Date: 2019-12-25 20:17:12 CET, cola version: 1.3.2
Document is loading...
All available functions which can be applied to this res_list object:
res_list
#> A 'ConsensusPartitionList' object with 24 methods.
#> On a matrix with 51882 rows and 180 columns.
#> Top rows are extracted by 'SD, CV, MAD, ATC' methods.
#> Subgroups are detected by 'hclust, kmeans, skmeans, pam, mclust, NMF' method.
#> Number of partitions are tried for k = 2, 3, 4, 5, 6.
#> Performed in total 30000 partitions by row resampling.
#>
#> Following methods can be applied to this 'ConsensusPartitionList' object:
#> [1] "cola_report" "collect_classes" "collect_plots" "collect_stats"
#> [5] "colnames" "functional_enrichment" "get_anno_col" "get_anno"
#> [9] "get_classes" "get_matrix" "get_membership" "get_stats"
#> [13] "is_best_k" "is_stable_k" "ncol" "nrow"
#> [17] "rownames" "show" "suggest_best_k" "test_to_known_factors"
#> [21] "top_rows_heatmap" "top_rows_overlap"
#>
#> You can get result for a single method by, e.g. object["SD", "hclust"] or object["SD:hclust"]
#> or a subset of methods by object[c("SD", "CV")], c("hclust", "kmeans")]
The call of run_all_consensus_partition_methods() was:
#> run_all_consensus_partition_methods(data = mat, mc.cores = 4, anno = anno)
Dimension of the input matrix:
mat = get_matrix(res_list)
dim(mat)
#> [1] 51882 180
The density distribution for each sample is visualized as in one column in the following heatmap. The clustering is based on the distance which is the Kolmogorov-Smirnov statistic between two distributions.
library(ComplexHeatmap)
densityHeatmap(mat, top_annotation = HeatmapAnnotation(df = get_anno(res_list),
col = get_anno_col(res_list)), ylab = "value", cluster_columns = TRUE, show_column_names = FALSE,
mc.cores = 4)
Folowing table shows the best k (number of partitions) for each combination
of top-value methods and partition methods. Clicking on the method name in
the table goes to the section for a single combination of methods.
The cola vignette explains the definition of the metrics used for determining the best number of partitions.
suggest_best_k(res_list)
| The best k | 1-PAC | Mean silhouette | Concordance | Optional k | ||
|---|---|---|---|---|---|---|
| SD:skmeans | 4 | 1.000 | 0.976 | 0.990 | ** | 2,3 |
| CV:pam | 2 | 1.000 | 0.978 | 0.990 | ** | |
| MAD:skmeans | 4 | 1.000 | 0.982 | 0.992 | ** | 2,3 |
| ATC:mclust | 2 | 1.000 | 1.000 | 1.000 | ** | |
| SD:kmeans | 4 | 0.997 | 0.950 | 0.971 | ** | |
| CV:NMF | 3 | 0.993 | 0.960 | 0.983 | ** | 2 |
| SD:pam | 2 | 0.965 | 0.962 | 0.983 | ** | |
| ATC:NMF | 3 | 0.958 | 0.942 | 0.976 | ** | 2 |
| SD:mclust | 4 | 0.957 | 0.919 | 0.970 | ** | 2 |
| MAD:mclust | 4 | 0.955 | 0.936 | 0.974 | ** | 2 |
| CV:mclust | 4 | 0.948 | 0.933 | 0.966 | * | 2 |
| MAD:NMF | 4 | 0.945 | 0.911 | 0.961 | * | 2,3 |
| CV:skmeans | 4 | 0.935 | 0.928 | 0.966 | * | 2,3 |
| SD:NMF | 4 | 0.921 | 0.901 | 0.957 | * | 2,3 |
| MAD:kmeans | 4 | 0.921 | 0.919 | 0.961 | * | 3 |
| ATC:pam | 6 | 0.918 | 0.876 | 0.919 | * | 2,3,5 |
| CV:kmeans | 4 | 0.913 | 0.918 | 0.941 | * | 2,3 |
| MAD:pam | 4 | 0.905 | 0.880 | 0.951 | * | 2 |
| ATC:kmeans | 5 | 0.903 | 0.923 | 0.931 | * | 2,3 |
| ATC:skmeans | 5 | 0.901 | 0.866 | 0.943 | * | 2,3 |
| MAD:hclust | 5 | 0.659 | 0.671 | 0.805 | ||
| ATC:hclust | 3 | 0.533 | 0.781 | 0.883 | ||
| CV:hclust | 3 | 0.470 | 0.623 | 0.822 | ||
| SD:hclust | 2 | 0.394 | 0.773 | 0.881 |
**: 1-PAC > 0.95, *: 1-PAC > 0.9
Cumulative distribution function curves of consensus matrix for all methods.
collect_plots(res_list, fun = plot_ecdf)
Consensus heatmaps for all methods. (What is a consensus heatmap?)
collect_plots(res_list, k = 2, fun = consensus_heatmap, mc.cores = 4)
collect_plots(res_list, k = 3, fun = consensus_heatmap, mc.cores = 4)
collect_plots(res_list, k = 4, fun = consensus_heatmap, mc.cores = 4)
collect_plots(res_list, k = 5, fun = consensus_heatmap, mc.cores = 4)
collect_plots(res_list, k = 6, fun = consensus_heatmap, mc.cores = 4)
Membership heatmaps for all methods. (What is a membership heatmap?)
collect_plots(res_list, k = 2, fun = membership_heatmap, mc.cores = 4)
collect_plots(res_list, k = 3, fun = membership_heatmap, mc.cores = 4)
collect_plots(res_list, k = 4, fun = membership_heatmap, mc.cores = 4)
collect_plots(res_list, k = 5, fun = membership_heatmap, mc.cores = 4)
collect_plots(res_list, k = 6, fun = membership_heatmap, mc.cores = 4)
Signature heatmaps for all methods. (What is a signature heatmap?)
Note in following heatmaps, rows are scaled.
collect_plots(res_list, k = 2, fun = get_signatures, mc.cores = 4)
collect_plots(res_list, k = 3, fun = get_signatures, mc.cores = 4)
collect_plots(res_list, k = 4, fun = get_signatures, mc.cores = 4)
collect_plots(res_list, k = 5, fun = get_signatures, mc.cores = 4)
collect_plots(res_list, k = 6, fun = get_signatures, mc.cores = 4)
The statistics used for measuring the stability of consensus partitioning. (How are they defined?)
get_stats(res_list, k = 2)
#> k 1-PAC mean_silhouette concordance area_increased Rand Jaccard
#> SD:NMF 2 0.942 0.938 0.975 0.501 0.498 0.498
#> CV:NMF 2 1.000 0.972 0.988 0.497 0.505 0.505
#> MAD:NMF 2 0.977 0.952 0.981 0.501 0.499 0.499
#> ATC:NMF 2 0.910 0.940 0.975 0.498 0.500 0.500
#> SD:skmeans 2 0.999 0.974 0.988 0.500 0.501 0.501
#> CV:skmeans 2 0.965 0.950 0.980 0.500 0.501 0.501
#> MAD:skmeans 2 0.988 0.967 0.986 0.500 0.500 0.500
#> ATC:skmeans 2 0.988 0.965 0.986 0.490 0.511 0.511
#> SD:mclust 2 1.000 0.997 0.999 0.328 0.672 0.672
#> CV:mclust 2 0.997 0.955 0.972 0.343 0.672 0.672
#> MAD:mclust 2 1.000 0.985 0.992 0.327 0.672 0.672
#> ATC:mclust 2 1.000 1.000 1.000 0.316 0.685 0.685
#> SD:kmeans 2 0.859 0.943 0.974 0.481 0.515 0.515
#> CV:kmeans 2 0.900 0.933 0.971 0.472 0.520 0.520
#> MAD:kmeans 2 0.858 0.960 0.980 0.480 0.515 0.515
#> ATC:kmeans 2 1.000 1.000 1.000 0.436 0.565 0.565
#> SD:pam 2 0.965 0.962 0.983 0.418 0.587 0.587
#> CV:pam 2 1.000 0.978 0.990 0.408 0.597 0.597
#> MAD:pam 2 1.000 0.970 0.985 0.418 0.592 0.592
#> ATC:pam 2 1.000 0.991 0.996 0.381 0.623 0.623
#> SD:hclust 2 0.394 0.773 0.881 0.449 0.539 0.539
#> CV:hclust 2 0.364 0.694 0.862 0.432 0.539 0.539
#> MAD:hclust 2 0.383 0.760 0.878 0.439 0.557 0.557
#> ATC:hclust 2 0.508 0.774 0.897 0.411 0.578 0.578
get_stats(res_list, k = 3)
#> k 1-PAC mean_silhouette concordance area_increased Rand Jaccard
#> SD:NMF 3 0.993 0.965 0.985 0.306 0.781 0.588
#> CV:NMF 3 0.993 0.960 0.983 0.311 0.773 0.581
#> MAD:NMF 3 1.000 0.967 0.987 0.305 0.781 0.587
#> ATC:NMF 3 0.958 0.942 0.976 0.319 0.774 0.578
#> SD:skmeans 3 1.000 0.971 0.989 0.290 0.800 0.621
#> CV:skmeans 3 1.000 0.970 0.988 0.292 0.800 0.621
#> MAD:skmeans 3 1.000 0.981 0.992 0.290 0.802 0.624
#> ATC:skmeans 3 1.000 0.974 0.990 0.284 0.825 0.669
#> SD:mclust 3 0.614 0.786 0.887 0.840 0.683 0.531
#> CV:mclust 3 0.789 0.893 0.944 0.816 0.686 0.536
#> MAD:mclust 3 0.631 0.768 0.881 0.846 0.682 0.529
#> ATC:mclust 3 0.671 0.880 0.908 0.936 0.691 0.548
#> SD:kmeans 3 0.856 0.945 0.972 0.349 0.749 0.551
#> CV:kmeans 3 1.000 0.980 0.992 0.370 0.738 0.540
#> MAD:kmeans 3 0.994 0.977 0.989 0.349 0.749 0.551
#> ATC:kmeans 3 1.000 0.987 0.995 0.494 0.678 0.479
#> SD:pam 3 0.750 0.880 0.942 0.545 0.708 0.526
#> CV:pam 3 0.669 0.806 0.901 0.537 0.731 0.566
#> MAD:pam 3 0.772 0.803 0.917 0.552 0.697 0.511
#> ATC:pam 3 1.000 0.963 0.984 0.674 0.691 0.523
#> SD:hclust 3 0.477 0.671 0.833 0.425 0.750 0.558
#> CV:hclust 3 0.470 0.623 0.822 0.479 0.699 0.488
#> MAD:hclust 3 0.492 0.648 0.828 0.448 0.740 0.550
#> ATC:hclust 3 0.533 0.781 0.883 0.527 0.668 0.476
get_stats(res_list, k = 4)
#> k 1-PAC mean_silhouette concordance area_increased Rand Jaccard
#> SD:NMF 4 0.921 0.901 0.957 0.0971 0.912 0.752
#> CV:NMF 4 0.832 0.847 0.917 0.1090 0.913 0.759
#> MAD:NMF 4 0.945 0.911 0.961 0.0887 0.923 0.783
#> ATC:NMF 4 0.866 0.879 0.938 0.0839 0.929 0.797
#> SD:skmeans 4 1.000 0.976 0.990 0.1262 0.908 0.745
#> CV:skmeans 4 0.935 0.928 0.966 0.1260 0.901 0.730
#> MAD:skmeans 4 1.000 0.982 0.992 0.1267 0.904 0.734
#> ATC:skmeans 4 0.897 0.875 0.919 0.0780 0.948 0.863
#> SD:mclust 4 0.957 0.919 0.970 0.2148 0.827 0.567
#> CV:mclust 4 0.948 0.933 0.966 0.1686 0.834 0.586
#> MAD:mclust 4 0.955 0.936 0.974 0.2090 0.824 0.561
#> ATC:mclust 4 0.673 0.752 0.815 0.1822 0.877 0.685
#> SD:kmeans 4 0.997 0.950 0.971 0.1553 0.862 0.627
#> CV:kmeans 4 0.913 0.918 0.941 0.1554 0.861 0.627
#> MAD:kmeans 4 0.921 0.919 0.961 0.1586 0.856 0.614
#> ATC:kmeans 4 0.742 0.734 0.854 0.1362 0.821 0.540
#> SD:pam 4 0.888 0.874 0.947 0.1609 0.832 0.564
#> CV:pam 4 0.783 0.779 0.909 0.1928 0.822 0.559
#> MAD:pam 4 0.905 0.880 0.951 0.1585 0.824 0.543
#> ATC:pam 4 0.885 0.936 0.960 0.1700 0.828 0.564
#> SD:hclust 4 0.595 0.622 0.812 0.1467 0.890 0.687
#> CV:hclust 4 0.532 0.582 0.776 0.1360 0.868 0.633
#> MAD:hclust 4 0.556 0.619 0.811 0.1509 0.882 0.667
#> ATC:hclust 4 0.665 0.693 0.833 0.1436 0.873 0.669
get_stats(res_list, k = 5)
#> k 1-PAC mean_silhouette concordance area_increased Rand Jaccard
#> SD:NMF 5 0.738 0.659 0.821 0.0665 0.950 0.826
#> CV:NMF 5 0.720 0.613 0.790 0.0648 0.959 0.860
#> MAD:NMF 5 0.754 0.677 0.837 0.0649 0.983 0.941
#> ATC:NMF 5 0.761 0.733 0.845 0.0557 0.969 0.894
#> SD:skmeans 5 0.869 0.771 0.883 0.0594 0.972 0.901
#> CV:skmeans 5 0.780 0.706 0.843 0.0549 0.979 0.926
#> MAD:skmeans 5 0.839 0.729 0.880 0.0520 0.960 0.858
#> ATC:skmeans 5 0.901 0.866 0.943 0.0702 0.939 0.820
#> SD:mclust 5 0.872 0.834 0.911 0.0606 0.943 0.789
#> CV:mclust 5 0.826 0.787 0.876 0.0588 0.934 0.763
#> MAD:mclust 5 0.844 0.821 0.904 0.0621 0.935 0.761
#> ATC:mclust 5 0.805 0.875 0.904 0.0683 0.862 0.572
#> SD:kmeans 5 0.824 0.703 0.830 0.0577 0.965 0.867
#> CV:kmeans 5 0.788 0.748 0.830 0.0618 0.966 0.867
#> MAD:kmeans 5 0.843 0.734 0.845 0.0565 0.980 0.921
#> ATC:kmeans 5 0.903 0.923 0.931 0.0707 0.914 0.682
#> SD:pam 5 0.839 0.773 0.836 0.0624 0.923 0.709
#> CV:pam 5 0.770 0.629 0.797 0.0648 0.925 0.722
#> MAD:pam 5 0.813 0.765 0.855 0.0593 0.928 0.724
#> ATC:pam 5 0.963 0.948 0.977 0.0594 0.954 0.819
#> SD:hclust 5 0.682 0.649 0.805 0.0520 0.943 0.783
#> CV:hclust 5 0.611 0.563 0.742 0.0625 0.900 0.640
#> MAD:hclust 5 0.659 0.671 0.805 0.0614 0.952 0.813
#> ATC:hclust 5 0.723 0.752 0.833 0.0790 0.871 0.580
get_stats(res_list, k = 6)
#> k 1-PAC mean_silhouette concordance area_increased Rand Jaccard
#> SD:NMF 6 0.735 0.630 0.804 0.0382 0.924 0.716
#> CV:NMF 6 0.725 0.612 0.795 0.0383 0.893 0.634
#> MAD:NMF 6 0.721 0.666 0.804 0.0444 0.887 0.639
#> ATC:NMF 6 0.726 0.590 0.797 0.0349 0.967 0.884
#> SD:skmeans 6 0.800 0.642 0.791 0.0345 0.944 0.790
#> CV:skmeans 6 0.749 0.535 0.736 0.0355 0.943 0.787
#> MAD:skmeans 6 0.806 0.692 0.818 0.0317 0.956 0.826
#> ATC:skmeans 6 0.843 0.757 0.888 0.0379 0.943 0.808
#> SD:mclust 6 0.833 0.766 0.861 0.0319 0.971 0.870
#> CV:mclust 6 0.779 0.758 0.843 0.0327 0.984 0.930
#> MAD:mclust 6 0.836 0.805 0.844 0.0317 0.967 0.853
#> ATC:mclust 6 0.807 0.801 0.852 0.0336 0.980 0.913
#> SD:kmeans 6 0.784 0.578 0.778 0.0388 0.911 0.661
#> CV:kmeans 6 0.767 0.593 0.755 0.0389 0.914 0.651
#> MAD:kmeans 6 0.790 0.666 0.775 0.0375 0.905 0.623
#> ATC:kmeans 6 0.850 0.761 0.849 0.0374 0.980 0.901
#> SD:pam 6 0.884 0.783 0.908 0.0433 0.944 0.735
#> CV:pam 6 0.874 0.849 0.922 0.0420 0.919 0.646
#> MAD:pam 6 0.851 0.743 0.881 0.0419 0.930 0.682
#> ATC:pam 6 0.918 0.876 0.919 0.0386 0.964 0.833
#> SD:hclust 6 0.718 0.628 0.792 0.0367 0.974 0.886
#> CV:hclust 6 0.669 0.573 0.703 0.0366 0.939 0.730
#> MAD:hclust 6 0.732 0.680 0.799 0.0375 0.950 0.775
#> ATC:hclust 6 0.731 0.690 0.825 0.0339 0.985 0.928
Following heatmap plots the partition for each combination of methods and the lightness correspond to the silhouette scores for samples in each method. On top the consensus subgroup is inferred from all methods by taking the mean silhouette scores as weight.
collect_stats(res_list, k = 2)
collect_stats(res_list, k = 3)
collect_stats(res_list, k = 4)
collect_stats(res_list, k = 5)
collect_stats(res_list, k = 6)
Collect partitions from all methods:
collect_classes(res_list, k = 2)
collect_classes(res_list, k = 3)
collect_classes(res_list, k = 4)
collect_classes(res_list, k = 5)
collect_classes(res_list, k = 6)
Overlap of top rows from different top-row methods:
top_rows_overlap(res_list, top_n = 1000, method = "euler")
top_rows_overlap(res_list, top_n = 2000, method = "euler")
top_rows_overlap(res_list, top_n = 3000, method = "euler")
top_rows_overlap(res_list, top_n = 4000, method = "euler")
top_rows_overlap(res_list, top_n = 5000, method = "euler")
Also visualize the correspondance of rankings between different top-row methods:
top_rows_overlap(res_list, top_n = 1000, method = "correspondance")
top_rows_overlap(res_list, top_n = 2000, method = "correspondance")
top_rows_overlap(res_list, top_n = 3000, method = "correspondance")
top_rows_overlap(res_list, top_n = 4000, method = "correspondance")
top_rows_overlap(res_list, top_n = 5000, method = "correspondance")
Heatmaps of the top rows:
top_rows_heatmap(res_list, top_n = 1000)
top_rows_heatmap(res_list, top_n = 2000)
top_rows_heatmap(res_list, top_n = 3000)
top_rows_heatmap(res_list, top_n = 4000)
top_rows_heatmap(res_list, top_n = 5000)
Test correlation between subgroups and known annotations. If the known annotation is numeric, one-way ANOVA test is applied, and if the known annotation is discrete, chi-squared contingency table test is applied.
test_to_known_factors(res_list, k = 2)
#> n disease.state(p) tissue(p) k
#> SD:NMF 173 1.11e-15 1.26e-18 2
#> CV:NMF 179 8.68e-14 7.25e-16 2
#> MAD:NMF 175 1.37e-14 1.72e-17 2
#> ATC:NMF 177 1.54e-14 4.45e-17 2
#> SD:skmeans 178 2.15e-14 6.35e-17 2
#> CV:skmeans 175 1.18e-14 1.97e-17 2
#> MAD:skmeans 178 4.21e-14 2.16e-16 2
#> ATC:skmeans 177 8.09e-14 4.73e-16 2
#> SD:mclust 180 8.42e-18 5.58e-18 2
#> CV:mclust 179 2.96e-17 1.95e-17 2
#> MAD:mclust 179 2.96e-17 1.95e-17 2
#> ATC:mclust 180 3.71e-17 6.12e-17 2
#> SD:kmeans 175 1.73e-13 1.15e-15 2
#> CV:kmeans 175 4.64e-13 2.01e-15 2
#> MAD:kmeans 179 2.39e-13 2.24e-15 2
#> ATC:kmeans 180 4.69e-12 7.98e-13 2
#> SD:pam 179 1.15e-15 1.20e-15 2
#> CV:pam 179 4.84e-16 7.06e-16 2
#> MAD:pam 179 1.15e-15 1.20e-15 2
#> ATC:pam 179 8.58e-15 8.60e-15 2
#> SD:hclust 167 1.13e-12 1.44e-14 2
#> CV:hclust 150 2.60e-13 6.85e-14 2
#> MAD:hclust 165 1.93e-12 1.42e-13 2
#> ATC:hclust 162 3.05e-16 2.16e-16 2
test_to_known_factors(res_list, k = 3)
#> n disease.state(p) tissue(p) k
#> SD:NMF 178 1.18e-24 7.88e-25 3
#> CV:NMF 178 2.65e-26 2.64e-26 3
#> MAD:NMF 177 3.82e-25 4.63e-25 3
#> ATC:NMF 177 6.35e-25 3.48e-24 3
#> SD:skmeans 177 7.65e-27 3.28e-26 3
#> CV:skmeans 176 2.23e-26 1.30e-25 3
#> MAD:skmeans 179 1.22e-26 1.16e-25 3
#> ATC:skmeans 176 4.05e-22 1.65e-22 3
#> SD:mclust 163 2.00e-29 1.69e-30 3
#> CV:mclust 174 3.98e-28 3.29e-29 3
#> MAD:mclust 156 5.67e-29 9.17e-30 3
#> ATC:mclust 179 5.72e-28 8.02e-29 3
#> SD:kmeans 177 2.01e-27 2.25e-28 3
#> CV:kmeans 178 7.92e-27 7.08e-28 3
#> MAD:kmeans 180 8.17e-27 9.10e-28 3
#> ATC:kmeans 179 5.26e-27 3.12e-28 3
#> SD:pam 173 5.05e-28 3.30e-29 3
#> CV:pam 166 6.12e-30 6.94e-32 3
#> MAD:pam 164 3.39e-29 7.07e-31 3
#> ATC:pam 177 1.73e-23 7.29e-24 3
#> SD:hclust 144 4.43e-15 4.86e-15 3
#> CV:hclust 136 3.42e-23 2.97e-23 3
#> MAD:hclust 149 2.20e-16 1.99e-16 3
#> ATC:hclust 166 4.49e-28 5.61e-29 3
test_to_known_factors(res_list, k = 4)
#> n disease.state(p) tissue(p) k
#> SD:NMF 172 1.64e-23 7.72e-21 4
#> CV:NMF 170 5.87e-23 1.85e-21 4
#> MAD:NMF 176 1.70e-25 1.32e-22 4
#> ATC:NMF 173 5.53e-21 1.32e-18 4
#> SD:skmeans 179 3.18e-26 7.74e-25 4
#> CV:skmeans 176 2.73e-26 2.22e-24 4
#> MAD:skmeans 179 3.18e-26 7.74e-25 4
#> ATC:skmeans 172 5.55e-23 4.05e-24 4
#> SD:mclust 171 1.28e-29 1.75e-30 4
#> CV:mclust 177 3.61e-29 3.94e-30 4
#> MAD:mclust 177 1.46e-28 1.27e-29 4
#> ATC:mclust 166 1.03e-32 3.23e-29 4
#> SD:kmeans 175 1.62e-27 3.49e-28 4
#> CV:kmeans 176 1.55e-26 3.41e-27 4
#> MAD:kmeans 172 1.98e-26 4.19e-27 4
#> ATC:kmeans 167 2.05e-25 1.69e-27 4
#> SD:pam 168 2.69e-28 3.94e-29 4
#> CV:pam 153 1.12e-25 2.80e-27 4
#> MAD:pam 166 4.70e-27 1.45e-27 4
#> ATC:pam 179 1.87e-27 3.77e-29 4
#> SD:hclust 132 1.53e-19 4.25e-18 4
#> CV:hclust 119 1.02e-20 1.40e-19 4
#> MAD:hclust 140 2.04e-22 4.06e-20 4
#> ATC:hclust 153 3.76e-26 5.44e-26 4
test_to_known_factors(res_list, k = 5)
#> n disease.state(p) tissue(p) k
#> SD:NMF 144 3.65e-21 3.31e-19 5
#> CV:NMF 133 2.19e-18 4.04e-19 5
#> MAD:NMF 143 1.82e-22 1.22e-21 5
#> ATC:NMF 159 2.48e-22 6.21e-20 5
#> SD:skmeans 162 3.14e-24 3.55e-23 5
#> CV:skmeans 147 4.07e-24 7.51e-23 5
#> MAD:skmeans 152 6.44e-22 1.09e-21 5
#> ATC:skmeans 166 9.55e-23 5.25e-22 5
#> SD:mclust 164 5.12e-33 4.31e-31 5
#> CV:mclust 151 1.06e-27 3.49e-29 5
#> MAD:mclust 162 7.05e-31 3.19e-29 5
#> ATC:mclust 172 5.57e-31 1.82e-27 5
#> SD:kmeans 141 2.39e-25 2.70e-25 5
#> CV:kmeans 164 2.78e-27 3.71e-28 5
#> MAD:kmeans 159 2.39e-28 1.74e-29 5
#> ATC:kmeans 177 1.37e-27 6.76e-27 5
#> SD:pam 160 3.88e-27 3.47e-27 5
#> CV:pam 133 4.41e-23 9.84e-25 5
#> MAD:pam 160 1.02e-28 2.86e-29 5
#> ATC:pam 177 3.08e-32 4.98e-29 5
#> SD:hclust 136 2.15e-17 1.50e-16 5
#> CV:hclust 111 2.57e-16 8.33e-16 5
#> MAD:hclust 142 9.41e-22 5.75e-21 5
#> ATC:hclust 143 1.20e-24 4.09e-23 5
test_to_known_factors(res_list, k = 6)
#> n disease.state(p) tissue(p) k
#> SD:NMF 135 3.60e-20 1.07e-18 6
#> CV:NMF 137 7.47e-20 3.82e-20 6
#> MAD:NMF 145 5.26e-21 3.97e-20 6
#> ATC:NMF 133 3.20e-21 4.33e-20 6
#> SD:skmeans 131 6.49e-22 1.16e-22 6
#> CV:skmeans 112 1.48e-16 5.21e-17 6
#> MAD:skmeans 149 4.10e-21 1.03e-20 6
#> ATC:skmeans 152 2.58e-20 3.91e-20 6
#> SD:mclust 160 1.92e-27 1.14e-26 6
#> CV:mclust 167 1.38e-32 8.00e-29 6
#> MAD:mclust 162 3.86e-27 1.24e-28 6
#> ATC:mclust 169 1.78e-27 2.62e-24 6
#> SD:kmeans 118 2.42e-19 1.76e-18 6
#> CV:kmeans 120 2.58e-19 3.90e-17 6
#> MAD:kmeans 146 3.96e-24 8.38e-24 6
#> ATC:kmeans 150 4.36e-25 3.47e-23 6
#> SD:pam 159 2.35e-23 4.76e-23 6
#> CV:pam 169 1.44e-25 1.83e-25 6
#> MAD:pam 153 8.34e-23 1.81e-22 6
#> ATC:pam 174 4.86e-31 5.83e-28 6
#> SD:hclust 133 2.12e-17 7.99e-16 6
#> CV:hclust 112 2.24e-19 6.24e-17 6
#> MAD:hclust 151 1.90e-24 1.04e-24 6
#> ATC:hclust 141 4.95e-25 4.34e-24 6
The object with results only for a single top-value method and a single partition method can be extracted as:
res = res_list["SD", "hclust"]
# you can also extract it by
# res = res_list["SD:hclust"]
A summary of res and all the functions that can be applied to it:
res
#> A 'ConsensusPartition' object with k = 2, 3, 4, 5, 6.
#> On a matrix with 51882 rows and 180 columns.
#> Top rows (1000, 2000, 3000, 4000, 5000) are extracted by 'SD' method.
#> Subgroups are detected by 'hclust' method.
#> Performed in total 1250 partitions by row resampling.
#> Best k for subgroups seems to be 2.
#>
#> Following methods can be applied to this 'ConsensusPartition' object:
#> [1] "cola_report" "collect_classes" "collect_plots"
#> [4] "collect_stats" "colnames" "compare_signatures"
#> [7] "consensus_heatmap" "dimension_reduction" "functional_enrichment"
#> [10] "get_anno_col" "get_anno" "get_classes"
#> [13] "get_consensus" "get_matrix" "get_membership"
#> [16] "get_param" "get_signatures" "get_stats"
#> [19] "is_best_k" "is_stable_k" "membership_heatmap"
#> [22] "ncol" "nrow" "plot_ecdf"
#> [25] "rownames" "select_partition_number" "show"
#> [28] "suggest_best_k" "test_to_known_factors"
collect_plots() function collects all the plots made from res for all k (number of partitions)
into one single page to provide an easy and fast comparison between different k.
collect_plots(res)
The plots are:
k and the heatmap of
predicted classes for each k.k.k.k.All the plots in panels can be made by individual functions and they are plotted later in this section.
select_partition_number() produces several plots showing different
statistics for choosing “optimized” k. There are following statistics:
k;k, the area increased is defined as \(A_k - A_{k-1}\).The detailed explanations of these statistics can be found in the cola vignette.
Generally speaking, lower PAC score, higher mean silhouette score or higher
concordance corresponds to better partition. Rand index and Jaccard index
measure how similar the current partition is compared to partition with k-1.
If they are too similar, we won't accept k is better than k-1.
select_partition_number(res)
The numeric values for all these statistics can be obtained by get_stats().
get_stats(res)
#> k 1-PAC mean_silhouette concordance area_increased Rand Jaccard
#> 2 2 0.394 0.773 0.881 0.4486 0.539 0.539
#> 3 3 0.477 0.671 0.833 0.4251 0.750 0.558
#> 4 4 0.595 0.622 0.812 0.1467 0.890 0.687
#> 5 5 0.682 0.649 0.805 0.0520 0.943 0.783
#> 6 6 0.718 0.628 0.792 0.0367 0.974 0.886
suggest_best_k() suggests the best \(k\) based on these statistics. The rules are as follows:
suggest_best_k(res)
#> [1] 2
Following shows the table of the partitions (You need to click the show/hide
code output link to see it). The membership matrix (columns with name p*)
is inferred by
clue::cl_consensus()
function with the SE method. Basically the value in the membership matrix
represents the probability to belong to a certain group. The finall class
label for an item is determined with the group with highest probability it
belongs to.
In get_classes() function, the entropy is calculated from the membership
matrix and the silhouette score is calculated from the consensus matrix.
cbind(get_classes(res, k = 2), get_membership(res, k = 2))
#> class entropy silhouette p1 p2
#> GSM97800 2 0.0000 0.8822 0.000 1.000
#> GSM97803 2 0.0000 0.8822 0.000 1.000
#> GSM97804 2 0.0000 0.8822 0.000 1.000
#> GSM97805 2 0.0000 0.8822 0.000 1.000
#> GSM97807 2 0.0000 0.8822 0.000 1.000
#> GSM97809 2 0.0000 0.8822 0.000 1.000
#> GSM97811 2 0.0000 0.8822 0.000 1.000
#> GSM97812 2 0.0000 0.8822 0.000 1.000
#> GSM97816 1 0.9833 0.4411 0.576 0.424
#> GSM97817 2 0.0000 0.8822 0.000 1.000
#> GSM97820 2 0.0000 0.8822 0.000 1.000
#> GSM97825 2 0.0000 0.8822 0.000 1.000
#> GSM97827 2 0.0000 0.8822 0.000 1.000
#> GSM97828 1 0.9833 0.4411 0.576 0.424
#> GSM97833 2 0.0000 0.8822 0.000 1.000
#> GSM97834 2 0.0000 0.8822 0.000 1.000
#> GSM97840 2 0.1184 0.8770 0.016 0.984
#> GSM97846 2 0.0000 0.8822 0.000 1.000
#> GSM97848 2 0.0000 0.8822 0.000 1.000
#> GSM97849 2 0.0000 0.8822 0.000 1.000
#> GSM97850 2 0.0000 0.8822 0.000 1.000
#> GSM97853 2 0.0000 0.8822 0.000 1.000
#> GSM97855 2 0.0000 0.8822 0.000 1.000
#> GSM97878 1 0.6148 0.8144 0.848 0.152
#> GSM97913 1 0.9754 0.4660 0.592 0.408
#> GSM97932 1 0.0000 0.8430 1.000 0.000
#> GSM97939 2 0.4815 0.8335 0.104 0.896
#> GSM97951 2 0.2603 0.8661 0.044 0.956
#> GSM97957 1 0.8909 0.6617 0.692 0.308
#> GSM97972 2 0.8386 0.6214 0.268 0.732
#> GSM97793 1 0.8909 0.6617 0.692 0.308
#> GSM97795 2 0.4161 0.8463 0.084 0.916
#> GSM97802 1 0.4939 0.8316 0.892 0.108
#> GSM97810 2 0.4431 0.8414 0.092 0.908
#> GSM97815 2 0.4815 0.8336 0.104 0.896
#> GSM97837 1 0.4298 0.8369 0.912 0.088
#> GSM97843 2 0.9963 0.0235 0.464 0.536
#> GSM97890 2 0.9460 0.4162 0.364 0.636
#> GSM97899 1 0.0000 0.8430 1.000 0.000
#> GSM97910 1 0.8499 0.7147 0.724 0.276
#> GSM97916 1 0.6623 0.8030 0.828 0.172
#> GSM97920 1 0.9248 0.6132 0.660 0.340
#> GSM97921 1 0.7139 0.7868 0.804 0.196
#> GSM97927 1 0.5842 0.8191 0.860 0.140
#> GSM97937 1 0.0376 0.8439 0.996 0.004
#> GSM97941 2 0.0938 0.8783 0.012 0.988
#> GSM97943 1 0.9833 0.4411 0.576 0.424
#> GSM97958 1 0.8081 0.7447 0.752 0.248
#> GSM97960 2 0.4022 0.8484 0.080 0.920
#> GSM97794 1 0.8555 0.7029 0.720 0.280
#> GSM97796 1 0.0000 0.8430 1.000 0.000
#> GSM97797 1 0.8267 0.7308 0.740 0.260
#> GSM97798 1 0.0000 0.8430 1.000 0.000
#> GSM97801 1 0.8267 0.7308 0.740 0.260
#> GSM97806 1 0.6343 0.8094 0.840 0.160
#> GSM97808 1 0.0000 0.8430 1.000 0.000
#> GSM97813 1 0.0672 0.8445 0.992 0.008
#> GSM97814 1 0.0000 0.8430 1.000 0.000
#> GSM97818 1 0.7453 0.7682 0.788 0.212
#> GSM97819 1 0.9044 0.6431 0.680 0.320
#> GSM97821 2 0.5946 0.8003 0.144 0.856
#> GSM97826 1 0.4298 0.8369 0.912 0.088
#> GSM97829 1 0.3274 0.8424 0.940 0.060
#> GSM97832 2 0.3431 0.8570 0.064 0.936
#> GSM97836 1 0.6973 0.7942 0.812 0.188
#> GSM97839 1 0.0000 0.8430 1.000 0.000
#> GSM97844 2 0.0000 0.8822 0.000 1.000
#> GSM97847 1 0.0672 0.8445 0.992 0.008
#> GSM97851 1 0.0000 0.8430 1.000 0.000
#> GSM97852 1 0.0672 0.8445 0.992 0.008
#> GSM97856 1 0.0000 0.8430 1.000 0.000
#> GSM97858 2 0.0000 0.8822 0.000 1.000
#> GSM97859 1 0.0672 0.8445 0.992 0.008
#> GSM97861 1 0.5519 0.8243 0.872 0.128
#> GSM97863 1 0.0000 0.8430 1.000 0.000
#> GSM97869 1 0.6712 0.8004 0.824 0.176
#> GSM97870 1 0.0672 0.8445 0.992 0.008
#> GSM97871 1 0.0000 0.8430 1.000 0.000
#> GSM97877 1 0.9754 0.4660 0.592 0.408
#> GSM97879 1 0.3274 0.8410 0.940 0.060
#> GSM97882 1 0.6343 0.8094 0.840 0.160
#> GSM97885 1 0.6531 0.8065 0.832 0.168
#> GSM97886 1 0.0000 0.8430 1.000 0.000
#> GSM97887 1 0.0000 0.8430 1.000 0.000
#> GSM97888 1 0.0000 0.8430 1.000 0.000
#> GSM97889 1 0.3431 0.8413 0.936 0.064
#> GSM97891 1 0.6887 0.7957 0.816 0.184
#> GSM97892 2 0.0000 0.8822 0.000 1.000
#> GSM97893 1 0.0000 0.8430 1.000 0.000
#> GSM97894 1 0.0000 0.8430 1.000 0.000
#> GSM97895 1 0.0000 0.8430 1.000 0.000
#> GSM97896 1 0.0000 0.8430 1.000 0.000
#> GSM97898 1 0.0000 0.8430 1.000 0.000
#> GSM97903 1 0.4161 0.8368 0.916 0.084
#> GSM97905 1 0.2603 0.8439 0.956 0.044
#> GSM97906 1 0.0000 0.8430 1.000 0.000
#> GSM97908 1 0.0938 0.8448 0.988 0.012
#> GSM97912 1 0.2603 0.8439 0.956 0.044
#> GSM97914 1 0.6973 0.7922 0.812 0.188
#> GSM97915 1 0.0000 0.8430 1.000 0.000
#> GSM97917 1 0.0000 0.8430 1.000 0.000
#> GSM97918 1 0.0000 0.8430 1.000 0.000
#> GSM97919 1 0.0000 0.8430 1.000 0.000
#> GSM97922 1 0.0672 0.8445 0.992 0.008
#> GSM97924 2 0.0000 0.8822 0.000 1.000
#> GSM97926 1 0.6973 0.7942 0.812 0.188
#> GSM97930 1 0.2778 0.8444 0.952 0.048
#> GSM97931 2 0.8386 0.6214 0.268 0.732
#> GSM97935 1 0.5629 0.8226 0.868 0.132
#> GSM97936 1 0.0000 0.8430 1.000 0.000
#> GSM97938 1 0.0000 0.8430 1.000 0.000
#> GSM97940 1 0.0000 0.8430 1.000 0.000
#> GSM97942 1 0.8861 0.6672 0.696 0.304
#> GSM97945 1 0.0376 0.8440 0.996 0.004
#> GSM97946 2 0.0000 0.8822 0.000 1.000
#> GSM97948 1 0.7453 0.7687 0.788 0.212
#> GSM97950 1 0.0000 0.8430 1.000 0.000
#> GSM97952 1 0.0000 0.8430 1.000 0.000
#> GSM97953 1 0.0376 0.8439 0.996 0.004
#> GSM97954 1 0.0672 0.8445 0.992 0.008
#> GSM97955 1 0.0000 0.8430 1.000 0.000
#> GSM97959 1 0.8813 0.6781 0.700 0.300
#> GSM97961 1 0.0000 0.8430 1.000 0.000
#> GSM97963 1 0.0000 0.8430 1.000 0.000
#> GSM97965 1 0.0000 0.8430 1.000 0.000
#> GSM97966 1 0.0000 0.8430 1.000 0.000
#> GSM97967 2 0.0000 0.8822 0.000 1.000
#> GSM97968 2 0.0000 0.8822 0.000 1.000
#> GSM97969 1 0.0376 0.8438 0.996 0.004
#> GSM97971 1 0.0672 0.8445 0.992 0.008
#> GSM97799 2 0.7219 0.7390 0.200 0.800
#> GSM97823 2 0.0000 0.8822 0.000 1.000
#> GSM97824 2 0.9491 0.3755 0.368 0.632
#> GSM97830 1 0.9129 0.6324 0.672 0.328
#> GSM97835 2 0.5294 0.8210 0.120 0.880
#> GSM97838 2 0.0000 0.8822 0.000 1.000
#> GSM97841 2 0.0000 0.8822 0.000 1.000
#> GSM97842 2 0.7056 0.7488 0.192 0.808
#> GSM97854 2 0.0000 0.8822 0.000 1.000
#> GSM97857 2 0.9522 0.3600 0.372 0.628
#> GSM97860 1 0.8909 0.6617 0.692 0.308
#> GSM97862 1 0.9983 0.2423 0.524 0.476
#> GSM97864 2 0.0000 0.8822 0.000 1.000
#> GSM97866 1 0.9988 0.2261 0.520 0.480
#> GSM97868 2 0.9044 0.5173 0.320 0.680
#> GSM97872 1 0.2778 0.8439 0.952 0.048
#> GSM97873 2 0.6973 0.7562 0.188 0.812
#> GSM97874 1 0.9129 0.6324 0.672 0.328
#> GSM97875 1 0.9044 0.6431 0.680 0.320
#> GSM97876 1 0.8909 0.6617 0.692 0.308
#> GSM97880 1 0.8909 0.6617 0.692 0.308
#> GSM97881 2 0.8327 0.6396 0.264 0.736
#> GSM97884 2 0.7745 0.7022 0.228 0.772
#> GSM97901 1 0.9988 0.2263 0.520 0.480
#> GSM97902 1 0.8081 0.7447 0.752 0.248
#> GSM97909 2 0.5842 0.8042 0.140 0.860
#> GSM97911 2 0.8327 0.6396 0.264 0.736
#> GSM97923 1 0.8909 0.6617 0.692 0.308
#> GSM97928 1 0.2778 0.8439 0.952 0.048
#> GSM97929 2 0.0000 0.8822 0.000 1.000
#> GSM97933 1 0.8909 0.6617 0.692 0.308
#> GSM97934 1 0.8909 0.6617 0.692 0.308
#> GSM97944 2 0.7219 0.7390 0.200 0.800
#> GSM97949 2 0.0000 0.8822 0.000 1.000
#> GSM97956 2 0.9896 0.1070 0.440 0.560
#> GSM97962 1 0.9393 0.5836 0.644 0.356
#> GSM97964 2 0.7815 0.6914 0.232 0.768
#> GSM97970 2 0.6973 0.7543 0.188 0.812
#> GSM97822 1 0.3584 0.8407 0.932 0.068
#> GSM97831 1 0.9170 0.6256 0.668 0.332
#> GSM97845 1 0.0672 0.8445 0.992 0.008
#> GSM97865 1 0.7950 0.7524 0.760 0.240
#> GSM97867 1 0.8909 0.6617 0.692 0.308
#> GSM97883 1 0.5629 0.8219 0.868 0.132
#> GSM97897 1 0.2236 0.8447 0.964 0.036
#> GSM97900 1 0.0000 0.8430 1.000 0.000
#> GSM97904 1 0.4298 0.8373 0.912 0.088
#> GSM97907 2 0.0000 0.8822 0.000 1.000
#> GSM97925 1 0.7453 0.7687 0.788 0.212
#> GSM97947 1 0.9044 0.6431 0.680 0.320
cbind(get_classes(res, k = 3), get_membership(res, k = 3))
#> class entropy silhouette p1 p2 p3
#> GSM97800 2 0.0000 0.8653 0.000 1.000 0.000
#> GSM97803 2 0.0000 0.8653 0.000 1.000 0.000
#> GSM97804 2 0.0000 0.8653 0.000 1.000 0.000
#> GSM97805 2 0.0000 0.8653 0.000 1.000 0.000
#> GSM97807 2 0.0000 0.8653 0.000 1.000 0.000
#> GSM97809 2 0.0000 0.8653 0.000 1.000 0.000
#> GSM97811 2 0.0000 0.8653 0.000 1.000 0.000
#> GSM97812 2 0.0000 0.8653 0.000 1.000 0.000
#> GSM97816 3 0.4121 0.6547 0.000 0.168 0.832
#> GSM97817 2 0.0000 0.8653 0.000 1.000 0.000
#> GSM97820 2 0.0000 0.8653 0.000 1.000 0.000
#> GSM97825 2 0.0000 0.8653 0.000 1.000 0.000
#> GSM97827 2 0.0000 0.8653 0.000 1.000 0.000
#> GSM97828 3 0.4121 0.6547 0.000 0.168 0.832
#> GSM97833 2 0.0000 0.8653 0.000 1.000 0.000
#> GSM97834 2 0.0000 0.8653 0.000 1.000 0.000
#> GSM97840 2 0.1529 0.8479 0.000 0.960 0.040
#> GSM97846 2 0.0000 0.8653 0.000 1.000 0.000
#> GSM97848 2 0.0000 0.8653 0.000 1.000 0.000
#> GSM97849 2 0.0000 0.8653 0.000 1.000 0.000
#> GSM97850 2 0.0000 0.8653 0.000 1.000 0.000
#> GSM97853 2 0.0000 0.8653 0.000 1.000 0.000
#> GSM97855 2 0.0000 0.8653 0.000 1.000 0.000
#> GSM97878 3 0.7112 0.6238 0.308 0.044 0.648
#> GSM97913 3 0.8437 0.5850 0.128 0.276 0.596
#> GSM97932 1 0.0000 0.8601 1.000 0.000 0.000
#> GSM97939 2 0.5138 0.6957 0.000 0.748 0.252
#> GSM97951 2 0.2356 0.8295 0.000 0.928 0.072
#> GSM97957 3 0.0892 0.7225 0.020 0.000 0.980
#> GSM97972 2 0.6793 0.2882 0.012 0.536 0.452
#> GSM97793 3 0.0892 0.7225 0.020 0.000 0.980
#> GSM97795 2 0.4452 0.7526 0.000 0.808 0.192
#> GSM97802 3 0.4974 0.6730 0.236 0.000 0.764
#> GSM97810 2 0.4842 0.7228 0.000 0.776 0.224
#> GSM97815 2 0.5178 0.6938 0.000 0.744 0.256
#> GSM97837 3 0.6244 0.3696 0.440 0.000 0.560
#> GSM97843 3 0.6051 0.4051 0.012 0.292 0.696
#> GSM97890 3 0.6973 0.0305 0.020 0.416 0.564
#> GSM97899 1 0.0000 0.8601 1.000 0.000 0.000
#> GSM97910 3 0.6271 0.7234 0.140 0.088 0.772
#> GSM97916 3 0.6964 0.6706 0.264 0.052 0.684
#> GSM97920 3 0.0983 0.7181 0.004 0.016 0.980
#> GSM97921 3 0.7885 0.5624 0.336 0.072 0.592
#> GSM97927 3 0.6217 0.6682 0.264 0.024 0.712
#> GSM97937 1 0.3619 0.7541 0.864 0.000 0.136
#> GSM97941 2 0.0892 0.8565 0.000 0.980 0.020
#> GSM97943 3 0.4121 0.6547 0.000 0.168 0.832
#> GSM97958 3 0.7058 0.7083 0.180 0.100 0.720
#> GSM97960 2 0.3816 0.7824 0.000 0.852 0.148
#> GSM97794 3 0.7954 0.6793 0.192 0.148 0.660
#> GSM97796 1 0.0000 0.8601 1.000 0.000 0.000
#> GSM97797 3 0.5851 0.7263 0.140 0.068 0.792
#> GSM97798 1 0.0000 0.8601 1.000 0.000 0.000
#> GSM97801 3 0.5851 0.7263 0.140 0.068 0.792
#> GSM97806 3 0.6490 0.6775 0.256 0.036 0.708
#> GSM97808 1 0.0000 0.8601 1.000 0.000 0.000
#> GSM97813 3 0.6305 0.2475 0.484 0.000 0.516
#> GSM97814 1 0.0000 0.8601 1.000 0.000 0.000
#> GSM97818 3 0.8337 0.6034 0.296 0.112 0.592
#> GSM97819 3 0.0424 0.7180 0.008 0.000 0.992
#> GSM97821 2 0.4887 0.7069 0.000 0.772 0.228
#> GSM97826 3 0.6215 0.4012 0.428 0.000 0.572
#> GSM97829 1 0.6647 0.1553 0.592 0.012 0.396
#> GSM97832 2 0.3482 0.7963 0.000 0.872 0.128
#> GSM97836 3 0.6232 0.7007 0.220 0.040 0.740
#> GSM97839 1 0.0000 0.8601 1.000 0.000 0.000
#> GSM97844 2 0.0000 0.8653 0.000 1.000 0.000
#> GSM97847 1 0.4291 0.6982 0.820 0.000 0.180
#> GSM97851 1 0.0000 0.8601 1.000 0.000 0.000
#> GSM97852 1 0.4291 0.6982 0.820 0.000 0.180
#> GSM97856 1 0.0000 0.8601 1.000 0.000 0.000
#> GSM97858 2 0.0000 0.8653 0.000 1.000 0.000
#> GSM97859 3 0.6291 0.2888 0.468 0.000 0.532
#> GSM97861 3 0.6388 0.6511 0.284 0.024 0.692
#> GSM97863 1 0.0000 0.8601 1.000 0.000 0.000
#> GSM97869 3 0.7022 0.6733 0.260 0.056 0.684
#> GSM97870 3 0.6291 0.2888 0.468 0.000 0.532
#> GSM97871 1 0.0000 0.8601 1.000 0.000 0.000
#> GSM97877 3 0.8437 0.5850 0.128 0.276 0.596
#> GSM97879 1 0.6879 0.0201 0.556 0.016 0.428
#> GSM97882 3 0.6526 0.6747 0.260 0.036 0.704
#> GSM97885 3 0.6526 0.6742 0.260 0.036 0.704
#> GSM97886 1 0.0000 0.8601 1.000 0.000 0.000
#> GSM97887 1 0.0000 0.8601 1.000 0.000 0.000
#> GSM97888 1 0.6260 -0.0185 0.552 0.000 0.448
#> GSM97889 3 0.5678 0.5893 0.316 0.000 0.684
#> GSM97891 3 0.5967 0.7014 0.216 0.032 0.752
#> GSM97892 2 0.0000 0.8653 0.000 1.000 0.000
#> GSM97893 1 0.4291 0.6828 0.820 0.000 0.180
#> GSM97894 1 0.0000 0.8601 1.000 0.000 0.000
#> GSM97895 1 0.0000 0.8601 1.000 0.000 0.000
#> GSM97896 1 0.6062 0.2239 0.616 0.000 0.384
#> GSM97898 1 0.0000 0.8601 1.000 0.000 0.000
#> GSM97903 1 0.7392 -0.2004 0.500 0.032 0.468
#> GSM97905 3 0.6140 0.4427 0.404 0.000 0.596
#> GSM97906 1 0.0000 0.8601 1.000 0.000 0.000
#> GSM97908 1 0.3686 0.7521 0.860 0.000 0.140
#> GSM97912 3 0.6140 0.4427 0.404 0.000 0.596
#> GSM97914 3 0.7694 0.6007 0.316 0.068 0.616
#> GSM97915 1 0.0000 0.8601 1.000 0.000 0.000
#> GSM97917 1 0.0000 0.8601 1.000 0.000 0.000
#> GSM97918 1 0.0000 0.8601 1.000 0.000 0.000
#> GSM97919 1 0.0000 0.8601 1.000 0.000 0.000
#> GSM97922 3 0.6291 0.2888 0.468 0.000 0.532
#> GSM97924 2 0.0000 0.8653 0.000 1.000 0.000
#> GSM97926 3 0.6232 0.7007 0.220 0.040 0.740
#> GSM97930 1 0.6274 -0.0643 0.544 0.000 0.456
#> GSM97931 2 0.6793 0.2882 0.012 0.536 0.452
#> GSM97935 3 0.6355 0.6553 0.280 0.024 0.696
#> GSM97936 1 0.1163 0.8445 0.972 0.000 0.028
#> GSM97938 1 0.1163 0.8437 0.972 0.000 0.028
#> GSM97940 1 0.0000 0.8601 1.000 0.000 0.000
#> GSM97942 3 0.1163 0.7232 0.028 0.000 0.972
#> GSM97945 1 0.4062 0.7207 0.836 0.000 0.164
#> GSM97946 2 0.0000 0.8653 0.000 1.000 0.000
#> GSM97948 3 0.3412 0.7197 0.124 0.000 0.876
#> GSM97950 1 0.0000 0.8601 1.000 0.000 0.000
#> GSM97952 1 0.0000 0.8601 1.000 0.000 0.000
#> GSM97953 1 0.2796 0.7980 0.908 0.000 0.092
#> GSM97954 1 0.5706 0.4161 0.680 0.000 0.320
#> GSM97955 1 0.0747 0.8523 0.984 0.000 0.016
#> GSM97959 3 0.8028 0.6752 0.168 0.176 0.656
#> GSM97961 1 0.0000 0.8601 1.000 0.000 0.000
#> GSM97963 1 0.0000 0.8601 1.000 0.000 0.000
#> GSM97965 1 0.0000 0.8601 1.000 0.000 0.000
#> GSM97966 1 0.0000 0.8601 1.000 0.000 0.000
#> GSM97967 2 0.0000 0.8653 0.000 1.000 0.000
#> GSM97968 2 0.0000 0.8653 0.000 1.000 0.000
#> GSM97969 1 0.6291 -0.0994 0.532 0.000 0.468
#> GSM97971 3 0.6299 0.2686 0.476 0.000 0.524
#> GSM97799 2 0.6180 0.4600 0.000 0.584 0.416
#> GSM97823 2 0.0000 0.8653 0.000 1.000 0.000
#> GSM97824 3 0.6330 0.1446 0.004 0.396 0.600
#> GSM97830 3 0.0848 0.7198 0.008 0.008 0.984
#> GSM97835 2 0.5465 0.6591 0.000 0.712 0.288
#> GSM97838 2 0.0000 0.8653 0.000 1.000 0.000
#> GSM97841 2 0.0000 0.8653 0.000 1.000 0.000
#> GSM97842 2 0.6154 0.4765 0.000 0.592 0.408
#> GSM97854 2 0.0000 0.8653 0.000 1.000 0.000
#> GSM97857 3 0.6045 0.1864 0.000 0.380 0.620
#> GSM97860 3 0.0892 0.7225 0.020 0.000 0.980
#> GSM97862 3 0.4465 0.5967 0.004 0.176 0.820
#> GSM97864 2 0.0000 0.8653 0.000 1.000 0.000
#> GSM97866 3 0.4629 0.5830 0.004 0.188 0.808
#> GSM97868 3 0.6260 -0.0823 0.000 0.448 0.552
#> GSM97872 3 0.5926 0.5380 0.356 0.000 0.644
#> GSM97873 2 0.6126 0.4959 0.000 0.600 0.400
#> GSM97874 3 0.0848 0.7198 0.008 0.008 0.984
#> GSM97875 3 0.0424 0.7180 0.008 0.000 0.992
#> GSM97876 3 0.0892 0.7225 0.020 0.000 0.980
#> GSM97880 3 0.0892 0.7225 0.020 0.000 0.980
#> GSM97881 2 0.6308 0.2711 0.000 0.508 0.492
#> GSM97884 2 0.6252 0.4032 0.000 0.556 0.444
#> GSM97901 3 0.4629 0.5827 0.004 0.188 0.808
#> GSM97902 3 0.7058 0.7083 0.180 0.100 0.720
#> GSM97909 2 0.4842 0.7115 0.000 0.776 0.224
#> GSM97911 2 0.6308 0.2711 0.000 0.508 0.492
#> GSM97923 3 0.0892 0.7225 0.020 0.000 0.980
#> GSM97928 3 0.5926 0.5380 0.356 0.000 0.644
#> GSM97929 2 0.0000 0.8653 0.000 1.000 0.000
#> GSM97933 3 0.0892 0.7225 0.020 0.000 0.980
#> GSM97934 3 0.0892 0.7225 0.020 0.000 0.980
#> GSM97944 2 0.6180 0.4600 0.000 0.584 0.416
#> GSM97949 2 0.0000 0.8653 0.000 1.000 0.000
#> GSM97956 3 0.5929 0.3636 0.004 0.320 0.676
#> GSM97962 3 0.2116 0.7184 0.012 0.040 0.948
#> GSM97964 2 0.6260 0.3836 0.000 0.552 0.448
#> GSM97970 2 0.6126 0.4928 0.000 0.600 0.400
#> GSM97822 3 0.5621 0.5991 0.308 0.000 0.692
#> GSM97831 3 0.1015 0.7199 0.008 0.012 0.980
#> GSM97845 1 0.5529 0.4766 0.704 0.000 0.296
#> GSM97865 3 0.6962 0.7089 0.184 0.092 0.724
#> GSM97867 3 0.0892 0.7225 0.020 0.000 0.980
#> GSM97883 3 0.4796 0.6871 0.220 0.000 0.780
#> GSM97897 3 0.6079 0.4846 0.388 0.000 0.612
#> GSM97900 1 0.0000 0.8601 1.000 0.000 0.000
#> GSM97904 3 0.5905 0.5660 0.352 0.000 0.648
#> GSM97907 2 0.0000 0.8653 0.000 1.000 0.000
#> GSM97925 3 0.3340 0.7203 0.120 0.000 0.880
#> GSM97947 3 0.0424 0.7180 0.008 0.000 0.992
cbind(get_classes(res, k = 4), get_membership(res, k = 4))
#> class entropy silhouette p1 p2 p3 p4
#> GSM97800 2 0.0000 0.8530 0.000 1.000 0.000 0.000
#> GSM97803 2 0.0000 0.8530 0.000 1.000 0.000 0.000
#> GSM97804 2 0.0000 0.8530 0.000 1.000 0.000 0.000
#> GSM97805 2 0.0000 0.8530 0.000 1.000 0.000 0.000
#> GSM97807 2 0.0000 0.8530 0.000 1.000 0.000 0.000
#> GSM97809 2 0.0000 0.8530 0.000 1.000 0.000 0.000
#> GSM97811 2 0.0000 0.8530 0.000 1.000 0.000 0.000
#> GSM97812 2 0.0000 0.8530 0.000 1.000 0.000 0.000
#> GSM97816 1 0.6245 0.3236 0.636 0.096 0.268 0.000
#> GSM97817 2 0.0000 0.8530 0.000 1.000 0.000 0.000
#> GSM97820 2 0.0000 0.8530 0.000 1.000 0.000 0.000
#> GSM97825 2 0.0000 0.8530 0.000 1.000 0.000 0.000
#> GSM97827 2 0.0000 0.8530 0.000 1.000 0.000 0.000
#> GSM97828 1 0.6245 0.3236 0.636 0.096 0.268 0.000
#> GSM97833 2 0.0000 0.8530 0.000 1.000 0.000 0.000
#> GSM97834 2 0.0000 0.8530 0.000 1.000 0.000 0.000
#> GSM97840 2 0.1576 0.8278 0.048 0.948 0.004 0.000
#> GSM97846 2 0.0000 0.8530 0.000 1.000 0.000 0.000
#> GSM97848 2 0.0000 0.8530 0.000 1.000 0.000 0.000
#> GSM97849 2 0.0000 0.8530 0.000 1.000 0.000 0.000
#> GSM97850 2 0.0000 0.8530 0.000 1.000 0.000 0.000
#> GSM97853 2 0.0000 0.8530 0.000 1.000 0.000 0.000
#> GSM97855 2 0.0000 0.8530 0.000 1.000 0.000 0.000
#> GSM97878 1 0.4333 0.6473 0.820 0.004 0.056 0.120
#> GSM97913 1 0.5364 0.4792 0.732 0.204 0.060 0.004
#> GSM97932 4 0.0188 0.8829 0.004 0.000 0.000 0.996
#> GSM97939 2 0.5669 0.6499 0.092 0.708 0.200 0.000
#> GSM97951 2 0.2739 0.8063 0.036 0.904 0.060 0.000
#> GSM97957 3 0.1302 0.6730 0.044 0.000 0.956 0.000
#> GSM97972 2 0.7483 0.2669 0.360 0.456 0.184 0.000
#> GSM97793 3 0.0921 0.6753 0.028 0.000 0.972 0.000
#> GSM97795 2 0.4701 0.7193 0.056 0.780 0.164 0.000
#> GSM97802 3 0.5730 0.2185 0.344 0.000 0.616 0.040
#> GSM97810 2 0.5267 0.6821 0.076 0.740 0.184 0.000
#> GSM97815 2 0.5681 0.6455 0.088 0.704 0.208 0.000
#> GSM97837 1 0.5309 0.5640 0.700 0.000 0.044 0.256
#> GSM97843 3 0.5522 0.4209 0.044 0.288 0.668 0.000
#> GSM97890 3 0.6400 0.0684 0.068 0.408 0.524 0.000
#> GSM97899 4 0.0188 0.8838 0.004 0.000 0.000 0.996
#> GSM97910 1 0.4623 0.5696 0.792 0.020 0.168 0.020
#> GSM97916 1 0.5241 0.6421 0.760 0.008 0.164 0.068
#> GSM97920 3 0.2888 0.6220 0.124 0.004 0.872 0.000
#> GSM97921 1 0.5774 0.6163 0.720 0.008 0.088 0.184
#> GSM97927 1 0.4920 0.6243 0.756 0.000 0.192 0.052
#> GSM97937 4 0.3710 0.7042 0.192 0.000 0.004 0.804
#> GSM97941 2 0.0779 0.8433 0.016 0.980 0.004 0.000
#> GSM97943 1 0.6245 0.3236 0.636 0.096 0.268 0.000
#> GSM97958 1 0.3472 0.6188 0.868 0.024 0.100 0.008
#> GSM97960 2 0.4205 0.7518 0.056 0.820 0.124 0.000
#> GSM97794 1 0.5455 0.6114 0.776 0.088 0.104 0.032
#> GSM97796 4 0.0000 0.8841 0.000 0.000 0.000 1.000
#> GSM97797 1 0.4572 0.5678 0.796 0.016 0.164 0.024
#> GSM97798 4 0.0188 0.8838 0.004 0.000 0.000 0.996
#> GSM97801 1 0.4572 0.5678 0.796 0.016 0.164 0.024
#> GSM97806 1 0.5257 0.6216 0.728 0.000 0.212 0.060
#> GSM97808 4 0.0188 0.8838 0.004 0.000 0.000 0.996
#> GSM97813 1 0.7866 0.2533 0.376 0.000 0.348 0.276
#> GSM97814 4 0.0188 0.8838 0.004 0.000 0.000 0.996
#> GSM97818 1 0.4796 0.6298 0.812 0.064 0.024 0.100
#> GSM97819 3 0.0469 0.6719 0.012 0.000 0.988 0.000
#> GSM97821 2 0.5369 0.6914 0.144 0.744 0.112 0.000
#> GSM97826 1 0.5596 0.5905 0.696 0.000 0.068 0.236
#> GSM97829 1 0.5337 0.2363 0.564 0.000 0.012 0.424
#> GSM97832 2 0.3793 0.7684 0.044 0.844 0.112 0.000
#> GSM97836 1 0.4635 0.6069 0.756 0.000 0.216 0.028
#> GSM97839 4 0.0000 0.8841 0.000 0.000 0.000 1.000
#> GSM97844 2 0.0000 0.8530 0.000 1.000 0.000 0.000
#> GSM97847 4 0.4456 0.5645 0.280 0.000 0.004 0.716
#> GSM97851 4 0.0188 0.8829 0.004 0.000 0.000 0.996
#> GSM97852 4 0.4456 0.5645 0.280 0.000 0.004 0.716
#> GSM97856 4 0.0000 0.8841 0.000 0.000 0.000 1.000
#> GSM97858 2 0.0000 0.8530 0.000 1.000 0.000 0.000
#> GSM97859 1 0.7830 0.2507 0.384 0.000 0.356 0.260
#> GSM97861 1 0.5240 0.6260 0.740 0.000 0.188 0.072
#> GSM97863 4 0.0000 0.8841 0.000 0.000 0.000 1.000
#> GSM97869 1 0.5125 0.6421 0.768 0.008 0.160 0.064
#> GSM97870 1 0.7830 0.2507 0.384 0.000 0.356 0.260
#> GSM97871 4 0.0000 0.8841 0.000 0.000 0.000 1.000
#> GSM97877 1 0.5364 0.4792 0.732 0.204 0.060 0.004
#> GSM97879 1 0.6844 0.3509 0.500 0.000 0.104 0.396
#> GSM97882 1 0.5328 0.6217 0.724 0.000 0.212 0.064
#> GSM97885 1 0.4990 0.6338 0.756 0.000 0.184 0.060
#> GSM97886 4 0.0188 0.8838 0.004 0.000 0.000 0.996
#> GSM97887 4 0.0188 0.8838 0.004 0.000 0.000 0.996
#> GSM97888 4 0.7918 -0.3158 0.332 0.000 0.316 0.352
#> GSM97889 3 0.6831 0.0732 0.352 0.000 0.536 0.112
#> GSM97891 1 0.4574 0.6039 0.756 0.000 0.220 0.024
#> GSM97892 2 0.0000 0.8530 0.000 1.000 0.000 0.000
#> GSM97893 4 0.4406 0.5130 0.300 0.000 0.000 0.700
#> GSM97894 4 0.0000 0.8841 0.000 0.000 0.000 1.000
#> GSM97895 4 0.0188 0.8829 0.004 0.000 0.000 0.996
#> GSM97896 4 0.7814 -0.1880 0.304 0.000 0.280 0.416
#> GSM97898 4 0.0188 0.8829 0.004 0.000 0.000 0.996
#> GSM97903 1 0.6637 0.4867 0.572 0.000 0.104 0.324
#> GSM97905 3 0.7550 -0.1372 0.372 0.000 0.436 0.192
#> GSM97906 4 0.0188 0.8838 0.004 0.000 0.000 0.996
#> GSM97908 4 0.3982 0.6712 0.220 0.000 0.004 0.776
#> GSM97912 3 0.7550 -0.1372 0.372 0.000 0.436 0.192
#> GSM97914 1 0.5324 0.6357 0.760 0.008 0.084 0.148
#> GSM97915 4 0.0000 0.8841 0.000 0.000 0.000 1.000
#> GSM97917 4 0.0188 0.8829 0.004 0.000 0.000 0.996
#> GSM97918 4 0.0188 0.8829 0.004 0.000 0.000 0.996
#> GSM97919 4 0.0000 0.8841 0.000 0.000 0.000 1.000
#> GSM97922 1 0.7830 0.2507 0.384 0.000 0.356 0.260
#> GSM97924 2 0.0000 0.8530 0.000 1.000 0.000 0.000
#> GSM97926 1 0.4635 0.6069 0.756 0.000 0.216 0.028
#> GSM97930 1 0.4936 0.4295 0.652 0.000 0.008 0.340
#> GSM97931 2 0.7483 0.2669 0.360 0.456 0.184 0.000
#> GSM97935 1 0.5212 0.6249 0.740 0.000 0.192 0.068
#> GSM97936 4 0.1118 0.8629 0.036 0.000 0.000 0.964
#> GSM97938 4 0.1474 0.8526 0.052 0.000 0.000 0.948
#> GSM97940 4 0.0188 0.8838 0.004 0.000 0.000 0.996
#> GSM97942 3 0.1118 0.6712 0.036 0.000 0.964 0.000
#> GSM97945 4 0.4974 0.5980 0.224 0.000 0.040 0.736
#> GSM97946 2 0.0000 0.8530 0.000 1.000 0.000 0.000
#> GSM97948 3 0.4507 0.4765 0.224 0.000 0.756 0.020
#> GSM97950 4 0.0188 0.8829 0.004 0.000 0.000 0.996
#> GSM97952 4 0.0000 0.8841 0.000 0.000 0.000 1.000
#> GSM97953 4 0.2773 0.7929 0.116 0.000 0.004 0.880
#> GSM97954 4 0.6182 0.0301 0.428 0.000 0.052 0.520
#> GSM97955 4 0.0657 0.8766 0.012 0.000 0.004 0.984
#> GSM97959 1 0.3734 0.5830 0.856 0.096 0.044 0.004
#> GSM97961 4 0.0188 0.8838 0.004 0.000 0.000 0.996
#> GSM97963 4 0.0188 0.8838 0.004 0.000 0.000 0.996
#> GSM97965 4 0.0188 0.8838 0.004 0.000 0.000 0.996
#> GSM97966 4 0.0188 0.8838 0.004 0.000 0.000 0.996
#> GSM97967 2 0.0000 0.8530 0.000 1.000 0.000 0.000
#> GSM97968 2 0.0000 0.8530 0.000 1.000 0.000 0.000
#> GSM97969 1 0.7916 0.2522 0.356 0.000 0.316 0.328
#> GSM97971 1 0.7849 0.2508 0.380 0.000 0.352 0.268
#> GSM97799 2 0.6653 0.4021 0.096 0.548 0.356 0.000
#> GSM97823 2 0.0000 0.8530 0.000 1.000 0.000 0.000
#> GSM97824 3 0.6421 0.1947 0.076 0.368 0.556 0.000
#> GSM97830 3 0.2011 0.6492 0.080 0.000 0.920 0.000
#> GSM97835 2 0.5995 0.6095 0.096 0.672 0.232 0.000
#> GSM97838 2 0.0000 0.8530 0.000 1.000 0.000 0.000
#> GSM97841 2 0.0000 0.8530 0.000 1.000 0.000 0.000
#> GSM97842 2 0.6627 0.4171 0.096 0.556 0.348 0.000
#> GSM97854 2 0.0000 0.8530 0.000 1.000 0.000 0.000
#> GSM97857 3 0.6482 0.2361 0.084 0.352 0.564 0.000
#> GSM97860 3 0.0921 0.6753 0.028 0.000 0.972 0.000
#> GSM97862 3 0.4669 0.5653 0.052 0.168 0.780 0.000
#> GSM97864 2 0.0000 0.8530 0.000 1.000 0.000 0.000
#> GSM97866 3 0.4798 0.5575 0.052 0.180 0.768 0.000
#> GSM97868 3 0.6642 -0.0444 0.084 0.424 0.492 0.000
#> GSM97872 1 0.7240 0.2458 0.456 0.000 0.400 0.144
#> GSM97873 2 0.6468 0.4356 0.084 0.568 0.348 0.000
#> GSM97874 3 0.2149 0.6440 0.088 0.000 0.912 0.000
#> GSM97875 3 0.0469 0.6719 0.012 0.000 0.988 0.000
#> GSM97876 3 0.0921 0.6753 0.028 0.000 0.972 0.000
#> GSM97880 3 0.0921 0.6753 0.028 0.000 0.972 0.000
#> GSM97881 2 0.6650 0.2227 0.084 0.484 0.432 0.000
#> GSM97884 2 0.6529 0.3510 0.080 0.532 0.388 0.000
#> GSM97901 3 0.4832 0.5577 0.056 0.176 0.768 0.000
#> GSM97902 1 0.3472 0.6188 0.868 0.024 0.100 0.008
#> GSM97909 2 0.5272 0.6990 0.136 0.752 0.112 0.000
#> GSM97911 2 0.6650 0.2227 0.084 0.484 0.432 0.000
#> GSM97923 3 0.0921 0.6753 0.028 0.000 0.972 0.000
#> GSM97928 1 0.7240 0.2458 0.456 0.000 0.400 0.144
#> GSM97929 2 0.0000 0.8530 0.000 1.000 0.000 0.000
#> GSM97933 3 0.1118 0.6740 0.036 0.000 0.964 0.000
#> GSM97934 3 0.1302 0.6730 0.044 0.000 0.956 0.000
#> GSM97944 2 0.6653 0.4021 0.096 0.548 0.356 0.000
#> GSM97949 2 0.0000 0.8530 0.000 1.000 0.000 0.000
#> GSM97956 3 0.5929 0.4002 0.064 0.296 0.640 0.000
#> GSM97962 3 0.2797 0.6620 0.068 0.032 0.900 0.000
#> GSM97964 2 0.6694 0.3194 0.092 0.516 0.392 0.000
#> GSM97970 2 0.6561 0.4327 0.092 0.564 0.344 0.000
#> GSM97822 3 0.6738 0.0853 0.352 0.000 0.544 0.104
#> GSM97831 3 0.2197 0.6485 0.080 0.004 0.916 0.000
#> GSM97845 4 0.5989 0.1578 0.400 0.000 0.044 0.556
#> GSM97865 1 0.3495 0.6228 0.868 0.020 0.100 0.012
#> GSM97867 3 0.0921 0.6753 0.028 0.000 0.972 0.000
#> GSM97883 3 0.5691 0.2796 0.304 0.000 0.648 0.048
#> GSM97897 3 0.7468 -0.0703 0.352 0.000 0.464 0.184
#> GSM97900 4 0.0188 0.8838 0.004 0.000 0.000 0.996
#> GSM97904 1 0.6990 0.4545 0.552 0.000 0.304 0.144
#> GSM97907 2 0.0000 0.8530 0.000 1.000 0.000 0.000
#> GSM97925 3 0.4399 0.4810 0.224 0.000 0.760 0.016
#> GSM97947 3 0.0469 0.6719 0.012 0.000 0.988 0.000
cbind(get_classes(res, k = 5), get_membership(res, k = 5))
#> class entropy silhouette p1 p2 p3 p4 p5
#> GSM97800 2 0.0000 0.85929 0.000 1.000 0.000 0.000 0.000
#> GSM97803 2 0.0000 0.85929 0.000 1.000 0.000 0.000 0.000
#> GSM97804 2 0.0000 0.85929 0.000 1.000 0.000 0.000 0.000
#> GSM97805 2 0.0000 0.85929 0.000 1.000 0.000 0.000 0.000
#> GSM97807 2 0.0000 0.85929 0.000 1.000 0.000 0.000 0.000
#> GSM97809 2 0.0000 0.85929 0.000 1.000 0.000 0.000 0.000
#> GSM97811 2 0.0000 0.85929 0.000 1.000 0.000 0.000 0.000
#> GSM97812 2 0.0000 0.85929 0.000 1.000 0.000 0.000 0.000
#> GSM97816 1 0.4650 0.43885 0.776 0.060 0.128 0.000 0.036
#> GSM97817 2 0.0000 0.85929 0.000 1.000 0.000 0.000 0.000
#> GSM97820 2 0.0000 0.85929 0.000 1.000 0.000 0.000 0.000
#> GSM97825 2 0.0000 0.85929 0.000 1.000 0.000 0.000 0.000
#> GSM97827 2 0.0000 0.85929 0.000 1.000 0.000 0.000 0.000
#> GSM97828 1 0.4650 0.43885 0.776 0.060 0.128 0.000 0.036
#> GSM97833 2 0.0000 0.85929 0.000 1.000 0.000 0.000 0.000
#> GSM97834 2 0.0000 0.85929 0.000 1.000 0.000 0.000 0.000
#> GSM97840 2 0.1788 0.82338 0.056 0.932 0.008 0.000 0.004
#> GSM97846 2 0.0000 0.85929 0.000 1.000 0.000 0.000 0.000
#> GSM97848 2 0.0000 0.85929 0.000 1.000 0.000 0.000 0.000
#> GSM97849 2 0.0000 0.85929 0.000 1.000 0.000 0.000 0.000
#> GSM97850 2 0.0000 0.85929 0.000 1.000 0.000 0.000 0.000
#> GSM97853 2 0.0000 0.85929 0.000 1.000 0.000 0.000 0.000
#> GSM97855 2 0.0000 0.85929 0.000 1.000 0.000 0.000 0.000
#> GSM97878 1 0.5241 0.56689 0.692 0.000 0.016 0.072 0.220
#> GSM97913 1 0.5458 0.49968 0.696 0.172 0.020 0.000 0.112
#> GSM97932 4 0.0798 0.88659 0.008 0.000 0.000 0.976 0.016
#> GSM97939 2 0.5567 0.61285 0.124 0.680 0.180 0.000 0.016
#> GSM97951 2 0.2741 0.80067 0.032 0.892 0.064 0.000 0.012
#> GSM97957 3 0.1697 0.74668 0.008 0.000 0.932 0.000 0.060
#> GSM97972 1 0.6281 -0.13382 0.468 0.420 0.096 0.000 0.016
#> GSM97793 3 0.1671 0.74542 0.000 0.000 0.924 0.000 0.076
#> GSM97795 2 0.4568 0.70595 0.084 0.768 0.136 0.000 0.012
#> GSM97802 5 0.3734 0.58976 0.004 0.000 0.240 0.004 0.752
#> GSM97810 2 0.5056 0.66176 0.100 0.724 0.164 0.000 0.012
#> GSM97815 2 0.5545 0.61043 0.116 0.680 0.188 0.000 0.016
#> GSM97837 1 0.6477 0.35612 0.532 0.000 0.012 0.160 0.296
#> GSM97843 3 0.5449 0.50609 0.036 0.280 0.648 0.000 0.036
#> GSM97890 3 0.6446 0.18014 0.052 0.392 0.496 0.000 0.060
#> GSM97899 4 0.0290 0.89302 0.000 0.000 0.000 0.992 0.008
#> GSM97910 1 0.3218 0.55790 0.860 0.000 0.032 0.012 0.096
#> GSM97916 1 0.5989 0.51974 0.552 0.004 0.048 0.028 0.368
#> GSM97920 3 0.3321 0.69164 0.136 0.000 0.832 0.000 0.032
#> GSM97921 1 0.6491 0.52220 0.608 0.000 0.044 0.148 0.200
#> GSM97927 1 0.5855 0.44266 0.496 0.000 0.052 0.020 0.432
#> GSM97937 4 0.4679 0.65088 0.136 0.000 0.000 0.740 0.124
#> GSM97941 2 0.0671 0.84896 0.016 0.980 0.004 0.000 0.000
#> GSM97943 1 0.4650 0.43885 0.776 0.060 0.128 0.000 0.036
#> GSM97958 1 0.4705 0.59484 0.724 0.008 0.052 0.000 0.216
#> GSM97960 2 0.4059 0.74158 0.068 0.808 0.112 0.000 0.012
#> GSM97794 1 0.6144 0.57292 0.636 0.072 0.040 0.008 0.244
#> GSM97796 4 0.0000 0.89360 0.000 0.000 0.000 1.000 0.000
#> GSM97797 1 0.3346 0.53224 0.856 0.000 0.036 0.016 0.092
#> GSM97798 4 0.0290 0.89302 0.000 0.000 0.000 0.992 0.008
#> GSM97801 1 0.3346 0.53224 0.856 0.000 0.036 0.016 0.092
#> GSM97806 1 0.6123 0.47098 0.496 0.000 0.068 0.024 0.412
#> GSM97808 4 0.0290 0.89302 0.000 0.000 0.000 0.992 0.008
#> GSM97813 5 0.3433 0.70272 0.008 0.000 0.024 0.136 0.832
#> GSM97814 4 0.0290 0.89302 0.000 0.000 0.000 0.992 0.008
#> GSM97818 1 0.5719 0.56595 0.688 0.048 0.004 0.064 0.196
#> GSM97819 3 0.1701 0.74028 0.016 0.000 0.936 0.000 0.048
#> GSM97821 2 0.5303 0.67756 0.136 0.732 0.084 0.000 0.048
#> GSM97826 1 0.6413 0.34628 0.524 0.000 0.012 0.140 0.324
#> GSM97829 1 0.6861 0.14956 0.400 0.000 0.004 0.340 0.256
#> GSM97832 2 0.3629 0.76108 0.072 0.832 0.092 0.000 0.004
#> GSM97836 1 0.5917 0.48718 0.532 0.000 0.076 0.012 0.380
#> GSM97839 4 0.0000 0.89360 0.000 0.000 0.000 1.000 0.000
#> GSM97844 2 0.0000 0.85929 0.000 1.000 0.000 0.000 0.000
#> GSM97847 4 0.5602 0.48036 0.216 0.000 0.000 0.636 0.148
#> GSM97851 4 0.0162 0.89245 0.004 0.000 0.000 0.996 0.000
#> GSM97852 4 0.5602 0.48036 0.216 0.000 0.000 0.636 0.148
#> GSM97856 4 0.0000 0.89360 0.000 0.000 0.000 1.000 0.000
#> GSM97858 2 0.0000 0.85929 0.000 1.000 0.000 0.000 0.000
#> GSM97859 5 0.3283 0.70531 0.008 0.000 0.028 0.116 0.848
#> GSM97861 1 0.6025 0.41464 0.476 0.000 0.048 0.032 0.444
#> GSM97863 4 0.0000 0.89360 0.000 0.000 0.000 1.000 0.000
#> GSM97869 1 0.5968 0.52520 0.560 0.004 0.048 0.028 0.360
#> GSM97870 5 0.3283 0.70531 0.008 0.000 0.028 0.116 0.848
#> GSM97871 4 0.0000 0.89360 0.000 0.000 0.000 1.000 0.000
#> GSM97877 1 0.5458 0.49968 0.696 0.172 0.020 0.000 0.112
#> GSM97879 5 0.7477 -0.04754 0.296 0.000 0.032 0.332 0.340
#> GSM97882 1 0.6127 0.46701 0.492 0.000 0.068 0.024 0.416
#> GSM97885 1 0.6024 0.48307 0.516 0.000 0.056 0.028 0.400
#> GSM97886 4 0.0290 0.89302 0.000 0.000 0.000 0.992 0.008
#> GSM97887 4 0.0290 0.89302 0.000 0.000 0.000 0.992 0.008
#> GSM97888 5 0.4004 0.65669 0.008 0.000 0.016 0.216 0.760
#> GSM97889 5 0.3734 0.65665 0.000 0.000 0.168 0.036 0.796
#> GSM97891 1 0.5856 0.47096 0.516 0.000 0.076 0.008 0.400
#> GSM97892 2 0.0000 0.85929 0.000 1.000 0.000 0.000 0.000
#> GSM97893 4 0.5759 0.41088 0.180 0.000 0.000 0.620 0.200
#> GSM97894 4 0.0000 0.89360 0.000 0.000 0.000 1.000 0.000
#> GSM97895 4 0.0798 0.88659 0.008 0.000 0.000 0.976 0.016
#> GSM97896 5 0.4423 0.57151 0.008 0.000 0.012 0.296 0.684
#> GSM97898 4 0.0451 0.89065 0.004 0.000 0.000 0.988 0.008
#> GSM97903 5 0.7087 -0.20757 0.372 0.000 0.016 0.232 0.380
#> GSM97905 5 0.4237 0.70155 0.012 0.000 0.112 0.080 0.796
#> GSM97906 4 0.0290 0.89302 0.000 0.000 0.000 0.992 0.008
#> GSM97908 4 0.5006 0.60490 0.180 0.000 0.000 0.704 0.116
#> GSM97912 5 0.4237 0.70155 0.012 0.000 0.112 0.080 0.796
#> GSM97914 1 0.5940 0.55236 0.652 0.000 0.032 0.108 0.208
#> GSM97915 4 0.0000 0.89360 0.000 0.000 0.000 1.000 0.000
#> GSM97917 4 0.0693 0.88742 0.012 0.000 0.000 0.980 0.008
#> GSM97918 4 0.0579 0.88912 0.008 0.000 0.000 0.984 0.008
#> GSM97919 4 0.0000 0.89360 0.000 0.000 0.000 1.000 0.000
#> GSM97922 5 0.3283 0.70531 0.008 0.000 0.028 0.116 0.848
#> GSM97924 2 0.0000 0.85929 0.000 1.000 0.000 0.000 0.000
#> GSM97926 1 0.5917 0.48718 0.532 0.000 0.076 0.012 0.380
#> GSM97930 1 0.6510 0.26224 0.488 0.000 0.000 0.260 0.252
#> GSM97931 1 0.6281 -0.13382 0.468 0.420 0.096 0.000 0.016
#> GSM97935 1 0.6013 0.41640 0.476 0.000 0.052 0.028 0.444
#> GSM97936 4 0.1403 0.86760 0.024 0.000 0.000 0.952 0.024
#> GSM97938 4 0.2230 0.84028 0.044 0.000 0.000 0.912 0.044
#> GSM97940 4 0.0290 0.89302 0.000 0.000 0.000 0.992 0.008
#> GSM97942 3 0.1792 0.73903 0.000 0.000 0.916 0.000 0.084
#> GSM97945 4 0.5234 0.55794 0.112 0.000 0.012 0.708 0.168
#> GSM97946 2 0.0000 0.85929 0.000 1.000 0.000 0.000 0.000
#> GSM97948 3 0.5258 0.14427 0.040 0.000 0.548 0.004 0.408
#> GSM97950 4 0.0693 0.88742 0.012 0.000 0.000 0.980 0.008
#> GSM97952 4 0.0000 0.89360 0.000 0.000 0.000 1.000 0.000
#> GSM97953 4 0.3593 0.76035 0.084 0.000 0.000 0.828 0.088
#> GSM97954 4 0.6700 -0.10379 0.252 0.000 0.000 0.416 0.332
#> GSM97955 4 0.0579 0.88825 0.008 0.000 0.000 0.984 0.008
#> GSM97959 1 0.4422 0.57686 0.776 0.068 0.012 0.000 0.144
#> GSM97961 4 0.0290 0.89302 0.000 0.000 0.000 0.992 0.008
#> GSM97963 4 0.0290 0.89302 0.000 0.000 0.000 0.992 0.008
#> GSM97965 4 0.0290 0.89302 0.000 0.000 0.000 0.992 0.008
#> GSM97966 4 0.0290 0.89302 0.000 0.000 0.000 0.992 0.008
#> GSM97967 2 0.0000 0.85929 0.000 1.000 0.000 0.000 0.000
#> GSM97968 2 0.0000 0.85929 0.000 1.000 0.000 0.000 0.000
#> GSM97969 5 0.3933 0.66969 0.008 0.000 0.020 0.196 0.776
#> GSM97971 5 0.3380 0.70537 0.008 0.000 0.028 0.124 0.840
#> GSM97799 2 0.6375 0.33334 0.120 0.524 0.340 0.000 0.016
#> GSM97823 2 0.0000 0.85929 0.000 1.000 0.000 0.000 0.000
#> GSM97824 3 0.6056 0.31027 0.096 0.344 0.548 0.000 0.012
#> GSM97830 3 0.2535 0.72566 0.076 0.000 0.892 0.000 0.032
#> GSM97835 2 0.5796 0.56846 0.120 0.648 0.216 0.000 0.016
#> GSM97838 2 0.0000 0.85929 0.000 1.000 0.000 0.000 0.000
#> GSM97841 2 0.0000 0.85929 0.000 1.000 0.000 0.000 0.000
#> GSM97842 2 0.6353 0.35104 0.120 0.532 0.332 0.000 0.016
#> GSM97854 2 0.0000 0.85929 0.000 1.000 0.000 0.000 0.000
#> GSM97857 3 0.5975 0.34540 0.092 0.332 0.564 0.000 0.012
#> GSM97860 3 0.1671 0.74542 0.000 0.000 0.924 0.000 0.076
#> GSM97862 3 0.4198 0.67139 0.048 0.144 0.792 0.000 0.016
#> GSM97864 2 0.0000 0.85929 0.000 1.000 0.000 0.000 0.000
#> GSM97866 3 0.4261 0.66367 0.048 0.160 0.780 0.000 0.012
#> GSM97868 3 0.6262 0.08282 0.096 0.400 0.488 0.000 0.016
#> GSM97872 5 0.6039 0.56746 0.156 0.000 0.124 0.052 0.668
#> GSM97873 2 0.6264 0.37034 0.112 0.544 0.328 0.000 0.016
#> GSM97874 3 0.2769 0.71910 0.092 0.000 0.876 0.000 0.032
#> GSM97875 3 0.1701 0.74028 0.016 0.000 0.936 0.000 0.048
#> GSM97876 3 0.1671 0.74542 0.000 0.000 0.924 0.000 0.076
#> GSM97880 3 0.1671 0.74542 0.000 0.000 0.924 0.000 0.076
#> GSM97881 2 0.6285 0.10949 0.096 0.460 0.428 0.000 0.016
#> GSM97884 2 0.6231 0.26644 0.096 0.508 0.380 0.000 0.016
#> GSM97901 3 0.4335 0.66315 0.064 0.152 0.776 0.000 0.008
#> GSM97902 1 0.4705 0.59484 0.724 0.008 0.052 0.000 0.216
#> GSM97909 2 0.5218 0.68620 0.128 0.740 0.084 0.000 0.048
#> GSM97911 2 0.6285 0.10949 0.096 0.460 0.428 0.000 0.016
#> GSM97923 3 0.1671 0.74542 0.000 0.000 0.924 0.000 0.076
#> GSM97928 5 0.6039 0.56746 0.156 0.000 0.124 0.052 0.668
#> GSM97929 2 0.0000 0.85929 0.000 1.000 0.000 0.000 0.000
#> GSM97933 3 0.1894 0.74552 0.008 0.000 0.920 0.000 0.072
#> GSM97934 3 0.1697 0.74668 0.008 0.000 0.932 0.000 0.060
#> GSM97944 2 0.6375 0.33334 0.120 0.524 0.340 0.000 0.016
#> GSM97949 2 0.0000 0.85929 0.000 1.000 0.000 0.000 0.000
#> GSM97956 3 0.5500 0.50186 0.084 0.268 0.640 0.000 0.008
#> GSM97962 3 0.2745 0.74403 0.028 0.024 0.896 0.000 0.052
#> GSM97964 2 0.6356 0.22563 0.108 0.492 0.384 0.000 0.016
#> GSM97970 2 0.6303 0.36726 0.116 0.540 0.328 0.000 0.016
#> GSM97822 5 0.3694 0.65284 0.000 0.000 0.172 0.032 0.796
#> GSM97831 3 0.2482 0.72319 0.084 0.000 0.892 0.000 0.024
#> GSM97845 4 0.6605 0.00712 0.236 0.000 0.000 0.452 0.312
#> GSM97865 1 0.4615 0.59423 0.724 0.004 0.052 0.000 0.220
#> GSM97867 3 0.1671 0.74542 0.000 0.000 0.924 0.000 0.076
#> GSM97883 5 0.4825 0.40087 0.012 0.000 0.368 0.012 0.608
#> GSM97897 5 0.4401 0.68497 0.000 0.000 0.132 0.104 0.764
#> GSM97900 4 0.0290 0.89302 0.000 0.000 0.000 0.992 0.008
#> GSM97904 5 0.6375 0.20818 0.280 0.000 0.076 0.056 0.588
#> GSM97907 2 0.0000 0.85929 0.000 1.000 0.000 0.000 0.000
#> GSM97925 3 0.5225 0.18993 0.040 0.000 0.564 0.004 0.392
#> GSM97947 3 0.1774 0.73911 0.016 0.000 0.932 0.000 0.052
cbind(get_classes(res, k = 6), get_membership(res, k = 6))
#> class entropy silhouette p1 p2 p3 p4 p5 p6
#> GSM97800 2 0.0000 0.8153 0.000 1.000 0.000 0.000 0.000 0.000
#> GSM97803 2 0.0000 0.8153 0.000 1.000 0.000 0.000 0.000 0.000
#> GSM97804 2 0.0000 0.8153 0.000 1.000 0.000 0.000 0.000 0.000
#> GSM97805 2 0.0000 0.8153 0.000 1.000 0.000 0.000 0.000 0.000
#> GSM97807 2 0.0000 0.8153 0.000 1.000 0.000 0.000 0.000 0.000
#> GSM97809 2 0.0000 0.8153 0.000 1.000 0.000 0.000 0.000 0.000
#> GSM97811 2 0.0000 0.8153 0.000 1.000 0.000 0.000 0.000 0.000
#> GSM97812 2 0.0000 0.8153 0.000 1.000 0.000 0.000 0.000 0.000
#> GSM97816 5 0.4904 0.5668 0.016 0.016 0.048 0.000 0.684 0.236
#> GSM97817 2 0.0000 0.8153 0.000 1.000 0.000 0.000 0.000 0.000
#> GSM97820 2 0.0000 0.8153 0.000 1.000 0.000 0.000 0.000 0.000
#> GSM97825 2 0.0000 0.8153 0.000 1.000 0.000 0.000 0.000 0.000
#> GSM97827 2 0.0000 0.8153 0.000 1.000 0.000 0.000 0.000 0.000
#> GSM97828 5 0.4904 0.5668 0.016 0.016 0.048 0.000 0.684 0.236
#> GSM97833 2 0.0000 0.8153 0.000 1.000 0.000 0.000 0.000 0.000
#> GSM97834 2 0.0000 0.8153 0.000 1.000 0.000 0.000 0.000 0.000
#> GSM97840 2 0.2070 0.7528 0.000 0.908 0.000 0.000 0.044 0.048
#> GSM97846 2 0.0000 0.8153 0.000 1.000 0.000 0.000 0.000 0.000
#> GSM97848 2 0.0000 0.8153 0.000 1.000 0.000 0.000 0.000 0.000
#> GSM97849 2 0.0000 0.8153 0.000 1.000 0.000 0.000 0.000 0.000
#> GSM97850 2 0.0000 0.8153 0.000 1.000 0.000 0.000 0.000 0.000
#> GSM97853 2 0.0000 0.8153 0.000 1.000 0.000 0.000 0.000 0.000
#> GSM97855 2 0.0000 0.8153 0.000 1.000 0.000 0.000 0.000 0.000
#> GSM97878 6 0.3080 0.5352 0.040 0.000 0.000 0.012 0.100 0.848
#> GSM97913 6 0.5381 0.0195 0.000 0.140 0.008 0.000 0.248 0.604
#> GSM97932 4 0.3671 0.8188 0.028 0.000 0.000 0.816 0.100 0.056
#> GSM97939 2 0.6112 0.4535 0.000 0.588 0.116 0.000 0.216 0.080
#> GSM97951 2 0.3105 0.7165 0.000 0.844 0.036 0.000 0.108 0.012
#> GSM97957 3 0.1434 0.7385 0.028 0.000 0.948 0.000 0.012 0.012
#> GSM97972 5 0.6722 0.3628 0.000 0.320 0.040 0.000 0.396 0.244
#> GSM97793 3 0.0935 0.7397 0.032 0.000 0.964 0.000 0.000 0.004
#> GSM97795 2 0.4885 0.5908 0.000 0.700 0.100 0.000 0.176 0.024
#> GSM97802 1 0.4496 0.6878 0.744 0.000 0.168 0.004 0.052 0.032
#> GSM97810 2 0.5670 0.5162 0.000 0.636 0.100 0.000 0.200 0.064
#> GSM97815 2 0.6116 0.4564 0.000 0.588 0.124 0.000 0.212 0.076
#> GSM97837 6 0.6124 0.4009 0.148 0.000 0.000 0.068 0.196 0.588
#> GSM97843 3 0.5334 0.4644 0.004 0.236 0.632 0.000 0.116 0.012
#> GSM97890 3 0.6864 0.2625 0.024 0.320 0.460 0.000 0.156 0.040
#> GSM97899 4 0.1082 0.8712 0.004 0.000 0.000 0.956 0.040 0.000
#> GSM97910 6 0.4682 -0.1364 0.020 0.000 0.016 0.000 0.416 0.548
#> GSM97916 6 0.4207 0.5993 0.192 0.004 0.020 0.004 0.028 0.752
#> GSM97920 3 0.3485 0.6466 0.004 0.000 0.784 0.000 0.184 0.028
#> GSM97921 6 0.4717 0.5138 0.028 0.000 0.012 0.096 0.116 0.748
#> GSM97927 6 0.4022 0.5920 0.232 0.000 0.004 0.012 0.020 0.732
#> GSM97937 4 0.5635 0.5317 0.084 0.000 0.000 0.612 0.052 0.252
#> GSM97941 2 0.0622 0.8019 0.000 0.980 0.000 0.000 0.012 0.008
#> GSM97943 5 0.4904 0.5668 0.016 0.016 0.048 0.000 0.684 0.236
#> GSM97958 6 0.3359 0.4737 0.024 0.000 0.020 0.000 0.136 0.820
#> GSM97960 2 0.4514 0.6343 0.000 0.744 0.068 0.000 0.152 0.036
#> GSM97794 6 0.4918 0.4631 0.076 0.044 0.016 0.000 0.124 0.740
#> GSM97796 4 0.0622 0.8740 0.012 0.000 0.000 0.980 0.000 0.008
#> GSM97797 5 0.4714 0.2159 0.024 0.000 0.012 0.000 0.508 0.456
#> GSM97798 4 0.1082 0.8712 0.004 0.000 0.000 0.956 0.040 0.000
#> GSM97801 5 0.4714 0.2159 0.024 0.000 0.012 0.000 0.508 0.456
#> GSM97806 6 0.4189 0.5973 0.232 0.000 0.024 0.004 0.016 0.724
#> GSM97808 4 0.1082 0.8712 0.004 0.000 0.000 0.956 0.040 0.000
#> GSM97813 1 0.2744 0.7619 0.864 0.000 0.000 0.064 0.000 0.072
#> GSM97814 4 0.1082 0.8712 0.004 0.000 0.000 0.956 0.040 0.000
#> GSM97818 6 0.4074 0.4712 0.032 0.024 0.000 0.020 0.132 0.792
#> GSM97819 3 0.1398 0.7219 0.008 0.000 0.940 0.000 0.052 0.000
#> GSM97821 2 0.5459 0.5462 0.008 0.680 0.052 0.000 0.160 0.100
#> GSM97826 6 0.6200 0.4004 0.176 0.000 0.000 0.060 0.192 0.572
#> GSM97829 6 0.6107 0.4001 0.100 0.000 0.000 0.244 0.080 0.576
#> GSM97832 2 0.4164 0.6529 0.000 0.764 0.064 0.000 0.152 0.020
#> GSM97836 6 0.4438 0.5776 0.224 0.000 0.024 0.000 0.040 0.712
#> GSM97839 4 0.0622 0.8740 0.012 0.000 0.000 0.980 0.000 0.008
#> GSM97844 2 0.0000 0.8153 0.000 1.000 0.000 0.000 0.000 0.000
#> GSM97847 4 0.5964 0.2828 0.092 0.000 0.000 0.508 0.044 0.356
#> GSM97851 4 0.2174 0.8582 0.016 0.000 0.000 0.912 0.036 0.036
#> GSM97852 4 0.5964 0.2828 0.092 0.000 0.000 0.508 0.044 0.356
#> GSM97856 4 0.0551 0.8745 0.008 0.000 0.000 0.984 0.004 0.004
#> GSM97858 2 0.0000 0.8153 0.000 1.000 0.000 0.000 0.000 0.000
#> GSM97859 1 0.2488 0.7639 0.880 0.000 0.000 0.044 0.000 0.076
#> GSM97861 6 0.4286 0.5804 0.248 0.000 0.004 0.024 0.016 0.708
#> GSM97863 4 0.0622 0.8740 0.012 0.000 0.000 0.980 0.000 0.008
#> GSM97869 6 0.4248 0.5981 0.188 0.004 0.020 0.004 0.032 0.752
#> GSM97870 1 0.2488 0.7639 0.880 0.000 0.000 0.044 0.000 0.076
#> GSM97871 4 0.0922 0.8741 0.004 0.000 0.000 0.968 0.024 0.004
#> GSM97877 6 0.5381 0.0195 0.000 0.140 0.008 0.000 0.248 0.604
#> GSM97879 6 0.6469 0.3093 0.220 0.000 0.000 0.268 0.036 0.476
#> GSM97882 6 0.4214 0.5968 0.236 0.000 0.024 0.004 0.016 0.720
#> GSM97885 6 0.4220 0.6007 0.228 0.000 0.012 0.004 0.032 0.724
#> GSM97886 4 0.1082 0.8712 0.004 0.000 0.000 0.956 0.040 0.000
#> GSM97887 4 0.1082 0.8712 0.004 0.000 0.000 0.956 0.040 0.000
#> GSM97888 1 0.3163 0.7218 0.820 0.000 0.000 0.140 0.000 0.040
#> GSM97889 1 0.3931 0.7328 0.812 0.000 0.096 0.012 0.044 0.036
#> GSM97891 6 0.4417 0.5778 0.220 0.000 0.024 0.004 0.032 0.720
#> GSM97892 2 0.0000 0.8153 0.000 1.000 0.000 0.000 0.000 0.000
#> GSM97893 4 0.6041 0.2676 0.104 0.000 0.000 0.512 0.044 0.340
#> GSM97894 4 0.0405 0.8744 0.008 0.000 0.000 0.988 0.000 0.004
#> GSM97895 4 0.3671 0.8188 0.028 0.000 0.000 0.816 0.100 0.056
#> GSM97896 1 0.3998 0.6075 0.728 0.000 0.000 0.236 0.016 0.020
#> GSM97898 4 0.2164 0.8566 0.016 0.000 0.000 0.912 0.028 0.044
#> GSM97903 6 0.5887 0.4599 0.232 0.000 0.000 0.156 0.032 0.580
#> GSM97905 1 0.4017 0.7636 0.812 0.000 0.068 0.028 0.020 0.072
#> GSM97906 4 0.1082 0.8712 0.004 0.000 0.000 0.956 0.040 0.000
#> GSM97908 4 0.5578 0.4861 0.072 0.000 0.000 0.588 0.044 0.296
#> GSM97912 1 0.4017 0.7636 0.812 0.000 0.068 0.028 0.020 0.072
#> GSM97914 6 0.4610 0.5229 0.040 0.000 0.012 0.056 0.136 0.756
#> GSM97915 4 0.0767 0.8739 0.012 0.000 0.000 0.976 0.004 0.008
#> GSM97917 4 0.2638 0.8434 0.016 0.000 0.000 0.884 0.040 0.060
#> GSM97918 4 0.2371 0.8513 0.016 0.000 0.000 0.900 0.032 0.052
#> GSM97919 4 0.1546 0.8700 0.020 0.000 0.000 0.944 0.020 0.016
#> GSM97922 1 0.2488 0.7639 0.880 0.000 0.000 0.044 0.000 0.076
#> GSM97924 2 0.0000 0.8153 0.000 1.000 0.000 0.000 0.000 0.000
#> GSM97926 6 0.4438 0.5776 0.224 0.000 0.024 0.000 0.040 0.712
#> GSM97930 6 0.5421 0.4708 0.100 0.000 0.000 0.172 0.060 0.668
#> GSM97931 5 0.6722 0.3628 0.000 0.320 0.040 0.000 0.396 0.244
#> GSM97935 6 0.4291 0.5805 0.248 0.000 0.004 0.020 0.020 0.708
#> GSM97936 4 0.2545 0.8470 0.028 0.000 0.000 0.892 0.028 0.052
#> GSM97938 4 0.4006 0.7779 0.048 0.000 0.000 0.792 0.044 0.116
#> GSM97940 4 0.1082 0.8712 0.004 0.000 0.000 0.956 0.040 0.000
#> GSM97942 3 0.1082 0.7359 0.040 0.000 0.956 0.000 0.000 0.004
#> GSM97945 4 0.5127 0.5786 0.104 0.000 0.000 0.668 0.024 0.204
#> GSM97946 2 0.0000 0.8153 0.000 1.000 0.000 0.000 0.000 0.000
#> GSM97948 3 0.5818 0.1491 0.332 0.000 0.548 0.004 0.040 0.076
#> GSM97950 4 0.2638 0.8471 0.016 0.000 0.000 0.884 0.040 0.060
#> GSM97952 4 0.0922 0.8741 0.004 0.000 0.000 0.968 0.024 0.004
#> GSM97953 4 0.5055 0.6704 0.080 0.000 0.000 0.696 0.048 0.176
#> GSM97954 6 0.6484 0.2582 0.228 0.000 0.000 0.308 0.028 0.436
#> GSM97955 4 0.1262 0.8742 0.008 0.000 0.000 0.956 0.016 0.020
#> GSM97959 6 0.4111 0.2949 0.004 0.036 0.004 0.000 0.232 0.724
#> GSM97961 4 0.1082 0.8712 0.004 0.000 0.000 0.956 0.040 0.000
#> GSM97963 4 0.1082 0.8712 0.004 0.000 0.000 0.956 0.040 0.000
#> GSM97965 4 0.1082 0.8712 0.004 0.000 0.000 0.956 0.040 0.000
#> GSM97966 4 0.1082 0.8712 0.004 0.000 0.000 0.956 0.040 0.000
#> GSM97967 2 0.0000 0.8153 0.000 1.000 0.000 0.000 0.000 0.000
#> GSM97968 2 0.0000 0.8153 0.000 1.000 0.000 0.000 0.000 0.000
#> GSM97969 1 0.3130 0.7281 0.828 0.000 0.000 0.124 0.000 0.048
#> GSM97971 1 0.2618 0.7629 0.872 0.000 0.000 0.052 0.000 0.076
#> GSM97799 2 0.6998 0.2304 0.000 0.436 0.256 0.000 0.224 0.084
#> GSM97823 2 0.0000 0.8153 0.000 1.000 0.000 0.000 0.000 0.000
#> GSM97824 3 0.6555 0.3094 0.000 0.276 0.484 0.000 0.188 0.052
#> GSM97830 3 0.2714 0.6909 0.004 0.000 0.848 0.000 0.136 0.012
#> GSM97835 2 0.6339 0.4181 0.000 0.560 0.152 0.000 0.212 0.076
#> GSM97838 2 0.0000 0.8153 0.000 1.000 0.000 0.000 0.000 0.000
#> GSM97841 2 0.0000 0.8153 0.000 1.000 0.000 0.000 0.000 0.000
#> GSM97842 2 0.6988 0.2409 0.000 0.440 0.248 0.000 0.228 0.084
#> GSM97854 2 0.0000 0.8153 0.000 1.000 0.000 0.000 0.000 0.000
#> GSM97857 3 0.6536 0.3263 0.000 0.264 0.492 0.000 0.192 0.052
#> GSM97860 3 0.0935 0.7397 0.032 0.000 0.964 0.000 0.000 0.004
#> GSM97862 3 0.5004 0.5950 0.004 0.100 0.712 0.000 0.148 0.036
#> GSM97864 2 0.0000 0.8153 0.000 1.000 0.000 0.000 0.000 0.000
#> GSM97866 3 0.5131 0.5841 0.004 0.112 0.700 0.000 0.148 0.036
#> GSM97868 3 0.6930 0.1654 0.000 0.320 0.408 0.000 0.200 0.072
#> GSM97872 1 0.5606 0.5626 0.632 0.000 0.068 0.016 0.036 0.248
#> GSM97873 2 0.6897 0.2609 0.000 0.452 0.248 0.000 0.224 0.076
#> GSM97874 3 0.2872 0.6829 0.004 0.000 0.832 0.000 0.152 0.012
#> GSM97875 3 0.1398 0.7219 0.008 0.000 0.940 0.000 0.052 0.000
#> GSM97876 3 0.0935 0.7397 0.032 0.000 0.964 0.000 0.000 0.004
#> GSM97880 3 0.0935 0.7397 0.032 0.000 0.964 0.000 0.000 0.004
#> GSM97881 2 0.7006 -0.0115 0.000 0.372 0.348 0.000 0.204 0.076
#> GSM97884 2 0.6989 0.1489 0.000 0.416 0.288 0.000 0.220 0.076
#> GSM97901 3 0.5034 0.5833 0.000 0.108 0.708 0.000 0.136 0.048
#> GSM97902 6 0.3359 0.4737 0.024 0.000 0.020 0.000 0.136 0.820
#> GSM97909 2 0.5383 0.5570 0.008 0.688 0.052 0.000 0.156 0.096
#> GSM97911 2 0.7006 -0.0115 0.000 0.372 0.348 0.000 0.204 0.076
#> GSM97923 3 0.0935 0.7397 0.032 0.000 0.964 0.000 0.000 0.004
#> GSM97928 1 0.5606 0.5626 0.632 0.000 0.068 0.016 0.036 0.248
#> GSM97929 2 0.0000 0.8153 0.000 1.000 0.000 0.000 0.000 0.000
#> GSM97933 3 0.1194 0.7386 0.032 0.000 0.956 0.000 0.004 0.008
#> GSM97934 3 0.1434 0.7385 0.028 0.000 0.948 0.000 0.012 0.012
#> GSM97944 2 0.6998 0.2304 0.000 0.436 0.256 0.000 0.224 0.084
#> GSM97949 2 0.0000 0.8153 0.000 1.000 0.000 0.000 0.000 0.000
#> GSM97956 3 0.6137 0.4299 0.000 0.208 0.572 0.000 0.168 0.052
#> GSM97962 3 0.2836 0.7234 0.028 0.004 0.880 0.000 0.052 0.036
#> GSM97964 2 0.6964 0.1024 0.000 0.404 0.312 0.000 0.212 0.072
#> GSM97970 2 0.6920 0.2611 0.000 0.452 0.248 0.000 0.220 0.080
#> GSM97822 1 0.3948 0.7303 0.808 0.000 0.100 0.008 0.044 0.040
#> GSM97831 3 0.2872 0.6859 0.004 0.000 0.832 0.000 0.152 0.012
#> GSM97845 6 0.6574 0.2175 0.208 0.000 0.000 0.340 0.036 0.416
#> GSM97865 6 0.3277 0.4823 0.024 0.000 0.020 0.000 0.128 0.828
#> GSM97867 3 0.0935 0.7397 0.032 0.000 0.964 0.000 0.000 0.004
#> GSM97883 1 0.5294 0.4590 0.564 0.000 0.352 0.004 0.012 0.068
#> GSM97897 1 0.4359 0.7423 0.792 0.000 0.080 0.064 0.040 0.024
#> GSM97900 4 0.1082 0.8712 0.004 0.000 0.000 0.956 0.040 0.000
#> GSM97904 1 0.5460 0.0450 0.484 0.000 0.020 0.020 0.032 0.444
#> GSM97907 2 0.0000 0.8153 0.000 1.000 0.000 0.000 0.000 0.000
#> GSM97925 3 0.5722 0.1933 0.320 0.000 0.564 0.004 0.036 0.076
#> GSM97947 3 0.1500 0.7207 0.012 0.000 0.936 0.000 0.052 0.000
Heatmaps for the consensus matrix. It visualizes the probability of two samples to be in a same group.
consensus_heatmap(res, k = 2)
consensus_heatmap(res, k = 3)
consensus_heatmap(res, k = 4)
consensus_heatmap(res, k = 5)
consensus_heatmap(res, k = 6)
Heatmaps for the membership of samples in all partitions to see how consistent they are:
membership_heatmap(res, k = 2)
membership_heatmap(res, k = 3)
membership_heatmap(res, k = 4)
membership_heatmap(res, k = 5)
membership_heatmap(res, k = 6)
As soon as we have had the classes for columns, we can look for signatures which are significantly different between classes which can be candidate marks for certain classes. Following are the heatmaps for signatures.
Signature heatmaps where rows are scaled:
get_signatures(res, k = 2)
get_signatures(res, k = 3)
get_signatures(res, k = 4)
get_signatures(res, k = 5)
get_signatures(res, k = 6)
Signature heatmaps where rows are not scaled:
get_signatures(res, k = 2, scale_rows = FALSE)
get_signatures(res, k = 3, scale_rows = FALSE)
get_signatures(res, k = 4, scale_rows = FALSE)
get_signatures(res, k = 5, scale_rows = FALSE)
get_signatures(res, k = 6, scale_rows = FALSE)
Compare the overlap of signatures from different k:
compare_signatures(res)
get_signature() returns a data frame invisibly. TO get the list of signatures, the function
call should be assigned to a variable explicitly. In following code, if plot argument is set
to FALSE, no heatmap is plotted while only the differential analysis is performed.
# code only for demonstration
tb = get_signature(res, k = ..., plot = FALSE)
An example of the output of tb is:
#> which_row fdr mean_1 mean_2 scaled_mean_1 scaled_mean_2 km
#> 1 38 0.042760348 8.373488 9.131774 -0.5533452 0.5164555 1
#> 2 40 0.018707592 7.106213 8.469186 -0.6173731 0.5762149 1
#> 3 55 0.019134737 10.221463 11.207825 -0.6159697 0.5749050 1
#> 4 59 0.006059896 5.921854 7.869574 -0.6899429 0.6439467 1
#> 5 60 0.018055526 8.928898 10.211722 -0.6204761 0.5791110 1
#> 6 98 0.009384629 15.714769 14.887706 0.6635654 -0.6193277 2
...
The columns in tb are:
which_row: row indices corresponding to the input matrix.fdr: FDR for the differential test. mean_x: The mean value in group x.scaled_mean_x: The mean value in group x after rows are scaled.km: Row groups if k-means clustering is applied to rows.UMAP plot which shows how samples are separated.
dimension_reduction(res, k = 2, method = "UMAP")
dimension_reduction(res, k = 3, method = "UMAP")
dimension_reduction(res, k = 4, method = "UMAP")
dimension_reduction(res, k = 5, method = "UMAP")
dimension_reduction(res, k = 6, method = "UMAP")
Following heatmap shows how subgroups are split when increasing k:
collect_classes(res)
Test correlation between subgroups and known annotations. If the known annotation is numeric, one-way ANOVA test is applied, and if the known annotation is discrete, chi-squared contingency table test is applied.
test_to_known_factors(res)
#> n disease.state(p) tissue(p) k
#> SD:hclust 167 1.13e-12 1.44e-14 2
#> SD:hclust 144 4.43e-15 4.86e-15 3
#> SD:hclust 132 1.53e-19 4.25e-18 4
#> SD:hclust 136 2.15e-17 1.50e-16 5
#> SD:hclust 133 2.12e-17 7.99e-16 6
If matrix rows can be associated to genes, consider to use functional_enrichment(res,
...) to perform function enrichment for the signature genes. See this vignette for more detailed explanations.
The object with results only for a single top-value method and a single partition method can be extracted as:
res = res_list["SD", "kmeans"]
# you can also extract it by
# res = res_list["SD:kmeans"]
A summary of res and all the functions that can be applied to it:
res
#> A 'ConsensusPartition' object with k = 2, 3, 4, 5, 6.
#> On a matrix with 51882 rows and 180 columns.
#> Top rows (1000, 2000, 3000, 4000, 5000) are extracted by 'SD' method.
#> Subgroups are detected by 'kmeans' method.
#> Performed in total 1250 partitions by row resampling.
#> Best k for subgroups seems to be 4.
#>
#> Following methods can be applied to this 'ConsensusPartition' object:
#> [1] "cola_report" "collect_classes" "collect_plots"
#> [4] "collect_stats" "colnames" "compare_signatures"
#> [7] "consensus_heatmap" "dimension_reduction" "functional_enrichment"
#> [10] "get_anno_col" "get_anno" "get_classes"
#> [13] "get_consensus" "get_matrix" "get_membership"
#> [16] "get_param" "get_signatures" "get_stats"
#> [19] "is_best_k" "is_stable_k" "membership_heatmap"
#> [22] "ncol" "nrow" "plot_ecdf"
#> [25] "rownames" "select_partition_number" "show"
#> [28] "suggest_best_k" "test_to_known_factors"
collect_plots() function collects all the plots made from res for all k (number of partitions)
into one single page to provide an easy and fast comparison between different k.
collect_plots(res)
The plots are:
k and the heatmap of
predicted classes for each k.k.k.k.All the plots in panels can be made by individual functions and they are plotted later in this section.
select_partition_number() produces several plots showing different
statistics for choosing “optimized” k. There are following statistics:
k;k, the area increased is defined as \(A_k - A_{k-1}\).The detailed explanations of these statistics can be found in the cola vignette.
Generally speaking, lower PAC score, higher mean silhouette score or higher
concordance corresponds to better partition. Rand index and Jaccard index
measure how similar the current partition is compared to partition with k-1.
If they are too similar, we won't accept k is better than k-1.
select_partition_number(res)
The numeric values for all these statistics can be obtained by get_stats().
get_stats(res)
#> k 1-PAC mean_silhouette concordance area_increased Rand Jaccard
#> 2 2 0.859 0.943 0.974 0.4808 0.515 0.515
#> 3 3 0.856 0.945 0.972 0.3488 0.749 0.551
#> 4 4 0.997 0.950 0.971 0.1553 0.862 0.627
#> 5 5 0.824 0.703 0.830 0.0577 0.965 0.867
#> 6 6 0.784 0.578 0.778 0.0388 0.911 0.661
suggest_best_k() suggests the best \(k\) based on these statistics. The rules are as follows:
suggest_best_k(res)
#> [1] 4
Following shows the table of the partitions (You need to click the show/hide
code output link to see it). The membership matrix (columns with name p*)
is inferred by
clue::cl_consensus()
function with the SE method. Basically the value in the membership matrix
represents the probability to belong to a certain group. The finall class
label for an item is determined with the group with highest probability it
belongs to.
In get_classes() function, the entropy is calculated from the membership
matrix and the silhouette score is calculated from the consensus matrix.
cbind(get_classes(res, k = 2), get_membership(res, k = 2))
#> class entropy silhouette p1 p2
#> GSM97800 2 0.0000 0.960 0.000 1.000
#> GSM97803 2 0.0000 0.960 0.000 1.000
#> GSM97804 2 0.0000 0.960 0.000 1.000
#> GSM97805 2 0.0000 0.960 0.000 1.000
#> GSM97807 2 0.0000 0.960 0.000 1.000
#> GSM97809 2 0.0000 0.960 0.000 1.000
#> GSM97811 2 0.0000 0.960 0.000 1.000
#> GSM97812 2 0.0000 0.960 0.000 1.000
#> GSM97816 2 0.0000 0.960 0.000 1.000
#> GSM97817 2 0.0000 0.960 0.000 1.000
#> GSM97820 2 0.0000 0.960 0.000 1.000
#> GSM97825 2 0.0000 0.960 0.000 1.000
#> GSM97827 2 0.0000 0.960 0.000 1.000
#> GSM97828 2 0.9552 0.447 0.376 0.624
#> GSM97833 2 0.0000 0.960 0.000 1.000
#> GSM97834 2 0.0000 0.960 0.000 1.000
#> GSM97840 2 0.0000 0.960 0.000 1.000
#> GSM97846 2 0.0000 0.960 0.000 1.000
#> GSM97848 2 0.0000 0.960 0.000 1.000
#> GSM97849 2 0.0000 0.960 0.000 1.000
#> GSM97850 2 0.0000 0.960 0.000 1.000
#> GSM97853 2 0.0000 0.960 0.000 1.000
#> GSM97855 2 0.0000 0.960 0.000 1.000
#> GSM97878 1 0.0000 0.980 1.000 0.000
#> GSM97913 2 0.0000 0.960 0.000 1.000
#> GSM97932 1 0.0000 0.980 1.000 0.000
#> GSM97939 2 0.0000 0.960 0.000 1.000
#> GSM97951 2 0.0000 0.960 0.000 1.000
#> GSM97957 1 0.9170 0.480 0.668 0.332
#> GSM97972 2 0.0376 0.957 0.004 0.996
#> GSM97793 1 0.0000 0.980 1.000 0.000
#> GSM97795 2 0.0000 0.960 0.000 1.000
#> GSM97802 1 0.0000 0.980 1.000 0.000
#> GSM97810 2 0.0000 0.960 0.000 1.000
#> GSM97815 2 0.0000 0.960 0.000 1.000
#> GSM97837 1 0.0000 0.980 1.000 0.000
#> GSM97843 1 0.9129 0.489 0.672 0.328
#> GSM97890 2 0.7219 0.785 0.200 0.800
#> GSM97899 1 0.0000 0.980 1.000 0.000
#> GSM97910 1 0.0000 0.980 1.000 0.000
#> GSM97916 1 0.0000 0.980 1.000 0.000
#> GSM97920 1 0.9170 0.480 0.668 0.332
#> GSM97921 1 0.0000 0.980 1.000 0.000
#> GSM97927 1 0.0000 0.980 1.000 0.000
#> GSM97937 1 0.0000 0.980 1.000 0.000
#> GSM97941 2 0.0000 0.960 0.000 1.000
#> GSM97943 1 0.0000 0.980 1.000 0.000
#> GSM97958 2 0.5842 0.857 0.140 0.860
#> GSM97960 2 0.0000 0.960 0.000 1.000
#> GSM97794 1 0.0000 0.980 1.000 0.000
#> GSM97796 1 0.0000 0.980 1.000 0.000
#> GSM97797 1 0.0000 0.980 1.000 0.000
#> GSM97798 1 0.0000 0.980 1.000 0.000
#> GSM97801 1 0.0000 0.980 1.000 0.000
#> GSM97806 1 0.0000 0.980 1.000 0.000
#> GSM97808 1 0.0000 0.980 1.000 0.000
#> GSM97813 1 0.0000 0.980 1.000 0.000
#> GSM97814 1 0.0000 0.980 1.000 0.000
#> GSM97818 1 0.0000 0.980 1.000 0.000
#> GSM97819 1 0.0000 0.980 1.000 0.000
#> GSM97821 2 0.0000 0.960 0.000 1.000
#> GSM97826 1 0.0000 0.980 1.000 0.000
#> GSM97829 1 0.0000 0.980 1.000 0.000
#> GSM97832 2 0.0000 0.960 0.000 1.000
#> GSM97836 1 0.0000 0.980 1.000 0.000
#> GSM97839 1 0.0000 0.980 1.000 0.000
#> GSM97844 2 0.0000 0.960 0.000 1.000
#> GSM97847 1 0.0000 0.980 1.000 0.000
#> GSM97851 1 0.0000 0.980 1.000 0.000
#> GSM97852 1 0.0000 0.980 1.000 0.000
#> GSM97856 1 0.0000 0.980 1.000 0.000
#> GSM97858 2 0.0000 0.960 0.000 1.000
#> GSM97859 1 0.0000 0.980 1.000 0.000
#> GSM97861 1 0.0000 0.980 1.000 0.000
#> GSM97863 1 0.0000 0.980 1.000 0.000
#> GSM97869 1 0.0000 0.980 1.000 0.000
#> GSM97870 1 0.0000 0.980 1.000 0.000
#> GSM97871 1 0.0000 0.980 1.000 0.000
#> GSM97877 2 0.0000 0.960 0.000 1.000
#> GSM97879 1 0.0000 0.980 1.000 0.000
#> GSM97882 1 0.0000 0.980 1.000 0.000
#> GSM97885 1 0.0000 0.980 1.000 0.000
#> GSM97886 1 0.0000 0.980 1.000 0.000
#> GSM97887 1 0.0000 0.980 1.000 0.000
#> GSM97888 1 0.0000 0.980 1.000 0.000
#> GSM97889 1 0.0000 0.980 1.000 0.000
#> GSM97891 1 0.0000 0.980 1.000 0.000
#> GSM97892 2 0.0000 0.960 0.000 1.000
#> GSM97893 1 0.0000 0.980 1.000 0.000
#> GSM97894 1 0.0000 0.980 1.000 0.000
#> GSM97895 1 0.0000 0.980 1.000 0.000
#> GSM97896 1 0.0000 0.980 1.000 0.000
#> GSM97898 1 0.0000 0.980 1.000 0.000
#> GSM97903 1 0.0000 0.980 1.000 0.000
#> GSM97905 1 0.0000 0.980 1.000 0.000
#> GSM97906 1 0.0000 0.980 1.000 0.000
#> GSM97908 1 0.0000 0.980 1.000 0.000
#> GSM97912 1 0.0000 0.980 1.000 0.000
#> GSM97914 1 0.0000 0.980 1.000 0.000
#> GSM97915 1 0.0000 0.980 1.000 0.000
#> GSM97917 1 0.0000 0.980 1.000 0.000
#> GSM97918 1 0.0000 0.980 1.000 0.000
#> GSM97919 1 0.0000 0.980 1.000 0.000
#> GSM97922 1 0.0000 0.980 1.000 0.000
#> GSM97924 2 0.0000 0.960 0.000 1.000
#> GSM97926 1 0.0000 0.980 1.000 0.000
#> GSM97930 1 0.0000 0.980 1.000 0.000
#> GSM97931 2 0.6048 0.849 0.148 0.852
#> GSM97935 1 0.0000 0.980 1.000 0.000
#> GSM97936 1 0.0000 0.980 1.000 0.000
#> GSM97938 1 0.0000 0.980 1.000 0.000
#> GSM97940 1 0.0000 0.980 1.000 0.000
#> GSM97942 1 0.0000 0.980 1.000 0.000
#> GSM97945 1 0.0000 0.980 1.000 0.000
#> GSM97946 2 0.0000 0.960 0.000 1.000
#> GSM97948 1 0.0000 0.980 1.000 0.000
#> GSM97950 1 0.0000 0.980 1.000 0.000
#> GSM97952 1 0.0000 0.980 1.000 0.000
#> GSM97953 1 0.0000 0.980 1.000 0.000
#> GSM97954 1 0.0000 0.980 1.000 0.000
#> GSM97955 1 0.0000 0.980 1.000 0.000
#> GSM97959 1 0.9000 0.508 0.684 0.316
#> GSM97961 1 0.0000 0.980 1.000 0.000
#> GSM97963 1 0.0000 0.980 1.000 0.000
#> GSM97965 1 0.0000 0.980 1.000 0.000
#> GSM97966 1 0.0000 0.980 1.000 0.000
#> GSM97967 2 0.0000 0.960 0.000 1.000
#> GSM97968 2 0.0000 0.960 0.000 1.000
#> GSM97969 1 0.0000 0.980 1.000 0.000
#> GSM97971 1 0.0000 0.980 1.000 0.000
#> GSM97799 2 0.0000 0.960 0.000 1.000
#> GSM97823 2 0.0000 0.960 0.000 1.000
#> GSM97824 2 0.6247 0.841 0.156 0.844
#> GSM97830 1 0.8813 0.550 0.700 0.300
#> GSM97835 2 0.0000 0.960 0.000 1.000
#> GSM97838 2 0.0000 0.960 0.000 1.000
#> GSM97841 2 0.0000 0.960 0.000 1.000
#> GSM97842 2 0.0000 0.960 0.000 1.000
#> GSM97854 2 0.0000 0.960 0.000 1.000
#> GSM97857 2 0.5737 0.860 0.136 0.864
#> GSM97860 1 0.0000 0.980 1.000 0.000
#> GSM97862 2 0.6247 0.841 0.156 0.844
#> GSM97864 2 0.0000 0.960 0.000 1.000
#> GSM97866 2 0.6247 0.841 0.156 0.844
#> GSM97868 2 0.5519 0.867 0.128 0.872
#> GSM97872 1 0.0000 0.980 1.000 0.000
#> GSM97873 2 0.0000 0.960 0.000 1.000
#> GSM97874 1 0.0000 0.980 1.000 0.000
#> GSM97875 1 0.9129 0.489 0.672 0.328
#> GSM97876 1 0.0000 0.980 1.000 0.000
#> GSM97880 1 0.0000 0.980 1.000 0.000
#> GSM97881 2 0.6148 0.845 0.152 0.848
#> GSM97884 2 0.0000 0.960 0.000 1.000
#> GSM97901 2 0.6801 0.812 0.180 0.820
#> GSM97902 1 0.0000 0.980 1.000 0.000
#> GSM97909 2 0.0000 0.960 0.000 1.000
#> GSM97911 2 0.6148 0.845 0.152 0.848
#> GSM97923 1 0.0000 0.980 1.000 0.000
#> GSM97928 1 0.0000 0.980 1.000 0.000
#> GSM97929 2 0.0000 0.960 0.000 1.000
#> GSM97933 1 0.0000 0.980 1.000 0.000
#> GSM97934 1 0.0000 0.980 1.000 0.000
#> GSM97944 2 0.0000 0.960 0.000 1.000
#> GSM97949 2 0.0000 0.960 0.000 1.000
#> GSM97956 2 0.6247 0.841 0.156 0.844
#> GSM97962 2 0.6247 0.841 0.156 0.844
#> GSM97964 2 0.6148 0.845 0.152 0.848
#> GSM97970 2 0.0000 0.960 0.000 1.000
#> GSM97822 1 0.0000 0.980 1.000 0.000
#> GSM97831 2 0.7528 0.762 0.216 0.784
#> GSM97845 1 0.0000 0.980 1.000 0.000
#> GSM97865 1 0.0000 0.980 1.000 0.000
#> GSM97867 1 0.0000 0.980 1.000 0.000
#> GSM97883 1 0.0000 0.980 1.000 0.000
#> GSM97897 1 0.0000 0.980 1.000 0.000
#> GSM97900 1 0.0000 0.980 1.000 0.000
#> GSM97904 1 0.0000 0.980 1.000 0.000
#> GSM97907 2 0.0000 0.960 0.000 1.000
#> GSM97925 1 0.0000 0.980 1.000 0.000
#> GSM97947 1 0.0000 0.980 1.000 0.000
cbind(get_classes(res, k = 3), get_membership(res, k = 3))
#> class entropy silhouette p1 p2 p3
#> GSM97800 2 0.0000 0.9826 0.000 1.000 0.000
#> GSM97803 2 0.0000 0.9826 0.000 1.000 0.000
#> GSM97804 2 0.0000 0.9826 0.000 1.000 0.000
#> GSM97805 2 0.0000 0.9826 0.000 1.000 0.000
#> GSM97807 2 0.0000 0.9826 0.000 1.000 0.000
#> GSM97809 2 0.0000 0.9826 0.000 1.000 0.000
#> GSM97811 2 0.0000 0.9826 0.000 1.000 0.000
#> GSM97812 2 0.0000 0.9826 0.000 1.000 0.000
#> GSM97816 3 0.0000 0.9844 0.000 0.000 1.000
#> GSM97817 2 0.0000 0.9826 0.000 1.000 0.000
#> GSM97820 2 0.0000 0.9826 0.000 1.000 0.000
#> GSM97825 2 0.0000 0.9826 0.000 1.000 0.000
#> GSM97827 2 0.0000 0.9826 0.000 1.000 0.000
#> GSM97828 3 0.0000 0.9844 0.000 0.000 1.000
#> GSM97833 2 0.0000 0.9826 0.000 1.000 0.000
#> GSM97834 2 0.0000 0.9826 0.000 1.000 0.000
#> GSM97840 2 0.0000 0.9826 0.000 1.000 0.000
#> GSM97846 2 0.0000 0.9826 0.000 1.000 0.000
#> GSM97848 2 0.0000 0.9826 0.000 1.000 0.000
#> GSM97849 2 0.0000 0.9826 0.000 1.000 0.000
#> GSM97850 2 0.0000 0.9826 0.000 1.000 0.000
#> GSM97853 2 0.0000 0.9826 0.000 1.000 0.000
#> GSM97855 2 0.0000 0.9826 0.000 1.000 0.000
#> GSM97878 1 0.3941 0.8613 0.844 0.000 0.156
#> GSM97913 2 0.5070 0.6915 0.004 0.772 0.224
#> GSM97932 1 0.0000 0.9555 1.000 0.000 0.000
#> GSM97939 3 0.0000 0.9844 0.000 0.000 1.000
#> GSM97951 2 0.0000 0.9826 0.000 1.000 0.000
#> GSM97957 3 0.0000 0.9844 0.000 0.000 1.000
#> GSM97972 3 0.0000 0.9844 0.000 0.000 1.000
#> GSM97793 3 0.0000 0.9844 0.000 0.000 1.000
#> GSM97795 2 0.0000 0.9826 0.000 1.000 0.000
#> GSM97802 3 0.0000 0.9844 0.000 0.000 1.000
#> GSM97810 3 0.4555 0.7376 0.000 0.200 0.800
#> GSM97815 3 0.0237 0.9803 0.000 0.004 0.996
#> GSM97837 1 0.2066 0.9297 0.940 0.000 0.060
#> GSM97843 3 0.0000 0.9844 0.000 0.000 1.000
#> GSM97890 3 0.0000 0.9844 0.000 0.000 1.000
#> GSM97899 1 0.0000 0.9555 1.000 0.000 0.000
#> GSM97910 3 0.1529 0.9389 0.040 0.000 0.960
#> GSM97916 1 0.4062 0.8528 0.836 0.000 0.164
#> GSM97920 3 0.0000 0.9844 0.000 0.000 1.000
#> GSM97921 1 0.3619 0.8807 0.864 0.000 0.136
#> GSM97927 1 0.3116 0.9035 0.892 0.000 0.108
#> GSM97937 1 0.0000 0.9555 1.000 0.000 0.000
#> GSM97941 2 0.0000 0.9826 0.000 1.000 0.000
#> GSM97943 3 0.0000 0.9844 0.000 0.000 1.000
#> GSM97958 3 0.0000 0.9844 0.000 0.000 1.000
#> GSM97960 2 0.0000 0.9826 0.000 1.000 0.000
#> GSM97794 1 0.4062 0.8528 0.836 0.000 0.164
#> GSM97796 1 0.0000 0.9555 1.000 0.000 0.000
#> GSM97797 1 0.4062 0.8528 0.836 0.000 0.164
#> GSM97798 1 0.0000 0.9555 1.000 0.000 0.000
#> GSM97801 1 0.3619 0.8807 0.864 0.000 0.136
#> GSM97806 1 0.0000 0.9555 1.000 0.000 0.000
#> GSM97808 1 0.0000 0.9555 1.000 0.000 0.000
#> GSM97813 1 0.0000 0.9555 1.000 0.000 0.000
#> GSM97814 1 0.0000 0.9555 1.000 0.000 0.000
#> GSM97818 1 0.3619 0.8807 0.864 0.000 0.136
#> GSM97819 3 0.0000 0.9844 0.000 0.000 1.000
#> GSM97821 3 0.5968 0.4228 0.000 0.364 0.636
#> GSM97826 1 0.0000 0.9555 1.000 0.000 0.000
#> GSM97829 1 0.2878 0.9111 0.904 0.000 0.096
#> GSM97832 2 0.6309 -0.0117 0.000 0.504 0.496
#> GSM97836 1 0.3116 0.9035 0.892 0.000 0.108
#> GSM97839 1 0.0000 0.9555 1.000 0.000 0.000
#> GSM97844 2 0.0000 0.9826 0.000 1.000 0.000
#> GSM97847 1 0.0000 0.9555 1.000 0.000 0.000
#> GSM97851 1 0.0000 0.9555 1.000 0.000 0.000
#> GSM97852 1 0.0000 0.9555 1.000 0.000 0.000
#> GSM97856 1 0.0000 0.9555 1.000 0.000 0.000
#> GSM97858 2 0.0000 0.9826 0.000 1.000 0.000
#> GSM97859 1 0.0237 0.9540 0.996 0.000 0.004
#> GSM97861 1 0.3116 0.9035 0.892 0.000 0.108
#> GSM97863 1 0.0000 0.9555 1.000 0.000 0.000
#> GSM97869 1 0.4002 0.8572 0.840 0.000 0.160
#> GSM97870 1 0.6274 0.2737 0.544 0.000 0.456
#> GSM97871 1 0.0000 0.9555 1.000 0.000 0.000
#> GSM97877 2 0.0000 0.9826 0.000 1.000 0.000
#> GSM97879 1 0.0000 0.9555 1.000 0.000 0.000
#> GSM97882 1 0.3038 0.9062 0.896 0.000 0.104
#> GSM97885 1 0.3116 0.9035 0.892 0.000 0.108
#> GSM97886 1 0.0000 0.9555 1.000 0.000 0.000
#> GSM97887 1 0.0000 0.9555 1.000 0.000 0.000
#> GSM97888 1 0.0000 0.9555 1.000 0.000 0.000
#> GSM97889 1 0.0000 0.9555 1.000 0.000 0.000
#> GSM97891 1 0.0237 0.9540 0.996 0.000 0.004
#> GSM97892 2 0.0000 0.9826 0.000 1.000 0.000
#> GSM97893 1 0.0000 0.9555 1.000 0.000 0.000
#> GSM97894 1 0.0000 0.9555 1.000 0.000 0.000
#> GSM97895 1 0.0000 0.9555 1.000 0.000 0.000
#> GSM97896 1 0.0000 0.9555 1.000 0.000 0.000
#> GSM97898 1 0.0000 0.9555 1.000 0.000 0.000
#> GSM97903 1 0.2878 0.9111 0.904 0.000 0.096
#> GSM97905 1 0.0000 0.9555 1.000 0.000 0.000
#> GSM97906 1 0.0000 0.9555 1.000 0.000 0.000
#> GSM97908 1 0.0000 0.9555 1.000 0.000 0.000
#> GSM97912 1 0.2537 0.9198 0.920 0.000 0.080
#> GSM97914 1 0.3619 0.8807 0.864 0.000 0.136
#> GSM97915 1 0.0000 0.9555 1.000 0.000 0.000
#> GSM97917 1 0.0000 0.9555 1.000 0.000 0.000
#> GSM97918 1 0.0000 0.9555 1.000 0.000 0.000
#> GSM97919 1 0.0000 0.9555 1.000 0.000 0.000
#> GSM97922 1 0.0000 0.9555 1.000 0.000 0.000
#> GSM97924 2 0.0000 0.9826 0.000 1.000 0.000
#> GSM97926 3 0.0000 0.9844 0.000 0.000 1.000
#> GSM97930 1 0.0000 0.9555 1.000 0.000 0.000
#> GSM97931 3 0.0000 0.9844 0.000 0.000 1.000
#> GSM97935 1 0.3116 0.9035 0.892 0.000 0.108
#> GSM97936 1 0.0000 0.9555 1.000 0.000 0.000
#> GSM97938 1 0.0000 0.9555 1.000 0.000 0.000
#> GSM97940 1 0.0000 0.9555 1.000 0.000 0.000
#> GSM97942 3 0.0000 0.9844 0.000 0.000 1.000
#> GSM97945 1 0.0000 0.9555 1.000 0.000 0.000
#> GSM97946 2 0.0000 0.9826 0.000 1.000 0.000
#> GSM97948 3 0.0000 0.9844 0.000 0.000 1.000
#> GSM97950 1 0.0000 0.9555 1.000 0.000 0.000
#> GSM97952 1 0.0000 0.9555 1.000 0.000 0.000
#> GSM97953 1 0.0000 0.9555 1.000 0.000 0.000
#> GSM97954 1 0.0000 0.9555 1.000 0.000 0.000
#> GSM97955 1 0.0000 0.9555 1.000 0.000 0.000
#> GSM97959 1 0.5757 0.8222 0.792 0.056 0.152
#> GSM97961 1 0.0000 0.9555 1.000 0.000 0.000
#> GSM97963 1 0.0000 0.9555 1.000 0.000 0.000
#> GSM97965 1 0.0000 0.9555 1.000 0.000 0.000
#> GSM97966 1 0.0000 0.9555 1.000 0.000 0.000
#> GSM97967 2 0.0000 0.9826 0.000 1.000 0.000
#> GSM97968 2 0.0000 0.9826 0.000 1.000 0.000
#> GSM97969 1 0.0000 0.9555 1.000 0.000 0.000
#> GSM97971 1 0.0000 0.9555 1.000 0.000 0.000
#> GSM97799 3 0.0000 0.9844 0.000 0.000 1.000
#> GSM97823 2 0.0000 0.9826 0.000 1.000 0.000
#> GSM97824 3 0.0000 0.9844 0.000 0.000 1.000
#> GSM97830 3 0.0000 0.9844 0.000 0.000 1.000
#> GSM97835 3 0.4121 0.7818 0.000 0.168 0.832
#> GSM97838 2 0.0000 0.9826 0.000 1.000 0.000
#> GSM97841 2 0.0000 0.9826 0.000 1.000 0.000
#> GSM97842 3 0.0000 0.9844 0.000 0.000 1.000
#> GSM97854 2 0.0000 0.9826 0.000 1.000 0.000
#> GSM97857 3 0.0000 0.9844 0.000 0.000 1.000
#> GSM97860 3 0.0000 0.9844 0.000 0.000 1.000
#> GSM97862 3 0.0000 0.9844 0.000 0.000 1.000
#> GSM97864 2 0.0000 0.9826 0.000 1.000 0.000
#> GSM97866 3 0.0000 0.9844 0.000 0.000 1.000
#> GSM97868 3 0.0000 0.9844 0.000 0.000 1.000
#> GSM97872 1 0.2959 0.9088 0.900 0.000 0.100
#> GSM97873 3 0.0000 0.9844 0.000 0.000 1.000
#> GSM97874 3 0.0000 0.9844 0.000 0.000 1.000
#> GSM97875 3 0.0000 0.9844 0.000 0.000 1.000
#> GSM97876 3 0.0000 0.9844 0.000 0.000 1.000
#> GSM97880 3 0.0000 0.9844 0.000 0.000 1.000
#> GSM97881 3 0.0000 0.9844 0.000 0.000 1.000
#> GSM97884 3 0.0000 0.9844 0.000 0.000 1.000
#> GSM97901 3 0.0000 0.9844 0.000 0.000 1.000
#> GSM97902 3 0.0000 0.9844 0.000 0.000 1.000
#> GSM97909 2 0.0000 0.9826 0.000 1.000 0.000
#> GSM97911 3 0.0000 0.9844 0.000 0.000 1.000
#> GSM97923 3 0.0000 0.9844 0.000 0.000 1.000
#> GSM97928 1 0.2959 0.9088 0.900 0.000 0.100
#> GSM97929 2 0.0000 0.9826 0.000 1.000 0.000
#> GSM97933 3 0.0000 0.9844 0.000 0.000 1.000
#> GSM97934 3 0.0000 0.9844 0.000 0.000 1.000
#> GSM97944 3 0.0000 0.9844 0.000 0.000 1.000
#> GSM97949 2 0.0000 0.9826 0.000 1.000 0.000
#> GSM97956 3 0.0000 0.9844 0.000 0.000 1.000
#> GSM97962 3 0.0000 0.9844 0.000 0.000 1.000
#> GSM97964 3 0.0000 0.9844 0.000 0.000 1.000
#> GSM97970 3 0.0000 0.9844 0.000 0.000 1.000
#> GSM97822 1 0.3116 0.9035 0.892 0.000 0.108
#> GSM97831 3 0.0000 0.9844 0.000 0.000 1.000
#> GSM97845 1 0.0000 0.9555 1.000 0.000 0.000
#> GSM97865 1 0.3551 0.8842 0.868 0.000 0.132
#> GSM97867 3 0.0000 0.9844 0.000 0.000 1.000
#> GSM97883 3 0.0000 0.9844 0.000 0.000 1.000
#> GSM97897 1 0.0000 0.9555 1.000 0.000 0.000
#> GSM97900 1 0.0000 0.9555 1.000 0.000 0.000
#> GSM97904 1 0.2959 0.9089 0.900 0.000 0.100
#> GSM97907 2 0.0000 0.9826 0.000 1.000 0.000
#> GSM97925 3 0.0000 0.9844 0.000 0.000 1.000
#> GSM97947 3 0.0000 0.9844 0.000 0.000 1.000
cbind(get_classes(res, k = 4), get_membership(res, k = 4))
#> class entropy silhouette p1 p2 p3 p4
#> GSM97800 2 0.0707 0.981 0.000 0.980 0.000 0.020
#> GSM97803 2 0.0592 0.982 0.000 0.984 0.000 0.016
#> GSM97804 2 0.0707 0.981 0.000 0.980 0.000 0.020
#> GSM97805 2 0.0707 0.981 0.000 0.980 0.000 0.020
#> GSM97807 2 0.0000 0.984 0.000 1.000 0.000 0.000
#> GSM97809 2 0.0000 0.984 0.000 1.000 0.000 0.000
#> GSM97811 2 0.0000 0.984 0.000 1.000 0.000 0.000
#> GSM97812 2 0.0000 0.984 0.000 1.000 0.000 0.000
#> GSM97816 3 0.2411 0.905 0.040 0.040 0.920 0.000
#> GSM97817 2 0.0000 0.984 0.000 1.000 0.000 0.000
#> GSM97820 2 0.0000 0.984 0.000 1.000 0.000 0.000
#> GSM97825 2 0.0000 0.984 0.000 1.000 0.000 0.000
#> GSM97827 2 0.0000 0.984 0.000 1.000 0.000 0.000
#> GSM97828 3 0.4967 0.192 0.452 0.000 0.548 0.000
#> GSM97833 2 0.0000 0.984 0.000 1.000 0.000 0.000
#> GSM97834 2 0.0000 0.984 0.000 1.000 0.000 0.000
#> GSM97840 2 0.0000 0.984 0.000 1.000 0.000 0.000
#> GSM97846 2 0.0000 0.984 0.000 1.000 0.000 0.000
#> GSM97848 2 0.0000 0.984 0.000 1.000 0.000 0.000
#> GSM97849 2 0.0000 0.984 0.000 1.000 0.000 0.000
#> GSM97850 2 0.0000 0.984 0.000 1.000 0.000 0.000
#> GSM97853 2 0.0000 0.984 0.000 1.000 0.000 0.000
#> GSM97855 2 0.0000 0.984 0.000 1.000 0.000 0.000
#> GSM97878 1 0.0188 0.962 0.996 0.000 0.004 0.000
#> GSM97913 1 0.0895 0.949 0.976 0.000 0.004 0.020
#> GSM97932 4 0.0707 1.000 0.020 0.000 0.000 0.980
#> GSM97939 3 0.0000 0.963 0.000 0.000 1.000 0.000
#> GSM97951 2 0.0000 0.984 0.000 1.000 0.000 0.000
#> GSM97957 3 0.0000 0.963 0.000 0.000 1.000 0.000
#> GSM97972 3 0.1302 0.930 0.044 0.000 0.956 0.000
#> GSM97793 3 0.0188 0.962 0.004 0.000 0.996 0.000
#> GSM97795 2 0.0707 0.981 0.000 0.980 0.000 0.020
#> GSM97802 3 0.0188 0.962 0.004 0.000 0.996 0.000
#> GSM97810 3 0.3569 0.742 0.000 0.196 0.804 0.000
#> GSM97815 3 0.0000 0.963 0.000 0.000 1.000 0.000
#> GSM97837 1 0.0000 0.962 1.000 0.000 0.000 0.000
#> GSM97843 3 0.0000 0.963 0.000 0.000 1.000 0.000
#> GSM97890 3 0.0000 0.963 0.000 0.000 1.000 0.000
#> GSM97899 4 0.0707 1.000 0.020 0.000 0.000 0.980
#> GSM97910 1 0.0817 0.947 0.976 0.000 0.024 0.000
#> GSM97916 1 0.0188 0.962 0.996 0.000 0.004 0.000
#> GSM97920 3 0.0000 0.963 0.000 0.000 1.000 0.000
#> GSM97921 1 0.0188 0.962 0.996 0.000 0.004 0.000
#> GSM97927 1 0.1022 0.957 0.968 0.000 0.000 0.032
#> GSM97937 1 0.0000 0.962 1.000 0.000 0.000 0.000
#> GSM97941 2 0.0000 0.984 0.000 1.000 0.000 0.000
#> GSM97943 1 0.0817 0.947 0.976 0.000 0.024 0.000
#> GSM97958 1 0.2081 0.898 0.916 0.000 0.084 0.000
#> GSM97960 2 0.0000 0.984 0.000 1.000 0.000 0.000
#> GSM97794 1 0.0188 0.962 0.996 0.000 0.004 0.000
#> GSM97796 4 0.0707 1.000 0.020 0.000 0.000 0.980
#> GSM97797 1 0.0188 0.962 0.996 0.000 0.004 0.000
#> GSM97798 4 0.0707 1.000 0.020 0.000 0.000 0.980
#> GSM97801 1 0.0188 0.962 0.996 0.000 0.004 0.000
#> GSM97806 1 0.1211 0.954 0.960 0.000 0.000 0.040
#> GSM97808 4 0.0707 1.000 0.020 0.000 0.000 0.980
#> GSM97813 1 0.1211 0.953 0.960 0.000 0.000 0.040
#> GSM97814 4 0.0707 1.000 0.020 0.000 0.000 0.980
#> GSM97818 1 0.0188 0.962 0.996 0.000 0.004 0.000
#> GSM97819 3 0.0188 0.962 0.004 0.000 0.996 0.000
#> GSM97821 3 0.6349 0.162 0.028 0.428 0.524 0.020
#> GSM97826 1 0.0000 0.962 1.000 0.000 0.000 0.000
#> GSM97829 1 0.0000 0.962 1.000 0.000 0.000 0.000
#> GSM97832 2 0.5400 0.369 0.000 0.608 0.372 0.020
#> GSM97836 1 0.1118 0.955 0.964 0.000 0.000 0.036
#> GSM97839 4 0.0707 1.000 0.020 0.000 0.000 0.980
#> GSM97844 2 0.0707 0.981 0.000 0.980 0.000 0.020
#> GSM97847 1 0.0188 0.962 0.996 0.000 0.000 0.004
#> GSM97851 4 0.0707 1.000 0.020 0.000 0.000 0.980
#> GSM97852 1 0.1211 0.954 0.960 0.000 0.000 0.040
#> GSM97856 4 0.0707 1.000 0.020 0.000 0.000 0.980
#> GSM97858 2 0.0707 0.981 0.000 0.980 0.000 0.020
#> GSM97859 1 0.1022 0.957 0.968 0.000 0.000 0.032
#> GSM97861 1 0.1118 0.955 0.964 0.000 0.000 0.036
#> GSM97863 4 0.0707 1.000 0.020 0.000 0.000 0.980
#> GSM97869 1 0.0188 0.962 0.996 0.000 0.004 0.000
#> GSM97870 1 0.0707 0.948 0.980 0.000 0.020 0.000
#> GSM97871 4 0.0707 1.000 0.020 0.000 0.000 0.980
#> GSM97877 1 0.2189 0.918 0.932 0.044 0.004 0.020
#> GSM97879 1 0.1211 0.954 0.960 0.000 0.000 0.040
#> GSM97882 1 0.1118 0.955 0.964 0.000 0.000 0.036
#> GSM97885 1 0.0000 0.962 1.000 0.000 0.000 0.000
#> GSM97886 4 0.0707 1.000 0.020 0.000 0.000 0.980
#> GSM97887 4 0.0707 1.000 0.020 0.000 0.000 0.980
#> GSM97888 4 0.0707 1.000 0.020 0.000 0.000 0.980
#> GSM97889 4 0.0817 0.996 0.024 0.000 0.000 0.976
#> GSM97891 1 0.1211 0.954 0.960 0.000 0.000 0.040
#> GSM97892 2 0.0707 0.981 0.000 0.980 0.000 0.020
#> GSM97893 4 0.0707 1.000 0.020 0.000 0.000 0.980
#> GSM97894 4 0.0707 1.000 0.020 0.000 0.000 0.980
#> GSM97895 4 0.0707 1.000 0.020 0.000 0.000 0.980
#> GSM97896 4 0.0707 1.000 0.020 0.000 0.000 0.980
#> GSM97898 4 0.0707 1.000 0.020 0.000 0.000 0.980
#> GSM97903 1 0.0188 0.962 0.996 0.000 0.004 0.000
#> GSM97905 1 0.3873 0.736 0.772 0.000 0.000 0.228
#> GSM97906 4 0.0707 1.000 0.020 0.000 0.000 0.980
#> GSM97908 1 0.2973 0.852 0.856 0.000 0.000 0.144
#> GSM97912 1 0.0000 0.962 1.000 0.000 0.000 0.000
#> GSM97914 1 0.0188 0.962 0.996 0.000 0.004 0.000
#> GSM97915 4 0.0707 1.000 0.020 0.000 0.000 0.980
#> GSM97917 4 0.0707 1.000 0.020 0.000 0.000 0.980
#> GSM97918 4 0.0707 1.000 0.020 0.000 0.000 0.980
#> GSM97919 4 0.0707 1.000 0.020 0.000 0.000 0.980
#> GSM97922 1 0.1389 0.949 0.952 0.000 0.000 0.048
#> GSM97924 2 0.0707 0.981 0.000 0.980 0.000 0.020
#> GSM97926 3 0.0469 0.955 0.012 0.000 0.988 0.000
#> GSM97930 1 0.0188 0.962 0.996 0.000 0.000 0.004
#> GSM97931 3 0.4817 0.391 0.388 0.000 0.612 0.000
#> GSM97935 1 0.1305 0.955 0.960 0.000 0.004 0.036
#> GSM97936 4 0.0707 1.000 0.020 0.000 0.000 0.980
#> GSM97938 1 0.4761 0.452 0.628 0.000 0.000 0.372
#> GSM97940 4 0.0707 1.000 0.020 0.000 0.000 0.980
#> GSM97942 3 0.0188 0.962 0.004 0.000 0.996 0.000
#> GSM97945 4 0.0707 1.000 0.020 0.000 0.000 0.980
#> GSM97946 2 0.0000 0.984 0.000 1.000 0.000 0.000
#> GSM97948 3 0.0188 0.962 0.004 0.000 0.996 0.000
#> GSM97950 4 0.0707 1.000 0.020 0.000 0.000 0.980
#> GSM97952 4 0.0707 1.000 0.020 0.000 0.000 0.980
#> GSM97953 1 0.0817 0.959 0.976 0.000 0.000 0.024
#> GSM97954 1 0.1211 0.954 0.960 0.000 0.000 0.040
#> GSM97955 4 0.0707 1.000 0.020 0.000 0.000 0.980
#> GSM97959 1 0.0188 0.962 0.996 0.000 0.004 0.000
#> GSM97961 4 0.0707 1.000 0.020 0.000 0.000 0.980
#> GSM97963 4 0.0707 1.000 0.020 0.000 0.000 0.980
#> GSM97965 4 0.0707 1.000 0.020 0.000 0.000 0.980
#> GSM97966 4 0.0707 1.000 0.020 0.000 0.000 0.980
#> GSM97967 2 0.0000 0.984 0.000 1.000 0.000 0.000
#> GSM97968 2 0.0000 0.984 0.000 1.000 0.000 0.000
#> GSM97969 1 0.3311 0.818 0.828 0.000 0.000 0.172
#> GSM97971 1 0.1022 0.957 0.968 0.000 0.000 0.032
#> GSM97799 3 0.0000 0.963 0.000 0.000 1.000 0.000
#> GSM97823 2 0.0000 0.984 0.000 1.000 0.000 0.000
#> GSM97824 3 0.0000 0.963 0.000 0.000 1.000 0.000
#> GSM97830 3 0.0188 0.962 0.004 0.000 0.996 0.000
#> GSM97835 3 0.1637 0.910 0.000 0.060 0.940 0.000
#> GSM97838 2 0.0707 0.981 0.000 0.980 0.000 0.020
#> GSM97841 2 0.0707 0.981 0.000 0.980 0.000 0.020
#> GSM97842 3 0.0000 0.963 0.000 0.000 1.000 0.000
#> GSM97854 2 0.0707 0.981 0.000 0.980 0.000 0.020
#> GSM97857 3 0.0000 0.963 0.000 0.000 1.000 0.000
#> GSM97860 3 0.0188 0.962 0.004 0.000 0.996 0.000
#> GSM97862 3 0.0000 0.963 0.000 0.000 1.000 0.000
#> GSM97864 2 0.0707 0.981 0.000 0.980 0.000 0.020
#> GSM97866 3 0.0000 0.963 0.000 0.000 1.000 0.000
#> GSM97868 3 0.0000 0.963 0.000 0.000 1.000 0.000
#> GSM97872 1 0.0000 0.962 1.000 0.000 0.000 0.000
#> GSM97873 3 0.0000 0.963 0.000 0.000 1.000 0.000
#> GSM97874 3 0.0188 0.962 0.004 0.000 0.996 0.000
#> GSM97875 3 0.0188 0.962 0.004 0.000 0.996 0.000
#> GSM97876 3 0.0188 0.962 0.004 0.000 0.996 0.000
#> GSM97880 3 0.0188 0.962 0.004 0.000 0.996 0.000
#> GSM97881 3 0.0000 0.963 0.000 0.000 1.000 0.000
#> GSM97884 3 0.0000 0.963 0.000 0.000 1.000 0.000
#> GSM97901 3 0.0000 0.963 0.000 0.000 1.000 0.000
#> GSM97902 1 0.0817 0.947 0.976 0.000 0.024 0.000
#> GSM97909 2 0.0895 0.978 0.000 0.976 0.004 0.020
#> GSM97911 3 0.0000 0.963 0.000 0.000 1.000 0.000
#> GSM97923 3 0.0188 0.962 0.004 0.000 0.996 0.000
#> GSM97928 1 0.0000 0.962 1.000 0.000 0.000 0.000
#> GSM97929 2 0.0707 0.981 0.000 0.980 0.000 0.020
#> GSM97933 3 0.0188 0.962 0.004 0.000 0.996 0.000
#> GSM97934 3 0.0188 0.962 0.004 0.000 0.996 0.000
#> GSM97944 3 0.0000 0.963 0.000 0.000 1.000 0.000
#> GSM97949 2 0.0000 0.984 0.000 1.000 0.000 0.000
#> GSM97956 3 0.0000 0.963 0.000 0.000 1.000 0.000
#> GSM97962 3 0.0000 0.963 0.000 0.000 1.000 0.000
#> GSM97964 3 0.0000 0.963 0.000 0.000 1.000 0.000
#> GSM97970 3 0.0000 0.963 0.000 0.000 1.000 0.000
#> GSM97822 1 0.1118 0.955 0.964 0.000 0.000 0.036
#> GSM97831 3 0.0000 0.963 0.000 0.000 1.000 0.000
#> GSM97845 1 0.1211 0.954 0.960 0.000 0.000 0.040
#> GSM97865 1 0.0188 0.962 0.996 0.000 0.004 0.000
#> GSM97867 3 0.0188 0.962 0.004 0.000 0.996 0.000
#> GSM97883 3 0.0188 0.962 0.004 0.000 0.996 0.000
#> GSM97897 4 0.0817 0.996 0.024 0.000 0.000 0.976
#> GSM97900 4 0.0707 1.000 0.020 0.000 0.000 0.980
#> GSM97904 1 0.0707 0.960 0.980 0.000 0.000 0.020
#> GSM97907 2 0.0707 0.981 0.000 0.980 0.000 0.020
#> GSM97925 3 0.0188 0.962 0.004 0.000 0.996 0.000
#> GSM97947 3 0.0188 0.962 0.004 0.000 0.996 0.000
cbind(get_classes(res, k = 5), get_membership(res, k = 5))
#> class entropy silhouette p1 p2 p3 p4 p5
#> GSM97800 2 0.1341 0.9304 0.000 0.944 0.000 0.000 0.056
#> GSM97803 2 0.1341 0.9304 0.000 0.944 0.000 0.000 0.056
#> GSM97804 2 0.1502 0.9299 0.004 0.940 0.000 0.000 0.056
#> GSM97805 2 0.1502 0.9299 0.004 0.940 0.000 0.000 0.056
#> GSM97807 2 0.0000 0.9404 0.000 1.000 0.000 0.000 0.000
#> GSM97809 2 0.0000 0.9404 0.000 1.000 0.000 0.000 0.000
#> GSM97811 2 0.0000 0.9404 0.000 1.000 0.000 0.000 0.000
#> GSM97812 2 0.0000 0.9404 0.000 1.000 0.000 0.000 0.000
#> GSM97816 1 0.6987 -0.0924 0.400 0.012 0.228 0.000 0.360
#> GSM97817 2 0.0000 0.9404 0.000 1.000 0.000 0.000 0.000
#> GSM97820 2 0.0000 0.9404 0.000 1.000 0.000 0.000 0.000
#> GSM97825 2 0.0000 0.9404 0.000 1.000 0.000 0.000 0.000
#> GSM97827 2 0.0000 0.9404 0.000 1.000 0.000 0.000 0.000
#> GSM97828 1 0.5792 0.1700 0.616 0.000 0.192 0.000 0.192
#> GSM97833 2 0.0000 0.9404 0.000 1.000 0.000 0.000 0.000
#> GSM97834 2 0.0000 0.9404 0.000 1.000 0.000 0.000 0.000
#> GSM97840 2 0.0000 0.9404 0.000 1.000 0.000 0.000 0.000
#> GSM97846 2 0.0162 0.9399 0.000 0.996 0.000 0.000 0.004
#> GSM97848 2 0.0000 0.9404 0.000 1.000 0.000 0.000 0.000
#> GSM97849 2 0.0000 0.9404 0.000 1.000 0.000 0.000 0.000
#> GSM97850 2 0.0000 0.9404 0.000 1.000 0.000 0.000 0.000
#> GSM97853 2 0.0000 0.9404 0.000 1.000 0.000 0.000 0.000
#> GSM97855 2 0.0000 0.9404 0.000 1.000 0.000 0.000 0.000
#> GSM97878 1 0.0955 0.5685 0.968 0.000 0.000 0.004 0.028
#> GSM97913 1 0.2966 0.4216 0.816 0.000 0.000 0.000 0.184
#> GSM97932 4 0.2732 0.8642 0.000 0.000 0.000 0.840 0.160
#> GSM97939 3 0.4015 0.7423 0.000 0.000 0.652 0.000 0.348
#> GSM97951 2 0.0671 0.9334 0.004 0.980 0.000 0.000 0.016
#> GSM97957 3 0.1121 0.8598 0.000 0.000 0.956 0.000 0.044
#> GSM97972 1 0.6659 -0.0936 0.396 0.000 0.228 0.000 0.376
#> GSM97793 3 0.0290 0.8618 0.000 0.000 0.992 0.000 0.008
#> GSM97795 2 0.4182 0.6194 0.004 0.644 0.000 0.000 0.352
#> GSM97802 3 0.4341 0.3580 0.008 0.000 0.628 0.000 0.364
#> GSM97810 3 0.5884 0.6039 0.000 0.112 0.536 0.000 0.352
#> GSM97815 3 0.3895 0.7601 0.000 0.000 0.680 0.000 0.320
#> GSM97837 1 0.2536 0.5722 0.868 0.000 0.000 0.004 0.128
#> GSM97843 3 0.0162 0.8635 0.000 0.000 0.996 0.000 0.004
#> GSM97890 3 0.1671 0.8695 0.000 0.000 0.924 0.000 0.076
#> GSM97899 4 0.0162 0.8902 0.000 0.000 0.000 0.996 0.004
#> GSM97910 1 0.1638 0.5439 0.932 0.000 0.004 0.000 0.064
#> GSM97916 1 0.0671 0.5699 0.980 0.000 0.000 0.004 0.016
#> GSM97920 3 0.1121 0.8598 0.000 0.000 0.956 0.000 0.044
#> GSM97921 1 0.0324 0.5748 0.992 0.000 0.000 0.004 0.004
#> GSM97927 1 0.4840 0.4661 0.640 0.000 0.000 0.040 0.320
#> GSM97937 1 0.3333 0.5626 0.788 0.000 0.000 0.004 0.208
#> GSM97941 2 0.2286 0.8592 0.004 0.888 0.000 0.000 0.108
#> GSM97943 1 0.2629 0.4815 0.860 0.000 0.004 0.000 0.136
#> GSM97958 1 0.4135 0.2127 0.656 0.000 0.004 0.000 0.340
#> GSM97960 2 0.4047 0.6046 0.004 0.676 0.000 0.000 0.320
#> GSM97794 1 0.1124 0.5610 0.960 0.000 0.000 0.004 0.036
#> GSM97796 4 0.2377 0.8824 0.000 0.000 0.000 0.872 0.128
#> GSM97797 1 0.1205 0.5587 0.956 0.000 0.000 0.004 0.040
#> GSM97798 4 0.0162 0.8902 0.000 0.000 0.000 0.996 0.004
#> GSM97801 1 0.1124 0.5632 0.960 0.000 0.000 0.004 0.036
#> GSM97806 1 0.3841 0.5599 0.780 0.000 0.000 0.032 0.188
#> GSM97808 4 0.0162 0.8902 0.000 0.000 0.000 0.996 0.004
#> GSM97813 1 0.5227 0.2834 0.508 0.000 0.000 0.044 0.448
#> GSM97814 4 0.0162 0.8902 0.000 0.000 0.000 0.996 0.004
#> GSM97818 1 0.0955 0.5649 0.968 0.000 0.000 0.004 0.028
#> GSM97819 3 0.0703 0.8644 0.000 0.000 0.976 0.000 0.024
#> GSM97821 5 0.7636 -0.0519 0.324 0.160 0.084 0.000 0.432
#> GSM97826 1 0.4135 0.4868 0.656 0.000 0.000 0.004 0.340
#> GSM97829 1 0.1638 0.5817 0.932 0.000 0.000 0.004 0.064
#> GSM97832 2 0.5853 0.3318 0.000 0.472 0.096 0.000 0.432
#> GSM97836 1 0.4679 0.4743 0.652 0.000 0.000 0.032 0.316
#> GSM97839 4 0.2377 0.8824 0.000 0.000 0.000 0.872 0.128
#> GSM97844 2 0.1502 0.9299 0.004 0.940 0.000 0.000 0.056
#> GSM97847 1 0.3671 0.5289 0.756 0.000 0.000 0.008 0.236
#> GSM97851 4 0.2732 0.8642 0.000 0.000 0.000 0.840 0.160
#> GSM97852 1 0.4540 0.4670 0.656 0.000 0.000 0.024 0.320
#> GSM97856 4 0.0162 0.8902 0.000 0.000 0.000 0.996 0.004
#> GSM97858 2 0.1502 0.9299 0.004 0.940 0.000 0.000 0.056
#> GSM97859 1 0.4861 0.3524 0.548 0.000 0.000 0.024 0.428
#> GSM97861 1 0.4768 0.4835 0.656 0.000 0.000 0.040 0.304
#> GSM97863 4 0.2377 0.8824 0.000 0.000 0.000 0.872 0.128
#> GSM97869 1 0.3715 0.5318 0.736 0.000 0.000 0.004 0.260
#> GSM97870 1 0.4455 0.4012 0.588 0.000 0.008 0.000 0.404
#> GSM97871 4 0.0162 0.8902 0.000 0.000 0.000 0.996 0.004
#> GSM97877 1 0.2966 0.4216 0.816 0.000 0.000 0.000 0.184
#> GSM97879 1 0.4425 0.5329 0.716 0.000 0.000 0.040 0.244
#> GSM97882 1 0.4679 0.4743 0.652 0.000 0.000 0.032 0.316
#> GSM97885 1 0.3861 0.5216 0.712 0.000 0.000 0.004 0.284
#> GSM97886 4 0.1341 0.8910 0.000 0.000 0.000 0.944 0.056
#> GSM97887 4 0.0162 0.8902 0.000 0.000 0.000 0.996 0.004
#> GSM97888 5 0.5206 -0.2450 0.044 0.000 0.000 0.428 0.528
#> GSM97889 4 0.5151 0.0615 0.044 0.000 0.000 0.560 0.396
#> GSM97891 1 0.4342 0.5362 0.728 0.000 0.000 0.040 0.232
#> GSM97892 2 0.1502 0.9299 0.004 0.940 0.000 0.000 0.056
#> GSM97893 4 0.3612 0.8246 0.028 0.000 0.000 0.800 0.172
#> GSM97894 4 0.2424 0.8811 0.000 0.000 0.000 0.868 0.132
#> GSM97895 4 0.2732 0.8642 0.000 0.000 0.000 0.840 0.160
#> GSM97896 4 0.4015 0.4093 0.000 0.000 0.000 0.652 0.348
#> GSM97898 4 0.2424 0.8811 0.000 0.000 0.000 0.868 0.132
#> GSM97903 1 0.1704 0.5834 0.928 0.000 0.000 0.004 0.068
#> GSM97905 5 0.7166 -0.0858 0.300 0.000 0.220 0.028 0.452
#> GSM97906 4 0.0162 0.8902 0.000 0.000 0.000 0.996 0.004
#> GSM97908 1 0.6297 0.1549 0.532 0.000 0.000 0.212 0.256
#> GSM97912 1 0.4651 0.3723 0.560 0.000 0.008 0.004 0.428
#> GSM97914 1 0.0451 0.5738 0.988 0.000 0.000 0.004 0.008
#> GSM97915 4 0.2424 0.8811 0.000 0.000 0.000 0.868 0.132
#> GSM97917 4 0.2732 0.8642 0.000 0.000 0.000 0.840 0.160
#> GSM97918 4 0.2424 0.8811 0.000 0.000 0.000 0.868 0.132
#> GSM97919 4 0.2424 0.8811 0.000 0.000 0.000 0.868 0.132
#> GSM97922 1 0.5293 0.2434 0.492 0.000 0.000 0.048 0.460
#> GSM97924 2 0.1502 0.9299 0.004 0.940 0.000 0.000 0.056
#> GSM97926 3 0.3732 0.8390 0.032 0.000 0.792 0.000 0.176
#> GSM97930 1 0.3388 0.5597 0.792 0.000 0.000 0.008 0.200
#> GSM97931 1 0.5717 0.0359 0.540 0.000 0.092 0.000 0.368
#> GSM97935 1 0.4708 0.4885 0.668 0.000 0.000 0.040 0.292
#> GSM97936 4 0.2127 0.8861 0.000 0.000 0.000 0.892 0.108
#> GSM97938 1 0.6723 -0.0762 0.412 0.000 0.000 0.324 0.264
#> GSM97940 4 0.0162 0.8902 0.000 0.000 0.000 0.996 0.004
#> GSM97942 3 0.0290 0.8618 0.000 0.000 0.992 0.000 0.008
#> GSM97945 4 0.0162 0.8902 0.000 0.000 0.000 0.996 0.004
#> GSM97946 2 0.0000 0.9404 0.000 1.000 0.000 0.000 0.000
#> GSM97948 3 0.3876 0.4437 0.000 0.000 0.684 0.000 0.316
#> GSM97950 4 0.1410 0.8909 0.000 0.000 0.000 0.940 0.060
#> GSM97952 4 0.0162 0.8902 0.000 0.000 0.000 0.996 0.004
#> GSM97953 1 0.3999 0.5366 0.740 0.000 0.000 0.020 0.240
#> GSM97954 1 0.4484 0.4816 0.668 0.000 0.000 0.024 0.308
#> GSM97955 4 0.2377 0.8824 0.000 0.000 0.000 0.872 0.128
#> GSM97959 1 0.1357 0.5538 0.948 0.000 0.000 0.004 0.048
#> GSM97961 4 0.1410 0.8909 0.000 0.000 0.000 0.940 0.060
#> GSM97963 4 0.0162 0.8902 0.000 0.000 0.000 0.996 0.004
#> GSM97965 4 0.0162 0.8902 0.000 0.000 0.000 0.996 0.004
#> GSM97966 4 0.0162 0.8902 0.000 0.000 0.000 0.996 0.004
#> GSM97967 2 0.0162 0.9399 0.000 0.996 0.000 0.000 0.004
#> GSM97968 2 0.0162 0.9398 0.004 0.996 0.000 0.000 0.000
#> GSM97969 5 0.5178 -0.4144 0.480 0.000 0.000 0.040 0.480
#> GSM97971 1 0.4867 0.3459 0.544 0.000 0.000 0.024 0.432
#> GSM97799 3 0.3210 0.8372 0.000 0.000 0.788 0.000 0.212
#> GSM97823 2 0.0000 0.9404 0.000 1.000 0.000 0.000 0.000
#> GSM97824 3 0.3480 0.8251 0.000 0.000 0.752 0.000 0.248
#> GSM97830 3 0.0290 0.8626 0.000 0.000 0.992 0.000 0.008
#> GSM97835 3 0.4540 0.7400 0.000 0.024 0.656 0.000 0.320
#> GSM97838 2 0.1502 0.9299 0.004 0.940 0.000 0.000 0.056
#> GSM97841 2 0.1502 0.9299 0.004 0.940 0.000 0.000 0.056
#> GSM97842 3 0.3366 0.8275 0.000 0.000 0.768 0.000 0.232
#> GSM97854 2 0.1502 0.9299 0.004 0.940 0.000 0.000 0.056
#> GSM97857 3 0.4015 0.7423 0.000 0.000 0.652 0.000 0.348
#> GSM97860 3 0.0290 0.8618 0.000 0.000 0.992 0.000 0.008
#> GSM97862 3 0.2329 0.8631 0.000 0.000 0.876 0.000 0.124
#> GSM97864 2 0.1502 0.9299 0.004 0.940 0.000 0.000 0.056
#> GSM97866 3 0.1792 0.8687 0.000 0.000 0.916 0.000 0.084
#> GSM97868 3 0.3109 0.8419 0.000 0.000 0.800 0.000 0.200
#> GSM97872 1 0.4288 0.4337 0.612 0.000 0.000 0.004 0.384
#> GSM97873 3 0.3336 0.8297 0.000 0.000 0.772 0.000 0.228
#> GSM97874 3 0.0404 0.8616 0.000 0.000 0.988 0.000 0.012
#> GSM97875 3 0.0609 0.8652 0.000 0.000 0.980 0.000 0.020
#> GSM97876 3 0.0290 0.8618 0.000 0.000 0.992 0.000 0.008
#> GSM97880 3 0.0404 0.8616 0.000 0.000 0.988 0.000 0.012
#> GSM97881 3 0.2605 0.8575 0.000 0.000 0.852 0.000 0.148
#> GSM97884 3 0.3210 0.8372 0.000 0.000 0.788 0.000 0.212
#> GSM97901 3 0.1792 0.8687 0.000 0.000 0.916 0.000 0.084
#> GSM97902 1 0.2629 0.4815 0.860 0.000 0.004 0.000 0.136
#> GSM97909 2 0.4403 0.5684 0.008 0.608 0.000 0.000 0.384
#> GSM97911 3 0.2605 0.8575 0.000 0.000 0.852 0.000 0.148
#> GSM97923 3 0.0290 0.8618 0.000 0.000 0.992 0.000 0.008
#> GSM97928 1 0.4321 0.4184 0.600 0.000 0.000 0.004 0.396
#> GSM97929 2 0.1502 0.9299 0.004 0.940 0.000 0.000 0.056
#> GSM97933 3 0.0609 0.8615 0.000 0.000 0.980 0.000 0.020
#> GSM97934 3 0.1121 0.8598 0.000 0.000 0.956 0.000 0.044
#> GSM97944 3 0.3210 0.8372 0.000 0.000 0.788 0.000 0.212
#> GSM97949 2 0.0000 0.9404 0.000 1.000 0.000 0.000 0.000
#> GSM97956 3 0.3274 0.8362 0.000 0.000 0.780 0.000 0.220
#> GSM97962 3 0.1792 0.8668 0.000 0.000 0.916 0.000 0.084
#> GSM97964 3 0.3336 0.8337 0.000 0.000 0.772 0.000 0.228
#> GSM97970 3 0.3336 0.8297 0.000 0.000 0.772 0.000 0.228
#> GSM97822 1 0.5133 0.3693 0.568 0.000 0.000 0.044 0.388
#> GSM97831 3 0.1410 0.8697 0.000 0.000 0.940 0.000 0.060
#> GSM97845 1 0.4404 0.5058 0.684 0.000 0.000 0.024 0.292
#> GSM97865 1 0.0324 0.5748 0.992 0.000 0.000 0.004 0.004
#> GSM97867 3 0.0290 0.8618 0.000 0.000 0.992 0.000 0.008
#> GSM97883 3 0.0404 0.8616 0.000 0.000 0.988 0.000 0.012
#> GSM97897 4 0.4015 0.3408 0.000 0.000 0.000 0.652 0.348
#> GSM97900 4 0.0162 0.8902 0.000 0.000 0.000 0.996 0.004
#> GSM97904 1 0.4574 0.3916 0.576 0.000 0.000 0.012 0.412
#> GSM97907 2 0.1502 0.9299 0.004 0.940 0.000 0.000 0.056
#> GSM97925 3 0.0290 0.8618 0.000 0.000 0.992 0.000 0.008
#> GSM97947 3 0.2020 0.8156 0.000 0.000 0.900 0.000 0.100
cbind(get_classes(res, k = 6), get_membership(res, k = 6))
#> class entropy silhouette p1 p2 p3 p4 p5 p6
#> GSM97800 2 0.2833 0.90180 0.008 0.864 0.000 0.000 0.088 0.040
#> GSM97803 2 0.2639 0.90368 0.008 0.876 0.000 0.000 0.084 0.032
#> GSM97804 2 0.2711 0.90305 0.008 0.872 0.000 0.000 0.084 0.036
#> GSM97805 2 0.2833 0.90180 0.008 0.864 0.000 0.000 0.088 0.040
#> GSM97807 2 0.0291 0.92697 0.000 0.992 0.000 0.000 0.004 0.004
#> GSM97809 2 0.0000 0.92779 0.000 1.000 0.000 0.000 0.000 0.000
#> GSM97811 2 0.0000 0.92779 0.000 1.000 0.000 0.000 0.000 0.000
#> GSM97812 2 0.0000 0.92779 0.000 1.000 0.000 0.000 0.000 0.000
#> GSM97816 6 0.4946 0.45788 0.000 0.000 0.284 0.000 0.100 0.616
#> GSM97817 2 0.0291 0.92697 0.000 0.992 0.000 0.000 0.004 0.004
#> GSM97820 2 0.0291 0.92697 0.000 0.992 0.000 0.000 0.004 0.004
#> GSM97825 2 0.0000 0.92779 0.000 1.000 0.000 0.000 0.000 0.000
#> GSM97827 2 0.0000 0.92779 0.000 1.000 0.000 0.000 0.000 0.000
#> GSM97828 6 0.4852 0.55916 0.048 0.000 0.064 0.000 0.176 0.712
#> GSM97833 2 0.0000 0.92779 0.000 1.000 0.000 0.000 0.000 0.000
#> GSM97834 2 0.0000 0.92779 0.000 1.000 0.000 0.000 0.000 0.000
#> GSM97840 2 0.0146 0.92697 0.000 0.996 0.000 0.000 0.000 0.004
#> GSM97846 2 0.0000 0.92779 0.000 1.000 0.000 0.000 0.000 0.000
#> GSM97848 2 0.0000 0.92779 0.000 1.000 0.000 0.000 0.000 0.000
#> GSM97849 2 0.0000 0.92779 0.000 1.000 0.000 0.000 0.000 0.000
#> GSM97850 2 0.0291 0.92697 0.000 0.992 0.000 0.000 0.004 0.004
#> GSM97853 2 0.0291 0.92697 0.000 0.992 0.000 0.000 0.004 0.004
#> GSM97855 2 0.0291 0.92697 0.000 0.992 0.000 0.000 0.004 0.004
#> GSM97878 6 0.3885 0.67666 0.220 0.000 0.000 0.000 0.044 0.736
#> GSM97913 6 0.3373 0.70209 0.140 0.000 0.012 0.000 0.032 0.816
#> GSM97932 4 0.2231 0.79049 0.004 0.000 0.000 0.900 0.068 0.028
#> GSM97939 3 0.2384 0.45120 0.000 0.000 0.888 0.000 0.064 0.048
#> GSM97951 2 0.0972 0.91399 0.000 0.964 0.000 0.000 0.028 0.008
#> GSM97957 3 0.4757 0.04546 0.000 0.000 0.480 0.000 0.472 0.048
#> GSM97972 6 0.4957 0.42483 0.000 0.000 0.332 0.000 0.084 0.584
#> GSM97793 3 0.3867 0.01924 0.000 0.000 0.512 0.000 0.488 0.000
#> GSM97795 2 0.6871 0.28142 0.008 0.408 0.380 0.000 0.128 0.076
#> GSM97802 1 0.5457 -0.12093 0.588 0.000 0.140 0.000 0.264 0.008
#> GSM97810 3 0.3906 0.38654 0.000 0.068 0.808 0.000 0.064 0.060
#> GSM97815 3 0.1863 0.46874 0.000 0.000 0.920 0.000 0.044 0.036
#> GSM97837 6 0.5358 0.35318 0.392 0.000 0.000 0.000 0.112 0.496
#> GSM97843 3 0.4089 0.04846 0.000 0.000 0.524 0.000 0.468 0.008
#> GSM97890 3 0.3508 0.36991 0.000 0.000 0.704 0.000 0.292 0.004
#> GSM97899 4 0.3749 0.83968 0.016 0.000 0.000 0.776 0.180 0.028
#> GSM97910 6 0.3269 0.70931 0.184 0.000 0.000 0.000 0.024 0.792
#> GSM97916 6 0.3342 0.68681 0.228 0.000 0.000 0.000 0.012 0.760
#> GSM97920 3 0.4757 0.04994 0.000 0.000 0.480 0.000 0.472 0.048
#> GSM97921 6 0.4294 0.64773 0.248 0.000 0.000 0.000 0.060 0.692
#> GSM97927 1 0.2611 0.63826 0.864 0.000 0.000 0.008 0.012 0.116
#> GSM97937 1 0.6560 0.17557 0.500 0.000 0.000 0.092 0.116 0.292
#> GSM97941 2 0.2201 0.87433 0.000 0.900 0.000 0.000 0.048 0.052
#> GSM97943 6 0.3557 0.69279 0.140 0.000 0.004 0.000 0.056 0.800
#> GSM97958 6 0.5260 0.53864 0.040 0.000 0.224 0.000 0.080 0.656
#> GSM97960 3 0.5582 -0.19466 0.000 0.448 0.460 0.000 0.044 0.048
#> GSM97794 6 0.3073 0.70418 0.204 0.000 0.000 0.000 0.008 0.788
#> GSM97796 4 0.0806 0.82472 0.000 0.000 0.000 0.972 0.008 0.020
#> GSM97797 6 0.3012 0.70738 0.196 0.000 0.000 0.000 0.008 0.796
#> GSM97798 4 0.3749 0.83968 0.016 0.000 0.000 0.776 0.180 0.028
#> GSM97801 6 0.3315 0.70722 0.200 0.000 0.000 0.000 0.020 0.780
#> GSM97806 1 0.4748 0.41209 0.624 0.000 0.000 0.008 0.052 0.316
#> GSM97808 4 0.3749 0.83968 0.016 0.000 0.000 0.776 0.180 0.028
#> GSM97813 1 0.0405 0.66365 0.988 0.000 0.000 0.008 0.004 0.000
#> GSM97814 4 0.3749 0.83968 0.016 0.000 0.000 0.776 0.180 0.028
#> GSM97818 6 0.3073 0.70418 0.204 0.000 0.000 0.000 0.008 0.788
#> GSM97819 3 0.4076 0.10624 0.000 0.000 0.540 0.000 0.452 0.008
#> GSM97821 6 0.6282 0.28473 0.004 0.036 0.376 0.000 0.124 0.460
#> GSM97826 1 0.4024 0.52587 0.744 0.000 0.000 0.000 0.072 0.184
#> GSM97829 6 0.4703 0.55208 0.312 0.000 0.000 0.000 0.068 0.620
#> GSM97832 3 0.6874 0.13306 0.004 0.240 0.504 0.000 0.120 0.132
#> GSM97836 1 0.2917 0.63080 0.840 0.000 0.000 0.008 0.016 0.136
#> GSM97839 4 0.0891 0.82212 0.000 0.000 0.000 0.968 0.008 0.024
#> GSM97844 2 0.2833 0.90180 0.008 0.864 0.000 0.000 0.088 0.040
#> GSM97847 1 0.7032 0.12943 0.400 0.000 0.000 0.152 0.108 0.340
#> GSM97851 4 0.2094 0.79291 0.004 0.000 0.000 0.908 0.064 0.024
#> GSM97852 1 0.7065 0.23895 0.428 0.000 0.000 0.172 0.108 0.292
#> GSM97856 4 0.3749 0.83968 0.016 0.000 0.000 0.776 0.180 0.028
#> GSM97858 2 0.2711 0.90305 0.008 0.872 0.000 0.000 0.084 0.036
#> GSM97859 1 0.0665 0.66446 0.980 0.000 0.000 0.008 0.004 0.008
#> GSM97861 1 0.3288 0.60626 0.800 0.000 0.000 0.008 0.016 0.176
#> GSM97863 4 0.0993 0.82102 0.000 0.000 0.000 0.964 0.012 0.024
#> GSM97869 1 0.3586 0.52497 0.720 0.000 0.000 0.000 0.012 0.268
#> GSM97870 1 0.0909 0.66121 0.968 0.000 0.000 0.000 0.012 0.020
#> GSM97871 4 0.3749 0.83968 0.016 0.000 0.000 0.776 0.180 0.028
#> GSM97877 6 0.3969 0.68663 0.124 0.008 0.020 0.000 0.052 0.796
#> GSM97879 1 0.4666 0.44579 0.644 0.000 0.000 0.008 0.052 0.296
#> GSM97882 1 0.2876 0.63213 0.844 0.000 0.000 0.008 0.016 0.132
#> GSM97885 1 0.3534 0.54504 0.740 0.000 0.000 0.000 0.016 0.244
#> GSM97886 4 0.2743 0.84081 0.000 0.000 0.000 0.828 0.164 0.008
#> GSM97887 4 0.3749 0.83968 0.016 0.000 0.000 0.776 0.180 0.028
#> GSM97888 1 0.3829 0.50585 0.760 0.000 0.000 0.200 0.016 0.024
#> GSM97889 1 0.4477 0.49293 0.748 0.000 0.000 0.144 0.076 0.032
#> GSM97891 1 0.4568 0.44648 0.648 0.000 0.000 0.008 0.044 0.300
#> GSM97892 2 0.2711 0.90305 0.008 0.872 0.000 0.000 0.084 0.036
#> GSM97893 4 0.3874 0.68382 0.076 0.000 0.000 0.800 0.100 0.024
#> GSM97894 4 0.1088 0.81959 0.000 0.000 0.000 0.960 0.016 0.024
#> GSM97895 4 0.2231 0.79049 0.004 0.000 0.000 0.900 0.068 0.028
#> GSM97896 1 0.5165 0.18612 0.588 0.000 0.000 0.332 0.060 0.020
#> GSM97898 4 0.0993 0.82102 0.000 0.000 0.000 0.964 0.012 0.024
#> GSM97903 6 0.4703 0.35252 0.380 0.000 0.000 0.000 0.052 0.568
#> GSM97905 1 0.3665 0.25950 0.696 0.000 0.004 0.000 0.296 0.004
#> GSM97906 4 0.3749 0.83968 0.016 0.000 0.000 0.776 0.180 0.028
#> GSM97908 4 0.7287 -0.29500 0.288 0.000 0.000 0.372 0.108 0.232
#> GSM97912 1 0.1003 0.65984 0.964 0.000 0.000 0.000 0.020 0.016
#> GSM97914 6 0.4239 0.65121 0.248 0.000 0.000 0.000 0.056 0.696
#> GSM97915 4 0.1088 0.81959 0.000 0.000 0.000 0.960 0.016 0.024
#> GSM97917 4 0.2320 0.78195 0.004 0.000 0.000 0.892 0.080 0.024
#> GSM97918 4 0.1088 0.81959 0.000 0.000 0.000 0.960 0.016 0.024
#> GSM97919 4 0.1492 0.81066 0.000 0.000 0.000 0.940 0.036 0.024
#> GSM97922 1 0.0405 0.66365 0.988 0.000 0.000 0.008 0.004 0.000
#> GSM97924 2 0.2711 0.90305 0.008 0.872 0.000 0.000 0.084 0.036
#> GSM97926 3 0.3168 0.47221 0.000 0.000 0.828 0.000 0.116 0.056
#> GSM97930 1 0.6882 0.13670 0.428 0.000 0.000 0.128 0.108 0.336
#> GSM97931 6 0.4892 0.49642 0.008 0.000 0.288 0.000 0.072 0.632
#> GSM97935 1 0.3502 0.59251 0.780 0.000 0.000 0.008 0.020 0.192
#> GSM97936 4 0.0820 0.82592 0.000 0.000 0.000 0.972 0.016 0.012
#> GSM97938 4 0.7080 -0.09261 0.260 0.000 0.000 0.448 0.124 0.168
#> GSM97940 4 0.3749 0.83968 0.016 0.000 0.000 0.776 0.180 0.028
#> GSM97942 3 0.3996 0.02184 0.000 0.000 0.512 0.000 0.484 0.004
#> GSM97945 4 0.3749 0.83968 0.016 0.000 0.000 0.776 0.180 0.028
#> GSM97946 2 0.0146 0.92781 0.000 0.996 0.000 0.000 0.000 0.004
#> GSM97948 5 0.5606 0.12454 0.424 0.000 0.124 0.000 0.448 0.004
#> GSM97950 4 0.2805 0.84077 0.000 0.000 0.000 0.828 0.160 0.012
#> GSM97952 4 0.3749 0.83968 0.016 0.000 0.000 0.776 0.180 0.028
#> GSM97953 1 0.6826 0.18074 0.476 0.000 0.000 0.120 0.124 0.280
#> GSM97954 1 0.6893 0.25488 0.460 0.000 0.000 0.144 0.108 0.288
#> GSM97955 4 0.0993 0.82098 0.000 0.000 0.000 0.964 0.012 0.024
#> GSM97959 6 0.2915 0.70960 0.184 0.000 0.000 0.000 0.008 0.808
#> GSM97961 4 0.2378 0.84038 0.000 0.000 0.000 0.848 0.152 0.000
#> GSM97963 4 0.3749 0.83968 0.016 0.000 0.000 0.776 0.180 0.028
#> GSM97965 4 0.3749 0.83968 0.016 0.000 0.000 0.776 0.180 0.028
#> GSM97966 4 0.3749 0.83968 0.016 0.000 0.000 0.776 0.180 0.028
#> GSM97967 2 0.0146 0.92790 0.000 0.996 0.000 0.000 0.004 0.000
#> GSM97968 2 0.0405 0.92717 0.000 0.988 0.000 0.000 0.004 0.008
#> GSM97969 1 0.1078 0.66288 0.964 0.000 0.000 0.016 0.012 0.008
#> GSM97971 1 0.0665 0.66446 0.980 0.000 0.000 0.008 0.004 0.008
#> GSM97799 3 0.0260 0.51044 0.000 0.000 0.992 0.000 0.008 0.000
#> GSM97823 2 0.0000 0.92779 0.000 1.000 0.000 0.000 0.000 0.000
#> GSM97824 3 0.1564 0.49749 0.000 0.000 0.936 0.000 0.024 0.040
#> GSM97830 3 0.4467 0.03643 0.000 0.000 0.508 0.000 0.464 0.028
#> GSM97835 3 0.2164 0.46237 0.000 0.016 0.912 0.000 0.044 0.028
#> GSM97838 2 0.2833 0.90180 0.008 0.864 0.000 0.000 0.088 0.040
#> GSM97841 2 0.2711 0.90305 0.008 0.872 0.000 0.000 0.084 0.036
#> GSM97842 3 0.0520 0.50518 0.000 0.000 0.984 0.000 0.008 0.008
#> GSM97854 2 0.2711 0.90305 0.008 0.872 0.000 0.000 0.084 0.036
#> GSM97857 3 0.2794 0.45428 0.000 0.000 0.860 0.000 0.060 0.080
#> GSM97860 3 0.3867 0.01924 0.000 0.000 0.512 0.000 0.488 0.000
#> GSM97862 3 0.3122 0.46348 0.000 0.000 0.804 0.000 0.176 0.020
#> GSM97864 2 0.2711 0.90305 0.008 0.872 0.000 0.000 0.084 0.036
#> GSM97866 3 0.3374 0.44253 0.000 0.000 0.772 0.000 0.208 0.020
#> GSM97868 3 0.0972 0.51092 0.000 0.000 0.964 0.000 0.028 0.008
#> GSM97872 1 0.1265 0.65784 0.948 0.000 0.000 0.000 0.008 0.044
#> GSM97873 3 0.0520 0.50518 0.000 0.000 0.984 0.000 0.008 0.008
#> GSM97874 3 0.4473 0.00161 0.000 0.000 0.492 0.000 0.480 0.028
#> GSM97875 3 0.4062 0.13365 0.000 0.000 0.552 0.000 0.440 0.008
#> GSM97876 3 0.3996 0.02184 0.000 0.000 0.512 0.000 0.484 0.004
#> GSM97880 3 0.3867 0.01924 0.000 0.000 0.512 0.000 0.488 0.000
#> GSM97881 3 0.2302 0.49247 0.000 0.000 0.872 0.000 0.120 0.008
#> GSM97884 3 0.0405 0.50740 0.000 0.000 0.988 0.000 0.008 0.004
#> GSM97901 3 0.3432 0.43619 0.000 0.000 0.764 0.000 0.216 0.020
#> GSM97902 6 0.3409 0.70018 0.144 0.000 0.004 0.000 0.044 0.808
#> GSM97909 2 0.7393 0.23281 0.008 0.376 0.328 0.000 0.116 0.172
#> GSM97911 3 0.2302 0.49247 0.000 0.000 0.872 0.000 0.120 0.008
#> GSM97923 3 0.3867 0.01924 0.000 0.000 0.512 0.000 0.488 0.000
#> GSM97928 1 0.1320 0.66005 0.948 0.000 0.000 0.000 0.016 0.036
#> GSM97929 2 0.2711 0.90305 0.008 0.872 0.000 0.000 0.084 0.036
#> GSM97933 5 0.4097 -0.49246 0.000 0.000 0.492 0.000 0.500 0.008
#> GSM97934 3 0.4757 0.04546 0.000 0.000 0.480 0.000 0.472 0.048
#> GSM97944 3 0.0260 0.51044 0.000 0.000 0.992 0.000 0.008 0.000
#> GSM97949 2 0.0405 0.92717 0.000 0.988 0.000 0.000 0.004 0.008
#> GSM97956 3 0.0692 0.51058 0.000 0.000 0.976 0.000 0.004 0.020
#> GSM97962 3 0.4443 0.26651 0.000 0.000 0.596 0.000 0.368 0.036
#> GSM97964 3 0.0914 0.50563 0.000 0.000 0.968 0.000 0.016 0.016
#> GSM97970 3 0.0260 0.50773 0.000 0.000 0.992 0.000 0.000 0.008
#> GSM97822 1 0.1426 0.65779 0.948 0.000 0.000 0.008 0.028 0.016
#> GSM97831 3 0.4047 0.35965 0.000 0.000 0.676 0.000 0.296 0.028
#> GSM97845 1 0.6759 0.29318 0.496 0.000 0.000 0.144 0.104 0.256
#> GSM97865 6 0.4294 0.64773 0.248 0.000 0.000 0.000 0.060 0.692
#> GSM97867 3 0.3867 0.01924 0.000 0.000 0.512 0.000 0.488 0.000
#> GSM97883 3 0.3998 -0.00343 0.004 0.000 0.504 0.000 0.492 0.000
#> GSM97897 1 0.5294 0.27020 0.612 0.000 0.000 0.288 0.072 0.028
#> GSM97900 4 0.3749 0.83968 0.016 0.000 0.000 0.776 0.180 0.028
#> GSM97904 1 0.1167 0.66417 0.960 0.000 0.000 0.008 0.020 0.012
#> GSM97907 2 0.2711 0.90305 0.008 0.872 0.000 0.000 0.084 0.036
#> GSM97925 3 0.3998 0.00596 0.000 0.000 0.504 0.000 0.492 0.004
#> GSM97947 3 0.4818 0.02269 0.036 0.000 0.496 0.000 0.460 0.008
Heatmaps for the consensus matrix. It visualizes the probability of two samples to be in a same group.
consensus_heatmap(res, k = 2)
consensus_heatmap(res, k = 3)
consensus_heatmap(res, k = 4)
consensus_heatmap(res, k = 5)
consensus_heatmap(res, k = 6)
Heatmaps for the membership of samples in all partitions to see how consistent they are:
membership_heatmap(res, k = 2)
membership_heatmap(res, k = 3)
membership_heatmap(res, k = 4)
membership_heatmap(res, k = 5)
membership_heatmap(res, k = 6)
As soon as we have had the classes for columns, we can look for signatures which are significantly different between classes which can be candidate marks for certain classes. Following are the heatmaps for signatures.
Signature heatmaps where rows are scaled:
get_signatures(res, k = 2)
get_signatures(res, k = 3)
get_signatures(res, k = 4)
get_signatures(res, k = 5)
get_signatures(res, k = 6)
Signature heatmaps where rows are not scaled:
get_signatures(res, k = 2, scale_rows = FALSE)
get_signatures(res, k = 3, scale_rows = FALSE)
get_signatures(res, k = 4, scale_rows = FALSE)
get_signatures(res, k = 5, scale_rows = FALSE)
get_signatures(res, k = 6, scale_rows = FALSE)
Compare the overlap of signatures from different k:
compare_signatures(res)
get_signature() returns a data frame invisibly. TO get the list of signatures, the function
call should be assigned to a variable explicitly. In following code, if plot argument is set
to FALSE, no heatmap is plotted while only the differential analysis is performed.
# code only for demonstration
tb = get_signature(res, k = ..., plot = FALSE)
An example of the output of tb is:
#> which_row fdr mean_1 mean_2 scaled_mean_1 scaled_mean_2 km
#> 1 38 0.042760348 8.373488 9.131774 -0.5533452 0.5164555 1
#> 2 40 0.018707592 7.106213 8.469186 -0.6173731 0.5762149 1
#> 3 55 0.019134737 10.221463 11.207825 -0.6159697 0.5749050 1
#> 4 59 0.006059896 5.921854 7.869574 -0.6899429 0.6439467 1
#> 5 60 0.018055526 8.928898 10.211722 -0.6204761 0.5791110 1
#> 6 98 0.009384629 15.714769 14.887706 0.6635654 -0.6193277 2
...
The columns in tb are:
which_row: row indices corresponding to the input matrix.fdr: FDR for the differential test. mean_x: The mean value in group x.scaled_mean_x: The mean value in group x after rows are scaled.km: Row groups if k-means clustering is applied to rows.UMAP plot which shows how samples are separated.
dimension_reduction(res, k = 2, method = "UMAP")
dimension_reduction(res, k = 3, method = "UMAP")
dimension_reduction(res, k = 4, method = "UMAP")
dimension_reduction(res, k = 5, method = "UMAP")
dimension_reduction(res, k = 6, method = "UMAP")
Following heatmap shows how subgroups are split when increasing k:
collect_classes(res)
Test correlation between subgroups and known annotations. If the known annotation is numeric, one-way ANOVA test is applied, and if the known annotation is discrete, chi-squared contingency table test is applied.
test_to_known_factors(res)
#> n disease.state(p) tissue(p) k
#> SD:kmeans 175 1.73e-13 1.15e-15 2
#> SD:kmeans 177 2.01e-27 2.25e-28 3
#> SD:kmeans 175 1.62e-27 3.49e-28 4
#> SD:kmeans 141 2.39e-25 2.70e-25 5
#> SD:kmeans 118 2.42e-19 1.76e-18 6
If matrix rows can be associated to genes, consider to use functional_enrichment(res,
...) to perform function enrichment for the signature genes. See this vignette for more detailed explanations.
The object with results only for a single top-value method and a single partition method can be extracted as:
res = res_list["SD", "skmeans"]
# you can also extract it by
# res = res_list["SD:skmeans"]
A summary of res and all the functions that can be applied to it:
res
#> A 'ConsensusPartition' object with k = 2, 3, 4, 5, 6.
#> On a matrix with 51882 rows and 180 columns.
#> Top rows (1000, 2000, 3000, 4000, 5000) are extracted by 'SD' method.
#> Subgroups are detected by 'skmeans' method.
#> Performed in total 1250 partitions by row resampling.
#> Best k for subgroups seems to be 4.
#>
#> Following methods can be applied to this 'ConsensusPartition' object:
#> [1] "cola_report" "collect_classes" "collect_plots"
#> [4] "collect_stats" "colnames" "compare_signatures"
#> [7] "consensus_heatmap" "dimension_reduction" "functional_enrichment"
#> [10] "get_anno_col" "get_anno" "get_classes"
#> [13] "get_consensus" "get_matrix" "get_membership"
#> [16] "get_param" "get_signatures" "get_stats"
#> [19] "is_best_k" "is_stable_k" "membership_heatmap"
#> [22] "ncol" "nrow" "plot_ecdf"
#> [25] "rownames" "select_partition_number" "show"
#> [28] "suggest_best_k" "test_to_known_factors"
collect_plots() function collects all the plots made from res for all k (number of partitions)
into one single page to provide an easy and fast comparison between different k.
collect_plots(res)
The plots are:
k and the heatmap of
predicted classes for each k.k.k.k.All the plots in panels can be made by individual functions and they are plotted later in this section.
select_partition_number() produces several plots showing different
statistics for choosing “optimized” k. There are following statistics:
k;k, the area increased is defined as \(A_k - A_{k-1}\).The detailed explanations of these statistics can be found in the cola vignette.
Generally speaking, lower PAC score, higher mean silhouette score or higher
concordance corresponds to better partition. Rand index and Jaccard index
measure how similar the current partition is compared to partition with k-1.
If they are too similar, we won't accept k is better than k-1.
select_partition_number(res)
The numeric values for all these statistics can be obtained by get_stats().
get_stats(res)
#> k 1-PAC mean_silhouette concordance area_increased Rand Jaccard
#> 2 2 0.999 0.974 0.988 0.5003 0.501 0.501
#> 3 3 1.000 0.971 0.989 0.2899 0.800 0.621
#> 4 4 1.000 0.976 0.990 0.1262 0.908 0.745
#> 5 5 0.869 0.771 0.883 0.0594 0.972 0.901
#> 6 6 0.800 0.642 0.791 0.0345 0.944 0.790
suggest_best_k() suggests the best \(k\) based on these statistics. The rules are as follows:
suggest_best_k(res)
#> [1] 4
#> attr(,"optional")
#> [1] 2 3
There is also optional best \(k\) = 2 3 that is worth to check.
Following shows the table of the partitions (You need to click the show/hide
code output link to see it). The membership matrix (columns with name p*)
is inferred by
clue::cl_consensus()
function with the SE method. Basically the value in the membership matrix
represents the probability to belong to a certain group. The finall class
label for an item is determined with the group with highest probability it
belongs to.
In get_classes() function, the entropy is calculated from the membership
matrix and the silhouette score is calculated from the consensus matrix.
cbind(get_classes(res, k = 2), get_membership(res, k = 2))
#> class entropy silhouette p1 p2
#> GSM97800 2 0.0000 0.995 0.000 1.000
#> GSM97803 2 0.0000 0.995 0.000 1.000
#> GSM97804 2 0.0000 0.995 0.000 1.000
#> GSM97805 2 0.0000 0.995 0.000 1.000
#> GSM97807 2 0.0000 0.995 0.000 1.000
#> GSM97809 2 0.0000 0.995 0.000 1.000
#> GSM97811 2 0.0000 0.995 0.000 1.000
#> GSM97812 2 0.0000 0.995 0.000 1.000
#> GSM97816 2 0.0000 0.995 0.000 1.000
#> GSM97817 2 0.0000 0.995 0.000 1.000
#> GSM97820 2 0.0000 0.995 0.000 1.000
#> GSM97825 2 0.0000 0.995 0.000 1.000
#> GSM97827 2 0.0000 0.995 0.000 1.000
#> GSM97828 2 0.0000 0.995 0.000 1.000
#> GSM97833 2 0.0000 0.995 0.000 1.000
#> GSM97834 2 0.0000 0.995 0.000 1.000
#> GSM97840 2 0.0000 0.995 0.000 1.000
#> GSM97846 2 0.0000 0.995 0.000 1.000
#> GSM97848 2 0.0000 0.995 0.000 1.000
#> GSM97849 2 0.0000 0.995 0.000 1.000
#> GSM97850 2 0.0000 0.995 0.000 1.000
#> GSM97853 2 0.0000 0.995 0.000 1.000
#> GSM97855 2 0.0000 0.995 0.000 1.000
#> GSM97878 1 0.0000 0.982 1.000 0.000
#> GSM97913 2 0.0000 0.995 0.000 1.000
#> GSM97932 1 0.0000 0.982 1.000 0.000
#> GSM97939 2 0.0000 0.995 0.000 1.000
#> GSM97951 2 0.0000 0.995 0.000 1.000
#> GSM97957 2 0.0000 0.995 0.000 1.000
#> GSM97972 2 0.0000 0.995 0.000 1.000
#> GSM97793 1 0.3733 0.918 0.928 0.072
#> GSM97795 2 0.0000 0.995 0.000 1.000
#> GSM97802 1 0.0000 0.982 1.000 0.000
#> GSM97810 2 0.0000 0.995 0.000 1.000
#> GSM97815 2 0.0000 0.995 0.000 1.000
#> GSM97837 1 0.0000 0.982 1.000 0.000
#> GSM97843 2 0.0000 0.995 0.000 1.000
#> GSM97890 2 0.0000 0.995 0.000 1.000
#> GSM97899 1 0.0000 0.982 1.000 0.000
#> GSM97910 1 0.0000 0.982 1.000 0.000
#> GSM97916 1 0.0000 0.982 1.000 0.000
#> GSM97920 2 0.0000 0.995 0.000 1.000
#> GSM97921 1 0.0000 0.982 1.000 0.000
#> GSM97927 1 0.0000 0.982 1.000 0.000
#> GSM97937 1 0.0000 0.982 1.000 0.000
#> GSM97941 2 0.0000 0.995 0.000 1.000
#> GSM97943 2 0.0000 0.995 0.000 1.000
#> GSM97958 2 0.0000 0.995 0.000 1.000
#> GSM97960 2 0.0000 0.995 0.000 1.000
#> GSM97794 1 0.3431 0.925 0.936 0.064
#> GSM97796 1 0.0000 0.982 1.000 0.000
#> GSM97797 1 0.7299 0.751 0.796 0.204
#> GSM97798 1 0.0000 0.982 1.000 0.000
#> GSM97801 1 0.0000 0.982 1.000 0.000
#> GSM97806 1 0.0000 0.982 1.000 0.000
#> GSM97808 1 0.0000 0.982 1.000 0.000
#> GSM97813 1 0.0000 0.982 1.000 0.000
#> GSM97814 1 0.0000 0.982 1.000 0.000
#> GSM97818 1 0.0000 0.982 1.000 0.000
#> GSM97819 1 0.3274 0.929 0.940 0.060
#> GSM97821 2 0.0000 0.995 0.000 1.000
#> GSM97826 1 0.0000 0.982 1.000 0.000
#> GSM97829 1 0.0000 0.982 1.000 0.000
#> GSM97832 2 0.0000 0.995 0.000 1.000
#> GSM97836 1 0.0000 0.982 1.000 0.000
#> GSM97839 1 0.0000 0.982 1.000 0.000
#> GSM97844 2 0.0000 0.995 0.000 1.000
#> GSM97847 1 0.0000 0.982 1.000 0.000
#> GSM97851 1 0.0000 0.982 1.000 0.000
#> GSM97852 1 0.0000 0.982 1.000 0.000
#> GSM97856 1 0.0000 0.982 1.000 0.000
#> GSM97858 2 0.0000 0.995 0.000 1.000
#> GSM97859 1 0.0000 0.982 1.000 0.000
#> GSM97861 1 0.0000 0.982 1.000 0.000
#> GSM97863 1 0.0000 0.982 1.000 0.000
#> GSM97869 1 0.0000 0.982 1.000 0.000
#> GSM97870 1 0.0000 0.982 1.000 0.000
#> GSM97871 1 0.0000 0.982 1.000 0.000
#> GSM97877 2 0.0000 0.995 0.000 1.000
#> GSM97879 1 0.0000 0.982 1.000 0.000
#> GSM97882 1 0.0000 0.982 1.000 0.000
#> GSM97885 1 0.0000 0.982 1.000 0.000
#> GSM97886 1 0.0000 0.982 1.000 0.000
#> GSM97887 1 0.0000 0.982 1.000 0.000
#> GSM97888 1 0.0000 0.982 1.000 0.000
#> GSM97889 1 0.0000 0.982 1.000 0.000
#> GSM97891 1 0.0000 0.982 1.000 0.000
#> GSM97892 2 0.0000 0.995 0.000 1.000
#> GSM97893 1 0.0000 0.982 1.000 0.000
#> GSM97894 1 0.0000 0.982 1.000 0.000
#> GSM97895 1 0.0000 0.982 1.000 0.000
#> GSM97896 1 0.0000 0.982 1.000 0.000
#> GSM97898 1 0.0000 0.982 1.000 0.000
#> GSM97903 1 0.0000 0.982 1.000 0.000
#> GSM97905 1 0.0000 0.982 1.000 0.000
#> GSM97906 1 0.0000 0.982 1.000 0.000
#> GSM97908 1 0.0000 0.982 1.000 0.000
#> GSM97912 1 0.0000 0.982 1.000 0.000
#> GSM97914 1 0.0000 0.982 1.000 0.000
#> GSM97915 1 0.0000 0.982 1.000 0.000
#> GSM97917 1 0.0000 0.982 1.000 0.000
#> GSM97918 1 0.0000 0.982 1.000 0.000
#> GSM97919 1 0.0000 0.982 1.000 0.000
#> GSM97922 1 0.0000 0.982 1.000 0.000
#> GSM97924 2 0.0000 0.995 0.000 1.000
#> GSM97926 1 0.9323 0.490 0.652 0.348
#> GSM97930 1 0.0000 0.982 1.000 0.000
#> GSM97931 2 0.0000 0.995 0.000 1.000
#> GSM97935 1 0.0000 0.982 1.000 0.000
#> GSM97936 1 0.0000 0.982 1.000 0.000
#> GSM97938 1 0.0000 0.982 1.000 0.000
#> GSM97940 1 0.0000 0.982 1.000 0.000
#> GSM97942 1 0.0000 0.982 1.000 0.000
#> GSM97945 1 0.0000 0.982 1.000 0.000
#> GSM97946 2 0.0000 0.995 0.000 1.000
#> GSM97948 1 0.0000 0.982 1.000 0.000
#> GSM97950 1 0.0000 0.982 1.000 0.000
#> GSM97952 1 0.0000 0.982 1.000 0.000
#> GSM97953 1 0.0000 0.982 1.000 0.000
#> GSM97954 1 0.0000 0.982 1.000 0.000
#> GSM97955 1 0.0000 0.982 1.000 0.000
#> GSM97959 2 0.4690 0.887 0.100 0.900
#> GSM97961 1 0.0000 0.982 1.000 0.000
#> GSM97963 1 0.0000 0.982 1.000 0.000
#> GSM97965 1 0.0000 0.982 1.000 0.000
#> GSM97966 1 0.0000 0.982 1.000 0.000
#> GSM97967 2 0.0000 0.995 0.000 1.000
#> GSM97968 2 0.0000 0.995 0.000 1.000
#> GSM97969 1 0.0000 0.982 1.000 0.000
#> GSM97971 1 0.0000 0.982 1.000 0.000
#> GSM97799 2 0.0000 0.995 0.000 1.000
#> GSM97823 2 0.0000 0.995 0.000 1.000
#> GSM97824 2 0.0000 0.995 0.000 1.000
#> GSM97830 2 0.0938 0.984 0.012 0.988
#> GSM97835 2 0.0000 0.995 0.000 1.000
#> GSM97838 2 0.0000 0.995 0.000 1.000
#> GSM97841 2 0.0000 0.995 0.000 1.000
#> GSM97842 2 0.0000 0.995 0.000 1.000
#> GSM97854 2 0.0000 0.995 0.000 1.000
#> GSM97857 2 0.0000 0.995 0.000 1.000
#> GSM97860 1 0.6712 0.796 0.824 0.176
#> GSM97862 2 0.0000 0.995 0.000 1.000
#> GSM97864 2 0.0000 0.995 0.000 1.000
#> GSM97866 2 0.0000 0.995 0.000 1.000
#> GSM97868 2 0.0000 0.995 0.000 1.000
#> GSM97872 1 0.0000 0.982 1.000 0.000
#> GSM97873 2 0.0000 0.995 0.000 1.000
#> GSM97874 1 0.6801 0.791 0.820 0.180
#> GSM97875 2 0.0376 0.991 0.004 0.996
#> GSM97876 2 0.7139 0.752 0.196 0.804
#> GSM97880 1 0.0000 0.982 1.000 0.000
#> GSM97881 2 0.0000 0.995 0.000 1.000
#> GSM97884 2 0.0000 0.995 0.000 1.000
#> GSM97901 2 0.0000 0.995 0.000 1.000
#> GSM97902 1 0.9427 0.446 0.640 0.360
#> GSM97909 2 0.0000 0.995 0.000 1.000
#> GSM97911 2 0.0000 0.995 0.000 1.000
#> GSM97923 1 0.4161 0.906 0.916 0.084
#> GSM97928 1 0.0000 0.982 1.000 0.000
#> GSM97929 2 0.0000 0.995 0.000 1.000
#> GSM97933 1 0.4431 0.898 0.908 0.092
#> GSM97934 2 0.4022 0.911 0.080 0.920
#> GSM97944 2 0.0000 0.995 0.000 1.000
#> GSM97949 2 0.0000 0.995 0.000 1.000
#> GSM97956 2 0.0000 0.995 0.000 1.000
#> GSM97962 2 0.0000 0.995 0.000 1.000
#> GSM97964 2 0.0000 0.995 0.000 1.000
#> GSM97970 2 0.0000 0.995 0.000 1.000
#> GSM97822 1 0.0000 0.982 1.000 0.000
#> GSM97831 2 0.0000 0.995 0.000 1.000
#> GSM97845 1 0.0000 0.982 1.000 0.000
#> GSM97865 1 0.0000 0.982 1.000 0.000
#> GSM97867 1 0.0000 0.982 1.000 0.000
#> GSM97883 1 0.0000 0.982 1.000 0.000
#> GSM97897 1 0.0000 0.982 1.000 0.000
#> GSM97900 1 0.0000 0.982 1.000 0.000
#> GSM97904 1 0.0000 0.982 1.000 0.000
#> GSM97907 2 0.0000 0.995 0.000 1.000
#> GSM97925 1 0.4161 0.906 0.916 0.084
#> GSM97947 1 0.0000 0.982 1.000 0.000
cbind(get_classes(res, k = 3), get_membership(res, k = 3))
#> class entropy silhouette p1 p2 p3
#> GSM97800 2 0.000 0.972 0.000 1.000 0.000
#> GSM97803 2 0.000 0.972 0.000 1.000 0.000
#> GSM97804 2 0.000 0.972 0.000 1.000 0.000
#> GSM97805 2 0.000 0.972 0.000 1.000 0.000
#> GSM97807 2 0.000 0.972 0.000 1.000 0.000
#> GSM97809 2 0.000 0.972 0.000 1.000 0.000
#> GSM97811 2 0.000 0.972 0.000 1.000 0.000
#> GSM97812 2 0.000 0.972 0.000 1.000 0.000
#> GSM97816 2 0.000 0.972 0.000 1.000 0.000
#> GSM97817 2 0.000 0.972 0.000 1.000 0.000
#> GSM97820 2 0.000 0.972 0.000 1.000 0.000
#> GSM97825 2 0.000 0.972 0.000 1.000 0.000
#> GSM97827 2 0.000 0.972 0.000 1.000 0.000
#> GSM97828 2 0.460 0.741 0.000 0.796 0.204
#> GSM97833 2 0.000 0.972 0.000 1.000 0.000
#> GSM97834 2 0.000 0.972 0.000 1.000 0.000
#> GSM97840 2 0.000 0.972 0.000 1.000 0.000
#> GSM97846 2 0.000 0.972 0.000 1.000 0.000
#> GSM97848 2 0.000 0.972 0.000 1.000 0.000
#> GSM97849 2 0.000 0.972 0.000 1.000 0.000
#> GSM97850 2 0.000 0.972 0.000 1.000 0.000
#> GSM97853 2 0.000 0.972 0.000 1.000 0.000
#> GSM97855 2 0.000 0.972 0.000 1.000 0.000
#> GSM97878 1 0.000 0.992 1.000 0.000 0.000
#> GSM97913 2 0.000 0.972 0.000 1.000 0.000
#> GSM97932 1 0.000 0.992 1.000 0.000 0.000
#> GSM97939 2 0.611 0.359 0.000 0.604 0.396
#> GSM97951 2 0.000 0.972 0.000 1.000 0.000
#> GSM97957 3 0.000 1.000 0.000 0.000 1.000
#> GSM97972 2 0.000 0.972 0.000 1.000 0.000
#> GSM97793 3 0.000 1.000 0.000 0.000 1.000
#> GSM97795 2 0.000 0.972 0.000 1.000 0.000
#> GSM97802 3 0.000 1.000 0.000 0.000 1.000
#> GSM97810 2 0.000 0.972 0.000 1.000 0.000
#> GSM97815 2 0.164 0.932 0.000 0.956 0.044
#> GSM97837 1 0.000 0.992 1.000 0.000 0.000
#> GSM97843 3 0.000 1.000 0.000 0.000 1.000
#> GSM97890 3 0.000 1.000 0.000 0.000 1.000
#> GSM97899 1 0.000 0.992 1.000 0.000 0.000
#> GSM97910 1 0.000 0.992 1.000 0.000 0.000
#> GSM97916 1 0.000 0.992 1.000 0.000 0.000
#> GSM97920 3 0.000 1.000 0.000 0.000 1.000
#> GSM97921 1 0.000 0.992 1.000 0.000 0.000
#> GSM97927 1 0.000 0.992 1.000 0.000 0.000
#> GSM97937 1 0.000 0.992 1.000 0.000 0.000
#> GSM97941 2 0.000 0.972 0.000 1.000 0.000
#> GSM97943 2 0.489 0.706 0.000 0.772 0.228
#> GSM97958 2 0.000 0.972 0.000 1.000 0.000
#> GSM97960 2 0.000 0.972 0.000 1.000 0.000
#> GSM97794 1 0.412 0.793 0.832 0.168 0.000
#> GSM97796 1 0.000 0.992 1.000 0.000 0.000
#> GSM97797 1 0.619 0.269 0.580 0.420 0.000
#> GSM97798 1 0.000 0.992 1.000 0.000 0.000
#> GSM97801 1 0.000 0.992 1.000 0.000 0.000
#> GSM97806 1 0.000 0.992 1.000 0.000 0.000
#> GSM97808 1 0.000 0.992 1.000 0.000 0.000
#> GSM97813 1 0.000 0.992 1.000 0.000 0.000
#> GSM97814 1 0.000 0.992 1.000 0.000 0.000
#> GSM97818 1 0.000 0.992 1.000 0.000 0.000
#> GSM97819 3 0.000 1.000 0.000 0.000 1.000
#> GSM97821 2 0.000 0.972 0.000 1.000 0.000
#> GSM97826 1 0.000 0.992 1.000 0.000 0.000
#> GSM97829 1 0.000 0.992 1.000 0.000 0.000
#> GSM97832 2 0.000 0.972 0.000 1.000 0.000
#> GSM97836 1 0.000 0.992 1.000 0.000 0.000
#> GSM97839 1 0.000 0.992 1.000 0.000 0.000
#> GSM97844 2 0.000 0.972 0.000 1.000 0.000
#> GSM97847 1 0.000 0.992 1.000 0.000 0.000
#> GSM97851 1 0.000 0.992 1.000 0.000 0.000
#> GSM97852 1 0.000 0.992 1.000 0.000 0.000
#> GSM97856 1 0.000 0.992 1.000 0.000 0.000
#> GSM97858 2 0.000 0.972 0.000 1.000 0.000
#> GSM97859 1 0.000 0.992 1.000 0.000 0.000
#> GSM97861 1 0.000 0.992 1.000 0.000 0.000
#> GSM97863 1 0.000 0.992 1.000 0.000 0.000
#> GSM97869 1 0.000 0.992 1.000 0.000 0.000
#> GSM97870 1 0.000 0.992 1.000 0.000 0.000
#> GSM97871 1 0.000 0.992 1.000 0.000 0.000
#> GSM97877 2 0.000 0.972 0.000 1.000 0.000
#> GSM97879 1 0.000 0.992 1.000 0.000 0.000
#> GSM97882 1 0.000 0.992 1.000 0.000 0.000
#> GSM97885 1 0.000 0.992 1.000 0.000 0.000
#> GSM97886 1 0.000 0.992 1.000 0.000 0.000
#> GSM97887 1 0.000 0.992 1.000 0.000 0.000
#> GSM97888 1 0.000 0.992 1.000 0.000 0.000
#> GSM97889 1 0.000 0.992 1.000 0.000 0.000
#> GSM97891 1 0.000 0.992 1.000 0.000 0.000
#> GSM97892 2 0.000 0.972 0.000 1.000 0.000
#> GSM97893 1 0.000 0.992 1.000 0.000 0.000
#> GSM97894 1 0.000 0.992 1.000 0.000 0.000
#> GSM97895 1 0.000 0.992 1.000 0.000 0.000
#> GSM97896 1 0.000 0.992 1.000 0.000 0.000
#> GSM97898 1 0.000 0.992 1.000 0.000 0.000
#> GSM97903 1 0.000 0.992 1.000 0.000 0.000
#> GSM97905 1 0.000 0.992 1.000 0.000 0.000
#> GSM97906 1 0.000 0.992 1.000 0.000 0.000
#> GSM97908 1 0.000 0.992 1.000 0.000 0.000
#> GSM97912 1 0.000 0.992 1.000 0.000 0.000
#> GSM97914 1 0.000 0.992 1.000 0.000 0.000
#> GSM97915 1 0.000 0.992 1.000 0.000 0.000
#> GSM97917 1 0.000 0.992 1.000 0.000 0.000
#> GSM97918 1 0.000 0.992 1.000 0.000 0.000
#> GSM97919 1 0.000 0.992 1.000 0.000 0.000
#> GSM97922 1 0.000 0.992 1.000 0.000 0.000
#> GSM97924 2 0.000 0.972 0.000 1.000 0.000
#> GSM97926 3 0.000 1.000 0.000 0.000 1.000
#> GSM97930 1 0.000 0.992 1.000 0.000 0.000
#> GSM97931 2 0.000 0.972 0.000 1.000 0.000
#> GSM97935 1 0.000 0.992 1.000 0.000 0.000
#> GSM97936 1 0.000 0.992 1.000 0.000 0.000
#> GSM97938 1 0.000 0.992 1.000 0.000 0.000
#> GSM97940 1 0.000 0.992 1.000 0.000 0.000
#> GSM97942 3 0.000 1.000 0.000 0.000 1.000
#> GSM97945 1 0.000 0.992 1.000 0.000 0.000
#> GSM97946 2 0.000 0.972 0.000 1.000 0.000
#> GSM97948 3 0.000 1.000 0.000 0.000 1.000
#> GSM97950 1 0.000 0.992 1.000 0.000 0.000
#> GSM97952 1 0.000 0.992 1.000 0.000 0.000
#> GSM97953 1 0.000 0.992 1.000 0.000 0.000
#> GSM97954 1 0.000 0.992 1.000 0.000 0.000
#> GSM97955 1 0.000 0.992 1.000 0.000 0.000
#> GSM97959 2 0.000 0.972 0.000 1.000 0.000
#> GSM97961 1 0.000 0.992 1.000 0.000 0.000
#> GSM97963 1 0.000 0.992 1.000 0.000 0.000
#> GSM97965 1 0.000 0.992 1.000 0.000 0.000
#> GSM97966 1 0.000 0.992 1.000 0.000 0.000
#> GSM97967 2 0.000 0.972 0.000 1.000 0.000
#> GSM97968 2 0.000 0.972 0.000 1.000 0.000
#> GSM97969 1 0.000 0.992 1.000 0.000 0.000
#> GSM97971 1 0.000 0.992 1.000 0.000 0.000
#> GSM97799 3 0.000 1.000 0.000 0.000 1.000
#> GSM97823 2 0.000 0.972 0.000 1.000 0.000
#> GSM97824 3 0.000 1.000 0.000 0.000 1.000
#> GSM97830 3 0.000 1.000 0.000 0.000 1.000
#> GSM97835 2 0.406 0.798 0.000 0.836 0.164
#> GSM97838 2 0.000 0.972 0.000 1.000 0.000
#> GSM97841 2 0.000 0.972 0.000 1.000 0.000
#> GSM97842 3 0.000 1.000 0.000 0.000 1.000
#> GSM97854 2 0.000 0.972 0.000 1.000 0.000
#> GSM97857 3 0.000 1.000 0.000 0.000 1.000
#> GSM97860 3 0.000 1.000 0.000 0.000 1.000
#> GSM97862 3 0.000 1.000 0.000 0.000 1.000
#> GSM97864 2 0.000 0.972 0.000 1.000 0.000
#> GSM97866 3 0.000 1.000 0.000 0.000 1.000
#> GSM97868 3 0.000 1.000 0.000 0.000 1.000
#> GSM97872 1 0.000 0.992 1.000 0.000 0.000
#> GSM97873 3 0.000 1.000 0.000 0.000 1.000
#> GSM97874 3 0.000 1.000 0.000 0.000 1.000
#> GSM97875 3 0.000 1.000 0.000 0.000 1.000
#> GSM97876 3 0.000 1.000 0.000 0.000 1.000
#> GSM97880 3 0.000 1.000 0.000 0.000 1.000
#> GSM97881 3 0.000 1.000 0.000 0.000 1.000
#> GSM97884 3 0.000 1.000 0.000 0.000 1.000
#> GSM97901 3 0.000 1.000 0.000 0.000 1.000
#> GSM97902 2 0.624 0.217 0.440 0.560 0.000
#> GSM97909 2 0.000 0.972 0.000 1.000 0.000
#> GSM97911 3 0.000 1.000 0.000 0.000 1.000
#> GSM97923 3 0.000 1.000 0.000 0.000 1.000
#> GSM97928 1 0.000 0.992 1.000 0.000 0.000
#> GSM97929 2 0.000 0.972 0.000 1.000 0.000
#> GSM97933 3 0.000 1.000 0.000 0.000 1.000
#> GSM97934 3 0.000 1.000 0.000 0.000 1.000
#> GSM97944 3 0.000 1.000 0.000 0.000 1.000
#> GSM97949 2 0.000 0.972 0.000 1.000 0.000
#> GSM97956 3 0.000 1.000 0.000 0.000 1.000
#> GSM97962 3 0.000 1.000 0.000 0.000 1.000
#> GSM97964 3 0.000 1.000 0.000 0.000 1.000
#> GSM97970 3 0.000 1.000 0.000 0.000 1.000
#> GSM97822 1 0.000 0.992 1.000 0.000 0.000
#> GSM97831 3 0.000 1.000 0.000 0.000 1.000
#> GSM97845 1 0.000 0.992 1.000 0.000 0.000
#> GSM97865 1 0.000 0.992 1.000 0.000 0.000
#> GSM97867 3 0.000 1.000 0.000 0.000 1.000
#> GSM97883 3 0.000 1.000 0.000 0.000 1.000
#> GSM97897 1 0.000 0.992 1.000 0.000 0.000
#> GSM97900 1 0.000 0.992 1.000 0.000 0.000
#> GSM97904 1 0.000 0.992 1.000 0.000 0.000
#> GSM97907 2 0.000 0.972 0.000 1.000 0.000
#> GSM97925 3 0.000 1.000 0.000 0.000 1.000
#> GSM97947 3 0.000 1.000 0.000 0.000 1.000
cbind(get_classes(res, k = 4), get_membership(res, k = 4))
#> class entropy silhouette p1 p2 p3 p4
#> GSM97800 2 0.0000 0.985 0.000 1.000 0.000 0.000
#> GSM97803 2 0.0000 0.985 0.000 1.000 0.000 0.000
#> GSM97804 2 0.0000 0.985 0.000 1.000 0.000 0.000
#> GSM97805 2 0.0000 0.985 0.000 1.000 0.000 0.000
#> GSM97807 2 0.0000 0.985 0.000 1.000 0.000 0.000
#> GSM97809 2 0.0000 0.985 0.000 1.000 0.000 0.000
#> GSM97811 2 0.0000 0.985 0.000 1.000 0.000 0.000
#> GSM97812 2 0.0000 0.985 0.000 1.000 0.000 0.000
#> GSM97816 2 0.0188 0.982 0.004 0.996 0.000 0.000
#> GSM97817 2 0.0000 0.985 0.000 1.000 0.000 0.000
#> GSM97820 2 0.0000 0.985 0.000 1.000 0.000 0.000
#> GSM97825 2 0.0000 0.985 0.000 1.000 0.000 0.000
#> GSM97827 2 0.0000 0.985 0.000 1.000 0.000 0.000
#> GSM97828 1 0.0000 0.965 1.000 0.000 0.000 0.000
#> GSM97833 2 0.0000 0.985 0.000 1.000 0.000 0.000
#> GSM97834 2 0.0000 0.985 0.000 1.000 0.000 0.000
#> GSM97840 2 0.0000 0.985 0.000 1.000 0.000 0.000
#> GSM97846 2 0.0000 0.985 0.000 1.000 0.000 0.000
#> GSM97848 2 0.0000 0.985 0.000 1.000 0.000 0.000
#> GSM97849 2 0.0000 0.985 0.000 1.000 0.000 0.000
#> GSM97850 2 0.0000 0.985 0.000 1.000 0.000 0.000
#> GSM97853 2 0.0000 0.985 0.000 1.000 0.000 0.000
#> GSM97855 2 0.0000 0.985 0.000 1.000 0.000 0.000
#> GSM97878 1 0.2868 0.843 0.864 0.000 0.000 0.136
#> GSM97913 2 0.4948 0.219 0.440 0.560 0.000 0.000
#> GSM97932 4 0.0000 0.995 0.000 0.000 0.000 1.000
#> GSM97939 2 0.3801 0.716 0.000 0.780 0.220 0.000
#> GSM97951 2 0.0000 0.985 0.000 1.000 0.000 0.000
#> GSM97957 3 0.0000 0.996 0.000 0.000 1.000 0.000
#> GSM97972 2 0.0188 0.982 0.004 0.996 0.000 0.000
#> GSM97793 3 0.0000 0.996 0.000 0.000 1.000 0.000
#> GSM97795 2 0.0000 0.985 0.000 1.000 0.000 0.000
#> GSM97802 3 0.2589 0.840 0.000 0.000 0.884 0.116
#> GSM97810 2 0.0000 0.985 0.000 1.000 0.000 0.000
#> GSM97815 2 0.0469 0.973 0.000 0.988 0.012 0.000
#> GSM97837 1 0.0000 0.965 1.000 0.000 0.000 0.000
#> GSM97843 3 0.0000 0.996 0.000 0.000 1.000 0.000
#> GSM97890 3 0.0000 0.996 0.000 0.000 1.000 0.000
#> GSM97899 4 0.0000 0.995 0.000 0.000 0.000 1.000
#> GSM97910 1 0.0000 0.965 1.000 0.000 0.000 0.000
#> GSM97916 1 0.0000 0.965 1.000 0.000 0.000 0.000
#> GSM97920 3 0.0000 0.996 0.000 0.000 1.000 0.000
#> GSM97921 1 0.0000 0.965 1.000 0.000 0.000 0.000
#> GSM97927 4 0.0000 0.995 0.000 0.000 0.000 1.000
#> GSM97937 1 0.2589 0.865 0.884 0.000 0.000 0.116
#> GSM97941 2 0.0000 0.985 0.000 1.000 0.000 0.000
#> GSM97943 1 0.0000 0.965 1.000 0.000 0.000 0.000
#> GSM97958 2 0.0188 0.982 0.004 0.996 0.000 0.000
#> GSM97960 2 0.0000 0.985 0.000 1.000 0.000 0.000
#> GSM97794 1 0.0000 0.965 1.000 0.000 0.000 0.000
#> GSM97796 4 0.0000 0.995 0.000 0.000 0.000 1.000
#> GSM97797 1 0.0000 0.965 1.000 0.000 0.000 0.000
#> GSM97798 4 0.0000 0.995 0.000 0.000 0.000 1.000
#> GSM97801 1 0.0000 0.965 1.000 0.000 0.000 0.000
#> GSM97806 4 0.0000 0.995 0.000 0.000 0.000 1.000
#> GSM97808 4 0.0000 0.995 0.000 0.000 0.000 1.000
#> GSM97813 4 0.0000 0.995 0.000 0.000 0.000 1.000
#> GSM97814 4 0.0000 0.995 0.000 0.000 0.000 1.000
#> GSM97818 1 0.0000 0.965 1.000 0.000 0.000 0.000
#> GSM97819 3 0.0000 0.996 0.000 0.000 1.000 0.000
#> GSM97821 2 0.0000 0.985 0.000 1.000 0.000 0.000
#> GSM97826 1 0.0188 0.963 0.996 0.000 0.000 0.004
#> GSM97829 1 0.0000 0.965 1.000 0.000 0.000 0.000
#> GSM97832 2 0.0000 0.985 0.000 1.000 0.000 0.000
#> GSM97836 4 0.0000 0.995 0.000 0.000 0.000 1.000
#> GSM97839 4 0.0000 0.995 0.000 0.000 0.000 1.000
#> GSM97844 2 0.0000 0.985 0.000 1.000 0.000 0.000
#> GSM97847 1 0.0707 0.953 0.980 0.000 0.000 0.020
#> GSM97851 4 0.0000 0.995 0.000 0.000 0.000 1.000
#> GSM97852 4 0.0000 0.995 0.000 0.000 0.000 1.000
#> GSM97856 4 0.0000 0.995 0.000 0.000 0.000 1.000
#> GSM97858 2 0.0000 0.985 0.000 1.000 0.000 0.000
#> GSM97859 4 0.0000 0.995 0.000 0.000 0.000 1.000
#> GSM97861 4 0.0000 0.995 0.000 0.000 0.000 1.000
#> GSM97863 4 0.0000 0.995 0.000 0.000 0.000 1.000
#> GSM97869 1 0.1211 0.937 0.960 0.000 0.000 0.040
#> GSM97870 4 0.0657 0.982 0.012 0.000 0.004 0.984
#> GSM97871 4 0.0000 0.995 0.000 0.000 0.000 1.000
#> GSM97877 2 0.0000 0.985 0.000 1.000 0.000 0.000
#> GSM97879 4 0.0000 0.995 0.000 0.000 0.000 1.000
#> GSM97882 4 0.0000 0.995 0.000 0.000 0.000 1.000
#> GSM97885 1 0.4585 0.524 0.668 0.000 0.000 0.332
#> GSM97886 4 0.0000 0.995 0.000 0.000 0.000 1.000
#> GSM97887 4 0.0000 0.995 0.000 0.000 0.000 1.000
#> GSM97888 4 0.0000 0.995 0.000 0.000 0.000 1.000
#> GSM97889 4 0.0000 0.995 0.000 0.000 0.000 1.000
#> GSM97891 4 0.0000 0.995 0.000 0.000 0.000 1.000
#> GSM97892 2 0.0000 0.985 0.000 1.000 0.000 0.000
#> GSM97893 4 0.0000 0.995 0.000 0.000 0.000 1.000
#> GSM97894 4 0.0000 0.995 0.000 0.000 0.000 1.000
#> GSM97895 4 0.0000 0.995 0.000 0.000 0.000 1.000
#> GSM97896 4 0.0000 0.995 0.000 0.000 0.000 1.000
#> GSM97898 4 0.0000 0.995 0.000 0.000 0.000 1.000
#> GSM97903 1 0.0188 0.963 0.996 0.000 0.000 0.004
#> GSM97905 4 0.0000 0.995 0.000 0.000 0.000 1.000
#> GSM97906 4 0.0000 0.995 0.000 0.000 0.000 1.000
#> GSM97908 4 0.1557 0.941 0.056 0.000 0.000 0.944
#> GSM97912 4 0.0336 0.988 0.008 0.000 0.000 0.992
#> GSM97914 1 0.0000 0.965 1.000 0.000 0.000 0.000
#> GSM97915 4 0.0000 0.995 0.000 0.000 0.000 1.000
#> GSM97917 4 0.0000 0.995 0.000 0.000 0.000 1.000
#> GSM97918 4 0.0000 0.995 0.000 0.000 0.000 1.000
#> GSM97919 4 0.0000 0.995 0.000 0.000 0.000 1.000
#> GSM97922 4 0.0000 0.995 0.000 0.000 0.000 1.000
#> GSM97924 2 0.0000 0.985 0.000 1.000 0.000 0.000
#> GSM97926 3 0.0000 0.996 0.000 0.000 1.000 0.000
#> GSM97930 1 0.0469 0.959 0.988 0.000 0.000 0.012
#> GSM97931 2 0.0000 0.985 0.000 1.000 0.000 0.000
#> GSM97935 4 0.0000 0.995 0.000 0.000 0.000 1.000
#> GSM97936 4 0.0000 0.995 0.000 0.000 0.000 1.000
#> GSM97938 4 0.0921 0.970 0.028 0.000 0.000 0.972
#> GSM97940 4 0.0000 0.995 0.000 0.000 0.000 1.000
#> GSM97942 3 0.0000 0.996 0.000 0.000 1.000 0.000
#> GSM97945 4 0.0000 0.995 0.000 0.000 0.000 1.000
#> GSM97946 2 0.0000 0.985 0.000 1.000 0.000 0.000
#> GSM97948 3 0.0000 0.996 0.000 0.000 1.000 0.000
#> GSM97950 4 0.0000 0.995 0.000 0.000 0.000 1.000
#> GSM97952 4 0.0000 0.995 0.000 0.000 0.000 1.000
#> GSM97953 4 0.2589 0.870 0.116 0.000 0.000 0.884
#> GSM97954 4 0.0921 0.970 0.028 0.000 0.000 0.972
#> GSM97955 4 0.0000 0.995 0.000 0.000 0.000 1.000
#> GSM97959 1 0.0188 0.962 0.996 0.004 0.000 0.000
#> GSM97961 4 0.0000 0.995 0.000 0.000 0.000 1.000
#> GSM97963 4 0.0000 0.995 0.000 0.000 0.000 1.000
#> GSM97965 4 0.0000 0.995 0.000 0.000 0.000 1.000
#> GSM97966 4 0.0000 0.995 0.000 0.000 0.000 1.000
#> GSM97967 2 0.0000 0.985 0.000 1.000 0.000 0.000
#> GSM97968 2 0.0000 0.985 0.000 1.000 0.000 0.000
#> GSM97969 4 0.0000 0.995 0.000 0.000 0.000 1.000
#> GSM97971 4 0.0000 0.995 0.000 0.000 0.000 1.000
#> GSM97799 3 0.0000 0.996 0.000 0.000 1.000 0.000
#> GSM97823 2 0.0000 0.985 0.000 1.000 0.000 0.000
#> GSM97824 3 0.0000 0.996 0.000 0.000 1.000 0.000
#> GSM97830 3 0.0000 0.996 0.000 0.000 1.000 0.000
#> GSM97835 2 0.1792 0.912 0.000 0.932 0.068 0.000
#> GSM97838 2 0.0000 0.985 0.000 1.000 0.000 0.000
#> GSM97841 2 0.0000 0.985 0.000 1.000 0.000 0.000
#> GSM97842 3 0.0000 0.996 0.000 0.000 1.000 0.000
#> GSM97854 2 0.0000 0.985 0.000 1.000 0.000 0.000
#> GSM97857 3 0.0000 0.996 0.000 0.000 1.000 0.000
#> GSM97860 3 0.0000 0.996 0.000 0.000 1.000 0.000
#> GSM97862 3 0.0000 0.996 0.000 0.000 1.000 0.000
#> GSM97864 2 0.0000 0.985 0.000 1.000 0.000 0.000
#> GSM97866 3 0.0000 0.996 0.000 0.000 1.000 0.000
#> GSM97868 3 0.0000 0.996 0.000 0.000 1.000 0.000
#> GSM97872 4 0.1474 0.946 0.052 0.000 0.000 0.948
#> GSM97873 3 0.0000 0.996 0.000 0.000 1.000 0.000
#> GSM97874 3 0.0000 0.996 0.000 0.000 1.000 0.000
#> GSM97875 3 0.0000 0.996 0.000 0.000 1.000 0.000
#> GSM97876 3 0.0000 0.996 0.000 0.000 1.000 0.000
#> GSM97880 3 0.0000 0.996 0.000 0.000 1.000 0.000
#> GSM97881 3 0.0000 0.996 0.000 0.000 1.000 0.000
#> GSM97884 3 0.0000 0.996 0.000 0.000 1.000 0.000
#> GSM97901 3 0.0000 0.996 0.000 0.000 1.000 0.000
#> GSM97902 1 0.0000 0.965 1.000 0.000 0.000 0.000
#> GSM97909 2 0.0000 0.985 0.000 1.000 0.000 0.000
#> GSM97911 3 0.0000 0.996 0.000 0.000 1.000 0.000
#> GSM97923 3 0.0000 0.996 0.000 0.000 1.000 0.000
#> GSM97928 4 0.0000 0.995 0.000 0.000 0.000 1.000
#> GSM97929 2 0.0000 0.985 0.000 1.000 0.000 0.000
#> GSM97933 3 0.0000 0.996 0.000 0.000 1.000 0.000
#> GSM97934 3 0.0000 0.996 0.000 0.000 1.000 0.000
#> GSM97944 3 0.0000 0.996 0.000 0.000 1.000 0.000
#> GSM97949 2 0.0000 0.985 0.000 1.000 0.000 0.000
#> GSM97956 3 0.0000 0.996 0.000 0.000 1.000 0.000
#> GSM97962 3 0.0000 0.996 0.000 0.000 1.000 0.000
#> GSM97964 3 0.0000 0.996 0.000 0.000 1.000 0.000
#> GSM97970 3 0.0000 0.996 0.000 0.000 1.000 0.000
#> GSM97822 4 0.0000 0.995 0.000 0.000 0.000 1.000
#> GSM97831 3 0.0000 0.996 0.000 0.000 1.000 0.000
#> GSM97845 4 0.0188 0.992 0.004 0.000 0.000 0.996
#> GSM97865 1 0.0000 0.965 1.000 0.000 0.000 0.000
#> GSM97867 3 0.0000 0.996 0.000 0.000 1.000 0.000
#> GSM97883 3 0.0000 0.996 0.000 0.000 1.000 0.000
#> GSM97897 4 0.0000 0.995 0.000 0.000 0.000 1.000
#> GSM97900 4 0.0000 0.995 0.000 0.000 0.000 1.000
#> GSM97904 4 0.0000 0.995 0.000 0.000 0.000 1.000
#> GSM97907 2 0.0000 0.985 0.000 1.000 0.000 0.000
#> GSM97925 3 0.0000 0.996 0.000 0.000 1.000 0.000
#> GSM97947 3 0.0000 0.996 0.000 0.000 1.000 0.000
cbind(get_classes(res, k = 5), get_membership(res, k = 5))
#> class entropy silhouette p1 p2 p3 p4 p5
#> GSM97800 2 0.0000 0.97543 0.000 1.000 0.000 0.000 0.000
#> GSM97803 2 0.0000 0.97543 0.000 1.000 0.000 0.000 0.000
#> GSM97804 2 0.0000 0.97543 0.000 1.000 0.000 0.000 0.000
#> GSM97805 2 0.0000 0.97543 0.000 1.000 0.000 0.000 0.000
#> GSM97807 2 0.0000 0.97543 0.000 1.000 0.000 0.000 0.000
#> GSM97809 2 0.0000 0.97543 0.000 1.000 0.000 0.000 0.000
#> GSM97811 2 0.0000 0.97543 0.000 1.000 0.000 0.000 0.000
#> GSM97812 2 0.0000 0.97543 0.000 1.000 0.000 0.000 0.000
#> GSM97816 2 0.2889 0.86035 0.084 0.872 0.000 0.000 0.044
#> GSM97817 2 0.0000 0.97543 0.000 1.000 0.000 0.000 0.000
#> GSM97820 2 0.0000 0.97543 0.000 1.000 0.000 0.000 0.000
#> GSM97825 2 0.0000 0.97543 0.000 1.000 0.000 0.000 0.000
#> GSM97827 2 0.0000 0.97543 0.000 1.000 0.000 0.000 0.000
#> GSM97828 1 0.1410 0.84791 0.940 0.000 0.000 0.000 0.060
#> GSM97833 2 0.0000 0.97543 0.000 1.000 0.000 0.000 0.000
#> GSM97834 2 0.0000 0.97543 0.000 1.000 0.000 0.000 0.000
#> GSM97840 2 0.0000 0.97543 0.000 1.000 0.000 0.000 0.000
#> GSM97846 2 0.0000 0.97543 0.000 1.000 0.000 0.000 0.000
#> GSM97848 2 0.0000 0.97543 0.000 1.000 0.000 0.000 0.000
#> GSM97849 2 0.0000 0.97543 0.000 1.000 0.000 0.000 0.000
#> GSM97850 2 0.0000 0.97543 0.000 1.000 0.000 0.000 0.000
#> GSM97853 2 0.0000 0.97543 0.000 1.000 0.000 0.000 0.000
#> GSM97855 2 0.0000 0.97543 0.000 1.000 0.000 0.000 0.000
#> GSM97878 1 0.4565 0.49794 0.664 0.000 0.000 0.308 0.028
#> GSM97913 2 0.4086 0.58780 0.284 0.704 0.000 0.000 0.012
#> GSM97932 4 0.0898 0.84580 0.008 0.000 0.000 0.972 0.020
#> GSM97939 3 0.4147 0.28773 0.000 0.316 0.676 0.000 0.008
#> GSM97951 2 0.0000 0.97543 0.000 1.000 0.000 0.000 0.000
#> GSM97957 3 0.4287 0.57870 0.000 0.000 0.540 0.000 0.460
#> GSM97972 2 0.3053 0.86358 0.076 0.872 0.008 0.000 0.044
#> GSM97793 3 0.4278 0.58192 0.000 0.000 0.548 0.000 0.452
#> GSM97795 2 0.0162 0.97286 0.000 0.996 0.000 0.000 0.004
#> GSM97802 5 0.3532 0.78130 0.000 0.000 0.128 0.048 0.824
#> GSM97810 2 0.0898 0.95308 0.000 0.972 0.020 0.000 0.008
#> GSM97815 2 0.4375 0.34921 0.000 0.576 0.420 0.000 0.004
#> GSM97837 1 0.0880 0.86382 0.968 0.000 0.000 0.000 0.032
#> GSM97843 3 0.4235 0.59649 0.000 0.000 0.576 0.000 0.424
#> GSM97890 3 0.0510 0.70880 0.000 0.000 0.984 0.000 0.016
#> GSM97899 4 0.0510 0.85611 0.000 0.000 0.000 0.984 0.016
#> GSM97910 1 0.0880 0.86016 0.968 0.000 0.000 0.000 0.032
#> GSM97916 1 0.1792 0.83264 0.916 0.000 0.000 0.000 0.084
#> GSM97920 3 0.4291 0.57395 0.000 0.000 0.536 0.000 0.464
#> GSM97921 1 0.1205 0.86247 0.956 0.000 0.000 0.004 0.040
#> GSM97927 4 0.4278 0.32228 0.000 0.000 0.000 0.548 0.452
#> GSM97937 1 0.3193 0.75104 0.840 0.000 0.000 0.132 0.028
#> GSM97941 2 0.0000 0.97543 0.000 1.000 0.000 0.000 0.000
#> GSM97943 1 0.1121 0.85604 0.956 0.000 0.000 0.000 0.044
#> GSM97958 2 0.3115 0.83649 0.112 0.852 0.000 0.000 0.036
#> GSM97960 2 0.0162 0.97286 0.000 0.996 0.000 0.000 0.004
#> GSM97794 1 0.0404 0.86307 0.988 0.000 0.000 0.000 0.012
#> GSM97796 4 0.0162 0.85489 0.000 0.000 0.000 0.996 0.004
#> GSM97797 1 0.0404 0.86307 0.988 0.000 0.000 0.000 0.012
#> GSM97798 4 0.0510 0.85611 0.000 0.000 0.000 0.984 0.016
#> GSM97801 1 0.0290 0.86392 0.992 0.000 0.000 0.000 0.008
#> GSM97806 4 0.0451 0.85583 0.004 0.000 0.000 0.988 0.008
#> GSM97808 4 0.0510 0.85611 0.000 0.000 0.000 0.984 0.016
#> GSM97813 4 0.4300 0.27988 0.000 0.000 0.000 0.524 0.476
#> GSM97814 4 0.0510 0.85611 0.000 0.000 0.000 0.984 0.016
#> GSM97818 1 0.0404 0.86307 0.988 0.000 0.000 0.000 0.012
#> GSM97819 3 0.3949 0.62479 0.000 0.000 0.668 0.000 0.332
#> GSM97821 2 0.0000 0.97543 0.000 1.000 0.000 0.000 0.000
#> GSM97826 1 0.3141 0.77361 0.832 0.000 0.000 0.016 0.152
#> GSM97829 1 0.0703 0.86458 0.976 0.000 0.000 0.000 0.024
#> GSM97832 2 0.0162 0.97286 0.000 0.996 0.000 0.000 0.004
#> GSM97836 4 0.3508 0.64965 0.000 0.000 0.000 0.748 0.252
#> GSM97839 4 0.0162 0.85489 0.000 0.000 0.000 0.996 0.004
#> GSM97844 2 0.0000 0.97543 0.000 1.000 0.000 0.000 0.000
#> GSM97847 1 0.4086 0.62276 0.736 0.000 0.000 0.240 0.024
#> GSM97851 4 0.0771 0.84789 0.004 0.000 0.000 0.976 0.020
#> GSM97852 4 0.1012 0.84350 0.012 0.000 0.000 0.968 0.020
#> GSM97856 4 0.0510 0.85611 0.000 0.000 0.000 0.984 0.016
#> GSM97858 2 0.0000 0.97543 0.000 1.000 0.000 0.000 0.000
#> GSM97859 4 0.4448 0.26706 0.004 0.000 0.000 0.516 0.480
#> GSM97861 4 0.0510 0.85611 0.000 0.000 0.000 0.984 0.016
#> GSM97863 4 0.0162 0.85489 0.000 0.000 0.000 0.996 0.004
#> GSM97869 1 0.4897 0.17468 0.516 0.000 0.000 0.024 0.460
#> GSM97870 5 0.1697 0.84000 0.008 0.000 0.000 0.060 0.932
#> GSM97871 4 0.0510 0.85611 0.000 0.000 0.000 0.984 0.016
#> GSM97877 2 0.0807 0.95662 0.012 0.976 0.000 0.000 0.012
#> GSM97879 4 0.0404 0.85616 0.000 0.000 0.000 0.988 0.012
#> GSM97882 4 0.4249 0.36585 0.000 0.000 0.000 0.568 0.432
#> GSM97885 1 0.6017 0.07735 0.480 0.000 0.000 0.116 0.404
#> GSM97886 4 0.0000 0.85512 0.000 0.000 0.000 1.000 0.000
#> GSM97887 4 0.0510 0.85611 0.000 0.000 0.000 0.984 0.016
#> GSM97888 4 0.4227 0.39669 0.000 0.000 0.000 0.580 0.420
#> GSM97889 4 0.4294 0.28643 0.000 0.000 0.000 0.532 0.468
#> GSM97891 4 0.0671 0.85525 0.004 0.000 0.000 0.980 0.016
#> GSM97892 2 0.0000 0.97543 0.000 1.000 0.000 0.000 0.000
#> GSM97893 4 0.1012 0.84350 0.012 0.000 0.000 0.968 0.020
#> GSM97894 4 0.0162 0.85489 0.000 0.000 0.000 0.996 0.004
#> GSM97895 4 0.0609 0.84971 0.000 0.000 0.000 0.980 0.020
#> GSM97896 4 0.4294 0.29456 0.000 0.000 0.000 0.532 0.468
#> GSM97898 4 0.0290 0.85389 0.000 0.000 0.000 0.992 0.008
#> GSM97903 1 0.2331 0.82006 0.900 0.000 0.000 0.080 0.020
#> GSM97905 5 0.1671 0.84031 0.000 0.000 0.000 0.076 0.924
#> GSM97906 4 0.0510 0.85611 0.000 0.000 0.000 0.984 0.016
#> GSM97908 4 0.1872 0.81140 0.052 0.000 0.000 0.928 0.020
#> GSM97912 5 0.3852 0.64739 0.020 0.000 0.000 0.220 0.760
#> GSM97914 1 0.0510 0.86471 0.984 0.000 0.000 0.000 0.016
#> GSM97915 4 0.0162 0.85489 0.000 0.000 0.000 0.996 0.004
#> GSM97917 4 0.0898 0.84580 0.008 0.000 0.000 0.972 0.020
#> GSM97918 4 0.0162 0.85489 0.000 0.000 0.000 0.996 0.004
#> GSM97919 4 0.0162 0.85489 0.000 0.000 0.000 0.996 0.004
#> GSM97922 4 0.4300 0.27988 0.000 0.000 0.000 0.524 0.476
#> GSM97924 2 0.0000 0.97543 0.000 1.000 0.000 0.000 0.000
#> GSM97926 3 0.0000 0.70834 0.000 0.000 1.000 0.000 0.000
#> GSM97930 1 0.2795 0.79964 0.872 0.000 0.000 0.100 0.028
#> GSM97931 2 0.0162 0.97286 0.000 0.996 0.000 0.000 0.004
#> GSM97935 4 0.0955 0.85127 0.004 0.000 0.000 0.968 0.028
#> GSM97936 4 0.0000 0.85512 0.000 0.000 0.000 1.000 0.000
#> GSM97938 4 0.1661 0.82573 0.036 0.000 0.000 0.940 0.024
#> GSM97940 4 0.0510 0.85611 0.000 0.000 0.000 0.984 0.016
#> GSM97942 3 0.4278 0.58192 0.000 0.000 0.548 0.000 0.452
#> GSM97945 4 0.0510 0.85611 0.000 0.000 0.000 0.984 0.016
#> GSM97946 2 0.0000 0.97543 0.000 1.000 0.000 0.000 0.000
#> GSM97948 5 0.1732 0.74797 0.000 0.000 0.080 0.000 0.920
#> GSM97950 4 0.0000 0.85512 0.000 0.000 0.000 1.000 0.000
#> GSM97952 4 0.0510 0.85611 0.000 0.000 0.000 0.984 0.016
#> GSM97953 4 0.2813 0.75761 0.108 0.000 0.000 0.868 0.024
#> GSM97954 4 0.1725 0.82088 0.044 0.000 0.000 0.936 0.020
#> GSM97955 4 0.0000 0.85512 0.000 0.000 0.000 1.000 0.000
#> GSM97959 1 0.0566 0.86248 0.984 0.004 0.000 0.000 0.012
#> GSM97961 4 0.0000 0.85512 0.000 0.000 0.000 1.000 0.000
#> GSM97963 4 0.0510 0.85611 0.000 0.000 0.000 0.984 0.016
#> GSM97965 4 0.0510 0.85611 0.000 0.000 0.000 0.984 0.016
#> GSM97966 4 0.0510 0.85611 0.000 0.000 0.000 0.984 0.016
#> GSM97967 2 0.0000 0.97543 0.000 1.000 0.000 0.000 0.000
#> GSM97968 2 0.0000 0.97543 0.000 1.000 0.000 0.000 0.000
#> GSM97969 4 0.3274 0.68575 0.000 0.000 0.000 0.780 0.220
#> GSM97971 4 0.4560 0.25648 0.008 0.000 0.000 0.508 0.484
#> GSM97799 3 0.0162 0.70711 0.000 0.000 0.996 0.000 0.004
#> GSM97823 2 0.0000 0.97543 0.000 1.000 0.000 0.000 0.000
#> GSM97824 3 0.0510 0.70582 0.000 0.000 0.984 0.000 0.016
#> GSM97830 3 0.4287 0.57755 0.000 0.000 0.540 0.000 0.460
#> GSM97835 3 0.4415 0.00866 0.000 0.444 0.552 0.000 0.004
#> GSM97838 2 0.0000 0.97543 0.000 1.000 0.000 0.000 0.000
#> GSM97841 2 0.0000 0.97543 0.000 1.000 0.000 0.000 0.000
#> GSM97842 3 0.0162 0.70711 0.000 0.000 0.996 0.000 0.004
#> GSM97854 2 0.0000 0.97543 0.000 1.000 0.000 0.000 0.000
#> GSM97857 3 0.0963 0.69342 0.000 0.000 0.964 0.000 0.036
#> GSM97860 3 0.4278 0.58192 0.000 0.000 0.548 0.000 0.452
#> GSM97862 3 0.0162 0.70922 0.000 0.000 0.996 0.000 0.004
#> GSM97864 2 0.0000 0.97543 0.000 1.000 0.000 0.000 0.000
#> GSM97866 3 0.0162 0.70922 0.000 0.000 0.996 0.000 0.004
#> GSM97868 3 0.0162 0.70922 0.000 0.000 0.996 0.000 0.004
#> GSM97872 4 0.5454 0.30076 0.064 0.000 0.000 0.532 0.404
#> GSM97873 3 0.0162 0.70711 0.000 0.000 0.996 0.000 0.004
#> GSM97874 3 0.4291 0.57395 0.000 0.000 0.536 0.000 0.464
#> GSM97875 3 0.3074 0.67085 0.000 0.000 0.804 0.000 0.196
#> GSM97876 3 0.4278 0.58192 0.000 0.000 0.548 0.000 0.452
#> GSM97880 3 0.4278 0.58192 0.000 0.000 0.548 0.000 0.452
#> GSM97881 3 0.0000 0.70834 0.000 0.000 1.000 0.000 0.000
#> GSM97884 3 0.0162 0.70711 0.000 0.000 0.996 0.000 0.004
#> GSM97901 3 0.0162 0.70922 0.000 0.000 0.996 0.000 0.004
#> GSM97902 1 0.1282 0.86021 0.952 0.000 0.000 0.004 0.044
#> GSM97909 2 0.0000 0.97543 0.000 1.000 0.000 0.000 0.000
#> GSM97911 3 0.0000 0.70834 0.000 0.000 1.000 0.000 0.000
#> GSM97923 3 0.4278 0.58192 0.000 0.000 0.548 0.000 0.452
#> GSM97928 4 0.3876 0.56212 0.000 0.000 0.000 0.684 0.316
#> GSM97929 2 0.0000 0.97543 0.000 1.000 0.000 0.000 0.000
#> GSM97933 3 0.4287 0.57856 0.000 0.000 0.540 0.000 0.460
#> GSM97934 3 0.4287 0.57870 0.000 0.000 0.540 0.000 0.460
#> GSM97944 3 0.0162 0.70711 0.000 0.000 0.996 0.000 0.004
#> GSM97949 2 0.0000 0.97543 0.000 1.000 0.000 0.000 0.000
#> GSM97956 3 0.0290 0.70839 0.000 0.000 0.992 0.000 0.008
#> GSM97962 3 0.2561 0.68184 0.000 0.000 0.856 0.000 0.144
#> GSM97964 3 0.0162 0.70743 0.000 0.000 0.996 0.000 0.004
#> GSM97970 3 0.0162 0.70711 0.000 0.000 0.996 0.000 0.004
#> GSM97822 4 0.4294 0.28643 0.000 0.000 0.000 0.532 0.468
#> GSM97831 3 0.1851 0.69926 0.000 0.000 0.912 0.000 0.088
#> GSM97845 4 0.1216 0.83888 0.020 0.000 0.000 0.960 0.020
#> GSM97865 1 0.1205 0.86247 0.956 0.000 0.000 0.004 0.040
#> GSM97867 3 0.4278 0.58192 0.000 0.000 0.548 0.000 0.452
#> GSM97883 3 0.4287 0.57515 0.000 0.000 0.540 0.000 0.460
#> GSM97897 4 0.4287 0.30432 0.000 0.000 0.000 0.540 0.460
#> GSM97900 4 0.0510 0.85611 0.000 0.000 0.000 0.984 0.016
#> GSM97904 4 0.2629 0.77628 0.004 0.000 0.000 0.860 0.136
#> GSM97907 2 0.0000 0.97543 0.000 1.000 0.000 0.000 0.000
#> GSM97925 3 0.4278 0.58192 0.000 0.000 0.548 0.000 0.452
#> GSM97947 3 0.4138 0.59502 0.000 0.000 0.616 0.000 0.384
cbind(get_classes(res, k = 6), get_membership(res, k = 6))
#> class entropy silhouette p1 p2 p3 p4 p5 p6
#> GSM97800 2 0.0146 0.9619 0.004 0.996 0.000 0.000 0.000 0.000
#> GSM97803 2 0.0146 0.9619 0.004 0.996 0.000 0.000 0.000 0.000
#> GSM97804 2 0.0146 0.9619 0.004 0.996 0.000 0.000 0.000 0.000
#> GSM97805 2 0.0146 0.9619 0.004 0.996 0.000 0.000 0.000 0.000
#> GSM97807 2 0.0000 0.9625 0.000 1.000 0.000 0.000 0.000 0.000
#> GSM97809 2 0.0000 0.9625 0.000 1.000 0.000 0.000 0.000 0.000
#> GSM97811 2 0.0000 0.9625 0.000 1.000 0.000 0.000 0.000 0.000
#> GSM97812 2 0.0000 0.9625 0.000 1.000 0.000 0.000 0.000 0.000
#> GSM97816 6 0.4357 0.0576 0.000 0.420 0.008 0.000 0.012 0.560
#> GSM97817 2 0.0000 0.9625 0.000 1.000 0.000 0.000 0.000 0.000
#> GSM97820 2 0.0000 0.9625 0.000 1.000 0.000 0.000 0.000 0.000
#> GSM97825 2 0.0000 0.9625 0.000 1.000 0.000 0.000 0.000 0.000
#> GSM97827 2 0.0000 0.9625 0.000 1.000 0.000 0.000 0.000 0.000
#> GSM97828 6 0.1340 0.4880 0.004 0.000 0.008 0.000 0.040 0.948
#> GSM97833 2 0.0000 0.9625 0.000 1.000 0.000 0.000 0.000 0.000
#> GSM97834 2 0.0000 0.9625 0.000 1.000 0.000 0.000 0.000 0.000
#> GSM97840 2 0.0000 0.9625 0.000 1.000 0.000 0.000 0.000 0.000
#> GSM97846 2 0.0000 0.9625 0.000 1.000 0.000 0.000 0.000 0.000
#> GSM97848 2 0.0000 0.9625 0.000 1.000 0.000 0.000 0.000 0.000
#> GSM97849 2 0.0000 0.9625 0.000 1.000 0.000 0.000 0.000 0.000
#> GSM97850 2 0.0000 0.9625 0.000 1.000 0.000 0.000 0.000 0.000
#> GSM97853 2 0.0000 0.9625 0.000 1.000 0.000 0.000 0.000 0.000
#> GSM97855 2 0.0000 0.9625 0.000 1.000 0.000 0.000 0.000 0.000
#> GSM97878 1 0.4636 0.1999 0.692 0.000 0.000 0.148 0.000 0.160
#> GSM97913 2 0.5451 0.1945 0.328 0.532 0.000 0.000 0.000 0.140
#> GSM97932 4 0.3073 0.7325 0.152 0.000 0.000 0.824 0.016 0.008
#> GSM97939 3 0.3089 0.5783 0.000 0.188 0.800 0.000 0.008 0.004
#> GSM97951 2 0.0000 0.9625 0.000 1.000 0.000 0.000 0.000 0.000
#> GSM97957 5 0.5065 0.6339 0.000 0.000 0.260 0.000 0.616 0.124
#> GSM97972 2 0.4725 0.3736 0.004 0.588 0.020 0.000 0.016 0.372
#> GSM97793 5 0.3409 0.6879 0.000 0.000 0.300 0.000 0.700 0.000
#> GSM97795 2 0.0291 0.9598 0.004 0.992 0.004 0.000 0.000 0.000
#> GSM97802 5 0.5807 0.1902 0.268 0.000 0.088 0.056 0.588 0.000
#> GSM97810 2 0.1501 0.8889 0.000 0.924 0.076 0.000 0.000 0.000
#> GSM97815 3 0.4015 0.3036 0.004 0.396 0.596 0.000 0.004 0.000
#> GSM97837 6 0.3706 0.4225 0.380 0.000 0.000 0.000 0.000 0.620
#> GSM97843 5 0.3907 0.5370 0.000 0.000 0.408 0.000 0.588 0.004
#> GSM97890 3 0.1814 0.7452 0.000 0.000 0.900 0.000 0.100 0.000
#> GSM97899 4 0.0146 0.7931 0.000 0.000 0.000 0.996 0.004 0.000
#> GSM97910 6 0.1918 0.5188 0.088 0.000 0.000 0.000 0.008 0.904
#> GSM97916 1 0.4246 -0.0116 0.580 0.000 0.000 0.000 0.020 0.400
#> GSM97920 5 0.5565 0.5795 0.000 0.000 0.240 0.000 0.552 0.208
#> GSM97921 6 0.3659 0.4332 0.364 0.000 0.000 0.000 0.000 0.636
#> GSM97927 4 0.5719 0.3133 0.248 0.000 0.000 0.520 0.232 0.000
#> GSM97937 1 0.6124 0.0788 0.444 0.000 0.000 0.172 0.016 0.368
#> GSM97941 2 0.0000 0.9625 0.000 1.000 0.000 0.000 0.000 0.000
#> GSM97943 6 0.1078 0.5054 0.012 0.000 0.008 0.000 0.016 0.964
#> GSM97958 2 0.4022 0.4500 0.008 0.628 0.004 0.000 0.000 0.360
#> GSM97960 2 0.0363 0.9539 0.000 0.988 0.012 0.000 0.000 0.000
#> GSM97794 1 0.3828 -0.0600 0.560 0.000 0.000 0.000 0.000 0.440
#> GSM97796 4 0.1563 0.7871 0.056 0.000 0.000 0.932 0.012 0.000
#> GSM97797 1 0.3864 -0.1320 0.520 0.000 0.000 0.000 0.000 0.480
#> GSM97798 4 0.0146 0.7931 0.000 0.000 0.000 0.996 0.004 0.000
#> GSM97801 6 0.3499 0.4059 0.320 0.000 0.000 0.000 0.000 0.680
#> GSM97806 4 0.1863 0.7458 0.104 0.000 0.000 0.896 0.000 0.000
#> GSM97808 4 0.0146 0.7931 0.000 0.000 0.000 0.996 0.004 0.000
#> GSM97813 4 0.6207 0.1405 0.332 0.000 0.000 0.384 0.280 0.004
#> GSM97814 4 0.0146 0.7931 0.000 0.000 0.000 0.996 0.004 0.000
#> GSM97818 1 0.3847 -0.0754 0.544 0.000 0.000 0.000 0.000 0.456
#> GSM97819 3 0.3862 -0.2815 0.000 0.000 0.524 0.000 0.476 0.000
#> GSM97821 2 0.0146 0.9619 0.004 0.996 0.000 0.000 0.000 0.000
#> GSM97826 1 0.6190 0.0778 0.508 0.000 0.000 0.060 0.100 0.332
#> GSM97829 6 0.3684 0.4266 0.372 0.000 0.000 0.000 0.000 0.628
#> GSM97832 2 0.0291 0.9598 0.004 0.992 0.004 0.000 0.000 0.000
#> GSM97836 4 0.3978 0.6279 0.160 0.000 0.000 0.756 0.084 0.000
#> GSM97839 4 0.1563 0.7871 0.056 0.000 0.000 0.932 0.012 0.000
#> GSM97844 2 0.0146 0.9619 0.004 0.996 0.000 0.000 0.000 0.000
#> GSM97847 1 0.5773 0.2018 0.552 0.000 0.000 0.284 0.016 0.148
#> GSM97851 4 0.2806 0.7450 0.136 0.000 0.000 0.844 0.016 0.004
#> GSM97852 4 0.3992 0.6209 0.264 0.000 0.000 0.708 0.016 0.012
#> GSM97856 4 0.0146 0.7931 0.000 0.000 0.000 0.996 0.004 0.000
#> GSM97858 2 0.0146 0.9619 0.004 0.996 0.000 0.000 0.000 0.000
#> GSM97859 4 0.6589 0.0804 0.344 0.000 0.000 0.352 0.280 0.024
#> GSM97861 4 0.0508 0.7902 0.012 0.000 0.000 0.984 0.004 0.000
#> GSM97863 4 0.1462 0.7877 0.056 0.000 0.000 0.936 0.008 0.000
#> GSM97869 1 0.5539 0.1517 0.604 0.000 0.000 0.016 0.232 0.148
#> GSM97870 5 0.5505 0.0908 0.320 0.000 0.000 0.028 0.572 0.080
#> GSM97871 4 0.0146 0.7931 0.000 0.000 0.000 0.996 0.004 0.000
#> GSM97877 2 0.3394 0.7214 0.200 0.776 0.000 0.000 0.000 0.024
#> GSM97879 4 0.0363 0.7925 0.012 0.000 0.000 0.988 0.000 0.000
#> GSM97882 4 0.5605 0.3586 0.244 0.000 0.000 0.544 0.212 0.000
#> GSM97885 1 0.7135 0.2001 0.464 0.000 0.000 0.188 0.164 0.184
#> GSM97886 4 0.0790 0.7922 0.032 0.000 0.000 0.968 0.000 0.000
#> GSM97887 4 0.0146 0.7931 0.000 0.000 0.000 0.996 0.004 0.000
#> GSM97888 4 0.5882 0.3285 0.280 0.000 0.000 0.476 0.244 0.000
#> GSM97889 4 0.5875 0.2591 0.264 0.000 0.000 0.480 0.256 0.000
#> GSM97891 4 0.1531 0.7560 0.068 0.000 0.000 0.928 0.000 0.004
#> GSM97892 2 0.0146 0.9619 0.004 0.996 0.000 0.000 0.000 0.000
#> GSM97893 4 0.3172 0.7288 0.152 0.000 0.000 0.820 0.016 0.012
#> GSM97894 4 0.1625 0.7859 0.060 0.000 0.000 0.928 0.012 0.000
#> GSM97895 4 0.2703 0.7551 0.116 0.000 0.000 0.860 0.016 0.008
#> GSM97896 4 0.5951 0.2580 0.272 0.000 0.000 0.456 0.272 0.000
#> GSM97898 4 0.1563 0.7871 0.056 0.000 0.000 0.932 0.012 0.000
#> GSM97903 1 0.4230 0.0286 0.612 0.000 0.000 0.024 0.000 0.364
#> GSM97905 5 0.3460 0.2964 0.220 0.000 0.000 0.020 0.760 0.000
#> GSM97906 4 0.0146 0.7931 0.000 0.000 0.000 0.996 0.004 0.000
#> GSM97908 4 0.4035 0.5981 0.272 0.000 0.000 0.700 0.016 0.012
#> GSM97912 5 0.6654 -0.2109 0.384 0.000 0.000 0.164 0.396 0.056
#> GSM97914 6 0.3823 0.3096 0.436 0.000 0.000 0.000 0.000 0.564
#> GSM97915 4 0.1563 0.7871 0.056 0.000 0.000 0.932 0.012 0.000
#> GSM97917 4 0.3147 0.7256 0.160 0.000 0.000 0.816 0.016 0.008
#> GSM97918 4 0.1584 0.7862 0.064 0.000 0.000 0.928 0.008 0.000
#> GSM97919 4 0.1913 0.7787 0.080 0.000 0.000 0.908 0.012 0.000
#> GSM97922 4 0.6200 0.1458 0.332 0.000 0.000 0.388 0.276 0.004
#> GSM97924 2 0.0146 0.9619 0.004 0.996 0.000 0.000 0.000 0.000
#> GSM97926 3 0.0865 0.8009 0.000 0.000 0.964 0.000 0.036 0.000
#> GSM97930 1 0.4614 0.0909 0.660 0.000 0.000 0.040 0.016 0.284
#> GSM97931 2 0.2517 0.8518 0.100 0.876 0.008 0.000 0.000 0.016
#> GSM97935 4 0.2070 0.7370 0.100 0.000 0.000 0.892 0.008 0.000
#> GSM97936 4 0.0713 0.7921 0.028 0.000 0.000 0.972 0.000 0.000
#> GSM97938 4 0.4112 0.6618 0.200 0.000 0.000 0.744 0.016 0.040
#> GSM97940 4 0.0146 0.7931 0.000 0.000 0.000 0.996 0.004 0.000
#> GSM97942 5 0.3446 0.6841 0.000 0.000 0.308 0.000 0.692 0.000
#> GSM97945 4 0.0146 0.7931 0.000 0.000 0.000 0.996 0.004 0.000
#> GSM97946 2 0.0000 0.9625 0.000 1.000 0.000 0.000 0.000 0.000
#> GSM97948 5 0.2740 0.4527 0.120 0.000 0.028 0.000 0.852 0.000
#> GSM97950 4 0.0935 0.7922 0.032 0.000 0.000 0.964 0.004 0.000
#> GSM97952 4 0.0146 0.7931 0.000 0.000 0.000 0.996 0.004 0.000
#> GSM97953 4 0.5231 0.4995 0.248 0.000 0.000 0.632 0.016 0.104
#> GSM97954 4 0.4621 0.4406 0.356 0.000 0.000 0.604 0.016 0.024
#> GSM97955 4 0.1265 0.7901 0.044 0.000 0.000 0.948 0.008 0.000
#> GSM97959 1 0.3833 -0.0673 0.556 0.000 0.000 0.000 0.000 0.444
#> GSM97961 4 0.0790 0.7922 0.032 0.000 0.000 0.968 0.000 0.000
#> GSM97963 4 0.0146 0.7931 0.000 0.000 0.000 0.996 0.004 0.000
#> GSM97965 4 0.0146 0.7931 0.000 0.000 0.000 0.996 0.004 0.000
#> GSM97966 4 0.0146 0.7931 0.000 0.000 0.000 0.996 0.004 0.000
#> GSM97967 2 0.0000 0.9625 0.000 1.000 0.000 0.000 0.000 0.000
#> GSM97968 2 0.0000 0.9625 0.000 1.000 0.000 0.000 0.000 0.000
#> GSM97969 4 0.5151 0.5724 0.208 0.000 0.000 0.636 0.152 0.004
#> GSM97971 1 0.6583 -0.1119 0.368 0.000 0.000 0.328 0.280 0.024
#> GSM97799 3 0.0260 0.8092 0.000 0.000 0.992 0.000 0.008 0.000
#> GSM97823 2 0.0000 0.9625 0.000 1.000 0.000 0.000 0.000 0.000
#> GSM97824 3 0.1720 0.7715 0.000 0.000 0.928 0.000 0.032 0.040
#> GSM97830 5 0.4892 0.6528 0.000 0.000 0.272 0.000 0.628 0.100
#> GSM97835 3 0.3215 0.5097 0.004 0.240 0.756 0.000 0.000 0.000
#> GSM97838 2 0.0146 0.9619 0.004 0.996 0.000 0.000 0.000 0.000
#> GSM97841 2 0.0146 0.9619 0.004 0.996 0.000 0.000 0.000 0.000
#> GSM97842 3 0.0146 0.8091 0.000 0.000 0.996 0.000 0.004 0.000
#> GSM97854 2 0.0146 0.9619 0.004 0.996 0.000 0.000 0.000 0.000
#> GSM97857 3 0.3388 0.6482 0.000 0.000 0.792 0.000 0.036 0.172
#> GSM97860 5 0.3428 0.6866 0.000 0.000 0.304 0.000 0.696 0.000
#> GSM97862 3 0.0632 0.8042 0.000 0.000 0.976 0.000 0.024 0.000
#> GSM97864 2 0.0146 0.9619 0.004 0.996 0.000 0.000 0.000 0.000
#> GSM97866 3 0.1265 0.7885 0.000 0.000 0.948 0.000 0.044 0.008
#> GSM97868 3 0.0632 0.8074 0.000 0.000 0.976 0.000 0.024 0.000
#> GSM97872 1 0.6694 -0.0776 0.428 0.000 0.000 0.328 0.192 0.052
#> GSM97873 3 0.0260 0.8092 0.000 0.000 0.992 0.000 0.008 0.000
#> GSM97874 5 0.4793 0.6621 0.000 0.000 0.252 0.000 0.648 0.100
#> GSM97875 3 0.3647 0.1609 0.000 0.000 0.640 0.000 0.360 0.000
#> GSM97876 5 0.3428 0.6866 0.000 0.000 0.304 0.000 0.696 0.000
#> GSM97880 5 0.3508 0.6892 0.000 0.000 0.292 0.000 0.704 0.004
#> GSM97881 3 0.0547 0.8079 0.000 0.000 0.980 0.000 0.020 0.000
#> GSM97884 3 0.0146 0.8091 0.000 0.000 0.996 0.000 0.004 0.000
#> GSM97901 3 0.1285 0.7851 0.000 0.000 0.944 0.000 0.052 0.004
#> GSM97902 6 0.1563 0.5125 0.056 0.000 0.000 0.000 0.012 0.932
#> GSM97909 2 0.0146 0.9619 0.004 0.996 0.000 0.000 0.000 0.000
#> GSM97911 3 0.0547 0.8079 0.000 0.000 0.980 0.000 0.020 0.000
#> GSM97923 5 0.3446 0.6841 0.000 0.000 0.308 0.000 0.692 0.000
#> GSM97928 4 0.5382 0.4642 0.288 0.000 0.000 0.564 0.148 0.000
#> GSM97929 2 0.0146 0.9619 0.004 0.996 0.000 0.000 0.000 0.000
#> GSM97933 5 0.3575 0.6880 0.000 0.000 0.284 0.000 0.708 0.008
#> GSM97934 5 0.5009 0.6396 0.000 0.000 0.256 0.000 0.624 0.120
#> GSM97944 3 0.0260 0.8092 0.000 0.000 0.992 0.000 0.008 0.000
#> GSM97949 2 0.0000 0.9625 0.000 1.000 0.000 0.000 0.000 0.000
#> GSM97956 3 0.0405 0.8080 0.000 0.000 0.988 0.000 0.008 0.004
#> GSM97962 3 0.4635 0.1938 0.000 0.000 0.608 0.000 0.336 0.056
#> GSM97964 3 0.0520 0.8036 0.000 0.000 0.984 0.000 0.008 0.008
#> GSM97970 3 0.0000 0.8083 0.000 0.000 1.000 0.000 0.000 0.000
#> GSM97822 4 0.5951 0.2237 0.276 0.000 0.000 0.456 0.268 0.000
#> GSM97831 3 0.4235 0.5122 0.000 0.000 0.724 0.000 0.192 0.084
#> GSM97845 4 0.4050 0.6425 0.232 0.000 0.000 0.728 0.016 0.024
#> GSM97865 6 0.3789 0.3529 0.416 0.000 0.000 0.000 0.000 0.584
#> GSM97867 5 0.3409 0.6879 0.000 0.000 0.300 0.000 0.700 0.000
#> GSM97883 5 0.3360 0.6865 0.004 0.000 0.264 0.000 0.732 0.000
#> GSM97897 4 0.5680 0.3222 0.252 0.000 0.000 0.528 0.220 0.000
#> GSM97900 4 0.0146 0.7931 0.000 0.000 0.000 0.996 0.004 0.000
#> GSM97904 4 0.3838 0.7023 0.096 0.000 0.000 0.784 0.116 0.004
#> GSM97907 2 0.0146 0.9619 0.004 0.996 0.000 0.000 0.000 0.000
#> GSM97925 5 0.3446 0.6841 0.000 0.000 0.308 0.000 0.692 0.000
#> GSM97947 5 0.4649 0.3373 0.040 0.000 0.468 0.000 0.492 0.000
Heatmaps for the consensus matrix. It visualizes the probability of two samples to be in a same group.
consensus_heatmap(res, k = 2)
consensus_heatmap(res, k = 3)
consensus_heatmap(res, k = 4)
consensus_heatmap(res, k = 5)
consensus_heatmap(res, k = 6)
Heatmaps for the membership of samples in all partitions to see how consistent they are:
membership_heatmap(res, k = 2)
membership_heatmap(res, k = 3)
membership_heatmap(res, k = 4)
membership_heatmap(res, k = 5)
membership_heatmap(res, k = 6)
As soon as we have had the classes for columns, we can look for signatures which are significantly different between classes which can be candidate marks for certain classes. Following are the heatmaps for signatures.
Signature heatmaps where rows are scaled:
get_signatures(res, k = 2)
get_signatures(res, k = 3)
get_signatures(res, k = 4)
get_signatures(res, k = 5)
get_signatures(res, k = 6)
Signature heatmaps where rows are not scaled:
get_signatures(res, k = 2, scale_rows = FALSE)
get_signatures(res, k = 3, scale_rows = FALSE)
get_signatures(res, k = 4, scale_rows = FALSE)
get_signatures(res, k = 5, scale_rows = FALSE)
get_signatures(res, k = 6, scale_rows = FALSE)
Compare the overlap of signatures from different k:
compare_signatures(res)
get_signature() returns a data frame invisibly. TO get the list of signatures, the function
call should be assigned to a variable explicitly. In following code, if plot argument is set
to FALSE, no heatmap is plotted while only the differential analysis is performed.
# code only for demonstration
tb = get_signature(res, k = ..., plot = FALSE)
An example of the output of tb is:
#> which_row fdr mean_1 mean_2 scaled_mean_1 scaled_mean_2 km
#> 1 38 0.042760348 8.373488 9.131774 -0.5533452 0.5164555 1
#> 2 40 0.018707592 7.106213 8.469186 -0.6173731 0.5762149 1
#> 3 55 0.019134737 10.221463 11.207825 -0.6159697 0.5749050 1
#> 4 59 0.006059896 5.921854 7.869574 -0.6899429 0.6439467 1
#> 5 60 0.018055526 8.928898 10.211722 -0.6204761 0.5791110 1
#> 6 98 0.009384629 15.714769 14.887706 0.6635654 -0.6193277 2
...
The columns in tb are:
which_row: row indices corresponding to the input matrix.fdr: FDR for the differential test. mean_x: The mean value in group x.scaled_mean_x: The mean value in group x after rows are scaled.km: Row groups if k-means clustering is applied to rows.UMAP plot which shows how samples are separated.
dimension_reduction(res, k = 2, method = "UMAP")
dimension_reduction(res, k = 3, method = "UMAP")
dimension_reduction(res, k = 4, method = "UMAP")
dimension_reduction(res, k = 5, method = "UMAP")
dimension_reduction(res, k = 6, method = "UMAP")
Following heatmap shows how subgroups are split when increasing k:
collect_classes(res)
Test correlation between subgroups and known annotations. If the known annotation is numeric, one-way ANOVA test is applied, and if the known annotation is discrete, chi-squared contingency table test is applied.
test_to_known_factors(res)
#> n disease.state(p) tissue(p) k
#> SD:skmeans 178 2.15e-14 6.35e-17 2
#> SD:skmeans 177 7.65e-27 3.28e-26 3
#> SD:skmeans 179 3.18e-26 7.74e-25 4
#> SD:skmeans 162 3.14e-24 3.55e-23 5
#> SD:skmeans 131 6.49e-22 1.16e-22 6
If matrix rows can be associated to genes, consider to use functional_enrichment(res,
...) to perform function enrichment for the signature genes. See this vignette for more detailed explanations.
The object with results only for a single top-value method and a single partition method can be extracted as:
res = res_list["SD", "pam"]
# you can also extract it by
# res = res_list["SD:pam"]
A summary of res and all the functions that can be applied to it:
res
#> A 'ConsensusPartition' object with k = 2, 3, 4, 5, 6.
#> On a matrix with 51882 rows and 180 columns.
#> Top rows (1000, 2000, 3000, 4000, 5000) are extracted by 'SD' method.
#> Subgroups are detected by 'pam' method.
#> Performed in total 1250 partitions by row resampling.
#> Best k for subgroups seems to be 2.
#>
#> Following methods can be applied to this 'ConsensusPartition' object:
#> [1] "cola_report" "collect_classes" "collect_plots"
#> [4] "collect_stats" "colnames" "compare_signatures"
#> [7] "consensus_heatmap" "dimension_reduction" "functional_enrichment"
#> [10] "get_anno_col" "get_anno" "get_classes"
#> [13] "get_consensus" "get_matrix" "get_membership"
#> [16] "get_param" "get_signatures" "get_stats"
#> [19] "is_best_k" "is_stable_k" "membership_heatmap"
#> [22] "ncol" "nrow" "plot_ecdf"
#> [25] "rownames" "select_partition_number" "show"
#> [28] "suggest_best_k" "test_to_known_factors"
collect_plots() function collects all the plots made from res for all k (number of partitions)
into one single page to provide an easy and fast comparison between different k.
collect_plots(res)
The plots are:
k and the heatmap of
predicted classes for each k.k.k.k.All the plots in panels can be made by individual functions and they are plotted later in this section.
select_partition_number() produces several plots showing different
statistics for choosing “optimized” k. There are following statistics:
k;k, the area increased is defined as \(A_k - A_{k-1}\).The detailed explanations of these statistics can be found in the cola vignette.
Generally speaking, lower PAC score, higher mean silhouette score or higher
concordance corresponds to better partition. Rand index and Jaccard index
measure how similar the current partition is compared to partition with k-1.
If they are too similar, we won't accept k is better than k-1.
select_partition_number(res)
The numeric values for all these statistics can be obtained by get_stats().
get_stats(res)
#> k 1-PAC mean_silhouette concordance area_increased Rand Jaccard
#> 2 2 0.965 0.962 0.983 0.4183 0.587 0.587
#> 3 3 0.750 0.880 0.942 0.5455 0.708 0.526
#> 4 4 0.888 0.874 0.947 0.1609 0.832 0.564
#> 5 5 0.839 0.773 0.836 0.0624 0.923 0.709
#> 6 6 0.884 0.783 0.908 0.0433 0.944 0.735
suggest_best_k() suggests the best \(k\) based on these statistics. The rules are as follows:
suggest_best_k(res)
#> [1] 2
Following shows the table of the partitions (You need to click the show/hide
code output link to see it). The membership matrix (columns with name p*)
is inferred by
clue::cl_consensus()
function with the SE method. Basically the value in the membership matrix
represents the probability to belong to a certain group. The finall class
label for an item is determined with the group with highest probability it
belongs to.
In get_classes() function, the entropy is calculated from the membership
matrix and the silhouette score is calculated from the consensus matrix.
cbind(get_classes(res, k = 2), get_membership(res, k = 2))
#> class entropy silhouette p1 p2
#> GSM97800 2 0.000 0.982 0.000 1.000
#> GSM97803 2 0.000 0.982 0.000 1.000
#> GSM97804 2 0.000 0.982 0.000 1.000
#> GSM97805 2 0.000 0.982 0.000 1.000
#> GSM97807 2 0.000 0.982 0.000 1.000
#> GSM97809 2 0.000 0.982 0.000 1.000
#> GSM97811 2 0.000 0.982 0.000 1.000
#> GSM97812 2 0.000 0.982 0.000 1.000
#> GSM97816 2 0.000 0.982 0.000 1.000
#> GSM97817 2 0.000 0.982 0.000 1.000
#> GSM97820 2 0.000 0.982 0.000 1.000
#> GSM97825 2 0.000 0.982 0.000 1.000
#> GSM97827 2 0.000 0.982 0.000 1.000
#> GSM97828 2 0.722 0.753 0.200 0.800
#> GSM97833 2 0.000 0.982 0.000 1.000
#> GSM97834 2 0.000 0.982 0.000 1.000
#> GSM97840 2 0.000 0.982 0.000 1.000
#> GSM97846 2 0.000 0.982 0.000 1.000
#> GSM97848 2 0.000 0.982 0.000 1.000
#> GSM97849 2 0.000 0.982 0.000 1.000
#> GSM97850 2 0.000 0.982 0.000 1.000
#> GSM97853 2 0.000 0.982 0.000 1.000
#> GSM97855 2 0.000 0.982 0.000 1.000
#> GSM97878 1 0.000 0.983 1.000 0.000
#> GSM97913 2 0.224 0.948 0.036 0.964
#> GSM97932 1 0.000 0.983 1.000 0.000
#> GSM97939 2 0.000 0.982 0.000 1.000
#> GSM97951 2 0.000 0.982 0.000 1.000
#> GSM97957 1 0.000 0.983 1.000 0.000
#> GSM97972 2 0.204 0.953 0.032 0.968
#> GSM97793 1 0.000 0.983 1.000 0.000
#> GSM97795 2 0.000 0.982 0.000 1.000
#> GSM97802 1 0.000 0.983 1.000 0.000
#> GSM97810 2 0.000 0.982 0.000 1.000
#> GSM97815 2 0.000 0.982 0.000 1.000
#> GSM97837 1 0.000 0.983 1.000 0.000
#> GSM97843 1 0.000 0.983 1.000 0.000
#> GSM97890 1 0.000 0.983 1.000 0.000
#> GSM97899 1 0.000 0.983 1.000 0.000
#> GSM97910 1 0.000 0.983 1.000 0.000
#> GSM97916 1 0.000 0.983 1.000 0.000
#> GSM97920 1 0.000 0.983 1.000 0.000
#> GSM97921 1 0.000 0.983 1.000 0.000
#> GSM97927 1 0.000 0.983 1.000 0.000
#> GSM97937 1 0.000 0.983 1.000 0.000
#> GSM97941 2 0.000 0.982 0.000 1.000
#> GSM97943 1 0.000 0.983 1.000 0.000
#> GSM97958 1 0.689 0.787 0.816 0.184
#> GSM97960 2 0.000 0.982 0.000 1.000
#> GSM97794 1 0.000 0.983 1.000 0.000
#> GSM97796 1 0.000 0.983 1.000 0.000
#> GSM97797 1 0.000 0.983 1.000 0.000
#> GSM97798 1 0.000 0.983 1.000 0.000
#> GSM97801 1 0.000 0.983 1.000 0.000
#> GSM97806 1 0.000 0.983 1.000 0.000
#> GSM97808 1 0.000 0.983 1.000 0.000
#> GSM97813 1 0.000 0.983 1.000 0.000
#> GSM97814 1 0.000 0.983 1.000 0.000
#> GSM97818 1 0.000 0.983 1.000 0.000
#> GSM97819 1 0.000 0.983 1.000 0.000
#> GSM97821 2 0.978 0.275 0.412 0.588
#> GSM97826 1 0.000 0.983 1.000 0.000
#> GSM97829 1 0.000 0.983 1.000 0.000
#> GSM97832 2 0.000 0.982 0.000 1.000
#> GSM97836 1 0.000 0.983 1.000 0.000
#> GSM97839 1 0.000 0.983 1.000 0.000
#> GSM97844 2 0.000 0.982 0.000 1.000
#> GSM97847 1 0.000 0.983 1.000 0.000
#> GSM97851 1 0.000 0.983 1.000 0.000
#> GSM97852 1 0.000 0.983 1.000 0.000
#> GSM97856 1 0.000 0.983 1.000 0.000
#> GSM97858 2 0.000 0.982 0.000 1.000
#> GSM97859 1 0.000 0.983 1.000 0.000
#> GSM97861 1 0.000 0.983 1.000 0.000
#> GSM97863 1 0.000 0.983 1.000 0.000
#> GSM97869 1 0.000 0.983 1.000 0.000
#> GSM97870 1 0.000 0.983 1.000 0.000
#> GSM97871 1 0.000 0.983 1.000 0.000
#> GSM97877 1 0.788 0.709 0.764 0.236
#> GSM97879 1 0.000 0.983 1.000 0.000
#> GSM97882 1 0.000 0.983 1.000 0.000
#> GSM97885 1 0.000 0.983 1.000 0.000
#> GSM97886 1 0.000 0.983 1.000 0.000
#> GSM97887 1 0.000 0.983 1.000 0.000
#> GSM97888 1 0.000 0.983 1.000 0.000
#> GSM97889 1 0.000 0.983 1.000 0.000
#> GSM97891 1 0.000 0.983 1.000 0.000
#> GSM97892 2 0.000 0.982 0.000 1.000
#> GSM97893 1 0.000 0.983 1.000 0.000
#> GSM97894 1 0.000 0.983 1.000 0.000
#> GSM97895 1 0.000 0.983 1.000 0.000
#> GSM97896 1 0.000 0.983 1.000 0.000
#> GSM97898 1 0.000 0.983 1.000 0.000
#> GSM97903 1 0.000 0.983 1.000 0.000
#> GSM97905 1 0.000 0.983 1.000 0.000
#> GSM97906 1 0.000 0.983 1.000 0.000
#> GSM97908 1 0.000 0.983 1.000 0.000
#> GSM97912 1 0.000 0.983 1.000 0.000
#> GSM97914 1 0.000 0.983 1.000 0.000
#> GSM97915 1 0.000 0.983 1.000 0.000
#> GSM97917 1 0.000 0.983 1.000 0.000
#> GSM97918 1 0.000 0.983 1.000 0.000
#> GSM97919 1 0.000 0.983 1.000 0.000
#> GSM97922 1 0.000 0.983 1.000 0.000
#> GSM97924 2 0.000 0.982 0.000 1.000
#> GSM97926 1 0.000 0.983 1.000 0.000
#> GSM97930 1 0.000 0.983 1.000 0.000
#> GSM97931 1 0.343 0.927 0.936 0.064
#> GSM97935 1 0.000 0.983 1.000 0.000
#> GSM97936 1 0.000 0.983 1.000 0.000
#> GSM97938 1 0.000 0.983 1.000 0.000
#> GSM97940 1 0.000 0.983 1.000 0.000
#> GSM97942 1 0.000 0.983 1.000 0.000
#> GSM97945 1 0.000 0.983 1.000 0.000
#> GSM97946 2 0.000 0.982 0.000 1.000
#> GSM97948 1 0.000 0.983 1.000 0.000
#> GSM97950 1 0.000 0.983 1.000 0.000
#> GSM97952 1 0.000 0.983 1.000 0.000
#> GSM97953 1 0.000 0.983 1.000 0.000
#> GSM97954 1 0.000 0.983 1.000 0.000
#> GSM97955 1 0.000 0.983 1.000 0.000
#> GSM97959 1 0.163 0.964 0.976 0.024
#> GSM97961 1 0.000 0.983 1.000 0.000
#> GSM97963 1 0.000 0.983 1.000 0.000
#> GSM97965 1 0.000 0.983 1.000 0.000
#> GSM97966 1 0.000 0.983 1.000 0.000
#> GSM97967 2 0.000 0.982 0.000 1.000
#> GSM97968 2 0.000 0.982 0.000 1.000
#> GSM97969 1 0.000 0.983 1.000 0.000
#> GSM97971 1 0.000 0.983 1.000 0.000
#> GSM97799 1 0.671 0.798 0.824 0.176
#> GSM97823 2 0.000 0.982 0.000 1.000
#> GSM97824 1 0.343 0.927 0.936 0.064
#> GSM97830 1 0.000 0.983 1.000 0.000
#> GSM97835 2 0.000 0.982 0.000 1.000
#> GSM97838 2 0.000 0.982 0.000 1.000
#> GSM97841 2 0.000 0.982 0.000 1.000
#> GSM97842 1 0.753 0.741 0.784 0.216
#> GSM97854 2 0.000 0.982 0.000 1.000
#> GSM97857 1 0.625 0.824 0.844 0.156
#> GSM97860 1 0.000 0.983 1.000 0.000
#> GSM97862 1 0.141 0.967 0.980 0.020
#> GSM97864 2 0.000 0.982 0.000 1.000
#> GSM97866 1 0.000 0.983 1.000 0.000
#> GSM97868 1 0.343 0.927 0.936 0.064
#> GSM97872 1 0.000 0.983 1.000 0.000
#> GSM97873 1 0.900 0.561 0.684 0.316
#> GSM97874 1 0.000 0.983 1.000 0.000
#> GSM97875 1 0.000 0.983 1.000 0.000
#> GSM97876 1 0.000 0.983 1.000 0.000
#> GSM97880 1 0.000 0.983 1.000 0.000
#> GSM97881 1 0.260 0.946 0.956 0.044
#> GSM97884 1 0.808 0.689 0.752 0.248
#> GSM97901 1 0.000 0.983 1.000 0.000
#> GSM97902 1 0.000 0.983 1.000 0.000
#> GSM97909 2 0.000 0.982 0.000 1.000
#> GSM97911 1 0.204 0.957 0.968 0.032
#> GSM97923 1 0.000 0.983 1.000 0.000
#> GSM97928 1 0.000 0.983 1.000 0.000
#> GSM97929 2 0.000 0.982 0.000 1.000
#> GSM97933 1 0.000 0.983 1.000 0.000
#> GSM97934 1 0.000 0.983 1.000 0.000
#> GSM97944 1 0.671 0.798 0.824 0.176
#> GSM97949 2 0.000 0.982 0.000 1.000
#> GSM97956 1 0.278 0.942 0.952 0.048
#> GSM97962 1 0.000 0.983 1.000 0.000
#> GSM97964 1 0.358 0.923 0.932 0.068
#> GSM97970 2 0.781 0.689 0.232 0.768
#> GSM97822 1 0.000 0.983 1.000 0.000
#> GSM97831 1 0.000 0.983 1.000 0.000
#> GSM97845 1 0.000 0.983 1.000 0.000
#> GSM97865 1 0.000 0.983 1.000 0.000
#> GSM97867 1 0.000 0.983 1.000 0.000
#> GSM97883 1 0.000 0.983 1.000 0.000
#> GSM97897 1 0.000 0.983 1.000 0.000
#> GSM97900 1 0.000 0.983 1.000 0.000
#> GSM97904 1 0.000 0.983 1.000 0.000
#> GSM97907 2 0.000 0.982 0.000 1.000
#> GSM97925 1 0.000 0.983 1.000 0.000
#> GSM97947 1 0.000 0.983 1.000 0.000
cbind(get_classes(res, k = 3), get_membership(res, k = 3))
#> class entropy silhouette p1 p2 p3
#> GSM97800 2 0.0000 0.9758 0.000 1.000 0.000
#> GSM97803 2 0.0000 0.9758 0.000 1.000 0.000
#> GSM97804 2 0.0000 0.9758 0.000 1.000 0.000
#> GSM97805 2 0.0000 0.9758 0.000 1.000 0.000
#> GSM97807 2 0.0000 0.9758 0.000 1.000 0.000
#> GSM97809 2 0.0000 0.9758 0.000 1.000 0.000
#> GSM97811 2 0.0000 0.9758 0.000 1.000 0.000
#> GSM97812 2 0.0000 0.9758 0.000 1.000 0.000
#> GSM97816 3 0.6192 0.2764 0.000 0.420 0.580
#> GSM97817 2 0.0000 0.9758 0.000 1.000 0.000
#> GSM97820 2 0.0000 0.9758 0.000 1.000 0.000
#> GSM97825 2 0.0000 0.9758 0.000 1.000 0.000
#> GSM97827 2 0.0000 0.9758 0.000 1.000 0.000
#> GSM97828 3 0.5229 0.8075 0.068 0.104 0.828
#> GSM97833 2 0.0000 0.9758 0.000 1.000 0.000
#> GSM97834 2 0.0000 0.9758 0.000 1.000 0.000
#> GSM97840 2 0.0000 0.9758 0.000 1.000 0.000
#> GSM97846 2 0.0000 0.9758 0.000 1.000 0.000
#> GSM97848 2 0.0000 0.9758 0.000 1.000 0.000
#> GSM97849 2 0.0000 0.9758 0.000 1.000 0.000
#> GSM97850 2 0.0000 0.9758 0.000 1.000 0.000
#> GSM97853 2 0.0000 0.9758 0.000 1.000 0.000
#> GSM97855 2 0.0000 0.9758 0.000 1.000 0.000
#> GSM97878 1 0.4654 0.7914 0.792 0.000 0.208
#> GSM97913 2 0.2918 0.9108 0.032 0.924 0.044
#> GSM97932 1 0.0000 0.9131 1.000 0.000 0.000
#> GSM97939 3 0.0000 0.9397 0.000 0.000 1.000
#> GSM97951 2 0.0000 0.9758 0.000 1.000 0.000
#> GSM97957 3 0.0000 0.9397 0.000 0.000 1.000
#> GSM97972 3 0.0000 0.9397 0.000 0.000 1.000
#> GSM97793 3 0.1163 0.9245 0.028 0.000 0.972
#> GSM97795 2 0.3816 0.8271 0.000 0.852 0.148
#> GSM97802 3 0.1860 0.9063 0.052 0.000 0.948
#> GSM97810 3 0.3816 0.7743 0.000 0.148 0.852
#> GSM97815 3 0.0000 0.9397 0.000 0.000 1.000
#> GSM97837 1 0.3941 0.8429 0.844 0.000 0.156
#> GSM97843 3 0.0000 0.9397 0.000 0.000 1.000
#> GSM97890 3 0.0237 0.9384 0.004 0.000 0.996
#> GSM97899 1 0.0000 0.9131 1.000 0.000 0.000
#> GSM97910 1 0.6126 0.4656 0.600 0.000 0.400
#> GSM97916 1 0.5968 0.5453 0.636 0.000 0.364
#> GSM97920 3 0.0000 0.9397 0.000 0.000 1.000
#> GSM97921 1 0.5178 0.7347 0.744 0.000 0.256
#> GSM97927 1 0.3686 0.8574 0.860 0.000 0.140
#> GSM97937 1 0.2448 0.8875 0.924 0.000 0.076
#> GSM97941 2 0.0000 0.9758 0.000 1.000 0.000
#> GSM97943 3 0.3816 0.7843 0.148 0.000 0.852
#> GSM97958 3 0.1031 0.9268 0.024 0.000 0.976
#> GSM97960 2 0.1860 0.9303 0.000 0.948 0.052
#> GSM97794 1 0.5216 0.7251 0.740 0.000 0.260
#> GSM97796 1 0.0000 0.9131 1.000 0.000 0.000
#> GSM97797 1 0.5733 0.6226 0.676 0.000 0.324
#> GSM97798 1 0.0000 0.9131 1.000 0.000 0.000
#> GSM97801 1 0.4235 0.8268 0.824 0.000 0.176
#> GSM97806 1 0.3192 0.8722 0.888 0.000 0.112
#> GSM97808 1 0.0000 0.9131 1.000 0.000 0.000
#> GSM97813 1 0.3192 0.8722 0.888 0.000 0.112
#> GSM97814 1 0.0000 0.9131 1.000 0.000 0.000
#> GSM97818 1 0.4062 0.8363 0.836 0.000 0.164
#> GSM97819 3 0.0237 0.9384 0.004 0.000 0.996
#> GSM97821 2 0.7299 0.2466 0.032 0.556 0.412
#> GSM97826 1 0.0237 0.9117 0.996 0.000 0.004
#> GSM97829 1 0.3752 0.8526 0.856 0.000 0.144
#> GSM97832 3 0.4974 0.6487 0.000 0.236 0.764
#> GSM97836 1 0.3267 0.8707 0.884 0.000 0.116
#> GSM97839 1 0.0000 0.9131 1.000 0.000 0.000
#> GSM97844 2 0.0000 0.9758 0.000 1.000 0.000
#> GSM97847 1 0.0000 0.9131 1.000 0.000 0.000
#> GSM97851 1 0.0000 0.9131 1.000 0.000 0.000
#> GSM97852 1 0.0000 0.9131 1.000 0.000 0.000
#> GSM97856 1 0.0000 0.9131 1.000 0.000 0.000
#> GSM97858 2 0.0000 0.9758 0.000 1.000 0.000
#> GSM97859 1 0.3192 0.8722 0.888 0.000 0.112
#> GSM97861 1 0.3879 0.8481 0.848 0.000 0.152
#> GSM97863 1 0.0000 0.9131 1.000 0.000 0.000
#> GSM97869 1 0.5733 0.6219 0.676 0.000 0.324
#> GSM97870 3 0.6192 0.1537 0.420 0.000 0.580
#> GSM97871 1 0.0000 0.9131 1.000 0.000 0.000
#> GSM97877 2 0.5094 0.7819 0.056 0.832 0.112
#> GSM97879 1 0.0000 0.9131 1.000 0.000 0.000
#> GSM97882 1 0.3192 0.8722 0.888 0.000 0.112
#> GSM97885 1 0.3340 0.8679 0.880 0.000 0.120
#> GSM97886 1 0.0000 0.9131 1.000 0.000 0.000
#> GSM97887 1 0.0000 0.9131 1.000 0.000 0.000
#> GSM97888 1 0.0000 0.9131 1.000 0.000 0.000
#> GSM97889 1 0.3686 0.8573 0.860 0.000 0.140
#> GSM97891 1 0.3192 0.8722 0.888 0.000 0.112
#> GSM97892 2 0.0000 0.9758 0.000 1.000 0.000
#> GSM97893 1 0.0000 0.9131 1.000 0.000 0.000
#> GSM97894 1 0.0000 0.9131 1.000 0.000 0.000
#> GSM97895 1 0.0000 0.9131 1.000 0.000 0.000
#> GSM97896 1 0.0000 0.9131 1.000 0.000 0.000
#> GSM97898 1 0.0000 0.9131 1.000 0.000 0.000
#> GSM97903 1 0.3192 0.8722 0.888 0.000 0.112
#> GSM97905 1 0.5948 0.5488 0.640 0.000 0.360
#> GSM97906 1 0.0000 0.9131 1.000 0.000 0.000
#> GSM97908 1 0.0000 0.9131 1.000 0.000 0.000
#> GSM97912 1 0.5835 0.5913 0.660 0.000 0.340
#> GSM97914 1 0.4654 0.7916 0.792 0.000 0.208
#> GSM97915 1 0.0000 0.9131 1.000 0.000 0.000
#> GSM97917 1 0.0000 0.9131 1.000 0.000 0.000
#> GSM97918 1 0.0000 0.9131 1.000 0.000 0.000
#> GSM97919 1 0.0000 0.9131 1.000 0.000 0.000
#> GSM97922 1 0.0000 0.9131 1.000 0.000 0.000
#> GSM97924 2 0.0000 0.9758 0.000 1.000 0.000
#> GSM97926 3 0.1860 0.9063 0.052 0.000 0.948
#> GSM97930 1 0.0000 0.9131 1.000 0.000 0.000
#> GSM97931 3 0.1753 0.9096 0.048 0.000 0.952
#> GSM97935 1 0.3192 0.8722 0.888 0.000 0.112
#> GSM97936 1 0.0000 0.9131 1.000 0.000 0.000
#> GSM97938 1 0.0000 0.9131 1.000 0.000 0.000
#> GSM97940 1 0.0000 0.9131 1.000 0.000 0.000
#> GSM97942 3 0.1289 0.9217 0.032 0.000 0.968
#> GSM97945 1 0.0000 0.9131 1.000 0.000 0.000
#> GSM97946 2 0.0000 0.9758 0.000 1.000 0.000
#> GSM97948 3 0.2796 0.8639 0.092 0.000 0.908
#> GSM97950 1 0.0000 0.9131 1.000 0.000 0.000
#> GSM97952 1 0.0000 0.9131 1.000 0.000 0.000
#> GSM97953 1 0.0000 0.9131 1.000 0.000 0.000
#> GSM97954 1 0.0000 0.9131 1.000 0.000 0.000
#> GSM97955 1 0.0000 0.9131 1.000 0.000 0.000
#> GSM97959 1 0.8495 0.5936 0.612 0.168 0.220
#> GSM97961 1 0.0000 0.9131 1.000 0.000 0.000
#> GSM97963 1 0.0000 0.9131 1.000 0.000 0.000
#> GSM97965 1 0.0000 0.9131 1.000 0.000 0.000
#> GSM97966 1 0.0000 0.9131 1.000 0.000 0.000
#> GSM97967 2 0.0000 0.9758 0.000 1.000 0.000
#> GSM97968 2 0.0000 0.9758 0.000 1.000 0.000
#> GSM97969 1 0.0000 0.9131 1.000 0.000 0.000
#> GSM97971 1 0.3192 0.8722 0.888 0.000 0.112
#> GSM97799 3 0.0000 0.9397 0.000 0.000 1.000
#> GSM97823 2 0.0000 0.9758 0.000 1.000 0.000
#> GSM97824 3 0.0000 0.9397 0.000 0.000 1.000
#> GSM97830 3 0.0000 0.9397 0.000 0.000 1.000
#> GSM97835 3 0.0424 0.9352 0.000 0.008 0.992
#> GSM97838 2 0.0000 0.9758 0.000 1.000 0.000
#> GSM97841 2 0.0000 0.9758 0.000 1.000 0.000
#> GSM97842 3 0.0000 0.9397 0.000 0.000 1.000
#> GSM97854 2 0.0000 0.9758 0.000 1.000 0.000
#> GSM97857 3 0.0000 0.9397 0.000 0.000 1.000
#> GSM97860 3 0.0000 0.9397 0.000 0.000 1.000
#> GSM97862 3 0.0000 0.9397 0.000 0.000 1.000
#> GSM97864 2 0.0000 0.9758 0.000 1.000 0.000
#> GSM97866 3 0.0000 0.9397 0.000 0.000 1.000
#> GSM97868 3 0.0000 0.9397 0.000 0.000 1.000
#> GSM97872 3 0.6140 0.2266 0.404 0.000 0.596
#> GSM97873 3 0.0000 0.9397 0.000 0.000 1.000
#> GSM97874 3 0.0000 0.9397 0.000 0.000 1.000
#> GSM97875 3 0.0237 0.9384 0.004 0.000 0.996
#> GSM97876 3 0.0000 0.9397 0.000 0.000 1.000
#> GSM97880 3 0.0000 0.9397 0.000 0.000 1.000
#> GSM97881 3 0.0237 0.9384 0.004 0.000 0.996
#> GSM97884 3 0.0000 0.9397 0.000 0.000 1.000
#> GSM97901 3 0.0000 0.9397 0.000 0.000 1.000
#> GSM97902 1 0.6267 0.3250 0.548 0.000 0.452
#> GSM97909 2 0.3412 0.8563 0.000 0.876 0.124
#> GSM97911 3 0.0000 0.9397 0.000 0.000 1.000
#> GSM97923 3 0.0000 0.9397 0.000 0.000 1.000
#> GSM97928 3 0.6295 -0.0253 0.472 0.000 0.528
#> GSM97929 2 0.0000 0.9758 0.000 1.000 0.000
#> GSM97933 3 0.0592 0.9342 0.012 0.000 0.988
#> GSM97934 3 0.0000 0.9397 0.000 0.000 1.000
#> GSM97944 3 0.0000 0.9397 0.000 0.000 1.000
#> GSM97949 2 0.0000 0.9758 0.000 1.000 0.000
#> GSM97956 3 0.0000 0.9397 0.000 0.000 1.000
#> GSM97962 3 0.0000 0.9397 0.000 0.000 1.000
#> GSM97964 3 0.0000 0.9397 0.000 0.000 1.000
#> GSM97970 3 0.0000 0.9397 0.000 0.000 1.000
#> GSM97822 1 0.3686 0.8571 0.860 0.000 0.140
#> GSM97831 3 0.0000 0.9397 0.000 0.000 1.000
#> GSM97845 1 0.0000 0.9131 1.000 0.000 0.000
#> GSM97865 1 0.3752 0.8538 0.856 0.000 0.144
#> GSM97867 3 0.0424 0.9367 0.008 0.000 0.992
#> GSM97883 3 0.1163 0.9248 0.028 0.000 0.972
#> GSM97897 1 0.0000 0.9131 1.000 0.000 0.000
#> GSM97900 1 0.0000 0.9131 1.000 0.000 0.000
#> GSM97904 1 0.4399 0.8162 0.812 0.000 0.188
#> GSM97907 2 0.0000 0.9758 0.000 1.000 0.000
#> GSM97925 3 0.0237 0.9384 0.004 0.000 0.996
#> GSM97947 3 0.1289 0.9217 0.032 0.000 0.968
cbind(get_classes(res, k = 4), get_membership(res, k = 4))
#> class entropy silhouette p1 p2 p3 p4
#> GSM97800 2 0.0000 0.9902 0.000 1.000 0.000 0.000
#> GSM97803 2 0.0000 0.9902 0.000 1.000 0.000 0.000
#> GSM97804 2 0.0000 0.9902 0.000 1.000 0.000 0.000
#> GSM97805 2 0.0000 0.9902 0.000 1.000 0.000 0.000
#> GSM97807 2 0.0000 0.9902 0.000 1.000 0.000 0.000
#> GSM97809 2 0.0000 0.9902 0.000 1.000 0.000 0.000
#> GSM97811 2 0.0000 0.9902 0.000 1.000 0.000 0.000
#> GSM97812 2 0.0000 0.9902 0.000 1.000 0.000 0.000
#> GSM97816 3 0.5649 0.3431 0.028 0.392 0.580 0.000
#> GSM97817 2 0.0000 0.9902 0.000 1.000 0.000 0.000
#> GSM97820 2 0.0000 0.9902 0.000 1.000 0.000 0.000
#> GSM97825 2 0.0000 0.9902 0.000 1.000 0.000 0.000
#> GSM97827 2 0.0000 0.9902 0.000 1.000 0.000 0.000
#> GSM97828 1 0.4967 0.2071 0.548 0.000 0.452 0.000
#> GSM97833 2 0.0000 0.9902 0.000 1.000 0.000 0.000
#> GSM97834 2 0.0000 0.9902 0.000 1.000 0.000 0.000
#> GSM97840 2 0.0000 0.9902 0.000 1.000 0.000 0.000
#> GSM97846 2 0.0000 0.9902 0.000 1.000 0.000 0.000
#> GSM97848 2 0.0000 0.9902 0.000 1.000 0.000 0.000
#> GSM97849 2 0.0000 0.9902 0.000 1.000 0.000 0.000
#> GSM97850 2 0.0000 0.9902 0.000 1.000 0.000 0.000
#> GSM97853 2 0.0000 0.9902 0.000 1.000 0.000 0.000
#> GSM97855 2 0.0000 0.9902 0.000 1.000 0.000 0.000
#> GSM97878 1 0.0000 0.8814 1.000 0.000 0.000 0.000
#> GSM97913 1 0.0000 0.8814 1.000 0.000 0.000 0.000
#> GSM97932 4 0.0000 0.9550 0.000 0.000 0.000 1.000
#> GSM97939 3 0.0000 0.9528 0.000 0.000 1.000 0.000
#> GSM97951 2 0.0000 0.9902 0.000 1.000 0.000 0.000
#> GSM97957 3 0.0000 0.9528 0.000 0.000 1.000 0.000
#> GSM97972 3 0.2647 0.8330 0.120 0.000 0.880 0.000
#> GSM97793 3 0.0000 0.9528 0.000 0.000 1.000 0.000
#> GSM97795 2 0.4543 0.5203 0.000 0.676 0.324 0.000
#> GSM97802 3 0.4072 0.6424 0.252 0.000 0.748 0.000
#> GSM97810 3 0.1302 0.9193 0.000 0.044 0.956 0.000
#> GSM97815 3 0.0336 0.9473 0.000 0.008 0.992 0.000
#> GSM97837 1 0.0000 0.8814 1.000 0.000 0.000 0.000
#> GSM97843 3 0.0000 0.9528 0.000 0.000 1.000 0.000
#> GSM97890 3 0.0000 0.9528 0.000 0.000 1.000 0.000
#> GSM97899 4 0.0000 0.9550 0.000 0.000 0.000 1.000
#> GSM97910 1 0.0000 0.8814 1.000 0.000 0.000 0.000
#> GSM97916 1 0.0000 0.8814 1.000 0.000 0.000 0.000
#> GSM97920 3 0.2081 0.8762 0.084 0.000 0.916 0.000
#> GSM97921 1 0.0000 0.8814 1.000 0.000 0.000 0.000
#> GSM97927 1 0.0707 0.8719 0.980 0.000 0.000 0.020
#> GSM97937 1 0.0000 0.8814 1.000 0.000 0.000 0.000
#> GSM97941 2 0.0000 0.9902 0.000 1.000 0.000 0.000
#> GSM97943 1 0.2868 0.7857 0.864 0.000 0.136 0.000
#> GSM97958 1 0.4989 0.1392 0.528 0.000 0.472 0.000
#> GSM97960 2 0.1118 0.9538 0.000 0.964 0.036 0.000
#> GSM97794 1 0.0000 0.8814 1.000 0.000 0.000 0.000
#> GSM97796 4 0.0000 0.9550 0.000 0.000 0.000 1.000
#> GSM97797 1 0.0000 0.8814 1.000 0.000 0.000 0.000
#> GSM97798 4 0.0000 0.9550 0.000 0.000 0.000 1.000
#> GSM97801 1 0.0000 0.8814 1.000 0.000 0.000 0.000
#> GSM97806 1 0.0000 0.8814 1.000 0.000 0.000 0.000
#> GSM97808 4 0.0000 0.9550 0.000 0.000 0.000 1.000
#> GSM97813 1 0.1302 0.8565 0.956 0.000 0.000 0.044
#> GSM97814 4 0.0000 0.9550 0.000 0.000 0.000 1.000
#> GSM97818 1 0.0000 0.8814 1.000 0.000 0.000 0.000
#> GSM97819 3 0.0000 0.9528 0.000 0.000 1.000 0.000
#> GSM97821 1 0.6764 0.3747 0.556 0.332 0.112 0.000
#> GSM97826 1 0.0000 0.8814 1.000 0.000 0.000 0.000
#> GSM97829 1 0.0000 0.8814 1.000 0.000 0.000 0.000
#> GSM97832 3 0.3123 0.7925 0.000 0.156 0.844 0.000
#> GSM97836 1 0.0000 0.8814 1.000 0.000 0.000 0.000
#> GSM97839 4 0.0000 0.9550 0.000 0.000 0.000 1.000
#> GSM97844 2 0.0000 0.9902 0.000 1.000 0.000 0.000
#> GSM97847 1 0.0000 0.8814 1.000 0.000 0.000 0.000
#> GSM97851 4 0.0000 0.9550 0.000 0.000 0.000 1.000
#> GSM97852 1 0.0000 0.8814 1.000 0.000 0.000 0.000
#> GSM97856 4 0.0000 0.9550 0.000 0.000 0.000 1.000
#> GSM97858 2 0.0000 0.9902 0.000 1.000 0.000 0.000
#> GSM97859 1 0.0000 0.8814 1.000 0.000 0.000 0.000
#> GSM97861 1 0.1211 0.8593 0.960 0.000 0.000 0.040
#> GSM97863 4 0.0000 0.9550 0.000 0.000 0.000 1.000
#> GSM97869 1 0.0000 0.8814 1.000 0.000 0.000 0.000
#> GSM97870 1 0.0336 0.8782 0.992 0.000 0.008 0.000
#> GSM97871 4 0.0000 0.9550 0.000 0.000 0.000 1.000
#> GSM97877 1 0.0188 0.8796 0.996 0.004 0.000 0.000
#> GSM97879 1 0.4843 0.3411 0.604 0.000 0.000 0.396
#> GSM97882 1 0.0000 0.8814 1.000 0.000 0.000 0.000
#> GSM97885 1 0.0000 0.8814 1.000 0.000 0.000 0.000
#> GSM97886 4 0.0000 0.9550 0.000 0.000 0.000 1.000
#> GSM97887 4 0.0000 0.9550 0.000 0.000 0.000 1.000
#> GSM97888 4 0.4103 0.6278 0.256 0.000 0.000 0.744
#> GSM97889 4 0.4482 0.6059 0.264 0.000 0.008 0.728
#> GSM97891 1 0.0188 0.8797 0.996 0.000 0.000 0.004
#> GSM97892 2 0.0000 0.9902 0.000 1.000 0.000 0.000
#> GSM97893 4 0.0000 0.9550 0.000 0.000 0.000 1.000
#> GSM97894 4 0.0000 0.9550 0.000 0.000 0.000 1.000
#> GSM97895 4 0.0000 0.9550 0.000 0.000 0.000 1.000
#> GSM97896 4 0.0000 0.9550 0.000 0.000 0.000 1.000
#> GSM97898 4 0.0000 0.9550 0.000 0.000 0.000 1.000
#> GSM97903 1 0.0000 0.8814 1.000 0.000 0.000 0.000
#> GSM97905 3 0.6139 0.1992 0.404 0.000 0.544 0.052
#> GSM97906 4 0.0000 0.9550 0.000 0.000 0.000 1.000
#> GSM97908 4 0.4996 0.0126 0.484 0.000 0.000 0.516
#> GSM97912 1 0.0921 0.8679 0.972 0.000 0.028 0.000
#> GSM97914 1 0.0000 0.8814 1.000 0.000 0.000 0.000
#> GSM97915 4 0.0000 0.9550 0.000 0.000 0.000 1.000
#> GSM97917 4 0.0000 0.9550 0.000 0.000 0.000 1.000
#> GSM97918 4 0.0000 0.9550 0.000 0.000 0.000 1.000
#> GSM97919 4 0.0000 0.9550 0.000 0.000 0.000 1.000
#> GSM97922 1 0.4605 0.4644 0.664 0.000 0.000 0.336
#> GSM97924 2 0.0000 0.9902 0.000 1.000 0.000 0.000
#> GSM97926 3 0.1118 0.9264 0.036 0.000 0.964 0.000
#> GSM97930 1 0.0000 0.8814 1.000 0.000 0.000 0.000
#> GSM97931 1 0.3726 0.6974 0.788 0.000 0.212 0.000
#> GSM97935 1 0.1118 0.8619 0.964 0.000 0.000 0.036
#> GSM97936 4 0.0000 0.9550 0.000 0.000 0.000 1.000
#> GSM97938 4 0.4134 0.6103 0.260 0.000 0.000 0.740
#> GSM97940 4 0.0000 0.9550 0.000 0.000 0.000 1.000
#> GSM97942 3 0.0000 0.9528 0.000 0.000 1.000 0.000
#> GSM97945 4 0.0000 0.9550 0.000 0.000 0.000 1.000
#> GSM97946 2 0.0000 0.9902 0.000 1.000 0.000 0.000
#> GSM97948 3 0.4193 0.6142 0.268 0.000 0.732 0.000
#> GSM97950 4 0.0000 0.9550 0.000 0.000 0.000 1.000
#> GSM97952 4 0.0000 0.9550 0.000 0.000 0.000 1.000
#> GSM97953 1 0.4040 0.6232 0.752 0.000 0.000 0.248
#> GSM97954 1 0.4008 0.6397 0.756 0.000 0.000 0.244
#> GSM97955 4 0.0000 0.9550 0.000 0.000 0.000 1.000
#> GSM97959 1 0.0000 0.8814 1.000 0.000 0.000 0.000
#> GSM97961 4 0.0000 0.9550 0.000 0.000 0.000 1.000
#> GSM97963 4 0.0000 0.9550 0.000 0.000 0.000 1.000
#> GSM97965 4 0.0000 0.9550 0.000 0.000 0.000 1.000
#> GSM97966 4 0.0000 0.9550 0.000 0.000 0.000 1.000
#> GSM97967 2 0.0000 0.9902 0.000 1.000 0.000 0.000
#> GSM97968 2 0.0000 0.9902 0.000 1.000 0.000 0.000
#> GSM97969 1 0.4761 0.3820 0.628 0.000 0.000 0.372
#> GSM97971 1 0.0000 0.8814 1.000 0.000 0.000 0.000
#> GSM97799 3 0.0000 0.9528 0.000 0.000 1.000 0.000
#> GSM97823 2 0.0000 0.9902 0.000 1.000 0.000 0.000
#> GSM97824 3 0.0000 0.9528 0.000 0.000 1.000 0.000
#> GSM97830 3 0.0000 0.9528 0.000 0.000 1.000 0.000
#> GSM97835 3 0.0921 0.9313 0.000 0.028 0.972 0.000
#> GSM97838 2 0.0000 0.9902 0.000 1.000 0.000 0.000
#> GSM97841 2 0.0000 0.9902 0.000 1.000 0.000 0.000
#> GSM97842 3 0.0000 0.9528 0.000 0.000 1.000 0.000
#> GSM97854 2 0.0000 0.9902 0.000 1.000 0.000 0.000
#> GSM97857 3 0.0000 0.9528 0.000 0.000 1.000 0.000
#> GSM97860 3 0.0000 0.9528 0.000 0.000 1.000 0.000
#> GSM97862 3 0.0000 0.9528 0.000 0.000 1.000 0.000
#> GSM97864 2 0.0000 0.9902 0.000 1.000 0.000 0.000
#> GSM97866 3 0.0000 0.9528 0.000 0.000 1.000 0.000
#> GSM97868 3 0.0000 0.9528 0.000 0.000 1.000 0.000
#> GSM97872 1 0.4866 0.3255 0.596 0.000 0.404 0.000
#> GSM97873 3 0.0000 0.9528 0.000 0.000 1.000 0.000
#> GSM97874 3 0.0000 0.9528 0.000 0.000 1.000 0.000
#> GSM97875 3 0.0000 0.9528 0.000 0.000 1.000 0.000
#> GSM97876 3 0.0000 0.9528 0.000 0.000 1.000 0.000
#> GSM97880 3 0.0000 0.9528 0.000 0.000 1.000 0.000
#> GSM97881 3 0.0000 0.9528 0.000 0.000 1.000 0.000
#> GSM97884 3 0.0000 0.9528 0.000 0.000 1.000 0.000
#> GSM97901 3 0.0000 0.9528 0.000 0.000 1.000 0.000
#> GSM97902 1 0.3569 0.7222 0.804 0.000 0.196 0.000
#> GSM97909 1 0.6200 0.3769 0.580 0.356 0.064 0.000
#> GSM97911 3 0.0000 0.9528 0.000 0.000 1.000 0.000
#> GSM97923 3 0.0000 0.9528 0.000 0.000 1.000 0.000
#> GSM97928 1 0.4898 0.2890 0.584 0.000 0.416 0.000
#> GSM97929 2 0.0000 0.9902 0.000 1.000 0.000 0.000
#> GSM97933 3 0.0000 0.9528 0.000 0.000 1.000 0.000
#> GSM97934 3 0.0000 0.9528 0.000 0.000 1.000 0.000
#> GSM97944 3 0.0000 0.9528 0.000 0.000 1.000 0.000
#> GSM97949 2 0.0000 0.9902 0.000 1.000 0.000 0.000
#> GSM97956 3 0.0000 0.9528 0.000 0.000 1.000 0.000
#> GSM97962 3 0.0000 0.9528 0.000 0.000 1.000 0.000
#> GSM97964 3 0.0000 0.9528 0.000 0.000 1.000 0.000
#> GSM97970 3 0.0000 0.9528 0.000 0.000 1.000 0.000
#> GSM97822 1 0.0921 0.8670 0.972 0.000 0.000 0.028
#> GSM97831 3 0.0000 0.9528 0.000 0.000 1.000 0.000
#> GSM97845 1 0.4193 0.6064 0.732 0.000 0.000 0.268
#> GSM97865 1 0.0000 0.8814 1.000 0.000 0.000 0.000
#> GSM97867 3 0.0000 0.9528 0.000 0.000 1.000 0.000
#> GSM97883 3 0.3266 0.7716 0.168 0.000 0.832 0.000
#> GSM97897 4 0.4040 0.6427 0.248 0.000 0.000 0.752
#> GSM97900 4 0.0000 0.9550 0.000 0.000 0.000 1.000
#> GSM97904 1 0.4372 0.6184 0.728 0.000 0.268 0.004
#> GSM97907 2 0.0000 0.9902 0.000 1.000 0.000 0.000
#> GSM97925 3 0.0000 0.9528 0.000 0.000 1.000 0.000
#> GSM97947 3 0.1118 0.9248 0.036 0.000 0.964 0.000
cbind(get_classes(res, k = 5), get_membership(res, k = 5))
#> class entropy silhouette p1 p2 p3 p4 p5
#> GSM97800 2 0.0000 0.9990 0.000 1.000 0.000 0.000 0.000
#> GSM97803 2 0.0000 0.9990 0.000 1.000 0.000 0.000 0.000
#> GSM97804 2 0.0000 0.9990 0.000 1.000 0.000 0.000 0.000
#> GSM97805 2 0.0000 0.9990 0.000 1.000 0.000 0.000 0.000
#> GSM97807 2 0.0000 0.9990 0.000 1.000 0.000 0.000 0.000
#> GSM97809 2 0.0000 0.9990 0.000 1.000 0.000 0.000 0.000
#> GSM97811 2 0.0000 0.9990 0.000 1.000 0.000 0.000 0.000
#> GSM97812 2 0.0000 0.9990 0.000 1.000 0.000 0.000 0.000
#> GSM97816 5 0.7711 -0.3835 0.052 0.304 0.284 0.000 0.360
#> GSM97817 2 0.0000 0.9990 0.000 1.000 0.000 0.000 0.000
#> GSM97820 2 0.0000 0.9990 0.000 1.000 0.000 0.000 0.000
#> GSM97825 2 0.0000 0.9990 0.000 1.000 0.000 0.000 0.000
#> GSM97827 2 0.0000 0.9990 0.000 1.000 0.000 0.000 0.000
#> GSM97828 1 0.6208 0.2018 0.480 0.000 0.144 0.000 0.376
#> GSM97833 2 0.0000 0.9990 0.000 1.000 0.000 0.000 0.000
#> GSM97834 2 0.0000 0.9990 0.000 1.000 0.000 0.000 0.000
#> GSM97840 2 0.0000 0.9990 0.000 1.000 0.000 0.000 0.000
#> GSM97846 2 0.0000 0.9990 0.000 1.000 0.000 0.000 0.000
#> GSM97848 2 0.0000 0.9990 0.000 1.000 0.000 0.000 0.000
#> GSM97849 2 0.0000 0.9990 0.000 1.000 0.000 0.000 0.000
#> GSM97850 2 0.0000 0.9990 0.000 1.000 0.000 0.000 0.000
#> GSM97853 2 0.0000 0.9990 0.000 1.000 0.000 0.000 0.000
#> GSM97855 2 0.0000 0.9990 0.000 1.000 0.000 0.000 0.000
#> GSM97878 1 0.3636 0.2606 0.728 0.000 0.000 0.000 0.272
#> GSM97913 1 0.0000 0.7617 1.000 0.000 0.000 0.000 0.000
#> GSM97932 4 0.0000 0.9767 0.000 0.000 0.000 1.000 0.000
#> GSM97939 3 0.2690 0.8085 0.000 0.000 0.844 0.000 0.156
#> GSM97951 2 0.0000 0.9990 0.000 1.000 0.000 0.000 0.000
#> GSM97957 3 0.4138 0.7545 0.000 0.000 0.616 0.000 0.384
#> GSM97972 3 0.6756 0.4016 0.264 0.000 0.372 0.000 0.364
#> GSM97793 3 0.3876 0.7279 0.000 0.000 0.684 0.000 0.316
#> GSM97795 3 0.4030 0.3488 0.000 0.352 0.648 0.000 0.000
#> GSM97802 3 0.6292 -0.2627 0.152 0.000 0.448 0.000 0.400
#> GSM97810 3 0.3438 0.7968 0.000 0.020 0.808 0.000 0.172
#> GSM97815 3 0.0290 0.8094 0.000 0.008 0.992 0.000 0.000
#> GSM97837 1 0.1197 0.7454 0.952 0.000 0.000 0.000 0.048
#> GSM97843 3 0.4138 0.7545 0.000 0.000 0.616 0.000 0.384
#> GSM97890 3 0.0000 0.8127 0.000 0.000 1.000 0.000 0.000
#> GSM97899 4 0.0000 0.9767 0.000 0.000 0.000 1.000 0.000
#> GSM97910 1 0.0000 0.7617 1.000 0.000 0.000 0.000 0.000
#> GSM97916 1 0.1270 0.7349 0.948 0.000 0.000 0.000 0.052
#> GSM97920 3 0.4599 0.7446 0.016 0.000 0.600 0.000 0.384
#> GSM97921 1 0.0880 0.7488 0.968 0.000 0.000 0.000 0.032
#> GSM97927 5 0.4227 0.6278 0.420 0.000 0.000 0.000 0.580
#> GSM97937 1 0.1341 0.7388 0.944 0.000 0.000 0.000 0.056
#> GSM97941 2 0.0000 0.9990 0.000 1.000 0.000 0.000 0.000
#> GSM97943 1 0.4436 0.4232 0.596 0.000 0.008 0.000 0.396
#> GSM97958 1 0.5702 0.4460 0.628 0.000 0.180 0.000 0.192
#> GSM97960 2 0.0880 0.9618 0.000 0.968 0.032 0.000 0.000
#> GSM97794 1 0.0000 0.7617 1.000 0.000 0.000 0.000 0.000
#> GSM97796 4 0.0000 0.9767 0.000 0.000 0.000 1.000 0.000
#> GSM97797 1 0.0000 0.7617 1.000 0.000 0.000 0.000 0.000
#> GSM97798 4 0.0000 0.9767 0.000 0.000 0.000 1.000 0.000
#> GSM97801 1 0.0000 0.7617 1.000 0.000 0.000 0.000 0.000
#> GSM97806 1 0.1792 0.7019 0.916 0.000 0.000 0.000 0.084
#> GSM97808 4 0.0000 0.9767 0.000 0.000 0.000 1.000 0.000
#> GSM97813 5 0.4470 0.6576 0.372 0.000 0.000 0.012 0.616
#> GSM97814 4 0.0000 0.9767 0.000 0.000 0.000 1.000 0.000
#> GSM97818 1 0.0000 0.7617 1.000 0.000 0.000 0.000 0.000
#> GSM97819 3 0.1671 0.8171 0.000 0.000 0.924 0.000 0.076
#> GSM97821 1 0.3957 0.4895 0.712 0.008 0.280 0.000 0.000
#> GSM97826 1 0.2280 0.6874 0.880 0.000 0.000 0.000 0.120
#> GSM97829 1 0.1478 0.7333 0.936 0.000 0.000 0.000 0.064
#> GSM97832 3 0.3123 0.7990 0.000 0.012 0.828 0.000 0.160
#> GSM97836 5 0.4242 0.6224 0.428 0.000 0.000 0.000 0.572
#> GSM97839 4 0.0000 0.9767 0.000 0.000 0.000 1.000 0.000
#> GSM97844 2 0.0000 0.9990 0.000 1.000 0.000 0.000 0.000
#> GSM97847 1 0.0609 0.7558 0.980 0.000 0.000 0.000 0.020
#> GSM97851 4 0.0000 0.9767 0.000 0.000 0.000 1.000 0.000
#> GSM97852 5 0.4306 0.5223 0.492 0.000 0.000 0.000 0.508
#> GSM97856 4 0.0000 0.9767 0.000 0.000 0.000 1.000 0.000
#> GSM97858 2 0.0000 0.9990 0.000 1.000 0.000 0.000 0.000
#> GSM97859 5 0.4138 0.6515 0.384 0.000 0.000 0.000 0.616
#> GSM97861 5 0.4604 0.6272 0.428 0.000 0.000 0.012 0.560
#> GSM97863 4 0.0000 0.9767 0.000 0.000 0.000 1.000 0.000
#> GSM97869 1 0.1410 0.7292 0.940 0.000 0.000 0.000 0.060
#> GSM97870 5 0.4114 0.6556 0.376 0.000 0.000 0.000 0.624
#> GSM97871 4 0.0000 0.9767 0.000 0.000 0.000 1.000 0.000
#> GSM97877 1 0.0000 0.7617 1.000 0.000 0.000 0.000 0.000
#> GSM97879 5 0.6250 0.4914 0.256 0.000 0.000 0.204 0.540
#> GSM97882 5 0.4278 0.6014 0.452 0.000 0.000 0.000 0.548
#> GSM97885 1 0.3816 0.2094 0.696 0.000 0.000 0.000 0.304
#> GSM97886 4 0.0000 0.9767 0.000 0.000 0.000 1.000 0.000
#> GSM97887 4 0.2852 0.7598 0.000 0.000 0.000 0.828 0.172
#> GSM97888 5 0.5854 0.5144 0.152 0.000 0.000 0.252 0.596
#> GSM97889 5 0.5750 0.5313 0.156 0.000 0.000 0.228 0.616
#> GSM97891 1 0.3003 0.4978 0.812 0.000 0.000 0.000 0.188
#> GSM97892 2 0.0000 0.9990 0.000 1.000 0.000 0.000 0.000
#> GSM97893 4 0.0609 0.9590 0.000 0.000 0.000 0.980 0.020
#> GSM97894 4 0.0000 0.9767 0.000 0.000 0.000 1.000 0.000
#> GSM97895 4 0.0162 0.9737 0.000 0.000 0.000 0.996 0.004
#> GSM97896 4 0.0510 0.9634 0.000 0.000 0.000 0.984 0.016
#> GSM97898 4 0.0000 0.9767 0.000 0.000 0.000 1.000 0.000
#> GSM97903 1 0.0290 0.7599 0.992 0.000 0.000 0.000 0.008
#> GSM97905 5 0.2890 0.5238 0.160 0.000 0.004 0.000 0.836
#> GSM97906 4 0.0000 0.9767 0.000 0.000 0.000 1.000 0.000
#> GSM97908 4 0.5808 0.0821 0.392 0.000 0.000 0.512 0.096
#> GSM97912 5 0.3999 0.6551 0.344 0.000 0.000 0.000 0.656
#> GSM97914 1 0.0000 0.7617 1.000 0.000 0.000 0.000 0.000
#> GSM97915 4 0.0000 0.9767 0.000 0.000 0.000 1.000 0.000
#> GSM97917 4 0.0000 0.9767 0.000 0.000 0.000 1.000 0.000
#> GSM97918 4 0.0000 0.9767 0.000 0.000 0.000 1.000 0.000
#> GSM97919 4 0.0000 0.9767 0.000 0.000 0.000 1.000 0.000
#> GSM97922 5 0.4470 0.6576 0.372 0.000 0.000 0.012 0.616
#> GSM97924 2 0.0000 0.9990 0.000 1.000 0.000 0.000 0.000
#> GSM97926 5 0.4555 0.1906 0.008 0.000 0.472 0.000 0.520
#> GSM97930 1 0.0609 0.7577 0.980 0.000 0.000 0.000 0.020
#> GSM97931 1 0.1571 0.7246 0.936 0.000 0.060 0.000 0.004
#> GSM97935 5 0.4610 0.6236 0.432 0.000 0.000 0.012 0.556
#> GSM97936 4 0.0162 0.9736 0.000 0.000 0.000 0.996 0.004
#> GSM97938 5 0.5889 0.1699 0.100 0.000 0.000 0.428 0.472
#> GSM97940 4 0.0000 0.9767 0.000 0.000 0.000 1.000 0.000
#> GSM97942 3 0.3242 0.7869 0.000 0.000 0.784 0.000 0.216
#> GSM97945 4 0.0000 0.9767 0.000 0.000 0.000 1.000 0.000
#> GSM97946 2 0.0000 0.9990 0.000 1.000 0.000 0.000 0.000
#> GSM97948 5 0.5125 0.5003 0.156 0.000 0.148 0.000 0.696
#> GSM97950 4 0.0000 0.9767 0.000 0.000 0.000 1.000 0.000
#> GSM97952 4 0.0000 0.9767 0.000 0.000 0.000 1.000 0.000
#> GSM97953 1 0.5519 0.3941 0.648 0.000 0.000 0.148 0.204
#> GSM97954 1 0.6191 -0.3426 0.440 0.000 0.000 0.136 0.424
#> GSM97955 4 0.0404 0.9664 0.000 0.000 0.000 0.988 0.012
#> GSM97959 1 0.0000 0.7617 1.000 0.000 0.000 0.000 0.000
#> GSM97961 4 0.0000 0.9767 0.000 0.000 0.000 1.000 0.000
#> GSM97963 4 0.0000 0.9767 0.000 0.000 0.000 1.000 0.000
#> GSM97965 4 0.0000 0.9767 0.000 0.000 0.000 1.000 0.000
#> GSM97966 4 0.0000 0.9767 0.000 0.000 0.000 1.000 0.000
#> GSM97967 2 0.0000 0.9990 0.000 1.000 0.000 0.000 0.000
#> GSM97968 2 0.0000 0.9990 0.000 1.000 0.000 0.000 0.000
#> GSM97969 5 0.4787 0.6563 0.364 0.000 0.000 0.028 0.608
#> GSM97971 5 0.4138 0.6515 0.384 0.000 0.000 0.000 0.616
#> GSM97799 3 0.0000 0.8127 0.000 0.000 1.000 0.000 0.000
#> GSM97823 2 0.0000 0.9990 0.000 1.000 0.000 0.000 0.000
#> GSM97824 3 0.2732 0.8018 0.000 0.000 0.840 0.000 0.160
#> GSM97830 3 0.4138 0.7545 0.000 0.000 0.616 0.000 0.384
#> GSM97835 3 0.0000 0.8127 0.000 0.000 1.000 0.000 0.000
#> GSM97838 2 0.0000 0.9990 0.000 1.000 0.000 0.000 0.000
#> GSM97841 2 0.0000 0.9990 0.000 1.000 0.000 0.000 0.000
#> GSM97842 3 0.0000 0.8127 0.000 0.000 1.000 0.000 0.000
#> GSM97854 2 0.0000 0.9990 0.000 1.000 0.000 0.000 0.000
#> GSM97857 3 0.4138 0.7545 0.000 0.000 0.616 0.000 0.384
#> GSM97860 3 0.3305 0.7877 0.000 0.000 0.776 0.000 0.224
#> GSM97862 3 0.1270 0.8180 0.000 0.000 0.948 0.000 0.052
#> GSM97864 2 0.0000 0.9990 0.000 1.000 0.000 0.000 0.000
#> GSM97866 3 0.3684 0.7928 0.000 0.000 0.720 0.000 0.280
#> GSM97868 3 0.0000 0.8127 0.000 0.000 1.000 0.000 0.000
#> GSM97872 5 0.4482 0.6519 0.348 0.000 0.016 0.000 0.636
#> GSM97873 3 0.0000 0.8127 0.000 0.000 1.000 0.000 0.000
#> GSM97874 3 0.4138 0.7545 0.000 0.000 0.616 0.000 0.384
#> GSM97875 3 0.0000 0.8127 0.000 0.000 1.000 0.000 0.000
#> GSM97876 3 0.2605 0.8093 0.000 0.000 0.852 0.000 0.148
#> GSM97880 3 0.4138 0.7545 0.000 0.000 0.616 0.000 0.384
#> GSM97881 3 0.0000 0.8127 0.000 0.000 1.000 0.000 0.000
#> GSM97884 3 0.0000 0.8127 0.000 0.000 1.000 0.000 0.000
#> GSM97901 3 0.0000 0.8127 0.000 0.000 1.000 0.000 0.000
#> GSM97902 1 0.4101 0.4308 0.628 0.000 0.000 0.000 0.372
#> GSM97909 1 0.5114 0.5068 0.708 0.044 0.216 0.000 0.032
#> GSM97911 3 0.0000 0.8127 0.000 0.000 1.000 0.000 0.000
#> GSM97923 3 0.3143 0.7947 0.000 0.000 0.796 0.000 0.204
#> GSM97928 5 0.5142 0.6375 0.392 0.000 0.044 0.000 0.564
#> GSM97929 2 0.0000 0.9990 0.000 1.000 0.000 0.000 0.000
#> GSM97933 3 0.4278 0.6977 0.000 0.000 0.548 0.000 0.452
#> GSM97934 3 0.4138 0.7545 0.000 0.000 0.616 0.000 0.384
#> GSM97944 3 0.0000 0.8127 0.000 0.000 1.000 0.000 0.000
#> GSM97949 2 0.0000 0.9990 0.000 1.000 0.000 0.000 0.000
#> GSM97956 3 0.2732 0.8018 0.000 0.000 0.840 0.000 0.160
#> GSM97962 3 0.4138 0.7545 0.000 0.000 0.616 0.000 0.384
#> GSM97964 3 0.2732 0.8018 0.000 0.000 0.840 0.000 0.160
#> GSM97970 3 0.0000 0.8127 0.000 0.000 1.000 0.000 0.000
#> GSM97822 5 0.4331 0.6481 0.400 0.000 0.000 0.004 0.596
#> GSM97831 3 0.4126 0.7560 0.000 0.000 0.620 0.000 0.380
#> GSM97845 1 0.6003 0.2419 0.584 0.000 0.000 0.192 0.224
#> GSM97865 1 0.2074 0.6900 0.896 0.000 0.000 0.000 0.104
#> GSM97867 3 0.3366 0.7855 0.000 0.000 0.768 0.000 0.232
#> GSM97883 5 0.4977 -0.3509 0.040 0.000 0.356 0.000 0.604
#> GSM97897 5 0.5827 0.5092 0.144 0.000 0.000 0.260 0.596
#> GSM97900 4 0.0000 0.9767 0.000 0.000 0.000 1.000 0.000
#> GSM97904 5 0.4060 0.5723 0.360 0.000 0.000 0.000 0.640
#> GSM97907 2 0.0000 0.9990 0.000 1.000 0.000 0.000 0.000
#> GSM97925 3 0.1270 0.8177 0.000 0.000 0.948 0.000 0.052
#> GSM97947 3 0.1341 0.7782 0.000 0.000 0.944 0.000 0.056
cbind(get_classes(res, k = 6), get_membership(res, k = 6))
#> class entropy silhouette p1 p2 p3 p4 p5 p6
#> GSM97800 2 0.0000 0.9999 0.000 1.000 0.000 0.000 0.000 0.000
#> GSM97803 2 0.0000 0.9999 0.000 1.000 0.000 0.000 0.000 0.000
#> GSM97804 2 0.0000 0.9999 0.000 1.000 0.000 0.000 0.000 0.000
#> GSM97805 2 0.0000 0.9999 0.000 1.000 0.000 0.000 0.000 0.000
#> GSM97807 2 0.0000 0.9999 0.000 1.000 0.000 0.000 0.000 0.000
#> GSM97809 2 0.0000 0.9999 0.000 1.000 0.000 0.000 0.000 0.000
#> GSM97811 2 0.0000 0.9999 0.000 1.000 0.000 0.000 0.000 0.000
#> GSM97812 2 0.0000 0.9999 0.000 1.000 0.000 0.000 0.000 0.000
#> GSM97816 5 0.2009 0.7566 0.000 0.024 0.000 0.000 0.908 0.068
#> GSM97817 2 0.0000 0.9999 0.000 1.000 0.000 0.000 0.000 0.000
#> GSM97820 2 0.0000 0.9999 0.000 1.000 0.000 0.000 0.000 0.000
#> GSM97825 2 0.0000 0.9999 0.000 1.000 0.000 0.000 0.000 0.000
#> GSM97827 2 0.0000 0.9999 0.000 1.000 0.000 0.000 0.000 0.000
#> GSM97828 5 0.0458 0.8049 0.000 0.000 0.000 0.000 0.984 0.016
#> GSM97833 2 0.0000 0.9999 0.000 1.000 0.000 0.000 0.000 0.000
#> GSM97834 2 0.0000 0.9999 0.000 1.000 0.000 0.000 0.000 0.000
#> GSM97840 2 0.0000 0.9999 0.000 1.000 0.000 0.000 0.000 0.000
#> GSM97846 2 0.0000 0.9999 0.000 1.000 0.000 0.000 0.000 0.000
#> GSM97848 2 0.0000 0.9999 0.000 1.000 0.000 0.000 0.000 0.000
#> GSM97849 2 0.0000 0.9999 0.000 1.000 0.000 0.000 0.000 0.000
#> GSM97850 2 0.0000 0.9999 0.000 1.000 0.000 0.000 0.000 0.000
#> GSM97853 2 0.0000 0.9999 0.000 1.000 0.000 0.000 0.000 0.000
#> GSM97855 2 0.0000 0.9999 0.000 1.000 0.000 0.000 0.000 0.000
#> GSM97878 6 0.3482 0.4487 0.316 0.000 0.000 0.000 0.000 0.684
#> GSM97913 6 0.0000 0.8403 0.000 0.000 0.000 0.000 0.000 1.000
#> GSM97932 4 0.0000 0.9672 0.000 0.000 0.000 1.000 0.000 0.000
#> GSM97939 3 0.3833 0.1956 0.000 0.000 0.556 0.000 0.444 0.000
#> GSM97951 2 0.0000 0.9999 0.000 1.000 0.000 0.000 0.000 0.000
#> GSM97957 5 0.0000 0.8120 0.000 0.000 0.000 0.000 1.000 0.000
#> GSM97972 5 0.2199 0.7449 0.000 0.000 0.020 0.000 0.892 0.088
#> GSM97793 5 0.4096 -0.0463 0.008 0.000 0.484 0.000 0.508 0.000
#> GSM97795 3 0.0000 0.8266 0.000 0.000 1.000 0.000 0.000 0.000
#> GSM97802 1 0.3515 0.5234 0.676 0.000 0.324 0.000 0.000 0.000
#> GSM97810 5 0.3866 -0.0768 0.000 0.000 0.484 0.000 0.516 0.000
#> GSM97815 3 0.0000 0.8266 0.000 0.000 1.000 0.000 0.000 0.000
#> GSM97837 6 0.1007 0.8289 0.044 0.000 0.000 0.000 0.000 0.956
#> GSM97843 5 0.0000 0.8120 0.000 0.000 0.000 0.000 1.000 0.000
#> GSM97890 3 0.0000 0.8266 0.000 0.000 1.000 0.000 0.000 0.000
#> GSM97899 4 0.0000 0.9672 0.000 0.000 0.000 1.000 0.000 0.000
#> GSM97910 6 0.0000 0.8403 0.000 0.000 0.000 0.000 0.000 1.000
#> GSM97916 6 0.2883 0.6616 0.212 0.000 0.000 0.000 0.000 0.788
#> GSM97920 5 0.0000 0.8120 0.000 0.000 0.000 0.000 1.000 0.000
#> GSM97921 6 0.0000 0.8403 0.000 0.000 0.000 0.000 0.000 1.000
#> GSM97927 1 0.1082 0.7926 0.956 0.000 0.000 0.000 0.004 0.040
#> GSM97937 6 0.2631 0.7466 0.180 0.000 0.000 0.000 0.000 0.820
#> GSM97941 2 0.0000 0.9999 0.000 1.000 0.000 0.000 0.000 0.000
#> GSM97943 5 0.1074 0.7935 0.028 0.000 0.000 0.000 0.960 0.012
#> GSM97958 6 0.4184 -0.0410 0.000 0.000 0.012 0.000 0.488 0.500
#> GSM97960 2 0.0146 0.9955 0.000 0.996 0.004 0.000 0.000 0.000
#> GSM97794 6 0.0000 0.8403 0.000 0.000 0.000 0.000 0.000 1.000
#> GSM97796 4 0.0000 0.9672 0.000 0.000 0.000 1.000 0.000 0.000
#> GSM97797 6 0.0000 0.8403 0.000 0.000 0.000 0.000 0.000 1.000
#> GSM97798 4 0.0000 0.9672 0.000 0.000 0.000 1.000 0.000 0.000
#> GSM97801 6 0.0000 0.8403 0.000 0.000 0.000 0.000 0.000 1.000
#> GSM97806 6 0.2491 0.7612 0.164 0.000 0.000 0.000 0.000 0.836
#> GSM97808 4 0.0000 0.9672 0.000 0.000 0.000 1.000 0.000 0.000
#> GSM97813 1 0.0260 0.7921 0.992 0.000 0.000 0.000 0.000 0.008
#> GSM97814 4 0.0000 0.9672 0.000 0.000 0.000 1.000 0.000 0.000
#> GSM97818 6 0.0000 0.8403 0.000 0.000 0.000 0.000 0.000 1.000
#> GSM97819 3 0.1895 0.7765 0.016 0.000 0.912 0.000 0.072 0.000
#> GSM97821 6 0.0547 0.8301 0.000 0.000 0.020 0.000 0.000 0.980
#> GSM97826 6 0.3804 0.4281 0.424 0.000 0.000 0.000 0.000 0.576
#> GSM97829 6 0.3101 0.6904 0.244 0.000 0.000 0.000 0.000 0.756
#> GSM97832 3 0.3867 0.0724 0.000 0.000 0.512 0.000 0.488 0.000
#> GSM97836 1 0.0865 0.7898 0.964 0.000 0.000 0.000 0.000 0.036
#> GSM97839 4 0.0000 0.9672 0.000 0.000 0.000 1.000 0.000 0.000
#> GSM97844 2 0.0000 0.9999 0.000 1.000 0.000 0.000 0.000 0.000
#> GSM97847 6 0.2300 0.7642 0.144 0.000 0.000 0.000 0.000 0.856
#> GSM97851 4 0.0000 0.9672 0.000 0.000 0.000 1.000 0.000 0.000
#> GSM97852 1 0.3288 0.5759 0.724 0.000 0.000 0.000 0.000 0.276
#> GSM97856 4 0.0000 0.9672 0.000 0.000 0.000 1.000 0.000 0.000
#> GSM97858 2 0.0000 0.9999 0.000 1.000 0.000 0.000 0.000 0.000
#> GSM97859 1 0.0363 0.7918 0.988 0.000 0.000 0.000 0.000 0.012
#> GSM97861 1 0.2597 0.7351 0.824 0.000 0.000 0.000 0.000 0.176
#> GSM97863 4 0.0000 0.9672 0.000 0.000 0.000 1.000 0.000 0.000
#> GSM97869 6 0.2996 0.6425 0.228 0.000 0.000 0.000 0.000 0.772
#> GSM97870 1 0.1812 0.7760 0.912 0.000 0.000 0.000 0.080 0.008
#> GSM97871 4 0.0000 0.9672 0.000 0.000 0.000 1.000 0.000 0.000
#> GSM97877 6 0.0000 0.8403 0.000 0.000 0.000 0.000 0.000 1.000
#> GSM97879 1 0.3819 0.6547 0.764 0.000 0.000 0.172 0.000 0.064
#> GSM97882 1 0.2793 0.7226 0.800 0.000 0.000 0.000 0.000 0.200
#> GSM97885 1 0.3866 0.0711 0.516 0.000 0.000 0.000 0.000 0.484
#> GSM97886 4 0.0000 0.9672 0.000 0.000 0.000 1.000 0.000 0.000
#> GSM97887 4 0.2491 0.7724 0.164 0.000 0.000 0.836 0.000 0.000
#> GSM97888 1 0.1267 0.7760 0.940 0.000 0.000 0.060 0.000 0.000
#> GSM97889 1 0.0260 0.7917 0.992 0.000 0.000 0.008 0.000 0.000
#> GSM97891 6 0.2762 0.6653 0.196 0.000 0.000 0.000 0.000 0.804
#> GSM97892 2 0.0000 0.9999 0.000 1.000 0.000 0.000 0.000 0.000
#> GSM97893 4 0.2300 0.8222 0.144 0.000 0.000 0.856 0.000 0.000
#> GSM97894 4 0.0000 0.9672 0.000 0.000 0.000 1.000 0.000 0.000
#> GSM97895 4 0.0000 0.9672 0.000 0.000 0.000 1.000 0.000 0.000
#> GSM97896 4 0.0937 0.9369 0.040 0.000 0.000 0.960 0.000 0.000
#> GSM97898 4 0.0000 0.9672 0.000 0.000 0.000 1.000 0.000 0.000
#> GSM97903 6 0.1765 0.7988 0.096 0.000 0.000 0.000 0.000 0.904
#> GSM97905 1 0.2664 0.7000 0.816 0.000 0.000 0.000 0.184 0.000
#> GSM97906 4 0.0000 0.9672 0.000 0.000 0.000 1.000 0.000 0.000
#> GSM97908 4 0.5989 0.0080 0.248 0.000 0.000 0.432 0.000 0.320
#> GSM97912 1 0.1333 0.7878 0.944 0.000 0.000 0.000 0.048 0.008
#> GSM97914 6 0.0000 0.8403 0.000 0.000 0.000 0.000 0.000 1.000
#> GSM97915 4 0.0000 0.9672 0.000 0.000 0.000 1.000 0.000 0.000
#> GSM97917 4 0.0000 0.9672 0.000 0.000 0.000 1.000 0.000 0.000
#> GSM97918 4 0.0000 0.9672 0.000 0.000 0.000 1.000 0.000 0.000
#> GSM97919 4 0.0000 0.9672 0.000 0.000 0.000 1.000 0.000 0.000
#> GSM97922 1 0.0260 0.7921 0.992 0.000 0.000 0.000 0.000 0.008
#> GSM97924 2 0.0000 0.9999 0.000 1.000 0.000 0.000 0.000 0.000
#> GSM97926 1 0.4397 0.4379 0.596 0.000 0.376 0.000 0.004 0.024
#> GSM97930 6 0.2597 0.7603 0.176 0.000 0.000 0.000 0.000 0.824
#> GSM97931 6 0.0405 0.8360 0.004 0.000 0.000 0.000 0.008 0.988
#> GSM97935 1 0.2793 0.7178 0.800 0.000 0.000 0.000 0.000 0.200
#> GSM97936 4 0.0632 0.9478 0.024 0.000 0.000 0.976 0.000 0.000
#> GSM97938 1 0.4634 0.5217 0.656 0.000 0.000 0.080 0.000 0.264
#> GSM97940 4 0.0000 0.9672 0.000 0.000 0.000 1.000 0.000 0.000
#> GSM97942 3 0.3110 0.6486 0.012 0.000 0.792 0.000 0.196 0.000
#> GSM97945 4 0.0000 0.9672 0.000 0.000 0.000 1.000 0.000 0.000
#> GSM97946 2 0.0000 0.9999 0.000 1.000 0.000 0.000 0.000 0.000
#> GSM97948 1 0.3130 0.7291 0.828 0.000 0.048 0.000 0.124 0.000
#> GSM97950 4 0.0000 0.9672 0.000 0.000 0.000 1.000 0.000 0.000
#> GSM97952 4 0.0000 0.9672 0.000 0.000 0.000 1.000 0.000 0.000
#> GSM97953 6 0.3695 0.4224 0.376 0.000 0.000 0.000 0.000 0.624
#> GSM97954 1 0.4264 0.4085 0.620 0.000 0.000 0.028 0.000 0.352
#> GSM97955 4 0.2219 0.8316 0.136 0.000 0.000 0.864 0.000 0.000
#> GSM97959 6 0.0000 0.8403 0.000 0.000 0.000 0.000 0.000 1.000
#> GSM97961 4 0.0000 0.9672 0.000 0.000 0.000 1.000 0.000 0.000
#> GSM97963 4 0.0000 0.9672 0.000 0.000 0.000 1.000 0.000 0.000
#> GSM97965 4 0.0000 0.9672 0.000 0.000 0.000 1.000 0.000 0.000
#> GSM97966 4 0.0000 0.9672 0.000 0.000 0.000 1.000 0.000 0.000
#> GSM97967 2 0.0000 0.9999 0.000 1.000 0.000 0.000 0.000 0.000
#> GSM97968 2 0.0000 0.9999 0.000 1.000 0.000 0.000 0.000 0.000
#> GSM97969 1 0.1176 0.7894 0.956 0.000 0.000 0.024 0.000 0.020
#> GSM97971 1 0.0260 0.7921 0.992 0.000 0.000 0.000 0.000 0.008
#> GSM97799 3 0.0000 0.8266 0.000 0.000 1.000 0.000 0.000 0.000
#> GSM97823 2 0.0000 0.9999 0.000 1.000 0.000 0.000 0.000 0.000
#> GSM97824 3 0.3868 0.0527 0.000 0.000 0.504 0.000 0.496 0.000
#> GSM97830 5 0.0000 0.8120 0.000 0.000 0.000 0.000 1.000 0.000
#> GSM97835 3 0.0000 0.8266 0.000 0.000 1.000 0.000 0.000 0.000
#> GSM97838 2 0.0000 0.9999 0.000 1.000 0.000 0.000 0.000 0.000
#> GSM97841 2 0.0000 0.9999 0.000 1.000 0.000 0.000 0.000 0.000
#> GSM97842 3 0.0000 0.8266 0.000 0.000 1.000 0.000 0.000 0.000
#> GSM97854 2 0.0000 0.9999 0.000 1.000 0.000 0.000 0.000 0.000
#> GSM97857 5 0.0000 0.8120 0.000 0.000 0.000 0.000 1.000 0.000
#> GSM97860 3 0.4095 0.0487 0.008 0.000 0.512 0.000 0.480 0.000
#> GSM97862 3 0.1204 0.7982 0.000 0.000 0.944 0.000 0.056 0.000
#> GSM97864 2 0.0000 0.9999 0.000 1.000 0.000 0.000 0.000 0.000
#> GSM97866 5 0.3838 0.0544 0.000 0.000 0.448 0.000 0.552 0.000
#> GSM97868 3 0.0000 0.8266 0.000 0.000 1.000 0.000 0.000 0.000
#> GSM97872 1 0.0291 0.7922 0.992 0.000 0.000 0.000 0.004 0.004
#> GSM97873 3 0.0000 0.8266 0.000 0.000 1.000 0.000 0.000 0.000
#> GSM97874 5 0.0260 0.8097 0.008 0.000 0.000 0.000 0.992 0.000
#> GSM97875 3 0.0000 0.8266 0.000 0.000 1.000 0.000 0.000 0.000
#> GSM97876 3 0.2631 0.7043 0.008 0.000 0.840 0.000 0.152 0.000
#> GSM97880 5 0.0260 0.8097 0.008 0.000 0.000 0.000 0.992 0.000
#> GSM97881 3 0.0000 0.8266 0.000 0.000 1.000 0.000 0.000 0.000
#> GSM97884 3 0.0000 0.8266 0.000 0.000 1.000 0.000 0.000 0.000
#> GSM97901 3 0.0363 0.8209 0.000 0.000 0.988 0.000 0.012 0.000
#> GSM97902 5 0.3833 0.1488 0.000 0.000 0.000 0.000 0.556 0.444
#> GSM97909 6 0.4141 0.6376 0.188 0.004 0.068 0.000 0.000 0.740
#> GSM97911 3 0.0000 0.8266 0.000 0.000 1.000 0.000 0.000 0.000
#> GSM97923 3 0.3534 0.5310 0.008 0.000 0.716 0.000 0.276 0.000
#> GSM97928 1 0.2416 0.7437 0.844 0.000 0.000 0.000 0.000 0.156
#> GSM97929 2 0.0000 0.9999 0.000 1.000 0.000 0.000 0.000 0.000
#> GSM97933 5 0.0260 0.8097 0.008 0.000 0.000 0.000 0.992 0.000
#> GSM97934 5 0.0000 0.8120 0.000 0.000 0.000 0.000 1.000 0.000
#> GSM97944 3 0.0000 0.8266 0.000 0.000 1.000 0.000 0.000 0.000
#> GSM97949 2 0.0000 0.9999 0.000 1.000 0.000 0.000 0.000 0.000
#> GSM97956 3 0.3867 0.0724 0.000 0.000 0.512 0.000 0.488 0.000
#> GSM97962 5 0.0000 0.8120 0.000 0.000 0.000 0.000 1.000 0.000
#> GSM97964 3 0.3857 0.1268 0.000 0.000 0.532 0.000 0.468 0.000
#> GSM97970 3 0.0000 0.8266 0.000 0.000 1.000 0.000 0.000 0.000
#> GSM97822 1 0.2378 0.7452 0.848 0.000 0.000 0.000 0.000 0.152
#> GSM97831 5 0.0000 0.8120 0.000 0.000 0.000 0.000 1.000 0.000
#> GSM97845 1 0.5421 -0.0553 0.452 0.000 0.000 0.116 0.000 0.432
#> GSM97865 6 0.0000 0.8403 0.000 0.000 0.000 0.000 0.000 1.000
#> GSM97867 5 0.4184 -0.0504 0.012 0.000 0.484 0.000 0.504 0.000
#> GSM97883 5 0.3578 0.3400 0.340 0.000 0.000 0.000 0.660 0.000
#> GSM97897 1 0.2454 0.7150 0.840 0.000 0.000 0.160 0.000 0.000
#> GSM97900 4 0.0000 0.9672 0.000 0.000 0.000 1.000 0.000 0.000
#> GSM97904 1 0.3861 0.5260 0.640 0.000 0.000 0.000 0.008 0.352
#> GSM97907 2 0.0000 0.9999 0.000 1.000 0.000 0.000 0.000 0.000
#> GSM97925 3 0.0865 0.8091 0.000 0.000 0.964 0.000 0.036 0.000
#> GSM97947 3 0.0547 0.8151 0.020 0.000 0.980 0.000 0.000 0.000
Heatmaps for the consensus matrix. It visualizes the probability of two samples to be in a same group.
consensus_heatmap(res, k = 2)
consensus_heatmap(res, k = 3)
consensus_heatmap(res, k = 4)
consensus_heatmap(res, k = 5)
consensus_heatmap(res, k = 6)
Heatmaps for the membership of samples in all partitions to see how consistent they are:
membership_heatmap(res, k = 2)
membership_heatmap(res, k = 3)
membership_heatmap(res, k = 4)
membership_heatmap(res, k = 5)
membership_heatmap(res, k = 6)
As soon as we have had the classes for columns, we can look for signatures which are significantly different between classes which can be candidate marks for certain classes. Following are the heatmaps for signatures.
Signature heatmaps where rows are scaled:
get_signatures(res, k = 2)
get_signatures(res, k = 3)
get_signatures(res, k = 4)
get_signatures(res, k = 5)
get_signatures(res, k = 6)
Signature heatmaps where rows are not scaled:
get_signatures(res, k = 2, scale_rows = FALSE)
get_signatures(res, k = 3, scale_rows = FALSE)
get_signatures(res, k = 4, scale_rows = FALSE)
get_signatures(res, k = 5, scale_rows = FALSE)
get_signatures(res, k = 6, scale_rows = FALSE)
Compare the overlap of signatures from different k:
compare_signatures(res)
get_signature() returns a data frame invisibly. TO get the list of signatures, the function
call should be assigned to a variable explicitly. In following code, if plot argument is set
to FALSE, no heatmap is plotted while only the differential analysis is performed.
# code only for demonstration
tb = get_signature(res, k = ..., plot = FALSE)
An example of the output of tb is:
#> which_row fdr mean_1 mean_2 scaled_mean_1 scaled_mean_2 km
#> 1 38 0.042760348 8.373488 9.131774 -0.5533452 0.5164555 1
#> 2 40 0.018707592 7.106213 8.469186 -0.6173731 0.5762149 1
#> 3 55 0.019134737 10.221463 11.207825 -0.6159697 0.5749050 1
#> 4 59 0.006059896 5.921854 7.869574 -0.6899429 0.6439467 1
#> 5 60 0.018055526 8.928898 10.211722 -0.6204761 0.5791110 1
#> 6 98 0.009384629 15.714769 14.887706 0.6635654 -0.6193277 2
...
The columns in tb are:
which_row: row indices corresponding to the input matrix.fdr: FDR for the differential test. mean_x: The mean value in group x.scaled_mean_x: The mean value in group x after rows are scaled.km: Row groups if k-means clustering is applied to rows.UMAP plot which shows how samples are separated.
dimension_reduction(res, k = 2, method = "UMAP")
dimension_reduction(res, k = 3, method = "UMAP")
dimension_reduction(res, k = 4, method = "UMAP")
dimension_reduction(res, k = 5, method = "UMAP")
dimension_reduction(res, k = 6, method = "UMAP")
Following heatmap shows how subgroups are split when increasing k:
collect_classes(res)
Test correlation between subgroups and known annotations. If the known annotation is numeric, one-way ANOVA test is applied, and if the known annotation is discrete, chi-squared contingency table test is applied.
test_to_known_factors(res)
#> n disease.state(p) tissue(p) k
#> SD:pam 179 1.15e-15 1.20e-15 2
#> SD:pam 173 5.05e-28 3.30e-29 3
#> SD:pam 168 2.69e-28 3.94e-29 4
#> SD:pam 160 3.88e-27 3.47e-27 5
#> SD:pam 159 2.35e-23 4.76e-23 6
If matrix rows can be associated to genes, consider to use functional_enrichment(res,
...) to perform function enrichment for the signature genes. See this vignette for more detailed explanations.
The object with results only for a single top-value method and a single partition method can be extracted as:
res = res_list["SD", "mclust"]
# you can also extract it by
# res = res_list["SD:mclust"]
A summary of res and all the functions that can be applied to it:
res
#> A 'ConsensusPartition' object with k = 2, 3, 4, 5, 6.
#> On a matrix with 51882 rows and 180 columns.
#> Top rows (1000, 2000, 3000, 4000, 5000) are extracted by 'SD' method.
#> Subgroups are detected by 'mclust' method.
#> Performed in total 1250 partitions by row resampling.
#> Best k for subgroups seems to be 4.
#>
#> Following methods can be applied to this 'ConsensusPartition' object:
#> [1] "cola_report" "collect_classes" "collect_plots"
#> [4] "collect_stats" "colnames" "compare_signatures"
#> [7] "consensus_heatmap" "dimension_reduction" "functional_enrichment"
#> [10] "get_anno_col" "get_anno" "get_classes"
#> [13] "get_consensus" "get_matrix" "get_membership"
#> [16] "get_param" "get_signatures" "get_stats"
#> [19] "is_best_k" "is_stable_k" "membership_heatmap"
#> [22] "ncol" "nrow" "plot_ecdf"
#> [25] "rownames" "select_partition_number" "show"
#> [28] "suggest_best_k" "test_to_known_factors"
collect_plots() function collects all the plots made from res for all k (number of partitions)
into one single page to provide an easy and fast comparison between different k.
collect_plots(res)
The plots are:
k and the heatmap of
predicted classes for each k.k.k.k.All the plots in panels can be made by individual functions and they are plotted later in this section.
select_partition_number() produces several plots showing different
statistics for choosing “optimized” k. There are following statistics:
k;k, the area increased is defined as \(A_k - A_{k-1}\).The detailed explanations of these statistics can be found in the cola vignette.
Generally speaking, lower PAC score, higher mean silhouette score or higher
concordance corresponds to better partition. Rand index and Jaccard index
measure how similar the current partition is compared to partition with k-1.
If they are too similar, we won't accept k is better than k-1.
select_partition_number(res)
The numeric values for all these statistics can be obtained by get_stats().
get_stats(res)
#> k 1-PAC mean_silhouette concordance area_increased Rand Jaccard
#> 2 2 1.000 0.997 0.999 0.3275 0.672 0.672
#> 3 3 0.614 0.786 0.887 0.8404 0.683 0.531
#> 4 4 0.957 0.919 0.970 0.2148 0.827 0.567
#> 5 5 0.872 0.834 0.911 0.0606 0.943 0.789
#> 6 6 0.833 0.766 0.861 0.0319 0.971 0.870
suggest_best_k() suggests the best \(k\) based on these statistics. The rules are as follows:
suggest_best_k(res)
#> [1] 4
#> attr(,"optional")
#> [1] 2
There is also optional best \(k\) = 2 that is worth to check.
Following shows the table of the partitions (You need to click the show/hide
code output link to see it). The membership matrix (columns with name p*)
is inferred by
clue::cl_consensus()
function with the SE method. Basically the value in the membership matrix
represents the probability to belong to a certain group. The finall class
label for an item is determined with the group with highest probability it
belongs to.
In get_classes() function, the entropy is calculated from the membership
matrix and the silhouette score is calculated from the consensus matrix.
cbind(get_classes(res, k = 2), get_membership(res, k = 2))
#> class entropy silhouette p1 p2
#> GSM97800 2 0.0000 0.993 0.000 1.000
#> GSM97803 2 0.0000 0.993 0.000 1.000
#> GSM97804 2 0.0000 0.993 0.000 1.000
#> GSM97805 2 0.0000 0.993 0.000 1.000
#> GSM97807 2 0.0000 0.993 0.000 1.000
#> GSM97809 2 0.0000 0.993 0.000 1.000
#> GSM97811 2 0.0000 0.993 0.000 1.000
#> GSM97812 2 0.0000 0.993 0.000 1.000
#> GSM97816 1 0.0000 1.000 1.000 0.000
#> GSM97817 2 0.0000 0.993 0.000 1.000
#> GSM97820 2 0.0000 0.993 0.000 1.000
#> GSM97825 2 0.0000 0.993 0.000 1.000
#> GSM97827 2 0.0000 0.993 0.000 1.000
#> GSM97828 1 0.0000 1.000 1.000 0.000
#> GSM97833 2 0.0000 0.993 0.000 1.000
#> GSM97834 2 0.0000 0.993 0.000 1.000
#> GSM97840 2 0.7815 0.698 0.232 0.768
#> GSM97846 2 0.0000 0.993 0.000 1.000
#> GSM97848 2 0.0000 0.993 0.000 1.000
#> GSM97849 2 0.0000 0.993 0.000 1.000
#> GSM97850 2 0.0000 0.993 0.000 1.000
#> GSM97853 2 0.0000 0.993 0.000 1.000
#> GSM97855 2 0.0000 0.993 0.000 1.000
#> GSM97878 1 0.0000 1.000 1.000 0.000
#> GSM97913 1 0.0000 1.000 1.000 0.000
#> GSM97932 1 0.0000 1.000 1.000 0.000
#> GSM97939 1 0.0000 1.000 1.000 0.000
#> GSM97951 2 0.0376 0.990 0.004 0.996
#> GSM97957 1 0.0000 1.000 1.000 0.000
#> GSM97972 1 0.0000 1.000 1.000 0.000
#> GSM97793 1 0.0000 1.000 1.000 0.000
#> GSM97795 1 0.0000 1.000 1.000 0.000
#> GSM97802 1 0.0000 1.000 1.000 0.000
#> GSM97810 1 0.0000 1.000 1.000 0.000
#> GSM97815 1 0.0000 1.000 1.000 0.000
#> GSM97837 1 0.0000 1.000 1.000 0.000
#> GSM97843 1 0.0000 1.000 1.000 0.000
#> GSM97890 1 0.0000 1.000 1.000 0.000
#> GSM97899 1 0.0000 1.000 1.000 0.000
#> GSM97910 1 0.0000 1.000 1.000 0.000
#> GSM97916 1 0.0000 1.000 1.000 0.000
#> GSM97920 1 0.0000 1.000 1.000 0.000
#> GSM97921 1 0.0000 1.000 1.000 0.000
#> GSM97927 1 0.0000 1.000 1.000 0.000
#> GSM97937 1 0.0000 1.000 1.000 0.000
#> GSM97941 1 0.0000 1.000 1.000 0.000
#> GSM97943 1 0.0000 1.000 1.000 0.000
#> GSM97958 1 0.0000 1.000 1.000 0.000
#> GSM97960 1 0.0000 1.000 1.000 0.000
#> GSM97794 1 0.0000 1.000 1.000 0.000
#> GSM97796 1 0.0000 1.000 1.000 0.000
#> GSM97797 1 0.0000 1.000 1.000 0.000
#> GSM97798 1 0.0000 1.000 1.000 0.000
#> GSM97801 1 0.0000 1.000 1.000 0.000
#> GSM97806 1 0.0000 1.000 1.000 0.000
#> GSM97808 1 0.0000 1.000 1.000 0.000
#> GSM97813 1 0.0000 1.000 1.000 0.000
#> GSM97814 1 0.0000 1.000 1.000 0.000
#> GSM97818 1 0.0000 1.000 1.000 0.000
#> GSM97819 1 0.0000 1.000 1.000 0.000
#> GSM97821 1 0.0000 1.000 1.000 0.000
#> GSM97826 1 0.0000 1.000 1.000 0.000
#> GSM97829 1 0.0000 1.000 1.000 0.000
#> GSM97832 1 0.0000 1.000 1.000 0.000
#> GSM97836 1 0.0000 1.000 1.000 0.000
#> GSM97839 1 0.0000 1.000 1.000 0.000
#> GSM97844 2 0.0000 0.993 0.000 1.000
#> GSM97847 1 0.0000 1.000 1.000 0.000
#> GSM97851 1 0.0000 1.000 1.000 0.000
#> GSM97852 1 0.0000 1.000 1.000 0.000
#> GSM97856 1 0.0000 1.000 1.000 0.000
#> GSM97858 2 0.0000 0.993 0.000 1.000
#> GSM97859 1 0.0000 1.000 1.000 0.000
#> GSM97861 1 0.0000 1.000 1.000 0.000
#> GSM97863 1 0.0000 1.000 1.000 0.000
#> GSM97869 1 0.0000 1.000 1.000 0.000
#> GSM97870 1 0.0000 1.000 1.000 0.000
#> GSM97871 1 0.0000 1.000 1.000 0.000
#> GSM97877 1 0.0000 1.000 1.000 0.000
#> GSM97879 1 0.0000 1.000 1.000 0.000
#> GSM97882 1 0.0000 1.000 1.000 0.000
#> GSM97885 1 0.0000 1.000 1.000 0.000
#> GSM97886 1 0.0000 1.000 1.000 0.000
#> GSM97887 1 0.0000 1.000 1.000 0.000
#> GSM97888 1 0.0000 1.000 1.000 0.000
#> GSM97889 1 0.0000 1.000 1.000 0.000
#> GSM97891 1 0.0000 1.000 1.000 0.000
#> GSM97892 2 0.0000 0.993 0.000 1.000
#> GSM97893 1 0.0000 1.000 1.000 0.000
#> GSM97894 1 0.0000 1.000 1.000 0.000
#> GSM97895 1 0.0000 1.000 1.000 0.000
#> GSM97896 1 0.0000 1.000 1.000 0.000
#> GSM97898 1 0.0000 1.000 1.000 0.000
#> GSM97903 1 0.0000 1.000 1.000 0.000
#> GSM97905 1 0.0000 1.000 1.000 0.000
#> GSM97906 1 0.0000 1.000 1.000 0.000
#> GSM97908 1 0.0000 1.000 1.000 0.000
#> GSM97912 1 0.0000 1.000 1.000 0.000
#> GSM97914 1 0.0000 1.000 1.000 0.000
#> GSM97915 1 0.0000 1.000 1.000 0.000
#> GSM97917 1 0.0000 1.000 1.000 0.000
#> GSM97918 1 0.0000 1.000 1.000 0.000
#> GSM97919 1 0.0000 1.000 1.000 0.000
#> GSM97922 1 0.0000 1.000 1.000 0.000
#> GSM97924 2 0.0000 0.993 0.000 1.000
#> GSM97926 1 0.0000 1.000 1.000 0.000
#> GSM97930 1 0.0000 1.000 1.000 0.000
#> GSM97931 1 0.0000 1.000 1.000 0.000
#> GSM97935 1 0.0000 1.000 1.000 0.000
#> GSM97936 1 0.0000 1.000 1.000 0.000
#> GSM97938 1 0.0000 1.000 1.000 0.000
#> GSM97940 1 0.0000 1.000 1.000 0.000
#> GSM97942 1 0.0000 1.000 1.000 0.000
#> GSM97945 1 0.0000 1.000 1.000 0.000
#> GSM97946 2 0.0000 0.993 0.000 1.000
#> GSM97948 1 0.0000 1.000 1.000 0.000
#> GSM97950 1 0.0000 1.000 1.000 0.000
#> GSM97952 1 0.0000 1.000 1.000 0.000
#> GSM97953 1 0.0000 1.000 1.000 0.000
#> GSM97954 1 0.0000 1.000 1.000 0.000
#> GSM97955 1 0.0000 1.000 1.000 0.000
#> GSM97959 1 0.0000 1.000 1.000 0.000
#> GSM97961 1 0.0000 1.000 1.000 0.000
#> GSM97963 1 0.0000 1.000 1.000 0.000
#> GSM97965 1 0.0000 1.000 1.000 0.000
#> GSM97966 1 0.0000 1.000 1.000 0.000
#> GSM97967 2 0.0000 0.993 0.000 1.000
#> GSM97968 2 0.0000 0.993 0.000 1.000
#> GSM97969 1 0.0000 1.000 1.000 0.000
#> GSM97971 1 0.0000 1.000 1.000 0.000
#> GSM97799 1 0.0000 1.000 1.000 0.000
#> GSM97823 2 0.0000 0.993 0.000 1.000
#> GSM97824 1 0.0000 1.000 1.000 0.000
#> GSM97830 1 0.0000 1.000 1.000 0.000
#> GSM97835 1 0.0000 1.000 1.000 0.000
#> GSM97838 2 0.0000 0.993 0.000 1.000
#> GSM97841 2 0.0000 0.993 0.000 1.000
#> GSM97842 1 0.0000 1.000 1.000 0.000
#> GSM97854 2 0.0000 0.993 0.000 1.000
#> GSM97857 1 0.0000 1.000 1.000 0.000
#> GSM97860 1 0.0000 1.000 1.000 0.000
#> GSM97862 1 0.0000 1.000 1.000 0.000
#> GSM97864 2 0.0000 0.993 0.000 1.000
#> GSM97866 1 0.0000 1.000 1.000 0.000
#> GSM97868 1 0.0000 1.000 1.000 0.000
#> GSM97872 1 0.0000 1.000 1.000 0.000
#> GSM97873 1 0.0000 1.000 1.000 0.000
#> GSM97874 1 0.0000 1.000 1.000 0.000
#> GSM97875 1 0.0000 1.000 1.000 0.000
#> GSM97876 1 0.0000 1.000 1.000 0.000
#> GSM97880 1 0.0000 1.000 1.000 0.000
#> GSM97881 1 0.0000 1.000 1.000 0.000
#> GSM97884 1 0.0000 1.000 1.000 0.000
#> GSM97901 1 0.0000 1.000 1.000 0.000
#> GSM97902 1 0.0000 1.000 1.000 0.000
#> GSM97909 1 0.0000 1.000 1.000 0.000
#> GSM97911 1 0.0000 1.000 1.000 0.000
#> GSM97923 1 0.0000 1.000 1.000 0.000
#> GSM97928 1 0.0000 1.000 1.000 0.000
#> GSM97929 2 0.0000 0.993 0.000 1.000
#> GSM97933 1 0.0000 1.000 1.000 0.000
#> GSM97934 1 0.0000 1.000 1.000 0.000
#> GSM97944 1 0.0000 1.000 1.000 0.000
#> GSM97949 2 0.0000 0.993 0.000 1.000
#> GSM97956 1 0.0000 1.000 1.000 0.000
#> GSM97962 1 0.0000 1.000 1.000 0.000
#> GSM97964 1 0.0000 1.000 1.000 0.000
#> GSM97970 1 0.0000 1.000 1.000 0.000
#> GSM97822 1 0.0000 1.000 1.000 0.000
#> GSM97831 1 0.0000 1.000 1.000 0.000
#> GSM97845 1 0.0000 1.000 1.000 0.000
#> GSM97865 1 0.0000 1.000 1.000 0.000
#> GSM97867 1 0.0000 1.000 1.000 0.000
#> GSM97883 1 0.0000 1.000 1.000 0.000
#> GSM97897 1 0.0000 1.000 1.000 0.000
#> GSM97900 1 0.0000 1.000 1.000 0.000
#> GSM97904 1 0.0000 1.000 1.000 0.000
#> GSM97907 2 0.0000 0.993 0.000 1.000
#> GSM97925 1 0.0000 1.000 1.000 0.000
#> GSM97947 1 0.0000 1.000 1.000 0.000
cbind(get_classes(res, k = 3), get_membership(res, k = 3))
#> class entropy silhouette p1 p2 p3
#> GSM97800 2 0.0000 0.990 0.000 1.000 0.000
#> GSM97803 2 0.0000 0.990 0.000 1.000 0.000
#> GSM97804 2 0.0000 0.990 0.000 1.000 0.000
#> GSM97805 2 0.0000 0.990 0.000 1.000 0.000
#> GSM97807 2 0.0000 0.990 0.000 1.000 0.000
#> GSM97809 2 0.0000 0.990 0.000 1.000 0.000
#> GSM97811 2 0.0000 0.990 0.000 1.000 0.000
#> GSM97812 2 0.0000 0.990 0.000 1.000 0.000
#> GSM97816 3 0.6079 0.244 0.388 0.000 0.612
#> GSM97817 2 0.0000 0.990 0.000 1.000 0.000
#> GSM97820 2 0.0000 0.990 0.000 1.000 0.000
#> GSM97825 2 0.0000 0.990 0.000 1.000 0.000
#> GSM97827 2 0.0000 0.990 0.000 1.000 0.000
#> GSM97828 3 0.6168 0.152 0.412 0.000 0.588
#> GSM97833 2 0.0000 0.990 0.000 1.000 0.000
#> GSM97834 2 0.0000 0.990 0.000 1.000 0.000
#> GSM97840 3 0.7970 0.478 0.080 0.324 0.596
#> GSM97846 2 0.0000 0.990 0.000 1.000 0.000
#> GSM97848 2 0.0000 0.990 0.000 1.000 0.000
#> GSM97849 2 0.0000 0.990 0.000 1.000 0.000
#> GSM97850 2 0.0000 0.990 0.000 1.000 0.000
#> GSM97853 2 0.0000 0.990 0.000 1.000 0.000
#> GSM97855 2 0.0000 0.990 0.000 1.000 0.000
#> GSM97878 1 0.5327 0.780 0.728 0.000 0.272
#> GSM97913 3 0.6095 0.230 0.392 0.000 0.608
#> GSM97932 1 0.0592 0.781 0.988 0.000 0.012
#> GSM97939 3 0.0000 0.859 0.000 0.000 1.000
#> GSM97951 2 0.5706 0.521 0.000 0.680 0.320
#> GSM97957 3 0.0000 0.859 0.000 0.000 1.000
#> GSM97972 3 0.6079 0.244 0.388 0.000 0.612
#> GSM97793 3 0.0000 0.859 0.000 0.000 1.000
#> GSM97795 3 0.0000 0.859 0.000 0.000 1.000
#> GSM97802 1 0.6308 0.258 0.508 0.000 0.492
#> GSM97810 3 0.0000 0.859 0.000 0.000 1.000
#> GSM97815 3 0.0000 0.859 0.000 0.000 1.000
#> GSM97837 1 0.5988 0.628 0.632 0.000 0.368
#> GSM97843 3 0.0000 0.859 0.000 0.000 1.000
#> GSM97890 3 0.0000 0.859 0.000 0.000 1.000
#> GSM97899 1 0.0000 0.778 1.000 0.000 0.000
#> GSM97910 1 0.6111 0.565 0.604 0.000 0.396
#> GSM97916 1 0.5560 0.745 0.700 0.000 0.300
#> GSM97920 3 0.0000 0.859 0.000 0.000 1.000
#> GSM97921 1 0.5138 0.801 0.748 0.000 0.252
#> GSM97927 1 0.4887 0.821 0.772 0.000 0.228
#> GSM97937 1 0.5216 0.793 0.740 0.000 0.260
#> GSM97941 3 0.6062 0.256 0.384 0.000 0.616
#> GSM97943 3 0.6192 0.117 0.420 0.000 0.580
#> GSM97958 3 0.6079 0.244 0.388 0.000 0.612
#> GSM97960 3 0.0000 0.859 0.000 0.000 1.000
#> GSM97794 1 0.5926 0.652 0.644 0.000 0.356
#> GSM97796 1 0.0000 0.778 1.000 0.000 0.000
#> GSM97797 1 0.6140 0.546 0.596 0.000 0.404
#> GSM97798 1 0.0000 0.778 1.000 0.000 0.000
#> GSM97801 1 0.5785 0.695 0.668 0.000 0.332
#> GSM97806 1 0.4887 0.821 0.772 0.000 0.228
#> GSM97808 1 0.0000 0.778 1.000 0.000 0.000
#> GSM97813 1 0.4842 0.822 0.776 0.000 0.224
#> GSM97814 1 0.0000 0.778 1.000 0.000 0.000
#> GSM97818 1 0.5926 0.652 0.644 0.000 0.356
#> GSM97819 3 0.0000 0.859 0.000 0.000 1.000
#> GSM97821 3 0.6062 0.256 0.384 0.000 0.616
#> GSM97826 1 0.5560 0.745 0.700 0.000 0.300
#> GSM97829 1 0.5591 0.740 0.696 0.000 0.304
#> GSM97832 3 0.0000 0.859 0.000 0.000 1.000
#> GSM97836 1 0.4887 0.821 0.772 0.000 0.228
#> GSM97839 1 0.0000 0.778 1.000 0.000 0.000
#> GSM97844 2 0.0000 0.990 0.000 1.000 0.000
#> GSM97847 1 0.4887 0.821 0.772 0.000 0.228
#> GSM97851 1 0.0000 0.778 1.000 0.000 0.000
#> GSM97852 1 0.4842 0.822 0.776 0.000 0.224
#> GSM97856 1 0.0000 0.778 1.000 0.000 0.000
#> GSM97858 2 0.0000 0.990 0.000 1.000 0.000
#> GSM97859 1 0.4887 0.821 0.772 0.000 0.228
#> GSM97861 1 0.4887 0.821 0.772 0.000 0.228
#> GSM97863 1 0.0000 0.778 1.000 0.000 0.000
#> GSM97869 1 0.5291 0.785 0.732 0.000 0.268
#> GSM97870 3 0.6154 0.169 0.408 0.000 0.592
#> GSM97871 1 0.0000 0.778 1.000 0.000 0.000
#> GSM97877 3 0.6095 0.230 0.392 0.000 0.608
#> GSM97879 1 0.4842 0.822 0.776 0.000 0.224
#> GSM97882 1 0.4842 0.822 0.776 0.000 0.224
#> GSM97885 1 0.4887 0.821 0.772 0.000 0.228
#> GSM97886 1 0.0000 0.778 1.000 0.000 0.000
#> GSM97887 1 0.0000 0.778 1.000 0.000 0.000
#> GSM97888 1 0.4842 0.822 0.776 0.000 0.224
#> GSM97889 1 0.4842 0.822 0.776 0.000 0.224
#> GSM97891 1 0.4887 0.821 0.772 0.000 0.228
#> GSM97892 2 0.0000 0.990 0.000 1.000 0.000
#> GSM97893 1 0.4842 0.822 0.776 0.000 0.224
#> GSM97894 1 0.0000 0.778 1.000 0.000 0.000
#> GSM97895 1 0.1031 0.783 0.976 0.000 0.024
#> GSM97896 1 0.0000 0.778 1.000 0.000 0.000
#> GSM97898 1 0.0000 0.778 1.000 0.000 0.000
#> GSM97903 1 0.4887 0.821 0.772 0.000 0.228
#> GSM97905 3 0.6062 0.251 0.384 0.000 0.616
#> GSM97906 1 0.0000 0.778 1.000 0.000 0.000
#> GSM97908 1 0.4842 0.822 0.776 0.000 0.224
#> GSM97912 1 0.6140 0.546 0.596 0.000 0.404
#> GSM97914 1 0.5363 0.776 0.724 0.000 0.276
#> GSM97915 1 0.0000 0.778 1.000 0.000 0.000
#> GSM97917 1 0.1031 0.783 0.976 0.000 0.024
#> GSM97918 1 0.0000 0.778 1.000 0.000 0.000
#> GSM97919 1 0.0000 0.778 1.000 0.000 0.000
#> GSM97922 1 0.4842 0.822 0.776 0.000 0.224
#> GSM97924 2 0.0000 0.990 0.000 1.000 0.000
#> GSM97926 3 0.4346 0.662 0.184 0.000 0.816
#> GSM97930 1 0.4887 0.821 0.772 0.000 0.228
#> GSM97931 3 0.6079 0.244 0.388 0.000 0.612
#> GSM97935 1 0.4887 0.821 0.772 0.000 0.228
#> GSM97936 1 0.4002 0.815 0.840 0.000 0.160
#> GSM97938 1 0.4931 0.818 0.768 0.000 0.232
#> GSM97940 1 0.0000 0.778 1.000 0.000 0.000
#> GSM97942 3 0.0000 0.859 0.000 0.000 1.000
#> GSM97945 1 0.4121 0.816 0.832 0.000 0.168
#> GSM97946 2 0.0000 0.990 0.000 1.000 0.000
#> GSM97948 3 0.4796 0.608 0.220 0.000 0.780
#> GSM97950 1 0.0000 0.778 1.000 0.000 0.000
#> GSM97952 1 0.0000 0.778 1.000 0.000 0.000
#> GSM97953 1 0.4931 0.818 0.768 0.000 0.232
#> GSM97954 1 0.4842 0.822 0.776 0.000 0.224
#> GSM97955 1 0.4346 0.819 0.816 0.000 0.184
#> GSM97959 3 0.6154 0.169 0.408 0.000 0.592
#> GSM97961 1 0.0000 0.778 1.000 0.000 0.000
#> GSM97963 1 0.0000 0.778 1.000 0.000 0.000
#> GSM97965 1 0.0000 0.778 1.000 0.000 0.000
#> GSM97966 1 0.0000 0.778 1.000 0.000 0.000
#> GSM97967 2 0.0000 0.990 0.000 1.000 0.000
#> GSM97968 2 0.0000 0.990 0.000 1.000 0.000
#> GSM97969 1 0.4887 0.821 0.772 0.000 0.228
#> GSM97971 1 0.4974 0.815 0.764 0.000 0.236
#> GSM97799 3 0.0000 0.859 0.000 0.000 1.000
#> GSM97823 2 0.0000 0.990 0.000 1.000 0.000
#> GSM97824 3 0.0000 0.859 0.000 0.000 1.000
#> GSM97830 3 0.0000 0.859 0.000 0.000 1.000
#> GSM97835 3 0.0000 0.859 0.000 0.000 1.000
#> GSM97838 2 0.0000 0.990 0.000 1.000 0.000
#> GSM97841 2 0.0000 0.990 0.000 1.000 0.000
#> GSM97842 3 0.0000 0.859 0.000 0.000 1.000
#> GSM97854 2 0.0000 0.990 0.000 1.000 0.000
#> GSM97857 3 0.0000 0.859 0.000 0.000 1.000
#> GSM97860 3 0.0000 0.859 0.000 0.000 1.000
#> GSM97862 3 0.0000 0.859 0.000 0.000 1.000
#> GSM97864 2 0.0000 0.990 0.000 1.000 0.000
#> GSM97866 3 0.0000 0.859 0.000 0.000 1.000
#> GSM97868 3 0.0000 0.859 0.000 0.000 1.000
#> GSM97872 1 0.5431 0.766 0.716 0.000 0.284
#> GSM97873 3 0.0000 0.859 0.000 0.000 1.000
#> GSM97874 3 0.0000 0.859 0.000 0.000 1.000
#> GSM97875 3 0.0000 0.859 0.000 0.000 1.000
#> GSM97876 3 0.0000 0.859 0.000 0.000 1.000
#> GSM97880 3 0.0000 0.859 0.000 0.000 1.000
#> GSM97881 3 0.0000 0.859 0.000 0.000 1.000
#> GSM97884 3 0.0000 0.859 0.000 0.000 1.000
#> GSM97901 3 0.0000 0.859 0.000 0.000 1.000
#> GSM97902 1 0.6308 0.267 0.508 0.000 0.492
#> GSM97909 3 0.6062 0.256 0.384 0.000 0.616
#> GSM97911 3 0.0000 0.859 0.000 0.000 1.000
#> GSM97923 3 0.0000 0.859 0.000 0.000 1.000
#> GSM97928 1 0.4887 0.821 0.772 0.000 0.228
#> GSM97929 2 0.0000 0.990 0.000 1.000 0.000
#> GSM97933 3 0.0000 0.859 0.000 0.000 1.000
#> GSM97934 3 0.0000 0.859 0.000 0.000 1.000
#> GSM97944 3 0.0000 0.859 0.000 0.000 1.000
#> GSM97949 2 0.0000 0.990 0.000 1.000 0.000
#> GSM97956 3 0.0000 0.859 0.000 0.000 1.000
#> GSM97962 3 0.0000 0.859 0.000 0.000 1.000
#> GSM97964 3 0.0000 0.859 0.000 0.000 1.000
#> GSM97970 3 0.0000 0.859 0.000 0.000 1.000
#> GSM97822 1 0.4842 0.822 0.776 0.000 0.224
#> GSM97831 3 0.0000 0.859 0.000 0.000 1.000
#> GSM97845 1 0.4842 0.822 0.776 0.000 0.224
#> GSM97865 1 0.5591 0.740 0.696 0.000 0.304
#> GSM97867 3 0.0000 0.859 0.000 0.000 1.000
#> GSM97883 3 0.0000 0.859 0.000 0.000 1.000
#> GSM97897 1 0.4346 0.819 0.816 0.000 0.184
#> GSM97900 1 0.0000 0.778 1.000 0.000 0.000
#> GSM97904 1 0.4887 0.821 0.772 0.000 0.228
#> GSM97907 2 0.0000 0.990 0.000 1.000 0.000
#> GSM97925 3 0.0000 0.859 0.000 0.000 1.000
#> GSM97947 3 0.0000 0.859 0.000 0.000 1.000
cbind(get_classes(res, k = 4), get_membership(res, k = 4))
#> class entropy silhouette p1 p2 p3 p4
#> GSM97800 2 0.0000 0.9844 0.000 1.000 0.000 0.000
#> GSM97803 2 0.0000 0.9844 0.000 1.000 0.000 0.000
#> GSM97804 2 0.0000 0.9844 0.000 1.000 0.000 0.000
#> GSM97805 2 0.0000 0.9844 0.000 1.000 0.000 0.000
#> GSM97807 2 0.0000 0.9844 0.000 1.000 0.000 0.000
#> GSM97809 2 0.0000 0.9844 0.000 1.000 0.000 0.000
#> GSM97811 2 0.0000 0.9844 0.000 1.000 0.000 0.000
#> GSM97812 2 0.0000 0.9844 0.000 1.000 0.000 0.000
#> GSM97816 3 0.4925 0.2918 0.428 0.000 0.572 0.000
#> GSM97817 2 0.0000 0.9844 0.000 1.000 0.000 0.000
#> GSM97820 2 0.0000 0.9844 0.000 1.000 0.000 0.000
#> GSM97825 2 0.0000 0.9844 0.000 1.000 0.000 0.000
#> GSM97827 2 0.0000 0.9844 0.000 1.000 0.000 0.000
#> GSM97828 3 0.4925 0.2918 0.428 0.000 0.572 0.000
#> GSM97833 2 0.0000 0.9844 0.000 1.000 0.000 0.000
#> GSM97834 2 0.0000 0.9844 0.000 1.000 0.000 0.000
#> GSM97840 2 0.5112 0.1958 0.436 0.560 0.004 0.000
#> GSM97846 2 0.0000 0.9844 0.000 1.000 0.000 0.000
#> GSM97848 2 0.0000 0.9844 0.000 1.000 0.000 0.000
#> GSM97849 2 0.0000 0.9844 0.000 1.000 0.000 0.000
#> GSM97850 2 0.0000 0.9844 0.000 1.000 0.000 0.000
#> GSM97853 2 0.0000 0.9844 0.000 1.000 0.000 0.000
#> GSM97855 2 0.0000 0.9844 0.000 1.000 0.000 0.000
#> GSM97878 1 0.0000 0.9758 1.000 0.000 0.000 0.000
#> GSM97913 1 0.0000 0.9758 1.000 0.000 0.000 0.000
#> GSM97932 4 0.0000 0.9327 0.000 0.000 0.000 1.000
#> GSM97939 3 0.0000 0.9495 0.000 0.000 1.000 0.000
#> GSM97951 2 0.0188 0.9797 0.004 0.996 0.000 0.000
#> GSM97957 3 0.0000 0.9495 0.000 0.000 1.000 0.000
#> GSM97972 3 0.4916 0.3025 0.424 0.000 0.576 0.000
#> GSM97793 3 0.0000 0.9495 0.000 0.000 1.000 0.000
#> GSM97795 3 0.0000 0.9495 0.000 0.000 1.000 0.000
#> GSM97802 1 0.0707 0.9555 0.980 0.000 0.020 0.000
#> GSM97810 3 0.0000 0.9495 0.000 0.000 1.000 0.000
#> GSM97815 3 0.0000 0.9495 0.000 0.000 1.000 0.000
#> GSM97837 1 0.0000 0.9758 1.000 0.000 0.000 0.000
#> GSM97843 3 0.0000 0.9495 0.000 0.000 1.000 0.000
#> GSM97890 3 0.0000 0.9495 0.000 0.000 1.000 0.000
#> GSM97899 4 0.0336 0.9274 0.008 0.000 0.000 0.992
#> GSM97910 1 0.0000 0.9758 1.000 0.000 0.000 0.000
#> GSM97916 1 0.0000 0.9758 1.000 0.000 0.000 0.000
#> GSM97920 3 0.0000 0.9495 0.000 0.000 1.000 0.000
#> GSM97921 1 0.0000 0.9758 1.000 0.000 0.000 0.000
#> GSM97927 1 0.0000 0.9758 1.000 0.000 0.000 0.000
#> GSM97937 1 0.0000 0.9758 1.000 0.000 0.000 0.000
#> GSM97941 1 0.2654 0.8537 0.888 0.108 0.004 0.000
#> GSM97943 3 0.4925 0.2918 0.428 0.000 0.572 0.000
#> GSM97958 1 0.0188 0.9724 0.996 0.000 0.004 0.000
#> GSM97960 3 0.0000 0.9495 0.000 0.000 1.000 0.000
#> GSM97794 1 0.0000 0.9758 1.000 0.000 0.000 0.000
#> GSM97796 4 0.0000 0.9327 0.000 0.000 0.000 1.000
#> GSM97797 1 0.0000 0.9758 1.000 0.000 0.000 0.000
#> GSM97798 4 0.0000 0.9327 0.000 0.000 0.000 1.000
#> GSM97801 1 0.0000 0.9758 1.000 0.000 0.000 0.000
#> GSM97806 1 0.0000 0.9758 1.000 0.000 0.000 0.000
#> GSM97808 4 0.0000 0.9327 0.000 0.000 0.000 1.000
#> GSM97813 1 0.0000 0.9758 1.000 0.000 0.000 0.000
#> GSM97814 4 0.0000 0.9327 0.000 0.000 0.000 1.000
#> GSM97818 1 0.0000 0.9758 1.000 0.000 0.000 0.000
#> GSM97819 3 0.0000 0.9495 0.000 0.000 1.000 0.000
#> GSM97821 1 0.0188 0.9724 0.996 0.000 0.004 0.000
#> GSM97826 1 0.0000 0.9758 1.000 0.000 0.000 0.000
#> GSM97829 1 0.0000 0.9758 1.000 0.000 0.000 0.000
#> GSM97832 3 0.0000 0.9495 0.000 0.000 1.000 0.000
#> GSM97836 1 0.0000 0.9758 1.000 0.000 0.000 0.000
#> GSM97839 4 0.0000 0.9327 0.000 0.000 0.000 1.000
#> GSM97844 2 0.0000 0.9844 0.000 1.000 0.000 0.000
#> GSM97847 1 0.0000 0.9758 1.000 0.000 0.000 0.000
#> GSM97851 4 0.0000 0.9327 0.000 0.000 0.000 1.000
#> GSM97852 1 0.0000 0.9758 1.000 0.000 0.000 0.000
#> GSM97856 4 0.0000 0.9327 0.000 0.000 0.000 1.000
#> GSM97858 2 0.0000 0.9844 0.000 1.000 0.000 0.000
#> GSM97859 1 0.0000 0.9758 1.000 0.000 0.000 0.000
#> GSM97861 1 0.0000 0.9758 1.000 0.000 0.000 0.000
#> GSM97863 4 0.0000 0.9327 0.000 0.000 0.000 1.000
#> GSM97869 1 0.0000 0.9758 1.000 0.000 0.000 0.000
#> GSM97870 1 0.1211 0.9333 0.960 0.000 0.040 0.000
#> GSM97871 4 0.0000 0.9327 0.000 0.000 0.000 1.000
#> GSM97877 1 0.0000 0.9758 1.000 0.000 0.000 0.000
#> GSM97879 1 0.0000 0.9758 1.000 0.000 0.000 0.000
#> GSM97882 1 0.0000 0.9758 1.000 0.000 0.000 0.000
#> GSM97885 1 0.0000 0.9758 1.000 0.000 0.000 0.000
#> GSM97886 4 0.0000 0.9327 0.000 0.000 0.000 1.000
#> GSM97887 4 0.3311 0.7917 0.172 0.000 0.000 0.828
#> GSM97888 1 0.0000 0.9758 1.000 0.000 0.000 0.000
#> GSM97889 1 0.0000 0.9758 1.000 0.000 0.000 0.000
#> GSM97891 1 0.0000 0.9758 1.000 0.000 0.000 0.000
#> GSM97892 2 0.0000 0.9844 0.000 1.000 0.000 0.000
#> GSM97893 1 0.0188 0.9727 0.996 0.000 0.000 0.004
#> GSM97894 4 0.0000 0.9327 0.000 0.000 0.000 1.000
#> GSM97895 1 0.4981 0.0497 0.536 0.000 0.000 0.464
#> GSM97896 4 0.3486 0.7718 0.188 0.000 0.000 0.812
#> GSM97898 4 0.0000 0.9327 0.000 0.000 0.000 1.000
#> GSM97903 1 0.0000 0.9758 1.000 0.000 0.000 0.000
#> GSM97905 1 0.0000 0.9758 1.000 0.000 0.000 0.000
#> GSM97906 4 0.1389 0.8968 0.048 0.000 0.000 0.952
#> GSM97908 1 0.0000 0.9758 1.000 0.000 0.000 0.000
#> GSM97912 1 0.0000 0.9758 1.000 0.000 0.000 0.000
#> GSM97914 1 0.0000 0.9758 1.000 0.000 0.000 0.000
#> GSM97915 4 0.0000 0.9327 0.000 0.000 0.000 1.000
#> GSM97917 4 0.3942 0.7044 0.236 0.000 0.000 0.764
#> GSM97918 4 0.0000 0.9327 0.000 0.000 0.000 1.000
#> GSM97919 4 0.0000 0.9327 0.000 0.000 0.000 1.000
#> GSM97922 1 0.0000 0.9758 1.000 0.000 0.000 0.000
#> GSM97924 2 0.0000 0.9844 0.000 1.000 0.000 0.000
#> GSM97926 3 0.4454 0.5652 0.308 0.000 0.692 0.000
#> GSM97930 1 0.0000 0.9758 1.000 0.000 0.000 0.000
#> GSM97931 1 0.0188 0.9724 0.996 0.000 0.004 0.000
#> GSM97935 1 0.0000 0.9758 1.000 0.000 0.000 0.000
#> GSM97936 4 0.4382 0.6003 0.296 0.000 0.000 0.704
#> GSM97938 1 0.0000 0.9758 1.000 0.000 0.000 0.000
#> GSM97940 4 0.0000 0.9327 0.000 0.000 0.000 1.000
#> GSM97942 3 0.0000 0.9495 0.000 0.000 1.000 0.000
#> GSM97945 4 0.4804 0.4120 0.384 0.000 0.000 0.616
#> GSM97946 2 0.0000 0.9844 0.000 1.000 0.000 0.000
#> GSM97948 1 0.4955 0.1644 0.556 0.000 0.444 0.000
#> GSM97950 4 0.0000 0.9327 0.000 0.000 0.000 1.000
#> GSM97952 4 0.0000 0.9327 0.000 0.000 0.000 1.000
#> GSM97953 1 0.0000 0.9758 1.000 0.000 0.000 0.000
#> GSM97954 1 0.0000 0.9758 1.000 0.000 0.000 0.000
#> GSM97955 4 0.4661 0.4971 0.348 0.000 0.000 0.652
#> GSM97959 1 0.0000 0.9758 1.000 0.000 0.000 0.000
#> GSM97961 4 0.0000 0.9327 0.000 0.000 0.000 1.000
#> GSM97963 4 0.0000 0.9327 0.000 0.000 0.000 1.000
#> GSM97965 4 0.0000 0.9327 0.000 0.000 0.000 1.000
#> GSM97966 4 0.0000 0.9327 0.000 0.000 0.000 1.000
#> GSM97967 2 0.0000 0.9844 0.000 1.000 0.000 0.000
#> GSM97968 2 0.0000 0.9844 0.000 1.000 0.000 0.000
#> GSM97969 1 0.0000 0.9758 1.000 0.000 0.000 0.000
#> GSM97971 1 0.0000 0.9758 1.000 0.000 0.000 0.000
#> GSM97799 3 0.0000 0.9495 0.000 0.000 1.000 0.000
#> GSM97823 2 0.0000 0.9844 0.000 1.000 0.000 0.000
#> GSM97824 3 0.0000 0.9495 0.000 0.000 1.000 0.000
#> GSM97830 3 0.0000 0.9495 0.000 0.000 1.000 0.000
#> GSM97835 3 0.0000 0.9495 0.000 0.000 1.000 0.000
#> GSM97838 2 0.0000 0.9844 0.000 1.000 0.000 0.000
#> GSM97841 2 0.0000 0.9844 0.000 1.000 0.000 0.000
#> GSM97842 3 0.0000 0.9495 0.000 0.000 1.000 0.000
#> GSM97854 2 0.0000 0.9844 0.000 1.000 0.000 0.000
#> GSM97857 3 0.0000 0.9495 0.000 0.000 1.000 0.000
#> GSM97860 3 0.0000 0.9495 0.000 0.000 1.000 0.000
#> GSM97862 3 0.0000 0.9495 0.000 0.000 1.000 0.000
#> GSM97864 2 0.0000 0.9844 0.000 1.000 0.000 0.000
#> GSM97866 3 0.0000 0.9495 0.000 0.000 1.000 0.000
#> GSM97868 3 0.0000 0.9495 0.000 0.000 1.000 0.000
#> GSM97872 1 0.0000 0.9758 1.000 0.000 0.000 0.000
#> GSM97873 3 0.0000 0.9495 0.000 0.000 1.000 0.000
#> GSM97874 3 0.0000 0.9495 0.000 0.000 1.000 0.000
#> GSM97875 3 0.0000 0.9495 0.000 0.000 1.000 0.000
#> GSM97876 3 0.0000 0.9495 0.000 0.000 1.000 0.000
#> GSM97880 3 0.0000 0.9495 0.000 0.000 1.000 0.000
#> GSM97881 3 0.0000 0.9495 0.000 0.000 1.000 0.000
#> GSM97884 3 0.0000 0.9495 0.000 0.000 1.000 0.000
#> GSM97901 3 0.0000 0.9495 0.000 0.000 1.000 0.000
#> GSM97902 1 0.0000 0.9758 1.000 0.000 0.000 0.000
#> GSM97909 1 0.0188 0.9724 0.996 0.000 0.004 0.000
#> GSM97911 3 0.0000 0.9495 0.000 0.000 1.000 0.000
#> GSM97923 3 0.0000 0.9495 0.000 0.000 1.000 0.000
#> GSM97928 1 0.0000 0.9758 1.000 0.000 0.000 0.000
#> GSM97929 2 0.0000 0.9844 0.000 1.000 0.000 0.000
#> GSM97933 3 0.0000 0.9495 0.000 0.000 1.000 0.000
#> GSM97934 3 0.0000 0.9495 0.000 0.000 1.000 0.000
#> GSM97944 3 0.0000 0.9495 0.000 0.000 1.000 0.000
#> GSM97949 2 0.0000 0.9844 0.000 1.000 0.000 0.000
#> GSM97956 3 0.0000 0.9495 0.000 0.000 1.000 0.000
#> GSM97962 3 0.0000 0.9495 0.000 0.000 1.000 0.000
#> GSM97964 3 0.0000 0.9495 0.000 0.000 1.000 0.000
#> GSM97970 3 0.0000 0.9495 0.000 0.000 1.000 0.000
#> GSM97822 1 0.0000 0.9758 1.000 0.000 0.000 0.000
#> GSM97831 3 0.0000 0.9495 0.000 0.000 1.000 0.000
#> GSM97845 1 0.0000 0.9758 1.000 0.000 0.000 0.000
#> GSM97865 1 0.0000 0.9758 1.000 0.000 0.000 0.000
#> GSM97867 3 0.0000 0.9495 0.000 0.000 1.000 0.000
#> GSM97883 3 0.0000 0.9495 0.000 0.000 1.000 0.000
#> GSM97897 1 0.0188 0.9727 0.996 0.000 0.000 0.004
#> GSM97900 1 0.3610 0.7174 0.800 0.000 0.000 0.200
#> GSM97904 1 0.0000 0.9758 1.000 0.000 0.000 0.000
#> GSM97907 2 0.0000 0.9844 0.000 1.000 0.000 0.000
#> GSM97925 3 0.0000 0.9495 0.000 0.000 1.000 0.000
#> GSM97947 3 0.0000 0.9495 0.000 0.000 1.000 0.000
cbind(get_classes(res, k = 5), get_membership(res, k = 5))
#> class entropy silhouette p1 p2 p3 p4 p5
#> GSM97800 2 0.0290 0.9590 0.000 0.992 0.000 0.000 0.008
#> GSM97803 2 0.0880 0.9561 0.000 0.968 0.000 0.000 0.032
#> GSM97804 2 0.0290 0.9590 0.000 0.992 0.000 0.000 0.008
#> GSM97805 2 0.0510 0.9585 0.000 0.984 0.000 0.000 0.016
#> GSM97807 2 0.2020 0.9353 0.000 0.900 0.000 0.000 0.100
#> GSM97809 2 0.2074 0.9336 0.000 0.896 0.000 0.000 0.104
#> GSM97811 2 0.0000 0.9593 0.000 1.000 0.000 0.000 0.000
#> GSM97812 2 0.0290 0.9590 0.000 0.992 0.000 0.000 0.008
#> GSM97816 5 0.3039 0.5667 0.000 0.000 0.192 0.000 0.808
#> GSM97817 2 0.0290 0.9590 0.000 0.992 0.000 0.000 0.008
#> GSM97820 2 0.2020 0.9353 0.000 0.900 0.000 0.000 0.100
#> GSM97825 2 0.0290 0.9590 0.000 0.992 0.000 0.000 0.008
#> GSM97827 2 0.0290 0.9590 0.000 0.992 0.000 0.000 0.008
#> GSM97828 5 0.4464 0.4015 0.028 0.000 0.288 0.000 0.684
#> GSM97833 2 0.0510 0.9585 0.000 0.984 0.000 0.000 0.016
#> GSM97834 2 0.0290 0.9590 0.000 0.992 0.000 0.000 0.008
#> GSM97840 5 0.4620 0.2374 0.028 0.320 0.000 0.000 0.652
#> GSM97846 2 0.0290 0.9590 0.000 0.992 0.000 0.000 0.008
#> GSM97848 2 0.1270 0.9517 0.000 0.948 0.000 0.000 0.052
#> GSM97849 2 0.0290 0.9590 0.000 0.992 0.000 0.000 0.008
#> GSM97850 2 0.2074 0.9336 0.000 0.896 0.000 0.000 0.104
#> GSM97853 2 0.0162 0.9593 0.000 0.996 0.000 0.000 0.004
#> GSM97855 2 0.3003 0.8484 0.000 0.812 0.000 0.000 0.188
#> GSM97878 1 0.0609 0.9346 0.980 0.000 0.000 0.000 0.020
#> GSM97913 1 0.4268 0.1444 0.556 0.000 0.000 0.000 0.444
#> GSM97932 4 0.0898 0.9469 0.020 0.000 0.000 0.972 0.008
#> GSM97939 5 0.3684 0.4188 0.000 0.000 0.280 0.000 0.720
#> GSM97951 5 0.4161 0.0823 0.000 0.392 0.000 0.000 0.608
#> GSM97957 3 0.0000 0.8695 0.000 0.000 1.000 0.000 0.000
#> GSM97972 5 0.3209 0.5781 0.008 0.000 0.180 0.000 0.812
#> GSM97793 3 0.0000 0.8695 0.000 0.000 1.000 0.000 0.000
#> GSM97795 5 0.2891 0.5800 0.000 0.000 0.176 0.000 0.824
#> GSM97802 1 0.2932 0.8198 0.864 0.000 0.104 0.000 0.032
#> GSM97810 5 0.2891 0.5800 0.000 0.000 0.176 0.000 0.824
#> GSM97815 5 0.2891 0.5800 0.000 0.000 0.176 0.000 0.824
#> GSM97837 1 0.1043 0.9312 0.960 0.000 0.000 0.000 0.040
#> GSM97843 3 0.0000 0.8695 0.000 0.000 1.000 0.000 0.000
#> GSM97890 3 0.2813 0.8376 0.000 0.000 0.832 0.000 0.168
#> GSM97899 4 0.0162 0.9615 0.004 0.000 0.000 0.996 0.000
#> GSM97910 1 0.1043 0.9312 0.960 0.000 0.000 0.000 0.040
#> GSM97916 1 0.0880 0.9318 0.968 0.000 0.000 0.000 0.032
#> GSM97920 3 0.0162 0.8695 0.000 0.000 0.996 0.000 0.004
#> GSM97921 1 0.0880 0.9318 0.968 0.000 0.000 0.000 0.032
#> GSM97927 1 0.0290 0.9338 0.992 0.000 0.000 0.000 0.008
#> GSM97937 1 0.1043 0.9312 0.960 0.000 0.000 0.000 0.040
#> GSM97941 5 0.5987 0.4578 0.272 0.156 0.000 0.000 0.572
#> GSM97943 5 0.6201 0.4167 0.216 0.000 0.232 0.000 0.552
#> GSM97958 5 0.4268 0.1822 0.444 0.000 0.000 0.000 0.556
#> GSM97960 5 0.2891 0.5800 0.000 0.000 0.176 0.000 0.824
#> GSM97794 1 0.0880 0.9318 0.968 0.000 0.000 0.000 0.032
#> GSM97796 4 0.0162 0.9625 0.000 0.000 0.000 0.996 0.004
#> GSM97797 1 0.0880 0.9318 0.968 0.000 0.000 0.000 0.032
#> GSM97798 4 0.0000 0.9628 0.000 0.000 0.000 1.000 0.000
#> GSM97801 1 0.1043 0.9312 0.960 0.000 0.000 0.000 0.040
#> GSM97806 1 0.0290 0.9338 0.992 0.000 0.000 0.000 0.008
#> GSM97808 4 0.0000 0.9628 0.000 0.000 0.000 1.000 0.000
#> GSM97813 1 0.0510 0.9320 0.984 0.000 0.000 0.000 0.016
#> GSM97814 4 0.0000 0.9628 0.000 0.000 0.000 1.000 0.000
#> GSM97818 1 0.0880 0.9318 0.968 0.000 0.000 0.000 0.032
#> GSM97819 3 0.2230 0.8570 0.000 0.000 0.884 0.000 0.116
#> GSM97821 5 0.4268 0.1822 0.444 0.000 0.000 0.000 0.556
#> GSM97826 1 0.1043 0.9312 0.960 0.000 0.000 0.000 0.040
#> GSM97829 1 0.1043 0.9312 0.960 0.000 0.000 0.000 0.040
#> GSM97832 5 0.2891 0.5800 0.000 0.000 0.176 0.000 0.824
#> GSM97836 1 0.0162 0.9352 0.996 0.000 0.000 0.000 0.004
#> GSM97839 4 0.0162 0.9625 0.000 0.000 0.000 0.996 0.004
#> GSM97844 2 0.0162 0.9593 0.000 0.996 0.000 0.000 0.004
#> GSM97847 1 0.0290 0.9338 0.992 0.000 0.000 0.000 0.008
#> GSM97851 4 0.0566 0.9557 0.012 0.000 0.000 0.984 0.004
#> GSM97852 1 0.0290 0.9338 0.992 0.000 0.000 0.000 0.008
#> GSM97856 4 0.0000 0.9628 0.000 0.000 0.000 1.000 0.000
#> GSM97858 2 0.0000 0.9593 0.000 1.000 0.000 0.000 0.000
#> GSM97859 1 0.0880 0.9334 0.968 0.000 0.000 0.000 0.032
#> GSM97861 1 0.0290 0.9338 0.992 0.000 0.000 0.000 0.008
#> GSM97863 4 0.0162 0.9625 0.000 0.000 0.000 0.996 0.004
#> GSM97869 1 0.0880 0.9318 0.968 0.000 0.000 0.000 0.032
#> GSM97870 1 0.1484 0.9216 0.944 0.000 0.008 0.000 0.048
#> GSM97871 4 0.0000 0.9628 0.000 0.000 0.000 1.000 0.000
#> GSM97877 1 0.4283 0.1040 0.544 0.000 0.000 0.000 0.456
#> GSM97879 1 0.0290 0.9338 0.992 0.000 0.000 0.000 0.008
#> GSM97882 1 0.0290 0.9338 0.992 0.000 0.000 0.000 0.008
#> GSM97885 1 0.0609 0.9355 0.980 0.000 0.000 0.000 0.020
#> GSM97886 4 0.1168 0.9300 0.032 0.000 0.000 0.960 0.008
#> GSM97887 4 0.3209 0.7289 0.180 0.000 0.000 0.812 0.008
#> GSM97888 1 0.2046 0.8740 0.916 0.000 0.000 0.068 0.016
#> GSM97889 1 0.0290 0.9338 0.992 0.000 0.000 0.000 0.008
#> GSM97891 1 0.0290 0.9338 0.992 0.000 0.000 0.000 0.008
#> GSM97892 2 0.1851 0.9400 0.000 0.912 0.000 0.000 0.088
#> GSM97893 1 0.1764 0.8793 0.928 0.000 0.000 0.064 0.008
#> GSM97894 4 0.0000 0.9628 0.000 0.000 0.000 1.000 0.000
#> GSM97895 1 0.4522 0.2103 0.552 0.000 0.000 0.440 0.008
#> GSM97896 4 0.3246 0.7231 0.184 0.000 0.000 0.808 0.008
#> GSM97898 4 0.0162 0.9625 0.000 0.000 0.000 0.996 0.004
#> GSM97903 1 0.0000 0.9349 1.000 0.000 0.000 0.000 0.000
#> GSM97905 1 0.1043 0.9312 0.960 0.000 0.000 0.000 0.040
#> GSM97906 4 0.0898 0.9473 0.020 0.000 0.000 0.972 0.008
#> GSM97908 1 0.0290 0.9338 0.992 0.000 0.000 0.000 0.008
#> GSM97912 1 0.1043 0.9312 0.960 0.000 0.000 0.000 0.040
#> GSM97914 1 0.0880 0.9318 0.968 0.000 0.000 0.000 0.032
#> GSM97915 4 0.0162 0.9625 0.000 0.000 0.000 0.996 0.004
#> GSM97917 4 0.3861 0.5879 0.264 0.000 0.000 0.728 0.008
#> GSM97918 4 0.0162 0.9625 0.000 0.000 0.000 0.996 0.004
#> GSM97919 4 0.0162 0.9625 0.000 0.000 0.000 0.996 0.004
#> GSM97922 1 0.0798 0.9294 0.976 0.000 0.000 0.008 0.016
#> GSM97924 2 0.2074 0.9336 0.000 0.896 0.000 0.000 0.104
#> GSM97926 3 0.6470 0.1282 0.348 0.000 0.460 0.000 0.192
#> GSM97930 1 0.0290 0.9338 0.992 0.000 0.000 0.000 0.008
#> GSM97931 5 0.4273 0.1705 0.448 0.000 0.000 0.000 0.552
#> GSM97935 1 0.0290 0.9338 0.992 0.000 0.000 0.000 0.008
#> GSM97936 4 0.0290 0.9593 0.008 0.000 0.000 0.992 0.000
#> GSM97938 1 0.0404 0.9346 0.988 0.000 0.000 0.000 0.012
#> GSM97940 4 0.0000 0.9628 0.000 0.000 0.000 1.000 0.000
#> GSM97942 3 0.1671 0.8649 0.000 0.000 0.924 0.000 0.076
#> GSM97945 4 0.0703 0.9467 0.024 0.000 0.000 0.976 0.000
#> GSM97946 2 0.2074 0.9336 0.000 0.896 0.000 0.000 0.104
#> GSM97948 1 0.4708 0.4530 0.668 0.000 0.292 0.000 0.040
#> GSM97950 4 0.0290 0.9596 0.000 0.000 0.000 0.992 0.008
#> GSM97952 4 0.0000 0.9628 0.000 0.000 0.000 1.000 0.000
#> GSM97953 1 0.0404 0.9346 0.988 0.000 0.000 0.000 0.012
#> GSM97954 1 0.0290 0.9338 0.992 0.000 0.000 0.000 0.008
#> GSM97955 4 0.0404 0.9570 0.012 0.000 0.000 0.988 0.000
#> GSM97959 1 0.1965 0.8784 0.904 0.000 0.000 0.000 0.096
#> GSM97961 4 0.0162 0.9625 0.000 0.000 0.000 0.996 0.004
#> GSM97963 4 0.0000 0.9628 0.000 0.000 0.000 1.000 0.000
#> GSM97965 4 0.0000 0.9628 0.000 0.000 0.000 1.000 0.000
#> GSM97966 4 0.0000 0.9628 0.000 0.000 0.000 1.000 0.000
#> GSM97967 2 0.0290 0.9590 0.000 0.992 0.000 0.000 0.008
#> GSM97968 5 0.4249 -0.0354 0.000 0.432 0.000 0.000 0.568
#> GSM97969 1 0.0162 0.9345 0.996 0.000 0.000 0.000 0.004
#> GSM97971 1 0.0609 0.9350 0.980 0.000 0.000 0.000 0.020
#> GSM97799 3 0.3242 0.8073 0.000 0.000 0.784 0.000 0.216
#> GSM97823 2 0.2074 0.9336 0.000 0.896 0.000 0.000 0.104
#> GSM97824 3 0.2690 0.8439 0.000 0.000 0.844 0.000 0.156
#> GSM97830 3 0.0000 0.8695 0.000 0.000 1.000 0.000 0.000
#> GSM97835 5 0.3143 0.5492 0.000 0.000 0.204 0.000 0.796
#> GSM97838 2 0.2074 0.9336 0.000 0.896 0.000 0.000 0.104
#> GSM97841 2 0.2074 0.9336 0.000 0.896 0.000 0.000 0.104
#> GSM97842 3 0.3949 0.6822 0.000 0.000 0.668 0.000 0.332
#> GSM97854 2 0.0794 0.9568 0.000 0.972 0.000 0.000 0.028
#> GSM97857 3 0.3796 0.7232 0.000 0.000 0.700 0.000 0.300
#> GSM97860 3 0.0000 0.8695 0.000 0.000 1.000 0.000 0.000
#> GSM97862 3 0.0000 0.8695 0.000 0.000 1.000 0.000 0.000
#> GSM97864 2 0.0290 0.9590 0.000 0.992 0.000 0.000 0.008
#> GSM97866 3 0.0000 0.8695 0.000 0.000 1.000 0.000 0.000
#> GSM97868 3 0.2329 0.8549 0.000 0.000 0.876 0.000 0.124
#> GSM97872 1 0.0880 0.9332 0.968 0.000 0.000 0.000 0.032
#> GSM97873 3 0.3949 0.6822 0.000 0.000 0.668 0.000 0.332
#> GSM97874 3 0.0000 0.8695 0.000 0.000 1.000 0.000 0.000
#> GSM97875 3 0.2732 0.8418 0.000 0.000 0.840 0.000 0.160
#> GSM97876 3 0.0000 0.8695 0.000 0.000 1.000 0.000 0.000
#> GSM97880 3 0.0000 0.8695 0.000 0.000 1.000 0.000 0.000
#> GSM97881 3 0.2773 0.8399 0.000 0.000 0.836 0.000 0.164
#> GSM97884 3 0.3876 0.7049 0.000 0.000 0.684 0.000 0.316
#> GSM97901 3 0.0000 0.8695 0.000 0.000 1.000 0.000 0.000
#> GSM97902 1 0.0963 0.9307 0.964 0.000 0.000 0.000 0.036
#> GSM97909 5 0.4242 0.2244 0.428 0.000 0.000 0.000 0.572
#> GSM97911 3 0.2773 0.8399 0.000 0.000 0.836 0.000 0.164
#> GSM97923 3 0.0000 0.8695 0.000 0.000 1.000 0.000 0.000
#> GSM97928 1 0.0000 0.9349 1.000 0.000 0.000 0.000 0.000
#> GSM97929 2 0.0290 0.9590 0.000 0.992 0.000 0.000 0.008
#> GSM97933 3 0.0000 0.8695 0.000 0.000 1.000 0.000 0.000
#> GSM97934 3 0.0000 0.8695 0.000 0.000 1.000 0.000 0.000
#> GSM97944 3 0.3242 0.8073 0.000 0.000 0.784 0.000 0.216
#> GSM97949 2 0.0290 0.9590 0.000 0.992 0.000 0.000 0.008
#> GSM97956 3 0.1121 0.8684 0.000 0.000 0.956 0.000 0.044
#> GSM97962 3 0.0000 0.8695 0.000 0.000 1.000 0.000 0.000
#> GSM97964 3 0.3684 0.7460 0.000 0.000 0.720 0.000 0.280
#> GSM97970 3 0.3730 0.7385 0.000 0.000 0.712 0.000 0.288
#> GSM97822 1 0.0290 0.9338 0.992 0.000 0.000 0.000 0.008
#> GSM97831 3 0.0000 0.8695 0.000 0.000 1.000 0.000 0.000
#> GSM97845 1 0.0404 0.9331 0.988 0.000 0.000 0.000 0.012
#> GSM97865 1 0.0880 0.9318 0.968 0.000 0.000 0.000 0.032
#> GSM97867 3 0.0000 0.8695 0.000 0.000 1.000 0.000 0.000
#> GSM97883 3 0.1792 0.8637 0.000 0.000 0.916 0.000 0.084
#> GSM97897 1 0.0579 0.9307 0.984 0.000 0.000 0.008 0.008
#> GSM97900 1 0.3282 0.7170 0.804 0.000 0.000 0.188 0.008
#> GSM97904 1 0.0290 0.9353 0.992 0.000 0.000 0.000 0.008
#> GSM97907 2 0.1341 0.9506 0.000 0.944 0.000 0.000 0.056
#> GSM97925 3 0.2813 0.8376 0.000 0.000 0.832 0.000 0.168
#> GSM97947 3 0.3132 0.8338 0.008 0.000 0.820 0.000 0.172
cbind(get_classes(res, k = 6), get_membership(res, k = 6))
#> class entropy silhouette p1 p2 p3 p4 p5 p6
#> GSM97800 2 0.0363 0.882 0.000 0.988 0.000 0.000 0.000 0.012
#> GSM97803 2 0.1501 0.887 0.000 0.924 0.000 0.000 0.000 0.076
#> GSM97804 2 0.0363 0.882 0.000 0.988 0.000 0.000 0.000 0.012
#> GSM97805 2 0.0790 0.887 0.000 0.968 0.000 0.000 0.000 0.032
#> GSM97807 2 0.2597 0.864 0.000 0.824 0.000 0.000 0.000 0.176
#> GSM97809 2 0.2730 0.856 0.000 0.808 0.000 0.000 0.000 0.192
#> GSM97811 2 0.1863 0.886 0.000 0.896 0.000 0.000 0.000 0.104
#> GSM97812 2 0.1556 0.859 0.000 0.920 0.000 0.000 0.000 0.080
#> GSM97816 5 0.5003 0.548 0.012 0.000 0.108 0.000 0.664 0.216
#> GSM97817 2 0.1556 0.859 0.000 0.920 0.000 0.000 0.000 0.080
#> GSM97820 2 0.2597 0.864 0.000 0.824 0.000 0.000 0.000 0.176
#> GSM97825 2 0.1556 0.859 0.000 0.920 0.000 0.000 0.000 0.080
#> GSM97827 2 0.1556 0.859 0.000 0.920 0.000 0.000 0.000 0.080
#> GSM97828 5 0.6078 0.514 0.060 0.000 0.132 0.000 0.580 0.228
#> GSM97833 2 0.1957 0.882 0.000 0.888 0.000 0.000 0.000 0.112
#> GSM97834 2 0.1556 0.859 0.000 0.920 0.000 0.000 0.000 0.080
#> GSM97840 6 0.5543 0.377 0.032 0.100 0.000 0.000 0.260 0.608
#> GSM97846 2 0.1556 0.859 0.000 0.920 0.000 0.000 0.000 0.080
#> GSM97848 2 0.2092 0.880 0.000 0.876 0.000 0.000 0.000 0.124
#> GSM97849 2 0.1556 0.859 0.000 0.920 0.000 0.000 0.000 0.080
#> GSM97850 2 0.2631 0.862 0.000 0.820 0.000 0.000 0.000 0.180
#> GSM97853 2 0.1387 0.864 0.000 0.932 0.000 0.000 0.000 0.068
#> GSM97855 2 0.4534 0.357 0.000 0.496 0.000 0.000 0.032 0.472
#> GSM97878 1 0.0692 0.885 0.976 0.000 0.000 0.000 0.004 0.020
#> GSM97913 6 0.6000 0.432 0.364 0.000 0.000 0.000 0.236 0.400
#> GSM97932 4 0.2373 0.912 0.024 0.000 0.000 0.888 0.004 0.084
#> GSM97939 5 0.1814 0.646 0.000 0.000 0.100 0.000 0.900 0.000
#> GSM97951 6 0.5738 0.330 0.000 0.284 0.000 0.000 0.208 0.508
#> GSM97957 3 0.0363 0.820 0.000 0.000 0.988 0.000 0.012 0.000
#> GSM97972 5 0.4816 0.551 0.016 0.000 0.100 0.000 0.696 0.188
#> GSM97793 3 0.0458 0.826 0.000 0.000 0.984 0.000 0.016 0.000
#> GSM97795 5 0.3608 0.567 0.000 0.000 0.064 0.000 0.788 0.148
#> GSM97802 1 0.3000 0.747 0.840 0.000 0.124 0.000 0.004 0.032
#> GSM97810 5 0.2852 0.624 0.000 0.000 0.064 0.000 0.856 0.080
#> GSM97815 5 0.1802 0.638 0.000 0.000 0.072 0.000 0.916 0.012
#> GSM97837 1 0.1421 0.875 0.944 0.000 0.000 0.000 0.028 0.028
#> GSM97843 3 0.0000 0.827 0.000 0.000 1.000 0.000 0.000 0.000
#> GSM97890 3 0.3309 0.645 0.000 0.000 0.720 0.000 0.280 0.000
#> GSM97899 4 0.0146 0.943 0.000 0.000 0.000 0.996 0.000 0.004
#> GSM97910 1 0.2145 0.849 0.900 0.000 0.000 0.000 0.028 0.072
#> GSM97916 1 0.1951 0.854 0.908 0.000 0.000 0.000 0.016 0.076
#> GSM97920 3 0.0458 0.827 0.000 0.000 0.984 0.000 0.016 0.000
#> GSM97921 1 0.0806 0.885 0.972 0.000 0.000 0.000 0.020 0.008
#> GSM97927 1 0.1501 0.883 0.924 0.000 0.000 0.000 0.000 0.076
#> GSM97937 1 0.0858 0.885 0.968 0.000 0.000 0.000 0.028 0.004
#> GSM97941 6 0.5822 0.364 0.132 0.020 0.000 0.000 0.312 0.536
#> GSM97943 5 0.6852 0.261 0.208 0.000 0.100 0.000 0.492 0.200
#> GSM97958 6 0.6131 0.383 0.332 0.000 0.000 0.000 0.332 0.336
#> GSM97960 5 0.3150 0.610 0.000 0.000 0.064 0.000 0.832 0.104
#> GSM97794 1 0.1908 0.845 0.900 0.000 0.000 0.000 0.004 0.096
#> GSM97796 4 0.1285 0.936 0.000 0.000 0.000 0.944 0.004 0.052
#> GSM97797 1 0.2442 0.793 0.852 0.000 0.000 0.000 0.004 0.144
#> GSM97798 4 0.0260 0.943 0.000 0.000 0.000 0.992 0.000 0.008
#> GSM97801 1 0.1845 0.863 0.920 0.000 0.000 0.000 0.028 0.052
#> GSM97806 1 0.1556 0.882 0.920 0.000 0.000 0.000 0.000 0.080
#> GSM97808 4 0.0260 0.943 0.000 0.000 0.000 0.992 0.000 0.008
#> GSM97813 1 0.1501 0.883 0.924 0.000 0.000 0.000 0.000 0.076
#> GSM97814 4 0.0260 0.943 0.000 0.000 0.000 0.992 0.000 0.008
#> GSM97818 1 0.1753 0.855 0.912 0.000 0.000 0.000 0.004 0.084
#> GSM97819 3 0.2378 0.762 0.000 0.000 0.848 0.000 0.152 0.000
#> GSM97821 5 0.5841 -0.305 0.192 0.000 0.000 0.000 0.436 0.372
#> GSM97826 1 0.0858 0.885 0.968 0.000 0.000 0.000 0.028 0.004
#> GSM97829 1 0.1257 0.879 0.952 0.000 0.000 0.000 0.028 0.020
#> GSM97832 5 0.3196 0.615 0.000 0.000 0.064 0.000 0.828 0.108
#> GSM97836 1 0.0000 0.889 1.000 0.000 0.000 0.000 0.000 0.000
#> GSM97839 4 0.1285 0.936 0.000 0.000 0.000 0.944 0.004 0.052
#> GSM97844 2 0.0547 0.884 0.000 0.980 0.000 0.000 0.000 0.020
#> GSM97847 1 0.1556 0.882 0.920 0.000 0.000 0.000 0.000 0.080
#> GSM97851 4 0.1542 0.934 0.008 0.000 0.000 0.936 0.004 0.052
#> GSM97852 1 0.1556 0.882 0.920 0.000 0.000 0.000 0.000 0.080
#> GSM97856 4 0.0146 0.943 0.000 0.000 0.000 0.996 0.000 0.004
#> GSM97858 2 0.2003 0.881 0.000 0.884 0.000 0.000 0.000 0.116
#> GSM97859 1 0.0508 0.887 0.984 0.000 0.000 0.000 0.012 0.004
#> GSM97861 1 0.1556 0.882 0.920 0.000 0.000 0.000 0.000 0.080
#> GSM97863 4 0.1285 0.936 0.000 0.000 0.000 0.944 0.004 0.052
#> GSM97869 1 0.1588 0.863 0.924 0.000 0.000 0.000 0.004 0.072
#> GSM97870 1 0.1857 0.863 0.924 0.000 0.004 0.000 0.044 0.028
#> GSM97871 4 0.0260 0.943 0.000 0.000 0.000 0.992 0.000 0.008
#> GSM97877 6 0.6021 0.436 0.360 0.000 0.000 0.000 0.244 0.396
#> GSM97879 1 0.1556 0.882 0.920 0.000 0.000 0.000 0.000 0.080
#> GSM97882 1 0.1501 0.883 0.924 0.000 0.000 0.000 0.000 0.076
#> GSM97885 1 0.1010 0.890 0.960 0.000 0.000 0.000 0.004 0.036
#> GSM97886 4 0.1983 0.895 0.020 0.000 0.000 0.908 0.000 0.072
#> GSM97887 4 0.3167 0.799 0.096 0.000 0.000 0.832 0.000 0.072
#> GSM97888 1 0.3175 0.799 0.832 0.000 0.000 0.088 0.000 0.080
#> GSM97889 1 0.1556 0.882 0.920 0.000 0.000 0.000 0.000 0.080
#> GSM97891 1 0.1556 0.882 0.920 0.000 0.000 0.000 0.000 0.080
#> GSM97892 2 0.2378 0.872 0.000 0.848 0.000 0.000 0.000 0.152
#> GSM97893 1 0.2608 0.846 0.872 0.000 0.000 0.048 0.000 0.080
#> GSM97894 4 0.0000 0.943 0.000 0.000 0.000 1.000 0.000 0.000
#> GSM97895 1 0.4988 0.132 0.484 0.000 0.000 0.448 0.000 0.068
#> GSM97896 4 0.3118 0.804 0.092 0.000 0.000 0.836 0.000 0.072
#> GSM97898 4 0.1285 0.936 0.000 0.000 0.000 0.944 0.004 0.052
#> GSM97903 1 0.0858 0.891 0.968 0.000 0.000 0.000 0.004 0.028
#> GSM97905 1 0.1257 0.878 0.952 0.000 0.000 0.000 0.020 0.028
#> GSM97906 4 0.1926 0.901 0.020 0.000 0.000 0.912 0.000 0.068
#> GSM97908 1 0.1556 0.882 0.920 0.000 0.000 0.000 0.000 0.080
#> GSM97912 1 0.1341 0.877 0.948 0.000 0.000 0.000 0.028 0.024
#> GSM97914 1 0.1500 0.872 0.936 0.000 0.000 0.000 0.012 0.052
#> GSM97915 4 0.1219 0.937 0.000 0.000 0.000 0.948 0.004 0.048
#> GSM97917 4 0.4270 0.690 0.156 0.000 0.000 0.740 0.004 0.100
#> GSM97918 4 0.1285 0.936 0.000 0.000 0.000 0.944 0.004 0.052
#> GSM97919 4 0.1285 0.936 0.000 0.000 0.000 0.944 0.004 0.052
#> GSM97922 1 0.1556 0.882 0.920 0.000 0.000 0.000 0.000 0.080
#> GSM97924 2 0.2730 0.856 0.000 0.808 0.000 0.000 0.000 0.192
#> GSM97926 3 0.6896 -0.145 0.316 0.000 0.348 0.000 0.288 0.048
#> GSM97930 1 0.1556 0.882 0.920 0.000 0.000 0.000 0.000 0.080
#> GSM97931 5 0.6082 -0.406 0.272 0.000 0.000 0.000 0.368 0.360
#> GSM97935 1 0.1556 0.882 0.920 0.000 0.000 0.000 0.000 0.080
#> GSM97936 4 0.0146 0.943 0.004 0.000 0.000 0.996 0.000 0.000
#> GSM97938 1 0.0363 0.890 0.988 0.000 0.000 0.000 0.000 0.012
#> GSM97940 4 0.0260 0.943 0.000 0.000 0.000 0.992 0.000 0.008
#> GSM97942 3 0.1501 0.806 0.000 0.000 0.924 0.000 0.076 0.000
#> GSM97945 4 0.1856 0.907 0.048 0.000 0.000 0.920 0.000 0.032
#> GSM97946 2 0.2730 0.856 0.000 0.808 0.000 0.000 0.000 0.192
#> GSM97948 1 0.4614 0.320 0.624 0.000 0.332 0.000 0.016 0.028
#> GSM97950 4 0.1701 0.904 0.008 0.000 0.000 0.920 0.000 0.072
#> GSM97952 4 0.0260 0.943 0.000 0.000 0.000 0.992 0.000 0.008
#> GSM97953 1 0.0458 0.889 0.984 0.000 0.000 0.000 0.000 0.016
#> GSM97954 1 0.1556 0.882 0.920 0.000 0.000 0.000 0.000 0.080
#> GSM97955 4 0.1219 0.921 0.048 0.000 0.000 0.948 0.000 0.004
#> GSM97959 1 0.4478 0.452 0.680 0.000 0.000 0.000 0.076 0.244
#> GSM97961 4 0.1285 0.936 0.000 0.000 0.000 0.944 0.004 0.052
#> GSM97963 4 0.0146 0.943 0.000 0.000 0.000 0.996 0.000 0.004
#> GSM97965 4 0.0000 0.943 0.000 0.000 0.000 1.000 0.000 0.000
#> GSM97966 4 0.0146 0.943 0.000 0.000 0.000 0.996 0.000 0.004
#> GSM97967 2 0.1501 0.860 0.000 0.924 0.000 0.000 0.000 0.076
#> GSM97968 6 0.5351 0.223 0.000 0.288 0.000 0.000 0.144 0.568
#> GSM97969 1 0.1387 0.885 0.932 0.000 0.000 0.000 0.000 0.068
#> GSM97971 1 0.0363 0.888 0.988 0.000 0.000 0.000 0.012 0.000
#> GSM97799 5 0.3515 0.422 0.000 0.000 0.324 0.000 0.676 0.000
#> GSM97823 2 0.2730 0.856 0.000 0.808 0.000 0.000 0.000 0.192
#> GSM97824 3 0.3175 0.675 0.000 0.000 0.744 0.000 0.256 0.000
#> GSM97830 3 0.0363 0.820 0.000 0.000 0.988 0.000 0.012 0.000
#> GSM97835 5 0.1610 0.642 0.000 0.000 0.084 0.000 0.916 0.000
#> GSM97838 2 0.2730 0.856 0.000 0.808 0.000 0.000 0.000 0.192
#> GSM97841 2 0.2697 0.858 0.000 0.812 0.000 0.000 0.000 0.188
#> GSM97842 5 0.3023 0.583 0.000 0.000 0.232 0.000 0.768 0.000
#> GSM97854 2 0.1327 0.888 0.000 0.936 0.000 0.000 0.000 0.064
#> GSM97857 3 0.3823 0.307 0.000 0.000 0.564 0.000 0.436 0.000
#> GSM97860 3 0.0000 0.827 0.000 0.000 1.000 0.000 0.000 0.000
#> GSM97862 3 0.0458 0.826 0.000 0.000 0.984 0.000 0.016 0.000
#> GSM97864 2 0.0363 0.882 0.000 0.988 0.000 0.000 0.000 0.012
#> GSM97866 3 0.0000 0.827 0.000 0.000 1.000 0.000 0.000 0.000
#> GSM97868 3 0.3330 0.642 0.000 0.000 0.716 0.000 0.284 0.000
#> GSM97872 1 0.0909 0.883 0.968 0.000 0.000 0.000 0.012 0.020
#> GSM97873 5 0.2941 0.598 0.000 0.000 0.220 0.000 0.780 0.000
#> GSM97874 3 0.0363 0.820 0.000 0.000 0.988 0.000 0.012 0.000
#> GSM97875 3 0.3244 0.658 0.000 0.000 0.732 0.000 0.268 0.000
#> GSM97876 3 0.0000 0.827 0.000 0.000 1.000 0.000 0.000 0.000
#> GSM97880 3 0.0000 0.827 0.000 0.000 1.000 0.000 0.000 0.000
#> GSM97881 3 0.3330 0.641 0.000 0.000 0.716 0.000 0.284 0.000
#> GSM97884 5 0.3175 0.548 0.000 0.000 0.256 0.000 0.744 0.000
#> GSM97901 3 0.0000 0.827 0.000 0.000 1.000 0.000 0.000 0.000
#> GSM97902 1 0.2726 0.798 0.856 0.000 0.000 0.000 0.032 0.112
#> GSM97909 5 0.5681 -0.293 0.156 0.000 0.000 0.000 0.428 0.416
#> GSM97911 3 0.3351 0.637 0.000 0.000 0.712 0.000 0.288 0.000
#> GSM97923 3 0.0000 0.827 0.000 0.000 1.000 0.000 0.000 0.000
#> GSM97928 1 0.0146 0.889 0.996 0.000 0.000 0.000 0.000 0.004
#> GSM97929 2 0.0363 0.882 0.000 0.988 0.000 0.000 0.000 0.012
#> GSM97933 3 0.0458 0.826 0.000 0.000 0.984 0.000 0.016 0.000
#> GSM97934 3 0.0363 0.820 0.000 0.000 0.988 0.000 0.012 0.000
#> GSM97944 5 0.3515 0.422 0.000 0.000 0.324 0.000 0.676 0.000
#> GSM97949 2 0.0363 0.882 0.000 0.988 0.000 0.000 0.000 0.012
#> GSM97956 3 0.2092 0.782 0.000 0.000 0.876 0.000 0.124 0.000
#> GSM97962 3 0.0146 0.827 0.000 0.000 0.996 0.000 0.004 0.000
#> GSM97964 3 0.3823 0.314 0.000 0.000 0.564 0.000 0.436 0.000
#> GSM97970 5 0.3221 0.536 0.000 0.000 0.264 0.000 0.736 0.000
#> GSM97822 1 0.1556 0.882 0.920 0.000 0.000 0.000 0.000 0.080
#> GSM97831 3 0.0363 0.820 0.000 0.000 0.988 0.000 0.012 0.000
#> GSM97845 1 0.1556 0.882 0.920 0.000 0.000 0.000 0.000 0.080
#> GSM97865 1 0.1219 0.876 0.948 0.000 0.000 0.000 0.004 0.048
#> GSM97867 3 0.0000 0.827 0.000 0.000 1.000 0.000 0.000 0.000
#> GSM97883 3 0.1387 0.809 0.000 0.000 0.932 0.000 0.068 0.000
#> GSM97897 1 0.1812 0.878 0.912 0.000 0.000 0.008 0.000 0.080
#> GSM97900 1 0.4406 0.598 0.696 0.000 0.000 0.224 0.000 0.080
#> GSM97904 1 0.0146 0.888 0.996 0.000 0.000 0.000 0.000 0.004
#> GSM97907 2 0.2631 0.862 0.000 0.820 0.000 0.000 0.000 0.180
#> GSM97925 3 0.3936 0.625 0.020 0.000 0.700 0.000 0.276 0.004
#> GSM97947 3 0.4555 0.585 0.040 0.000 0.672 0.000 0.272 0.016
Heatmaps for the consensus matrix. It visualizes the probability of two samples to be in a same group.
consensus_heatmap(res, k = 2)
consensus_heatmap(res, k = 3)
consensus_heatmap(res, k = 4)
consensus_heatmap(res, k = 5)
consensus_heatmap(res, k = 6)
Heatmaps for the membership of samples in all partitions to see how consistent they are:
membership_heatmap(res, k = 2)
membership_heatmap(res, k = 3)
membership_heatmap(res, k = 4)
membership_heatmap(res, k = 5)
membership_heatmap(res, k = 6)
As soon as we have had the classes for columns, we can look for signatures which are significantly different between classes which can be candidate marks for certain classes. Following are the heatmaps for signatures.
Signature heatmaps where rows are scaled:
get_signatures(res, k = 2)
get_signatures(res, k = 3)
get_signatures(res, k = 4)
get_signatures(res, k = 5)
get_signatures(res, k = 6)
Signature heatmaps where rows are not scaled:
get_signatures(res, k = 2, scale_rows = FALSE)
get_signatures(res, k = 3, scale_rows = FALSE)
get_signatures(res, k = 4, scale_rows = FALSE)
get_signatures(res, k = 5, scale_rows = FALSE)
get_signatures(res, k = 6, scale_rows = FALSE)
Compare the overlap of signatures from different k:
compare_signatures(res)
get_signature() returns a data frame invisibly. TO get the list of signatures, the function
call should be assigned to a variable explicitly. In following code, if plot argument is set
to FALSE, no heatmap is plotted while only the differential analysis is performed.
# code only for demonstration
tb = get_signature(res, k = ..., plot = FALSE)
An example of the output of tb is:
#> which_row fdr mean_1 mean_2 scaled_mean_1 scaled_mean_2 km
#> 1 38 0.042760348 8.373488 9.131774 -0.5533452 0.5164555 1
#> 2 40 0.018707592 7.106213 8.469186 -0.6173731 0.5762149 1
#> 3 55 0.019134737 10.221463 11.207825 -0.6159697 0.5749050 1
#> 4 59 0.006059896 5.921854 7.869574 -0.6899429 0.6439467 1
#> 5 60 0.018055526 8.928898 10.211722 -0.6204761 0.5791110 1
#> 6 98 0.009384629 15.714769 14.887706 0.6635654 -0.6193277 2
...
The columns in tb are:
which_row: row indices corresponding to the input matrix.fdr: FDR for the differential test. mean_x: The mean value in group x.scaled_mean_x: The mean value in group x after rows are scaled.km: Row groups if k-means clustering is applied to rows.UMAP plot which shows how samples are separated.
dimension_reduction(res, k = 2, method = "UMAP")
dimension_reduction(res, k = 3, method = "UMAP")
dimension_reduction(res, k = 4, method = "UMAP")
dimension_reduction(res, k = 5, method = "UMAP")
dimension_reduction(res, k = 6, method = "UMAP")
Following heatmap shows how subgroups are split when increasing k:
collect_classes(res)
Test correlation between subgroups and known annotations. If the known annotation is numeric, one-way ANOVA test is applied, and if the known annotation is discrete, chi-squared contingency table test is applied.
test_to_known_factors(res)
#> n disease.state(p) tissue(p) k
#> SD:mclust 180 8.42e-18 5.58e-18 2
#> SD:mclust 163 2.00e-29 1.69e-30 3
#> SD:mclust 171 1.28e-29 1.75e-30 4
#> SD:mclust 164 5.12e-33 4.31e-31 5
#> SD:mclust 160 1.92e-27 1.14e-26 6
If matrix rows can be associated to genes, consider to use functional_enrichment(res,
...) to perform function enrichment for the signature genes. See this vignette for more detailed explanations.
The object with results only for a single top-value method and a single partition method can be extracted as:
res = res_list["SD", "NMF"]
# you can also extract it by
# res = res_list["SD:NMF"]
A summary of res and all the functions that can be applied to it:
res
#> A 'ConsensusPartition' object with k = 2, 3, 4, 5, 6.
#> On a matrix with 51882 rows and 180 columns.
#> Top rows (1000, 2000, 3000, 4000, 5000) are extracted by 'SD' method.
#> Subgroups are detected by 'NMF' method.
#> Performed in total 1250 partitions by row resampling.
#> Best k for subgroups seems to be 4.
#>
#> Following methods can be applied to this 'ConsensusPartition' object:
#> [1] "cola_report" "collect_classes" "collect_plots"
#> [4] "collect_stats" "colnames" "compare_signatures"
#> [7] "consensus_heatmap" "dimension_reduction" "functional_enrichment"
#> [10] "get_anno_col" "get_anno" "get_classes"
#> [13] "get_consensus" "get_matrix" "get_membership"
#> [16] "get_param" "get_signatures" "get_stats"
#> [19] "is_best_k" "is_stable_k" "membership_heatmap"
#> [22] "ncol" "nrow" "plot_ecdf"
#> [25] "rownames" "select_partition_number" "show"
#> [28] "suggest_best_k" "test_to_known_factors"
collect_plots() function collects all the plots made from res for all k (number of partitions)
into one single page to provide an easy and fast comparison between different k.
collect_plots(res)
The plots are:
k and the heatmap of
predicted classes for each k.k.k.k.All the plots in panels can be made by individual functions and they are plotted later in this section.
select_partition_number() produces several plots showing different
statistics for choosing “optimized” k. There are following statistics:
k;k, the area increased is defined as \(A_k - A_{k-1}\).The detailed explanations of these statistics can be found in the cola vignette.
Generally speaking, lower PAC score, higher mean silhouette score or higher
concordance corresponds to better partition. Rand index and Jaccard index
measure how similar the current partition is compared to partition with k-1.
If they are too similar, we won't accept k is better than k-1.
select_partition_number(res)
The numeric values for all these statistics can be obtained by get_stats().
get_stats(res)
#> k 1-PAC mean_silhouette concordance area_increased Rand Jaccard
#> 2 2 0.942 0.938 0.975 0.5014 0.498 0.498
#> 3 3 0.993 0.965 0.985 0.3057 0.781 0.588
#> 4 4 0.921 0.901 0.957 0.0971 0.912 0.752
#> 5 5 0.738 0.659 0.821 0.0665 0.950 0.826
#> 6 6 0.735 0.630 0.804 0.0382 0.924 0.716
suggest_best_k() suggests the best \(k\) based on these statistics. The rules are as follows:
suggest_best_k(res)
#> [1] 4
#> attr(,"optional")
#> [1] 2 3
There is also optional best \(k\) = 2 3 that is worth to check.
Following shows the table of the partitions (You need to click the show/hide
code output link to see it). The membership matrix (columns with name p*)
is inferred by
clue::cl_consensus()
function with the SE method. Basically the value in the membership matrix
represents the probability to belong to a certain group. The finall class
label for an item is determined with the group with highest probability it
belongs to.
In get_classes() function, the entropy is calculated from the membership
matrix and the silhouette score is calculated from the consensus matrix.
cbind(get_classes(res, k = 2), get_membership(res, k = 2))
#> class entropy silhouette p1 p2
#> GSM97800 2 0.0000 0.984 0.000 1.000
#> GSM97803 2 0.0000 0.984 0.000 1.000
#> GSM97804 2 0.0000 0.984 0.000 1.000
#> GSM97805 2 0.0000 0.984 0.000 1.000
#> GSM97807 2 0.0000 0.984 0.000 1.000
#> GSM97809 2 0.0000 0.984 0.000 1.000
#> GSM97811 2 0.0000 0.984 0.000 1.000
#> GSM97812 2 0.0000 0.984 0.000 1.000
#> GSM97816 2 0.0000 0.984 0.000 1.000
#> GSM97817 2 0.0000 0.984 0.000 1.000
#> GSM97820 2 0.0000 0.984 0.000 1.000
#> GSM97825 2 0.0000 0.984 0.000 1.000
#> GSM97827 2 0.0000 0.984 0.000 1.000
#> GSM97828 2 0.0000 0.984 0.000 1.000
#> GSM97833 2 0.0000 0.984 0.000 1.000
#> GSM97834 2 0.0000 0.984 0.000 1.000
#> GSM97840 2 0.0000 0.984 0.000 1.000
#> GSM97846 2 0.0000 0.984 0.000 1.000
#> GSM97848 2 0.0000 0.984 0.000 1.000
#> GSM97849 2 0.0000 0.984 0.000 1.000
#> GSM97850 2 0.0000 0.984 0.000 1.000
#> GSM97853 2 0.0000 0.984 0.000 1.000
#> GSM97855 2 0.0000 0.984 0.000 1.000
#> GSM97878 1 0.0000 0.965 1.000 0.000
#> GSM97913 2 0.0000 0.984 0.000 1.000
#> GSM97932 1 0.0000 0.965 1.000 0.000
#> GSM97939 2 0.0000 0.984 0.000 1.000
#> GSM97951 2 0.0000 0.984 0.000 1.000
#> GSM97957 2 0.0000 0.984 0.000 1.000
#> GSM97972 2 0.0000 0.984 0.000 1.000
#> GSM97793 1 0.8267 0.656 0.740 0.260
#> GSM97795 2 0.0000 0.984 0.000 1.000
#> GSM97802 1 0.9988 0.112 0.520 0.480
#> GSM97810 2 0.0000 0.984 0.000 1.000
#> GSM97815 2 0.0000 0.984 0.000 1.000
#> GSM97837 1 0.0000 0.965 1.000 0.000
#> GSM97843 2 0.0000 0.984 0.000 1.000
#> GSM97890 2 0.0000 0.984 0.000 1.000
#> GSM97899 1 0.0000 0.965 1.000 0.000
#> GSM97910 1 0.6531 0.792 0.832 0.168
#> GSM97916 1 0.0000 0.965 1.000 0.000
#> GSM97920 2 0.0000 0.984 0.000 1.000
#> GSM97921 1 0.0000 0.965 1.000 0.000
#> GSM97927 1 0.0000 0.965 1.000 0.000
#> GSM97937 1 0.0000 0.965 1.000 0.000
#> GSM97941 2 0.0000 0.984 0.000 1.000
#> GSM97943 2 0.2236 0.950 0.036 0.964
#> GSM97958 2 0.0000 0.984 0.000 1.000
#> GSM97960 2 0.0000 0.984 0.000 1.000
#> GSM97794 1 0.6148 0.813 0.848 0.152
#> GSM97796 1 0.0000 0.965 1.000 0.000
#> GSM97797 1 0.9983 0.127 0.524 0.476
#> GSM97798 1 0.0000 0.965 1.000 0.000
#> GSM97801 1 0.0000 0.965 1.000 0.000
#> GSM97806 1 0.0000 0.965 1.000 0.000
#> GSM97808 1 0.0000 0.965 1.000 0.000
#> GSM97813 1 0.0000 0.965 1.000 0.000
#> GSM97814 1 0.0000 0.965 1.000 0.000
#> GSM97818 1 0.0000 0.965 1.000 0.000
#> GSM97819 1 0.7376 0.738 0.792 0.208
#> GSM97821 2 0.0000 0.984 0.000 1.000
#> GSM97826 1 0.0000 0.965 1.000 0.000
#> GSM97829 1 0.0000 0.965 1.000 0.000
#> GSM97832 2 0.0000 0.984 0.000 1.000
#> GSM97836 1 0.0000 0.965 1.000 0.000
#> GSM97839 1 0.0000 0.965 1.000 0.000
#> GSM97844 2 0.0000 0.984 0.000 1.000
#> GSM97847 1 0.0000 0.965 1.000 0.000
#> GSM97851 1 0.0000 0.965 1.000 0.000
#> GSM97852 1 0.0000 0.965 1.000 0.000
#> GSM97856 1 0.0000 0.965 1.000 0.000
#> GSM97858 2 0.0000 0.984 0.000 1.000
#> GSM97859 1 0.0000 0.965 1.000 0.000
#> GSM97861 1 0.0000 0.965 1.000 0.000
#> GSM97863 1 0.0000 0.965 1.000 0.000
#> GSM97869 1 0.0000 0.965 1.000 0.000
#> GSM97870 1 0.0000 0.965 1.000 0.000
#> GSM97871 1 0.0000 0.965 1.000 0.000
#> GSM97877 2 0.0000 0.984 0.000 1.000
#> GSM97879 1 0.0000 0.965 1.000 0.000
#> GSM97882 1 0.0000 0.965 1.000 0.000
#> GSM97885 1 0.0000 0.965 1.000 0.000
#> GSM97886 1 0.0000 0.965 1.000 0.000
#> GSM97887 1 0.0000 0.965 1.000 0.000
#> GSM97888 1 0.0000 0.965 1.000 0.000
#> GSM97889 1 0.0000 0.965 1.000 0.000
#> GSM97891 1 0.0000 0.965 1.000 0.000
#> GSM97892 2 0.0000 0.984 0.000 1.000
#> GSM97893 1 0.0000 0.965 1.000 0.000
#> GSM97894 1 0.0000 0.965 1.000 0.000
#> GSM97895 1 0.0000 0.965 1.000 0.000
#> GSM97896 1 0.0000 0.965 1.000 0.000
#> GSM97898 1 0.0000 0.965 1.000 0.000
#> GSM97903 1 0.0000 0.965 1.000 0.000
#> GSM97905 1 0.0000 0.965 1.000 0.000
#> GSM97906 1 0.0000 0.965 1.000 0.000
#> GSM97908 1 0.0000 0.965 1.000 0.000
#> GSM97912 1 0.0000 0.965 1.000 0.000
#> GSM97914 1 0.0000 0.965 1.000 0.000
#> GSM97915 1 0.0000 0.965 1.000 0.000
#> GSM97917 1 0.0000 0.965 1.000 0.000
#> GSM97918 1 0.0000 0.965 1.000 0.000
#> GSM97919 1 0.0000 0.965 1.000 0.000
#> GSM97922 1 0.0000 0.965 1.000 0.000
#> GSM97924 2 0.0000 0.984 0.000 1.000
#> GSM97926 1 0.9522 0.432 0.628 0.372
#> GSM97930 1 0.0000 0.965 1.000 0.000
#> GSM97931 2 0.0000 0.984 0.000 1.000
#> GSM97935 1 0.0000 0.965 1.000 0.000
#> GSM97936 1 0.0000 0.965 1.000 0.000
#> GSM97938 1 0.0000 0.965 1.000 0.000
#> GSM97940 1 0.0000 0.965 1.000 0.000
#> GSM97942 1 0.1414 0.948 0.980 0.020
#> GSM97945 1 0.0000 0.965 1.000 0.000
#> GSM97946 2 0.0000 0.984 0.000 1.000
#> GSM97948 1 0.0000 0.965 1.000 0.000
#> GSM97950 1 0.0000 0.965 1.000 0.000
#> GSM97952 1 0.0000 0.965 1.000 0.000
#> GSM97953 1 0.0000 0.965 1.000 0.000
#> GSM97954 1 0.0000 0.965 1.000 0.000
#> GSM97955 1 0.0000 0.965 1.000 0.000
#> GSM97959 2 0.5842 0.829 0.140 0.860
#> GSM97961 1 0.0000 0.965 1.000 0.000
#> GSM97963 1 0.0000 0.965 1.000 0.000
#> GSM97965 1 0.0000 0.965 1.000 0.000
#> GSM97966 1 0.0000 0.965 1.000 0.000
#> GSM97967 2 0.0000 0.984 0.000 1.000
#> GSM97968 2 0.0000 0.984 0.000 1.000
#> GSM97969 1 0.0000 0.965 1.000 0.000
#> GSM97971 1 0.0000 0.965 1.000 0.000
#> GSM97799 2 0.0000 0.984 0.000 1.000
#> GSM97823 2 0.0000 0.984 0.000 1.000
#> GSM97824 2 0.0000 0.984 0.000 1.000
#> GSM97830 2 0.0000 0.984 0.000 1.000
#> GSM97835 2 0.0000 0.984 0.000 1.000
#> GSM97838 2 0.0000 0.984 0.000 1.000
#> GSM97841 2 0.0000 0.984 0.000 1.000
#> GSM97842 2 0.0000 0.984 0.000 1.000
#> GSM97854 2 0.0000 0.984 0.000 1.000
#> GSM97857 2 0.0000 0.984 0.000 1.000
#> GSM97860 2 0.9129 0.494 0.328 0.672
#> GSM97862 2 0.0000 0.984 0.000 1.000
#> GSM97864 2 0.0000 0.984 0.000 1.000
#> GSM97866 2 0.0000 0.984 0.000 1.000
#> GSM97868 2 0.0000 0.984 0.000 1.000
#> GSM97872 1 0.0000 0.965 1.000 0.000
#> GSM97873 2 0.0000 0.984 0.000 1.000
#> GSM97874 2 0.5842 0.828 0.140 0.860
#> GSM97875 2 0.0000 0.984 0.000 1.000
#> GSM97876 2 0.0672 0.977 0.008 0.992
#> GSM97880 1 0.4431 0.881 0.908 0.092
#> GSM97881 2 0.0000 0.984 0.000 1.000
#> GSM97884 2 0.0000 0.984 0.000 1.000
#> GSM97901 2 0.0000 0.984 0.000 1.000
#> GSM97902 2 0.2043 0.954 0.032 0.968
#> GSM97909 2 0.0000 0.984 0.000 1.000
#> GSM97911 2 0.0000 0.984 0.000 1.000
#> GSM97923 1 0.9608 0.402 0.616 0.384
#> GSM97928 1 0.0000 0.965 1.000 0.000
#> GSM97929 2 0.0000 0.984 0.000 1.000
#> GSM97933 1 0.9963 0.168 0.536 0.464
#> GSM97934 2 0.7453 0.721 0.212 0.788
#> GSM97944 2 0.0000 0.984 0.000 1.000
#> GSM97949 2 0.0000 0.984 0.000 1.000
#> GSM97956 2 0.0000 0.984 0.000 1.000
#> GSM97962 2 0.0000 0.984 0.000 1.000
#> GSM97964 2 0.0000 0.984 0.000 1.000
#> GSM97970 2 0.0000 0.984 0.000 1.000
#> GSM97822 1 0.0000 0.965 1.000 0.000
#> GSM97831 2 0.0000 0.984 0.000 1.000
#> GSM97845 1 0.0000 0.965 1.000 0.000
#> GSM97865 1 0.0000 0.965 1.000 0.000
#> GSM97867 1 0.0000 0.965 1.000 0.000
#> GSM97883 1 0.2948 0.920 0.948 0.052
#> GSM97897 1 0.0000 0.965 1.000 0.000
#> GSM97900 1 0.0000 0.965 1.000 0.000
#> GSM97904 1 0.0000 0.965 1.000 0.000
#> GSM97907 2 0.0000 0.984 0.000 1.000
#> GSM97925 2 0.9635 0.339 0.388 0.612
#> GSM97947 1 0.3274 0.913 0.940 0.060
cbind(get_classes(res, k = 3), get_membership(res, k = 3))
#> class entropy silhouette p1 p2 p3
#> GSM97800 2 0.0000 0.982 0.000 1.000 0.000
#> GSM97803 2 0.0000 0.982 0.000 1.000 0.000
#> GSM97804 2 0.0000 0.982 0.000 1.000 0.000
#> GSM97805 2 0.0000 0.982 0.000 1.000 0.000
#> GSM97807 2 0.0000 0.982 0.000 1.000 0.000
#> GSM97809 2 0.0000 0.982 0.000 1.000 0.000
#> GSM97811 2 0.0000 0.982 0.000 1.000 0.000
#> GSM97812 2 0.0000 0.982 0.000 1.000 0.000
#> GSM97816 2 0.0000 0.982 0.000 1.000 0.000
#> GSM97817 2 0.0000 0.982 0.000 1.000 0.000
#> GSM97820 2 0.0000 0.982 0.000 1.000 0.000
#> GSM97825 2 0.0000 0.982 0.000 1.000 0.000
#> GSM97827 2 0.0000 0.982 0.000 1.000 0.000
#> GSM97828 2 0.2448 0.907 0.000 0.924 0.076
#> GSM97833 2 0.0000 0.982 0.000 1.000 0.000
#> GSM97834 2 0.0000 0.982 0.000 1.000 0.000
#> GSM97840 2 0.0000 0.982 0.000 1.000 0.000
#> GSM97846 2 0.0000 0.982 0.000 1.000 0.000
#> GSM97848 2 0.0000 0.982 0.000 1.000 0.000
#> GSM97849 2 0.0000 0.982 0.000 1.000 0.000
#> GSM97850 2 0.0000 0.982 0.000 1.000 0.000
#> GSM97853 2 0.0000 0.982 0.000 1.000 0.000
#> GSM97855 2 0.0000 0.982 0.000 1.000 0.000
#> GSM97878 1 0.0000 0.988 1.000 0.000 0.000
#> GSM97913 2 0.0000 0.982 0.000 1.000 0.000
#> GSM97932 1 0.0000 0.988 1.000 0.000 0.000
#> GSM97939 3 0.2796 0.891 0.000 0.092 0.908
#> GSM97951 2 0.0000 0.982 0.000 1.000 0.000
#> GSM97957 3 0.0000 0.980 0.000 0.000 1.000
#> GSM97972 2 0.0000 0.982 0.000 1.000 0.000
#> GSM97793 3 0.0000 0.980 0.000 0.000 1.000
#> GSM97795 2 0.0237 0.979 0.000 0.996 0.004
#> GSM97802 3 0.0237 0.977 0.000 0.004 0.996
#> GSM97810 2 0.2878 0.887 0.000 0.904 0.096
#> GSM97815 2 0.2959 0.883 0.000 0.900 0.100
#> GSM97837 1 0.3267 0.869 0.884 0.000 0.116
#> GSM97843 3 0.0000 0.980 0.000 0.000 1.000
#> GSM97890 3 0.0000 0.980 0.000 0.000 1.000
#> GSM97899 1 0.0000 0.988 1.000 0.000 0.000
#> GSM97910 1 0.5111 0.800 0.820 0.036 0.144
#> GSM97916 1 0.0000 0.988 1.000 0.000 0.000
#> GSM97920 3 0.0000 0.980 0.000 0.000 1.000
#> GSM97921 1 0.0000 0.988 1.000 0.000 0.000
#> GSM97927 1 0.0000 0.988 1.000 0.000 0.000
#> GSM97937 1 0.0000 0.988 1.000 0.000 0.000
#> GSM97941 2 0.0000 0.982 0.000 1.000 0.000
#> GSM97943 3 0.6487 0.611 0.032 0.268 0.700
#> GSM97958 2 0.0000 0.982 0.000 1.000 0.000
#> GSM97960 2 0.0237 0.979 0.000 0.996 0.004
#> GSM97794 1 0.3619 0.840 0.864 0.136 0.000
#> GSM97796 1 0.0000 0.988 1.000 0.000 0.000
#> GSM97797 2 0.6286 0.128 0.464 0.536 0.000
#> GSM97798 1 0.0000 0.988 1.000 0.000 0.000
#> GSM97801 1 0.0000 0.988 1.000 0.000 0.000
#> GSM97806 1 0.0000 0.988 1.000 0.000 0.000
#> GSM97808 1 0.0000 0.988 1.000 0.000 0.000
#> GSM97813 1 0.0000 0.988 1.000 0.000 0.000
#> GSM97814 1 0.0000 0.988 1.000 0.000 0.000
#> GSM97818 1 0.0747 0.974 0.984 0.016 0.000
#> GSM97819 3 0.0000 0.980 0.000 0.000 1.000
#> GSM97821 2 0.0000 0.982 0.000 1.000 0.000
#> GSM97826 1 0.0000 0.988 1.000 0.000 0.000
#> GSM97829 1 0.0000 0.988 1.000 0.000 0.000
#> GSM97832 2 0.1163 0.958 0.000 0.972 0.028
#> GSM97836 1 0.5968 0.427 0.636 0.000 0.364
#> GSM97839 1 0.0000 0.988 1.000 0.000 0.000
#> GSM97844 2 0.0000 0.982 0.000 1.000 0.000
#> GSM97847 1 0.0000 0.988 1.000 0.000 0.000
#> GSM97851 1 0.0000 0.988 1.000 0.000 0.000
#> GSM97852 1 0.0000 0.988 1.000 0.000 0.000
#> GSM97856 1 0.0000 0.988 1.000 0.000 0.000
#> GSM97858 2 0.0000 0.982 0.000 1.000 0.000
#> GSM97859 1 0.1411 0.956 0.964 0.000 0.036
#> GSM97861 1 0.0000 0.988 1.000 0.000 0.000
#> GSM97863 1 0.0000 0.988 1.000 0.000 0.000
#> GSM97869 1 0.0000 0.988 1.000 0.000 0.000
#> GSM97870 3 0.0000 0.980 0.000 0.000 1.000
#> GSM97871 1 0.0000 0.988 1.000 0.000 0.000
#> GSM97877 2 0.0000 0.982 0.000 1.000 0.000
#> GSM97879 1 0.0000 0.988 1.000 0.000 0.000
#> GSM97882 1 0.0000 0.988 1.000 0.000 0.000
#> GSM97885 1 0.0000 0.988 1.000 0.000 0.000
#> GSM97886 1 0.0000 0.988 1.000 0.000 0.000
#> GSM97887 1 0.0000 0.988 1.000 0.000 0.000
#> GSM97888 1 0.0000 0.988 1.000 0.000 0.000
#> GSM97889 1 0.0237 0.985 0.996 0.000 0.004
#> GSM97891 1 0.0000 0.988 1.000 0.000 0.000
#> GSM97892 2 0.0000 0.982 0.000 1.000 0.000
#> GSM97893 1 0.0000 0.988 1.000 0.000 0.000
#> GSM97894 1 0.0000 0.988 1.000 0.000 0.000
#> GSM97895 1 0.0000 0.988 1.000 0.000 0.000
#> GSM97896 1 0.0000 0.988 1.000 0.000 0.000
#> GSM97898 1 0.0000 0.988 1.000 0.000 0.000
#> GSM97903 1 0.0000 0.988 1.000 0.000 0.000
#> GSM97905 3 0.0000 0.980 0.000 0.000 1.000
#> GSM97906 1 0.0000 0.988 1.000 0.000 0.000
#> GSM97908 1 0.0000 0.988 1.000 0.000 0.000
#> GSM97912 3 0.3686 0.827 0.140 0.000 0.860
#> GSM97914 1 0.0000 0.988 1.000 0.000 0.000
#> GSM97915 1 0.0000 0.988 1.000 0.000 0.000
#> GSM97917 1 0.0000 0.988 1.000 0.000 0.000
#> GSM97918 1 0.0000 0.988 1.000 0.000 0.000
#> GSM97919 1 0.0000 0.988 1.000 0.000 0.000
#> GSM97922 1 0.0000 0.988 1.000 0.000 0.000
#> GSM97924 2 0.0000 0.982 0.000 1.000 0.000
#> GSM97926 3 0.0000 0.980 0.000 0.000 1.000
#> GSM97930 1 0.0000 0.988 1.000 0.000 0.000
#> GSM97931 2 0.0000 0.982 0.000 1.000 0.000
#> GSM97935 1 0.0000 0.988 1.000 0.000 0.000
#> GSM97936 1 0.0000 0.988 1.000 0.000 0.000
#> GSM97938 1 0.0000 0.988 1.000 0.000 0.000
#> GSM97940 1 0.0000 0.988 1.000 0.000 0.000
#> GSM97942 3 0.0000 0.980 0.000 0.000 1.000
#> GSM97945 1 0.0000 0.988 1.000 0.000 0.000
#> GSM97946 2 0.0000 0.982 0.000 1.000 0.000
#> GSM97948 3 0.0000 0.980 0.000 0.000 1.000
#> GSM97950 1 0.0000 0.988 1.000 0.000 0.000
#> GSM97952 1 0.0000 0.988 1.000 0.000 0.000
#> GSM97953 1 0.0000 0.988 1.000 0.000 0.000
#> GSM97954 1 0.0000 0.988 1.000 0.000 0.000
#> GSM97955 1 0.0000 0.988 1.000 0.000 0.000
#> GSM97959 2 0.2878 0.876 0.096 0.904 0.000
#> GSM97961 1 0.0000 0.988 1.000 0.000 0.000
#> GSM97963 1 0.0000 0.988 1.000 0.000 0.000
#> GSM97965 1 0.0000 0.988 1.000 0.000 0.000
#> GSM97966 1 0.0000 0.988 1.000 0.000 0.000
#> GSM97967 2 0.0000 0.982 0.000 1.000 0.000
#> GSM97968 2 0.0000 0.982 0.000 1.000 0.000
#> GSM97969 1 0.0000 0.988 1.000 0.000 0.000
#> GSM97971 1 0.1860 0.940 0.948 0.000 0.052
#> GSM97799 3 0.0000 0.980 0.000 0.000 1.000
#> GSM97823 2 0.0000 0.982 0.000 1.000 0.000
#> GSM97824 3 0.0000 0.980 0.000 0.000 1.000
#> GSM97830 3 0.0000 0.980 0.000 0.000 1.000
#> GSM97835 3 0.5678 0.544 0.000 0.316 0.684
#> GSM97838 2 0.0000 0.982 0.000 1.000 0.000
#> GSM97841 2 0.0000 0.982 0.000 1.000 0.000
#> GSM97842 3 0.0000 0.980 0.000 0.000 1.000
#> GSM97854 2 0.0000 0.982 0.000 1.000 0.000
#> GSM97857 3 0.0000 0.980 0.000 0.000 1.000
#> GSM97860 3 0.0000 0.980 0.000 0.000 1.000
#> GSM97862 3 0.0000 0.980 0.000 0.000 1.000
#> GSM97864 2 0.0000 0.982 0.000 1.000 0.000
#> GSM97866 3 0.0000 0.980 0.000 0.000 1.000
#> GSM97868 3 0.0000 0.980 0.000 0.000 1.000
#> GSM97872 1 0.0000 0.988 1.000 0.000 0.000
#> GSM97873 3 0.0237 0.977 0.000 0.004 0.996
#> GSM97874 3 0.0000 0.980 0.000 0.000 1.000
#> GSM97875 3 0.0000 0.980 0.000 0.000 1.000
#> GSM97876 3 0.0000 0.980 0.000 0.000 1.000
#> GSM97880 3 0.0000 0.980 0.000 0.000 1.000
#> GSM97881 3 0.0000 0.980 0.000 0.000 1.000
#> GSM97884 3 0.1163 0.956 0.000 0.028 0.972
#> GSM97901 3 0.0000 0.980 0.000 0.000 1.000
#> GSM97902 2 0.0592 0.970 0.012 0.988 0.000
#> GSM97909 2 0.0000 0.982 0.000 1.000 0.000
#> GSM97911 3 0.0000 0.980 0.000 0.000 1.000
#> GSM97923 3 0.0000 0.980 0.000 0.000 1.000
#> GSM97928 1 0.0000 0.988 1.000 0.000 0.000
#> GSM97929 2 0.0000 0.982 0.000 1.000 0.000
#> GSM97933 3 0.0000 0.980 0.000 0.000 1.000
#> GSM97934 3 0.0000 0.980 0.000 0.000 1.000
#> GSM97944 3 0.0000 0.980 0.000 0.000 1.000
#> GSM97949 2 0.0000 0.982 0.000 1.000 0.000
#> GSM97956 3 0.0000 0.980 0.000 0.000 1.000
#> GSM97962 3 0.0000 0.980 0.000 0.000 1.000
#> GSM97964 3 0.0000 0.980 0.000 0.000 1.000
#> GSM97970 3 0.0000 0.980 0.000 0.000 1.000
#> GSM97822 1 0.0000 0.988 1.000 0.000 0.000
#> GSM97831 3 0.0000 0.980 0.000 0.000 1.000
#> GSM97845 1 0.0000 0.988 1.000 0.000 0.000
#> GSM97865 1 0.0000 0.988 1.000 0.000 0.000
#> GSM97867 3 0.0000 0.980 0.000 0.000 1.000
#> GSM97883 3 0.0000 0.980 0.000 0.000 1.000
#> GSM97897 1 0.0000 0.988 1.000 0.000 0.000
#> GSM97900 1 0.0000 0.988 1.000 0.000 0.000
#> GSM97904 1 0.0237 0.985 0.996 0.000 0.004
#> GSM97907 2 0.0000 0.982 0.000 1.000 0.000
#> GSM97925 3 0.0000 0.980 0.000 0.000 1.000
#> GSM97947 3 0.0000 0.980 0.000 0.000 1.000
cbind(get_classes(res, k = 4), get_membership(res, k = 4))
#> class entropy silhouette p1 p2 p3 p4
#> GSM97800 2 0.0000 0.9894 0.000 1.000 0.000 0.000
#> GSM97803 2 0.0000 0.9894 0.000 1.000 0.000 0.000
#> GSM97804 2 0.0000 0.9894 0.000 1.000 0.000 0.000
#> GSM97805 2 0.0000 0.9894 0.000 1.000 0.000 0.000
#> GSM97807 2 0.0000 0.9894 0.000 1.000 0.000 0.000
#> GSM97809 2 0.0000 0.9894 0.000 1.000 0.000 0.000
#> GSM97811 2 0.0000 0.9894 0.000 1.000 0.000 0.000
#> GSM97812 2 0.0000 0.9894 0.000 1.000 0.000 0.000
#> GSM97816 1 0.0817 0.8049 0.976 0.024 0.000 0.000
#> GSM97817 2 0.0000 0.9894 0.000 1.000 0.000 0.000
#> GSM97820 2 0.0000 0.9894 0.000 1.000 0.000 0.000
#> GSM97825 2 0.0000 0.9894 0.000 1.000 0.000 0.000
#> GSM97827 2 0.0000 0.9894 0.000 1.000 0.000 0.000
#> GSM97828 1 0.0188 0.8142 0.996 0.000 0.004 0.000
#> GSM97833 2 0.0000 0.9894 0.000 1.000 0.000 0.000
#> GSM97834 2 0.0000 0.9894 0.000 1.000 0.000 0.000
#> GSM97840 2 0.0188 0.9866 0.004 0.996 0.000 0.000
#> GSM97846 2 0.0000 0.9894 0.000 1.000 0.000 0.000
#> GSM97848 2 0.0000 0.9894 0.000 1.000 0.000 0.000
#> GSM97849 2 0.0000 0.9894 0.000 1.000 0.000 0.000
#> GSM97850 2 0.0000 0.9894 0.000 1.000 0.000 0.000
#> GSM97853 2 0.0000 0.9894 0.000 1.000 0.000 0.000
#> GSM97855 2 0.0188 0.9866 0.004 0.996 0.000 0.000
#> GSM97878 4 0.1211 0.9521 0.040 0.000 0.000 0.960
#> GSM97913 2 0.0592 0.9772 0.016 0.984 0.000 0.000
#> GSM97932 4 0.1118 0.9548 0.036 0.000 0.000 0.964
#> GSM97939 3 0.2021 0.8769 0.012 0.056 0.932 0.000
#> GSM97951 2 0.0000 0.9894 0.000 1.000 0.000 0.000
#> GSM97957 1 0.4222 0.5658 0.728 0.000 0.272 0.000
#> GSM97972 1 0.2831 0.7471 0.876 0.120 0.004 0.000
#> GSM97793 3 0.0336 0.9299 0.008 0.000 0.992 0.000
#> GSM97795 2 0.0000 0.9894 0.000 1.000 0.000 0.000
#> GSM97802 3 0.1302 0.8865 0.000 0.000 0.956 0.044
#> GSM97810 2 0.1722 0.9302 0.008 0.944 0.048 0.000
#> GSM97815 2 0.0469 0.9781 0.000 0.988 0.012 0.000
#> GSM97837 1 0.0000 0.8156 1.000 0.000 0.000 0.000
#> GSM97843 3 0.0469 0.9285 0.012 0.000 0.988 0.000
#> GSM97890 3 0.0000 0.9300 0.000 0.000 1.000 0.000
#> GSM97899 4 0.0000 0.9689 0.000 0.000 0.000 1.000
#> GSM97910 1 0.0000 0.8156 1.000 0.000 0.000 0.000
#> GSM97916 4 0.3311 0.8050 0.172 0.000 0.000 0.828
#> GSM97920 1 0.4948 0.1536 0.560 0.000 0.440 0.000
#> GSM97921 1 0.2647 0.7773 0.880 0.000 0.000 0.120
#> GSM97927 4 0.0000 0.9689 0.000 0.000 0.000 1.000
#> GSM97937 1 0.2469 0.7840 0.892 0.000 0.000 0.108
#> GSM97941 2 0.0000 0.9894 0.000 1.000 0.000 0.000
#> GSM97943 1 0.0188 0.8146 0.996 0.000 0.004 0.000
#> GSM97958 2 0.2814 0.8502 0.132 0.868 0.000 0.000
#> GSM97960 2 0.0000 0.9894 0.000 1.000 0.000 0.000
#> GSM97794 4 0.2546 0.8992 0.028 0.060 0.000 0.912
#> GSM97796 4 0.0188 0.9688 0.004 0.000 0.000 0.996
#> GSM97797 1 0.4434 0.6684 0.756 0.016 0.000 0.228
#> GSM97798 4 0.0000 0.9689 0.000 0.000 0.000 1.000
#> GSM97801 1 0.0000 0.8156 1.000 0.000 0.000 0.000
#> GSM97806 4 0.0000 0.9689 0.000 0.000 0.000 1.000
#> GSM97808 4 0.0000 0.9689 0.000 0.000 0.000 1.000
#> GSM97813 4 0.0000 0.9689 0.000 0.000 0.000 1.000
#> GSM97814 4 0.0000 0.9689 0.000 0.000 0.000 1.000
#> GSM97818 4 0.4313 0.6456 0.260 0.004 0.000 0.736
#> GSM97819 3 0.0000 0.9300 0.000 0.000 1.000 0.000
#> GSM97821 2 0.0000 0.9894 0.000 1.000 0.000 0.000
#> GSM97826 1 0.0336 0.8153 0.992 0.000 0.000 0.008
#> GSM97829 1 0.0592 0.8143 0.984 0.000 0.000 0.016
#> GSM97832 2 0.2197 0.9122 0.080 0.916 0.004 0.000
#> GSM97836 3 0.4992 0.0765 0.000 0.000 0.524 0.476
#> GSM97839 4 0.0188 0.9688 0.004 0.000 0.000 0.996
#> GSM97844 2 0.0000 0.9894 0.000 1.000 0.000 0.000
#> GSM97847 4 0.1211 0.9521 0.040 0.000 0.000 0.960
#> GSM97851 4 0.0921 0.9597 0.028 0.000 0.000 0.972
#> GSM97852 4 0.0707 0.9636 0.020 0.000 0.000 0.980
#> GSM97856 4 0.0000 0.9689 0.000 0.000 0.000 1.000
#> GSM97858 2 0.0000 0.9894 0.000 1.000 0.000 0.000
#> GSM97859 4 0.0469 0.9674 0.012 0.000 0.000 0.988
#> GSM97861 4 0.0000 0.9689 0.000 0.000 0.000 1.000
#> GSM97863 4 0.0188 0.9688 0.004 0.000 0.000 0.996
#> GSM97869 4 0.0188 0.9688 0.004 0.000 0.000 0.996
#> GSM97870 3 0.2814 0.8278 0.132 0.000 0.868 0.000
#> GSM97871 4 0.0000 0.9689 0.000 0.000 0.000 1.000
#> GSM97877 2 0.0000 0.9894 0.000 1.000 0.000 0.000
#> GSM97879 4 0.0336 0.9679 0.008 0.000 0.000 0.992
#> GSM97882 4 0.0000 0.9689 0.000 0.000 0.000 1.000
#> GSM97885 4 0.0188 0.9688 0.004 0.000 0.000 0.996
#> GSM97886 4 0.0000 0.9689 0.000 0.000 0.000 1.000
#> GSM97887 4 0.0336 0.9645 0.000 0.000 0.008 0.992
#> GSM97888 4 0.0188 0.9688 0.004 0.000 0.000 0.996
#> GSM97889 4 0.2589 0.8412 0.000 0.000 0.116 0.884
#> GSM97891 4 0.0000 0.9689 0.000 0.000 0.000 1.000
#> GSM97892 2 0.0000 0.9894 0.000 1.000 0.000 0.000
#> GSM97893 4 0.1118 0.9548 0.036 0.000 0.000 0.964
#> GSM97894 4 0.0000 0.9689 0.000 0.000 0.000 1.000
#> GSM97895 4 0.1118 0.9548 0.036 0.000 0.000 0.964
#> GSM97896 4 0.0000 0.9689 0.000 0.000 0.000 1.000
#> GSM97898 4 0.0336 0.9679 0.008 0.000 0.000 0.992
#> GSM97903 4 0.1022 0.9574 0.032 0.000 0.000 0.968
#> GSM97905 3 0.0336 0.9299 0.008 0.000 0.992 0.000
#> GSM97906 4 0.0000 0.9689 0.000 0.000 0.000 1.000
#> GSM97908 4 0.0921 0.9598 0.028 0.000 0.000 0.972
#> GSM97912 1 0.2773 0.7586 0.880 0.000 0.116 0.004
#> GSM97914 1 0.4730 0.4352 0.636 0.000 0.000 0.364
#> GSM97915 4 0.0000 0.9689 0.000 0.000 0.000 1.000
#> GSM97917 4 0.1118 0.9548 0.036 0.000 0.000 0.964
#> GSM97918 4 0.0469 0.9668 0.012 0.000 0.000 0.988
#> GSM97919 4 0.0592 0.9653 0.016 0.000 0.000 0.984
#> GSM97922 4 0.0188 0.9688 0.004 0.000 0.000 0.996
#> GSM97924 2 0.0000 0.9894 0.000 1.000 0.000 0.000
#> GSM97926 3 0.0000 0.9300 0.000 0.000 1.000 0.000
#> GSM97930 4 0.1716 0.9320 0.064 0.000 0.000 0.936
#> GSM97931 2 0.0000 0.9894 0.000 1.000 0.000 0.000
#> GSM97935 4 0.0000 0.9689 0.000 0.000 0.000 1.000
#> GSM97936 4 0.0000 0.9689 0.000 0.000 0.000 1.000
#> GSM97938 4 0.2589 0.8744 0.116 0.000 0.000 0.884
#> GSM97940 4 0.0000 0.9689 0.000 0.000 0.000 1.000
#> GSM97942 3 0.0000 0.9300 0.000 0.000 1.000 0.000
#> GSM97945 4 0.0000 0.9689 0.000 0.000 0.000 1.000
#> GSM97946 2 0.0000 0.9894 0.000 1.000 0.000 0.000
#> GSM97948 3 0.0000 0.9300 0.000 0.000 1.000 0.000
#> GSM97950 4 0.0188 0.9688 0.004 0.000 0.000 0.996
#> GSM97952 4 0.0000 0.9689 0.000 0.000 0.000 1.000
#> GSM97953 4 0.4888 0.2635 0.412 0.000 0.000 0.588
#> GSM97954 4 0.0817 0.9618 0.024 0.000 0.000 0.976
#> GSM97955 4 0.0188 0.9688 0.004 0.000 0.000 0.996
#> GSM97959 2 0.3443 0.7801 0.016 0.848 0.000 0.136
#> GSM97961 4 0.0188 0.9688 0.004 0.000 0.000 0.996
#> GSM97963 4 0.0000 0.9689 0.000 0.000 0.000 1.000
#> GSM97965 4 0.0000 0.9689 0.000 0.000 0.000 1.000
#> GSM97966 4 0.0000 0.9689 0.000 0.000 0.000 1.000
#> GSM97967 2 0.0000 0.9894 0.000 1.000 0.000 0.000
#> GSM97968 2 0.0336 0.9836 0.008 0.992 0.000 0.000
#> GSM97969 4 0.0707 0.9636 0.020 0.000 0.000 0.980
#> GSM97971 4 0.1489 0.9478 0.044 0.000 0.004 0.952
#> GSM97799 3 0.0000 0.9300 0.000 0.000 1.000 0.000
#> GSM97823 2 0.0000 0.9894 0.000 1.000 0.000 0.000
#> GSM97824 3 0.2868 0.8217 0.136 0.000 0.864 0.000
#> GSM97830 3 0.2011 0.8799 0.080 0.000 0.920 0.000
#> GSM97835 3 0.4992 0.0934 0.000 0.476 0.524 0.000
#> GSM97838 2 0.0000 0.9894 0.000 1.000 0.000 0.000
#> GSM97841 2 0.0000 0.9894 0.000 1.000 0.000 0.000
#> GSM97842 3 0.0000 0.9300 0.000 0.000 1.000 0.000
#> GSM97854 2 0.0000 0.9894 0.000 1.000 0.000 0.000
#> GSM97857 1 0.3024 0.7189 0.852 0.000 0.148 0.000
#> GSM97860 3 0.0336 0.9299 0.008 0.000 0.992 0.000
#> GSM97862 3 0.0336 0.9299 0.008 0.000 0.992 0.000
#> GSM97864 2 0.0000 0.9894 0.000 1.000 0.000 0.000
#> GSM97866 3 0.0336 0.9299 0.008 0.000 0.992 0.000
#> GSM97868 3 0.0336 0.9299 0.008 0.000 0.992 0.000
#> GSM97872 1 0.4008 0.6654 0.756 0.000 0.000 0.244
#> GSM97873 3 0.0000 0.9300 0.000 0.000 1.000 0.000
#> GSM97874 3 0.4817 0.3573 0.388 0.000 0.612 0.000
#> GSM97875 3 0.0000 0.9300 0.000 0.000 1.000 0.000
#> GSM97876 3 0.0336 0.9299 0.008 0.000 0.992 0.000
#> GSM97880 3 0.1211 0.9112 0.040 0.000 0.960 0.000
#> GSM97881 3 0.0000 0.9300 0.000 0.000 1.000 0.000
#> GSM97884 3 0.0188 0.9277 0.000 0.004 0.996 0.000
#> GSM97901 3 0.0336 0.9299 0.008 0.000 0.992 0.000
#> GSM97902 1 0.0000 0.8156 1.000 0.000 0.000 0.000
#> GSM97909 2 0.0000 0.9894 0.000 1.000 0.000 0.000
#> GSM97911 3 0.0000 0.9300 0.000 0.000 1.000 0.000
#> GSM97923 3 0.0188 0.9301 0.004 0.000 0.996 0.000
#> GSM97928 4 0.0469 0.9668 0.012 0.000 0.000 0.988
#> GSM97929 2 0.0000 0.9894 0.000 1.000 0.000 0.000
#> GSM97933 3 0.2704 0.8341 0.124 0.000 0.876 0.000
#> GSM97934 1 0.4697 0.4153 0.644 0.000 0.356 0.000
#> GSM97944 3 0.0000 0.9300 0.000 0.000 1.000 0.000
#> GSM97949 2 0.0000 0.9894 0.000 1.000 0.000 0.000
#> GSM97956 3 0.0469 0.9285 0.012 0.000 0.988 0.000
#> GSM97962 3 0.3610 0.7381 0.200 0.000 0.800 0.000
#> GSM97964 3 0.0469 0.9285 0.012 0.000 0.988 0.000
#> GSM97970 3 0.0000 0.9300 0.000 0.000 1.000 0.000
#> GSM97822 4 0.0921 0.9484 0.000 0.000 0.028 0.972
#> GSM97831 3 0.1389 0.9058 0.048 0.000 0.952 0.000
#> GSM97845 4 0.1118 0.9548 0.036 0.000 0.000 0.964
#> GSM97865 1 0.4996 0.0792 0.516 0.000 0.000 0.484
#> GSM97867 3 0.0336 0.9299 0.008 0.000 0.992 0.000
#> GSM97883 3 0.0469 0.9285 0.012 0.000 0.988 0.000
#> GSM97897 4 0.1637 0.9139 0.000 0.000 0.060 0.940
#> GSM97900 4 0.0336 0.9645 0.000 0.000 0.008 0.992
#> GSM97904 4 0.1256 0.9486 0.008 0.000 0.028 0.964
#> GSM97907 2 0.0000 0.9894 0.000 1.000 0.000 0.000
#> GSM97925 3 0.0000 0.9300 0.000 0.000 1.000 0.000
#> GSM97947 3 0.0000 0.9300 0.000 0.000 1.000 0.000
cbind(get_classes(res, k = 5), get_membership(res, k = 5))
#> class entropy silhouette p1 p2 p3 p4 p5
#> GSM97800 2 0.0000 0.9494 0.000 1.000 0.000 0.000 0.000
#> GSM97803 2 0.0000 0.9494 0.000 1.000 0.000 0.000 0.000
#> GSM97804 2 0.0609 0.9434 0.000 0.980 0.000 0.000 0.020
#> GSM97805 2 0.0510 0.9448 0.000 0.984 0.000 0.000 0.016
#> GSM97807 2 0.0162 0.9486 0.004 0.996 0.000 0.000 0.000
#> GSM97809 2 0.0162 0.9486 0.004 0.996 0.000 0.000 0.000
#> GSM97811 2 0.0000 0.9494 0.000 1.000 0.000 0.000 0.000
#> GSM97812 2 0.0000 0.9494 0.000 1.000 0.000 0.000 0.000
#> GSM97816 1 0.0566 0.6902 0.984 0.012 0.000 0.000 0.004
#> GSM97817 2 0.0000 0.9494 0.000 1.000 0.000 0.000 0.000
#> GSM97820 2 0.0000 0.9494 0.000 1.000 0.000 0.000 0.000
#> GSM97825 2 0.0162 0.9487 0.000 0.996 0.000 0.000 0.004
#> GSM97827 2 0.0000 0.9494 0.000 1.000 0.000 0.000 0.000
#> GSM97828 1 0.0404 0.6904 0.988 0.000 0.000 0.000 0.012
#> GSM97833 2 0.0000 0.9494 0.000 1.000 0.000 0.000 0.000
#> GSM97834 2 0.0000 0.9494 0.000 1.000 0.000 0.000 0.000
#> GSM97840 2 0.0162 0.9486 0.004 0.996 0.000 0.000 0.000
#> GSM97846 2 0.0000 0.9494 0.000 1.000 0.000 0.000 0.000
#> GSM97848 2 0.0000 0.9494 0.000 1.000 0.000 0.000 0.000
#> GSM97849 2 0.0000 0.9494 0.000 1.000 0.000 0.000 0.000
#> GSM97850 2 0.0000 0.9494 0.000 1.000 0.000 0.000 0.000
#> GSM97853 2 0.0000 0.9494 0.000 1.000 0.000 0.000 0.000
#> GSM97855 2 0.0609 0.9410 0.020 0.980 0.000 0.000 0.000
#> GSM97878 5 0.4820 0.5449 0.000 0.008 0.052 0.232 0.708
#> GSM97913 2 0.4663 0.4268 0.020 0.604 0.000 0.000 0.376
#> GSM97932 5 0.4542 0.7136 0.008 0.000 0.000 0.456 0.536
#> GSM97939 3 0.4711 0.7394 0.032 0.124 0.772 0.000 0.072
#> GSM97951 2 0.0162 0.9486 0.004 0.996 0.000 0.000 0.000
#> GSM97957 1 0.4835 0.2517 0.592 0.000 0.380 0.000 0.028
#> GSM97972 1 0.6432 0.4754 0.568 0.288 0.032 0.000 0.112
#> GSM97793 3 0.2233 0.8395 0.004 0.000 0.892 0.000 0.104
#> GSM97795 2 0.0932 0.9393 0.004 0.972 0.004 0.000 0.020
#> GSM97802 4 0.6797 -0.0247 0.000 0.004 0.340 0.420 0.236
#> GSM97810 2 0.4230 0.6795 0.016 0.764 0.196 0.000 0.024
#> GSM97815 2 0.4286 0.6075 0.004 0.716 0.260 0.000 0.020
#> GSM97837 1 0.2389 0.6875 0.880 0.000 0.000 0.004 0.116
#> GSM97843 3 0.1670 0.8587 0.012 0.000 0.936 0.000 0.052
#> GSM97890 3 0.1571 0.8560 0.004 0.000 0.936 0.000 0.060
#> GSM97899 4 0.0880 0.6800 0.000 0.000 0.000 0.968 0.032
#> GSM97910 1 0.2011 0.6884 0.908 0.000 0.000 0.004 0.088
#> GSM97916 4 0.6455 -0.2606 0.264 0.000 0.000 0.500 0.236
#> GSM97920 1 0.4238 0.5831 0.768 0.000 0.164 0.000 0.068
#> GSM97921 1 0.5335 0.5409 0.668 0.000 0.000 0.132 0.200
#> GSM97927 4 0.2127 0.6358 0.000 0.000 0.000 0.892 0.108
#> GSM97937 1 0.5922 0.2980 0.504 0.000 0.000 0.108 0.388
#> GSM97941 2 0.0162 0.9486 0.004 0.996 0.000 0.000 0.000
#> GSM97943 1 0.0613 0.6909 0.984 0.004 0.004 0.000 0.008
#> GSM97958 2 0.4729 0.6845 0.180 0.748 0.000 0.024 0.048
#> GSM97960 2 0.0290 0.9469 0.000 0.992 0.000 0.000 0.008
#> GSM97794 4 0.6498 -0.4257 0.024 0.104 0.000 0.472 0.400
#> GSM97796 4 0.2179 0.6325 0.000 0.000 0.000 0.888 0.112
#> GSM97797 1 0.5556 0.3258 0.524 0.000 0.000 0.072 0.404
#> GSM97798 4 0.0510 0.6850 0.000 0.000 0.000 0.984 0.016
#> GSM97801 1 0.2648 0.6674 0.848 0.000 0.000 0.000 0.152
#> GSM97806 4 0.2605 0.5814 0.000 0.000 0.000 0.852 0.148
#> GSM97808 4 0.0510 0.6843 0.000 0.000 0.000 0.984 0.016
#> GSM97813 4 0.3280 0.5852 0.000 0.000 0.012 0.812 0.176
#> GSM97814 4 0.0290 0.6851 0.000 0.000 0.000 0.992 0.008
#> GSM97818 4 0.6637 -0.2536 0.368 0.008 0.000 0.452 0.172
#> GSM97819 3 0.0880 0.8627 0.000 0.000 0.968 0.000 0.032
#> GSM97821 2 0.1285 0.9308 0.004 0.956 0.004 0.000 0.036
#> GSM97826 1 0.3445 0.6620 0.824 0.000 0.000 0.036 0.140
#> GSM97829 1 0.3993 0.6232 0.756 0.000 0.000 0.028 0.216
#> GSM97832 2 0.5274 0.4410 0.336 0.612 0.012 0.000 0.040
#> GSM97836 3 0.4449 0.3412 0.004 0.000 0.636 0.352 0.008
#> GSM97839 4 0.2471 0.6042 0.000 0.000 0.000 0.864 0.136
#> GSM97844 2 0.0404 0.9464 0.000 0.988 0.000 0.000 0.012
#> GSM97847 5 0.4731 0.7149 0.016 0.000 0.000 0.456 0.528
#> GSM97851 5 0.4304 0.6698 0.000 0.000 0.000 0.484 0.516
#> GSM97852 5 0.4306 0.6536 0.000 0.000 0.000 0.492 0.508
#> GSM97856 4 0.1341 0.6650 0.000 0.000 0.000 0.944 0.056
#> GSM97858 2 0.0609 0.9434 0.000 0.980 0.000 0.000 0.020
#> GSM97859 4 0.3731 0.5859 0.012 0.000 0.016 0.800 0.172
#> GSM97861 4 0.1830 0.6589 0.000 0.000 0.008 0.924 0.068
#> GSM97863 4 0.2179 0.6330 0.000 0.000 0.000 0.888 0.112
#> GSM97869 4 0.3544 0.5869 0.004 0.000 0.008 0.788 0.200
#> GSM97870 3 0.6945 0.2516 0.324 0.000 0.472 0.024 0.180
#> GSM97871 4 0.0794 0.6799 0.000 0.000 0.000 0.972 0.028
#> GSM97877 2 0.2230 0.8582 0.000 0.884 0.000 0.000 0.116
#> GSM97879 4 0.0794 0.6814 0.000 0.000 0.000 0.972 0.028
#> GSM97882 4 0.0963 0.6835 0.000 0.000 0.000 0.964 0.036
#> GSM97885 4 0.0794 0.6846 0.000 0.000 0.000 0.972 0.028
#> GSM97886 4 0.3143 0.4842 0.000 0.000 0.000 0.796 0.204
#> GSM97887 4 0.1043 0.6782 0.000 0.000 0.000 0.960 0.040
#> GSM97888 4 0.3336 0.5723 0.000 0.000 0.000 0.772 0.228
#> GSM97889 4 0.5408 0.3719 0.000 0.000 0.120 0.652 0.228
#> GSM97891 4 0.2020 0.6718 0.000 0.000 0.000 0.900 0.100
#> GSM97892 2 0.0000 0.9494 0.000 1.000 0.000 0.000 0.000
#> GSM97893 4 0.4415 -0.2808 0.008 0.000 0.000 0.604 0.388
#> GSM97894 4 0.4171 -0.2594 0.000 0.000 0.000 0.604 0.396
#> GSM97895 5 0.4297 0.6933 0.000 0.000 0.000 0.472 0.528
#> GSM97896 4 0.2732 0.6300 0.000 0.000 0.000 0.840 0.160
#> GSM97898 4 0.3561 0.3579 0.000 0.000 0.000 0.740 0.260
#> GSM97903 4 0.4238 -0.1544 0.004 0.000 0.000 0.628 0.368
#> GSM97905 3 0.3264 0.8248 0.016 0.000 0.820 0.000 0.164
#> GSM97906 4 0.0290 0.6851 0.000 0.000 0.000 0.992 0.008
#> GSM97908 5 0.4644 0.7072 0.012 0.000 0.000 0.460 0.528
#> GSM97912 1 0.6941 0.2914 0.460 0.000 0.308 0.016 0.216
#> GSM97914 1 0.5656 0.3454 0.624 0.000 0.000 0.236 0.140
#> GSM97915 4 0.4227 -0.3747 0.000 0.000 0.000 0.580 0.420
#> GSM97917 5 0.4434 0.7117 0.004 0.000 0.000 0.460 0.536
#> GSM97918 4 0.3480 0.3687 0.000 0.000 0.000 0.752 0.248
#> GSM97919 4 0.4294 -0.5538 0.000 0.000 0.000 0.532 0.468
#> GSM97922 4 0.2377 0.6440 0.000 0.000 0.000 0.872 0.128
#> GSM97924 2 0.0162 0.9488 0.000 0.996 0.000 0.000 0.004
#> GSM97926 3 0.2011 0.8482 0.004 0.000 0.908 0.000 0.088
#> GSM97930 5 0.4894 0.7077 0.024 0.000 0.000 0.456 0.520
#> GSM97931 2 0.3229 0.8478 0.008 0.860 0.044 0.000 0.088
#> GSM97935 4 0.1197 0.6759 0.000 0.000 0.000 0.952 0.048
#> GSM97936 4 0.2280 0.6184 0.000 0.000 0.000 0.880 0.120
#> GSM97938 5 0.5319 0.6572 0.044 0.000 0.008 0.360 0.588
#> GSM97940 4 0.0000 0.6856 0.000 0.000 0.000 1.000 0.000
#> GSM97942 3 0.1041 0.8587 0.004 0.000 0.964 0.000 0.032
#> GSM97945 4 0.0609 0.6850 0.000 0.000 0.000 0.980 0.020
#> GSM97946 2 0.0000 0.9494 0.000 1.000 0.000 0.000 0.000
#> GSM97948 3 0.2894 0.8374 0.008 0.000 0.860 0.008 0.124
#> GSM97950 4 0.2690 0.5628 0.000 0.000 0.000 0.844 0.156
#> GSM97952 4 0.0404 0.6849 0.000 0.000 0.000 0.988 0.012
#> GSM97953 5 0.6256 0.4752 0.188 0.000 0.004 0.248 0.560
#> GSM97954 4 0.4562 -0.6678 0.008 0.000 0.000 0.496 0.496
#> GSM97955 4 0.2732 0.5753 0.000 0.000 0.000 0.840 0.160
#> GSM97959 2 0.4545 0.6420 0.000 0.752 0.000 0.116 0.132
#> GSM97961 4 0.1671 0.6544 0.000 0.000 0.000 0.924 0.076
#> GSM97963 4 0.0404 0.6851 0.000 0.000 0.000 0.988 0.012
#> GSM97965 4 0.0404 0.6858 0.000 0.000 0.000 0.988 0.012
#> GSM97966 4 0.0703 0.6830 0.000 0.000 0.000 0.976 0.024
#> GSM97967 2 0.0000 0.9494 0.000 1.000 0.000 0.000 0.000
#> GSM97968 2 0.0794 0.9357 0.028 0.972 0.000 0.000 0.000
#> GSM97969 4 0.3684 0.3281 0.000 0.000 0.000 0.720 0.280
#> GSM97971 4 0.5370 0.4430 0.048 0.000 0.028 0.668 0.256
#> GSM97799 3 0.1788 0.8573 0.004 0.008 0.932 0.000 0.056
#> GSM97823 2 0.0000 0.9494 0.000 1.000 0.000 0.000 0.000
#> GSM97824 3 0.4541 0.7634 0.136 0.000 0.752 0.000 0.112
#> GSM97830 3 0.4094 0.7891 0.128 0.000 0.788 0.000 0.084
#> GSM97835 3 0.5123 0.3962 0.004 0.336 0.616 0.000 0.044
#> GSM97838 2 0.0510 0.9451 0.000 0.984 0.000 0.000 0.016
#> GSM97841 2 0.0162 0.9487 0.000 0.996 0.000 0.000 0.004
#> GSM97842 3 0.1740 0.8600 0.000 0.012 0.932 0.000 0.056
#> GSM97854 2 0.0510 0.9451 0.000 0.984 0.000 0.000 0.016
#> GSM97857 1 0.5068 0.2294 0.572 0.000 0.388 0.000 0.040
#> GSM97860 3 0.2136 0.8468 0.008 0.000 0.904 0.000 0.088
#> GSM97862 3 0.1106 0.8627 0.012 0.000 0.964 0.000 0.024
#> GSM97864 2 0.0162 0.9487 0.000 0.996 0.000 0.000 0.004
#> GSM97866 3 0.1701 0.8581 0.016 0.000 0.936 0.000 0.048
#> GSM97868 3 0.2011 0.8564 0.004 0.000 0.908 0.000 0.088
#> GSM97872 5 0.7194 -0.3808 0.400 0.000 0.092 0.084 0.424
#> GSM97873 3 0.1216 0.8576 0.000 0.020 0.960 0.000 0.020
#> GSM97874 3 0.4924 0.5767 0.272 0.000 0.668 0.000 0.060
#> GSM97875 3 0.2179 0.8494 0.000 0.000 0.888 0.000 0.112
#> GSM97876 3 0.1628 0.8610 0.008 0.000 0.936 0.000 0.056
#> GSM97880 3 0.2104 0.8647 0.024 0.000 0.916 0.000 0.060
#> GSM97881 3 0.0955 0.8603 0.004 0.000 0.968 0.000 0.028
#> GSM97884 3 0.3474 0.8255 0.008 0.020 0.824 0.000 0.148
#> GSM97901 3 0.2189 0.8553 0.012 0.000 0.904 0.000 0.084
#> GSM97902 1 0.5067 0.6342 0.696 0.072 0.008 0.000 0.224
#> GSM97909 2 0.0703 0.9382 0.000 0.976 0.000 0.000 0.024
#> GSM97911 3 0.0609 0.8603 0.000 0.000 0.980 0.000 0.020
#> GSM97923 3 0.1877 0.8604 0.012 0.000 0.924 0.000 0.064
#> GSM97928 4 0.4727 0.3829 0.012 0.000 0.012 0.636 0.340
#> GSM97929 2 0.0290 0.9478 0.000 0.992 0.000 0.000 0.008
#> GSM97933 3 0.4386 0.7692 0.096 0.000 0.764 0.000 0.140
#> GSM97934 3 0.5431 0.1816 0.424 0.000 0.516 0.000 0.060
#> GSM97944 3 0.1740 0.8569 0.000 0.012 0.932 0.000 0.056
#> GSM97949 2 0.0162 0.9483 0.000 0.996 0.000 0.000 0.004
#> GSM97956 3 0.2873 0.8429 0.020 0.000 0.860 0.000 0.120
#> GSM97962 3 0.3608 0.8010 0.112 0.000 0.824 0.000 0.064
#> GSM97964 3 0.3309 0.8275 0.036 0.000 0.836 0.000 0.128
#> GSM97970 3 0.1412 0.8601 0.004 0.008 0.952 0.000 0.036
#> GSM97822 4 0.4612 0.4654 0.000 0.000 0.056 0.712 0.232
#> GSM97831 3 0.2376 0.8564 0.052 0.000 0.904 0.000 0.044
#> GSM97845 4 0.3143 0.4828 0.000 0.000 0.000 0.796 0.204
#> GSM97865 1 0.7006 -0.2068 0.384 0.008 0.000 0.276 0.332
#> GSM97867 3 0.1444 0.8603 0.012 0.000 0.948 0.000 0.040
#> GSM97883 3 0.3238 0.8239 0.028 0.000 0.836 0.000 0.136
#> GSM97897 4 0.4434 0.4850 0.000 0.000 0.056 0.736 0.208
#> GSM97900 4 0.1043 0.6807 0.000 0.000 0.000 0.960 0.040
#> GSM97904 4 0.4183 0.5382 0.000 0.000 0.084 0.780 0.136
#> GSM97907 2 0.0404 0.9464 0.000 0.988 0.000 0.000 0.012
#> GSM97925 3 0.2536 0.8468 0.004 0.000 0.868 0.000 0.128
#> GSM97947 3 0.3402 0.8016 0.004 0.000 0.804 0.008 0.184
cbind(get_classes(res, k = 6), get_membership(res, k = 6))
#> class entropy silhouette p1 p2 p3 p4 p5 p6
#> GSM97800 2 0.0146 0.9298 0.000 0.996 0.000 0.000 0.004 0.000
#> GSM97803 2 0.0260 0.9292 0.000 0.992 0.000 0.000 0.008 0.000
#> GSM97804 2 0.0632 0.9240 0.000 0.976 0.000 0.000 0.024 0.000
#> GSM97805 2 0.0458 0.9270 0.000 0.984 0.000 0.000 0.016 0.000
#> GSM97807 2 0.0260 0.9293 0.000 0.992 0.000 0.000 0.008 0.000
#> GSM97809 2 0.0260 0.9293 0.000 0.992 0.000 0.000 0.008 0.000
#> GSM97811 2 0.0146 0.9303 0.000 0.996 0.000 0.000 0.004 0.000
#> GSM97812 2 0.0146 0.9303 0.000 0.996 0.000 0.000 0.004 0.000
#> GSM97816 6 0.0146 0.6277 0.000 0.000 0.000 0.000 0.004 0.996
#> GSM97817 2 0.0000 0.9302 0.000 1.000 0.000 0.000 0.000 0.000
#> GSM97820 2 0.0146 0.9303 0.000 0.996 0.000 0.000 0.004 0.000
#> GSM97825 2 0.0146 0.9303 0.000 0.996 0.000 0.000 0.004 0.000
#> GSM97827 2 0.0146 0.9303 0.000 0.996 0.000 0.000 0.004 0.000
#> GSM97828 6 0.0260 0.6278 0.000 0.000 0.000 0.000 0.008 0.992
#> GSM97833 2 0.0146 0.9303 0.000 0.996 0.000 0.000 0.004 0.000
#> GSM97834 2 0.0146 0.9303 0.000 0.996 0.000 0.000 0.004 0.000
#> GSM97840 2 0.0146 0.9303 0.000 0.996 0.000 0.000 0.004 0.000
#> GSM97846 2 0.0000 0.9302 0.000 1.000 0.000 0.000 0.000 0.000
#> GSM97848 2 0.0146 0.9303 0.000 0.996 0.000 0.000 0.004 0.000
#> GSM97849 2 0.0146 0.9303 0.000 0.996 0.000 0.000 0.004 0.000
#> GSM97850 2 0.0000 0.9302 0.000 1.000 0.000 0.000 0.000 0.000
#> GSM97853 2 0.0146 0.9303 0.000 0.996 0.000 0.000 0.004 0.000
#> GSM97855 2 0.0603 0.9246 0.000 0.980 0.000 0.000 0.016 0.004
#> GSM97878 1 0.2294 0.6246 0.892 0.000 0.000 0.072 0.036 0.000
#> GSM97913 1 0.4273 0.2074 0.616 0.364 0.000 0.004 0.008 0.008
#> GSM97932 1 0.2623 0.6753 0.852 0.000 0.000 0.132 0.016 0.000
#> GSM97939 3 0.4073 0.6572 0.012 0.088 0.772 0.000 0.128 0.000
#> GSM97951 2 0.0363 0.9278 0.000 0.988 0.000 0.000 0.012 0.000
#> GSM97957 3 0.5255 0.3817 0.024 0.000 0.600 0.000 0.068 0.308
#> GSM97972 2 0.8456 -0.2893 0.176 0.336 0.068 0.004 0.152 0.264
#> GSM97793 3 0.1265 0.7891 0.008 0.000 0.948 0.000 0.044 0.000
#> GSM97795 2 0.0692 0.9240 0.004 0.976 0.000 0.000 0.020 0.000
#> GSM97802 5 0.6505 0.5410 0.008 0.012 0.276 0.276 0.428 0.000
#> GSM97810 2 0.5929 0.2342 0.028 0.536 0.340 0.000 0.084 0.012
#> GSM97815 2 0.3711 0.5998 0.000 0.720 0.260 0.000 0.020 0.000
#> GSM97837 6 0.3976 0.5777 0.196 0.000 0.000 0.004 0.052 0.748
#> GSM97843 3 0.1524 0.7835 0.008 0.000 0.932 0.000 0.060 0.000
#> GSM97890 3 0.1074 0.7894 0.012 0.000 0.960 0.000 0.028 0.000
#> GSM97899 4 0.1245 0.7448 0.032 0.000 0.000 0.952 0.016 0.000
#> GSM97910 6 0.2052 0.6206 0.004 0.000 0.000 0.028 0.056 0.912
#> GSM97916 6 0.6950 -0.1655 0.288 0.000 0.000 0.284 0.056 0.372
#> GSM97920 6 0.1713 0.5968 0.000 0.000 0.044 0.000 0.028 0.928
#> GSM97921 6 0.7579 0.0211 0.308 0.000 0.004 0.252 0.128 0.308
#> GSM97927 4 0.2263 0.6780 0.016 0.000 0.000 0.884 0.100 0.000
#> GSM97937 1 0.5961 0.3338 0.624 0.000 0.004 0.080 0.104 0.188
#> GSM97941 2 0.0291 0.9291 0.004 0.992 0.000 0.000 0.004 0.000
#> GSM97943 6 0.0972 0.6252 0.008 0.000 0.000 0.000 0.028 0.964
#> GSM97958 2 0.6943 0.3907 0.056 0.584 0.004 0.080 0.156 0.120
#> GSM97960 2 0.1152 0.9043 0.000 0.952 0.004 0.000 0.044 0.000
#> GSM97794 1 0.7415 0.4318 0.484 0.156 0.000 0.204 0.128 0.028
#> GSM97796 4 0.3103 0.6328 0.208 0.000 0.000 0.784 0.008 0.000
#> GSM97797 6 0.5977 0.3209 0.320 0.004 0.000 0.020 0.132 0.524
#> GSM97798 4 0.0806 0.7377 0.008 0.000 0.000 0.972 0.020 0.000
#> GSM97801 6 0.1003 0.6286 0.016 0.000 0.000 0.000 0.020 0.964
#> GSM97806 4 0.3834 0.6382 0.108 0.000 0.000 0.776 0.116 0.000
#> GSM97808 4 0.0806 0.7376 0.008 0.000 0.000 0.972 0.020 0.000
#> GSM97813 4 0.5275 0.1882 0.044 0.000 0.020 0.564 0.364 0.008
#> GSM97814 4 0.0820 0.7443 0.016 0.000 0.000 0.972 0.012 0.000
#> GSM97818 1 0.7037 0.3210 0.380 0.020 0.000 0.268 0.028 0.304
#> GSM97819 3 0.0865 0.7900 0.000 0.000 0.964 0.000 0.036 0.000
#> GSM97821 2 0.2703 0.8354 0.008 0.860 0.000 0.016 0.116 0.000
#> GSM97826 1 0.4821 -0.1149 0.484 0.000 0.000 0.008 0.036 0.472
#> GSM97829 6 0.4486 0.5417 0.192 0.000 0.000 0.048 0.032 0.728
#> GSM97832 6 0.4477 0.3686 0.004 0.292 0.008 0.000 0.032 0.664
#> GSM97836 3 0.5236 0.2237 0.040 0.000 0.660 0.220 0.080 0.000
#> GSM97839 4 0.2738 0.6601 0.176 0.000 0.000 0.820 0.004 0.000
#> GSM97844 2 0.0603 0.9257 0.004 0.980 0.000 0.000 0.016 0.000
#> GSM97847 1 0.2454 0.6833 0.840 0.000 0.000 0.160 0.000 0.000
#> GSM97851 1 0.2730 0.6825 0.836 0.000 0.000 0.152 0.012 0.000
#> GSM97852 1 0.2994 0.6821 0.788 0.000 0.000 0.208 0.004 0.000
#> GSM97856 4 0.1563 0.7428 0.056 0.000 0.000 0.932 0.012 0.000
#> GSM97858 2 0.0547 0.9257 0.000 0.980 0.000 0.000 0.020 0.000
#> GSM97859 4 0.6102 0.1250 0.108 0.000 0.032 0.524 0.328 0.008
#> GSM97861 4 0.1124 0.7302 0.008 0.000 0.000 0.956 0.036 0.000
#> GSM97863 4 0.3261 0.6359 0.204 0.000 0.000 0.780 0.016 0.000
#> GSM97869 4 0.5933 0.1516 0.108 0.004 0.012 0.516 0.352 0.008
#> GSM97870 6 0.7022 -0.3750 0.000 0.000 0.324 0.060 0.288 0.328
#> GSM97871 4 0.1297 0.7455 0.040 0.000 0.000 0.948 0.012 0.000
#> GSM97877 2 0.3622 0.6576 0.236 0.744 0.000 0.004 0.016 0.000
#> GSM97879 4 0.1780 0.7381 0.048 0.000 0.000 0.924 0.028 0.000
#> GSM97882 4 0.2263 0.7282 0.048 0.000 0.000 0.896 0.056 0.000
#> GSM97885 4 0.1845 0.7201 0.028 0.000 0.000 0.920 0.052 0.000
#> GSM97886 4 0.3412 0.6547 0.128 0.000 0.000 0.808 0.064 0.000
#> GSM97887 4 0.1398 0.7375 0.008 0.000 0.000 0.940 0.052 0.000
#> GSM97888 4 0.5974 0.0965 0.336 0.000 0.000 0.428 0.236 0.000
#> GSM97889 4 0.5767 -0.1640 0.024 0.000 0.096 0.480 0.400 0.000
#> GSM97891 4 0.3313 0.6857 0.060 0.000 0.000 0.816 0.124 0.000
#> GSM97892 2 0.0146 0.9300 0.000 0.996 0.000 0.000 0.004 0.000
#> GSM97893 1 0.4654 0.4151 0.544 0.000 0.000 0.412 0.044 0.000
#> GSM97894 1 0.3984 0.4279 0.596 0.000 0.000 0.396 0.008 0.000
#> GSM97895 1 0.2748 0.6740 0.848 0.000 0.000 0.128 0.024 0.000
#> GSM97896 4 0.5658 0.2096 0.188 0.000 0.000 0.520 0.292 0.000
#> GSM97898 4 0.4336 -0.1617 0.476 0.000 0.000 0.504 0.020 0.000
#> GSM97903 1 0.4238 0.3106 0.540 0.000 0.000 0.444 0.016 0.000
#> GSM97905 3 0.4444 0.5643 0.108 0.000 0.708 0.000 0.184 0.000
#> GSM97906 4 0.0458 0.7403 0.000 0.000 0.000 0.984 0.016 0.000
#> GSM97908 1 0.2912 0.6835 0.816 0.000 0.000 0.172 0.012 0.000
#> GSM97912 5 0.7416 0.2817 0.108 0.000 0.368 0.024 0.372 0.128
#> GSM97914 6 0.7069 0.1429 0.236 0.000 0.000 0.232 0.096 0.436
#> GSM97915 1 0.3852 0.4700 0.612 0.000 0.000 0.384 0.004 0.000
#> GSM97917 1 0.3213 0.6433 0.820 0.000 0.000 0.132 0.048 0.000
#> GSM97918 4 0.3799 0.4605 0.276 0.000 0.000 0.704 0.020 0.000
#> GSM97919 1 0.3564 0.6296 0.724 0.000 0.000 0.264 0.012 0.000
#> GSM97922 4 0.5663 0.1940 0.156 0.000 0.004 0.524 0.316 0.000
#> GSM97924 2 0.0260 0.9292 0.000 0.992 0.000 0.000 0.008 0.000
#> GSM97926 3 0.2112 0.7714 0.016 0.000 0.896 0.000 0.088 0.000
#> GSM97930 1 0.2973 0.6769 0.836 0.000 0.000 0.136 0.024 0.004
#> GSM97931 2 0.4695 0.6869 0.044 0.732 0.052 0.000 0.168 0.004
#> GSM97935 4 0.1500 0.7244 0.012 0.000 0.000 0.936 0.052 0.000
#> GSM97936 4 0.2815 0.6907 0.120 0.000 0.000 0.848 0.032 0.000
#> GSM97938 1 0.3508 0.5778 0.812 0.000 0.004 0.104 0.080 0.000
#> GSM97940 4 0.0891 0.7444 0.024 0.000 0.000 0.968 0.008 0.000
#> GSM97942 3 0.0972 0.7918 0.008 0.000 0.964 0.000 0.028 0.000
#> GSM97945 4 0.1341 0.7434 0.024 0.000 0.000 0.948 0.028 0.000
#> GSM97946 2 0.0000 0.9302 0.000 1.000 0.000 0.000 0.000 0.000
#> GSM97948 3 0.4328 0.4526 0.004 0.000 0.672 0.040 0.284 0.000
#> GSM97950 4 0.2942 0.6660 0.132 0.000 0.000 0.836 0.032 0.000
#> GSM97952 4 0.0692 0.7453 0.020 0.000 0.000 0.976 0.004 0.000
#> GSM97953 1 0.5567 0.4698 0.684 0.000 0.012 0.124 0.116 0.064
#> GSM97954 1 0.3109 0.6713 0.772 0.000 0.000 0.224 0.004 0.000
#> GSM97955 4 0.2871 0.6472 0.192 0.000 0.000 0.804 0.004 0.000
#> GSM97959 2 0.4497 0.5531 0.244 0.692 0.000 0.052 0.012 0.000
#> GSM97961 4 0.1643 0.7306 0.068 0.000 0.000 0.924 0.008 0.000
#> GSM97963 4 0.0891 0.7409 0.008 0.000 0.000 0.968 0.024 0.000
#> GSM97965 4 0.0717 0.7450 0.016 0.000 0.000 0.976 0.008 0.000
#> GSM97966 4 0.1152 0.7295 0.004 0.000 0.000 0.952 0.044 0.000
#> GSM97967 2 0.0146 0.9303 0.000 0.996 0.000 0.000 0.004 0.000
#> GSM97968 2 0.1477 0.8965 0.004 0.940 0.000 0.000 0.008 0.048
#> GSM97969 1 0.5213 0.1853 0.488 0.000 0.000 0.420 0.092 0.000
#> GSM97971 4 0.7050 -0.2313 0.128 0.000 0.044 0.396 0.392 0.040
#> GSM97799 3 0.1745 0.7847 0.012 0.000 0.920 0.000 0.068 0.000
#> GSM97823 2 0.0146 0.9303 0.000 0.996 0.000 0.000 0.004 0.000
#> GSM97824 3 0.4372 0.6815 0.020 0.000 0.752 0.000 0.136 0.092
#> GSM97830 3 0.4537 0.5319 0.004 0.000 0.680 0.000 0.068 0.248
#> GSM97835 3 0.5587 0.1480 0.004 0.356 0.508 0.000 0.132 0.000
#> GSM97838 2 0.0603 0.9257 0.004 0.980 0.000 0.000 0.016 0.000
#> GSM97841 2 0.0146 0.9298 0.000 0.996 0.000 0.000 0.004 0.000
#> GSM97842 3 0.2125 0.7794 0.004 0.016 0.908 0.000 0.068 0.004
#> GSM97854 2 0.0363 0.9282 0.000 0.988 0.000 0.000 0.012 0.000
#> GSM97857 3 0.5600 0.3804 0.048 0.000 0.600 0.000 0.076 0.276
#> GSM97860 3 0.1757 0.7832 0.008 0.000 0.916 0.000 0.076 0.000
#> GSM97862 3 0.0692 0.7912 0.004 0.000 0.976 0.000 0.020 0.000
#> GSM97864 2 0.0146 0.9298 0.000 0.996 0.000 0.000 0.004 0.000
#> GSM97866 3 0.0865 0.7878 0.000 0.000 0.964 0.000 0.036 0.000
#> GSM97868 3 0.2264 0.7773 0.012 0.000 0.888 0.000 0.096 0.004
#> GSM97872 1 0.5859 0.2850 0.648 0.000 0.100 0.024 0.184 0.044
#> GSM97873 3 0.0976 0.7913 0.008 0.016 0.968 0.000 0.008 0.000
#> GSM97874 3 0.5224 0.4162 0.004 0.000 0.616 0.000 0.136 0.244
#> GSM97875 3 0.2805 0.7215 0.004 0.000 0.812 0.000 0.184 0.000
#> GSM97876 3 0.1267 0.7877 0.000 0.000 0.940 0.000 0.060 0.000
#> GSM97880 3 0.1625 0.7872 0.012 0.000 0.928 0.000 0.060 0.000
#> GSM97881 3 0.1074 0.7883 0.012 0.000 0.960 0.000 0.028 0.000
#> GSM97884 3 0.4229 0.6210 0.008 0.056 0.728 0.000 0.208 0.000
#> GSM97901 3 0.1531 0.7870 0.000 0.000 0.928 0.000 0.068 0.004
#> GSM97902 6 0.6822 0.4759 0.208 0.068 0.004 0.036 0.116 0.568
#> GSM97909 2 0.0922 0.9204 0.004 0.968 0.000 0.004 0.024 0.000
#> GSM97911 3 0.0993 0.7886 0.012 0.000 0.964 0.000 0.024 0.000
#> GSM97923 3 0.1471 0.7889 0.004 0.000 0.932 0.000 0.064 0.000
#> GSM97928 5 0.7018 0.3308 0.216 0.012 0.060 0.252 0.460 0.000
#> GSM97929 2 0.0363 0.9282 0.000 0.988 0.000 0.000 0.012 0.000
#> GSM97933 3 0.4034 0.6764 0.052 0.000 0.776 0.000 0.148 0.024
#> GSM97934 3 0.4736 0.5925 0.040 0.000 0.724 0.000 0.072 0.164
#> GSM97944 3 0.1757 0.7880 0.012 0.008 0.928 0.000 0.052 0.000
#> GSM97949 2 0.0146 0.9303 0.000 0.996 0.000 0.000 0.004 0.000
#> GSM97956 3 0.2980 0.7068 0.008 0.000 0.800 0.000 0.192 0.000
#> GSM97962 3 0.2257 0.7697 0.016 0.000 0.904 0.000 0.060 0.020
#> GSM97964 3 0.3345 0.6805 0.028 0.000 0.788 0.000 0.184 0.000
#> GSM97970 3 0.1578 0.7868 0.012 0.004 0.936 0.000 0.048 0.000
#> GSM97822 4 0.5311 0.0446 0.032 0.000 0.044 0.528 0.396 0.000
#> GSM97831 3 0.2325 0.7746 0.008 0.000 0.900 0.000 0.044 0.048
#> GSM97845 4 0.3694 0.5427 0.232 0.000 0.000 0.740 0.028 0.000
#> GSM97865 1 0.7534 0.2451 0.416 0.020 0.004 0.300 0.100 0.160
#> GSM97867 3 0.0806 0.7899 0.008 0.000 0.972 0.000 0.020 0.000
#> GSM97883 3 0.4052 0.5504 0.020 0.000 0.708 0.000 0.260 0.012
#> GSM97897 4 0.4873 0.2624 0.020 0.000 0.040 0.612 0.328 0.000
#> GSM97900 4 0.1845 0.7363 0.028 0.000 0.000 0.920 0.052 0.000
#> GSM97904 5 0.7148 0.4996 0.076 0.000 0.272 0.320 0.332 0.000
#> GSM97907 2 0.0692 0.9241 0.004 0.976 0.000 0.000 0.020 0.000
#> GSM97925 3 0.2704 0.7511 0.016 0.000 0.844 0.000 0.140 0.000
#> GSM97947 3 0.4334 0.2288 0.000 0.000 0.568 0.024 0.408 0.000
Heatmaps for the consensus matrix. It visualizes the probability of two samples to be in a same group.
consensus_heatmap(res, k = 2)
consensus_heatmap(res, k = 3)
consensus_heatmap(res, k = 4)
consensus_heatmap(res, k = 5)
consensus_heatmap(res, k = 6)
Heatmaps for the membership of samples in all partitions to see how consistent they are:
membership_heatmap(res, k = 2)
membership_heatmap(res, k = 3)
membership_heatmap(res, k = 4)
membership_heatmap(res, k = 5)
membership_heatmap(res, k = 6)
As soon as we have had the classes for columns, we can look for signatures which are significantly different between classes which can be candidate marks for certain classes. Following are the heatmaps for signatures.
Signature heatmaps where rows are scaled:
get_signatures(res, k = 2)
get_signatures(res, k = 3)
get_signatures(res, k = 4)
get_signatures(res, k = 5)
get_signatures(res, k = 6)
Signature heatmaps where rows are not scaled:
get_signatures(res, k = 2, scale_rows = FALSE)
get_signatures(res, k = 3, scale_rows = FALSE)
get_signatures(res, k = 4, scale_rows = FALSE)
get_signatures(res, k = 5, scale_rows = FALSE)
get_signatures(res, k = 6, scale_rows = FALSE)
Compare the overlap of signatures from different k:
compare_signatures(res)
get_signature() returns a data frame invisibly. TO get the list of signatures, the function
call should be assigned to a variable explicitly. In following code, if plot argument is set
to FALSE, no heatmap is plotted while only the differential analysis is performed.
# code only for demonstration
tb = get_signature(res, k = ..., plot = FALSE)
An example of the output of tb is:
#> which_row fdr mean_1 mean_2 scaled_mean_1 scaled_mean_2 km
#> 1 38 0.042760348 8.373488 9.131774 -0.5533452 0.5164555 1
#> 2 40 0.018707592 7.106213 8.469186 -0.6173731 0.5762149 1
#> 3 55 0.019134737 10.221463 11.207825 -0.6159697 0.5749050 1
#> 4 59 0.006059896 5.921854 7.869574 -0.6899429 0.6439467 1
#> 5 60 0.018055526 8.928898 10.211722 -0.6204761 0.5791110 1
#> 6 98 0.009384629 15.714769 14.887706 0.6635654 -0.6193277 2
...
The columns in tb are:
which_row: row indices corresponding to the input matrix.fdr: FDR for the differential test. mean_x: The mean value in group x.scaled_mean_x: The mean value in group x after rows are scaled.km: Row groups if k-means clustering is applied to rows.UMAP plot which shows how samples are separated.
dimension_reduction(res, k = 2, method = "UMAP")
dimension_reduction(res, k = 3, method = "UMAP")
dimension_reduction(res, k = 4, method = "UMAP")
dimension_reduction(res, k = 5, method = "UMAP")
dimension_reduction(res, k = 6, method = "UMAP")
Following heatmap shows how subgroups are split when increasing k:
collect_classes(res)
Test correlation between subgroups and known annotations. If the known annotation is numeric, one-way ANOVA test is applied, and if the known annotation is discrete, chi-squared contingency table test is applied.
test_to_known_factors(res)
#> n disease.state(p) tissue(p) k
#> SD:NMF 173 1.11e-15 1.26e-18 2
#> SD:NMF 178 1.18e-24 7.88e-25 3
#> SD:NMF 172 1.64e-23 7.72e-21 4
#> SD:NMF 144 3.65e-21 3.31e-19 5
#> SD:NMF 135 3.60e-20 1.07e-18 6
If matrix rows can be associated to genes, consider to use functional_enrichment(res,
...) to perform function enrichment for the signature genes. See this vignette for more detailed explanations.
The object with results only for a single top-value method and a single partition method can be extracted as:
res = res_list["CV", "hclust"]
# you can also extract it by
# res = res_list["CV:hclust"]
A summary of res and all the functions that can be applied to it:
res
#> A 'ConsensusPartition' object with k = 2, 3, 4, 5, 6.
#> On a matrix with 51882 rows and 180 columns.
#> Top rows (1000, 2000, 3000, 4000, 5000) are extracted by 'CV' method.
#> Subgroups are detected by 'hclust' method.
#> Performed in total 1250 partitions by row resampling.
#> Best k for subgroups seems to be 3.
#>
#> Following methods can be applied to this 'ConsensusPartition' object:
#> [1] "cola_report" "collect_classes" "collect_plots"
#> [4] "collect_stats" "colnames" "compare_signatures"
#> [7] "consensus_heatmap" "dimension_reduction" "functional_enrichment"
#> [10] "get_anno_col" "get_anno" "get_classes"
#> [13] "get_consensus" "get_matrix" "get_membership"
#> [16] "get_param" "get_signatures" "get_stats"
#> [19] "is_best_k" "is_stable_k" "membership_heatmap"
#> [22] "ncol" "nrow" "plot_ecdf"
#> [25] "rownames" "select_partition_number" "show"
#> [28] "suggest_best_k" "test_to_known_factors"
collect_plots() function collects all the plots made from res for all k (number of partitions)
into one single page to provide an easy and fast comparison between different k.
collect_plots(res)
The plots are:
k and the heatmap of
predicted classes for each k.k.k.k.All the plots in panels can be made by individual functions and they are plotted later in this section.
select_partition_number() produces several plots showing different
statistics for choosing “optimized” k. There are following statistics:
k;k, the area increased is defined as \(A_k - A_{k-1}\).The detailed explanations of these statistics can be found in the cola vignette.
Generally speaking, lower PAC score, higher mean silhouette score or higher
concordance corresponds to better partition. Rand index and Jaccard index
measure how similar the current partition is compared to partition with k-1.
If they are too similar, we won't accept k is better than k-1.
select_partition_number(res)
The numeric values for all these statistics can be obtained by get_stats().
get_stats(res)
#> k 1-PAC mean_silhouette concordance area_increased Rand Jaccard
#> 2 2 0.364 0.694 0.862 0.4320 0.539 0.539
#> 3 3 0.470 0.623 0.822 0.4790 0.699 0.488
#> 4 4 0.532 0.582 0.776 0.1360 0.868 0.633
#> 5 5 0.611 0.563 0.742 0.0625 0.900 0.640
#> 6 6 0.669 0.573 0.703 0.0366 0.939 0.730
suggest_best_k() suggests the best \(k\) based on these statistics. The rules are as follows:
suggest_best_k(res)
#> [1] 3
Following shows the table of the partitions (You need to click the show/hide
code output link to see it). The membership matrix (columns with name p*)
is inferred by
clue::cl_consensus()
function with the SE method. Basically the value in the membership matrix
represents the probability to belong to a certain group. The finall class
label for an item is determined with the group with highest probability it
belongs to.
In get_classes() function, the entropy is calculated from the membership
matrix and the silhouette score is calculated from the consensus matrix.
cbind(get_classes(res, k = 2), get_membership(res, k = 2))
#> class entropy silhouette p1 p2
#> GSM97800 2 0.0000 0.79300 0.000 1.000
#> GSM97803 2 0.0000 0.79300 0.000 1.000
#> GSM97804 2 0.0000 0.79300 0.000 1.000
#> GSM97805 2 0.0000 0.79300 0.000 1.000
#> GSM97807 2 0.0000 0.79300 0.000 1.000
#> GSM97809 2 0.0000 0.79300 0.000 1.000
#> GSM97811 2 0.0000 0.79300 0.000 1.000
#> GSM97812 2 0.0000 0.79300 0.000 1.000
#> GSM97816 2 0.9988 0.04925 0.480 0.520
#> GSM97817 2 0.0000 0.79300 0.000 1.000
#> GSM97820 2 0.0000 0.79300 0.000 1.000
#> GSM97825 2 0.0000 0.79300 0.000 1.000
#> GSM97827 2 0.0000 0.79300 0.000 1.000
#> GSM97828 2 0.9988 0.04925 0.480 0.520
#> GSM97833 2 0.0000 0.79300 0.000 1.000
#> GSM97834 2 0.0000 0.79300 0.000 1.000
#> GSM97840 2 0.4022 0.75351 0.080 0.920
#> GSM97846 2 0.0000 0.79300 0.000 1.000
#> GSM97848 2 0.0000 0.79300 0.000 1.000
#> GSM97849 2 0.0000 0.79300 0.000 1.000
#> GSM97850 2 0.0000 0.79300 0.000 1.000
#> GSM97853 2 0.0000 0.79300 0.000 1.000
#> GSM97855 2 0.0000 0.79300 0.000 1.000
#> GSM97878 1 0.6438 0.77564 0.836 0.164
#> GSM97913 2 1.0000 0.03291 0.496 0.504
#> GSM97932 1 0.0000 0.83756 1.000 0.000
#> GSM97939 2 0.8443 0.59304 0.272 0.728
#> GSM97951 2 0.5519 0.72560 0.128 0.872
#> GSM97957 1 0.8861 0.61654 0.696 0.304
#> GSM97972 2 0.9427 0.44795 0.360 0.640
#> GSM97793 1 0.8144 0.69212 0.748 0.252
#> GSM97795 2 0.8386 0.59767 0.268 0.732
#> GSM97802 1 0.5629 0.80073 0.868 0.132
#> GSM97810 2 0.8327 0.60256 0.264 0.736
#> GSM97815 2 0.8386 0.59767 0.268 0.732
#> GSM97837 1 0.0938 0.83882 0.988 0.012
#> GSM97843 1 0.9323 0.52867 0.652 0.348
#> GSM97890 1 0.9635 0.43208 0.612 0.388
#> GSM97899 1 0.0000 0.83756 1.000 0.000
#> GSM97910 1 0.9775 0.34247 0.588 0.412
#> GSM97916 1 0.6973 0.75761 0.812 0.188
#> GSM97920 1 0.9248 0.54864 0.660 0.340
#> GSM97921 1 0.4298 0.82308 0.912 0.088
#> GSM97927 1 0.5519 0.80519 0.872 0.128
#> GSM97937 1 0.1184 0.83907 0.984 0.016
#> GSM97941 2 0.1184 0.78641 0.016 0.984
#> GSM97943 2 0.9988 0.04925 0.480 0.520
#> GSM97958 1 0.9323 0.52664 0.652 0.348
#> GSM97960 2 0.7056 0.67643 0.192 0.808
#> GSM97794 1 0.9286 0.52226 0.656 0.344
#> GSM97796 1 0.0000 0.83756 1.000 0.000
#> GSM97797 1 0.9775 0.34518 0.588 0.412
#> GSM97798 1 0.0000 0.83756 1.000 0.000
#> GSM97801 1 0.9427 0.48201 0.640 0.360
#> GSM97806 1 0.5408 0.80785 0.876 0.124
#> GSM97808 1 0.0000 0.83756 1.000 0.000
#> GSM97813 1 0.0672 0.83881 0.992 0.008
#> GSM97814 1 0.0000 0.83756 1.000 0.000
#> GSM97818 1 0.5519 0.79625 0.872 0.128
#> GSM97819 1 0.8144 0.69212 0.748 0.252
#> GSM97821 2 0.9850 0.29088 0.428 0.572
#> GSM97826 1 0.0672 0.83847 0.992 0.008
#> GSM97829 1 0.3584 0.83182 0.932 0.068
#> GSM97832 2 0.6531 0.69736 0.168 0.832
#> GSM97836 1 0.6887 0.76734 0.816 0.184
#> GSM97839 1 0.0000 0.83756 1.000 0.000
#> GSM97844 2 0.0000 0.79300 0.000 1.000
#> GSM97847 1 0.0376 0.83819 0.996 0.004
#> GSM97851 1 0.0000 0.83756 1.000 0.000
#> GSM97852 1 0.0376 0.83819 0.996 0.004
#> GSM97856 1 0.0000 0.83756 1.000 0.000
#> GSM97858 2 0.0000 0.79300 0.000 1.000
#> GSM97859 1 0.0672 0.83881 0.992 0.008
#> GSM97861 1 0.5519 0.80519 0.872 0.128
#> GSM97863 1 0.0000 0.83756 1.000 0.000
#> GSM97869 1 0.6887 0.76184 0.816 0.184
#> GSM97870 1 0.0672 0.83881 0.992 0.008
#> GSM97871 1 0.0000 0.83756 1.000 0.000
#> GSM97877 2 1.0000 0.02583 0.496 0.504
#> GSM97879 1 0.3584 0.82963 0.932 0.068
#> GSM97882 1 0.5294 0.80966 0.880 0.120
#> GSM97885 1 0.5519 0.80558 0.872 0.128
#> GSM97886 1 0.0000 0.83756 1.000 0.000
#> GSM97887 1 0.0000 0.83756 1.000 0.000
#> GSM97888 1 0.0000 0.83756 1.000 0.000
#> GSM97889 1 0.5178 0.81025 0.884 0.116
#> GSM97891 1 0.6247 0.78876 0.844 0.156
#> GSM97892 2 0.0000 0.79300 0.000 1.000
#> GSM97893 1 0.0000 0.83756 1.000 0.000
#> GSM97894 1 0.0000 0.83756 1.000 0.000
#> GSM97895 1 0.0000 0.83756 1.000 0.000
#> GSM97896 1 0.0000 0.83756 1.000 0.000
#> GSM97898 1 0.0000 0.83756 1.000 0.000
#> GSM97903 1 0.2948 0.83363 0.948 0.052
#> GSM97905 1 0.2423 0.83642 0.960 0.040
#> GSM97906 1 0.0000 0.83756 1.000 0.000
#> GSM97908 1 0.0938 0.83909 0.988 0.012
#> GSM97912 1 0.0938 0.83884 0.988 0.012
#> GSM97914 1 0.4939 0.81448 0.892 0.108
#> GSM97915 1 0.0000 0.83756 1.000 0.000
#> GSM97917 1 0.0000 0.83756 1.000 0.000
#> GSM97918 1 0.0000 0.83756 1.000 0.000
#> GSM97919 1 0.0000 0.83756 1.000 0.000
#> GSM97922 1 0.0672 0.83881 0.992 0.008
#> GSM97924 2 0.0000 0.79300 0.000 1.000
#> GSM97926 1 0.6887 0.76734 0.816 0.184
#> GSM97930 1 0.0672 0.83879 0.992 0.008
#> GSM97931 2 0.9552 0.42167 0.376 0.624
#> GSM97935 1 0.5519 0.80519 0.872 0.128
#> GSM97936 1 0.0376 0.83819 0.996 0.004
#> GSM97938 1 0.0000 0.83756 1.000 0.000
#> GSM97940 1 0.0000 0.83756 1.000 0.000
#> GSM97942 1 0.8144 0.69212 0.748 0.252
#> GSM97945 1 0.0000 0.83756 1.000 0.000
#> GSM97946 2 0.0000 0.79300 0.000 1.000
#> GSM97948 1 0.7950 0.70576 0.760 0.240
#> GSM97950 1 0.0000 0.83756 1.000 0.000
#> GSM97952 1 0.0000 0.83756 1.000 0.000
#> GSM97953 1 0.0000 0.83756 1.000 0.000
#> GSM97954 1 0.1184 0.83862 0.984 0.016
#> GSM97955 1 0.0000 0.83756 1.000 0.000
#> GSM97959 1 0.9983 0.07578 0.524 0.476
#> GSM97961 1 0.0000 0.83756 1.000 0.000
#> GSM97963 1 0.0000 0.83756 1.000 0.000
#> GSM97965 1 0.0000 0.83756 1.000 0.000
#> GSM97966 1 0.0000 0.83756 1.000 0.000
#> GSM97967 2 0.0000 0.79300 0.000 1.000
#> GSM97968 2 0.0000 0.79300 0.000 1.000
#> GSM97969 1 0.0376 0.83819 0.996 0.004
#> GSM97971 1 0.0672 0.83881 0.992 0.008
#> GSM97799 2 0.9248 0.48705 0.340 0.660
#> GSM97823 2 0.0000 0.79300 0.000 1.000
#> GSM97824 2 0.9993 0.04706 0.484 0.516
#> GSM97830 1 0.8267 0.68162 0.740 0.260
#> GSM97835 2 0.8555 0.58127 0.280 0.720
#> GSM97838 2 0.0000 0.79300 0.000 1.000
#> GSM97841 2 0.0000 0.79300 0.000 1.000
#> GSM97842 2 0.9170 0.50099 0.332 0.668
#> GSM97854 2 0.0000 0.79300 0.000 1.000
#> GSM97857 2 1.0000 -0.02282 0.500 0.500
#> GSM97860 1 0.8144 0.69212 0.748 0.252
#> GSM97862 1 0.9686 0.41037 0.604 0.396
#> GSM97864 2 0.0000 0.79300 0.000 1.000
#> GSM97866 1 0.9754 0.37403 0.592 0.408
#> GSM97868 1 0.9661 0.42242 0.608 0.392
#> GSM97872 1 0.4161 0.82470 0.916 0.084
#> GSM97873 2 0.9686 0.35564 0.396 0.604
#> GSM97874 1 0.8144 0.69212 0.748 0.252
#> GSM97875 1 0.8144 0.69212 0.748 0.252
#> GSM97876 1 0.8144 0.69212 0.748 0.252
#> GSM97880 1 0.8144 0.69212 0.748 0.252
#> GSM97881 1 0.9686 0.41009 0.604 0.396
#> GSM97884 2 0.9552 0.40960 0.376 0.624
#> GSM97901 1 0.9710 0.39930 0.600 0.400
#> GSM97902 1 0.9795 0.33238 0.584 0.416
#> GSM97909 2 0.9427 0.45706 0.360 0.640
#> GSM97911 1 0.9686 0.41009 0.604 0.396
#> GSM97923 1 0.8144 0.69212 0.748 0.252
#> GSM97928 1 0.4298 0.82332 0.912 0.088
#> GSM97929 2 0.0000 0.79300 0.000 1.000
#> GSM97933 1 0.8813 0.62298 0.700 0.300
#> GSM97934 1 0.8813 0.62298 0.700 0.300
#> GSM97944 2 0.9248 0.48705 0.340 0.660
#> GSM97949 2 0.0000 0.79300 0.000 1.000
#> GSM97956 2 1.0000 -0.00743 0.496 0.504
#> GSM97962 1 0.8813 0.62298 0.700 0.300
#> GSM97964 2 0.9933 0.17501 0.452 0.548
#> GSM97970 2 0.9993 0.04218 0.484 0.516
#> GSM97822 1 0.5178 0.81025 0.884 0.116
#> GSM97831 1 0.8909 0.60929 0.692 0.308
#> GSM97845 1 0.0672 0.83883 0.992 0.008
#> GSM97865 1 0.5737 0.80191 0.864 0.136
#> GSM97867 1 0.8144 0.69212 0.748 0.252
#> GSM97883 1 0.2778 0.83526 0.952 0.048
#> GSM97897 1 0.4431 0.82199 0.908 0.092
#> GSM97900 1 0.0000 0.83756 1.000 0.000
#> GSM97904 1 0.4431 0.82450 0.908 0.092
#> GSM97907 2 0.0000 0.79300 0.000 1.000
#> GSM97925 1 0.8016 0.70115 0.756 0.244
#> GSM97947 1 0.8144 0.69212 0.748 0.252
cbind(get_classes(res, k = 3), get_membership(res, k = 3))
#> class entropy silhouette p1 p2 p3
#> GSM97800 2 0.0000 0.8533 0.000 1.000 0.000
#> GSM97803 2 0.0000 0.8533 0.000 1.000 0.000
#> GSM97804 2 0.0000 0.8533 0.000 1.000 0.000
#> GSM97805 2 0.0000 0.8533 0.000 1.000 0.000
#> GSM97807 2 0.0000 0.8533 0.000 1.000 0.000
#> GSM97809 2 0.0000 0.8533 0.000 1.000 0.000
#> GSM97811 2 0.0000 0.8533 0.000 1.000 0.000
#> GSM97812 2 0.0000 0.8533 0.000 1.000 0.000
#> GSM97816 3 0.6264 0.4269 0.004 0.380 0.616
#> GSM97817 2 0.0000 0.8533 0.000 1.000 0.000
#> GSM97820 2 0.0000 0.8533 0.000 1.000 0.000
#> GSM97825 2 0.0000 0.8533 0.000 1.000 0.000
#> GSM97827 2 0.0000 0.8533 0.000 1.000 0.000
#> GSM97828 3 0.6264 0.4269 0.004 0.380 0.616
#> GSM97833 2 0.0000 0.8533 0.000 1.000 0.000
#> GSM97834 2 0.0000 0.8533 0.000 1.000 0.000
#> GSM97840 2 0.2959 0.7638 0.000 0.900 0.100
#> GSM97846 2 0.0000 0.8533 0.000 1.000 0.000
#> GSM97848 2 0.0000 0.8533 0.000 1.000 0.000
#> GSM97849 2 0.0000 0.8533 0.000 1.000 0.000
#> GSM97850 2 0.0000 0.8533 0.000 1.000 0.000
#> GSM97853 2 0.0000 0.8533 0.000 1.000 0.000
#> GSM97855 2 0.0000 0.8533 0.000 1.000 0.000
#> GSM97878 3 0.8887 0.1915 0.424 0.120 0.456
#> GSM97913 2 0.8983 -0.2672 0.128 0.444 0.428
#> GSM97932 1 0.0000 0.8375 1.000 0.000 0.000
#> GSM97939 2 0.6235 0.1560 0.000 0.564 0.436
#> GSM97951 2 0.4654 0.6401 0.000 0.792 0.208
#> GSM97957 3 0.2200 0.7011 0.004 0.056 0.940
#> GSM97972 2 0.6813 -0.0471 0.012 0.520 0.468
#> GSM97793 3 0.0237 0.7012 0.004 0.000 0.996
#> GSM97795 2 0.6235 0.1584 0.000 0.564 0.436
#> GSM97802 3 0.3816 0.6326 0.148 0.000 0.852
#> GSM97810 2 0.6204 0.1905 0.000 0.576 0.424
#> GSM97815 2 0.6244 0.1458 0.000 0.560 0.440
#> GSM97837 1 0.5397 0.6427 0.720 0.000 0.280
#> GSM97843 3 0.2878 0.6850 0.000 0.096 0.904
#> GSM97890 3 0.3752 0.6682 0.000 0.144 0.856
#> GSM97899 1 0.0000 0.8375 1.000 0.000 0.000
#> GSM97910 3 0.8371 0.5476 0.116 0.292 0.592
#> GSM97916 3 0.8825 0.3944 0.336 0.132 0.532
#> GSM97920 3 0.2959 0.6902 0.000 0.100 0.900
#> GSM97921 1 0.7610 0.3235 0.564 0.048 0.388
#> GSM97927 3 0.7997 0.3499 0.360 0.072 0.568
#> GSM97937 1 0.4504 0.7424 0.804 0.000 0.196
#> GSM97941 2 0.1163 0.8326 0.000 0.972 0.028
#> GSM97943 3 0.6264 0.4269 0.004 0.380 0.616
#> GSM97958 3 0.8322 0.5837 0.124 0.268 0.608
#> GSM97960 2 0.5650 0.4643 0.000 0.688 0.312
#> GSM97794 3 0.9268 0.5356 0.208 0.268 0.524
#> GSM97796 1 0.0000 0.8375 1.000 0.000 0.000
#> GSM97797 3 0.8622 0.5337 0.132 0.296 0.572
#> GSM97798 1 0.0000 0.8375 1.000 0.000 0.000
#> GSM97801 3 0.8795 0.5689 0.168 0.256 0.576
#> GSM97806 3 0.7919 0.3068 0.380 0.064 0.556
#> GSM97808 1 0.0000 0.8375 1.000 0.000 0.000
#> GSM97813 1 0.5733 0.5874 0.676 0.000 0.324
#> GSM97814 1 0.0000 0.8375 1.000 0.000 0.000
#> GSM97818 1 0.8228 0.2694 0.552 0.084 0.364
#> GSM97819 3 0.0237 0.7012 0.004 0.000 0.996
#> GSM97821 2 0.8774 -0.1306 0.112 0.476 0.412
#> GSM97826 1 0.5216 0.6656 0.740 0.000 0.260
#> GSM97829 1 0.6956 0.5463 0.660 0.040 0.300
#> GSM97832 2 0.5178 0.5653 0.000 0.744 0.256
#> GSM97836 3 0.7728 0.5126 0.276 0.084 0.640
#> GSM97839 1 0.0000 0.8375 1.000 0.000 0.000
#> GSM97844 2 0.0000 0.8533 0.000 1.000 0.000
#> GSM97847 1 0.3412 0.7935 0.876 0.000 0.124
#> GSM97851 1 0.0000 0.8375 1.000 0.000 0.000
#> GSM97852 1 0.3267 0.7977 0.884 0.000 0.116
#> GSM97856 1 0.0000 0.8375 1.000 0.000 0.000
#> GSM97858 2 0.0000 0.8533 0.000 1.000 0.000
#> GSM97859 1 0.5785 0.5765 0.668 0.000 0.332
#> GSM97861 3 0.7980 0.3597 0.356 0.072 0.572
#> GSM97863 1 0.0000 0.8375 1.000 0.000 0.000
#> GSM97869 3 0.8806 0.3816 0.344 0.128 0.528
#> GSM97870 1 0.5835 0.5640 0.660 0.000 0.340
#> GSM97871 1 0.0000 0.8375 1.000 0.000 0.000
#> GSM97877 3 0.8844 0.2566 0.116 0.440 0.444
#> GSM97879 1 0.7561 0.1433 0.516 0.040 0.444
#> GSM97882 3 0.7809 0.3217 0.372 0.060 0.568
#> GSM97885 3 0.8013 0.3397 0.364 0.072 0.564
#> GSM97886 1 0.0592 0.8356 0.988 0.000 0.012
#> GSM97887 1 0.0000 0.8375 1.000 0.000 0.000
#> GSM97888 1 0.4062 0.7690 0.836 0.000 0.164
#> GSM97889 3 0.4121 0.6137 0.168 0.000 0.832
#> GSM97891 3 0.7995 0.4697 0.304 0.088 0.608
#> GSM97892 2 0.0000 0.8533 0.000 1.000 0.000
#> GSM97893 1 0.3038 0.8035 0.896 0.000 0.104
#> GSM97894 1 0.0000 0.8375 1.000 0.000 0.000
#> GSM97895 1 0.0237 0.8367 0.996 0.000 0.004
#> GSM97896 1 0.2878 0.8087 0.904 0.000 0.096
#> GSM97898 1 0.0000 0.8375 1.000 0.000 0.000
#> GSM97903 1 0.7091 0.2862 0.560 0.024 0.416
#> GSM97905 3 0.6309 -0.1661 0.496 0.000 0.504
#> GSM97906 1 0.0000 0.8375 1.000 0.000 0.000
#> GSM97908 1 0.4235 0.7517 0.824 0.000 0.176
#> GSM97912 1 0.6252 0.3152 0.556 0.000 0.444
#> GSM97914 1 0.8063 0.0314 0.488 0.064 0.448
#> GSM97915 1 0.0000 0.8375 1.000 0.000 0.000
#> GSM97917 1 0.0592 0.8358 0.988 0.000 0.012
#> GSM97918 1 0.0000 0.8375 1.000 0.000 0.000
#> GSM97919 1 0.0000 0.8375 1.000 0.000 0.000
#> GSM97922 1 0.5810 0.5698 0.664 0.000 0.336
#> GSM97924 2 0.0000 0.8533 0.000 1.000 0.000
#> GSM97926 3 0.7728 0.5126 0.276 0.084 0.640
#> GSM97930 1 0.4291 0.7491 0.820 0.000 0.180
#> GSM97931 2 0.7652 -0.0641 0.044 0.512 0.444
#> GSM97935 3 0.7962 0.3684 0.352 0.072 0.576
#> GSM97936 1 0.1529 0.8288 0.960 0.000 0.040
#> GSM97938 1 0.2796 0.8133 0.908 0.000 0.092
#> GSM97940 1 0.0000 0.8375 1.000 0.000 0.000
#> GSM97942 3 0.0237 0.7012 0.004 0.000 0.996
#> GSM97945 1 0.0892 0.8338 0.980 0.000 0.020
#> GSM97946 2 0.0000 0.8533 0.000 1.000 0.000
#> GSM97948 3 0.0892 0.7011 0.020 0.000 0.980
#> GSM97950 1 0.0000 0.8375 1.000 0.000 0.000
#> GSM97952 1 0.0000 0.8375 1.000 0.000 0.000
#> GSM97953 1 0.2796 0.8130 0.908 0.000 0.092
#> GSM97954 1 0.5156 0.7121 0.776 0.008 0.216
#> GSM97955 1 0.0747 0.8355 0.984 0.000 0.016
#> GSM97959 3 0.9302 0.2969 0.160 0.420 0.420
#> GSM97961 1 0.0000 0.8375 1.000 0.000 0.000
#> GSM97963 1 0.0000 0.8375 1.000 0.000 0.000
#> GSM97965 1 0.0000 0.8375 1.000 0.000 0.000
#> GSM97966 1 0.0000 0.8375 1.000 0.000 0.000
#> GSM97967 2 0.0000 0.8533 0.000 1.000 0.000
#> GSM97968 2 0.0237 0.8504 0.000 0.996 0.004
#> GSM97969 1 0.5760 0.5830 0.672 0.000 0.328
#> GSM97971 1 0.5760 0.5817 0.672 0.000 0.328
#> GSM97799 3 0.6286 0.1471 0.000 0.464 0.536
#> GSM97823 2 0.0000 0.8533 0.000 1.000 0.000
#> GSM97824 3 0.5650 0.5115 0.000 0.312 0.688
#> GSM97830 3 0.0661 0.7021 0.004 0.008 0.988
#> GSM97835 2 0.6267 0.1046 0.000 0.548 0.452
#> GSM97838 2 0.0000 0.8533 0.000 1.000 0.000
#> GSM97841 2 0.0000 0.8533 0.000 1.000 0.000
#> GSM97842 3 0.6307 0.0782 0.000 0.488 0.512
#> GSM97854 2 0.0000 0.8533 0.000 1.000 0.000
#> GSM97857 3 0.5785 0.5321 0.004 0.300 0.696
#> GSM97860 3 0.0237 0.7012 0.004 0.000 0.996
#> GSM97862 3 0.4121 0.6579 0.000 0.168 0.832
#> GSM97864 2 0.0000 0.8533 0.000 1.000 0.000
#> GSM97866 3 0.4399 0.6468 0.000 0.188 0.812
#> GSM97868 3 0.3752 0.6674 0.000 0.144 0.856
#> GSM97872 3 0.5882 0.3690 0.348 0.000 0.652
#> GSM97873 3 0.6180 0.3079 0.000 0.416 0.584
#> GSM97874 3 0.0237 0.7012 0.004 0.000 0.996
#> GSM97875 3 0.0237 0.7012 0.004 0.000 0.996
#> GSM97876 3 0.0237 0.7012 0.004 0.000 0.996
#> GSM97880 3 0.0237 0.7012 0.004 0.000 0.996
#> GSM97881 3 0.3879 0.6640 0.000 0.152 0.848
#> GSM97884 3 0.6244 0.2359 0.000 0.440 0.560
#> GSM97901 3 0.4178 0.6557 0.000 0.172 0.828
#> GSM97902 3 0.8113 0.5299 0.092 0.312 0.596
#> GSM97909 2 0.8143 0.1372 0.080 0.560 0.360
#> GSM97911 3 0.3879 0.6640 0.000 0.152 0.848
#> GSM97923 3 0.0237 0.7012 0.004 0.000 0.996
#> GSM97928 3 0.5835 0.3870 0.340 0.000 0.660
#> GSM97929 2 0.0000 0.8533 0.000 1.000 0.000
#> GSM97933 3 0.2096 0.7013 0.004 0.052 0.944
#> GSM97934 3 0.2096 0.7013 0.004 0.052 0.944
#> GSM97944 3 0.6286 0.1471 0.000 0.464 0.536
#> GSM97949 2 0.0000 0.8533 0.000 1.000 0.000
#> GSM97956 3 0.5560 0.5276 0.000 0.300 0.700
#> GSM97962 3 0.2096 0.7013 0.004 0.052 0.944
#> GSM97964 3 0.5905 0.4484 0.000 0.352 0.648
#> GSM97970 3 0.5497 0.5275 0.000 0.292 0.708
#> GSM97822 3 0.4178 0.6098 0.172 0.000 0.828
#> GSM97831 3 0.2301 0.7005 0.004 0.060 0.936
#> GSM97845 1 0.4750 0.7206 0.784 0.000 0.216
#> GSM97865 3 0.8243 0.1898 0.420 0.076 0.504
#> GSM97867 3 0.0237 0.7012 0.004 0.000 0.996
#> GSM97883 3 0.6252 0.0285 0.444 0.000 0.556
#> GSM97897 3 0.5016 0.5507 0.240 0.000 0.760
#> GSM97900 1 0.0000 0.8375 1.000 0.000 0.000
#> GSM97904 1 0.7801 0.1830 0.520 0.052 0.428
#> GSM97907 2 0.0000 0.8533 0.000 1.000 0.000
#> GSM97925 3 0.0592 0.7025 0.012 0.000 0.988
#> GSM97947 3 0.0237 0.7012 0.004 0.000 0.996
cbind(get_classes(res, k = 4), get_membership(res, k = 4))
#> class entropy silhouette p1 p2 p3 p4
#> GSM97800 2 0.0000 0.88945 0.000 1.000 0.000 0.000
#> GSM97803 2 0.0000 0.88945 0.000 1.000 0.000 0.000
#> GSM97804 2 0.0000 0.88945 0.000 1.000 0.000 0.000
#> GSM97805 2 0.0000 0.88945 0.000 1.000 0.000 0.000
#> GSM97807 2 0.0000 0.88945 0.000 1.000 0.000 0.000
#> GSM97809 2 0.0000 0.88945 0.000 1.000 0.000 0.000
#> GSM97811 2 0.0000 0.88945 0.000 1.000 0.000 0.000
#> GSM97812 2 0.0000 0.88945 0.000 1.000 0.000 0.000
#> GSM97816 1 0.7341 0.20977 0.528 0.220 0.252 0.000
#> GSM97817 2 0.0000 0.88945 0.000 1.000 0.000 0.000
#> GSM97820 2 0.0000 0.88945 0.000 1.000 0.000 0.000
#> GSM97825 2 0.0000 0.88945 0.000 1.000 0.000 0.000
#> GSM97827 2 0.0000 0.88945 0.000 1.000 0.000 0.000
#> GSM97828 1 0.7341 0.20977 0.528 0.220 0.252 0.000
#> GSM97833 2 0.0000 0.88945 0.000 1.000 0.000 0.000
#> GSM97834 2 0.0000 0.88945 0.000 1.000 0.000 0.000
#> GSM97840 2 0.3636 0.71342 0.172 0.820 0.008 0.000
#> GSM97846 2 0.0000 0.88945 0.000 1.000 0.000 0.000
#> GSM97848 2 0.0000 0.88945 0.000 1.000 0.000 0.000
#> GSM97849 2 0.0000 0.88945 0.000 1.000 0.000 0.000
#> GSM97850 2 0.0000 0.88945 0.000 1.000 0.000 0.000
#> GSM97853 2 0.0000 0.88945 0.000 1.000 0.000 0.000
#> GSM97855 2 0.0000 0.88945 0.000 1.000 0.000 0.000
#> GSM97878 1 0.4912 0.51630 0.796 0.020 0.052 0.132
#> GSM97913 1 0.5627 0.42697 0.684 0.268 0.040 0.008
#> GSM97932 4 0.2345 0.78207 0.100 0.000 0.000 0.900
#> GSM97939 2 0.7681 0.02152 0.252 0.456 0.292 0.000
#> GSM97951 2 0.5619 0.57840 0.124 0.724 0.152 0.000
#> GSM97957 3 0.2928 0.65105 0.108 0.012 0.880 0.000
#> GSM97972 1 0.7677 0.09835 0.412 0.372 0.216 0.000
#> GSM97793 3 0.0188 0.65469 0.004 0.000 0.996 0.000
#> GSM97795 2 0.7658 0.00605 0.236 0.456 0.308 0.000
#> GSM97802 3 0.5631 0.32302 0.224 0.000 0.700 0.076
#> GSM97810 2 0.7613 0.06414 0.240 0.472 0.288 0.000
#> GSM97815 2 0.7694 -0.01410 0.244 0.448 0.308 0.000
#> GSM97837 4 0.5982 0.38988 0.436 0.000 0.040 0.524
#> GSM97843 3 0.4127 0.63844 0.124 0.052 0.824 0.000
#> GSM97890 3 0.5113 0.61294 0.152 0.088 0.760 0.000
#> GSM97899 4 0.0000 0.80233 0.000 0.000 0.000 1.000
#> GSM97910 1 0.6999 0.39736 0.644 0.132 0.196 0.028
#> GSM97916 1 0.7362 0.56200 0.632 0.048 0.144 0.176
#> GSM97920 3 0.4793 0.57912 0.204 0.040 0.756 0.000
#> GSM97921 1 0.6818 0.10500 0.532 0.004 0.092 0.372
#> GSM97927 1 0.7090 0.52812 0.588 0.004 0.204 0.204
#> GSM97937 4 0.5582 0.55740 0.348 0.000 0.032 0.620
#> GSM97941 2 0.1474 0.84704 0.052 0.948 0.000 0.000
#> GSM97943 1 0.7319 0.21301 0.532 0.220 0.248 0.000
#> GSM97958 1 0.7026 0.45383 0.644 0.144 0.184 0.028
#> GSM97960 2 0.6826 0.36701 0.172 0.600 0.228 0.000
#> GSM97794 1 0.6821 0.51665 0.688 0.144 0.108 0.060
#> GSM97796 4 0.0707 0.80195 0.020 0.000 0.000 0.980
#> GSM97797 1 0.6530 0.44521 0.692 0.136 0.144 0.028
#> GSM97798 4 0.0000 0.80233 0.000 0.000 0.000 1.000
#> GSM97801 1 0.7004 0.43817 0.668 0.108 0.168 0.056
#> GSM97806 1 0.7048 0.53738 0.592 0.004 0.184 0.220
#> GSM97808 4 0.0000 0.80233 0.000 0.000 0.000 1.000
#> GSM97813 4 0.7098 0.41131 0.244 0.000 0.192 0.564
#> GSM97814 4 0.0000 0.80233 0.000 0.000 0.000 1.000
#> GSM97818 1 0.7010 0.19554 0.552 0.028 0.064 0.356
#> GSM97819 3 0.0188 0.65469 0.004 0.000 0.996 0.000
#> GSM97821 1 0.7484 0.23937 0.472 0.364 0.160 0.004
#> GSM97826 4 0.5964 0.42610 0.424 0.000 0.040 0.536
#> GSM97829 1 0.6781 -0.17025 0.472 0.016 0.056 0.456
#> GSM97832 2 0.6324 0.48155 0.172 0.660 0.168 0.000
#> GSM97836 1 0.7253 0.42325 0.548 0.008 0.304 0.140
#> GSM97839 4 0.0707 0.80195 0.020 0.000 0.000 0.980
#> GSM97844 2 0.0000 0.88945 0.000 1.000 0.000 0.000
#> GSM97847 4 0.4655 0.64295 0.312 0.000 0.004 0.684
#> GSM97851 4 0.1637 0.79373 0.060 0.000 0.000 0.940
#> GSM97852 4 0.4608 0.65086 0.304 0.000 0.004 0.692
#> GSM97856 4 0.0188 0.80287 0.004 0.000 0.000 0.996
#> GSM97858 2 0.0000 0.88945 0.000 1.000 0.000 0.000
#> GSM97859 4 0.7145 0.39857 0.252 0.000 0.192 0.556
#> GSM97861 1 0.7059 0.52795 0.592 0.004 0.204 0.200
#> GSM97863 4 0.0707 0.80195 0.020 0.000 0.000 0.980
#> GSM97869 1 0.7280 0.56218 0.636 0.044 0.140 0.180
#> GSM97870 4 0.7190 0.38397 0.260 0.000 0.192 0.548
#> GSM97871 4 0.0000 0.80233 0.000 0.000 0.000 1.000
#> GSM97877 1 0.5696 0.42113 0.680 0.264 0.052 0.004
#> GSM97879 1 0.7265 0.29962 0.512 0.004 0.140 0.344
#> GSM97882 1 0.6917 0.52838 0.592 0.000 0.200 0.208
#> GSM97885 1 0.6996 0.53409 0.600 0.004 0.196 0.200
#> GSM97886 4 0.0779 0.80063 0.016 0.000 0.004 0.980
#> GSM97887 4 0.0000 0.80233 0.000 0.000 0.000 1.000
#> GSM97888 4 0.5066 0.68424 0.148 0.000 0.088 0.764
#> GSM97889 3 0.5851 0.28707 0.236 0.000 0.680 0.084
#> GSM97891 1 0.6291 0.51808 0.680 0.008 0.192 0.120
#> GSM97892 2 0.0000 0.88945 0.000 1.000 0.000 0.000
#> GSM97893 4 0.4422 0.68071 0.256 0.000 0.008 0.736
#> GSM97894 4 0.1022 0.80250 0.032 0.000 0.000 0.968
#> GSM97895 4 0.2345 0.78316 0.100 0.000 0.000 0.900
#> GSM97896 4 0.3900 0.74679 0.084 0.000 0.072 0.844
#> GSM97898 4 0.1118 0.79903 0.036 0.000 0.000 0.964
#> GSM97903 1 0.7106 0.19590 0.504 0.004 0.116 0.376
#> GSM97905 4 0.7863 -0.02723 0.276 0.000 0.344 0.380
#> GSM97906 4 0.0188 0.80287 0.004 0.000 0.000 0.996
#> GSM97908 4 0.5708 0.47692 0.416 0.000 0.028 0.556
#> GSM97912 4 0.7799 0.10153 0.308 0.000 0.272 0.420
#> GSM97914 1 0.7087 0.35404 0.564 0.008 0.124 0.304
#> GSM97915 4 0.1302 0.79827 0.044 0.000 0.000 0.956
#> GSM97917 4 0.2814 0.77300 0.132 0.000 0.000 0.868
#> GSM97918 4 0.0592 0.80207 0.016 0.000 0.000 0.984
#> GSM97919 4 0.2345 0.78207 0.100 0.000 0.000 0.900
#> GSM97922 4 0.7168 0.39090 0.256 0.000 0.192 0.552
#> GSM97924 2 0.0000 0.88945 0.000 1.000 0.000 0.000
#> GSM97926 1 0.7253 0.42325 0.548 0.008 0.304 0.140
#> GSM97930 4 0.4950 0.54852 0.376 0.000 0.004 0.620
#> GSM97931 1 0.7534 0.14962 0.448 0.360 0.192 0.000
#> GSM97935 1 0.7028 0.52888 0.596 0.004 0.204 0.196
#> GSM97936 4 0.2530 0.77927 0.100 0.000 0.004 0.896
#> GSM97938 4 0.4678 0.69940 0.232 0.000 0.024 0.744
#> GSM97940 4 0.0000 0.80233 0.000 0.000 0.000 1.000
#> GSM97942 3 0.0592 0.65284 0.016 0.000 0.984 0.000
#> GSM97945 4 0.1059 0.79878 0.016 0.000 0.012 0.972
#> GSM97946 2 0.0000 0.88945 0.000 1.000 0.000 0.000
#> GSM97948 3 0.1722 0.64001 0.048 0.000 0.944 0.008
#> GSM97950 4 0.0336 0.80109 0.008 0.000 0.000 0.992
#> GSM97952 4 0.0000 0.80233 0.000 0.000 0.000 1.000
#> GSM97953 4 0.4678 0.69935 0.232 0.000 0.024 0.744
#> GSM97954 4 0.5821 0.47459 0.368 0.000 0.040 0.592
#> GSM97955 4 0.0895 0.80136 0.020 0.000 0.004 0.976
#> GSM97959 1 0.4789 0.45377 0.740 0.236 0.020 0.004
#> GSM97961 4 0.0000 0.80233 0.000 0.000 0.000 1.000
#> GSM97963 4 0.0000 0.80233 0.000 0.000 0.000 1.000
#> GSM97965 4 0.0000 0.80233 0.000 0.000 0.000 1.000
#> GSM97966 4 0.0000 0.80233 0.000 0.000 0.000 1.000
#> GSM97967 2 0.0000 0.88945 0.000 1.000 0.000 0.000
#> GSM97968 2 0.0469 0.88034 0.012 0.988 0.000 0.000
#> GSM97969 4 0.7006 0.44314 0.216 0.000 0.204 0.580
#> GSM97971 4 0.7122 0.40569 0.248 0.000 0.192 0.560
#> GSM97799 3 0.7775 0.21809 0.244 0.352 0.404 0.000
#> GSM97823 2 0.0000 0.88945 0.000 1.000 0.000 0.000
#> GSM97824 3 0.7173 0.42280 0.228 0.216 0.556 0.000
#> GSM97830 3 0.0817 0.65698 0.024 0.000 0.976 0.000
#> GSM97835 2 0.7758 -0.05595 0.260 0.432 0.308 0.000
#> GSM97838 2 0.0000 0.88945 0.000 1.000 0.000 0.000
#> GSM97841 2 0.0000 0.88945 0.000 1.000 0.000 0.000
#> GSM97842 3 0.7800 0.18502 0.248 0.372 0.380 0.000
#> GSM97854 2 0.0000 0.88945 0.000 1.000 0.000 0.000
#> GSM97857 3 0.7140 0.43099 0.236 0.204 0.560 0.000
#> GSM97860 3 0.0188 0.65469 0.004 0.000 0.996 0.000
#> GSM97862 3 0.5610 0.58389 0.176 0.104 0.720 0.000
#> GSM97864 2 0.0000 0.88945 0.000 1.000 0.000 0.000
#> GSM97866 3 0.5963 0.55442 0.196 0.116 0.688 0.000
#> GSM97868 3 0.5077 0.61362 0.160 0.080 0.760 0.000
#> GSM97872 3 0.7541 -0.19927 0.388 0.000 0.424 0.188
#> GSM97873 3 0.7687 0.27350 0.240 0.312 0.448 0.000
#> GSM97874 3 0.0188 0.65469 0.004 0.000 0.996 0.000
#> GSM97875 3 0.0188 0.65469 0.004 0.000 0.996 0.000
#> GSM97876 3 0.0188 0.65469 0.004 0.000 0.996 0.000
#> GSM97880 3 0.0000 0.65471 0.000 0.000 1.000 0.000
#> GSM97881 3 0.5220 0.60691 0.156 0.092 0.752 0.000
#> GSM97884 3 0.7724 0.24688 0.240 0.328 0.432 0.000
#> GSM97901 3 0.5540 0.58713 0.164 0.108 0.728 0.000
#> GSM97902 1 0.7985 0.35241 0.548 0.184 0.228 0.040
#> GSM97909 1 0.6653 0.10660 0.480 0.436 0.084 0.000
#> GSM97911 3 0.5220 0.60691 0.156 0.092 0.752 0.000
#> GSM97923 3 0.0188 0.65469 0.004 0.000 0.996 0.000
#> GSM97928 3 0.7514 -0.18713 0.384 0.000 0.432 0.184
#> GSM97929 2 0.0000 0.88945 0.000 1.000 0.000 0.000
#> GSM97933 3 0.2867 0.65207 0.104 0.012 0.884 0.000
#> GSM97934 3 0.2867 0.65207 0.104 0.012 0.884 0.000
#> GSM97944 3 0.7775 0.21809 0.244 0.352 0.404 0.000
#> GSM97949 2 0.0000 0.88945 0.000 1.000 0.000 0.000
#> GSM97956 3 0.7091 0.43671 0.224 0.208 0.568 0.000
#> GSM97962 3 0.2867 0.65207 0.104 0.012 0.884 0.000
#> GSM97964 3 0.7538 0.33976 0.260 0.248 0.492 0.000
#> GSM97970 3 0.6769 0.47875 0.172 0.220 0.608 0.000
#> GSM97822 3 0.5910 0.27276 0.244 0.000 0.672 0.084
#> GSM97831 3 0.2813 0.65634 0.080 0.024 0.896 0.000
#> GSM97845 4 0.5659 0.50719 0.368 0.000 0.032 0.600
#> GSM97865 1 0.7007 0.46184 0.612 0.016 0.124 0.248
#> GSM97867 3 0.0188 0.65469 0.004 0.000 0.996 0.000
#> GSM97883 3 0.7852 -0.26230 0.276 0.000 0.392 0.332
#> GSM97897 3 0.6664 0.17668 0.232 0.000 0.616 0.152
#> GSM97900 4 0.0000 0.80233 0.000 0.000 0.000 1.000
#> GSM97904 1 0.7657 0.18053 0.456 0.012 0.148 0.384
#> GSM97907 2 0.0000 0.88945 0.000 1.000 0.000 0.000
#> GSM97925 3 0.1398 0.64747 0.040 0.000 0.956 0.004
#> GSM97947 3 0.0188 0.65469 0.004 0.000 0.996 0.000
cbind(get_classes(res, k = 5), get_membership(res, k = 5))
#> class entropy silhouette p1 p2 p3 p4 p5
#> GSM97800 2 0.0000 0.94932 0.000 1.000 0.000 0.000 0.000
#> GSM97803 2 0.0000 0.94932 0.000 1.000 0.000 0.000 0.000
#> GSM97804 2 0.0000 0.94932 0.000 1.000 0.000 0.000 0.000
#> GSM97805 2 0.0000 0.94932 0.000 1.000 0.000 0.000 0.000
#> GSM97807 2 0.0000 0.94932 0.000 1.000 0.000 0.000 0.000
#> GSM97809 2 0.0000 0.94932 0.000 1.000 0.000 0.000 0.000
#> GSM97811 2 0.0000 0.94932 0.000 1.000 0.000 0.000 0.000
#> GSM97812 2 0.0000 0.94932 0.000 1.000 0.000 0.000 0.000
#> GSM97816 5 0.5028 0.51615 0.048 0.080 0.116 0.000 0.756
#> GSM97817 2 0.0000 0.94932 0.000 1.000 0.000 0.000 0.000
#> GSM97820 2 0.0000 0.94932 0.000 1.000 0.000 0.000 0.000
#> GSM97825 2 0.0000 0.94932 0.000 1.000 0.000 0.000 0.000
#> GSM97827 2 0.0000 0.94932 0.000 1.000 0.000 0.000 0.000
#> GSM97828 5 0.5028 0.51615 0.048 0.080 0.116 0.000 0.756
#> GSM97833 2 0.0000 0.94932 0.000 1.000 0.000 0.000 0.000
#> GSM97834 2 0.0000 0.94932 0.000 1.000 0.000 0.000 0.000
#> GSM97840 2 0.3845 0.64700 0.024 0.768 0.000 0.000 0.208
#> GSM97846 2 0.0000 0.94932 0.000 1.000 0.000 0.000 0.000
#> GSM97848 2 0.0000 0.94932 0.000 1.000 0.000 0.000 0.000
#> GSM97849 2 0.0000 0.94932 0.000 1.000 0.000 0.000 0.000
#> GSM97850 2 0.0000 0.94932 0.000 1.000 0.000 0.000 0.000
#> GSM97853 2 0.0000 0.94932 0.000 1.000 0.000 0.000 0.000
#> GSM97855 2 0.0000 0.94932 0.000 1.000 0.000 0.000 0.000
#> GSM97878 1 0.4714 0.26782 0.576 0.000 0.012 0.004 0.408
#> GSM97913 5 0.5375 0.39028 0.196 0.124 0.004 0.000 0.676
#> GSM97932 4 0.3845 0.65278 0.208 0.000 0.000 0.768 0.024
#> GSM97939 5 0.6405 0.49835 0.000 0.364 0.176 0.000 0.460
#> GSM97951 2 0.5164 0.33261 0.000 0.672 0.096 0.000 0.232
#> GSM97957 3 0.3053 0.66352 0.008 0.000 0.828 0.000 0.164
#> GSM97972 5 0.6009 0.56462 0.040 0.240 0.084 0.000 0.636
#> GSM97793 3 0.0000 0.70427 0.000 0.000 1.000 0.000 0.000
#> GSM97795 5 0.6494 0.48914 0.000 0.364 0.192 0.000 0.444
#> GSM97802 3 0.6172 0.16480 0.368 0.000 0.536 0.044 0.052
#> GSM97810 5 0.6401 0.49260 0.000 0.380 0.172 0.000 0.448
#> GSM97815 5 0.6483 0.49292 0.000 0.356 0.192 0.000 0.452
#> GSM97837 1 0.6459 0.19506 0.484 0.000 0.016 0.380 0.120
#> GSM97843 3 0.4197 0.61549 0.012 0.024 0.760 0.000 0.204
#> GSM97890 3 0.4957 0.50978 0.008 0.040 0.664 0.000 0.288
#> GSM97899 4 0.0000 0.75644 0.000 0.000 0.000 1.000 0.000
#> GSM97910 5 0.5640 0.35107 0.168 0.008 0.100 0.024 0.700
#> GSM97916 5 0.7504 -0.52475 0.400 0.008 0.060 0.132 0.400
#> GSM97920 3 0.4616 0.51582 0.028 0.004 0.680 0.000 0.288
#> GSM97921 1 0.7138 0.49200 0.476 0.000 0.032 0.280 0.212
#> GSM97927 1 0.7703 0.57616 0.428 0.000 0.096 0.152 0.324
#> GSM97937 4 0.6028 0.08834 0.424 0.000 0.012 0.484 0.080
#> GSM97941 2 0.1704 0.87464 0.004 0.928 0.000 0.000 0.068
#> GSM97943 5 0.4981 0.51743 0.048 0.080 0.112 0.000 0.760
#> GSM97958 5 0.6715 0.13512 0.304 0.064 0.052 0.016 0.564
#> GSM97960 2 0.6113 -0.19703 0.000 0.524 0.144 0.000 0.332
#> GSM97794 5 0.7091 0.03490 0.300 0.064 0.040 0.048 0.548
#> GSM97796 4 0.0880 0.75332 0.032 0.000 0.000 0.968 0.000
#> GSM97797 5 0.5922 0.30454 0.220 0.024 0.068 0.020 0.668
#> GSM97798 4 0.0000 0.75644 0.000 0.000 0.000 1.000 0.000
#> GSM97801 5 0.5931 0.27335 0.216 0.000 0.096 0.036 0.652
#> GSM97806 1 0.7684 0.59365 0.440 0.000 0.088 0.168 0.304
#> GSM97808 4 0.0000 0.75644 0.000 0.000 0.000 1.000 0.000
#> GSM97813 4 0.6837 -0.05766 0.372 0.000 0.140 0.460 0.028
#> GSM97814 4 0.0000 0.75644 0.000 0.000 0.000 1.000 0.000
#> GSM97818 1 0.7205 0.52462 0.496 0.020 0.012 0.252 0.220
#> GSM97819 3 0.0912 0.69729 0.012 0.000 0.972 0.000 0.016
#> GSM97821 5 0.7884 0.47233 0.156 0.296 0.104 0.004 0.440
#> GSM97826 1 0.5925 0.14868 0.528 0.000 0.016 0.388 0.068
#> GSM97829 1 0.6837 0.38347 0.476 0.000 0.020 0.332 0.172
#> GSM97832 2 0.5538 0.09040 0.000 0.596 0.092 0.000 0.312
#> GSM97836 1 0.8056 0.43122 0.372 0.000 0.204 0.108 0.316
#> GSM97839 4 0.0880 0.75332 0.032 0.000 0.000 0.968 0.000
#> GSM97844 2 0.0000 0.94932 0.000 1.000 0.000 0.000 0.000
#> GSM97847 4 0.5118 0.29601 0.412 0.000 0.000 0.548 0.040
#> GSM97851 4 0.2513 0.72107 0.116 0.000 0.000 0.876 0.008
#> GSM97852 4 0.5103 0.31567 0.404 0.000 0.000 0.556 0.040
#> GSM97856 4 0.0290 0.75652 0.008 0.000 0.000 0.992 0.000
#> GSM97858 2 0.0000 0.94932 0.000 1.000 0.000 0.000 0.000
#> GSM97859 4 0.6847 -0.07906 0.380 0.000 0.140 0.452 0.028
#> GSM97861 1 0.7709 0.57196 0.424 0.000 0.096 0.152 0.328
#> GSM97863 4 0.0609 0.75533 0.020 0.000 0.000 0.980 0.000
#> GSM97869 1 0.7509 0.50527 0.404 0.008 0.056 0.140 0.392
#> GSM97870 4 0.6858 -0.11113 0.392 0.000 0.140 0.440 0.028
#> GSM97871 4 0.0000 0.75644 0.000 0.000 0.000 1.000 0.000
#> GSM97877 5 0.5436 0.40720 0.176 0.124 0.012 0.000 0.688
#> GSM97879 1 0.7545 0.59327 0.460 0.000 0.064 0.260 0.216
#> GSM97882 1 0.7722 0.59116 0.436 0.000 0.096 0.160 0.308
#> GSM97885 1 0.7638 0.57809 0.436 0.000 0.092 0.148 0.324
#> GSM97886 4 0.1041 0.74901 0.032 0.000 0.000 0.964 0.004
#> GSM97887 4 0.0000 0.75644 0.000 0.000 0.000 1.000 0.000
#> GSM97888 4 0.5060 0.47049 0.240 0.000 0.064 0.688 0.008
#> GSM97889 3 0.6220 0.11608 0.392 0.000 0.512 0.044 0.052
#> GSM97891 1 0.7069 0.44263 0.444 0.000 0.084 0.080 0.392
#> GSM97892 2 0.0000 0.94932 0.000 1.000 0.000 0.000 0.000
#> GSM97893 4 0.4836 0.39326 0.356 0.000 0.000 0.612 0.032
#> GSM97894 4 0.1502 0.74862 0.056 0.000 0.000 0.940 0.004
#> GSM97895 4 0.3562 0.66473 0.196 0.000 0.000 0.788 0.016
#> GSM97896 4 0.3904 0.62343 0.156 0.000 0.052 0.792 0.000
#> GSM97898 4 0.1768 0.74113 0.072 0.000 0.000 0.924 0.004
#> GSM97903 1 0.7241 0.56064 0.488 0.000 0.048 0.276 0.188
#> GSM97905 1 0.7318 0.38926 0.448 0.000 0.244 0.272 0.036
#> GSM97906 4 0.0162 0.75639 0.004 0.000 0.000 0.996 0.000
#> GSM97908 1 0.6205 -0.05712 0.460 0.000 0.004 0.416 0.120
#> GSM97912 1 0.6971 0.35689 0.496 0.000 0.172 0.300 0.032
#> GSM97914 1 0.7320 0.58778 0.472 0.000 0.044 0.232 0.252
#> GSM97915 4 0.2068 0.73432 0.092 0.000 0.000 0.904 0.004
#> GSM97917 4 0.3789 0.64099 0.212 0.000 0.000 0.768 0.020
#> GSM97918 4 0.0880 0.75370 0.032 0.000 0.000 0.968 0.000
#> GSM97919 4 0.3745 0.66034 0.196 0.000 0.000 0.780 0.024
#> GSM97922 4 0.6851 -0.08819 0.384 0.000 0.140 0.448 0.028
#> GSM97924 2 0.0000 0.94932 0.000 1.000 0.000 0.000 0.000
#> GSM97926 1 0.8056 0.43122 0.372 0.000 0.204 0.108 0.316
#> GSM97930 1 0.5351 -0.07309 0.484 0.000 0.000 0.464 0.052
#> GSM97931 5 0.6258 0.57124 0.064 0.228 0.080 0.000 0.628
#> GSM97935 1 0.7751 0.57039 0.416 0.000 0.100 0.152 0.332
#> GSM97936 4 0.2920 0.69195 0.132 0.000 0.000 0.852 0.016
#> GSM97938 4 0.5179 0.41878 0.352 0.000 0.004 0.600 0.044
#> GSM97940 4 0.0000 0.75644 0.000 0.000 0.000 1.000 0.000
#> GSM97942 3 0.0798 0.70191 0.016 0.000 0.976 0.000 0.008
#> GSM97945 4 0.1026 0.74830 0.024 0.000 0.004 0.968 0.004
#> GSM97946 2 0.0000 0.94932 0.000 1.000 0.000 0.000 0.000
#> GSM97948 3 0.2124 0.68362 0.056 0.000 0.916 0.000 0.028
#> GSM97950 4 0.0510 0.75631 0.016 0.000 0.000 0.984 0.000
#> GSM97952 4 0.0000 0.75644 0.000 0.000 0.000 1.000 0.000
#> GSM97953 4 0.5126 0.41850 0.356 0.000 0.004 0.600 0.040
#> GSM97954 4 0.6237 -0.10369 0.440 0.000 0.024 0.460 0.076
#> GSM97955 4 0.0992 0.75143 0.024 0.000 0.000 0.968 0.008
#> GSM97959 5 0.5205 0.33734 0.224 0.104 0.000 0.000 0.672
#> GSM97961 4 0.0000 0.75644 0.000 0.000 0.000 1.000 0.000
#> GSM97963 4 0.0000 0.75644 0.000 0.000 0.000 1.000 0.000
#> GSM97965 4 0.0000 0.75644 0.000 0.000 0.000 1.000 0.000
#> GSM97966 4 0.0000 0.75644 0.000 0.000 0.000 1.000 0.000
#> GSM97967 2 0.0000 0.94932 0.000 1.000 0.000 0.000 0.000
#> GSM97968 2 0.0609 0.92856 0.000 0.980 0.000 0.000 0.020
#> GSM97969 4 0.7000 0.00966 0.336 0.000 0.144 0.480 0.040
#> GSM97971 4 0.6842 -0.06670 0.376 0.000 0.140 0.456 0.028
#> GSM97799 5 0.6626 0.43370 0.000 0.272 0.272 0.000 0.456
#> GSM97823 2 0.0000 0.94932 0.000 1.000 0.000 0.000 0.000
#> GSM97824 5 0.6359 0.06139 0.004 0.140 0.416 0.000 0.440
#> GSM97830 3 0.1357 0.70183 0.004 0.000 0.948 0.000 0.048
#> GSM97835 5 0.6401 0.50001 0.000 0.336 0.184 0.000 0.480
#> GSM97838 2 0.0000 0.94932 0.000 1.000 0.000 0.000 0.000
#> GSM97841 2 0.0000 0.94932 0.000 1.000 0.000 0.000 0.000
#> GSM97842 5 0.6562 0.46032 0.000 0.284 0.244 0.000 0.472
#> GSM97854 2 0.0000 0.94932 0.000 1.000 0.000 0.000 0.000
#> GSM97857 3 0.6504 -0.07948 0.012 0.132 0.428 0.000 0.428
#> GSM97860 3 0.0000 0.70427 0.000 0.000 1.000 0.000 0.000
#> GSM97862 3 0.5424 0.41030 0.008 0.056 0.600 0.000 0.336
#> GSM97864 2 0.0000 0.94932 0.000 1.000 0.000 0.000 0.000
#> GSM97866 3 0.5507 0.31831 0.008 0.052 0.556 0.000 0.384
#> GSM97868 3 0.4906 0.52135 0.008 0.036 0.664 0.000 0.292
#> GSM97872 1 0.6506 0.37253 0.576 0.000 0.284 0.076 0.064
#> GSM97873 5 0.6813 0.36972 0.008 0.228 0.308 0.000 0.456
#> GSM97874 3 0.0162 0.70488 0.000 0.000 0.996 0.000 0.004
#> GSM97875 3 0.0912 0.69729 0.012 0.000 0.972 0.000 0.016
#> GSM97876 3 0.0324 0.70414 0.004 0.000 0.992 0.000 0.004
#> GSM97880 3 0.0290 0.70385 0.000 0.000 0.992 0.000 0.008
#> GSM97881 3 0.5017 0.49781 0.008 0.040 0.652 0.000 0.300
#> GSM97884 5 0.6701 0.41539 0.004 0.240 0.288 0.000 0.468
#> GSM97901 3 0.5309 0.41145 0.004 0.056 0.604 0.000 0.336
#> GSM97902 5 0.6833 0.39839 0.180 0.064 0.096 0.028 0.632
#> GSM97909 5 0.6223 0.49756 0.096 0.316 0.024 0.000 0.564
#> GSM97911 3 0.5017 0.49781 0.008 0.040 0.652 0.000 0.300
#> GSM97923 3 0.0000 0.70427 0.000 0.000 1.000 0.000 0.000
#> GSM97928 1 0.6542 0.35374 0.568 0.000 0.292 0.072 0.068
#> GSM97929 2 0.0000 0.94932 0.000 1.000 0.000 0.000 0.000
#> GSM97933 3 0.3013 0.66601 0.008 0.000 0.832 0.000 0.160
#> GSM97934 3 0.3013 0.66601 0.008 0.000 0.832 0.000 0.160
#> GSM97944 5 0.6626 0.43370 0.000 0.272 0.272 0.000 0.456
#> GSM97949 2 0.0000 0.94932 0.000 1.000 0.000 0.000 0.000
#> GSM97956 3 0.6333 -0.07194 0.004 0.136 0.432 0.000 0.428
#> GSM97962 3 0.3013 0.66601 0.008 0.000 0.832 0.000 0.160
#> GSM97964 5 0.6615 0.25920 0.012 0.160 0.344 0.000 0.484
#> GSM97970 3 0.6331 0.15209 0.004 0.152 0.508 0.000 0.336
#> GSM97822 3 0.6232 0.10012 0.400 0.000 0.504 0.044 0.052
#> GSM97831 3 0.3132 0.65504 0.008 0.000 0.820 0.000 0.172
#> GSM97845 4 0.6040 -0.06036 0.452 0.000 0.012 0.456 0.080
#> GSM97865 1 0.7244 0.55333 0.432 0.000 0.036 0.192 0.340
#> GSM97867 3 0.0000 0.70427 0.000 0.000 1.000 0.000 0.000
#> GSM97883 1 0.7372 0.42886 0.440 0.000 0.292 0.228 0.040
#> GSM97897 3 0.6821 -0.03780 0.396 0.000 0.456 0.104 0.044
#> GSM97900 4 0.0000 0.75644 0.000 0.000 0.000 1.000 0.000
#> GSM97904 1 0.7695 0.49794 0.420 0.000 0.072 0.308 0.200
#> GSM97907 2 0.0000 0.94932 0.000 1.000 0.000 0.000 0.000
#> GSM97925 3 0.1907 0.68974 0.044 0.000 0.928 0.000 0.028
#> GSM97947 3 0.0912 0.69729 0.012 0.000 0.972 0.000 0.016
cbind(get_classes(res, k = 6), get_membership(res, k = 6))
#> class entropy silhouette p1 p2 p3 p4 p5 p6
#> GSM97800 2 0.0000 0.9474 0.000 1.000 0.000 0.000 0.000 0.000
#> GSM97803 2 0.0000 0.9474 0.000 1.000 0.000 0.000 0.000 0.000
#> GSM97804 2 0.0000 0.9474 0.000 1.000 0.000 0.000 0.000 0.000
#> GSM97805 2 0.0000 0.9474 0.000 1.000 0.000 0.000 0.000 0.000
#> GSM97807 2 0.0000 0.9474 0.000 1.000 0.000 0.000 0.000 0.000
#> GSM97809 2 0.0000 0.9474 0.000 1.000 0.000 0.000 0.000 0.000
#> GSM97811 2 0.0000 0.9474 0.000 1.000 0.000 0.000 0.000 0.000
#> GSM97812 2 0.0000 0.9474 0.000 1.000 0.000 0.000 0.000 0.000
#> GSM97816 6 0.4902 0.5145 0.076 0.052 0.044 0.000 0.068 0.760
#> GSM97817 2 0.0000 0.9474 0.000 1.000 0.000 0.000 0.000 0.000
#> GSM97820 2 0.0000 0.9474 0.000 1.000 0.000 0.000 0.000 0.000
#> GSM97825 2 0.0000 0.9474 0.000 1.000 0.000 0.000 0.000 0.000
#> GSM97827 2 0.0000 0.9474 0.000 1.000 0.000 0.000 0.000 0.000
#> GSM97828 6 0.4902 0.5145 0.076 0.052 0.044 0.000 0.068 0.760
#> GSM97833 2 0.0000 0.9474 0.000 1.000 0.000 0.000 0.000 0.000
#> GSM97834 2 0.0000 0.9474 0.000 1.000 0.000 0.000 0.000 0.000
#> GSM97840 2 0.4330 0.6520 0.028 0.760 0.000 0.000 0.076 0.136
#> GSM97846 2 0.0000 0.9474 0.000 1.000 0.000 0.000 0.000 0.000
#> GSM97848 2 0.0000 0.9474 0.000 1.000 0.000 0.000 0.000 0.000
#> GSM97849 2 0.0000 0.9474 0.000 1.000 0.000 0.000 0.000 0.000
#> GSM97850 2 0.0000 0.9474 0.000 1.000 0.000 0.000 0.000 0.000
#> GSM97853 2 0.0000 0.9474 0.000 1.000 0.000 0.000 0.000 0.000
#> GSM97855 2 0.0000 0.9474 0.000 1.000 0.000 0.000 0.000 0.000
#> GSM97878 1 0.5637 0.1577 0.540 0.000 0.008 0.000 0.312 0.140
#> GSM97913 6 0.6761 0.2680 0.284 0.100 0.000 0.000 0.136 0.480
#> GSM97932 4 0.4772 0.6268 0.096 0.000 0.000 0.700 0.188 0.016
#> GSM97939 6 0.5365 0.5404 0.004 0.320 0.116 0.000 0.000 0.560
#> GSM97951 2 0.4597 0.2957 0.000 0.652 0.072 0.000 0.000 0.276
#> GSM97957 3 0.3323 0.7132 0.008 0.000 0.780 0.000 0.008 0.204
#> GSM97972 6 0.4980 0.5813 0.040 0.196 0.032 0.000 0.024 0.708
#> GSM97793 3 0.0748 0.7456 0.004 0.000 0.976 0.000 0.004 0.016
#> GSM97795 6 0.5486 0.5345 0.000 0.316 0.132 0.000 0.004 0.548
#> GSM97802 5 0.6312 0.7767 0.244 0.000 0.276 0.012 0.464 0.004
#> GSM97810 6 0.5365 0.5346 0.000 0.332 0.112 0.000 0.004 0.552
#> GSM97815 6 0.5461 0.5375 0.000 0.308 0.132 0.000 0.004 0.556
#> GSM97837 1 0.7117 0.2912 0.368 0.000 0.008 0.304 0.268 0.052
#> GSM97843 3 0.3668 0.6737 0.008 0.000 0.728 0.000 0.008 0.256
#> GSM97890 3 0.4058 0.5408 0.004 0.008 0.616 0.000 0.000 0.372
#> GSM97899 4 0.0000 0.7727 0.000 0.000 0.000 1.000 0.000 0.000
#> GSM97910 6 0.5755 0.3350 0.252 0.004 0.032 0.012 0.080 0.620
#> GSM97916 1 0.5737 0.3908 0.628 0.004 0.016 0.100 0.020 0.232
#> GSM97920 3 0.5070 0.5346 0.044 0.004 0.644 0.000 0.032 0.276
#> GSM97921 1 0.6956 0.4211 0.492 0.000 0.004 0.228 0.172 0.104
#> GSM97927 1 0.4918 0.4161 0.720 0.000 0.032 0.112 0.004 0.132
#> GSM97937 4 0.6495 -0.1379 0.360 0.000 0.000 0.384 0.232 0.024
#> GSM97941 2 0.1787 0.8666 0.004 0.920 0.000 0.000 0.008 0.068
#> GSM97943 6 0.4889 0.5158 0.080 0.052 0.040 0.000 0.068 0.760
#> GSM97958 1 0.6151 -0.0227 0.448 0.044 0.008 0.000 0.080 0.420
#> GSM97960 2 0.5404 -0.2696 0.000 0.488 0.100 0.000 0.004 0.408
#> GSM97794 1 0.6865 0.0685 0.428 0.044 0.008 0.040 0.076 0.404
#> GSM97796 4 0.1401 0.7674 0.020 0.000 0.000 0.948 0.028 0.004
#> GSM97797 6 0.6046 0.2803 0.276 0.012 0.020 0.008 0.108 0.576
#> GSM97798 4 0.0000 0.7727 0.000 0.000 0.000 1.000 0.000 0.000
#> GSM97801 6 0.6204 0.2729 0.268 0.000 0.036 0.016 0.116 0.564
#> GSM97806 1 0.5173 0.4319 0.712 0.000 0.032 0.124 0.016 0.116
#> GSM97808 4 0.0000 0.7727 0.000 0.000 0.000 1.000 0.000 0.000
#> GSM97813 4 0.6838 -0.3169 0.352 0.000 0.048 0.356 0.244 0.000
#> GSM97814 4 0.0000 0.7727 0.000 0.000 0.000 1.000 0.000 0.000
#> GSM97818 1 0.7368 0.4099 0.448 0.016 0.000 0.212 0.224 0.100
#> GSM97819 3 0.1218 0.7179 0.004 0.000 0.956 0.000 0.028 0.012
#> GSM97821 6 0.7952 0.3811 0.280 0.272 0.076 0.000 0.052 0.320
#> GSM97826 1 0.6665 0.2915 0.356 0.000 0.004 0.308 0.312 0.020
#> GSM97829 1 0.7258 0.3899 0.428 0.000 0.008 0.260 0.212 0.092
#> GSM97832 2 0.5012 -0.0142 0.004 0.560 0.056 0.000 0.004 0.376
#> GSM97836 1 0.6109 0.2999 0.624 0.000 0.132 0.084 0.008 0.152
#> GSM97839 4 0.1401 0.7674 0.020 0.000 0.000 0.948 0.028 0.004
#> GSM97844 2 0.0000 0.9474 0.000 1.000 0.000 0.000 0.000 0.000
#> GSM97847 4 0.6220 0.1149 0.308 0.000 0.000 0.448 0.232 0.012
#> GSM97851 4 0.3127 0.7291 0.040 0.000 0.000 0.844 0.104 0.012
#> GSM97852 4 0.6196 0.1347 0.304 0.000 0.000 0.456 0.228 0.012
#> GSM97856 4 0.0405 0.7724 0.008 0.000 0.000 0.988 0.004 0.000
#> GSM97858 2 0.0000 0.9474 0.000 1.000 0.000 0.000 0.000 0.000
#> GSM97859 1 0.6846 0.2200 0.356 0.000 0.048 0.348 0.248 0.000
#> GSM97861 1 0.5063 0.4130 0.712 0.000 0.032 0.112 0.008 0.136
#> GSM97863 4 0.1053 0.7698 0.012 0.000 0.000 0.964 0.020 0.004
#> GSM97869 1 0.5993 0.3887 0.616 0.004 0.016 0.100 0.036 0.228
#> GSM97870 1 0.6842 0.2236 0.368 0.000 0.048 0.336 0.248 0.000
#> GSM97871 4 0.0000 0.7727 0.000 0.000 0.000 1.000 0.000 0.000
#> GSM97877 6 0.6759 0.2850 0.280 0.100 0.004 0.000 0.120 0.496
#> GSM97879 1 0.6018 0.4610 0.624 0.000 0.020 0.212 0.060 0.084
#> GSM97882 1 0.5164 0.4252 0.708 0.000 0.032 0.120 0.012 0.128
#> GSM97885 1 0.4913 0.4222 0.724 0.000 0.028 0.108 0.008 0.132
#> GSM97886 4 0.1536 0.7658 0.020 0.000 0.000 0.944 0.024 0.012
#> GSM97887 4 0.0000 0.7727 0.000 0.000 0.000 1.000 0.000 0.000
#> GSM97888 4 0.5434 0.3906 0.156 0.000 0.024 0.640 0.180 0.000
#> GSM97889 5 0.6248 0.7963 0.248 0.000 0.252 0.012 0.484 0.004
#> GSM97891 1 0.5446 0.3279 0.688 0.000 0.036 0.056 0.040 0.180
#> GSM97892 2 0.0000 0.9474 0.000 1.000 0.000 0.000 0.000 0.000
#> GSM97893 4 0.5747 0.2647 0.272 0.000 0.000 0.544 0.176 0.008
#> GSM97894 4 0.2078 0.7600 0.032 0.000 0.000 0.916 0.040 0.012
#> GSM97895 4 0.4733 0.6321 0.084 0.000 0.000 0.712 0.180 0.024
#> GSM97896 4 0.4425 0.5942 0.088 0.000 0.024 0.760 0.124 0.004
#> GSM97898 4 0.2333 0.7527 0.040 0.000 0.000 0.896 0.060 0.004
#> GSM97903 1 0.6325 0.4579 0.588 0.000 0.016 0.224 0.100 0.072
#> GSM97905 1 0.7440 -0.0746 0.384 0.000 0.140 0.180 0.292 0.004
#> GSM97906 4 0.0146 0.7723 0.004 0.000 0.000 0.996 0.000 0.000
#> GSM97908 4 0.6906 -0.0406 0.352 0.000 0.004 0.360 0.240 0.044
#> GSM97912 1 0.6997 0.0563 0.404 0.000 0.064 0.204 0.324 0.004
#> GSM97914 1 0.6668 0.4450 0.548 0.000 0.004 0.192 0.132 0.124
#> GSM97915 4 0.2563 0.7467 0.028 0.000 0.000 0.880 0.084 0.008
#> GSM97917 4 0.5095 0.5702 0.152 0.000 0.000 0.672 0.160 0.016
#> GSM97918 4 0.1515 0.7678 0.028 0.000 0.000 0.944 0.020 0.008
#> GSM97919 4 0.4510 0.6499 0.084 0.000 0.000 0.728 0.172 0.016
#> GSM97922 1 0.6853 0.2162 0.356 0.000 0.048 0.344 0.252 0.000
#> GSM97924 2 0.0000 0.9474 0.000 1.000 0.000 0.000 0.000 0.000
#> GSM97926 1 0.6109 0.2999 0.624 0.000 0.132 0.084 0.008 0.152
#> GSM97930 4 0.6421 -0.1896 0.356 0.000 0.000 0.372 0.256 0.016
#> GSM97931 6 0.5662 0.5825 0.076 0.192 0.032 0.000 0.036 0.664
#> GSM97935 1 0.5167 0.4122 0.704 0.000 0.036 0.112 0.008 0.140
#> GSM97936 4 0.3770 0.6719 0.100 0.000 0.000 0.796 0.096 0.008
#> GSM97938 4 0.6112 0.2450 0.268 0.000 0.000 0.488 0.232 0.012
#> GSM97940 4 0.0000 0.7727 0.000 0.000 0.000 1.000 0.000 0.000
#> GSM97942 3 0.1065 0.7389 0.020 0.000 0.964 0.000 0.008 0.008
#> GSM97945 4 0.1116 0.7636 0.028 0.000 0.004 0.960 0.008 0.000
#> GSM97946 2 0.0000 0.9474 0.000 1.000 0.000 0.000 0.000 0.000
#> GSM97948 3 0.2351 0.6914 0.052 0.000 0.900 0.000 0.036 0.012
#> GSM97950 4 0.0820 0.7724 0.012 0.000 0.000 0.972 0.016 0.000
#> GSM97952 4 0.0000 0.7727 0.000 0.000 0.000 1.000 0.000 0.000
#> GSM97953 4 0.6112 0.2443 0.268 0.000 0.000 0.488 0.232 0.012
#> GSM97954 1 0.6586 0.2790 0.424 0.000 0.012 0.364 0.176 0.024
#> GSM97955 4 0.1074 0.7665 0.028 0.000 0.000 0.960 0.012 0.000
#> GSM97959 6 0.6684 0.1912 0.316 0.080 0.000 0.000 0.140 0.464
#> GSM97961 4 0.0000 0.7727 0.000 0.000 0.000 1.000 0.000 0.000
#> GSM97963 4 0.0000 0.7727 0.000 0.000 0.000 1.000 0.000 0.000
#> GSM97965 4 0.0000 0.7727 0.000 0.000 0.000 1.000 0.000 0.000
#> GSM97966 4 0.0000 0.7727 0.000 0.000 0.000 1.000 0.000 0.000
#> GSM97967 2 0.0000 0.9474 0.000 1.000 0.000 0.000 0.000 0.000
#> GSM97968 2 0.0717 0.9247 0.000 0.976 0.000 0.000 0.008 0.016
#> GSM97969 4 0.7069 -0.2419 0.308 0.000 0.052 0.388 0.244 0.008
#> GSM97971 1 0.6846 0.2190 0.352 0.000 0.048 0.352 0.248 0.000
#> GSM97799 6 0.5775 0.4857 0.004 0.220 0.216 0.000 0.004 0.556
#> GSM97823 2 0.0000 0.9474 0.000 1.000 0.000 0.000 0.000 0.000
#> GSM97824 6 0.5322 0.1596 0.004 0.088 0.352 0.000 0.004 0.552
#> GSM97830 3 0.1643 0.7554 0.008 0.000 0.924 0.000 0.000 0.068
#> GSM97835 6 0.5474 0.5422 0.004 0.284 0.128 0.000 0.004 0.580
#> GSM97838 2 0.0146 0.9436 0.000 0.996 0.000 0.000 0.004 0.000
#> GSM97841 2 0.0000 0.9474 0.000 1.000 0.000 0.000 0.000 0.000
#> GSM97842 6 0.5655 0.5086 0.004 0.228 0.188 0.000 0.004 0.576
#> GSM97854 2 0.0000 0.9474 0.000 1.000 0.000 0.000 0.000 0.000
#> GSM97857 6 0.5318 0.1191 0.004 0.084 0.368 0.000 0.004 0.540
#> GSM97860 3 0.0508 0.7466 0.004 0.000 0.984 0.000 0.000 0.012
#> GSM97862 3 0.4415 0.4365 0.004 0.020 0.556 0.000 0.000 0.420
#> GSM97864 2 0.0000 0.9474 0.000 1.000 0.000 0.000 0.000 0.000
#> GSM97866 3 0.4466 0.3036 0.004 0.020 0.500 0.000 0.000 0.476
#> GSM97868 3 0.4058 0.5531 0.004 0.008 0.616 0.000 0.000 0.372
#> GSM97872 5 0.5785 0.5788 0.344 0.000 0.072 0.032 0.544 0.008
#> GSM97873 6 0.5531 0.4392 0.004 0.180 0.240 0.000 0.000 0.576
#> GSM97874 3 0.0748 0.7487 0.004 0.000 0.976 0.000 0.004 0.016
#> GSM97875 3 0.1116 0.7142 0.004 0.000 0.960 0.000 0.028 0.008
#> GSM97876 3 0.0717 0.7439 0.008 0.000 0.976 0.000 0.000 0.016
#> GSM97880 3 0.0922 0.7479 0.004 0.000 0.968 0.000 0.004 0.024
#> GSM97881 3 0.4090 0.5271 0.004 0.008 0.604 0.000 0.000 0.384
#> GSM97884 6 0.5689 0.4761 0.004 0.184 0.220 0.000 0.008 0.584
#> GSM97901 3 0.4547 0.4237 0.004 0.020 0.552 0.000 0.004 0.420
#> GSM97902 6 0.6207 0.3566 0.252 0.040 0.024 0.016 0.064 0.604
#> GSM97909 6 0.6682 0.4511 0.176 0.288 0.012 0.000 0.040 0.484
#> GSM97911 3 0.4090 0.5271 0.004 0.008 0.604 0.000 0.000 0.384
#> GSM97923 3 0.0405 0.7446 0.004 0.000 0.988 0.000 0.000 0.008
#> GSM97928 5 0.5698 0.5967 0.336 0.000 0.072 0.028 0.556 0.008
#> GSM97929 2 0.0000 0.9474 0.000 1.000 0.000 0.000 0.000 0.000
#> GSM97933 3 0.3292 0.7154 0.008 0.000 0.784 0.000 0.008 0.200
#> GSM97934 3 0.3292 0.7154 0.008 0.000 0.784 0.000 0.008 0.200
#> GSM97944 6 0.5775 0.4857 0.004 0.220 0.216 0.000 0.004 0.556
#> GSM97949 2 0.0000 0.9474 0.000 1.000 0.000 0.000 0.000 0.000
#> GSM97956 6 0.5334 0.0933 0.004 0.084 0.376 0.000 0.004 0.532
#> GSM97962 3 0.3292 0.7154 0.008 0.000 0.784 0.000 0.008 0.200
#> GSM97964 6 0.5298 0.3444 0.004 0.112 0.276 0.000 0.004 0.604
#> GSM97970 3 0.5516 0.1226 0.004 0.112 0.460 0.000 0.000 0.424
#> GSM97822 5 0.6247 0.7971 0.256 0.000 0.244 0.012 0.484 0.004
#> GSM97831 3 0.3103 0.7063 0.008 0.000 0.784 0.000 0.000 0.208
#> GSM97845 1 0.6242 0.2119 0.424 0.000 0.000 0.376 0.180 0.020
#> GSM97865 1 0.6657 0.3987 0.536 0.000 0.000 0.148 0.124 0.192
#> GSM97867 3 0.0748 0.7456 0.004 0.000 0.976 0.000 0.004 0.016
#> GSM97883 1 0.7538 -0.1706 0.380 0.000 0.204 0.152 0.260 0.004
#> GSM97897 5 0.6944 0.7589 0.256 0.000 0.208 0.072 0.460 0.004
#> GSM97900 4 0.0000 0.7727 0.000 0.000 0.000 1.000 0.000 0.000
#> GSM97904 1 0.7366 0.3011 0.472 0.000 0.028 0.228 0.180 0.092
#> GSM97907 2 0.0000 0.9474 0.000 1.000 0.000 0.000 0.000 0.000
#> GSM97925 3 0.1991 0.7073 0.044 0.000 0.920 0.000 0.024 0.012
#> GSM97947 3 0.1116 0.7142 0.004 0.000 0.960 0.000 0.028 0.008
Heatmaps for the consensus matrix. It visualizes the probability of two samples to be in a same group.
consensus_heatmap(res, k = 2)
consensus_heatmap(res, k = 3)
consensus_heatmap(res, k = 4)
consensus_heatmap(res, k = 5)
consensus_heatmap(res, k = 6)
Heatmaps for the membership of samples in all partitions to see how consistent they are:
membership_heatmap(res, k = 2)
membership_heatmap(res, k = 3)
membership_heatmap(res, k = 4)
membership_heatmap(res, k = 5)
membership_heatmap(res, k = 6)
As soon as we have had the classes for columns, we can look for signatures which are significantly different between classes which can be candidate marks for certain classes. Following are the heatmaps for signatures.
Signature heatmaps where rows are scaled:
get_signatures(res, k = 2)
get_signatures(res, k = 3)
get_signatures(res, k = 4)
get_signatures(res, k = 5)
get_signatures(res, k = 6)
Signature heatmaps where rows are not scaled:
get_signatures(res, k = 2, scale_rows = FALSE)
get_signatures(res, k = 3, scale_rows = FALSE)
get_signatures(res, k = 4, scale_rows = FALSE)
get_signatures(res, k = 5, scale_rows = FALSE)
get_signatures(res, k = 6, scale_rows = FALSE)
Compare the overlap of signatures from different k:
compare_signatures(res)
get_signature() returns a data frame invisibly. TO get the list of signatures, the function
call should be assigned to a variable explicitly. In following code, if plot argument is set
to FALSE, no heatmap is plotted while only the differential analysis is performed.
# code only for demonstration
tb = get_signature(res, k = ..., plot = FALSE)
An example of the output of tb is:
#> which_row fdr mean_1 mean_2 scaled_mean_1 scaled_mean_2 km
#> 1 38 0.042760348 8.373488 9.131774 -0.5533452 0.5164555 1
#> 2 40 0.018707592 7.106213 8.469186 -0.6173731 0.5762149 1
#> 3 55 0.019134737 10.221463 11.207825 -0.6159697 0.5749050 1
#> 4 59 0.006059896 5.921854 7.869574 -0.6899429 0.6439467 1
#> 5 60 0.018055526 8.928898 10.211722 -0.6204761 0.5791110 1
#> 6 98 0.009384629 15.714769 14.887706 0.6635654 -0.6193277 2
...
The columns in tb are:
which_row: row indices corresponding to the input matrix.fdr: FDR for the differential test. mean_x: The mean value in group x.scaled_mean_x: The mean value in group x after rows are scaled.km: Row groups if k-means clustering is applied to rows.UMAP plot which shows how samples are separated.
dimension_reduction(res, k = 2, method = "UMAP")
dimension_reduction(res, k = 3, method = "UMAP")
dimension_reduction(res, k = 4, method = "UMAP")
dimension_reduction(res, k = 5, method = "UMAP")
dimension_reduction(res, k = 6, method = "UMAP")
Following heatmap shows how subgroups are split when increasing k:
collect_classes(res)
Test correlation between subgroups and known annotations. If the known annotation is numeric, one-way ANOVA test is applied, and if the known annotation is discrete, chi-squared contingency table test is applied.
test_to_known_factors(res)
#> n disease.state(p) tissue(p) k
#> CV:hclust 150 2.60e-13 6.85e-14 2
#> CV:hclust 136 3.42e-23 2.97e-23 3
#> CV:hclust 119 1.02e-20 1.40e-19 4
#> CV:hclust 111 2.57e-16 8.33e-16 5
#> CV:hclust 112 2.24e-19 6.24e-17 6
If matrix rows can be associated to genes, consider to use functional_enrichment(res,
...) to perform function enrichment for the signature genes. See this vignette for more detailed explanations.
The object with results only for a single top-value method and a single partition method can be extracted as:
res = res_list["CV", "kmeans"]
# you can also extract it by
# res = res_list["CV:kmeans"]
A summary of res and all the functions that can be applied to it:
res
#> A 'ConsensusPartition' object with k = 2, 3, 4, 5, 6.
#> On a matrix with 51882 rows and 180 columns.
#> Top rows (1000, 2000, 3000, 4000, 5000) are extracted by 'CV' method.
#> Subgroups are detected by 'kmeans' method.
#> Performed in total 1250 partitions by row resampling.
#> Best k for subgroups seems to be 4.
#>
#> Following methods can be applied to this 'ConsensusPartition' object:
#> [1] "cola_report" "collect_classes" "collect_plots"
#> [4] "collect_stats" "colnames" "compare_signatures"
#> [7] "consensus_heatmap" "dimension_reduction" "functional_enrichment"
#> [10] "get_anno_col" "get_anno" "get_classes"
#> [13] "get_consensus" "get_matrix" "get_membership"
#> [16] "get_param" "get_signatures" "get_stats"
#> [19] "is_best_k" "is_stable_k" "membership_heatmap"
#> [22] "ncol" "nrow" "plot_ecdf"
#> [25] "rownames" "select_partition_number" "show"
#> [28] "suggest_best_k" "test_to_known_factors"
collect_plots() function collects all the plots made from res for all k (number of partitions)
into one single page to provide an easy and fast comparison between different k.
collect_plots(res)
The plots are:
k and the heatmap of
predicted classes for each k.k.k.k.All the plots in panels can be made by individual functions and they are plotted later in this section.
select_partition_number() produces several plots showing different
statistics for choosing “optimized” k. There are following statistics:
k;k, the area increased is defined as \(A_k - A_{k-1}\).The detailed explanations of these statistics can be found in the cola vignette.
Generally speaking, lower PAC score, higher mean silhouette score or higher
concordance corresponds to better partition. Rand index and Jaccard index
measure how similar the current partition is compared to partition with k-1.
If they are too similar, we won't accept k is better than k-1.
select_partition_number(res)
The numeric values for all these statistics can be obtained by get_stats().
get_stats(res)
#> k 1-PAC mean_silhouette concordance area_increased Rand Jaccard
#> 2 2 0.900 0.933 0.971 0.4719 0.520 0.520
#> 3 3 1.000 0.980 0.992 0.3698 0.738 0.540
#> 4 4 0.913 0.918 0.941 0.1554 0.861 0.627
#> 5 5 0.788 0.748 0.830 0.0618 0.966 0.867
#> 6 6 0.767 0.593 0.755 0.0389 0.914 0.651
suggest_best_k() suggests the best \(k\) based on these statistics. The rules are as follows:
suggest_best_k(res)
#> [1] 4
#> attr(,"optional")
#> [1] 2 3
There is also optional best \(k\) = 2 3 that is worth to check.
Following shows the table of the partitions (You need to click the show/hide
code output link to see it). The membership matrix (columns with name p*)
is inferred by
clue::cl_consensus()
function with the SE method. Basically the value in the membership matrix
represents the probability to belong to a certain group. The finall class
label for an item is determined with the group with highest probability it
belongs to.
In get_classes() function, the entropy is calculated from the membership
matrix and the silhouette score is calculated from the consensus matrix.
cbind(get_classes(res, k = 2), get_membership(res, k = 2))
#> class entropy silhouette p1 p2
#> GSM97800 2 0.0000 0.943 0.000 1.000
#> GSM97803 2 0.0000 0.943 0.000 1.000
#> GSM97804 2 0.0000 0.943 0.000 1.000
#> GSM97805 2 0.0000 0.943 0.000 1.000
#> GSM97807 2 0.0000 0.943 0.000 1.000
#> GSM97809 2 0.0000 0.943 0.000 1.000
#> GSM97811 2 0.0000 0.943 0.000 1.000
#> GSM97812 2 0.0000 0.943 0.000 1.000
#> GSM97816 2 0.0000 0.943 0.000 1.000
#> GSM97817 2 0.0000 0.943 0.000 1.000
#> GSM97820 2 0.0000 0.943 0.000 1.000
#> GSM97825 2 0.0000 0.943 0.000 1.000
#> GSM97827 2 0.0000 0.943 0.000 1.000
#> GSM97828 1 0.9795 0.206 0.584 0.416
#> GSM97833 2 0.0000 0.943 0.000 1.000
#> GSM97834 2 0.0000 0.943 0.000 1.000
#> GSM97840 2 0.0000 0.943 0.000 1.000
#> GSM97846 2 0.0000 0.943 0.000 1.000
#> GSM97848 2 0.0000 0.943 0.000 1.000
#> GSM97849 2 0.0000 0.943 0.000 1.000
#> GSM97850 2 0.0000 0.943 0.000 1.000
#> GSM97853 2 0.0000 0.943 0.000 1.000
#> GSM97855 2 0.0000 0.943 0.000 1.000
#> GSM97878 1 0.0000 0.987 1.000 0.000
#> GSM97913 2 0.0376 0.940 0.004 0.996
#> GSM97932 1 0.0000 0.987 1.000 0.000
#> GSM97939 2 0.0000 0.943 0.000 1.000
#> GSM97951 2 0.0000 0.943 0.000 1.000
#> GSM97957 1 0.2778 0.937 0.952 0.048
#> GSM97972 2 0.0000 0.943 0.000 1.000
#> GSM97793 1 0.0000 0.987 1.000 0.000
#> GSM97795 2 0.0000 0.943 0.000 1.000
#> GSM97802 1 0.0000 0.987 1.000 0.000
#> GSM97810 2 0.0000 0.943 0.000 1.000
#> GSM97815 2 0.0000 0.943 0.000 1.000
#> GSM97837 1 0.0000 0.987 1.000 0.000
#> GSM97843 1 0.3274 0.924 0.940 0.060
#> GSM97890 2 0.9896 0.302 0.440 0.560
#> GSM97899 1 0.0000 0.987 1.000 0.000
#> GSM97910 1 0.0000 0.987 1.000 0.000
#> GSM97916 1 0.0000 0.987 1.000 0.000
#> GSM97920 1 0.2603 0.942 0.956 0.044
#> GSM97921 1 0.0000 0.987 1.000 0.000
#> GSM97927 1 0.0000 0.987 1.000 0.000
#> GSM97937 1 0.0000 0.987 1.000 0.000
#> GSM97941 2 0.0000 0.943 0.000 1.000
#> GSM97943 1 0.0000 0.987 1.000 0.000
#> GSM97958 2 0.7139 0.774 0.196 0.804
#> GSM97960 2 0.0000 0.943 0.000 1.000
#> GSM97794 1 0.0000 0.987 1.000 0.000
#> GSM97796 1 0.0000 0.987 1.000 0.000
#> GSM97797 1 0.0000 0.987 1.000 0.000
#> GSM97798 1 0.0000 0.987 1.000 0.000
#> GSM97801 1 0.0000 0.987 1.000 0.000
#> GSM97806 1 0.0000 0.987 1.000 0.000
#> GSM97808 1 0.0000 0.987 1.000 0.000
#> GSM97813 1 0.0000 0.987 1.000 0.000
#> GSM97814 1 0.0000 0.987 1.000 0.000
#> GSM97818 1 0.0000 0.987 1.000 0.000
#> GSM97819 1 0.0000 0.987 1.000 0.000
#> GSM97821 2 0.0000 0.943 0.000 1.000
#> GSM97826 1 0.0000 0.987 1.000 0.000
#> GSM97829 1 0.0000 0.987 1.000 0.000
#> GSM97832 2 0.0000 0.943 0.000 1.000
#> GSM97836 1 0.0000 0.987 1.000 0.000
#> GSM97839 1 0.0000 0.987 1.000 0.000
#> GSM97844 2 0.0000 0.943 0.000 1.000
#> GSM97847 1 0.0000 0.987 1.000 0.000
#> GSM97851 1 0.0000 0.987 1.000 0.000
#> GSM97852 1 0.0000 0.987 1.000 0.000
#> GSM97856 1 0.0000 0.987 1.000 0.000
#> GSM97858 2 0.0000 0.943 0.000 1.000
#> GSM97859 1 0.0000 0.987 1.000 0.000
#> GSM97861 1 0.0000 0.987 1.000 0.000
#> GSM97863 1 0.0000 0.987 1.000 0.000
#> GSM97869 1 0.0000 0.987 1.000 0.000
#> GSM97870 1 0.0000 0.987 1.000 0.000
#> GSM97871 1 0.0000 0.987 1.000 0.000
#> GSM97877 2 0.0000 0.943 0.000 1.000
#> GSM97879 1 0.0000 0.987 1.000 0.000
#> GSM97882 1 0.0000 0.987 1.000 0.000
#> GSM97885 1 0.0000 0.987 1.000 0.000
#> GSM97886 1 0.0000 0.987 1.000 0.000
#> GSM97887 1 0.0000 0.987 1.000 0.000
#> GSM97888 1 0.0000 0.987 1.000 0.000
#> GSM97889 1 0.0000 0.987 1.000 0.000
#> GSM97891 1 0.0000 0.987 1.000 0.000
#> GSM97892 2 0.0000 0.943 0.000 1.000
#> GSM97893 1 0.0000 0.987 1.000 0.000
#> GSM97894 1 0.0000 0.987 1.000 0.000
#> GSM97895 1 0.0000 0.987 1.000 0.000
#> GSM97896 1 0.0000 0.987 1.000 0.000
#> GSM97898 1 0.0000 0.987 1.000 0.000
#> GSM97903 1 0.0000 0.987 1.000 0.000
#> GSM97905 1 0.0000 0.987 1.000 0.000
#> GSM97906 1 0.0000 0.987 1.000 0.000
#> GSM97908 1 0.0000 0.987 1.000 0.000
#> GSM97912 1 0.0000 0.987 1.000 0.000
#> GSM97914 1 0.0000 0.987 1.000 0.000
#> GSM97915 1 0.0000 0.987 1.000 0.000
#> GSM97917 1 0.0000 0.987 1.000 0.000
#> GSM97918 1 0.0000 0.987 1.000 0.000
#> GSM97919 1 0.0000 0.987 1.000 0.000
#> GSM97922 1 0.0000 0.987 1.000 0.000
#> GSM97924 2 0.0000 0.943 0.000 1.000
#> GSM97926 1 0.0000 0.987 1.000 0.000
#> GSM97930 1 0.0000 0.987 1.000 0.000
#> GSM97931 2 0.7674 0.741 0.224 0.776
#> GSM97935 1 0.0000 0.987 1.000 0.000
#> GSM97936 1 0.0000 0.987 1.000 0.000
#> GSM97938 1 0.0000 0.987 1.000 0.000
#> GSM97940 1 0.0000 0.987 1.000 0.000
#> GSM97942 1 0.0000 0.987 1.000 0.000
#> GSM97945 1 0.0000 0.987 1.000 0.000
#> GSM97946 2 0.0000 0.943 0.000 1.000
#> GSM97948 1 0.0000 0.987 1.000 0.000
#> GSM97950 1 0.0000 0.987 1.000 0.000
#> GSM97952 1 0.0000 0.987 1.000 0.000
#> GSM97953 1 0.0000 0.987 1.000 0.000
#> GSM97954 1 0.0000 0.987 1.000 0.000
#> GSM97955 1 0.0000 0.987 1.000 0.000
#> GSM97959 1 0.8327 0.607 0.736 0.264
#> GSM97961 1 0.0000 0.987 1.000 0.000
#> GSM97963 1 0.0000 0.987 1.000 0.000
#> GSM97965 1 0.0000 0.987 1.000 0.000
#> GSM97966 1 0.0000 0.987 1.000 0.000
#> GSM97967 2 0.0000 0.943 0.000 1.000
#> GSM97968 2 0.0000 0.943 0.000 1.000
#> GSM97969 1 0.0000 0.987 1.000 0.000
#> GSM97971 1 0.0000 0.987 1.000 0.000
#> GSM97799 2 0.0000 0.943 0.000 1.000
#> GSM97823 2 0.0000 0.943 0.000 1.000
#> GSM97824 2 0.7883 0.725 0.236 0.764
#> GSM97830 1 0.1843 0.959 0.972 0.028
#> GSM97835 2 0.0000 0.943 0.000 1.000
#> GSM97838 2 0.0000 0.943 0.000 1.000
#> GSM97841 2 0.0000 0.943 0.000 1.000
#> GSM97842 2 0.0000 0.943 0.000 1.000
#> GSM97854 2 0.0000 0.943 0.000 1.000
#> GSM97857 2 0.7453 0.755 0.212 0.788
#> GSM97860 1 0.0000 0.987 1.000 0.000
#> GSM97862 2 0.8861 0.616 0.304 0.696
#> GSM97864 2 0.0000 0.943 0.000 1.000
#> GSM97866 2 0.8608 0.651 0.284 0.716
#> GSM97868 2 0.7453 0.755 0.212 0.788
#> GSM97872 1 0.0000 0.987 1.000 0.000
#> GSM97873 2 0.0000 0.943 0.000 1.000
#> GSM97874 1 0.0000 0.987 1.000 0.000
#> GSM97875 1 0.1184 0.971 0.984 0.016
#> GSM97876 1 0.0000 0.987 1.000 0.000
#> GSM97880 1 0.0000 0.987 1.000 0.000
#> GSM97881 2 0.7815 0.730 0.232 0.768
#> GSM97884 2 0.0000 0.943 0.000 1.000
#> GSM97901 2 0.9944 0.252 0.456 0.544
#> GSM97902 1 0.0000 0.987 1.000 0.000
#> GSM97909 2 0.0000 0.943 0.000 1.000
#> GSM97911 2 0.7815 0.730 0.232 0.768
#> GSM97923 1 0.0000 0.987 1.000 0.000
#> GSM97928 1 0.0000 0.987 1.000 0.000
#> GSM97929 2 0.0000 0.943 0.000 1.000
#> GSM97933 1 0.0000 0.987 1.000 0.000
#> GSM97934 1 0.0000 0.987 1.000 0.000
#> GSM97944 2 0.0000 0.943 0.000 1.000
#> GSM97949 2 0.0000 0.943 0.000 1.000
#> GSM97956 2 0.7883 0.725 0.236 0.764
#> GSM97962 2 0.9754 0.389 0.408 0.592
#> GSM97964 2 0.7139 0.774 0.196 0.804
#> GSM97970 2 0.0000 0.943 0.000 1.000
#> GSM97822 1 0.0000 0.987 1.000 0.000
#> GSM97831 1 0.9850 0.164 0.572 0.428
#> GSM97845 1 0.0000 0.987 1.000 0.000
#> GSM97865 1 0.0000 0.987 1.000 0.000
#> GSM97867 1 0.0000 0.987 1.000 0.000
#> GSM97883 1 0.0000 0.987 1.000 0.000
#> GSM97897 1 0.0000 0.987 1.000 0.000
#> GSM97900 1 0.0000 0.987 1.000 0.000
#> GSM97904 1 0.0000 0.987 1.000 0.000
#> GSM97907 2 0.0000 0.943 0.000 1.000
#> GSM97925 1 0.0000 0.987 1.000 0.000
#> GSM97947 1 0.0000 0.987 1.000 0.000
cbind(get_classes(res, k = 3), get_membership(res, k = 3))
#> class entropy silhouette p1 p2 p3
#> GSM97800 2 0.0000 1.000 0.000 1.000 0.000
#> GSM97803 2 0.0000 1.000 0.000 1.000 0.000
#> GSM97804 2 0.0000 1.000 0.000 1.000 0.000
#> GSM97805 2 0.0000 1.000 0.000 1.000 0.000
#> GSM97807 2 0.0000 1.000 0.000 1.000 0.000
#> GSM97809 2 0.0000 1.000 0.000 1.000 0.000
#> GSM97811 2 0.0000 1.000 0.000 1.000 0.000
#> GSM97812 2 0.0000 1.000 0.000 1.000 0.000
#> GSM97816 3 0.0000 0.977 0.000 0.000 1.000
#> GSM97817 2 0.0000 1.000 0.000 1.000 0.000
#> GSM97820 2 0.0000 1.000 0.000 1.000 0.000
#> GSM97825 2 0.0000 1.000 0.000 1.000 0.000
#> GSM97827 2 0.0000 1.000 0.000 1.000 0.000
#> GSM97828 3 0.0000 0.977 0.000 0.000 1.000
#> GSM97833 2 0.0000 1.000 0.000 1.000 0.000
#> GSM97834 2 0.0000 1.000 0.000 1.000 0.000
#> GSM97840 2 0.0000 1.000 0.000 1.000 0.000
#> GSM97846 2 0.0000 1.000 0.000 1.000 0.000
#> GSM97848 2 0.0000 1.000 0.000 1.000 0.000
#> GSM97849 2 0.0000 1.000 0.000 1.000 0.000
#> GSM97850 2 0.0000 1.000 0.000 1.000 0.000
#> GSM97853 2 0.0000 1.000 0.000 1.000 0.000
#> GSM97855 2 0.0000 1.000 0.000 1.000 0.000
#> GSM97878 1 0.2356 0.922 0.928 0.000 0.072
#> GSM97913 3 0.6192 0.304 0.000 0.420 0.580
#> GSM97932 1 0.0000 0.997 1.000 0.000 0.000
#> GSM97939 3 0.0000 0.977 0.000 0.000 1.000
#> GSM97951 2 0.0000 1.000 0.000 1.000 0.000
#> GSM97957 3 0.0000 0.977 0.000 0.000 1.000
#> GSM97972 3 0.0000 0.977 0.000 0.000 1.000
#> GSM97793 3 0.0000 0.977 0.000 0.000 1.000
#> GSM97795 2 0.0000 1.000 0.000 1.000 0.000
#> GSM97802 3 0.0000 0.977 0.000 0.000 1.000
#> GSM97810 3 0.6154 0.340 0.000 0.408 0.592
#> GSM97815 3 0.0000 0.977 0.000 0.000 1.000
#> GSM97837 1 0.0000 0.997 1.000 0.000 0.000
#> GSM97843 3 0.0000 0.977 0.000 0.000 1.000
#> GSM97890 3 0.0000 0.977 0.000 0.000 1.000
#> GSM97899 1 0.0000 0.997 1.000 0.000 0.000
#> GSM97910 3 0.0000 0.977 0.000 0.000 1.000
#> GSM97916 1 0.0237 0.994 0.996 0.000 0.004
#> GSM97920 3 0.0000 0.977 0.000 0.000 1.000
#> GSM97921 1 0.0000 0.997 1.000 0.000 0.000
#> GSM97927 1 0.0000 0.997 1.000 0.000 0.000
#> GSM97937 1 0.0000 0.997 1.000 0.000 0.000
#> GSM97941 2 0.0000 1.000 0.000 1.000 0.000
#> GSM97943 3 0.0000 0.977 0.000 0.000 1.000
#> GSM97958 3 0.0000 0.977 0.000 0.000 1.000
#> GSM97960 2 0.0000 1.000 0.000 1.000 0.000
#> GSM97794 1 0.0237 0.994 0.996 0.000 0.004
#> GSM97796 1 0.0000 0.997 1.000 0.000 0.000
#> GSM97797 1 0.3412 0.860 0.876 0.000 0.124
#> GSM97798 1 0.0000 0.997 1.000 0.000 0.000
#> GSM97801 1 0.0237 0.994 0.996 0.000 0.004
#> GSM97806 1 0.0000 0.997 1.000 0.000 0.000
#> GSM97808 1 0.0000 0.997 1.000 0.000 0.000
#> GSM97813 1 0.0000 0.997 1.000 0.000 0.000
#> GSM97814 1 0.0000 0.997 1.000 0.000 0.000
#> GSM97818 1 0.0000 0.997 1.000 0.000 0.000
#> GSM97819 3 0.0000 0.977 0.000 0.000 1.000
#> GSM97821 3 0.3340 0.854 0.000 0.120 0.880
#> GSM97826 1 0.0000 0.997 1.000 0.000 0.000
#> GSM97829 1 0.0000 0.997 1.000 0.000 0.000
#> GSM97832 3 0.5560 0.585 0.000 0.300 0.700
#> GSM97836 1 0.0000 0.997 1.000 0.000 0.000
#> GSM97839 1 0.0000 0.997 1.000 0.000 0.000
#> GSM97844 2 0.0000 1.000 0.000 1.000 0.000
#> GSM97847 1 0.0000 0.997 1.000 0.000 0.000
#> GSM97851 1 0.0000 0.997 1.000 0.000 0.000
#> GSM97852 1 0.0000 0.997 1.000 0.000 0.000
#> GSM97856 1 0.0000 0.997 1.000 0.000 0.000
#> GSM97858 2 0.0000 1.000 0.000 1.000 0.000
#> GSM97859 1 0.0000 0.997 1.000 0.000 0.000
#> GSM97861 1 0.0000 0.997 1.000 0.000 0.000
#> GSM97863 1 0.0000 0.997 1.000 0.000 0.000
#> GSM97869 1 0.0000 0.997 1.000 0.000 0.000
#> GSM97870 1 0.0000 0.997 1.000 0.000 0.000
#> GSM97871 1 0.0000 0.997 1.000 0.000 0.000
#> GSM97877 2 0.0000 1.000 0.000 1.000 0.000
#> GSM97879 1 0.0000 0.997 1.000 0.000 0.000
#> GSM97882 1 0.0000 0.997 1.000 0.000 0.000
#> GSM97885 1 0.0000 0.997 1.000 0.000 0.000
#> GSM97886 1 0.0000 0.997 1.000 0.000 0.000
#> GSM97887 1 0.0000 0.997 1.000 0.000 0.000
#> GSM97888 1 0.0000 0.997 1.000 0.000 0.000
#> GSM97889 1 0.0000 0.997 1.000 0.000 0.000
#> GSM97891 1 0.0000 0.997 1.000 0.000 0.000
#> GSM97892 2 0.0000 1.000 0.000 1.000 0.000
#> GSM97893 1 0.0000 0.997 1.000 0.000 0.000
#> GSM97894 1 0.0000 0.997 1.000 0.000 0.000
#> GSM97895 1 0.0000 0.997 1.000 0.000 0.000
#> GSM97896 1 0.0000 0.997 1.000 0.000 0.000
#> GSM97898 1 0.0000 0.997 1.000 0.000 0.000
#> GSM97903 1 0.0000 0.997 1.000 0.000 0.000
#> GSM97905 1 0.0000 0.997 1.000 0.000 0.000
#> GSM97906 1 0.0000 0.997 1.000 0.000 0.000
#> GSM97908 1 0.0000 0.997 1.000 0.000 0.000
#> GSM97912 1 0.0000 0.997 1.000 0.000 0.000
#> GSM97914 1 0.0000 0.997 1.000 0.000 0.000
#> GSM97915 1 0.0000 0.997 1.000 0.000 0.000
#> GSM97917 1 0.0000 0.997 1.000 0.000 0.000
#> GSM97918 1 0.0000 0.997 1.000 0.000 0.000
#> GSM97919 1 0.0000 0.997 1.000 0.000 0.000
#> GSM97922 1 0.0000 0.997 1.000 0.000 0.000
#> GSM97924 2 0.0000 1.000 0.000 1.000 0.000
#> GSM97926 3 0.0000 0.977 0.000 0.000 1.000
#> GSM97930 1 0.0000 0.997 1.000 0.000 0.000
#> GSM97931 3 0.0000 0.977 0.000 0.000 1.000
#> GSM97935 1 0.0000 0.997 1.000 0.000 0.000
#> GSM97936 1 0.0000 0.997 1.000 0.000 0.000
#> GSM97938 1 0.0000 0.997 1.000 0.000 0.000
#> GSM97940 1 0.0000 0.997 1.000 0.000 0.000
#> GSM97942 3 0.0000 0.977 0.000 0.000 1.000
#> GSM97945 1 0.0000 0.997 1.000 0.000 0.000
#> GSM97946 2 0.0000 1.000 0.000 1.000 0.000
#> GSM97948 3 0.0000 0.977 0.000 0.000 1.000
#> GSM97950 1 0.0000 0.997 1.000 0.000 0.000
#> GSM97952 1 0.0000 0.997 1.000 0.000 0.000
#> GSM97953 1 0.0000 0.997 1.000 0.000 0.000
#> GSM97954 1 0.0000 0.997 1.000 0.000 0.000
#> GSM97955 1 0.0000 0.997 1.000 0.000 0.000
#> GSM97959 1 0.0424 0.990 0.992 0.008 0.000
#> GSM97961 1 0.0000 0.997 1.000 0.000 0.000
#> GSM97963 1 0.0000 0.997 1.000 0.000 0.000
#> GSM97965 1 0.0000 0.997 1.000 0.000 0.000
#> GSM97966 1 0.0000 0.997 1.000 0.000 0.000
#> GSM97967 2 0.0000 1.000 0.000 1.000 0.000
#> GSM97968 2 0.0000 1.000 0.000 1.000 0.000
#> GSM97969 1 0.0000 0.997 1.000 0.000 0.000
#> GSM97971 1 0.0000 0.997 1.000 0.000 0.000
#> GSM97799 3 0.0000 0.977 0.000 0.000 1.000
#> GSM97823 2 0.0000 1.000 0.000 1.000 0.000
#> GSM97824 3 0.0000 0.977 0.000 0.000 1.000
#> GSM97830 3 0.0000 0.977 0.000 0.000 1.000
#> GSM97835 3 0.0000 0.977 0.000 0.000 1.000
#> GSM97838 2 0.0000 1.000 0.000 1.000 0.000
#> GSM97841 2 0.0000 1.000 0.000 1.000 0.000
#> GSM97842 3 0.0000 0.977 0.000 0.000 1.000
#> GSM97854 2 0.0000 1.000 0.000 1.000 0.000
#> GSM97857 3 0.0000 0.977 0.000 0.000 1.000
#> GSM97860 3 0.0000 0.977 0.000 0.000 1.000
#> GSM97862 3 0.0000 0.977 0.000 0.000 1.000
#> GSM97864 2 0.0000 1.000 0.000 1.000 0.000
#> GSM97866 3 0.0000 0.977 0.000 0.000 1.000
#> GSM97868 3 0.0000 0.977 0.000 0.000 1.000
#> GSM97872 1 0.0000 0.997 1.000 0.000 0.000
#> GSM97873 3 0.0000 0.977 0.000 0.000 1.000
#> GSM97874 3 0.0000 0.977 0.000 0.000 1.000
#> GSM97875 3 0.0000 0.977 0.000 0.000 1.000
#> GSM97876 3 0.0000 0.977 0.000 0.000 1.000
#> GSM97880 3 0.0000 0.977 0.000 0.000 1.000
#> GSM97881 3 0.0000 0.977 0.000 0.000 1.000
#> GSM97884 3 0.0000 0.977 0.000 0.000 1.000
#> GSM97901 3 0.0000 0.977 0.000 0.000 1.000
#> GSM97902 3 0.0000 0.977 0.000 0.000 1.000
#> GSM97909 2 0.0000 1.000 0.000 1.000 0.000
#> GSM97911 3 0.0000 0.977 0.000 0.000 1.000
#> GSM97923 3 0.0000 0.977 0.000 0.000 1.000
#> GSM97928 1 0.0000 0.997 1.000 0.000 0.000
#> GSM97929 2 0.0000 1.000 0.000 1.000 0.000
#> GSM97933 3 0.0000 0.977 0.000 0.000 1.000
#> GSM97934 3 0.0000 0.977 0.000 0.000 1.000
#> GSM97944 3 0.0000 0.977 0.000 0.000 1.000
#> GSM97949 2 0.0000 1.000 0.000 1.000 0.000
#> GSM97956 3 0.0000 0.977 0.000 0.000 1.000
#> GSM97962 3 0.0000 0.977 0.000 0.000 1.000
#> GSM97964 3 0.0000 0.977 0.000 0.000 1.000
#> GSM97970 3 0.0000 0.977 0.000 0.000 1.000
#> GSM97822 1 0.0000 0.997 1.000 0.000 0.000
#> GSM97831 3 0.0000 0.977 0.000 0.000 1.000
#> GSM97845 1 0.0000 0.997 1.000 0.000 0.000
#> GSM97865 1 0.0000 0.997 1.000 0.000 0.000
#> GSM97867 3 0.0000 0.977 0.000 0.000 1.000
#> GSM97883 3 0.0000 0.977 0.000 0.000 1.000
#> GSM97897 1 0.0000 0.997 1.000 0.000 0.000
#> GSM97900 1 0.0000 0.997 1.000 0.000 0.000
#> GSM97904 1 0.0000 0.997 1.000 0.000 0.000
#> GSM97907 2 0.0000 1.000 0.000 1.000 0.000
#> GSM97925 3 0.0000 0.977 0.000 0.000 1.000
#> GSM97947 3 0.0000 0.977 0.000 0.000 1.000
cbind(get_classes(res, k = 4), get_membership(res, k = 4))
#> class entropy silhouette p1 p2 p3 p4
#> GSM97800 2 0.1022 0.984 0.032 0.968 0.000 0.000
#> GSM97803 2 0.0921 0.985 0.028 0.972 0.000 0.000
#> GSM97804 2 0.1022 0.984 0.032 0.968 0.000 0.000
#> GSM97805 2 0.1022 0.984 0.032 0.968 0.000 0.000
#> GSM97807 2 0.0000 0.989 0.000 1.000 0.000 0.000
#> GSM97809 2 0.0000 0.989 0.000 1.000 0.000 0.000
#> GSM97811 2 0.0000 0.989 0.000 1.000 0.000 0.000
#> GSM97812 2 0.0000 0.989 0.000 1.000 0.000 0.000
#> GSM97816 3 0.4188 0.736 0.244 0.004 0.752 0.000
#> GSM97817 2 0.0000 0.989 0.000 1.000 0.000 0.000
#> GSM97820 2 0.0000 0.989 0.000 1.000 0.000 0.000
#> GSM97825 2 0.0000 0.989 0.000 1.000 0.000 0.000
#> GSM97827 2 0.0000 0.989 0.000 1.000 0.000 0.000
#> GSM97828 3 0.4981 0.258 0.464 0.000 0.536 0.000
#> GSM97833 2 0.0000 0.989 0.000 1.000 0.000 0.000
#> GSM97834 2 0.0000 0.989 0.000 1.000 0.000 0.000
#> GSM97840 2 0.0000 0.989 0.000 1.000 0.000 0.000
#> GSM97846 2 0.0000 0.989 0.000 1.000 0.000 0.000
#> GSM97848 2 0.0000 0.989 0.000 1.000 0.000 0.000
#> GSM97849 2 0.0000 0.989 0.000 1.000 0.000 0.000
#> GSM97850 2 0.0000 0.989 0.000 1.000 0.000 0.000
#> GSM97853 2 0.0000 0.989 0.000 1.000 0.000 0.000
#> GSM97855 2 0.0000 0.989 0.000 1.000 0.000 0.000
#> GSM97878 1 0.1118 0.884 0.964 0.000 0.000 0.036
#> GSM97913 1 0.0188 0.859 0.996 0.000 0.004 0.000
#> GSM97932 4 0.0000 0.991 0.000 0.000 0.000 1.000
#> GSM97939 3 0.1118 0.937 0.036 0.000 0.964 0.000
#> GSM97951 2 0.0000 0.989 0.000 1.000 0.000 0.000
#> GSM97957 3 0.0000 0.945 0.000 0.000 1.000 0.000
#> GSM97972 3 0.4134 0.716 0.260 0.000 0.740 0.000
#> GSM97793 3 0.0188 0.945 0.004 0.000 0.996 0.000
#> GSM97795 2 0.1211 0.980 0.040 0.960 0.000 0.000
#> GSM97802 3 0.0188 0.945 0.004 0.000 0.996 0.000
#> GSM97810 3 0.6252 0.191 0.056 0.432 0.512 0.000
#> GSM97815 3 0.1637 0.926 0.060 0.000 0.940 0.000
#> GSM97837 1 0.2149 0.896 0.912 0.000 0.000 0.088
#> GSM97843 3 0.0000 0.945 0.000 0.000 1.000 0.000
#> GSM97890 3 0.0000 0.945 0.000 0.000 1.000 0.000
#> GSM97899 4 0.0000 0.991 0.000 0.000 0.000 1.000
#> GSM97910 1 0.1211 0.857 0.960 0.000 0.040 0.000
#> GSM97916 1 0.1211 0.886 0.960 0.000 0.000 0.040
#> GSM97920 3 0.0000 0.945 0.000 0.000 1.000 0.000
#> GSM97921 1 0.1867 0.897 0.928 0.000 0.000 0.072
#> GSM97927 1 0.3907 0.835 0.768 0.000 0.000 0.232
#> GSM97937 1 0.2216 0.896 0.908 0.000 0.000 0.092
#> GSM97941 2 0.0188 0.988 0.004 0.996 0.000 0.000
#> GSM97943 1 0.1302 0.856 0.956 0.000 0.044 0.000
#> GSM97958 1 0.1118 0.856 0.964 0.000 0.036 0.000
#> GSM97960 2 0.0817 0.985 0.024 0.976 0.000 0.000
#> GSM97794 1 0.1022 0.882 0.968 0.000 0.000 0.032
#> GSM97796 4 0.0000 0.991 0.000 0.000 0.000 1.000
#> GSM97797 1 0.1022 0.882 0.968 0.000 0.000 0.032
#> GSM97798 4 0.0000 0.991 0.000 0.000 0.000 1.000
#> GSM97801 1 0.1389 0.890 0.952 0.000 0.000 0.048
#> GSM97806 1 0.3907 0.835 0.768 0.000 0.000 0.232
#> GSM97808 4 0.0000 0.991 0.000 0.000 0.000 1.000
#> GSM97813 1 0.4843 0.590 0.604 0.000 0.000 0.396
#> GSM97814 4 0.0000 0.991 0.000 0.000 0.000 1.000
#> GSM97818 1 0.1474 0.891 0.948 0.000 0.000 0.052
#> GSM97819 3 0.0188 0.945 0.004 0.000 0.996 0.000
#> GSM97821 3 0.5375 0.743 0.116 0.140 0.744 0.000
#> GSM97826 1 0.2216 0.896 0.908 0.000 0.000 0.092
#> GSM97829 1 0.1867 0.897 0.928 0.000 0.000 0.072
#> GSM97832 3 0.6400 0.242 0.068 0.408 0.524 0.000
#> GSM97836 1 0.3873 0.836 0.772 0.000 0.000 0.228
#> GSM97839 4 0.0000 0.991 0.000 0.000 0.000 1.000
#> GSM97844 2 0.1022 0.984 0.032 0.968 0.000 0.000
#> GSM97847 1 0.1940 0.897 0.924 0.000 0.000 0.076
#> GSM97851 4 0.0000 0.991 0.000 0.000 0.000 1.000
#> GSM97852 1 0.3726 0.847 0.788 0.000 0.000 0.212
#> GSM97856 4 0.0000 0.991 0.000 0.000 0.000 1.000
#> GSM97858 2 0.1022 0.984 0.032 0.968 0.000 0.000
#> GSM97859 1 0.4008 0.825 0.756 0.000 0.000 0.244
#> GSM97861 1 0.3907 0.835 0.768 0.000 0.000 0.232
#> GSM97863 4 0.0000 0.991 0.000 0.000 0.000 1.000
#> GSM97869 1 0.1389 0.890 0.952 0.000 0.000 0.048
#> GSM97870 1 0.1978 0.896 0.928 0.000 0.004 0.068
#> GSM97871 4 0.0000 0.991 0.000 0.000 0.000 1.000
#> GSM97877 1 0.0336 0.857 0.992 0.008 0.000 0.000
#> GSM97879 1 0.3907 0.835 0.768 0.000 0.000 0.232
#> GSM97882 1 0.3873 0.836 0.772 0.000 0.000 0.228
#> GSM97885 1 0.1867 0.897 0.928 0.000 0.000 0.072
#> GSM97886 4 0.0000 0.991 0.000 0.000 0.000 1.000
#> GSM97887 4 0.0000 0.991 0.000 0.000 0.000 1.000
#> GSM97888 4 0.0000 0.991 0.000 0.000 0.000 1.000
#> GSM97889 4 0.0336 0.983 0.008 0.000 0.000 0.992
#> GSM97891 1 0.3907 0.835 0.768 0.000 0.000 0.232
#> GSM97892 2 0.1022 0.984 0.032 0.968 0.000 0.000
#> GSM97893 4 0.0000 0.991 0.000 0.000 0.000 1.000
#> GSM97894 4 0.0000 0.991 0.000 0.000 0.000 1.000
#> GSM97895 4 0.0000 0.991 0.000 0.000 0.000 1.000
#> GSM97896 4 0.0000 0.991 0.000 0.000 0.000 1.000
#> GSM97898 4 0.0000 0.991 0.000 0.000 0.000 1.000
#> GSM97903 1 0.1867 0.897 0.928 0.000 0.000 0.072
#> GSM97905 1 0.6788 0.632 0.592 0.000 0.144 0.264
#> GSM97906 4 0.0000 0.991 0.000 0.000 0.000 1.000
#> GSM97908 1 0.4643 0.692 0.656 0.000 0.000 0.344
#> GSM97912 1 0.2149 0.896 0.912 0.000 0.000 0.088
#> GSM97914 1 0.1867 0.897 0.928 0.000 0.000 0.072
#> GSM97915 4 0.0000 0.991 0.000 0.000 0.000 1.000
#> GSM97917 4 0.0000 0.991 0.000 0.000 0.000 1.000
#> GSM97918 4 0.0000 0.991 0.000 0.000 0.000 1.000
#> GSM97919 4 0.0000 0.991 0.000 0.000 0.000 1.000
#> GSM97922 4 0.4250 0.493 0.276 0.000 0.000 0.724
#> GSM97924 2 0.1022 0.984 0.032 0.968 0.000 0.000
#> GSM97926 3 0.1118 0.938 0.036 0.000 0.964 0.000
#> GSM97930 1 0.1940 0.897 0.924 0.000 0.000 0.076
#> GSM97931 3 0.3873 0.758 0.228 0.000 0.772 0.000
#> GSM97935 1 0.3907 0.835 0.768 0.000 0.000 0.232
#> GSM97936 4 0.0000 0.991 0.000 0.000 0.000 1.000
#> GSM97938 1 0.4040 0.810 0.752 0.000 0.000 0.248
#> GSM97940 4 0.0000 0.991 0.000 0.000 0.000 1.000
#> GSM97942 3 0.0188 0.945 0.004 0.000 0.996 0.000
#> GSM97945 4 0.0000 0.991 0.000 0.000 0.000 1.000
#> GSM97946 2 0.0000 0.989 0.000 1.000 0.000 0.000
#> GSM97948 3 0.0336 0.943 0.008 0.000 0.992 0.000
#> GSM97950 4 0.0000 0.991 0.000 0.000 0.000 1.000
#> GSM97952 4 0.0000 0.991 0.000 0.000 0.000 1.000
#> GSM97953 1 0.2216 0.896 0.908 0.000 0.000 0.092
#> GSM97954 1 0.3907 0.836 0.768 0.000 0.000 0.232
#> GSM97955 4 0.0000 0.991 0.000 0.000 0.000 1.000
#> GSM97959 1 0.1209 0.881 0.964 0.000 0.004 0.032
#> GSM97961 4 0.0000 0.991 0.000 0.000 0.000 1.000
#> GSM97963 4 0.0000 0.991 0.000 0.000 0.000 1.000
#> GSM97965 4 0.0000 0.991 0.000 0.000 0.000 1.000
#> GSM97966 4 0.0000 0.991 0.000 0.000 0.000 1.000
#> GSM97967 2 0.0000 0.989 0.000 1.000 0.000 0.000
#> GSM97968 2 0.0000 0.989 0.000 1.000 0.000 0.000
#> GSM97969 1 0.4331 0.776 0.712 0.000 0.000 0.288
#> GSM97971 1 0.4103 0.814 0.744 0.000 0.000 0.256
#> GSM97799 3 0.1118 0.937 0.036 0.000 0.964 0.000
#> GSM97823 2 0.0000 0.989 0.000 1.000 0.000 0.000
#> GSM97824 3 0.0921 0.939 0.028 0.000 0.972 0.000
#> GSM97830 3 0.0188 0.945 0.004 0.000 0.996 0.000
#> GSM97835 3 0.1637 0.926 0.060 0.000 0.940 0.000
#> GSM97838 2 0.1022 0.984 0.032 0.968 0.000 0.000
#> GSM97841 2 0.1022 0.984 0.032 0.968 0.000 0.000
#> GSM97842 3 0.1118 0.937 0.036 0.000 0.964 0.000
#> GSM97854 2 0.1022 0.984 0.032 0.968 0.000 0.000
#> GSM97857 3 0.0921 0.939 0.028 0.000 0.972 0.000
#> GSM97860 3 0.0188 0.945 0.004 0.000 0.996 0.000
#> GSM97862 3 0.0000 0.945 0.000 0.000 1.000 0.000
#> GSM97864 2 0.1022 0.984 0.032 0.968 0.000 0.000
#> GSM97866 3 0.0000 0.945 0.000 0.000 1.000 0.000
#> GSM97868 3 0.0921 0.939 0.028 0.000 0.972 0.000
#> GSM97872 1 0.2149 0.896 0.912 0.000 0.000 0.088
#> GSM97873 3 0.1118 0.937 0.036 0.000 0.964 0.000
#> GSM97874 3 0.0188 0.945 0.004 0.000 0.996 0.000
#> GSM97875 3 0.0188 0.945 0.004 0.000 0.996 0.000
#> GSM97876 3 0.0188 0.945 0.004 0.000 0.996 0.000
#> GSM97880 3 0.0188 0.945 0.004 0.000 0.996 0.000
#> GSM97881 3 0.0000 0.945 0.000 0.000 1.000 0.000
#> GSM97884 3 0.1118 0.937 0.036 0.000 0.964 0.000
#> GSM97901 3 0.0000 0.945 0.000 0.000 1.000 0.000
#> GSM97902 1 0.1302 0.856 0.956 0.000 0.044 0.000
#> GSM97909 2 0.1867 0.955 0.072 0.928 0.000 0.000
#> GSM97911 3 0.0000 0.945 0.000 0.000 1.000 0.000
#> GSM97923 3 0.0188 0.945 0.004 0.000 0.996 0.000
#> GSM97928 1 0.2216 0.896 0.908 0.000 0.000 0.092
#> GSM97929 2 0.1022 0.984 0.032 0.968 0.000 0.000
#> GSM97933 3 0.0000 0.945 0.000 0.000 1.000 0.000
#> GSM97934 3 0.0000 0.945 0.000 0.000 1.000 0.000
#> GSM97944 3 0.1118 0.937 0.036 0.000 0.964 0.000
#> GSM97949 2 0.0000 0.989 0.000 1.000 0.000 0.000
#> GSM97956 3 0.0921 0.939 0.028 0.000 0.972 0.000
#> GSM97962 3 0.0000 0.945 0.000 0.000 1.000 0.000
#> GSM97964 3 0.1118 0.937 0.036 0.000 0.964 0.000
#> GSM97970 3 0.1118 0.937 0.036 0.000 0.964 0.000
#> GSM97822 1 0.3873 0.836 0.772 0.000 0.000 0.228
#> GSM97831 3 0.0000 0.945 0.000 0.000 1.000 0.000
#> GSM97845 1 0.4040 0.822 0.752 0.000 0.000 0.248
#> GSM97865 1 0.1716 0.895 0.936 0.000 0.000 0.064
#> GSM97867 3 0.0188 0.945 0.004 0.000 0.996 0.000
#> GSM97883 3 0.0188 0.945 0.004 0.000 0.996 0.000
#> GSM97897 4 0.0000 0.991 0.000 0.000 0.000 1.000
#> GSM97900 4 0.0000 0.991 0.000 0.000 0.000 1.000
#> GSM97904 1 0.2149 0.896 0.912 0.000 0.000 0.088
#> GSM97907 2 0.1022 0.984 0.032 0.968 0.000 0.000
#> GSM97925 3 0.0188 0.945 0.004 0.000 0.996 0.000
#> GSM97947 3 0.0188 0.945 0.004 0.000 0.996 0.000
cbind(get_classes(res, k = 5), get_membership(res, k = 5))
#> class entropy silhouette p1 p2 p3 p4 p5
#> GSM97800 2 0.2280 0.9037 0.000 0.880 0.000 0.000 0.120
#> GSM97803 2 0.2179 0.9058 0.000 0.888 0.000 0.000 0.112
#> GSM97804 2 0.2179 0.9058 0.000 0.888 0.000 0.000 0.112
#> GSM97805 2 0.2280 0.9037 0.000 0.880 0.000 0.000 0.120
#> GSM97807 2 0.0290 0.9338 0.000 0.992 0.000 0.000 0.008
#> GSM97809 2 0.0000 0.9352 0.000 1.000 0.000 0.000 0.000
#> GSM97811 2 0.0000 0.9352 0.000 1.000 0.000 0.000 0.000
#> GSM97812 2 0.0000 0.9352 0.000 1.000 0.000 0.000 0.000
#> GSM97816 5 0.6368 0.4685 0.356 0.000 0.172 0.000 0.472
#> GSM97817 2 0.0290 0.9338 0.000 0.992 0.000 0.000 0.008
#> GSM97820 2 0.0290 0.9338 0.000 0.992 0.000 0.000 0.008
#> GSM97825 2 0.0000 0.9352 0.000 1.000 0.000 0.000 0.000
#> GSM97827 2 0.0000 0.9352 0.000 1.000 0.000 0.000 0.000
#> GSM97828 1 0.6518 -0.1841 0.484 0.000 0.240 0.000 0.276
#> GSM97833 2 0.0000 0.9352 0.000 1.000 0.000 0.000 0.000
#> GSM97834 2 0.0000 0.9352 0.000 1.000 0.000 0.000 0.000
#> GSM97840 2 0.0000 0.9352 0.000 1.000 0.000 0.000 0.000
#> GSM97846 2 0.0000 0.9352 0.000 1.000 0.000 0.000 0.000
#> GSM97848 2 0.0000 0.9352 0.000 1.000 0.000 0.000 0.000
#> GSM97849 2 0.0000 0.9352 0.000 1.000 0.000 0.000 0.000
#> GSM97850 2 0.0290 0.9338 0.000 0.992 0.000 0.000 0.008
#> GSM97853 2 0.0290 0.9338 0.000 0.992 0.000 0.000 0.008
#> GSM97855 2 0.0290 0.9338 0.000 0.992 0.000 0.000 0.008
#> GSM97878 1 0.2719 0.6316 0.852 0.000 0.000 0.004 0.144
#> GSM97913 1 0.3586 0.4714 0.736 0.000 0.000 0.000 0.264
#> GSM97932 4 0.2471 0.8560 0.000 0.000 0.000 0.864 0.136
#> GSM97939 3 0.3932 0.6608 0.000 0.000 0.672 0.000 0.328
#> GSM97951 2 0.0000 0.9352 0.000 1.000 0.000 0.000 0.000
#> GSM97957 3 0.1768 0.8017 0.004 0.000 0.924 0.000 0.072
#> GSM97972 5 0.6399 0.4642 0.360 0.000 0.176 0.000 0.464
#> GSM97793 3 0.0162 0.8171 0.004 0.000 0.996 0.000 0.000
#> GSM97795 2 0.4074 0.5211 0.000 0.636 0.000 0.000 0.364
#> GSM97802 3 0.5064 0.2931 0.080 0.000 0.672 0.000 0.248
#> GSM97810 5 0.6755 0.1197 0.000 0.264 0.360 0.000 0.376
#> GSM97815 3 0.3999 0.6168 0.000 0.000 0.656 0.000 0.344
#> GSM97837 1 0.2389 0.7016 0.880 0.000 0.000 0.004 0.116
#> GSM97843 3 0.0671 0.8207 0.004 0.000 0.980 0.000 0.016
#> GSM97890 3 0.2230 0.8054 0.000 0.000 0.884 0.000 0.116
#> GSM97899 4 0.1121 0.9033 0.000 0.000 0.000 0.956 0.044
#> GSM97910 1 0.2648 0.6214 0.848 0.000 0.000 0.000 0.152
#> GSM97916 1 0.2488 0.6535 0.872 0.000 0.000 0.004 0.124
#> GSM97920 3 0.1124 0.8175 0.004 0.000 0.960 0.000 0.036
#> GSM97921 1 0.2068 0.6662 0.904 0.000 0.000 0.004 0.092
#> GSM97927 1 0.4674 0.6801 0.708 0.000 0.000 0.060 0.232
#> GSM97937 1 0.2707 0.7047 0.876 0.000 0.000 0.024 0.100
#> GSM97941 2 0.0794 0.9259 0.000 0.972 0.000 0.000 0.028
#> GSM97943 1 0.3395 0.5327 0.764 0.000 0.000 0.000 0.236
#> GSM97958 1 0.4341 0.1135 0.592 0.000 0.004 0.000 0.404
#> GSM97960 2 0.4029 0.5013 0.000 0.680 0.004 0.000 0.316
#> GSM97794 1 0.2674 0.6320 0.856 0.000 0.000 0.004 0.140
#> GSM97796 4 0.1478 0.8937 0.000 0.000 0.000 0.936 0.064
#> GSM97797 1 0.2763 0.6283 0.848 0.000 0.000 0.004 0.148
#> GSM97798 4 0.1121 0.9033 0.000 0.000 0.000 0.956 0.044
#> GSM97801 1 0.2763 0.6280 0.848 0.000 0.000 0.004 0.148
#> GSM97806 1 0.3888 0.7099 0.796 0.000 0.000 0.056 0.148
#> GSM97808 4 0.1121 0.9033 0.000 0.000 0.000 0.956 0.044
#> GSM97813 1 0.5968 0.5596 0.512 0.000 0.000 0.116 0.372
#> GSM97814 4 0.1121 0.9033 0.000 0.000 0.000 0.956 0.044
#> GSM97818 1 0.2629 0.6327 0.860 0.000 0.000 0.004 0.136
#> GSM97819 3 0.0162 0.8189 0.000 0.000 0.996 0.000 0.004
#> GSM97821 5 0.6610 0.4215 0.180 0.020 0.252 0.000 0.548
#> GSM97826 1 0.4167 0.6939 0.724 0.000 0.000 0.024 0.252
#> GSM97829 1 0.2179 0.6862 0.896 0.000 0.000 0.004 0.100
#> GSM97832 5 0.6494 0.3116 0.000 0.256 0.252 0.000 0.492
#> GSM97836 1 0.4490 0.6872 0.724 0.000 0.000 0.052 0.224
#> GSM97839 4 0.1608 0.8915 0.000 0.000 0.000 0.928 0.072
#> GSM97844 2 0.2280 0.9037 0.000 0.880 0.000 0.000 0.120
#> GSM97847 1 0.3506 0.6887 0.824 0.000 0.000 0.044 0.132
#> GSM97851 4 0.2230 0.8690 0.000 0.000 0.000 0.884 0.116
#> GSM97852 1 0.4819 0.6754 0.716 0.000 0.000 0.092 0.192
#> GSM97856 4 0.1121 0.9033 0.000 0.000 0.000 0.956 0.044
#> GSM97858 2 0.2179 0.9058 0.000 0.888 0.000 0.000 0.112
#> GSM97859 1 0.5168 0.6348 0.592 0.000 0.000 0.052 0.356
#> GSM97861 1 0.4558 0.6853 0.724 0.000 0.000 0.060 0.216
#> GSM97863 4 0.1544 0.8926 0.000 0.000 0.000 0.932 0.068
#> GSM97869 1 0.3123 0.7025 0.812 0.000 0.000 0.004 0.184
#> GSM97870 1 0.3957 0.6835 0.712 0.000 0.008 0.000 0.280
#> GSM97871 4 0.1121 0.9033 0.000 0.000 0.000 0.956 0.044
#> GSM97877 1 0.3715 0.4793 0.736 0.004 0.000 0.000 0.260
#> GSM97879 1 0.3734 0.7123 0.812 0.000 0.000 0.060 0.128
#> GSM97882 1 0.4629 0.6796 0.704 0.000 0.000 0.052 0.244
#> GSM97885 1 0.3333 0.7003 0.788 0.000 0.000 0.004 0.208
#> GSM97886 4 0.0000 0.9006 0.000 0.000 0.000 1.000 0.000
#> GSM97887 4 0.1121 0.9033 0.000 0.000 0.000 0.956 0.044
#> GSM97888 4 0.6032 0.4132 0.124 0.000 0.000 0.508 0.368
#> GSM97889 4 0.6121 0.5076 0.120 0.000 0.016 0.592 0.272
#> GSM97891 1 0.3821 0.7089 0.800 0.000 0.000 0.052 0.148
#> GSM97892 2 0.2179 0.9058 0.000 0.888 0.000 0.000 0.112
#> GSM97893 4 0.4179 0.7764 0.072 0.000 0.000 0.776 0.152
#> GSM97894 4 0.1671 0.8902 0.000 0.000 0.000 0.924 0.076
#> GSM97895 4 0.2561 0.8514 0.000 0.000 0.000 0.856 0.144
#> GSM97896 4 0.4555 0.6530 0.020 0.000 0.000 0.636 0.344
#> GSM97898 4 0.1671 0.8902 0.000 0.000 0.000 0.924 0.076
#> GSM97903 1 0.0671 0.6960 0.980 0.000 0.000 0.004 0.016
#> GSM97905 5 0.7472 -0.2421 0.304 0.000 0.308 0.032 0.356
#> GSM97906 4 0.1121 0.9033 0.000 0.000 0.000 0.956 0.044
#> GSM97908 1 0.5990 0.4759 0.560 0.000 0.000 0.296 0.144
#> GSM97912 1 0.4298 0.6571 0.640 0.000 0.008 0.000 0.352
#> GSM97914 1 0.2124 0.6600 0.900 0.000 0.000 0.004 0.096
#> GSM97915 4 0.1671 0.8902 0.000 0.000 0.000 0.924 0.076
#> GSM97917 4 0.2561 0.8507 0.000 0.000 0.000 0.856 0.144
#> GSM97918 4 0.1121 0.8972 0.000 0.000 0.000 0.956 0.044
#> GSM97919 4 0.1671 0.8902 0.000 0.000 0.000 0.924 0.076
#> GSM97922 1 0.6564 0.4417 0.420 0.000 0.000 0.204 0.376
#> GSM97924 2 0.2179 0.9058 0.000 0.888 0.000 0.000 0.112
#> GSM97926 3 0.3013 0.7861 0.008 0.000 0.832 0.000 0.160
#> GSM97930 1 0.3400 0.6908 0.828 0.000 0.000 0.036 0.136
#> GSM97931 5 0.6575 0.4657 0.368 0.000 0.208 0.000 0.424
#> GSM97935 1 0.4558 0.6853 0.724 0.000 0.000 0.060 0.216
#> GSM97936 4 0.0290 0.9008 0.000 0.000 0.000 0.992 0.008
#> GSM97938 1 0.5083 0.6288 0.700 0.000 0.000 0.140 0.160
#> GSM97940 4 0.1121 0.9033 0.000 0.000 0.000 0.956 0.044
#> GSM97942 3 0.0162 0.8171 0.004 0.000 0.996 0.000 0.000
#> GSM97945 4 0.1121 0.9033 0.000 0.000 0.000 0.956 0.044
#> GSM97946 2 0.0000 0.9352 0.000 1.000 0.000 0.000 0.000
#> GSM97948 3 0.3596 0.5044 0.012 0.000 0.776 0.000 0.212
#> GSM97950 4 0.0162 0.9007 0.000 0.000 0.000 0.996 0.004
#> GSM97952 4 0.1121 0.9033 0.000 0.000 0.000 0.956 0.044
#> GSM97953 1 0.2653 0.7047 0.880 0.000 0.000 0.024 0.096
#> GSM97954 1 0.4718 0.6786 0.728 0.000 0.000 0.092 0.180
#> GSM97955 4 0.1478 0.8938 0.000 0.000 0.000 0.936 0.064
#> GSM97959 1 0.2763 0.6257 0.848 0.000 0.000 0.004 0.148
#> GSM97961 4 0.0162 0.9007 0.000 0.000 0.000 0.996 0.004
#> GSM97963 4 0.1121 0.9033 0.000 0.000 0.000 0.956 0.044
#> GSM97965 4 0.1121 0.9033 0.000 0.000 0.000 0.956 0.044
#> GSM97966 4 0.1121 0.9033 0.000 0.000 0.000 0.956 0.044
#> GSM97967 2 0.0000 0.9352 0.000 1.000 0.000 0.000 0.000
#> GSM97968 2 0.0510 0.9338 0.000 0.984 0.000 0.000 0.016
#> GSM97969 1 0.5606 0.6163 0.568 0.000 0.000 0.088 0.344
#> GSM97971 1 0.5168 0.6348 0.592 0.000 0.000 0.052 0.356
#> GSM97799 3 0.3452 0.7361 0.000 0.000 0.756 0.000 0.244
#> GSM97823 2 0.0000 0.9352 0.000 1.000 0.000 0.000 0.000
#> GSM97824 3 0.3837 0.6884 0.000 0.000 0.692 0.000 0.308
#> GSM97830 3 0.0162 0.8171 0.004 0.000 0.996 0.000 0.000
#> GSM97835 3 0.4060 0.5890 0.000 0.000 0.640 0.000 0.360
#> GSM97838 2 0.2280 0.9037 0.000 0.880 0.000 0.000 0.120
#> GSM97841 2 0.2179 0.9058 0.000 0.888 0.000 0.000 0.112
#> GSM97842 3 0.3561 0.7240 0.000 0.000 0.740 0.000 0.260
#> GSM97854 2 0.2179 0.9058 0.000 0.888 0.000 0.000 0.112
#> GSM97857 3 0.3932 0.6608 0.000 0.000 0.672 0.000 0.328
#> GSM97860 3 0.0162 0.8171 0.004 0.000 0.996 0.000 0.000
#> GSM97862 3 0.2732 0.7909 0.000 0.000 0.840 0.000 0.160
#> GSM97864 2 0.2179 0.9058 0.000 0.888 0.000 0.000 0.112
#> GSM97866 3 0.1544 0.8205 0.000 0.000 0.932 0.000 0.068
#> GSM97868 3 0.3305 0.7517 0.000 0.000 0.776 0.000 0.224
#> GSM97872 1 0.3550 0.7059 0.760 0.000 0.000 0.004 0.236
#> GSM97873 3 0.3561 0.7240 0.000 0.000 0.740 0.000 0.260
#> GSM97874 3 0.0162 0.8171 0.004 0.000 0.996 0.000 0.000
#> GSM97875 3 0.0162 0.8189 0.000 0.000 0.996 0.000 0.004
#> GSM97876 3 0.0162 0.8171 0.004 0.000 0.996 0.000 0.000
#> GSM97880 3 0.0162 0.8171 0.004 0.000 0.996 0.000 0.000
#> GSM97881 3 0.2605 0.7941 0.000 0.000 0.852 0.000 0.148
#> GSM97884 3 0.3561 0.7240 0.000 0.000 0.740 0.000 0.260
#> GSM97901 3 0.1478 0.8205 0.000 0.000 0.936 0.000 0.064
#> GSM97902 1 0.3336 0.5409 0.772 0.000 0.000 0.000 0.228
#> GSM97909 5 0.5785 0.0172 0.092 0.404 0.000 0.000 0.504
#> GSM97911 3 0.2605 0.7941 0.000 0.000 0.852 0.000 0.148
#> GSM97923 3 0.0162 0.8171 0.004 0.000 0.996 0.000 0.000
#> GSM97928 1 0.3906 0.6902 0.704 0.000 0.000 0.004 0.292
#> GSM97929 2 0.2179 0.9058 0.000 0.888 0.000 0.000 0.112
#> GSM97933 3 0.1638 0.8005 0.004 0.000 0.932 0.000 0.064
#> GSM97934 3 0.1768 0.8017 0.004 0.000 0.924 0.000 0.072
#> GSM97944 3 0.3452 0.7361 0.000 0.000 0.756 0.000 0.244
#> GSM97949 2 0.0290 0.9338 0.000 0.992 0.000 0.000 0.008
#> GSM97956 3 0.3730 0.7078 0.000 0.000 0.712 0.000 0.288
#> GSM97962 3 0.1952 0.8043 0.004 0.000 0.912 0.000 0.084
#> GSM97964 3 0.3837 0.6884 0.000 0.000 0.692 0.000 0.308
#> GSM97970 3 0.3561 0.7240 0.000 0.000 0.740 0.000 0.260
#> GSM97822 1 0.4878 0.6674 0.676 0.000 0.000 0.060 0.264
#> GSM97831 3 0.0963 0.8224 0.000 0.000 0.964 0.000 0.036
#> GSM97845 1 0.4768 0.6807 0.724 0.000 0.000 0.096 0.180
#> GSM97865 1 0.2011 0.6682 0.908 0.000 0.000 0.004 0.088
#> GSM97867 3 0.0162 0.8171 0.004 0.000 0.996 0.000 0.000
#> GSM97883 3 0.0566 0.8150 0.004 0.000 0.984 0.000 0.012
#> GSM97897 4 0.4080 0.7008 0.020 0.000 0.000 0.728 0.252
#> GSM97900 4 0.1121 0.9033 0.000 0.000 0.000 0.956 0.044
#> GSM97904 1 0.3949 0.6883 0.696 0.000 0.000 0.004 0.300
#> GSM97907 2 0.2179 0.9058 0.000 0.888 0.000 0.000 0.112
#> GSM97925 3 0.0162 0.8171 0.004 0.000 0.996 0.000 0.000
#> GSM97947 3 0.0865 0.8063 0.004 0.000 0.972 0.000 0.024
cbind(get_classes(res, k = 6), get_membership(res, k = 6))
#> class entropy silhouette p1 p2 p3 p4 p5 p6
#> GSM97800 2 0.3664 0.877074 0.020 0.812 0.000 0.000 0.108 0.060
#> GSM97803 2 0.3371 0.881078 0.020 0.832 0.000 0.000 0.104 0.044
#> GSM97804 2 0.3605 0.876599 0.020 0.816 0.000 0.000 0.108 0.056
#> GSM97805 2 0.3721 0.874925 0.020 0.808 0.000 0.000 0.108 0.064
#> GSM97807 2 0.0458 0.924655 0.000 0.984 0.000 0.000 0.000 0.016
#> GSM97809 2 0.0000 0.927243 0.000 1.000 0.000 0.000 0.000 0.000
#> GSM97811 2 0.0000 0.927243 0.000 1.000 0.000 0.000 0.000 0.000
#> GSM97812 2 0.0000 0.927243 0.000 1.000 0.000 0.000 0.000 0.000
#> GSM97816 6 0.5128 0.100044 0.000 0.000 0.084 0.000 0.412 0.504
#> GSM97817 2 0.0458 0.924655 0.000 0.984 0.000 0.000 0.000 0.016
#> GSM97820 2 0.0458 0.924655 0.000 0.984 0.000 0.000 0.000 0.016
#> GSM97825 2 0.0000 0.927243 0.000 1.000 0.000 0.000 0.000 0.000
#> GSM97827 2 0.0000 0.927243 0.000 1.000 0.000 0.000 0.000 0.000
#> GSM97828 6 0.5361 0.427259 0.008 0.000 0.180 0.000 0.192 0.620
#> GSM97833 2 0.0000 0.927243 0.000 1.000 0.000 0.000 0.000 0.000
#> GSM97834 2 0.0000 0.927243 0.000 1.000 0.000 0.000 0.000 0.000
#> GSM97840 2 0.0000 0.927243 0.000 1.000 0.000 0.000 0.000 0.000
#> GSM97846 2 0.0000 0.927243 0.000 1.000 0.000 0.000 0.000 0.000
#> GSM97848 2 0.0000 0.927243 0.000 1.000 0.000 0.000 0.000 0.000
#> GSM97849 2 0.0000 0.927243 0.000 1.000 0.000 0.000 0.000 0.000
#> GSM97850 2 0.0458 0.924655 0.000 0.984 0.000 0.000 0.000 0.016
#> GSM97853 2 0.0458 0.924655 0.000 0.984 0.000 0.000 0.000 0.016
#> GSM97855 2 0.0458 0.924655 0.000 0.984 0.000 0.000 0.000 0.016
#> GSM97878 6 0.3053 0.649380 0.168 0.000 0.000 0.000 0.020 0.812
#> GSM97913 6 0.3112 0.641668 0.096 0.000 0.000 0.000 0.068 0.836
#> GSM97932 4 0.5419 0.674965 0.136 0.000 0.000 0.620 0.228 0.016
#> GSM97939 5 0.4524 0.294135 0.000 0.000 0.404 0.000 0.560 0.036
#> GSM97951 2 0.0000 0.927243 0.000 1.000 0.000 0.000 0.000 0.000
#> GSM97957 3 0.2822 0.622389 0.000 0.000 0.852 0.000 0.108 0.040
#> GSM97972 6 0.5027 0.044868 0.000 0.000 0.072 0.000 0.440 0.488
#> GSM97793 3 0.0000 0.707057 0.000 0.000 1.000 0.000 0.000 0.000
#> GSM97795 5 0.5350 -0.067460 0.020 0.424 0.000 0.000 0.496 0.060
#> GSM97802 1 0.4772 0.063042 0.516 0.000 0.444 0.000 0.028 0.012
#> GSM97810 5 0.5793 0.446161 0.000 0.124 0.228 0.000 0.604 0.044
#> GSM97815 5 0.4444 0.252463 0.000 0.000 0.436 0.000 0.536 0.028
#> GSM97837 6 0.5649 0.066280 0.396 0.000 0.000 0.000 0.152 0.452
#> GSM97843 3 0.1124 0.705083 0.000 0.000 0.956 0.000 0.036 0.008
#> GSM97890 3 0.3151 0.542728 0.000 0.000 0.748 0.000 0.252 0.000
#> GSM97899 4 0.0547 0.858925 0.020 0.000 0.000 0.980 0.000 0.000
#> GSM97910 6 0.3268 0.660109 0.144 0.000 0.000 0.000 0.044 0.812
#> GSM97916 6 0.2996 0.601162 0.228 0.000 0.000 0.000 0.000 0.772
#> GSM97920 3 0.1261 0.697520 0.000 0.000 0.952 0.000 0.024 0.024
#> GSM97921 6 0.4771 0.488147 0.256 0.000 0.000 0.000 0.096 0.648
#> GSM97927 1 0.4108 0.506288 0.724 0.000 0.000 0.032 0.012 0.232
#> GSM97937 1 0.5819 0.028637 0.420 0.000 0.000 0.000 0.184 0.396
#> GSM97941 2 0.1845 0.889810 0.000 0.920 0.000 0.000 0.028 0.052
#> GSM97943 6 0.4321 0.610001 0.096 0.000 0.012 0.000 0.144 0.748
#> GSM97958 6 0.3834 0.534639 0.024 0.000 0.000 0.000 0.268 0.708
#> GSM97960 5 0.4578 0.108501 0.000 0.444 0.000 0.000 0.520 0.036
#> GSM97794 6 0.2738 0.652894 0.176 0.000 0.000 0.000 0.004 0.820
#> GSM97796 4 0.3690 0.826971 0.068 0.000 0.000 0.804 0.116 0.012
#> GSM97797 6 0.2814 0.656002 0.172 0.000 0.000 0.000 0.008 0.820
#> GSM97798 4 0.0547 0.858925 0.020 0.000 0.000 0.980 0.000 0.000
#> GSM97801 6 0.2950 0.661298 0.148 0.000 0.000 0.000 0.024 0.828
#> GSM97806 1 0.5036 0.263521 0.528 0.000 0.000 0.028 0.028 0.416
#> GSM97808 4 0.0547 0.858925 0.020 0.000 0.000 0.980 0.000 0.000
#> GSM97813 1 0.1716 0.564114 0.932 0.000 0.000 0.036 0.004 0.028
#> GSM97814 4 0.0547 0.858925 0.020 0.000 0.000 0.980 0.000 0.000
#> GSM97818 6 0.2697 0.643704 0.188 0.000 0.000 0.000 0.000 0.812
#> GSM97819 3 0.0790 0.705671 0.000 0.000 0.968 0.000 0.032 0.000
#> GSM97821 5 0.5525 0.184682 0.016 0.008 0.064 0.000 0.512 0.400
#> GSM97826 1 0.5051 0.433125 0.652 0.000 0.000 0.004 0.156 0.188
#> GSM97829 6 0.5173 0.314748 0.324 0.000 0.000 0.000 0.108 0.568
#> GSM97832 5 0.5904 0.460840 0.004 0.104 0.156 0.000 0.640 0.096
#> GSM97836 1 0.4135 0.498127 0.712 0.000 0.000 0.028 0.012 0.248
#> GSM97839 4 0.3690 0.826971 0.068 0.000 0.000 0.804 0.116 0.012
#> GSM97844 2 0.3721 0.874925 0.020 0.808 0.000 0.000 0.108 0.064
#> GSM97847 1 0.6275 0.157669 0.432 0.000 0.000 0.016 0.212 0.340
#> GSM97851 4 0.5291 0.693501 0.124 0.000 0.000 0.636 0.224 0.016
#> GSM97852 1 0.6423 0.247054 0.472 0.000 0.000 0.032 0.212 0.284
#> GSM97856 4 0.0547 0.858925 0.020 0.000 0.000 0.980 0.000 0.000
#> GSM97858 2 0.3544 0.877147 0.020 0.820 0.000 0.000 0.108 0.052
#> GSM97859 1 0.1826 0.568157 0.924 0.000 0.000 0.020 0.004 0.052
#> GSM97861 1 0.4316 0.482310 0.688 0.000 0.000 0.032 0.012 0.268
#> GSM97863 4 0.3690 0.826971 0.068 0.000 0.000 0.804 0.116 0.012
#> GSM97869 1 0.3428 0.451527 0.696 0.000 0.000 0.000 0.000 0.304
#> GSM97870 1 0.2723 0.546477 0.852 0.000 0.016 0.000 0.004 0.128
#> GSM97871 4 0.0547 0.858925 0.020 0.000 0.000 0.980 0.000 0.000
#> GSM97877 6 0.3123 0.644818 0.112 0.000 0.000 0.000 0.056 0.832
#> GSM97879 1 0.5209 0.259352 0.524 0.000 0.000 0.040 0.028 0.408
#> GSM97882 1 0.3726 0.515176 0.752 0.000 0.000 0.028 0.004 0.216
#> GSM97885 1 0.3802 0.440547 0.676 0.000 0.000 0.000 0.012 0.312
#> GSM97886 4 0.1262 0.857428 0.016 0.000 0.000 0.956 0.020 0.008
#> GSM97887 4 0.0547 0.858925 0.020 0.000 0.000 0.980 0.000 0.000
#> GSM97888 1 0.3780 0.400298 0.760 0.000 0.000 0.204 0.020 0.016
#> GSM97889 1 0.4344 0.078753 0.556 0.000 0.016 0.424 0.004 0.000
#> GSM97891 1 0.4795 0.303451 0.556 0.000 0.000 0.028 0.016 0.400
#> GSM97892 2 0.3605 0.876599 0.020 0.816 0.000 0.000 0.108 0.056
#> GSM97893 4 0.6223 0.443588 0.256 0.000 0.000 0.492 0.232 0.020
#> GSM97894 4 0.3870 0.820194 0.072 0.000 0.000 0.788 0.128 0.012
#> GSM97895 4 0.5579 0.649356 0.156 0.000 0.000 0.600 0.228 0.016
#> GSM97896 1 0.4358 -0.014260 0.596 0.000 0.000 0.380 0.016 0.008
#> GSM97898 4 0.3870 0.820194 0.072 0.000 0.000 0.788 0.128 0.012
#> GSM97903 6 0.4101 0.421837 0.308 0.000 0.000 0.000 0.028 0.664
#> GSM97905 1 0.4048 0.336680 0.644 0.000 0.340 0.000 0.004 0.012
#> GSM97906 4 0.0547 0.858925 0.020 0.000 0.000 0.980 0.000 0.000
#> GSM97908 1 0.7430 0.173656 0.372 0.000 0.000 0.140 0.252 0.236
#> GSM97912 1 0.1949 0.559758 0.904 0.000 0.004 0.000 0.004 0.088
#> GSM97914 6 0.3980 0.582732 0.216 0.000 0.000 0.000 0.052 0.732
#> GSM97915 4 0.3870 0.820194 0.072 0.000 0.000 0.788 0.128 0.012
#> GSM97917 4 0.5728 0.630288 0.160 0.000 0.000 0.584 0.236 0.020
#> GSM97918 4 0.3543 0.829951 0.052 0.000 0.000 0.812 0.124 0.012
#> GSM97919 4 0.3870 0.820194 0.072 0.000 0.000 0.788 0.128 0.012
#> GSM97922 1 0.1471 0.540691 0.932 0.000 0.000 0.064 0.004 0.000
#> GSM97924 2 0.3544 0.877147 0.020 0.820 0.000 0.000 0.108 0.052
#> GSM97926 3 0.4278 0.368295 0.000 0.000 0.632 0.000 0.336 0.032
#> GSM97930 1 0.6196 0.165202 0.444 0.000 0.000 0.012 0.216 0.328
#> GSM97931 6 0.4855 0.108081 0.000 0.000 0.064 0.000 0.380 0.556
#> GSM97935 1 0.4316 0.482310 0.688 0.000 0.000 0.032 0.012 0.268
#> GSM97936 4 0.1737 0.855465 0.020 0.000 0.000 0.932 0.040 0.008
#> GSM97938 1 0.6818 0.195911 0.432 0.000 0.000 0.056 0.260 0.252
#> GSM97940 4 0.0547 0.858925 0.020 0.000 0.000 0.980 0.000 0.000
#> GSM97942 3 0.0363 0.707009 0.000 0.000 0.988 0.000 0.012 0.000
#> GSM97945 4 0.0547 0.858925 0.020 0.000 0.000 0.980 0.000 0.000
#> GSM97946 2 0.0000 0.927243 0.000 1.000 0.000 0.000 0.000 0.000
#> GSM97948 3 0.4046 0.239055 0.368 0.000 0.620 0.000 0.008 0.004
#> GSM97950 4 0.1515 0.856730 0.020 0.000 0.000 0.944 0.028 0.008
#> GSM97952 4 0.0547 0.858925 0.020 0.000 0.000 0.980 0.000 0.000
#> GSM97953 1 0.5962 0.030600 0.416 0.000 0.000 0.004 0.188 0.392
#> GSM97954 1 0.6464 0.232604 0.472 0.000 0.000 0.036 0.208 0.284
#> GSM97955 4 0.3646 0.826559 0.072 0.000 0.000 0.804 0.116 0.008
#> GSM97959 6 0.2778 0.657074 0.168 0.000 0.000 0.000 0.008 0.824
#> GSM97961 4 0.1485 0.856744 0.028 0.000 0.000 0.944 0.024 0.004
#> GSM97963 4 0.0547 0.858925 0.020 0.000 0.000 0.980 0.000 0.000
#> GSM97965 4 0.0547 0.858925 0.020 0.000 0.000 0.980 0.000 0.000
#> GSM97966 4 0.0547 0.858925 0.020 0.000 0.000 0.980 0.000 0.000
#> GSM97967 2 0.0000 0.927243 0.000 1.000 0.000 0.000 0.000 0.000
#> GSM97968 2 0.0891 0.923279 0.000 0.968 0.000 0.000 0.008 0.024
#> GSM97969 1 0.2027 0.559486 0.920 0.000 0.000 0.032 0.032 0.016
#> GSM97971 1 0.1826 0.568157 0.924 0.000 0.000 0.020 0.004 0.052
#> GSM97799 3 0.3860 0.000425 0.000 0.000 0.528 0.000 0.472 0.000
#> GSM97823 2 0.0000 0.927243 0.000 1.000 0.000 0.000 0.000 0.000
#> GSM97824 5 0.4377 0.197252 0.000 0.000 0.436 0.000 0.540 0.024
#> GSM97830 3 0.0260 0.706953 0.000 0.000 0.992 0.000 0.000 0.008
#> GSM97835 5 0.4366 0.258085 0.000 0.000 0.428 0.000 0.548 0.024
#> GSM97838 2 0.3721 0.874925 0.020 0.808 0.000 0.000 0.108 0.064
#> GSM97841 2 0.3544 0.877147 0.020 0.820 0.000 0.000 0.108 0.052
#> GSM97842 3 0.3867 -0.059078 0.000 0.000 0.512 0.000 0.488 0.000
#> GSM97854 2 0.3544 0.877147 0.020 0.820 0.000 0.000 0.108 0.052
#> GSM97857 5 0.4863 0.268000 0.000 0.000 0.412 0.000 0.528 0.060
#> GSM97860 3 0.0146 0.707596 0.000 0.000 0.996 0.000 0.004 0.000
#> GSM97862 3 0.3634 0.472048 0.000 0.000 0.696 0.000 0.296 0.008
#> GSM97864 2 0.3544 0.877147 0.020 0.820 0.000 0.000 0.108 0.052
#> GSM97866 3 0.3073 0.599941 0.000 0.000 0.788 0.000 0.204 0.008
#> GSM97868 3 0.3817 0.137869 0.000 0.000 0.568 0.000 0.432 0.000
#> GSM97872 1 0.4302 0.497325 0.728 0.000 0.000 0.000 0.116 0.156
#> GSM97873 3 0.3866 -0.044765 0.000 0.000 0.516 0.000 0.484 0.000
#> GSM97874 3 0.0000 0.707057 0.000 0.000 1.000 0.000 0.000 0.000
#> GSM97875 3 0.0865 0.704932 0.000 0.000 0.964 0.000 0.036 0.000
#> GSM97876 3 0.0000 0.707057 0.000 0.000 1.000 0.000 0.000 0.000
#> GSM97880 3 0.0000 0.707057 0.000 0.000 1.000 0.000 0.000 0.000
#> GSM97881 3 0.3515 0.429356 0.000 0.000 0.676 0.000 0.324 0.000
#> GSM97884 3 0.3864 -0.028620 0.000 0.000 0.520 0.000 0.480 0.000
#> GSM97901 3 0.3012 0.608277 0.000 0.000 0.796 0.000 0.196 0.008
#> GSM97902 6 0.4259 0.623576 0.104 0.000 0.012 0.000 0.128 0.756
#> GSM97909 5 0.6068 0.203392 0.016 0.168 0.000 0.000 0.472 0.344
#> GSM97911 3 0.3531 0.421263 0.000 0.000 0.672 0.000 0.328 0.000
#> GSM97923 3 0.0146 0.707596 0.000 0.000 0.996 0.000 0.004 0.000
#> GSM97928 1 0.3862 0.528341 0.772 0.000 0.000 0.000 0.096 0.132
#> GSM97929 2 0.3544 0.877147 0.020 0.820 0.000 0.000 0.108 0.052
#> GSM97933 3 0.2537 0.636662 0.000 0.000 0.872 0.000 0.096 0.032
#> GSM97934 3 0.2822 0.622389 0.000 0.000 0.852 0.000 0.108 0.040
#> GSM97944 3 0.3860 0.000425 0.000 0.000 0.528 0.000 0.472 0.000
#> GSM97949 2 0.0458 0.924655 0.000 0.984 0.000 0.000 0.000 0.016
#> GSM97956 5 0.4331 0.124447 0.000 0.000 0.464 0.000 0.516 0.020
#> GSM97962 3 0.3139 0.615221 0.000 0.000 0.816 0.000 0.152 0.032
#> GSM97964 5 0.4377 0.197252 0.000 0.000 0.436 0.000 0.540 0.024
#> GSM97970 3 0.3864 -0.028620 0.000 0.000 0.520 0.000 0.480 0.000
#> GSM97822 1 0.3343 0.533502 0.812 0.000 0.000 0.040 0.004 0.144
#> GSM97831 3 0.2070 0.676801 0.000 0.000 0.892 0.000 0.100 0.008
#> GSM97845 1 0.6437 0.253324 0.464 0.000 0.000 0.032 0.208 0.296
#> GSM97865 6 0.4771 0.489721 0.256 0.000 0.000 0.000 0.096 0.648
#> GSM97867 3 0.0000 0.707057 0.000 0.000 1.000 0.000 0.000 0.000
#> GSM97883 3 0.0951 0.691410 0.020 0.000 0.968 0.000 0.008 0.004
#> GSM97897 4 0.3998 0.101750 0.492 0.000 0.000 0.504 0.004 0.000
#> GSM97900 4 0.0547 0.858925 0.020 0.000 0.000 0.980 0.000 0.000
#> GSM97904 1 0.3235 0.544078 0.820 0.000 0.000 0.000 0.052 0.128
#> GSM97907 2 0.3544 0.877147 0.020 0.820 0.000 0.000 0.108 0.052
#> GSM97925 3 0.0632 0.706712 0.000 0.000 0.976 0.000 0.024 0.000
#> GSM97947 3 0.1863 0.674418 0.044 0.000 0.920 0.000 0.036 0.000
Heatmaps for the consensus matrix. It visualizes the probability of two samples to be in a same group.
consensus_heatmap(res, k = 2)
consensus_heatmap(res, k = 3)
consensus_heatmap(res, k = 4)
consensus_heatmap(res, k = 5)
consensus_heatmap(res, k = 6)
Heatmaps for the membership of samples in all partitions to see how consistent they are:
membership_heatmap(res, k = 2)
membership_heatmap(res, k = 3)
membership_heatmap(res, k = 4)
membership_heatmap(res, k = 5)
membership_heatmap(res, k = 6)
As soon as we have had the classes for columns, we can look for signatures which are significantly different between classes which can be candidate marks for certain classes. Following are the heatmaps for signatures.
Signature heatmaps where rows are scaled:
get_signatures(res, k = 2)
get_signatures(res, k = 3)
get_signatures(res, k = 4)
get_signatures(res, k = 5)
get_signatures(res, k = 6)
Signature heatmaps where rows are not scaled:
get_signatures(res, k = 2, scale_rows = FALSE)
get_signatures(res, k = 3, scale_rows = FALSE)
get_signatures(res, k = 4, scale_rows = FALSE)
get_signatures(res, k = 5, scale_rows = FALSE)
get_signatures(res, k = 6, scale_rows = FALSE)
Compare the overlap of signatures from different k:
compare_signatures(res)
get_signature() returns a data frame invisibly. TO get the list of signatures, the function
call should be assigned to a variable explicitly. In following code, if plot argument is set
to FALSE, no heatmap is plotted while only the differential analysis is performed.
# code only for demonstration
tb = get_signature(res, k = ..., plot = FALSE)
An example of the output of tb is:
#> which_row fdr mean_1 mean_2 scaled_mean_1 scaled_mean_2 km
#> 1 38 0.042760348 8.373488 9.131774 -0.5533452 0.5164555 1
#> 2 40 0.018707592 7.106213 8.469186 -0.6173731 0.5762149 1
#> 3 55 0.019134737 10.221463 11.207825 -0.6159697 0.5749050 1
#> 4 59 0.006059896 5.921854 7.869574 -0.6899429 0.6439467 1
#> 5 60 0.018055526 8.928898 10.211722 -0.6204761 0.5791110 1
#> 6 98 0.009384629 15.714769 14.887706 0.6635654 -0.6193277 2
...
The columns in tb are:
which_row: row indices corresponding to the input matrix.fdr: FDR for the differential test. mean_x: The mean value in group x.scaled_mean_x: The mean value in group x after rows are scaled.km: Row groups if k-means clustering is applied to rows.UMAP plot which shows how samples are separated.
dimension_reduction(res, k = 2, method = "UMAP")
dimension_reduction(res, k = 3, method = "UMAP")
dimension_reduction(res, k = 4, method = "UMAP")
dimension_reduction(res, k = 5, method = "UMAP")
dimension_reduction(res, k = 6, method = "UMAP")
Following heatmap shows how subgroups are split when increasing k:
collect_classes(res)
Test correlation between subgroups and known annotations. If the known annotation is numeric, one-way ANOVA test is applied, and if the known annotation is discrete, chi-squared contingency table test is applied.
test_to_known_factors(res)
#> n disease.state(p) tissue(p) k
#> CV:kmeans 175 4.64e-13 2.01e-15 2
#> CV:kmeans 178 7.92e-27 7.08e-28 3
#> CV:kmeans 176 1.55e-26 3.41e-27 4
#> CV:kmeans 164 2.78e-27 3.71e-28 5
#> CV:kmeans 120 2.58e-19 3.90e-17 6
If matrix rows can be associated to genes, consider to use functional_enrichment(res,
...) to perform function enrichment for the signature genes. See this vignette for more detailed explanations.
The object with results only for a single top-value method and a single partition method can be extracted as:
res = res_list["CV", "skmeans"]
# you can also extract it by
# res = res_list["CV:skmeans"]
A summary of res and all the functions that can be applied to it:
res
#> A 'ConsensusPartition' object with k = 2, 3, 4, 5, 6.
#> On a matrix with 51882 rows and 180 columns.
#> Top rows (1000, 2000, 3000, 4000, 5000) are extracted by 'CV' method.
#> Subgroups are detected by 'skmeans' method.
#> Performed in total 1250 partitions by row resampling.
#> Best k for subgroups seems to be 4.
#>
#> Following methods can be applied to this 'ConsensusPartition' object:
#> [1] "cola_report" "collect_classes" "collect_plots"
#> [4] "collect_stats" "colnames" "compare_signatures"
#> [7] "consensus_heatmap" "dimension_reduction" "functional_enrichment"
#> [10] "get_anno_col" "get_anno" "get_classes"
#> [13] "get_consensus" "get_matrix" "get_membership"
#> [16] "get_param" "get_signatures" "get_stats"
#> [19] "is_best_k" "is_stable_k" "membership_heatmap"
#> [22] "ncol" "nrow" "plot_ecdf"
#> [25] "rownames" "select_partition_number" "show"
#> [28] "suggest_best_k" "test_to_known_factors"
collect_plots() function collects all the plots made from res for all k (number of partitions)
into one single page to provide an easy and fast comparison between different k.
collect_plots(res)
The plots are:
k and the heatmap of
predicted classes for each k.k.k.k.All the plots in panels can be made by individual functions and they are plotted later in this section.
select_partition_number() produces several plots showing different
statistics for choosing “optimized” k. There are following statistics:
k;k, the area increased is defined as \(A_k - A_{k-1}\).The detailed explanations of these statistics can be found in the cola vignette.
Generally speaking, lower PAC score, higher mean silhouette score or higher
concordance corresponds to better partition. Rand index and Jaccard index
measure how similar the current partition is compared to partition with k-1.
If they are too similar, we won't accept k is better than k-1.
select_partition_number(res)
The numeric values for all these statistics can be obtained by get_stats().
get_stats(res)
#> k 1-PAC mean_silhouette concordance area_increased Rand Jaccard
#> 2 2 0.965 0.950 0.980 0.4997 0.501 0.501
#> 3 3 1.000 0.970 0.988 0.2919 0.800 0.621
#> 4 4 0.935 0.928 0.966 0.1260 0.901 0.730
#> 5 5 0.780 0.706 0.843 0.0549 0.979 0.926
#> 6 6 0.749 0.535 0.736 0.0355 0.943 0.787
suggest_best_k() suggests the best \(k\) based on these statistics. The rules are as follows:
suggest_best_k(res)
#> [1] 4
#> attr(,"optional")
#> [1] 2 3
There is also optional best \(k\) = 2 3 that is worth to check.
Following shows the table of the partitions (You need to click the show/hide
code output link to see it). The membership matrix (columns with name p*)
is inferred by
clue::cl_consensus()
function with the SE method. Basically the value in the membership matrix
represents the probability to belong to a certain group. The finall class
label for an item is determined with the group with highest probability it
belongs to.
In get_classes() function, the entropy is calculated from the membership
matrix and the silhouette score is calculated from the consensus matrix.
cbind(get_classes(res, k = 2), get_membership(res, k = 2))
#> class entropy silhouette p1 p2
#> GSM97800 2 0.0000 0.984 0.000 1.000
#> GSM97803 2 0.0000 0.984 0.000 1.000
#> GSM97804 2 0.0000 0.984 0.000 1.000
#> GSM97805 2 0.0000 0.984 0.000 1.000
#> GSM97807 2 0.0000 0.984 0.000 1.000
#> GSM97809 2 0.0000 0.984 0.000 1.000
#> GSM97811 2 0.0000 0.984 0.000 1.000
#> GSM97812 2 0.0000 0.984 0.000 1.000
#> GSM97816 2 0.0000 0.984 0.000 1.000
#> GSM97817 2 0.0000 0.984 0.000 1.000
#> GSM97820 2 0.0000 0.984 0.000 1.000
#> GSM97825 2 0.0000 0.984 0.000 1.000
#> GSM97827 2 0.0000 0.984 0.000 1.000
#> GSM97828 2 0.0000 0.984 0.000 1.000
#> GSM97833 2 0.0000 0.984 0.000 1.000
#> GSM97834 2 0.0000 0.984 0.000 1.000
#> GSM97840 2 0.0000 0.984 0.000 1.000
#> GSM97846 2 0.0000 0.984 0.000 1.000
#> GSM97848 2 0.0000 0.984 0.000 1.000
#> GSM97849 2 0.0000 0.984 0.000 1.000
#> GSM97850 2 0.0000 0.984 0.000 1.000
#> GSM97853 2 0.0000 0.984 0.000 1.000
#> GSM97855 2 0.0000 0.984 0.000 1.000
#> GSM97878 1 0.0000 0.975 1.000 0.000
#> GSM97913 2 0.0000 0.984 0.000 1.000
#> GSM97932 1 0.0000 0.975 1.000 0.000
#> GSM97939 2 0.0000 0.984 0.000 1.000
#> GSM97951 2 0.0000 0.984 0.000 1.000
#> GSM97957 2 0.0000 0.984 0.000 1.000
#> GSM97972 2 0.0000 0.984 0.000 1.000
#> GSM97793 1 0.6048 0.819 0.852 0.148
#> GSM97795 2 0.0000 0.984 0.000 1.000
#> GSM97802 1 0.0000 0.975 1.000 0.000
#> GSM97810 2 0.0000 0.984 0.000 1.000
#> GSM97815 2 0.0000 0.984 0.000 1.000
#> GSM97837 1 0.0000 0.975 1.000 0.000
#> GSM97843 2 0.0000 0.984 0.000 1.000
#> GSM97890 2 0.0000 0.984 0.000 1.000
#> GSM97899 1 0.0000 0.975 1.000 0.000
#> GSM97910 1 0.0000 0.975 1.000 0.000
#> GSM97916 1 0.0000 0.975 1.000 0.000
#> GSM97920 2 0.1843 0.958 0.028 0.972
#> GSM97921 1 0.0000 0.975 1.000 0.000
#> GSM97927 1 0.0000 0.975 1.000 0.000
#> GSM97937 1 0.0000 0.975 1.000 0.000
#> GSM97941 2 0.0000 0.984 0.000 1.000
#> GSM97943 2 0.7299 0.739 0.204 0.796
#> GSM97958 2 0.0000 0.984 0.000 1.000
#> GSM97960 2 0.0000 0.984 0.000 1.000
#> GSM97794 1 0.0938 0.964 0.988 0.012
#> GSM97796 1 0.0000 0.975 1.000 0.000
#> GSM97797 1 0.8909 0.557 0.692 0.308
#> GSM97798 1 0.0000 0.975 1.000 0.000
#> GSM97801 1 0.0000 0.975 1.000 0.000
#> GSM97806 1 0.0000 0.975 1.000 0.000
#> GSM97808 1 0.0000 0.975 1.000 0.000
#> GSM97813 1 0.0000 0.975 1.000 0.000
#> GSM97814 1 0.0000 0.975 1.000 0.000
#> GSM97818 1 0.0000 0.975 1.000 0.000
#> GSM97819 1 0.0672 0.968 0.992 0.008
#> GSM97821 2 0.0000 0.984 0.000 1.000
#> GSM97826 1 0.0000 0.975 1.000 0.000
#> GSM97829 1 0.0000 0.975 1.000 0.000
#> GSM97832 2 0.0000 0.984 0.000 1.000
#> GSM97836 1 0.0000 0.975 1.000 0.000
#> GSM97839 1 0.0000 0.975 1.000 0.000
#> GSM97844 2 0.0000 0.984 0.000 1.000
#> GSM97847 1 0.0000 0.975 1.000 0.000
#> GSM97851 1 0.0000 0.975 1.000 0.000
#> GSM97852 1 0.0000 0.975 1.000 0.000
#> GSM97856 1 0.0000 0.975 1.000 0.000
#> GSM97858 2 0.0000 0.984 0.000 1.000
#> GSM97859 1 0.0000 0.975 1.000 0.000
#> GSM97861 1 0.0000 0.975 1.000 0.000
#> GSM97863 1 0.0000 0.975 1.000 0.000
#> GSM97869 1 0.0000 0.975 1.000 0.000
#> GSM97870 1 0.0000 0.975 1.000 0.000
#> GSM97871 1 0.0000 0.975 1.000 0.000
#> GSM97877 2 0.0000 0.984 0.000 1.000
#> GSM97879 1 0.0000 0.975 1.000 0.000
#> GSM97882 1 0.0000 0.975 1.000 0.000
#> GSM97885 1 0.0000 0.975 1.000 0.000
#> GSM97886 1 0.0000 0.975 1.000 0.000
#> GSM97887 1 0.0000 0.975 1.000 0.000
#> GSM97888 1 0.0000 0.975 1.000 0.000
#> GSM97889 1 0.0000 0.975 1.000 0.000
#> GSM97891 1 0.0000 0.975 1.000 0.000
#> GSM97892 2 0.0000 0.984 0.000 1.000
#> GSM97893 1 0.0000 0.975 1.000 0.000
#> GSM97894 1 0.0000 0.975 1.000 0.000
#> GSM97895 1 0.0000 0.975 1.000 0.000
#> GSM97896 1 0.0000 0.975 1.000 0.000
#> GSM97898 1 0.0000 0.975 1.000 0.000
#> GSM97903 1 0.0000 0.975 1.000 0.000
#> GSM97905 1 0.0000 0.975 1.000 0.000
#> GSM97906 1 0.0000 0.975 1.000 0.000
#> GSM97908 1 0.0000 0.975 1.000 0.000
#> GSM97912 1 0.0000 0.975 1.000 0.000
#> GSM97914 1 0.0000 0.975 1.000 0.000
#> GSM97915 1 0.0000 0.975 1.000 0.000
#> GSM97917 1 0.0000 0.975 1.000 0.000
#> GSM97918 1 0.0000 0.975 1.000 0.000
#> GSM97919 1 0.0000 0.975 1.000 0.000
#> GSM97922 1 0.0000 0.975 1.000 0.000
#> GSM97924 2 0.0000 0.984 0.000 1.000
#> GSM97926 1 0.8144 0.669 0.748 0.252
#> GSM97930 1 0.0000 0.975 1.000 0.000
#> GSM97931 2 0.0000 0.984 0.000 1.000
#> GSM97935 1 0.0000 0.975 1.000 0.000
#> GSM97936 1 0.0000 0.975 1.000 0.000
#> GSM97938 1 0.0000 0.975 1.000 0.000
#> GSM97940 1 0.0000 0.975 1.000 0.000
#> GSM97942 1 0.0000 0.975 1.000 0.000
#> GSM97945 1 0.0000 0.975 1.000 0.000
#> GSM97946 2 0.0000 0.984 0.000 1.000
#> GSM97948 1 0.0000 0.975 1.000 0.000
#> GSM97950 1 0.0000 0.975 1.000 0.000
#> GSM97952 1 0.0000 0.975 1.000 0.000
#> GSM97953 1 0.0000 0.975 1.000 0.000
#> GSM97954 1 0.0000 0.975 1.000 0.000
#> GSM97955 1 0.0000 0.975 1.000 0.000
#> GSM97959 2 0.3584 0.916 0.068 0.932
#> GSM97961 1 0.0000 0.975 1.000 0.000
#> GSM97963 1 0.0000 0.975 1.000 0.000
#> GSM97965 1 0.0000 0.975 1.000 0.000
#> GSM97966 1 0.0000 0.975 1.000 0.000
#> GSM97967 2 0.0000 0.984 0.000 1.000
#> GSM97968 2 0.0000 0.984 0.000 1.000
#> GSM97969 1 0.0000 0.975 1.000 0.000
#> GSM97971 1 0.0000 0.975 1.000 0.000
#> GSM97799 2 0.0000 0.984 0.000 1.000
#> GSM97823 2 0.0000 0.984 0.000 1.000
#> GSM97824 2 0.0000 0.984 0.000 1.000
#> GSM97830 2 0.6712 0.780 0.176 0.824
#> GSM97835 2 0.0000 0.984 0.000 1.000
#> GSM97838 2 0.0000 0.984 0.000 1.000
#> GSM97841 2 0.0000 0.984 0.000 1.000
#> GSM97842 2 0.0000 0.984 0.000 1.000
#> GSM97854 2 0.0000 0.984 0.000 1.000
#> GSM97857 2 0.0000 0.984 0.000 1.000
#> GSM97860 1 0.9460 0.441 0.636 0.364
#> GSM97862 2 0.0000 0.984 0.000 1.000
#> GSM97864 2 0.0000 0.984 0.000 1.000
#> GSM97866 2 0.0000 0.984 0.000 1.000
#> GSM97868 2 0.0000 0.984 0.000 1.000
#> GSM97872 1 0.0000 0.975 1.000 0.000
#> GSM97873 2 0.0000 0.984 0.000 1.000
#> GSM97874 1 0.9393 0.460 0.644 0.356
#> GSM97875 2 0.1414 0.966 0.020 0.980
#> GSM97876 2 0.9580 0.374 0.380 0.620
#> GSM97880 1 0.0000 0.975 1.000 0.000
#> GSM97881 2 0.0000 0.984 0.000 1.000
#> GSM97884 2 0.0000 0.984 0.000 1.000
#> GSM97901 2 0.0000 0.984 0.000 1.000
#> GSM97902 1 0.9970 0.129 0.532 0.468
#> GSM97909 2 0.0000 0.984 0.000 1.000
#> GSM97911 2 0.0000 0.984 0.000 1.000
#> GSM97923 1 0.0376 0.971 0.996 0.004
#> GSM97928 1 0.0000 0.975 1.000 0.000
#> GSM97929 2 0.0000 0.984 0.000 1.000
#> GSM97933 1 0.8144 0.670 0.748 0.252
#> GSM97934 2 0.9608 0.362 0.384 0.616
#> GSM97944 2 0.0000 0.984 0.000 1.000
#> GSM97949 2 0.0000 0.984 0.000 1.000
#> GSM97956 2 0.0000 0.984 0.000 1.000
#> GSM97962 2 0.0000 0.984 0.000 1.000
#> GSM97964 2 0.0000 0.984 0.000 1.000
#> GSM97970 2 0.0000 0.984 0.000 1.000
#> GSM97822 1 0.0000 0.975 1.000 0.000
#> GSM97831 2 0.0000 0.984 0.000 1.000
#> GSM97845 1 0.0000 0.975 1.000 0.000
#> GSM97865 1 0.0000 0.975 1.000 0.000
#> GSM97867 1 0.0000 0.975 1.000 0.000
#> GSM97883 1 0.0000 0.975 1.000 0.000
#> GSM97897 1 0.0000 0.975 1.000 0.000
#> GSM97900 1 0.0000 0.975 1.000 0.000
#> GSM97904 1 0.0000 0.975 1.000 0.000
#> GSM97907 2 0.0000 0.984 0.000 1.000
#> GSM97925 1 0.7299 0.745 0.796 0.204
#> GSM97947 1 0.0000 0.975 1.000 0.000
cbind(get_classes(res, k = 3), get_membership(res, k = 3))
#> class entropy silhouette p1 p2 p3
#> GSM97800 2 0.0000 0.972 0.000 1.000 0.000
#> GSM97803 2 0.0000 0.972 0.000 1.000 0.000
#> GSM97804 2 0.0000 0.972 0.000 1.000 0.000
#> GSM97805 2 0.0000 0.972 0.000 1.000 0.000
#> GSM97807 2 0.0000 0.972 0.000 1.000 0.000
#> GSM97809 2 0.0000 0.972 0.000 1.000 0.000
#> GSM97811 2 0.0000 0.972 0.000 1.000 0.000
#> GSM97812 2 0.0000 0.972 0.000 1.000 0.000
#> GSM97816 2 0.0000 0.972 0.000 1.000 0.000
#> GSM97817 2 0.0000 0.972 0.000 1.000 0.000
#> GSM97820 2 0.0000 0.972 0.000 1.000 0.000
#> GSM97825 2 0.0000 0.972 0.000 1.000 0.000
#> GSM97827 2 0.0000 0.972 0.000 1.000 0.000
#> GSM97828 2 0.6111 0.357 0.000 0.604 0.396
#> GSM97833 2 0.0000 0.972 0.000 1.000 0.000
#> GSM97834 2 0.0000 0.972 0.000 1.000 0.000
#> GSM97840 2 0.0000 0.972 0.000 1.000 0.000
#> GSM97846 2 0.0000 0.972 0.000 1.000 0.000
#> GSM97848 2 0.0000 0.972 0.000 1.000 0.000
#> GSM97849 2 0.0000 0.972 0.000 1.000 0.000
#> GSM97850 2 0.0000 0.972 0.000 1.000 0.000
#> GSM97853 2 0.0000 0.972 0.000 1.000 0.000
#> GSM97855 2 0.0000 0.972 0.000 1.000 0.000
#> GSM97878 1 0.0000 0.993 1.000 0.000 0.000
#> GSM97913 2 0.0000 0.972 0.000 1.000 0.000
#> GSM97932 1 0.0000 0.993 1.000 0.000 0.000
#> GSM97939 2 0.2959 0.874 0.000 0.900 0.100
#> GSM97951 2 0.0000 0.972 0.000 1.000 0.000
#> GSM97957 3 0.0000 0.999 0.000 0.000 1.000
#> GSM97972 2 0.0000 0.972 0.000 1.000 0.000
#> GSM97793 3 0.0000 0.999 0.000 0.000 1.000
#> GSM97795 2 0.0000 0.972 0.000 1.000 0.000
#> GSM97802 3 0.0747 0.981 0.016 0.000 0.984
#> GSM97810 2 0.0000 0.972 0.000 1.000 0.000
#> GSM97815 2 0.0000 0.972 0.000 1.000 0.000
#> GSM97837 1 0.0000 0.993 1.000 0.000 0.000
#> GSM97843 3 0.0000 0.999 0.000 0.000 1.000
#> GSM97890 3 0.0000 0.999 0.000 0.000 1.000
#> GSM97899 1 0.0000 0.993 1.000 0.000 0.000
#> GSM97910 1 0.2711 0.899 0.912 0.000 0.088
#> GSM97916 1 0.0000 0.993 1.000 0.000 0.000
#> GSM97920 3 0.0000 0.999 0.000 0.000 1.000
#> GSM97921 1 0.0000 0.993 1.000 0.000 0.000
#> GSM97927 1 0.0000 0.993 1.000 0.000 0.000
#> GSM97937 1 0.0000 0.993 1.000 0.000 0.000
#> GSM97941 2 0.0000 0.972 0.000 1.000 0.000
#> GSM97943 2 0.8010 0.282 0.068 0.548 0.384
#> GSM97958 2 0.0000 0.972 0.000 1.000 0.000
#> GSM97960 2 0.0000 0.972 0.000 1.000 0.000
#> GSM97794 1 0.0424 0.985 0.992 0.008 0.000
#> GSM97796 1 0.0000 0.993 1.000 0.000 0.000
#> GSM97797 2 0.5926 0.445 0.356 0.644 0.000
#> GSM97798 1 0.0000 0.993 1.000 0.000 0.000
#> GSM97801 1 0.0000 0.993 1.000 0.000 0.000
#> GSM97806 1 0.0000 0.993 1.000 0.000 0.000
#> GSM97808 1 0.0000 0.993 1.000 0.000 0.000
#> GSM97813 1 0.0000 0.993 1.000 0.000 0.000
#> GSM97814 1 0.0000 0.993 1.000 0.000 0.000
#> GSM97818 1 0.0000 0.993 1.000 0.000 0.000
#> GSM97819 3 0.0000 0.999 0.000 0.000 1.000
#> GSM97821 2 0.0000 0.972 0.000 1.000 0.000
#> GSM97826 1 0.0000 0.993 1.000 0.000 0.000
#> GSM97829 1 0.0000 0.993 1.000 0.000 0.000
#> GSM97832 2 0.0000 0.972 0.000 1.000 0.000
#> GSM97836 1 0.0000 0.993 1.000 0.000 0.000
#> GSM97839 1 0.0000 0.993 1.000 0.000 0.000
#> GSM97844 2 0.0000 0.972 0.000 1.000 0.000
#> GSM97847 1 0.0000 0.993 1.000 0.000 0.000
#> GSM97851 1 0.0000 0.993 1.000 0.000 0.000
#> GSM97852 1 0.0000 0.993 1.000 0.000 0.000
#> GSM97856 1 0.0000 0.993 1.000 0.000 0.000
#> GSM97858 2 0.0000 0.972 0.000 1.000 0.000
#> GSM97859 1 0.0000 0.993 1.000 0.000 0.000
#> GSM97861 1 0.0000 0.993 1.000 0.000 0.000
#> GSM97863 1 0.0000 0.993 1.000 0.000 0.000
#> GSM97869 1 0.0000 0.993 1.000 0.000 0.000
#> GSM97870 1 0.0000 0.993 1.000 0.000 0.000
#> GSM97871 1 0.0000 0.993 1.000 0.000 0.000
#> GSM97877 2 0.0000 0.972 0.000 1.000 0.000
#> GSM97879 1 0.0000 0.993 1.000 0.000 0.000
#> GSM97882 1 0.0000 0.993 1.000 0.000 0.000
#> GSM97885 1 0.0000 0.993 1.000 0.000 0.000
#> GSM97886 1 0.0000 0.993 1.000 0.000 0.000
#> GSM97887 1 0.0000 0.993 1.000 0.000 0.000
#> GSM97888 1 0.0000 0.993 1.000 0.000 0.000
#> GSM97889 1 0.0000 0.993 1.000 0.000 0.000
#> GSM97891 1 0.0000 0.993 1.000 0.000 0.000
#> GSM97892 2 0.0000 0.972 0.000 1.000 0.000
#> GSM97893 1 0.0000 0.993 1.000 0.000 0.000
#> GSM97894 1 0.0000 0.993 1.000 0.000 0.000
#> GSM97895 1 0.0000 0.993 1.000 0.000 0.000
#> GSM97896 1 0.0000 0.993 1.000 0.000 0.000
#> GSM97898 1 0.0000 0.993 1.000 0.000 0.000
#> GSM97903 1 0.0000 0.993 1.000 0.000 0.000
#> GSM97905 1 0.0000 0.993 1.000 0.000 0.000
#> GSM97906 1 0.0000 0.993 1.000 0.000 0.000
#> GSM97908 1 0.0000 0.993 1.000 0.000 0.000
#> GSM97912 1 0.0000 0.993 1.000 0.000 0.000
#> GSM97914 1 0.0000 0.993 1.000 0.000 0.000
#> GSM97915 1 0.0000 0.993 1.000 0.000 0.000
#> GSM97917 1 0.0000 0.993 1.000 0.000 0.000
#> GSM97918 1 0.0000 0.993 1.000 0.000 0.000
#> GSM97919 1 0.0000 0.993 1.000 0.000 0.000
#> GSM97922 1 0.0000 0.993 1.000 0.000 0.000
#> GSM97924 2 0.0000 0.972 0.000 1.000 0.000
#> GSM97926 3 0.0000 0.999 0.000 0.000 1.000
#> GSM97930 1 0.0000 0.993 1.000 0.000 0.000
#> GSM97931 2 0.0000 0.972 0.000 1.000 0.000
#> GSM97935 1 0.0000 0.993 1.000 0.000 0.000
#> GSM97936 1 0.0000 0.993 1.000 0.000 0.000
#> GSM97938 1 0.0000 0.993 1.000 0.000 0.000
#> GSM97940 1 0.0000 0.993 1.000 0.000 0.000
#> GSM97942 3 0.0000 0.999 0.000 0.000 1.000
#> GSM97945 1 0.0000 0.993 1.000 0.000 0.000
#> GSM97946 2 0.0000 0.972 0.000 1.000 0.000
#> GSM97948 3 0.0000 0.999 0.000 0.000 1.000
#> GSM97950 1 0.0000 0.993 1.000 0.000 0.000
#> GSM97952 1 0.0000 0.993 1.000 0.000 0.000
#> GSM97953 1 0.0000 0.993 1.000 0.000 0.000
#> GSM97954 1 0.0000 0.993 1.000 0.000 0.000
#> GSM97955 1 0.0000 0.993 1.000 0.000 0.000
#> GSM97959 2 0.0000 0.972 0.000 1.000 0.000
#> GSM97961 1 0.0000 0.993 1.000 0.000 0.000
#> GSM97963 1 0.0000 0.993 1.000 0.000 0.000
#> GSM97965 1 0.0000 0.993 1.000 0.000 0.000
#> GSM97966 1 0.0000 0.993 1.000 0.000 0.000
#> GSM97967 2 0.0000 0.972 0.000 1.000 0.000
#> GSM97968 2 0.0000 0.972 0.000 1.000 0.000
#> GSM97969 1 0.0000 0.993 1.000 0.000 0.000
#> GSM97971 1 0.0000 0.993 1.000 0.000 0.000
#> GSM97799 3 0.0000 0.999 0.000 0.000 1.000
#> GSM97823 2 0.0000 0.972 0.000 1.000 0.000
#> GSM97824 3 0.0000 0.999 0.000 0.000 1.000
#> GSM97830 3 0.0000 0.999 0.000 0.000 1.000
#> GSM97835 2 0.4605 0.739 0.000 0.796 0.204
#> GSM97838 2 0.0000 0.972 0.000 1.000 0.000
#> GSM97841 2 0.0000 0.972 0.000 1.000 0.000
#> GSM97842 3 0.0424 0.991 0.000 0.008 0.992
#> GSM97854 2 0.0000 0.972 0.000 1.000 0.000
#> GSM97857 3 0.0000 0.999 0.000 0.000 1.000
#> GSM97860 3 0.0000 0.999 0.000 0.000 1.000
#> GSM97862 3 0.0000 0.999 0.000 0.000 1.000
#> GSM97864 2 0.0000 0.972 0.000 1.000 0.000
#> GSM97866 3 0.0000 0.999 0.000 0.000 1.000
#> GSM97868 3 0.0000 0.999 0.000 0.000 1.000
#> GSM97872 1 0.0000 0.993 1.000 0.000 0.000
#> GSM97873 3 0.0000 0.999 0.000 0.000 1.000
#> GSM97874 3 0.0000 0.999 0.000 0.000 1.000
#> GSM97875 3 0.0000 0.999 0.000 0.000 1.000
#> GSM97876 3 0.0000 0.999 0.000 0.000 1.000
#> GSM97880 3 0.0000 0.999 0.000 0.000 1.000
#> GSM97881 3 0.0000 0.999 0.000 0.000 1.000
#> GSM97884 3 0.0000 0.999 0.000 0.000 1.000
#> GSM97901 3 0.0000 0.999 0.000 0.000 1.000
#> GSM97902 1 0.9022 0.102 0.480 0.384 0.136
#> GSM97909 2 0.0000 0.972 0.000 1.000 0.000
#> GSM97911 3 0.0000 0.999 0.000 0.000 1.000
#> GSM97923 3 0.0000 0.999 0.000 0.000 1.000
#> GSM97928 1 0.0000 0.993 1.000 0.000 0.000
#> GSM97929 2 0.0000 0.972 0.000 1.000 0.000
#> GSM97933 3 0.0000 0.999 0.000 0.000 1.000
#> GSM97934 3 0.0000 0.999 0.000 0.000 1.000
#> GSM97944 3 0.0000 0.999 0.000 0.000 1.000
#> GSM97949 2 0.0000 0.972 0.000 1.000 0.000
#> GSM97956 3 0.0000 0.999 0.000 0.000 1.000
#> GSM97962 3 0.0000 0.999 0.000 0.000 1.000
#> GSM97964 3 0.0000 0.999 0.000 0.000 1.000
#> GSM97970 3 0.0000 0.999 0.000 0.000 1.000
#> GSM97822 1 0.0000 0.993 1.000 0.000 0.000
#> GSM97831 3 0.0000 0.999 0.000 0.000 1.000
#> GSM97845 1 0.0000 0.993 1.000 0.000 0.000
#> GSM97865 1 0.0000 0.993 1.000 0.000 0.000
#> GSM97867 3 0.0000 0.999 0.000 0.000 1.000
#> GSM97883 3 0.0000 0.999 0.000 0.000 1.000
#> GSM97897 1 0.0000 0.993 1.000 0.000 0.000
#> GSM97900 1 0.0000 0.993 1.000 0.000 0.000
#> GSM97904 1 0.0000 0.993 1.000 0.000 0.000
#> GSM97907 2 0.0000 0.972 0.000 1.000 0.000
#> GSM97925 3 0.0000 0.999 0.000 0.000 1.000
#> GSM97947 3 0.0000 0.999 0.000 0.000 1.000
cbind(get_classes(res, k = 4), get_membership(res, k = 4))
#> class entropy silhouette p1 p2 p3 p4
#> GSM97800 2 0.0000 0.9867 0.000 1.000 0.000 0.000
#> GSM97803 2 0.0000 0.9867 0.000 1.000 0.000 0.000
#> GSM97804 2 0.0000 0.9867 0.000 1.000 0.000 0.000
#> GSM97805 2 0.0000 0.9867 0.000 1.000 0.000 0.000
#> GSM97807 2 0.0000 0.9867 0.000 1.000 0.000 0.000
#> GSM97809 2 0.0000 0.9867 0.000 1.000 0.000 0.000
#> GSM97811 2 0.0000 0.9867 0.000 1.000 0.000 0.000
#> GSM97812 2 0.0000 0.9867 0.000 1.000 0.000 0.000
#> GSM97816 2 0.1389 0.9453 0.048 0.952 0.000 0.000
#> GSM97817 2 0.0000 0.9867 0.000 1.000 0.000 0.000
#> GSM97820 2 0.0000 0.9867 0.000 1.000 0.000 0.000
#> GSM97825 2 0.0000 0.9867 0.000 1.000 0.000 0.000
#> GSM97827 2 0.0000 0.9867 0.000 1.000 0.000 0.000
#> GSM97828 1 0.3672 0.7421 0.824 0.012 0.164 0.000
#> GSM97833 2 0.0000 0.9867 0.000 1.000 0.000 0.000
#> GSM97834 2 0.0000 0.9867 0.000 1.000 0.000 0.000
#> GSM97840 2 0.0000 0.9867 0.000 1.000 0.000 0.000
#> GSM97846 2 0.0000 0.9867 0.000 1.000 0.000 0.000
#> GSM97848 2 0.0000 0.9867 0.000 1.000 0.000 0.000
#> GSM97849 2 0.0000 0.9867 0.000 1.000 0.000 0.000
#> GSM97850 2 0.0000 0.9867 0.000 1.000 0.000 0.000
#> GSM97853 2 0.0000 0.9867 0.000 1.000 0.000 0.000
#> GSM97855 2 0.0000 0.9867 0.000 1.000 0.000 0.000
#> GSM97878 1 0.3219 0.8131 0.836 0.000 0.000 0.164
#> GSM97913 2 0.2530 0.8733 0.112 0.888 0.000 0.000
#> GSM97932 4 0.1211 0.9246 0.040 0.000 0.000 0.960
#> GSM97939 2 0.2281 0.8831 0.000 0.904 0.096 0.000
#> GSM97951 2 0.0000 0.9867 0.000 1.000 0.000 0.000
#> GSM97957 3 0.0000 0.9985 0.000 0.000 1.000 0.000
#> GSM97972 2 0.0592 0.9739 0.016 0.984 0.000 0.000
#> GSM97793 3 0.0000 0.9985 0.000 0.000 1.000 0.000
#> GSM97795 2 0.0000 0.9867 0.000 1.000 0.000 0.000
#> GSM97802 4 0.5168 0.0345 0.004 0.000 0.492 0.504
#> GSM97810 2 0.0000 0.9867 0.000 1.000 0.000 0.000
#> GSM97815 2 0.0188 0.9830 0.000 0.996 0.004 0.000
#> GSM97837 1 0.2408 0.8598 0.896 0.000 0.000 0.104
#> GSM97843 3 0.0000 0.9985 0.000 0.000 1.000 0.000
#> GSM97890 3 0.0000 0.9985 0.000 0.000 1.000 0.000
#> GSM97899 4 0.0000 0.9453 0.000 0.000 0.000 1.000
#> GSM97910 1 0.0188 0.8870 0.996 0.000 0.000 0.004
#> GSM97916 1 0.0469 0.8857 0.988 0.000 0.000 0.012
#> GSM97920 3 0.0000 0.9985 0.000 0.000 1.000 0.000
#> GSM97921 1 0.0188 0.8870 0.996 0.000 0.000 0.004
#> GSM97927 4 0.1118 0.9269 0.036 0.000 0.000 0.964
#> GSM97937 1 0.2973 0.8323 0.856 0.000 0.000 0.144
#> GSM97941 2 0.0000 0.9867 0.000 1.000 0.000 0.000
#> GSM97943 1 0.0000 0.8849 1.000 0.000 0.000 0.000
#> GSM97958 2 0.4008 0.6893 0.244 0.756 0.000 0.000
#> GSM97960 2 0.0000 0.9867 0.000 1.000 0.000 0.000
#> GSM97794 1 0.0188 0.8870 0.996 0.000 0.000 0.004
#> GSM97796 4 0.0188 0.9451 0.004 0.000 0.000 0.996
#> GSM97797 1 0.0188 0.8870 0.996 0.000 0.000 0.004
#> GSM97798 4 0.0000 0.9453 0.000 0.000 0.000 1.000
#> GSM97801 1 0.0188 0.8870 0.996 0.000 0.000 0.004
#> GSM97806 4 0.2011 0.8869 0.080 0.000 0.000 0.920
#> GSM97808 4 0.0000 0.9453 0.000 0.000 0.000 1.000
#> GSM97813 4 0.0188 0.9442 0.004 0.000 0.000 0.996
#> GSM97814 4 0.0000 0.9453 0.000 0.000 0.000 1.000
#> GSM97818 1 0.0188 0.8870 0.996 0.000 0.000 0.004
#> GSM97819 3 0.0000 0.9985 0.000 0.000 1.000 0.000
#> GSM97821 2 0.0000 0.9867 0.000 1.000 0.000 0.000
#> GSM97826 1 0.4746 0.4991 0.632 0.000 0.000 0.368
#> GSM97829 1 0.2281 0.8648 0.904 0.000 0.000 0.096
#> GSM97832 2 0.0000 0.9867 0.000 1.000 0.000 0.000
#> GSM97836 4 0.0592 0.9405 0.016 0.000 0.000 0.984
#> GSM97839 4 0.0336 0.9443 0.008 0.000 0.000 0.992
#> GSM97844 2 0.0000 0.9867 0.000 1.000 0.000 0.000
#> GSM97847 1 0.3726 0.7558 0.788 0.000 0.000 0.212
#> GSM97851 4 0.1118 0.9278 0.036 0.000 0.000 0.964
#> GSM97852 4 0.3726 0.7384 0.212 0.000 0.000 0.788
#> GSM97856 4 0.0000 0.9453 0.000 0.000 0.000 1.000
#> GSM97858 2 0.0000 0.9867 0.000 1.000 0.000 0.000
#> GSM97859 4 0.0188 0.9442 0.004 0.000 0.000 0.996
#> GSM97861 4 0.0592 0.9393 0.016 0.000 0.000 0.984
#> GSM97863 4 0.0336 0.9443 0.008 0.000 0.000 0.992
#> GSM97869 1 0.4925 0.2896 0.572 0.000 0.000 0.428
#> GSM97870 4 0.0469 0.9422 0.012 0.000 0.000 0.988
#> GSM97871 4 0.0000 0.9453 0.000 0.000 0.000 1.000
#> GSM97877 2 0.0000 0.9867 0.000 1.000 0.000 0.000
#> GSM97879 4 0.0817 0.9385 0.024 0.000 0.000 0.976
#> GSM97882 4 0.0592 0.9406 0.016 0.000 0.000 0.984
#> GSM97885 4 0.4356 0.5801 0.292 0.000 0.000 0.708
#> GSM97886 4 0.0336 0.9443 0.008 0.000 0.000 0.992
#> GSM97887 4 0.0000 0.9453 0.000 0.000 0.000 1.000
#> GSM97888 4 0.0336 0.9448 0.008 0.000 0.000 0.992
#> GSM97889 4 0.0188 0.9442 0.004 0.000 0.000 0.996
#> GSM97891 4 0.3074 0.8066 0.152 0.000 0.000 0.848
#> GSM97892 2 0.0000 0.9867 0.000 1.000 0.000 0.000
#> GSM97893 4 0.1211 0.9246 0.040 0.000 0.000 0.960
#> GSM97894 4 0.0188 0.9451 0.004 0.000 0.000 0.996
#> GSM97895 4 0.0921 0.9335 0.028 0.000 0.000 0.972
#> GSM97896 4 0.0188 0.9442 0.004 0.000 0.000 0.996
#> GSM97898 4 0.0336 0.9443 0.008 0.000 0.000 0.992
#> GSM97903 1 0.2345 0.8572 0.900 0.000 0.000 0.100
#> GSM97905 4 0.0188 0.9442 0.004 0.000 0.000 0.996
#> GSM97906 4 0.0000 0.9453 0.000 0.000 0.000 1.000
#> GSM97908 4 0.3649 0.7318 0.204 0.000 0.000 0.796
#> GSM97912 4 0.1022 0.9331 0.032 0.000 0.000 0.968
#> GSM97914 1 0.0188 0.8870 0.996 0.000 0.000 0.004
#> GSM97915 4 0.0336 0.9443 0.008 0.000 0.000 0.992
#> GSM97917 4 0.1474 0.9147 0.052 0.000 0.000 0.948
#> GSM97918 4 0.0469 0.9429 0.012 0.000 0.000 0.988
#> GSM97919 4 0.0336 0.9443 0.008 0.000 0.000 0.992
#> GSM97922 4 0.0188 0.9442 0.004 0.000 0.000 0.996
#> GSM97924 2 0.0000 0.9867 0.000 1.000 0.000 0.000
#> GSM97926 3 0.0000 0.9985 0.000 0.000 1.000 0.000
#> GSM97930 1 0.1302 0.8830 0.956 0.000 0.000 0.044
#> GSM97931 2 0.0000 0.9867 0.000 1.000 0.000 0.000
#> GSM97935 4 0.2530 0.8514 0.112 0.000 0.000 0.888
#> GSM97936 4 0.0188 0.9451 0.004 0.000 0.000 0.996
#> GSM97938 4 0.4500 0.5053 0.316 0.000 0.000 0.684
#> GSM97940 4 0.0000 0.9453 0.000 0.000 0.000 1.000
#> GSM97942 3 0.0000 0.9985 0.000 0.000 1.000 0.000
#> GSM97945 4 0.0000 0.9453 0.000 0.000 0.000 1.000
#> GSM97946 2 0.0000 0.9867 0.000 1.000 0.000 0.000
#> GSM97948 3 0.1209 0.9559 0.004 0.000 0.964 0.032
#> GSM97950 4 0.0000 0.9453 0.000 0.000 0.000 1.000
#> GSM97952 4 0.0000 0.9453 0.000 0.000 0.000 1.000
#> GSM97953 1 0.4776 0.4815 0.624 0.000 0.000 0.376
#> GSM97954 4 0.4331 0.5938 0.288 0.000 0.000 0.712
#> GSM97955 4 0.0188 0.9451 0.004 0.000 0.000 0.996
#> GSM97959 1 0.0469 0.8799 0.988 0.012 0.000 0.000
#> GSM97961 4 0.0188 0.9451 0.004 0.000 0.000 0.996
#> GSM97963 4 0.0000 0.9453 0.000 0.000 0.000 1.000
#> GSM97965 4 0.0000 0.9453 0.000 0.000 0.000 1.000
#> GSM97966 4 0.0000 0.9453 0.000 0.000 0.000 1.000
#> GSM97967 2 0.0000 0.9867 0.000 1.000 0.000 0.000
#> GSM97968 2 0.0000 0.9867 0.000 1.000 0.000 0.000
#> GSM97969 4 0.0707 0.9387 0.020 0.000 0.000 0.980
#> GSM97971 4 0.0336 0.9448 0.008 0.000 0.000 0.992
#> GSM97799 3 0.0000 0.9985 0.000 0.000 1.000 0.000
#> GSM97823 2 0.0000 0.9867 0.000 1.000 0.000 0.000
#> GSM97824 3 0.0000 0.9985 0.000 0.000 1.000 0.000
#> GSM97830 3 0.0000 0.9985 0.000 0.000 1.000 0.000
#> GSM97835 2 0.2921 0.8276 0.000 0.860 0.140 0.000
#> GSM97838 2 0.0000 0.9867 0.000 1.000 0.000 0.000
#> GSM97841 2 0.0000 0.9867 0.000 1.000 0.000 0.000
#> GSM97842 3 0.0469 0.9840 0.000 0.012 0.988 0.000
#> GSM97854 2 0.0000 0.9867 0.000 1.000 0.000 0.000
#> GSM97857 3 0.0000 0.9985 0.000 0.000 1.000 0.000
#> GSM97860 3 0.0000 0.9985 0.000 0.000 1.000 0.000
#> GSM97862 3 0.0000 0.9985 0.000 0.000 1.000 0.000
#> GSM97864 2 0.0000 0.9867 0.000 1.000 0.000 0.000
#> GSM97866 3 0.0000 0.9985 0.000 0.000 1.000 0.000
#> GSM97868 3 0.0000 0.9985 0.000 0.000 1.000 0.000
#> GSM97872 4 0.3569 0.7469 0.196 0.000 0.000 0.804
#> GSM97873 3 0.0000 0.9985 0.000 0.000 1.000 0.000
#> GSM97874 3 0.0000 0.9985 0.000 0.000 1.000 0.000
#> GSM97875 3 0.0000 0.9985 0.000 0.000 1.000 0.000
#> GSM97876 3 0.0000 0.9985 0.000 0.000 1.000 0.000
#> GSM97880 3 0.0000 0.9985 0.000 0.000 1.000 0.000
#> GSM97881 3 0.0000 0.9985 0.000 0.000 1.000 0.000
#> GSM97884 3 0.0000 0.9985 0.000 0.000 1.000 0.000
#> GSM97901 3 0.0000 0.9985 0.000 0.000 1.000 0.000
#> GSM97902 1 0.1677 0.8819 0.948 0.000 0.012 0.040
#> GSM97909 2 0.0000 0.9867 0.000 1.000 0.000 0.000
#> GSM97911 3 0.0000 0.9985 0.000 0.000 1.000 0.000
#> GSM97923 3 0.0000 0.9985 0.000 0.000 1.000 0.000
#> GSM97928 4 0.0469 0.9432 0.012 0.000 0.000 0.988
#> GSM97929 2 0.0000 0.9867 0.000 1.000 0.000 0.000
#> GSM97933 3 0.0000 0.9985 0.000 0.000 1.000 0.000
#> GSM97934 3 0.0000 0.9985 0.000 0.000 1.000 0.000
#> GSM97944 3 0.0000 0.9985 0.000 0.000 1.000 0.000
#> GSM97949 2 0.0000 0.9867 0.000 1.000 0.000 0.000
#> GSM97956 3 0.0000 0.9985 0.000 0.000 1.000 0.000
#> GSM97962 3 0.0000 0.9985 0.000 0.000 1.000 0.000
#> GSM97964 3 0.0000 0.9985 0.000 0.000 1.000 0.000
#> GSM97970 3 0.0000 0.9985 0.000 0.000 1.000 0.000
#> GSM97822 4 0.0188 0.9442 0.004 0.000 0.000 0.996
#> GSM97831 3 0.0000 0.9985 0.000 0.000 1.000 0.000
#> GSM97845 4 0.3528 0.7569 0.192 0.000 0.000 0.808
#> GSM97865 1 0.0188 0.8870 0.996 0.000 0.000 0.004
#> GSM97867 3 0.0000 0.9985 0.000 0.000 1.000 0.000
#> GSM97883 3 0.0000 0.9985 0.000 0.000 1.000 0.000
#> GSM97897 4 0.0188 0.9442 0.004 0.000 0.000 0.996
#> GSM97900 4 0.0000 0.9453 0.000 0.000 0.000 1.000
#> GSM97904 4 0.0188 0.9451 0.004 0.000 0.000 0.996
#> GSM97907 2 0.0000 0.9867 0.000 1.000 0.000 0.000
#> GSM97925 3 0.0000 0.9985 0.000 0.000 1.000 0.000
#> GSM97947 3 0.0000 0.9985 0.000 0.000 1.000 0.000
cbind(get_classes(res, k = 5), get_membership(res, k = 5))
#> class entropy silhouette p1 p2 p3 p4 p5
#> GSM97800 2 0.0000 0.9500 0.000 1.000 0.000 0.000 0.000
#> GSM97803 2 0.0000 0.9500 0.000 1.000 0.000 0.000 0.000
#> GSM97804 2 0.0000 0.9500 0.000 1.000 0.000 0.000 0.000
#> GSM97805 2 0.0000 0.9500 0.000 1.000 0.000 0.000 0.000
#> GSM97807 2 0.0000 0.9500 0.000 1.000 0.000 0.000 0.000
#> GSM97809 2 0.0000 0.9500 0.000 1.000 0.000 0.000 0.000
#> GSM97811 2 0.0000 0.9500 0.000 1.000 0.000 0.000 0.000
#> GSM97812 2 0.0000 0.9500 0.000 1.000 0.000 0.000 0.000
#> GSM97816 2 0.6679 0.2664 0.252 0.516 0.012 0.000 0.220
#> GSM97817 2 0.0000 0.9500 0.000 1.000 0.000 0.000 0.000
#> GSM97820 2 0.0000 0.9500 0.000 1.000 0.000 0.000 0.000
#> GSM97825 2 0.0000 0.9500 0.000 1.000 0.000 0.000 0.000
#> GSM97827 2 0.0000 0.9500 0.000 1.000 0.000 0.000 0.000
#> GSM97828 1 0.5646 0.4831 0.556 0.012 0.056 0.000 0.376
#> GSM97833 2 0.0000 0.9500 0.000 1.000 0.000 0.000 0.000
#> GSM97834 2 0.0000 0.9500 0.000 1.000 0.000 0.000 0.000
#> GSM97840 2 0.0000 0.9500 0.000 1.000 0.000 0.000 0.000
#> GSM97846 2 0.0000 0.9500 0.000 1.000 0.000 0.000 0.000
#> GSM97848 2 0.0000 0.9500 0.000 1.000 0.000 0.000 0.000
#> GSM97849 2 0.0000 0.9500 0.000 1.000 0.000 0.000 0.000
#> GSM97850 2 0.0000 0.9500 0.000 1.000 0.000 0.000 0.000
#> GSM97853 2 0.0000 0.9500 0.000 1.000 0.000 0.000 0.000
#> GSM97855 2 0.0000 0.9500 0.000 1.000 0.000 0.000 0.000
#> GSM97878 1 0.6054 0.3711 0.568 0.000 0.000 0.260 0.172
#> GSM97913 2 0.3942 0.6918 0.232 0.748 0.000 0.000 0.020
#> GSM97932 4 0.4325 0.6020 0.064 0.000 0.000 0.756 0.180
#> GSM97939 2 0.5150 0.5558 0.000 0.652 0.272 0.000 0.076
#> GSM97951 2 0.0000 0.9500 0.000 1.000 0.000 0.000 0.000
#> GSM97957 3 0.4225 0.7585 0.004 0.000 0.632 0.000 0.364
#> GSM97972 2 0.4765 0.6877 0.092 0.736 0.004 0.000 0.168
#> GSM97793 3 0.3534 0.8308 0.000 0.000 0.744 0.000 0.256
#> GSM97795 2 0.0000 0.9500 0.000 1.000 0.000 0.000 0.000
#> GSM97802 5 0.6718 0.4103 0.000 0.000 0.260 0.328 0.412
#> GSM97810 2 0.1205 0.9181 0.000 0.956 0.004 0.000 0.040
#> GSM97815 2 0.2020 0.8624 0.000 0.900 0.100 0.000 0.000
#> GSM97837 1 0.4815 0.6426 0.692 0.000 0.000 0.064 0.244
#> GSM97843 3 0.2891 0.8593 0.000 0.000 0.824 0.000 0.176
#> GSM97890 3 0.1197 0.8612 0.000 0.000 0.952 0.000 0.048
#> GSM97899 4 0.0162 0.7205 0.000 0.000 0.000 0.996 0.004
#> GSM97910 1 0.3010 0.6596 0.824 0.000 0.004 0.000 0.172
#> GSM97916 1 0.2930 0.6391 0.832 0.000 0.000 0.004 0.164
#> GSM97920 3 0.3895 0.8009 0.000 0.000 0.680 0.000 0.320
#> GSM97921 1 0.3203 0.7035 0.820 0.000 0.000 0.012 0.168
#> GSM97927 4 0.4157 0.4080 0.020 0.000 0.000 0.716 0.264
#> GSM97937 1 0.5962 0.5064 0.584 0.000 0.000 0.168 0.248
#> GSM97941 2 0.0000 0.9500 0.000 1.000 0.000 0.000 0.000
#> GSM97943 1 0.4238 0.5819 0.628 0.000 0.004 0.000 0.368
#> GSM97958 2 0.6100 0.2859 0.308 0.540 0.000 0.000 0.152
#> GSM97960 2 0.0000 0.9500 0.000 1.000 0.000 0.000 0.000
#> GSM97794 1 0.0794 0.6971 0.972 0.000 0.000 0.000 0.028
#> GSM97796 4 0.2006 0.7169 0.012 0.000 0.000 0.916 0.072
#> GSM97797 1 0.1043 0.6948 0.960 0.000 0.000 0.000 0.040
#> GSM97798 4 0.0404 0.7180 0.000 0.000 0.000 0.988 0.012
#> GSM97801 1 0.1341 0.7014 0.944 0.000 0.000 0.000 0.056
#> GSM97806 4 0.2570 0.6828 0.084 0.000 0.000 0.888 0.028
#> GSM97808 4 0.0404 0.7180 0.000 0.000 0.000 0.988 0.012
#> GSM97813 4 0.4015 0.3557 0.000 0.000 0.000 0.652 0.348
#> GSM97814 4 0.0404 0.7180 0.000 0.000 0.000 0.988 0.012
#> GSM97818 1 0.1205 0.7049 0.956 0.000 0.000 0.004 0.040
#> GSM97819 3 0.2377 0.8576 0.000 0.000 0.872 0.000 0.128
#> GSM97821 2 0.0000 0.9500 0.000 1.000 0.000 0.000 0.000
#> GSM97826 5 0.6779 -0.0597 0.324 0.000 0.000 0.288 0.388
#> GSM97829 1 0.5195 0.6210 0.676 0.000 0.000 0.108 0.216
#> GSM97832 2 0.0451 0.9422 0.000 0.988 0.004 0.000 0.008
#> GSM97836 4 0.3690 0.5552 0.020 0.000 0.000 0.780 0.200
#> GSM97839 4 0.2130 0.7145 0.012 0.000 0.000 0.908 0.080
#> GSM97844 2 0.0000 0.9500 0.000 1.000 0.000 0.000 0.000
#> GSM97847 1 0.6599 0.1724 0.436 0.000 0.000 0.344 0.220
#> GSM97851 4 0.4298 0.6030 0.060 0.000 0.000 0.756 0.184
#> GSM97852 4 0.6133 0.3260 0.220 0.000 0.000 0.564 0.216
#> GSM97856 4 0.0162 0.7198 0.000 0.000 0.000 0.996 0.004
#> GSM97858 2 0.0000 0.9500 0.000 1.000 0.000 0.000 0.000
#> GSM97859 4 0.4403 0.3053 0.008 0.000 0.000 0.608 0.384
#> GSM97861 4 0.1800 0.6953 0.020 0.000 0.000 0.932 0.048
#> GSM97863 4 0.2017 0.7158 0.008 0.000 0.000 0.912 0.080
#> GSM97869 1 0.6392 0.0377 0.468 0.000 0.000 0.176 0.356
#> GSM97870 4 0.4489 0.0553 0.008 0.000 0.000 0.572 0.420
#> GSM97871 4 0.0404 0.7180 0.000 0.000 0.000 0.988 0.012
#> GSM97877 2 0.2966 0.8166 0.136 0.848 0.000 0.000 0.016
#> GSM97879 4 0.2012 0.7072 0.060 0.000 0.000 0.920 0.020
#> GSM97882 4 0.3728 0.4827 0.008 0.000 0.000 0.748 0.244
#> GSM97885 4 0.6245 0.0402 0.236 0.000 0.000 0.544 0.220
#> GSM97886 4 0.1082 0.7218 0.008 0.000 0.000 0.964 0.028
#> GSM97887 4 0.0510 0.7163 0.000 0.000 0.000 0.984 0.016
#> GSM97888 4 0.3949 0.5035 0.004 0.000 0.000 0.696 0.300
#> GSM97889 4 0.3636 0.4179 0.000 0.000 0.000 0.728 0.272
#> GSM97891 4 0.3035 0.6367 0.112 0.000 0.000 0.856 0.032
#> GSM97892 2 0.0000 0.9500 0.000 1.000 0.000 0.000 0.000
#> GSM97893 4 0.4832 0.5523 0.088 0.000 0.000 0.712 0.200
#> GSM97894 4 0.2408 0.7092 0.016 0.000 0.000 0.892 0.092
#> GSM97895 4 0.3958 0.6315 0.044 0.000 0.000 0.780 0.176
#> GSM97896 4 0.3969 0.4635 0.004 0.000 0.000 0.692 0.304
#> GSM97898 4 0.2573 0.7024 0.016 0.000 0.000 0.880 0.104
#> GSM97903 1 0.5466 0.4389 0.640 0.000 0.000 0.244 0.116
#> GSM97905 5 0.4350 0.2589 0.004 0.000 0.000 0.408 0.588
#> GSM97906 4 0.0404 0.7180 0.000 0.000 0.000 0.988 0.012
#> GSM97908 4 0.5514 0.4605 0.172 0.000 0.000 0.652 0.176
#> GSM97912 5 0.5443 -0.0197 0.060 0.000 0.000 0.436 0.504
#> GSM97914 1 0.2513 0.7073 0.876 0.000 0.000 0.008 0.116
#> GSM97915 4 0.2189 0.7131 0.012 0.000 0.000 0.904 0.084
#> GSM97917 4 0.4841 0.5455 0.084 0.000 0.000 0.708 0.208
#> GSM97918 4 0.2654 0.7041 0.032 0.000 0.000 0.884 0.084
#> GSM97919 4 0.2915 0.6910 0.024 0.000 0.000 0.860 0.116
#> GSM97922 4 0.4354 0.3421 0.008 0.000 0.000 0.624 0.368
#> GSM97924 2 0.0000 0.9500 0.000 1.000 0.000 0.000 0.000
#> GSM97926 3 0.0510 0.8578 0.000 0.000 0.984 0.000 0.016
#> GSM97930 1 0.5902 0.4774 0.600 0.000 0.000 0.192 0.208
#> GSM97931 2 0.2467 0.8813 0.052 0.908 0.024 0.000 0.016
#> GSM97935 4 0.3359 0.6226 0.084 0.000 0.000 0.844 0.072
#> GSM97936 4 0.1251 0.7210 0.008 0.000 0.000 0.956 0.036
#> GSM97938 4 0.6244 0.2633 0.200 0.000 0.000 0.540 0.260
#> GSM97940 4 0.0404 0.7180 0.000 0.000 0.000 0.988 0.012
#> GSM97942 3 0.3336 0.8370 0.000 0.000 0.772 0.000 0.228
#> GSM97945 4 0.0000 0.7200 0.000 0.000 0.000 1.000 0.000
#> GSM97946 2 0.0000 0.9500 0.000 1.000 0.000 0.000 0.000
#> GSM97948 5 0.5880 -0.2386 0.000 0.000 0.416 0.100 0.484
#> GSM97950 4 0.1357 0.7235 0.004 0.000 0.000 0.948 0.048
#> GSM97952 4 0.0290 0.7189 0.000 0.000 0.000 0.992 0.008
#> GSM97953 4 0.6732 -0.1261 0.352 0.000 0.000 0.392 0.256
#> GSM97954 4 0.5725 0.4178 0.224 0.000 0.000 0.620 0.156
#> GSM97955 4 0.1764 0.7194 0.008 0.000 0.000 0.928 0.064
#> GSM97959 1 0.1965 0.6714 0.924 0.052 0.000 0.000 0.024
#> GSM97961 4 0.1484 0.7212 0.008 0.000 0.000 0.944 0.048
#> GSM97963 4 0.0162 0.7194 0.000 0.000 0.000 0.996 0.004
#> GSM97965 4 0.0290 0.7208 0.000 0.000 0.000 0.992 0.008
#> GSM97966 4 0.0404 0.7180 0.000 0.000 0.000 0.988 0.012
#> GSM97967 2 0.0000 0.9500 0.000 1.000 0.000 0.000 0.000
#> GSM97968 2 0.0000 0.9500 0.000 1.000 0.000 0.000 0.000
#> GSM97969 4 0.3999 0.6191 0.020 0.000 0.000 0.740 0.240
#> GSM97971 4 0.4825 0.2583 0.024 0.000 0.000 0.568 0.408
#> GSM97799 3 0.0162 0.8545 0.000 0.000 0.996 0.000 0.004
#> GSM97823 2 0.0000 0.9500 0.000 1.000 0.000 0.000 0.000
#> GSM97824 3 0.2377 0.8109 0.000 0.000 0.872 0.000 0.128
#> GSM97830 3 0.3586 0.8317 0.000 0.000 0.736 0.000 0.264
#> GSM97835 2 0.4288 0.4467 0.000 0.612 0.384 0.000 0.004
#> GSM97838 2 0.0000 0.9500 0.000 1.000 0.000 0.000 0.000
#> GSM97841 2 0.0000 0.9500 0.000 1.000 0.000 0.000 0.000
#> GSM97842 3 0.0324 0.8534 0.000 0.004 0.992 0.000 0.004
#> GSM97854 2 0.0000 0.9500 0.000 1.000 0.000 0.000 0.000
#> GSM97857 3 0.3196 0.7728 0.004 0.000 0.804 0.000 0.192
#> GSM97860 3 0.3452 0.8332 0.000 0.000 0.756 0.000 0.244
#> GSM97862 3 0.0290 0.8545 0.000 0.000 0.992 0.000 0.008
#> GSM97864 2 0.0000 0.9500 0.000 1.000 0.000 0.000 0.000
#> GSM97866 3 0.0880 0.8605 0.000 0.000 0.968 0.000 0.032
#> GSM97868 3 0.0404 0.8599 0.000 0.000 0.988 0.000 0.012
#> GSM97872 4 0.6210 0.1918 0.148 0.000 0.000 0.492 0.360
#> GSM97873 3 0.0162 0.8545 0.000 0.000 0.996 0.000 0.004
#> GSM97874 3 0.3586 0.8297 0.000 0.000 0.736 0.000 0.264
#> GSM97875 3 0.1908 0.8616 0.000 0.000 0.908 0.000 0.092
#> GSM97876 3 0.3480 0.8338 0.000 0.000 0.752 0.000 0.248
#> GSM97880 3 0.3561 0.8297 0.000 0.000 0.740 0.000 0.260
#> GSM97881 3 0.0290 0.8567 0.000 0.000 0.992 0.000 0.008
#> GSM97884 3 0.0290 0.8542 0.000 0.000 0.992 0.000 0.008
#> GSM97901 3 0.0794 0.8602 0.000 0.000 0.972 0.000 0.028
#> GSM97902 1 0.4494 0.5968 0.608 0.000 0.000 0.012 0.380
#> GSM97909 2 0.0000 0.9500 0.000 1.000 0.000 0.000 0.000
#> GSM97911 3 0.0290 0.8567 0.000 0.000 0.992 0.000 0.008
#> GSM97923 3 0.3395 0.8354 0.000 0.000 0.764 0.000 0.236
#> GSM97928 4 0.4873 0.5460 0.068 0.000 0.000 0.688 0.244
#> GSM97929 2 0.0000 0.9500 0.000 1.000 0.000 0.000 0.000
#> GSM97933 3 0.4015 0.7865 0.000 0.000 0.652 0.000 0.348
#> GSM97934 3 0.4114 0.7590 0.000 0.000 0.624 0.000 0.376
#> GSM97944 3 0.0162 0.8545 0.000 0.000 0.996 0.000 0.004
#> GSM97949 2 0.0000 0.9500 0.000 1.000 0.000 0.000 0.000
#> GSM97956 3 0.1270 0.8448 0.000 0.000 0.948 0.000 0.052
#> GSM97962 3 0.3586 0.8097 0.000 0.000 0.736 0.000 0.264
#> GSM97964 3 0.1732 0.8314 0.000 0.000 0.920 0.000 0.080
#> GSM97970 3 0.0162 0.8545 0.000 0.000 0.996 0.000 0.004
#> GSM97822 4 0.3752 0.3784 0.000 0.000 0.000 0.708 0.292
#> GSM97831 3 0.2377 0.8640 0.000 0.000 0.872 0.000 0.128
#> GSM97845 4 0.5602 0.4556 0.164 0.000 0.000 0.640 0.196
#> GSM97865 1 0.3280 0.7026 0.812 0.000 0.000 0.012 0.176
#> GSM97867 3 0.3480 0.8329 0.000 0.000 0.752 0.000 0.248
#> GSM97883 3 0.3999 0.7677 0.000 0.000 0.656 0.000 0.344
#> GSM97897 4 0.3366 0.4886 0.000 0.000 0.000 0.768 0.232
#> GSM97900 4 0.0404 0.7180 0.000 0.000 0.000 0.988 0.012
#> GSM97904 4 0.4420 0.5669 0.028 0.000 0.000 0.692 0.280
#> GSM97907 2 0.0000 0.9500 0.000 1.000 0.000 0.000 0.000
#> GSM97925 3 0.3074 0.8447 0.000 0.000 0.804 0.000 0.196
#> GSM97947 3 0.3160 0.8400 0.000 0.000 0.808 0.004 0.188
cbind(get_classes(res, k = 6), get_membership(res, k = 6))
#> class entropy silhouette p1 p2 p3 p4 p5 p6
#> GSM97800 2 0.1092 0.9223 0.020 0.960 0.000 0.000 0.020 0.000
#> GSM97803 2 0.1003 0.9237 0.016 0.964 0.000 0.000 0.020 0.000
#> GSM97804 2 0.1176 0.9212 0.024 0.956 0.000 0.000 0.020 0.000
#> GSM97805 2 0.1176 0.9212 0.024 0.956 0.000 0.000 0.020 0.000
#> GSM97807 2 0.0000 0.9282 0.000 1.000 0.000 0.000 0.000 0.000
#> GSM97809 2 0.0000 0.9282 0.000 1.000 0.000 0.000 0.000 0.000
#> GSM97811 2 0.0000 0.9282 0.000 1.000 0.000 0.000 0.000 0.000
#> GSM97812 2 0.0000 0.9282 0.000 1.000 0.000 0.000 0.000 0.000
#> GSM97816 2 0.7153 -0.1796 0.040 0.372 0.020 0.000 0.236 0.332
#> GSM97817 2 0.0000 0.9282 0.000 1.000 0.000 0.000 0.000 0.000
#> GSM97820 2 0.0000 0.9282 0.000 1.000 0.000 0.000 0.000 0.000
#> GSM97825 2 0.0000 0.9282 0.000 1.000 0.000 0.000 0.000 0.000
#> GSM97827 2 0.0000 0.9282 0.000 1.000 0.000 0.000 0.000 0.000
#> GSM97828 6 0.6664 0.4456 0.064 0.016 0.132 0.000 0.256 0.532
#> GSM97833 2 0.0000 0.9282 0.000 1.000 0.000 0.000 0.000 0.000
#> GSM97834 2 0.0000 0.9282 0.000 1.000 0.000 0.000 0.000 0.000
#> GSM97840 2 0.0000 0.9282 0.000 1.000 0.000 0.000 0.000 0.000
#> GSM97846 2 0.0000 0.9282 0.000 1.000 0.000 0.000 0.000 0.000
#> GSM97848 2 0.0000 0.9282 0.000 1.000 0.000 0.000 0.000 0.000
#> GSM97849 2 0.0000 0.9282 0.000 1.000 0.000 0.000 0.000 0.000
#> GSM97850 2 0.0146 0.9278 0.004 0.996 0.000 0.000 0.000 0.000
#> GSM97853 2 0.0000 0.9282 0.000 1.000 0.000 0.000 0.000 0.000
#> GSM97855 2 0.0000 0.9282 0.000 1.000 0.000 0.000 0.000 0.000
#> GSM97878 6 0.7109 0.2752 0.352 0.000 0.000 0.160 0.112 0.376
#> GSM97913 2 0.6194 0.4522 0.088 0.592 0.000 0.000 0.148 0.172
#> GSM97932 4 0.4643 0.4528 0.304 0.000 0.000 0.640 0.008 0.048
#> GSM97939 5 0.5528 0.0478 0.012 0.448 0.068 0.000 0.464 0.008
#> GSM97951 2 0.0000 0.9282 0.000 1.000 0.000 0.000 0.000 0.000
#> GSM97957 3 0.4054 0.4728 0.024 0.000 0.736 0.000 0.220 0.020
#> GSM97972 2 0.5977 0.4166 0.040 0.580 0.000 0.000 0.220 0.160
#> GSM97793 3 0.0000 0.6140 0.000 0.000 1.000 0.000 0.000 0.000
#> GSM97795 2 0.1633 0.9113 0.024 0.932 0.000 0.000 0.044 0.000
#> GSM97802 1 0.7180 0.3431 0.364 0.000 0.272 0.280 0.084 0.000
#> GSM97810 2 0.1787 0.8815 0.008 0.920 0.000 0.000 0.068 0.004
#> GSM97815 2 0.4046 0.7067 0.028 0.744 0.020 0.000 0.208 0.000
#> GSM97837 6 0.5072 0.5169 0.308 0.000 0.000 0.044 0.032 0.616
#> GSM97843 3 0.3073 0.4631 0.008 0.000 0.788 0.000 0.204 0.000
#> GSM97890 3 0.3817 -0.2992 0.000 0.000 0.568 0.000 0.432 0.000
#> GSM97899 4 0.0000 0.6775 0.000 0.000 0.000 1.000 0.000 0.000
#> GSM97910 6 0.4085 0.5838 0.048 0.000 0.028 0.000 0.152 0.772
#> GSM97916 6 0.5658 0.4656 0.348 0.000 0.000 0.004 0.144 0.504
#> GSM97920 3 0.3642 0.5484 0.012 0.000 0.800 0.000 0.140 0.048
#> GSM97921 6 0.4107 0.5825 0.228 0.000 0.000 0.024 0.020 0.728
#> GSM97927 4 0.4489 0.1097 0.328 0.000 0.000 0.632 0.008 0.032
#> GSM97937 6 0.5924 0.2785 0.348 0.000 0.000 0.156 0.012 0.484
#> GSM97941 2 0.0000 0.9282 0.000 1.000 0.000 0.000 0.000 0.000
#> GSM97943 6 0.5699 0.5074 0.096 0.000 0.060 0.000 0.220 0.624
#> GSM97958 2 0.6275 0.0522 0.048 0.464 0.000 0.000 0.120 0.368
#> GSM97960 2 0.0777 0.9156 0.004 0.972 0.000 0.000 0.024 0.000
#> GSM97794 6 0.4858 0.5723 0.180 0.000 0.000 0.000 0.156 0.664
#> GSM97796 4 0.2219 0.6603 0.136 0.000 0.000 0.864 0.000 0.000
#> GSM97797 6 0.4634 0.5736 0.144 0.000 0.000 0.000 0.164 0.692
#> GSM97798 4 0.0260 0.6753 0.008 0.000 0.000 0.992 0.000 0.000
#> GSM97801 6 0.3918 0.6084 0.108 0.000 0.000 0.000 0.124 0.768
#> GSM97806 4 0.3505 0.6153 0.092 0.000 0.000 0.824 0.016 0.068
#> GSM97808 4 0.0260 0.6753 0.008 0.000 0.000 0.992 0.000 0.000
#> GSM97813 4 0.4461 -0.1964 0.464 0.000 0.000 0.512 0.020 0.004
#> GSM97814 4 0.0260 0.6753 0.008 0.000 0.000 0.992 0.000 0.000
#> GSM97818 6 0.4358 0.5942 0.184 0.000 0.000 0.000 0.100 0.716
#> GSM97819 3 0.3101 0.3753 0.000 0.000 0.756 0.000 0.244 0.000
#> GSM97821 2 0.1633 0.9115 0.024 0.932 0.000 0.000 0.044 0.000
#> GSM97826 1 0.5457 0.2503 0.604 0.000 0.000 0.212 0.008 0.176
#> GSM97829 6 0.5636 0.4653 0.296 0.000 0.000 0.088 0.036 0.580
#> GSM97832 2 0.1616 0.9119 0.020 0.932 0.000 0.000 0.048 0.000
#> GSM97836 4 0.3450 0.5001 0.208 0.000 0.000 0.772 0.012 0.008
#> GSM97839 4 0.2544 0.6555 0.140 0.000 0.000 0.852 0.004 0.004
#> GSM97844 2 0.1176 0.9212 0.024 0.956 0.000 0.000 0.020 0.000
#> GSM97847 1 0.6454 0.0280 0.416 0.000 0.000 0.296 0.020 0.268
#> GSM97851 4 0.4555 0.4525 0.308 0.000 0.000 0.640 0.004 0.048
#> GSM97852 4 0.5641 0.2132 0.364 0.000 0.000 0.504 0.008 0.124
#> GSM97856 4 0.0000 0.6775 0.000 0.000 0.000 1.000 0.000 0.000
#> GSM97858 2 0.1176 0.9212 0.024 0.956 0.000 0.000 0.020 0.000
#> GSM97859 1 0.4429 0.3012 0.548 0.000 0.000 0.424 0.028 0.000
#> GSM97861 4 0.1594 0.6435 0.052 0.000 0.000 0.932 0.000 0.016
#> GSM97863 4 0.2520 0.6515 0.152 0.000 0.000 0.844 0.004 0.000
#> GSM97869 1 0.6101 0.0557 0.576 0.000 0.000 0.104 0.076 0.244
#> GSM97870 1 0.6319 0.4460 0.524 0.000 0.084 0.328 0.036 0.028
#> GSM97871 4 0.0146 0.6765 0.004 0.000 0.000 0.996 0.000 0.000
#> GSM97877 2 0.5350 0.6333 0.080 0.688 0.000 0.000 0.108 0.124
#> GSM97879 4 0.2065 0.6525 0.052 0.000 0.000 0.912 0.004 0.032
#> GSM97882 4 0.4380 0.2014 0.312 0.000 0.000 0.652 0.024 0.012
#> GSM97885 4 0.6033 -0.2304 0.360 0.000 0.000 0.480 0.024 0.136
#> GSM97886 4 0.1644 0.6772 0.076 0.000 0.000 0.920 0.004 0.000
#> GSM97887 4 0.0260 0.6753 0.008 0.000 0.000 0.992 0.000 0.000
#> GSM97888 4 0.4199 0.1543 0.416 0.000 0.000 0.568 0.016 0.000
#> GSM97889 4 0.3852 0.1630 0.324 0.000 0.000 0.664 0.012 0.000
#> GSM97891 4 0.3956 0.5133 0.072 0.000 0.000 0.792 0.024 0.112
#> GSM97892 2 0.1003 0.9234 0.016 0.964 0.000 0.000 0.020 0.000
#> GSM97893 4 0.4901 0.4035 0.316 0.000 0.000 0.608 0.004 0.072
#> GSM97894 4 0.2879 0.6367 0.176 0.000 0.000 0.816 0.004 0.004
#> GSM97895 4 0.4347 0.4909 0.288 0.000 0.000 0.668 0.004 0.040
#> GSM97896 4 0.4049 0.3268 0.332 0.000 0.000 0.648 0.020 0.000
#> GSM97898 4 0.3089 0.6244 0.188 0.000 0.000 0.800 0.004 0.008
#> GSM97903 6 0.6966 0.2908 0.320 0.000 0.000 0.168 0.092 0.420
#> GSM97905 1 0.6285 0.3016 0.400 0.000 0.392 0.188 0.020 0.000
#> GSM97906 4 0.0260 0.6753 0.008 0.000 0.000 0.992 0.000 0.000
#> GSM97908 4 0.5212 0.3719 0.312 0.000 0.000 0.588 0.008 0.092
#> GSM97912 1 0.5141 0.4741 0.648 0.000 0.036 0.272 0.028 0.016
#> GSM97914 6 0.3750 0.6022 0.200 0.000 0.000 0.016 0.020 0.764
#> GSM97915 4 0.2595 0.6476 0.160 0.000 0.000 0.836 0.004 0.000
#> GSM97917 4 0.4976 0.3842 0.324 0.000 0.000 0.596 0.004 0.076
#> GSM97918 4 0.3277 0.6186 0.188 0.000 0.000 0.792 0.004 0.016
#> GSM97919 4 0.3340 0.6141 0.196 0.000 0.000 0.784 0.004 0.016
#> GSM97922 1 0.4366 0.2607 0.548 0.000 0.000 0.428 0.024 0.000
#> GSM97924 2 0.1003 0.9233 0.020 0.964 0.000 0.000 0.016 0.000
#> GSM97926 3 0.3868 -0.4597 0.000 0.000 0.508 0.000 0.492 0.000
#> GSM97930 1 0.6034 -0.3517 0.444 0.000 0.000 0.112 0.032 0.412
#> GSM97931 2 0.5531 0.6594 0.064 0.684 0.016 0.000 0.160 0.076
#> GSM97935 4 0.3650 0.4899 0.116 0.000 0.000 0.792 0.000 0.092
#> GSM97936 4 0.1531 0.6790 0.068 0.000 0.000 0.928 0.004 0.000
#> GSM97938 4 0.6335 -0.0652 0.356 0.000 0.000 0.404 0.016 0.224
#> GSM97940 4 0.0146 0.6765 0.004 0.000 0.000 0.996 0.000 0.000
#> GSM97942 3 0.0790 0.6134 0.000 0.000 0.968 0.000 0.032 0.000
#> GSM97945 4 0.0000 0.6775 0.000 0.000 0.000 1.000 0.000 0.000
#> GSM97946 2 0.0000 0.9282 0.000 1.000 0.000 0.000 0.000 0.000
#> GSM97948 3 0.4533 0.3634 0.216 0.000 0.712 0.036 0.036 0.000
#> GSM97950 4 0.1610 0.6774 0.084 0.000 0.000 0.916 0.000 0.000
#> GSM97952 4 0.0146 0.6765 0.004 0.000 0.000 0.996 0.000 0.000
#> GSM97953 6 0.6552 -0.0817 0.324 0.000 0.000 0.312 0.020 0.344
#> GSM97954 4 0.5728 0.1984 0.364 0.000 0.000 0.500 0.012 0.124
#> GSM97955 4 0.1908 0.6750 0.096 0.000 0.000 0.900 0.004 0.000
#> GSM97959 6 0.5698 0.5504 0.136 0.072 0.000 0.000 0.144 0.648
#> GSM97961 4 0.1700 0.6773 0.080 0.000 0.000 0.916 0.004 0.000
#> GSM97963 4 0.0000 0.6775 0.000 0.000 0.000 1.000 0.000 0.000
#> GSM97965 4 0.0000 0.6775 0.000 0.000 0.000 1.000 0.000 0.000
#> GSM97966 4 0.0260 0.6753 0.008 0.000 0.000 0.992 0.000 0.000
#> GSM97967 2 0.0000 0.9282 0.000 1.000 0.000 0.000 0.000 0.000
#> GSM97968 2 0.0000 0.9282 0.000 1.000 0.000 0.000 0.000 0.000
#> GSM97969 4 0.4464 0.4451 0.340 0.000 0.000 0.624 0.008 0.028
#> GSM97971 1 0.4273 0.3607 0.596 0.000 0.000 0.380 0.024 0.000
#> GSM97799 5 0.3854 0.5324 0.000 0.000 0.464 0.000 0.536 0.000
#> GSM97823 2 0.0000 0.9282 0.000 1.000 0.000 0.000 0.000 0.000
#> GSM97824 5 0.3986 0.4749 0.004 0.000 0.384 0.000 0.608 0.004
#> GSM97830 3 0.1444 0.6107 0.000 0.000 0.928 0.000 0.072 0.000
#> GSM97835 5 0.5667 0.2157 0.024 0.360 0.092 0.000 0.524 0.000
#> GSM97838 2 0.1088 0.9224 0.024 0.960 0.000 0.000 0.016 0.000
#> GSM97841 2 0.1088 0.9226 0.024 0.960 0.000 0.000 0.016 0.000
#> GSM97842 5 0.3966 0.5555 0.000 0.004 0.444 0.000 0.552 0.000
#> GSM97854 2 0.1176 0.9212 0.024 0.956 0.000 0.000 0.020 0.000
#> GSM97857 5 0.4835 0.3100 0.040 0.000 0.340 0.000 0.604 0.016
#> GSM97860 3 0.0865 0.6143 0.000 0.000 0.964 0.000 0.036 0.000
#> GSM97862 3 0.3993 -0.4468 0.004 0.000 0.520 0.000 0.476 0.000
#> GSM97864 2 0.1176 0.9212 0.024 0.956 0.000 0.000 0.020 0.000
#> GSM97866 3 0.4098 -0.3530 0.004 0.000 0.548 0.000 0.444 0.004
#> GSM97868 3 0.3864 -0.4418 0.000 0.000 0.520 0.000 0.480 0.000
#> GSM97872 1 0.5888 0.1489 0.500 0.000 0.000 0.364 0.028 0.108
#> GSM97873 5 0.3971 0.5556 0.004 0.000 0.448 0.000 0.548 0.000
#> GSM97874 3 0.0692 0.6131 0.000 0.000 0.976 0.000 0.020 0.004
#> GSM97875 3 0.3464 0.2026 0.000 0.000 0.688 0.000 0.312 0.000
#> GSM97876 3 0.0790 0.6127 0.000 0.000 0.968 0.000 0.032 0.000
#> GSM97880 3 0.0713 0.6076 0.000 0.000 0.972 0.000 0.028 0.000
#> GSM97881 3 0.3869 -0.4959 0.000 0.000 0.500 0.000 0.500 0.000
#> GSM97884 5 0.3975 0.5545 0.004 0.000 0.452 0.000 0.544 0.000
#> GSM97901 3 0.3930 -0.2344 0.004 0.000 0.576 0.000 0.420 0.000
#> GSM97902 6 0.6340 0.5125 0.140 0.000 0.064 0.012 0.196 0.588
#> GSM97909 2 0.1003 0.9233 0.020 0.964 0.000 0.000 0.016 0.000
#> GSM97911 5 0.3866 0.4834 0.000 0.000 0.484 0.000 0.516 0.000
#> GSM97923 3 0.0632 0.6136 0.000 0.000 0.976 0.000 0.024 0.000
#> GSM97928 4 0.5051 0.3437 0.304 0.000 0.000 0.612 0.012 0.072
#> GSM97929 2 0.1176 0.9212 0.024 0.956 0.000 0.000 0.020 0.000
#> GSM97933 3 0.2631 0.5459 0.012 0.000 0.856 0.000 0.128 0.004
#> GSM97934 3 0.3829 0.4901 0.016 0.000 0.760 0.000 0.200 0.024
#> GSM97944 5 0.3847 0.5482 0.000 0.000 0.456 0.000 0.544 0.000
#> GSM97949 2 0.0000 0.9282 0.000 1.000 0.000 0.000 0.000 0.000
#> GSM97956 5 0.4195 0.4864 0.004 0.000 0.440 0.000 0.548 0.008
#> GSM97962 3 0.4368 0.2999 0.020 0.000 0.640 0.000 0.328 0.012
#> GSM97964 5 0.4090 0.4877 0.008 0.000 0.384 0.000 0.604 0.004
#> GSM97970 5 0.3975 0.5545 0.004 0.000 0.452 0.000 0.544 0.000
#> GSM97822 4 0.4474 -0.1179 0.412 0.000 0.000 0.560 0.024 0.004
#> GSM97831 3 0.3672 0.2348 0.008 0.000 0.688 0.000 0.304 0.000
#> GSM97845 4 0.5365 0.3057 0.332 0.000 0.000 0.552 0.004 0.112
#> GSM97865 6 0.4691 0.5725 0.256 0.000 0.000 0.024 0.044 0.676
#> GSM97867 3 0.0260 0.6138 0.000 0.000 0.992 0.000 0.008 0.000
#> GSM97883 3 0.2655 0.5549 0.060 0.000 0.876 0.000 0.060 0.004
#> GSM97897 4 0.3215 0.3769 0.240 0.000 0.000 0.756 0.004 0.000
#> GSM97900 4 0.0260 0.6753 0.008 0.000 0.000 0.992 0.000 0.000
#> GSM97904 4 0.5254 0.3375 0.312 0.000 0.000 0.600 0.032 0.056
#> GSM97907 2 0.1176 0.9212 0.024 0.956 0.000 0.000 0.020 0.000
#> GSM97925 3 0.1531 0.5996 0.004 0.000 0.928 0.000 0.068 0.000
#> GSM97947 3 0.3588 0.5202 0.060 0.000 0.788 0.000 0.152 0.000
Heatmaps for the consensus matrix. It visualizes the probability of two samples to be in a same group.
consensus_heatmap(res, k = 2)
consensus_heatmap(res, k = 3)
consensus_heatmap(res, k = 4)
consensus_heatmap(res, k = 5)
consensus_heatmap(res, k = 6)
Heatmaps for the membership of samples in all partitions to see how consistent they are:
membership_heatmap(res, k = 2)
membership_heatmap(res, k = 3)
membership_heatmap(res, k = 4)
membership_heatmap(res, k = 5)
membership_heatmap(res, k = 6)
As soon as we have had the classes for columns, we can look for signatures which are significantly different between classes which can be candidate marks for certain classes. Following are the heatmaps for signatures.
Signature heatmaps where rows are scaled:
get_signatures(res, k = 2)
get_signatures(res, k = 3)
get_signatures(res, k = 4)
get_signatures(res, k = 5)
get_signatures(res, k = 6)
Signature heatmaps where rows are not scaled:
get_signatures(res, k = 2, scale_rows = FALSE)
get_signatures(res, k = 3, scale_rows = FALSE)
get_signatures(res, k = 4, scale_rows = FALSE)
get_signatures(res, k = 5, scale_rows = FALSE)
get_signatures(res, k = 6, scale_rows = FALSE)
Compare the overlap of signatures from different k:
compare_signatures(res)
get_signature() returns a data frame invisibly. TO get the list of signatures, the function
call should be assigned to a variable explicitly. In following code, if plot argument is set
to FALSE, no heatmap is plotted while only the differential analysis is performed.
# code only for demonstration
tb = get_signature(res, k = ..., plot = FALSE)
An example of the output of tb is:
#> which_row fdr mean_1 mean_2 scaled_mean_1 scaled_mean_2 km
#> 1 38 0.042760348 8.373488 9.131774 -0.5533452 0.5164555 1
#> 2 40 0.018707592 7.106213 8.469186 -0.6173731 0.5762149 1
#> 3 55 0.019134737 10.221463 11.207825 -0.6159697 0.5749050 1
#> 4 59 0.006059896 5.921854 7.869574 -0.6899429 0.6439467 1
#> 5 60 0.018055526 8.928898 10.211722 -0.6204761 0.5791110 1
#> 6 98 0.009384629 15.714769 14.887706 0.6635654 -0.6193277 2
...
The columns in tb are:
which_row: row indices corresponding to the input matrix.fdr: FDR for the differential test. mean_x: The mean value in group x.scaled_mean_x: The mean value in group x after rows are scaled.km: Row groups if k-means clustering is applied to rows.UMAP plot which shows how samples are separated.
dimension_reduction(res, k = 2, method = "UMAP")
dimension_reduction(res, k = 3, method = "UMAP")
dimension_reduction(res, k = 4, method = "UMAP")
dimension_reduction(res, k = 5, method = "UMAP")
dimension_reduction(res, k = 6, method = "UMAP")
Following heatmap shows how subgroups are split when increasing k:
collect_classes(res)
Test correlation between subgroups and known annotations. If the known annotation is numeric, one-way ANOVA test is applied, and if the known annotation is discrete, chi-squared contingency table test is applied.
test_to_known_factors(res)
#> n disease.state(p) tissue(p) k
#> CV:skmeans 175 1.18e-14 1.97e-17 2
#> CV:skmeans 176 2.23e-26 1.30e-25 3
#> CV:skmeans 176 2.73e-26 2.22e-24 4
#> CV:skmeans 147 4.07e-24 7.51e-23 5
#> CV:skmeans 112 1.48e-16 5.21e-17 6
If matrix rows can be associated to genes, consider to use functional_enrichment(res,
...) to perform function enrichment for the signature genes. See this vignette for more detailed explanations.
The object with results only for a single top-value method and a single partition method can be extracted as:
res = res_list["CV", "pam"]
# you can also extract it by
# res = res_list["CV:pam"]
A summary of res and all the functions that can be applied to it:
res
#> A 'ConsensusPartition' object with k = 2, 3, 4, 5, 6.
#> On a matrix with 51882 rows and 180 columns.
#> Top rows (1000, 2000, 3000, 4000, 5000) are extracted by 'CV' method.
#> Subgroups are detected by 'pam' method.
#> Performed in total 1250 partitions by row resampling.
#> Best k for subgroups seems to be 2.
#>
#> Following methods can be applied to this 'ConsensusPartition' object:
#> [1] "cola_report" "collect_classes" "collect_plots"
#> [4] "collect_stats" "colnames" "compare_signatures"
#> [7] "consensus_heatmap" "dimension_reduction" "functional_enrichment"
#> [10] "get_anno_col" "get_anno" "get_classes"
#> [13] "get_consensus" "get_matrix" "get_membership"
#> [16] "get_param" "get_signatures" "get_stats"
#> [19] "is_best_k" "is_stable_k" "membership_heatmap"
#> [22] "ncol" "nrow" "plot_ecdf"
#> [25] "rownames" "select_partition_number" "show"
#> [28] "suggest_best_k" "test_to_known_factors"
collect_plots() function collects all the plots made from res for all k (number of partitions)
into one single page to provide an easy and fast comparison between different k.
collect_plots(res)
The plots are:
k and the heatmap of
predicted classes for each k.k.k.k.All the plots in panels can be made by individual functions and they are plotted later in this section.
select_partition_number() produces several plots showing different
statistics for choosing “optimized” k. There are following statistics:
k;k, the area increased is defined as \(A_k - A_{k-1}\).The detailed explanations of these statistics can be found in the cola vignette.
Generally speaking, lower PAC score, higher mean silhouette score or higher
concordance corresponds to better partition. Rand index and Jaccard index
measure how similar the current partition is compared to partition with k-1.
If they are too similar, we won't accept k is better than k-1.
select_partition_number(res)
The numeric values for all these statistics can be obtained by get_stats().
get_stats(res)
#> k 1-PAC mean_silhouette concordance area_increased Rand Jaccard
#> 2 2 1.000 0.978 0.990 0.4077 0.597 0.597
#> 3 3 0.669 0.806 0.901 0.5370 0.731 0.566
#> 4 4 0.783 0.779 0.909 0.1928 0.822 0.559
#> 5 5 0.770 0.629 0.797 0.0648 0.925 0.722
#> 6 6 0.874 0.849 0.922 0.0420 0.919 0.646
suggest_best_k() suggests the best \(k\) based on these statistics. The rules are as follows:
suggest_best_k(res)
#> [1] 2
Following shows the table of the partitions (You need to click the show/hide
code output link to see it). The membership matrix (columns with name p*)
is inferred by
clue::cl_consensus()
function with the SE method. Basically the value in the membership matrix
represents the probability to belong to a certain group. The finall class
label for an item is determined with the group with highest probability it
belongs to.
In get_classes() function, the entropy is calculated from the membership
matrix and the silhouette score is calculated from the consensus matrix.
cbind(get_classes(res, k = 2), get_membership(res, k = 2))
#> class entropy silhouette p1 p2
#> GSM97800 2 0.0000 0.990 0.000 1.000
#> GSM97803 2 0.0000 0.990 0.000 1.000
#> GSM97804 2 0.0000 0.990 0.000 1.000
#> GSM97805 2 0.0000 0.990 0.000 1.000
#> GSM97807 2 0.0000 0.990 0.000 1.000
#> GSM97809 2 0.0000 0.990 0.000 1.000
#> GSM97811 2 0.0000 0.990 0.000 1.000
#> GSM97812 2 0.0000 0.990 0.000 1.000
#> GSM97816 2 0.0000 0.990 0.000 1.000
#> GSM97817 2 0.0000 0.990 0.000 1.000
#> GSM97820 2 0.0000 0.990 0.000 1.000
#> GSM97825 2 0.0000 0.990 0.000 1.000
#> GSM97827 2 0.0000 0.990 0.000 1.000
#> GSM97828 2 0.6343 0.811 0.160 0.840
#> GSM97833 2 0.0000 0.990 0.000 1.000
#> GSM97834 2 0.0000 0.990 0.000 1.000
#> GSM97840 2 0.0000 0.990 0.000 1.000
#> GSM97846 2 0.0000 0.990 0.000 1.000
#> GSM97848 2 0.0000 0.990 0.000 1.000
#> GSM97849 2 0.0000 0.990 0.000 1.000
#> GSM97850 2 0.0000 0.990 0.000 1.000
#> GSM97853 2 0.0000 0.990 0.000 1.000
#> GSM97855 2 0.0000 0.990 0.000 1.000
#> GSM97878 1 0.0000 0.990 1.000 0.000
#> GSM97913 2 0.7745 0.704 0.228 0.772
#> GSM97932 1 0.0000 0.990 1.000 0.000
#> GSM97939 2 0.0000 0.990 0.000 1.000
#> GSM97951 2 0.0000 0.990 0.000 1.000
#> GSM97957 1 0.0000 0.990 1.000 0.000
#> GSM97972 2 0.0938 0.980 0.012 0.988
#> GSM97793 1 0.0000 0.990 1.000 0.000
#> GSM97795 2 0.0000 0.990 0.000 1.000
#> GSM97802 1 0.0000 0.990 1.000 0.000
#> GSM97810 2 0.0000 0.990 0.000 1.000
#> GSM97815 2 0.0000 0.990 0.000 1.000
#> GSM97837 1 0.0000 0.990 1.000 0.000
#> GSM97843 1 0.0000 0.990 1.000 0.000
#> GSM97890 1 0.0000 0.990 1.000 0.000
#> GSM97899 1 0.0000 0.990 1.000 0.000
#> GSM97910 1 0.0000 0.990 1.000 0.000
#> GSM97916 1 0.0000 0.990 1.000 0.000
#> GSM97920 1 0.0000 0.990 1.000 0.000
#> GSM97921 1 0.0000 0.990 1.000 0.000
#> GSM97927 1 0.0000 0.990 1.000 0.000
#> GSM97937 1 0.0000 0.990 1.000 0.000
#> GSM97941 2 0.0000 0.990 0.000 1.000
#> GSM97943 1 0.0000 0.990 1.000 0.000
#> GSM97958 1 0.6623 0.795 0.828 0.172
#> GSM97960 2 0.0000 0.990 0.000 1.000
#> GSM97794 1 0.0000 0.990 1.000 0.000
#> GSM97796 1 0.0000 0.990 1.000 0.000
#> GSM97797 1 0.0000 0.990 1.000 0.000
#> GSM97798 1 0.0000 0.990 1.000 0.000
#> GSM97801 1 0.0000 0.990 1.000 0.000
#> GSM97806 1 0.0000 0.990 1.000 0.000
#> GSM97808 1 0.0000 0.990 1.000 0.000
#> GSM97813 1 0.0000 0.990 1.000 0.000
#> GSM97814 1 0.0000 0.990 1.000 0.000
#> GSM97818 1 0.0000 0.990 1.000 0.000
#> GSM97819 1 0.0000 0.990 1.000 0.000
#> GSM97821 1 0.6247 0.819 0.844 0.156
#> GSM97826 1 0.0000 0.990 1.000 0.000
#> GSM97829 1 0.0000 0.990 1.000 0.000
#> GSM97832 2 0.0000 0.990 0.000 1.000
#> GSM97836 1 0.0000 0.990 1.000 0.000
#> GSM97839 1 0.0000 0.990 1.000 0.000
#> GSM97844 2 0.0000 0.990 0.000 1.000
#> GSM97847 1 0.0000 0.990 1.000 0.000
#> GSM97851 1 0.0000 0.990 1.000 0.000
#> GSM97852 1 0.0000 0.990 1.000 0.000
#> GSM97856 1 0.0000 0.990 1.000 0.000
#> GSM97858 2 0.0000 0.990 0.000 1.000
#> GSM97859 1 0.0000 0.990 1.000 0.000
#> GSM97861 1 0.0000 0.990 1.000 0.000
#> GSM97863 1 0.0000 0.990 1.000 0.000
#> GSM97869 1 0.0000 0.990 1.000 0.000
#> GSM97870 1 0.0000 0.990 1.000 0.000
#> GSM97871 1 0.0000 0.990 1.000 0.000
#> GSM97877 1 0.1633 0.969 0.976 0.024
#> GSM97879 1 0.0000 0.990 1.000 0.000
#> GSM97882 1 0.0000 0.990 1.000 0.000
#> GSM97885 1 0.0000 0.990 1.000 0.000
#> GSM97886 1 0.0000 0.990 1.000 0.000
#> GSM97887 1 0.0000 0.990 1.000 0.000
#> GSM97888 1 0.0000 0.990 1.000 0.000
#> GSM97889 1 0.0000 0.990 1.000 0.000
#> GSM97891 1 0.0000 0.990 1.000 0.000
#> GSM97892 2 0.0000 0.990 0.000 1.000
#> GSM97893 1 0.0000 0.990 1.000 0.000
#> GSM97894 1 0.0000 0.990 1.000 0.000
#> GSM97895 1 0.0000 0.990 1.000 0.000
#> GSM97896 1 0.0000 0.990 1.000 0.000
#> GSM97898 1 0.0000 0.990 1.000 0.000
#> GSM97903 1 0.0000 0.990 1.000 0.000
#> GSM97905 1 0.0000 0.990 1.000 0.000
#> GSM97906 1 0.0000 0.990 1.000 0.000
#> GSM97908 1 0.0000 0.990 1.000 0.000
#> GSM97912 1 0.0000 0.990 1.000 0.000
#> GSM97914 1 0.0000 0.990 1.000 0.000
#> GSM97915 1 0.0000 0.990 1.000 0.000
#> GSM97917 1 0.0000 0.990 1.000 0.000
#> GSM97918 1 0.0000 0.990 1.000 0.000
#> GSM97919 1 0.0000 0.990 1.000 0.000
#> GSM97922 1 0.0000 0.990 1.000 0.000
#> GSM97924 2 0.0000 0.990 0.000 1.000
#> GSM97926 1 0.0000 0.990 1.000 0.000
#> GSM97930 1 0.0000 0.990 1.000 0.000
#> GSM97931 1 0.0000 0.990 1.000 0.000
#> GSM97935 1 0.0000 0.990 1.000 0.000
#> GSM97936 1 0.0000 0.990 1.000 0.000
#> GSM97938 1 0.0000 0.990 1.000 0.000
#> GSM97940 1 0.0000 0.990 1.000 0.000
#> GSM97942 1 0.0000 0.990 1.000 0.000
#> GSM97945 1 0.0000 0.990 1.000 0.000
#> GSM97946 2 0.0000 0.990 0.000 1.000
#> GSM97948 1 0.0000 0.990 1.000 0.000
#> GSM97950 1 0.0000 0.990 1.000 0.000
#> GSM97952 1 0.0000 0.990 1.000 0.000
#> GSM97953 1 0.0000 0.990 1.000 0.000
#> GSM97954 1 0.0000 0.990 1.000 0.000
#> GSM97955 1 0.0000 0.990 1.000 0.000
#> GSM97959 1 0.1414 0.972 0.980 0.020
#> GSM97961 1 0.0000 0.990 1.000 0.000
#> GSM97963 1 0.0000 0.990 1.000 0.000
#> GSM97965 1 0.0000 0.990 1.000 0.000
#> GSM97966 1 0.0000 0.990 1.000 0.000
#> GSM97967 2 0.0000 0.990 0.000 1.000
#> GSM97968 2 0.0000 0.990 0.000 1.000
#> GSM97969 1 0.0000 0.990 1.000 0.000
#> GSM97971 1 0.0000 0.990 1.000 0.000
#> GSM97799 1 0.0938 0.980 0.988 0.012
#> GSM97823 2 0.0000 0.990 0.000 1.000
#> GSM97824 1 0.0000 0.990 1.000 0.000
#> GSM97830 1 0.0000 0.990 1.000 0.000
#> GSM97835 2 0.3114 0.936 0.056 0.944
#> GSM97838 2 0.0000 0.990 0.000 1.000
#> GSM97841 2 0.0000 0.990 0.000 1.000
#> GSM97842 1 0.6247 0.819 0.844 0.156
#> GSM97854 2 0.0000 0.990 0.000 1.000
#> GSM97857 1 0.0672 0.983 0.992 0.008
#> GSM97860 1 0.0000 0.990 1.000 0.000
#> GSM97862 1 0.0000 0.990 1.000 0.000
#> GSM97864 2 0.0000 0.990 0.000 1.000
#> GSM97866 1 0.0000 0.990 1.000 0.000
#> GSM97868 1 0.0000 0.990 1.000 0.000
#> GSM97872 1 0.0000 0.990 1.000 0.000
#> GSM97873 1 0.6343 0.813 0.840 0.160
#> GSM97874 1 0.0000 0.990 1.000 0.000
#> GSM97875 1 0.0000 0.990 1.000 0.000
#> GSM97876 1 0.0000 0.990 1.000 0.000
#> GSM97880 1 0.0000 0.990 1.000 0.000
#> GSM97881 1 0.0000 0.990 1.000 0.000
#> GSM97884 1 0.4690 0.889 0.900 0.100
#> GSM97901 1 0.0000 0.990 1.000 0.000
#> GSM97902 1 0.0000 0.990 1.000 0.000
#> GSM97909 2 0.0938 0.980 0.012 0.988
#> GSM97911 1 0.0000 0.990 1.000 0.000
#> GSM97923 1 0.0000 0.990 1.000 0.000
#> GSM97928 1 0.0000 0.990 1.000 0.000
#> GSM97929 2 0.0000 0.990 0.000 1.000
#> GSM97933 1 0.0000 0.990 1.000 0.000
#> GSM97934 1 0.0000 0.990 1.000 0.000
#> GSM97944 1 0.2423 0.953 0.960 0.040
#> GSM97949 2 0.0000 0.990 0.000 1.000
#> GSM97956 1 0.0000 0.990 1.000 0.000
#> GSM97962 1 0.0000 0.990 1.000 0.000
#> GSM97964 1 0.0000 0.990 1.000 0.000
#> GSM97970 1 0.9775 0.309 0.588 0.412
#> GSM97822 1 0.0000 0.990 1.000 0.000
#> GSM97831 1 0.0000 0.990 1.000 0.000
#> GSM97845 1 0.0000 0.990 1.000 0.000
#> GSM97865 1 0.0000 0.990 1.000 0.000
#> GSM97867 1 0.0000 0.990 1.000 0.000
#> GSM97883 1 0.0000 0.990 1.000 0.000
#> GSM97897 1 0.0000 0.990 1.000 0.000
#> GSM97900 1 0.0000 0.990 1.000 0.000
#> GSM97904 1 0.0000 0.990 1.000 0.000
#> GSM97907 2 0.0000 0.990 0.000 1.000
#> GSM97925 1 0.0000 0.990 1.000 0.000
#> GSM97947 1 0.0000 0.990 1.000 0.000
cbind(get_classes(res, k = 3), get_membership(res, k = 3))
#> class entropy silhouette p1 p2 p3
#> GSM97800 2 0.0000 0.9909 0.000 1.000 0.000
#> GSM97803 2 0.0000 0.9909 0.000 1.000 0.000
#> GSM97804 2 0.0000 0.9909 0.000 1.000 0.000
#> GSM97805 2 0.0000 0.9909 0.000 1.000 0.000
#> GSM97807 2 0.0000 0.9909 0.000 1.000 0.000
#> GSM97809 2 0.0000 0.9909 0.000 1.000 0.000
#> GSM97811 2 0.0000 0.9909 0.000 1.000 0.000
#> GSM97812 2 0.0000 0.9909 0.000 1.000 0.000
#> GSM97816 3 0.5529 0.4968 0.000 0.296 0.704
#> GSM97817 2 0.0000 0.9909 0.000 1.000 0.000
#> GSM97820 2 0.0000 0.9909 0.000 1.000 0.000
#> GSM97825 2 0.0000 0.9909 0.000 1.000 0.000
#> GSM97827 2 0.0000 0.9909 0.000 1.000 0.000
#> GSM97828 3 0.2434 0.8328 0.036 0.024 0.940
#> GSM97833 2 0.0000 0.9909 0.000 1.000 0.000
#> GSM97834 2 0.0000 0.9909 0.000 1.000 0.000
#> GSM97840 2 0.0000 0.9909 0.000 1.000 0.000
#> GSM97846 2 0.0000 0.9909 0.000 1.000 0.000
#> GSM97848 2 0.0000 0.9909 0.000 1.000 0.000
#> GSM97849 2 0.0000 0.9909 0.000 1.000 0.000
#> GSM97850 2 0.0000 0.9909 0.000 1.000 0.000
#> GSM97853 2 0.0000 0.9909 0.000 1.000 0.000
#> GSM97855 2 0.0000 0.9909 0.000 1.000 0.000
#> GSM97878 1 0.5058 0.7671 0.756 0.000 0.244
#> GSM97913 3 0.7581 0.2552 0.044 0.408 0.548
#> GSM97932 1 0.0000 0.8462 1.000 0.000 0.000
#> GSM97939 3 0.4504 0.6400 0.000 0.196 0.804
#> GSM97951 2 0.0000 0.9909 0.000 1.000 0.000
#> GSM97957 3 0.0000 0.8576 0.000 0.000 1.000
#> GSM97972 3 0.2959 0.7713 0.000 0.100 0.900
#> GSM97793 3 0.6235 -0.0323 0.436 0.000 0.564
#> GSM97795 2 0.2711 0.8969 0.000 0.912 0.088
#> GSM97802 1 0.5810 0.6614 0.664 0.000 0.336
#> GSM97810 3 0.6252 0.1585 0.000 0.444 0.556
#> GSM97815 3 0.3686 0.7455 0.000 0.140 0.860
#> GSM97837 3 0.5138 0.6167 0.252 0.000 0.748
#> GSM97843 3 0.0000 0.8576 0.000 0.000 1.000
#> GSM97890 1 0.6295 0.3700 0.528 0.000 0.472
#> GSM97899 1 0.0000 0.8462 1.000 0.000 0.000
#> GSM97910 3 0.5678 0.4652 0.316 0.000 0.684
#> GSM97916 1 0.5016 0.7703 0.760 0.000 0.240
#> GSM97920 3 0.0000 0.8576 0.000 0.000 1.000
#> GSM97921 3 0.6026 0.3038 0.376 0.000 0.624
#> GSM97927 1 0.4796 0.7841 0.780 0.000 0.220
#> GSM97937 1 0.3752 0.8160 0.856 0.000 0.144
#> GSM97941 2 0.0000 0.9909 0.000 1.000 0.000
#> GSM97943 3 0.2448 0.8085 0.076 0.000 0.924
#> GSM97958 3 0.1267 0.8448 0.004 0.024 0.972
#> GSM97960 2 0.1753 0.9438 0.000 0.952 0.048
#> GSM97794 1 0.5058 0.7671 0.756 0.000 0.244
#> GSM97796 1 0.0000 0.8462 1.000 0.000 0.000
#> GSM97797 1 0.5098 0.7640 0.752 0.000 0.248
#> GSM97798 1 0.0000 0.8462 1.000 0.000 0.000
#> GSM97801 3 0.5621 0.4909 0.308 0.000 0.692
#> GSM97806 1 0.4796 0.7841 0.780 0.000 0.220
#> GSM97808 1 0.0000 0.8462 1.000 0.000 0.000
#> GSM97813 1 0.0892 0.8448 0.980 0.000 0.020
#> GSM97814 1 0.0000 0.8462 1.000 0.000 0.000
#> GSM97818 1 0.5291 0.7458 0.732 0.000 0.268
#> GSM97819 1 0.6215 0.4830 0.572 0.000 0.428
#> GSM97821 1 0.7379 0.6045 0.616 0.048 0.336
#> GSM97826 1 0.0000 0.8462 1.000 0.000 0.000
#> GSM97829 1 0.4931 0.7764 0.768 0.000 0.232
#> GSM97832 3 0.4974 0.5782 0.000 0.236 0.764
#> GSM97836 1 0.4842 0.7816 0.776 0.000 0.224
#> GSM97839 1 0.0000 0.8462 1.000 0.000 0.000
#> GSM97844 2 0.0000 0.9909 0.000 1.000 0.000
#> GSM97847 1 0.0747 0.8453 0.984 0.000 0.016
#> GSM97851 1 0.0000 0.8462 1.000 0.000 0.000
#> GSM97852 1 0.3340 0.8234 0.880 0.000 0.120
#> GSM97856 1 0.0000 0.8462 1.000 0.000 0.000
#> GSM97858 2 0.0000 0.9909 0.000 1.000 0.000
#> GSM97859 1 0.4702 0.7883 0.788 0.000 0.212
#> GSM97861 1 0.5138 0.7618 0.748 0.000 0.252
#> GSM97863 1 0.0000 0.8462 1.000 0.000 0.000
#> GSM97869 1 0.5058 0.7671 0.756 0.000 0.244
#> GSM97870 1 0.5016 0.7706 0.760 0.000 0.240
#> GSM97871 1 0.0000 0.8462 1.000 0.000 0.000
#> GSM97877 1 0.7372 0.7173 0.688 0.092 0.220
#> GSM97879 1 0.3686 0.8171 0.860 0.000 0.140
#> GSM97882 1 0.4796 0.7841 0.780 0.000 0.220
#> GSM97885 1 0.4796 0.7841 0.780 0.000 0.220
#> GSM97886 1 0.0000 0.8462 1.000 0.000 0.000
#> GSM97887 1 0.0000 0.8462 1.000 0.000 0.000
#> GSM97888 1 0.0000 0.8462 1.000 0.000 0.000
#> GSM97889 1 0.4931 0.7784 0.768 0.000 0.232
#> GSM97891 1 0.4796 0.7841 0.780 0.000 0.220
#> GSM97892 2 0.0000 0.9909 0.000 1.000 0.000
#> GSM97893 1 0.0000 0.8462 1.000 0.000 0.000
#> GSM97894 1 0.0000 0.8462 1.000 0.000 0.000
#> GSM97895 1 0.0000 0.8462 1.000 0.000 0.000
#> GSM97896 1 0.0000 0.8462 1.000 0.000 0.000
#> GSM97898 1 0.0000 0.8462 1.000 0.000 0.000
#> GSM97903 1 0.4796 0.7841 0.780 0.000 0.220
#> GSM97905 1 0.4842 0.7816 0.776 0.000 0.224
#> GSM97906 1 0.0000 0.8462 1.000 0.000 0.000
#> GSM97908 1 0.0000 0.8462 1.000 0.000 0.000
#> GSM97912 1 0.4931 0.7767 0.768 0.000 0.232
#> GSM97914 1 0.4931 0.7760 0.768 0.000 0.232
#> GSM97915 1 0.0000 0.8462 1.000 0.000 0.000
#> GSM97917 1 0.0000 0.8462 1.000 0.000 0.000
#> GSM97918 1 0.0000 0.8462 1.000 0.000 0.000
#> GSM97919 1 0.0000 0.8462 1.000 0.000 0.000
#> GSM97922 1 0.0000 0.8462 1.000 0.000 0.000
#> GSM97924 2 0.0000 0.9909 0.000 1.000 0.000
#> GSM97926 1 0.5650 0.6941 0.688 0.000 0.312
#> GSM97930 1 0.1163 0.8436 0.972 0.000 0.028
#> GSM97931 1 0.5733 0.6781 0.676 0.000 0.324
#> GSM97935 1 0.4842 0.7816 0.776 0.000 0.224
#> GSM97936 1 0.0000 0.8462 1.000 0.000 0.000
#> GSM97938 1 0.1411 0.8424 0.964 0.000 0.036
#> GSM97940 1 0.0000 0.8462 1.000 0.000 0.000
#> GSM97942 1 0.5988 0.6085 0.632 0.000 0.368
#> GSM97945 1 0.0000 0.8462 1.000 0.000 0.000
#> GSM97946 2 0.0000 0.9909 0.000 1.000 0.000
#> GSM97948 1 0.5650 0.6941 0.688 0.000 0.312
#> GSM97950 1 0.0000 0.8462 1.000 0.000 0.000
#> GSM97952 1 0.0000 0.8462 1.000 0.000 0.000
#> GSM97953 1 0.0000 0.8462 1.000 0.000 0.000
#> GSM97954 1 0.0000 0.8462 1.000 0.000 0.000
#> GSM97955 1 0.0000 0.8462 1.000 0.000 0.000
#> GSM97959 1 0.6719 0.7564 0.744 0.096 0.160
#> GSM97961 1 0.0000 0.8462 1.000 0.000 0.000
#> GSM97963 1 0.0000 0.8462 1.000 0.000 0.000
#> GSM97965 1 0.0000 0.8462 1.000 0.000 0.000
#> GSM97966 1 0.0000 0.8462 1.000 0.000 0.000
#> GSM97967 2 0.0000 0.9909 0.000 1.000 0.000
#> GSM97968 2 0.0000 0.9909 0.000 1.000 0.000
#> GSM97969 1 0.0747 0.8451 0.984 0.000 0.016
#> GSM97971 1 0.2625 0.8322 0.916 0.000 0.084
#> GSM97799 3 0.0592 0.8523 0.012 0.000 0.988
#> GSM97823 2 0.0000 0.9909 0.000 1.000 0.000
#> GSM97824 3 0.0000 0.8576 0.000 0.000 1.000
#> GSM97830 3 0.0000 0.8576 0.000 0.000 1.000
#> GSM97835 3 0.0592 0.8520 0.000 0.012 0.988
#> GSM97838 2 0.0000 0.9909 0.000 1.000 0.000
#> GSM97841 2 0.0000 0.9909 0.000 1.000 0.000
#> GSM97842 3 0.0000 0.8576 0.000 0.000 1.000
#> GSM97854 2 0.0000 0.9909 0.000 1.000 0.000
#> GSM97857 3 0.0000 0.8576 0.000 0.000 1.000
#> GSM97860 3 0.1529 0.8339 0.040 0.000 0.960
#> GSM97862 3 0.0000 0.8576 0.000 0.000 1.000
#> GSM97864 2 0.0000 0.9909 0.000 1.000 0.000
#> GSM97866 3 0.0000 0.8576 0.000 0.000 1.000
#> GSM97868 3 0.0000 0.8576 0.000 0.000 1.000
#> GSM97872 1 0.5948 0.6120 0.640 0.000 0.360
#> GSM97873 3 0.0000 0.8576 0.000 0.000 1.000
#> GSM97874 3 0.0000 0.8576 0.000 0.000 1.000
#> GSM97875 1 0.6307 0.3221 0.512 0.000 0.488
#> GSM97876 3 0.0000 0.8576 0.000 0.000 1.000
#> GSM97880 3 0.0000 0.8576 0.000 0.000 1.000
#> GSM97881 3 0.5968 0.2412 0.364 0.000 0.636
#> GSM97884 3 0.0000 0.8576 0.000 0.000 1.000
#> GSM97901 3 0.0000 0.8576 0.000 0.000 1.000
#> GSM97902 3 0.4702 0.6598 0.212 0.000 0.788
#> GSM97909 2 0.4963 0.7291 0.008 0.792 0.200
#> GSM97911 3 0.0892 0.8478 0.020 0.000 0.980
#> GSM97923 3 0.5016 0.5742 0.240 0.000 0.760
#> GSM97928 1 0.5560 0.7108 0.700 0.000 0.300
#> GSM97929 2 0.0000 0.9909 0.000 1.000 0.000
#> GSM97933 3 0.1289 0.8412 0.032 0.000 0.968
#> GSM97934 3 0.0000 0.8576 0.000 0.000 1.000
#> GSM97944 3 0.0000 0.8576 0.000 0.000 1.000
#> GSM97949 2 0.0000 0.9909 0.000 1.000 0.000
#> GSM97956 3 0.0000 0.8576 0.000 0.000 1.000
#> GSM97962 3 0.0000 0.8576 0.000 0.000 1.000
#> GSM97964 3 0.0000 0.8576 0.000 0.000 1.000
#> GSM97970 3 0.0000 0.8576 0.000 0.000 1.000
#> GSM97822 1 0.5178 0.7583 0.744 0.000 0.256
#> GSM97831 3 0.0000 0.8576 0.000 0.000 1.000
#> GSM97845 1 0.0000 0.8462 1.000 0.000 0.000
#> GSM97865 3 0.5138 0.5988 0.252 0.000 0.748
#> GSM97867 3 0.6260 -0.1086 0.448 0.000 0.552
#> GSM97883 3 0.5591 0.4614 0.304 0.000 0.696
#> GSM97897 1 0.0424 0.8459 0.992 0.000 0.008
#> GSM97900 1 0.0000 0.8462 1.000 0.000 0.000
#> GSM97904 1 0.5216 0.7536 0.740 0.000 0.260
#> GSM97907 2 0.0000 0.9909 0.000 1.000 0.000
#> GSM97925 1 0.6299 0.3586 0.524 0.000 0.476
#> GSM97947 1 0.6045 0.5868 0.620 0.000 0.380
cbind(get_classes(res, k = 4), get_membership(res, k = 4))
#> class entropy silhouette p1 p2 p3 p4
#> GSM97800 2 0.0000 0.9763 0.000 1.000 0.000 0.000
#> GSM97803 2 0.0000 0.9763 0.000 1.000 0.000 0.000
#> GSM97804 2 0.0000 0.9763 0.000 1.000 0.000 0.000
#> GSM97805 2 0.0000 0.9763 0.000 1.000 0.000 0.000
#> GSM97807 2 0.0000 0.9763 0.000 1.000 0.000 0.000
#> GSM97809 2 0.0000 0.9763 0.000 1.000 0.000 0.000
#> GSM97811 2 0.0000 0.9763 0.000 1.000 0.000 0.000
#> GSM97812 2 0.0000 0.9763 0.000 1.000 0.000 0.000
#> GSM97816 3 0.5610 0.6301 0.104 0.176 0.720 0.000
#> GSM97817 2 0.0000 0.9763 0.000 1.000 0.000 0.000
#> GSM97820 2 0.0000 0.9763 0.000 1.000 0.000 0.000
#> GSM97825 2 0.0000 0.9763 0.000 1.000 0.000 0.000
#> GSM97827 2 0.0000 0.9763 0.000 1.000 0.000 0.000
#> GSM97828 3 0.4011 0.6574 0.208 0.008 0.784 0.000
#> GSM97833 2 0.0000 0.9763 0.000 1.000 0.000 0.000
#> GSM97834 2 0.0000 0.9763 0.000 1.000 0.000 0.000
#> GSM97840 2 0.0000 0.9763 0.000 1.000 0.000 0.000
#> GSM97846 2 0.0000 0.9763 0.000 1.000 0.000 0.000
#> GSM97848 2 0.0000 0.9763 0.000 1.000 0.000 0.000
#> GSM97849 2 0.0000 0.9763 0.000 1.000 0.000 0.000
#> GSM97850 2 0.0000 0.9763 0.000 1.000 0.000 0.000
#> GSM97853 2 0.0000 0.9763 0.000 1.000 0.000 0.000
#> GSM97855 2 0.0000 0.9763 0.000 1.000 0.000 0.000
#> GSM97878 1 0.0336 0.8048 0.992 0.000 0.008 0.000
#> GSM97913 1 0.7397 -0.0290 0.428 0.164 0.408 0.000
#> GSM97932 4 0.0000 0.9658 0.000 0.000 0.000 1.000
#> GSM97939 3 0.0336 0.8557 0.000 0.008 0.992 0.000
#> GSM97951 2 0.0000 0.9763 0.000 1.000 0.000 0.000
#> GSM97957 3 0.0000 0.8599 0.000 0.000 1.000 0.000
#> GSM97972 3 0.4313 0.5791 0.260 0.004 0.736 0.000
#> GSM97793 3 0.4277 0.5366 0.280 0.000 0.720 0.000
#> GSM97795 2 0.4222 0.6024 0.000 0.728 0.272 0.000
#> GSM97802 1 0.4855 0.3416 0.600 0.000 0.400 0.000
#> GSM97810 3 0.5000 -0.0105 0.000 0.500 0.500 0.000
#> GSM97815 3 0.2149 0.7974 0.000 0.088 0.912 0.000
#> GSM97837 1 0.4933 0.1831 0.568 0.000 0.432 0.000
#> GSM97843 3 0.0000 0.8599 0.000 0.000 1.000 0.000
#> GSM97890 3 0.4790 0.3043 0.380 0.000 0.620 0.000
#> GSM97899 4 0.0000 0.9658 0.000 0.000 0.000 1.000
#> GSM97910 1 0.4955 0.1517 0.556 0.000 0.444 0.000
#> GSM97916 1 0.0000 0.8057 1.000 0.000 0.000 0.000
#> GSM97920 3 0.1474 0.8284 0.052 0.000 0.948 0.000
#> GSM97921 1 0.4356 0.4910 0.708 0.000 0.292 0.000
#> GSM97927 1 0.0000 0.8057 1.000 0.000 0.000 0.000
#> GSM97937 1 0.0000 0.8057 1.000 0.000 0.000 0.000
#> GSM97941 2 0.0000 0.9763 0.000 1.000 0.000 0.000
#> GSM97943 3 0.4941 0.1992 0.436 0.000 0.564 0.000
#> GSM97958 3 0.4713 0.3911 0.360 0.000 0.640 0.000
#> GSM97960 2 0.2469 0.8568 0.000 0.892 0.108 0.000
#> GSM97794 1 0.0000 0.8057 1.000 0.000 0.000 0.000
#> GSM97796 4 0.0000 0.9658 0.000 0.000 0.000 1.000
#> GSM97797 1 0.0336 0.8045 0.992 0.000 0.008 0.000
#> GSM97798 4 0.0000 0.9658 0.000 0.000 0.000 1.000
#> GSM97801 1 0.4730 0.3563 0.636 0.000 0.364 0.000
#> GSM97806 1 0.0000 0.8057 1.000 0.000 0.000 0.000
#> GSM97808 4 0.0000 0.9658 0.000 0.000 0.000 1.000
#> GSM97813 1 0.0188 0.8057 0.996 0.000 0.000 0.004
#> GSM97814 4 0.0000 0.9658 0.000 0.000 0.000 1.000
#> GSM97818 1 0.0707 0.7988 0.980 0.000 0.020 0.000
#> GSM97819 1 0.4961 0.2163 0.552 0.000 0.448 0.000
#> GSM97821 1 0.5179 0.5953 0.728 0.052 0.220 0.000
#> GSM97826 1 0.2814 0.7448 0.868 0.000 0.000 0.132
#> GSM97829 1 0.0000 0.8057 1.000 0.000 0.000 0.000
#> GSM97832 3 0.1022 0.8417 0.000 0.032 0.968 0.000
#> GSM97836 1 0.0592 0.8024 0.984 0.000 0.016 0.000
#> GSM97839 4 0.0000 0.9658 0.000 0.000 0.000 1.000
#> GSM97844 2 0.0000 0.9763 0.000 1.000 0.000 0.000
#> GSM97847 1 0.0336 0.8049 0.992 0.000 0.000 0.008
#> GSM97851 4 0.0000 0.9658 0.000 0.000 0.000 1.000
#> GSM97852 1 0.0000 0.8057 1.000 0.000 0.000 0.000
#> GSM97856 4 0.0000 0.9658 0.000 0.000 0.000 1.000
#> GSM97858 2 0.0000 0.9763 0.000 1.000 0.000 0.000
#> GSM97859 1 0.0188 0.8057 0.996 0.000 0.000 0.004
#> GSM97861 1 0.0188 0.8055 0.996 0.000 0.004 0.000
#> GSM97863 4 0.0000 0.9658 0.000 0.000 0.000 1.000
#> GSM97869 1 0.0000 0.8057 1.000 0.000 0.000 0.000
#> GSM97870 1 0.0188 0.8056 0.996 0.000 0.004 0.000
#> GSM97871 4 0.0000 0.9658 0.000 0.000 0.000 1.000
#> GSM97877 1 0.0000 0.8057 1.000 0.000 0.000 0.000
#> GSM97879 1 0.3024 0.7383 0.852 0.000 0.000 0.148
#> GSM97882 1 0.0592 0.8024 0.984 0.000 0.016 0.000
#> GSM97885 1 0.0000 0.8057 1.000 0.000 0.000 0.000
#> GSM97886 4 0.0000 0.9658 0.000 0.000 0.000 1.000
#> GSM97887 4 0.5050 0.2045 0.408 0.000 0.004 0.588
#> GSM97888 1 0.4661 0.4697 0.652 0.000 0.000 0.348
#> GSM97889 1 0.4599 0.7167 0.800 0.000 0.088 0.112
#> GSM97891 1 0.0000 0.8057 1.000 0.000 0.000 0.000
#> GSM97892 2 0.0000 0.9763 0.000 1.000 0.000 0.000
#> GSM97893 4 0.0000 0.9658 0.000 0.000 0.000 1.000
#> GSM97894 4 0.3172 0.7823 0.160 0.000 0.000 0.840
#> GSM97895 4 0.3123 0.7895 0.156 0.000 0.000 0.844
#> GSM97896 4 0.1637 0.9128 0.060 0.000 0.000 0.940
#> GSM97898 4 0.0000 0.9658 0.000 0.000 0.000 1.000
#> GSM97903 1 0.0000 0.8057 1.000 0.000 0.000 0.000
#> GSM97905 1 0.3831 0.6621 0.792 0.000 0.204 0.004
#> GSM97906 4 0.0469 0.9561 0.012 0.000 0.000 0.988
#> GSM97908 1 0.4998 0.0890 0.512 0.000 0.000 0.488
#> GSM97912 1 0.3080 0.7555 0.880 0.000 0.096 0.024
#> GSM97914 1 0.0000 0.8057 1.000 0.000 0.000 0.000
#> GSM97915 4 0.0000 0.9658 0.000 0.000 0.000 1.000
#> GSM97917 4 0.0000 0.9658 0.000 0.000 0.000 1.000
#> GSM97918 4 0.0000 0.9658 0.000 0.000 0.000 1.000
#> GSM97919 4 0.0000 0.9658 0.000 0.000 0.000 1.000
#> GSM97922 1 0.4624 0.4791 0.660 0.000 0.000 0.340
#> GSM97924 2 0.0000 0.9763 0.000 1.000 0.000 0.000
#> GSM97926 1 0.4406 0.5326 0.700 0.000 0.300 0.000
#> GSM97930 1 0.0336 0.8047 0.992 0.000 0.000 0.008
#> GSM97931 1 0.1792 0.7787 0.932 0.000 0.068 0.000
#> GSM97935 1 0.0000 0.8057 1.000 0.000 0.000 0.000
#> GSM97936 4 0.0000 0.9658 0.000 0.000 0.000 1.000
#> GSM97938 1 0.1792 0.7813 0.932 0.000 0.000 0.068
#> GSM97940 4 0.0000 0.9658 0.000 0.000 0.000 1.000
#> GSM97942 1 0.4977 0.1858 0.540 0.000 0.460 0.000
#> GSM97945 4 0.0000 0.9658 0.000 0.000 0.000 1.000
#> GSM97946 2 0.0000 0.9763 0.000 1.000 0.000 0.000
#> GSM97948 1 0.2868 0.7295 0.864 0.000 0.136 0.000
#> GSM97950 4 0.0000 0.9658 0.000 0.000 0.000 1.000
#> GSM97952 4 0.0000 0.9658 0.000 0.000 0.000 1.000
#> GSM97953 1 0.3311 0.7156 0.828 0.000 0.000 0.172
#> GSM97954 1 0.4804 0.3971 0.616 0.000 0.000 0.384
#> GSM97955 4 0.0000 0.9658 0.000 0.000 0.000 1.000
#> GSM97959 1 0.0336 0.8040 0.992 0.000 0.008 0.000
#> GSM97961 4 0.0000 0.9658 0.000 0.000 0.000 1.000
#> GSM97963 4 0.0000 0.9658 0.000 0.000 0.000 1.000
#> GSM97965 4 0.0000 0.9658 0.000 0.000 0.000 1.000
#> GSM97966 4 0.0000 0.9658 0.000 0.000 0.000 1.000
#> GSM97967 2 0.0000 0.9763 0.000 1.000 0.000 0.000
#> GSM97968 2 0.0000 0.9763 0.000 1.000 0.000 0.000
#> GSM97969 1 0.4933 0.2777 0.568 0.000 0.000 0.432
#> GSM97971 1 0.0000 0.8057 1.000 0.000 0.000 0.000
#> GSM97799 3 0.0336 0.8565 0.008 0.000 0.992 0.000
#> GSM97823 2 0.0000 0.9763 0.000 1.000 0.000 0.000
#> GSM97824 3 0.0000 0.8599 0.000 0.000 1.000 0.000
#> GSM97830 3 0.0000 0.8599 0.000 0.000 1.000 0.000
#> GSM97835 3 0.0000 0.8599 0.000 0.000 1.000 0.000
#> GSM97838 2 0.0000 0.9763 0.000 1.000 0.000 0.000
#> GSM97841 2 0.0000 0.9763 0.000 1.000 0.000 0.000
#> GSM97842 3 0.0000 0.8599 0.000 0.000 1.000 0.000
#> GSM97854 2 0.0000 0.9763 0.000 1.000 0.000 0.000
#> GSM97857 3 0.0000 0.8599 0.000 0.000 1.000 0.000
#> GSM97860 3 0.1211 0.8363 0.040 0.000 0.960 0.000
#> GSM97862 3 0.0000 0.8599 0.000 0.000 1.000 0.000
#> GSM97864 2 0.0000 0.9763 0.000 1.000 0.000 0.000
#> GSM97866 3 0.0000 0.8599 0.000 0.000 1.000 0.000
#> GSM97868 3 0.0000 0.8599 0.000 0.000 1.000 0.000
#> GSM97872 1 0.4222 0.5944 0.728 0.000 0.272 0.000
#> GSM97873 3 0.0000 0.8599 0.000 0.000 1.000 0.000
#> GSM97874 3 0.0000 0.8599 0.000 0.000 1.000 0.000
#> GSM97875 3 0.4746 0.3360 0.368 0.000 0.632 0.000
#> GSM97876 3 0.0000 0.8599 0.000 0.000 1.000 0.000
#> GSM97880 3 0.0000 0.8599 0.000 0.000 1.000 0.000
#> GSM97881 3 0.4164 0.5625 0.264 0.000 0.736 0.000
#> GSM97884 3 0.0000 0.8599 0.000 0.000 1.000 0.000
#> GSM97901 3 0.0000 0.8599 0.000 0.000 1.000 0.000
#> GSM97902 1 0.4989 0.0642 0.528 0.000 0.472 0.000
#> GSM97909 2 0.7463 0.0646 0.384 0.440 0.176 0.000
#> GSM97911 3 0.0707 0.8500 0.020 0.000 0.980 0.000
#> GSM97923 3 0.3400 0.6914 0.180 0.000 0.820 0.000
#> GSM97928 1 0.3907 0.6306 0.768 0.000 0.232 0.000
#> GSM97929 2 0.0000 0.9763 0.000 1.000 0.000 0.000
#> GSM97933 3 0.1557 0.8239 0.056 0.000 0.944 0.000
#> GSM97934 3 0.0188 0.8583 0.004 0.000 0.996 0.000
#> GSM97944 3 0.0000 0.8599 0.000 0.000 1.000 0.000
#> GSM97949 2 0.0000 0.9763 0.000 1.000 0.000 0.000
#> GSM97956 3 0.0000 0.8599 0.000 0.000 1.000 0.000
#> GSM97962 3 0.0000 0.8599 0.000 0.000 1.000 0.000
#> GSM97964 3 0.0000 0.8599 0.000 0.000 1.000 0.000
#> GSM97970 3 0.0000 0.8599 0.000 0.000 1.000 0.000
#> GSM97822 1 0.0469 0.8037 0.988 0.000 0.012 0.000
#> GSM97831 3 0.0000 0.8599 0.000 0.000 1.000 0.000
#> GSM97845 4 0.2647 0.8463 0.120 0.000 0.000 0.880
#> GSM97865 1 0.4817 0.2933 0.612 0.000 0.388 0.000
#> GSM97867 3 0.4543 0.4419 0.324 0.000 0.676 0.000
#> GSM97883 3 0.4730 0.3635 0.364 0.000 0.636 0.000
#> GSM97897 1 0.4697 0.4505 0.644 0.000 0.000 0.356
#> GSM97900 4 0.1940 0.8923 0.076 0.000 0.000 0.924
#> GSM97904 1 0.0336 0.8047 0.992 0.000 0.008 0.000
#> GSM97907 2 0.0000 0.9763 0.000 1.000 0.000 0.000
#> GSM97925 3 0.4843 0.2620 0.396 0.000 0.604 0.000
#> GSM97947 1 0.5000 0.0683 0.504 0.000 0.496 0.000
cbind(get_classes(res, k = 5), get_membership(res, k = 5))
#> class entropy silhouette p1 p2 p3 p4 p5
#> GSM97800 2 0.0000 0.9814 0.000 1.000 0.000 0.000 0.000
#> GSM97803 2 0.0000 0.9814 0.000 1.000 0.000 0.000 0.000
#> GSM97804 2 0.0000 0.9814 0.000 1.000 0.000 0.000 0.000
#> GSM97805 2 0.0000 0.9814 0.000 1.000 0.000 0.000 0.000
#> GSM97807 2 0.0000 0.9814 0.000 1.000 0.000 0.000 0.000
#> GSM97809 2 0.0000 0.9814 0.000 1.000 0.000 0.000 0.000
#> GSM97811 2 0.0000 0.9814 0.000 1.000 0.000 0.000 0.000
#> GSM97812 2 0.0000 0.9814 0.000 1.000 0.000 0.000 0.000
#> GSM97816 3 0.4968 0.4137 0.016 0.140 0.740 0.000 0.104
#> GSM97817 2 0.0000 0.9814 0.000 1.000 0.000 0.000 0.000
#> GSM97820 2 0.0000 0.9814 0.000 1.000 0.000 0.000 0.000
#> GSM97825 2 0.0000 0.9814 0.000 1.000 0.000 0.000 0.000
#> GSM97827 2 0.0000 0.9814 0.000 1.000 0.000 0.000 0.000
#> GSM97828 3 0.3476 0.4329 0.020 0.000 0.804 0.000 0.176
#> GSM97833 2 0.0000 0.9814 0.000 1.000 0.000 0.000 0.000
#> GSM97834 2 0.0000 0.9814 0.000 1.000 0.000 0.000 0.000
#> GSM97840 2 0.0000 0.9814 0.000 1.000 0.000 0.000 0.000
#> GSM97846 2 0.0000 0.9814 0.000 1.000 0.000 0.000 0.000
#> GSM97848 2 0.0000 0.9814 0.000 1.000 0.000 0.000 0.000
#> GSM97849 2 0.0000 0.9814 0.000 1.000 0.000 0.000 0.000
#> GSM97850 2 0.0000 0.9814 0.000 1.000 0.000 0.000 0.000
#> GSM97853 2 0.0000 0.9814 0.000 1.000 0.000 0.000 0.000
#> GSM97855 2 0.0000 0.9814 0.000 1.000 0.000 0.000 0.000
#> GSM97878 1 0.1270 0.6723 0.948 0.000 0.000 0.000 0.052
#> GSM97913 5 0.7345 0.3708 0.160 0.072 0.268 0.000 0.500
#> GSM97932 4 0.0162 0.9704 0.000 0.000 0.000 0.996 0.004
#> GSM97939 3 0.2280 0.6597 0.000 0.000 0.880 0.000 0.120
#> GSM97951 2 0.0000 0.9814 0.000 1.000 0.000 0.000 0.000
#> GSM97957 3 0.0290 0.6409 0.000 0.000 0.992 0.000 0.008
#> GSM97972 3 0.4456 0.2760 0.020 0.000 0.660 0.000 0.320
#> GSM97793 1 0.6499 0.0286 0.440 0.000 0.368 0.000 0.192
#> GSM97795 2 0.5929 0.0183 0.000 0.464 0.104 0.000 0.432
#> GSM97802 1 0.4333 0.4930 0.752 0.000 0.060 0.000 0.188
#> GSM97810 3 0.4287 0.0571 0.000 0.460 0.540 0.000 0.000
#> GSM97815 3 0.5678 0.5633 0.000 0.084 0.524 0.000 0.392
#> GSM97837 5 0.6362 0.3727 0.184 0.000 0.320 0.000 0.496
#> GSM97843 3 0.1965 0.6561 0.000 0.000 0.904 0.000 0.096
#> GSM97890 5 0.6232 -0.4201 0.152 0.000 0.356 0.000 0.492
#> GSM97899 4 0.0000 0.9717 0.000 0.000 0.000 1.000 0.000
#> GSM97910 5 0.6229 0.3834 0.192 0.000 0.268 0.000 0.540
#> GSM97916 1 0.4297 -0.0257 0.528 0.000 0.000 0.000 0.472
#> GSM97920 3 0.2179 0.6578 0.000 0.000 0.888 0.000 0.112
#> GSM97921 5 0.6180 0.2565 0.360 0.000 0.144 0.000 0.496
#> GSM97927 1 0.0510 0.6725 0.984 0.000 0.000 0.000 0.016
#> GSM97937 1 0.4297 -0.0241 0.528 0.000 0.000 0.000 0.472
#> GSM97941 2 0.0000 0.9814 0.000 1.000 0.000 0.000 0.000
#> GSM97943 3 0.4794 0.0720 0.032 0.000 0.624 0.000 0.344
#> GSM97958 5 0.5443 0.1607 0.060 0.000 0.436 0.000 0.504
#> GSM97960 2 0.2605 0.7923 0.000 0.852 0.148 0.000 0.000
#> GSM97794 1 0.4307 -0.0826 0.504 0.000 0.000 0.000 0.496
#> GSM97796 4 0.0000 0.9717 0.000 0.000 0.000 1.000 0.000
#> GSM97797 1 0.4452 -0.0907 0.500 0.000 0.004 0.000 0.496
#> GSM97798 4 0.0000 0.9717 0.000 0.000 0.000 1.000 0.000
#> GSM97801 5 0.6459 0.3567 0.244 0.000 0.256 0.000 0.500
#> GSM97806 1 0.4171 0.2188 0.604 0.000 0.000 0.000 0.396
#> GSM97808 4 0.0000 0.9717 0.000 0.000 0.000 1.000 0.000
#> GSM97813 1 0.0162 0.6718 0.996 0.000 0.000 0.000 0.004
#> GSM97814 4 0.0000 0.9717 0.000 0.000 0.000 1.000 0.000
#> GSM97818 5 0.4452 0.0273 0.496 0.000 0.004 0.000 0.500
#> GSM97819 1 0.6651 -0.0163 0.444 0.000 0.300 0.000 0.256
#> GSM97821 5 0.3339 0.1939 0.072 0.004 0.072 0.000 0.852
#> GSM97826 1 0.5785 0.2359 0.568 0.000 0.000 0.112 0.320
#> GSM97829 1 0.2929 0.5748 0.840 0.000 0.008 0.000 0.152
#> GSM97832 3 0.3231 0.6525 0.000 0.004 0.800 0.000 0.196
#> GSM97836 1 0.1608 0.6658 0.928 0.000 0.000 0.000 0.072
#> GSM97839 4 0.0000 0.9717 0.000 0.000 0.000 1.000 0.000
#> GSM97844 2 0.0000 0.9814 0.000 1.000 0.000 0.000 0.000
#> GSM97847 5 0.4452 0.0206 0.496 0.000 0.000 0.004 0.500
#> GSM97851 4 0.0162 0.9704 0.000 0.000 0.000 0.996 0.004
#> GSM97852 1 0.0404 0.6706 0.988 0.000 0.000 0.000 0.012
#> GSM97856 4 0.0000 0.9717 0.000 0.000 0.000 1.000 0.000
#> GSM97858 2 0.0000 0.9814 0.000 1.000 0.000 0.000 0.000
#> GSM97859 1 0.0162 0.6728 0.996 0.000 0.000 0.004 0.000
#> GSM97861 1 0.0703 0.6728 0.976 0.000 0.000 0.000 0.024
#> GSM97863 4 0.0162 0.9704 0.000 0.000 0.000 0.996 0.004
#> GSM97869 1 0.3707 0.3986 0.716 0.000 0.000 0.000 0.284
#> GSM97870 1 0.0404 0.6733 0.988 0.000 0.000 0.000 0.012
#> GSM97871 4 0.0000 0.9717 0.000 0.000 0.000 1.000 0.000
#> GSM97877 5 0.4307 0.0159 0.500 0.000 0.000 0.000 0.500
#> GSM97879 1 0.2408 0.6535 0.892 0.000 0.000 0.092 0.016
#> GSM97882 1 0.0794 0.6732 0.972 0.000 0.000 0.000 0.028
#> GSM97885 1 0.3636 0.4212 0.728 0.000 0.000 0.000 0.272
#> GSM97886 4 0.0000 0.9717 0.000 0.000 0.000 1.000 0.000
#> GSM97887 1 0.4505 0.3455 0.604 0.000 0.000 0.384 0.012
#> GSM97888 1 0.3086 0.5780 0.816 0.000 0.000 0.180 0.004
#> GSM97889 1 0.2342 0.6628 0.916 0.000 0.020 0.024 0.040
#> GSM97891 1 0.4210 0.1366 0.588 0.000 0.000 0.000 0.412
#> GSM97892 2 0.0000 0.9814 0.000 1.000 0.000 0.000 0.000
#> GSM97893 4 0.0162 0.9704 0.000 0.000 0.000 0.996 0.004
#> GSM97894 4 0.3430 0.6996 0.220 0.000 0.000 0.776 0.004
#> GSM97895 4 0.3177 0.7173 0.208 0.000 0.000 0.792 0.000
#> GSM97896 4 0.1768 0.9033 0.072 0.000 0.000 0.924 0.004
#> GSM97898 4 0.0162 0.9704 0.000 0.000 0.000 0.996 0.004
#> GSM97903 1 0.4030 0.2686 0.648 0.000 0.000 0.000 0.352
#> GSM97905 1 0.2859 0.6393 0.876 0.000 0.056 0.000 0.068
#> GSM97906 4 0.0510 0.9590 0.016 0.000 0.000 0.984 0.000
#> GSM97908 1 0.5956 0.2236 0.476 0.000 0.000 0.416 0.108
#> GSM97912 1 0.2104 0.6647 0.924 0.000 0.024 0.008 0.044
#> GSM97914 1 0.4307 -0.0826 0.504 0.000 0.000 0.000 0.496
#> GSM97915 4 0.0162 0.9704 0.000 0.000 0.000 0.996 0.004
#> GSM97917 4 0.0162 0.9704 0.000 0.000 0.000 0.996 0.004
#> GSM97918 4 0.0000 0.9717 0.000 0.000 0.000 1.000 0.000
#> GSM97919 4 0.0000 0.9717 0.000 0.000 0.000 1.000 0.000
#> GSM97922 1 0.2233 0.6421 0.892 0.000 0.000 0.104 0.004
#> GSM97924 2 0.0000 0.9814 0.000 1.000 0.000 0.000 0.000
#> GSM97926 1 0.2798 0.6151 0.852 0.000 0.008 0.000 0.140
#> GSM97930 5 0.4452 0.0236 0.496 0.000 0.000 0.004 0.500
#> GSM97931 5 0.4718 0.0207 0.444 0.000 0.016 0.000 0.540
#> GSM97935 1 0.0963 0.6640 0.964 0.000 0.000 0.000 0.036
#> GSM97936 4 0.0000 0.9717 0.000 0.000 0.000 1.000 0.000
#> GSM97938 1 0.2754 0.6471 0.880 0.000 0.000 0.040 0.080
#> GSM97940 4 0.0000 0.9717 0.000 0.000 0.000 1.000 0.000
#> GSM97942 1 0.6374 0.0858 0.468 0.000 0.172 0.000 0.360
#> GSM97945 4 0.0000 0.9717 0.000 0.000 0.000 1.000 0.000
#> GSM97946 2 0.0000 0.9814 0.000 1.000 0.000 0.000 0.000
#> GSM97948 1 0.2597 0.6385 0.884 0.000 0.024 0.000 0.092
#> GSM97950 4 0.0000 0.9717 0.000 0.000 0.000 1.000 0.000
#> GSM97952 4 0.0000 0.9717 0.000 0.000 0.000 1.000 0.000
#> GSM97953 1 0.5026 0.5206 0.716 0.000 0.004 0.120 0.160
#> GSM97954 1 0.3727 0.5593 0.768 0.000 0.000 0.216 0.016
#> GSM97955 4 0.0162 0.9704 0.000 0.000 0.000 0.996 0.004
#> GSM97959 5 0.4307 0.0175 0.500 0.000 0.000 0.000 0.500
#> GSM97961 4 0.0000 0.9717 0.000 0.000 0.000 1.000 0.000
#> GSM97963 4 0.0000 0.9717 0.000 0.000 0.000 1.000 0.000
#> GSM97965 4 0.0000 0.9717 0.000 0.000 0.000 1.000 0.000
#> GSM97966 4 0.0000 0.9717 0.000 0.000 0.000 1.000 0.000
#> GSM97967 2 0.0000 0.9814 0.000 1.000 0.000 0.000 0.000
#> GSM97968 2 0.0000 0.9814 0.000 1.000 0.000 0.000 0.000
#> GSM97969 1 0.3196 0.5745 0.804 0.000 0.000 0.192 0.004
#> GSM97971 1 0.0162 0.6713 0.996 0.000 0.000 0.000 0.004
#> GSM97799 3 0.4306 0.5654 0.000 0.000 0.508 0.000 0.492
#> GSM97823 2 0.0000 0.9814 0.000 1.000 0.000 0.000 0.000
#> GSM97824 3 0.1851 0.6544 0.000 0.000 0.912 0.000 0.088
#> GSM97830 3 0.0290 0.6409 0.000 0.000 0.992 0.000 0.008
#> GSM97835 3 0.4306 0.5654 0.000 0.000 0.508 0.000 0.492
#> GSM97838 2 0.0000 0.9814 0.000 1.000 0.000 0.000 0.000
#> GSM97841 2 0.0000 0.9814 0.000 1.000 0.000 0.000 0.000
#> GSM97842 3 0.4306 0.5654 0.000 0.000 0.508 0.000 0.492
#> GSM97854 2 0.0000 0.9814 0.000 1.000 0.000 0.000 0.000
#> GSM97857 3 0.1270 0.6526 0.000 0.000 0.948 0.000 0.052
#> GSM97860 3 0.4620 0.5662 0.016 0.000 0.592 0.000 0.392
#> GSM97862 3 0.4138 0.6047 0.000 0.000 0.616 0.000 0.384
#> GSM97864 2 0.0000 0.9814 0.000 1.000 0.000 0.000 0.000
#> GSM97866 3 0.1197 0.6539 0.000 0.000 0.952 0.000 0.048
#> GSM97868 3 0.4304 0.5697 0.000 0.000 0.516 0.000 0.484
#> GSM97872 1 0.2516 0.6039 0.860 0.000 0.140 0.000 0.000
#> GSM97873 3 0.4306 0.5654 0.000 0.000 0.508 0.000 0.492
#> GSM97874 3 0.2179 0.6414 0.004 0.000 0.896 0.000 0.100
#> GSM97875 5 0.5761 -0.4951 0.088 0.000 0.420 0.000 0.492
#> GSM97876 3 0.4242 0.5656 0.000 0.000 0.572 0.000 0.428
#> GSM97880 3 0.0404 0.6422 0.000 0.000 0.988 0.000 0.012
#> GSM97881 5 0.5880 -0.4848 0.100 0.000 0.416 0.000 0.484
#> GSM97884 3 0.4287 0.5812 0.000 0.000 0.540 0.000 0.460
#> GSM97901 3 0.4161 0.6016 0.000 0.000 0.608 0.000 0.392
#> GSM97902 3 0.5836 -0.1687 0.100 0.000 0.516 0.000 0.384
#> GSM97909 5 0.3413 0.3432 0.132 0.016 0.016 0.000 0.836
#> GSM97911 3 0.4451 0.5616 0.004 0.000 0.504 0.000 0.492
#> GSM97923 3 0.5810 0.4657 0.092 0.000 0.480 0.000 0.428
#> GSM97928 1 0.3035 0.6114 0.856 0.000 0.112 0.000 0.032
#> GSM97929 2 0.0000 0.9814 0.000 1.000 0.000 0.000 0.000
#> GSM97933 3 0.3037 0.5686 0.100 0.000 0.860 0.000 0.040
#> GSM97934 3 0.0451 0.6391 0.004 0.000 0.988 0.000 0.008
#> GSM97944 3 0.4306 0.5654 0.000 0.000 0.508 0.000 0.492
#> GSM97949 2 0.0000 0.9814 0.000 1.000 0.000 0.000 0.000
#> GSM97956 3 0.2179 0.6593 0.000 0.000 0.888 0.000 0.112
#> GSM97962 3 0.0609 0.6477 0.000 0.000 0.980 0.000 0.020
#> GSM97964 3 0.2561 0.6587 0.000 0.000 0.856 0.000 0.144
#> GSM97970 3 0.4273 0.5857 0.000 0.000 0.552 0.000 0.448
#> GSM97822 1 0.0963 0.6722 0.964 0.000 0.000 0.000 0.036
#> GSM97831 3 0.0000 0.6427 0.000 0.000 1.000 0.000 0.000
#> GSM97845 4 0.3921 0.7600 0.072 0.000 0.000 0.800 0.128
#> GSM97865 5 0.6448 0.3323 0.272 0.000 0.228 0.000 0.500
#> GSM97867 3 0.6195 0.3799 0.208 0.000 0.552 0.000 0.240
#> GSM97883 3 0.5313 0.1494 0.388 0.000 0.556 0.000 0.056
#> GSM97897 1 0.2329 0.6312 0.876 0.000 0.000 0.124 0.000
#> GSM97900 4 0.1851 0.8873 0.088 0.000 0.000 0.912 0.000
#> GSM97904 1 0.1522 0.6622 0.944 0.000 0.012 0.000 0.044
#> GSM97907 2 0.0000 0.9814 0.000 1.000 0.000 0.000 0.000
#> GSM97925 5 0.6002 -0.4614 0.116 0.000 0.392 0.000 0.492
#> GSM97947 5 0.6334 -0.1196 0.388 0.000 0.160 0.000 0.452
cbind(get_classes(res, k = 6), get_membership(res, k = 6))
#> class entropy silhouette p1 p2 p3 p4 p5 p6
#> GSM97800 2 0.0000 1.0000 0.000 1.000 0.000 0.000 0.000 0.000
#> GSM97803 2 0.0000 1.0000 0.000 1.000 0.000 0.000 0.000 0.000
#> GSM97804 2 0.0000 1.0000 0.000 1.000 0.000 0.000 0.000 0.000
#> GSM97805 2 0.0000 1.0000 0.000 1.000 0.000 0.000 0.000 0.000
#> GSM97807 2 0.0000 1.0000 0.000 1.000 0.000 0.000 0.000 0.000
#> GSM97809 2 0.0000 1.0000 0.000 1.000 0.000 0.000 0.000 0.000
#> GSM97811 2 0.0000 1.0000 0.000 1.000 0.000 0.000 0.000 0.000
#> GSM97812 2 0.0000 1.0000 0.000 1.000 0.000 0.000 0.000 0.000
#> GSM97816 5 0.2402 0.8361 0.000 0.000 0.012 0.000 0.868 0.120
#> GSM97817 2 0.0000 1.0000 0.000 1.000 0.000 0.000 0.000 0.000
#> GSM97820 2 0.0000 1.0000 0.000 1.000 0.000 0.000 0.000 0.000
#> GSM97825 2 0.0000 1.0000 0.000 1.000 0.000 0.000 0.000 0.000
#> GSM97827 2 0.0000 1.0000 0.000 1.000 0.000 0.000 0.000 0.000
#> GSM97828 5 0.1391 0.8604 0.000 0.000 0.016 0.000 0.944 0.040
#> GSM97833 2 0.0000 1.0000 0.000 1.000 0.000 0.000 0.000 0.000
#> GSM97834 2 0.0000 1.0000 0.000 1.000 0.000 0.000 0.000 0.000
#> GSM97840 2 0.0000 1.0000 0.000 1.000 0.000 0.000 0.000 0.000
#> GSM97846 2 0.0000 1.0000 0.000 1.000 0.000 0.000 0.000 0.000
#> GSM97848 2 0.0000 1.0000 0.000 1.000 0.000 0.000 0.000 0.000
#> GSM97849 2 0.0000 1.0000 0.000 1.000 0.000 0.000 0.000 0.000
#> GSM97850 2 0.0000 1.0000 0.000 1.000 0.000 0.000 0.000 0.000
#> GSM97853 2 0.0000 1.0000 0.000 1.000 0.000 0.000 0.000 0.000
#> GSM97855 2 0.0000 1.0000 0.000 1.000 0.000 0.000 0.000 0.000
#> GSM97878 1 0.1141 0.8427 0.948 0.000 0.000 0.000 0.000 0.052
#> GSM97913 6 0.0291 0.8642 0.000 0.004 0.000 0.000 0.004 0.992
#> GSM97932 4 0.0405 0.9628 0.004 0.000 0.000 0.988 0.000 0.008
#> GSM97939 5 0.2697 0.8316 0.000 0.000 0.188 0.000 0.812 0.000
#> GSM97951 2 0.0000 1.0000 0.000 1.000 0.000 0.000 0.000 0.000
#> GSM97957 5 0.0000 0.8518 0.000 0.000 0.000 0.000 1.000 0.000
#> GSM97972 5 0.3055 0.8542 0.000 0.000 0.096 0.000 0.840 0.064
#> GSM97793 1 0.5975 0.1481 0.420 0.000 0.232 0.000 0.348 0.000
#> GSM97795 3 0.0146 0.8882 0.000 0.004 0.996 0.000 0.000 0.000
#> GSM97802 1 0.2697 0.7256 0.812 0.000 0.188 0.000 0.000 0.000
#> GSM97810 5 0.3215 0.6654 0.000 0.240 0.004 0.000 0.756 0.000
#> GSM97815 3 0.1814 0.8148 0.000 0.000 0.900 0.000 0.100 0.000
#> GSM97837 6 0.0146 0.8652 0.000 0.000 0.000 0.000 0.004 0.996
#> GSM97843 5 0.2454 0.8471 0.000 0.000 0.160 0.000 0.840 0.000
#> GSM97890 3 0.0000 0.8902 0.000 0.000 1.000 0.000 0.000 0.000
#> GSM97899 4 0.0000 0.9663 0.000 0.000 0.000 1.000 0.000 0.000
#> GSM97910 6 0.0260 0.8641 0.000 0.000 0.000 0.000 0.008 0.992
#> GSM97916 6 0.2631 0.7590 0.180 0.000 0.000 0.000 0.000 0.820
#> GSM97920 5 0.2416 0.8441 0.000 0.000 0.156 0.000 0.844 0.000
#> GSM97921 6 0.0260 0.8671 0.008 0.000 0.000 0.000 0.000 0.992
#> GSM97927 1 0.0632 0.8492 0.976 0.000 0.000 0.000 0.000 0.024
#> GSM97937 6 0.2562 0.7640 0.172 0.000 0.000 0.000 0.000 0.828
#> GSM97941 2 0.0000 1.0000 0.000 1.000 0.000 0.000 0.000 0.000
#> GSM97943 5 0.2048 0.8350 0.000 0.000 0.000 0.000 0.880 0.120
#> GSM97958 5 0.3999 0.1620 0.000 0.000 0.004 0.000 0.500 0.496
#> GSM97960 2 0.0000 1.0000 0.000 1.000 0.000 0.000 0.000 0.000
#> GSM97794 6 0.0260 0.8671 0.008 0.000 0.000 0.000 0.000 0.992
#> GSM97796 4 0.0000 0.9663 0.000 0.000 0.000 1.000 0.000 0.000
#> GSM97797 6 0.0260 0.8671 0.008 0.000 0.000 0.000 0.000 0.992
#> GSM97798 4 0.0000 0.9663 0.000 0.000 0.000 1.000 0.000 0.000
#> GSM97801 6 0.0146 0.8653 0.000 0.000 0.000 0.000 0.004 0.996
#> GSM97806 6 0.3563 0.5153 0.336 0.000 0.000 0.000 0.000 0.664
#> GSM97808 4 0.0000 0.9663 0.000 0.000 0.000 1.000 0.000 0.000
#> GSM97813 1 0.0260 0.8489 0.992 0.000 0.000 0.000 0.000 0.008
#> GSM97814 4 0.0000 0.9663 0.000 0.000 0.000 1.000 0.000 0.000
#> GSM97818 6 0.0146 0.8669 0.004 0.000 0.000 0.000 0.000 0.996
#> GSM97819 3 0.4405 0.0732 0.472 0.000 0.504 0.000 0.024 0.000
#> GSM97821 6 0.3464 0.5175 0.000 0.000 0.312 0.000 0.000 0.688
#> GSM97826 6 0.5211 0.2724 0.388 0.000 0.000 0.096 0.000 0.516
#> GSM97829 1 0.3383 0.6036 0.728 0.000 0.000 0.000 0.004 0.268
#> GSM97832 5 0.3578 0.6293 0.000 0.000 0.340 0.000 0.660 0.000
#> GSM97836 1 0.0937 0.8455 0.960 0.000 0.000 0.000 0.000 0.040
#> GSM97839 4 0.0000 0.9663 0.000 0.000 0.000 1.000 0.000 0.000
#> GSM97844 2 0.0000 1.0000 0.000 1.000 0.000 0.000 0.000 0.000
#> GSM97847 6 0.0260 0.8654 0.008 0.000 0.000 0.000 0.000 0.992
#> GSM97851 4 0.0405 0.9628 0.004 0.000 0.000 0.988 0.000 0.008
#> GSM97852 1 0.0937 0.8472 0.960 0.000 0.000 0.000 0.000 0.040
#> GSM97856 4 0.0000 0.9663 0.000 0.000 0.000 1.000 0.000 0.000
#> GSM97858 2 0.0000 1.0000 0.000 1.000 0.000 0.000 0.000 0.000
#> GSM97859 1 0.0000 0.8492 1.000 0.000 0.000 0.000 0.000 0.000
#> GSM97861 1 0.1007 0.8447 0.956 0.000 0.000 0.000 0.000 0.044
#> GSM97863 4 0.0291 0.9639 0.004 0.000 0.000 0.992 0.000 0.004
#> GSM97869 6 0.3868 0.0766 0.492 0.000 0.000 0.000 0.000 0.508
#> GSM97870 1 0.0000 0.8492 1.000 0.000 0.000 0.000 0.000 0.000
#> GSM97871 4 0.0000 0.9663 0.000 0.000 0.000 1.000 0.000 0.000
#> GSM97877 6 0.0260 0.8671 0.008 0.000 0.000 0.000 0.000 0.992
#> GSM97879 1 0.1124 0.8486 0.956 0.000 0.000 0.008 0.000 0.036
#> GSM97882 1 0.0000 0.8492 1.000 0.000 0.000 0.000 0.000 0.000
#> GSM97885 1 0.3695 0.3487 0.624 0.000 0.000 0.000 0.000 0.376
#> GSM97886 4 0.0000 0.9663 0.000 0.000 0.000 1.000 0.000 0.000
#> GSM97887 1 0.3428 0.5790 0.696 0.000 0.000 0.304 0.000 0.000
#> GSM97888 1 0.2212 0.7877 0.880 0.000 0.000 0.112 0.000 0.008
#> GSM97889 1 0.0405 0.8501 0.988 0.000 0.000 0.004 0.008 0.000
#> GSM97891 6 0.2454 0.7632 0.160 0.000 0.000 0.000 0.000 0.840
#> GSM97892 2 0.0000 1.0000 0.000 1.000 0.000 0.000 0.000 0.000
#> GSM97893 4 0.0405 0.9628 0.004 0.000 0.000 0.988 0.000 0.008
#> GSM97894 4 0.3314 0.6348 0.256 0.000 0.000 0.740 0.000 0.004
#> GSM97895 4 0.3081 0.7043 0.220 0.000 0.000 0.776 0.000 0.004
#> GSM97896 4 0.1958 0.8851 0.100 0.000 0.000 0.896 0.000 0.004
#> GSM97898 4 0.0405 0.9628 0.004 0.000 0.000 0.988 0.000 0.008
#> GSM97903 6 0.3717 0.4346 0.384 0.000 0.000 0.000 0.000 0.616
#> GSM97905 1 0.2048 0.7984 0.880 0.000 0.000 0.000 0.120 0.000
#> GSM97906 4 0.0458 0.9562 0.016 0.000 0.000 0.984 0.000 0.000
#> GSM97908 1 0.5911 0.1989 0.432 0.000 0.000 0.356 0.000 0.212
#> GSM97912 1 0.1643 0.8304 0.924 0.000 0.000 0.000 0.068 0.008
#> GSM97914 6 0.0260 0.8671 0.008 0.000 0.000 0.000 0.000 0.992
#> GSM97915 4 0.0405 0.9628 0.004 0.000 0.000 0.988 0.000 0.008
#> GSM97917 4 0.0405 0.9628 0.004 0.000 0.000 0.988 0.000 0.008
#> GSM97918 4 0.0146 0.9652 0.000 0.000 0.000 0.996 0.000 0.004
#> GSM97919 4 0.0000 0.9663 0.000 0.000 0.000 1.000 0.000 0.000
#> GSM97922 1 0.0405 0.8496 0.988 0.000 0.000 0.008 0.000 0.004
#> GSM97924 2 0.0000 1.0000 0.000 1.000 0.000 0.000 0.000 0.000
#> GSM97926 1 0.1152 0.8419 0.952 0.000 0.044 0.000 0.000 0.004
#> GSM97930 6 0.0260 0.8666 0.008 0.000 0.000 0.000 0.000 0.992
#> GSM97931 6 0.2313 0.8209 0.100 0.000 0.012 0.000 0.004 0.884
#> GSM97935 1 0.1957 0.8133 0.888 0.000 0.000 0.000 0.000 0.112
#> GSM97936 4 0.0000 0.9663 0.000 0.000 0.000 1.000 0.000 0.000
#> GSM97938 1 0.2595 0.7606 0.836 0.000 0.000 0.004 0.000 0.160
#> GSM97940 4 0.0000 0.9663 0.000 0.000 0.000 1.000 0.000 0.000
#> GSM97942 3 0.4421 0.7051 0.156 0.000 0.716 0.000 0.128 0.000
#> GSM97945 4 0.0000 0.9663 0.000 0.000 0.000 1.000 0.000 0.000
#> GSM97946 2 0.0000 1.0000 0.000 1.000 0.000 0.000 0.000 0.000
#> GSM97948 1 0.1204 0.8380 0.944 0.000 0.000 0.000 0.056 0.000
#> GSM97950 4 0.0146 0.9652 0.000 0.000 0.000 0.996 0.000 0.004
#> GSM97952 4 0.0000 0.9663 0.000 0.000 0.000 1.000 0.000 0.000
#> GSM97953 1 0.4836 0.4934 0.632 0.000 0.000 0.076 0.004 0.288
#> GSM97954 1 0.2783 0.7615 0.836 0.000 0.000 0.148 0.000 0.016
#> GSM97955 4 0.0291 0.9639 0.004 0.000 0.000 0.992 0.000 0.004
#> GSM97959 6 0.0146 0.8669 0.004 0.000 0.000 0.000 0.000 0.996
#> GSM97961 4 0.0000 0.9663 0.000 0.000 0.000 1.000 0.000 0.000
#> GSM97963 4 0.0000 0.9663 0.000 0.000 0.000 1.000 0.000 0.000
#> GSM97965 4 0.0000 0.9663 0.000 0.000 0.000 1.000 0.000 0.000
#> GSM97966 4 0.0000 0.9663 0.000 0.000 0.000 1.000 0.000 0.000
#> GSM97967 2 0.0000 1.0000 0.000 1.000 0.000 0.000 0.000 0.000
#> GSM97968 2 0.0000 1.0000 0.000 1.000 0.000 0.000 0.000 0.000
#> GSM97969 1 0.1970 0.8091 0.900 0.000 0.000 0.092 0.000 0.008
#> GSM97971 1 0.0260 0.8502 0.992 0.000 0.000 0.000 0.000 0.008
#> GSM97799 3 0.0000 0.8902 0.000 0.000 1.000 0.000 0.000 0.000
#> GSM97823 2 0.0000 1.0000 0.000 1.000 0.000 0.000 0.000 0.000
#> GSM97824 5 0.2527 0.8429 0.000 0.000 0.168 0.000 0.832 0.000
#> GSM97830 5 0.0000 0.8518 0.000 0.000 0.000 0.000 1.000 0.000
#> GSM97835 3 0.0000 0.8902 0.000 0.000 1.000 0.000 0.000 0.000
#> GSM97838 2 0.0000 1.0000 0.000 1.000 0.000 0.000 0.000 0.000
#> GSM97841 2 0.0000 1.0000 0.000 1.000 0.000 0.000 0.000 0.000
#> GSM97842 3 0.0000 0.8902 0.000 0.000 1.000 0.000 0.000 0.000
#> GSM97854 2 0.0000 1.0000 0.000 1.000 0.000 0.000 0.000 0.000
#> GSM97857 5 0.2178 0.8568 0.000 0.000 0.132 0.000 0.868 0.000
#> GSM97860 3 0.2912 0.7697 0.000 0.000 0.784 0.000 0.216 0.000
#> GSM97862 3 0.2378 0.7874 0.000 0.000 0.848 0.000 0.152 0.000
#> GSM97864 2 0.0000 1.0000 0.000 1.000 0.000 0.000 0.000 0.000
#> GSM97866 5 0.2092 0.8577 0.000 0.000 0.124 0.000 0.876 0.000
#> GSM97868 3 0.0000 0.8902 0.000 0.000 1.000 0.000 0.000 0.000
#> GSM97872 1 0.2340 0.7708 0.852 0.000 0.000 0.000 0.148 0.000
#> GSM97873 3 0.0000 0.8902 0.000 0.000 1.000 0.000 0.000 0.000
#> GSM97874 5 0.1908 0.7951 0.000 0.000 0.096 0.000 0.900 0.004
#> GSM97875 3 0.0000 0.8902 0.000 0.000 1.000 0.000 0.000 0.000
#> GSM97876 3 0.2491 0.8032 0.000 0.000 0.836 0.000 0.164 0.000
#> GSM97880 5 0.0000 0.8518 0.000 0.000 0.000 0.000 1.000 0.000
#> GSM97881 3 0.0260 0.8877 0.000 0.000 0.992 0.000 0.008 0.000
#> GSM97884 3 0.0000 0.8902 0.000 0.000 1.000 0.000 0.000 0.000
#> GSM97901 3 0.2823 0.7128 0.000 0.000 0.796 0.000 0.204 0.000
#> GSM97902 5 0.2872 0.7853 0.140 0.000 0.000 0.000 0.836 0.024
#> GSM97909 6 0.1958 0.8078 0.004 0.000 0.100 0.000 0.000 0.896
#> GSM97911 3 0.0000 0.8902 0.000 0.000 1.000 0.000 0.000 0.000
#> GSM97923 3 0.2491 0.8032 0.000 0.000 0.836 0.000 0.164 0.000
#> GSM97928 1 0.1082 0.8462 0.956 0.000 0.000 0.000 0.004 0.040
#> GSM97929 2 0.0000 1.0000 0.000 1.000 0.000 0.000 0.000 0.000
#> GSM97933 5 0.1003 0.8547 0.016 0.000 0.020 0.000 0.964 0.000
#> GSM97934 5 0.0000 0.8518 0.000 0.000 0.000 0.000 1.000 0.000
#> GSM97944 3 0.0000 0.8902 0.000 0.000 1.000 0.000 0.000 0.000
#> GSM97949 2 0.0000 1.0000 0.000 1.000 0.000 0.000 0.000 0.000
#> GSM97956 5 0.2597 0.8392 0.000 0.000 0.176 0.000 0.824 0.000
#> GSM97962 5 0.1327 0.8655 0.000 0.000 0.064 0.000 0.936 0.000
#> GSM97964 5 0.2664 0.8337 0.000 0.000 0.184 0.000 0.816 0.000
#> GSM97970 3 0.0000 0.8902 0.000 0.000 1.000 0.000 0.000 0.000
#> GSM97822 1 0.0458 0.8502 0.984 0.000 0.000 0.000 0.000 0.016
#> GSM97831 5 0.0547 0.8588 0.000 0.000 0.020 0.000 0.980 0.000
#> GSM97845 4 0.3679 0.7061 0.040 0.000 0.000 0.760 0.000 0.200
#> GSM97865 6 0.0405 0.8661 0.008 0.000 0.000 0.000 0.004 0.988
#> GSM97867 3 0.5618 0.4895 0.252 0.000 0.540 0.000 0.208 0.000
#> GSM97883 1 0.3782 0.3130 0.588 0.000 0.000 0.000 0.412 0.000
#> GSM97897 1 0.0865 0.8446 0.964 0.000 0.000 0.036 0.000 0.000
#> GSM97900 4 0.1957 0.8578 0.112 0.000 0.000 0.888 0.000 0.000
#> GSM97904 1 0.1663 0.8233 0.912 0.000 0.000 0.000 0.000 0.088
#> GSM97907 2 0.0000 1.0000 0.000 1.000 0.000 0.000 0.000 0.000
#> GSM97925 3 0.0260 0.8876 0.000 0.000 0.992 0.000 0.008 0.000
#> GSM97947 3 0.2318 0.8500 0.044 0.000 0.892 0.000 0.064 0.000
Heatmaps for the consensus matrix. It visualizes the probability of two samples to be in a same group.
consensus_heatmap(res, k = 2)
consensus_heatmap(res, k = 3)
consensus_heatmap(res, k = 4)
consensus_heatmap(res, k = 5)
consensus_heatmap(res, k = 6)
Heatmaps for the membership of samples in all partitions to see how consistent they are:
membership_heatmap(res, k = 2)
membership_heatmap(res, k = 3)
membership_heatmap(res, k = 4)
membership_heatmap(res, k = 5)
membership_heatmap(res, k = 6)
As soon as we have had the classes for columns, we can look for signatures which are significantly different between classes which can be candidate marks for certain classes. Following are the heatmaps for signatures.
Signature heatmaps where rows are scaled:
get_signatures(res, k = 2)
get_signatures(res, k = 3)
get_signatures(res, k = 4)
get_signatures(res, k = 5)
get_signatures(res, k = 6)
Signature heatmaps where rows are not scaled:
get_signatures(res, k = 2, scale_rows = FALSE)
get_signatures(res, k = 3, scale_rows = FALSE)
get_signatures(res, k = 4, scale_rows = FALSE)
get_signatures(res, k = 5, scale_rows = FALSE)
get_signatures(res, k = 6, scale_rows = FALSE)
Compare the overlap of signatures from different k:
compare_signatures(res)
get_signature() returns a data frame invisibly. TO get the list of signatures, the function
call should be assigned to a variable explicitly. In following code, if plot argument is set
to FALSE, no heatmap is plotted while only the differential analysis is performed.
# code only for demonstration
tb = get_signature(res, k = ..., plot = FALSE)
An example of the output of tb is:
#> which_row fdr mean_1 mean_2 scaled_mean_1 scaled_mean_2 km
#> 1 38 0.042760348 8.373488 9.131774 -0.5533452 0.5164555 1
#> 2 40 0.018707592 7.106213 8.469186 -0.6173731 0.5762149 1
#> 3 55 0.019134737 10.221463 11.207825 -0.6159697 0.5749050 1
#> 4 59 0.006059896 5.921854 7.869574 -0.6899429 0.6439467 1
#> 5 60 0.018055526 8.928898 10.211722 -0.6204761 0.5791110 1
#> 6 98 0.009384629 15.714769 14.887706 0.6635654 -0.6193277 2
...
The columns in tb are:
which_row: row indices corresponding to the input matrix.fdr: FDR for the differential test. mean_x: The mean value in group x.scaled_mean_x: The mean value in group x after rows are scaled.km: Row groups if k-means clustering is applied to rows.UMAP plot which shows how samples are separated.
dimension_reduction(res, k = 2, method = "UMAP")
dimension_reduction(res, k = 3, method = "UMAP")
dimension_reduction(res, k = 4, method = "UMAP")
dimension_reduction(res, k = 5, method = "UMAP")
dimension_reduction(res, k = 6, method = "UMAP")
Following heatmap shows how subgroups are split when increasing k:
collect_classes(res)
Test correlation between subgroups and known annotations. If the known annotation is numeric, one-way ANOVA test is applied, and if the known annotation is discrete, chi-squared contingency table test is applied.
test_to_known_factors(res)
#> n disease.state(p) tissue(p) k
#> CV:pam 179 4.84e-16 7.06e-16 2
#> CV:pam 166 6.12e-30 6.94e-32 3
#> CV:pam 153 1.12e-25 2.80e-27 4
#> CV:pam 133 4.41e-23 9.84e-25 5
#> CV:pam 169 1.44e-25 1.83e-25 6
If matrix rows can be associated to genes, consider to use functional_enrichment(res,
...) to perform function enrichment for the signature genes. See this vignette for more detailed explanations.
The object with results only for a single top-value method and a single partition method can be extracted as:
res = res_list["CV", "mclust"]
# you can also extract it by
# res = res_list["CV:mclust"]
A summary of res and all the functions that can be applied to it:
res
#> A 'ConsensusPartition' object with k = 2, 3, 4, 5, 6.
#> On a matrix with 51882 rows and 180 columns.
#> Top rows (1000, 2000, 3000, 4000, 5000) are extracted by 'CV' method.
#> Subgroups are detected by 'mclust' method.
#> Performed in total 1250 partitions by row resampling.
#> Best k for subgroups seems to be 4.
#>
#> Following methods can be applied to this 'ConsensusPartition' object:
#> [1] "cola_report" "collect_classes" "collect_plots"
#> [4] "collect_stats" "colnames" "compare_signatures"
#> [7] "consensus_heatmap" "dimension_reduction" "functional_enrichment"
#> [10] "get_anno_col" "get_anno" "get_classes"
#> [13] "get_consensus" "get_matrix" "get_membership"
#> [16] "get_param" "get_signatures" "get_stats"
#> [19] "is_best_k" "is_stable_k" "membership_heatmap"
#> [22] "ncol" "nrow" "plot_ecdf"
#> [25] "rownames" "select_partition_number" "show"
#> [28] "suggest_best_k" "test_to_known_factors"
collect_plots() function collects all the plots made from res for all k (number of partitions)
into one single page to provide an easy and fast comparison between different k.
collect_plots(res)
The plots are:
k and the heatmap of
predicted classes for each k.k.k.k.All the plots in panels can be made by individual functions and they are plotted later in this section.
select_partition_number() produces several plots showing different
statistics for choosing “optimized” k. There are following statistics:
k;k, the area increased is defined as \(A_k - A_{k-1}\).The detailed explanations of these statistics can be found in the cola vignette.
Generally speaking, lower PAC score, higher mean silhouette score or higher
concordance corresponds to better partition. Rand index and Jaccard index
measure how similar the current partition is compared to partition with k-1.
If they are too similar, we won't accept k is better than k-1.
select_partition_number(res)
The numeric values for all these statistics can be obtained by get_stats().
get_stats(res)
#> k 1-PAC mean_silhouette concordance area_increased Rand Jaccard
#> 2 2 0.997 0.955 0.972 0.3433 0.672 0.672
#> 3 3 0.789 0.893 0.944 0.8159 0.686 0.536
#> 4 4 0.948 0.933 0.966 0.1686 0.834 0.586
#> 5 5 0.826 0.787 0.876 0.0588 0.934 0.763
#> 6 6 0.779 0.758 0.843 0.0327 0.984 0.930
suggest_best_k() suggests the best \(k\) based on these statistics. The rules are as follows:
suggest_best_k(res)
#> [1] 4
#> attr(,"optional")
#> [1] 2
There is also optional best \(k\) = 2 that is worth to check.
Following shows the table of the partitions (You need to click the show/hide
code output link to see it). The membership matrix (columns with name p*)
is inferred by
clue::cl_consensus()
function with the SE method. Basically the value in the membership matrix
represents the probability to belong to a certain group. The finall class
label for an item is determined with the group with highest probability it
belongs to.
In get_classes() function, the entropy is calculated from the membership
matrix and the silhouette score is calculated from the consensus matrix.
cbind(get_classes(res, k = 2), get_membership(res, k = 2))
#> class entropy silhouette p1 p2
#> GSM97800 2 0.0000 0.987 0.000 1.000
#> GSM97803 2 0.0000 0.987 0.000 1.000
#> GSM97804 2 0.0000 0.987 0.000 1.000
#> GSM97805 2 0.0000 0.987 0.000 1.000
#> GSM97807 2 0.0000 0.987 0.000 1.000
#> GSM97809 2 0.0000 0.987 0.000 1.000
#> GSM97811 2 0.0000 0.987 0.000 1.000
#> GSM97812 2 0.0000 0.987 0.000 1.000
#> GSM97816 1 0.4562 0.927 0.904 0.096
#> GSM97817 2 0.0000 0.987 0.000 1.000
#> GSM97820 2 0.0000 0.987 0.000 1.000
#> GSM97825 2 0.0000 0.987 0.000 1.000
#> GSM97827 2 0.0000 0.987 0.000 1.000
#> GSM97828 1 0.3584 0.939 0.932 0.068
#> GSM97833 2 0.0000 0.987 0.000 1.000
#> GSM97834 2 0.0000 0.987 0.000 1.000
#> GSM97840 2 0.9833 0.178 0.424 0.576
#> GSM97846 2 0.0000 0.987 0.000 1.000
#> GSM97848 2 0.0000 0.987 0.000 1.000
#> GSM97849 2 0.0000 0.987 0.000 1.000
#> GSM97850 2 0.0000 0.987 0.000 1.000
#> GSM97853 2 0.0000 0.987 0.000 1.000
#> GSM97855 2 0.0000 0.987 0.000 1.000
#> GSM97878 1 0.0000 0.965 1.000 0.000
#> GSM97913 1 0.0000 0.965 1.000 0.000
#> GSM97932 1 0.0000 0.965 1.000 0.000
#> GSM97939 1 0.4562 0.927 0.904 0.096
#> GSM97951 2 0.0000 0.987 0.000 1.000
#> GSM97957 1 0.4562 0.927 0.904 0.096
#> GSM97972 1 0.4431 0.929 0.908 0.092
#> GSM97793 1 0.4562 0.927 0.904 0.096
#> GSM97795 1 0.6623 0.848 0.828 0.172
#> GSM97802 1 0.0000 0.965 1.000 0.000
#> GSM97810 1 0.4562 0.927 0.904 0.096
#> GSM97815 1 0.4562 0.927 0.904 0.096
#> GSM97837 1 0.0000 0.965 1.000 0.000
#> GSM97843 1 0.4562 0.927 0.904 0.096
#> GSM97890 1 0.4562 0.927 0.904 0.096
#> GSM97899 1 0.0000 0.965 1.000 0.000
#> GSM97910 1 0.0000 0.965 1.000 0.000
#> GSM97916 1 0.0000 0.965 1.000 0.000
#> GSM97920 1 0.4562 0.927 0.904 0.096
#> GSM97921 1 0.0000 0.965 1.000 0.000
#> GSM97927 1 0.0000 0.965 1.000 0.000
#> GSM97937 1 0.0000 0.965 1.000 0.000
#> GSM97941 1 0.4690 0.924 0.900 0.100
#> GSM97943 1 0.0000 0.965 1.000 0.000
#> GSM97958 1 0.0000 0.965 1.000 0.000
#> GSM97960 1 0.5519 0.898 0.872 0.128
#> GSM97794 1 0.0000 0.965 1.000 0.000
#> GSM97796 1 0.0000 0.965 1.000 0.000
#> GSM97797 1 0.0000 0.965 1.000 0.000
#> GSM97798 1 0.0000 0.965 1.000 0.000
#> GSM97801 1 0.0000 0.965 1.000 0.000
#> GSM97806 1 0.0000 0.965 1.000 0.000
#> GSM97808 1 0.0000 0.965 1.000 0.000
#> GSM97813 1 0.0000 0.965 1.000 0.000
#> GSM97814 1 0.0000 0.965 1.000 0.000
#> GSM97818 1 0.0000 0.965 1.000 0.000
#> GSM97819 1 0.4562 0.927 0.904 0.096
#> GSM97821 1 0.0000 0.965 1.000 0.000
#> GSM97826 1 0.0000 0.965 1.000 0.000
#> GSM97829 1 0.0000 0.965 1.000 0.000
#> GSM97832 1 0.4562 0.927 0.904 0.096
#> GSM97836 1 0.0000 0.965 1.000 0.000
#> GSM97839 1 0.0000 0.965 1.000 0.000
#> GSM97844 2 0.0000 0.987 0.000 1.000
#> GSM97847 1 0.0000 0.965 1.000 0.000
#> GSM97851 1 0.0000 0.965 1.000 0.000
#> GSM97852 1 0.0000 0.965 1.000 0.000
#> GSM97856 1 0.0000 0.965 1.000 0.000
#> GSM97858 2 0.0000 0.987 0.000 1.000
#> GSM97859 1 0.0000 0.965 1.000 0.000
#> GSM97861 1 0.0000 0.965 1.000 0.000
#> GSM97863 1 0.0000 0.965 1.000 0.000
#> GSM97869 1 0.0000 0.965 1.000 0.000
#> GSM97870 1 0.0000 0.965 1.000 0.000
#> GSM97871 1 0.0000 0.965 1.000 0.000
#> GSM97877 1 0.0000 0.965 1.000 0.000
#> GSM97879 1 0.0000 0.965 1.000 0.000
#> GSM97882 1 0.0000 0.965 1.000 0.000
#> GSM97885 1 0.0000 0.965 1.000 0.000
#> GSM97886 1 0.0000 0.965 1.000 0.000
#> GSM97887 1 0.0000 0.965 1.000 0.000
#> GSM97888 1 0.0000 0.965 1.000 0.000
#> GSM97889 1 0.0000 0.965 1.000 0.000
#> GSM97891 1 0.0000 0.965 1.000 0.000
#> GSM97892 2 0.0000 0.987 0.000 1.000
#> GSM97893 1 0.0000 0.965 1.000 0.000
#> GSM97894 1 0.0000 0.965 1.000 0.000
#> GSM97895 1 0.0000 0.965 1.000 0.000
#> GSM97896 1 0.0000 0.965 1.000 0.000
#> GSM97898 1 0.0000 0.965 1.000 0.000
#> GSM97903 1 0.0000 0.965 1.000 0.000
#> GSM97905 1 0.0000 0.965 1.000 0.000
#> GSM97906 1 0.0000 0.965 1.000 0.000
#> GSM97908 1 0.0000 0.965 1.000 0.000
#> GSM97912 1 0.0000 0.965 1.000 0.000
#> GSM97914 1 0.0000 0.965 1.000 0.000
#> GSM97915 1 0.0000 0.965 1.000 0.000
#> GSM97917 1 0.0000 0.965 1.000 0.000
#> GSM97918 1 0.0000 0.965 1.000 0.000
#> GSM97919 1 0.0000 0.965 1.000 0.000
#> GSM97922 1 0.0000 0.965 1.000 0.000
#> GSM97924 2 0.0000 0.987 0.000 1.000
#> GSM97926 1 0.0000 0.965 1.000 0.000
#> GSM97930 1 0.0000 0.965 1.000 0.000
#> GSM97931 1 0.0000 0.965 1.000 0.000
#> GSM97935 1 0.0000 0.965 1.000 0.000
#> GSM97936 1 0.0000 0.965 1.000 0.000
#> GSM97938 1 0.0000 0.965 1.000 0.000
#> GSM97940 1 0.0000 0.965 1.000 0.000
#> GSM97942 1 0.4562 0.927 0.904 0.096
#> GSM97945 1 0.0000 0.965 1.000 0.000
#> GSM97946 2 0.0000 0.987 0.000 1.000
#> GSM97948 1 0.0000 0.965 1.000 0.000
#> GSM97950 1 0.0000 0.965 1.000 0.000
#> GSM97952 1 0.0000 0.965 1.000 0.000
#> GSM97953 1 0.0000 0.965 1.000 0.000
#> GSM97954 1 0.0000 0.965 1.000 0.000
#> GSM97955 1 0.0000 0.965 1.000 0.000
#> GSM97959 1 0.0000 0.965 1.000 0.000
#> GSM97961 1 0.0000 0.965 1.000 0.000
#> GSM97963 1 0.0000 0.965 1.000 0.000
#> GSM97965 1 0.0000 0.965 1.000 0.000
#> GSM97966 1 0.0000 0.965 1.000 0.000
#> GSM97967 2 0.0000 0.987 0.000 1.000
#> GSM97968 2 0.0672 0.979 0.008 0.992
#> GSM97969 1 0.0000 0.965 1.000 0.000
#> GSM97971 1 0.0000 0.965 1.000 0.000
#> GSM97799 1 0.4562 0.927 0.904 0.096
#> GSM97823 2 0.0000 0.987 0.000 1.000
#> GSM97824 1 0.4562 0.927 0.904 0.096
#> GSM97830 1 0.4562 0.927 0.904 0.096
#> GSM97835 1 0.4562 0.927 0.904 0.096
#> GSM97838 2 0.0000 0.987 0.000 1.000
#> GSM97841 2 0.0000 0.987 0.000 1.000
#> GSM97842 1 0.4562 0.927 0.904 0.096
#> GSM97854 2 0.0000 0.987 0.000 1.000
#> GSM97857 1 0.4562 0.927 0.904 0.096
#> GSM97860 1 0.4562 0.927 0.904 0.096
#> GSM97862 1 0.4562 0.927 0.904 0.096
#> GSM97864 2 0.0000 0.987 0.000 1.000
#> GSM97866 1 0.4562 0.927 0.904 0.096
#> GSM97868 1 0.4562 0.927 0.904 0.096
#> GSM97872 1 0.0000 0.965 1.000 0.000
#> GSM97873 1 0.4562 0.927 0.904 0.096
#> GSM97874 1 0.4562 0.927 0.904 0.096
#> GSM97875 1 0.4562 0.927 0.904 0.096
#> GSM97876 1 0.4562 0.927 0.904 0.096
#> GSM97880 1 0.4562 0.927 0.904 0.096
#> GSM97881 1 0.4562 0.927 0.904 0.096
#> GSM97884 1 0.4562 0.927 0.904 0.096
#> GSM97901 1 0.4562 0.927 0.904 0.096
#> GSM97902 1 0.0000 0.965 1.000 0.000
#> GSM97909 1 0.3733 0.938 0.928 0.072
#> GSM97911 1 0.4562 0.927 0.904 0.096
#> GSM97923 1 0.4562 0.927 0.904 0.096
#> GSM97928 1 0.0000 0.965 1.000 0.000
#> GSM97929 2 0.0000 0.987 0.000 1.000
#> GSM97933 1 0.4562 0.927 0.904 0.096
#> GSM97934 1 0.4562 0.927 0.904 0.096
#> GSM97944 1 0.4562 0.927 0.904 0.096
#> GSM97949 2 0.0000 0.987 0.000 1.000
#> GSM97956 1 0.4562 0.927 0.904 0.096
#> GSM97962 1 0.4562 0.927 0.904 0.096
#> GSM97964 1 0.4562 0.927 0.904 0.096
#> GSM97970 1 0.4562 0.927 0.904 0.096
#> GSM97822 1 0.0000 0.965 1.000 0.000
#> GSM97831 1 0.4562 0.927 0.904 0.096
#> GSM97845 1 0.0000 0.965 1.000 0.000
#> GSM97865 1 0.0000 0.965 1.000 0.000
#> GSM97867 1 0.4562 0.927 0.904 0.096
#> GSM97883 1 0.4298 0.931 0.912 0.088
#> GSM97897 1 0.0000 0.965 1.000 0.000
#> GSM97900 1 0.0000 0.965 1.000 0.000
#> GSM97904 1 0.0000 0.965 1.000 0.000
#> GSM97907 2 0.0000 0.987 0.000 1.000
#> GSM97925 1 0.0672 0.963 0.992 0.008
#> GSM97947 1 0.0672 0.963 0.992 0.008
cbind(get_classes(res, k = 3), get_membership(res, k = 3))
#> class entropy silhouette p1 p2 p3
#> GSM97800 2 0.0000 0.97533 0.000 1.000 0.000
#> GSM97803 2 0.0000 0.97533 0.000 1.000 0.000
#> GSM97804 2 0.0000 0.97533 0.000 1.000 0.000
#> GSM97805 2 0.0000 0.97533 0.000 1.000 0.000
#> GSM97807 2 0.0000 0.97533 0.000 1.000 0.000
#> GSM97809 2 0.0000 0.97533 0.000 1.000 0.000
#> GSM97811 2 0.0000 0.97533 0.000 1.000 0.000
#> GSM97812 2 0.0000 0.97533 0.000 1.000 0.000
#> GSM97816 3 0.3752 0.82080 0.144 0.000 0.856
#> GSM97817 2 0.0000 0.97533 0.000 1.000 0.000
#> GSM97820 2 0.0000 0.97533 0.000 1.000 0.000
#> GSM97825 2 0.0000 0.97533 0.000 1.000 0.000
#> GSM97827 2 0.0000 0.97533 0.000 1.000 0.000
#> GSM97828 3 0.3816 0.81698 0.148 0.000 0.852
#> GSM97833 2 0.0000 0.97533 0.000 1.000 0.000
#> GSM97834 2 0.0000 0.97533 0.000 1.000 0.000
#> GSM97840 3 0.6254 0.74794 0.188 0.056 0.756
#> GSM97846 2 0.0000 0.97533 0.000 1.000 0.000
#> GSM97848 2 0.0000 0.97533 0.000 1.000 0.000
#> GSM97849 2 0.0000 0.97533 0.000 1.000 0.000
#> GSM97850 2 0.0000 0.97533 0.000 1.000 0.000
#> GSM97853 2 0.0000 0.97533 0.000 1.000 0.000
#> GSM97855 2 0.2711 0.88805 0.000 0.912 0.088
#> GSM97878 1 0.3038 0.90907 0.896 0.000 0.104
#> GSM97913 3 0.4931 0.71624 0.232 0.000 0.768
#> GSM97932 1 0.1163 0.93525 0.972 0.000 0.028
#> GSM97939 3 0.0000 0.92292 0.000 0.000 1.000
#> GSM97951 2 0.5882 0.47131 0.000 0.652 0.348
#> GSM97957 3 0.0000 0.92292 0.000 0.000 1.000
#> GSM97972 3 0.3941 0.80907 0.156 0.000 0.844
#> GSM97793 3 0.0000 0.92292 0.000 0.000 1.000
#> GSM97795 3 0.0000 0.92292 0.000 0.000 1.000
#> GSM97802 1 0.5591 0.62352 0.696 0.000 0.304
#> GSM97810 3 0.0000 0.92292 0.000 0.000 1.000
#> GSM97815 3 0.0000 0.92292 0.000 0.000 1.000
#> GSM97837 1 0.3551 0.88460 0.868 0.000 0.132
#> GSM97843 3 0.0000 0.92292 0.000 0.000 1.000
#> GSM97890 3 0.0000 0.92292 0.000 0.000 1.000
#> GSM97899 1 0.0000 0.92890 1.000 0.000 0.000
#> GSM97910 1 0.5058 0.73720 0.756 0.000 0.244
#> GSM97916 1 0.3038 0.90904 0.896 0.000 0.104
#> GSM97920 3 0.0000 0.92292 0.000 0.000 1.000
#> GSM97921 1 0.3340 0.89545 0.880 0.000 0.120
#> GSM97927 1 0.1753 0.93680 0.952 0.000 0.048
#> GSM97937 1 0.3116 0.90432 0.892 0.000 0.108
#> GSM97941 3 0.4842 0.72857 0.224 0.000 0.776
#> GSM97943 3 0.6305 0.00855 0.484 0.000 0.516
#> GSM97958 3 0.5397 0.63088 0.280 0.000 0.720
#> GSM97960 3 0.0000 0.92292 0.000 0.000 1.000
#> GSM97794 1 0.4555 0.80414 0.800 0.000 0.200
#> GSM97796 1 0.0000 0.92890 1.000 0.000 0.000
#> GSM97797 1 0.5431 0.66864 0.716 0.000 0.284
#> GSM97798 1 0.0000 0.92890 1.000 0.000 0.000
#> GSM97801 1 0.3482 0.88837 0.872 0.000 0.128
#> GSM97806 1 0.1753 0.93680 0.952 0.000 0.048
#> GSM97808 1 0.0000 0.92890 1.000 0.000 0.000
#> GSM97813 1 0.1411 0.93636 0.964 0.000 0.036
#> GSM97814 1 0.0000 0.92890 1.000 0.000 0.000
#> GSM97818 1 0.3482 0.88834 0.872 0.000 0.128
#> GSM97819 3 0.0424 0.91892 0.008 0.000 0.992
#> GSM97821 3 0.4842 0.72857 0.224 0.000 0.776
#> GSM97826 1 0.3038 0.90800 0.896 0.000 0.104
#> GSM97829 1 0.3267 0.89871 0.884 0.000 0.116
#> GSM97832 3 0.0000 0.92292 0.000 0.000 1.000
#> GSM97836 1 0.1753 0.93680 0.952 0.000 0.048
#> GSM97839 1 0.0000 0.92890 1.000 0.000 0.000
#> GSM97844 2 0.0000 0.97533 0.000 1.000 0.000
#> GSM97847 1 0.1753 0.93680 0.952 0.000 0.048
#> GSM97851 1 0.1163 0.93525 0.972 0.000 0.028
#> GSM97852 1 0.1753 0.93680 0.952 0.000 0.048
#> GSM97856 1 0.0000 0.92890 1.000 0.000 0.000
#> GSM97858 2 0.0747 0.96114 0.000 0.984 0.016
#> GSM97859 1 0.1753 0.93680 0.952 0.000 0.048
#> GSM97861 1 0.1860 0.93573 0.948 0.000 0.052
#> GSM97863 1 0.0000 0.92890 1.000 0.000 0.000
#> GSM97869 1 0.2261 0.92972 0.932 0.000 0.068
#> GSM97870 1 0.5216 0.70849 0.740 0.000 0.260
#> GSM97871 1 0.0000 0.92890 1.000 0.000 0.000
#> GSM97877 3 0.4842 0.72857 0.224 0.000 0.776
#> GSM97879 1 0.1753 0.93680 0.952 0.000 0.048
#> GSM97882 1 0.1753 0.93680 0.952 0.000 0.048
#> GSM97885 1 0.1753 0.93680 0.952 0.000 0.048
#> GSM97886 1 0.0000 0.92890 1.000 0.000 0.000
#> GSM97887 1 0.0000 0.92890 1.000 0.000 0.000
#> GSM97888 1 0.1643 0.93695 0.956 0.000 0.044
#> GSM97889 1 0.1753 0.93680 0.952 0.000 0.048
#> GSM97891 1 0.1753 0.93680 0.952 0.000 0.048
#> GSM97892 2 0.0000 0.97533 0.000 1.000 0.000
#> GSM97893 1 0.1643 0.93685 0.956 0.000 0.044
#> GSM97894 1 0.0000 0.92890 1.000 0.000 0.000
#> GSM97895 1 0.1643 0.93685 0.956 0.000 0.044
#> GSM97896 1 0.0000 0.92890 1.000 0.000 0.000
#> GSM97898 1 0.0000 0.92890 1.000 0.000 0.000
#> GSM97903 1 0.1753 0.93680 0.952 0.000 0.048
#> GSM97905 3 0.5988 0.40909 0.368 0.000 0.632
#> GSM97906 1 0.0000 0.92890 1.000 0.000 0.000
#> GSM97908 1 0.1753 0.93680 0.952 0.000 0.048
#> GSM97912 1 0.3619 0.88063 0.864 0.000 0.136
#> GSM97914 1 0.3116 0.90565 0.892 0.000 0.108
#> GSM97915 1 0.0000 0.92890 1.000 0.000 0.000
#> GSM97917 1 0.1643 0.93685 0.956 0.000 0.044
#> GSM97918 1 0.0000 0.92890 1.000 0.000 0.000
#> GSM97919 1 0.0000 0.92890 1.000 0.000 0.000
#> GSM97922 1 0.0424 0.93114 0.992 0.000 0.008
#> GSM97924 2 0.0000 0.97533 0.000 1.000 0.000
#> GSM97926 3 0.4346 0.77908 0.184 0.000 0.816
#> GSM97930 1 0.2261 0.92919 0.932 0.000 0.068
#> GSM97931 3 0.4842 0.72857 0.224 0.000 0.776
#> GSM97935 1 0.2066 0.93304 0.940 0.000 0.060
#> GSM97936 1 0.0237 0.92988 0.996 0.000 0.004
#> GSM97938 1 0.3192 0.90193 0.888 0.000 0.112
#> GSM97940 1 0.0000 0.92890 1.000 0.000 0.000
#> GSM97942 3 0.0424 0.91892 0.008 0.000 0.992
#> GSM97945 1 0.0424 0.93102 0.992 0.000 0.008
#> GSM97946 2 0.0000 0.97533 0.000 1.000 0.000
#> GSM97948 3 0.4931 0.71201 0.232 0.000 0.768
#> GSM97950 1 0.0000 0.92890 1.000 0.000 0.000
#> GSM97952 1 0.0000 0.92890 1.000 0.000 0.000
#> GSM97953 1 0.3116 0.90432 0.892 0.000 0.108
#> GSM97954 1 0.1753 0.93680 0.952 0.000 0.048
#> GSM97955 1 0.1411 0.93646 0.964 0.000 0.036
#> GSM97959 1 0.6308 0.07120 0.508 0.000 0.492
#> GSM97961 1 0.0000 0.92890 1.000 0.000 0.000
#> GSM97963 1 0.0000 0.92890 1.000 0.000 0.000
#> GSM97965 1 0.0000 0.92890 1.000 0.000 0.000
#> GSM97966 1 0.0000 0.92890 1.000 0.000 0.000
#> GSM97967 2 0.0000 0.97533 0.000 1.000 0.000
#> GSM97968 2 0.6045 0.39259 0.000 0.620 0.380
#> GSM97969 1 0.1753 0.93680 0.952 0.000 0.048
#> GSM97971 1 0.2261 0.92910 0.932 0.000 0.068
#> GSM97799 3 0.0000 0.92292 0.000 0.000 1.000
#> GSM97823 2 0.0000 0.97533 0.000 1.000 0.000
#> GSM97824 3 0.0000 0.92292 0.000 0.000 1.000
#> GSM97830 3 0.0000 0.92292 0.000 0.000 1.000
#> GSM97835 3 0.0000 0.92292 0.000 0.000 1.000
#> GSM97838 2 0.0000 0.97533 0.000 1.000 0.000
#> GSM97841 2 0.0000 0.97533 0.000 1.000 0.000
#> GSM97842 3 0.0000 0.92292 0.000 0.000 1.000
#> GSM97854 2 0.0000 0.97533 0.000 1.000 0.000
#> GSM97857 3 0.0000 0.92292 0.000 0.000 1.000
#> GSM97860 3 0.0000 0.92292 0.000 0.000 1.000
#> GSM97862 3 0.0000 0.92292 0.000 0.000 1.000
#> GSM97864 2 0.0000 0.97533 0.000 1.000 0.000
#> GSM97866 3 0.0000 0.92292 0.000 0.000 1.000
#> GSM97868 3 0.0000 0.92292 0.000 0.000 1.000
#> GSM97872 1 0.3340 0.89552 0.880 0.000 0.120
#> GSM97873 3 0.0000 0.92292 0.000 0.000 1.000
#> GSM97874 3 0.0000 0.92292 0.000 0.000 1.000
#> GSM97875 3 0.0000 0.92292 0.000 0.000 1.000
#> GSM97876 3 0.0000 0.92292 0.000 0.000 1.000
#> GSM97880 3 0.0000 0.92292 0.000 0.000 1.000
#> GSM97881 3 0.0000 0.92292 0.000 0.000 1.000
#> GSM97884 3 0.0000 0.92292 0.000 0.000 1.000
#> GSM97901 3 0.0000 0.92292 0.000 0.000 1.000
#> GSM97902 1 0.6192 0.33469 0.580 0.000 0.420
#> GSM97909 3 0.4842 0.72857 0.224 0.000 0.776
#> GSM97911 3 0.0000 0.92292 0.000 0.000 1.000
#> GSM97923 3 0.0000 0.92292 0.000 0.000 1.000
#> GSM97928 1 0.1964 0.93440 0.944 0.000 0.056
#> GSM97929 2 0.0000 0.97533 0.000 1.000 0.000
#> GSM97933 3 0.0000 0.92292 0.000 0.000 1.000
#> GSM97934 3 0.0000 0.92292 0.000 0.000 1.000
#> GSM97944 3 0.0000 0.92292 0.000 0.000 1.000
#> GSM97949 2 0.0000 0.97533 0.000 1.000 0.000
#> GSM97956 3 0.0000 0.92292 0.000 0.000 1.000
#> GSM97962 3 0.0000 0.92292 0.000 0.000 1.000
#> GSM97964 3 0.0000 0.92292 0.000 0.000 1.000
#> GSM97970 3 0.0000 0.92292 0.000 0.000 1.000
#> GSM97822 1 0.1964 0.93453 0.944 0.000 0.056
#> GSM97831 3 0.0000 0.92292 0.000 0.000 1.000
#> GSM97845 1 0.1753 0.93680 0.952 0.000 0.048
#> GSM97865 1 0.3412 0.89195 0.876 0.000 0.124
#> GSM97867 3 0.0000 0.92292 0.000 0.000 1.000
#> GSM97883 3 0.0424 0.91892 0.008 0.000 0.992
#> GSM97897 1 0.0000 0.92890 1.000 0.000 0.000
#> GSM97900 1 0.0000 0.92890 1.000 0.000 0.000
#> GSM97904 1 0.3038 0.90824 0.896 0.000 0.104
#> GSM97907 2 0.0000 0.97533 0.000 1.000 0.000
#> GSM97925 3 0.0424 0.91892 0.008 0.000 0.992
#> GSM97947 3 0.0424 0.91892 0.008 0.000 0.992
cbind(get_classes(res, k = 4), get_membership(res, k = 4))
#> class entropy silhouette p1 p2 p3 p4
#> GSM97800 2 0.0000 0.979 0.000 1.000 0.000 0.000
#> GSM97803 2 0.0000 0.979 0.000 1.000 0.000 0.000
#> GSM97804 2 0.0000 0.979 0.000 1.000 0.000 0.000
#> GSM97805 2 0.0000 0.979 0.000 1.000 0.000 0.000
#> GSM97807 2 0.0000 0.979 0.000 1.000 0.000 0.000
#> GSM97809 2 0.0000 0.979 0.000 1.000 0.000 0.000
#> GSM97811 2 0.0000 0.979 0.000 1.000 0.000 0.000
#> GSM97812 2 0.0000 0.979 0.000 1.000 0.000 0.000
#> GSM97816 3 0.1256 0.960 0.028 0.000 0.964 0.008
#> GSM97817 2 0.0000 0.979 0.000 1.000 0.000 0.000
#> GSM97820 2 0.0000 0.979 0.000 1.000 0.000 0.000
#> GSM97825 2 0.0000 0.979 0.000 1.000 0.000 0.000
#> GSM97827 2 0.0000 0.979 0.000 1.000 0.000 0.000
#> GSM97828 3 0.1388 0.957 0.028 0.000 0.960 0.012
#> GSM97833 2 0.0000 0.979 0.000 1.000 0.000 0.000
#> GSM97834 2 0.0000 0.979 0.000 1.000 0.000 0.000
#> GSM97840 2 0.3972 0.715 0.204 0.788 0.000 0.008
#> GSM97846 2 0.0000 0.979 0.000 1.000 0.000 0.000
#> GSM97848 2 0.0000 0.979 0.000 1.000 0.000 0.000
#> GSM97849 2 0.0000 0.979 0.000 1.000 0.000 0.000
#> GSM97850 2 0.0000 0.979 0.000 1.000 0.000 0.000
#> GSM97853 2 0.0000 0.979 0.000 1.000 0.000 0.000
#> GSM97855 2 0.0000 0.979 0.000 1.000 0.000 0.000
#> GSM97878 1 0.0000 0.948 1.000 0.000 0.000 0.000
#> GSM97913 1 0.0336 0.944 0.992 0.000 0.000 0.008
#> GSM97932 4 0.3837 0.706 0.224 0.000 0.000 0.776
#> GSM97939 3 0.0524 0.977 0.004 0.000 0.988 0.008
#> GSM97951 2 0.0188 0.975 0.004 0.996 0.000 0.000
#> GSM97957 3 0.0188 0.979 0.004 0.000 0.996 0.000
#> GSM97972 3 0.1256 0.960 0.028 0.000 0.964 0.008
#> GSM97793 3 0.0000 0.980 0.000 0.000 1.000 0.000
#> GSM97795 3 0.0524 0.976 0.000 0.004 0.988 0.008
#> GSM97802 1 0.1284 0.945 0.964 0.000 0.012 0.024
#> GSM97810 3 0.0524 0.977 0.004 0.000 0.988 0.008
#> GSM97815 3 0.0336 0.978 0.000 0.000 0.992 0.008
#> GSM97837 1 0.0188 0.949 0.996 0.000 0.000 0.004
#> GSM97843 3 0.0000 0.980 0.000 0.000 1.000 0.000
#> GSM97890 3 0.0000 0.980 0.000 0.000 1.000 0.000
#> GSM97899 4 0.0921 0.939 0.028 0.000 0.000 0.972
#> GSM97910 1 0.0469 0.949 0.988 0.000 0.000 0.012
#> GSM97916 1 0.0000 0.948 1.000 0.000 0.000 0.000
#> GSM97920 3 0.0188 0.979 0.004 0.000 0.996 0.000
#> GSM97921 1 0.0188 0.949 0.996 0.000 0.000 0.004
#> GSM97927 1 0.0921 0.946 0.972 0.000 0.000 0.028
#> GSM97937 1 0.0336 0.949 0.992 0.000 0.000 0.008
#> GSM97941 2 0.5212 0.291 0.420 0.572 0.000 0.008
#> GSM97943 3 0.3718 0.793 0.168 0.000 0.820 0.012
#> GSM97958 1 0.0336 0.944 0.992 0.000 0.000 0.008
#> GSM97960 3 0.0712 0.975 0.004 0.004 0.984 0.008
#> GSM97794 1 0.0336 0.944 0.992 0.000 0.000 0.008
#> GSM97796 4 0.0336 0.953 0.008 0.000 0.000 0.992
#> GSM97797 1 0.0336 0.944 0.992 0.000 0.000 0.008
#> GSM97798 4 0.0336 0.953 0.008 0.000 0.000 0.992
#> GSM97801 1 0.0188 0.949 0.996 0.000 0.000 0.004
#> GSM97806 1 0.0469 0.950 0.988 0.000 0.000 0.012
#> GSM97808 4 0.0336 0.953 0.008 0.000 0.000 0.992
#> GSM97813 1 0.2149 0.906 0.912 0.000 0.000 0.088
#> GSM97814 4 0.0336 0.953 0.008 0.000 0.000 0.992
#> GSM97818 1 0.0000 0.948 1.000 0.000 0.000 0.000
#> GSM97819 3 0.0707 0.965 0.020 0.000 0.980 0.000
#> GSM97821 1 0.0524 0.945 0.988 0.000 0.004 0.008
#> GSM97826 1 0.0336 0.949 0.992 0.000 0.000 0.008
#> GSM97829 1 0.0336 0.949 0.992 0.000 0.000 0.008
#> GSM97832 3 0.0524 0.977 0.004 0.000 0.988 0.008
#> GSM97836 1 0.0921 0.946 0.972 0.000 0.000 0.028
#> GSM97839 4 0.0336 0.953 0.008 0.000 0.000 0.992
#> GSM97844 2 0.0000 0.979 0.000 1.000 0.000 0.000
#> GSM97847 1 0.0921 0.947 0.972 0.000 0.000 0.028
#> GSM97851 4 0.3400 0.774 0.180 0.000 0.000 0.820
#> GSM97852 1 0.1211 0.941 0.960 0.000 0.000 0.040
#> GSM97856 4 0.0336 0.953 0.008 0.000 0.000 0.992
#> GSM97858 2 0.0188 0.975 0.004 0.996 0.000 0.000
#> GSM97859 1 0.1022 0.945 0.968 0.000 0.000 0.032
#> GSM97861 1 0.0921 0.946 0.972 0.000 0.000 0.028
#> GSM97863 4 0.0336 0.953 0.008 0.000 0.000 0.992
#> GSM97869 1 0.0000 0.948 1.000 0.000 0.000 0.000
#> GSM97870 1 0.0707 0.948 0.980 0.000 0.000 0.020
#> GSM97871 4 0.0336 0.953 0.008 0.000 0.000 0.992
#> GSM97877 1 0.0336 0.944 0.992 0.000 0.000 0.008
#> GSM97879 1 0.1022 0.944 0.968 0.000 0.000 0.032
#> GSM97882 1 0.0921 0.946 0.972 0.000 0.000 0.028
#> GSM97885 1 0.0188 0.949 0.996 0.000 0.000 0.004
#> GSM97886 1 0.4304 0.650 0.716 0.000 0.000 0.284
#> GSM97887 1 0.4477 0.596 0.688 0.000 0.000 0.312
#> GSM97888 1 0.1716 0.925 0.936 0.000 0.000 0.064
#> GSM97889 1 0.1118 0.943 0.964 0.000 0.000 0.036
#> GSM97891 1 0.0336 0.949 0.992 0.000 0.000 0.008
#> GSM97892 2 0.0000 0.979 0.000 1.000 0.000 0.000
#> GSM97893 1 0.3311 0.818 0.828 0.000 0.000 0.172
#> GSM97894 4 0.0336 0.953 0.008 0.000 0.000 0.992
#> GSM97895 1 0.2281 0.899 0.904 0.000 0.000 0.096
#> GSM97896 4 0.4941 0.174 0.436 0.000 0.000 0.564
#> GSM97898 4 0.0336 0.953 0.008 0.000 0.000 0.992
#> GSM97903 1 0.0188 0.949 0.996 0.000 0.000 0.004
#> GSM97905 1 0.1174 0.942 0.968 0.000 0.020 0.012
#> GSM97906 4 0.0469 0.951 0.012 0.000 0.000 0.988
#> GSM97908 1 0.1302 0.939 0.956 0.000 0.000 0.044
#> GSM97912 1 0.0188 0.949 0.996 0.000 0.000 0.004
#> GSM97914 1 0.0000 0.948 1.000 0.000 0.000 0.000
#> GSM97915 4 0.0336 0.953 0.008 0.000 0.000 0.992
#> GSM97917 1 0.3311 0.818 0.828 0.000 0.000 0.172
#> GSM97918 4 0.0336 0.953 0.008 0.000 0.000 0.992
#> GSM97919 4 0.0469 0.951 0.012 0.000 0.000 0.988
#> GSM97922 1 0.3123 0.837 0.844 0.000 0.000 0.156
#> GSM97924 2 0.0000 0.979 0.000 1.000 0.000 0.000
#> GSM97926 1 0.5459 0.217 0.552 0.000 0.432 0.016
#> GSM97930 1 0.0707 0.948 0.980 0.000 0.000 0.020
#> GSM97931 1 0.0524 0.945 0.988 0.000 0.004 0.008
#> GSM97935 1 0.0000 0.948 1.000 0.000 0.000 0.000
#> GSM97936 4 0.1474 0.921 0.052 0.000 0.000 0.948
#> GSM97938 1 0.0336 0.949 0.992 0.000 0.000 0.008
#> GSM97940 4 0.0336 0.953 0.008 0.000 0.000 0.992
#> GSM97942 3 0.0817 0.961 0.024 0.000 0.976 0.000
#> GSM97945 4 0.1716 0.911 0.064 0.000 0.000 0.936
#> GSM97946 2 0.0000 0.979 0.000 1.000 0.000 0.000
#> GSM97948 1 0.1629 0.939 0.952 0.000 0.024 0.024
#> GSM97950 1 0.4331 0.643 0.712 0.000 0.000 0.288
#> GSM97952 4 0.0336 0.953 0.008 0.000 0.000 0.992
#> GSM97953 1 0.0336 0.949 0.992 0.000 0.000 0.008
#> GSM97954 1 0.1118 0.943 0.964 0.000 0.000 0.036
#> GSM97955 4 0.1940 0.899 0.076 0.000 0.000 0.924
#> GSM97959 1 0.0336 0.944 0.992 0.000 0.000 0.008
#> GSM97961 4 0.0336 0.953 0.008 0.000 0.000 0.992
#> GSM97963 4 0.0336 0.953 0.008 0.000 0.000 0.992
#> GSM97965 4 0.0336 0.953 0.008 0.000 0.000 0.992
#> GSM97966 4 0.0336 0.953 0.008 0.000 0.000 0.992
#> GSM97967 2 0.0000 0.979 0.000 1.000 0.000 0.000
#> GSM97968 2 0.0188 0.975 0.004 0.996 0.000 0.000
#> GSM97969 1 0.1022 0.945 0.968 0.000 0.000 0.032
#> GSM97971 1 0.0592 0.949 0.984 0.000 0.000 0.016
#> GSM97799 3 0.0188 0.979 0.000 0.000 0.996 0.004
#> GSM97823 2 0.0000 0.979 0.000 1.000 0.000 0.000
#> GSM97824 3 0.0188 0.979 0.004 0.000 0.996 0.000
#> GSM97830 3 0.0000 0.980 0.000 0.000 1.000 0.000
#> GSM97835 3 0.0336 0.978 0.000 0.000 0.992 0.008
#> GSM97838 2 0.0000 0.979 0.000 1.000 0.000 0.000
#> GSM97841 2 0.0000 0.979 0.000 1.000 0.000 0.000
#> GSM97842 3 0.0336 0.978 0.000 0.000 0.992 0.008
#> GSM97854 2 0.0000 0.979 0.000 1.000 0.000 0.000
#> GSM97857 3 0.0376 0.979 0.004 0.000 0.992 0.004
#> GSM97860 3 0.0000 0.980 0.000 0.000 1.000 0.000
#> GSM97862 3 0.0000 0.980 0.000 0.000 1.000 0.000
#> GSM97864 2 0.0000 0.979 0.000 1.000 0.000 0.000
#> GSM97866 3 0.0000 0.980 0.000 0.000 1.000 0.000
#> GSM97868 3 0.0000 0.980 0.000 0.000 1.000 0.000
#> GSM97872 1 0.0188 0.949 0.996 0.000 0.000 0.004
#> GSM97873 3 0.0188 0.979 0.000 0.000 0.996 0.004
#> GSM97874 3 0.0000 0.980 0.000 0.000 1.000 0.000
#> GSM97875 3 0.0000 0.980 0.000 0.000 1.000 0.000
#> GSM97876 3 0.0000 0.980 0.000 0.000 1.000 0.000
#> GSM97880 3 0.0000 0.980 0.000 0.000 1.000 0.000
#> GSM97881 3 0.0000 0.980 0.000 0.000 1.000 0.000
#> GSM97884 3 0.0188 0.979 0.000 0.000 0.996 0.004
#> GSM97901 3 0.0000 0.980 0.000 0.000 1.000 0.000
#> GSM97902 1 0.2255 0.885 0.920 0.000 0.068 0.012
#> GSM97909 1 0.0524 0.944 0.988 0.004 0.000 0.008
#> GSM97911 3 0.0000 0.980 0.000 0.000 1.000 0.000
#> GSM97923 3 0.0000 0.980 0.000 0.000 1.000 0.000
#> GSM97928 1 0.0336 0.949 0.992 0.000 0.000 0.008
#> GSM97929 2 0.0000 0.979 0.000 1.000 0.000 0.000
#> GSM97933 3 0.0188 0.979 0.004 0.000 0.996 0.000
#> GSM97934 3 0.0188 0.979 0.004 0.000 0.996 0.000
#> GSM97944 3 0.0188 0.979 0.000 0.000 0.996 0.004
#> GSM97949 2 0.0000 0.979 0.000 1.000 0.000 0.000
#> GSM97956 3 0.0188 0.979 0.004 0.000 0.996 0.000
#> GSM97962 3 0.0188 0.979 0.004 0.000 0.996 0.000
#> GSM97964 3 0.0376 0.979 0.004 0.000 0.992 0.004
#> GSM97970 3 0.0188 0.979 0.000 0.000 0.996 0.004
#> GSM97822 1 0.0921 0.946 0.972 0.000 0.000 0.028
#> GSM97831 3 0.0000 0.980 0.000 0.000 1.000 0.000
#> GSM97845 1 0.1211 0.941 0.960 0.000 0.000 0.040
#> GSM97865 1 0.0000 0.948 1.000 0.000 0.000 0.000
#> GSM97867 3 0.0000 0.980 0.000 0.000 1.000 0.000
#> GSM97883 3 0.1389 0.939 0.048 0.000 0.952 0.000
#> GSM97897 1 0.2760 0.867 0.872 0.000 0.000 0.128
#> GSM97900 1 0.3123 0.836 0.844 0.000 0.000 0.156
#> GSM97904 1 0.0707 0.948 0.980 0.000 0.000 0.020
#> GSM97907 2 0.0000 0.979 0.000 1.000 0.000 0.000
#> GSM97925 3 0.2859 0.854 0.112 0.000 0.880 0.008
#> GSM97947 3 0.4420 0.663 0.240 0.000 0.748 0.012
cbind(get_classes(res, k = 5), get_membership(res, k = 5))
#> class entropy silhouette p1 p2 p3 p4 p5
#> GSM97800 2 0.1341 0.94955 0.000 0.944 0.000 0.000 0.056
#> GSM97803 2 0.1341 0.94955 0.000 0.944 0.000 0.000 0.056
#> GSM97804 2 0.1341 0.94955 0.000 0.944 0.000 0.000 0.056
#> GSM97805 2 0.1341 0.94955 0.000 0.944 0.000 0.000 0.056
#> GSM97807 2 0.0000 0.96492 0.000 1.000 0.000 0.000 0.000
#> GSM97809 2 0.0000 0.96492 0.000 1.000 0.000 0.000 0.000
#> GSM97811 2 0.0162 0.96356 0.000 0.996 0.000 0.000 0.004
#> GSM97812 2 0.0000 0.96492 0.000 1.000 0.000 0.000 0.000
#> GSM97816 5 0.4640 0.31748 0.016 0.000 0.400 0.000 0.584
#> GSM97817 2 0.0000 0.96492 0.000 1.000 0.000 0.000 0.000
#> GSM97820 2 0.0000 0.96492 0.000 1.000 0.000 0.000 0.000
#> GSM97825 2 0.0000 0.96492 0.000 1.000 0.000 0.000 0.000
#> GSM97827 2 0.0000 0.96492 0.000 1.000 0.000 0.000 0.000
#> GSM97828 3 0.4747 -0.11034 0.016 0.000 0.496 0.000 0.488
#> GSM97833 2 0.0000 0.96492 0.000 1.000 0.000 0.000 0.000
#> GSM97834 2 0.0000 0.96492 0.000 1.000 0.000 0.000 0.000
#> GSM97840 5 0.5663 0.05644 0.080 0.412 0.000 0.000 0.508
#> GSM97846 2 0.0000 0.96492 0.000 1.000 0.000 0.000 0.000
#> GSM97848 2 0.0000 0.96492 0.000 1.000 0.000 0.000 0.000
#> GSM97849 2 0.0000 0.96492 0.000 1.000 0.000 0.000 0.000
#> GSM97850 2 0.0000 0.96492 0.000 1.000 0.000 0.000 0.000
#> GSM97853 2 0.0000 0.96492 0.000 1.000 0.000 0.000 0.000
#> GSM97855 2 0.1571 0.91635 0.004 0.936 0.000 0.000 0.060
#> GSM97878 1 0.1851 0.88342 0.912 0.000 0.000 0.000 0.088
#> GSM97913 5 0.4278 0.08858 0.452 0.000 0.000 0.000 0.548
#> GSM97932 4 0.3039 0.74288 0.192 0.000 0.000 0.808 0.000
#> GSM97939 5 0.3957 0.47457 0.008 0.000 0.280 0.000 0.712
#> GSM97951 2 0.3728 0.67389 0.008 0.748 0.000 0.000 0.244
#> GSM97957 3 0.0771 0.89445 0.004 0.000 0.976 0.000 0.020
#> GSM97972 5 0.4640 0.31748 0.016 0.000 0.400 0.000 0.584
#> GSM97793 3 0.0609 0.89521 0.000 0.000 0.980 0.000 0.020
#> GSM97795 5 0.3910 0.48380 0.008 0.000 0.272 0.000 0.720
#> GSM97802 1 0.3002 0.85897 0.856 0.000 0.028 0.000 0.116
#> GSM97810 5 0.4016 0.48442 0.012 0.000 0.272 0.000 0.716
#> GSM97815 5 0.3992 0.48573 0.012 0.000 0.268 0.000 0.720
#> GSM97837 1 0.2377 0.87336 0.872 0.000 0.000 0.000 0.128
#> GSM97843 3 0.0162 0.89608 0.000 0.000 0.996 0.000 0.004
#> GSM97890 3 0.0609 0.89416 0.000 0.000 0.980 0.000 0.020
#> GSM97899 4 0.0404 0.91694 0.012 0.000 0.000 0.988 0.000
#> GSM97910 1 0.2280 0.87630 0.880 0.000 0.000 0.000 0.120
#> GSM97916 1 0.1851 0.88342 0.912 0.000 0.000 0.000 0.088
#> GSM97920 3 0.0290 0.89570 0.000 0.000 0.992 0.000 0.008
#> GSM97921 1 0.2127 0.88055 0.892 0.000 0.000 0.000 0.108
#> GSM97927 1 0.0579 0.88691 0.984 0.000 0.000 0.008 0.008
#> GSM97937 1 0.2329 0.87494 0.876 0.000 0.000 0.000 0.124
#> GSM97941 5 0.6109 0.34771 0.172 0.272 0.000 0.000 0.556
#> GSM97943 5 0.6175 0.36571 0.148 0.000 0.344 0.000 0.508
#> GSM97958 5 0.4278 0.08354 0.452 0.000 0.000 0.000 0.548
#> GSM97960 5 0.4039 0.48504 0.008 0.004 0.268 0.000 0.720
#> GSM97794 1 0.2230 0.87663 0.884 0.000 0.000 0.000 0.116
#> GSM97796 4 0.0000 0.92313 0.000 0.000 0.000 1.000 0.000
#> GSM97797 1 0.2230 0.87663 0.884 0.000 0.000 0.000 0.116
#> GSM97798 4 0.0000 0.92313 0.000 0.000 0.000 1.000 0.000
#> GSM97801 1 0.2329 0.87494 0.876 0.000 0.000 0.000 0.124
#> GSM97806 1 0.0290 0.88412 0.992 0.000 0.000 0.008 0.000
#> GSM97808 4 0.0000 0.92313 0.000 0.000 0.000 1.000 0.000
#> GSM97813 1 0.1197 0.86432 0.952 0.000 0.000 0.048 0.000
#> GSM97814 4 0.0000 0.92313 0.000 0.000 0.000 1.000 0.000
#> GSM97818 1 0.1908 0.88538 0.908 0.000 0.000 0.000 0.092
#> GSM97819 3 0.1493 0.87165 0.024 0.000 0.948 0.000 0.028
#> GSM97821 5 0.4287 0.07156 0.460 0.000 0.000 0.000 0.540
#> GSM97826 1 0.2074 0.88242 0.896 0.000 0.000 0.000 0.104
#> GSM97829 1 0.2329 0.87494 0.876 0.000 0.000 0.000 0.124
#> GSM97832 5 0.3910 0.48380 0.008 0.000 0.272 0.000 0.720
#> GSM97836 1 0.1638 0.88976 0.932 0.000 0.000 0.004 0.064
#> GSM97839 4 0.0000 0.92313 0.000 0.000 0.000 1.000 0.000
#> GSM97844 2 0.1341 0.94955 0.000 0.944 0.000 0.000 0.056
#> GSM97847 1 0.0324 0.88534 0.992 0.000 0.000 0.004 0.004
#> GSM97851 4 0.2648 0.78793 0.152 0.000 0.000 0.848 0.000
#> GSM97852 1 0.0290 0.88412 0.992 0.000 0.000 0.008 0.000
#> GSM97856 4 0.0000 0.92313 0.000 0.000 0.000 1.000 0.000
#> GSM97858 2 0.0404 0.96344 0.000 0.988 0.000 0.000 0.012
#> GSM97859 1 0.1628 0.89059 0.936 0.000 0.000 0.008 0.056
#> GSM97861 1 0.0290 0.88412 0.992 0.000 0.000 0.008 0.000
#> GSM97863 4 0.0000 0.92313 0.000 0.000 0.000 1.000 0.000
#> GSM97869 1 0.1671 0.88704 0.924 0.000 0.000 0.000 0.076
#> GSM97870 1 0.2280 0.87720 0.880 0.000 0.000 0.000 0.120
#> GSM97871 4 0.0000 0.92313 0.000 0.000 0.000 1.000 0.000
#> GSM97877 5 0.4278 0.08858 0.452 0.000 0.000 0.000 0.548
#> GSM97879 1 0.0290 0.88412 0.992 0.000 0.000 0.008 0.000
#> GSM97882 1 0.0451 0.88430 0.988 0.000 0.000 0.008 0.004
#> GSM97885 1 0.0290 0.88412 0.992 0.000 0.000 0.008 0.000
#> GSM97886 1 0.4114 0.35416 0.624 0.000 0.000 0.376 0.000
#> GSM97887 1 0.4273 0.11701 0.552 0.000 0.000 0.448 0.000
#> GSM97888 1 0.1341 0.85899 0.944 0.000 0.000 0.056 0.000
#> GSM97889 1 0.0579 0.88378 0.984 0.000 0.000 0.008 0.008
#> GSM97891 1 0.0290 0.88412 0.992 0.000 0.000 0.008 0.000
#> GSM97892 2 0.1197 0.95255 0.000 0.952 0.000 0.000 0.048
#> GSM97893 1 0.2286 0.80569 0.888 0.000 0.000 0.108 0.004
#> GSM97894 4 0.0510 0.91735 0.016 0.000 0.000 0.984 0.000
#> GSM97895 1 0.0794 0.87421 0.972 0.000 0.000 0.028 0.000
#> GSM97896 4 0.3913 0.54772 0.324 0.000 0.000 0.676 0.000
#> GSM97898 4 0.0000 0.92313 0.000 0.000 0.000 1.000 0.000
#> GSM97903 1 0.0162 0.88676 0.996 0.000 0.000 0.000 0.004
#> GSM97905 1 0.2984 0.85932 0.860 0.000 0.032 0.000 0.108
#> GSM97906 4 0.1671 0.87649 0.076 0.000 0.000 0.924 0.000
#> GSM97908 1 0.0290 0.88412 0.992 0.000 0.000 0.008 0.000
#> GSM97912 1 0.2280 0.87579 0.880 0.000 0.000 0.000 0.120
#> GSM97914 1 0.1732 0.88747 0.920 0.000 0.000 0.000 0.080
#> GSM97915 4 0.0000 0.92313 0.000 0.000 0.000 1.000 0.000
#> GSM97917 1 0.2719 0.76363 0.852 0.000 0.000 0.144 0.004
#> GSM97918 4 0.0510 0.91601 0.016 0.000 0.000 0.984 0.000
#> GSM97919 4 0.0609 0.91552 0.020 0.000 0.000 0.980 0.000
#> GSM97922 1 0.2329 0.79318 0.876 0.000 0.000 0.124 0.000
#> GSM97924 2 0.0290 0.96381 0.000 0.992 0.000 0.000 0.008
#> GSM97926 1 0.6532 -0.00423 0.448 0.000 0.348 0.000 0.204
#> GSM97930 1 0.0162 0.88607 0.996 0.000 0.000 0.000 0.004
#> GSM97931 5 0.4648 0.07513 0.464 0.000 0.012 0.000 0.524
#> GSM97935 1 0.0162 0.88510 0.996 0.000 0.000 0.004 0.000
#> GSM97936 4 0.1544 0.87527 0.068 0.000 0.000 0.932 0.000
#> GSM97938 1 0.2329 0.87494 0.876 0.000 0.000 0.000 0.124
#> GSM97940 4 0.0000 0.92313 0.000 0.000 0.000 1.000 0.000
#> GSM97942 3 0.1668 0.86686 0.028 0.000 0.940 0.000 0.032
#> GSM97945 4 0.2605 0.82126 0.148 0.000 0.000 0.852 0.000
#> GSM97946 2 0.0000 0.96492 0.000 1.000 0.000 0.000 0.000
#> GSM97948 1 0.3593 0.82880 0.824 0.000 0.060 0.000 0.116
#> GSM97950 4 0.4307 0.04631 0.500 0.000 0.000 0.500 0.000
#> GSM97952 4 0.0000 0.92313 0.000 0.000 0.000 1.000 0.000
#> GSM97953 1 0.2329 0.87494 0.876 0.000 0.000 0.000 0.124
#> GSM97954 1 0.0566 0.88314 0.984 0.000 0.000 0.012 0.004
#> GSM97955 4 0.2179 0.83643 0.112 0.000 0.000 0.888 0.000
#> GSM97959 1 0.2852 0.83400 0.828 0.000 0.000 0.000 0.172
#> GSM97961 4 0.0000 0.92313 0.000 0.000 0.000 1.000 0.000
#> GSM97963 4 0.0000 0.92313 0.000 0.000 0.000 1.000 0.000
#> GSM97965 4 0.0000 0.92313 0.000 0.000 0.000 1.000 0.000
#> GSM97966 4 0.0162 0.92190 0.004 0.000 0.000 0.996 0.000
#> GSM97967 2 0.0000 0.96492 0.000 1.000 0.000 0.000 0.000
#> GSM97968 2 0.4182 0.47790 0.004 0.644 0.000 0.000 0.352
#> GSM97969 1 0.0798 0.88841 0.976 0.000 0.000 0.008 0.016
#> GSM97971 1 0.1608 0.88984 0.928 0.000 0.000 0.000 0.072
#> GSM97799 3 0.3274 0.70086 0.000 0.000 0.780 0.000 0.220
#> GSM97823 2 0.0000 0.96492 0.000 1.000 0.000 0.000 0.000
#> GSM97824 3 0.0955 0.88747 0.004 0.000 0.968 0.000 0.028
#> GSM97830 3 0.0510 0.89573 0.000 0.000 0.984 0.000 0.016
#> GSM97835 5 0.3684 0.47135 0.000 0.000 0.280 0.000 0.720
#> GSM97838 2 0.0404 0.96344 0.000 0.988 0.000 0.000 0.012
#> GSM97841 2 0.0609 0.96138 0.000 0.980 0.000 0.000 0.020
#> GSM97842 5 0.4273 0.11054 0.000 0.000 0.448 0.000 0.552
#> GSM97854 2 0.1341 0.94955 0.000 0.944 0.000 0.000 0.056
#> GSM97857 3 0.2439 0.81459 0.004 0.000 0.876 0.000 0.120
#> GSM97860 3 0.0609 0.89490 0.000 0.000 0.980 0.000 0.020
#> GSM97862 3 0.0404 0.89479 0.000 0.000 0.988 0.000 0.012
#> GSM97864 2 0.1341 0.94955 0.000 0.944 0.000 0.000 0.056
#> GSM97866 3 0.0510 0.89573 0.000 0.000 0.984 0.000 0.016
#> GSM97868 3 0.0609 0.89200 0.000 0.000 0.980 0.000 0.020
#> GSM97872 1 0.2280 0.87579 0.880 0.000 0.000 0.000 0.120
#> GSM97873 5 0.4291 0.05758 0.000 0.000 0.464 0.000 0.536
#> GSM97874 3 0.0510 0.89573 0.000 0.000 0.984 0.000 0.016
#> GSM97875 3 0.0771 0.89423 0.004 0.000 0.976 0.000 0.020
#> GSM97876 3 0.0609 0.89490 0.000 0.000 0.980 0.000 0.020
#> GSM97880 3 0.0510 0.89573 0.000 0.000 0.984 0.000 0.016
#> GSM97881 3 0.0290 0.89612 0.000 0.000 0.992 0.000 0.008
#> GSM97884 3 0.4088 0.42567 0.000 0.000 0.632 0.000 0.368
#> GSM97901 3 0.0510 0.89573 0.000 0.000 0.984 0.000 0.016
#> GSM97902 1 0.4909 0.27456 0.560 0.000 0.028 0.000 0.412
#> GSM97909 5 0.4287 0.07156 0.460 0.000 0.000 0.000 0.540
#> GSM97911 3 0.0404 0.89495 0.000 0.000 0.988 0.000 0.012
#> GSM97923 3 0.0609 0.89490 0.000 0.000 0.980 0.000 0.020
#> GSM97928 1 0.1671 0.88717 0.924 0.000 0.000 0.000 0.076
#> GSM97929 2 0.1341 0.94955 0.000 0.944 0.000 0.000 0.056
#> GSM97933 3 0.0324 0.89624 0.004 0.000 0.992 0.000 0.004
#> GSM97934 3 0.0771 0.89445 0.004 0.000 0.976 0.000 0.020
#> GSM97944 3 0.2966 0.74679 0.000 0.000 0.816 0.000 0.184
#> GSM97949 2 0.0609 0.96138 0.000 0.980 0.000 0.000 0.020
#> GSM97956 3 0.0510 0.89384 0.000 0.000 0.984 0.000 0.016
#> GSM97962 3 0.0566 0.89560 0.004 0.000 0.984 0.000 0.012
#> GSM97964 3 0.3048 0.74960 0.004 0.000 0.820 0.000 0.176
#> GSM97970 3 0.3876 0.53773 0.000 0.000 0.684 0.000 0.316
#> GSM97822 1 0.0579 0.88378 0.984 0.000 0.000 0.008 0.008
#> GSM97831 3 0.0609 0.89490 0.000 0.000 0.980 0.000 0.020
#> GSM97845 1 0.0451 0.88429 0.988 0.000 0.000 0.008 0.004
#> GSM97865 1 0.1965 0.88249 0.904 0.000 0.000 0.000 0.096
#> GSM97867 3 0.0703 0.89342 0.000 0.000 0.976 0.000 0.024
#> GSM97883 3 0.2124 0.83564 0.056 0.000 0.916 0.000 0.028
#> GSM97897 1 0.1410 0.85493 0.940 0.000 0.000 0.060 0.000
#> GSM97900 1 0.1851 0.82907 0.912 0.000 0.000 0.088 0.000
#> GSM97904 1 0.2020 0.88222 0.900 0.000 0.000 0.000 0.100
#> GSM97907 2 0.1410 0.94841 0.000 0.940 0.000 0.000 0.060
#> GSM97925 3 0.4210 0.63597 0.096 0.000 0.780 0.000 0.124
#> GSM97947 3 0.5264 0.39538 0.196 0.000 0.676 0.000 0.128
cbind(get_classes(res, k = 6), get_membership(res, k = 6))
#> class entropy silhouette p1 p2 p3 p4 p5 p6
#> GSM97800 2 0.3765 0.737 0.000 0.596 0.000 0.000 0.000 NA
#> GSM97803 2 0.3747 0.740 0.000 0.604 0.000 0.000 0.000 NA
#> GSM97804 2 0.3789 0.731 0.000 0.584 0.000 0.000 0.000 NA
#> GSM97805 2 0.3804 0.727 0.000 0.576 0.000 0.000 0.000 NA
#> GSM97807 2 0.0146 0.818 0.000 0.996 0.000 0.000 0.000 NA
#> GSM97809 2 0.0458 0.814 0.000 0.984 0.000 0.000 0.000 NA
#> GSM97811 2 0.0000 0.819 0.000 1.000 0.000 0.000 0.000 NA
#> GSM97812 2 0.0000 0.819 0.000 1.000 0.000 0.000 0.000 NA
#> GSM97816 5 0.4186 0.591 0.000 0.000 0.192 0.000 0.728 NA
#> GSM97817 2 0.0547 0.820 0.000 0.980 0.000 0.000 0.000 NA
#> GSM97820 2 0.0363 0.815 0.000 0.988 0.000 0.000 0.000 NA
#> GSM97825 2 0.0146 0.819 0.000 0.996 0.000 0.000 0.000 NA
#> GSM97827 2 0.0146 0.819 0.000 0.996 0.000 0.000 0.000 NA
#> GSM97828 5 0.4317 0.505 0.000 0.000 0.252 0.000 0.688 NA
#> GSM97833 2 0.0000 0.819 0.000 1.000 0.000 0.000 0.000 NA
#> GSM97834 2 0.0146 0.819 0.000 0.996 0.000 0.000 0.000 NA
#> GSM97840 5 0.5109 0.372 0.028 0.280 0.000 0.000 0.632 NA
#> GSM97846 2 0.0260 0.820 0.000 0.992 0.000 0.000 0.000 NA
#> GSM97848 2 0.0260 0.817 0.000 0.992 0.000 0.000 0.000 NA
#> GSM97849 2 0.0000 0.819 0.000 1.000 0.000 0.000 0.000 NA
#> GSM97850 2 0.0790 0.819 0.000 0.968 0.000 0.000 0.000 NA
#> GSM97853 2 0.0000 0.819 0.000 1.000 0.000 0.000 0.000 NA
#> GSM97855 2 0.4301 0.583 0.000 0.696 0.000 0.000 0.240 NA
#> GSM97878 1 0.2581 0.849 0.856 0.000 0.000 0.000 0.128 NA
#> GSM97913 5 0.3398 0.565 0.252 0.000 0.000 0.000 0.740 NA
#> GSM97932 4 0.3652 0.566 0.324 0.000 0.000 0.672 0.000 NA
#> GSM97939 5 0.4368 0.644 0.000 0.000 0.088 0.000 0.708 NA
#> GSM97951 2 0.4933 0.313 0.000 0.536 0.000 0.000 0.396 NA
#> GSM97957 3 0.0146 0.829 0.000 0.000 0.996 0.000 0.004 NA
#> GSM97972 5 0.4294 0.598 0.004 0.000 0.188 0.000 0.728 NA
#> GSM97793 3 0.1789 0.828 0.000 0.000 0.924 0.000 0.044 NA
#> GSM97795 5 0.3627 0.667 0.000 0.000 0.080 0.000 0.792 NA
#> GSM97802 1 0.4526 0.760 0.740 0.000 0.092 0.000 0.144 NA
#> GSM97810 5 0.4030 0.660 0.000 0.000 0.080 0.000 0.748 NA
#> GSM97815 5 0.4300 0.647 0.000 0.000 0.080 0.000 0.712 NA
#> GSM97837 1 0.3806 0.817 0.776 0.000 0.000 0.000 0.136 NA
#> GSM97843 3 0.0632 0.833 0.000 0.000 0.976 0.000 0.024 NA
#> GSM97890 3 0.3274 0.804 0.000 0.000 0.824 0.000 0.096 NA
#> GSM97899 4 0.0000 0.903 0.000 0.000 0.000 1.000 0.000 NA
#> GSM97910 1 0.3588 0.823 0.788 0.000 0.000 0.000 0.152 NA
#> GSM97916 1 0.2446 0.851 0.864 0.000 0.000 0.000 0.124 NA
#> GSM97920 3 0.0935 0.833 0.000 0.000 0.964 0.000 0.032 NA
#> GSM97921 1 0.2624 0.851 0.856 0.000 0.000 0.000 0.124 NA
#> GSM97927 1 0.0260 0.863 0.992 0.000 0.000 0.000 0.008 NA
#> GSM97937 1 0.3637 0.827 0.792 0.000 0.000 0.000 0.124 NA
#> GSM97941 5 0.5072 0.544 0.084 0.172 0.000 0.000 0.696 NA
#> GSM97943 5 0.5752 0.548 0.144 0.000 0.184 0.000 0.624 NA
#> GSM97958 5 0.3314 0.590 0.224 0.000 0.000 0.000 0.764 NA
#> GSM97960 5 0.3893 0.664 0.000 0.000 0.080 0.000 0.764 NA
#> GSM97794 1 0.2482 0.848 0.848 0.000 0.000 0.000 0.148 NA
#> GSM97796 4 0.0363 0.903 0.000 0.000 0.000 0.988 0.000 NA
#> GSM97797 1 0.2730 0.844 0.836 0.000 0.000 0.000 0.152 NA
#> GSM97798 4 0.0000 0.903 0.000 0.000 0.000 1.000 0.000 NA
#> GSM97801 1 0.3806 0.817 0.776 0.000 0.000 0.000 0.136 NA
#> GSM97806 1 0.0000 0.862 1.000 0.000 0.000 0.000 0.000 NA
#> GSM97808 4 0.0000 0.903 0.000 0.000 0.000 1.000 0.000 NA
#> GSM97813 1 0.0935 0.847 0.964 0.000 0.000 0.032 0.000 NA
#> GSM97814 4 0.0000 0.903 0.000 0.000 0.000 1.000 0.000 NA
#> GSM97818 1 0.2003 0.858 0.884 0.000 0.000 0.000 0.116 NA
#> GSM97819 3 0.2658 0.817 0.000 0.000 0.864 0.000 0.100 NA
#> GSM97821 5 0.3534 0.573 0.244 0.000 0.000 0.000 0.740 NA
#> GSM97826 1 0.3534 0.831 0.800 0.000 0.000 0.000 0.124 NA
#> GSM97829 1 0.3727 0.822 0.784 0.000 0.000 0.000 0.128 NA
#> GSM97832 5 0.4127 0.657 0.000 0.000 0.088 0.000 0.740 NA
#> GSM97836 1 0.1267 0.865 0.940 0.000 0.000 0.000 0.060 NA
#> GSM97839 4 0.0363 0.903 0.000 0.000 0.000 0.988 0.000 NA
#> GSM97844 2 0.3804 0.727 0.000 0.576 0.000 0.000 0.000 NA
#> GSM97847 1 0.0000 0.862 1.000 0.000 0.000 0.000 0.000 NA
#> GSM97851 4 0.3383 0.633 0.268 0.000 0.000 0.728 0.000 NA
#> GSM97852 1 0.0000 0.862 1.000 0.000 0.000 0.000 0.000 NA
#> GSM97856 4 0.0000 0.903 0.000 0.000 0.000 1.000 0.000 NA
#> GSM97858 2 0.2912 0.793 0.000 0.784 0.000 0.000 0.000 NA
#> GSM97859 1 0.1625 0.865 0.928 0.000 0.000 0.000 0.060 NA
#> GSM97861 1 0.0000 0.862 1.000 0.000 0.000 0.000 0.000 NA
#> GSM97863 4 0.0363 0.903 0.000 0.000 0.000 0.988 0.000 NA
#> GSM97869 1 0.2100 0.857 0.884 0.000 0.000 0.000 0.112 NA
#> GSM97870 1 0.3821 0.813 0.772 0.000 0.000 0.000 0.148 NA
#> GSM97871 4 0.0000 0.903 0.000 0.000 0.000 1.000 0.000 NA
#> GSM97877 5 0.3398 0.565 0.252 0.000 0.000 0.000 0.740 NA
#> GSM97879 1 0.0000 0.862 1.000 0.000 0.000 0.000 0.000 NA
#> GSM97882 1 0.0000 0.862 1.000 0.000 0.000 0.000 0.000 NA
#> GSM97885 1 0.0000 0.862 1.000 0.000 0.000 0.000 0.000 NA
#> GSM97886 1 0.3636 0.448 0.676 0.000 0.000 0.320 0.000 NA
#> GSM97887 1 0.3756 0.357 0.644 0.000 0.000 0.352 0.000 NA
#> GSM97888 1 0.1152 0.841 0.952 0.000 0.000 0.044 0.000 NA
#> GSM97889 1 0.0146 0.861 0.996 0.000 0.000 0.000 0.000 NA
#> GSM97891 1 0.0000 0.862 1.000 0.000 0.000 0.000 0.000 NA
#> GSM97892 2 0.3797 0.729 0.000 0.580 0.000 0.000 0.000 NA
#> GSM97893 1 0.1644 0.813 0.920 0.000 0.000 0.076 0.000 NA
#> GSM97894 4 0.0405 0.903 0.004 0.000 0.000 0.988 0.000 NA
#> GSM97895 1 0.0146 0.861 0.996 0.000 0.000 0.004 0.000 NA
#> GSM97896 4 0.3769 0.516 0.356 0.000 0.000 0.640 0.000 NA
#> GSM97898 4 0.0363 0.903 0.000 0.000 0.000 0.988 0.000 NA
#> GSM97903 1 0.0000 0.862 1.000 0.000 0.000 0.000 0.000 NA
#> GSM97905 1 0.3582 0.798 0.768 0.000 0.000 0.000 0.196 NA
#> GSM97906 4 0.2320 0.805 0.132 0.000 0.000 0.864 0.000 NA
#> GSM97908 1 0.0000 0.862 1.000 0.000 0.000 0.000 0.000 NA
#> GSM97912 1 0.3767 0.819 0.780 0.000 0.000 0.000 0.132 NA
#> GSM97914 1 0.2053 0.858 0.888 0.000 0.000 0.000 0.108 NA
#> GSM97915 4 0.0363 0.903 0.000 0.000 0.000 0.988 0.000 NA
#> GSM97917 1 0.2491 0.717 0.836 0.000 0.000 0.164 0.000 NA
#> GSM97918 4 0.1563 0.866 0.056 0.000 0.000 0.932 0.000 NA
#> GSM97919 4 0.1225 0.887 0.036 0.000 0.000 0.952 0.000 NA
#> GSM97922 1 0.2234 0.769 0.872 0.000 0.000 0.124 0.000 NA
#> GSM97924 2 0.2941 0.795 0.000 0.780 0.000 0.000 0.000 NA
#> GSM97926 3 0.6602 0.138 0.232 0.000 0.464 0.000 0.260 NA
#> GSM97930 1 0.0000 0.862 1.000 0.000 0.000 0.000 0.000 NA
#> GSM97931 5 0.3770 0.562 0.244 0.000 0.000 0.000 0.728 NA
#> GSM97935 1 0.0146 0.861 0.996 0.000 0.000 0.000 0.000 NA
#> GSM97936 4 0.0632 0.893 0.024 0.000 0.000 0.976 0.000 NA
#> GSM97938 1 0.3686 0.824 0.788 0.000 0.000 0.000 0.124 NA
#> GSM97940 4 0.0000 0.903 0.000 0.000 0.000 1.000 0.000 NA
#> GSM97942 3 0.2679 0.816 0.000 0.000 0.864 0.000 0.096 NA
#> GSM97945 4 0.2378 0.805 0.152 0.000 0.000 0.848 0.000 NA
#> GSM97946 2 0.0363 0.815 0.000 0.988 0.000 0.000 0.000 NA
#> GSM97948 1 0.5775 0.573 0.608 0.000 0.160 0.000 0.196 NA
#> GSM97950 4 0.3986 0.251 0.464 0.000 0.000 0.532 0.000 NA
#> GSM97952 4 0.0000 0.903 0.000 0.000 0.000 1.000 0.000 NA
#> GSM97953 1 0.3686 0.824 0.788 0.000 0.000 0.000 0.124 NA
#> GSM97954 1 0.0000 0.862 1.000 0.000 0.000 0.000 0.000 NA
#> GSM97955 4 0.2260 0.783 0.140 0.000 0.000 0.860 0.000 NA
#> GSM97959 1 0.3975 0.323 0.544 0.000 0.000 0.000 0.452 NA
#> GSM97961 4 0.0363 0.903 0.000 0.000 0.000 0.988 0.000 NA
#> GSM97963 4 0.0146 0.903 0.000 0.000 0.000 0.996 0.000 NA
#> GSM97965 4 0.0260 0.903 0.000 0.000 0.000 0.992 0.000 NA
#> GSM97966 4 0.0260 0.901 0.008 0.000 0.000 0.992 0.000 NA
#> GSM97967 2 0.0260 0.820 0.000 0.992 0.000 0.000 0.000 NA
#> GSM97968 2 0.5029 0.174 0.000 0.484 0.000 0.000 0.444 NA
#> GSM97969 1 0.0458 0.864 0.984 0.000 0.000 0.000 0.016 NA
#> GSM97971 1 0.2509 0.860 0.876 0.000 0.000 0.000 0.088 NA
#> GSM97799 3 0.5600 0.514 0.000 0.000 0.528 0.000 0.176 NA
#> GSM97823 2 0.0458 0.814 0.000 0.984 0.000 0.000 0.000 NA
#> GSM97824 3 0.2250 0.819 0.000 0.000 0.888 0.000 0.092 NA
#> GSM97830 3 0.0603 0.825 0.000 0.000 0.980 0.000 0.004 NA
#> GSM97835 5 0.4468 0.635 0.000 0.000 0.092 0.000 0.696 NA
#> GSM97838 2 0.2762 0.796 0.000 0.804 0.000 0.000 0.000 NA
#> GSM97841 2 0.3695 0.749 0.000 0.624 0.000 0.000 0.000 NA
#> GSM97842 3 0.5991 0.345 0.000 0.000 0.436 0.000 0.256 NA
#> GSM97854 2 0.3804 0.727 0.000 0.576 0.000 0.000 0.000 NA
#> GSM97857 3 0.3431 0.731 0.000 0.000 0.756 0.000 0.228 NA
#> GSM97860 3 0.0603 0.825 0.000 0.000 0.980 0.000 0.004 NA
#> GSM97862 3 0.0777 0.833 0.000 0.000 0.972 0.000 0.024 NA
#> GSM97864 2 0.3804 0.727 0.000 0.576 0.000 0.000 0.000 NA
#> GSM97866 3 0.0000 0.830 0.000 0.000 1.000 0.000 0.000 NA
#> GSM97868 3 0.3268 0.798 0.000 0.000 0.824 0.000 0.100 NA
#> GSM97872 1 0.3686 0.824 0.788 0.000 0.000 0.000 0.124 NA
#> GSM97873 3 0.5971 0.365 0.000 0.000 0.444 0.000 0.252 NA
#> GSM97874 3 0.0603 0.825 0.000 0.000 0.980 0.000 0.004 NA
#> GSM97875 3 0.2586 0.814 0.000 0.000 0.868 0.000 0.100 NA
#> GSM97876 3 0.0603 0.825 0.000 0.000 0.980 0.000 0.004 NA
#> GSM97880 3 0.0508 0.827 0.000 0.000 0.984 0.000 0.004 NA
#> GSM97881 3 0.3118 0.804 0.000 0.000 0.836 0.000 0.092 NA
#> GSM97884 3 0.5921 0.398 0.000 0.000 0.460 0.000 0.240 NA
#> GSM97901 3 0.0405 0.831 0.000 0.000 0.988 0.000 0.008 NA
#> GSM97902 1 0.5196 0.297 0.504 0.000 0.012 0.000 0.424 NA
#> GSM97909 5 0.3946 0.590 0.228 0.016 0.000 0.000 0.736 NA
#> GSM97911 3 0.3221 0.800 0.000 0.000 0.828 0.000 0.096 NA
#> GSM97923 3 0.0858 0.824 0.000 0.000 0.968 0.000 0.004 NA
#> GSM97928 1 0.2212 0.857 0.880 0.000 0.000 0.000 0.112 NA
#> GSM97929 2 0.3804 0.727 0.000 0.576 0.000 0.000 0.000 NA
#> GSM97933 3 0.0632 0.832 0.000 0.000 0.976 0.000 0.024 NA
#> GSM97934 3 0.0291 0.828 0.000 0.000 0.992 0.000 0.004 NA
#> GSM97944 3 0.5597 0.517 0.000 0.000 0.532 0.000 0.180 NA
#> GSM97949 2 0.3547 0.763 0.000 0.668 0.000 0.000 0.000 NA
#> GSM97956 3 0.1633 0.830 0.000 0.000 0.932 0.000 0.044 NA
#> GSM97962 3 0.0713 0.833 0.000 0.000 0.972 0.000 0.028 NA
#> GSM97964 3 0.4332 0.651 0.000 0.000 0.672 0.000 0.276 NA
#> GSM97970 3 0.5824 0.432 0.000 0.000 0.484 0.000 0.216 NA
#> GSM97822 1 0.0146 0.861 0.996 0.000 0.000 0.000 0.000 NA
#> GSM97831 3 0.0405 0.827 0.000 0.000 0.988 0.000 0.004 NA
#> GSM97845 1 0.0000 0.862 1.000 0.000 0.000 0.000 0.000 NA
#> GSM97865 1 0.2346 0.852 0.868 0.000 0.000 0.000 0.124 NA
#> GSM97867 3 0.1074 0.821 0.000 0.000 0.960 0.000 0.012 NA
#> GSM97883 3 0.2565 0.818 0.008 0.000 0.872 0.000 0.104 NA
#> GSM97897 1 0.1124 0.844 0.956 0.000 0.000 0.036 0.000 NA
#> GSM97900 1 0.1700 0.813 0.916 0.000 0.000 0.080 0.000 NA
#> GSM97904 1 0.3193 0.841 0.824 0.000 0.000 0.000 0.124 NA
#> GSM97907 2 0.3797 0.729 0.000 0.580 0.000 0.000 0.000 NA
#> GSM97925 3 0.4663 0.657 0.012 0.000 0.680 0.000 0.244 NA
#> GSM97947 3 0.5305 0.598 0.048 0.000 0.648 0.000 0.236 NA
Heatmaps for the consensus matrix. It visualizes the probability of two samples to be in a same group.
consensus_heatmap(res, k = 2)
consensus_heatmap(res, k = 3)
consensus_heatmap(res, k = 4)
consensus_heatmap(res, k = 5)
consensus_heatmap(res, k = 6)
Heatmaps for the membership of samples in all partitions to see how consistent they are:
membership_heatmap(res, k = 2)
membership_heatmap(res, k = 3)
membership_heatmap(res, k = 4)
membership_heatmap(res, k = 5)
membership_heatmap(res, k = 6)
As soon as we have had the classes for columns, we can look for signatures which are significantly different between classes which can be candidate marks for certain classes. Following are the heatmaps for signatures.
Signature heatmaps where rows are scaled:
get_signatures(res, k = 2)
get_signatures(res, k = 3)
get_signatures(res, k = 4)
get_signatures(res, k = 5)
get_signatures(res, k = 6)
Signature heatmaps where rows are not scaled:
get_signatures(res, k = 2, scale_rows = FALSE)
get_signatures(res, k = 3, scale_rows = FALSE)
get_signatures(res, k = 4, scale_rows = FALSE)
get_signatures(res, k = 5, scale_rows = FALSE)
get_signatures(res, k = 6, scale_rows = FALSE)
Compare the overlap of signatures from different k:
compare_signatures(res)
get_signature() returns a data frame invisibly. TO get the list of signatures, the function
call should be assigned to a variable explicitly. In following code, if plot argument is set
to FALSE, no heatmap is plotted while only the differential analysis is performed.
# code only for demonstration
tb = get_signature(res, k = ..., plot = FALSE)
An example of the output of tb is:
#> which_row fdr mean_1 mean_2 scaled_mean_1 scaled_mean_2 km
#> 1 38 0.042760348 8.373488 9.131774 -0.5533452 0.5164555 1
#> 2 40 0.018707592 7.106213 8.469186 -0.6173731 0.5762149 1
#> 3 55 0.019134737 10.221463 11.207825 -0.6159697 0.5749050 1
#> 4 59 0.006059896 5.921854 7.869574 -0.6899429 0.6439467 1
#> 5 60 0.018055526 8.928898 10.211722 -0.6204761 0.5791110 1
#> 6 98 0.009384629 15.714769 14.887706 0.6635654 -0.6193277 2
...
The columns in tb are:
which_row: row indices corresponding to the input matrix.fdr: FDR for the differential test. mean_x: The mean value in group x.scaled_mean_x: The mean value in group x after rows are scaled.km: Row groups if k-means clustering is applied to rows.UMAP plot which shows how samples are separated.
dimension_reduction(res, k = 2, method = "UMAP")
dimension_reduction(res, k = 3, method = "UMAP")
dimension_reduction(res, k = 4, method = "UMAP")
dimension_reduction(res, k = 5, method = "UMAP")
dimension_reduction(res, k = 6, method = "UMAP")
Following heatmap shows how subgroups are split when increasing k:
collect_classes(res)
Test correlation between subgroups and known annotations. If the known annotation is numeric, one-way ANOVA test is applied, and if the known annotation is discrete, chi-squared contingency table test is applied.
test_to_known_factors(res)
#> n disease.state(p) tissue(p) k
#> CV:mclust 179 2.96e-17 1.95e-17 2
#> CV:mclust 174 3.98e-28 3.29e-29 3
#> CV:mclust 177 3.61e-29 3.94e-30 4
#> CV:mclust 151 1.06e-27 3.49e-29 5
#> CV:mclust 167 1.38e-32 8.00e-29 6
If matrix rows can be associated to genes, consider to use functional_enrichment(res,
...) to perform function enrichment for the signature genes. See this vignette for more detailed explanations.
The object with results only for a single top-value method and a single partition method can be extracted as:
res = res_list["CV", "NMF"]
# you can also extract it by
# res = res_list["CV:NMF"]
A summary of res and all the functions that can be applied to it:
res
#> A 'ConsensusPartition' object with k = 2, 3, 4, 5, 6.
#> On a matrix with 51882 rows and 180 columns.
#> Top rows (1000, 2000, 3000, 4000, 5000) are extracted by 'CV' method.
#> Subgroups are detected by 'NMF' method.
#> Performed in total 1250 partitions by row resampling.
#> Best k for subgroups seems to be 3.
#>
#> Following methods can be applied to this 'ConsensusPartition' object:
#> [1] "cola_report" "collect_classes" "collect_plots"
#> [4] "collect_stats" "colnames" "compare_signatures"
#> [7] "consensus_heatmap" "dimension_reduction" "functional_enrichment"
#> [10] "get_anno_col" "get_anno" "get_classes"
#> [13] "get_consensus" "get_matrix" "get_membership"
#> [16] "get_param" "get_signatures" "get_stats"
#> [19] "is_best_k" "is_stable_k" "membership_heatmap"
#> [22] "ncol" "nrow" "plot_ecdf"
#> [25] "rownames" "select_partition_number" "show"
#> [28] "suggest_best_k" "test_to_known_factors"
collect_plots() function collects all the plots made from res for all k (number of partitions)
into one single page to provide an easy and fast comparison between different k.
collect_plots(res)
The plots are:
k and the heatmap of
predicted classes for each k.k.k.k.All the plots in panels can be made by individual functions and they are plotted later in this section.
select_partition_number() produces several plots showing different
statistics for choosing “optimized” k. There are following statistics:
k;k, the area increased is defined as \(A_k - A_{k-1}\).The detailed explanations of these statistics can be found in the cola vignette.
Generally speaking, lower PAC score, higher mean silhouette score or higher
concordance corresponds to better partition. Rand index and Jaccard index
measure how similar the current partition is compared to partition with k-1.
If they are too similar, we won't accept k is better than k-1.
select_partition_number(res)
The numeric values for all these statistics can be obtained by get_stats().
get_stats(res)
#> k 1-PAC mean_silhouette concordance area_increased Rand Jaccard
#> 2 2 1.000 0.972 0.988 0.4972 0.505 0.505
#> 3 3 0.993 0.960 0.983 0.3108 0.773 0.581
#> 4 4 0.832 0.847 0.917 0.1090 0.913 0.759
#> 5 5 0.720 0.613 0.790 0.0648 0.959 0.860
#> 6 6 0.725 0.612 0.795 0.0383 0.893 0.634
suggest_best_k() suggests the best \(k\) based on these statistics. The rules are as follows:
suggest_best_k(res)
#> [1] 3
#> attr(,"optional")
#> [1] 2
There is also optional best \(k\) = 2 that is worth to check.
Following shows the table of the partitions (You need to click the show/hide
code output link to see it). The membership matrix (columns with name p*)
is inferred by
clue::cl_consensus()
function with the SE method. Basically the value in the membership matrix
represents the probability to belong to a certain group. The finall class
label for an item is determined with the group with highest probability it
belongs to.
In get_classes() function, the entropy is calculated from the membership
matrix and the silhouette score is calculated from the consensus matrix.
cbind(get_classes(res, k = 2), get_membership(res, k = 2))
#> class entropy silhouette p1 p2
#> GSM97800 2 0.0000 0.995 0.000 1.000
#> GSM97803 2 0.0000 0.995 0.000 1.000
#> GSM97804 2 0.0000 0.995 0.000 1.000
#> GSM97805 2 0.0000 0.995 0.000 1.000
#> GSM97807 2 0.0000 0.995 0.000 1.000
#> GSM97809 2 0.0000 0.995 0.000 1.000
#> GSM97811 2 0.0000 0.995 0.000 1.000
#> GSM97812 2 0.0000 0.995 0.000 1.000
#> GSM97816 2 0.0000 0.995 0.000 1.000
#> GSM97817 2 0.0000 0.995 0.000 1.000
#> GSM97820 2 0.0000 0.995 0.000 1.000
#> GSM97825 2 0.0000 0.995 0.000 1.000
#> GSM97827 2 0.0000 0.995 0.000 1.000
#> GSM97828 2 0.0000 0.995 0.000 1.000
#> GSM97833 2 0.0000 0.995 0.000 1.000
#> GSM97834 2 0.0000 0.995 0.000 1.000
#> GSM97840 2 0.0000 0.995 0.000 1.000
#> GSM97846 2 0.0000 0.995 0.000 1.000
#> GSM97848 2 0.0000 0.995 0.000 1.000
#> GSM97849 2 0.0000 0.995 0.000 1.000
#> GSM97850 2 0.0000 0.995 0.000 1.000
#> GSM97853 2 0.0000 0.995 0.000 1.000
#> GSM97855 2 0.0000 0.995 0.000 1.000
#> GSM97878 1 0.0000 0.982 1.000 0.000
#> GSM97913 2 0.0000 0.995 0.000 1.000
#> GSM97932 1 0.0000 0.982 1.000 0.000
#> GSM97939 2 0.0000 0.995 0.000 1.000
#> GSM97951 2 0.0000 0.995 0.000 1.000
#> GSM97957 2 0.0000 0.995 0.000 1.000
#> GSM97972 2 0.0000 0.995 0.000 1.000
#> GSM97793 1 0.0000 0.982 1.000 0.000
#> GSM97795 2 0.0000 0.995 0.000 1.000
#> GSM97802 1 0.0000 0.982 1.000 0.000
#> GSM97810 2 0.0000 0.995 0.000 1.000
#> GSM97815 2 0.0000 0.995 0.000 1.000
#> GSM97837 1 0.0000 0.982 1.000 0.000
#> GSM97843 2 0.0376 0.991 0.004 0.996
#> GSM97890 2 0.0000 0.995 0.000 1.000
#> GSM97899 1 0.0000 0.982 1.000 0.000
#> GSM97910 1 0.0000 0.982 1.000 0.000
#> GSM97916 1 0.0000 0.982 1.000 0.000
#> GSM97920 2 0.0376 0.991 0.004 0.996
#> GSM97921 1 0.0000 0.982 1.000 0.000
#> GSM97927 1 0.0000 0.982 1.000 0.000
#> GSM97937 1 0.0000 0.982 1.000 0.000
#> GSM97941 2 0.0000 0.995 0.000 1.000
#> GSM97943 1 0.9850 0.275 0.572 0.428
#> GSM97958 2 0.0000 0.995 0.000 1.000
#> GSM97960 2 0.0000 0.995 0.000 1.000
#> GSM97794 1 0.1633 0.962 0.976 0.024
#> GSM97796 1 0.0000 0.982 1.000 0.000
#> GSM97797 1 0.7950 0.695 0.760 0.240
#> GSM97798 1 0.0000 0.982 1.000 0.000
#> GSM97801 1 0.0000 0.982 1.000 0.000
#> GSM97806 1 0.0000 0.982 1.000 0.000
#> GSM97808 1 0.0000 0.982 1.000 0.000
#> GSM97813 1 0.0000 0.982 1.000 0.000
#> GSM97814 1 0.0000 0.982 1.000 0.000
#> GSM97818 1 0.0000 0.982 1.000 0.000
#> GSM97819 1 0.0000 0.982 1.000 0.000
#> GSM97821 2 0.0000 0.995 0.000 1.000
#> GSM97826 1 0.0000 0.982 1.000 0.000
#> GSM97829 1 0.0000 0.982 1.000 0.000
#> GSM97832 2 0.0000 0.995 0.000 1.000
#> GSM97836 1 0.0000 0.982 1.000 0.000
#> GSM97839 1 0.0000 0.982 1.000 0.000
#> GSM97844 2 0.0000 0.995 0.000 1.000
#> GSM97847 1 0.0000 0.982 1.000 0.000
#> GSM97851 1 0.0000 0.982 1.000 0.000
#> GSM97852 1 0.0000 0.982 1.000 0.000
#> GSM97856 1 0.0000 0.982 1.000 0.000
#> GSM97858 2 0.0000 0.995 0.000 1.000
#> GSM97859 1 0.0000 0.982 1.000 0.000
#> GSM97861 1 0.0000 0.982 1.000 0.000
#> GSM97863 1 0.0000 0.982 1.000 0.000
#> GSM97869 1 0.0000 0.982 1.000 0.000
#> GSM97870 1 0.0000 0.982 1.000 0.000
#> GSM97871 1 0.0000 0.982 1.000 0.000
#> GSM97877 2 0.0000 0.995 0.000 1.000
#> GSM97879 1 0.0000 0.982 1.000 0.000
#> GSM97882 1 0.0000 0.982 1.000 0.000
#> GSM97885 1 0.0000 0.982 1.000 0.000
#> GSM97886 1 0.0000 0.982 1.000 0.000
#> GSM97887 1 0.0000 0.982 1.000 0.000
#> GSM97888 1 0.0000 0.982 1.000 0.000
#> GSM97889 1 0.0000 0.982 1.000 0.000
#> GSM97891 1 0.0000 0.982 1.000 0.000
#> GSM97892 2 0.0000 0.995 0.000 1.000
#> GSM97893 1 0.0000 0.982 1.000 0.000
#> GSM97894 1 0.0000 0.982 1.000 0.000
#> GSM97895 1 0.0000 0.982 1.000 0.000
#> GSM97896 1 0.0000 0.982 1.000 0.000
#> GSM97898 1 0.0000 0.982 1.000 0.000
#> GSM97903 1 0.0000 0.982 1.000 0.000
#> GSM97905 1 0.0000 0.982 1.000 0.000
#> GSM97906 1 0.0000 0.982 1.000 0.000
#> GSM97908 1 0.0000 0.982 1.000 0.000
#> GSM97912 1 0.0000 0.982 1.000 0.000
#> GSM97914 1 0.0000 0.982 1.000 0.000
#> GSM97915 1 0.0000 0.982 1.000 0.000
#> GSM97917 1 0.0000 0.982 1.000 0.000
#> GSM97918 1 0.0000 0.982 1.000 0.000
#> GSM97919 1 0.0000 0.982 1.000 0.000
#> GSM97922 1 0.0000 0.982 1.000 0.000
#> GSM97924 2 0.0000 0.995 0.000 1.000
#> GSM97926 1 0.2043 0.955 0.968 0.032
#> GSM97930 1 0.0000 0.982 1.000 0.000
#> GSM97931 2 0.0000 0.995 0.000 1.000
#> GSM97935 1 0.0000 0.982 1.000 0.000
#> GSM97936 1 0.0000 0.982 1.000 0.000
#> GSM97938 1 0.0000 0.982 1.000 0.000
#> GSM97940 1 0.0000 0.982 1.000 0.000
#> GSM97942 1 0.0000 0.982 1.000 0.000
#> GSM97945 1 0.0000 0.982 1.000 0.000
#> GSM97946 2 0.0000 0.995 0.000 1.000
#> GSM97948 1 0.0000 0.982 1.000 0.000
#> GSM97950 1 0.0000 0.982 1.000 0.000
#> GSM97952 1 0.0000 0.982 1.000 0.000
#> GSM97953 1 0.0000 0.982 1.000 0.000
#> GSM97954 1 0.0000 0.982 1.000 0.000
#> GSM97955 1 0.0000 0.982 1.000 0.000
#> GSM97959 2 0.6801 0.776 0.180 0.820
#> GSM97961 1 0.0000 0.982 1.000 0.000
#> GSM97963 1 0.0000 0.982 1.000 0.000
#> GSM97965 1 0.0000 0.982 1.000 0.000
#> GSM97966 1 0.0000 0.982 1.000 0.000
#> GSM97967 2 0.0000 0.995 0.000 1.000
#> GSM97968 2 0.0000 0.995 0.000 1.000
#> GSM97969 1 0.0000 0.982 1.000 0.000
#> GSM97971 1 0.0000 0.982 1.000 0.000
#> GSM97799 2 0.0000 0.995 0.000 1.000
#> GSM97823 2 0.0000 0.995 0.000 1.000
#> GSM97824 2 0.0000 0.995 0.000 1.000
#> GSM97830 2 0.3584 0.925 0.068 0.932
#> GSM97835 2 0.0000 0.995 0.000 1.000
#> GSM97838 2 0.0000 0.995 0.000 1.000
#> GSM97841 2 0.0000 0.995 0.000 1.000
#> GSM97842 2 0.0000 0.995 0.000 1.000
#> GSM97854 2 0.0000 0.995 0.000 1.000
#> GSM97857 2 0.0000 0.995 0.000 1.000
#> GSM97860 1 0.2603 0.943 0.956 0.044
#> GSM97862 2 0.0000 0.995 0.000 1.000
#> GSM97864 2 0.0000 0.995 0.000 1.000
#> GSM97866 2 0.0000 0.995 0.000 1.000
#> GSM97868 2 0.0000 0.995 0.000 1.000
#> GSM97872 1 0.0000 0.982 1.000 0.000
#> GSM97873 2 0.0000 0.995 0.000 1.000
#> GSM97874 1 0.3274 0.928 0.940 0.060
#> GSM97875 2 0.5737 0.840 0.136 0.864
#> GSM97876 1 0.8861 0.581 0.696 0.304
#> GSM97880 1 0.0000 0.982 1.000 0.000
#> GSM97881 2 0.0000 0.995 0.000 1.000
#> GSM97884 2 0.0000 0.995 0.000 1.000
#> GSM97901 2 0.0000 0.995 0.000 1.000
#> GSM97902 1 0.9000 0.552 0.684 0.316
#> GSM97909 2 0.0000 0.995 0.000 1.000
#> GSM97911 2 0.0000 0.995 0.000 1.000
#> GSM97923 1 0.0000 0.982 1.000 0.000
#> GSM97928 1 0.0000 0.982 1.000 0.000
#> GSM97929 2 0.0000 0.995 0.000 1.000
#> GSM97933 1 0.4022 0.908 0.920 0.080
#> GSM97934 1 0.6801 0.787 0.820 0.180
#> GSM97944 2 0.0000 0.995 0.000 1.000
#> GSM97949 2 0.0000 0.995 0.000 1.000
#> GSM97956 2 0.0000 0.995 0.000 1.000
#> GSM97962 2 0.0000 0.995 0.000 1.000
#> GSM97964 2 0.0000 0.995 0.000 1.000
#> GSM97970 2 0.0000 0.995 0.000 1.000
#> GSM97822 1 0.0000 0.982 1.000 0.000
#> GSM97831 2 0.0000 0.995 0.000 1.000
#> GSM97845 1 0.0000 0.982 1.000 0.000
#> GSM97865 1 0.0000 0.982 1.000 0.000
#> GSM97867 1 0.0000 0.982 1.000 0.000
#> GSM97883 1 0.0000 0.982 1.000 0.000
#> GSM97897 1 0.0000 0.982 1.000 0.000
#> GSM97900 1 0.0000 0.982 1.000 0.000
#> GSM97904 1 0.0000 0.982 1.000 0.000
#> GSM97907 2 0.0000 0.995 0.000 1.000
#> GSM97925 1 0.4690 0.886 0.900 0.100
#> GSM97947 1 0.0000 0.982 1.000 0.000
cbind(get_classes(res, k = 3), get_membership(res, k = 3))
#> class entropy silhouette p1 p2 p3
#> GSM97800 2 0.0000 0.9754 0.000 1.000 0.000
#> GSM97803 2 0.0000 0.9754 0.000 1.000 0.000
#> GSM97804 2 0.0000 0.9754 0.000 1.000 0.000
#> GSM97805 2 0.0000 0.9754 0.000 1.000 0.000
#> GSM97807 2 0.0000 0.9754 0.000 1.000 0.000
#> GSM97809 2 0.0000 0.9754 0.000 1.000 0.000
#> GSM97811 2 0.0000 0.9754 0.000 1.000 0.000
#> GSM97812 2 0.0000 0.9754 0.000 1.000 0.000
#> GSM97816 2 0.0000 0.9754 0.000 1.000 0.000
#> GSM97817 2 0.0000 0.9754 0.000 1.000 0.000
#> GSM97820 2 0.0000 0.9754 0.000 1.000 0.000
#> GSM97825 2 0.0000 0.9754 0.000 1.000 0.000
#> GSM97827 2 0.0000 0.9754 0.000 1.000 0.000
#> GSM97828 2 0.2165 0.9173 0.000 0.936 0.064
#> GSM97833 2 0.0000 0.9754 0.000 1.000 0.000
#> GSM97834 2 0.0000 0.9754 0.000 1.000 0.000
#> GSM97840 2 0.0000 0.9754 0.000 1.000 0.000
#> GSM97846 2 0.0000 0.9754 0.000 1.000 0.000
#> GSM97848 2 0.0000 0.9754 0.000 1.000 0.000
#> GSM97849 2 0.0000 0.9754 0.000 1.000 0.000
#> GSM97850 2 0.0000 0.9754 0.000 1.000 0.000
#> GSM97853 2 0.0000 0.9754 0.000 1.000 0.000
#> GSM97855 2 0.0000 0.9754 0.000 1.000 0.000
#> GSM97878 1 0.0000 0.9855 1.000 0.000 0.000
#> GSM97913 2 0.0000 0.9754 0.000 1.000 0.000
#> GSM97932 1 0.0000 0.9855 1.000 0.000 0.000
#> GSM97939 3 0.5363 0.6122 0.000 0.276 0.724
#> GSM97951 2 0.0000 0.9754 0.000 1.000 0.000
#> GSM97957 3 0.0000 0.9862 0.000 0.000 1.000
#> GSM97972 2 0.0000 0.9754 0.000 1.000 0.000
#> GSM97793 3 0.0000 0.9862 0.000 0.000 1.000
#> GSM97795 2 0.0424 0.9694 0.000 0.992 0.008
#> GSM97802 3 0.0000 0.9862 0.000 0.000 1.000
#> GSM97810 2 0.0424 0.9694 0.000 0.992 0.008
#> GSM97815 2 0.3941 0.8083 0.000 0.844 0.156
#> GSM97837 1 0.0000 0.9855 1.000 0.000 0.000
#> GSM97843 3 0.0000 0.9862 0.000 0.000 1.000
#> GSM97890 3 0.0000 0.9862 0.000 0.000 1.000
#> GSM97899 1 0.0000 0.9855 1.000 0.000 0.000
#> GSM97910 3 0.4235 0.7813 0.176 0.000 0.824
#> GSM97916 1 0.0000 0.9855 1.000 0.000 0.000
#> GSM97920 3 0.0000 0.9862 0.000 0.000 1.000
#> GSM97921 1 0.0000 0.9855 1.000 0.000 0.000
#> GSM97927 1 0.0000 0.9855 1.000 0.000 0.000
#> GSM97937 1 0.0000 0.9855 1.000 0.000 0.000
#> GSM97941 2 0.0000 0.9754 0.000 1.000 0.000
#> GSM97943 2 0.9947 0.0471 0.292 0.380 0.328
#> GSM97958 2 0.0000 0.9754 0.000 1.000 0.000
#> GSM97960 2 0.0237 0.9724 0.000 0.996 0.004
#> GSM97794 1 0.0592 0.9746 0.988 0.012 0.000
#> GSM97796 1 0.0000 0.9855 1.000 0.000 0.000
#> GSM97797 1 0.4178 0.7865 0.828 0.172 0.000
#> GSM97798 1 0.0000 0.9855 1.000 0.000 0.000
#> GSM97801 1 0.0000 0.9855 1.000 0.000 0.000
#> GSM97806 1 0.0000 0.9855 1.000 0.000 0.000
#> GSM97808 1 0.0000 0.9855 1.000 0.000 0.000
#> GSM97813 1 0.0000 0.9855 1.000 0.000 0.000
#> GSM97814 1 0.0000 0.9855 1.000 0.000 0.000
#> GSM97818 1 0.0000 0.9855 1.000 0.000 0.000
#> GSM97819 3 0.0000 0.9862 0.000 0.000 1.000
#> GSM97821 2 0.0000 0.9754 0.000 1.000 0.000
#> GSM97826 1 0.0000 0.9855 1.000 0.000 0.000
#> GSM97829 1 0.0000 0.9855 1.000 0.000 0.000
#> GSM97832 2 0.2878 0.8826 0.000 0.904 0.096
#> GSM97836 1 0.4235 0.7846 0.824 0.000 0.176
#> GSM97839 1 0.0000 0.9855 1.000 0.000 0.000
#> GSM97844 2 0.0000 0.9754 0.000 1.000 0.000
#> GSM97847 1 0.0000 0.9855 1.000 0.000 0.000
#> GSM97851 1 0.0000 0.9855 1.000 0.000 0.000
#> GSM97852 1 0.0000 0.9855 1.000 0.000 0.000
#> GSM97856 1 0.0000 0.9855 1.000 0.000 0.000
#> GSM97858 2 0.0000 0.9754 0.000 1.000 0.000
#> GSM97859 1 0.0424 0.9786 0.992 0.000 0.008
#> GSM97861 1 0.0000 0.9855 1.000 0.000 0.000
#> GSM97863 1 0.0000 0.9855 1.000 0.000 0.000
#> GSM97869 1 0.0000 0.9855 1.000 0.000 0.000
#> GSM97870 3 0.0237 0.9824 0.004 0.000 0.996
#> GSM97871 1 0.0000 0.9855 1.000 0.000 0.000
#> GSM97877 2 0.0000 0.9754 0.000 1.000 0.000
#> GSM97879 1 0.0000 0.9855 1.000 0.000 0.000
#> GSM97882 1 0.0000 0.9855 1.000 0.000 0.000
#> GSM97885 1 0.0000 0.9855 1.000 0.000 0.000
#> GSM97886 1 0.0000 0.9855 1.000 0.000 0.000
#> GSM97887 1 0.0000 0.9855 1.000 0.000 0.000
#> GSM97888 1 0.0000 0.9855 1.000 0.000 0.000
#> GSM97889 1 0.1163 0.9600 0.972 0.000 0.028
#> GSM97891 1 0.0000 0.9855 1.000 0.000 0.000
#> GSM97892 2 0.0000 0.9754 0.000 1.000 0.000
#> GSM97893 1 0.0000 0.9855 1.000 0.000 0.000
#> GSM97894 1 0.0000 0.9855 1.000 0.000 0.000
#> GSM97895 1 0.0000 0.9855 1.000 0.000 0.000
#> GSM97896 1 0.0000 0.9855 1.000 0.000 0.000
#> GSM97898 1 0.0000 0.9855 1.000 0.000 0.000
#> GSM97903 1 0.0000 0.9855 1.000 0.000 0.000
#> GSM97905 3 0.0424 0.9784 0.008 0.000 0.992
#> GSM97906 1 0.0000 0.9855 1.000 0.000 0.000
#> GSM97908 1 0.0000 0.9855 1.000 0.000 0.000
#> GSM97912 1 0.5363 0.6212 0.724 0.000 0.276
#> GSM97914 1 0.0000 0.9855 1.000 0.000 0.000
#> GSM97915 1 0.0000 0.9855 1.000 0.000 0.000
#> GSM97917 1 0.0000 0.9855 1.000 0.000 0.000
#> GSM97918 1 0.0000 0.9855 1.000 0.000 0.000
#> GSM97919 1 0.0000 0.9855 1.000 0.000 0.000
#> GSM97922 1 0.0000 0.9855 1.000 0.000 0.000
#> GSM97924 2 0.0000 0.9754 0.000 1.000 0.000
#> GSM97926 3 0.0000 0.9862 0.000 0.000 1.000
#> GSM97930 1 0.0000 0.9855 1.000 0.000 0.000
#> GSM97931 2 0.1289 0.9486 0.000 0.968 0.032
#> GSM97935 1 0.0000 0.9855 1.000 0.000 0.000
#> GSM97936 1 0.0000 0.9855 1.000 0.000 0.000
#> GSM97938 1 0.0000 0.9855 1.000 0.000 0.000
#> GSM97940 1 0.0000 0.9855 1.000 0.000 0.000
#> GSM97942 3 0.0000 0.9862 0.000 0.000 1.000
#> GSM97945 1 0.0000 0.9855 1.000 0.000 0.000
#> GSM97946 2 0.0000 0.9754 0.000 1.000 0.000
#> GSM97948 3 0.0000 0.9862 0.000 0.000 1.000
#> GSM97950 1 0.0000 0.9855 1.000 0.000 0.000
#> GSM97952 1 0.0000 0.9855 1.000 0.000 0.000
#> GSM97953 1 0.0000 0.9855 1.000 0.000 0.000
#> GSM97954 1 0.0000 0.9855 1.000 0.000 0.000
#> GSM97955 1 0.0000 0.9855 1.000 0.000 0.000
#> GSM97959 2 0.5560 0.5658 0.300 0.700 0.000
#> GSM97961 1 0.0000 0.9855 1.000 0.000 0.000
#> GSM97963 1 0.0000 0.9855 1.000 0.000 0.000
#> GSM97965 1 0.0000 0.9855 1.000 0.000 0.000
#> GSM97966 1 0.0000 0.9855 1.000 0.000 0.000
#> GSM97967 2 0.0000 0.9754 0.000 1.000 0.000
#> GSM97968 2 0.0000 0.9754 0.000 1.000 0.000
#> GSM97969 1 0.0000 0.9855 1.000 0.000 0.000
#> GSM97971 1 0.0000 0.9855 1.000 0.000 0.000
#> GSM97799 3 0.0000 0.9862 0.000 0.000 1.000
#> GSM97823 2 0.0000 0.9754 0.000 1.000 0.000
#> GSM97824 3 0.0000 0.9862 0.000 0.000 1.000
#> GSM97830 3 0.0000 0.9862 0.000 0.000 1.000
#> GSM97835 3 0.2959 0.8819 0.000 0.100 0.900
#> GSM97838 2 0.0000 0.9754 0.000 1.000 0.000
#> GSM97841 2 0.0000 0.9754 0.000 1.000 0.000
#> GSM97842 3 0.0000 0.9862 0.000 0.000 1.000
#> GSM97854 2 0.0000 0.9754 0.000 1.000 0.000
#> GSM97857 3 0.0424 0.9794 0.000 0.008 0.992
#> GSM97860 3 0.0000 0.9862 0.000 0.000 1.000
#> GSM97862 3 0.0000 0.9862 0.000 0.000 1.000
#> GSM97864 2 0.0000 0.9754 0.000 1.000 0.000
#> GSM97866 3 0.0000 0.9862 0.000 0.000 1.000
#> GSM97868 3 0.0000 0.9862 0.000 0.000 1.000
#> GSM97872 1 0.0000 0.9855 1.000 0.000 0.000
#> GSM97873 3 0.0000 0.9862 0.000 0.000 1.000
#> GSM97874 3 0.0000 0.9862 0.000 0.000 1.000
#> GSM97875 3 0.0000 0.9862 0.000 0.000 1.000
#> GSM97876 3 0.0000 0.9862 0.000 0.000 1.000
#> GSM97880 3 0.0000 0.9862 0.000 0.000 1.000
#> GSM97881 3 0.0000 0.9862 0.000 0.000 1.000
#> GSM97884 3 0.0000 0.9862 0.000 0.000 1.000
#> GSM97901 3 0.0000 0.9862 0.000 0.000 1.000
#> GSM97902 1 0.6244 0.2037 0.560 0.440 0.000
#> GSM97909 2 0.0000 0.9754 0.000 1.000 0.000
#> GSM97911 3 0.0000 0.9862 0.000 0.000 1.000
#> GSM97923 3 0.0000 0.9862 0.000 0.000 1.000
#> GSM97928 1 0.0000 0.9855 1.000 0.000 0.000
#> GSM97929 2 0.0000 0.9754 0.000 1.000 0.000
#> GSM97933 3 0.0000 0.9862 0.000 0.000 1.000
#> GSM97934 3 0.0000 0.9862 0.000 0.000 1.000
#> GSM97944 3 0.0000 0.9862 0.000 0.000 1.000
#> GSM97949 2 0.0000 0.9754 0.000 1.000 0.000
#> GSM97956 3 0.0000 0.9862 0.000 0.000 1.000
#> GSM97962 3 0.0000 0.9862 0.000 0.000 1.000
#> GSM97964 3 0.0424 0.9794 0.000 0.008 0.992
#> GSM97970 3 0.0000 0.9862 0.000 0.000 1.000
#> GSM97822 1 0.0000 0.9855 1.000 0.000 0.000
#> GSM97831 3 0.0000 0.9862 0.000 0.000 1.000
#> GSM97845 1 0.0000 0.9855 1.000 0.000 0.000
#> GSM97865 1 0.0000 0.9855 1.000 0.000 0.000
#> GSM97867 3 0.0000 0.9862 0.000 0.000 1.000
#> GSM97883 3 0.0000 0.9862 0.000 0.000 1.000
#> GSM97897 1 0.0000 0.9855 1.000 0.000 0.000
#> GSM97900 1 0.0424 0.9786 0.992 0.000 0.008
#> GSM97904 1 0.0000 0.9855 1.000 0.000 0.000
#> GSM97907 2 0.0000 0.9754 0.000 1.000 0.000
#> GSM97925 3 0.0000 0.9862 0.000 0.000 1.000
#> GSM97947 3 0.0000 0.9862 0.000 0.000 1.000
cbind(get_classes(res, k = 4), get_membership(res, k = 4))
#> class entropy silhouette p1 p2 p3 p4
#> GSM97800 2 0.0000 0.9696 0.000 1.000 0.000 0.000
#> GSM97803 2 0.0000 0.9696 0.000 1.000 0.000 0.000
#> GSM97804 2 0.0000 0.9696 0.000 1.000 0.000 0.000
#> GSM97805 2 0.0000 0.9696 0.000 1.000 0.000 0.000
#> GSM97807 2 0.0000 0.9696 0.000 1.000 0.000 0.000
#> GSM97809 2 0.0000 0.9696 0.000 1.000 0.000 0.000
#> GSM97811 2 0.0000 0.9696 0.000 1.000 0.000 0.000
#> GSM97812 2 0.0000 0.9696 0.000 1.000 0.000 0.000
#> GSM97816 1 0.2589 0.7242 0.912 0.044 0.044 0.000
#> GSM97817 2 0.0000 0.9696 0.000 1.000 0.000 0.000
#> GSM97820 2 0.0000 0.9696 0.000 1.000 0.000 0.000
#> GSM97825 2 0.0000 0.9696 0.000 1.000 0.000 0.000
#> GSM97827 2 0.0000 0.9696 0.000 1.000 0.000 0.000
#> GSM97828 1 0.1716 0.7307 0.936 0.000 0.064 0.000
#> GSM97833 2 0.0000 0.9696 0.000 1.000 0.000 0.000
#> GSM97834 2 0.0000 0.9696 0.000 1.000 0.000 0.000
#> GSM97840 2 0.0000 0.9696 0.000 1.000 0.000 0.000
#> GSM97846 2 0.0000 0.9696 0.000 1.000 0.000 0.000
#> GSM97848 2 0.0000 0.9696 0.000 1.000 0.000 0.000
#> GSM97849 2 0.0000 0.9696 0.000 1.000 0.000 0.000
#> GSM97850 2 0.0000 0.9696 0.000 1.000 0.000 0.000
#> GSM97853 2 0.0000 0.9696 0.000 1.000 0.000 0.000
#> GSM97855 2 0.0000 0.9696 0.000 1.000 0.000 0.000
#> GSM97878 4 0.2197 0.9073 0.080 0.000 0.004 0.916
#> GSM97913 2 0.0336 0.9623 0.008 0.992 0.000 0.000
#> GSM97932 4 0.1637 0.9183 0.060 0.000 0.000 0.940
#> GSM97939 3 0.6356 0.5246 0.320 0.084 0.596 0.000
#> GSM97951 2 0.0000 0.9696 0.000 1.000 0.000 0.000
#> GSM97957 1 0.3688 0.6049 0.792 0.000 0.208 0.000
#> GSM97972 1 0.2494 0.7276 0.916 0.036 0.048 0.000
#> GSM97793 3 0.1792 0.8651 0.068 0.000 0.932 0.000
#> GSM97795 2 0.0895 0.9508 0.004 0.976 0.020 0.000
#> GSM97802 3 0.3463 0.7287 0.040 0.000 0.864 0.096
#> GSM97810 2 0.5179 0.6218 0.220 0.728 0.052 0.000
#> GSM97815 2 0.2814 0.8306 0.000 0.868 0.132 0.000
#> GSM97837 1 0.1545 0.7459 0.952 0.000 0.008 0.040
#> GSM97843 3 0.2921 0.8383 0.140 0.000 0.860 0.000
#> GSM97890 3 0.0469 0.8599 0.012 0.000 0.988 0.000
#> GSM97899 4 0.0707 0.9295 0.020 0.000 0.000 0.980
#> GSM97910 1 0.5030 0.6389 0.752 0.000 0.188 0.060
#> GSM97916 4 0.1211 0.9268 0.040 0.000 0.000 0.960
#> GSM97920 3 0.4907 0.4412 0.420 0.000 0.580 0.000
#> GSM97921 1 0.4790 0.3912 0.620 0.000 0.000 0.380
#> GSM97927 4 0.0592 0.9330 0.016 0.000 0.000 0.984
#> GSM97937 1 0.3764 0.6898 0.784 0.000 0.000 0.216
#> GSM97941 2 0.0000 0.9696 0.000 1.000 0.000 0.000
#> GSM97943 1 0.1716 0.7308 0.936 0.000 0.064 0.000
#> GSM97958 1 0.5050 0.2466 0.588 0.408 0.000 0.004
#> GSM97960 2 0.0000 0.9696 0.000 1.000 0.000 0.000
#> GSM97794 4 0.2255 0.8894 0.012 0.068 0.000 0.920
#> GSM97796 4 0.0188 0.9324 0.004 0.000 0.000 0.996
#> GSM97797 4 0.4260 0.7314 0.020 0.180 0.004 0.796
#> GSM97798 4 0.1624 0.9186 0.028 0.000 0.020 0.952
#> GSM97801 1 0.2611 0.7402 0.896 0.000 0.008 0.096
#> GSM97806 4 0.1520 0.9206 0.024 0.000 0.020 0.956
#> GSM97808 4 0.0592 0.9303 0.016 0.000 0.000 0.984
#> GSM97813 4 0.0779 0.9325 0.016 0.000 0.004 0.980
#> GSM97814 4 0.1284 0.9243 0.024 0.000 0.012 0.964
#> GSM97818 4 0.5007 0.4374 0.356 0.008 0.000 0.636
#> GSM97819 3 0.0469 0.8635 0.012 0.000 0.988 0.000
#> GSM97821 2 0.1807 0.9190 0.008 0.940 0.052 0.000
#> GSM97826 1 0.3569 0.7037 0.804 0.000 0.000 0.196
#> GSM97829 1 0.3837 0.6839 0.776 0.000 0.000 0.224
#> GSM97832 2 0.5140 0.6793 0.144 0.760 0.096 0.000
#> GSM97836 4 0.5131 0.5879 0.028 0.000 0.280 0.692
#> GSM97839 4 0.0000 0.9324 0.000 0.000 0.000 1.000
#> GSM97844 2 0.0000 0.9696 0.000 1.000 0.000 0.000
#> GSM97847 4 0.1867 0.9117 0.072 0.000 0.000 0.928
#> GSM97851 4 0.1389 0.9239 0.048 0.000 0.000 0.952
#> GSM97852 4 0.1211 0.9268 0.040 0.000 0.000 0.960
#> GSM97856 4 0.1510 0.9207 0.028 0.000 0.016 0.956
#> GSM97858 2 0.0000 0.9696 0.000 1.000 0.000 0.000
#> GSM97859 4 0.1706 0.9277 0.036 0.000 0.016 0.948
#> GSM97861 4 0.1510 0.9233 0.028 0.000 0.016 0.956
#> GSM97863 4 0.0336 0.9323 0.008 0.000 0.000 0.992
#> GSM97869 4 0.1059 0.9307 0.016 0.000 0.012 0.972
#> GSM97870 3 0.4925 0.4282 0.428 0.000 0.572 0.000
#> GSM97871 4 0.1042 0.9275 0.020 0.000 0.008 0.972
#> GSM97877 2 0.0000 0.9696 0.000 1.000 0.000 0.000
#> GSM97879 4 0.0707 0.9314 0.020 0.000 0.000 0.980
#> GSM97882 4 0.2644 0.8873 0.032 0.000 0.060 0.908
#> GSM97885 4 0.0469 0.9322 0.012 0.000 0.000 0.988
#> GSM97886 4 0.1510 0.9207 0.028 0.000 0.016 0.956
#> GSM97887 4 0.3372 0.8480 0.036 0.000 0.096 0.868
#> GSM97888 4 0.0707 0.9306 0.020 0.000 0.000 0.980
#> GSM97889 4 0.4988 0.6616 0.036 0.000 0.236 0.728
#> GSM97891 4 0.2131 0.9061 0.036 0.000 0.032 0.932
#> GSM97892 2 0.0000 0.9696 0.000 1.000 0.000 0.000
#> GSM97893 4 0.2011 0.9055 0.080 0.000 0.000 0.920
#> GSM97894 4 0.0707 0.9329 0.020 0.000 0.000 0.980
#> GSM97895 4 0.1389 0.9242 0.048 0.000 0.000 0.952
#> GSM97896 4 0.0592 0.9303 0.016 0.000 0.000 0.984
#> GSM97898 4 0.0592 0.9319 0.016 0.000 0.000 0.984
#> GSM97903 4 0.1211 0.9268 0.040 0.000 0.000 0.960
#> GSM97905 3 0.2593 0.8561 0.104 0.000 0.892 0.004
#> GSM97906 4 0.0592 0.9307 0.016 0.000 0.000 0.984
#> GSM97908 4 0.1302 0.9255 0.044 0.000 0.000 0.956
#> GSM97912 1 0.2813 0.7329 0.896 0.000 0.080 0.024
#> GSM97914 4 0.4222 0.6338 0.272 0.000 0.000 0.728
#> GSM97915 4 0.0707 0.9333 0.020 0.000 0.000 0.980
#> GSM97917 4 0.1867 0.9113 0.072 0.000 0.000 0.928
#> GSM97918 4 0.1118 0.9279 0.036 0.000 0.000 0.964
#> GSM97919 4 0.0921 0.9304 0.028 0.000 0.000 0.972
#> GSM97922 4 0.0592 0.9322 0.016 0.000 0.000 0.984
#> GSM97924 2 0.0000 0.9696 0.000 1.000 0.000 0.000
#> GSM97926 3 0.1356 0.8425 0.032 0.000 0.960 0.008
#> GSM97930 4 0.3219 0.8203 0.164 0.000 0.000 0.836
#> GSM97931 2 0.2048 0.9075 0.008 0.928 0.064 0.000
#> GSM97935 4 0.1109 0.9274 0.028 0.000 0.004 0.968
#> GSM97936 4 0.0817 0.9285 0.024 0.000 0.000 0.976
#> GSM97938 4 0.3356 0.8096 0.176 0.000 0.000 0.824
#> GSM97940 4 0.1388 0.9226 0.028 0.000 0.012 0.960
#> GSM97942 3 0.0921 0.8670 0.028 0.000 0.972 0.000
#> GSM97945 4 0.0469 0.9324 0.012 0.000 0.000 0.988
#> GSM97946 2 0.0000 0.9696 0.000 1.000 0.000 0.000
#> GSM97948 3 0.1610 0.8362 0.032 0.000 0.952 0.016
#> GSM97950 4 0.0817 0.9313 0.024 0.000 0.000 0.976
#> GSM97952 4 0.1004 0.9274 0.024 0.000 0.004 0.972
#> GSM97953 1 0.4605 0.5093 0.664 0.000 0.000 0.336
#> GSM97954 4 0.1302 0.9255 0.044 0.000 0.000 0.956
#> GSM97955 4 0.0817 0.9307 0.024 0.000 0.000 0.976
#> GSM97959 2 0.5847 0.2276 0.036 0.560 0.000 0.404
#> GSM97961 4 0.0592 0.9319 0.016 0.000 0.000 0.984
#> GSM97963 4 0.0336 0.9326 0.008 0.000 0.000 0.992
#> GSM97965 4 0.0336 0.9319 0.008 0.000 0.000 0.992
#> GSM97966 4 0.0707 0.9295 0.020 0.000 0.000 0.980
#> GSM97967 2 0.0000 0.9696 0.000 1.000 0.000 0.000
#> GSM97968 2 0.0000 0.9696 0.000 1.000 0.000 0.000
#> GSM97969 4 0.1211 0.9268 0.040 0.000 0.000 0.960
#> GSM97971 4 0.1807 0.9216 0.052 0.000 0.008 0.940
#> GSM97799 3 0.0592 0.8566 0.016 0.000 0.984 0.000
#> GSM97823 2 0.0000 0.9696 0.000 1.000 0.000 0.000
#> GSM97824 3 0.4898 0.4169 0.416 0.000 0.584 0.000
#> GSM97830 3 0.3074 0.8307 0.152 0.000 0.848 0.000
#> GSM97835 3 0.3402 0.7203 0.004 0.164 0.832 0.000
#> GSM97838 2 0.0000 0.9696 0.000 1.000 0.000 0.000
#> GSM97841 2 0.0000 0.9696 0.000 1.000 0.000 0.000
#> GSM97842 3 0.1256 0.8651 0.028 0.008 0.964 0.000
#> GSM97854 2 0.0000 0.9696 0.000 1.000 0.000 0.000
#> GSM97857 1 0.3311 0.6484 0.828 0.000 0.172 0.000
#> GSM97860 3 0.2011 0.8636 0.080 0.000 0.920 0.000
#> GSM97862 3 0.2408 0.8548 0.104 0.000 0.896 0.000
#> GSM97864 2 0.0000 0.9696 0.000 1.000 0.000 0.000
#> GSM97866 3 0.2868 0.8403 0.136 0.000 0.864 0.000
#> GSM97868 3 0.1716 0.8662 0.064 0.000 0.936 0.000
#> GSM97872 1 0.3088 0.7346 0.864 0.000 0.008 0.128
#> GSM97873 3 0.0817 0.8673 0.024 0.000 0.976 0.000
#> GSM97874 3 0.3649 0.7903 0.204 0.000 0.796 0.000
#> GSM97875 3 0.0707 0.8545 0.020 0.000 0.980 0.000
#> GSM97876 3 0.1389 0.8678 0.048 0.000 0.952 0.000
#> GSM97880 3 0.3486 0.8079 0.188 0.000 0.812 0.000
#> GSM97881 3 0.0469 0.8655 0.012 0.000 0.988 0.000
#> GSM97884 3 0.1452 0.8652 0.036 0.008 0.956 0.000
#> GSM97901 3 0.2081 0.8614 0.084 0.000 0.916 0.000
#> GSM97902 1 0.1733 0.7448 0.948 0.000 0.024 0.028
#> GSM97909 2 0.0779 0.9535 0.004 0.980 0.016 0.000
#> GSM97911 3 0.0336 0.8643 0.008 0.000 0.992 0.000
#> GSM97923 3 0.0817 0.8668 0.024 0.000 0.976 0.000
#> GSM97928 4 0.1637 0.9207 0.060 0.000 0.000 0.940
#> GSM97929 2 0.0000 0.9696 0.000 1.000 0.000 0.000
#> GSM97933 1 0.4250 0.4898 0.724 0.000 0.276 0.000
#> GSM97934 1 0.3649 0.6115 0.796 0.000 0.204 0.000
#> GSM97944 3 0.0469 0.8586 0.012 0.000 0.988 0.000
#> GSM97949 2 0.0000 0.9696 0.000 1.000 0.000 0.000
#> GSM97956 3 0.3610 0.7869 0.200 0.000 0.800 0.000
#> GSM97962 1 0.4941 -0.0203 0.564 0.000 0.436 0.000
#> GSM97964 3 0.4941 0.3993 0.436 0.000 0.564 0.000
#> GSM97970 3 0.1022 0.8676 0.032 0.000 0.968 0.000
#> GSM97822 4 0.4755 0.7149 0.040 0.000 0.200 0.760
#> GSM97831 3 0.3311 0.8165 0.172 0.000 0.828 0.000
#> GSM97845 4 0.1716 0.9160 0.064 0.000 0.000 0.936
#> GSM97865 1 0.3975 0.6729 0.760 0.000 0.000 0.240
#> GSM97867 3 0.2011 0.8633 0.080 0.000 0.920 0.000
#> GSM97883 3 0.4134 0.7254 0.260 0.000 0.740 0.000
#> GSM97897 4 0.3764 0.8255 0.040 0.000 0.116 0.844
#> GSM97900 4 0.2871 0.8752 0.032 0.000 0.072 0.896
#> GSM97904 4 0.1824 0.9212 0.060 0.000 0.004 0.936
#> GSM97907 2 0.0000 0.9696 0.000 1.000 0.000 0.000
#> GSM97925 3 0.1545 0.8349 0.040 0.000 0.952 0.008
#> GSM97947 3 0.1913 0.8240 0.040 0.000 0.940 0.020
cbind(get_classes(res, k = 5), get_membership(res, k = 5))
#> class entropy silhouette p1 p2 p3 p4 p5
#> GSM97800 2 0.0404 0.9185 0.000 0.988 0.000 0.000 0.012
#> GSM97803 2 0.0162 0.9201 0.000 0.996 0.000 0.000 0.004
#> GSM97804 2 0.1124 0.9059 0.004 0.960 0.000 0.000 0.036
#> GSM97805 2 0.0771 0.9140 0.004 0.976 0.000 0.000 0.020
#> GSM97807 2 0.0404 0.9173 0.000 0.988 0.000 0.000 0.012
#> GSM97809 2 0.0404 0.9173 0.000 0.988 0.000 0.000 0.012
#> GSM97811 2 0.0000 0.9205 0.000 1.000 0.000 0.000 0.000
#> GSM97812 2 0.0000 0.9205 0.000 1.000 0.000 0.000 0.000
#> GSM97816 1 0.5118 0.1356 0.584 0.004 0.036 0.000 0.376
#> GSM97817 2 0.0162 0.9198 0.000 0.996 0.000 0.000 0.004
#> GSM97820 2 0.0000 0.9205 0.000 1.000 0.000 0.000 0.000
#> GSM97825 2 0.0000 0.9205 0.000 1.000 0.000 0.000 0.000
#> GSM97827 2 0.0000 0.9205 0.000 1.000 0.000 0.000 0.000
#> GSM97828 1 0.4947 0.1607 0.576 0.004 0.024 0.000 0.396
#> GSM97833 2 0.0000 0.9205 0.000 1.000 0.000 0.000 0.000
#> GSM97834 2 0.0000 0.9205 0.000 1.000 0.000 0.000 0.000
#> GSM97840 2 0.0404 0.9173 0.000 0.988 0.000 0.000 0.012
#> GSM97846 2 0.0000 0.9205 0.000 1.000 0.000 0.000 0.000
#> GSM97848 2 0.0000 0.9205 0.000 1.000 0.000 0.000 0.000
#> GSM97849 2 0.0000 0.9205 0.000 1.000 0.000 0.000 0.000
#> GSM97850 2 0.0000 0.9205 0.000 1.000 0.000 0.000 0.000
#> GSM97853 2 0.0000 0.9205 0.000 1.000 0.000 0.000 0.000
#> GSM97855 2 0.0771 0.9123 0.004 0.976 0.000 0.000 0.020
#> GSM97878 1 0.7922 0.2850 0.424 0.004 0.140 0.116 0.316
#> GSM97913 2 0.6167 0.1495 0.392 0.504 0.000 0.016 0.088
#> GSM97932 4 0.4781 0.4898 0.428 0.000 0.000 0.552 0.020
#> GSM97939 3 0.5785 -0.0907 0.012 0.072 0.568 0.000 0.348
#> GSM97951 2 0.0609 0.9146 0.000 0.980 0.000 0.000 0.020
#> GSM97957 5 0.6754 0.7311 0.276 0.000 0.324 0.000 0.400
#> GSM97972 1 0.5711 0.1730 0.600 0.044 0.032 0.000 0.324
#> GSM97793 3 0.3661 0.5352 0.000 0.000 0.724 0.000 0.276
#> GSM97795 2 0.1106 0.9039 0.000 0.964 0.012 0.000 0.024
#> GSM97802 3 0.6605 0.0858 0.000 0.000 0.432 0.348 0.220
#> GSM97810 2 0.6604 0.1791 0.012 0.532 0.224 0.000 0.232
#> GSM97815 2 0.5080 0.3952 0.000 0.604 0.348 0.000 0.048
#> GSM97837 1 0.4025 0.3287 0.700 0.000 0.008 0.000 0.292
#> GSM97843 3 0.2127 0.6360 0.000 0.000 0.892 0.000 0.108
#> GSM97890 3 0.1410 0.6755 0.000 0.000 0.940 0.000 0.060
#> GSM97899 4 0.1444 0.7889 0.040 0.000 0.000 0.948 0.012
#> GSM97910 1 0.6820 0.1415 0.436 0.004 0.124 0.024 0.412
#> GSM97916 4 0.4588 0.6465 0.308 0.000 0.012 0.668 0.012
#> GSM97920 3 0.6609 -0.3958 0.216 0.000 0.416 0.000 0.368
#> GSM97921 1 0.5059 0.4508 0.668 0.000 0.000 0.076 0.256
#> GSM97927 4 0.1697 0.7637 0.008 0.000 0.000 0.932 0.060
#> GSM97937 1 0.4465 0.4768 0.732 0.000 0.000 0.056 0.212
#> GSM97941 2 0.0510 0.9162 0.000 0.984 0.000 0.000 0.016
#> GSM97943 1 0.5492 -0.0235 0.536 0.004 0.056 0.000 0.404
#> GSM97958 1 0.7023 0.0553 0.380 0.292 0.000 0.008 0.320
#> GSM97960 2 0.1492 0.8942 0.004 0.948 0.008 0.000 0.040
#> GSM97794 4 0.7189 0.1890 0.400 0.048 0.000 0.408 0.144
#> GSM97796 4 0.1892 0.7833 0.080 0.000 0.000 0.916 0.004
#> GSM97797 1 0.6310 0.3985 0.576 0.024 0.004 0.096 0.300
#> GSM97798 4 0.1205 0.7752 0.004 0.000 0.000 0.956 0.040
#> GSM97801 1 0.3812 0.4774 0.780 0.000 0.004 0.020 0.196
#> GSM97806 4 0.2561 0.7821 0.096 0.000 0.000 0.884 0.020
#> GSM97808 4 0.0963 0.7758 0.000 0.000 0.000 0.964 0.036
#> GSM97813 4 0.2017 0.7527 0.008 0.000 0.000 0.912 0.080
#> GSM97814 4 0.0807 0.7841 0.012 0.000 0.000 0.976 0.012
#> GSM97818 1 0.6268 0.2616 0.508 0.004 0.000 0.348 0.140
#> GSM97819 3 0.1608 0.6687 0.000 0.000 0.928 0.000 0.072
#> GSM97821 2 0.0854 0.9136 0.000 0.976 0.008 0.004 0.012
#> GSM97826 1 0.4612 0.4886 0.736 0.000 0.000 0.084 0.180
#> GSM97829 1 0.3735 0.4951 0.828 0.000 0.008 0.064 0.100
#> GSM97832 2 0.7248 0.3629 0.152 0.552 0.104 0.000 0.192
#> GSM97836 4 0.5292 0.4510 0.024 0.000 0.328 0.620 0.028
#> GSM97839 4 0.2864 0.7651 0.136 0.000 0.000 0.852 0.012
#> GSM97844 2 0.0162 0.9198 0.000 0.996 0.000 0.000 0.004
#> GSM97847 4 0.4718 0.4683 0.444 0.000 0.000 0.540 0.016
#> GSM97851 4 0.4327 0.6014 0.360 0.000 0.000 0.632 0.008
#> GSM97852 4 0.4538 0.5885 0.364 0.000 0.000 0.620 0.016
#> GSM97856 4 0.2359 0.7871 0.060 0.000 0.000 0.904 0.036
#> GSM97858 2 0.0671 0.9157 0.004 0.980 0.000 0.000 0.016
#> GSM97859 4 0.2158 0.7903 0.052 0.000 0.008 0.920 0.020
#> GSM97861 4 0.2722 0.7243 0.008 0.000 0.004 0.868 0.120
#> GSM97863 4 0.1831 0.7844 0.076 0.000 0.000 0.920 0.004
#> GSM97869 4 0.2844 0.7304 0.028 0.000 0.004 0.876 0.092
#> GSM97870 3 0.6381 -0.1532 0.060 0.000 0.560 0.060 0.320
#> GSM97871 4 0.0898 0.7864 0.020 0.000 0.000 0.972 0.008
#> GSM97877 2 0.3359 0.7407 0.164 0.816 0.000 0.000 0.020
#> GSM97879 4 0.0880 0.7878 0.032 0.000 0.000 0.968 0.000
#> GSM97882 4 0.1299 0.7826 0.008 0.000 0.020 0.960 0.012
#> GSM97885 4 0.0566 0.7828 0.004 0.000 0.000 0.984 0.012
#> GSM97886 4 0.6053 0.5683 0.232 0.000 0.004 0.592 0.172
#> GSM97887 4 0.2796 0.7460 0.008 0.000 0.008 0.868 0.116
#> GSM97888 4 0.4059 0.7484 0.172 0.000 0.000 0.776 0.052
#> GSM97889 4 0.5258 0.4730 0.000 0.000 0.140 0.680 0.180
#> GSM97891 4 0.2149 0.7864 0.036 0.000 0.000 0.916 0.048
#> GSM97892 2 0.0000 0.9205 0.000 1.000 0.000 0.000 0.000
#> GSM97893 4 0.4238 0.5984 0.368 0.000 0.000 0.628 0.004
#> GSM97894 4 0.4840 0.6243 0.320 0.000 0.000 0.640 0.040
#> GSM97895 4 0.4640 0.5351 0.400 0.000 0.000 0.584 0.016
#> GSM97896 4 0.0703 0.7884 0.024 0.000 0.000 0.976 0.000
#> GSM97898 4 0.3421 0.7315 0.204 0.000 0.000 0.788 0.008
#> GSM97903 4 0.4402 0.6020 0.352 0.000 0.000 0.636 0.012
#> GSM97905 3 0.3642 0.5972 0.020 0.000 0.820 0.016 0.144
#> GSM97906 4 0.0404 0.7830 0.000 0.000 0.000 0.988 0.012
#> GSM97908 4 0.5981 0.3959 0.404 0.000 0.000 0.484 0.112
#> GSM97912 5 0.7230 0.5636 0.348 0.000 0.260 0.020 0.372
#> GSM97914 4 0.6418 -0.1664 0.412 0.000 0.000 0.416 0.172
#> GSM97915 4 0.4360 0.6693 0.284 0.000 0.000 0.692 0.024
#> GSM97917 4 0.4481 0.5233 0.416 0.000 0.000 0.576 0.008
#> GSM97918 4 0.3300 0.7368 0.204 0.000 0.000 0.792 0.004
#> GSM97919 4 0.4608 0.6195 0.336 0.000 0.000 0.640 0.024
#> GSM97922 4 0.0992 0.7875 0.024 0.000 0.000 0.968 0.008
#> GSM97924 2 0.0566 0.9164 0.004 0.984 0.000 0.000 0.012
#> GSM97926 3 0.1965 0.6645 0.000 0.000 0.904 0.000 0.096
#> GSM97930 1 0.4610 -0.1972 0.556 0.000 0.000 0.432 0.012
#> GSM97931 2 0.7522 -0.0183 0.028 0.376 0.292 0.004 0.300
#> GSM97935 4 0.1357 0.7723 0.004 0.000 0.000 0.948 0.048
#> GSM97936 4 0.3283 0.7623 0.140 0.000 0.000 0.832 0.028
#> GSM97938 1 0.5470 0.0953 0.588 0.000 0.000 0.332 0.080
#> GSM97940 4 0.0693 0.7844 0.008 0.000 0.000 0.980 0.012
#> GSM97942 3 0.0703 0.6766 0.000 0.000 0.976 0.000 0.024
#> GSM97945 4 0.1195 0.7781 0.012 0.000 0.000 0.960 0.028
#> GSM97946 2 0.0290 0.9187 0.000 0.992 0.000 0.000 0.008
#> GSM97948 3 0.3250 0.6283 0.004 0.000 0.820 0.008 0.168
#> GSM97950 4 0.1768 0.7871 0.072 0.000 0.000 0.924 0.004
#> GSM97952 4 0.0771 0.7815 0.004 0.000 0.000 0.976 0.020
#> GSM97953 1 0.3849 0.4946 0.808 0.000 0.000 0.112 0.080
#> GSM97954 4 0.5028 0.5164 0.400 0.000 0.000 0.564 0.036
#> GSM97955 4 0.1952 0.7849 0.084 0.000 0.000 0.912 0.004
#> GSM97959 2 0.6890 -0.0297 0.260 0.468 0.000 0.260 0.012
#> GSM97961 4 0.1341 0.7874 0.056 0.000 0.000 0.944 0.000
#> GSM97963 4 0.0955 0.7782 0.004 0.000 0.000 0.968 0.028
#> GSM97965 4 0.0162 0.7844 0.004 0.000 0.000 0.996 0.000
#> GSM97966 4 0.0963 0.7745 0.000 0.000 0.000 0.964 0.036
#> GSM97967 2 0.0000 0.9205 0.000 1.000 0.000 0.000 0.000
#> GSM97968 2 0.1403 0.8969 0.024 0.952 0.000 0.000 0.024
#> GSM97969 4 0.4958 0.5192 0.400 0.000 0.000 0.568 0.032
#> GSM97971 4 0.5046 0.6140 0.088 0.000 0.012 0.720 0.180
#> GSM97799 3 0.2471 0.6670 0.000 0.000 0.864 0.000 0.136
#> GSM97823 2 0.0290 0.9187 0.000 0.992 0.000 0.000 0.008
#> GSM97824 5 0.5895 0.2447 0.100 0.000 0.440 0.000 0.460
#> GSM97830 3 0.4302 0.5932 0.032 0.000 0.720 0.000 0.248
#> GSM97835 3 0.5107 0.3906 0.000 0.204 0.688 0.000 0.108
#> GSM97838 2 0.0671 0.9157 0.004 0.980 0.000 0.000 0.016
#> GSM97841 2 0.0000 0.9205 0.000 1.000 0.000 0.000 0.000
#> GSM97842 3 0.2964 0.6497 0.004 0.004 0.840 0.000 0.152
#> GSM97854 2 0.0671 0.9157 0.004 0.980 0.000 0.000 0.016
#> GSM97857 5 0.6790 0.7250 0.288 0.000 0.336 0.000 0.376
#> GSM97860 3 0.2471 0.6504 0.000 0.000 0.864 0.000 0.136
#> GSM97862 3 0.1851 0.6496 0.000 0.000 0.912 0.000 0.088
#> GSM97864 2 0.0000 0.9205 0.000 1.000 0.000 0.000 0.000
#> GSM97866 3 0.2773 0.5857 0.000 0.000 0.836 0.000 0.164
#> GSM97868 3 0.2798 0.6650 0.008 0.000 0.852 0.000 0.140
#> GSM97872 1 0.7052 0.2632 0.520 0.000 0.072 0.112 0.296
#> GSM97873 3 0.1041 0.6761 0.000 0.004 0.964 0.000 0.032
#> GSM97874 3 0.4430 0.4998 0.036 0.000 0.708 0.000 0.256
#> GSM97875 3 0.2813 0.6569 0.000 0.000 0.832 0.000 0.168
#> GSM97876 3 0.2488 0.6666 0.004 0.000 0.872 0.000 0.124
#> GSM97880 3 0.4066 0.6087 0.044 0.000 0.768 0.000 0.188
#> GSM97881 3 0.1544 0.6743 0.000 0.000 0.932 0.000 0.068
#> GSM97884 3 0.3628 0.6064 0.000 0.012 0.772 0.000 0.216
#> GSM97901 3 0.3659 0.5913 0.012 0.000 0.768 0.000 0.220
#> GSM97902 1 0.4168 0.4476 0.784 0.004 0.036 0.008 0.168
#> GSM97909 2 0.1704 0.8704 0.000 0.928 0.004 0.000 0.068
#> GSM97911 3 0.1608 0.6736 0.000 0.000 0.928 0.000 0.072
#> GSM97923 3 0.2707 0.6704 0.008 0.000 0.860 0.000 0.132
#> GSM97928 4 0.3767 0.7090 0.068 0.000 0.000 0.812 0.120
#> GSM97929 2 0.0162 0.9198 0.000 0.996 0.000 0.000 0.004
#> GSM97933 3 0.6247 -0.5139 0.152 0.000 0.484 0.000 0.364
#> GSM97934 3 0.6796 -0.7820 0.288 0.000 0.360 0.000 0.352
#> GSM97944 3 0.2605 0.6650 0.000 0.000 0.852 0.000 0.148
#> GSM97949 2 0.0290 0.9194 0.000 0.992 0.000 0.000 0.008
#> GSM97956 3 0.4787 0.3686 0.036 0.000 0.640 0.000 0.324
#> GSM97962 3 0.5968 -0.2428 0.156 0.000 0.576 0.000 0.268
#> GSM97964 3 0.4898 -0.0576 0.032 0.000 0.592 0.000 0.376
#> GSM97970 3 0.0703 0.6763 0.000 0.000 0.976 0.000 0.024
#> GSM97822 4 0.4088 0.6245 0.000 0.000 0.056 0.776 0.168
#> GSM97831 3 0.2563 0.6568 0.008 0.000 0.872 0.000 0.120
#> GSM97845 4 0.3333 0.7314 0.208 0.000 0.000 0.788 0.004
#> GSM97865 1 0.5392 0.4393 0.652 0.004 0.000 0.092 0.252
#> GSM97867 3 0.2127 0.6599 0.000 0.000 0.892 0.000 0.108
#> GSM97883 3 0.3779 0.4527 0.012 0.000 0.752 0.000 0.236
#> GSM97897 4 0.3608 0.6647 0.000 0.000 0.040 0.812 0.148
#> GSM97900 4 0.1787 0.7797 0.016 0.000 0.004 0.936 0.044
#> GSM97904 4 0.5282 0.6173 0.144 0.000 0.008 0.700 0.148
#> GSM97907 2 0.0510 0.9172 0.000 0.984 0.000 0.000 0.016
#> GSM97925 3 0.3837 0.5642 0.000 0.000 0.692 0.000 0.308
#> GSM97947 3 0.3768 0.6286 0.008 0.000 0.760 0.004 0.228
cbind(get_classes(res, k = 6), get_membership(res, k = 6))
#> class entropy silhouette p1 p2 p3 p4 p5 p6
#> GSM97800 2 0.0260 0.93458 0.000 0.992 0.000 0.000 0.008 0.000
#> GSM97803 2 0.0363 0.93356 0.000 0.988 0.000 0.000 0.012 0.000
#> GSM97804 2 0.1285 0.90925 0.004 0.944 0.000 0.000 0.052 0.000
#> GSM97805 2 0.1138 0.92186 0.012 0.960 0.000 0.000 0.024 0.004
#> GSM97807 2 0.0000 0.93515 0.000 1.000 0.000 0.000 0.000 0.000
#> GSM97809 2 0.0260 0.93416 0.000 0.992 0.000 0.000 0.000 0.008
#> GSM97811 2 0.0000 0.93515 0.000 1.000 0.000 0.000 0.000 0.000
#> GSM97812 2 0.0000 0.93515 0.000 1.000 0.000 0.000 0.000 0.000
#> GSM97816 6 0.1078 0.57583 0.000 0.008 0.012 0.000 0.016 0.964
#> GSM97817 2 0.0000 0.93515 0.000 1.000 0.000 0.000 0.000 0.000
#> GSM97820 2 0.0146 0.93507 0.004 0.996 0.000 0.000 0.000 0.000
#> GSM97825 2 0.0000 0.93515 0.000 1.000 0.000 0.000 0.000 0.000
#> GSM97827 2 0.0146 0.93509 0.004 0.996 0.000 0.000 0.000 0.000
#> GSM97828 6 0.1810 0.57689 0.020 0.004 0.008 0.000 0.036 0.932
#> GSM97833 2 0.0000 0.93515 0.000 1.000 0.000 0.000 0.000 0.000
#> GSM97834 2 0.0000 0.93515 0.000 1.000 0.000 0.000 0.000 0.000
#> GSM97840 2 0.0146 0.93503 0.000 0.996 0.000 0.000 0.000 0.004
#> GSM97846 2 0.0000 0.93515 0.000 1.000 0.000 0.000 0.000 0.000
#> GSM97848 2 0.0291 0.93430 0.000 0.992 0.000 0.000 0.004 0.004
#> GSM97849 2 0.0291 0.93429 0.004 0.992 0.000 0.000 0.004 0.000
#> GSM97850 2 0.0000 0.93515 0.000 1.000 0.000 0.000 0.000 0.000
#> GSM97853 2 0.0146 0.93508 0.000 0.996 0.000 0.000 0.004 0.000
#> GSM97855 2 0.1082 0.91058 0.004 0.956 0.000 0.000 0.000 0.040
#> GSM97878 1 0.3202 0.55707 0.844 0.000 0.028 0.028 0.100 0.000
#> GSM97913 1 0.3940 0.31001 0.704 0.272 0.000 0.000 0.016 0.008
#> GSM97932 1 0.2662 0.70949 0.840 0.000 0.000 0.152 0.004 0.004
#> GSM97939 3 0.4346 0.59092 0.016 0.036 0.776 0.000 0.132 0.040
#> GSM97951 2 0.0291 0.93487 0.004 0.992 0.000 0.000 0.004 0.000
#> GSM97957 3 0.5770 0.25227 0.028 0.000 0.500 0.000 0.092 0.380
#> GSM97972 6 0.7080 0.45615 0.204 0.080 0.060 0.004 0.096 0.556
#> GSM97793 3 0.4700 0.18816 0.060 0.000 0.600 0.000 0.340 0.000
#> GSM97795 2 0.1053 0.92279 0.012 0.964 0.000 0.000 0.020 0.004
#> GSM97802 4 0.6363 0.18170 0.016 0.004 0.280 0.492 0.204 0.004
#> GSM97810 2 0.6532 -0.14648 0.016 0.452 0.388 0.000 0.080 0.064
#> GSM97815 2 0.4779 0.48829 0.020 0.692 0.232 0.000 0.048 0.008
#> GSM97837 6 0.3134 0.57541 0.168 0.000 0.000 0.000 0.024 0.808
#> GSM97843 3 0.1605 0.66676 0.016 0.000 0.936 0.000 0.044 0.004
#> GSM97890 3 0.1643 0.65353 0.000 0.000 0.924 0.000 0.068 0.008
#> GSM97899 4 0.0935 0.79416 0.032 0.000 0.000 0.964 0.004 0.000
#> GSM97910 6 0.4981 0.42488 0.028 0.000 0.036 0.020 0.228 0.688
#> GSM97916 4 0.6349 0.31715 0.288 0.000 0.008 0.540 0.068 0.096
#> GSM97920 6 0.4060 0.41683 0.000 0.000 0.120 0.004 0.112 0.764
#> GSM97921 6 0.5916 0.19229 0.372 0.000 0.000 0.084 0.044 0.500
#> GSM97927 4 0.0909 0.79302 0.012 0.000 0.000 0.968 0.020 0.000
#> GSM97937 1 0.4976 0.15154 0.556 0.000 0.000 0.020 0.036 0.388
#> GSM97941 2 0.0291 0.93499 0.004 0.992 0.000 0.000 0.000 0.004
#> GSM97943 6 0.1787 0.57190 0.016 0.000 0.020 0.000 0.032 0.932
#> GSM97958 6 0.7406 0.19479 0.056 0.364 0.020 0.036 0.104 0.420
#> GSM97960 2 0.1980 0.87000 0.000 0.920 0.036 0.000 0.036 0.008
#> GSM97794 1 0.7807 0.38811 0.456 0.092 0.000 0.164 0.212 0.076
#> GSM97796 4 0.3023 0.66414 0.232 0.000 0.000 0.768 0.000 0.000
#> GSM97797 5 0.6834 -0.29614 0.224 0.016 0.000 0.024 0.396 0.340
#> GSM97798 4 0.1321 0.79056 0.020 0.000 0.000 0.952 0.024 0.004
#> GSM97801 6 0.2928 0.56099 0.056 0.000 0.000 0.004 0.084 0.856
#> GSM97806 4 0.2848 0.75556 0.124 0.000 0.000 0.848 0.024 0.004
#> GSM97808 4 0.0806 0.79491 0.020 0.000 0.000 0.972 0.008 0.000
#> GSM97813 4 0.2679 0.76507 0.040 0.000 0.000 0.864 0.096 0.000
#> GSM97814 4 0.1138 0.79462 0.024 0.000 0.000 0.960 0.012 0.004
#> GSM97818 6 0.6276 0.03486 0.296 0.008 0.000 0.160 0.024 0.512
#> GSM97819 3 0.1429 0.66662 0.004 0.000 0.940 0.000 0.052 0.004
#> GSM97821 2 0.2395 0.86981 0.016 0.896 0.000 0.012 0.072 0.004
#> GSM97826 1 0.5159 0.30430 0.568 0.000 0.000 0.048 0.024 0.360
#> GSM97829 1 0.5410 -0.07412 0.488 0.000 0.004 0.024 0.048 0.436
#> GSM97832 6 0.5740 0.28139 0.004 0.212 0.040 0.000 0.120 0.624
#> GSM97836 3 0.6140 -0.02244 0.112 0.000 0.448 0.400 0.040 0.000
#> GSM97839 4 0.3426 0.58333 0.276 0.000 0.000 0.720 0.004 0.000
#> GSM97844 2 0.0622 0.93146 0.008 0.980 0.000 0.000 0.012 0.000
#> GSM97847 1 0.2762 0.71937 0.804 0.000 0.000 0.196 0.000 0.000
#> GSM97851 1 0.2933 0.71874 0.796 0.000 0.000 0.200 0.004 0.000
#> GSM97852 1 0.2854 0.71758 0.792 0.000 0.000 0.208 0.000 0.000
#> GSM97856 4 0.1865 0.79450 0.040 0.000 0.000 0.920 0.040 0.000
#> GSM97858 2 0.0725 0.92994 0.012 0.976 0.000 0.000 0.012 0.000
#> GSM97859 4 0.4653 0.71269 0.104 0.000 0.040 0.756 0.092 0.008
#> GSM97861 4 0.1313 0.78892 0.016 0.000 0.004 0.952 0.028 0.000
#> GSM97863 4 0.2854 0.69056 0.208 0.000 0.000 0.792 0.000 0.000
#> GSM97869 4 0.4268 0.71690 0.092 0.000 0.004 0.772 0.112 0.020
#> GSM97870 3 0.7620 -0.07549 0.016 0.000 0.336 0.248 0.096 0.304
#> GSM97871 4 0.1124 0.79548 0.036 0.000 0.000 0.956 0.008 0.000
#> GSM97877 2 0.3547 0.54525 0.300 0.696 0.000 0.000 0.004 0.000
#> GSM97879 4 0.1606 0.79138 0.056 0.000 0.000 0.932 0.004 0.008
#> GSM97882 4 0.1793 0.79418 0.032 0.000 0.004 0.928 0.036 0.000
#> GSM97885 4 0.0993 0.79549 0.024 0.000 0.000 0.964 0.012 0.000
#> GSM97886 4 0.5964 0.11700 0.152 0.000 0.000 0.420 0.416 0.012
#> GSM97887 4 0.2825 0.73367 0.012 0.000 0.008 0.844 0.136 0.000
#> GSM97888 4 0.5600 0.39111 0.308 0.000 0.000 0.560 0.116 0.016
#> GSM97889 4 0.4387 0.63358 0.012 0.000 0.076 0.732 0.180 0.000
#> GSM97891 4 0.2322 0.78694 0.036 0.000 0.000 0.896 0.064 0.004
#> GSM97892 2 0.0363 0.93356 0.000 0.988 0.000 0.000 0.012 0.000
#> GSM97893 1 0.3767 0.67486 0.708 0.000 0.000 0.276 0.012 0.004
#> GSM97894 1 0.3748 0.62346 0.688 0.000 0.000 0.300 0.012 0.000
#> GSM97895 1 0.3622 0.71245 0.792 0.000 0.000 0.164 0.024 0.020
#> GSM97896 4 0.3699 0.66353 0.212 0.000 0.000 0.752 0.036 0.000
#> GSM97898 1 0.3955 0.46183 0.608 0.000 0.000 0.384 0.008 0.000
#> GSM97903 4 0.4097 -0.07271 0.488 0.000 0.000 0.504 0.008 0.000
#> GSM97905 3 0.3748 0.62583 0.092 0.000 0.792 0.004 0.112 0.000
#> GSM97906 4 0.0820 0.79627 0.012 0.000 0.000 0.972 0.016 0.000
#> GSM97908 1 0.3284 0.71378 0.800 0.000 0.000 0.168 0.032 0.000
#> GSM97912 3 0.7353 0.22491 0.080 0.000 0.484 0.040 0.164 0.232
#> GSM97914 6 0.6362 0.10356 0.204 0.000 0.000 0.276 0.032 0.488
#> GSM97915 1 0.3819 0.55435 0.652 0.000 0.000 0.340 0.008 0.000
#> GSM97917 1 0.3880 0.70544 0.772 0.000 0.000 0.176 0.024 0.028
#> GSM97918 4 0.3810 0.08840 0.428 0.000 0.000 0.572 0.000 0.000
#> GSM97919 1 0.3349 0.69579 0.748 0.000 0.000 0.244 0.008 0.000
#> GSM97922 4 0.3683 0.70622 0.160 0.000 0.004 0.784 0.052 0.000
#> GSM97924 2 0.0653 0.93232 0.004 0.980 0.000 0.000 0.012 0.004
#> GSM97926 3 0.2745 0.63288 0.020 0.000 0.860 0.000 0.112 0.008
#> GSM97930 1 0.3800 0.71421 0.776 0.000 0.000 0.176 0.020 0.028
#> GSM97931 5 0.7336 0.22846 0.112 0.292 0.176 0.000 0.412 0.008
#> GSM97935 4 0.0622 0.79423 0.008 0.000 0.000 0.980 0.012 0.000
#> GSM97936 4 0.3351 0.71486 0.160 0.000 0.000 0.800 0.040 0.000
#> GSM97938 1 0.3413 0.59630 0.836 0.000 0.000 0.072 0.024 0.068
#> GSM97940 4 0.0806 0.79523 0.020 0.000 0.000 0.972 0.008 0.000
#> GSM97942 3 0.1155 0.66550 0.004 0.000 0.956 0.000 0.036 0.004
#> GSM97945 4 0.0632 0.79459 0.024 0.000 0.000 0.976 0.000 0.000
#> GSM97946 2 0.0146 0.93494 0.004 0.996 0.000 0.000 0.000 0.000
#> GSM97948 3 0.4255 0.23342 0.016 0.000 0.600 0.004 0.380 0.000
#> GSM97950 4 0.2913 0.70410 0.180 0.000 0.000 0.812 0.004 0.004
#> GSM97952 4 0.0405 0.79525 0.008 0.000 0.000 0.988 0.004 0.000
#> GSM97953 1 0.4953 0.30150 0.644 0.000 0.000 0.044 0.032 0.280
#> GSM97954 1 0.3190 0.71305 0.772 0.000 0.000 0.220 0.008 0.000
#> GSM97955 4 0.2883 0.68039 0.212 0.000 0.000 0.788 0.000 0.000
#> GSM97959 2 0.6145 0.12095 0.324 0.528 0.000 0.104 0.012 0.032
#> GSM97961 4 0.1663 0.77048 0.088 0.000 0.000 0.912 0.000 0.000
#> GSM97963 4 0.0458 0.79487 0.016 0.000 0.000 0.984 0.000 0.000
#> GSM97965 4 0.0363 0.79473 0.012 0.000 0.000 0.988 0.000 0.000
#> GSM97966 4 0.0622 0.79521 0.012 0.000 0.000 0.980 0.008 0.000
#> GSM97967 2 0.0146 0.93508 0.000 0.996 0.000 0.000 0.004 0.000
#> GSM97968 2 0.3608 0.59837 0.000 0.716 0.000 0.000 0.012 0.272
#> GSM97969 1 0.3813 0.70552 0.736 0.000 0.000 0.236 0.020 0.008
#> GSM97971 4 0.6699 0.50047 0.176 0.000 0.052 0.580 0.144 0.048
#> GSM97799 3 0.2646 0.63098 0.004 0.000 0.852 0.004 0.136 0.004
#> GSM97823 2 0.0405 0.93295 0.000 0.988 0.000 0.000 0.004 0.008
#> GSM97824 3 0.4606 0.56805 0.012 0.000 0.716 0.000 0.172 0.100
#> GSM97830 3 0.5945 -0.18881 0.000 0.000 0.416 0.004 0.396 0.184
#> GSM97835 3 0.6335 -0.20774 0.008 0.280 0.460 0.000 0.244 0.008
#> GSM97838 2 0.0622 0.93146 0.008 0.980 0.000 0.000 0.012 0.000
#> GSM97841 2 0.0146 0.93494 0.004 0.996 0.000 0.000 0.000 0.000
#> GSM97842 3 0.2356 0.65796 0.004 0.008 0.884 0.000 0.100 0.004
#> GSM97854 2 0.0858 0.92663 0.004 0.968 0.000 0.000 0.028 0.000
#> GSM97857 3 0.5908 0.25363 0.032 0.000 0.504 0.000 0.104 0.360
#> GSM97860 3 0.3523 0.55365 0.040 0.000 0.780 0.000 0.180 0.000
#> GSM97862 3 0.0767 0.66709 0.004 0.000 0.976 0.000 0.008 0.012
#> GSM97864 2 0.0291 0.93455 0.004 0.992 0.000 0.000 0.004 0.000
#> GSM97866 3 0.1590 0.66275 0.008 0.000 0.936 0.000 0.048 0.008
#> GSM97868 3 0.3438 0.55540 0.008 0.000 0.764 0.000 0.220 0.008
#> GSM97872 1 0.5262 0.52972 0.732 0.000 0.040 0.064 0.088 0.076
#> GSM97873 3 0.1872 0.66213 0.004 0.004 0.920 0.000 0.064 0.008
#> GSM97874 5 0.5592 0.17018 0.056 0.000 0.400 0.000 0.504 0.040
#> GSM97875 3 0.3052 0.59161 0.000 0.000 0.780 0.004 0.216 0.000
#> GSM97876 3 0.1958 0.65705 0.000 0.000 0.896 0.000 0.100 0.004
#> GSM97880 3 0.3816 0.61059 0.008 0.000 0.780 0.000 0.156 0.056
#> GSM97881 3 0.1588 0.65003 0.000 0.000 0.924 0.000 0.072 0.004
#> GSM97884 3 0.3171 0.63478 0.008 0.004 0.812 0.000 0.168 0.008
#> GSM97901 3 0.2121 0.65908 0.000 0.000 0.892 0.000 0.096 0.012
#> GSM97902 6 0.5686 0.44561 0.336 0.004 0.020 0.012 0.064 0.564
#> GSM97909 2 0.1313 0.91610 0.016 0.952 0.000 0.004 0.028 0.000
#> GSM97911 3 0.1757 0.64775 0.000 0.000 0.916 0.000 0.076 0.008
#> GSM97923 3 0.3693 0.51359 0.004 0.000 0.708 0.000 0.280 0.008
#> GSM97928 4 0.7323 0.16273 0.248 0.000 0.084 0.460 0.184 0.024
#> GSM97929 2 0.0436 0.93409 0.004 0.988 0.000 0.000 0.004 0.004
#> GSM97933 3 0.5022 0.53947 0.060 0.000 0.712 0.000 0.140 0.088
#> GSM97934 3 0.6060 0.31274 0.056 0.000 0.548 0.000 0.104 0.292
#> GSM97944 3 0.2497 0.64569 0.008 0.000 0.872 0.004 0.112 0.004
#> GSM97949 2 0.0000 0.93515 0.000 1.000 0.000 0.000 0.000 0.000
#> GSM97956 3 0.3672 0.61653 0.008 0.000 0.780 0.000 0.176 0.036
#> GSM97962 3 0.4572 0.56901 0.032 0.000 0.744 0.000 0.124 0.100
#> GSM97964 3 0.3862 0.60647 0.016 0.004 0.784 0.000 0.160 0.036
#> GSM97970 3 0.1970 0.64539 0.008 0.000 0.900 0.000 0.092 0.000
#> GSM97822 4 0.3840 0.68862 0.012 0.000 0.056 0.784 0.148 0.000
#> GSM97831 3 0.3227 0.62337 0.000 0.000 0.824 0.000 0.116 0.060
#> GSM97845 4 0.4083 0.50237 0.284 0.000 0.000 0.688 0.008 0.020
#> GSM97865 1 0.5899 -0.00687 0.488 0.000 0.000 0.080 0.044 0.388
#> GSM97867 3 0.3272 0.61330 0.048 0.000 0.824 0.000 0.124 0.004
#> GSM97883 3 0.3229 0.61528 0.004 0.000 0.804 0.000 0.172 0.020
#> GSM97897 4 0.3015 0.73625 0.012 0.000 0.024 0.844 0.120 0.000
#> GSM97900 4 0.2519 0.76651 0.044 0.000 0.000 0.884 0.068 0.004
#> GSM97904 1 0.8364 0.12450 0.332 0.000 0.220 0.208 0.184 0.056
#> GSM97907 2 0.0692 0.93042 0.004 0.976 0.000 0.000 0.020 0.000
#> GSM97925 5 0.4257 -0.13235 0.004 0.000 0.484 0.004 0.504 0.004
#> GSM97947 3 0.4263 0.09851 0.000 0.000 0.504 0.016 0.480 0.000
Heatmaps for the consensus matrix. It visualizes the probability of two samples to be in a same group.
consensus_heatmap(res, k = 2)
consensus_heatmap(res, k = 3)
consensus_heatmap(res, k = 4)
consensus_heatmap(res, k = 5)
consensus_heatmap(res, k = 6)
Heatmaps for the membership of samples in all partitions to see how consistent they are:
membership_heatmap(res, k = 2)
membership_heatmap(res, k = 3)
membership_heatmap(res, k = 4)
membership_heatmap(res, k = 5)
membership_heatmap(res, k = 6)
As soon as we have had the classes for columns, we can look for signatures which are significantly different between classes which can be candidate marks for certain classes. Following are the heatmaps for signatures.
Signature heatmaps where rows are scaled:
get_signatures(res, k = 2)
get_signatures(res, k = 3)
get_signatures(res, k = 4)
get_signatures(res, k = 5)
get_signatures(res, k = 6)
Signature heatmaps where rows are not scaled:
get_signatures(res, k = 2, scale_rows = FALSE)
get_signatures(res, k = 3, scale_rows = FALSE)
get_signatures(res, k = 4, scale_rows = FALSE)
get_signatures(res, k = 5, scale_rows = FALSE)
get_signatures(res, k = 6, scale_rows = FALSE)
Compare the overlap of signatures from different k:
compare_signatures(res)
get_signature() returns a data frame invisibly. TO get the list of signatures, the function
call should be assigned to a variable explicitly. In following code, if plot argument is set
to FALSE, no heatmap is plotted while only the differential analysis is performed.
# code only for demonstration
tb = get_signature(res, k = ..., plot = FALSE)
An example of the output of tb is:
#> which_row fdr mean_1 mean_2 scaled_mean_1 scaled_mean_2 km
#> 1 38 0.042760348 8.373488 9.131774 -0.5533452 0.5164555 1
#> 2 40 0.018707592 7.106213 8.469186 -0.6173731 0.5762149 1
#> 3 55 0.019134737 10.221463 11.207825 -0.6159697 0.5749050 1
#> 4 59 0.006059896 5.921854 7.869574 -0.6899429 0.6439467 1
#> 5 60 0.018055526 8.928898 10.211722 -0.6204761 0.5791110 1
#> 6 98 0.009384629 15.714769 14.887706 0.6635654 -0.6193277 2
...
The columns in tb are:
which_row: row indices corresponding to the input matrix.fdr: FDR for the differential test. mean_x: The mean value in group x.scaled_mean_x: The mean value in group x after rows are scaled.km: Row groups if k-means clustering is applied to rows.UMAP plot which shows how samples are separated.
dimension_reduction(res, k = 2, method = "UMAP")
dimension_reduction(res, k = 3, method = "UMAP")
dimension_reduction(res, k = 4, method = "UMAP")
dimension_reduction(res, k = 5, method = "UMAP")
dimension_reduction(res, k = 6, method = "UMAP")
Following heatmap shows how subgroups are split when increasing k:
collect_classes(res)
Test correlation between subgroups and known annotations. If the known annotation is numeric, one-way ANOVA test is applied, and if the known annotation is discrete, chi-squared contingency table test is applied.
test_to_known_factors(res)
#> n disease.state(p) tissue(p) k
#> CV:NMF 179 8.68e-14 7.25e-16 2
#> CV:NMF 178 2.65e-26 2.64e-26 3
#> CV:NMF 170 5.87e-23 1.85e-21 4
#> CV:NMF 133 2.19e-18 4.04e-19 5
#> CV:NMF 137 7.47e-20 3.82e-20 6
If matrix rows can be associated to genes, consider to use functional_enrichment(res,
...) to perform function enrichment for the signature genes. See this vignette for more detailed explanations.
The object with results only for a single top-value method and a single partition method can be extracted as:
res = res_list["MAD", "hclust"]
# you can also extract it by
# res = res_list["MAD:hclust"]
A summary of res and all the functions that can be applied to it:
res
#> A 'ConsensusPartition' object with k = 2, 3, 4, 5, 6.
#> On a matrix with 51882 rows and 180 columns.
#> Top rows (1000, 2000, 3000, 4000, 5000) are extracted by 'MAD' method.
#> Subgroups are detected by 'hclust' method.
#> Performed in total 1250 partitions by row resampling.
#> Best k for subgroups seems to be 5.
#>
#> Following methods can be applied to this 'ConsensusPartition' object:
#> [1] "cola_report" "collect_classes" "collect_plots"
#> [4] "collect_stats" "colnames" "compare_signatures"
#> [7] "consensus_heatmap" "dimension_reduction" "functional_enrichment"
#> [10] "get_anno_col" "get_anno" "get_classes"
#> [13] "get_consensus" "get_matrix" "get_membership"
#> [16] "get_param" "get_signatures" "get_stats"
#> [19] "is_best_k" "is_stable_k" "membership_heatmap"
#> [22] "ncol" "nrow" "plot_ecdf"
#> [25] "rownames" "select_partition_number" "show"
#> [28] "suggest_best_k" "test_to_known_factors"
collect_plots() function collects all the plots made from res for all k (number of partitions)
into one single page to provide an easy and fast comparison between different k.
collect_plots(res)
The plots are:
k and the heatmap of
predicted classes for each k.k.k.k.All the plots in panels can be made by individual functions and they are plotted later in this section.
select_partition_number() produces several plots showing different
statistics for choosing “optimized” k. There are following statistics:
k;k, the area increased is defined as \(A_k - A_{k-1}\).The detailed explanations of these statistics can be found in the cola vignette.
Generally speaking, lower PAC score, higher mean silhouette score or higher
concordance corresponds to better partition. Rand index and Jaccard index
measure how similar the current partition is compared to partition with k-1.
If they are too similar, we won't accept k is better than k-1.
select_partition_number(res)
The numeric values for all these statistics can be obtained by get_stats().
get_stats(res)
#> k 1-PAC mean_silhouette concordance area_increased Rand Jaccard
#> 2 2 0.383 0.760 0.878 0.4395 0.557 0.557
#> 3 3 0.492 0.648 0.828 0.4479 0.740 0.550
#> 4 4 0.556 0.619 0.811 0.1509 0.882 0.667
#> 5 5 0.659 0.671 0.805 0.0614 0.952 0.813
#> 6 6 0.732 0.680 0.799 0.0375 0.950 0.775
suggest_best_k() suggests the best \(k\) based on these statistics. The rules are as follows:
suggest_best_k(res)
#> [1] 5
Following shows the table of the partitions (You need to click the show/hide
code output link to see it). The membership matrix (columns with name p*)
is inferred by
clue::cl_consensus()
function with the SE method. Basically the value in the membership matrix
represents the probability to belong to a certain group. The finall class
label for an item is determined with the group with highest probability it
belongs to.
In get_classes() function, the entropy is calculated from the membership
matrix and the silhouette score is calculated from the consensus matrix.
cbind(get_classes(res, k = 2), get_membership(res, k = 2))
#> class entropy silhouette p1 p2
#> GSM97800 2 0.0000 0.8781 0.000 1.000
#> GSM97803 2 0.0000 0.8781 0.000 1.000
#> GSM97804 2 0.0000 0.8781 0.000 1.000
#> GSM97805 2 0.0000 0.8781 0.000 1.000
#> GSM97807 2 0.0000 0.8781 0.000 1.000
#> GSM97809 2 0.0000 0.8781 0.000 1.000
#> GSM97811 2 0.0000 0.8781 0.000 1.000
#> GSM97812 2 0.0000 0.8781 0.000 1.000
#> GSM97816 1 0.9988 0.2673 0.520 0.480
#> GSM97817 2 0.0000 0.8781 0.000 1.000
#> GSM97820 2 0.0000 0.8781 0.000 1.000
#> GSM97825 2 0.0000 0.8781 0.000 1.000
#> GSM97827 2 0.0000 0.8781 0.000 1.000
#> GSM97828 1 0.9988 0.2673 0.520 0.480
#> GSM97833 2 0.0000 0.8781 0.000 1.000
#> GSM97834 2 0.0000 0.8781 0.000 1.000
#> GSM97840 2 0.0376 0.8760 0.004 0.996
#> GSM97846 2 0.0000 0.8781 0.000 1.000
#> GSM97848 2 0.0000 0.8781 0.000 1.000
#> GSM97849 2 0.0000 0.8781 0.000 1.000
#> GSM97850 2 0.0000 0.8781 0.000 1.000
#> GSM97853 2 0.0000 0.8781 0.000 1.000
#> GSM97855 2 0.0000 0.8781 0.000 1.000
#> GSM97878 1 0.6887 0.7917 0.816 0.184
#> GSM97913 1 0.9922 0.3388 0.552 0.448
#> GSM97932 1 0.0000 0.8408 1.000 0.000
#> GSM97939 2 0.6343 0.7718 0.160 0.840
#> GSM97951 2 0.4431 0.8263 0.092 0.908
#> GSM97957 1 0.8608 0.6915 0.716 0.284
#> GSM97972 2 0.8861 0.5401 0.304 0.696
#> GSM97793 1 0.8499 0.7001 0.724 0.276
#> GSM97795 2 0.6148 0.7799 0.152 0.848
#> GSM97802 1 0.3274 0.8403 0.940 0.060
#> GSM97810 2 0.6343 0.7718 0.160 0.840
#> GSM97815 2 0.6438 0.7678 0.164 0.836
#> GSM97837 1 0.3584 0.8383 0.932 0.068
#> GSM97843 1 0.9686 0.4891 0.604 0.396
#> GSM97890 1 0.9933 0.3397 0.548 0.452
#> GSM97899 1 0.0000 0.8408 1.000 0.000
#> GSM97910 1 0.6531 0.8031 0.832 0.168
#> GSM97916 1 0.6048 0.8130 0.852 0.148
#> GSM97920 1 0.9000 0.6513 0.684 0.316
#> GSM97921 1 0.7219 0.7812 0.800 0.200
#> GSM97927 1 0.5519 0.8211 0.872 0.128
#> GSM97937 1 0.0938 0.8429 0.988 0.012
#> GSM97941 2 0.0000 0.8781 0.000 1.000
#> GSM97943 1 0.9988 0.2673 0.520 0.480
#> GSM97958 1 0.7883 0.7484 0.764 0.236
#> GSM97960 2 0.5408 0.8035 0.124 0.876
#> GSM97794 1 0.9209 0.6029 0.664 0.336
#> GSM97796 1 0.0000 0.8408 1.000 0.000
#> GSM97797 1 0.7219 0.7822 0.800 0.200
#> GSM97798 1 0.0000 0.8408 1.000 0.000
#> GSM97801 1 0.6148 0.8119 0.848 0.152
#> GSM97806 1 0.6148 0.8110 0.848 0.152
#> GSM97808 1 0.0000 0.8408 1.000 0.000
#> GSM97813 1 0.0938 0.8431 0.988 0.012
#> GSM97814 1 0.0000 0.8408 1.000 0.000
#> GSM97818 1 0.6973 0.7880 0.812 0.188
#> GSM97819 1 0.8608 0.6918 0.716 0.284
#> GSM97821 2 0.7674 0.6884 0.224 0.776
#> GSM97826 1 0.3584 0.8383 0.932 0.068
#> GSM97829 1 0.5059 0.8279 0.888 0.112
#> GSM97832 2 0.5294 0.8070 0.120 0.880
#> GSM97836 1 0.6623 0.8012 0.828 0.172
#> GSM97839 1 0.0000 0.8408 1.000 0.000
#> GSM97844 2 0.0000 0.8781 0.000 1.000
#> GSM97847 1 0.0938 0.8429 0.988 0.012
#> GSM97851 1 0.0000 0.8408 1.000 0.000
#> GSM97852 1 0.0938 0.8429 0.988 0.012
#> GSM97856 1 0.0000 0.8408 1.000 0.000
#> GSM97858 2 0.0000 0.8781 0.000 1.000
#> GSM97859 1 0.0938 0.8431 0.988 0.012
#> GSM97861 1 0.5519 0.8211 0.872 0.128
#> GSM97863 1 0.0000 0.8408 1.000 0.000
#> GSM97869 1 0.6048 0.8130 0.852 0.148
#> GSM97870 1 0.1184 0.8435 0.984 0.016
#> GSM97871 1 0.0000 0.8408 1.000 0.000
#> GSM97877 1 0.9983 0.2558 0.524 0.476
#> GSM97879 1 0.4161 0.8347 0.916 0.084
#> GSM97882 1 0.6148 0.8110 0.848 0.152
#> GSM97885 1 0.6048 0.8130 0.852 0.148
#> GSM97886 1 0.0000 0.8408 1.000 0.000
#> GSM97887 1 0.0000 0.8408 1.000 0.000
#> GSM97888 1 0.0000 0.8408 1.000 0.000
#> GSM97889 1 0.1843 0.8436 0.972 0.028
#> GSM97891 1 0.6247 0.8091 0.844 0.156
#> GSM97892 2 0.0000 0.8781 0.000 1.000
#> GSM97893 1 0.0000 0.8408 1.000 0.000
#> GSM97894 1 0.0000 0.8408 1.000 0.000
#> GSM97895 1 0.0000 0.8408 1.000 0.000
#> GSM97896 1 0.0000 0.8408 1.000 0.000
#> GSM97898 1 0.0000 0.8408 1.000 0.000
#> GSM97903 1 0.4431 0.8330 0.908 0.092
#> GSM97905 1 0.1414 0.8433 0.980 0.020
#> GSM97906 1 0.0000 0.8408 1.000 0.000
#> GSM97908 1 0.0938 0.8432 0.988 0.012
#> GSM97912 1 0.1414 0.8433 0.980 0.020
#> GSM97914 1 0.6247 0.8101 0.844 0.156
#> GSM97915 1 0.0000 0.8408 1.000 0.000
#> GSM97917 1 0.0000 0.8408 1.000 0.000
#> GSM97918 1 0.0000 0.8408 1.000 0.000
#> GSM97919 1 0.0000 0.8408 1.000 0.000
#> GSM97922 1 0.0938 0.8431 0.988 0.012
#> GSM97924 2 0.0000 0.8781 0.000 1.000
#> GSM97926 1 0.6623 0.8012 0.828 0.172
#> GSM97930 1 0.2043 0.8431 0.968 0.032
#> GSM97931 2 0.8861 0.5401 0.304 0.696
#> GSM97935 1 0.5519 0.8211 0.872 0.128
#> GSM97936 1 0.0000 0.8408 1.000 0.000
#> GSM97938 1 0.0000 0.8408 1.000 0.000
#> GSM97940 1 0.0000 0.8408 1.000 0.000
#> GSM97942 1 0.8499 0.7001 0.724 0.276
#> GSM97945 1 0.0000 0.8408 1.000 0.000
#> GSM97946 2 0.0000 0.8781 0.000 1.000
#> GSM97948 1 0.7219 0.7712 0.800 0.200
#> GSM97950 1 0.0000 0.8408 1.000 0.000
#> GSM97952 1 0.0000 0.8408 1.000 0.000
#> GSM97953 1 0.0376 0.8418 0.996 0.004
#> GSM97954 1 0.1843 0.8433 0.972 0.028
#> GSM97955 1 0.0000 0.8408 1.000 0.000
#> GSM97959 1 0.9710 0.4835 0.600 0.400
#> GSM97961 1 0.0000 0.8408 1.000 0.000
#> GSM97963 1 0.0000 0.8408 1.000 0.000
#> GSM97965 1 0.0000 0.8408 1.000 0.000
#> GSM97966 1 0.0000 0.8408 1.000 0.000
#> GSM97967 2 0.0000 0.8781 0.000 1.000
#> GSM97968 2 0.0000 0.8781 0.000 1.000
#> GSM97969 1 0.0376 0.8416 0.996 0.004
#> GSM97971 1 0.0938 0.8431 0.988 0.012
#> GSM97799 2 0.8207 0.6403 0.256 0.744
#> GSM97823 2 0.0000 0.8781 0.000 1.000
#> GSM97824 2 0.9933 0.0338 0.452 0.548
#> GSM97830 1 0.8713 0.6819 0.708 0.292
#> GSM97835 2 0.6623 0.7590 0.172 0.828
#> GSM97838 2 0.0000 0.8781 0.000 1.000
#> GSM97841 2 0.0000 0.8781 0.000 1.000
#> GSM97842 2 0.8386 0.6202 0.268 0.732
#> GSM97854 2 0.0000 0.8781 0.000 1.000
#> GSM97857 2 0.9933 0.0338 0.452 0.548
#> GSM97860 1 0.8499 0.7001 0.724 0.276
#> GSM97862 1 0.9427 0.5725 0.640 0.360
#> GSM97864 2 0.0000 0.8781 0.000 1.000
#> GSM97866 1 0.9427 0.5725 0.640 0.360
#> GSM97868 1 0.9881 0.3900 0.564 0.436
#> GSM97872 1 0.2423 0.8429 0.960 0.040
#> GSM97873 2 0.8081 0.6542 0.248 0.752
#> GSM97874 1 0.8861 0.6682 0.696 0.304
#> GSM97875 1 0.8608 0.6918 0.716 0.284
#> GSM97876 1 0.8499 0.7001 0.724 0.276
#> GSM97880 1 0.8499 0.7001 0.724 0.276
#> GSM97881 1 0.9963 0.3023 0.536 0.464
#> GSM97884 2 0.8955 0.5135 0.312 0.688
#> GSM97901 1 0.9427 0.5725 0.640 0.360
#> GSM97902 1 0.7815 0.7525 0.768 0.232
#> GSM97909 2 0.7674 0.6884 0.224 0.776
#> GSM97911 1 0.9963 0.3023 0.536 0.464
#> GSM97923 1 0.8499 0.7001 0.724 0.276
#> GSM97928 1 0.2423 0.8429 0.960 0.040
#> GSM97929 2 0.0000 0.8781 0.000 1.000
#> GSM97933 1 0.8608 0.6915 0.716 0.284
#> GSM97934 1 0.8608 0.6915 0.716 0.284
#> GSM97944 2 0.8207 0.6403 0.256 0.744
#> GSM97949 2 0.0000 0.8781 0.000 1.000
#> GSM97956 2 0.9970 -0.0447 0.468 0.532
#> GSM97962 1 0.8909 0.6597 0.692 0.308
#> GSM97964 2 0.9129 0.4749 0.328 0.672
#> GSM97970 2 0.7453 0.7089 0.212 0.788
#> GSM97822 1 0.2043 0.8434 0.968 0.032
#> GSM97831 1 0.8909 0.6599 0.692 0.308
#> GSM97845 1 0.1184 0.8432 0.984 0.016
#> GSM97865 1 0.7602 0.7642 0.780 0.220
#> GSM97867 1 0.8499 0.7001 0.724 0.276
#> GSM97883 1 0.3733 0.8378 0.928 0.072
#> GSM97897 1 0.0938 0.8431 0.988 0.012
#> GSM97900 1 0.0000 0.8408 1.000 0.000
#> GSM97904 1 0.1414 0.8442 0.980 0.020
#> GSM97907 2 0.0000 0.8781 0.000 1.000
#> GSM97925 1 0.7219 0.7712 0.800 0.200
#> GSM97947 1 0.8608 0.6918 0.716 0.284
cbind(get_classes(res, k = 3), get_membership(res, k = 3))
#> class entropy silhouette p1 p2 p3
#> GSM97800 2 0.0000 0.8661 0.000 1.000 0.000
#> GSM97803 2 0.0000 0.8661 0.000 1.000 0.000
#> GSM97804 2 0.0000 0.8661 0.000 1.000 0.000
#> GSM97805 2 0.0000 0.8661 0.000 1.000 0.000
#> GSM97807 2 0.0000 0.8661 0.000 1.000 0.000
#> GSM97809 2 0.0000 0.8661 0.000 1.000 0.000
#> GSM97811 2 0.0000 0.8661 0.000 1.000 0.000
#> GSM97812 2 0.0000 0.8661 0.000 1.000 0.000
#> GSM97816 3 0.5815 0.5077 0.004 0.304 0.692
#> GSM97817 2 0.0000 0.8661 0.000 1.000 0.000
#> GSM97820 2 0.0000 0.8661 0.000 1.000 0.000
#> GSM97825 2 0.0000 0.8661 0.000 1.000 0.000
#> GSM97827 2 0.0000 0.8661 0.000 1.000 0.000
#> GSM97828 3 0.5815 0.5077 0.004 0.304 0.692
#> GSM97833 2 0.0000 0.8661 0.000 1.000 0.000
#> GSM97834 2 0.0000 0.8661 0.000 1.000 0.000
#> GSM97840 2 0.0747 0.8561 0.000 0.984 0.016
#> GSM97846 2 0.0000 0.8661 0.000 1.000 0.000
#> GSM97848 2 0.0000 0.8661 0.000 1.000 0.000
#> GSM97849 2 0.0000 0.8661 0.000 1.000 0.000
#> GSM97850 2 0.0000 0.8661 0.000 1.000 0.000
#> GSM97853 2 0.0000 0.8661 0.000 1.000 0.000
#> GSM97855 2 0.0000 0.8661 0.000 1.000 0.000
#> GSM97878 3 0.7872 0.6151 0.296 0.084 0.620
#> GSM97913 3 0.8068 0.5143 0.088 0.316 0.596
#> GSM97932 1 0.0000 0.8451 1.000 0.000 0.000
#> GSM97939 2 0.5621 0.5838 0.000 0.692 0.308
#> GSM97951 2 0.3816 0.7608 0.000 0.852 0.148
#> GSM97957 3 0.0848 0.7085 0.008 0.008 0.984
#> GSM97972 2 0.6912 0.2061 0.016 0.540 0.444
#> GSM97793 3 0.0424 0.7060 0.008 0.000 0.992
#> GSM97795 2 0.5497 0.6091 0.000 0.708 0.292
#> GSM97802 3 0.5138 0.6147 0.252 0.000 0.748
#> GSM97810 2 0.5621 0.5838 0.000 0.692 0.308
#> GSM97815 2 0.5733 0.5629 0.000 0.676 0.324
#> GSM97837 3 0.6280 0.3108 0.460 0.000 0.540
#> GSM97843 3 0.3784 0.6545 0.004 0.132 0.864
#> GSM97890 3 0.4399 0.5979 0.000 0.188 0.812
#> GSM97899 1 0.0424 0.8412 0.992 0.000 0.008
#> GSM97910 3 0.7027 0.6150 0.296 0.044 0.660
#> GSM97916 3 0.7600 0.5767 0.328 0.060 0.612
#> GSM97920 3 0.1765 0.7122 0.004 0.040 0.956
#> GSM97921 3 0.7925 0.5943 0.316 0.080 0.604
#> GSM97927 3 0.7310 0.5335 0.360 0.040 0.600
#> GSM97937 1 0.2625 0.7889 0.916 0.000 0.084
#> GSM97941 2 0.0000 0.8661 0.000 1.000 0.000
#> GSM97943 3 0.5815 0.5077 0.004 0.304 0.692
#> GSM97958 3 0.7741 0.6621 0.216 0.116 0.668
#> GSM97960 2 0.4702 0.7001 0.000 0.788 0.212
#> GSM97794 3 0.8711 0.6262 0.184 0.224 0.592
#> GSM97796 1 0.0000 0.8451 1.000 0.000 0.000
#> GSM97797 3 0.7454 0.6469 0.252 0.080 0.668
#> GSM97798 1 0.0000 0.8451 1.000 0.000 0.000
#> GSM97801 3 0.7190 0.5856 0.320 0.044 0.636
#> GSM97806 3 0.7580 0.5631 0.340 0.056 0.604
#> GSM97808 1 0.0000 0.8451 1.000 0.000 0.000
#> GSM97813 1 0.6302 -0.0700 0.520 0.000 0.480
#> GSM97814 1 0.0000 0.8451 1.000 0.000 0.000
#> GSM97818 3 0.7992 0.5717 0.328 0.080 0.592
#> GSM97819 3 0.0000 0.7052 0.000 0.000 1.000
#> GSM97821 2 0.5733 0.5235 0.000 0.676 0.324
#> GSM97826 3 0.6274 0.3224 0.456 0.000 0.544
#> GSM97829 3 0.7223 0.4062 0.424 0.028 0.548
#> GSM97832 2 0.4399 0.7240 0.000 0.812 0.188
#> GSM97836 3 0.7065 0.6296 0.276 0.052 0.672
#> GSM97839 1 0.0000 0.8451 1.000 0.000 0.000
#> GSM97844 2 0.0000 0.8661 0.000 1.000 0.000
#> GSM97847 1 0.4178 0.6964 0.828 0.000 0.172
#> GSM97851 1 0.0000 0.8451 1.000 0.000 0.000
#> GSM97852 1 0.4178 0.6964 0.828 0.000 0.172
#> GSM97856 1 0.0000 0.8451 1.000 0.000 0.000
#> GSM97858 2 0.0000 0.8661 0.000 1.000 0.000
#> GSM97859 1 0.6307 -0.0984 0.512 0.000 0.488
#> GSM97861 3 0.7310 0.5335 0.360 0.040 0.600
#> GSM97863 1 0.0000 0.8451 1.000 0.000 0.000
#> GSM97869 3 0.7600 0.5767 0.328 0.060 0.612
#> GSM97870 1 0.6308 -0.1101 0.508 0.000 0.492
#> GSM97871 1 0.0000 0.8451 1.000 0.000 0.000
#> GSM97877 3 0.7905 0.4720 0.072 0.340 0.588
#> GSM97879 3 0.6804 0.3223 0.460 0.012 0.528
#> GSM97882 3 0.7537 0.5721 0.332 0.056 0.612
#> GSM97885 3 0.7600 0.5767 0.328 0.060 0.612
#> GSM97886 1 0.0000 0.8451 1.000 0.000 0.000
#> GSM97887 1 0.0000 0.8451 1.000 0.000 0.000
#> GSM97888 1 0.5291 0.5344 0.732 0.000 0.268
#> GSM97889 3 0.5810 0.5136 0.336 0.000 0.664
#> GSM97891 3 0.7467 0.5852 0.320 0.056 0.624
#> GSM97892 2 0.0000 0.8661 0.000 1.000 0.000
#> GSM97893 1 0.1529 0.8219 0.960 0.000 0.040
#> GSM97894 1 0.0000 0.8451 1.000 0.000 0.000
#> GSM97895 1 0.0000 0.8451 1.000 0.000 0.000
#> GSM97896 1 0.5216 0.5693 0.740 0.000 0.260
#> GSM97898 1 0.0000 0.8451 1.000 0.000 0.000
#> GSM97903 3 0.7054 0.3337 0.456 0.020 0.524
#> GSM97905 3 0.6235 0.3033 0.436 0.000 0.564
#> GSM97906 1 0.0000 0.8451 1.000 0.000 0.000
#> GSM97908 1 0.4062 0.7069 0.836 0.000 0.164
#> GSM97912 3 0.6235 0.3033 0.436 0.000 0.564
#> GSM97914 3 0.7306 0.5703 0.340 0.044 0.616
#> GSM97915 1 0.0000 0.8451 1.000 0.000 0.000
#> GSM97917 1 0.0000 0.8451 1.000 0.000 0.000
#> GSM97918 1 0.0000 0.8451 1.000 0.000 0.000
#> GSM97919 1 0.0000 0.8451 1.000 0.000 0.000
#> GSM97922 1 0.6307 -0.0984 0.512 0.000 0.488
#> GSM97924 2 0.0000 0.8661 0.000 1.000 0.000
#> GSM97926 3 0.7065 0.6296 0.276 0.052 0.672
#> GSM97930 1 0.6140 0.1641 0.596 0.000 0.404
#> GSM97931 2 0.6912 0.2061 0.016 0.540 0.444
#> GSM97935 3 0.7310 0.5335 0.360 0.040 0.600
#> GSM97936 1 0.0237 0.8429 0.996 0.000 0.004
#> GSM97938 1 0.1031 0.8325 0.976 0.000 0.024
#> GSM97940 1 0.0000 0.8451 1.000 0.000 0.000
#> GSM97942 3 0.0424 0.7060 0.008 0.000 0.992
#> GSM97945 1 0.3192 0.7609 0.888 0.000 0.112
#> GSM97946 2 0.0000 0.8661 0.000 1.000 0.000
#> GSM97948 3 0.3116 0.6918 0.108 0.000 0.892
#> GSM97950 1 0.0000 0.8451 1.000 0.000 0.000
#> GSM97952 1 0.0000 0.8451 1.000 0.000 0.000
#> GSM97953 1 0.1289 0.8277 0.968 0.000 0.032
#> GSM97954 1 0.6008 0.2668 0.628 0.000 0.372
#> GSM97955 1 0.0424 0.8416 0.992 0.000 0.008
#> GSM97959 3 0.8233 0.5892 0.116 0.272 0.612
#> GSM97961 1 0.0000 0.8451 1.000 0.000 0.000
#> GSM97963 1 0.0000 0.8451 1.000 0.000 0.000
#> GSM97965 1 0.0000 0.8451 1.000 0.000 0.000
#> GSM97966 1 0.0000 0.8451 1.000 0.000 0.000
#> GSM97967 2 0.0000 0.8661 0.000 1.000 0.000
#> GSM97968 2 0.0000 0.8661 0.000 1.000 0.000
#> GSM97969 1 0.6140 0.2023 0.596 0.000 0.404
#> GSM97971 1 0.6307 -0.0984 0.512 0.000 0.488
#> GSM97799 2 0.6295 0.2582 0.000 0.528 0.472
#> GSM97823 2 0.0000 0.8661 0.000 1.000 0.000
#> GSM97824 3 0.5621 0.4216 0.000 0.308 0.692
#> GSM97830 3 0.0424 0.7071 0.000 0.008 0.992
#> GSM97835 2 0.5988 0.4906 0.000 0.632 0.368
#> GSM97838 2 0.0000 0.8661 0.000 1.000 0.000
#> GSM97841 2 0.0000 0.8661 0.000 1.000 0.000
#> GSM97842 2 0.6302 0.2329 0.000 0.520 0.480
#> GSM97854 2 0.0000 0.8661 0.000 1.000 0.000
#> GSM97857 3 0.5621 0.4216 0.000 0.308 0.692
#> GSM97860 3 0.0424 0.7060 0.008 0.000 0.992
#> GSM97862 3 0.2448 0.6947 0.000 0.076 0.924
#> GSM97864 2 0.0000 0.8661 0.000 1.000 0.000
#> GSM97866 3 0.2448 0.6947 0.000 0.076 0.924
#> GSM97868 3 0.4178 0.6191 0.000 0.172 0.828
#> GSM97872 3 0.5733 0.5369 0.324 0.000 0.676
#> GSM97873 2 0.6274 0.2882 0.000 0.544 0.456
#> GSM97874 3 0.1031 0.7105 0.000 0.024 0.976
#> GSM97875 3 0.0000 0.7052 0.000 0.000 1.000
#> GSM97876 3 0.0424 0.7060 0.008 0.000 0.992
#> GSM97880 3 0.0424 0.7060 0.008 0.000 0.992
#> GSM97881 3 0.4555 0.5853 0.000 0.200 0.800
#> GSM97884 3 0.6295 -0.0729 0.000 0.472 0.528
#> GSM97901 3 0.2448 0.6947 0.000 0.076 0.924
#> GSM97902 3 0.7717 0.6610 0.220 0.112 0.668
#> GSM97909 2 0.5733 0.5235 0.000 0.676 0.324
#> GSM97911 3 0.4555 0.5853 0.000 0.200 0.800
#> GSM97923 3 0.0424 0.7060 0.008 0.000 0.992
#> GSM97928 3 0.5733 0.5369 0.324 0.000 0.676
#> GSM97929 2 0.0000 0.8661 0.000 1.000 0.000
#> GSM97933 3 0.0848 0.7085 0.008 0.008 0.984
#> GSM97934 3 0.0848 0.7085 0.008 0.008 0.984
#> GSM97944 2 0.6295 0.2582 0.000 0.528 0.472
#> GSM97949 2 0.0000 0.8661 0.000 1.000 0.000
#> GSM97956 3 0.5465 0.4565 0.000 0.288 0.712
#> GSM97962 3 0.1711 0.7097 0.008 0.032 0.960
#> GSM97964 3 0.6286 -0.0307 0.000 0.464 0.536
#> GSM97970 2 0.6168 0.3998 0.000 0.588 0.412
#> GSM97822 3 0.5678 0.5433 0.316 0.000 0.684
#> GSM97831 3 0.1031 0.7081 0.000 0.024 0.976
#> GSM97845 1 0.5327 0.5280 0.728 0.000 0.272
#> GSM97865 3 0.7673 0.6545 0.236 0.100 0.664
#> GSM97867 3 0.0424 0.7060 0.008 0.000 0.992
#> GSM97883 3 0.5363 0.6010 0.276 0.000 0.724
#> GSM97897 3 0.6111 0.3924 0.396 0.000 0.604
#> GSM97900 1 0.0000 0.8451 1.000 0.000 0.000
#> GSM97904 1 0.6274 -0.0242 0.544 0.000 0.456
#> GSM97907 2 0.0000 0.8661 0.000 1.000 0.000
#> GSM97925 3 0.3116 0.6918 0.108 0.000 0.892
#> GSM97947 3 0.0237 0.7060 0.004 0.000 0.996
cbind(get_classes(res, k = 4), get_membership(res, k = 4))
#> class entropy silhouette p1 p2 p3 p4
#> GSM97800 2 0.0000 0.8631 0.000 1.000 0.000 0.000
#> GSM97803 2 0.0000 0.8631 0.000 1.000 0.000 0.000
#> GSM97804 2 0.0000 0.8631 0.000 1.000 0.000 0.000
#> GSM97805 2 0.0000 0.8631 0.000 1.000 0.000 0.000
#> GSM97807 2 0.0000 0.8631 0.000 1.000 0.000 0.000
#> GSM97809 2 0.0000 0.8631 0.000 1.000 0.000 0.000
#> GSM97811 2 0.0000 0.8631 0.000 1.000 0.000 0.000
#> GSM97812 2 0.0000 0.8631 0.000 1.000 0.000 0.000
#> GSM97816 1 0.6102 0.4061 0.672 0.212 0.116 0.000
#> GSM97817 2 0.0000 0.8631 0.000 1.000 0.000 0.000
#> GSM97820 2 0.0000 0.8631 0.000 1.000 0.000 0.000
#> GSM97825 2 0.0000 0.8631 0.000 1.000 0.000 0.000
#> GSM97827 2 0.0000 0.8631 0.000 1.000 0.000 0.000
#> GSM97828 1 0.6102 0.4061 0.672 0.212 0.116 0.000
#> GSM97833 2 0.0000 0.8631 0.000 1.000 0.000 0.000
#> GSM97834 2 0.0000 0.8631 0.000 1.000 0.000 0.000
#> GSM97840 2 0.0592 0.8523 0.016 0.984 0.000 0.000
#> GSM97846 2 0.0000 0.8631 0.000 1.000 0.000 0.000
#> GSM97848 2 0.0000 0.8631 0.000 1.000 0.000 0.000
#> GSM97849 2 0.0000 0.8631 0.000 1.000 0.000 0.000
#> GSM97850 2 0.0000 0.8631 0.000 1.000 0.000 0.000
#> GSM97853 2 0.0000 0.8631 0.000 1.000 0.000 0.000
#> GSM97855 2 0.0000 0.8631 0.000 1.000 0.000 0.000
#> GSM97878 1 0.3639 0.6903 0.868 0.024 0.020 0.088
#> GSM97913 1 0.4364 0.5235 0.764 0.220 0.016 0.000
#> GSM97932 4 0.0188 0.8280 0.004 0.000 0.000 0.996
#> GSM97939 2 0.6655 0.5561 0.184 0.624 0.192 0.000
#> GSM97951 2 0.4426 0.7409 0.096 0.812 0.092 0.000
#> GSM97957 3 0.1867 0.6876 0.072 0.000 0.928 0.000
#> GSM97972 1 0.6389 -0.0932 0.488 0.448 0.064 0.000
#> GSM97793 3 0.0469 0.6927 0.012 0.000 0.988 0.000
#> GSM97795 2 0.6416 0.5842 0.152 0.648 0.200 0.000
#> GSM97802 3 0.6613 0.2858 0.288 0.000 0.596 0.116
#> GSM97810 2 0.6655 0.5561 0.184 0.624 0.192 0.000
#> GSM97815 2 0.6750 0.5378 0.180 0.612 0.208 0.000
#> GSM97837 1 0.4767 0.5906 0.724 0.000 0.020 0.256
#> GSM97843 3 0.4898 0.6343 0.116 0.104 0.780 0.000
#> GSM97890 3 0.5462 0.5854 0.112 0.152 0.736 0.000
#> GSM97899 4 0.0524 0.8242 0.004 0.000 0.008 0.988
#> GSM97910 1 0.4001 0.6807 0.840 0.004 0.048 0.108
#> GSM97916 1 0.6039 0.6700 0.720 0.016 0.128 0.136
#> GSM97920 3 0.4836 0.5076 0.320 0.008 0.672 0.000
#> GSM97921 1 0.4413 0.6746 0.812 0.008 0.040 0.140
#> GSM97927 1 0.6037 0.6313 0.688 0.000 0.156 0.156
#> GSM97937 4 0.3486 0.6783 0.188 0.000 0.000 0.812
#> GSM97941 2 0.0000 0.8631 0.000 1.000 0.000 0.000
#> GSM97943 1 0.6102 0.4061 0.672 0.212 0.116 0.000
#> GSM97958 1 0.3289 0.6571 0.892 0.028 0.052 0.028
#> GSM97960 2 0.5470 0.6790 0.116 0.736 0.148 0.000
#> GSM97794 1 0.6740 0.5970 0.692 0.156 0.088 0.064
#> GSM97796 4 0.0000 0.8293 0.000 0.000 0.000 1.000
#> GSM97797 1 0.4247 0.6737 0.844 0.028 0.044 0.084
#> GSM97798 4 0.0000 0.8293 0.000 0.000 0.000 1.000
#> GSM97801 1 0.4388 0.6735 0.812 0.004 0.048 0.136
#> GSM97806 1 0.6456 0.6514 0.684 0.016 0.148 0.152
#> GSM97808 4 0.0000 0.8293 0.000 0.000 0.000 1.000
#> GSM97813 4 0.7906 -0.1112 0.316 0.000 0.316 0.368
#> GSM97814 4 0.0000 0.8293 0.000 0.000 0.000 1.000
#> GSM97818 1 0.4072 0.6866 0.828 0.052 0.000 0.120
#> GSM97819 3 0.0188 0.6924 0.004 0.000 0.996 0.000
#> GSM97821 2 0.6259 0.4730 0.300 0.616 0.084 0.000
#> GSM97826 1 0.4838 0.5964 0.724 0.000 0.024 0.252
#> GSM97829 1 0.5135 0.6328 0.728 0.004 0.036 0.232
#> GSM97832 2 0.5042 0.7076 0.096 0.768 0.136 0.000
#> GSM97836 1 0.6915 0.5426 0.616 0.016 0.256 0.112
#> GSM97839 4 0.0000 0.8293 0.000 0.000 0.000 1.000
#> GSM97844 2 0.0000 0.8631 0.000 1.000 0.000 0.000
#> GSM97847 4 0.4431 0.5001 0.304 0.000 0.000 0.696
#> GSM97851 4 0.0188 0.8280 0.004 0.000 0.000 0.996
#> GSM97852 4 0.4431 0.5001 0.304 0.000 0.000 0.696
#> GSM97856 4 0.0000 0.8293 0.000 0.000 0.000 1.000
#> GSM97858 2 0.0000 0.8631 0.000 1.000 0.000 0.000
#> GSM97859 4 0.7913 -0.1259 0.316 0.000 0.324 0.360
#> GSM97861 1 0.6037 0.6313 0.688 0.000 0.156 0.156
#> GSM97863 4 0.0000 0.8293 0.000 0.000 0.000 1.000
#> GSM97869 1 0.6039 0.6700 0.720 0.016 0.128 0.136
#> GSM97870 4 0.7912 -0.1246 0.312 0.000 0.328 0.360
#> GSM97871 4 0.0000 0.8293 0.000 0.000 0.000 1.000
#> GSM97877 1 0.4776 0.4988 0.732 0.244 0.024 0.000
#> GSM97879 1 0.6195 0.5821 0.648 0.000 0.100 0.252
#> GSM97882 1 0.6455 0.6471 0.684 0.016 0.156 0.144
#> GSM97885 1 0.6039 0.6700 0.720 0.016 0.128 0.136
#> GSM97886 4 0.0000 0.8293 0.000 0.000 0.000 1.000
#> GSM97887 4 0.0000 0.8293 0.000 0.000 0.000 1.000
#> GSM97888 4 0.6790 0.3737 0.196 0.000 0.196 0.608
#> GSM97889 3 0.7336 0.1823 0.284 0.000 0.520 0.196
#> GSM97891 1 0.6528 0.6297 0.676 0.016 0.172 0.136
#> GSM97892 2 0.0000 0.8631 0.000 1.000 0.000 0.000
#> GSM97893 4 0.2469 0.7593 0.108 0.000 0.000 0.892
#> GSM97894 4 0.0000 0.8293 0.000 0.000 0.000 1.000
#> GSM97895 4 0.0188 0.8280 0.004 0.000 0.000 0.996
#> GSM97896 4 0.6723 0.4031 0.188 0.000 0.196 0.616
#> GSM97898 4 0.0188 0.8280 0.004 0.000 0.000 0.996
#> GSM97903 1 0.5397 0.6169 0.708 0.004 0.044 0.244
#> GSM97905 3 0.7878 -0.0753 0.324 0.000 0.384 0.292
#> GSM97906 4 0.0000 0.8293 0.000 0.000 0.000 1.000
#> GSM97908 4 0.4431 0.5073 0.304 0.000 0.000 0.696
#> GSM97912 3 0.7878 -0.0753 0.324 0.000 0.384 0.292
#> GSM97914 1 0.4362 0.6914 0.816 0.008 0.040 0.136
#> GSM97915 4 0.0188 0.8280 0.004 0.000 0.000 0.996
#> GSM97917 4 0.0592 0.8229 0.016 0.000 0.000 0.984
#> GSM97918 4 0.0188 0.8280 0.004 0.000 0.000 0.996
#> GSM97919 4 0.0188 0.8280 0.004 0.000 0.000 0.996
#> GSM97922 4 0.7913 -0.1259 0.316 0.000 0.324 0.360
#> GSM97924 2 0.0000 0.8631 0.000 1.000 0.000 0.000
#> GSM97926 1 0.6915 0.5426 0.616 0.016 0.256 0.112
#> GSM97930 1 0.4817 0.3452 0.612 0.000 0.000 0.388
#> GSM97931 1 0.6389 -0.0932 0.488 0.448 0.064 0.000
#> GSM97935 1 0.6037 0.6313 0.688 0.000 0.156 0.156
#> GSM97936 4 0.0376 0.8257 0.004 0.000 0.004 0.992
#> GSM97938 4 0.1940 0.7828 0.076 0.000 0.000 0.924
#> GSM97940 4 0.0000 0.8293 0.000 0.000 0.000 1.000
#> GSM97942 3 0.0469 0.6927 0.012 0.000 0.988 0.000
#> GSM97945 4 0.4553 0.6415 0.180 0.000 0.040 0.780
#> GSM97946 2 0.0000 0.8631 0.000 1.000 0.000 0.000
#> GSM97948 3 0.4428 0.5832 0.124 0.000 0.808 0.068
#> GSM97950 4 0.0336 0.8270 0.008 0.000 0.000 0.992
#> GSM97952 4 0.0000 0.8293 0.000 0.000 0.000 1.000
#> GSM97953 4 0.2081 0.7767 0.084 0.000 0.000 0.916
#> GSM97954 1 0.5808 0.2386 0.544 0.000 0.032 0.424
#> GSM97955 4 0.0376 0.8260 0.004 0.000 0.004 0.992
#> GSM97959 1 0.3907 0.5705 0.808 0.180 0.008 0.004
#> GSM97961 4 0.0000 0.8293 0.000 0.000 0.000 1.000
#> GSM97963 4 0.0000 0.8293 0.000 0.000 0.000 1.000
#> GSM97965 4 0.0000 0.8293 0.000 0.000 0.000 1.000
#> GSM97966 4 0.0000 0.8293 0.000 0.000 0.000 1.000
#> GSM97967 2 0.0000 0.8631 0.000 1.000 0.000 0.000
#> GSM97968 2 0.0000 0.8631 0.000 1.000 0.000 0.000
#> GSM97969 4 0.7677 0.0702 0.272 0.000 0.268 0.460
#> GSM97971 4 0.7913 -0.1259 0.316 0.000 0.324 0.360
#> GSM97799 2 0.7392 0.2560 0.172 0.472 0.356 0.000
#> GSM97823 2 0.0000 0.8631 0.000 1.000 0.000 0.000
#> GSM97824 3 0.6640 0.4241 0.128 0.268 0.604 0.000
#> GSM97830 3 0.3528 0.6329 0.192 0.000 0.808 0.000
#> GSM97835 2 0.7082 0.4632 0.184 0.564 0.252 0.000
#> GSM97838 2 0.0000 0.8631 0.000 1.000 0.000 0.000
#> GSM97841 2 0.0000 0.8631 0.000 1.000 0.000 0.000
#> GSM97842 2 0.7379 0.2384 0.168 0.468 0.364 0.000
#> GSM97854 2 0.0000 0.8631 0.000 1.000 0.000 0.000
#> GSM97857 3 0.6811 0.4175 0.144 0.268 0.588 0.000
#> GSM97860 3 0.0469 0.6927 0.012 0.000 0.988 0.000
#> GSM97862 3 0.3858 0.6618 0.100 0.056 0.844 0.000
#> GSM97864 2 0.0000 0.8631 0.000 1.000 0.000 0.000
#> GSM97866 3 0.3796 0.6635 0.096 0.056 0.848 0.000
#> GSM97868 3 0.5380 0.5965 0.120 0.136 0.744 0.000
#> GSM97872 3 0.7381 0.1040 0.328 0.000 0.492 0.180
#> GSM97873 2 0.7375 0.2934 0.176 0.488 0.336 0.000
#> GSM97874 3 0.4313 0.5713 0.260 0.004 0.736 0.000
#> GSM97875 3 0.0188 0.6924 0.004 0.000 0.996 0.000
#> GSM97876 3 0.0469 0.6927 0.012 0.000 0.988 0.000
#> GSM97880 3 0.0469 0.6927 0.012 0.000 0.988 0.000
#> GSM97881 3 0.5708 0.5697 0.124 0.160 0.716 0.000
#> GSM97884 2 0.7546 0.0676 0.188 0.408 0.404 0.000
#> GSM97901 3 0.3858 0.6618 0.100 0.056 0.844 0.000
#> GSM97902 1 0.3285 0.6600 0.892 0.024 0.052 0.032
#> GSM97909 2 0.6238 0.4781 0.296 0.620 0.084 0.000
#> GSM97911 3 0.5708 0.5697 0.124 0.160 0.716 0.000
#> GSM97923 3 0.0469 0.6927 0.012 0.000 0.988 0.000
#> GSM97928 3 0.7381 0.1040 0.328 0.000 0.492 0.180
#> GSM97929 2 0.0000 0.8631 0.000 1.000 0.000 0.000
#> GSM97933 3 0.0921 0.6934 0.028 0.000 0.972 0.000
#> GSM97934 3 0.1867 0.6876 0.072 0.000 0.928 0.000
#> GSM97944 2 0.7392 0.2560 0.172 0.472 0.356 0.000
#> GSM97949 2 0.0000 0.8631 0.000 1.000 0.000 0.000
#> GSM97956 3 0.6495 0.4534 0.124 0.252 0.624 0.000
#> GSM97962 3 0.2174 0.6914 0.052 0.020 0.928 0.000
#> GSM97964 3 0.7546 -0.0757 0.188 0.400 0.412 0.000
#> GSM97970 2 0.7312 0.3820 0.188 0.520 0.292 0.000
#> GSM97822 3 0.7237 0.1893 0.296 0.000 0.528 0.176
#> GSM97831 3 0.4136 0.6298 0.196 0.016 0.788 0.000
#> GSM97845 4 0.5550 0.1482 0.428 0.000 0.020 0.552
#> GSM97865 1 0.3081 0.6670 0.900 0.016 0.044 0.040
#> GSM97867 3 0.0469 0.6927 0.012 0.000 0.988 0.000
#> GSM97883 3 0.6961 0.1861 0.316 0.000 0.548 0.136
#> GSM97897 3 0.7643 0.1026 0.276 0.000 0.468 0.256
#> GSM97900 4 0.0000 0.8293 0.000 0.000 0.000 1.000
#> GSM97904 1 0.7749 0.2292 0.408 0.000 0.236 0.356
#> GSM97907 2 0.0000 0.8631 0.000 1.000 0.000 0.000
#> GSM97925 3 0.4482 0.5829 0.128 0.000 0.804 0.068
#> GSM97947 3 0.0376 0.6928 0.004 0.000 0.992 0.004
cbind(get_classes(res, k = 5), get_membership(res, k = 5))
#> class entropy silhouette p1 p2 p3 p4 p5
#> GSM97800 2 0.0000 0.85410 0.000 1.000 0.000 0.000 0.000
#> GSM97803 2 0.0000 0.85410 0.000 1.000 0.000 0.000 0.000
#> GSM97804 2 0.0000 0.85410 0.000 1.000 0.000 0.000 0.000
#> GSM97805 2 0.0000 0.85410 0.000 1.000 0.000 0.000 0.000
#> GSM97807 2 0.0000 0.85410 0.000 1.000 0.000 0.000 0.000
#> GSM97809 2 0.0000 0.85410 0.000 1.000 0.000 0.000 0.000
#> GSM97811 2 0.0000 0.85410 0.000 1.000 0.000 0.000 0.000
#> GSM97812 2 0.0000 0.85410 0.000 1.000 0.000 0.000 0.000
#> GSM97816 1 0.5857 0.44473 0.684 0.148 0.048 0.000 0.120
#> GSM97817 2 0.0000 0.85410 0.000 1.000 0.000 0.000 0.000
#> GSM97820 2 0.0000 0.85410 0.000 1.000 0.000 0.000 0.000
#> GSM97825 2 0.0000 0.85410 0.000 1.000 0.000 0.000 0.000
#> GSM97827 2 0.0000 0.85410 0.000 1.000 0.000 0.000 0.000
#> GSM97828 1 0.5857 0.44473 0.684 0.148 0.048 0.000 0.120
#> GSM97833 2 0.0000 0.85410 0.000 1.000 0.000 0.000 0.000
#> GSM97834 2 0.0000 0.85410 0.000 1.000 0.000 0.000 0.000
#> GSM97840 2 0.0609 0.84053 0.020 0.980 0.000 0.000 0.000
#> GSM97846 2 0.0000 0.85410 0.000 1.000 0.000 0.000 0.000
#> GSM97848 2 0.0000 0.85410 0.000 1.000 0.000 0.000 0.000
#> GSM97849 2 0.0000 0.85410 0.000 1.000 0.000 0.000 0.000
#> GSM97850 2 0.0000 0.85410 0.000 1.000 0.000 0.000 0.000
#> GSM97853 2 0.0000 0.85410 0.000 1.000 0.000 0.000 0.000
#> GSM97855 2 0.0000 0.85410 0.000 1.000 0.000 0.000 0.000
#> GSM97878 1 0.4174 0.62953 0.764 0.004 0.004 0.028 0.200
#> GSM97913 1 0.4767 0.53764 0.732 0.180 0.004 0.000 0.084
#> GSM97932 4 0.0404 0.89170 0.000 0.000 0.000 0.988 0.012
#> GSM97939 2 0.7014 0.43011 0.224 0.548 0.172 0.000 0.056
#> GSM97951 2 0.4584 0.70327 0.120 0.780 0.072 0.000 0.028
#> GSM97957 3 0.2304 0.76993 0.048 0.000 0.908 0.000 0.044
#> GSM97972 1 0.5931 0.05577 0.548 0.372 0.036 0.000 0.044
#> GSM97793 3 0.1043 0.76674 0.000 0.000 0.960 0.000 0.040
#> GSM97795 2 0.6904 0.46240 0.188 0.572 0.180 0.000 0.060
#> GSM97802 5 0.4190 0.62009 0.012 0.000 0.256 0.008 0.724
#> GSM97810 2 0.7014 0.43011 0.224 0.548 0.172 0.000 0.056
#> GSM97815 2 0.7182 0.39293 0.220 0.528 0.192 0.000 0.060
#> GSM97837 1 0.5915 0.49937 0.584 0.000 0.000 0.152 0.264
#> GSM97843 3 0.4499 0.74877 0.108 0.076 0.788 0.000 0.028
#> GSM97890 3 0.5203 0.70904 0.120 0.120 0.732 0.000 0.028
#> GSM97899 4 0.0613 0.88983 0.004 0.000 0.004 0.984 0.008
#> GSM97910 1 0.4201 0.60173 0.752 0.000 0.000 0.044 0.204
#> GSM97916 1 0.5851 0.58570 0.604 0.000 0.048 0.040 0.308
#> GSM97920 3 0.5252 0.57377 0.292 0.000 0.632 0.000 0.076
#> GSM97921 1 0.4754 0.61133 0.748 0.000 0.008 0.100 0.144
#> GSM97927 1 0.6238 0.48747 0.524 0.000 0.040 0.060 0.376
#> GSM97937 4 0.4528 0.64443 0.144 0.000 0.000 0.752 0.104
#> GSM97941 2 0.0000 0.85410 0.000 1.000 0.000 0.000 0.000
#> GSM97943 1 0.5857 0.44473 0.684 0.148 0.048 0.000 0.120
#> GSM97958 1 0.3361 0.63206 0.844 0.008 0.020 0.004 0.124
#> GSM97960 2 0.5764 0.61129 0.148 0.688 0.124 0.000 0.040
#> GSM97794 1 0.6375 0.58411 0.664 0.112 0.044 0.020 0.160
#> GSM97796 4 0.0000 0.89559 0.000 0.000 0.000 1.000 0.000
#> GSM97797 1 0.4166 0.60292 0.772 0.020 0.000 0.020 0.188
#> GSM97798 4 0.0162 0.89586 0.000 0.000 0.000 0.996 0.004
#> GSM97801 1 0.4618 0.57742 0.724 0.000 0.000 0.068 0.208
#> GSM97806 1 0.6260 0.54202 0.568 0.000 0.048 0.064 0.320
#> GSM97808 4 0.0162 0.89586 0.000 0.000 0.000 0.996 0.004
#> GSM97813 5 0.4734 0.74955 0.016 0.000 0.040 0.220 0.724
#> GSM97814 4 0.0162 0.89586 0.000 0.000 0.000 0.996 0.004
#> GSM97818 1 0.5289 0.61395 0.720 0.036 0.004 0.056 0.184
#> GSM97819 3 0.0794 0.77090 0.000 0.000 0.972 0.000 0.028
#> GSM97821 2 0.6407 0.40369 0.312 0.564 0.060 0.000 0.064
#> GSM97826 1 0.5915 0.50086 0.584 0.000 0.000 0.152 0.264
#> GSM97829 1 0.5654 0.53329 0.628 0.000 0.000 0.148 0.224
#> GSM97832 2 0.5398 0.64433 0.100 0.724 0.132 0.000 0.044
#> GSM97836 1 0.6799 0.47075 0.512 0.000 0.132 0.036 0.320
#> GSM97839 4 0.0000 0.89559 0.000 0.000 0.000 1.000 0.000
#> GSM97844 2 0.0000 0.85410 0.000 1.000 0.000 0.000 0.000
#> GSM97847 4 0.5975 0.35037 0.224 0.000 0.000 0.588 0.188
#> GSM97851 4 0.0290 0.89271 0.000 0.000 0.000 0.992 0.008
#> GSM97852 4 0.5975 0.35037 0.224 0.000 0.000 0.588 0.188
#> GSM97856 4 0.0000 0.89559 0.000 0.000 0.000 1.000 0.000
#> GSM97858 2 0.0000 0.85410 0.000 1.000 0.000 0.000 0.000
#> GSM97859 5 0.4673 0.75499 0.016 0.000 0.040 0.212 0.732
#> GSM97861 1 0.6238 0.48747 0.524 0.000 0.040 0.060 0.376
#> GSM97863 4 0.0000 0.89559 0.000 0.000 0.000 1.000 0.000
#> GSM97869 1 0.5851 0.58570 0.604 0.000 0.048 0.040 0.308
#> GSM97870 5 0.4744 0.75511 0.016 0.000 0.044 0.212 0.728
#> GSM97871 4 0.0162 0.89586 0.000 0.000 0.000 0.996 0.004
#> GSM97877 1 0.4767 0.51690 0.724 0.200 0.004 0.000 0.072
#> GSM97879 1 0.6471 0.37818 0.476 0.000 0.012 0.132 0.380
#> GSM97882 1 0.6177 0.53962 0.568 0.000 0.048 0.056 0.328
#> GSM97885 1 0.5851 0.58570 0.604 0.000 0.048 0.040 0.308
#> GSM97886 4 0.0162 0.89586 0.000 0.000 0.000 0.996 0.004
#> GSM97887 4 0.0162 0.89586 0.000 0.000 0.000 0.996 0.004
#> GSM97888 5 0.4740 0.34114 0.000 0.000 0.016 0.468 0.516
#> GSM97889 5 0.4444 0.71668 0.000 0.000 0.180 0.072 0.748
#> GSM97891 1 0.6170 0.51836 0.556 0.000 0.052 0.048 0.344
#> GSM97892 2 0.0000 0.85410 0.000 1.000 0.000 0.000 0.000
#> GSM97893 4 0.3051 0.78475 0.060 0.000 0.000 0.864 0.076
#> GSM97894 4 0.0000 0.89559 0.000 0.000 0.000 1.000 0.000
#> GSM97895 4 0.0404 0.89170 0.000 0.000 0.000 0.988 0.012
#> GSM97896 4 0.4907 -0.28949 0.000 0.000 0.024 0.492 0.484
#> GSM97898 4 0.0290 0.89271 0.000 0.000 0.000 0.992 0.008
#> GSM97903 1 0.6000 0.49498 0.552 0.000 0.004 0.116 0.328
#> GSM97905 5 0.4925 0.76216 0.020 0.000 0.084 0.152 0.744
#> GSM97906 4 0.0162 0.89586 0.000 0.000 0.000 0.996 0.004
#> GSM97908 4 0.5892 0.36141 0.220 0.000 0.000 0.600 0.180
#> GSM97912 5 0.4925 0.76216 0.020 0.000 0.084 0.152 0.744
#> GSM97914 1 0.4752 0.62653 0.732 0.000 0.012 0.056 0.200
#> GSM97915 4 0.0162 0.89434 0.000 0.000 0.000 0.996 0.004
#> GSM97917 4 0.1211 0.87682 0.016 0.000 0.000 0.960 0.024
#> GSM97918 4 0.0290 0.89402 0.000 0.000 0.000 0.992 0.008
#> GSM97919 4 0.0290 0.89271 0.000 0.000 0.000 0.992 0.008
#> GSM97922 5 0.4673 0.75499 0.016 0.000 0.040 0.212 0.732
#> GSM97924 2 0.0000 0.85410 0.000 1.000 0.000 0.000 0.000
#> GSM97926 1 0.6799 0.47075 0.512 0.000 0.132 0.036 0.320
#> GSM97930 1 0.6523 0.29080 0.484 0.000 0.000 0.268 0.248
#> GSM97931 1 0.5931 0.05577 0.548 0.372 0.036 0.000 0.044
#> GSM97935 1 0.6238 0.48747 0.524 0.000 0.040 0.060 0.376
#> GSM97936 4 0.0880 0.87805 0.000 0.000 0.000 0.968 0.032
#> GSM97938 4 0.2645 0.81434 0.068 0.000 0.000 0.888 0.044
#> GSM97940 4 0.0162 0.89586 0.000 0.000 0.000 0.996 0.004
#> GSM97942 3 0.1043 0.76674 0.000 0.000 0.960 0.000 0.040
#> GSM97945 4 0.4450 0.63265 0.080 0.000 0.004 0.764 0.152
#> GSM97946 2 0.0000 0.85410 0.000 1.000 0.000 0.000 0.000
#> GSM97948 3 0.4747 0.42610 0.036 0.000 0.676 0.004 0.284
#> GSM97950 4 0.0671 0.88895 0.004 0.000 0.000 0.980 0.016
#> GSM97952 4 0.0162 0.89586 0.000 0.000 0.000 0.996 0.004
#> GSM97953 4 0.3055 0.79072 0.072 0.000 0.000 0.864 0.064
#> GSM97954 1 0.6905 0.14629 0.396 0.000 0.004 0.300 0.300
#> GSM97955 4 0.0324 0.89315 0.004 0.000 0.000 0.992 0.004
#> GSM97959 1 0.4239 0.57294 0.784 0.132 0.004 0.000 0.080
#> GSM97961 4 0.0162 0.89586 0.000 0.000 0.000 0.996 0.004
#> GSM97963 4 0.0162 0.89586 0.000 0.000 0.000 0.996 0.004
#> GSM97965 4 0.0162 0.89586 0.000 0.000 0.000 0.996 0.004
#> GSM97966 4 0.0162 0.89586 0.000 0.000 0.000 0.996 0.004
#> GSM97967 2 0.0000 0.85410 0.000 1.000 0.000 0.000 0.000
#> GSM97968 2 0.0000 0.85410 0.000 1.000 0.000 0.000 0.000
#> GSM97969 5 0.5037 0.65800 0.008 0.000 0.036 0.320 0.636
#> GSM97971 5 0.4673 0.75499 0.016 0.000 0.040 0.212 0.732
#> GSM97799 2 0.7581 0.00450 0.204 0.392 0.348 0.000 0.056
#> GSM97823 2 0.0000 0.85410 0.000 1.000 0.000 0.000 0.000
#> GSM97824 3 0.6497 0.57023 0.152 0.196 0.608 0.000 0.044
#> GSM97830 3 0.3882 0.71783 0.168 0.000 0.788 0.000 0.044
#> GSM97835 2 0.7418 0.29994 0.220 0.484 0.236 0.000 0.060
#> GSM97838 2 0.0000 0.85410 0.000 1.000 0.000 0.000 0.000
#> GSM97841 2 0.0000 0.85410 0.000 1.000 0.000 0.000 0.000
#> GSM97842 2 0.7553 -0.00831 0.196 0.392 0.356 0.000 0.056
#> GSM97854 2 0.0000 0.85410 0.000 1.000 0.000 0.000 0.000
#> GSM97857 3 0.6661 0.56151 0.164 0.196 0.592 0.000 0.048
#> GSM97860 3 0.1043 0.76674 0.000 0.000 0.960 0.000 0.040
#> GSM97862 3 0.3100 0.76731 0.092 0.020 0.868 0.000 0.020
#> GSM97864 2 0.0000 0.85410 0.000 1.000 0.000 0.000 0.000
#> GSM97866 3 0.3043 0.76815 0.088 0.020 0.872 0.000 0.020
#> GSM97868 3 0.4746 0.72197 0.124 0.100 0.760 0.000 0.016
#> GSM97872 5 0.4964 0.69370 0.036 0.000 0.172 0.052 0.740
#> GSM97873 2 0.7613 0.05380 0.204 0.404 0.332 0.000 0.060
#> GSM97874 3 0.4693 0.64489 0.244 0.000 0.700 0.000 0.056
#> GSM97875 3 0.0794 0.77090 0.000 0.000 0.972 0.000 0.028
#> GSM97876 3 0.1043 0.76674 0.000 0.000 0.960 0.000 0.040
#> GSM97880 3 0.1043 0.76674 0.000 0.000 0.960 0.000 0.040
#> GSM97881 3 0.5165 0.69740 0.128 0.124 0.728 0.000 0.020
#> GSM97884 3 0.7628 0.14554 0.220 0.332 0.392 0.000 0.056
#> GSM97901 3 0.3100 0.76731 0.092 0.020 0.868 0.000 0.020
#> GSM97902 1 0.3127 0.63097 0.848 0.000 0.020 0.004 0.128
#> GSM97909 2 0.6392 0.40965 0.308 0.568 0.060 0.000 0.064
#> GSM97911 3 0.5165 0.69740 0.128 0.124 0.728 0.000 0.020
#> GSM97923 3 0.1121 0.76483 0.000 0.000 0.956 0.000 0.044
#> GSM97928 5 0.4964 0.69370 0.036 0.000 0.172 0.052 0.740
#> GSM97929 2 0.0000 0.85410 0.000 1.000 0.000 0.000 0.000
#> GSM97933 3 0.1364 0.77153 0.012 0.000 0.952 0.000 0.036
#> GSM97934 3 0.2304 0.76993 0.048 0.000 0.908 0.000 0.044
#> GSM97944 2 0.7581 0.00450 0.204 0.392 0.348 0.000 0.056
#> GSM97949 2 0.0000 0.85410 0.000 1.000 0.000 0.000 0.000
#> GSM97956 3 0.6344 0.59257 0.148 0.180 0.628 0.000 0.044
#> GSM97962 3 0.2278 0.77687 0.044 0.008 0.916 0.000 0.032
#> GSM97964 3 0.7667 0.17437 0.220 0.324 0.396 0.000 0.060
#> GSM97970 2 0.7578 0.18716 0.220 0.440 0.280 0.000 0.060
#> GSM97822 5 0.4587 0.70036 0.012 0.000 0.188 0.052 0.748
#> GSM97831 3 0.3771 0.72365 0.164 0.000 0.796 0.000 0.040
#> GSM97845 4 0.6825 -0.07540 0.288 0.000 0.004 0.432 0.276
#> GSM97865 1 0.2886 0.63288 0.844 0.000 0.008 0.000 0.148
#> GSM97867 3 0.1043 0.76674 0.000 0.000 0.960 0.000 0.040
#> GSM97883 5 0.5197 0.62733 0.024 0.000 0.276 0.036 0.664
#> GSM97897 5 0.5159 0.73657 0.000 0.000 0.164 0.144 0.692
#> GSM97900 4 0.0162 0.89586 0.000 0.000 0.000 0.996 0.004
#> GSM97904 5 0.7066 0.46574 0.192 0.000 0.040 0.256 0.512
#> GSM97907 2 0.0000 0.85410 0.000 1.000 0.000 0.000 0.000
#> GSM97925 3 0.4818 0.42650 0.040 0.000 0.672 0.004 0.284
#> GSM97947 3 0.0880 0.77064 0.000 0.000 0.968 0.000 0.032
cbind(get_classes(res, k = 6), get_membership(res, k = 6))
#> class entropy silhouette p1 p2 p3 p4 p5 p6
#> GSM97800 2 0.0000 0.9050 0.000 1.000 0.000 0.000 0.000 0.000
#> GSM97803 2 0.0000 0.9050 0.000 1.000 0.000 0.000 0.000 0.000
#> GSM97804 2 0.0000 0.9050 0.000 1.000 0.000 0.000 0.000 0.000
#> GSM97805 2 0.0000 0.9050 0.000 1.000 0.000 0.000 0.000 0.000
#> GSM97807 2 0.0146 0.9022 0.000 0.996 0.000 0.000 0.004 0.000
#> GSM97809 2 0.0146 0.9022 0.000 0.996 0.000 0.000 0.004 0.000
#> GSM97811 2 0.0000 0.9050 0.000 1.000 0.000 0.000 0.000 0.000
#> GSM97812 2 0.0000 0.9050 0.000 1.000 0.000 0.000 0.000 0.000
#> GSM97816 5 0.3309 0.0827 0.028 0.004 0.004 0.000 0.816 0.148
#> GSM97817 2 0.0000 0.9050 0.000 1.000 0.000 0.000 0.000 0.000
#> GSM97820 2 0.0000 0.9050 0.000 1.000 0.000 0.000 0.000 0.000
#> GSM97825 2 0.0000 0.9050 0.000 1.000 0.000 0.000 0.000 0.000
#> GSM97827 2 0.0000 0.9050 0.000 1.000 0.000 0.000 0.000 0.000
#> GSM97828 5 0.3309 0.0827 0.028 0.004 0.004 0.000 0.816 0.148
#> GSM97833 2 0.0000 0.9050 0.000 1.000 0.000 0.000 0.000 0.000
#> GSM97834 2 0.0000 0.9050 0.000 1.000 0.000 0.000 0.000 0.000
#> GSM97840 2 0.1245 0.8577 0.000 0.952 0.000 0.000 0.032 0.016
#> GSM97846 2 0.0000 0.9050 0.000 1.000 0.000 0.000 0.000 0.000
#> GSM97848 2 0.0000 0.9050 0.000 1.000 0.000 0.000 0.000 0.000
#> GSM97849 2 0.0000 0.9050 0.000 1.000 0.000 0.000 0.000 0.000
#> GSM97850 2 0.0000 0.9050 0.000 1.000 0.000 0.000 0.000 0.000
#> GSM97853 2 0.0000 0.9050 0.000 1.000 0.000 0.000 0.000 0.000
#> GSM97855 2 0.0146 0.9022 0.000 0.996 0.000 0.000 0.004 0.000
#> GSM97878 6 0.2800 0.6647 0.036 0.000 0.000 0.004 0.100 0.860
#> GSM97913 6 0.5492 0.3786 0.028 0.080 0.000 0.000 0.316 0.576
#> GSM97932 4 0.0748 0.9057 0.004 0.000 0.000 0.976 0.004 0.016
#> GSM97939 5 0.6113 0.5549 0.000 0.400 0.096 0.000 0.456 0.048
#> GSM97951 2 0.4649 0.2496 0.000 0.656 0.036 0.000 0.288 0.020
#> GSM97957 3 0.2071 0.7773 0.028 0.000 0.916 0.000 0.044 0.012
#> GSM97972 5 0.6170 0.3647 0.020 0.208 0.000 0.000 0.500 0.272
#> GSM97793 3 0.0458 0.7807 0.016 0.000 0.984 0.000 0.000 0.000
#> GSM97795 2 0.6239 -0.5038 0.004 0.444 0.108 0.000 0.404 0.040
#> GSM97802 1 0.2745 0.6516 0.860 0.000 0.112 0.000 0.008 0.020
#> GSM97810 5 0.6113 0.5549 0.000 0.400 0.096 0.000 0.456 0.048
#> GSM97815 5 0.6393 0.5824 0.004 0.388 0.116 0.000 0.444 0.048
#> GSM97837 6 0.5524 0.5145 0.072 0.000 0.000 0.080 0.196 0.652
#> GSM97843 3 0.4700 0.6787 0.016 0.040 0.732 0.000 0.180 0.032
#> GSM97890 3 0.5119 0.5567 0.004 0.068 0.672 0.000 0.224 0.032
#> GSM97899 4 0.0748 0.9077 0.016 0.000 0.000 0.976 0.004 0.004
#> GSM97910 6 0.4643 0.5664 0.048 0.000 0.000 0.008 0.304 0.640
#> GSM97916 6 0.4699 0.6493 0.156 0.000 0.004 0.012 0.108 0.720
#> GSM97920 3 0.5106 0.5464 0.024 0.000 0.600 0.000 0.324 0.052
#> GSM97921 6 0.5144 0.6408 0.052 0.000 0.000 0.080 0.180 0.688
#> GSM97927 6 0.5336 0.5739 0.240 0.000 0.004 0.028 0.084 0.644
#> GSM97937 4 0.4492 0.5632 0.052 0.000 0.000 0.680 0.008 0.260
#> GSM97941 2 0.0547 0.8865 0.000 0.980 0.000 0.000 0.020 0.000
#> GSM97943 5 0.3309 0.0827 0.028 0.004 0.004 0.000 0.816 0.148
#> GSM97958 6 0.4265 0.6323 0.044 0.004 0.004 0.000 0.236 0.712
#> GSM97960 2 0.5516 -0.1640 0.000 0.552 0.068 0.000 0.348 0.032
#> GSM97794 6 0.6069 0.5417 0.080 0.060 0.004 0.008 0.252 0.596
#> GSM97796 4 0.0146 0.9118 0.004 0.000 0.000 0.996 0.000 0.000
#> GSM97797 6 0.4363 0.5577 0.040 0.000 0.000 0.000 0.324 0.636
#> GSM97798 4 0.0508 0.9114 0.012 0.000 0.000 0.984 0.004 0.000
#> GSM97801 6 0.5027 0.5303 0.040 0.000 0.000 0.032 0.312 0.616
#> GSM97806 6 0.5323 0.6113 0.200 0.000 0.000 0.032 0.112 0.656
#> GSM97808 4 0.0508 0.9114 0.012 0.000 0.000 0.984 0.004 0.000
#> GSM97813 1 0.4074 0.7510 0.748 0.000 0.000 0.160 0.000 0.092
#> GSM97814 4 0.0405 0.9119 0.008 0.000 0.000 0.988 0.004 0.000
#> GSM97818 6 0.4407 0.6456 0.068 0.012 0.000 0.016 0.144 0.760
#> GSM97819 3 0.0291 0.7798 0.004 0.000 0.992 0.000 0.004 0.000
#> GSM97821 2 0.5985 -0.3757 0.000 0.416 0.008 0.000 0.404 0.172
#> GSM97826 6 0.5573 0.5183 0.080 0.000 0.000 0.076 0.196 0.648
#> GSM97829 6 0.5608 0.5329 0.044 0.000 0.000 0.100 0.236 0.620
#> GSM97832 2 0.5335 0.0869 0.000 0.616 0.080 0.000 0.276 0.028
#> GSM97836 6 0.6264 0.5593 0.204 0.000 0.088 0.004 0.116 0.588
#> GSM97839 4 0.0146 0.9118 0.004 0.000 0.000 0.996 0.000 0.000
#> GSM97844 2 0.0000 0.9050 0.000 1.000 0.000 0.000 0.000 0.000
#> GSM97847 4 0.4989 0.2302 0.060 0.000 0.000 0.528 0.004 0.408
#> GSM97851 4 0.0405 0.9085 0.000 0.000 0.000 0.988 0.004 0.008
#> GSM97852 4 0.4989 0.2302 0.060 0.000 0.000 0.528 0.004 0.408
#> GSM97856 4 0.0146 0.9118 0.004 0.000 0.000 0.996 0.000 0.000
#> GSM97858 2 0.0000 0.9050 0.000 1.000 0.000 0.000 0.000 0.000
#> GSM97859 1 0.3967 0.7558 0.760 0.000 0.000 0.148 0.000 0.092
#> GSM97861 6 0.5336 0.5739 0.240 0.000 0.004 0.028 0.084 0.644
#> GSM97863 4 0.0146 0.9118 0.004 0.000 0.000 0.996 0.000 0.000
#> GSM97869 6 0.4699 0.6493 0.156 0.000 0.004 0.012 0.108 0.720
#> GSM97870 1 0.4107 0.7554 0.756 0.000 0.004 0.148 0.000 0.092
#> GSM97871 4 0.0405 0.9119 0.008 0.000 0.000 0.988 0.004 0.000
#> GSM97877 6 0.5717 0.2996 0.024 0.100 0.000 0.000 0.348 0.528
#> GSM97879 6 0.4654 0.5164 0.252 0.000 0.000 0.060 0.012 0.676
#> GSM97882 6 0.5234 0.6087 0.208 0.000 0.000 0.024 0.112 0.656
#> GSM97885 6 0.4732 0.6483 0.160 0.000 0.004 0.012 0.108 0.716
#> GSM97886 4 0.0405 0.9119 0.008 0.000 0.000 0.988 0.004 0.000
#> GSM97887 4 0.0508 0.9114 0.012 0.000 0.000 0.984 0.004 0.000
#> GSM97888 1 0.4703 0.4676 0.544 0.000 0.000 0.408 0.000 0.048
#> GSM97889 1 0.2430 0.7120 0.900 0.000 0.048 0.036 0.004 0.012
#> GSM97891 6 0.5328 0.5908 0.220 0.000 0.004 0.016 0.116 0.644
#> GSM97892 2 0.0000 0.9050 0.000 1.000 0.000 0.000 0.000 0.000
#> GSM97893 4 0.2877 0.7888 0.020 0.000 0.000 0.848 0.008 0.124
#> GSM97894 4 0.0146 0.9118 0.004 0.000 0.000 0.996 0.000 0.000
#> GSM97895 4 0.0748 0.9057 0.004 0.000 0.000 0.976 0.004 0.016
#> GSM97896 1 0.4456 0.3462 0.524 0.000 0.000 0.448 0.000 0.028
#> GSM97898 4 0.0405 0.9085 0.000 0.000 0.000 0.988 0.004 0.008
#> GSM97903 6 0.4003 0.5958 0.156 0.000 0.000 0.056 0.016 0.772
#> GSM97905 1 0.3771 0.7541 0.800 0.000 0.012 0.100 0.000 0.088
#> GSM97906 4 0.0508 0.9114 0.012 0.000 0.000 0.984 0.004 0.000
#> GSM97908 4 0.4822 0.2817 0.048 0.000 0.000 0.548 0.004 0.400
#> GSM97912 1 0.3771 0.7541 0.800 0.000 0.012 0.100 0.000 0.088
#> GSM97914 6 0.3486 0.6696 0.048 0.000 0.000 0.016 0.116 0.820
#> GSM97915 4 0.0146 0.9101 0.000 0.000 0.000 0.996 0.004 0.000
#> GSM97917 4 0.1226 0.8890 0.004 0.000 0.000 0.952 0.004 0.040
#> GSM97918 4 0.0436 0.9090 0.004 0.000 0.000 0.988 0.004 0.004
#> GSM97919 4 0.0551 0.9088 0.004 0.000 0.000 0.984 0.004 0.008
#> GSM97922 1 0.3967 0.7558 0.760 0.000 0.000 0.148 0.000 0.092
#> GSM97924 2 0.0000 0.9050 0.000 1.000 0.000 0.000 0.000 0.000
#> GSM97926 6 0.6264 0.5593 0.204 0.000 0.088 0.004 0.116 0.588
#> GSM97930 6 0.5145 0.4547 0.100 0.000 0.000 0.192 0.032 0.676
#> GSM97931 5 0.6170 0.3647 0.020 0.208 0.000 0.000 0.500 0.272
#> GSM97935 6 0.5336 0.5739 0.240 0.000 0.004 0.028 0.084 0.644
#> GSM97936 4 0.1418 0.8798 0.024 0.000 0.000 0.944 0.000 0.032
#> GSM97938 4 0.2961 0.7854 0.020 0.000 0.000 0.840 0.008 0.132
#> GSM97940 4 0.0405 0.9119 0.008 0.000 0.000 0.988 0.004 0.000
#> GSM97942 3 0.0458 0.7807 0.016 0.000 0.984 0.000 0.000 0.000
#> GSM97945 4 0.3978 0.6639 0.084 0.000 0.000 0.756 0.000 0.160
#> GSM97946 2 0.0146 0.9022 0.000 0.996 0.000 0.000 0.004 0.000
#> GSM97948 3 0.5189 0.4399 0.280 0.000 0.624 0.000 0.024 0.072
#> GSM97950 4 0.0603 0.9058 0.004 0.000 0.000 0.980 0.000 0.016
#> GSM97952 4 0.0405 0.9119 0.008 0.000 0.000 0.988 0.004 0.000
#> GSM97953 4 0.3423 0.7480 0.036 0.000 0.000 0.808 0.008 0.148
#> GSM97954 6 0.5277 0.3503 0.156 0.000 0.000 0.224 0.004 0.616
#> GSM97955 4 0.0603 0.9091 0.004 0.000 0.000 0.980 0.000 0.016
#> GSM97959 6 0.5017 0.4515 0.020 0.048 0.000 0.000 0.336 0.596
#> GSM97961 4 0.0405 0.9119 0.008 0.000 0.000 0.988 0.004 0.000
#> GSM97963 4 0.0405 0.9119 0.008 0.000 0.000 0.988 0.004 0.000
#> GSM97965 4 0.0405 0.9119 0.008 0.000 0.000 0.988 0.004 0.000
#> GSM97966 4 0.0508 0.9114 0.012 0.000 0.000 0.984 0.004 0.000
#> GSM97967 2 0.0000 0.9050 0.000 1.000 0.000 0.000 0.000 0.000
#> GSM97968 2 0.0146 0.9022 0.000 0.996 0.000 0.000 0.004 0.000
#> GSM97969 1 0.4654 0.6666 0.652 0.000 0.000 0.268 0.000 0.080
#> GSM97971 1 0.3967 0.7558 0.760 0.000 0.000 0.148 0.000 0.092
#> GSM97799 5 0.6950 0.5951 0.004 0.276 0.276 0.000 0.396 0.048
#> GSM97823 2 0.0000 0.9050 0.000 1.000 0.000 0.000 0.000 0.000
#> GSM97824 3 0.6024 0.2230 0.000 0.136 0.556 0.000 0.268 0.040
#> GSM97830 3 0.3799 0.6985 0.012 0.000 0.756 0.000 0.208 0.024
#> GSM97835 5 0.6651 0.6456 0.004 0.340 0.164 0.000 0.444 0.048
#> GSM97838 2 0.0000 0.9050 0.000 1.000 0.000 0.000 0.000 0.000
#> GSM97841 2 0.0000 0.9050 0.000 1.000 0.000 0.000 0.000 0.000
#> GSM97842 5 0.6901 0.5838 0.004 0.268 0.284 0.000 0.400 0.044
#> GSM97854 2 0.0000 0.9050 0.000 1.000 0.000 0.000 0.000 0.000
#> GSM97857 3 0.6245 0.2073 0.004 0.136 0.540 0.000 0.276 0.044
#> GSM97860 3 0.0458 0.7807 0.016 0.000 0.984 0.000 0.000 0.000
#> GSM97862 3 0.3393 0.7315 0.004 0.012 0.824 0.000 0.128 0.032
#> GSM97864 2 0.0000 0.9050 0.000 1.000 0.000 0.000 0.000 0.000
#> GSM97866 3 0.3319 0.7336 0.004 0.012 0.828 0.000 0.128 0.028
#> GSM97868 3 0.4714 0.6070 0.000 0.052 0.700 0.000 0.216 0.032
#> GSM97872 1 0.3363 0.6753 0.844 0.000 0.040 0.020 0.008 0.088
#> GSM97873 5 0.6903 0.6105 0.004 0.276 0.256 0.000 0.416 0.048
#> GSM97874 3 0.4531 0.6185 0.016 0.000 0.668 0.000 0.280 0.036
#> GSM97875 3 0.0291 0.7798 0.004 0.000 0.992 0.000 0.004 0.000
#> GSM97876 3 0.0458 0.7807 0.016 0.000 0.984 0.000 0.000 0.000
#> GSM97880 3 0.0458 0.7807 0.016 0.000 0.984 0.000 0.000 0.000
#> GSM97881 3 0.5241 0.5327 0.004 0.072 0.656 0.000 0.236 0.032
#> GSM97884 5 0.6917 0.5100 0.004 0.212 0.308 0.000 0.420 0.056
#> GSM97901 3 0.3393 0.7315 0.004 0.012 0.824 0.000 0.128 0.032
#> GSM97902 6 0.4188 0.6351 0.048 0.000 0.004 0.000 0.236 0.712
#> GSM97909 2 0.5983 -0.3583 0.000 0.424 0.008 0.000 0.396 0.172
#> GSM97911 3 0.5241 0.5327 0.004 0.072 0.656 0.000 0.236 0.032
#> GSM97923 3 0.0547 0.7795 0.020 0.000 0.980 0.000 0.000 0.000
#> GSM97928 1 0.3363 0.6753 0.844 0.000 0.040 0.020 0.008 0.088
#> GSM97929 2 0.0000 0.9050 0.000 1.000 0.000 0.000 0.000 0.000
#> GSM97933 3 0.1059 0.7821 0.016 0.000 0.964 0.000 0.016 0.004
#> GSM97934 3 0.2071 0.7773 0.028 0.000 0.916 0.000 0.044 0.012
#> GSM97944 5 0.6950 0.5951 0.004 0.276 0.276 0.000 0.396 0.048
#> GSM97949 2 0.0000 0.9050 0.000 1.000 0.000 0.000 0.000 0.000
#> GSM97956 3 0.5857 0.3004 0.000 0.120 0.580 0.000 0.260 0.040
#> GSM97962 3 0.2101 0.7777 0.016 0.008 0.920 0.000 0.040 0.016
#> GSM97964 5 0.6779 0.4864 0.000 0.204 0.320 0.000 0.420 0.056
#> GSM97970 5 0.6843 0.6375 0.004 0.320 0.212 0.000 0.416 0.048
#> GSM97822 1 0.2276 0.6962 0.908 0.000 0.052 0.016 0.004 0.020
#> GSM97831 3 0.3910 0.7001 0.012 0.000 0.740 0.000 0.224 0.024
#> GSM97845 6 0.5660 0.1668 0.140 0.000 0.000 0.364 0.004 0.492
#> GSM97865 6 0.3912 0.6435 0.044 0.000 0.000 0.000 0.224 0.732
#> GSM97867 3 0.0458 0.7807 0.016 0.000 0.984 0.000 0.000 0.000
#> GSM97883 1 0.4576 0.5989 0.696 0.000 0.220 0.008 0.000 0.076
#> GSM97897 1 0.3142 0.7312 0.840 0.000 0.044 0.108 0.000 0.008
#> GSM97900 4 0.0508 0.9114 0.012 0.000 0.000 0.984 0.004 0.000
#> GSM97904 1 0.5910 0.3933 0.508 0.000 0.000 0.192 0.008 0.292
#> GSM97907 2 0.0000 0.9050 0.000 1.000 0.000 0.000 0.000 0.000
#> GSM97925 3 0.5236 0.4400 0.280 0.000 0.620 0.000 0.024 0.076
#> GSM97947 3 0.0405 0.7801 0.008 0.000 0.988 0.000 0.004 0.000
Heatmaps for the consensus matrix. It visualizes the probability of two samples to be in a same group.
consensus_heatmap(res, k = 2)
consensus_heatmap(res, k = 3)
consensus_heatmap(res, k = 4)
consensus_heatmap(res, k = 5)
consensus_heatmap(res, k = 6)
Heatmaps for the membership of samples in all partitions to see how consistent they are:
membership_heatmap(res, k = 2)
membership_heatmap(res, k = 3)
membership_heatmap(res, k = 4)
membership_heatmap(res, k = 5)
membership_heatmap(res, k = 6)
As soon as we have had the classes for columns, we can look for signatures which are significantly different between classes which can be candidate marks for certain classes. Following are the heatmaps for signatures.
Signature heatmaps where rows are scaled:
get_signatures(res, k = 2)
get_signatures(res, k = 3)
get_signatures(res, k = 4)
get_signatures(res, k = 5)
get_signatures(res, k = 6)
Signature heatmaps where rows are not scaled:
get_signatures(res, k = 2, scale_rows = FALSE)
get_signatures(res, k = 3, scale_rows = FALSE)
get_signatures(res, k = 4, scale_rows = FALSE)
get_signatures(res, k = 5, scale_rows = FALSE)
get_signatures(res, k = 6, scale_rows = FALSE)
Compare the overlap of signatures from different k:
compare_signatures(res)
get_signature() returns a data frame invisibly. TO get the list of signatures, the function
call should be assigned to a variable explicitly. In following code, if plot argument is set
to FALSE, no heatmap is plotted while only the differential analysis is performed.
# code only for demonstration
tb = get_signature(res, k = ..., plot = FALSE)
An example of the output of tb is:
#> which_row fdr mean_1 mean_2 scaled_mean_1 scaled_mean_2 km
#> 1 38 0.042760348 8.373488 9.131774 -0.5533452 0.5164555 1
#> 2 40 0.018707592 7.106213 8.469186 -0.6173731 0.5762149 1
#> 3 55 0.019134737 10.221463 11.207825 -0.6159697 0.5749050 1
#> 4 59 0.006059896 5.921854 7.869574 -0.6899429 0.6439467 1
#> 5 60 0.018055526 8.928898 10.211722 -0.6204761 0.5791110 1
#> 6 98 0.009384629 15.714769 14.887706 0.6635654 -0.6193277 2
...
The columns in tb are:
which_row: row indices corresponding to the input matrix.fdr: FDR for the differential test. mean_x: The mean value in group x.scaled_mean_x: The mean value in group x after rows are scaled.km: Row groups if k-means clustering is applied to rows.UMAP plot which shows how samples are separated.
dimension_reduction(res, k = 2, method = "UMAP")
dimension_reduction(res, k = 3, method = "UMAP")
dimension_reduction(res, k = 4, method = "UMAP")
dimension_reduction(res, k = 5, method = "UMAP")
dimension_reduction(res, k = 6, method = "UMAP")
Following heatmap shows how subgroups are split when increasing k:
collect_classes(res)
Test correlation between subgroups and known annotations. If the known annotation is numeric, one-way ANOVA test is applied, and if the known annotation is discrete, chi-squared contingency table test is applied.
test_to_known_factors(res)
#> n disease.state(p) tissue(p) k
#> MAD:hclust 165 1.93e-12 1.42e-13 2
#> MAD:hclust 149 2.20e-16 1.99e-16 3
#> MAD:hclust 140 2.04e-22 4.06e-20 4
#> MAD:hclust 142 9.41e-22 5.75e-21 5
#> MAD:hclust 151 1.90e-24 1.04e-24 6
If matrix rows can be associated to genes, consider to use functional_enrichment(res,
...) to perform function enrichment for the signature genes. See this vignette for more detailed explanations.
The object with results only for a single top-value method and a single partition method can be extracted as:
res = res_list["MAD", "kmeans"]
# you can also extract it by
# res = res_list["MAD:kmeans"]
A summary of res and all the functions that can be applied to it:
res
#> A 'ConsensusPartition' object with k = 2, 3, 4, 5, 6.
#> On a matrix with 51882 rows and 180 columns.
#> Top rows (1000, 2000, 3000, 4000, 5000) are extracted by 'MAD' method.
#> Subgroups are detected by 'kmeans' method.
#> Performed in total 1250 partitions by row resampling.
#> Best k for subgroups seems to be 4.
#>
#> Following methods can be applied to this 'ConsensusPartition' object:
#> [1] "cola_report" "collect_classes" "collect_plots"
#> [4] "collect_stats" "colnames" "compare_signatures"
#> [7] "consensus_heatmap" "dimension_reduction" "functional_enrichment"
#> [10] "get_anno_col" "get_anno" "get_classes"
#> [13] "get_consensus" "get_matrix" "get_membership"
#> [16] "get_param" "get_signatures" "get_stats"
#> [19] "is_best_k" "is_stable_k" "membership_heatmap"
#> [22] "ncol" "nrow" "plot_ecdf"
#> [25] "rownames" "select_partition_number" "show"
#> [28] "suggest_best_k" "test_to_known_factors"
collect_plots() function collects all the plots made from res for all k (number of partitions)
into one single page to provide an easy and fast comparison between different k.
collect_plots(res)
The plots are:
k and the heatmap of
predicted classes for each k.k.k.k.All the plots in panels can be made by individual functions and they are plotted later in this section.
select_partition_number() produces several plots showing different
statistics for choosing “optimized” k. There are following statistics:
k;k, the area increased is defined as \(A_k - A_{k-1}\).The detailed explanations of these statistics can be found in the cola vignette.
Generally speaking, lower PAC score, higher mean silhouette score or higher
concordance corresponds to better partition. Rand index and Jaccard index
measure how similar the current partition is compared to partition with k-1.
If they are too similar, we won't accept k is better than k-1.
select_partition_number(res)
The numeric values for all these statistics can be obtained by get_stats().
get_stats(res)
#> k 1-PAC mean_silhouette concordance area_increased Rand Jaccard
#> 2 2 0.858 0.960 0.980 0.4801 0.515 0.515
#> 3 3 0.994 0.977 0.989 0.3495 0.749 0.551
#> 4 4 0.921 0.919 0.961 0.1586 0.856 0.614
#> 5 5 0.843 0.734 0.845 0.0565 0.980 0.921
#> 6 6 0.790 0.666 0.775 0.0375 0.905 0.623
suggest_best_k() suggests the best \(k\) based on these statistics. The rules are as follows:
suggest_best_k(res)
#> [1] 4
#> attr(,"optional")
#> [1] 3
There is also optional best \(k\) = 3 that is worth to check.
Following shows the table of the partitions (You need to click the show/hide
code output link to see it). The membership matrix (columns with name p*)
is inferred by
clue::cl_consensus()
function with the SE method. Basically the value in the membership matrix
represents the probability to belong to a certain group. The finall class
label for an item is determined with the group with highest probability it
belongs to.
In get_classes() function, the entropy is calculated from the membership
matrix and the silhouette score is calculated from the consensus matrix.
cbind(get_classes(res, k = 2), get_membership(res, k = 2))
#> class entropy silhouette p1 p2
#> GSM97800 2 0.0000 0.965 0.000 1.000
#> GSM97803 2 0.0000 0.965 0.000 1.000
#> GSM97804 2 0.0000 0.965 0.000 1.000
#> GSM97805 2 0.0000 0.965 0.000 1.000
#> GSM97807 2 0.0000 0.965 0.000 1.000
#> GSM97809 2 0.0000 0.965 0.000 1.000
#> GSM97811 2 0.0000 0.965 0.000 1.000
#> GSM97812 2 0.0000 0.965 0.000 1.000
#> GSM97816 2 0.0000 0.965 0.000 1.000
#> GSM97817 2 0.0000 0.965 0.000 1.000
#> GSM97820 2 0.0000 0.965 0.000 1.000
#> GSM97825 2 0.0000 0.965 0.000 1.000
#> GSM97827 2 0.0000 0.965 0.000 1.000
#> GSM97828 2 0.9754 0.364 0.408 0.592
#> GSM97833 2 0.0000 0.965 0.000 1.000
#> GSM97834 2 0.0000 0.965 0.000 1.000
#> GSM97840 2 0.0000 0.965 0.000 1.000
#> GSM97846 2 0.0000 0.965 0.000 1.000
#> GSM97848 2 0.0000 0.965 0.000 1.000
#> GSM97849 2 0.0000 0.965 0.000 1.000
#> GSM97850 2 0.0000 0.965 0.000 1.000
#> GSM97853 2 0.0000 0.965 0.000 1.000
#> GSM97855 2 0.0000 0.965 0.000 1.000
#> GSM97878 1 0.0000 0.990 1.000 0.000
#> GSM97913 2 0.0000 0.965 0.000 1.000
#> GSM97932 1 0.0000 0.990 1.000 0.000
#> GSM97939 2 0.0000 0.965 0.000 1.000
#> GSM97951 2 0.0000 0.965 0.000 1.000
#> GSM97957 1 0.5737 0.837 0.864 0.136
#> GSM97972 2 0.0376 0.962 0.004 0.996
#> GSM97793 1 0.0000 0.990 1.000 0.000
#> GSM97795 2 0.0000 0.965 0.000 1.000
#> GSM97802 1 0.0000 0.990 1.000 0.000
#> GSM97810 2 0.0000 0.965 0.000 1.000
#> GSM97815 2 0.0000 0.965 0.000 1.000
#> GSM97837 1 0.0000 0.990 1.000 0.000
#> GSM97843 1 0.4939 0.873 0.892 0.108
#> GSM97890 2 0.6623 0.823 0.172 0.828
#> GSM97899 1 0.0000 0.990 1.000 0.000
#> GSM97910 1 0.0000 0.990 1.000 0.000
#> GSM97916 1 0.0000 0.990 1.000 0.000
#> GSM97920 1 0.5737 0.837 0.864 0.136
#> GSM97921 1 0.0000 0.990 1.000 0.000
#> GSM97927 1 0.0000 0.990 1.000 0.000
#> GSM97937 1 0.0000 0.990 1.000 0.000
#> GSM97941 2 0.0000 0.965 0.000 1.000
#> GSM97943 1 0.0000 0.990 1.000 0.000
#> GSM97958 2 0.5519 0.873 0.128 0.872
#> GSM97960 2 0.0000 0.965 0.000 1.000
#> GSM97794 1 0.0000 0.990 1.000 0.000
#> GSM97796 1 0.0000 0.990 1.000 0.000
#> GSM97797 1 0.0000 0.990 1.000 0.000
#> GSM97798 1 0.0000 0.990 1.000 0.000
#> GSM97801 1 0.0000 0.990 1.000 0.000
#> GSM97806 1 0.0000 0.990 1.000 0.000
#> GSM97808 1 0.0000 0.990 1.000 0.000
#> GSM97813 1 0.0000 0.990 1.000 0.000
#> GSM97814 1 0.0000 0.990 1.000 0.000
#> GSM97818 1 0.0000 0.990 1.000 0.000
#> GSM97819 1 0.0000 0.990 1.000 0.000
#> GSM97821 2 0.0000 0.965 0.000 1.000
#> GSM97826 1 0.0000 0.990 1.000 0.000
#> GSM97829 1 0.0000 0.990 1.000 0.000
#> GSM97832 2 0.0000 0.965 0.000 1.000
#> GSM97836 1 0.0000 0.990 1.000 0.000
#> GSM97839 1 0.0000 0.990 1.000 0.000
#> GSM97844 2 0.0000 0.965 0.000 1.000
#> GSM97847 1 0.0000 0.990 1.000 0.000
#> GSM97851 1 0.0000 0.990 1.000 0.000
#> GSM97852 1 0.0000 0.990 1.000 0.000
#> GSM97856 1 0.0000 0.990 1.000 0.000
#> GSM97858 2 0.0000 0.965 0.000 1.000
#> GSM97859 1 0.0000 0.990 1.000 0.000
#> GSM97861 1 0.0000 0.990 1.000 0.000
#> GSM97863 1 0.0000 0.990 1.000 0.000
#> GSM97869 1 0.0000 0.990 1.000 0.000
#> GSM97870 1 0.0000 0.990 1.000 0.000
#> GSM97871 1 0.0000 0.990 1.000 0.000
#> GSM97877 2 0.0000 0.965 0.000 1.000
#> GSM97879 1 0.0000 0.990 1.000 0.000
#> GSM97882 1 0.0000 0.990 1.000 0.000
#> GSM97885 1 0.0000 0.990 1.000 0.000
#> GSM97886 1 0.0000 0.990 1.000 0.000
#> GSM97887 1 0.0000 0.990 1.000 0.000
#> GSM97888 1 0.0000 0.990 1.000 0.000
#> GSM97889 1 0.0000 0.990 1.000 0.000
#> GSM97891 1 0.0000 0.990 1.000 0.000
#> GSM97892 2 0.0000 0.965 0.000 1.000
#> GSM97893 1 0.0000 0.990 1.000 0.000
#> GSM97894 1 0.0000 0.990 1.000 0.000
#> GSM97895 1 0.0000 0.990 1.000 0.000
#> GSM97896 1 0.0000 0.990 1.000 0.000
#> GSM97898 1 0.0000 0.990 1.000 0.000
#> GSM97903 1 0.0000 0.990 1.000 0.000
#> GSM97905 1 0.0000 0.990 1.000 0.000
#> GSM97906 1 0.0000 0.990 1.000 0.000
#> GSM97908 1 0.0000 0.990 1.000 0.000
#> GSM97912 1 0.0000 0.990 1.000 0.000
#> GSM97914 1 0.0000 0.990 1.000 0.000
#> GSM97915 1 0.0000 0.990 1.000 0.000
#> GSM97917 1 0.0000 0.990 1.000 0.000
#> GSM97918 1 0.0000 0.990 1.000 0.000
#> GSM97919 1 0.0000 0.990 1.000 0.000
#> GSM97922 1 0.0000 0.990 1.000 0.000
#> GSM97924 2 0.0000 0.965 0.000 1.000
#> GSM97926 1 0.0000 0.990 1.000 0.000
#> GSM97930 1 0.0000 0.990 1.000 0.000
#> GSM97931 2 0.4815 0.893 0.104 0.896
#> GSM97935 1 0.0000 0.990 1.000 0.000
#> GSM97936 1 0.0000 0.990 1.000 0.000
#> GSM97938 1 0.0000 0.990 1.000 0.000
#> GSM97940 1 0.0000 0.990 1.000 0.000
#> GSM97942 1 0.0000 0.990 1.000 0.000
#> GSM97945 1 0.0000 0.990 1.000 0.000
#> GSM97946 2 0.0000 0.965 0.000 1.000
#> GSM97948 1 0.0000 0.990 1.000 0.000
#> GSM97950 1 0.0000 0.990 1.000 0.000
#> GSM97952 1 0.0000 0.990 1.000 0.000
#> GSM97953 1 0.0000 0.990 1.000 0.000
#> GSM97954 1 0.0000 0.990 1.000 0.000
#> GSM97955 1 0.0000 0.990 1.000 0.000
#> GSM97959 1 0.8443 0.607 0.728 0.272
#> GSM97961 1 0.0000 0.990 1.000 0.000
#> GSM97963 1 0.0000 0.990 1.000 0.000
#> GSM97965 1 0.0000 0.990 1.000 0.000
#> GSM97966 1 0.0000 0.990 1.000 0.000
#> GSM97967 2 0.0000 0.965 0.000 1.000
#> GSM97968 2 0.0000 0.965 0.000 1.000
#> GSM97969 1 0.0000 0.990 1.000 0.000
#> GSM97971 1 0.0000 0.990 1.000 0.000
#> GSM97799 2 0.0000 0.965 0.000 1.000
#> GSM97823 2 0.0000 0.965 0.000 1.000
#> GSM97824 2 0.5629 0.869 0.132 0.868
#> GSM97830 1 0.5519 0.847 0.872 0.128
#> GSM97835 2 0.0000 0.965 0.000 1.000
#> GSM97838 2 0.0000 0.965 0.000 1.000
#> GSM97841 2 0.0000 0.965 0.000 1.000
#> GSM97842 2 0.0000 0.965 0.000 1.000
#> GSM97854 2 0.0000 0.965 0.000 1.000
#> GSM97857 2 0.5629 0.869 0.132 0.868
#> GSM97860 1 0.0000 0.990 1.000 0.000
#> GSM97862 2 0.5629 0.869 0.132 0.868
#> GSM97864 2 0.0000 0.965 0.000 1.000
#> GSM97866 2 0.5629 0.869 0.132 0.868
#> GSM97868 2 0.4939 0.890 0.108 0.892
#> GSM97872 1 0.0000 0.990 1.000 0.000
#> GSM97873 2 0.0000 0.965 0.000 1.000
#> GSM97874 1 0.0000 0.990 1.000 0.000
#> GSM97875 1 0.8207 0.643 0.744 0.256
#> GSM97876 1 0.0672 0.982 0.992 0.008
#> GSM97880 1 0.0000 0.990 1.000 0.000
#> GSM97881 2 0.5629 0.869 0.132 0.868
#> GSM97884 2 0.0000 0.965 0.000 1.000
#> GSM97901 2 0.6801 0.812 0.180 0.820
#> GSM97902 1 0.0000 0.990 1.000 0.000
#> GSM97909 2 0.0000 0.965 0.000 1.000
#> GSM97911 2 0.5629 0.869 0.132 0.868
#> GSM97923 1 0.0000 0.990 1.000 0.000
#> GSM97928 1 0.0000 0.990 1.000 0.000
#> GSM97929 2 0.0000 0.965 0.000 1.000
#> GSM97933 1 0.0000 0.990 1.000 0.000
#> GSM97934 1 0.0000 0.990 1.000 0.000
#> GSM97944 2 0.0000 0.965 0.000 1.000
#> GSM97949 2 0.0000 0.965 0.000 1.000
#> GSM97956 2 0.5629 0.869 0.132 0.868
#> GSM97962 2 0.5629 0.869 0.132 0.868
#> GSM97964 2 0.5629 0.869 0.132 0.868
#> GSM97970 2 0.0000 0.965 0.000 1.000
#> GSM97822 1 0.0000 0.990 1.000 0.000
#> GSM97831 2 0.7056 0.796 0.192 0.808
#> GSM97845 1 0.0000 0.990 1.000 0.000
#> GSM97865 1 0.0000 0.990 1.000 0.000
#> GSM97867 1 0.0000 0.990 1.000 0.000
#> GSM97883 1 0.0000 0.990 1.000 0.000
#> GSM97897 1 0.0000 0.990 1.000 0.000
#> GSM97900 1 0.0000 0.990 1.000 0.000
#> GSM97904 1 0.0000 0.990 1.000 0.000
#> GSM97907 2 0.0000 0.965 0.000 1.000
#> GSM97925 1 0.0000 0.990 1.000 0.000
#> GSM97947 1 0.0000 0.990 1.000 0.000
cbind(get_classes(res, k = 3), get_membership(res, k = 3))
#> class entropy silhouette p1 p2 p3
#> GSM97800 2 0.0000 0.990 0.000 1.000 0.000
#> GSM97803 2 0.0000 0.990 0.000 1.000 0.000
#> GSM97804 2 0.0000 0.990 0.000 1.000 0.000
#> GSM97805 2 0.0000 0.990 0.000 1.000 0.000
#> GSM97807 2 0.0000 0.990 0.000 1.000 0.000
#> GSM97809 2 0.0000 0.990 0.000 1.000 0.000
#> GSM97811 2 0.0000 0.990 0.000 1.000 0.000
#> GSM97812 2 0.0000 0.990 0.000 1.000 0.000
#> GSM97816 3 0.0000 0.990 0.000 0.000 1.000
#> GSM97817 2 0.0000 0.990 0.000 1.000 0.000
#> GSM97820 2 0.0000 0.990 0.000 1.000 0.000
#> GSM97825 2 0.0000 0.990 0.000 1.000 0.000
#> GSM97827 2 0.0000 0.990 0.000 1.000 0.000
#> GSM97828 3 0.0000 0.990 0.000 0.000 1.000
#> GSM97833 2 0.0000 0.990 0.000 1.000 0.000
#> GSM97834 2 0.0000 0.990 0.000 1.000 0.000
#> GSM97840 2 0.0000 0.990 0.000 1.000 0.000
#> GSM97846 2 0.0000 0.990 0.000 1.000 0.000
#> GSM97848 2 0.0000 0.990 0.000 1.000 0.000
#> GSM97849 2 0.0000 0.990 0.000 1.000 0.000
#> GSM97850 2 0.0000 0.990 0.000 1.000 0.000
#> GSM97853 2 0.0000 0.990 0.000 1.000 0.000
#> GSM97855 2 0.0000 0.990 0.000 1.000 0.000
#> GSM97878 1 0.3482 0.862 0.872 0.000 0.128
#> GSM97913 2 0.3267 0.863 0.000 0.884 0.116
#> GSM97932 1 0.0000 0.988 1.000 0.000 0.000
#> GSM97939 3 0.0000 0.990 0.000 0.000 1.000
#> GSM97951 2 0.0000 0.990 0.000 1.000 0.000
#> GSM97957 3 0.0000 0.990 0.000 0.000 1.000
#> GSM97972 3 0.0000 0.990 0.000 0.000 1.000
#> GSM97793 3 0.0000 0.990 0.000 0.000 1.000
#> GSM97795 2 0.0000 0.990 0.000 1.000 0.000
#> GSM97802 3 0.0000 0.990 0.000 0.000 1.000
#> GSM97810 3 0.4062 0.801 0.000 0.164 0.836
#> GSM97815 3 0.0000 0.990 0.000 0.000 1.000
#> GSM97837 1 0.0000 0.988 1.000 0.000 0.000
#> GSM97843 3 0.0000 0.990 0.000 0.000 1.000
#> GSM97890 3 0.0000 0.990 0.000 0.000 1.000
#> GSM97899 1 0.0000 0.988 1.000 0.000 0.000
#> GSM97910 3 0.1964 0.926 0.056 0.000 0.944
#> GSM97916 1 0.3752 0.843 0.856 0.000 0.144
#> GSM97920 3 0.0000 0.990 0.000 0.000 1.000
#> GSM97921 1 0.0000 0.988 1.000 0.000 0.000
#> GSM97927 1 0.0000 0.988 1.000 0.000 0.000
#> GSM97937 1 0.0000 0.988 1.000 0.000 0.000
#> GSM97941 2 0.0000 0.990 0.000 1.000 0.000
#> GSM97943 3 0.0000 0.990 0.000 0.000 1.000
#> GSM97958 3 0.0000 0.990 0.000 0.000 1.000
#> GSM97960 2 0.0000 0.990 0.000 1.000 0.000
#> GSM97794 1 0.3752 0.843 0.856 0.000 0.144
#> GSM97796 1 0.0000 0.988 1.000 0.000 0.000
#> GSM97797 1 0.3879 0.833 0.848 0.000 0.152
#> GSM97798 1 0.0000 0.988 1.000 0.000 0.000
#> GSM97801 1 0.0747 0.975 0.984 0.000 0.016
#> GSM97806 1 0.0000 0.988 1.000 0.000 0.000
#> GSM97808 1 0.0000 0.988 1.000 0.000 0.000
#> GSM97813 1 0.0000 0.988 1.000 0.000 0.000
#> GSM97814 1 0.0000 0.988 1.000 0.000 0.000
#> GSM97818 1 0.0592 0.978 0.988 0.000 0.012
#> GSM97819 3 0.0000 0.990 0.000 0.000 1.000
#> GSM97821 3 0.5178 0.655 0.000 0.256 0.744
#> GSM97826 1 0.0000 0.988 1.000 0.000 0.000
#> GSM97829 1 0.0000 0.988 1.000 0.000 0.000
#> GSM97832 2 0.5706 0.524 0.000 0.680 0.320
#> GSM97836 1 0.0000 0.988 1.000 0.000 0.000
#> GSM97839 1 0.0000 0.988 1.000 0.000 0.000
#> GSM97844 2 0.0000 0.990 0.000 1.000 0.000
#> GSM97847 1 0.0000 0.988 1.000 0.000 0.000
#> GSM97851 1 0.0000 0.988 1.000 0.000 0.000
#> GSM97852 1 0.0000 0.988 1.000 0.000 0.000
#> GSM97856 1 0.0000 0.988 1.000 0.000 0.000
#> GSM97858 2 0.0000 0.990 0.000 1.000 0.000
#> GSM97859 1 0.0000 0.988 1.000 0.000 0.000
#> GSM97861 1 0.0000 0.988 1.000 0.000 0.000
#> GSM97863 1 0.0000 0.988 1.000 0.000 0.000
#> GSM97869 1 0.3752 0.843 0.856 0.000 0.144
#> GSM97870 1 0.0892 0.971 0.980 0.000 0.020
#> GSM97871 1 0.0000 0.988 1.000 0.000 0.000
#> GSM97877 2 0.0000 0.990 0.000 1.000 0.000
#> GSM97879 1 0.0000 0.988 1.000 0.000 0.000
#> GSM97882 1 0.0000 0.988 1.000 0.000 0.000
#> GSM97885 1 0.0000 0.988 1.000 0.000 0.000
#> GSM97886 1 0.0000 0.988 1.000 0.000 0.000
#> GSM97887 1 0.0000 0.988 1.000 0.000 0.000
#> GSM97888 1 0.0000 0.988 1.000 0.000 0.000
#> GSM97889 1 0.0000 0.988 1.000 0.000 0.000
#> GSM97891 1 0.0000 0.988 1.000 0.000 0.000
#> GSM97892 2 0.0000 0.990 0.000 1.000 0.000
#> GSM97893 1 0.0000 0.988 1.000 0.000 0.000
#> GSM97894 1 0.0000 0.988 1.000 0.000 0.000
#> GSM97895 1 0.0000 0.988 1.000 0.000 0.000
#> GSM97896 1 0.0000 0.988 1.000 0.000 0.000
#> GSM97898 1 0.0000 0.988 1.000 0.000 0.000
#> GSM97903 1 0.0000 0.988 1.000 0.000 0.000
#> GSM97905 1 0.0000 0.988 1.000 0.000 0.000
#> GSM97906 1 0.0000 0.988 1.000 0.000 0.000
#> GSM97908 1 0.0000 0.988 1.000 0.000 0.000
#> GSM97912 1 0.0000 0.988 1.000 0.000 0.000
#> GSM97914 1 0.0592 0.978 0.988 0.000 0.012
#> GSM97915 1 0.0000 0.988 1.000 0.000 0.000
#> GSM97917 1 0.0000 0.988 1.000 0.000 0.000
#> GSM97918 1 0.0000 0.988 1.000 0.000 0.000
#> GSM97919 1 0.0000 0.988 1.000 0.000 0.000
#> GSM97922 1 0.0000 0.988 1.000 0.000 0.000
#> GSM97924 2 0.0000 0.990 0.000 1.000 0.000
#> GSM97926 3 0.0000 0.990 0.000 0.000 1.000
#> GSM97930 1 0.0000 0.988 1.000 0.000 0.000
#> GSM97931 3 0.0000 0.990 0.000 0.000 1.000
#> GSM97935 1 0.0000 0.988 1.000 0.000 0.000
#> GSM97936 1 0.0000 0.988 1.000 0.000 0.000
#> GSM97938 1 0.0000 0.988 1.000 0.000 0.000
#> GSM97940 1 0.0000 0.988 1.000 0.000 0.000
#> GSM97942 3 0.0000 0.990 0.000 0.000 1.000
#> GSM97945 1 0.0000 0.988 1.000 0.000 0.000
#> GSM97946 2 0.0000 0.990 0.000 1.000 0.000
#> GSM97948 3 0.0000 0.990 0.000 0.000 1.000
#> GSM97950 1 0.0000 0.988 1.000 0.000 0.000
#> GSM97952 1 0.0000 0.988 1.000 0.000 0.000
#> GSM97953 1 0.0000 0.988 1.000 0.000 0.000
#> GSM97954 1 0.0000 0.988 1.000 0.000 0.000
#> GSM97955 1 0.0000 0.988 1.000 0.000 0.000
#> GSM97959 1 0.5954 0.781 0.792 0.116 0.092
#> GSM97961 1 0.0000 0.988 1.000 0.000 0.000
#> GSM97963 1 0.0000 0.988 1.000 0.000 0.000
#> GSM97965 1 0.0000 0.988 1.000 0.000 0.000
#> GSM97966 1 0.0000 0.988 1.000 0.000 0.000
#> GSM97967 2 0.0000 0.990 0.000 1.000 0.000
#> GSM97968 2 0.0000 0.990 0.000 1.000 0.000
#> GSM97969 1 0.0000 0.988 1.000 0.000 0.000
#> GSM97971 1 0.0000 0.988 1.000 0.000 0.000
#> GSM97799 3 0.0000 0.990 0.000 0.000 1.000
#> GSM97823 2 0.0000 0.990 0.000 1.000 0.000
#> GSM97824 3 0.0000 0.990 0.000 0.000 1.000
#> GSM97830 3 0.0000 0.990 0.000 0.000 1.000
#> GSM97835 3 0.0592 0.979 0.000 0.012 0.988
#> GSM97838 2 0.0000 0.990 0.000 1.000 0.000
#> GSM97841 2 0.0000 0.990 0.000 1.000 0.000
#> GSM97842 3 0.0000 0.990 0.000 0.000 1.000
#> GSM97854 2 0.0000 0.990 0.000 1.000 0.000
#> GSM97857 3 0.0000 0.990 0.000 0.000 1.000
#> GSM97860 3 0.0000 0.990 0.000 0.000 1.000
#> GSM97862 3 0.0000 0.990 0.000 0.000 1.000
#> GSM97864 2 0.0000 0.990 0.000 1.000 0.000
#> GSM97866 3 0.0000 0.990 0.000 0.000 1.000
#> GSM97868 3 0.0000 0.990 0.000 0.000 1.000
#> GSM97872 1 0.0000 0.988 1.000 0.000 0.000
#> GSM97873 3 0.0000 0.990 0.000 0.000 1.000
#> GSM97874 3 0.0000 0.990 0.000 0.000 1.000
#> GSM97875 3 0.0000 0.990 0.000 0.000 1.000
#> GSM97876 3 0.0000 0.990 0.000 0.000 1.000
#> GSM97880 3 0.0000 0.990 0.000 0.000 1.000
#> GSM97881 3 0.0000 0.990 0.000 0.000 1.000
#> GSM97884 3 0.0000 0.990 0.000 0.000 1.000
#> GSM97901 3 0.0000 0.990 0.000 0.000 1.000
#> GSM97902 3 0.0000 0.990 0.000 0.000 1.000
#> GSM97909 2 0.0000 0.990 0.000 1.000 0.000
#> GSM97911 3 0.0000 0.990 0.000 0.000 1.000
#> GSM97923 3 0.0000 0.990 0.000 0.000 1.000
#> GSM97928 1 0.0000 0.988 1.000 0.000 0.000
#> GSM97929 2 0.0000 0.990 0.000 1.000 0.000
#> GSM97933 3 0.0000 0.990 0.000 0.000 1.000
#> GSM97934 3 0.0000 0.990 0.000 0.000 1.000
#> GSM97944 3 0.0000 0.990 0.000 0.000 1.000
#> GSM97949 2 0.0000 0.990 0.000 1.000 0.000
#> GSM97956 3 0.0000 0.990 0.000 0.000 1.000
#> GSM97962 3 0.0000 0.990 0.000 0.000 1.000
#> GSM97964 3 0.0000 0.990 0.000 0.000 1.000
#> GSM97970 3 0.0000 0.990 0.000 0.000 1.000
#> GSM97822 1 0.0000 0.988 1.000 0.000 0.000
#> GSM97831 3 0.0000 0.990 0.000 0.000 1.000
#> GSM97845 1 0.0000 0.988 1.000 0.000 0.000
#> GSM97865 1 0.0592 0.978 0.988 0.000 0.012
#> GSM97867 3 0.0000 0.990 0.000 0.000 1.000
#> GSM97883 3 0.0000 0.990 0.000 0.000 1.000
#> GSM97897 1 0.0000 0.988 1.000 0.000 0.000
#> GSM97900 1 0.0000 0.988 1.000 0.000 0.000
#> GSM97904 1 0.0000 0.988 1.000 0.000 0.000
#> GSM97907 2 0.0000 0.990 0.000 1.000 0.000
#> GSM97925 3 0.0000 0.990 0.000 0.000 1.000
#> GSM97947 3 0.0000 0.990 0.000 0.000 1.000
cbind(get_classes(res, k = 4), get_membership(res, k = 4))
#> class entropy silhouette p1 p2 p3 p4
#> GSM97800 2 0.0336 0.995 0.008 0.992 0.000 0.000
#> GSM97803 2 0.0336 0.995 0.008 0.992 0.000 0.000
#> GSM97804 2 0.0336 0.995 0.008 0.992 0.000 0.000
#> GSM97805 2 0.0336 0.995 0.008 0.992 0.000 0.000
#> GSM97807 2 0.0000 0.996 0.000 1.000 0.000 0.000
#> GSM97809 2 0.0000 0.996 0.000 1.000 0.000 0.000
#> GSM97811 2 0.0000 0.996 0.000 1.000 0.000 0.000
#> GSM97812 2 0.0000 0.996 0.000 1.000 0.000 0.000
#> GSM97816 3 0.7145 0.464 0.252 0.192 0.556 0.000
#> GSM97817 2 0.0000 0.996 0.000 1.000 0.000 0.000
#> GSM97820 2 0.0000 0.996 0.000 1.000 0.000 0.000
#> GSM97825 2 0.0000 0.996 0.000 1.000 0.000 0.000
#> GSM97827 2 0.0000 0.996 0.000 1.000 0.000 0.000
#> GSM97828 1 0.4134 0.613 0.740 0.000 0.260 0.000
#> GSM97833 2 0.0000 0.996 0.000 1.000 0.000 0.000
#> GSM97834 2 0.0000 0.996 0.000 1.000 0.000 0.000
#> GSM97840 2 0.0000 0.996 0.000 1.000 0.000 0.000
#> GSM97846 2 0.0000 0.996 0.000 1.000 0.000 0.000
#> GSM97848 2 0.0000 0.996 0.000 1.000 0.000 0.000
#> GSM97849 2 0.0000 0.996 0.000 1.000 0.000 0.000
#> GSM97850 2 0.0000 0.996 0.000 1.000 0.000 0.000
#> GSM97853 2 0.0000 0.996 0.000 1.000 0.000 0.000
#> GSM97855 2 0.0000 0.996 0.000 1.000 0.000 0.000
#> GSM97878 1 0.0336 0.918 0.992 0.000 0.000 0.008
#> GSM97913 1 0.0000 0.913 1.000 0.000 0.000 0.000
#> GSM97932 4 0.0000 0.975 0.000 0.000 0.000 1.000
#> GSM97939 3 0.0000 0.963 0.000 0.000 1.000 0.000
#> GSM97951 2 0.0000 0.996 0.000 1.000 0.000 0.000
#> GSM97957 3 0.0000 0.963 0.000 0.000 1.000 0.000
#> GSM97972 3 0.4250 0.638 0.276 0.000 0.724 0.000
#> GSM97793 3 0.0000 0.963 0.000 0.000 1.000 0.000
#> GSM97795 2 0.0336 0.995 0.008 0.992 0.000 0.000
#> GSM97802 3 0.0000 0.963 0.000 0.000 1.000 0.000
#> GSM97810 3 0.3688 0.723 0.000 0.208 0.792 0.000
#> GSM97815 3 0.0000 0.963 0.000 0.000 1.000 0.000
#> GSM97837 1 0.0336 0.918 0.992 0.000 0.000 0.008
#> GSM97843 3 0.0000 0.963 0.000 0.000 1.000 0.000
#> GSM97890 3 0.0000 0.963 0.000 0.000 1.000 0.000
#> GSM97899 4 0.0000 0.975 0.000 0.000 0.000 1.000
#> GSM97910 1 0.0336 0.912 0.992 0.000 0.008 0.000
#> GSM97916 1 0.0336 0.918 0.992 0.000 0.000 0.008
#> GSM97920 3 0.0000 0.963 0.000 0.000 1.000 0.000
#> GSM97921 1 0.0336 0.918 0.992 0.000 0.000 0.008
#> GSM97927 1 0.2408 0.888 0.896 0.000 0.000 0.104
#> GSM97937 1 0.0336 0.918 0.992 0.000 0.000 0.008
#> GSM97941 2 0.0000 0.996 0.000 1.000 0.000 0.000
#> GSM97943 1 0.0336 0.912 0.992 0.000 0.008 0.000
#> GSM97958 1 0.0336 0.912 0.992 0.000 0.008 0.000
#> GSM97960 2 0.0000 0.996 0.000 1.000 0.000 0.000
#> GSM97794 1 0.0336 0.918 0.992 0.000 0.000 0.008
#> GSM97796 4 0.0000 0.975 0.000 0.000 0.000 1.000
#> GSM97797 1 0.0336 0.918 0.992 0.000 0.000 0.008
#> GSM97798 4 0.0000 0.975 0.000 0.000 0.000 1.000
#> GSM97801 1 0.0336 0.918 0.992 0.000 0.000 0.008
#> GSM97806 1 0.2530 0.884 0.888 0.000 0.000 0.112
#> GSM97808 4 0.0000 0.975 0.000 0.000 0.000 1.000
#> GSM97813 1 0.4985 0.248 0.532 0.000 0.000 0.468
#> GSM97814 4 0.0000 0.975 0.000 0.000 0.000 1.000
#> GSM97818 1 0.0336 0.918 0.992 0.000 0.000 0.008
#> GSM97819 3 0.0000 0.963 0.000 0.000 1.000 0.000
#> GSM97821 3 0.7768 0.208 0.260 0.312 0.428 0.000
#> GSM97826 1 0.0336 0.918 0.992 0.000 0.000 0.008
#> GSM97829 1 0.0336 0.918 0.992 0.000 0.000 0.008
#> GSM97832 2 0.1970 0.932 0.008 0.932 0.060 0.000
#> GSM97836 1 0.2530 0.884 0.888 0.000 0.000 0.112
#> GSM97839 4 0.0000 0.975 0.000 0.000 0.000 1.000
#> GSM97844 2 0.0336 0.995 0.008 0.992 0.000 0.000
#> GSM97847 1 0.0336 0.918 0.992 0.000 0.000 0.008
#> GSM97851 4 0.0000 0.975 0.000 0.000 0.000 1.000
#> GSM97852 1 0.2530 0.884 0.888 0.000 0.000 0.112
#> GSM97856 4 0.0000 0.975 0.000 0.000 0.000 1.000
#> GSM97858 2 0.0336 0.995 0.008 0.992 0.000 0.000
#> GSM97859 1 0.2081 0.897 0.916 0.000 0.000 0.084
#> GSM97861 1 0.2530 0.884 0.888 0.000 0.000 0.112
#> GSM97863 4 0.0000 0.975 0.000 0.000 0.000 1.000
#> GSM97869 1 0.0336 0.918 0.992 0.000 0.000 0.008
#> GSM97870 1 0.0336 0.918 0.992 0.000 0.000 0.008
#> GSM97871 4 0.0000 0.975 0.000 0.000 0.000 1.000
#> GSM97877 1 0.1940 0.859 0.924 0.076 0.000 0.000
#> GSM97879 1 0.2530 0.884 0.888 0.000 0.000 0.112
#> GSM97882 1 0.2530 0.884 0.888 0.000 0.000 0.112
#> GSM97885 1 0.0336 0.918 0.992 0.000 0.000 0.008
#> GSM97886 4 0.0000 0.975 0.000 0.000 0.000 1.000
#> GSM97887 4 0.0000 0.975 0.000 0.000 0.000 1.000
#> GSM97888 4 0.0000 0.975 0.000 0.000 0.000 1.000
#> GSM97889 4 0.0000 0.975 0.000 0.000 0.000 1.000
#> GSM97891 1 0.2530 0.884 0.888 0.000 0.000 0.112
#> GSM97892 2 0.0336 0.995 0.008 0.992 0.000 0.000
#> GSM97893 4 0.0000 0.975 0.000 0.000 0.000 1.000
#> GSM97894 4 0.0000 0.975 0.000 0.000 0.000 1.000
#> GSM97895 4 0.0000 0.975 0.000 0.000 0.000 1.000
#> GSM97896 4 0.0000 0.975 0.000 0.000 0.000 1.000
#> GSM97898 4 0.0000 0.975 0.000 0.000 0.000 1.000
#> GSM97903 1 0.0336 0.918 0.992 0.000 0.000 0.008
#> GSM97905 4 0.5000 -0.165 0.496 0.000 0.000 0.504
#> GSM97906 4 0.0000 0.975 0.000 0.000 0.000 1.000
#> GSM97908 1 0.4522 0.605 0.680 0.000 0.000 0.320
#> GSM97912 1 0.0921 0.914 0.972 0.000 0.000 0.028
#> GSM97914 1 0.0336 0.918 0.992 0.000 0.000 0.008
#> GSM97915 4 0.0000 0.975 0.000 0.000 0.000 1.000
#> GSM97917 4 0.0000 0.975 0.000 0.000 0.000 1.000
#> GSM97918 4 0.0000 0.975 0.000 0.000 0.000 1.000
#> GSM97919 4 0.0000 0.975 0.000 0.000 0.000 1.000
#> GSM97922 1 0.4998 0.181 0.512 0.000 0.000 0.488
#> GSM97924 2 0.0336 0.995 0.008 0.992 0.000 0.000
#> GSM97926 3 0.0000 0.963 0.000 0.000 1.000 0.000
#> GSM97930 1 0.0336 0.918 0.992 0.000 0.000 0.008
#> GSM97931 3 0.4866 0.381 0.404 0.000 0.596 0.000
#> GSM97935 1 0.2530 0.884 0.888 0.000 0.000 0.112
#> GSM97936 4 0.0000 0.975 0.000 0.000 0.000 1.000
#> GSM97938 4 0.4624 0.389 0.340 0.000 0.000 0.660
#> GSM97940 4 0.0000 0.975 0.000 0.000 0.000 1.000
#> GSM97942 3 0.0000 0.963 0.000 0.000 1.000 0.000
#> GSM97945 4 0.0000 0.975 0.000 0.000 0.000 1.000
#> GSM97946 2 0.0000 0.996 0.000 1.000 0.000 0.000
#> GSM97948 3 0.0000 0.963 0.000 0.000 1.000 0.000
#> GSM97950 4 0.0000 0.975 0.000 0.000 0.000 1.000
#> GSM97952 4 0.0000 0.975 0.000 0.000 0.000 1.000
#> GSM97953 1 0.3311 0.818 0.828 0.000 0.000 0.172
#> GSM97954 1 0.2530 0.884 0.888 0.000 0.000 0.112
#> GSM97955 4 0.0000 0.975 0.000 0.000 0.000 1.000
#> GSM97959 1 0.0336 0.918 0.992 0.000 0.000 0.008
#> GSM97961 4 0.0000 0.975 0.000 0.000 0.000 1.000
#> GSM97963 4 0.0000 0.975 0.000 0.000 0.000 1.000
#> GSM97965 4 0.0000 0.975 0.000 0.000 0.000 1.000
#> GSM97966 4 0.0000 0.975 0.000 0.000 0.000 1.000
#> GSM97967 2 0.0000 0.996 0.000 1.000 0.000 0.000
#> GSM97968 2 0.0000 0.996 0.000 1.000 0.000 0.000
#> GSM97969 1 0.4972 0.287 0.544 0.000 0.000 0.456
#> GSM97971 1 0.2408 0.888 0.896 0.000 0.000 0.104
#> GSM97799 3 0.0000 0.963 0.000 0.000 1.000 0.000
#> GSM97823 2 0.0000 0.996 0.000 1.000 0.000 0.000
#> GSM97824 3 0.0000 0.963 0.000 0.000 1.000 0.000
#> GSM97830 3 0.0000 0.963 0.000 0.000 1.000 0.000
#> GSM97835 3 0.0188 0.959 0.000 0.004 0.996 0.000
#> GSM97838 2 0.0336 0.995 0.008 0.992 0.000 0.000
#> GSM97841 2 0.0336 0.995 0.008 0.992 0.000 0.000
#> GSM97842 3 0.0000 0.963 0.000 0.000 1.000 0.000
#> GSM97854 2 0.0336 0.995 0.008 0.992 0.000 0.000
#> GSM97857 3 0.0000 0.963 0.000 0.000 1.000 0.000
#> GSM97860 3 0.0000 0.963 0.000 0.000 1.000 0.000
#> GSM97862 3 0.0000 0.963 0.000 0.000 1.000 0.000
#> GSM97864 2 0.0336 0.995 0.008 0.992 0.000 0.000
#> GSM97866 3 0.0000 0.963 0.000 0.000 1.000 0.000
#> GSM97868 3 0.0000 0.963 0.000 0.000 1.000 0.000
#> GSM97872 1 0.0336 0.918 0.992 0.000 0.000 0.008
#> GSM97873 3 0.0000 0.963 0.000 0.000 1.000 0.000
#> GSM97874 3 0.0000 0.963 0.000 0.000 1.000 0.000
#> GSM97875 3 0.0000 0.963 0.000 0.000 1.000 0.000
#> GSM97876 3 0.0000 0.963 0.000 0.000 1.000 0.000
#> GSM97880 3 0.0000 0.963 0.000 0.000 1.000 0.000
#> GSM97881 3 0.0000 0.963 0.000 0.000 1.000 0.000
#> GSM97884 3 0.0000 0.963 0.000 0.000 1.000 0.000
#> GSM97901 3 0.0000 0.963 0.000 0.000 1.000 0.000
#> GSM97902 1 0.0336 0.912 0.992 0.000 0.008 0.000
#> GSM97909 2 0.0336 0.995 0.008 0.992 0.000 0.000
#> GSM97911 3 0.0000 0.963 0.000 0.000 1.000 0.000
#> GSM97923 3 0.0000 0.963 0.000 0.000 1.000 0.000
#> GSM97928 1 0.0469 0.917 0.988 0.000 0.000 0.012
#> GSM97929 2 0.0336 0.995 0.008 0.992 0.000 0.000
#> GSM97933 3 0.0000 0.963 0.000 0.000 1.000 0.000
#> GSM97934 3 0.0000 0.963 0.000 0.000 1.000 0.000
#> GSM97944 3 0.0000 0.963 0.000 0.000 1.000 0.000
#> GSM97949 2 0.0000 0.996 0.000 1.000 0.000 0.000
#> GSM97956 3 0.0000 0.963 0.000 0.000 1.000 0.000
#> GSM97962 3 0.0000 0.963 0.000 0.000 1.000 0.000
#> GSM97964 3 0.0000 0.963 0.000 0.000 1.000 0.000
#> GSM97970 3 0.0000 0.963 0.000 0.000 1.000 0.000
#> GSM97822 1 0.2530 0.884 0.888 0.000 0.000 0.112
#> GSM97831 3 0.0000 0.963 0.000 0.000 1.000 0.000
#> GSM97845 1 0.2530 0.884 0.888 0.000 0.000 0.112
#> GSM97865 1 0.0336 0.918 0.992 0.000 0.000 0.008
#> GSM97867 3 0.0000 0.963 0.000 0.000 1.000 0.000
#> GSM97883 3 0.0000 0.963 0.000 0.000 1.000 0.000
#> GSM97897 4 0.0000 0.975 0.000 0.000 0.000 1.000
#> GSM97900 4 0.0000 0.975 0.000 0.000 0.000 1.000
#> GSM97904 1 0.2149 0.895 0.912 0.000 0.000 0.088
#> GSM97907 2 0.0336 0.995 0.008 0.992 0.000 0.000
#> GSM97925 3 0.0000 0.963 0.000 0.000 1.000 0.000
#> GSM97947 3 0.0000 0.963 0.000 0.000 1.000 0.000
cbind(get_classes(res, k = 5), get_membership(res, k = 5))
#> class entropy silhouette p1 p2 p3 p4 p5
#> GSM97800 2 0.1671 0.9171 0.000 0.924 0.000 0.000 0.076
#> GSM97803 2 0.1671 0.9171 0.000 0.924 0.000 0.000 0.076
#> GSM97804 2 0.1671 0.9171 0.000 0.924 0.000 0.000 0.076
#> GSM97805 2 0.1671 0.9171 0.000 0.924 0.000 0.000 0.076
#> GSM97807 2 0.0000 0.9326 0.000 1.000 0.000 0.000 0.000
#> GSM97809 2 0.0000 0.9326 0.000 1.000 0.000 0.000 0.000
#> GSM97811 2 0.0000 0.9326 0.000 1.000 0.000 0.000 0.000
#> GSM97812 2 0.0000 0.9326 0.000 1.000 0.000 0.000 0.000
#> GSM97816 5 0.6832 0.4844 0.420 0.052 0.092 0.000 0.436
#> GSM97817 2 0.0290 0.9320 0.000 0.992 0.000 0.000 0.008
#> GSM97820 2 0.0000 0.9326 0.000 1.000 0.000 0.000 0.000
#> GSM97825 2 0.0290 0.9320 0.000 0.992 0.000 0.000 0.008
#> GSM97827 2 0.0000 0.9326 0.000 1.000 0.000 0.000 0.000
#> GSM97828 1 0.5510 0.0143 0.648 0.000 0.144 0.000 0.208
#> GSM97833 2 0.0000 0.9326 0.000 1.000 0.000 0.000 0.000
#> GSM97834 2 0.0290 0.9320 0.000 0.992 0.000 0.000 0.008
#> GSM97840 2 0.0000 0.9326 0.000 1.000 0.000 0.000 0.000
#> GSM97846 2 0.0290 0.9320 0.000 0.992 0.000 0.000 0.008
#> GSM97848 2 0.0000 0.9326 0.000 1.000 0.000 0.000 0.000
#> GSM97849 2 0.0000 0.9326 0.000 1.000 0.000 0.000 0.000
#> GSM97850 2 0.0000 0.9326 0.000 1.000 0.000 0.000 0.000
#> GSM97853 2 0.0000 0.9326 0.000 1.000 0.000 0.000 0.000
#> GSM97855 2 0.0000 0.9326 0.000 1.000 0.000 0.000 0.000
#> GSM97878 1 0.1197 0.5829 0.952 0.000 0.000 0.000 0.048
#> GSM97913 1 0.3003 0.3751 0.812 0.000 0.000 0.000 0.188
#> GSM97932 4 0.0162 0.9222 0.000 0.000 0.000 0.996 0.004
#> GSM97939 3 0.4201 0.6232 0.000 0.000 0.592 0.000 0.408
#> GSM97951 2 0.0510 0.9240 0.000 0.984 0.000 0.000 0.016
#> GSM97957 3 0.1270 0.8076 0.000 0.000 0.948 0.000 0.052
#> GSM97972 5 0.6269 0.4760 0.408 0.000 0.148 0.000 0.444
#> GSM97793 3 0.0000 0.8099 0.000 0.000 1.000 0.000 0.000
#> GSM97795 2 0.4256 0.3187 0.000 0.564 0.000 0.000 0.436
#> GSM97802 3 0.4235 0.3227 0.008 0.000 0.656 0.000 0.336
#> GSM97810 3 0.5668 0.4727 0.000 0.080 0.504 0.000 0.416
#> GSM97815 3 0.4150 0.6410 0.000 0.000 0.612 0.000 0.388
#> GSM97837 1 0.2377 0.6589 0.872 0.000 0.000 0.000 0.128
#> GSM97843 3 0.0162 0.8110 0.000 0.000 0.996 0.000 0.004
#> GSM97890 3 0.2020 0.8113 0.000 0.000 0.900 0.000 0.100
#> GSM97899 4 0.1341 0.9207 0.000 0.000 0.000 0.944 0.056
#> GSM97910 1 0.1608 0.5612 0.928 0.000 0.000 0.000 0.072
#> GSM97916 1 0.0162 0.6156 0.996 0.000 0.000 0.000 0.004
#> GSM97920 3 0.1197 0.8091 0.000 0.000 0.952 0.000 0.048
#> GSM97921 1 0.0162 0.6142 0.996 0.000 0.000 0.000 0.004
#> GSM97927 1 0.5056 0.6596 0.596 0.000 0.000 0.044 0.360
#> GSM97937 1 0.3143 0.6801 0.796 0.000 0.000 0.000 0.204
#> GSM97941 2 0.1671 0.8706 0.000 0.924 0.000 0.000 0.076
#> GSM97943 1 0.2179 0.5199 0.888 0.000 0.000 0.000 0.112
#> GSM97958 1 0.4161 -0.2281 0.608 0.000 0.000 0.000 0.392
#> GSM97960 2 0.4150 0.3035 0.000 0.612 0.000 0.000 0.388
#> GSM97794 1 0.1410 0.5728 0.940 0.000 0.000 0.000 0.060
#> GSM97796 4 0.0162 0.9222 0.000 0.000 0.000 0.996 0.004
#> GSM97797 1 0.1410 0.5728 0.940 0.000 0.000 0.000 0.060
#> GSM97798 4 0.1341 0.9207 0.000 0.000 0.000 0.944 0.056
#> GSM97801 1 0.1341 0.5741 0.944 0.000 0.000 0.000 0.056
#> GSM97806 1 0.4355 0.6917 0.732 0.000 0.000 0.044 0.224
#> GSM97808 4 0.1341 0.9207 0.000 0.000 0.000 0.944 0.056
#> GSM97813 1 0.5684 0.5820 0.488 0.000 0.000 0.080 0.432
#> GSM97814 4 0.1341 0.9207 0.000 0.000 0.000 0.944 0.056
#> GSM97818 1 0.1410 0.5728 0.940 0.000 0.000 0.000 0.060
#> GSM97819 3 0.0290 0.8112 0.000 0.000 0.992 0.000 0.008
#> GSM97821 5 0.5814 0.4806 0.400 0.020 0.052 0.000 0.528
#> GSM97826 1 0.3895 0.6837 0.680 0.000 0.000 0.000 0.320
#> GSM97829 1 0.1671 0.6495 0.924 0.000 0.000 0.000 0.076
#> GSM97832 5 0.4648 -0.2051 0.000 0.464 0.012 0.000 0.524
#> GSM97836 1 0.5016 0.6648 0.608 0.000 0.000 0.044 0.348
#> GSM97839 4 0.0162 0.9222 0.000 0.000 0.000 0.996 0.004
#> GSM97844 2 0.1671 0.9171 0.000 0.924 0.000 0.000 0.076
#> GSM97847 1 0.3283 0.6724 0.832 0.000 0.000 0.028 0.140
#> GSM97851 4 0.0162 0.9222 0.000 0.000 0.000 0.996 0.004
#> GSM97852 1 0.4982 0.6782 0.692 0.000 0.000 0.088 0.220
#> GSM97856 4 0.1341 0.9207 0.000 0.000 0.000 0.944 0.056
#> GSM97858 2 0.1671 0.9171 0.000 0.924 0.000 0.000 0.076
#> GSM97859 1 0.5151 0.6424 0.560 0.000 0.000 0.044 0.396
#> GSM97861 1 0.5043 0.6616 0.600 0.000 0.000 0.044 0.356
#> GSM97863 4 0.0162 0.9222 0.000 0.000 0.000 0.996 0.004
#> GSM97869 1 0.3876 0.6773 0.684 0.000 0.000 0.000 0.316
#> GSM97870 1 0.4798 0.6455 0.580 0.000 0.024 0.000 0.396
#> GSM97871 4 0.1341 0.9207 0.000 0.000 0.000 0.944 0.056
#> GSM97877 1 0.3756 0.2221 0.744 0.008 0.000 0.000 0.248
#> GSM97879 1 0.4793 0.6859 0.684 0.000 0.000 0.056 0.260
#> GSM97882 1 0.5016 0.6648 0.608 0.000 0.000 0.044 0.348
#> GSM97885 1 0.3857 0.6853 0.688 0.000 0.000 0.000 0.312
#> GSM97886 4 0.0162 0.9228 0.000 0.000 0.000 0.996 0.004
#> GSM97887 4 0.1341 0.9207 0.000 0.000 0.000 0.944 0.056
#> GSM97888 4 0.5014 0.4767 0.040 0.000 0.000 0.592 0.368
#> GSM97889 4 0.5052 0.4616 0.036 0.000 0.000 0.552 0.412
#> GSM97891 1 0.4413 0.6920 0.724 0.000 0.000 0.044 0.232
#> GSM97892 2 0.1671 0.9171 0.000 0.924 0.000 0.000 0.076
#> GSM97893 4 0.0992 0.9049 0.024 0.000 0.000 0.968 0.008
#> GSM97894 4 0.0162 0.9222 0.000 0.000 0.000 0.996 0.004
#> GSM97895 4 0.0162 0.9222 0.000 0.000 0.000 0.996 0.004
#> GSM97896 4 0.3661 0.6966 0.000 0.000 0.000 0.724 0.276
#> GSM97898 4 0.0162 0.9222 0.000 0.000 0.000 0.996 0.004
#> GSM97903 1 0.2074 0.6628 0.896 0.000 0.000 0.000 0.104
#> GSM97905 5 0.7564 -0.3469 0.264 0.000 0.256 0.052 0.428
#> GSM97906 4 0.1341 0.9207 0.000 0.000 0.000 0.944 0.056
#> GSM97908 1 0.5523 0.4570 0.592 0.000 0.000 0.320 0.088
#> GSM97912 1 0.4810 0.6491 0.580 0.000 0.012 0.008 0.400
#> GSM97914 1 0.0162 0.6142 0.996 0.000 0.000 0.000 0.004
#> GSM97915 4 0.0162 0.9222 0.000 0.000 0.000 0.996 0.004
#> GSM97917 4 0.0162 0.9222 0.000 0.000 0.000 0.996 0.004
#> GSM97918 4 0.0162 0.9222 0.000 0.000 0.000 0.996 0.004
#> GSM97919 4 0.0162 0.9222 0.000 0.000 0.000 0.996 0.004
#> GSM97922 1 0.5638 0.5862 0.492 0.000 0.000 0.076 0.432
#> GSM97924 2 0.1671 0.9171 0.000 0.924 0.000 0.000 0.076
#> GSM97926 3 0.3039 0.7878 0.000 0.000 0.808 0.000 0.192
#> GSM97930 1 0.2605 0.6763 0.852 0.000 0.000 0.000 0.148
#> GSM97931 1 0.5895 -0.5539 0.460 0.000 0.100 0.000 0.440
#> GSM97935 1 0.5056 0.6596 0.596 0.000 0.000 0.044 0.360
#> GSM97936 4 0.0290 0.9227 0.000 0.000 0.000 0.992 0.008
#> GSM97938 4 0.5086 0.3746 0.304 0.000 0.000 0.636 0.060
#> GSM97940 4 0.1341 0.9207 0.000 0.000 0.000 0.944 0.056
#> GSM97942 3 0.0162 0.8103 0.000 0.000 0.996 0.000 0.004
#> GSM97945 4 0.1341 0.9207 0.000 0.000 0.000 0.944 0.056
#> GSM97946 2 0.0000 0.9326 0.000 1.000 0.000 0.000 0.000
#> GSM97948 3 0.3884 0.4203 0.004 0.000 0.708 0.000 0.288
#> GSM97950 4 0.0000 0.9226 0.000 0.000 0.000 1.000 0.000
#> GSM97952 4 0.1341 0.9207 0.000 0.000 0.000 0.944 0.056
#> GSM97953 1 0.4400 0.6770 0.744 0.000 0.000 0.060 0.196
#> GSM97954 1 0.4986 0.6808 0.688 0.000 0.000 0.084 0.228
#> GSM97955 4 0.0290 0.9227 0.000 0.000 0.000 0.992 0.008
#> GSM97959 1 0.1544 0.5649 0.932 0.000 0.000 0.000 0.068
#> GSM97961 4 0.0290 0.9227 0.000 0.000 0.000 0.992 0.008
#> GSM97963 4 0.1341 0.9207 0.000 0.000 0.000 0.944 0.056
#> GSM97965 4 0.1341 0.9207 0.000 0.000 0.000 0.944 0.056
#> GSM97966 4 0.1341 0.9207 0.000 0.000 0.000 0.944 0.056
#> GSM97967 2 0.0290 0.9320 0.000 0.992 0.000 0.000 0.008
#> GSM97968 2 0.0000 0.9326 0.000 1.000 0.000 0.000 0.000
#> GSM97969 1 0.6180 0.5508 0.460 0.000 0.000 0.136 0.404
#> GSM97971 1 0.5159 0.6401 0.556 0.000 0.000 0.044 0.400
#> GSM97799 3 0.3796 0.7344 0.000 0.000 0.700 0.000 0.300
#> GSM97823 2 0.0000 0.9326 0.000 1.000 0.000 0.000 0.000
#> GSM97824 3 0.3949 0.7118 0.000 0.000 0.668 0.000 0.332
#> GSM97830 3 0.0162 0.8110 0.000 0.000 0.996 0.000 0.004
#> GSM97835 3 0.4161 0.6364 0.000 0.000 0.608 0.000 0.392
#> GSM97838 2 0.1671 0.9171 0.000 0.924 0.000 0.000 0.076
#> GSM97841 2 0.1671 0.9171 0.000 0.924 0.000 0.000 0.076
#> GSM97842 3 0.3837 0.7285 0.000 0.000 0.692 0.000 0.308
#> GSM97854 2 0.1671 0.9171 0.000 0.924 0.000 0.000 0.076
#> GSM97857 3 0.4192 0.6235 0.000 0.000 0.596 0.000 0.404
#> GSM97860 3 0.0000 0.8099 0.000 0.000 1.000 0.000 0.000
#> GSM97862 3 0.2852 0.7968 0.000 0.000 0.828 0.000 0.172
#> GSM97864 2 0.1671 0.9171 0.000 0.924 0.000 0.000 0.076
#> GSM97866 3 0.2020 0.8132 0.000 0.000 0.900 0.000 0.100
#> GSM97868 3 0.3707 0.7444 0.000 0.000 0.716 0.000 0.284
#> GSM97872 1 0.4171 0.6573 0.604 0.000 0.000 0.000 0.396
#> GSM97873 3 0.3837 0.7285 0.000 0.000 0.692 0.000 0.308
#> GSM97874 3 0.0000 0.8099 0.000 0.000 1.000 0.000 0.000
#> GSM97875 3 0.0404 0.8120 0.000 0.000 0.988 0.000 0.012
#> GSM97876 3 0.0000 0.8099 0.000 0.000 1.000 0.000 0.000
#> GSM97880 3 0.0000 0.8099 0.000 0.000 1.000 0.000 0.000
#> GSM97881 3 0.3003 0.7907 0.000 0.000 0.812 0.000 0.188
#> GSM97884 3 0.3837 0.7285 0.000 0.000 0.692 0.000 0.308
#> GSM97901 3 0.2020 0.8132 0.000 0.000 0.900 0.000 0.100
#> GSM97902 1 0.2605 0.4516 0.852 0.000 0.000 0.000 0.148
#> GSM97909 2 0.4559 0.1551 0.008 0.512 0.000 0.000 0.480
#> GSM97911 3 0.3003 0.7907 0.000 0.000 0.812 0.000 0.188
#> GSM97923 3 0.0000 0.8099 0.000 0.000 1.000 0.000 0.000
#> GSM97928 1 0.4171 0.6573 0.604 0.000 0.000 0.000 0.396
#> GSM97929 2 0.1671 0.9171 0.000 0.924 0.000 0.000 0.076
#> GSM97933 3 0.0609 0.8052 0.000 0.000 0.980 0.000 0.020
#> GSM97934 3 0.0880 0.8044 0.000 0.000 0.968 0.000 0.032
#> GSM97944 3 0.3796 0.7344 0.000 0.000 0.700 0.000 0.300
#> GSM97949 2 0.0000 0.9326 0.000 1.000 0.000 0.000 0.000
#> GSM97956 3 0.3774 0.7383 0.000 0.000 0.704 0.000 0.296
#> GSM97962 3 0.1908 0.8126 0.000 0.000 0.908 0.000 0.092
#> GSM97964 3 0.3913 0.7196 0.000 0.000 0.676 0.000 0.324
#> GSM97970 3 0.3837 0.7285 0.000 0.000 0.692 0.000 0.308
#> GSM97822 1 0.5188 0.6295 0.540 0.000 0.000 0.044 0.416
#> GSM97831 3 0.1908 0.8137 0.000 0.000 0.908 0.000 0.092
#> GSM97845 1 0.5336 0.6707 0.628 0.000 0.000 0.084 0.288
#> GSM97865 1 0.0162 0.6142 0.996 0.000 0.000 0.000 0.004
#> GSM97867 3 0.0000 0.8099 0.000 0.000 1.000 0.000 0.000
#> GSM97883 3 0.0404 0.8042 0.000 0.000 0.988 0.000 0.012
#> GSM97897 4 0.4101 0.5785 0.000 0.000 0.000 0.628 0.372
#> GSM97900 4 0.1341 0.9207 0.000 0.000 0.000 0.944 0.056
#> GSM97904 1 0.5086 0.6448 0.564 0.000 0.000 0.040 0.396
#> GSM97907 2 0.1671 0.9171 0.000 0.924 0.000 0.000 0.076
#> GSM97925 3 0.0162 0.8103 0.000 0.000 0.996 0.000 0.004
#> GSM97947 3 0.0794 0.8020 0.000 0.000 0.972 0.000 0.028
cbind(get_classes(res, k = 6), get_membership(res, k = 6))
#> class entropy silhouette p1 p2 p3 p4 p5 p6
#> GSM97800 2 0.3219 0.90538 0.020 0.848 0.000 0.000 0.068 0.064
#> GSM97803 2 0.3219 0.90538 0.020 0.848 0.000 0.000 0.068 0.064
#> GSM97804 2 0.3219 0.90538 0.020 0.848 0.000 0.000 0.068 0.064
#> GSM97805 2 0.3219 0.90538 0.020 0.848 0.000 0.000 0.068 0.064
#> GSM97807 2 0.0146 0.93947 0.000 0.996 0.000 0.000 0.000 0.004
#> GSM97809 2 0.0146 0.93947 0.000 0.996 0.000 0.000 0.000 0.004
#> GSM97811 2 0.0146 0.93947 0.000 0.996 0.000 0.000 0.000 0.004
#> GSM97812 2 0.0000 0.94049 0.000 1.000 0.000 0.000 0.000 0.000
#> GSM97816 6 0.4273 0.39834 0.000 0.012 0.012 0.000 0.348 0.628
#> GSM97817 2 0.0000 0.94049 0.000 1.000 0.000 0.000 0.000 0.000
#> GSM97820 2 0.0000 0.94049 0.000 1.000 0.000 0.000 0.000 0.000
#> GSM97825 2 0.0000 0.94049 0.000 1.000 0.000 0.000 0.000 0.000
#> GSM97827 2 0.0000 0.94049 0.000 1.000 0.000 0.000 0.000 0.000
#> GSM97828 6 0.4968 0.59717 0.080 0.000 0.088 0.000 0.108 0.724
#> GSM97833 2 0.0000 0.94049 0.000 1.000 0.000 0.000 0.000 0.000
#> GSM97834 2 0.0000 0.94049 0.000 1.000 0.000 0.000 0.000 0.000
#> GSM97840 2 0.0146 0.93947 0.000 0.996 0.000 0.000 0.000 0.004
#> GSM97846 2 0.0000 0.94049 0.000 1.000 0.000 0.000 0.000 0.000
#> GSM97848 2 0.0000 0.94049 0.000 1.000 0.000 0.000 0.000 0.000
#> GSM97849 2 0.0000 0.94049 0.000 1.000 0.000 0.000 0.000 0.000
#> GSM97850 2 0.0000 0.94049 0.000 1.000 0.000 0.000 0.000 0.000
#> GSM97853 2 0.0000 0.94049 0.000 1.000 0.000 0.000 0.000 0.000
#> GSM97855 2 0.0146 0.93947 0.000 0.996 0.000 0.000 0.000 0.004
#> GSM97878 6 0.3713 0.64639 0.224 0.000 0.000 0.000 0.032 0.744
#> GSM97913 6 0.3354 0.68090 0.128 0.000 0.000 0.000 0.060 0.812
#> GSM97932 4 0.4198 0.79526 0.016 0.000 0.000 0.732 0.212 0.040
#> GSM97939 5 0.4736 0.56302 0.000 0.000 0.352 0.000 0.588 0.060
#> GSM97951 2 0.1594 0.89914 0.000 0.932 0.000 0.000 0.052 0.016
#> GSM97957 3 0.2190 0.73519 0.000 0.000 0.900 0.000 0.060 0.040
#> GSM97972 6 0.4237 0.34221 0.000 0.000 0.020 0.000 0.396 0.584
#> GSM97793 3 0.0000 0.77771 0.000 0.000 1.000 0.000 0.000 0.000
#> GSM97795 5 0.5049 0.06862 0.008 0.384 0.000 0.000 0.548 0.060
#> GSM97802 1 0.4889 -0.00281 0.504 0.000 0.436 0.000 0.060 0.000
#> GSM97810 5 0.5433 0.53708 0.000 0.044 0.284 0.000 0.608 0.064
#> GSM97815 5 0.4806 0.56923 0.000 0.000 0.380 0.000 0.560 0.060
#> GSM97837 1 0.5611 0.08595 0.484 0.000 0.000 0.000 0.152 0.364
#> GSM97843 3 0.0520 0.77749 0.000 0.000 0.984 0.000 0.008 0.008
#> GSM97890 3 0.3023 0.52257 0.000 0.000 0.768 0.000 0.232 0.000
#> GSM97899 4 0.0000 0.88182 0.000 0.000 0.000 1.000 0.000 0.000
#> GSM97910 6 0.3520 0.68402 0.188 0.000 0.000 0.000 0.036 0.776
#> GSM97916 6 0.3668 0.52903 0.328 0.000 0.000 0.000 0.004 0.668
#> GSM97920 3 0.2201 0.73793 0.000 0.000 0.900 0.000 0.052 0.048
#> GSM97921 6 0.4482 0.50788 0.324 0.000 0.000 0.000 0.048 0.628
#> GSM97927 1 0.2734 0.64833 0.864 0.000 0.000 0.024 0.008 0.104
#> GSM97937 1 0.5643 0.33003 0.536 0.000 0.000 0.000 0.216 0.248
#> GSM97941 2 0.2912 0.83045 0.000 0.852 0.000 0.000 0.076 0.072
#> GSM97943 6 0.3821 0.67579 0.148 0.000 0.000 0.000 0.080 0.772
#> GSM97958 6 0.4402 0.58287 0.060 0.000 0.000 0.000 0.268 0.672
#> GSM97960 5 0.4828 0.28398 0.000 0.368 0.000 0.000 0.568 0.064
#> GSM97794 6 0.3404 0.67129 0.224 0.000 0.000 0.000 0.016 0.760
#> GSM97796 4 0.2964 0.86597 0.004 0.000 0.000 0.848 0.108 0.040
#> GSM97797 6 0.3558 0.68057 0.212 0.000 0.000 0.000 0.028 0.760
#> GSM97798 4 0.0000 0.88182 0.000 0.000 0.000 1.000 0.000 0.000
#> GSM97801 6 0.3424 0.67462 0.204 0.000 0.000 0.000 0.024 0.772
#> GSM97806 1 0.4965 0.48800 0.644 0.000 0.000 0.024 0.056 0.276
#> GSM97808 4 0.0000 0.88182 0.000 0.000 0.000 1.000 0.000 0.000
#> GSM97813 1 0.1194 0.66335 0.956 0.000 0.000 0.032 0.004 0.008
#> GSM97814 4 0.0000 0.88182 0.000 0.000 0.000 1.000 0.000 0.000
#> GSM97818 6 0.2969 0.66470 0.224 0.000 0.000 0.000 0.000 0.776
#> GSM97819 3 0.1075 0.76563 0.000 0.000 0.952 0.000 0.048 0.000
#> GSM97821 6 0.4222 0.20024 0.008 0.004 0.000 0.000 0.472 0.516
#> GSM97826 1 0.4849 0.48119 0.664 0.000 0.000 0.000 0.148 0.188
#> GSM97829 6 0.5029 0.16086 0.444 0.000 0.000 0.000 0.072 0.484
#> GSM97832 5 0.4985 0.37866 0.000 0.240 0.004 0.000 0.644 0.112
#> GSM97836 1 0.2833 0.64779 0.860 0.000 0.000 0.024 0.012 0.104
#> GSM97839 4 0.2964 0.86597 0.004 0.000 0.000 0.848 0.108 0.040
#> GSM97844 2 0.3219 0.90538 0.020 0.848 0.000 0.000 0.068 0.064
#> GSM97847 1 0.5851 0.26521 0.476 0.000 0.000 0.000 0.220 0.304
#> GSM97851 4 0.3727 0.82217 0.004 0.000 0.000 0.768 0.188 0.040
#> GSM97852 1 0.6271 0.40311 0.516 0.000 0.000 0.032 0.220 0.232
#> GSM97856 4 0.0000 0.88182 0.000 0.000 0.000 1.000 0.000 0.000
#> GSM97858 2 0.3219 0.90538 0.020 0.848 0.000 0.000 0.068 0.064
#> GSM97859 1 0.0837 0.66759 0.972 0.000 0.000 0.020 0.004 0.004
#> GSM97861 1 0.2781 0.64823 0.860 0.000 0.000 0.024 0.008 0.108
#> GSM97863 4 0.2964 0.86597 0.004 0.000 0.000 0.848 0.108 0.040
#> GSM97869 1 0.2994 0.56956 0.788 0.000 0.000 0.000 0.004 0.208
#> GSM97870 1 0.0909 0.66084 0.968 0.000 0.020 0.000 0.000 0.012
#> GSM97871 4 0.0000 0.88182 0.000 0.000 0.000 1.000 0.000 0.000
#> GSM97877 6 0.3748 0.66151 0.108 0.000 0.000 0.000 0.108 0.784
#> GSM97879 1 0.5179 0.50106 0.648 0.000 0.000 0.048 0.052 0.252
#> GSM97882 1 0.2734 0.64833 0.864 0.000 0.000 0.024 0.008 0.104
#> GSM97885 1 0.3190 0.57615 0.772 0.000 0.000 0.000 0.008 0.220
#> GSM97886 4 0.1168 0.88126 0.000 0.000 0.000 0.956 0.028 0.016
#> GSM97887 4 0.0146 0.88063 0.000 0.000 0.000 0.996 0.004 0.000
#> GSM97888 1 0.5341 0.22465 0.600 0.000 0.000 0.304 0.060 0.036
#> GSM97889 1 0.4168 0.15532 0.584 0.000 0.000 0.400 0.016 0.000
#> GSM97891 1 0.4637 0.54311 0.692 0.000 0.000 0.024 0.048 0.236
#> GSM97892 2 0.3219 0.90538 0.020 0.848 0.000 0.000 0.068 0.064
#> GSM97893 4 0.4957 0.72963 0.048 0.000 0.000 0.668 0.244 0.040
#> GSM97894 4 0.2964 0.86597 0.004 0.000 0.000 0.848 0.108 0.040
#> GSM97895 4 0.4198 0.79526 0.016 0.000 0.000 0.732 0.212 0.040
#> GSM97896 4 0.4434 0.32496 0.412 0.000 0.000 0.564 0.012 0.012
#> GSM97898 4 0.2964 0.86597 0.004 0.000 0.000 0.848 0.108 0.040
#> GSM97903 6 0.4676 0.20183 0.428 0.000 0.000 0.000 0.044 0.528
#> GSM97905 1 0.4201 0.43984 0.708 0.000 0.252 0.028 0.008 0.004
#> GSM97906 4 0.0000 0.88182 0.000 0.000 0.000 1.000 0.000 0.000
#> GSM97908 1 0.7273 0.27363 0.404 0.000 0.000 0.120 0.252 0.224
#> GSM97912 1 0.0924 0.66546 0.972 0.000 0.008 0.008 0.004 0.008
#> GSM97914 6 0.4326 0.53977 0.300 0.000 0.000 0.000 0.044 0.656
#> GSM97915 4 0.2964 0.86597 0.004 0.000 0.000 0.848 0.108 0.040
#> GSM97917 4 0.4329 0.77801 0.016 0.000 0.000 0.712 0.232 0.040
#> GSM97918 4 0.2775 0.86798 0.000 0.000 0.000 0.856 0.104 0.040
#> GSM97919 4 0.3054 0.86276 0.004 0.000 0.000 0.840 0.116 0.040
#> GSM97922 1 0.1194 0.66335 0.956 0.000 0.000 0.032 0.004 0.008
#> GSM97924 2 0.3219 0.90538 0.020 0.848 0.000 0.000 0.068 0.064
#> GSM97926 3 0.3830 0.03981 0.000 0.000 0.620 0.000 0.376 0.004
#> GSM97930 1 0.5805 0.27028 0.488 0.000 0.000 0.000 0.212 0.300
#> GSM97931 6 0.3899 0.40954 0.000 0.000 0.008 0.000 0.364 0.628
#> GSM97935 1 0.2871 0.64189 0.852 0.000 0.000 0.024 0.008 0.116
#> GSM97936 4 0.2009 0.87702 0.000 0.000 0.000 0.908 0.068 0.024
#> GSM97938 4 0.7614 -0.09362 0.264 0.000 0.000 0.308 0.260 0.168
#> GSM97940 4 0.0000 0.88182 0.000 0.000 0.000 1.000 0.000 0.000
#> GSM97942 3 0.0260 0.77592 0.000 0.000 0.992 0.000 0.008 0.000
#> GSM97945 4 0.0000 0.88182 0.000 0.000 0.000 1.000 0.000 0.000
#> GSM97946 2 0.0146 0.93947 0.000 0.996 0.000 0.000 0.000 0.004
#> GSM97948 3 0.3969 0.31435 0.332 0.000 0.652 0.000 0.016 0.000
#> GSM97950 4 0.1341 0.88052 0.000 0.000 0.000 0.948 0.028 0.024
#> GSM97952 4 0.0000 0.88182 0.000 0.000 0.000 1.000 0.000 0.000
#> GSM97953 1 0.6208 0.35406 0.520 0.000 0.000 0.028 0.224 0.228
#> GSM97954 1 0.6234 0.40375 0.524 0.000 0.000 0.032 0.220 0.224
#> GSM97955 4 0.2775 0.86797 0.000 0.000 0.000 0.856 0.104 0.040
#> GSM97959 6 0.3345 0.68207 0.204 0.000 0.000 0.000 0.020 0.776
#> GSM97961 4 0.1003 0.88129 0.000 0.000 0.000 0.964 0.020 0.016
#> GSM97963 4 0.0000 0.88182 0.000 0.000 0.000 1.000 0.000 0.000
#> GSM97965 4 0.0000 0.88182 0.000 0.000 0.000 1.000 0.000 0.000
#> GSM97966 4 0.0000 0.88182 0.000 0.000 0.000 1.000 0.000 0.000
#> GSM97967 2 0.0000 0.94049 0.000 1.000 0.000 0.000 0.000 0.000
#> GSM97968 2 0.0291 0.93943 0.000 0.992 0.000 0.000 0.004 0.004
#> GSM97969 1 0.2095 0.65515 0.916 0.000 0.000 0.040 0.028 0.016
#> GSM97971 1 0.0837 0.66759 0.972 0.000 0.000 0.020 0.004 0.004
#> GSM97799 5 0.3866 0.50912 0.000 0.000 0.484 0.000 0.516 0.000
#> GSM97823 2 0.0146 0.93947 0.000 0.996 0.000 0.000 0.000 0.004
#> GSM97824 5 0.4385 0.51030 0.000 0.000 0.444 0.000 0.532 0.024
#> GSM97830 3 0.1074 0.77075 0.000 0.000 0.960 0.000 0.012 0.028
#> GSM97835 5 0.4593 0.57281 0.000 0.000 0.380 0.000 0.576 0.044
#> GSM97838 2 0.3219 0.90538 0.020 0.848 0.000 0.000 0.068 0.064
#> GSM97841 2 0.3219 0.90538 0.020 0.848 0.000 0.000 0.068 0.064
#> GSM97842 5 0.3862 0.52517 0.000 0.000 0.476 0.000 0.524 0.000
#> GSM97854 2 0.3219 0.90538 0.020 0.848 0.000 0.000 0.068 0.064
#> GSM97857 5 0.5179 0.53668 0.000 0.000 0.392 0.000 0.516 0.092
#> GSM97860 3 0.0000 0.77771 0.000 0.000 1.000 0.000 0.000 0.000
#> GSM97862 3 0.3835 0.32237 0.000 0.000 0.684 0.000 0.300 0.016
#> GSM97864 2 0.3219 0.90538 0.020 0.848 0.000 0.000 0.068 0.064
#> GSM97866 3 0.3404 0.53347 0.000 0.000 0.760 0.000 0.224 0.016
#> GSM97868 3 0.3838 -0.32958 0.000 0.000 0.552 0.000 0.448 0.000
#> GSM97872 1 0.1297 0.66053 0.948 0.000 0.000 0.000 0.012 0.040
#> GSM97873 5 0.3862 0.52517 0.000 0.000 0.476 0.000 0.524 0.000
#> GSM97874 3 0.0858 0.77223 0.000 0.000 0.968 0.000 0.004 0.028
#> GSM97875 3 0.1204 0.75954 0.000 0.000 0.944 0.000 0.056 0.000
#> GSM97876 3 0.0000 0.77771 0.000 0.000 1.000 0.000 0.000 0.000
#> GSM97880 3 0.0000 0.77771 0.000 0.000 1.000 0.000 0.000 0.000
#> GSM97881 3 0.3672 0.07898 0.000 0.000 0.632 0.000 0.368 0.000
#> GSM97884 5 0.3864 0.51855 0.000 0.000 0.480 0.000 0.520 0.000
#> GSM97901 3 0.3404 0.53347 0.000 0.000 0.760 0.000 0.224 0.016
#> GSM97902 6 0.3641 0.67900 0.140 0.000 0.000 0.000 0.072 0.788
#> GSM97909 5 0.6036 0.21273 0.008 0.288 0.000 0.000 0.484 0.220
#> GSM97911 3 0.3672 0.07898 0.000 0.000 0.632 0.000 0.368 0.000
#> GSM97923 3 0.0000 0.77771 0.000 0.000 1.000 0.000 0.000 0.000
#> GSM97928 1 0.1138 0.66251 0.960 0.000 0.000 0.004 0.012 0.024
#> GSM97929 2 0.3219 0.90538 0.020 0.848 0.000 0.000 0.068 0.064
#> GSM97933 3 0.0865 0.76114 0.000 0.000 0.964 0.000 0.036 0.000
#> GSM97934 3 0.2001 0.73931 0.000 0.000 0.912 0.000 0.048 0.040
#> GSM97944 5 0.3866 0.50912 0.000 0.000 0.484 0.000 0.516 0.000
#> GSM97949 2 0.0000 0.94049 0.000 1.000 0.000 0.000 0.000 0.000
#> GSM97956 5 0.3995 0.50539 0.000 0.000 0.480 0.000 0.516 0.004
#> GSM97962 3 0.2945 0.66292 0.000 0.000 0.824 0.000 0.156 0.020
#> GSM97964 5 0.3843 0.53097 0.000 0.000 0.452 0.000 0.548 0.000
#> GSM97970 5 0.3862 0.52517 0.000 0.000 0.476 0.000 0.524 0.000
#> GSM97822 1 0.2016 0.65957 0.920 0.000 0.000 0.024 0.016 0.040
#> GSM97831 3 0.3377 0.60127 0.000 0.000 0.784 0.000 0.188 0.028
#> GSM97845 1 0.5860 0.45297 0.588 0.000 0.000 0.032 0.216 0.164
#> GSM97865 6 0.4393 0.52166 0.316 0.000 0.000 0.000 0.044 0.640
#> GSM97867 3 0.0146 0.77642 0.000 0.000 0.996 0.000 0.004 0.000
#> GSM97883 3 0.1082 0.74487 0.040 0.000 0.956 0.000 0.004 0.000
#> GSM97897 4 0.4264 0.11425 0.488 0.000 0.000 0.496 0.016 0.000
#> GSM97900 4 0.0146 0.88063 0.000 0.000 0.000 0.996 0.004 0.000
#> GSM97904 1 0.0891 0.66910 0.968 0.000 0.000 0.024 0.008 0.000
#> GSM97907 2 0.3219 0.90538 0.020 0.848 0.000 0.000 0.068 0.064
#> GSM97925 3 0.0260 0.77592 0.000 0.000 0.992 0.000 0.008 0.000
#> GSM97947 3 0.1719 0.75333 0.016 0.000 0.924 0.000 0.060 0.000
Heatmaps for the consensus matrix. It visualizes the probability of two samples to be in a same group.
consensus_heatmap(res, k = 2)
consensus_heatmap(res, k = 3)
consensus_heatmap(res, k = 4)
consensus_heatmap(res, k = 5)
consensus_heatmap(res, k = 6)
Heatmaps for the membership of samples in all partitions to see how consistent they are:
membership_heatmap(res, k = 2)
membership_heatmap(res, k = 3)
membership_heatmap(res, k = 4)
membership_heatmap(res, k = 5)
membership_heatmap(res, k = 6)
As soon as we have had the classes for columns, we can look for signatures which are significantly different between classes which can be candidate marks for certain classes. Following are the heatmaps for signatures.
Signature heatmaps where rows are scaled:
get_signatures(res, k = 2)
get_signatures(res, k = 3)
get_signatures(res, k = 4)
get_signatures(res, k = 5)
get_signatures(res, k = 6)
Signature heatmaps where rows are not scaled:
get_signatures(res, k = 2, scale_rows = FALSE)
get_signatures(res, k = 3, scale_rows = FALSE)
get_signatures(res, k = 4, scale_rows = FALSE)
get_signatures(res, k = 5, scale_rows = FALSE)
get_signatures(res, k = 6, scale_rows = FALSE)
Compare the overlap of signatures from different k:
compare_signatures(res)
get_signature() returns a data frame invisibly. TO get the list of signatures, the function
call should be assigned to a variable explicitly. In following code, if plot argument is set
to FALSE, no heatmap is plotted while only the differential analysis is performed.
# code only for demonstration
tb = get_signature(res, k = ..., plot = FALSE)
An example of the output of tb is:
#> which_row fdr mean_1 mean_2 scaled_mean_1 scaled_mean_2 km
#> 1 38 0.042760348 8.373488 9.131774 -0.5533452 0.5164555 1
#> 2 40 0.018707592 7.106213 8.469186 -0.6173731 0.5762149 1
#> 3 55 0.019134737 10.221463 11.207825 -0.6159697 0.5749050 1
#> 4 59 0.006059896 5.921854 7.869574 -0.6899429 0.6439467 1
#> 5 60 0.018055526 8.928898 10.211722 -0.6204761 0.5791110 1
#> 6 98 0.009384629 15.714769 14.887706 0.6635654 -0.6193277 2
...
The columns in tb are:
which_row: row indices corresponding to the input matrix.fdr: FDR for the differential test. mean_x: The mean value in group x.scaled_mean_x: The mean value in group x after rows are scaled.km: Row groups if k-means clustering is applied to rows.UMAP plot which shows how samples are separated.
dimension_reduction(res, k = 2, method = "UMAP")
dimension_reduction(res, k = 3, method = "UMAP")
dimension_reduction(res, k = 4, method = "UMAP")
dimension_reduction(res, k = 5, method = "UMAP")
dimension_reduction(res, k = 6, method = "UMAP")
Following heatmap shows how subgroups are split when increasing k:
collect_classes(res)
Test correlation between subgroups and known annotations. If the known annotation is numeric, one-way ANOVA test is applied, and if the known annotation is discrete, chi-squared contingency table test is applied.
test_to_known_factors(res)
#> n disease.state(p) tissue(p) k
#> MAD:kmeans 179 2.39e-13 2.24e-15 2
#> MAD:kmeans 180 8.17e-27 9.10e-28 3
#> MAD:kmeans 172 1.98e-26 4.19e-27 4
#> MAD:kmeans 159 2.39e-28 1.74e-29 5
#> MAD:kmeans 146 3.96e-24 8.38e-24 6
If matrix rows can be associated to genes, consider to use functional_enrichment(res,
...) to perform function enrichment for the signature genes. See this vignette for more detailed explanations.
The object with results only for a single top-value method and a single partition method can be extracted as:
res = res_list["MAD", "skmeans"]
# you can also extract it by
# res = res_list["MAD:skmeans"]
A summary of res and all the functions that can be applied to it:
res
#> A 'ConsensusPartition' object with k = 2, 3, 4, 5, 6.
#> On a matrix with 51882 rows and 180 columns.
#> Top rows (1000, 2000, 3000, 4000, 5000) are extracted by 'MAD' method.
#> Subgroups are detected by 'skmeans' method.
#> Performed in total 1250 partitions by row resampling.
#> Best k for subgroups seems to be 4.
#>
#> Following methods can be applied to this 'ConsensusPartition' object:
#> [1] "cola_report" "collect_classes" "collect_plots"
#> [4] "collect_stats" "colnames" "compare_signatures"
#> [7] "consensus_heatmap" "dimension_reduction" "functional_enrichment"
#> [10] "get_anno_col" "get_anno" "get_classes"
#> [13] "get_consensus" "get_matrix" "get_membership"
#> [16] "get_param" "get_signatures" "get_stats"
#> [19] "is_best_k" "is_stable_k" "membership_heatmap"
#> [22] "ncol" "nrow" "plot_ecdf"
#> [25] "rownames" "select_partition_number" "show"
#> [28] "suggest_best_k" "test_to_known_factors"
collect_plots() function collects all the plots made from res for all k (number of partitions)
into one single page to provide an easy and fast comparison between different k.
collect_plots(res)
The plots are:
k and the heatmap of
predicted classes for each k.k.k.k.All the plots in panels can be made by individual functions and they are plotted later in this section.
select_partition_number() produces several plots showing different
statistics for choosing “optimized” k. There are following statistics:
k;k, the area increased is defined as \(A_k - A_{k-1}\).The detailed explanations of these statistics can be found in the cola vignette.
Generally speaking, lower PAC score, higher mean silhouette score or higher
concordance corresponds to better partition. Rand index and Jaccard index
measure how similar the current partition is compared to partition with k-1.
If they are too similar, we won't accept k is better than k-1.
select_partition_number(res)
The numeric values for all these statistics can be obtained by get_stats().
get_stats(res)
#> k 1-PAC mean_silhouette concordance area_increased Rand Jaccard
#> 2 2 0.988 0.967 0.986 0.4999 0.500 0.500
#> 3 3 1.000 0.981 0.992 0.2900 0.802 0.624
#> 4 4 1.000 0.982 0.992 0.1267 0.904 0.734
#> 5 5 0.839 0.729 0.880 0.0520 0.960 0.858
#> 6 6 0.806 0.692 0.818 0.0317 0.956 0.826
suggest_best_k() suggests the best \(k\) based on these statistics. The rules are as follows:
suggest_best_k(res)
#> [1] 4
#> attr(,"optional")
#> [1] 2 3
There is also optional best \(k\) = 2 3 that is worth to check.
Following shows the table of the partitions (You need to click the show/hide
code output link to see it). The membership matrix (columns with name p*)
is inferred by
clue::cl_consensus()
function with the SE method. Basically the value in the membership matrix
represents the probability to belong to a certain group. The finall class
label for an item is determined with the group with highest probability it
belongs to.
In get_classes() function, the entropy is calculated from the membership
matrix and the silhouette score is calculated from the consensus matrix.
cbind(get_classes(res, k = 2), get_membership(res, k = 2))
#> class entropy silhouette p1 p2
#> GSM97800 2 0.0000 0.983 0.000 1.000
#> GSM97803 2 0.0000 0.983 0.000 1.000
#> GSM97804 2 0.0000 0.983 0.000 1.000
#> GSM97805 2 0.0000 0.983 0.000 1.000
#> GSM97807 2 0.0000 0.983 0.000 1.000
#> GSM97809 2 0.0000 0.983 0.000 1.000
#> GSM97811 2 0.0000 0.983 0.000 1.000
#> GSM97812 2 0.0000 0.983 0.000 1.000
#> GSM97816 2 0.0000 0.983 0.000 1.000
#> GSM97817 2 0.0000 0.983 0.000 1.000
#> GSM97820 2 0.0000 0.983 0.000 1.000
#> GSM97825 2 0.0000 0.983 0.000 1.000
#> GSM97827 2 0.0000 0.983 0.000 1.000
#> GSM97828 2 0.0000 0.983 0.000 1.000
#> GSM97833 2 0.0000 0.983 0.000 1.000
#> GSM97834 2 0.0000 0.983 0.000 1.000
#> GSM97840 2 0.0000 0.983 0.000 1.000
#> GSM97846 2 0.0000 0.983 0.000 1.000
#> GSM97848 2 0.0000 0.983 0.000 1.000
#> GSM97849 2 0.0000 0.983 0.000 1.000
#> GSM97850 2 0.0000 0.983 0.000 1.000
#> GSM97853 2 0.0000 0.983 0.000 1.000
#> GSM97855 2 0.0000 0.983 0.000 1.000
#> GSM97878 1 0.0000 0.988 1.000 0.000
#> GSM97913 2 0.0000 0.983 0.000 1.000
#> GSM97932 1 0.0000 0.988 1.000 0.000
#> GSM97939 2 0.0000 0.983 0.000 1.000
#> GSM97951 2 0.0000 0.983 0.000 1.000
#> GSM97957 2 0.0000 0.983 0.000 1.000
#> GSM97972 2 0.0000 0.983 0.000 1.000
#> GSM97793 1 0.0376 0.985 0.996 0.004
#> GSM97795 2 0.0000 0.983 0.000 1.000
#> GSM97802 1 0.0000 0.988 1.000 0.000
#> GSM97810 2 0.0000 0.983 0.000 1.000
#> GSM97815 2 0.0000 0.983 0.000 1.000
#> GSM97837 1 0.0000 0.988 1.000 0.000
#> GSM97843 2 0.0000 0.983 0.000 1.000
#> GSM97890 2 0.0000 0.983 0.000 1.000
#> GSM97899 1 0.0000 0.988 1.000 0.000
#> GSM97910 1 0.0000 0.988 1.000 0.000
#> GSM97916 1 0.0000 0.988 1.000 0.000
#> GSM97920 2 0.0000 0.983 0.000 1.000
#> GSM97921 1 0.0000 0.988 1.000 0.000
#> GSM97927 1 0.0000 0.988 1.000 0.000
#> GSM97937 1 0.0000 0.988 1.000 0.000
#> GSM97941 2 0.0000 0.983 0.000 1.000
#> GSM97943 2 0.5737 0.837 0.136 0.864
#> GSM97958 2 0.0000 0.983 0.000 1.000
#> GSM97960 2 0.0000 0.983 0.000 1.000
#> GSM97794 1 0.4690 0.883 0.900 0.100
#> GSM97796 1 0.0000 0.988 1.000 0.000
#> GSM97797 1 0.8443 0.625 0.728 0.272
#> GSM97798 1 0.0000 0.988 1.000 0.000
#> GSM97801 1 0.0000 0.988 1.000 0.000
#> GSM97806 1 0.0000 0.988 1.000 0.000
#> GSM97808 1 0.0000 0.988 1.000 0.000
#> GSM97813 1 0.0000 0.988 1.000 0.000
#> GSM97814 1 0.0000 0.988 1.000 0.000
#> GSM97818 1 0.0000 0.988 1.000 0.000
#> GSM97819 1 0.0376 0.985 0.996 0.004
#> GSM97821 2 0.0000 0.983 0.000 1.000
#> GSM97826 1 0.0000 0.988 1.000 0.000
#> GSM97829 1 0.0000 0.988 1.000 0.000
#> GSM97832 2 0.0000 0.983 0.000 1.000
#> GSM97836 1 0.0000 0.988 1.000 0.000
#> GSM97839 1 0.0000 0.988 1.000 0.000
#> GSM97844 2 0.0000 0.983 0.000 1.000
#> GSM97847 1 0.0000 0.988 1.000 0.000
#> GSM97851 1 0.0000 0.988 1.000 0.000
#> GSM97852 1 0.0000 0.988 1.000 0.000
#> GSM97856 1 0.0000 0.988 1.000 0.000
#> GSM97858 2 0.0000 0.983 0.000 1.000
#> GSM97859 1 0.0000 0.988 1.000 0.000
#> GSM97861 1 0.0000 0.988 1.000 0.000
#> GSM97863 1 0.0000 0.988 1.000 0.000
#> GSM97869 1 0.0000 0.988 1.000 0.000
#> GSM97870 1 0.0000 0.988 1.000 0.000
#> GSM97871 1 0.0000 0.988 1.000 0.000
#> GSM97877 2 0.0000 0.983 0.000 1.000
#> GSM97879 1 0.0000 0.988 1.000 0.000
#> GSM97882 1 0.0000 0.988 1.000 0.000
#> GSM97885 1 0.0000 0.988 1.000 0.000
#> GSM97886 1 0.0000 0.988 1.000 0.000
#> GSM97887 1 0.0000 0.988 1.000 0.000
#> GSM97888 1 0.0000 0.988 1.000 0.000
#> GSM97889 1 0.0000 0.988 1.000 0.000
#> GSM97891 1 0.0000 0.988 1.000 0.000
#> GSM97892 2 0.0000 0.983 0.000 1.000
#> GSM97893 1 0.0000 0.988 1.000 0.000
#> GSM97894 1 0.0000 0.988 1.000 0.000
#> GSM97895 1 0.0000 0.988 1.000 0.000
#> GSM97896 1 0.0000 0.988 1.000 0.000
#> GSM97898 1 0.0000 0.988 1.000 0.000
#> GSM97903 1 0.0000 0.988 1.000 0.000
#> GSM97905 1 0.0000 0.988 1.000 0.000
#> GSM97906 1 0.0000 0.988 1.000 0.000
#> GSM97908 1 0.0000 0.988 1.000 0.000
#> GSM97912 1 0.0000 0.988 1.000 0.000
#> GSM97914 1 0.0000 0.988 1.000 0.000
#> GSM97915 1 0.0000 0.988 1.000 0.000
#> GSM97917 1 0.0000 0.988 1.000 0.000
#> GSM97918 1 0.0000 0.988 1.000 0.000
#> GSM97919 1 0.0000 0.988 1.000 0.000
#> GSM97922 1 0.0000 0.988 1.000 0.000
#> GSM97924 2 0.0000 0.983 0.000 1.000
#> GSM97926 2 0.9209 0.499 0.336 0.664
#> GSM97930 1 0.0000 0.988 1.000 0.000
#> GSM97931 2 0.0000 0.983 0.000 1.000
#> GSM97935 1 0.0000 0.988 1.000 0.000
#> GSM97936 1 0.0000 0.988 1.000 0.000
#> GSM97938 1 0.0000 0.988 1.000 0.000
#> GSM97940 1 0.0000 0.988 1.000 0.000
#> GSM97942 1 0.0000 0.988 1.000 0.000
#> GSM97945 1 0.0000 0.988 1.000 0.000
#> GSM97946 2 0.0000 0.983 0.000 1.000
#> GSM97948 1 0.0000 0.988 1.000 0.000
#> GSM97950 1 0.0000 0.988 1.000 0.000
#> GSM97952 1 0.0000 0.988 1.000 0.000
#> GSM97953 1 0.0000 0.988 1.000 0.000
#> GSM97954 1 0.0000 0.988 1.000 0.000
#> GSM97955 1 0.0000 0.988 1.000 0.000
#> GSM97959 2 0.4939 0.871 0.108 0.892
#> GSM97961 1 0.0000 0.988 1.000 0.000
#> GSM97963 1 0.0000 0.988 1.000 0.000
#> GSM97965 1 0.0000 0.988 1.000 0.000
#> GSM97966 1 0.0000 0.988 1.000 0.000
#> GSM97967 2 0.0000 0.983 0.000 1.000
#> GSM97968 2 0.0000 0.983 0.000 1.000
#> GSM97969 1 0.0000 0.988 1.000 0.000
#> GSM97971 1 0.0000 0.988 1.000 0.000
#> GSM97799 2 0.0000 0.983 0.000 1.000
#> GSM97823 2 0.0000 0.983 0.000 1.000
#> GSM97824 2 0.0000 0.983 0.000 1.000
#> GSM97830 2 0.1843 0.957 0.028 0.972
#> GSM97835 2 0.0000 0.983 0.000 1.000
#> GSM97838 2 0.0000 0.983 0.000 1.000
#> GSM97841 2 0.0000 0.983 0.000 1.000
#> GSM97842 2 0.0000 0.983 0.000 1.000
#> GSM97854 2 0.0000 0.983 0.000 1.000
#> GSM97857 2 0.0000 0.983 0.000 1.000
#> GSM97860 1 0.6247 0.812 0.844 0.156
#> GSM97862 2 0.0000 0.983 0.000 1.000
#> GSM97864 2 0.0000 0.983 0.000 1.000
#> GSM97866 2 0.0000 0.983 0.000 1.000
#> GSM97868 2 0.0000 0.983 0.000 1.000
#> GSM97872 1 0.0000 0.988 1.000 0.000
#> GSM97873 2 0.0000 0.983 0.000 1.000
#> GSM97874 1 0.8661 0.595 0.712 0.288
#> GSM97875 2 0.0000 0.983 0.000 1.000
#> GSM97876 2 0.9170 0.508 0.332 0.668
#> GSM97880 1 0.0000 0.988 1.000 0.000
#> GSM97881 2 0.0000 0.983 0.000 1.000
#> GSM97884 2 0.0000 0.983 0.000 1.000
#> GSM97901 2 0.0000 0.983 0.000 1.000
#> GSM97902 1 0.8555 0.612 0.720 0.280
#> GSM97909 2 0.0000 0.983 0.000 1.000
#> GSM97911 2 0.0000 0.983 0.000 1.000
#> GSM97923 1 0.0376 0.985 0.996 0.004
#> GSM97928 1 0.0000 0.988 1.000 0.000
#> GSM97929 2 0.0000 0.983 0.000 1.000
#> GSM97933 1 0.0000 0.988 1.000 0.000
#> GSM97934 2 0.9815 0.282 0.420 0.580
#> GSM97944 2 0.0000 0.983 0.000 1.000
#> GSM97949 2 0.0000 0.983 0.000 1.000
#> GSM97956 2 0.0000 0.983 0.000 1.000
#> GSM97962 2 0.0000 0.983 0.000 1.000
#> GSM97964 2 0.0000 0.983 0.000 1.000
#> GSM97970 2 0.0000 0.983 0.000 1.000
#> GSM97822 1 0.0000 0.988 1.000 0.000
#> GSM97831 2 0.0000 0.983 0.000 1.000
#> GSM97845 1 0.0000 0.988 1.000 0.000
#> GSM97865 1 0.0000 0.988 1.000 0.000
#> GSM97867 1 0.0000 0.988 1.000 0.000
#> GSM97883 1 0.0000 0.988 1.000 0.000
#> GSM97897 1 0.0000 0.988 1.000 0.000
#> GSM97900 1 0.0000 0.988 1.000 0.000
#> GSM97904 1 0.0000 0.988 1.000 0.000
#> GSM97907 2 0.0000 0.983 0.000 1.000
#> GSM97925 1 0.0000 0.988 1.000 0.000
#> GSM97947 1 0.0000 0.988 1.000 0.000
cbind(get_classes(res, k = 3), get_membership(res, k = 3))
#> class entropy silhouette p1 p2 p3
#> GSM97800 2 0.0000 0.9869 0.000 1.000 0.000
#> GSM97803 2 0.0000 0.9869 0.000 1.000 0.000
#> GSM97804 2 0.0000 0.9869 0.000 1.000 0.000
#> GSM97805 2 0.0000 0.9869 0.000 1.000 0.000
#> GSM97807 2 0.0000 0.9869 0.000 1.000 0.000
#> GSM97809 2 0.0000 0.9869 0.000 1.000 0.000
#> GSM97811 2 0.0000 0.9869 0.000 1.000 0.000
#> GSM97812 2 0.0000 0.9869 0.000 1.000 0.000
#> GSM97816 2 0.0000 0.9869 0.000 1.000 0.000
#> GSM97817 2 0.0000 0.9869 0.000 1.000 0.000
#> GSM97820 2 0.0000 0.9869 0.000 1.000 0.000
#> GSM97825 2 0.0000 0.9869 0.000 1.000 0.000
#> GSM97827 2 0.0000 0.9869 0.000 1.000 0.000
#> GSM97828 2 0.2711 0.8991 0.000 0.912 0.088
#> GSM97833 2 0.0000 0.9869 0.000 1.000 0.000
#> GSM97834 2 0.0000 0.9869 0.000 1.000 0.000
#> GSM97840 2 0.0000 0.9869 0.000 1.000 0.000
#> GSM97846 2 0.0000 0.9869 0.000 1.000 0.000
#> GSM97848 2 0.0000 0.9869 0.000 1.000 0.000
#> GSM97849 2 0.0000 0.9869 0.000 1.000 0.000
#> GSM97850 2 0.0000 0.9869 0.000 1.000 0.000
#> GSM97853 2 0.0000 0.9869 0.000 1.000 0.000
#> GSM97855 2 0.0000 0.9869 0.000 1.000 0.000
#> GSM97878 1 0.0000 0.9915 1.000 0.000 0.000
#> GSM97913 2 0.0000 0.9869 0.000 1.000 0.000
#> GSM97932 1 0.0000 0.9915 1.000 0.000 0.000
#> GSM97939 2 0.3038 0.8805 0.000 0.896 0.104
#> GSM97951 2 0.0000 0.9869 0.000 1.000 0.000
#> GSM97957 3 0.0000 0.9996 0.000 0.000 1.000
#> GSM97972 2 0.0000 0.9869 0.000 1.000 0.000
#> GSM97793 3 0.0000 0.9996 0.000 0.000 1.000
#> GSM97795 2 0.0000 0.9869 0.000 1.000 0.000
#> GSM97802 3 0.0000 0.9996 0.000 0.000 1.000
#> GSM97810 2 0.0000 0.9869 0.000 1.000 0.000
#> GSM97815 2 0.0000 0.9869 0.000 1.000 0.000
#> GSM97837 1 0.0000 0.9915 1.000 0.000 0.000
#> GSM97843 3 0.0000 0.9996 0.000 0.000 1.000
#> GSM97890 3 0.0000 0.9996 0.000 0.000 1.000
#> GSM97899 1 0.0000 0.9915 1.000 0.000 0.000
#> GSM97910 1 0.0000 0.9915 1.000 0.000 0.000
#> GSM97916 1 0.0000 0.9915 1.000 0.000 0.000
#> GSM97920 3 0.0000 0.9996 0.000 0.000 1.000
#> GSM97921 1 0.0000 0.9915 1.000 0.000 0.000
#> GSM97927 1 0.0000 0.9915 1.000 0.000 0.000
#> GSM97937 1 0.0000 0.9915 1.000 0.000 0.000
#> GSM97941 2 0.0000 0.9869 0.000 1.000 0.000
#> GSM97943 2 0.6470 0.7257 0.148 0.760 0.092
#> GSM97958 2 0.0000 0.9869 0.000 1.000 0.000
#> GSM97960 2 0.0000 0.9869 0.000 1.000 0.000
#> GSM97794 1 0.4062 0.7984 0.836 0.164 0.000
#> GSM97796 1 0.0000 0.9915 1.000 0.000 0.000
#> GSM97797 2 0.5058 0.6765 0.244 0.756 0.000
#> GSM97798 1 0.0000 0.9915 1.000 0.000 0.000
#> GSM97801 1 0.0000 0.9915 1.000 0.000 0.000
#> GSM97806 1 0.0000 0.9915 1.000 0.000 0.000
#> GSM97808 1 0.0000 0.9915 1.000 0.000 0.000
#> GSM97813 1 0.0000 0.9915 1.000 0.000 0.000
#> GSM97814 1 0.0000 0.9915 1.000 0.000 0.000
#> GSM97818 1 0.0000 0.9915 1.000 0.000 0.000
#> GSM97819 3 0.0000 0.9996 0.000 0.000 1.000
#> GSM97821 2 0.0000 0.9869 0.000 1.000 0.000
#> GSM97826 1 0.0000 0.9915 1.000 0.000 0.000
#> GSM97829 1 0.0000 0.9915 1.000 0.000 0.000
#> GSM97832 2 0.0000 0.9869 0.000 1.000 0.000
#> GSM97836 1 0.0000 0.9915 1.000 0.000 0.000
#> GSM97839 1 0.0000 0.9915 1.000 0.000 0.000
#> GSM97844 2 0.0000 0.9869 0.000 1.000 0.000
#> GSM97847 1 0.0000 0.9915 1.000 0.000 0.000
#> GSM97851 1 0.0000 0.9915 1.000 0.000 0.000
#> GSM97852 1 0.0000 0.9915 1.000 0.000 0.000
#> GSM97856 1 0.0000 0.9915 1.000 0.000 0.000
#> GSM97858 2 0.0000 0.9869 0.000 1.000 0.000
#> GSM97859 1 0.0000 0.9915 1.000 0.000 0.000
#> GSM97861 1 0.0000 0.9915 1.000 0.000 0.000
#> GSM97863 1 0.0000 0.9915 1.000 0.000 0.000
#> GSM97869 1 0.0000 0.9915 1.000 0.000 0.000
#> GSM97870 1 0.0000 0.9915 1.000 0.000 0.000
#> GSM97871 1 0.0000 0.9915 1.000 0.000 0.000
#> GSM97877 2 0.0000 0.9869 0.000 1.000 0.000
#> GSM97879 1 0.0000 0.9915 1.000 0.000 0.000
#> GSM97882 1 0.0000 0.9915 1.000 0.000 0.000
#> GSM97885 1 0.0000 0.9915 1.000 0.000 0.000
#> GSM97886 1 0.0000 0.9915 1.000 0.000 0.000
#> GSM97887 1 0.0000 0.9915 1.000 0.000 0.000
#> GSM97888 1 0.0000 0.9915 1.000 0.000 0.000
#> GSM97889 1 0.0000 0.9915 1.000 0.000 0.000
#> GSM97891 1 0.0000 0.9915 1.000 0.000 0.000
#> GSM97892 2 0.0000 0.9869 0.000 1.000 0.000
#> GSM97893 1 0.0000 0.9915 1.000 0.000 0.000
#> GSM97894 1 0.0000 0.9915 1.000 0.000 0.000
#> GSM97895 1 0.0000 0.9915 1.000 0.000 0.000
#> GSM97896 1 0.0000 0.9915 1.000 0.000 0.000
#> GSM97898 1 0.0000 0.9915 1.000 0.000 0.000
#> GSM97903 1 0.0000 0.9915 1.000 0.000 0.000
#> GSM97905 1 0.0000 0.9915 1.000 0.000 0.000
#> GSM97906 1 0.0000 0.9915 1.000 0.000 0.000
#> GSM97908 1 0.0000 0.9915 1.000 0.000 0.000
#> GSM97912 1 0.0000 0.9915 1.000 0.000 0.000
#> GSM97914 1 0.0000 0.9915 1.000 0.000 0.000
#> GSM97915 1 0.0000 0.9915 1.000 0.000 0.000
#> GSM97917 1 0.0000 0.9915 1.000 0.000 0.000
#> GSM97918 1 0.0000 0.9915 1.000 0.000 0.000
#> GSM97919 1 0.0000 0.9915 1.000 0.000 0.000
#> GSM97922 1 0.0000 0.9915 1.000 0.000 0.000
#> GSM97924 2 0.0000 0.9869 0.000 1.000 0.000
#> GSM97926 3 0.0000 0.9996 0.000 0.000 1.000
#> GSM97930 1 0.0000 0.9915 1.000 0.000 0.000
#> GSM97931 2 0.0000 0.9869 0.000 1.000 0.000
#> GSM97935 1 0.0000 0.9915 1.000 0.000 0.000
#> GSM97936 1 0.0000 0.9915 1.000 0.000 0.000
#> GSM97938 1 0.0000 0.9915 1.000 0.000 0.000
#> GSM97940 1 0.0000 0.9915 1.000 0.000 0.000
#> GSM97942 3 0.0000 0.9996 0.000 0.000 1.000
#> GSM97945 1 0.0000 0.9915 1.000 0.000 0.000
#> GSM97946 2 0.0000 0.9869 0.000 1.000 0.000
#> GSM97948 3 0.0000 0.9996 0.000 0.000 1.000
#> GSM97950 1 0.0000 0.9915 1.000 0.000 0.000
#> GSM97952 1 0.0000 0.9915 1.000 0.000 0.000
#> GSM97953 1 0.0000 0.9915 1.000 0.000 0.000
#> GSM97954 1 0.0000 0.9915 1.000 0.000 0.000
#> GSM97955 1 0.0000 0.9915 1.000 0.000 0.000
#> GSM97959 2 0.0000 0.9869 0.000 1.000 0.000
#> GSM97961 1 0.0000 0.9915 1.000 0.000 0.000
#> GSM97963 1 0.0000 0.9915 1.000 0.000 0.000
#> GSM97965 1 0.0000 0.9915 1.000 0.000 0.000
#> GSM97966 1 0.0000 0.9915 1.000 0.000 0.000
#> GSM97967 2 0.0000 0.9869 0.000 1.000 0.000
#> GSM97968 2 0.0000 0.9869 0.000 1.000 0.000
#> GSM97969 1 0.0000 0.9915 1.000 0.000 0.000
#> GSM97971 1 0.0000 0.9915 1.000 0.000 0.000
#> GSM97799 3 0.0000 0.9996 0.000 0.000 1.000
#> GSM97823 2 0.0000 0.9869 0.000 1.000 0.000
#> GSM97824 3 0.0000 0.9996 0.000 0.000 1.000
#> GSM97830 3 0.0000 0.9996 0.000 0.000 1.000
#> GSM97835 2 0.0592 0.9763 0.000 0.988 0.012
#> GSM97838 2 0.0000 0.9869 0.000 1.000 0.000
#> GSM97841 2 0.0000 0.9869 0.000 1.000 0.000
#> GSM97842 3 0.0747 0.9835 0.000 0.016 0.984
#> GSM97854 2 0.0000 0.9869 0.000 1.000 0.000
#> GSM97857 3 0.0000 0.9996 0.000 0.000 1.000
#> GSM97860 3 0.0000 0.9996 0.000 0.000 1.000
#> GSM97862 3 0.0000 0.9996 0.000 0.000 1.000
#> GSM97864 2 0.0000 0.9869 0.000 1.000 0.000
#> GSM97866 3 0.0000 0.9996 0.000 0.000 1.000
#> GSM97868 3 0.0000 0.9996 0.000 0.000 1.000
#> GSM97872 1 0.0000 0.9915 1.000 0.000 0.000
#> GSM97873 3 0.0000 0.9996 0.000 0.000 1.000
#> GSM97874 3 0.0000 0.9996 0.000 0.000 1.000
#> GSM97875 3 0.0000 0.9996 0.000 0.000 1.000
#> GSM97876 3 0.0000 0.9996 0.000 0.000 1.000
#> GSM97880 3 0.0000 0.9996 0.000 0.000 1.000
#> GSM97881 3 0.0000 0.9996 0.000 0.000 1.000
#> GSM97884 3 0.0000 0.9996 0.000 0.000 1.000
#> GSM97901 3 0.0000 0.9996 0.000 0.000 1.000
#> GSM97902 1 0.6307 0.0341 0.512 0.488 0.000
#> GSM97909 2 0.0000 0.9869 0.000 1.000 0.000
#> GSM97911 3 0.0000 0.9996 0.000 0.000 1.000
#> GSM97923 3 0.0000 0.9996 0.000 0.000 1.000
#> GSM97928 1 0.0000 0.9915 1.000 0.000 0.000
#> GSM97929 2 0.0000 0.9869 0.000 1.000 0.000
#> GSM97933 3 0.0000 0.9996 0.000 0.000 1.000
#> GSM97934 3 0.0000 0.9996 0.000 0.000 1.000
#> GSM97944 3 0.0000 0.9996 0.000 0.000 1.000
#> GSM97949 2 0.0000 0.9869 0.000 1.000 0.000
#> GSM97956 3 0.0000 0.9996 0.000 0.000 1.000
#> GSM97962 3 0.0000 0.9996 0.000 0.000 1.000
#> GSM97964 3 0.0000 0.9996 0.000 0.000 1.000
#> GSM97970 3 0.0000 0.9996 0.000 0.000 1.000
#> GSM97822 1 0.0000 0.9915 1.000 0.000 0.000
#> GSM97831 3 0.0000 0.9996 0.000 0.000 1.000
#> GSM97845 1 0.0000 0.9915 1.000 0.000 0.000
#> GSM97865 1 0.0000 0.9915 1.000 0.000 0.000
#> GSM97867 3 0.0000 0.9996 0.000 0.000 1.000
#> GSM97883 3 0.0000 0.9996 0.000 0.000 1.000
#> GSM97897 1 0.0000 0.9915 1.000 0.000 0.000
#> GSM97900 1 0.0000 0.9915 1.000 0.000 0.000
#> GSM97904 1 0.0000 0.9915 1.000 0.000 0.000
#> GSM97907 2 0.0000 0.9869 0.000 1.000 0.000
#> GSM97925 3 0.0000 0.9996 0.000 0.000 1.000
#> GSM97947 3 0.0000 0.9996 0.000 0.000 1.000
cbind(get_classes(res, k = 4), get_membership(res, k = 4))
#> class entropy silhouette p1 p2 p3 p4
#> GSM97800 2 0.0000 0.999 0.000 1.000 0.000 0.000
#> GSM97803 2 0.0000 0.999 0.000 1.000 0.000 0.000
#> GSM97804 2 0.0000 0.999 0.000 1.000 0.000 0.000
#> GSM97805 2 0.0000 0.999 0.000 1.000 0.000 0.000
#> GSM97807 2 0.0000 0.999 0.000 1.000 0.000 0.000
#> GSM97809 2 0.0000 0.999 0.000 1.000 0.000 0.000
#> GSM97811 2 0.0000 0.999 0.000 1.000 0.000 0.000
#> GSM97812 2 0.0000 0.999 0.000 1.000 0.000 0.000
#> GSM97816 2 0.0188 0.995 0.004 0.996 0.000 0.000
#> GSM97817 2 0.0000 0.999 0.000 1.000 0.000 0.000
#> GSM97820 2 0.0000 0.999 0.000 1.000 0.000 0.000
#> GSM97825 2 0.0000 0.999 0.000 1.000 0.000 0.000
#> GSM97827 2 0.0000 0.999 0.000 1.000 0.000 0.000
#> GSM97828 1 0.0000 0.951 1.000 0.000 0.000 0.000
#> GSM97833 2 0.0000 0.999 0.000 1.000 0.000 0.000
#> GSM97834 2 0.0000 0.999 0.000 1.000 0.000 0.000
#> GSM97840 2 0.0000 0.999 0.000 1.000 0.000 0.000
#> GSM97846 2 0.0000 0.999 0.000 1.000 0.000 0.000
#> GSM97848 2 0.0000 0.999 0.000 1.000 0.000 0.000
#> GSM97849 2 0.0000 0.999 0.000 1.000 0.000 0.000
#> GSM97850 2 0.0000 0.999 0.000 1.000 0.000 0.000
#> GSM97853 2 0.0000 0.999 0.000 1.000 0.000 0.000
#> GSM97855 2 0.0000 0.999 0.000 1.000 0.000 0.000
#> GSM97878 1 0.1557 0.909 0.944 0.000 0.000 0.056
#> GSM97913 1 0.4817 0.366 0.612 0.388 0.000 0.000
#> GSM97932 4 0.0000 0.998 0.000 0.000 0.000 1.000
#> GSM97939 2 0.1022 0.963 0.000 0.968 0.032 0.000
#> GSM97951 2 0.0000 0.999 0.000 1.000 0.000 0.000
#> GSM97957 3 0.0000 0.994 0.000 0.000 1.000 0.000
#> GSM97972 2 0.0000 0.999 0.000 1.000 0.000 0.000
#> GSM97793 3 0.0000 0.994 0.000 0.000 1.000 0.000
#> GSM97795 2 0.0000 0.999 0.000 1.000 0.000 0.000
#> GSM97802 3 0.3172 0.773 0.000 0.000 0.840 0.160
#> GSM97810 2 0.0000 0.999 0.000 1.000 0.000 0.000
#> GSM97815 2 0.0000 0.999 0.000 1.000 0.000 0.000
#> GSM97837 1 0.0000 0.951 1.000 0.000 0.000 0.000
#> GSM97843 3 0.0000 0.994 0.000 0.000 1.000 0.000
#> GSM97890 3 0.0000 0.994 0.000 0.000 1.000 0.000
#> GSM97899 4 0.0000 0.998 0.000 0.000 0.000 1.000
#> GSM97910 1 0.0000 0.951 1.000 0.000 0.000 0.000
#> GSM97916 1 0.0000 0.951 1.000 0.000 0.000 0.000
#> GSM97920 3 0.0000 0.994 0.000 0.000 1.000 0.000
#> GSM97921 1 0.0000 0.951 1.000 0.000 0.000 0.000
#> GSM97927 4 0.0000 0.998 0.000 0.000 0.000 1.000
#> GSM97937 1 0.4164 0.650 0.736 0.000 0.000 0.264
#> GSM97941 2 0.0000 0.999 0.000 1.000 0.000 0.000
#> GSM97943 1 0.0000 0.951 1.000 0.000 0.000 0.000
#> GSM97958 2 0.0469 0.988 0.012 0.988 0.000 0.000
#> GSM97960 2 0.0000 0.999 0.000 1.000 0.000 0.000
#> GSM97794 1 0.0000 0.951 1.000 0.000 0.000 0.000
#> GSM97796 4 0.0000 0.998 0.000 0.000 0.000 1.000
#> GSM97797 1 0.0000 0.951 1.000 0.000 0.000 0.000
#> GSM97798 4 0.0000 0.998 0.000 0.000 0.000 1.000
#> GSM97801 1 0.0000 0.951 1.000 0.000 0.000 0.000
#> GSM97806 4 0.0000 0.998 0.000 0.000 0.000 1.000
#> GSM97808 4 0.0000 0.998 0.000 0.000 0.000 1.000
#> GSM97813 4 0.0000 0.998 0.000 0.000 0.000 1.000
#> GSM97814 4 0.0000 0.998 0.000 0.000 0.000 1.000
#> GSM97818 1 0.0000 0.951 1.000 0.000 0.000 0.000
#> GSM97819 3 0.0000 0.994 0.000 0.000 1.000 0.000
#> GSM97821 2 0.0000 0.999 0.000 1.000 0.000 0.000
#> GSM97826 1 0.0188 0.949 0.996 0.000 0.000 0.004
#> GSM97829 1 0.0000 0.951 1.000 0.000 0.000 0.000
#> GSM97832 2 0.0000 0.999 0.000 1.000 0.000 0.000
#> GSM97836 4 0.0000 0.998 0.000 0.000 0.000 1.000
#> GSM97839 4 0.0000 0.998 0.000 0.000 0.000 1.000
#> GSM97844 2 0.0000 0.999 0.000 1.000 0.000 0.000
#> GSM97847 1 0.0817 0.935 0.976 0.000 0.000 0.024
#> GSM97851 4 0.0000 0.998 0.000 0.000 0.000 1.000
#> GSM97852 4 0.0000 0.998 0.000 0.000 0.000 1.000
#> GSM97856 4 0.0000 0.998 0.000 0.000 0.000 1.000
#> GSM97858 2 0.0000 0.999 0.000 1.000 0.000 0.000
#> GSM97859 4 0.0000 0.998 0.000 0.000 0.000 1.000
#> GSM97861 4 0.0000 0.998 0.000 0.000 0.000 1.000
#> GSM97863 4 0.0000 0.998 0.000 0.000 0.000 1.000
#> GSM97869 1 0.1557 0.909 0.944 0.000 0.000 0.056
#> GSM97870 4 0.0188 0.994 0.004 0.000 0.000 0.996
#> GSM97871 4 0.0000 0.998 0.000 0.000 0.000 1.000
#> GSM97877 2 0.0000 0.999 0.000 1.000 0.000 0.000
#> GSM97879 4 0.0000 0.998 0.000 0.000 0.000 1.000
#> GSM97882 4 0.0000 0.998 0.000 0.000 0.000 1.000
#> GSM97885 1 0.3610 0.754 0.800 0.000 0.000 0.200
#> GSM97886 4 0.0000 0.998 0.000 0.000 0.000 1.000
#> GSM97887 4 0.0000 0.998 0.000 0.000 0.000 1.000
#> GSM97888 4 0.0000 0.998 0.000 0.000 0.000 1.000
#> GSM97889 4 0.0000 0.998 0.000 0.000 0.000 1.000
#> GSM97891 4 0.0000 0.998 0.000 0.000 0.000 1.000
#> GSM97892 2 0.0000 0.999 0.000 1.000 0.000 0.000
#> GSM97893 4 0.0000 0.998 0.000 0.000 0.000 1.000
#> GSM97894 4 0.0000 0.998 0.000 0.000 0.000 1.000
#> GSM97895 4 0.0000 0.998 0.000 0.000 0.000 1.000
#> GSM97896 4 0.0000 0.998 0.000 0.000 0.000 1.000
#> GSM97898 4 0.0000 0.998 0.000 0.000 0.000 1.000
#> GSM97903 1 0.0188 0.949 0.996 0.000 0.000 0.004
#> GSM97905 4 0.0000 0.998 0.000 0.000 0.000 1.000
#> GSM97906 4 0.0000 0.998 0.000 0.000 0.000 1.000
#> GSM97908 4 0.0817 0.975 0.024 0.000 0.000 0.976
#> GSM97912 4 0.0000 0.998 0.000 0.000 0.000 1.000
#> GSM97914 1 0.0000 0.951 1.000 0.000 0.000 0.000
#> GSM97915 4 0.0000 0.998 0.000 0.000 0.000 1.000
#> GSM97917 4 0.0000 0.998 0.000 0.000 0.000 1.000
#> GSM97918 4 0.0000 0.998 0.000 0.000 0.000 1.000
#> GSM97919 4 0.0000 0.998 0.000 0.000 0.000 1.000
#> GSM97922 4 0.0000 0.998 0.000 0.000 0.000 1.000
#> GSM97924 2 0.0000 0.999 0.000 1.000 0.000 0.000
#> GSM97926 3 0.0000 0.994 0.000 0.000 1.000 0.000
#> GSM97930 1 0.0000 0.951 1.000 0.000 0.000 0.000
#> GSM97931 2 0.0000 0.999 0.000 1.000 0.000 0.000
#> GSM97935 4 0.0000 0.998 0.000 0.000 0.000 1.000
#> GSM97936 4 0.0000 0.998 0.000 0.000 0.000 1.000
#> GSM97938 4 0.0188 0.994 0.004 0.000 0.000 0.996
#> GSM97940 4 0.0000 0.998 0.000 0.000 0.000 1.000
#> GSM97942 3 0.0000 0.994 0.000 0.000 1.000 0.000
#> GSM97945 4 0.0000 0.998 0.000 0.000 0.000 1.000
#> GSM97946 2 0.0000 0.999 0.000 1.000 0.000 0.000
#> GSM97948 3 0.0000 0.994 0.000 0.000 1.000 0.000
#> GSM97950 4 0.0000 0.998 0.000 0.000 0.000 1.000
#> GSM97952 4 0.0000 0.998 0.000 0.000 0.000 1.000
#> GSM97953 4 0.1211 0.958 0.040 0.000 0.000 0.960
#> GSM97954 4 0.0188 0.994 0.004 0.000 0.000 0.996
#> GSM97955 4 0.0000 0.998 0.000 0.000 0.000 1.000
#> GSM97959 1 0.0000 0.951 1.000 0.000 0.000 0.000
#> GSM97961 4 0.0000 0.998 0.000 0.000 0.000 1.000
#> GSM97963 4 0.0000 0.998 0.000 0.000 0.000 1.000
#> GSM97965 4 0.0000 0.998 0.000 0.000 0.000 1.000
#> GSM97966 4 0.0000 0.998 0.000 0.000 0.000 1.000
#> GSM97967 2 0.0000 0.999 0.000 1.000 0.000 0.000
#> GSM97968 2 0.0000 0.999 0.000 1.000 0.000 0.000
#> GSM97969 4 0.0000 0.998 0.000 0.000 0.000 1.000
#> GSM97971 4 0.0000 0.998 0.000 0.000 0.000 1.000
#> GSM97799 3 0.0000 0.994 0.000 0.000 1.000 0.000
#> GSM97823 2 0.0000 0.999 0.000 1.000 0.000 0.000
#> GSM97824 3 0.0000 0.994 0.000 0.000 1.000 0.000
#> GSM97830 3 0.0000 0.994 0.000 0.000 1.000 0.000
#> GSM97835 2 0.0000 0.999 0.000 1.000 0.000 0.000
#> GSM97838 2 0.0000 0.999 0.000 1.000 0.000 0.000
#> GSM97841 2 0.0000 0.999 0.000 1.000 0.000 0.000
#> GSM97842 3 0.0817 0.966 0.000 0.024 0.976 0.000
#> GSM97854 2 0.0000 0.999 0.000 1.000 0.000 0.000
#> GSM97857 3 0.0000 0.994 0.000 0.000 1.000 0.000
#> GSM97860 3 0.0000 0.994 0.000 0.000 1.000 0.000
#> GSM97862 3 0.0000 0.994 0.000 0.000 1.000 0.000
#> GSM97864 2 0.0000 0.999 0.000 1.000 0.000 0.000
#> GSM97866 3 0.0000 0.994 0.000 0.000 1.000 0.000
#> GSM97868 3 0.0000 0.994 0.000 0.000 1.000 0.000
#> GSM97872 4 0.1792 0.926 0.068 0.000 0.000 0.932
#> GSM97873 3 0.0000 0.994 0.000 0.000 1.000 0.000
#> GSM97874 3 0.0000 0.994 0.000 0.000 1.000 0.000
#> GSM97875 3 0.0000 0.994 0.000 0.000 1.000 0.000
#> GSM97876 3 0.0000 0.994 0.000 0.000 1.000 0.000
#> GSM97880 3 0.0000 0.994 0.000 0.000 1.000 0.000
#> GSM97881 3 0.0000 0.994 0.000 0.000 1.000 0.000
#> GSM97884 3 0.0000 0.994 0.000 0.000 1.000 0.000
#> GSM97901 3 0.0000 0.994 0.000 0.000 1.000 0.000
#> GSM97902 1 0.0000 0.951 1.000 0.000 0.000 0.000
#> GSM97909 2 0.0000 0.999 0.000 1.000 0.000 0.000
#> GSM97911 3 0.0000 0.994 0.000 0.000 1.000 0.000
#> GSM97923 3 0.0000 0.994 0.000 0.000 1.000 0.000
#> GSM97928 4 0.0000 0.998 0.000 0.000 0.000 1.000
#> GSM97929 2 0.0000 0.999 0.000 1.000 0.000 0.000
#> GSM97933 3 0.0000 0.994 0.000 0.000 1.000 0.000
#> GSM97934 3 0.0000 0.994 0.000 0.000 1.000 0.000
#> GSM97944 3 0.0000 0.994 0.000 0.000 1.000 0.000
#> GSM97949 2 0.0000 0.999 0.000 1.000 0.000 0.000
#> GSM97956 3 0.0000 0.994 0.000 0.000 1.000 0.000
#> GSM97962 3 0.0000 0.994 0.000 0.000 1.000 0.000
#> GSM97964 3 0.0000 0.994 0.000 0.000 1.000 0.000
#> GSM97970 3 0.0000 0.994 0.000 0.000 1.000 0.000
#> GSM97822 4 0.0000 0.998 0.000 0.000 0.000 1.000
#> GSM97831 3 0.0000 0.994 0.000 0.000 1.000 0.000
#> GSM97845 4 0.0000 0.998 0.000 0.000 0.000 1.000
#> GSM97865 1 0.0000 0.951 1.000 0.000 0.000 0.000
#> GSM97867 3 0.0000 0.994 0.000 0.000 1.000 0.000
#> GSM97883 3 0.0000 0.994 0.000 0.000 1.000 0.000
#> GSM97897 4 0.0000 0.998 0.000 0.000 0.000 1.000
#> GSM97900 4 0.0000 0.998 0.000 0.000 0.000 1.000
#> GSM97904 4 0.0000 0.998 0.000 0.000 0.000 1.000
#> GSM97907 2 0.0000 0.999 0.000 1.000 0.000 0.000
#> GSM97925 3 0.0000 0.994 0.000 0.000 1.000 0.000
#> GSM97947 3 0.0000 0.994 0.000 0.000 1.000 0.000
cbind(get_classes(res, k = 5), get_membership(res, k = 5))
#> class entropy silhouette p1 p2 p3 p4 p5
#> GSM97800 2 0.0000 0.9732 0.000 1.000 0.000 0.000 0.000
#> GSM97803 2 0.0000 0.9732 0.000 1.000 0.000 0.000 0.000
#> GSM97804 2 0.0000 0.9732 0.000 1.000 0.000 0.000 0.000
#> GSM97805 2 0.0000 0.9732 0.000 1.000 0.000 0.000 0.000
#> GSM97807 2 0.0000 0.9732 0.000 1.000 0.000 0.000 0.000
#> GSM97809 2 0.0000 0.9732 0.000 1.000 0.000 0.000 0.000
#> GSM97811 2 0.0000 0.9732 0.000 1.000 0.000 0.000 0.000
#> GSM97812 2 0.0000 0.9732 0.000 1.000 0.000 0.000 0.000
#> GSM97816 2 0.4449 0.7544 0.112 0.776 0.008 0.000 0.104
#> GSM97817 2 0.0000 0.9732 0.000 1.000 0.000 0.000 0.000
#> GSM97820 2 0.0000 0.9732 0.000 1.000 0.000 0.000 0.000
#> GSM97825 2 0.0000 0.9732 0.000 1.000 0.000 0.000 0.000
#> GSM97827 2 0.0000 0.9732 0.000 1.000 0.000 0.000 0.000
#> GSM97828 1 0.2563 0.8174 0.872 0.000 0.008 0.000 0.120
#> GSM97833 2 0.0000 0.9732 0.000 1.000 0.000 0.000 0.000
#> GSM97834 2 0.0000 0.9732 0.000 1.000 0.000 0.000 0.000
#> GSM97840 2 0.0000 0.9732 0.000 1.000 0.000 0.000 0.000
#> GSM97846 2 0.0000 0.9732 0.000 1.000 0.000 0.000 0.000
#> GSM97848 2 0.0000 0.9732 0.000 1.000 0.000 0.000 0.000
#> GSM97849 2 0.0000 0.9732 0.000 1.000 0.000 0.000 0.000
#> GSM97850 2 0.0000 0.9732 0.000 1.000 0.000 0.000 0.000
#> GSM97853 2 0.0000 0.9732 0.000 1.000 0.000 0.000 0.000
#> GSM97855 2 0.0000 0.9732 0.000 1.000 0.000 0.000 0.000
#> GSM97878 1 0.4519 0.6815 0.720 0.000 0.000 0.228 0.052
#> GSM97913 2 0.5036 0.2488 0.404 0.560 0.000 0.000 0.036
#> GSM97932 4 0.0671 0.9020 0.004 0.000 0.000 0.980 0.016
#> GSM97939 3 0.5036 -0.0202 0.000 0.452 0.516 0.000 0.032
#> GSM97951 2 0.0000 0.9732 0.000 1.000 0.000 0.000 0.000
#> GSM97957 5 0.4283 0.2051 0.000 0.000 0.456 0.000 0.544
#> GSM97972 2 0.3617 0.8283 0.060 0.836 0.008 0.000 0.096
#> GSM97793 3 0.4305 -0.2092 0.000 0.000 0.512 0.000 0.488
#> GSM97795 2 0.0162 0.9704 0.000 0.996 0.004 0.000 0.000
#> GSM97802 5 0.4468 0.3231 0.000 0.000 0.240 0.044 0.716
#> GSM97810 2 0.1106 0.9467 0.000 0.964 0.024 0.000 0.012
#> GSM97815 2 0.3480 0.6805 0.000 0.752 0.248 0.000 0.000
#> GSM97837 1 0.0703 0.8616 0.976 0.000 0.000 0.000 0.024
#> GSM97843 3 0.4182 0.0195 0.000 0.000 0.600 0.000 0.400
#> GSM97890 3 0.0963 0.6232 0.000 0.000 0.964 0.000 0.036
#> GSM97899 4 0.0404 0.9056 0.000 0.000 0.000 0.988 0.012
#> GSM97910 1 0.1410 0.8520 0.940 0.000 0.000 0.000 0.060
#> GSM97916 1 0.2329 0.8324 0.876 0.000 0.000 0.000 0.124
#> GSM97920 5 0.4305 0.1840 0.000 0.000 0.488 0.000 0.512
#> GSM97921 1 0.1522 0.8593 0.944 0.000 0.000 0.012 0.044
#> GSM97927 4 0.3999 0.6696 0.000 0.000 0.000 0.656 0.344
#> GSM97937 1 0.4697 0.3748 0.592 0.000 0.000 0.388 0.020
#> GSM97941 2 0.0000 0.9732 0.000 1.000 0.000 0.000 0.000
#> GSM97943 1 0.2233 0.8293 0.892 0.000 0.004 0.000 0.104
#> GSM97958 2 0.3840 0.7912 0.116 0.808 0.000 0.000 0.076
#> GSM97960 2 0.0451 0.9651 0.000 0.988 0.008 0.000 0.004
#> GSM97794 1 0.0963 0.8582 0.964 0.000 0.000 0.000 0.036
#> GSM97796 4 0.0290 0.9048 0.000 0.000 0.000 0.992 0.008
#> GSM97797 1 0.0963 0.8582 0.964 0.000 0.000 0.000 0.036
#> GSM97798 4 0.0510 0.9058 0.000 0.000 0.000 0.984 0.016
#> GSM97801 1 0.0510 0.8600 0.984 0.000 0.000 0.000 0.016
#> GSM97806 4 0.1018 0.9019 0.016 0.000 0.000 0.968 0.016
#> GSM97808 4 0.0510 0.9058 0.000 0.000 0.000 0.984 0.016
#> GSM97813 4 0.4030 0.6598 0.000 0.000 0.000 0.648 0.352
#> GSM97814 4 0.0510 0.9058 0.000 0.000 0.000 0.984 0.016
#> GSM97818 1 0.0880 0.8586 0.968 0.000 0.000 0.000 0.032
#> GSM97819 3 0.3932 0.2009 0.000 0.000 0.672 0.000 0.328
#> GSM97821 2 0.0000 0.9732 0.000 1.000 0.000 0.000 0.000
#> GSM97826 1 0.3267 0.8173 0.844 0.000 0.000 0.044 0.112
#> GSM97829 1 0.0898 0.8625 0.972 0.000 0.000 0.008 0.020
#> GSM97832 2 0.0000 0.9732 0.000 1.000 0.000 0.000 0.000
#> GSM97836 4 0.3366 0.7791 0.000 0.000 0.000 0.768 0.232
#> GSM97839 4 0.0290 0.9048 0.000 0.000 0.000 0.992 0.008
#> GSM97844 2 0.0000 0.9732 0.000 1.000 0.000 0.000 0.000
#> GSM97847 1 0.4354 0.6599 0.712 0.000 0.000 0.256 0.032
#> GSM97851 4 0.0671 0.9020 0.004 0.000 0.000 0.980 0.016
#> GSM97852 4 0.1648 0.8822 0.040 0.000 0.000 0.940 0.020
#> GSM97856 4 0.0404 0.9056 0.000 0.000 0.000 0.988 0.012
#> GSM97858 2 0.0000 0.9732 0.000 1.000 0.000 0.000 0.000
#> GSM97859 4 0.4045 0.6578 0.000 0.000 0.000 0.644 0.356
#> GSM97861 4 0.0963 0.9019 0.000 0.000 0.000 0.964 0.036
#> GSM97863 4 0.0290 0.9048 0.000 0.000 0.000 0.992 0.008
#> GSM97869 1 0.5131 0.5756 0.588 0.000 0.000 0.048 0.364
#> GSM97870 5 0.4524 0.0412 0.020 0.000 0.000 0.336 0.644
#> GSM97871 4 0.0404 0.9056 0.000 0.000 0.000 0.988 0.012
#> GSM97877 2 0.1124 0.9421 0.004 0.960 0.000 0.000 0.036
#> GSM97879 4 0.0566 0.9057 0.004 0.000 0.000 0.984 0.012
#> GSM97882 4 0.3684 0.7373 0.000 0.000 0.000 0.720 0.280
#> GSM97885 1 0.5788 0.5675 0.580 0.000 0.000 0.120 0.300
#> GSM97886 4 0.0162 0.9059 0.000 0.000 0.000 0.996 0.004
#> GSM97887 4 0.0510 0.9058 0.000 0.000 0.000 0.984 0.016
#> GSM97888 4 0.3305 0.7840 0.000 0.000 0.000 0.776 0.224
#> GSM97889 4 0.3983 0.6736 0.000 0.000 0.000 0.660 0.340
#> GSM97891 4 0.0798 0.9042 0.008 0.000 0.000 0.976 0.016
#> GSM97892 2 0.0000 0.9732 0.000 1.000 0.000 0.000 0.000
#> GSM97893 4 0.0671 0.9020 0.004 0.000 0.000 0.980 0.016
#> GSM97894 4 0.0162 0.9055 0.000 0.000 0.000 0.996 0.004
#> GSM97895 4 0.0510 0.9030 0.000 0.000 0.000 0.984 0.016
#> GSM97896 4 0.3561 0.7549 0.000 0.000 0.000 0.740 0.260
#> GSM97898 4 0.0404 0.9041 0.000 0.000 0.000 0.988 0.012
#> GSM97903 1 0.2914 0.8293 0.872 0.000 0.000 0.076 0.052
#> GSM97905 5 0.3534 0.3025 0.000 0.000 0.000 0.256 0.744
#> GSM97906 4 0.0510 0.9058 0.000 0.000 0.000 0.984 0.016
#> GSM97908 4 0.2464 0.8335 0.096 0.000 0.000 0.888 0.016
#> GSM97912 4 0.4696 0.5190 0.016 0.000 0.000 0.556 0.428
#> GSM97914 1 0.0000 0.8606 1.000 0.000 0.000 0.000 0.000
#> GSM97915 4 0.0404 0.9055 0.000 0.000 0.000 0.988 0.012
#> GSM97917 4 0.0912 0.8992 0.012 0.000 0.000 0.972 0.016
#> GSM97918 4 0.0290 0.9048 0.000 0.000 0.000 0.992 0.008
#> GSM97919 4 0.0404 0.9041 0.000 0.000 0.000 0.988 0.012
#> GSM97922 4 0.4045 0.6578 0.000 0.000 0.000 0.644 0.356
#> GSM97924 2 0.0000 0.9732 0.000 1.000 0.000 0.000 0.000
#> GSM97926 3 0.0609 0.6297 0.000 0.000 0.980 0.000 0.020
#> GSM97930 1 0.3130 0.8182 0.856 0.000 0.000 0.096 0.048
#> GSM97931 2 0.0451 0.9651 0.000 0.988 0.004 0.000 0.008
#> GSM97935 4 0.2077 0.8787 0.008 0.000 0.000 0.908 0.084
#> GSM97936 4 0.0290 0.9057 0.000 0.000 0.000 0.992 0.008
#> GSM97938 4 0.1117 0.8961 0.020 0.000 0.000 0.964 0.016
#> GSM97940 4 0.0510 0.9058 0.000 0.000 0.000 0.984 0.016
#> GSM97942 3 0.4304 -0.2067 0.000 0.000 0.516 0.000 0.484
#> GSM97945 4 0.0510 0.9058 0.000 0.000 0.000 0.984 0.016
#> GSM97946 2 0.0000 0.9732 0.000 1.000 0.000 0.000 0.000
#> GSM97948 5 0.3160 0.3724 0.000 0.000 0.188 0.004 0.808
#> GSM97950 4 0.0000 0.9058 0.000 0.000 0.000 1.000 0.000
#> GSM97952 4 0.0510 0.9058 0.000 0.000 0.000 0.984 0.016
#> GSM97953 4 0.2046 0.8636 0.068 0.000 0.000 0.916 0.016
#> GSM97954 4 0.2208 0.8565 0.072 0.000 0.000 0.908 0.020
#> GSM97955 4 0.0162 0.9054 0.000 0.000 0.000 0.996 0.004
#> GSM97959 1 0.1124 0.8578 0.960 0.004 0.000 0.000 0.036
#> GSM97961 4 0.0000 0.9058 0.000 0.000 0.000 1.000 0.000
#> GSM97963 4 0.0510 0.9058 0.000 0.000 0.000 0.984 0.016
#> GSM97965 4 0.0404 0.9056 0.000 0.000 0.000 0.988 0.012
#> GSM97966 4 0.0510 0.9058 0.000 0.000 0.000 0.984 0.016
#> GSM97967 2 0.0000 0.9732 0.000 1.000 0.000 0.000 0.000
#> GSM97968 2 0.0000 0.9732 0.000 1.000 0.000 0.000 0.000
#> GSM97969 4 0.1410 0.8927 0.000 0.000 0.000 0.940 0.060
#> GSM97971 4 0.4196 0.6535 0.004 0.000 0.000 0.640 0.356
#> GSM97799 3 0.0162 0.6319 0.000 0.000 0.996 0.000 0.004
#> GSM97823 2 0.0000 0.9732 0.000 1.000 0.000 0.000 0.000
#> GSM97824 3 0.1270 0.6000 0.000 0.000 0.948 0.000 0.052
#> GSM97830 3 0.4307 -0.2615 0.000 0.000 0.500 0.000 0.500
#> GSM97835 3 0.4305 -0.1135 0.000 0.488 0.512 0.000 0.000
#> GSM97838 2 0.0000 0.9732 0.000 1.000 0.000 0.000 0.000
#> GSM97841 2 0.0000 0.9732 0.000 1.000 0.000 0.000 0.000
#> GSM97842 3 0.0162 0.6297 0.000 0.004 0.996 0.000 0.000
#> GSM97854 2 0.0000 0.9732 0.000 1.000 0.000 0.000 0.000
#> GSM97857 3 0.2020 0.5573 0.000 0.000 0.900 0.000 0.100
#> GSM97860 3 0.4305 -0.2092 0.000 0.000 0.512 0.000 0.488
#> GSM97862 3 0.0510 0.6314 0.000 0.000 0.984 0.000 0.016
#> GSM97864 2 0.0000 0.9732 0.000 1.000 0.000 0.000 0.000
#> GSM97866 3 0.0510 0.6314 0.000 0.000 0.984 0.000 0.016
#> GSM97868 3 0.0404 0.6323 0.000 0.000 0.988 0.000 0.012
#> GSM97872 4 0.4548 0.7396 0.052 0.000 0.000 0.716 0.232
#> GSM97873 3 0.0162 0.6319 0.000 0.000 0.996 0.000 0.004
#> GSM97874 5 0.4306 0.1616 0.000 0.000 0.492 0.000 0.508
#> GSM97875 3 0.2773 0.4977 0.000 0.000 0.836 0.000 0.164
#> GSM97876 3 0.4305 -0.2092 0.000 0.000 0.512 0.000 0.488
#> GSM97880 3 0.4305 -0.2092 0.000 0.000 0.512 0.000 0.488
#> GSM97881 3 0.0404 0.6314 0.000 0.000 0.988 0.000 0.012
#> GSM97884 3 0.0162 0.6319 0.000 0.000 0.996 0.000 0.004
#> GSM97901 3 0.0510 0.6314 0.000 0.000 0.984 0.000 0.016
#> GSM97902 1 0.2179 0.8365 0.896 0.000 0.000 0.004 0.100
#> GSM97909 2 0.0000 0.9732 0.000 1.000 0.000 0.000 0.000
#> GSM97911 3 0.0404 0.6314 0.000 0.000 0.988 0.000 0.012
#> GSM97923 3 0.4305 -0.2092 0.000 0.000 0.512 0.000 0.488
#> GSM97928 4 0.2813 0.8338 0.000 0.000 0.000 0.832 0.168
#> GSM97929 2 0.0000 0.9732 0.000 1.000 0.000 0.000 0.000
#> GSM97933 5 0.4297 0.1900 0.000 0.000 0.472 0.000 0.528
#> GSM97934 5 0.4291 0.2128 0.000 0.000 0.464 0.000 0.536
#> GSM97944 3 0.0162 0.6319 0.000 0.000 0.996 0.000 0.004
#> GSM97949 2 0.0000 0.9732 0.000 1.000 0.000 0.000 0.000
#> GSM97956 3 0.0404 0.6273 0.000 0.000 0.988 0.000 0.012
#> GSM97962 3 0.3274 0.4516 0.000 0.000 0.780 0.000 0.220
#> GSM97964 3 0.0510 0.6249 0.000 0.000 0.984 0.000 0.016
#> GSM97970 3 0.0000 0.6312 0.000 0.000 1.000 0.000 0.000
#> GSM97822 4 0.4030 0.6611 0.000 0.000 0.000 0.648 0.352
#> GSM97831 3 0.1478 0.6105 0.000 0.000 0.936 0.000 0.064
#> GSM97845 4 0.1399 0.8907 0.028 0.000 0.000 0.952 0.020
#> GSM97865 1 0.1522 0.8590 0.944 0.000 0.000 0.012 0.044
#> GSM97867 3 0.4305 -0.2092 0.000 0.000 0.512 0.000 0.488
#> GSM97883 5 0.4235 0.2700 0.000 0.000 0.424 0.000 0.576
#> GSM97897 4 0.3857 0.7047 0.000 0.000 0.000 0.688 0.312
#> GSM97900 4 0.0510 0.9058 0.000 0.000 0.000 0.984 0.016
#> GSM97904 4 0.2020 0.8700 0.000 0.000 0.000 0.900 0.100
#> GSM97907 2 0.0000 0.9732 0.000 1.000 0.000 0.000 0.000
#> GSM97925 3 0.4304 -0.2067 0.000 0.000 0.516 0.000 0.484
#> GSM97947 3 0.4171 0.0278 0.000 0.000 0.604 0.000 0.396
cbind(get_classes(res, k = 6), get_membership(res, k = 6))
#> class entropy silhouette p1 p2 p3 p4 p5 p6
#> GSM97800 2 0.0000 0.9392 0.000 1.000 0.000 0.000 0.000 0.000
#> GSM97803 2 0.0000 0.9392 0.000 1.000 0.000 0.000 0.000 0.000
#> GSM97804 2 0.0000 0.9392 0.000 1.000 0.000 0.000 0.000 0.000
#> GSM97805 2 0.0000 0.9392 0.000 1.000 0.000 0.000 0.000 0.000
#> GSM97807 2 0.0146 0.9379 0.000 0.996 0.000 0.000 0.004 0.000
#> GSM97809 2 0.0146 0.9379 0.000 0.996 0.000 0.000 0.004 0.000
#> GSM97811 2 0.0146 0.9379 0.000 0.996 0.000 0.000 0.004 0.000
#> GSM97812 2 0.0000 0.9392 0.000 1.000 0.000 0.000 0.000 0.000
#> GSM97816 2 0.7529 -0.1628 0.172 0.360 0.008 0.000 0.140 0.320
#> GSM97817 2 0.0000 0.9392 0.000 1.000 0.000 0.000 0.000 0.000
#> GSM97820 2 0.0000 0.9392 0.000 1.000 0.000 0.000 0.000 0.000
#> GSM97825 2 0.0000 0.9392 0.000 1.000 0.000 0.000 0.000 0.000
#> GSM97827 2 0.0000 0.9392 0.000 1.000 0.000 0.000 0.000 0.000
#> GSM97828 6 0.5387 0.5534 0.176 0.004 0.008 0.000 0.180 0.632
#> GSM97833 2 0.0000 0.9392 0.000 1.000 0.000 0.000 0.000 0.000
#> GSM97834 2 0.0000 0.9392 0.000 1.000 0.000 0.000 0.000 0.000
#> GSM97840 2 0.0146 0.9379 0.000 0.996 0.000 0.000 0.004 0.000
#> GSM97846 2 0.0000 0.9392 0.000 1.000 0.000 0.000 0.000 0.000
#> GSM97848 2 0.0000 0.9392 0.000 1.000 0.000 0.000 0.000 0.000
#> GSM97849 2 0.0000 0.9392 0.000 1.000 0.000 0.000 0.000 0.000
#> GSM97850 2 0.0000 0.9392 0.000 1.000 0.000 0.000 0.000 0.000
#> GSM97853 2 0.0000 0.9392 0.000 1.000 0.000 0.000 0.000 0.000
#> GSM97855 2 0.0146 0.9379 0.000 0.996 0.000 0.000 0.004 0.000
#> GSM97878 6 0.6838 0.5532 0.284 0.000 0.000 0.124 0.120 0.472
#> GSM97913 2 0.7314 -0.1928 0.176 0.392 0.000 0.000 0.144 0.288
#> GSM97932 4 0.2333 0.7741 0.040 0.000 0.000 0.896 0.004 0.060
#> GSM97939 3 0.4074 0.3784 0.004 0.324 0.656 0.000 0.016 0.000
#> GSM97951 2 0.0146 0.9379 0.000 0.996 0.000 0.000 0.004 0.000
#> GSM97957 5 0.5023 0.7023 0.044 0.000 0.296 0.000 0.628 0.032
#> GSM97972 2 0.6776 0.3895 0.144 0.564 0.016 0.000 0.128 0.148
#> GSM97793 5 0.3390 0.8105 0.000 0.000 0.296 0.000 0.704 0.000
#> GSM97795 2 0.0458 0.9286 0.000 0.984 0.016 0.000 0.000 0.000
#> GSM97802 1 0.6495 0.0480 0.480 0.000 0.116 0.076 0.328 0.000
#> GSM97810 2 0.1398 0.8924 0.000 0.940 0.052 0.000 0.008 0.000
#> GSM97815 2 0.3634 0.4561 0.000 0.644 0.356 0.000 0.000 0.000
#> GSM97837 6 0.2366 0.6749 0.056 0.000 0.000 0.020 0.024 0.900
#> GSM97843 5 0.3961 0.5991 0.004 0.000 0.440 0.000 0.556 0.000
#> GSM97890 3 0.2092 0.7204 0.000 0.000 0.876 0.000 0.124 0.000
#> GSM97899 4 0.0603 0.8214 0.016 0.000 0.000 0.980 0.004 0.000
#> GSM97910 6 0.3953 0.6312 0.132 0.000 0.000 0.000 0.104 0.764
#> GSM97916 6 0.5330 0.5862 0.396 0.000 0.000 0.000 0.108 0.496
#> GSM97920 5 0.5857 0.6651 0.056 0.000 0.280 0.000 0.576 0.088
#> GSM97921 6 0.3806 0.6822 0.160 0.000 0.000 0.020 0.036 0.784
#> GSM97927 4 0.4080 -0.2856 0.456 0.000 0.000 0.536 0.008 0.000
#> GSM97937 6 0.5503 0.0183 0.076 0.000 0.000 0.400 0.020 0.504
#> GSM97941 2 0.0146 0.9379 0.000 0.996 0.000 0.000 0.004 0.000
#> GSM97943 6 0.4974 0.5624 0.192 0.000 0.000 0.000 0.160 0.648
#> GSM97958 2 0.6270 0.4056 0.112 0.580 0.000 0.000 0.108 0.200
#> GSM97960 2 0.0547 0.9257 0.000 0.980 0.020 0.000 0.000 0.000
#> GSM97794 6 0.5190 0.6551 0.272 0.000 0.000 0.000 0.132 0.596
#> GSM97796 4 0.0777 0.8178 0.024 0.000 0.000 0.972 0.000 0.004
#> GSM97797 6 0.5089 0.6609 0.244 0.000 0.000 0.000 0.136 0.620
#> GSM97798 4 0.0891 0.8190 0.024 0.000 0.000 0.968 0.008 0.000
#> GSM97801 6 0.2563 0.6831 0.052 0.000 0.000 0.000 0.072 0.876
#> GSM97806 4 0.2581 0.7205 0.128 0.000 0.000 0.856 0.000 0.016
#> GSM97808 4 0.0891 0.8190 0.024 0.000 0.000 0.968 0.008 0.000
#> GSM97813 1 0.3864 0.3579 0.520 0.000 0.000 0.480 0.000 0.000
#> GSM97814 4 0.0777 0.8202 0.024 0.000 0.000 0.972 0.004 0.000
#> GSM97818 6 0.4769 0.6697 0.264 0.000 0.000 0.000 0.092 0.644
#> GSM97819 3 0.3817 -0.2806 0.000 0.000 0.568 0.000 0.432 0.000
#> GSM97821 2 0.0260 0.9348 0.000 0.992 0.000 0.000 0.008 0.000
#> GSM97826 6 0.5368 0.4205 0.252 0.000 0.000 0.116 0.016 0.616
#> GSM97829 6 0.2401 0.6747 0.048 0.000 0.000 0.024 0.028 0.900
#> GSM97832 2 0.0146 0.9379 0.000 0.996 0.000 0.000 0.004 0.000
#> GSM97836 4 0.3421 0.4988 0.256 0.000 0.000 0.736 0.008 0.000
#> GSM97839 4 0.0777 0.8178 0.024 0.000 0.000 0.972 0.000 0.004
#> GSM97844 2 0.0000 0.9392 0.000 1.000 0.000 0.000 0.000 0.000
#> GSM97847 6 0.6363 0.2162 0.200 0.000 0.000 0.340 0.024 0.436
#> GSM97851 4 0.2066 0.7827 0.040 0.000 0.000 0.908 0.000 0.052
#> GSM97852 4 0.3225 0.7070 0.080 0.000 0.000 0.828 0.000 0.092
#> GSM97856 4 0.0603 0.8216 0.016 0.000 0.000 0.980 0.004 0.000
#> GSM97858 2 0.0000 0.9392 0.000 1.000 0.000 0.000 0.000 0.000
#> GSM97859 1 0.4242 0.4460 0.536 0.000 0.000 0.448 0.000 0.016
#> GSM97861 4 0.1918 0.7770 0.088 0.000 0.000 0.904 0.008 0.000
#> GSM97863 4 0.0777 0.8178 0.024 0.000 0.000 0.972 0.000 0.004
#> GSM97869 1 0.4346 -0.1689 0.712 0.000 0.000 0.020 0.036 0.232
#> GSM97870 1 0.6504 0.4711 0.540 0.000 0.000 0.200 0.180 0.080
#> GSM97871 4 0.0777 0.8202 0.024 0.000 0.000 0.972 0.004 0.000
#> GSM97877 2 0.5239 0.5746 0.160 0.680 0.000 0.000 0.120 0.040
#> GSM97879 4 0.0922 0.8227 0.024 0.000 0.000 0.968 0.004 0.004
#> GSM97882 4 0.3923 -0.0560 0.416 0.000 0.000 0.580 0.004 0.000
#> GSM97885 1 0.5964 -0.0993 0.548 0.000 0.000 0.116 0.040 0.296
#> GSM97886 4 0.0000 0.8221 0.000 0.000 0.000 1.000 0.000 0.000
#> GSM97887 4 0.0891 0.8190 0.024 0.000 0.000 0.968 0.008 0.000
#> GSM97888 4 0.3221 0.5141 0.264 0.000 0.000 0.736 0.000 0.000
#> GSM97889 4 0.3862 -0.0115 0.388 0.000 0.000 0.608 0.004 0.000
#> GSM97891 4 0.2784 0.7124 0.132 0.000 0.000 0.848 0.012 0.008
#> GSM97892 2 0.0000 0.9392 0.000 1.000 0.000 0.000 0.000 0.000
#> GSM97893 4 0.2272 0.7777 0.040 0.000 0.000 0.900 0.004 0.056
#> GSM97894 4 0.0508 0.8205 0.012 0.000 0.000 0.984 0.000 0.004
#> GSM97895 4 0.2074 0.7871 0.036 0.000 0.000 0.912 0.004 0.048
#> GSM97896 4 0.3601 0.3493 0.312 0.000 0.000 0.684 0.004 0.000
#> GSM97898 4 0.0777 0.8178 0.024 0.000 0.000 0.972 0.000 0.004
#> GSM97903 6 0.5759 0.6449 0.276 0.000 0.000 0.044 0.096 0.584
#> GSM97905 5 0.5649 -0.1950 0.396 0.000 0.000 0.152 0.452 0.000
#> GSM97906 4 0.0777 0.8202 0.024 0.000 0.000 0.972 0.004 0.000
#> GSM97908 4 0.3101 0.6859 0.032 0.000 0.000 0.820 0.000 0.148
#> GSM97912 1 0.5498 0.5159 0.524 0.000 0.000 0.384 0.032 0.060
#> GSM97914 6 0.3429 0.6948 0.144 0.000 0.000 0.016 0.028 0.812
#> GSM97915 4 0.0777 0.8178 0.024 0.000 0.000 0.972 0.000 0.004
#> GSM97917 4 0.2258 0.7745 0.044 0.000 0.000 0.896 0.000 0.060
#> GSM97918 4 0.0820 0.8182 0.016 0.000 0.000 0.972 0.000 0.012
#> GSM97919 4 0.0777 0.8178 0.024 0.000 0.000 0.972 0.000 0.004
#> GSM97922 1 0.3860 0.3995 0.528 0.000 0.000 0.472 0.000 0.000
#> GSM97924 2 0.0000 0.9392 0.000 1.000 0.000 0.000 0.000 0.000
#> GSM97926 3 0.1349 0.7904 0.004 0.000 0.940 0.000 0.056 0.000
#> GSM97930 6 0.5843 0.6053 0.264 0.000 0.000 0.104 0.048 0.584
#> GSM97931 2 0.3370 0.8103 0.060 0.848 0.012 0.000 0.064 0.016
#> GSM97935 4 0.3301 0.6118 0.216 0.000 0.000 0.772 0.008 0.004
#> GSM97936 4 0.0146 0.8222 0.004 0.000 0.000 0.996 0.000 0.000
#> GSM97938 4 0.3269 0.7108 0.052 0.000 0.000 0.832 0.008 0.108
#> GSM97940 4 0.0777 0.8202 0.024 0.000 0.000 0.972 0.004 0.000
#> GSM97942 5 0.3446 0.8068 0.000 0.000 0.308 0.000 0.692 0.000
#> GSM97945 4 0.0891 0.8190 0.024 0.000 0.000 0.968 0.008 0.000
#> GSM97946 2 0.0000 0.9392 0.000 1.000 0.000 0.000 0.000 0.000
#> GSM97948 5 0.4801 0.5389 0.280 0.000 0.088 0.000 0.632 0.000
#> GSM97950 4 0.0000 0.8221 0.000 0.000 0.000 1.000 0.000 0.000
#> GSM97952 4 0.0777 0.8202 0.024 0.000 0.000 0.972 0.004 0.000
#> GSM97953 4 0.4003 0.6243 0.056 0.000 0.000 0.772 0.016 0.156
#> GSM97954 4 0.3118 0.7164 0.072 0.000 0.000 0.836 0.000 0.092
#> GSM97955 4 0.0508 0.8209 0.012 0.000 0.000 0.984 0.000 0.004
#> GSM97959 6 0.5183 0.6607 0.264 0.004 0.000 0.000 0.120 0.612
#> GSM97961 4 0.0000 0.8221 0.000 0.000 0.000 1.000 0.000 0.000
#> GSM97963 4 0.0777 0.8202 0.024 0.000 0.000 0.972 0.004 0.000
#> GSM97965 4 0.0777 0.8202 0.024 0.000 0.000 0.972 0.004 0.000
#> GSM97966 4 0.0891 0.8190 0.024 0.000 0.000 0.968 0.008 0.000
#> GSM97967 2 0.0000 0.9392 0.000 1.000 0.000 0.000 0.000 0.000
#> GSM97968 2 0.0146 0.9379 0.000 0.996 0.000 0.000 0.004 0.000
#> GSM97969 4 0.2443 0.7739 0.096 0.000 0.000 0.880 0.004 0.020
#> GSM97971 1 0.4453 0.4536 0.528 0.000 0.000 0.444 0.000 0.028
#> GSM97799 3 0.0260 0.8109 0.000 0.000 0.992 0.000 0.008 0.000
#> GSM97823 2 0.0146 0.9379 0.000 0.996 0.000 0.000 0.004 0.000
#> GSM97824 3 0.2060 0.7675 0.016 0.000 0.900 0.000 0.084 0.000
#> GSM97830 5 0.4877 0.7507 0.032 0.000 0.324 0.000 0.616 0.028
#> GSM97835 3 0.3351 0.4238 0.000 0.288 0.712 0.000 0.000 0.000
#> GSM97838 2 0.0000 0.9392 0.000 1.000 0.000 0.000 0.000 0.000
#> GSM97841 2 0.0000 0.9392 0.000 1.000 0.000 0.000 0.000 0.000
#> GSM97842 3 0.0000 0.8106 0.000 0.000 1.000 0.000 0.000 0.000
#> GSM97854 2 0.0000 0.9392 0.000 1.000 0.000 0.000 0.000 0.000
#> GSM97857 3 0.3689 0.6718 0.072 0.000 0.800 0.000 0.120 0.008
#> GSM97860 5 0.3428 0.8087 0.000 0.000 0.304 0.000 0.696 0.000
#> GSM97862 3 0.1152 0.8048 0.004 0.000 0.952 0.000 0.044 0.000
#> GSM97864 2 0.0000 0.9392 0.000 1.000 0.000 0.000 0.000 0.000
#> GSM97866 3 0.1219 0.8032 0.004 0.000 0.948 0.000 0.048 0.000
#> GSM97868 3 0.1285 0.8024 0.004 0.000 0.944 0.000 0.052 0.000
#> GSM97872 4 0.5583 -0.0645 0.308 0.000 0.000 0.540 0.004 0.148
#> GSM97873 3 0.0260 0.8109 0.000 0.000 0.992 0.000 0.008 0.000
#> GSM97874 5 0.4605 0.7860 0.028 0.000 0.276 0.000 0.668 0.028
#> GSM97875 3 0.3266 0.3906 0.000 0.000 0.728 0.000 0.272 0.000
#> GSM97876 5 0.3446 0.8080 0.000 0.000 0.308 0.000 0.692 0.000
#> GSM97880 5 0.3330 0.8101 0.000 0.000 0.284 0.000 0.716 0.000
#> GSM97881 3 0.0632 0.8096 0.000 0.000 0.976 0.000 0.024 0.000
#> GSM97884 3 0.0146 0.8109 0.000 0.000 0.996 0.000 0.004 0.000
#> GSM97901 3 0.1588 0.7861 0.004 0.000 0.924 0.000 0.072 0.000
#> GSM97902 6 0.4788 0.5756 0.180 0.000 0.000 0.004 0.132 0.684
#> GSM97909 2 0.0000 0.9392 0.000 1.000 0.000 0.000 0.000 0.000
#> GSM97911 3 0.0632 0.8097 0.000 0.000 0.976 0.000 0.024 0.000
#> GSM97923 5 0.3446 0.8080 0.000 0.000 0.308 0.000 0.692 0.000
#> GSM97928 4 0.3731 0.5304 0.240 0.000 0.000 0.736 0.004 0.020
#> GSM97929 2 0.0000 0.9392 0.000 1.000 0.000 0.000 0.000 0.000
#> GSM97933 5 0.3360 0.8044 0.004 0.000 0.264 0.000 0.732 0.000
#> GSM97934 5 0.4719 0.7450 0.044 0.000 0.248 0.000 0.680 0.028
#> GSM97944 3 0.0260 0.8109 0.000 0.000 0.992 0.000 0.008 0.000
#> GSM97949 2 0.0000 0.9392 0.000 1.000 0.000 0.000 0.000 0.000
#> GSM97956 3 0.1082 0.8051 0.004 0.000 0.956 0.000 0.040 0.000
#> GSM97962 3 0.4026 0.1083 0.012 0.000 0.612 0.000 0.376 0.000
#> GSM97964 3 0.1010 0.8015 0.004 0.000 0.960 0.000 0.036 0.000
#> GSM97970 3 0.0000 0.8106 0.000 0.000 1.000 0.000 0.000 0.000
#> GSM97822 4 0.3868 -0.3893 0.496 0.000 0.000 0.504 0.000 0.000
#> GSM97831 3 0.3755 0.6048 0.032 0.000 0.780 0.000 0.172 0.016
#> GSM97845 4 0.2724 0.7448 0.052 0.000 0.000 0.864 0.000 0.084
#> GSM97865 6 0.4338 0.6793 0.200 0.000 0.000 0.024 0.044 0.732
#> GSM97867 5 0.3390 0.8105 0.000 0.000 0.296 0.000 0.704 0.000
#> GSM97883 5 0.4368 0.7563 0.088 0.000 0.204 0.000 0.708 0.000
#> GSM97897 4 0.3789 0.2281 0.332 0.000 0.000 0.660 0.008 0.000
#> GSM97900 4 0.0891 0.8190 0.024 0.000 0.000 0.968 0.008 0.000
#> GSM97904 4 0.2917 0.7228 0.136 0.000 0.000 0.840 0.008 0.016
#> GSM97907 2 0.0000 0.9392 0.000 1.000 0.000 0.000 0.000 0.000
#> GSM97925 5 0.3499 0.7988 0.000 0.000 0.320 0.000 0.680 0.000
#> GSM97947 5 0.4651 0.4687 0.040 0.000 0.476 0.000 0.484 0.000
Heatmaps for the consensus matrix. It visualizes the probability of two samples to be in a same group.
consensus_heatmap(res, k = 2)
consensus_heatmap(res, k = 3)
consensus_heatmap(res, k = 4)
consensus_heatmap(res, k = 5)
consensus_heatmap(res, k = 6)
Heatmaps for the membership of samples in all partitions to see how consistent they are:
membership_heatmap(res, k = 2)
membership_heatmap(res, k = 3)
membership_heatmap(res, k = 4)
membership_heatmap(res, k = 5)
membership_heatmap(res, k = 6)
As soon as we have had the classes for columns, we can look for signatures which are significantly different between classes which can be candidate marks for certain classes. Following are the heatmaps for signatures.
Signature heatmaps where rows are scaled:
get_signatures(res, k = 2)
get_signatures(res, k = 3)
get_signatures(res, k = 4)
get_signatures(res, k = 5)
get_signatures(res, k = 6)
Signature heatmaps where rows are not scaled:
get_signatures(res, k = 2, scale_rows = FALSE)
get_signatures(res, k = 3, scale_rows = FALSE)
get_signatures(res, k = 4, scale_rows = FALSE)
get_signatures(res, k = 5, scale_rows = FALSE)
get_signatures(res, k = 6, scale_rows = FALSE)
Compare the overlap of signatures from different k:
compare_signatures(res)
get_signature() returns a data frame invisibly. TO get the list of signatures, the function
call should be assigned to a variable explicitly. In following code, if plot argument is set
to FALSE, no heatmap is plotted while only the differential analysis is performed.
# code only for demonstration
tb = get_signature(res, k = ..., plot = FALSE)
An example of the output of tb is:
#> which_row fdr mean_1 mean_2 scaled_mean_1 scaled_mean_2 km
#> 1 38 0.042760348 8.373488 9.131774 -0.5533452 0.5164555 1
#> 2 40 0.018707592 7.106213 8.469186 -0.6173731 0.5762149 1
#> 3 55 0.019134737 10.221463 11.207825 -0.6159697 0.5749050 1
#> 4 59 0.006059896 5.921854 7.869574 -0.6899429 0.6439467 1
#> 5 60 0.018055526 8.928898 10.211722 -0.6204761 0.5791110 1
#> 6 98 0.009384629 15.714769 14.887706 0.6635654 -0.6193277 2
...
The columns in tb are:
which_row: row indices corresponding to the input matrix.fdr: FDR for the differential test. mean_x: The mean value in group x.scaled_mean_x: The mean value in group x after rows are scaled.km: Row groups if k-means clustering is applied to rows.UMAP plot which shows how samples are separated.
dimension_reduction(res, k = 2, method = "UMAP")
dimension_reduction(res, k = 3, method = "UMAP")
dimension_reduction(res, k = 4, method = "UMAP")
dimension_reduction(res, k = 5, method = "UMAP")
dimension_reduction(res, k = 6, method = "UMAP")
Following heatmap shows how subgroups are split when increasing k:
collect_classes(res)
Test correlation between subgroups and known annotations. If the known annotation is numeric, one-way ANOVA test is applied, and if the known annotation is discrete, chi-squared contingency table test is applied.
test_to_known_factors(res)
#> n disease.state(p) tissue(p) k
#> MAD:skmeans 178 4.21e-14 2.16e-16 2
#> MAD:skmeans 179 1.22e-26 1.16e-25 3
#> MAD:skmeans 179 3.18e-26 7.74e-25 4
#> MAD:skmeans 152 6.44e-22 1.09e-21 5
#> MAD:skmeans 149 4.10e-21 1.03e-20 6
If matrix rows can be associated to genes, consider to use functional_enrichment(res,
...) to perform function enrichment for the signature genes. See this vignette for more detailed explanations.
The object with results only for a single top-value method and a single partition method can be extracted as:
res = res_list["MAD", "pam"]
# you can also extract it by
# res = res_list["MAD:pam"]
A summary of res and all the functions that can be applied to it:
res
#> A 'ConsensusPartition' object with k = 2, 3, 4, 5, 6.
#> On a matrix with 51882 rows and 180 columns.
#> Top rows (1000, 2000, 3000, 4000, 5000) are extracted by 'MAD' method.
#> Subgroups are detected by 'pam' method.
#> Performed in total 1250 partitions by row resampling.
#> Best k for subgroups seems to be 4.
#>
#> Following methods can be applied to this 'ConsensusPartition' object:
#> [1] "cola_report" "collect_classes" "collect_plots"
#> [4] "collect_stats" "colnames" "compare_signatures"
#> [7] "consensus_heatmap" "dimension_reduction" "functional_enrichment"
#> [10] "get_anno_col" "get_anno" "get_classes"
#> [13] "get_consensus" "get_matrix" "get_membership"
#> [16] "get_param" "get_signatures" "get_stats"
#> [19] "is_best_k" "is_stable_k" "membership_heatmap"
#> [22] "ncol" "nrow" "plot_ecdf"
#> [25] "rownames" "select_partition_number" "show"
#> [28] "suggest_best_k" "test_to_known_factors"
collect_plots() function collects all the plots made from res for all k (number of partitions)
into one single page to provide an easy and fast comparison between different k.
collect_plots(res)
The plots are:
k and the heatmap of
predicted classes for each k.k.k.k.All the plots in panels can be made by individual functions and they are plotted later in this section.
select_partition_number() produces several plots showing different
statistics for choosing “optimized” k. There are following statistics:
k;k, the area increased is defined as \(A_k - A_{k-1}\).The detailed explanations of these statistics can be found in the cola vignette.
Generally speaking, lower PAC score, higher mean silhouette score or higher
concordance corresponds to better partition. Rand index and Jaccard index
measure how similar the current partition is compared to partition with k-1.
If they are too similar, we won't accept k is better than k-1.
select_partition_number(res)
The numeric values for all these statistics can be obtained by get_stats().
get_stats(res)
#> k 1-PAC mean_silhouette concordance area_increased Rand Jaccard
#> 2 2 1.000 0.970 0.985 0.4177 0.592 0.592
#> 3 3 0.772 0.803 0.917 0.5521 0.697 0.511
#> 4 4 0.905 0.880 0.951 0.1585 0.824 0.543
#> 5 5 0.813 0.765 0.855 0.0593 0.928 0.724
#> 6 6 0.851 0.743 0.881 0.0419 0.930 0.682
suggest_best_k() suggests the best \(k\) based on these statistics. The rules are as follows:
suggest_best_k(res)
#> [1] 4
#> attr(,"optional")
#> [1] 2
There is also optional best \(k\) = 2 that is worth to check.
Following shows the table of the partitions (You need to click the show/hide
code output link to see it). The membership matrix (columns with name p*)
is inferred by
clue::cl_consensus()
function with the SE method. Basically the value in the membership matrix
represents the probability to belong to a certain group. The finall class
label for an item is determined with the group with highest probability it
belongs to.
In get_classes() function, the entropy is calculated from the membership
matrix and the silhouette score is calculated from the consensus matrix.
cbind(get_classes(res, k = 2), get_membership(res, k = 2))
#> class entropy silhouette p1 p2
#> GSM97800 2 0.0000 0.997 0.000 1.000
#> GSM97803 2 0.0000 0.997 0.000 1.000
#> GSM97804 2 0.0000 0.997 0.000 1.000
#> GSM97805 2 0.0000 0.997 0.000 1.000
#> GSM97807 2 0.0000 0.997 0.000 1.000
#> GSM97809 2 0.0000 0.997 0.000 1.000
#> GSM97811 2 0.0000 0.997 0.000 1.000
#> GSM97812 2 0.0000 0.997 0.000 1.000
#> GSM97816 2 0.0000 0.997 0.000 1.000
#> GSM97817 2 0.0000 0.997 0.000 1.000
#> GSM97820 2 0.0000 0.997 0.000 1.000
#> GSM97825 2 0.0000 0.997 0.000 1.000
#> GSM97827 2 0.0000 0.997 0.000 1.000
#> GSM97828 2 0.0938 0.986 0.012 0.988
#> GSM97833 2 0.0000 0.997 0.000 1.000
#> GSM97834 2 0.0000 0.997 0.000 1.000
#> GSM97840 2 0.0000 0.997 0.000 1.000
#> GSM97846 2 0.0000 0.997 0.000 1.000
#> GSM97848 2 0.0000 0.997 0.000 1.000
#> GSM97849 2 0.0000 0.997 0.000 1.000
#> GSM97850 2 0.0000 0.997 0.000 1.000
#> GSM97853 2 0.0000 0.997 0.000 1.000
#> GSM97855 2 0.0000 0.997 0.000 1.000
#> GSM97878 1 0.0000 0.980 1.000 0.000
#> GSM97913 2 0.1414 0.978 0.020 0.980
#> GSM97932 1 0.0000 0.980 1.000 0.000
#> GSM97939 2 0.0000 0.997 0.000 1.000
#> GSM97951 2 0.0000 0.997 0.000 1.000
#> GSM97957 1 0.2043 0.961 0.968 0.032
#> GSM97972 2 0.2603 0.953 0.044 0.956
#> GSM97793 1 0.0000 0.980 1.000 0.000
#> GSM97795 2 0.0000 0.997 0.000 1.000
#> GSM97802 1 0.0000 0.980 1.000 0.000
#> GSM97810 2 0.0000 0.997 0.000 1.000
#> GSM97815 2 0.0000 0.997 0.000 1.000
#> GSM97837 1 0.0000 0.980 1.000 0.000
#> GSM97843 1 0.2948 0.947 0.948 0.052
#> GSM97890 1 0.2948 0.947 0.948 0.052
#> GSM97899 1 0.0000 0.980 1.000 0.000
#> GSM97910 1 0.0000 0.980 1.000 0.000
#> GSM97916 1 0.0000 0.980 1.000 0.000
#> GSM97920 1 0.2948 0.947 0.948 0.052
#> GSM97921 1 0.0000 0.980 1.000 0.000
#> GSM97927 1 0.0000 0.980 1.000 0.000
#> GSM97937 1 0.0000 0.980 1.000 0.000
#> GSM97941 2 0.0000 0.997 0.000 1.000
#> GSM97943 1 0.0672 0.976 0.992 0.008
#> GSM97958 1 0.5519 0.871 0.872 0.128
#> GSM97960 2 0.0000 0.997 0.000 1.000
#> GSM97794 1 0.0672 0.976 0.992 0.008
#> GSM97796 1 0.0000 0.980 1.000 0.000
#> GSM97797 1 0.2236 0.959 0.964 0.036
#> GSM97798 1 0.0000 0.980 1.000 0.000
#> GSM97801 1 0.0000 0.980 1.000 0.000
#> GSM97806 1 0.0000 0.980 1.000 0.000
#> GSM97808 1 0.0000 0.980 1.000 0.000
#> GSM97813 1 0.0000 0.980 1.000 0.000
#> GSM97814 1 0.0000 0.980 1.000 0.000
#> GSM97818 1 0.0000 0.980 1.000 0.000
#> GSM97819 1 0.0000 0.980 1.000 0.000
#> GSM97821 1 0.9909 0.250 0.556 0.444
#> GSM97826 1 0.0000 0.980 1.000 0.000
#> GSM97829 1 0.0000 0.980 1.000 0.000
#> GSM97832 2 0.0000 0.997 0.000 1.000
#> GSM97836 1 0.0000 0.980 1.000 0.000
#> GSM97839 1 0.0000 0.980 1.000 0.000
#> GSM97844 2 0.0000 0.997 0.000 1.000
#> GSM97847 1 0.0000 0.980 1.000 0.000
#> GSM97851 1 0.0000 0.980 1.000 0.000
#> GSM97852 1 0.0000 0.980 1.000 0.000
#> GSM97856 1 0.0000 0.980 1.000 0.000
#> GSM97858 2 0.0000 0.997 0.000 1.000
#> GSM97859 1 0.0000 0.980 1.000 0.000
#> GSM97861 1 0.0000 0.980 1.000 0.000
#> GSM97863 1 0.0000 0.980 1.000 0.000
#> GSM97869 1 0.0376 0.978 0.996 0.004
#> GSM97870 1 0.0000 0.980 1.000 0.000
#> GSM97871 1 0.0000 0.980 1.000 0.000
#> GSM97877 1 0.9170 0.543 0.668 0.332
#> GSM97879 1 0.0000 0.980 1.000 0.000
#> GSM97882 1 0.0000 0.980 1.000 0.000
#> GSM97885 1 0.0000 0.980 1.000 0.000
#> GSM97886 1 0.0000 0.980 1.000 0.000
#> GSM97887 1 0.0000 0.980 1.000 0.000
#> GSM97888 1 0.0000 0.980 1.000 0.000
#> GSM97889 1 0.0000 0.980 1.000 0.000
#> GSM97891 1 0.0000 0.980 1.000 0.000
#> GSM97892 2 0.0000 0.997 0.000 1.000
#> GSM97893 1 0.0000 0.980 1.000 0.000
#> GSM97894 1 0.0000 0.980 1.000 0.000
#> GSM97895 1 0.0000 0.980 1.000 0.000
#> GSM97896 1 0.0000 0.980 1.000 0.000
#> GSM97898 1 0.0000 0.980 1.000 0.000
#> GSM97903 1 0.0000 0.980 1.000 0.000
#> GSM97905 1 0.0000 0.980 1.000 0.000
#> GSM97906 1 0.0000 0.980 1.000 0.000
#> GSM97908 1 0.0000 0.980 1.000 0.000
#> GSM97912 1 0.0000 0.980 1.000 0.000
#> GSM97914 1 0.0000 0.980 1.000 0.000
#> GSM97915 1 0.0000 0.980 1.000 0.000
#> GSM97917 1 0.0000 0.980 1.000 0.000
#> GSM97918 1 0.0000 0.980 1.000 0.000
#> GSM97919 1 0.0000 0.980 1.000 0.000
#> GSM97922 1 0.0000 0.980 1.000 0.000
#> GSM97924 2 0.0000 0.997 0.000 1.000
#> GSM97926 1 0.0672 0.976 0.992 0.008
#> GSM97930 1 0.0000 0.980 1.000 0.000
#> GSM97931 1 0.2948 0.947 0.948 0.052
#> GSM97935 1 0.0000 0.980 1.000 0.000
#> GSM97936 1 0.0000 0.980 1.000 0.000
#> GSM97938 1 0.0000 0.980 1.000 0.000
#> GSM97940 1 0.0000 0.980 1.000 0.000
#> GSM97942 1 0.0000 0.980 1.000 0.000
#> GSM97945 1 0.0000 0.980 1.000 0.000
#> GSM97946 2 0.0000 0.997 0.000 1.000
#> GSM97948 1 0.0000 0.980 1.000 0.000
#> GSM97950 1 0.0000 0.980 1.000 0.000
#> GSM97952 1 0.0000 0.980 1.000 0.000
#> GSM97953 1 0.0000 0.980 1.000 0.000
#> GSM97954 1 0.0000 0.980 1.000 0.000
#> GSM97955 1 0.0000 0.980 1.000 0.000
#> GSM97959 1 0.4562 0.906 0.904 0.096
#> GSM97961 1 0.0000 0.980 1.000 0.000
#> GSM97963 1 0.0000 0.980 1.000 0.000
#> GSM97965 1 0.0000 0.980 1.000 0.000
#> GSM97966 1 0.0000 0.980 1.000 0.000
#> GSM97967 2 0.0000 0.997 0.000 1.000
#> GSM97968 2 0.0000 0.997 0.000 1.000
#> GSM97969 1 0.0000 0.980 1.000 0.000
#> GSM97971 1 0.0000 0.980 1.000 0.000
#> GSM97799 1 0.2948 0.947 0.948 0.052
#> GSM97823 2 0.0000 0.997 0.000 1.000
#> GSM97824 1 0.2948 0.947 0.948 0.052
#> GSM97830 1 0.0672 0.976 0.992 0.008
#> GSM97835 2 0.0000 0.997 0.000 1.000
#> GSM97838 2 0.0000 0.997 0.000 1.000
#> GSM97841 2 0.0000 0.997 0.000 1.000
#> GSM97842 1 0.5737 0.862 0.864 0.136
#> GSM97854 2 0.0000 0.997 0.000 1.000
#> GSM97857 1 0.5294 0.880 0.880 0.120
#> GSM97860 1 0.0000 0.980 1.000 0.000
#> GSM97862 1 0.2948 0.947 0.948 0.052
#> GSM97864 2 0.0000 0.997 0.000 1.000
#> GSM97866 1 0.2948 0.947 0.948 0.052
#> GSM97868 1 0.2948 0.947 0.948 0.052
#> GSM97872 1 0.0000 0.980 1.000 0.000
#> GSM97873 1 0.6438 0.827 0.836 0.164
#> GSM97874 1 0.0376 0.978 0.996 0.004
#> GSM97875 1 0.0938 0.974 0.988 0.012
#> GSM97876 1 0.0000 0.980 1.000 0.000
#> GSM97880 1 0.0000 0.980 1.000 0.000
#> GSM97881 1 0.2948 0.947 0.948 0.052
#> GSM97884 1 0.4431 0.911 0.908 0.092
#> GSM97901 1 0.2948 0.947 0.948 0.052
#> GSM97902 1 0.0376 0.978 0.996 0.004
#> GSM97909 2 0.0000 0.997 0.000 1.000
#> GSM97911 1 0.2948 0.947 0.948 0.052
#> GSM97923 1 0.0000 0.980 1.000 0.000
#> GSM97928 1 0.0000 0.980 1.000 0.000
#> GSM97929 2 0.0000 0.997 0.000 1.000
#> GSM97933 1 0.0672 0.976 0.992 0.008
#> GSM97934 1 0.0672 0.976 0.992 0.008
#> GSM97944 1 0.3733 0.930 0.928 0.072
#> GSM97949 2 0.0000 0.997 0.000 1.000
#> GSM97956 1 0.2948 0.947 0.948 0.052
#> GSM97962 1 0.2948 0.947 0.948 0.052
#> GSM97964 1 0.2948 0.947 0.948 0.052
#> GSM97970 2 0.4022 0.911 0.080 0.920
#> GSM97822 1 0.0000 0.980 1.000 0.000
#> GSM97831 1 0.2948 0.947 0.948 0.052
#> GSM97845 1 0.0000 0.980 1.000 0.000
#> GSM97865 1 0.0000 0.980 1.000 0.000
#> GSM97867 1 0.0000 0.980 1.000 0.000
#> GSM97883 1 0.0000 0.980 1.000 0.000
#> GSM97897 1 0.0000 0.980 1.000 0.000
#> GSM97900 1 0.0000 0.980 1.000 0.000
#> GSM97904 1 0.0000 0.980 1.000 0.000
#> GSM97907 2 0.0000 0.997 0.000 1.000
#> GSM97925 1 0.0000 0.980 1.000 0.000
#> GSM97947 1 0.0000 0.980 1.000 0.000
cbind(get_classes(res, k = 3), get_membership(res, k = 3))
#> class entropy silhouette p1 p2 p3
#> GSM97800 2 0.0000 0.9705 0.000 1.000 0.000
#> GSM97803 2 0.0000 0.9705 0.000 1.000 0.000
#> GSM97804 2 0.0000 0.9705 0.000 1.000 0.000
#> GSM97805 2 0.0000 0.9705 0.000 1.000 0.000
#> GSM97807 2 0.0000 0.9705 0.000 1.000 0.000
#> GSM97809 2 0.0000 0.9705 0.000 1.000 0.000
#> GSM97811 2 0.0000 0.9705 0.000 1.000 0.000
#> GSM97812 2 0.0000 0.9705 0.000 1.000 0.000
#> GSM97816 2 0.5785 0.5032 0.000 0.668 0.332
#> GSM97817 2 0.0000 0.9705 0.000 1.000 0.000
#> GSM97820 2 0.0000 0.9705 0.000 1.000 0.000
#> GSM97825 2 0.0000 0.9705 0.000 1.000 0.000
#> GSM97827 2 0.0000 0.9705 0.000 1.000 0.000
#> GSM97828 3 0.5760 0.4154 0.000 0.328 0.672
#> GSM97833 2 0.0000 0.9705 0.000 1.000 0.000
#> GSM97834 2 0.0000 0.9705 0.000 1.000 0.000
#> GSM97840 2 0.0000 0.9705 0.000 1.000 0.000
#> GSM97846 2 0.0000 0.9705 0.000 1.000 0.000
#> GSM97848 2 0.0000 0.9705 0.000 1.000 0.000
#> GSM97849 2 0.0000 0.9705 0.000 1.000 0.000
#> GSM97850 2 0.0000 0.9705 0.000 1.000 0.000
#> GSM97853 2 0.0000 0.9705 0.000 1.000 0.000
#> GSM97855 2 0.0000 0.9705 0.000 1.000 0.000
#> GSM97878 1 0.6286 0.3124 0.536 0.000 0.464
#> GSM97913 2 0.2772 0.8799 0.080 0.916 0.004
#> GSM97932 1 0.0000 0.8637 1.000 0.000 0.000
#> GSM97939 3 0.4399 0.6777 0.000 0.188 0.812
#> GSM97951 2 0.0000 0.9705 0.000 1.000 0.000
#> GSM97957 3 0.0000 0.8990 0.000 0.000 1.000
#> GSM97972 3 0.3116 0.7907 0.000 0.108 0.892
#> GSM97793 3 0.0592 0.8924 0.012 0.000 0.988
#> GSM97795 2 0.0892 0.9539 0.000 0.980 0.020
#> GSM97802 3 0.0747 0.8897 0.016 0.000 0.984
#> GSM97810 3 0.5678 0.4339 0.000 0.316 0.684
#> GSM97815 3 0.0000 0.8990 0.000 0.000 1.000
#> GSM97837 1 0.0237 0.8613 0.996 0.000 0.004
#> GSM97843 3 0.0000 0.8990 0.000 0.000 1.000
#> GSM97890 3 0.0000 0.8990 0.000 0.000 1.000
#> GSM97899 1 0.0000 0.8637 1.000 0.000 0.000
#> GSM97910 3 0.6307 -0.1747 0.488 0.000 0.512
#> GSM97916 1 0.6252 0.3707 0.556 0.000 0.444
#> GSM97920 3 0.0000 0.8990 0.000 0.000 1.000
#> GSM97921 1 0.5760 0.6195 0.672 0.000 0.328
#> GSM97927 1 0.5650 0.6419 0.688 0.000 0.312
#> GSM97937 1 0.0000 0.8637 1.000 0.000 0.000
#> GSM97941 2 0.0000 0.9705 0.000 1.000 0.000
#> GSM97943 3 0.0892 0.8857 0.020 0.000 0.980
#> GSM97958 3 0.0424 0.8951 0.008 0.000 0.992
#> GSM97960 2 0.6079 0.3825 0.000 0.612 0.388
#> GSM97794 3 0.6307 -0.1747 0.488 0.000 0.512
#> GSM97796 1 0.0000 0.8637 1.000 0.000 0.000
#> GSM97797 3 0.6309 -0.2029 0.496 0.000 0.504
#> GSM97798 1 0.0000 0.8637 1.000 0.000 0.000
#> GSM97801 1 0.5650 0.6419 0.688 0.000 0.312
#> GSM97806 1 0.5650 0.6419 0.688 0.000 0.312
#> GSM97808 1 0.0000 0.8637 1.000 0.000 0.000
#> GSM97813 1 0.5465 0.6662 0.712 0.000 0.288
#> GSM97814 1 0.0000 0.8637 1.000 0.000 0.000
#> GSM97818 1 0.5810 0.6064 0.664 0.000 0.336
#> GSM97819 3 0.0000 0.8990 0.000 0.000 1.000
#> GSM97821 3 0.6255 0.5003 0.012 0.320 0.668
#> GSM97826 1 0.0000 0.8637 1.000 0.000 0.000
#> GSM97829 1 0.5591 0.6504 0.696 0.000 0.304
#> GSM97832 3 0.5706 0.4269 0.000 0.320 0.680
#> GSM97836 1 0.5882 0.5884 0.652 0.000 0.348
#> GSM97839 1 0.0000 0.8637 1.000 0.000 0.000
#> GSM97844 2 0.0000 0.9705 0.000 1.000 0.000
#> GSM97847 1 0.0000 0.8637 1.000 0.000 0.000
#> GSM97851 1 0.0000 0.8637 1.000 0.000 0.000
#> GSM97852 1 0.1163 0.8499 0.972 0.000 0.028
#> GSM97856 1 0.0000 0.8637 1.000 0.000 0.000
#> GSM97858 2 0.0000 0.9705 0.000 1.000 0.000
#> GSM97859 1 0.5650 0.6419 0.688 0.000 0.312
#> GSM97861 1 0.6305 0.2479 0.516 0.000 0.484
#> GSM97863 1 0.0000 0.8637 1.000 0.000 0.000
#> GSM97869 3 0.6307 -0.1738 0.488 0.000 0.512
#> GSM97870 3 0.6168 0.1257 0.412 0.000 0.588
#> GSM97871 1 0.0000 0.8637 1.000 0.000 0.000
#> GSM97877 2 0.6313 0.4471 0.016 0.676 0.308
#> GSM97879 1 0.0237 0.8619 0.996 0.000 0.004
#> GSM97882 1 0.5650 0.6419 0.688 0.000 0.312
#> GSM97885 1 0.5650 0.6419 0.688 0.000 0.312
#> GSM97886 1 0.0000 0.8637 1.000 0.000 0.000
#> GSM97887 1 0.0000 0.8637 1.000 0.000 0.000
#> GSM97888 1 0.0000 0.8637 1.000 0.000 0.000
#> GSM97889 1 0.4121 0.7632 0.832 0.000 0.168
#> GSM97891 1 0.5650 0.6419 0.688 0.000 0.312
#> GSM97892 2 0.0000 0.9705 0.000 1.000 0.000
#> GSM97893 1 0.0000 0.8637 1.000 0.000 0.000
#> GSM97894 1 0.0000 0.8637 1.000 0.000 0.000
#> GSM97895 1 0.0000 0.8637 1.000 0.000 0.000
#> GSM97896 1 0.0000 0.8637 1.000 0.000 0.000
#> GSM97898 1 0.0000 0.8637 1.000 0.000 0.000
#> GSM97903 1 0.5650 0.6419 0.688 0.000 0.312
#> GSM97905 1 0.5706 0.6319 0.680 0.000 0.320
#> GSM97906 1 0.0000 0.8637 1.000 0.000 0.000
#> GSM97908 1 0.0000 0.8637 1.000 0.000 0.000
#> GSM97912 1 0.5706 0.6312 0.680 0.000 0.320
#> GSM97914 1 0.6008 0.5412 0.628 0.000 0.372
#> GSM97915 1 0.0000 0.8637 1.000 0.000 0.000
#> GSM97917 1 0.0000 0.8637 1.000 0.000 0.000
#> GSM97918 1 0.0000 0.8637 1.000 0.000 0.000
#> GSM97919 1 0.0000 0.8637 1.000 0.000 0.000
#> GSM97922 1 0.0000 0.8637 1.000 0.000 0.000
#> GSM97924 2 0.0000 0.9705 0.000 1.000 0.000
#> GSM97926 3 0.0747 0.8897 0.016 0.000 0.984
#> GSM97930 1 0.0000 0.8637 1.000 0.000 0.000
#> GSM97931 3 0.0747 0.8897 0.016 0.000 0.984
#> GSM97935 1 0.5650 0.6419 0.688 0.000 0.312
#> GSM97936 1 0.0000 0.8637 1.000 0.000 0.000
#> GSM97938 1 0.0000 0.8637 1.000 0.000 0.000
#> GSM97940 1 0.0000 0.8637 1.000 0.000 0.000
#> GSM97942 3 0.0237 0.8973 0.004 0.000 0.996
#> GSM97945 1 0.0000 0.8637 1.000 0.000 0.000
#> GSM97946 2 0.0000 0.9705 0.000 1.000 0.000
#> GSM97948 3 0.0747 0.8897 0.016 0.000 0.984
#> GSM97950 1 0.0000 0.8637 1.000 0.000 0.000
#> GSM97952 1 0.0000 0.8637 1.000 0.000 0.000
#> GSM97953 1 0.0000 0.8637 1.000 0.000 0.000
#> GSM97954 1 0.0000 0.8637 1.000 0.000 0.000
#> GSM97955 1 0.0000 0.8637 1.000 0.000 0.000
#> GSM97959 1 0.9050 0.3231 0.484 0.140 0.376
#> GSM97961 1 0.0000 0.8637 1.000 0.000 0.000
#> GSM97963 1 0.0000 0.8637 1.000 0.000 0.000
#> GSM97965 1 0.0000 0.8637 1.000 0.000 0.000
#> GSM97966 1 0.0000 0.8637 1.000 0.000 0.000
#> GSM97967 2 0.0000 0.9705 0.000 1.000 0.000
#> GSM97968 2 0.0000 0.9705 0.000 1.000 0.000
#> GSM97969 1 0.0000 0.8637 1.000 0.000 0.000
#> GSM97971 1 0.5465 0.6661 0.712 0.000 0.288
#> GSM97799 3 0.0000 0.8990 0.000 0.000 1.000
#> GSM97823 2 0.0000 0.9705 0.000 1.000 0.000
#> GSM97824 3 0.0000 0.8990 0.000 0.000 1.000
#> GSM97830 3 0.0000 0.8990 0.000 0.000 1.000
#> GSM97835 3 0.0237 0.8970 0.000 0.004 0.996
#> GSM97838 2 0.0000 0.9705 0.000 1.000 0.000
#> GSM97841 2 0.0000 0.9705 0.000 1.000 0.000
#> GSM97842 3 0.0000 0.8990 0.000 0.000 1.000
#> GSM97854 2 0.0000 0.9705 0.000 1.000 0.000
#> GSM97857 3 0.0000 0.8990 0.000 0.000 1.000
#> GSM97860 3 0.0000 0.8990 0.000 0.000 1.000
#> GSM97862 3 0.0000 0.8990 0.000 0.000 1.000
#> GSM97864 2 0.0000 0.9705 0.000 1.000 0.000
#> GSM97866 3 0.0000 0.8990 0.000 0.000 1.000
#> GSM97868 3 0.0000 0.8990 0.000 0.000 1.000
#> GSM97872 3 0.5785 0.3815 0.332 0.000 0.668
#> GSM97873 3 0.0000 0.8990 0.000 0.000 1.000
#> GSM97874 3 0.0000 0.8990 0.000 0.000 1.000
#> GSM97875 3 0.0000 0.8990 0.000 0.000 1.000
#> GSM97876 3 0.0000 0.8990 0.000 0.000 1.000
#> GSM97880 3 0.0000 0.8990 0.000 0.000 1.000
#> GSM97881 3 0.0000 0.8990 0.000 0.000 1.000
#> GSM97884 3 0.0000 0.8990 0.000 0.000 1.000
#> GSM97901 3 0.0000 0.8990 0.000 0.000 1.000
#> GSM97902 3 0.6204 0.0694 0.424 0.000 0.576
#> GSM97909 2 0.0747 0.9574 0.000 0.984 0.016
#> GSM97911 3 0.0000 0.8990 0.000 0.000 1.000
#> GSM97923 3 0.0000 0.8990 0.000 0.000 1.000
#> GSM97928 3 0.1529 0.8683 0.040 0.000 0.960
#> GSM97929 2 0.0000 0.9705 0.000 1.000 0.000
#> GSM97933 3 0.0237 0.8974 0.004 0.000 0.996
#> GSM97934 3 0.0000 0.8990 0.000 0.000 1.000
#> GSM97944 3 0.0000 0.8990 0.000 0.000 1.000
#> GSM97949 2 0.0000 0.9705 0.000 1.000 0.000
#> GSM97956 3 0.0000 0.8990 0.000 0.000 1.000
#> GSM97962 3 0.0000 0.8990 0.000 0.000 1.000
#> GSM97964 3 0.0000 0.8990 0.000 0.000 1.000
#> GSM97970 3 0.0000 0.8990 0.000 0.000 1.000
#> GSM97822 1 0.5678 0.6371 0.684 0.000 0.316
#> GSM97831 3 0.0000 0.8990 0.000 0.000 1.000
#> GSM97845 1 0.0000 0.8637 1.000 0.000 0.000
#> GSM97865 1 0.5988 0.5491 0.632 0.000 0.368
#> GSM97867 3 0.0237 0.8974 0.004 0.000 0.996
#> GSM97883 3 0.0237 0.8974 0.004 0.000 0.996
#> GSM97897 1 0.0000 0.8637 1.000 0.000 0.000
#> GSM97900 1 0.0000 0.8637 1.000 0.000 0.000
#> GSM97904 1 0.5706 0.6318 0.680 0.000 0.320
#> GSM97907 2 0.0000 0.9705 0.000 1.000 0.000
#> GSM97925 3 0.0237 0.8973 0.004 0.000 0.996
#> GSM97947 3 0.0592 0.8924 0.012 0.000 0.988
cbind(get_classes(res, k = 4), get_membership(res, k = 4))
#> class entropy silhouette p1 p2 p3 p4
#> GSM97800 2 0.0000 0.9841 0.000 1.000 0.000 0.000
#> GSM97803 2 0.0000 0.9841 0.000 1.000 0.000 0.000
#> GSM97804 2 0.0000 0.9841 0.000 1.000 0.000 0.000
#> GSM97805 2 0.0000 0.9841 0.000 1.000 0.000 0.000
#> GSM97807 2 0.0000 0.9841 0.000 1.000 0.000 0.000
#> GSM97809 2 0.0000 0.9841 0.000 1.000 0.000 0.000
#> GSM97811 2 0.0000 0.9841 0.000 1.000 0.000 0.000
#> GSM97812 2 0.0000 0.9841 0.000 1.000 0.000 0.000
#> GSM97816 2 0.5060 0.2597 0.004 0.584 0.412 0.000
#> GSM97817 2 0.0000 0.9841 0.000 1.000 0.000 0.000
#> GSM97820 2 0.0000 0.9841 0.000 1.000 0.000 0.000
#> GSM97825 2 0.0000 0.9841 0.000 1.000 0.000 0.000
#> GSM97827 2 0.0000 0.9841 0.000 1.000 0.000 0.000
#> GSM97828 3 0.4193 0.6123 0.268 0.000 0.732 0.000
#> GSM97833 2 0.0000 0.9841 0.000 1.000 0.000 0.000
#> GSM97834 2 0.0000 0.9841 0.000 1.000 0.000 0.000
#> GSM97840 2 0.0000 0.9841 0.000 1.000 0.000 0.000
#> GSM97846 2 0.0000 0.9841 0.000 1.000 0.000 0.000
#> GSM97848 2 0.0000 0.9841 0.000 1.000 0.000 0.000
#> GSM97849 2 0.0000 0.9841 0.000 1.000 0.000 0.000
#> GSM97850 2 0.0000 0.9841 0.000 1.000 0.000 0.000
#> GSM97853 2 0.0000 0.9841 0.000 1.000 0.000 0.000
#> GSM97855 2 0.0000 0.9841 0.000 1.000 0.000 0.000
#> GSM97878 1 0.0000 0.9050 1.000 0.000 0.000 0.000
#> GSM97913 1 0.0000 0.9050 1.000 0.000 0.000 0.000
#> GSM97932 4 0.0000 0.9344 0.000 0.000 0.000 1.000
#> GSM97939 3 0.0000 0.9645 0.000 0.000 1.000 0.000
#> GSM97951 2 0.0000 0.9841 0.000 1.000 0.000 0.000
#> GSM97957 3 0.0000 0.9645 0.000 0.000 1.000 0.000
#> GSM97972 3 0.0376 0.9595 0.004 0.004 0.992 0.000
#> GSM97793 3 0.0000 0.9645 0.000 0.000 1.000 0.000
#> GSM97795 2 0.3172 0.8052 0.000 0.840 0.160 0.000
#> GSM97802 1 0.4996 0.1305 0.516 0.000 0.484 0.000
#> GSM97810 3 0.0469 0.9556 0.000 0.012 0.988 0.000
#> GSM97815 3 0.0188 0.9617 0.000 0.004 0.996 0.000
#> GSM97837 1 0.0000 0.9050 1.000 0.000 0.000 0.000
#> GSM97843 3 0.0000 0.9645 0.000 0.000 1.000 0.000
#> GSM97890 3 0.0000 0.9645 0.000 0.000 1.000 0.000
#> GSM97899 4 0.0000 0.9344 0.000 0.000 0.000 1.000
#> GSM97910 1 0.0000 0.9050 1.000 0.000 0.000 0.000
#> GSM97916 1 0.0000 0.9050 1.000 0.000 0.000 0.000
#> GSM97920 3 0.1867 0.8945 0.072 0.000 0.928 0.000
#> GSM97921 1 0.0000 0.9050 1.000 0.000 0.000 0.000
#> GSM97927 1 0.0469 0.8993 0.988 0.000 0.000 0.012
#> GSM97937 1 0.0336 0.9015 0.992 0.000 0.000 0.008
#> GSM97941 2 0.0000 0.9841 0.000 1.000 0.000 0.000
#> GSM97943 1 0.0188 0.9034 0.996 0.000 0.004 0.000
#> GSM97958 1 0.4888 0.3346 0.588 0.000 0.412 0.000
#> GSM97960 3 0.4985 0.1190 0.000 0.468 0.532 0.000
#> GSM97794 1 0.0000 0.9050 1.000 0.000 0.000 0.000
#> GSM97796 4 0.0000 0.9344 0.000 0.000 0.000 1.000
#> GSM97797 1 0.0000 0.9050 1.000 0.000 0.000 0.000
#> GSM97798 4 0.0000 0.9344 0.000 0.000 0.000 1.000
#> GSM97801 1 0.0000 0.9050 1.000 0.000 0.000 0.000
#> GSM97806 1 0.0000 0.9050 1.000 0.000 0.000 0.000
#> GSM97808 4 0.0000 0.9344 0.000 0.000 0.000 1.000
#> GSM97813 1 0.0707 0.8950 0.980 0.000 0.000 0.020
#> GSM97814 4 0.0000 0.9344 0.000 0.000 0.000 1.000
#> GSM97818 1 0.0000 0.9050 1.000 0.000 0.000 0.000
#> GSM97819 3 0.0000 0.9645 0.000 0.000 1.000 0.000
#> GSM97821 1 0.5593 0.6534 0.708 0.080 0.212 0.000
#> GSM97826 1 0.0000 0.9050 1.000 0.000 0.000 0.000
#> GSM97829 1 0.0188 0.9035 0.996 0.000 0.000 0.004
#> GSM97832 3 0.1389 0.9239 0.000 0.048 0.952 0.000
#> GSM97836 1 0.0000 0.9050 1.000 0.000 0.000 0.000
#> GSM97839 4 0.0000 0.9344 0.000 0.000 0.000 1.000
#> GSM97844 2 0.0000 0.9841 0.000 1.000 0.000 0.000
#> GSM97847 1 0.0469 0.8984 0.988 0.000 0.000 0.012
#> GSM97851 4 0.0000 0.9344 0.000 0.000 0.000 1.000
#> GSM97852 1 0.0188 0.9035 0.996 0.000 0.000 0.004
#> GSM97856 4 0.0000 0.9344 0.000 0.000 0.000 1.000
#> GSM97858 2 0.0000 0.9841 0.000 1.000 0.000 0.000
#> GSM97859 1 0.0000 0.9050 1.000 0.000 0.000 0.000
#> GSM97861 1 0.0469 0.8993 0.988 0.000 0.000 0.012
#> GSM97863 4 0.0000 0.9344 0.000 0.000 0.000 1.000
#> GSM97869 1 0.0000 0.9050 1.000 0.000 0.000 0.000
#> GSM97870 1 0.1211 0.8818 0.960 0.000 0.040 0.000
#> GSM97871 4 0.0000 0.9344 0.000 0.000 0.000 1.000
#> GSM97877 1 0.0000 0.9050 1.000 0.000 0.000 0.000
#> GSM97879 4 0.4866 0.3846 0.404 0.000 0.000 0.596
#> GSM97882 1 0.0000 0.9050 1.000 0.000 0.000 0.000
#> GSM97885 1 0.0000 0.9050 1.000 0.000 0.000 0.000
#> GSM97886 4 0.0000 0.9344 0.000 0.000 0.000 1.000
#> GSM97887 4 0.0000 0.9344 0.000 0.000 0.000 1.000
#> GSM97888 4 0.4643 0.4419 0.344 0.000 0.000 0.656
#> GSM97889 1 0.4999 0.0492 0.508 0.000 0.000 0.492
#> GSM97891 1 0.0000 0.9050 1.000 0.000 0.000 0.000
#> GSM97892 2 0.0000 0.9841 0.000 1.000 0.000 0.000
#> GSM97893 4 0.0000 0.9344 0.000 0.000 0.000 1.000
#> GSM97894 4 0.0000 0.9344 0.000 0.000 0.000 1.000
#> GSM97895 4 0.0000 0.9344 0.000 0.000 0.000 1.000
#> GSM97896 4 0.0000 0.9344 0.000 0.000 0.000 1.000
#> GSM97898 4 0.0000 0.9344 0.000 0.000 0.000 1.000
#> GSM97903 1 0.0000 0.9050 1.000 0.000 0.000 0.000
#> GSM97905 1 0.7085 0.4913 0.568 0.000 0.232 0.200
#> GSM97906 4 0.0000 0.9344 0.000 0.000 0.000 1.000
#> GSM97908 4 0.4843 0.4081 0.396 0.000 0.000 0.604
#> GSM97912 1 0.1584 0.8813 0.952 0.000 0.036 0.012
#> GSM97914 1 0.0000 0.9050 1.000 0.000 0.000 0.000
#> GSM97915 4 0.0000 0.9344 0.000 0.000 0.000 1.000
#> GSM97917 4 0.0000 0.9344 0.000 0.000 0.000 1.000
#> GSM97918 4 0.0000 0.9344 0.000 0.000 0.000 1.000
#> GSM97919 4 0.0000 0.9344 0.000 0.000 0.000 1.000
#> GSM97922 1 0.3356 0.7349 0.824 0.000 0.000 0.176
#> GSM97924 2 0.0000 0.9841 0.000 1.000 0.000 0.000
#> GSM97926 3 0.0000 0.9645 0.000 0.000 1.000 0.000
#> GSM97930 1 0.0000 0.9050 1.000 0.000 0.000 0.000
#> GSM97931 1 0.4382 0.5841 0.704 0.000 0.296 0.000
#> GSM97935 1 0.0000 0.9050 1.000 0.000 0.000 0.000
#> GSM97936 4 0.0000 0.9344 0.000 0.000 0.000 1.000
#> GSM97938 4 0.1637 0.8839 0.060 0.000 0.000 0.940
#> GSM97940 4 0.0000 0.9344 0.000 0.000 0.000 1.000
#> GSM97942 3 0.0000 0.9645 0.000 0.000 1.000 0.000
#> GSM97945 4 0.0000 0.9344 0.000 0.000 0.000 1.000
#> GSM97946 2 0.0000 0.9841 0.000 1.000 0.000 0.000
#> GSM97948 1 0.4948 0.2685 0.560 0.000 0.440 0.000
#> GSM97950 4 0.0000 0.9344 0.000 0.000 0.000 1.000
#> GSM97952 4 0.0000 0.9344 0.000 0.000 0.000 1.000
#> GSM97953 4 0.4941 0.3059 0.436 0.000 0.000 0.564
#> GSM97954 1 0.3528 0.6984 0.808 0.000 0.000 0.192
#> GSM97955 4 0.0000 0.9344 0.000 0.000 0.000 1.000
#> GSM97959 1 0.0000 0.9050 1.000 0.000 0.000 0.000
#> GSM97961 4 0.0000 0.9344 0.000 0.000 0.000 1.000
#> GSM97963 4 0.0000 0.9344 0.000 0.000 0.000 1.000
#> GSM97965 4 0.0000 0.9344 0.000 0.000 0.000 1.000
#> GSM97966 4 0.0000 0.9344 0.000 0.000 0.000 1.000
#> GSM97967 2 0.0000 0.9841 0.000 1.000 0.000 0.000
#> GSM97968 2 0.0000 0.9841 0.000 1.000 0.000 0.000
#> GSM97969 4 0.4877 0.3689 0.408 0.000 0.000 0.592
#> GSM97971 1 0.0469 0.8993 0.988 0.000 0.000 0.012
#> GSM97799 3 0.0000 0.9645 0.000 0.000 1.000 0.000
#> GSM97823 2 0.0000 0.9841 0.000 1.000 0.000 0.000
#> GSM97824 3 0.0000 0.9645 0.000 0.000 1.000 0.000
#> GSM97830 3 0.0000 0.9645 0.000 0.000 1.000 0.000
#> GSM97835 3 0.0188 0.9616 0.000 0.004 0.996 0.000
#> GSM97838 2 0.0000 0.9841 0.000 1.000 0.000 0.000
#> GSM97841 2 0.0000 0.9841 0.000 1.000 0.000 0.000
#> GSM97842 3 0.0000 0.9645 0.000 0.000 1.000 0.000
#> GSM97854 2 0.0000 0.9841 0.000 1.000 0.000 0.000
#> GSM97857 3 0.0000 0.9645 0.000 0.000 1.000 0.000
#> GSM97860 3 0.0000 0.9645 0.000 0.000 1.000 0.000
#> GSM97862 3 0.0000 0.9645 0.000 0.000 1.000 0.000
#> GSM97864 2 0.0000 0.9841 0.000 1.000 0.000 0.000
#> GSM97866 3 0.0000 0.9645 0.000 0.000 1.000 0.000
#> GSM97868 3 0.0000 0.9645 0.000 0.000 1.000 0.000
#> GSM97872 1 0.4647 0.6039 0.704 0.000 0.288 0.008
#> GSM97873 3 0.0000 0.9645 0.000 0.000 1.000 0.000
#> GSM97874 3 0.0000 0.9645 0.000 0.000 1.000 0.000
#> GSM97875 3 0.0000 0.9645 0.000 0.000 1.000 0.000
#> GSM97876 3 0.0000 0.9645 0.000 0.000 1.000 0.000
#> GSM97880 3 0.0000 0.9645 0.000 0.000 1.000 0.000
#> GSM97881 3 0.0000 0.9645 0.000 0.000 1.000 0.000
#> GSM97884 3 0.0000 0.9645 0.000 0.000 1.000 0.000
#> GSM97901 3 0.0000 0.9645 0.000 0.000 1.000 0.000
#> GSM97902 1 0.2704 0.8186 0.876 0.000 0.124 0.000
#> GSM97909 1 0.4761 0.4997 0.664 0.332 0.004 0.000
#> GSM97911 3 0.0000 0.9645 0.000 0.000 1.000 0.000
#> GSM97923 3 0.0000 0.9645 0.000 0.000 1.000 0.000
#> GSM97928 3 0.4898 0.2129 0.416 0.000 0.584 0.000
#> GSM97929 2 0.0000 0.9841 0.000 1.000 0.000 0.000
#> GSM97933 3 0.0000 0.9645 0.000 0.000 1.000 0.000
#> GSM97934 3 0.0000 0.9645 0.000 0.000 1.000 0.000
#> GSM97944 3 0.0000 0.9645 0.000 0.000 1.000 0.000
#> GSM97949 2 0.0000 0.9841 0.000 1.000 0.000 0.000
#> GSM97956 3 0.0000 0.9645 0.000 0.000 1.000 0.000
#> GSM97962 3 0.0000 0.9645 0.000 0.000 1.000 0.000
#> GSM97964 3 0.0000 0.9645 0.000 0.000 1.000 0.000
#> GSM97970 3 0.0000 0.9645 0.000 0.000 1.000 0.000
#> GSM97822 1 0.0188 0.9035 0.996 0.000 0.000 0.004
#> GSM97831 3 0.0000 0.9645 0.000 0.000 1.000 0.000
#> GSM97845 4 0.4643 0.5114 0.344 0.000 0.000 0.656
#> GSM97865 1 0.0000 0.9050 1.000 0.000 0.000 0.000
#> GSM97867 3 0.0000 0.9645 0.000 0.000 1.000 0.000
#> GSM97883 3 0.3123 0.7874 0.156 0.000 0.844 0.000
#> GSM97897 4 0.2760 0.8097 0.128 0.000 0.000 0.872
#> GSM97900 4 0.0000 0.9344 0.000 0.000 0.000 1.000
#> GSM97904 1 0.2473 0.8504 0.908 0.000 0.080 0.012
#> GSM97907 2 0.0000 0.9841 0.000 1.000 0.000 0.000
#> GSM97925 3 0.0188 0.9615 0.004 0.000 0.996 0.000
#> GSM97947 3 0.1940 0.8898 0.076 0.000 0.924 0.000
cbind(get_classes(res, k = 5), get_membership(res, k = 5))
#> class entropy silhouette p1 p2 p3 p4 p5
#> GSM97800 2 0.0000 0.9642 0.000 1.000 0.000 0.000 0.000
#> GSM97803 2 0.0000 0.9642 0.000 1.000 0.000 0.000 0.000
#> GSM97804 2 0.0000 0.9642 0.000 1.000 0.000 0.000 0.000
#> GSM97805 2 0.0000 0.9642 0.000 1.000 0.000 0.000 0.000
#> GSM97807 2 0.0000 0.9642 0.000 1.000 0.000 0.000 0.000
#> GSM97809 2 0.0000 0.9642 0.000 1.000 0.000 0.000 0.000
#> GSM97811 2 0.0000 0.9642 0.000 1.000 0.000 0.000 0.000
#> GSM97812 2 0.0000 0.9642 0.000 1.000 0.000 0.000 0.000
#> GSM97816 2 0.6612 0.0421 0.000 0.460 0.264 0.000 0.276
#> GSM97817 2 0.0000 0.9642 0.000 1.000 0.000 0.000 0.000
#> GSM97820 2 0.0000 0.9642 0.000 1.000 0.000 0.000 0.000
#> GSM97825 2 0.0000 0.9642 0.000 1.000 0.000 0.000 0.000
#> GSM97827 2 0.0000 0.9642 0.000 1.000 0.000 0.000 0.000
#> GSM97828 5 0.4101 -0.1772 0.004 0.000 0.332 0.000 0.664
#> GSM97833 2 0.0000 0.9642 0.000 1.000 0.000 0.000 0.000
#> GSM97834 2 0.0000 0.9642 0.000 1.000 0.000 0.000 0.000
#> GSM97840 2 0.0000 0.9642 0.000 1.000 0.000 0.000 0.000
#> GSM97846 2 0.0000 0.9642 0.000 1.000 0.000 0.000 0.000
#> GSM97848 2 0.0000 0.9642 0.000 1.000 0.000 0.000 0.000
#> GSM97849 2 0.0000 0.9642 0.000 1.000 0.000 0.000 0.000
#> GSM97850 2 0.0000 0.9642 0.000 1.000 0.000 0.000 0.000
#> GSM97853 2 0.0000 0.9642 0.000 1.000 0.000 0.000 0.000
#> GSM97855 2 0.0000 0.9642 0.000 1.000 0.000 0.000 0.000
#> GSM97878 1 0.4283 -0.3651 0.544 0.000 0.000 0.000 0.456
#> GSM97913 5 0.4015 0.8024 0.348 0.000 0.000 0.000 0.652
#> GSM97932 4 0.0162 0.9498 0.000 0.000 0.000 0.996 0.004
#> GSM97939 3 0.1732 0.8377 0.000 0.000 0.920 0.000 0.080
#> GSM97951 2 0.0000 0.9642 0.000 1.000 0.000 0.000 0.000
#> GSM97957 3 0.3684 0.8001 0.000 0.000 0.720 0.000 0.280
#> GSM97972 3 0.4256 0.6489 0.000 0.000 0.564 0.000 0.436
#> GSM97793 3 0.6046 0.3237 0.344 0.000 0.524 0.000 0.132
#> GSM97795 2 0.4227 0.3518 0.000 0.580 0.420 0.000 0.000
#> GSM97802 1 0.3838 0.4970 0.716 0.000 0.280 0.000 0.004
#> GSM97810 3 0.3427 0.8096 0.000 0.012 0.796 0.000 0.192
#> GSM97815 3 0.0000 0.8331 0.000 0.000 1.000 0.000 0.000
#> GSM97837 5 0.4283 0.6519 0.456 0.000 0.000 0.000 0.544
#> GSM97843 3 0.3684 0.8001 0.000 0.000 0.720 0.000 0.280
#> GSM97890 3 0.0000 0.8331 0.000 0.000 1.000 0.000 0.000
#> GSM97899 4 0.0000 0.9526 0.000 0.000 0.000 1.000 0.000
#> GSM97910 5 0.3999 0.8032 0.344 0.000 0.000 0.000 0.656
#> GSM97916 5 0.4030 0.8000 0.352 0.000 0.000 0.000 0.648
#> GSM97920 3 0.3707 0.7986 0.000 0.000 0.716 0.000 0.284
#> GSM97921 5 0.3913 0.8012 0.324 0.000 0.000 0.000 0.676
#> GSM97927 1 0.1851 0.6605 0.912 0.000 0.000 0.000 0.088
#> GSM97937 1 0.4278 -0.4728 0.548 0.000 0.000 0.000 0.452
#> GSM97941 2 0.0000 0.9642 0.000 1.000 0.000 0.000 0.000
#> GSM97943 5 0.2953 0.5961 0.144 0.000 0.012 0.000 0.844
#> GSM97958 5 0.2171 0.4749 0.024 0.000 0.064 0.000 0.912
#> GSM97960 2 0.4482 0.3053 0.000 0.612 0.376 0.000 0.012
#> GSM97794 5 0.4015 0.8024 0.348 0.000 0.000 0.000 0.652
#> GSM97796 4 0.0000 0.9526 0.000 0.000 0.000 1.000 0.000
#> GSM97797 5 0.4015 0.8024 0.348 0.000 0.000 0.000 0.652
#> GSM97798 4 0.0000 0.9526 0.000 0.000 0.000 1.000 0.000
#> GSM97801 5 0.3913 0.8010 0.324 0.000 0.000 0.000 0.676
#> GSM97806 1 0.3730 0.3403 0.712 0.000 0.000 0.000 0.288
#> GSM97808 4 0.0000 0.9526 0.000 0.000 0.000 1.000 0.000
#> GSM97813 1 0.0290 0.6914 0.992 0.000 0.000 0.008 0.000
#> GSM97814 4 0.0000 0.9526 0.000 0.000 0.000 1.000 0.000
#> GSM97818 5 0.3999 0.8023 0.344 0.000 0.000 0.000 0.656
#> GSM97819 3 0.2563 0.8249 0.008 0.000 0.872 0.000 0.120
#> GSM97821 5 0.5670 0.6173 0.192 0.000 0.176 0.000 0.632
#> GSM97826 5 0.4307 0.6177 0.496 0.000 0.000 0.000 0.504
#> GSM97829 5 0.4114 0.7619 0.376 0.000 0.000 0.000 0.624
#> GSM97832 3 0.3994 0.7996 0.000 0.040 0.772 0.000 0.188
#> GSM97836 1 0.2648 0.6093 0.848 0.000 0.000 0.000 0.152
#> GSM97839 4 0.0000 0.9526 0.000 0.000 0.000 1.000 0.000
#> GSM97844 2 0.0000 0.9642 0.000 1.000 0.000 0.000 0.000
#> GSM97847 5 0.4165 0.7958 0.320 0.000 0.000 0.008 0.672
#> GSM97851 4 0.0000 0.9526 0.000 0.000 0.000 1.000 0.000
#> GSM97852 1 0.3424 0.5085 0.760 0.000 0.000 0.000 0.240
#> GSM97856 4 0.0000 0.9526 0.000 0.000 0.000 1.000 0.000
#> GSM97858 2 0.0000 0.9642 0.000 1.000 0.000 0.000 0.000
#> GSM97859 1 0.0000 0.6904 1.000 0.000 0.000 0.000 0.000
#> GSM97861 1 0.2020 0.6610 0.900 0.000 0.000 0.000 0.100
#> GSM97863 4 0.0000 0.9526 0.000 0.000 0.000 1.000 0.000
#> GSM97869 5 0.4101 0.7797 0.372 0.000 0.000 0.000 0.628
#> GSM97870 1 0.0000 0.6904 1.000 0.000 0.000 0.000 0.000
#> GSM97871 4 0.0000 0.9526 0.000 0.000 0.000 1.000 0.000
#> GSM97877 5 0.4015 0.8024 0.348 0.000 0.000 0.000 0.652
#> GSM97879 1 0.5398 0.5175 0.648 0.000 0.000 0.240 0.112
#> GSM97882 1 0.2605 0.6130 0.852 0.000 0.000 0.000 0.148
#> GSM97885 5 0.4287 0.6185 0.460 0.000 0.000 0.000 0.540
#> GSM97886 4 0.0000 0.9526 0.000 0.000 0.000 1.000 0.000
#> GSM97887 4 0.3636 0.5841 0.272 0.000 0.000 0.728 0.000
#> GSM97888 1 0.3607 0.5413 0.752 0.000 0.000 0.244 0.004
#> GSM97889 1 0.2629 0.6234 0.860 0.000 0.000 0.136 0.004
#> GSM97891 1 0.2966 0.5697 0.816 0.000 0.000 0.000 0.184
#> GSM97892 2 0.0000 0.9642 0.000 1.000 0.000 0.000 0.000
#> GSM97893 4 0.0162 0.9498 0.000 0.000 0.000 0.996 0.004
#> GSM97894 4 0.0000 0.9526 0.000 0.000 0.000 1.000 0.000
#> GSM97895 4 0.0671 0.9377 0.016 0.000 0.000 0.980 0.004
#> GSM97896 4 0.0703 0.9340 0.024 0.000 0.000 0.976 0.000
#> GSM97898 4 0.0000 0.9526 0.000 0.000 0.000 1.000 0.000
#> GSM97903 5 0.4015 0.8004 0.348 0.000 0.000 0.000 0.652
#> GSM97905 1 0.2516 0.6276 0.860 0.000 0.000 0.000 0.140
#> GSM97906 4 0.0000 0.9526 0.000 0.000 0.000 1.000 0.000
#> GSM97908 4 0.6189 -0.0418 0.140 0.000 0.000 0.476 0.384
#> GSM97912 1 0.0794 0.6876 0.972 0.000 0.000 0.000 0.028
#> GSM97914 5 0.3932 0.8016 0.328 0.000 0.000 0.000 0.672
#> GSM97915 4 0.0000 0.9526 0.000 0.000 0.000 1.000 0.000
#> GSM97917 4 0.0000 0.9526 0.000 0.000 0.000 1.000 0.000
#> GSM97918 4 0.0000 0.9526 0.000 0.000 0.000 1.000 0.000
#> GSM97919 4 0.0000 0.9526 0.000 0.000 0.000 1.000 0.000
#> GSM97922 1 0.0162 0.6900 0.996 0.000 0.000 0.000 0.004
#> GSM97924 2 0.0000 0.9642 0.000 1.000 0.000 0.000 0.000
#> GSM97926 3 0.4450 -0.0254 0.488 0.000 0.508 0.000 0.004
#> GSM97930 5 0.3932 0.7997 0.328 0.000 0.000 0.000 0.672
#> GSM97931 5 0.5423 0.6660 0.224 0.000 0.124 0.000 0.652
#> GSM97935 1 0.2605 0.6130 0.852 0.000 0.000 0.000 0.148
#> GSM97936 4 0.0000 0.9526 0.000 0.000 0.000 1.000 0.000
#> GSM97938 4 0.5765 0.3125 0.304 0.000 0.000 0.580 0.116
#> GSM97940 4 0.0000 0.9526 0.000 0.000 0.000 1.000 0.000
#> GSM97942 3 0.5964 0.3374 0.340 0.000 0.536 0.000 0.124
#> GSM97945 4 0.0000 0.9526 0.000 0.000 0.000 1.000 0.000
#> GSM97946 2 0.0000 0.9642 0.000 1.000 0.000 0.000 0.000
#> GSM97948 1 0.4723 0.5408 0.736 0.000 0.136 0.000 0.128
#> GSM97950 4 0.0000 0.9526 0.000 0.000 0.000 1.000 0.000
#> GSM97952 4 0.0000 0.9526 0.000 0.000 0.000 1.000 0.000
#> GSM97953 1 0.6180 0.4159 0.556 0.000 0.000 0.224 0.220
#> GSM97954 1 0.5136 0.4318 0.660 0.000 0.000 0.080 0.260
#> GSM97955 4 0.0162 0.9495 0.004 0.000 0.000 0.996 0.000
#> GSM97959 5 0.4015 0.8024 0.348 0.000 0.000 0.000 0.652
#> GSM97961 4 0.0000 0.9526 0.000 0.000 0.000 1.000 0.000
#> GSM97963 4 0.0000 0.9526 0.000 0.000 0.000 1.000 0.000
#> GSM97965 4 0.0000 0.9526 0.000 0.000 0.000 1.000 0.000
#> GSM97966 4 0.0000 0.9526 0.000 0.000 0.000 1.000 0.000
#> GSM97967 2 0.0000 0.9642 0.000 1.000 0.000 0.000 0.000
#> GSM97968 2 0.0000 0.9642 0.000 1.000 0.000 0.000 0.000
#> GSM97969 1 0.3675 0.5861 0.788 0.000 0.000 0.188 0.024
#> GSM97971 1 0.0000 0.6904 1.000 0.000 0.000 0.000 0.000
#> GSM97799 3 0.0000 0.8331 0.000 0.000 1.000 0.000 0.000
#> GSM97823 2 0.0000 0.9642 0.000 1.000 0.000 0.000 0.000
#> GSM97824 3 0.3039 0.8119 0.000 0.000 0.808 0.000 0.192
#> GSM97830 3 0.3707 0.7997 0.000 0.000 0.716 0.000 0.284
#> GSM97835 3 0.0000 0.8331 0.000 0.000 1.000 0.000 0.000
#> GSM97838 2 0.0000 0.9642 0.000 1.000 0.000 0.000 0.000
#> GSM97841 2 0.0000 0.9642 0.000 1.000 0.000 0.000 0.000
#> GSM97842 3 0.0000 0.8331 0.000 0.000 1.000 0.000 0.000
#> GSM97854 2 0.0000 0.9642 0.000 1.000 0.000 0.000 0.000
#> GSM97857 3 0.3684 0.8001 0.000 0.000 0.720 0.000 0.280
#> GSM97860 3 0.2561 0.8193 0.000 0.000 0.856 0.000 0.144
#> GSM97862 3 0.0404 0.8341 0.000 0.000 0.988 0.000 0.012
#> GSM97864 2 0.0000 0.9642 0.000 1.000 0.000 0.000 0.000
#> GSM97866 3 0.1851 0.8394 0.000 0.000 0.912 0.000 0.088
#> GSM97868 3 0.0000 0.8331 0.000 0.000 1.000 0.000 0.000
#> GSM97872 1 0.2208 0.6515 0.908 0.000 0.072 0.000 0.020
#> GSM97873 3 0.0000 0.8331 0.000 0.000 1.000 0.000 0.000
#> GSM97874 3 0.3876 0.7903 0.000 0.000 0.684 0.000 0.316
#> GSM97875 3 0.0162 0.8323 0.000 0.000 0.996 0.000 0.004
#> GSM97876 3 0.2377 0.8198 0.000 0.000 0.872 0.000 0.128
#> GSM97880 3 0.4066 0.7847 0.004 0.000 0.672 0.000 0.324
#> GSM97881 3 0.0000 0.8331 0.000 0.000 1.000 0.000 0.000
#> GSM97884 3 0.0000 0.8331 0.000 0.000 1.000 0.000 0.000
#> GSM97901 3 0.0404 0.8341 0.000 0.000 0.988 0.000 0.012
#> GSM97902 5 0.1444 0.5162 0.040 0.000 0.012 0.000 0.948
#> GSM97909 5 0.7431 0.4243 0.216 0.232 0.064 0.000 0.488
#> GSM97911 3 0.0000 0.8331 0.000 0.000 1.000 0.000 0.000
#> GSM97923 3 0.2424 0.8180 0.000 0.000 0.868 0.000 0.132
#> GSM97928 1 0.4641 0.0343 0.532 0.000 0.456 0.000 0.012
#> GSM97929 2 0.0000 0.9642 0.000 1.000 0.000 0.000 0.000
#> GSM97933 3 0.5915 0.6783 0.124 0.000 0.552 0.000 0.324
#> GSM97934 3 0.3730 0.7984 0.000 0.000 0.712 0.000 0.288
#> GSM97944 3 0.0000 0.8331 0.000 0.000 1.000 0.000 0.000
#> GSM97949 2 0.0000 0.9642 0.000 1.000 0.000 0.000 0.000
#> GSM97956 3 0.3039 0.8119 0.000 0.000 0.808 0.000 0.192
#> GSM97962 3 0.3684 0.8001 0.000 0.000 0.720 0.000 0.280
#> GSM97964 3 0.2471 0.8272 0.000 0.000 0.864 0.000 0.136
#> GSM97970 3 0.0000 0.8331 0.000 0.000 1.000 0.000 0.000
#> GSM97822 1 0.0290 0.6898 0.992 0.000 0.000 0.000 0.008
#> GSM97831 3 0.3684 0.8001 0.000 0.000 0.720 0.000 0.280
#> GSM97845 4 0.5093 0.5517 0.180 0.000 0.000 0.696 0.124
#> GSM97865 5 0.3913 0.8010 0.324 0.000 0.000 0.000 0.676
#> GSM97867 3 0.3521 0.8037 0.040 0.000 0.820 0.000 0.140
#> GSM97883 3 0.5935 0.5620 0.268 0.000 0.580 0.000 0.152
#> GSM97897 1 0.3949 0.4052 0.668 0.000 0.000 0.332 0.000
#> GSM97900 4 0.0000 0.9526 0.000 0.000 0.000 1.000 0.000
#> GSM97904 1 0.2179 0.6755 0.888 0.000 0.000 0.000 0.112
#> GSM97907 2 0.0000 0.9642 0.000 1.000 0.000 0.000 0.000
#> GSM97925 3 0.4390 0.7105 0.156 0.000 0.760 0.000 0.084
#> GSM97947 3 0.4196 0.3450 0.356 0.000 0.640 0.000 0.004
cbind(get_classes(res, k = 6), get_membership(res, k = 6))
#> class entropy silhouette p1 p2 p3 p4 p5 p6
#> GSM97800 2 0.0000 0.9920 0.000 1.000 0.000 0.000 0.000 0.000
#> GSM97803 2 0.0000 0.9920 0.000 1.000 0.000 0.000 0.000 0.000
#> GSM97804 2 0.0000 0.9920 0.000 1.000 0.000 0.000 0.000 0.000
#> GSM97805 2 0.0000 0.9920 0.000 1.000 0.000 0.000 0.000 0.000
#> GSM97807 2 0.0000 0.9920 0.000 1.000 0.000 0.000 0.000 0.000
#> GSM97809 2 0.0000 0.9920 0.000 1.000 0.000 0.000 0.000 0.000
#> GSM97811 2 0.0000 0.9920 0.000 1.000 0.000 0.000 0.000 0.000
#> GSM97812 2 0.0000 0.9920 0.000 1.000 0.000 0.000 0.000 0.000
#> GSM97816 5 0.4723 0.4911 0.000 0.272 0.032 0.000 0.664 0.032
#> GSM97817 2 0.0000 0.9920 0.000 1.000 0.000 0.000 0.000 0.000
#> GSM97820 2 0.0000 0.9920 0.000 1.000 0.000 0.000 0.000 0.000
#> GSM97825 2 0.0000 0.9920 0.000 1.000 0.000 0.000 0.000 0.000
#> GSM97827 2 0.0000 0.9920 0.000 1.000 0.000 0.000 0.000 0.000
#> GSM97828 5 0.3269 0.6352 0.000 0.000 0.024 0.000 0.792 0.184
#> GSM97833 2 0.0000 0.9920 0.000 1.000 0.000 0.000 0.000 0.000
#> GSM97834 2 0.0000 0.9920 0.000 1.000 0.000 0.000 0.000 0.000
#> GSM97840 2 0.0000 0.9920 0.000 1.000 0.000 0.000 0.000 0.000
#> GSM97846 2 0.0000 0.9920 0.000 1.000 0.000 0.000 0.000 0.000
#> GSM97848 2 0.0000 0.9920 0.000 1.000 0.000 0.000 0.000 0.000
#> GSM97849 2 0.0000 0.9920 0.000 1.000 0.000 0.000 0.000 0.000
#> GSM97850 2 0.0000 0.9920 0.000 1.000 0.000 0.000 0.000 0.000
#> GSM97853 2 0.0000 0.9920 0.000 1.000 0.000 0.000 0.000 0.000
#> GSM97855 2 0.0000 0.9920 0.000 1.000 0.000 0.000 0.000 0.000
#> GSM97878 6 0.3240 0.5670 0.244 0.000 0.004 0.000 0.000 0.752
#> GSM97913 6 0.1610 0.7344 0.084 0.000 0.000 0.000 0.000 0.916
#> GSM97932 4 0.0858 0.9337 0.000 0.000 0.000 0.968 0.004 0.028
#> GSM97939 3 0.3789 0.1347 0.000 0.000 0.584 0.000 0.416 0.000
#> GSM97951 2 0.0000 0.9920 0.000 1.000 0.000 0.000 0.000 0.000
#> GSM97957 5 0.0865 0.7565 0.000 0.000 0.036 0.000 0.964 0.000
#> GSM97972 5 0.2384 0.7365 0.000 0.000 0.048 0.000 0.888 0.064
#> GSM97793 3 0.4704 0.5702 0.100 0.000 0.664 0.000 0.236 0.000
#> GSM97795 3 0.0937 0.8070 0.000 0.040 0.960 0.000 0.000 0.000
#> GSM97802 1 0.4281 0.6063 0.708 0.000 0.220 0.000 0.072 0.000
#> GSM97810 5 0.3101 0.6332 0.000 0.000 0.244 0.000 0.756 0.000
#> GSM97815 3 0.0146 0.8472 0.000 0.000 0.996 0.000 0.004 0.000
#> GSM97837 6 0.3512 0.5140 0.272 0.000 0.000 0.000 0.008 0.720
#> GSM97843 5 0.0937 0.7564 0.000 0.000 0.040 0.000 0.960 0.000
#> GSM97890 3 0.0146 0.8472 0.000 0.000 0.996 0.000 0.004 0.000
#> GSM97899 4 0.0000 0.9595 0.000 0.000 0.000 1.000 0.000 0.000
#> GSM97910 6 0.1556 0.7350 0.080 0.000 0.000 0.000 0.000 0.920
#> GSM97916 6 0.2562 0.6844 0.172 0.000 0.000 0.000 0.000 0.828
#> GSM97920 5 0.0865 0.7565 0.000 0.000 0.036 0.000 0.964 0.000
#> GSM97921 6 0.0790 0.7325 0.032 0.000 0.000 0.000 0.000 0.968
#> GSM97927 1 0.3052 0.6477 0.780 0.000 0.004 0.000 0.000 0.216
#> GSM97937 6 0.3992 0.3836 0.364 0.000 0.000 0.000 0.012 0.624
#> GSM97941 2 0.0000 0.9920 0.000 1.000 0.000 0.000 0.000 0.000
#> GSM97943 6 0.5075 0.0633 0.076 0.000 0.000 0.000 0.460 0.464
#> GSM97958 6 0.4282 0.1680 0.000 0.000 0.020 0.000 0.420 0.560
#> GSM97960 2 0.3652 0.5798 0.000 0.720 0.016 0.000 0.264 0.000
#> GSM97794 6 0.1610 0.7344 0.084 0.000 0.000 0.000 0.000 0.916
#> GSM97796 4 0.0000 0.9595 0.000 0.000 0.000 1.000 0.000 0.000
#> GSM97797 6 0.1610 0.7344 0.084 0.000 0.000 0.000 0.000 0.916
#> GSM97798 4 0.0000 0.9595 0.000 0.000 0.000 1.000 0.000 0.000
#> GSM97801 6 0.0000 0.7258 0.000 0.000 0.000 0.000 0.000 1.000
#> GSM97806 6 0.4103 0.0261 0.448 0.000 0.004 0.000 0.004 0.544
#> GSM97808 4 0.0000 0.9595 0.000 0.000 0.000 1.000 0.000 0.000
#> GSM97813 1 0.0520 0.7620 0.984 0.000 0.000 0.000 0.008 0.008
#> GSM97814 4 0.0000 0.9595 0.000 0.000 0.000 1.000 0.000 0.000
#> GSM97818 6 0.1204 0.7345 0.056 0.000 0.000 0.000 0.000 0.944
#> GSM97819 5 0.4844 -0.0332 0.056 0.000 0.440 0.000 0.504 0.000
#> GSM97821 6 0.3996 0.6282 0.080 0.000 0.168 0.000 0.000 0.752
#> GSM97826 6 0.4109 0.3965 0.412 0.000 0.000 0.000 0.012 0.576
#> GSM97829 6 0.1367 0.7134 0.044 0.000 0.000 0.000 0.012 0.944
#> GSM97832 5 0.3874 0.6270 0.000 0.040 0.228 0.000 0.732 0.000
#> GSM97836 1 0.3565 0.5313 0.692 0.000 0.004 0.000 0.000 0.304
#> GSM97839 4 0.0000 0.9595 0.000 0.000 0.000 1.000 0.000 0.000
#> GSM97844 2 0.0000 0.9920 0.000 1.000 0.000 0.000 0.000 0.000
#> GSM97847 6 0.0291 0.7253 0.004 0.000 0.000 0.000 0.004 0.992
#> GSM97851 4 0.0000 0.9595 0.000 0.000 0.000 1.000 0.000 0.000
#> GSM97852 6 0.4114 -0.1410 0.460 0.000 0.004 0.000 0.004 0.532
#> GSM97856 4 0.0000 0.9595 0.000 0.000 0.000 1.000 0.000 0.000
#> GSM97858 2 0.0000 0.9920 0.000 1.000 0.000 0.000 0.000 0.000
#> GSM97859 1 0.0725 0.7618 0.976 0.000 0.000 0.000 0.012 0.012
#> GSM97861 1 0.3290 0.6340 0.744 0.000 0.004 0.000 0.000 0.252
#> GSM97863 4 0.0000 0.9595 0.000 0.000 0.000 1.000 0.000 0.000
#> GSM97869 6 0.2793 0.6658 0.200 0.000 0.000 0.000 0.000 0.800
#> GSM97870 1 0.0520 0.7620 0.984 0.000 0.000 0.000 0.008 0.008
#> GSM97871 4 0.0000 0.9595 0.000 0.000 0.000 1.000 0.000 0.000
#> GSM97877 6 0.1610 0.7344 0.084 0.000 0.000 0.000 0.000 0.916
#> GSM97879 1 0.5862 0.4546 0.516 0.000 0.004 0.172 0.004 0.304
#> GSM97882 1 0.3584 0.5261 0.688 0.000 0.004 0.000 0.000 0.308
#> GSM97885 6 0.3428 0.5358 0.304 0.000 0.000 0.000 0.000 0.696
#> GSM97886 4 0.0000 0.9595 0.000 0.000 0.000 1.000 0.000 0.000
#> GSM97887 4 0.3446 0.4904 0.308 0.000 0.000 0.692 0.000 0.000
#> GSM97888 1 0.2501 0.7225 0.888 0.000 0.000 0.072 0.012 0.028
#> GSM97889 1 0.0363 0.7618 0.988 0.000 0.000 0.012 0.000 0.000
#> GSM97891 1 0.3907 0.3363 0.588 0.000 0.004 0.000 0.000 0.408
#> GSM97892 2 0.0000 0.9920 0.000 1.000 0.000 0.000 0.000 0.000
#> GSM97893 4 0.0363 0.9505 0.000 0.000 0.000 0.988 0.000 0.012
#> GSM97894 4 0.0000 0.9595 0.000 0.000 0.000 1.000 0.000 0.000
#> GSM97895 4 0.1138 0.9293 0.024 0.000 0.000 0.960 0.004 0.012
#> GSM97896 4 0.0790 0.9344 0.032 0.000 0.000 0.968 0.000 0.000
#> GSM97898 4 0.0000 0.9595 0.000 0.000 0.000 1.000 0.000 0.000
#> GSM97903 6 0.1411 0.7337 0.060 0.000 0.000 0.000 0.004 0.936
#> GSM97905 1 0.1082 0.7572 0.956 0.000 0.000 0.000 0.040 0.004
#> GSM97906 4 0.0000 0.9595 0.000 0.000 0.000 1.000 0.000 0.000
#> GSM97908 6 0.4290 0.4173 0.020 0.000 0.004 0.324 0.004 0.648
#> GSM97912 1 0.0520 0.7620 0.984 0.000 0.000 0.000 0.008 0.008
#> GSM97914 6 0.0713 0.7322 0.028 0.000 0.000 0.000 0.000 0.972
#> GSM97915 4 0.0000 0.9595 0.000 0.000 0.000 1.000 0.000 0.000
#> GSM97917 4 0.0000 0.9595 0.000 0.000 0.000 1.000 0.000 0.000
#> GSM97918 4 0.0000 0.9595 0.000 0.000 0.000 1.000 0.000 0.000
#> GSM97919 4 0.0000 0.9595 0.000 0.000 0.000 1.000 0.000 0.000
#> GSM97922 1 0.0725 0.7616 0.976 0.000 0.000 0.000 0.012 0.012
#> GSM97924 2 0.0000 0.9920 0.000 1.000 0.000 0.000 0.000 0.000
#> GSM97926 1 0.4639 0.2411 0.512 0.000 0.448 0.000 0.040 0.000
#> GSM97930 6 0.0603 0.7297 0.016 0.000 0.000 0.000 0.004 0.980
#> GSM97931 6 0.4418 0.6556 0.084 0.000 0.108 0.000 0.044 0.764
#> GSM97935 1 0.3565 0.5313 0.692 0.000 0.004 0.000 0.000 0.304
#> GSM97936 4 0.0000 0.9595 0.000 0.000 0.000 1.000 0.000 0.000
#> GSM97938 4 0.6062 -0.0588 0.320 0.000 0.000 0.444 0.004 0.232
#> GSM97940 4 0.0000 0.9595 0.000 0.000 0.000 1.000 0.000 0.000
#> GSM97942 3 0.4039 0.6467 0.060 0.000 0.732 0.000 0.208 0.000
#> GSM97945 4 0.0000 0.9595 0.000 0.000 0.000 1.000 0.000 0.000
#> GSM97946 2 0.0000 0.9920 0.000 1.000 0.000 0.000 0.000 0.000
#> GSM97948 1 0.4447 0.6112 0.704 0.000 0.064 0.000 0.224 0.008
#> GSM97950 4 0.0000 0.9595 0.000 0.000 0.000 1.000 0.000 0.000
#> GSM97952 4 0.0000 0.9595 0.000 0.000 0.000 1.000 0.000 0.000
#> GSM97953 6 0.4841 -0.1639 0.452 0.000 0.000 0.032 0.012 0.504
#> GSM97954 6 0.4728 -0.1138 0.464 0.000 0.004 0.028 0.004 0.500
#> GSM97955 4 0.0146 0.9563 0.004 0.000 0.000 0.996 0.000 0.000
#> GSM97959 6 0.1610 0.7344 0.084 0.000 0.000 0.000 0.000 0.916
#> GSM97961 4 0.0000 0.9595 0.000 0.000 0.000 1.000 0.000 0.000
#> GSM97963 4 0.0000 0.9595 0.000 0.000 0.000 1.000 0.000 0.000
#> GSM97965 4 0.0000 0.9595 0.000 0.000 0.000 1.000 0.000 0.000
#> GSM97966 4 0.0000 0.9595 0.000 0.000 0.000 1.000 0.000 0.000
#> GSM97967 2 0.0000 0.9920 0.000 1.000 0.000 0.000 0.000 0.000
#> GSM97968 2 0.0000 0.9920 0.000 1.000 0.000 0.000 0.000 0.000
#> GSM97969 1 0.4600 0.6482 0.716 0.000 0.000 0.132 0.008 0.144
#> GSM97971 1 0.0622 0.7620 0.980 0.000 0.000 0.000 0.012 0.008
#> GSM97799 3 0.0146 0.8472 0.000 0.000 0.996 0.000 0.004 0.000
#> GSM97823 2 0.0000 0.9920 0.000 1.000 0.000 0.000 0.000 0.000
#> GSM97824 5 0.3101 0.6312 0.000 0.000 0.244 0.000 0.756 0.000
#> GSM97830 5 0.1152 0.7556 0.004 0.000 0.044 0.000 0.952 0.000
#> GSM97835 3 0.0146 0.8472 0.000 0.000 0.996 0.000 0.004 0.000
#> GSM97838 2 0.0000 0.9920 0.000 1.000 0.000 0.000 0.000 0.000
#> GSM97841 2 0.0000 0.9920 0.000 1.000 0.000 0.000 0.000 0.000
#> GSM97842 3 0.0260 0.8449 0.000 0.000 0.992 0.000 0.008 0.000
#> GSM97854 2 0.0000 0.9920 0.000 1.000 0.000 0.000 0.000 0.000
#> GSM97857 5 0.0865 0.7565 0.000 0.000 0.036 0.000 0.964 0.000
#> GSM97860 5 0.4080 -0.0433 0.008 0.000 0.456 0.000 0.536 0.000
#> GSM97862 3 0.3531 0.3898 0.000 0.000 0.672 0.000 0.328 0.000
#> GSM97864 2 0.0000 0.9920 0.000 1.000 0.000 0.000 0.000 0.000
#> GSM97866 5 0.3847 0.1941 0.000 0.000 0.456 0.000 0.544 0.000
#> GSM97868 3 0.0260 0.8455 0.000 0.000 0.992 0.000 0.008 0.000
#> GSM97872 1 0.2445 0.7097 0.872 0.000 0.000 0.000 0.108 0.020
#> GSM97873 3 0.0146 0.8472 0.000 0.000 0.996 0.000 0.004 0.000
#> GSM97874 5 0.0972 0.7445 0.008 0.000 0.028 0.000 0.964 0.000
#> GSM97875 3 0.0146 0.8472 0.000 0.000 0.996 0.000 0.004 0.000
#> GSM97876 3 0.3741 0.5473 0.008 0.000 0.672 0.000 0.320 0.000
#> GSM97880 5 0.0622 0.7471 0.008 0.000 0.012 0.000 0.980 0.000
#> GSM97881 3 0.0146 0.8472 0.000 0.000 0.996 0.000 0.004 0.000
#> GSM97884 3 0.0146 0.8472 0.000 0.000 0.996 0.000 0.004 0.000
#> GSM97901 3 0.3531 0.3898 0.000 0.000 0.672 0.000 0.328 0.000
#> GSM97902 5 0.3961 0.1244 0.000 0.000 0.004 0.000 0.556 0.440
#> GSM97909 6 0.6926 0.3716 0.172 0.228 0.116 0.000 0.000 0.484
#> GSM97911 3 0.0146 0.8472 0.000 0.000 0.996 0.000 0.004 0.000
#> GSM97923 3 0.3271 0.6546 0.008 0.000 0.760 0.000 0.232 0.000
#> GSM97928 1 0.4340 0.6315 0.740 0.000 0.024 0.000 0.184 0.052
#> GSM97929 2 0.0000 0.9920 0.000 1.000 0.000 0.000 0.000 0.000
#> GSM97933 5 0.0622 0.7471 0.008 0.000 0.012 0.000 0.980 0.000
#> GSM97934 5 0.1010 0.7563 0.004 0.000 0.036 0.000 0.960 0.000
#> GSM97944 3 0.0146 0.8472 0.000 0.000 0.996 0.000 0.004 0.000
#> GSM97949 2 0.0000 0.9920 0.000 1.000 0.000 0.000 0.000 0.000
#> GSM97956 5 0.3101 0.6320 0.000 0.000 0.244 0.000 0.756 0.000
#> GSM97962 5 0.0865 0.7565 0.000 0.000 0.036 0.000 0.964 0.000
#> GSM97964 5 0.3647 0.4823 0.000 0.000 0.360 0.000 0.640 0.000
#> GSM97970 3 0.0146 0.8472 0.000 0.000 0.996 0.000 0.004 0.000
#> GSM97822 1 0.1588 0.7481 0.924 0.000 0.004 0.000 0.000 0.072
#> GSM97831 5 0.1267 0.7517 0.000 0.000 0.060 0.000 0.940 0.000
#> GSM97845 4 0.4648 0.4289 0.040 0.000 0.004 0.624 0.004 0.328
#> GSM97865 6 0.0146 0.7273 0.004 0.000 0.000 0.000 0.000 0.996
#> GSM97867 5 0.5491 0.1473 0.144 0.000 0.332 0.000 0.524 0.000
#> GSM97883 5 0.4500 0.2134 0.392 0.000 0.036 0.000 0.572 0.000
#> GSM97897 1 0.2738 0.6508 0.820 0.000 0.000 0.176 0.004 0.000
#> GSM97900 4 0.0000 0.9595 0.000 0.000 0.000 1.000 0.000 0.000
#> GSM97904 1 0.2810 0.7055 0.832 0.000 0.004 0.000 0.008 0.156
#> GSM97907 2 0.0000 0.9920 0.000 1.000 0.000 0.000 0.000 0.000
#> GSM97925 3 0.2668 0.7175 0.004 0.000 0.828 0.000 0.168 0.000
#> GSM97947 3 0.2814 0.7040 0.172 0.000 0.820 0.000 0.008 0.000
Heatmaps for the consensus matrix. It visualizes the probability of two samples to be in a same group.
consensus_heatmap(res, k = 2)
consensus_heatmap(res, k = 3)
consensus_heatmap(res, k = 4)
consensus_heatmap(res, k = 5)
consensus_heatmap(res, k = 6)
Heatmaps for the membership of samples in all partitions to see how consistent they are:
membership_heatmap(res, k = 2)
membership_heatmap(res, k = 3)
membership_heatmap(res, k = 4)
membership_heatmap(res, k = 5)
membership_heatmap(res, k = 6)
As soon as we have had the classes for columns, we can look for signatures which are significantly different between classes which can be candidate marks for certain classes. Following are the heatmaps for signatures.
Signature heatmaps where rows are scaled:
get_signatures(res, k = 2)
get_signatures(res, k = 3)
get_signatures(res, k = 4)
get_signatures(res, k = 5)
get_signatures(res, k = 6)
Signature heatmaps where rows are not scaled:
get_signatures(res, k = 2, scale_rows = FALSE)
get_signatures(res, k = 3, scale_rows = FALSE)
get_signatures(res, k = 4, scale_rows = FALSE)
get_signatures(res, k = 5, scale_rows = FALSE)
get_signatures(res, k = 6, scale_rows = FALSE)
Compare the overlap of signatures from different k:
compare_signatures(res)
get_signature() returns a data frame invisibly. TO get the list of signatures, the function
call should be assigned to a variable explicitly. In following code, if plot argument is set
to FALSE, no heatmap is plotted while only the differential analysis is performed.
# code only for demonstration
tb = get_signature(res, k = ..., plot = FALSE)
An example of the output of tb is:
#> which_row fdr mean_1 mean_2 scaled_mean_1 scaled_mean_2 km
#> 1 38 0.042760348 8.373488 9.131774 -0.5533452 0.5164555 1
#> 2 40 0.018707592 7.106213 8.469186 -0.6173731 0.5762149 1
#> 3 55 0.019134737 10.221463 11.207825 -0.6159697 0.5749050 1
#> 4 59 0.006059896 5.921854 7.869574 -0.6899429 0.6439467 1
#> 5 60 0.018055526 8.928898 10.211722 -0.6204761 0.5791110 1
#> 6 98 0.009384629 15.714769 14.887706 0.6635654 -0.6193277 2
...
The columns in tb are:
which_row: row indices corresponding to the input matrix.fdr: FDR for the differential test. mean_x: The mean value in group x.scaled_mean_x: The mean value in group x after rows are scaled.km: Row groups if k-means clustering is applied to rows.UMAP plot which shows how samples are separated.
dimension_reduction(res, k = 2, method = "UMAP")
dimension_reduction(res, k = 3, method = "UMAP")
dimension_reduction(res, k = 4, method = "UMAP")
dimension_reduction(res, k = 5, method = "UMAP")
dimension_reduction(res, k = 6, method = "UMAP")
Following heatmap shows how subgroups are split when increasing k:
collect_classes(res)
Test correlation between subgroups and known annotations. If the known annotation is numeric, one-way ANOVA test is applied, and if the known annotation is discrete, chi-squared contingency table test is applied.
test_to_known_factors(res)
#> n disease.state(p) tissue(p) k
#> MAD:pam 179 1.15e-15 1.20e-15 2
#> MAD:pam 164 3.39e-29 7.07e-31 3
#> MAD:pam 166 4.70e-27 1.45e-27 4
#> MAD:pam 160 1.02e-28 2.86e-29 5
#> MAD:pam 153 8.34e-23 1.81e-22 6
If matrix rows can be associated to genes, consider to use functional_enrichment(res,
...) to perform function enrichment for the signature genes. See this vignette for more detailed explanations.
The object with results only for a single top-value method and a single partition method can be extracted as:
res = res_list["MAD", "mclust"]
# you can also extract it by
# res = res_list["MAD:mclust"]
A summary of res and all the functions that can be applied to it:
res
#> A 'ConsensusPartition' object with k = 2, 3, 4, 5, 6.
#> On a matrix with 51882 rows and 180 columns.
#> Top rows (1000, 2000, 3000, 4000, 5000) are extracted by 'MAD' method.
#> Subgroups are detected by 'mclust' method.
#> Performed in total 1250 partitions by row resampling.
#> Best k for subgroups seems to be 4.
#>
#> Following methods can be applied to this 'ConsensusPartition' object:
#> [1] "cola_report" "collect_classes" "collect_plots"
#> [4] "collect_stats" "colnames" "compare_signatures"
#> [7] "consensus_heatmap" "dimension_reduction" "functional_enrichment"
#> [10] "get_anno_col" "get_anno" "get_classes"
#> [13] "get_consensus" "get_matrix" "get_membership"
#> [16] "get_param" "get_signatures" "get_stats"
#> [19] "is_best_k" "is_stable_k" "membership_heatmap"
#> [22] "ncol" "nrow" "plot_ecdf"
#> [25] "rownames" "select_partition_number" "show"
#> [28] "suggest_best_k" "test_to_known_factors"
collect_plots() function collects all the plots made from res for all k (number of partitions)
into one single page to provide an easy and fast comparison between different k.
collect_plots(res)
The plots are:
k and the heatmap of
predicted classes for each k.k.k.k.All the plots in panels can be made by individual functions and they are plotted later in this section.
select_partition_number() produces several plots showing different
statistics for choosing “optimized” k. There are following statistics:
k;k, the area increased is defined as \(A_k - A_{k-1}\).The detailed explanations of these statistics can be found in the cola vignette.
Generally speaking, lower PAC score, higher mean silhouette score or higher
concordance corresponds to better partition. Rand index and Jaccard index
measure how similar the current partition is compared to partition with k-1.
If they are too similar, we won't accept k is better than k-1.
select_partition_number(res)
The numeric values for all these statistics can be obtained by get_stats().
get_stats(res)
#> k 1-PAC mean_silhouette concordance area_increased Rand Jaccard
#> 2 2 1.000 0.985 0.992 0.3272 0.672 0.672
#> 3 3 0.631 0.768 0.881 0.8461 0.682 0.529
#> 4 4 0.955 0.936 0.974 0.2090 0.824 0.561
#> 5 5 0.844 0.821 0.904 0.0621 0.935 0.761
#> 6 6 0.836 0.805 0.844 0.0317 0.967 0.853
suggest_best_k() suggests the best \(k\) based on these statistics. The rules are as follows:
suggest_best_k(res)
#> [1] 4
#> attr(,"optional")
#> [1] 2
There is also optional best \(k\) = 2 that is worth to check.
Following shows the table of the partitions (You need to click the show/hide
code output link to see it). The membership matrix (columns with name p*)
is inferred by
clue::cl_consensus()
function with the SE method. Basically the value in the membership matrix
represents the probability to belong to a certain group. The finall class
label for an item is determined with the group with highest probability it
belongs to.
In get_classes() function, the entropy is calculated from the membership
matrix and the silhouette score is calculated from the consensus matrix.
cbind(get_classes(res, k = 2), get_membership(res, k = 2))
#> class entropy silhouette p1 p2
#> GSM97800 2 0.0000 0.981 0.000 1.000
#> GSM97803 2 0.0000 0.981 0.000 1.000
#> GSM97804 2 0.0000 0.981 0.000 1.000
#> GSM97805 2 0.0000 0.981 0.000 1.000
#> GSM97807 2 0.0000 0.981 0.000 1.000
#> GSM97809 2 0.0000 0.981 0.000 1.000
#> GSM97811 2 0.0000 0.981 0.000 1.000
#> GSM97812 2 0.0000 0.981 0.000 1.000
#> GSM97816 1 0.0000 0.994 1.000 0.000
#> GSM97817 2 0.0000 0.981 0.000 1.000
#> GSM97820 2 0.0000 0.981 0.000 1.000
#> GSM97825 2 0.0000 0.981 0.000 1.000
#> GSM97827 2 0.0000 0.981 0.000 1.000
#> GSM97828 1 0.0000 0.994 1.000 0.000
#> GSM97833 2 0.0000 0.981 0.000 1.000
#> GSM97834 2 0.0000 0.981 0.000 1.000
#> GSM97840 2 0.9635 0.369 0.388 0.612
#> GSM97846 2 0.0000 0.981 0.000 1.000
#> GSM97848 2 0.0000 0.981 0.000 1.000
#> GSM97849 2 0.0000 0.981 0.000 1.000
#> GSM97850 2 0.0000 0.981 0.000 1.000
#> GSM97853 2 0.0000 0.981 0.000 1.000
#> GSM97855 2 0.0000 0.981 0.000 1.000
#> GSM97878 1 0.0000 0.994 1.000 0.000
#> GSM97913 1 0.0000 0.994 1.000 0.000
#> GSM97932 1 0.0000 0.994 1.000 0.000
#> GSM97939 1 0.1184 0.989 0.984 0.016
#> GSM97951 2 0.8499 0.619 0.276 0.724
#> GSM97957 1 0.1184 0.989 0.984 0.016
#> GSM97972 1 0.0376 0.993 0.996 0.004
#> GSM97793 1 0.1184 0.989 0.984 0.016
#> GSM97795 1 0.1184 0.989 0.984 0.016
#> GSM97802 1 0.0000 0.994 1.000 0.000
#> GSM97810 1 0.1184 0.989 0.984 0.016
#> GSM97815 1 0.1184 0.989 0.984 0.016
#> GSM97837 1 0.0000 0.994 1.000 0.000
#> GSM97843 1 0.1184 0.989 0.984 0.016
#> GSM97890 1 0.1184 0.989 0.984 0.016
#> GSM97899 1 0.0000 0.994 1.000 0.000
#> GSM97910 1 0.0000 0.994 1.000 0.000
#> GSM97916 1 0.0000 0.994 1.000 0.000
#> GSM97920 1 0.1184 0.989 0.984 0.016
#> GSM97921 1 0.0000 0.994 1.000 0.000
#> GSM97927 1 0.0000 0.994 1.000 0.000
#> GSM97937 1 0.0000 0.994 1.000 0.000
#> GSM97941 1 0.1184 0.989 0.984 0.016
#> GSM97943 1 0.0000 0.994 1.000 0.000
#> GSM97958 1 0.0000 0.994 1.000 0.000
#> GSM97960 1 0.1184 0.989 0.984 0.016
#> GSM97794 1 0.0000 0.994 1.000 0.000
#> GSM97796 1 0.0000 0.994 1.000 0.000
#> GSM97797 1 0.0000 0.994 1.000 0.000
#> GSM97798 1 0.0000 0.994 1.000 0.000
#> GSM97801 1 0.0000 0.994 1.000 0.000
#> GSM97806 1 0.0000 0.994 1.000 0.000
#> GSM97808 1 0.0000 0.994 1.000 0.000
#> GSM97813 1 0.0000 0.994 1.000 0.000
#> GSM97814 1 0.0000 0.994 1.000 0.000
#> GSM97818 1 0.0000 0.994 1.000 0.000
#> GSM97819 1 0.1184 0.989 0.984 0.016
#> GSM97821 1 0.0672 0.992 0.992 0.008
#> GSM97826 1 0.0000 0.994 1.000 0.000
#> GSM97829 1 0.0000 0.994 1.000 0.000
#> GSM97832 1 0.1184 0.989 0.984 0.016
#> GSM97836 1 0.0000 0.994 1.000 0.000
#> GSM97839 1 0.0000 0.994 1.000 0.000
#> GSM97844 2 0.0000 0.981 0.000 1.000
#> GSM97847 1 0.0000 0.994 1.000 0.000
#> GSM97851 1 0.0000 0.994 1.000 0.000
#> GSM97852 1 0.0000 0.994 1.000 0.000
#> GSM97856 1 0.0000 0.994 1.000 0.000
#> GSM97858 2 0.0000 0.981 0.000 1.000
#> GSM97859 1 0.0000 0.994 1.000 0.000
#> GSM97861 1 0.0000 0.994 1.000 0.000
#> GSM97863 1 0.0000 0.994 1.000 0.000
#> GSM97869 1 0.0000 0.994 1.000 0.000
#> GSM97870 1 0.0000 0.994 1.000 0.000
#> GSM97871 1 0.0000 0.994 1.000 0.000
#> GSM97877 1 0.0000 0.994 1.000 0.000
#> GSM97879 1 0.0000 0.994 1.000 0.000
#> GSM97882 1 0.0000 0.994 1.000 0.000
#> GSM97885 1 0.0000 0.994 1.000 0.000
#> GSM97886 1 0.0000 0.994 1.000 0.000
#> GSM97887 1 0.0000 0.994 1.000 0.000
#> GSM97888 1 0.0000 0.994 1.000 0.000
#> GSM97889 1 0.0000 0.994 1.000 0.000
#> GSM97891 1 0.0000 0.994 1.000 0.000
#> GSM97892 2 0.0000 0.981 0.000 1.000
#> GSM97893 1 0.0000 0.994 1.000 0.000
#> GSM97894 1 0.0000 0.994 1.000 0.000
#> GSM97895 1 0.0000 0.994 1.000 0.000
#> GSM97896 1 0.0000 0.994 1.000 0.000
#> GSM97898 1 0.0000 0.994 1.000 0.000
#> GSM97903 1 0.0000 0.994 1.000 0.000
#> GSM97905 1 0.0000 0.994 1.000 0.000
#> GSM97906 1 0.0000 0.994 1.000 0.000
#> GSM97908 1 0.0000 0.994 1.000 0.000
#> GSM97912 1 0.0000 0.994 1.000 0.000
#> GSM97914 1 0.0000 0.994 1.000 0.000
#> GSM97915 1 0.0000 0.994 1.000 0.000
#> GSM97917 1 0.0000 0.994 1.000 0.000
#> GSM97918 1 0.0000 0.994 1.000 0.000
#> GSM97919 1 0.0000 0.994 1.000 0.000
#> GSM97922 1 0.0000 0.994 1.000 0.000
#> GSM97924 2 0.0000 0.981 0.000 1.000
#> GSM97926 1 0.0672 0.992 0.992 0.008
#> GSM97930 1 0.0000 0.994 1.000 0.000
#> GSM97931 1 0.0000 0.994 1.000 0.000
#> GSM97935 1 0.0000 0.994 1.000 0.000
#> GSM97936 1 0.0000 0.994 1.000 0.000
#> GSM97938 1 0.0000 0.994 1.000 0.000
#> GSM97940 1 0.0000 0.994 1.000 0.000
#> GSM97942 1 0.1184 0.989 0.984 0.016
#> GSM97945 1 0.0000 0.994 1.000 0.000
#> GSM97946 2 0.0000 0.981 0.000 1.000
#> GSM97948 1 0.0376 0.993 0.996 0.004
#> GSM97950 1 0.0000 0.994 1.000 0.000
#> GSM97952 1 0.0000 0.994 1.000 0.000
#> GSM97953 1 0.0000 0.994 1.000 0.000
#> GSM97954 1 0.0000 0.994 1.000 0.000
#> GSM97955 1 0.0000 0.994 1.000 0.000
#> GSM97959 1 0.0000 0.994 1.000 0.000
#> GSM97961 1 0.0000 0.994 1.000 0.000
#> GSM97963 1 0.0000 0.994 1.000 0.000
#> GSM97965 1 0.0000 0.994 1.000 0.000
#> GSM97966 1 0.0000 0.994 1.000 0.000
#> GSM97967 2 0.0000 0.981 0.000 1.000
#> GSM97968 2 0.0000 0.981 0.000 1.000
#> GSM97969 1 0.0000 0.994 1.000 0.000
#> GSM97971 1 0.0000 0.994 1.000 0.000
#> GSM97799 1 0.1184 0.989 0.984 0.016
#> GSM97823 2 0.0000 0.981 0.000 1.000
#> GSM97824 1 0.1184 0.989 0.984 0.016
#> GSM97830 1 0.1184 0.989 0.984 0.016
#> GSM97835 1 0.1184 0.989 0.984 0.016
#> GSM97838 2 0.0000 0.981 0.000 1.000
#> GSM97841 2 0.0000 0.981 0.000 1.000
#> GSM97842 1 0.1184 0.989 0.984 0.016
#> GSM97854 2 0.0000 0.981 0.000 1.000
#> GSM97857 1 0.1184 0.989 0.984 0.016
#> GSM97860 1 0.1184 0.989 0.984 0.016
#> GSM97862 1 0.1184 0.989 0.984 0.016
#> GSM97864 2 0.0000 0.981 0.000 1.000
#> GSM97866 1 0.1184 0.989 0.984 0.016
#> GSM97868 1 0.1184 0.989 0.984 0.016
#> GSM97872 1 0.0000 0.994 1.000 0.000
#> GSM97873 1 0.1184 0.989 0.984 0.016
#> GSM97874 1 0.1184 0.989 0.984 0.016
#> GSM97875 1 0.1184 0.989 0.984 0.016
#> GSM97876 1 0.1184 0.989 0.984 0.016
#> GSM97880 1 0.1184 0.989 0.984 0.016
#> GSM97881 1 0.1184 0.989 0.984 0.016
#> GSM97884 1 0.1184 0.989 0.984 0.016
#> GSM97901 1 0.1184 0.989 0.984 0.016
#> GSM97902 1 0.0000 0.994 1.000 0.000
#> GSM97909 1 0.1184 0.989 0.984 0.016
#> GSM97911 1 0.1184 0.989 0.984 0.016
#> GSM97923 1 0.1184 0.989 0.984 0.016
#> GSM97928 1 0.0000 0.994 1.000 0.000
#> GSM97929 2 0.0000 0.981 0.000 1.000
#> GSM97933 1 0.1184 0.989 0.984 0.016
#> GSM97934 1 0.1184 0.989 0.984 0.016
#> GSM97944 1 0.1184 0.989 0.984 0.016
#> GSM97949 2 0.0000 0.981 0.000 1.000
#> GSM97956 1 0.1184 0.989 0.984 0.016
#> GSM97962 1 0.1184 0.989 0.984 0.016
#> GSM97964 1 0.1184 0.989 0.984 0.016
#> GSM97970 1 0.1184 0.989 0.984 0.016
#> GSM97822 1 0.0000 0.994 1.000 0.000
#> GSM97831 1 0.1184 0.989 0.984 0.016
#> GSM97845 1 0.0000 0.994 1.000 0.000
#> GSM97865 1 0.0000 0.994 1.000 0.000
#> GSM97867 1 0.1184 0.989 0.984 0.016
#> GSM97883 1 0.1184 0.989 0.984 0.016
#> GSM97897 1 0.0000 0.994 1.000 0.000
#> GSM97900 1 0.0000 0.994 1.000 0.000
#> GSM97904 1 0.0000 0.994 1.000 0.000
#> GSM97907 2 0.0000 0.981 0.000 1.000
#> GSM97925 1 0.1184 0.989 0.984 0.016
#> GSM97947 1 0.1184 0.989 0.984 0.016
cbind(get_classes(res, k = 3), get_membership(res, k = 3))
#> class entropy silhouette p1 p2 p3
#> GSM97800 2 0.0000 0.989 0.000 1.000 0.000
#> GSM97803 2 0.0000 0.989 0.000 1.000 0.000
#> GSM97804 2 0.0000 0.989 0.000 1.000 0.000
#> GSM97805 2 0.0000 0.989 0.000 1.000 0.000
#> GSM97807 2 0.0000 0.989 0.000 1.000 0.000
#> GSM97809 2 0.0000 0.989 0.000 1.000 0.000
#> GSM97811 2 0.0000 0.989 0.000 1.000 0.000
#> GSM97812 2 0.0000 0.989 0.000 1.000 0.000
#> GSM97816 3 0.5905 0.322 0.352 0.000 0.648
#> GSM97817 2 0.0000 0.989 0.000 1.000 0.000
#> GSM97820 2 0.0000 0.989 0.000 1.000 0.000
#> GSM97825 2 0.0000 0.989 0.000 1.000 0.000
#> GSM97827 2 0.0000 0.989 0.000 1.000 0.000
#> GSM97828 3 0.6008 0.256 0.372 0.000 0.628
#> GSM97833 2 0.0000 0.989 0.000 1.000 0.000
#> GSM97834 2 0.0000 0.989 0.000 1.000 0.000
#> GSM97840 3 0.8550 0.465 0.176 0.216 0.608
#> GSM97846 2 0.0000 0.989 0.000 1.000 0.000
#> GSM97848 2 0.0000 0.989 0.000 1.000 0.000
#> GSM97849 2 0.0000 0.989 0.000 1.000 0.000
#> GSM97850 2 0.0000 0.989 0.000 1.000 0.000
#> GSM97853 2 0.0000 0.989 0.000 1.000 0.000
#> GSM97855 2 0.0000 0.989 0.000 1.000 0.000
#> GSM97878 1 0.5882 0.670 0.652 0.000 0.348
#> GSM97913 3 0.5988 0.270 0.368 0.000 0.632
#> GSM97932 1 0.1411 0.767 0.964 0.000 0.036
#> GSM97939 3 0.0000 0.865 0.000 0.000 1.000
#> GSM97951 2 0.6148 0.428 0.004 0.640 0.356
#> GSM97957 3 0.0000 0.865 0.000 0.000 1.000
#> GSM97972 3 0.5905 0.322 0.352 0.000 0.648
#> GSM97793 3 0.0000 0.865 0.000 0.000 1.000
#> GSM97795 3 0.0000 0.865 0.000 0.000 1.000
#> GSM97802 3 0.5926 0.309 0.356 0.000 0.644
#> GSM97810 3 0.0000 0.865 0.000 0.000 1.000
#> GSM97815 3 0.0000 0.865 0.000 0.000 1.000
#> GSM97837 1 0.6244 0.486 0.560 0.000 0.440
#> GSM97843 3 0.0000 0.865 0.000 0.000 1.000
#> GSM97890 3 0.0000 0.865 0.000 0.000 1.000
#> GSM97899 1 0.0000 0.760 1.000 0.000 0.000
#> GSM97910 1 0.6244 0.486 0.560 0.000 0.440
#> GSM97916 1 0.5968 0.646 0.636 0.000 0.364
#> GSM97920 3 0.0000 0.865 0.000 0.000 1.000
#> GSM97921 1 0.5905 0.665 0.648 0.000 0.352
#> GSM97927 1 0.5327 0.755 0.728 0.000 0.272
#> GSM97937 1 0.5926 0.658 0.644 0.000 0.356
#> GSM97941 3 0.5905 0.322 0.352 0.000 0.648
#> GSM97943 3 0.6154 0.111 0.408 0.000 0.592
#> GSM97958 3 0.5968 0.284 0.364 0.000 0.636
#> GSM97960 3 0.0000 0.865 0.000 0.000 1.000
#> GSM97794 1 0.6244 0.486 0.560 0.000 0.440
#> GSM97796 1 0.0000 0.760 1.000 0.000 0.000
#> GSM97797 1 0.6252 0.475 0.556 0.000 0.444
#> GSM97798 1 0.0000 0.760 1.000 0.000 0.000
#> GSM97801 1 0.6192 0.535 0.580 0.000 0.420
#> GSM97806 1 0.5327 0.755 0.728 0.000 0.272
#> GSM97808 1 0.0000 0.760 1.000 0.000 0.000
#> GSM97813 1 0.4235 0.780 0.824 0.000 0.176
#> GSM97814 1 0.0000 0.760 1.000 0.000 0.000
#> GSM97818 1 0.6244 0.486 0.560 0.000 0.440
#> GSM97819 3 0.0000 0.865 0.000 0.000 1.000
#> GSM97821 3 0.5882 0.332 0.348 0.000 0.652
#> GSM97826 1 0.6154 0.561 0.592 0.000 0.408
#> GSM97829 1 0.6008 0.632 0.628 0.000 0.372
#> GSM97832 3 0.0000 0.865 0.000 0.000 1.000
#> GSM97836 1 0.5327 0.755 0.728 0.000 0.272
#> GSM97839 1 0.0000 0.760 1.000 0.000 0.000
#> GSM97844 2 0.0000 0.989 0.000 1.000 0.000
#> GSM97847 1 0.5327 0.755 0.728 0.000 0.272
#> GSM97851 1 0.0000 0.760 1.000 0.000 0.000
#> GSM97852 1 0.5327 0.755 0.728 0.000 0.272
#> GSM97856 1 0.0000 0.760 1.000 0.000 0.000
#> GSM97858 2 0.0000 0.989 0.000 1.000 0.000
#> GSM97859 1 0.5529 0.732 0.704 0.000 0.296
#> GSM97861 1 0.5327 0.755 0.728 0.000 0.272
#> GSM97863 1 0.0000 0.760 1.000 0.000 0.000
#> GSM97869 1 0.5905 0.665 0.648 0.000 0.352
#> GSM97870 3 0.6095 0.180 0.392 0.000 0.608
#> GSM97871 1 0.0000 0.760 1.000 0.000 0.000
#> GSM97877 3 0.5926 0.310 0.356 0.000 0.644
#> GSM97879 1 0.5327 0.755 0.728 0.000 0.272
#> GSM97882 1 0.5327 0.755 0.728 0.000 0.272
#> GSM97885 1 0.5327 0.755 0.728 0.000 0.272
#> GSM97886 1 0.0000 0.760 1.000 0.000 0.000
#> GSM97887 1 0.0000 0.760 1.000 0.000 0.000
#> GSM97888 1 0.4178 0.780 0.828 0.000 0.172
#> GSM97889 1 0.5327 0.755 0.728 0.000 0.272
#> GSM97891 1 0.5327 0.755 0.728 0.000 0.272
#> GSM97892 2 0.0000 0.989 0.000 1.000 0.000
#> GSM97893 1 0.3879 0.781 0.848 0.000 0.152
#> GSM97894 1 0.0000 0.760 1.000 0.000 0.000
#> GSM97895 1 0.2711 0.776 0.912 0.000 0.088
#> GSM97896 1 0.0000 0.760 1.000 0.000 0.000
#> GSM97898 1 0.0000 0.760 1.000 0.000 0.000
#> GSM97903 1 0.5327 0.755 0.728 0.000 0.272
#> GSM97905 3 0.6140 0.128 0.404 0.000 0.596
#> GSM97906 1 0.0000 0.760 1.000 0.000 0.000
#> GSM97908 1 0.4235 0.780 0.824 0.000 0.176
#> GSM97912 1 0.6244 0.486 0.560 0.000 0.440
#> GSM97914 1 0.5905 0.665 0.648 0.000 0.352
#> GSM97915 1 0.0000 0.760 1.000 0.000 0.000
#> GSM97917 1 0.2261 0.773 0.932 0.000 0.068
#> GSM97918 1 0.0000 0.760 1.000 0.000 0.000
#> GSM97919 1 0.0000 0.760 1.000 0.000 0.000
#> GSM97922 1 0.4121 0.780 0.832 0.000 0.168
#> GSM97924 2 0.0000 0.989 0.000 1.000 0.000
#> GSM97926 3 0.0237 0.861 0.004 0.000 0.996
#> GSM97930 1 0.5363 0.751 0.724 0.000 0.276
#> GSM97931 3 0.5905 0.322 0.352 0.000 0.648
#> GSM97935 1 0.5327 0.755 0.728 0.000 0.272
#> GSM97936 1 0.2711 0.777 0.912 0.000 0.088
#> GSM97938 1 0.4504 0.777 0.804 0.000 0.196
#> GSM97940 1 0.0000 0.760 1.000 0.000 0.000
#> GSM97942 3 0.0000 0.865 0.000 0.000 1.000
#> GSM97945 1 0.2796 0.777 0.908 0.000 0.092
#> GSM97946 2 0.0000 0.989 0.000 1.000 0.000
#> GSM97948 3 0.1529 0.829 0.040 0.000 0.960
#> GSM97950 1 0.0000 0.760 1.000 0.000 0.000
#> GSM97952 1 0.0000 0.760 1.000 0.000 0.000
#> GSM97953 1 0.5621 0.719 0.692 0.000 0.308
#> GSM97954 1 0.5016 0.766 0.760 0.000 0.240
#> GSM97955 1 0.3619 0.781 0.864 0.000 0.136
#> GSM97959 3 0.6140 0.129 0.404 0.000 0.596
#> GSM97961 1 0.0000 0.760 1.000 0.000 0.000
#> GSM97963 1 0.0000 0.760 1.000 0.000 0.000
#> GSM97965 1 0.0000 0.760 1.000 0.000 0.000
#> GSM97966 1 0.0000 0.760 1.000 0.000 0.000
#> GSM97967 2 0.0000 0.989 0.000 1.000 0.000
#> GSM97968 2 0.0592 0.977 0.000 0.988 0.012
#> GSM97969 1 0.4291 0.779 0.820 0.000 0.180
#> GSM97971 1 0.5785 0.691 0.668 0.000 0.332
#> GSM97799 3 0.0000 0.865 0.000 0.000 1.000
#> GSM97823 2 0.0000 0.989 0.000 1.000 0.000
#> GSM97824 3 0.0000 0.865 0.000 0.000 1.000
#> GSM97830 3 0.0000 0.865 0.000 0.000 1.000
#> GSM97835 3 0.0000 0.865 0.000 0.000 1.000
#> GSM97838 2 0.0000 0.989 0.000 1.000 0.000
#> GSM97841 2 0.0000 0.989 0.000 1.000 0.000
#> GSM97842 3 0.0000 0.865 0.000 0.000 1.000
#> GSM97854 2 0.0000 0.989 0.000 1.000 0.000
#> GSM97857 3 0.0000 0.865 0.000 0.000 1.000
#> GSM97860 3 0.0000 0.865 0.000 0.000 1.000
#> GSM97862 3 0.0000 0.865 0.000 0.000 1.000
#> GSM97864 2 0.0000 0.989 0.000 1.000 0.000
#> GSM97866 3 0.0000 0.865 0.000 0.000 1.000
#> GSM97868 3 0.0000 0.865 0.000 0.000 1.000
#> GSM97872 1 0.5948 0.652 0.640 0.000 0.360
#> GSM97873 3 0.0000 0.865 0.000 0.000 1.000
#> GSM97874 3 0.0000 0.865 0.000 0.000 1.000
#> GSM97875 3 0.0000 0.865 0.000 0.000 1.000
#> GSM97876 3 0.0000 0.865 0.000 0.000 1.000
#> GSM97880 3 0.0000 0.865 0.000 0.000 1.000
#> GSM97881 3 0.0000 0.865 0.000 0.000 1.000
#> GSM97884 3 0.0000 0.865 0.000 0.000 1.000
#> GSM97901 3 0.0000 0.865 0.000 0.000 1.000
#> GSM97902 1 0.6280 0.428 0.540 0.000 0.460
#> GSM97909 3 0.5882 0.332 0.348 0.000 0.652
#> GSM97911 3 0.0000 0.865 0.000 0.000 1.000
#> GSM97923 3 0.0000 0.865 0.000 0.000 1.000
#> GSM97928 1 0.5327 0.755 0.728 0.000 0.272
#> GSM97929 2 0.0000 0.989 0.000 1.000 0.000
#> GSM97933 3 0.0000 0.865 0.000 0.000 1.000
#> GSM97934 3 0.0000 0.865 0.000 0.000 1.000
#> GSM97944 3 0.0000 0.865 0.000 0.000 1.000
#> GSM97949 2 0.0000 0.989 0.000 1.000 0.000
#> GSM97956 3 0.0000 0.865 0.000 0.000 1.000
#> GSM97962 3 0.0000 0.865 0.000 0.000 1.000
#> GSM97964 3 0.0000 0.865 0.000 0.000 1.000
#> GSM97970 3 0.0000 0.865 0.000 0.000 1.000
#> GSM97822 1 0.5327 0.755 0.728 0.000 0.272
#> GSM97831 3 0.0000 0.865 0.000 0.000 1.000
#> GSM97845 1 0.4842 0.770 0.776 0.000 0.224
#> GSM97865 1 0.6008 0.632 0.628 0.000 0.372
#> GSM97867 3 0.0000 0.865 0.000 0.000 1.000
#> GSM97883 3 0.0000 0.865 0.000 0.000 1.000
#> GSM97897 1 0.2537 0.776 0.920 0.000 0.080
#> GSM97900 1 0.0000 0.760 1.000 0.000 0.000
#> GSM97904 1 0.5363 0.751 0.724 0.000 0.276
#> GSM97907 2 0.0000 0.989 0.000 1.000 0.000
#> GSM97925 3 0.0000 0.865 0.000 0.000 1.000
#> GSM97947 3 0.0000 0.865 0.000 0.000 1.000
cbind(get_classes(res, k = 4), get_membership(res, k = 4))
#> class entropy silhouette p1 p2 p3 p4
#> GSM97800 2 0.0000 0.984 0.000 1.000 0.000 0.000
#> GSM97803 2 0.0000 0.984 0.000 1.000 0.000 0.000
#> GSM97804 2 0.0000 0.984 0.000 1.000 0.000 0.000
#> GSM97805 2 0.0000 0.984 0.000 1.000 0.000 0.000
#> GSM97807 2 0.0000 0.984 0.000 1.000 0.000 0.000
#> GSM97809 2 0.0000 0.984 0.000 1.000 0.000 0.000
#> GSM97811 2 0.0000 0.984 0.000 1.000 0.000 0.000
#> GSM97812 2 0.0000 0.984 0.000 1.000 0.000 0.000
#> GSM97816 3 0.3610 0.753 0.200 0.000 0.800 0.000
#> GSM97817 2 0.0000 0.984 0.000 1.000 0.000 0.000
#> GSM97820 2 0.0000 0.984 0.000 1.000 0.000 0.000
#> GSM97825 2 0.0000 0.984 0.000 1.000 0.000 0.000
#> GSM97827 2 0.0000 0.984 0.000 1.000 0.000 0.000
#> GSM97828 3 0.3610 0.753 0.200 0.000 0.800 0.000
#> GSM97833 2 0.0000 0.984 0.000 1.000 0.000 0.000
#> GSM97834 2 0.0000 0.984 0.000 1.000 0.000 0.000
#> GSM97840 2 0.4741 0.509 0.328 0.668 0.004 0.000
#> GSM97846 2 0.0000 0.984 0.000 1.000 0.000 0.000
#> GSM97848 2 0.0000 0.984 0.000 1.000 0.000 0.000
#> GSM97849 2 0.0000 0.984 0.000 1.000 0.000 0.000
#> GSM97850 2 0.0000 0.984 0.000 1.000 0.000 0.000
#> GSM97853 2 0.0000 0.984 0.000 1.000 0.000 0.000
#> GSM97855 2 0.0000 0.984 0.000 1.000 0.000 0.000
#> GSM97878 1 0.0000 0.977 1.000 0.000 0.000 0.000
#> GSM97913 1 0.0000 0.977 1.000 0.000 0.000 0.000
#> GSM97932 4 0.0921 0.913 0.028 0.000 0.000 0.972
#> GSM97939 3 0.0000 0.969 0.000 0.000 1.000 0.000
#> GSM97951 2 0.1637 0.912 0.060 0.940 0.000 0.000
#> GSM97957 3 0.0000 0.969 0.000 0.000 1.000 0.000
#> GSM97972 3 0.3486 0.768 0.188 0.000 0.812 0.000
#> GSM97793 3 0.0000 0.969 0.000 0.000 1.000 0.000
#> GSM97795 3 0.1474 0.925 0.052 0.000 0.948 0.000
#> GSM97802 1 0.2011 0.890 0.920 0.000 0.080 0.000
#> GSM97810 3 0.1474 0.925 0.052 0.000 0.948 0.000
#> GSM97815 3 0.1474 0.925 0.052 0.000 0.948 0.000
#> GSM97837 1 0.0000 0.977 1.000 0.000 0.000 0.000
#> GSM97843 3 0.0000 0.969 0.000 0.000 1.000 0.000
#> GSM97890 3 0.0000 0.969 0.000 0.000 1.000 0.000
#> GSM97899 4 0.0336 0.924 0.008 0.000 0.000 0.992
#> GSM97910 1 0.0000 0.977 1.000 0.000 0.000 0.000
#> GSM97916 1 0.0000 0.977 1.000 0.000 0.000 0.000
#> GSM97920 3 0.0000 0.969 0.000 0.000 1.000 0.000
#> GSM97921 1 0.0000 0.977 1.000 0.000 0.000 0.000
#> GSM97927 1 0.0000 0.977 1.000 0.000 0.000 0.000
#> GSM97937 1 0.0000 0.977 1.000 0.000 0.000 0.000
#> GSM97941 1 0.2530 0.867 0.896 0.100 0.004 0.000
#> GSM97943 3 0.4103 0.675 0.256 0.000 0.744 0.000
#> GSM97958 1 0.0188 0.973 0.996 0.000 0.004 0.000
#> GSM97960 3 0.1474 0.925 0.052 0.000 0.948 0.000
#> GSM97794 1 0.0000 0.977 1.000 0.000 0.000 0.000
#> GSM97796 4 0.0000 0.928 0.000 0.000 0.000 1.000
#> GSM97797 1 0.0000 0.977 1.000 0.000 0.000 0.000
#> GSM97798 4 0.0000 0.928 0.000 0.000 0.000 1.000
#> GSM97801 1 0.0000 0.977 1.000 0.000 0.000 0.000
#> GSM97806 1 0.0000 0.977 1.000 0.000 0.000 0.000
#> GSM97808 4 0.0000 0.928 0.000 0.000 0.000 1.000
#> GSM97813 1 0.0000 0.977 1.000 0.000 0.000 0.000
#> GSM97814 4 0.0000 0.928 0.000 0.000 0.000 1.000
#> GSM97818 1 0.0000 0.977 1.000 0.000 0.000 0.000
#> GSM97819 3 0.0000 0.969 0.000 0.000 1.000 0.000
#> GSM97821 1 0.0188 0.973 0.996 0.000 0.004 0.000
#> GSM97826 1 0.0000 0.977 1.000 0.000 0.000 0.000
#> GSM97829 1 0.0000 0.977 1.000 0.000 0.000 0.000
#> GSM97832 3 0.1474 0.925 0.052 0.000 0.948 0.000
#> GSM97836 1 0.0000 0.977 1.000 0.000 0.000 0.000
#> GSM97839 4 0.0000 0.928 0.000 0.000 0.000 1.000
#> GSM97844 2 0.0000 0.984 0.000 1.000 0.000 0.000
#> GSM97847 1 0.0000 0.977 1.000 0.000 0.000 0.000
#> GSM97851 4 0.0000 0.928 0.000 0.000 0.000 1.000
#> GSM97852 1 0.0000 0.977 1.000 0.000 0.000 0.000
#> GSM97856 4 0.0000 0.928 0.000 0.000 0.000 1.000
#> GSM97858 2 0.0000 0.984 0.000 1.000 0.000 0.000
#> GSM97859 1 0.0000 0.977 1.000 0.000 0.000 0.000
#> GSM97861 1 0.0000 0.977 1.000 0.000 0.000 0.000
#> GSM97863 4 0.0000 0.928 0.000 0.000 0.000 1.000
#> GSM97869 1 0.0000 0.977 1.000 0.000 0.000 0.000
#> GSM97870 1 0.1867 0.899 0.928 0.000 0.072 0.000
#> GSM97871 4 0.0000 0.928 0.000 0.000 0.000 1.000
#> GSM97877 1 0.0000 0.977 1.000 0.000 0.000 0.000
#> GSM97879 1 0.0000 0.977 1.000 0.000 0.000 0.000
#> GSM97882 1 0.0000 0.977 1.000 0.000 0.000 0.000
#> GSM97885 1 0.0000 0.977 1.000 0.000 0.000 0.000
#> GSM97886 4 0.2647 0.843 0.120 0.000 0.000 0.880
#> GSM97887 1 0.4907 0.221 0.580 0.000 0.000 0.420
#> GSM97888 1 0.0000 0.977 1.000 0.000 0.000 0.000
#> GSM97889 1 0.0000 0.977 1.000 0.000 0.000 0.000
#> GSM97891 1 0.0000 0.977 1.000 0.000 0.000 0.000
#> GSM97892 2 0.0000 0.984 0.000 1.000 0.000 0.000
#> GSM97893 1 0.1474 0.928 0.948 0.000 0.000 0.052
#> GSM97894 4 0.0000 0.928 0.000 0.000 0.000 1.000
#> GSM97895 1 0.1792 0.912 0.932 0.000 0.000 0.068
#> GSM97896 4 0.4992 0.133 0.476 0.000 0.000 0.524
#> GSM97898 4 0.0000 0.928 0.000 0.000 0.000 1.000
#> GSM97903 1 0.0000 0.977 1.000 0.000 0.000 0.000
#> GSM97905 1 0.0188 0.973 0.996 0.000 0.004 0.000
#> GSM97906 4 0.1474 0.897 0.052 0.000 0.000 0.948
#> GSM97908 1 0.0000 0.977 1.000 0.000 0.000 0.000
#> GSM97912 1 0.0000 0.977 1.000 0.000 0.000 0.000
#> GSM97914 1 0.0000 0.977 1.000 0.000 0.000 0.000
#> GSM97915 4 0.0000 0.928 0.000 0.000 0.000 1.000
#> GSM97917 4 0.4967 0.217 0.452 0.000 0.000 0.548
#> GSM97918 4 0.0000 0.928 0.000 0.000 0.000 1.000
#> GSM97919 4 0.0000 0.928 0.000 0.000 0.000 1.000
#> GSM97922 1 0.0000 0.977 1.000 0.000 0.000 0.000
#> GSM97924 2 0.0000 0.984 0.000 1.000 0.000 0.000
#> GSM97926 3 0.2760 0.837 0.128 0.000 0.872 0.000
#> GSM97930 1 0.0000 0.977 1.000 0.000 0.000 0.000
#> GSM97931 1 0.0188 0.973 0.996 0.000 0.004 0.000
#> GSM97935 1 0.0000 0.977 1.000 0.000 0.000 0.000
#> GSM97936 4 0.3074 0.809 0.152 0.000 0.000 0.848
#> GSM97938 1 0.0000 0.977 1.000 0.000 0.000 0.000
#> GSM97940 4 0.0000 0.928 0.000 0.000 0.000 1.000
#> GSM97942 3 0.0000 0.969 0.000 0.000 1.000 0.000
#> GSM97945 4 0.3569 0.767 0.196 0.000 0.000 0.804
#> GSM97946 2 0.0000 0.984 0.000 1.000 0.000 0.000
#> GSM97948 1 0.4585 0.513 0.668 0.000 0.332 0.000
#> GSM97950 4 0.1867 0.882 0.072 0.000 0.000 0.928
#> GSM97952 4 0.0000 0.928 0.000 0.000 0.000 1.000
#> GSM97953 1 0.0000 0.977 1.000 0.000 0.000 0.000
#> GSM97954 1 0.0000 0.977 1.000 0.000 0.000 0.000
#> GSM97955 4 0.3486 0.777 0.188 0.000 0.000 0.812
#> GSM97959 1 0.0000 0.977 1.000 0.000 0.000 0.000
#> GSM97961 4 0.0000 0.928 0.000 0.000 0.000 1.000
#> GSM97963 4 0.0000 0.928 0.000 0.000 0.000 1.000
#> GSM97965 4 0.0000 0.928 0.000 0.000 0.000 1.000
#> GSM97966 4 0.0000 0.928 0.000 0.000 0.000 1.000
#> GSM97967 2 0.0000 0.984 0.000 1.000 0.000 0.000
#> GSM97968 2 0.1474 0.921 0.052 0.948 0.000 0.000
#> GSM97969 1 0.0000 0.977 1.000 0.000 0.000 0.000
#> GSM97971 1 0.0000 0.977 1.000 0.000 0.000 0.000
#> GSM97799 3 0.0000 0.969 0.000 0.000 1.000 0.000
#> GSM97823 2 0.0000 0.984 0.000 1.000 0.000 0.000
#> GSM97824 3 0.0000 0.969 0.000 0.000 1.000 0.000
#> GSM97830 3 0.0000 0.969 0.000 0.000 1.000 0.000
#> GSM97835 3 0.0000 0.969 0.000 0.000 1.000 0.000
#> GSM97838 2 0.0000 0.984 0.000 1.000 0.000 0.000
#> GSM97841 2 0.0000 0.984 0.000 1.000 0.000 0.000
#> GSM97842 3 0.0000 0.969 0.000 0.000 1.000 0.000
#> GSM97854 2 0.0000 0.984 0.000 1.000 0.000 0.000
#> GSM97857 3 0.0000 0.969 0.000 0.000 1.000 0.000
#> GSM97860 3 0.0000 0.969 0.000 0.000 1.000 0.000
#> GSM97862 3 0.0000 0.969 0.000 0.000 1.000 0.000
#> GSM97864 2 0.0000 0.984 0.000 1.000 0.000 0.000
#> GSM97866 3 0.0000 0.969 0.000 0.000 1.000 0.000
#> GSM97868 3 0.0000 0.969 0.000 0.000 1.000 0.000
#> GSM97872 1 0.0000 0.977 1.000 0.000 0.000 0.000
#> GSM97873 3 0.0000 0.969 0.000 0.000 1.000 0.000
#> GSM97874 3 0.0000 0.969 0.000 0.000 1.000 0.000
#> GSM97875 3 0.0000 0.969 0.000 0.000 1.000 0.000
#> GSM97876 3 0.0000 0.969 0.000 0.000 1.000 0.000
#> GSM97880 3 0.0000 0.969 0.000 0.000 1.000 0.000
#> GSM97881 3 0.0000 0.969 0.000 0.000 1.000 0.000
#> GSM97884 3 0.0000 0.969 0.000 0.000 1.000 0.000
#> GSM97901 3 0.0000 0.969 0.000 0.000 1.000 0.000
#> GSM97902 1 0.0000 0.977 1.000 0.000 0.000 0.000
#> GSM97909 1 0.0188 0.973 0.996 0.000 0.004 0.000
#> GSM97911 3 0.0000 0.969 0.000 0.000 1.000 0.000
#> GSM97923 3 0.0000 0.969 0.000 0.000 1.000 0.000
#> GSM97928 1 0.0000 0.977 1.000 0.000 0.000 0.000
#> GSM97929 2 0.0000 0.984 0.000 1.000 0.000 0.000
#> GSM97933 3 0.0000 0.969 0.000 0.000 1.000 0.000
#> GSM97934 3 0.0000 0.969 0.000 0.000 1.000 0.000
#> GSM97944 3 0.0000 0.969 0.000 0.000 1.000 0.000
#> GSM97949 2 0.0000 0.984 0.000 1.000 0.000 0.000
#> GSM97956 3 0.0000 0.969 0.000 0.000 1.000 0.000
#> GSM97962 3 0.0000 0.969 0.000 0.000 1.000 0.000
#> GSM97964 3 0.0000 0.969 0.000 0.000 1.000 0.000
#> GSM97970 3 0.0000 0.969 0.000 0.000 1.000 0.000
#> GSM97822 1 0.0000 0.977 1.000 0.000 0.000 0.000
#> GSM97831 3 0.0000 0.969 0.000 0.000 1.000 0.000
#> GSM97845 1 0.0000 0.977 1.000 0.000 0.000 0.000
#> GSM97865 1 0.0000 0.977 1.000 0.000 0.000 0.000
#> GSM97867 3 0.0000 0.969 0.000 0.000 1.000 0.000
#> GSM97883 3 0.0000 0.969 0.000 0.000 1.000 0.000
#> GSM97897 1 0.0592 0.963 0.984 0.000 0.000 0.016
#> GSM97900 1 0.2760 0.835 0.872 0.000 0.000 0.128
#> GSM97904 1 0.0000 0.977 1.000 0.000 0.000 0.000
#> GSM97907 2 0.0000 0.984 0.000 1.000 0.000 0.000
#> GSM97925 3 0.0000 0.969 0.000 0.000 1.000 0.000
#> GSM97947 3 0.0000 0.969 0.000 0.000 1.000 0.000
cbind(get_classes(res, k = 5), get_membership(res, k = 5))
#> class entropy silhouette p1 p2 p3 p4 p5
#> GSM97800 2 0.0000 0.9709 0.000 1.000 0.000 0.000 0.000
#> GSM97803 2 0.0000 0.9709 0.000 1.000 0.000 0.000 0.000
#> GSM97804 2 0.0000 0.9709 0.000 1.000 0.000 0.000 0.000
#> GSM97805 2 0.0000 0.9709 0.000 1.000 0.000 0.000 0.000
#> GSM97807 2 0.1608 0.9368 0.000 0.928 0.000 0.000 0.072
#> GSM97809 2 0.1608 0.9368 0.000 0.928 0.000 0.000 0.072
#> GSM97811 2 0.0000 0.9709 0.000 1.000 0.000 0.000 0.000
#> GSM97812 2 0.0000 0.9709 0.000 1.000 0.000 0.000 0.000
#> GSM97816 5 0.4325 0.5642 0.064 0.000 0.180 0.000 0.756
#> GSM97817 2 0.0000 0.9709 0.000 1.000 0.000 0.000 0.000
#> GSM97820 2 0.1608 0.9368 0.000 0.928 0.000 0.000 0.072
#> GSM97825 2 0.0000 0.9709 0.000 1.000 0.000 0.000 0.000
#> GSM97827 2 0.0000 0.9709 0.000 1.000 0.000 0.000 0.000
#> GSM97828 5 0.4360 0.5618 0.064 0.000 0.184 0.000 0.752
#> GSM97833 2 0.0000 0.9709 0.000 1.000 0.000 0.000 0.000
#> GSM97834 2 0.0000 0.9709 0.000 1.000 0.000 0.000 0.000
#> GSM97840 5 0.5274 0.2796 0.064 0.336 0.000 0.000 0.600
#> GSM97846 2 0.0000 0.9709 0.000 1.000 0.000 0.000 0.000
#> GSM97848 2 0.0703 0.9617 0.000 0.976 0.000 0.000 0.024
#> GSM97849 2 0.0000 0.9709 0.000 1.000 0.000 0.000 0.000
#> GSM97850 2 0.1608 0.9368 0.000 0.928 0.000 0.000 0.072
#> GSM97853 2 0.0000 0.9709 0.000 1.000 0.000 0.000 0.000
#> GSM97855 2 0.4390 0.3214 0.004 0.568 0.000 0.000 0.428
#> GSM97878 1 0.0162 0.9168 0.996 0.000 0.000 0.000 0.004
#> GSM97913 5 0.4297 0.3235 0.472 0.000 0.000 0.000 0.528
#> GSM97932 4 0.3090 0.8077 0.104 0.000 0.000 0.856 0.040
#> GSM97939 5 0.3642 0.4413 0.008 0.000 0.232 0.000 0.760
#> GSM97951 5 0.4533 -0.0177 0.008 0.448 0.000 0.000 0.544
#> GSM97957 3 0.0000 0.8891 0.000 0.000 1.000 0.000 0.000
#> GSM97972 5 0.4360 0.5615 0.064 0.000 0.184 0.000 0.752
#> GSM97793 3 0.0000 0.8891 0.000 0.000 1.000 0.000 0.000
#> GSM97795 5 0.2753 0.5645 0.008 0.000 0.136 0.000 0.856
#> GSM97802 1 0.3461 0.6078 0.772 0.000 0.224 0.000 0.004
#> GSM97810 5 0.3013 0.5501 0.008 0.000 0.160 0.000 0.832
#> GSM97815 5 0.3093 0.5423 0.008 0.000 0.168 0.000 0.824
#> GSM97837 1 0.0162 0.9168 0.996 0.000 0.000 0.000 0.004
#> GSM97843 3 0.0162 0.8893 0.000 0.000 0.996 0.000 0.004
#> GSM97890 3 0.2516 0.8655 0.000 0.000 0.860 0.000 0.140
#> GSM97899 4 0.0000 0.9362 0.000 0.000 0.000 1.000 0.000
#> GSM97910 1 0.0162 0.9168 0.996 0.000 0.000 0.000 0.004
#> GSM97916 1 0.0162 0.9168 0.996 0.000 0.000 0.000 0.004
#> GSM97920 3 0.0000 0.8891 0.000 0.000 1.000 0.000 0.000
#> GSM97921 1 0.0162 0.9168 0.996 0.000 0.000 0.000 0.004
#> GSM97927 1 0.1270 0.9124 0.948 0.000 0.000 0.000 0.052
#> GSM97937 1 0.0000 0.9175 1.000 0.000 0.000 0.000 0.000
#> GSM97941 5 0.5953 0.4884 0.336 0.124 0.000 0.000 0.540
#> GSM97943 5 0.6178 0.4705 0.296 0.000 0.168 0.000 0.536
#> GSM97958 5 0.4302 0.3034 0.480 0.000 0.000 0.000 0.520
#> GSM97960 5 0.2753 0.5645 0.008 0.000 0.136 0.000 0.856
#> GSM97794 1 0.0162 0.9168 0.996 0.000 0.000 0.000 0.004
#> GSM97796 4 0.0162 0.9338 0.004 0.000 0.000 0.996 0.000
#> GSM97797 1 0.0290 0.9150 0.992 0.000 0.000 0.000 0.008
#> GSM97798 4 0.0000 0.9362 0.000 0.000 0.000 1.000 0.000
#> GSM97801 1 0.0162 0.9168 0.996 0.000 0.000 0.000 0.004
#> GSM97806 1 0.1270 0.9124 0.948 0.000 0.000 0.000 0.052
#> GSM97808 4 0.0000 0.9362 0.000 0.000 0.000 1.000 0.000
#> GSM97813 1 0.1270 0.9124 0.948 0.000 0.000 0.000 0.052
#> GSM97814 4 0.0000 0.9362 0.000 0.000 0.000 1.000 0.000
#> GSM97818 1 0.0162 0.9168 0.996 0.000 0.000 0.000 0.004
#> GSM97819 3 0.2280 0.8751 0.000 0.000 0.880 0.000 0.120
#> GSM97821 5 0.4297 0.3235 0.472 0.000 0.000 0.000 0.528
#> GSM97826 1 0.0162 0.9168 0.996 0.000 0.000 0.000 0.004
#> GSM97829 1 0.0162 0.9168 0.996 0.000 0.000 0.000 0.004
#> GSM97832 5 0.3013 0.5501 0.008 0.000 0.160 0.000 0.832
#> GSM97836 1 0.0162 0.9178 0.996 0.000 0.000 0.000 0.004
#> GSM97839 4 0.0000 0.9362 0.000 0.000 0.000 1.000 0.000
#> GSM97844 2 0.0000 0.9709 0.000 1.000 0.000 0.000 0.000
#> GSM97847 1 0.1270 0.9124 0.948 0.000 0.000 0.000 0.052
#> GSM97851 4 0.0290 0.9315 0.008 0.000 0.000 0.992 0.000
#> GSM97852 1 0.1270 0.9124 0.948 0.000 0.000 0.000 0.052
#> GSM97856 4 0.0000 0.9362 0.000 0.000 0.000 1.000 0.000
#> GSM97858 2 0.0000 0.9709 0.000 1.000 0.000 0.000 0.000
#> GSM97859 1 0.0000 0.9175 1.000 0.000 0.000 0.000 0.000
#> GSM97861 1 0.1270 0.9124 0.948 0.000 0.000 0.000 0.052
#> GSM97863 4 0.0000 0.9362 0.000 0.000 0.000 1.000 0.000
#> GSM97869 1 0.0162 0.9168 0.996 0.000 0.000 0.000 0.004
#> GSM97870 1 0.1701 0.8579 0.936 0.000 0.016 0.000 0.048
#> GSM97871 4 0.0000 0.9362 0.000 0.000 0.000 1.000 0.000
#> GSM97877 5 0.4297 0.3235 0.472 0.000 0.000 0.000 0.528
#> GSM97879 1 0.1270 0.9124 0.948 0.000 0.000 0.000 0.052
#> GSM97882 1 0.1270 0.9124 0.948 0.000 0.000 0.000 0.052
#> GSM97885 1 0.0963 0.9155 0.964 0.000 0.000 0.000 0.036
#> GSM97886 4 0.2409 0.8573 0.068 0.000 0.000 0.900 0.032
#> GSM97887 1 0.5297 0.0433 0.476 0.000 0.000 0.476 0.048
#> GSM97888 1 0.4369 0.6753 0.740 0.000 0.000 0.208 0.052
#> GSM97889 1 0.1270 0.9124 0.948 0.000 0.000 0.000 0.052
#> GSM97891 1 0.1270 0.9124 0.948 0.000 0.000 0.000 0.052
#> GSM97892 2 0.0000 0.9709 0.000 1.000 0.000 0.000 0.000
#> GSM97893 1 0.4272 0.6929 0.752 0.000 0.000 0.196 0.052
#> GSM97894 4 0.0000 0.9362 0.000 0.000 0.000 1.000 0.000
#> GSM97895 1 0.4548 0.6366 0.716 0.000 0.000 0.232 0.052
#> GSM97896 4 0.5142 0.3625 0.348 0.000 0.000 0.600 0.052
#> GSM97898 4 0.0000 0.9362 0.000 0.000 0.000 1.000 0.000
#> GSM97903 1 0.0794 0.9166 0.972 0.000 0.000 0.000 0.028
#> GSM97905 1 0.0162 0.9168 0.996 0.000 0.000 0.000 0.004
#> GSM97906 4 0.1557 0.8989 0.008 0.000 0.000 0.940 0.052
#> GSM97908 1 0.1270 0.9124 0.948 0.000 0.000 0.000 0.052
#> GSM97912 1 0.0162 0.9168 0.996 0.000 0.000 0.000 0.004
#> GSM97914 1 0.0162 0.9168 0.996 0.000 0.000 0.000 0.004
#> GSM97915 4 0.0000 0.9362 0.000 0.000 0.000 1.000 0.000
#> GSM97917 4 0.5272 0.2202 0.396 0.000 0.000 0.552 0.052
#> GSM97918 4 0.0000 0.9362 0.000 0.000 0.000 1.000 0.000
#> GSM97919 4 0.0000 0.9362 0.000 0.000 0.000 1.000 0.000
#> GSM97922 1 0.1670 0.9061 0.936 0.000 0.000 0.012 0.052
#> GSM97924 2 0.1608 0.9368 0.000 0.928 0.000 0.000 0.072
#> GSM97926 3 0.5956 0.3553 0.296 0.000 0.564 0.000 0.140
#> GSM97930 1 0.1270 0.9124 0.948 0.000 0.000 0.000 0.052
#> GSM97931 5 0.4297 0.3235 0.472 0.000 0.000 0.000 0.528
#> GSM97935 1 0.1270 0.9124 0.948 0.000 0.000 0.000 0.052
#> GSM97936 4 0.0290 0.9308 0.008 0.000 0.000 0.992 0.000
#> GSM97938 1 0.0609 0.9174 0.980 0.000 0.000 0.000 0.020
#> GSM97940 4 0.0000 0.9362 0.000 0.000 0.000 1.000 0.000
#> GSM97942 3 0.2179 0.8777 0.000 0.000 0.888 0.000 0.112
#> GSM97945 4 0.2300 0.8639 0.072 0.000 0.000 0.904 0.024
#> GSM97946 2 0.1608 0.9368 0.000 0.928 0.000 0.000 0.072
#> GSM97948 1 0.4817 0.4290 0.680 0.000 0.264 0.000 0.056
#> GSM97950 4 0.2450 0.8620 0.052 0.000 0.000 0.900 0.048
#> GSM97952 4 0.0000 0.9362 0.000 0.000 0.000 1.000 0.000
#> GSM97953 1 0.0000 0.9175 1.000 0.000 0.000 0.000 0.000
#> GSM97954 1 0.1270 0.9124 0.948 0.000 0.000 0.000 0.052
#> GSM97955 4 0.1792 0.8614 0.084 0.000 0.000 0.916 0.000
#> GSM97959 1 0.3336 0.6067 0.772 0.000 0.000 0.000 0.228
#> GSM97961 4 0.0000 0.9362 0.000 0.000 0.000 1.000 0.000
#> GSM97963 4 0.0000 0.9362 0.000 0.000 0.000 1.000 0.000
#> GSM97965 4 0.0000 0.9362 0.000 0.000 0.000 1.000 0.000
#> GSM97966 4 0.0000 0.9362 0.000 0.000 0.000 1.000 0.000
#> GSM97967 2 0.0000 0.9709 0.000 1.000 0.000 0.000 0.000
#> GSM97968 5 0.4533 -0.0165 0.008 0.448 0.000 0.000 0.544
#> GSM97969 1 0.1270 0.9124 0.948 0.000 0.000 0.000 0.052
#> GSM97971 1 0.0000 0.9175 1.000 0.000 0.000 0.000 0.000
#> GSM97799 3 0.3143 0.8310 0.000 0.000 0.796 0.000 0.204
#> GSM97823 2 0.1608 0.9368 0.000 0.928 0.000 0.000 0.072
#> GSM97824 3 0.2020 0.8803 0.000 0.000 0.900 0.000 0.100
#> GSM97830 3 0.0000 0.8891 0.000 0.000 1.000 0.000 0.000
#> GSM97835 5 0.2813 0.5310 0.000 0.000 0.168 0.000 0.832
#> GSM97838 2 0.0609 0.9635 0.000 0.980 0.000 0.000 0.020
#> GSM97841 2 0.0794 0.9599 0.000 0.972 0.000 0.000 0.028
#> GSM97842 3 0.4262 0.5081 0.000 0.000 0.560 0.000 0.440
#> GSM97854 2 0.0000 0.9709 0.000 1.000 0.000 0.000 0.000
#> GSM97857 3 0.3395 0.7962 0.000 0.000 0.764 0.000 0.236
#> GSM97860 3 0.0000 0.8891 0.000 0.000 1.000 0.000 0.000
#> GSM97862 3 0.0000 0.8891 0.000 0.000 1.000 0.000 0.000
#> GSM97864 2 0.0000 0.9709 0.000 1.000 0.000 0.000 0.000
#> GSM97866 3 0.0000 0.8891 0.000 0.000 1.000 0.000 0.000
#> GSM97868 3 0.2230 0.8770 0.000 0.000 0.884 0.000 0.116
#> GSM97872 1 0.0000 0.9175 1.000 0.000 0.000 0.000 0.000
#> GSM97873 3 0.3966 0.6947 0.000 0.000 0.664 0.000 0.336
#> GSM97874 3 0.0000 0.8891 0.000 0.000 1.000 0.000 0.000
#> GSM97875 3 0.2280 0.8751 0.000 0.000 0.880 0.000 0.120
#> GSM97876 3 0.0000 0.8891 0.000 0.000 1.000 0.000 0.000
#> GSM97880 3 0.0000 0.8891 0.000 0.000 1.000 0.000 0.000
#> GSM97881 3 0.2329 0.8734 0.000 0.000 0.876 0.000 0.124
#> GSM97884 3 0.3752 0.7494 0.000 0.000 0.708 0.000 0.292
#> GSM97901 3 0.0000 0.8891 0.000 0.000 1.000 0.000 0.000
#> GSM97902 1 0.0510 0.9093 0.984 0.000 0.000 0.000 0.016
#> GSM97909 5 0.4297 0.3235 0.472 0.000 0.000 0.000 0.528
#> GSM97911 3 0.2424 0.8696 0.000 0.000 0.868 0.000 0.132
#> GSM97923 3 0.0000 0.8891 0.000 0.000 1.000 0.000 0.000
#> GSM97928 1 0.0290 0.9178 0.992 0.000 0.000 0.000 0.008
#> GSM97929 2 0.0000 0.9709 0.000 1.000 0.000 0.000 0.000
#> GSM97933 3 0.0290 0.8894 0.000 0.000 0.992 0.000 0.008
#> GSM97934 3 0.0000 0.8891 0.000 0.000 1.000 0.000 0.000
#> GSM97944 3 0.3143 0.8310 0.000 0.000 0.796 0.000 0.204
#> GSM97949 2 0.0000 0.9709 0.000 1.000 0.000 0.000 0.000
#> GSM97956 3 0.0510 0.8891 0.000 0.000 0.984 0.000 0.016
#> GSM97962 3 0.0000 0.8891 0.000 0.000 1.000 0.000 0.000
#> GSM97964 3 0.3242 0.8177 0.000 0.000 0.784 0.000 0.216
#> GSM97970 3 0.4030 0.6572 0.000 0.000 0.648 0.000 0.352
#> GSM97822 1 0.1270 0.9124 0.948 0.000 0.000 0.000 0.052
#> GSM97831 3 0.0000 0.8891 0.000 0.000 1.000 0.000 0.000
#> GSM97845 1 0.1270 0.9124 0.948 0.000 0.000 0.000 0.052
#> GSM97865 1 0.0162 0.9168 0.996 0.000 0.000 0.000 0.004
#> GSM97867 3 0.0000 0.8891 0.000 0.000 1.000 0.000 0.000
#> GSM97883 3 0.2179 0.8771 0.000 0.000 0.888 0.000 0.112
#> GSM97897 1 0.2300 0.8832 0.908 0.000 0.000 0.040 0.052
#> GSM97900 1 0.4461 0.6575 0.728 0.000 0.000 0.220 0.052
#> GSM97904 1 0.0000 0.9175 1.000 0.000 0.000 0.000 0.000
#> GSM97907 2 0.0000 0.9709 0.000 1.000 0.000 0.000 0.000
#> GSM97925 3 0.3445 0.8512 0.036 0.000 0.824 0.000 0.140
#> GSM97947 3 0.3283 0.8565 0.028 0.000 0.832 0.000 0.140
cbind(get_classes(res, k = 6), get_membership(res, k = 6))
#> class entropy silhouette p1 p2 p3 p4 p5 p6
#> GSM97800 2 0.0146 0.96802 0.000 0.996 0.000 0.000 0.004 0.000
#> GSM97803 2 0.0000 0.96830 0.000 1.000 0.000 0.000 0.000 0.000
#> GSM97804 2 0.0146 0.96802 0.000 0.996 0.000 0.000 0.004 0.000
#> GSM97805 2 0.0000 0.96830 0.000 1.000 0.000 0.000 0.000 0.000
#> GSM97807 2 0.2384 0.92111 0.000 0.884 0.000 0.000 0.084 0.032
#> GSM97809 2 0.2384 0.92111 0.000 0.884 0.000 0.000 0.084 0.032
#> GSM97811 2 0.1204 0.95408 0.000 0.944 0.000 0.000 0.056 0.000
#> GSM97812 2 0.0363 0.96760 0.000 0.988 0.000 0.000 0.012 0.000
#> GSM97816 6 0.5744 -0.00522 0.012 0.000 0.128 0.000 0.356 0.504
#> GSM97817 2 0.0146 0.96802 0.000 0.996 0.000 0.000 0.004 0.000
#> GSM97820 2 0.2230 0.92642 0.000 0.892 0.000 0.000 0.084 0.024
#> GSM97825 2 0.0146 0.96802 0.000 0.996 0.000 0.000 0.004 0.000
#> GSM97827 2 0.0146 0.96802 0.000 0.996 0.000 0.000 0.004 0.000
#> GSM97828 6 0.5851 0.00034 0.016 0.000 0.128 0.000 0.372 0.484
#> GSM97833 2 0.1075 0.95579 0.000 0.952 0.000 0.000 0.048 0.000
#> GSM97834 2 0.0146 0.96802 0.000 0.996 0.000 0.000 0.004 0.000
#> GSM97840 6 0.1599 0.48546 0.024 0.028 0.000 0.000 0.008 0.940
#> GSM97846 2 0.0146 0.96802 0.000 0.996 0.000 0.000 0.004 0.000
#> GSM97848 2 0.1297 0.95502 0.000 0.948 0.000 0.000 0.040 0.012
#> GSM97849 2 0.0260 0.96811 0.000 0.992 0.000 0.000 0.008 0.000
#> GSM97850 2 0.2230 0.92642 0.000 0.892 0.000 0.000 0.084 0.024
#> GSM97853 2 0.0260 0.96811 0.000 0.992 0.000 0.000 0.008 0.000
#> GSM97855 6 0.5011 0.20442 0.000 0.368 0.000 0.000 0.080 0.552
#> GSM97878 1 0.2058 0.90424 0.908 0.000 0.000 0.000 0.056 0.036
#> GSM97913 6 0.3679 0.50705 0.176 0.000 0.000 0.000 0.052 0.772
#> GSM97932 4 0.2706 0.77892 0.160 0.000 0.000 0.832 0.000 0.008
#> GSM97939 5 0.4360 0.57700 0.000 0.000 0.060 0.000 0.680 0.260
#> GSM97951 6 0.4172 0.33166 0.000 0.280 0.000 0.000 0.040 0.680
#> GSM97957 3 0.0146 0.89500 0.000 0.000 0.996 0.000 0.000 0.004
#> GSM97972 6 0.5800 -0.06014 0.016 0.000 0.144 0.000 0.300 0.540
#> GSM97793 3 0.0146 0.89586 0.000 0.000 0.996 0.000 0.004 0.000
#> GSM97795 5 0.4702 0.31163 0.000 0.000 0.044 0.000 0.496 0.460
#> GSM97802 1 0.4599 0.58294 0.680 0.000 0.252 0.000 0.012 0.056
#> GSM97810 5 0.4698 0.32770 0.000 0.000 0.044 0.000 0.504 0.452
#> GSM97815 5 0.4393 0.51994 0.000 0.000 0.044 0.000 0.640 0.316
#> GSM97837 1 0.2201 0.90027 0.900 0.000 0.000 0.000 0.048 0.052
#> GSM97843 3 0.0000 0.89591 0.000 0.000 1.000 0.000 0.000 0.000
#> GSM97890 3 0.2527 0.80844 0.000 0.000 0.832 0.000 0.168 0.000
#> GSM97899 4 0.0000 0.92285 0.000 0.000 0.000 1.000 0.000 0.000
#> GSM97910 1 0.2856 0.87555 0.856 0.000 0.000 0.000 0.076 0.068
#> GSM97916 1 0.2798 0.87486 0.852 0.000 0.000 0.000 0.112 0.036
#> GSM97920 3 0.0146 0.89500 0.000 0.000 0.996 0.000 0.000 0.004
#> GSM97921 1 0.2058 0.90451 0.908 0.000 0.000 0.000 0.056 0.036
#> GSM97927 1 0.0146 0.91730 0.996 0.000 0.000 0.000 0.004 0.000
#> GSM97937 1 0.1151 0.91648 0.956 0.000 0.000 0.000 0.012 0.032
#> GSM97941 6 0.1390 0.49988 0.032 0.016 0.000 0.000 0.004 0.948
#> GSM97943 6 0.6977 0.06838 0.116 0.000 0.132 0.000 0.344 0.408
#> GSM97958 6 0.3770 0.46554 0.244 0.000 0.000 0.000 0.028 0.728
#> GSM97960 5 0.4695 0.33594 0.000 0.000 0.044 0.000 0.508 0.448
#> GSM97794 1 0.3352 0.84726 0.816 0.000 0.000 0.000 0.112 0.072
#> GSM97796 4 0.0405 0.92214 0.000 0.000 0.000 0.988 0.004 0.008
#> GSM97797 1 0.3878 0.80068 0.772 0.000 0.000 0.000 0.112 0.116
#> GSM97798 4 0.0146 0.92217 0.000 0.000 0.000 0.996 0.004 0.000
#> GSM97801 1 0.2625 0.88541 0.872 0.000 0.000 0.000 0.072 0.056
#> GSM97806 1 0.0146 0.91730 0.996 0.000 0.000 0.000 0.004 0.000
#> GSM97808 4 0.0146 0.92217 0.000 0.000 0.000 0.996 0.004 0.000
#> GSM97813 1 0.0260 0.91642 0.992 0.000 0.000 0.000 0.008 0.000
#> GSM97814 4 0.0146 0.92217 0.000 0.000 0.000 0.996 0.004 0.000
#> GSM97818 1 0.3241 0.85399 0.824 0.000 0.000 0.000 0.112 0.064
#> GSM97819 3 0.2048 0.84541 0.000 0.000 0.880 0.000 0.120 0.000
#> GSM97821 6 0.3268 0.51194 0.100 0.000 0.000 0.000 0.076 0.824
#> GSM97826 1 0.1649 0.91241 0.932 0.000 0.000 0.000 0.036 0.032
#> GSM97829 1 0.1649 0.91180 0.932 0.000 0.000 0.000 0.032 0.036
#> GSM97832 6 0.4757 -0.34941 0.000 0.000 0.048 0.000 0.468 0.484
#> GSM97836 1 0.0632 0.91868 0.976 0.000 0.000 0.000 0.000 0.024
#> GSM97839 4 0.0405 0.92214 0.000 0.000 0.000 0.988 0.004 0.008
#> GSM97844 2 0.0000 0.96830 0.000 1.000 0.000 0.000 0.000 0.000
#> GSM97847 1 0.0146 0.91730 0.996 0.000 0.000 0.000 0.004 0.000
#> GSM97851 4 0.1606 0.88182 0.056 0.000 0.000 0.932 0.004 0.008
#> GSM97852 1 0.0146 0.91730 0.996 0.000 0.000 0.000 0.004 0.000
#> GSM97856 4 0.0000 0.92285 0.000 0.000 0.000 1.000 0.000 0.000
#> GSM97858 2 0.0260 0.96824 0.000 0.992 0.000 0.000 0.008 0.000
#> GSM97859 1 0.1151 0.91648 0.956 0.000 0.000 0.000 0.012 0.032
#> GSM97861 1 0.0000 0.91787 1.000 0.000 0.000 0.000 0.000 0.000
#> GSM97863 4 0.0405 0.92214 0.000 0.000 0.000 0.988 0.004 0.008
#> GSM97869 1 0.2798 0.87486 0.852 0.000 0.000 0.000 0.112 0.036
#> GSM97870 1 0.1563 0.91019 0.932 0.000 0.000 0.000 0.012 0.056
#> GSM97871 4 0.0000 0.92285 0.000 0.000 0.000 1.000 0.000 0.000
#> GSM97877 6 0.2848 0.51482 0.176 0.000 0.000 0.000 0.008 0.816
#> GSM97879 1 0.0146 0.91730 0.996 0.000 0.000 0.000 0.004 0.000
#> GSM97882 1 0.0146 0.91730 0.996 0.000 0.000 0.000 0.004 0.000
#> GSM97885 1 0.0405 0.91940 0.988 0.000 0.000 0.000 0.004 0.008
#> GSM97886 4 0.1398 0.89135 0.052 0.000 0.000 0.940 0.008 0.000
#> GSM97887 4 0.4018 0.29604 0.412 0.000 0.000 0.580 0.008 0.000
#> GSM97888 1 0.2402 0.79335 0.856 0.000 0.000 0.140 0.004 0.000
#> GSM97889 1 0.0146 0.91730 0.996 0.000 0.000 0.000 0.004 0.000
#> GSM97891 1 0.0146 0.91730 0.996 0.000 0.000 0.000 0.004 0.000
#> GSM97892 2 0.0909 0.96008 0.000 0.968 0.000 0.000 0.012 0.020
#> GSM97893 1 0.2420 0.80705 0.864 0.000 0.000 0.128 0.004 0.004
#> GSM97894 4 0.0000 0.92285 0.000 0.000 0.000 1.000 0.000 0.000
#> GSM97895 1 0.2595 0.77944 0.836 0.000 0.000 0.160 0.004 0.000
#> GSM97896 4 0.3512 0.58728 0.272 0.000 0.000 0.720 0.008 0.000
#> GSM97898 4 0.0405 0.92214 0.000 0.000 0.000 0.988 0.004 0.008
#> GSM97903 1 0.1858 0.90277 0.912 0.000 0.000 0.000 0.076 0.012
#> GSM97905 1 0.1434 0.91320 0.940 0.000 0.000 0.000 0.012 0.048
#> GSM97906 4 0.1010 0.90477 0.036 0.000 0.000 0.960 0.004 0.000
#> GSM97908 1 0.0146 0.91730 0.996 0.000 0.000 0.000 0.004 0.000
#> GSM97912 1 0.1297 0.91517 0.948 0.000 0.000 0.000 0.012 0.040
#> GSM97914 1 0.2752 0.87739 0.856 0.000 0.000 0.000 0.108 0.036
#> GSM97915 4 0.0405 0.92214 0.000 0.000 0.000 0.988 0.004 0.008
#> GSM97917 4 0.3713 0.59424 0.284 0.000 0.000 0.704 0.004 0.008
#> GSM97918 4 0.0405 0.92214 0.000 0.000 0.000 0.988 0.004 0.008
#> GSM97919 4 0.0405 0.92214 0.000 0.000 0.000 0.988 0.004 0.008
#> GSM97922 1 0.0405 0.91482 0.988 0.000 0.000 0.004 0.008 0.000
#> GSM97924 2 0.2230 0.92642 0.000 0.892 0.000 0.000 0.084 0.024
#> GSM97926 3 0.5303 0.57096 0.068 0.000 0.664 0.000 0.208 0.060
#> GSM97930 1 0.0363 0.91792 0.988 0.000 0.000 0.000 0.012 0.000
#> GSM97931 6 0.3607 0.50765 0.112 0.000 0.000 0.000 0.092 0.796
#> GSM97935 1 0.0146 0.91730 0.996 0.000 0.000 0.000 0.004 0.000
#> GSM97936 4 0.0937 0.90341 0.040 0.000 0.000 0.960 0.000 0.000
#> GSM97938 1 0.0820 0.91938 0.972 0.000 0.000 0.000 0.012 0.016
#> GSM97940 4 0.0000 0.92285 0.000 0.000 0.000 1.000 0.000 0.000
#> GSM97942 3 0.1556 0.86814 0.000 0.000 0.920 0.000 0.080 0.000
#> GSM97945 4 0.2219 0.81786 0.136 0.000 0.000 0.864 0.000 0.000
#> GSM97946 2 0.2384 0.92111 0.000 0.884 0.000 0.000 0.084 0.032
#> GSM97948 1 0.5284 0.32887 0.552 0.000 0.368 0.000 0.024 0.056
#> GSM97950 4 0.1049 0.90606 0.032 0.000 0.000 0.960 0.008 0.000
#> GSM97952 4 0.0000 0.92285 0.000 0.000 0.000 1.000 0.000 0.000
#> GSM97953 1 0.1074 0.91806 0.960 0.000 0.000 0.000 0.012 0.028
#> GSM97954 1 0.0146 0.91730 0.996 0.000 0.000 0.000 0.004 0.000
#> GSM97955 4 0.2454 0.78257 0.160 0.000 0.000 0.840 0.000 0.000
#> GSM97959 6 0.4958 0.30902 0.364 0.000 0.000 0.000 0.076 0.560
#> GSM97961 4 0.0405 0.92214 0.000 0.000 0.000 0.988 0.004 0.008
#> GSM97963 4 0.0000 0.92285 0.000 0.000 0.000 1.000 0.000 0.000
#> GSM97965 4 0.0146 0.92277 0.000 0.000 0.000 0.996 0.004 0.000
#> GSM97966 4 0.0146 0.92217 0.000 0.000 0.000 0.996 0.004 0.000
#> GSM97967 2 0.0146 0.96802 0.000 0.996 0.000 0.000 0.004 0.000
#> GSM97968 6 0.4751 0.30794 0.000 0.312 0.000 0.000 0.072 0.616
#> GSM97969 1 0.0260 0.91642 0.992 0.000 0.000 0.000 0.008 0.000
#> GSM97971 1 0.1245 0.91693 0.952 0.000 0.000 0.000 0.016 0.032
#> GSM97799 5 0.3309 0.64639 0.000 0.000 0.280 0.000 0.720 0.000
#> GSM97823 2 0.2309 0.92384 0.000 0.888 0.000 0.000 0.084 0.028
#> GSM97824 3 0.2300 0.82919 0.000 0.000 0.856 0.000 0.144 0.000
#> GSM97830 3 0.0146 0.89500 0.000 0.000 0.996 0.000 0.000 0.004
#> GSM97835 5 0.3989 0.57599 0.000 0.000 0.044 0.000 0.720 0.236
#> GSM97838 2 0.1765 0.94403 0.000 0.924 0.000 0.000 0.052 0.024
#> GSM97841 2 0.0993 0.95866 0.000 0.964 0.000 0.000 0.012 0.024
#> GSM97842 5 0.3954 0.67883 0.000 0.000 0.204 0.000 0.740 0.056
#> GSM97854 2 0.0000 0.96830 0.000 1.000 0.000 0.000 0.000 0.000
#> GSM97857 3 0.3489 0.61200 0.000 0.000 0.708 0.000 0.288 0.004
#> GSM97860 3 0.0000 0.89591 0.000 0.000 1.000 0.000 0.000 0.000
#> GSM97862 3 0.0000 0.89591 0.000 0.000 1.000 0.000 0.000 0.000
#> GSM97864 2 0.0146 0.96802 0.000 0.996 0.000 0.000 0.004 0.000
#> GSM97866 3 0.0000 0.89591 0.000 0.000 1.000 0.000 0.000 0.000
#> GSM97868 3 0.2631 0.79691 0.000 0.000 0.820 0.000 0.180 0.000
#> GSM97872 1 0.1225 0.91573 0.952 0.000 0.000 0.000 0.012 0.036
#> GSM97873 5 0.3470 0.67085 0.000 0.000 0.248 0.000 0.740 0.012
#> GSM97874 3 0.0146 0.89500 0.000 0.000 0.996 0.000 0.000 0.004
#> GSM97875 3 0.2454 0.81465 0.000 0.000 0.840 0.000 0.160 0.000
#> GSM97876 3 0.0000 0.89591 0.000 0.000 1.000 0.000 0.000 0.000
#> GSM97880 3 0.0000 0.89591 0.000 0.000 1.000 0.000 0.000 0.000
#> GSM97881 3 0.2562 0.80441 0.000 0.000 0.828 0.000 0.172 0.000
#> GSM97884 5 0.3198 0.66352 0.000 0.000 0.260 0.000 0.740 0.000
#> GSM97901 3 0.0000 0.89591 0.000 0.000 1.000 0.000 0.000 0.000
#> GSM97902 1 0.3612 0.82421 0.796 0.000 0.000 0.000 0.100 0.104
#> GSM97909 6 0.2376 0.49323 0.044 0.000 0.000 0.000 0.068 0.888
#> GSM97911 3 0.2597 0.80098 0.000 0.000 0.824 0.000 0.176 0.000
#> GSM97923 3 0.0000 0.89591 0.000 0.000 1.000 0.000 0.000 0.000
#> GSM97928 1 0.0891 0.91822 0.968 0.000 0.000 0.000 0.008 0.024
#> GSM97929 2 0.0146 0.96802 0.000 0.996 0.000 0.000 0.004 0.000
#> GSM97933 3 0.0146 0.89586 0.000 0.000 0.996 0.000 0.004 0.000
#> GSM97934 3 0.0000 0.89591 0.000 0.000 1.000 0.000 0.000 0.000
#> GSM97944 5 0.3309 0.64639 0.000 0.000 0.280 0.000 0.720 0.000
#> GSM97949 2 0.0000 0.96830 0.000 1.000 0.000 0.000 0.000 0.000
#> GSM97956 3 0.1141 0.88150 0.000 0.000 0.948 0.000 0.052 0.000
#> GSM97962 3 0.0146 0.89598 0.000 0.000 0.996 0.000 0.004 0.000
#> GSM97964 3 0.3390 0.59931 0.000 0.000 0.704 0.000 0.296 0.000
#> GSM97970 5 0.4038 0.67936 0.000 0.000 0.216 0.000 0.728 0.056
#> GSM97822 1 0.0146 0.91730 0.996 0.000 0.000 0.000 0.004 0.000
#> GSM97831 3 0.0146 0.89500 0.000 0.000 0.996 0.000 0.000 0.004
#> GSM97845 1 0.0146 0.91730 0.996 0.000 0.000 0.000 0.004 0.000
#> GSM97865 1 0.2798 0.87486 0.852 0.000 0.000 0.000 0.112 0.036
#> GSM97867 3 0.0000 0.89591 0.000 0.000 1.000 0.000 0.000 0.000
#> GSM97883 3 0.0632 0.89103 0.000 0.000 0.976 0.000 0.024 0.000
#> GSM97897 1 0.0806 0.90626 0.972 0.000 0.000 0.020 0.008 0.000
#> GSM97900 1 0.3271 0.66176 0.760 0.000 0.000 0.232 0.008 0.000
#> GSM97904 1 0.1049 0.91704 0.960 0.000 0.000 0.000 0.008 0.032
#> GSM97907 2 0.0000 0.96830 0.000 1.000 0.000 0.000 0.000 0.000
#> GSM97925 3 0.3494 0.77766 0.004 0.000 0.792 0.000 0.168 0.036
#> GSM97947 3 0.3248 0.79108 0.000 0.000 0.804 0.000 0.164 0.032
Heatmaps for the consensus matrix. It visualizes the probability of two samples to be in a same group.
consensus_heatmap(res, k = 2)
consensus_heatmap(res, k = 3)
consensus_heatmap(res, k = 4)
consensus_heatmap(res, k = 5)
consensus_heatmap(res, k = 6)
Heatmaps for the membership of samples in all partitions to see how consistent they are:
membership_heatmap(res, k = 2)
membership_heatmap(res, k = 3)
membership_heatmap(res, k = 4)
membership_heatmap(res, k = 5)
membership_heatmap(res, k = 6)
As soon as we have had the classes for columns, we can look for signatures which are significantly different between classes which can be candidate marks for certain classes. Following are the heatmaps for signatures.
Signature heatmaps where rows are scaled:
get_signatures(res, k = 2)
get_signatures(res, k = 3)
get_signatures(res, k = 4)
get_signatures(res, k = 5)
get_signatures(res, k = 6)
Signature heatmaps where rows are not scaled:
get_signatures(res, k = 2, scale_rows = FALSE)
get_signatures(res, k = 3, scale_rows = FALSE)
get_signatures(res, k = 4, scale_rows = FALSE)
get_signatures(res, k = 5, scale_rows = FALSE)
get_signatures(res, k = 6, scale_rows = FALSE)
Compare the overlap of signatures from different k:
compare_signatures(res)
get_signature() returns a data frame invisibly. TO get the list of signatures, the function
call should be assigned to a variable explicitly. In following code, if plot argument is set
to FALSE, no heatmap is plotted while only the differential analysis is performed.
# code only for demonstration
tb = get_signature(res, k = ..., plot = FALSE)
An example of the output of tb is:
#> which_row fdr mean_1 mean_2 scaled_mean_1 scaled_mean_2 km
#> 1 38 0.042760348 8.373488 9.131774 -0.5533452 0.5164555 1
#> 2 40 0.018707592 7.106213 8.469186 -0.6173731 0.5762149 1
#> 3 55 0.019134737 10.221463 11.207825 -0.6159697 0.5749050 1
#> 4 59 0.006059896 5.921854 7.869574 -0.6899429 0.6439467 1
#> 5 60 0.018055526 8.928898 10.211722 -0.6204761 0.5791110 1
#> 6 98 0.009384629 15.714769 14.887706 0.6635654 -0.6193277 2
...
The columns in tb are:
which_row: row indices corresponding to the input matrix.fdr: FDR for the differential test. mean_x: The mean value in group x.scaled_mean_x: The mean value in group x after rows are scaled.km: Row groups if k-means clustering is applied to rows.UMAP plot which shows how samples are separated.
dimension_reduction(res, k = 2, method = "UMAP")
dimension_reduction(res, k = 3, method = "UMAP")
dimension_reduction(res, k = 4, method = "UMAP")
dimension_reduction(res, k = 5, method = "UMAP")
dimension_reduction(res, k = 6, method = "UMAP")
Following heatmap shows how subgroups are split when increasing k:
collect_classes(res)
Test correlation between subgroups and known annotations. If the known annotation is numeric, one-way ANOVA test is applied, and if the known annotation is discrete, chi-squared contingency table test is applied.
test_to_known_factors(res)
#> n disease.state(p) tissue(p) k
#> MAD:mclust 179 2.96e-17 1.95e-17 2
#> MAD:mclust 156 5.67e-29 9.17e-30 3
#> MAD:mclust 177 1.46e-28 1.27e-29 4
#> MAD:mclust 162 7.05e-31 3.19e-29 5
#> MAD:mclust 162 3.86e-27 1.24e-28 6
If matrix rows can be associated to genes, consider to use functional_enrichment(res,
...) to perform function enrichment for the signature genes. See this vignette for more detailed explanations.
The object with results only for a single top-value method and a single partition method can be extracted as:
res = res_list["MAD", "NMF"]
# you can also extract it by
# res = res_list["MAD:NMF"]
A summary of res and all the functions that can be applied to it:
res
#> A 'ConsensusPartition' object with k = 2, 3, 4, 5, 6.
#> On a matrix with 51882 rows and 180 columns.
#> Top rows (1000, 2000, 3000, 4000, 5000) are extracted by 'MAD' method.
#> Subgroups are detected by 'NMF' method.
#> Performed in total 1250 partitions by row resampling.
#> Best k for subgroups seems to be 4.
#>
#> Following methods can be applied to this 'ConsensusPartition' object:
#> [1] "cola_report" "collect_classes" "collect_plots"
#> [4] "collect_stats" "colnames" "compare_signatures"
#> [7] "consensus_heatmap" "dimension_reduction" "functional_enrichment"
#> [10] "get_anno_col" "get_anno" "get_classes"
#> [13] "get_consensus" "get_matrix" "get_membership"
#> [16] "get_param" "get_signatures" "get_stats"
#> [19] "is_best_k" "is_stable_k" "membership_heatmap"
#> [22] "ncol" "nrow" "plot_ecdf"
#> [25] "rownames" "select_partition_number" "show"
#> [28] "suggest_best_k" "test_to_known_factors"
collect_plots() function collects all the plots made from res for all k (number of partitions)
into one single page to provide an easy and fast comparison between different k.
collect_plots(res)
The plots are:
k and the heatmap of
predicted classes for each k.k.k.k.All the plots in panels can be made by individual functions and they are plotted later in this section.
select_partition_number() produces several plots showing different
statistics for choosing “optimized” k. There are following statistics:
k;k, the area increased is defined as \(A_k - A_{k-1}\).The detailed explanations of these statistics can be found in the cola vignette.
Generally speaking, lower PAC score, higher mean silhouette score or higher
concordance corresponds to better partition. Rand index and Jaccard index
measure how similar the current partition is compared to partition with k-1.
If they are too similar, we won't accept k is better than k-1.
select_partition_number(res)
The numeric values for all these statistics can be obtained by get_stats().
get_stats(res)
#> k 1-PAC mean_silhouette concordance area_increased Rand Jaccard
#> 2 2 0.977 0.952 0.981 0.5008 0.499 0.499
#> 3 3 1.000 0.967 0.987 0.3054 0.781 0.587
#> 4 4 0.945 0.911 0.961 0.0887 0.923 0.783
#> 5 5 0.754 0.677 0.837 0.0649 0.983 0.941
#> 6 6 0.721 0.666 0.804 0.0444 0.887 0.639
suggest_best_k() suggests the best \(k\) based on these statistics. The rules are as follows:
suggest_best_k(res)
#> [1] 4
#> attr(,"optional")
#> [1] 2 3
There is also optional best \(k\) = 2 3 that is worth to check.
Following shows the table of the partitions (You need to click the show/hide
code output link to see it). The membership matrix (columns with name p*)
is inferred by
clue::cl_consensus()
function with the SE method. Basically the value in the membership matrix
represents the probability to belong to a certain group. The finall class
label for an item is determined with the group with highest probability it
belongs to.
In get_classes() function, the entropy is calculated from the membership
matrix and the silhouette score is calculated from the consensus matrix.
cbind(get_classes(res, k = 2), get_membership(res, k = 2))
#> class entropy silhouette p1 p2
#> GSM97800 2 0.0000 0.980 0.000 1.000
#> GSM97803 2 0.0000 0.980 0.000 1.000
#> GSM97804 2 0.0000 0.980 0.000 1.000
#> GSM97805 2 0.0000 0.980 0.000 1.000
#> GSM97807 2 0.0000 0.980 0.000 1.000
#> GSM97809 2 0.0000 0.980 0.000 1.000
#> GSM97811 2 0.0000 0.980 0.000 1.000
#> GSM97812 2 0.0000 0.980 0.000 1.000
#> GSM97816 2 0.0000 0.980 0.000 1.000
#> GSM97817 2 0.0000 0.980 0.000 1.000
#> GSM97820 2 0.0000 0.980 0.000 1.000
#> GSM97825 2 0.0000 0.980 0.000 1.000
#> GSM97827 2 0.0000 0.980 0.000 1.000
#> GSM97828 2 0.0000 0.980 0.000 1.000
#> GSM97833 2 0.0000 0.980 0.000 1.000
#> GSM97834 2 0.0000 0.980 0.000 1.000
#> GSM97840 2 0.0000 0.980 0.000 1.000
#> GSM97846 2 0.0000 0.980 0.000 1.000
#> GSM97848 2 0.0000 0.980 0.000 1.000
#> GSM97849 2 0.0000 0.980 0.000 1.000
#> GSM97850 2 0.0000 0.980 0.000 1.000
#> GSM97853 2 0.0000 0.980 0.000 1.000
#> GSM97855 2 0.0000 0.980 0.000 1.000
#> GSM97878 1 0.0376 0.977 0.996 0.004
#> GSM97913 2 0.0000 0.980 0.000 1.000
#> GSM97932 1 0.0000 0.980 1.000 0.000
#> GSM97939 2 0.0000 0.980 0.000 1.000
#> GSM97951 2 0.0000 0.980 0.000 1.000
#> GSM97957 2 0.0000 0.980 0.000 1.000
#> GSM97972 2 0.0000 0.980 0.000 1.000
#> GSM97793 1 0.2948 0.934 0.948 0.052
#> GSM97795 2 0.0000 0.980 0.000 1.000
#> GSM97802 1 0.7376 0.741 0.792 0.208
#> GSM97810 2 0.0000 0.980 0.000 1.000
#> GSM97815 2 0.0000 0.980 0.000 1.000
#> GSM97837 1 0.0000 0.980 1.000 0.000
#> GSM97843 2 0.0376 0.976 0.004 0.996
#> GSM97890 2 0.0000 0.980 0.000 1.000
#> GSM97899 1 0.0000 0.980 1.000 0.000
#> GSM97910 1 0.3114 0.931 0.944 0.056
#> GSM97916 1 0.0000 0.980 1.000 0.000
#> GSM97920 2 0.0000 0.980 0.000 1.000
#> GSM97921 1 0.0000 0.980 1.000 0.000
#> GSM97927 1 0.0000 0.980 1.000 0.000
#> GSM97937 1 0.0000 0.980 1.000 0.000
#> GSM97941 2 0.0000 0.980 0.000 1.000
#> GSM97943 2 0.5294 0.854 0.120 0.880
#> GSM97958 2 0.0000 0.980 0.000 1.000
#> GSM97960 2 0.0000 0.980 0.000 1.000
#> GSM97794 1 0.6148 0.820 0.848 0.152
#> GSM97796 1 0.0000 0.980 1.000 0.000
#> GSM97797 2 0.9881 0.216 0.436 0.564
#> GSM97798 1 0.0000 0.980 1.000 0.000
#> GSM97801 1 0.0000 0.980 1.000 0.000
#> GSM97806 1 0.0000 0.980 1.000 0.000
#> GSM97808 1 0.0000 0.980 1.000 0.000
#> GSM97813 1 0.0000 0.980 1.000 0.000
#> GSM97814 1 0.0000 0.980 1.000 0.000
#> GSM97818 1 0.0672 0.973 0.992 0.008
#> GSM97819 1 0.4815 0.879 0.896 0.104
#> GSM97821 2 0.0000 0.980 0.000 1.000
#> GSM97826 1 0.0000 0.980 1.000 0.000
#> GSM97829 1 0.0000 0.980 1.000 0.000
#> GSM97832 2 0.0000 0.980 0.000 1.000
#> GSM97836 1 0.0000 0.980 1.000 0.000
#> GSM97839 1 0.0000 0.980 1.000 0.000
#> GSM97844 2 0.0000 0.980 0.000 1.000
#> GSM97847 1 0.0000 0.980 1.000 0.000
#> GSM97851 1 0.0000 0.980 1.000 0.000
#> GSM97852 1 0.0000 0.980 1.000 0.000
#> GSM97856 1 0.0000 0.980 1.000 0.000
#> GSM97858 2 0.0000 0.980 0.000 1.000
#> GSM97859 1 0.0000 0.980 1.000 0.000
#> GSM97861 1 0.0000 0.980 1.000 0.000
#> GSM97863 1 0.0000 0.980 1.000 0.000
#> GSM97869 1 0.0000 0.980 1.000 0.000
#> GSM97870 1 0.0000 0.980 1.000 0.000
#> GSM97871 1 0.0000 0.980 1.000 0.000
#> GSM97877 2 0.0000 0.980 0.000 1.000
#> GSM97879 1 0.0000 0.980 1.000 0.000
#> GSM97882 1 0.0000 0.980 1.000 0.000
#> GSM97885 1 0.0000 0.980 1.000 0.000
#> GSM97886 1 0.0000 0.980 1.000 0.000
#> GSM97887 1 0.0000 0.980 1.000 0.000
#> GSM97888 1 0.0000 0.980 1.000 0.000
#> GSM97889 1 0.0000 0.980 1.000 0.000
#> GSM97891 1 0.0000 0.980 1.000 0.000
#> GSM97892 2 0.0000 0.980 0.000 1.000
#> GSM97893 1 0.0000 0.980 1.000 0.000
#> GSM97894 1 0.0000 0.980 1.000 0.000
#> GSM97895 1 0.0000 0.980 1.000 0.000
#> GSM97896 1 0.0000 0.980 1.000 0.000
#> GSM97898 1 0.0000 0.980 1.000 0.000
#> GSM97903 1 0.0000 0.980 1.000 0.000
#> GSM97905 1 0.0000 0.980 1.000 0.000
#> GSM97906 1 0.0000 0.980 1.000 0.000
#> GSM97908 1 0.0000 0.980 1.000 0.000
#> GSM97912 1 0.0000 0.980 1.000 0.000
#> GSM97914 1 0.0000 0.980 1.000 0.000
#> GSM97915 1 0.0000 0.980 1.000 0.000
#> GSM97917 1 0.0000 0.980 1.000 0.000
#> GSM97918 1 0.0000 0.980 1.000 0.000
#> GSM97919 1 0.0000 0.980 1.000 0.000
#> GSM97922 1 0.0000 0.980 1.000 0.000
#> GSM97924 2 0.0000 0.980 0.000 1.000
#> GSM97926 1 0.9754 0.318 0.592 0.408
#> GSM97930 1 0.0000 0.980 1.000 0.000
#> GSM97931 2 0.0000 0.980 0.000 1.000
#> GSM97935 1 0.0000 0.980 1.000 0.000
#> GSM97936 1 0.0000 0.980 1.000 0.000
#> GSM97938 1 0.0000 0.980 1.000 0.000
#> GSM97940 1 0.0000 0.980 1.000 0.000
#> GSM97942 1 0.0000 0.980 1.000 0.000
#> GSM97945 1 0.0000 0.980 1.000 0.000
#> GSM97946 2 0.0000 0.980 0.000 1.000
#> GSM97948 1 0.0000 0.980 1.000 0.000
#> GSM97950 1 0.0000 0.980 1.000 0.000
#> GSM97952 1 0.0000 0.980 1.000 0.000
#> GSM97953 1 0.0000 0.980 1.000 0.000
#> GSM97954 1 0.0000 0.980 1.000 0.000
#> GSM97955 1 0.0000 0.980 1.000 0.000
#> GSM97959 2 0.5408 0.849 0.124 0.876
#> GSM97961 1 0.0000 0.980 1.000 0.000
#> GSM97963 1 0.0000 0.980 1.000 0.000
#> GSM97965 1 0.0000 0.980 1.000 0.000
#> GSM97966 1 0.0000 0.980 1.000 0.000
#> GSM97967 2 0.0000 0.980 0.000 1.000
#> GSM97968 2 0.0000 0.980 0.000 1.000
#> GSM97969 1 0.0000 0.980 1.000 0.000
#> GSM97971 1 0.0000 0.980 1.000 0.000
#> GSM97799 2 0.0000 0.980 0.000 1.000
#> GSM97823 2 0.0000 0.980 0.000 1.000
#> GSM97824 2 0.0000 0.980 0.000 1.000
#> GSM97830 2 0.0000 0.980 0.000 1.000
#> GSM97835 2 0.0000 0.980 0.000 1.000
#> GSM97838 2 0.0000 0.980 0.000 1.000
#> GSM97841 2 0.0000 0.980 0.000 1.000
#> GSM97842 2 0.0000 0.980 0.000 1.000
#> GSM97854 2 0.0000 0.980 0.000 1.000
#> GSM97857 2 0.0000 0.980 0.000 1.000
#> GSM97860 1 0.9661 0.364 0.608 0.392
#> GSM97862 2 0.0000 0.980 0.000 1.000
#> GSM97864 2 0.0000 0.980 0.000 1.000
#> GSM97866 2 0.0000 0.980 0.000 1.000
#> GSM97868 2 0.0000 0.980 0.000 1.000
#> GSM97872 1 0.0000 0.980 1.000 0.000
#> GSM97873 2 0.0000 0.980 0.000 1.000
#> GSM97874 2 0.9491 0.411 0.368 0.632
#> GSM97875 2 0.0000 0.980 0.000 1.000
#> GSM97876 2 0.1843 0.954 0.028 0.972
#> GSM97880 1 0.0000 0.980 1.000 0.000
#> GSM97881 2 0.0000 0.980 0.000 1.000
#> GSM97884 2 0.0000 0.980 0.000 1.000
#> GSM97901 2 0.0000 0.980 0.000 1.000
#> GSM97902 2 0.4022 0.900 0.080 0.920
#> GSM97909 2 0.0000 0.980 0.000 1.000
#> GSM97911 2 0.0000 0.980 0.000 1.000
#> GSM97923 1 0.3274 0.927 0.940 0.060
#> GSM97928 1 0.0000 0.980 1.000 0.000
#> GSM97929 2 0.0000 0.980 0.000 1.000
#> GSM97933 1 0.4562 0.889 0.904 0.096
#> GSM97934 2 0.9970 0.105 0.468 0.532
#> GSM97944 2 0.0000 0.980 0.000 1.000
#> GSM97949 2 0.0000 0.980 0.000 1.000
#> GSM97956 2 0.0000 0.980 0.000 1.000
#> GSM97962 2 0.0000 0.980 0.000 1.000
#> GSM97964 2 0.0000 0.980 0.000 1.000
#> GSM97970 2 0.0000 0.980 0.000 1.000
#> GSM97822 1 0.0000 0.980 1.000 0.000
#> GSM97831 2 0.0000 0.980 0.000 1.000
#> GSM97845 1 0.0000 0.980 1.000 0.000
#> GSM97865 1 0.0000 0.980 1.000 0.000
#> GSM97867 1 0.0000 0.980 1.000 0.000
#> GSM97883 1 0.1843 0.956 0.972 0.028
#> GSM97897 1 0.0000 0.980 1.000 0.000
#> GSM97900 1 0.0000 0.980 1.000 0.000
#> GSM97904 1 0.0000 0.980 1.000 0.000
#> GSM97907 2 0.0000 0.980 0.000 1.000
#> GSM97925 1 0.8499 0.626 0.724 0.276
#> GSM97947 1 0.0000 0.980 1.000 0.000
cbind(get_classes(res, k = 3), get_membership(res, k = 3))
#> class entropy silhouette p1 p2 p3
#> GSM97800 2 0.0000 0.981 0.000 1.000 0.000
#> GSM97803 2 0.0000 0.981 0.000 1.000 0.000
#> GSM97804 2 0.0000 0.981 0.000 1.000 0.000
#> GSM97805 2 0.0000 0.981 0.000 1.000 0.000
#> GSM97807 2 0.0000 0.981 0.000 1.000 0.000
#> GSM97809 2 0.0000 0.981 0.000 1.000 0.000
#> GSM97811 2 0.0000 0.981 0.000 1.000 0.000
#> GSM97812 2 0.0000 0.981 0.000 1.000 0.000
#> GSM97816 2 0.0000 0.981 0.000 1.000 0.000
#> GSM97817 2 0.0000 0.981 0.000 1.000 0.000
#> GSM97820 2 0.0000 0.981 0.000 1.000 0.000
#> GSM97825 2 0.0000 0.981 0.000 1.000 0.000
#> GSM97827 2 0.0000 0.981 0.000 1.000 0.000
#> GSM97828 2 0.0000 0.981 0.000 1.000 0.000
#> GSM97833 2 0.0000 0.981 0.000 1.000 0.000
#> GSM97834 2 0.0000 0.981 0.000 1.000 0.000
#> GSM97840 2 0.0000 0.981 0.000 1.000 0.000
#> GSM97846 2 0.0000 0.981 0.000 1.000 0.000
#> GSM97848 2 0.0000 0.981 0.000 1.000 0.000
#> GSM97849 2 0.0000 0.981 0.000 1.000 0.000
#> GSM97850 2 0.0000 0.981 0.000 1.000 0.000
#> GSM97853 2 0.0000 0.981 0.000 1.000 0.000
#> GSM97855 2 0.0000 0.981 0.000 1.000 0.000
#> GSM97878 1 0.0000 0.997 1.000 0.000 0.000
#> GSM97913 2 0.0000 0.981 0.000 1.000 0.000
#> GSM97932 1 0.0000 0.997 1.000 0.000 0.000
#> GSM97939 3 0.3551 0.832 0.000 0.132 0.868
#> GSM97951 2 0.0000 0.981 0.000 1.000 0.000
#> GSM97957 3 0.0000 0.971 0.000 0.000 1.000
#> GSM97972 2 0.0000 0.981 0.000 1.000 0.000
#> GSM97793 3 0.0000 0.971 0.000 0.000 1.000
#> GSM97795 2 0.0000 0.981 0.000 1.000 0.000
#> GSM97802 3 0.0000 0.971 0.000 0.000 1.000
#> GSM97810 2 0.0892 0.963 0.000 0.980 0.020
#> GSM97815 2 0.4062 0.798 0.000 0.836 0.164
#> GSM97837 1 0.0000 0.997 1.000 0.000 0.000
#> GSM97843 3 0.0000 0.971 0.000 0.000 1.000
#> GSM97890 3 0.0000 0.971 0.000 0.000 1.000
#> GSM97899 1 0.0000 0.997 1.000 0.000 0.000
#> GSM97910 1 0.1774 0.960 0.960 0.024 0.016
#> GSM97916 1 0.0000 0.997 1.000 0.000 0.000
#> GSM97920 3 0.0000 0.971 0.000 0.000 1.000
#> GSM97921 1 0.0000 0.997 1.000 0.000 0.000
#> GSM97927 1 0.0000 0.997 1.000 0.000 0.000
#> GSM97937 1 0.0000 0.997 1.000 0.000 0.000
#> GSM97941 2 0.0000 0.981 0.000 1.000 0.000
#> GSM97943 2 0.7265 0.595 0.076 0.684 0.240
#> GSM97958 2 0.0000 0.981 0.000 1.000 0.000
#> GSM97960 2 0.0000 0.981 0.000 1.000 0.000
#> GSM97794 1 0.3686 0.835 0.860 0.140 0.000
#> GSM97796 1 0.0000 0.997 1.000 0.000 0.000
#> GSM97797 2 0.6026 0.403 0.376 0.624 0.000
#> GSM97798 1 0.0000 0.997 1.000 0.000 0.000
#> GSM97801 1 0.0000 0.997 1.000 0.000 0.000
#> GSM97806 1 0.0000 0.997 1.000 0.000 0.000
#> GSM97808 1 0.0000 0.997 1.000 0.000 0.000
#> GSM97813 1 0.0000 0.997 1.000 0.000 0.000
#> GSM97814 1 0.0000 0.997 1.000 0.000 0.000
#> GSM97818 1 0.0237 0.993 0.996 0.004 0.000
#> GSM97819 3 0.0000 0.971 0.000 0.000 1.000
#> GSM97821 2 0.0000 0.981 0.000 1.000 0.000
#> GSM97826 1 0.0000 0.997 1.000 0.000 0.000
#> GSM97829 1 0.0000 0.997 1.000 0.000 0.000
#> GSM97832 2 0.0000 0.981 0.000 1.000 0.000
#> GSM97836 3 0.6244 0.232 0.440 0.000 0.560
#> GSM97839 1 0.0000 0.997 1.000 0.000 0.000
#> GSM97844 2 0.0000 0.981 0.000 1.000 0.000
#> GSM97847 1 0.0000 0.997 1.000 0.000 0.000
#> GSM97851 1 0.0000 0.997 1.000 0.000 0.000
#> GSM97852 1 0.0000 0.997 1.000 0.000 0.000
#> GSM97856 1 0.0000 0.997 1.000 0.000 0.000
#> GSM97858 2 0.0000 0.981 0.000 1.000 0.000
#> GSM97859 1 0.0747 0.982 0.984 0.000 0.016
#> GSM97861 1 0.0000 0.997 1.000 0.000 0.000
#> GSM97863 1 0.0000 0.997 1.000 0.000 0.000
#> GSM97869 1 0.0000 0.997 1.000 0.000 0.000
#> GSM97870 3 0.0000 0.971 0.000 0.000 1.000
#> GSM97871 1 0.0000 0.997 1.000 0.000 0.000
#> GSM97877 2 0.0000 0.981 0.000 1.000 0.000
#> GSM97879 1 0.0000 0.997 1.000 0.000 0.000
#> GSM97882 1 0.0000 0.997 1.000 0.000 0.000
#> GSM97885 1 0.0000 0.997 1.000 0.000 0.000
#> GSM97886 1 0.0000 0.997 1.000 0.000 0.000
#> GSM97887 1 0.0000 0.997 1.000 0.000 0.000
#> GSM97888 1 0.0000 0.997 1.000 0.000 0.000
#> GSM97889 1 0.0000 0.997 1.000 0.000 0.000
#> GSM97891 1 0.0000 0.997 1.000 0.000 0.000
#> GSM97892 2 0.0000 0.981 0.000 1.000 0.000
#> GSM97893 1 0.0000 0.997 1.000 0.000 0.000
#> GSM97894 1 0.0000 0.997 1.000 0.000 0.000
#> GSM97895 1 0.0000 0.997 1.000 0.000 0.000
#> GSM97896 1 0.0000 0.997 1.000 0.000 0.000
#> GSM97898 1 0.0000 0.997 1.000 0.000 0.000
#> GSM97903 1 0.0000 0.997 1.000 0.000 0.000
#> GSM97905 3 0.0000 0.971 0.000 0.000 1.000
#> GSM97906 1 0.0000 0.997 1.000 0.000 0.000
#> GSM97908 1 0.0000 0.997 1.000 0.000 0.000
#> GSM97912 3 0.6274 0.172 0.456 0.000 0.544
#> GSM97914 1 0.0000 0.997 1.000 0.000 0.000
#> GSM97915 1 0.0000 0.997 1.000 0.000 0.000
#> GSM97917 1 0.0000 0.997 1.000 0.000 0.000
#> GSM97918 1 0.0000 0.997 1.000 0.000 0.000
#> GSM97919 1 0.0000 0.997 1.000 0.000 0.000
#> GSM97922 1 0.0000 0.997 1.000 0.000 0.000
#> GSM97924 2 0.0000 0.981 0.000 1.000 0.000
#> GSM97926 3 0.0000 0.971 0.000 0.000 1.000
#> GSM97930 1 0.0000 0.997 1.000 0.000 0.000
#> GSM97931 2 0.0000 0.981 0.000 1.000 0.000
#> GSM97935 1 0.0000 0.997 1.000 0.000 0.000
#> GSM97936 1 0.0000 0.997 1.000 0.000 0.000
#> GSM97938 1 0.0000 0.997 1.000 0.000 0.000
#> GSM97940 1 0.0000 0.997 1.000 0.000 0.000
#> GSM97942 3 0.0000 0.971 0.000 0.000 1.000
#> GSM97945 1 0.0000 0.997 1.000 0.000 0.000
#> GSM97946 2 0.0000 0.981 0.000 1.000 0.000
#> GSM97948 3 0.0000 0.971 0.000 0.000 1.000
#> GSM97950 1 0.0000 0.997 1.000 0.000 0.000
#> GSM97952 1 0.0000 0.997 1.000 0.000 0.000
#> GSM97953 1 0.0000 0.997 1.000 0.000 0.000
#> GSM97954 1 0.0000 0.997 1.000 0.000 0.000
#> GSM97955 1 0.0000 0.997 1.000 0.000 0.000
#> GSM97959 2 0.2625 0.890 0.084 0.916 0.000
#> GSM97961 1 0.0000 0.997 1.000 0.000 0.000
#> GSM97963 1 0.0000 0.997 1.000 0.000 0.000
#> GSM97965 1 0.0000 0.997 1.000 0.000 0.000
#> GSM97966 1 0.0000 0.997 1.000 0.000 0.000
#> GSM97967 2 0.0000 0.981 0.000 1.000 0.000
#> GSM97968 2 0.0000 0.981 0.000 1.000 0.000
#> GSM97969 1 0.0000 0.997 1.000 0.000 0.000
#> GSM97971 1 0.0237 0.994 0.996 0.000 0.004
#> GSM97799 3 0.0000 0.971 0.000 0.000 1.000
#> GSM97823 2 0.0000 0.981 0.000 1.000 0.000
#> GSM97824 3 0.0000 0.971 0.000 0.000 1.000
#> GSM97830 3 0.0000 0.971 0.000 0.000 1.000
#> GSM97835 3 0.3879 0.806 0.000 0.152 0.848
#> GSM97838 2 0.0000 0.981 0.000 1.000 0.000
#> GSM97841 2 0.0000 0.981 0.000 1.000 0.000
#> GSM97842 3 0.0237 0.968 0.000 0.004 0.996
#> GSM97854 2 0.0000 0.981 0.000 1.000 0.000
#> GSM97857 3 0.0424 0.965 0.000 0.008 0.992
#> GSM97860 3 0.0000 0.971 0.000 0.000 1.000
#> GSM97862 3 0.0000 0.971 0.000 0.000 1.000
#> GSM97864 2 0.0000 0.981 0.000 1.000 0.000
#> GSM97866 3 0.0000 0.971 0.000 0.000 1.000
#> GSM97868 3 0.0000 0.971 0.000 0.000 1.000
#> GSM97872 1 0.0000 0.997 1.000 0.000 0.000
#> GSM97873 3 0.0000 0.971 0.000 0.000 1.000
#> GSM97874 3 0.0000 0.971 0.000 0.000 1.000
#> GSM97875 3 0.0000 0.971 0.000 0.000 1.000
#> GSM97876 3 0.0000 0.971 0.000 0.000 1.000
#> GSM97880 3 0.0000 0.971 0.000 0.000 1.000
#> GSM97881 3 0.0000 0.971 0.000 0.000 1.000
#> GSM97884 3 0.0237 0.968 0.000 0.004 0.996
#> GSM97901 3 0.0000 0.971 0.000 0.000 1.000
#> GSM97902 2 0.1529 0.940 0.040 0.960 0.000
#> GSM97909 2 0.0000 0.981 0.000 1.000 0.000
#> GSM97911 3 0.0000 0.971 0.000 0.000 1.000
#> GSM97923 3 0.0000 0.971 0.000 0.000 1.000
#> GSM97928 1 0.0000 0.997 1.000 0.000 0.000
#> GSM97929 2 0.0000 0.981 0.000 1.000 0.000
#> GSM97933 3 0.0000 0.971 0.000 0.000 1.000
#> GSM97934 3 0.0000 0.971 0.000 0.000 1.000
#> GSM97944 3 0.0000 0.971 0.000 0.000 1.000
#> GSM97949 2 0.0000 0.981 0.000 1.000 0.000
#> GSM97956 3 0.0000 0.971 0.000 0.000 1.000
#> GSM97962 3 0.0000 0.971 0.000 0.000 1.000
#> GSM97964 3 0.0000 0.971 0.000 0.000 1.000
#> GSM97970 3 0.0000 0.971 0.000 0.000 1.000
#> GSM97822 1 0.0000 0.997 1.000 0.000 0.000
#> GSM97831 3 0.0000 0.971 0.000 0.000 1.000
#> GSM97845 1 0.0000 0.997 1.000 0.000 0.000
#> GSM97865 1 0.0000 0.997 1.000 0.000 0.000
#> GSM97867 3 0.0000 0.971 0.000 0.000 1.000
#> GSM97883 3 0.0000 0.971 0.000 0.000 1.000
#> GSM97897 1 0.0237 0.993 0.996 0.000 0.004
#> GSM97900 1 0.0000 0.997 1.000 0.000 0.000
#> GSM97904 1 0.0000 0.997 1.000 0.000 0.000
#> GSM97907 2 0.0000 0.981 0.000 1.000 0.000
#> GSM97925 3 0.0000 0.971 0.000 0.000 1.000
#> GSM97947 3 0.0000 0.971 0.000 0.000 1.000
cbind(get_classes(res, k = 4), get_membership(res, k = 4))
#> class entropy silhouette p1 p2 p3 p4
#> GSM97800 2 0.0000 0.9880 0.000 1.000 0.000 0.000
#> GSM97803 2 0.0000 0.9880 0.000 1.000 0.000 0.000
#> GSM97804 2 0.0000 0.9880 0.000 1.000 0.000 0.000
#> GSM97805 2 0.0000 0.9880 0.000 1.000 0.000 0.000
#> GSM97807 2 0.0000 0.9880 0.000 1.000 0.000 0.000
#> GSM97809 2 0.0000 0.9880 0.000 1.000 0.000 0.000
#> GSM97811 2 0.0000 0.9880 0.000 1.000 0.000 0.000
#> GSM97812 2 0.0000 0.9880 0.000 1.000 0.000 0.000
#> GSM97816 4 0.0376 0.8468 0.000 0.004 0.004 0.992
#> GSM97817 2 0.0000 0.9880 0.000 1.000 0.000 0.000
#> GSM97820 2 0.0000 0.9880 0.000 1.000 0.000 0.000
#> GSM97825 2 0.0000 0.9880 0.000 1.000 0.000 0.000
#> GSM97827 2 0.0000 0.9880 0.000 1.000 0.000 0.000
#> GSM97828 4 0.0188 0.8480 0.000 0.000 0.004 0.996
#> GSM97833 2 0.0000 0.9880 0.000 1.000 0.000 0.000
#> GSM97834 2 0.0000 0.9880 0.000 1.000 0.000 0.000
#> GSM97840 2 0.0188 0.9852 0.000 0.996 0.000 0.004
#> GSM97846 2 0.0000 0.9880 0.000 1.000 0.000 0.000
#> GSM97848 2 0.0000 0.9880 0.000 1.000 0.000 0.000
#> GSM97849 2 0.0000 0.9880 0.000 1.000 0.000 0.000
#> GSM97850 2 0.0000 0.9880 0.000 1.000 0.000 0.000
#> GSM97853 2 0.0000 0.9880 0.000 1.000 0.000 0.000
#> GSM97855 2 0.0336 0.9822 0.000 0.992 0.000 0.008
#> GSM97878 1 0.0376 0.9707 0.992 0.004 0.000 0.004
#> GSM97913 2 0.0000 0.9880 0.000 1.000 0.000 0.000
#> GSM97932 1 0.0336 0.9707 0.992 0.000 0.000 0.008
#> GSM97939 3 0.4378 0.7249 0.000 0.164 0.796 0.040
#> GSM97951 2 0.0000 0.9880 0.000 1.000 0.000 0.000
#> GSM97957 4 0.2814 0.7570 0.000 0.000 0.132 0.868
#> GSM97972 4 0.1398 0.8314 0.000 0.040 0.004 0.956
#> GSM97793 3 0.0336 0.9220 0.000 0.000 0.992 0.008
#> GSM97795 2 0.0000 0.9880 0.000 1.000 0.000 0.000
#> GSM97802 3 0.1191 0.8987 0.024 0.004 0.968 0.004
#> GSM97810 2 0.0927 0.9661 0.000 0.976 0.016 0.008
#> GSM97815 2 0.1867 0.9097 0.000 0.928 0.072 0.000
#> GSM97837 4 0.0188 0.8480 0.000 0.000 0.004 0.996
#> GSM97843 3 0.0707 0.9200 0.000 0.000 0.980 0.020
#> GSM97890 3 0.0188 0.9205 0.000 0.000 0.996 0.004
#> GSM97899 1 0.0000 0.9736 1.000 0.000 0.000 0.000
#> GSM97910 4 0.0188 0.8480 0.000 0.000 0.004 0.996
#> GSM97916 1 0.0336 0.9707 0.992 0.000 0.000 0.008
#> GSM97920 4 0.4907 0.1557 0.000 0.000 0.420 0.580
#> GSM97921 4 0.4477 0.5552 0.312 0.000 0.000 0.688
#> GSM97927 1 0.0188 0.9719 0.996 0.000 0.004 0.000
#> GSM97937 4 0.3975 0.6764 0.240 0.000 0.000 0.760
#> GSM97941 2 0.0000 0.9880 0.000 1.000 0.000 0.000
#> GSM97943 4 0.0188 0.8480 0.000 0.000 0.004 0.996
#> GSM97958 2 0.1940 0.9162 0.000 0.924 0.000 0.076
#> GSM97960 2 0.0000 0.9880 0.000 1.000 0.000 0.000
#> GSM97794 1 0.1118 0.9388 0.964 0.036 0.000 0.000
#> GSM97796 1 0.0000 0.9736 1.000 0.000 0.000 0.000
#> GSM97797 1 0.5792 0.5961 0.708 0.124 0.000 0.168
#> GSM97798 1 0.0188 0.9719 0.996 0.000 0.000 0.004
#> GSM97801 4 0.0817 0.8477 0.024 0.000 0.000 0.976
#> GSM97806 1 0.0188 0.9719 0.996 0.000 0.000 0.004
#> GSM97808 1 0.0000 0.9736 1.000 0.000 0.000 0.000
#> GSM97813 1 0.0000 0.9736 1.000 0.000 0.000 0.000
#> GSM97814 1 0.0000 0.9736 1.000 0.000 0.000 0.000
#> GSM97818 1 0.3975 0.6764 0.760 0.000 0.000 0.240
#> GSM97819 3 0.0188 0.9205 0.000 0.000 0.996 0.004
#> GSM97821 2 0.0000 0.9880 0.000 1.000 0.000 0.000
#> GSM97826 4 0.0817 0.8481 0.024 0.000 0.000 0.976
#> GSM97829 4 0.1474 0.8349 0.052 0.000 0.000 0.948
#> GSM97832 2 0.2281 0.8963 0.000 0.904 0.000 0.096
#> GSM97836 3 0.5155 0.0973 0.468 0.000 0.528 0.004
#> GSM97839 1 0.0000 0.9736 1.000 0.000 0.000 0.000
#> GSM97844 2 0.0000 0.9880 0.000 1.000 0.000 0.000
#> GSM97847 1 0.0336 0.9707 0.992 0.000 0.000 0.008
#> GSM97851 1 0.0188 0.9725 0.996 0.000 0.000 0.004
#> GSM97852 1 0.0188 0.9725 0.996 0.000 0.000 0.004
#> GSM97856 1 0.0000 0.9736 1.000 0.000 0.000 0.000
#> GSM97858 2 0.0000 0.9880 0.000 1.000 0.000 0.000
#> GSM97859 1 0.0000 0.9736 1.000 0.000 0.000 0.000
#> GSM97861 1 0.0376 0.9697 0.992 0.000 0.004 0.004
#> GSM97863 1 0.0000 0.9736 1.000 0.000 0.000 0.000
#> GSM97869 1 0.0000 0.9736 1.000 0.000 0.000 0.000
#> GSM97870 3 0.4277 0.6513 0.000 0.000 0.720 0.280
#> GSM97871 1 0.0000 0.9736 1.000 0.000 0.000 0.000
#> GSM97877 2 0.0000 0.9880 0.000 1.000 0.000 0.000
#> GSM97879 1 0.0000 0.9736 1.000 0.000 0.000 0.000
#> GSM97882 1 0.0524 0.9669 0.988 0.000 0.008 0.004
#> GSM97885 1 0.0000 0.9736 1.000 0.000 0.000 0.000
#> GSM97886 1 0.0000 0.9736 1.000 0.000 0.000 0.000
#> GSM97887 1 0.0657 0.9638 0.984 0.000 0.012 0.004
#> GSM97888 1 0.0000 0.9736 1.000 0.000 0.000 0.000
#> GSM97889 1 0.0779 0.9606 0.980 0.000 0.016 0.004
#> GSM97891 1 0.0524 0.9669 0.988 0.000 0.008 0.004
#> GSM97892 2 0.0000 0.9880 0.000 1.000 0.000 0.000
#> GSM97893 1 0.0469 0.9681 0.988 0.000 0.000 0.012
#> GSM97894 1 0.0000 0.9736 1.000 0.000 0.000 0.000
#> GSM97895 1 0.0336 0.9707 0.992 0.000 0.000 0.008
#> GSM97896 1 0.0000 0.9736 1.000 0.000 0.000 0.000
#> GSM97898 1 0.0000 0.9736 1.000 0.000 0.000 0.000
#> GSM97903 1 0.0188 0.9725 0.996 0.000 0.000 0.004
#> GSM97905 3 0.1059 0.9159 0.012 0.000 0.972 0.016
#> GSM97906 1 0.0000 0.9736 1.000 0.000 0.000 0.000
#> GSM97908 1 0.0188 0.9725 0.996 0.000 0.000 0.004
#> GSM97912 4 0.1489 0.8403 0.044 0.000 0.004 0.952
#> GSM97914 1 0.4134 0.6426 0.740 0.000 0.000 0.260
#> GSM97915 1 0.0000 0.9736 1.000 0.000 0.000 0.000
#> GSM97917 1 0.0336 0.9707 0.992 0.000 0.000 0.008
#> GSM97918 1 0.0000 0.9736 1.000 0.000 0.000 0.000
#> GSM97919 1 0.0000 0.9736 1.000 0.000 0.000 0.000
#> GSM97922 1 0.0000 0.9736 1.000 0.000 0.000 0.000
#> GSM97924 2 0.0000 0.9880 0.000 1.000 0.000 0.000
#> GSM97926 3 0.0188 0.9205 0.000 0.000 0.996 0.004
#> GSM97930 1 0.0817 0.9588 0.976 0.000 0.000 0.024
#> GSM97931 2 0.0000 0.9880 0.000 1.000 0.000 0.000
#> GSM97935 1 0.0000 0.9736 1.000 0.000 0.000 0.000
#> GSM97936 1 0.0000 0.9736 1.000 0.000 0.000 0.000
#> GSM97938 1 0.0707 0.9621 0.980 0.000 0.000 0.020
#> GSM97940 1 0.0188 0.9719 0.996 0.000 0.000 0.004
#> GSM97942 3 0.0188 0.9205 0.000 0.000 0.996 0.004
#> GSM97945 1 0.0000 0.9736 1.000 0.000 0.000 0.000
#> GSM97946 2 0.0000 0.9880 0.000 1.000 0.000 0.000
#> GSM97948 3 0.0188 0.9205 0.000 0.000 0.996 0.004
#> GSM97950 1 0.0000 0.9736 1.000 0.000 0.000 0.000
#> GSM97952 1 0.0000 0.9736 1.000 0.000 0.000 0.000
#> GSM97953 1 0.3074 0.8141 0.848 0.000 0.000 0.152
#> GSM97954 1 0.0188 0.9725 0.996 0.000 0.000 0.004
#> GSM97955 1 0.0000 0.9736 1.000 0.000 0.000 0.000
#> GSM97959 2 0.3764 0.6577 0.216 0.784 0.000 0.000
#> GSM97961 1 0.0000 0.9736 1.000 0.000 0.000 0.000
#> GSM97963 1 0.0000 0.9736 1.000 0.000 0.000 0.000
#> GSM97965 1 0.0000 0.9736 1.000 0.000 0.000 0.000
#> GSM97966 1 0.0000 0.9736 1.000 0.000 0.000 0.000
#> GSM97967 2 0.0000 0.9880 0.000 1.000 0.000 0.000
#> GSM97968 2 0.0188 0.9852 0.000 0.996 0.000 0.004
#> GSM97969 1 0.0188 0.9725 0.996 0.000 0.000 0.004
#> GSM97971 1 0.1302 0.9423 0.956 0.000 0.000 0.044
#> GSM97799 3 0.0188 0.9205 0.000 0.000 0.996 0.004
#> GSM97823 2 0.0000 0.9880 0.000 1.000 0.000 0.000
#> GSM97824 3 0.3942 0.7105 0.000 0.000 0.764 0.236
#> GSM97830 3 0.2281 0.8719 0.000 0.000 0.904 0.096
#> GSM97835 3 0.4250 0.5648 0.000 0.276 0.724 0.000
#> GSM97838 2 0.0000 0.9880 0.000 1.000 0.000 0.000
#> GSM97841 2 0.0000 0.9880 0.000 1.000 0.000 0.000
#> GSM97842 3 0.0188 0.9219 0.000 0.000 0.996 0.004
#> GSM97854 2 0.0000 0.9880 0.000 1.000 0.000 0.000
#> GSM97857 4 0.2011 0.8041 0.000 0.000 0.080 0.920
#> GSM97860 3 0.0592 0.9209 0.000 0.000 0.984 0.016
#> GSM97862 3 0.0469 0.9216 0.000 0.000 0.988 0.012
#> GSM97864 2 0.0000 0.9880 0.000 1.000 0.000 0.000
#> GSM97866 3 0.0817 0.9186 0.000 0.000 0.976 0.024
#> GSM97868 3 0.0469 0.9216 0.000 0.000 0.988 0.012
#> GSM97872 4 0.4907 0.2991 0.420 0.000 0.000 0.580
#> GSM97873 3 0.0188 0.9219 0.000 0.000 0.996 0.004
#> GSM97874 3 0.4454 0.5989 0.000 0.000 0.692 0.308
#> GSM97875 3 0.0188 0.9205 0.000 0.000 0.996 0.004
#> GSM97876 3 0.0336 0.9220 0.000 0.000 0.992 0.008
#> GSM97880 3 0.1557 0.9024 0.000 0.000 0.944 0.056
#> GSM97881 3 0.0000 0.9214 0.000 0.000 1.000 0.000
#> GSM97884 3 0.0188 0.9204 0.000 0.004 0.996 0.000
#> GSM97901 3 0.0707 0.9200 0.000 0.000 0.980 0.020
#> GSM97902 4 0.1059 0.8450 0.012 0.016 0.000 0.972
#> GSM97909 2 0.0000 0.9880 0.000 1.000 0.000 0.000
#> GSM97911 3 0.0000 0.9214 0.000 0.000 1.000 0.000
#> GSM97923 3 0.0469 0.9216 0.000 0.000 0.988 0.012
#> GSM97928 1 0.0188 0.9725 0.996 0.000 0.000 0.004
#> GSM97929 2 0.0000 0.9880 0.000 1.000 0.000 0.000
#> GSM97933 3 0.3266 0.7995 0.000 0.000 0.832 0.168
#> GSM97934 4 0.4072 0.6026 0.000 0.000 0.252 0.748
#> GSM97944 3 0.0000 0.9214 0.000 0.000 1.000 0.000
#> GSM97949 2 0.0000 0.9880 0.000 1.000 0.000 0.000
#> GSM97956 3 0.1211 0.9116 0.000 0.000 0.960 0.040
#> GSM97962 3 0.4008 0.6992 0.000 0.000 0.756 0.244
#> GSM97964 3 0.1389 0.9073 0.000 0.000 0.952 0.048
#> GSM97970 3 0.0336 0.9220 0.000 0.000 0.992 0.008
#> GSM97822 1 0.0895 0.9569 0.976 0.000 0.020 0.004
#> GSM97831 3 0.1557 0.9024 0.000 0.000 0.944 0.056
#> GSM97845 1 0.0336 0.9707 0.992 0.000 0.000 0.008
#> GSM97865 1 0.4855 0.2950 0.600 0.000 0.000 0.400
#> GSM97867 3 0.0592 0.9209 0.000 0.000 0.984 0.016
#> GSM97883 3 0.1302 0.9095 0.000 0.000 0.956 0.044
#> GSM97897 1 0.0657 0.9638 0.984 0.000 0.012 0.004
#> GSM97900 1 0.0657 0.9638 0.984 0.000 0.012 0.004
#> GSM97904 1 0.0188 0.9725 0.996 0.000 0.000 0.004
#> GSM97907 2 0.0000 0.9880 0.000 1.000 0.000 0.000
#> GSM97925 3 0.0188 0.9205 0.000 0.000 0.996 0.004
#> GSM97947 3 0.0188 0.9205 0.000 0.000 0.996 0.004
cbind(get_classes(res, k = 5), get_membership(res, k = 5))
#> class entropy silhouette p1 p2 p3 p4 p5
#> GSM97800 2 0.0162 0.95462 0.000 0.996 0.000 0.000 0.004
#> GSM97803 2 0.0162 0.95462 0.000 0.996 0.000 0.000 0.004
#> GSM97804 2 0.0290 0.95371 0.000 0.992 0.000 0.000 0.008
#> GSM97805 2 0.0162 0.95462 0.000 0.996 0.000 0.000 0.004
#> GSM97807 2 0.0451 0.95135 0.004 0.988 0.000 0.000 0.008
#> GSM97809 2 0.0451 0.95135 0.004 0.988 0.000 0.000 0.008
#> GSM97811 2 0.0000 0.95456 0.000 1.000 0.000 0.000 0.000
#> GSM97812 2 0.0162 0.95390 0.000 0.996 0.000 0.000 0.004
#> GSM97816 1 0.0162 0.59919 0.996 0.004 0.000 0.000 0.000
#> GSM97817 2 0.0162 0.95462 0.000 0.996 0.000 0.000 0.004
#> GSM97820 2 0.0000 0.95456 0.000 1.000 0.000 0.000 0.000
#> GSM97825 2 0.0162 0.95390 0.000 0.996 0.000 0.000 0.004
#> GSM97827 2 0.0162 0.95390 0.000 0.996 0.000 0.000 0.004
#> GSM97828 1 0.0162 0.59926 0.996 0.000 0.000 0.000 0.004
#> GSM97833 2 0.0000 0.95456 0.000 1.000 0.000 0.000 0.000
#> GSM97834 2 0.0000 0.95456 0.000 1.000 0.000 0.000 0.000
#> GSM97840 2 0.0451 0.95281 0.008 0.988 0.000 0.000 0.004
#> GSM97846 2 0.0000 0.95456 0.000 1.000 0.000 0.000 0.000
#> GSM97848 2 0.0162 0.95390 0.000 0.996 0.000 0.000 0.004
#> GSM97849 2 0.0162 0.95390 0.000 0.996 0.000 0.000 0.004
#> GSM97850 2 0.0162 0.95462 0.000 0.996 0.000 0.000 0.004
#> GSM97853 2 0.0162 0.95390 0.000 0.996 0.000 0.000 0.004
#> GSM97855 2 0.1012 0.94071 0.020 0.968 0.000 0.000 0.012
#> GSM97878 5 0.5803 0.16847 0.016 0.020 0.032 0.344 0.588
#> GSM97913 2 0.5754 0.49074 0.080 0.640 0.000 0.024 0.256
#> GSM97932 4 0.4576 0.36663 0.016 0.000 0.000 0.608 0.376
#> GSM97939 3 0.6261 0.55909 0.036 0.144 0.628 0.000 0.192
#> GSM97951 2 0.0671 0.94712 0.004 0.980 0.000 0.000 0.016
#> GSM97957 1 0.5656 0.41769 0.588 0.000 0.308 0.000 0.104
#> GSM97972 1 0.4761 0.47371 0.728 0.168 0.000 0.000 0.104
#> GSM97793 3 0.2852 0.78568 0.000 0.000 0.828 0.000 0.172
#> GSM97795 2 0.0579 0.95011 0.000 0.984 0.008 0.000 0.008
#> GSM97802 3 0.6900 -0.00077 0.000 0.004 0.396 0.316 0.284
#> GSM97810 2 0.2681 0.86693 0.004 0.892 0.052 0.000 0.052
#> GSM97815 2 0.4657 0.51683 0.000 0.668 0.296 0.000 0.036
#> GSM97837 1 0.2813 0.57040 0.832 0.000 0.000 0.000 0.168
#> GSM97843 3 0.1168 0.83569 0.008 0.000 0.960 0.000 0.032
#> GSM97890 3 0.2329 0.81137 0.000 0.000 0.876 0.000 0.124
#> GSM97899 4 0.0794 0.72033 0.000 0.000 0.000 0.972 0.028
#> GSM97910 1 0.3795 0.54122 0.804 0.004 0.008 0.020 0.164
#> GSM97916 4 0.4193 0.59742 0.040 0.000 0.000 0.748 0.212
#> GSM97920 1 0.3282 0.52642 0.804 0.000 0.188 0.000 0.008
#> GSM97921 1 0.5726 0.17134 0.612 0.000 0.000 0.140 0.248
#> GSM97927 4 0.2813 0.61962 0.000 0.000 0.000 0.832 0.168
#> GSM97937 1 0.5989 0.00640 0.536 0.000 0.000 0.128 0.336
#> GSM97941 2 0.0000 0.95456 0.000 1.000 0.000 0.000 0.000
#> GSM97943 1 0.1478 0.59737 0.936 0.000 0.000 0.000 0.064
#> GSM97958 2 0.3275 0.83706 0.068 0.860 0.000 0.008 0.064
#> GSM97960 2 0.1430 0.91914 0.000 0.944 0.004 0.000 0.052
#> GSM97794 4 0.6530 0.17790 0.036 0.124 0.000 0.572 0.268
#> GSM97796 4 0.1608 0.71879 0.000 0.000 0.000 0.928 0.072
#> GSM97797 1 0.7558 -0.17144 0.404 0.068 0.000 0.168 0.360
#> GSM97798 4 0.1608 0.69973 0.000 0.000 0.000 0.928 0.072
#> GSM97801 1 0.3724 0.48407 0.788 0.000 0.000 0.028 0.184
#> GSM97806 4 0.2471 0.68647 0.000 0.000 0.000 0.864 0.136
#> GSM97808 4 0.1792 0.69264 0.000 0.000 0.000 0.916 0.084
#> GSM97813 4 0.2280 0.68101 0.000 0.000 0.000 0.880 0.120
#> GSM97814 4 0.1121 0.71117 0.000 0.000 0.000 0.956 0.044
#> GSM97818 4 0.6839 -0.04043 0.232 0.020 0.000 0.512 0.236
#> GSM97819 3 0.1197 0.83270 0.000 0.000 0.952 0.000 0.048
#> GSM97821 2 0.0880 0.94176 0.000 0.968 0.000 0.000 0.032
#> GSM97826 1 0.2873 0.57416 0.860 0.000 0.000 0.020 0.120
#> GSM97829 1 0.4238 0.44663 0.768 0.000 0.000 0.068 0.164
#> GSM97832 2 0.4054 0.69067 0.236 0.744 0.008 0.000 0.012
#> GSM97836 4 0.4561 -0.08935 0.000 0.000 0.488 0.504 0.008
#> GSM97839 4 0.2648 0.68096 0.000 0.000 0.000 0.848 0.152
#> GSM97844 2 0.0162 0.95462 0.000 0.996 0.000 0.000 0.004
#> GSM97847 4 0.4570 0.42016 0.020 0.000 0.000 0.632 0.348
#> GSM97851 4 0.4118 0.47332 0.004 0.000 0.000 0.660 0.336
#> GSM97852 4 0.4047 0.49260 0.004 0.000 0.000 0.676 0.320
#> GSM97856 4 0.1732 0.71342 0.000 0.000 0.000 0.920 0.080
#> GSM97858 2 0.0290 0.95371 0.000 0.992 0.000 0.000 0.008
#> GSM97859 4 0.2517 0.68572 0.004 0.000 0.008 0.884 0.104
#> GSM97861 4 0.1851 0.69015 0.000 0.000 0.000 0.912 0.088
#> GSM97863 4 0.1732 0.71680 0.000 0.000 0.000 0.920 0.080
#> GSM97869 4 0.2068 0.70068 0.000 0.000 0.004 0.904 0.092
#> GSM97870 3 0.6831 0.28566 0.304 0.000 0.508 0.028 0.160
#> GSM97871 4 0.0404 0.72053 0.000 0.000 0.000 0.988 0.012
#> GSM97877 2 0.0865 0.94189 0.000 0.972 0.000 0.004 0.024
#> GSM97879 4 0.0609 0.72157 0.000 0.000 0.000 0.980 0.020
#> GSM97882 4 0.0794 0.72078 0.000 0.000 0.000 0.972 0.028
#> GSM97885 4 0.1270 0.71245 0.000 0.000 0.000 0.948 0.052
#> GSM97886 4 0.3242 0.62856 0.000 0.000 0.000 0.784 0.216
#> GSM97887 4 0.1121 0.71456 0.000 0.000 0.000 0.956 0.044
#> GSM97888 4 0.2230 0.71279 0.000 0.000 0.000 0.884 0.116
#> GSM97889 4 0.5335 0.28141 0.000 0.000 0.096 0.644 0.260
#> GSM97891 4 0.2179 0.70360 0.000 0.000 0.000 0.888 0.112
#> GSM97892 2 0.0162 0.95462 0.000 0.996 0.000 0.000 0.004
#> GSM97893 4 0.3689 0.57947 0.004 0.000 0.000 0.740 0.256
#> GSM97894 4 0.3424 0.61387 0.000 0.000 0.000 0.760 0.240
#> GSM97895 4 0.4313 0.42641 0.008 0.000 0.000 0.636 0.356
#> GSM97896 4 0.2377 0.68951 0.000 0.000 0.000 0.872 0.128
#> GSM97898 4 0.3143 0.64707 0.000 0.000 0.000 0.796 0.204
#> GSM97903 4 0.3628 0.61712 0.012 0.000 0.000 0.772 0.216
#> GSM97905 3 0.3767 0.76404 0.008 0.000 0.800 0.024 0.168
#> GSM97906 4 0.1043 0.71257 0.000 0.000 0.000 0.960 0.040
#> GSM97908 4 0.4538 0.39370 0.016 0.000 0.000 0.620 0.364
#> GSM97912 1 0.7002 0.33289 0.480 0.000 0.208 0.024 0.288
#> GSM97914 4 0.6206 0.02849 0.252 0.000 0.000 0.548 0.200
#> GSM97915 4 0.3534 0.59108 0.000 0.000 0.000 0.744 0.256
#> GSM97917 4 0.4380 0.38504 0.008 0.000 0.000 0.616 0.376
#> GSM97918 4 0.1851 0.71451 0.000 0.000 0.000 0.912 0.088
#> GSM97919 4 0.3814 0.56325 0.004 0.000 0.000 0.720 0.276
#> GSM97922 4 0.2280 0.68461 0.000 0.000 0.000 0.880 0.120
#> GSM97924 2 0.0162 0.95462 0.000 0.996 0.000 0.000 0.004
#> GSM97926 3 0.2280 0.81535 0.000 0.000 0.880 0.000 0.120
#> GSM97930 4 0.4798 0.29718 0.024 0.000 0.000 0.580 0.396
#> GSM97931 2 0.5372 0.62694 0.012 0.692 0.084 0.004 0.208
#> GSM97935 4 0.1792 0.69192 0.000 0.000 0.000 0.916 0.084
#> GSM97936 4 0.2471 0.68392 0.000 0.000 0.000 0.864 0.136
#> GSM97938 4 0.4885 0.24523 0.028 0.000 0.000 0.572 0.400
#> GSM97940 4 0.0963 0.71613 0.000 0.000 0.000 0.964 0.036
#> GSM97942 3 0.1544 0.83086 0.000 0.000 0.932 0.000 0.068
#> GSM97945 4 0.1478 0.70480 0.000 0.000 0.000 0.936 0.064
#> GSM97946 2 0.0162 0.95409 0.004 0.996 0.000 0.000 0.000
#> GSM97948 3 0.2732 0.79733 0.000 0.000 0.840 0.000 0.160
#> GSM97950 4 0.1671 0.71778 0.000 0.000 0.000 0.924 0.076
#> GSM97952 4 0.0703 0.71586 0.000 0.000 0.000 0.976 0.024
#> GSM97953 4 0.5906 -0.07616 0.104 0.000 0.000 0.492 0.404
#> GSM97954 4 0.4288 0.47781 0.012 0.000 0.000 0.664 0.324
#> GSM97955 4 0.1341 0.72038 0.000 0.000 0.000 0.944 0.056
#> GSM97959 2 0.4125 0.56362 0.004 0.748 0.000 0.224 0.024
#> GSM97961 4 0.0963 0.72004 0.000 0.000 0.000 0.964 0.036
#> GSM97963 4 0.1544 0.70273 0.000 0.000 0.000 0.932 0.068
#> GSM97965 4 0.1197 0.70949 0.000 0.000 0.000 0.952 0.048
#> GSM97966 4 0.1908 0.68624 0.000 0.000 0.000 0.908 0.092
#> GSM97967 2 0.0162 0.95390 0.000 0.996 0.000 0.000 0.004
#> GSM97968 2 0.0671 0.94876 0.016 0.980 0.000 0.000 0.004
#> GSM97969 4 0.2536 0.69978 0.004 0.000 0.000 0.868 0.128
#> GSM97971 4 0.5281 0.44217 0.040 0.000 0.028 0.668 0.264
#> GSM97799 3 0.1270 0.83352 0.000 0.000 0.948 0.000 0.052
#> GSM97823 2 0.0162 0.95409 0.004 0.996 0.000 0.000 0.000
#> GSM97824 3 0.5440 0.58025 0.184 0.000 0.660 0.000 0.156
#> GSM97830 3 0.3517 0.80159 0.068 0.000 0.832 0.000 0.100
#> GSM97835 3 0.5459 0.49511 0.000 0.236 0.644 0.000 0.120
#> GSM97838 2 0.0162 0.95462 0.000 0.996 0.000 0.000 0.004
#> GSM97841 2 0.0162 0.95462 0.000 0.996 0.000 0.000 0.004
#> GSM97842 3 0.1281 0.83848 0.000 0.012 0.956 0.000 0.032
#> GSM97854 2 0.0290 0.95371 0.000 0.992 0.000 0.000 0.008
#> GSM97857 1 0.5373 0.45482 0.632 0.000 0.276 0.000 0.092
#> GSM97860 3 0.2648 0.80066 0.000 0.000 0.848 0.000 0.152
#> GSM97862 3 0.1124 0.83393 0.004 0.000 0.960 0.000 0.036
#> GSM97864 2 0.0162 0.95462 0.000 0.996 0.000 0.000 0.004
#> GSM97866 3 0.2172 0.81882 0.016 0.000 0.908 0.000 0.076
#> GSM97868 3 0.2280 0.81313 0.000 0.000 0.880 0.000 0.120
#> GSM97872 5 0.7195 -0.12536 0.356 0.000 0.040 0.168 0.436
#> GSM97873 3 0.0898 0.83915 0.000 0.008 0.972 0.000 0.020
#> GSM97874 3 0.5602 0.58201 0.196 0.000 0.640 0.000 0.164
#> GSM97875 3 0.1270 0.83619 0.000 0.000 0.948 0.000 0.052
#> GSM97876 3 0.0955 0.83527 0.004 0.000 0.968 0.000 0.028
#> GSM97880 3 0.2079 0.82777 0.020 0.000 0.916 0.000 0.064
#> GSM97881 3 0.1043 0.83658 0.000 0.000 0.960 0.000 0.040
#> GSM97884 3 0.3250 0.77718 0.008 0.004 0.820 0.000 0.168
#> GSM97901 3 0.1557 0.82938 0.008 0.000 0.940 0.000 0.052
#> GSM97902 1 0.4922 0.48963 0.716 0.036 0.000 0.028 0.220
#> GSM97909 2 0.0290 0.95371 0.000 0.992 0.000 0.000 0.008
#> GSM97911 3 0.0404 0.83781 0.000 0.000 0.988 0.000 0.012
#> GSM97923 3 0.1484 0.83892 0.008 0.000 0.944 0.000 0.048
#> GSM97928 4 0.4256 0.20852 0.000 0.000 0.000 0.564 0.436
#> GSM97929 2 0.0290 0.95371 0.000 0.992 0.000 0.000 0.008
#> GSM97933 3 0.5137 0.63460 0.096 0.000 0.676 0.000 0.228
#> GSM97934 1 0.5717 0.29055 0.540 0.000 0.368 0.000 0.092
#> GSM97944 3 0.0880 0.83704 0.000 0.000 0.968 0.000 0.032
#> GSM97949 2 0.0162 0.95390 0.000 0.996 0.000 0.000 0.004
#> GSM97956 3 0.3327 0.77882 0.028 0.000 0.828 0.000 0.144
#> GSM97962 3 0.4637 0.68717 0.160 0.000 0.740 0.000 0.100
#> GSM97964 3 0.4743 0.67420 0.048 0.004 0.700 0.000 0.248
#> GSM97970 3 0.1608 0.83014 0.000 0.000 0.928 0.000 0.072
#> GSM97822 4 0.3789 0.54319 0.000 0.000 0.020 0.768 0.212
#> GSM97831 3 0.3141 0.81566 0.040 0.000 0.852 0.000 0.108
#> GSM97845 4 0.1571 0.71904 0.004 0.000 0.000 0.936 0.060
#> GSM97865 4 0.7082 -0.47898 0.348 0.012 0.000 0.376 0.264
#> GSM97867 3 0.1952 0.83351 0.004 0.000 0.912 0.000 0.084
#> GSM97883 3 0.3944 0.74055 0.032 0.000 0.768 0.000 0.200
#> GSM97897 4 0.3757 0.54054 0.000 0.000 0.020 0.772 0.208
#> GSM97900 4 0.0880 0.71843 0.000 0.000 0.000 0.968 0.032
#> GSM97904 4 0.4602 0.42391 0.000 0.000 0.028 0.656 0.316
#> GSM97907 2 0.0290 0.95371 0.000 0.992 0.000 0.000 0.008
#> GSM97925 3 0.3039 0.77213 0.000 0.000 0.808 0.000 0.192
#> GSM97947 3 0.1792 0.83593 0.000 0.000 0.916 0.000 0.084
cbind(get_classes(res, k = 6), get_membership(res, k = 6))
#> class entropy silhouette p1 p2 p3 p4 p5 p6
#> GSM97800 2 0.0260 0.9285 0.000 0.992 0.000 0.000 NA 0.000
#> GSM97803 2 0.0291 0.9276 0.000 0.992 0.000 0.000 NA 0.004
#> GSM97804 2 0.1003 0.9175 0.000 0.964 0.004 0.000 NA 0.004
#> GSM97805 2 0.0603 0.9252 0.000 0.980 0.000 0.000 NA 0.004
#> GSM97807 2 0.0458 0.9266 0.000 0.984 0.000 0.000 NA 0.000
#> GSM97809 2 0.0603 0.9255 0.000 0.980 0.000 0.000 NA 0.004
#> GSM97811 2 0.0260 0.9284 0.000 0.992 0.000 0.000 NA 0.000
#> GSM97812 2 0.0363 0.9277 0.000 0.988 0.000 0.000 NA 0.000
#> GSM97816 6 0.0603 0.7711 0.004 0.000 0.000 0.000 NA 0.980
#> GSM97817 2 0.0146 0.9282 0.000 0.996 0.000 0.000 NA 0.000
#> GSM97820 2 0.0363 0.9277 0.000 0.988 0.000 0.000 NA 0.000
#> GSM97825 2 0.0260 0.9284 0.000 0.992 0.000 0.000 NA 0.000
#> GSM97827 2 0.0260 0.9284 0.000 0.992 0.000 0.000 NA 0.000
#> GSM97828 6 0.0291 0.7712 0.004 0.000 0.000 0.000 NA 0.992
#> GSM97833 2 0.0260 0.9284 0.000 0.992 0.000 0.000 NA 0.000
#> GSM97834 2 0.0146 0.9288 0.000 0.996 0.000 0.000 NA 0.000
#> GSM97840 2 0.0146 0.9289 0.000 0.996 0.000 0.000 NA 0.004
#> GSM97846 2 0.0000 0.9285 0.000 1.000 0.000 0.000 NA 0.000
#> GSM97848 2 0.0363 0.9277 0.000 0.988 0.000 0.000 NA 0.000
#> GSM97849 2 0.0260 0.9284 0.000 0.992 0.000 0.000 NA 0.000
#> GSM97850 2 0.0146 0.9287 0.000 0.996 0.000 0.000 NA 0.000
#> GSM97853 2 0.0363 0.9277 0.000 0.988 0.000 0.000 NA 0.000
#> GSM97855 2 0.1245 0.9100 0.000 0.952 0.000 0.000 NA 0.032
#> GSM97878 1 0.3311 0.6294 0.844 0.004 0.016 0.084 NA 0.000
#> GSM97913 1 0.4822 0.2540 0.640 0.304 0.000 0.012 NA 0.012
#> GSM97932 1 0.2743 0.6900 0.828 0.000 0.000 0.164 NA 0.000
#> GSM97939 3 0.5471 0.5432 0.016 0.192 0.644 0.000 NA 0.008
#> GSM97951 2 0.0260 0.9287 0.000 0.992 0.000 0.000 NA 0.000
#> GSM97957 3 0.6198 0.4218 0.044 0.000 0.548 0.000 NA 0.236
#> GSM97972 2 0.8530 -0.4208 0.240 0.264 0.064 0.000 NA 0.244
#> GSM97793 3 0.2848 0.7531 0.008 0.000 0.816 0.000 NA 0.000
#> GSM97795 2 0.0520 0.9262 0.000 0.984 0.008 0.000 NA 0.000
#> GSM97802 4 0.6292 0.2755 0.012 0.008 0.264 0.492 NA 0.000
#> GSM97810 2 0.5700 0.4665 0.044 0.632 0.208 0.000 NA 0.004
#> GSM97815 2 0.3602 0.6601 0.000 0.760 0.208 0.000 NA 0.000
#> GSM97837 6 0.5306 0.4508 0.316 0.000 0.000 0.008 NA 0.576
#> GSM97843 3 0.1745 0.7764 0.012 0.000 0.920 0.000 NA 0.000
#> GSM97890 3 0.3368 0.7277 0.012 0.000 0.756 0.000 NA 0.000
#> GSM97899 4 0.2122 0.7341 0.076 0.000 0.000 0.900 NA 0.000
#> GSM97910 6 0.3054 0.7432 0.016 0.000 0.000 0.036 NA 0.852
#> GSM97916 4 0.7203 -0.1059 0.344 0.004 0.000 0.388 NA 0.140
#> GSM97920 6 0.1765 0.7535 0.000 0.000 0.052 0.000 NA 0.924
#> GSM97921 1 0.6868 0.3186 0.524 0.004 0.000 0.136 NA 0.180
#> GSM97927 4 0.1970 0.7098 0.008 0.000 0.000 0.900 NA 0.000
#> GSM97937 1 0.4939 0.4354 0.716 0.000 0.000 0.044 NA 0.112
#> GSM97941 2 0.0000 0.9285 0.000 1.000 0.000 0.000 NA 0.000
#> GSM97943 6 0.1594 0.7598 0.016 0.000 0.000 0.000 NA 0.932
#> GSM97958 2 0.6413 0.5237 0.072 0.652 0.016 0.072 NA 0.052
#> GSM97960 2 0.1760 0.8871 0.004 0.928 0.020 0.000 NA 0.000
#> GSM97794 1 0.6662 0.5505 0.552 0.100 0.000 0.232 NA 0.016
#> GSM97796 4 0.3634 0.5505 0.296 0.000 0.000 0.696 NA 0.000
#> GSM97797 1 0.6801 0.1351 0.504 0.032 0.000 0.032 NA 0.260
#> GSM97798 4 0.0603 0.7457 0.004 0.000 0.000 0.980 NA 0.000
#> GSM97801 6 0.1794 0.7647 0.040 0.000 0.000 0.000 NA 0.924
#> GSM97806 4 0.4358 0.5961 0.196 0.000 0.000 0.712 NA 0.000
#> GSM97808 4 0.0458 0.7454 0.000 0.000 0.000 0.984 NA 0.000
#> GSM97813 4 0.3480 0.6844 0.044 0.000 0.008 0.808 NA 0.000
#> GSM97814 4 0.0909 0.7500 0.020 0.000 0.000 0.968 NA 0.000
#> GSM97818 1 0.6339 0.5467 0.528 0.012 0.000 0.260 NA 0.176
#> GSM97819 3 0.1141 0.7744 0.000 0.000 0.948 0.000 NA 0.000
#> GSM97821 2 0.2915 0.8411 0.016 0.868 0.008 0.012 NA 0.004
#> GSM97826 6 0.4724 0.4742 0.320 0.000 0.000 0.024 NA 0.628
#> GSM97829 6 0.5637 0.1215 0.372 0.000 0.000 0.080 NA 0.520
#> GSM97832 6 0.3932 0.5402 0.000 0.248 0.004 0.000 NA 0.720
#> GSM97836 3 0.6334 0.2568 0.068 0.000 0.500 0.324 NA 0.000
#> GSM97839 4 0.4076 0.2670 0.396 0.000 0.000 0.592 NA 0.000
#> GSM97844 2 0.0405 0.9269 0.000 0.988 0.000 0.000 NA 0.004
#> GSM97847 1 0.2562 0.6913 0.828 0.000 0.000 0.172 NA 0.000
#> GSM97851 1 0.2848 0.6925 0.816 0.000 0.000 0.176 NA 0.000
#> GSM97852 1 0.3103 0.6725 0.784 0.000 0.000 0.208 NA 0.000
#> GSM97856 4 0.2618 0.7178 0.116 0.000 0.000 0.860 NA 0.000
#> GSM97858 2 0.0692 0.9227 0.000 0.976 0.000 0.000 NA 0.004
#> GSM97859 4 0.5033 0.6204 0.092 0.000 0.048 0.716 NA 0.004
#> GSM97861 4 0.0891 0.7463 0.008 0.000 0.000 0.968 NA 0.000
#> GSM97863 4 0.3512 0.5826 0.272 0.000 0.000 0.720 NA 0.000
#> GSM97869 4 0.4390 0.6566 0.124 0.008 0.004 0.748 NA 0.000
#> GSM97870 3 0.7820 -0.0973 0.012 0.000 0.308 0.244 NA 0.288
#> GSM97871 4 0.1802 0.7394 0.072 0.000 0.000 0.916 NA 0.000
#> GSM97877 2 0.3306 0.7826 0.120 0.828 0.004 0.000 NA 0.004
#> GSM97879 4 0.2164 0.7366 0.068 0.000 0.000 0.900 NA 0.000
#> GSM97882 4 0.2568 0.7432 0.068 0.000 0.000 0.876 NA 0.000
#> GSM97885 4 0.1575 0.7463 0.032 0.000 0.000 0.936 NA 0.000
#> GSM97886 4 0.4720 0.4067 0.304 0.000 0.000 0.624 NA 0.000
#> GSM97887 4 0.1498 0.7476 0.028 0.000 0.000 0.940 NA 0.000
#> GSM97888 4 0.4580 0.4594 0.336 0.000 0.000 0.612 NA 0.000
#> GSM97889 4 0.4515 0.5833 0.016 0.000 0.072 0.720 NA 0.000
#> GSM97891 4 0.3834 0.6708 0.116 0.000 0.000 0.776 NA 0.000
#> GSM97892 2 0.0405 0.9282 0.000 0.988 0.000 0.000 NA 0.004
#> GSM97893 1 0.4908 0.5490 0.596 0.000 0.000 0.332 NA 0.004
#> GSM97894 1 0.4250 0.1764 0.528 0.000 0.000 0.456 NA 0.000
#> GSM97895 1 0.3278 0.6844 0.808 0.000 0.000 0.152 NA 0.000
#> GSM97896 4 0.4196 0.6491 0.144 0.000 0.000 0.740 NA 0.000
#> GSM97898 1 0.4091 0.1353 0.520 0.000 0.000 0.472 NA 0.000
#> GSM97903 4 0.4620 0.0981 0.428 0.000 0.000 0.532 NA 0.000
#> GSM97905 3 0.3578 0.7168 0.052 0.000 0.784 0.000 NA 0.000
#> GSM97906 4 0.0622 0.7497 0.012 0.000 0.000 0.980 NA 0.000
#> GSM97908 1 0.2948 0.6842 0.804 0.000 0.000 0.188 NA 0.000
#> GSM97912 3 0.7519 0.2460 0.048 0.000 0.424 0.076 NA 0.144
#> GSM97914 1 0.6807 0.4619 0.436 0.000 0.000 0.312 NA 0.184
#> GSM97915 1 0.4026 0.4066 0.612 0.000 0.000 0.376 NA 0.000
#> GSM97917 1 0.3352 0.6599 0.820 0.000 0.000 0.120 NA 0.004
#> GSM97918 4 0.3564 0.5450 0.264 0.000 0.000 0.724 NA 0.000
#> GSM97919 1 0.3847 0.4702 0.644 0.000 0.000 0.348 NA 0.000
#> GSM97922 4 0.4419 0.6331 0.136 0.000 0.004 0.728 NA 0.000
#> GSM97924 2 0.0405 0.9271 0.000 0.988 0.000 0.000 NA 0.004
#> GSM97926 3 0.3541 0.7109 0.012 0.000 0.728 0.000 NA 0.000
#> GSM97930 1 0.2692 0.6849 0.840 0.000 0.000 0.148 NA 0.000
#> GSM97931 2 0.5679 0.3859 0.040 0.560 0.064 0.000 NA 0.004
#> GSM97935 4 0.1049 0.7453 0.008 0.000 0.000 0.960 NA 0.000
#> GSM97936 4 0.3582 0.5752 0.252 0.000 0.000 0.732 NA 0.000
#> GSM97938 1 0.3337 0.6269 0.824 0.000 0.004 0.108 NA 0.000
#> GSM97940 4 0.1049 0.7509 0.032 0.000 0.000 0.960 NA 0.000
#> GSM97942 3 0.2357 0.7734 0.012 0.000 0.872 0.000 NA 0.000
#> GSM97945 4 0.1492 0.7482 0.036 0.000 0.000 0.940 NA 0.000
#> GSM97946 2 0.0146 0.9287 0.000 0.996 0.000 0.000 NA 0.000
#> GSM97948 3 0.4077 0.6680 0.012 0.000 0.660 0.008 NA 0.000
#> GSM97950 4 0.3514 0.5942 0.228 0.000 0.000 0.752 NA 0.000
#> GSM97952 4 0.0858 0.7488 0.028 0.000 0.000 0.968 NA 0.000
#> GSM97953 1 0.4793 0.5544 0.744 0.000 0.004 0.100 NA 0.056
#> GSM97954 1 0.3398 0.6227 0.740 0.000 0.000 0.252 NA 0.000
#> GSM97955 4 0.2948 0.6732 0.188 0.000 0.000 0.804 NA 0.000
#> GSM97959 2 0.4075 0.6091 0.184 0.740 0.000 0.076 NA 0.000
#> GSM97961 4 0.2257 0.7153 0.116 0.000 0.000 0.876 NA 0.000
#> GSM97963 4 0.1003 0.7504 0.020 0.000 0.000 0.964 NA 0.000
#> GSM97965 4 0.1151 0.7507 0.032 0.000 0.000 0.956 NA 0.000
#> GSM97966 4 0.1010 0.7390 0.004 0.000 0.000 0.960 NA 0.000
#> GSM97967 2 0.0260 0.9284 0.000 0.992 0.000 0.000 NA 0.000
#> GSM97968 2 0.1753 0.8741 0.000 0.912 0.000 0.000 NA 0.084
#> GSM97969 4 0.4189 0.3891 0.376 0.000 0.000 0.604 NA 0.000
#> GSM97971 4 0.7214 0.3261 0.120 0.000 0.164 0.492 NA 0.016
#> GSM97799 3 0.2213 0.7729 0.008 0.004 0.888 0.000 NA 0.000
#> GSM97823 2 0.0405 0.9280 0.000 0.988 0.000 0.000 NA 0.004
#> GSM97824 3 0.4101 0.6921 0.032 0.000 0.768 0.000 NA 0.040
#> GSM97830 3 0.4853 0.6630 0.012 0.000 0.692 0.000 NA 0.172
#> GSM97835 3 0.5945 0.3425 0.008 0.304 0.496 0.000 NA 0.000
#> GSM97838 2 0.0291 0.9276 0.000 0.992 0.000 0.000 NA 0.004
#> GSM97841 2 0.0146 0.9282 0.000 0.996 0.000 0.000 NA 0.000
#> GSM97842 3 0.1370 0.7798 0.004 0.012 0.948 0.000 NA 0.000
#> GSM97854 2 0.0603 0.9243 0.000 0.980 0.000 0.000 NA 0.004
#> GSM97857 3 0.6361 0.4507 0.072 0.000 0.556 0.000 NA 0.204
#> GSM97860 3 0.3136 0.7526 0.016 0.000 0.796 0.000 NA 0.000
#> GSM97862 3 0.0865 0.7781 0.000 0.000 0.964 0.000 NA 0.000
#> GSM97864 2 0.0146 0.9282 0.000 0.996 0.000 0.000 NA 0.000
#> GSM97866 3 0.1398 0.7707 0.008 0.000 0.940 0.000 NA 0.000
#> GSM97868 3 0.3376 0.7328 0.016 0.000 0.764 0.000 NA 0.000
#> GSM97872 1 0.6447 0.2830 0.580 0.000 0.096 0.052 NA 0.036
#> GSM97873 3 0.1946 0.7797 0.004 0.012 0.912 0.000 NA 0.000
#> GSM97874 3 0.5909 0.3736 0.012 0.000 0.448 0.000 NA 0.144
#> GSM97875 3 0.1765 0.7784 0.000 0.000 0.904 0.000 NA 0.000
#> GSM97876 3 0.0713 0.7766 0.000 0.000 0.972 0.000 NA 0.000
#> GSM97880 3 0.1908 0.7686 0.028 0.000 0.916 0.000 NA 0.000
#> GSM97881 3 0.2312 0.7717 0.012 0.000 0.876 0.000 NA 0.000
#> GSM97884 3 0.3314 0.7389 0.004 0.048 0.820 0.000 NA 0.000
#> GSM97901 3 0.1461 0.7763 0.016 0.000 0.940 0.000 NA 0.000
#> GSM97902 1 0.6562 -0.1185 0.460 0.032 0.000 0.028 NA 0.372
#> GSM97909 2 0.0692 0.9231 0.000 0.976 0.000 0.000 NA 0.004
#> GSM97911 3 0.1866 0.7768 0.008 0.000 0.908 0.000 NA 0.000
#> GSM97923 3 0.2118 0.7764 0.008 0.000 0.888 0.000 NA 0.000
#> GSM97928 4 0.7526 0.1413 0.132 0.012 0.144 0.408 NA 0.004
#> GSM97929 2 0.0146 0.9282 0.000 0.996 0.000 0.000 NA 0.000
#> GSM97933 3 0.4988 0.6230 0.096 0.000 0.684 0.000 NA 0.024
#> GSM97934 3 0.5682 0.5805 0.068 0.000 0.648 0.000 NA 0.136
#> GSM97944 3 0.2009 0.7751 0.008 0.004 0.904 0.000 NA 0.000
#> GSM97949 2 0.0363 0.9278 0.000 0.988 0.000 0.000 NA 0.000
#> GSM97956 3 0.2592 0.7483 0.016 0.000 0.864 0.000 NA 0.004
#> GSM97962 3 0.3142 0.7379 0.044 0.000 0.840 0.000 NA 0.008
#> GSM97964 3 0.3834 0.6855 0.028 0.008 0.748 0.000 NA 0.000
#> GSM97970 3 0.2773 0.7607 0.008 0.004 0.836 0.000 NA 0.000
#> GSM97822 4 0.4431 0.6172 0.036 0.000 0.048 0.740 NA 0.000
#> GSM97831 3 0.3834 0.7423 0.012 0.000 0.776 0.000 NA 0.044
#> GSM97845 4 0.3037 0.6702 0.176 0.000 0.000 0.808 NA 0.000
#> GSM97865 1 0.6934 0.3896 0.552 0.024 0.000 0.140 NA 0.116
#> GSM97867 3 0.1858 0.7814 0.012 0.000 0.912 0.000 NA 0.000
#> GSM97883 3 0.3374 0.7087 0.020 0.000 0.772 0.000 NA 0.000
#> GSM97897 4 0.3767 0.6402 0.020 0.000 0.028 0.780 NA 0.000
#> GSM97900 4 0.1934 0.7433 0.040 0.000 0.000 0.916 NA 0.000
#> GSM97904 3 0.7563 0.1616 0.160 0.004 0.384 0.224 NA 0.000
#> GSM97907 2 0.0935 0.9161 0.000 0.964 0.000 0.000 NA 0.004
#> GSM97925 3 0.3725 0.6788 0.008 0.000 0.676 0.000 NA 0.000
#> GSM97947 3 0.3833 0.6990 0.004 0.000 0.708 0.016 NA 0.000
Heatmaps for the consensus matrix. It visualizes the probability of two samples to be in a same group.
consensus_heatmap(res, k = 2)
consensus_heatmap(res, k = 3)
consensus_heatmap(res, k = 4)
consensus_heatmap(res, k = 5)
consensus_heatmap(res, k = 6)
Heatmaps for the membership of samples in all partitions to see how consistent they are:
membership_heatmap(res, k = 2)
membership_heatmap(res, k = 3)
membership_heatmap(res, k = 4)
membership_heatmap(res, k = 5)
membership_heatmap(res, k = 6)
As soon as we have had the classes for columns, we can look for signatures which are significantly different between classes which can be candidate marks for certain classes. Following are the heatmaps for signatures.
Signature heatmaps where rows are scaled:
get_signatures(res, k = 2)
get_signatures(res, k = 3)
get_signatures(res, k = 4)
get_signatures(res, k = 5)
get_signatures(res, k = 6)
Signature heatmaps where rows are not scaled:
get_signatures(res, k = 2, scale_rows = FALSE)
get_signatures(res, k = 3, scale_rows = FALSE)
get_signatures(res, k = 4, scale_rows = FALSE)
get_signatures(res, k = 5, scale_rows = FALSE)
get_signatures(res, k = 6, scale_rows = FALSE)
Compare the overlap of signatures from different k:
compare_signatures(res)
get_signature() returns a data frame invisibly. TO get the list of signatures, the function
call should be assigned to a variable explicitly. In following code, if plot argument is set
to FALSE, no heatmap is plotted while only the differential analysis is performed.
# code only for demonstration
tb = get_signature(res, k = ..., plot = FALSE)
An example of the output of tb is:
#> which_row fdr mean_1 mean_2 scaled_mean_1 scaled_mean_2 km
#> 1 38 0.042760348 8.373488 9.131774 -0.5533452 0.5164555 1
#> 2 40 0.018707592 7.106213 8.469186 -0.6173731 0.5762149 1
#> 3 55 0.019134737 10.221463 11.207825 -0.6159697 0.5749050 1
#> 4 59 0.006059896 5.921854 7.869574 -0.6899429 0.6439467 1
#> 5 60 0.018055526 8.928898 10.211722 -0.6204761 0.5791110 1
#> 6 98 0.009384629 15.714769 14.887706 0.6635654 -0.6193277 2
...
The columns in tb are:
which_row: row indices corresponding to the input matrix.fdr: FDR for the differential test. mean_x: The mean value in group x.scaled_mean_x: The mean value in group x after rows are scaled.km: Row groups if k-means clustering is applied to rows.UMAP plot which shows how samples are separated.
dimension_reduction(res, k = 2, method = "UMAP")
dimension_reduction(res, k = 3, method = "UMAP")
dimension_reduction(res, k = 4, method = "UMAP")
dimension_reduction(res, k = 5, method = "UMAP")
dimension_reduction(res, k = 6, method = "UMAP")
Following heatmap shows how subgroups are split when increasing k:
collect_classes(res)
Test correlation between subgroups and known annotations. If the known annotation is numeric, one-way ANOVA test is applied, and if the known annotation is discrete, chi-squared contingency table test is applied.
test_to_known_factors(res)
#> n disease.state(p) tissue(p) k
#> MAD:NMF 175 1.37e-14 1.72e-17 2
#> MAD:NMF 177 3.82e-25 4.63e-25 3
#> MAD:NMF 176 1.70e-25 1.32e-22 4
#> MAD:NMF 143 1.82e-22 1.22e-21 5
#> MAD:NMF 145 5.26e-21 3.97e-20 6
If matrix rows can be associated to genes, consider to use functional_enrichment(res,
...) to perform function enrichment for the signature genes. See this vignette for more detailed explanations.
The object with results only for a single top-value method and a single partition method can be extracted as:
res = res_list["ATC", "hclust"]
# you can also extract it by
# res = res_list["ATC:hclust"]
A summary of res and all the functions that can be applied to it:
res
#> A 'ConsensusPartition' object with k = 2, 3, 4, 5, 6.
#> On a matrix with 51882 rows and 180 columns.
#> Top rows (1000, 2000, 3000, 4000, 5000) are extracted by 'ATC' method.
#> Subgroups are detected by 'hclust' method.
#> Performed in total 1250 partitions by row resampling.
#> Best k for subgroups seems to be 3.
#>
#> Following methods can be applied to this 'ConsensusPartition' object:
#> [1] "cola_report" "collect_classes" "collect_plots"
#> [4] "collect_stats" "colnames" "compare_signatures"
#> [7] "consensus_heatmap" "dimension_reduction" "functional_enrichment"
#> [10] "get_anno_col" "get_anno" "get_classes"
#> [13] "get_consensus" "get_matrix" "get_membership"
#> [16] "get_param" "get_signatures" "get_stats"
#> [19] "is_best_k" "is_stable_k" "membership_heatmap"
#> [22] "ncol" "nrow" "plot_ecdf"
#> [25] "rownames" "select_partition_number" "show"
#> [28] "suggest_best_k" "test_to_known_factors"
collect_plots() function collects all the plots made from res for all k (number of partitions)
into one single page to provide an easy and fast comparison between different k.
collect_plots(res)
The plots are:
k and the heatmap of
predicted classes for each k.k.k.k.All the plots in panels can be made by individual functions and they are plotted later in this section.
select_partition_number() produces several plots showing different
statistics for choosing “optimized” k. There are following statistics:
k;k, the area increased is defined as \(A_k - A_{k-1}\).The detailed explanations of these statistics can be found in the cola vignette.
Generally speaking, lower PAC score, higher mean silhouette score or higher
concordance corresponds to better partition. Rand index and Jaccard index
measure how similar the current partition is compared to partition with k-1.
If they are too similar, we won't accept k is better than k-1.
select_partition_number(res)
The numeric values for all these statistics can be obtained by get_stats().
get_stats(res)
#> k 1-PAC mean_silhouette concordance area_increased Rand Jaccard
#> 2 2 0.508 0.774 0.897 0.4113 0.578 0.578
#> 3 3 0.533 0.781 0.883 0.5269 0.668 0.476
#> 4 4 0.665 0.693 0.833 0.1436 0.873 0.669
#> 5 5 0.723 0.752 0.833 0.0790 0.871 0.580
#> 6 6 0.731 0.690 0.825 0.0339 0.985 0.928
suggest_best_k() suggests the best \(k\) based on these statistics. The rules are as follows:
suggest_best_k(res)
#> [1] 3
Following shows the table of the partitions (You need to click the show/hide
code output link to see it). The membership matrix (columns with name p*)
is inferred by
clue::cl_consensus()
function with the SE method. Basically the value in the membership matrix
represents the probability to belong to a certain group. The finall class
label for an item is determined with the group with highest probability it
belongs to.
In get_classes() function, the entropy is calculated from the membership
matrix and the silhouette score is calculated from the consensus matrix.
cbind(get_classes(res, k = 2), get_membership(res, k = 2))
#> class entropy silhouette p1 p2
#> GSM97800 2 0.0000 0.84277 0.000 1.000
#> GSM97803 2 0.0000 0.84277 0.000 1.000
#> GSM97804 2 0.0000 0.84277 0.000 1.000
#> GSM97805 2 0.0000 0.84277 0.000 1.000
#> GSM97807 2 0.0000 0.84277 0.000 1.000
#> GSM97809 2 0.0000 0.84277 0.000 1.000
#> GSM97811 2 0.0000 0.84277 0.000 1.000
#> GSM97812 2 0.0000 0.84277 0.000 1.000
#> GSM97816 1 0.9491 0.48834 0.632 0.368
#> GSM97817 2 0.0000 0.84277 0.000 1.000
#> GSM97820 2 0.0000 0.84277 0.000 1.000
#> GSM97825 2 0.0000 0.84277 0.000 1.000
#> GSM97827 2 0.0000 0.84277 0.000 1.000
#> GSM97828 1 0.9491 0.48834 0.632 0.368
#> GSM97833 2 0.0000 0.84277 0.000 1.000
#> GSM97834 2 0.0000 0.84277 0.000 1.000
#> GSM97840 2 0.7139 0.69198 0.196 0.804
#> GSM97846 2 0.0000 0.84277 0.000 1.000
#> GSM97848 2 0.0000 0.84277 0.000 1.000
#> GSM97849 2 0.0000 0.84277 0.000 1.000
#> GSM97850 2 0.0000 0.84277 0.000 1.000
#> GSM97853 2 0.0000 0.84277 0.000 1.000
#> GSM97855 2 0.0376 0.84085 0.004 0.996
#> GSM97878 1 0.7139 0.76822 0.804 0.196
#> GSM97913 1 0.7528 0.74706 0.784 0.216
#> GSM97932 1 0.0000 0.88154 1.000 0.000
#> GSM97939 2 0.9686 0.36390 0.396 0.604
#> GSM97951 2 0.7139 0.69198 0.196 0.804
#> GSM97957 1 0.7815 0.73939 0.768 0.232
#> GSM97972 2 0.9686 0.36424 0.396 0.604
#> GSM97793 1 0.7883 0.73535 0.764 0.236
#> GSM97795 2 0.2043 0.82431 0.032 0.968
#> GSM97802 1 0.6343 0.80149 0.840 0.160
#> GSM97810 2 0.9393 0.45774 0.356 0.644
#> GSM97815 2 0.9491 0.43233 0.368 0.632
#> GSM97837 1 0.0000 0.88154 1.000 0.000
#> GSM97843 1 0.7883 0.73562 0.764 0.236
#> GSM97890 1 0.8144 0.71670 0.748 0.252
#> GSM97899 1 0.0000 0.88154 1.000 0.000
#> GSM97910 1 0.6887 0.78438 0.816 0.184
#> GSM97916 1 0.3879 0.85258 0.924 0.076
#> GSM97920 1 0.8016 0.72818 0.756 0.244
#> GSM97921 1 0.2423 0.86843 0.960 0.040
#> GSM97927 1 0.0000 0.88154 1.000 0.000
#> GSM97937 1 0.0000 0.88154 1.000 0.000
#> GSM97941 2 0.7219 0.68761 0.200 0.800
#> GSM97943 1 0.7219 0.77162 0.800 0.200
#> GSM97958 1 0.8608 0.64365 0.716 0.284
#> GSM97960 2 0.9170 0.50190 0.332 0.668
#> GSM97794 1 0.4298 0.84724 0.912 0.088
#> GSM97796 1 0.0000 0.88154 1.000 0.000
#> GSM97797 1 0.7139 0.76822 0.804 0.196
#> GSM97798 1 0.0000 0.88154 1.000 0.000
#> GSM97801 1 0.1843 0.87289 0.972 0.028
#> GSM97806 1 0.0000 0.88154 1.000 0.000
#> GSM97808 1 0.0000 0.88154 1.000 0.000
#> GSM97813 1 0.0000 0.88154 1.000 0.000
#> GSM97814 1 0.0000 0.88154 1.000 0.000
#> GSM97818 1 0.2778 0.86516 0.952 0.048
#> GSM97819 1 0.7950 0.73109 0.760 0.240
#> GSM97821 1 0.9977 0.10253 0.528 0.472
#> GSM97826 1 0.0000 0.88154 1.000 0.000
#> GSM97829 1 0.0376 0.88055 0.996 0.004
#> GSM97832 2 0.9427 0.44984 0.360 0.640
#> GSM97836 1 0.3879 0.85258 0.924 0.076
#> GSM97839 1 0.0000 0.88154 1.000 0.000
#> GSM97844 2 0.0000 0.84277 0.000 1.000
#> GSM97847 1 0.0000 0.88154 1.000 0.000
#> GSM97851 1 0.0000 0.88154 1.000 0.000
#> GSM97852 1 0.0000 0.88154 1.000 0.000
#> GSM97856 1 0.0000 0.88154 1.000 0.000
#> GSM97858 2 0.0000 0.84277 0.000 1.000
#> GSM97859 1 0.0000 0.88154 1.000 0.000
#> GSM97861 1 0.0376 0.88056 0.996 0.004
#> GSM97863 1 0.0000 0.88154 1.000 0.000
#> GSM97869 1 0.3879 0.85258 0.924 0.076
#> GSM97870 1 0.0000 0.88154 1.000 0.000
#> GSM97871 1 0.0000 0.88154 1.000 0.000
#> GSM97877 2 0.9686 0.36389 0.396 0.604
#> GSM97879 1 0.0000 0.88154 1.000 0.000
#> GSM97882 1 0.0000 0.88154 1.000 0.000
#> GSM97885 1 0.0000 0.88154 1.000 0.000
#> GSM97886 1 0.0000 0.88154 1.000 0.000
#> GSM97887 1 0.0000 0.88154 1.000 0.000
#> GSM97888 1 0.0000 0.88154 1.000 0.000
#> GSM97889 1 0.0000 0.88154 1.000 0.000
#> GSM97891 1 0.0000 0.88154 1.000 0.000
#> GSM97892 2 0.0000 0.84277 0.000 1.000
#> GSM97893 1 0.0000 0.88154 1.000 0.000
#> GSM97894 1 0.0000 0.88154 1.000 0.000
#> GSM97895 1 0.0000 0.88154 1.000 0.000
#> GSM97896 1 0.0000 0.88154 1.000 0.000
#> GSM97898 1 0.0000 0.88154 1.000 0.000
#> GSM97903 1 0.0000 0.88154 1.000 0.000
#> GSM97905 1 0.0000 0.88154 1.000 0.000
#> GSM97906 1 0.0000 0.88154 1.000 0.000
#> GSM97908 1 0.0000 0.88154 1.000 0.000
#> GSM97912 1 0.0000 0.88154 1.000 0.000
#> GSM97914 1 0.0376 0.88055 0.996 0.004
#> GSM97915 1 0.0000 0.88154 1.000 0.000
#> GSM97917 1 0.0000 0.88154 1.000 0.000
#> GSM97918 1 0.0000 0.88154 1.000 0.000
#> GSM97919 1 0.0000 0.88154 1.000 0.000
#> GSM97922 1 0.0000 0.88154 1.000 0.000
#> GSM97924 2 0.0000 0.84277 0.000 1.000
#> GSM97926 1 0.3879 0.85258 0.924 0.076
#> GSM97930 1 0.0000 0.88154 1.000 0.000
#> GSM97931 2 0.9686 0.36424 0.396 0.604
#> GSM97935 1 0.0000 0.88154 1.000 0.000
#> GSM97936 1 0.0000 0.88154 1.000 0.000
#> GSM97938 1 0.0000 0.88154 1.000 0.000
#> GSM97940 1 0.0000 0.88154 1.000 0.000
#> GSM97942 1 0.7883 0.73535 0.764 0.236
#> GSM97945 1 0.0000 0.88154 1.000 0.000
#> GSM97946 2 0.0000 0.84277 0.000 1.000
#> GSM97948 1 0.0376 0.88057 0.996 0.004
#> GSM97950 1 0.0000 0.88154 1.000 0.000
#> GSM97952 1 0.0000 0.88154 1.000 0.000
#> GSM97953 1 0.0000 0.88154 1.000 0.000
#> GSM97954 1 0.0000 0.88154 1.000 0.000
#> GSM97955 1 0.0000 0.88154 1.000 0.000
#> GSM97959 1 0.9087 0.57438 0.676 0.324
#> GSM97961 1 0.0000 0.88154 1.000 0.000
#> GSM97963 1 0.0000 0.88154 1.000 0.000
#> GSM97965 1 0.0000 0.88154 1.000 0.000
#> GSM97966 1 0.0000 0.88154 1.000 0.000
#> GSM97967 2 0.0000 0.84277 0.000 1.000
#> GSM97968 2 0.0376 0.84085 0.004 0.996
#> GSM97969 1 0.0000 0.88154 1.000 0.000
#> GSM97971 1 0.0000 0.88154 1.000 0.000
#> GSM97799 1 1.0000 0.00781 0.500 0.500
#> GSM97823 2 0.0000 0.84277 0.000 1.000
#> GSM97824 1 0.8327 0.70058 0.736 0.264
#> GSM97830 1 0.8081 0.72185 0.752 0.248
#> GSM97835 2 0.9427 0.44984 0.360 0.640
#> GSM97838 2 0.0000 0.84277 0.000 1.000
#> GSM97841 2 0.0000 0.84277 0.000 1.000
#> GSM97842 2 0.9896 0.22089 0.440 0.560
#> GSM97854 2 0.0000 0.84277 0.000 1.000
#> GSM97857 1 0.8327 0.70058 0.736 0.264
#> GSM97860 1 0.7883 0.73535 0.764 0.236
#> GSM97862 1 0.8267 0.70533 0.740 0.260
#> GSM97864 2 0.0000 0.84277 0.000 1.000
#> GSM97866 1 0.8267 0.70533 0.740 0.260
#> GSM97868 1 0.8267 0.70587 0.740 0.260
#> GSM97872 1 0.0672 0.87937 0.992 0.008
#> GSM97873 2 0.9686 0.36390 0.396 0.604
#> GSM97874 1 0.8081 0.72185 0.752 0.248
#> GSM97875 1 0.7950 0.73109 0.760 0.240
#> GSM97876 1 0.7883 0.73535 0.764 0.236
#> GSM97880 1 0.7883 0.73535 0.764 0.236
#> GSM97881 1 0.8499 0.68075 0.724 0.276
#> GSM97884 2 0.9954 0.14378 0.460 0.540
#> GSM97901 1 0.8267 0.70533 0.740 0.260
#> GSM97902 1 0.7745 0.73569 0.772 0.228
#> GSM97909 2 0.9686 0.36389 0.396 0.604
#> GSM97911 1 0.8499 0.68075 0.724 0.276
#> GSM97923 1 0.7883 0.73535 0.764 0.236
#> GSM97928 1 0.0000 0.88154 1.000 0.000
#> GSM97929 2 0.0000 0.84277 0.000 1.000
#> GSM97933 1 0.7815 0.73939 0.768 0.232
#> GSM97934 1 0.7815 0.73939 0.768 0.232
#> GSM97944 2 1.0000 -0.03392 0.500 0.500
#> GSM97949 2 0.0000 0.84277 0.000 1.000
#> GSM97956 1 0.8327 0.70005 0.736 0.264
#> GSM97962 1 0.8267 0.70587 0.740 0.260
#> GSM97964 1 0.8555 0.67407 0.720 0.280
#> GSM97970 2 1.0000 -0.03392 0.500 0.500
#> GSM97822 1 0.0000 0.88154 1.000 0.000
#> GSM97831 1 0.8144 0.71694 0.748 0.252
#> GSM97845 1 0.0000 0.88154 1.000 0.000
#> GSM97865 1 0.4939 0.83558 0.892 0.108
#> GSM97867 1 0.7883 0.73535 0.764 0.236
#> GSM97883 1 0.3431 0.85882 0.936 0.064
#> GSM97897 1 0.0000 0.88154 1.000 0.000
#> GSM97900 1 0.0000 0.88154 1.000 0.000
#> GSM97904 1 0.0000 0.88154 1.000 0.000
#> GSM97907 2 0.0000 0.84277 0.000 1.000
#> GSM97925 1 0.3733 0.85542 0.928 0.072
#> GSM97947 1 0.7950 0.73109 0.760 0.240
cbind(get_classes(res, k = 3), get_membership(res, k = 3))
#> class entropy silhouette p1 p2 p3
#> GSM97800 2 0.0000 0.995 0.000 1.000 0.000
#> GSM97803 2 0.0000 0.995 0.000 1.000 0.000
#> GSM97804 2 0.0000 0.995 0.000 1.000 0.000
#> GSM97805 2 0.0000 0.995 0.000 1.000 0.000
#> GSM97807 2 0.0000 0.995 0.000 1.000 0.000
#> GSM97809 2 0.0000 0.995 0.000 1.000 0.000
#> GSM97811 2 0.0000 0.995 0.000 1.000 0.000
#> GSM97812 2 0.0000 0.995 0.000 1.000 0.000
#> GSM97816 3 0.0592 0.766 0.000 0.012 0.988
#> GSM97817 2 0.0000 0.995 0.000 1.000 0.000
#> GSM97820 2 0.0000 0.995 0.000 1.000 0.000
#> GSM97825 2 0.0000 0.995 0.000 1.000 0.000
#> GSM97827 2 0.0000 0.995 0.000 1.000 0.000
#> GSM97828 3 0.0592 0.766 0.000 0.012 0.988
#> GSM97833 2 0.0000 0.995 0.000 1.000 0.000
#> GSM97834 2 0.0000 0.995 0.000 1.000 0.000
#> GSM97840 3 0.6309 0.104 0.000 0.496 0.504
#> GSM97846 2 0.0000 0.995 0.000 1.000 0.000
#> GSM97848 2 0.0000 0.995 0.000 1.000 0.000
#> GSM97849 2 0.0000 0.995 0.000 1.000 0.000
#> GSM97850 2 0.0000 0.995 0.000 1.000 0.000
#> GSM97853 2 0.0000 0.995 0.000 1.000 0.000
#> GSM97855 2 0.0424 0.988 0.000 0.992 0.008
#> GSM97878 3 0.4346 0.716 0.184 0.000 0.816
#> GSM97913 3 0.4047 0.747 0.148 0.004 0.848
#> GSM97932 1 0.0000 0.881 1.000 0.000 0.000
#> GSM97939 3 0.5098 0.611 0.000 0.248 0.752
#> GSM97951 3 0.6309 0.104 0.000 0.496 0.504
#> GSM97957 3 0.3482 0.790 0.128 0.000 0.872
#> GSM97972 3 0.5098 0.610 0.000 0.248 0.752
#> GSM97793 3 0.3412 0.793 0.124 0.000 0.876
#> GSM97795 2 0.3816 0.810 0.000 0.852 0.148
#> GSM97802 3 0.4555 0.719 0.200 0.000 0.800
#> GSM97810 3 0.5465 0.557 0.000 0.288 0.712
#> GSM97815 3 0.5363 0.574 0.000 0.276 0.724
#> GSM97837 1 0.4796 0.725 0.780 0.000 0.220
#> GSM97843 3 0.3412 0.793 0.124 0.000 0.876
#> GSM97890 3 0.3116 0.798 0.108 0.000 0.892
#> GSM97899 1 0.0000 0.881 1.000 0.000 0.000
#> GSM97910 3 0.5397 0.606 0.280 0.000 0.720
#> GSM97916 3 0.6225 0.244 0.432 0.000 0.568
#> GSM97920 3 0.3340 0.794 0.120 0.000 0.880
#> GSM97921 1 0.6180 0.301 0.584 0.000 0.416
#> GSM97927 1 0.5138 0.693 0.748 0.000 0.252
#> GSM97937 1 0.1753 0.862 0.952 0.000 0.048
#> GSM97941 3 0.6308 0.119 0.000 0.492 0.508
#> GSM97943 3 0.4235 0.747 0.176 0.000 0.824
#> GSM97958 3 0.5105 0.757 0.124 0.048 0.828
#> GSM97960 3 0.5706 0.509 0.000 0.320 0.680
#> GSM97794 3 0.6192 0.270 0.420 0.000 0.580
#> GSM97796 1 0.0000 0.881 1.000 0.000 0.000
#> GSM97797 3 0.4291 0.720 0.180 0.000 0.820
#> GSM97798 1 0.0000 0.881 1.000 0.000 0.000
#> GSM97801 1 0.6008 0.442 0.628 0.000 0.372
#> GSM97806 1 0.5098 0.698 0.752 0.000 0.248
#> GSM97808 1 0.0000 0.881 1.000 0.000 0.000
#> GSM97813 1 0.0000 0.881 1.000 0.000 0.000
#> GSM97814 1 0.0000 0.881 1.000 0.000 0.000
#> GSM97818 1 0.6286 0.155 0.536 0.000 0.464
#> GSM97819 3 0.3267 0.795 0.116 0.000 0.884
#> GSM97821 3 0.5573 0.706 0.044 0.160 0.796
#> GSM97826 1 0.3752 0.804 0.856 0.000 0.144
#> GSM97829 1 0.5560 0.602 0.700 0.000 0.300
#> GSM97832 3 0.5431 0.563 0.000 0.284 0.716
#> GSM97836 3 0.6215 0.258 0.428 0.000 0.572
#> GSM97839 1 0.0000 0.881 1.000 0.000 0.000
#> GSM97844 2 0.0000 0.995 0.000 1.000 0.000
#> GSM97847 1 0.0000 0.881 1.000 0.000 0.000
#> GSM97851 1 0.0000 0.881 1.000 0.000 0.000
#> GSM97852 1 0.0000 0.881 1.000 0.000 0.000
#> GSM97856 1 0.0000 0.881 1.000 0.000 0.000
#> GSM97858 2 0.0000 0.995 0.000 1.000 0.000
#> GSM97859 1 0.3267 0.827 0.884 0.000 0.116
#> GSM97861 1 0.5291 0.670 0.732 0.000 0.268
#> GSM97863 1 0.0000 0.881 1.000 0.000 0.000
#> GSM97869 3 0.6225 0.244 0.432 0.000 0.568
#> GSM97870 1 0.3267 0.827 0.884 0.000 0.116
#> GSM97871 1 0.0000 0.881 1.000 0.000 0.000
#> GSM97877 3 0.5098 0.613 0.000 0.248 0.752
#> GSM97879 1 0.4399 0.759 0.812 0.000 0.188
#> GSM97882 1 0.5098 0.698 0.752 0.000 0.248
#> GSM97885 1 0.5138 0.694 0.748 0.000 0.252
#> GSM97886 1 0.0000 0.881 1.000 0.000 0.000
#> GSM97887 1 0.0000 0.881 1.000 0.000 0.000
#> GSM97888 1 0.0000 0.881 1.000 0.000 0.000
#> GSM97889 1 0.2537 0.848 0.920 0.000 0.080
#> GSM97891 1 0.5138 0.693 0.748 0.000 0.252
#> GSM97892 2 0.0000 0.995 0.000 1.000 0.000
#> GSM97893 1 0.0000 0.881 1.000 0.000 0.000
#> GSM97894 1 0.0000 0.881 1.000 0.000 0.000
#> GSM97895 1 0.0000 0.881 1.000 0.000 0.000
#> GSM97896 1 0.0000 0.881 1.000 0.000 0.000
#> GSM97898 1 0.0000 0.881 1.000 0.000 0.000
#> GSM97903 1 0.5706 0.576 0.680 0.000 0.320
#> GSM97905 1 0.2711 0.843 0.912 0.000 0.088
#> GSM97906 1 0.0000 0.881 1.000 0.000 0.000
#> GSM97908 1 0.0237 0.879 0.996 0.000 0.004
#> GSM97912 1 0.2711 0.843 0.912 0.000 0.088
#> GSM97914 1 0.5678 0.582 0.684 0.000 0.316
#> GSM97915 1 0.0000 0.881 1.000 0.000 0.000
#> GSM97917 1 0.0000 0.881 1.000 0.000 0.000
#> GSM97918 1 0.0000 0.881 1.000 0.000 0.000
#> GSM97919 1 0.0000 0.881 1.000 0.000 0.000
#> GSM97922 1 0.0000 0.881 1.000 0.000 0.000
#> GSM97924 2 0.0000 0.995 0.000 1.000 0.000
#> GSM97926 3 0.6215 0.258 0.428 0.000 0.572
#> GSM97930 1 0.4605 0.741 0.796 0.000 0.204
#> GSM97931 3 0.5098 0.610 0.000 0.248 0.752
#> GSM97935 1 0.5138 0.693 0.748 0.000 0.252
#> GSM97936 1 0.0000 0.881 1.000 0.000 0.000
#> GSM97938 1 0.0000 0.881 1.000 0.000 0.000
#> GSM97940 1 0.0000 0.881 1.000 0.000 0.000
#> GSM97942 3 0.3412 0.793 0.124 0.000 0.876
#> GSM97945 1 0.0000 0.881 1.000 0.000 0.000
#> GSM97946 2 0.0000 0.995 0.000 1.000 0.000
#> GSM97948 1 0.5835 0.533 0.660 0.000 0.340
#> GSM97950 1 0.0000 0.881 1.000 0.000 0.000
#> GSM97952 1 0.0000 0.881 1.000 0.000 0.000
#> GSM97953 1 0.0000 0.881 1.000 0.000 0.000
#> GSM97954 1 0.4452 0.755 0.808 0.000 0.192
#> GSM97955 1 0.0000 0.881 1.000 0.000 0.000
#> GSM97959 3 0.4253 0.775 0.080 0.048 0.872
#> GSM97961 1 0.0000 0.881 1.000 0.000 0.000
#> GSM97963 1 0.0000 0.881 1.000 0.000 0.000
#> GSM97965 1 0.0000 0.881 1.000 0.000 0.000
#> GSM97966 1 0.0000 0.881 1.000 0.000 0.000
#> GSM97967 2 0.0000 0.995 0.000 1.000 0.000
#> GSM97968 2 0.0424 0.988 0.000 0.992 0.008
#> GSM97969 1 0.1753 0.863 0.952 0.000 0.048
#> GSM97971 1 0.2448 0.848 0.924 0.000 0.076
#> GSM97799 3 0.4291 0.707 0.008 0.152 0.840
#> GSM97823 2 0.0000 0.995 0.000 1.000 0.000
#> GSM97824 3 0.3618 0.800 0.104 0.012 0.884
#> GSM97830 3 0.3192 0.797 0.112 0.000 0.888
#> GSM97835 3 0.5431 0.563 0.000 0.284 0.716
#> GSM97838 2 0.0000 0.995 0.000 1.000 0.000
#> GSM97841 2 0.0000 0.995 0.000 1.000 0.000
#> GSM97842 3 0.4605 0.656 0.000 0.204 0.796
#> GSM97854 2 0.0000 0.995 0.000 1.000 0.000
#> GSM97857 3 0.3618 0.800 0.104 0.012 0.884
#> GSM97860 3 0.3412 0.793 0.124 0.000 0.876
#> GSM97862 3 0.3454 0.799 0.104 0.008 0.888
#> GSM97864 2 0.0000 0.995 0.000 1.000 0.000
#> GSM97866 3 0.3454 0.799 0.104 0.008 0.888
#> GSM97868 3 0.3454 0.799 0.104 0.008 0.888
#> GSM97872 1 0.5621 0.591 0.692 0.000 0.308
#> GSM97873 3 0.5098 0.611 0.000 0.248 0.752
#> GSM97874 3 0.3192 0.797 0.112 0.000 0.888
#> GSM97875 3 0.3267 0.795 0.116 0.000 0.884
#> GSM97876 3 0.3412 0.793 0.124 0.000 0.876
#> GSM97880 3 0.3412 0.793 0.124 0.000 0.876
#> GSM97881 3 0.3129 0.798 0.088 0.008 0.904
#> GSM97884 3 0.4346 0.675 0.000 0.184 0.816
#> GSM97901 3 0.3454 0.799 0.104 0.008 0.888
#> GSM97902 3 0.3551 0.760 0.132 0.000 0.868
#> GSM97909 3 0.5098 0.613 0.000 0.248 0.752
#> GSM97911 3 0.3129 0.798 0.088 0.008 0.904
#> GSM97923 3 0.3412 0.793 0.124 0.000 0.876
#> GSM97928 1 0.5098 0.697 0.752 0.000 0.248
#> GSM97929 2 0.0000 0.995 0.000 1.000 0.000
#> GSM97933 3 0.3482 0.790 0.128 0.000 0.872
#> GSM97934 3 0.3482 0.790 0.128 0.000 0.872
#> GSM97944 3 0.4291 0.707 0.008 0.152 0.840
#> GSM97949 2 0.0000 0.995 0.000 1.000 0.000
#> GSM97956 3 0.3375 0.800 0.100 0.008 0.892
#> GSM97962 3 0.3454 0.799 0.104 0.008 0.888
#> GSM97964 3 0.3043 0.797 0.084 0.008 0.908
#> GSM97970 3 0.4291 0.707 0.008 0.152 0.840
#> GSM97822 1 0.3551 0.810 0.868 0.000 0.132
#> GSM97831 3 0.3116 0.797 0.108 0.000 0.892
#> GSM97845 1 0.0000 0.881 1.000 0.000 0.000
#> GSM97865 3 0.6192 0.289 0.420 0.000 0.580
#> GSM97867 3 0.3412 0.793 0.124 0.000 0.876
#> GSM97883 1 0.6274 0.177 0.544 0.000 0.456
#> GSM97897 1 0.0424 0.878 0.992 0.000 0.008
#> GSM97900 1 0.0000 0.881 1.000 0.000 0.000
#> GSM97904 1 0.5216 0.677 0.740 0.000 0.260
#> GSM97907 2 0.0000 0.995 0.000 1.000 0.000
#> GSM97925 3 0.6244 0.221 0.440 0.000 0.560
#> GSM97947 3 0.3267 0.795 0.116 0.000 0.884
cbind(get_classes(res, k = 4), get_membership(res, k = 4))
#> class entropy silhouette p1 p2 p3 p4
#> GSM97800 2 0.0000 0.9874 0.000 1.000 0.000 0.000
#> GSM97803 2 0.0000 0.9874 0.000 1.000 0.000 0.000
#> GSM97804 2 0.0000 0.9874 0.000 1.000 0.000 0.000
#> GSM97805 2 0.0000 0.9874 0.000 1.000 0.000 0.000
#> GSM97807 2 0.0000 0.9874 0.000 1.000 0.000 0.000
#> GSM97809 2 0.0000 0.9874 0.000 1.000 0.000 0.000
#> GSM97811 2 0.0000 0.9874 0.000 1.000 0.000 0.000
#> GSM97812 2 0.0000 0.9874 0.000 1.000 0.000 0.000
#> GSM97816 4 0.4746 0.3933 0.000 0.000 0.368 0.632
#> GSM97817 2 0.0000 0.9874 0.000 1.000 0.000 0.000
#> GSM97820 2 0.0000 0.9874 0.000 1.000 0.000 0.000
#> GSM97825 2 0.0000 0.9874 0.000 1.000 0.000 0.000
#> GSM97827 2 0.0000 0.9874 0.000 1.000 0.000 0.000
#> GSM97828 4 0.4746 0.3933 0.000 0.000 0.368 0.632
#> GSM97833 2 0.0000 0.9874 0.000 1.000 0.000 0.000
#> GSM97834 2 0.0000 0.9874 0.000 1.000 0.000 0.000
#> GSM97840 4 0.4814 0.5845 0.000 0.316 0.008 0.676
#> GSM97846 2 0.0000 0.9874 0.000 1.000 0.000 0.000
#> GSM97848 2 0.0000 0.9874 0.000 1.000 0.000 0.000
#> GSM97849 2 0.0000 0.9874 0.000 1.000 0.000 0.000
#> GSM97850 2 0.0000 0.9874 0.000 1.000 0.000 0.000
#> GSM97853 2 0.0000 0.9874 0.000 1.000 0.000 0.000
#> GSM97855 2 0.1637 0.9283 0.000 0.940 0.000 0.060
#> GSM97878 3 0.4776 0.4704 0.024 0.000 0.732 0.244
#> GSM97913 3 0.4304 0.4067 0.000 0.000 0.716 0.284
#> GSM97932 1 0.0000 0.8398 1.000 0.000 0.000 0.000
#> GSM97939 4 0.3687 0.8038 0.000 0.080 0.064 0.856
#> GSM97951 4 0.4814 0.5845 0.000 0.316 0.008 0.676
#> GSM97957 3 0.2760 0.6620 0.000 0.000 0.872 0.128
#> GSM97972 4 0.3354 0.8071 0.000 0.084 0.044 0.872
#> GSM97793 3 0.2760 0.6617 0.000 0.000 0.872 0.128
#> GSM97795 2 0.4356 0.5578 0.000 0.708 0.000 0.292
#> GSM97802 3 0.2469 0.6349 0.000 0.000 0.892 0.108
#> GSM97810 4 0.2867 0.7991 0.000 0.104 0.012 0.884
#> GSM97815 4 0.2909 0.8032 0.000 0.092 0.020 0.888
#> GSM97837 1 0.6367 0.4077 0.540 0.000 0.392 0.068
#> GSM97843 3 0.3074 0.6603 0.000 0.000 0.848 0.152
#> GSM97890 3 0.3444 0.6486 0.000 0.000 0.816 0.184
#> GSM97899 1 0.0000 0.8398 1.000 0.000 0.000 0.000
#> GSM97910 3 0.5700 0.5845 0.120 0.000 0.716 0.164
#> GSM97916 3 0.5332 0.5419 0.184 0.000 0.736 0.080
#> GSM97920 3 0.4262 0.6020 0.008 0.000 0.756 0.236
#> GSM97921 3 0.6360 0.1339 0.420 0.000 0.516 0.064
#> GSM97927 1 0.6506 0.2369 0.468 0.000 0.460 0.072
#> GSM97937 1 0.2282 0.8069 0.924 0.000 0.052 0.024
#> GSM97941 4 0.4792 0.5924 0.000 0.312 0.008 0.680
#> GSM97943 3 0.4808 0.5816 0.028 0.000 0.736 0.236
#> GSM97958 3 0.5151 -0.0894 0.004 0.000 0.532 0.464
#> GSM97960 4 0.3324 0.7853 0.000 0.136 0.012 0.852
#> GSM97794 3 0.5517 0.5376 0.184 0.000 0.724 0.092
#> GSM97796 1 0.0000 0.8398 1.000 0.000 0.000 0.000
#> GSM97797 3 0.4744 0.4723 0.024 0.000 0.736 0.240
#> GSM97798 1 0.0000 0.8398 1.000 0.000 0.000 0.000
#> GSM97801 3 0.6543 0.0855 0.372 0.000 0.544 0.084
#> GSM97806 1 0.6506 0.2477 0.472 0.000 0.456 0.072
#> GSM97808 1 0.0000 0.8398 1.000 0.000 0.000 0.000
#> GSM97813 1 0.3550 0.7757 0.860 0.000 0.096 0.044
#> GSM97814 1 0.0000 0.8398 1.000 0.000 0.000 0.000
#> GSM97818 3 0.6351 0.3616 0.268 0.000 0.628 0.104
#> GSM97819 3 0.3172 0.6515 0.000 0.000 0.840 0.160
#> GSM97821 4 0.4706 0.6947 0.000 0.028 0.224 0.748
#> GSM97826 1 0.5986 0.5537 0.620 0.000 0.320 0.060
#> GSM97829 3 0.6506 -0.2067 0.456 0.000 0.472 0.072
#> GSM97832 4 0.2924 0.8016 0.000 0.100 0.016 0.884
#> GSM97836 3 0.5226 0.5458 0.180 0.000 0.744 0.076
#> GSM97839 1 0.0000 0.8398 1.000 0.000 0.000 0.000
#> GSM97844 2 0.0000 0.9874 0.000 1.000 0.000 0.000
#> GSM97847 1 0.0376 0.8381 0.992 0.000 0.004 0.004
#> GSM97851 1 0.0000 0.8398 1.000 0.000 0.000 0.000
#> GSM97852 1 0.0376 0.8381 0.992 0.000 0.004 0.004
#> GSM97856 1 0.0000 0.8398 1.000 0.000 0.000 0.000
#> GSM97858 2 0.0000 0.9874 0.000 1.000 0.000 0.000
#> GSM97859 1 0.5906 0.5866 0.644 0.000 0.292 0.064
#> GSM97861 3 0.6506 -0.2196 0.456 0.000 0.472 0.072
#> GSM97863 1 0.0000 0.8398 1.000 0.000 0.000 0.000
#> GSM97869 3 0.5332 0.5419 0.184 0.000 0.736 0.080
#> GSM97870 1 0.5906 0.5866 0.644 0.000 0.292 0.064
#> GSM97871 1 0.0000 0.8398 1.000 0.000 0.000 0.000
#> GSM97877 4 0.3107 0.8046 0.000 0.080 0.036 0.884
#> GSM97879 1 0.6079 0.5650 0.628 0.000 0.300 0.072
#> GSM97882 1 0.6506 0.2477 0.472 0.000 0.456 0.072
#> GSM97885 1 0.6506 0.2364 0.468 0.000 0.460 0.072
#> GSM97886 1 0.0188 0.8378 0.996 0.000 0.000 0.004
#> GSM97887 1 0.0000 0.8398 1.000 0.000 0.000 0.000
#> GSM97888 1 0.0000 0.8398 1.000 0.000 0.000 0.000
#> GSM97889 1 0.5463 0.6402 0.692 0.000 0.256 0.052
#> GSM97891 1 0.6506 0.2369 0.468 0.000 0.460 0.072
#> GSM97892 2 0.0000 0.9874 0.000 1.000 0.000 0.000
#> GSM97893 1 0.0000 0.8398 1.000 0.000 0.000 0.000
#> GSM97894 1 0.0000 0.8398 1.000 0.000 0.000 0.000
#> GSM97895 1 0.0000 0.8398 1.000 0.000 0.000 0.000
#> GSM97896 1 0.0000 0.8398 1.000 0.000 0.000 0.000
#> GSM97898 1 0.0000 0.8398 1.000 0.000 0.000 0.000
#> GSM97903 3 0.6562 -0.0728 0.404 0.000 0.516 0.080
#> GSM97905 1 0.5648 0.6348 0.684 0.000 0.252 0.064
#> GSM97906 1 0.0000 0.8398 1.000 0.000 0.000 0.000
#> GSM97908 1 0.0524 0.8361 0.988 0.000 0.004 0.008
#> GSM97912 1 0.5619 0.6385 0.688 0.000 0.248 0.064
#> GSM97914 1 0.6315 0.2065 0.508 0.000 0.432 0.060
#> GSM97915 1 0.0000 0.8398 1.000 0.000 0.000 0.000
#> GSM97917 1 0.0000 0.8398 1.000 0.000 0.000 0.000
#> GSM97918 1 0.0000 0.8398 1.000 0.000 0.000 0.000
#> GSM97919 1 0.0000 0.8398 1.000 0.000 0.000 0.000
#> GSM97922 1 0.3550 0.7757 0.860 0.000 0.096 0.044
#> GSM97924 2 0.0000 0.9874 0.000 1.000 0.000 0.000
#> GSM97926 3 0.5226 0.5458 0.180 0.000 0.744 0.076
#> GSM97930 1 0.6179 0.5324 0.608 0.000 0.320 0.072
#> GSM97931 4 0.3354 0.8071 0.000 0.084 0.044 0.872
#> GSM97935 1 0.6506 0.2369 0.468 0.000 0.460 0.072
#> GSM97936 1 0.0188 0.8391 0.996 0.000 0.000 0.004
#> GSM97938 1 0.0188 0.8391 0.996 0.000 0.000 0.004
#> GSM97940 1 0.0000 0.8398 1.000 0.000 0.000 0.000
#> GSM97942 3 0.2760 0.6617 0.000 0.000 0.872 0.128
#> GSM97945 1 0.0657 0.8354 0.984 0.000 0.012 0.004
#> GSM97946 2 0.0000 0.9874 0.000 1.000 0.000 0.000
#> GSM97948 3 0.6500 0.0200 0.376 0.000 0.544 0.080
#> GSM97950 1 0.0000 0.8398 1.000 0.000 0.000 0.000
#> GSM97952 1 0.0000 0.8398 1.000 0.000 0.000 0.000
#> GSM97953 1 0.0188 0.8391 0.996 0.000 0.000 0.004
#> GSM97954 1 0.6121 0.5526 0.620 0.000 0.308 0.072
#> GSM97955 1 0.0376 0.8381 0.992 0.000 0.004 0.004
#> GSM97959 4 0.4888 0.3599 0.000 0.000 0.412 0.588
#> GSM97961 1 0.0000 0.8398 1.000 0.000 0.000 0.000
#> GSM97963 1 0.0000 0.8398 1.000 0.000 0.000 0.000
#> GSM97965 1 0.0000 0.8398 1.000 0.000 0.000 0.000
#> GSM97966 1 0.0000 0.8398 1.000 0.000 0.000 0.000
#> GSM97967 2 0.0000 0.9874 0.000 1.000 0.000 0.000
#> GSM97968 2 0.1557 0.9324 0.000 0.944 0.000 0.056
#> GSM97969 1 0.3764 0.7565 0.844 0.000 0.116 0.040
#> GSM97971 1 0.5180 0.6896 0.740 0.000 0.196 0.064
#> GSM97799 4 0.5078 0.6141 0.000 0.028 0.272 0.700
#> GSM97823 2 0.0000 0.9874 0.000 1.000 0.000 0.000
#> GSM97824 3 0.3873 0.6088 0.000 0.000 0.772 0.228
#> GSM97830 3 0.3610 0.6235 0.000 0.000 0.800 0.200
#> GSM97835 4 0.2924 0.8016 0.000 0.100 0.016 0.884
#> GSM97838 2 0.0000 0.9874 0.000 1.000 0.000 0.000
#> GSM97841 2 0.0000 0.9874 0.000 1.000 0.000 0.000
#> GSM97842 4 0.4374 0.7752 0.000 0.068 0.120 0.812
#> GSM97854 2 0.0000 0.9874 0.000 1.000 0.000 0.000
#> GSM97857 3 0.3873 0.6088 0.000 0.000 0.772 0.228
#> GSM97860 3 0.2760 0.6617 0.000 0.000 0.872 0.128
#> GSM97862 3 0.3801 0.6120 0.000 0.000 0.780 0.220
#> GSM97864 2 0.0000 0.9874 0.000 1.000 0.000 0.000
#> GSM97866 3 0.3801 0.6120 0.000 0.000 0.780 0.220
#> GSM97868 3 0.3837 0.6124 0.000 0.000 0.776 0.224
#> GSM97872 3 0.6477 -0.1221 0.420 0.000 0.508 0.072
#> GSM97873 4 0.3687 0.8038 0.000 0.080 0.064 0.856
#> GSM97874 3 0.3219 0.6461 0.000 0.000 0.836 0.164
#> GSM97875 3 0.3172 0.6515 0.000 0.000 0.840 0.160
#> GSM97876 3 0.2760 0.6617 0.000 0.000 0.872 0.128
#> GSM97880 3 0.2760 0.6617 0.000 0.000 0.872 0.128
#> GSM97881 3 0.4072 0.5794 0.000 0.000 0.748 0.252
#> GSM97884 4 0.5021 0.7299 0.000 0.064 0.180 0.756
#> GSM97901 3 0.3801 0.6120 0.000 0.000 0.780 0.220
#> GSM97902 3 0.4343 0.4558 0.004 0.000 0.732 0.264
#> GSM97909 4 0.3107 0.8046 0.000 0.080 0.036 0.884
#> GSM97911 3 0.4072 0.5794 0.000 0.000 0.748 0.252
#> GSM97923 3 0.2760 0.6617 0.000 0.000 0.872 0.128
#> GSM97928 1 0.6557 0.2704 0.476 0.000 0.448 0.076
#> GSM97929 2 0.0000 0.9874 0.000 1.000 0.000 0.000
#> GSM97933 3 0.2760 0.6620 0.000 0.000 0.872 0.128
#> GSM97934 3 0.2760 0.6620 0.000 0.000 0.872 0.128
#> GSM97944 4 0.5078 0.6141 0.000 0.028 0.272 0.700
#> GSM97949 2 0.0000 0.9874 0.000 1.000 0.000 0.000
#> GSM97956 3 0.3942 0.6004 0.000 0.000 0.764 0.236
#> GSM97962 3 0.3837 0.6124 0.000 0.000 0.776 0.224
#> GSM97964 3 0.4382 0.5187 0.000 0.000 0.704 0.296
#> GSM97970 4 0.5078 0.6141 0.000 0.028 0.272 0.700
#> GSM97822 1 0.5847 0.5438 0.628 0.000 0.320 0.052
#> GSM97831 3 0.3649 0.6228 0.000 0.000 0.796 0.204
#> GSM97845 1 0.0376 0.8381 0.992 0.000 0.004 0.004
#> GSM97865 3 0.5535 0.5459 0.192 0.000 0.720 0.088
#> GSM97867 3 0.2760 0.6617 0.000 0.000 0.872 0.128
#> GSM97883 3 0.5859 0.3860 0.284 0.000 0.652 0.064
#> GSM97897 1 0.3734 0.7682 0.848 0.000 0.108 0.044
#> GSM97900 1 0.0000 0.8398 1.000 0.000 0.000 0.000
#> GSM97904 1 0.6503 0.2754 0.480 0.000 0.448 0.072
#> GSM97907 2 0.0000 0.9874 0.000 1.000 0.000 0.000
#> GSM97925 3 0.5395 0.5398 0.172 0.000 0.736 0.092
#> GSM97947 3 0.3172 0.6515 0.000 0.000 0.840 0.160
cbind(get_classes(res, k = 5), get_membership(res, k = 5))
#> class entropy silhouette p1 p2 p3 p4 p5
#> GSM97800 2 0.0000 0.9842 0.000 1.000 0.000 0.000 0.000
#> GSM97803 2 0.0000 0.9842 0.000 1.000 0.000 0.000 0.000
#> GSM97804 2 0.0000 0.9842 0.000 1.000 0.000 0.000 0.000
#> GSM97805 2 0.0000 0.9842 0.000 1.000 0.000 0.000 0.000
#> GSM97807 2 0.0000 0.9842 0.000 1.000 0.000 0.000 0.000
#> GSM97809 2 0.0000 0.9842 0.000 1.000 0.000 0.000 0.000
#> GSM97811 2 0.0000 0.9842 0.000 1.000 0.000 0.000 0.000
#> GSM97812 2 0.0000 0.9842 0.000 1.000 0.000 0.000 0.000
#> GSM97816 5 0.6351 0.3844 0.184 0.000 0.316 0.000 0.500
#> GSM97817 2 0.0000 0.9842 0.000 1.000 0.000 0.000 0.000
#> GSM97820 2 0.0000 0.9842 0.000 1.000 0.000 0.000 0.000
#> GSM97825 2 0.0000 0.9842 0.000 1.000 0.000 0.000 0.000
#> GSM97827 2 0.0000 0.9842 0.000 1.000 0.000 0.000 0.000
#> GSM97828 5 0.6351 0.3844 0.184 0.000 0.316 0.000 0.500
#> GSM97833 2 0.0000 0.9842 0.000 1.000 0.000 0.000 0.000
#> GSM97834 2 0.0000 0.9842 0.000 1.000 0.000 0.000 0.000
#> GSM97840 5 0.4080 0.6283 0.000 0.252 0.020 0.000 0.728
#> GSM97846 2 0.0000 0.9842 0.000 1.000 0.000 0.000 0.000
#> GSM97848 2 0.0000 0.9842 0.000 1.000 0.000 0.000 0.000
#> GSM97849 2 0.0000 0.9842 0.000 1.000 0.000 0.000 0.000
#> GSM97850 2 0.0000 0.9842 0.000 1.000 0.000 0.000 0.000
#> GSM97853 2 0.0000 0.9842 0.000 1.000 0.000 0.000 0.000
#> GSM97855 2 0.1908 0.8924 0.000 0.908 0.000 0.000 0.092
#> GSM97878 1 0.6112 0.0342 0.516 0.000 0.344 0.000 0.140
#> GSM97913 1 0.6358 -0.0235 0.492 0.000 0.328 0.000 0.180
#> GSM97932 4 0.0963 0.9138 0.036 0.000 0.000 0.964 0.000
#> GSM97939 5 0.2484 0.7847 0.004 0.028 0.068 0.000 0.900
#> GSM97951 5 0.4080 0.6283 0.000 0.252 0.020 0.000 0.728
#> GSM97957 3 0.1894 0.8545 0.072 0.000 0.920 0.000 0.008
#> GSM97972 5 0.2299 0.7885 0.004 0.032 0.052 0.000 0.912
#> GSM97793 3 0.1732 0.8510 0.080 0.000 0.920 0.000 0.000
#> GSM97795 2 0.4015 0.4506 0.000 0.652 0.000 0.000 0.348
#> GSM97802 3 0.3885 0.7379 0.176 0.000 0.784 0.000 0.040
#> GSM97810 5 0.1648 0.7846 0.000 0.040 0.020 0.000 0.940
#> GSM97815 5 0.1579 0.7863 0.000 0.032 0.024 0.000 0.944
#> GSM97837 1 0.4998 0.5702 0.632 0.000 0.032 0.328 0.008
#> GSM97843 3 0.2136 0.8521 0.088 0.000 0.904 0.000 0.008
#> GSM97890 3 0.2390 0.8498 0.084 0.000 0.896 0.000 0.020
#> GSM97899 4 0.0000 0.9262 0.000 0.000 0.000 1.000 0.000
#> GSM97910 3 0.6909 0.0260 0.412 0.000 0.424 0.036 0.128
#> GSM97916 1 0.5011 0.4315 0.660 0.000 0.292 0.012 0.036
#> GSM97920 3 0.4808 0.7389 0.136 0.000 0.728 0.000 0.136
#> GSM97921 1 0.6721 0.5721 0.520 0.000 0.208 0.256 0.016
#> GSM97927 1 0.5376 0.6919 0.688 0.000 0.104 0.196 0.012
#> GSM97937 4 0.2377 0.8183 0.128 0.000 0.000 0.872 0.000
#> GSM97941 5 0.4054 0.6335 0.000 0.248 0.020 0.000 0.732
#> GSM97943 3 0.6248 0.4595 0.300 0.000 0.524 0.000 0.176
#> GSM97958 5 0.6593 0.2543 0.352 0.000 0.216 0.000 0.432
#> GSM97960 5 0.2208 0.7750 0.000 0.072 0.020 0.000 0.908
#> GSM97794 1 0.4969 0.4356 0.668 0.000 0.284 0.012 0.036
#> GSM97796 4 0.0000 0.9262 0.000 0.000 0.000 1.000 0.000
#> GSM97797 1 0.6112 0.0257 0.516 0.000 0.344 0.000 0.140
#> GSM97798 4 0.0000 0.9262 0.000 0.000 0.000 1.000 0.000
#> GSM97801 1 0.5778 0.6498 0.660 0.000 0.156 0.168 0.016
#> GSM97806 1 0.5437 0.6916 0.680 0.000 0.104 0.204 0.012
#> GSM97808 4 0.0000 0.9262 0.000 0.000 0.000 1.000 0.000
#> GSM97813 4 0.4522 0.3731 0.316 0.000 0.000 0.660 0.024
#> GSM97814 4 0.0000 0.9262 0.000 0.000 0.000 1.000 0.000
#> GSM97818 1 0.4404 0.5642 0.748 0.000 0.204 0.040 0.008
#> GSM97819 3 0.0955 0.8484 0.028 0.000 0.968 0.000 0.004
#> GSM97821 5 0.4372 0.7005 0.120 0.004 0.100 0.000 0.776
#> GSM97826 1 0.5335 0.4462 0.548 0.000 0.032 0.408 0.012
#> GSM97829 1 0.5636 0.6660 0.652 0.000 0.092 0.240 0.016
#> GSM97832 5 0.1741 0.7863 0.000 0.040 0.024 0.000 0.936
#> GSM97836 1 0.5050 0.4239 0.652 0.000 0.300 0.012 0.036
#> GSM97839 4 0.0000 0.9262 0.000 0.000 0.000 1.000 0.000
#> GSM97844 2 0.0000 0.9842 0.000 1.000 0.000 0.000 0.000
#> GSM97847 4 0.1478 0.8935 0.064 0.000 0.000 0.936 0.000
#> GSM97851 4 0.0000 0.9262 0.000 0.000 0.000 1.000 0.000
#> GSM97852 4 0.1478 0.8935 0.064 0.000 0.000 0.936 0.000
#> GSM97856 4 0.0000 0.9262 0.000 0.000 0.000 1.000 0.000
#> GSM97858 2 0.0000 0.9842 0.000 1.000 0.000 0.000 0.000
#> GSM97859 1 0.5609 0.4918 0.564 0.000 0.048 0.372 0.016
#> GSM97861 1 0.5460 0.6895 0.684 0.000 0.120 0.184 0.012
#> GSM97863 4 0.0000 0.9262 0.000 0.000 0.000 1.000 0.000
#> GSM97869 1 0.5011 0.4315 0.660 0.000 0.292 0.012 0.036
#> GSM97870 1 0.5609 0.4918 0.564 0.000 0.048 0.372 0.016
#> GSM97871 4 0.0000 0.9262 0.000 0.000 0.000 1.000 0.000
#> GSM97877 5 0.2184 0.7852 0.028 0.028 0.020 0.000 0.924
#> GSM97879 1 0.4718 0.3538 0.540 0.000 0.016 0.444 0.000
#> GSM97882 1 0.5437 0.6916 0.680 0.000 0.104 0.204 0.012
#> GSM97885 1 0.5422 0.6915 0.684 0.000 0.108 0.196 0.012
#> GSM97886 4 0.0324 0.9206 0.004 0.000 0.000 0.992 0.004
#> GSM97887 4 0.0000 0.9262 0.000 0.000 0.000 1.000 0.000
#> GSM97888 4 0.0703 0.9140 0.024 0.000 0.000 0.976 0.000
#> GSM97889 1 0.6324 0.3243 0.452 0.000 0.084 0.440 0.024
#> GSM97891 1 0.5376 0.6919 0.688 0.000 0.104 0.196 0.012
#> GSM97892 2 0.0000 0.9842 0.000 1.000 0.000 0.000 0.000
#> GSM97893 4 0.0609 0.9201 0.020 0.000 0.000 0.980 0.000
#> GSM97894 4 0.0000 0.9262 0.000 0.000 0.000 1.000 0.000
#> GSM97895 4 0.0963 0.9138 0.036 0.000 0.000 0.964 0.000
#> GSM97896 4 0.0703 0.9142 0.024 0.000 0.000 0.976 0.000
#> GSM97898 4 0.0000 0.9262 0.000 0.000 0.000 1.000 0.000
#> GSM97903 1 0.4711 0.6795 0.736 0.000 0.116 0.148 0.000
#> GSM97905 1 0.5084 0.3312 0.520 0.000 0.012 0.452 0.016
#> GSM97906 4 0.0000 0.9262 0.000 0.000 0.000 1.000 0.000
#> GSM97908 4 0.1544 0.8942 0.068 0.000 0.000 0.932 0.000
#> GSM97912 1 0.5092 0.3056 0.508 0.000 0.012 0.464 0.016
#> GSM97914 1 0.6124 0.6397 0.584 0.000 0.128 0.276 0.012
#> GSM97915 4 0.0000 0.9262 0.000 0.000 0.000 1.000 0.000
#> GSM97917 4 0.0609 0.9201 0.020 0.000 0.000 0.980 0.000
#> GSM97918 4 0.0000 0.9262 0.000 0.000 0.000 1.000 0.000
#> GSM97919 4 0.0000 0.9262 0.000 0.000 0.000 1.000 0.000
#> GSM97922 4 0.4522 0.3731 0.316 0.000 0.000 0.660 0.024
#> GSM97924 2 0.0000 0.9842 0.000 1.000 0.000 0.000 0.000
#> GSM97926 1 0.5050 0.4239 0.652 0.000 0.300 0.012 0.036
#> GSM97930 1 0.4682 0.4036 0.564 0.000 0.016 0.420 0.000
#> GSM97931 5 0.2299 0.7885 0.004 0.032 0.052 0.000 0.912
#> GSM97935 1 0.5376 0.6919 0.688 0.000 0.104 0.196 0.012
#> GSM97936 4 0.1121 0.9074 0.044 0.000 0.000 0.956 0.000
#> GSM97938 4 0.1197 0.9051 0.048 0.000 0.000 0.952 0.000
#> GSM97940 4 0.0000 0.9262 0.000 0.000 0.000 1.000 0.000
#> GSM97942 3 0.1792 0.8502 0.084 0.000 0.916 0.000 0.000
#> GSM97945 4 0.1831 0.8786 0.076 0.000 0.004 0.920 0.000
#> GSM97946 2 0.0000 0.9842 0.000 1.000 0.000 0.000 0.000
#> GSM97948 1 0.4835 0.6575 0.724 0.000 0.156 0.120 0.000
#> GSM97950 4 0.0609 0.9201 0.020 0.000 0.000 0.980 0.000
#> GSM97952 4 0.0000 0.9262 0.000 0.000 0.000 1.000 0.000
#> GSM97953 4 0.1197 0.9051 0.048 0.000 0.000 0.952 0.000
#> GSM97954 1 0.4708 0.3706 0.548 0.000 0.016 0.436 0.000
#> GSM97955 4 0.1341 0.8996 0.056 0.000 0.000 0.944 0.000
#> GSM97959 5 0.6080 0.4809 0.272 0.000 0.168 0.000 0.560
#> GSM97961 4 0.0000 0.9262 0.000 0.000 0.000 1.000 0.000
#> GSM97963 4 0.0000 0.9262 0.000 0.000 0.000 1.000 0.000
#> GSM97965 4 0.0000 0.9262 0.000 0.000 0.000 1.000 0.000
#> GSM97966 4 0.0000 0.9262 0.000 0.000 0.000 1.000 0.000
#> GSM97967 2 0.0000 0.9842 0.000 1.000 0.000 0.000 0.000
#> GSM97968 2 0.1792 0.9004 0.000 0.916 0.000 0.000 0.084
#> GSM97969 4 0.4853 0.3867 0.296 0.000 0.032 0.664 0.008
#> GSM97971 4 0.4888 -0.1983 0.472 0.000 0.004 0.508 0.016
#> GSM97799 5 0.4457 0.4992 0.012 0.000 0.368 0.000 0.620
#> GSM97823 2 0.0000 0.9842 0.000 1.000 0.000 0.000 0.000
#> GSM97824 3 0.3622 0.8085 0.056 0.000 0.820 0.000 0.124
#> GSM97830 3 0.3955 0.7985 0.084 0.000 0.800 0.000 0.116
#> GSM97835 5 0.1741 0.7863 0.000 0.040 0.024 0.000 0.936
#> GSM97838 2 0.0000 0.9842 0.000 1.000 0.000 0.000 0.000
#> GSM97841 2 0.0000 0.9842 0.000 1.000 0.000 0.000 0.000
#> GSM97842 5 0.3584 0.7575 0.012 0.028 0.132 0.000 0.828
#> GSM97854 2 0.0000 0.9842 0.000 1.000 0.000 0.000 0.000
#> GSM97857 3 0.3622 0.8085 0.056 0.000 0.820 0.000 0.124
#> GSM97860 3 0.1792 0.8502 0.084 0.000 0.916 0.000 0.000
#> GSM97862 3 0.2685 0.8234 0.028 0.000 0.880 0.000 0.092
#> GSM97864 2 0.0000 0.9842 0.000 1.000 0.000 0.000 0.000
#> GSM97866 3 0.2685 0.8234 0.028 0.000 0.880 0.000 0.092
#> GSM97868 3 0.3527 0.8127 0.056 0.000 0.828 0.000 0.116
#> GSM97872 1 0.5025 0.6798 0.724 0.000 0.116 0.152 0.008
#> GSM97873 5 0.2484 0.7847 0.004 0.028 0.068 0.000 0.900
#> GSM97874 3 0.3362 0.8280 0.080 0.000 0.844 0.000 0.076
#> GSM97875 3 0.0955 0.8484 0.028 0.000 0.968 0.000 0.004
#> GSM97876 3 0.1671 0.8540 0.076 0.000 0.924 0.000 0.000
#> GSM97880 3 0.1732 0.8510 0.080 0.000 0.920 0.000 0.000
#> GSM97881 3 0.3051 0.7983 0.028 0.000 0.852 0.000 0.120
#> GSM97884 5 0.4215 0.6913 0.008 0.024 0.220 0.000 0.748
#> GSM97901 3 0.2685 0.8234 0.028 0.000 0.880 0.000 0.092
#> GSM97902 1 0.6422 -0.1071 0.460 0.000 0.360 0.000 0.180
#> GSM97909 5 0.2184 0.7852 0.028 0.028 0.020 0.000 0.924
#> GSM97911 3 0.3051 0.7983 0.028 0.000 0.852 0.000 0.120
#> GSM97923 3 0.1792 0.8502 0.084 0.000 0.916 0.000 0.000
#> GSM97928 1 0.5519 0.6890 0.680 0.000 0.108 0.196 0.016
#> GSM97929 2 0.0000 0.9842 0.000 1.000 0.000 0.000 0.000
#> GSM97933 3 0.1894 0.8545 0.072 0.000 0.920 0.000 0.008
#> GSM97934 3 0.1894 0.8545 0.072 0.000 0.920 0.000 0.008
#> GSM97944 5 0.4457 0.4992 0.012 0.000 0.368 0.000 0.620
#> GSM97949 2 0.0000 0.9842 0.000 1.000 0.000 0.000 0.000
#> GSM97956 3 0.3192 0.8117 0.040 0.000 0.848 0.000 0.112
#> GSM97962 3 0.3527 0.8127 0.056 0.000 0.828 0.000 0.116
#> GSM97964 3 0.3650 0.7407 0.028 0.000 0.796 0.000 0.176
#> GSM97970 5 0.4457 0.4992 0.012 0.000 0.368 0.000 0.620
#> GSM97822 1 0.6582 0.4584 0.480 0.000 0.116 0.380 0.024
#> GSM97831 3 0.3780 0.8059 0.072 0.000 0.812 0.000 0.116
#> GSM97845 4 0.1478 0.8937 0.064 0.000 0.000 0.936 0.000
#> GSM97865 1 0.5924 0.4229 0.616 0.000 0.284 0.040 0.060
#> GSM97867 3 0.1732 0.8510 0.080 0.000 0.920 0.000 0.000
#> GSM97883 1 0.6302 0.4453 0.520 0.000 0.356 0.108 0.016
#> GSM97897 4 0.4564 0.4722 0.272 0.000 0.008 0.696 0.024
#> GSM97900 4 0.0000 0.9262 0.000 0.000 0.000 1.000 0.000
#> GSM97904 1 0.4964 0.6924 0.700 0.000 0.096 0.204 0.000
#> GSM97907 2 0.0000 0.9842 0.000 1.000 0.000 0.000 0.000
#> GSM97925 1 0.4446 0.2641 0.592 0.000 0.400 0.008 0.000
#> GSM97947 3 0.0955 0.8484 0.028 0.000 0.968 0.000 0.004
cbind(get_classes(res, k = 6), get_membership(res, k = 6))
#> class entropy silhouette p1 p2 p3 p4 p5 p6
#> GSM97800 2 0.0000 0.9831 0.000 1.000 0.000 0.000 0.000 0.000
#> GSM97803 2 0.0000 0.9831 0.000 1.000 0.000 0.000 0.000 0.000
#> GSM97804 2 0.0000 0.9831 0.000 1.000 0.000 0.000 0.000 0.000
#> GSM97805 2 0.0000 0.9831 0.000 1.000 0.000 0.000 0.000 0.000
#> GSM97807 2 0.0000 0.9831 0.000 1.000 0.000 0.000 0.000 0.000
#> GSM97809 2 0.0000 0.9831 0.000 1.000 0.000 0.000 0.000 0.000
#> GSM97811 2 0.0000 0.9831 0.000 1.000 0.000 0.000 0.000 0.000
#> GSM97812 2 0.0000 0.9831 0.000 1.000 0.000 0.000 0.000 0.000
#> GSM97816 6 0.5502 0.4320 0.008 0.000 0.100 0.000 0.408 0.484
#> GSM97817 2 0.0000 0.9831 0.000 1.000 0.000 0.000 0.000 0.000
#> GSM97820 2 0.0000 0.9831 0.000 1.000 0.000 0.000 0.000 0.000
#> GSM97825 2 0.0000 0.9831 0.000 1.000 0.000 0.000 0.000 0.000
#> GSM97827 2 0.0000 0.9831 0.000 1.000 0.000 0.000 0.000 0.000
#> GSM97828 6 0.5502 0.4320 0.008 0.000 0.100 0.000 0.408 0.484
#> GSM97833 2 0.0000 0.9831 0.000 1.000 0.000 0.000 0.000 0.000
#> GSM97834 2 0.0000 0.9831 0.000 1.000 0.000 0.000 0.000 0.000
#> GSM97840 5 0.3189 0.4489 0.000 0.236 0.000 0.000 0.760 0.004
#> GSM97846 2 0.0000 0.9831 0.000 1.000 0.000 0.000 0.000 0.000
#> GSM97848 2 0.0000 0.9831 0.000 1.000 0.000 0.000 0.000 0.000
#> GSM97849 2 0.0000 0.9831 0.000 1.000 0.000 0.000 0.000 0.000
#> GSM97850 2 0.0000 0.9831 0.000 1.000 0.000 0.000 0.000 0.000
#> GSM97853 2 0.0000 0.9831 0.000 1.000 0.000 0.000 0.000 0.000
#> GSM97855 2 0.1858 0.8861 0.000 0.904 0.000 0.000 0.092 0.004
#> GSM97878 1 0.6066 -0.2736 0.456 0.000 0.148 0.000 0.020 0.376
#> GSM97913 1 0.6519 -0.3770 0.416 0.000 0.132 0.000 0.060 0.392
#> GSM97932 4 0.3737 0.7678 0.044 0.000 0.000 0.780 0.008 0.168
#> GSM97939 5 0.1794 0.6794 0.000 0.016 0.024 0.000 0.932 0.028
#> GSM97951 5 0.3189 0.4489 0.000 0.236 0.000 0.000 0.760 0.004
#> GSM97957 3 0.1753 0.7674 0.084 0.000 0.912 0.000 0.000 0.004
#> GSM97972 5 0.1346 0.6797 0.000 0.016 0.008 0.000 0.952 0.024
#> GSM97793 3 0.1814 0.7619 0.100 0.000 0.900 0.000 0.000 0.000
#> GSM97795 2 0.3659 0.4083 0.000 0.636 0.000 0.000 0.364 0.000
#> GSM97802 3 0.4906 0.5791 0.080 0.000 0.656 0.000 0.012 0.252
#> GSM97810 5 0.0777 0.6815 0.000 0.024 0.000 0.000 0.972 0.004
#> GSM97815 5 0.0458 0.6832 0.000 0.016 0.000 0.000 0.984 0.000
#> GSM97837 1 0.4087 0.5714 0.720 0.000 0.012 0.240 0.000 0.028
#> GSM97843 3 0.2573 0.7579 0.112 0.000 0.864 0.000 0.000 0.024
#> GSM97890 3 0.3455 0.7599 0.088 0.000 0.828 0.000 0.016 0.068
#> GSM97899 4 0.0146 0.8990 0.004 0.000 0.000 0.996 0.000 0.000
#> GSM97910 1 0.7132 -0.0734 0.456 0.000 0.248 0.004 0.108 0.184
#> GSM97916 1 0.4546 0.3859 0.728 0.000 0.132 0.000 0.012 0.128
#> GSM97920 3 0.5562 0.5549 0.144 0.000 0.660 0.000 0.132 0.064
#> GSM97921 1 0.6331 0.4991 0.560 0.000 0.076 0.216 0.000 0.148
#> GSM97927 1 0.4418 0.6227 0.764 0.000 0.044 0.108 0.000 0.084
#> GSM97937 4 0.3715 0.7335 0.188 0.000 0.000 0.764 0.000 0.048
#> GSM97941 5 0.3163 0.4536 0.000 0.232 0.000 0.000 0.764 0.004
#> GSM97943 3 0.7454 -0.1737 0.288 0.000 0.356 0.000 0.148 0.208
#> GSM97958 5 0.7102 -0.3588 0.296 0.000 0.080 0.000 0.384 0.240
#> GSM97960 5 0.1349 0.6610 0.000 0.056 0.000 0.000 0.940 0.004
#> GSM97794 1 0.4659 0.3711 0.716 0.000 0.132 0.000 0.012 0.140
#> GSM97796 4 0.0000 0.9002 0.000 0.000 0.000 1.000 0.000 0.000
#> GSM97797 1 0.6026 -0.2849 0.452 0.000 0.140 0.000 0.020 0.388
#> GSM97798 4 0.0000 0.9002 0.000 0.000 0.000 1.000 0.000 0.000
#> GSM97801 1 0.4426 0.5543 0.768 0.000 0.060 0.092 0.000 0.080
#> GSM97806 1 0.4503 0.6239 0.756 0.000 0.044 0.116 0.000 0.084
#> GSM97808 4 0.0000 0.9002 0.000 0.000 0.000 1.000 0.000 0.000
#> GSM97813 4 0.5029 0.3181 0.276 0.000 0.000 0.612 0.000 0.112
#> GSM97814 4 0.0000 0.9002 0.000 0.000 0.000 1.000 0.000 0.000
#> GSM97818 1 0.3703 0.5051 0.812 0.000 0.084 0.020 0.000 0.084
#> GSM97819 3 0.2443 0.7476 0.020 0.000 0.880 0.000 0.004 0.096
#> GSM97821 5 0.4385 0.4268 0.100 0.000 0.024 0.000 0.756 0.120
#> GSM97826 1 0.4444 0.5296 0.644 0.000 0.008 0.316 0.000 0.032
#> GSM97829 1 0.4136 0.5895 0.768 0.000 0.036 0.156 0.000 0.040
#> GSM97832 5 0.0632 0.6836 0.000 0.024 0.000 0.000 0.976 0.000
#> GSM97836 1 0.4538 0.3840 0.728 0.000 0.144 0.000 0.012 0.116
#> GSM97839 4 0.0000 0.9002 0.000 0.000 0.000 1.000 0.000 0.000
#> GSM97844 2 0.0000 0.9831 0.000 1.000 0.000 0.000 0.000 0.000
#> GSM97847 4 0.3130 0.8116 0.124 0.000 0.000 0.828 0.000 0.048
#> GSM97851 4 0.0000 0.9002 0.000 0.000 0.000 1.000 0.000 0.000
#> GSM97852 4 0.3130 0.8116 0.124 0.000 0.000 0.828 0.000 0.048
#> GSM97856 4 0.0000 0.9002 0.000 0.000 0.000 1.000 0.000 0.000
#> GSM97858 2 0.0000 0.9831 0.000 1.000 0.000 0.000 0.000 0.000
#> GSM97859 1 0.5223 0.5717 0.628 0.000 0.020 0.264 0.000 0.088
#> GSM97861 1 0.4705 0.6230 0.744 0.000 0.060 0.108 0.000 0.088
#> GSM97863 4 0.0000 0.9002 0.000 0.000 0.000 1.000 0.000 0.000
#> GSM97869 1 0.4546 0.3859 0.728 0.000 0.132 0.000 0.012 0.128
#> GSM97870 1 0.5223 0.5717 0.628 0.000 0.020 0.264 0.000 0.088
#> GSM97871 4 0.0000 0.9002 0.000 0.000 0.000 1.000 0.000 0.000
#> GSM97877 5 0.1332 0.6746 0.008 0.012 0.000 0.000 0.952 0.028
#> GSM97879 1 0.4105 0.4476 0.632 0.000 0.000 0.348 0.000 0.020
#> GSM97882 1 0.4503 0.6239 0.756 0.000 0.044 0.116 0.000 0.084
#> GSM97885 1 0.4523 0.6237 0.756 0.000 0.048 0.112 0.000 0.084
#> GSM97886 4 0.0632 0.8847 0.000 0.000 0.000 0.976 0.000 0.024
#> GSM97887 4 0.0000 0.9002 0.000 0.000 0.000 1.000 0.000 0.000
#> GSM97888 4 0.0713 0.8853 0.028 0.000 0.000 0.972 0.000 0.000
#> GSM97889 1 0.6211 0.4090 0.484 0.000 0.036 0.340 0.000 0.140
#> GSM97891 1 0.4418 0.6227 0.764 0.000 0.044 0.108 0.000 0.084
#> GSM97892 2 0.0000 0.9831 0.000 1.000 0.000 0.000 0.000 0.000
#> GSM97893 4 0.1480 0.8795 0.020 0.000 0.000 0.940 0.000 0.040
#> GSM97894 4 0.0000 0.9002 0.000 0.000 0.000 1.000 0.000 0.000
#> GSM97895 4 0.4034 0.7533 0.064 0.000 0.000 0.760 0.008 0.168
#> GSM97896 4 0.0632 0.8875 0.024 0.000 0.000 0.976 0.000 0.000
#> GSM97898 4 0.0000 0.9002 0.000 0.000 0.000 1.000 0.000 0.000
#> GSM97903 1 0.3168 0.6073 0.852 0.000 0.048 0.076 0.000 0.024
#> GSM97905 1 0.5376 0.4316 0.528 0.000 0.008 0.372 0.000 0.092
#> GSM97906 4 0.0000 0.9002 0.000 0.000 0.000 1.000 0.000 0.000
#> GSM97908 4 0.3193 0.8116 0.124 0.000 0.000 0.824 0.000 0.052
#> GSM97912 1 0.5425 0.3804 0.496 0.000 0.008 0.404 0.000 0.092
#> GSM97914 1 0.5060 0.5871 0.684 0.000 0.052 0.204 0.000 0.060
#> GSM97915 4 0.0000 0.9002 0.000 0.000 0.000 1.000 0.000 0.000
#> GSM97917 4 0.1480 0.8795 0.020 0.000 0.000 0.940 0.000 0.040
#> GSM97918 4 0.0000 0.9002 0.000 0.000 0.000 1.000 0.000 0.000
#> GSM97919 4 0.0000 0.9002 0.000 0.000 0.000 1.000 0.000 0.000
#> GSM97922 4 0.5029 0.3181 0.276 0.000 0.000 0.612 0.000 0.112
#> GSM97924 2 0.0000 0.9831 0.000 1.000 0.000 0.000 0.000 0.000
#> GSM97926 1 0.4538 0.3840 0.728 0.000 0.144 0.000 0.012 0.116
#> GSM97930 1 0.4048 0.4708 0.644 0.000 0.004 0.340 0.000 0.012
#> GSM97931 5 0.1346 0.6797 0.000 0.016 0.008 0.000 0.952 0.024
#> GSM97935 1 0.4418 0.6227 0.764 0.000 0.044 0.108 0.000 0.084
#> GSM97936 4 0.2908 0.8267 0.104 0.000 0.000 0.848 0.000 0.048
#> GSM97938 4 0.2954 0.8243 0.108 0.000 0.000 0.844 0.000 0.048
#> GSM97940 4 0.0000 0.9002 0.000 0.000 0.000 1.000 0.000 0.000
#> GSM97942 3 0.1863 0.7604 0.104 0.000 0.896 0.000 0.000 0.000
#> GSM97945 4 0.3307 0.7907 0.148 0.000 0.000 0.808 0.000 0.044
#> GSM97946 2 0.0000 0.9831 0.000 1.000 0.000 0.000 0.000 0.000
#> GSM97948 1 0.3099 0.5973 0.848 0.000 0.084 0.060 0.000 0.008
#> GSM97950 4 0.1480 0.8795 0.020 0.000 0.000 0.940 0.000 0.040
#> GSM97952 4 0.0000 0.9002 0.000 0.000 0.000 1.000 0.000 0.000
#> GSM97953 4 0.2954 0.8243 0.108 0.000 0.000 0.844 0.000 0.048
#> GSM97954 1 0.4092 0.4531 0.636 0.000 0.000 0.344 0.000 0.020
#> GSM97955 4 0.3044 0.8179 0.116 0.000 0.000 0.836 0.000 0.048
#> GSM97959 5 0.6366 -0.1246 0.212 0.000 0.048 0.000 0.528 0.212
#> GSM97961 4 0.0000 0.9002 0.000 0.000 0.000 1.000 0.000 0.000
#> GSM97963 4 0.0000 0.9002 0.000 0.000 0.000 1.000 0.000 0.000
#> GSM97965 4 0.0000 0.9002 0.000 0.000 0.000 1.000 0.000 0.000
#> GSM97966 4 0.0000 0.9002 0.000 0.000 0.000 1.000 0.000 0.000
#> GSM97967 2 0.0000 0.9831 0.000 1.000 0.000 0.000 0.000 0.000
#> GSM97968 2 0.1663 0.8941 0.000 0.912 0.000 0.000 0.088 0.000
#> GSM97969 4 0.4607 0.2192 0.392 0.000 0.008 0.572 0.000 0.028
#> GSM97971 1 0.5281 0.2645 0.464 0.000 0.004 0.448 0.000 0.084
#> GSM97799 5 0.4711 0.3425 0.000 0.000 0.280 0.000 0.640 0.080
#> GSM97823 2 0.0000 0.9831 0.000 1.000 0.000 0.000 0.000 0.000
#> GSM97824 3 0.5018 0.7058 0.052 0.000 0.712 0.000 0.128 0.108
#> GSM97830 3 0.4560 0.6637 0.100 0.000 0.748 0.000 0.116 0.036
#> GSM97835 5 0.0632 0.6836 0.000 0.024 0.000 0.000 0.976 0.000
#> GSM97838 2 0.0000 0.9831 0.000 1.000 0.000 0.000 0.000 0.000
#> GSM97841 2 0.0000 0.9831 0.000 1.000 0.000 0.000 0.000 0.000
#> GSM97842 5 0.3017 0.6286 0.000 0.016 0.064 0.000 0.860 0.060
#> GSM97854 2 0.0000 0.9831 0.000 1.000 0.000 0.000 0.000 0.000
#> GSM97857 3 0.5018 0.7058 0.052 0.000 0.712 0.000 0.128 0.108
#> GSM97860 3 0.1863 0.7604 0.104 0.000 0.896 0.000 0.000 0.000
#> GSM97862 3 0.4670 0.7116 0.028 0.000 0.732 0.000 0.112 0.128
#> GSM97864 2 0.0000 0.9831 0.000 1.000 0.000 0.000 0.000 0.000
#> GSM97866 3 0.4670 0.7116 0.028 0.000 0.732 0.000 0.112 0.128
#> GSM97868 3 0.4940 0.7108 0.052 0.000 0.720 0.000 0.120 0.108
#> GSM97872 1 0.3445 0.6049 0.836 0.000 0.048 0.080 0.000 0.036
#> GSM97873 5 0.1794 0.6794 0.000 0.016 0.024 0.000 0.932 0.028
#> GSM97874 3 0.3673 0.7172 0.100 0.000 0.804 0.000 0.088 0.008
#> GSM97875 3 0.2443 0.7476 0.020 0.000 0.880 0.000 0.004 0.096
#> GSM97876 3 0.1866 0.7689 0.084 0.000 0.908 0.000 0.000 0.008
#> GSM97880 3 0.1814 0.7619 0.100 0.000 0.900 0.000 0.000 0.000
#> GSM97881 3 0.4709 0.6912 0.016 0.000 0.716 0.000 0.140 0.128
#> GSM97884 5 0.3998 0.5410 0.000 0.012 0.116 0.000 0.780 0.092
#> GSM97901 3 0.4670 0.7116 0.028 0.000 0.732 0.000 0.112 0.128
#> GSM97902 6 0.6505 0.1126 0.400 0.000 0.144 0.000 0.052 0.404
#> GSM97909 5 0.1332 0.6746 0.008 0.012 0.000 0.000 0.952 0.028
#> GSM97911 3 0.4709 0.6912 0.016 0.000 0.716 0.000 0.140 0.128
#> GSM97923 3 0.1863 0.7604 0.104 0.000 0.896 0.000 0.000 0.000
#> GSM97928 1 0.4775 0.6174 0.732 0.000 0.044 0.104 0.000 0.120
#> GSM97929 2 0.0000 0.9831 0.000 1.000 0.000 0.000 0.000 0.000
#> GSM97933 3 0.1753 0.7674 0.084 0.000 0.912 0.000 0.000 0.004
#> GSM97934 3 0.1753 0.7674 0.084 0.000 0.912 0.000 0.000 0.004
#> GSM97944 5 0.4711 0.3425 0.000 0.000 0.280 0.000 0.640 0.080
#> GSM97949 2 0.0000 0.9831 0.000 1.000 0.000 0.000 0.000 0.000
#> GSM97956 3 0.4784 0.7075 0.032 0.000 0.724 0.000 0.124 0.120
#> GSM97962 3 0.4897 0.7115 0.052 0.000 0.724 0.000 0.120 0.104
#> GSM97964 3 0.5076 0.6301 0.016 0.000 0.668 0.000 0.196 0.120
#> GSM97970 5 0.4711 0.3425 0.000 0.000 0.280 0.000 0.640 0.080
#> GSM97822 1 0.6289 0.4889 0.516 0.000 0.052 0.296 0.000 0.136
#> GSM97831 3 0.4232 0.6894 0.068 0.000 0.776 0.000 0.116 0.040
#> GSM97845 4 0.3130 0.8119 0.124 0.000 0.000 0.828 0.000 0.048
#> GSM97865 1 0.5515 0.3563 0.676 0.000 0.104 0.020 0.032 0.168
#> GSM97867 3 0.1814 0.7619 0.100 0.000 0.900 0.000 0.000 0.000
#> GSM97883 1 0.6125 0.3918 0.532 0.000 0.308 0.060 0.000 0.100
#> GSM97897 4 0.4756 0.4733 0.200 0.000 0.000 0.672 0.000 0.128
#> GSM97900 4 0.0000 0.9002 0.000 0.000 0.000 1.000 0.000 0.000
#> GSM97904 1 0.3051 0.6228 0.844 0.000 0.036 0.112 0.000 0.008
#> GSM97907 2 0.0000 0.9831 0.000 1.000 0.000 0.000 0.000 0.000
#> GSM97925 1 0.4105 0.2597 0.632 0.000 0.348 0.000 0.000 0.020
#> GSM97947 3 0.2443 0.7476 0.020 0.000 0.880 0.000 0.004 0.096
Heatmaps for the consensus matrix. It visualizes the probability of two samples to be in a same group.
consensus_heatmap(res, k = 2)
consensus_heatmap(res, k = 3)
consensus_heatmap(res, k = 4)
consensus_heatmap(res, k = 5)
consensus_heatmap(res, k = 6)
Heatmaps for the membership of samples in all partitions to see how consistent they are:
membership_heatmap(res, k = 2)
membership_heatmap(res, k = 3)
membership_heatmap(res, k = 4)
membership_heatmap(res, k = 5)
membership_heatmap(res, k = 6)
As soon as we have had the classes for columns, we can look for signatures which are significantly different between classes which can be candidate marks for certain classes. Following are the heatmaps for signatures.
Signature heatmaps where rows are scaled:
get_signatures(res, k = 2)
get_signatures(res, k = 3)
get_signatures(res, k = 4)
get_signatures(res, k = 5)
get_signatures(res, k = 6)
Signature heatmaps where rows are not scaled:
get_signatures(res, k = 2, scale_rows = FALSE)
get_signatures(res, k = 3, scale_rows = FALSE)
get_signatures(res, k = 4, scale_rows = FALSE)
get_signatures(res, k = 5, scale_rows = FALSE)
get_signatures(res, k = 6, scale_rows = FALSE)
Compare the overlap of signatures from different k:
compare_signatures(res)
get_signature() returns a data frame invisibly. TO get the list of signatures, the function
call should be assigned to a variable explicitly. In following code, if plot argument is set
to FALSE, no heatmap is plotted while only the differential analysis is performed.
# code only for demonstration
tb = get_signature(res, k = ..., plot = FALSE)
An example of the output of tb is:
#> which_row fdr mean_1 mean_2 scaled_mean_1 scaled_mean_2 km
#> 1 38 0.042760348 8.373488 9.131774 -0.5533452 0.5164555 1
#> 2 40 0.018707592 7.106213 8.469186 -0.6173731 0.5762149 1
#> 3 55 0.019134737 10.221463 11.207825 -0.6159697 0.5749050 1
#> 4 59 0.006059896 5.921854 7.869574 -0.6899429 0.6439467 1
#> 5 60 0.018055526 8.928898 10.211722 -0.6204761 0.5791110 1
#> 6 98 0.009384629 15.714769 14.887706 0.6635654 -0.6193277 2
...
The columns in tb are:
which_row: row indices corresponding to the input matrix.fdr: FDR for the differential test. mean_x: The mean value in group x.scaled_mean_x: The mean value in group x after rows are scaled.km: Row groups if k-means clustering is applied to rows.UMAP plot which shows how samples are separated.
dimension_reduction(res, k = 2, method = "UMAP")
dimension_reduction(res, k = 3, method = "UMAP")
dimension_reduction(res, k = 4, method = "UMAP")
dimension_reduction(res, k = 5, method = "UMAP")
dimension_reduction(res, k = 6, method = "UMAP")
Following heatmap shows how subgroups are split when increasing k:
collect_classes(res)
Test correlation between subgroups and known annotations. If the known annotation is numeric, one-way ANOVA test is applied, and if the known annotation is discrete, chi-squared contingency table test is applied.
test_to_known_factors(res)
#> n disease.state(p) tissue(p) k
#> ATC:hclust 162 3.05e-16 2.16e-16 2
#> ATC:hclust 166 4.49e-28 5.61e-29 3
#> ATC:hclust 153 3.76e-26 5.44e-26 4
#> ATC:hclust 143 1.20e-24 4.09e-23 5
#> ATC:hclust 141 4.95e-25 4.34e-24 6
If matrix rows can be associated to genes, consider to use functional_enrichment(res,
...) to perform function enrichment for the signature genes. See this vignette for more detailed explanations.
The object with results only for a single top-value method and a single partition method can be extracted as:
res = res_list["ATC", "kmeans"]
# you can also extract it by
# res = res_list["ATC:kmeans"]
A summary of res and all the functions that can be applied to it:
res
#> A 'ConsensusPartition' object with k = 2, 3, 4, 5, 6.
#> On a matrix with 51882 rows and 180 columns.
#> Top rows (1000, 2000, 3000, 4000, 5000) are extracted by 'ATC' method.
#> Subgroups are detected by 'kmeans' method.
#> Performed in total 1250 partitions by row resampling.
#> Best k for subgroups seems to be 5.
#>
#> Following methods can be applied to this 'ConsensusPartition' object:
#> [1] "cola_report" "collect_classes" "collect_plots"
#> [4] "collect_stats" "colnames" "compare_signatures"
#> [7] "consensus_heatmap" "dimension_reduction" "functional_enrichment"
#> [10] "get_anno_col" "get_anno" "get_classes"
#> [13] "get_consensus" "get_matrix" "get_membership"
#> [16] "get_param" "get_signatures" "get_stats"
#> [19] "is_best_k" "is_stable_k" "membership_heatmap"
#> [22] "ncol" "nrow" "plot_ecdf"
#> [25] "rownames" "select_partition_number" "show"
#> [28] "suggest_best_k" "test_to_known_factors"
collect_plots() function collects all the plots made from res for all k (number of partitions)
into one single page to provide an easy and fast comparison between different k.
collect_plots(res)
The plots are:
k and the heatmap of
predicted classes for each k.k.k.k.All the plots in panels can be made by individual functions and they are plotted later in this section.
select_partition_number() produces several plots showing different
statistics for choosing “optimized” k. There are following statistics:
k;k, the area increased is defined as \(A_k - A_{k-1}\).The detailed explanations of these statistics can be found in the cola vignette.
Generally speaking, lower PAC score, higher mean silhouette score or higher
concordance corresponds to better partition. Rand index and Jaccard index
measure how similar the current partition is compared to partition with k-1.
If they are too similar, we won't accept k is better than k-1.
select_partition_number(res)
The numeric values for all these statistics can be obtained by get_stats().
get_stats(res)
#> k 1-PAC mean_silhouette concordance area_increased Rand Jaccard
#> 2 2 1.000 1.000 1.000 0.4358 0.565 0.565
#> 3 3 1.000 0.987 0.995 0.4943 0.678 0.479
#> 4 4 0.742 0.734 0.854 0.1362 0.821 0.540
#> 5 5 0.903 0.923 0.931 0.0707 0.914 0.682
#> 6 6 0.850 0.761 0.849 0.0374 0.980 0.901
suggest_best_k() suggests the best \(k\) based on these statistics. The rules are as follows:
suggest_best_k(res)
#> [1] 5
#> attr(,"optional")
#> [1] 2 3
There is also optional best \(k\) = 2 3 that is worth to check.
Following shows the table of the partitions (You need to click the show/hide
code output link to see it). The membership matrix (columns with name p*)
is inferred by
clue::cl_consensus()
function with the SE method. Basically the value in the membership matrix
represents the probability to belong to a certain group. The finall class
label for an item is determined with the group with highest probability it
belongs to.
In get_classes() function, the entropy is calculated from the membership
matrix and the silhouette score is calculated from the consensus matrix.
cbind(get_classes(res, k = 2), get_membership(res, k = 2))
#> class entropy silhouette p1 p2
#> GSM97800 2 0.0000 1.000 0.000 1.000
#> GSM97803 2 0.0000 1.000 0.000 1.000
#> GSM97804 2 0.0000 1.000 0.000 1.000
#> GSM97805 2 0.0000 1.000 0.000 1.000
#> GSM97807 2 0.0000 1.000 0.000 1.000
#> GSM97809 2 0.0000 1.000 0.000 1.000
#> GSM97811 2 0.0000 1.000 0.000 1.000
#> GSM97812 2 0.0000 1.000 0.000 1.000
#> GSM97816 2 0.0000 1.000 0.000 1.000
#> GSM97817 2 0.0000 1.000 0.000 1.000
#> GSM97820 2 0.0000 1.000 0.000 1.000
#> GSM97825 2 0.0000 1.000 0.000 1.000
#> GSM97827 2 0.0000 1.000 0.000 1.000
#> GSM97828 1 0.0000 1.000 1.000 0.000
#> GSM97833 2 0.0000 1.000 0.000 1.000
#> GSM97834 2 0.0000 1.000 0.000 1.000
#> GSM97840 2 0.0000 1.000 0.000 1.000
#> GSM97846 2 0.0000 1.000 0.000 1.000
#> GSM97848 2 0.0000 1.000 0.000 1.000
#> GSM97849 2 0.0000 1.000 0.000 1.000
#> GSM97850 2 0.0000 1.000 0.000 1.000
#> GSM97853 2 0.0000 1.000 0.000 1.000
#> GSM97855 2 0.0000 1.000 0.000 1.000
#> GSM97878 1 0.0000 1.000 1.000 0.000
#> GSM97913 1 0.0376 0.996 0.996 0.004
#> GSM97932 1 0.0000 1.000 1.000 0.000
#> GSM97939 2 0.0000 1.000 0.000 1.000
#> GSM97951 2 0.0000 1.000 0.000 1.000
#> GSM97957 1 0.0000 1.000 1.000 0.000
#> GSM97972 2 0.0000 1.000 0.000 1.000
#> GSM97793 1 0.0000 1.000 1.000 0.000
#> GSM97795 2 0.0000 1.000 0.000 1.000
#> GSM97802 1 0.0000 1.000 1.000 0.000
#> GSM97810 2 0.0000 1.000 0.000 1.000
#> GSM97815 2 0.0000 1.000 0.000 1.000
#> GSM97837 1 0.0000 1.000 1.000 0.000
#> GSM97843 1 0.0000 1.000 1.000 0.000
#> GSM97890 1 0.0000 1.000 1.000 0.000
#> GSM97899 1 0.0000 1.000 1.000 0.000
#> GSM97910 1 0.0000 1.000 1.000 0.000
#> GSM97916 1 0.0000 1.000 1.000 0.000
#> GSM97920 1 0.0000 1.000 1.000 0.000
#> GSM97921 1 0.0000 1.000 1.000 0.000
#> GSM97927 1 0.0000 1.000 1.000 0.000
#> GSM97937 1 0.0000 1.000 1.000 0.000
#> GSM97941 2 0.0000 1.000 0.000 1.000
#> GSM97943 1 0.0000 1.000 1.000 0.000
#> GSM97958 1 0.0000 1.000 1.000 0.000
#> GSM97960 2 0.0000 1.000 0.000 1.000
#> GSM97794 1 0.0000 1.000 1.000 0.000
#> GSM97796 1 0.0000 1.000 1.000 0.000
#> GSM97797 1 0.0000 1.000 1.000 0.000
#> GSM97798 1 0.0000 1.000 1.000 0.000
#> GSM97801 1 0.0000 1.000 1.000 0.000
#> GSM97806 1 0.0000 1.000 1.000 0.000
#> GSM97808 1 0.0000 1.000 1.000 0.000
#> GSM97813 1 0.0000 1.000 1.000 0.000
#> GSM97814 1 0.0000 1.000 1.000 0.000
#> GSM97818 1 0.0000 1.000 1.000 0.000
#> GSM97819 1 0.0000 1.000 1.000 0.000
#> GSM97821 2 0.0000 1.000 0.000 1.000
#> GSM97826 1 0.0000 1.000 1.000 0.000
#> GSM97829 1 0.0000 1.000 1.000 0.000
#> GSM97832 2 0.0000 1.000 0.000 1.000
#> GSM97836 1 0.0000 1.000 1.000 0.000
#> GSM97839 1 0.0000 1.000 1.000 0.000
#> GSM97844 2 0.0000 1.000 0.000 1.000
#> GSM97847 1 0.0000 1.000 1.000 0.000
#> GSM97851 1 0.0000 1.000 1.000 0.000
#> GSM97852 1 0.0000 1.000 1.000 0.000
#> GSM97856 1 0.0000 1.000 1.000 0.000
#> GSM97858 2 0.0000 1.000 0.000 1.000
#> GSM97859 1 0.0000 1.000 1.000 0.000
#> GSM97861 1 0.0000 1.000 1.000 0.000
#> GSM97863 1 0.0000 1.000 1.000 0.000
#> GSM97869 1 0.0000 1.000 1.000 0.000
#> GSM97870 1 0.0000 1.000 1.000 0.000
#> GSM97871 1 0.0000 1.000 1.000 0.000
#> GSM97877 2 0.0000 1.000 0.000 1.000
#> GSM97879 1 0.0000 1.000 1.000 0.000
#> GSM97882 1 0.0000 1.000 1.000 0.000
#> GSM97885 1 0.0000 1.000 1.000 0.000
#> GSM97886 1 0.0000 1.000 1.000 0.000
#> GSM97887 1 0.0000 1.000 1.000 0.000
#> GSM97888 1 0.0000 1.000 1.000 0.000
#> GSM97889 1 0.0000 1.000 1.000 0.000
#> GSM97891 1 0.0000 1.000 1.000 0.000
#> GSM97892 2 0.0000 1.000 0.000 1.000
#> GSM97893 1 0.0000 1.000 1.000 0.000
#> GSM97894 1 0.0000 1.000 1.000 0.000
#> GSM97895 1 0.0000 1.000 1.000 0.000
#> GSM97896 1 0.0000 1.000 1.000 0.000
#> GSM97898 1 0.0000 1.000 1.000 0.000
#> GSM97903 1 0.0000 1.000 1.000 0.000
#> GSM97905 1 0.0000 1.000 1.000 0.000
#> GSM97906 1 0.0000 1.000 1.000 0.000
#> GSM97908 1 0.0000 1.000 1.000 0.000
#> GSM97912 1 0.0000 1.000 1.000 0.000
#> GSM97914 1 0.0000 1.000 1.000 0.000
#> GSM97915 1 0.0000 1.000 1.000 0.000
#> GSM97917 1 0.0000 1.000 1.000 0.000
#> GSM97918 1 0.0000 1.000 1.000 0.000
#> GSM97919 1 0.0000 1.000 1.000 0.000
#> GSM97922 1 0.0000 1.000 1.000 0.000
#> GSM97924 2 0.0000 1.000 0.000 1.000
#> GSM97926 1 0.0000 1.000 1.000 0.000
#> GSM97930 1 0.0000 1.000 1.000 0.000
#> GSM97931 2 0.0000 1.000 0.000 1.000
#> GSM97935 1 0.0000 1.000 1.000 0.000
#> GSM97936 1 0.0000 1.000 1.000 0.000
#> GSM97938 1 0.0000 1.000 1.000 0.000
#> GSM97940 1 0.0000 1.000 1.000 0.000
#> GSM97942 1 0.0000 1.000 1.000 0.000
#> GSM97945 1 0.0000 1.000 1.000 0.000
#> GSM97946 2 0.0000 1.000 0.000 1.000
#> GSM97948 1 0.0000 1.000 1.000 0.000
#> GSM97950 1 0.0000 1.000 1.000 0.000
#> GSM97952 1 0.0000 1.000 1.000 0.000
#> GSM97953 1 0.0000 1.000 1.000 0.000
#> GSM97954 1 0.0000 1.000 1.000 0.000
#> GSM97955 1 0.0000 1.000 1.000 0.000
#> GSM97959 1 0.0000 1.000 1.000 0.000
#> GSM97961 1 0.0000 1.000 1.000 0.000
#> GSM97963 1 0.0000 1.000 1.000 0.000
#> GSM97965 1 0.0000 1.000 1.000 0.000
#> GSM97966 1 0.0000 1.000 1.000 0.000
#> GSM97967 2 0.0000 1.000 0.000 1.000
#> GSM97968 2 0.0000 1.000 0.000 1.000
#> GSM97969 1 0.0000 1.000 1.000 0.000
#> GSM97971 1 0.0000 1.000 1.000 0.000
#> GSM97799 2 0.0000 1.000 0.000 1.000
#> GSM97823 2 0.0000 1.000 0.000 1.000
#> GSM97824 1 0.0000 1.000 1.000 0.000
#> GSM97830 1 0.0000 1.000 1.000 0.000
#> GSM97835 2 0.0000 1.000 0.000 1.000
#> GSM97838 2 0.0000 1.000 0.000 1.000
#> GSM97841 2 0.0000 1.000 0.000 1.000
#> GSM97842 2 0.0000 1.000 0.000 1.000
#> GSM97854 2 0.0000 1.000 0.000 1.000
#> GSM97857 1 0.0000 1.000 1.000 0.000
#> GSM97860 1 0.0000 1.000 1.000 0.000
#> GSM97862 1 0.0000 1.000 1.000 0.000
#> GSM97864 2 0.0000 1.000 0.000 1.000
#> GSM97866 1 0.0000 1.000 1.000 0.000
#> GSM97868 1 0.0000 1.000 1.000 0.000
#> GSM97872 1 0.0000 1.000 1.000 0.000
#> GSM97873 2 0.0000 1.000 0.000 1.000
#> GSM97874 1 0.0000 1.000 1.000 0.000
#> GSM97875 1 0.0000 1.000 1.000 0.000
#> GSM97876 1 0.0000 1.000 1.000 0.000
#> GSM97880 1 0.0000 1.000 1.000 0.000
#> GSM97881 1 0.0000 1.000 1.000 0.000
#> GSM97884 2 0.0000 1.000 0.000 1.000
#> GSM97901 1 0.0000 1.000 1.000 0.000
#> GSM97902 1 0.0000 1.000 1.000 0.000
#> GSM97909 2 0.0000 1.000 0.000 1.000
#> GSM97911 1 0.0000 1.000 1.000 0.000
#> GSM97923 1 0.0000 1.000 1.000 0.000
#> GSM97928 1 0.0000 1.000 1.000 0.000
#> GSM97929 2 0.0000 1.000 0.000 1.000
#> GSM97933 1 0.0000 1.000 1.000 0.000
#> GSM97934 1 0.0000 1.000 1.000 0.000
#> GSM97944 2 0.0000 1.000 0.000 1.000
#> GSM97949 2 0.0000 1.000 0.000 1.000
#> GSM97956 1 0.0000 1.000 1.000 0.000
#> GSM97962 1 0.0000 1.000 1.000 0.000
#> GSM97964 1 0.0000 1.000 1.000 0.000
#> GSM97970 2 0.0000 1.000 0.000 1.000
#> GSM97822 1 0.0000 1.000 1.000 0.000
#> GSM97831 1 0.0000 1.000 1.000 0.000
#> GSM97845 1 0.0000 1.000 1.000 0.000
#> GSM97865 1 0.0000 1.000 1.000 0.000
#> GSM97867 1 0.0000 1.000 1.000 0.000
#> GSM97883 1 0.0000 1.000 1.000 0.000
#> GSM97897 1 0.0000 1.000 1.000 0.000
#> GSM97900 1 0.0000 1.000 1.000 0.000
#> GSM97904 1 0.0000 1.000 1.000 0.000
#> GSM97907 2 0.0000 1.000 0.000 1.000
#> GSM97925 1 0.0000 1.000 1.000 0.000
#> GSM97947 1 0.0000 1.000 1.000 0.000
cbind(get_classes(res, k = 3), get_membership(res, k = 3))
#> class entropy silhouette p1 p2 p3
#> GSM97800 2 0.0000 1.000 0.000 1.000 0.000
#> GSM97803 2 0.0000 1.000 0.000 1.000 0.000
#> GSM97804 2 0.0000 1.000 0.000 1.000 0.000
#> GSM97805 2 0.0000 1.000 0.000 1.000 0.000
#> GSM97807 2 0.0000 1.000 0.000 1.000 0.000
#> GSM97809 2 0.0000 1.000 0.000 1.000 0.000
#> GSM97811 2 0.0000 1.000 0.000 1.000 0.000
#> GSM97812 2 0.0000 1.000 0.000 1.000 0.000
#> GSM97816 3 0.0000 0.986 0.000 0.000 1.000
#> GSM97817 2 0.0000 1.000 0.000 1.000 0.000
#> GSM97820 2 0.0000 1.000 0.000 1.000 0.000
#> GSM97825 2 0.0000 1.000 0.000 1.000 0.000
#> GSM97827 2 0.0000 1.000 0.000 1.000 0.000
#> GSM97828 3 0.0000 0.986 0.000 0.000 1.000
#> GSM97833 2 0.0000 1.000 0.000 1.000 0.000
#> GSM97834 2 0.0000 1.000 0.000 1.000 0.000
#> GSM97840 2 0.0000 1.000 0.000 1.000 0.000
#> GSM97846 2 0.0000 1.000 0.000 1.000 0.000
#> GSM97848 2 0.0000 1.000 0.000 1.000 0.000
#> GSM97849 2 0.0000 1.000 0.000 1.000 0.000
#> GSM97850 2 0.0000 1.000 0.000 1.000 0.000
#> GSM97853 2 0.0000 1.000 0.000 1.000 0.000
#> GSM97855 2 0.0000 1.000 0.000 1.000 0.000
#> GSM97878 3 0.0000 0.986 0.000 0.000 1.000
#> GSM97913 3 0.0000 0.986 0.000 0.000 1.000
#> GSM97932 1 0.0000 0.998 1.000 0.000 0.000
#> GSM97939 3 0.0000 0.986 0.000 0.000 1.000
#> GSM97951 2 0.0000 1.000 0.000 1.000 0.000
#> GSM97957 3 0.0000 0.986 0.000 0.000 1.000
#> GSM97972 3 0.0000 0.986 0.000 0.000 1.000
#> GSM97793 3 0.0000 0.986 0.000 0.000 1.000
#> GSM97795 2 0.0000 1.000 0.000 1.000 0.000
#> GSM97802 3 0.0000 0.986 0.000 0.000 1.000
#> GSM97810 3 0.0000 0.986 0.000 0.000 1.000
#> GSM97815 3 0.0000 0.986 0.000 0.000 1.000
#> GSM97837 1 0.0000 0.998 1.000 0.000 0.000
#> GSM97843 3 0.0000 0.986 0.000 0.000 1.000
#> GSM97890 3 0.0000 0.986 0.000 0.000 1.000
#> GSM97899 1 0.0000 0.998 1.000 0.000 0.000
#> GSM97910 3 0.0000 0.986 0.000 0.000 1.000
#> GSM97916 3 0.2796 0.887 0.092 0.000 0.908
#> GSM97920 3 0.0000 0.986 0.000 0.000 1.000
#> GSM97921 1 0.0237 0.994 0.996 0.000 0.004
#> GSM97927 1 0.0000 0.998 1.000 0.000 0.000
#> GSM97937 1 0.0000 0.998 1.000 0.000 0.000
#> GSM97941 2 0.0000 1.000 0.000 1.000 0.000
#> GSM97943 3 0.0000 0.986 0.000 0.000 1.000
#> GSM97958 3 0.0000 0.986 0.000 0.000 1.000
#> GSM97960 2 0.0000 1.000 0.000 1.000 0.000
#> GSM97794 3 0.0000 0.986 0.000 0.000 1.000
#> GSM97796 1 0.0000 0.998 1.000 0.000 0.000
#> GSM97797 3 0.0000 0.986 0.000 0.000 1.000
#> GSM97798 1 0.0000 0.998 1.000 0.000 0.000
#> GSM97801 3 0.4121 0.792 0.168 0.000 0.832
#> GSM97806 1 0.0000 0.998 1.000 0.000 0.000
#> GSM97808 1 0.0000 0.998 1.000 0.000 0.000
#> GSM97813 1 0.0000 0.998 1.000 0.000 0.000
#> GSM97814 1 0.0000 0.998 1.000 0.000 0.000
#> GSM97818 3 0.0747 0.970 0.016 0.000 0.984
#> GSM97819 3 0.0000 0.986 0.000 0.000 1.000
#> GSM97821 3 0.0000 0.986 0.000 0.000 1.000
#> GSM97826 1 0.0000 0.998 1.000 0.000 0.000
#> GSM97829 1 0.0000 0.998 1.000 0.000 0.000
#> GSM97832 3 0.0000 0.986 0.000 0.000 1.000
#> GSM97836 1 0.2796 0.893 0.908 0.000 0.092
#> GSM97839 1 0.0000 0.998 1.000 0.000 0.000
#> GSM97844 2 0.0000 1.000 0.000 1.000 0.000
#> GSM97847 1 0.0000 0.998 1.000 0.000 0.000
#> GSM97851 1 0.0000 0.998 1.000 0.000 0.000
#> GSM97852 1 0.0000 0.998 1.000 0.000 0.000
#> GSM97856 1 0.0000 0.998 1.000 0.000 0.000
#> GSM97858 2 0.0000 1.000 0.000 1.000 0.000
#> GSM97859 1 0.0000 0.998 1.000 0.000 0.000
#> GSM97861 1 0.0000 0.998 1.000 0.000 0.000
#> GSM97863 1 0.0000 0.998 1.000 0.000 0.000
#> GSM97869 3 0.2796 0.887 0.092 0.000 0.908
#> GSM97870 1 0.0000 0.998 1.000 0.000 0.000
#> GSM97871 1 0.0000 0.998 1.000 0.000 0.000
#> GSM97877 3 0.0000 0.986 0.000 0.000 1.000
#> GSM97879 1 0.0000 0.998 1.000 0.000 0.000
#> GSM97882 1 0.0000 0.998 1.000 0.000 0.000
#> GSM97885 1 0.0000 0.998 1.000 0.000 0.000
#> GSM97886 1 0.0000 0.998 1.000 0.000 0.000
#> GSM97887 1 0.0000 0.998 1.000 0.000 0.000
#> GSM97888 1 0.0000 0.998 1.000 0.000 0.000
#> GSM97889 1 0.0000 0.998 1.000 0.000 0.000
#> GSM97891 1 0.0424 0.990 0.992 0.000 0.008
#> GSM97892 2 0.0000 1.000 0.000 1.000 0.000
#> GSM97893 1 0.0000 0.998 1.000 0.000 0.000
#> GSM97894 1 0.0000 0.998 1.000 0.000 0.000
#> GSM97895 1 0.0000 0.998 1.000 0.000 0.000
#> GSM97896 1 0.0000 0.998 1.000 0.000 0.000
#> GSM97898 1 0.0000 0.998 1.000 0.000 0.000
#> GSM97903 1 0.0237 0.994 0.996 0.000 0.004
#> GSM97905 1 0.0000 0.998 1.000 0.000 0.000
#> GSM97906 1 0.0000 0.998 1.000 0.000 0.000
#> GSM97908 1 0.0000 0.998 1.000 0.000 0.000
#> GSM97912 1 0.0000 0.998 1.000 0.000 0.000
#> GSM97914 1 0.0000 0.998 1.000 0.000 0.000
#> GSM97915 1 0.0000 0.998 1.000 0.000 0.000
#> GSM97917 1 0.0000 0.998 1.000 0.000 0.000
#> GSM97918 1 0.0000 0.998 1.000 0.000 0.000
#> GSM97919 1 0.0000 0.998 1.000 0.000 0.000
#> GSM97922 1 0.0000 0.998 1.000 0.000 0.000
#> GSM97924 2 0.0000 1.000 0.000 1.000 0.000
#> GSM97926 3 0.0000 0.986 0.000 0.000 1.000
#> GSM97930 1 0.0000 0.998 1.000 0.000 0.000
#> GSM97931 3 0.0000 0.986 0.000 0.000 1.000
#> GSM97935 1 0.0424 0.990 0.992 0.000 0.008
#> GSM97936 1 0.0000 0.998 1.000 0.000 0.000
#> GSM97938 1 0.0000 0.998 1.000 0.000 0.000
#> GSM97940 1 0.0000 0.998 1.000 0.000 0.000
#> GSM97942 3 0.0000 0.986 0.000 0.000 1.000
#> GSM97945 1 0.0000 0.998 1.000 0.000 0.000
#> GSM97946 2 0.0000 1.000 0.000 1.000 0.000
#> GSM97948 1 0.0000 0.998 1.000 0.000 0.000
#> GSM97950 1 0.0000 0.998 1.000 0.000 0.000
#> GSM97952 1 0.0000 0.998 1.000 0.000 0.000
#> GSM97953 1 0.0000 0.998 1.000 0.000 0.000
#> GSM97954 1 0.0000 0.998 1.000 0.000 0.000
#> GSM97955 1 0.0000 0.998 1.000 0.000 0.000
#> GSM97959 3 0.0000 0.986 0.000 0.000 1.000
#> GSM97961 1 0.0000 0.998 1.000 0.000 0.000
#> GSM97963 1 0.0000 0.998 1.000 0.000 0.000
#> GSM97965 1 0.0000 0.998 1.000 0.000 0.000
#> GSM97966 1 0.0000 0.998 1.000 0.000 0.000
#> GSM97967 2 0.0000 1.000 0.000 1.000 0.000
#> GSM97968 2 0.0000 1.000 0.000 1.000 0.000
#> GSM97969 1 0.0000 0.998 1.000 0.000 0.000
#> GSM97971 1 0.0000 0.998 1.000 0.000 0.000
#> GSM97799 3 0.0000 0.986 0.000 0.000 1.000
#> GSM97823 2 0.0000 1.000 0.000 1.000 0.000
#> GSM97824 3 0.0000 0.986 0.000 0.000 1.000
#> GSM97830 3 0.0000 0.986 0.000 0.000 1.000
#> GSM97835 3 0.0237 0.982 0.000 0.004 0.996
#> GSM97838 2 0.0000 1.000 0.000 1.000 0.000
#> GSM97841 2 0.0000 1.000 0.000 1.000 0.000
#> GSM97842 3 0.0000 0.986 0.000 0.000 1.000
#> GSM97854 2 0.0000 1.000 0.000 1.000 0.000
#> GSM97857 3 0.0000 0.986 0.000 0.000 1.000
#> GSM97860 3 0.0000 0.986 0.000 0.000 1.000
#> GSM97862 3 0.0000 0.986 0.000 0.000 1.000
#> GSM97864 2 0.0000 1.000 0.000 1.000 0.000
#> GSM97866 3 0.0000 0.986 0.000 0.000 1.000
#> GSM97868 3 0.0000 0.986 0.000 0.000 1.000
#> GSM97872 3 0.0000 0.986 0.000 0.000 1.000
#> GSM97873 3 0.0000 0.986 0.000 0.000 1.000
#> GSM97874 3 0.0000 0.986 0.000 0.000 1.000
#> GSM97875 3 0.0000 0.986 0.000 0.000 1.000
#> GSM97876 3 0.0000 0.986 0.000 0.000 1.000
#> GSM97880 3 0.0000 0.986 0.000 0.000 1.000
#> GSM97881 3 0.0000 0.986 0.000 0.000 1.000
#> GSM97884 3 0.0000 0.986 0.000 0.000 1.000
#> GSM97901 3 0.0000 0.986 0.000 0.000 1.000
#> GSM97902 3 0.0000 0.986 0.000 0.000 1.000
#> GSM97909 3 0.0000 0.986 0.000 0.000 1.000
#> GSM97911 3 0.0000 0.986 0.000 0.000 1.000
#> GSM97923 3 0.0000 0.986 0.000 0.000 1.000
#> GSM97928 1 0.0000 0.998 1.000 0.000 0.000
#> GSM97929 2 0.0000 1.000 0.000 1.000 0.000
#> GSM97933 3 0.0000 0.986 0.000 0.000 1.000
#> GSM97934 3 0.0000 0.986 0.000 0.000 1.000
#> GSM97944 3 0.0000 0.986 0.000 0.000 1.000
#> GSM97949 2 0.0000 1.000 0.000 1.000 0.000
#> GSM97956 3 0.0000 0.986 0.000 0.000 1.000
#> GSM97962 3 0.0000 0.986 0.000 0.000 1.000
#> GSM97964 3 0.0000 0.986 0.000 0.000 1.000
#> GSM97970 3 0.0000 0.986 0.000 0.000 1.000
#> GSM97822 1 0.0000 0.998 1.000 0.000 0.000
#> GSM97831 3 0.0000 0.986 0.000 0.000 1.000
#> GSM97845 1 0.0000 0.998 1.000 0.000 0.000
#> GSM97865 3 0.6215 0.259 0.428 0.000 0.572
#> GSM97867 3 0.1289 0.953 0.032 0.000 0.968
#> GSM97883 3 0.0000 0.986 0.000 0.000 1.000
#> GSM97897 1 0.0000 0.998 1.000 0.000 0.000
#> GSM97900 1 0.0000 0.998 1.000 0.000 0.000
#> GSM97904 1 0.0000 0.998 1.000 0.000 0.000
#> GSM97907 2 0.0000 1.000 0.000 1.000 0.000
#> GSM97925 3 0.0000 0.986 0.000 0.000 1.000
#> GSM97947 3 0.0000 0.986 0.000 0.000 1.000
cbind(get_classes(res, k = 4), get_membership(res, k = 4))
#> class entropy silhouette p1 p2 p3 p4
#> GSM97800 2 0.0000 0.9858 0.000 1.000 0.000 0.000
#> GSM97803 2 0.0000 0.9858 0.000 1.000 0.000 0.000
#> GSM97804 2 0.0000 0.9858 0.000 1.000 0.000 0.000
#> GSM97805 2 0.0000 0.9858 0.000 1.000 0.000 0.000
#> GSM97807 2 0.0000 0.9858 0.000 1.000 0.000 0.000
#> GSM97809 2 0.0000 0.9858 0.000 1.000 0.000 0.000
#> GSM97811 2 0.0000 0.9858 0.000 1.000 0.000 0.000
#> GSM97812 2 0.0000 0.9858 0.000 1.000 0.000 0.000
#> GSM97816 3 0.0336 0.7146 0.008 0.000 0.992 0.000
#> GSM97817 2 0.0000 0.9858 0.000 1.000 0.000 0.000
#> GSM97820 2 0.0000 0.9858 0.000 1.000 0.000 0.000
#> GSM97825 2 0.0000 0.9858 0.000 1.000 0.000 0.000
#> GSM97827 2 0.0000 0.9858 0.000 1.000 0.000 0.000
#> GSM97828 3 0.4697 0.7156 0.356 0.000 0.644 0.000
#> GSM97833 2 0.0000 0.9858 0.000 1.000 0.000 0.000
#> GSM97834 2 0.0000 0.9858 0.000 1.000 0.000 0.000
#> GSM97840 2 0.4040 0.7405 0.000 0.752 0.248 0.000
#> GSM97846 2 0.0000 0.9858 0.000 1.000 0.000 0.000
#> GSM97848 2 0.0000 0.9858 0.000 1.000 0.000 0.000
#> GSM97849 2 0.0000 0.9858 0.000 1.000 0.000 0.000
#> GSM97850 2 0.0000 0.9858 0.000 1.000 0.000 0.000
#> GSM97853 2 0.0000 0.9858 0.000 1.000 0.000 0.000
#> GSM97855 2 0.0000 0.9858 0.000 1.000 0.000 0.000
#> GSM97878 1 0.0188 0.6458 0.996 0.000 0.004 0.000
#> GSM97913 3 0.0817 0.7105 0.024 0.000 0.976 0.000
#> GSM97932 4 0.0188 0.9493 0.004 0.000 0.000 0.996
#> GSM97939 3 0.0336 0.7146 0.008 0.000 0.992 0.000
#> GSM97951 2 0.4040 0.7405 0.000 0.752 0.248 0.000
#> GSM97957 3 0.4996 0.6052 0.484 0.000 0.516 0.000
#> GSM97972 3 0.0336 0.7146 0.008 0.000 0.992 0.000
#> GSM97793 3 0.4996 0.6052 0.484 0.000 0.516 0.000
#> GSM97795 2 0.2011 0.9182 0.000 0.920 0.080 0.000
#> GSM97802 3 0.4790 0.6972 0.380 0.000 0.620 0.000
#> GSM97810 3 0.0336 0.7146 0.008 0.000 0.992 0.000
#> GSM97815 3 0.0336 0.7146 0.008 0.000 0.992 0.000
#> GSM97837 1 0.4564 0.6143 0.672 0.000 0.000 0.328
#> GSM97843 3 0.5000 0.5899 0.496 0.000 0.504 0.000
#> GSM97890 3 0.4356 0.7360 0.292 0.000 0.708 0.000
#> GSM97899 4 0.0000 0.9499 0.000 0.000 0.000 1.000
#> GSM97910 1 0.0188 0.6458 0.996 0.000 0.004 0.000
#> GSM97916 1 0.0657 0.6586 0.984 0.000 0.004 0.012
#> GSM97920 3 0.5000 0.5899 0.496 0.000 0.504 0.000
#> GSM97921 1 0.2345 0.7115 0.900 0.000 0.000 0.100
#> GSM97927 1 0.3837 0.7073 0.776 0.000 0.000 0.224
#> GSM97937 1 0.4817 0.5169 0.612 0.000 0.000 0.388
#> GSM97941 3 0.5296 -0.3133 0.008 0.496 0.496 0.000
#> GSM97943 1 0.0336 0.6416 0.992 0.000 0.008 0.000
#> GSM97958 3 0.1940 0.7244 0.076 0.000 0.924 0.000
#> GSM97960 3 0.5028 -0.0228 0.004 0.400 0.596 0.000
#> GSM97794 1 0.0336 0.6468 0.992 0.000 0.008 0.000
#> GSM97796 4 0.0188 0.9493 0.004 0.000 0.000 0.996
#> GSM97797 1 0.0336 0.6468 0.992 0.000 0.008 0.000
#> GSM97798 4 0.0000 0.9499 0.000 0.000 0.000 1.000
#> GSM97801 1 0.0000 0.6493 1.000 0.000 0.000 0.000
#> GSM97806 1 0.4103 0.6892 0.744 0.000 0.000 0.256
#> GSM97808 4 0.0000 0.9499 0.000 0.000 0.000 1.000
#> GSM97813 4 0.0000 0.9499 0.000 0.000 0.000 1.000
#> GSM97814 4 0.0000 0.9499 0.000 0.000 0.000 1.000
#> GSM97818 1 0.0524 0.6547 0.988 0.000 0.004 0.008
#> GSM97819 3 0.4996 0.6052 0.484 0.000 0.516 0.000
#> GSM97821 3 0.0336 0.7146 0.008 0.000 0.992 0.000
#> GSM97826 1 0.4697 0.5750 0.644 0.000 0.000 0.356
#> GSM97829 1 0.3311 0.7239 0.828 0.000 0.000 0.172
#> GSM97832 3 0.0336 0.7146 0.008 0.000 0.992 0.000
#> GSM97836 1 0.0921 0.6697 0.972 0.000 0.000 0.028
#> GSM97839 4 0.0188 0.9493 0.004 0.000 0.000 0.996
#> GSM97844 2 0.0000 0.9858 0.000 1.000 0.000 0.000
#> GSM97847 1 0.4790 0.5334 0.620 0.000 0.000 0.380
#> GSM97851 4 0.0188 0.9493 0.004 0.000 0.000 0.996
#> GSM97852 1 0.4967 0.3634 0.548 0.000 0.000 0.452
#> GSM97856 4 0.0000 0.9499 0.000 0.000 0.000 1.000
#> GSM97858 2 0.0000 0.9858 0.000 1.000 0.000 0.000
#> GSM97859 1 0.4522 0.6311 0.680 0.000 0.000 0.320
#> GSM97861 1 0.3219 0.7257 0.836 0.000 0.000 0.164
#> GSM97863 4 0.0188 0.9493 0.004 0.000 0.000 0.996
#> GSM97869 1 0.0657 0.6586 0.984 0.000 0.004 0.012
#> GSM97870 1 0.1022 0.6728 0.968 0.000 0.000 0.032
#> GSM97871 4 0.0000 0.9499 0.000 0.000 0.000 1.000
#> GSM97877 3 0.0336 0.7146 0.008 0.000 0.992 0.000
#> GSM97879 1 0.4776 0.5482 0.624 0.000 0.000 0.376
#> GSM97882 1 0.4431 0.6496 0.696 0.000 0.000 0.304
#> GSM97885 1 0.4431 0.6496 0.696 0.000 0.000 0.304
#> GSM97886 4 0.0000 0.9499 0.000 0.000 0.000 1.000
#> GSM97887 4 0.0000 0.9499 0.000 0.000 0.000 1.000
#> GSM97888 4 0.0000 0.9499 0.000 0.000 0.000 1.000
#> GSM97889 1 0.4564 0.6216 0.672 0.000 0.000 0.328
#> GSM97891 1 0.3649 0.7161 0.796 0.000 0.000 0.204
#> GSM97892 2 0.0000 0.9858 0.000 1.000 0.000 0.000
#> GSM97893 4 0.0188 0.9493 0.004 0.000 0.000 0.996
#> GSM97894 4 0.0000 0.9499 0.000 0.000 0.000 1.000
#> GSM97895 4 0.0188 0.9493 0.004 0.000 0.000 0.996
#> GSM97896 4 0.0000 0.9499 0.000 0.000 0.000 1.000
#> GSM97898 4 0.0188 0.9493 0.004 0.000 0.000 0.996
#> GSM97903 1 0.3569 0.7174 0.804 0.000 0.000 0.196
#> GSM97905 1 0.4585 0.6143 0.668 0.000 0.000 0.332
#> GSM97906 4 0.0000 0.9499 0.000 0.000 0.000 1.000
#> GSM97908 4 0.4996 -0.2006 0.484 0.000 0.000 0.516
#> GSM97912 1 0.5000 0.2425 0.504 0.000 0.000 0.496
#> GSM97914 1 0.3610 0.7161 0.800 0.000 0.000 0.200
#> GSM97915 4 0.0188 0.9493 0.004 0.000 0.000 0.996
#> GSM97917 4 0.0188 0.9493 0.004 0.000 0.000 0.996
#> GSM97918 4 0.0188 0.9493 0.004 0.000 0.000 0.996
#> GSM97919 4 0.0188 0.9493 0.004 0.000 0.000 0.996
#> GSM97922 4 0.0000 0.9499 0.000 0.000 0.000 1.000
#> GSM97924 2 0.0000 0.9858 0.000 1.000 0.000 0.000
#> GSM97926 3 0.4790 0.6973 0.380 0.000 0.620 0.000
#> GSM97930 1 0.4382 0.6537 0.704 0.000 0.000 0.296
#> GSM97931 3 0.0336 0.7146 0.008 0.000 0.992 0.000
#> GSM97935 1 0.3975 0.6995 0.760 0.000 0.000 0.240
#> GSM97936 4 0.0188 0.9493 0.004 0.000 0.000 0.996
#> GSM97938 4 0.4996 -0.2006 0.484 0.000 0.000 0.516
#> GSM97940 4 0.0000 0.9499 0.000 0.000 0.000 1.000
#> GSM97942 1 0.4855 -0.3872 0.600 0.000 0.400 0.000
#> GSM97945 4 0.0188 0.9465 0.004 0.000 0.000 0.996
#> GSM97946 2 0.0000 0.9858 0.000 1.000 0.000 0.000
#> GSM97948 1 0.1118 0.6756 0.964 0.000 0.000 0.036
#> GSM97950 4 0.0188 0.9493 0.004 0.000 0.000 0.996
#> GSM97952 4 0.0000 0.9499 0.000 0.000 0.000 1.000
#> GSM97953 1 0.4522 0.6248 0.680 0.000 0.000 0.320
#> GSM97954 1 0.4776 0.5413 0.624 0.000 0.000 0.376
#> GSM97955 4 0.0188 0.9493 0.004 0.000 0.000 0.996
#> GSM97959 1 0.4981 0.0855 0.536 0.000 0.464 0.000
#> GSM97961 4 0.0188 0.9493 0.004 0.000 0.000 0.996
#> GSM97963 4 0.0000 0.9499 0.000 0.000 0.000 1.000
#> GSM97965 4 0.0000 0.9499 0.000 0.000 0.000 1.000
#> GSM97966 4 0.0000 0.9499 0.000 0.000 0.000 1.000
#> GSM97967 2 0.0000 0.9858 0.000 1.000 0.000 0.000
#> GSM97968 2 0.0000 0.9858 0.000 1.000 0.000 0.000
#> GSM97969 1 0.4477 0.6394 0.688 0.000 0.000 0.312
#> GSM97971 1 0.5000 0.2425 0.504 0.000 0.000 0.496
#> GSM97799 3 0.0000 0.7156 0.000 0.000 1.000 0.000
#> GSM97823 2 0.0000 0.9858 0.000 1.000 0.000 0.000
#> GSM97824 3 0.4072 0.7435 0.252 0.000 0.748 0.000
#> GSM97830 3 0.4996 0.6052 0.484 0.000 0.516 0.000
#> GSM97835 3 0.0336 0.7146 0.008 0.000 0.992 0.000
#> GSM97838 2 0.0000 0.9858 0.000 1.000 0.000 0.000
#> GSM97841 2 0.0000 0.9858 0.000 1.000 0.000 0.000
#> GSM97842 3 0.0188 0.7152 0.004 0.000 0.996 0.000
#> GSM97854 2 0.0000 0.9858 0.000 1.000 0.000 0.000
#> GSM97857 3 0.4103 0.7429 0.256 0.000 0.744 0.000
#> GSM97860 3 0.5000 0.5899 0.496 0.000 0.504 0.000
#> GSM97862 3 0.4304 0.7380 0.284 0.000 0.716 0.000
#> GSM97864 2 0.0000 0.9858 0.000 1.000 0.000 0.000
#> GSM97866 3 0.4543 0.7250 0.324 0.000 0.676 0.000
#> GSM97868 3 0.4072 0.7435 0.252 0.000 0.748 0.000
#> GSM97872 1 0.0336 0.6444 0.992 0.000 0.008 0.000
#> GSM97873 3 0.0188 0.7152 0.004 0.000 0.996 0.000
#> GSM97874 3 0.5000 0.5899 0.496 0.000 0.504 0.000
#> GSM97875 3 0.4730 0.7053 0.364 0.000 0.636 0.000
#> GSM97876 3 0.4996 0.6052 0.484 0.000 0.516 0.000
#> GSM97880 3 0.5000 0.5830 0.500 0.000 0.500 0.000
#> GSM97881 3 0.4072 0.7435 0.252 0.000 0.748 0.000
#> GSM97884 3 0.0000 0.7156 0.000 0.000 1.000 0.000
#> GSM97901 3 0.4564 0.7235 0.328 0.000 0.672 0.000
#> GSM97902 1 0.4998 -0.5909 0.512 0.000 0.488 0.000
#> GSM97909 3 0.0336 0.7146 0.008 0.000 0.992 0.000
#> GSM97911 3 0.4040 0.7436 0.248 0.000 0.752 0.000
#> GSM97923 1 0.4999 -0.5854 0.508 0.000 0.492 0.000
#> GSM97928 1 0.2647 0.7194 0.880 0.000 0.000 0.120
#> GSM97929 2 0.0000 0.9858 0.000 1.000 0.000 0.000
#> GSM97933 3 0.5000 0.5899 0.496 0.000 0.504 0.000
#> GSM97934 3 0.5000 0.5899 0.496 0.000 0.504 0.000
#> GSM97944 3 0.0000 0.7156 0.000 0.000 1.000 0.000
#> GSM97949 2 0.0000 0.9858 0.000 1.000 0.000 0.000
#> GSM97956 3 0.4072 0.7435 0.252 0.000 0.748 0.000
#> GSM97962 3 0.4331 0.7370 0.288 0.000 0.712 0.000
#> GSM97964 3 0.4072 0.7435 0.252 0.000 0.748 0.000
#> GSM97970 3 0.0000 0.7156 0.000 0.000 1.000 0.000
#> GSM97822 1 0.4008 0.6971 0.756 0.000 0.000 0.244
#> GSM97831 3 0.4730 0.7053 0.364 0.000 0.636 0.000
#> GSM97845 4 0.4999 -0.2253 0.492 0.000 0.000 0.508
#> GSM97865 1 0.1211 0.6815 0.960 0.000 0.000 0.040
#> GSM97867 1 0.4843 -0.3771 0.604 0.000 0.396 0.000
#> GSM97883 1 0.0469 0.6426 0.988 0.000 0.012 0.000
#> GSM97897 4 0.0000 0.9499 0.000 0.000 0.000 1.000
#> GSM97900 4 0.0000 0.9499 0.000 0.000 0.000 1.000
#> GSM97904 1 0.1792 0.6941 0.932 0.000 0.000 0.068
#> GSM97907 2 0.0000 0.9858 0.000 1.000 0.000 0.000
#> GSM97925 3 0.5000 0.5899 0.496 0.000 0.504 0.000
#> GSM97947 3 0.5000 0.5899 0.496 0.000 0.504 0.000
cbind(get_classes(res, k = 5), get_membership(res, k = 5))
#> class entropy silhouette p1 p2 p3 p4 p5
#> GSM97800 2 0.0000 0.9900 0.000 1.000 0.000 0.000 0.000
#> GSM97803 2 0.0000 0.9900 0.000 1.000 0.000 0.000 0.000
#> GSM97804 2 0.0000 0.9900 0.000 1.000 0.000 0.000 0.000
#> GSM97805 2 0.0000 0.9900 0.000 1.000 0.000 0.000 0.000
#> GSM97807 2 0.0290 0.9902 0.008 0.992 0.000 0.000 0.000
#> GSM97809 2 0.0609 0.9872 0.020 0.980 0.000 0.000 0.000
#> GSM97811 2 0.0290 0.9902 0.008 0.992 0.000 0.000 0.000
#> GSM97812 2 0.0290 0.9902 0.008 0.992 0.000 0.000 0.000
#> GSM97816 5 0.3039 0.9293 0.000 0.000 0.192 0.000 0.808
#> GSM97817 2 0.0290 0.9902 0.008 0.992 0.000 0.000 0.000
#> GSM97820 2 0.0290 0.9902 0.008 0.992 0.000 0.000 0.000
#> GSM97825 2 0.0290 0.9902 0.008 0.992 0.000 0.000 0.000
#> GSM97827 2 0.0290 0.9902 0.008 0.992 0.000 0.000 0.000
#> GSM97828 3 0.0290 0.9474 0.000 0.000 0.992 0.000 0.008
#> GSM97833 2 0.0290 0.9902 0.008 0.992 0.000 0.000 0.000
#> GSM97834 2 0.0290 0.9902 0.008 0.992 0.000 0.000 0.000
#> GSM97840 5 0.3462 0.7278 0.012 0.196 0.000 0.000 0.792
#> GSM97846 2 0.0290 0.9902 0.008 0.992 0.000 0.000 0.000
#> GSM97848 2 0.0290 0.9902 0.008 0.992 0.000 0.000 0.000
#> GSM97849 2 0.0290 0.9902 0.008 0.992 0.000 0.000 0.000
#> GSM97850 2 0.0290 0.9880 0.008 0.992 0.000 0.000 0.000
#> GSM97853 2 0.0290 0.9902 0.008 0.992 0.000 0.000 0.000
#> GSM97855 2 0.0404 0.9865 0.012 0.988 0.000 0.000 0.000
#> GSM97878 1 0.2864 0.9037 0.864 0.000 0.024 0.000 0.112
#> GSM97913 5 0.2110 0.8288 0.016 0.000 0.072 0.000 0.912
#> GSM97932 4 0.1197 0.9622 0.000 0.000 0.000 0.952 0.048
#> GSM97939 5 0.3039 0.9293 0.000 0.000 0.192 0.000 0.808
#> GSM97951 5 0.3462 0.7278 0.012 0.196 0.000 0.000 0.792
#> GSM97957 3 0.0510 0.9508 0.016 0.000 0.984 0.000 0.000
#> GSM97972 5 0.3039 0.9293 0.000 0.000 0.192 0.000 0.808
#> GSM97793 3 0.0404 0.9511 0.012 0.000 0.988 0.000 0.000
#> GSM97795 2 0.2864 0.8312 0.012 0.852 0.000 0.000 0.136
#> GSM97802 3 0.0703 0.9389 0.024 0.000 0.976 0.000 0.000
#> GSM97810 5 0.3039 0.9293 0.000 0.000 0.192 0.000 0.808
#> GSM97815 5 0.3039 0.9293 0.000 0.000 0.192 0.000 0.808
#> GSM97837 1 0.2932 0.9131 0.864 0.000 0.004 0.020 0.112
#> GSM97843 3 0.0510 0.9508 0.016 0.000 0.984 0.000 0.000
#> GSM97890 3 0.0162 0.9481 0.000 0.000 0.996 0.000 0.004
#> GSM97899 4 0.0162 0.9730 0.004 0.000 0.000 0.996 0.000
#> GSM97910 1 0.3339 0.8909 0.840 0.000 0.048 0.000 0.112
#> GSM97916 1 0.2813 0.9048 0.868 0.000 0.024 0.000 0.108
#> GSM97920 3 0.0510 0.9508 0.016 0.000 0.984 0.000 0.000
#> GSM97921 1 0.2802 0.9108 0.876 0.000 0.016 0.008 0.100
#> GSM97927 1 0.0932 0.9177 0.972 0.000 0.004 0.020 0.004
#> GSM97937 1 0.2864 0.9127 0.864 0.000 0.000 0.024 0.112
#> GSM97941 5 0.3381 0.7618 0.000 0.176 0.016 0.000 0.808
#> GSM97943 3 0.5995 -0.0677 0.420 0.000 0.468 0.000 0.112
#> GSM97958 5 0.2813 0.9141 0.000 0.000 0.168 0.000 0.832
#> GSM97960 5 0.3798 0.8253 0.000 0.128 0.064 0.000 0.808
#> GSM97794 1 0.2864 0.9037 0.864 0.000 0.024 0.000 0.112
#> GSM97796 4 0.0703 0.9715 0.000 0.000 0.000 0.976 0.024
#> GSM97797 1 0.3192 0.8960 0.848 0.000 0.040 0.000 0.112
#> GSM97798 4 0.0162 0.9730 0.004 0.000 0.000 0.996 0.000
#> GSM97801 1 0.2915 0.9050 0.860 0.000 0.024 0.000 0.116
#> GSM97806 1 0.0932 0.9177 0.972 0.000 0.004 0.020 0.004
#> GSM97808 4 0.0162 0.9730 0.004 0.000 0.000 0.996 0.000
#> GSM97813 4 0.2286 0.8858 0.108 0.000 0.000 0.888 0.004
#> GSM97814 4 0.0162 0.9730 0.004 0.000 0.000 0.996 0.000
#> GSM97818 1 0.2864 0.9037 0.864 0.000 0.024 0.000 0.112
#> GSM97819 3 0.0510 0.9508 0.016 0.000 0.984 0.000 0.000
#> GSM97821 5 0.2929 0.9253 0.000 0.000 0.180 0.000 0.820
#> GSM97826 1 0.2813 0.9138 0.868 0.000 0.000 0.024 0.108
#> GSM97829 1 0.2959 0.9126 0.864 0.000 0.008 0.016 0.112
#> GSM97832 5 0.3039 0.9293 0.000 0.000 0.192 0.000 0.808
#> GSM97836 1 0.0865 0.9144 0.972 0.000 0.024 0.000 0.004
#> GSM97839 4 0.0703 0.9715 0.000 0.000 0.000 0.976 0.024
#> GSM97844 2 0.0000 0.9900 0.000 1.000 0.000 0.000 0.000
#> GSM97847 1 0.2915 0.9119 0.860 0.000 0.000 0.024 0.116
#> GSM97851 4 0.0703 0.9715 0.000 0.000 0.000 0.976 0.024
#> GSM97852 1 0.2278 0.9023 0.908 0.000 0.000 0.060 0.032
#> GSM97856 4 0.0162 0.9730 0.004 0.000 0.000 0.996 0.000
#> GSM97858 2 0.0404 0.9865 0.012 0.988 0.000 0.000 0.000
#> GSM97859 1 0.1211 0.9150 0.960 0.000 0.000 0.024 0.016
#> GSM97861 1 0.0968 0.9179 0.972 0.000 0.012 0.012 0.004
#> GSM97863 4 0.0703 0.9715 0.000 0.000 0.000 0.976 0.024
#> GSM97869 1 0.1403 0.9135 0.952 0.000 0.024 0.000 0.024
#> GSM97870 1 0.0992 0.9160 0.968 0.000 0.024 0.000 0.008
#> GSM97871 4 0.0162 0.9728 0.000 0.000 0.000 0.996 0.004
#> GSM97877 5 0.2852 0.9210 0.000 0.000 0.172 0.000 0.828
#> GSM97879 1 0.1741 0.9184 0.936 0.000 0.000 0.024 0.040
#> GSM97882 1 0.0865 0.9171 0.972 0.000 0.000 0.024 0.004
#> GSM97885 1 0.0865 0.9171 0.972 0.000 0.000 0.024 0.004
#> GSM97886 4 0.0566 0.9711 0.004 0.000 0.000 0.984 0.012
#> GSM97887 4 0.0451 0.9717 0.004 0.000 0.000 0.988 0.008
#> GSM97888 4 0.0579 0.9705 0.008 0.000 0.000 0.984 0.008
#> GSM97889 1 0.1403 0.9142 0.952 0.000 0.000 0.024 0.024
#> GSM97891 1 0.0932 0.9177 0.972 0.000 0.004 0.020 0.004
#> GSM97892 2 0.0000 0.9900 0.000 1.000 0.000 0.000 0.000
#> GSM97893 4 0.1270 0.9597 0.000 0.000 0.000 0.948 0.052
#> GSM97894 4 0.0162 0.9730 0.004 0.000 0.000 0.996 0.000
#> GSM97895 4 0.2077 0.9348 0.008 0.000 0.000 0.908 0.084
#> GSM97896 4 0.0451 0.9717 0.004 0.000 0.000 0.988 0.008
#> GSM97898 4 0.0703 0.9715 0.000 0.000 0.000 0.976 0.024
#> GSM97903 1 0.2395 0.9191 0.904 0.000 0.008 0.016 0.072
#> GSM97905 1 0.1377 0.9168 0.956 0.000 0.004 0.020 0.020
#> GSM97906 4 0.0162 0.9730 0.004 0.000 0.000 0.996 0.000
#> GSM97908 1 0.4312 0.8505 0.772 0.000 0.000 0.104 0.124
#> GSM97912 1 0.2773 0.8555 0.868 0.000 0.000 0.112 0.020
#> GSM97914 1 0.2692 0.9142 0.884 0.000 0.008 0.016 0.092
#> GSM97915 4 0.0703 0.9715 0.000 0.000 0.000 0.976 0.024
#> GSM97917 4 0.0794 0.9702 0.000 0.000 0.000 0.972 0.028
#> GSM97918 4 0.0703 0.9715 0.000 0.000 0.000 0.976 0.024
#> GSM97919 4 0.0703 0.9715 0.000 0.000 0.000 0.976 0.024
#> GSM97922 4 0.1197 0.9452 0.048 0.000 0.000 0.952 0.000
#> GSM97924 2 0.0404 0.9865 0.012 0.988 0.000 0.000 0.000
#> GSM97926 3 0.0000 0.9492 0.000 0.000 1.000 0.000 0.000
#> GSM97930 1 0.2864 0.9127 0.864 0.000 0.000 0.024 0.112
#> GSM97931 5 0.3039 0.9293 0.000 0.000 0.192 0.000 0.808
#> GSM97935 1 0.0932 0.9177 0.972 0.000 0.004 0.020 0.004
#> GSM97936 4 0.0703 0.9715 0.000 0.000 0.000 0.976 0.024
#> GSM97938 1 0.5450 0.7038 0.652 0.000 0.000 0.216 0.132
#> GSM97940 4 0.0162 0.9730 0.004 0.000 0.000 0.996 0.000
#> GSM97942 3 0.1205 0.9220 0.040 0.000 0.956 0.000 0.004
#> GSM97945 4 0.4141 0.6423 0.248 0.000 0.000 0.728 0.024
#> GSM97946 2 0.0404 0.9865 0.012 0.988 0.000 0.000 0.000
#> GSM97948 1 0.0865 0.9144 0.972 0.000 0.024 0.000 0.004
#> GSM97950 4 0.0880 0.9695 0.000 0.000 0.000 0.968 0.032
#> GSM97952 4 0.0162 0.9730 0.004 0.000 0.000 0.996 0.000
#> GSM97953 1 0.2880 0.9137 0.868 0.000 0.004 0.020 0.108
#> GSM97954 1 0.1818 0.9182 0.932 0.000 0.000 0.024 0.044
#> GSM97955 4 0.0703 0.9715 0.000 0.000 0.000 0.976 0.024
#> GSM97959 1 0.5178 0.2833 0.484 0.000 0.040 0.000 0.476
#> GSM97961 4 0.0609 0.9720 0.000 0.000 0.000 0.980 0.020
#> GSM97963 4 0.0162 0.9730 0.004 0.000 0.000 0.996 0.000
#> GSM97965 4 0.0324 0.9731 0.004 0.000 0.000 0.992 0.004
#> GSM97966 4 0.0162 0.9730 0.004 0.000 0.000 0.996 0.000
#> GSM97967 2 0.0290 0.9902 0.008 0.992 0.000 0.000 0.000
#> GSM97968 2 0.0404 0.9865 0.012 0.988 0.000 0.000 0.000
#> GSM97969 1 0.1579 0.9144 0.944 0.000 0.000 0.024 0.032
#> GSM97971 1 0.1648 0.9081 0.940 0.000 0.000 0.040 0.020
#> GSM97799 5 0.3661 0.8386 0.000 0.000 0.276 0.000 0.724
#> GSM97823 2 0.0290 0.9902 0.008 0.992 0.000 0.000 0.000
#> GSM97824 3 0.0162 0.9481 0.000 0.000 0.996 0.000 0.004
#> GSM97830 3 0.0404 0.9511 0.012 0.000 0.988 0.000 0.000
#> GSM97835 5 0.3039 0.9293 0.000 0.000 0.192 0.000 0.808
#> GSM97838 2 0.0404 0.9865 0.012 0.988 0.000 0.000 0.000
#> GSM97841 2 0.0404 0.9865 0.012 0.988 0.000 0.000 0.000
#> GSM97842 5 0.3039 0.9293 0.000 0.000 0.192 0.000 0.808
#> GSM97854 2 0.0000 0.9900 0.000 1.000 0.000 0.000 0.000
#> GSM97857 3 0.0703 0.9312 0.000 0.000 0.976 0.000 0.024
#> GSM97860 3 0.0510 0.9508 0.016 0.000 0.984 0.000 0.000
#> GSM97862 3 0.0162 0.9481 0.000 0.000 0.996 0.000 0.004
#> GSM97864 2 0.0290 0.9902 0.008 0.992 0.000 0.000 0.000
#> GSM97866 3 0.0162 0.9481 0.000 0.000 0.996 0.000 0.004
#> GSM97868 3 0.0162 0.9481 0.000 0.000 0.996 0.000 0.004
#> GSM97872 1 0.3506 0.8870 0.832 0.000 0.064 0.000 0.104
#> GSM97873 5 0.3039 0.9293 0.000 0.000 0.192 0.000 0.808
#> GSM97874 3 0.0510 0.9508 0.016 0.000 0.984 0.000 0.000
#> GSM97875 3 0.0324 0.9497 0.004 0.000 0.992 0.000 0.004
#> GSM97876 3 0.0404 0.9511 0.012 0.000 0.988 0.000 0.000
#> GSM97880 3 0.0510 0.9508 0.016 0.000 0.984 0.000 0.000
#> GSM97881 3 0.0162 0.9481 0.000 0.000 0.996 0.000 0.004
#> GSM97884 5 0.3039 0.9293 0.000 0.000 0.192 0.000 0.808
#> GSM97901 3 0.0162 0.9481 0.000 0.000 0.996 0.000 0.004
#> GSM97902 3 0.5303 0.5243 0.232 0.000 0.660 0.000 0.108
#> GSM97909 5 0.2929 0.9253 0.000 0.000 0.180 0.000 0.820
#> GSM97911 3 0.0290 0.9446 0.000 0.000 0.992 0.000 0.008
#> GSM97923 3 0.0510 0.9508 0.016 0.000 0.984 0.000 0.000
#> GSM97928 1 0.0968 0.9196 0.972 0.000 0.012 0.012 0.004
#> GSM97929 2 0.0000 0.9900 0.000 1.000 0.000 0.000 0.000
#> GSM97933 3 0.0510 0.9508 0.016 0.000 0.984 0.000 0.000
#> GSM97934 3 0.0510 0.9508 0.016 0.000 0.984 0.000 0.000
#> GSM97944 5 0.3661 0.8386 0.000 0.000 0.276 0.000 0.724
#> GSM97949 2 0.0000 0.9900 0.000 1.000 0.000 0.000 0.000
#> GSM97956 3 0.0162 0.9481 0.000 0.000 0.996 0.000 0.004
#> GSM97962 3 0.0162 0.9481 0.000 0.000 0.996 0.000 0.004
#> GSM97964 3 0.0162 0.9481 0.000 0.000 0.996 0.000 0.004
#> GSM97970 5 0.3039 0.9293 0.000 0.000 0.192 0.000 0.808
#> GSM97822 1 0.0932 0.9177 0.972 0.000 0.004 0.020 0.004
#> GSM97831 3 0.0324 0.9497 0.004 0.000 0.992 0.000 0.004
#> GSM97845 1 0.3521 0.8235 0.820 0.000 0.000 0.140 0.040
#> GSM97865 1 0.2720 0.9105 0.880 0.000 0.020 0.004 0.096
#> GSM97867 3 0.1251 0.9224 0.036 0.000 0.956 0.000 0.008
#> GSM97883 1 0.4276 0.3601 0.616 0.000 0.380 0.000 0.004
#> GSM97897 4 0.1478 0.9315 0.064 0.000 0.000 0.936 0.000
#> GSM97900 4 0.0451 0.9717 0.004 0.000 0.000 0.988 0.008
#> GSM97904 1 0.1310 0.9159 0.956 0.000 0.024 0.000 0.020
#> GSM97907 2 0.0404 0.9865 0.012 0.988 0.000 0.000 0.000
#> GSM97925 3 0.0703 0.9443 0.024 0.000 0.976 0.000 0.000
#> GSM97947 3 0.0510 0.9508 0.016 0.000 0.984 0.000 0.000
cbind(get_classes(res, k = 6), get_membership(res, k = 6))
#> class entropy silhouette p1 p2 p3 p4 p5 p6
#> GSM97800 2 0.0790 0.9454 0.000 0.968 0.000 0.000 0.000 0.032
#> GSM97803 2 0.0790 0.9454 0.000 0.968 0.000 0.000 0.000 0.032
#> GSM97804 2 0.0790 0.9454 0.000 0.968 0.000 0.000 0.000 0.032
#> GSM97805 2 0.0790 0.9454 0.000 0.968 0.000 0.000 0.000 0.032
#> GSM97807 2 0.0000 0.9473 0.000 1.000 0.000 0.000 0.000 0.000
#> GSM97809 2 0.2092 0.9016 0.000 0.876 0.000 0.000 0.000 0.124
#> GSM97811 2 0.0000 0.9473 0.000 1.000 0.000 0.000 0.000 0.000
#> GSM97812 2 0.0000 0.9473 0.000 1.000 0.000 0.000 0.000 0.000
#> GSM97816 5 0.3464 0.8649 0.000 0.000 0.084 0.000 0.808 0.108
#> GSM97817 2 0.0000 0.9473 0.000 1.000 0.000 0.000 0.000 0.000
#> GSM97820 2 0.0000 0.9473 0.000 1.000 0.000 0.000 0.000 0.000
#> GSM97825 2 0.0000 0.9473 0.000 1.000 0.000 0.000 0.000 0.000
#> GSM97827 2 0.0000 0.9473 0.000 1.000 0.000 0.000 0.000 0.000
#> GSM97828 3 0.2912 0.8379 0.000 0.000 0.784 0.000 0.000 0.216
#> GSM97833 2 0.0000 0.9473 0.000 1.000 0.000 0.000 0.000 0.000
#> GSM97834 2 0.0000 0.9473 0.000 1.000 0.000 0.000 0.000 0.000
#> GSM97840 5 0.3821 0.7483 0.000 0.080 0.000 0.000 0.772 0.148
#> GSM97846 2 0.0458 0.9450 0.000 0.984 0.000 0.000 0.000 0.016
#> GSM97848 2 0.0000 0.9473 0.000 1.000 0.000 0.000 0.000 0.000
#> GSM97849 2 0.0000 0.9473 0.000 1.000 0.000 0.000 0.000 0.000
#> GSM97850 2 0.1863 0.9165 0.000 0.896 0.000 0.000 0.000 0.104
#> GSM97853 2 0.0000 0.9473 0.000 1.000 0.000 0.000 0.000 0.000
#> GSM97855 2 0.2632 0.8824 0.000 0.832 0.000 0.000 0.004 0.164
#> GSM97878 6 0.3864 0.2330 0.480 0.000 0.000 0.000 0.000 0.520
#> GSM97913 5 0.3764 0.7091 0.008 0.000 0.012 0.000 0.724 0.256
#> GSM97932 4 0.2308 0.9148 0.000 0.000 0.000 0.892 0.040 0.068
#> GSM97939 5 0.1779 0.8942 0.000 0.000 0.064 0.000 0.920 0.016
#> GSM97951 5 0.3770 0.7517 0.000 0.076 0.000 0.000 0.776 0.148
#> GSM97957 3 0.2135 0.9031 0.000 0.000 0.872 0.000 0.000 0.128
#> GSM97972 5 0.2179 0.8931 0.000 0.000 0.064 0.000 0.900 0.036
#> GSM97793 3 0.1863 0.9076 0.000 0.000 0.896 0.000 0.000 0.104
#> GSM97795 2 0.5643 0.3126 0.000 0.496 0.000 0.000 0.340 0.164
#> GSM97802 3 0.3301 0.8110 0.100 0.000 0.828 0.000 0.004 0.068
#> GSM97810 5 0.1471 0.8936 0.000 0.000 0.064 0.000 0.932 0.004
#> GSM97815 5 0.1327 0.8941 0.000 0.000 0.064 0.000 0.936 0.000
#> GSM97837 1 0.3298 0.4418 0.756 0.000 0.000 0.000 0.008 0.236
#> GSM97843 3 0.1863 0.9076 0.000 0.000 0.896 0.000 0.000 0.104
#> GSM97890 3 0.1588 0.8884 0.000 0.000 0.924 0.000 0.004 0.072
#> GSM97899 4 0.0000 0.9367 0.000 0.000 0.000 1.000 0.000 0.000
#> GSM97910 6 0.4476 0.4283 0.308 0.000 0.052 0.000 0.000 0.640
#> GSM97916 1 0.3747 0.0688 0.604 0.000 0.000 0.000 0.000 0.396
#> GSM97920 3 0.2135 0.9031 0.000 0.000 0.872 0.000 0.000 0.128
#> GSM97921 1 0.3804 0.1261 0.576 0.000 0.000 0.000 0.000 0.424
#> GSM97927 1 0.2632 0.5588 0.832 0.000 0.000 0.000 0.004 0.164
#> GSM97937 1 0.3133 0.4885 0.780 0.000 0.000 0.000 0.008 0.212
#> GSM97941 5 0.2179 0.8372 0.000 0.064 0.000 0.000 0.900 0.036
#> GSM97943 6 0.5428 0.3903 0.176 0.000 0.252 0.000 0.000 0.572
#> GSM97958 5 0.3848 0.7866 0.000 0.000 0.040 0.000 0.736 0.224
#> GSM97960 5 0.2123 0.8531 0.000 0.052 0.012 0.000 0.912 0.024
#> GSM97794 6 0.3860 0.2743 0.472 0.000 0.000 0.000 0.000 0.528
#> GSM97796 4 0.1528 0.9308 0.000 0.000 0.000 0.936 0.016 0.048
#> GSM97797 6 0.3966 0.3190 0.444 0.000 0.004 0.000 0.000 0.552
#> GSM97798 4 0.0000 0.9367 0.000 0.000 0.000 1.000 0.000 0.000
#> GSM97801 1 0.3782 -0.0212 0.588 0.000 0.000 0.000 0.000 0.412
#> GSM97806 1 0.2527 0.5571 0.832 0.000 0.000 0.000 0.000 0.168
#> GSM97808 4 0.0000 0.9367 0.000 0.000 0.000 1.000 0.000 0.000
#> GSM97813 4 0.3975 0.4518 0.392 0.000 0.000 0.600 0.008 0.000
#> GSM97814 4 0.0000 0.9367 0.000 0.000 0.000 1.000 0.000 0.000
#> GSM97818 6 0.3867 0.2122 0.488 0.000 0.000 0.000 0.000 0.512
#> GSM97819 3 0.0692 0.9031 0.000 0.000 0.976 0.000 0.004 0.020
#> GSM97821 5 0.1719 0.8916 0.000 0.000 0.060 0.000 0.924 0.016
#> GSM97826 1 0.3043 0.4967 0.792 0.000 0.000 0.000 0.008 0.200
#> GSM97829 1 0.3101 0.4351 0.756 0.000 0.000 0.000 0.000 0.244
#> GSM97832 5 0.1327 0.8941 0.000 0.000 0.064 0.000 0.936 0.000
#> GSM97836 1 0.2527 0.5571 0.832 0.000 0.000 0.000 0.000 0.168
#> GSM97839 4 0.1528 0.9308 0.000 0.000 0.000 0.936 0.016 0.048
#> GSM97844 2 0.0790 0.9454 0.000 0.968 0.000 0.000 0.000 0.032
#> GSM97847 1 0.3509 0.4649 0.744 0.000 0.000 0.000 0.016 0.240
#> GSM97851 4 0.1528 0.9308 0.000 0.000 0.000 0.936 0.016 0.048
#> GSM97852 1 0.3380 0.5291 0.832 0.000 0.000 0.056 0.016 0.096
#> GSM97856 4 0.0000 0.9367 0.000 0.000 0.000 1.000 0.000 0.000
#> GSM97858 2 0.2300 0.8973 0.000 0.856 0.000 0.000 0.000 0.144
#> GSM97859 1 0.0405 0.6115 0.988 0.000 0.000 0.000 0.008 0.004
#> GSM97861 1 0.2527 0.5571 0.832 0.000 0.000 0.000 0.000 0.168
#> GSM97863 4 0.1528 0.9308 0.000 0.000 0.000 0.936 0.016 0.048
#> GSM97869 1 0.3221 0.3898 0.736 0.000 0.000 0.000 0.000 0.264
#> GSM97870 1 0.0777 0.6123 0.972 0.000 0.000 0.000 0.004 0.024
#> GSM97871 4 0.0000 0.9367 0.000 0.000 0.000 1.000 0.000 0.000
#> GSM97877 5 0.1856 0.8854 0.000 0.000 0.048 0.000 0.920 0.032
#> GSM97879 1 0.2489 0.5710 0.860 0.000 0.000 0.000 0.012 0.128
#> GSM97882 1 0.2632 0.5588 0.832 0.000 0.000 0.000 0.004 0.164
#> GSM97885 1 0.2632 0.5588 0.832 0.000 0.000 0.000 0.004 0.164
#> GSM97886 4 0.0993 0.9288 0.000 0.000 0.000 0.964 0.024 0.012
#> GSM97887 4 0.0363 0.9350 0.000 0.000 0.000 0.988 0.012 0.000
#> GSM97888 4 0.0622 0.9324 0.008 0.000 0.000 0.980 0.012 0.000
#> GSM97889 1 0.0508 0.6106 0.984 0.000 0.000 0.000 0.012 0.004
#> GSM97891 1 0.2562 0.5524 0.828 0.000 0.000 0.000 0.000 0.172
#> GSM97892 2 0.0790 0.9454 0.000 0.968 0.000 0.000 0.000 0.032
#> GSM97893 4 0.3329 0.8765 0.072 0.000 0.000 0.844 0.032 0.052
#> GSM97894 4 0.0000 0.9367 0.000 0.000 0.000 1.000 0.000 0.000
#> GSM97895 4 0.5043 0.7428 0.124 0.000 0.000 0.708 0.048 0.120
#> GSM97896 4 0.0363 0.9350 0.000 0.000 0.000 0.988 0.012 0.000
#> GSM97898 4 0.1528 0.9308 0.000 0.000 0.000 0.936 0.016 0.048
#> GSM97903 1 0.3607 0.3632 0.652 0.000 0.000 0.000 0.000 0.348
#> GSM97905 1 0.0405 0.6118 0.988 0.000 0.000 0.000 0.004 0.008
#> GSM97906 4 0.0000 0.9367 0.000 0.000 0.000 1.000 0.000 0.000
#> GSM97908 1 0.4334 0.4254 0.708 0.000 0.000 0.028 0.024 0.240
#> GSM97912 1 0.1124 0.5871 0.956 0.000 0.000 0.036 0.008 0.000
#> GSM97914 1 0.3706 0.2950 0.620 0.000 0.000 0.000 0.000 0.380
#> GSM97915 4 0.1528 0.9308 0.000 0.000 0.000 0.936 0.016 0.048
#> GSM97917 4 0.1765 0.9273 0.000 0.000 0.000 0.924 0.024 0.052
#> GSM97918 4 0.1528 0.9308 0.000 0.000 0.000 0.936 0.016 0.048
#> GSM97919 4 0.1528 0.9308 0.000 0.000 0.000 0.936 0.016 0.048
#> GSM97922 4 0.1866 0.8800 0.084 0.000 0.000 0.908 0.008 0.000
#> GSM97924 2 0.2416 0.8983 0.000 0.844 0.000 0.000 0.000 0.156
#> GSM97926 3 0.1588 0.8884 0.000 0.000 0.924 0.000 0.004 0.072
#> GSM97930 1 0.3725 0.4077 0.676 0.000 0.000 0.000 0.008 0.316
#> GSM97931 5 0.2179 0.8931 0.000 0.000 0.064 0.000 0.900 0.036
#> GSM97935 1 0.2562 0.5524 0.828 0.000 0.000 0.000 0.000 0.172
#> GSM97936 4 0.2313 0.9166 0.036 0.000 0.000 0.904 0.016 0.044
#> GSM97938 1 0.5229 0.2994 0.636 0.000 0.000 0.096 0.020 0.248
#> GSM97940 4 0.0000 0.9367 0.000 0.000 0.000 1.000 0.000 0.000
#> GSM97942 3 0.2266 0.9008 0.012 0.000 0.880 0.000 0.000 0.108
#> GSM97945 4 0.4766 0.3513 0.400 0.000 0.000 0.552 0.004 0.044
#> GSM97946 2 0.2260 0.8993 0.000 0.860 0.000 0.000 0.000 0.140
#> GSM97948 1 0.1588 0.6055 0.924 0.000 0.000 0.000 0.004 0.072
#> GSM97950 4 0.1765 0.9273 0.000 0.000 0.000 0.924 0.024 0.052
#> GSM97952 4 0.0000 0.9367 0.000 0.000 0.000 1.000 0.000 0.000
#> GSM97953 1 0.3133 0.4885 0.780 0.000 0.000 0.000 0.008 0.212
#> GSM97954 1 0.2531 0.5699 0.856 0.000 0.000 0.000 0.012 0.132
#> GSM97955 4 0.2231 0.9196 0.028 0.000 0.000 0.908 0.016 0.048
#> GSM97959 6 0.5899 0.3251 0.252 0.000 0.000 0.000 0.276 0.472
#> GSM97961 4 0.1434 0.9315 0.000 0.000 0.000 0.940 0.012 0.048
#> GSM97963 4 0.0000 0.9367 0.000 0.000 0.000 1.000 0.000 0.000
#> GSM97965 4 0.0000 0.9367 0.000 0.000 0.000 1.000 0.000 0.000
#> GSM97966 4 0.0000 0.9367 0.000 0.000 0.000 1.000 0.000 0.000
#> GSM97967 2 0.0458 0.9450 0.000 0.984 0.000 0.000 0.000 0.016
#> GSM97968 2 0.2632 0.8824 0.000 0.832 0.000 0.000 0.004 0.164
#> GSM97969 1 0.2230 0.5918 0.892 0.000 0.000 0.000 0.024 0.084
#> GSM97971 1 0.0520 0.6119 0.984 0.000 0.000 0.000 0.008 0.008
#> GSM97799 5 0.4377 0.7406 0.000 0.000 0.244 0.000 0.688 0.068
#> GSM97823 2 0.0000 0.9473 0.000 1.000 0.000 0.000 0.000 0.000
#> GSM97824 3 0.2112 0.8805 0.000 0.000 0.896 0.000 0.016 0.088
#> GSM97830 3 0.2135 0.9031 0.000 0.000 0.872 0.000 0.000 0.128
#> GSM97835 5 0.1327 0.8941 0.000 0.000 0.064 0.000 0.936 0.000
#> GSM97838 2 0.2300 0.8973 0.000 0.856 0.000 0.000 0.000 0.144
#> GSM97841 2 0.2260 0.8993 0.000 0.860 0.000 0.000 0.000 0.140
#> GSM97842 5 0.3700 0.8379 0.000 0.000 0.152 0.000 0.780 0.068
#> GSM97854 2 0.0790 0.9454 0.000 0.968 0.000 0.000 0.000 0.032
#> GSM97857 3 0.2672 0.8562 0.000 0.000 0.868 0.000 0.052 0.080
#> GSM97860 3 0.1863 0.9076 0.000 0.000 0.896 0.000 0.000 0.104
#> GSM97862 3 0.1643 0.8894 0.000 0.000 0.924 0.000 0.008 0.068
#> GSM97864 2 0.0458 0.9450 0.000 0.984 0.000 0.000 0.000 0.016
#> GSM97866 3 0.1196 0.8984 0.000 0.000 0.952 0.000 0.008 0.040
#> GSM97868 3 0.1625 0.8910 0.000 0.000 0.928 0.000 0.012 0.060
#> GSM97872 1 0.5492 -0.2863 0.472 0.000 0.128 0.000 0.000 0.400
#> GSM97873 5 0.2030 0.8924 0.000 0.000 0.064 0.000 0.908 0.028
#> GSM97874 3 0.2092 0.9030 0.000 0.000 0.876 0.000 0.000 0.124
#> GSM97875 3 0.0692 0.9031 0.000 0.000 0.976 0.000 0.004 0.020
#> GSM97876 3 0.1814 0.9084 0.000 0.000 0.900 0.000 0.000 0.100
#> GSM97880 3 0.1863 0.9076 0.000 0.000 0.896 0.000 0.000 0.104
#> GSM97881 3 0.1858 0.8839 0.000 0.000 0.912 0.000 0.012 0.076
#> GSM97884 5 0.3700 0.8379 0.000 0.000 0.152 0.000 0.780 0.068
#> GSM97901 3 0.1082 0.8993 0.000 0.000 0.956 0.000 0.004 0.040
#> GSM97902 6 0.4657 0.3911 0.100 0.000 0.228 0.000 0.000 0.672
#> GSM97909 5 0.1807 0.8911 0.000 0.000 0.060 0.000 0.920 0.020
#> GSM97911 3 0.1858 0.8839 0.000 0.000 0.912 0.000 0.012 0.076
#> GSM97923 3 0.2006 0.9065 0.004 0.000 0.892 0.000 0.000 0.104
#> GSM97928 1 0.1387 0.6124 0.932 0.000 0.000 0.000 0.000 0.068
#> GSM97929 2 0.0790 0.9454 0.000 0.968 0.000 0.000 0.000 0.032
#> GSM97933 3 0.1863 0.9076 0.000 0.000 0.896 0.000 0.000 0.104
#> GSM97934 3 0.2135 0.9031 0.000 0.000 0.872 0.000 0.000 0.128
#> GSM97944 5 0.4377 0.7406 0.000 0.000 0.244 0.000 0.688 0.068
#> GSM97949 2 0.0458 0.9463 0.000 0.984 0.000 0.000 0.000 0.016
#> GSM97956 3 0.1757 0.8861 0.000 0.000 0.916 0.000 0.008 0.076
#> GSM97962 3 0.2416 0.9062 0.000 0.000 0.844 0.000 0.000 0.156
#> GSM97964 3 0.1858 0.8839 0.000 0.000 0.912 0.000 0.012 0.076
#> GSM97970 5 0.3736 0.8352 0.000 0.000 0.156 0.000 0.776 0.068
#> GSM97822 1 0.2632 0.5588 0.832 0.000 0.000 0.000 0.004 0.164
#> GSM97831 3 0.1556 0.9113 0.000 0.000 0.920 0.000 0.000 0.080
#> GSM97845 1 0.3630 0.4653 0.816 0.000 0.000 0.100 0.020 0.064
#> GSM97865 1 0.3860 -0.1344 0.528 0.000 0.000 0.000 0.000 0.472
#> GSM97867 3 0.2480 0.8964 0.024 0.000 0.872 0.000 0.000 0.104
#> GSM97883 1 0.5556 -0.1350 0.504 0.000 0.348 0.000 0.000 0.148
#> GSM97897 4 0.2302 0.8447 0.120 0.000 0.000 0.872 0.008 0.000
#> GSM97900 4 0.0363 0.9350 0.000 0.000 0.000 0.988 0.012 0.000
#> GSM97904 1 0.0405 0.6132 0.988 0.000 0.000 0.000 0.004 0.008
#> GSM97907 2 0.2454 0.8962 0.000 0.840 0.000 0.000 0.000 0.160
#> GSM97925 3 0.2118 0.9061 0.008 0.000 0.888 0.000 0.000 0.104
#> GSM97947 3 0.0951 0.9023 0.008 0.000 0.968 0.000 0.004 0.020
Heatmaps for the consensus matrix. It visualizes the probability of two samples to be in a same group.
consensus_heatmap(res, k = 2)
consensus_heatmap(res, k = 3)
consensus_heatmap(res, k = 4)
consensus_heatmap(res, k = 5)
consensus_heatmap(res, k = 6)
Heatmaps for the membership of samples in all partitions to see how consistent they are:
membership_heatmap(res, k = 2)
membership_heatmap(res, k = 3)
membership_heatmap(res, k = 4)
membership_heatmap(res, k = 5)
membership_heatmap(res, k = 6)
As soon as we have had the classes for columns, we can look for signatures which are significantly different between classes which can be candidate marks for certain classes. Following are the heatmaps for signatures.
Signature heatmaps where rows are scaled:
get_signatures(res, k = 2)
get_signatures(res, k = 3)
get_signatures(res, k = 4)
get_signatures(res, k = 5)
get_signatures(res, k = 6)
Signature heatmaps where rows are not scaled:
get_signatures(res, k = 2, scale_rows = FALSE)
get_signatures(res, k = 3, scale_rows = FALSE)
get_signatures(res, k = 4, scale_rows = FALSE)
get_signatures(res, k = 5, scale_rows = FALSE)
get_signatures(res, k = 6, scale_rows = FALSE)
Compare the overlap of signatures from different k:
compare_signatures(res)
get_signature() returns a data frame invisibly. TO get the list of signatures, the function
call should be assigned to a variable explicitly. In following code, if plot argument is set
to FALSE, no heatmap is plotted while only the differential analysis is performed.
# code only for demonstration
tb = get_signature(res, k = ..., plot = FALSE)
An example of the output of tb is:
#> which_row fdr mean_1 mean_2 scaled_mean_1 scaled_mean_2 km
#> 1 38 0.042760348 8.373488 9.131774 -0.5533452 0.5164555 1
#> 2 40 0.018707592 7.106213 8.469186 -0.6173731 0.5762149 1
#> 3 55 0.019134737 10.221463 11.207825 -0.6159697 0.5749050 1
#> 4 59 0.006059896 5.921854 7.869574 -0.6899429 0.6439467 1
#> 5 60 0.018055526 8.928898 10.211722 -0.6204761 0.5791110 1
#> 6 98 0.009384629 15.714769 14.887706 0.6635654 -0.6193277 2
...
The columns in tb are:
which_row: row indices corresponding to the input matrix.fdr: FDR for the differential test. mean_x: The mean value in group x.scaled_mean_x: The mean value in group x after rows are scaled.km: Row groups if k-means clustering is applied to rows.UMAP plot which shows how samples are separated.
dimension_reduction(res, k = 2, method = "UMAP")
dimension_reduction(res, k = 3, method = "UMAP")
dimension_reduction(res, k = 4, method = "UMAP")
dimension_reduction(res, k = 5, method = "UMAP")
dimension_reduction(res, k = 6, method = "UMAP")
Following heatmap shows how subgroups are split when increasing k:
collect_classes(res)
Test correlation between subgroups and known annotations. If the known annotation is numeric, one-way ANOVA test is applied, and if the known annotation is discrete, chi-squared contingency table test is applied.
test_to_known_factors(res)
#> n disease.state(p) tissue(p) k
#> ATC:kmeans 180 4.69e-12 7.98e-13 2
#> ATC:kmeans 179 5.26e-27 3.12e-28 3
#> ATC:kmeans 167 2.05e-25 1.69e-27 4
#> ATC:kmeans 177 1.37e-27 6.76e-27 5
#> ATC:kmeans 150 4.36e-25 3.47e-23 6
If matrix rows can be associated to genes, consider to use functional_enrichment(res,
...) to perform function enrichment for the signature genes. See this vignette for more detailed explanations.
The object with results only for a single top-value method and a single partition method can be extracted as:
res = res_list["ATC", "skmeans"]
# you can also extract it by
# res = res_list["ATC:skmeans"]
A summary of res and all the functions that can be applied to it:
res
#> A 'ConsensusPartition' object with k = 2, 3, 4, 5, 6.
#> On a matrix with 51882 rows and 180 columns.
#> Top rows (1000, 2000, 3000, 4000, 5000) are extracted by 'ATC' method.
#> Subgroups are detected by 'skmeans' method.
#> Performed in total 1250 partitions by row resampling.
#> Best k for subgroups seems to be 5.
#>
#> Following methods can be applied to this 'ConsensusPartition' object:
#> [1] "cola_report" "collect_classes" "collect_plots"
#> [4] "collect_stats" "colnames" "compare_signatures"
#> [7] "consensus_heatmap" "dimension_reduction" "functional_enrichment"
#> [10] "get_anno_col" "get_anno" "get_classes"
#> [13] "get_consensus" "get_matrix" "get_membership"
#> [16] "get_param" "get_signatures" "get_stats"
#> [19] "is_best_k" "is_stable_k" "membership_heatmap"
#> [22] "ncol" "nrow" "plot_ecdf"
#> [25] "rownames" "select_partition_number" "show"
#> [28] "suggest_best_k" "test_to_known_factors"
collect_plots() function collects all the plots made from res for all k (number of partitions)
into one single page to provide an easy and fast comparison between different k.
collect_plots(res)
The plots are:
k and the heatmap of
predicted classes for each k.k.k.k.All the plots in panels can be made by individual functions and they are plotted later in this section.
select_partition_number() produces several plots showing different
statistics for choosing “optimized” k. There are following statistics:
k;k, the area increased is defined as \(A_k - A_{k-1}\).The detailed explanations of these statistics can be found in the cola vignette.
Generally speaking, lower PAC score, higher mean silhouette score or higher
concordance corresponds to better partition. Rand index and Jaccard index
measure how similar the current partition is compared to partition with k-1.
If they are too similar, we won't accept k is better than k-1.
select_partition_number(res)
The numeric values for all these statistics can be obtained by get_stats().
get_stats(res)
#> k 1-PAC mean_silhouette concordance area_increased Rand Jaccard
#> 2 2 0.988 0.965 0.986 0.4901 0.511 0.511
#> 3 3 1.000 0.974 0.990 0.2844 0.825 0.669
#> 4 4 0.897 0.875 0.919 0.0780 0.948 0.863
#> 5 5 0.901 0.866 0.943 0.0702 0.939 0.820
#> 6 6 0.843 0.757 0.888 0.0379 0.943 0.808
suggest_best_k() suggests the best \(k\) based on these statistics. The rules are as follows:
suggest_best_k(res)
#> [1] 5
#> attr(,"optional")
#> [1] 2 3
There is also optional best \(k\) = 2 3 that is worth to check.
Following shows the table of the partitions (You need to click the show/hide
code output link to see it). The membership matrix (columns with name p*)
is inferred by
clue::cl_consensus()
function with the SE method. Basically the value in the membership matrix
represents the probability to belong to a certain group. The finall class
label for an item is determined with the group with highest probability it
belongs to.
In get_classes() function, the entropy is calculated from the membership
matrix and the silhouette score is calculated from the consensus matrix.
cbind(get_classes(res, k = 2), get_membership(res, k = 2))
#> class entropy silhouette p1 p2
#> GSM97800 2 0.000 0.986 0.000 1.000
#> GSM97803 2 0.000 0.986 0.000 1.000
#> GSM97804 2 0.000 0.986 0.000 1.000
#> GSM97805 2 0.000 0.986 0.000 1.000
#> GSM97807 2 0.000 0.986 0.000 1.000
#> GSM97809 2 0.000 0.986 0.000 1.000
#> GSM97811 2 0.000 0.986 0.000 1.000
#> GSM97812 2 0.000 0.986 0.000 1.000
#> GSM97816 2 0.000 0.986 0.000 1.000
#> GSM97817 2 0.000 0.986 0.000 1.000
#> GSM97820 2 0.000 0.986 0.000 1.000
#> GSM97825 2 0.000 0.986 0.000 1.000
#> GSM97827 2 0.000 0.986 0.000 1.000
#> GSM97828 2 0.000 0.986 0.000 1.000
#> GSM97833 2 0.000 0.986 0.000 1.000
#> GSM97834 2 0.000 0.986 0.000 1.000
#> GSM97840 2 0.000 0.986 0.000 1.000
#> GSM97846 2 0.000 0.986 0.000 1.000
#> GSM97848 2 0.000 0.986 0.000 1.000
#> GSM97849 2 0.000 0.986 0.000 1.000
#> GSM97850 2 0.000 0.986 0.000 1.000
#> GSM97853 2 0.000 0.986 0.000 1.000
#> GSM97855 2 0.000 0.986 0.000 1.000
#> GSM97878 1 0.000 0.985 1.000 0.000
#> GSM97913 2 0.000 0.986 0.000 1.000
#> GSM97932 1 0.000 0.985 1.000 0.000
#> GSM97939 2 0.000 0.986 0.000 1.000
#> GSM97951 2 0.000 0.986 0.000 1.000
#> GSM97957 1 0.680 0.777 0.820 0.180
#> GSM97972 2 0.000 0.986 0.000 1.000
#> GSM97793 1 0.971 0.336 0.600 0.400
#> GSM97795 2 0.000 0.986 0.000 1.000
#> GSM97802 1 0.689 0.771 0.816 0.184
#> GSM97810 2 0.000 0.986 0.000 1.000
#> GSM97815 2 0.000 0.986 0.000 1.000
#> GSM97837 1 0.000 0.985 1.000 0.000
#> GSM97843 1 0.000 0.985 1.000 0.000
#> GSM97890 2 0.000 0.986 0.000 1.000
#> GSM97899 1 0.000 0.985 1.000 0.000
#> GSM97910 1 0.000 0.985 1.000 0.000
#> GSM97916 1 0.000 0.985 1.000 0.000
#> GSM97920 1 0.000 0.985 1.000 0.000
#> GSM97921 1 0.000 0.985 1.000 0.000
#> GSM97927 1 0.000 0.985 1.000 0.000
#> GSM97937 1 0.000 0.985 1.000 0.000
#> GSM97941 2 0.000 0.986 0.000 1.000
#> GSM97943 1 0.000 0.985 1.000 0.000
#> GSM97958 2 0.000 0.986 0.000 1.000
#> GSM97960 2 0.000 0.986 0.000 1.000
#> GSM97794 1 0.000 0.985 1.000 0.000
#> GSM97796 1 0.000 0.985 1.000 0.000
#> GSM97797 1 0.000 0.985 1.000 0.000
#> GSM97798 1 0.000 0.985 1.000 0.000
#> GSM97801 1 0.000 0.985 1.000 0.000
#> GSM97806 1 0.000 0.985 1.000 0.000
#> GSM97808 1 0.000 0.985 1.000 0.000
#> GSM97813 1 0.000 0.985 1.000 0.000
#> GSM97814 1 0.000 0.985 1.000 0.000
#> GSM97818 1 0.000 0.985 1.000 0.000
#> GSM97819 1 0.000 0.985 1.000 0.000
#> GSM97821 2 0.000 0.986 0.000 1.000
#> GSM97826 1 0.000 0.985 1.000 0.000
#> GSM97829 1 0.000 0.985 1.000 0.000
#> GSM97832 2 0.000 0.986 0.000 1.000
#> GSM97836 1 0.000 0.985 1.000 0.000
#> GSM97839 1 0.000 0.985 1.000 0.000
#> GSM97844 2 0.000 0.986 0.000 1.000
#> GSM97847 1 0.000 0.985 1.000 0.000
#> GSM97851 1 0.000 0.985 1.000 0.000
#> GSM97852 1 0.000 0.985 1.000 0.000
#> GSM97856 1 0.000 0.985 1.000 0.000
#> GSM97858 2 0.000 0.986 0.000 1.000
#> GSM97859 1 0.000 0.985 1.000 0.000
#> GSM97861 1 0.000 0.985 1.000 0.000
#> GSM97863 1 0.000 0.985 1.000 0.000
#> GSM97869 1 0.000 0.985 1.000 0.000
#> GSM97870 1 0.000 0.985 1.000 0.000
#> GSM97871 1 0.000 0.985 1.000 0.000
#> GSM97877 2 0.000 0.986 0.000 1.000
#> GSM97879 1 0.000 0.985 1.000 0.000
#> GSM97882 1 0.000 0.985 1.000 0.000
#> GSM97885 1 0.000 0.985 1.000 0.000
#> GSM97886 1 0.000 0.985 1.000 0.000
#> GSM97887 1 0.000 0.985 1.000 0.000
#> GSM97888 1 0.000 0.985 1.000 0.000
#> GSM97889 1 0.000 0.985 1.000 0.000
#> GSM97891 1 0.000 0.985 1.000 0.000
#> GSM97892 2 0.000 0.986 0.000 1.000
#> GSM97893 1 0.000 0.985 1.000 0.000
#> GSM97894 1 0.000 0.985 1.000 0.000
#> GSM97895 1 0.000 0.985 1.000 0.000
#> GSM97896 1 0.000 0.985 1.000 0.000
#> GSM97898 1 0.000 0.985 1.000 0.000
#> GSM97903 1 0.000 0.985 1.000 0.000
#> GSM97905 1 0.000 0.985 1.000 0.000
#> GSM97906 1 0.000 0.985 1.000 0.000
#> GSM97908 1 0.000 0.985 1.000 0.000
#> GSM97912 1 0.000 0.985 1.000 0.000
#> GSM97914 1 0.000 0.985 1.000 0.000
#> GSM97915 1 0.000 0.985 1.000 0.000
#> GSM97917 1 0.000 0.985 1.000 0.000
#> GSM97918 1 0.000 0.985 1.000 0.000
#> GSM97919 1 0.000 0.985 1.000 0.000
#> GSM97922 1 0.000 0.985 1.000 0.000
#> GSM97924 2 0.000 0.986 0.000 1.000
#> GSM97926 1 0.605 0.821 0.852 0.148
#> GSM97930 1 0.000 0.985 1.000 0.000
#> GSM97931 2 0.000 0.986 0.000 1.000
#> GSM97935 1 0.000 0.985 1.000 0.000
#> GSM97936 1 0.000 0.985 1.000 0.000
#> GSM97938 1 0.000 0.985 1.000 0.000
#> GSM97940 1 0.000 0.985 1.000 0.000
#> GSM97942 1 0.000 0.985 1.000 0.000
#> GSM97945 1 0.000 0.985 1.000 0.000
#> GSM97946 2 0.000 0.986 0.000 1.000
#> GSM97948 1 0.000 0.985 1.000 0.000
#> GSM97950 1 0.000 0.985 1.000 0.000
#> GSM97952 1 0.000 0.985 1.000 0.000
#> GSM97953 1 0.000 0.985 1.000 0.000
#> GSM97954 1 0.000 0.985 1.000 0.000
#> GSM97955 1 0.000 0.985 1.000 0.000
#> GSM97959 2 0.971 0.329 0.400 0.600
#> GSM97961 1 0.000 0.985 1.000 0.000
#> GSM97963 1 0.000 0.985 1.000 0.000
#> GSM97965 1 0.000 0.985 1.000 0.000
#> GSM97966 1 0.000 0.985 1.000 0.000
#> GSM97967 2 0.000 0.986 0.000 1.000
#> GSM97968 2 0.000 0.986 0.000 1.000
#> GSM97969 1 0.000 0.985 1.000 0.000
#> GSM97971 1 0.000 0.985 1.000 0.000
#> GSM97799 2 0.000 0.986 0.000 1.000
#> GSM97823 2 0.000 0.986 0.000 1.000
#> GSM97824 2 0.000 0.986 0.000 1.000
#> GSM97830 1 0.971 0.336 0.600 0.400
#> GSM97835 2 0.000 0.986 0.000 1.000
#> GSM97838 2 0.000 0.986 0.000 1.000
#> GSM97841 2 0.000 0.986 0.000 1.000
#> GSM97842 2 0.000 0.986 0.000 1.000
#> GSM97854 2 0.000 0.986 0.000 1.000
#> GSM97857 2 0.000 0.986 0.000 1.000
#> GSM97860 1 0.000 0.985 1.000 0.000
#> GSM97862 2 0.000 0.986 0.000 1.000
#> GSM97864 2 0.000 0.986 0.000 1.000
#> GSM97866 2 0.000 0.986 0.000 1.000
#> GSM97868 2 0.000 0.986 0.000 1.000
#> GSM97872 1 0.000 0.985 1.000 0.000
#> GSM97873 2 0.000 0.986 0.000 1.000
#> GSM97874 1 0.000 0.985 1.000 0.000
#> GSM97875 2 0.745 0.730 0.212 0.788
#> GSM97876 1 0.788 0.691 0.764 0.236
#> GSM97880 1 0.000 0.985 1.000 0.000
#> GSM97881 2 0.000 0.986 0.000 1.000
#> GSM97884 2 0.000 0.986 0.000 1.000
#> GSM97901 2 0.714 0.754 0.196 0.804
#> GSM97902 1 0.000 0.985 1.000 0.000
#> GSM97909 2 0.000 0.986 0.000 1.000
#> GSM97911 2 0.000 0.986 0.000 1.000
#> GSM97923 1 0.000 0.985 1.000 0.000
#> GSM97928 1 0.000 0.985 1.000 0.000
#> GSM97929 2 0.000 0.986 0.000 1.000
#> GSM97933 1 0.000 0.985 1.000 0.000
#> GSM97934 1 0.000 0.985 1.000 0.000
#> GSM97944 2 0.000 0.986 0.000 1.000
#> GSM97949 2 0.000 0.986 0.000 1.000
#> GSM97956 2 0.000 0.986 0.000 1.000
#> GSM97962 2 0.000 0.986 0.000 1.000
#> GSM97964 2 0.000 0.986 0.000 1.000
#> GSM97970 2 0.000 0.986 0.000 1.000
#> GSM97822 1 0.000 0.985 1.000 0.000
#> GSM97831 2 0.722 0.748 0.200 0.800
#> GSM97845 1 0.000 0.985 1.000 0.000
#> GSM97865 1 0.000 0.985 1.000 0.000
#> GSM97867 1 0.000 0.985 1.000 0.000
#> GSM97883 1 0.000 0.985 1.000 0.000
#> GSM97897 1 0.000 0.985 1.000 0.000
#> GSM97900 1 0.000 0.985 1.000 0.000
#> GSM97904 1 0.000 0.985 1.000 0.000
#> GSM97907 2 0.000 0.986 0.000 1.000
#> GSM97925 1 0.000 0.985 1.000 0.000
#> GSM97947 1 0.000 0.985 1.000 0.000
cbind(get_classes(res, k = 3), get_membership(res, k = 3))
#> class entropy silhouette p1 p2 p3
#> GSM97800 2 0.0000 0.971 0.000 1.000 0.000
#> GSM97803 2 0.0000 0.971 0.000 1.000 0.000
#> GSM97804 2 0.0000 0.971 0.000 1.000 0.000
#> GSM97805 2 0.0000 0.971 0.000 1.000 0.000
#> GSM97807 2 0.0000 0.971 0.000 1.000 0.000
#> GSM97809 2 0.0000 0.971 0.000 1.000 0.000
#> GSM97811 2 0.0000 0.971 0.000 1.000 0.000
#> GSM97812 2 0.0000 0.971 0.000 1.000 0.000
#> GSM97816 2 0.0000 0.971 0.000 1.000 0.000
#> GSM97817 2 0.0000 0.971 0.000 1.000 0.000
#> GSM97820 2 0.0000 0.971 0.000 1.000 0.000
#> GSM97825 2 0.0000 0.971 0.000 1.000 0.000
#> GSM97827 2 0.0000 0.971 0.000 1.000 0.000
#> GSM97828 3 0.0000 0.996 0.000 0.000 1.000
#> GSM97833 2 0.0000 0.971 0.000 1.000 0.000
#> GSM97834 2 0.0000 0.971 0.000 1.000 0.000
#> GSM97840 2 0.0000 0.971 0.000 1.000 0.000
#> GSM97846 2 0.0000 0.971 0.000 1.000 0.000
#> GSM97848 2 0.0000 0.971 0.000 1.000 0.000
#> GSM97849 2 0.0000 0.971 0.000 1.000 0.000
#> GSM97850 2 0.0000 0.971 0.000 1.000 0.000
#> GSM97853 2 0.0000 0.971 0.000 1.000 0.000
#> GSM97855 2 0.0000 0.971 0.000 1.000 0.000
#> GSM97878 1 0.0000 1.000 1.000 0.000 0.000
#> GSM97913 2 0.0000 0.971 0.000 1.000 0.000
#> GSM97932 1 0.0000 1.000 1.000 0.000 0.000
#> GSM97939 2 0.0000 0.971 0.000 1.000 0.000
#> GSM97951 2 0.0000 0.971 0.000 1.000 0.000
#> GSM97957 3 0.0000 0.996 0.000 0.000 1.000
#> GSM97972 2 0.0000 0.971 0.000 1.000 0.000
#> GSM97793 3 0.0000 0.996 0.000 0.000 1.000
#> GSM97795 2 0.0000 0.971 0.000 1.000 0.000
#> GSM97802 3 0.0000 0.996 0.000 0.000 1.000
#> GSM97810 2 0.0000 0.971 0.000 1.000 0.000
#> GSM97815 2 0.0000 0.971 0.000 1.000 0.000
#> GSM97837 1 0.0000 1.000 1.000 0.000 0.000
#> GSM97843 3 0.0000 0.996 0.000 0.000 1.000
#> GSM97890 3 0.0000 0.996 0.000 0.000 1.000
#> GSM97899 1 0.0000 1.000 1.000 0.000 0.000
#> GSM97910 1 0.0000 1.000 1.000 0.000 0.000
#> GSM97916 1 0.0000 1.000 1.000 0.000 0.000
#> GSM97920 3 0.0000 0.996 0.000 0.000 1.000
#> GSM97921 1 0.0000 1.000 1.000 0.000 0.000
#> GSM97927 1 0.0000 1.000 1.000 0.000 0.000
#> GSM97937 1 0.0000 1.000 1.000 0.000 0.000
#> GSM97941 2 0.0000 0.971 0.000 1.000 0.000
#> GSM97943 1 0.0000 1.000 1.000 0.000 0.000
#> GSM97958 2 0.0000 0.971 0.000 1.000 0.000
#> GSM97960 2 0.0000 0.971 0.000 1.000 0.000
#> GSM97794 1 0.0000 1.000 1.000 0.000 0.000
#> GSM97796 1 0.0000 1.000 1.000 0.000 0.000
#> GSM97797 1 0.0000 1.000 1.000 0.000 0.000
#> GSM97798 1 0.0000 1.000 1.000 0.000 0.000
#> GSM97801 1 0.0000 1.000 1.000 0.000 0.000
#> GSM97806 1 0.0000 1.000 1.000 0.000 0.000
#> GSM97808 1 0.0000 1.000 1.000 0.000 0.000
#> GSM97813 1 0.0000 1.000 1.000 0.000 0.000
#> GSM97814 1 0.0000 1.000 1.000 0.000 0.000
#> GSM97818 1 0.0000 1.000 1.000 0.000 0.000
#> GSM97819 3 0.0000 0.996 0.000 0.000 1.000
#> GSM97821 2 0.0000 0.971 0.000 1.000 0.000
#> GSM97826 1 0.0000 1.000 1.000 0.000 0.000
#> GSM97829 1 0.0000 1.000 1.000 0.000 0.000
#> GSM97832 2 0.0000 0.971 0.000 1.000 0.000
#> GSM97836 1 0.0000 1.000 1.000 0.000 0.000
#> GSM97839 1 0.0000 1.000 1.000 0.000 0.000
#> GSM97844 2 0.0000 0.971 0.000 1.000 0.000
#> GSM97847 1 0.0000 1.000 1.000 0.000 0.000
#> GSM97851 1 0.0000 1.000 1.000 0.000 0.000
#> GSM97852 1 0.0000 1.000 1.000 0.000 0.000
#> GSM97856 1 0.0000 1.000 1.000 0.000 0.000
#> GSM97858 2 0.0000 0.971 0.000 1.000 0.000
#> GSM97859 1 0.0000 1.000 1.000 0.000 0.000
#> GSM97861 1 0.0000 1.000 1.000 0.000 0.000
#> GSM97863 1 0.0000 1.000 1.000 0.000 0.000
#> GSM97869 1 0.0000 1.000 1.000 0.000 0.000
#> GSM97870 1 0.0000 1.000 1.000 0.000 0.000
#> GSM97871 1 0.0000 1.000 1.000 0.000 0.000
#> GSM97877 2 0.0000 0.971 0.000 1.000 0.000
#> GSM97879 1 0.0000 1.000 1.000 0.000 0.000
#> GSM97882 1 0.0000 1.000 1.000 0.000 0.000
#> GSM97885 1 0.0000 1.000 1.000 0.000 0.000
#> GSM97886 1 0.0000 1.000 1.000 0.000 0.000
#> GSM97887 1 0.0000 1.000 1.000 0.000 0.000
#> GSM97888 1 0.0000 1.000 1.000 0.000 0.000
#> GSM97889 1 0.0000 1.000 1.000 0.000 0.000
#> GSM97891 1 0.0000 1.000 1.000 0.000 0.000
#> GSM97892 2 0.0000 0.971 0.000 1.000 0.000
#> GSM97893 1 0.0000 1.000 1.000 0.000 0.000
#> GSM97894 1 0.0000 1.000 1.000 0.000 0.000
#> GSM97895 1 0.0000 1.000 1.000 0.000 0.000
#> GSM97896 1 0.0000 1.000 1.000 0.000 0.000
#> GSM97898 1 0.0000 1.000 1.000 0.000 0.000
#> GSM97903 1 0.0000 1.000 1.000 0.000 0.000
#> GSM97905 1 0.0000 1.000 1.000 0.000 0.000
#> GSM97906 1 0.0000 1.000 1.000 0.000 0.000
#> GSM97908 1 0.0000 1.000 1.000 0.000 0.000
#> GSM97912 1 0.0000 1.000 1.000 0.000 0.000
#> GSM97914 1 0.0000 1.000 1.000 0.000 0.000
#> GSM97915 1 0.0000 1.000 1.000 0.000 0.000
#> GSM97917 1 0.0000 1.000 1.000 0.000 0.000
#> GSM97918 1 0.0000 1.000 1.000 0.000 0.000
#> GSM97919 1 0.0000 1.000 1.000 0.000 0.000
#> GSM97922 1 0.0000 1.000 1.000 0.000 0.000
#> GSM97924 2 0.0000 0.971 0.000 1.000 0.000
#> GSM97926 3 0.0000 0.996 0.000 0.000 1.000
#> GSM97930 1 0.0000 1.000 1.000 0.000 0.000
#> GSM97931 2 0.0000 0.971 0.000 1.000 0.000
#> GSM97935 1 0.0000 1.000 1.000 0.000 0.000
#> GSM97936 1 0.0000 1.000 1.000 0.000 0.000
#> GSM97938 1 0.0000 1.000 1.000 0.000 0.000
#> GSM97940 1 0.0000 1.000 1.000 0.000 0.000
#> GSM97942 3 0.3038 0.874 0.104 0.000 0.896
#> GSM97945 1 0.0000 1.000 1.000 0.000 0.000
#> GSM97946 2 0.0000 0.971 0.000 1.000 0.000
#> GSM97948 1 0.0000 1.000 1.000 0.000 0.000
#> GSM97950 1 0.0000 1.000 1.000 0.000 0.000
#> GSM97952 1 0.0000 1.000 1.000 0.000 0.000
#> GSM97953 1 0.0000 1.000 1.000 0.000 0.000
#> GSM97954 1 0.0000 1.000 1.000 0.000 0.000
#> GSM97955 1 0.0000 1.000 1.000 0.000 0.000
#> GSM97959 2 0.6168 0.309 0.412 0.588 0.000
#> GSM97961 1 0.0000 1.000 1.000 0.000 0.000
#> GSM97963 1 0.0000 1.000 1.000 0.000 0.000
#> GSM97965 1 0.0000 1.000 1.000 0.000 0.000
#> GSM97966 1 0.0000 1.000 1.000 0.000 0.000
#> GSM97967 2 0.0000 0.971 0.000 1.000 0.000
#> GSM97968 2 0.0000 0.971 0.000 1.000 0.000
#> GSM97969 1 0.0000 1.000 1.000 0.000 0.000
#> GSM97971 1 0.0000 1.000 1.000 0.000 0.000
#> GSM97799 2 0.6126 0.355 0.000 0.600 0.400
#> GSM97823 2 0.0000 0.971 0.000 1.000 0.000
#> GSM97824 3 0.0000 0.996 0.000 0.000 1.000
#> GSM97830 3 0.0000 0.996 0.000 0.000 1.000
#> GSM97835 2 0.0000 0.971 0.000 1.000 0.000
#> GSM97838 2 0.0000 0.971 0.000 1.000 0.000
#> GSM97841 2 0.0000 0.971 0.000 1.000 0.000
#> GSM97842 2 0.0000 0.971 0.000 1.000 0.000
#> GSM97854 2 0.0000 0.971 0.000 1.000 0.000
#> GSM97857 3 0.0592 0.984 0.000 0.012 0.988
#> GSM97860 3 0.0000 0.996 0.000 0.000 1.000
#> GSM97862 3 0.0000 0.996 0.000 0.000 1.000
#> GSM97864 2 0.0000 0.971 0.000 1.000 0.000
#> GSM97866 3 0.0000 0.996 0.000 0.000 1.000
#> GSM97868 3 0.0000 0.996 0.000 0.000 1.000
#> GSM97872 1 0.0000 1.000 1.000 0.000 0.000
#> GSM97873 2 0.0000 0.971 0.000 1.000 0.000
#> GSM97874 3 0.0000 0.996 0.000 0.000 1.000
#> GSM97875 3 0.0000 0.996 0.000 0.000 1.000
#> GSM97876 3 0.0000 0.996 0.000 0.000 1.000
#> GSM97880 3 0.0000 0.996 0.000 0.000 1.000
#> GSM97881 3 0.0000 0.996 0.000 0.000 1.000
#> GSM97884 2 0.0000 0.971 0.000 1.000 0.000
#> GSM97901 3 0.0000 0.996 0.000 0.000 1.000
#> GSM97902 1 0.0000 1.000 1.000 0.000 0.000
#> GSM97909 2 0.0000 0.971 0.000 1.000 0.000
#> GSM97911 3 0.0000 0.996 0.000 0.000 1.000
#> GSM97923 3 0.0000 0.996 0.000 0.000 1.000
#> GSM97928 1 0.0000 1.000 1.000 0.000 0.000
#> GSM97929 2 0.0000 0.971 0.000 1.000 0.000
#> GSM97933 3 0.0000 0.996 0.000 0.000 1.000
#> GSM97934 3 0.0000 0.996 0.000 0.000 1.000
#> GSM97944 2 0.6126 0.355 0.000 0.600 0.400
#> GSM97949 2 0.0000 0.971 0.000 1.000 0.000
#> GSM97956 3 0.0000 0.996 0.000 0.000 1.000
#> GSM97962 3 0.0000 0.996 0.000 0.000 1.000
#> GSM97964 3 0.0000 0.996 0.000 0.000 1.000
#> GSM97970 2 0.6126 0.355 0.000 0.600 0.400
#> GSM97822 1 0.0000 1.000 1.000 0.000 0.000
#> GSM97831 3 0.0000 0.996 0.000 0.000 1.000
#> GSM97845 1 0.0000 1.000 1.000 0.000 0.000
#> GSM97865 1 0.0000 1.000 1.000 0.000 0.000
#> GSM97867 3 0.0000 0.996 0.000 0.000 1.000
#> GSM97883 1 0.1289 0.967 0.968 0.000 0.032
#> GSM97897 1 0.0000 1.000 1.000 0.000 0.000
#> GSM97900 1 0.0000 1.000 1.000 0.000 0.000
#> GSM97904 1 0.0000 1.000 1.000 0.000 0.000
#> GSM97907 2 0.0000 0.971 0.000 1.000 0.000
#> GSM97925 3 0.0237 0.992 0.004 0.000 0.996
#> GSM97947 3 0.0000 0.996 0.000 0.000 1.000
cbind(get_classes(res, k = 4), get_membership(res, k = 4))
#> class entropy silhouette p1 p2 p3 p4
#> GSM97800 2 0.0000 0.9868 0.000 1.000 0.000 0.000
#> GSM97803 2 0.0000 0.9868 0.000 1.000 0.000 0.000
#> GSM97804 2 0.0000 0.9868 0.000 1.000 0.000 0.000
#> GSM97805 2 0.0000 0.9868 0.000 1.000 0.000 0.000
#> GSM97807 2 0.0000 0.9868 0.000 1.000 0.000 0.000
#> GSM97809 2 0.0000 0.9868 0.000 1.000 0.000 0.000
#> GSM97811 2 0.0000 0.9868 0.000 1.000 0.000 0.000
#> GSM97812 2 0.0000 0.9868 0.000 1.000 0.000 0.000
#> GSM97816 2 0.0000 0.9868 0.000 1.000 0.000 0.000
#> GSM97817 2 0.0000 0.9868 0.000 1.000 0.000 0.000
#> GSM97820 2 0.0000 0.9868 0.000 1.000 0.000 0.000
#> GSM97825 2 0.0000 0.9868 0.000 1.000 0.000 0.000
#> GSM97827 2 0.0000 0.9868 0.000 1.000 0.000 0.000
#> GSM97828 3 0.3444 0.6363 0.000 0.000 0.816 0.184
#> GSM97833 2 0.0000 0.9868 0.000 1.000 0.000 0.000
#> GSM97834 2 0.0000 0.9868 0.000 1.000 0.000 0.000
#> GSM97840 2 0.0000 0.9868 0.000 1.000 0.000 0.000
#> GSM97846 2 0.0000 0.9868 0.000 1.000 0.000 0.000
#> GSM97848 2 0.0000 0.9868 0.000 1.000 0.000 0.000
#> GSM97849 2 0.0000 0.9868 0.000 1.000 0.000 0.000
#> GSM97850 2 0.0000 0.9868 0.000 1.000 0.000 0.000
#> GSM97853 2 0.0000 0.9868 0.000 1.000 0.000 0.000
#> GSM97855 2 0.0000 0.9868 0.000 1.000 0.000 0.000
#> GSM97878 1 0.4643 0.6572 0.656 0.000 0.000 0.344
#> GSM97913 2 0.3569 0.7695 0.000 0.804 0.000 0.196
#> GSM97932 1 0.0000 0.9474 1.000 0.000 0.000 0.000
#> GSM97939 2 0.0000 0.9868 0.000 1.000 0.000 0.000
#> GSM97951 2 0.0000 0.9868 0.000 1.000 0.000 0.000
#> GSM97957 3 0.0000 0.8161 0.000 0.000 1.000 0.000
#> GSM97972 2 0.0000 0.9868 0.000 1.000 0.000 0.000
#> GSM97793 3 0.0000 0.8161 0.000 0.000 1.000 0.000
#> GSM97795 2 0.0000 0.9868 0.000 1.000 0.000 0.000
#> GSM97802 4 0.4917 0.8411 0.008 0.000 0.336 0.656
#> GSM97810 2 0.0000 0.9868 0.000 1.000 0.000 0.000
#> GSM97815 2 0.0000 0.9868 0.000 1.000 0.000 0.000
#> GSM97837 1 0.3873 0.7819 0.772 0.000 0.000 0.228
#> GSM97843 3 0.0000 0.8161 0.000 0.000 1.000 0.000
#> GSM97890 4 0.4643 0.8521 0.000 0.000 0.344 0.656
#> GSM97899 1 0.0000 0.9474 1.000 0.000 0.000 0.000
#> GSM97910 1 0.7846 0.0387 0.392 0.000 0.272 0.336
#> GSM97916 1 0.3024 0.8618 0.852 0.000 0.000 0.148
#> GSM97920 3 0.0000 0.8161 0.000 0.000 1.000 0.000
#> GSM97921 1 0.2921 0.8671 0.860 0.000 0.000 0.140
#> GSM97927 1 0.0000 0.9474 1.000 0.000 0.000 0.000
#> GSM97937 1 0.2011 0.9051 0.920 0.000 0.000 0.080
#> GSM97941 2 0.0000 0.9868 0.000 1.000 0.000 0.000
#> GSM97943 3 0.5193 0.4878 0.020 0.000 0.656 0.324
#> GSM97958 2 0.0000 0.9868 0.000 1.000 0.000 0.000
#> GSM97960 2 0.0000 0.9868 0.000 1.000 0.000 0.000
#> GSM97794 1 0.4643 0.6572 0.656 0.000 0.000 0.344
#> GSM97796 1 0.0000 0.9474 1.000 0.000 0.000 0.000
#> GSM97797 1 0.4643 0.6572 0.656 0.000 0.000 0.344
#> GSM97798 1 0.0000 0.9474 1.000 0.000 0.000 0.000
#> GSM97801 1 0.4564 0.6732 0.672 0.000 0.000 0.328
#> GSM97806 1 0.0469 0.9420 0.988 0.000 0.000 0.012
#> GSM97808 1 0.0000 0.9474 1.000 0.000 0.000 0.000
#> GSM97813 1 0.0000 0.9474 1.000 0.000 0.000 0.000
#> GSM97814 1 0.0000 0.9474 1.000 0.000 0.000 0.000
#> GSM97818 1 0.4643 0.6572 0.656 0.000 0.000 0.344
#> GSM97819 3 0.4989 -0.5048 0.000 0.000 0.528 0.472
#> GSM97821 2 0.0000 0.9868 0.000 1.000 0.000 0.000
#> GSM97826 1 0.2081 0.9027 0.916 0.000 0.000 0.084
#> GSM97829 1 0.3873 0.7819 0.772 0.000 0.000 0.228
#> GSM97832 2 0.0000 0.9868 0.000 1.000 0.000 0.000
#> GSM97836 1 0.0000 0.9474 1.000 0.000 0.000 0.000
#> GSM97839 1 0.0000 0.9474 1.000 0.000 0.000 0.000
#> GSM97844 2 0.0000 0.9868 0.000 1.000 0.000 0.000
#> GSM97847 1 0.2011 0.9051 0.920 0.000 0.000 0.080
#> GSM97851 1 0.0000 0.9474 1.000 0.000 0.000 0.000
#> GSM97852 1 0.0000 0.9474 1.000 0.000 0.000 0.000
#> GSM97856 1 0.0000 0.9474 1.000 0.000 0.000 0.000
#> GSM97858 2 0.0000 0.9868 0.000 1.000 0.000 0.000
#> GSM97859 1 0.0000 0.9474 1.000 0.000 0.000 0.000
#> GSM97861 1 0.0000 0.9474 1.000 0.000 0.000 0.000
#> GSM97863 1 0.0000 0.9474 1.000 0.000 0.000 0.000
#> GSM97869 1 0.1792 0.9107 0.932 0.000 0.000 0.068
#> GSM97870 1 0.0000 0.9474 1.000 0.000 0.000 0.000
#> GSM97871 1 0.0000 0.9474 1.000 0.000 0.000 0.000
#> GSM97877 2 0.0000 0.9868 0.000 1.000 0.000 0.000
#> GSM97879 1 0.0000 0.9474 1.000 0.000 0.000 0.000
#> GSM97882 1 0.0336 0.9438 0.992 0.000 0.000 0.008
#> GSM97885 1 0.0336 0.9438 0.992 0.000 0.000 0.008
#> GSM97886 1 0.0000 0.9474 1.000 0.000 0.000 0.000
#> GSM97887 1 0.0000 0.9474 1.000 0.000 0.000 0.000
#> GSM97888 1 0.0000 0.9474 1.000 0.000 0.000 0.000
#> GSM97889 1 0.0000 0.9474 1.000 0.000 0.000 0.000
#> GSM97891 1 0.0592 0.9401 0.984 0.000 0.000 0.016
#> GSM97892 2 0.0000 0.9868 0.000 1.000 0.000 0.000
#> GSM97893 1 0.0000 0.9474 1.000 0.000 0.000 0.000
#> GSM97894 1 0.0000 0.9474 1.000 0.000 0.000 0.000
#> GSM97895 1 0.0000 0.9474 1.000 0.000 0.000 0.000
#> GSM97896 1 0.0000 0.9474 1.000 0.000 0.000 0.000
#> GSM97898 1 0.0000 0.9474 1.000 0.000 0.000 0.000
#> GSM97903 1 0.2973 0.8649 0.856 0.000 0.000 0.144
#> GSM97905 1 0.0000 0.9474 1.000 0.000 0.000 0.000
#> GSM97906 1 0.0000 0.9474 1.000 0.000 0.000 0.000
#> GSM97908 1 0.1940 0.9075 0.924 0.000 0.000 0.076
#> GSM97912 1 0.0000 0.9474 1.000 0.000 0.000 0.000
#> GSM97914 1 0.3024 0.8618 0.852 0.000 0.000 0.148
#> GSM97915 1 0.0000 0.9474 1.000 0.000 0.000 0.000
#> GSM97917 1 0.0000 0.9474 1.000 0.000 0.000 0.000
#> GSM97918 1 0.0000 0.9474 1.000 0.000 0.000 0.000
#> GSM97919 1 0.0000 0.9474 1.000 0.000 0.000 0.000
#> GSM97922 1 0.0000 0.9474 1.000 0.000 0.000 0.000
#> GSM97924 2 0.0000 0.9868 0.000 1.000 0.000 0.000
#> GSM97926 4 0.4643 0.8521 0.000 0.000 0.344 0.656
#> GSM97930 1 0.2921 0.8671 0.860 0.000 0.000 0.140
#> GSM97931 2 0.0000 0.9868 0.000 1.000 0.000 0.000
#> GSM97935 1 0.0592 0.9401 0.984 0.000 0.000 0.016
#> GSM97936 1 0.0000 0.9474 1.000 0.000 0.000 0.000
#> GSM97938 1 0.1940 0.9075 0.924 0.000 0.000 0.076
#> GSM97940 1 0.0000 0.9474 1.000 0.000 0.000 0.000
#> GSM97942 3 0.0469 0.8038 0.012 0.000 0.988 0.000
#> GSM97945 1 0.0000 0.9474 1.000 0.000 0.000 0.000
#> GSM97946 2 0.0000 0.9868 0.000 1.000 0.000 0.000
#> GSM97948 1 0.0000 0.9474 1.000 0.000 0.000 0.000
#> GSM97950 1 0.0000 0.9474 1.000 0.000 0.000 0.000
#> GSM97952 1 0.0000 0.9474 1.000 0.000 0.000 0.000
#> GSM97953 1 0.1867 0.9098 0.928 0.000 0.000 0.072
#> GSM97954 1 0.0000 0.9474 1.000 0.000 0.000 0.000
#> GSM97955 1 0.0000 0.9474 1.000 0.000 0.000 0.000
#> GSM97959 2 0.7146 0.3173 0.148 0.516 0.000 0.336
#> GSM97961 1 0.0000 0.9474 1.000 0.000 0.000 0.000
#> GSM97963 1 0.0000 0.9474 1.000 0.000 0.000 0.000
#> GSM97965 1 0.0000 0.9474 1.000 0.000 0.000 0.000
#> GSM97966 1 0.0000 0.9474 1.000 0.000 0.000 0.000
#> GSM97967 2 0.0000 0.9868 0.000 1.000 0.000 0.000
#> GSM97968 2 0.0000 0.9868 0.000 1.000 0.000 0.000
#> GSM97969 1 0.0000 0.9474 1.000 0.000 0.000 0.000
#> GSM97971 1 0.0000 0.9474 1.000 0.000 0.000 0.000
#> GSM97799 4 0.6084 0.7538 0.000 0.092 0.252 0.656
#> GSM97823 2 0.0000 0.9868 0.000 1.000 0.000 0.000
#> GSM97824 4 0.4643 0.8521 0.000 0.000 0.344 0.656
#> GSM97830 3 0.0000 0.8161 0.000 0.000 1.000 0.000
#> GSM97835 2 0.0000 0.9868 0.000 1.000 0.000 0.000
#> GSM97838 2 0.0000 0.9868 0.000 1.000 0.000 0.000
#> GSM97841 2 0.0000 0.9868 0.000 1.000 0.000 0.000
#> GSM97842 4 0.4661 0.4121 0.000 0.348 0.000 0.652
#> GSM97854 2 0.0000 0.9868 0.000 1.000 0.000 0.000
#> GSM97857 4 0.4800 0.8492 0.000 0.004 0.340 0.656
#> GSM97860 3 0.0000 0.8161 0.000 0.000 1.000 0.000
#> GSM97862 4 0.4643 0.8521 0.000 0.000 0.344 0.656
#> GSM97864 2 0.0000 0.9868 0.000 1.000 0.000 0.000
#> GSM97866 4 0.4643 0.8521 0.000 0.000 0.344 0.656
#> GSM97868 4 0.4643 0.8521 0.000 0.000 0.344 0.656
#> GSM97872 1 0.4922 0.7448 0.736 0.000 0.036 0.228
#> GSM97873 2 0.0336 0.9787 0.000 0.992 0.000 0.008
#> GSM97874 3 0.0000 0.8161 0.000 0.000 1.000 0.000
#> GSM97875 4 0.4967 0.6605 0.000 0.000 0.452 0.548
#> GSM97876 3 0.0000 0.8161 0.000 0.000 1.000 0.000
#> GSM97880 3 0.0000 0.8161 0.000 0.000 1.000 0.000
#> GSM97881 4 0.4643 0.8521 0.000 0.000 0.344 0.656
#> GSM97884 4 0.4661 0.4121 0.000 0.348 0.000 0.652
#> GSM97901 4 0.4643 0.8521 0.000 0.000 0.344 0.656
#> GSM97902 3 0.7621 0.2780 0.212 0.000 0.444 0.344
#> GSM97909 2 0.0000 0.9868 0.000 1.000 0.000 0.000
#> GSM97911 4 0.4643 0.8521 0.000 0.000 0.344 0.656
#> GSM97923 3 0.0000 0.8161 0.000 0.000 1.000 0.000
#> GSM97928 1 0.0000 0.9474 1.000 0.000 0.000 0.000
#> GSM97929 2 0.0000 0.9868 0.000 1.000 0.000 0.000
#> GSM97933 3 0.0000 0.8161 0.000 0.000 1.000 0.000
#> GSM97934 3 0.0000 0.8161 0.000 0.000 1.000 0.000
#> GSM97944 4 0.6084 0.7538 0.000 0.092 0.252 0.656
#> GSM97949 2 0.0000 0.9868 0.000 1.000 0.000 0.000
#> GSM97956 4 0.4643 0.8521 0.000 0.000 0.344 0.656
#> GSM97962 3 0.3444 0.5375 0.000 0.000 0.816 0.184
#> GSM97964 4 0.4643 0.8521 0.000 0.000 0.344 0.656
#> GSM97970 4 0.6084 0.7538 0.000 0.092 0.252 0.656
#> GSM97822 1 0.0000 0.9474 1.000 0.000 0.000 0.000
#> GSM97831 3 0.3219 0.5619 0.000 0.000 0.836 0.164
#> GSM97845 1 0.0000 0.9474 1.000 0.000 0.000 0.000
#> GSM97865 1 0.3024 0.8618 0.852 0.000 0.000 0.148
#> GSM97867 3 0.0336 0.8091 0.008 0.000 0.992 0.000
#> GSM97883 1 0.4072 0.6545 0.748 0.000 0.252 0.000
#> GSM97897 1 0.0000 0.9474 1.000 0.000 0.000 0.000
#> GSM97900 1 0.0000 0.9474 1.000 0.000 0.000 0.000
#> GSM97904 1 0.0000 0.9474 1.000 0.000 0.000 0.000
#> GSM97907 2 0.0000 0.9868 0.000 1.000 0.000 0.000
#> GSM97925 3 0.0336 0.8091 0.008 0.000 0.992 0.000
#> GSM97947 3 0.4989 -0.5048 0.000 0.000 0.528 0.472
cbind(get_classes(res, k = 5), get_membership(res, k = 5))
#> class entropy silhouette p1 p2 p3 p4 p5
#> GSM97800 2 0.0000 0.991 0.000 1.000 0.000 0.000 0.000
#> GSM97803 2 0.0000 0.991 0.000 1.000 0.000 0.000 0.000
#> GSM97804 2 0.0000 0.991 0.000 1.000 0.000 0.000 0.000
#> GSM97805 2 0.0000 0.991 0.000 1.000 0.000 0.000 0.000
#> GSM97807 2 0.0000 0.991 0.000 1.000 0.000 0.000 0.000
#> GSM97809 2 0.0000 0.991 0.000 1.000 0.000 0.000 0.000
#> GSM97811 2 0.0000 0.991 0.000 1.000 0.000 0.000 0.000
#> GSM97812 2 0.0000 0.991 0.000 1.000 0.000 0.000 0.000
#> GSM97816 2 0.0000 0.991 0.000 1.000 0.000 0.000 0.000
#> GSM97817 2 0.0000 0.991 0.000 1.000 0.000 0.000 0.000
#> GSM97820 2 0.0000 0.991 0.000 1.000 0.000 0.000 0.000
#> GSM97825 2 0.0000 0.991 0.000 1.000 0.000 0.000 0.000
#> GSM97827 2 0.0000 0.991 0.000 1.000 0.000 0.000 0.000
#> GSM97828 5 0.2230 0.838 0.116 0.000 0.000 0.000 0.884
#> GSM97833 2 0.0000 0.991 0.000 1.000 0.000 0.000 0.000
#> GSM97834 2 0.0000 0.991 0.000 1.000 0.000 0.000 0.000
#> GSM97840 2 0.0000 0.991 0.000 1.000 0.000 0.000 0.000
#> GSM97846 2 0.0000 0.991 0.000 1.000 0.000 0.000 0.000
#> GSM97848 2 0.0000 0.991 0.000 1.000 0.000 0.000 0.000
#> GSM97849 2 0.0000 0.991 0.000 1.000 0.000 0.000 0.000
#> GSM97850 2 0.0000 0.991 0.000 1.000 0.000 0.000 0.000
#> GSM97853 2 0.0000 0.991 0.000 1.000 0.000 0.000 0.000
#> GSM97855 2 0.0000 0.991 0.000 1.000 0.000 0.000 0.000
#> GSM97878 1 0.0703 0.633 0.976 0.000 0.000 0.024 0.000
#> GSM97913 2 0.4161 0.425 0.392 0.608 0.000 0.000 0.000
#> GSM97932 4 0.0162 0.914 0.004 0.000 0.000 0.996 0.000
#> GSM97939 2 0.0000 0.991 0.000 1.000 0.000 0.000 0.000
#> GSM97951 2 0.0000 0.991 0.000 1.000 0.000 0.000 0.000
#> GSM97957 5 0.0510 0.933 0.000 0.000 0.016 0.000 0.984
#> GSM97972 2 0.0000 0.991 0.000 1.000 0.000 0.000 0.000
#> GSM97793 5 0.0510 0.933 0.000 0.000 0.016 0.000 0.984
#> GSM97795 2 0.0000 0.991 0.000 1.000 0.000 0.000 0.000
#> GSM97802 3 0.1117 0.927 0.016 0.000 0.964 0.000 0.020
#> GSM97810 2 0.0000 0.991 0.000 1.000 0.000 0.000 0.000
#> GSM97815 2 0.0000 0.991 0.000 1.000 0.000 0.000 0.000
#> GSM97837 4 0.3774 0.491 0.296 0.000 0.000 0.704 0.000
#> GSM97843 5 0.0510 0.933 0.000 0.000 0.016 0.000 0.984
#> GSM97890 3 0.1410 0.916 0.000 0.000 0.940 0.000 0.060
#> GSM97899 4 0.0000 0.916 0.000 0.000 0.000 1.000 0.000
#> GSM97910 1 0.2136 0.628 0.904 0.000 0.000 0.088 0.008
#> GSM97916 1 0.4570 0.552 0.648 0.000 0.004 0.332 0.016
#> GSM97920 5 0.0671 0.930 0.004 0.000 0.016 0.000 0.980
#> GSM97921 4 0.4060 0.285 0.360 0.000 0.000 0.640 0.000
#> GSM97927 4 0.2393 0.846 0.080 0.000 0.004 0.900 0.016
#> GSM97937 4 0.2329 0.795 0.124 0.000 0.000 0.876 0.000
#> GSM97941 2 0.0000 0.991 0.000 1.000 0.000 0.000 0.000
#> GSM97943 5 0.4126 0.460 0.380 0.000 0.000 0.000 0.620
#> GSM97958 2 0.0000 0.991 0.000 1.000 0.000 0.000 0.000
#> GSM97960 2 0.0000 0.991 0.000 1.000 0.000 0.000 0.000
#> GSM97794 1 0.0162 0.617 0.996 0.000 0.000 0.004 0.000
#> GSM97796 4 0.0000 0.916 0.000 0.000 0.000 1.000 0.000
#> GSM97797 1 0.0510 0.628 0.984 0.000 0.000 0.016 0.000
#> GSM97798 4 0.0000 0.916 0.000 0.000 0.000 1.000 0.000
#> GSM97801 1 0.3336 0.582 0.772 0.000 0.000 0.228 0.000
#> GSM97806 4 0.3456 0.685 0.204 0.000 0.004 0.788 0.004
#> GSM97808 4 0.0000 0.916 0.000 0.000 0.000 1.000 0.000
#> GSM97813 4 0.1179 0.899 0.016 0.000 0.004 0.964 0.016
#> GSM97814 4 0.0000 0.916 0.000 0.000 0.000 1.000 0.000
#> GSM97818 1 0.0510 0.628 0.984 0.000 0.000 0.016 0.000
#> GSM97819 3 0.2852 0.796 0.000 0.000 0.828 0.000 0.172
#> GSM97821 2 0.0000 0.991 0.000 1.000 0.000 0.000 0.000
#> GSM97826 4 0.2773 0.738 0.164 0.000 0.000 0.836 0.000
#> GSM97829 4 0.3774 0.491 0.296 0.000 0.000 0.704 0.000
#> GSM97832 2 0.0000 0.991 0.000 1.000 0.000 0.000 0.000
#> GSM97836 4 0.2074 0.864 0.060 0.000 0.004 0.920 0.016
#> GSM97839 4 0.0000 0.916 0.000 0.000 0.000 1.000 0.000
#> GSM97844 2 0.0000 0.991 0.000 1.000 0.000 0.000 0.000
#> GSM97847 4 0.2773 0.754 0.164 0.000 0.000 0.836 0.000
#> GSM97851 4 0.0000 0.916 0.000 0.000 0.000 1.000 0.000
#> GSM97852 4 0.0000 0.916 0.000 0.000 0.000 1.000 0.000
#> GSM97856 4 0.0000 0.916 0.000 0.000 0.000 1.000 0.000
#> GSM97858 2 0.0000 0.991 0.000 1.000 0.000 0.000 0.000
#> GSM97859 4 0.1179 0.899 0.016 0.000 0.004 0.964 0.016
#> GSM97861 4 0.0566 0.909 0.012 0.000 0.000 0.984 0.004
#> GSM97863 4 0.0000 0.916 0.000 0.000 0.000 1.000 0.000
#> GSM97869 4 0.4889 -0.192 0.476 0.000 0.004 0.504 0.016
#> GSM97870 4 0.1179 0.899 0.016 0.000 0.004 0.964 0.016
#> GSM97871 4 0.0000 0.916 0.000 0.000 0.000 1.000 0.000
#> GSM97877 2 0.0000 0.991 0.000 1.000 0.000 0.000 0.000
#> GSM97879 4 0.0000 0.916 0.000 0.000 0.000 1.000 0.000
#> GSM97882 4 0.3575 0.713 0.180 0.000 0.004 0.800 0.016
#> GSM97885 4 0.3752 0.680 0.200 0.000 0.004 0.780 0.016
#> GSM97886 4 0.0000 0.916 0.000 0.000 0.000 1.000 0.000
#> GSM97887 4 0.0162 0.915 0.000 0.000 0.000 0.996 0.004
#> GSM97888 4 0.0404 0.912 0.000 0.000 0.000 0.988 0.012
#> GSM97889 4 0.1179 0.899 0.016 0.000 0.004 0.964 0.016
#> GSM97891 4 0.3974 0.628 0.228 0.000 0.004 0.752 0.016
#> GSM97892 2 0.0000 0.991 0.000 1.000 0.000 0.000 0.000
#> GSM97893 4 0.0000 0.916 0.000 0.000 0.000 1.000 0.000
#> GSM97894 4 0.0000 0.916 0.000 0.000 0.000 1.000 0.000
#> GSM97895 4 0.0162 0.914 0.004 0.000 0.000 0.996 0.000
#> GSM97896 4 0.0290 0.913 0.000 0.000 0.000 0.992 0.008
#> GSM97898 4 0.0000 0.916 0.000 0.000 0.000 1.000 0.000
#> GSM97903 1 0.4249 0.407 0.568 0.000 0.000 0.432 0.000
#> GSM97905 4 0.0162 0.914 0.004 0.000 0.000 0.996 0.000
#> GSM97906 4 0.0000 0.916 0.000 0.000 0.000 1.000 0.000
#> GSM97908 4 0.1965 0.829 0.096 0.000 0.000 0.904 0.000
#> GSM97912 4 0.1179 0.899 0.016 0.000 0.004 0.964 0.016
#> GSM97914 1 0.4192 0.472 0.596 0.000 0.000 0.404 0.000
#> GSM97915 4 0.0000 0.916 0.000 0.000 0.000 1.000 0.000
#> GSM97917 4 0.0000 0.916 0.000 0.000 0.000 1.000 0.000
#> GSM97918 4 0.0000 0.916 0.000 0.000 0.000 1.000 0.000
#> GSM97919 4 0.0000 0.916 0.000 0.000 0.000 1.000 0.000
#> GSM97922 4 0.1074 0.900 0.012 0.000 0.004 0.968 0.016
#> GSM97924 2 0.0000 0.991 0.000 1.000 0.000 0.000 0.000
#> GSM97926 3 0.0162 0.947 0.000 0.000 0.996 0.000 0.004
#> GSM97930 1 0.4302 0.274 0.520 0.000 0.000 0.480 0.000
#> GSM97931 2 0.0000 0.991 0.000 1.000 0.000 0.000 0.000
#> GSM97935 4 0.4004 0.620 0.232 0.000 0.004 0.748 0.016
#> GSM97936 4 0.0000 0.916 0.000 0.000 0.000 1.000 0.000
#> GSM97938 4 0.2020 0.825 0.100 0.000 0.000 0.900 0.000
#> GSM97940 4 0.0000 0.916 0.000 0.000 0.000 1.000 0.000
#> GSM97942 5 0.0510 0.933 0.000 0.000 0.016 0.000 0.984
#> GSM97945 4 0.0000 0.916 0.000 0.000 0.000 1.000 0.000
#> GSM97946 2 0.0000 0.991 0.000 1.000 0.000 0.000 0.000
#> GSM97948 4 0.1179 0.899 0.016 0.000 0.004 0.964 0.016
#> GSM97950 4 0.0000 0.916 0.000 0.000 0.000 1.000 0.000
#> GSM97952 4 0.0000 0.916 0.000 0.000 0.000 1.000 0.000
#> GSM97953 4 0.2020 0.825 0.100 0.000 0.000 0.900 0.000
#> GSM97954 4 0.0162 0.914 0.004 0.000 0.000 0.996 0.000
#> GSM97955 4 0.0000 0.916 0.000 0.000 0.000 1.000 0.000
#> GSM97959 1 0.3010 0.471 0.824 0.172 0.000 0.004 0.000
#> GSM97961 4 0.0000 0.916 0.000 0.000 0.000 1.000 0.000
#> GSM97963 4 0.0000 0.916 0.000 0.000 0.000 1.000 0.000
#> GSM97965 4 0.0000 0.916 0.000 0.000 0.000 1.000 0.000
#> GSM97966 4 0.0000 0.916 0.000 0.000 0.000 1.000 0.000
#> GSM97967 2 0.0000 0.991 0.000 1.000 0.000 0.000 0.000
#> GSM97968 2 0.0000 0.991 0.000 1.000 0.000 0.000 0.000
#> GSM97969 4 0.0000 0.916 0.000 0.000 0.000 1.000 0.000
#> GSM97971 4 0.0798 0.905 0.008 0.000 0.000 0.976 0.016
#> GSM97799 3 0.1043 0.926 0.000 0.040 0.960 0.000 0.000
#> GSM97823 2 0.0000 0.991 0.000 1.000 0.000 0.000 0.000
#> GSM97824 3 0.0162 0.947 0.000 0.000 0.996 0.000 0.004
#> GSM97830 5 0.0510 0.933 0.000 0.000 0.016 0.000 0.984
#> GSM97835 2 0.0000 0.991 0.000 1.000 0.000 0.000 0.000
#> GSM97838 2 0.0000 0.991 0.000 1.000 0.000 0.000 0.000
#> GSM97841 2 0.0000 0.991 0.000 1.000 0.000 0.000 0.000
#> GSM97842 3 0.1341 0.909 0.000 0.056 0.944 0.000 0.000
#> GSM97854 2 0.0000 0.991 0.000 1.000 0.000 0.000 0.000
#> GSM97857 3 0.0162 0.947 0.000 0.000 0.996 0.000 0.004
#> GSM97860 5 0.0510 0.933 0.000 0.000 0.016 0.000 0.984
#> GSM97862 3 0.0162 0.947 0.000 0.000 0.996 0.000 0.004
#> GSM97864 2 0.0000 0.991 0.000 1.000 0.000 0.000 0.000
#> GSM97866 3 0.0162 0.947 0.000 0.000 0.996 0.000 0.004
#> GSM97868 3 0.1851 0.893 0.000 0.000 0.912 0.000 0.088
#> GSM97872 4 0.3928 0.483 0.296 0.000 0.000 0.700 0.004
#> GSM97873 2 0.1965 0.885 0.000 0.904 0.096 0.000 0.000
#> GSM97874 5 0.0510 0.933 0.000 0.000 0.016 0.000 0.984
#> GSM97875 3 0.1965 0.884 0.000 0.000 0.904 0.000 0.096
#> GSM97876 5 0.0510 0.933 0.000 0.000 0.016 0.000 0.984
#> GSM97880 5 0.0510 0.933 0.000 0.000 0.016 0.000 0.984
#> GSM97881 3 0.0162 0.947 0.000 0.000 0.996 0.000 0.004
#> GSM97884 3 0.1544 0.894 0.000 0.068 0.932 0.000 0.000
#> GSM97901 3 0.0162 0.947 0.000 0.000 0.996 0.000 0.004
#> GSM97902 1 0.1310 0.614 0.956 0.000 0.000 0.020 0.024
#> GSM97909 2 0.0000 0.991 0.000 1.000 0.000 0.000 0.000
#> GSM97911 3 0.0162 0.947 0.000 0.000 0.996 0.000 0.004
#> GSM97923 5 0.0510 0.933 0.000 0.000 0.016 0.000 0.984
#> GSM97928 4 0.0162 0.914 0.004 0.000 0.000 0.996 0.000
#> GSM97929 2 0.0000 0.991 0.000 1.000 0.000 0.000 0.000
#> GSM97933 5 0.0510 0.933 0.000 0.000 0.016 0.000 0.984
#> GSM97934 5 0.0510 0.933 0.000 0.000 0.016 0.000 0.984
#> GSM97944 3 0.1043 0.926 0.000 0.040 0.960 0.000 0.000
#> GSM97949 2 0.0000 0.991 0.000 1.000 0.000 0.000 0.000
#> GSM97956 3 0.0162 0.947 0.000 0.000 0.996 0.000 0.004
#> GSM97962 5 0.3274 0.716 0.000 0.000 0.220 0.000 0.780
#> GSM97964 3 0.0162 0.947 0.000 0.000 0.996 0.000 0.004
#> GSM97970 3 0.0963 0.929 0.000 0.036 0.964 0.000 0.000
#> GSM97822 4 0.2393 0.846 0.080 0.000 0.004 0.900 0.016
#> GSM97831 5 0.4291 0.117 0.000 0.000 0.464 0.000 0.536
#> GSM97845 4 0.0000 0.916 0.000 0.000 0.000 1.000 0.000
#> GSM97865 1 0.4219 0.449 0.584 0.000 0.000 0.416 0.000
#> GSM97867 5 0.0510 0.933 0.000 0.000 0.016 0.000 0.984
#> GSM97883 4 0.4881 0.089 0.016 0.000 0.004 0.520 0.460
#> GSM97897 4 0.1179 0.899 0.016 0.000 0.004 0.964 0.016
#> GSM97900 4 0.0000 0.916 0.000 0.000 0.000 1.000 0.000
#> GSM97904 4 0.0162 0.915 0.000 0.000 0.000 0.996 0.004
#> GSM97907 2 0.0000 0.991 0.000 1.000 0.000 0.000 0.000
#> GSM97925 5 0.0671 0.930 0.004 0.000 0.016 0.000 0.980
#> GSM97947 3 0.3086 0.783 0.004 0.000 0.816 0.000 0.180
cbind(get_classes(res, k = 6), get_membership(res, k = 6))
#> class entropy silhouette p1 p2 p3 p4 p5 p6
#> GSM97800 2 0.0000 0.9761 0.000 1.000 0.000 0.000 0.000 0.000
#> GSM97803 2 0.0000 0.9761 0.000 1.000 0.000 0.000 0.000 0.000
#> GSM97804 2 0.0000 0.9761 0.000 1.000 0.000 0.000 0.000 0.000
#> GSM97805 2 0.0000 0.9761 0.000 1.000 0.000 0.000 0.000 0.000
#> GSM97807 2 0.0000 0.9761 0.000 1.000 0.000 0.000 0.000 0.000
#> GSM97809 2 0.0000 0.9761 0.000 1.000 0.000 0.000 0.000 0.000
#> GSM97811 2 0.0000 0.9761 0.000 1.000 0.000 0.000 0.000 0.000
#> GSM97812 2 0.0000 0.9761 0.000 1.000 0.000 0.000 0.000 0.000
#> GSM97816 2 0.3911 0.4352 0.000 0.624 0.000 0.000 0.008 0.368
#> GSM97817 2 0.0000 0.9761 0.000 1.000 0.000 0.000 0.000 0.000
#> GSM97820 2 0.0000 0.9761 0.000 1.000 0.000 0.000 0.000 0.000
#> GSM97825 2 0.0000 0.9761 0.000 1.000 0.000 0.000 0.000 0.000
#> GSM97827 2 0.0000 0.9761 0.000 1.000 0.000 0.000 0.000 0.000
#> GSM97828 6 0.3823 0.0645 0.000 0.000 0.000 0.000 0.436 0.564
#> GSM97833 2 0.0000 0.9761 0.000 1.000 0.000 0.000 0.000 0.000
#> GSM97834 2 0.0000 0.9761 0.000 1.000 0.000 0.000 0.000 0.000
#> GSM97840 2 0.0000 0.9761 0.000 1.000 0.000 0.000 0.000 0.000
#> GSM97846 2 0.0000 0.9761 0.000 1.000 0.000 0.000 0.000 0.000
#> GSM97848 2 0.0000 0.9761 0.000 1.000 0.000 0.000 0.000 0.000
#> GSM97849 2 0.0000 0.9761 0.000 1.000 0.000 0.000 0.000 0.000
#> GSM97850 2 0.0000 0.9761 0.000 1.000 0.000 0.000 0.000 0.000
#> GSM97853 2 0.0000 0.9761 0.000 1.000 0.000 0.000 0.000 0.000
#> GSM97855 2 0.0000 0.9761 0.000 1.000 0.000 0.000 0.000 0.000
#> GSM97878 1 0.3984 -0.3354 0.648 0.000 0.000 0.016 0.000 0.336
#> GSM97913 2 0.5993 -0.1174 0.272 0.440 0.000 0.000 0.000 0.288
#> GSM97932 4 0.0405 0.8611 0.008 0.000 0.000 0.988 0.000 0.004
#> GSM97939 2 0.0000 0.9761 0.000 1.000 0.000 0.000 0.000 0.000
#> GSM97951 2 0.0000 0.9761 0.000 1.000 0.000 0.000 0.000 0.000
#> GSM97957 5 0.1387 0.8400 0.000 0.000 0.000 0.000 0.932 0.068
#> GSM97972 2 0.1007 0.9377 0.000 0.956 0.000 0.000 0.000 0.044
#> GSM97793 5 0.0260 0.8673 0.000 0.000 0.000 0.000 0.992 0.008
#> GSM97795 2 0.0000 0.9761 0.000 1.000 0.000 0.000 0.000 0.000
#> GSM97802 3 0.5856 0.5233 0.228 0.000 0.608 0.000 0.076 0.088
#> GSM97810 2 0.0000 0.9761 0.000 1.000 0.000 0.000 0.000 0.000
#> GSM97815 2 0.0000 0.9761 0.000 1.000 0.000 0.000 0.000 0.000
#> GSM97837 4 0.4416 0.5062 0.124 0.000 0.000 0.716 0.000 0.160
#> GSM97843 5 0.0508 0.8640 0.004 0.000 0.000 0.000 0.984 0.012
#> GSM97890 3 0.2592 0.8226 0.004 0.000 0.864 0.000 0.116 0.016
#> GSM97899 4 0.0363 0.8674 0.012 0.000 0.000 0.988 0.000 0.000
#> GSM97910 6 0.3513 0.6423 0.144 0.000 0.000 0.060 0.000 0.796
#> GSM97916 1 0.1152 0.0953 0.952 0.000 0.000 0.044 0.000 0.004
#> GSM97920 5 0.3547 0.4479 0.000 0.000 0.000 0.000 0.668 0.332
#> GSM97921 4 0.4282 0.5021 0.192 0.000 0.000 0.720 0.000 0.088
#> GSM97927 1 0.3862 0.3370 0.524 0.000 0.000 0.476 0.000 0.000
#> GSM97937 4 0.2799 0.7305 0.076 0.000 0.000 0.860 0.000 0.064
#> GSM97941 2 0.0000 0.9761 0.000 1.000 0.000 0.000 0.000 0.000
#> GSM97943 6 0.4166 0.3497 0.028 0.000 0.000 0.000 0.324 0.648
#> GSM97958 2 0.2404 0.8532 0.016 0.872 0.000 0.000 0.000 0.112
#> GSM97960 2 0.0000 0.9761 0.000 1.000 0.000 0.000 0.000 0.000
#> GSM97794 1 0.3515 -0.3148 0.676 0.000 0.000 0.000 0.000 0.324
#> GSM97796 4 0.0000 0.8675 0.000 0.000 0.000 1.000 0.000 0.000
#> GSM97797 6 0.3867 0.4500 0.488 0.000 0.000 0.000 0.000 0.512
#> GSM97798 4 0.0458 0.8663 0.016 0.000 0.000 0.984 0.000 0.000
#> GSM97801 6 0.4389 0.5750 0.188 0.000 0.000 0.100 0.000 0.712
#> GSM97806 1 0.3868 0.3449 0.504 0.000 0.000 0.496 0.000 0.000
#> GSM97808 4 0.0458 0.8663 0.016 0.000 0.000 0.984 0.000 0.000
#> GSM97813 4 0.2969 0.6204 0.224 0.000 0.000 0.776 0.000 0.000
#> GSM97814 4 0.0363 0.8674 0.012 0.000 0.000 0.988 0.000 0.000
#> GSM97818 1 0.3531 -0.3225 0.672 0.000 0.000 0.000 0.000 0.328
#> GSM97819 3 0.3624 0.7614 0.000 0.000 0.784 0.000 0.156 0.060
#> GSM97821 2 0.0363 0.9668 0.000 0.988 0.000 0.000 0.000 0.012
#> GSM97826 4 0.3092 0.7004 0.104 0.000 0.000 0.836 0.000 0.060
#> GSM97829 4 0.4382 0.5140 0.124 0.000 0.000 0.720 0.000 0.156
#> GSM97832 2 0.0000 0.9761 0.000 1.000 0.000 0.000 0.000 0.000
#> GSM97836 4 0.3866 -0.2593 0.484 0.000 0.000 0.516 0.000 0.000
#> GSM97839 4 0.0000 0.8675 0.000 0.000 0.000 1.000 0.000 0.000
#> GSM97844 2 0.0000 0.9761 0.000 1.000 0.000 0.000 0.000 0.000
#> GSM97847 4 0.2613 0.7198 0.140 0.000 0.000 0.848 0.000 0.012
#> GSM97851 4 0.0000 0.8675 0.000 0.000 0.000 1.000 0.000 0.000
#> GSM97852 4 0.0260 0.8650 0.008 0.000 0.000 0.992 0.000 0.000
#> GSM97856 4 0.0363 0.8674 0.012 0.000 0.000 0.988 0.000 0.000
#> GSM97858 2 0.0000 0.9761 0.000 1.000 0.000 0.000 0.000 0.000
#> GSM97859 4 0.3023 0.6062 0.232 0.000 0.000 0.768 0.000 0.000
#> GSM97861 4 0.1610 0.8132 0.084 0.000 0.000 0.916 0.000 0.000
#> GSM97863 4 0.0000 0.8675 0.000 0.000 0.000 1.000 0.000 0.000
#> GSM97869 1 0.2340 0.2766 0.852 0.000 0.000 0.148 0.000 0.000
#> GSM97870 4 0.3076 0.5907 0.240 0.000 0.000 0.760 0.000 0.000
#> GSM97871 4 0.0363 0.8674 0.012 0.000 0.000 0.988 0.000 0.000
#> GSM97877 2 0.0363 0.9668 0.000 0.988 0.000 0.000 0.000 0.012
#> GSM97879 4 0.0000 0.8675 0.000 0.000 0.000 1.000 0.000 0.000
#> GSM97882 1 0.3843 0.3957 0.548 0.000 0.000 0.452 0.000 0.000
#> GSM97885 1 0.3817 0.4320 0.568 0.000 0.000 0.432 0.000 0.000
#> GSM97886 4 0.0363 0.8674 0.012 0.000 0.000 0.988 0.000 0.000
#> GSM97887 4 0.0458 0.8663 0.016 0.000 0.000 0.984 0.000 0.000
#> GSM97888 4 0.0937 0.8518 0.040 0.000 0.000 0.960 0.000 0.000
#> GSM97889 4 0.2941 0.6271 0.220 0.000 0.000 0.780 0.000 0.000
#> GSM97891 1 0.3854 0.4102 0.536 0.000 0.000 0.464 0.000 0.000
#> GSM97892 2 0.0000 0.9761 0.000 1.000 0.000 0.000 0.000 0.000
#> GSM97893 4 0.0000 0.8675 0.000 0.000 0.000 1.000 0.000 0.000
#> GSM97894 4 0.0363 0.8674 0.012 0.000 0.000 0.988 0.000 0.000
#> GSM97895 4 0.0622 0.8557 0.012 0.000 0.000 0.980 0.000 0.008
#> GSM97896 4 0.0937 0.8523 0.040 0.000 0.000 0.960 0.000 0.000
#> GSM97898 4 0.0000 0.8675 0.000 0.000 0.000 1.000 0.000 0.000
#> GSM97903 4 0.4185 -0.3518 0.492 0.000 0.000 0.496 0.000 0.012
#> GSM97905 4 0.0865 0.8556 0.036 0.000 0.000 0.964 0.000 0.000
#> GSM97906 4 0.0363 0.8674 0.012 0.000 0.000 0.988 0.000 0.000
#> GSM97908 4 0.1588 0.8034 0.072 0.000 0.000 0.924 0.000 0.004
#> GSM97912 4 0.2969 0.6204 0.224 0.000 0.000 0.776 0.000 0.000
#> GSM97914 1 0.5127 0.3400 0.528 0.000 0.000 0.384 0.000 0.088
#> GSM97915 4 0.0000 0.8675 0.000 0.000 0.000 1.000 0.000 0.000
#> GSM97917 4 0.0000 0.8675 0.000 0.000 0.000 1.000 0.000 0.000
#> GSM97918 4 0.0000 0.8675 0.000 0.000 0.000 1.000 0.000 0.000
#> GSM97919 4 0.0000 0.8675 0.000 0.000 0.000 1.000 0.000 0.000
#> GSM97922 4 0.2969 0.6204 0.224 0.000 0.000 0.776 0.000 0.000
#> GSM97924 2 0.0000 0.9761 0.000 1.000 0.000 0.000 0.000 0.000
#> GSM97926 3 0.1007 0.8837 0.000 0.000 0.956 0.000 0.000 0.044
#> GSM97930 4 0.4823 -0.0690 0.388 0.000 0.000 0.552 0.000 0.060
#> GSM97931 2 0.0000 0.9761 0.000 1.000 0.000 0.000 0.000 0.000
#> GSM97935 1 0.3717 0.4893 0.616 0.000 0.000 0.384 0.000 0.000
#> GSM97936 4 0.0000 0.8675 0.000 0.000 0.000 1.000 0.000 0.000
#> GSM97938 4 0.2512 0.7556 0.060 0.000 0.000 0.880 0.000 0.060
#> GSM97940 4 0.0363 0.8674 0.012 0.000 0.000 0.988 0.000 0.000
#> GSM97942 5 0.0777 0.8576 0.004 0.000 0.000 0.000 0.972 0.024
#> GSM97945 4 0.0000 0.8675 0.000 0.000 0.000 1.000 0.000 0.000
#> GSM97946 2 0.0000 0.9761 0.000 1.000 0.000 0.000 0.000 0.000
#> GSM97948 4 0.4107 0.4965 0.256 0.000 0.000 0.708 0.012 0.024
#> GSM97950 4 0.0000 0.8675 0.000 0.000 0.000 1.000 0.000 0.000
#> GSM97952 4 0.0363 0.8674 0.012 0.000 0.000 0.988 0.000 0.000
#> GSM97953 4 0.2325 0.7702 0.048 0.000 0.000 0.892 0.000 0.060
#> GSM97954 4 0.0146 0.8657 0.004 0.000 0.000 0.996 0.000 0.000
#> GSM97955 4 0.0000 0.8675 0.000 0.000 0.000 1.000 0.000 0.000
#> GSM97959 1 0.5519 -0.3809 0.520 0.148 0.000 0.000 0.000 0.332
#> GSM97961 4 0.0000 0.8675 0.000 0.000 0.000 1.000 0.000 0.000
#> GSM97963 4 0.0363 0.8674 0.012 0.000 0.000 0.988 0.000 0.000
#> GSM97965 4 0.0363 0.8674 0.012 0.000 0.000 0.988 0.000 0.000
#> GSM97966 4 0.0458 0.8663 0.016 0.000 0.000 0.984 0.000 0.000
#> GSM97967 2 0.0000 0.9761 0.000 1.000 0.000 0.000 0.000 0.000
#> GSM97968 2 0.0000 0.9761 0.000 1.000 0.000 0.000 0.000 0.000
#> GSM97969 4 0.0458 0.8663 0.016 0.000 0.000 0.984 0.000 0.000
#> GSM97971 4 0.2527 0.7085 0.168 0.000 0.000 0.832 0.000 0.000
#> GSM97799 3 0.0547 0.8848 0.000 0.020 0.980 0.000 0.000 0.000
#> GSM97823 2 0.0000 0.9761 0.000 1.000 0.000 0.000 0.000 0.000
#> GSM97824 3 0.0146 0.8888 0.000 0.000 0.996 0.000 0.000 0.004
#> GSM97830 5 0.1714 0.8220 0.000 0.000 0.000 0.000 0.908 0.092
#> GSM97835 2 0.0000 0.9761 0.000 1.000 0.000 0.000 0.000 0.000
#> GSM97838 2 0.0000 0.9761 0.000 1.000 0.000 0.000 0.000 0.000
#> GSM97841 2 0.0000 0.9761 0.000 1.000 0.000 0.000 0.000 0.000
#> GSM97842 3 0.0865 0.8723 0.000 0.036 0.964 0.000 0.000 0.000
#> GSM97854 2 0.0000 0.9761 0.000 1.000 0.000 0.000 0.000 0.000
#> GSM97857 3 0.1814 0.8406 0.000 0.000 0.900 0.000 0.000 0.100
#> GSM97860 5 0.0405 0.8655 0.004 0.000 0.000 0.000 0.988 0.008
#> GSM97862 3 0.0713 0.8878 0.000 0.000 0.972 0.000 0.000 0.028
#> GSM97864 2 0.0000 0.9761 0.000 1.000 0.000 0.000 0.000 0.000
#> GSM97866 3 0.0713 0.8878 0.000 0.000 0.972 0.000 0.000 0.028
#> GSM97868 3 0.1663 0.8454 0.000 0.000 0.912 0.000 0.088 0.000
#> GSM97872 4 0.4883 0.4517 0.124 0.000 0.000 0.688 0.012 0.176
#> GSM97873 2 0.2003 0.8484 0.000 0.884 0.116 0.000 0.000 0.000
#> GSM97874 5 0.1075 0.8520 0.000 0.000 0.000 0.000 0.952 0.048
#> GSM97875 3 0.3138 0.8078 0.000 0.000 0.832 0.000 0.108 0.060
#> GSM97876 5 0.0146 0.8676 0.000 0.000 0.000 0.000 0.996 0.004
#> GSM97880 5 0.0260 0.8673 0.000 0.000 0.000 0.000 0.992 0.008
#> GSM97881 3 0.0000 0.8888 0.000 0.000 1.000 0.000 0.000 0.000
#> GSM97884 3 0.0937 0.8685 0.000 0.040 0.960 0.000 0.000 0.000
#> GSM97901 3 0.0713 0.8878 0.000 0.000 0.972 0.000 0.000 0.028
#> GSM97902 6 0.2833 0.6471 0.148 0.000 0.000 0.012 0.004 0.836
#> GSM97909 2 0.0146 0.9731 0.000 0.996 0.000 0.000 0.000 0.004
#> GSM97911 3 0.0000 0.8888 0.000 0.000 1.000 0.000 0.000 0.000
#> GSM97923 5 0.0405 0.8655 0.004 0.000 0.000 0.000 0.988 0.008
#> GSM97928 4 0.1168 0.8477 0.028 0.000 0.000 0.956 0.000 0.016
#> GSM97929 2 0.0000 0.9761 0.000 1.000 0.000 0.000 0.000 0.000
#> GSM97933 5 0.0260 0.8673 0.000 0.000 0.000 0.000 0.992 0.008
#> GSM97934 5 0.1204 0.8478 0.000 0.000 0.000 0.000 0.944 0.056
#> GSM97944 3 0.0547 0.8848 0.000 0.020 0.980 0.000 0.000 0.000
#> GSM97949 2 0.0000 0.9761 0.000 1.000 0.000 0.000 0.000 0.000
#> GSM97956 3 0.0146 0.8891 0.000 0.000 0.996 0.000 0.000 0.004
#> GSM97962 5 0.4145 0.5258 0.000 0.000 0.252 0.000 0.700 0.048
#> GSM97964 3 0.0000 0.8888 0.000 0.000 1.000 0.000 0.000 0.000
#> GSM97970 3 0.0547 0.8848 0.000 0.020 0.980 0.000 0.000 0.000
#> GSM97822 1 0.3995 0.3230 0.516 0.000 0.000 0.480 0.000 0.004
#> GSM97831 3 0.5054 0.3296 0.000 0.000 0.548 0.000 0.368 0.084
#> GSM97845 4 0.0000 0.8675 0.000 0.000 0.000 1.000 0.000 0.000
#> GSM97865 1 0.5274 0.3672 0.492 0.000 0.000 0.408 0.000 0.100
#> GSM97867 5 0.0146 0.8672 0.004 0.000 0.000 0.000 0.996 0.000
#> GSM97883 5 0.6551 0.1094 0.280 0.000 0.000 0.176 0.488 0.056
#> GSM97897 4 0.2969 0.6204 0.224 0.000 0.000 0.776 0.000 0.000
#> GSM97900 4 0.0458 0.8663 0.016 0.000 0.000 0.984 0.000 0.000
#> GSM97904 4 0.0632 0.8629 0.024 0.000 0.000 0.976 0.000 0.000
#> GSM97907 2 0.0000 0.9761 0.000 1.000 0.000 0.000 0.000 0.000
#> GSM97925 5 0.2203 0.7955 0.016 0.000 0.000 0.004 0.896 0.084
#> GSM97947 3 0.4862 0.6430 0.012 0.000 0.672 0.000 0.228 0.088
Heatmaps for the consensus matrix. It visualizes the probability of two samples to be in a same group.
consensus_heatmap(res, k = 2)
consensus_heatmap(res, k = 3)
consensus_heatmap(res, k = 4)
consensus_heatmap(res, k = 5)
consensus_heatmap(res, k = 6)
Heatmaps for the membership of samples in all partitions to see how consistent they are:
membership_heatmap(res, k = 2)
membership_heatmap(res, k = 3)
membership_heatmap(res, k = 4)
membership_heatmap(res, k = 5)
membership_heatmap(res, k = 6)
As soon as we have had the classes for columns, we can look for signatures which are significantly different between classes which can be candidate marks for certain classes. Following are the heatmaps for signatures.
Signature heatmaps where rows are scaled:
get_signatures(res, k = 2)
get_signatures(res, k = 3)
get_signatures(res, k = 4)
get_signatures(res, k = 5)
get_signatures(res, k = 6)
Signature heatmaps where rows are not scaled:
get_signatures(res, k = 2, scale_rows = FALSE)
get_signatures(res, k = 3, scale_rows = FALSE)
get_signatures(res, k = 4, scale_rows = FALSE)
get_signatures(res, k = 5, scale_rows = FALSE)
get_signatures(res, k = 6, scale_rows = FALSE)
Compare the overlap of signatures from different k:
compare_signatures(res)
get_signature() returns a data frame invisibly. TO get the list of signatures, the function
call should be assigned to a variable explicitly. In following code, if plot argument is set
to FALSE, no heatmap is plotted while only the differential analysis is performed.
# code only for demonstration
tb = get_signature(res, k = ..., plot = FALSE)
An example of the output of tb is:
#> which_row fdr mean_1 mean_2 scaled_mean_1 scaled_mean_2 km
#> 1 38 0.042760348 8.373488 9.131774 -0.5533452 0.5164555 1
#> 2 40 0.018707592 7.106213 8.469186 -0.6173731 0.5762149 1
#> 3 55 0.019134737 10.221463 11.207825 -0.6159697 0.5749050 1
#> 4 59 0.006059896 5.921854 7.869574 -0.6899429 0.6439467 1
#> 5 60 0.018055526 8.928898 10.211722 -0.6204761 0.5791110 1
#> 6 98 0.009384629 15.714769 14.887706 0.6635654 -0.6193277 2
...
The columns in tb are:
which_row: row indices corresponding to the input matrix.fdr: FDR for the differential test. mean_x: The mean value in group x.scaled_mean_x: The mean value in group x after rows are scaled.km: Row groups if k-means clustering is applied to rows.UMAP plot which shows how samples are separated.
dimension_reduction(res, k = 2, method = "UMAP")
dimension_reduction(res, k = 3, method = "UMAP")
dimension_reduction(res, k = 4, method = "UMAP")
dimension_reduction(res, k = 5, method = "UMAP")
dimension_reduction(res, k = 6, method = "UMAP")
Following heatmap shows how subgroups are split when increasing k:
collect_classes(res)
Test correlation between subgroups and known annotations. If the known annotation is numeric, one-way ANOVA test is applied, and if the known annotation is discrete, chi-squared contingency table test is applied.
test_to_known_factors(res)
#> n disease.state(p) tissue(p) k
#> ATC:skmeans 177 8.09e-14 4.73e-16 2
#> ATC:skmeans 176 4.05e-22 1.65e-22 3
#> ATC:skmeans 172 5.55e-23 4.05e-24 4
#> ATC:skmeans 166 9.55e-23 5.25e-22 5
#> ATC:skmeans 152 2.58e-20 3.91e-20 6
If matrix rows can be associated to genes, consider to use functional_enrichment(res,
...) to perform function enrichment for the signature genes. See this vignette for more detailed explanations.
The object with results only for a single top-value method and a single partition method can be extracted as:
res = res_list["ATC", "pam"]
# you can also extract it by
# res = res_list["ATC:pam"]
A summary of res and all the functions that can be applied to it:
res
#> A 'ConsensusPartition' object with k = 2, 3, 4, 5, 6.
#> On a matrix with 51882 rows and 180 columns.
#> Top rows (1000, 2000, 3000, 4000, 5000) are extracted by 'ATC' method.
#> Subgroups are detected by 'pam' method.
#> Performed in total 1250 partitions by row resampling.
#> Best k for subgroups seems to be 6.
#>
#> Following methods can be applied to this 'ConsensusPartition' object:
#> [1] "cola_report" "collect_classes" "collect_plots"
#> [4] "collect_stats" "colnames" "compare_signatures"
#> [7] "consensus_heatmap" "dimension_reduction" "functional_enrichment"
#> [10] "get_anno_col" "get_anno" "get_classes"
#> [13] "get_consensus" "get_matrix" "get_membership"
#> [16] "get_param" "get_signatures" "get_stats"
#> [19] "is_best_k" "is_stable_k" "membership_heatmap"
#> [22] "ncol" "nrow" "plot_ecdf"
#> [25] "rownames" "select_partition_number" "show"
#> [28] "suggest_best_k" "test_to_known_factors"
collect_plots() function collects all the plots made from res for all k (number of partitions)
into one single page to provide an easy and fast comparison between different k.
collect_plots(res)
The plots are:
k and the heatmap of
predicted classes for each k.k.k.k.All the plots in panels can be made by individual functions and they are plotted later in this section.
select_partition_number() produces several plots showing different
statistics for choosing “optimized” k. There are following statistics:
k;k, the area increased is defined as \(A_k - A_{k-1}\).The detailed explanations of these statistics can be found in the cola vignette.
Generally speaking, lower PAC score, higher mean silhouette score or higher
concordance corresponds to better partition. Rand index and Jaccard index
measure how similar the current partition is compared to partition with k-1.
If they are too similar, we won't accept k is better than k-1.
select_partition_number(res)
The numeric values for all these statistics can be obtained by get_stats().
get_stats(res)
#> k 1-PAC mean_silhouette concordance area_increased Rand Jaccard
#> 2 2 1.000 0.991 0.996 0.3812 0.623 0.623
#> 3 3 1.000 0.963 0.984 0.6736 0.691 0.523
#> 4 4 0.885 0.936 0.960 0.1700 0.828 0.564
#> 5 5 0.963 0.948 0.977 0.0594 0.954 0.819
#> 6 6 0.918 0.876 0.919 0.0386 0.964 0.833
suggest_best_k() suggests the best \(k\) based on these statistics. The rules are as follows:
suggest_best_k(res)
#> [1] 6
#> attr(,"optional")
#> [1] 2 3 5
There is also optional best \(k\) = 2 3 5 that is worth to check.
Following shows the table of the partitions (You need to click the show/hide
code output link to see it). The membership matrix (columns with name p*)
is inferred by
clue::cl_consensus()
function with the SE method. Basically the value in the membership matrix
represents the probability to belong to a certain group. The finall class
label for an item is determined with the group with highest probability it
belongs to.
In get_classes() function, the entropy is calculated from the membership
matrix and the silhouette score is calculated from the consensus matrix.
cbind(get_classes(res, k = 2), get_membership(res, k = 2))
#> class entropy silhouette p1 p2
#> GSM97800 2 0.000 1.000 0.000 1.000
#> GSM97803 2 0.000 1.000 0.000 1.000
#> GSM97804 2 0.000 1.000 0.000 1.000
#> GSM97805 2 0.000 1.000 0.000 1.000
#> GSM97807 2 0.000 1.000 0.000 1.000
#> GSM97809 2 0.000 1.000 0.000 1.000
#> GSM97811 2 0.000 1.000 0.000 1.000
#> GSM97812 2 0.000 1.000 0.000 1.000
#> GSM97816 1 0.963 0.367 0.612 0.388
#> GSM97817 2 0.000 1.000 0.000 1.000
#> GSM97820 2 0.000 1.000 0.000 1.000
#> GSM97825 2 0.000 1.000 0.000 1.000
#> GSM97827 2 0.000 1.000 0.000 1.000
#> GSM97828 1 0.000 0.995 1.000 0.000
#> GSM97833 2 0.000 1.000 0.000 1.000
#> GSM97834 2 0.000 1.000 0.000 1.000
#> GSM97840 2 0.000 1.000 0.000 1.000
#> GSM97846 2 0.000 1.000 0.000 1.000
#> GSM97848 2 0.000 1.000 0.000 1.000
#> GSM97849 2 0.000 1.000 0.000 1.000
#> GSM97850 2 0.000 1.000 0.000 1.000
#> GSM97853 2 0.000 1.000 0.000 1.000
#> GSM97855 2 0.000 1.000 0.000 1.000
#> GSM97878 1 0.000 0.995 1.000 0.000
#> GSM97913 1 0.000 0.995 1.000 0.000
#> GSM97932 1 0.000 0.995 1.000 0.000
#> GSM97939 1 0.000 0.995 1.000 0.000
#> GSM97951 2 0.000 1.000 0.000 1.000
#> GSM97957 1 0.000 0.995 1.000 0.000
#> GSM97972 1 0.000 0.995 1.000 0.000
#> GSM97793 1 0.000 0.995 1.000 0.000
#> GSM97795 2 0.000 1.000 0.000 1.000
#> GSM97802 1 0.000 0.995 1.000 0.000
#> GSM97810 2 0.000 1.000 0.000 1.000
#> GSM97815 2 0.000 1.000 0.000 1.000
#> GSM97837 1 0.000 0.995 1.000 0.000
#> GSM97843 1 0.000 0.995 1.000 0.000
#> GSM97890 1 0.000 0.995 1.000 0.000
#> GSM97899 1 0.000 0.995 1.000 0.000
#> GSM97910 1 0.000 0.995 1.000 0.000
#> GSM97916 1 0.000 0.995 1.000 0.000
#> GSM97920 1 0.000 0.995 1.000 0.000
#> GSM97921 1 0.000 0.995 1.000 0.000
#> GSM97927 1 0.000 0.995 1.000 0.000
#> GSM97937 1 0.000 0.995 1.000 0.000
#> GSM97941 2 0.000 1.000 0.000 1.000
#> GSM97943 1 0.000 0.995 1.000 0.000
#> GSM97958 1 0.000 0.995 1.000 0.000
#> GSM97960 2 0.000 1.000 0.000 1.000
#> GSM97794 1 0.000 0.995 1.000 0.000
#> GSM97796 1 0.000 0.995 1.000 0.000
#> GSM97797 1 0.000 0.995 1.000 0.000
#> GSM97798 1 0.000 0.995 1.000 0.000
#> GSM97801 1 0.000 0.995 1.000 0.000
#> GSM97806 1 0.000 0.995 1.000 0.000
#> GSM97808 1 0.000 0.995 1.000 0.000
#> GSM97813 1 0.000 0.995 1.000 0.000
#> GSM97814 1 0.000 0.995 1.000 0.000
#> GSM97818 1 0.000 0.995 1.000 0.000
#> GSM97819 1 0.000 0.995 1.000 0.000
#> GSM97821 1 0.000 0.995 1.000 0.000
#> GSM97826 1 0.000 0.995 1.000 0.000
#> GSM97829 1 0.000 0.995 1.000 0.000
#> GSM97832 2 0.000 1.000 0.000 1.000
#> GSM97836 1 0.000 0.995 1.000 0.000
#> GSM97839 1 0.000 0.995 1.000 0.000
#> GSM97844 2 0.000 1.000 0.000 1.000
#> GSM97847 1 0.000 0.995 1.000 0.000
#> GSM97851 1 0.000 0.995 1.000 0.000
#> GSM97852 1 0.000 0.995 1.000 0.000
#> GSM97856 1 0.000 0.995 1.000 0.000
#> GSM97858 2 0.000 1.000 0.000 1.000
#> GSM97859 1 0.000 0.995 1.000 0.000
#> GSM97861 1 0.000 0.995 1.000 0.000
#> GSM97863 1 0.000 0.995 1.000 0.000
#> GSM97869 1 0.000 0.995 1.000 0.000
#> GSM97870 1 0.000 0.995 1.000 0.000
#> GSM97871 1 0.000 0.995 1.000 0.000
#> GSM97877 1 0.827 0.649 0.740 0.260
#> GSM97879 1 0.000 0.995 1.000 0.000
#> GSM97882 1 0.000 0.995 1.000 0.000
#> GSM97885 1 0.000 0.995 1.000 0.000
#> GSM97886 1 0.000 0.995 1.000 0.000
#> GSM97887 1 0.000 0.995 1.000 0.000
#> GSM97888 1 0.000 0.995 1.000 0.000
#> GSM97889 1 0.000 0.995 1.000 0.000
#> GSM97891 1 0.000 0.995 1.000 0.000
#> GSM97892 2 0.000 1.000 0.000 1.000
#> GSM97893 1 0.000 0.995 1.000 0.000
#> GSM97894 1 0.000 0.995 1.000 0.000
#> GSM97895 1 0.000 0.995 1.000 0.000
#> GSM97896 1 0.000 0.995 1.000 0.000
#> GSM97898 1 0.000 0.995 1.000 0.000
#> GSM97903 1 0.000 0.995 1.000 0.000
#> GSM97905 1 0.000 0.995 1.000 0.000
#> GSM97906 1 0.000 0.995 1.000 0.000
#> GSM97908 1 0.000 0.995 1.000 0.000
#> GSM97912 1 0.000 0.995 1.000 0.000
#> GSM97914 1 0.000 0.995 1.000 0.000
#> GSM97915 1 0.000 0.995 1.000 0.000
#> GSM97917 1 0.000 0.995 1.000 0.000
#> GSM97918 1 0.000 0.995 1.000 0.000
#> GSM97919 1 0.000 0.995 1.000 0.000
#> GSM97922 1 0.000 0.995 1.000 0.000
#> GSM97924 2 0.000 1.000 0.000 1.000
#> GSM97926 1 0.000 0.995 1.000 0.000
#> GSM97930 1 0.000 0.995 1.000 0.000
#> GSM97931 1 0.000 0.995 1.000 0.000
#> GSM97935 1 0.000 0.995 1.000 0.000
#> GSM97936 1 0.000 0.995 1.000 0.000
#> GSM97938 1 0.000 0.995 1.000 0.000
#> GSM97940 1 0.000 0.995 1.000 0.000
#> GSM97942 1 0.000 0.995 1.000 0.000
#> GSM97945 1 0.000 0.995 1.000 0.000
#> GSM97946 2 0.000 1.000 0.000 1.000
#> GSM97948 1 0.000 0.995 1.000 0.000
#> GSM97950 1 0.000 0.995 1.000 0.000
#> GSM97952 1 0.000 0.995 1.000 0.000
#> GSM97953 1 0.000 0.995 1.000 0.000
#> GSM97954 1 0.000 0.995 1.000 0.000
#> GSM97955 1 0.000 0.995 1.000 0.000
#> GSM97959 1 0.000 0.995 1.000 0.000
#> GSM97961 1 0.000 0.995 1.000 0.000
#> GSM97963 1 0.000 0.995 1.000 0.000
#> GSM97965 1 0.000 0.995 1.000 0.000
#> GSM97966 1 0.000 0.995 1.000 0.000
#> GSM97967 2 0.000 1.000 0.000 1.000
#> GSM97968 2 0.000 1.000 0.000 1.000
#> GSM97969 1 0.000 0.995 1.000 0.000
#> GSM97971 1 0.000 0.995 1.000 0.000
#> GSM97799 1 0.000 0.995 1.000 0.000
#> GSM97823 2 0.000 1.000 0.000 1.000
#> GSM97824 1 0.000 0.995 1.000 0.000
#> GSM97830 1 0.000 0.995 1.000 0.000
#> GSM97835 2 0.000 1.000 0.000 1.000
#> GSM97838 2 0.000 1.000 0.000 1.000
#> GSM97841 2 0.000 1.000 0.000 1.000
#> GSM97842 1 0.000 0.995 1.000 0.000
#> GSM97854 2 0.000 1.000 0.000 1.000
#> GSM97857 1 0.000 0.995 1.000 0.000
#> GSM97860 1 0.000 0.995 1.000 0.000
#> GSM97862 1 0.000 0.995 1.000 0.000
#> GSM97864 2 0.000 1.000 0.000 1.000
#> GSM97866 1 0.000 0.995 1.000 0.000
#> GSM97868 1 0.000 0.995 1.000 0.000
#> GSM97872 1 0.000 0.995 1.000 0.000
#> GSM97873 1 0.000 0.995 1.000 0.000
#> GSM97874 1 0.000 0.995 1.000 0.000
#> GSM97875 1 0.000 0.995 1.000 0.000
#> GSM97876 1 0.000 0.995 1.000 0.000
#> GSM97880 1 0.000 0.995 1.000 0.000
#> GSM97881 1 0.000 0.995 1.000 0.000
#> GSM97884 1 0.000 0.995 1.000 0.000
#> GSM97901 1 0.000 0.995 1.000 0.000
#> GSM97902 1 0.000 0.995 1.000 0.000
#> GSM97909 2 0.141 0.979 0.020 0.980
#> GSM97911 1 0.000 0.995 1.000 0.000
#> GSM97923 1 0.000 0.995 1.000 0.000
#> GSM97928 1 0.000 0.995 1.000 0.000
#> GSM97929 2 0.000 1.000 0.000 1.000
#> GSM97933 1 0.000 0.995 1.000 0.000
#> GSM97934 1 0.000 0.995 1.000 0.000
#> GSM97944 1 0.000 0.995 1.000 0.000
#> GSM97949 2 0.000 1.000 0.000 1.000
#> GSM97956 1 0.000 0.995 1.000 0.000
#> GSM97962 1 0.000 0.995 1.000 0.000
#> GSM97964 1 0.000 0.995 1.000 0.000
#> GSM97970 1 0.000 0.995 1.000 0.000
#> GSM97822 1 0.000 0.995 1.000 0.000
#> GSM97831 1 0.000 0.995 1.000 0.000
#> GSM97845 1 0.000 0.995 1.000 0.000
#> GSM97865 1 0.000 0.995 1.000 0.000
#> GSM97867 1 0.000 0.995 1.000 0.000
#> GSM97883 1 0.000 0.995 1.000 0.000
#> GSM97897 1 0.000 0.995 1.000 0.000
#> GSM97900 1 0.000 0.995 1.000 0.000
#> GSM97904 1 0.000 0.995 1.000 0.000
#> GSM97907 2 0.000 1.000 0.000 1.000
#> GSM97925 1 0.000 0.995 1.000 0.000
#> GSM97947 1 0.000 0.995 1.000 0.000
cbind(get_classes(res, k = 3), get_membership(res, k = 3))
#> class entropy silhouette p1 p2 p3
#> GSM97800 2 0.0000 1.0000 0.000 1 0.000
#> GSM97803 2 0.0000 1.0000 0.000 1 0.000
#> GSM97804 2 0.0000 1.0000 0.000 1 0.000
#> GSM97805 2 0.0000 1.0000 0.000 1 0.000
#> GSM97807 2 0.0000 1.0000 0.000 1 0.000
#> GSM97809 2 0.0000 1.0000 0.000 1 0.000
#> GSM97811 2 0.0000 1.0000 0.000 1 0.000
#> GSM97812 2 0.0000 1.0000 0.000 1 0.000
#> GSM97816 3 0.0000 0.9735 0.000 0 1.000
#> GSM97817 2 0.0000 1.0000 0.000 1 0.000
#> GSM97820 2 0.0000 1.0000 0.000 1 0.000
#> GSM97825 2 0.0000 1.0000 0.000 1 0.000
#> GSM97827 2 0.0000 1.0000 0.000 1 0.000
#> GSM97828 3 0.0000 0.9735 0.000 0 1.000
#> GSM97833 2 0.0000 1.0000 0.000 1 0.000
#> GSM97834 2 0.0000 1.0000 0.000 1 0.000
#> GSM97840 2 0.0000 1.0000 0.000 1 0.000
#> GSM97846 2 0.0000 1.0000 0.000 1 0.000
#> GSM97848 2 0.0000 1.0000 0.000 1 0.000
#> GSM97849 2 0.0000 1.0000 0.000 1 0.000
#> GSM97850 2 0.0000 1.0000 0.000 1 0.000
#> GSM97853 2 0.0000 1.0000 0.000 1 0.000
#> GSM97855 2 0.0000 1.0000 0.000 1 0.000
#> GSM97878 3 0.0000 0.9735 0.000 0 1.000
#> GSM97913 3 0.0000 0.9735 0.000 0 1.000
#> GSM97932 1 0.0000 0.9848 1.000 0 0.000
#> GSM97939 3 0.0000 0.9735 0.000 0 1.000
#> GSM97951 2 0.0000 1.0000 0.000 1 0.000
#> GSM97957 3 0.0000 0.9735 0.000 0 1.000
#> GSM97972 3 0.0000 0.9735 0.000 0 1.000
#> GSM97793 3 0.0000 0.9735 0.000 0 1.000
#> GSM97795 2 0.0000 1.0000 0.000 1 0.000
#> GSM97802 3 0.0000 0.9735 0.000 0 1.000
#> GSM97810 3 0.0000 0.9735 0.000 0 1.000
#> GSM97815 3 0.0000 0.9735 0.000 0 1.000
#> GSM97837 1 0.0000 0.9848 1.000 0 0.000
#> GSM97843 3 0.0000 0.9735 0.000 0 1.000
#> GSM97890 3 0.0000 0.9735 0.000 0 1.000
#> GSM97899 1 0.0000 0.9848 1.000 0 0.000
#> GSM97910 3 0.0000 0.9735 0.000 0 1.000
#> GSM97916 3 0.0424 0.9690 0.008 0 0.992
#> GSM97920 3 0.0000 0.9735 0.000 0 1.000
#> GSM97921 3 0.1411 0.9504 0.036 0 0.964
#> GSM97927 3 0.1860 0.9389 0.052 0 0.948
#> GSM97937 1 0.0000 0.9848 1.000 0 0.000
#> GSM97941 2 0.0000 1.0000 0.000 1 0.000
#> GSM97943 3 0.0000 0.9735 0.000 0 1.000
#> GSM97958 3 0.0000 0.9735 0.000 0 1.000
#> GSM97960 2 0.0000 1.0000 0.000 1 0.000
#> GSM97794 3 0.0000 0.9735 0.000 0 1.000
#> GSM97796 1 0.0000 0.9848 1.000 0 0.000
#> GSM97797 3 0.0000 0.9735 0.000 0 1.000
#> GSM97798 1 0.0000 0.9848 1.000 0 0.000
#> GSM97801 3 0.0424 0.9690 0.008 0 0.992
#> GSM97806 3 0.1860 0.9389 0.052 0 0.948
#> GSM97808 1 0.0000 0.9848 1.000 0 0.000
#> GSM97813 1 0.0000 0.9848 1.000 0 0.000
#> GSM97814 1 0.0000 0.9848 1.000 0 0.000
#> GSM97818 3 0.0000 0.9735 0.000 0 1.000
#> GSM97819 3 0.0000 0.9735 0.000 0 1.000
#> GSM97821 3 0.0000 0.9735 0.000 0 1.000
#> GSM97826 1 0.0000 0.9848 1.000 0 0.000
#> GSM97829 3 0.4931 0.7228 0.232 0 0.768
#> GSM97832 3 0.0000 0.9735 0.000 0 1.000
#> GSM97836 3 0.0747 0.9640 0.016 0 0.984
#> GSM97839 1 0.0000 0.9848 1.000 0 0.000
#> GSM97844 2 0.0000 1.0000 0.000 1 0.000
#> GSM97847 1 0.0000 0.9848 1.000 0 0.000
#> GSM97851 1 0.0000 0.9848 1.000 0 0.000
#> GSM97852 1 0.0000 0.9848 1.000 0 0.000
#> GSM97856 1 0.0000 0.9848 1.000 0 0.000
#> GSM97858 2 0.0000 1.0000 0.000 1 0.000
#> GSM97859 3 0.4796 0.7412 0.220 0 0.780
#> GSM97861 3 0.1860 0.9389 0.052 0 0.948
#> GSM97863 1 0.0000 0.9848 1.000 0 0.000
#> GSM97869 3 0.0000 0.9735 0.000 0 1.000
#> GSM97870 3 0.3412 0.8662 0.124 0 0.876
#> GSM97871 1 0.0000 0.9848 1.000 0 0.000
#> GSM97877 3 0.0000 0.9735 0.000 0 1.000
#> GSM97879 1 0.0000 0.9848 1.000 0 0.000
#> GSM97882 3 0.3551 0.8573 0.132 0 0.868
#> GSM97885 1 0.6309 -0.0419 0.504 0 0.496
#> GSM97886 1 0.0000 0.9848 1.000 0 0.000
#> GSM97887 1 0.0000 0.9848 1.000 0 0.000
#> GSM97888 1 0.0000 0.9848 1.000 0 0.000
#> GSM97889 3 0.5926 0.4863 0.356 0 0.644
#> GSM97891 3 0.1860 0.9389 0.052 0 0.948
#> GSM97892 2 0.0000 1.0000 0.000 1 0.000
#> GSM97893 1 0.0000 0.9848 1.000 0 0.000
#> GSM97894 1 0.0000 0.9848 1.000 0 0.000
#> GSM97895 1 0.0000 0.9848 1.000 0 0.000
#> GSM97896 1 0.0000 0.9848 1.000 0 0.000
#> GSM97898 1 0.0000 0.9848 1.000 0 0.000
#> GSM97903 3 0.1860 0.9389 0.052 0 0.948
#> GSM97905 3 0.6235 0.2747 0.436 0 0.564
#> GSM97906 1 0.0000 0.9848 1.000 0 0.000
#> GSM97908 1 0.0000 0.9848 1.000 0 0.000
#> GSM97912 1 0.0000 0.9848 1.000 0 0.000
#> GSM97914 3 0.1964 0.9359 0.056 0 0.944
#> GSM97915 1 0.0000 0.9848 1.000 0 0.000
#> GSM97917 1 0.0000 0.9848 1.000 0 0.000
#> GSM97918 1 0.0000 0.9848 1.000 0 0.000
#> GSM97919 1 0.0000 0.9848 1.000 0 0.000
#> GSM97922 1 0.0000 0.9848 1.000 0 0.000
#> GSM97924 2 0.0000 1.0000 0.000 1 0.000
#> GSM97926 3 0.0000 0.9735 0.000 0 1.000
#> GSM97930 1 0.4178 0.7712 0.828 0 0.172
#> GSM97931 3 0.0000 0.9735 0.000 0 1.000
#> GSM97935 3 0.1860 0.9389 0.052 0 0.948
#> GSM97936 1 0.0000 0.9848 1.000 0 0.000
#> GSM97938 1 0.0000 0.9848 1.000 0 0.000
#> GSM97940 1 0.0000 0.9848 1.000 0 0.000
#> GSM97942 3 0.0000 0.9735 0.000 0 1.000
#> GSM97945 1 0.0000 0.9848 1.000 0 0.000
#> GSM97946 2 0.0000 1.0000 0.000 1 0.000
#> GSM97948 3 0.1860 0.9389 0.052 0 0.948
#> GSM97950 1 0.0000 0.9848 1.000 0 0.000
#> GSM97952 1 0.0000 0.9848 1.000 0 0.000
#> GSM97953 1 0.0000 0.9848 1.000 0 0.000
#> GSM97954 1 0.0000 0.9848 1.000 0 0.000
#> GSM97955 1 0.0000 0.9848 1.000 0 0.000
#> GSM97959 3 0.0000 0.9735 0.000 0 1.000
#> GSM97961 1 0.0000 0.9848 1.000 0 0.000
#> GSM97963 1 0.0000 0.9848 1.000 0 0.000
#> GSM97965 1 0.0000 0.9848 1.000 0 0.000
#> GSM97966 1 0.0000 0.9848 1.000 0 0.000
#> GSM97967 2 0.0000 1.0000 0.000 1 0.000
#> GSM97968 2 0.0000 1.0000 0.000 1 0.000
#> GSM97969 1 0.0000 0.9848 1.000 0 0.000
#> GSM97971 1 0.0000 0.9848 1.000 0 0.000
#> GSM97799 3 0.0000 0.9735 0.000 0 1.000
#> GSM97823 2 0.0000 1.0000 0.000 1 0.000
#> GSM97824 3 0.0000 0.9735 0.000 0 1.000
#> GSM97830 3 0.0000 0.9735 0.000 0 1.000
#> GSM97835 3 0.0000 0.9735 0.000 0 1.000
#> GSM97838 2 0.0000 1.0000 0.000 1 0.000
#> GSM97841 2 0.0000 1.0000 0.000 1 0.000
#> GSM97842 3 0.0000 0.9735 0.000 0 1.000
#> GSM97854 2 0.0000 1.0000 0.000 1 0.000
#> GSM97857 3 0.0000 0.9735 0.000 0 1.000
#> GSM97860 3 0.0000 0.9735 0.000 0 1.000
#> GSM97862 3 0.0000 0.9735 0.000 0 1.000
#> GSM97864 2 0.0000 1.0000 0.000 1 0.000
#> GSM97866 3 0.0000 0.9735 0.000 0 1.000
#> GSM97868 3 0.0000 0.9735 0.000 0 1.000
#> GSM97872 3 0.0000 0.9735 0.000 0 1.000
#> GSM97873 3 0.0000 0.9735 0.000 0 1.000
#> GSM97874 3 0.0000 0.9735 0.000 0 1.000
#> GSM97875 3 0.0000 0.9735 0.000 0 1.000
#> GSM97876 3 0.0000 0.9735 0.000 0 1.000
#> GSM97880 3 0.0000 0.9735 0.000 0 1.000
#> GSM97881 3 0.0000 0.9735 0.000 0 1.000
#> GSM97884 3 0.0000 0.9735 0.000 0 1.000
#> GSM97901 3 0.0000 0.9735 0.000 0 1.000
#> GSM97902 3 0.0000 0.9735 0.000 0 1.000
#> GSM97909 3 0.0000 0.9735 0.000 0 1.000
#> GSM97911 3 0.0000 0.9735 0.000 0 1.000
#> GSM97923 3 0.0000 0.9735 0.000 0 1.000
#> GSM97928 3 0.0424 0.9690 0.008 0 0.992
#> GSM97929 2 0.0000 1.0000 0.000 1 0.000
#> GSM97933 3 0.0000 0.9735 0.000 0 1.000
#> GSM97934 3 0.0000 0.9735 0.000 0 1.000
#> GSM97944 3 0.0000 0.9735 0.000 0 1.000
#> GSM97949 2 0.0000 1.0000 0.000 1 0.000
#> GSM97956 3 0.0000 0.9735 0.000 0 1.000
#> GSM97962 3 0.0000 0.9735 0.000 0 1.000
#> GSM97964 3 0.0000 0.9735 0.000 0 1.000
#> GSM97970 3 0.0000 0.9735 0.000 0 1.000
#> GSM97822 3 0.1860 0.9389 0.052 0 0.948
#> GSM97831 3 0.0000 0.9735 0.000 0 1.000
#> GSM97845 1 0.0000 0.9848 1.000 0 0.000
#> GSM97865 3 0.0424 0.9690 0.008 0 0.992
#> GSM97867 3 0.0000 0.9735 0.000 0 1.000
#> GSM97883 3 0.0000 0.9735 0.000 0 1.000
#> GSM97897 1 0.0000 0.9848 1.000 0 0.000
#> GSM97900 1 0.0000 0.9848 1.000 0 0.000
#> GSM97904 3 0.3482 0.8620 0.128 0 0.872
#> GSM97907 2 0.0000 1.0000 0.000 1 0.000
#> GSM97925 3 0.0000 0.9735 0.000 0 1.000
#> GSM97947 3 0.0000 0.9735 0.000 0 1.000
cbind(get_classes(res, k = 4), get_membership(res, k = 4))
#> class entropy silhouette p1 p2 p3 p4
#> GSM97800 2 0.0000 0.985 0.000 1.000 0.000 0.000
#> GSM97803 2 0.0000 0.985 0.000 1.000 0.000 0.000
#> GSM97804 2 0.0000 0.985 0.000 1.000 0.000 0.000
#> GSM97805 2 0.0000 0.985 0.000 1.000 0.000 0.000
#> GSM97807 2 0.0000 0.985 0.000 1.000 0.000 0.000
#> GSM97809 2 0.0000 0.985 0.000 1.000 0.000 0.000
#> GSM97811 2 0.0000 0.985 0.000 1.000 0.000 0.000
#> GSM97812 2 0.0000 0.985 0.000 1.000 0.000 0.000
#> GSM97816 3 0.0000 0.919 0.000 0.000 1.000 0.000
#> GSM97817 2 0.0000 0.985 0.000 1.000 0.000 0.000
#> GSM97820 2 0.0000 0.985 0.000 1.000 0.000 0.000
#> GSM97825 2 0.0000 0.985 0.000 1.000 0.000 0.000
#> GSM97827 2 0.0000 0.985 0.000 1.000 0.000 0.000
#> GSM97828 3 0.1022 0.925 0.032 0.000 0.968 0.000
#> GSM97833 2 0.0000 0.985 0.000 1.000 0.000 0.000
#> GSM97834 2 0.0000 0.985 0.000 1.000 0.000 0.000
#> GSM97840 2 0.1118 0.959 0.000 0.964 0.036 0.000
#> GSM97846 2 0.0000 0.985 0.000 1.000 0.000 0.000
#> GSM97848 2 0.0000 0.985 0.000 1.000 0.000 0.000
#> GSM97849 2 0.0000 0.985 0.000 1.000 0.000 0.000
#> GSM97850 2 0.0000 0.985 0.000 1.000 0.000 0.000
#> GSM97853 2 0.0000 0.985 0.000 1.000 0.000 0.000
#> GSM97855 2 0.0000 0.985 0.000 1.000 0.000 0.000
#> GSM97878 1 0.0000 0.956 1.000 0.000 0.000 0.000
#> GSM97913 3 0.0336 0.917 0.008 0.000 0.992 0.000
#> GSM97932 4 0.0000 0.989 0.000 0.000 0.000 1.000
#> GSM97939 3 0.0000 0.919 0.000 0.000 1.000 0.000
#> GSM97951 2 0.1118 0.959 0.000 0.964 0.036 0.000
#> GSM97957 3 0.3356 0.879 0.176 0.000 0.824 0.000
#> GSM97972 3 0.0000 0.919 0.000 0.000 1.000 0.000
#> GSM97793 3 0.3356 0.879 0.176 0.000 0.824 0.000
#> GSM97795 2 0.0817 0.968 0.000 0.976 0.024 0.000
#> GSM97802 3 0.2081 0.914 0.084 0.000 0.916 0.000
#> GSM97810 3 0.0000 0.919 0.000 0.000 1.000 0.000
#> GSM97815 3 0.0000 0.919 0.000 0.000 1.000 0.000
#> GSM97837 1 0.3311 0.793 0.828 0.000 0.000 0.172
#> GSM97843 3 0.3444 0.875 0.184 0.000 0.816 0.000
#> GSM97890 3 0.1118 0.925 0.036 0.000 0.964 0.000
#> GSM97899 4 0.0000 0.989 0.000 0.000 0.000 1.000
#> GSM97910 1 0.0000 0.956 1.000 0.000 0.000 0.000
#> GSM97916 1 0.0000 0.956 1.000 0.000 0.000 0.000
#> GSM97920 3 0.3266 0.883 0.168 0.000 0.832 0.000
#> GSM97921 1 0.0000 0.956 1.000 0.000 0.000 0.000
#> GSM97927 1 0.0000 0.956 1.000 0.000 0.000 0.000
#> GSM97937 1 0.1118 0.940 0.964 0.000 0.000 0.036
#> GSM97941 2 0.3444 0.812 0.000 0.816 0.184 0.000
#> GSM97943 1 0.0000 0.956 1.000 0.000 0.000 0.000
#> GSM97958 3 0.0000 0.919 0.000 0.000 1.000 0.000
#> GSM97960 2 0.4661 0.540 0.000 0.652 0.348 0.000
#> GSM97794 1 0.0000 0.956 1.000 0.000 0.000 0.000
#> GSM97796 4 0.0000 0.989 0.000 0.000 0.000 1.000
#> GSM97797 1 0.0000 0.956 1.000 0.000 0.000 0.000
#> GSM97798 4 0.0000 0.989 0.000 0.000 0.000 1.000
#> GSM97801 1 0.0000 0.956 1.000 0.000 0.000 0.000
#> GSM97806 1 0.0000 0.956 1.000 0.000 0.000 0.000
#> GSM97808 4 0.0000 0.989 0.000 0.000 0.000 1.000
#> GSM97813 1 0.4941 0.279 0.564 0.000 0.000 0.436
#> GSM97814 4 0.0000 0.989 0.000 0.000 0.000 1.000
#> GSM97818 1 0.0000 0.956 1.000 0.000 0.000 0.000
#> GSM97819 3 0.3444 0.875 0.184 0.000 0.816 0.000
#> GSM97821 3 0.0000 0.919 0.000 0.000 1.000 0.000
#> GSM97826 1 0.1389 0.931 0.952 0.000 0.000 0.048
#> GSM97829 1 0.0188 0.955 0.996 0.000 0.000 0.004
#> GSM97832 3 0.0000 0.919 0.000 0.000 1.000 0.000
#> GSM97836 1 0.0000 0.956 1.000 0.000 0.000 0.000
#> GSM97839 4 0.0000 0.989 0.000 0.000 0.000 1.000
#> GSM97844 2 0.0000 0.985 0.000 1.000 0.000 0.000
#> GSM97847 1 0.0336 0.955 0.992 0.000 0.000 0.008
#> GSM97851 4 0.0000 0.989 0.000 0.000 0.000 1.000
#> GSM97852 1 0.1118 0.940 0.964 0.000 0.000 0.036
#> GSM97856 4 0.0000 0.989 0.000 0.000 0.000 1.000
#> GSM97858 2 0.0000 0.985 0.000 1.000 0.000 0.000
#> GSM97859 1 0.0469 0.953 0.988 0.000 0.000 0.012
#> GSM97861 1 0.0000 0.956 1.000 0.000 0.000 0.000
#> GSM97863 4 0.0000 0.989 0.000 0.000 0.000 1.000
#> GSM97869 1 0.0000 0.956 1.000 0.000 0.000 0.000
#> GSM97870 1 0.0000 0.956 1.000 0.000 0.000 0.000
#> GSM97871 4 0.0000 0.989 0.000 0.000 0.000 1.000
#> GSM97877 3 0.0000 0.919 0.000 0.000 1.000 0.000
#> GSM97879 1 0.1118 0.940 0.964 0.000 0.000 0.036
#> GSM97882 1 0.0336 0.955 0.992 0.000 0.000 0.008
#> GSM97885 1 0.0336 0.955 0.992 0.000 0.000 0.008
#> GSM97886 4 0.0000 0.989 0.000 0.000 0.000 1.000
#> GSM97887 4 0.0000 0.989 0.000 0.000 0.000 1.000
#> GSM97888 4 0.0000 0.989 0.000 0.000 0.000 1.000
#> GSM97889 1 0.0817 0.947 0.976 0.000 0.000 0.024
#> GSM97891 1 0.0000 0.956 1.000 0.000 0.000 0.000
#> GSM97892 2 0.0000 0.985 0.000 1.000 0.000 0.000
#> GSM97893 4 0.0000 0.989 0.000 0.000 0.000 1.000
#> GSM97894 4 0.0000 0.989 0.000 0.000 0.000 1.000
#> GSM97895 4 0.0000 0.989 0.000 0.000 0.000 1.000
#> GSM97896 4 0.0000 0.989 0.000 0.000 0.000 1.000
#> GSM97898 4 0.0000 0.989 0.000 0.000 0.000 1.000
#> GSM97903 1 0.0000 0.956 1.000 0.000 0.000 0.000
#> GSM97905 1 0.1118 0.940 0.964 0.000 0.000 0.036
#> GSM97906 4 0.0000 0.989 0.000 0.000 0.000 1.000
#> GSM97908 1 0.4103 0.677 0.744 0.000 0.000 0.256
#> GSM97912 1 0.3123 0.816 0.844 0.000 0.000 0.156
#> GSM97914 1 0.0000 0.956 1.000 0.000 0.000 0.000
#> GSM97915 4 0.0000 0.989 0.000 0.000 0.000 1.000
#> GSM97917 4 0.0000 0.989 0.000 0.000 0.000 1.000
#> GSM97918 4 0.0000 0.989 0.000 0.000 0.000 1.000
#> GSM97919 4 0.0000 0.989 0.000 0.000 0.000 1.000
#> GSM97922 4 0.0000 0.989 0.000 0.000 0.000 1.000
#> GSM97924 2 0.0000 0.985 0.000 1.000 0.000 0.000
#> GSM97926 3 0.3444 0.875 0.184 0.000 0.816 0.000
#> GSM97930 1 0.0336 0.955 0.992 0.000 0.000 0.008
#> GSM97931 3 0.0000 0.919 0.000 0.000 1.000 0.000
#> GSM97935 1 0.0000 0.956 1.000 0.000 0.000 0.000
#> GSM97936 4 0.0000 0.989 0.000 0.000 0.000 1.000
#> GSM97938 4 0.4040 0.645 0.248 0.000 0.000 0.752
#> GSM97940 4 0.0000 0.989 0.000 0.000 0.000 1.000
#> GSM97942 3 0.3726 0.848 0.212 0.000 0.788 0.000
#> GSM97945 4 0.2647 0.839 0.120 0.000 0.000 0.880
#> GSM97946 2 0.0000 0.985 0.000 1.000 0.000 0.000
#> GSM97948 1 0.0000 0.956 1.000 0.000 0.000 0.000
#> GSM97950 4 0.0000 0.989 0.000 0.000 0.000 1.000
#> GSM97952 4 0.0000 0.989 0.000 0.000 0.000 1.000
#> GSM97953 1 0.0707 0.949 0.980 0.000 0.000 0.020
#> GSM97954 1 0.1118 0.940 0.964 0.000 0.000 0.036
#> GSM97955 4 0.0000 0.989 0.000 0.000 0.000 1.000
#> GSM97959 1 0.3311 0.798 0.828 0.000 0.172 0.000
#> GSM97961 4 0.0000 0.989 0.000 0.000 0.000 1.000
#> GSM97963 4 0.0000 0.989 0.000 0.000 0.000 1.000
#> GSM97965 4 0.0000 0.989 0.000 0.000 0.000 1.000
#> GSM97966 4 0.0000 0.989 0.000 0.000 0.000 1.000
#> GSM97967 2 0.0000 0.985 0.000 1.000 0.000 0.000
#> GSM97968 2 0.0000 0.985 0.000 1.000 0.000 0.000
#> GSM97969 1 0.1118 0.940 0.964 0.000 0.000 0.036
#> GSM97971 1 0.1474 0.930 0.948 0.000 0.000 0.052
#> GSM97799 3 0.0000 0.919 0.000 0.000 1.000 0.000
#> GSM97823 2 0.0000 0.985 0.000 1.000 0.000 0.000
#> GSM97824 3 0.1118 0.925 0.036 0.000 0.964 0.000
#> GSM97830 3 0.3172 0.887 0.160 0.000 0.840 0.000
#> GSM97835 3 0.0000 0.919 0.000 0.000 1.000 0.000
#> GSM97838 2 0.0000 0.985 0.000 1.000 0.000 0.000
#> GSM97841 2 0.0000 0.985 0.000 1.000 0.000 0.000
#> GSM97842 3 0.0000 0.919 0.000 0.000 1.000 0.000
#> GSM97854 2 0.0000 0.985 0.000 1.000 0.000 0.000
#> GSM97857 3 0.1118 0.925 0.036 0.000 0.964 0.000
#> GSM97860 3 0.3444 0.875 0.184 0.000 0.816 0.000
#> GSM97862 3 0.1118 0.925 0.036 0.000 0.964 0.000
#> GSM97864 2 0.0000 0.985 0.000 1.000 0.000 0.000
#> GSM97866 3 0.1118 0.925 0.036 0.000 0.964 0.000
#> GSM97868 3 0.1118 0.925 0.036 0.000 0.964 0.000
#> GSM97872 3 0.3528 0.868 0.192 0.000 0.808 0.000
#> GSM97873 3 0.0000 0.919 0.000 0.000 1.000 0.000
#> GSM97874 3 0.3444 0.875 0.184 0.000 0.816 0.000
#> GSM97875 3 0.1118 0.925 0.036 0.000 0.964 0.000
#> GSM97876 3 0.3074 0.890 0.152 0.000 0.848 0.000
#> GSM97880 3 0.3444 0.875 0.184 0.000 0.816 0.000
#> GSM97881 3 0.1118 0.925 0.036 0.000 0.964 0.000
#> GSM97884 3 0.0000 0.919 0.000 0.000 1.000 0.000
#> GSM97901 3 0.1118 0.925 0.036 0.000 0.964 0.000
#> GSM97902 3 0.3726 0.848 0.212 0.000 0.788 0.000
#> GSM97909 3 0.0000 0.919 0.000 0.000 1.000 0.000
#> GSM97911 3 0.1118 0.925 0.036 0.000 0.964 0.000
#> GSM97923 3 0.3444 0.875 0.184 0.000 0.816 0.000
#> GSM97928 1 0.0000 0.956 1.000 0.000 0.000 0.000
#> GSM97929 2 0.0000 0.985 0.000 1.000 0.000 0.000
#> GSM97933 3 0.3444 0.875 0.184 0.000 0.816 0.000
#> GSM97934 3 0.3444 0.875 0.184 0.000 0.816 0.000
#> GSM97944 3 0.0000 0.919 0.000 0.000 1.000 0.000
#> GSM97949 2 0.0000 0.985 0.000 1.000 0.000 0.000
#> GSM97956 3 0.1118 0.925 0.036 0.000 0.964 0.000
#> GSM97962 3 0.1118 0.925 0.036 0.000 0.964 0.000
#> GSM97964 3 0.1118 0.925 0.036 0.000 0.964 0.000
#> GSM97970 3 0.0000 0.919 0.000 0.000 1.000 0.000
#> GSM97822 1 0.0000 0.956 1.000 0.000 0.000 0.000
#> GSM97831 3 0.1118 0.925 0.036 0.000 0.964 0.000
#> GSM97845 1 0.3726 0.741 0.788 0.000 0.000 0.212
#> GSM97865 1 0.0000 0.956 1.000 0.000 0.000 0.000
#> GSM97867 3 0.3444 0.875 0.184 0.000 0.816 0.000
#> GSM97883 3 0.3569 0.864 0.196 0.000 0.804 0.000
#> GSM97897 4 0.0000 0.989 0.000 0.000 0.000 1.000
#> GSM97900 4 0.0000 0.989 0.000 0.000 0.000 1.000
#> GSM97904 1 0.0000 0.956 1.000 0.000 0.000 0.000
#> GSM97907 2 0.0000 0.985 0.000 1.000 0.000 0.000
#> GSM97925 3 0.3444 0.875 0.184 0.000 0.816 0.000
#> GSM97947 3 0.3444 0.875 0.184 0.000 0.816 0.000
cbind(get_classes(res, k = 5), get_membership(res, k = 5))
#> class entropy silhouette p1 p2 p3 p4 p5
#> GSM97800 2 0.0000 0.979 0.000 1.000 0.000 0.000 0.000
#> GSM97803 2 0.0000 0.979 0.000 1.000 0.000 0.000 0.000
#> GSM97804 2 0.0000 0.979 0.000 1.000 0.000 0.000 0.000
#> GSM97805 2 0.0000 0.979 0.000 1.000 0.000 0.000 0.000
#> GSM97807 2 0.0000 0.979 0.000 1.000 0.000 0.000 0.000
#> GSM97809 2 0.0000 0.979 0.000 1.000 0.000 0.000 0.000
#> GSM97811 2 0.0000 0.979 0.000 1.000 0.000 0.000 0.000
#> GSM97812 2 0.0000 0.979 0.000 1.000 0.000 0.000 0.000
#> GSM97816 5 0.0000 1.000 0.000 0.000 0.000 0.000 1.000
#> GSM97817 2 0.0000 0.979 0.000 1.000 0.000 0.000 0.000
#> GSM97820 2 0.0000 0.979 0.000 1.000 0.000 0.000 0.000
#> GSM97825 2 0.0000 0.979 0.000 1.000 0.000 0.000 0.000
#> GSM97827 2 0.0000 0.979 0.000 1.000 0.000 0.000 0.000
#> GSM97828 3 0.0000 0.956 0.000 0.000 1.000 0.000 0.000
#> GSM97833 2 0.0000 0.979 0.000 1.000 0.000 0.000 0.000
#> GSM97834 2 0.0000 0.979 0.000 1.000 0.000 0.000 0.000
#> GSM97840 2 0.4287 0.162 0.000 0.540 0.000 0.000 0.460
#> GSM97846 2 0.0000 0.979 0.000 1.000 0.000 0.000 0.000
#> GSM97848 2 0.0000 0.979 0.000 1.000 0.000 0.000 0.000
#> GSM97849 2 0.0000 0.979 0.000 1.000 0.000 0.000 0.000
#> GSM97850 2 0.0000 0.979 0.000 1.000 0.000 0.000 0.000
#> GSM97853 2 0.0000 0.979 0.000 1.000 0.000 0.000 0.000
#> GSM97855 2 0.0000 0.979 0.000 1.000 0.000 0.000 0.000
#> GSM97878 1 0.0404 0.956 0.988 0.000 0.012 0.000 0.000
#> GSM97913 5 0.0000 1.000 0.000 0.000 0.000 0.000 1.000
#> GSM97932 4 0.0000 0.989 0.000 0.000 0.000 1.000 0.000
#> GSM97939 5 0.0000 1.000 0.000 0.000 0.000 0.000 1.000
#> GSM97951 5 0.0162 0.995 0.000 0.004 0.000 0.000 0.996
#> GSM97957 3 0.0000 0.956 0.000 0.000 1.000 0.000 0.000
#> GSM97972 5 0.0000 1.000 0.000 0.000 0.000 0.000 1.000
#> GSM97793 3 0.0000 0.956 0.000 0.000 1.000 0.000 0.000
#> GSM97795 2 0.3661 0.616 0.000 0.724 0.000 0.000 0.276
#> GSM97802 3 0.0162 0.956 0.000 0.000 0.996 0.000 0.004
#> GSM97810 5 0.0000 1.000 0.000 0.000 0.000 0.000 1.000
#> GSM97815 5 0.0000 1.000 0.000 0.000 0.000 0.000 1.000
#> GSM97837 1 0.2127 0.863 0.892 0.000 0.000 0.108 0.000
#> GSM97843 3 0.0162 0.955 0.004 0.000 0.996 0.000 0.000
#> GSM97890 3 0.0162 0.956 0.000 0.000 0.996 0.000 0.004
#> GSM97899 4 0.0000 0.989 0.000 0.000 0.000 1.000 0.000
#> GSM97910 1 0.0404 0.956 0.988 0.000 0.012 0.000 0.000
#> GSM97916 1 0.0000 0.964 1.000 0.000 0.000 0.000 0.000
#> GSM97920 3 0.0000 0.956 0.000 0.000 1.000 0.000 0.000
#> GSM97921 1 0.0000 0.964 1.000 0.000 0.000 0.000 0.000
#> GSM97927 1 0.0000 0.964 1.000 0.000 0.000 0.000 0.000
#> GSM97937 1 0.0000 0.964 1.000 0.000 0.000 0.000 0.000
#> GSM97941 5 0.0000 1.000 0.000 0.000 0.000 0.000 1.000
#> GSM97943 1 0.2230 0.859 0.884 0.000 0.116 0.000 0.000
#> GSM97958 5 0.0000 1.000 0.000 0.000 0.000 0.000 1.000
#> GSM97960 5 0.0000 1.000 0.000 0.000 0.000 0.000 1.000
#> GSM97794 1 0.0404 0.956 0.988 0.000 0.012 0.000 0.000
#> GSM97796 4 0.0000 0.989 0.000 0.000 0.000 1.000 0.000
#> GSM97797 1 0.0404 0.956 0.988 0.000 0.012 0.000 0.000
#> GSM97798 4 0.0000 0.989 0.000 0.000 0.000 1.000 0.000
#> GSM97801 1 0.0000 0.964 1.000 0.000 0.000 0.000 0.000
#> GSM97806 1 0.0000 0.964 1.000 0.000 0.000 0.000 0.000
#> GSM97808 4 0.0000 0.989 0.000 0.000 0.000 1.000 0.000
#> GSM97813 1 0.4262 0.252 0.560 0.000 0.000 0.440 0.000
#> GSM97814 4 0.0000 0.989 0.000 0.000 0.000 1.000 0.000
#> GSM97818 1 0.0000 0.964 1.000 0.000 0.000 0.000 0.000
#> GSM97819 3 0.0000 0.956 0.000 0.000 1.000 0.000 0.000
#> GSM97821 5 0.0000 1.000 0.000 0.000 0.000 0.000 1.000
#> GSM97826 1 0.0162 0.961 0.996 0.000 0.000 0.004 0.000
#> GSM97829 1 0.0000 0.964 1.000 0.000 0.000 0.000 0.000
#> GSM97832 5 0.0000 1.000 0.000 0.000 0.000 0.000 1.000
#> GSM97836 1 0.0000 0.964 1.000 0.000 0.000 0.000 0.000
#> GSM97839 4 0.0000 0.989 0.000 0.000 0.000 1.000 0.000
#> GSM97844 2 0.0000 0.979 0.000 1.000 0.000 0.000 0.000
#> GSM97847 1 0.0000 0.964 1.000 0.000 0.000 0.000 0.000
#> GSM97851 4 0.0000 0.989 0.000 0.000 0.000 1.000 0.000
#> GSM97852 1 0.0000 0.964 1.000 0.000 0.000 0.000 0.000
#> GSM97856 4 0.0000 0.989 0.000 0.000 0.000 1.000 0.000
#> GSM97858 2 0.0000 0.979 0.000 1.000 0.000 0.000 0.000
#> GSM97859 1 0.0000 0.964 1.000 0.000 0.000 0.000 0.000
#> GSM97861 1 0.0000 0.964 1.000 0.000 0.000 0.000 0.000
#> GSM97863 4 0.0000 0.989 0.000 0.000 0.000 1.000 0.000
#> GSM97869 1 0.0000 0.964 1.000 0.000 0.000 0.000 0.000
#> GSM97870 1 0.0000 0.964 1.000 0.000 0.000 0.000 0.000
#> GSM97871 4 0.0000 0.989 0.000 0.000 0.000 1.000 0.000
#> GSM97877 5 0.0000 1.000 0.000 0.000 0.000 0.000 1.000
#> GSM97879 1 0.0000 0.964 1.000 0.000 0.000 0.000 0.000
#> GSM97882 1 0.0000 0.964 1.000 0.000 0.000 0.000 0.000
#> GSM97885 1 0.0000 0.964 1.000 0.000 0.000 0.000 0.000
#> GSM97886 4 0.0000 0.989 0.000 0.000 0.000 1.000 0.000
#> GSM97887 4 0.0000 0.989 0.000 0.000 0.000 1.000 0.000
#> GSM97888 4 0.0000 0.989 0.000 0.000 0.000 1.000 0.000
#> GSM97889 1 0.0000 0.964 1.000 0.000 0.000 0.000 0.000
#> GSM97891 1 0.0000 0.964 1.000 0.000 0.000 0.000 0.000
#> GSM97892 2 0.0000 0.979 0.000 1.000 0.000 0.000 0.000
#> GSM97893 4 0.0000 0.989 0.000 0.000 0.000 1.000 0.000
#> GSM97894 4 0.0000 0.989 0.000 0.000 0.000 1.000 0.000
#> GSM97895 4 0.0000 0.989 0.000 0.000 0.000 1.000 0.000
#> GSM97896 4 0.0000 0.989 0.000 0.000 0.000 1.000 0.000
#> GSM97898 4 0.0000 0.989 0.000 0.000 0.000 1.000 0.000
#> GSM97903 1 0.0000 0.964 1.000 0.000 0.000 0.000 0.000
#> GSM97905 1 0.0000 0.964 1.000 0.000 0.000 0.000 0.000
#> GSM97906 4 0.0000 0.989 0.000 0.000 0.000 1.000 0.000
#> GSM97908 1 0.3074 0.763 0.804 0.000 0.000 0.196 0.000
#> GSM97912 1 0.2230 0.857 0.884 0.000 0.000 0.116 0.000
#> GSM97914 1 0.0000 0.964 1.000 0.000 0.000 0.000 0.000
#> GSM97915 4 0.0000 0.989 0.000 0.000 0.000 1.000 0.000
#> GSM97917 4 0.0000 0.989 0.000 0.000 0.000 1.000 0.000
#> GSM97918 4 0.0000 0.989 0.000 0.000 0.000 1.000 0.000
#> GSM97919 4 0.0000 0.989 0.000 0.000 0.000 1.000 0.000
#> GSM97922 4 0.0000 0.989 0.000 0.000 0.000 1.000 0.000
#> GSM97924 2 0.0000 0.979 0.000 1.000 0.000 0.000 0.000
#> GSM97926 3 0.2179 0.890 0.100 0.000 0.896 0.000 0.004
#> GSM97930 1 0.0000 0.964 1.000 0.000 0.000 0.000 0.000
#> GSM97931 5 0.0000 1.000 0.000 0.000 0.000 0.000 1.000
#> GSM97935 1 0.0000 0.964 1.000 0.000 0.000 0.000 0.000
#> GSM97936 4 0.0000 0.989 0.000 0.000 0.000 1.000 0.000
#> GSM97938 4 0.3480 0.651 0.248 0.000 0.000 0.752 0.000
#> GSM97940 4 0.0000 0.989 0.000 0.000 0.000 1.000 0.000
#> GSM97942 3 0.2690 0.829 0.156 0.000 0.844 0.000 0.000
#> GSM97945 4 0.1965 0.871 0.096 0.000 0.000 0.904 0.000
#> GSM97946 2 0.0000 0.979 0.000 1.000 0.000 0.000 0.000
#> GSM97948 1 0.0290 0.959 0.992 0.000 0.008 0.000 0.000
#> GSM97950 4 0.0000 0.989 0.000 0.000 0.000 1.000 0.000
#> GSM97952 4 0.0000 0.989 0.000 0.000 0.000 1.000 0.000
#> GSM97953 1 0.0000 0.964 1.000 0.000 0.000 0.000 0.000
#> GSM97954 1 0.0000 0.964 1.000 0.000 0.000 0.000 0.000
#> GSM97955 4 0.0000 0.989 0.000 0.000 0.000 1.000 0.000
#> GSM97959 1 0.2690 0.809 0.844 0.000 0.000 0.000 0.156
#> GSM97961 4 0.0000 0.989 0.000 0.000 0.000 1.000 0.000
#> GSM97963 4 0.0000 0.989 0.000 0.000 0.000 1.000 0.000
#> GSM97965 4 0.0000 0.989 0.000 0.000 0.000 1.000 0.000
#> GSM97966 4 0.0000 0.989 0.000 0.000 0.000 1.000 0.000
#> GSM97967 2 0.0000 0.979 0.000 1.000 0.000 0.000 0.000
#> GSM97968 2 0.0000 0.979 0.000 1.000 0.000 0.000 0.000
#> GSM97969 1 0.0000 0.964 1.000 0.000 0.000 0.000 0.000
#> GSM97971 1 0.1043 0.932 0.960 0.000 0.000 0.040 0.000
#> GSM97799 3 0.1197 0.930 0.000 0.000 0.952 0.000 0.048
#> GSM97823 2 0.0000 0.979 0.000 1.000 0.000 0.000 0.000
#> GSM97824 3 0.0162 0.956 0.000 0.000 0.996 0.000 0.004
#> GSM97830 3 0.0000 0.956 0.000 0.000 1.000 0.000 0.000
#> GSM97835 5 0.0000 1.000 0.000 0.000 0.000 0.000 1.000
#> GSM97838 2 0.0000 0.979 0.000 1.000 0.000 0.000 0.000
#> GSM97841 2 0.0000 0.979 0.000 1.000 0.000 0.000 0.000
#> GSM97842 3 0.1197 0.930 0.000 0.000 0.952 0.000 0.048
#> GSM97854 2 0.0000 0.979 0.000 1.000 0.000 0.000 0.000
#> GSM97857 3 0.0162 0.956 0.000 0.000 0.996 0.000 0.004
#> GSM97860 3 0.0000 0.956 0.000 0.000 1.000 0.000 0.000
#> GSM97862 3 0.0162 0.956 0.000 0.000 0.996 0.000 0.004
#> GSM97864 2 0.0000 0.979 0.000 1.000 0.000 0.000 0.000
#> GSM97866 3 0.0000 0.956 0.000 0.000 1.000 0.000 0.000
#> GSM97868 3 0.0162 0.956 0.000 0.000 0.996 0.000 0.004
#> GSM97872 3 0.2377 0.863 0.128 0.000 0.872 0.000 0.000
#> GSM97873 5 0.0000 1.000 0.000 0.000 0.000 0.000 1.000
#> GSM97874 3 0.0290 0.954 0.008 0.000 0.992 0.000 0.000
#> GSM97875 3 0.0162 0.956 0.000 0.000 0.996 0.000 0.004
#> GSM97876 3 0.0000 0.956 0.000 0.000 1.000 0.000 0.000
#> GSM97880 3 0.1908 0.896 0.092 0.000 0.908 0.000 0.000
#> GSM97881 3 0.0162 0.956 0.000 0.000 0.996 0.000 0.004
#> GSM97884 3 0.4219 0.336 0.000 0.000 0.584 0.000 0.416
#> GSM97901 3 0.0000 0.956 0.000 0.000 1.000 0.000 0.000
#> GSM97902 3 0.1608 0.908 0.072 0.000 0.928 0.000 0.000
#> GSM97909 5 0.0000 1.000 0.000 0.000 0.000 0.000 1.000
#> GSM97911 3 0.0162 0.956 0.000 0.000 0.996 0.000 0.004
#> GSM97923 3 0.1908 0.896 0.092 0.000 0.908 0.000 0.000
#> GSM97928 1 0.0000 0.964 1.000 0.000 0.000 0.000 0.000
#> GSM97929 2 0.0000 0.979 0.000 1.000 0.000 0.000 0.000
#> GSM97933 3 0.0162 0.955 0.004 0.000 0.996 0.000 0.000
#> GSM97934 3 0.0000 0.956 0.000 0.000 1.000 0.000 0.000
#> GSM97944 3 0.1197 0.930 0.000 0.000 0.952 0.000 0.048
#> GSM97949 2 0.0000 0.979 0.000 1.000 0.000 0.000 0.000
#> GSM97956 3 0.0162 0.956 0.000 0.000 0.996 0.000 0.004
#> GSM97962 3 0.0000 0.956 0.000 0.000 1.000 0.000 0.000
#> GSM97964 3 0.0162 0.956 0.000 0.000 0.996 0.000 0.004
#> GSM97970 3 0.1197 0.930 0.000 0.000 0.952 0.000 0.048
#> GSM97822 1 0.0000 0.964 1.000 0.000 0.000 0.000 0.000
#> GSM97831 3 0.0000 0.956 0.000 0.000 1.000 0.000 0.000
#> GSM97845 1 0.3003 0.773 0.812 0.000 0.000 0.188 0.000
#> GSM97865 1 0.0000 0.964 1.000 0.000 0.000 0.000 0.000
#> GSM97867 3 0.2020 0.890 0.100 0.000 0.900 0.000 0.000
#> GSM97883 3 0.2179 0.879 0.112 0.000 0.888 0.000 0.000
#> GSM97897 4 0.0000 0.989 0.000 0.000 0.000 1.000 0.000
#> GSM97900 4 0.0000 0.989 0.000 0.000 0.000 1.000 0.000
#> GSM97904 1 0.0510 0.953 0.984 0.000 0.016 0.000 0.000
#> GSM97907 2 0.0000 0.979 0.000 1.000 0.000 0.000 0.000
#> GSM97925 3 0.0794 0.944 0.028 0.000 0.972 0.000 0.000
#> GSM97947 3 0.1851 0.900 0.088 0.000 0.912 0.000 0.000
cbind(get_classes(res, k = 6), get_membership(res, k = 6))
#> class entropy silhouette p1 p2 p3 p4 p5 p6
#> GSM97800 2 0.0000 0.9787 0.000 1.000 0.000 0.000 0.000 0.000
#> GSM97803 2 0.0000 0.9787 0.000 1.000 0.000 0.000 0.000 0.000
#> GSM97804 2 0.0000 0.9787 0.000 1.000 0.000 0.000 0.000 0.000
#> GSM97805 2 0.0000 0.9787 0.000 1.000 0.000 0.000 0.000 0.000
#> GSM97807 2 0.0000 0.9787 0.000 1.000 0.000 0.000 0.000 0.000
#> GSM97809 2 0.0000 0.9787 0.000 1.000 0.000 0.000 0.000 0.000
#> GSM97811 2 0.0000 0.9787 0.000 1.000 0.000 0.000 0.000 0.000
#> GSM97812 2 0.0000 0.9787 0.000 1.000 0.000 0.000 0.000 0.000
#> GSM97816 5 0.3847 0.1712 0.000 0.000 0.000 0.000 0.544 0.456
#> GSM97817 2 0.0000 0.9787 0.000 1.000 0.000 0.000 0.000 0.000
#> GSM97820 2 0.0000 0.9787 0.000 1.000 0.000 0.000 0.000 0.000
#> GSM97825 2 0.0000 0.9787 0.000 1.000 0.000 0.000 0.000 0.000
#> GSM97827 2 0.0000 0.9787 0.000 1.000 0.000 0.000 0.000 0.000
#> GSM97828 6 0.3221 0.8619 0.000 0.000 0.264 0.000 0.000 0.736
#> GSM97833 2 0.0000 0.9787 0.000 1.000 0.000 0.000 0.000 0.000
#> GSM97834 2 0.0000 0.9787 0.000 1.000 0.000 0.000 0.000 0.000
#> GSM97840 2 0.3854 0.1414 0.000 0.536 0.000 0.000 0.464 0.000
#> GSM97846 2 0.0000 0.9787 0.000 1.000 0.000 0.000 0.000 0.000
#> GSM97848 2 0.0000 0.9787 0.000 1.000 0.000 0.000 0.000 0.000
#> GSM97849 2 0.0000 0.9787 0.000 1.000 0.000 0.000 0.000 0.000
#> GSM97850 2 0.0000 0.9787 0.000 1.000 0.000 0.000 0.000 0.000
#> GSM97853 2 0.0000 0.9787 0.000 1.000 0.000 0.000 0.000 0.000
#> GSM97855 2 0.0000 0.9787 0.000 1.000 0.000 0.000 0.000 0.000
#> GSM97878 1 0.0146 0.8693 0.996 0.000 0.004 0.000 0.000 0.000
#> GSM97913 5 0.0000 0.9578 0.000 0.000 0.000 0.000 1.000 0.000
#> GSM97932 4 0.0000 0.9754 0.000 0.000 0.000 1.000 0.000 0.000
#> GSM97939 5 0.0000 0.9578 0.000 0.000 0.000 0.000 1.000 0.000
#> GSM97951 5 0.0000 0.9578 0.000 0.000 0.000 0.000 1.000 0.000
#> GSM97957 6 0.3221 0.8619 0.000 0.000 0.264 0.000 0.000 0.736
#> GSM97972 5 0.0000 0.9578 0.000 0.000 0.000 0.000 1.000 0.000
#> GSM97793 6 0.3198 0.8623 0.000 0.000 0.260 0.000 0.000 0.740
#> GSM97795 2 0.3309 0.6036 0.000 0.720 0.000 0.000 0.280 0.000
#> GSM97802 3 0.2527 0.7058 0.000 0.000 0.832 0.000 0.000 0.168
#> GSM97810 5 0.0000 0.9578 0.000 0.000 0.000 0.000 1.000 0.000
#> GSM97815 5 0.0000 0.9578 0.000 0.000 0.000 0.000 1.000 0.000
#> GSM97837 1 0.1075 0.8426 0.952 0.000 0.000 0.048 0.000 0.000
#> GSM97843 6 0.3482 0.7923 0.000 0.000 0.316 0.000 0.000 0.684
#> GSM97890 3 0.0146 0.8832 0.000 0.000 0.996 0.000 0.000 0.004
#> GSM97899 4 0.0000 0.9754 0.000 0.000 0.000 1.000 0.000 0.000
#> GSM97910 1 0.0713 0.8563 0.972 0.000 0.000 0.000 0.000 0.028
#> GSM97916 1 0.0000 0.8708 1.000 0.000 0.000 0.000 0.000 0.000
#> GSM97920 6 0.3198 0.8623 0.000 0.000 0.260 0.000 0.000 0.740
#> GSM97921 1 0.3076 0.8287 0.760 0.000 0.000 0.000 0.000 0.240
#> GSM97927 1 0.3198 0.8225 0.740 0.000 0.000 0.000 0.000 0.260
#> GSM97937 1 0.0000 0.8708 1.000 0.000 0.000 0.000 0.000 0.000
#> GSM97941 5 0.0000 0.9578 0.000 0.000 0.000 0.000 1.000 0.000
#> GSM97943 6 0.3221 0.5974 0.264 0.000 0.000 0.000 0.000 0.736
#> GSM97958 5 0.0000 0.9578 0.000 0.000 0.000 0.000 1.000 0.000
#> GSM97960 5 0.0000 0.9578 0.000 0.000 0.000 0.000 1.000 0.000
#> GSM97794 1 0.0000 0.8708 1.000 0.000 0.000 0.000 0.000 0.000
#> GSM97796 4 0.0000 0.9754 0.000 0.000 0.000 1.000 0.000 0.000
#> GSM97797 1 0.0000 0.8708 1.000 0.000 0.000 0.000 0.000 0.000
#> GSM97798 4 0.0000 0.9754 0.000 0.000 0.000 1.000 0.000 0.000
#> GSM97801 1 0.0865 0.8507 0.964 0.000 0.000 0.000 0.000 0.036
#> GSM97806 1 0.3198 0.8225 0.740 0.000 0.000 0.000 0.000 0.260
#> GSM97808 4 0.0000 0.9754 0.000 0.000 0.000 1.000 0.000 0.000
#> GSM97813 4 0.5978 -0.0545 0.296 0.000 0.000 0.444 0.000 0.260
#> GSM97814 4 0.0000 0.9754 0.000 0.000 0.000 1.000 0.000 0.000
#> GSM97818 1 0.0000 0.8708 1.000 0.000 0.000 0.000 0.000 0.000
#> GSM97819 3 0.0000 0.8861 0.000 0.000 1.000 0.000 0.000 0.000
#> GSM97821 5 0.0000 0.9578 0.000 0.000 0.000 0.000 1.000 0.000
#> GSM97826 1 0.0000 0.8708 1.000 0.000 0.000 0.000 0.000 0.000
#> GSM97829 1 0.0000 0.8708 1.000 0.000 0.000 0.000 0.000 0.000
#> GSM97832 5 0.0000 0.9578 0.000 0.000 0.000 0.000 1.000 0.000
#> GSM97836 1 0.3198 0.8225 0.740 0.000 0.000 0.000 0.000 0.260
#> GSM97839 4 0.0000 0.9754 0.000 0.000 0.000 1.000 0.000 0.000
#> GSM97844 2 0.0000 0.9787 0.000 1.000 0.000 0.000 0.000 0.000
#> GSM97847 1 0.0000 0.8708 1.000 0.000 0.000 0.000 0.000 0.000
#> GSM97851 4 0.0000 0.9754 0.000 0.000 0.000 1.000 0.000 0.000
#> GSM97852 1 0.0000 0.8708 1.000 0.000 0.000 0.000 0.000 0.000
#> GSM97856 4 0.0000 0.9754 0.000 0.000 0.000 1.000 0.000 0.000
#> GSM97858 2 0.0000 0.9787 0.000 1.000 0.000 0.000 0.000 0.000
#> GSM97859 1 0.3198 0.8225 0.740 0.000 0.000 0.000 0.000 0.260
#> GSM97861 1 0.3198 0.8225 0.740 0.000 0.000 0.000 0.000 0.260
#> GSM97863 4 0.0000 0.9754 0.000 0.000 0.000 1.000 0.000 0.000
#> GSM97869 1 0.3198 0.8225 0.740 0.000 0.000 0.000 0.000 0.260
#> GSM97870 1 0.3198 0.8225 0.740 0.000 0.000 0.000 0.000 0.260
#> GSM97871 4 0.0000 0.9754 0.000 0.000 0.000 1.000 0.000 0.000
#> GSM97877 5 0.0000 0.9578 0.000 0.000 0.000 0.000 1.000 0.000
#> GSM97879 1 0.0000 0.8708 1.000 0.000 0.000 0.000 0.000 0.000
#> GSM97882 1 0.3198 0.8225 0.740 0.000 0.000 0.000 0.000 0.260
#> GSM97885 1 0.0000 0.8708 1.000 0.000 0.000 0.000 0.000 0.000
#> GSM97886 4 0.0000 0.9754 0.000 0.000 0.000 1.000 0.000 0.000
#> GSM97887 4 0.0000 0.9754 0.000 0.000 0.000 1.000 0.000 0.000
#> GSM97888 4 0.0000 0.9754 0.000 0.000 0.000 1.000 0.000 0.000
#> GSM97889 1 0.3198 0.8225 0.740 0.000 0.000 0.000 0.000 0.260
#> GSM97891 1 0.3198 0.8225 0.740 0.000 0.000 0.000 0.000 0.260
#> GSM97892 2 0.0000 0.9787 0.000 1.000 0.000 0.000 0.000 0.000
#> GSM97893 4 0.0000 0.9754 0.000 0.000 0.000 1.000 0.000 0.000
#> GSM97894 4 0.0000 0.9754 0.000 0.000 0.000 1.000 0.000 0.000
#> GSM97895 4 0.0000 0.9754 0.000 0.000 0.000 1.000 0.000 0.000
#> GSM97896 4 0.0000 0.9754 0.000 0.000 0.000 1.000 0.000 0.000
#> GSM97898 4 0.0000 0.9754 0.000 0.000 0.000 1.000 0.000 0.000
#> GSM97903 1 0.0000 0.8708 1.000 0.000 0.000 0.000 0.000 0.000
#> GSM97905 1 0.3221 0.8201 0.736 0.000 0.000 0.000 0.000 0.264
#> GSM97906 4 0.0000 0.9754 0.000 0.000 0.000 1.000 0.000 0.000
#> GSM97908 1 0.2178 0.7671 0.868 0.000 0.000 0.132 0.000 0.000
#> GSM97912 1 0.1663 0.8109 0.912 0.000 0.000 0.088 0.000 0.000
#> GSM97914 1 0.0000 0.8708 1.000 0.000 0.000 0.000 0.000 0.000
#> GSM97915 4 0.0000 0.9754 0.000 0.000 0.000 1.000 0.000 0.000
#> GSM97917 4 0.0000 0.9754 0.000 0.000 0.000 1.000 0.000 0.000
#> GSM97918 4 0.0000 0.9754 0.000 0.000 0.000 1.000 0.000 0.000
#> GSM97919 4 0.0000 0.9754 0.000 0.000 0.000 1.000 0.000 0.000
#> GSM97922 4 0.0000 0.9754 0.000 0.000 0.000 1.000 0.000 0.000
#> GSM97924 2 0.0000 0.9787 0.000 1.000 0.000 0.000 0.000 0.000
#> GSM97926 3 0.3863 0.5531 0.028 0.000 0.712 0.000 0.000 0.260
#> GSM97930 1 0.0000 0.8708 1.000 0.000 0.000 0.000 0.000 0.000
#> GSM97931 5 0.0713 0.9386 0.000 0.000 0.028 0.000 0.972 0.000
#> GSM97935 1 0.3198 0.8225 0.740 0.000 0.000 0.000 0.000 0.260
#> GSM97936 4 0.0000 0.9754 0.000 0.000 0.000 1.000 0.000 0.000
#> GSM97938 4 0.3645 0.6687 0.236 0.000 0.000 0.740 0.000 0.024
#> GSM97940 4 0.0000 0.9754 0.000 0.000 0.000 1.000 0.000 0.000
#> GSM97942 6 0.1257 0.6333 0.028 0.000 0.020 0.000 0.000 0.952
#> GSM97945 4 0.0865 0.9357 0.036 0.000 0.000 0.964 0.000 0.000
#> GSM97946 2 0.0000 0.9787 0.000 1.000 0.000 0.000 0.000 0.000
#> GSM97948 1 0.3221 0.8201 0.736 0.000 0.000 0.000 0.000 0.264
#> GSM97950 4 0.0000 0.9754 0.000 0.000 0.000 1.000 0.000 0.000
#> GSM97952 4 0.0000 0.9754 0.000 0.000 0.000 1.000 0.000 0.000
#> GSM97953 1 0.0865 0.8684 0.964 0.000 0.000 0.000 0.000 0.036
#> GSM97954 1 0.0000 0.8708 1.000 0.000 0.000 0.000 0.000 0.000
#> GSM97955 4 0.0000 0.9754 0.000 0.000 0.000 1.000 0.000 0.000
#> GSM97959 1 0.2003 0.7844 0.884 0.000 0.000 0.000 0.116 0.000
#> GSM97961 4 0.0000 0.9754 0.000 0.000 0.000 1.000 0.000 0.000
#> GSM97963 4 0.0000 0.9754 0.000 0.000 0.000 1.000 0.000 0.000
#> GSM97965 4 0.0000 0.9754 0.000 0.000 0.000 1.000 0.000 0.000
#> GSM97966 4 0.0000 0.9754 0.000 0.000 0.000 1.000 0.000 0.000
#> GSM97967 2 0.0000 0.9787 0.000 1.000 0.000 0.000 0.000 0.000
#> GSM97968 2 0.0000 0.9787 0.000 1.000 0.000 0.000 0.000 0.000
#> GSM97969 1 0.0000 0.8708 1.000 0.000 0.000 0.000 0.000 0.000
#> GSM97971 1 0.4613 0.7600 0.660 0.000 0.000 0.080 0.000 0.260
#> GSM97799 3 0.0000 0.8861 0.000 0.000 1.000 0.000 0.000 0.000
#> GSM97823 2 0.0000 0.9787 0.000 1.000 0.000 0.000 0.000 0.000
#> GSM97824 3 0.0000 0.8861 0.000 0.000 1.000 0.000 0.000 0.000
#> GSM97830 6 0.3221 0.8619 0.000 0.000 0.264 0.000 0.000 0.736
#> GSM97835 5 0.1556 0.8947 0.000 0.000 0.080 0.000 0.920 0.000
#> GSM97838 2 0.0000 0.9787 0.000 1.000 0.000 0.000 0.000 0.000
#> GSM97841 2 0.0000 0.9787 0.000 1.000 0.000 0.000 0.000 0.000
#> GSM97842 3 0.0000 0.8861 0.000 0.000 1.000 0.000 0.000 0.000
#> GSM97854 2 0.0000 0.9787 0.000 1.000 0.000 0.000 0.000 0.000
#> GSM97857 3 0.1556 0.8167 0.000 0.000 0.920 0.000 0.080 0.000
#> GSM97860 6 0.3198 0.8623 0.000 0.000 0.260 0.000 0.000 0.740
#> GSM97862 3 0.0000 0.8861 0.000 0.000 1.000 0.000 0.000 0.000
#> GSM97864 2 0.0000 0.9787 0.000 1.000 0.000 0.000 0.000 0.000
#> GSM97866 3 0.0000 0.8861 0.000 0.000 1.000 0.000 0.000 0.000
#> GSM97868 3 0.0000 0.8861 0.000 0.000 1.000 0.000 0.000 0.000
#> GSM97872 6 0.1913 0.6270 0.012 0.000 0.080 0.000 0.000 0.908
#> GSM97873 5 0.1556 0.8947 0.000 0.000 0.080 0.000 0.920 0.000
#> GSM97874 6 0.3198 0.8623 0.000 0.000 0.260 0.000 0.000 0.740
#> GSM97875 3 0.0000 0.8861 0.000 0.000 1.000 0.000 0.000 0.000
#> GSM97876 6 0.3221 0.8619 0.000 0.000 0.264 0.000 0.000 0.736
#> GSM97880 6 0.3198 0.8623 0.000 0.000 0.260 0.000 0.000 0.740
#> GSM97881 3 0.0000 0.8861 0.000 0.000 1.000 0.000 0.000 0.000
#> GSM97884 3 0.3789 0.2722 0.000 0.000 0.584 0.000 0.416 0.000
#> GSM97901 3 0.0000 0.8861 0.000 0.000 1.000 0.000 0.000 0.000
#> GSM97902 3 0.5170 0.0761 0.112 0.000 0.576 0.000 0.000 0.312
#> GSM97909 5 0.0000 0.9578 0.000 0.000 0.000 0.000 1.000 0.000
#> GSM97911 3 0.0000 0.8861 0.000 0.000 1.000 0.000 0.000 0.000
#> GSM97923 6 0.3076 0.8506 0.000 0.000 0.240 0.000 0.000 0.760
#> GSM97928 1 0.2762 0.8393 0.804 0.000 0.000 0.000 0.000 0.196
#> GSM97929 2 0.0000 0.9787 0.000 1.000 0.000 0.000 0.000 0.000
#> GSM97933 6 0.3221 0.8619 0.000 0.000 0.264 0.000 0.000 0.736
#> GSM97934 6 0.3221 0.8619 0.000 0.000 0.264 0.000 0.000 0.736
#> GSM97944 3 0.0000 0.8861 0.000 0.000 1.000 0.000 0.000 0.000
#> GSM97949 2 0.0000 0.9787 0.000 1.000 0.000 0.000 0.000 0.000
#> GSM97956 3 0.0000 0.8861 0.000 0.000 1.000 0.000 0.000 0.000
#> GSM97962 6 0.3244 0.8584 0.000 0.000 0.268 0.000 0.000 0.732
#> GSM97964 3 0.0000 0.8861 0.000 0.000 1.000 0.000 0.000 0.000
#> GSM97970 3 0.0000 0.8861 0.000 0.000 1.000 0.000 0.000 0.000
#> GSM97822 1 0.3198 0.8225 0.740 0.000 0.000 0.000 0.000 0.260
#> GSM97831 3 0.3371 0.3783 0.000 0.000 0.708 0.000 0.000 0.292
#> GSM97845 1 0.2697 0.6985 0.812 0.000 0.000 0.188 0.000 0.000
#> GSM97865 1 0.0000 0.8708 1.000 0.000 0.000 0.000 0.000 0.000
#> GSM97867 6 0.0000 0.6600 0.000 0.000 0.000 0.000 0.000 1.000
#> GSM97883 6 0.0858 0.6391 0.028 0.000 0.004 0.000 0.000 0.968
#> GSM97897 4 0.0000 0.9754 0.000 0.000 0.000 1.000 0.000 0.000
#> GSM97900 4 0.0000 0.9754 0.000 0.000 0.000 1.000 0.000 0.000
#> GSM97904 1 0.3221 0.8202 0.736 0.000 0.000 0.000 0.000 0.264
#> GSM97907 2 0.0000 0.9787 0.000 1.000 0.000 0.000 0.000 0.000
#> GSM97925 3 0.0622 0.8716 0.012 0.000 0.980 0.000 0.000 0.008
#> GSM97947 3 0.3175 0.6834 0.028 0.000 0.808 0.000 0.000 0.164
Heatmaps for the consensus matrix. It visualizes the probability of two samples to be in a same group.
consensus_heatmap(res, k = 2)
consensus_heatmap(res, k = 3)
consensus_heatmap(res, k = 4)
consensus_heatmap(res, k = 5)
consensus_heatmap(res, k = 6)
Heatmaps for the membership of samples in all partitions to see how consistent they are:
membership_heatmap(res, k = 2)
membership_heatmap(res, k = 3)
membership_heatmap(res, k = 4)
membership_heatmap(res, k = 5)
membership_heatmap(res, k = 6)
As soon as we have had the classes for columns, we can look for signatures which are significantly different between classes which can be candidate marks for certain classes. Following are the heatmaps for signatures.
Signature heatmaps where rows are scaled:
get_signatures(res, k = 2)
get_signatures(res, k = 3)
get_signatures(res, k = 4)
get_signatures(res, k = 5)
get_signatures(res, k = 6)
Signature heatmaps where rows are not scaled:
get_signatures(res, k = 2, scale_rows = FALSE)
get_signatures(res, k = 3, scale_rows = FALSE)
get_signatures(res, k = 4, scale_rows = FALSE)
get_signatures(res, k = 5, scale_rows = FALSE)
get_signatures(res, k = 6, scale_rows = FALSE)
Compare the overlap of signatures from different k:
compare_signatures(res)
get_signature() returns a data frame invisibly. TO get the list of signatures, the function
call should be assigned to a variable explicitly. In following code, if plot argument is set
to FALSE, no heatmap is plotted while only the differential analysis is performed.
# code only for demonstration
tb = get_signature(res, k = ..., plot = FALSE)
An example of the output of tb is:
#> which_row fdr mean_1 mean_2 scaled_mean_1 scaled_mean_2 km
#> 1 38 0.042760348 8.373488 9.131774 -0.5533452 0.5164555 1
#> 2 40 0.018707592 7.106213 8.469186 -0.6173731 0.5762149 1
#> 3 55 0.019134737 10.221463 11.207825 -0.6159697 0.5749050 1
#> 4 59 0.006059896 5.921854 7.869574 -0.6899429 0.6439467 1
#> 5 60 0.018055526 8.928898 10.211722 -0.6204761 0.5791110 1
#> 6 98 0.009384629 15.714769 14.887706 0.6635654 -0.6193277 2
...
The columns in tb are:
which_row: row indices corresponding to the input matrix.fdr: FDR for the differential test. mean_x: The mean value in group x.scaled_mean_x: The mean value in group x after rows are scaled.km: Row groups if k-means clustering is applied to rows.UMAP plot which shows how samples are separated.
dimension_reduction(res, k = 2, method = "UMAP")
dimension_reduction(res, k = 3, method = "UMAP")
dimension_reduction(res, k = 4, method = "UMAP")
dimension_reduction(res, k = 5, method = "UMAP")
dimension_reduction(res, k = 6, method = "UMAP")
Following heatmap shows how subgroups are split when increasing k:
collect_classes(res)
Test correlation between subgroups and known annotations. If the known annotation is numeric, one-way ANOVA test is applied, and if the known annotation is discrete, chi-squared contingency table test is applied.
test_to_known_factors(res)
#> n disease.state(p) tissue(p) k
#> ATC:pam 179 8.58e-15 8.60e-15 2
#> ATC:pam 177 1.73e-23 7.29e-24 3
#> ATC:pam 179 1.87e-27 3.77e-29 4
#> ATC:pam 177 3.08e-32 4.98e-29 5
#> ATC:pam 174 4.86e-31 5.83e-28 6
If matrix rows can be associated to genes, consider to use functional_enrichment(res,
...) to perform function enrichment for the signature genes. See this vignette for more detailed explanations.
The object with results only for a single top-value method and a single partition method can be extracted as:
res = res_list["ATC", "mclust"]
# you can also extract it by
# res = res_list["ATC:mclust"]
A summary of res and all the functions that can be applied to it:
res
#> A 'ConsensusPartition' object with k = 2, 3, 4, 5, 6.
#> On a matrix with 51882 rows and 180 columns.
#> Top rows (1000, 2000, 3000, 4000, 5000) are extracted by 'ATC' method.
#> Subgroups are detected by 'mclust' method.
#> Performed in total 1250 partitions by row resampling.
#> Best k for subgroups seems to be 2.
#>
#> Following methods can be applied to this 'ConsensusPartition' object:
#> [1] "cola_report" "collect_classes" "collect_plots"
#> [4] "collect_stats" "colnames" "compare_signatures"
#> [7] "consensus_heatmap" "dimension_reduction" "functional_enrichment"
#> [10] "get_anno_col" "get_anno" "get_classes"
#> [13] "get_consensus" "get_matrix" "get_membership"
#> [16] "get_param" "get_signatures" "get_stats"
#> [19] "is_best_k" "is_stable_k" "membership_heatmap"
#> [22] "ncol" "nrow" "plot_ecdf"
#> [25] "rownames" "select_partition_number" "show"
#> [28] "suggest_best_k" "test_to_known_factors"
collect_plots() function collects all the plots made from res for all k (number of partitions)
into one single page to provide an easy and fast comparison between different k.
collect_plots(res)
The plots are:
k and the heatmap of
predicted classes for each k.k.k.k.All the plots in panels can be made by individual functions and they are plotted later in this section.
select_partition_number() produces several plots showing different
statistics for choosing “optimized” k. There are following statistics:
k;k, the area increased is defined as \(A_k - A_{k-1}\).The detailed explanations of these statistics can be found in the cola vignette.
Generally speaking, lower PAC score, higher mean silhouette score or higher
concordance corresponds to better partition. Rand index and Jaccard index
measure how similar the current partition is compared to partition with k-1.
If they are too similar, we won't accept k is better than k-1.
select_partition_number(res)
The numeric values for all these statistics can be obtained by get_stats().
get_stats(res)
#> k 1-PAC mean_silhouette concordance area_increased Rand Jaccard
#> 2 2 1.000 1.000 1.000 0.3157 0.685 0.685
#> 3 3 0.671 0.880 0.908 0.9357 0.691 0.548
#> 4 4 0.673 0.752 0.815 0.1822 0.877 0.685
#> 5 5 0.805 0.875 0.904 0.0683 0.862 0.572
#> 6 6 0.807 0.801 0.852 0.0336 0.980 0.913
suggest_best_k() suggests the best \(k\) based on these statistics. The rules are as follows:
suggest_best_k(res)
#> [1] 2
Following shows the table of the partitions (You need to click the show/hide
code output link to see it). The membership matrix (columns with name p*)
is inferred by
clue::cl_consensus()
function with the SE method. Basically the value in the membership matrix
represents the probability to belong to a certain group. The finall class
label for an item is determined with the group with highest probability it
belongs to.
In get_classes() function, the entropy is calculated from the membership
matrix and the silhouette score is calculated from the consensus matrix.
cbind(get_classes(res, k = 2), get_membership(res, k = 2))
#> class entropy silhouette p1 p2
#> GSM97800 2 0.0000 1.000 0.000 1.000
#> GSM97803 2 0.0000 1.000 0.000 1.000
#> GSM97804 2 0.0000 1.000 0.000 1.000
#> GSM97805 2 0.0000 1.000 0.000 1.000
#> GSM97807 2 0.0000 1.000 0.000 1.000
#> GSM97809 2 0.0000 1.000 0.000 1.000
#> GSM97811 2 0.0000 1.000 0.000 1.000
#> GSM97812 2 0.0000 1.000 0.000 1.000
#> GSM97816 1 0.0000 1.000 1.000 0.000
#> GSM97817 2 0.0000 1.000 0.000 1.000
#> GSM97820 2 0.0000 1.000 0.000 1.000
#> GSM97825 2 0.0000 1.000 0.000 1.000
#> GSM97827 2 0.0000 1.000 0.000 1.000
#> GSM97828 1 0.0000 1.000 1.000 0.000
#> GSM97833 2 0.0000 1.000 0.000 1.000
#> GSM97834 2 0.0000 1.000 0.000 1.000
#> GSM97840 1 0.0376 0.996 0.996 0.004
#> GSM97846 2 0.0000 1.000 0.000 1.000
#> GSM97848 2 0.0000 1.000 0.000 1.000
#> GSM97849 2 0.0000 1.000 0.000 1.000
#> GSM97850 2 0.0000 1.000 0.000 1.000
#> GSM97853 2 0.0000 1.000 0.000 1.000
#> GSM97855 2 0.0000 1.000 0.000 1.000
#> GSM97878 1 0.0000 1.000 1.000 0.000
#> GSM97913 1 0.0000 1.000 1.000 0.000
#> GSM97932 1 0.0000 1.000 1.000 0.000
#> GSM97939 1 0.0000 1.000 1.000 0.000
#> GSM97951 1 0.0000 1.000 1.000 0.000
#> GSM97957 1 0.0000 1.000 1.000 0.000
#> GSM97972 1 0.0000 1.000 1.000 0.000
#> GSM97793 1 0.0000 1.000 1.000 0.000
#> GSM97795 1 0.0000 1.000 1.000 0.000
#> GSM97802 1 0.0000 1.000 1.000 0.000
#> GSM97810 1 0.0000 1.000 1.000 0.000
#> GSM97815 1 0.0000 1.000 1.000 0.000
#> GSM97837 1 0.0000 1.000 1.000 0.000
#> GSM97843 1 0.0000 1.000 1.000 0.000
#> GSM97890 1 0.0000 1.000 1.000 0.000
#> GSM97899 1 0.0000 1.000 1.000 0.000
#> GSM97910 1 0.0000 1.000 1.000 0.000
#> GSM97916 1 0.0000 1.000 1.000 0.000
#> GSM97920 1 0.0000 1.000 1.000 0.000
#> GSM97921 1 0.0000 1.000 1.000 0.000
#> GSM97927 1 0.0000 1.000 1.000 0.000
#> GSM97937 1 0.0000 1.000 1.000 0.000
#> GSM97941 1 0.0000 1.000 1.000 0.000
#> GSM97943 1 0.0000 1.000 1.000 0.000
#> GSM97958 1 0.0000 1.000 1.000 0.000
#> GSM97960 1 0.0000 1.000 1.000 0.000
#> GSM97794 1 0.0000 1.000 1.000 0.000
#> GSM97796 1 0.0000 1.000 1.000 0.000
#> GSM97797 1 0.0000 1.000 1.000 0.000
#> GSM97798 1 0.0000 1.000 1.000 0.000
#> GSM97801 1 0.0000 1.000 1.000 0.000
#> GSM97806 1 0.0000 1.000 1.000 0.000
#> GSM97808 1 0.0000 1.000 1.000 0.000
#> GSM97813 1 0.0000 1.000 1.000 0.000
#> GSM97814 1 0.0000 1.000 1.000 0.000
#> GSM97818 1 0.0000 1.000 1.000 0.000
#> GSM97819 1 0.0000 1.000 1.000 0.000
#> GSM97821 1 0.0000 1.000 1.000 0.000
#> GSM97826 1 0.0000 1.000 1.000 0.000
#> GSM97829 1 0.0000 1.000 1.000 0.000
#> GSM97832 1 0.0000 1.000 1.000 0.000
#> GSM97836 1 0.0000 1.000 1.000 0.000
#> GSM97839 1 0.0000 1.000 1.000 0.000
#> GSM97844 2 0.0000 1.000 0.000 1.000
#> GSM97847 1 0.0000 1.000 1.000 0.000
#> GSM97851 1 0.0000 1.000 1.000 0.000
#> GSM97852 1 0.0000 1.000 1.000 0.000
#> GSM97856 1 0.0000 1.000 1.000 0.000
#> GSM97858 2 0.0000 1.000 0.000 1.000
#> GSM97859 1 0.0000 1.000 1.000 0.000
#> GSM97861 1 0.0000 1.000 1.000 0.000
#> GSM97863 1 0.0000 1.000 1.000 0.000
#> GSM97869 1 0.0000 1.000 1.000 0.000
#> GSM97870 1 0.0000 1.000 1.000 0.000
#> GSM97871 1 0.0000 1.000 1.000 0.000
#> GSM97877 1 0.0000 1.000 1.000 0.000
#> GSM97879 1 0.0000 1.000 1.000 0.000
#> GSM97882 1 0.0000 1.000 1.000 0.000
#> GSM97885 1 0.0000 1.000 1.000 0.000
#> GSM97886 1 0.0000 1.000 1.000 0.000
#> GSM97887 1 0.0000 1.000 1.000 0.000
#> GSM97888 1 0.0000 1.000 1.000 0.000
#> GSM97889 1 0.0000 1.000 1.000 0.000
#> GSM97891 1 0.0000 1.000 1.000 0.000
#> GSM97892 2 0.0000 1.000 0.000 1.000
#> GSM97893 1 0.0000 1.000 1.000 0.000
#> GSM97894 1 0.0000 1.000 1.000 0.000
#> GSM97895 1 0.0000 1.000 1.000 0.000
#> GSM97896 1 0.0000 1.000 1.000 0.000
#> GSM97898 1 0.0000 1.000 1.000 0.000
#> GSM97903 1 0.0000 1.000 1.000 0.000
#> GSM97905 1 0.0000 1.000 1.000 0.000
#> GSM97906 1 0.0000 1.000 1.000 0.000
#> GSM97908 1 0.0000 1.000 1.000 0.000
#> GSM97912 1 0.0000 1.000 1.000 0.000
#> GSM97914 1 0.0000 1.000 1.000 0.000
#> GSM97915 1 0.0000 1.000 1.000 0.000
#> GSM97917 1 0.0000 1.000 1.000 0.000
#> GSM97918 1 0.0000 1.000 1.000 0.000
#> GSM97919 1 0.0000 1.000 1.000 0.000
#> GSM97922 1 0.0000 1.000 1.000 0.000
#> GSM97924 2 0.0000 1.000 0.000 1.000
#> GSM97926 1 0.0000 1.000 1.000 0.000
#> GSM97930 1 0.0000 1.000 1.000 0.000
#> GSM97931 1 0.0000 1.000 1.000 0.000
#> GSM97935 1 0.0000 1.000 1.000 0.000
#> GSM97936 1 0.0000 1.000 1.000 0.000
#> GSM97938 1 0.0000 1.000 1.000 0.000
#> GSM97940 1 0.0000 1.000 1.000 0.000
#> GSM97942 1 0.0000 1.000 1.000 0.000
#> GSM97945 1 0.0000 1.000 1.000 0.000
#> GSM97946 2 0.0000 1.000 0.000 1.000
#> GSM97948 1 0.0000 1.000 1.000 0.000
#> GSM97950 1 0.0000 1.000 1.000 0.000
#> GSM97952 1 0.0000 1.000 1.000 0.000
#> GSM97953 1 0.0000 1.000 1.000 0.000
#> GSM97954 1 0.0000 1.000 1.000 0.000
#> GSM97955 1 0.0000 1.000 1.000 0.000
#> GSM97959 1 0.0000 1.000 1.000 0.000
#> GSM97961 1 0.0000 1.000 1.000 0.000
#> GSM97963 1 0.0000 1.000 1.000 0.000
#> GSM97965 1 0.0000 1.000 1.000 0.000
#> GSM97966 1 0.0000 1.000 1.000 0.000
#> GSM97967 2 0.0000 1.000 0.000 1.000
#> GSM97968 2 0.0000 1.000 0.000 1.000
#> GSM97969 1 0.0000 1.000 1.000 0.000
#> GSM97971 1 0.0000 1.000 1.000 0.000
#> GSM97799 1 0.0000 1.000 1.000 0.000
#> GSM97823 2 0.0000 1.000 0.000 1.000
#> GSM97824 1 0.0000 1.000 1.000 0.000
#> GSM97830 1 0.0000 1.000 1.000 0.000
#> GSM97835 1 0.0000 1.000 1.000 0.000
#> GSM97838 2 0.0000 1.000 0.000 1.000
#> GSM97841 2 0.0000 1.000 0.000 1.000
#> GSM97842 1 0.0000 1.000 1.000 0.000
#> GSM97854 2 0.0000 1.000 0.000 1.000
#> GSM97857 1 0.0000 1.000 1.000 0.000
#> GSM97860 1 0.0000 1.000 1.000 0.000
#> GSM97862 1 0.0000 1.000 1.000 0.000
#> GSM97864 2 0.0000 1.000 0.000 1.000
#> GSM97866 1 0.0000 1.000 1.000 0.000
#> GSM97868 1 0.0000 1.000 1.000 0.000
#> GSM97872 1 0.0000 1.000 1.000 0.000
#> GSM97873 1 0.0000 1.000 1.000 0.000
#> GSM97874 1 0.0000 1.000 1.000 0.000
#> GSM97875 1 0.0000 1.000 1.000 0.000
#> GSM97876 1 0.0000 1.000 1.000 0.000
#> GSM97880 1 0.0000 1.000 1.000 0.000
#> GSM97881 1 0.0000 1.000 1.000 0.000
#> GSM97884 1 0.0000 1.000 1.000 0.000
#> GSM97901 1 0.0000 1.000 1.000 0.000
#> GSM97902 1 0.0000 1.000 1.000 0.000
#> GSM97909 1 0.0000 1.000 1.000 0.000
#> GSM97911 1 0.0000 1.000 1.000 0.000
#> GSM97923 1 0.0000 1.000 1.000 0.000
#> GSM97928 1 0.0000 1.000 1.000 0.000
#> GSM97929 2 0.0000 1.000 0.000 1.000
#> GSM97933 1 0.0000 1.000 1.000 0.000
#> GSM97934 1 0.0000 1.000 1.000 0.000
#> GSM97944 1 0.0000 1.000 1.000 0.000
#> GSM97949 2 0.0000 1.000 0.000 1.000
#> GSM97956 1 0.0000 1.000 1.000 0.000
#> GSM97962 1 0.0000 1.000 1.000 0.000
#> GSM97964 1 0.0000 1.000 1.000 0.000
#> GSM97970 1 0.0000 1.000 1.000 0.000
#> GSM97822 1 0.0000 1.000 1.000 0.000
#> GSM97831 1 0.0000 1.000 1.000 0.000
#> GSM97845 1 0.0000 1.000 1.000 0.000
#> GSM97865 1 0.0000 1.000 1.000 0.000
#> GSM97867 1 0.0000 1.000 1.000 0.000
#> GSM97883 1 0.0000 1.000 1.000 0.000
#> GSM97897 1 0.0000 1.000 1.000 0.000
#> GSM97900 1 0.0000 1.000 1.000 0.000
#> GSM97904 1 0.0000 1.000 1.000 0.000
#> GSM97907 2 0.0000 1.000 0.000 1.000
#> GSM97925 1 0.0000 1.000 1.000 0.000
#> GSM97947 1 0.0000 1.000 1.000 0.000
cbind(get_classes(res, k = 3), get_membership(res, k = 3))
#> class entropy silhouette p1 p2 p3
#> GSM97800 2 0.0000 0.985 0.000 1.000 0.000
#> GSM97803 2 0.0000 0.985 0.000 1.000 0.000
#> GSM97804 2 0.0000 0.985 0.000 1.000 0.000
#> GSM97805 2 0.0000 0.985 0.000 1.000 0.000
#> GSM97807 2 0.0000 0.985 0.000 1.000 0.000
#> GSM97809 2 0.0000 0.985 0.000 1.000 0.000
#> GSM97811 2 0.0000 0.985 0.000 1.000 0.000
#> GSM97812 2 0.0000 0.985 0.000 1.000 0.000
#> GSM97816 3 0.0237 0.994 0.004 0.000 0.996
#> GSM97817 2 0.0000 0.985 0.000 1.000 0.000
#> GSM97820 2 0.0000 0.985 0.000 1.000 0.000
#> GSM97825 2 0.0000 0.985 0.000 1.000 0.000
#> GSM97827 2 0.0000 0.985 0.000 1.000 0.000
#> GSM97828 3 0.0237 0.994 0.004 0.000 0.996
#> GSM97833 2 0.0000 0.985 0.000 1.000 0.000
#> GSM97834 2 0.0000 0.985 0.000 1.000 0.000
#> GSM97840 3 0.0747 0.981 0.000 0.016 0.984
#> GSM97846 2 0.0000 0.985 0.000 1.000 0.000
#> GSM97848 2 0.0000 0.985 0.000 1.000 0.000
#> GSM97849 2 0.0000 0.985 0.000 1.000 0.000
#> GSM97850 2 0.0000 0.985 0.000 1.000 0.000
#> GSM97853 2 0.0000 0.985 0.000 1.000 0.000
#> GSM97855 2 0.4654 0.712 0.000 0.792 0.208
#> GSM97878 1 0.6079 0.675 0.612 0.000 0.388
#> GSM97913 1 0.6204 0.617 0.576 0.000 0.424
#> GSM97932 1 0.1753 0.825 0.952 0.000 0.048
#> GSM97939 3 0.0000 0.999 0.000 0.000 1.000
#> GSM97951 3 0.0424 0.991 0.000 0.008 0.992
#> GSM97957 3 0.0000 0.999 0.000 0.000 1.000
#> GSM97972 3 0.0000 0.999 0.000 0.000 1.000
#> GSM97793 3 0.0000 0.999 0.000 0.000 1.000
#> GSM97795 3 0.0000 0.999 0.000 0.000 1.000
#> GSM97802 3 0.0000 0.999 0.000 0.000 1.000
#> GSM97810 3 0.0000 0.999 0.000 0.000 1.000
#> GSM97815 3 0.0000 0.999 0.000 0.000 1.000
#> GSM97837 1 0.6045 0.682 0.620 0.000 0.380
#> GSM97843 3 0.0000 0.999 0.000 0.000 1.000
#> GSM97890 3 0.0000 0.999 0.000 0.000 1.000
#> GSM97899 1 0.0592 0.808 0.988 0.000 0.012
#> GSM97910 1 0.6079 0.675 0.612 0.000 0.388
#> GSM97916 1 0.5835 0.727 0.660 0.000 0.340
#> GSM97920 3 0.0000 0.999 0.000 0.000 1.000
#> GSM97921 1 0.4842 0.811 0.776 0.000 0.224
#> GSM97927 1 0.5591 0.757 0.696 0.000 0.304
#> GSM97937 1 0.3482 0.838 0.872 0.000 0.128
#> GSM97941 3 0.0424 0.990 0.008 0.000 0.992
#> GSM97943 1 0.6215 0.611 0.572 0.000 0.428
#> GSM97958 1 0.6204 0.617 0.576 0.000 0.424
#> GSM97960 3 0.0000 0.999 0.000 0.000 1.000
#> GSM97794 1 0.6079 0.675 0.612 0.000 0.388
#> GSM97796 1 0.0000 0.802 1.000 0.000 0.000
#> GSM97797 1 0.6079 0.675 0.612 0.000 0.388
#> GSM97798 1 0.0000 0.802 1.000 0.000 0.000
#> GSM97801 1 0.6079 0.675 0.612 0.000 0.388
#> GSM97806 1 0.4605 0.820 0.796 0.000 0.204
#> GSM97808 1 0.0000 0.802 1.000 0.000 0.000
#> GSM97813 1 0.3551 0.832 0.868 0.000 0.132
#> GSM97814 1 0.0000 0.802 1.000 0.000 0.000
#> GSM97818 1 0.6079 0.675 0.612 0.000 0.388
#> GSM97819 3 0.0000 0.999 0.000 0.000 1.000
#> GSM97821 3 0.0424 0.990 0.008 0.000 0.992
#> GSM97826 1 0.4121 0.832 0.832 0.000 0.168
#> GSM97829 1 0.6062 0.679 0.616 0.000 0.384
#> GSM97832 3 0.0000 0.999 0.000 0.000 1.000
#> GSM97836 1 0.6079 0.675 0.612 0.000 0.388
#> GSM97839 1 0.0000 0.802 1.000 0.000 0.000
#> GSM97844 2 0.0000 0.985 0.000 1.000 0.000
#> GSM97847 1 0.3116 0.838 0.892 0.000 0.108
#> GSM97851 1 0.0000 0.802 1.000 0.000 0.000
#> GSM97852 1 0.3116 0.838 0.892 0.000 0.108
#> GSM97856 1 0.0000 0.802 1.000 0.000 0.000
#> GSM97858 2 0.0000 0.985 0.000 1.000 0.000
#> GSM97859 1 0.4654 0.818 0.792 0.000 0.208
#> GSM97861 1 0.4702 0.816 0.788 0.000 0.212
#> GSM97863 1 0.0000 0.802 1.000 0.000 0.000
#> GSM97869 1 0.6026 0.689 0.624 0.000 0.376
#> GSM97870 1 0.6215 0.611 0.572 0.000 0.428
#> GSM97871 1 0.0000 0.802 1.000 0.000 0.000
#> GSM97877 3 0.0424 0.990 0.008 0.000 0.992
#> GSM97879 1 0.3038 0.838 0.896 0.000 0.104
#> GSM97882 1 0.4796 0.813 0.780 0.000 0.220
#> GSM97885 1 0.4002 0.834 0.840 0.000 0.160
#> GSM97886 1 0.3941 0.835 0.844 0.000 0.156
#> GSM97887 1 0.2625 0.836 0.916 0.000 0.084
#> GSM97888 1 0.2356 0.832 0.928 0.000 0.072
#> GSM97889 1 0.4555 0.821 0.800 0.000 0.200
#> GSM97891 1 0.5363 0.778 0.724 0.000 0.276
#> GSM97892 2 0.0000 0.985 0.000 1.000 0.000
#> GSM97893 1 0.2796 0.836 0.908 0.000 0.092
#> GSM97894 1 0.0000 0.802 1.000 0.000 0.000
#> GSM97895 1 0.4555 0.822 0.800 0.000 0.200
#> GSM97896 1 0.1529 0.822 0.960 0.000 0.040
#> GSM97898 1 0.0000 0.802 1.000 0.000 0.000
#> GSM97903 1 0.4291 0.829 0.820 0.000 0.180
#> GSM97905 1 0.5948 0.706 0.640 0.000 0.360
#> GSM97906 1 0.0000 0.802 1.000 0.000 0.000
#> GSM97908 1 0.3038 0.838 0.896 0.000 0.104
#> GSM97912 1 0.4002 0.834 0.840 0.000 0.160
#> GSM97914 1 0.4235 0.830 0.824 0.000 0.176
#> GSM97915 1 0.0000 0.802 1.000 0.000 0.000
#> GSM97917 1 0.2165 0.830 0.936 0.000 0.064
#> GSM97918 1 0.0000 0.802 1.000 0.000 0.000
#> GSM97919 1 0.0000 0.802 1.000 0.000 0.000
#> GSM97922 1 0.1163 0.817 0.972 0.000 0.028
#> GSM97924 2 0.0000 0.985 0.000 1.000 0.000
#> GSM97926 3 0.0000 0.999 0.000 0.000 1.000
#> GSM97930 1 0.3340 0.838 0.880 0.000 0.120
#> GSM97931 3 0.0000 0.999 0.000 0.000 1.000
#> GSM97935 1 0.5785 0.733 0.668 0.000 0.332
#> GSM97936 1 0.2878 0.837 0.904 0.000 0.096
#> GSM97938 1 0.3686 0.837 0.860 0.000 0.140
#> GSM97940 1 0.0000 0.802 1.000 0.000 0.000
#> GSM97942 3 0.0000 0.999 0.000 0.000 1.000
#> GSM97945 1 0.2878 0.837 0.904 0.000 0.096
#> GSM97946 2 0.0000 0.985 0.000 1.000 0.000
#> GSM97948 1 0.6215 0.611 0.572 0.000 0.428
#> GSM97950 1 0.2796 0.836 0.908 0.000 0.092
#> GSM97952 1 0.0000 0.802 1.000 0.000 0.000
#> GSM97953 1 0.6045 0.682 0.620 0.000 0.380
#> GSM97954 1 0.3038 0.838 0.896 0.000 0.104
#> GSM97955 1 0.2878 0.837 0.904 0.000 0.096
#> GSM97959 1 0.6204 0.617 0.576 0.000 0.424
#> GSM97961 1 0.0000 0.802 1.000 0.000 0.000
#> GSM97963 1 0.0000 0.802 1.000 0.000 0.000
#> GSM97965 1 0.0000 0.802 1.000 0.000 0.000
#> GSM97966 1 0.0000 0.802 1.000 0.000 0.000
#> GSM97967 2 0.0000 0.985 0.000 1.000 0.000
#> GSM97968 2 0.5098 0.638 0.000 0.752 0.248
#> GSM97969 1 0.4931 0.806 0.768 0.000 0.232
#> GSM97971 1 0.3482 0.838 0.872 0.000 0.128
#> GSM97799 3 0.0000 0.999 0.000 0.000 1.000
#> GSM97823 2 0.0000 0.985 0.000 1.000 0.000
#> GSM97824 3 0.0000 0.999 0.000 0.000 1.000
#> GSM97830 3 0.0000 0.999 0.000 0.000 1.000
#> GSM97835 3 0.0000 0.999 0.000 0.000 1.000
#> GSM97838 2 0.0000 0.985 0.000 1.000 0.000
#> GSM97841 2 0.0000 0.985 0.000 1.000 0.000
#> GSM97842 3 0.0000 0.999 0.000 0.000 1.000
#> GSM97854 2 0.0000 0.985 0.000 1.000 0.000
#> GSM97857 3 0.0000 0.999 0.000 0.000 1.000
#> GSM97860 3 0.0000 0.999 0.000 0.000 1.000
#> GSM97862 3 0.0000 0.999 0.000 0.000 1.000
#> GSM97864 2 0.0000 0.985 0.000 1.000 0.000
#> GSM97866 3 0.0000 0.999 0.000 0.000 1.000
#> GSM97868 3 0.0000 0.999 0.000 0.000 1.000
#> GSM97872 1 0.6140 0.651 0.596 0.000 0.404
#> GSM97873 3 0.0000 0.999 0.000 0.000 1.000
#> GSM97874 3 0.0000 0.999 0.000 0.000 1.000
#> GSM97875 3 0.0000 0.999 0.000 0.000 1.000
#> GSM97876 3 0.0000 0.999 0.000 0.000 1.000
#> GSM97880 3 0.0000 0.999 0.000 0.000 1.000
#> GSM97881 3 0.0000 0.999 0.000 0.000 1.000
#> GSM97884 3 0.0000 0.999 0.000 0.000 1.000
#> GSM97901 3 0.0000 0.999 0.000 0.000 1.000
#> GSM97902 1 0.6095 0.669 0.608 0.000 0.392
#> GSM97909 3 0.0424 0.990 0.008 0.000 0.992
#> GSM97911 3 0.0000 0.999 0.000 0.000 1.000
#> GSM97923 3 0.0000 0.999 0.000 0.000 1.000
#> GSM97928 1 0.5465 0.770 0.712 0.000 0.288
#> GSM97929 2 0.0000 0.985 0.000 1.000 0.000
#> GSM97933 3 0.0000 0.999 0.000 0.000 1.000
#> GSM97934 3 0.0000 0.999 0.000 0.000 1.000
#> GSM97944 3 0.0000 0.999 0.000 0.000 1.000
#> GSM97949 2 0.0000 0.985 0.000 1.000 0.000
#> GSM97956 3 0.0000 0.999 0.000 0.000 1.000
#> GSM97962 3 0.0000 0.999 0.000 0.000 1.000
#> GSM97964 3 0.0000 0.999 0.000 0.000 1.000
#> GSM97970 3 0.0000 0.999 0.000 0.000 1.000
#> GSM97822 1 0.6045 0.682 0.620 0.000 0.380
#> GSM97831 3 0.0000 0.999 0.000 0.000 1.000
#> GSM97845 1 0.2878 0.837 0.904 0.000 0.096
#> GSM97865 1 0.5216 0.790 0.740 0.000 0.260
#> GSM97867 3 0.0000 0.999 0.000 0.000 1.000
#> GSM97883 1 0.6307 0.476 0.512 0.000 0.488
#> GSM97897 1 0.4002 0.827 0.840 0.000 0.160
#> GSM97900 1 0.2878 0.837 0.904 0.000 0.096
#> GSM97904 1 0.6079 0.675 0.612 0.000 0.388
#> GSM97907 2 0.0000 0.985 0.000 1.000 0.000
#> GSM97925 3 0.0000 0.999 0.000 0.000 1.000
#> GSM97947 3 0.0000 0.999 0.000 0.000 1.000
cbind(get_classes(res, k = 4), get_membership(res, k = 4))
#> class entropy silhouette p1 p2 p3 p4
#> GSM97800 2 0.0000 0.9760 0.000 1.000 0.000 0.000
#> GSM97803 2 0.0000 0.9760 0.000 1.000 0.000 0.000
#> GSM97804 2 0.0000 0.9760 0.000 1.000 0.000 0.000
#> GSM97805 2 0.0000 0.9760 0.000 1.000 0.000 0.000
#> GSM97807 2 0.0000 0.9760 0.000 1.000 0.000 0.000
#> GSM97809 2 0.0000 0.9760 0.000 1.000 0.000 0.000
#> GSM97811 2 0.0000 0.9760 0.000 1.000 0.000 0.000
#> GSM97812 2 0.0000 0.9760 0.000 1.000 0.000 0.000
#> GSM97816 4 0.5742 0.6011 0.036 0.000 0.368 0.596
#> GSM97817 2 0.0000 0.9760 0.000 1.000 0.000 0.000
#> GSM97820 2 0.0000 0.9760 0.000 1.000 0.000 0.000
#> GSM97825 2 0.0000 0.9760 0.000 1.000 0.000 0.000
#> GSM97827 2 0.0000 0.9760 0.000 1.000 0.000 0.000
#> GSM97828 4 0.5807 0.6025 0.040 0.000 0.364 0.596
#> GSM97833 2 0.0000 0.9760 0.000 1.000 0.000 0.000
#> GSM97834 2 0.0000 0.9760 0.000 1.000 0.000 0.000
#> GSM97840 4 0.5540 0.6877 0.028 0.004 0.320 0.648
#> GSM97846 2 0.0000 0.9760 0.000 1.000 0.000 0.000
#> GSM97848 2 0.0000 0.9760 0.000 1.000 0.000 0.000
#> GSM97849 2 0.0000 0.9760 0.000 1.000 0.000 0.000
#> GSM97850 2 0.0000 0.9760 0.000 1.000 0.000 0.000
#> GSM97853 2 0.0000 0.9760 0.000 1.000 0.000 0.000
#> GSM97855 2 0.4993 0.5874 0.000 0.712 0.028 0.260
#> GSM97878 4 0.5344 0.4302 0.300 0.000 0.032 0.668
#> GSM97913 4 0.4907 0.6934 0.060 0.000 0.176 0.764
#> GSM97932 1 0.2737 0.7925 0.888 0.000 0.008 0.104
#> GSM97939 4 0.4967 0.5461 0.000 0.000 0.452 0.548
#> GSM97951 4 0.4936 0.6461 0.000 0.004 0.372 0.624
#> GSM97957 3 0.1297 0.8651 0.020 0.000 0.964 0.016
#> GSM97972 4 0.4790 0.6399 0.000 0.000 0.380 0.620
#> GSM97793 3 0.1297 0.8651 0.020 0.000 0.964 0.016
#> GSM97795 4 0.4955 0.5597 0.000 0.000 0.444 0.556
#> GSM97802 3 0.7355 -0.1669 0.172 0.000 0.488 0.340
#> GSM97810 4 0.4916 0.5886 0.000 0.000 0.424 0.576
#> GSM97815 4 0.4967 0.5461 0.000 0.000 0.452 0.548
#> GSM97837 4 0.5673 0.3174 0.372 0.000 0.032 0.596
#> GSM97843 3 0.1929 0.8537 0.036 0.000 0.940 0.024
#> GSM97890 3 0.1302 0.8436 0.000 0.000 0.956 0.044
#> GSM97899 1 0.3024 0.7697 0.852 0.000 0.000 0.148
#> GSM97910 4 0.6522 0.6559 0.144 0.000 0.224 0.632
#> GSM97916 1 0.4795 0.6826 0.696 0.000 0.012 0.292
#> GSM97920 3 0.2021 0.8421 0.040 0.000 0.936 0.024
#> GSM97921 1 0.4372 0.7034 0.728 0.000 0.004 0.268
#> GSM97927 1 0.3725 0.7520 0.812 0.000 0.008 0.180
#> GSM97937 1 0.3768 0.7634 0.808 0.000 0.008 0.184
#> GSM97941 4 0.5343 0.6903 0.028 0.000 0.316 0.656
#> GSM97943 4 0.6189 0.6539 0.092 0.000 0.268 0.640
#> GSM97958 4 0.4877 0.6990 0.044 0.000 0.204 0.752
#> GSM97960 4 0.4961 0.5534 0.000 0.000 0.448 0.552
#> GSM97794 4 0.6106 0.3349 0.332 0.000 0.064 0.604
#> GSM97796 1 0.4008 0.7346 0.756 0.000 0.000 0.244
#> GSM97797 4 0.5783 0.6499 0.172 0.000 0.120 0.708
#> GSM97798 1 0.3801 0.7339 0.780 0.000 0.000 0.220
#> GSM97801 4 0.6650 0.6268 0.200 0.000 0.176 0.624
#> GSM97806 1 0.3681 0.7560 0.816 0.000 0.008 0.176
#> GSM97808 1 0.3837 0.7333 0.776 0.000 0.000 0.224
#> GSM97813 1 0.2281 0.7969 0.904 0.000 0.000 0.096
#> GSM97814 1 0.3801 0.7339 0.780 0.000 0.000 0.220
#> GSM97818 4 0.5018 0.3479 0.332 0.000 0.012 0.656
#> GSM97819 3 0.0921 0.8644 0.028 0.000 0.972 0.000
#> GSM97821 4 0.5344 0.6952 0.032 0.000 0.300 0.668
#> GSM97826 1 0.3893 0.7546 0.796 0.000 0.008 0.196
#> GSM97829 1 0.5263 0.2726 0.544 0.000 0.008 0.448
#> GSM97832 4 0.4961 0.5534 0.000 0.000 0.448 0.552
#> GSM97836 1 0.3583 0.7468 0.816 0.000 0.004 0.180
#> GSM97839 1 0.4040 0.7346 0.752 0.000 0.000 0.248
#> GSM97844 2 0.0000 0.9760 0.000 1.000 0.000 0.000
#> GSM97847 1 0.3306 0.7671 0.840 0.000 0.004 0.156
#> GSM97851 1 0.4072 0.7346 0.748 0.000 0.000 0.252
#> GSM97852 1 0.3052 0.7805 0.860 0.000 0.004 0.136
#> GSM97856 1 0.3837 0.7339 0.776 0.000 0.000 0.224
#> GSM97858 2 0.0000 0.9760 0.000 1.000 0.000 0.000
#> GSM97859 1 0.2859 0.7889 0.880 0.000 0.008 0.112
#> GSM97861 1 0.3448 0.7611 0.828 0.000 0.004 0.168
#> GSM97863 1 0.4072 0.7346 0.748 0.000 0.000 0.252
#> GSM97869 1 0.4049 0.7437 0.780 0.000 0.008 0.212
#> GSM97870 1 0.7847 -0.3183 0.384 0.000 0.268 0.348
#> GSM97871 1 0.3873 0.7326 0.772 0.000 0.000 0.228
#> GSM97877 4 0.5254 0.6957 0.028 0.000 0.300 0.672
#> GSM97879 1 0.2593 0.7967 0.892 0.000 0.004 0.104
#> GSM97882 1 0.3539 0.7599 0.820 0.000 0.004 0.176
#> GSM97885 1 0.3668 0.7597 0.808 0.000 0.004 0.188
#> GSM97886 1 0.2799 0.7941 0.884 0.000 0.008 0.108
#> GSM97887 1 0.2401 0.7963 0.904 0.000 0.004 0.092
#> GSM97888 1 0.2011 0.7986 0.920 0.000 0.000 0.080
#> GSM97889 1 0.2401 0.7954 0.904 0.000 0.004 0.092
#> GSM97891 1 0.3852 0.7517 0.808 0.000 0.012 0.180
#> GSM97892 2 0.0000 0.9760 0.000 1.000 0.000 0.000
#> GSM97893 1 0.2124 0.8008 0.924 0.000 0.008 0.068
#> GSM97894 1 0.3801 0.7339 0.780 0.000 0.000 0.220
#> GSM97895 1 0.3768 0.7629 0.808 0.000 0.008 0.184
#> GSM97896 1 0.1940 0.7994 0.924 0.000 0.000 0.076
#> GSM97898 1 0.4072 0.7346 0.748 0.000 0.000 0.252
#> GSM97903 1 0.4343 0.7157 0.732 0.000 0.004 0.264
#> GSM97905 1 0.2918 0.7851 0.876 0.000 0.008 0.116
#> GSM97906 1 0.3801 0.7339 0.780 0.000 0.000 0.220
#> GSM97908 1 0.3355 0.7775 0.836 0.000 0.004 0.160
#> GSM97912 1 0.2480 0.7944 0.904 0.000 0.008 0.088
#> GSM97914 1 0.4535 0.6861 0.704 0.000 0.004 0.292
#> GSM97915 1 0.3801 0.7339 0.780 0.000 0.000 0.220
#> GSM97917 1 0.2675 0.7897 0.892 0.000 0.008 0.100
#> GSM97918 1 0.4072 0.7346 0.748 0.000 0.000 0.252
#> GSM97919 1 0.4072 0.7346 0.748 0.000 0.000 0.252
#> GSM97922 1 0.2647 0.8005 0.880 0.000 0.000 0.120
#> GSM97924 2 0.0000 0.9760 0.000 1.000 0.000 0.000
#> GSM97926 3 0.5228 0.5999 0.120 0.000 0.756 0.124
#> GSM97930 1 0.3908 0.7435 0.784 0.000 0.004 0.212
#> GSM97931 4 0.4790 0.6399 0.000 0.000 0.380 0.620
#> GSM97935 1 0.3893 0.7450 0.796 0.000 0.008 0.196
#> GSM97936 1 0.3583 0.7791 0.816 0.000 0.004 0.180
#> GSM97938 1 0.3498 0.7748 0.832 0.000 0.008 0.160
#> GSM97940 1 0.3801 0.7339 0.780 0.000 0.000 0.220
#> GSM97942 3 0.2413 0.8202 0.064 0.000 0.916 0.020
#> GSM97945 1 0.2197 0.7979 0.916 0.000 0.004 0.080
#> GSM97946 2 0.0000 0.9760 0.000 1.000 0.000 0.000
#> GSM97948 1 0.7235 -0.0886 0.480 0.000 0.148 0.372
#> GSM97950 1 0.1545 0.7997 0.952 0.000 0.008 0.040
#> GSM97952 1 0.3801 0.7339 0.780 0.000 0.000 0.220
#> GSM97953 1 0.4262 0.7216 0.756 0.000 0.008 0.236
#> GSM97954 1 0.2944 0.7834 0.868 0.000 0.004 0.128
#> GSM97955 1 0.3539 0.7789 0.820 0.000 0.004 0.176
#> GSM97959 4 0.5102 0.6558 0.136 0.000 0.100 0.764
#> GSM97961 1 0.4360 0.7367 0.744 0.000 0.008 0.248
#> GSM97963 1 0.3982 0.7355 0.776 0.000 0.004 0.220
#> GSM97965 1 0.3873 0.7326 0.772 0.000 0.000 0.228
#> GSM97966 1 0.3801 0.7339 0.780 0.000 0.000 0.220
#> GSM97967 2 0.0000 0.9760 0.000 1.000 0.000 0.000
#> GSM97968 2 0.6876 0.1398 0.000 0.532 0.116 0.352
#> GSM97969 1 0.3351 0.7831 0.844 0.000 0.008 0.148
#> GSM97971 1 0.2412 0.7947 0.908 0.000 0.008 0.084
#> GSM97799 3 0.1557 0.8331 0.000 0.000 0.944 0.056
#> GSM97823 2 0.0000 0.9760 0.000 1.000 0.000 0.000
#> GSM97824 3 0.0672 0.8668 0.008 0.000 0.984 0.008
#> GSM97830 3 0.1297 0.8651 0.020 0.000 0.964 0.016
#> GSM97835 4 0.4992 0.4750 0.000 0.000 0.476 0.524
#> GSM97838 2 0.0000 0.9760 0.000 1.000 0.000 0.000
#> GSM97841 2 0.0000 0.9760 0.000 1.000 0.000 0.000
#> GSM97842 3 0.3649 0.6283 0.000 0.000 0.796 0.204
#> GSM97854 2 0.0000 0.9760 0.000 1.000 0.000 0.000
#> GSM97857 3 0.4990 0.0384 0.008 0.000 0.640 0.352
#> GSM97860 3 0.1297 0.8651 0.020 0.000 0.964 0.016
#> GSM97862 3 0.0336 0.8676 0.008 0.000 0.992 0.000
#> GSM97864 2 0.0000 0.9760 0.000 1.000 0.000 0.000
#> GSM97866 3 0.0336 0.8676 0.008 0.000 0.992 0.000
#> GSM97868 3 0.1635 0.8489 0.008 0.000 0.948 0.044
#> GSM97872 4 0.6612 0.6446 0.132 0.000 0.256 0.612
#> GSM97873 3 0.4522 0.3078 0.000 0.000 0.680 0.320
#> GSM97874 3 0.1297 0.8651 0.020 0.000 0.964 0.016
#> GSM97875 3 0.0188 0.8662 0.004 0.000 0.996 0.000
#> GSM97876 3 0.0336 0.8676 0.008 0.000 0.992 0.000
#> GSM97880 3 0.1297 0.8651 0.020 0.000 0.964 0.016
#> GSM97881 3 0.0188 0.8629 0.000 0.000 0.996 0.004
#> GSM97884 3 0.2216 0.7997 0.000 0.000 0.908 0.092
#> GSM97901 3 0.0336 0.8676 0.008 0.000 0.992 0.000
#> GSM97902 4 0.6147 0.6809 0.128 0.000 0.200 0.672
#> GSM97909 4 0.5277 0.6943 0.028 0.000 0.304 0.668
#> GSM97911 3 0.0469 0.8615 0.000 0.000 0.988 0.012
#> GSM97923 3 0.0804 0.8680 0.012 0.000 0.980 0.008
#> GSM97928 1 0.3583 0.7535 0.816 0.000 0.004 0.180
#> GSM97929 2 0.0000 0.9760 0.000 1.000 0.000 0.000
#> GSM97933 3 0.1297 0.8651 0.020 0.000 0.964 0.016
#> GSM97934 3 0.1297 0.8651 0.020 0.000 0.964 0.016
#> GSM97944 3 0.1557 0.8331 0.000 0.000 0.944 0.056
#> GSM97949 2 0.0707 0.9554 0.000 0.980 0.020 0.000
#> GSM97956 3 0.1256 0.8596 0.008 0.000 0.964 0.028
#> GSM97962 3 0.0672 0.8679 0.008 0.000 0.984 0.008
#> GSM97964 3 0.1557 0.8331 0.000 0.000 0.944 0.056
#> GSM97970 3 0.1716 0.8272 0.000 0.000 0.936 0.064
#> GSM97822 1 0.4542 0.7014 0.752 0.000 0.020 0.228
#> GSM97831 3 0.1297 0.8651 0.020 0.000 0.964 0.016
#> GSM97845 1 0.1576 0.8015 0.948 0.000 0.004 0.048
#> GSM97865 1 0.4585 0.6357 0.668 0.000 0.000 0.332
#> GSM97867 3 0.1297 0.8651 0.020 0.000 0.964 0.016
#> GSM97883 3 0.7148 0.1743 0.220 0.000 0.560 0.220
#> GSM97897 1 0.2281 0.7966 0.904 0.000 0.000 0.096
#> GSM97900 1 0.2412 0.7947 0.908 0.000 0.008 0.084
#> GSM97904 1 0.4019 0.7280 0.792 0.000 0.012 0.196
#> GSM97907 2 0.0000 0.9760 0.000 1.000 0.000 0.000
#> GSM97925 3 0.5913 0.4666 0.180 0.000 0.696 0.124
#> GSM97947 3 0.1474 0.8379 0.052 0.000 0.948 0.000
cbind(get_classes(res, k = 5), get_membership(res, k = 5))
#> class entropy silhouette p1 p2 p3 p4 p5
#> GSM97800 2 0.0000 0.9996 0.000 1.000 0.000 0.000 0.000
#> GSM97803 2 0.0000 0.9996 0.000 1.000 0.000 0.000 0.000
#> GSM97804 2 0.0000 0.9996 0.000 1.000 0.000 0.000 0.000
#> GSM97805 2 0.0000 0.9996 0.000 1.000 0.000 0.000 0.000
#> GSM97807 2 0.0000 0.9996 0.000 1.000 0.000 0.000 0.000
#> GSM97809 2 0.0000 0.9996 0.000 1.000 0.000 0.000 0.000
#> GSM97811 2 0.0000 0.9996 0.000 1.000 0.000 0.000 0.000
#> GSM97812 2 0.0000 0.9996 0.000 1.000 0.000 0.000 0.000
#> GSM97816 5 0.4715 0.8281 0.072 0.000 0.068 0.076 0.784
#> GSM97817 2 0.0000 0.9996 0.000 1.000 0.000 0.000 0.000
#> GSM97820 2 0.0000 0.9996 0.000 1.000 0.000 0.000 0.000
#> GSM97825 2 0.0000 0.9996 0.000 1.000 0.000 0.000 0.000
#> GSM97827 2 0.0000 0.9996 0.000 1.000 0.000 0.000 0.000
#> GSM97828 5 0.4774 0.8248 0.076 0.000 0.068 0.076 0.780
#> GSM97833 2 0.0000 0.9996 0.000 1.000 0.000 0.000 0.000
#> GSM97834 2 0.0000 0.9996 0.000 1.000 0.000 0.000 0.000
#> GSM97840 5 0.2418 0.8980 0.044 0.024 0.020 0.000 0.912
#> GSM97846 2 0.0000 0.9996 0.000 1.000 0.000 0.000 0.000
#> GSM97848 2 0.0000 0.9996 0.000 1.000 0.000 0.000 0.000
#> GSM97849 2 0.0000 0.9996 0.000 1.000 0.000 0.000 0.000
#> GSM97850 2 0.0000 0.9996 0.000 1.000 0.000 0.000 0.000
#> GSM97853 2 0.0000 0.9996 0.000 1.000 0.000 0.000 0.000
#> GSM97855 5 0.3395 0.6774 0.000 0.236 0.000 0.000 0.764
#> GSM97878 1 0.2771 0.8322 0.860 0.000 0.000 0.012 0.128
#> GSM97913 5 0.1671 0.8889 0.076 0.000 0.000 0.000 0.924
#> GSM97932 1 0.3661 0.6163 0.724 0.000 0.000 0.276 0.000
#> GSM97939 5 0.1915 0.9072 0.040 0.000 0.032 0.000 0.928
#> GSM97951 5 0.1915 0.9072 0.040 0.000 0.032 0.000 0.928
#> GSM97957 3 0.3340 0.8732 0.016 0.000 0.860 0.076 0.048
#> GSM97972 5 0.3245 0.8881 0.048 0.000 0.044 0.036 0.872
#> GSM97793 3 0.3340 0.8732 0.016 0.000 0.860 0.076 0.048
#> GSM97795 5 0.1915 0.9072 0.040 0.000 0.032 0.000 0.928
#> GSM97802 5 0.5408 0.2530 0.060 0.000 0.408 0.000 0.532
#> GSM97810 5 0.1915 0.9072 0.040 0.000 0.032 0.000 0.928
#> GSM97815 5 0.2153 0.9044 0.040 0.000 0.044 0.000 0.916
#> GSM97837 1 0.3854 0.7705 0.816 0.000 0.004 0.080 0.100
#> GSM97843 3 0.1124 0.9034 0.000 0.000 0.960 0.004 0.036
#> GSM97890 3 0.1043 0.9035 0.000 0.000 0.960 0.000 0.040
#> GSM97899 4 0.3455 0.8627 0.208 0.000 0.000 0.784 0.008
#> GSM97910 1 0.4326 0.7294 0.776 0.000 0.004 0.080 0.140
#> GSM97916 1 0.1549 0.8896 0.944 0.000 0.000 0.016 0.040
#> GSM97920 3 0.3385 0.8503 0.056 0.000 0.864 0.044 0.036
#> GSM97921 1 0.1310 0.8913 0.956 0.000 0.000 0.024 0.020
#> GSM97927 1 0.1943 0.8909 0.924 0.000 0.000 0.020 0.056
#> GSM97937 1 0.1285 0.8902 0.956 0.000 0.004 0.036 0.004
#> GSM97941 5 0.1845 0.9026 0.056 0.000 0.016 0.000 0.928
#> GSM97943 1 0.4737 0.7119 0.756 0.000 0.016 0.080 0.148
#> GSM97958 5 0.1952 0.8865 0.084 0.000 0.004 0.000 0.912
#> GSM97960 5 0.2153 0.9044 0.040 0.000 0.044 0.000 0.916
#> GSM97794 1 0.2305 0.8608 0.896 0.000 0.000 0.012 0.092
#> GSM97796 4 0.2179 0.9527 0.112 0.000 0.000 0.888 0.000
#> GSM97797 1 0.2997 0.8154 0.840 0.000 0.000 0.012 0.148
#> GSM97798 4 0.2280 0.9525 0.120 0.000 0.000 0.880 0.000
#> GSM97801 1 0.4149 0.7447 0.792 0.000 0.004 0.080 0.124
#> GSM97806 1 0.1907 0.8916 0.928 0.000 0.000 0.028 0.044
#> GSM97808 4 0.2329 0.9503 0.124 0.000 0.000 0.876 0.000
#> GSM97813 1 0.1978 0.8916 0.928 0.000 0.004 0.044 0.024
#> GSM97814 4 0.2230 0.9522 0.116 0.000 0.000 0.884 0.000
#> GSM97818 1 0.2624 0.8422 0.872 0.000 0.000 0.012 0.116
#> GSM97819 3 0.0451 0.9077 0.000 0.000 0.988 0.004 0.008
#> GSM97821 5 0.1914 0.9025 0.060 0.000 0.016 0.000 0.924
#> GSM97826 1 0.1569 0.8874 0.944 0.000 0.004 0.044 0.008
#> GSM97829 1 0.2813 0.8351 0.884 0.000 0.004 0.048 0.064
#> GSM97832 5 0.2153 0.9044 0.040 0.000 0.044 0.000 0.916
#> GSM97836 1 0.2321 0.8911 0.912 0.000 0.008 0.024 0.056
#> GSM97839 4 0.2179 0.9527 0.112 0.000 0.000 0.888 0.000
#> GSM97844 2 0.0000 0.9996 0.000 1.000 0.000 0.000 0.000
#> GSM97847 1 0.1956 0.8708 0.916 0.000 0.000 0.076 0.008
#> GSM97851 4 0.2179 0.9527 0.112 0.000 0.000 0.888 0.000
#> GSM97852 1 0.2249 0.8669 0.896 0.000 0.000 0.096 0.008
#> GSM97856 4 0.2329 0.9508 0.124 0.000 0.000 0.876 0.000
#> GSM97858 2 0.0000 0.9996 0.000 1.000 0.000 0.000 0.000
#> GSM97859 1 0.1901 0.8908 0.932 0.000 0.004 0.040 0.024
#> GSM97861 1 0.1915 0.8915 0.928 0.000 0.000 0.032 0.040
#> GSM97863 4 0.2230 0.9514 0.116 0.000 0.000 0.884 0.000
#> GSM97869 1 0.1943 0.8900 0.924 0.000 0.000 0.020 0.056
#> GSM97870 1 0.3508 0.8271 0.848 0.000 0.076 0.012 0.064
#> GSM97871 4 0.2179 0.9527 0.112 0.000 0.000 0.888 0.000
#> GSM97877 5 0.1809 0.9008 0.060 0.000 0.012 0.000 0.928
#> GSM97879 1 0.2011 0.8713 0.908 0.000 0.000 0.088 0.004
#> GSM97882 1 0.1965 0.8916 0.924 0.000 0.000 0.024 0.052
#> GSM97885 1 0.1915 0.8923 0.928 0.000 0.000 0.040 0.032
#> GSM97886 1 0.1492 0.8931 0.948 0.000 0.004 0.040 0.008
#> GSM97887 1 0.1885 0.8898 0.932 0.000 0.004 0.044 0.020
#> GSM97888 1 0.2608 0.8707 0.888 0.000 0.004 0.088 0.020
#> GSM97889 1 0.1630 0.8929 0.944 0.000 0.004 0.036 0.016
#> GSM97891 1 0.1965 0.8910 0.924 0.000 0.000 0.024 0.052
#> GSM97892 2 0.0000 0.9996 0.000 1.000 0.000 0.000 0.000
#> GSM97893 1 0.2228 0.8671 0.900 0.000 0.004 0.092 0.004
#> GSM97894 4 0.2280 0.9525 0.120 0.000 0.000 0.880 0.000
#> GSM97895 1 0.1285 0.8902 0.956 0.000 0.004 0.036 0.004
#> GSM97896 1 0.2932 0.8514 0.864 0.000 0.004 0.112 0.020
#> GSM97898 4 0.2179 0.9527 0.112 0.000 0.000 0.888 0.000
#> GSM97903 1 0.1310 0.8909 0.956 0.000 0.000 0.020 0.024
#> GSM97905 1 0.1885 0.8898 0.932 0.000 0.004 0.044 0.020
#> GSM97906 4 0.2230 0.9522 0.116 0.000 0.000 0.884 0.000
#> GSM97908 1 0.2179 0.8536 0.896 0.000 0.000 0.100 0.004
#> GSM97912 1 0.1885 0.8898 0.932 0.000 0.004 0.044 0.020
#> GSM97914 1 0.1211 0.8913 0.960 0.000 0.000 0.024 0.016
#> GSM97915 4 0.2179 0.9527 0.112 0.000 0.000 0.888 0.000
#> GSM97917 4 0.4430 0.2916 0.456 0.000 0.004 0.540 0.000
#> GSM97918 4 0.2230 0.9514 0.116 0.000 0.000 0.884 0.000
#> GSM97919 4 0.2179 0.9527 0.112 0.000 0.000 0.888 0.000
#> GSM97922 1 0.4482 0.3833 0.636 0.000 0.000 0.348 0.016
#> GSM97924 2 0.0000 0.9996 0.000 1.000 0.000 0.000 0.000
#> GSM97926 3 0.1571 0.8963 0.000 0.000 0.936 0.004 0.060
#> GSM97930 1 0.1894 0.8724 0.920 0.000 0.000 0.072 0.008
#> GSM97931 5 0.1915 0.9072 0.040 0.000 0.032 0.000 0.928
#> GSM97935 1 0.2012 0.8891 0.920 0.000 0.000 0.020 0.060
#> GSM97936 4 0.4286 0.6411 0.340 0.000 0.004 0.652 0.004
#> GSM97938 1 0.1990 0.8751 0.920 0.000 0.004 0.068 0.008
#> GSM97940 4 0.2280 0.9525 0.120 0.000 0.000 0.880 0.000
#> GSM97942 3 0.1282 0.9012 0.000 0.000 0.952 0.004 0.044
#> GSM97945 1 0.2304 0.8643 0.892 0.000 0.000 0.100 0.008
#> GSM97946 2 0.0000 0.9996 0.000 1.000 0.000 0.000 0.000
#> GSM97948 1 0.3673 0.8464 0.836 0.000 0.060 0.012 0.092
#> GSM97950 1 0.2228 0.8671 0.900 0.000 0.004 0.092 0.004
#> GSM97952 4 0.2329 0.9508 0.124 0.000 0.000 0.876 0.000
#> GSM97953 1 0.1074 0.8879 0.968 0.000 0.004 0.016 0.012
#> GSM97954 1 0.1732 0.8683 0.920 0.000 0.000 0.080 0.000
#> GSM97955 4 0.3550 0.8337 0.236 0.000 0.000 0.760 0.004
#> GSM97959 1 0.4307 0.0749 0.500 0.000 0.000 0.000 0.500
#> GSM97961 4 0.2230 0.9514 0.116 0.000 0.000 0.884 0.000
#> GSM97963 4 0.2280 0.9525 0.120 0.000 0.000 0.880 0.000
#> GSM97965 4 0.2179 0.9527 0.112 0.000 0.000 0.888 0.000
#> GSM97966 4 0.2280 0.9525 0.120 0.000 0.000 0.880 0.000
#> GSM97967 2 0.0000 0.9996 0.000 1.000 0.000 0.000 0.000
#> GSM97968 5 0.3242 0.7058 0.000 0.216 0.000 0.000 0.784
#> GSM97969 1 0.1492 0.8916 0.948 0.000 0.004 0.040 0.008
#> GSM97971 1 0.1862 0.8893 0.932 0.000 0.004 0.048 0.016
#> GSM97799 3 0.1478 0.8878 0.000 0.000 0.936 0.000 0.064
#> GSM97823 2 0.0000 0.9996 0.000 1.000 0.000 0.000 0.000
#> GSM97824 3 0.0703 0.9078 0.000 0.000 0.976 0.000 0.024
#> GSM97830 3 0.3340 0.8732 0.016 0.000 0.860 0.076 0.048
#> GSM97835 5 0.2153 0.9044 0.040 0.000 0.044 0.000 0.916
#> GSM97838 2 0.0000 0.9996 0.000 1.000 0.000 0.000 0.000
#> GSM97841 2 0.0000 0.9996 0.000 1.000 0.000 0.000 0.000
#> GSM97842 3 0.4088 0.3624 0.000 0.000 0.632 0.000 0.368
#> GSM97854 2 0.0000 0.9996 0.000 1.000 0.000 0.000 0.000
#> GSM97857 3 0.4848 0.7208 0.052 0.000 0.756 0.040 0.152
#> GSM97860 3 0.2072 0.9001 0.016 0.000 0.928 0.036 0.020
#> GSM97862 3 0.0290 0.9087 0.000 0.000 0.992 0.000 0.008
#> GSM97864 2 0.0000 0.9996 0.000 1.000 0.000 0.000 0.000
#> GSM97866 3 0.0404 0.9090 0.000 0.000 0.988 0.000 0.012
#> GSM97868 3 0.0703 0.9078 0.000 0.000 0.976 0.000 0.024
#> GSM97872 1 0.4240 0.7595 0.792 0.000 0.008 0.088 0.112
#> GSM97873 5 0.4696 0.3037 0.016 0.000 0.428 0.000 0.556
#> GSM97874 3 0.3340 0.8732 0.016 0.000 0.860 0.076 0.048
#> GSM97875 3 0.0671 0.9100 0.004 0.000 0.980 0.000 0.016
#> GSM97876 3 0.0451 0.9092 0.004 0.000 0.988 0.000 0.008
#> GSM97880 3 0.3340 0.8732 0.016 0.000 0.860 0.076 0.048
#> GSM97881 3 0.0404 0.9087 0.000 0.000 0.988 0.000 0.012
#> GSM97884 3 0.1792 0.8727 0.000 0.000 0.916 0.000 0.084
#> GSM97901 3 0.0404 0.9090 0.000 0.000 0.988 0.000 0.012
#> GSM97902 1 0.5706 0.2714 0.540 0.000 0.004 0.076 0.380
#> GSM97909 5 0.1914 0.9025 0.060 0.000 0.016 0.000 0.924
#> GSM97911 3 0.0510 0.9081 0.000 0.000 0.984 0.000 0.016
#> GSM97923 3 0.0798 0.9082 0.016 0.000 0.976 0.000 0.008
#> GSM97928 1 0.2103 0.8914 0.920 0.000 0.004 0.020 0.056
#> GSM97929 2 0.0000 0.9996 0.000 1.000 0.000 0.000 0.000
#> GSM97933 3 0.1612 0.9045 0.016 0.000 0.948 0.024 0.012
#> GSM97934 3 0.3340 0.8732 0.016 0.000 0.860 0.076 0.048
#> GSM97944 3 0.1270 0.8954 0.000 0.000 0.948 0.000 0.052
#> GSM97949 2 0.0451 0.9867 0.000 0.988 0.008 0.000 0.004
#> GSM97956 3 0.0609 0.9074 0.000 0.000 0.980 0.000 0.020
#> GSM97962 3 0.2037 0.8971 0.012 0.000 0.920 0.064 0.004
#> GSM97964 3 0.0703 0.9062 0.000 0.000 0.976 0.000 0.024
#> GSM97970 3 0.1732 0.8758 0.000 0.000 0.920 0.000 0.080
#> GSM97822 1 0.2172 0.8913 0.916 0.000 0.004 0.020 0.060
#> GSM97831 3 0.3033 0.8817 0.016 0.000 0.876 0.076 0.032
#> GSM97845 1 0.2074 0.8629 0.896 0.000 0.000 0.104 0.000
#> GSM97865 1 0.1364 0.8891 0.952 0.000 0.000 0.012 0.036
#> GSM97867 3 0.3157 0.8800 0.016 0.000 0.872 0.060 0.052
#> GSM97883 3 0.5869 0.0286 0.428 0.000 0.484 0.004 0.084
#> GSM97897 1 0.1996 0.8926 0.928 0.000 0.004 0.032 0.036
#> GSM97900 1 0.1885 0.8898 0.932 0.000 0.004 0.044 0.020
#> GSM97904 1 0.2122 0.8900 0.924 0.000 0.008 0.032 0.036
#> GSM97907 2 0.0000 0.9996 0.000 1.000 0.000 0.000 0.000
#> GSM97925 3 0.2597 0.8682 0.040 0.000 0.896 0.004 0.060
#> GSM97947 3 0.0865 0.9045 0.000 0.000 0.972 0.004 0.024
cbind(get_classes(res, k = 6), get_membership(res, k = 6))
#> class entropy silhouette p1 p2 p3 p4 p5 p6
#> GSM97800 2 0.0000 0.9994 0.000 1.000 0.000 0.000 0.000 0.000
#> GSM97803 2 0.0000 0.9994 0.000 1.000 0.000 0.000 0.000 0.000
#> GSM97804 2 0.0000 0.9994 0.000 1.000 0.000 0.000 0.000 0.000
#> GSM97805 2 0.0000 0.9994 0.000 1.000 0.000 0.000 0.000 0.000
#> GSM97807 2 0.0000 0.9994 0.000 1.000 0.000 0.000 0.000 0.000
#> GSM97809 2 0.0000 0.9994 0.000 1.000 0.000 0.000 0.000 0.000
#> GSM97811 2 0.0000 0.9994 0.000 1.000 0.000 0.000 0.000 0.000
#> GSM97812 2 0.0000 0.9994 0.000 1.000 0.000 0.000 0.000 0.000
#> GSM97816 5 0.4592 0.6820 0.000 0.000 0.028 0.032 0.680 0.260
#> GSM97817 2 0.0000 0.9994 0.000 1.000 0.000 0.000 0.000 0.000
#> GSM97820 2 0.0000 0.9994 0.000 1.000 0.000 0.000 0.000 0.000
#> GSM97825 2 0.0000 0.9994 0.000 1.000 0.000 0.000 0.000 0.000
#> GSM97827 2 0.0000 0.9994 0.000 1.000 0.000 0.000 0.000 0.000
#> GSM97828 5 0.4683 0.6728 0.000 0.000 0.032 0.032 0.672 0.264
#> GSM97833 2 0.0000 0.9994 0.000 1.000 0.000 0.000 0.000 0.000
#> GSM97834 2 0.0000 0.9994 0.000 1.000 0.000 0.000 0.000 0.000
#> GSM97840 5 0.1471 0.8634 0.000 0.064 0.000 0.000 0.932 0.004
#> GSM97846 2 0.0000 0.9994 0.000 1.000 0.000 0.000 0.000 0.000
#> GSM97848 2 0.0000 0.9994 0.000 1.000 0.000 0.000 0.000 0.000
#> GSM97849 2 0.0000 0.9994 0.000 1.000 0.000 0.000 0.000 0.000
#> GSM97850 2 0.0000 0.9994 0.000 1.000 0.000 0.000 0.000 0.000
#> GSM97853 2 0.0000 0.9994 0.000 1.000 0.000 0.000 0.000 0.000
#> GSM97855 5 0.2912 0.7164 0.000 0.216 0.000 0.000 0.784 0.000
#> GSM97878 1 0.3101 0.7683 0.820 0.000 0.000 0.000 0.148 0.032
#> GSM97913 5 0.1151 0.8765 0.032 0.000 0.000 0.000 0.956 0.012
#> GSM97932 1 0.3136 0.6742 0.768 0.000 0.000 0.228 0.000 0.004
#> GSM97939 5 0.1204 0.9043 0.000 0.000 0.056 0.000 0.944 0.000
#> GSM97951 5 0.0000 0.9008 0.000 0.000 0.000 0.000 1.000 0.000
#> GSM97957 6 0.3695 0.9700 0.000 0.000 0.376 0.000 0.000 0.624
#> GSM97972 5 0.1707 0.9029 0.000 0.000 0.056 0.012 0.928 0.004
#> GSM97793 6 0.3695 0.9700 0.000 0.000 0.376 0.000 0.000 0.624
#> GSM97795 5 0.1075 0.9073 0.000 0.000 0.048 0.000 0.952 0.000
#> GSM97802 3 0.5351 0.0559 0.100 0.000 0.524 0.000 0.372 0.004
#> GSM97810 5 0.1075 0.9073 0.000 0.000 0.048 0.000 0.952 0.000
#> GSM97815 5 0.1141 0.9065 0.000 0.000 0.052 0.000 0.948 0.000
#> GSM97837 1 0.2492 0.7726 0.888 0.000 0.000 0.036 0.068 0.008
#> GSM97843 3 0.0458 0.7358 0.000 0.000 0.984 0.000 0.000 0.016
#> GSM97890 3 0.0146 0.7342 0.000 0.000 0.996 0.000 0.000 0.004
#> GSM97899 4 0.3853 0.7889 0.156 0.000 0.000 0.780 0.052 0.012
#> GSM97910 1 0.3645 0.7437 0.820 0.000 0.000 0.036 0.096 0.048
#> GSM97916 1 0.2110 0.8214 0.900 0.000 0.000 0.012 0.084 0.004
#> GSM97920 3 0.3011 0.5344 0.000 0.000 0.800 0.004 0.004 0.192
#> GSM97921 1 0.1340 0.8233 0.948 0.000 0.000 0.004 0.040 0.008
#> GSM97927 1 0.5349 0.8091 0.684 0.000 0.004 0.060 0.084 0.168
#> GSM97937 1 0.0405 0.8195 0.988 0.000 0.000 0.008 0.000 0.004
#> GSM97941 5 0.0291 0.8992 0.004 0.000 0.000 0.000 0.992 0.004
#> GSM97943 1 0.4164 0.7311 0.796 0.000 0.012 0.036 0.100 0.056
#> GSM97958 5 0.1682 0.8514 0.052 0.000 0.000 0.000 0.928 0.020
#> GSM97960 5 0.1075 0.9073 0.000 0.000 0.048 0.000 0.952 0.000
#> GSM97794 1 0.2639 0.8120 0.876 0.000 0.000 0.008 0.084 0.032
#> GSM97796 4 0.1010 0.9072 0.036 0.000 0.000 0.960 0.000 0.004
#> GSM97797 1 0.3388 0.7575 0.792 0.000 0.000 0.000 0.172 0.036
#> GSM97798 4 0.2740 0.8813 0.060 0.000 0.000 0.864 0.000 0.076
#> GSM97801 1 0.3432 0.7436 0.836 0.000 0.000 0.036 0.084 0.044
#> GSM97806 1 0.5302 0.8098 0.688 0.000 0.004 0.060 0.080 0.168
#> GSM97808 4 0.2740 0.8813 0.060 0.000 0.000 0.864 0.000 0.076
#> GSM97813 1 0.4000 0.8143 0.764 0.000 0.000 0.064 0.008 0.164
#> GSM97814 4 0.2129 0.9042 0.056 0.000 0.000 0.904 0.000 0.040
#> GSM97818 1 0.3023 0.7746 0.828 0.000 0.000 0.000 0.140 0.032
#> GSM97819 3 0.1556 0.7068 0.000 0.000 0.920 0.000 0.000 0.080
#> GSM97821 5 0.0291 0.8992 0.004 0.000 0.000 0.000 0.992 0.004
#> GSM97826 1 0.0405 0.8187 0.988 0.000 0.000 0.004 0.000 0.008
#> GSM97829 1 0.1949 0.7927 0.924 0.000 0.000 0.036 0.020 0.020
#> GSM97832 5 0.1285 0.9065 0.000 0.000 0.052 0.000 0.944 0.004
#> GSM97836 1 0.4755 0.8157 0.732 0.000 0.008 0.060 0.036 0.164
#> GSM97839 4 0.1010 0.9072 0.036 0.000 0.000 0.960 0.000 0.004
#> GSM97844 2 0.0000 0.9994 0.000 1.000 0.000 0.000 0.000 0.000
#> GSM97847 1 0.2151 0.8237 0.904 0.000 0.000 0.016 0.072 0.008
#> GSM97851 4 0.1010 0.9072 0.036 0.000 0.000 0.960 0.000 0.004
#> GSM97852 1 0.2939 0.8276 0.860 0.000 0.000 0.060 0.072 0.008
#> GSM97856 4 0.2046 0.9053 0.060 0.000 0.000 0.908 0.000 0.032
#> GSM97858 2 0.0260 0.9905 0.000 0.992 0.000 0.000 0.008 0.000
#> GSM97859 1 0.3752 0.8127 0.772 0.000 0.000 0.064 0.000 0.164
#> GSM97861 1 0.4818 0.8162 0.720 0.000 0.000 0.060 0.056 0.164
#> GSM97863 4 0.1010 0.9072 0.036 0.000 0.000 0.960 0.000 0.004
#> GSM97869 1 0.4975 0.8197 0.716 0.000 0.000 0.060 0.084 0.140
#> GSM97870 1 0.5366 0.7678 0.684 0.000 0.124 0.020 0.020 0.152
#> GSM97871 4 0.1124 0.9070 0.036 0.000 0.000 0.956 0.000 0.008
#> GSM97877 5 0.0291 0.8992 0.004 0.000 0.000 0.000 0.992 0.004
#> GSM97879 1 0.2007 0.8330 0.916 0.000 0.000 0.036 0.044 0.004
#> GSM97882 1 0.5349 0.8091 0.684 0.000 0.004 0.060 0.084 0.168
#> GSM97885 1 0.5164 0.8105 0.692 0.000 0.000 0.060 0.080 0.168
#> GSM97886 1 0.2685 0.8321 0.868 0.000 0.000 0.060 0.000 0.072
#> GSM97887 1 0.3752 0.8127 0.772 0.000 0.000 0.064 0.000 0.164
#> GSM97888 1 0.3860 0.8091 0.764 0.000 0.000 0.072 0.000 0.164
#> GSM97889 1 0.3695 0.8145 0.776 0.000 0.000 0.060 0.000 0.164
#> GSM97891 1 0.5349 0.8091 0.684 0.000 0.004 0.060 0.084 0.168
#> GSM97892 2 0.0000 0.9994 0.000 1.000 0.000 0.000 0.000 0.000
#> GSM97893 1 0.1471 0.8284 0.932 0.000 0.000 0.064 0.000 0.004
#> GSM97894 4 0.1908 0.9072 0.056 0.000 0.000 0.916 0.000 0.028
#> GSM97895 1 0.0520 0.8192 0.984 0.000 0.000 0.008 0.000 0.008
#> GSM97896 1 0.4154 0.7931 0.740 0.000 0.000 0.096 0.000 0.164
#> GSM97898 4 0.1010 0.9072 0.036 0.000 0.000 0.960 0.000 0.004
#> GSM97903 1 0.2002 0.8225 0.908 0.000 0.000 0.012 0.076 0.004
#> GSM97905 1 0.3752 0.8127 0.772 0.000 0.000 0.064 0.000 0.164
#> GSM97906 4 0.1845 0.9072 0.052 0.000 0.000 0.920 0.000 0.028
#> GSM97908 1 0.2151 0.8221 0.904 0.000 0.000 0.016 0.072 0.008
#> GSM97912 1 0.3752 0.8127 0.772 0.000 0.000 0.064 0.000 0.164
#> GSM97914 1 0.2013 0.8208 0.908 0.000 0.000 0.008 0.076 0.008
#> GSM97915 4 0.0937 0.9077 0.040 0.000 0.000 0.960 0.000 0.000
#> GSM97917 4 0.3817 0.1862 0.432 0.000 0.000 0.568 0.000 0.000
#> GSM97918 4 0.1010 0.9072 0.036 0.000 0.000 0.960 0.000 0.004
#> GSM97919 4 0.1010 0.9072 0.036 0.000 0.000 0.960 0.000 0.004
#> GSM97922 1 0.5869 0.4898 0.540 0.000 0.000 0.304 0.024 0.132
#> GSM97924 2 0.0000 0.9994 0.000 1.000 0.000 0.000 0.000 0.000
#> GSM97926 3 0.0146 0.7343 0.000 0.000 0.996 0.000 0.004 0.000
#> GSM97930 1 0.1957 0.8217 0.912 0.000 0.000 0.008 0.072 0.008
#> GSM97931 5 0.1141 0.9065 0.000 0.000 0.052 0.000 0.948 0.000
#> GSM97935 1 0.5212 0.8097 0.688 0.000 0.000 0.060 0.084 0.168
#> GSM97936 4 0.4981 0.3580 0.340 0.000 0.000 0.584 0.072 0.004
#> GSM97938 1 0.0520 0.8187 0.984 0.000 0.000 0.008 0.000 0.008
#> GSM97940 4 0.1908 0.9072 0.056 0.000 0.000 0.916 0.000 0.028
#> GSM97942 3 0.0937 0.7314 0.000 0.000 0.960 0.000 0.000 0.040
#> GSM97945 1 0.4987 0.8164 0.712 0.000 0.000 0.064 0.072 0.152
#> GSM97946 2 0.0000 0.9994 0.000 1.000 0.000 0.000 0.000 0.000
#> GSM97948 1 0.5591 0.7814 0.676 0.000 0.100 0.032 0.028 0.164
#> GSM97950 1 0.1686 0.8295 0.924 0.000 0.000 0.064 0.000 0.012
#> GSM97952 4 0.1970 0.9061 0.060 0.000 0.000 0.912 0.000 0.028
#> GSM97953 1 0.0972 0.8116 0.964 0.000 0.000 0.028 0.000 0.008
#> GSM97954 1 0.1230 0.8263 0.956 0.000 0.000 0.008 0.028 0.008
#> GSM97955 4 0.4332 0.6449 0.228 0.000 0.000 0.700 0.072 0.000
#> GSM97959 1 0.4574 0.2847 0.524 0.000 0.000 0.000 0.440 0.036
#> GSM97961 4 0.1010 0.9072 0.036 0.000 0.000 0.960 0.000 0.004
#> GSM97963 4 0.1719 0.9074 0.060 0.000 0.000 0.924 0.000 0.016
#> GSM97965 4 0.1010 0.9072 0.036 0.000 0.000 0.960 0.000 0.004
#> GSM97966 4 0.2512 0.8920 0.060 0.000 0.000 0.880 0.000 0.060
#> GSM97967 2 0.0000 0.9994 0.000 1.000 0.000 0.000 0.000 0.000
#> GSM97968 5 0.2730 0.7464 0.000 0.192 0.000 0.000 0.808 0.000
#> GSM97969 1 0.1092 0.8303 0.960 0.000 0.000 0.020 0.000 0.020
#> GSM97971 1 0.3752 0.8127 0.772 0.000 0.000 0.064 0.000 0.164
#> GSM97799 3 0.0725 0.7267 0.000 0.000 0.976 0.000 0.012 0.012
#> GSM97823 2 0.0000 0.9994 0.000 1.000 0.000 0.000 0.000 0.000
#> GSM97824 3 0.1141 0.7269 0.000 0.000 0.948 0.000 0.000 0.052
#> GSM97830 6 0.3695 0.9700 0.000 0.000 0.376 0.000 0.000 0.624
#> GSM97835 5 0.1387 0.8956 0.000 0.000 0.068 0.000 0.932 0.000
#> GSM97838 2 0.0000 0.9994 0.000 1.000 0.000 0.000 0.000 0.000
#> GSM97841 2 0.0000 0.9994 0.000 1.000 0.000 0.000 0.000 0.000
#> GSM97842 3 0.2070 0.6428 0.000 0.000 0.896 0.000 0.092 0.012
#> GSM97854 2 0.0000 0.9994 0.000 1.000 0.000 0.000 0.000 0.000
#> GSM97857 3 0.5307 0.0196 0.000 0.000 0.564 0.012 0.340 0.084
#> GSM97860 3 0.3843 -0.5487 0.000 0.000 0.548 0.000 0.000 0.452
#> GSM97862 3 0.2092 0.6648 0.000 0.000 0.876 0.000 0.000 0.124
#> GSM97864 2 0.0000 0.9994 0.000 1.000 0.000 0.000 0.000 0.000
#> GSM97866 3 0.1814 0.6916 0.000 0.000 0.900 0.000 0.000 0.100
#> GSM97868 3 0.0146 0.7354 0.000 0.000 0.996 0.000 0.000 0.004
#> GSM97872 1 0.3896 0.7403 0.820 0.000 0.016 0.036 0.076 0.052
#> GSM97873 3 0.4047 0.1746 0.000 0.000 0.604 0.000 0.384 0.012
#> GSM97874 6 0.3695 0.9700 0.000 0.000 0.376 0.000 0.000 0.624
#> GSM97875 3 0.1610 0.7037 0.000 0.000 0.916 0.000 0.000 0.084
#> GSM97876 3 0.1610 0.7037 0.000 0.000 0.916 0.000 0.000 0.084
#> GSM97880 6 0.3695 0.9700 0.000 0.000 0.376 0.000 0.000 0.624
#> GSM97881 3 0.1152 0.7257 0.000 0.000 0.952 0.000 0.004 0.044
#> GSM97884 3 0.1802 0.6714 0.000 0.000 0.916 0.000 0.072 0.012
#> GSM97901 3 0.2135 0.6591 0.000 0.000 0.872 0.000 0.000 0.128
#> GSM97902 1 0.5028 0.5105 0.644 0.000 0.004 0.032 0.280 0.040
#> GSM97909 5 0.0291 0.8992 0.004 0.000 0.000 0.000 0.992 0.004
#> GSM97911 3 0.0891 0.7349 0.000 0.000 0.968 0.000 0.008 0.024
#> GSM97923 3 0.1714 0.6984 0.000 0.000 0.908 0.000 0.000 0.092
#> GSM97928 1 0.4440 0.8173 0.744 0.000 0.000 0.060 0.032 0.164
#> GSM97929 2 0.0000 0.9994 0.000 1.000 0.000 0.000 0.000 0.000
#> GSM97933 3 0.2883 0.5074 0.000 0.000 0.788 0.000 0.000 0.212
#> GSM97934 6 0.3695 0.9700 0.000 0.000 0.376 0.000 0.000 0.624
#> GSM97944 3 0.0725 0.7267 0.000 0.000 0.976 0.000 0.012 0.012
#> GSM97949 2 0.0260 0.9905 0.000 0.992 0.000 0.000 0.008 0.000
#> GSM97956 3 0.0146 0.7342 0.000 0.000 0.996 0.000 0.000 0.004
#> GSM97962 3 0.3531 0.0661 0.000 0.000 0.672 0.000 0.000 0.328
#> GSM97964 3 0.0520 0.7303 0.000 0.000 0.984 0.000 0.008 0.008
#> GSM97970 3 0.1151 0.7102 0.000 0.000 0.956 0.000 0.032 0.012
#> GSM97822 1 0.5349 0.8091 0.684 0.000 0.004 0.060 0.084 0.168
#> GSM97831 6 0.3857 0.7873 0.000 0.000 0.468 0.000 0.000 0.532
#> GSM97845 1 0.1983 0.8330 0.916 0.000 0.000 0.060 0.012 0.012
#> GSM97865 1 0.2586 0.8126 0.880 0.000 0.000 0.008 0.080 0.032
#> GSM97867 3 0.3727 -0.3271 0.000 0.000 0.612 0.000 0.000 0.388
#> GSM97883 3 0.3921 0.1352 0.308 0.000 0.676 0.000 0.004 0.012
#> GSM97897 1 0.4348 0.8157 0.748 0.000 0.000 0.064 0.024 0.164
#> GSM97900 1 0.3752 0.8127 0.772 0.000 0.000 0.064 0.000 0.164
#> GSM97904 1 0.3796 0.8189 0.780 0.000 0.004 0.048 0.004 0.164
#> GSM97907 2 0.0000 0.9994 0.000 1.000 0.000 0.000 0.000 0.000
#> GSM97925 3 0.0363 0.7323 0.000 0.000 0.988 0.000 0.012 0.000
#> GSM97947 3 0.1327 0.7165 0.000 0.000 0.936 0.000 0.000 0.064
Heatmaps for the consensus matrix. It visualizes the probability of two samples to be in a same group.
consensus_heatmap(res, k = 2)
consensus_heatmap(res, k = 3)
consensus_heatmap(res, k = 4)
consensus_heatmap(res, k = 5)
consensus_heatmap(res, k = 6)
Heatmaps for the membership of samples in all partitions to see how consistent they are:
membership_heatmap(res, k = 2)
membership_heatmap(res, k = 3)
membership_heatmap(res, k = 4)
membership_heatmap(res, k = 5)
membership_heatmap(res, k = 6)
As soon as we have had the classes for columns, we can look for signatures which are significantly different between classes which can be candidate marks for certain classes. Following are the heatmaps for signatures.
Signature heatmaps where rows are scaled:
get_signatures(res, k = 2)
get_signatures(res, k = 3)
get_signatures(res, k = 4)
get_signatures(res, k = 5)
get_signatures(res, k = 6)
Signature heatmaps where rows are not scaled:
get_signatures(res, k = 2, scale_rows = FALSE)
get_signatures(res, k = 3, scale_rows = FALSE)
get_signatures(res, k = 4, scale_rows = FALSE)
get_signatures(res, k = 5, scale_rows = FALSE)
get_signatures(res, k = 6, scale_rows = FALSE)
Compare the overlap of signatures from different k:
compare_signatures(res)
get_signature() returns a data frame invisibly. TO get the list of signatures, the function
call should be assigned to a variable explicitly. In following code, if plot argument is set
to FALSE, no heatmap is plotted while only the differential analysis is performed.
# code only for demonstration
tb = get_signature(res, k = ..., plot = FALSE)
An example of the output of tb is:
#> which_row fdr mean_1 mean_2 scaled_mean_1 scaled_mean_2 km
#> 1 38 0.042760348 8.373488 9.131774 -0.5533452 0.5164555 1
#> 2 40 0.018707592 7.106213 8.469186 -0.6173731 0.5762149 1
#> 3 55 0.019134737 10.221463 11.207825 -0.6159697 0.5749050 1
#> 4 59 0.006059896 5.921854 7.869574 -0.6899429 0.6439467 1
#> 5 60 0.018055526 8.928898 10.211722 -0.6204761 0.5791110 1
#> 6 98 0.009384629 15.714769 14.887706 0.6635654 -0.6193277 2
...
The columns in tb are:
which_row: row indices corresponding to the input matrix.fdr: FDR for the differential test. mean_x: The mean value in group x.scaled_mean_x: The mean value in group x after rows are scaled.km: Row groups if k-means clustering is applied to rows.UMAP plot which shows how samples are separated.
dimension_reduction(res, k = 2, method = "UMAP")
dimension_reduction(res, k = 3, method = "UMAP")
dimension_reduction(res, k = 4, method = "UMAP")
dimension_reduction(res, k = 5, method = "UMAP")
dimension_reduction(res, k = 6, method = "UMAP")
Following heatmap shows how subgroups are split when increasing k:
collect_classes(res)
Test correlation between subgroups and known annotations. If the known annotation is numeric, one-way ANOVA test is applied, and if the known annotation is discrete, chi-squared contingency table test is applied.
test_to_known_factors(res)
#> n disease.state(p) tissue(p) k
#> ATC:mclust 180 3.71e-17 6.12e-17 2
#> ATC:mclust 179 5.72e-28 8.02e-29 3
#> ATC:mclust 166 1.03e-32 3.23e-29 4
#> ATC:mclust 172 5.57e-31 1.82e-27 5
#> ATC:mclust 169 1.78e-27 2.62e-24 6
If matrix rows can be associated to genes, consider to use functional_enrichment(res,
...) to perform function enrichment for the signature genes. See this vignette for more detailed explanations.
The object with results only for a single top-value method and a single partition method can be extracted as:
res = res_list["ATC", "NMF"]
# you can also extract it by
# res = res_list["ATC:NMF"]
A summary of res and all the functions that can be applied to it:
res
#> A 'ConsensusPartition' object with k = 2, 3, 4, 5, 6.
#> On a matrix with 51882 rows and 180 columns.
#> Top rows (1000, 2000, 3000, 4000, 5000) are extracted by 'ATC' method.
#> Subgroups are detected by 'NMF' method.
#> Performed in total 1250 partitions by row resampling.
#> Best k for subgroups seems to be 3.
#>
#> Following methods can be applied to this 'ConsensusPartition' object:
#> [1] "cola_report" "collect_classes" "collect_plots"
#> [4] "collect_stats" "colnames" "compare_signatures"
#> [7] "consensus_heatmap" "dimension_reduction" "functional_enrichment"
#> [10] "get_anno_col" "get_anno" "get_classes"
#> [13] "get_consensus" "get_matrix" "get_membership"
#> [16] "get_param" "get_signatures" "get_stats"
#> [19] "is_best_k" "is_stable_k" "membership_heatmap"
#> [22] "ncol" "nrow" "plot_ecdf"
#> [25] "rownames" "select_partition_number" "show"
#> [28] "suggest_best_k" "test_to_known_factors"
collect_plots() function collects all the plots made from res for all k (number of partitions)
into one single page to provide an easy and fast comparison between different k.
collect_plots(res)
The plots are:
k and the heatmap of
predicted classes for each k.k.k.k.All the plots in panels can be made by individual functions and they are plotted later in this section.
select_partition_number() produces several plots showing different
statistics for choosing “optimized” k. There are following statistics:
k;k, the area increased is defined as \(A_k - A_{k-1}\).The detailed explanations of these statistics can be found in the cola vignette.
Generally speaking, lower PAC score, higher mean silhouette score or higher
concordance corresponds to better partition. Rand index and Jaccard index
measure how similar the current partition is compared to partition with k-1.
If they are too similar, we won't accept k is better than k-1.
select_partition_number(res)
The numeric values for all these statistics can be obtained by get_stats().
get_stats(res)
#> k 1-PAC mean_silhouette concordance area_increased Rand Jaccard
#> 2 2 0.910 0.940 0.975 0.4983 0.500 0.500
#> 3 3 0.958 0.942 0.976 0.3191 0.774 0.578
#> 4 4 0.866 0.879 0.938 0.0839 0.929 0.797
#> 5 5 0.761 0.733 0.845 0.0557 0.969 0.894
#> 6 6 0.726 0.590 0.797 0.0349 0.967 0.884
suggest_best_k() suggests the best \(k\) based on these statistics. The rules are as follows:
suggest_best_k(res)
#> [1] 3
#> attr(,"optional")
#> [1] 2
There is also optional best \(k\) = 2 that is worth to check.
Following shows the table of the partitions (You need to click the show/hide
code output link to see it). The membership matrix (columns with name p*)
is inferred by
clue::cl_consensus()
function with the SE method. Basically the value in the membership matrix
represents the probability to belong to a certain group. The finall class
label for an item is determined with the group with highest probability it
belongs to.
In get_classes() function, the entropy is calculated from the membership
matrix and the silhouette score is calculated from the consensus matrix.
cbind(get_classes(res, k = 2), get_membership(res, k = 2))
#> class entropy silhouette p1 p2
#> GSM97800 2 0.000 0.971 0.000 1.000
#> GSM97803 2 0.000 0.971 0.000 1.000
#> GSM97804 2 0.000 0.971 0.000 1.000
#> GSM97805 2 0.000 0.971 0.000 1.000
#> GSM97807 2 0.000 0.971 0.000 1.000
#> GSM97809 2 0.000 0.971 0.000 1.000
#> GSM97811 2 0.000 0.971 0.000 1.000
#> GSM97812 2 0.000 0.971 0.000 1.000
#> GSM97816 2 0.000 0.971 0.000 1.000
#> GSM97817 2 0.000 0.971 0.000 1.000
#> GSM97820 2 0.000 0.971 0.000 1.000
#> GSM97825 2 0.000 0.971 0.000 1.000
#> GSM97827 2 0.000 0.971 0.000 1.000
#> GSM97828 2 0.000 0.971 0.000 1.000
#> GSM97833 2 0.000 0.971 0.000 1.000
#> GSM97834 2 0.000 0.971 0.000 1.000
#> GSM97840 2 0.000 0.971 0.000 1.000
#> GSM97846 2 0.000 0.971 0.000 1.000
#> GSM97848 2 0.000 0.971 0.000 1.000
#> GSM97849 2 0.000 0.971 0.000 1.000
#> GSM97850 2 0.000 0.971 0.000 1.000
#> GSM97853 2 0.000 0.971 0.000 1.000
#> GSM97855 2 0.000 0.971 0.000 1.000
#> GSM97878 1 0.242 0.942 0.960 0.040
#> GSM97913 2 0.000 0.971 0.000 1.000
#> GSM97932 1 0.000 0.976 1.000 0.000
#> GSM97939 2 0.000 0.971 0.000 1.000
#> GSM97951 2 0.000 0.971 0.000 1.000
#> GSM97957 2 0.615 0.806 0.152 0.848
#> GSM97972 2 0.000 0.971 0.000 1.000
#> GSM97793 2 0.000 0.971 0.000 1.000
#> GSM97795 2 0.000 0.971 0.000 1.000
#> GSM97802 2 0.994 0.153 0.456 0.544
#> GSM97810 2 0.000 0.971 0.000 1.000
#> GSM97815 2 0.000 0.971 0.000 1.000
#> GSM97837 1 0.000 0.976 1.000 0.000
#> GSM97843 1 0.895 0.561 0.688 0.312
#> GSM97890 2 0.000 0.971 0.000 1.000
#> GSM97899 1 0.000 0.976 1.000 0.000
#> GSM97910 1 0.311 0.927 0.944 0.056
#> GSM97916 1 0.000 0.976 1.000 0.000
#> GSM97920 2 0.850 0.614 0.276 0.724
#> GSM97921 1 0.000 0.976 1.000 0.000
#> GSM97927 1 0.000 0.976 1.000 0.000
#> GSM97937 1 0.000 0.976 1.000 0.000
#> GSM97941 2 0.000 0.971 0.000 1.000
#> GSM97943 1 0.653 0.804 0.832 0.168
#> GSM97958 2 0.000 0.971 0.000 1.000
#> GSM97960 2 0.000 0.971 0.000 1.000
#> GSM97794 1 0.584 0.839 0.860 0.140
#> GSM97796 1 0.000 0.976 1.000 0.000
#> GSM97797 1 0.904 0.543 0.680 0.320
#> GSM97798 1 0.000 0.976 1.000 0.000
#> GSM97801 1 0.000 0.976 1.000 0.000
#> GSM97806 1 0.000 0.976 1.000 0.000
#> GSM97808 1 0.000 0.976 1.000 0.000
#> GSM97813 1 0.000 0.976 1.000 0.000
#> GSM97814 1 0.000 0.976 1.000 0.000
#> GSM97818 1 0.118 0.963 0.984 0.016
#> GSM97819 1 0.850 0.632 0.724 0.276
#> GSM97821 2 0.000 0.971 0.000 1.000
#> GSM97826 1 0.000 0.976 1.000 0.000
#> GSM97829 1 0.000 0.976 1.000 0.000
#> GSM97832 2 0.000 0.971 0.000 1.000
#> GSM97836 1 0.000 0.976 1.000 0.000
#> GSM97839 1 0.000 0.976 1.000 0.000
#> GSM97844 2 0.000 0.971 0.000 1.000
#> GSM97847 1 0.000 0.976 1.000 0.000
#> GSM97851 1 0.000 0.976 1.000 0.000
#> GSM97852 1 0.000 0.976 1.000 0.000
#> GSM97856 1 0.000 0.976 1.000 0.000
#> GSM97858 2 0.000 0.971 0.000 1.000
#> GSM97859 1 0.000 0.976 1.000 0.000
#> GSM97861 1 0.000 0.976 1.000 0.000
#> GSM97863 1 0.000 0.976 1.000 0.000
#> GSM97869 1 0.000 0.976 1.000 0.000
#> GSM97870 1 0.000 0.976 1.000 0.000
#> GSM97871 1 0.000 0.976 1.000 0.000
#> GSM97877 2 0.000 0.971 0.000 1.000
#> GSM97879 1 0.000 0.976 1.000 0.000
#> GSM97882 1 0.000 0.976 1.000 0.000
#> GSM97885 1 0.000 0.976 1.000 0.000
#> GSM97886 1 0.000 0.976 1.000 0.000
#> GSM97887 1 0.000 0.976 1.000 0.000
#> GSM97888 1 0.000 0.976 1.000 0.000
#> GSM97889 1 0.000 0.976 1.000 0.000
#> GSM97891 1 0.000 0.976 1.000 0.000
#> GSM97892 2 0.000 0.971 0.000 1.000
#> GSM97893 1 0.000 0.976 1.000 0.000
#> GSM97894 1 0.000 0.976 1.000 0.000
#> GSM97895 1 0.000 0.976 1.000 0.000
#> GSM97896 1 0.000 0.976 1.000 0.000
#> GSM97898 1 0.000 0.976 1.000 0.000
#> GSM97903 1 0.000 0.976 1.000 0.000
#> GSM97905 1 0.000 0.976 1.000 0.000
#> GSM97906 1 0.000 0.976 1.000 0.000
#> GSM97908 1 0.000 0.976 1.000 0.000
#> GSM97912 1 0.000 0.976 1.000 0.000
#> GSM97914 1 0.000 0.976 1.000 0.000
#> GSM97915 1 0.000 0.976 1.000 0.000
#> GSM97917 1 0.000 0.976 1.000 0.000
#> GSM97918 1 0.000 0.976 1.000 0.000
#> GSM97919 1 0.000 0.976 1.000 0.000
#> GSM97922 1 0.000 0.976 1.000 0.000
#> GSM97924 2 0.000 0.971 0.000 1.000
#> GSM97926 2 0.983 0.258 0.424 0.576
#> GSM97930 1 0.000 0.976 1.000 0.000
#> GSM97931 2 0.000 0.971 0.000 1.000
#> GSM97935 1 0.000 0.976 1.000 0.000
#> GSM97936 1 0.000 0.976 1.000 0.000
#> GSM97938 1 0.000 0.976 1.000 0.000
#> GSM97940 1 0.000 0.976 1.000 0.000
#> GSM97942 1 0.000 0.976 1.000 0.000
#> GSM97945 1 0.000 0.976 1.000 0.000
#> GSM97946 2 0.000 0.971 0.000 1.000
#> GSM97948 1 0.000 0.976 1.000 0.000
#> GSM97950 1 0.000 0.976 1.000 0.000
#> GSM97952 1 0.000 0.976 1.000 0.000
#> GSM97953 1 0.000 0.976 1.000 0.000
#> GSM97954 1 0.000 0.976 1.000 0.000
#> GSM97955 1 0.000 0.976 1.000 0.000
#> GSM97959 2 0.998 0.080 0.476 0.524
#> GSM97961 1 0.000 0.976 1.000 0.000
#> GSM97963 1 0.000 0.976 1.000 0.000
#> GSM97965 1 0.000 0.976 1.000 0.000
#> GSM97966 1 0.000 0.976 1.000 0.000
#> GSM97967 2 0.000 0.971 0.000 1.000
#> GSM97968 2 0.000 0.971 0.000 1.000
#> GSM97969 1 0.000 0.976 1.000 0.000
#> GSM97971 1 0.000 0.976 1.000 0.000
#> GSM97799 2 0.000 0.971 0.000 1.000
#> GSM97823 2 0.000 0.971 0.000 1.000
#> GSM97824 2 0.000 0.971 0.000 1.000
#> GSM97830 2 0.000 0.971 0.000 1.000
#> GSM97835 2 0.000 0.971 0.000 1.000
#> GSM97838 2 0.000 0.971 0.000 1.000
#> GSM97841 2 0.000 0.971 0.000 1.000
#> GSM97842 2 0.000 0.971 0.000 1.000
#> GSM97854 2 0.000 0.971 0.000 1.000
#> GSM97857 2 0.000 0.971 0.000 1.000
#> GSM97860 1 0.697 0.776 0.812 0.188
#> GSM97862 2 0.000 0.971 0.000 1.000
#> GSM97864 2 0.000 0.971 0.000 1.000
#> GSM97866 2 0.000 0.971 0.000 1.000
#> GSM97868 2 0.000 0.971 0.000 1.000
#> GSM97872 1 0.000 0.976 1.000 0.000
#> GSM97873 2 0.000 0.971 0.000 1.000
#> GSM97874 1 0.745 0.741 0.788 0.212
#> GSM97875 2 0.000 0.971 0.000 1.000
#> GSM97876 2 0.821 0.650 0.256 0.744
#> GSM97880 1 0.000 0.976 1.000 0.000
#> GSM97881 2 0.000 0.971 0.000 1.000
#> GSM97884 2 0.000 0.971 0.000 1.000
#> GSM97901 2 0.000 0.971 0.000 1.000
#> GSM97902 2 0.775 0.697 0.228 0.772
#> GSM97909 2 0.000 0.971 0.000 1.000
#> GSM97911 2 0.000 0.971 0.000 1.000
#> GSM97923 1 0.000 0.976 1.000 0.000
#> GSM97928 1 0.000 0.976 1.000 0.000
#> GSM97929 2 0.000 0.971 0.000 1.000
#> GSM97933 1 0.584 0.839 0.860 0.140
#> GSM97934 1 0.625 0.820 0.844 0.156
#> GSM97944 2 0.000 0.971 0.000 1.000
#> GSM97949 2 0.000 0.971 0.000 1.000
#> GSM97956 2 0.000 0.971 0.000 1.000
#> GSM97962 2 0.000 0.971 0.000 1.000
#> GSM97964 2 0.000 0.971 0.000 1.000
#> GSM97970 2 0.000 0.971 0.000 1.000
#> GSM97822 1 0.000 0.976 1.000 0.000
#> GSM97831 2 0.000 0.971 0.000 1.000
#> GSM97845 1 0.000 0.976 1.000 0.000
#> GSM97865 1 0.000 0.976 1.000 0.000
#> GSM97867 1 0.000 0.976 1.000 0.000
#> GSM97883 1 0.000 0.976 1.000 0.000
#> GSM97897 1 0.000 0.976 1.000 0.000
#> GSM97900 1 0.000 0.976 1.000 0.000
#> GSM97904 1 0.000 0.976 1.000 0.000
#> GSM97907 2 0.000 0.971 0.000 1.000
#> GSM97925 1 0.644 0.809 0.836 0.164
#> GSM97947 1 0.118 0.963 0.984 0.016
cbind(get_classes(res, k = 3), get_membership(res, k = 3))
#> class entropy silhouette p1 p2 p3
#> GSM97800 2 0.0000 0.9686 0.000 1.000 0.000
#> GSM97803 2 0.0000 0.9686 0.000 1.000 0.000
#> GSM97804 2 0.0000 0.9686 0.000 1.000 0.000
#> GSM97805 2 0.0000 0.9686 0.000 1.000 0.000
#> GSM97807 2 0.0000 0.9686 0.000 1.000 0.000
#> GSM97809 2 0.0000 0.9686 0.000 1.000 0.000
#> GSM97811 2 0.0000 0.9686 0.000 1.000 0.000
#> GSM97812 2 0.0000 0.9686 0.000 1.000 0.000
#> GSM97816 2 0.5397 0.6131 0.000 0.720 0.280
#> GSM97817 2 0.0000 0.9686 0.000 1.000 0.000
#> GSM97820 2 0.0000 0.9686 0.000 1.000 0.000
#> GSM97825 2 0.0000 0.9686 0.000 1.000 0.000
#> GSM97827 2 0.0000 0.9686 0.000 1.000 0.000
#> GSM97828 3 0.0000 0.9786 0.000 0.000 1.000
#> GSM97833 2 0.0000 0.9686 0.000 1.000 0.000
#> GSM97834 2 0.0000 0.9686 0.000 1.000 0.000
#> GSM97840 2 0.0000 0.9686 0.000 1.000 0.000
#> GSM97846 2 0.0000 0.9686 0.000 1.000 0.000
#> GSM97848 2 0.0000 0.9686 0.000 1.000 0.000
#> GSM97849 2 0.0000 0.9686 0.000 1.000 0.000
#> GSM97850 2 0.0000 0.9686 0.000 1.000 0.000
#> GSM97853 2 0.0000 0.9686 0.000 1.000 0.000
#> GSM97855 2 0.0000 0.9686 0.000 1.000 0.000
#> GSM97878 1 0.3412 0.8542 0.876 0.124 0.000
#> GSM97913 2 0.0000 0.9686 0.000 1.000 0.000
#> GSM97932 1 0.0000 0.9751 1.000 0.000 0.000
#> GSM97939 2 0.6305 0.0887 0.000 0.516 0.484
#> GSM97951 2 0.0000 0.9686 0.000 1.000 0.000
#> GSM97957 3 0.0000 0.9786 0.000 0.000 1.000
#> GSM97972 2 0.0000 0.9686 0.000 1.000 0.000
#> GSM97793 3 0.0000 0.9786 0.000 0.000 1.000
#> GSM97795 2 0.0000 0.9686 0.000 1.000 0.000
#> GSM97802 3 0.0000 0.9786 0.000 0.000 1.000
#> GSM97810 2 0.0000 0.9686 0.000 1.000 0.000
#> GSM97815 2 0.0892 0.9518 0.000 0.980 0.020
#> GSM97837 1 0.2796 0.8944 0.908 0.000 0.092
#> GSM97843 3 0.0000 0.9786 0.000 0.000 1.000
#> GSM97890 3 0.0000 0.9786 0.000 0.000 1.000
#> GSM97899 1 0.0000 0.9751 1.000 0.000 0.000
#> GSM97910 1 0.6793 0.5493 0.672 0.036 0.292
#> GSM97916 1 0.0000 0.9751 1.000 0.000 0.000
#> GSM97920 3 0.0000 0.9786 0.000 0.000 1.000
#> GSM97921 1 0.0000 0.9751 1.000 0.000 0.000
#> GSM97927 1 0.0000 0.9751 1.000 0.000 0.000
#> GSM97937 1 0.0000 0.9751 1.000 0.000 0.000
#> GSM97941 2 0.0000 0.9686 0.000 1.000 0.000
#> GSM97943 3 0.0000 0.9786 0.000 0.000 1.000
#> GSM97958 2 0.0000 0.9686 0.000 1.000 0.000
#> GSM97960 2 0.0237 0.9654 0.000 0.996 0.004
#> GSM97794 1 0.4605 0.7465 0.796 0.204 0.000
#> GSM97796 1 0.0000 0.9751 1.000 0.000 0.000
#> GSM97797 1 0.6252 0.2117 0.556 0.444 0.000
#> GSM97798 1 0.0000 0.9751 1.000 0.000 0.000
#> GSM97801 1 0.1643 0.9401 0.956 0.000 0.044
#> GSM97806 1 0.0000 0.9751 1.000 0.000 0.000
#> GSM97808 1 0.0000 0.9751 1.000 0.000 0.000
#> GSM97813 1 0.0000 0.9751 1.000 0.000 0.000
#> GSM97814 1 0.0000 0.9751 1.000 0.000 0.000
#> GSM97818 1 0.2625 0.8994 0.916 0.084 0.000
#> GSM97819 3 0.0000 0.9786 0.000 0.000 1.000
#> GSM97821 2 0.0000 0.9686 0.000 1.000 0.000
#> GSM97826 1 0.0000 0.9751 1.000 0.000 0.000
#> GSM97829 1 0.0000 0.9751 1.000 0.000 0.000
#> GSM97832 2 0.2165 0.9100 0.000 0.936 0.064
#> GSM97836 3 0.6126 0.3149 0.400 0.000 0.600
#> GSM97839 1 0.0000 0.9751 1.000 0.000 0.000
#> GSM97844 2 0.0000 0.9686 0.000 1.000 0.000
#> GSM97847 1 0.0000 0.9751 1.000 0.000 0.000
#> GSM97851 1 0.0000 0.9751 1.000 0.000 0.000
#> GSM97852 1 0.0000 0.9751 1.000 0.000 0.000
#> GSM97856 1 0.0000 0.9751 1.000 0.000 0.000
#> GSM97858 2 0.0000 0.9686 0.000 1.000 0.000
#> GSM97859 1 0.3941 0.8199 0.844 0.000 0.156
#> GSM97861 1 0.0000 0.9751 1.000 0.000 0.000
#> GSM97863 1 0.0000 0.9751 1.000 0.000 0.000
#> GSM97869 1 0.0424 0.9691 0.992 0.008 0.000
#> GSM97870 3 0.0000 0.9786 0.000 0.000 1.000
#> GSM97871 1 0.0000 0.9751 1.000 0.000 0.000
#> GSM97877 2 0.0000 0.9686 0.000 1.000 0.000
#> GSM97879 1 0.0000 0.9751 1.000 0.000 0.000
#> GSM97882 1 0.0000 0.9751 1.000 0.000 0.000
#> GSM97885 1 0.0000 0.9751 1.000 0.000 0.000
#> GSM97886 1 0.0000 0.9751 1.000 0.000 0.000
#> GSM97887 1 0.0000 0.9751 1.000 0.000 0.000
#> GSM97888 1 0.0000 0.9751 1.000 0.000 0.000
#> GSM97889 1 0.0592 0.9664 0.988 0.000 0.012
#> GSM97891 1 0.0000 0.9751 1.000 0.000 0.000
#> GSM97892 2 0.0000 0.9686 0.000 1.000 0.000
#> GSM97893 1 0.0000 0.9751 1.000 0.000 0.000
#> GSM97894 1 0.0000 0.9751 1.000 0.000 0.000
#> GSM97895 1 0.0000 0.9751 1.000 0.000 0.000
#> GSM97896 1 0.0000 0.9751 1.000 0.000 0.000
#> GSM97898 1 0.0000 0.9751 1.000 0.000 0.000
#> GSM97903 1 0.0000 0.9751 1.000 0.000 0.000
#> GSM97905 3 0.0747 0.9636 0.016 0.000 0.984
#> GSM97906 1 0.0000 0.9751 1.000 0.000 0.000
#> GSM97908 1 0.0000 0.9751 1.000 0.000 0.000
#> GSM97912 1 0.4702 0.7381 0.788 0.000 0.212
#> GSM97914 1 0.0000 0.9751 1.000 0.000 0.000
#> GSM97915 1 0.0000 0.9751 1.000 0.000 0.000
#> GSM97917 1 0.0000 0.9751 1.000 0.000 0.000
#> GSM97918 1 0.0000 0.9751 1.000 0.000 0.000
#> GSM97919 1 0.0000 0.9751 1.000 0.000 0.000
#> GSM97922 1 0.0000 0.9751 1.000 0.000 0.000
#> GSM97924 2 0.0000 0.9686 0.000 1.000 0.000
#> GSM97926 3 0.0000 0.9786 0.000 0.000 1.000
#> GSM97930 1 0.0000 0.9751 1.000 0.000 0.000
#> GSM97931 2 0.0000 0.9686 0.000 1.000 0.000
#> GSM97935 1 0.0000 0.9751 1.000 0.000 0.000
#> GSM97936 1 0.0000 0.9751 1.000 0.000 0.000
#> GSM97938 1 0.0000 0.9751 1.000 0.000 0.000
#> GSM97940 1 0.0000 0.9751 1.000 0.000 0.000
#> GSM97942 3 0.0000 0.9786 0.000 0.000 1.000
#> GSM97945 1 0.0000 0.9751 1.000 0.000 0.000
#> GSM97946 2 0.0000 0.9686 0.000 1.000 0.000
#> GSM97948 3 0.0000 0.9786 0.000 0.000 1.000
#> GSM97950 1 0.0000 0.9751 1.000 0.000 0.000
#> GSM97952 1 0.0000 0.9751 1.000 0.000 0.000
#> GSM97953 1 0.2711 0.8984 0.912 0.000 0.088
#> GSM97954 1 0.0000 0.9751 1.000 0.000 0.000
#> GSM97955 1 0.0000 0.9751 1.000 0.000 0.000
#> GSM97959 2 0.5621 0.5397 0.308 0.692 0.000
#> GSM97961 1 0.0000 0.9751 1.000 0.000 0.000
#> GSM97963 1 0.0000 0.9751 1.000 0.000 0.000
#> GSM97965 1 0.0000 0.9751 1.000 0.000 0.000
#> GSM97966 1 0.0000 0.9751 1.000 0.000 0.000
#> GSM97967 2 0.0000 0.9686 0.000 1.000 0.000
#> GSM97968 2 0.0000 0.9686 0.000 1.000 0.000
#> GSM97969 1 0.0000 0.9751 1.000 0.000 0.000
#> GSM97971 1 0.0592 0.9664 0.988 0.000 0.012
#> GSM97799 3 0.0000 0.9786 0.000 0.000 1.000
#> GSM97823 2 0.0000 0.9686 0.000 1.000 0.000
#> GSM97824 3 0.0000 0.9786 0.000 0.000 1.000
#> GSM97830 3 0.0000 0.9786 0.000 0.000 1.000
#> GSM97835 2 0.5650 0.5563 0.000 0.688 0.312
#> GSM97838 2 0.0000 0.9686 0.000 1.000 0.000
#> GSM97841 2 0.0000 0.9686 0.000 1.000 0.000
#> GSM97842 3 0.1860 0.9276 0.000 0.052 0.948
#> GSM97854 2 0.0000 0.9686 0.000 1.000 0.000
#> GSM97857 3 0.0000 0.9786 0.000 0.000 1.000
#> GSM97860 3 0.0000 0.9786 0.000 0.000 1.000
#> GSM97862 3 0.0000 0.9786 0.000 0.000 1.000
#> GSM97864 2 0.0000 0.9686 0.000 1.000 0.000
#> GSM97866 3 0.0000 0.9786 0.000 0.000 1.000
#> GSM97868 3 0.0000 0.9786 0.000 0.000 1.000
#> GSM97872 3 0.2711 0.8872 0.088 0.000 0.912
#> GSM97873 3 0.4702 0.7119 0.000 0.212 0.788
#> GSM97874 3 0.0000 0.9786 0.000 0.000 1.000
#> GSM97875 3 0.0000 0.9786 0.000 0.000 1.000
#> GSM97876 3 0.0000 0.9786 0.000 0.000 1.000
#> GSM97880 3 0.0000 0.9786 0.000 0.000 1.000
#> GSM97881 3 0.0000 0.9786 0.000 0.000 1.000
#> GSM97884 3 0.0000 0.9786 0.000 0.000 1.000
#> GSM97901 3 0.0000 0.9786 0.000 0.000 1.000
#> GSM97902 2 0.3619 0.8210 0.136 0.864 0.000
#> GSM97909 2 0.0000 0.9686 0.000 1.000 0.000
#> GSM97911 3 0.0000 0.9786 0.000 0.000 1.000
#> GSM97923 3 0.0000 0.9786 0.000 0.000 1.000
#> GSM97928 1 0.1860 0.9331 0.948 0.000 0.052
#> GSM97929 2 0.0000 0.9686 0.000 1.000 0.000
#> GSM97933 3 0.0000 0.9786 0.000 0.000 1.000
#> GSM97934 3 0.0000 0.9786 0.000 0.000 1.000
#> GSM97944 3 0.0000 0.9786 0.000 0.000 1.000
#> GSM97949 2 0.0000 0.9686 0.000 1.000 0.000
#> GSM97956 3 0.0000 0.9786 0.000 0.000 1.000
#> GSM97962 3 0.0000 0.9786 0.000 0.000 1.000
#> GSM97964 3 0.0000 0.9786 0.000 0.000 1.000
#> GSM97970 3 0.0000 0.9786 0.000 0.000 1.000
#> GSM97822 1 0.0000 0.9751 1.000 0.000 0.000
#> GSM97831 3 0.0000 0.9786 0.000 0.000 1.000
#> GSM97845 1 0.0000 0.9751 1.000 0.000 0.000
#> GSM97865 1 0.0000 0.9751 1.000 0.000 0.000
#> GSM97867 3 0.0000 0.9786 0.000 0.000 1.000
#> GSM97883 3 0.0000 0.9786 0.000 0.000 1.000
#> GSM97897 1 0.0000 0.9751 1.000 0.000 0.000
#> GSM97900 1 0.0000 0.9751 1.000 0.000 0.000
#> GSM97904 3 0.3482 0.8427 0.128 0.000 0.872
#> GSM97907 2 0.0000 0.9686 0.000 1.000 0.000
#> GSM97925 3 0.0000 0.9786 0.000 0.000 1.000
#> GSM97947 3 0.0000 0.9786 0.000 0.000 1.000
cbind(get_classes(res, k = 4), get_membership(res, k = 4))
#> class entropy silhouette p1 p2 p3 p4
#> GSM97800 2 0.0188 0.968 0.000 0.996 0.000 0.004
#> GSM97803 2 0.0188 0.968 0.000 0.996 0.000 0.004
#> GSM97804 2 0.0336 0.968 0.000 0.992 0.000 0.008
#> GSM97805 2 0.0336 0.967 0.000 0.992 0.000 0.008
#> GSM97807 2 0.0188 0.968 0.000 0.996 0.000 0.004
#> GSM97809 2 0.0336 0.967 0.000 0.992 0.000 0.008
#> GSM97811 2 0.0000 0.968 0.000 1.000 0.000 0.000
#> GSM97812 2 0.0336 0.967 0.000 0.992 0.000 0.008
#> GSM97816 4 0.2036 0.776 0.000 0.032 0.032 0.936
#> GSM97817 2 0.0000 0.968 0.000 1.000 0.000 0.000
#> GSM97820 2 0.0336 0.967 0.000 0.992 0.000 0.008
#> GSM97825 2 0.0188 0.968 0.000 0.996 0.000 0.004
#> GSM97827 2 0.0000 0.968 0.000 1.000 0.000 0.000
#> GSM97828 4 0.1767 0.779 0.000 0.012 0.044 0.944
#> GSM97833 2 0.0188 0.968 0.000 0.996 0.000 0.004
#> GSM97834 2 0.0000 0.968 0.000 1.000 0.000 0.000
#> GSM97840 2 0.0188 0.968 0.000 0.996 0.000 0.004
#> GSM97846 2 0.0188 0.968 0.000 0.996 0.000 0.004
#> GSM97848 2 0.0469 0.965 0.000 0.988 0.000 0.012
#> GSM97849 2 0.0188 0.968 0.000 0.996 0.000 0.004
#> GSM97850 2 0.0188 0.968 0.000 0.996 0.000 0.004
#> GSM97853 2 0.0336 0.967 0.000 0.992 0.000 0.008
#> GSM97855 2 0.0592 0.962 0.000 0.984 0.000 0.016
#> GSM97878 1 0.4100 0.816 0.832 0.092 0.000 0.076
#> GSM97913 2 0.1305 0.944 0.004 0.960 0.000 0.036
#> GSM97932 1 0.1022 0.945 0.968 0.000 0.000 0.032
#> GSM97939 2 0.5182 0.537 0.000 0.684 0.288 0.028
#> GSM97951 2 0.0188 0.968 0.000 0.996 0.000 0.004
#> GSM97957 4 0.3907 0.702 0.000 0.000 0.232 0.768
#> GSM97972 4 0.4361 0.674 0.000 0.208 0.020 0.772
#> GSM97793 3 0.3486 0.746 0.000 0.000 0.812 0.188
#> GSM97795 2 0.0188 0.968 0.000 0.996 0.000 0.004
#> GSM97802 3 0.1388 0.876 0.028 0.000 0.960 0.012
#> GSM97810 2 0.0592 0.963 0.000 0.984 0.000 0.016
#> GSM97815 2 0.0657 0.964 0.000 0.984 0.004 0.012
#> GSM97837 4 0.2197 0.768 0.080 0.000 0.004 0.916
#> GSM97843 3 0.1211 0.895 0.000 0.000 0.960 0.040
#> GSM97890 3 0.0188 0.903 0.000 0.000 0.996 0.004
#> GSM97899 1 0.0336 0.954 0.992 0.000 0.000 0.008
#> GSM97910 4 0.2057 0.782 0.032 0.008 0.020 0.940
#> GSM97916 1 0.1004 0.950 0.972 0.000 0.004 0.024
#> GSM97920 4 0.4072 0.677 0.000 0.000 0.252 0.748
#> GSM97921 1 0.4356 0.613 0.708 0.000 0.000 0.292
#> GSM97927 1 0.0672 0.952 0.984 0.000 0.008 0.008
#> GSM97937 1 0.4304 0.626 0.716 0.000 0.000 0.284
#> GSM97941 2 0.0336 0.967 0.000 0.992 0.000 0.008
#> GSM97943 4 0.1722 0.779 0.000 0.008 0.048 0.944
#> GSM97958 2 0.0707 0.961 0.000 0.980 0.000 0.020
#> GSM97960 2 0.0336 0.967 0.000 0.992 0.000 0.008
#> GSM97794 1 0.4465 0.756 0.800 0.144 0.000 0.056
#> GSM97796 1 0.0336 0.955 0.992 0.000 0.000 0.008
#> GSM97797 4 0.6084 0.629 0.204 0.120 0.000 0.676
#> GSM97798 1 0.0188 0.955 0.996 0.000 0.000 0.004
#> GSM97801 4 0.1443 0.778 0.028 0.004 0.008 0.960
#> GSM97806 1 0.0657 0.952 0.984 0.000 0.004 0.012
#> GSM97808 1 0.0188 0.955 0.996 0.000 0.000 0.004
#> GSM97813 1 0.0672 0.952 0.984 0.000 0.008 0.008
#> GSM97814 1 0.0188 0.955 0.996 0.000 0.000 0.004
#> GSM97818 1 0.5311 0.495 0.648 0.024 0.000 0.328
#> GSM97819 3 0.0188 0.905 0.000 0.000 0.996 0.004
#> GSM97821 2 0.0817 0.959 0.000 0.976 0.000 0.024
#> GSM97826 4 0.3688 0.676 0.208 0.000 0.000 0.792
#> GSM97829 4 0.2589 0.750 0.116 0.000 0.000 0.884
#> GSM97832 2 0.4955 0.583 0.000 0.708 0.024 0.268
#> GSM97836 3 0.2796 0.788 0.092 0.000 0.892 0.016
#> GSM97839 1 0.0336 0.955 0.992 0.000 0.000 0.008
#> GSM97844 2 0.0188 0.968 0.000 0.996 0.000 0.004
#> GSM97847 1 0.0921 0.947 0.972 0.000 0.000 0.028
#> GSM97851 1 0.0592 0.953 0.984 0.000 0.000 0.016
#> GSM97852 1 0.0469 0.954 0.988 0.000 0.000 0.012
#> GSM97856 1 0.0336 0.954 0.992 0.000 0.000 0.008
#> GSM97858 2 0.0188 0.968 0.000 0.996 0.000 0.004
#> GSM97859 1 0.3401 0.798 0.840 0.000 0.152 0.008
#> GSM97861 1 0.0336 0.954 0.992 0.000 0.000 0.008
#> GSM97863 1 0.0188 0.955 0.996 0.000 0.000 0.004
#> GSM97869 1 0.1339 0.943 0.964 0.008 0.004 0.024
#> GSM97870 3 0.0592 0.904 0.000 0.000 0.984 0.016
#> GSM97871 1 0.0188 0.955 0.996 0.000 0.000 0.004
#> GSM97877 2 0.0592 0.963 0.000 0.984 0.000 0.016
#> GSM97879 1 0.0592 0.953 0.984 0.000 0.000 0.016
#> GSM97882 1 0.0657 0.952 0.984 0.000 0.004 0.012
#> GSM97885 1 0.0188 0.956 0.996 0.000 0.000 0.004
#> GSM97886 1 0.0188 0.955 0.996 0.000 0.000 0.004
#> GSM97887 1 0.0927 0.947 0.976 0.000 0.016 0.008
#> GSM97888 1 0.0336 0.954 0.992 0.000 0.000 0.008
#> GSM97889 1 0.2773 0.850 0.880 0.000 0.116 0.004
#> GSM97891 1 0.0657 0.952 0.984 0.000 0.004 0.012
#> GSM97892 2 0.0000 0.968 0.000 1.000 0.000 0.000
#> GSM97893 1 0.0921 0.947 0.972 0.000 0.000 0.028
#> GSM97894 1 0.0188 0.955 0.996 0.000 0.000 0.004
#> GSM97895 1 0.3311 0.816 0.828 0.000 0.000 0.172
#> GSM97896 1 0.0336 0.954 0.992 0.000 0.000 0.008
#> GSM97898 1 0.0336 0.955 0.992 0.000 0.000 0.008
#> GSM97903 1 0.0817 0.950 0.976 0.000 0.000 0.024
#> GSM97905 3 0.3984 0.724 0.132 0.000 0.828 0.040
#> GSM97906 1 0.0188 0.955 0.996 0.000 0.000 0.004
#> GSM97908 1 0.0921 0.947 0.972 0.000 0.000 0.028
#> GSM97912 1 0.0657 0.951 0.984 0.000 0.012 0.004
#> GSM97914 1 0.1022 0.946 0.968 0.000 0.000 0.032
#> GSM97915 1 0.0000 0.955 1.000 0.000 0.000 0.000
#> GSM97917 1 0.0592 0.953 0.984 0.000 0.000 0.016
#> GSM97918 1 0.0469 0.954 0.988 0.000 0.000 0.012
#> GSM97919 1 0.0336 0.955 0.992 0.000 0.000 0.008
#> GSM97922 1 0.0336 0.954 0.992 0.000 0.000 0.008
#> GSM97924 2 0.0188 0.968 0.000 0.996 0.000 0.004
#> GSM97926 3 0.0336 0.902 0.000 0.000 0.992 0.008
#> GSM97930 1 0.1118 0.943 0.964 0.000 0.000 0.036
#> GSM97931 2 0.0707 0.961 0.000 0.980 0.000 0.020
#> GSM97935 1 0.0336 0.954 0.992 0.000 0.000 0.008
#> GSM97936 1 0.0000 0.955 1.000 0.000 0.000 0.000
#> GSM97938 1 0.2760 0.859 0.872 0.000 0.000 0.128
#> GSM97940 1 0.0188 0.955 0.996 0.000 0.000 0.004
#> GSM97942 3 0.0188 0.905 0.000 0.000 0.996 0.004
#> GSM97945 1 0.0000 0.955 1.000 0.000 0.000 0.000
#> GSM97946 2 0.0188 0.968 0.000 0.996 0.000 0.004
#> GSM97948 3 0.1610 0.869 0.032 0.000 0.952 0.016
#> GSM97950 1 0.0592 0.953 0.984 0.000 0.000 0.016
#> GSM97952 1 0.0336 0.954 0.992 0.000 0.000 0.008
#> GSM97953 4 0.4353 0.660 0.232 0.000 0.012 0.756
#> GSM97954 1 0.0921 0.947 0.972 0.000 0.000 0.028
#> GSM97955 1 0.0336 0.955 0.992 0.000 0.000 0.008
#> GSM97959 2 0.5660 0.282 0.396 0.576 0.000 0.028
#> GSM97961 1 0.0336 0.955 0.992 0.000 0.000 0.008
#> GSM97963 1 0.0188 0.955 0.996 0.000 0.000 0.004
#> GSM97965 1 0.0000 0.955 1.000 0.000 0.000 0.000
#> GSM97966 1 0.0336 0.954 0.992 0.000 0.000 0.008
#> GSM97967 2 0.0188 0.968 0.000 0.996 0.000 0.004
#> GSM97968 2 0.0336 0.967 0.000 0.992 0.000 0.008
#> GSM97969 1 0.1022 0.947 0.968 0.000 0.000 0.032
#> GSM97971 1 0.0376 0.955 0.992 0.000 0.004 0.004
#> GSM97799 3 0.0000 0.904 0.000 0.000 1.000 0.000
#> GSM97823 2 0.0592 0.963 0.000 0.984 0.000 0.016
#> GSM97824 3 0.3444 0.750 0.000 0.000 0.816 0.184
#> GSM97830 4 0.4761 0.481 0.000 0.000 0.372 0.628
#> GSM97835 2 0.1706 0.930 0.000 0.948 0.036 0.016
#> GSM97838 2 0.0188 0.968 0.000 0.996 0.000 0.004
#> GSM97841 2 0.0188 0.968 0.000 0.996 0.000 0.004
#> GSM97842 3 0.1356 0.878 0.000 0.032 0.960 0.008
#> GSM97854 2 0.0188 0.968 0.000 0.996 0.000 0.004
#> GSM97857 4 0.3444 0.738 0.000 0.000 0.184 0.816
#> GSM97860 3 0.1302 0.894 0.000 0.000 0.956 0.044
#> GSM97862 3 0.1022 0.899 0.000 0.000 0.968 0.032
#> GSM97864 2 0.0188 0.968 0.000 0.996 0.000 0.004
#> GSM97866 3 0.1022 0.899 0.000 0.000 0.968 0.032
#> GSM97868 3 0.1637 0.884 0.000 0.000 0.940 0.060
#> GSM97872 4 0.2921 0.761 0.000 0.000 0.140 0.860
#> GSM97873 3 0.4319 0.567 0.000 0.228 0.760 0.012
#> GSM97874 4 0.4961 0.281 0.000 0.000 0.448 0.552
#> GSM97875 3 0.0000 0.904 0.000 0.000 1.000 0.000
#> GSM97876 3 0.0707 0.903 0.000 0.000 0.980 0.020
#> GSM97880 3 0.4564 0.477 0.000 0.000 0.672 0.328
#> GSM97881 3 0.0000 0.904 0.000 0.000 1.000 0.000
#> GSM97884 3 0.0000 0.904 0.000 0.000 1.000 0.000
#> GSM97901 3 0.1022 0.899 0.000 0.000 0.968 0.032
#> GSM97902 4 0.3768 0.690 0.008 0.184 0.000 0.808
#> GSM97909 2 0.0817 0.959 0.000 0.976 0.000 0.024
#> GSM97911 3 0.0000 0.904 0.000 0.000 1.000 0.000
#> GSM97923 3 0.0469 0.904 0.000 0.000 0.988 0.012
#> GSM97928 1 0.3306 0.789 0.840 0.000 0.156 0.004
#> GSM97929 2 0.0188 0.968 0.000 0.996 0.000 0.004
#> GSM97933 3 0.2589 0.834 0.000 0.000 0.884 0.116
#> GSM97934 4 0.3837 0.710 0.000 0.000 0.224 0.776
#> GSM97944 3 0.0000 0.904 0.000 0.000 1.000 0.000
#> GSM97949 2 0.0188 0.968 0.000 0.996 0.000 0.004
#> GSM97956 3 0.1637 0.884 0.000 0.000 0.940 0.060
#> GSM97962 4 0.4855 0.428 0.000 0.000 0.400 0.600
#> GSM97964 3 0.0188 0.905 0.000 0.000 0.996 0.004
#> GSM97970 3 0.0188 0.905 0.000 0.000 0.996 0.004
#> GSM97822 1 0.3547 0.808 0.840 0.000 0.144 0.016
#> GSM97831 3 0.4277 0.585 0.000 0.000 0.720 0.280
#> GSM97845 1 0.0592 0.953 0.984 0.000 0.000 0.016
#> GSM97865 1 0.1389 0.936 0.952 0.000 0.000 0.048
#> GSM97867 3 0.1792 0.879 0.000 0.000 0.932 0.068
#> GSM97883 3 0.0336 0.905 0.000 0.000 0.992 0.008
#> GSM97897 1 0.0927 0.947 0.976 0.000 0.016 0.008
#> GSM97900 1 0.0336 0.954 0.992 0.000 0.000 0.008
#> GSM97904 3 0.5500 0.118 0.464 0.000 0.520 0.016
#> GSM97907 2 0.0188 0.968 0.000 0.996 0.000 0.004
#> GSM97925 3 0.0336 0.902 0.000 0.000 0.992 0.008
#> GSM97947 3 0.0524 0.898 0.004 0.000 0.988 0.008
cbind(get_classes(res, k = 5), get_membership(res, k = 5))
#> class entropy silhouette p1 p2 p3 p4 p5
#> GSM97800 2 0.0703 0.8936 0.000 0.976 0.000 0.000 0.024
#> GSM97803 2 0.0324 0.8967 0.004 0.992 0.000 0.000 0.004
#> GSM97804 2 0.0794 0.8955 0.000 0.972 0.000 0.000 0.028
#> GSM97805 2 0.0510 0.8968 0.000 0.984 0.000 0.000 0.016
#> GSM97807 2 0.0566 0.8951 0.004 0.984 0.000 0.000 0.012
#> GSM97809 2 0.0451 0.8957 0.004 0.988 0.000 0.000 0.008
#> GSM97811 2 0.0404 0.8957 0.000 0.988 0.000 0.000 0.012
#> GSM97812 2 0.0703 0.8936 0.000 0.976 0.000 0.000 0.024
#> GSM97816 1 0.1306 0.6634 0.960 0.016 0.008 0.000 0.016
#> GSM97817 2 0.0609 0.8946 0.000 0.980 0.000 0.000 0.020
#> GSM97820 2 0.0566 0.8951 0.004 0.984 0.000 0.000 0.012
#> GSM97825 2 0.0794 0.8927 0.000 0.972 0.000 0.000 0.028
#> GSM97827 2 0.0703 0.8939 0.000 0.976 0.000 0.000 0.024
#> GSM97828 1 0.1059 0.6671 0.968 0.004 0.008 0.000 0.020
#> GSM97833 2 0.0404 0.8957 0.000 0.988 0.000 0.000 0.012
#> GSM97834 2 0.0609 0.8946 0.000 0.980 0.000 0.000 0.020
#> GSM97840 2 0.2338 0.8509 0.004 0.884 0.000 0.000 0.112
#> GSM97846 2 0.0880 0.8909 0.000 0.968 0.000 0.000 0.032
#> GSM97848 2 0.0771 0.8941 0.004 0.976 0.000 0.000 0.020
#> GSM97849 2 0.0510 0.8951 0.000 0.984 0.000 0.000 0.016
#> GSM97850 2 0.0566 0.8960 0.004 0.984 0.000 0.000 0.012
#> GSM97853 2 0.0771 0.8941 0.004 0.976 0.000 0.000 0.020
#> GSM97855 2 0.0955 0.8947 0.004 0.968 0.000 0.000 0.028
#> GSM97878 5 0.5828 0.5367 0.072 0.044 0.004 0.204 0.676
#> GSM97913 5 0.4906 0.3358 0.028 0.324 0.000 0.008 0.640
#> GSM97932 4 0.3789 0.6991 0.016 0.000 0.000 0.760 0.224
#> GSM97939 2 0.6411 0.0988 0.004 0.440 0.408 0.000 0.148
#> GSM97951 2 0.2377 0.8391 0.000 0.872 0.000 0.000 0.128
#> GSM97957 1 0.3760 0.6241 0.784 0.000 0.188 0.000 0.028
#> GSM97972 1 0.4831 0.4762 0.740 0.176 0.016 0.000 0.068
#> GSM97793 3 0.3485 0.7735 0.124 0.000 0.828 0.000 0.048
#> GSM97795 2 0.1608 0.8813 0.000 0.928 0.000 0.000 0.072
#> GSM97802 3 0.4751 0.6381 0.000 0.000 0.732 0.152 0.116
#> GSM97810 2 0.3039 0.7864 0.000 0.808 0.000 0.000 0.192
#> GSM97815 2 0.4138 0.7607 0.000 0.776 0.064 0.000 0.160
#> GSM97837 1 0.2629 0.6301 0.860 0.000 0.000 0.004 0.136
#> GSM97843 3 0.1012 0.8629 0.012 0.000 0.968 0.000 0.020
#> GSM97890 3 0.1121 0.8589 0.000 0.000 0.956 0.000 0.044
#> GSM97899 4 0.0162 0.8404 0.000 0.000 0.000 0.996 0.004
#> GSM97910 1 0.2020 0.6504 0.900 0.000 0.000 0.000 0.100
#> GSM97916 4 0.5501 0.2823 0.064 0.000 0.004 0.572 0.360
#> GSM97920 1 0.2795 0.6641 0.872 0.000 0.100 0.000 0.028
#> GSM97921 4 0.6824 -0.3911 0.324 0.000 0.000 0.344 0.332
#> GSM97927 4 0.2574 0.7882 0.000 0.000 0.012 0.876 0.112
#> GSM97937 4 0.6319 0.1854 0.204 0.000 0.000 0.524 0.272
#> GSM97941 2 0.2329 0.8417 0.000 0.876 0.000 0.000 0.124
#> GSM97943 1 0.1018 0.6721 0.968 0.000 0.016 0.000 0.016
#> GSM97958 2 0.3934 0.6732 0.008 0.716 0.000 0.000 0.276
#> GSM97960 2 0.1410 0.8826 0.000 0.940 0.000 0.000 0.060
#> GSM97794 5 0.5896 0.5211 0.032 0.068 0.000 0.284 0.616
#> GSM97796 4 0.2074 0.8171 0.000 0.000 0.000 0.896 0.104
#> GSM97797 5 0.6022 0.0421 0.396 0.020 0.000 0.068 0.516
#> GSM97798 4 0.0963 0.8353 0.000 0.000 0.000 0.964 0.036
#> GSM97801 1 0.2377 0.6331 0.872 0.000 0.000 0.000 0.128
#> GSM97806 4 0.2536 0.8097 0.000 0.000 0.004 0.868 0.128
#> GSM97808 4 0.1121 0.8326 0.000 0.000 0.000 0.956 0.044
#> GSM97813 4 0.2077 0.8063 0.000 0.000 0.008 0.908 0.084
#> GSM97814 4 0.0404 0.8405 0.000 0.000 0.000 0.988 0.012
#> GSM97818 1 0.6526 -0.1075 0.528 0.008 0.000 0.260 0.204
#> GSM97819 3 0.0671 0.8646 0.004 0.000 0.980 0.000 0.016
#> GSM97821 2 0.3366 0.7459 0.000 0.768 0.000 0.000 0.232
#> GSM97826 1 0.3090 0.5807 0.860 0.000 0.000 0.088 0.052
#> GSM97829 1 0.4657 0.4141 0.668 0.000 0.000 0.036 0.296
#> GSM97832 2 0.6241 0.0907 0.412 0.468 0.008 0.000 0.112
#> GSM97836 3 0.3906 0.7152 0.000 0.000 0.800 0.132 0.068
#> GSM97839 4 0.1965 0.8214 0.000 0.000 0.000 0.904 0.096
#> GSM97844 2 0.0880 0.8905 0.000 0.968 0.000 0.000 0.032
#> GSM97847 4 0.4193 0.6541 0.024 0.000 0.000 0.720 0.256
#> GSM97851 4 0.2690 0.7823 0.000 0.000 0.000 0.844 0.156
#> GSM97852 4 0.3519 0.7233 0.008 0.000 0.000 0.776 0.216
#> GSM97856 4 0.0162 0.8405 0.000 0.000 0.000 0.996 0.004
#> GSM97858 2 0.1608 0.8738 0.000 0.928 0.000 0.000 0.072
#> GSM97859 4 0.4535 0.6111 0.000 0.000 0.140 0.752 0.108
#> GSM97861 4 0.0880 0.8400 0.000 0.000 0.000 0.968 0.032
#> GSM97863 4 0.1732 0.8280 0.000 0.000 0.000 0.920 0.080
#> GSM97869 4 0.4594 0.5385 0.004 0.012 0.012 0.692 0.280
#> GSM97870 3 0.5880 0.5873 0.056 0.000 0.684 0.156 0.104
#> GSM97871 4 0.0510 0.8408 0.000 0.000 0.000 0.984 0.016
#> GSM97877 2 0.3210 0.7674 0.000 0.788 0.000 0.000 0.212
#> GSM97879 4 0.1638 0.8373 0.004 0.000 0.000 0.932 0.064
#> GSM97882 4 0.1952 0.8177 0.000 0.000 0.004 0.912 0.084
#> GSM97885 4 0.2411 0.8113 0.008 0.000 0.000 0.884 0.108
#> GSM97886 4 0.1478 0.8400 0.000 0.000 0.000 0.936 0.064
#> GSM97887 4 0.1197 0.8317 0.000 0.000 0.000 0.952 0.048
#> GSM97888 4 0.1121 0.8316 0.000 0.000 0.000 0.956 0.044
#> GSM97889 4 0.3159 0.7592 0.000 0.000 0.056 0.856 0.088
#> GSM97891 4 0.1124 0.8411 0.000 0.000 0.004 0.960 0.036
#> GSM97892 2 0.0510 0.8944 0.000 0.984 0.000 0.000 0.016
#> GSM97893 4 0.2124 0.8288 0.004 0.000 0.000 0.900 0.096
#> GSM97894 4 0.0290 0.8408 0.000 0.000 0.000 0.992 0.008
#> GSM97895 4 0.4655 0.6250 0.052 0.000 0.000 0.700 0.248
#> GSM97896 4 0.1270 0.8284 0.000 0.000 0.000 0.948 0.052
#> GSM97898 4 0.1410 0.8341 0.000 0.000 0.000 0.940 0.060
#> GSM97903 4 0.2270 0.8293 0.020 0.000 0.000 0.904 0.076
#> GSM97905 3 0.5508 0.3244 0.024 0.000 0.608 0.328 0.040
#> GSM97906 4 0.0404 0.8395 0.000 0.000 0.000 0.988 0.012
#> GSM97908 4 0.4040 0.6447 0.012 0.000 0.000 0.712 0.276
#> GSM97912 4 0.1792 0.8110 0.000 0.000 0.000 0.916 0.084
#> GSM97914 4 0.4902 0.5361 0.048 0.000 0.000 0.648 0.304
#> GSM97915 4 0.1851 0.8252 0.000 0.000 0.000 0.912 0.088
#> GSM97917 4 0.3388 0.7351 0.008 0.000 0.000 0.792 0.200
#> GSM97918 4 0.2280 0.8088 0.000 0.000 0.000 0.880 0.120
#> GSM97919 4 0.2561 0.7916 0.000 0.000 0.000 0.856 0.144
#> GSM97922 4 0.1410 0.8240 0.000 0.000 0.000 0.940 0.060
#> GSM97924 2 0.0451 0.8962 0.004 0.988 0.000 0.000 0.008
#> GSM97926 3 0.1270 0.8561 0.000 0.000 0.948 0.000 0.052
#> GSM97930 4 0.4329 0.6484 0.032 0.000 0.000 0.716 0.252
#> GSM97931 2 0.3266 0.7788 0.000 0.796 0.004 0.000 0.200
#> GSM97935 4 0.1410 0.8285 0.000 0.000 0.000 0.940 0.060
#> GSM97936 4 0.1792 0.8283 0.000 0.000 0.000 0.916 0.084
#> GSM97938 4 0.5062 0.5503 0.068 0.000 0.000 0.656 0.276
#> GSM97940 4 0.0703 0.8375 0.000 0.000 0.000 0.976 0.024
#> GSM97942 3 0.0955 0.8640 0.004 0.000 0.968 0.000 0.028
#> GSM97945 4 0.0609 0.8412 0.000 0.000 0.000 0.980 0.020
#> GSM97946 2 0.0566 0.8962 0.004 0.984 0.000 0.000 0.012
#> GSM97948 3 0.3339 0.7901 0.000 0.000 0.836 0.040 0.124
#> GSM97950 4 0.2966 0.7692 0.000 0.000 0.000 0.816 0.184
#> GSM97952 4 0.0000 0.8403 0.000 0.000 0.000 1.000 0.000
#> GSM97953 1 0.6693 0.1245 0.524 0.000 0.020 0.172 0.284
#> GSM97954 4 0.2873 0.8035 0.020 0.000 0.000 0.860 0.120
#> GSM97955 4 0.1478 0.8348 0.000 0.000 0.000 0.936 0.064
#> GSM97959 2 0.6875 -0.1975 0.008 0.448 0.000 0.268 0.276
#> GSM97961 4 0.1197 0.8406 0.000 0.000 0.000 0.952 0.048
#> GSM97963 4 0.0290 0.8399 0.000 0.000 0.000 0.992 0.008
#> GSM97965 4 0.0290 0.8400 0.000 0.000 0.000 0.992 0.008
#> GSM97966 4 0.1121 0.8326 0.000 0.000 0.000 0.956 0.044
#> GSM97967 2 0.0963 0.8891 0.000 0.964 0.000 0.000 0.036
#> GSM97968 2 0.1041 0.8941 0.004 0.964 0.000 0.000 0.032
#> GSM97969 4 0.1997 0.8261 0.040 0.000 0.000 0.924 0.036
#> GSM97971 4 0.1357 0.8300 0.004 0.000 0.000 0.948 0.048
#> GSM97799 3 0.0963 0.8601 0.000 0.000 0.964 0.000 0.036
#> GSM97823 2 0.0771 0.8941 0.004 0.976 0.000 0.000 0.020
#> GSM97824 3 0.2969 0.7854 0.128 0.000 0.852 0.000 0.020
#> GSM97830 1 0.4624 0.4271 0.636 0.000 0.340 0.000 0.024
#> GSM97835 2 0.5635 0.4643 0.000 0.620 0.252 0.000 0.128
#> GSM97838 2 0.1341 0.8813 0.000 0.944 0.000 0.000 0.056
#> GSM97841 2 0.0703 0.8926 0.000 0.976 0.000 0.000 0.024
#> GSM97842 3 0.2653 0.8263 0.000 0.024 0.880 0.000 0.096
#> GSM97854 2 0.0510 0.8961 0.000 0.984 0.000 0.000 0.016
#> GSM97857 1 0.4806 0.5730 0.688 0.000 0.252 0.000 0.060
#> GSM97860 3 0.1750 0.8526 0.028 0.000 0.936 0.000 0.036
#> GSM97862 3 0.0807 0.8643 0.012 0.000 0.976 0.000 0.012
#> GSM97864 2 0.0703 0.8933 0.000 0.976 0.000 0.000 0.024
#> GSM97866 3 0.0693 0.8636 0.012 0.000 0.980 0.000 0.008
#> GSM97868 3 0.1018 0.8613 0.016 0.000 0.968 0.000 0.016
#> GSM97872 1 0.5136 0.6064 0.692 0.000 0.128 0.000 0.180
#> GSM97873 3 0.3051 0.7834 0.000 0.076 0.864 0.000 0.060
#> GSM97874 3 0.4787 0.1865 0.432 0.000 0.548 0.000 0.020
#> GSM97875 3 0.0880 0.8622 0.000 0.000 0.968 0.000 0.032
#> GSM97876 3 0.1399 0.8602 0.020 0.000 0.952 0.000 0.028
#> GSM97880 3 0.4754 0.5670 0.264 0.000 0.684 0.000 0.052
#> GSM97881 3 0.0794 0.8619 0.000 0.000 0.972 0.000 0.028
#> GSM97884 3 0.1124 0.8633 0.004 0.000 0.960 0.000 0.036
#> GSM97901 3 0.1012 0.8599 0.020 0.000 0.968 0.000 0.012
#> GSM97902 1 0.5410 0.4276 0.620 0.024 0.012 0.016 0.328
#> GSM97909 2 0.3074 0.7827 0.000 0.804 0.000 0.000 0.196
#> GSM97911 3 0.0404 0.8639 0.000 0.000 0.988 0.000 0.012
#> GSM97923 3 0.0912 0.8612 0.012 0.000 0.972 0.000 0.016
#> GSM97928 4 0.4686 0.6833 0.000 0.000 0.104 0.736 0.160
#> GSM97929 2 0.0794 0.8958 0.000 0.972 0.000 0.000 0.028
#> GSM97933 3 0.3506 0.7737 0.132 0.000 0.824 0.000 0.044
#> GSM97934 1 0.4797 0.5300 0.660 0.000 0.296 0.000 0.044
#> GSM97944 3 0.0609 0.8626 0.000 0.000 0.980 0.000 0.020
#> GSM97949 2 0.0703 0.8967 0.000 0.976 0.000 0.000 0.024
#> GSM97956 3 0.1012 0.8615 0.012 0.000 0.968 0.000 0.020
#> GSM97962 3 0.5111 0.0231 0.464 0.000 0.500 0.000 0.036
#> GSM97964 3 0.0898 0.8640 0.008 0.000 0.972 0.000 0.020
#> GSM97970 3 0.1197 0.8579 0.000 0.000 0.952 0.000 0.048
#> GSM97822 4 0.5264 0.4803 0.000 0.000 0.196 0.676 0.128
#> GSM97831 3 0.4675 0.3738 0.380 0.000 0.600 0.000 0.020
#> GSM97845 4 0.1831 0.8315 0.004 0.000 0.000 0.920 0.076
#> GSM97865 4 0.3759 0.7755 0.092 0.000 0.000 0.816 0.092
#> GSM97867 3 0.2504 0.8269 0.064 0.000 0.896 0.000 0.040
#> GSM97883 3 0.2293 0.8447 0.016 0.000 0.900 0.000 0.084
#> GSM97897 4 0.1956 0.8122 0.000 0.000 0.008 0.916 0.076
#> GSM97900 4 0.0609 0.8400 0.000 0.000 0.000 0.980 0.020
#> GSM97904 4 0.5028 0.1835 0.008 0.000 0.420 0.552 0.020
#> GSM97907 2 0.2020 0.8585 0.000 0.900 0.000 0.000 0.100
#> GSM97925 3 0.1965 0.8397 0.000 0.000 0.904 0.000 0.096
#> GSM97947 3 0.1410 0.8543 0.000 0.000 0.940 0.000 0.060
cbind(get_classes(res, k = 6), get_membership(res, k = 6))
#> class entropy silhouette p1 p2 p3 p4 p5 p6
#> GSM97800 2 0.0508 0.9106 0.004 0.984 0.000 0.000 0.012 0.000
#> GSM97803 2 0.0405 0.9114 0.004 0.988 0.000 0.000 0.008 0.000
#> GSM97804 2 0.0717 0.9102 0.016 0.976 0.000 0.000 0.008 0.000
#> GSM97805 2 0.0622 0.9113 0.008 0.980 0.000 0.000 0.012 0.000
#> GSM97807 2 0.0725 0.9101 0.012 0.976 0.000 0.000 0.012 0.000
#> GSM97809 2 0.0993 0.9077 0.012 0.964 0.000 0.000 0.024 0.000
#> GSM97811 2 0.0146 0.9106 0.004 0.996 0.000 0.000 0.000 0.000
#> GSM97812 2 0.0146 0.9106 0.004 0.996 0.000 0.000 0.000 0.000
#> GSM97816 6 0.0692 0.6600 0.000 0.004 0.000 0.000 0.020 0.976
#> GSM97817 2 0.0146 0.9106 0.004 0.996 0.000 0.000 0.000 0.000
#> GSM97820 2 0.0717 0.9093 0.008 0.976 0.000 0.000 0.016 0.000
#> GSM97825 2 0.0146 0.9106 0.004 0.996 0.000 0.000 0.000 0.000
#> GSM97827 2 0.0146 0.9106 0.004 0.996 0.000 0.000 0.000 0.000
#> GSM97828 6 0.0405 0.6607 0.000 0.004 0.000 0.000 0.008 0.988
#> GSM97833 2 0.0146 0.9106 0.004 0.996 0.000 0.000 0.000 0.000
#> GSM97834 2 0.0146 0.9106 0.004 0.996 0.000 0.000 0.000 0.000
#> GSM97840 2 0.1995 0.8883 0.052 0.912 0.000 0.000 0.036 0.000
#> GSM97846 2 0.0405 0.9095 0.008 0.988 0.000 0.000 0.004 0.000
#> GSM97848 2 0.0622 0.9078 0.008 0.980 0.000 0.000 0.012 0.000
#> GSM97849 2 0.0291 0.9098 0.004 0.992 0.000 0.000 0.004 0.000
#> GSM97850 2 0.0692 0.9098 0.004 0.976 0.000 0.000 0.020 0.000
#> GSM97853 2 0.0508 0.9087 0.012 0.984 0.000 0.000 0.004 0.000
#> GSM97855 2 0.1232 0.9061 0.016 0.956 0.000 0.000 0.024 0.004
#> GSM97878 1 0.3924 0.0153 0.816 0.004 0.016 0.088 0.060 0.016
#> GSM97913 1 0.3232 0.1222 0.844 0.108 0.000 0.012 0.024 0.012
#> GSM97932 4 0.4076 0.1489 0.428 0.000 0.000 0.564 0.004 0.004
#> GSM97939 2 0.5921 0.0910 0.180 0.432 0.384 0.000 0.004 0.000
#> GSM97951 2 0.2277 0.8751 0.076 0.892 0.000 0.000 0.032 0.000
#> GSM97957 6 0.5862 0.3110 0.008 0.000 0.236 0.000 0.224 0.532
#> GSM97972 6 0.7894 0.1880 0.044 0.256 0.080 0.000 0.308 0.312
#> GSM97793 3 0.4659 0.5985 0.004 0.000 0.612 0.000 0.336 0.048
#> GSM97795 2 0.1528 0.8952 0.048 0.936 0.000 0.000 0.016 0.000
#> GSM97802 3 0.5757 0.3452 0.004 0.004 0.556 0.192 0.244 0.000
#> GSM97810 2 0.4276 0.7639 0.176 0.752 0.020 0.000 0.048 0.004
#> GSM97815 2 0.5003 0.6633 0.120 0.704 0.140 0.000 0.036 0.000
#> GSM97837 6 0.3018 0.5528 0.168 0.000 0.000 0.012 0.004 0.816
#> GSM97843 3 0.3058 0.7644 0.024 0.000 0.840 0.000 0.124 0.012
#> GSM97890 3 0.2001 0.7757 0.040 0.000 0.912 0.000 0.048 0.000
#> GSM97899 4 0.0972 0.6946 0.008 0.000 0.000 0.964 0.028 0.000
#> GSM97910 6 0.2772 0.6340 0.040 0.000 0.000 0.004 0.092 0.864
#> GSM97916 4 0.7923 -0.2489 0.236 0.000 0.036 0.380 0.228 0.120
#> GSM97920 6 0.1261 0.6564 0.000 0.000 0.024 0.000 0.024 0.952
#> GSM97921 1 0.5984 -0.2661 0.532 0.000 0.000 0.328 0.080 0.060
#> GSM97927 4 0.3912 0.5392 0.004 0.000 0.044 0.748 0.204 0.000
#> GSM97937 4 0.5067 -0.1362 0.456 0.000 0.000 0.488 0.032 0.024
#> GSM97941 2 0.2066 0.8810 0.072 0.904 0.000 0.000 0.024 0.000
#> GSM97943 6 0.0405 0.6610 0.000 0.004 0.000 0.000 0.008 0.988
#> GSM97958 2 0.5698 0.5249 0.304 0.568 0.004 0.012 0.108 0.004
#> GSM97960 2 0.1049 0.9068 0.032 0.960 0.000 0.000 0.008 0.000
#> GSM97794 1 0.6377 0.0934 0.584 0.056 0.000 0.144 0.200 0.016
#> GSM97796 4 0.2883 0.5869 0.212 0.000 0.000 0.788 0.000 0.000
#> GSM97797 1 0.5874 0.0688 0.584 0.012 0.000 0.036 0.084 0.284
#> GSM97798 4 0.1267 0.6853 0.000 0.000 0.000 0.940 0.060 0.000
#> GSM97801 6 0.1584 0.6447 0.064 0.000 0.000 0.000 0.008 0.928
#> GSM97806 4 0.4000 0.6079 0.164 0.000 0.008 0.764 0.064 0.000
#> GSM97808 4 0.1444 0.6814 0.000 0.000 0.000 0.928 0.072 0.000
#> GSM97813 4 0.4924 0.4281 0.008 0.000 0.112 0.668 0.212 0.000
#> GSM97814 4 0.0717 0.6956 0.008 0.000 0.000 0.976 0.016 0.000
#> GSM97818 6 0.6192 -0.0805 0.160 0.000 0.000 0.240 0.048 0.552
#> GSM97819 3 0.1196 0.7900 0.008 0.000 0.952 0.000 0.040 0.000
#> GSM97821 2 0.4881 0.6476 0.232 0.648 0.000 0.000 0.120 0.000
#> GSM97826 6 0.2493 0.5815 0.036 0.000 0.000 0.076 0.004 0.884
#> GSM97829 6 0.5643 -0.1407 0.404 0.000 0.000 0.076 0.028 0.492
#> GSM97832 6 0.5067 0.3171 0.044 0.328 0.004 0.000 0.020 0.604
#> GSM97836 3 0.5127 0.5566 0.060 0.000 0.700 0.152 0.088 0.000
#> GSM97839 4 0.2300 0.6483 0.144 0.000 0.000 0.856 0.000 0.000
#> GSM97844 2 0.0891 0.9074 0.024 0.968 0.000 0.000 0.008 0.000
#> GSM97847 4 0.3982 0.0646 0.460 0.000 0.000 0.536 0.004 0.000
#> GSM97851 4 0.3482 0.4262 0.316 0.000 0.000 0.684 0.000 0.000
#> GSM97852 4 0.3782 0.2206 0.412 0.000 0.000 0.588 0.000 0.000
#> GSM97856 4 0.1418 0.6952 0.032 0.000 0.000 0.944 0.024 0.000
#> GSM97858 2 0.1492 0.8992 0.036 0.940 0.000 0.000 0.024 0.000
#> GSM97859 4 0.5785 0.2644 0.008 0.000 0.196 0.568 0.224 0.004
#> GSM97861 4 0.1152 0.6931 0.004 0.000 0.000 0.952 0.044 0.000
#> GSM97863 4 0.2219 0.6537 0.136 0.000 0.000 0.864 0.000 0.000
#> GSM97869 4 0.5535 0.4128 0.128 0.004 0.012 0.624 0.228 0.004
#> GSM97870 4 0.7644 -0.1428 0.008 0.000 0.312 0.324 0.224 0.132
#> GSM97871 4 0.1267 0.6872 0.060 0.000 0.000 0.940 0.000 0.000
#> GSM97877 2 0.3776 0.7728 0.188 0.760 0.000 0.000 0.052 0.000
#> GSM97879 4 0.2350 0.6734 0.100 0.000 0.000 0.880 0.020 0.000
#> GSM97882 4 0.2588 0.6550 0.012 0.000 0.004 0.860 0.124 0.000
#> GSM97885 4 0.3190 0.6611 0.056 0.000 0.000 0.844 0.088 0.012
#> GSM97886 4 0.3595 0.6160 0.084 0.000 0.000 0.796 0.120 0.000
#> GSM97887 4 0.2400 0.6621 0.004 0.000 0.008 0.872 0.116 0.000
#> GSM97888 4 0.2288 0.6617 0.004 0.000 0.004 0.876 0.116 0.000
#> GSM97889 4 0.4924 0.4232 0.008 0.000 0.112 0.668 0.212 0.000
#> GSM97891 4 0.2340 0.6809 0.044 0.000 0.004 0.896 0.056 0.000
#> GSM97892 2 0.0725 0.9102 0.012 0.976 0.000 0.000 0.012 0.000
#> GSM97893 4 0.2680 0.6597 0.108 0.000 0.000 0.860 0.032 0.000
#> GSM97894 4 0.1657 0.6902 0.056 0.000 0.000 0.928 0.016 0.000
#> GSM97895 4 0.4741 0.0467 0.420 0.000 0.000 0.536 0.040 0.004
#> GSM97896 4 0.2513 0.6458 0.008 0.000 0.000 0.852 0.140 0.000
#> GSM97898 4 0.2191 0.6618 0.120 0.000 0.000 0.876 0.004 0.000
#> GSM97903 4 0.2685 0.6837 0.080 0.000 0.000 0.872 0.044 0.004
#> GSM97905 3 0.5667 0.1230 0.016 0.000 0.564 0.324 0.084 0.012
#> GSM97906 4 0.0458 0.6940 0.000 0.000 0.000 0.984 0.016 0.000
#> GSM97908 4 0.3991 0.0261 0.472 0.000 0.000 0.524 0.004 0.000
#> GSM97912 4 0.3667 0.5713 0.008 0.000 0.032 0.776 0.184 0.000
#> GSM97914 1 0.4403 -0.1277 0.508 0.000 0.000 0.468 0.024 0.000
#> GSM97915 4 0.2491 0.6355 0.164 0.000 0.000 0.836 0.000 0.000
#> GSM97917 4 0.3934 0.2752 0.376 0.000 0.000 0.616 0.008 0.000
#> GSM97918 4 0.2933 0.5926 0.200 0.000 0.000 0.796 0.004 0.000
#> GSM97919 4 0.3482 0.4283 0.316 0.000 0.000 0.684 0.000 0.000
#> GSM97922 4 0.2595 0.6297 0.004 0.000 0.000 0.836 0.160 0.000
#> GSM97924 2 0.0820 0.9098 0.012 0.972 0.000 0.000 0.016 0.000
#> GSM97926 3 0.2190 0.7695 0.060 0.000 0.900 0.000 0.040 0.000
#> GSM97930 4 0.3966 0.1146 0.444 0.000 0.000 0.552 0.004 0.000
#> GSM97931 2 0.3821 0.7474 0.220 0.740 0.000 0.000 0.040 0.000
#> GSM97935 4 0.2243 0.6595 0.004 0.000 0.004 0.880 0.112 0.000
#> GSM97936 4 0.2260 0.6518 0.140 0.000 0.000 0.860 0.000 0.000
#> GSM97938 1 0.5741 -0.2294 0.448 0.000 0.004 0.440 0.092 0.016
#> GSM97940 4 0.0547 0.6933 0.000 0.000 0.000 0.980 0.020 0.000
#> GSM97942 3 0.1807 0.7885 0.020 0.000 0.920 0.000 0.060 0.000
#> GSM97945 4 0.1141 0.6888 0.052 0.000 0.000 0.948 0.000 0.000
#> GSM97946 2 0.0508 0.9104 0.004 0.984 0.000 0.000 0.012 0.000
#> GSM97948 3 0.5212 0.4957 0.028 0.000 0.608 0.048 0.312 0.004
#> GSM97950 4 0.4011 0.4020 0.304 0.000 0.000 0.672 0.024 0.000
#> GSM97952 4 0.0508 0.6949 0.004 0.000 0.000 0.984 0.012 0.000
#> GSM97953 5 0.7789 0.0000 0.312 0.000 0.032 0.240 0.328 0.088
#> GSM97954 4 0.2572 0.6558 0.136 0.000 0.000 0.852 0.012 0.000
#> GSM97955 4 0.2178 0.6561 0.132 0.000 0.000 0.868 0.000 0.000
#> GSM97959 2 0.7456 -0.1917 0.312 0.340 0.000 0.196 0.152 0.000
#> GSM97961 4 0.1563 0.6859 0.056 0.000 0.000 0.932 0.012 0.000
#> GSM97963 4 0.0146 0.6948 0.000 0.000 0.000 0.996 0.004 0.000
#> GSM97965 4 0.0713 0.6930 0.028 0.000 0.000 0.972 0.000 0.000
#> GSM97966 4 0.1644 0.6789 0.004 0.000 0.000 0.920 0.076 0.000
#> GSM97967 2 0.0405 0.9095 0.004 0.988 0.000 0.000 0.008 0.000
#> GSM97968 2 0.0717 0.9107 0.008 0.976 0.000 0.000 0.016 0.000
#> GSM97969 4 0.3067 0.6468 0.020 0.000 0.000 0.844 0.116 0.020
#> GSM97971 4 0.2944 0.6373 0.012 0.000 0.000 0.832 0.148 0.008
#> GSM97799 3 0.0993 0.7832 0.012 0.000 0.964 0.000 0.024 0.000
#> GSM97823 2 0.1151 0.9030 0.012 0.956 0.000 0.000 0.032 0.000
#> GSM97824 3 0.3964 0.7178 0.012 0.000 0.764 0.000 0.176 0.048
#> GSM97830 6 0.5354 0.4126 0.004 0.000 0.176 0.000 0.212 0.608
#> GSM97835 2 0.5357 0.4757 0.128 0.600 0.264 0.000 0.008 0.000
#> GSM97838 2 0.1168 0.9044 0.028 0.956 0.000 0.000 0.016 0.000
#> GSM97841 2 0.0622 0.9103 0.012 0.980 0.000 0.000 0.008 0.000
#> GSM97842 3 0.3382 0.7530 0.124 0.008 0.820 0.000 0.048 0.000
#> GSM97854 2 0.0725 0.9102 0.012 0.976 0.000 0.000 0.012 0.000
#> GSM97857 3 0.6578 0.2689 0.032 0.000 0.428 0.000 0.292 0.248
#> GSM97860 3 0.4078 0.7114 0.024 0.000 0.740 0.000 0.212 0.024
#> GSM97862 3 0.1777 0.7886 0.024 0.000 0.928 0.000 0.044 0.004
#> GSM97864 2 0.0291 0.9112 0.004 0.992 0.000 0.000 0.004 0.000
#> GSM97866 3 0.1194 0.7897 0.004 0.000 0.956 0.000 0.032 0.008
#> GSM97868 3 0.2996 0.7647 0.016 0.000 0.832 0.000 0.144 0.008
#> GSM97872 1 0.8102 -0.2856 0.320 0.000 0.180 0.028 0.208 0.264
#> GSM97873 3 0.3341 0.7340 0.088 0.060 0.836 0.000 0.016 0.000
#> GSM97874 3 0.5574 0.2435 0.008 0.000 0.472 0.000 0.108 0.412
#> GSM97875 3 0.1411 0.7756 0.004 0.000 0.936 0.000 0.060 0.000
#> GSM97876 3 0.1806 0.7878 0.000 0.000 0.908 0.000 0.088 0.004
#> GSM97880 3 0.5052 0.5718 0.004 0.000 0.592 0.000 0.320 0.084
#> GSM97881 3 0.0891 0.7832 0.008 0.000 0.968 0.000 0.024 0.000
#> GSM97884 3 0.1700 0.7809 0.004 0.000 0.916 0.000 0.080 0.000
#> GSM97901 3 0.1542 0.7865 0.004 0.000 0.936 0.000 0.052 0.008
#> GSM97902 1 0.7538 -0.2418 0.376 0.008 0.020 0.056 0.296 0.244
#> GSM97909 2 0.3595 0.8072 0.144 0.796 0.000 0.004 0.056 0.000
#> GSM97911 3 0.0777 0.7850 0.004 0.000 0.972 0.000 0.024 0.000
#> GSM97923 3 0.1615 0.7874 0.004 0.000 0.928 0.000 0.064 0.004
#> GSM97928 4 0.6159 0.0135 0.312 0.000 0.120 0.520 0.048 0.000
#> GSM97929 2 0.0260 0.9106 0.008 0.992 0.000 0.000 0.000 0.000
#> GSM97933 3 0.4684 0.6372 0.008 0.000 0.656 0.000 0.276 0.060
#> GSM97934 3 0.6225 0.2498 0.008 0.000 0.428 0.000 0.292 0.272
#> GSM97944 3 0.0909 0.7839 0.012 0.000 0.968 0.000 0.020 0.000
#> GSM97949 2 0.0000 0.9107 0.000 1.000 0.000 0.000 0.000 0.000
#> GSM97956 3 0.1882 0.7864 0.012 0.000 0.920 0.000 0.060 0.008
#> GSM97962 3 0.5840 0.4369 0.008 0.000 0.508 0.000 0.316 0.168
#> GSM97964 3 0.1411 0.7877 0.004 0.000 0.936 0.000 0.060 0.000
#> GSM97970 3 0.1549 0.7811 0.020 0.000 0.936 0.000 0.044 0.000
#> GSM97822 4 0.5951 0.1944 0.012 0.000 0.232 0.528 0.228 0.000
#> GSM97831 3 0.5016 0.2639 0.004 0.000 0.504 0.000 0.060 0.432
#> GSM97845 4 0.2340 0.6504 0.148 0.000 0.000 0.852 0.000 0.000
#> GSM97865 4 0.4845 0.5007 0.148 0.000 0.000 0.724 0.060 0.068
#> GSM97867 3 0.4067 0.6725 0.000 0.000 0.700 0.000 0.260 0.040
#> GSM97883 3 0.2989 0.7169 0.008 0.000 0.812 0.004 0.176 0.000
#> GSM97897 4 0.3245 0.5917 0.004 0.000 0.016 0.796 0.184 0.000
#> GSM97900 4 0.1349 0.6913 0.004 0.000 0.000 0.940 0.056 0.000
#> GSM97904 4 0.6311 -0.3013 0.016 0.000 0.284 0.448 0.252 0.000
#> GSM97907 2 0.1700 0.8938 0.048 0.928 0.000 0.000 0.024 0.000
#> GSM97925 3 0.3611 0.7321 0.096 0.000 0.796 0.000 0.108 0.000
#> GSM97947 3 0.2706 0.7127 0.008 0.000 0.832 0.000 0.160 0.000
Heatmaps for the consensus matrix. It visualizes the probability of two samples to be in a same group.
consensus_heatmap(res, k = 2)
consensus_heatmap(res, k = 3)
consensus_heatmap(res, k = 4)
consensus_heatmap(res, k = 5)
consensus_heatmap(res, k = 6)
Heatmaps for the membership of samples in all partitions to see how consistent they are:
membership_heatmap(res, k = 2)
membership_heatmap(res, k = 3)
membership_heatmap(res, k = 4)
membership_heatmap(res, k = 5)
membership_heatmap(res, k = 6)
As soon as we have had the classes for columns, we can look for signatures which are significantly different between classes which can be candidate marks for certain classes. Following are the heatmaps for signatures.
Signature heatmaps where rows are scaled:
get_signatures(res, k = 2)
get_signatures(res, k = 3)
get_signatures(res, k = 4)
get_signatures(res, k = 5)
get_signatures(res, k = 6)
Signature heatmaps where rows are not scaled:
get_signatures(res, k = 2, scale_rows = FALSE)
get_signatures(res, k = 3, scale_rows = FALSE)
get_signatures(res, k = 4, scale_rows = FALSE)
get_signatures(res, k = 5, scale_rows = FALSE)
get_signatures(res, k = 6, scale_rows = FALSE)
Compare the overlap of signatures from different k:
compare_signatures(res)
get_signature() returns a data frame invisibly. TO get the list of signatures, the function
call should be assigned to a variable explicitly. In following code, if plot argument is set
to FALSE, no heatmap is plotted while only the differential analysis is performed.
# code only for demonstration
tb = get_signature(res, k = ..., plot = FALSE)
An example of the output of tb is:
#> which_row fdr mean_1 mean_2 scaled_mean_1 scaled_mean_2 km
#> 1 38 0.042760348 8.373488 9.131774 -0.5533452 0.5164555 1
#> 2 40 0.018707592 7.106213 8.469186 -0.6173731 0.5762149 1
#> 3 55 0.019134737 10.221463 11.207825 -0.6159697 0.5749050 1
#> 4 59 0.006059896 5.921854 7.869574 -0.6899429 0.6439467 1
#> 5 60 0.018055526 8.928898 10.211722 -0.6204761 0.5791110 1
#> 6 98 0.009384629 15.714769 14.887706 0.6635654 -0.6193277 2
...
The columns in tb are:
which_row: row indices corresponding to the input matrix.fdr: FDR for the differential test. mean_x: The mean value in group x.scaled_mean_x: The mean value in group x after rows are scaled.km: Row groups if k-means clustering is applied to rows.UMAP plot which shows how samples are separated.
dimension_reduction(res, k = 2, method = "UMAP")
dimension_reduction(res, k = 3, method = "UMAP")
dimension_reduction(res, k = 4, method = "UMAP")
dimension_reduction(res, k = 5, method = "UMAP")
dimension_reduction(res, k = 6, method = "UMAP")
Following heatmap shows how subgroups are split when increasing k:
collect_classes(res)
Test correlation between subgroups and known annotations. If the known annotation is numeric, one-way ANOVA test is applied, and if the known annotation is discrete, chi-squared contingency table test is applied.
test_to_known_factors(res)
#> n disease.state(p) tissue(p) k
#> ATC:NMF 177 1.54e-14 4.45e-17 2
#> ATC:NMF 177 6.35e-25 3.48e-24 3
#> ATC:NMF 173 5.53e-21 1.32e-18 4
#> ATC:NMF 159 2.48e-22 6.21e-20 5
#> ATC:NMF 133 3.20e-21 4.33e-20 6
If matrix rows can be associated to genes, consider to use functional_enrichment(res,
...) to perform function enrichment for the signature genes. See this vignette for more detailed explanations.
sessionInfo()
#> R version 3.6.0 (2019-04-26)
#> Platform: x86_64-pc-linux-gnu (64-bit)
#> Running under: CentOS Linux 7 (Core)
#>
#> Matrix products: default
#> BLAS: /usr/lib64/libblas.so.3.4.2
#> LAPACK: /usr/lib64/liblapack.so.3.4.2
#>
#> locale:
#> [1] LC_CTYPE=en_GB.UTF-8 LC_NUMERIC=C LC_TIME=en_GB.UTF-8
#> [4] LC_COLLATE=en_GB.UTF-8 LC_MONETARY=en_GB.UTF-8 LC_MESSAGES=en_GB.UTF-8
#> [7] LC_PAPER=en_GB.UTF-8 LC_NAME=C LC_ADDRESS=C
#> [10] LC_TELEPHONE=C LC_MEASUREMENT=en_GB.UTF-8 LC_IDENTIFICATION=C
#>
#> attached base packages:
#> [1] grid stats graphics grDevices utils datasets methods base
#>
#> other attached packages:
#> [1] genefilter_1.66.0 ComplexHeatmap_2.3.1 markdown_1.1 knitr_1.26
#> [5] GetoptLong_0.1.7 cola_1.3.2
#>
#> loaded via a namespace (and not attached):
#> [1] circlize_0.4.8 shape_1.4.4 xfun_0.11 slam_0.1-46
#> [5] lattice_0.20-38 splines_3.6.0 colorspace_1.4-1 vctrs_0.2.0
#> [9] stats4_3.6.0 blob_1.2.0 XML_3.98-1.20 survival_2.44-1.1
#> [13] rlang_0.4.2 pillar_1.4.2 DBI_1.0.0 BiocGenerics_0.30.0
#> [17] bit64_0.9-7 RColorBrewer_1.1-2 matrixStats_0.55.0 stringr_1.4.0
#> [21] GlobalOptions_0.1.1 evaluate_0.14 memoise_1.1.0 Biobase_2.44.0
#> [25] IRanges_2.18.3 parallel_3.6.0 AnnotationDbi_1.46.1 highr_0.8
#> [29] Rcpp_1.0.3 xtable_1.8-4 backports_1.1.5 S4Vectors_0.22.1
#> [33] annotate_1.62.0 skmeans_0.2-11 bit_1.1-14 microbenchmark_1.4-7
#> [37] brew_1.0-6 impute_1.58.0 rjson_0.2.20 png_0.1-7
#> [41] digest_0.6.23 stringi_1.4.3 polyclip_1.10-0 clue_0.3-57
#> [45] tools_3.6.0 bitops_1.0-6 magrittr_1.5 eulerr_6.0.0
#> [49] RCurl_1.95-4.12 RSQLite_2.1.4 tibble_2.1.3 cluster_2.1.0
#> [53] crayon_1.3.4 pkgconfig_2.0.3 zeallot_0.1.0 Matrix_1.2-17
#> [57] xml2_1.2.2 httr_1.4.1 R6_2.4.1 mclust_5.4.5
#> [61] compiler_3.6.0