Date: 2019-12-25 20:17:16 CET, cola version: 1.3.2
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All available functions which can be applied to this res_list object:
res_list
#> A 'ConsensusPartitionList' object with 24 methods.
#> On a matrix with 12013 rows and 164 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] 12013 164
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 | ||
|---|---|---|---|---|---|
| SD:mclust | 2 | 1.000 | 0.977 | 0.990 | ** |
| MAD:mclust | 2 | 1.000 | 0.973 | 0.988 | ** |
| ATC:hclust | 2 | 1.000 | 0.983 | 0.992 | ** |
| ATC:kmeans | 2 | 1.000 | 0.999 | 1.000 | ** |
| ATC:pam | 2 | 1.000 | 0.989 | 0.995 | ** |
| ATC:mclust | 2 | 1.000 | 0.986 | 0.994 | ** |
| SD:pam | 2 | 0.999 | 0.973 | 0.988 | ** |
| CV:mclust | 2 | 0.996 | 0.949 | 0.966 | ** |
| CV:kmeans | 3 | 0.989 | 0.958 | 0.978 | ** |
| SD:kmeans | 3 | 0.958 | 0.936 | 0.956 | ** |
| ATC:NMF | 2 | 0.949 | 0.950 | 0.978 | * |
| ATC:skmeans | 2 | 0.936 | 0.914 | 0.967 | * |
| MAD:pam | 2 | 0.908 | 0.936 | 0.969 | * |
| MAD:kmeans | 3 | 0.902 | 0.913 | 0.954 | * |
| SD:skmeans | 3 | 0.836 | 0.888 | 0.945 | |
| MAD:NMF | 2 | 0.788 | 0.877 | 0.948 | |
| SD:hclust | 4 | 0.742 | 0.826 | 0.902 | |
| CV:skmeans | 3 | 0.673 | 0.821 | 0.912 | |
| MAD:skmeans | 2 | 0.647 | 0.839 | 0.928 | |
| CV:NMF | 3 | 0.631 | 0.811 | 0.898 | |
| SD:NMF | 3 | 0.594 | 0.781 | 0.881 | |
| CV:hclust | 6 | 0.512 | 0.692 | 0.864 | |
| MAD:hclust | 3 | 0.479 | 0.863 | 0.843 | |
| CV:pam | 3 | 0.307 | 0.677 | 0.798 |
**: 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 0.858 0.923 0.965 0.438 0.569 0.569
#> CV:NMF 2 0.734 0.862 0.942 0.432 0.569 0.569
#> MAD:NMF 2 0.788 0.877 0.948 0.451 0.548 0.548
#> ATC:NMF 2 0.949 0.950 0.978 0.374 0.629 0.629
#> SD:skmeans 2 0.740 0.868 0.943 0.477 0.533 0.533
#> CV:skmeans 2 0.573 0.803 0.909 0.492 0.512 0.512
#> MAD:skmeans 2 0.647 0.839 0.928 0.490 0.508 0.508
#> ATC:skmeans 2 0.936 0.914 0.967 0.455 0.556 0.556
#> SD:mclust 2 1.000 0.977 0.990 0.310 0.684 0.684
#> CV:mclust 2 0.996 0.949 0.966 0.317 0.707 0.707
#> MAD:mclust 2 1.000 0.973 0.988 0.315 0.692 0.692
#> ATC:mclust 2 1.000 0.986 0.994 0.302 0.692 0.692
#> SD:kmeans 2 0.518 0.904 0.919 0.318 0.699 0.699
#> CV:kmeans 2 0.444 0.680 0.811 0.345 0.699 0.699
#> MAD:kmeans 2 0.490 0.860 0.892 0.328 0.707 0.707
#> ATC:kmeans 2 1.000 0.999 1.000 0.294 0.707 0.707
#> SD:pam 2 0.999 0.973 0.988 0.302 0.707 0.707
#> CV:pam 2 0.885 0.937 0.969 0.295 0.732 0.732
#> MAD:pam 2 0.908 0.936 0.969 0.328 0.684 0.684
#> ATC:pam 2 1.000 0.989 0.995 0.287 0.715 0.715
#> SD:hclust 2 0.703 0.950 0.912 0.195 0.715 0.715
#> CV:hclust 2 0.694 0.908 0.953 0.091 0.976 0.976
#> MAD:hclust 2 0.639 0.824 0.911 0.143 0.988 0.988
#> ATC:hclust 2 1.000 0.983 0.992 0.308 0.699 0.699
get_stats(res_list, k = 3)
#> k 1-PAC mean_silhouette concordance area_increased Rand Jaccard
#> SD:NMF 3 0.594 0.781 0.881 0.4403 0.749 0.575
#> CV:NMF 3 0.631 0.811 0.898 0.4756 0.709 0.523
#> MAD:NMF 3 0.626 0.783 0.884 0.4216 0.720 0.525
#> ATC:NMF 3 0.585 0.759 0.878 0.6662 0.648 0.476
#> SD:skmeans 3 0.836 0.888 0.945 0.3655 0.745 0.553
#> CV:skmeans 3 0.673 0.821 0.912 0.3289 0.746 0.545
#> MAD:skmeans 3 0.683 0.831 0.916 0.3379 0.762 0.565
#> ATC:skmeans 3 0.835 0.867 0.943 0.4552 0.710 0.511
#> SD:mclust 3 0.516 0.528 0.819 0.8417 0.722 0.607
#> CV:mclust 3 0.477 0.724 0.801 0.8186 0.738 0.634
#> MAD:mclust 3 0.546 0.676 0.808 0.8429 0.696 0.569
#> ATC:mclust 3 0.424 0.536 0.731 0.8756 0.648 0.502
#> SD:kmeans 3 0.958 0.936 0.956 0.7764 0.731 0.617
#> CV:kmeans 3 0.989 0.958 0.978 0.6327 0.731 0.617
#> MAD:kmeans 3 0.902 0.913 0.954 0.7788 0.712 0.592
#> ATC:kmeans 3 0.544 0.809 0.870 0.8955 0.715 0.598
#> SD:pam 3 0.399 0.728 0.843 1.0683 0.669 0.532
#> CV:pam 3 0.307 0.677 0.798 1.0915 0.638 0.509
#> MAD:pam 3 0.342 0.722 0.817 0.9089 0.687 0.547
#> ATC:pam 3 0.689 0.885 0.923 1.0854 0.664 0.535
#> SD:hclust 3 0.543 0.886 0.923 0.7011 0.990 0.986
#> CV:hclust 3 0.504 0.796 0.888 1.1371 1.000 1.000
#> MAD:hclust 3 0.479 0.863 0.843 0.9107 0.707 0.703
#> ATC:hclust 3 1.000 0.977 0.990 0.0262 0.996 0.994
get_stats(res_list, k = 4)
#> k 1-PAC mean_silhouette concordance area_increased Rand Jaccard
#> SD:NMF 4 0.590 0.660 0.819 0.1768 0.805 0.516
#> CV:NMF 4 0.496 0.583 0.751 0.1590 0.850 0.609
#> MAD:NMF 4 0.543 0.642 0.799 0.1619 0.808 0.517
#> ATC:NMF 4 0.654 0.728 0.851 0.1191 0.851 0.636
#> SD:skmeans 4 0.592 0.684 0.825 0.1447 0.833 0.565
#> CV:skmeans 4 0.520 0.530 0.736 0.1426 0.872 0.651
#> MAD:skmeans 4 0.516 0.623 0.780 0.1405 0.846 0.591
#> ATC:skmeans 4 0.745 0.830 0.901 0.1143 0.791 0.484
#> SD:mclust 4 0.642 0.786 0.856 0.2342 0.729 0.456
#> CV:mclust 4 0.622 0.693 0.798 0.2058 0.815 0.615
#> MAD:mclust 4 0.647 0.767 0.856 0.2293 0.789 0.530
#> ATC:mclust 4 0.660 0.684 0.867 0.2097 0.851 0.641
#> SD:kmeans 4 0.617 0.624 0.759 0.2198 0.787 0.538
#> CV:kmeans 4 0.699 0.694 0.829 0.1511 0.965 0.920
#> MAD:kmeans 4 0.635 0.663 0.789 0.1860 0.852 0.649
#> ATC:kmeans 4 0.596 0.776 0.847 0.2241 0.761 0.507
#> SD:pam 4 0.395 0.504 0.711 0.1134 0.914 0.778
#> CV:pam 4 0.320 0.518 0.710 0.1065 0.954 0.885
#> MAD:pam 4 0.387 0.556 0.746 0.1382 0.870 0.675
#> ATC:pam 4 0.676 0.846 0.914 0.0456 0.973 0.933
#> SD:hclust 4 0.742 0.826 0.902 0.2171 0.932 0.904
#> CV:hclust 4 0.434 0.804 0.863 0.6884 0.709 0.702
#> MAD:hclust 4 0.380 0.849 0.893 0.3673 1.000 1.000
#> ATC:hclust 4 0.884 0.933 0.953 0.1131 1.000 1.000
get_stats(res_list, k = 5)
#> k 1-PAC mean_silhouette concordance area_increased Rand Jaccard
#> SD:NMF 5 0.552 0.507 0.726 0.0577 0.935 0.767
#> CV:NMF 5 0.509 0.472 0.640 0.0668 0.896 0.646
#> MAD:NMF 5 0.536 0.507 0.707 0.0610 0.933 0.754
#> ATC:NMF 5 0.584 0.671 0.792 0.0507 0.947 0.841
#> SD:skmeans 5 0.549 0.523 0.689 0.0637 0.951 0.807
#> CV:skmeans 5 0.493 0.384 0.631 0.0642 0.931 0.749
#> MAD:skmeans 5 0.487 0.441 0.644 0.0643 0.957 0.836
#> ATC:skmeans 5 0.825 0.844 0.913 0.0761 0.834 0.475
#> SD:mclust 5 0.774 0.790 0.867 0.0490 0.928 0.763
#> CV:mclust 5 0.565 0.548 0.738 0.0656 0.905 0.727
#> MAD:mclust 5 0.730 0.743 0.855 0.0536 0.955 0.841
#> ATC:mclust 5 0.656 0.593 0.811 0.0848 0.830 0.552
#> SD:kmeans 5 0.630 0.733 0.815 0.0860 0.884 0.631
#> CV:kmeans 5 0.608 0.581 0.707 0.1018 0.810 0.545
#> MAD:kmeans 5 0.592 0.658 0.783 0.0830 0.876 0.613
#> ATC:kmeans 5 0.705 0.553 0.795 0.0901 0.991 0.971
#> SD:pam 5 0.401 0.497 0.713 0.0385 0.951 0.850
#> CV:pam 5 0.318 0.443 0.680 0.0312 0.993 0.980
#> MAD:pam 5 0.407 0.520 0.708 0.0450 0.974 0.913
#> ATC:pam 5 0.703 0.811 0.879 0.1712 0.819 0.553
#> SD:hclust 5 0.590 0.804 0.896 0.1549 0.961 0.939
#> CV:hclust 5 0.408 0.745 0.878 0.2463 0.990 0.985
#> MAD:hclust 5 0.571 0.732 0.881 0.1796 0.971 0.958
#> ATC:hclust 5 0.518 0.743 0.856 0.2990 0.952 0.931
get_stats(res_list, k = 6)
#> k 1-PAC mean_silhouette concordance area_increased Rand Jaccard
#> SD:NMF 6 0.550 0.447 0.647 0.0403 0.921 0.694
#> CV:NMF 6 0.527 0.420 0.608 0.0425 0.929 0.713
#> MAD:NMF 6 0.555 0.441 0.652 0.0401 0.952 0.797
#> ATC:NMF 6 0.581 0.592 0.737 0.0519 0.967 0.894
#> SD:skmeans 6 0.566 0.483 0.632 0.0404 0.952 0.792
#> CV:skmeans 6 0.516 0.328 0.568 0.0395 0.937 0.742
#> MAD:skmeans 6 0.506 0.323 0.580 0.0404 0.912 0.665
#> ATC:skmeans 6 0.762 0.689 0.777 0.0371 0.955 0.786
#> SD:mclust 6 0.734 0.695 0.845 0.0721 0.880 0.586
#> CV:mclust 6 0.637 0.713 0.804 0.0267 0.941 0.809
#> MAD:mclust 6 0.732 0.687 0.839 0.0616 0.907 0.652
#> ATC:mclust 6 0.696 0.704 0.806 0.0414 0.874 0.619
#> SD:kmeans 6 0.709 0.719 0.821 0.0409 0.967 0.867
#> CV:kmeans 6 0.607 0.666 0.737 0.0539 0.923 0.719
#> MAD:kmeans 6 0.650 0.687 0.770 0.0433 0.978 0.908
#> ATC:kmeans 6 0.702 0.623 0.712 0.0502 0.831 0.495
#> SD:pam 6 0.433 0.435 0.661 0.0365 0.944 0.816
#> CV:pam 6 0.300 0.441 0.657 0.0233 0.985 0.959
#> MAD:pam 6 0.416 0.534 0.687 0.0255 0.983 0.942
#> ATC:pam 6 0.813 0.830 0.919 0.0317 0.986 0.944
#> SD:hclust 6 0.492 0.780 0.871 0.0848 0.990 0.983
#> CV:hclust 6 0.512 0.692 0.864 0.0995 0.899 0.852
#> MAD:hclust 6 0.444 0.761 0.864 0.1352 0.909 0.863
#> ATC:hclust 6 0.460 0.565 0.806 0.1128 0.863 0.789
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 tissue(p) k
#> SD:NMF 160 2.84e-17 2
#> CV:NMF 152 9.03e-20 2
#> MAD:NMF 154 6.80e-16 2
#> ATC:NMF 162 2.59e-20 2
#> SD:skmeans 153 7.04e-16 2
#> CV:skmeans 145 2.41e-11 2
#> MAD:skmeans 154 1.42e-13 2
#> ATC:skmeans 154 6.47e-14 2
#> SD:mclust 162 2.52e-28 2
#> CV:mclust 162 2.11e-29 2
#> MAD:mclust 163 1.65e-27 2
#> ATC:mclust 163 1.69e-28 2
#> SD:kmeans 164 1.13e-28 2
#> CV:kmeans 127 1.04e-23 2
#> MAD:kmeans 164 9.07e-30 2
#> ATC:kmeans 164 1.08e-29 2
#> SD:pam 162 2.11e-29 2
#> CV:pam 162 6.78e-35 2
#> MAD:pam 161 3.77e-28 2
#> ATC:pam 163 8.95e-31 2
#> SD:hclust 163 8.88e-31 2
#> CV:hclust 163 8.71e-01 2
#> MAD:hclust 160 NA 2
#> ATC:hclust 164 1.48e-28 2
test_to_known_factors(res_list, k = 3)
#> n tissue(p) k
#> SD:NMF 152 1.20e-23 3
#> CV:NMF 153 3.86e-23 3
#> MAD:NMF 148 3.75e-23 3
#> ATC:NMF 146 1.08e-29 3
#> SD:skmeans 155 1.30e-23 3
#> CV:skmeans 150 2.73e-25 3
#> MAD:skmeans 152 4.40e-25 3
#> ATC:skmeans 152 1.74e-17 3
#> SD:mclust 101 3.32e-24 3
#> CV:mclust 160 1.60e-32 3
#> MAD:mclust 154 1.31e-32 3
#> ATC:mclust 116 2.03e-24 3
#> SD:kmeans 162 2.03e-32 3
#> CV:kmeans 162 8.65e-32 3
#> MAD:kmeans 158 1.15e-33 3
#> ATC:kmeans 155 5.49e-29 3
#> SD:pam 140 2.22e-24 3
#> CV:pam 138 7.78e-28 3
#> MAD:pam 146 9.94e-26 3
#> ATC:pam 162 2.66e-31 3
#> SD:hclust 156 2.04e-29 3
#> CV:hclust 159 NA 3
#> MAD:hclust 156 2.63e-27 3
#> ATC:hclust 164 2.47e-29 3
test_to_known_factors(res_list, k = 4)
#> n tissue(p) k
#> SD:NMF 130 7.88e-25 4
#> CV:NMF 115 5.29e-20 4
#> MAD:NMF 132 4.45e-23 4
#> ATC:NMF 147 9.00e-28 4
#> SD:skmeans 131 1.20e-23 4
#> CV:skmeans 95 1.50e-18 4
#> MAD:skmeans 118 1.91e-20 4
#> ATC:skmeans 156 2.10e-24 4
#> SD:mclust 153 4.45e-34 4
#> CV:mclust 138 1.65e-31 4
#> MAD:mclust 151 1.96e-33 4
#> ATC:mclust 124 4.61e-25 4
#> SD:kmeans 142 2.48e-34 4
#> CV:kmeans 149 5.89e-29 4
#> MAD:kmeans 141 1.39e-34 4
#> ATC:kmeans 154 2.31e-30 4
#> SD:pam 96 2.26e-15 4
#> CV:pam 104 7.81e-21 4
#> MAD:pam 112 4.41e-19 4
#> ATC:pam 161 8.41e-34 4
#> SD:hclust 151 5.36e-37 4
#> CV:hclust 146 1.71e-27 4
#> MAD:hclust 155 3.15e-29 4
#> ATC:hclust 162 1.39e-30 4
test_to_known_factors(res_list, k = 5)
#> n tissue(p) k
#> SD:NMF 104 4.81e-20 5
#> CV:NMF 88 1.27e-15 5
#> MAD:NMF 103 2.76e-20 5
#> ATC:NMF 143 3.75e-24 5
#> SD:skmeans 94 7.96e-16 5
#> CV:skmeans 61 3.46e-11 5
#> MAD:skmeans 83 1.50e-15 5
#> ATC:skmeans 156 7.48e-25 5
#> SD:mclust 151 1.71e-33 5
#> CV:mclust 113 1.86e-35 5
#> MAD:mclust 146 4.05e-32 5
#> ATC:mclust 113 6.43e-21 5
#> SD:kmeans 144 1.64e-37 5
#> CV:kmeans 105 6.44e-22 5
#> MAD:kmeans 124 1.20e-34 5
#> ATC:kmeans 114 2.22e-25 5
#> SD:pam 97 1.98e-17 5
#> CV:pam 92 4.76e-19 5
#> MAD:pam 104 3.14e-20 5
#> ATC:pam 156 1.57e-31 5
#> SD:hclust 149 2.80e-35 5
#> CV:hclust 138 6.14e-26 5
#> MAD:hclust 144 4.87e-25 5
#> ATC:hclust 146 7.83e-34 5
test_to_known_factors(res_list, k = 6)
#> n tissue(p) k
#> SD:NMF 82 4.72e-18 6
#> CV:NMF 66 1.16e-12 6
#> MAD:NMF 75 1.15e-15 6
#> ATC:NMF 126 2.60e-22 6
#> SD:skmeans 76 4.58e-13 6
#> CV:skmeans 57 4.83e-10 6
#> MAD:skmeans 46 2.66e-08 6
#> ATC:skmeans 135 2.30e-30 6
#> SD:mclust 137 2.03e-29 6
#> CV:mclust 148 2.16e-32 6
#> MAD:mclust 138 7.04e-31 6
#> ATC:mclust 144 5.57e-27 6
#> SD:kmeans 143 5.24e-35 6
#> CV:kmeans 136 7.64e-35 6
#> MAD:kmeans 139 4.66e-36 6
#> ATC:kmeans 108 1.03e-22 6
#> SD:pam 78 3.06e-12 6
#> CV:pam 95 1.12e-17 6
#> MAD:pam 117 1.59e-22 6
#> ATC:pam 153 1.45e-29 6
#> SD:hclust 144 2.47e-33 6
#> CV:hclust 144 2.86e-33 6
#> MAD:hclust 150 2.74e-32 6
#> ATC:hclust 120 1.33e-22 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 12013 rows and 164 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 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 0.703 0.950 0.912 0.1952 0.715 0.715
#> 3 3 0.543 0.886 0.923 0.7011 0.990 0.986
#> 4 4 0.742 0.826 0.902 0.2171 0.932 0.904
#> 5 5 0.590 0.804 0.896 0.1549 0.961 0.939
#> 6 6 0.492 0.780 0.871 0.0848 0.990 0.983
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
#> GSM152839 1 0.0376 0.96261 0.996 0.004
#> GSM152840 1 0.3584 0.89164 0.932 0.068
#> GSM152841 1 0.0672 0.96400 0.992 0.008
#> GSM152842 1 0.1414 0.94864 0.980 0.020
#> GSM152843 1 0.0672 0.96446 0.992 0.008
#> GSM152844 1 0.3733 0.88512 0.928 0.072
#> GSM152845 1 0.5629 0.76767 0.868 0.132
#> GSM152846 1 0.4298 0.85622 0.912 0.088
#> GSM152847 1 0.0672 0.96030 0.992 0.008
#> GSM152848 1 0.0376 0.96261 0.996 0.004
#> GSM152849 1 0.0672 0.96359 0.992 0.008
#> GSM152850 1 0.0938 0.96494 0.988 0.012
#> GSM152851 1 0.0672 0.96543 0.992 0.008
#> GSM152852 1 0.3733 0.88512 0.928 0.072
#> GSM152853 1 0.3733 0.88512 0.928 0.072
#> GSM152854 1 0.3879 0.88376 0.924 0.076
#> GSM152855 1 0.1414 0.96018 0.980 0.020
#> GSM153238 1 0.2778 0.92625 0.952 0.048
#> GSM153239 1 0.3584 0.89222 0.932 0.068
#> GSM153240 1 0.0000 0.96474 1.000 0.000
#> GSM153241 1 0.0376 0.96261 0.996 0.004
#> GSM153242 1 0.3879 0.88673 0.924 0.076
#> GSM153243 1 0.1414 0.96229 0.980 0.020
#> GSM153244 1 0.0672 0.96543 0.992 0.008
#> GSM153245 1 0.2778 0.92007 0.952 0.048
#> GSM153246 1 0.5294 0.77761 0.880 0.120
#> GSM153247 1 0.1414 0.95909 0.980 0.020
#> GSM153248 1 0.0672 0.96518 0.992 0.008
#> GSM153249 1 0.0000 0.96474 1.000 0.000
#> GSM153250 1 0.0376 0.96551 0.996 0.004
#> GSM153251 1 0.2778 0.92434 0.952 0.048
#> GSM153252 1 0.0000 0.96474 1.000 0.000
#> GSM153253 1 0.0376 0.96518 0.996 0.004
#> GSM153254 1 0.0376 0.96548 0.996 0.004
#> GSM153255 1 0.0000 0.96474 1.000 0.000
#> GSM153256 1 0.0000 0.96474 1.000 0.000
#> GSM153257 1 0.0000 0.96474 1.000 0.000
#> GSM153258 1 0.0672 0.96507 0.992 0.008
#> GSM153259 1 0.0938 0.96430 0.988 0.012
#> GSM153260 1 0.2423 0.94064 0.960 0.040
#> GSM153261 1 0.2236 0.94423 0.964 0.036
#> GSM153262 1 0.0376 0.96518 0.996 0.004
#> GSM153263 1 0.0672 0.96507 0.992 0.008
#> GSM153264 1 0.0672 0.96507 0.992 0.008
#> GSM153265 1 0.0376 0.96518 0.996 0.004
#> GSM153266 1 0.0938 0.96363 0.988 0.012
#> GSM153267 1 0.0000 0.96474 1.000 0.000
#> GSM153268 1 0.1414 0.95309 0.980 0.020
#> GSM153269 1 0.0376 0.96551 0.996 0.004
#> GSM153270 1 0.0376 0.96548 0.996 0.004
#> GSM153271 1 0.0376 0.96551 0.996 0.004
#> GSM153272 1 0.0000 0.96474 1.000 0.000
#> GSM153273 1 0.0938 0.96363 0.988 0.012
#> GSM153274 1 0.0000 0.96474 1.000 0.000
#> GSM153275 1 0.0000 0.96474 1.000 0.000
#> GSM153276 1 0.0376 0.96551 0.996 0.004
#> GSM153277 1 0.0376 0.96518 0.996 0.004
#> GSM153278 1 0.0938 0.96440 0.988 0.012
#> GSM153279 1 0.0672 0.96543 0.992 0.008
#> GSM153280 1 0.0376 0.96518 0.996 0.004
#> GSM153281 1 0.0000 0.96474 1.000 0.000
#> GSM153282 1 0.0376 0.96518 0.996 0.004
#> GSM153283 1 0.0672 0.96507 0.992 0.008
#> GSM153284 1 0.0000 0.96474 1.000 0.000
#> GSM153285 1 0.0376 0.96518 0.996 0.004
#> GSM153286 1 0.0000 0.96474 1.000 0.000
#> GSM153287 1 0.0376 0.96518 0.996 0.004
#> GSM153288 1 0.0000 0.96474 1.000 0.000
#> GSM153289 1 0.1414 0.96018 0.980 0.020
#> GSM153290 1 0.0376 0.96518 0.996 0.004
#> GSM153291 1 0.0000 0.96474 1.000 0.000
#> GSM153292 1 0.0376 0.96518 0.996 0.004
#> GSM153293 1 0.0000 0.96474 1.000 0.000
#> GSM153294 1 0.0672 0.96518 0.992 0.008
#> GSM153295 1 0.0376 0.96261 0.996 0.004
#> GSM153054 1 0.1414 0.96240 0.980 0.020
#> GSM153055 1 0.0672 0.96507 0.992 0.008
#> GSM153056 1 0.0376 0.96261 0.996 0.004
#> GSM153057 1 0.1414 0.96089 0.980 0.020
#> GSM153058 1 0.3114 0.91257 0.944 0.056
#> GSM153059 1 0.1633 0.95773 0.976 0.024
#> GSM153060 1 0.3584 0.87575 0.932 0.068
#> GSM153061 1 0.1633 0.94401 0.976 0.024
#> GSM153062 1 0.9922 -0.00395 0.552 0.448
#> GSM153063 1 0.2423 0.93643 0.960 0.040
#> GSM153064 1 0.0938 0.96363 0.988 0.012
#> GSM153065 1 0.2603 0.93730 0.956 0.044
#> GSM153066 1 0.7299 0.54875 0.796 0.204
#> GSM153067 1 0.0000 0.96474 1.000 0.000
#> GSM153068 1 0.2043 0.95086 0.968 0.032
#> GSM153069 1 0.0000 0.96474 1.000 0.000
#> GSM153070 1 0.0376 0.96551 0.996 0.004
#> GSM153071 1 0.1184 0.96238 0.984 0.016
#> GSM153072 1 0.1184 0.96238 0.984 0.016
#> GSM153073 1 0.0000 0.96474 1.000 0.000
#> GSM153074 1 0.0000 0.96474 1.000 0.000
#> GSM153075 1 0.0672 0.96507 0.992 0.008
#> GSM153076 1 0.0000 0.96474 1.000 0.000
#> GSM153077 1 0.1184 0.96238 0.984 0.016
#> GSM153078 1 0.0672 0.96446 0.992 0.008
#> GSM153079 1 0.1414 0.96018 0.980 0.020
#> GSM153080 1 0.2043 0.95161 0.968 0.032
#> GSM153081 1 0.1184 0.96238 0.984 0.016
#> GSM153082 1 0.1414 0.96061 0.980 0.020
#> GSM153083 1 0.1184 0.96238 0.984 0.016
#> GSM153084 1 0.2423 0.94000 0.960 0.040
#> GSM153085 1 0.1184 0.96238 0.984 0.016
#> GSM153086 1 0.1184 0.96238 0.984 0.016
#> GSM153087 1 0.0000 0.96474 1.000 0.000
#> GSM153088 1 0.0000 0.96474 1.000 0.000
#> GSM153089 1 0.3274 0.90530 0.940 0.060
#> GSM153090 1 0.0000 0.96474 1.000 0.000
#> GSM153091 1 0.0938 0.96363 0.988 0.012
#> GSM153092 1 0.0672 0.96507 0.992 0.008
#> GSM153093 1 0.0000 0.96474 1.000 0.000
#> GSM153094 1 0.0938 0.96363 0.988 0.012
#> GSM153095 1 0.1414 0.96031 0.980 0.020
#> GSM153096 1 0.0938 0.96363 0.988 0.012
#> GSM153097 1 0.0938 0.96363 0.988 0.012
#> GSM153098 1 0.0376 0.96548 0.996 0.004
#> GSM153099 1 0.0376 0.96551 0.996 0.004
#> GSM153100 1 0.0672 0.96507 0.992 0.008
#> GSM153101 1 0.1184 0.96238 0.984 0.016
#> GSM153102 1 0.1184 0.96196 0.984 0.016
#> GSM153103 1 0.1184 0.96238 0.984 0.016
#> GSM153104 1 0.0376 0.96518 0.996 0.004
#> GSM153106 1 0.1414 0.96018 0.980 0.020
#> GSM153107 1 0.1414 0.96018 0.980 0.020
#> GSM153108 1 0.0376 0.96518 0.996 0.004
#> GSM153109 1 0.1184 0.96196 0.984 0.016
#> GSM153110 1 0.0672 0.96507 0.992 0.008
#> GSM153111 1 0.1184 0.96238 0.984 0.016
#> GSM153112 1 0.0938 0.96363 0.988 0.012
#> GSM153113 1 0.1414 0.96057 0.980 0.020
#> GSM153114 1 0.1414 0.96018 0.980 0.020
#> GSM187532 2 0.9710 0.99868 0.400 0.600
#> GSM187533 2 0.9710 0.99868 0.400 0.600
#> GSM187534 2 0.9710 0.99868 0.400 0.600
#> GSM187535 1 0.5737 0.73807 0.864 0.136
#> GSM152906 2 0.9710 0.99868 0.400 0.600
#> GSM152907 2 0.9754 0.98633 0.408 0.592
#> GSM152908 2 0.9710 0.99868 0.400 0.600
#> GSM152909 2 0.9710 0.99868 0.400 0.600
#> GSM152910 2 0.9710 0.99868 0.400 0.600
#> GSM152911 2 0.9710 0.99868 0.400 0.600
#> GSM152912 2 0.9710 0.99868 0.400 0.600
#> GSM152913 2 0.9710 0.99868 0.400 0.600
#> GSM152914 2 0.9710 0.99868 0.400 0.600
#> GSM152915 2 0.9710 0.99868 0.400 0.600
#> GSM152916 2 0.9710 0.99868 0.400 0.600
#> GSM152917 2 0.9710 0.99868 0.400 0.600
#> GSM152918 2 0.9710 0.99868 0.400 0.600
#> GSM152919 2 0.9710 0.99868 0.400 0.600
#> GSM152920 2 0.9710 0.99868 0.400 0.600
#> GSM152921 2 0.9710 0.99868 0.400 0.600
#> GSM152922 2 0.9710 0.99868 0.400 0.600
#> GSM152923 2 0.9710 0.99868 0.400 0.600
#> GSM152924 2 0.9710 0.99868 0.400 0.600
#> GSM152925 2 0.9710 0.99868 0.400 0.600
#> GSM152926 2 0.9754 0.98633 0.408 0.592
#> GSM152927 2 0.9710 0.99868 0.400 0.600
#> GSM152928 2 0.9732 0.99277 0.404 0.596
#> GSM152929 2 0.9710 0.99868 0.400 0.600
#> GSM152930 2 0.9710 0.99868 0.400 0.600
cbind(get_classes(res, k = 3), get_membership(res, k = 3))
#> class entropy silhouette p1 p2 p3
#> GSM152839 1 0.1015 0.9283 0.980 0.012 0.008
#> GSM152840 1 0.8410 0.4107 0.620 0.164 0.216
#> GSM152841 1 0.3129 0.8828 0.904 0.008 0.088
#> GSM152842 1 0.3889 0.8585 0.884 0.032 0.084
#> GSM152843 1 0.1919 0.9202 0.956 0.024 0.020
#> GSM152844 1 0.8587 0.3689 0.604 0.176 0.220
#> GSM152845 1 0.9591 -0.0593 0.472 0.296 0.232
#> GSM152846 1 0.8878 0.2874 0.576 0.208 0.216
#> GSM152847 1 0.2443 0.9090 0.940 0.028 0.032
#> GSM152848 1 0.1170 0.9261 0.976 0.016 0.008
#> GSM152849 1 0.1751 0.9247 0.960 0.012 0.028
#> GSM152850 1 0.1751 0.9265 0.960 0.012 0.028
#> GSM152851 1 0.1315 0.9286 0.972 0.020 0.008
#> GSM152852 1 0.8350 0.4266 0.628 0.176 0.196
#> GSM152853 1 0.8473 0.3966 0.616 0.176 0.208
#> GSM152854 1 0.7160 0.6154 0.720 0.148 0.132
#> GSM152855 1 0.1163 0.9280 0.972 0.028 0.000
#> GSM153238 1 0.3742 0.8844 0.892 0.072 0.036
#> GSM153239 1 0.7633 0.5583 0.684 0.132 0.184
#> GSM153240 1 0.0475 0.9291 0.992 0.004 0.004
#> GSM153241 1 0.1999 0.9172 0.952 0.012 0.036
#> GSM153242 1 0.7451 0.5899 0.700 0.156 0.144
#> GSM153243 1 0.1919 0.9236 0.956 0.024 0.020
#> GSM153244 1 0.1182 0.9294 0.976 0.012 0.012
#> GSM153245 1 0.5883 0.7599 0.796 0.092 0.112
#> GSM153246 1 0.8394 0.1460 0.576 0.108 0.316
#> GSM153247 1 0.2569 0.9147 0.936 0.032 0.032
#> GSM153248 1 0.1182 0.9307 0.976 0.012 0.012
#> GSM153249 1 0.0661 0.9295 0.988 0.004 0.008
#> GSM153250 1 0.0848 0.9303 0.984 0.008 0.008
#> GSM153251 1 0.5020 0.7950 0.836 0.108 0.056
#> GSM153252 1 0.0661 0.9299 0.988 0.004 0.008
#> GSM153253 1 0.1585 0.9238 0.964 0.008 0.028
#> GSM153254 1 0.1015 0.9304 0.980 0.008 0.012
#> GSM153255 1 0.0829 0.9291 0.984 0.004 0.012
#> GSM153256 1 0.0661 0.9289 0.988 0.004 0.008
#> GSM153257 1 0.0829 0.9291 0.984 0.004 0.012
#> GSM153258 1 0.1015 0.9302 0.980 0.012 0.008
#> GSM153259 1 0.1129 0.9290 0.976 0.020 0.004
#> GSM153260 1 0.4194 0.8595 0.876 0.064 0.060
#> GSM153261 1 0.2903 0.9038 0.924 0.048 0.028
#> GSM153262 1 0.1453 0.9259 0.968 0.008 0.024
#> GSM153263 1 0.0829 0.9295 0.984 0.012 0.004
#> GSM153264 1 0.1170 0.9292 0.976 0.016 0.008
#> GSM153265 1 0.1711 0.9220 0.960 0.008 0.032
#> GSM153266 1 0.1129 0.9289 0.976 0.020 0.004
#> GSM153267 1 0.0661 0.9299 0.988 0.004 0.008
#> GSM153268 1 0.4256 0.8442 0.868 0.036 0.096
#> GSM153269 1 0.0424 0.9297 0.992 0.008 0.000
#> GSM153270 1 0.0661 0.9299 0.988 0.008 0.004
#> GSM153271 1 0.0661 0.9295 0.988 0.008 0.004
#> GSM153272 1 0.0661 0.9289 0.988 0.004 0.008
#> GSM153273 1 0.1315 0.9277 0.972 0.020 0.008
#> GSM153274 1 0.0661 0.9292 0.988 0.004 0.008
#> GSM153275 1 0.0829 0.9291 0.984 0.004 0.012
#> GSM153276 1 0.0424 0.9297 0.992 0.008 0.000
#> GSM153277 1 0.1585 0.9239 0.964 0.008 0.028
#> GSM153278 1 0.1774 0.9286 0.960 0.016 0.024
#> GSM153279 1 0.1182 0.9294 0.976 0.012 0.012
#> GSM153280 1 0.1585 0.9239 0.964 0.008 0.028
#> GSM153281 1 0.0661 0.9299 0.988 0.004 0.008
#> GSM153282 1 0.1585 0.9240 0.964 0.008 0.028
#> GSM153283 1 0.1129 0.9297 0.976 0.020 0.004
#> GSM153284 1 0.0475 0.9291 0.992 0.004 0.004
#> GSM153285 1 0.1453 0.9254 0.968 0.008 0.024
#> GSM153286 1 0.0661 0.9297 0.988 0.004 0.008
#> GSM153287 1 0.1015 0.9296 0.980 0.008 0.012
#> GSM153288 1 0.0829 0.9300 0.984 0.004 0.012
#> GSM153289 1 0.1163 0.9280 0.972 0.028 0.000
#> GSM153290 1 0.0848 0.9298 0.984 0.008 0.008
#> GSM153291 1 0.0983 0.9291 0.980 0.004 0.016
#> GSM153292 1 0.1315 0.9286 0.972 0.008 0.020
#> GSM153293 1 0.0661 0.9289 0.988 0.004 0.008
#> GSM153294 1 0.1337 0.9306 0.972 0.012 0.016
#> GSM153295 1 0.1774 0.9234 0.960 0.024 0.016
#> GSM153054 1 0.2443 0.9212 0.940 0.032 0.028
#> GSM153055 1 0.0592 0.9295 0.988 0.012 0.000
#> GSM153056 1 0.1751 0.9251 0.960 0.012 0.028
#> GSM153057 1 0.1751 0.9244 0.960 0.028 0.012
#> GSM153058 1 0.5915 0.7358 0.792 0.128 0.080
#> GSM153059 1 0.2443 0.9146 0.940 0.032 0.028
#> GSM153060 1 0.5678 0.7134 0.776 0.032 0.192
#> GSM153061 1 0.5455 0.7474 0.788 0.028 0.184
#> GSM153062 3 0.3686 0.0000 0.140 0.000 0.860
#> GSM153063 1 0.4288 0.8546 0.872 0.060 0.068
#> GSM153064 1 0.1170 0.9284 0.976 0.016 0.008
#> GSM153065 1 0.4379 0.8512 0.868 0.060 0.072
#> GSM153066 1 0.6556 0.5708 0.692 0.276 0.032
#> GSM153067 1 0.0829 0.9291 0.984 0.004 0.012
#> GSM153068 1 0.4423 0.8542 0.864 0.048 0.088
#> GSM153069 1 0.0829 0.9291 0.984 0.004 0.012
#> GSM153070 1 0.0848 0.9303 0.984 0.008 0.008
#> GSM153071 1 0.1774 0.9288 0.960 0.024 0.016
#> GSM153072 1 0.1620 0.9284 0.964 0.024 0.012
#> GSM153073 1 0.0475 0.9291 0.992 0.004 0.004
#> GSM153074 1 0.0475 0.9291 0.992 0.004 0.004
#> GSM153075 1 0.0592 0.9295 0.988 0.012 0.000
#> GSM153076 1 0.0661 0.9292 0.988 0.004 0.008
#> GSM153077 1 0.1453 0.9287 0.968 0.024 0.008
#> GSM153078 1 0.1636 0.9261 0.964 0.020 0.016
#> GSM153079 1 0.1163 0.9280 0.972 0.028 0.000
#> GSM153080 1 0.2527 0.9164 0.936 0.044 0.020
#> GSM153081 1 0.1267 0.9289 0.972 0.024 0.004
#> GSM153082 1 0.1453 0.9276 0.968 0.024 0.008
#> GSM153083 1 0.1129 0.9287 0.976 0.020 0.004
#> GSM153084 1 0.3183 0.8850 0.908 0.076 0.016
#> GSM153085 1 0.0892 0.9286 0.980 0.020 0.000
#> GSM153086 1 0.1315 0.9278 0.972 0.020 0.008
#> GSM153087 1 0.0661 0.9304 0.988 0.008 0.004
#> GSM153088 1 0.0475 0.9291 0.992 0.004 0.004
#> GSM153089 1 0.6039 0.7430 0.788 0.104 0.108
#> GSM153090 1 0.0661 0.9289 0.988 0.004 0.008
#> GSM153091 1 0.1170 0.9284 0.976 0.016 0.008
#> GSM153092 1 0.1170 0.9303 0.976 0.016 0.008
#> GSM153093 1 0.0661 0.9289 0.988 0.004 0.008
#> GSM153094 1 0.1315 0.9277 0.972 0.020 0.008
#> GSM153095 1 0.2050 0.9227 0.952 0.020 0.028
#> GSM153096 1 0.1315 0.9277 0.972 0.020 0.008
#> GSM153097 1 0.1315 0.9277 0.972 0.020 0.008
#> GSM153098 1 0.1015 0.9308 0.980 0.012 0.008
#> GSM153099 1 0.0829 0.9300 0.984 0.012 0.004
#> GSM153100 1 0.0829 0.9294 0.984 0.012 0.004
#> GSM153101 1 0.1315 0.9281 0.972 0.020 0.008
#> GSM153102 1 0.0892 0.9289 0.980 0.020 0.000
#> GSM153103 1 0.1129 0.9287 0.976 0.020 0.004
#> GSM153104 1 0.1015 0.9289 0.980 0.008 0.012
#> GSM153106 1 0.1163 0.9280 0.972 0.028 0.000
#> GSM153107 1 0.1163 0.9280 0.972 0.028 0.000
#> GSM153108 1 0.0661 0.9299 0.988 0.008 0.004
#> GSM153109 1 0.0892 0.9289 0.980 0.020 0.000
#> GSM153110 1 0.1170 0.9285 0.976 0.016 0.008
#> GSM153111 1 0.1315 0.9278 0.972 0.020 0.008
#> GSM153112 1 0.1170 0.9284 0.976 0.016 0.008
#> GSM153113 1 0.1315 0.9282 0.972 0.020 0.008
#> GSM153114 1 0.1163 0.9280 0.972 0.028 0.000
#> GSM187532 2 0.3192 0.9931 0.112 0.888 0.000
#> GSM187533 2 0.3340 0.9867 0.120 0.880 0.000
#> GSM187534 2 0.3340 0.9867 0.120 0.880 0.000
#> GSM187535 1 0.3752 0.8187 0.856 0.144 0.000
#> GSM152906 2 0.3267 0.9933 0.116 0.884 0.000
#> GSM152907 2 0.3412 0.9811 0.124 0.876 0.000
#> GSM152908 2 0.3192 0.9931 0.112 0.888 0.000
#> GSM152909 2 0.3192 0.9931 0.112 0.888 0.000
#> GSM152910 2 0.3192 0.9931 0.112 0.888 0.000
#> GSM152911 2 0.3267 0.9933 0.116 0.884 0.000
#> GSM152912 2 0.3192 0.9931 0.112 0.888 0.000
#> GSM152913 2 0.3192 0.9931 0.112 0.888 0.000
#> GSM152914 2 0.3267 0.9933 0.116 0.884 0.000
#> GSM152915 2 0.3267 0.9933 0.116 0.884 0.000
#> GSM152916 2 0.3192 0.9931 0.112 0.888 0.000
#> GSM152917 2 0.3267 0.9933 0.116 0.884 0.000
#> GSM152918 2 0.3267 0.9933 0.116 0.884 0.000
#> GSM152919 2 0.3267 0.9933 0.116 0.884 0.000
#> GSM152920 2 0.3192 0.9931 0.112 0.888 0.000
#> GSM152921 2 0.3192 0.9931 0.112 0.888 0.000
#> GSM152922 2 0.3192 0.9931 0.112 0.888 0.000
#> GSM152923 2 0.3267 0.9933 0.116 0.884 0.000
#> GSM152924 2 0.3192 0.9931 0.112 0.888 0.000
#> GSM152925 2 0.3192 0.9931 0.112 0.888 0.000
#> GSM152926 2 0.3412 0.9811 0.124 0.876 0.000
#> GSM152927 2 0.3192 0.9931 0.112 0.888 0.000
#> GSM152928 2 0.3267 0.9911 0.116 0.884 0.000
#> GSM152929 2 0.3267 0.9933 0.116 0.884 0.000
#> GSM152930 2 0.3267 0.9933 0.116 0.884 0.000
cbind(get_classes(res, k = 4), get_membership(res, k = 4))
#> class entropy silhouette p1 p2 p3 p4
#> GSM152839 1 0.1388 0.8947 0.960 0.000 0.012 0.028
#> GSM152840 3 0.7164 0.8108 0.384 0.108 0.500 0.008
#> GSM152841 1 0.3808 0.7263 0.824 0.012 0.160 0.004
#> GSM152842 1 0.4284 0.6343 0.780 0.000 0.020 0.200
#> GSM152843 1 0.2234 0.8672 0.924 0.004 0.008 0.064
#> GSM152844 3 0.7038 0.8727 0.336 0.120 0.540 0.004
#> GSM152845 3 0.8136 0.6047 0.248 0.240 0.488 0.024
#> GSM152846 3 0.7659 0.8484 0.324 0.152 0.508 0.016
#> GSM152847 1 0.3160 0.8020 0.872 0.000 0.020 0.108
#> GSM152848 1 0.1151 0.8919 0.968 0.000 0.008 0.024
#> GSM152849 1 0.2408 0.8703 0.920 0.004 0.016 0.060
#> GSM152850 1 0.2307 0.8827 0.928 0.008 0.016 0.048
#> GSM152851 1 0.2032 0.8835 0.936 0.028 0.036 0.000
#> GSM152852 3 0.6941 0.8637 0.360 0.120 0.520 0.000
#> GSM152853 3 0.6894 0.8759 0.344 0.120 0.536 0.000
#> GSM152854 1 0.7527 -0.5134 0.516 0.112 0.348 0.024
#> GSM152855 1 0.1648 0.8927 0.956 0.016 0.016 0.012
#> GSM153238 1 0.4343 0.7665 0.840 0.044 0.032 0.084
#> GSM153239 1 0.7324 -0.7118 0.456 0.108 0.424 0.012
#> GSM153240 1 0.0859 0.8955 0.980 0.008 0.008 0.004
#> GSM153241 1 0.2797 0.8623 0.908 0.008 0.028 0.056
#> GSM153242 1 0.8054 -0.5552 0.500 0.132 0.324 0.044
#> GSM153243 1 0.2807 0.8760 0.912 0.020 0.024 0.044
#> GSM153244 1 0.1593 0.8928 0.956 0.016 0.024 0.004
#> GSM153245 1 0.7137 -0.0473 0.620 0.068 0.256 0.056
#> GSM153246 4 0.5759 0.0973 0.276 0.020 0.028 0.676
#> GSM153247 1 0.3030 0.8500 0.900 0.020 0.020 0.060
#> GSM153248 1 0.1271 0.8986 0.968 0.012 0.012 0.008
#> GSM153249 1 0.1114 0.8965 0.972 0.008 0.016 0.004
#> GSM153250 1 0.0992 0.8973 0.976 0.012 0.004 0.008
#> GSM153251 1 0.6266 0.3635 0.700 0.080 0.192 0.028
#> GSM153252 1 0.1174 0.8939 0.968 0.012 0.020 0.000
#> GSM153253 1 0.2125 0.8749 0.932 0.012 0.052 0.004
#> GSM153254 1 0.1821 0.8961 0.948 0.012 0.032 0.008
#> GSM153255 1 0.1042 0.8939 0.972 0.008 0.020 0.000
#> GSM153256 1 0.0672 0.8956 0.984 0.008 0.008 0.000
#> GSM153257 1 0.0992 0.8949 0.976 0.008 0.012 0.004
#> GSM153258 1 0.1262 0.8979 0.968 0.016 0.008 0.008
#> GSM153259 1 0.1124 0.8962 0.972 0.012 0.004 0.012
#> GSM153260 1 0.4692 0.7186 0.812 0.044 0.024 0.120
#> GSM153261 1 0.3491 0.8439 0.884 0.044 0.044 0.028
#> GSM153262 1 0.1771 0.8874 0.948 0.012 0.036 0.004
#> GSM153263 1 0.1114 0.8974 0.972 0.016 0.008 0.004
#> GSM153264 1 0.1394 0.8981 0.964 0.012 0.008 0.016
#> GSM153265 1 0.2207 0.8760 0.928 0.012 0.056 0.004
#> GSM153266 1 0.1526 0.8955 0.960 0.012 0.012 0.016
#> GSM153267 1 0.0804 0.8958 0.980 0.008 0.012 0.000
#> GSM153268 1 0.4900 0.4904 0.732 0.032 0.236 0.000
#> GSM153269 1 0.0992 0.8968 0.976 0.012 0.008 0.004
#> GSM153270 1 0.0937 0.8979 0.976 0.012 0.012 0.000
#> GSM153271 1 0.0804 0.8963 0.980 0.012 0.008 0.000
#> GSM153272 1 0.0804 0.8946 0.980 0.008 0.012 0.000
#> GSM153273 1 0.1394 0.8931 0.964 0.012 0.008 0.016
#> GSM153274 1 0.1229 0.8957 0.968 0.008 0.020 0.004
#> GSM153275 1 0.0859 0.8962 0.980 0.008 0.008 0.004
#> GSM153276 1 0.1124 0.8970 0.972 0.012 0.012 0.004
#> GSM153277 1 0.1909 0.8812 0.940 0.008 0.048 0.004
#> GSM153278 1 0.1917 0.8923 0.944 0.008 0.012 0.036
#> GSM153279 1 0.1484 0.8954 0.960 0.016 0.020 0.004
#> GSM153280 1 0.1953 0.8811 0.940 0.012 0.044 0.004
#> GSM153281 1 0.1584 0.8867 0.952 0.012 0.036 0.000
#> GSM153282 1 0.2040 0.8778 0.936 0.012 0.048 0.004
#> GSM153283 1 0.0992 0.8981 0.976 0.012 0.004 0.008
#> GSM153284 1 0.0992 0.8964 0.976 0.008 0.012 0.004
#> GSM153285 1 0.1863 0.8835 0.944 0.012 0.040 0.004
#> GSM153286 1 0.0927 0.8951 0.976 0.008 0.016 0.000
#> GSM153287 1 0.1151 0.8937 0.968 0.008 0.024 0.000
#> GSM153288 1 0.1042 0.8942 0.972 0.008 0.020 0.000
#> GSM153289 1 0.1648 0.8927 0.956 0.016 0.016 0.012
#> GSM153290 1 0.1674 0.8893 0.952 0.012 0.032 0.004
#> GSM153291 1 0.1256 0.8915 0.964 0.008 0.028 0.000
#> GSM153292 1 0.1356 0.8910 0.960 0.008 0.032 0.000
#> GSM153293 1 0.0672 0.8950 0.984 0.008 0.008 0.000
#> GSM153294 1 0.1404 0.8984 0.964 0.012 0.012 0.012
#> GSM153295 1 0.1510 0.8880 0.956 0.000 0.016 0.028
#> GSM153054 1 0.2694 0.8746 0.916 0.016 0.024 0.044
#> GSM153055 1 0.1182 0.8983 0.968 0.016 0.016 0.000
#> GSM153056 1 0.1771 0.8888 0.948 0.004 0.012 0.036
#> GSM153057 1 0.2616 0.8756 0.920 0.036 0.028 0.016
#> GSM153058 1 0.7577 -0.0333 0.620 0.112 0.196 0.072
#> GSM153059 1 0.3301 0.8534 0.892 0.040 0.044 0.024
#> GSM153060 1 0.5873 0.1923 0.632 0.004 0.044 0.320
#> GSM153061 1 0.5137 0.3835 0.680 0.000 0.024 0.296
#> GSM153062 4 0.6606 0.3597 0.052 0.012 0.440 0.496
#> GSM153063 1 0.5619 0.5752 0.756 0.056 0.152 0.036
#> GSM153064 1 0.1271 0.8936 0.968 0.012 0.008 0.012
#> GSM153065 1 0.4846 0.7135 0.804 0.044 0.028 0.124
#> GSM153066 1 0.6457 0.1487 0.640 0.276 0.020 0.064
#> GSM153067 1 0.1042 0.8939 0.972 0.008 0.020 0.000
#> GSM153068 1 0.4687 0.6812 0.796 0.028 0.020 0.156
#> GSM153069 1 0.1042 0.8939 0.972 0.008 0.020 0.000
#> GSM153070 1 0.0992 0.8973 0.976 0.012 0.004 0.008
#> GSM153071 1 0.1975 0.8928 0.944 0.012 0.016 0.028
#> GSM153072 1 0.1853 0.8921 0.948 0.012 0.012 0.028
#> GSM153073 1 0.0336 0.8957 0.992 0.008 0.000 0.000
#> GSM153074 1 0.1114 0.8956 0.972 0.008 0.016 0.004
#> GSM153075 1 0.1059 0.8976 0.972 0.016 0.012 0.000
#> GSM153076 1 0.1139 0.8971 0.972 0.008 0.012 0.008
#> GSM153077 1 0.1526 0.8961 0.960 0.012 0.012 0.016
#> GSM153078 1 0.2040 0.8816 0.936 0.004 0.012 0.048
#> GSM153079 1 0.1648 0.8927 0.956 0.016 0.016 0.012
#> GSM153080 1 0.3250 0.8420 0.888 0.024 0.072 0.016
#> GSM153081 1 0.1526 0.8962 0.960 0.012 0.012 0.016
#> GSM153082 1 0.1884 0.8913 0.948 0.016 0.016 0.020
#> GSM153083 1 0.1648 0.8934 0.956 0.012 0.016 0.016
#> GSM153084 1 0.3740 0.8077 0.864 0.088 0.020 0.028
#> GSM153085 1 0.1404 0.8948 0.964 0.012 0.012 0.012
#> GSM153086 1 0.1762 0.8918 0.952 0.012 0.016 0.020
#> GSM153087 1 0.0712 0.8984 0.984 0.004 0.008 0.004
#> GSM153088 1 0.0672 0.8951 0.984 0.008 0.008 0.000
#> GSM153089 1 0.6330 0.3192 0.692 0.088 0.196 0.024
#> GSM153090 1 0.0672 0.8956 0.984 0.008 0.008 0.000
#> GSM153091 1 0.1271 0.8936 0.968 0.012 0.008 0.012
#> GSM153092 1 0.1271 0.8987 0.968 0.012 0.008 0.012
#> GSM153093 1 0.0672 0.8950 0.984 0.008 0.008 0.000
#> GSM153094 1 0.1394 0.8931 0.964 0.012 0.008 0.016
#> GSM153095 1 0.2730 0.8779 0.916 0.020 0.028 0.036
#> GSM153096 1 0.1394 0.8931 0.964 0.012 0.008 0.016
#> GSM153097 1 0.1394 0.8931 0.964 0.012 0.008 0.016
#> GSM153098 1 0.1271 0.8991 0.968 0.012 0.008 0.012
#> GSM153099 1 0.0992 0.8970 0.976 0.012 0.004 0.008
#> GSM153100 1 0.0992 0.8973 0.976 0.012 0.004 0.008
#> GSM153101 1 0.1884 0.8930 0.948 0.020 0.016 0.016
#> GSM153102 1 0.1648 0.8937 0.956 0.016 0.016 0.012
#> GSM153103 1 0.1640 0.8937 0.956 0.012 0.020 0.012
#> GSM153104 1 0.1575 0.8901 0.956 0.012 0.028 0.004
#> GSM153106 1 0.1648 0.8927 0.956 0.016 0.016 0.012
#> GSM153107 1 0.1648 0.8927 0.956 0.016 0.016 0.012
#> GSM153108 1 0.0992 0.8976 0.976 0.008 0.012 0.004
#> GSM153109 1 0.1648 0.8937 0.956 0.016 0.016 0.012
#> GSM153110 1 0.1262 0.8947 0.968 0.008 0.008 0.016
#> GSM153111 1 0.1762 0.8918 0.952 0.012 0.016 0.020
#> GSM153112 1 0.1271 0.8936 0.968 0.012 0.008 0.012
#> GSM153113 1 0.1998 0.8913 0.944 0.020 0.016 0.020
#> GSM153114 1 0.1648 0.8927 0.956 0.016 0.016 0.012
#> GSM187532 2 0.1022 0.9891 0.032 0.968 0.000 0.000
#> GSM187533 2 0.1389 0.9759 0.048 0.952 0.000 0.000
#> GSM187534 2 0.1389 0.9759 0.048 0.952 0.000 0.000
#> GSM187535 1 0.3726 0.7479 0.844 0.132 0.012 0.012
#> GSM152906 2 0.1211 0.9886 0.040 0.960 0.000 0.000
#> GSM152907 2 0.1389 0.9784 0.048 0.952 0.000 0.000
#> GSM152908 2 0.1022 0.9891 0.032 0.968 0.000 0.000
#> GSM152909 2 0.1022 0.9891 0.032 0.968 0.000 0.000
#> GSM152910 2 0.1022 0.9891 0.032 0.968 0.000 0.000
#> GSM152911 2 0.1118 0.9907 0.036 0.964 0.000 0.000
#> GSM152912 2 0.1022 0.9891 0.032 0.968 0.000 0.000
#> GSM152913 2 0.1022 0.9891 0.032 0.968 0.000 0.000
#> GSM152914 2 0.1118 0.9907 0.036 0.964 0.000 0.000
#> GSM152915 2 0.1118 0.9907 0.036 0.964 0.000 0.000
#> GSM152916 2 0.1118 0.9902 0.036 0.964 0.000 0.000
#> GSM152917 2 0.1118 0.9907 0.036 0.964 0.000 0.000
#> GSM152918 2 0.1118 0.9907 0.036 0.964 0.000 0.000
#> GSM152919 2 0.1118 0.9907 0.036 0.964 0.000 0.000
#> GSM152920 2 0.1022 0.9891 0.032 0.968 0.000 0.000
#> GSM152921 2 0.1022 0.9891 0.032 0.968 0.000 0.000
#> GSM152922 2 0.1022 0.9891 0.032 0.968 0.000 0.000
#> GSM152923 2 0.1211 0.9886 0.040 0.960 0.000 0.000
#> GSM152924 2 0.1118 0.9902 0.036 0.964 0.000 0.000
#> GSM152925 2 0.1118 0.9902 0.036 0.964 0.000 0.000
#> GSM152926 2 0.1389 0.9784 0.048 0.952 0.000 0.000
#> GSM152927 2 0.1118 0.9902 0.036 0.964 0.000 0.000
#> GSM152928 2 0.1211 0.9874 0.040 0.960 0.000 0.000
#> GSM152929 2 0.1211 0.9886 0.040 0.960 0.000 0.000
#> GSM152930 2 0.1211 0.9886 0.040 0.960 0.000 0.000
cbind(get_classes(res, k = 5), get_membership(res, k = 5))
#> class entropy silhouette p1 p2 p3 p4 p5
#> GSM152839 1 0.2103 0.88478 0.920 0.000 0.020 0.004 0.056
#> GSM152840 3 0.3933 0.70997 0.196 0.000 0.776 0.008 0.020
#> GSM152841 1 0.4301 0.70199 0.768 0.004 0.188 0.012 0.028
#> GSM152842 1 0.4891 0.14081 0.564 0.004 0.008 0.008 0.416
#> GSM152843 1 0.3422 0.81225 0.832 0.004 0.020 0.004 0.140
#> GSM152844 3 0.3124 0.68000 0.144 0.000 0.840 0.008 0.008
#> GSM152845 3 0.5867 0.43439 0.104 0.116 0.716 0.036 0.028
#> GSM152846 3 0.4352 0.61448 0.132 0.032 0.800 0.020 0.016
#> GSM152847 1 0.4153 0.65529 0.736 0.000 0.020 0.004 0.240
#> GSM152848 1 0.1701 0.88428 0.936 0.000 0.016 0.000 0.048
#> GSM152849 1 0.3281 0.82074 0.840 0.004 0.016 0.004 0.136
#> GSM152850 1 0.2574 0.86889 0.896 0.008 0.012 0.004 0.080
#> GSM152851 1 0.2569 0.87133 0.904 0.008 0.056 0.004 0.028
#> GSM152852 3 0.3320 0.70409 0.164 0.000 0.820 0.004 0.012
#> GSM152853 3 0.3044 0.68980 0.148 0.000 0.840 0.004 0.008
#> GSM152854 3 0.5740 0.50738 0.328 0.004 0.596 0.016 0.056
#> GSM152855 1 0.1913 0.88245 0.932 0.016 0.008 0.000 0.044
#> GSM153238 1 0.4860 0.66512 0.744 0.040 0.016 0.012 0.188
#> GSM153239 3 0.5321 0.58113 0.296 0.016 0.648 0.008 0.032
#> GSM153240 1 0.1173 0.88984 0.964 0.004 0.012 0.000 0.020
#> GSM153241 1 0.3479 0.83080 0.852 0.004 0.040 0.012 0.092
#> GSM153242 3 0.6556 0.49248 0.324 0.024 0.556 0.020 0.076
#> GSM153243 1 0.2951 0.86273 0.880 0.016 0.016 0.004 0.084
#> GSM153244 1 0.1977 0.88522 0.936 0.008 0.024 0.008 0.024
#> GSM153245 1 0.6764 -0.47990 0.432 0.000 0.432 0.056 0.080
#> GSM153246 5 0.5323 -0.70612 0.024 0.004 0.096 0.152 0.724
#> GSM153247 1 0.3623 0.80242 0.828 0.020 0.008 0.008 0.136
#> GSM153248 1 0.1280 0.88906 0.960 0.008 0.000 0.008 0.024
#> GSM153249 1 0.1533 0.88674 0.952 0.004 0.016 0.004 0.024
#> GSM153250 1 0.1087 0.88849 0.968 0.008 0.008 0.000 0.016
#> GSM153251 1 0.6103 0.22347 0.604 0.028 0.304 0.020 0.044
#> GSM153252 1 0.1808 0.87998 0.936 0.004 0.040 0.000 0.020
#> GSM153253 1 0.2853 0.85450 0.888 0.004 0.068 0.008 0.032
#> GSM153254 1 0.2026 0.88860 0.932 0.004 0.032 0.008 0.024
#> GSM153255 1 0.1721 0.88201 0.944 0.004 0.028 0.004 0.020
#> GSM153256 1 0.1121 0.88726 0.968 0.004 0.008 0.004 0.016
#> GSM153257 1 0.1347 0.88590 0.960 0.004 0.020 0.008 0.008
#> GSM153258 1 0.1299 0.88912 0.960 0.012 0.008 0.000 0.020
#> GSM153259 1 0.1364 0.88505 0.952 0.012 0.000 0.000 0.036
#> GSM153260 1 0.5684 0.53385 0.684 0.036 0.028 0.028 0.224
#> GSM153261 1 0.4431 0.78529 0.808 0.040 0.040 0.012 0.100
#> GSM153262 1 0.2386 0.87450 0.912 0.004 0.048 0.004 0.032
#> GSM153263 1 0.1200 0.89086 0.964 0.012 0.016 0.000 0.008
#> GSM153264 1 0.1569 0.88833 0.948 0.008 0.012 0.000 0.032
#> GSM153265 1 0.2816 0.85868 0.892 0.004 0.064 0.012 0.028
#> GSM153266 1 0.1921 0.88498 0.932 0.012 0.012 0.000 0.044
#> GSM153267 1 0.1074 0.88620 0.968 0.004 0.016 0.000 0.012
#> GSM153268 1 0.4821 0.45351 0.660 0.004 0.308 0.008 0.020
#> GSM153269 1 0.1200 0.88737 0.964 0.008 0.012 0.000 0.016
#> GSM153270 1 0.1362 0.89006 0.960 0.008 0.012 0.004 0.016
#> GSM153271 1 0.1095 0.88657 0.968 0.008 0.012 0.000 0.012
#> GSM153272 1 0.1334 0.88850 0.960 0.004 0.012 0.004 0.020
#> GSM153273 1 0.1522 0.88129 0.944 0.012 0.000 0.000 0.044
#> GSM153274 1 0.1334 0.88700 0.960 0.004 0.020 0.004 0.012
#> GSM153275 1 0.1143 0.88667 0.968 0.004 0.008 0.008 0.012
#> GSM153276 1 0.1200 0.88894 0.964 0.008 0.016 0.000 0.012
#> GSM153277 1 0.2388 0.87303 0.912 0.004 0.056 0.008 0.020
#> GSM153278 1 0.2400 0.87910 0.908 0.008 0.008 0.008 0.068
#> GSM153279 1 0.1884 0.88645 0.940 0.008 0.020 0.008 0.024
#> GSM153280 1 0.2411 0.87033 0.912 0.004 0.052 0.008 0.024
#> GSM153281 1 0.2264 0.86713 0.912 0.004 0.060 0.000 0.024
#> GSM153282 1 0.2616 0.86021 0.900 0.004 0.064 0.008 0.024
#> GSM153283 1 0.1059 0.88858 0.968 0.008 0.004 0.000 0.020
#> GSM153284 1 0.1016 0.88793 0.972 0.004 0.008 0.004 0.012
#> GSM153285 1 0.2569 0.86517 0.904 0.004 0.056 0.008 0.028
#> GSM153286 1 0.1278 0.88758 0.960 0.004 0.020 0.000 0.016
#> GSM153287 1 0.1814 0.88112 0.940 0.004 0.028 0.004 0.024
#> GSM153288 1 0.1646 0.88175 0.944 0.004 0.032 0.000 0.020
#> GSM153289 1 0.1913 0.88245 0.932 0.016 0.008 0.000 0.044
#> GSM153290 1 0.2386 0.87249 0.912 0.004 0.048 0.004 0.032
#> GSM153291 1 0.1603 0.88285 0.948 0.004 0.032 0.004 0.012
#> GSM153292 1 0.2071 0.87637 0.928 0.004 0.036 0.004 0.028
#> GSM153293 1 0.1121 0.88691 0.968 0.004 0.008 0.004 0.016
#> GSM153294 1 0.1369 0.88857 0.956 0.008 0.000 0.008 0.028
#> GSM153295 1 0.2331 0.86934 0.908 0.000 0.024 0.004 0.064
#> GSM153054 1 0.3340 0.84742 0.860 0.016 0.028 0.004 0.092
#> GSM153055 1 0.1419 0.89097 0.956 0.012 0.016 0.000 0.016
#> GSM153056 1 0.2388 0.87210 0.904 0.004 0.012 0.004 0.076
#> GSM153057 1 0.3507 0.85236 0.864 0.024 0.036 0.012 0.064
#> GSM153058 1 0.7226 -0.33382 0.472 0.024 0.372 0.088 0.044
#> GSM153059 1 0.4049 0.81979 0.832 0.028 0.044 0.012 0.084
#> GSM153060 5 0.6986 -0.14762 0.400 0.004 0.060 0.084 0.452
#> GSM153061 1 0.6789 -0.00299 0.544 0.004 0.024 0.168 0.260
#> GSM153062 4 0.1074 0.00000 0.004 0.000 0.012 0.968 0.016
#> GSM153063 1 0.6076 0.48570 0.656 0.020 0.208 0.016 0.100
#> GSM153064 1 0.1444 0.88171 0.948 0.012 0.000 0.000 0.040
#> GSM153065 1 0.5841 0.53739 0.688 0.036 0.032 0.040 0.204
#> GSM153066 1 0.6786 0.02502 0.540 0.284 0.012 0.016 0.148
#> GSM153067 1 0.1721 0.88144 0.944 0.004 0.028 0.004 0.020
#> GSM153068 1 0.6051 0.36561 0.620 0.028 0.016 0.052 0.284
#> GSM153069 1 0.1622 0.88302 0.948 0.004 0.028 0.004 0.016
#> GSM153070 1 0.0854 0.88814 0.976 0.008 0.004 0.000 0.012
#> GSM153071 1 0.2387 0.87868 0.908 0.012 0.004 0.008 0.068
#> GSM153072 1 0.2388 0.87824 0.904 0.012 0.004 0.004 0.076
#> GSM153073 1 0.0775 0.88854 0.980 0.004 0.004 0.004 0.008
#> GSM153074 1 0.1538 0.88596 0.952 0.004 0.020 0.004 0.020
#> GSM153075 1 0.1413 0.89123 0.956 0.012 0.012 0.000 0.020
#> GSM153076 1 0.1517 0.88888 0.952 0.004 0.012 0.004 0.028
#> GSM153077 1 0.1925 0.88653 0.936 0.012 0.012 0.004 0.036
#> GSM153078 1 0.2612 0.86879 0.892 0.004 0.016 0.004 0.084
#> GSM153079 1 0.1913 0.88245 0.932 0.016 0.008 0.000 0.044
#> GSM153080 1 0.3842 0.82087 0.836 0.012 0.084 0.008 0.060
#> GSM153081 1 0.1844 0.88642 0.936 0.012 0.012 0.000 0.040
#> GSM153082 1 0.2005 0.88270 0.924 0.016 0.004 0.000 0.056
#> GSM153083 1 0.1757 0.88219 0.936 0.012 0.004 0.000 0.048
#> GSM153084 1 0.4194 0.76548 0.808 0.092 0.012 0.004 0.084
#> GSM153085 1 0.1892 0.88552 0.936 0.012 0.008 0.004 0.040
#> GSM153086 1 0.1970 0.87782 0.924 0.012 0.004 0.000 0.060
#> GSM153087 1 0.1173 0.89157 0.964 0.000 0.012 0.004 0.020
#> GSM153088 1 0.0968 0.88530 0.972 0.004 0.012 0.000 0.012
#> GSM153089 1 0.6624 0.28452 0.608 0.048 0.256 0.028 0.060
#> GSM153090 1 0.1016 0.88584 0.972 0.004 0.008 0.004 0.012
#> GSM153091 1 0.1364 0.88238 0.952 0.012 0.000 0.000 0.036
#> GSM153092 1 0.1087 0.88929 0.968 0.008 0.008 0.000 0.016
#> GSM153093 1 0.1016 0.88585 0.972 0.004 0.012 0.004 0.008
#> GSM153094 1 0.1444 0.88224 0.948 0.012 0.000 0.000 0.040
#> GSM153095 1 0.3258 0.85401 0.864 0.020 0.020 0.004 0.092
#> GSM153096 1 0.1364 0.88299 0.952 0.012 0.000 0.000 0.036
#> GSM153097 1 0.1597 0.88028 0.940 0.012 0.000 0.000 0.048
#> GSM153098 1 0.1441 0.89050 0.956 0.008 0.004 0.008 0.024
#> GSM153099 1 0.0960 0.88864 0.972 0.008 0.004 0.000 0.016
#> GSM153100 1 0.0960 0.88726 0.972 0.008 0.004 0.000 0.016
#> GSM153101 1 0.2457 0.87968 0.908 0.020 0.008 0.004 0.060
#> GSM153102 1 0.1836 0.88246 0.936 0.016 0.008 0.000 0.040
#> GSM153103 1 0.1996 0.88068 0.928 0.012 0.012 0.000 0.048
#> GSM153104 1 0.1996 0.87879 0.932 0.004 0.040 0.008 0.016
#> GSM153106 1 0.1913 0.88245 0.932 0.016 0.008 0.000 0.044
#> GSM153107 1 0.1913 0.88245 0.932 0.016 0.008 0.000 0.044
#> GSM153108 1 0.1533 0.88838 0.952 0.004 0.016 0.004 0.024
#> GSM153109 1 0.1836 0.88246 0.936 0.016 0.008 0.000 0.040
#> GSM153110 1 0.1408 0.88319 0.948 0.008 0.000 0.000 0.044
#> GSM153111 1 0.1830 0.88054 0.932 0.012 0.004 0.000 0.052
#> GSM153112 1 0.1444 0.88171 0.948 0.012 0.000 0.000 0.040
#> GSM153113 1 0.2457 0.87842 0.908 0.020 0.008 0.004 0.060
#> GSM153114 1 0.1913 0.88245 0.932 0.016 0.008 0.000 0.044
#> GSM187532 2 0.0290 0.98861 0.008 0.992 0.000 0.000 0.000
#> GSM187533 2 0.0703 0.97459 0.024 0.976 0.000 0.000 0.000
#> GSM187534 2 0.0703 0.97459 0.024 0.976 0.000 0.000 0.000
#> GSM187535 1 0.3635 0.77625 0.824 0.132 0.008 0.000 0.036
#> GSM152906 2 0.0510 0.98812 0.016 0.984 0.000 0.000 0.000
#> GSM152907 2 0.0703 0.97735 0.024 0.976 0.000 0.000 0.000
#> GSM152908 2 0.0290 0.98861 0.008 0.992 0.000 0.000 0.000
#> GSM152909 2 0.0290 0.98861 0.008 0.992 0.000 0.000 0.000
#> GSM152910 2 0.0290 0.98861 0.008 0.992 0.000 0.000 0.000
#> GSM152911 2 0.0404 0.99081 0.012 0.988 0.000 0.000 0.000
#> GSM152912 2 0.0290 0.98861 0.008 0.992 0.000 0.000 0.000
#> GSM152913 2 0.0290 0.98861 0.008 0.992 0.000 0.000 0.000
#> GSM152914 2 0.0404 0.99081 0.012 0.988 0.000 0.000 0.000
#> GSM152915 2 0.0404 0.99081 0.012 0.988 0.000 0.000 0.000
#> GSM152916 2 0.0404 0.99049 0.012 0.988 0.000 0.000 0.000
#> GSM152917 2 0.0404 0.99081 0.012 0.988 0.000 0.000 0.000
#> GSM152918 2 0.0404 0.99081 0.012 0.988 0.000 0.000 0.000
#> GSM152919 2 0.0404 0.99081 0.012 0.988 0.000 0.000 0.000
#> GSM152920 2 0.0290 0.98861 0.008 0.992 0.000 0.000 0.000
#> GSM152921 2 0.0290 0.98861 0.008 0.992 0.000 0.000 0.000
#> GSM152922 2 0.0290 0.98861 0.008 0.992 0.000 0.000 0.000
#> GSM152923 2 0.0510 0.98812 0.016 0.984 0.000 0.000 0.000
#> GSM152924 2 0.0404 0.99049 0.012 0.988 0.000 0.000 0.000
#> GSM152925 2 0.0404 0.99049 0.012 0.988 0.000 0.000 0.000
#> GSM152926 2 0.0703 0.97735 0.024 0.976 0.000 0.000 0.000
#> GSM152927 2 0.0404 0.99049 0.012 0.988 0.000 0.000 0.000
#> GSM152928 2 0.0510 0.98710 0.016 0.984 0.000 0.000 0.000
#> GSM152929 2 0.0510 0.98812 0.016 0.984 0.000 0.000 0.000
#> GSM152930 2 0.0510 0.98812 0.016 0.984 0.000 0.000 0.000
cbind(get_classes(res, k = 6), get_membership(res, k = 6))
#> class entropy silhouette p1 p2 p3 p4 p5 p6
#> GSM152839 1 0.2468 0.8720 0.880 0.000 0.008 0.016 0.000 0.096
#> GSM152840 4 0.3451 0.5529 0.156 0.000 0.012 0.804 0.000 0.028
#> GSM152841 1 0.3867 0.7015 0.748 0.000 0.000 0.200 0.000 0.052
#> GSM152842 1 0.6406 -0.0488 0.460 0.000 0.240 0.012 0.008 0.280
#> GSM152843 1 0.3988 0.7919 0.776 0.000 0.060 0.016 0.000 0.148
#> GSM152844 4 0.2020 0.5537 0.096 0.000 0.008 0.896 0.000 0.000
#> GSM152845 4 0.5985 0.1189 0.024 0.072 0.036 0.672 0.032 0.164
#> GSM152846 4 0.4388 0.3465 0.048 0.016 0.024 0.796 0.020 0.096
#> GSM152847 1 0.4864 0.5185 0.624 0.000 0.056 0.012 0.000 0.308
#> GSM152848 1 0.2269 0.8715 0.896 0.000 0.012 0.012 0.000 0.080
#> GSM152849 1 0.3764 0.7874 0.784 0.000 0.044 0.012 0.000 0.160
#> GSM152850 1 0.2793 0.8477 0.856 0.000 0.028 0.000 0.004 0.112
#> GSM152851 1 0.2796 0.8466 0.872 0.004 0.004 0.064 0.000 0.056
#> GSM152852 4 0.3377 0.5538 0.104 0.000 0.020 0.836 0.004 0.036
#> GSM152853 4 0.2051 0.5553 0.096 0.000 0.004 0.896 0.000 0.004
#> GSM152854 4 0.5957 0.4224 0.260 0.000 0.040 0.592 0.012 0.096
#> GSM152855 1 0.2356 0.8625 0.884 0.008 0.004 0.004 0.000 0.100
#> GSM153238 1 0.5044 0.5614 0.640 0.020 0.036 0.008 0.004 0.292
#> GSM153239 4 0.4932 0.4581 0.240 0.000 0.012 0.660 0.000 0.088
#> GSM153240 1 0.1225 0.8731 0.952 0.000 0.000 0.012 0.000 0.036
#> GSM153241 1 0.3900 0.8093 0.808 0.000 0.032 0.044 0.008 0.108
#> GSM153242 4 0.6411 0.4148 0.232 0.004 0.040 0.564 0.012 0.148
#> GSM153243 1 0.3460 0.8394 0.824 0.004 0.028 0.012 0.004 0.128
#> GSM153244 1 0.2010 0.8673 0.920 0.004 0.004 0.036 0.000 0.036
#> GSM153245 4 0.6953 0.1774 0.376 0.000 0.048 0.428 0.040 0.108
#> GSM153246 3 0.3306 0.0000 0.004 0.000 0.828 0.004 0.120 0.044
#> GSM153247 1 0.3896 0.7700 0.768 0.012 0.024 0.008 0.000 0.188
#> GSM153248 1 0.1901 0.8731 0.912 0.004 0.000 0.008 0.000 0.076
#> GSM153249 1 0.1092 0.8697 0.960 0.000 0.000 0.020 0.000 0.020
#> GSM153250 1 0.1036 0.8724 0.964 0.000 0.008 0.004 0.000 0.024
#> GSM153251 1 0.6545 0.0684 0.524 0.016 0.020 0.296 0.016 0.128
#> GSM153252 1 0.1616 0.8650 0.932 0.000 0.000 0.048 0.000 0.020
#> GSM153253 1 0.2672 0.8338 0.868 0.000 0.000 0.080 0.000 0.052
#> GSM153254 1 0.2138 0.8718 0.908 0.004 0.000 0.036 0.000 0.052
#> GSM153255 1 0.1575 0.8648 0.936 0.000 0.000 0.032 0.000 0.032
#> GSM153256 1 0.1151 0.8702 0.956 0.000 0.000 0.012 0.000 0.032
#> GSM153257 1 0.1257 0.8690 0.952 0.000 0.000 0.028 0.000 0.020
#> GSM153258 1 0.1410 0.8742 0.944 0.004 0.008 0.000 0.000 0.044
#> GSM153259 1 0.1812 0.8658 0.912 0.008 0.000 0.000 0.000 0.080
#> GSM153260 1 0.5565 0.2887 0.540 0.004 0.088 0.008 0.004 0.356
#> GSM153261 1 0.4516 0.7668 0.756 0.024 0.024 0.028 0.004 0.164
#> GSM153262 1 0.2401 0.8529 0.892 0.000 0.004 0.060 0.000 0.044
#> GSM153263 1 0.1598 0.8776 0.940 0.004 0.008 0.008 0.000 0.040
#> GSM153264 1 0.1888 0.8747 0.916 0.004 0.012 0.000 0.000 0.068
#> GSM153265 1 0.2672 0.8392 0.868 0.000 0.000 0.080 0.000 0.052
#> GSM153266 1 0.2144 0.8722 0.896 0.004 0.004 0.004 0.000 0.092
#> GSM153267 1 0.1092 0.8687 0.960 0.000 0.000 0.020 0.000 0.020
#> GSM153268 1 0.4563 0.4327 0.628 0.000 0.000 0.316 0.000 0.056
#> GSM153269 1 0.1036 0.8727 0.964 0.000 0.004 0.008 0.000 0.024
#> GSM153270 1 0.1464 0.8744 0.944 0.004 0.000 0.016 0.000 0.036
#> GSM153271 1 0.1251 0.8704 0.956 0.000 0.008 0.012 0.000 0.024
#> GSM153272 1 0.1245 0.8710 0.952 0.000 0.000 0.016 0.000 0.032
#> GSM153273 1 0.1806 0.8628 0.908 0.004 0.000 0.000 0.000 0.088
#> GSM153274 1 0.1257 0.8716 0.952 0.000 0.000 0.020 0.000 0.028
#> GSM153275 1 0.1074 0.8692 0.960 0.000 0.000 0.012 0.000 0.028
#> GSM153276 1 0.1053 0.8724 0.964 0.000 0.004 0.012 0.000 0.020
#> GSM153277 1 0.2318 0.8550 0.892 0.000 0.000 0.064 0.000 0.044
#> GSM153278 1 0.2923 0.8604 0.856 0.000 0.024 0.004 0.008 0.108
#> GSM153279 1 0.1788 0.8679 0.928 0.004 0.000 0.028 0.000 0.040
#> GSM153280 1 0.2250 0.8501 0.896 0.000 0.000 0.064 0.000 0.040
#> GSM153281 1 0.2294 0.8473 0.892 0.000 0.000 0.072 0.000 0.036
#> GSM153282 1 0.2488 0.8393 0.880 0.000 0.000 0.076 0.000 0.044
#> GSM153283 1 0.1477 0.8748 0.940 0.004 0.008 0.000 0.000 0.048
#> GSM153284 1 0.1194 0.8724 0.956 0.000 0.004 0.008 0.000 0.032
#> GSM153285 1 0.2506 0.8426 0.880 0.000 0.000 0.068 0.000 0.052
#> GSM153286 1 0.1485 0.8710 0.944 0.000 0.004 0.024 0.000 0.028
#> GSM153287 1 0.1572 0.8645 0.936 0.000 0.000 0.036 0.000 0.028
#> GSM153288 1 0.1644 0.8651 0.932 0.000 0.000 0.040 0.000 0.028
#> GSM153289 1 0.2356 0.8625 0.884 0.008 0.004 0.004 0.000 0.100
#> GSM153290 1 0.2407 0.8516 0.892 0.000 0.004 0.056 0.000 0.048
#> GSM153291 1 0.1636 0.8688 0.936 0.000 0.004 0.036 0.000 0.024
#> GSM153292 1 0.1713 0.8617 0.928 0.000 0.000 0.044 0.000 0.028
#> GSM153293 1 0.1168 0.8711 0.956 0.000 0.000 0.016 0.000 0.028
#> GSM153294 1 0.2009 0.8715 0.904 0.004 0.000 0.008 0.000 0.084
#> GSM153295 1 0.2840 0.8514 0.868 0.000 0.016 0.020 0.004 0.092
#> GSM153054 1 0.3534 0.8308 0.816 0.008 0.012 0.020 0.004 0.140
#> GSM153055 1 0.1476 0.8758 0.948 0.004 0.008 0.012 0.000 0.028
#> GSM153056 1 0.3067 0.8507 0.852 0.000 0.024 0.016 0.004 0.104
#> GSM153057 1 0.3612 0.8373 0.824 0.012 0.004 0.040 0.008 0.112
#> GSM153058 1 0.7253 -0.4597 0.384 0.004 0.012 0.376 0.100 0.124
#> GSM153059 1 0.4290 0.8011 0.780 0.016 0.012 0.048 0.008 0.136
#> GSM153060 6 0.7447 0.0000 0.128 0.000 0.288 0.048 0.084 0.452
#> GSM153061 1 0.6933 -0.3568 0.388 0.000 0.088 0.000 0.160 0.364
#> GSM153062 5 0.0622 0.0000 0.000 0.000 0.008 0.000 0.980 0.012
#> GSM153063 1 0.6254 0.3938 0.588 0.004 0.028 0.188 0.016 0.176
#> GSM153064 1 0.1700 0.8650 0.916 0.004 0.000 0.000 0.000 0.080
#> GSM153065 1 0.5700 0.2955 0.548 0.004 0.068 0.012 0.016 0.352
#> GSM153066 1 0.6713 -0.1232 0.440 0.252 0.020 0.004 0.008 0.276
#> GSM153067 1 0.1498 0.8648 0.940 0.000 0.000 0.032 0.000 0.028
#> GSM153068 1 0.6229 0.1784 0.516 0.004 0.112 0.004 0.036 0.328
#> GSM153069 1 0.1418 0.8664 0.944 0.000 0.000 0.032 0.000 0.024
#> GSM153070 1 0.1049 0.8728 0.960 0.000 0.008 0.000 0.000 0.032
#> GSM153071 1 0.2543 0.8603 0.868 0.004 0.008 0.000 0.004 0.116
#> GSM153072 1 0.2587 0.8625 0.864 0.004 0.008 0.000 0.004 0.120
#> GSM153073 1 0.1138 0.8738 0.960 0.000 0.004 0.012 0.000 0.024
#> GSM153074 1 0.1092 0.8688 0.960 0.000 0.000 0.020 0.000 0.020
#> GSM153075 1 0.1476 0.8762 0.948 0.004 0.008 0.012 0.000 0.028
#> GSM153076 1 0.1605 0.8739 0.936 0.000 0.004 0.016 0.000 0.044
#> GSM153077 1 0.2113 0.8715 0.896 0.004 0.008 0.000 0.000 0.092
#> GSM153078 1 0.3281 0.8449 0.828 0.000 0.036 0.012 0.000 0.124
#> GSM153079 1 0.2356 0.8625 0.884 0.008 0.004 0.004 0.000 0.100
#> GSM153080 1 0.3905 0.8151 0.792 0.008 0.004 0.088 0.000 0.108
#> GSM153081 1 0.2504 0.8667 0.876 0.004 0.012 0.004 0.000 0.104
#> GSM153082 1 0.2163 0.8655 0.892 0.008 0.000 0.004 0.000 0.096
#> GSM153083 1 0.2356 0.8601 0.884 0.004 0.008 0.004 0.000 0.100
#> GSM153084 1 0.3946 0.7612 0.768 0.076 0.000 0.004 0.000 0.152
#> GSM153085 1 0.2001 0.8732 0.900 0.004 0.000 0.004 0.000 0.092
#> GSM153086 1 0.2386 0.8572 0.876 0.004 0.004 0.004 0.000 0.112
#> GSM153087 1 0.1320 0.8763 0.948 0.000 0.000 0.016 0.000 0.036
#> GSM153088 1 0.1346 0.8693 0.952 0.000 0.008 0.016 0.000 0.024
#> GSM153089 1 0.6909 0.1505 0.536 0.028 0.024 0.220 0.020 0.172
#> GSM153090 1 0.1138 0.8694 0.960 0.000 0.004 0.012 0.000 0.024
#> GSM153091 1 0.1531 0.8678 0.928 0.004 0.000 0.000 0.000 0.068
#> GSM153092 1 0.1413 0.8746 0.948 0.004 0.008 0.004 0.000 0.036
#> GSM153093 1 0.1003 0.8681 0.964 0.000 0.000 0.020 0.000 0.016
#> GSM153094 1 0.1753 0.8644 0.912 0.004 0.000 0.000 0.000 0.084
#> GSM153095 1 0.3185 0.8416 0.836 0.008 0.016 0.012 0.000 0.128
#> GSM153096 1 0.1949 0.8643 0.904 0.004 0.004 0.000 0.000 0.088
#> GSM153097 1 0.1908 0.8604 0.900 0.004 0.000 0.000 0.000 0.096
#> GSM153098 1 0.1410 0.8769 0.944 0.004 0.000 0.008 0.000 0.044
#> GSM153099 1 0.0790 0.8744 0.968 0.000 0.000 0.000 0.000 0.032
#> GSM153100 1 0.1750 0.8732 0.928 0.004 0.004 0.008 0.000 0.056
#> GSM153101 1 0.2261 0.8649 0.884 0.008 0.000 0.004 0.000 0.104
#> GSM153102 1 0.2306 0.8613 0.888 0.008 0.004 0.004 0.000 0.096
#> GSM153103 1 0.2476 0.8575 0.868 0.004 0.004 0.004 0.000 0.120
#> GSM153104 1 0.1995 0.8576 0.912 0.000 0.000 0.052 0.000 0.036
#> GSM153106 1 0.2356 0.8625 0.884 0.008 0.004 0.004 0.000 0.100
#> GSM153107 1 0.2356 0.8625 0.884 0.008 0.004 0.004 0.000 0.100
#> GSM153108 1 0.1592 0.8740 0.940 0.000 0.008 0.020 0.000 0.032
#> GSM153109 1 0.2306 0.8613 0.888 0.008 0.004 0.004 0.000 0.096
#> GSM153110 1 0.1753 0.8648 0.912 0.004 0.000 0.000 0.000 0.084
#> GSM153111 1 0.2356 0.8588 0.884 0.004 0.008 0.004 0.000 0.100
#> GSM153112 1 0.1700 0.8650 0.916 0.004 0.000 0.000 0.000 0.080
#> GSM153113 1 0.2308 0.8618 0.880 0.008 0.000 0.004 0.000 0.108
#> GSM153114 1 0.2356 0.8625 0.884 0.008 0.004 0.004 0.000 0.100
#> GSM187532 2 0.0000 0.9907 0.000 1.000 0.000 0.000 0.000 0.000
#> GSM187533 2 0.0820 0.9707 0.012 0.972 0.000 0.000 0.000 0.016
#> GSM187534 2 0.0820 0.9707 0.012 0.972 0.000 0.000 0.000 0.016
#> GSM187535 1 0.3622 0.7904 0.800 0.124 0.000 0.004 0.000 0.072
#> GSM152906 2 0.0291 0.9901 0.004 0.992 0.000 0.000 0.000 0.004
#> GSM152907 2 0.0508 0.9800 0.012 0.984 0.000 0.000 0.000 0.004
#> GSM152908 2 0.0000 0.9907 0.000 1.000 0.000 0.000 0.000 0.000
#> GSM152909 2 0.0146 0.9895 0.000 0.996 0.000 0.000 0.000 0.004
#> GSM152910 2 0.0000 0.9907 0.000 1.000 0.000 0.000 0.000 0.000
#> GSM152911 2 0.0146 0.9908 0.000 0.996 0.000 0.000 0.000 0.004
#> GSM152912 2 0.0000 0.9907 0.000 1.000 0.000 0.000 0.000 0.000
#> GSM152913 2 0.0146 0.9892 0.000 0.996 0.000 0.000 0.000 0.004
#> GSM152914 2 0.0146 0.9908 0.000 0.996 0.000 0.000 0.000 0.004
#> GSM152915 2 0.0146 0.9908 0.000 0.996 0.000 0.000 0.000 0.004
#> GSM152916 2 0.0146 0.9905 0.004 0.996 0.000 0.000 0.000 0.000
#> GSM152917 2 0.0146 0.9908 0.000 0.996 0.000 0.000 0.000 0.004
#> GSM152918 2 0.0146 0.9908 0.000 0.996 0.000 0.000 0.000 0.004
#> GSM152919 2 0.0146 0.9908 0.000 0.996 0.000 0.000 0.000 0.004
#> GSM152920 2 0.0000 0.9907 0.000 1.000 0.000 0.000 0.000 0.000
#> GSM152921 2 0.0000 0.9907 0.000 1.000 0.000 0.000 0.000 0.000
#> GSM152922 2 0.0000 0.9907 0.000 1.000 0.000 0.000 0.000 0.000
#> GSM152923 2 0.0291 0.9901 0.004 0.992 0.000 0.000 0.000 0.004
#> GSM152924 2 0.0146 0.9905 0.004 0.996 0.000 0.000 0.000 0.000
#> GSM152925 2 0.0146 0.9905 0.004 0.996 0.000 0.000 0.000 0.000
#> GSM152926 2 0.0508 0.9800 0.012 0.984 0.000 0.000 0.000 0.004
#> GSM152927 2 0.0146 0.9905 0.004 0.996 0.000 0.000 0.000 0.000
#> GSM152928 2 0.0260 0.9854 0.008 0.992 0.000 0.000 0.000 0.000
#> GSM152929 2 0.0291 0.9901 0.004 0.992 0.000 0.000 0.000 0.004
#> GSM152930 2 0.0291 0.9901 0.004 0.992 0.000 0.000 0.000 0.004
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)
#> Error in mat[ceiling(1:nr/h_ratio), ceiling(1:nc/w_ratio), drop = FALSE]: subscript out of bounds
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 tissue(p) k
#> SD:hclust 163 8.88e-31 2
#> SD:hclust 156 2.04e-29 3
#> SD:hclust 151 5.36e-37 4
#> SD:hclust 149 2.80e-35 5
#> SD:hclust 144 2.47e-33 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 12013 rows and 164 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 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 0.518 0.904 0.919 0.3178 0.699 0.699
#> 3 3 0.958 0.936 0.956 0.7764 0.731 0.617
#> 4 4 0.617 0.624 0.759 0.2198 0.787 0.538
#> 5 5 0.630 0.733 0.815 0.0860 0.884 0.631
#> 6 6 0.709 0.719 0.821 0.0409 0.967 0.867
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
#> GSM152839 1 0.7056 0.823 0.808 0.192
#> GSM152840 1 0.7299 0.816 0.796 0.204
#> GSM152841 1 0.0000 0.928 1.000 0.000
#> GSM152842 1 0.7299 0.816 0.796 0.204
#> GSM152843 1 0.7299 0.816 0.796 0.204
#> GSM152844 1 0.7299 0.816 0.796 0.204
#> GSM152845 1 0.7299 0.816 0.796 0.204
#> GSM152846 1 0.7299 0.816 0.796 0.204
#> GSM152847 1 0.7299 0.816 0.796 0.204
#> GSM152848 1 0.0000 0.928 1.000 0.000
#> GSM152849 1 0.7299 0.816 0.796 0.204
#> GSM152850 1 0.7299 0.816 0.796 0.204
#> GSM152851 1 0.4562 0.878 0.904 0.096
#> GSM152852 1 0.7299 0.816 0.796 0.204
#> GSM152853 1 0.7299 0.816 0.796 0.204
#> GSM152854 1 0.7299 0.816 0.796 0.204
#> GSM152855 1 0.0000 0.928 1.000 0.000
#> GSM153238 1 0.7299 0.816 0.796 0.204
#> GSM153239 1 0.7299 0.816 0.796 0.204
#> GSM153240 1 0.0000 0.928 1.000 0.000
#> GSM153241 1 0.7299 0.816 0.796 0.204
#> GSM153242 1 0.7299 0.816 0.796 0.204
#> GSM153243 1 0.7299 0.816 0.796 0.204
#> GSM153244 1 0.0000 0.928 1.000 0.000
#> GSM153245 1 0.7299 0.816 0.796 0.204
#> GSM153246 1 0.7299 0.816 0.796 0.204
#> GSM153247 1 0.6887 0.828 0.816 0.184
#> GSM153248 1 0.0000 0.928 1.000 0.000
#> GSM153249 1 0.0000 0.928 1.000 0.000
#> GSM153250 1 0.0000 0.928 1.000 0.000
#> GSM153251 1 0.7299 0.816 0.796 0.204
#> GSM153252 1 0.0000 0.928 1.000 0.000
#> GSM153253 1 0.0000 0.928 1.000 0.000
#> GSM153254 1 0.3114 0.899 0.944 0.056
#> GSM153255 1 0.0000 0.928 1.000 0.000
#> GSM153256 1 0.0000 0.928 1.000 0.000
#> GSM153257 1 0.0000 0.928 1.000 0.000
#> GSM153258 1 0.0000 0.928 1.000 0.000
#> GSM153259 1 0.0000 0.928 1.000 0.000
#> GSM153260 1 0.7299 0.816 0.796 0.204
#> GSM153261 1 0.7299 0.816 0.796 0.204
#> GSM153262 1 0.0000 0.928 1.000 0.000
#> GSM153263 1 0.0000 0.928 1.000 0.000
#> GSM153264 1 0.0000 0.928 1.000 0.000
#> GSM153265 1 0.0000 0.928 1.000 0.000
#> GSM153266 1 0.0000 0.928 1.000 0.000
#> GSM153267 1 0.0000 0.928 1.000 0.000
#> GSM153268 1 0.6343 0.842 0.840 0.160
#> GSM153269 1 0.0000 0.928 1.000 0.000
#> GSM153270 1 0.0000 0.928 1.000 0.000
#> GSM153271 1 0.0000 0.928 1.000 0.000
#> GSM153272 1 0.0000 0.928 1.000 0.000
#> GSM153273 1 0.0000 0.928 1.000 0.000
#> GSM153274 1 0.0000 0.928 1.000 0.000
#> GSM153275 1 0.0000 0.928 1.000 0.000
#> GSM153276 1 0.0000 0.928 1.000 0.000
#> GSM153277 1 0.0000 0.928 1.000 0.000
#> GSM153278 1 0.7299 0.816 0.796 0.204
#> GSM153279 1 0.0376 0.927 0.996 0.004
#> GSM153280 1 0.0000 0.928 1.000 0.000
#> GSM153281 1 0.0000 0.928 1.000 0.000
#> GSM153282 1 0.0376 0.927 0.996 0.004
#> GSM153283 1 0.0000 0.928 1.000 0.000
#> GSM153284 1 0.0000 0.928 1.000 0.000
#> GSM153285 1 0.0000 0.928 1.000 0.000
#> GSM153286 1 0.0000 0.928 1.000 0.000
#> GSM153287 1 0.0000 0.928 1.000 0.000
#> GSM153288 1 0.0000 0.928 1.000 0.000
#> GSM153289 1 0.0000 0.928 1.000 0.000
#> GSM153290 1 0.0000 0.928 1.000 0.000
#> GSM153291 1 0.0000 0.928 1.000 0.000
#> GSM153292 1 0.0000 0.928 1.000 0.000
#> GSM153293 1 0.0000 0.928 1.000 0.000
#> GSM153294 1 0.0000 0.928 1.000 0.000
#> GSM153295 1 0.0376 0.927 0.996 0.004
#> GSM153054 1 0.0000 0.928 1.000 0.000
#> GSM153055 1 0.0000 0.928 1.000 0.000
#> GSM153056 1 0.7299 0.816 0.796 0.204
#> GSM153057 1 0.6801 0.830 0.820 0.180
#> GSM153058 1 0.7299 0.816 0.796 0.204
#> GSM153059 1 0.7139 0.820 0.804 0.196
#> GSM153060 1 0.7299 0.816 0.796 0.204
#> GSM153061 1 0.7299 0.816 0.796 0.204
#> GSM153062 1 0.7299 0.816 0.796 0.204
#> GSM153063 1 0.7299 0.816 0.796 0.204
#> GSM153064 1 0.0000 0.928 1.000 0.000
#> GSM153065 1 0.7299 0.816 0.796 0.204
#> GSM153066 2 0.5946 0.778 0.144 0.856
#> GSM153067 1 0.0000 0.928 1.000 0.000
#> GSM153068 1 0.7299 0.816 0.796 0.204
#> GSM153069 1 0.0000 0.928 1.000 0.000
#> GSM153070 1 0.0000 0.928 1.000 0.000
#> GSM153071 1 0.0376 0.927 0.996 0.004
#> GSM153072 1 0.0000 0.928 1.000 0.000
#> GSM153073 1 0.0000 0.928 1.000 0.000
#> GSM153074 1 0.0000 0.928 1.000 0.000
#> GSM153075 1 0.0000 0.928 1.000 0.000
#> GSM153076 1 0.0000 0.928 1.000 0.000
#> GSM153077 1 0.0000 0.928 1.000 0.000
#> GSM153078 1 0.1184 0.921 0.984 0.016
#> GSM153079 1 0.0000 0.928 1.000 0.000
#> GSM153080 1 0.7299 0.816 0.796 0.204
#> GSM153081 1 0.0000 0.928 1.000 0.000
#> GSM153082 1 0.0000 0.928 1.000 0.000
#> GSM153083 1 0.0000 0.928 1.000 0.000
#> GSM153084 1 0.0000 0.928 1.000 0.000
#> GSM153085 1 0.0000 0.928 1.000 0.000
#> GSM153086 1 0.0000 0.928 1.000 0.000
#> GSM153087 1 0.0000 0.928 1.000 0.000
#> GSM153088 1 0.0000 0.928 1.000 0.000
#> GSM153089 1 0.7299 0.816 0.796 0.204
#> GSM153090 1 0.0000 0.928 1.000 0.000
#> GSM153091 1 0.0000 0.928 1.000 0.000
#> GSM153092 1 0.0000 0.928 1.000 0.000
#> GSM153093 1 0.0000 0.928 1.000 0.000
#> GSM153094 1 0.0000 0.928 1.000 0.000
#> GSM153095 1 0.0000 0.928 1.000 0.000
#> GSM153096 1 0.0000 0.928 1.000 0.000
#> GSM153097 1 0.0000 0.928 1.000 0.000
#> GSM153098 1 0.0000 0.928 1.000 0.000
#> GSM153099 1 0.0000 0.928 1.000 0.000
#> GSM153100 1 0.0000 0.928 1.000 0.000
#> GSM153101 1 0.0376 0.927 0.996 0.004
#> GSM153102 1 0.0000 0.928 1.000 0.000
#> GSM153103 1 0.0000 0.928 1.000 0.000
#> GSM153104 1 0.0000 0.928 1.000 0.000
#> GSM153106 1 0.0000 0.928 1.000 0.000
#> GSM153107 1 0.0000 0.928 1.000 0.000
#> GSM153108 1 0.0000 0.928 1.000 0.000
#> GSM153109 1 0.0000 0.928 1.000 0.000
#> GSM153110 1 0.0000 0.928 1.000 0.000
#> GSM153111 1 0.0000 0.928 1.000 0.000
#> GSM153112 1 0.0000 0.928 1.000 0.000
#> GSM153113 1 0.0000 0.928 1.000 0.000
#> GSM153114 1 0.0000 0.928 1.000 0.000
#> GSM187532 2 0.0376 0.789 0.004 0.996
#> GSM187533 2 0.7299 0.964 0.204 0.796
#> GSM187534 2 0.7299 0.964 0.204 0.796
#> GSM187535 2 0.7299 0.964 0.204 0.796
#> GSM152906 2 0.7299 0.964 0.204 0.796
#> GSM152907 2 0.7299 0.964 0.204 0.796
#> GSM152908 2 0.7299 0.964 0.204 0.796
#> GSM152909 2 0.1843 0.814 0.028 0.972
#> GSM152910 2 0.5178 0.897 0.116 0.884
#> GSM152911 2 0.7299 0.964 0.204 0.796
#> GSM152912 2 0.7299 0.964 0.204 0.796
#> GSM152913 2 0.4562 0.879 0.096 0.904
#> GSM152914 2 0.7299 0.964 0.204 0.796
#> GSM152915 2 0.7299 0.964 0.204 0.796
#> GSM152916 2 0.7299 0.964 0.204 0.796
#> GSM152917 2 0.7299 0.964 0.204 0.796
#> GSM152918 2 0.7299 0.964 0.204 0.796
#> GSM152919 2 0.7299 0.964 0.204 0.796
#> GSM152920 2 0.7299 0.964 0.204 0.796
#> GSM152921 2 0.7299 0.964 0.204 0.796
#> GSM152922 2 0.7219 0.962 0.200 0.800
#> GSM152923 2 0.7299 0.964 0.204 0.796
#> GSM152924 2 0.7299 0.964 0.204 0.796
#> GSM152925 2 0.7299 0.964 0.204 0.796
#> GSM152926 2 0.7299 0.964 0.204 0.796
#> GSM152927 2 0.5408 0.903 0.124 0.876
#> GSM152928 2 0.7299 0.964 0.204 0.796
#> GSM152929 2 0.7299 0.964 0.204 0.796
#> GSM152930 2 0.7299 0.964 0.204 0.796
cbind(get_classes(res, k = 3), get_membership(res, k = 3))
#> class entropy silhouette p1 p2 p3
#> GSM152839 1 0.6062 0.403 0.616 0.000 0.384
#> GSM152840 3 0.2165 0.936 0.064 0.000 0.936
#> GSM152841 1 0.1031 0.952 0.976 0.000 0.024
#> GSM152842 3 0.1411 0.944 0.036 0.000 0.964
#> GSM152843 3 0.1289 0.945 0.032 0.000 0.968
#> GSM152844 3 0.2165 0.936 0.064 0.000 0.936
#> GSM152845 3 0.1289 0.945 0.032 0.000 0.968
#> GSM152846 3 0.2165 0.936 0.064 0.000 0.936
#> GSM152847 3 0.1411 0.944 0.036 0.000 0.964
#> GSM152848 1 0.1289 0.959 0.968 0.000 0.032
#> GSM152849 3 0.1411 0.944 0.036 0.000 0.964
#> GSM152850 3 0.3267 0.878 0.116 0.000 0.884
#> GSM152851 1 0.5465 0.592 0.712 0.000 0.288
#> GSM152852 3 0.2165 0.936 0.064 0.000 0.936
#> GSM152853 3 0.2165 0.936 0.064 0.000 0.936
#> GSM152854 3 0.2165 0.936 0.064 0.000 0.936
#> GSM152855 1 0.0237 0.959 0.996 0.000 0.004
#> GSM153238 3 0.2261 0.925 0.068 0.000 0.932
#> GSM153239 3 0.2261 0.934 0.068 0.000 0.932
#> GSM153240 1 0.0424 0.958 0.992 0.000 0.008
#> GSM153241 3 0.1289 0.945 0.032 0.000 0.968
#> GSM153242 3 0.2165 0.936 0.064 0.000 0.936
#> GSM153243 3 0.1753 0.938 0.048 0.000 0.952
#> GSM153244 1 0.1411 0.946 0.964 0.000 0.036
#> GSM153245 3 0.2165 0.936 0.064 0.000 0.936
#> GSM153246 3 0.1289 0.945 0.032 0.000 0.968
#> GSM153247 3 0.4796 0.742 0.220 0.000 0.780
#> GSM153248 1 0.1289 0.959 0.968 0.000 0.032
#> GSM153249 1 0.0424 0.958 0.992 0.000 0.008
#> GSM153250 1 0.1163 0.960 0.972 0.000 0.028
#> GSM153251 3 0.2066 0.938 0.060 0.000 0.940
#> GSM153252 1 0.0424 0.958 0.992 0.000 0.008
#> GSM153253 1 0.1289 0.948 0.968 0.000 0.032
#> GSM153254 1 0.4887 0.727 0.772 0.000 0.228
#> GSM153255 1 0.0424 0.958 0.992 0.000 0.008
#> GSM153256 1 0.0237 0.959 0.996 0.000 0.004
#> GSM153257 1 0.0424 0.958 0.992 0.000 0.008
#> GSM153258 1 0.1289 0.959 0.968 0.000 0.032
#> GSM153259 1 0.1289 0.959 0.968 0.000 0.032
#> GSM153260 3 0.1753 0.938 0.048 0.000 0.952
#> GSM153261 3 0.1529 0.942 0.040 0.000 0.960
#> GSM153262 1 0.1031 0.952 0.976 0.000 0.024
#> GSM153263 1 0.1289 0.959 0.968 0.000 0.032
#> GSM153264 1 0.1289 0.959 0.968 0.000 0.032
#> GSM153265 1 0.1163 0.950 0.972 0.000 0.028
#> GSM153266 1 0.1289 0.959 0.968 0.000 0.032
#> GSM153267 1 0.0424 0.960 0.992 0.000 0.008
#> GSM153268 1 0.5733 0.509 0.676 0.000 0.324
#> GSM153269 1 0.0592 0.960 0.988 0.000 0.012
#> GSM153270 1 0.0592 0.959 0.988 0.000 0.012
#> GSM153271 1 0.0747 0.960 0.984 0.000 0.016
#> GSM153272 1 0.0424 0.958 0.992 0.000 0.008
#> GSM153273 1 0.1289 0.959 0.968 0.000 0.032
#> GSM153274 1 0.0592 0.960 0.988 0.000 0.012
#> GSM153275 1 0.0592 0.959 0.988 0.000 0.012
#> GSM153276 1 0.0747 0.960 0.984 0.000 0.016
#> GSM153277 1 0.1163 0.950 0.972 0.000 0.028
#> GSM153278 3 0.1964 0.935 0.056 0.000 0.944
#> GSM153279 1 0.1031 0.952 0.976 0.000 0.024
#> GSM153280 1 0.1163 0.950 0.972 0.000 0.028
#> GSM153281 1 0.1163 0.950 0.972 0.000 0.028
#> GSM153282 1 0.1163 0.950 0.972 0.000 0.028
#> GSM153283 1 0.1289 0.959 0.968 0.000 0.032
#> GSM153284 1 0.0424 0.958 0.992 0.000 0.008
#> GSM153285 1 0.1411 0.946 0.964 0.000 0.036
#> GSM153286 1 0.0424 0.958 0.992 0.000 0.008
#> GSM153287 1 0.0747 0.956 0.984 0.000 0.016
#> GSM153288 1 0.0424 0.958 0.992 0.000 0.008
#> GSM153289 1 0.0000 0.959 1.000 0.000 0.000
#> GSM153290 1 0.1163 0.951 0.972 0.000 0.028
#> GSM153291 1 0.0424 0.958 0.992 0.000 0.008
#> GSM153292 1 0.0892 0.954 0.980 0.000 0.020
#> GSM153293 1 0.0237 0.959 0.996 0.000 0.004
#> GSM153294 1 0.1289 0.959 0.968 0.000 0.032
#> GSM153295 1 0.0592 0.957 0.988 0.000 0.012
#> GSM153054 1 0.2711 0.923 0.912 0.000 0.088
#> GSM153055 1 0.0592 0.960 0.988 0.000 0.012
#> GSM153056 3 0.1643 0.942 0.044 0.000 0.956
#> GSM153057 3 0.5016 0.706 0.240 0.000 0.760
#> GSM153058 3 0.1411 0.945 0.036 0.000 0.964
#> GSM153059 3 0.2625 0.912 0.084 0.000 0.916
#> GSM153060 3 0.1289 0.945 0.032 0.000 0.968
#> GSM153061 3 0.1529 0.942 0.040 0.000 0.960
#> GSM153062 3 0.1289 0.945 0.032 0.000 0.968
#> GSM153063 3 0.1964 0.939 0.056 0.000 0.944
#> GSM153064 1 0.1289 0.959 0.968 0.000 0.032
#> GSM153065 3 0.1643 0.940 0.044 0.000 0.956
#> GSM153066 3 0.6952 0.053 0.016 0.480 0.504
#> GSM153067 1 0.0424 0.958 0.992 0.000 0.008
#> GSM153068 3 0.1411 0.944 0.036 0.000 0.964
#> GSM153069 1 0.0747 0.956 0.984 0.000 0.016
#> GSM153070 1 0.1289 0.959 0.968 0.000 0.032
#> GSM153071 1 0.2448 0.934 0.924 0.000 0.076
#> GSM153072 1 0.2537 0.930 0.920 0.000 0.080
#> GSM153073 1 0.1289 0.959 0.968 0.000 0.032
#> GSM153074 1 0.0424 0.958 0.992 0.000 0.008
#> GSM153075 1 0.0424 0.958 0.992 0.000 0.008
#> GSM153076 1 0.1163 0.960 0.972 0.000 0.028
#> GSM153077 1 0.1289 0.959 0.968 0.000 0.032
#> GSM153078 1 0.4002 0.840 0.840 0.000 0.160
#> GSM153079 1 0.1289 0.959 0.968 0.000 0.032
#> GSM153080 3 0.2711 0.921 0.088 0.000 0.912
#> GSM153081 1 0.1289 0.959 0.968 0.000 0.032
#> GSM153082 1 0.1289 0.959 0.968 0.000 0.032
#> GSM153083 1 0.1860 0.950 0.948 0.000 0.052
#> GSM153084 1 0.4802 0.823 0.824 0.020 0.156
#> GSM153085 1 0.1289 0.959 0.968 0.000 0.032
#> GSM153086 1 0.2066 0.945 0.940 0.000 0.060
#> GSM153087 1 0.0424 0.958 0.992 0.000 0.008
#> GSM153088 1 0.1163 0.960 0.972 0.000 0.028
#> GSM153089 3 0.2066 0.938 0.060 0.000 0.940
#> GSM153090 1 0.1163 0.960 0.972 0.000 0.028
#> GSM153091 1 0.1289 0.959 0.968 0.000 0.032
#> GSM153092 1 0.1163 0.960 0.972 0.000 0.028
#> GSM153093 1 0.0424 0.958 0.992 0.000 0.008
#> GSM153094 1 0.1289 0.959 0.968 0.000 0.032
#> GSM153095 1 0.2165 0.943 0.936 0.000 0.064
#> GSM153096 1 0.1289 0.959 0.968 0.000 0.032
#> GSM153097 1 0.1289 0.959 0.968 0.000 0.032
#> GSM153098 1 0.1289 0.959 0.968 0.000 0.032
#> GSM153099 1 0.0424 0.958 0.992 0.000 0.008
#> GSM153100 1 0.1289 0.959 0.968 0.000 0.032
#> GSM153101 1 0.2356 0.937 0.928 0.000 0.072
#> GSM153102 1 0.1860 0.950 0.948 0.000 0.052
#> GSM153103 1 0.1964 0.947 0.944 0.000 0.056
#> GSM153104 1 0.1031 0.952 0.976 0.000 0.024
#> GSM153106 1 0.1031 0.960 0.976 0.000 0.024
#> GSM153107 1 0.1289 0.959 0.968 0.000 0.032
#> GSM153108 1 0.0592 0.960 0.988 0.000 0.012
#> GSM153109 1 0.1860 0.950 0.948 0.000 0.052
#> GSM153110 1 0.1289 0.959 0.968 0.000 0.032
#> GSM153111 1 0.1289 0.959 0.968 0.000 0.032
#> GSM153112 1 0.1289 0.959 0.968 0.000 0.032
#> GSM153113 1 0.1411 0.958 0.964 0.000 0.036
#> GSM153114 1 0.0424 0.958 0.992 0.000 0.008
#> GSM187532 2 0.0000 0.986 0.000 1.000 0.000
#> GSM187533 2 0.0000 0.986 0.000 1.000 0.000
#> GSM187534 2 0.0000 0.986 0.000 1.000 0.000
#> GSM187535 2 0.3845 0.825 0.116 0.872 0.012
#> GSM152906 2 0.0592 0.985 0.000 0.988 0.012
#> GSM152907 2 0.0592 0.985 0.000 0.988 0.012
#> GSM152908 2 0.0892 0.983 0.000 0.980 0.020
#> GSM152909 2 0.0747 0.985 0.000 0.984 0.016
#> GSM152910 2 0.0892 0.983 0.000 0.980 0.020
#> GSM152911 2 0.0424 0.986 0.000 0.992 0.008
#> GSM152912 2 0.0892 0.983 0.000 0.980 0.020
#> GSM152913 2 0.0424 0.986 0.000 0.992 0.008
#> GSM152914 2 0.0424 0.986 0.000 0.992 0.008
#> GSM152915 2 0.0424 0.986 0.000 0.992 0.008
#> GSM152916 2 0.0592 0.985 0.000 0.988 0.012
#> GSM152917 2 0.0424 0.986 0.000 0.992 0.008
#> GSM152918 2 0.0424 0.986 0.000 0.992 0.008
#> GSM152919 2 0.0424 0.986 0.000 0.992 0.008
#> GSM152920 2 0.0892 0.983 0.000 0.980 0.020
#> GSM152921 2 0.0892 0.983 0.000 0.980 0.020
#> GSM152922 2 0.0892 0.983 0.000 0.980 0.020
#> GSM152923 2 0.0592 0.985 0.000 0.988 0.012
#> GSM152924 2 0.0592 0.985 0.000 0.988 0.012
#> GSM152925 2 0.0592 0.985 0.000 0.988 0.012
#> GSM152926 2 0.0592 0.985 0.000 0.988 0.012
#> GSM152927 2 0.0592 0.985 0.000 0.988 0.012
#> GSM152928 2 0.0592 0.985 0.000 0.988 0.012
#> GSM152929 2 0.0592 0.985 0.000 0.988 0.012
#> GSM152930 2 0.0592 0.985 0.000 0.988 0.012
cbind(get_classes(res, k = 4), get_membership(res, k = 4))
#> class entropy silhouette p1 p2 p3 p4
#> GSM152839 1 0.6739 0.2496 0.612 0.000 0.216 0.172
#> GSM152840 3 0.0895 0.7726 0.004 0.000 0.976 0.020
#> GSM152841 4 0.4008 0.6350 0.000 0.000 0.244 0.756
#> GSM152842 3 0.4713 0.8528 0.360 0.000 0.640 0.000
#> GSM152843 3 0.4936 0.8327 0.372 0.000 0.624 0.004
#> GSM152844 3 0.0524 0.7820 0.004 0.000 0.988 0.008
#> GSM152845 3 0.3942 0.8667 0.236 0.000 0.764 0.000
#> GSM152846 3 0.1576 0.8112 0.048 0.000 0.948 0.004
#> GSM152847 3 0.4920 0.8355 0.368 0.000 0.628 0.004
#> GSM152848 1 0.4996 0.6077 0.516 0.000 0.000 0.484
#> GSM152849 3 0.4872 0.8443 0.356 0.000 0.640 0.004
#> GSM152850 1 0.5420 -0.3568 0.624 0.000 0.352 0.024
#> GSM152851 4 0.5182 0.5382 0.028 0.000 0.288 0.684
#> GSM152852 3 0.0376 0.7850 0.004 0.000 0.992 0.004
#> GSM152853 3 0.0779 0.7760 0.004 0.000 0.980 0.016
#> GSM152854 3 0.3791 0.8639 0.200 0.000 0.796 0.004
#> GSM152855 4 0.0592 0.7470 0.016 0.000 0.000 0.984
#> GSM153238 1 0.4632 -0.3236 0.688 0.000 0.308 0.004
#> GSM153239 3 0.0657 0.7791 0.004 0.000 0.984 0.012
#> GSM153240 4 0.2589 0.7191 0.000 0.000 0.116 0.884
#> GSM153241 3 0.4837 0.8539 0.348 0.000 0.648 0.004
#> GSM153242 3 0.2466 0.8301 0.096 0.000 0.900 0.004
#> GSM153243 1 0.5088 -0.5619 0.572 0.000 0.424 0.004
#> GSM153244 4 0.3539 0.6851 0.004 0.000 0.176 0.820
#> GSM153245 3 0.1305 0.8038 0.036 0.000 0.960 0.004
#> GSM153246 3 0.4564 0.8656 0.328 0.000 0.672 0.000
#> GSM153247 1 0.5343 -0.0608 0.708 0.000 0.240 0.052
#> GSM153248 1 0.4992 0.6208 0.524 0.000 0.000 0.476
#> GSM153249 4 0.2921 0.7106 0.000 0.000 0.140 0.860
#> GSM153250 4 0.2760 0.6117 0.128 0.000 0.000 0.872
#> GSM153251 3 0.4372 0.8718 0.268 0.000 0.728 0.004
#> GSM153252 4 0.0592 0.7512 0.000 0.000 0.016 0.984
#> GSM153253 4 0.3764 0.6633 0.000 0.000 0.216 0.784
#> GSM153254 1 0.7859 0.1511 0.376 0.000 0.272 0.352
#> GSM153255 4 0.0336 0.7517 0.000 0.000 0.008 0.992
#> GSM153256 4 0.0817 0.7422 0.024 0.000 0.000 0.976
#> GSM153257 4 0.0469 0.7518 0.000 0.000 0.012 0.988
#> GSM153258 4 0.4996 -0.5509 0.484 0.000 0.000 0.516
#> GSM153259 1 0.4985 0.6323 0.532 0.000 0.000 0.468
#> GSM153260 1 0.5143 -0.6234 0.540 0.000 0.456 0.004
#> GSM153261 3 0.5163 0.7113 0.480 0.000 0.516 0.004
#> GSM153262 4 0.3400 0.6893 0.000 0.000 0.180 0.820
#> GSM153263 4 0.3975 0.3419 0.240 0.000 0.000 0.760
#> GSM153264 1 0.4981 0.6381 0.536 0.000 0.000 0.464
#> GSM153265 4 0.3726 0.6669 0.000 0.000 0.212 0.788
#> GSM153266 1 0.4989 0.6291 0.528 0.000 0.000 0.472
#> GSM153267 4 0.0817 0.7422 0.024 0.000 0.000 0.976
#> GSM153268 4 0.4964 0.4524 0.004 0.000 0.380 0.616
#> GSM153269 4 0.0817 0.7422 0.024 0.000 0.000 0.976
#> GSM153270 4 0.1118 0.7320 0.036 0.000 0.000 0.964
#> GSM153271 4 0.2216 0.6679 0.092 0.000 0.000 0.908
#> GSM153272 4 0.0336 0.7517 0.000 0.000 0.008 0.992
#> GSM153273 1 0.4985 0.6323 0.532 0.000 0.000 0.468
#> GSM153274 4 0.0707 0.7448 0.020 0.000 0.000 0.980
#> GSM153275 4 0.0592 0.7469 0.016 0.000 0.000 0.984
#> GSM153276 4 0.0707 0.7460 0.020 0.000 0.000 0.980
#> GSM153277 4 0.3172 0.7017 0.000 0.000 0.160 0.840
#> GSM153278 1 0.5112 -0.5643 0.560 0.000 0.436 0.004
#> GSM153279 4 0.3400 0.6893 0.000 0.000 0.180 0.820
#> GSM153280 4 0.3726 0.6669 0.000 0.000 0.212 0.788
#> GSM153281 4 0.3569 0.6781 0.000 0.000 0.196 0.804
#> GSM153282 4 0.3764 0.6637 0.000 0.000 0.216 0.784
#> GSM153283 1 0.4996 0.6099 0.516 0.000 0.000 0.484
#> GSM153284 4 0.0524 0.7505 0.008 0.000 0.004 0.988
#> GSM153285 4 0.3726 0.6669 0.000 0.000 0.212 0.788
#> GSM153286 4 0.0707 0.7451 0.020 0.000 0.000 0.980
#> GSM153287 4 0.3123 0.7034 0.000 0.000 0.156 0.844
#> GSM153288 4 0.0336 0.7496 0.008 0.000 0.000 0.992
#> GSM153289 4 0.0921 0.7400 0.028 0.000 0.000 0.972
#> GSM153290 4 0.3688 0.6697 0.000 0.000 0.208 0.792
#> GSM153291 4 0.0592 0.7511 0.000 0.000 0.016 0.984
#> GSM153292 4 0.3486 0.6840 0.000 0.000 0.188 0.812
#> GSM153293 4 0.0707 0.7451 0.020 0.000 0.000 0.980
#> GSM153294 1 0.4998 0.5971 0.512 0.000 0.000 0.488
#> GSM153295 4 0.0895 0.7474 0.020 0.000 0.004 0.976
#> GSM153054 1 0.5070 0.6471 0.580 0.000 0.004 0.416
#> GSM153055 4 0.2216 0.6702 0.092 0.000 0.000 0.908
#> GSM153056 3 0.5376 0.7953 0.396 0.000 0.588 0.016
#> GSM153057 1 0.6097 -0.4081 0.580 0.000 0.364 0.056
#> GSM153058 3 0.4331 0.8686 0.288 0.000 0.712 0.000
#> GSM153059 1 0.4950 -0.4625 0.620 0.000 0.376 0.004
#> GSM153060 3 0.4564 0.8664 0.328 0.000 0.672 0.000
#> GSM153061 3 0.4855 0.8605 0.352 0.000 0.644 0.004
#> GSM153062 3 0.4477 0.8638 0.312 0.000 0.688 0.000
#> GSM153063 3 0.4103 0.8718 0.256 0.000 0.744 0.000
#> GSM153064 1 0.4994 0.6139 0.520 0.000 0.000 0.480
#> GSM153065 3 0.4920 0.8481 0.368 0.000 0.628 0.004
#> GSM153066 1 0.5031 -0.0210 0.768 0.092 0.140 0.000
#> GSM153067 4 0.0188 0.7515 0.000 0.000 0.004 0.996
#> GSM153068 3 0.4585 0.8622 0.332 0.000 0.668 0.000
#> GSM153069 4 0.3123 0.7034 0.000 0.000 0.156 0.844
#> GSM153070 4 0.4907 -0.3803 0.420 0.000 0.000 0.580
#> GSM153071 1 0.4978 0.5995 0.664 0.000 0.012 0.324
#> GSM153072 1 0.5050 0.6456 0.588 0.000 0.004 0.408
#> GSM153073 1 0.4996 0.6100 0.516 0.000 0.000 0.484
#> GSM153074 4 0.0188 0.7515 0.000 0.000 0.004 0.996
#> GSM153075 4 0.0779 0.7487 0.016 0.000 0.004 0.980
#> GSM153076 4 0.4643 -0.0688 0.344 0.000 0.000 0.656
#> GSM153077 1 0.4972 0.6439 0.544 0.000 0.000 0.456
#> GSM153078 1 0.5697 0.5585 0.664 0.000 0.056 0.280
#> GSM153079 1 0.4967 0.6463 0.548 0.000 0.000 0.452
#> GSM153080 3 0.5389 0.7375 0.308 0.000 0.660 0.032
#> GSM153081 1 0.4981 0.6381 0.536 0.000 0.000 0.464
#> GSM153082 1 0.4989 0.6248 0.528 0.000 0.000 0.472
#> GSM153083 1 0.5112 0.6507 0.560 0.000 0.004 0.436
#> GSM153084 1 0.4332 0.5148 0.792 0.000 0.032 0.176
#> GSM153085 1 0.4933 0.6499 0.568 0.000 0.000 0.432
#> GSM153086 1 0.5088 0.6504 0.572 0.000 0.004 0.424
#> GSM153087 4 0.0336 0.7520 0.000 0.000 0.008 0.992
#> GSM153088 4 0.2814 0.6046 0.132 0.000 0.000 0.868
#> GSM153089 3 0.4018 0.8679 0.224 0.000 0.772 0.004
#> GSM153090 4 0.2081 0.6785 0.084 0.000 0.000 0.916
#> GSM153091 1 0.4989 0.6248 0.528 0.000 0.000 0.472
#> GSM153092 4 0.4999 -0.5726 0.492 0.000 0.000 0.508
#> GSM153093 4 0.0469 0.7516 0.000 0.000 0.012 0.988
#> GSM153094 1 0.4977 0.6393 0.540 0.000 0.000 0.460
#> GSM153095 1 0.4964 0.6307 0.616 0.000 0.004 0.380
#> GSM153096 1 0.4992 0.6208 0.524 0.000 0.000 0.476
#> GSM153097 1 0.4961 0.6479 0.552 0.000 0.000 0.448
#> GSM153098 4 0.4941 -0.4040 0.436 0.000 0.000 0.564
#> GSM153099 4 0.0707 0.7451 0.020 0.000 0.000 0.980
#> GSM153100 1 0.5000 0.5854 0.504 0.000 0.000 0.496
#> GSM153101 1 0.4964 0.6335 0.616 0.000 0.004 0.380
#> GSM153102 1 0.5126 0.6491 0.552 0.000 0.004 0.444
#> GSM153103 1 0.5028 0.6439 0.596 0.000 0.004 0.400
#> GSM153104 4 0.3172 0.7017 0.000 0.000 0.160 0.840
#> GSM153106 4 0.4955 -0.4313 0.444 0.000 0.000 0.556
#> GSM153107 4 0.4998 -0.5575 0.488 0.000 0.000 0.512
#> GSM153108 4 0.2999 0.6053 0.132 0.000 0.004 0.864
#> GSM153109 1 0.5126 0.6494 0.552 0.000 0.004 0.444
#> GSM153110 1 0.4972 0.6435 0.544 0.000 0.000 0.456
#> GSM153111 1 0.4961 0.6479 0.552 0.000 0.000 0.448
#> GSM153112 4 0.4981 -0.4876 0.464 0.000 0.000 0.536
#> GSM153113 1 0.4955 0.6496 0.556 0.000 0.000 0.444
#> GSM153114 4 0.0779 0.7487 0.016 0.000 0.004 0.980
#> GSM187532 2 0.1489 0.9456 0.044 0.952 0.004 0.000
#> GSM187533 2 0.1022 0.9467 0.032 0.968 0.000 0.000
#> GSM187534 2 0.1356 0.9461 0.032 0.960 0.008 0.000
#> GSM187535 2 0.7120 0.4014 0.284 0.572 0.008 0.136
#> GSM152906 2 0.2675 0.9371 0.100 0.892 0.008 0.000
#> GSM152907 2 0.2675 0.9371 0.100 0.892 0.008 0.000
#> GSM152908 2 0.0336 0.9461 0.008 0.992 0.000 0.000
#> GSM152909 2 0.0707 0.9419 0.020 0.980 0.000 0.000
#> GSM152910 2 0.0336 0.9461 0.008 0.992 0.000 0.000
#> GSM152911 2 0.0000 0.9475 0.000 1.000 0.000 0.000
#> GSM152912 2 0.0336 0.9461 0.008 0.992 0.000 0.000
#> GSM152913 2 0.0188 0.9469 0.004 0.996 0.000 0.000
#> GSM152914 2 0.0000 0.9475 0.000 1.000 0.000 0.000
#> GSM152915 2 0.0000 0.9475 0.000 1.000 0.000 0.000
#> GSM152916 2 0.2611 0.9376 0.096 0.896 0.008 0.000
#> GSM152917 2 0.0000 0.9475 0.000 1.000 0.000 0.000
#> GSM152918 2 0.0000 0.9475 0.000 1.000 0.000 0.000
#> GSM152919 2 0.0000 0.9475 0.000 1.000 0.000 0.000
#> GSM152920 2 0.0336 0.9461 0.008 0.992 0.000 0.000
#> GSM152921 2 0.0336 0.9461 0.008 0.992 0.000 0.000
#> GSM152922 2 0.0336 0.9461 0.008 0.992 0.000 0.000
#> GSM152923 2 0.2675 0.9371 0.100 0.892 0.008 0.000
#> GSM152924 2 0.2675 0.9371 0.100 0.892 0.008 0.000
#> GSM152925 2 0.2675 0.9371 0.100 0.892 0.008 0.000
#> GSM152926 2 0.2675 0.9371 0.100 0.892 0.008 0.000
#> GSM152927 2 0.2675 0.9371 0.100 0.892 0.008 0.000
#> GSM152928 2 0.2675 0.9371 0.100 0.892 0.008 0.000
#> GSM152929 2 0.2675 0.9371 0.100 0.892 0.008 0.000
#> GSM152930 2 0.2675 0.9371 0.100 0.892 0.008 0.000
cbind(get_classes(res, k = 5), get_membership(res, k = 5))
#> class entropy silhouette p1 p2 p3 p4 p5
#> GSM152839 3 0.6683 0.4509 0.332 0.000 0.528 0.072 0.068
#> GSM152840 5 0.5177 0.8070 0.000 0.000 0.220 0.104 0.676
#> GSM152841 4 0.2929 0.7089 0.000 0.000 0.000 0.820 0.180
#> GSM152842 3 0.3339 0.5571 0.040 0.000 0.836 0.000 0.124
#> GSM152843 3 0.4316 0.5988 0.080 0.000 0.784 0.008 0.128
#> GSM152844 5 0.5013 0.8480 0.000 0.000 0.240 0.080 0.680
#> GSM152845 5 0.4375 0.6368 0.004 0.000 0.420 0.000 0.576
#> GSM152846 5 0.4622 0.8315 0.000 0.000 0.264 0.044 0.692
#> GSM152847 3 0.3888 0.5968 0.076 0.000 0.804 0.000 0.120
#> GSM152848 1 0.5201 0.7666 0.712 0.000 0.052 0.200 0.036
#> GSM152849 3 0.3934 0.5917 0.076 0.000 0.800 0.000 0.124
#> GSM152850 3 0.5124 0.5817 0.260 0.000 0.668 0.004 0.068
#> GSM152851 4 0.3366 0.7073 0.000 0.000 0.032 0.828 0.140
#> GSM152852 5 0.4959 0.8471 0.000 0.000 0.240 0.076 0.684
#> GSM152853 5 0.4960 0.8470 0.000 0.000 0.232 0.080 0.688
#> GSM152854 5 0.4291 0.5230 0.000 0.000 0.464 0.000 0.536
#> GSM152855 4 0.2707 0.8519 0.100 0.000 0.000 0.876 0.024
#> GSM153238 3 0.4473 0.4615 0.412 0.000 0.580 0.000 0.008
#> GSM153239 5 0.5117 0.8443 0.000 0.000 0.240 0.088 0.672
#> GSM153240 4 0.1568 0.8535 0.036 0.000 0.000 0.944 0.020
#> GSM153241 3 0.3493 0.5877 0.060 0.000 0.832 0.000 0.108
#> GSM153242 5 0.5264 0.7442 0.000 0.000 0.392 0.052 0.556
#> GSM153243 3 0.3455 0.6234 0.208 0.000 0.784 0.000 0.008
#> GSM153244 4 0.1883 0.8205 0.012 0.000 0.008 0.932 0.048
#> GSM153245 5 0.5422 0.8120 0.004 0.000 0.308 0.072 0.616
#> GSM153246 3 0.3882 0.2834 0.020 0.000 0.756 0.000 0.224
#> GSM153247 3 0.4950 0.4781 0.384 0.000 0.588 0.008 0.020
#> GSM153248 1 0.1965 0.8518 0.904 0.000 0.000 0.096 0.000
#> GSM153249 4 0.1668 0.8434 0.028 0.000 0.000 0.940 0.032
#> GSM153250 4 0.4706 0.5156 0.316 0.000 0.008 0.656 0.020
#> GSM153251 3 0.4244 0.2670 0.012 0.000 0.728 0.012 0.248
#> GSM153252 4 0.2233 0.8573 0.080 0.000 0.000 0.904 0.016
#> GSM153253 4 0.2516 0.7504 0.000 0.000 0.000 0.860 0.140
#> GSM153254 4 0.7549 -0.0834 0.228 0.000 0.296 0.424 0.052
#> GSM153255 4 0.2130 0.8576 0.080 0.000 0.000 0.908 0.012
#> GSM153256 4 0.2616 0.8491 0.100 0.000 0.000 0.880 0.020
#> GSM153257 4 0.2233 0.8573 0.080 0.000 0.000 0.904 0.016
#> GSM153258 1 0.4352 0.7590 0.732 0.000 0.012 0.236 0.020
#> GSM153259 1 0.1965 0.8518 0.904 0.000 0.000 0.096 0.000
#> GSM153260 3 0.3805 0.6286 0.184 0.000 0.784 0.000 0.032
#> GSM153261 3 0.4021 0.6246 0.200 0.000 0.764 0.000 0.036
#> GSM153262 4 0.1357 0.8239 0.004 0.000 0.000 0.948 0.048
#> GSM153263 4 0.4888 -0.0284 0.472 0.000 0.004 0.508 0.016
#> GSM153264 1 0.4231 0.8069 0.776 0.000 0.028 0.176 0.020
#> GSM153265 4 0.2424 0.7581 0.000 0.000 0.000 0.868 0.132
#> GSM153266 1 0.3900 0.8139 0.788 0.000 0.012 0.180 0.020
#> GSM153267 4 0.2616 0.8491 0.100 0.000 0.000 0.880 0.020
#> GSM153268 4 0.4384 0.4219 0.000 0.000 0.016 0.660 0.324
#> GSM153269 4 0.2932 0.8400 0.112 0.000 0.004 0.864 0.020
#> GSM153270 4 0.2304 0.8532 0.100 0.000 0.000 0.892 0.008
#> GSM153271 4 0.4245 0.6825 0.236 0.000 0.008 0.736 0.020
#> GSM153272 4 0.1892 0.8576 0.080 0.000 0.000 0.916 0.004
#> GSM153273 1 0.1965 0.8518 0.904 0.000 0.000 0.096 0.000
#> GSM153274 4 0.2880 0.8426 0.108 0.000 0.004 0.868 0.020
#> GSM153275 4 0.2616 0.8495 0.100 0.000 0.000 0.880 0.020
#> GSM153276 4 0.3166 0.8417 0.104 0.000 0.016 0.860 0.020
#> GSM153277 4 0.1701 0.8317 0.016 0.000 0.000 0.936 0.048
#> GSM153278 3 0.5030 0.6044 0.220 0.000 0.696 0.004 0.080
#> GSM153279 4 0.1544 0.8047 0.000 0.000 0.000 0.932 0.068
#> GSM153280 4 0.2230 0.7689 0.000 0.000 0.000 0.884 0.116
#> GSM153281 4 0.1544 0.8062 0.000 0.000 0.000 0.932 0.068
#> GSM153282 4 0.2605 0.7423 0.000 0.000 0.000 0.852 0.148
#> GSM153283 1 0.4097 0.7867 0.756 0.000 0.008 0.216 0.020
#> GSM153284 4 0.2249 0.8541 0.096 0.000 0.000 0.896 0.008
#> GSM153285 4 0.2648 0.7402 0.000 0.000 0.000 0.848 0.152
#> GSM153286 4 0.2464 0.8521 0.096 0.000 0.000 0.888 0.016
#> GSM153287 4 0.1469 0.8360 0.016 0.000 0.000 0.948 0.036
#> GSM153288 4 0.2361 0.8531 0.096 0.000 0.000 0.892 0.012
#> GSM153289 4 0.3152 0.8267 0.136 0.000 0.000 0.840 0.024
#> GSM153290 4 0.2230 0.7693 0.000 0.000 0.000 0.884 0.116
#> GSM153291 4 0.2172 0.8573 0.076 0.000 0.000 0.908 0.016
#> GSM153292 4 0.1197 0.8200 0.000 0.000 0.000 0.952 0.048
#> GSM153293 4 0.2179 0.8537 0.100 0.000 0.000 0.896 0.004
#> GSM153294 1 0.2377 0.8444 0.872 0.000 0.000 0.128 0.000
#> GSM153295 4 0.2859 0.8509 0.096 0.000 0.012 0.876 0.016
#> GSM153054 1 0.2554 0.8393 0.892 0.000 0.036 0.072 0.000
#> GSM153055 4 0.3678 0.7841 0.168 0.000 0.008 0.804 0.020
#> GSM153056 3 0.4754 0.6104 0.112 0.000 0.760 0.016 0.112
#> GSM153057 3 0.4761 0.5841 0.256 0.000 0.700 0.024 0.020
#> GSM153058 3 0.4329 0.0880 0.016 0.000 0.672 0.000 0.312
#> GSM153059 3 0.4169 0.5961 0.256 0.000 0.724 0.004 0.016
#> GSM153060 3 0.4132 0.2121 0.020 0.000 0.720 0.000 0.260
#> GSM153061 3 0.2873 0.4648 0.020 0.000 0.860 0.000 0.120
#> GSM153062 3 0.4626 -0.2047 0.020 0.000 0.616 0.000 0.364
#> GSM153063 3 0.4408 0.2699 0.008 0.000 0.736 0.032 0.224
#> GSM153064 1 0.2127 0.8501 0.892 0.000 0.000 0.108 0.000
#> GSM153065 3 0.2580 0.5997 0.064 0.000 0.892 0.000 0.044
#> GSM153066 1 0.5241 -0.1622 0.528 0.016 0.436 0.000 0.020
#> GSM153067 4 0.2233 0.8573 0.080 0.000 0.000 0.904 0.016
#> GSM153068 3 0.2305 0.5180 0.012 0.000 0.896 0.000 0.092
#> GSM153069 4 0.1549 0.8343 0.016 0.000 0.000 0.944 0.040
#> GSM153070 1 0.4879 0.5165 0.612 0.000 0.008 0.360 0.020
#> GSM153071 1 0.5116 0.4274 0.640 0.000 0.304 0.052 0.004
#> GSM153072 1 0.2790 0.8256 0.880 0.000 0.052 0.068 0.000
#> GSM153073 1 0.3899 0.8072 0.780 0.000 0.008 0.192 0.020
#> GSM153074 4 0.1732 0.8575 0.080 0.000 0.000 0.920 0.000
#> GSM153075 4 0.2124 0.8558 0.096 0.000 0.004 0.900 0.000
#> GSM153076 1 0.5035 0.3276 0.548 0.000 0.008 0.424 0.020
#> GSM153077 1 0.4119 0.8170 0.792 0.000 0.032 0.156 0.020
#> GSM153078 1 0.6568 0.1672 0.500 0.000 0.372 0.088 0.040
#> GSM153079 1 0.2354 0.8461 0.904 0.000 0.008 0.076 0.012
#> GSM153080 3 0.6624 0.4834 0.164 0.000 0.612 0.064 0.160
#> GSM153081 1 0.3992 0.8242 0.812 0.000 0.028 0.128 0.032
#> GSM153082 1 0.2011 0.8503 0.908 0.000 0.004 0.088 0.000
#> GSM153083 1 0.2460 0.8407 0.900 0.000 0.024 0.072 0.004
#> GSM153084 1 0.3851 0.5747 0.768 0.000 0.212 0.016 0.004
#> GSM153085 1 0.3334 0.8257 0.852 0.000 0.064 0.080 0.004
#> GSM153086 1 0.2535 0.8363 0.892 0.000 0.032 0.076 0.000
#> GSM153087 4 0.2642 0.8584 0.084 0.000 0.004 0.888 0.024
#> GSM153088 4 0.4630 0.5544 0.300 0.000 0.008 0.672 0.020
#> GSM153089 3 0.4984 -0.1156 0.008 0.000 0.620 0.028 0.344
#> GSM153090 4 0.4158 0.7017 0.224 0.000 0.008 0.748 0.020
#> GSM153091 1 0.1965 0.8518 0.904 0.000 0.000 0.096 0.000
#> GSM153092 1 0.3912 0.7770 0.752 0.000 0.000 0.228 0.020
#> GSM153093 4 0.1892 0.8575 0.080 0.000 0.000 0.916 0.004
#> GSM153094 1 0.2124 0.8519 0.900 0.000 0.004 0.096 0.000
#> GSM153095 1 0.3169 0.7927 0.856 0.000 0.084 0.060 0.000
#> GSM153096 1 0.1965 0.8518 0.904 0.000 0.000 0.096 0.000
#> GSM153097 1 0.2077 0.8483 0.908 0.000 0.008 0.084 0.000
#> GSM153098 1 0.3210 0.7745 0.788 0.000 0.000 0.212 0.000
#> GSM153099 4 0.2773 0.8425 0.112 0.000 0.000 0.868 0.020
#> GSM153100 1 0.3048 0.8262 0.820 0.000 0.000 0.176 0.004
#> GSM153101 1 0.2927 0.8068 0.872 0.000 0.068 0.060 0.000
#> GSM153102 1 0.3018 0.8375 0.872 0.000 0.036 0.084 0.008
#> GSM153103 1 0.2949 0.8221 0.876 0.000 0.052 0.068 0.004
#> GSM153104 4 0.1626 0.8334 0.016 0.000 0.000 0.940 0.044
#> GSM153106 1 0.3427 0.8049 0.796 0.000 0.000 0.192 0.012
#> GSM153107 1 0.3399 0.8259 0.812 0.000 0.000 0.168 0.020
#> GSM153108 4 0.4029 0.5632 0.316 0.000 0.000 0.680 0.004
#> GSM153109 1 0.2824 0.8455 0.880 0.000 0.024 0.088 0.008
#> GSM153110 1 0.1965 0.8518 0.904 0.000 0.000 0.096 0.000
#> GSM153111 1 0.2193 0.8505 0.900 0.000 0.008 0.092 0.000
#> GSM153112 1 0.3003 0.8003 0.812 0.000 0.000 0.188 0.000
#> GSM153113 1 0.2569 0.8301 0.892 0.000 0.040 0.068 0.000
#> GSM153114 4 0.2561 0.8546 0.096 0.000 0.000 0.884 0.020
#> GSM187532 2 0.2756 0.9190 0.024 0.880 0.004 0.000 0.092
#> GSM187533 2 0.2331 0.9227 0.020 0.900 0.000 0.000 0.080
#> GSM187534 2 0.2236 0.9250 0.024 0.908 0.000 0.000 0.068
#> GSM187535 1 0.5966 0.1773 0.544 0.368 0.000 0.020 0.068
#> GSM152906 2 0.3051 0.9145 0.028 0.852 0.000 0.000 0.120
#> GSM152907 2 0.3051 0.9145 0.028 0.852 0.000 0.000 0.120
#> GSM152908 2 0.1965 0.9112 0.024 0.924 0.000 0.000 0.052
#> GSM152909 2 0.1981 0.9076 0.016 0.920 0.000 0.000 0.064
#> GSM152910 2 0.1965 0.9112 0.024 0.924 0.000 0.000 0.052
#> GSM152911 2 0.0000 0.9271 0.000 1.000 0.000 0.000 0.000
#> GSM152912 2 0.1965 0.9112 0.024 0.924 0.000 0.000 0.052
#> GSM152913 2 0.0794 0.9233 0.000 0.972 0.000 0.000 0.028
#> GSM152914 2 0.0000 0.9271 0.000 1.000 0.000 0.000 0.000
#> GSM152915 2 0.0000 0.9271 0.000 1.000 0.000 0.000 0.000
#> GSM152916 2 0.3099 0.9138 0.028 0.848 0.000 0.000 0.124
#> GSM152917 2 0.0162 0.9275 0.000 0.996 0.000 0.000 0.004
#> GSM152918 2 0.0162 0.9275 0.000 0.996 0.000 0.000 0.004
#> GSM152919 2 0.0162 0.9275 0.000 0.996 0.000 0.000 0.004
#> GSM152920 2 0.1965 0.9112 0.024 0.924 0.000 0.000 0.052
#> GSM152921 2 0.1965 0.9112 0.024 0.924 0.000 0.000 0.052
#> GSM152922 2 0.1965 0.9112 0.024 0.924 0.000 0.000 0.052
#> GSM152923 2 0.3051 0.9145 0.028 0.852 0.000 0.000 0.120
#> GSM152924 2 0.3099 0.9138 0.028 0.848 0.000 0.000 0.124
#> GSM152925 2 0.3099 0.9138 0.028 0.848 0.000 0.000 0.124
#> GSM152926 2 0.3051 0.9145 0.028 0.852 0.000 0.000 0.120
#> GSM152927 2 0.3099 0.9138 0.028 0.848 0.000 0.000 0.124
#> GSM152928 2 0.3099 0.9138 0.028 0.848 0.000 0.000 0.124
#> GSM152929 2 0.3051 0.9145 0.028 0.852 0.000 0.000 0.120
#> GSM152930 2 0.3051 0.9145 0.028 0.852 0.000 0.000 0.120
cbind(get_classes(res, k = 6), get_membership(res, k = 6))
#> class entropy silhouette p1 p2 p3 p4 p5 p6
#> GSM152839 3 0.5280 0.4998 0.140 0.000 0.704 0.020 0.104 0.032
#> GSM152840 6 0.2257 0.8053 0.000 0.000 0.040 0.048 0.008 0.904
#> GSM152841 4 0.3122 0.7155 0.000 0.000 0.000 0.804 0.020 0.176
#> GSM152842 3 0.3852 0.4723 0.020 0.000 0.796 0.000 0.120 0.064
#> GSM152843 3 0.4394 0.5210 0.044 0.000 0.772 0.004 0.112 0.068
#> GSM152844 6 0.2009 0.8172 0.000 0.000 0.040 0.040 0.004 0.916
#> GSM152845 6 0.4371 0.6468 0.008 0.000 0.120 0.000 0.132 0.740
#> GSM152846 6 0.2519 0.8009 0.000 0.000 0.044 0.016 0.048 0.892
#> GSM152847 3 0.4131 0.5141 0.036 0.000 0.784 0.000 0.108 0.072
#> GSM152848 1 0.6589 0.5755 0.580 0.000 0.132 0.156 0.120 0.012
#> GSM152849 3 0.4239 0.5174 0.036 0.000 0.784 0.004 0.096 0.080
#> GSM152850 3 0.4634 0.5397 0.100 0.000 0.756 0.008 0.100 0.036
#> GSM152851 4 0.3562 0.7411 0.000 0.000 0.036 0.824 0.040 0.100
#> GSM152852 6 0.2255 0.8150 0.000 0.000 0.044 0.024 0.024 0.908
#> GSM152853 6 0.2009 0.8172 0.000 0.000 0.040 0.040 0.004 0.916
#> GSM152854 6 0.4107 0.4808 0.000 0.000 0.280 0.000 0.036 0.684
#> GSM152855 4 0.2442 0.8542 0.048 0.000 0.000 0.884 0.068 0.000
#> GSM153238 3 0.4246 0.4134 0.268 0.000 0.692 0.000 0.028 0.012
#> GSM153239 6 0.2815 0.8090 0.000 0.000 0.056 0.044 0.024 0.876
#> GSM153240 4 0.1732 0.8543 0.004 0.000 0.004 0.920 0.072 0.000
#> GSM153241 3 0.3730 0.5156 0.028 0.000 0.812 0.000 0.100 0.060
#> GSM153242 6 0.4691 0.6087 0.000 0.000 0.196 0.008 0.100 0.696
#> GSM153243 3 0.2571 0.5580 0.064 0.000 0.876 0.000 0.060 0.000
#> GSM153244 4 0.2613 0.8302 0.016 0.000 0.028 0.896 0.044 0.016
#> GSM153245 6 0.4409 0.6932 0.000 0.000 0.156 0.028 0.068 0.748
#> GSM153246 5 0.6101 0.8250 0.020 0.000 0.388 0.000 0.440 0.152
#> GSM153247 3 0.3791 0.4944 0.200 0.000 0.760 0.000 0.032 0.008
#> GSM153248 1 0.0865 0.8539 0.964 0.000 0.000 0.036 0.000 0.000
#> GSM153249 4 0.1350 0.8431 0.008 0.000 0.000 0.952 0.020 0.020
#> GSM153250 4 0.5422 0.2263 0.376 0.000 0.008 0.520 0.096 0.000
#> GSM153251 3 0.4710 0.2130 0.004 0.000 0.688 0.000 0.112 0.196
#> GSM153252 4 0.1232 0.8539 0.024 0.000 0.000 0.956 0.016 0.004
#> GSM153253 4 0.2445 0.7853 0.000 0.000 0.000 0.872 0.020 0.108
#> GSM153254 3 0.6024 0.1344 0.084 0.000 0.508 0.360 0.044 0.004
#> GSM153255 4 0.1261 0.8587 0.024 0.000 0.000 0.952 0.024 0.000
#> GSM153256 4 0.3073 0.8365 0.080 0.000 0.000 0.840 0.080 0.000
#> GSM153257 4 0.1261 0.8590 0.024 0.000 0.000 0.952 0.024 0.000
#> GSM153258 1 0.4988 0.6965 0.688 0.000 0.028 0.192 0.092 0.000
#> GSM153259 1 0.0937 0.8540 0.960 0.000 0.000 0.040 0.000 0.000
#> GSM153260 3 0.2760 0.5382 0.052 0.000 0.868 0.000 0.076 0.004
#> GSM153261 3 0.2860 0.5658 0.068 0.000 0.872 0.000 0.028 0.032
#> GSM153262 4 0.1257 0.8359 0.000 0.000 0.000 0.952 0.020 0.028
#> GSM153263 1 0.5190 0.2897 0.524 0.000 0.004 0.392 0.080 0.000
#> GSM153264 1 0.5172 0.7224 0.704 0.000 0.076 0.124 0.096 0.000
#> GSM153265 4 0.2301 0.7943 0.000 0.000 0.000 0.884 0.020 0.096
#> GSM153266 1 0.4445 0.7611 0.756 0.000 0.032 0.116 0.096 0.000
#> GSM153267 4 0.3054 0.8404 0.072 0.000 0.004 0.848 0.076 0.000
#> GSM153268 4 0.4241 0.3959 0.000 0.000 0.004 0.628 0.020 0.348
#> GSM153269 4 0.3366 0.8263 0.092 0.000 0.004 0.824 0.080 0.000
#> GSM153270 4 0.2803 0.8522 0.064 0.000 0.012 0.872 0.052 0.000
#> GSM153271 4 0.5059 0.5107 0.284 0.000 0.008 0.620 0.088 0.000
#> GSM153272 4 0.2119 0.8575 0.036 0.000 0.000 0.904 0.060 0.000
#> GSM153273 1 0.0865 0.8539 0.964 0.000 0.000 0.036 0.000 0.000
#> GSM153274 4 0.3272 0.8352 0.076 0.000 0.008 0.836 0.080 0.000
#> GSM153275 4 0.2994 0.8432 0.064 0.000 0.004 0.852 0.080 0.000
#> GSM153276 4 0.3430 0.8385 0.060 0.000 0.028 0.836 0.076 0.000
#> GSM153277 4 0.1268 0.8411 0.004 0.000 0.000 0.952 0.008 0.036
#> GSM153278 3 0.3760 0.5687 0.076 0.000 0.820 0.004 0.068 0.032
#> GSM153279 4 0.1774 0.8361 0.004 0.000 0.016 0.936 0.020 0.024
#> GSM153280 4 0.2147 0.8024 0.000 0.000 0.000 0.896 0.020 0.084
#> GSM153281 4 0.1408 0.8318 0.000 0.000 0.000 0.944 0.020 0.036
#> GSM153282 4 0.2491 0.7792 0.000 0.000 0.000 0.868 0.020 0.112
#> GSM153283 1 0.4717 0.7346 0.724 0.000 0.028 0.152 0.096 0.000
#> GSM153284 4 0.2451 0.8537 0.056 0.000 0.000 0.884 0.060 0.000
#> GSM153285 4 0.2581 0.7742 0.000 0.000 0.000 0.860 0.020 0.120
#> GSM153286 4 0.2910 0.8424 0.068 0.000 0.000 0.852 0.080 0.000
#> GSM153287 4 0.1092 0.8392 0.000 0.000 0.000 0.960 0.020 0.020
#> GSM153288 4 0.2442 0.8537 0.048 0.000 0.000 0.884 0.068 0.000
#> GSM153289 4 0.3575 0.7962 0.128 0.000 0.000 0.796 0.076 0.000
#> GSM153290 4 0.1983 0.8093 0.000 0.000 0.000 0.908 0.020 0.072
#> GSM153291 4 0.1321 0.8548 0.024 0.000 0.000 0.952 0.020 0.004
#> GSM153292 4 0.1408 0.8315 0.000 0.000 0.000 0.944 0.020 0.036
#> GSM153293 4 0.2745 0.8474 0.068 0.000 0.000 0.864 0.068 0.000
#> GSM153294 1 0.0937 0.8541 0.960 0.000 0.000 0.040 0.000 0.000
#> GSM153295 4 0.2852 0.8451 0.064 0.000 0.000 0.856 0.080 0.000
#> GSM153054 1 0.2507 0.8339 0.892 0.000 0.056 0.036 0.016 0.000
#> GSM153055 4 0.4200 0.7831 0.128 0.000 0.028 0.772 0.072 0.000
#> GSM153056 3 0.3942 0.5574 0.048 0.000 0.816 0.012 0.076 0.048
#> GSM153057 3 0.3533 0.5475 0.104 0.000 0.820 0.016 0.060 0.000
#> GSM153058 3 0.4756 0.1607 0.000 0.000 0.664 0.000 0.112 0.224
#> GSM153059 3 0.3402 0.5360 0.104 0.000 0.820 0.000 0.072 0.004
#> GSM153060 5 0.6224 0.8521 0.016 0.000 0.372 0.000 0.420 0.192
#> GSM153061 3 0.5506 -0.5954 0.016 0.000 0.524 0.000 0.372 0.088
#> GSM153062 5 0.6216 0.7466 0.016 0.000 0.276 0.000 0.476 0.232
#> GSM153063 3 0.5204 0.1404 0.000 0.000 0.660 0.020 0.128 0.192
#> GSM153064 1 0.1007 0.8539 0.956 0.000 0.000 0.044 0.000 0.000
#> GSM153065 3 0.3161 0.4053 0.008 0.000 0.828 0.000 0.136 0.028
#> GSM153066 3 0.5477 0.2455 0.392 0.012 0.528 0.000 0.048 0.020
#> GSM153067 4 0.1334 0.8555 0.032 0.000 0.000 0.948 0.020 0.000
#> GSM153068 3 0.3283 0.3505 0.000 0.000 0.804 0.000 0.160 0.036
#> GSM153069 4 0.1092 0.8392 0.000 0.000 0.000 0.960 0.020 0.020
#> GSM153070 1 0.5727 0.3965 0.536 0.000 0.028 0.340 0.096 0.000
#> GSM153071 3 0.4574 0.1888 0.464 0.000 0.508 0.012 0.016 0.000
#> GSM153072 1 0.2669 0.7988 0.864 0.000 0.108 0.024 0.004 0.000
#> GSM153073 1 0.4363 0.7548 0.752 0.000 0.020 0.140 0.088 0.000
#> GSM153074 4 0.1124 0.8582 0.036 0.000 0.000 0.956 0.008 0.000
#> GSM153075 4 0.1873 0.8602 0.048 0.000 0.008 0.924 0.020 0.000
#> GSM153076 1 0.5246 0.5095 0.592 0.000 0.012 0.308 0.088 0.000
#> GSM153077 1 0.5142 0.7277 0.708 0.000 0.080 0.116 0.096 0.000
#> GSM153078 3 0.6124 0.3235 0.276 0.000 0.560 0.040 0.116 0.008
#> GSM153079 1 0.1464 0.8511 0.944 0.000 0.016 0.036 0.004 0.000
#> GSM153080 3 0.4859 0.5073 0.072 0.000 0.756 0.080 0.020 0.072
#> GSM153081 1 0.4930 0.7475 0.728 0.000 0.088 0.084 0.100 0.000
#> GSM153082 1 0.1320 0.8507 0.948 0.000 0.016 0.036 0.000 0.000
#> GSM153083 1 0.1320 0.8507 0.948 0.000 0.016 0.036 0.000 0.000
#> GSM153084 1 0.3534 0.5308 0.740 0.000 0.244 0.000 0.016 0.000
#> GSM153085 1 0.3092 0.8229 0.852 0.000 0.088 0.044 0.016 0.000
#> GSM153086 1 0.1334 0.8487 0.948 0.000 0.020 0.032 0.000 0.000
#> GSM153087 4 0.2325 0.8605 0.044 0.000 0.008 0.900 0.048 0.000
#> GSM153088 4 0.5560 0.3094 0.344 0.000 0.016 0.540 0.100 0.000
#> GSM153089 3 0.5248 -0.0486 0.004 0.000 0.568 0.004 0.084 0.340
#> GSM153090 4 0.4815 0.6133 0.236 0.000 0.008 0.668 0.088 0.000
#> GSM153091 1 0.0865 0.8539 0.964 0.000 0.000 0.036 0.000 0.000
#> GSM153092 1 0.3821 0.7659 0.776 0.000 0.004 0.156 0.064 0.000
#> GSM153093 4 0.1829 0.8590 0.024 0.000 0.000 0.920 0.056 0.000
#> GSM153094 1 0.1225 0.8520 0.952 0.000 0.012 0.036 0.000 0.000
#> GSM153095 1 0.2745 0.7769 0.860 0.000 0.112 0.020 0.008 0.000
#> GSM153096 1 0.0937 0.8540 0.960 0.000 0.000 0.040 0.000 0.000
#> GSM153097 1 0.1320 0.8507 0.948 0.000 0.016 0.036 0.000 0.000
#> GSM153098 1 0.1663 0.8380 0.912 0.000 0.000 0.088 0.000 0.000
#> GSM153099 4 0.3054 0.8409 0.076 0.000 0.004 0.848 0.072 0.000
#> GSM153100 1 0.2618 0.8191 0.860 0.000 0.000 0.116 0.024 0.000
#> GSM153101 1 0.1889 0.8250 0.920 0.000 0.056 0.020 0.004 0.000
#> GSM153102 1 0.1794 0.8427 0.924 0.000 0.040 0.036 0.000 0.000
#> GSM153103 1 0.1780 0.8395 0.924 0.000 0.048 0.028 0.000 0.000
#> GSM153104 4 0.1257 0.8359 0.000 0.000 0.000 0.952 0.020 0.028
#> GSM153106 1 0.2214 0.8416 0.892 0.000 0.004 0.092 0.012 0.000
#> GSM153107 1 0.2398 0.8404 0.888 0.000 0.004 0.080 0.028 0.000
#> GSM153108 4 0.3653 0.5822 0.300 0.000 0.000 0.692 0.008 0.000
#> GSM153109 1 0.1492 0.8488 0.940 0.000 0.024 0.036 0.000 0.000
#> GSM153110 1 0.0865 0.8539 0.964 0.000 0.000 0.036 0.000 0.000
#> GSM153111 1 0.1124 0.8528 0.956 0.000 0.008 0.036 0.000 0.000
#> GSM153112 1 0.1501 0.8432 0.924 0.000 0.000 0.076 0.000 0.000
#> GSM153113 1 0.1682 0.8282 0.928 0.000 0.052 0.020 0.000 0.000
#> GSM153114 4 0.2136 0.8583 0.048 0.000 0.000 0.904 0.048 0.000
#> GSM187532 2 0.3544 0.8379 0.012 0.816 0.008 0.000 0.132 0.032
#> GSM187533 2 0.2755 0.8584 0.008 0.864 0.004 0.000 0.108 0.016
#> GSM187534 2 0.2800 0.8601 0.008 0.860 0.004 0.000 0.112 0.016
#> GSM187535 1 0.5265 0.5185 0.656 0.216 0.004 0.020 0.104 0.000
#> GSM152906 2 0.3151 0.8397 0.000 0.748 0.000 0.000 0.252 0.000
#> GSM152907 2 0.3151 0.8397 0.000 0.748 0.000 0.000 0.252 0.000
#> GSM152908 2 0.1625 0.8520 0.000 0.928 0.000 0.000 0.060 0.012
#> GSM152909 2 0.2815 0.8236 0.012 0.864 0.000 0.000 0.096 0.028
#> GSM152910 2 0.1625 0.8520 0.000 0.928 0.000 0.000 0.060 0.012
#> GSM152911 2 0.0363 0.8696 0.000 0.988 0.000 0.000 0.000 0.012
#> GSM152912 2 0.1625 0.8520 0.000 0.928 0.000 0.000 0.060 0.012
#> GSM152913 2 0.0984 0.8672 0.008 0.968 0.000 0.000 0.012 0.012
#> GSM152914 2 0.0508 0.8702 0.000 0.984 0.000 0.000 0.004 0.012
#> GSM152915 2 0.0363 0.8696 0.000 0.988 0.000 0.000 0.000 0.012
#> GSM152916 2 0.3175 0.8386 0.000 0.744 0.000 0.000 0.256 0.000
#> GSM152917 2 0.0508 0.8702 0.000 0.984 0.000 0.000 0.004 0.012
#> GSM152918 2 0.0508 0.8702 0.000 0.984 0.000 0.000 0.004 0.012
#> GSM152919 2 0.0508 0.8702 0.000 0.984 0.000 0.000 0.004 0.012
#> GSM152920 2 0.1625 0.8520 0.000 0.928 0.000 0.000 0.060 0.012
#> GSM152921 2 0.1625 0.8520 0.000 0.928 0.000 0.000 0.060 0.012
#> GSM152922 2 0.1625 0.8520 0.000 0.928 0.000 0.000 0.060 0.012
#> GSM152923 2 0.3151 0.8397 0.000 0.748 0.000 0.000 0.252 0.000
#> GSM152924 2 0.3175 0.8386 0.000 0.744 0.000 0.000 0.256 0.000
#> GSM152925 2 0.3198 0.8372 0.000 0.740 0.000 0.000 0.260 0.000
#> GSM152926 2 0.3151 0.8397 0.000 0.748 0.000 0.000 0.252 0.000
#> GSM152927 2 0.3175 0.8386 0.000 0.744 0.000 0.000 0.256 0.000
#> GSM152928 2 0.3198 0.8372 0.000 0.740 0.000 0.000 0.260 0.000
#> GSM152929 2 0.3151 0.8397 0.000 0.748 0.000 0.000 0.252 0.000
#> GSM152930 2 0.3151 0.8397 0.000 0.748 0.000 0.000 0.252 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 tissue(p) k
#> SD:kmeans 164 1.13e-28 2
#> SD:kmeans 162 2.03e-32 3
#> SD:kmeans 142 2.48e-34 4
#> SD:kmeans 144 1.64e-37 5
#> SD:kmeans 143 5.24e-35 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 12013 rows and 164 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 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 0.740 0.868 0.943 0.4771 0.533 0.533
#> 3 3 0.836 0.888 0.945 0.3655 0.745 0.553
#> 4 4 0.592 0.684 0.825 0.1447 0.833 0.565
#> 5 5 0.549 0.523 0.689 0.0637 0.951 0.807
#> 6 6 0.566 0.483 0.632 0.0404 0.952 0.792
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
#> GSM152839 1 0.0000 0.9333 1.000 0.000
#> GSM152840 1 0.0000 0.9333 1.000 0.000
#> GSM152841 1 0.0000 0.9333 1.000 0.000
#> GSM152842 1 0.1633 0.9198 0.976 0.024
#> GSM152843 1 0.0000 0.9333 1.000 0.000
#> GSM152844 1 0.0376 0.9311 0.996 0.004
#> GSM152845 2 0.0000 0.9449 0.000 1.000
#> GSM152846 1 0.6343 0.7983 0.840 0.160
#> GSM152847 1 0.0000 0.9333 1.000 0.000
#> GSM152848 1 0.0000 0.9333 1.000 0.000
#> GSM152849 1 0.0000 0.9333 1.000 0.000
#> GSM152850 1 0.2423 0.9096 0.960 0.040
#> GSM152851 1 0.0000 0.9333 1.000 0.000
#> GSM152852 1 0.5842 0.8199 0.860 0.140
#> GSM152853 1 0.0000 0.9333 1.000 0.000
#> GSM152854 1 0.6801 0.7732 0.820 0.180
#> GSM152855 1 0.0000 0.9333 1.000 0.000
#> GSM153238 2 0.0376 0.9430 0.004 0.996
#> GSM153239 1 0.0000 0.9333 1.000 0.000
#> GSM153240 1 0.0000 0.9333 1.000 0.000
#> GSM153241 1 0.0000 0.9333 1.000 0.000
#> GSM153242 1 0.9909 0.2130 0.556 0.444
#> GSM153243 2 0.0000 0.9449 0.000 1.000
#> GSM153244 1 0.3584 0.8885 0.932 0.068
#> GSM153245 1 0.0000 0.9333 1.000 0.000
#> GSM153246 1 0.9983 0.0959 0.524 0.476
#> GSM153247 1 0.9710 0.3476 0.600 0.400
#> GSM153248 2 0.9970 0.0776 0.468 0.532
#> GSM153249 1 0.0000 0.9333 1.000 0.000
#> GSM153250 1 0.0000 0.9333 1.000 0.000
#> GSM153251 2 0.9491 0.4179 0.368 0.632
#> GSM153252 1 0.0000 0.9333 1.000 0.000
#> GSM153253 1 0.0000 0.9333 1.000 0.000
#> GSM153254 1 0.6801 0.7738 0.820 0.180
#> GSM153255 1 0.0000 0.9333 1.000 0.000
#> GSM153256 1 0.0000 0.9333 1.000 0.000
#> GSM153257 1 0.0000 0.9333 1.000 0.000
#> GSM153258 1 0.0376 0.9312 0.996 0.004
#> GSM153259 1 0.7883 0.6917 0.764 0.236
#> GSM153260 2 0.6343 0.7931 0.160 0.840
#> GSM153261 2 0.9460 0.4303 0.364 0.636
#> GSM153262 1 0.0000 0.9333 1.000 0.000
#> GSM153263 1 0.0000 0.9333 1.000 0.000
#> GSM153264 1 0.0376 0.9311 0.996 0.004
#> GSM153265 1 0.0000 0.9333 1.000 0.000
#> GSM153266 1 0.0000 0.9333 1.000 0.000
#> GSM153267 1 0.0000 0.9333 1.000 0.000
#> GSM153268 1 0.0000 0.9333 1.000 0.000
#> GSM153269 1 0.0000 0.9333 1.000 0.000
#> GSM153270 1 0.0000 0.9333 1.000 0.000
#> GSM153271 1 0.0000 0.9333 1.000 0.000
#> GSM153272 1 0.0000 0.9333 1.000 0.000
#> GSM153273 1 0.8608 0.6145 0.716 0.284
#> GSM153274 1 0.0000 0.9333 1.000 0.000
#> GSM153275 1 0.0000 0.9333 1.000 0.000
#> GSM153276 1 0.0000 0.9333 1.000 0.000
#> GSM153277 1 0.0000 0.9333 1.000 0.000
#> GSM153278 1 0.1414 0.9225 0.980 0.020
#> GSM153279 1 0.0000 0.9333 1.000 0.000
#> GSM153280 1 0.0000 0.9333 1.000 0.000
#> GSM153281 1 0.0000 0.9333 1.000 0.000
#> GSM153282 1 0.0000 0.9333 1.000 0.000
#> GSM153283 1 0.0000 0.9333 1.000 0.000
#> GSM153284 1 0.0000 0.9333 1.000 0.000
#> GSM153285 1 0.0000 0.9333 1.000 0.000
#> GSM153286 1 0.0000 0.9333 1.000 0.000
#> GSM153287 1 0.0000 0.9333 1.000 0.000
#> GSM153288 1 0.0000 0.9333 1.000 0.000
#> GSM153289 1 0.0000 0.9333 1.000 0.000
#> GSM153290 1 0.0000 0.9333 1.000 0.000
#> GSM153291 1 0.0000 0.9333 1.000 0.000
#> GSM153292 1 0.0000 0.9333 1.000 0.000
#> GSM153293 1 0.0000 0.9333 1.000 0.000
#> GSM153294 1 0.8713 0.6061 0.708 0.292
#> GSM153295 1 0.0000 0.9333 1.000 0.000
#> GSM153054 1 0.8499 0.6320 0.724 0.276
#> GSM153055 1 0.0000 0.9333 1.000 0.000
#> GSM153056 1 0.0000 0.9333 1.000 0.000
#> GSM153057 1 0.9491 0.4349 0.632 0.368
#> GSM153058 1 0.8909 0.5657 0.692 0.308
#> GSM153059 2 0.4690 0.8645 0.100 0.900
#> GSM153060 1 0.9393 0.4629 0.644 0.356
#> GSM153061 2 0.4298 0.8793 0.088 0.912
#> GSM153062 2 0.2043 0.9257 0.032 0.968
#> GSM153063 1 0.6438 0.7922 0.836 0.164
#> GSM153064 1 0.4562 0.8610 0.904 0.096
#> GSM153065 2 0.0000 0.9449 0.000 1.000
#> GSM153066 2 0.0000 0.9449 0.000 1.000
#> GSM153067 1 0.0000 0.9333 1.000 0.000
#> GSM153068 2 0.8267 0.6436 0.260 0.740
#> GSM153069 1 0.0000 0.9333 1.000 0.000
#> GSM153070 1 0.0000 0.9333 1.000 0.000
#> GSM153071 1 0.3879 0.8828 0.924 0.076
#> GSM153072 2 0.6712 0.7827 0.176 0.824
#> GSM153073 1 0.0000 0.9333 1.000 0.000
#> GSM153074 1 0.0000 0.9333 1.000 0.000
#> GSM153075 1 0.0000 0.9333 1.000 0.000
#> GSM153076 1 0.0000 0.9333 1.000 0.000
#> GSM153077 1 0.3431 0.8912 0.936 0.064
#> GSM153078 1 0.3584 0.8901 0.932 0.068
#> GSM153079 2 0.2948 0.9102 0.052 0.948
#> GSM153080 1 0.0000 0.9333 1.000 0.000
#> GSM153081 1 0.0000 0.9333 1.000 0.000
#> GSM153082 2 0.0376 0.9430 0.004 0.996
#> GSM153083 2 0.0000 0.9449 0.000 1.000
#> GSM153084 2 0.0000 0.9449 0.000 1.000
#> GSM153085 2 0.3431 0.9033 0.064 0.936
#> GSM153086 2 0.0938 0.9391 0.012 0.988
#> GSM153087 1 0.0000 0.9333 1.000 0.000
#> GSM153088 1 0.0000 0.9333 1.000 0.000
#> GSM153089 2 0.9866 0.2317 0.432 0.568
#> GSM153090 1 0.0000 0.9333 1.000 0.000
#> GSM153091 2 0.3879 0.8891 0.076 0.924
#> GSM153092 1 0.3274 0.8965 0.940 0.060
#> GSM153093 1 0.0000 0.9333 1.000 0.000
#> GSM153094 2 0.0672 0.9411 0.008 0.992
#> GSM153095 2 0.5842 0.8205 0.140 0.860
#> GSM153096 1 0.9522 0.4337 0.628 0.372
#> GSM153097 2 0.1184 0.9365 0.016 0.984
#> GSM153098 1 0.8443 0.6363 0.728 0.272
#> GSM153099 1 0.0000 0.9333 1.000 0.000
#> GSM153100 1 0.2948 0.9009 0.948 0.052
#> GSM153101 2 0.4815 0.8645 0.104 0.896
#> GSM153102 2 0.0000 0.9449 0.000 1.000
#> GSM153103 2 0.2236 0.9227 0.036 0.964
#> GSM153104 1 0.0000 0.9333 1.000 0.000
#> GSM153106 1 0.5737 0.8280 0.864 0.136
#> GSM153107 1 0.3114 0.8990 0.944 0.056
#> GSM153108 1 0.0672 0.9290 0.992 0.008
#> GSM153109 2 0.0000 0.9449 0.000 1.000
#> GSM153110 1 0.9732 0.3533 0.596 0.404
#> GSM153111 2 0.0672 0.9411 0.008 0.992
#> GSM153112 1 0.8207 0.6618 0.744 0.256
#> GSM153113 2 0.0000 0.9449 0.000 1.000
#> GSM153114 1 0.0000 0.9333 1.000 0.000
#> GSM187532 2 0.0000 0.9449 0.000 1.000
#> GSM187533 2 0.0000 0.9449 0.000 1.000
#> GSM187534 2 0.0000 0.9449 0.000 1.000
#> GSM187535 2 0.0000 0.9449 0.000 1.000
#> GSM152906 2 0.0000 0.9449 0.000 1.000
#> GSM152907 2 0.0000 0.9449 0.000 1.000
#> GSM152908 2 0.0000 0.9449 0.000 1.000
#> GSM152909 2 0.0000 0.9449 0.000 1.000
#> GSM152910 2 0.0000 0.9449 0.000 1.000
#> GSM152911 2 0.0000 0.9449 0.000 1.000
#> GSM152912 2 0.0000 0.9449 0.000 1.000
#> GSM152913 2 0.0000 0.9449 0.000 1.000
#> GSM152914 2 0.0000 0.9449 0.000 1.000
#> GSM152915 2 0.0000 0.9449 0.000 1.000
#> GSM152916 2 0.0000 0.9449 0.000 1.000
#> GSM152917 2 0.0000 0.9449 0.000 1.000
#> GSM152918 2 0.0000 0.9449 0.000 1.000
#> GSM152919 2 0.0000 0.9449 0.000 1.000
#> GSM152920 2 0.0000 0.9449 0.000 1.000
#> GSM152921 2 0.0000 0.9449 0.000 1.000
#> GSM152922 2 0.0000 0.9449 0.000 1.000
#> GSM152923 2 0.0000 0.9449 0.000 1.000
#> GSM152924 2 0.0000 0.9449 0.000 1.000
#> GSM152925 2 0.0000 0.9449 0.000 1.000
#> GSM152926 2 0.0000 0.9449 0.000 1.000
#> GSM152927 2 0.0000 0.9449 0.000 1.000
#> GSM152928 2 0.0000 0.9449 0.000 1.000
#> GSM152929 2 0.0000 0.9449 0.000 1.000
#> GSM152930 2 0.0000 0.9449 0.000 1.000
cbind(get_classes(res, k = 3), get_membership(res, k = 3))
#> class entropy silhouette p1 p2 p3
#> GSM152839 3 0.4291 0.7776 0.180 0.000 0.820
#> GSM152840 3 0.0592 0.9349 0.012 0.000 0.988
#> GSM152841 1 0.2537 0.9024 0.920 0.000 0.080
#> GSM152842 3 0.0000 0.9398 0.000 0.000 1.000
#> GSM152843 3 0.0424 0.9370 0.008 0.000 0.992
#> GSM152844 3 0.0000 0.9398 0.000 0.000 1.000
#> GSM152845 3 0.0237 0.9380 0.000 0.004 0.996
#> GSM152846 3 0.0000 0.9398 0.000 0.000 1.000
#> GSM152847 3 0.0000 0.9398 0.000 0.000 1.000
#> GSM152848 1 0.5178 0.6680 0.744 0.000 0.256
#> GSM152849 3 0.0000 0.9398 0.000 0.000 1.000
#> GSM152850 3 0.0892 0.9302 0.020 0.000 0.980
#> GSM152851 3 0.3752 0.8221 0.144 0.000 0.856
#> GSM152852 3 0.0000 0.9398 0.000 0.000 1.000
#> GSM152853 3 0.0000 0.9398 0.000 0.000 1.000
#> GSM152854 3 0.0000 0.9398 0.000 0.000 1.000
#> GSM152855 1 0.0000 0.9381 1.000 0.000 0.000
#> GSM153238 3 0.0592 0.9345 0.000 0.012 0.988
#> GSM153239 3 0.0237 0.9385 0.004 0.000 0.996
#> GSM153240 1 0.0237 0.9373 0.996 0.000 0.004
#> GSM153241 3 0.0000 0.9398 0.000 0.000 1.000
#> GSM153242 3 0.0000 0.9398 0.000 0.000 1.000
#> GSM153243 3 0.2165 0.8959 0.000 0.064 0.936
#> GSM153244 1 0.7074 0.0559 0.500 0.020 0.480
#> GSM153245 3 0.0000 0.9398 0.000 0.000 1.000
#> GSM153246 3 0.0000 0.9398 0.000 0.000 1.000
#> GSM153247 3 0.1129 0.9303 0.020 0.004 0.976
#> GSM153248 1 0.4062 0.8024 0.836 0.164 0.000
#> GSM153249 1 0.0000 0.9381 1.000 0.000 0.000
#> GSM153250 1 0.0000 0.9381 1.000 0.000 0.000
#> GSM153251 3 0.0000 0.9398 0.000 0.000 1.000
#> GSM153252 1 0.0000 0.9381 1.000 0.000 0.000
#> GSM153253 1 0.2448 0.9064 0.924 0.000 0.076
#> GSM153254 3 0.4174 0.8543 0.092 0.036 0.872
#> GSM153255 1 0.0000 0.9381 1.000 0.000 0.000
#> GSM153256 1 0.0000 0.9381 1.000 0.000 0.000
#> GSM153257 1 0.0000 0.9381 1.000 0.000 0.000
#> GSM153258 1 0.0237 0.9377 0.996 0.000 0.004
#> GSM153259 1 0.2356 0.8990 0.928 0.072 0.000
#> GSM153260 3 0.0892 0.9300 0.000 0.020 0.980
#> GSM153261 3 0.0000 0.9398 0.000 0.000 1.000
#> GSM153262 1 0.1529 0.9265 0.960 0.000 0.040
#> GSM153263 1 0.0000 0.9381 1.000 0.000 0.000
#> GSM153264 1 0.2711 0.8913 0.912 0.000 0.088
#> GSM153265 1 0.2625 0.9006 0.916 0.000 0.084
#> GSM153266 1 0.3340 0.8611 0.880 0.000 0.120
#> GSM153267 1 0.0000 0.9381 1.000 0.000 0.000
#> GSM153268 1 0.6062 0.4165 0.616 0.000 0.384
#> GSM153269 1 0.0000 0.9381 1.000 0.000 0.000
#> GSM153270 1 0.3192 0.8715 0.888 0.000 0.112
#> GSM153271 1 0.0000 0.9381 1.000 0.000 0.000
#> GSM153272 1 0.0000 0.9381 1.000 0.000 0.000
#> GSM153273 1 0.4033 0.8312 0.856 0.136 0.008
#> GSM153274 1 0.0592 0.9362 0.988 0.000 0.012
#> GSM153275 1 0.0000 0.9381 1.000 0.000 0.000
#> GSM153276 1 0.0747 0.9353 0.984 0.000 0.016
#> GSM153277 1 0.1529 0.9271 0.960 0.000 0.040
#> GSM153278 3 0.0000 0.9398 0.000 0.000 1.000
#> GSM153279 1 0.6168 0.3318 0.588 0.000 0.412
#> GSM153280 1 0.2356 0.9098 0.928 0.000 0.072
#> GSM153281 1 0.1411 0.9281 0.964 0.000 0.036
#> GSM153282 1 0.2796 0.8939 0.908 0.000 0.092
#> GSM153283 1 0.0000 0.9381 1.000 0.000 0.000
#> GSM153284 1 0.0000 0.9381 1.000 0.000 0.000
#> GSM153285 1 0.2711 0.8968 0.912 0.000 0.088
#> GSM153286 1 0.0000 0.9381 1.000 0.000 0.000
#> GSM153287 1 0.0000 0.9381 1.000 0.000 0.000
#> GSM153288 1 0.0000 0.9381 1.000 0.000 0.000
#> GSM153289 1 0.0000 0.9381 1.000 0.000 0.000
#> GSM153290 1 0.2796 0.8945 0.908 0.000 0.092
#> GSM153291 1 0.0000 0.9381 1.000 0.000 0.000
#> GSM153292 1 0.0237 0.9373 0.996 0.000 0.004
#> GSM153293 1 0.0000 0.9381 1.000 0.000 0.000
#> GSM153294 1 0.1753 0.9173 0.952 0.048 0.000
#> GSM153295 1 0.0000 0.9381 1.000 0.000 0.000
#> GSM153054 3 0.7959 0.5305 0.288 0.092 0.620
#> GSM153055 1 0.2165 0.9130 0.936 0.000 0.064
#> GSM153056 3 0.0592 0.9350 0.012 0.000 0.988
#> GSM153057 3 0.2383 0.9080 0.044 0.016 0.940
#> GSM153058 3 0.0000 0.9398 0.000 0.000 1.000
#> GSM153059 3 0.2165 0.8973 0.000 0.064 0.936
#> GSM153060 3 0.0000 0.9398 0.000 0.000 1.000
#> GSM153061 3 0.0000 0.9398 0.000 0.000 1.000
#> GSM153062 3 0.0000 0.9398 0.000 0.000 1.000
#> GSM153063 3 0.0000 0.9398 0.000 0.000 1.000
#> GSM153064 1 0.0237 0.9372 0.996 0.004 0.000
#> GSM153065 3 0.2066 0.8996 0.000 0.060 0.940
#> GSM153066 2 0.0747 0.9409 0.000 0.984 0.016
#> GSM153067 1 0.0000 0.9381 1.000 0.000 0.000
#> GSM153068 3 0.0000 0.9398 0.000 0.000 1.000
#> GSM153069 1 0.0000 0.9381 1.000 0.000 0.000
#> GSM153070 1 0.1031 0.9325 0.976 0.000 0.024
#> GSM153071 3 0.5070 0.7170 0.224 0.004 0.772
#> GSM153072 3 0.8607 0.4878 0.152 0.256 0.592
#> GSM153073 1 0.0000 0.9381 1.000 0.000 0.000
#> GSM153074 1 0.0000 0.9381 1.000 0.000 0.000
#> GSM153075 1 0.1860 0.9215 0.948 0.000 0.052
#> GSM153076 1 0.0000 0.9381 1.000 0.000 0.000
#> GSM153077 1 0.4342 0.8438 0.856 0.024 0.120
#> GSM153078 3 0.5378 0.6969 0.236 0.008 0.756
#> GSM153079 2 0.6915 0.7036 0.140 0.736 0.124
#> GSM153080 3 0.0000 0.9398 0.000 0.000 1.000
#> GSM153081 1 0.3879 0.8228 0.848 0.000 0.152
#> GSM153082 2 0.0892 0.9383 0.020 0.980 0.000
#> GSM153083 2 0.0000 0.9518 0.000 1.000 0.000
#> GSM153084 2 0.0000 0.9518 0.000 1.000 0.000
#> GSM153085 2 0.8464 0.4699 0.132 0.596 0.272
#> GSM153086 2 0.2116 0.9177 0.040 0.948 0.012
#> GSM153087 1 0.1529 0.9270 0.960 0.000 0.040
#> GSM153088 1 0.0000 0.9381 1.000 0.000 0.000
#> GSM153089 3 0.0000 0.9398 0.000 0.000 1.000
#> GSM153090 1 0.0000 0.9381 1.000 0.000 0.000
#> GSM153091 2 0.4062 0.7900 0.164 0.836 0.000
#> GSM153092 1 0.2173 0.9149 0.944 0.048 0.008
#> GSM153093 1 0.0000 0.9381 1.000 0.000 0.000
#> GSM153094 2 0.1643 0.9194 0.044 0.956 0.000
#> GSM153095 2 0.8212 0.4561 0.104 0.600 0.296
#> GSM153096 1 0.4351 0.7948 0.828 0.168 0.004
#> GSM153097 2 0.1964 0.9085 0.056 0.944 0.000
#> GSM153098 1 0.2261 0.9029 0.932 0.068 0.000
#> GSM153099 1 0.0000 0.9381 1.000 0.000 0.000
#> GSM153100 1 0.0237 0.9372 0.996 0.004 0.000
#> GSM153101 3 0.8464 0.4687 0.128 0.280 0.592
#> GSM153102 2 0.6673 0.6580 0.056 0.720 0.224
#> GSM153103 2 0.7425 0.4611 0.052 0.620 0.328
#> GSM153104 1 0.2066 0.9171 0.940 0.000 0.060
#> GSM153106 1 0.0747 0.9337 0.984 0.016 0.000
#> GSM153107 1 0.0424 0.9364 0.992 0.008 0.000
#> GSM153108 1 0.2400 0.9115 0.932 0.004 0.064
#> GSM153109 2 0.0000 0.9518 0.000 1.000 0.000
#> GSM153110 1 0.7209 0.3917 0.604 0.360 0.036
#> GSM153111 2 0.1860 0.9125 0.052 0.948 0.000
#> GSM153112 1 0.1411 0.9237 0.964 0.036 0.000
#> GSM153113 2 0.0000 0.9518 0.000 1.000 0.000
#> GSM153114 1 0.0000 0.9381 1.000 0.000 0.000
#> GSM187532 2 0.0000 0.9518 0.000 1.000 0.000
#> GSM187533 2 0.0000 0.9518 0.000 1.000 0.000
#> GSM187534 2 0.0000 0.9518 0.000 1.000 0.000
#> GSM187535 2 0.0000 0.9518 0.000 1.000 0.000
#> GSM152906 2 0.0000 0.9518 0.000 1.000 0.000
#> GSM152907 2 0.0000 0.9518 0.000 1.000 0.000
#> GSM152908 2 0.0000 0.9518 0.000 1.000 0.000
#> GSM152909 2 0.0000 0.9518 0.000 1.000 0.000
#> GSM152910 2 0.0000 0.9518 0.000 1.000 0.000
#> GSM152911 2 0.0000 0.9518 0.000 1.000 0.000
#> GSM152912 2 0.0000 0.9518 0.000 1.000 0.000
#> GSM152913 2 0.0000 0.9518 0.000 1.000 0.000
#> GSM152914 2 0.0000 0.9518 0.000 1.000 0.000
#> GSM152915 2 0.0000 0.9518 0.000 1.000 0.000
#> GSM152916 2 0.0000 0.9518 0.000 1.000 0.000
#> GSM152917 2 0.0000 0.9518 0.000 1.000 0.000
#> GSM152918 2 0.0000 0.9518 0.000 1.000 0.000
#> GSM152919 2 0.0000 0.9518 0.000 1.000 0.000
#> GSM152920 2 0.0000 0.9518 0.000 1.000 0.000
#> GSM152921 2 0.0000 0.9518 0.000 1.000 0.000
#> GSM152922 2 0.0000 0.9518 0.000 1.000 0.000
#> GSM152923 2 0.0000 0.9518 0.000 1.000 0.000
#> GSM152924 2 0.0000 0.9518 0.000 1.000 0.000
#> GSM152925 2 0.0000 0.9518 0.000 1.000 0.000
#> GSM152926 2 0.0000 0.9518 0.000 1.000 0.000
#> GSM152927 2 0.0000 0.9518 0.000 1.000 0.000
#> GSM152928 2 0.0000 0.9518 0.000 1.000 0.000
#> GSM152929 2 0.0000 0.9518 0.000 1.000 0.000
#> GSM152930 2 0.0000 0.9518 0.000 1.000 0.000
cbind(get_classes(res, k = 4), get_membership(res, k = 4))
#> class entropy silhouette p1 p2 p3 p4
#> GSM152839 3 0.6871 0.4449 0.240 0.000 0.592 0.168
#> GSM152840 3 0.4372 0.6929 0.004 0.000 0.728 0.268
#> GSM152841 4 0.1305 0.7580 0.004 0.000 0.036 0.960
#> GSM152842 3 0.0707 0.8617 0.020 0.000 0.980 0.000
#> GSM152843 3 0.3732 0.8175 0.092 0.000 0.852 0.056
#> GSM152844 3 0.2197 0.8544 0.004 0.000 0.916 0.080
#> GSM152845 3 0.1139 0.8635 0.008 0.012 0.972 0.008
#> GSM152846 3 0.1824 0.8597 0.004 0.000 0.936 0.060
#> GSM152847 3 0.1978 0.8499 0.068 0.000 0.928 0.004
#> GSM152848 1 0.6916 0.4663 0.588 0.000 0.176 0.236
#> GSM152849 3 0.1109 0.8620 0.028 0.000 0.968 0.004
#> GSM152850 3 0.4399 0.7168 0.212 0.000 0.768 0.020
#> GSM152851 4 0.5097 0.1138 0.004 0.000 0.428 0.568
#> GSM152852 3 0.1867 0.8584 0.000 0.000 0.928 0.072
#> GSM152853 3 0.3355 0.8094 0.004 0.000 0.836 0.160
#> GSM152854 3 0.0779 0.8633 0.004 0.000 0.980 0.016
#> GSM152855 4 0.4040 0.6851 0.248 0.000 0.000 0.752
#> GSM153238 3 0.3495 0.8037 0.140 0.016 0.844 0.000
#> GSM153239 3 0.3257 0.8158 0.004 0.000 0.844 0.152
#> GSM153240 4 0.2799 0.7731 0.108 0.000 0.008 0.884
#> GSM153241 3 0.1059 0.8655 0.016 0.000 0.972 0.012
#> GSM153242 3 0.1635 0.8634 0.008 0.000 0.948 0.044
#> GSM153243 3 0.3320 0.8227 0.056 0.068 0.876 0.000
#> GSM153244 4 0.6629 0.4824 0.076 0.028 0.244 0.652
#> GSM153245 3 0.2773 0.8395 0.004 0.000 0.880 0.116
#> GSM153246 3 0.0000 0.8610 0.000 0.000 1.000 0.000
#> GSM153247 3 0.4521 0.8145 0.092 0.024 0.828 0.056
#> GSM153248 1 0.1743 0.6354 0.940 0.004 0.000 0.056
#> GSM153249 4 0.1109 0.7724 0.028 0.000 0.004 0.968
#> GSM153250 1 0.4941 0.1407 0.564 0.000 0.000 0.436
#> GSM153251 3 0.0895 0.8637 0.004 0.000 0.976 0.020
#> GSM153252 4 0.1890 0.7776 0.056 0.000 0.008 0.936
#> GSM153253 4 0.1356 0.7637 0.008 0.000 0.032 0.960
#> GSM153254 3 0.7696 0.4555 0.084 0.060 0.552 0.304
#> GSM153255 4 0.2149 0.7697 0.088 0.000 0.000 0.912
#> GSM153256 4 0.4697 0.5201 0.356 0.000 0.000 0.644
#> GSM153257 4 0.2944 0.7696 0.128 0.000 0.004 0.868
#> GSM153258 1 0.5105 0.5165 0.696 0.000 0.028 0.276
#> GSM153259 1 0.1489 0.6334 0.952 0.004 0.000 0.044
#> GSM153260 3 0.2928 0.8311 0.108 0.012 0.880 0.000
#> GSM153261 3 0.1118 0.8598 0.036 0.000 0.964 0.000
#> GSM153262 4 0.1406 0.7680 0.016 0.000 0.024 0.960
#> GSM153263 1 0.4977 0.0867 0.540 0.000 0.000 0.460
#> GSM153264 1 0.4257 0.6214 0.812 0.000 0.048 0.140
#> GSM153265 4 0.2053 0.7465 0.004 0.000 0.072 0.924
#> GSM153266 1 0.5766 0.5844 0.704 0.000 0.104 0.192
#> GSM153267 4 0.4522 0.5826 0.320 0.000 0.000 0.680
#> GSM153268 4 0.3088 0.6893 0.008 0.000 0.128 0.864
#> GSM153269 4 0.4898 0.3831 0.416 0.000 0.000 0.584
#> GSM153270 4 0.6815 0.4206 0.284 0.000 0.136 0.580
#> GSM153271 1 0.4992 -0.0325 0.524 0.000 0.000 0.476
#> GSM153272 4 0.3219 0.7484 0.164 0.000 0.000 0.836
#> GSM153273 1 0.2401 0.6369 0.904 0.000 0.004 0.092
#> GSM153274 4 0.5252 0.5368 0.336 0.000 0.020 0.644
#> GSM153275 4 0.4164 0.6605 0.264 0.000 0.000 0.736
#> GSM153276 4 0.5417 0.6284 0.240 0.000 0.056 0.704
#> GSM153277 4 0.3216 0.7636 0.076 0.000 0.044 0.880
#> GSM153278 3 0.3172 0.8009 0.160 0.000 0.840 0.000
#> GSM153279 4 0.4919 0.5803 0.048 0.000 0.200 0.752
#> GSM153280 4 0.1677 0.7555 0.012 0.000 0.040 0.948
#> GSM153281 4 0.1406 0.7704 0.024 0.000 0.016 0.960
#> GSM153282 4 0.1661 0.7504 0.004 0.000 0.052 0.944
#> GSM153283 1 0.4008 0.5423 0.756 0.000 0.000 0.244
#> GSM153284 4 0.3311 0.7404 0.172 0.000 0.000 0.828
#> GSM153285 4 0.1854 0.7562 0.012 0.000 0.048 0.940
#> GSM153286 4 0.4134 0.6673 0.260 0.000 0.000 0.740
#> GSM153287 4 0.0779 0.7688 0.016 0.000 0.004 0.980
#> GSM153288 4 0.3219 0.7498 0.164 0.000 0.000 0.836
#> GSM153289 4 0.4746 0.4759 0.368 0.000 0.000 0.632
#> GSM153290 4 0.1677 0.7567 0.012 0.000 0.040 0.948
#> GSM153291 4 0.1940 0.7729 0.076 0.000 0.000 0.924
#> GSM153292 4 0.0524 0.7678 0.008 0.000 0.004 0.988
#> GSM153293 4 0.4164 0.6621 0.264 0.000 0.000 0.736
#> GSM153294 1 0.4855 0.5522 0.712 0.020 0.000 0.268
#> GSM153295 4 0.4644 0.6919 0.228 0.000 0.024 0.748
#> GSM153054 1 0.6504 0.4374 0.632 0.020 0.284 0.064
#> GSM153055 4 0.6495 0.3744 0.356 0.000 0.084 0.560
#> GSM153056 3 0.3647 0.8269 0.040 0.000 0.852 0.108
#> GSM153057 3 0.6327 0.7003 0.116 0.032 0.712 0.140
#> GSM153058 3 0.0804 0.8638 0.008 0.000 0.980 0.012
#> GSM153059 3 0.5035 0.7507 0.068 0.136 0.784 0.012
#> GSM153060 3 0.0188 0.8616 0.000 0.000 0.996 0.004
#> GSM153061 3 0.0469 0.8596 0.012 0.000 0.988 0.000
#> GSM153062 3 0.0000 0.8610 0.000 0.000 1.000 0.000
#> GSM153063 3 0.1978 0.8615 0.004 0.000 0.928 0.068
#> GSM153064 1 0.2469 0.6317 0.892 0.000 0.000 0.108
#> GSM153065 3 0.3144 0.8242 0.044 0.072 0.884 0.000
#> GSM153066 2 0.2255 0.8805 0.012 0.920 0.068 0.000
#> GSM153067 4 0.2999 0.7672 0.132 0.000 0.004 0.864
#> GSM153068 3 0.0000 0.8610 0.000 0.000 1.000 0.000
#> GSM153069 4 0.0657 0.7692 0.012 0.000 0.004 0.984
#> GSM153070 1 0.6069 0.3397 0.588 0.000 0.056 0.356
#> GSM153071 3 0.7685 0.1068 0.288 0.000 0.456 0.256
#> GSM153072 1 0.7568 0.4320 0.588 0.076 0.264 0.072
#> GSM153073 1 0.4053 0.5681 0.768 0.000 0.004 0.228
#> GSM153074 4 0.2760 0.7648 0.128 0.000 0.000 0.872
#> GSM153075 4 0.4656 0.7350 0.136 0.000 0.072 0.792
#> GSM153076 1 0.4477 0.4483 0.688 0.000 0.000 0.312
#> GSM153077 1 0.4644 0.6249 0.800 0.004 0.064 0.132
#> GSM153078 3 0.7470 0.2394 0.344 0.012 0.508 0.136
#> GSM153079 1 0.5644 0.5557 0.712 0.220 0.060 0.008
#> GSM153080 3 0.3443 0.8184 0.016 0.000 0.848 0.136
#> GSM153081 1 0.4093 0.6321 0.832 0.000 0.072 0.096
#> GSM153082 2 0.5367 0.4945 0.304 0.664 0.000 0.032
#> GSM153083 1 0.4981 0.0415 0.536 0.464 0.000 0.000
#> GSM153084 2 0.2255 0.8898 0.068 0.920 0.012 0.000
#> GSM153085 1 0.9291 0.3261 0.400 0.272 0.228 0.100
#> GSM153086 1 0.4387 0.5508 0.752 0.236 0.012 0.000
#> GSM153087 4 0.4617 0.7150 0.204 0.000 0.032 0.764
#> GSM153088 1 0.4877 0.2053 0.592 0.000 0.000 0.408
#> GSM153089 3 0.2140 0.8639 0.008 0.008 0.932 0.052
#> GSM153090 4 0.4994 0.1697 0.480 0.000 0.000 0.520
#> GSM153091 1 0.3813 0.6217 0.828 0.148 0.000 0.024
#> GSM153092 1 0.5309 0.5215 0.688 0.028 0.004 0.280
#> GSM153093 4 0.2149 0.7740 0.088 0.000 0.000 0.912
#> GSM153094 1 0.4817 0.2941 0.612 0.388 0.000 0.000
#> GSM153095 2 0.9279 -0.0412 0.268 0.404 0.228 0.100
#> GSM153096 1 0.2457 0.6387 0.912 0.008 0.004 0.076
#> GSM153097 1 0.3032 0.6219 0.868 0.124 0.008 0.000
#> GSM153098 1 0.5906 0.1907 0.528 0.036 0.000 0.436
#> GSM153099 4 0.5736 0.5340 0.328 0.000 0.044 0.628
#> GSM153100 1 0.4866 0.2935 0.596 0.000 0.000 0.404
#> GSM153101 1 0.8869 0.1527 0.412 0.148 0.352 0.088
#> GSM153102 1 0.9395 0.2659 0.376 0.312 0.192 0.120
#> GSM153103 1 0.6623 0.4447 0.620 0.148 0.232 0.000
#> GSM153104 4 0.1406 0.7691 0.016 0.000 0.024 0.960
#> GSM153106 1 0.5399 0.0774 0.520 0.012 0.000 0.468
#> GSM153107 1 0.4677 0.4780 0.680 0.004 0.000 0.316
#> GSM153108 4 0.5579 0.5708 0.252 0.000 0.060 0.688
#> GSM153109 2 0.4543 0.5320 0.324 0.676 0.000 0.000
#> GSM153110 1 0.1911 0.6342 0.944 0.032 0.004 0.020
#> GSM153111 1 0.5148 0.3662 0.640 0.348 0.008 0.004
#> GSM153112 1 0.4452 0.5589 0.732 0.008 0.000 0.260
#> GSM153113 2 0.2281 0.8677 0.096 0.904 0.000 0.000
#> GSM153114 4 0.3172 0.7519 0.160 0.000 0.000 0.840
#> GSM187532 2 0.0336 0.9460 0.000 0.992 0.008 0.000
#> GSM187533 2 0.0188 0.9514 0.004 0.996 0.000 0.000
#> GSM187534 2 0.0188 0.9514 0.004 0.996 0.000 0.000
#> GSM187535 2 0.0817 0.9356 0.024 0.976 0.000 0.000
#> GSM152906 2 0.0000 0.9511 0.000 1.000 0.000 0.000
#> GSM152907 2 0.0000 0.9511 0.000 1.000 0.000 0.000
#> GSM152908 2 0.0188 0.9514 0.004 0.996 0.000 0.000
#> GSM152909 2 0.0188 0.9514 0.004 0.996 0.000 0.000
#> GSM152910 2 0.0188 0.9514 0.004 0.996 0.000 0.000
#> GSM152911 2 0.0188 0.9514 0.004 0.996 0.000 0.000
#> GSM152912 2 0.0188 0.9514 0.004 0.996 0.000 0.000
#> GSM152913 2 0.0000 0.9511 0.000 1.000 0.000 0.000
#> GSM152914 2 0.0188 0.9514 0.004 0.996 0.000 0.000
#> GSM152915 2 0.0188 0.9514 0.004 0.996 0.000 0.000
#> GSM152916 2 0.0000 0.9511 0.000 1.000 0.000 0.000
#> GSM152917 2 0.0188 0.9514 0.004 0.996 0.000 0.000
#> GSM152918 2 0.0188 0.9514 0.004 0.996 0.000 0.000
#> GSM152919 2 0.0188 0.9514 0.004 0.996 0.000 0.000
#> GSM152920 2 0.0188 0.9514 0.004 0.996 0.000 0.000
#> GSM152921 2 0.0188 0.9514 0.004 0.996 0.000 0.000
#> GSM152922 2 0.0188 0.9514 0.004 0.996 0.000 0.000
#> GSM152923 2 0.0000 0.9511 0.000 1.000 0.000 0.000
#> GSM152924 2 0.0000 0.9511 0.000 1.000 0.000 0.000
#> GSM152925 2 0.0000 0.9511 0.000 1.000 0.000 0.000
#> GSM152926 2 0.0000 0.9511 0.000 1.000 0.000 0.000
#> GSM152927 2 0.0000 0.9511 0.000 1.000 0.000 0.000
#> GSM152928 2 0.0000 0.9511 0.000 1.000 0.000 0.000
#> GSM152929 2 0.0000 0.9511 0.000 1.000 0.000 0.000
#> GSM152930 2 0.0000 0.9511 0.000 1.000 0.000 0.000
cbind(get_classes(res, k = 5), get_membership(res, k = 5))
#> class entropy silhouette p1 p2 p3 p4 p5
#> GSM152839 3 0.7979 0.3590 0.124 0.000 0.412 0.168 0.296
#> GSM152840 3 0.5483 0.3947 0.004 0.000 0.504 0.440 0.052
#> GSM152841 4 0.0912 0.5943 0.000 0.000 0.012 0.972 0.016
#> GSM152842 3 0.3398 0.7284 0.024 0.000 0.828 0.004 0.144
#> GSM152843 3 0.6418 0.6374 0.076 0.000 0.612 0.076 0.236
#> GSM152844 3 0.4284 0.6945 0.000 0.000 0.736 0.224 0.040
#> GSM152845 3 0.2018 0.7427 0.008 0.008 0.932 0.012 0.040
#> GSM152846 3 0.3319 0.7392 0.008 0.000 0.852 0.100 0.040
#> GSM152847 3 0.5013 0.7041 0.056 0.000 0.728 0.028 0.188
#> GSM152848 5 0.7635 0.2837 0.208 0.000 0.176 0.116 0.500
#> GSM152849 3 0.3350 0.7358 0.040 0.000 0.844 0.004 0.112
#> GSM152850 3 0.6148 0.4925 0.096 0.000 0.544 0.016 0.344
#> GSM152851 4 0.5847 0.3350 0.028 0.000 0.268 0.628 0.076
#> GSM152852 3 0.4184 0.7199 0.004 0.000 0.772 0.176 0.048
#> GSM152853 3 0.5128 0.5749 0.000 0.000 0.604 0.344 0.052
#> GSM152854 3 0.2609 0.7450 0.004 0.000 0.896 0.052 0.048
#> GSM152855 4 0.5783 0.3231 0.100 0.000 0.000 0.540 0.360
#> GSM153238 3 0.5360 0.6366 0.196 0.020 0.704 0.004 0.076
#> GSM153239 3 0.5301 0.6472 0.004 0.000 0.648 0.272 0.076
#> GSM153240 4 0.4863 0.4676 0.048 0.000 0.000 0.656 0.296
#> GSM153241 3 0.4682 0.7321 0.036 0.000 0.760 0.040 0.164
#> GSM153242 3 0.3523 0.7378 0.004 0.000 0.832 0.120 0.044
#> GSM153243 3 0.5741 0.6607 0.080 0.072 0.700 0.000 0.148
#> GSM153244 4 0.7950 0.1841 0.068 0.028 0.256 0.484 0.164
#> GSM153245 3 0.4681 0.7048 0.004 0.000 0.728 0.204 0.064
#> GSM153246 3 0.1205 0.7358 0.004 0.000 0.956 0.000 0.040
#> GSM153247 3 0.7927 0.5515 0.132 0.052 0.552 0.100 0.164
#> GSM153248 1 0.4649 0.3386 0.720 0.012 0.000 0.036 0.232
#> GSM153249 4 0.3116 0.6038 0.064 0.000 0.000 0.860 0.076
#> GSM153250 5 0.6030 0.5908 0.196 0.000 0.000 0.224 0.580
#> GSM153251 3 0.2916 0.7476 0.012 0.000 0.884 0.048 0.056
#> GSM153252 4 0.4031 0.5865 0.044 0.000 0.000 0.772 0.184
#> GSM153253 4 0.1568 0.5967 0.000 0.000 0.020 0.944 0.036
#> GSM153254 3 0.9091 0.2088 0.124 0.060 0.352 0.280 0.184
#> GSM153255 4 0.3690 0.5595 0.020 0.000 0.000 0.780 0.200
#> GSM153256 4 0.6373 -0.2024 0.164 0.000 0.000 0.420 0.416
#> GSM153257 4 0.4708 0.5321 0.068 0.000 0.000 0.712 0.220
#> GSM153258 5 0.6755 0.5057 0.320 0.000 0.020 0.164 0.496
#> GSM153259 1 0.3912 0.3730 0.768 0.000 0.004 0.020 0.208
#> GSM153260 3 0.5157 0.6727 0.128 0.008 0.712 0.000 0.152
#> GSM153261 3 0.3507 0.7362 0.060 0.000 0.844 0.008 0.088
#> GSM153262 4 0.3631 0.6014 0.012 0.000 0.024 0.820 0.144
#> GSM153263 5 0.6751 0.4616 0.296 0.000 0.000 0.296 0.408
#> GSM153264 5 0.6209 0.4101 0.312 0.000 0.040 0.072 0.576
#> GSM153265 4 0.3646 0.5661 0.020 0.000 0.064 0.844 0.072
#> GSM153266 5 0.6988 0.2984 0.356 0.000 0.052 0.116 0.476
#> GSM153267 4 0.6037 -0.0757 0.116 0.000 0.000 0.444 0.440
#> GSM153268 4 0.3270 0.5403 0.004 0.000 0.100 0.852 0.044
#> GSM153269 5 0.6194 0.3990 0.156 0.000 0.000 0.328 0.516
#> GSM153270 4 0.8108 -0.0778 0.188 0.000 0.124 0.372 0.316
#> GSM153271 5 0.6396 0.4341 0.188 0.000 0.000 0.324 0.488
#> GSM153272 4 0.4817 0.4532 0.044 0.000 0.000 0.656 0.300
#> GSM153273 1 0.4392 0.3866 0.748 0.004 0.000 0.048 0.200
#> GSM153274 4 0.6989 -0.0531 0.116 0.000 0.048 0.424 0.412
#> GSM153275 4 0.6282 0.0331 0.156 0.000 0.000 0.476 0.368
#> GSM153276 4 0.7102 -0.1008 0.112 0.000 0.060 0.436 0.392
#> GSM153277 4 0.5802 0.5325 0.084 0.000 0.060 0.688 0.168
#> GSM153278 3 0.6296 0.5978 0.120 0.000 0.604 0.032 0.244
#> GSM153279 4 0.6931 0.3443 0.104 0.000 0.212 0.580 0.104
#> GSM153280 4 0.2804 0.5694 0.008 0.000 0.056 0.888 0.048
#> GSM153281 4 0.2362 0.6099 0.008 0.000 0.008 0.900 0.084
#> GSM153282 4 0.2456 0.5821 0.008 0.000 0.064 0.904 0.024
#> GSM153283 5 0.6404 0.4966 0.360 0.000 0.008 0.140 0.492
#> GSM153284 4 0.5687 0.3550 0.104 0.000 0.000 0.580 0.316
#> GSM153285 4 0.1997 0.5984 0.016 0.000 0.024 0.932 0.028
#> GSM153286 4 0.5691 0.2114 0.088 0.000 0.000 0.536 0.376
#> GSM153287 4 0.2233 0.5989 0.016 0.000 0.000 0.904 0.080
#> GSM153288 4 0.5027 0.4251 0.056 0.000 0.000 0.640 0.304
#> GSM153289 4 0.6150 0.1227 0.132 0.000 0.000 0.464 0.404
#> GSM153290 4 0.2591 0.5907 0.020 0.000 0.044 0.904 0.032
#> GSM153291 4 0.4170 0.5694 0.048 0.000 0.000 0.760 0.192
#> GSM153292 4 0.1981 0.6068 0.016 0.000 0.000 0.920 0.064
#> GSM153293 4 0.6180 0.0161 0.136 0.000 0.000 0.460 0.404
#> GSM153294 1 0.5948 0.2165 0.632 0.012 0.000 0.172 0.184
#> GSM153295 5 0.6722 -0.0861 0.076 0.000 0.056 0.432 0.436
#> GSM153054 1 0.7642 0.2872 0.524 0.024 0.184 0.056 0.212
#> GSM153055 4 0.7350 -0.0845 0.120 0.000 0.076 0.404 0.400
#> GSM153056 3 0.6827 0.6001 0.072 0.000 0.588 0.140 0.200
#> GSM153057 3 0.7638 0.5248 0.108 0.016 0.532 0.116 0.228
#> GSM153058 3 0.3027 0.7492 0.012 0.000 0.876 0.040 0.072
#> GSM153059 3 0.6825 0.6142 0.088 0.108 0.644 0.024 0.136
#> GSM153060 3 0.1757 0.7394 0.004 0.000 0.936 0.012 0.048
#> GSM153061 3 0.2141 0.7388 0.016 0.000 0.916 0.004 0.064
#> GSM153062 3 0.0865 0.7339 0.000 0.000 0.972 0.004 0.024
#> GSM153063 3 0.4650 0.7337 0.036 0.000 0.772 0.140 0.052
#> GSM153064 1 0.4096 0.3546 0.772 0.000 0.000 0.052 0.176
#> GSM153065 3 0.4755 0.6915 0.084 0.056 0.780 0.000 0.080
#> GSM153066 2 0.4045 0.7730 0.064 0.824 0.076 0.000 0.036
#> GSM153067 4 0.4734 0.5531 0.108 0.000 0.000 0.732 0.160
#> GSM153068 3 0.1571 0.7389 0.004 0.000 0.936 0.000 0.060
#> GSM153069 4 0.2390 0.6030 0.020 0.000 0.000 0.896 0.084
#> GSM153070 5 0.6762 0.5654 0.256 0.000 0.024 0.188 0.532
#> GSM153071 3 0.8377 0.1080 0.244 0.000 0.368 0.188 0.200
#> GSM153072 1 0.8296 0.3614 0.492 0.072 0.156 0.064 0.216
#> GSM153073 5 0.6461 0.4961 0.344 0.000 0.008 0.152 0.496
#> GSM153074 4 0.4528 0.5454 0.060 0.000 0.000 0.728 0.212
#> GSM153075 4 0.7381 0.1906 0.124 0.000 0.080 0.448 0.348
#> GSM153076 5 0.6503 0.5749 0.300 0.000 0.000 0.220 0.480
#> GSM153077 5 0.6071 0.3299 0.352 0.000 0.048 0.044 0.556
#> GSM153078 3 0.8004 0.1104 0.184 0.004 0.372 0.092 0.348
#> GSM153079 1 0.6873 0.4188 0.568 0.112 0.060 0.004 0.256
#> GSM153080 3 0.6593 0.5989 0.068 0.000 0.584 0.260 0.088
#> GSM153081 5 0.5667 0.2860 0.296 0.000 0.040 0.040 0.624
#> GSM153082 2 0.6743 -0.0756 0.384 0.476 0.016 0.012 0.112
#> GSM153083 1 0.6380 0.3900 0.520 0.336 0.012 0.000 0.132
#> GSM153084 2 0.5181 0.6196 0.188 0.720 0.048 0.000 0.044
#> GSM153085 1 0.9682 0.2485 0.272 0.224 0.148 0.108 0.248
#> GSM153086 1 0.5445 0.4796 0.712 0.140 0.020 0.004 0.124
#> GSM153087 4 0.6918 0.3145 0.100 0.000 0.072 0.536 0.292
#> GSM153088 5 0.6033 0.6106 0.220 0.000 0.000 0.200 0.580
#> GSM153089 3 0.5454 0.7080 0.036 0.008 0.724 0.156 0.076
#> GSM153090 5 0.5939 0.5349 0.148 0.000 0.000 0.276 0.576
#> GSM153091 1 0.4944 0.4637 0.724 0.156 0.000 0.004 0.116
#> GSM153092 1 0.7352 -0.1380 0.452 0.008 0.040 0.156 0.344
#> GSM153093 4 0.4823 0.4895 0.052 0.000 0.000 0.672 0.276
#> GSM153094 1 0.5956 0.4299 0.608 0.256 0.004 0.004 0.128
#> GSM153095 1 0.9359 0.3296 0.344 0.248 0.196 0.092 0.120
#> GSM153096 1 0.4743 0.3688 0.728 0.004 0.004 0.056 0.208
#> GSM153097 1 0.4578 0.4648 0.772 0.068 0.012 0.004 0.144
#> GSM153098 1 0.6631 -0.0763 0.476 0.012 0.000 0.352 0.160
#> GSM153099 5 0.6959 0.1733 0.136 0.000 0.036 0.392 0.436
#> GSM153100 1 0.6714 -0.2491 0.424 0.000 0.000 0.296 0.280
#> GSM153101 1 0.8879 0.2846 0.408 0.092 0.268 0.084 0.148
#> GSM153102 1 0.9019 0.3781 0.436 0.188 0.144 0.096 0.136
#> GSM153103 1 0.7608 0.4061 0.528 0.100 0.164 0.008 0.200
#> GSM153104 4 0.3189 0.6099 0.020 0.000 0.032 0.868 0.080
#> GSM153106 1 0.6928 -0.1766 0.380 0.004 0.000 0.316 0.300
#> GSM153107 1 0.6688 -0.1026 0.452 0.000 0.012 0.164 0.372
#> GSM153108 4 0.7364 0.3172 0.204 0.000 0.108 0.536 0.152
#> GSM153109 2 0.6514 -0.0229 0.392 0.488 0.012 0.012 0.096
#> GSM153110 1 0.3426 0.4187 0.836 0.008 0.008 0.012 0.136
#> GSM153111 1 0.5886 0.4141 0.588 0.288 0.000 0.004 0.120
#> GSM153112 1 0.5998 0.0676 0.604 0.004 0.000 0.192 0.200
#> GSM153113 2 0.3535 0.7472 0.164 0.808 0.000 0.000 0.028
#> GSM153114 4 0.5491 0.4396 0.088 0.000 0.000 0.600 0.312
#> GSM187532 2 0.1205 0.9052 0.000 0.956 0.040 0.000 0.004
#> GSM187533 2 0.0324 0.9360 0.004 0.992 0.000 0.000 0.004
#> GSM187534 2 0.0451 0.9339 0.008 0.988 0.000 0.000 0.004
#> GSM187535 2 0.2304 0.8666 0.048 0.908 0.000 0.000 0.044
#> GSM152906 2 0.0162 0.9374 0.000 0.996 0.000 0.000 0.004
#> GSM152907 2 0.0000 0.9384 0.000 1.000 0.000 0.000 0.000
#> GSM152908 2 0.0000 0.9384 0.000 1.000 0.000 0.000 0.000
#> GSM152909 2 0.0162 0.9374 0.000 0.996 0.000 0.000 0.004
#> GSM152910 2 0.0162 0.9374 0.000 0.996 0.000 0.000 0.004
#> GSM152911 2 0.0000 0.9384 0.000 1.000 0.000 0.000 0.000
#> GSM152912 2 0.0162 0.9374 0.000 0.996 0.000 0.000 0.004
#> GSM152913 2 0.0000 0.9384 0.000 1.000 0.000 0.000 0.000
#> GSM152914 2 0.0000 0.9384 0.000 1.000 0.000 0.000 0.000
#> GSM152915 2 0.0000 0.9384 0.000 1.000 0.000 0.000 0.000
#> GSM152916 2 0.0000 0.9384 0.000 1.000 0.000 0.000 0.000
#> GSM152917 2 0.0000 0.9384 0.000 1.000 0.000 0.000 0.000
#> GSM152918 2 0.0000 0.9384 0.000 1.000 0.000 0.000 0.000
#> GSM152919 2 0.0000 0.9384 0.000 1.000 0.000 0.000 0.000
#> GSM152920 2 0.0162 0.9374 0.000 0.996 0.000 0.000 0.004
#> GSM152921 2 0.0000 0.9384 0.000 1.000 0.000 0.000 0.000
#> GSM152922 2 0.0162 0.9374 0.000 0.996 0.000 0.000 0.004
#> GSM152923 2 0.0000 0.9384 0.000 1.000 0.000 0.000 0.000
#> GSM152924 2 0.0162 0.9374 0.000 0.996 0.000 0.000 0.004
#> GSM152925 2 0.0290 0.9370 0.000 0.992 0.000 0.000 0.008
#> GSM152926 2 0.0162 0.9374 0.000 0.996 0.000 0.000 0.004
#> GSM152927 2 0.0290 0.9370 0.000 0.992 0.000 0.000 0.008
#> GSM152928 2 0.0324 0.9357 0.004 0.992 0.000 0.000 0.004
#> GSM152929 2 0.0162 0.9374 0.000 0.996 0.000 0.000 0.004
#> GSM152930 2 0.0162 0.9374 0.000 0.996 0.000 0.000 0.004
cbind(get_classes(res, k = 6), get_membership(res, k = 6))
#> class entropy silhouette p1 p2 p3 p4 p5 p6
#> GSM152839 3 0.8606 0.17276 0.140 0.000 0.300 0.100 NA 0.216
#> GSM152840 3 0.6010 0.23745 0.008 0.000 0.436 0.432 NA 0.020
#> GSM152841 4 0.3145 0.56177 0.008 0.000 0.060 0.864 NA 0.036
#> GSM152842 3 0.3744 0.65187 0.004 0.000 0.784 0.008 NA 0.036
#> GSM152843 3 0.7150 0.51396 0.056 0.000 0.500 0.044 NA 0.160
#> GSM152844 3 0.4730 0.60059 0.004 0.000 0.680 0.232 NA 0.004
#> GSM152845 3 0.3536 0.65607 0.008 0.040 0.840 0.024 NA 0.004
#> GSM152846 3 0.4309 0.64141 0.004 0.000 0.748 0.140 NA 0.004
#> GSM152847 3 0.6604 0.56664 0.056 0.000 0.572 0.028 NA 0.148
#> GSM152848 6 0.8249 0.22058 0.140 0.000 0.140 0.108 NA 0.412
#> GSM152849 3 0.5442 0.63194 0.032 0.000 0.648 0.020 NA 0.056
#> GSM152850 3 0.7528 0.34507 0.096 0.000 0.388 0.016 NA 0.224
#> GSM152851 4 0.6973 0.34105 0.016 0.000 0.188 0.528 NA 0.104
#> GSM152852 3 0.4732 0.63245 0.012 0.000 0.716 0.160 NA 0.004
#> GSM152853 3 0.5616 0.47009 0.004 0.000 0.548 0.332 NA 0.012
#> GSM152854 3 0.4230 0.66612 0.004 0.000 0.756 0.076 NA 0.008
#> GSM152855 4 0.6940 -0.02286 0.124 0.000 0.000 0.396 NA 0.364
#> GSM153238 3 0.6736 0.49740 0.164 0.020 0.544 0.004 NA 0.048
#> GSM153239 3 0.6001 0.54606 0.012 0.000 0.564 0.260 NA 0.016
#> GSM153240 4 0.5811 0.34211 0.036 0.000 0.008 0.564 NA 0.316
#> GSM153241 3 0.6703 0.59105 0.028 0.000 0.560 0.076 NA 0.112
#> GSM153242 3 0.4250 0.65130 0.004 0.000 0.744 0.108 NA 0.000
#> GSM153243 3 0.6279 0.55689 0.068 0.064 0.580 0.000 NA 0.028
#> GSM153244 4 0.8267 0.22288 0.056 0.016 0.196 0.408 NA 0.104
#> GSM153245 3 0.5802 0.54479 0.008 0.000 0.568 0.276 NA 0.012
#> GSM153246 3 0.2149 0.65219 0.004 0.000 0.888 0.000 NA 0.004
#> GSM153247 3 0.8198 0.38638 0.124 0.016 0.424 0.076 NA 0.104
#> GSM153248 1 0.5878 0.32354 0.564 0.008 0.000 0.028 NA 0.300
#> GSM153249 4 0.4330 0.54436 0.056 0.000 0.000 0.764 NA 0.136
#> GSM153250 6 0.5481 0.52331 0.124 0.000 0.000 0.156 NA 0.664
#> GSM153251 3 0.4791 0.66329 0.020 0.012 0.740 0.064 NA 0.008
#> GSM153252 4 0.5340 0.48781 0.056 0.000 0.004 0.652 NA 0.236
#> GSM153253 4 0.2532 0.56988 0.000 0.000 0.036 0.892 NA 0.020
#> GSM153254 3 0.8951 0.23342 0.076 0.048 0.296 0.224 NA 0.088
#> GSM153255 4 0.4733 0.44035 0.024 0.000 0.000 0.668 NA 0.264
#> GSM153256 6 0.6290 0.36980 0.112 0.000 0.000 0.296 NA 0.524
#> GSM153257 4 0.5713 0.34591 0.052 0.000 0.000 0.564 NA 0.316
#> GSM153258 6 0.7445 0.31732 0.216 0.000 0.020 0.124 NA 0.460
#> GSM153259 1 0.5309 0.34602 0.632 0.000 0.000 0.028 NA 0.252
#> GSM153260 3 0.6260 0.55644 0.092 0.012 0.592 0.004 NA 0.064
#> GSM153261 3 0.5720 0.62256 0.056 0.000 0.644 0.020 NA 0.060
#> GSM153262 4 0.5216 0.54368 0.044 0.000 0.024 0.720 NA 0.128
#> GSM153263 6 0.7288 0.40103 0.244 0.000 0.000 0.236 NA 0.400
#> GSM153264 6 0.6400 0.23617 0.212 0.000 0.048 0.016 NA 0.572
#> GSM153265 4 0.4958 0.53792 0.028 0.000 0.080 0.752 NA 0.064
#> GSM153266 6 0.7571 0.19725 0.232 0.000 0.040 0.096 NA 0.456
#> GSM153267 6 0.6369 0.36288 0.092 0.000 0.008 0.268 NA 0.552
#> GSM153268 4 0.4170 0.50514 0.004 0.000 0.132 0.776 NA 0.020
#> GSM153269 6 0.5459 0.41268 0.052 0.000 0.000 0.236 NA 0.636
#> GSM153270 4 0.8492 -0.11835 0.176 0.000 0.076 0.316 NA 0.252
#> GSM153271 6 0.5549 0.44321 0.096 0.000 0.000 0.244 NA 0.620
#> GSM153272 4 0.5278 0.20048 0.040 0.000 0.000 0.516 NA 0.412
#> GSM153273 1 0.5657 0.35300 0.632 0.000 0.008 0.068 NA 0.236
#> GSM153274 6 0.7173 0.33599 0.064 0.000 0.032 0.284 NA 0.468
#> GSM153275 6 0.6780 0.18508 0.116 0.000 0.008 0.368 NA 0.432
#> GSM153276 6 0.7356 0.14524 0.028 0.000 0.056 0.340 NA 0.376
#> GSM153277 4 0.6752 0.42302 0.068 0.000 0.064 0.596 NA 0.132
#> GSM153278 3 0.7510 0.46085 0.080 0.000 0.436 0.040 NA 0.164
#> GSM153279 4 0.7218 0.37509 0.048 0.000 0.096 0.532 NA 0.140
#> GSM153280 4 0.4399 0.55953 0.020 0.000 0.068 0.788 NA 0.044
#> GSM153281 4 0.4130 0.56516 0.008 0.000 0.024 0.784 NA 0.132
#> GSM153282 4 0.3313 0.56901 0.004 0.000 0.040 0.852 NA 0.044
#> GSM153283 6 0.6305 0.39622 0.212 0.000 0.008 0.096 NA 0.588
#> GSM153284 4 0.6842 0.14929 0.092 0.000 0.004 0.460 NA 0.316
#> GSM153285 4 0.3689 0.56539 0.020 0.000 0.064 0.836 NA 0.036
#> GSM153286 6 0.5414 -0.02783 0.032 0.000 0.000 0.448 NA 0.472
#> GSM153287 4 0.3507 0.55581 0.020 0.000 0.000 0.820 NA 0.116
#> GSM153288 4 0.5972 0.27203 0.076 0.000 0.000 0.524 NA 0.340
#> GSM153289 6 0.7082 0.16192 0.156 0.000 0.000 0.340 NA 0.392
#> GSM153290 4 0.3693 0.57557 0.004 0.000 0.052 0.828 NA 0.064
#> GSM153291 4 0.4956 0.51058 0.072 0.000 0.000 0.704 NA 0.176
#> GSM153292 4 0.2722 0.57058 0.016 0.000 0.008 0.876 NA 0.088
#> GSM153293 6 0.6385 0.03242 0.096 0.000 0.000 0.416 NA 0.416
#> GSM153294 1 0.6836 0.11681 0.496 0.000 0.000 0.168 NA 0.228
#> GSM153295 4 0.7441 -0.08667 0.060 0.000 0.052 0.384 NA 0.364
#> GSM153054 1 0.8320 0.21303 0.368 0.004 0.220 0.052 NA 0.188
#> GSM153055 6 0.8024 0.32987 0.116 0.000 0.064 0.256 NA 0.400
#> GSM153056 3 0.7679 0.45795 0.036 0.000 0.432 0.116 NA 0.164
#> GSM153057 3 0.8177 0.46566 0.056 0.028 0.432 0.096 NA 0.132
#> GSM153058 3 0.3657 0.66439 0.004 0.000 0.788 0.012 NA 0.024
#> GSM153059 3 0.7687 0.45271 0.084 0.112 0.516 0.024 NA 0.060
#> GSM153060 3 0.2446 0.66010 0.000 0.000 0.864 0.012 NA 0.000
#> GSM153061 3 0.2544 0.65098 0.012 0.000 0.864 0.000 NA 0.004
#> GSM153062 3 0.2001 0.65120 0.000 0.000 0.900 0.004 NA 0.004
#> GSM153063 3 0.5658 0.63397 0.016 0.000 0.644 0.152 NA 0.020
#> GSM153064 1 0.5270 0.32087 0.644 0.000 0.000 0.056 NA 0.248
#> GSM153065 3 0.5469 0.60625 0.048 0.068 0.692 0.000 NA 0.028
#> GSM153066 2 0.4840 0.67987 0.052 0.744 0.092 0.000 NA 0.008
#> GSM153067 4 0.6064 0.35486 0.132 0.000 0.000 0.588 NA 0.216
#> GSM153068 3 0.3419 0.65182 0.020 0.000 0.820 0.004 NA 0.020
#> GSM153069 4 0.2393 0.56619 0.004 0.000 0.000 0.884 NA 0.092
#> GSM153070 6 0.6913 0.40073 0.216 0.000 0.020 0.116 NA 0.536
#> GSM153071 3 0.8845 -0.00177 0.188 0.000 0.256 0.148 NA 0.160
#> GSM153072 1 0.8426 0.31863 0.400 0.040 0.152 0.032 NA 0.144
#> GSM153073 6 0.6358 0.37761 0.172 0.000 0.004 0.088 NA 0.584
#> GSM153074 4 0.5964 0.38348 0.076 0.000 0.000 0.576 NA 0.268
#> GSM153075 4 0.8007 0.10698 0.104 0.000 0.060 0.388 NA 0.264
#> GSM153076 6 0.6194 0.36302 0.272 0.000 0.000 0.128 NA 0.544
#> GSM153077 6 0.6175 0.28588 0.184 0.004 0.024 0.028 NA 0.612
#> GSM153078 3 0.8198 0.13485 0.112 0.000 0.316 0.056 NA 0.272
#> GSM153079 1 0.7765 0.37450 0.468 0.128 0.028 0.012 NA 0.192
#> GSM153080 3 0.7447 0.46673 0.036 0.000 0.440 0.256 NA 0.068
#> GSM153081 6 0.7513 0.15095 0.224 0.000 0.088 0.036 NA 0.456
#> GSM153082 2 0.7944 -0.38518 0.336 0.364 0.012 0.032 NA 0.120
#> GSM153083 1 0.6757 0.43385 0.532 0.236 0.012 0.000 NA 0.088
#> GSM153084 2 0.6135 0.46070 0.164 0.632 0.060 0.000 NA 0.024
#> GSM153085 1 0.9383 0.29209 0.288 0.176 0.108 0.048 NA 0.184
#> GSM153086 1 0.5886 0.47448 0.676 0.096 0.032 0.000 NA 0.092
#> GSM153087 4 0.7379 0.11184 0.068 0.000 0.044 0.448 NA 0.292
#> GSM153088 6 0.4813 0.51546 0.072 0.000 0.000 0.112 NA 0.736
#> GSM153089 3 0.5584 0.64152 0.032 0.020 0.684 0.124 NA 0.004
#> GSM153090 6 0.5368 0.52830 0.088 0.000 0.000 0.156 NA 0.680
#> GSM153091 1 0.6238 0.43208 0.616 0.116 0.004 0.012 NA 0.184
#> GSM153092 6 0.7979 0.16615 0.300 0.012 0.028 0.120 NA 0.380
#> GSM153093 4 0.5673 0.40857 0.044 0.000 0.012 0.616 NA 0.264
#> GSM153094 1 0.7156 0.41517 0.496 0.244 0.008 0.008 NA 0.128
#> GSM153095 1 0.9017 0.36055 0.356 0.232 0.096 0.052 NA 0.108
#> GSM153096 1 0.6150 0.36112 0.608 0.000 0.012 0.072 NA 0.208
#> GSM153097 1 0.5886 0.45898 0.644 0.072 0.008 0.000 NA 0.160
#> GSM153098 1 0.7529 -0.08943 0.368 0.012 0.000 0.312 NA 0.196
#> GSM153099 6 0.7987 0.32563 0.156 0.000 0.048 0.268 NA 0.388
#> GSM153100 1 0.7257 -0.01291 0.428 0.000 0.004 0.212 NA 0.248
#> GSM153101 1 0.9151 0.28322 0.368 0.084 0.188 0.092 NA 0.100
#> GSM153102 1 0.9060 0.35862 0.364 0.156 0.132 0.076 NA 0.064
#> GSM153103 1 0.8013 0.34226 0.404 0.064 0.116 0.000 NA 0.164
#> GSM153104 4 0.5036 0.56204 0.036 0.000 0.028 0.732 NA 0.136
#> GSM153106 1 0.7958 -0.02206 0.344 0.012 0.004 0.232 NA 0.232
#> GSM153107 1 0.7215 0.07428 0.440 0.008 0.000 0.136 NA 0.288
#> GSM153108 4 0.7907 0.21824 0.192 0.004 0.060 0.456 NA 0.176
#> GSM153109 1 0.6855 0.35424 0.448 0.360 0.028 0.004 NA 0.036
#> GSM153110 1 0.4377 0.41887 0.740 0.004 0.004 0.004 NA 0.176
#> GSM153111 1 0.6722 0.43453 0.532 0.216 0.004 0.000 NA 0.140
#> GSM153112 1 0.6291 0.22499 0.556 0.000 0.000 0.156 NA 0.224
#> GSM153113 2 0.4568 0.61458 0.188 0.720 0.000 0.000 NA 0.020
#> GSM153114 4 0.6879 0.17422 0.124 0.000 0.000 0.456 NA 0.300
#> GSM187532 2 0.1649 0.88263 0.000 0.932 0.036 0.000 NA 0.000
#> GSM187533 2 0.0405 0.93002 0.004 0.988 0.000 0.000 NA 0.000
#> GSM187534 2 0.0547 0.93067 0.000 0.980 0.000 0.000 NA 0.000
#> GSM187535 2 0.3177 0.81475 0.072 0.852 0.000 0.000 NA 0.024
#> GSM152906 2 0.0777 0.92883 0.004 0.972 0.000 0.000 NA 0.000
#> GSM152907 2 0.0692 0.92942 0.004 0.976 0.000 0.000 NA 0.000
#> GSM152908 2 0.0000 0.93146 0.000 1.000 0.000 0.000 NA 0.000
#> GSM152909 2 0.0405 0.92800 0.000 0.988 0.004 0.000 NA 0.000
#> GSM152910 2 0.0000 0.93146 0.000 1.000 0.000 0.000 NA 0.000
#> GSM152911 2 0.0146 0.93101 0.000 0.996 0.000 0.000 NA 0.000
#> GSM152912 2 0.0000 0.93146 0.000 1.000 0.000 0.000 NA 0.000
#> GSM152913 2 0.0260 0.93146 0.000 0.992 0.000 0.000 NA 0.000
#> GSM152914 2 0.0146 0.93101 0.000 0.996 0.000 0.000 NA 0.000
#> GSM152915 2 0.0146 0.93101 0.000 0.996 0.000 0.000 NA 0.000
#> GSM152916 2 0.0603 0.93044 0.004 0.980 0.000 0.000 NA 0.000
#> GSM152917 2 0.0146 0.93101 0.000 0.996 0.000 0.000 NA 0.000
#> GSM152918 2 0.0260 0.93146 0.000 0.992 0.000 0.000 NA 0.000
#> GSM152919 2 0.0146 0.93101 0.000 0.996 0.000 0.000 NA 0.000
#> GSM152920 2 0.0000 0.93146 0.000 1.000 0.000 0.000 NA 0.000
#> GSM152921 2 0.0000 0.93146 0.000 1.000 0.000 0.000 NA 0.000
#> GSM152922 2 0.0000 0.93146 0.000 1.000 0.000 0.000 NA 0.000
#> GSM152923 2 0.0777 0.92883 0.004 0.972 0.000 0.000 NA 0.000
#> GSM152924 2 0.0692 0.92951 0.004 0.976 0.000 0.000 NA 0.000
#> GSM152925 2 0.0777 0.92883 0.004 0.972 0.000 0.000 NA 0.000
#> GSM152926 2 0.0777 0.92883 0.004 0.972 0.000 0.000 NA 0.000
#> GSM152927 2 0.0777 0.92883 0.004 0.972 0.000 0.000 NA 0.000
#> GSM152928 2 0.1124 0.92231 0.008 0.956 0.000 0.000 NA 0.000
#> GSM152929 2 0.0777 0.92883 0.004 0.972 0.000 0.000 NA 0.000
#> GSM152930 2 0.0777 0.92883 0.004 0.972 0.000 0.000 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 tissue(p) k
#> SD:skmeans 153 7.04e-16 2
#> SD:skmeans 155 1.30e-23 3
#> SD:skmeans 131 1.20e-23 4
#> SD:skmeans 94 7.96e-16 5
#> SD:skmeans 76 4.58e-13 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 12013 rows and 164 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 0.999 0.973 0.988 0.3025 0.707 0.707
#> 3 3 0.399 0.728 0.843 1.0683 0.669 0.532
#> 4 4 0.395 0.504 0.711 0.1134 0.914 0.778
#> 5 5 0.401 0.497 0.713 0.0385 0.951 0.850
#> 6 6 0.433 0.435 0.661 0.0365 0.944 0.816
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
#> GSM152839 1 0.0000 0.988 1.000 0.000
#> GSM152840 1 0.0000 0.988 1.000 0.000
#> GSM152841 1 0.0000 0.988 1.000 0.000
#> GSM152842 1 0.0000 0.988 1.000 0.000
#> GSM152843 1 0.0000 0.988 1.000 0.000
#> GSM152844 1 0.0000 0.988 1.000 0.000
#> GSM152845 1 0.0376 0.985 0.996 0.004
#> GSM152846 1 0.0000 0.988 1.000 0.000
#> GSM152847 1 0.0000 0.988 1.000 0.000
#> GSM152848 1 0.0000 0.988 1.000 0.000
#> GSM152849 1 0.0000 0.988 1.000 0.000
#> GSM152850 1 0.0000 0.988 1.000 0.000
#> GSM152851 1 0.0000 0.988 1.000 0.000
#> GSM152852 1 0.0000 0.988 1.000 0.000
#> GSM152853 1 0.0000 0.988 1.000 0.000
#> GSM152854 1 0.0000 0.988 1.000 0.000
#> GSM152855 1 0.0000 0.988 1.000 0.000
#> GSM153238 1 0.0000 0.988 1.000 0.000
#> GSM153239 1 0.0000 0.988 1.000 0.000
#> GSM153240 1 0.0000 0.988 1.000 0.000
#> GSM153241 1 0.0000 0.988 1.000 0.000
#> GSM153242 1 0.0000 0.988 1.000 0.000
#> GSM153243 1 0.1414 0.972 0.980 0.020
#> GSM153244 1 0.0000 0.988 1.000 0.000
#> GSM153245 1 0.0000 0.988 1.000 0.000
#> GSM153246 1 0.0000 0.988 1.000 0.000
#> GSM153247 1 0.0000 0.988 1.000 0.000
#> GSM153248 1 0.0000 0.988 1.000 0.000
#> GSM153249 1 0.0000 0.988 1.000 0.000
#> GSM153250 1 0.0000 0.988 1.000 0.000
#> GSM153251 1 0.0000 0.988 1.000 0.000
#> GSM153252 1 0.0000 0.988 1.000 0.000
#> GSM153253 1 0.0000 0.988 1.000 0.000
#> GSM153254 1 0.0000 0.988 1.000 0.000
#> GSM153255 1 0.0000 0.988 1.000 0.000
#> GSM153256 1 0.0000 0.988 1.000 0.000
#> GSM153257 1 0.0000 0.988 1.000 0.000
#> GSM153258 1 0.0000 0.988 1.000 0.000
#> GSM153259 1 0.0000 0.988 1.000 0.000
#> GSM153260 1 0.0000 0.988 1.000 0.000
#> GSM153261 1 0.0000 0.988 1.000 0.000
#> GSM153262 1 0.0000 0.988 1.000 0.000
#> GSM153263 1 0.0000 0.988 1.000 0.000
#> GSM153264 1 0.0000 0.988 1.000 0.000
#> GSM153265 1 0.0000 0.988 1.000 0.000
#> GSM153266 1 0.0000 0.988 1.000 0.000
#> GSM153267 1 0.0000 0.988 1.000 0.000
#> GSM153268 1 0.0000 0.988 1.000 0.000
#> GSM153269 1 0.0000 0.988 1.000 0.000
#> GSM153270 1 0.0000 0.988 1.000 0.000
#> GSM153271 1 0.0000 0.988 1.000 0.000
#> GSM153272 1 0.0000 0.988 1.000 0.000
#> GSM153273 1 0.0000 0.988 1.000 0.000
#> GSM153274 1 0.0000 0.988 1.000 0.000
#> GSM153275 1 0.0000 0.988 1.000 0.000
#> GSM153276 1 0.0000 0.988 1.000 0.000
#> GSM153277 1 0.0000 0.988 1.000 0.000
#> GSM153278 1 0.0000 0.988 1.000 0.000
#> GSM153279 1 0.0000 0.988 1.000 0.000
#> GSM153280 1 0.0000 0.988 1.000 0.000
#> GSM153281 1 0.0000 0.988 1.000 0.000
#> GSM153282 1 0.0000 0.988 1.000 0.000
#> GSM153283 1 0.0000 0.988 1.000 0.000
#> GSM153284 1 0.0000 0.988 1.000 0.000
#> GSM153285 1 0.0000 0.988 1.000 0.000
#> GSM153286 1 0.0000 0.988 1.000 0.000
#> GSM153287 1 0.0000 0.988 1.000 0.000
#> GSM153288 1 0.0000 0.988 1.000 0.000
#> GSM153289 1 0.0000 0.988 1.000 0.000
#> GSM153290 1 0.0000 0.988 1.000 0.000
#> GSM153291 1 0.0000 0.988 1.000 0.000
#> GSM153292 1 0.0000 0.988 1.000 0.000
#> GSM153293 1 0.0000 0.988 1.000 0.000
#> GSM153294 1 0.0376 0.985 0.996 0.004
#> GSM153295 1 0.0000 0.988 1.000 0.000
#> GSM153054 1 0.0000 0.988 1.000 0.000
#> GSM153055 1 0.0000 0.988 1.000 0.000
#> GSM153056 1 0.0000 0.988 1.000 0.000
#> GSM153057 1 0.0000 0.988 1.000 0.000
#> GSM153058 1 0.0000 0.988 1.000 0.000
#> GSM153059 1 0.0000 0.988 1.000 0.000
#> GSM153060 1 0.0000 0.988 1.000 0.000
#> GSM153061 1 0.0000 0.988 1.000 0.000
#> GSM153062 1 0.5178 0.870 0.884 0.116
#> GSM153063 1 0.0000 0.988 1.000 0.000
#> GSM153064 1 0.0000 0.988 1.000 0.000
#> GSM153065 1 0.2778 0.945 0.952 0.048
#> GSM153066 2 0.6887 0.780 0.184 0.816
#> GSM153067 1 0.0000 0.988 1.000 0.000
#> GSM153068 1 0.0000 0.988 1.000 0.000
#> GSM153069 1 0.0000 0.988 1.000 0.000
#> GSM153070 1 0.0000 0.988 1.000 0.000
#> GSM153071 1 0.0000 0.988 1.000 0.000
#> GSM153072 1 0.0000 0.988 1.000 0.000
#> GSM153073 1 0.0000 0.988 1.000 0.000
#> GSM153074 1 0.0000 0.988 1.000 0.000
#> GSM153075 1 0.0000 0.988 1.000 0.000
#> GSM153076 1 0.0000 0.988 1.000 0.000
#> GSM153077 1 0.0000 0.988 1.000 0.000
#> GSM153078 1 0.0000 0.988 1.000 0.000
#> GSM153079 1 0.0672 0.982 0.992 0.008
#> GSM153080 1 0.0000 0.988 1.000 0.000
#> GSM153081 1 0.0000 0.988 1.000 0.000
#> GSM153082 1 0.4815 0.884 0.896 0.104
#> GSM153083 1 0.4161 0.907 0.916 0.084
#> GSM153084 1 0.4939 0.881 0.892 0.108
#> GSM153085 1 0.0000 0.988 1.000 0.000
#> GSM153086 1 0.2043 0.960 0.968 0.032
#> GSM153087 1 0.0000 0.988 1.000 0.000
#> GSM153088 1 0.0000 0.988 1.000 0.000
#> GSM153089 1 0.0000 0.988 1.000 0.000
#> GSM153090 1 0.0000 0.988 1.000 0.000
#> GSM153091 1 0.3584 0.924 0.932 0.068
#> GSM153092 1 0.0000 0.988 1.000 0.000
#> GSM153093 1 0.0000 0.988 1.000 0.000
#> GSM153094 1 0.1843 0.964 0.972 0.028
#> GSM153095 1 0.0000 0.988 1.000 0.000
#> GSM153096 1 0.0000 0.988 1.000 0.000
#> GSM153097 1 0.0376 0.985 0.996 0.004
#> GSM153098 1 0.0376 0.985 0.996 0.004
#> GSM153099 1 0.0000 0.988 1.000 0.000
#> GSM153100 1 0.0000 0.988 1.000 0.000
#> GSM153101 1 0.0000 0.988 1.000 0.000
#> GSM153102 1 0.0000 0.988 1.000 0.000
#> GSM153103 1 0.0000 0.988 1.000 0.000
#> GSM153104 1 0.0000 0.988 1.000 0.000
#> GSM153106 1 0.0000 0.988 1.000 0.000
#> GSM153107 1 0.0000 0.988 1.000 0.000
#> GSM153108 1 0.0000 0.988 1.000 0.000
#> GSM153109 1 0.6438 0.808 0.836 0.164
#> GSM153110 1 0.0938 0.978 0.988 0.012
#> GSM153111 1 0.1414 0.971 0.980 0.020
#> GSM153112 1 0.0000 0.988 1.000 0.000
#> GSM153113 1 0.9580 0.388 0.620 0.380
#> GSM153114 1 0.0000 0.988 1.000 0.000
#> GSM187532 2 0.0672 0.980 0.008 0.992
#> GSM187533 2 0.4161 0.908 0.084 0.916
#> GSM187534 2 0.4815 0.887 0.104 0.896
#> GSM187535 1 0.9580 0.386 0.620 0.380
#> GSM152906 2 0.0000 0.985 0.000 1.000
#> GSM152907 2 0.0000 0.985 0.000 1.000
#> GSM152908 2 0.0000 0.985 0.000 1.000
#> GSM152909 2 0.0000 0.985 0.000 1.000
#> GSM152910 2 0.0000 0.985 0.000 1.000
#> GSM152911 2 0.0000 0.985 0.000 1.000
#> GSM152912 2 0.0000 0.985 0.000 1.000
#> GSM152913 2 0.0000 0.985 0.000 1.000
#> GSM152914 2 0.0000 0.985 0.000 1.000
#> GSM152915 2 0.0000 0.985 0.000 1.000
#> GSM152916 2 0.0000 0.985 0.000 1.000
#> GSM152917 2 0.0000 0.985 0.000 1.000
#> GSM152918 2 0.0000 0.985 0.000 1.000
#> GSM152919 2 0.0000 0.985 0.000 1.000
#> GSM152920 2 0.0000 0.985 0.000 1.000
#> GSM152921 2 0.0000 0.985 0.000 1.000
#> GSM152922 2 0.0000 0.985 0.000 1.000
#> GSM152923 2 0.0000 0.985 0.000 1.000
#> GSM152924 2 0.0000 0.985 0.000 1.000
#> GSM152925 2 0.0000 0.985 0.000 1.000
#> GSM152926 2 0.0376 0.982 0.004 0.996
#> GSM152927 2 0.0000 0.985 0.000 1.000
#> GSM152928 2 0.1633 0.967 0.024 0.976
#> GSM152929 2 0.0000 0.985 0.000 1.000
#> GSM152930 2 0.0000 0.985 0.000 1.000
cbind(get_classes(res, k = 3), get_membership(res, k = 3))
#> class entropy silhouette p1 p2 p3
#> GSM152839 1 0.4842 0.7515 0.776 0.000 0.224
#> GSM152840 3 0.3038 0.8009 0.104 0.000 0.896
#> GSM152841 3 0.4504 0.7482 0.196 0.000 0.804
#> GSM152842 1 0.3619 0.7946 0.864 0.000 0.136
#> GSM152843 1 0.1411 0.7884 0.964 0.000 0.036
#> GSM152844 3 0.2537 0.8083 0.080 0.000 0.920
#> GSM152845 3 0.0892 0.8011 0.020 0.000 0.980
#> GSM152846 3 0.1860 0.8073 0.052 0.000 0.948
#> GSM152847 1 0.1529 0.7900 0.960 0.000 0.040
#> GSM152848 1 0.6111 0.4863 0.604 0.000 0.396
#> GSM152849 3 0.6168 0.2208 0.412 0.000 0.588
#> GSM152850 1 0.5859 0.5970 0.656 0.000 0.344
#> GSM152851 3 0.1163 0.7986 0.028 0.000 0.972
#> GSM152852 3 0.1031 0.8000 0.024 0.000 0.976
#> GSM152853 3 0.3686 0.7902 0.140 0.000 0.860
#> GSM152854 3 0.3619 0.7935 0.136 0.000 0.864
#> GSM152855 3 0.0592 0.8006 0.012 0.000 0.988
#> GSM153238 1 0.3116 0.7902 0.892 0.000 0.108
#> GSM153239 3 0.6180 0.3239 0.416 0.000 0.584
#> GSM153240 1 0.6140 0.3364 0.596 0.000 0.404
#> GSM153241 1 0.6280 0.0956 0.540 0.000 0.460
#> GSM153242 3 0.5291 0.6797 0.268 0.000 0.732
#> GSM153243 1 0.3192 0.7920 0.888 0.000 0.112
#> GSM153244 3 0.4931 0.7086 0.232 0.000 0.768
#> GSM153245 1 0.6168 0.3671 0.588 0.000 0.412
#> GSM153246 1 0.5216 0.7143 0.740 0.000 0.260
#> GSM153247 1 0.2625 0.7960 0.916 0.000 0.084
#> GSM153248 1 0.4504 0.7703 0.804 0.000 0.196
#> GSM153249 1 0.4121 0.7734 0.832 0.000 0.168
#> GSM153250 1 0.1643 0.7871 0.956 0.000 0.044
#> GSM153251 1 0.5327 0.6639 0.728 0.000 0.272
#> GSM153252 1 0.6079 0.4994 0.612 0.000 0.388
#> GSM153253 3 0.3816 0.7867 0.148 0.000 0.852
#> GSM153254 3 0.5948 0.4356 0.360 0.000 0.640
#> GSM153255 1 0.3192 0.7943 0.888 0.000 0.112
#> GSM153256 1 0.2165 0.7972 0.936 0.000 0.064
#> GSM153257 1 0.1529 0.7835 0.960 0.000 0.040
#> GSM153258 1 0.3686 0.7920 0.860 0.000 0.140
#> GSM153259 1 0.6111 0.4316 0.604 0.000 0.396
#> GSM153260 1 0.4235 0.7795 0.824 0.000 0.176
#> GSM153261 3 0.0747 0.8000 0.016 0.000 0.984
#> GSM153262 3 0.4002 0.7590 0.160 0.000 0.840
#> GSM153263 3 0.5706 0.4512 0.320 0.000 0.680
#> GSM153264 1 0.5859 0.5549 0.656 0.000 0.344
#> GSM153265 3 0.2878 0.8071 0.096 0.000 0.904
#> GSM153266 1 0.4121 0.7780 0.832 0.000 0.168
#> GSM153267 1 0.4750 0.7556 0.784 0.000 0.216
#> GSM153268 3 0.3340 0.7938 0.120 0.000 0.880
#> GSM153269 1 0.2959 0.8011 0.900 0.000 0.100
#> GSM153270 1 0.2066 0.7907 0.940 0.000 0.060
#> GSM153271 1 0.0892 0.7811 0.980 0.000 0.020
#> GSM153272 1 0.5098 0.7111 0.752 0.000 0.248
#> GSM153273 1 0.2537 0.8004 0.920 0.000 0.080
#> GSM153274 1 0.2711 0.8001 0.912 0.000 0.088
#> GSM153275 1 0.4750 0.6695 0.784 0.000 0.216
#> GSM153276 1 0.2959 0.7987 0.900 0.000 0.100
#> GSM153277 3 0.1753 0.8003 0.048 0.000 0.952
#> GSM153278 1 0.6126 0.3094 0.600 0.000 0.400
#> GSM153279 3 0.6062 0.3791 0.384 0.000 0.616
#> GSM153280 3 0.2959 0.8016 0.100 0.000 0.900
#> GSM153281 3 0.6154 0.3640 0.408 0.000 0.592
#> GSM153282 3 0.3879 0.7781 0.152 0.000 0.848
#> GSM153283 1 0.4504 0.7578 0.804 0.000 0.196
#> GSM153284 1 0.4178 0.7814 0.828 0.000 0.172
#> GSM153285 3 0.3879 0.7795 0.152 0.000 0.848
#> GSM153286 1 0.1529 0.7832 0.960 0.000 0.040
#> GSM153287 1 0.5291 0.6977 0.732 0.000 0.268
#> GSM153288 1 0.5254 0.6868 0.736 0.000 0.264
#> GSM153289 3 0.0592 0.7986 0.012 0.000 0.988
#> GSM153290 3 0.2066 0.7966 0.060 0.000 0.940
#> GSM153291 3 0.2448 0.8114 0.076 0.000 0.924
#> GSM153292 3 0.5621 0.6119 0.308 0.000 0.692
#> GSM153293 3 0.6192 0.1960 0.420 0.000 0.580
#> GSM153294 1 0.1031 0.7853 0.976 0.000 0.024
#> GSM153295 3 0.1643 0.8041 0.044 0.000 0.956
#> GSM153054 1 0.0237 0.7788 0.996 0.000 0.004
#> GSM153055 3 0.6267 0.2980 0.452 0.000 0.548
#> GSM153056 1 0.5760 0.6263 0.672 0.000 0.328
#> GSM153057 3 0.3619 0.7974 0.136 0.000 0.864
#> GSM153058 1 0.6308 -0.0104 0.508 0.000 0.492
#> GSM153059 3 0.2537 0.8040 0.080 0.000 0.920
#> GSM153060 1 0.2711 0.8009 0.912 0.000 0.088
#> GSM153061 3 0.5560 0.5729 0.300 0.000 0.700
#> GSM153062 1 0.8295 0.2061 0.548 0.088 0.364
#> GSM153063 1 0.5733 0.6442 0.676 0.000 0.324
#> GSM153064 1 0.5926 0.5736 0.644 0.000 0.356
#> GSM153065 3 0.4094 0.8027 0.100 0.028 0.872
#> GSM153066 2 0.5696 0.7729 0.064 0.800 0.136
#> GSM153067 1 0.2878 0.8026 0.904 0.000 0.096
#> GSM153068 1 0.6267 0.3218 0.548 0.000 0.452
#> GSM153069 3 0.6274 0.1445 0.456 0.000 0.544
#> GSM153070 1 0.1031 0.7834 0.976 0.000 0.024
#> GSM153071 1 0.3551 0.7846 0.868 0.000 0.132
#> GSM153072 1 0.3412 0.7969 0.876 0.000 0.124
#> GSM153073 1 0.0892 0.7836 0.980 0.000 0.020
#> GSM153074 3 0.5988 0.4726 0.368 0.000 0.632
#> GSM153075 3 0.1643 0.8062 0.044 0.000 0.956
#> GSM153076 1 0.3619 0.7922 0.864 0.000 0.136
#> GSM153077 1 0.2959 0.7932 0.900 0.000 0.100
#> GSM153078 1 0.6305 0.1488 0.516 0.000 0.484
#> GSM153079 3 0.1860 0.8006 0.052 0.000 0.948
#> GSM153080 3 0.3686 0.7906 0.140 0.000 0.860
#> GSM153081 3 0.4062 0.7540 0.164 0.000 0.836
#> GSM153082 3 0.7076 0.5548 0.256 0.060 0.684
#> GSM153083 1 0.3682 0.7908 0.876 0.008 0.116
#> GSM153084 1 0.6948 0.2017 0.512 0.016 0.472
#> GSM153085 1 0.5138 0.7368 0.748 0.000 0.252
#> GSM153086 1 0.1860 0.7895 0.948 0.000 0.052
#> GSM153087 1 0.2356 0.8003 0.928 0.000 0.072
#> GSM153088 1 0.1031 0.7821 0.976 0.000 0.024
#> GSM153089 3 0.3038 0.8065 0.104 0.000 0.896
#> GSM153090 1 0.2261 0.7918 0.932 0.000 0.068
#> GSM153091 1 0.2165 0.7863 0.936 0.000 0.064
#> GSM153092 1 0.5327 0.6685 0.728 0.000 0.272
#> GSM153093 1 0.2448 0.7949 0.924 0.000 0.076
#> GSM153094 1 0.5882 0.5773 0.652 0.000 0.348
#> GSM153095 1 0.5327 0.6783 0.728 0.000 0.272
#> GSM153096 1 0.5397 0.6775 0.720 0.000 0.280
#> GSM153097 1 0.5058 0.7325 0.756 0.000 0.244
#> GSM153098 1 0.4931 0.7340 0.768 0.000 0.232
#> GSM153099 1 0.2959 0.7972 0.900 0.000 0.100
#> GSM153100 3 0.3482 0.8010 0.128 0.000 0.872
#> GSM153101 3 0.2066 0.8071 0.060 0.000 0.940
#> GSM153102 3 0.1964 0.8069 0.056 0.000 0.944
#> GSM153103 1 0.1860 0.7922 0.948 0.000 0.052
#> GSM153104 1 0.3816 0.7884 0.852 0.000 0.148
#> GSM153106 3 0.0747 0.7988 0.016 0.000 0.984
#> GSM153107 3 0.1643 0.8009 0.044 0.000 0.956
#> GSM153108 3 0.2878 0.8093 0.096 0.000 0.904
#> GSM153109 3 0.7839 0.2842 0.380 0.060 0.560
#> GSM153110 1 0.1860 0.7841 0.948 0.000 0.052
#> GSM153111 1 0.2878 0.7966 0.904 0.000 0.096
#> GSM153112 1 0.5835 0.5989 0.660 0.000 0.340
#> GSM153113 3 0.9964 0.0259 0.336 0.296 0.368
#> GSM153114 3 0.1163 0.8028 0.028 0.000 0.972
#> GSM187532 2 0.2165 0.9309 0.000 0.936 0.064
#> GSM187533 2 0.3116 0.8754 0.000 0.892 0.108
#> GSM187534 2 0.3482 0.8496 0.000 0.872 0.128
#> GSM187535 3 0.2569 0.7885 0.032 0.032 0.936
#> GSM152906 2 0.0000 0.9783 0.000 1.000 0.000
#> GSM152907 2 0.0000 0.9783 0.000 1.000 0.000
#> GSM152908 2 0.0000 0.9783 0.000 1.000 0.000
#> GSM152909 2 0.0000 0.9783 0.000 1.000 0.000
#> GSM152910 2 0.0000 0.9783 0.000 1.000 0.000
#> GSM152911 2 0.0000 0.9783 0.000 1.000 0.000
#> GSM152912 2 0.0000 0.9783 0.000 1.000 0.000
#> GSM152913 2 0.0000 0.9783 0.000 1.000 0.000
#> GSM152914 2 0.0000 0.9783 0.000 1.000 0.000
#> GSM152915 2 0.0000 0.9783 0.000 1.000 0.000
#> GSM152916 2 0.0000 0.9783 0.000 1.000 0.000
#> GSM152917 2 0.0000 0.9783 0.000 1.000 0.000
#> GSM152918 2 0.0000 0.9783 0.000 1.000 0.000
#> GSM152919 2 0.0000 0.9783 0.000 1.000 0.000
#> GSM152920 2 0.0000 0.9783 0.000 1.000 0.000
#> GSM152921 2 0.0000 0.9783 0.000 1.000 0.000
#> GSM152922 2 0.0000 0.9783 0.000 1.000 0.000
#> GSM152923 2 0.0000 0.9783 0.000 1.000 0.000
#> GSM152924 2 0.0000 0.9783 0.000 1.000 0.000
#> GSM152925 2 0.0000 0.9783 0.000 1.000 0.000
#> GSM152926 2 0.1031 0.9579 0.024 0.976 0.000
#> GSM152927 2 0.0000 0.9783 0.000 1.000 0.000
#> GSM152928 2 0.2527 0.9310 0.020 0.936 0.044
#> GSM152929 2 0.0000 0.9783 0.000 1.000 0.000
#> GSM152930 2 0.0000 0.9783 0.000 1.000 0.000
cbind(get_classes(res, k = 4), get_membership(res, k = 4))
#> class entropy silhouette p1 p2 p3 p4
#> GSM152839 1 0.4671 0.63745 0.752 0.000 0.220 0.028
#> GSM152840 3 0.5493 -0.06119 0.016 0.000 0.528 0.456
#> GSM152841 3 0.6407 -0.04448 0.068 0.000 0.520 0.412
#> GSM152842 1 0.5793 0.46221 0.628 0.000 0.048 0.324
#> GSM152843 1 0.2048 0.69166 0.928 0.000 0.008 0.064
#> GSM152844 4 0.5861 0.13786 0.032 0.000 0.480 0.488
#> GSM152845 3 0.1545 0.56974 0.008 0.000 0.952 0.040
#> GSM152846 3 0.4781 0.48560 0.036 0.000 0.752 0.212
#> GSM152847 1 0.2124 0.69683 0.932 0.000 0.040 0.028
#> GSM152848 1 0.7047 0.20693 0.444 0.000 0.436 0.120
#> GSM152849 3 0.5060 0.11092 0.412 0.000 0.584 0.004
#> GSM152850 1 0.5414 0.45908 0.604 0.000 0.376 0.020
#> GSM152851 3 0.4304 0.36613 0.000 0.000 0.716 0.284
#> GSM152852 3 0.2944 0.52322 0.004 0.000 0.868 0.128
#> GSM152853 3 0.5805 0.12997 0.036 0.000 0.576 0.388
#> GSM152854 3 0.4869 0.51383 0.132 0.000 0.780 0.088
#> GSM152855 3 0.0188 0.56630 0.000 0.000 0.996 0.004
#> GSM153238 1 0.5265 0.65095 0.748 0.000 0.160 0.092
#> GSM153239 3 0.7863 -0.27958 0.276 0.000 0.380 0.344
#> GSM153240 1 0.7659 -0.14998 0.460 0.000 0.244 0.296
#> GSM153241 1 0.6901 0.14165 0.488 0.000 0.404 0.108
#> GSM153242 3 0.6843 0.04072 0.112 0.000 0.532 0.356
#> GSM153243 1 0.3441 0.69410 0.856 0.000 0.120 0.024
#> GSM153244 3 0.5756 0.40921 0.224 0.000 0.692 0.084
#> GSM153245 4 0.7512 0.48018 0.348 0.000 0.192 0.460
#> GSM153246 1 0.7352 0.17400 0.496 0.000 0.176 0.328
#> GSM153247 1 0.4188 0.68179 0.824 0.000 0.112 0.064
#> GSM153248 1 0.4214 0.66023 0.780 0.000 0.204 0.016
#> GSM153249 4 0.6607 0.23206 0.444 0.000 0.080 0.476
#> GSM153250 1 0.1629 0.68622 0.952 0.000 0.024 0.024
#> GSM153251 1 0.6116 0.56916 0.668 0.000 0.220 0.112
#> GSM153252 4 0.7485 0.42879 0.336 0.000 0.192 0.472
#> GSM153253 4 0.5775 0.30353 0.032 0.000 0.408 0.560
#> GSM153254 3 0.6936 0.21720 0.224 0.000 0.588 0.188
#> GSM153255 4 0.6082 0.00970 0.476 0.000 0.044 0.480
#> GSM153256 1 0.5131 0.50933 0.692 0.000 0.028 0.280
#> GSM153257 1 0.3032 0.67797 0.868 0.000 0.008 0.124
#> GSM153258 1 0.2345 0.69728 0.900 0.000 0.100 0.000
#> GSM153259 1 0.5600 0.41079 0.596 0.000 0.376 0.028
#> GSM153260 1 0.5250 0.65600 0.744 0.000 0.176 0.080
#> GSM153261 3 0.1489 0.56888 0.004 0.000 0.952 0.044
#> GSM153262 3 0.5354 0.43215 0.056 0.000 0.712 0.232
#> GSM153263 3 0.5977 0.34781 0.192 0.000 0.688 0.120
#> GSM153264 1 0.6966 0.36693 0.540 0.000 0.328 0.132
#> GSM153265 3 0.5630 0.19017 0.032 0.000 0.608 0.360
#> GSM153266 1 0.6357 0.55707 0.656 0.000 0.184 0.160
#> GSM153267 1 0.4524 0.65261 0.768 0.000 0.204 0.028
#> GSM153268 4 0.5288 0.15879 0.008 0.000 0.472 0.520
#> GSM153269 1 0.2611 0.70108 0.896 0.000 0.096 0.008
#> GSM153270 1 0.1767 0.68857 0.944 0.000 0.012 0.044
#> GSM153271 1 0.1151 0.68298 0.968 0.000 0.008 0.024
#> GSM153272 1 0.6854 0.41513 0.596 0.000 0.172 0.232
#> GSM153273 1 0.3497 0.68298 0.860 0.000 0.036 0.104
#> GSM153274 1 0.2489 0.70074 0.912 0.000 0.068 0.020
#> GSM153275 1 0.6936 0.15062 0.568 0.000 0.148 0.284
#> GSM153276 1 0.3168 0.69651 0.884 0.000 0.056 0.060
#> GSM153277 3 0.4661 0.24036 0.000 0.000 0.652 0.348
#> GSM153278 1 0.5472 0.45550 0.676 0.000 0.280 0.044
#> GSM153279 4 0.7666 0.25194 0.212 0.000 0.388 0.400
#> GSM153280 3 0.5673 0.31620 0.052 0.000 0.660 0.288
#> GSM153281 4 0.7253 0.45549 0.172 0.000 0.308 0.520
#> GSM153282 4 0.5969 0.31307 0.044 0.000 0.392 0.564
#> GSM153283 1 0.6546 0.53379 0.636 0.000 0.192 0.172
#> GSM153284 1 0.6554 0.10776 0.520 0.000 0.080 0.400
#> GSM153285 4 0.6340 0.30219 0.064 0.000 0.408 0.528
#> GSM153286 1 0.2741 0.68366 0.892 0.000 0.012 0.096
#> GSM153287 4 0.6468 0.40095 0.348 0.000 0.084 0.568
#> GSM153288 4 0.6949 0.45216 0.348 0.000 0.124 0.528
#> GSM153289 3 0.1151 0.56742 0.008 0.000 0.968 0.024
#> GSM153290 3 0.5244 -0.00949 0.008 0.000 0.556 0.436
#> GSM153291 3 0.4808 0.44835 0.028 0.000 0.736 0.236
#> GSM153292 4 0.6784 0.39078 0.104 0.000 0.368 0.528
#> GSM153293 3 0.7622 -0.01379 0.280 0.000 0.472 0.248
#> GSM153294 1 0.1059 0.68849 0.972 0.000 0.012 0.016
#> GSM153295 3 0.4095 0.51076 0.024 0.000 0.804 0.172
#> GSM153054 1 0.0937 0.68603 0.976 0.000 0.012 0.012
#> GSM153055 3 0.7901 -0.25125 0.312 0.000 0.372 0.316
#> GSM153056 1 0.5367 0.54155 0.664 0.000 0.304 0.032
#> GSM153057 3 0.3658 0.53074 0.144 0.000 0.836 0.020
#> GSM153058 1 0.5517 0.24919 0.568 0.000 0.412 0.020
#> GSM153059 3 0.1975 0.57064 0.048 0.000 0.936 0.016
#> GSM153060 1 0.4985 0.66306 0.768 0.000 0.080 0.152
#> GSM153061 3 0.6303 0.37184 0.192 0.000 0.660 0.148
#> GSM153062 1 0.9112 -0.22700 0.380 0.092 0.180 0.348
#> GSM153063 1 0.7556 0.11436 0.488 0.000 0.264 0.248
#> GSM153064 1 0.6658 0.35747 0.532 0.000 0.376 0.092
#> GSM153065 3 0.4676 0.55089 0.084 0.016 0.816 0.084
#> GSM153066 2 0.7589 0.58112 0.056 0.600 0.232 0.112
#> GSM153067 1 0.5735 0.19153 0.576 0.000 0.032 0.392
#> GSM153068 1 0.7558 0.11497 0.444 0.000 0.360 0.196
#> GSM153069 4 0.6964 0.50516 0.188 0.000 0.228 0.584
#> GSM153070 1 0.0336 0.68286 0.992 0.000 0.008 0.000
#> GSM153071 1 0.6796 0.46134 0.596 0.000 0.152 0.252
#> GSM153072 1 0.3224 0.69929 0.864 0.000 0.120 0.016
#> GSM153073 1 0.0672 0.68503 0.984 0.000 0.008 0.008
#> GSM153074 3 0.7734 -0.11293 0.272 0.000 0.444 0.284
#> GSM153075 3 0.2596 0.56487 0.024 0.000 0.908 0.068
#> GSM153076 1 0.3404 0.69449 0.864 0.000 0.104 0.032
#> GSM153077 1 0.3638 0.67867 0.848 0.000 0.120 0.032
#> GSM153078 3 0.6268 -0.09518 0.448 0.000 0.496 0.056
#> GSM153079 3 0.0895 0.56687 0.004 0.000 0.976 0.020
#> GSM153080 3 0.6367 0.17986 0.080 0.000 0.584 0.336
#> GSM153081 3 0.3266 0.53795 0.108 0.000 0.868 0.024
#> GSM153082 3 0.6195 0.39232 0.188 0.024 0.704 0.084
#> GSM153083 1 0.2899 0.69811 0.880 0.004 0.112 0.004
#> GSM153084 3 0.5653 -0.03601 0.448 0.004 0.532 0.016
#> GSM153085 1 0.5156 0.62268 0.720 0.000 0.236 0.044
#> GSM153086 1 0.1109 0.69256 0.968 0.000 0.028 0.004
#> GSM153087 1 0.3778 0.69249 0.848 0.000 0.052 0.100
#> GSM153088 1 0.1059 0.68316 0.972 0.000 0.016 0.012
#> GSM153089 3 0.5453 0.33604 0.036 0.000 0.660 0.304
#> GSM153090 1 0.1488 0.69054 0.956 0.000 0.032 0.012
#> GSM153091 1 0.1209 0.68664 0.964 0.000 0.032 0.004
#> GSM153092 1 0.5074 0.61901 0.724 0.000 0.236 0.040
#> GSM153093 1 0.4088 0.66751 0.820 0.000 0.040 0.140
#> GSM153094 1 0.5313 0.45138 0.608 0.000 0.376 0.016
#> GSM153095 1 0.5182 0.55137 0.684 0.000 0.288 0.028
#> GSM153096 1 0.6572 0.45155 0.608 0.000 0.272 0.120
#> GSM153097 1 0.5200 0.60229 0.700 0.000 0.264 0.036
#> GSM153098 1 0.7164 0.39848 0.556 0.000 0.240 0.204
#> GSM153099 1 0.5011 0.64007 0.764 0.000 0.076 0.160
#> GSM153100 3 0.5851 0.33067 0.068 0.000 0.660 0.272
#> GSM153101 3 0.3907 0.54411 0.032 0.000 0.828 0.140
#> GSM153102 3 0.3760 0.53656 0.028 0.000 0.836 0.136
#> GSM153103 1 0.1635 0.69573 0.948 0.000 0.044 0.008
#> GSM153104 1 0.6412 0.24225 0.572 0.000 0.080 0.348
#> GSM153106 3 0.0336 0.56590 0.000 0.000 0.992 0.008
#> GSM153107 3 0.0469 0.56693 0.012 0.000 0.988 0.000
#> GSM153108 3 0.4986 0.47792 0.044 0.000 0.740 0.216
#> GSM153109 3 0.5841 0.18385 0.384 0.024 0.584 0.008
#> GSM153110 1 0.1042 0.68559 0.972 0.000 0.020 0.008
#> GSM153111 1 0.1970 0.69982 0.932 0.000 0.060 0.008
#> GSM153112 1 0.7193 0.30427 0.508 0.000 0.340 0.152
#> GSM153113 3 0.8611 0.04708 0.312 0.268 0.388 0.032
#> GSM153114 3 0.0592 0.56780 0.016 0.000 0.984 0.000
#> GSM187532 2 0.4424 0.84549 0.000 0.812 0.100 0.088
#> GSM187533 2 0.3280 0.82165 0.000 0.860 0.124 0.016
#> GSM187534 2 0.4070 0.80614 0.000 0.824 0.132 0.044
#> GSM187535 3 0.1191 0.56406 0.004 0.004 0.968 0.024
#> GSM152906 2 0.2704 0.88854 0.000 0.876 0.000 0.124
#> GSM152907 2 0.0817 0.89491 0.000 0.976 0.000 0.024
#> GSM152908 2 0.3873 0.82831 0.000 0.772 0.000 0.228
#> GSM152909 2 0.4008 0.83026 0.000 0.756 0.000 0.244
#> GSM152910 2 0.3873 0.82831 0.000 0.772 0.000 0.228
#> GSM152911 2 0.0000 0.89438 0.000 1.000 0.000 0.000
#> GSM152912 2 0.3873 0.82831 0.000 0.772 0.000 0.228
#> GSM152913 2 0.0469 0.89451 0.000 0.988 0.000 0.012
#> GSM152914 2 0.0000 0.89438 0.000 1.000 0.000 0.000
#> GSM152915 2 0.0000 0.89438 0.000 1.000 0.000 0.000
#> GSM152916 2 0.2704 0.88854 0.000 0.876 0.000 0.124
#> GSM152917 2 0.0000 0.89438 0.000 1.000 0.000 0.000
#> GSM152918 2 0.0000 0.89438 0.000 1.000 0.000 0.000
#> GSM152919 2 0.0000 0.89438 0.000 1.000 0.000 0.000
#> GSM152920 2 0.3873 0.82831 0.000 0.772 0.000 0.228
#> GSM152921 2 0.3907 0.82884 0.000 0.768 0.000 0.232
#> GSM152922 2 0.4008 0.82999 0.000 0.756 0.000 0.244
#> GSM152923 2 0.2704 0.88854 0.000 0.876 0.000 0.124
#> GSM152924 2 0.2704 0.88854 0.000 0.876 0.000 0.124
#> GSM152925 2 0.2704 0.88854 0.000 0.876 0.000 0.124
#> GSM152926 2 0.3280 0.88242 0.016 0.860 0.000 0.124
#> GSM152927 2 0.2704 0.88854 0.000 0.876 0.000 0.124
#> GSM152928 2 0.5287 0.83841 0.028 0.780 0.064 0.128
#> GSM152929 2 0.2704 0.88854 0.000 0.876 0.000 0.124
#> GSM152930 2 0.2704 0.88854 0.000 0.876 0.000 0.124
cbind(get_classes(res, k = 5), get_membership(res, k = 5))
#> class entropy silhouette p1 p2 p3 p4 p5
#> GSM152839 1 0.4080 0.66031 0.760 0.000 0.212 0.012 0.016
#> GSM152840 4 0.4552 0.22468 0.008 0.000 0.468 0.524 0.000
#> GSM152841 4 0.5351 0.19995 0.052 0.000 0.464 0.484 0.000
#> GSM152842 1 0.5355 0.42458 0.576 0.000 0.032 0.376 0.016
#> GSM152843 1 0.2017 0.69636 0.912 0.000 0.008 0.080 0.000
#> GSM152844 4 0.4588 0.39659 0.016 0.000 0.380 0.604 0.000
#> GSM152845 3 0.1591 0.59301 0.004 0.000 0.940 0.052 0.004
#> GSM152846 3 0.4564 0.44431 0.024 0.000 0.696 0.272 0.008
#> GSM152847 1 0.2140 0.70281 0.924 0.000 0.040 0.024 0.012
#> GSM152848 1 0.6734 0.20690 0.412 0.000 0.408 0.168 0.012
#> GSM152849 3 0.4613 0.07889 0.408 0.000 0.580 0.008 0.004
#> GSM152850 1 0.4994 0.49942 0.604 0.000 0.364 0.020 0.012
#> GSM152851 3 0.3949 0.29512 0.000 0.000 0.668 0.332 0.000
#> GSM152852 3 0.2753 0.52684 0.008 0.000 0.856 0.136 0.000
#> GSM152853 3 0.4882 -0.06571 0.024 0.000 0.532 0.444 0.000
#> GSM152854 3 0.4503 0.51463 0.124 0.000 0.756 0.120 0.000
#> GSM152855 3 0.0290 0.58976 0.000 0.000 0.992 0.008 0.000
#> GSM153238 1 0.5269 0.64648 0.708 0.000 0.144 0.136 0.012
#> GSM153239 4 0.6597 0.32349 0.224 0.000 0.332 0.444 0.000
#> GSM153240 1 0.6726 -0.05809 0.464 0.000 0.200 0.328 0.008
#> GSM153241 1 0.6454 0.18220 0.456 0.000 0.396 0.140 0.008
#> GSM153242 3 0.5684 -0.11712 0.080 0.000 0.488 0.432 0.000
#> GSM153243 1 0.3680 0.69919 0.832 0.000 0.108 0.048 0.012
#> GSM153244 3 0.5060 0.42199 0.224 0.000 0.684 0.092 0.000
#> GSM153245 4 0.6040 0.51694 0.284 0.000 0.156 0.560 0.000
#> GSM153246 1 0.6385 0.21764 0.472 0.000 0.132 0.388 0.008
#> GSM153247 1 0.4298 0.68365 0.788 0.000 0.096 0.108 0.008
#> GSM153248 1 0.4377 0.66558 0.756 0.000 0.192 0.044 0.008
#> GSM153249 4 0.5375 0.35998 0.368 0.000 0.064 0.568 0.000
#> GSM153250 1 0.1405 0.69010 0.956 0.000 0.016 0.020 0.008
#> GSM153251 1 0.5437 0.58362 0.652 0.000 0.220 0.128 0.000
#> GSM153252 4 0.6179 0.47643 0.268 0.000 0.164 0.564 0.004
#> GSM153253 4 0.4297 0.49434 0.020 0.000 0.288 0.692 0.000
#> GSM153254 3 0.6043 0.25742 0.176 0.000 0.572 0.252 0.000
#> GSM153255 4 0.4920 0.24031 0.384 0.000 0.032 0.584 0.000
#> GSM153256 1 0.4473 0.48779 0.656 0.000 0.020 0.324 0.000
#> GSM153257 1 0.2561 0.68286 0.856 0.000 0.000 0.144 0.000
#> GSM153258 1 0.2439 0.70011 0.876 0.000 0.120 0.004 0.000
#> GSM153259 1 0.5261 0.47655 0.600 0.000 0.352 0.036 0.012
#> GSM153260 1 0.5049 0.66942 0.732 0.000 0.148 0.104 0.016
#> GSM153261 3 0.1970 0.59040 0.004 0.000 0.924 0.060 0.012
#> GSM153262 3 0.4594 0.41191 0.036 0.000 0.680 0.284 0.000
#> GSM153263 3 0.5420 0.40513 0.148 0.000 0.676 0.172 0.004
#> GSM153264 1 0.6615 0.38200 0.504 0.000 0.312 0.172 0.012
#> GSM153265 3 0.5077 -0.05052 0.036 0.000 0.536 0.428 0.000
#> GSM153266 1 0.6056 0.55275 0.616 0.000 0.164 0.208 0.012
#> GSM153267 1 0.4313 0.66219 0.752 0.000 0.208 0.028 0.012
#> GSM153268 4 0.4354 0.41018 0.008 0.000 0.368 0.624 0.000
#> GSM153269 1 0.2464 0.70575 0.892 0.000 0.092 0.012 0.004
#> GSM153270 1 0.1662 0.69321 0.936 0.000 0.004 0.056 0.004
#> GSM153271 1 0.0968 0.68658 0.972 0.000 0.004 0.012 0.012
#> GSM153272 1 0.6172 0.46118 0.584 0.000 0.164 0.244 0.008
#> GSM153273 1 0.3491 0.68746 0.836 0.000 0.028 0.124 0.012
#> GSM153274 1 0.2476 0.70531 0.904 0.000 0.064 0.020 0.012
#> GSM153275 1 0.6274 0.10800 0.532 0.000 0.120 0.336 0.012
#> GSM153276 1 0.2867 0.70077 0.880 0.000 0.044 0.072 0.004
#> GSM153277 3 0.4126 0.13838 0.000 0.000 0.620 0.380 0.000
#> GSM153278 1 0.4843 0.50607 0.676 0.000 0.276 0.044 0.004
#> GSM153279 4 0.6114 0.34912 0.152 0.000 0.312 0.536 0.000
#> GSM153280 3 0.4851 0.19976 0.036 0.000 0.624 0.340 0.000
#> GSM153281 4 0.5644 0.55180 0.144 0.000 0.228 0.628 0.000
#> GSM153282 4 0.4252 0.48657 0.020 0.000 0.280 0.700 0.000
#> GSM153283 1 0.6244 0.53853 0.596 0.000 0.160 0.228 0.016
#> GSM153284 1 0.5491 0.09441 0.480 0.000 0.044 0.468 0.008
#> GSM153285 4 0.4797 0.48758 0.044 0.000 0.296 0.660 0.000
#> GSM153286 1 0.2295 0.69243 0.900 0.000 0.004 0.088 0.008
#> GSM153287 4 0.4615 0.51236 0.252 0.000 0.048 0.700 0.000
#> GSM153288 4 0.5213 0.51280 0.276 0.000 0.068 0.652 0.004
#> GSM153289 3 0.1205 0.58982 0.004 0.000 0.956 0.040 0.000
#> GSM153290 4 0.4450 0.18361 0.004 0.000 0.488 0.508 0.000
#> GSM153291 3 0.4380 0.39129 0.020 0.000 0.676 0.304 0.000
#> GSM153292 4 0.5105 0.53594 0.076 0.000 0.264 0.660 0.000
#> GSM153293 3 0.6817 0.07448 0.248 0.000 0.464 0.280 0.008
#> GSM153294 1 0.1588 0.69627 0.948 0.000 0.016 0.028 0.008
#> GSM153295 3 0.3849 0.50602 0.016 0.000 0.752 0.232 0.000
#> GSM153054 1 0.1200 0.69225 0.964 0.000 0.008 0.016 0.012
#> GSM153055 4 0.7104 0.28178 0.276 0.000 0.344 0.368 0.012
#> GSM153056 1 0.4957 0.56290 0.648 0.000 0.312 0.028 0.012
#> GSM153057 3 0.3238 0.54711 0.136 0.000 0.836 0.028 0.000
#> GSM153058 1 0.4817 0.30567 0.572 0.000 0.404 0.024 0.000
#> GSM153059 3 0.1741 0.59541 0.040 0.000 0.936 0.024 0.000
#> GSM153060 1 0.5037 0.65345 0.724 0.000 0.080 0.180 0.016
#> GSM153061 3 0.6151 0.36917 0.176 0.000 0.604 0.208 0.012
#> GSM153062 4 0.8158 0.24383 0.244 0.076 0.092 0.504 0.084
#> GSM153063 1 0.6621 0.07536 0.448 0.000 0.240 0.312 0.000
#> GSM153064 1 0.6260 0.40855 0.516 0.000 0.360 0.112 0.012
#> GSM153065 3 0.5000 0.54956 0.076 0.020 0.764 0.124 0.016
#> GSM153066 2 0.8066 0.20809 0.036 0.448 0.228 0.044 0.244
#> GSM153067 1 0.4830 -0.02536 0.492 0.000 0.020 0.488 0.000
#> GSM153068 1 0.6815 0.21642 0.432 0.000 0.304 0.260 0.004
#> GSM153069 4 0.4680 0.56038 0.128 0.000 0.132 0.740 0.000
#> GSM153070 1 0.0290 0.68732 0.992 0.000 0.008 0.000 0.000
#> GSM153071 1 0.6225 0.37000 0.516 0.000 0.136 0.344 0.004
#> GSM153072 1 0.2773 0.70567 0.868 0.000 0.112 0.020 0.000
#> GSM153073 1 0.0981 0.68941 0.972 0.000 0.008 0.012 0.008
#> GSM153074 3 0.6705 -0.19243 0.252 0.000 0.412 0.336 0.000
#> GSM153075 3 0.2457 0.57716 0.016 0.000 0.900 0.076 0.008
#> GSM153076 1 0.3293 0.70025 0.852 0.000 0.108 0.028 0.012
#> GSM153077 1 0.3533 0.68391 0.840 0.000 0.108 0.040 0.012
#> GSM153078 1 0.5904 0.19557 0.460 0.000 0.460 0.068 0.012
#> GSM153079 3 0.0880 0.59044 0.000 0.000 0.968 0.032 0.000
#> GSM153080 3 0.5562 0.00407 0.072 0.000 0.520 0.408 0.000
#> GSM153081 3 0.3030 0.56596 0.088 0.000 0.868 0.040 0.004
#> GSM153082 3 0.5812 0.43698 0.160 0.016 0.684 0.128 0.012
#> GSM153083 1 0.2672 0.70309 0.872 0.000 0.116 0.008 0.004
#> GSM153084 3 0.5484 0.00352 0.424 0.008 0.532 0.016 0.020
#> GSM153085 1 0.4722 0.64399 0.716 0.000 0.232 0.040 0.012
#> GSM153086 1 0.1493 0.69776 0.948 0.000 0.024 0.000 0.028
#> GSM153087 1 0.3400 0.69978 0.840 0.000 0.040 0.116 0.004
#> GSM153088 1 0.0981 0.68625 0.972 0.000 0.008 0.008 0.012
#> GSM153089 3 0.5068 0.14492 0.032 0.000 0.580 0.384 0.004
#> GSM153090 1 0.1507 0.69330 0.952 0.000 0.024 0.012 0.012
#> GSM153091 1 0.1173 0.69042 0.964 0.000 0.020 0.004 0.012
#> GSM153092 1 0.4820 0.62772 0.708 0.000 0.232 0.052 0.008
#> GSM153093 1 0.3731 0.66546 0.800 0.000 0.040 0.160 0.000
#> GSM153094 1 0.5039 0.46632 0.604 0.000 0.360 0.028 0.008
#> GSM153095 1 0.5082 0.54840 0.656 0.000 0.292 0.040 0.012
#> GSM153096 1 0.6162 0.47665 0.584 0.000 0.248 0.160 0.008
#> GSM153097 1 0.5145 0.61345 0.676 0.000 0.256 0.056 0.012
#> GSM153098 1 0.6696 0.39799 0.512 0.000 0.220 0.256 0.012
#> GSM153099 1 0.4634 0.64543 0.740 0.000 0.072 0.184 0.004
#> GSM153100 3 0.5331 0.13316 0.060 0.000 0.568 0.372 0.000
#> GSM153101 3 0.4121 0.54855 0.036 0.000 0.784 0.168 0.012
#> GSM153102 3 0.3757 0.53878 0.024 0.000 0.808 0.156 0.012
#> GSM153103 1 0.1568 0.70137 0.944 0.000 0.036 0.020 0.000
#> GSM153104 1 0.5551 0.03161 0.488 0.000 0.068 0.444 0.000
#> GSM153106 3 0.0404 0.58838 0.000 0.000 0.988 0.012 0.000
#> GSM153107 3 0.0162 0.58935 0.000 0.000 0.996 0.004 0.000
#> GSM153108 3 0.4752 0.39638 0.036 0.000 0.648 0.316 0.000
#> GSM153109 3 0.5644 0.15229 0.376 0.028 0.568 0.016 0.012
#> GSM153110 1 0.0981 0.68896 0.972 0.000 0.008 0.008 0.012
#> GSM153111 1 0.2074 0.70524 0.924 0.004 0.056 0.008 0.008
#> GSM153112 1 0.6771 0.34753 0.484 0.000 0.300 0.204 0.012
#> GSM153113 3 0.7986 0.04674 0.300 0.256 0.376 0.060 0.008
#> GSM153114 3 0.0324 0.58840 0.004 0.000 0.992 0.004 0.000
#> GSM187532 2 0.5452 0.58325 0.000 0.692 0.100 0.020 0.188
#> GSM187533 2 0.4111 0.45707 0.000 0.816 0.100 0.036 0.048
#> GSM187534 2 0.4834 0.46820 0.000 0.752 0.132 0.016 0.100
#> GSM187535 3 0.1117 0.58912 0.000 0.000 0.964 0.020 0.016
#> GSM152906 2 0.4201 0.70408 0.000 0.592 0.000 0.000 0.408
#> GSM152907 2 0.1430 0.59066 0.000 0.944 0.000 0.004 0.052
#> GSM152908 5 0.5548 0.97890 0.000 0.440 0.000 0.068 0.492
#> GSM152909 5 0.5542 0.97833 0.000 0.432 0.000 0.068 0.500
#> GSM152910 5 0.5538 0.97571 0.000 0.428 0.000 0.068 0.504
#> GSM152911 2 0.0162 0.55760 0.000 0.996 0.000 0.004 0.000
#> GSM152912 5 0.5546 0.97945 0.000 0.436 0.000 0.068 0.496
#> GSM152913 2 0.1668 0.48569 0.000 0.940 0.000 0.032 0.028
#> GSM152914 2 0.0162 0.55760 0.000 0.996 0.000 0.004 0.000
#> GSM152915 2 0.0162 0.55760 0.000 0.996 0.000 0.004 0.000
#> GSM152916 2 0.4192 0.70413 0.000 0.596 0.000 0.000 0.404
#> GSM152917 2 0.0162 0.55760 0.000 0.996 0.000 0.004 0.000
#> GSM152918 2 0.0162 0.55760 0.000 0.996 0.000 0.004 0.000
#> GSM152919 2 0.0162 0.55760 0.000 0.996 0.000 0.004 0.000
#> GSM152920 5 0.5548 0.97890 0.000 0.440 0.000 0.068 0.492
#> GSM152921 5 0.5546 0.98006 0.000 0.436 0.000 0.068 0.496
#> GSM152922 5 0.5476 0.92327 0.000 0.388 0.000 0.068 0.544
#> GSM152923 2 0.4201 0.70408 0.000 0.592 0.000 0.000 0.408
#> GSM152924 2 0.4201 0.70408 0.000 0.592 0.000 0.000 0.408
#> GSM152925 2 0.4201 0.70408 0.000 0.592 0.000 0.000 0.408
#> GSM152926 2 0.4658 0.69134 0.016 0.576 0.000 0.000 0.408
#> GSM152927 2 0.4210 0.70237 0.000 0.588 0.000 0.000 0.412
#> GSM152928 2 0.4582 0.68799 0.012 0.572 0.000 0.000 0.416
#> GSM152929 2 0.4201 0.70408 0.000 0.592 0.000 0.000 0.408
#> GSM152930 2 0.4201 0.70408 0.000 0.592 0.000 0.000 0.408
cbind(get_classes(res, k = 6), get_membership(res, k = 6))
#> class entropy silhouette p1 p2 p3 p4 p5 p6
#> GSM152839 1 0.3504 0.65185 0.776 0.000 0.196 0.004 0.000 0.024
#> GSM152840 4 0.4344 0.29689 0.008 0.000 0.412 0.568 0.000 0.012
#> GSM152841 4 0.4576 0.31536 0.040 0.000 0.400 0.560 0.000 0.000
#> GSM152842 1 0.5227 0.36889 0.536 0.000 0.024 0.392 0.000 0.048
#> GSM152843 1 0.2554 0.67613 0.876 0.000 0.000 0.076 0.000 0.048
#> GSM152844 4 0.3733 0.48323 0.008 0.000 0.288 0.700 0.000 0.004
#> GSM152845 3 0.1549 0.61166 0.000 0.000 0.936 0.044 0.000 0.020
#> GSM152846 3 0.4593 0.44769 0.008 0.000 0.660 0.280 0.000 0.052
#> GSM152847 1 0.2183 0.68571 0.912 0.000 0.040 0.028 0.000 0.020
#> GSM152848 1 0.6737 0.18599 0.396 0.000 0.376 0.164 0.000 0.064
#> GSM152849 3 0.4662 0.00822 0.424 0.000 0.540 0.008 0.000 0.028
#> GSM152850 1 0.5042 0.47412 0.588 0.000 0.344 0.020 0.000 0.048
#> GSM152851 3 0.3940 0.31547 0.004 0.000 0.652 0.336 0.000 0.008
#> GSM152852 3 0.2794 0.53199 0.004 0.000 0.840 0.144 0.000 0.012
#> GSM152853 4 0.4096 0.13633 0.008 0.000 0.484 0.508 0.000 0.000
#> GSM152854 3 0.4550 0.53719 0.116 0.000 0.744 0.112 0.000 0.028
#> GSM152855 3 0.0260 0.60711 0.000 0.000 0.992 0.008 0.000 0.000
#> GSM153238 1 0.6045 0.57501 0.616 0.000 0.108 0.156 0.000 0.120
#> GSM153239 4 0.6213 0.33783 0.164 0.000 0.300 0.504 0.000 0.032
#> GSM153240 1 0.6314 -0.08369 0.452 0.000 0.192 0.332 0.000 0.024
#> GSM153241 1 0.6784 0.12773 0.396 0.000 0.384 0.132 0.000 0.088
#> GSM153242 4 0.5302 0.19561 0.056 0.000 0.424 0.500 0.000 0.020
#> GSM153243 1 0.3930 0.68048 0.812 0.004 0.068 0.056 0.000 0.060
#> GSM153244 3 0.4741 0.47135 0.216 0.000 0.688 0.084 0.000 0.012
#> GSM153245 4 0.4915 0.46438 0.260 0.000 0.108 0.632 0.000 0.000
#> GSM153246 4 0.6642 -0.13316 0.316 0.008 0.120 0.488 0.000 0.068
#> GSM153247 1 0.4878 0.64712 0.732 0.000 0.076 0.100 0.000 0.092
#> GSM153248 1 0.5281 0.62920 0.680 0.000 0.140 0.044 0.000 0.136
#> GSM153249 4 0.4569 0.37670 0.320 0.000 0.028 0.636 0.000 0.016
#> GSM153250 1 0.0862 0.66481 0.972 0.000 0.004 0.008 0.000 0.016
#> GSM153251 1 0.5847 0.54838 0.596 0.000 0.224 0.140 0.000 0.040
#> GSM153252 4 0.5534 0.47094 0.220 0.000 0.156 0.608 0.000 0.016
#> GSM153253 4 0.3136 0.53058 0.016 0.000 0.188 0.796 0.000 0.000
#> GSM153254 3 0.5492 0.32428 0.140 0.000 0.580 0.272 0.000 0.008
#> GSM153255 4 0.4308 0.39105 0.300 0.000 0.028 0.664 0.000 0.008
#> GSM153256 1 0.4787 0.40041 0.608 0.000 0.020 0.340 0.000 0.032
#> GSM153257 1 0.2402 0.66858 0.868 0.000 0.000 0.120 0.000 0.012
#> GSM153258 1 0.2263 0.68037 0.884 0.000 0.100 0.000 0.000 0.016
#> GSM153259 1 0.6024 0.46853 0.552 0.000 0.276 0.040 0.000 0.132
#> GSM153260 1 0.5277 0.63797 0.696 0.000 0.116 0.104 0.000 0.084
#> GSM153261 3 0.2240 0.60989 0.016 0.000 0.908 0.044 0.000 0.032
#> GSM153262 3 0.4322 0.42767 0.032 0.000 0.672 0.288 0.000 0.008
#> GSM153263 3 0.5780 0.42697 0.128 0.000 0.628 0.184 0.000 0.060
#> GSM153264 1 0.6722 0.27215 0.436 0.000 0.336 0.160 0.000 0.068
#> GSM153265 4 0.4701 0.12610 0.008 0.000 0.480 0.484 0.000 0.028
#> GSM153266 1 0.6560 0.45717 0.532 0.000 0.172 0.212 0.000 0.084
#> GSM153267 1 0.3916 0.64856 0.748 0.000 0.212 0.016 0.000 0.024
#> GSM153268 4 0.3330 0.48508 0.000 0.000 0.284 0.716 0.000 0.000
#> GSM153269 1 0.2121 0.68721 0.892 0.000 0.096 0.000 0.000 0.012
#> GSM153270 1 0.1633 0.67107 0.932 0.000 0.000 0.044 0.000 0.024
#> GSM153271 1 0.0603 0.66089 0.980 0.000 0.000 0.004 0.000 0.016
#> GSM153272 1 0.5734 0.46029 0.576 0.000 0.172 0.236 0.000 0.016
#> GSM153273 1 0.4090 0.65254 0.760 0.000 0.008 0.076 0.000 0.156
#> GSM153274 1 0.2445 0.68564 0.896 0.000 0.056 0.020 0.000 0.028
#> GSM153275 1 0.6445 -0.15579 0.440 0.000 0.100 0.384 0.000 0.076
#> GSM153276 1 0.2687 0.68643 0.876 0.000 0.044 0.072 0.000 0.008
#> GSM153277 3 0.3923 0.07153 0.000 0.000 0.580 0.416 0.000 0.004
#> GSM153278 1 0.4854 0.48507 0.664 0.000 0.260 0.044 0.000 0.032
#> GSM153279 4 0.4745 0.40766 0.088 0.000 0.268 0.644 0.000 0.000
#> GSM153280 3 0.4364 0.17147 0.024 0.000 0.608 0.364 0.000 0.004
#> GSM153281 4 0.4328 0.55589 0.092 0.000 0.192 0.716 0.000 0.000
#> GSM153282 4 0.2664 0.51005 0.000 0.000 0.184 0.816 0.000 0.000
#> GSM153283 1 0.6311 0.46049 0.536 0.000 0.152 0.256 0.000 0.056
#> GSM153284 4 0.5355 0.04221 0.408 0.000 0.024 0.512 0.000 0.056
#> GSM153285 4 0.3825 0.53589 0.032 0.000 0.220 0.744 0.000 0.004
#> GSM153286 1 0.1926 0.67627 0.912 0.000 0.000 0.068 0.000 0.020
#> GSM153287 4 0.3071 0.45842 0.180 0.000 0.016 0.804 0.000 0.000
#> GSM153288 4 0.4098 0.44884 0.220 0.000 0.036 0.732 0.000 0.012
#> GSM153289 3 0.0937 0.60870 0.000 0.000 0.960 0.040 0.000 0.000
#> GSM153290 4 0.3765 0.33399 0.000 0.000 0.404 0.596 0.000 0.000
#> GSM153291 3 0.4405 0.26623 0.020 0.000 0.604 0.368 0.000 0.008
#> GSM153292 4 0.4147 0.54615 0.044 0.000 0.196 0.744 0.000 0.016
#> GSM153293 3 0.6333 0.15927 0.232 0.000 0.456 0.292 0.000 0.020
#> GSM153294 1 0.2237 0.67281 0.896 0.000 0.004 0.020 0.000 0.080
#> GSM153295 3 0.3936 0.52961 0.012 0.000 0.736 0.228 0.000 0.024
#> GSM153054 1 0.2655 0.66103 0.848 0.000 0.004 0.008 0.000 0.140
#> GSM153055 4 0.6819 0.30573 0.248 0.000 0.284 0.416 0.000 0.052
#> GSM153056 1 0.4986 0.55115 0.620 0.000 0.300 0.012 0.000 0.068
#> GSM153057 3 0.3140 0.58961 0.096 0.000 0.848 0.020 0.000 0.036
#> GSM153058 1 0.4652 0.29223 0.560 0.000 0.404 0.024 0.000 0.012
#> GSM153059 3 0.1675 0.61420 0.032 0.000 0.936 0.024 0.000 0.008
#> GSM153060 1 0.4969 0.63407 0.712 0.000 0.064 0.156 0.000 0.068
#> GSM153061 3 0.6517 0.38229 0.148 0.000 0.544 0.212 0.000 0.096
#> GSM153062 6 0.6277 0.00000 0.088 0.000 0.020 0.264 0.056 0.572
#> GSM153063 1 0.6430 -0.03429 0.416 0.000 0.196 0.360 0.000 0.028
#> GSM153064 1 0.6891 0.38919 0.448 0.000 0.304 0.100 0.000 0.148
#> GSM153065 3 0.5199 0.54160 0.036 0.000 0.692 0.112 0.004 0.156
#> GSM153066 5 0.8321 0.22670 0.040 0.208 0.212 0.028 0.404 0.108
#> GSM153067 4 0.4158 0.29450 0.416 0.000 0.008 0.572 0.000 0.004
#> GSM153068 1 0.6734 0.24190 0.404 0.000 0.276 0.280 0.000 0.040
#> GSM153069 4 0.3112 0.50395 0.096 0.000 0.068 0.836 0.000 0.000
#> GSM153070 1 0.1036 0.66663 0.964 0.000 0.008 0.004 0.000 0.024
#> GSM153071 1 0.6560 0.26949 0.444 0.000 0.136 0.356 0.000 0.064
#> GSM153072 1 0.3479 0.68741 0.820 0.000 0.084 0.008 0.000 0.088
#> GSM153073 1 0.0717 0.66651 0.976 0.000 0.008 0.000 0.000 0.016
#> GSM153074 3 0.6278 -0.17185 0.228 0.000 0.396 0.364 0.000 0.012
#> GSM153075 3 0.3041 0.59171 0.012 0.000 0.856 0.068 0.000 0.064
#> GSM153076 1 0.2844 0.68520 0.860 0.000 0.104 0.020 0.000 0.016
#> GSM153077 1 0.3170 0.66153 0.840 0.000 0.112 0.032 0.000 0.016
#> GSM153078 1 0.5870 0.17546 0.452 0.000 0.432 0.060 0.000 0.056
#> GSM153079 3 0.0972 0.60953 0.000 0.000 0.964 0.028 0.000 0.008
#> GSM153080 3 0.5559 -0.10391 0.060 0.000 0.456 0.452 0.000 0.032
#> GSM153081 3 0.3097 0.59018 0.080 0.000 0.856 0.036 0.000 0.028
#> GSM153082 3 0.6145 0.44793 0.140 0.000 0.620 0.084 0.008 0.148
#> GSM153083 1 0.3096 0.68883 0.840 0.000 0.108 0.004 0.000 0.048
#> GSM153084 3 0.5801 0.08193 0.348 0.000 0.508 0.008 0.004 0.132
#> GSM153085 1 0.4224 0.64651 0.736 0.000 0.204 0.020 0.000 0.040
#> GSM153086 1 0.2604 0.67991 0.884 0.008 0.020 0.008 0.000 0.080
#> GSM153087 1 0.3559 0.68523 0.820 0.000 0.036 0.112 0.000 0.032
#> GSM153088 1 0.0790 0.66315 0.968 0.000 0.000 0.000 0.000 0.032
#> GSM153089 3 0.5346 -0.03642 0.028 0.000 0.488 0.436 0.000 0.048
#> GSM153090 1 0.1138 0.67138 0.960 0.000 0.012 0.004 0.000 0.024
#> GSM153091 1 0.2377 0.65844 0.868 0.000 0.004 0.004 0.000 0.124
#> GSM153092 1 0.5115 0.61194 0.684 0.000 0.196 0.056 0.000 0.064
#> GSM153093 1 0.3411 0.63965 0.804 0.000 0.024 0.160 0.000 0.012
#> GSM153094 1 0.5265 0.42084 0.560 0.000 0.360 0.024 0.000 0.056
#> GSM153095 1 0.5803 0.49312 0.588 0.000 0.256 0.040 0.000 0.116
#> GSM153096 1 0.5985 0.44183 0.560 0.000 0.232 0.180 0.000 0.028
#> GSM153097 1 0.5755 0.58083 0.612 0.000 0.232 0.056 0.000 0.100
#> GSM153098 1 0.7118 0.36417 0.448 0.000 0.188 0.240 0.000 0.124
#> GSM153099 1 0.4811 0.62556 0.704 0.000 0.064 0.196 0.000 0.036
#> GSM153100 3 0.4983 -0.06217 0.036 0.000 0.492 0.456 0.000 0.016
#> GSM153101 3 0.4861 0.53431 0.016 0.000 0.696 0.172 0.000 0.116
#> GSM153102 3 0.4343 0.53442 0.020 0.000 0.748 0.160 0.000 0.072
#> GSM153103 1 0.2463 0.68119 0.892 0.000 0.020 0.020 0.000 0.068
#> GSM153104 4 0.5093 0.23206 0.420 0.000 0.052 0.516 0.000 0.012
#> GSM153106 3 0.0603 0.60638 0.000 0.000 0.980 0.016 0.000 0.004
#> GSM153107 3 0.0146 0.60801 0.000 0.000 0.996 0.004 0.000 0.000
#> GSM153108 3 0.5045 0.33967 0.032 0.000 0.580 0.356 0.000 0.032
#> GSM153109 3 0.5989 0.07263 0.356 0.000 0.512 0.016 0.016 0.100
#> GSM153110 1 0.2482 0.65432 0.848 0.000 0.000 0.004 0.000 0.148
#> GSM153111 1 0.3227 0.68619 0.840 0.000 0.052 0.012 0.000 0.096
#> GSM153112 1 0.7416 0.31956 0.388 0.000 0.256 0.196 0.000 0.160
#> GSM153113 3 0.8299 -0.13302 0.264 0.004 0.308 0.044 0.248 0.132
#> GSM153114 3 0.0363 0.60463 0.000 0.000 0.988 0.012 0.000 0.000
#> GSM187532 5 0.5765 0.47830 0.000 0.184 0.088 0.004 0.644 0.080
#> GSM187533 5 0.4206 0.65222 0.000 0.020 0.080 0.004 0.776 0.120
#> GSM187534 5 0.4431 0.58303 0.000 0.100 0.136 0.012 0.748 0.004
#> GSM187535 3 0.1138 0.60950 0.000 0.012 0.960 0.024 0.000 0.004
#> GSM152906 2 0.3851 0.18243 0.000 0.540 0.000 0.000 0.460 0.000
#> GSM152907 5 0.1267 0.75043 0.000 0.060 0.000 0.000 0.940 0.000
#> GSM152908 2 0.5894 0.18341 0.000 0.452 0.000 0.000 0.216 0.332
#> GSM152909 2 0.5894 0.18341 0.000 0.452 0.000 0.000 0.216 0.332
#> GSM152910 2 0.5841 0.18361 0.000 0.464 0.000 0.000 0.204 0.332
#> GSM152911 5 0.0000 0.79959 0.000 0.000 0.000 0.000 1.000 0.000
#> GSM152912 2 0.5859 0.18473 0.000 0.460 0.000 0.000 0.208 0.332
#> GSM152913 5 0.2333 0.71520 0.000 0.024 0.000 0.000 0.884 0.092
#> GSM152914 5 0.0000 0.79959 0.000 0.000 0.000 0.000 1.000 0.000
#> GSM152915 5 0.0000 0.79959 0.000 0.000 0.000 0.000 1.000 0.000
#> GSM152916 2 0.3867 0.12405 0.000 0.512 0.000 0.000 0.488 0.000
#> GSM152917 5 0.0000 0.79959 0.000 0.000 0.000 0.000 1.000 0.000
#> GSM152918 5 0.0000 0.79959 0.000 0.000 0.000 0.000 1.000 0.000
#> GSM152919 5 0.0000 0.79959 0.000 0.000 0.000 0.000 1.000 0.000
#> GSM152920 2 0.5894 0.18341 0.000 0.452 0.000 0.000 0.216 0.332
#> GSM152921 2 0.5877 0.18377 0.000 0.456 0.000 0.000 0.212 0.332
#> GSM152922 2 0.5600 0.16829 0.000 0.508 0.000 0.000 0.160 0.332
#> GSM152923 2 0.3851 0.18243 0.000 0.540 0.000 0.000 0.460 0.000
#> GSM152924 2 0.3851 0.18243 0.000 0.540 0.000 0.000 0.460 0.000
#> GSM152925 2 0.3851 0.18243 0.000 0.540 0.000 0.000 0.460 0.000
#> GSM152926 2 0.4161 0.16716 0.012 0.540 0.000 0.000 0.448 0.000
#> GSM152927 2 0.3851 0.18243 0.000 0.540 0.000 0.000 0.460 0.000
#> GSM152928 2 0.3851 0.18243 0.000 0.540 0.000 0.000 0.460 0.000
#> GSM152929 2 0.3851 0.18243 0.000 0.540 0.000 0.000 0.460 0.000
#> GSM152930 2 0.3851 0.18243 0.000 0.540 0.000 0.000 0.460 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 tissue(p) k
#> SD:pam 162 2.11e-29 2
#> SD:pam 140 2.22e-24 3
#> SD:pam 96 2.26e-15 4
#> SD:pam 97 1.98e-17 5
#> SD:pam 78 3.06e-12 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 12013 rows and 164 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 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 0.977 0.990 0.3103 0.684 0.684
#> 3 3 0.516 0.528 0.819 0.8417 0.722 0.607
#> 4 4 0.642 0.786 0.856 0.2342 0.729 0.456
#> 5 5 0.774 0.790 0.867 0.0490 0.928 0.763
#> 6 6 0.734 0.695 0.845 0.0721 0.880 0.586
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
#> GSM152839 1 0.0000 0.997 1.000 0.000
#> GSM152840 1 0.0000 0.997 1.000 0.000
#> GSM152841 1 0.0000 0.997 1.000 0.000
#> GSM152842 1 0.0376 0.993 0.996 0.004
#> GSM152843 1 0.0376 0.993 0.996 0.004
#> GSM152844 1 0.0000 0.997 1.000 0.000
#> GSM152845 1 0.4815 0.880 0.896 0.104
#> GSM152846 1 0.0000 0.997 1.000 0.000
#> GSM152847 1 0.0376 0.993 0.996 0.004
#> GSM152848 1 0.0000 0.997 1.000 0.000
#> GSM152849 1 0.0000 0.997 1.000 0.000
#> GSM152850 1 0.0000 0.997 1.000 0.000
#> GSM152851 1 0.0000 0.997 1.000 0.000
#> GSM152852 1 0.0000 0.997 1.000 0.000
#> GSM152853 1 0.0000 0.997 1.000 0.000
#> GSM152854 1 0.0000 0.997 1.000 0.000
#> GSM152855 1 0.0000 0.997 1.000 0.000
#> GSM153238 1 0.0000 0.997 1.000 0.000
#> GSM153239 1 0.0000 0.997 1.000 0.000
#> GSM153240 1 0.0000 0.997 1.000 0.000
#> GSM153241 1 0.0000 0.997 1.000 0.000
#> GSM153242 1 0.0000 0.997 1.000 0.000
#> GSM153243 1 0.1184 0.982 0.984 0.016
#> GSM153244 1 0.0000 0.997 1.000 0.000
#> GSM153245 1 0.0000 0.997 1.000 0.000
#> GSM153246 1 0.0000 0.997 1.000 0.000
#> GSM153247 1 0.0000 0.997 1.000 0.000
#> GSM153248 1 0.0000 0.997 1.000 0.000
#> GSM153249 1 0.0000 0.997 1.000 0.000
#> GSM153250 1 0.0000 0.997 1.000 0.000
#> GSM153251 1 0.0000 0.997 1.000 0.000
#> GSM153252 1 0.0000 0.997 1.000 0.000
#> GSM153253 1 0.0000 0.997 1.000 0.000
#> GSM153254 1 0.0000 0.997 1.000 0.000
#> GSM153255 1 0.0000 0.997 1.000 0.000
#> GSM153256 1 0.0000 0.997 1.000 0.000
#> GSM153257 1 0.0000 0.997 1.000 0.000
#> GSM153258 1 0.0000 0.997 1.000 0.000
#> GSM153259 1 0.0000 0.997 1.000 0.000
#> GSM153260 1 0.0000 0.997 1.000 0.000
#> GSM153261 1 0.0000 0.997 1.000 0.000
#> GSM153262 1 0.0000 0.997 1.000 0.000
#> GSM153263 1 0.0000 0.997 1.000 0.000
#> GSM153264 1 0.0000 0.997 1.000 0.000
#> GSM153265 1 0.0000 0.997 1.000 0.000
#> GSM153266 1 0.0000 0.997 1.000 0.000
#> GSM153267 1 0.0000 0.997 1.000 0.000
#> GSM153268 1 0.0000 0.997 1.000 0.000
#> GSM153269 1 0.0000 0.997 1.000 0.000
#> GSM153270 1 0.0000 0.997 1.000 0.000
#> GSM153271 1 0.0000 0.997 1.000 0.000
#> GSM153272 1 0.0000 0.997 1.000 0.000
#> GSM153273 1 0.0000 0.997 1.000 0.000
#> GSM153274 1 0.0000 0.997 1.000 0.000
#> GSM153275 1 0.0000 0.997 1.000 0.000
#> GSM153276 1 0.0000 0.997 1.000 0.000
#> GSM153277 1 0.0000 0.997 1.000 0.000
#> GSM153278 1 0.0000 0.997 1.000 0.000
#> GSM153279 1 0.0000 0.997 1.000 0.000
#> GSM153280 1 0.0000 0.997 1.000 0.000
#> GSM153281 1 0.0000 0.997 1.000 0.000
#> GSM153282 1 0.0000 0.997 1.000 0.000
#> GSM153283 1 0.0000 0.997 1.000 0.000
#> GSM153284 1 0.0000 0.997 1.000 0.000
#> GSM153285 1 0.0000 0.997 1.000 0.000
#> GSM153286 1 0.0000 0.997 1.000 0.000
#> GSM153287 1 0.0000 0.997 1.000 0.000
#> GSM153288 1 0.0000 0.997 1.000 0.000
#> GSM153289 1 0.0000 0.997 1.000 0.000
#> GSM153290 1 0.0000 0.997 1.000 0.000
#> GSM153291 1 0.0000 0.997 1.000 0.000
#> GSM153292 1 0.0000 0.997 1.000 0.000
#> GSM153293 1 0.0000 0.997 1.000 0.000
#> GSM153294 1 0.0000 0.997 1.000 0.000
#> GSM153295 1 0.0000 0.997 1.000 0.000
#> GSM153054 1 0.0000 0.997 1.000 0.000
#> GSM153055 1 0.0000 0.997 1.000 0.000
#> GSM153056 1 0.0000 0.997 1.000 0.000
#> GSM153057 1 0.0000 0.997 1.000 0.000
#> GSM153058 1 0.0000 0.997 1.000 0.000
#> GSM153059 1 0.0000 0.997 1.000 0.000
#> GSM153060 1 0.0000 0.997 1.000 0.000
#> GSM153061 1 0.0000 0.997 1.000 0.000
#> GSM153062 1 0.0000 0.997 1.000 0.000
#> GSM153063 1 0.0000 0.997 1.000 0.000
#> GSM153064 1 0.0000 0.997 1.000 0.000
#> GSM153065 1 0.0000 0.997 1.000 0.000
#> GSM153066 2 0.9661 0.392 0.392 0.608
#> GSM153067 1 0.0000 0.997 1.000 0.000
#> GSM153068 1 0.0000 0.997 1.000 0.000
#> GSM153069 1 0.0000 0.997 1.000 0.000
#> GSM153070 1 0.0000 0.997 1.000 0.000
#> GSM153071 1 0.0000 0.997 1.000 0.000
#> GSM153072 1 0.0000 0.997 1.000 0.000
#> GSM153073 1 0.0000 0.997 1.000 0.000
#> GSM153074 1 0.0000 0.997 1.000 0.000
#> GSM153075 1 0.0000 0.997 1.000 0.000
#> GSM153076 1 0.0000 0.997 1.000 0.000
#> GSM153077 1 0.0000 0.997 1.000 0.000
#> GSM153078 1 0.0000 0.997 1.000 0.000
#> GSM153079 1 0.0672 0.990 0.992 0.008
#> GSM153080 1 0.0000 0.997 1.000 0.000
#> GSM153081 1 0.0000 0.997 1.000 0.000
#> GSM153082 1 0.2043 0.966 0.968 0.032
#> GSM153083 1 0.2423 0.958 0.960 0.040
#> GSM153084 2 0.9815 0.315 0.420 0.580
#> GSM153085 1 0.0000 0.997 1.000 0.000
#> GSM153086 1 0.0376 0.993 0.996 0.004
#> GSM153087 1 0.0000 0.997 1.000 0.000
#> GSM153088 1 0.0000 0.997 1.000 0.000
#> GSM153089 1 0.0000 0.997 1.000 0.000
#> GSM153090 1 0.0000 0.997 1.000 0.000
#> GSM153091 1 0.0672 0.990 0.992 0.008
#> GSM153092 1 0.0000 0.997 1.000 0.000
#> GSM153093 1 0.0000 0.997 1.000 0.000
#> GSM153094 1 0.1633 0.974 0.976 0.024
#> GSM153095 1 0.0000 0.997 1.000 0.000
#> GSM153096 1 0.0000 0.997 1.000 0.000
#> GSM153097 1 0.0376 0.993 0.996 0.004
#> GSM153098 1 0.0376 0.993 0.996 0.004
#> GSM153099 1 0.0000 0.997 1.000 0.000
#> GSM153100 1 0.0000 0.997 1.000 0.000
#> GSM153101 1 0.0000 0.997 1.000 0.000
#> GSM153102 1 0.0672 0.990 0.992 0.008
#> GSM153103 1 0.0000 0.997 1.000 0.000
#> GSM153104 1 0.0000 0.997 1.000 0.000
#> GSM153106 1 0.0000 0.997 1.000 0.000
#> GSM153107 1 0.0000 0.997 1.000 0.000
#> GSM153108 1 0.0000 0.997 1.000 0.000
#> GSM153109 1 0.5519 0.850 0.872 0.128
#> GSM153110 1 0.0376 0.993 0.996 0.004
#> GSM153111 1 0.1414 0.979 0.980 0.020
#> GSM153112 1 0.0000 0.997 1.000 0.000
#> GSM153113 2 0.8861 0.582 0.304 0.696
#> GSM153114 1 0.0000 0.997 1.000 0.000
#> GSM187532 2 0.0000 0.961 0.000 1.000
#> GSM187533 2 0.0000 0.961 0.000 1.000
#> GSM187534 2 0.0000 0.961 0.000 1.000
#> GSM187535 2 0.4431 0.877 0.092 0.908
#> GSM152906 2 0.0000 0.961 0.000 1.000
#> GSM152907 2 0.0000 0.961 0.000 1.000
#> GSM152908 2 0.0000 0.961 0.000 1.000
#> GSM152909 2 0.0000 0.961 0.000 1.000
#> GSM152910 2 0.0000 0.961 0.000 1.000
#> GSM152911 2 0.0000 0.961 0.000 1.000
#> GSM152912 2 0.0000 0.961 0.000 1.000
#> GSM152913 2 0.0000 0.961 0.000 1.000
#> GSM152914 2 0.0000 0.961 0.000 1.000
#> GSM152915 2 0.0000 0.961 0.000 1.000
#> GSM152916 2 0.0000 0.961 0.000 1.000
#> GSM152917 2 0.0000 0.961 0.000 1.000
#> GSM152918 2 0.0000 0.961 0.000 1.000
#> GSM152919 2 0.0000 0.961 0.000 1.000
#> GSM152920 2 0.0000 0.961 0.000 1.000
#> GSM152921 2 0.0000 0.961 0.000 1.000
#> GSM152922 2 0.0000 0.961 0.000 1.000
#> GSM152923 2 0.0000 0.961 0.000 1.000
#> GSM152924 2 0.0000 0.961 0.000 1.000
#> GSM152925 2 0.0000 0.961 0.000 1.000
#> GSM152926 2 0.0000 0.961 0.000 1.000
#> GSM152927 2 0.0000 0.961 0.000 1.000
#> GSM152928 2 0.0000 0.961 0.000 1.000
#> GSM152929 2 0.0000 0.961 0.000 1.000
#> GSM152930 2 0.0000 0.961 0.000 1.000
cbind(get_classes(res, k = 3), get_membership(res, k = 3))
#> class entropy silhouette p1 p2 p3
#> GSM152839 1 0.3879 0.5640 0.848 0.000 0.152
#> GSM152840 3 0.0747 0.5193 0.016 0.000 0.984
#> GSM152841 3 0.6215 0.4041 0.428 0.000 0.572
#> GSM152842 1 0.6274 0.0914 0.544 0.000 0.456
#> GSM152843 1 0.6267 0.0978 0.548 0.000 0.452
#> GSM152844 3 0.0747 0.5193 0.016 0.000 0.984
#> GSM152845 3 0.6033 0.2344 0.336 0.004 0.660
#> GSM152846 3 0.0747 0.5193 0.016 0.000 0.984
#> GSM152847 1 0.6274 0.0914 0.544 0.000 0.456
#> GSM152848 1 0.0237 0.6900 0.996 0.000 0.004
#> GSM152849 1 0.6291 0.0735 0.532 0.000 0.468
#> GSM152850 1 0.6008 0.2201 0.628 0.000 0.372
#> GSM152851 3 0.6215 0.4041 0.428 0.000 0.572
#> GSM152852 3 0.0747 0.5193 0.016 0.000 0.984
#> GSM152853 3 0.0747 0.5193 0.016 0.000 0.984
#> GSM152854 3 0.5591 0.2795 0.304 0.000 0.696
#> GSM152855 1 0.5905 0.2153 0.648 0.000 0.352
#> GSM153238 1 0.6235 0.1234 0.564 0.000 0.436
#> GSM153239 3 0.1163 0.5192 0.028 0.000 0.972
#> GSM153240 1 0.6168 0.0207 0.588 0.000 0.412
#> GSM153241 1 0.6235 0.1246 0.564 0.000 0.436
#> GSM153242 3 0.0747 0.5193 0.016 0.000 0.984
#> GSM153243 1 0.6252 0.1105 0.556 0.000 0.444
#> GSM153244 3 0.6235 0.3912 0.436 0.000 0.564
#> GSM153245 3 0.0747 0.5193 0.016 0.000 0.984
#> GSM153246 3 0.6295 0.0262 0.472 0.000 0.528
#> GSM153247 1 0.4121 0.5455 0.832 0.000 0.168
#> GSM153248 1 0.0000 0.6905 1.000 0.000 0.000
#> GSM153249 3 0.6309 0.2644 0.500 0.000 0.500
#> GSM153250 1 0.1289 0.6857 0.968 0.000 0.032
#> GSM153251 3 0.5138 0.3451 0.252 0.000 0.748
#> GSM153252 1 0.6140 0.0697 0.596 0.000 0.404
#> GSM153253 3 0.6215 0.4041 0.428 0.000 0.572
#> GSM153254 1 0.4702 0.5374 0.788 0.000 0.212
#> GSM153255 1 0.6192 0.0177 0.580 0.000 0.420
#> GSM153256 1 0.4002 0.5845 0.840 0.000 0.160
#> GSM153257 1 0.6140 0.0703 0.596 0.000 0.404
#> GSM153258 1 0.0424 0.6908 0.992 0.000 0.008
#> GSM153259 1 0.0237 0.6910 0.996 0.000 0.004
#> GSM153260 1 0.6274 0.0914 0.544 0.000 0.456
#> GSM153261 1 0.6299 0.0584 0.524 0.000 0.476
#> GSM153262 1 0.6267 -0.1108 0.548 0.000 0.452
#> GSM153263 1 0.1964 0.6775 0.944 0.000 0.056
#> GSM153264 1 0.0000 0.6905 1.000 0.000 0.000
#> GSM153265 3 0.6215 0.4041 0.428 0.000 0.572
#> GSM153266 1 0.0237 0.6900 0.996 0.000 0.004
#> GSM153267 1 0.3038 0.6474 0.896 0.000 0.104
#> GSM153268 3 0.6126 0.4168 0.400 0.000 0.600
#> GSM153269 1 0.3412 0.6262 0.876 0.000 0.124
#> GSM153270 1 0.3816 0.5995 0.852 0.000 0.148
#> GSM153271 1 0.2448 0.6666 0.924 0.000 0.076
#> GSM153272 1 0.6168 0.0449 0.588 0.000 0.412
#> GSM153273 1 0.0237 0.6910 0.996 0.000 0.004
#> GSM153274 1 0.2878 0.6543 0.904 0.000 0.096
#> GSM153275 1 0.5058 0.4572 0.756 0.000 0.244
#> GSM153276 1 0.4504 0.5293 0.804 0.000 0.196
#> GSM153277 3 0.6309 0.2537 0.496 0.000 0.504
#> GSM153278 1 0.6180 0.1540 0.584 0.000 0.416
#> GSM153279 3 0.6286 0.3357 0.464 0.000 0.536
#> GSM153280 3 0.6215 0.4041 0.428 0.000 0.572
#> GSM153281 3 0.6299 0.3099 0.476 0.000 0.524
#> GSM153282 3 0.6215 0.4041 0.428 0.000 0.572
#> GSM153283 1 0.0237 0.6900 0.996 0.000 0.004
#> GSM153284 1 0.6126 0.0829 0.600 0.000 0.400
#> GSM153285 3 0.6225 0.3992 0.432 0.000 0.568
#> GSM153286 1 0.6111 0.0938 0.604 0.000 0.396
#> GSM153287 1 0.6309 -0.2820 0.504 0.000 0.496
#> GSM153288 1 0.5859 0.2374 0.656 0.000 0.344
#> GSM153289 1 0.4346 0.5533 0.816 0.000 0.184
#> GSM153290 3 0.6215 0.4041 0.428 0.000 0.572
#> GSM153291 1 0.6180 0.0209 0.584 0.000 0.416
#> GSM153292 3 0.6244 0.3874 0.440 0.000 0.560
#> GSM153293 1 0.5058 0.4573 0.756 0.000 0.244
#> GSM153294 1 0.0237 0.6910 0.996 0.000 0.004
#> GSM153295 1 0.2625 0.6562 0.916 0.000 0.084
#> GSM153054 1 0.0592 0.6874 0.988 0.000 0.012
#> GSM153055 1 0.2066 0.6704 0.940 0.000 0.060
#> GSM153056 1 0.6180 0.1528 0.584 0.000 0.416
#> GSM153057 1 0.3267 0.6470 0.884 0.000 0.116
#> GSM153058 3 0.6204 0.0888 0.424 0.000 0.576
#> GSM153059 1 0.3941 0.5607 0.844 0.000 0.156
#> GSM153060 3 0.6267 0.0680 0.452 0.000 0.548
#> GSM153061 1 0.6302 0.0496 0.520 0.000 0.480
#> GSM153062 3 0.6111 0.1651 0.396 0.000 0.604
#> GSM153063 3 0.4121 0.4315 0.168 0.000 0.832
#> GSM153064 1 0.0237 0.6910 0.996 0.000 0.004
#> GSM153065 1 0.6274 0.0914 0.544 0.000 0.456
#> GSM153066 1 0.6860 0.4109 0.732 0.176 0.092
#> GSM153067 1 0.6140 0.0266 0.596 0.000 0.404
#> GSM153068 1 0.6302 0.0496 0.520 0.000 0.480
#> GSM153069 3 0.6309 0.2753 0.496 0.000 0.504
#> GSM153070 1 0.1411 0.6841 0.964 0.000 0.036
#> GSM153071 1 0.1289 0.6762 0.968 0.000 0.032
#> GSM153072 1 0.0000 0.6905 1.000 0.000 0.000
#> GSM153073 1 0.0424 0.6906 0.992 0.000 0.008
#> GSM153074 1 0.6126 0.0415 0.600 0.000 0.400
#> GSM153075 1 0.5810 0.2372 0.664 0.000 0.336
#> GSM153076 1 0.1163 0.6862 0.972 0.000 0.028
#> GSM153077 1 0.0000 0.6905 1.000 0.000 0.000
#> GSM153078 1 0.1163 0.6785 0.972 0.000 0.028
#> GSM153079 1 0.0000 0.6905 1.000 0.000 0.000
#> GSM153080 1 0.6308 0.0408 0.508 0.000 0.492
#> GSM153081 1 0.0237 0.6909 0.996 0.000 0.004
#> GSM153082 1 0.0000 0.6905 1.000 0.000 0.000
#> GSM153083 1 0.0000 0.6905 1.000 0.000 0.000
#> GSM153084 1 0.2569 0.6567 0.936 0.032 0.032
#> GSM153085 1 0.0892 0.6827 0.980 0.000 0.020
#> GSM153086 1 0.0000 0.6905 1.000 0.000 0.000
#> GSM153087 1 0.5621 0.3127 0.692 0.000 0.308
#> GSM153088 1 0.0747 0.6878 0.984 0.000 0.016
#> GSM153089 3 0.2165 0.5026 0.064 0.000 0.936
#> GSM153090 1 0.1753 0.6813 0.952 0.000 0.048
#> GSM153091 1 0.0000 0.6905 1.000 0.000 0.000
#> GSM153092 1 0.1860 0.6744 0.948 0.000 0.052
#> GSM153093 1 0.6192 0.0177 0.580 0.000 0.420
#> GSM153094 1 0.0000 0.6905 1.000 0.000 0.000
#> GSM153095 1 0.0747 0.6847 0.984 0.000 0.016
#> GSM153096 1 0.0237 0.6910 0.996 0.000 0.004
#> GSM153097 1 0.0000 0.6905 1.000 0.000 0.000
#> GSM153098 1 0.2878 0.6429 0.904 0.000 0.096
#> GSM153099 1 0.2796 0.6578 0.908 0.000 0.092
#> GSM153100 1 0.1860 0.6744 0.948 0.000 0.052
#> GSM153101 1 0.1529 0.6703 0.960 0.000 0.040
#> GSM153102 1 0.2711 0.6631 0.912 0.000 0.088
#> GSM153103 1 0.0424 0.6883 0.992 0.000 0.008
#> GSM153104 3 0.6307 0.2821 0.488 0.000 0.512
#> GSM153106 1 0.2066 0.6704 0.940 0.000 0.060
#> GSM153107 1 0.0747 0.6894 0.984 0.000 0.016
#> GSM153108 1 0.4291 0.5558 0.820 0.000 0.180
#> GSM153109 1 0.0237 0.6897 0.996 0.000 0.004
#> GSM153110 1 0.0000 0.6905 1.000 0.000 0.000
#> GSM153111 1 0.0000 0.6905 1.000 0.000 0.000
#> GSM153112 1 0.1411 0.6826 0.964 0.000 0.036
#> GSM153113 1 0.2749 0.6393 0.924 0.064 0.012
#> GSM153114 1 0.6168 0.0243 0.588 0.000 0.412
#> GSM187532 2 0.0000 0.9796 0.000 1.000 0.000
#> GSM187533 2 0.0000 0.9796 0.000 1.000 0.000
#> GSM187534 2 0.0000 0.9796 0.000 1.000 0.000
#> GSM187535 2 0.6267 0.1871 0.452 0.548 0.000
#> GSM152906 2 0.0000 0.9796 0.000 1.000 0.000
#> GSM152907 2 0.0000 0.9796 0.000 1.000 0.000
#> GSM152908 2 0.0000 0.9796 0.000 1.000 0.000
#> GSM152909 2 0.0000 0.9796 0.000 1.000 0.000
#> GSM152910 2 0.0000 0.9796 0.000 1.000 0.000
#> GSM152911 2 0.0000 0.9796 0.000 1.000 0.000
#> GSM152912 2 0.0000 0.9796 0.000 1.000 0.000
#> GSM152913 2 0.0000 0.9796 0.000 1.000 0.000
#> GSM152914 2 0.0000 0.9796 0.000 1.000 0.000
#> GSM152915 2 0.0000 0.9796 0.000 1.000 0.000
#> GSM152916 2 0.0000 0.9796 0.000 1.000 0.000
#> GSM152917 2 0.0000 0.9796 0.000 1.000 0.000
#> GSM152918 2 0.0000 0.9796 0.000 1.000 0.000
#> GSM152919 2 0.0000 0.9796 0.000 1.000 0.000
#> GSM152920 2 0.0000 0.9796 0.000 1.000 0.000
#> GSM152921 2 0.0000 0.9796 0.000 1.000 0.000
#> GSM152922 2 0.0000 0.9796 0.000 1.000 0.000
#> GSM152923 2 0.0000 0.9796 0.000 1.000 0.000
#> GSM152924 2 0.0000 0.9796 0.000 1.000 0.000
#> GSM152925 2 0.0000 0.9796 0.000 1.000 0.000
#> GSM152926 2 0.0000 0.9796 0.000 1.000 0.000
#> GSM152927 2 0.0000 0.9796 0.000 1.000 0.000
#> GSM152928 2 0.0424 0.9712 0.008 0.992 0.000
#> GSM152929 2 0.0000 0.9796 0.000 1.000 0.000
#> GSM152930 2 0.0000 0.9796 0.000 1.000 0.000
cbind(get_classes(res, k = 4), get_membership(res, k = 4))
#> class entropy silhouette p1 p2 p3 p4
#> GSM152839 1 0.4936 0.5036 0.652 0.000 0.340 0.008
#> GSM152840 3 0.4585 0.7197 0.000 0.000 0.668 0.332
#> GSM152841 4 0.2773 0.8064 0.116 0.000 0.004 0.880
#> GSM152842 3 0.1792 0.8198 0.068 0.000 0.932 0.000
#> GSM152843 3 0.1867 0.8198 0.072 0.000 0.928 0.000
#> GSM152844 3 0.4477 0.7327 0.000 0.000 0.688 0.312
#> GSM152845 3 0.5111 0.7961 0.056 0.000 0.740 0.204
#> GSM152846 3 0.4608 0.7394 0.004 0.000 0.692 0.304
#> GSM152847 3 0.1867 0.8195 0.072 0.000 0.928 0.000
#> GSM152848 1 0.2466 0.8301 0.900 0.000 0.096 0.004
#> GSM152849 3 0.1792 0.8198 0.068 0.000 0.932 0.000
#> GSM152850 3 0.4134 0.6556 0.260 0.000 0.740 0.000
#> GSM152851 4 0.7034 -0.0284 0.120 0.000 0.412 0.468
#> GSM152852 3 0.4454 0.7354 0.000 0.000 0.692 0.308
#> GSM152853 3 0.4477 0.7327 0.000 0.000 0.688 0.312
#> GSM152854 3 0.5109 0.7986 0.060 0.000 0.744 0.196
#> GSM152855 1 0.6222 -0.2087 0.532 0.000 0.056 0.412
#> GSM153238 3 0.2868 0.7930 0.136 0.000 0.864 0.000
#> GSM153239 3 0.4661 0.7075 0.000 0.000 0.652 0.348
#> GSM153240 4 0.4576 0.8176 0.260 0.000 0.012 0.728
#> GSM153241 3 0.2469 0.8088 0.108 0.000 0.892 0.000
#> GSM153242 3 0.4608 0.7394 0.004 0.000 0.692 0.304
#> GSM153243 3 0.2408 0.8104 0.104 0.000 0.896 0.000
#> GSM153244 4 0.4336 0.7694 0.128 0.000 0.060 0.812
#> GSM153245 3 0.4477 0.7327 0.000 0.000 0.688 0.312
#> GSM153246 3 0.2363 0.8209 0.056 0.000 0.920 0.024
#> GSM153247 3 0.5040 0.4528 0.364 0.000 0.628 0.008
#> GSM153248 1 0.0188 0.8675 0.996 0.000 0.000 0.004
#> GSM153249 4 0.3726 0.8432 0.212 0.000 0.000 0.788
#> GSM153250 1 0.1706 0.8500 0.948 0.000 0.016 0.036
#> GSM153251 3 0.5432 0.7920 0.068 0.000 0.716 0.216
#> GSM153252 4 0.6158 0.6275 0.384 0.000 0.056 0.560
#> GSM153253 4 0.2589 0.8074 0.116 0.000 0.000 0.884
#> GSM153254 3 0.6906 0.4180 0.408 0.000 0.484 0.108
#> GSM153255 4 0.4868 0.8156 0.256 0.000 0.024 0.720
#> GSM153256 1 0.2926 0.8115 0.896 0.000 0.048 0.056
#> GSM153257 4 0.6179 0.6095 0.392 0.000 0.056 0.552
#> GSM153258 1 0.0336 0.8673 0.992 0.000 0.000 0.008
#> GSM153259 1 0.0188 0.8675 0.996 0.000 0.000 0.004
#> GSM153260 3 0.2216 0.8149 0.092 0.000 0.908 0.000
#> GSM153261 3 0.1792 0.8209 0.068 0.000 0.932 0.000
#> GSM153262 4 0.4018 0.8411 0.224 0.000 0.004 0.772
#> GSM153263 1 0.1820 0.8479 0.944 0.000 0.020 0.036
#> GSM153264 1 0.0336 0.8674 0.992 0.000 0.000 0.008
#> GSM153265 4 0.2773 0.8066 0.116 0.000 0.004 0.880
#> GSM153266 1 0.2198 0.8461 0.920 0.000 0.072 0.008
#> GSM153267 1 0.2751 0.8169 0.904 0.000 0.056 0.040
#> GSM153268 4 0.6110 0.4503 0.100 0.000 0.240 0.660
#> GSM153269 1 0.2411 0.8314 0.920 0.000 0.040 0.040
#> GSM153270 1 0.3521 0.7823 0.864 0.000 0.052 0.084
#> GSM153271 1 0.2319 0.8338 0.924 0.000 0.040 0.036
#> GSM153272 4 0.5937 0.7049 0.340 0.000 0.052 0.608
#> GSM153273 1 0.0336 0.8673 0.992 0.000 0.000 0.008
#> GSM153274 1 0.2670 0.8206 0.908 0.000 0.052 0.040
#> GSM153275 1 0.5184 0.5380 0.732 0.000 0.056 0.212
#> GSM153276 1 0.4010 0.6980 0.816 0.000 0.028 0.156
#> GSM153277 4 0.3870 0.8432 0.208 0.000 0.004 0.788
#> GSM153278 3 0.3172 0.7727 0.160 0.000 0.840 0.000
#> GSM153279 4 0.3597 0.8121 0.148 0.000 0.016 0.836
#> GSM153280 4 0.2589 0.8074 0.116 0.000 0.000 0.884
#> GSM153281 4 0.3945 0.8428 0.216 0.000 0.004 0.780
#> GSM153282 4 0.2589 0.8074 0.116 0.000 0.000 0.884
#> GSM153283 1 0.0921 0.8607 0.972 0.000 0.000 0.028
#> GSM153284 4 0.6235 0.5488 0.420 0.000 0.056 0.524
#> GSM153285 4 0.2647 0.8106 0.120 0.000 0.000 0.880
#> GSM153286 4 0.6257 0.5083 0.436 0.000 0.056 0.508
#> GSM153287 4 0.3837 0.8414 0.224 0.000 0.000 0.776
#> GSM153288 1 0.6222 -0.2123 0.532 0.000 0.056 0.412
#> GSM153289 1 0.3533 0.7779 0.864 0.000 0.056 0.080
#> GSM153290 4 0.2589 0.8074 0.116 0.000 0.000 0.884
#> GSM153291 4 0.4228 0.8370 0.232 0.000 0.008 0.760
#> GSM153292 4 0.2814 0.8175 0.132 0.000 0.000 0.868
#> GSM153293 1 0.3732 0.7599 0.852 0.000 0.056 0.092
#> GSM153294 1 0.0524 0.8679 0.988 0.000 0.008 0.004
#> GSM153295 1 0.3219 0.8309 0.868 0.000 0.112 0.020
#> GSM153054 1 0.3356 0.7615 0.824 0.000 0.176 0.000
#> GSM153055 1 0.0817 0.8631 0.976 0.000 0.000 0.024
#> GSM153056 3 0.2345 0.8132 0.100 0.000 0.900 0.000
#> GSM153057 3 0.6077 0.2466 0.460 0.000 0.496 0.044
#> GSM153058 3 0.4898 0.8089 0.072 0.000 0.772 0.156
#> GSM153059 3 0.5143 0.7740 0.172 0.000 0.752 0.076
#> GSM153060 3 0.2926 0.8192 0.056 0.000 0.896 0.048
#> GSM153061 3 0.1902 0.8207 0.064 0.000 0.932 0.004
#> GSM153062 3 0.4415 0.8069 0.056 0.000 0.804 0.140
#> GSM153063 3 0.5219 0.7793 0.044 0.000 0.712 0.244
#> GSM153064 1 0.0592 0.8653 0.984 0.000 0.000 0.016
#> GSM153065 3 0.1792 0.8198 0.068 0.000 0.932 0.000
#> GSM153066 3 0.5088 0.7958 0.128 0.040 0.792 0.040
#> GSM153067 4 0.3873 0.8404 0.228 0.000 0.000 0.772
#> GSM153068 3 0.2179 0.8213 0.064 0.000 0.924 0.012
#> GSM153069 4 0.3837 0.8414 0.224 0.000 0.000 0.776
#> GSM153070 1 0.0707 0.8647 0.980 0.000 0.000 0.020
#> GSM153071 1 0.3219 0.7734 0.836 0.000 0.164 0.000
#> GSM153072 1 0.2704 0.8104 0.876 0.000 0.124 0.000
#> GSM153073 1 0.0469 0.8663 0.988 0.000 0.000 0.012
#> GSM153074 4 0.4122 0.8361 0.236 0.000 0.004 0.760
#> GSM153075 4 0.5288 0.4576 0.472 0.000 0.008 0.520
#> GSM153076 1 0.1929 0.8455 0.940 0.000 0.024 0.036
#> GSM153077 1 0.0376 0.8679 0.992 0.000 0.004 0.004
#> GSM153078 1 0.3837 0.7045 0.776 0.000 0.224 0.000
#> GSM153079 1 0.2216 0.8289 0.908 0.000 0.092 0.000
#> GSM153080 3 0.5375 0.7727 0.140 0.000 0.744 0.116
#> GSM153081 1 0.1174 0.8674 0.968 0.000 0.020 0.012
#> GSM153082 1 0.2589 0.8107 0.884 0.000 0.116 0.000
#> GSM153083 1 0.1474 0.8525 0.948 0.000 0.052 0.000
#> GSM153084 3 0.5372 0.2831 0.444 0.000 0.544 0.012
#> GSM153085 1 0.2704 0.8054 0.876 0.000 0.124 0.000
#> GSM153086 1 0.0336 0.8672 0.992 0.000 0.008 0.000
#> GSM153087 1 0.6168 -0.1131 0.556 0.000 0.056 0.388
#> GSM153088 1 0.1118 0.8565 0.964 0.000 0.000 0.036
#> GSM153089 3 0.4908 0.7498 0.016 0.000 0.692 0.292
#> GSM153090 1 0.1820 0.8481 0.944 0.000 0.020 0.036
#> GSM153091 1 0.2530 0.8139 0.888 0.000 0.112 0.000
#> GSM153092 1 0.0592 0.8657 0.984 0.000 0.000 0.016
#> GSM153093 4 0.5697 0.7756 0.280 0.000 0.056 0.664
#> GSM153094 1 0.2589 0.8107 0.884 0.000 0.116 0.000
#> GSM153095 1 0.2918 0.8125 0.876 0.000 0.116 0.008
#> GSM153096 1 0.0000 0.8676 1.000 0.000 0.000 0.000
#> GSM153097 1 0.0921 0.8613 0.972 0.000 0.028 0.000
#> GSM153098 1 0.0469 0.8679 0.988 0.000 0.000 0.012
#> GSM153099 1 0.2589 0.8254 0.912 0.000 0.044 0.044
#> GSM153100 1 0.0336 0.8679 0.992 0.000 0.000 0.008
#> GSM153101 1 0.3688 0.7189 0.792 0.000 0.208 0.000
#> GSM153102 1 0.2670 0.8301 0.908 0.000 0.052 0.040
#> GSM153103 1 0.3172 0.7762 0.840 0.000 0.160 0.000
#> GSM153104 4 0.3494 0.8371 0.172 0.000 0.004 0.824
#> GSM153106 1 0.0469 0.8666 0.988 0.000 0.000 0.012
#> GSM153107 1 0.0336 0.8673 0.992 0.000 0.000 0.008
#> GSM153108 1 0.3257 0.7409 0.844 0.000 0.004 0.152
#> GSM153109 1 0.2647 0.8078 0.880 0.000 0.120 0.000
#> GSM153110 1 0.0188 0.8673 0.996 0.000 0.004 0.000
#> GSM153111 1 0.0921 0.8615 0.972 0.000 0.028 0.000
#> GSM153112 1 0.0188 0.8676 0.996 0.000 0.004 0.000
#> GSM153113 1 0.2868 0.7996 0.864 0.000 0.136 0.000
#> GSM153114 4 0.4857 0.7950 0.284 0.000 0.016 0.700
#> GSM187532 2 0.2408 0.8512 0.000 0.896 0.104 0.000
#> GSM187533 2 0.0000 0.9730 0.000 1.000 0.000 0.000
#> GSM187534 2 0.0000 0.9730 0.000 1.000 0.000 0.000
#> GSM187535 2 0.7044 -0.0330 0.428 0.452 0.120 0.000
#> GSM152906 2 0.0000 0.9730 0.000 1.000 0.000 0.000
#> GSM152907 2 0.0000 0.9730 0.000 1.000 0.000 0.000
#> GSM152908 2 0.0000 0.9730 0.000 1.000 0.000 0.000
#> GSM152909 2 0.0000 0.9730 0.000 1.000 0.000 0.000
#> GSM152910 2 0.0000 0.9730 0.000 1.000 0.000 0.000
#> GSM152911 2 0.0000 0.9730 0.000 1.000 0.000 0.000
#> GSM152912 2 0.0000 0.9730 0.000 1.000 0.000 0.000
#> GSM152913 2 0.0000 0.9730 0.000 1.000 0.000 0.000
#> GSM152914 2 0.0000 0.9730 0.000 1.000 0.000 0.000
#> GSM152915 2 0.0000 0.9730 0.000 1.000 0.000 0.000
#> GSM152916 2 0.0000 0.9730 0.000 1.000 0.000 0.000
#> GSM152917 2 0.0000 0.9730 0.000 1.000 0.000 0.000
#> GSM152918 2 0.0000 0.9730 0.000 1.000 0.000 0.000
#> GSM152919 2 0.0000 0.9730 0.000 1.000 0.000 0.000
#> GSM152920 2 0.0000 0.9730 0.000 1.000 0.000 0.000
#> GSM152921 2 0.0000 0.9730 0.000 1.000 0.000 0.000
#> GSM152922 2 0.0000 0.9730 0.000 1.000 0.000 0.000
#> GSM152923 2 0.0000 0.9730 0.000 1.000 0.000 0.000
#> GSM152924 2 0.0000 0.9730 0.000 1.000 0.000 0.000
#> GSM152925 2 0.0000 0.9730 0.000 1.000 0.000 0.000
#> GSM152926 2 0.0000 0.9730 0.000 1.000 0.000 0.000
#> GSM152927 2 0.0000 0.9730 0.000 1.000 0.000 0.000
#> GSM152928 2 0.0188 0.9681 0.004 0.996 0.000 0.000
#> GSM152929 2 0.0000 0.9730 0.000 1.000 0.000 0.000
#> GSM152930 2 0.0000 0.9730 0.000 1.000 0.000 0.000
cbind(get_classes(res, k = 5), get_membership(res, k = 5))
#> class entropy silhouette p1 p2 p3 p4 p5
#> GSM152839 1 0.3772 0.7294 0.792 0.000 0.036 0.000 0.172
#> GSM152840 5 0.0000 0.8296 0.000 0.000 0.000 0.000 1.000
#> GSM152841 4 0.3266 0.7666 0.000 0.000 0.200 0.796 0.004
#> GSM152842 3 0.3684 0.8310 0.000 0.000 0.720 0.000 0.280
#> GSM152843 3 0.5598 0.6954 0.112 0.000 0.612 0.000 0.276
#> GSM152844 5 0.0000 0.8296 0.000 0.000 0.000 0.000 1.000
#> GSM152845 5 0.2179 0.7481 0.000 0.000 0.112 0.000 0.888
#> GSM152846 5 0.0000 0.8296 0.000 0.000 0.000 0.000 1.000
#> GSM152847 3 0.3661 0.8333 0.000 0.000 0.724 0.000 0.276
#> GSM152848 1 0.0671 0.8893 0.980 0.000 0.016 0.004 0.000
#> GSM152849 3 0.4229 0.8283 0.020 0.000 0.704 0.000 0.276
#> GSM152850 3 0.6405 0.4495 0.252 0.000 0.512 0.000 0.236
#> GSM152851 4 0.3929 0.5985 0.000 0.000 0.028 0.764 0.208
#> GSM152852 5 0.0000 0.8296 0.000 0.000 0.000 0.000 1.000
#> GSM152853 5 0.0000 0.8296 0.000 0.000 0.000 0.000 1.000
#> GSM152854 5 0.2605 0.6988 0.000 0.000 0.148 0.000 0.852
#> GSM152855 1 0.5450 0.2176 0.496 0.000 0.060 0.444 0.000
#> GSM153238 3 0.4276 0.8224 0.028 0.000 0.716 0.000 0.256
#> GSM153239 5 0.1270 0.7809 0.000 0.000 0.000 0.052 0.948
#> GSM153240 4 0.1012 0.7709 0.012 0.000 0.020 0.968 0.000
#> GSM153241 3 0.4691 0.8067 0.044 0.000 0.680 0.000 0.276
#> GSM153242 5 0.0000 0.8296 0.000 0.000 0.000 0.000 1.000
#> GSM153243 3 0.3790 0.8341 0.004 0.000 0.724 0.000 0.272
#> GSM153244 4 0.3769 0.6360 0.000 0.000 0.032 0.788 0.180
#> GSM153245 5 0.0000 0.8296 0.000 0.000 0.000 0.000 1.000
#> GSM153246 3 0.3876 0.7971 0.000 0.000 0.684 0.000 0.316
#> GSM153247 1 0.6049 0.3075 0.576 0.000 0.192 0.000 0.232
#> GSM153248 1 0.0162 0.8884 0.996 0.000 0.004 0.000 0.000
#> GSM153249 4 0.2605 0.7808 0.000 0.000 0.148 0.852 0.000
#> GSM153250 1 0.1469 0.8804 0.948 0.000 0.036 0.016 0.000
#> GSM153251 5 0.1410 0.8001 0.000 0.000 0.060 0.000 0.940
#> GSM153252 4 0.4985 0.5457 0.244 0.000 0.076 0.680 0.000
#> GSM153253 4 0.3266 0.7666 0.000 0.000 0.200 0.796 0.004
#> GSM153254 1 0.5361 0.5733 0.664 0.000 0.016 0.064 0.256
#> GSM153255 4 0.1408 0.7628 0.008 0.000 0.044 0.948 0.000
#> GSM153256 1 0.4649 0.7152 0.720 0.000 0.068 0.212 0.000
#> GSM153257 4 0.4879 0.5710 0.228 0.000 0.076 0.696 0.000
#> GSM153258 1 0.0510 0.8894 0.984 0.000 0.000 0.016 0.000
#> GSM153259 1 0.0671 0.8895 0.980 0.000 0.004 0.016 0.000
#> GSM153260 3 0.3790 0.8341 0.004 0.000 0.724 0.000 0.272
#> GSM153261 3 0.3661 0.8333 0.000 0.000 0.724 0.000 0.276
#> GSM153262 4 0.0510 0.7790 0.000 0.000 0.016 0.984 0.000
#> GSM153263 1 0.1403 0.8829 0.952 0.000 0.024 0.024 0.000
#> GSM153264 1 0.0324 0.8893 0.992 0.000 0.004 0.004 0.000
#> GSM153265 4 0.3074 0.7701 0.000 0.000 0.196 0.804 0.000
#> GSM153266 1 0.0671 0.8896 0.980 0.000 0.016 0.004 0.000
#> GSM153267 1 0.4421 0.7456 0.748 0.000 0.068 0.184 0.000
#> GSM153268 4 0.3829 0.7560 0.000 0.000 0.196 0.776 0.028
#> GSM153269 1 0.4649 0.7152 0.720 0.000 0.068 0.212 0.000
#> GSM153270 1 0.3875 0.7834 0.792 0.000 0.048 0.160 0.000
#> GSM153271 1 0.1907 0.8728 0.928 0.000 0.044 0.028 0.000
#> GSM153272 4 0.4113 0.6587 0.140 0.000 0.076 0.784 0.000
#> GSM153273 1 0.0290 0.8903 0.992 0.000 0.000 0.008 0.000
#> GSM153274 1 0.3970 0.7812 0.788 0.000 0.056 0.156 0.000
#> GSM153275 1 0.4930 0.6676 0.684 0.000 0.072 0.244 0.000
#> GSM153276 1 0.4104 0.7385 0.748 0.000 0.032 0.220 0.000
#> GSM153277 4 0.1197 0.7829 0.000 0.000 0.048 0.952 0.000
#> GSM153278 3 0.5577 0.6964 0.120 0.000 0.624 0.000 0.256
#> GSM153279 4 0.4618 0.7403 0.032 0.000 0.116 0.780 0.072
#> GSM153280 4 0.3109 0.7687 0.000 0.000 0.200 0.800 0.000
#> GSM153281 4 0.2424 0.7826 0.000 0.000 0.132 0.868 0.000
#> GSM153282 4 0.3109 0.7687 0.000 0.000 0.200 0.800 0.000
#> GSM153283 1 0.0162 0.8884 0.996 0.000 0.004 0.000 0.000
#> GSM153284 4 0.5192 0.4701 0.280 0.000 0.076 0.644 0.000
#> GSM153285 4 0.3231 0.7685 0.000 0.000 0.196 0.800 0.004
#> GSM153286 4 0.5290 0.4241 0.300 0.000 0.076 0.624 0.000
#> GSM153287 4 0.2773 0.7778 0.000 0.000 0.164 0.836 0.000
#> GSM153288 4 0.5648 -0.0900 0.448 0.000 0.076 0.476 0.000
#> GSM153289 1 0.4795 0.6957 0.704 0.000 0.072 0.224 0.000
#> GSM153290 4 0.3109 0.7687 0.000 0.000 0.200 0.800 0.000
#> GSM153291 4 0.0794 0.7701 0.000 0.000 0.028 0.972 0.000
#> GSM153292 4 0.3109 0.7687 0.000 0.000 0.200 0.800 0.000
#> GSM153293 1 0.5028 0.6455 0.668 0.000 0.072 0.260 0.000
#> GSM153294 1 0.0290 0.8893 0.992 0.000 0.008 0.000 0.000
#> GSM153295 1 0.4094 0.7318 0.780 0.000 0.020 0.020 0.180
#> GSM153054 1 0.0798 0.8895 0.976 0.000 0.016 0.008 0.000
#> GSM153055 1 0.2361 0.8530 0.892 0.000 0.012 0.096 0.000
#> GSM153056 3 0.6712 0.3324 0.300 0.000 0.424 0.000 0.276
#> GSM153057 1 0.4315 0.6510 0.728 0.000 0.012 0.016 0.244
#> GSM153058 5 0.4768 -0.0280 0.024 0.000 0.384 0.000 0.592
#> GSM153059 1 0.6920 -0.2305 0.424 0.000 0.316 0.008 0.252
#> GSM153060 3 0.4283 0.5370 0.000 0.000 0.544 0.000 0.456
#> GSM153061 3 0.3684 0.8310 0.000 0.000 0.720 0.000 0.280
#> GSM153062 5 0.3857 0.3285 0.000 0.000 0.312 0.000 0.688
#> GSM153063 5 0.1121 0.8095 0.000 0.000 0.044 0.000 0.956
#> GSM153064 1 0.0671 0.8892 0.980 0.000 0.004 0.016 0.000
#> GSM153065 3 0.3684 0.8310 0.000 0.000 0.720 0.000 0.280
#> GSM153066 3 0.5246 0.7896 0.024 0.040 0.664 0.000 0.272
#> GSM153067 4 0.0609 0.7719 0.000 0.000 0.020 0.980 0.000
#> GSM153068 3 0.3684 0.8310 0.000 0.000 0.720 0.000 0.280
#> GSM153069 4 0.2773 0.7778 0.000 0.000 0.164 0.836 0.000
#> GSM153070 1 0.0510 0.8894 0.984 0.000 0.000 0.016 0.000
#> GSM153071 1 0.0671 0.8895 0.980 0.000 0.004 0.016 0.000
#> GSM153072 1 0.0912 0.8898 0.972 0.000 0.012 0.016 0.000
#> GSM153073 1 0.0510 0.8894 0.984 0.000 0.000 0.016 0.000
#> GSM153074 4 0.1331 0.7651 0.008 0.000 0.040 0.952 0.000
#> GSM153075 4 0.4835 0.2368 0.380 0.000 0.028 0.592 0.000
#> GSM153076 1 0.1469 0.8804 0.948 0.000 0.036 0.016 0.000
#> GSM153077 1 0.0451 0.8899 0.988 0.000 0.004 0.008 0.000
#> GSM153078 1 0.2338 0.8213 0.884 0.000 0.112 0.004 0.000
#> GSM153079 1 0.0579 0.8901 0.984 0.000 0.008 0.008 0.000
#> GSM153080 5 0.6987 -0.0271 0.344 0.000 0.140 0.040 0.476
#> GSM153081 1 0.0162 0.8884 0.996 0.000 0.004 0.000 0.000
#> GSM153082 1 0.0162 0.8884 0.996 0.000 0.004 0.000 0.000
#> GSM153083 1 0.0162 0.8884 0.996 0.000 0.004 0.000 0.000
#> GSM153084 1 0.3628 0.6913 0.772 0.000 0.012 0.000 0.216
#> GSM153085 1 0.0693 0.8900 0.980 0.000 0.008 0.012 0.000
#> GSM153086 1 0.0451 0.8892 0.988 0.000 0.008 0.004 0.000
#> GSM153087 1 0.5488 0.2653 0.508 0.000 0.064 0.428 0.000
#> GSM153088 1 0.0566 0.8898 0.984 0.000 0.012 0.004 0.000
#> GSM153089 5 0.0162 0.8284 0.000 0.000 0.004 0.000 0.996
#> GSM153090 1 0.1568 0.8789 0.944 0.000 0.036 0.020 0.000
#> GSM153091 1 0.0162 0.8884 0.996 0.000 0.004 0.000 0.000
#> GSM153092 1 0.0912 0.8879 0.972 0.000 0.012 0.016 0.000
#> GSM153093 4 0.2989 0.7237 0.060 0.000 0.072 0.868 0.000
#> GSM153094 1 0.0162 0.8884 0.996 0.000 0.004 0.000 0.000
#> GSM153095 1 0.0671 0.8895 0.980 0.000 0.004 0.016 0.000
#> GSM153096 1 0.0404 0.8901 0.988 0.000 0.000 0.012 0.000
#> GSM153097 1 0.0162 0.8884 0.996 0.000 0.004 0.000 0.000
#> GSM153098 1 0.2462 0.8378 0.880 0.000 0.008 0.112 0.000
#> GSM153099 1 0.3291 0.8215 0.840 0.000 0.040 0.120 0.000
#> GSM153100 1 0.0671 0.8897 0.980 0.000 0.004 0.016 0.000
#> GSM153101 1 0.0992 0.8871 0.968 0.000 0.024 0.008 0.000
#> GSM153102 1 0.1179 0.8878 0.964 0.000 0.004 0.016 0.016
#> GSM153103 1 0.0898 0.8885 0.972 0.000 0.020 0.008 0.000
#> GSM153104 4 0.0880 0.7813 0.000 0.000 0.032 0.968 0.000
#> GSM153106 1 0.1444 0.8775 0.948 0.000 0.012 0.040 0.000
#> GSM153107 1 0.0510 0.8894 0.984 0.000 0.000 0.016 0.000
#> GSM153108 1 0.3970 0.7462 0.752 0.000 0.024 0.224 0.000
#> GSM153109 1 0.0162 0.8884 0.996 0.000 0.004 0.000 0.000
#> GSM153110 1 0.0451 0.8899 0.988 0.000 0.004 0.008 0.000
#> GSM153111 1 0.0162 0.8884 0.996 0.000 0.004 0.000 0.000
#> GSM153112 1 0.0162 0.8893 0.996 0.000 0.004 0.000 0.000
#> GSM153113 1 0.0566 0.8871 0.984 0.000 0.004 0.000 0.012
#> GSM153114 4 0.2149 0.7503 0.036 0.000 0.048 0.916 0.000
#> GSM187532 2 0.0794 0.9632 0.000 0.972 0.000 0.000 0.028
#> GSM187533 2 0.0000 0.9971 0.000 1.000 0.000 0.000 0.000
#> GSM187534 2 0.0162 0.9942 0.004 0.996 0.000 0.000 0.000
#> GSM187535 1 0.3989 0.6634 0.728 0.260 0.004 0.000 0.008
#> GSM152906 2 0.0000 0.9971 0.000 1.000 0.000 0.000 0.000
#> GSM152907 2 0.0510 0.9837 0.016 0.984 0.000 0.000 0.000
#> GSM152908 2 0.0000 0.9971 0.000 1.000 0.000 0.000 0.000
#> GSM152909 2 0.0000 0.9971 0.000 1.000 0.000 0.000 0.000
#> GSM152910 2 0.0000 0.9971 0.000 1.000 0.000 0.000 0.000
#> GSM152911 2 0.0000 0.9971 0.000 1.000 0.000 0.000 0.000
#> GSM152912 2 0.0000 0.9971 0.000 1.000 0.000 0.000 0.000
#> GSM152913 2 0.0000 0.9971 0.000 1.000 0.000 0.000 0.000
#> GSM152914 2 0.0000 0.9971 0.000 1.000 0.000 0.000 0.000
#> GSM152915 2 0.0000 0.9971 0.000 1.000 0.000 0.000 0.000
#> GSM152916 2 0.0000 0.9971 0.000 1.000 0.000 0.000 0.000
#> GSM152917 2 0.0000 0.9971 0.000 1.000 0.000 0.000 0.000
#> GSM152918 2 0.0000 0.9971 0.000 1.000 0.000 0.000 0.000
#> GSM152919 2 0.0000 0.9971 0.000 1.000 0.000 0.000 0.000
#> GSM152920 2 0.0000 0.9971 0.000 1.000 0.000 0.000 0.000
#> GSM152921 2 0.0000 0.9971 0.000 1.000 0.000 0.000 0.000
#> GSM152922 2 0.0000 0.9971 0.000 1.000 0.000 0.000 0.000
#> GSM152923 2 0.0000 0.9971 0.000 1.000 0.000 0.000 0.000
#> GSM152924 2 0.0000 0.9971 0.000 1.000 0.000 0.000 0.000
#> GSM152925 2 0.0000 0.9971 0.000 1.000 0.000 0.000 0.000
#> GSM152926 2 0.0510 0.9837 0.016 0.984 0.000 0.000 0.000
#> GSM152927 2 0.0000 0.9971 0.000 1.000 0.000 0.000 0.000
#> GSM152928 2 0.0162 0.9942 0.004 0.996 0.000 0.000 0.000
#> GSM152929 2 0.0000 0.9971 0.000 1.000 0.000 0.000 0.000
#> GSM152930 2 0.0000 0.9971 0.000 1.000 0.000 0.000 0.000
cbind(get_classes(res, k = 6), get_membership(res, k = 6))
#> class entropy silhouette p1 p2 p3 p4 p5 p6
#> GSM152839 1 0.5310 0.61647 0.616 0.000 0.184 0.196 0.000 0.004
#> GSM152840 6 0.0260 0.83956 0.000 0.000 0.008 0.000 0.000 0.992
#> GSM152841 5 0.0000 0.85875 0.000 0.000 0.000 0.000 1.000 0.000
#> GSM152842 3 0.0405 0.73375 0.004 0.000 0.988 0.000 0.000 0.008
#> GSM152843 3 0.4207 0.60910 0.176 0.000 0.744 0.072 0.000 0.008
#> GSM152844 6 0.0260 0.83956 0.000 0.000 0.008 0.000 0.000 0.992
#> GSM152845 3 0.3810 0.13638 0.000 0.000 0.572 0.000 0.000 0.428
#> GSM152846 6 0.0363 0.84002 0.000 0.000 0.012 0.000 0.000 0.988
#> GSM152847 3 0.0146 0.73237 0.004 0.000 0.996 0.000 0.000 0.000
#> GSM152848 1 0.2854 0.75073 0.792 0.000 0.000 0.208 0.000 0.000
#> GSM152849 3 0.1970 0.71814 0.092 0.000 0.900 0.000 0.000 0.008
#> GSM152850 3 0.3997 0.60924 0.216 0.000 0.736 0.044 0.000 0.004
#> GSM152851 5 0.4378 0.60673 0.000 0.000 0.040 0.016 0.704 0.240
#> GSM152852 6 0.0260 0.83956 0.000 0.000 0.008 0.000 0.000 0.992
#> GSM152853 6 0.0260 0.83956 0.000 0.000 0.008 0.000 0.000 0.992
#> GSM152854 3 0.3857 -0.00839 0.000 0.000 0.532 0.000 0.000 0.468
#> GSM152855 4 0.1088 0.75571 0.016 0.000 0.000 0.960 0.024 0.000
#> GSM153238 3 0.1471 0.73160 0.064 0.000 0.932 0.000 0.000 0.004
#> GSM153239 6 0.2744 0.79216 0.000 0.000 0.072 0.000 0.064 0.864
#> GSM153240 4 0.3937 0.11807 0.004 0.000 0.000 0.572 0.424 0.000
#> GSM153241 3 0.2619 0.71471 0.072 0.000 0.880 0.040 0.000 0.008
#> GSM153242 6 0.0632 0.83868 0.000 0.000 0.024 0.000 0.000 0.976
#> GSM153243 3 0.1010 0.73546 0.036 0.000 0.960 0.000 0.000 0.004
#> GSM153244 5 0.4427 0.71119 0.008 0.000 0.020 0.060 0.752 0.160
#> GSM153245 6 0.1556 0.81188 0.000 0.000 0.080 0.000 0.000 0.920
#> GSM153246 3 0.1349 0.71384 0.000 0.000 0.940 0.004 0.000 0.056
#> GSM153247 1 0.5540 0.09506 0.504 0.000 0.392 0.092 0.004 0.008
#> GSM153248 1 0.2300 0.76615 0.856 0.000 0.000 0.144 0.000 0.000
#> GSM153249 5 0.1327 0.85510 0.000 0.000 0.000 0.064 0.936 0.000
#> GSM153250 1 0.3847 0.48312 0.544 0.000 0.000 0.456 0.000 0.000
#> GSM153251 6 0.3810 0.25941 0.000 0.000 0.428 0.000 0.000 0.572
#> GSM153252 4 0.1367 0.74049 0.012 0.000 0.000 0.944 0.044 0.000
#> GSM153253 5 0.0000 0.85875 0.000 0.000 0.000 0.000 1.000 0.000
#> GSM153254 3 0.8022 0.17307 0.300 0.000 0.320 0.180 0.028 0.172
#> GSM153255 4 0.3742 0.31243 0.004 0.000 0.000 0.648 0.348 0.000
#> GSM153256 4 0.1327 0.73931 0.064 0.000 0.000 0.936 0.000 0.000
#> GSM153257 4 0.0717 0.75177 0.008 0.000 0.000 0.976 0.016 0.000
#> GSM153258 1 0.3266 0.71962 0.728 0.000 0.000 0.272 0.000 0.000
#> GSM153259 1 0.2562 0.76111 0.828 0.000 0.000 0.172 0.000 0.000
#> GSM153260 3 0.0405 0.73375 0.004 0.000 0.988 0.000 0.000 0.008
#> GSM153261 3 0.0291 0.73324 0.004 0.000 0.992 0.000 0.000 0.004
#> GSM153262 5 0.3899 0.40504 0.004 0.000 0.000 0.404 0.592 0.000
#> GSM153263 1 0.3823 0.51977 0.564 0.000 0.000 0.436 0.000 0.000
#> GSM153264 1 0.1910 0.76603 0.892 0.000 0.000 0.108 0.000 0.000
#> GSM153265 5 0.0363 0.86086 0.000 0.000 0.000 0.012 0.988 0.000
#> GSM153266 1 0.2854 0.75003 0.792 0.000 0.000 0.208 0.000 0.000
#> GSM153267 4 0.2762 0.57089 0.196 0.000 0.000 0.804 0.000 0.000
#> GSM153268 5 0.0632 0.84727 0.000 0.000 0.000 0.000 0.976 0.024
#> GSM153269 4 0.1387 0.73961 0.068 0.000 0.000 0.932 0.000 0.000
#> GSM153270 4 0.3499 0.29372 0.320 0.000 0.000 0.680 0.000 0.000
#> GSM153271 1 0.3869 0.37330 0.500 0.000 0.000 0.500 0.000 0.000
#> GSM153272 4 0.1333 0.72999 0.008 0.000 0.000 0.944 0.048 0.000
#> GSM153273 1 0.3198 0.72796 0.740 0.000 0.000 0.260 0.000 0.000
#> GSM153274 4 0.3446 0.31043 0.308 0.000 0.000 0.692 0.000 0.000
#> GSM153275 4 0.0458 0.75526 0.016 0.000 0.000 0.984 0.000 0.000
#> GSM153276 4 0.2340 0.66258 0.148 0.000 0.000 0.852 0.000 0.000
#> GSM153277 5 0.3565 0.62136 0.004 0.000 0.000 0.304 0.692 0.000
#> GSM153278 3 0.3539 0.63796 0.208 0.000 0.768 0.016 0.000 0.008
#> GSM153279 5 0.5342 0.63328 0.016 0.000 0.012 0.216 0.656 0.100
#> GSM153280 5 0.0000 0.85875 0.000 0.000 0.000 0.000 1.000 0.000
#> GSM153281 5 0.2730 0.76861 0.000 0.000 0.000 0.192 0.808 0.000
#> GSM153282 5 0.0000 0.85875 0.000 0.000 0.000 0.000 1.000 0.000
#> GSM153283 1 0.3221 0.72122 0.736 0.000 0.000 0.264 0.000 0.000
#> GSM153284 4 0.0508 0.75192 0.004 0.000 0.000 0.984 0.012 0.000
#> GSM153285 5 0.0458 0.86088 0.000 0.000 0.000 0.016 0.984 0.000
#> GSM153286 4 0.0717 0.75101 0.008 0.000 0.000 0.976 0.016 0.000
#> GSM153287 5 0.1267 0.85627 0.000 0.000 0.000 0.060 0.940 0.000
#> GSM153288 4 0.0405 0.75372 0.008 0.000 0.000 0.988 0.004 0.000
#> GSM153289 4 0.1204 0.74702 0.056 0.000 0.000 0.944 0.000 0.000
#> GSM153290 5 0.0000 0.85875 0.000 0.000 0.000 0.000 1.000 0.000
#> GSM153291 4 0.3966 -0.00398 0.004 0.000 0.000 0.552 0.444 0.000
#> GSM153292 5 0.0000 0.85875 0.000 0.000 0.000 0.000 1.000 0.000
#> GSM153293 4 0.0632 0.75603 0.024 0.000 0.000 0.976 0.000 0.000
#> GSM153294 1 0.3756 0.58059 0.600 0.000 0.000 0.400 0.000 0.000
#> GSM153295 1 0.4367 0.60757 0.604 0.000 0.032 0.364 0.000 0.000
#> GSM153054 1 0.2070 0.76633 0.896 0.000 0.012 0.092 0.000 0.000
#> GSM153055 1 0.3866 0.38592 0.516 0.000 0.000 0.484 0.000 0.000
#> GSM153056 3 0.4700 0.57066 0.180 0.000 0.700 0.112 0.000 0.008
#> GSM153057 1 0.5660 0.39857 0.572 0.000 0.288 0.124 0.008 0.008
#> GSM153058 3 0.3245 0.56666 0.008 0.000 0.764 0.000 0.000 0.228
#> GSM153059 3 0.4691 0.47489 0.388 0.000 0.576 0.008 0.008 0.020
#> GSM153060 3 0.2100 0.67812 0.000 0.000 0.884 0.004 0.000 0.112
#> GSM153061 3 0.0508 0.73098 0.000 0.000 0.984 0.004 0.000 0.012
#> GSM153062 3 0.2902 0.59436 0.000 0.000 0.800 0.004 0.000 0.196
#> GSM153063 6 0.3684 0.39565 0.000 0.000 0.372 0.000 0.000 0.628
#> GSM153064 1 0.3747 0.59023 0.604 0.000 0.000 0.396 0.000 0.000
#> GSM153065 3 0.0508 0.73344 0.004 0.000 0.984 0.000 0.000 0.012
#> GSM153066 3 0.4292 0.59312 0.244 0.020 0.712 0.000 0.008 0.016
#> GSM153067 4 0.3747 0.20161 0.000 0.000 0.000 0.604 0.396 0.000
#> GSM153068 3 0.0363 0.73141 0.000 0.000 0.988 0.000 0.000 0.012
#> GSM153069 5 0.1267 0.85627 0.000 0.000 0.000 0.060 0.940 0.000
#> GSM153070 1 0.3563 0.66494 0.664 0.000 0.000 0.336 0.000 0.000
#> GSM153071 1 0.2706 0.76249 0.832 0.000 0.008 0.160 0.000 0.000
#> GSM153072 1 0.1010 0.75356 0.960 0.000 0.004 0.036 0.000 0.000
#> GSM153073 1 0.3076 0.73777 0.760 0.000 0.000 0.240 0.000 0.000
#> GSM153074 4 0.3052 0.56655 0.004 0.000 0.000 0.780 0.216 0.000
#> GSM153075 4 0.3841 0.66398 0.068 0.000 0.000 0.764 0.168 0.000
#> GSM153076 1 0.3847 0.48234 0.544 0.000 0.000 0.456 0.000 0.000
#> GSM153077 1 0.1444 0.76219 0.928 0.000 0.000 0.072 0.000 0.000
#> GSM153078 1 0.3655 0.73231 0.792 0.000 0.112 0.096 0.000 0.000
#> GSM153079 1 0.0458 0.74361 0.984 0.000 0.000 0.016 0.000 0.000
#> GSM153080 3 0.6396 0.48085 0.124 0.000 0.584 0.112 0.004 0.176
#> GSM153081 1 0.2260 0.76547 0.860 0.000 0.000 0.140 0.000 0.000
#> GSM153082 1 0.0363 0.74487 0.988 0.000 0.000 0.012 0.000 0.000
#> GSM153083 1 0.0458 0.74361 0.984 0.000 0.000 0.016 0.000 0.000
#> GSM153084 1 0.3741 0.37752 0.740 0.004 0.240 0.004 0.008 0.004
#> GSM153085 1 0.0363 0.74521 0.988 0.000 0.000 0.012 0.000 0.000
#> GSM153086 1 0.0458 0.74361 0.984 0.000 0.000 0.016 0.000 0.000
#> GSM153087 4 0.1088 0.75791 0.024 0.000 0.000 0.960 0.016 0.000
#> GSM153088 1 0.3684 0.62089 0.628 0.000 0.000 0.372 0.000 0.000
#> GSM153089 6 0.3266 0.59066 0.000 0.000 0.272 0.000 0.000 0.728
#> GSM153090 1 0.3857 0.45733 0.532 0.000 0.000 0.468 0.000 0.000
#> GSM153091 1 0.0790 0.75216 0.968 0.000 0.000 0.032 0.000 0.000
#> GSM153092 1 0.3351 0.70517 0.712 0.000 0.000 0.288 0.000 0.000
#> GSM153093 4 0.1918 0.70655 0.008 0.000 0.000 0.904 0.088 0.000
#> GSM153094 1 0.0363 0.74539 0.988 0.000 0.000 0.012 0.000 0.000
#> GSM153095 1 0.0713 0.75297 0.972 0.000 0.000 0.028 0.000 0.000
#> GSM153096 1 0.2793 0.75422 0.800 0.000 0.000 0.200 0.000 0.000
#> GSM153097 1 0.0547 0.74550 0.980 0.000 0.000 0.020 0.000 0.000
#> GSM153098 4 0.3823 -0.12452 0.436 0.000 0.000 0.564 0.000 0.000
#> GSM153099 4 0.3828 -0.21302 0.440 0.000 0.000 0.560 0.000 0.000
#> GSM153100 1 0.3717 0.60592 0.616 0.000 0.000 0.384 0.000 0.000
#> GSM153101 1 0.1219 0.75895 0.948 0.000 0.004 0.048 0.000 0.000
#> GSM153102 1 0.1116 0.75364 0.960 0.000 0.004 0.028 0.008 0.000
#> GSM153103 1 0.0603 0.74377 0.980 0.000 0.004 0.016 0.000 0.000
#> GSM153104 5 0.3076 0.71837 0.000 0.000 0.000 0.240 0.760 0.000
#> GSM153106 1 0.3866 0.39472 0.516 0.000 0.000 0.484 0.000 0.000
#> GSM153107 1 0.3515 0.67606 0.676 0.000 0.000 0.324 0.000 0.000
#> GSM153108 4 0.4310 0.10209 0.396 0.000 0.000 0.580 0.024 0.000
#> GSM153109 1 0.0000 0.73803 1.000 0.000 0.000 0.000 0.000 0.000
#> GSM153110 1 0.1814 0.76631 0.900 0.000 0.000 0.100 0.000 0.000
#> GSM153111 1 0.0458 0.74361 0.984 0.000 0.000 0.016 0.000 0.000
#> GSM153112 1 0.3695 0.61520 0.624 0.000 0.000 0.376 0.000 0.000
#> GSM153113 1 0.0363 0.74024 0.988 0.000 0.000 0.012 0.000 0.000
#> GSM153114 4 0.2996 0.54084 0.000 0.000 0.000 0.772 0.228 0.000
#> GSM187532 2 0.0520 0.96332 0.000 0.984 0.008 0.000 0.000 0.008
#> GSM187533 2 0.0000 0.97986 0.000 1.000 0.000 0.000 0.000 0.000
#> GSM187534 2 0.0000 0.97986 0.000 1.000 0.000 0.000 0.000 0.000
#> GSM187535 2 0.3937 0.36307 0.424 0.572 0.000 0.004 0.000 0.000
#> GSM152906 2 0.0000 0.97986 0.000 1.000 0.000 0.000 0.000 0.000
#> GSM152907 2 0.0508 0.96786 0.012 0.984 0.000 0.004 0.000 0.000
#> GSM152908 2 0.0000 0.97986 0.000 1.000 0.000 0.000 0.000 0.000
#> GSM152909 2 0.0000 0.97986 0.000 1.000 0.000 0.000 0.000 0.000
#> GSM152910 2 0.0000 0.97986 0.000 1.000 0.000 0.000 0.000 0.000
#> GSM152911 2 0.0000 0.97986 0.000 1.000 0.000 0.000 0.000 0.000
#> GSM152912 2 0.0000 0.97986 0.000 1.000 0.000 0.000 0.000 0.000
#> GSM152913 2 0.0000 0.97986 0.000 1.000 0.000 0.000 0.000 0.000
#> GSM152914 2 0.0000 0.97986 0.000 1.000 0.000 0.000 0.000 0.000
#> GSM152915 2 0.0000 0.97986 0.000 1.000 0.000 0.000 0.000 0.000
#> GSM152916 2 0.0000 0.97986 0.000 1.000 0.000 0.000 0.000 0.000
#> GSM152917 2 0.0000 0.97986 0.000 1.000 0.000 0.000 0.000 0.000
#> GSM152918 2 0.0000 0.97986 0.000 1.000 0.000 0.000 0.000 0.000
#> GSM152919 2 0.0000 0.97986 0.000 1.000 0.000 0.000 0.000 0.000
#> GSM152920 2 0.0000 0.97986 0.000 1.000 0.000 0.000 0.000 0.000
#> GSM152921 2 0.0000 0.97986 0.000 1.000 0.000 0.000 0.000 0.000
#> GSM152922 2 0.0000 0.97986 0.000 1.000 0.000 0.000 0.000 0.000
#> GSM152923 2 0.0000 0.97986 0.000 1.000 0.000 0.000 0.000 0.000
#> GSM152924 2 0.0000 0.97986 0.000 1.000 0.000 0.000 0.000 0.000
#> GSM152925 2 0.0000 0.97986 0.000 1.000 0.000 0.000 0.000 0.000
#> GSM152926 2 0.0508 0.96786 0.012 0.984 0.000 0.004 0.000 0.000
#> GSM152927 2 0.0000 0.97986 0.000 1.000 0.000 0.000 0.000 0.000
#> GSM152928 2 0.0146 0.97611 0.004 0.996 0.000 0.000 0.000 0.000
#> GSM152929 2 0.0000 0.97986 0.000 1.000 0.000 0.000 0.000 0.000
#> GSM152930 2 0.0000 0.97986 0.000 1.000 0.000 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 tissue(p) k
#> SD:mclust 162 2.52e-28 2
#> SD:mclust 101 3.32e-24 3
#> SD:mclust 153 4.45e-34 4
#> SD:mclust 151 1.71e-33 5
#> SD:mclust 137 2.03e-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["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 12013 rows and 164 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 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 0.858 0.923 0.965 0.4385 0.569 0.569
#> 3 3 0.594 0.781 0.881 0.4403 0.749 0.575
#> 4 4 0.590 0.660 0.819 0.1768 0.805 0.516
#> 5 5 0.552 0.507 0.726 0.0577 0.935 0.767
#> 6 6 0.550 0.447 0.647 0.0403 0.921 0.694
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
#> GSM152839 1 0.0000 0.964 1.000 0.000
#> GSM152840 1 0.0000 0.964 1.000 0.000
#> GSM152841 1 0.0000 0.964 1.000 0.000
#> GSM152842 1 0.0000 0.964 1.000 0.000
#> GSM152843 1 0.0000 0.964 1.000 0.000
#> GSM152844 1 0.0000 0.964 1.000 0.000
#> GSM152845 2 0.0672 0.957 0.008 0.992
#> GSM152846 1 0.0672 0.960 0.992 0.008
#> GSM152847 1 0.0000 0.964 1.000 0.000
#> GSM152848 1 0.0000 0.964 1.000 0.000
#> GSM152849 1 0.0000 0.964 1.000 0.000
#> GSM152850 1 0.0000 0.964 1.000 0.000
#> GSM152851 1 0.0000 0.964 1.000 0.000
#> GSM152852 1 0.0000 0.964 1.000 0.000
#> GSM152853 1 0.0000 0.964 1.000 0.000
#> GSM152854 1 0.0000 0.964 1.000 0.000
#> GSM152855 1 0.0000 0.964 1.000 0.000
#> GSM153238 2 0.8499 0.639 0.276 0.724
#> GSM153239 1 0.0000 0.964 1.000 0.000
#> GSM153240 1 0.0000 0.964 1.000 0.000
#> GSM153241 1 0.0000 0.964 1.000 0.000
#> GSM153242 1 0.5842 0.836 0.860 0.140
#> GSM153243 2 0.3114 0.925 0.056 0.944
#> GSM153244 1 0.4431 0.892 0.908 0.092
#> GSM153245 1 0.0000 0.964 1.000 0.000
#> GSM153246 1 0.0000 0.964 1.000 0.000
#> GSM153247 1 0.4815 0.880 0.896 0.104
#> GSM153248 1 0.7602 0.734 0.780 0.220
#> GSM153249 1 0.0000 0.964 1.000 0.000
#> GSM153250 1 0.0000 0.964 1.000 0.000
#> GSM153251 1 0.9944 0.167 0.544 0.456
#> GSM153252 1 0.0000 0.964 1.000 0.000
#> GSM153253 1 0.0000 0.964 1.000 0.000
#> GSM153254 1 0.3274 0.922 0.940 0.060
#> GSM153255 1 0.0000 0.964 1.000 0.000
#> GSM153256 1 0.0000 0.964 1.000 0.000
#> GSM153257 1 0.0000 0.964 1.000 0.000
#> GSM153258 1 0.0000 0.964 1.000 0.000
#> GSM153259 1 0.0672 0.959 0.992 0.008
#> GSM153260 1 0.9286 0.486 0.656 0.344
#> GSM153261 1 0.1184 0.954 0.984 0.016
#> GSM153262 1 0.0000 0.964 1.000 0.000
#> GSM153263 1 0.0000 0.964 1.000 0.000
#> GSM153264 1 0.0000 0.964 1.000 0.000
#> GSM153265 1 0.0000 0.964 1.000 0.000
#> GSM153266 1 0.0000 0.964 1.000 0.000
#> GSM153267 1 0.0000 0.964 1.000 0.000
#> GSM153268 1 0.0000 0.964 1.000 0.000
#> GSM153269 1 0.0000 0.964 1.000 0.000
#> GSM153270 1 0.0000 0.964 1.000 0.000
#> GSM153271 1 0.0000 0.964 1.000 0.000
#> GSM153272 1 0.0000 0.964 1.000 0.000
#> GSM153273 1 0.4022 0.902 0.920 0.080
#> GSM153274 1 0.0000 0.964 1.000 0.000
#> GSM153275 1 0.0000 0.964 1.000 0.000
#> GSM153276 1 0.0000 0.964 1.000 0.000
#> GSM153277 1 0.0000 0.964 1.000 0.000
#> GSM153278 1 0.0000 0.964 1.000 0.000
#> GSM153279 1 0.0000 0.964 1.000 0.000
#> GSM153280 1 0.0000 0.964 1.000 0.000
#> GSM153281 1 0.0000 0.964 1.000 0.000
#> GSM153282 1 0.0000 0.964 1.000 0.000
#> GSM153283 1 0.0000 0.964 1.000 0.000
#> GSM153284 1 0.0000 0.964 1.000 0.000
#> GSM153285 1 0.0000 0.964 1.000 0.000
#> GSM153286 1 0.0000 0.964 1.000 0.000
#> GSM153287 1 0.0000 0.964 1.000 0.000
#> GSM153288 1 0.0000 0.964 1.000 0.000
#> GSM153289 1 0.0000 0.964 1.000 0.000
#> GSM153290 1 0.0000 0.964 1.000 0.000
#> GSM153291 1 0.0000 0.964 1.000 0.000
#> GSM153292 1 0.0000 0.964 1.000 0.000
#> GSM153293 1 0.0000 0.964 1.000 0.000
#> GSM153294 1 0.6438 0.812 0.836 0.164
#> GSM153295 1 0.0000 0.964 1.000 0.000
#> GSM153054 1 0.2043 0.943 0.968 0.032
#> GSM153055 1 0.0000 0.964 1.000 0.000
#> GSM153056 1 0.0000 0.964 1.000 0.000
#> GSM153057 1 0.3114 0.925 0.944 0.056
#> GSM153058 1 0.1414 0.952 0.980 0.020
#> GSM153059 2 0.6887 0.784 0.184 0.816
#> GSM153060 1 0.0376 0.962 0.996 0.004
#> GSM153061 1 0.4431 0.893 0.908 0.092
#> GSM153062 2 0.3431 0.917 0.064 0.936
#> GSM153063 1 0.0376 0.962 0.996 0.004
#> GSM153064 1 0.0000 0.964 1.000 0.000
#> GSM153065 2 0.0000 0.961 0.000 1.000
#> GSM153066 2 0.0000 0.961 0.000 1.000
#> GSM153067 1 0.0000 0.964 1.000 0.000
#> GSM153068 1 0.9922 0.189 0.552 0.448
#> GSM153069 1 0.0000 0.964 1.000 0.000
#> GSM153070 1 0.0000 0.964 1.000 0.000
#> GSM153071 1 0.0376 0.962 0.996 0.004
#> GSM153072 1 0.6247 0.821 0.844 0.156
#> GSM153073 1 0.0000 0.964 1.000 0.000
#> GSM153074 1 0.0000 0.964 1.000 0.000
#> GSM153075 1 0.0000 0.964 1.000 0.000
#> GSM153076 1 0.0000 0.964 1.000 0.000
#> GSM153077 1 0.1184 0.954 0.984 0.016
#> GSM153078 1 0.0672 0.959 0.992 0.008
#> GSM153079 2 0.5629 0.850 0.132 0.868
#> GSM153080 1 0.0000 0.964 1.000 0.000
#> GSM153081 1 0.0000 0.964 1.000 0.000
#> GSM153082 2 0.0672 0.957 0.008 0.992
#> GSM153083 2 0.0000 0.961 0.000 1.000
#> GSM153084 2 0.0000 0.961 0.000 1.000
#> GSM153085 2 0.9087 0.538 0.324 0.676
#> GSM153086 2 0.3879 0.907 0.076 0.924
#> GSM153087 1 0.0000 0.964 1.000 0.000
#> GSM153088 1 0.0000 0.964 1.000 0.000
#> GSM153089 1 0.9358 0.466 0.648 0.352
#> GSM153090 1 0.0000 0.964 1.000 0.000
#> GSM153091 2 0.2043 0.942 0.032 0.968
#> GSM153092 1 0.2603 0.934 0.956 0.044
#> GSM153093 1 0.0000 0.964 1.000 0.000
#> GSM153094 2 0.0000 0.961 0.000 1.000
#> GSM153095 2 0.8608 0.618 0.284 0.716
#> GSM153096 1 0.4161 0.900 0.916 0.084
#> GSM153097 2 0.3274 0.921 0.060 0.940
#> GSM153098 1 0.7602 0.730 0.780 0.220
#> GSM153099 1 0.0000 0.964 1.000 0.000
#> GSM153100 1 0.0672 0.959 0.992 0.008
#> GSM153101 1 0.8386 0.652 0.732 0.268
#> GSM153102 2 0.4939 0.876 0.108 0.892
#> GSM153103 2 0.7602 0.733 0.220 0.780
#> GSM153104 1 0.0000 0.964 1.000 0.000
#> GSM153106 1 0.4022 0.904 0.920 0.080
#> GSM153107 1 0.0376 0.962 0.996 0.004
#> GSM153108 1 0.0000 0.964 1.000 0.000
#> GSM153109 2 0.0000 0.961 0.000 1.000
#> GSM153110 1 0.5737 0.840 0.864 0.136
#> GSM153111 2 0.1414 0.950 0.020 0.980
#> GSM153112 1 0.6247 0.820 0.844 0.156
#> GSM153113 2 0.0000 0.961 0.000 1.000
#> GSM153114 1 0.0000 0.964 1.000 0.000
#> GSM187532 2 0.0000 0.961 0.000 1.000
#> GSM187533 2 0.0000 0.961 0.000 1.000
#> GSM187534 2 0.0000 0.961 0.000 1.000
#> GSM187535 2 0.0000 0.961 0.000 1.000
#> GSM152906 2 0.0000 0.961 0.000 1.000
#> GSM152907 2 0.0000 0.961 0.000 1.000
#> GSM152908 2 0.0000 0.961 0.000 1.000
#> GSM152909 2 0.0000 0.961 0.000 1.000
#> GSM152910 2 0.0000 0.961 0.000 1.000
#> GSM152911 2 0.0000 0.961 0.000 1.000
#> GSM152912 2 0.0000 0.961 0.000 1.000
#> GSM152913 2 0.0000 0.961 0.000 1.000
#> GSM152914 2 0.0000 0.961 0.000 1.000
#> GSM152915 2 0.0000 0.961 0.000 1.000
#> GSM152916 2 0.0000 0.961 0.000 1.000
#> GSM152917 2 0.0000 0.961 0.000 1.000
#> GSM152918 2 0.0000 0.961 0.000 1.000
#> GSM152919 2 0.0000 0.961 0.000 1.000
#> GSM152920 2 0.0000 0.961 0.000 1.000
#> GSM152921 2 0.0000 0.961 0.000 1.000
#> GSM152922 2 0.0000 0.961 0.000 1.000
#> GSM152923 2 0.0000 0.961 0.000 1.000
#> GSM152924 2 0.0000 0.961 0.000 1.000
#> GSM152925 2 0.0000 0.961 0.000 1.000
#> GSM152926 2 0.0000 0.961 0.000 1.000
#> GSM152927 2 0.0000 0.961 0.000 1.000
#> GSM152928 2 0.0000 0.961 0.000 1.000
#> GSM152929 2 0.0000 0.961 0.000 1.000
#> GSM152930 2 0.0000 0.961 0.000 1.000
cbind(get_classes(res, k = 3), get_membership(res, k = 3))
#> class entropy silhouette p1 p2 p3
#> GSM152839 3 0.6280 0.1432 0.460 0.000 0.540
#> GSM152840 3 0.4062 0.8033 0.164 0.000 0.836
#> GSM152841 1 0.3192 0.8627 0.888 0.000 0.112
#> GSM152842 3 0.2711 0.8320 0.088 0.000 0.912
#> GSM152843 3 0.4931 0.7274 0.232 0.000 0.768
#> GSM152844 3 0.1643 0.8341 0.044 0.000 0.956
#> GSM152845 3 0.2711 0.7465 0.000 0.088 0.912
#> GSM152846 3 0.0424 0.8219 0.000 0.008 0.992
#> GSM152847 3 0.4399 0.7815 0.188 0.000 0.812
#> GSM152848 1 0.3941 0.8306 0.844 0.000 0.156
#> GSM152849 3 0.2261 0.8346 0.068 0.000 0.932
#> GSM152850 3 0.4654 0.7601 0.208 0.000 0.792
#> GSM152851 3 0.5138 0.7009 0.252 0.000 0.748
#> GSM152852 3 0.0892 0.8303 0.020 0.000 0.980
#> GSM152853 3 0.2356 0.8339 0.072 0.000 0.928
#> GSM152854 3 0.0747 0.8290 0.016 0.000 0.984
#> GSM152855 1 0.0424 0.8820 0.992 0.008 0.000
#> GSM153238 3 0.1411 0.8033 0.000 0.036 0.964
#> GSM153239 3 0.4062 0.8056 0.164 0.000 0.836
#> GSM153240 1 0.2796 0.8728 0.908 0.000 0.092
#> GSM153241 3 0.4062 0.8050 0.164 0.000 0.836
#> GSM153242 3 0.1170 0.8182 0.008 0.016 0.976
#> GSM153243 3 0.2448 0.7642 0.000 0.076 0.924
#> GSM153244 1 0.5737 0.6912 0.732 0.012 0.256
#> GSM153245 3 0.3267 0.8260 0.116 0.000 0.884
#> GSM153246 3 0.0475 0.8239 0.004 0.004 0.992
#> GSM153247 3 0.3412 0.8251 0.124 0.000 0.876
#> GSM153248 1 0.5378 0.6390 0.756 0.236 0.008
#> GSM153249 1 0.0424 0.8819 0.992 0.000 0.008
#> GSM153250 1 0.0424 0.8820 0.992 0.008 0.000
#> GSM153251 3 0.1411 0.8015 0.000 0.036 0.964
#> GSM153252 1 0.2796 0.8731 0.908 0.000 0.092
#> GSM153253 1 0.3879 0.8344 0.848 0.000 0.152
#> GSM153254 3 0.4796 0.7467 0.220 0.000 0.780
#> GSM153255 1 0.0424 0.8872 0.992 0.000 0.008
#> GSM153256 1 0.0892 0.8871 0.980 0.000 0.020
#> GSM153257 1 0.1529 0.8894 0.960 0.000 0.040
#> GSM153258 1 0.0424 0.8879 0.992 0.000 0.008
#> GSM153259 1 0.0661 0.8821 0.988 0.008 0.004
#> GSM153260 3 0.1482 0.8211 0.012 0.020 0.968
#> GSM153261 3 0.0983 0.8295 0.016 0.004 0.980
#> GSM153262 1 0.3941 0.8314 0.844 0.000 0.156
#> GSM153263 1 0.0424 0.8874 0.992 0.000 0.008
#> GSM153264 1 0.1753 0.8887 0.952 0.000 0.048
#> GSM153265 1 0.5291 0.6847 0.732 0.000 0.268
#> GSM153266 1 0.4002 0.8280 0.840 0.000 0.160
#> GSM153267 1 0.0892 0.8894 0.980 0.000 0.020
#> GSM153268 1 0.6168 0.3484 0.588 0.000 0.412
#> GSM153269 1 0.0237 0.8860 0.996 0.000 0.004
#> GSM153270 1 0.3686 0.8435 0.860 0.000 0.140
#> GSM153271 1 0.0661 0.8799 0.988 0.004 0.008
#> GSM153272 1 0.1411 0.8894 0.964 0.000 0.036
#> GSM153273 1 0.2774 0.8371 0.920 0.072 0.008
#> GSM153274 1 0.2711 0.8752 0.912 0.000 0.088
#> GSM153275 1 0.1643 0.8889 0.956 0.000 0.044
#> GSM153276 1 0.3192 0.8626 0.888 0.000 0.112
#> GSM153277 1 0.4121 0.8197 0.832 0.000 0.168
#> GSM153278 3 0.4002 0.8062 0.160 0.000 0.840
#> GSM153279 1 0.6045 0.4390 0.620 0.000 0.380
#> GSM153280 1 0.5254 0.6902 0.736 0.000 0.264
#> GSM153281 1 0.3752 0.8403 0.856 0.000 0.144
#> GSM153282 1 0.4931 0.7407 0.768 0.000 0.232
#> GSM153283 1 0.1031 0.8899 0.976 0.000 0.024
#> GSM153284 1 0.1163 0.8898 0.972 0.000 0.028
#> GSM153285 1 0.4399 0.8003 0.812 0.000 0.188
#> GSM153286 1 0.1163 0.8895 0.972 0.000 0.028
#> GSM153287 1 0.1529 0.8893 0.960 0.000 0.040
#> GSM153288 1 0.0747 0.8888 0.984 0.000 0.016
#> GSM153289 1 0.0661 0.8799 0.988 0.008 0.004
#> GSM153290 1 0.4121 0.8193 0.832 0.000 0.168
#> GSM153291 1 0.0892 0.8892 0.980 0.000 0.020
#> GSM153292 1 0.2165 0.8843 0.936 0.000 0.064
#> GSM153293 1 0.0424 0.8852 0.992 0.000 0.008
#> GSM153294 1 0.5831 0.5506 0.708 0.284 0.008
#> GSM153295 1 0.3686 0.8435 0.860 0.000 0.140
#> GSM153054 1 0.6225 0.2848 0.568 0.000 0.432
#> GSM153055 1 0.2261 0.8834 0.932 0.000 0.068
#> GSM153056 3 0.5465 0.6359 0.288 0.000 0.712
#> GSM153057 3 0.4235 0.7963 0.176 0.000 0.824
#> GSM153058 3 0.1163 0.8325 0.028 0.000 0.972
#> GSM153059 3 0.2902 0.7897 0.016 0.064 0.920
#> GSM153060 3 0.0829 0.8262 0.012 0.004 0.984
#> GSM153061 3 0.0424 0.8219 0.000 0.008 0.992
#> GSM153062 3 0.1753 0.7899 0.000 0.048 0.952
#> GSM153063 3 0.1529 0.8340 0.040 0.000 0.960
#> GSM153064 1 0.0424 0.8820 0.992 0.008 0.000
#> GSM153065 3 0.2711 0.7477 0.000 0.088 0.912
#> GSM153066 2 0.6274 0.3633 0.000 0.544 0.456
#> GSM153067 1 0.1315 0.8704 0.972 0.020 0.008
#> GSM153068 3 0.1289 0.8051 0.000 0.032 0.968
#> GSM153069 1 0.1289 0.8897 0.968 0.000 0.032
#> GSM153070 1 0.1411 0.8901 0.964 0.000 0.036
#> GSM153071 1 0.5948 0.4843 0.640 0.000 0.360
#> GSM153072 1 0.5406 0.7456 0.764 0.012 0.224
#> GSM153073 1 0.0237 0.8840 0.996 0.004 0.000
#> GSM153074 1 0.0592 0.8840 0.988 0.000 0.012
#> GSM153075 1 0.2959 0.8697 0.900 0.000 0.100
#> GSM153076 1 0.0424 0.8819 0.992 0.000 0.008
#> GSM153077 1 0.0475 0.8852 0.992 0.004 0.004
#> GSM153078 3 0.5621 0.5937 0.308 0.000 0.692
#> GSM153079 2 0.5580 0.6538 0.256 0.736 0.008
#> GSM153080 3 0.4062 0.8037 0.164 0.000 0.836
#> GSM153081 1 0.2261 0.8842 0.932 0.000 0.068
#> GSM153082 2 0.3129 0.8178 0.088 0.904 0.008
#> GSM153083 2 0.1129 0.8549 0.020 0.976 0.004
#> GSM153084 2 0.3752 0.8267 0.000 0.856 0.144
#> GSM153085 2 0.9967 -0.1029 0.340 0.364 0.296
#> GSM153086 2 0.4994 0.7629 0.160 0.816 0.024
#> GSM153087 1 0.2356 0.8815 0.928 0.000 0.072
#> GSM153088 1 0.0424 0.8874 0.992 0.000 0.008
#> GSM153089 3 0.1129 0.8150 0.004 0.020 0.976
#> GSM153090 1 0.1289 0.8895 0.968 0.000 0.032
#> GSM153091 2 0.4912 0.7237 0.196 0.796 0.008
#> GSM153092 1 0.1315 0.8859 0.972 0.008 0.020
#> GSM153093 1 0.1643 0.8889 0.956 0.000 0.044
#> GSM153094 2 0.3349 0.8067 0.108 0.888 0.004
#> GSM153095 2 0.9970 -0.0383 0.348 0.356 0.296
#> GSM153096 1 0.2680 0.8412 0.924 0.068 0.008
#> GSM153097 2 0.4473 0.7586 0.164 0.828 0.008
#> GSM153098 1 0.5928 0.5268 0.696 0.296 0.008
#> GSM153099 1 0.3412 0.8549 0.876 0.000 0.124
#> GSM153100 1 0.1129 0.8747 0.976 0.020 0.004
#> GSM153101 3 0.6539 0.6176 0.288 0.028 0.684
#> GSM153102 2 0.8376 0.2296 0.084 0.496 0.420
#> GSM153103 3 0.9560 0.2392 0.212 0.324 0.464
#> GSM153104 1 0.3482 0.8527 0.872 0.000 0.128
#> GSM153106 1 0.3896 0.7818 0.864 0.128 0.008
#> GSM153107 1 0.0983 0.8771 0.980 0.016 0.004
#> GSM153108 1 0.2356 0.8835 0.928 0.000 0.072
#> GSM153109 2 0.2187 0.8565 0.028 0.948 0.024
#> GSM153110 1 0.2711 0.8306 0.912 0.088 0.000
#> GSM153111 2 0.3454 0.8067 0.104 0.888 0.008
#> GSM153112 1 0.5378 0.6392 0.756 0.236 0.008
#> GSM153113 2 0.0237 0.8583 0.000 0.996 0.004
#> GSM153114 1 0.0237 0.8865 0.996 0.000 0.004
#> GSM187532 3 0.6302 -0.2198 0.000 0.480 0.520
#> GSM187533 2 0.3340 0.8401 0.000 0.880 0.120
#> GSM187534 2 0.2261 0.8585 0.000 0.932 0.068
#> GSM187535 2 0.2063 0.8409 0.044 0.948 0.008
#> GSM152906 2 0.0237 0.8597 0.000 0.996 0.004
#> GSM152907 2 0.0592 0.8584 0.000 0.988 0.012
#> GSM152908 2 0.1289 0.8635 0.000 0.968 0.032
#> GSM152909 2 0.6180 0.4586 0.000 0.584 0.416
#> GSM152910 2 0.4750 0.7671 0.000 0.784 0.216
#> GSM152911 2 0.2066 0.8598 0.000 0.940 0.060
#> GSM152912 2 0.2261 0.8580 0.000 0.932 0.068
#> GSM152913 2 0.5058 0.7367 0.000 0.756 0.244
#> GSM152914 2 0.1411 0.8632 0.000 0.964 0.036
#> GSM152915 2 0.1289 0.8635 0.000 0.968 0.032
#> GSM152916 2 0.3686 0.8290 0.000 0.860 0.140
#> GSM152917 2 0.0747 0.8621 0.000 0.984 0.016
#> GSM152918 2 0.0424 0.8572 0.000 0.992 0.008
#> GSM152919 2 0.0747 0.8621 0.000 0.984 0.016
#> GSM152920 2 0.1643 0.8624 0.000 0.956 0.044
#> GSM152921 2 0.1289 0.8635 0.000 0.968 0.032
#> GSM152922 2 0.3267 0.8422 0.000 0.884 0.116
#> GSM152923 2 0.1163 0.8634 0.000 0.972 0.028
#> GSM152924 2 0.2878 0.8499 0.000 0.904 0.096
#> GSM152925 2 0.3482 0.8359 0.000 0.872 0.128
#> GSM152926 2 0.0000 0.8590 0.000 1.000 0.000
#> GSM152927 2 0.4504 0.7862 0.000 0.804 0.196
#> GSM152928 2 0.3551 0.8345 0.000 0.868 0.132
#> GSM152929 2 0.1163 0.8634 0.000 0.972 0.028
#> GSM152930 2 0.1031 0.8631 0.000 0.976 0.024
cbind(get_classes(res, k = 4), get_membership(res, k = 4))
#> class entropy silhouette p1 p2 p3 p4
#> GSM152839 1 0.6070 0.1340 0.548 0.000 0.404 0.048
#> GSM152840 4 0.4994 0.0339 0.000 0.000 0.480 0.520
#> GSM152841 4 0.2081 0.7743 0.000 0.000 0.084 0.916
#> GSM152842 3 0.4950 0.4406 0.376 0.004 0.620 0.000
#> GSM152843 3 0.4877 0.5087 0.328 0.000 0.664 0.008
#> GSM152844 3 0.5038 0.4990 0.000 0.020 0.684 0.296
#> GSM152845 3 0.2383 0.6980 0.004 0.048 0.924 0.024
#> GSM152846 3 0.4050 0.6532 0.000 0.024 0.808 0.168
#> GSM152847 3 0.4981 0.2240 0.464 0.000 0.536 0.000
#> GSM152848 1 0.3128 0.7745 0.884 0.000 0.040 0.076
#> GSM152849 3 0.3688 0.6579 0.208 0.000 0.792 0.000
#> GSM152850 1 0.4509 0.4713 0.708 0.004 0.288 0.000
#> GSM152851 4 0.5766 0.2128 0.000 0.032 0.404 0.564
#> GSM152852 3 0.4579 0.6125 0.004 0.020 0.764 0.212
#> GSM152853 3 0.5339 0.3223 0.000 0.016 0.600 0.384
#> GSM152854 3 0.2884 0.7049 0.004 0.028 0.900 0.068
#> GSM152855 4 0.3052 0.7543 0.136 0.004 0.000 0.860
#> GSM153238 3 0.4422 0.6123 0.256 0.008 0.736 0.000
#> GSM153239 3 0.5024 0.3947 0.000 0.008 0.632 0.360
#> GSM153240 4 0.1042 0.8101 0.020 0.000 0.008 0.972
#> GSM153241 3 0.3172 0.6881 0.160 0.000 0.840 0.000
#> GSM153242 3 0.4551 0.6589 0.004 0.044 0.796 0.156
#> GSM153243 3 0.5384 0.5161 0.324 0.028 0.648 0.000
#> GSM153244 4 0.4482 0.6868 0.000 0.068 0.128 0.804
#> GSM153245 3 0.4917 0.4561 0.004 0.004 0.664 0.328
#> GSM153246 3 0.1637 0.7189 0.060 0.000 0.940 0.000
#> GSM153247 3 0.4560 0.5687 0.296 0.004 0.700 0.000
#> GSM153248 1 0.1913 0.7739 0.940 0.040 0.000 0.020
#> GSM153249 4 0.0188 0.8076 0.004 0.000 0.000 0.996
#> GSM153250 1 0.3710 0.7146 0.804 0.004 0.000 0.192
#> GSM153251 3 0.3648 0.6902 0.004 0.056 0.864 0.076
#> GSM153252 4 0.2480 0.7914 0.088 0.000 0.008 0.904
#> GSM153253 4 0.2345 0.7661 0.000 0.000 0.100 0.900
#> GSM153254 3 0.6087 0.2167 0.000 0.048 0.540 0.412
#> GSM153255 4 0.0817 0.8091 0.024 0.000 0.000 0.976
#> GSM153256 4 0.4992 0.0835 0.476 0.000 0.000 0.524
#> GSM153257 4 0.1305 0.8087 0.036 0.000 0.004 0.960
#> GSM153258 1 0.2831 0.7701 0.876 0.004 0.000 0.120
#> GSM153259 1 0.1807 0.7802 0.940 0.008 0.000 0.052
#> GSM153260 3 0.5292 0.1972 0.480 0.008 0.512 0.000
#> GSM153261 3 0.2654 0.7076 0.108 0.004 0.888 0.000
#> GSM153262 4 0.1545 0.8013 0.008 0.000 0.040 0.952
#> GSM153263 1 0.3219 0.7408 0.836 0.000 0.000 0.164
#> GSM153264 1 0.1452 0.7656 0.956 0.000 0.036 0.008
#> GSM153265 4 0.2760 0.7435 0.000 0.000 0.128 0.872
#> GSM153266 1 0.2089 0.7652 0.932 0.000 0.048 0.020
#> GSM153267 4 0.4907 0.2653 0.420 0.000 0.000 0.580
#> GSM153268 4 0.3356 0.6982 0.000 0.000 0.176 0.824
#> GSM153269 1 0.4916 0.2408 0.576 0.000 0.000 0.424
#> GSM153270 4 0.5113 0.6164 0.252 0.000 0.036 0.712
#> GSM153271 1 0.4964 0.3867 0.616 0.004 0.000 0.380
#> GSM153272 4 0.1716 0.7987 0.064 0.000 0.000 0.936
#> GSM153273 1 0.3215 0.7729 0.876 0.032 0.000 0.092
#> GSM153274 4 0.5295 0.0290 0.488 0.000 0.008 0.504
#> GSM153275 4 0.4188 0.6399 0.244 0.000 0.004 0.752
#> GSM153276 4 0.4744 0.6478 0.240 0.000 0.024 0.736
#> GSM153277 4 0.1824 0.7921 0.004 0.000 0.060 0.936
#> GSM153278 3 0.4961 0.2854 0.448 0.000 0.552 0.000
#> GSM153279 4 0.3486 0.6828 0.000 0.000 0.188 0.812
#> GSM153280 4 0.3428 0.7216 0.000 0.012 0.144 0.844
#> GSM153281 4 0.1661 0.7955 0.004 0.000 0.052 0.944
#> GSM153282 4 0.2589 0.7545 0.000 0.000 0.116 0.884
#> GSM153283 1 0.2198 0.7796 0.920 0.000 0.008 0.072
#> GSM153284 4 0.1211 0.8074 0.040 0.000 0.000 0.960
#> GSM153285 4 0.2647 0.7535 0.000 0.000 0.120 0.880
#> GSM153286 4 0.2530 0.7731 0.112 0.000 0.000 0.888
#> GSM153287 4 0.0336 0.8066 0.000 0.000 0.008 0.992
#> GSM153288 4 0.2760 0.7609 0.128 0.000 0.000 0.872
#> GSM153289 4 0.4761 0.3944 0.372 0.000 0.000 0.628
#> GSM153290 4 0.2530 0.7599 0.000 0.000 0.112 0.888
#> GSM153291 4 0.0707 0.8094 0.020 0.000 0.000 0.980
#> GSM153292 4 0.1151 0.8006 0.000 0.008 0.024 0.968
#> GSM153293 4 0.4250 0.5818 0.276 0.000 0.000 0.724
#> GSM153294 1 0.7325 0.4568 0.528 0.264 0.000 0.208
#> GSM153295 1 0.5496 0.5281 0.652 0.000 0.036 0.312
#> GSM153054 1 0.3402 0.6695 0.832 0.000 0.164 0.004
#> GSM153055 4 0.4905 0.4390 0.364 0.000 0.004 0.632
#> GSM153056 3 0.5453 0.5335 0.320 0.000 0.648 0.032
#> GSM153057 3 0.4730 0.6659 0.188 0.004 0.772 0.036
#> GSM153058 3 0.2392 0.7242 0.052 0.008 0.924 0.016
#> GSM153059 3 0.2739 0.7162 0.060 0.036 0.904 0.000
#> GSM153060 3 0.1209 0.7218 0.032 0.000 0.964 0.004
#> GSM153061 3 0.3157 0.6925 0.144 0.004 0.852 0.000
#> GSM153062 3 0.1394 0.7179 0.016 0.012 0.964 0.008
#> GSM153063 3 0.3900 0.6585 0.000 0.020 0.816 0.164
#> GSM153064 1 0.3893 0.7086 0.796 0.008 0.000 0.196
#> GSM153065 3 0.4706 0.6177 0.248 0.020 0.732 0.000
#> GSM153066 3 0.6664 0.5239 0.216 0.164 0.620 0.000
#> GSM153067 4 0.0817 0.8089 0.024 0.000 0.000 0.976
#> GSM153068 3 0.2197 0.7138 0.080 0.004 0.916 0.000
#> GSM153069 4 0.0336 0.8068 0.000 0.000 0.008 0.992
#> GSM153070 1 0.3142 0.7673 0.860 0.000 0.008 0.132
#> GSM153071 1 0.4074 0.6254 0.792 0.004 0.196 0.008
#> GSM153072 1 0.2796 0.7263 0.892 0.008 0.096 0.004
#> GSM153073 1 0.1545 0.7802 0.952 0.008 0.000 0.040
#> GSM153074 4 0.0817 0.8089 0.024 0.000 0.000 0.976
#> GSM153075 4 0.1059 0.8074 0.012 0.000 0.016 0.972
#> GSM153076 1 0.2589 0.7705 0.884 0.000 0.000 0.116
#> GSM153077 1 0.1674 0.7657 0.952 0.012 0.032 0.004
#> GSM153078 1 0.4850 0.4584 0.696 0.008 0.292 0.004
#> GSM153079 1 0.2499 0.7586 0.920 0.032 0.044 0.004
#> GSM153080 3 0.4136 0.6499 0.016 0.000 0.788 0.196
#> GSM153081 1 0.1545 0.7645 0.952 0.000 0.040 0.008
#> GSM153082 2 0.5276 0.2743 0.432 0.560 0.004 0.004
#> GSM153083 1 0.3398 0.7307 0.872 0.068 0.060 0.000
#> GSM153084 2 0.7159 0.4591 0.244 0.556 0.200 0.000
#> GSM153085 1 0.4063 0.6532 0.808 0.016 0.172 0.004
#> GSM153086 1 0.2623 0.7410 0.908 0.028 0.064 0.000
#> GSM153087 4 0.2412 0.7931 0.084 0.000 0.008 0.908
#> GSM153088 1 0.2197 0.7789 0.916 0.000 0.004 0.080
#> GSM153089 3 0.4171 0.6723 0.000 0.060 0.824 0.116
#> GSM153090 1 0.3032 0.7691 0.868 0.000 0.008 0.124
#> GSM153091 1 0.4482 0.5691 0.728 0.264 0.000 0.008
#> GSM153092 1 0.5716 0.5655 0.668 0.060 0.000 0.272
#> GSM153093 4 0.1022 0.8091 0.032 0.000 0.000 0.968
#> GSM153094 2 0.4936 0.4278 0.372 0.624 0.000 0.004
#> GSM153095 1 0.8086 0.1415 0.444 0.288 0.256 0.012
#> GSM153096 1 0.2984 0.7752 0.888 0.028 0.000 0.084
#> GSM153097 1 0.1913 0.7617 0.940 0.040 0.020 0.000
#> GSM153098 4 0.7743 0.1527 0.256 0.308 0.000 0.436
#> GSM153099 4 0.5271 0.4601 0.340 0.000 0.020 0.640
#> GSM153100 1 0.6014 0.3664 0.588 0.052 0.000 0.360
#> GSM153101 1 0.4567 0.5550 0.748 0.012 0.236 0.004
#> GSM153102 2 0.7274 0.1918 0.068 0.488 0.412 0.032
#> GSM153103 1 0.4036 0.6615 0.816 0.020 0.160 0.004
#> GSM153104 4 0.1389 0.7955 0.000 0.000 0.048 0.952
#> GSM153106 4 0.7120 0.4107 0.224 0.212 0.000 0.564
#> GSM153107 1 0.3862 0.7397 0.824 0.024 0.000 0.152
#> GSM153108 4 0.1443 0.8053 0.004 0.008 0.028 0.960
#> GSM153109 2 0.3447 0.8174 0.128 0.852 0.020 0.000
#> GSM153110 1 0.1271 0.7716 0.968 0.012 0.012 0.008
#> GSM153111 1 0.2909 0.7395 0.888 0.092 0.020 0.000
#> GSM153112 1 0.7293 0.4575 0.536 0.248 0.000 0.216
#> GSM153113 2 0.2281 0.8488 0.096 0.904 0.000 0.000
#> GSM153114 4 0.1022 0.8096 0.032 0.000 0.000 0.968
#> GSM187532 3 0.5310 0.0721 0.012 0.412 0.576 0.000
#> GSM187533 2 0.2300 0.8710 0.016 0.920 0.064 0.000
#> GSM187534 2 0.1584 0.8812 0.036 0.952 0.012 0.000
#> GSM187535 2 0.1389 0.8713 0.048 0.952 0.000 0.000
#> GSM152906 2 0.1389 0.8746 0.048 0.952 0.000 0.000
#> GSM152907 2 0.1297 0.8723 0.000 0.964 0.020 0.016
#> GSM152908 2 0.0469 0.8788 0.000 0.988 0.012 0.000
#> GSM152909 2 0.5125 0.4656 0.004 0.616 0.376 0.004
#> GSM152910 2 0.3306 0.8074 0.004 0.840 0.156 0.000
#> GSM152911 2 0.1305 0.8765 0.004 0.960 0.036 0.000
#> GSM152912 2 0.1022 0.8760 0.000 0.968 0.032 0.000
#> GSM152913 2 0.3486 0.7745 0.000 0.812 0.188 0.000
#> GSM152914 2 0.0804 0.8814 0.012 0.980 0.008 0.000
#> GSM152915 2 0.0376 0.8790 0.000 0.992 0.004 0.004
#> GSM152916 2 0.2796 0.8569 0.016 0.892 0.092 0.000
#> GSM152917 2 0.0469 0.8806 0.012 0.988 0.000 0.000
#> GSM152918 2 0.1209 0.8778 0.032 0.964 0.000 0.004
#> GSM152919 2 0.0921 0.8799 0.028 0.972 0.000 0.000
#> GSM152920 2 0.0707 0.8788 0.000 0.980 0.020 0.000
#> GSM152921 2 0.0469 0.8788 0.000 0.988 0.012 0.000
#> GSM152922 2 0.1867 0.8621 0.000 0.928 0.072 0.000
#> GSM152923 2 0.0921 0.8799 0.028 0.972 0.000 0.000
#> GSM152924 2 0.2882 0.8596 0.024 0.892 0.084 0.000
#> GSM152925 2 0.2635 0.8645 0.020 0.904 0.076 0.000
#> GSM152926 2 0.1109 0.8797 0.028 0.968 0.000 0.004
#> GSM152927 2 0.3946 0.7980 0.020 0.812 0.168 0.000
#> GSM152928 2 0.4227 0.8221 0.060 0.820 0.120 0.000
#> GSM152929 2 0.1118 0.8776 0.036 0.964 0.000 0.000
#> GSM152930 2 0.1022 0.8788 0.032 0.968 0.000 0.000
cbind(get_classes(res, k = 5), get_membership(res, k = 5))
#> class entropy silhouette p1 p2 p3 p4 p5
#> GSM152839 1 0.5872 0.232103 0.548 0.000 0.376 0.032 0.044
#> GSM152840 4 0.5306 0.350201 0.000 0.000 0.316 0.612 0.072
#> GSM152841 4 0.1830 0.739078 0.000 0.000 0.028 0.932 0.040
#> GSM152842 3 0.4629 0.526761 0.244 0.000 0.704 0.000 0.052
#> GSM152843 3 0.4457 0.572859 0.208 0.000 0.740 0.004 0.048
#> GSM152844 3 0.6220 0.327187 0.000 0.004 0.508 0.356 0.132
#> GSM152845 3 0.4953 0.536209 0.000 0.024 0.688 0.028 0.260
#> GSM152846 3 0.6233 0.474099 0.000 0.012 0.592 0.180 0.216
#> GSM152847 3 0.5066 0.395929 0.344 0.000 0.608 0.000 0.048
#> GSM152848 1 0.3528 0.588379 0.848 0.000 0.084 0.016 0.052
#> GSM152849 3 0.4637 0.605903 0.160 0.000 0.748 0.004 0.088
#> GSM152850 1 0.5193 0.286859 0.584 0.000 0.364 0.000 0.052
#> GSM152851 4 0.5067 0.532421 0.000 0.008 0.224 0.696 0.072
#> GSM152852 3 0.6517 0.436151 0.000 0.012 0.548 0.220 0.220
#> GSM152853 4 0.5895 -0.096482 0.000 0.000 0.440 0.460 0.100
#> GSM152854 3 0.4619 0.606560 0.012 0.012 0.776 0.056 0.144
#> GSM152855 4 0.6678 0.228140 0.292 0.004 0.000 0.472 0.232
#> GSM153238 3 0.4891 0.569341 0.112 0.000 0.716 0.000 0.172
#> GSM153239 3 0.5414 0.244644 0.000 0.000 0.528 0.412 0.060
#> GSM153240 4 0.2972 0.744602 0.084 0.000 0.004 0.872 0.040
#> GSM153241 3 0.2830 0.640096 0.080 0.000 0.876 0.000 0.044
#> GSM153242 3 0.5752 0.538648 0.004 0.024 0.680 0.184 0.108
#> GSM153243 3 0.4999 0.552574 0.216 0.012 0.708 0.000 0.064
#> GSM153244 4 0.4854 0.666134 0.004 0.076 0.056 0.780 0.084
#> GSM153245 3 0.5297 0.370795 0.000 0.000 0.580 0.360 0.060
#> GSM153246 3 0.1356 0.642768 0.012 0.000 0.956 0.004 0.028
#> GSM153247 3 0.5634 0.484801 0.116 0.000 0.648 0.008 0.228
#> GSM153248 1 0.4411 0.507536 0.724 0.012 0.008 0.008 0.248
#> GSM153249 4 0.1300 0.751198 0.016 0.000 0.000 0.956 0.028
#> GSM153250 1 0.3085 0.576087 0.852 0.000 0.000 0.116 0.032
#> GSM153251 3 0.4872 0.599888 0.004 0.044 0.776 0.088 0.088
#> GSM153252 4 0.3806 0.703446 0.152 0.000 0.004 0.804 0.040
#> GSM153253 4 0.1661 0.739522 0.000 0.000 0.036 0.940 0.024
#> GSM153254 4 0.7607 -0.000679 0.004 0.060 0.340 0.424 0.172
#> GSM153255 4 0.1502 0.749275 0.056 0.000 0.000 0.940 0.004
#> GSM153256 1 0.4969 0.282039 0.588 0.000 0.000 0.376 0.036
#> GSM153257 4 0.2754 0.743316 0.080 0.000 0.004 0.884 0.032
#> GSM153258 1 0.2965 0.592732 0.884 0.004 0.008 0.052 0.052
#> GSM153259 1 0.4098 0.471285 0.716 0.004 0.004 0.004 0.272
#> GSM153260 3 0.5579 0.431109 0.300 0.000 0.600 0.000 0.100
#> GSM153261 3 0.5148 0.564006 0.072 0.008 0.684 0.000 0.236
#> GSM153262 4 0.2519 0.750737 0.036 0.000 0.004 0.900 0.060
#> GSM153263 1 0.3967 0.572373 0.808 0.000 0.004 0.088 0.100
#> GSM153264 1 0.2344 0.594719 0.904 0.000 0.064 0.000 0.032
#> GSM153265 4 0.2504 0.724382 0.000 0.000 0.064 0.896 0.040
#> GSM153266 1 0.2659 0.599076 0.888 0.000 0.060 0.000 0.052
#> GSM153267 1 0.4875 0.208312 0.576 0.000 0.004 0.400 0.020
#> GSM153268 4 0.3037 0.697834 0.000 0.000 0.100 0.860 0.040
#> GSM153269 1 0.4562 0.406787 0.676 0.000 0.000 0.292 0.032
#> GSM153270 4 0.5935 0.462005 0.288 0.000 0.020 0.604 0.088
#> GSM153271 1 0.4847 0.471161 0.692 0.000 0.000 0.240 0.068
#> GSM153272 4 0.3055 0.715452 0.144 0.000 0.000 0.840 0.016
#> GSM153273 1 0.3790 0.584539 0.816 0.012 0.000 0.036 0.136
#> GSM153274 1 0.5980 0.356465 0.584 0.000 0.044 0.324 0.048
#> GSM153275 4 0.5047 0.379885 0.376 0.000 0.004 0.588 0.032
#> GSM153276 4 0.5958 0.305846 0.384 0.000 0.036 0.536 0.044
#> GSM153277 4 0.3455 0.725696 0.020 0.000 0.024 0.844 0.112
#> GSM153278 3 0.5825 0.344179 0.360 0.000 0.536 0.000 0.104
#> GSM153279 4 0.3599 0.706149 0.004 0.000 0.104 0.832 0.060
#> GSM153280 4 0.3209 0.708510 0.000 0.004 0.060 0.860 0.076
#> GSM153281 4 0.0854 0.750336 0.004 0.000 0.012 0.976 0.008
#> GSM153282 4 0.1872 0.734335 0.000 0.000 0.052 0.928 0.020
#> GSM153283 1 0.1485 0.604568 0.948 0.000 0.020 0.000 0.032
#> GSM153284 4 0.3131 0.734611 0.104 0.000 0.008 0.860 0.028
#> GSM153285 4 0.2228 0.733123 0.000 0.000 0.048 0.912 0.040
#> GSM153286 4 0.4026 0.620772 0.244 0.000 0.000 0.736 0.020
#> GSM153287 4 0.1281 0.751336 0.012 0.000 0.000 0.956 0.032
#> GSM153288 4 0.3671 0.634492 0.236 0.000 0.000 0.756 0.008
#> GSM153289 1 0.6823 0.059187 0.448 0.008 0.000 0.320 0.224
#> GSM153290 4 0.2491 0.730303 0.000 0.000 0.036 0.896 0.068
#> GSM153291 4 0.3058 0.732921 0.096 0.000 0.000 0.860 0.044
#> GSM153292 4 0.0671 0.747083 0.000 0.000 0.004 0.980 0.016
#> GSM153293 4 0.5213 0.302448 0.396 0.000 0.000 0.556 0.048
#> GSM153294 1 0.7504 0.146140 0.484 0.144 0.004 0.076 0.292
#> GSM153295 1 0.5250 0.481409 0.708 0.000 0.020 0.188 0.084
#> GSM153054 1 0.6654 0.268083 0.480 0.004 0.232 0.000 0.284
#> GSM153055 1 0.6689 0.083381 0.492 0.020 0.040 0.396 0.052
#> GSM153056 3 0.5425 0.462844 0.308 0.000 0.628 0.024 0.040
#> GSM153057 3 0.6525 0.515049 0.204 0.008 0.604 0.024 0.160
#> GSM153058 3 0.4030 0.644227 0.064 0.004 0.832 0.040 0.060
#> GSM153059 3 0.5518 0.601734 0.056 0.044 0.720 0.012 0.168
#> GSM153060 3 0.1914 0.642389 0.008 0.000 0.928 0.008 0.056
#> GSM153061 3 0.3390 0.622664 0.060 0.000 0.840 0.000 0.100
#> GSM153062 3 0.1442 0.639367 0.000 0.004 0.952 0.012 0.032
#> GSM153063 3 0.5010 0.526525 0.000 0.000 0.688 0.224 0.088
#> GSM153064 1 0.3731 0.578044 0.816 0.000 0.000 0.072 0.112
#> GSM153065 3 0.4971 0.571185 0.176 0.000 0.708 0.000 0.116
#> GSM153066 3 0.6223 0.424713 0.052 0.080 0.616 0.000 0.252
#> GSM153067 4 0.2074 0.749052 0.036 0.000 0.000 0.920 0.044
#> GSM153068 3 0.1739 0.643741 0.032 0.000 0.940 0.004 0.024
#> GSM153069 4 0.0404 0.749838 0.012 0.000 0.000 0.988 0.000
#> GSM153070 1 0.3611 0.604155 0.856 0.004 0.036 0.044 0.060
#> GSM153071 1 0.7511 0.147264 0.408 0.016 0.304 0.016 0.256
#> GSM153072 1 0.6503 0.379534 0.580 0.024 0.192 0.000 0.204
#> GSM153073 1 0.3194 0.602567 0.868 0.008 0.028 0.008 0.088
#> GSM153074 4 0.2077 0.741609 0.084 0.000 0.000 0.908 0.008
#> GSM153075 4 0.6063 0.562450 0.108 0.032 0.004 0.652 0.204
#> GSM153076 1 0.2390 0.605871 0.908 0.000 0.004 0.044 0.044
#> GSM153077 1 0.2616 0.583946 0.880 0.000 0.100 0.000 0.020
#> GSM153078 1 0.5037 0.341227 0.616 0.000 0.336 0.000 0.048
#> GSM153079 1 0.5834 0.096670 0.536 0.028 0.044 0.000 0.392
#> GSM153080 3 0.5005 0.549751 0.008 0.000 0.708 0.208 0.076
#> GSM153081 1 0.3507 0.567180 0.828 0.000 0.052 0.000 0.120
#> GSM153082 2 0.7472 -0.156322 0.308 0.388 0.036 0.000 0.268
#> GSM153083 1 0.5358 0.474884 0.684 0.024 0.064 0.000 0.228
#> GSM153084 2 0.8099 -0.104791 0.120 0.400 0.216 0.000 0.264
#> GSM153085 1 0.6631 0.341534 0.564 0.020 0.244 0.004 0.168
#> GSM153086 1 0.4696 0.525693 0.736 0.000 0.108 0.000 0.156
#> GSM153087 4 0.5511 0.640647 0.148 0.000 0.044 0.712 0.096
#> GSM153088 1 0.2095 0.607955 0.928 0.000 0.024 0.028 0.020
#> GSM153089 3 0.6152 0.519427 0.000 0.032 0.636 0.140 0.192
#> GSM153090 1 0.2341 0.604354 0.912 0.000 0.020 0.056 0.012
#> GSM153091 1 0.4935 0.484450 0.724 0.160 0.000 0.004 0.112
#> GSM153092 1 0.5040 0.511013 0.744 0.020 0.004 0.148 0.084
#> GSM153093 4 0.1914 0.750684 0.060 0.000 0.000 0.924 0.016
#> GSM153094 1 0.5884 -0.141444 0.480 0.420 0.000 0.000 0.100
#> GSM153095 5 0.8345 0.259010 0.204 0.132 0.224 0.012 0.428
#> GSM153096 1 0.3056 0.588419 0.860 0.008 0.000 0.020 0.112
#> GSM153097 1 0.4132 0.549457 0.760 0.004 0.032 0.000 0.204
#> GSM153098 4 0.8111 -0.185993 0.264 0.096 0.000 0.332 0.308
#> GSM153099 4 0.5481 0.103892 0.456 0.000 0.032 0.496 0.016
#> GSM153100 1 0.6096 0.376437 0.620 0.024 0.000 0.236 0.120
#> GSM153101 1 0.6717 0.088809 0.416 0.000 0.264 0.000 0.320
#> GSM153102 5 0.7173 0.276977 0.024 0.168 0.204 0.036 0.568
#> GSM153103 1 0.5480 0.442134 0.656 0.000 0.176 0.000 0.168
#> GSM153104 4 0.1787 0.749637 0.004 0.000 0.016 0.936 0.044
#> GSM153106 5 0.7683 0.368981 0.248 0.096 0.000 0.184 0.472
#> GSM153107 5 0.6135 0.095447 0.440 0.024 0.008 0.048 0.480
#> GSM153108 4 0.4706 0.695040 0.112 0.000 0.016 0.764 0.108
#> GSM153109 5 0.6669 -0.003289 0.144 0.404 0.016 0.000 0.436
#> GSM153110 1 0.2825 0.590709 0.860 0.000 0.016 0.000 0.124
#> GSM153111 1 0.5816 0.379342 0.608 0.056 0.032 0.000 0.304
#> GSM153112 1 0.7298 0.302824 0.536 0.092 0.000 0.156 0.216
#> GSM153113 2 0.4387 0.616384 0.028 0.732 0.008 0.000 0.232
#> GSM153114 4 0.6426 0.374053 0.188 0.008 0.000 0.544 0.260
#> GSM187532 3 0.6811 0.029687 0.000 0.256 0.432 0.004 0.308
#> GSM187533 2 0.4696 0.344240 0.000 0.556 0.016 0.000 0.428
#> GSM187534 2 0.3774 0.600982 0.000 0.704 0.000 0.000 0.296
#> GSM187535 2 0.5607 0.331568 0.064 0.524 0.000 0.004 0.408
#> GSM152906 2 0.3863 0.659637 0.012 0.740 0.000 0.000 0.248
#> GSM152907 2 0.2112 0.714175 0.000 0.908 0.004 0.004 0.084
#> GSM152908 2 0.1671 0.694167 0.000 0.924 0.000 0.000 0.076
#> GSM152909 2 0.6358 0.267743 0.000 0.540 0.192 0.004 0.264
#> GSM152910 2 0.3681 0.637378 0.000 0.808 0.044 0.000 0.148
#> GSM152911 2 0.1282 0.706277 0.000 0.952 0.004 0.000 0.044
#> GSM152912 2 0.2127 0.682698 0.000 0.892 0.000 0.000 0.108
#> GSM152913 2 0.3806 0.658012 0.000 0.812 0.084 0.000 0.104
#> GSM152914 2 0.0290 0.713332 0.000 0.992 0.000 0.000 0.008
#> GSM152915 2 0.0794 0.710433 0.000 0.972 0.000 0.000 0.028
#> GSM152916 2 0.3659 0.680359 0.000 0.768 0.012 0.000 0.220
#> GSM152917 2 0.0963 0.714425 0.000 0.964 0.000 0.000 0.036
#> GSM152918 2 0.1638 0.711349 0.004 0.932 0.000 0.000 0.064
#> GSM152919 2 0.1121 0.715245 0.000 0.956 0.000 0.000 0.044
#> GSM152920 2 0.1965 0.686764 0.000 0.904 0.000 0.000 0.096
#> GSM152921 2 0.1732 0.695263 0.000 0.920 0.000 0.000 0.080
#> GSM152922 2 0.3106 0.653712 0.000 0.840 0.020 0.000 0.140
#> GSM152923 2 0.3461 0.675477 0.004 0.772 0.000 0.000 0.224
#> GSM152924 2 0.4518 0.614004 0.004 0.660 0.016 0.000 0.320
#> GSM152925 2 0.4639 0.588562 0.000 0.632 0.024 0.000 0.344
#> GSM152926 2 0.4066 0.613334 0.004 0.672 0.000 0.000 0.324
#> GSM152927 2 0.5308 0.572404 0.000 0.620 0.076 0.000 0.304
#> GSM152928 2 0.5892 0.345946 0.016 0.472 0.060 0.000 0.452
#> GSM152929 2 0.4003 0.633816 0.008 0.704 0.000 0.000 0.288
#> GSM152930 2 0.3231 0.685043 0.004 0.800 0.000 0.000 0.196
cbind(get_classes(res, k = 6), get_membership(res, k = 6))
#> class entropy silhouette p1 p2 p3 p4 p5 p6
#> GSM152839 1 0.5708 0.1480 0.528 0.000 0.368 0.008 0.024 0.072
#> GSM152840 4 0.6311 0.2609 0.000 0.000 0.236 0.516 0.036 0.212
#> GSM152841 4 0.2408 0.7174 0.000 0.000 0.012 0.876 0.004 0.108
#> GSM152842 3 0.4158 0.5369 0.204 0.000 0.740 0.000 0.020 0.036
#> GSM152843 3 0.5314 0.5020 0.244 0.000 0.652 0.012 0.028 0.064
#> GSM152844 3 0.6797 0.0413 0.000 0.000 0.368 0.248 0.044 0.340
#> GSM152845 6 0.5631 -0.1020 0.000 0.024 0.380 0.012 0.056 0.528
#> GSM152846 6 0.6203 -0.1544 0.000 0.000 0.416 0.100 0.052 0.432
#> GSM152847 3 0.5481 0.4171 0.324 0.000 0.580 0.004 0.032 0.060
#> GSM152848 1 0.3880 0.6219 0.816 0.000 0.080 0.016 0.020 0.068
#> GSM152849 3 0.6737 0.4414 0.180 0.004 0.516 0.008 0.052 0.240
#> GSM152850 1 0.5153 0.2238 0.564 0.000 0.372 0.004 0.028 0.032
#> GSM152851 4 0.5228 0.5650 0.000 0.032 0.172 0.700 0.020 0.076
#> GSM152852 6 0.6435 -0.0577 0.000 0.008 0.340 0.124 0.044 0.484
#> GSM152853 4 0.6516 -0.0128 0.000 0.000 0.312 0.408 0.024 0.256
#> GSM152854 3 0.5921 0.3310 0.012 0.036 0.556 0.040 0.016 0.340
#> GSM152855 6 0.7365 0.1701 0.264 0.024 0.000 0.260 0.056 0.396
#> GSM153238 3 0.5872 0.4716 0.052 0.000 0.612 0.000 0.184 0.152
#> GSM153239 3 0.6279 0.1170 0.000 0.000 0.436 0.364 0.024 0.176
#> GSM153240 4 0.5024 0.6438 0.156 0.000 0.016 0.692 0.004 0.132
#> GSM153241 3 0.4535 0.5573 0.104 0.004 0.760 0.012 0.012 0.108
#> GSM153242 3 0.6215 0.3313 0.000 0.032 0.560 0.112 0.020 0.276
#> GSM153243 3 0.6302 0.4687 0.256 0.024 0.568 0.000 0.036 0.116
#> GSM153244 4 0.6228 0.5340 0.016 0.168 0.060 0.636 0.012 0.108
#> GSM153245 3 0.5773 0.2678 0.000 0.004 0.576 0.292 0.032 0.096
#> GSM153246 3 0.2136 0.5536 0.016 0.000 0.908 0.000 0.012 0.064
#> GSM153247 3 0.6675 0.4307 0.052 0.008 0.588 0.036 0.200 0.116
#> GSM153248 1 0.5711 0.4276 0.536 0.000 0.012 0.016 0.356 0.080
#> GSM153249 4 0.1819 0.7355 0.008 0.000 0.004 0.932 0.032 0.024
#> GSM153250 1 0.3014 0.6382 0.864 0.000 0.024 0.080 0.004 0.028
#> GSM153251 3 0.5500 0.4800 0.008 0.036 0.700 0.056 0.036 0.164
#> GSM153252 4 0.3951 0.7112 0.072 0.000 0.012 0.816 0.048 0.052
#> GSM153253 4 0.2402 0.7227 0.000 0.000 0.032 0.896 0.012 0.060
#> GSM153254 6 0.7864 0.1083 0.008 0.180 0.220 0.232 0.004 0.356
#> GSM153255 4 0.2493 0.7244 0.076 0.000 0.000 0.884 0.004 0.036
#> GSM153256 1 0.5164 0.4358 0.612 0.000 0.004 0.312 0.036 0.036
#> GSM153257 4 0.3121 0.7269 0.044 0.000 0.012 0.868 0.028 0.048
#> GSM153258 1 0.3369 0.6336 0.852 0.000 0.016 0.024 0.040 0.068
#> GSM153259 1 0.5543 0.4975 0.588 0.000 0.000 0.012 0.256 0.144
#> GSM153260 3 0.6599 0.4601 0.264 0.016 0.536 0.000 0.064 0.120
#> GSM153261 3 0.5971 0.3525 0.032 0.012 0.528 0.000 0.080 0.348
#> GSM153262 4 0.4229 0.7032 0.032 0.000 0.016 0.792 0.056 0.104
#> GSM153263 1 0.4762 0.6208 0.740 0.000 0.000 0.076 0.112 0.072
#> GSM153264 1 0.2485 0.6314 0.884 0.000 0.084 0.000 0.024 0.008
#> GSM153265 4 0.3720 0.6778 0.000 0.000 0.052 0.788 0.008 0.152
#> GSM153266 1 0.2880 0.6469 0.872 0.000 0.056 0.000 0.048 0.024
#> GSM153267 1 0.5334 0.4266 0.616 0.004 0.020 0.304 0.016 0.040
#> GSM153268 4 0.3822 0.6671 0.000 0.000 0.060 0.788 0.012 0.140
#> GSM153269 1 0.4149 0.5864 0.764 0.000 0.012 0.172 0.012 0.040
#> GSM153270 4 0.7461 0.2450 0.272 0.000 0.096 0.472 0.088 0.072
#> GSM153271 1 0.4896 0.5835 0.704 0.000 0.016 0.204 0.056 0.020
#> GSM153272 4 0.3578 0.6749 0.160 0.000 0.000 0.796 0.016 0.028
#> GSM153273 1 0.5326 0.6094 0.672 0.000 0.004 0.052 0.200 0.072
#> GSM153274 1 0.6938 0.3041 0.480 0.004 0.124 0.316 0.028 0.048
#> GSM153275 4 0.5698 0.1874 0.404 0.000 0.024 0.504 0.016 0.052
#> GSM153276 1 0.6702 0.0432 0.424 0.004 0.076 0.400 0.008 0.088
#> GSM153277 4 0.4869 0.5521 0.032 0.000 0.012 0.628 0.012 0.316
#> GSM153278 3 0.5892 0.2981 0.376 0.008 0.496 0.000 0.016 0.104
#> GSM153279 4 0.3798 0.6957 0.000 0.004 0.072 0.820 0.044 0.060
#> GSM153280 4 0.3393 0.6813 0.000 0.000 0.020 0.784 0.004 0.192
#> GSM153281 4 0.1655 0.7373 0.008 0.000 0.008 0.932 0.000 0.052
#> GSM153282 4 0.2182 0.7233 0.000 0.000 0.020 0.900 0.004 0.076
#> GSM153283 1 0.2295 0.6484 0.908 0.000 0.016 0.004 0.048 0.024
#> GSM153284 4 0.4610 0.6383 0.192 0.004 0.008 0.724 0.008 0.064
#> GSM153285 4 0.2339 0.7284 0.000 0.000 0.020 0.896 0.012 0.072
#> GSM153286 4 0.4933 0.5202 0.276 0.000 0.000 0.636 0.008 0.080
#> GSM153287 4 0.1570 0.7329 0.004 0.000 0.008 0.944 0.016 0.028
#> GSM153288 4 0.4436 0.5894 0.236 0.000 0.000 0.704 0.020 0.040
#> GSM153289 1 0.7268 -0.0263 0.360 0.008 0.000 0.208 0.080 0.344
#> GSM153290 4 0.2700 0.7092 0.000 0.000 0.004 0.836 0.004 0.156
#> GSM153291 4 0.4029 0.6872 0.068 0.000 0.000 0.784 0.024 0.124
#> GSM153292 4 0.1511 0.7331 0.000 0.000 0.004 0.940 0.012 0.044
#> GSM153293 4 0.6102 0.1495 0.368 0.000 0.000 0.488 0.056 0.088
#> GSM153294 5 0.7443 0.1009 0.248 0.036 0.008 0.136 0.488 0.084
#> GSM153295 1 0.6509 0.4970 0.596 0.000 0.028 0.188 0.084 0.104
#> GSM153054 1 0.6996 0.2025 0.372 0.000 0.224 0.004 0.344 0.056
#> GSM153055 1 0.7975 0.3154 0.452 0.104 0.100 0.256 0.016 0.072
#> GSM153056 3 0.5912 0.4799 0.284 0.000 0.580 0.028 0.016 0.092
#> GSM153057 3 0.6736 0.5057 0.180 0.036 0.596 0.020 0.040 0.128
#> GSM153058 3 0.4064 0.5428 0.040 0.016 0.792 0.008 0.008 0.136
#> GSM153059 3 0.6136 0.4506 0.072 0.072 0.580 0.000 0.012 0.264
#> GSM153060 3 0.2702 0.5489 0.008 0.004 0.892 0.024 0.020 0.052
#> GSM153061 3 0.4094 0.5387 0.036 0.000 0.788 0.000 0.076 0.100
#> GSM153062 3 0.2518 0.5354 0.000 0.012 0.880 0.000 0.016 0.092
#> GSM153063 3 0.5788 0.3955 0.000 0.008 0.644 0.188 0.064 0.096
#> GSM153064 1 0.5419 0.6018 0.668 0.000 0.000 0.056 0.168 0.108
#> GSM153065 3 0.6319 0.5104 0.160 0.016 0.592 0.000 0.052 0.180
#> GSM153066 3 0.6600 0.3691 0.024 0.048 0.560 0.000 0.176 0.192
#> GSM153067 4 0.3029 0.7230 0.028 0.000 0.004 0.868 0.060 0.040
#> GSM153068 3 0.2345 0.5656 0.036 0.000 0.904 0.000 0.024 0.036
#> GSM153069 4 0.1320 0.7358 0.016 0.000 0.000 0.948 0.000 0.036
#> GSM153070 1 0.4781 0.6190 0.776 0.008 0.072 0.032 0.048 0.064
#> GSM153071 3 0.8121 0.2641 0.148 0.008 0.408 0.064 0.264 0.108
#> GSM153072 1 0.7267 0.1671 0.388 0.000 0.264 0.012 0.272 0.064
#> GSM153073 1 0.3954 0.6403 0.808 0.000 0.076 0.016 0.084 0.016
#> GSM153074 4 0.2350 0.7273 0.076 0.000 0.000 0.888 0.000 0.036
#> GSM153075 4 0.7397 0.2130 0.116 0.096 0.008 0.448 0.024 0.308
#> GSM153076 1 0.2929 0.6503 0.868 0.000 0.008 0.040 0.076 0.008
#> GSM153077 1 0.3939 0.5944 0.796 0.008 0.132 0.000 0.040 0.024
#> GSM153078 1 0.5745 0.3667 0.612 0.008 0.272 0.008 0.040 0.060
#> GSM153079 1 0.6658 0.1295 0.432 0.032 0.024 0.000 0.128 0.384
#> GSM153080 3 0.6376 0.3638 0.000 0.000 0.564 0.172 0.084 0.180
#> GSM153081 1 0.4809 0.5683 0.720 0.000 0.048 0.000 0.068 0.164
#> GSM153082 5 0.8463 0.2965 0.176 0.204 0.060 0.040 0.424 0.096
#> GSM153083 1 0.5586 0.5680 0.640 0.008 0.060 0.000 0.232 0.060
#> GSM153084 2 0.8485 -0.1139 0.060 0.284 0.212 0.000 0.248 0.196
#> GSM153085 3 0.7696 0.1115 0.312 0.016 0.332 0.008 0.256 0.076
#> GSM153086 1 0.5826 0.5438 0.624 0.000 0.116 0.000 0.192 0.068
#> GSM153087 4 0.6248 0.5610 0.148 0.000 0.096 0.636 0.032 0.088
#> GSM153088 1 0.2852 0.6367 0.880 0.000 0.064 0.016 0.020 0.020
#> GSM153089 3 0.6856 0.2713 0.000 0.052 0.500 0.076 0.060 0.312
#> GSM153090 1 0.3786 0.6378 0.832 0.000 0.056 0.052 0.032 0.028
#> GSM153091 1 0.5380 0.5853 0.680 0.088 0.000 0.016 0.184 0.032
#> GSM153092 1 0.5453 0.5853 0.724 0.040 0.012 0.068 0.040 0.116
#> GSM153093 4 0.2288 0.7307 0.072 0.000 0.000 0.896 0.004 0.028
#> GSM153094 1 0.5670 0.3586 0.568 0.324 0.004 0.000 0.052 0.052
#> GSM153095 5 0.7279 0.2107 0.076 0.016 0.172 0.032 0.540 0.164
#> GSM153096 1 0.3878 0.6371 0.792 0.000 0.000 0.020 0.128 0.060
#> GSM153097 1 0.4348 0.6025 0.732 0.000 0.028 0.000 0.200 0.040
#> GSM153098 5 0.7275 0.1736 0.128 0.036 0.004 0.256 0.496 0.080
#> GSM153099 1 0.5854 0.1324 0.484 0.000 0.024 0.416 0.024 0.052
#> GSM153100 1 0.6178 0.4652 0.592 0.000 0.000 0.176 0.084 0.148
#> GSM153101 5 0.7766 -0.0135 0.236 0.000 0.232 0.008 0.348 0.176
#> GSM153102 6 0.5518 0.3753 0.048 0.052 0.060 0.020 0.088 0.732
#> GSM153103 1 0.6069 0.5276 0.608 0.000 0.136 0.000 0.168 0.088
#> GSM153104 4 0.2535 0.7253 0.000 0.000 0.012 0.888 0.036 0.064
#> GSM153106 6 0.7518 0.3243 0.204 0.092 0.000 0.084 0.116 0.504
#> GSM153107 6 0.7269 0.2216 0.268 0.036 0.008 0.052 0.152 0.484
#> GSM153108 4 0.6340 0.3933 0.072 0.012 0.004 0.540 0.064 0.308
#> GSM153109 6 0.6653 0.2548 0.152 0.176 0.004 0.000 0.116 0.552
#> GSM153110 1 0.4272 0.6271 0.772 0.008 0.016 0.000 0.124 0.080
#> GSM153111 1 0.5059 0.4707 0.592 0.004 0.020 0.000 0.344 0.040
#> GSM153112 1 0.7103 0.3087 0.444 0.028 0.000 0.128 0.332 0.068
#> GSM153113 2 0.6741 -0.0311 0.020 0.424 0.016 0.012 0.384 0.144
#> GSM153114 6 0.7521 0.1488 0.160 0.056 0.004 0.304 0.048 0.428
#> GSM187532 6 0.7180 0.1104 0.000 0.280 0.272 0.000 0.084 0.364
#> GSM187533 6 0.6358 -0.1118 0.004 0.400 0.020 0.000 0.176 0.400
#> GSM187534 2 0.5701 0.2548 0.004 0.544 0.000 0.000 0.256 0.196
#> GSM187535 5 0.7157 0.0726 0.056 0.272 0.000 0.008 0.368 0.296
#> GSM152906 5 0.4847 0.3746 0.032 0.360 0.000 0.000 0.588 0.020
#> GSM152907 2 0.4079 0.2129 0.000 0.608 0.000 0.004 0.380 0.008
#> GSM152908 2 0.0717 0.6961 0.000 0.976 0.000 0.000 0.016 0.008
#> GSM152909 2 0.5847 0.2993 0.000 0.580 0.128 0.000 0.036 0.256
#> GSM152910 2 0.2255 0.6598 0.000 0.908 0.024 0.000 0.024 0.044
#> GSM152911 2 0.1152 0.6918 0.000 0.952 0.000 0.000 0.044 0.004
#> GSM152912 2 0.0692 0.6911 0.000 0.976 0.000 0.000 0.004 0.020
#> GSM152913 2 0.3823 0.6495 0.000 0.808 0.052 0.000 0.100 0.040
#> GSM152914 2 0.2473 0.6430 0.000 0.856 0.000 0.000 0.136 0.008
#> GSM152915 2 0.1643 0.6843 0.000 0.924 0.000 0.000 0.068 0.008
#> GSM152916 5 0.5057 0.2592 0.000 0.412 0.016 0.000 0.528 0.044
#> GSM152917 2 0.2805 0.5975 0.000 0.812 0.000 0.000 0.184 0.004
#> GSM152918 2 0.3136 0.5444 0.000 0.768 0.000 0.000 0.228 0.004
#> GSM152919 2 0.3357 0.5464 0.004 0.764 0.000 0.000 0.224 0.008
#> GSM152920 2 0.0717 0.6927 0.000 0.976 0.000 0.000 0.008 0.016
#> GSM152921 2 0.0692 0.6957 0.000 0.976 0.000 0.000 0.020 0.004
#> GSM152922 2 0.1265 0.6775 0.000 0.948 0.008 0.000 0.000 0.044
#> GSM152923 5 0.4261 0.2982 0.008 0.416 0.000 0.000 0.568 0.008
#> GSM152924 5 0.4634 0.4456 0.004 0.244 0.012 0.000 0.688 0.052
#> GSM152925 5 0.4459 0.4287 0.000 0.276 0.024 0.000 0.676 0.024
#> GSM152926 5 0.4226 0.4162 0.016 0.328 0.000 0.004 0.648 0.004
#> GSM152927 5 0.5577 0.4088 0.004 0.272 0.052 0.000 0.612 0.060
#> GSM152928 5 0.4835 0.4452 0.020 0.096 0.060 0.000 0.756 0.068
#> GSM152929 5 0.4174 0.3931 0.016 0.352 0.000 0.000 0.628 0.004
#> GSM152930 5 0.4471 0.2369 0.016 0.444 0.000 0.000 0.532 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 tissue(p) k
#> SD:NMF 160 2.84e-17 2
#> SD:NMF 152 1.20e-23 3
#> SD:NMF 130 7.88e-25 4
#> SD:NMF 104 4.81e-20 5
#> SD:NMF 82 4.72e-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 12013 rows and 164 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 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 0.694 0.908 0.953 0.0910 0.976 0.976
#> 3 3 0.504 0.796 0.888 1.1371 1.000 1.000
#> 4 4 0.434 0.804 0.863 0.6884 0.709 0.702
#> 5 5 0.408 0.745 0.878 0.2463 0.990 0.985
#> 6 6 0.512 0.692 0.864 0.0995 0.899 0.852
suggest_best_k() suggests the best \(k\) based on these statistics. The rules are as follows:
suggest_best_k(res)
#> [1] 6
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
#> GSM152839 1 0.0672 0.943 0.992 0.008
#> GSM152840 1 0.3274 0.919 0.940 0.060
#> GSM152841 1 0.0000 0.944 1.000 0.000
#> GSM152842 1 0.6247 0.781 0.844 0.156
#> GSM152843 1 0.3274 0.913 0.940 0.060
#> GSM152844 1 0.4690 0.883 0.900 0.100
#> GSM152845 1 0.4939 0.886 0.892 0.108
#> GSM152846 1 0.3879 0.901 0.924 0.076
#> GSM152847 1 0.3431 0.910 0.936 0.064
#> GSM152848 1 0.0376 0.944 0.996 0.004
#> GSM152849 1 0.3114 0.922 0.944 0.056
#> GSM152850 1 0.1843 0.939 0.972 0.028
#> GSM152851 1 0.0938 0.943 0.988 0.012
#> GSM152852 1 0.3584 0.914 0.932 0.068
#> GSM152853 1 0.4161 0.897 0.916 0.084
#> GSM152854 1 0.3431 0.918 0.936 0.064
#> GSM152855 1 0.0000 0.944 1.000 0.000
#> GSM153238 1 0.4298 0.896 0.912 0.088
#> GSM153239 1 0.3584 0.910 0.932 0.068
#> GSM153240 1 0.0376 0.944 0.996 0.004
#> GSM153241 1 0.1843 0.934 0.972 0.028
#> GSM153242 1 0.4562 0.892 0.904 0.096
#> GSM153243 1 0.1184 0.943 0.984 0.016
#> GSM153244 1 0.0376 0.944 0.996 0.004
#> GSM153245 1 0.4690 0.875 0.900 0.100
#> GSM153246 2 0.9522 0.583 0.372 0.628
#> GSM153247 1 0.4161 0.898 0.916 0.084
#> GSM153248 1 0.0000 0.944 1.000 0.000
#> GSM153249 1 0.0672 0.943 0.992 0.008
#> GSM153250 1 0.0000 0.944 1.000 0.000
#> GSM153251 1 0.3733 0.915 0.928 0.072
#> GSM153252 1 0.0000 0.944 1.000 0.000
#> GSM153253 1 0.0376 0.944 0.996 0.004
#> GSM153254 1 0.0376 0.944 0.996 0.004
#> GSM153255 1 0.0000 0.944 1.000 0.000
#> GSM153256 1 0.0000 0.944 1.000 0.000
#> GSM153257 1 0.0000 0.944 1.000 0.000
#> GSM153258 1 0.0000 0.944 1.000 0.000
#> GSM153259 1 0.0376 0.944 0.996 0.004
#> GSM153260 1 0.3879 0.910 0.924 0.076
#> GSM153261 1 0.2043 0.934 0.968 0.032
#> GSM153262 1 0.0376 0.944 0.996 0.004
#> GSM153263 1 0.0000 0.944 1.000 0.000
#> GSM153264 1 0.0376 0.944 0.996 0.004
#> GSM153265 1 0.0000 0.944 1.000 0.000
#> GSM153266 1 0.0000 0.944 1.000 0.000
#> GSM153267 1 0.0000 0.944 1.000 0.000
#> GSM153268 1 0.0672 0.944 0.992 0.008
#> GSM153269 1 0.0000 0.944 1.000 0.000
#> GSM153270 1 0.0000 0.944 1.000 0.000
#> GSM153271 1 0.0000 0.944 1.000 0.000
#> GSM153272 1 0.0000 0.944 1.000 0.000
#> GSM153273 1 0.0376 0.944 0.996 0.004
#> GSM153274 1 0.0672 0.943 0.992 0.008
#> GSM153275 1 0.0376 0.944 0.996 0.004
#> GSM153276 1 0.0672 0.944 0.992 0.008
#> GSM153277 1 0.0376 0.944 0.996 0.004
#> GSM153278 1 0.2423 0.927 0.960 0.040
#> GSM153279 1 0.0376 0.944 0.996 0.004
#> GSM153280 1 0.0000 0.944 1.000 0.000
#> GSM153281 1 0.0376 0.944 0.996 0.004
#> GSM153282 1 0.0376 0.944 0.996 0.004
#> GSM153283 1 0.0000 0.944 1.000 0.000
#> GSM153284 1 0.0376 0.944 0.996 0.004
#> GSM153285 1 0.0376 0.944 0.996 0.004
#> GSM153286 1 0.0000 0.944 1.000 0.000
#> GSM153287 1 0.0376 0.944 0.996 0.004
#> GSM153288 1 0.0000 0.944 1.000 0.000
#> GSM153289 1 0.0000 0.944 1.000 0.000
#> GSM153290 1 0.0000 0.944 1.000 0.000
#> GSM153291 1 0.0000 0.944 1.000 0.000
#> GSM153292 1 0.0376 0.944 0.996 0.004
#> GSM153293 1 0.0376 0.944 0.996 0.004
#> GSM153294 1 0.0376 0.944 0.996 0.004
#> GSM153295 1 0.2778 0.920 0.952 0.048
#> GSM153054 1 0.2423 0.931 0.960 0.040
#> GSM153055 1 0.0000 0.944 1.000 0.000
#> GSM153056 1 0.2423 0.928 0.960 0.040
#> GSM153057 1 0.1184 0.943 0.984 0.016
#> GSM153058 1 0.5408 0.861 0.876 0.124
#> GSM153059 1 0.1633 0.939 0.976 0.024
#> GSM153060 1 0.9209 0.287 0.664 0.336
#> GSM153061 1 0.8555 0.500 0.720 0.280
#> GSM153062 2 0.5178 0.703 0.116 0.884
#> GSM153063 1 0.4022 0.896 0.920 0.080
#> GSM153064 1 0.0376 0.944 0.996 0.004
#> GSM153065 1 0.4022 0.906 0.920 0.080
#> GSM153066 1 0.4562 0.891 0.904 0.096
#> GSM153067 1 0.0376 0.944 0.996 0.004
#> GSM153068 1 0.6247 0.799 0.844 0.156
#> GSM153069 1 0.0376 0.944 0.996 0.004
#> GSM153070 1 0.0000 0.944 1.000 0.000
#> GSM153071 1 0.0376 0.944 0.996 0.004
#> GSM153072 1 0.0672 0.943 0.992 0.008
#> GSM153073 1 0.0000 0.944 1.000 0.000
#> GSM153074 1 0.0376 0.944 0.996 0.004
#> GSM153075 1 0.0000 0.944 1.000 0.000
#> GSM153076 1 0.0000 0.944 1.000 0.000
#> GSM153077 1 0.0000 0.944 1.000 0.000
#> GSM153078 1 0.0672 0.944 0.992 0.008
#> GSM153079 1 0.0000 0.944 1.000 0.000
#> GSM153080 1 0.1414 0.941 0.980 0.020
#> GSM153081 1 0.0000 0.944 1.000 0.000
#> GSM153082 1 0.0376 0.944 0.996 0.004
#> GSM153083 1 0.0000 0.944 1.000 0.000
#> GSM153084 1 0.2236 0.934 0.964 0.036
#> GSM153085 1 0.0672 0.944 0.992 0.008
#> GSM153086 1 0.0672 0.943 0.992 0.008
#> GSM153087 1 0.0376 0.944 0.996 0.004
#> GSM153088 1 0.0000 0.944 1.000 0.000
#> GSM153089 1 0.3584 0.917 0.932 0.068
#> GSM153090 1 0.0000 0.944 1.000 0.000
#> GSM153091 1 0.0376 0.944 0.996 0.004
#> GSM153092 1 0.0000 0.944 1.000 0.000
#> GSM153093 1 0.0376 0.944 0.996 0.004
#> GSM153094 1 0.0376 0.944 0.996 0.004
#> GSM153095 1 0.0938 0.943 0.988 0.012
#> GSM153096 1 0.0376 0.944 0.996 0.004
#> GSM153097 1 0.0000 0.944 1.000 0.000
#> GSM153098 1 0.0672 0.943 0.992 0.008
#> GSM153099 1 0.0000 0.944 1.000 0.000
#> GSM153100 1 0.0000 0.944 1.000 0.000
#> GSM153101 1 0.1633 0.939 0.976 0.024
#> GSM153102 1 0.1184 0.940 0.984 0.016
#> GSM153103 1 0.0672 0.943 0.992 0.008
#> GSM153104 1 0.0672 0.943 0.992 0.008
#> GSM153106 1 0.0000 0.944 1.000 0.000
#> GSM153107 1 0.0000 0.944 1.000 0.000
#> GSM153108 1 0.0000 0.944 1.000 0.000
#> GSM153109 1 0.1184 0.940 0.984 0.016
#> GSM153110 1 0.0000 0.944 1.000 0.000
#> GSM153111 1 0.0000 0.944 1.000 0.000
#> GSM153112 1 0.0376 0.944 0.996 0.004
#> GSM153113 1 0.1414 0.939 0.980 0.020
#> GSM153114 1 0.0000 0.944 1.000 0.000
#> GSM187532 1 0.5178 0.868 0.884 0.116
#> GSM187533 1 0.5737 0.847 0.864 0.136
#> GSM187534 1 0.5737 0.847 0.864 0.136
#> GSM187535 1 0.1184 0.940 0.984 0.016
#> GSM152906 1 0.5946 0.836 0.856 0.144
#> GSM152907 1 0.5946 0.836 0.856 0.144
#> GSM152908 1 0.5842 0.838 0.860 0.140
#> GSM152909 1 0.5946 0.837 0.856 0.144
#> GSM152910 1 0.5946 0.834 0.856 0.144
#> GSM152911 1 0.5842 0.838 0.860 0.140
#> GSM152912 1 0.5842 0.838 0.860 0.140
#> GSM152913 1 0.6048 0.829 0.852 0.148
#> GSM152914 1 0.5842 0.838 0.860 0.140
#> GSM152915 1 0.5842 0.838 0.860 0.140
#> GSM152916 1 0.5842 0.838 0.860 0.140
#> GSM152917 1 0.5842 0.838 0.860 0.140
#> GSM152918 1 0.5842 0.838 0.860 0.140
#> GSM152919 1 0.5737 0.843 0.864 0.136
#> GSM152920 1 0.5842 0.838 0.860 0.140
#> GSM152921 1 0.5842 0.838 0.860 0.140
#> GSM152922 1 0.5946 0.834 0.856 0.144
#> GSM152923 1 0.5946 0.836 0.856 0.144
#> GSM152924 1 0.5842 0.838 0.860 0.140
#> GSM152925 1 0.5842 0.838 0.860 0.140
#> GSM152926 1 0.5946 0.836 0.856 0.144
#> GSM152927 1 0.5629 0.847 0.868 0.132
#> GSM152928 1 0.4562 0.885 0.904 0.096
#> GSM152929 1 0.5946 0.836 0.856 0.144
#> GSM152930 1 0.5946 0.836 0.856 0.144
cbind(get_classes(res, k = 3), get_membership(res, k = 3))
#> class entropy silhouette p1 p2 p3
#> GSM152839 1 0.1031 0.8839 0.976 0.024 0.000
#> GSM152840 1 0.4915 0.8087 0.832 0.132 0.036
#> GSM152841 1 0.0237 0.8848 0.996 0.000 0.004
#> GSM152842 1 0.7557 0.4721 0.656 0.264 0.080
#> GSM152843 1 0.3337 0.8508 0.908 0.060 0.032
#> GSM152844 1 0.5852 0.7690 0.788 0.152 0.060
#> GSM152845 1 0.6079 0.7449 0.748 0.216 0.036
#> GSM152846 1 0.5581 0.7788 0.792 0.168 0.040
#> GSM152847 1 0.4618 0.8015 0.840 0.136 0.024
#> GSM152848 1 0.0747 0.8839 0.984 0.016 0.000
#> GSM152849 1 0.3091 0.8580 0.912 0.072 0.016
#> GSM152850 1 0.2173 0.8747 0.944 0.048 0.008
#> GSM152851 1 0.1453 0.8824 0.968 0.024 0.008
#> GSM152852 1 0.4575 0.8079 0.828 0.160 0.012
#> GSM152853 1 0.5454 0.7848 0.804 0.152 0.044
#> GSM152854 1 0.4805 0.7983 0.812 0.176 0.012
#> GSM152855 1 0.0592 0.8851 0.988 0.012 0.000
#> GSM153238 1 0.5519 0.7994 0.812 0.120 0.068
#> GSM153239 1 0.5222 0.7963 0.816 0.144 0.040
#> GSM153240 1 0.0237 0.8844 0.996 0.004 0.000
#> GSM153241 1 0.2492 0.8672 0.936 0.048 0.016
#> GSM153242 1 0.6119 0.7569 0.772 0.164 0.064
#> GSM153243 1 0.1453 0.8828 0.968 0.024 0.008
#> GSM153244 1 0.0747 0.8857 0.984 0.016 0.000
#> GSM153245 1 0.6383 0.7326 0.768 0.128 0.104
#> GSM153246 2 0.8549 0.0000 0.100 0.516 0.384
#> GSM153247 1 0.5416 0.7989 0.820 0.100 0.080
#> GSM153248 1 0.0424 0.8843 0.992 0.008 0.000
#> GSM153249 1 0.0592 0.8855 0.988 0.012 0.000
#> GSM153250 1 0.0424 0.8848 0.992 0.008 0.000
#> GSM153251 1 0.5173 0.8012 0.816 0.148 0.036
#> GSM153252 1 0.0237 0.8848 0.996 0.000 0.004
#> GSM153253 1 0.0424 0.8842 0.992 0.008 0.000
#> GSM153254 1 0.0592 0.8862 0.988 0.012 0.000
#> GSM153255 1 0.0000 0.8839 1.000 0.000 0.000
#> GSM153256 1 0.0424 0.8848 0.992 0.008 0.000
#> GSM153257 1 0.0237 0.8839 0.996 0.004 0.000
#> GSM153258 1 0.0424 0.8847 0.992 0.008 0.000
#> GSM153259 1 0.0747 0.8849 0.984 0.016 0.000
#> GSM153260 1 0.4748 0.8085 0.832 0.144 0.024
#> GSM153261 1 0.3083 0.8650 0.916 0.060 0.024
#> GSM153262 1 0.0424 0.8839 0.992 0.008 0.000
#> GSM153263 1 0.0237 0.8846 0.996 0.004 0.000
#> GSM153264 1 0.0424 0.8842 0.992 0.008 0.000
#> GSM153265 1 0.0000 0.8839 1.000 0.000 0.000
#> GSM153266 1 0.0237 0.8839 0.996 0.004 0.000
#> GSM153267 1 0.0237 0.8839 0.996 0.004 0.000
#> GSM153268 1 0.1399 0.8821 0.968 0.028 0.004
#> GSM153269 1 0.0424 0.8848 0.992 0.008 0.000
#> GSM153270 1 0.0424 0.8848 0.992 0.008 0.000
#> GSM153271 1 0.0424 0.8848 0.992 0.008 0.000
#> GSM153272 1 0.0000 0.8839 1.000 0.000 0.000
#> GSM153273 1 0.0592 0.8848 0.988 0.012 0.000
#> GSM153274 1 0.0892 0.8853 0.980 0.020 0.000
#> GSM153275 1 0.0592 0.8851 0.988 0.012 0.000
#> GSM153276 1 0.0424 0.8853 0.992 0.008 0.000
#> GSM153277 1 0.0424 0.8852 0.992 0.008 0.000
#> GSM153278 1 0.2663 0.8630 0.932 0.044 0.024
#> GSM153279 1 0.0592 0.8857 0.988 0.012 0.000
#> GSM153280 1 0.0237 0.8846 0.996 0.004 0.000
#> GSM153281 1 0.0475 0.8849 0.992 0.004 0.004
#> GSM153282 1 0.0475 0.8849 0.992 0.004 0.004
#> GSM153283 1 0.0592 0.8845 0.988 0.012 0.000
#> GSM153284 1 0.0424 0.8852 0.992 0.008 0.000
#> GSM153285 1 0.0237 0.8844 0.996 0.004 0.000
#> GSM153286 1 0.0237 0.8846 0.996 0.004 0.000
#> GSM153287 1 0.0661 0.8852 0.988 0.008 0.004
#> GSM153288 1 0.0000 0.8839 1.000 0.000 0.000
#> GSM153289 1 0.0592 0.8851 0.988 0.012 0.000
#> GSM153290 1 0.0237 0.8846 0.996 0.004 0.000
#> GSM153291 1 0.0424 0.8848 0.992 0.008 0.000
#> GSM153292 1 0.0661 0.8852 0.988 0.008 0.004
#> GSM153293 1 0.0592 0.8855 0.988 0.012 0.000
#> GSM153294 1 0.0747 0.8849 0.984 0.016 0.000
#> GSM153295 1 0.3415 0.8430 0.900 0.080 0.020
#> GSM153054 1 0.3009 0.8636 0.920 0.052 0.028
#> GSM153055 1 0.0000 0.8839 1.000 0.000 0.000
#> GSM153056 1 0.2434 0.8655 0.940 0.036 0.024
#> GSM153057 1 0.1399 0.8835 0.968 0.028 0.004
#> GSM153058 1 0.6530 0.7462 0.760 0.120 0.120
#> GSM153059 1 0.2116 0.8766 0.948 0.040 0.012
#> GSM153060 1 0.9646 -0.1548 0.468 0.272 0.260
#> GSM153061 1 0.9386 0.0596 0.512 0.244 0.244
#> GSM153062 3 0.0983 0.0000 0.004 0.016 0.980
#> GSM153063 1 0.5662 0.7793 0.808 0.100 0.092
#> GSM153064 1 0.0747 0.8849 0.984 0.016 0.000
#> GSM153065 1 0.5634 0.7822 0.800 0.144 0.056
#> GSM153066 1 0.5330 0.7974 0.812 0.144 0.044
#> GSM153067 1 0.0237 0.8848 0.996 0.004 0.000
#> GSM153068 1 0.7298 0.6430 0.700 0.200 0.100
#> GSM153069 1 0.0237 0.8844 0.996 0.004 0.000
#> GSM153070 1 0.0237 0.8839 0.996 0.004 0.000
#> GSM153071 1 0.1129 0.8855 0.976 0.020 0.004
#> GSM153072 1 0.1315 0.8838 0.972 0.020 0.008
#> GSM153073 1 0.0424 0.8848 0.992 0.008 0.000
#> GSM153074 1 0.0424 0.8848 0.992 0.008 0.000
#> GSM153075 1 0.0424 0.8850 0.992 0.008 0.000
#> GSM153076 1 0.0424 0.8847 0.992 0.008 0.000
#> GSM153077 1 0.0424 0.8853 0.992 0.008 0.000
#> GSM153078 1 0.1031 0.8847 0.976 0.024 0.000
#> GSM153079 1 0.0592 0.8851 0.988 0.012 0.000
#> GSM153080 1 0.1950 0.8796 0.952 0.040 0.008
#> GSM153081 1 0.0592 0.8851 0.988 0.012 0.000
#> GSM153082 1 0.0592 0.8860 0.988 0.012 0.000
#> GSM153083 1 0.0747 0.8852 0.984 0.016 0.000
#> GSM153084 1 0.3370 0.8585 0.904 0.072 0.024
#> GSM153085 1 0.1182 0.8848 0.976 0.012 0.012
#> GSM153086 1 0.1031 0.8842 0.976 0.024 0.000
#> GSM153087 1 0.0424 0.8839 0.992 0.008 0.000
#> GSM153088 1 0.0424 0.8848 0.992 0.008 0.000
#> GSM153089 1 0.5058 0.8092 0.820 0.148 0.032
#> GSM153090 1 0.0424 0.8848 0.992 0.008 0.000
#> GSM153091 1 0.0747 0.8849 0.984 0.016 0.000
#> GSM153092 1 0.0237 0.8846 0.996 0.004 0.000
#> GSM153093 1 0.0424 0.8853 0.992 0.008 0.000
#> GSM153094 1 0.0747 0.8856 0.984 0.016 0.000
#> GSM153095 1 0.1267 0.8841 0.972 0.024 0.004
#> GSM153096 1 0.0592 0.8848 0.988 0.012 0.000
#> GSM153097 1 0.0592 0.8851 0.988 0.012 0.000
#> GSM153098 1 0.0592 0.8856 0.988 0.012 0.000
#> GSM153099 1 0.0424 0.8848 0.992 0.008 0.000
#> GSM153100 1 0.0424 0.8843 0.992 0.008 0.000
#> GSM153101 1 0.2339 0.8739 0.940 0.048 0.012
#> GSM153102 1 0.1289 0.8820 0.968 0.032 0.000
#> GSM153103 1 0.0747 0.8853 0.984 0.016 0.000
#> GSM153104 1 0.0592 0.8834 0.988 0.012 0.000
#> GSM153106 1 0.0592 0.8851 0.988 0.012 0.000
#> GSM153107 1 0.0592 0.8851 0.988 0.012 0.000
#> GSM153108 1 0.0237 0.8846 0.996 0.004 0.000
#> GSM153109 1 0.1289 0.8816 0.968 0.032 0.000
#> GSM153110 1 0.0424 0.8843 0.992 0.008 0.000
#> GSM153111 1 0.0747 0.8852 0.984 0.016 0.000
#> GSM153112 1 0.0747 0.8849 0.984 0.016 0.000
#> GSM153113 1 0.2066 0.8712 0.940 0.060 0.000
#> GSM153114 1 0.0592 0.8851 0.988 0.012 0.000
#> GSM187532 1 0.5873 0.6602 0.684 0.312 0.004
#> GSM187533 1 0.5905 0.6182 0.648 0.352 0.000
#> GSM187534 1 0.5905 0.6182 0.648 0.352 0.000
#> GSM187535 1 0.1411 0.8815 0.964 0.036 0.000
#> GSM152906 1 0.6008 0.5911 0.628 0.372 0.000
#> GSM152907 1 0.5988 0.5969 0.632 0.368 0.000
#> GSM152908 1 0.5988 0.5954 0.632 0.368 0.000
#> GSM152909 1 0.5926 0.6120 0.644 0.356 0.000
#> GSM152910 1 0.6008 0.5897 0.628 0.372 0.000
#> GSM152911 1 0.5988 0.5954 0.632 0.368 0.000
#> GSM152912 1 0.5988 0.5954 0.632 0.368 0.000
#> GSM152913 1 0.6228 0.5836 0.624 0.372 0.004
#> GSM152914 1 0.5988 0.5954 0.632 0.368 0.000
#> GSM152915 1 0.5988 0.5954 0.632 0.368 0.000
#> GSM152916 1 0.5988 0.5954 0.632 0.368 0.000
#> GSM152917 1 0.5988 0.5954 0.632 0.368 0.000
#> GSM152918 1 0.5988 0.5954 0.632 0.368 0.000
#> GSM152919 1 0.5968 0.6008 0.636 0.364 0.000
#> GSM152920 1 0.5988 0.5954 0.632 0.368 0.000
#> GSM152921 1 0.5988 0.5954 0.632 0.368 0.000
#> GSM152922 1 0.6008 0.5897 0.628 0.372 0.000
#> GSM152923 1 0.6008 0.5911 0.628 0.372 0.000
#> GSM152924 1 0.5988 0.5954 0.632 0.368 0.000
#> GSM152925 1 0.5968 0.6008 0.636 0.364 0.000
#> GSM152926 1 0.6008 0.5911 0.628 0.372 0.000
#> GSM152927 1 0.5948 0.6060 0.640 0.360 0.000
#> GSM152928 1 0.6096 0.6821 0.704 0.280 0.016
#> GSM152929 1 0.6008 0.5911 0.628 0.372 0.000
#> GSM152930 1 0.6008 0.5911 0.628 0.372 0.000
cbind(get_classes(res, k = 4), get_membership(res, k = 4))
#> class entropy silhouette p1 p2 p3 p4
#> GSM152839 1 0.1406 0.8923 0.960 0.024 0.016 0.000
#> GSM152840 1 0.6162 0.5622 0.708 0.192 0.068 0.032
#> GSM152841 1 0.0376 0.8958 0.992 0.004 0.004 0.000
#> GSM152842 1 0.6788 -0.0527 0.520 0.048 0.408 0.024
#> GSM152843 1 0.3494 0.8249 0.876 0.028 0.080 0.016
#> GSM152844 1 0.7002 0.4520 0.652 0.208 0.092 0.048
#> GSM152845 1 0.7363 -0.0790 0.548 0.336 0.076 0.040
#> GSM152846 1 0.6948 0.4086 0.644 0.224 0.096 0.036
#> GSM152847 1 0.5451 0.6480 0.740 0.084 0.172 0.004
#> GSM152848 1 0.1297 0.8935 0.964 0.016 0.020 0.000
#> GSM152849 1 0.3769 0.8141 0.864 0.052 0.072 0.012
#> GSM152850 1 0.2814 0.8535 0.908 0.032 0.052 0.008
#> GSM152851 1 0.1697 0.8849 0.952 0.028 0.016 0.004
#> GSM152852 1 0.5775 0.5367 0.696 0.212 0.092 0.000
#> GSM152853 1 0.6610 0.4934 0.672 0.196 0.108 0.024
#> GSM152854 1 0.5848 0.4922 0.684 0.228 0.088 0.000
#> GSM152855 1 0.0895 0.8946 0.976 0.020 0.004 0.000
#> GSM153238 1 0.6391 0.5862 0.708 0.160 0.092 0.040
#> GSM153239 1 0.6502 0.5080 0.680 0.196 0.100 0.024
#> GSM153240 1 0.0188 0.8955 0.996 0.000 0.004 0.000
#> GSM153241 1 0.3455 0.8291 0.880 0.044 0.064 0.012
#> GSM153242 1 0.7236 0.3322 0.628 0.220 0.108 0.044
#> GSM153243 1 0.2328 0.8671 0.924 0.056 0.016 0.004
#> GSM153244 1 0.1042 0.8955 0.972 0.020 0.008 0.000
#> GSM153245 1 0.7445 0.4582 0.644 0.140 0.136 0.080
#> GSM153246 3 0.6020 -0.6628 0.004 0.128 0.700 0.168
#> GSM153247 1 0.6857 0.5402 0.680 0.140 0.132 0.048
#> GSM153248 1 0.0524 0.8951 0.988 0.008 0.004 0.000
#> GSM153249 1 0.0524 0.8963 0.988 0.008 0.004 0.000
#> GSM153250 1 0.0376 0.8956 0.992 0.004 0.004 0.000
#> GSM153251 1 0.6307 0.4528 0.676 0.236 0.060 0.028
#> GSM153252 1 0.0188 0.8957 0.996 0.000 0.004 0.000
#> GSM153253 1 0.0657 0.8953 0.984 0.004 0.012 0.000
#> GSM153254 1 0.0657 0.8970 0.984 0.012 0.004 0.000
#> GSM153255 1 0.0000 0.8946 1.000 0.000 0.000 0.000
#> GSM153256 1 0.0376 0.8956 0.992 0.004 0.004 0.000
#> GSM153257 1 0.0336 0.8956 0.992 0.000 0.008 0.000
#> GSM153258 1 0.0336 0.8957 0.992 0.008 0.000 0.000
#> GSM153259 1 0.0707 0.8954 0.980 0.020 0.000 0.000
#> GSM153260 1 0.6233 0.5028 0.700 0.192 0.084 0.024
#> GSM153261 1 0.4014 0.8053 0.852 0.084 0.048 0.016
#> GSM153262 1 0.0336 0.8956 0.992 0.000 0.008 0.000
#> GSM153263 1 0.0376 0.8959 0.992 0.004 0.004 0.000
#> GSM153264 1 0.0804 0.8946 0.980 0.012 0.008 0.000
#> GSM153265 1 0.0000 0.8946 1.000 0.000 0.000 0.000
#> GSM153266 1 0.0524 0.8954 0.988 0.008 0.004 0.000
#> GSM153267 1 0.0188 0.8950 0.996 0.000 0.004 0.000
#> GSM153268 1 0.1913 0.8775 0.940 0.040 0.020 0.000
#> GSM153269 1 0.0376 0.8956 0.992 0.004 0.004 0.000
#> GSM153270 1 0.0657 0.8959 0.984 0.012 0.004 0.000
#> GSM153271 1 0.0376 0.8956 0.992 0.004 0.004 0.000
#> GSM153272 1 0.0000 0.8946 1.000 0.000 0.000 0.000
#> GSM153273 1 0.0895 0.8938 0.976 0.020 0.004 0.000
#> GSM153274 1 0.0937 0.8968 0.976 0.012 0.012 0.000
#> GSM153275 1 0.0524 0.8958 0.988 0.008 0.004 0.000
#> GSM153276 1 0.0524 0.8966 0.988 0.008 0.004 0.000
#> GSM153277 1 0.0376 0.8961 0.992 0.004 0.004 0.000
#> GSM153278 1 0.3465 0.8281 0.880 0.072 0.028 0.020
#> GSM153279 1 0.0657 0.8967 0.984 0.012 0.004 0.000
#> GSM153280 1 0.0188 0.8953 0.996 0.004 0.000 0.000
#> GSM153281 1 0.0469 0.8963 0.988 0.000 0.012 0.000
#> GSM153282 1 0.0336 0.8958 0.992 0.000 0.008 0.000
#> GSM153283 1 0.0524 0.8963 0.988 0.008 0.004 0.000
#> GSM153284 1 0.0524 0.8969 0.988 0.004 0.008 0.000
#> GSM153285 1 0.0336 0.8964 0.992 0.000 0.008 0.000
#> GSM153286 1 0.0188 0.8953 0.996 0.004 0.000 0.000
#> GSM153287 1 0.0524 0.8962 0.988 0.004 0.008 0.000
#> GSM153288 1 0.0000 0.8946 1.000 0.000 0.000 0.000
#> GSM153289 1 0.0895 0.8946 0.976 0.020 0.004 0.000
#> GSM153290 1 0.0188 0.8953 0.996 0.004 0.000 0.000
#> GSM153291 1 0.0376 0.8956 0.992 0.004 0.004 0.000
#> GSM153292 1 0.0524 0.8962 0.988 0.004 0.008 0.000
#> GSM153293 1 0.0524 0.8961 0.988 0.008 0.004 0.000
#> GSM153294 1 0.1004 0.8933 0.972 0.024 0.004 0.000
#> GSM153295 1 0.3726 0.8100 0.864 0.032 0.088 0.016
#> GSM153054 1 0.3599 0.8293 0.876 0.040 0.064 0.020
#> GSM153055 1 0.0188 0.8955 0.996 0.004 0.000 0.000
#> GSM153056 1 0.3178 0.8399 0.896 0.052 0.032 0.020
#> GSM153057 1 0.2099 0.8780 0.936 0.040 0.020 0.004
#> GSM153058 1 0.7611 0.3344 0.616 0.196 0.068 0.120
#> GSM153059 1 0.3029 0.8393 0.896 0.068 0.028 0.008
#> GSM153060 3 0.8588 0.0524 0.316 0.076 0.468 0.140
#> GSM153061 1 0.8483 -0.4984 0.404 0.048 0.384 0.164
#> GSM153062 4 0.0469 0.0000 0.000 0.000 0.012 0.988
#> GSM153063 1 0.6856 0.5492 0.688 0.132 0.116 0.064
#> GSM153064 1 0.0895 0.8949 0.976 0.020 0.004 0.000
#> GSM153065 1 0.6847 0.3952 0.656 0.220 0.080 0.044
#> GSM153066 1 0.6722 0.4257 0.648 0.240 0.084 0.028
#> GSM153067 1 0.0188 0.8956 0.996 0.004 0.000 0.000
#> GSM153068 1 0.7898 0.1307 0.548 0.152 0.260 0.040
#> GSM153069 1 0.0188 0.8955 0.996 0.000 0.004 0.000
#> GSM153070 1 0.0188 0.8950 0.996 0.000 0.004 0.000
#> GSM153071 1 0.1443 0.8918 0.960 0.028 0.008 0.004
#> GSM153072 1 0.1617 0.8907 0.956 0.024 0.012 0.008
#> GSM153073 1 0.0524 0.8961 0.988 0.004 0.008 0.000
#> GSM153074 1 0.0376 0.8958 0.992 0.004 0.004 0.000
#> GSM153075 1 0.0376 0.8960 0.992 0.004 0.004 0.000
#> GSM153076 1 0.0524 0.8957 0.988 0.008 0.004 0.000
#> GSM153077 1 0.0524 0.8967 0.988 0.008 0.004 0.000
#> GSM153078 1 0.1510 0.8898 0.956 0.028 0.016 0.000
#> GSM153079 1 0.1042 0.8937 0.972 0.020 0.008 0.000
#> GSM153080 1 0.2275 0.8726 0.928 0.048 0.020 0.004
#> GSM153081 1 0.0937 0.8955 0.976 0.012 0.012 0.000
#> GSM153082 1 0.0817 0.8952 0.976 0.024 0.000 0.000
#> GSM153083 1 0.1004 0.8931 0.972 0.024 0.004 0.000
#> GSM153084 1 0.4273 0.7511 0.820 0.136 0.036 0.008
#> GSM153085 1 0.1443 0.8897 0.960 0.028 0.008 0.004
#> GSM153086 1 0.1576 0.8808 0.948 0.048 0.004 0.000
#> GSM153087 1 0.0524 0.8966 0.988 0.004 0.008 0.000
#> GSM153088 1 0.0376 0.8956 0.992 0.004 0.004 0.000
#> GSM153089 1 0.6295 0.3905 0.652 0.272 0.056 0.020
#> GSM153090 1 0.0376 0.8956 0.992 0.004 0.004 0.000
#> GSM153091 1 0.1004 0.8933 0.972 0.024 0.004 0.000
#> GSM153092 1 0.0376 0.8959 0.992 0.004 0.004 0.000
#> GSM153093 1 0.0376 0.8963 0.992 0.004 0.004 0.000
#> GSM153094 1 0.0779 0.8964 0.980 0.016 0.004 0.000
#> GSM153095 1 0.1677 0.8831 0.948 0.040 0.012 0.000
#> GSM153096 1 0.0895 0.8938 0.976 0.020 0.004 0.000
#> GSM153097 1 0.0895 0.8938 0.976 0.020 0.004 0.000
#> GSM153098 1 0.0779 0.8954 0.980 0.016 0.004 0.000
#> GSM153099 1 0.0376 0.8956 0.992 0.004 0.004 0.000
#> GSM153100 1 0.0524 0.8951 0.988 0.008 0.004 0.000
#> GSM153101 1 0.2363 0.8659 0.920 0.056 0.024 0.000
#> GSM153102 1 0.1398 0.8859 0.956 0.040 0.004 0.000
#> GSM153103 1 0.1004 0.8930 0.972 0.024 0.004 0.000
#> GSM153104 1 0.0469 0.8953 0.988 0.000 0.012 0.000
#> GSM153106 1 0.1042 0.8937 0.972 0.020 0.008 0.000
#> GSM153107 1 0.1042 0.8937 0.972 0.020 0.008 0.000
#> GSM153108 1 0.0188 0.8953 0.996 0.004 0.000 0.000
#> GSM153109 1 0.1398 0.8849 0.956 0.040 0.004 0.000
#> GSM153110 1 0.0469 0.8954 0.988 0.012 0.000 0.000
#> GSM153111 1 0.1109 0.8919 0.968 0.028 0.004 0.000
#> GSM153112 1 0.1004 0.8933 0.972 0.024 0.004 0.000
#> GSM153113 1 0.2334 0.8417 0.908 0.088 0.004 0.000
#> GSM153114 1 0.0895 0.8946 0.976 0.020 0.004 0.000
#> GSM187532 2 0.5681 0.8082 0.360 0.612 0.016 0.012
#> GSM187533 2 0.4431 0.9290 0.304 0.696 0.000 0.000
#> GSM187534 2 0.4431 0.9290 0.304 0.696 0.000 0.000
#> GSM187535 1 0.1635 0.8821 0.948 0.044 0.008 0.000
#> GSM152906 2 0.4193 0.9642 0.268 0.732 0.000 0.000
#> GSM152907 2 0.4250 0.9656 0.276 0.724 0.000 0.000
#> GSM152908 2 0.4222 0.9676 0.272 0.728 0.000 0.000
#> GSM152909 2 0.4899 0.9257 0.300 0.688 0.004 0.008
#> GSM152910 2 0.4401 0.9673 0.272 0.724 0.000 0.004
#> GSM152911 2 0.4250 0.9683 0.276 0.724 0.000 0.000
#> GSM152912 2 0.4222 0.9676 0.272 0.728 0.000 0.000
#> GSM152913 2 0.4511 0.9607 0.268 0.724 0.000 0.008
#> GSM152914 2 0.4250 0.9683 0.276 0.724 0.000 0.000
#> GSM152915 2 0.4250 0.9683 0.276 0.724 0.000 0.000
#> GSM152916 2 0.4250 0.9672 0.276 0.724 0.000 0.000
#> GSM152917 2 0.4250 0.9683 0.276 0.724 0.000 0.000
#> GSM152918 2 0.4250 0.9683 0.276 0.724 0.000 0.000
#> GSM152919 2 0.4356 0.9512 0.292 0.708 0.000 0.000
#> GSM152920 2 0.4222 0.9676 0.272 0.728 0.000 0.000
#> GSM152921 2 0.4222 0.9676 0.272 0.728 0.000 0.000
#> GSM152922 2 0.4401 0.9673 0.272 0.724 0.000 0.004
#> GSM152923 2 0.4193 0.9642 0.268 0.732 0.000 0.000
#> GSM152924 2 0.4250 0.9672 0.276 0.724 0.000 0.000
#> GSM152925 2 0.4277 0.9651 0.280 0.720 0.000 0.000
#> GSM152926 2 0.4193 0.9642 0.268 0.732 0.000 0.000
#> GSM152927 2 0.4456 0.9642 0.280 0.716 0.004 0.000
#> GSM152928 2 0.5670 0.7596 0.392 0.584 0.016 0.008
#> GSM152929 2 0.4193 0.9642 0.268 0.732 0.000 0.000
#> GSM152930 2 0.4193 0.9642 0.268 0.732 0.000 0.000
cbind(get_classes(res, k = 5), get_membership(res, k = 5))
#> class entropy silhouette p1 p2 p3 p4 p5
#> GSM152839 1 0.1651 0.86437 0.944 0.012 0.008 0.000 0.036
#> GSM152840 1 0.6203 0.25541 0.584 0.072 0.020 0.012 0.312
#> GSM152841 1 0.0898 0.86843 0.972 0.008 0.000 0.000 0.020
#> GSM152842 1 0.6620 -0.39378 0.452 0.008 0.404 0.008 0.128
#> GSM152843 1 0.3736 0.74415 0.824 0.000 0.072 0.004 0.100
#> GSM152844 1 0.6403 0.01404 0.516 0.080 0.012 0.016 0.376
#> GSM152845 1 0.7678 -0.26537 0.416 0.296 0.028 0.016 0.244
#> GSM152846 1 0.7110 0.15588 0.548 0.168 0.044 0.008 0.232
#> GSM152847 1 0.5982 0.40065 0.644 0.012 0.124 0.008 0.212
#> GSM152848 1 0.1471 0.86324 0.952 0.004 0.020 0.000 0.024
#> GSM152849 1 0.4228 0.74058 0.812 0.028 0.052 0.004 0.104
#> GSM152850 1 0.3135 0.80398 0.868 0.020 0.024 0.000 0.088
#> GSM152851 1 0.1904 0.85303 0.936 0.020 0.016 0.000 0.028
#> GSM152852 1 0.6742 0.16591 0.548 0.136 0.040 0.000 0.276
#> GSM152853 1 0.6718 0.07430 0.532 0.076 0.056 0.004 0.332
#> GSM152854 1 0.6784 0.22683 0.568 0.152 0.036 0.004 0.240
#> GSM152855 1 0.0981 0.86698 0.972 0.012 0.008 0.000 0.008
#> GSM153238 1 0.6737 0.38890 0.624 0.140 0.048 0.016 0.172
#> GSM153239 1 0.6743 0.16442 0.556 0.104 0.032 0.012 0.296
#> GSM153240 1 0.0451 0.86783 0.988 0.004 0.000 0.000 0.008
#> GSM153241 1 0.3877 0.74673 0.816 0.016 0.040 0.000 0.128
#> GSM153242 1 0.7903 -0.09499 0.488 0.180 0.060 0.028 0.244
#> GSM153243 1 0.3089 0.81489 0.872 0.040 0.012 0.000 0.076
#> GSM153244 1 0.1278 0.86821 0.960 0.020 0.004 0.000 0.016
#> GSM153245 1 0.7181 0.15301 0.564 0.040 0.096 0.040 0.260
#> GSM153246 5 0.6948 0.00000 0.000 0.052 0.376 0.108 0.464
#> GSM153247 1 0.7313 0.32119 0.600 0.104 0.112 0.028 0.156
#> GSM153248 1 0.0727 0.86744 0.980 0.004 0.012 0.000 0.004
#> GSM153249 1 0.0854 0.86850 0.976 0.012 0.004 0.000 0.008
#> GSM153250 1 0.0613 0.86730 0.984 0.008 0.004 0.000 0.004
#> GSM153251 1 0.6958 0.19143 0.564 0.228 0.032 0.012 0.164
#> GSM153252 1 0.0566 0.86870 0.984 0.004 0.000 0.000 0.012
#> GSM153253 1 0.0740 0.86900 0.980 0.004 0.008 0.000 0.008
#> GSM153254 1 0.1267 0.86740 0.960 0.024 0.004 0.000 0.012
#> GSM153255 1 0.0324 0.86668 0.992 0.004 0.000 0.000 0.004
#> GSM153256 1 0.0613 0.86730 0.984 0.008 0.004 0.000 0.004
#> GSM153257 1 0.0740 0.86771 0.980 0.004 0.008 0.000 0.008
#> GSM153258 1 0.0324 0.86794 0.992 0.004 0.004 0.000 0.000
#> GSM153259 1 0.0854 0.86868 0.976 0.012 0.008 0.000 0.004
#> GSM153260 1 0.6872 0.25185 0.596 0.180 0.052 0.008 0.164
#> GSM153261 1 0.4605 0.71981 0.788 0.048 0.032 0.008 0.124
#> GSM153262 1 0.0579 0.86858 0.984 0.000 0.008 0.000 0.008
#> GSM153263 1 0.0740 0.86944 0.980 0.008 0.004 0.000 0.008
#> GSM153264 1 0.1179 0.86738 0.964 0.004 0.016 0.000 0.016
#> GSM153265 1 0.0451 0.86800 0.988 0.004 0.000 0.000 0.008
#> GSM153266 1 0.0807 0.86787 0.976 0.000 0.012 0.000 0.012
#> GSM153267 1 0.0613 0.86686 0.984 0.004 0.004 0.000 0.008
#> GSM153268 1 0.2456 0.83404 0.904 0.024 0.008 0.000 0.064
#> GSM153269 1 0.0613 0.86730 0.984 0.008 0.004 0.000 0.004
#> GSM153270 1 0.0981 0.86957 0.972 0.012 0.008 0.000 0.008
#> GSM153271 1 0.0613 0.86730 0.984 0.008 0.004 0.000 0.004
#> GSM153272 1 0.0324 0.86668 0.992 0.004 0.000 0.000 0.004
#> GSM153273 1 0.1306 0.86418 0.960 0.016 0.016 0.000 0.008
#> GSM153274 1 0.1074 0.86988 0.968 0.016 0.012 0.000 0.004
#> GSM153275 1 0.0854 0.86812 0.976 0.012 0.004 0.000 0.008
#> GSM153276 1 0.0807 0.87011 0.976 0.012 0.000 0.000 0.012
#> GSM153277 1 0.0451 0.86865 0.988 0.008 0.004 0.000 0.000
#> GSM153278 1 0.3323 0.79340 0.864 0.028 0.020 0.004 0.084
#> GSM153279 1 0.0898 0.86875 0.972 0.020 0.008 0.000 0.000
#> GSM153280 1 0.0579 0.86825 0.984 0.008 0.000 0.000 0.008
#> GSM153281 1 0.0727 0.86967 0.980 0.004 0.004 0.000 0.012
#> GSM153282 1 0.0613 0.86866 0.984 0.004 0.004 0.000 0.008
#> GSM153283 1 0.0727 0.86843 0.980 0.004 0.012 0.000 0.004
#> GSM153284 1 0.0854 0.86917 0.976 0.008 0.004 0.000 0.012
#> GSM153285 1 0.0613 0.86963 0.984 0.004 0.004 0.000 0.008
#> GSM153286 1 0.0451 0.86706 0.988 0.008 0.000 0.000 0.004
#> GSM153287 1 0.0854 0.86828 0.976 0.008 0.004 0.000 0.012
#> GSM153288 1 0.0324 0.86668 0.992 0.004 0.000 0.000 0.004
#> GSM153289 1 0.0981 0.86698 0.972 0.012 0.008 0.000 0.008
#> GSM153290 1 0.0566 0.86821 0.984 0.012 0.000 0.000 0.004
#> GSM153291 1 0.0613 0.86730 0.984 0.008 0.004 0.000 0.004
#> GSM153292 1 0.0854 0.86828 0.976 0.008 0.004 0.000 0.012
#> GSM153293 1 0.0727 0.86808 0.980 0.012 0.004 0.000 0.004
#> GSM153294 1 0.1200 0.86705 0.964 0.016 0.012 0.000 0.008
#> GSM153295 1 0.3688 0.73532 0.816 0.000 0.060 0.000 0.124
#> GSM153054 1 0.3888 0.75820 0.828 0.020 0.040 0.004 0.108
#> GSM153055 1 0.0671 0.86878 0.980 0.004 0.000 0.000 0.016
#> GSM153056 1 0.2858 0.80269 0.876 0.008 0.012 0.004 0.100
#> GSM153057 1 0.2756 0.83770 0.900 0.036 0.020 0.004 0.040
#> GSM153058 1 0.8103 -0.00887 0.516 0.152 0.036 0.112 0.184
#> GSM153059 1 0.3490 0.79383 0.856 0.068 0.028 0.000 0.048
#> GSM153060 3 0.4673 -0.40596 0.096 0.008 0.784 0.092 0.020
#> GSM153061 3 0.8260 0.30344 0.320 0.044 0.432 0.112 0.092
#> GSM153062 4 0.0898 0.00000 0.000 0.000 0.020 0.972 0.008
#> GSM153063 1 0.6988 0.30685 0.604 0.084 0.060 0.032 0.220
#> GSM153064 1 0.0968 0.86747 0.972 0.012 0.012 0.000 0.004
#> GSM153065 1 0.7603 0.06129 0.540 0.212 0.068 0.024 0.156
#> GSM153066 1 0.7369 0.08934 0.532 0.240 0.056 0.012 0.160
#> GSM153067 1 0.0451 0.86787 0.988 0.008 0.000 0.000 0.004
#> GSM153068 1 0.8191 -0.33396 0.444 0.148 0.280 0.020 0.108
#> GSM153069 1 0.0451 0.86783 0.988 0.004 0.000 0.000 0.008
#> GSM153070 1 0.0486 0.86693 0.988 0.004 0.004 0.000 0.004
#> GSM153071 1 0.1623 0.86342 0.948 0.016 0.016 0.000 0.020
#> GSM153072 1 0.1904 0.85917 0.936 0.016 0.028 0.000 0.020
#> GSM153073 1 0.0613 0.86850 0.984 0.004 0.008 0.000 0.004
#> GSM153074 1 0.0740 0.86791 0.980 0.008 0.004 0.000 0.008
#> GSM153075 1 0.0693 0.87043 0.980 0.012 0.000 0.000 0.008
#> GSM153076 1 0.0613 0.86827 0.984 0.004 0.008 0.000 0.004
#> GSM153077 1 0.0867 0.87011 0.976 0.008 0.008 0.000 0.008
#> GSM153078 1 0.2124 0.85125 0.924 0.012 0.020 0.000 0.044
#> GSM153079 1 0.1095 0.86622 0.968 0.012 0.012 0.000 0.008
#> GSM153080 1 0.2971 0.81947 0.880 0.032 0.016 0.000 0.072
#> GSM153081 1 0.0960 0.86759 0.972 0.008 0.016 0.000 0.004
#> GSM153082 1 0.1299 0.86621 0.960 0.020 0.008 0.000 0.012
#> GSM153083 1 0.1518 0.86180 0.952 0.020 0.016 0.000 0.012
#> GSM153084 1 0.4820 0.66590 0.764 0.144 0.028 0.004 0.060
#> GSM153085 1 0.1978 0.85321 0.932 0.032 0.012 0.000 0.024
#> GSM153086 1 0.1913 0.85167 0.932 0.044 0.016 0.000 0.008
#> GSM153087 1 0.0740 0.86995 0.980 0.008 0.008 0.000 0.004
#> GSM153088 1 0.0486 0.86787 0.988 0.004 0.004 0.000 0.004
#> GSM153089 1 0.6953 0.12408 0.536 0.268 0.028 0.008 0.160
#> GSM153090 1 0.0740 0.86747 0.980 0.008 0.004 0.000 0.008
#> GSM153091 1 0.1200 0.86705 0.964 0.016 0.012 0.000 0.008
#> GSM153092 1 0.0486 0.86827 0.988 0.004 0.004 0.000 0.004
#> GSM153093 1 0.0740 0.86812 0.980 0.008 0.004 0.000 0.008
#> GSM153094 1 0.1200 0.86772 0.964 0.016 0.012 0.000 0.008
#> GSM153095 1 0.2152 0.84823 0.920 0.032 0.004 0.000 0.044
#> GSM153096 1 0.1179 0.86454 0.964 0.016 0.016 0.000 0.004
#> GSM153097 1 0.1419 0.86284 0.956 0.016 0.016 0.000 0.012
#> GSM153098 1 0.0833 0.86982 0.976 0.016 0.004 0.000 0.004
#> GSM153099 1 0.0740 0.86837 0.980 0.008 0.008 0.000 0.004
#> GSM153100 1 0.0566 0.86670 0.984 0.004 0.012 0.000 0.000
#> GSM153101 1 0.2940 0.82310 0.888 0.040 0.040 0.000 0.032
#> GSM153102 1 0.1836 0.85524 0.936 0.040 0.016 0.000 0.008
#> GSM153103 1 0.1710 0.86138 0.944 0.024 0.012 0.000 0.020
#> GSM153104 1 0.0613 0.86859 0.984 0.004 0.008 0.000 0.004
#> GSM153106 1 0.1095 0.86622 0.968 0.012 0.012 0.000 0.008
#> GSM153107 1 0.1095 0.86622 0.968 0.012 0.012 0.000 0.008
#> GSM153108 1 0.0451 0.86899 0.988 0.008 0.000 0.000 0.004
#> GSM153109 1 0.1836 0.85390 0.936 0.040 0.016 0.000 0.008
#> GSM153110 1 0.0854 0.86716 0.976 0.008 0.012 0.000 0.004
#> GSM153111 1 0.1612 0.86048 0.948 0.024 0.016 0.000 0.012
#> GSM153112 1 0.1074 0.86613 0.968 0.016 0.012 0.000 0.004
#> GSM153113 1 0.2747 0.81050 0.884 0.088 0.012 0.000 0.016
#> GSM153114 1 0.0981 0.86698 0.972 0.012 0.008 0.000 0.008
#> GSM187532 2 0.4895 0.75778 0.192 0.736 0.012 0.008 0.052
#> GSM187533 2 0.2953 0.91697 0.144 0.844 0.000 0.000 0.012
#> GSM187534 2 0.2953 0.91697 0.144 0.844 0.000 0.000 0.012
#> GSM187535 1 0.1651 0.85947 0.944 0.036 0.012 0.000 0.008
#> GSM152906 2 0.2389 0.96151 0.116 0.880 0.000 0.000 0.004
#> GSM152907 2 0.2488 0.95532 0.124 0.872 0.000 0.000 0.004
#> GSM152908 2 0.2074 0.95705 0.104 0.896 0.000 0.000 0.000
#> GSM152909 2 0.3401 0.92170 0.116 0.844 0.004 0.004 0.032
#> GSM152910 2 0.2392 0.95512 0.104 0.888 0.000 0.004 0.004
#> GSM152911 2 0.2286 0.96026 0.108 0.888 0.000 0.000 0.004
#> GSM152912 2 0.2074 0.95705 0.104 0.896 0.000 0.000 0.000
#> GSM152913 2 0.2588 0.94537 0.100 0.884 0.000 0.008 0.008
#> GSM152914 2 0.2286 0.96026 0.108 0.888 0.000 0.000 0.004
#> GSM152915 2 0.2286 0.96026 0.108 0.888 0.000 0.000 0.004
#> GSM152916 2 0.2280 0.95911 0.120 0.880 0.000 0.000 0.000
#> GSM152917 2 0.2286 0.96026 0.108 0.888 0.000 0.000 0.004
#> GSM152918 2 0.2286 0.96026 0.108 0.888 0.000 0.000 0.004
#> GSM152919 2 0.2488 0.95201 0.124 0.872 0.000 0.000 0.004
#> GSM152920 2 0.2074 0.95705 0.104 0.896 0.000 0.000 0.000
#> GSM152921 2 0.2074 0.95705 0.104 0.896 0.000 0.000 0.000
#> GSM152922 2 0.2392 0.95512 0.104 0.888 0.000 0.004 0.004
#> GSM152923 2 0.2389 0.96151 0.116 0.880 0.000 0.000 0.004
#> GSM152924 2 0.2280 0.95911 0.120 0.880 0.000 0.000 0.000
#> GSM152925 2 0.2439 0.95901 0.120 0.876 0.000 0.000 0.004
#> GSM152926 2 0.2389 0.96151 0.116 0.880 0.000 0.000 0.004
#> GSM152927 2 0.2513 0.95871 0.116 0.876 0.000 0.000 0.008
#> GSM152928 2 0.4668 0.72960 0.220 0.732 0.024 0.004 0.020
#> GSM152929 2 0.2389 0.96151 0.116 0.880 0.000 0.000 0.004
#> GSM152930 2 0.2389 0.96151 0.116 0.880 0.000 0.000 0.004
cbind(get_classes(res, k = 6), get_membership(res, k = 6))
#> class entropy silhouette p1 p2 p3 p4 p5 p6
#> GSM152839 1 0.1810 0.837 0.932 0.020 0.008 0.036 0.000 0.004
#> GSM152840 4 0.5452 0.648 0.408 0.008 0.032 0.520 0.004 0.028
#> GSM152841 1 0.0922 0.848 0.968 0.004 0.000 0.024 0.000 0.004
#> GSM152842 3 0.6726 -0.504 0.404 0.028 0.416 0.112 0.000 0.040
#> GSM152843 1 0.3841 0.620 0.804 0.008 0.064 0.112 0.000 0.012
#> GSM152844 4 0.5913 0.630 0.324 0.016 0.028 0.568 0.012 0.052
#> GSM152845 4 0.7269 0.437 0.252 0.204 0.016 0.460 0.008 0.060
#> GSM152846 4 0.6540 0.667 0.376 0.092 0.020 0.468 0.004 0.040
#> GSM152847 1 0.6836 -0.285 0.560 0.032 0.100 0.204 0.000 0.104
#> GSM152848 1 0.1666 0.835 0.936 0.008 0.020 0.036 0.000 0.000
#> GSM152849 1 0.4424 0.597 0.784 0.028 0.056 0.100 0.000 0.032
#> GSM152850 1 0.3455 0.703 0.836 0.016 0.020 0.104 0.000 0.024
#> GSM152851 1 0.1908 0.814 0.924 0.020 0.012 0.044 0.000 0.000
#> GSM152852 4 0.5587 0.706 0.360 0.068 0.016 0.544 0.000 0.012
#> GSM152853 4 0.5279 0.649 0.340 0.012 0.048 0.584 0.000 0.016
#> GSM152854 4 0.6332 0.655 0.412 0.088 0.016 0.444 0.000 0.040
#> GSM152855 1 0.0984 0.847 0.968 0.012 0.008 0.012 0.000 0.000
#> GSM153238 1 0.7267 -0.197 0.560 0.132 0.032 0.152 0.020 0.104
#> GSM153239 4 0.6678 0.665 0.396 0.056 0.036 0.456 0.012 0.044
#> GSM153240 1 0.0405 0.848 0.988 0.004 0.000 0.008 0.000 0.000
#> GSM153241 1 0.4100 0.578 0.776 0.016 0.040 0.156 0.000 0.012
#> GSM153242 4 0.7708 0.564 0.304 0.108 0.036 0.440 0.020 0.092
#> GSM153243 1 0.3241 0.744 0.852 0.044 0.008 0.080 0.000 0.016
#> GSM153244 1 0.1401 0.844 0.948 0.020 0.000 0.028 0.000 0.004
#> GSM153245 1 0.7232 -0.716 0.428 0.008 0.088 0.364 0.032 0.080
#> GSM153246 6 0.4720 0.000 0.000 0.000 0.200 0.016 0.084 0.700
#> GSM153247 1 0.7723 -0.247 0.548 0.104 0.092 0.124 0.032 0.100
#> GSM153248 1 0.0964 0.848 0.968 0.004 0.012 0.016 0.000 0.000
#> GSM153249 1 0.0767 0.849 0.976 0.012 0.004 0.008 0.000 0.000
#> GSM153250 1 0.0665 0.847 0.980 0.008 0.004 0.008 0.000 0.000
#> GSM153251 1 0.7406 -0.642 0.444 0.184 0.020 0.276 0.008 0.068
#> GSM153252 1 0.0653 0.849 0.980 0.004 0.000 0.012 0.000 0.004
#> GSM153253 1 0.0798 0.848 0.976 0.004 0.004 0.012 0.000 0.004
#> GSM153254 1 0.1261 0.843 0.952 0.024 0.000 0.024 0.000 0.000
#> GSM153255 1 0.0405 0.847 0.988 0.004 0.000 0.008 0.000 0.000
#> GSM153256 1 0.0665 0.847 0.980 0.008 0.004 0.008 0.000 0.000
#> GSM153257 1 0.0862 0.849 0.972 0.004 0.008 0.016 0.000 0.000
#> GSM153258 1 0.0551 0.849 0.984 0.004 0.004 0.008 0.000 0.000
#> GSM153259 1 0.0984 0.849 0.968 0.012 0.008 0.012 0.000 0.000
#> GSM153260 1 0.7194 -0.553 0.492 0.156 0.032 0.244 0.000 0.076
#> GSM153261 1 0.5112 0.455 0.720 0.044 0.032 0.168 0.004 0.032
#> GSM153262 1 0.0622 0.849 0.980 0.000 0.008 0.012 0.000 0.000
#> GSM153263 1 0.0862 0.850 0.972 0.008 0.004 0.016 0.000 0.000
#> GSM153264 1 0.1419 0.846 0.952 0.012 0.016 0.016 0.000 0.004
#> GSM153265 1 0.0405 0.848 0.988 0.004 0.000 0.008 0.000 0.000
#> GSM153266 1 0.0993 0.847 0.964 0.000 0.012 0.024 0.000 0.000
#> GSM153267 1 0.0748 0.848 0.976 0.004 0.004 0.016 0.000 0.000
#> GSM153268 1 0.2382 0.787 0.896 0.020 0.004 0.072 0.000 0.008
#> GSM153269 1 0.0665 0.847 0.980 0.008 0.004 0.008 0.000 0.000
#> GSM153270 1 0.0984 0.851 0.968 0.012 0.008 0.012 0.000 0.000
#> GSM153271 1 0.0665 0.847 0.980 0.008 0.004 0.008 0.000 0.000
#> GSM153272 1 0.0291 0.846 0.992 0.004 0.000 0.004 0.000 0.000
#> GSM153273 1 0.1542 0.840 0.944 0.016 0.016 0.024 0.000 0.000
#> GSM153274 1 0.1173 0.849 0.960 0.016 0.008 0.016 0.000 0.000
#> GSM153275 1 0.0870 0.848 0.972 0.012 0.004 0.012 0.000 0.000
#> GSM153276 1 0.0725 0.851 0.976 0.012 0.000 0.012 0.000 0.000
#> GSM153277 1 0.0520 0.849 0.984 0.008 0.000 0.008 0.000 0.000
#> GSM153278 1 0.3876 0.646 0.808 0.024 0.020 0.120 0.000 0.028
#> GSM153279 1 0.0837 0.849 0.972 0.020 0.004 0.004 0.000 0.000
#> GSM153280 1 0.0622 0.849 0.980 0.008 0.000 0.012 0.000 0.000
#> GSM153281 1 0.0665 0.850 0.980 0.004 0.000 0.008 0.000 0.008
#> GSM153282 1 0.0653 0.849 0.980 0.004 0.000 0.012 0.000 0.004
#> GSM153283 1 0.0870 0.849 0.972 0.004 0.012 0.012 0.000 0.000
#> GSM153284 1 0.0767 0.850 0.976 0.008 0.004 0.012 0.000 0.000
#> GSM153285 1 0.0696 0.850 0.980 0.004 0.004 0.008 0.000 0.004
#> GSM153286 1 0.0405 0.847 0.988 0.008 0.000 0.004 0.000 0.000
#> GSM153287 1 0.0810 0.849 0.976 0.008 0.004 0.008 0.000 0.004
#> GSM153288 1 0.0405 0.847 0.988 0.004 0.000 0.008 0.000 0.000
#> GSM153289 1 0.0984 0.847 0.968 0.012 0.008 0.012 0.000 0.000
#> GSM153290 1 0.0622 0.849 0.980 0.012 0.000 0.008 0.000 0.000
#> GSM153291 1 0.0665 0.847 0.980 0.008 0.004 0.008 0.000 0.000
#> GSM153292 1 0.0810 0.849 0.976 0.008 0.004 0.008 0.000 0.004
#> GSM153293 1 0.0767 0.848 0.976 0.012 0.004 0.008 0.000 0.000
#> GSM153294 1 0.1275 0.847 0.956 0.016 0.012 0.016 0.000 0.000
#> GSM153295 1 0.4086 0.600 0.796 0.008 0.056 0.108 0.000 0.032
#> GSM153054 1 0.4273 0.633 0.800 0.028 0.044 0.052 0.000 0.076
#> GSM153055 1 0.0767 0.850 0.976 0.008 0.000 0.012 0.000 0.004
#> GSM153056 1 0.3291 0.691 0.832 0.004 0.016 0.124 0.000 0.024
#> GSM153057 1 0.2949 0.781 0.876 0.036 0.020 0.056 0.000 0.012
#> GSM153058 1 0.8005 -0.763 0.396 0.100 0.024 0.324 0.112 0.044
#> GSM153059 1 0.3784 0.687 0.820 0.064 0.020 0.084 0.000 0.012
#> GSM153060 3 0.2750 -0.725 0.020 0.000 0.880 0.012 0.076 0.012
#> GSM153061 1 0.9380 -0.662 0.252 0.052 0.232 0.224 0.100 0.140
#> GSM153062 5 0.0363 0.000 0.000 0.000 0.012 0.000 0.988 0.000
#> GSM153063 1 0.7525 -0.437 0.528 0.076 0.044 0.220 0.036 0.096
#> GSM153064 1 0.1180 0.847 0.960 0.012 0.012 0.016 0.000 0.000
#> GSM153065 1 0.7927 -0.607 0.452 0.184 0.052 0.224 0.020 0.068
#> GSM153066 1 0.7582 -0.393 0.492 0.236 0.044 0.124 0.012 0.092
#> GSM153067 1 0.0622 0.850 0.980 0.008 0.000 0.012 0.000 0.000
#> GSM153068 1 0.8317 -0.687 0.360 0.132 0.288 0.156 0.012 0.052
#> GSM153069 1 0.0508 0.848 0.984 0.004 0.000 0.012 0.000 0.000
#> GSM153070 1 0.0436 0.847 0.988 0.004 0.004 0.004 0.000 0.000
#> GSM153071 1 0.1811 0.835 0.936 0.020 0.012 0.020 0.000 0.012
#> GSM153072 1 0.2145 0.826 0.920 0.016 0.020 0.032 0.000 0.012
#> GSM153073 1 0.0767 0.849 0.976 0.004 0.008 0.012 0.000 0.000
#> GSM153074 1 0.0767 0.849 0.976 0.008 0.004 0.012 0.000 0.000
#> GSM153075 1 0.0725 0.851 0.976 0.012 0.000 0.012 0.000 0.000
#> GSM153076 1 0.0767 0.849 0.976 0.004 0.008 0.012 0.000 0.000
#> GSM153077 1 0.1026 0.850 0.968 0.008 0.008 0.012 0.000 0.004
#> GSM153078 1 0.2383 0.815 0.908 0.016 0.020 0.040 0.000 0.016
#> GSM153079 1 0.1269 0.845 0.956 0.012 0.012 0.020 0.000 0.000
#> GSM153080 1 0.2940 0.767 0.872 0.036 0.008 0.068 0.000 0.016
#> GSM153081 1 0.0976 0.848 0.968 0.008 0.016 0.008 0.000 0.000
#> GSM153082 1 0.1495 0.841 0.948 0.020 0.008 0.020 0.000 0.004
#> GSM153083 1 0.1787 0.833 0.932 0.020 0.016 0.032 0.000 0.000
#> GSM153084 1 0.5132 0.458 0.724 0.136 0.020 0.088 0.004 0.028
#> GSM153085 1 0.2044 0.824 0.924 0.032 0.016 0.020 0.000 0.008
#> GSM153086 1 0.1913 0.822 0.924 0.044 0.016 0.016 0.000 0.000
#> GSM153087 1 0.0779 0.851 0.976 0.008 0.008 0.008 0.000 0.000
#> GSM153088 1 0.0551 0.849 0.984 0.004 0.004 0.008 0.000 0.000
#> GSM153089 1 0.7246 -0.642 0.420 0.224 0.024 0.288 0.004 0.040
#> GSM153090 1 0.0870 0.849 0.972 0.012 0.004 0.012 0.000 0.000
#> GSM153091 1 0.1275 0.847 0.956 0.016 0.012 0.016 0.000 0.000
#> GSM153092 1 0.0653 0.849 0.980 0.004 0.004 0.012 0.000 0.000
#> GSM153093 1 0.0665 0.848 0.980 0.008 0.004 0.008 0.000 0.000
#> GSM153094 1 0.1364 0.846 0.952 0.016 0.012 0.020 0.000 0.000
#> GSM153095 1 0.2315 0.810 0.908 0.032 0.004 0.040 0.000 0.016
#> GSM153096 1 0.1458 0.840 0.948 0.016 0.016 0.020 0.000 0.000
#> GSM153097 1 0.1766 0.834 0.936 0.016 0.016 0.028 0.000 0.004
#> GSM153098 1 0.1059 0.850 0.964 0.016 0.004 0.016 0.000 0.000
#> GSM153099 1 0.0665 0.848 0.980 0.008 0.008 0.004 0.000 0.000
#> GSM153100 1 0.0767 0.847 0.976 0.004 0.012 0.008 0.000 0.000
#> GSM153101 1 0.3070 0.768 0.872 0.044 0.024 0.044 0.000 0.016
#> GSM153102 1 0.2239 0.817 0.912 0.040 0.016 0.028 0.000 0.004
#> GSM153103 1 0.1882 0.831 0.928 0.024 0.020 0.028 0.000 0.000
#> GSM153104 1 0.0653 0.848 0.980 0.004 0.004 0.012 0.000 0.000
#> GSM153106 1 0.1086 0.846 0.964 0.012 0.012 0.012 0.000 0.000
#> GSM153107 1 0.1086 0.846 0.964 0.012 0.012 0.012 0.000 0.000
#> GSM153108 1 0.0520 0.851 0.984 0.008 0.000 0.008 0.000 0.000
#> GSM153109 1 0.2239 0.814 0.912 0.040 0.016 0.028 0.000 0.004
#> GSM153110 1 0.0984 0.847 0.968 0.008 0.012 0.012 0.000 0.000
#> GSM153111 1 0.1794 0.831 0.932 0.024 0.016 0.028 0.000 0.000
#> GSM153112 1 0.1275 0.845 0.956 0.016 0.012 0.016 0.000 0.000
#> GSM153113 1 0.2610 0.763 0.880 0.088 0.012 0.016 0.000 0.004
#> GSM153114 1 0.0984 0.847 0.968 0.012 0.008 0.012 0.000 0.000
#> GSM187532 2 0.4652 0.772 0.140 0.748 0.008 0.068 0.000 0.036
#> GSM187533 2 0.2742 0.910 0.128 0.852 0.000 0.012 0.000 0.008
#> GSM187534 2 0.2742 0.910 0.128 0.852 0.000 0.012 0.000 0.008
#> GSM187535 1 0.1585 0.836 0.940 0.036 0.012 0.012 0.000 0.000
#> GSM152906 2 0.1908 0.960 0.096 0.900 0.000 0.000 0.000 0.004
#> GSM152907 2 0.2006 0.953 0.104 0.892 0.000 0.000 0.000 0.004
#> GSM152908 2 0.1610 0.956 0.084 0.916 0.000 0.000 0.000 0.000
#> GSM152909 2 0.3152 0.910 0.084 0.852 0.000 0.032 0.000 0.032
#> GSM152910 2 0.1913 0.946 0.080 0.908 0.000 0.000 0.000 0.012
#> GSM152911 2 0.1918 0.958 0.088 0.904 0.000 0.000 0.000 0.008
#> GSM152912 2 0.1610 0.956 0.084 0.916 0.000 0.000 0.000 0.000
#> GSM152913 2 0.2265 0.932 0.076 0.896 0.000 0.004 0.000 0.024
#> GSM152914 2 0.1806 0.959 0.088 0.908 0.000 0.000 0.000 0.004
#> GSM152915 2 0.1806 0.959 0.088 0.908 0.000 0.000 0.000 0.004
#> GSM152916 2 0.1814 0.957 0.100 0.900 0.000 0.000 0.000 0.000
#> GSM152917 2 0.1806 0.959 0.088 0.908 0.000 0.000 0.000 0.004
#> GSM152918 2 0.1806 0.959 0.088 0.908 0.000 0.000 0.000 0.004
#> GSM152919 2 0.2006 0.950 0.104 0.892 0.000 0.000 0.000 0.004
#> GSM152920 2 0.1610 0.956 0.084 0.916 0.000 0.000 0.000 0.000
#> GSM152921 2 0.1610 0.956 0.084 0.916 0.000 0.000 0.000 0.000
#> GSM152922 2 0.1913 0.946 0.080 0.908 0.000 0.000 0.000 0.012
#> GSM152923 2 0.1908 0.960 0.096 0.900 0.000 0.000 0.000 0.004
#> GSM152924 2 0.1814 0.957 0.100 0.900 0.000 0.000 0.000 0.000
#> GSM152925 2 0.1958 0.957 0.100 0.896 0.000 0.004 0.000 0.000
#> GSM152926 2 0.1908 0.960 0.096 0.900 0.000 0.000 0.000 0.004
#> GSM152927 2 0.2020 0.957 0.096 0.896 0.000 0.008 0.000 0.000
#> GSM152928 2 0.4330 0.739 0.188 0.748 0.020 0.028 0.000 0.016
#> GSM152929 2 0.1908 0.960 0.096 0.900 0.000 0.000 0.000 0.004
#> GSM152930 2 0.1908 0.960 0.096 0.900 0.000 0.000 0.000 0.004
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)
#> Error in mat[ceiling(1:nr/h_ratio), ceiling(1:nc/w_ratio), drop = FALSE]: subscript out of bounds
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 tissue(p) k
#> CV:hclust 163 8.71e-01 2
#> CV:hclust 159 NA 3
#> CV:hclust 146 1.71e-27 4
#> CV:hclust 138 6.14e-26 5
#> CV:hclust 144 2.86e-33 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 12013 rows and 164 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 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 0.444 0.680 0.811 0.3447 0.699 0.699
#> 3 3 0.989 0.958 0.978 0.6327 0.731 0.617
#> 4 4 0.699 0.694 0.829 0.1511 0.965 0.920
#> 5 5 0.608 0.581 0.707 0.1018 0.810 0.545
#> 6 6 0.607 0.666 0.737 0.0539 0.923 0.719
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
#> GSM152839 1 0.8763 0.543 0.704 0.296
#> GSM152840 1 0.9988 0.436 0.520 0.480
#> GSM152841 1 0.0376 0.757 0.996 0.004
#> GSM152842 1 0.9988 0.436 0.520 0.480
#> GSM152843 1 0.9988 0.436 0.520 0.480
#> GSM152844 1 0.9988 0.436 0.520 0.480
#> GSM152845 1 0.9988 0.436 0.520 0.480
#> GSM152846 1 0.9988 0.436 0.520 0.480
#> GSM152847 1 0.9988 0.436 0.520 0.480
#> GSM152848 1 0.0376 0.757 0.996 0.004
#> GSM152849 1 0.9988 0.436 0.520 0.480
#> GSM152850 1 0.9983 0.437 0.524 0.476
#> GSM152851 1 0.7883 0.596 0.764 0.236
#> GSM152852 1 0.9983 0.437 0.524 0.476
#> GSM152853 1 0.9988 0.436 0.520 0.480
#> GSM152854 1 0.9988 0.436 0.520 0.480
#> GSM152855 1 0.0000 0.757 1.000 0.000
#> GSM153238 1 0.9988 0.436 0.520 0.480
#> GSM153239 1 0.9988 0.436 0.520 0.480
#> GSM153240 1 0.0376 0.757 0.996 0.004
#> GSM153241 1 0.9988 0.436 0.520 0.480
#> GSM153242 1 0.9988 0.436 0.520 0.480
#> GSM153243 1 0.9988 0.436 0.520 0.480
#> GSM153244 1 0.0376 0.757 0.996 0.004
#> GSM153245 1 0.9988 0.436 0.520 0.480
#> GSM153246 1 0.9988 0.436 0.520 0.480
#> GSM153247 1 0.9988 0.436 0.520 0.480
#> GSM153248 1 0.0000 0.757 1.000 0.000
#> GSM153249 1 0.0000 0.757 1.000 0.000
#> GSM153250 1 0.0000 0.757 1.000 0.000
#> GSM153251 1 0.9988 0.436 0.520 0.480
#> GSM153252 1 0.0672 0.757 0.992 0.008
#> GSM153253 1 0.1414 0.752 0.980 0.020
#> GSM153254 1 0.1414 0.752 0.980 0.020
#> GSM153255 1 0.0000 0.757 1.000 0.000
#> GSM153256 1 0.0000 0.757 1.000 0.000
#> GSM153257 1 0.0000 0.757 1.000 0.000
#> GSM153258 1 0.0000 0.757 1.000 0.000
#> GSM153259 1 0.0000 0.757 1.000 0.000
#> GSM153260 1 0.9988 0.436 0.520 0.480
#> GSM153261 1 0.9988 0.436 0.520 0.480
#> GSM153262 1 0.0376 0.757 0.996 0.004
#> GSM153263 1 0.0000 0.757 1.000 0.000
#> GSM153264 1 0.0000 0.757 1.000 0.000
#> GSM153265 1 0.0672 0.757 0.992 0.008
#> GSM153266 1 0.0376 0.757 0.996 0.004
#> GSM153267 1 0.0000 0.757 1.000 0.000
#> GSM153268 1 0.6343 0.651 0.840 0.160
#> GSM153269 1 0.0000 0.757 1.000 0.000
#> GSM153270 1 0.0376 0.757 0.996 0.004
#> GSM153271 1 0.0000 0.757 1.000 0.000
#> GSM153272 1 0.0376 0.757 0.996 0.004
#> GSM153273 1 0.0000 0.757 1.000 0.000
#> GSM153274 1 0.0376 0.757 0.996 0.004
#> GSM153275 1 0.0000 0.757 1.000 0.000
#> GSM153276 1 0.1633 0.750 0.976 0.024
#> GSM153277 1 0.0672 0.757 0.992 0.008
#> GSM153278 1 0.9988 0.436 0.520 0.480
#> GSM153279 1 0.1414 0.752 0.980 0.020
#> GSM153280 1 0.0672 0.757 0.992 0.008
#> GSM153281 1 0.1633 0.750 0.976 0.024
#> GSM153282 1 0.0938 0.755 0.988 0.012
#> GSM153283 1 0.0000 0.757 1.000 0.000
#> GSM153284 1 0.0000 0.757 1.000 0.000
#> GSM153285 1 0.0938 0.755 0.988 0.012
#> GSM153286 1 0.0000 0.757 1.000 0.000
#> GSM153287 1 0.0672 0.757 0.992 0.008
#> GSM153288 1 0.0000 0.757 1.000 0.000
#> GSM153289 1 0.0000 0.757 1.000 0.000
#> GSM153290 1 0.1184 0.754 0.984 0.016
#> GSM153291 1 0.0000 0.757 1.000 0.000
#> GSM153292 1 0.0376 0.757 0.996 0.004
#> GSM153293 1 0.0000 0.757 1.000 0.000
#> GSM153294 1 0.0000 0.757 1.000 0.000
#> GSM153295 1 0.6438 0.651 0.836 0.164
#> GSM153054 1 0.5178 0.687 0.884 0.116
#> GSM153055 1 0.0000 0.757 1.000 0.000
#> GSM153056 1 0.9977 0.439 0.528 0.472
#> GSM153057 1 0.8144 0.571 0.748 0.252
#> GSM153058 1 0.9988 0.436 0.520 0.480
#> GSM153059 1 0.9286 0.510 0.656 0.344
#> GSM153060 1 0.9988 0.436 0.520 0.480
#> GSM153061 1 0.9988 0.436 0.520 0.480
#> GSM153062 1 0.9988 0.436 0.520 0.480
#> GSM153063 1 0.9988 0.436 0.520 0.480
#> GSM153064 1 0.0000 0.757 1.000 0.000
#> GSM153065 1 0.9988 0.436 0.520 0.480
#> GSM153066 2 0.9522 -0.177 0.372 0.628
#> GSM153067 1 0.0000 0.757 1.000 0.000
#> GSM153068 1 0.9988 0.436 0.520 0.480
#> GSM153069 1 0.0376 0.757 0.996 0.004
#> GSM153070 1 0.0000 0.757 1.000 0.000
#> GSM153071 1 0.8081 0.584 0.752 0.248
#> GSM153072 1 0.5842 0.669 0.860 0.140
#> GSM153073 1 0.0000 0.757 1.000 0.000
#> GSM153074 1 0.0000 0.757 1.000 0.000
#> GSM153075 1 0.0000 0.757 1.000 0.000
#> GSM153076 1 0.0000 0.757 1.000 0.000
#> GSM153077 1 0.0000 0.757 1.000 0.000
#> GSM153078 1 0.4690 0.700 0.900 0.100
#> GSM153079 1 0.0000 0.757 1.000 0.000
#> GSM153080 1 0.9988 0.436 0.520 0.480
#> GSM153081 1 0.0000 0.757 1.000 0.000
#> GSM153082 1 0.0000 0.757 1.000 0.000
#> GSM153083 1 0.0376 0.755 0.996 0.004
#> GSM153084 1 0.2236 0.740 0.964 0.036
#> GSM153085 1 0.4022 0.714 0.920 0.080
#> GSM153086 1 0.0672 0.753 0.992 0.008
#> GSM153087 1 0.0376 0.757 0.996 0.004
#> GSM153088 1 0.0000 0.757 1.000 0.000
#> GSM153089 1 0.9988 0.436 0.520 0.480
#> GSM153090 1 0.0000 0.757 1.000 0.000
#> GSM153091 1 0.0000 0.757 1.000 0.000
#> GSM153092 1 0.0000 0.757 1.000 0.000
#> GSM153093 1 0.0000 0.757 1.000 0.000
#> GSM153094 1 0.0000 0.757 1.000 0.000
#> GSM153095 1 0.2603 0.736 0.956 0.044
#> GSM153096 1 0.0000 0.757 1.000 0.000
#> GSM153097 1 0.0000 0.757 1.000 0.000
#> GSM153098 1 0.0000 0.757 1.000 0.000
#> GSM153099 1 0.0376 0.757 0.996 0.004
#> GSM153100 1 0.0000 0.757 1.000 0.000
#> GSM153101 1 0.4562 0.701 0.904 0.096
#> GSM153102 1 0.0000 0.757 1.000 0.000
#> GSM153103 1 0.0938 0.752 0.988 0.012
#> GSM153104 1 0.0938 0.755 0.988 0.012
#> GSM153106 1 0.0000 0.757 1.000 0.000
#> GSM153107 1 0.0000 0.757 1.000 0.000
#> GSM153108 1 0.0000 0.757 1.000 0.000
#> GSM153109 1 0.0376 0.755 0.996 0.004
#> GSM153110 1 0.0000 0.757 1.000 0.000
#> GSM153111 1 0.0376 0.755 0.996 0.004
#> GSM153112 1 0.0000 0.757 1.000 0.000
#> GSM153113 1 0.0672 0.753 0.992 0.008
#> GSM153114 1 0.0000 0.757 1.000 0.000
#> GSM187532 2 0.2778 0.413 0.048 0.952
#> GSM187533 2 0.9954 0.842 0.460 0.540
#> GSM187534 2 0.9970 0.845 0.468 0.532
#> GSM187535 2 0.9988 0.834 0.480 0.520
#> GSM152906 2 0.9977 0.846 0.472 0.528
#> GSM152907 2 0.9977 0.846 0.472 0.528
#> GSM152908 2 0.9977 0.846 0.472 0.528
#> GSM152909 2 0.3733 0.489 0.072 0.928
#> GSM152910 2 0.6438 0.572 0.164 0.836
#> GSM152911 2 0.9977 0.846 0.472 0.528
#> GSM152912 2 0.9970 0.846 0.468 0.532
#> GSM152913 2 0.5294 0.533 0.120 0.880
#> GSM152914 2 0.9977 0.846 0.472 0.528
#> GSM152915 2 0.9977 0.846 0.472 0.528
#> GSM152916 2 0.9881 0.824 0.436 0.564
#> GSM152917 2 0.9977 0.846 0.472 0.528
#> GSM152918 2 0.9977 0.846 0.472 0.528
#> GSM152919 2 0.9977 0.846 0.472 0.528
#> GSM152920 2 0.9977 0.846 0.472 0.528
#> GSM152921 2 0.9977 0.846 0.472 0.528
#> GSM152922 2 0.9963 0.844 0.464 0.536
#> GSM152923 2 0.9977 0.846 0.472 0.528
#> GSM152924 2 0.9954 0.842 0.460 0.540
#> GSM152925 2 0.9866 0.820 0.432 0.568
#> GSM152926 2 0.9977 0.846 0.472 0.528
#> GSM152927 2 0.6343 0.568 0.160 0.840
#> GSM152928 2 0.9881 0.824 0.436 0.564
#> GSM152929 2 0.9977 0.846 0.472 0.528
#> GSM152930 2 0.9977 0.846 0.472 0.528
cbind(get_classes(res, k = 3), get_membership(res, k = 3))
#> class entropy silhouette p1 p2 p3
#> GSM152839 1 0.4452 0.7616 0.808 0.000 0.192
#> GSM152840 3 0.0661 0.9622 0.008 0.004 0.988
#> GSM152841 1 0.0000 0.9838 1.000 0.000 0.000
#> GSM152842 3 0.0661 0.9617 0.008 0.004 0.988
#> GSM152843 3 0.0424 0.9623 0.008 0.000 0.992
#> GSM152844 3 0.0661 0.9622 0.008 0.004 0.988
#> GSM152845 3 0.0661 0.9622 0.008 0.004 0.988
#> GSM152846 3 0.0661 0.9622 0.008 0.004 0.988
#> GSM152847 3 0.0424 0.9623 0.008 0.000 0.992
#> GSM152848 1 0.0424 0.9777 0.992 0.000 0.008
#> GSM152849 3 0.0424 0.9623 0.008 0.000 0.992
#> GSM152850 3 0.2066 0.9035 0.060 0.000 0.940
#> GSM152851 1 0.4346 0.7817 0.816 0.000 0.184
#> GSM152852 3 0.0661 0.9622 0.008 0.004 0.988
#> GSM152853 3 0.0661 0.9622 0.008 0.004 0.988
#> GSM152854 3 0.0661 0.9622 0.008 0.004 0.988
#> GSM152855 1 0.0000 0.9838 1.000 0.000 0.000
#> GSM153238 3 0.0424 0.9623 0.008 0.000 0.992
#> GSM153239 3 0.0661 0.9622 0.008 0.004 0.988
#> GSM153240 1 0.0000 0.9838 1.000 0.000 0.000
#> GSM153241 3 0.0661 0.9617 0.008 0.004 0.988
#> GSM153242 3 0.0661 0.9622 0.008 0.004 0.988
#> GSM153243 3 0.0424 0.9623 0.008 0.000 0.992
#> GSM153244 1 0.0000 0.9838 1.000 0.000 0.000
#> GSM153245 3 0.0661 0.9622 0.008 0.004 0.988
#> GSM153246 3 0.1170 0.9577 0.008 0.016 0.976
#> GSM153247 3 0.0661 0.9617 0.008 0.004 0.988
#> GSM153248 1 0.0000 0.9838 1.000 0.000 0.000
#> GSM153249 1 0.0000 0.9838 1.000 0.000 0.000
#> GSM153250 1 0.0000 0.9838 1.000 0.000 0.000
#> GSM153251 3 0.0424 0.9623 0.008 0.000 0.992
#> GSM153252 1 0.0000 0.9838 1.000 0.000 0.000
#> GSM153253 1 0.0000 0.9838 1.000 0.000 0.000
#> GSM153254 1 0.0000 0.9838 1.000 0.000 0.000
#> GSM153255 1 0.0000 0.9838 1.000 0.000 0.000
#> GSM153256 1 0.0000 0.9838 1.000 0.000 0.000
#> GSM153257 1 0.0000 0.9838 1.000 0.000 0.000
#> GSM153258 1 0.0000 0.9838 1.000 0.000 0.000
#> GSM153259 1 0.0000 0.9838 1.000 0.000 0.000
#> GSM153260 3 0.0424 0.9623 0.008 0.000 0.992
#> GSM153261 3 0.0424 0.9623 0.008 0.000 0.992
#> GSM153262 1 0.0000 0.9838 1.000 0.000 0.000
#> GSM153263 1 0.0000 0.9838 1.000 0.000 0.000
#> GSM153264 1 0.0000 0.9838 1.000 0.000 0.000
#> GSM153265 1 0.0000 0.9838 1.000 0.000 0.000
#> GSM153266 1 0.0000 0.9838 1.000 0.000 0.000
#> GSM153267 1 0.0000 0.9838 1.000 0.000 0.000
#> GSM153268 1 0.0747 0.9709 0.984 0.000 0.016
#> GSM153269 1 0.0000 0.9838 1.000 0.000 0.000
#> GSM153270 1 0.0237 0.9807 0.996 0.000 0.004
#> GSM153271 1 0.0000 0.9838 1.000 0.000 0.000
#> GSM153272 1 0.0000 0.9838 1.000 0.000 0.000
#> GSM153273 1 0.0000 0.9838 1.000 0.000 0.000
#> GSM153274 1 0.0000 0.9838 1.000 0.000 0.000
#> GSM153275 1 0.0000 0.9838 1.000 0.000 0.000
#> GSM153276 1 0.0000 0.9838 1.000 0.000 0.000
#> GSM153277 1 0.0000 0.9838 1.000 0.000 0.000
#> GSM153278 3 0.0892 0.9521 0.020 0.000 0.980
#> GSM153279 1 0.0237 0.9806 0.996 0.000 0.004
#> GSM153280 1 0.0000 0.9838 1.000 0.000 0.000
#> GSM153281 1 0.0237 0.9805 0.996 0.000 0.004
#> GSM153282 1 0.0000 0.9838 1.000 0.000 0.000
#> GSM153283 1 0.0000 0.9838 1.000 0.000 0.000
#> GSM153284 1 0.0000 0.9838 1.000 0.000 0.000
#> GSM153285 1 0.0000 0.9838 1.000 0.000 0.000
#> GSM153286 1 0.0000 0.9838 1.000 0.000 0.000
#> GSM153287 1 0.0000 0.9838 1.000 0.000 0.000
#> GSM153288 1 0.0000 0.9838 1.000 0.000 0.000
#> GSM153289 1 0.0000 0.9838 1.000 0.000 0.000
#> GSM153290 1 0.0000 0.9838 1.000 0.000 0.000
#> GSM153291 1 0.0000 0.9838 1.000 0.000 0.000
#> GSM153292 1 0.0000 0.9838 1.000 0.000 0.000
#> GSM153293 1 0.0000 0.9838 1.000 0.000 0.000
#> GSM153294 1 0.0000 0.9838 1.000 0.000 0.000
#> GSM153295 1 0.1529 0.9511 0.960 0.000 0.040
#> GSM153054 1 0.3619 0.8470 0.864 0.000 0.136
#> GSM153055 1 0.0000 0.9838 1.000 0.000 0.000
#> GSM153056 3 0.1031 0.9479 0.024 0.000 0.976
#> GSM153057 3 0.6305 0.0876 0.484 0.000 0.516
#> GSM153058 3 0.0424 0.9623 0.008 0.000 0.992
#> GSM153059 3 0.5497 0.5709 0.292 0.000 0.708
#> GSM153060 3 0.1170 0.9577 0.008 0.016 0.976
#> GSM153061 3 0.1015 0.9584 0.008 0.012 0.980
#> GSM153062 3 0.1170 0.9577 0.008 0.016 0.976
#> GSM153063 3 0.0661 0.9617 0.008 0.004 0.988
#> GSM153064 1 0.0000 0.9838 1.000 0.000 0.000
#> GSM153065 3 0.0661 0.9617 0.008 0.004 0.988
#> GSM153066 3 0.0424 0.9623 0.008 0.000 0.992
#> GSM153067 1 0.0000 0.9838 1.000 0.000 0.000
#> GSM153068 3 0.0661 0.9617 0.008 0.004 0.988
#> GSM153069 1 0.0000 0.9838 1.000 0.000 0.000
#> GSM153070 1 0.0000 0.9838 1.000 0.000 0.000
#> GSM153071 1 0.6026 0.3999 0.624 0.000 0.376
#> GSM153072 1 0.4121 0.8043 0.832 0.000 0.168
#> GSM153073 1 0.0000 0.9838 1.000 0.000 0.000
#> GSM153074 1 0.0000 0.9838 1.000 0.000 0.000
#> GSM153075 1 0.0000 0.9838 1.000 0.000 0.000
#> GSM153076 1 0.0000 0.9838 1.000 0.000 0.000
#> GSM153077 1 0.0000 0.9838 1.000 0.000 0.000
#> GSM153078 1 0.3038 0.8854 0.896 0.000 0.104
#> GSM153079 1 0.0000 0.9838 1.000 0.000 0.000
#> GSM153080 3 0.1643 0.9230 0.044 0.000 0.956
#> GSM153081 1 0.0237 0.9807 0.996 0.000 0.004
#> GSM153082 1 0.0000 0.9838 1.000 0.000 0.000
#> GSM153083 1 0.0000 0.9838 1.000 0.000 0.000
#> GSM153084 1 0.2486 0.9251 0.932 0.008 0.060
#> GSM153085 1 0.2448 0.9150 0.924 0.000 0.076
#> GSM153086 1 0.0000 0.9838 1.000 0.000 0.000
#> GSM153087 1 0.0000 0.9838 1.000 0.000 0.000
#> GSM153088 1 0.0000 0.9838 1.000 0.000 0.000
#> GSM153089 3 0.0661 0.9622 0.008 0.004 0.988
#> GSM153090 1 0.0000 0.9838 1.000 0.000 0.000
#> GSM153091 1 0.0000 0.9838 1.000 0.000 0.000
#> GSM153092 1 0.0000 0.9838 1.000 0.000 0.000
#> GSM153093 1 0.0000 0.9838 1.000 0.000 0.000
#> GSM153094 1 0.0000 0.9838 1.000 0.000 0.000
#> GSM153095 1 0.1529 0.9509 0.960 0.000 0.040
#> GSM153096 1 0.0000 0.9838 1.000 0.000 0.000
#> GSM153097 1 0.0000 0.9838 1.000 0.000 0.000
#> GSM153098 1 0.0000 0.9838 1.000 0.000 0.000
#> GSM153099 1 0.0000 0.9838 1.000 0.000 0.000
#> GSM153100 1 0.0000 0.9838 1.000 0.000 0.000
#> GSM153101 1 0.2959 0.8890 0.900 0.000 0.100
#> GSM153102 1 0.0000 0.9838 1.000 0.000 0.000
#> GSM153103 1 0.0424 0.9779 0.992 0.000 0.008
#> GSM153104 1 0.0000 0.9838 1.000 0.000 0.000
#> GSM153106 1 0.0000 0.9838 1.000 0.000 0.000
#> GSM153107 1 0.0000 0.9838 1.000 0.000 0.000
#> GSM153108 1 0.0000 0.9838 1.000 0.000 0.000
#> GSM153109 1 0.0000 0.9838 1.000 0.000 0.000
#> GSM153110 1 0.0000 0.9838 1.000 0.000 0.000
#> GSM153111 1 0.0000 0.9838 1.000 0.000 0.000
#> GSM153112 1 0.0000 0.9838 1.000 0.000 0.000
#> GSM153113 1 0.0237 0.9808 0.996 0.004 0.000
#> GSM153114 1 0.0000 0.9838 1.000 0.000 0.000
#> GSM187532 2 0.4702 0.7283 0.000 0.788 0.212
#> GSM187533 2 0.0747 0.9857 0.016 0.984 0.000
#> GSM187534 2 0.0747 0.9857 0.016 0.984 0.000
#> GSM187535 2 0.2584 0.9249 0.064 0.928 0.008
#> GSM152906 2 0.1170 0.9850 0.016 0.976 0.008
#> GSM152907 2 0.1170 0.9850 0.016 0.976 0.008
#> GSM152908 2 0.0747 0.9857 0.016 0.984 0.000
#> GSM152909 2 0.0661 0.9745 0.004 0.988 0.008
#> GSM152910 2 0.0848 0.9787 0.008 0.984 0.008
#> GSM152911 2 0.0747 0.9857 0.016 0.984 0.000
#> GSM152912 2 0.0747 0.9857 0.016 0.984 0.000
#> GSM152913 2 0.0475 0.9748 0.004 0.992 0.004
#> GSM152914 2 0.0747 0.9857 0.016 0.984 0.000
#> GSM152915 2 0.0747 0.9857 0.016 0.984 0.000
#> GSM152916 2 0.1170 0.9850 0.016 0.976 0.008
#> GSM152917 2 0.0747 0.9857 0.016 0.984 0.000
#> GSM152918 2 0.0747 0.9857 0.016 0.984 0.000
#> GSM152919 2 0.0747 0.9857 0.016 0.984 0.000
#> GSM152920 2 0.0747 0.9857 0.016 0.984 0.000
#> GSM152921 2 0.0747 0.9857 0.016 0.984 0.000
#> GSM152922 2 0.0747 0.9857 0.016 0.984 0.000
#> GSM152923 2 0.1170 0.9850 0.016 0.976 0.008
#> GSM152924 2 0.1170 0.9850 0.016 0.976 0.008
#> GSM152925 2 0.1170 0.9850 0.016 0.976 0.008
#> GSM152926 2 0.1170 0.9850 0.016 0.976 0.008
#> GSM152927 2 0.1170 0.9785 0.008 0.976 0.016
#> GSM152928 2 0.1337 0.9832 0.016 0.972 0.012
#> GSM152929 2 0.1170 0.9850 0.016 0.976 0.008
#> GSM152930 2 0.1170 0.9850 0.016 0.976 0.008
cbind(get_classes(res, k = 4), get_membership(res, k = 4))
#> class entropy silhouette p1 p2 p3 p4
#> GSM152839 4 0.7918 0.6462 0.332 0.000 0.316 0.352
#> GSM152840 3 0.2921 0.7533 0.000 0.000 0.860 0.140
#> GSM152841 1 0.1474 0.7416 0.948 0.000 0.000 0.052
#> GSM152842 3 0.3942 0.7647 0.000 0.000 0.764 0.236
#> GSM152843 3 0.3486 0.7685 0.000 0.000 0.812 0.188
#> GSM152844 3 0.2589 0.7502 0.000 0.000 0.884 0.116
#> GSM152845 3 0.3649 0.7736 0.000 0.000 0.796 0.204
#> GSM152846 3 0.3356 0.7472 0.000 0.000 0.824 0.176
#> GSM152847 3 0.3569 0.7763 0.000 0.000 0.804 0.196
#> GSM152848 1 0.3444 0.6968 0.816 0.000 0.000 0.184
#> GSM152849 3 0.3801 0.7517 0.000 0.000 0.780 0.220
#> GSM152850 3 0.5138 0.5969 0.008 0.000 0.600 0.392
#> GSM152851 1 0.7062 -0.3860 0.572 0.000 0.224 0.204
#> GSM152852 3 0.3266 0.7555 0.000 0.000 0.832 0.168
#> GSM152853 3 0.2589 0.7502 0.000 0.000 0.884 0.116
#> GSM152854 3 0.2704 0.7688 0.000 0.000 0.876 0.124
#> GSM152855 1 0.1022 0.7747 0.968 0.000 0.000 0.032
#> GSM153238 3 0.4941 0.6888 0.000 0.000 0.564 0.436
#> GSM153239 3 0.3074 0.7470 0.000 0.000 0.848 0.152
#> GSM153240 1 0.0592 0.7678 0.984 0.000 0.000 0.016
#> GSM153241 3 0.3266 0.7805 0.000 0.000 0.832 0.168
#> GSM153242 3 0.3873 0.7656 0.000 0.000 0.772 0.228
#> GSM153243 3 0.4866 0.6633 0.000 0.000 0.596 0.404
#> GSM153244 1 0.1209 0.7631 0.964 0.000 0.004 0.032
#> GSM153245 3 0.2704 0.7648 0.000 0.000 0.876 0.124
#> GSM153246 3 0.4677 0.7053 0.000 0.004 0.680 0.316
#> GSM153247 3 0.4877 0.7156 0.000 0.000 0.592 0.408
#> GSM153248 1 0.3837 0.6389 0.776 0.000 0.000 0.224
#> GSM153249 1 0.0592 0.7678 0.984 0.000 0.000 0.016
#> GSM153250 1 0.1302 0.7744 0.956 0.000 0.000 0.044
#> GSM153251 3 0.4008 0.7851 0.000 0.000 0.756 0.244
#> GSM153252 1 0.1022 0.7622 0.968 0.000 0.000 0.032
#> GSM153253 1 0.1489 0.7469 0.952 0.000 0.004 0.044
#> GSM153254 1 0.5227 0.3057 0.704 0.000 0.040 0.256
#> GSM153255 1 0.0469 0.7695 0.988 0.000 0.000 0.012
#> GSM153256 1 0.0469 0.7747 0.988 0.000 0.000 0.012
#> GSM153257 1 0.0707 0.7723 0.980 0.000 0.000 0.020
#> GSM153258 1 0.2921 0.7322 0.860 0.000 0.000 0.140
#> GSM153259 1 0.3873 0.6338 0.772 0.000 0.000 0.228
#> GSM153260 3 0.4500 0.7609 0.000 0.000 0.684 0.316
#> GSM153261 3 0.4679 0.7028 0.000 0.000 0.648 0.352
#> GSM153262 1 0.1302 0.7670 0.956 0.000 0.000 0.044
#> GSM153263 1 0.2647 0.7466 0.880 0.000 0.000 0.120
#> GSM153264 1 0.3975 0.6186 0.760 0.000 0.000 0.240
#> GSM153265 1 0.1302 0.7554 0.956 0.000 0.000 0.044
#> GSM153266 1 0.4008 0.6099 0.756 0.000 0.000 0.244
#> GSM153267 1 0.0000 0.7729 1.000 0.000 0.000 0.000
#> GSM153268 1 0.5894 0.0934 0.692 0.000 0.200 0.108
#> GSM153269 1 0.1118 0.7747 0.964 0.000 0.000 0.036
#> GSM153270 1 0.1557 0.7758 0.944 0.000 0.000 0.056
#> GSM153271 1 0.1211 0.7744 0.960 0.000 0.000 0.040
#> GSM153272 1 0.0592 0.7678 0.984 0.000 0.000 0.016
#> GSM153273 1 0.3801 0.6419 0.780 0.000 0.000 0.220
#> GSM153274 1 0.1474 0.7739 0.948 0.000 0.000 0.052
#> GSM153275 1 0.0469 0.7748 0.988 0.000 0.000 0.012
#> GSM153276 1 0.1474 0.7735 0.948 0.000 0.000 0.052
#> GSM153277 1 0.0921 0.7665 0.972 0.000 0.000 0.028
#> GSM153278 3 0.4936 0.6196 0.004 0.000 0.624 0.372
#> GSM153279 1 0.1557 0.7435 0.944 0.000 0.000 0.056
#> GSM153280 1 0.1211 0.7526 0.960 0.000 0.000 0.040
#> GSM153281 1 0.1302 0.7503 0.956 0.000 0.000 0.044
#> GSM153282 1 0.1302 0.7495 0.956 0.000 0.000 0.044
#> GSM153283 1 0.3024 0.7228 0.852 0.000 0.000 0.148
#> GSM153284 1 0.0469 0.7754 0.988 0.000 0.000 0.012
#> GSM153285 1 0.1398 0.7498 0.956 0.000 0.004 0.040
#> GSM153286 1 0.0000 0.7729 1.000 0.000 0.000 0.000
#> GSM153287 1 0.0921 0.7616 0.972 0.000 0.000 0.028
#> GSM153288 1 0.0188 0.7716 0.996 0.000 0.000 0.004
#> GSM153289 1 0.1557 0.7741 0.944 0.000 0.000 0.056
#> GSM153290 1 0.1211 0.7526 0.960 0.000 0.000 0.040
#> GSM153291 1 0.0469 0.7693 0.988 0.000 0.000 0.012
#> GSM153292 1 0.1022 0.7589 0.968 0.000 0.000 0.032
#> GSM153293 1 0.0188 0.7738 0.996 0.000 0.000 0.004
#> GSM153294 1 0.3444 0.6846 0.816 0.000 0.000 0.184
#> GSM153295 1 0.2408 0.7388 0.920 0.000 0.036 0.044
#> GSM153054 1 0.6038 -0.3301 0.532 0.000 0.044 0.424
#> GSM153055 1 0.1637 0.7742 0.940 0.000 0.000 0.060
#> GSM153056 3 0.4718 0.7122 0.012 0.000 0.708 0.280
#> GSM153057 3 0.7853 -0.4345 0.268 0.000 0.368 0.364
#> GSM153058 3 0.3837 0.7876 0.000 0.000 0.776 0.224
#> GSM153059 3 0.6887 0.3300 0.104 0.000 0.456 0.440
#> GSM153060 3 0.4560 0.7146 0.000 0.004 0.700 0.296
#> GSM153061 3 0.4608 0.7171 0.000 0.004 0.692 0.304
#> GSM153062 3 0.4720 0.7017 0.000 0.004 0.672 0.324
#> GSM153063 3 0.4103 0.7699 0.000 0.000 0.744 0.256
#> GSM153064 1 0.3444 0.6844 0.816 0.000 0.000 0.184
#> GSM153065 3 0.4040 0.7796 0.000 0.000 0.752 0.248
#> GSM153066 3 0.4985 0.6445 0.000 0.000 0.532 0.468
#> GSM153067 1 0.0592 0.7712 0.984 0.000 0.000 0.016
#> GSM153068 3 0.4277 0.7558 0.000 0.000 0.720 0.280
#> GSM153069 1 0.0707 0.7658 0.980 0.000 0.000 0.020
#> GSM153070 1 0.2704 0.7429 0.876 0.000 0.000 0.124
#> GSM153071 4 0.7648 0.7667 0.348 0.000 0.216 0.436
#> GSM153072 4 0.6745 0.6735 0.428 0.000 0.092 0.480
#> GSM153073 1 0.3649 0.6695 0.796 0.000 0.000 0.204
#> GSM153074 1 0.0336 0.7705 0.992 0.000 0.000 0.008
#> GSM153075 1 0.0469 0.7734 0.988 0.000 0.000 0.012
#> GSM153076 1 0.2760 0.7414 0.872 0.000 0.000 0.128
#> GSM153077 1 0.4356 0.5026 0.708 0.000 0.000 0.292
#> GSM153078 4 0.7448 0.7421 0.400 0.000 0.172 0.428
#> GSM153079 1 0.4250 0.5512 0.724 0.000 0.000 0.276
#> GSM153080 3 0.5386 0.6555 0.024 0.000 0.632 0.344
#> GSM153081 1 0.4222 0.5614 0.728 0.000 0.000 0.272
#> GSM153082 1 0.3942 0.6202 0.764 0.000 0.000 0.236
#> GSM153083 1 0.4564 0.4062 0.672 0.000 0.000 0.328
#> GSM153084 4 0.7211 0.7688 0.352 0.004 0.132 0.512
#> GSM153085 1 0.6323 -0.4998 0.500 0.000 0.060 0.440
#> GSM153086 1 0.5183 -0.0175 0.584 0.000 0.008 0.408
#> GSM153087 1 0.1302 0.7683 0.956 0.000 0.000 0.044
#> GSM153088 1 0.1792 0.7678 0.932 0.000 0.000 0.068
#> GSM153089 3 0.3907 0.7841 0.000 0.000 0.768 0.232
#> GSM153090 1 0.1637 0.7701 0.940 0.000 0.000 0.060
#> GSM153091 1 0.3873 0.6347 0.772 0.000 0.000 0.228
#> GSM153092 1 0.3123 0.7148 0.844 0.000 0.000 0.156
#> GSM153093 1 0.0336 0.7737 0.992 0.000 0.000 0.008
#> GSM153094 1 0.3975 0.6197 0.760 0.000 0.000 0.240
#> GSM153095 1 0.5586 -0.3721 0.528 0.000 0.020 0.452
#> GSM153096 1 0.3801 0.6429 0.780 0.000 0.000 0.220
#> GSM153097 1 0.4585 0.3882 0.668 0.000 0.000 0.332
#> GSM153098 1 0.3123 0.7132 0.844 0.000 0.000 0.156
#> GSM153099 1 0.0336 0.7713 0.992 0.000 0.000 0.008
#> GSM153100 1 0.3024 0.7209 0.852 0.000 0.000 0.148
#> GSM153101 1 0.6504 -0.5609 0.476 0.000 0.072 0.452
#> GSM153102 1 0.4277 0.5188 0.720 0.000 0.000 0.280
#> GSM153103 1 0.5750 -0.3259 0.532 0.000 0.028 0.440
#> GSM153104 1 0.0921 0.7616 0.972 0.000 0.000 0.028
#> GSM153106 1 0.2868 0.7393 0.864 0.000 0.000 0.136
#> GSM153107 1 0.3172 0.7242 0.840 0.000 0.000 0.160
#> GSM153108 1 0.2011 0.7656 0.920 0.000 0.000 0.080
#> GSM153109 1 0.4250 0.5341 0.724 0.000 0.000 0.276
#> GSM153110 1 0.3907 0.6245 0.768 0.000 0.000 0.232
#> GSM153111 1 0.4454 0.4596 0.692 0.000 0.000 0.308
#> GSM153112 1 0.3219 0.7086 0.836 0.000 0.000 0.164
#> GSM153113 1 0.4804 0.0997 0.616 0.000 0.000 0.384
#> GSM153114 1 0.1211 0.7749 0.960 0.000 0.000 0.040
#> GSM187532 2 0.5700 0.6756 0.000 0.716 0.120 0.164
#> GSM187533 2 0.1109 0.9626 0.004 0.968 0.000 0.028
#> GSM187534 2 0.1004 0.9631 0.004 0.972 0.000 0.024
#> GSM187535 2 0.4093 0.8109 0.072 0.832 0.000 0.096
#> GSM152906 2 0.1109 0.9620 0.004 0.968 0.000 0.028
#> GSM152907 2 0.1109 0.9620 0.004 0.968 0.000 0.028
#> GSM152908 2 0.1109 0.9632 0.004 0.968 0.000 0.028
#> GSM152909 2 0.1930 0.9530 0.004 0.936 0.004 0.056
#> GSM152910 2 0.1305 0.9621 0.004 0.960 0.000 0.036
#> GSM152911 2 0.0779 0.9649 0.004 0.980 0.000 0.016
#> GSM152912 2 0.1109 0.9632 0.004 0.968 0.000 0.028
#> GSM152913 2 0.1305 0.9631 0.004 0.960 0.000 0.036
#> GSM152914 2 0.0779 0.9649 0.004 0.980 0.000 0.016
#> GSM152915 2 0.0779 0.9649 0.004 0.980 0.000 0.016
#> GSM152916 2 0.1305 0.9608 0.004 0.960 0.000 0.036
#> GSM152917 2 0.0779 0.9649 0.004 0.980 0.000 0.016
#> GSM152918 2 0.0779 0.9649 0.004 0.980 0.000 0.016
#> GSM152919 2 0.0779 0.9649 0.004 0.980 0.000 0.016
#> GSM152920 2 0.1109 0.9632 0.004 0.968 0.000 0.028
#> GSM152921 2 0.1109 0.9632 0.004 0.968 0.000 0.028
#> GSM152922 2 0.1109 0.9632 0.004 0.968 0.000 0.028
#> GSM152923 2 0.1109 0.9620 0.004 0.968 0.000 0.028
#> GSM152924 2 0.1398 0.9599 0.004 0.956 0.000 0.040
#> GSM152925 2 0.1398 0.9599 0.004 0.956 0.000 0.040
#> GSM152926 2 0.1109 0.9620 0.004 0.968 0.000 0.028
#> GSM152927 2 0.1398 0.9599 0.004 0.956 0.000 0.040
#> GSM152928 2 0.2164 0.9420 0.004 0.924 0.004 0.068
#> GSM152929 2 0.1109 0.9620 0.004 0.968 0.000 0.028
#> GSM152930 2 0.1109 0.9620 0.004 0.968 0.000 0.028
cbind(get_classes(res, k = 5), get_membership(res, k = 5))
#> class entropy silhouette p1 p2 p3 p4 p5
#> GSM152839 3 0.6291 0.2028 0.392 0.000 0.492 0.100 0.016
#> GSM152840 3 0.6315 0.1727 0.008 0.000 0.560 0.260 0.172
#> GSM152841 4 0.3876 0.8620 0.316 0.000 0.000 0.684 0.000
#> GSM152842 3 0.4582 -0.2914 0.000 0.000 0.572 0.012 0.416
#> GSM152843 3 0.4755 0.3822 0.056 0.000 0.780 0.080 0.084
#> GSM152844 3 0.6504 0.0639 0.000 0.000 0.488 0.240 0.272
#> GSM152845 3 0.6233 0.0593 0.000 0.000 0.520 0.168 0.312
#> GSM152846 3 0.6564 -0.0791 0.000 0.000 0.420 0.204 0.376
#> GSM152847 3 0.4626 0.3706 0.044 0.000 0.784 0.064 0.108
#> GSM152848 1 0.4130 0.4808 0.768 0.000 0.024 0.196 0.012
#> GSM152849 3 0.3923 0.4109 0.064 0.000 0.832 0.036 0.068
#> GSM152850 3 0.4986 0.3945 0.240 0.000 0.700 0.028 0.032
#> GSM152851 4 0.6084 0.3066 0.188 0.000 0.200 0.604 0.008
#> GSM152852 3 0.6243 0.1391 0.000 0.000 0.544 0.240 0.216
#> GSM152853 3 0.6474 0.0697 0.000 0.000 0.496 0.240 0.264
#> GSM152854 3 0.5476 0.2333 0.000 0.000 0.656 0.184 0.160
#> GSM152855 4 0.4723 0.7865 0.448 0.000 0.000 0.536 0.016
#> GSM153238 3 0.6112 0.3583 0.164 0.000 0.648 0.036 0.152
#> GSM153239 3 0.6598 -0.0171 0.000 0.000 0.452 0.232 0.316
#> GSM153240 4 0.4211 0.8940 0.360 0.000 0.000 0.636 0.004
#> GSM153241 3 0.4848 0.3315 0.040 0.000 0.756 0.052 0.152
#> GSM153242 3 0.6456 -0.0341 0.000 0.000 0.468 0.192 0.340
#> GSM153243 3 0.4778 0.4044 0.188 0.000 0.740 0.020 0.052
#> GSM153244 4 0.4225 0.8950 0.364 0.000 0.000 0.632 0.004
#> GSM153245 3 0.6233 0.0155 0.000 0.000 0.520 0.168 0.312
#> GSM153246 5 0.3282 0.7792 0.000 0.000 0.188 0.008 0.804
#> GSM153247 3 0.5956 0.2864 0.128 0.000 0.628 0.016 0.228
#> GSM153248 1 0.2011 0.6388 0.908 0.000 0.000 0.088 0.004
#> GSM153249 4 0.4045 0.8926 0.356 0.000 0.000 0.644 0.000
#> GSM153250 4 0.4306 0.7109 0.492 0.000 0.000 0.508 0.000
#> GSM153251 3 0.4489 0.2710 0.000 0.000 0.740 0.068 0.192
#> GSM153252 4 0.4347 0.8940 0.356 0.000 0.004 0.636 0.004
#> GSM153253 4 0.4162 0.8589 0.312 0.000 0.004 0.680 0.004
#> GSM153254 1 0.6780 -0.0258 0.408 0.000 0.196 0.388 0.008
#> GSM153255 4 0.4074 0.8937 0.364 0.000 0.000 0.636 0.000
#> GSM153256 4 0.4359 0.8664 0.412 0.000 0.000 0.584 0.004
#> GSM153257 4 0.4238 0.8943 0.368 0.000 0.000 0.628 0.004
#> GSM153258 1 0.3790 0.2879 0.724 0.000 0.000 0.272 0.004
#> GSM153259 1 0.2249 0.6352 0.896 0.000 0.000 0.096 0.008
#> GSM153260 3 0.5557 0.2384 0.052 0.000 0.652 0.032 0.264
#> GSM153261 3 0.5214 0.4118 0.156 0.000 0.728 0.032 0.084
#> GSM153262 4 0.4238 0.8924 0.368 0.000 0.000 0.628 0.004
#> GSM153263 1 0.4252 -0.0777 0.652 0.000 0.000 0.340 0.008
#> GSM153264 1 0.2589 0.6314 0.888 0.000 0.008 0.092 0.012
#> GSM153265 4 0.4286 0.8829 0.340 0.000 0.004 0.652 0.004
#> GSM153266 1 0.2589 0.6375 0.888 0.000 0.012 0.092 0.008
#> GSM153267 4 0.4288 0.8890 0.384 0.000 0.000 0.612 0.004
#> GSM153268 4 0.3839 0.4279 0.108 0.000 0.072 0.816 0.004
#> GSM153269 4 0.4528 0.8179 0.444 0.000 0.000 0.548 0.008
#> GSM153270 4 0.4645 0.8289 0.424 0.000 0.004 0.564 0.008
#> GSM153271 4 0.4430 0.7932 0.456 0.000 0.000 0.540 0.004
#> GSM153272 4 0.4225 0.8937 0.364 0.000 0.000 0.632 0.004
#> GSM153273 1 0.2136 0.6402 0.904 0.000 0.000 0.088 0.008
#> GSM153274 4 0.4684 0.8007 0.452 0.000 0.004 0.536 0.008
#> GSM153275 4 0.4375 0.8599 0.420 0.000 0.000 0.576 0.004
#> GSM153276 4 0.4709 0.8449 0.400 0.000 0.008 0.584 0.008
#> GSM153277 4 0.4347 0.8926 0.356 0.000 0.004 0.636 0.004
#> GSM153278 3 0.4716 0.4112 0.204 0.000 0.736 0.024 0.036
#> GSM153279 4 0.4435 0.8594 0.336 0.000 0.016 0.648 0.000
#> GSM153280 4 0.4135 0.8842 0.340 0.000 0.000 0.656 0.004
#> GSM153281 4 0.4047 0.8690 0.320 0.000 0.004 0.676 0.000
#> GSM153282 4 0.3895 0.8684 0.320 0.000 0.000 0.680 0.000
#> GSM153283 1 0.3700 0.4013 0.752 0.000 0.000 0.240 0.008
#> GSM153284 4 0.4235 0.8566 0.424 0.000 0.000 0.576 0.000
#> GSM153285 4 0.4084 0.8773 0.328 0.000 0.000 0.668 0.004
#> GSM153286 4 0.4171 0.8817 0.396 0.000 0.000 0.604 0.000
#> GSM153287 4 0.4015 0.8911 0.348 0.000 0.000 0.652 0.000
#> GSM153288 4 0.4192 0.8768 0.404 0.000 0.000 0.596 0.000
#> GSM153289 1 0.4744 -0.6303 0.508 0.000 0.000 0.476 0.016
#> GSM153290 4 0.4166 0.8889 0.348 0.000 0.000 0.648 0.004
#> GSM153291 4 0.4211 0.8943 0.360 0.000 0.000 0.636 0.004
#> GSM153292 4 0.4166 0.8913 0.348 0.000 0.000 0.648 0.004
#> GSM153293 4 0.4350 0.8737 0.408 0.000 0.000 0.588 0.004
#> GSM153294 1 0.2929 0.5903 0.840 0.000 0.000 0.152 0.008
#> GSM153295 4 0.5407 0.8008 0.392 0.000 0.028 0.560 0.020
#> GSM153054 1 0.4181 0.5659 0.780 0.000 0.172 0.032 0.016
#> GSM153055 4 0.4560 0.7560 0.484 0.000 0.000 0.508 0.008
#> GSM153056 3 0.4680 0.4313 0.124 0.000 0.776 0.060 0.040
#> GSM153057 3 0.6143 0.2529 0.384 0.000 0.524 0.040 0.052
#> GSM153058 3 0.5165 0.2478 0.008 0.000 0.696 0.088 0.208
#> GSM153059 3 0.5968 0.3549 0.260 0.000 0.628 0.040 0.072
#> GSM153060 5 0.3491 0.7890 0.000 0.000 0.228 0.004 0.768
#> GSM153061 5 0.4029 0.7277 0.000 0.000 0.316 0.004 0.680
#> GSM153062 5 0.3123 0.7689 0.000 0.000 0.184 0.004 0.812
#> GSM153063 3 0.4871 -0.1319 0.004 0.000 0.604 0.024 0.368
#> GSM153064 1 0.2886 0.5928 0.844 0.000 0.000 0.148 0.008
#> GSM153065 3 0.4958 -0.0738 0.004 0.000 0.616 0.032 0.348
#> GSM153066 3 0.6068 0.3661 0.216 0.000 0.640 0.036 0.108
#> GSM153067 4 0.4211 0.8939 0.360 0.000 0.000 0.636 0.004
#> GSM153068 5 0.4748 0.3533 0.000 0.000 0.492 0.016 0.492
#> GSM153069 4 0.4015 0.8908 0.348 0.000 0.000 0.652 0.000
#> GSM153070 1 0.4151 -0.0508 0.652 0.000 0.000 0.344 0.004
#> GSM153071 1 0.6424 -0.2073 0.472 0.000 0.420 0.056 0.052
#> GSM153072 1 0.5087 0.3393 0.692 0.000 0.244 0.028 0.036
#> GSM153073 1 0.3087 0.5814 0.836 0.000 0.004 0.152 0.008
#> GSM153074 4 0.4251 0.8931 0.372 0.000 0.000 0.624 0.004
#> GSM153075 4 0.4359 0.8660 0.412 0.000 0.000 0.584 0.004
#> GSM153076 1 0.3809 0.3294 0.736 0.000 0.000 0.256 0.008
#> GSM153077 1 0.2886 0.6354 0.884 0.000 0.036 0.068 0.012
#> GSM153078 1 0.5848 0.1418 0.556 0.000 0.364 0.060 0.020
#> GSM153079 1 0.2312 0.6459 0.912 0.000 0.016 0.060 0.012
#> GSM153080 3 0.5219 0.4332 0.152 0.000 0.724 0.100 0.024
#> GSM153081 1 0.3059 0.6405 0.868 0.000 0.016 0.096 0.020
#> GSM153082 1 0.2645 0.6418 0.884 0.000 0.008 0.096 0.012
#> GSM153083 1 0.1483 0.6345 0.952 0.000 0.028 0.008 0.012
#> GSM153084 1 0.5855 -0.0147 0.576 0.000 0.344 0.040 0.040
#> GSM153085 1 0.4836 0.4309 0.724 0.000 0.212 0.044 0.020
#> GSM153086 1 0.2589 0.5962 0.888 0.000 0.092 0.012 0.008
#> GSM153087 4 0.4553 0.8728 0.384 0.000 0.008 0.604 0.004
#> GSM153088 1 0.4522 -0.5405 0.552 0.000 0.000 0.440 0.008
#> GSM153089 3 0.4490 0.3057 0.004 0.000 0.756 0.072 0.168
#> GSM153090 1 0.4446 -0.6501 0.520 0.000 0.000 0.476 0.004
#> GSM153091 1 0.2304 0.6323 0.892 0.000 0.000 0.100 0.008
#> GSM153092 1 0.3177 0.4828 0.792 0.000 0.000 0.208 0.000
#> GSM153093 4 0.4331 0.8786 0.400 0.000 0.000 0.596 0.004
#> GSM153094 1 0.2228 0.6368 0.900 0.000 0.004 0.092 0.004
#> GSM153095 1 0.5078 0.3475 0.692 0.000 0.244 0.040 0.024
#> GSM153096 1 0.2179 0.6325 0.896 0.000 0.000 0.100 0.004
#> GSM153097 1 0.1455 0.6310 0.952 0.000 0.032 0.008 0.008
#> GSM153098 1 0.3196 0.5365 0.804 0.000 0.000 0.192 0.004
#> GSM153099 4 0.4114 0.8928 0.376 0.000 0.000 0.624 0.000
#> GSM153100 1 0.3366 0.4797 0.784 0.000 0.000 0.212 0.004
#> GSM153101 1 0.3769 0.4886 0.796 0.000 0.176 0.016 0.012
#> GSM153102 1 0.2409 0.6423 0.908 0.000 0.028 0.056 0.008
#> GSM153103 1 0.3592 0.5159 0.808 0.000 0.168 0.012 0.012
#> GSM153104 4 0.4286 0.8876 0.340 0.000 0.004 0.652 0.004
#> GSM153106 1 0.4249 0.2164 0.688 0.000 0.000 0.296 0.016
#> GSM153107 1 0.3759 0.4582 0.764 0.000 0.000 0.220 0.016
#> GSM153108 1 0.4390 -0.4506 0.568 0.000 0.000 0.428 0.004
#> GSM153109 1 0.1788 0.6459 0.932 0.000 0.004 0.056 0.008
#> GSM153110 1 0.2077 0.6415 0.908 0.000 0.000 0.084 0.008
#> GSM153111 1 0.1153 0.6343 0.964 0.000 0.024 0.004 0.008
#> GSM153112 1 0.3388 0.5029 0.792 0.000 0.000 0.200 0.008
#> GSM153113 1 0.4053 0.5600 0.812 0.004 0.128 0.036 0.020
#> GSM153114 4 0.4727 0.7763 0.452 0.000 0.000 0.532 0.016
#> GSM187532 2 0.6840 0.5960 0.020 0.624 0.168 0.056 0.132
#> GSM187533 2 0.3096 0.9056 0.008 0.868 0.000 0.040 0.084
#> GSM187534 2 0.2838 0.9094 0.008 0.884 0.000 0.036 0.072
#> GSM187535 2 0.5995 0.4508 0.312 0.592 0.000 0.052 0.044
#> GSM152906 2 0.1750 0.9193 0.000 0.936 0.000 0.036 0.028
#> GSM152907 2 0.1750 0.9193 0.000 0.936 0.000 0.036 0.028
#> GSM152908 2 0.1485 0.9145 0.000 0.948 0.000 0.020 0.032
#> GSM152909 2 0.2894 0.8931 0.000 0.876 0.004 0.036 0.084
#> GSM152910 2 0.1725 0.9140 0.000 0.936 0.000 0.020 0.044
#> GSM152911 2 0.0451 0.9223 0.000 0.988 0.000 0.004 0.008
#> GSM152912 2 0.1485 0.9145 0.000 0.948 0.000 0.020 0.032
#> GSM152913 2 0.2264 0.9100 0.000 0.912 0.004 0.024 0.060
#> GSM152914 2 0.0000 0.9235 0.000 1.000 0.000 0.000 0.000
#> GSM152915 2 0.0000 0.9235 0.000 1.000 0.000 0.000 0.000
#> GSM152916 2 0.2446 0.9137 0.000 0.900 0.000 0.044 0.056
#> GSM152917 2 0.0000 0.9235 0.000 1.000 0.000 0.000 0.000
#> GSM152918 2 0.0000 0.9235 0.000 1.000 0.000 0.000 0.000
#> GSM152919 2 0.0000 0.9235 0.000 1.000 0.000 0.000 0.000
#> GSM152920 2 0.1485 0.9145 0.000 0.948 0.000 0.020 0.032
#> GSM152921 2 0.1485 0.9145 0.000 0.948 0.000 0.020 0.032
#> GSM152922 2 0.1485 0.9145 0.000 0.948 0.000 0.020 0.032
#> GSM152923 2 0.1750 0.9193 0.000 0.936 0.000 0.036 0.028
#> GSM152924 2 0.2588 0.9115 0.000 0.892 0.000 0.048 0.060
#> GSM152925 2 0.2654 0.9101 0.000 0.888 0.000 0.048 0.064
#> GSM152926 2 0.1750 0.9193 0.000 0.936 0.000 0.036 0.028
#> GSM152927 2 0.2446 0.9137 0.000 0.900 0.000 0.044 0.056
#> GSM152928 2 0.4623 0.8526 0.048 0.808 0.024 0.052 0.068
#> GSM152929 2 0.1750 0.9193 0.000 0.936 0.000 0.036 0.028
#> GSM152930 2 0.1750 0.9193 0.000 0.936 0.000 0.036 0.028
cbind(get_classes(res, k = 6), get_membership(res, k = 6))
#> class entropy silhouette p1 p2 p3 p4 p5 p6
#> GSM152839 3 0.7226 0.3724 0.320 0.000 0.440 0.120 0.024 0.096
#> GSM152840 6 0.3239 0.7766 0.008 0.000 0.104 0.032 0.012 0.844
#> GSM152841 4 0.1598 0.8036 0.004 0.000 0.008 0.940 0.008 0.040
#> GSM152842 3 0.5726 0.0512 0.016 0.000 0.580 0.000 0.224 0.180
#> GSM152843 3 0.5511 0.4403 0.084 0.000 0.560 0.004 0.016 0.336
#> GSM152844 6 0.2730 0.7886 0.004 0.000 0.092 0.008 0.024 0.872
#> GSM152845 6 0.4208 0.6951 0.024 0.000 0.200 0.000 0.036 0.740
#> GSM152846 6 0.3237 0.7663 0.008 0.000 0.100 0.000 0.056 0.836
#> GSM152847 3 0.5223 0.4790 0.072 0.000 0.628 0.000 0.028 0.272
#> GSM152848 1 0.5092 0.5990 0.560 0.000 0.028 0.376 0.036 0.000
#> GSM152849 3 0.5267 0.5224 0.096 0.000 0.616 0.000 0.016 0.272
#> GSM152850 3 0.5515 0.5886 0.244 0.000 0.608 0.000 0.020 0.128
#> GSM152851 4 0.5248 0.5646 0.076 0.000 0.112 0.724 0.024 0.064
#> GSM152852 6 0.2169 0.7916 0.008 0.000 0.080 0.012 0.000 0.900
#> GSM152853 6 0.2538 0.7900 0.004 0.000 0.076 0.012 0.020 0.888
#> GSM152854 6 0.3633 0.7256 0.004 0.000 0.252 0.000 0.012 0.732
#> GSM152855 4 0.3638 0.7156 0.172 0.000 0.000 0.784 0.036 0.008
#> GSM153238 3 0.4445 0.5981 0.196 0.000 0.728 0.000 0.028 0.048
#> GSM153239 6 0.4045 0.7461 0.004 0.000 0.136 0.008 0.076 0.776
#> GSM153240 4 0.0767 0.8309 0.012 0.000 0.000 0.976 0.008 0.004
#> GSM153241 3 0.5707 0.4789 0.080 0.000 0.588 0.008 0.032 0.292
#> GSM153242 6 0.4663 0.6212 0.004 0.000 0.272 0.000 0.068 0.656
#> GSM153243 3 0.4098 0.6048 0.220 0.000 0.732 0.000 0.012 0.036
#> GSM153244 4 0.2135 0.8296 0.044 0.000 0.012 0.916 0.024 0.004
#> GSM153245 6 0.5425 0.5915 0.008 0.000 0.264 0.012 0.100 0.616
#> GSM153246 5 0.4923 0.7881 0.000 0.000 0.168 0.000 0.656 0.176
#> GSM153247 3 0.5127 0.5310 0.144 0.000 0.696 0.000 0.116 0.044
#> GSM153248 1 0.3265 0.7655 0.748 0.000 0.004 0.248 0.000 0.000
#> GSM153249 4 0.0820 0.8293 0.016 0.000 0.000 0.972 0.000 0.012
#> GSM153250 4 0.3894 0.5747 0.244 0.000 0.004 0.728 0.020 0.004
#> GSM153251 3 0.4649 0.3296 0.020 0.000 0.656 0.000 0.036 0.288
#> GSM153252 4 0.0653 0.8272 0.000 0.000 0.004 0.980 0.004 0.012
#> GSM153253 4 0.1772 0.8127 0.020 0.000 0.008 0.936 0.008 0.028
#> GSM153254 4 0.6050 0.2469 0.212 0.000 0.204 0.560 0.012 0.012
#> GSM153255 4 0.0717 0.8302 0.016 0.000 0.000 0.976 0.000 0.008
#> GSM153256 4 0.2445 0.7915 0.108 0.000 0.000 0.872 0.020 0.000
#> GSM153257 4 0.1647 0.8316 0.032 0.000 0.008 0.940 0.016 0.004
#> GSM153258 1 0.4764 0.3677 0.492 0.000 0.008 0.472 0.024 0.004
#> GSM153259 1 0.3337 0.7629 0.736 0.000 0.000 0.260 0.004 0.000
#> GSM153260 3 0.5131 0.4758 0.052 0.000 0.676 0.004 0.048 0.220
#> GSM153261 3 0.4825 0.6102 0.184 0.000 0.692 0.000 0.012 0.112
#> GSM153262 4 0.1699 0.8259 0.040 0.000 0.008 0.936 0.004 0.012
#> GSM153263 4 0.4635 -0.3261 0.476 0.000 0.008 0.492 0.024 0.000
#> GSM153264 1 0.4470 0.7158 0.660 0.000 0.016 0.296 0.028 0.000
#> GSM153265 4 0.1375 0.8205 0.004 0.000 0.008 0.952 0.008 0.028
#> GSM153266 1 0.4113 0.7341 0.668 0.000 0.008 0.308 0.016 0.000
#> GSM153267 4 0.1988 0.8175 0.072 0.000 0.004 0.912 0.008 0.004
#> GSM153268 4 0.3995 0.5672 0.016 0.000 0.012 0.740 0.008 0.224
#> GSM153269 4 0.3053 0.7521 0.144 0.000 0.004 0.828 0.024 0.000
#> GSM153270 4 0.3569 0.7418 0.152 0.000 0.016 0.804 0.024 0.004
#> GSM153271 4 0.3277 0.6951 0.188 0.000 0.004 0.792 0.016 0.000
#> GSM153272 4 0.0653 0.8301 0.012 0.000 0.000 0.980 0.004 0.004
#> GSM153273 1 0.3198 0.7614 0.740 0.000 0.000 0.260 0.000 0.000
#> GSM153274 4 0.3279 0.7568 0.148 0.000 0.008 0.816 0.028 0.000
#> GSM153275 4 0.2320 0.7898 0.132 0.000 0.000 0.864 0.004 0.000
#> GSM153276 4 0.2849 0.8123 0.084 0.000 0.020 0.872 0.016 0.008
#> GSM153277 4 0.1293 0.8296 0.016 0.000 0.004 0.956 0.004 0.020
#> GSM153278 3 0.5389 0.5993 0.224 0.000 0.636 0.004 0.016 0.120
#> GSM153279 4 0.1604 0.8154 0.024 0.000 0.016 0.944 0.008 0.008
#> GSM153280 4 0.1452 0.8191 0.004 0.000 0.008 0.948 0.008 0.032
#> GSM153281 4 0.1936 0.8001 0.016 0.000 0.012 0.928 0.008 0.036
#> GSM153282 4 0.1382 0.8099 0.000 0.000 0.008 0.948 0.008 0.036
#> GSM153283 1 0.4630 0.5783 0.560 0.000 0.008 0.404 0.028 0.000
#> GSM153284 4 0.2261 0.8031 0.104 0.000 0.004 0.884 0.008 0.000
#> GSM153285 4 0.1261 0.8171 0.004 0.000 0.004 0.956 0.008 0.028
#> GSM153286 4 0.1801 0.8219 0.056 0.000 0.000 0.924 0.016 0.004
#> GSM153287 4 0.0862 0.8235 0.004 0.000 0.008 0.972 0.000 0.016
#> GSM153288 4 0.1738 0.8232 0.052 0.000 0.000 0.928 0.016 0.004
#> GSM153289 4 0.4178 0.5681 0.248 0.000 0.000 0.708 0.036 0.008
#> GSM153290 4 0.1261 0.8224 0.004 0.000 0.008 0.956 0.004 0.028
#> GSM153291 4 0.1168 0.8307 0.028 0.000 0.000 0.956 0.000 0.016
#> GSM153292 4 0.1007 0.8223 0.004 0.000 0.008 0.968 0.004 0.016
#> GSM153293 4 0.2146 0.7975 0.116 0.000 0.000 0.880 0.004 0.000
#> GSM153294 1 0.3789 0.7132 0.668 0.000 0.000 0.324 0.004 0.004
#> GSM153295 4 0.3110 0.8084 0.072 0.000 0.012 0.864 0.020 0.032
#> GSM153054 1 0.4640 0.6060 0.728 0.000 0.140 0.116 0.004 0.012
#> GSM153055 4 0.3806 0.7264 0.168 0.000 0.020 0.780 0.032 0.000
#> GSM153056 3 0.5889 0.5721 0.144 0.000 0.616 0.024 0.016 0.200
#> GSM153057 3 0.5198 0.4706 0.352 0.000 0.576 0.048 0.020 0.004
#> GSM153058 3 0.5294 0.3025 0.028 0.000 0.612 0.000 0.072 0.288
#> GSM153059 3 0.4511 0.5743 0.252 0.000 0.696 0.012 0.024 0.016
#> GSM153060 5 0.5468 0.7925 0.004 0.000 0.276 0.000 0.572 0.148
#> GSM153061 5 0.5838 0.6796 0.016 0.000 0.364 0.000 0.492 0.128
#> GSM153062 5 0.5008 0.7859 0.008 0.000 0.172 0.000 0.668 0.152
#> GSM153063 3 0.5158 0.3271 0.028 0.000 0.680 0.000 0.144 0.148
#> GSM153064 1 0.3601 0.7293 0.684 0.000 0.000 0.312 0.004 0.000
#> GSM153065 3 0.5031 0.3490 0.028 0.000 0.688 0.000 0.104 0.180
#> GSM153066 3 0.5178 0.5723 0.244 0.000 0.652 0.000 0.040 0.064
#> GSM153067 4 0.0806 0.8303 0.020 0.000 0.000 0.972 0.000 0.008
#> GSM153068 3 0.5843 -0.1010 0.016 0.000 0.556 0.000 0.248 0.180
#> GSM153069 4 0.0458 0.8254 0.000 0.000 0.000 0.984 0.000 0.016
#> GSM153070 4 0.4387 0.0250 0.404 0.000 0.004 0.572 0.020 0.000
#> GSM153071 3 0.5341 0.4034 0.388 0.000 0.532 0.052 0.028 0.000
#> GSM153072 1 0.5073 0.3467 0.656 0.000 0.256 0.056 0.028 0.004
#> GSM153073 1 0.4450 0.6880 0.628 0.000 0.008 0.336 0.028 0.000
#> GSM153074 4 0.1141 0.8269 0.052 0.000 0.000 0.948 0.000 0.000
#> GSM153075 4 0.2492 0.8183 0.080 0.000 0.004 0.888 0.020 0.008
#> GSM153076 1 0.4433 0.5390 0.560 0.000 0.008 0.416 0.016 0.000
#> GSM153077 1 0.4616 0.7369 0.692 0.000 0.036 0.240 0.032 0.000
#> GSM153078 1 0.6174 -0.1928 0.436 0.000 0.432 0.088 0.024 0.020
#> GSM153079 1 0.3973 0.7636 0.744 0.000 0.004 0.216 0.028 0.008
#> GSM153080 3 0.6012 0.5591 0.144 0.000 0.572 0.020 0.012 0.252
#> GSM153081 1 0.4788 0.7443 0.672 0.000 0.016 0.256 0.052 0.004
#> GSM153082 1 0.3702 0.7636 0.720 0.000 0.004 0.264 0.012 0.000
#> GSM153083 1 0.3463 0.7431 0.800 0.000 0.032 0.160 0.008 0.000
#> GSM153084 1 0.4883 -0.0732 0.588 0.000 0.360 0.012 0.036 0.004
#> GSM153085 1 0.5099 0.4034 0.672 0.000 0.216 0.076 0.036 0.000
#> GSM153086 1 0.3469 0.6846 0.812 0.000 0.064 0.120 0.004 0.000
#> GSM153087 4 0.2489 0.8182 0.052 0.000 0.016 0.900 0.020 0.012
#> GSM153088 4 0.4375 0.3956 0.316 0.000 0.008 0.648 0.028 0.000
#> GSM153089 3 0.5130 0.3714 0.048 0.000 0.624 0.000 0.036 0.292
#> GSM153090 4 0.3905 0.5637 0.256 0.000 0.004 0.716 0.024 0.000
#> GSM153091 1 0.3360 0.7608 0.732 0.000 0.000 0.264 0.004 0.000
#> GSM153092 1 0.4262 0.5366 0.560 0.000 0.004 0.424 0.012 0.000
#> GSM153093 4 0.2230 0.8114 0.084 0.000 0.000 0.892 0.024 0.000
#> GSM153094 1 0.3337 0.7614 0.736 0.000 0.000 0.260 0.004 0.000
#> GSM153095 1 0.5059 0.2768 0.660 0.000 0.260 0.040 0.028 0.012
#> GSM153096 1 0.3314 0.7636 0.740 0.000 0.000 0.256 0.004 0.000
#> GSM153097 1 0.3263 0.7565 0.800 0.000 0.020 0.176 0.004 0.000
#> GSM153098 1 0.3634 0.6721 0.644 0.000 0.000 0.356 0.000 0.000
#> GSM153099 4 0.1851 0.8252 0.056 0.000 0.004 0.924 0.012 0.004
#> GSM153100 1 0.3706 0.6380 0.620 0.000 0.000 0.380 0.000 0.000
#> GSM153101 1 0.4256 0.5618 0.772 0.000 0.132 0.072 0.012 0.012
#> GSM153102 1 0.3892 0.7614 0.752 0.000 0.020 0.208 0.020 0.000
#> GSM153103 1 0.4233 0.5763 0.760 0.000 0.140 0.088 0.008 0.004
#> GSM153104 4 0.0914 0.8224 0.000 0.000 0.016 0.968 0.000 0.016
#> GSM153106 4 0.4814 -0.2642 0.452 0.000 0.000 0.504 0.036 0.008
#> GSM153107 1 0.4736 0.4737 0.528 0.000 0.000 0.432 0.032 0.008
#> GSM153108 4 0.3632 0.6359 0.228 0.000 0.004 0.752 0.008 0.008
#> GSM153109 1 0.3604 0.7633 0.760 0.000 0.012 0.216 0.012 0.000
#> GSM153110 1 0.3198 0.7627 0.740 0.000 0.000 0.260 0.000 0.000
#> GSM153111 1 0.3154 0.7594 0.800 0.000 0.012 0.184 0.004 0.000
#> GSM153112 1 0.3945 0.6377 0.612 0.000 0.000 0.380 0.008 0.000
#> GSM153113 1 0.4076 0.5706 0.776 0.000 0.124 0.088 0.008 0.004
#> GSM153114 4 0.3672 0.7154 0.176 0.000 0.000 0.780 0.036 0.008
#> GSM187532 2 0.7873 0.3287 0.084 0.452 0.212 0.000 0.156 0.096
#> GSM187533 2 0.3941 0.8325 0.044 0.800 0.012 0.000 0.124 0.020
#> GSM187534 2 0.3722 0.8396 0.036 0.812 0.012 0.000 0.124 0.016
#> GSM187535 2 0.6089 0.2822 0.372 0.496 0.000 0.040 0.084 0.008
#> GSM152906 2 0.2367 0.8615 0.016 0.888 0.000 0.000 0.088 0.008
#> GSM152907 2 0.2367 0.8615 0.016 0.888 0.000 0.000 0.088 0.008
#> GSM152908 2 0.1716 0.8566 0.028 0.932 0.004 0.000 0.036 0.000
#> GSM152909 2 0.4875 0.7836 0.064 0.744 0.032 0.000 0.132 0.028
#> GSM152910 2 0.2420 0.8517 0.032 0.888 0.004 0.000 0.076 0.000
#> GSM152911 2 0.0405 0.8690 0.004 0.988 0.000 0.000 0.008 0.000
#> GSM152912 2 0.1716 0.8566 0.028 0.932 0.004 0.000 0.036 0.000
#> GSM152913 2 0.3522 0.8345 0.036 0.832 0.024 0.000 0.100 0.008
#> GSM152914 2 0.0000 0.8706 0.000 1.000 0.000 0.000 0.000 0.000
#> GSM152915 2 0.0000 0.8706 0.000 1.000 0.000 0.000 0.000 0.000
#> GSM152916 2 0.3595 0.8407 0.036 0.796 0.000 0.000 0.156 0.012
#> GSM152917 2 0.0146 0.8709 0.000 0.996 0.000 0.000 0.004 0.000
#> GSM152918 2 0.0146 0.8709 0.000 0.996 0.000 0.000 0.004 0.000
#> GSM152919 2 0.0146 0.8709 0.000 0.996 0.000 0.000 0.004 0.000
#> GSM152920 2 0.1716 0.8566 0.028 0.932 0.004 0.000 0.036 0.000
#> GSM152921 2 0.1716 0.8566 0.028 0.932 0.004 0.000 0.036 0.000
#> GSM152922 2 0.1788 0.8554 0.028 0.928 0.004 0.000 0.040 0.000
#> GSM152923 2 0.2367 0.8615 0.016 0.888 0.000 0.000 0.088 0.008
#> GSM152924 2 0.3721 0.8385 0.036 0.788 0.000 0.000 0.160 0.016
#> GSM152925 2 0.3757 0.8373 0.036 0.784 0.000 0.000 0.164 0.016
#> GSM152926 2 0.2418 0.8610 0.016 0.884 0.000 0.000 0.092 0.008
#> GSM152927 2 0.3595 0.8407 0.036 0.796 0.000 0.000 0.156 0.012
#> GSM152928 2 0.4963 0.7792 0.092 0.712 0.020 0.000 0.164 0.012
#> GSM152929 2 0.2418 0.8610 0.016 0.884 0.000 0.000 0.092 0.008
#> GSM152930 2 0.2367 0.8615 0.016 0.888 0.000 0.000 0.088 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 tissue(p) k
#> CV:kmeans 127 1.04e-23 2
#> CV:kmeans 162 8.65e-32 3
#> CV:kmeans 149 5.89e-29 4
#> CV:kmeans 105 6.44e-22 5
#> CV:kmeans 136 7.64e-35 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 12013 rows and 164 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 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 0.573 0.803 0.909 0.4923 0.512 0.512
#> 3 3 0.673 0.821 0.912 0.3289 0.746 0.545
#> 4 4 0.520 0.530 0.736 0.1426 0.872 0.651
#> 5 5 0.493 0.384 0.631 0.0642 0.931 0.749
#> 6 6 0.516 0.328 0.568 0.0395 0.937 0.742
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
#> GSM152839 1 0.0672 0.8960 0.992 0.008
#> GSM152840 1 0.5408 0.8139 0.876 0.124
#> GSM152841 1 0.0000 0.8982 1.000 0.000
#> GSM152842 2 0.9522 0.4369 0.372 0.628
#> GSM152843 1 0.6438 0.7736 0.836 0.164
#> GSM152844 1 0.9580 0.4125 0.620 0.380
#> GSM152845 2 0.0938 0.8966 0.012 0.988
#> GSM152846 2 0.6712 0.7909 0.176 0.824
#> GSM152847 1 0.8144 0.6610 0.748 0.252
#> GSM152848 1 0.0000 0.8982 1.000 0.000
#> GSM152849 1 0.9635 0.3955 0.612 0.388
#> GSM152850 1 0.9661 0.3821 0.608 0.392
#> GSM152851 1 0.9358 0.4837 0.648 0.352
#> GSM152852 2 0.9922 0.2133 0.448 0.552
#> GSM152853 1 0.7528 0.7106 0.784 0.216
#> GSM152854 2 0.7056 0.7748 0.192 0.808
#> GSM152855 1 0.0376 0.8975 0.996 0.004
#> GSM153238 2 0.1414 0.8954 0.020 0.980
#> GSM153239 1 0.9209 0.5155 0.664 0.336
#> GSM153240 1 0.0000 0.8982 1.000 0.000
#> GSM153241 1 0.9608 0.4057 0.616 0.384
#> GSM153242 2 0.3584 0.8787 0.068 0.932
#> GSM153243 2 0.1184 0.8963 0.016 0.984
#> GSM153244 1 0.9129 0.5230 0.672 0.328
#> GSM153245 1 0.9710 0.3597 0.600 0.400
#> GSM153246 2 0.2603 0.8886 0.044 0.956
#> GSM153247 2 0.5842 0.8287 0.140 0.860
#> GSM153248 1 0.5737 0.8069 0.864 0.136
#> GSM153249 1 0.0376 0.8975 0.996 0.004
#> GSM153250 1 0.0000 0.8982 1.000 0.000
#> GSM153251 2 0.2603 0.8885 0.044 0.956
#> GSM153252 1 0.0376 0.8973 0.996 0.004
#> GSM153253 1 0.0376 0.8974 0.996 0.004
#> GSM153254 1 0.9754 0.3312 0.592 0.408
#> GSM153255 1 0.0000 0.8982 1.000 0.000
#> GSM153256 1 0.0376 0.8975 0.996 0.004
#> GSM153257 1 0.0000 0.8982 1.000 0.000
#> GSM153258 1 0.0672 0.8963 0.992 0.008
#> GSM153259 1 0.2423 0.8802 0.960 0.040
#> GSM153260 2 0.2948 0.8871 0.052 0.948
#> GSM153261 2 0.4815 0.8598 0.104 0.896
#> GSM153262 1 0.0000 0.8982 1.000 0.000
#> GSM153263 1 0.0672 0.8963 0.992 0.008
#> GSM153264 1 0.0672 0.8976 0.992 0.008
#> GSM153265 1 0.0672 0.8960 0.992 0.008
#> GSM153266 1 0.0672 0.8971 0.992 0.008
#> GSM153267 1 0.0000 0.8982 1.000 0.000
#> GSM153268 1 0.0672 0.8960 0.992 0.008
#> GSM153269 1 0.0000 0.8982 1.000 0.000
#> GSM153270 1 0.0376 0.8973 0.996 0.004
#> GSM153271 1 0.0000 0.8982 1.000 0.000
#> GSM153272 1 0.0000 0.8982 1.000 0.000
#> GSM153273 1 0.3431 0.8702 0.936 0.064
#> GSM153274 1 0.1184 0.8939 0.984 0.016
#> GSM153275 1 0.0672 0.8965 0.992 0.008
#> GSM153276 1 0.0672 0.8960 0.992 0.008
#> GSM153277 1 0.0000 0.8982 1.000 0.000
#> GSM153278 1 0.9815 0.3033 0.580 0.420
#> GSM153279 1 0.3274 0.8707 0.940 0.060
#> GSM153280 1 0.0376 0.8973 0.996 0.004
#> GSM153281 1 0.0672 0.8960 0.992 0.008
#> GSM153282 1 0.0376 0.8973 0.996 0.004
#> GSM153283 1 0.0376 0.8975 0.996 0.004
#> GSM153284 1 0.0000 0.8982 1.000 0.000
#> GSM153285 1 0.0000 0.8982 1.000 0.000
#> GSM153286 1 0.0000 0.8982 1.000 0.000
#> GSM153287 1 0.0000 0.8982 1.000 0.000
#> GSM153288 1 0.0000 0.8982 1.000 0.000
#> GSM153289 1 0.0376 0.8975 0.996 0.004
#> GSM153290 1 0.0376 0.8973 0.996 0.004
#> GSM153291 1 0.0000 0.8982 1.000 0.000
#> GSM153292 1 0.0376 0.8973 0.996 0.004
#> GSM153293 1 0.0672 0.8964 0.992 0.008
#> GSM153294 1 0.3431 0.8681 0.936 0.064
#> GSM153295 1 0.0672 0.8960 0.992 0.008
#> GSM153054 1 0.9833 0.2985 0.576 0.424
#> GSM153055 1 0.3274 0.8704 0.940 0.060
#> GSM153056 1 0.6048 0.7925 0.852 0.148
#> GSM153057 2 0.9815 0.3322 0.420 0.580
#> GSM153058 2 0.5946 0.8267 0.144 0.856
#> GSM153059 2 0.3274 0.8864 0.060 0.940
#> GSM153060 2 0.3431 0.8808 0.064 0.936
#> GSM153061 2 0.2043 0.8917 0.032 0.968
#> GSM153062 2 0.1843 0.8930 0.028 0.972
#> GSM153063 2 0.7745 0.7237 0.228 0.772
#> GSM153064 1 0.2043 0.8839 0.968 0.032
#> GSM153065 2 0.1414 0.8955 0.020 0.980
#> GSM153066 2 0.0672 0.8972 0.008 0.992
#> GSM153067 1 0.0376 0.8975 0.996 0.004
#> GSM153068 2 0.2043 0.8917 0.032 0.968
#> GSM153069 1 0.0000 0.8982 1.000 0.000
#> GSM153070 1 0.0000 0.8982 1.000 0.000
#> GSM153071 2 0.9833 0.2557 0.424 0.576
#> GSM153072 2 0.9635 0.4109 0.388 0.612
#> GSM153073 1 0.0000 0.8982 1.000 0.000
#> GSM153074 1 0.0376 0.8975 0.996 0.004
#> GSM153075 1 0.0000 0.8982 1.000 0.000
#> GSM153076 1 0.0376 0.8975 0.996 0.004
#> GSM153077 1 0.6247 0.7897 0.844 0.156
#> GSM153078 1 0.9608 0.4207 0.616 0.384
#> GSM153079 1 0.9998 0.0101 0.508 0.492
#> GSM153080 1 0.9608 0.4069 0.616 0.384
#> GSM153081 1 0.0672 0.8963 0.992 0.008
#> GSM153082 2 0.7219 0.7618 0.200 0.800
#> GSM153083 2 0.4298 0.8599 0.088 0.912
#> GSM153084 2 0.0000 0.8973 0.000 1.000
#> GSM153085 2 0.6148 0.8251 0.152 0.848
#> GSM153086 2 0.7528 0.7408 0.216 0.784
#> GSM153087 1 0.0672 0.8960 0.992 0.008
#> GSM153088 1 0.0000 0.8982 1.000 0.000
#> GSM153089 2 0.2043 0.8939 0.032 0.968
#> GSM153090 1 0.0000 0.8982 1.000 0.000
#> GSM153091 1 0.9815 0.2798 0.580 0.420
#> GSM153092 1 0.4562 0.8445 0.904 0.096
#> GSM153093 1 0.0000 0.8982 1.000 0.000
#> GSM153094 1 0.9998 0.0213 0.508 0.492
#> GSM153095 2 0.7376 0.7499 0.208 0.792
#> GSM153096 1 0.4298 0.8518 0.912 0.088
#> GSM153097 2 0.8955 0.5784 0.312 0.688
#> GSM153098 1 0.2603 0.8792 0.956 0.044
#> GSM153099 1 0.0376 0.8974 0.996 0.004
#> GSM153100 1 0.2603 0.8789 0.956 0.044
#> GSM153101 2 0.7528 0.7401 0.216 0.784
#> GSM153102 2 0.7815 0.7180 0.232 0.768
#> GSM153103 2 0.8207 0.6759 0.256 0.744
#> GSM153104 1 0.0672 0.8960 0.992 0.008
#> GSM153106 1 0.1633 0.8912 0.976 0.024
#> GSM153107 1 0.2423 0.8826 0.960 0.040
#> GSM153108 1 0.2043 0.8886 0.968 0.032
#> GSM153109 2 0.6343 0.8009 0.160 0.840
#> GSM153110 1 0.7139 0.7426 0.804 0.196
#> GSM153111 2 0.7453 0.7456 0.212 0.788
#> GSM153112 1 0.3114 0.8730 0.944 0.056
#> GSM153113 2 0.1633 0.8946 0.024 0.976
#> GSM153114 1 0.0672 0.8963 0.992 0.008
#> GSM187532 2 0.0000 0.8973 0.000 1.000
#> GSM187533 2 0.0672 0.8989 0.008 0.992
#> GSM187534 2 0.0376 0.8984 0.004 0.996
#> GSM187535 2 0.7219 0.7477 0.200 0.800
#> GSM152906 2 0.0672 0.8989 0.008 0.992
#> GSM152907 2 0.0672 0.8989 0.008 0.992
#> GSM152908 2 0.0672 0.8989 0.008 0.992
#> GSM152909 2 0.0000 0.8973 0.000 1.000
#> GSM152910 2 0.0000 0.8973 0.000 1.000
#> GSM152911 2 0.0672 0.8989 0.008 0.992
#> GSM152912 2 0.0672 0.8989 0.008 0.992
#> GSM152913 2 0.0000 0.8973 0.000 1.000
#> GSM152914 2 0.0672 0.8989 0.008 0.992
#> GSM152915 2 0.0672 0.8989 0.008 0.992
#> GSM152916 2 0.0376 0.8982 0.004 0.996
#> GSM152917 2 0.0672 0.8989 0.008 0.992
#> GSM152918 2 0.0672 0.8989 0.008 0.992
#> GSM152919 2 0.0672 0.8989 0.008 0.992
#> GSM152920 2 0.0672 0.8989 0.008 0.992
#> GSM152921 2 0.0672 0.8989 0.008 0.992
#> GSM152922 2 0.0376 0.8982 0.004 0.996
#> GSM152923 2 0.0672 0.8989 0.008 0.992
#> GSM152924 2 0.0672 0.8989 0.008 0.992
#> GSM152925 2 0.0000 0.8973 0.000 1.000
#> GSM152926 2 0.0672 0.8989 0.008 0.992
#> GSM152927 2 0.0376 0.8982 0.004 0.996
#> GSM152928 2 0.0000 0.8973 0.000 1.000
#> GSM152929 2 0.0672 0.8989 0.008 0.992
#> GSM152930 2 0.0672 0.8989 0.008 0.992
cbind(get_classes(res, k = 3), get_membership(res, k = 3))
#> class entropy silhouette p1 p2 p3
#> GSM152839 3 0.4654 0.71895 0.208 0.000 0.792
#> GSM152840 3 0.0000 0.91514 0.000 0.000 1.000
#> GSM152841 1 0.0424 0.89776 0.992 0.000 0.008
#> GSM152842 3 0.0000 0.91514 0.000 0.000 1.000
#> GSM152843 3 0.0000 0.91514 0.000 0.000 1.000
#> GSM152844 3 0.0000 0.91514 0.000 0.000 1.000
#> GSM152845 3 0.0000 0.91514 0.000 0.000 1.000
#> GSM152846 3 0.0000 0.91514 0.000 0.000 1.000
#> GSM152847 3 0.0000 0.91514 0.000 0.000 1.000
#> GSM152848 1 0.6095 0.40278 0.608 0.000 0.392
#> GSM152849 3 0.0000 0.91514 0.000 0.000 1.000
#> GSM152850 3 0.0000 0.91514 0.000 0.000 1.000
#> GSM152851 3 0.4326 0.79851 0.144 0.012 0.844
#> GSM152852 3 0.0000 0.91514 0.000 0.000 1.000
#> GSM152853 3 0.0000 0.91514 0.000 0.000 1.000
#> GSM152854 3 0.0000 0.91514 0.000 0.000 1.000
#> GSM152855 1 0.0000 0.89826 1.000 0.000 0.000
#> GSM153238 3 0.0000 0.91514 0.000 0.000 1.000
#> GSM153239 3 0.0000 0.91514 0.000 0.000 1.000
#> GSM153240 1 0.0000 0.89826 1.000 0.000 0.000
#> GSM153241 3 0.0000 0.91514 0.000 0.000 1.000
#> GSM153242 3 0.0000 0.91514 0.000 0.000 1.000
#> GSM153243 3 0.0000 0.91514 0.000 0.000 1.000
#> GSM153244 1 0.9783 0.14686 0.432 0.256 0.312
#> GSM153245 3 0.0000 0.91514 0.000 0.000 1.000
#> GSM153246 3 0.0000 0.91514 0.000 0.000 1.000
#> GSM153247 3 0.0592 0.90805 0.000 0.012 0.988
#> GSM153248 1 0.5115 0.70704 0.768 0.228 0.004
#> GSM153249 1 0.0000 0.89826 1.000 0.000 0.000
#> GSM153250 1 0.0000 0.89826 1.000 0.000 0.000
#> GSM153251 3 0.0000 0.91514 0.000 0.000 1.000
#> GSM153252 1 0.0000 0.89826 1.000 0.000 0.000
#> GSM153253 1 0.1753 0.88864 0.952 0.000 0.048
#> GSM153254 3 0.9283 0.31053 0.320 0.180 0.500
#> GSM153255 1 0.0000 0.89826 1.000 0.000 0.000
#> GSM153256 1 0.0000 0.89826 1.000 0.000 0.000
#> GSM153257 1 0.0000 0.89826 1.000 0.000 0.000
#> GSM153258 1 0.0237 0.89760 0.996 0.004 0.000
#> GSM153259 1 0.2959 0.84993 0.900 0.100 0.000
#> GSM153260 3 0.0000 0.91514 0.000 0.000 1.000
#> GSM153261 3 0.0000 0.91514 0.000 0.000 1.000
#> GSM153262 1 0.1411 0.89198 0.964 0.000 0.036
#> GSM153263 1 0.0000 0.89826 1.000 0.000 0.000
#> GSM153264 1 0.5536 0.74995 0.776 0.024 0.200
#> GSM153265 1 0.2796 0.86635 0.908 0.000 0.092
#> GSM153266 1 0.6284 0.58661 0.680 0.016 0.304
#> GSM153267 1 0.0000 0.89826 1.000 0.000 0.000
#> GSM153268 1 0.5397 0.64901 0.720 0.000 0.280
#> GSM153269 1 0.0000 0.89826 1.000 0.000 0.000
#> GSM153270 1 0.5254 0.67409 0.736 0.000 0.264
#> GSM153271 1 0.0000 0.89826 1.000 0.000 0.000
#> GSM153272 1 0.0000 0.89826 1.000 0.000 0.000
#> GSM153273 1 0.5378 0.69626 0.756 0.236 0.008
#> GSM153274 1 0.3607 0.84950 0.880 0.008 0.112
#> GSM153275 1 0.0000 0.89826 1.000 0.000 0.000
#> GSM153276 1 0.3686 0.82828 0.860 0.000 0.140
#> GSM153277 1 0.0747 0.89688 0.984 0.000 0.016
#> GSM153278 3 0.0000 0.91514 0.000 0.000 1.000
#> GSM153279 1 0.6641 0.22722 0.544 0.008 0.448
#> GSM153280 1 0.1031 0.89532 0.976 0.000 0.024
#> GSM153281 1 0.2165 0.88164 0.936 0.000 0.064
#> GSM153282 1 0.2448 0.87571 0.924 0.000 0.076
#> GSM153283 1 0.0000 0.89826 1.000 0.000 0.000
#> GSM153284 1 0.0000 0.89826 1.000 0.000 0.000
#> GSM153285 1 0.2165 0.88198 0.936 0.000 0.064
#> GSM153286 1 0.0000 0.89826 1.000 0.000 0.000
#> GSM153287 1 0.0000 0.89826 1.000 0.000 0.000
#> GSM153288 1 0.0000 0.89826 1.000 0.000 0.000
#> GSM153289 1 0.0000 0.89826 1.000 0.000 0.000
#> GSM153290 1 0.2448 0.87628 0.924 0.000 0.076
#> GSM153291 1 0.0000 0.89826 1.000 0.000 0.000
#> GSM153292 1 0.0424 0.89786 0.992 0.000 0.008
#> GSM153293 1 0.0000 0.89826 1.000 0.000 0.000
#> GSM153294 1 0.5254 0.65974 0.736 0.264 0.000
#> GSM153295 1 0.5291 0.66957 0.732 0.000 0.268
#> GSM153054 3 0.6174 0.73579 0.168 0.064 0.768
#> GSM153055 1 0.6348 0.73403 0.752 0.060 0.188
#> GSM153056 3 0.0424 0.91043 0.008 0.000 0.992
#> GSM153057 3 0.4357 0.83346 0.080 0.052 0.868
#> GSM153058 3 0.0000 0.91514 0.000 0.000 1.000
#> GSM153059 3 0.4249 0.82100 0.028 0.108 0.864
#> GSM153060 3 0.0000 0.91514 0.000 0.000 1.000
#> GSM153061 3 0.0000 0.91514 0.000 0.000 1.000
#> GSM153062 3 0.0000 0.91514 0.000 0.000 1.000
#> GSM153063 3 0.0000 0.91514 0.000 0.000 1.000
#> GSM153064 1 0.1643 0.88354 0.956 0.044 0.000
#> GSM153065 3 0.0237 0.91275 0.000 0.004 0.996
#> GSM153066 3 0.6126 0.33708 0.000 0.400 0.600
#> GSM153067 1 0.0000 0.89826 1.000 0.000 0.000
#> GSM153068 3 0.0000 0.91514 0.000 0.000 1.000
#> GSM153069 1 0.0000 0.89826 1.000 0.000 0.000
#> GSM153070 1 0.1399 0.89404 0.968 0.004 0.028
#> GSM153071 3 0.4411 0.79920 0.140 0.016 0.844
#> GSM153072 3 0.6920 0.70755 0.132 0.132 0.736
#> GSM153073 1 0.0000 0.89826 1.000 0.000 0.000
#> GSM153074 1 0.0000 0.89826 1.000 0.000 0.000
#> GSM153075 1 0.4015 0.85235 0.876 0.028 0.096
#> GSM153076 1 0.0000 0.89826 1.000 0.000 0.000
#> GSM153077 1 0.8726 0.42805 0.564 0.140 0.296
#> GSM153078 3 0.5412 0.75552 0.172 0.032 0.796
#> GSM153079 2 0.9460 0.08861 0.396 0.424 0.180
#> GSM153080 3 0.0237 0.91289 0.004 0.000 0.996
#> GSM153081 1 0.4235 0.79049 0.824 0.000 0.176
#> GSM153082 2 0.2680 0.87126 0.068 0.924 0.008
#> GSM153083 2 0.1170 0.90765 0.008 0.976 0.016
#> GSM153084 2 0.3412 0.81482 0.000 0.876 0.124
#> GSM153085 3 0.8408 0.35457 0.100 0.344 0.556
#> GSM153086 2 0.8455 0.41976 0.120 0.584 0.296
#> GSM153087 1 0.4937 0.80973 0.824 0.028 0.148
#> GSM153088 1 0.0424 0.89791 0.992 0.000 0.008
#> GSM153089 3 0.0237 0.91297 0.000 0.004 0.996
#> GSM153090 1 0.0000 0.89826 1.000 0.000 0.000
#> GSM153091 2 0.5016 0.66767 0.240 0.760 0.000
#> GSM153092 1 0.4291 0.80214 0.840 0.152 0.008
#> GSM153093 1 0.0000 0.89826 1.000 0.000 0.000
#> GSM153094 2 0.4235 0.76565 0.176 0.824 0.000
#> GSM153095 3 0.8939 -0.00189 0.124 0.436 0.440
#> GSM153096 1 0.7014 0.67015 0.712 0.208 0.080
#> GSM153097 2 0.5058 0.78175 0.148 0.820 0.032
#> GSM153098 1 0.2878 0.85465 0.904 0.096 0.000
#> GSM153099 1 0.2878 0.86402 0.904 0.000 0.096
#> GSM153100 1 0.2537 0.86540 0.920 0.080 0.000
#> GSM153101 3 0.8593 0.49566 0.156 0.248 0.596
#> GSM153102 2 0.9302 0.38145 0.236 0.524 0.240
#> GSM153103 2 0.9431 0.02427 0.176 0.424 0.400
#> GSM153104 1 0.2625 0.87170 0.916 0.000 0.084
#> GSM153106 1 0.0592 0.89597 0.988 0.012 0.000
#> GSM153107 1 0.2261 0.87176 0.932 0.068 0.000
#> GSM153108 1 0.5060 0.82750 0.836 0.064 0.100
#> GSM153109 2 0.1765 0.89301 0.040 0.956 0.004
#> GSM153110 1 0.7690 0.22982 0.536 0.416 0.048
#> GSM153111 2 0.3207 0.85507 0.084 0.904 0.012
#> GSM153112 1 0.4235 0.77948 0.824 0.176 0.000
#> GSM153113 2 0.0424 0.91501 0.000 0.992 0.008
#> GSM153114 1 0.0000 0.89826 1.000 0.000 0.000
#> GSM187532 2 0.4504 0.72176 0.000 0.804 0.196
#> GSM187533 2 0.0000 0.91927 0.000 1.000 0.000
#> GSM187534 2 0.0000 0.91927 0.000 1.000 0.000
#> GSM187535 2 0.0000 0.91927 0.000 1.000 0.000
#> GSM152906 2 0.0000 0.91927 0.000 1.000 0.000
#> GSM152907 2 0.0000 0.91927 0.000 1.000 0.000
#> GSM152908 2 0.0000 0.91927 0.000 1.000 0.000
#> GSM152909 2 0.0424 0.91489 0.000 0.992 0.008
#> GSM152910 2 0.0000 0.91927 0.000 1.000 0.000
#> GSM152911 2 0.0000 0.91927 0.000 1.000 0.000
#> GSM152912 2 0.0000 0.91927 0.000 1.000 0.000
#> GSM152913 2 0.0237 0.91709 0.000 0.996 0.004
#> GSM152914 2 0.0000 0.91927 0.000 1.000 0.000
#> GSM152915 2 0.0000 0.91927 0.000 1.000 0.000
#> GSM152916 2 0.0000 0.91927 0.000 1.000 0.000
#> GSM152917 2 0.0000 0.91927 0.000 1.000 0.000
#> GSM152918 2 0.0000 0.91927 0.000 1.000 0.000
#> GSM152919 2 0.0000 0.91927 0.000 1.000 0.000
#> GSM152920 2 0.0000 0.91927 0.000 1.000 0.000
#> GSM152921 2 0.0000 0.91927 0.000 1.000 0.000
#> GSM152922 2 0.0000 0.91927 0.000 1.000 0.000
#> GSM152923 2 0.0000 0.91927 0.000 1.000 0.000
#> GSM152924 2 0.0000 0.91927 0.000 1.000 0.000
#> GSM152925 2 0.0000 0.91927 0.000 1.000 0.000
#> GSM152926 2 0.0000 0.91927 0.000 1.000 0.000
#> GSM152927 2 0.0000 0.91927 0.000 1.000 0.000
#> GSM152928 2 0.0000 0.91927 0.000 1.000 0.000
#> GSM152929 2 0.0000 0.91927 0.000 1.000 0.000
#> GSM152930 2 0.0000 0.91927 0.000 1.000 0.000
cbind(get_classes(res, k = 4), get_membership(res, k = 4))
#> class entropy silhouette p1 p2 p3 p4
#> GSM152839 3 0.7634 0.05374 0.300 0.000 0.464 0.236
#> GSM152840 3 0.1970 0.81456 0.008 0.000 0.932 0.060
#> GSM152841 4 0.1902 0.59800 0.064 0.000 0.004 0.932
#> GSM152842 3 0.0000 0.82446 0.000 0.000 1.000 0.000
#> GSM152843 3 0.2965 0.79928 0.072 0.000 0.892 0.036
#> GSM152844 3 0.0469 0.82569 0.000 0.000 0.988 0.012
#> GSM152845 3 0.0188 0.82492 0.000 0.000 0.996 0.004
#> GSM152846 3 0.0376 0.82564 0.004 0.000 0.992 0.004
#> GSM152847 3 0.1042 0.82597 0.020 0.000 0.972 0.008
#> GSM152848 1 0.7605 0.14683 0.452 0.000 0.212 0.336
#> GSM152849 3 0.1970 0.81681 0.060 0.000 0.932 0.008
#> GSM152850 3 0.3443 0.76409 0.136 0.000 0.848 0.016
#> GSM152851 3 0.6925 0.31440 0.080 0.016 0.560 0.344
#> GSM152852 3 0.1004 0.82567 0.004 0.000 0.972 0.024
#> GSM152853 3 0.1557 0.81744 0.000 0.000 0.944 0.056
#> GSM152854 3 0.0524 0.82584 0.004 0.000 0.988 0.008
#> GSM152855 4 0.4843 0.41204 0.396 0.000 0.000 0.604
#> GSM153238 3 0.1398 0.82398 0.040 0.004 0.956 0.000
#> GSM153239 3 0.1584 0.82309 0.012 0.000 0.952 0.036
#> GSM153240 4 0.3764 0.59513 0.216 0.000 0.000 0.784
#> GSM153241 3 0.2443 0.81288 0.060 0.000 0.916 0.024
#> GSM153242 3 0.0188 0.82506 0.004 0.000 0.996 0.000
#> GSM153243 3 0.1807 0.81898 0.052 0.008 0.940 0.000
#> GSM153244 4 0.9737 -0.13523 0.268 0.172 0.208 0.352
#> GSM153245 3 0.0937 0.82643 0.012 0.000 0.976 0.012
#> GSM153246 3 0.0188 0.82497 0.004 0.000 0.996 0.000
#> GSM153247 3 0.1871 0.82233 0.024 0.016 0.948 0.012
#> GSM153248 1 0.6373 0.39906 0.648 0.136 0.000 0.216
#> GSM153249 4 0.3024 0.59912 0.148 0.000 0.000 0.852
#> GSM153250 4 0.4961 0.24843 0.448 0.000 0.000 0.552
#> GSM153251 3 0.0000 0.82446 0.000 0.000 1.000 0.000
#> GSM153252 4 0.4248 0.60022 0.220 0.000 0.012 0.768
#> GSM153253 4 0.3810 0.59343 0.092 0.000 0.060 0.848
#> GSM153254 3 0.9865 -0.26783 0.200 0.204 0.304 0.292
#> GSM153255 4 0.2868 0.60235 0.136 0.000 0.000 0.864
#> GSM153256 4 0.4830 0.41060 0.392 0.000 0.000 0.608
#> GSM153257 4 0.4250 0.55294 0.276 0.000 0.000 0.724
#> GSM153258 1 0.4866 0.07291 0.596 0.000 0.000 0.404
#> GSM153259 1 0.5137 0.35924 0.716 0.040 0.000 0.244
#> GSM153260 3 0.1109 0.82612 0.028 0.004 0.968 0.000
#> GSM153261 3 0.1576 0.82288 0.048 0.000 0.948 0.004
#> GSM153262 4 0.4576 0.57494 0.260 0.000 0.012 0.728
#> GSM153263 1 0.4955 -0.10017 0.556 0.000 0.000 0.444
#> GSM153264 1 0.6050 0.31451 0.664 0.004 0.076 0.256
#> GSM153265 4 0.5798 0.52056 0.208 0.000 0.096 0.696
#> GSM153266 1 0.7384 0.16678 0.476 0.000 0.172 0.352
#> GSM153267 4 0.4543 0.52144 0.324 0.000 0.000 0.676
#> GSM153268 4 0.5522 0.39604 0.080 0.000 0.204 0.716
#> GSM153269 4 0.4855 0.39704 0.400 0.000 0.000 0.600
#> GSM153270 4 0.7277 0.16425 0.360 0.000 0.156 0.484
#> GSM153271 4 0.4961 0.25723 0.448 0.000 0.000 0.552
#> GSM153272 4 0.3266 0.60582 0.168 0.000 0.000 0.832
#> GSM153273 1 0.6639 0.32570 0.584 0.092 0.004 0.320
#> GSM153274 4 0.7038 0.17672 0.416 0.004 0.104 0.476
#> GSM153275 4 0.4761 0.48381 0.332 0.000 0.004 0.664
#> GSM153276 4 0.6124 0.45041 0.276 0.000 0.084 0.640
#> GSM153277 4 0.5161 0.50113 0.300 0.000 0.024 0.676
#> GSM153278 3 0.3324 0.77110 0.136 0.000 0.852 0.012
#> GSM153279 4 0.7177 0.23582 0.172 0.004 0.256 0.568
#> GSM153280 4 0.4008 0.58677 0.148 0.000 0.032 0.820
#> GSM153281 4 0.4440 0.59244 0.136 0.000 0.060 0.804
#> GSM153282 4 0.3286 0.59752 0.080 0.000 0.044 0.876
#> GSM153283 1 0.4907 0.02930 0.580 0.000 0.000 0.420
#> GSM153284 4 0.4406 0.52943 0.300 0.000 0.000 0.700
#> GSM153285 4 0.3958 0.60917 0.160 0.000 0.024 0.816
#> GSM153286 4 0.4222 0.54761 0.272 0.000 0.000 0.728
#> GSM153287 4 0.1792 0.59689 0.068 0.000 0.000 0.932
#> GSM153288 4 0.4134 0.58359 0.260 0.000 0.000 0.740
#> GSM153289 4 0.4985 0.25883 0.468 0.000 0.000 0.532
#> GSM153290 4 0.4149 0.59253 0.152 0.000 0.036 0.812
#> GSM153291 4 0.3356 0.59010 0.176 0.000 0.000 0.824
#> GSM153292 4 0.1940 0.59834 0.076 0.000 0.000 0.924
#> GSM153293 4 0.4304 0.54183 0.284 0.000 0.000 0.716
#> GSM153294 1 0.7343 0.16719 0.424 0.156 0.000 0.420
#> GSM153295 4 0.7469 0.16141 0.312 0.000 0.200 0.488
#> GSM153054 3 0.8605 0.05861 0.304 0.056 0.456 0.184
#> GSM153055 4 0.8069 0.04075 0.376 0.064 0.092 0.468
#> GSM153056 3 0.4780 0.71243 0.116 0.000 0.788 0.096
#> GSM153057 3 0.7685 0.46199 0.220 0.064 0.600 0.116
#> GSM153058 3 0.0524 0.82655 0.008 0.000 0.988 0.004
#> GSM153059 3 0.7537 0.52142 0.144 0.172 0.624 0.060
#> GSM153060 3 0.0000 0.82446 0.000 0.000 1.000 0.000
#> GSM153061 3 0.0000 0.82446 0.000 0.000 1.000 0.000
#> GSM153062 3 0.0000 0.82446 0.000 0.000 1.000 0.000
#> GSM153063 3 0.1406 0.82480 0.016 0.000 0.960 0.024
#> GSM153064 1 0.5189 0.21725 0.616 0.012 0.000 0.372
#> GSM153065 3 0.0469 0.82634 0.012 0.000 0.988 0.000
#> GSM153066 3 0.5807 0.44426 0.044 0.344 0.612 0.000
#> GSM153067 4 0.4134 0.54746 0.260 0.000 0.000 0.740
#> GSM153068 3 0.0000 0.82446 0.000 0.000 1.000 0.000
#> GSM153069 4 0.2149 0.60256 0.088 0.000 0.000 0.912
#> GSM153070 1 0.6024 0.01558 0.540 0.000 0.044 0.416
#> GSM153071 3 0.7265 0.48658 0.164 0.028 0.620 0.188
#> GSM153072 3 0.9036 0.01601 0.332 0.132 0.416 0.120
#> GSM153073 1 0.4998 -0.14749 0.512 0.000 0.000 0.488
#> GSM153074 4 0.3942 0.57550 0.236 0.000 0.000 0.764
#> GSM153075 4 0.6789 0.35549 0.352 0.012 0.076 0.560
#> GSM153076 1 0.4925 -0.01603 0.572 0.000 0.000 0.428
#> GSM153077 1 0.8239 0.33228 0.544 0.080 0.128 0.248
#> GSM153078 3 0.8353 0.21924 0.300 0.056 0.492 0.152
#> GSM153079 1 0.7513 0.39042 0.620 0.180 0.052 0.148
#> GSM153080 3 0.3935 0.75822 0.060 0.000 0.840 0.100
#> GSM153081 1 0.5596 0.30669 0.696 0.000 0.068 0.236
#> GSM153082 2 0.7036 0.34665 0.276 0.600 0.020 0.104
#> GSM153083 2 0.6326 0.31775 0.376 0.572 0.024 0.028
#> GSM153084 2 0.6181 0.59708 0.120 0.700 0.168 0.012
#> GSM153085 3 0.9658 -0.11624 0.260 0.276 0.332 0.132
#> GSM153086 1 0.8469 0.36717 0.492 0.296 0.140 0.072
#> GSM153087 4 0.7031 0.36190 0.248 0.012 0.136 0.604
#> GSM153088 1 0.4941 -0.04067 0.564 0.000 0.000 0.436
#> GSM153089 3 0.0804 0.82768 0.008 0.000 0.980 0.012
#> GSM153090 4 0.4977 0.28239 0.460 0.000 0.000 0.540
#> GSM153091 1 0.7200 0.35421 0.484 0.372 0.000 0.144
#> GSM153092 1 0.6891 0.24811 0.548 0.092 0.008 0.352
#> GSM153093 4 0.4072 0.57573 0.252 0.000 0.000 0.748
#> GSM153094 2 0.6979 0.01073 0.376 0.504 0.000 0.120
#> GSM153095 1 0.9929 0.25360 0.300 0.228 0.264 0.208
#> GSM153096 1 0.7224 0.35708 0.584 0.108 0.024 0.284
#> GSM153097 1 0.7017 0.35039 0.564 0.340 0.028 0.068
#> GSM153098 4 0.6148 0.04994 0.468 0.048 0.000 0.484
#> GSM153099 4 0.6585 0.38498 0.312 0.000 0.104 0.584
#> GSM153100 1 0.6392 -0.00404 0.484 0.064 0.000 0.452
#> GSM153101 3 0.9286 -0.12255 0.324 0.236 0.352 0.088
#> GSM153102 1 0.9816 0.29120 0.312 0.292 0.172 0.224
#> GSM153103 1 0.9361 0.31894 0.404 0.252 0.232 0.112
#> GSM153104 4 0.4605 0.56928 0.132 0.000 0.072 0.796
#> GSM153106 1 0.5163 -0.16095 0.516 0.004 0.000 0.480
#> GSM153107 1 0.5237 0.14916 0.628 0.016 0.000 0.356
#> GSM153108 4 0.6988 0.27380 0.384 0.036 0.048 0.532
#> GSM153109 2 0.7211 0.16525 0.352 0.532 0.016 0.100
#> GSM153110 1 0.7012 0.42263 0.652 0.160 0.032 0.156
#> GSM153111 1 0.7053 0.09704 0.484 0.432 0.032 0.052
#> GSM153112 1 0.6392 0.12017 0.528 0.068 0.000 0.404
#> GSM153113 2 0.4238 0.72907 0.176 0.796 0.000 0.028
#> GSM153114 4 0.4817 0.38630 0.388 0.000 0.000 0.612
#> GSM187532 2 0.4054 0.68684 0.016 0.796 0.188 0.000
#> GSM187533 2 0.0188 0.91079 0.004 0.996 0.000 0.000
#> GSM187534 2 0.0188 0.91079 0.004 0.996 0.000 0.000
#> GSM187535 2 0.2867 0.82120 0.104 0.884 0.000 0.012
#> GSM152906 2 0.0000 0.91327 0.000 1.000 0.000 0.000
#> GSM152907 2 0.0000 0.91327 0.000 1.000 0.000 0.000
#> GSM152908 2 0.0000 0.91327 0.000 1.000 0.000 0.000
#> GSM152909 2 0.0592 0.90142 0.000 0.984 0.016 0.000
#> GSM152910 2 0.0000 0.91327 0.000 1.000 0.000 0.000
#> GSM152911 2 0.0000 0.91327 0.000 1.000 0.000 0.000
#> GSM152912 2 0.0000 0.91327 0.000 1.000 0.000 0.000
#> GSM152913 2 0.0336 0.90771 0.000 0.992 0.008 0.000
#> GSM152914 2 0.0000 0.91327 0.000 1.000 0.000 0.000
#> GSM152915 2 0.0000 0.91327 0.000 1.000 0.000 0.000
#> GSM152916 2 0.0000 0.91327 0.000 1.000 0.000 0.000
#> GSM152917 2 0.0000 0.91327 0.000 1.000 0.000 0.000
#> GSM152918 2 0.0000 0.91327 0.000 1.000 0.000 0.000
#> GSM152919 2 0.0000 0.91327 0.000 1.000 0.000 0.000
#> GSM152920 2 0.0000 0.91327 0.000 1.000 0.000 0.000
#> GSM152921 2 0.0000 0.91327 0.000 1.000 0.000 0.000
#> GSM152922 2 0.0000 0.91327 0.000 1.000 0.000 0.000
#> GSM152923 2 0.0000 0.91327 0.000 1.000 0.000 0.000
#> GSM152924 2 0.0000 0.91327 0.000 1.000 0.000 0.000
#> GSM152925 2 0.0000 0.91327 0.000 1.000 0.000 0.000
#> GSM152926 2 0.0000 0.91327 0.000 1.000 0.000 0.000
#> GSM152927 2 0.0188 0.91057 0.000 0.996 0.004 0.000
#> GSM152928 2 0.1042 0.89388 0.008 0.972 0.020 0.000
#> GSM152929 2 0.0000 0.91327 0.000 1.000 0.000 0.000
#> GSM152930 2 0.0000 0.91327 0.000 1.000 0.000 0.000
cbind(get_classes(res, k = 5), get_membership(res, k = 5))
#> class entropy silhouette p1 p2 p3 p4 p5
#> GSM152839 3 0.8362 -0.13843 0.232 0.000 0.364 0.164 0.240
#> GSM152840 3 0.4299 0.70904 0.016 0.000 0.796 0.100 0.088
#> GSM152841 4 0.4160 0.41715 0.068 0.000 0.016 0.804 0.112
#> GSM152842 3 0.1883 0.75537 0.012 0.000 0.932 0.008 0.048
#> GSM152843 3 0.6050 0.59843 0.088 0.000 0.656 0.056 0.200
#> GSM152844 3 0.2585 0.75177 0.004 0.000 0.896 0.036 0.064
#> GSM152845 3 0.1285 0.74971 0.004 0.004 0.956 0.000 0.036
#> GSM152846 3 0.1989 0.75409 0.016 0.000 0.932 0.020 0.032
#> GSM152847 3 0.3906 0.73554 0.032 0.000 0.816 0.024 0.128
#> GSM152848 1 0.8379 0.08141 0.368 0.000 0.180 0.220 0.232
#> GSM152849 3 0.3895 0.73823 0.052 0.000 0.824 0.020 0.104
#> GSM152850 3 0.6634 0.44715 0.160 0.000 0.576 0.036 0.228
#> GSM152851 3 0.8407 -0.04052 0.112 0.020 0.400 0.296 0.172
#> GSM152852 3 0.3481 0.73995 0.004 0.000 0.840 0.056 0.100
#> GSM152853 3 0.3800 0.72050 0.000 0.000 0.812 0.108 0.080
#> GSM152854 3 0.1956 0.75383 0.012 0.000 0.928 0.008 0.052
#> GSM152855 1 0.5168 0.03277 0.508 0.000 0.000 0.452 0.040
#> GSM153238 3 0.3189 0.74342 0.016 0.004 0.848 0.004 0.128
#> GSM153239 3 0.3854 0.73400 0.012 0.000 0.824 0.068 0.096
#> GSM153240 4 0.5768 0.35096 0.212 0.000 0.008 0.640 0.140
#> GSM153241 3 0.4599 0.71472 0.048 0.000 0.784 0.052 0.116
#> GSM153242 3 0.1845 0.75472 0.000 0.000 0.928 0.016 0.056
#> GSM153243 3 0.4242 0.71003 0.028 0.024 0.792 0.004 0.152
#> GSM153244 4 0.9578 -0.04703 0.216 0.124 0.176 0.340 0.144
#> GSM153245 3 0.3429 0.75049 0.012 0.000 0.848 0.040 0.100
#> GSM153246 3 0.0794 0.74500 0.000 0.000 0.972 0.000 0.028
#> GSM153247 3 0.4828 0.69736 0.056 0.016 0.776 0.024 0.128
#> GSM153248 1 0.7515 0.15686 0.440 0.072 0.000 0.160 0.328
#> GSM153249 4 0.5502 0.37307 0.192 0.000 0.000 0.652 0.156
#> GSM153250 4 0.6247 0.04509 0.428 0.000 0.000 0.428 0.144
#> GSM153251 3 0.1822 0.75526 0.004 0.004 0.932 0.004 0.056
#> GSM153252 4 0.5608 0.39543 0.168 0.000 0.012 0.672 0.148
#> GSM153253 4 0.5525 0.41104 0.096 0.000 0.052 0.716 0.136
#> GSM153254 4 0.9848 -0.25627 0.160 0.136 0.232 0.240 0.232
#> GSM153255 4 0.3863 0.40304 0.152 0.000 0.000 0.796 0.052
#> GSM153256 4 0.6322 0.18042 0.324 0.000 0.000 0.500 0.176
#> GSM153257 4 0.5848 0.37603 0.224 0.000 0.008 0.628 0.140
#> GSM153258 1 0.7147 0.26072 0.432 0.000 0.020 0.272 0.276
#> GSM153259 1 0.6812 0.29006 0.504 0.020 0.000 0.188 0.288
#> GSM153260 3 0.4019 0.72178 0.052 0.004 0.792 0.000 0.152
#> GSM153261 3 0.3209 0.74373 0.028 0.000 0.848 0.004 0.120
#> GSM153262 4 0.6973 0.16355 0.316 0.000 0.028 0.480 0.176
#> GSM153263 1 0.6182 0.19671 0.520 0.000 0.000 0.324 0.156
#> GSM153264 1 0.7395 0.22193 0.476 0.000 0.076 0.144 0.304
#> GSM153265 4 0.7051 0.29591 0.164 0.000 0.076 0.564 0.196
#> GSM153266 1 0.8261 0.14646 0.392 0.004 0.128 0.200 0.276
#> GSM153267 4 0.6362 0.22716 0.320 0.000 0.000 0.496 0.184
#> GSM153268 4 0.6666 0.29974 0.072 0.000 0.152 0.612 0.164
#> GSM153269 4 0.6434 0.11961 0.368 0.000 0.000 0.452 0.180
#> GSM153270 4 0.8210 0.00196 0.232 0.000 0.120 0.352 0.296
#> GSM153271 4 0.6102 0.19773 0.340 0.000 0.000 0.520 0.140
#> GSM153272 4 0.4800 0.39410 0.196 0.000 0.000 0.716 0.088
#> GSM153273 5 0.7653 -0.24262 0.348 0.040 0.004 0.248 0.360
#> GSM153274 4 0.8102 0.01851 0.280 0.000 0.096 0.348 0.276
#> GSM153275 4 0.6653 0.16167 0.320 0.000 0.000 0.436 0.244
#> GSM153276 4 0.7794 0.22397 0.244 0.000 0.092 0.448 0.216
#> GSM153277 4 0.7188 0.26289 0.216 0.000 0.064 0.532 0.188
#> GSM153278 3 0.6563 0.50642 0.108 0.000 0.592 0.056 0.244
#> GSM153279 4 0.8012 0.15647 0.156 0.004 0.244 0.456 0.140
#> GSM153280 4 0.6271 0.34686 0.120 0.000 0.068 0.652 0.160
#> GSM153281 4 0.5685 0.40911 0.104 0.000 0.044 0.696 0.156
#> GSM153282 4 0.5248 0.39910 0.068 0.000 0.064 0.740 0.128
#> GSM153283 1 0.6891 0.18426 0.440 0.000 0.008 0.296 0.256
#> GSM153284 4 0.6335 0.26025 0.276 0.000 0.000 0.520 0.204
#> GSM153285 4 0.5538 0.39925 0.092 0.000 0.044 0.708 0.156
#> GSM153286 4 0.5617 0.29559 0.256 0.000 0.000 0.620 0.124
#> GSM153287 4 0.2482 0.41882 0.084 0.000 0.000 0.892 0.024
#> GSM153288 4 0.5353 0.31417 0.272 0.000 0.000 0.636 0.092
#> GSM153289 1 0.5215 0.15456 0.592 0.000 0.000 0.352 0.056
#> GSM153290 4 0.6474 0.32164 0.192 0.000 0.056 0.620 0.132
#> GSM153291 4 0.5325 0.28591 0.308 0.000 0.000 0.616 0.076
#> GSM153292 4 0.4277 0.42432 0.100 0.000 0.004 0.784 0.112
#> GSM153293 4 0.6004 0.22532 0.372 0.000 0.000 0.508 0.120
#> GSM153294 4 0.7883 -0.09864 0.248 0.072 0.000 0.344 0.336
#> GSM153295 4 0.8341 0.05306 0.224 0.000 0.216 0.380 0.180
#> GSM153054 3 0.9108 -0.30910 0.192 0.048 0.356 0.156 0.248
#> GSM153055 4 0.8909 -0.10470 0.264 0.084 0.052 0.324 0.276
#> GSM153056 3 0.6308 0.56393 0.068 0.000 0.644 0.108 0.180
#> GSM153057 3 0.8712 0.00811 0.184 0.060 0.424 0.088 0.244
#> GSM153058 3 0.2416 0.75706 0.012 0.000 0.888 0.000 0.100
#> GSM153059 3 0.8809 -0.03023 0.092 0.204 0.432 0.072 0.200
#> GSM153060 3 0.1041 0.74852 0.004 0.000 0.964 0.000 0.032
#> GSM153061 3 0.1041 0.74866 0.004 0.000 0.964 0.000 0.032
#> GSM153062 3 0.0865 0.74568 0.004 0.000 0.972 0.000 0.024
#> GSM153063 3 0.3110 0.75162 0.024 0.000 0.872 0.024 0.080
#> GSM153064 5 0.6927 -0.30041 0.352 0.004 0.000 0.284 0.360
#> GSM153065 3 0.1768 0.75284 0.004 0.000 0.924 0.000 0.072
#> GSM153066 3 0.6872 0.02460 0.036 0.368 0.468 0.000 0.128
#> GSM153067 4 0.5668 0.35159 0.172 0.000 0.000 0.632 0.196
#> GSM153068 3 0.1197 0.75086 0.000 0.000 0.952 0.000 0.048
#> GSM153069 4 0.3291 0.42426 0.088 0.000 0.000 0.848 0.064
#> GSM153070 1 0.7333 0.11704 0.404 0.004 0.020 0.312 0.260
#> GSM153071 3 0.8506 0.07678 0.144 0.028 0.448 0.176 0.204
#> GSM153072 5 0.9056 0.26925 0.168 0.072 0.296 0.108 0.356
#> GSM153073 1 0.6785 0.08402 0.376 0.000 0.000 0.340 0.284
#> GSM153074 4 0.5530 0.34552 0.228 0.000 0.000 0.640 0.132
#> GSM153075 1 0.7805 0.03337 0.380 0.012 0.048 0.360 0.200
#> GSM153076 1 0.6659 0.08272 0.428 0.000 0.000 0.332 0.240
#> GSM153077 5 0.8954 -0.10482 0.324 0.064 0.096 0.180 0.336
#> GSM153078 3 0.9134 -0.29819 0.264 0.052 0.336 0.132 0.216
#> GSM153079 1 0.7642 -0.05178 0.584 0.132 0.084 0.056 0.144
#> GSM153080 3 0.6313 0.57423 0.060 0.000 0.644 0.132 0.164
#> GSM153081 1 0.5871 0.27140 0.680 0.000 0.048 0.108 0.164
#> GSM153082 2 0.8759 -0.41036 0.236 0.372 0.032 0.112 0.248
#> GSM153083 2 0.8285 -0.40963 0.280 0.364 0.052 0.028 0.276
#> GSM153084 2 0.7673 0.15090 0.088 0.548 0.160 0.024 0.180
#> GSM153085 5 0.9143 0.34656 0.140 0.160 0.212 0.084 0.404
#> GSM153086 5 0.9110 0.33336 0.252 0.208 0.128 0.056 0.356
#> GSM153087 4 0.8054 0.14936 0.188 0.008 0.088 0.404 0.312
#> GSM153088 1 0.6993 0.15317 0.428 0.000 0.012 0.312 0.248
#> GSM153089 3 0.3139 0.75216 0.008 0.008 0.860 0.012 0.112
#> GSM153090 1 0.6561 0.01255 0.424 0.000 0.000 0.372 0.204
#> GSM153091 1 0.8318 -0.14230 0.344 0.220 0.000 0.144 0.292
#> GSM153092 1 0.8147 0.25371 0.404 0.076 0.012 0.252 0.256
#> GSM153093 4 0.6606 0.19868 0.336 0.000 0.008 0.480 0.176
#> GSM153094 2 0.8188 -0.43594 0.236 0.356 0.000 0.116 0.292
#> GSM153095 5 0.9579 0.31841 0.120 0.180 0.220 0.144 0.336
#> GSM153096 1 0.8260 0.12284 0.360 0.048 0.040 0.196 0.356
#> GSM153097 5 0.8353 0.23799 0.312 0.228 0.028 0.064 0.368
#> GSM153098 4 0.7259 -0.06093 0.304 0.020 0.000 0.380 0.296
#> GSM153099 4 0.7735 0.18853 0.232 0.000 0.084 0.452 0.232
#> GSM153100 1 0.7628 0.12559 0.380 0.048 0.004 0.364 0.204
#> GSM153101 5 0.9224 0.32847 0.176 0.172 0.296 0.052 0.304
#> GSM153102 5 0.9852 0.18965 0.244 0.184 0.132 0.192 0.248
#> GSM153103 5 0.9541 0.25967 0.284 0.152 0.140 0.120 0.304
#> GSM153104 4 0.6659 0.36573 0.144 0.000 0.072 0.612 0.172
#> GSM153106 1 0.5837 0.17753 0.532 0.004 0.000 0.376 0.088
#> GSM153107 1 0.5516 0.31282 0.668 0.004 0.004 0.212 0.112
#> GSM153108 4 0.8215 -0.00132 0.320 0.032 0.064 0.408 0.176
#> GSM153109 2 0.8670 -0.27824 0.240 0.420 0.036 0.128 0.176
#> GSM153110 1 0.7679 -0.03368 0.412 0.096 0.012 0.096 0.384
#> GSM153111 5 0.8847 0.24547 0.280 0.280 0.040 0.092 0.308
#> GSM153112 4 0.7858 -0.16928 0.324 0.064 0.000 0.324 0.288
#> GSM153113 2 0.6155 0.45931 0.100 0.672 0.012 0.044 0.172
#> GSM153114 1 0.5443 0.04615 0.504 0.000 0.000 0.436 0.060
#> GSM187532 2 0.4370 0.49030 0.000 0.724 0.236 0.000 0.040
#> GSM187533 2 0.0771 0.84837 0.020 0.976 0.000 0.000 0.004
#> GSM187534 2 0.0566 0.85428 0.012 0.984 0.000 0.000 0.004
#> GSM187535 2 0.4004 0.59910 0.216 0.760 0.000 0.008 0.016
#> GSM152906 2 0.0000 0.86357 0.000 1.000 0.000 0.000 0.000
#> GSM152907 2 0.0000 0.86357 0.000 1.000 0.000 0.000 0.000
#> GSM152908 2 0.0000 0.86357 0.000 1.000 0.000 0.000 0.000
#> GSM152909 2 0.0451 0.85615 0.000 0.988 0.008 0.000 0.004
#> GSM152910 2 0.0000 0.86357 0.000 1.000 0.000 0.000 0.000
#> GSM152911 2 0.0000 0.86357 0.000 1.000 0.000 0.000 0.000
#> GSM152912 2 0.0000 0.86357 0.000 1.000 0.000 0.000 0.000
#> GSM152913 2 0.1195 0.83221 0.000 0.960 0.028 0.000 0.012
#> GSM152914 2 0.0000 0.86357 0.000 1.000 0.000 0.000 0.000
#> GSM152915 2 0.0000 0.86357 0.000 1.000 0.000 0.000 0.000
#> GSM152916 2 0.0000 0.86357 0.000 1.000 0.000 0.000 0.000
#> GSM152917 2 0.0000 0.86357 0.000 1.000 0.000 0.000 0.000
#> GSM152918 2 0.0000 0.86357 0.000 1.000 0.000 0.000 0.000
#> GSM152919 2 0.0000 0.86357 0.000 1.000 0.000 0.000 0.000
#> GSM152920 2 0.0000 0.86357 0.000 1.000 0.000 0.000 0.000
#> GSM152921 2 0.0000 0.86357 0.000 1.000 0.000 0.000 0.000
#> GSM152922 2 0.0000 0.86357 0.000 1.000 0.000 0.000 0.000
#> GSM152923 2 0.0000 0.86357 0.000 1.000 0.000 0.000 0.000
#> GSM152924 2 0.0000 0.86357 0.000 1.000 0.000 0.000 0.000
#> GSM152925 2 0.0000 0.86357 0.000 1.000 0.000 0.000 0.000
#> GSM152926 2 0.0000 0.86357 0.000 1.000 0.000 0.000 0.000
#> GSM152927 2 0.0451 0.85648 0.000 0.988 0.008 0.000 0.004
#> GSM152928 2 0.1471 0.82962 0.004 0.952 0.024 0.000 0.020
#> GSM152929 2 0.0000 0.86357 0.000 1.000 0.000 0.000 0.000
#> GSM152930 2 0.0000 0.86357 0.000 1.000 0.000 0.000 0.000
cbind(get_classes(res, k = 6), get_membership(res, k = 6))
#> class entropy silhouette p1 p2 p3 p4 p5 p6
#> GSM152839 6 0.8737 0.27027 0.188 0.000 0.224 0.112 0.184 0.292
#> GSM152840 3 0.5943 0.52335 0.020 0.000 0.636 0.116 0.044 0.184
#> GSM152841 4 0.5262 0.40058 0.080 0.000 0.012 0.716 0.108 0.084
#> GSM152842 3 0.3001 0.63147 0.020 0.000 0.860 0.008 0.016 0.096
#> GSM152843 3 0.6887 0.41314 0.108 0.000 0.580 0.064 0.080 0.168
#> GSM152844 3 0.4057 0.62250 0.004 0.000 0.776 0.064 0.012 0.144
#> GSM152845 3 0.2846 0.63576 0.008 0.004 0.856 0.000 0.016 0.116
#> GSM152846 3 0.2715 0.63458 0.000 0.000 0.860 0.024 0.004 0.112
#> GSM152847 3 0.5398 0.56633 0.064 0.000 0.660 0.012 0.040 0.224
#> GSM152848 5 0.8637 -0.10552 0.220 0.000 0.176 0.104 0.320 0.180
#> GSM152849 3 0.5482 0.57671 0.060 0.000 0.680 0.020 0.056 0.184
#> GSM152850 3 0.7768 0.03195 0.140 0.000 0.436 0.048 0.128 0.248
#> GSM152851 3 0.8788 -0.30004 0.072 0.028 0.300 0.276 0.104 0.220
#> GSM152852 3 0.4654 0.61167 0.024 0.000 0.752 0.056 0.024 0.144
#> GSM152853 3 0.4677 0.58893 0.004 0.000 0.732 0.100 0.020 0.144
#> GSM152854 3 0.3669 0.63200 0.008 0.004 0.784 0.000 0.028 0.176
#> GSM152855 5 0.5740 0.09700 0.072 0.000 0.000 0.348 0.536 0.044
#> GSM153238 3 0.5163 0.56762 0.084 0.012 0.712 0.004 0.032 0.156
#> GSM153239 3 0.5263 0.56857 0.016 0.000 0.680 0.092 0.020 0.192
#> GSM153240 4 0.6955 0.28445 0.128 0.000 0.016 0.524 0.220 0.112
#> GSM153241 3 0.5835 0.54530 0.064 0.004 0.676 0.032 0.068 0.156
#> GSM153242 3 0.3184 0.63681 0.012 0.000 0.824 0.012 0.004 0.148
#> GSM153243 3 0.6359 0.47398 0.060 0.040 0.596 0.004 0.060 0.240
#> GSM153244 4 0.9532 -0.01344 0.148 0.104 0.096 0.296 0.220 0.136
#> GSM153245 3 0.4829 0.61319 0.020 0.000 0.744 0.064 0.036 0.136
#> GSM153246 3 0.1075 0.62081 0.000 0.000 0.952 0.000 0.000 0.048
#> GSM153247 3 0.6520 0.50573 0.064 0.028 0.636 0.040 0.064 0.168
#> GSM153248 1 0.7675 0.21284 0.464 0.060 0.000 0.148 0.228 0.100
#> GSM153249 4 0.5576 0.36044 0.196 0.000 0.000 0.636 0.128 0.040
#> GSM153250 4 0.7061 0.04969 0.224 0.000 0.000 0.396 0.300 0.080
#> GSM153251 3 0.3952 0.62838 0.016 0.016 0.792 0.016 0.008 0.152
#> GSM153252 4 0.6693 0.33582 0.164 0.000 0.008 0.552 0.176 0.100
#> GSM153253 4 0.6721 0.37609 0.080 0.000 0.044 0.592 0.140 0.144
#> GSM153254 6 0.9670 0.23094 0.128 0.088 0.188 0.216 0.128 0.252
#> GSM153255 4 0.4914 0.38858 0.104 0.000 0.000 0.724 0.116 0.056
#> GSM153256 4 0.7065 0.10207 0.252 0.000 0.004 0.388 0.296 0.060
#> GSM153257 4 0.6583 0.33120 0.136 0.000 0.004 0.560 0.184 0.116
#> GSM153258 5 0.7698 0.13503 0.268 0.000 0.016 0.240 0.360 0.116
#> GSM153259 1 0.7495 0.05550 0.448 0.020 0.012 0.152 0.284 0.084
#> GSM153260 3 0.5114 0.57451 0.032 0.012 0.692 0.008 0.040 0.216
#> GSM153261 3 0.5130 0.55407 0.040 0.000 0.672 0.008 0.048 0.232
#> GSM153262 4 0.7246 0.24952 0.116 0.000 0.016 0.476 0.240 0.152
#> GSM153263 5 0.7517 0.07040 0.288 0.000 0.000 0.284 0.292 0.136
#> GSM153264 5 0.8046 0.06168 0.312 0.004 0.032 0.128 0.332 0.192
#> GSM153265 4 0.8075 0.23189 0.116 0.000 0.100 0.440 0.168 0.176
#> GSM153266 5 0.8835 -0.05586 0.244 0.012 0.088 0.136 0.260 0.260
#> GSM153267 4 0.7223 0.20621 0.232 0.000 0.008 0.436 0.236 0.088
#> GSM153268 4 0.7434 0.28688 0.096 0.000 0.112 0.528 0.096 0.168
#> GSM153269 5 0.7389 -0.01317 0.236 0.000 0.004 0.312 0.348 0.100
#> GSM153270 4 0.8889 -0.00998 0.184 0.004 0.136 0.292 0.160 0.224
#> GSM153271 4 0.6795 0.14279 0.320 0.000 0.000 0.416 0.208 0.056
#> GSM153272 4 0.5922 0.35302 0.112 0.000 0.004 0.616 0.208 0.060
#> GSM153273 1 0.7557 0.19093 0.476 0.036 0.008 0.252 0.116 0.112
#> GSM153274 1 0.8674 -0.07743 0.284 0.004 0.092 0.256 0.232 0.132
#> GSM153275 4 0.7463 0.18865 0.256 0.000 0.020 0.428 0.200 0.096
#> GSM153276 4 0.8014 0.17374 0.180 0.000 0.060 0.424 0.196 0.140
#> GSM153277 4 0.7944 0.17852 0.156 0.000 0.040 0.404 0.232 0.168
#> GSM153278 3 0.7269 0.18920 0.116 0.004 0.484 0.028 0.096 0.272
#> GSM153279 4 0.8613 -0.01592 0.160 0.000 0.184 0.340 0.116 0.200
#> GSM153280 4 0.6905 0.31590 0.076 0.000 0.040 0.548 0.220 0.116
#> GSM153281 4 0.6729 0.36397 0.096 0.000 0.064 0.604 0.096 0.140
#> GSM153282 4 0.7111 0.32841 0.108 0.000 0.092 0.568 0.088 0.144
#> GSM153283 1 0.7370 -0.06619 0.376 0.000 0.004 0.256 0.264 0.100
#> GSM153284 4 0.7025 0.25802 0.208 0.000 0.008 0.480 0.220 0.084
#> GSM153285 4 0.6847 0.36308 0.112 0.000 0.036 0.576 0.120 0.156
#> GSM153286 4 0.6570 0.29368 0.216 0.000 0.000 0.516 0.200 0.068
#> GSM153287 4 0.3528 0.41418 0.076 0.000 0.000 0.832 0.044 0.048
#> GSM153288 4 0.5874 0.35282 0.136 0.000 0.000 0.628 0.160 0.076
#> GSM153289 5 0.5114 0.18570 0.072 0.000 0.000 0.280 0.628 0.020
#> GSM153290 4 0.6944 0.27262 0.076 0.000 0.048 0.532 0.252 0.092
#> GSM153291 4 0.5446 0.26136 0.064 0.000 0.000 0.564 0.340 0.032
#> GSM153292 4 0.5487 0.41019 0.136 0.000 0.008 0.688 0.080 0.088
#> GSM153293 4 0.6497 0.20169 0.156 0.000 0.000 0.468 0.324 0.052
#> GSM153294 1 0.7855 0.12361 0.392 0.088 0.000 0.316 0.120 0.084
#> GSM153295 5 0.8584 0.00579 0.084 0.000 0.192 0.268 0.284 0.172
#> GSM153054 3 0.8997 -0.37349 0.244 0.028 0.316 0.096 0.132 0.184
#> GSM153055 4 0.9328 -0.03031 0.192 0.072 0.064 0.284 0.224 0.164
#> GSM153056 3 0.7333 0.27020 0.084 0.000 0.516 0.076 0.104 0.220
#> GSM153057 3 0.8510 -0.09897 0.176 0.044 0.428 0.048 0.156 0.148
#> GSM153058 3 0.3875 0.63141 0.016 0.000 0.772 0.008 0.020 0.184
#> GSM153059 3 0.8722 -0.12394 0.088 0.140 0.388 0.028 0.140 0.216
#> GSM153060 3 0.1757 0.62721 0.008 0.000 0.916 0.000 0.000 0.076
#> GSM153061 3 0.1615 0.62526 0.004 0.000 0.928 0.000 0.004 0.064
#> GSM153062 3 0.1007 0.61960 0.000 0.000 0.956 0.000 0.000 0.044
#> GSM153063 3 0.4268 0.61830 0.024 0.000 0.788 0.044 0.028 0.116
#> GSM153064 1 0.7052 0.14237 0.480 0.008 0.000 0.248 0.164 0.100
#> GSM153065 3 0.3201 0.63138 0.008 0.000 0.824 0.000 0.028 0.140
#> GSM153066 3 0.7325 -0.10549 0.036 0.360 0.404 0.008 0.044 0.148
#> GSM153067 4 0.5806 0.35612 0.220 0.000 0.000 0.612 0.112 0.056
#> GSM153068 3 0.2865 0.63432 0.012 0.000 0.840 0.000 0.008 0.140
#> GSM153069 4 0.4347 0.40947 0.088 0.000 0.000 0.772 0.092 0.048
#> GSM153070 5 0.7926 0.10252 0.304 0.000 0.036 0.244 0.316 0.100
#> GSM153071 3 0.8789 -0.21827 0.132 0.020 0.368 0.192 0.100 0.188
#> GSM153072 6 0.9431 0.32794 0.216 0.072 0.240 0.080 0.144 0.248
#> GSM153073 1 0.7297 -0.07867 0.368 0.000 0.000 0.288 0.236 0.108
#> GSM153074 4 0.6617 0.34549 0.208 0.000 0.000 0.520 0.192 0.080
#> GSM153075 5 0.7688 0.03124 0.096 0.004 0.040 0.280 0.432 0.148
#> GSM153076 1 0.6991 -0.04612 0.388 0.000 0.000 0.276 0.272 0.064
#> GSM153077 1 0.8537 -0.03888 0.312 0.020 0.056 0.112 0.304 0.196
#> GSM153078 3 0.9281 -0.45580 0.148 0.040 0.256 0.100 0.208 0.248
#> GSM153079 5 0.7626 0.06873 0.156 0.068 0.044 0.052 0.544 0.136
#> GSM153080 3 0.7099 0.31603 0.064 0.000 0.504 0.092 0.064 0.276
#> GSM153081 5 0.6711 0.21284 0.168 0.000 0.028 0.092 0.580 0.132
#> GSM153082 2 0.9141 -0.39684 0.260 0.316 0.048 0.116 0.112 0.148
#> GSM153083 2 0.8255 -0.30775 0.292 0.348 0.032 0.016 0.180 0.132
#> GSM153084 2 0.8142 0.06679 0.108 0.476 0.132 0.020 0.088 0.176
#> GSM153085 6 0.9698 0.17979 0.204 0.136 0.136 0.100 0.152 0.272
#> GSM153086 1 0.8885 -0.09220 0.392 0.104 0.124 0.044 0.136 0.200
#> GSM153087 4 0.8386 0.18242 0.204 0.012 0.064 0.400 0.136 0.184
#> GSM153088 5 0.7442 0.11192 0.296 0.000 0.000 0.232 0.340 0.132
#> GSM153089 3 0.5410 0.58207 0.048 0.020 0.720 0.036 0.032 0.144
#> GSM153090 5 0.7553 0.01355 0.268 0.000 0.004 0.300 0.308 0.120
#> GSM153091 1 0.8208 0.23347 0.412 0.200 0.000 0.124 0.168 0.096
#> GSM153092 1 0.8813 0.05036 0.288 0.076 0.016 0.192 0.276 0.152
#> GSM153093 4 0.7181 0.28067 0.224 0.000 0.008 0.472 0.180 0.116
#> GSM153094 1 0.8487 0.10001 0.300 0.288 0.000 0.092 0.188 0.132
#> GSM153095 1 0.9649 -0.19448 0.260 0.192 0.132 0.104 0.100 0.212
#> GSM153096 1 0.8774 0.12833 0.352 0.060 0.036 0.224 0.208 0.120
#> GSM153097 1 0.8531 0.11138 0.416 0.160 0.032 0.056 0.176 0.160
#> GSM153098 1 0.7357 -0.01899 0.368 0.028 0.008 0.356 0.204 0.036
#> GSM153099 4 0.8460 0.09021 0.244 0.000 0.084 0.328 0.136 0.208
#> GSM153100 4 0.7899 -0.05400 0.268 0.036 0.000 0.304 0.300 0.092
#> GSM153101 6 0.9514 0.28674 0.216 0.084 0.212 0.068 0.192 0.228
#> GSM153102 5 0.9792 -0.17033 0.216 0.164 0.100 0.136 0.232 0.152
#> GSM153103 1 0.9531 -0.25228 0.240 0.116 0.152 0.060 0.196 0.236
#> GSM153104 4 0.6379 0.38033 0.064 0.000 0.076 0.640 0.108 0.112
#> GSM153106 5 0.5460 0.20092 0.084 0.004 0.000 0.264 0.620 0.028
#> GSM153107 5 0.5313 0.22770 0.120 0.004 0.000 0.120 0.696 0.060
#> GSM153108 4 0.8682 -0.03440 0.200 0.020 0.064 0.300 0.292 0.124
#> GSM153109 2 0.8768 -0.36186 0.208 0.332 0.036 0.056 0.252 0.116
#> GSM153110 1 0.7256 0.23583 0.560 0.092 0.020 0.060 0.196 0.072
#> GSM153111 1 0.8937 0.07071 0.332 0.236 0.032 0.076 0.176 0.148
#> GSM153112 1 0.7912 0.12361 0.408 0.072 0.000 0.256 0.184 0.080
#> GSM153113 2 0.7999 0.16468 0.156 0.508 0.032 0.076 0.100 0.128
#> GSM153114 5 0.5622 0.10526 0.060 0.000 0.000 0.336 0.556 0.048
#> GSM187532 2 0.4848 0.51819 0.008 0.696 0.212 0.000 0.016 0.068
#> GSM187533 2 0.1682 0.83065 0.000 0.928 0.000 0.000 0.052 0.020
#> GSM187534 2 0.1480 0.83780 0.000 0.940 0.000 0.000 0.040 0.020
#> GSM187535 2 0.5180 0.51204 0.048 0.664 0.000 0.016 0.244 0.028
#> GSM152906 2 0.1049 0.85306 0.008 0.960 0.000 0.000 0.000 0.032
#> GSM152907 2 0.0891 0.85452 0.008 0.968 0.000 0.000 0.000 0.024
#> GSM152908 2 0.0146 0.85562 0.000 0.996 0.000 0.000 0.000 0.004
#> GSM152909 2 0.1377 0.84326 0.004 0.952 0.016 0.000 0.004 0.024
#> GSM152910 2 0.0692 0.85553 0.004 0.976 0.000 0.000 0.000 0.020
#> GSM152911 2 0.0146 0.85617 0.000 0.996 0.000 0.000 0.000 0.004
#> GSM152912 2 0.0260 0.85503 0.000 0.992 0.000 0.000 0.000 0.008
#> GSM152913 2 0.1786 0.82930 0.004 0.932 0.032 0.000 0.004 0.028
#> GSM152914 2 0.0260 0.85503 0.000 0.992 0.000 0.000 0.000 0.008
#> GSM152915 2 0.0146 0.85557 0.000 0.996 0.000 0.000 0.000 0.004
#> GSM152916 2 0.1074 0.85466 0.012 0.960 0.000 0.000 0.000 0.028
#> GSM152917 2 0.0146 0.85557 0.000 0.996 0.000 0.000 0.000 0.004
#> GSM152918 2 0.0508 0.85645 0.004 0.984 0.000 0.000 0.000 0.012
#> GSM152919 2 0.0260 0.85610 0.000 0.992 0.000 0.000 0.000 0.008
#> GSM152920 2 0.0146 0.85562 0.000 0.996 0.000 0.000 0.000 0.004
#> GSM152921 2 0.0000 0.85593 0.000 1.000 0.000 0.000 0.000 0.000
#> GSM152922 2 0.0291 0.85557 0.004 0.992 0.000 0.000 0.000 0.004
#> GSM152923 2 0.1049 0.85306 0.008 0.960 0.000 0.000 0.000 0.032
#> GSM152924 2 0.1367 0.85112 0.012 0.944 0.000 0.000 0.000 0.044
#> GSM152925 2 0.1296 0.85240 0.012 0.952 0.000 0.000 0.004 0.032
#> GSM152926 2 0.1245 0.85252 0.016 0.952 0.000 0.000 0.000 0.032
#> GSM152927 2 0.1850 0.84507 0.016 0.924 0.008 0.000 0.000 0.052
#> GSM152928 2 0.3388 0.78523 0.024 0.848 0.040 0.000 0.012 0.076
#> GSM152929 2 0.1151 0.85256 0.012 0.956 0.000 0.000 0.000 0.032
#> GSM152930 2 0.0972 0.85407 0.008 0.964 0.000 0.000 0.000 0.028
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 tissue(p) k
#> CV:skmeans 145 2.41e-11 2
#> CV:skmeans 150 2.73e-25 3
#> CV:skmeans 95 1.50e-18 4
#> CV:skmeans 61 3.46e-11 5
#> CV:skmeans 57 4.83e-10 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 12013 rows and 164 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 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 0.885 0.937 0.969 0.2950 0.732 0.732
#> 3 3 0.307 0.677 0.798 1.0915 0.638 0.509
#> 4 4 0.320 0.518 0.710 0.1065 0.954 0.885
#> 5 5 0.318 0.443 0.680 0.0312 0.993 0.980
#> 6 6 0.300 0.441 0.657 0.0233 0.985 0.959
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
#> GSM152839 1 0.0376 0.9689 0.996 0.004
#> GSM152840 1 0.0376 0.9689 0.996 0.004
#> GSM152841 1 0.0000 0.9687 1.000 0.000
#> GSM152842 1 0.0376 0.9689 0.996 0.004
#> GSM152843 1 0.0000 0.9687 1.000 0.000
#> GSM152844 1 0.0000 0.9687 1.000 0.000
#> GSM152845 1 0.0000 0.9687 1.000 0.000
#> GSM152846 1 0.1633 0.9599 0.976 0.024
#> GSM152847 1 0.0376 0.9680 0.996 0.004
#> GSM152848 1 0.0938 0.9664 0.988 0.012
#> GSM152849 1 0.0000 0.9687 1.000 0.000
#> GSM152850 1 0.0672 0.9681 0.992 0.008
#> GSM152851 1 0.1184 0.9642 0.984 0.016
#> GSM152852 1 0.0376 0.9689 0.996 0.004
#> GSM152853 1 0.0000 0.9687 1.000 0.000
#> GSM152854 1 0.1843 0.9574 0.972 0.028
#> GSM152855 1 0.0376 0.9689 0.996 0.004
#> GSM153238 1 0.0000 0.9687 1.000 0.000
#> GSM153239 1 0.0938 0.9668 0.988 0.012
#> GSM153240 1 0.0376 0.9689 0.996 0.004
#> GSM153241 1 0.0672 0.9682 0.992 0.008
#> GSM153242 1 0.0672 0.9682 0.992 0.008
#> GSM153243 1 0.2948 0.9348 0.948 0.052
#> GSM153244 1 0.0938 0.9664 0.988 0.012
#> GSM153245 1 0.0376 0.9689 0.996 0.004
#> GSM153246 1 0.2423 0.9441 0.960 0.040
#> GSM153247 1 0.0672 0.9664 0.992 0.008
#> GSM153248 1 0.1184 0.9626 0.984 0.016
#> GSM153249 1 0.0672 0.9664 0.992 0.008
#> GSM153250 1 0.0000 0.9687 1.000 0.000
#> GSM153251 1 0.0672 0.9666 0.992 0.008
#> GSM153252 1 0.0376 0.9689 0.996 0.004
#> GSM153253 1 0.0376 0.9689 0.996 0.004
#> GSM153254 1 0.0000 0.9687 1.000 0.000
#> GSM153255 1 0.0376 0.9689 0.996 0.004
#> GSM153256 1 0.0000 0.9687 1.000 0.000
#> GSM153257 1 0.0000 0.9687 1.000 0.000
#> GSM153258 1 0.0000 0.9687 1.000 0.000
#> GSM153259 1 0.0376 0.9680 0.996 0.004
#> GSM153260 1 0.1633 0.9598 0.976 0.024
#> GSM153261 1 0.0376 0.9689 0.996 0.004
#> GSM153262 1 0.0376 0.9689 0.996 0.004
#> GSM153263 1 0.0376 0.9689 0.996 0.004
#> GSM153264 1 0.0376 0.9689 0.996 0.004
#> GSM153265 1 0.0376 0.9689 0.996 0.004
#> GSM153266 1 0.0376 0.9689 0.996 0.004
#> GSM153267 1 0.0376 0.9689 0.996 0.004
#> GSM153268 1 0.0000 0.9687 1.000 0.000
#> GSM153269 1 0.0376 0.9689 0.996 0.004
#> GSM153270 1 0.0000 0.9687 1.000 0.000
#> GSM153271 1 0.0000 0.9687 1.000 0.000
#> GSM153272 1 0.0376 0.9689 0.996 0.004
#> GSM153273 1 0.1184 0.9624 0.984 0.016
#> GSM153274 1 0.0000 0.9687 1.000 0.000
#> GSM153275 1 0.0376 0.9689 0.996 0.004
#> GSM153276 1 0.0376 0.9689 0.996 0.004
#> GSM153277 1 0.0376 0.9689 0.996 0.004
#> GSM153278 1 0.0000 0.9687 1.000 0.000
#> GSM153279 1 0.0000 0.9687 1.000 0.000
#> GSM153280 1 0.0376 0.9689 0.996 0.004
#> GSM153281 1 0.0000 0.9687 1.000 0.000
#> GSM153282 1 0.0672 0.9681 0.992 0.008
#> GSM153283 1 0.0376 0.9689 0.996 0.004
#> GSM153284 1 0.0672 0.9681 0.992 0.008
#> GSM153285 1 0.0376 0.9689 0.996 0.004
#> GSM153286 1 0.0000 0.9687 1.000 0.000
#> GSM153287 1 0.0376 0.9689 0.996 0.004
#> GSM153288 1 0.0376 0.9689 0.996 0.004
#> GSM153289 1 0.0376 0.9689 0.996 0.004
#> GSM153290 1 0.0376 0.9689 0.996 0.004
#> GSM153291 1 0.0376 0.9689 0.996 0.004
#> GSM153292 1 0.0376 0.9689 0.996 0.004
#> GSM153293 1 0.0376 0.9689 0.996 0.004
#> GSM153294 1 0.7528 0.7405 0.784 0.216
#> GSM153295 1 0.0376 0.9689 0.996 0.004
#> GSM153054 1 0.3733 0.9170 0.928 0.072
#> GSM153055 1 0.0938 0.9666 0.988 0.012
#> GSM153056 1 0.0376 0.9689 0.996 0.004
#> GSM153057 1 0.0376 0.9689 0.996 0.004
#> GSM153058 1 0.0000 0.9687 1.000 0.000
#> GSM153059 1 0.0000 0.9687 1.000 0.000
#> GSM153060 1 0.0000 0.9687 1.000 0.000
#> GSM153061 1 0.0000 0.9687 1.000 0.000
#> GSM153062 1 0.8555 0.6404 0.720 0.280
#> GSM153063 1 0.1414 0.9597 0.980 0.020
#> GSM153064 1 0.0672 0.9682 0.992 0.008
#> GSM153065 1 0.4939 0.8871 0.892 0.108
#> GSM153066 1 0.7528 0.7286 0.784 0.216
#> GSM153067 1 0.1414 0.9600 0.980 0.020
#> GSM153068 1 0.0000 0.9687 1.000 0.000
#> GSM153069 1 0.0000 0.9687 1.000 0.000
#> GSM153070 1 0.0000 0.9687 1.000 0.000
#> GSM153071 1 0.0376 0.9679 0.996 0.004
#> GSM153072 1 0.5178 0.8750 0.884 0.116
#> GSM153073 1 0.0938 0.9644 0.988 0.012
#> GSM153074 1 0.0000 0.9687 1.000 0.000
#> GSM153075 1 0.0376 0.9689 0.996 0.004
#> GSM153076 1 0.0376 0.9680 0.996 0.004
#> GSM153077 1 0.1184 0.9622 0.984 0.016
#> GSM153078 1 0.0000 0.9687 1.000 0.000
#> GSM153079 1 0.0672 0.9681 0.992 0.008
#> GSM153080 1 0.0376 0.9689 0.996 0.004
#> GSM153081 1 0.0672 0.9681 0.992 0.008
#> GSM153082 1 0.6531 0.8172 0.832 0.168
#> GSM153083 1 0.5408 0.8670 0.876 0.124
#> GSM153084 1 0.6531 0.8151 0.832 0.168
#> GSM153085 1 0.0000 0.9687 1.000 0.000
#> GSM153086 1 0.3584 0.9193 0.932 0.068
#> GSM153087 1 0.0938 0.9643 0.988 0.012
#> GSM153088 1 0.0000 0.9687 1.000 0.000
#> GSM153089 1 0.0000 0.9687 1.000 0.000
#> GSM153090 1 0.0000 0.9687 1.000 0.000
#> GSM153091 2 0.9970 0.0907 0.468 0.532
#> GSM153092 1 0.0000 0.9687 1.000 0.000
#> GSM153093 1 0.1184 0.9647 0.984 0.016
#> GSM153094 1 0.1843 0.9544 0.972 0.028
#> GSM153095 1 0.0672 0.9667 0.992 0.008
#> GSM153096 1 0.1633 0.9563 0.976 0.024
#> GSM153097 1 0.3584 0.9208 0.932 0.068
#> GSM153098 1 0.2043 0.9518 0.968 0.032
#> GSM153099 1 0.0000 0.9687 1.000 0.000
#> GSM153100 1 0.0376 0.9689 0.996 0.004
#> GSM153101 1 0.0376 0.9689 0.996 0.004
#> GSM153102 1 0.0376 0.9689 0.996 0.004
#> GSM153103 1 0.0000 0.9687 1.000 0.000
#> GSM153104 1 0.0000 0.9687 1.000 0.000
#> GSM153106 1 0.0376 0.9689 0.996 0.004
#> GSM153107 1 0.0376 0.9689 0.996 0.004
#> GSM153108 1 0.0000 0.9687 1.000 0.000
#> GSM153109 1 0.5059 0.8831 0.888 0.112
#> GSM153110 1 0.3879 0.9133 0.924 0.076
#> GSM153111 1 0.7376 0.7595 0.792 0.208
#> GSM153112 1 0.4815 0.8918 0.896 0.104
#> GSM153113 1 0.8861 0.5888 0.696 0.304
#> GSM153114 1 0.0376 0.9689 0.996 0.004
#> GSM187532 1 0.8813 0.5741 0.700 0.300
#> GSM187533 1 0.8144 0.6864 0.748 0.252
#> GSM187534 1 0.9944 0.1957 0.544 0.456
#> GSM187535 1 0.5059 0.8810 0.888 0.112
#> GSM152906 2 0.0376 0.9669 0.004 0.996
#> GSM152907 2 0.0000 0.9673 0.000 1.000
#> GSM152908 2 0.0000 0.9673 0.000 1.000
#> GSM152909 2 0.0376 0.9669 0.004 0.996
#> GSM152910 2 0.0000 0.9673 0.000 1.000
#> GSM152911 2 0.0000 0.9673 0.000 1.000
#> GSM152912 2 0.0376 0.9669 0.004 0.996
#> GSM152913 2 0.0000 0.9673 0.000 1.000
#> GSM152914 2 0.0000 0.9673 0.000 1.000
#> GSM152915 2 0.0000 0.9673 0.000 1.000
#> GSM152916 2 0.0376 0.9669 0.004 0.996
#> GSM152917 2 0.0376 0.9669 0.004 0.996
#> GSM152918 2 0.0376 0.9669 0.004 0.996
#> GSM152919 2 0.0000 0.9673 0.000 1.000
#> GSM152920 2 0.0000 0.9673 0.000 1.000
#> GSM152921 2 0.0000 0.9673 0.000 1.000
#> GSM152922 2 0.0000 0.9673 0.000 1.000
#> GSM152923 2 0.0376 0.9669 0.004 0.996
#> GSM152924 2 0.4431 0.8877 0.092 0.908
#> GSM152925 2 0.0376 0.9669 0.004 0.996
#> GSM152926 2 0.4022 0.9047 0.080 0.920
#> GSM152927 2 0.0376 0.9669 0.004 0.996
#> GSM152928 2 0.5178 0.8622 0.116 0.884
#> GSM152929 2 0.0376 0.9669 0.004 0.996
#> GSM152930 2 0.0000 0.9673 0.000 1.000
cbind(get_classes(res, k = 3), get_membership(res, k = 3))
#> class entropy silhouette p1 p2 p3
#> GSM152839 1 0.5760 0.6209 0.672 0.000 0.328
#> GSM152840 3 0.5254 0.6434 0.264 0.000 0.736
#> GSM152841 1 0.5327 0.6838 0.728 0.000 0.272
#> GSM152842 1 0.5810 0.5502 0.664 0.000 0.336
#> GSM152843 1 0.2537 0.7656 0.920 0.000 0.080
#> GSM152844 3 0.5968 0.5584 0.364 0.000 0.636
#> GSM152845 3 0.1860 0.7358 0.052 0.000 0.948
#> GSM152846 3 0.5650 0.6182 0.312 0.000 0.688
#> GSM152847 1 0.3941 0.7754 0.844 0.000 0.156
#> GSM152848 3 0.4974 0.5984 0.236 0.000 0.764
#> GSM152849 3 0.4002 0.7221 0.160 0.000 0.840
#> GSM152850 1 0.6298 0.5765 0.608 0.004 0.388
#> GSM152851 3 0.3030 0.7365 0.092 0.004 0.904
#> GSM152852 3 0.2356 0.7329 0.072 0.000 0.928
#> GSM152853 3 0.5706 0.5861 0.320 0.000 0.680
#> GSM152854 3 0.3031 0.7425 0.076 0.012 0.912
#> GSM152855 3 0.1529 0.7290 0.040 0.000 0.960
#> GSM153238 1 0.2959 0.7666 0.900 0.000 0.100
#> GSM153239 3 0.6140 0.4665 0.404 0.000 0.596
#> GSM153240 3 0.6008 0.4531 0.372 0.000 0.628
#> GSM153241 3 0.5138 0.6645 0.252 0.000 0.748
#> GSM153242 3 0.5591 0.5804 0.304 0.000 0.696
#> GSM153243 1 0.5020 0.7139 0.796 0.012 0.192
#> GSM153244 3 0.3686 0.7352 0.140 0.000 0.860
#> GSM153245 1 0.6302 0.0409 0.520 0.000 0.480
#> GSM153246 1 0.6410 0.1494 0.576 0.004 0.420
#> GSM153247 1 0.1964 0.7428 0.944 0.000 0.056
#> GSM153248 1 0.4293 0.7708 0.832 0.004 0.164
#> GSM153249 1 0.2261 0.7503 0.932 0.000 0.068
#> GSM153250 1 0.2959 0.7596 0.900 0.000 0.100
#> GSM153251 1 0.4887 0.7162 0.772 0.000 0.228
#> GSM153252 1 0.5859 0.6241 0.656 0.000 0.344
#> GSM153253 3 0.4887 0.6740 0.228 0.000 0.772
#> GSM153254 3 0.4750 0.7041 0.216 0.000 0.784
#> GSM153255 1 0.4887 0.7371 0.772 0.000 0.228
#> GSM153256 1 0.3038 0.7742 0.896 0.000 0.104
#> GSM153257 1 0.2537 0.7568 0.920 0.000 0.080
#> GSM153258 3 0.6008 0.3208 0.372 0.000 0.628
#> GSM153259 3 0.5926 0.4999 0.356 0.000 0.644
#> GSM153260 3 0.6667 0.4136 0.368 0.016 0.616
#> GSM153261 3 0.3038 0.7358 0.104 0.000 0.896
#> GSM153262 3 0.5098 0.6568 0.248 0.000 0.752
#> GSM153263 3 0.5465 0.5250 0.288 0.000 0.712
#> GSM153264 3 0.5706 0.4780 0.320 0.000 0.680
#> GSM153265 3 0.1289 0.7334 0.032 0.000 0.968
#> GSM153266 1 0.4931 0.7514 0.768 0.000 0.232
#> GSM153267 1 0.5363 0.6899 0.724 0.000 0.276
#> GSM153268 3 0.5016 0.6757 0.240 0.000 0.760
#> GSM153269 1 0.5098 0.7412 0.752 0.000 0.248
#> GSM153270 1 0.2711 0.7416 0.912 0.000 0.088
#> GSM153271 1 0.2796 0.7499 0.908 0.000 0.092
#> GSM153272 1 0.6045 0.5813 0.620 0.000 0.380
#> GSM153273 1 0.5553 0.6724 0.724 0.004 0.272
#> GSM153274 1 0.4887 0.7493 0.772 0.000 0.228
#> GSM153275 3 0.5560 0.6209 0.300 0.000 0.700
#> GSM153276 1 0.5835 0.6542 0.660 0.000 0.340
#> GSM153277 3 0.1753 0.7359 0.048 0.000 0.952
#> GSM153278 3 0.6154 0.4561 0.408 0.000 0.592
#> GSM153279 3 0.6045 0.4275 0.380 0.000 0.620
#> GSM153280 3 0.3412 0.7303 0.124 0.000 0.876
#> GSM153281 1 0.6305 0.1070 0.516 0.000 0.484
#> GSM153282 3 0.3879 0.7316 0.152 0.000 0.848
#> GSM153283 1 0.5397 0.6814 0.720 0.000 0.280
#> GSM153284 1 0.6192 0.4365 0.580 0.000 0.420
#> GSM153285 3 0.6280 0.2193 0.460 0.000 0.540
#> GSM153286 1 0.4750 0.7551 0.784 0.000 0.216
#> GSM153287 1 0.3340 0.7728 0.880 0.000 0.120
#> GSM153288 3 0.6309 -0.0793 0.500 0.000 0.500
#> GSM153289 3 0.1289 0.7310 0.032 0.000 0.968
#> GSM153290 3 0.1860 0.7357 0.052 0.000 0.948
#> GSM153291 3 0.1411 0.7362 0.036 0.000 0.964
#> GSM153292 3 0.5465 0.6392 0.288 0.000 0.712
#> GSM153293 3 0.5327 0.5699 0.272 0.000 0.728
#> GSM153294 1 0.6613 0.6898 0.740 0.072 0.188
#> GSM153295 3 0.1031 0.7330 0.024 0.000 0.976
#> GSM153054 1 0.2651 0.7285 0.928 0.012 0.060
#> GSM153055 3 0.3482 0.7382 0.128 0.000 0.872
#> GSM153056 1 0.5760 0.6454 0.672 0.000 0.328
#> GSM153057 3 0.1860 0.7377 0.052 0.000 0.948
#> GSM153058 1 0.5785 0.5148 0.668 0.000 0.332
#> GSM153059 3 0.4504 0.7050 0.196 0.000 0.804
#> GSM153060 1 0.2711 0.7594 0.912 0.000 0.088
#> GSM153061 3 0.5785 0.6027 0.332 0.000 0.668
#> GSM153062 3 0.9252 0.3245 0.372 0.160 0.468
#> GSM153063 1 0.3752 0.7662 0.856 0.000 0.144
#> GSM153064 1 0.5650 0.6794 0.688 0.000 0.312
#> GSM153065 3 0.5566 0.7204 0.108 0.080 0.812
#> GSM153066 3 0.9343 0.2873 0.348 0.176 0.476
#> GSM153067 1 0.3686 0.7707 0.860 0.000 0.140
#> GSM153068 3 0.6126 0.3394 0.400 0.000 0.600
#> GSM153069 1 0.6008 0.4992 0.628 0.000 0.372
#> GSM153070 1 0.4178 0.7630 0.828 0.000 0.172
#> GSM153071 1 0.3941 0.7418 0.844 0.000 0.156
#> GSM153072 1 0.3695 0.7698 0.880 0.012 0.108
#> GSM153073 1 0.1964 0.7535 0.944 0.000 0.056
#> GSM153074 1 0.6215 0.4681 0.572 0.000 0.428
#> GSM153075 3 0.1411 0.7314 0.036 0.000 0.964
#> GSM153076 1 0.3879 0.7665 0.848 0.000 0.152
#> GSM153077 1 0.3412 0.7728 0.876 0.000 0.124
#> GSM153078 3 0.4555 0.7148 0.200 0.000 0.800
#> GSM153079 3 0.0592 0.7307 0.012 0.000 0.988
#> GSM153080 3 0.4702 0.6923 0.212 0.000 0.788
#> GSM153081 3 0.1753 0.7306 0.048 0.000 0.952
#> GSM153082 3 0.7588 0.6422 0.196 0.120 0.684
#> GSM153083 1 0.5778 0.7539 0.768 0.032 0.200
#> GSM153084 3 0.8204 0.5196 0.316 0.096 0.588
#> GSM153085 1 0.4702 0.7475 0.788 0.000 0.212
#> GSM153086 1 0.5737 0.7093 0.732 0.012 0.256
#> GSM153087 1 0.3112 0.7739 0.900 0.004 0.096
#> GSM153088 1 0.3267 0.7633 0.884 0.000 0.116
#> GSM153089 3 0.2796 0.7320 0.092 0.000 0.908
#> GSM153090 1 0.3619 0.7632 0.864 0.000 0.136
#> GSM153091 1 0.4399 0.7312 0.864 0.092 0.044
#> GSM153092 3 0.5988 0.4551 0.368 0.000 0.632
#> GSM153093 1 0.3619 0.7713 0.864 0.000 0.136
#> GSM153094 3 0.6672 -0.1523 0.472 0.008 0.520
#> GSM153095 1 0.5785 0.5292 0.668 0.000 0.332
#> GSM153096 3 0.6154 0.4263 0.408 0.000 0.592
#> GSM153097 1 0.7208 0.5509 0.620 0.040 0.340
#> GSM153098 1 0.5797 0.6157 0.712 0.008 0.280
#> GSM153099 1 0.6286 0.2512 0.536 0.000 0.464
#> GSM153100 3 0.3116 0.7430 0.108 0.000 0.892
#> GSM153101 3 0.2165 0.7299 0.064 0.000 0.936
#> GSM153102 3 0.1289 0.7320 0.032 0.000 0.968
#> GSM153103 1 0.4235 0.7608 0.824 0.000 0.176
#> GSM153104 1 0.5835 0.4309 0.660 0.000 0.340
#> GSM153106 3 0.0424 0.7305 0.008 0.000 0.992
#> GSM153107 3 0.1031 0.7317 0.024 0.000 0.976
#> GSM153108 3 0.3816 0.7361 0.148 0.000 0.852
#> GSM153109 3 0.7184 0.5835 0.240 0.072 0.688
#> GSM153110 1 0.3112 0.7468 0.916 0.028 0.056
#> GSM153111 1 0.5236 0.7516 0.804 0.028 0.168
#> GSM153112 1 0.7940 0.5458 0.592 0.076 0.332
#> GSM153113 3 0.9425 -0.0668 0.392 0.176 0.432
#> GSM153114 3 0.0592 0.7294 0.012 0.000 0.988
#> GSM187532 3 0.7954 0.5763 0.148 0.192 0.660
#> GSM187533 3 0.4731 0.6952 0.032 0.128 0.840
#> GSM187534 3 0.6386 0.3373 0.004 0.412 0.584
#> GSM187535 3 0.2152 0.7331 0.036 0.016 0.948
#> GSM152906 2 0.0000 0.9793 0.000 1.000 0.000
#> GSM152907 2 0.0000 0.9793 0.000 1.000 0.000
#> GSM152908 2 0.0000 0.9793 0.000 1.000 0.000
#> GSM152909 2 0.0424 0.9732 0.008 0.992 0.000
#> GSM152910 2 0.0000 0.9793 0.000 1.000 0.000
#> GSM152911 2 0.0000 0.9793 0.000 1.000 0.000
#> GSM152912 2 0.0000 0.9793 0.000 1.000 0.000
#> GSM152913 2 0.0000 0.9793 0.000 1.000 0.000
#> GSM152914 2 0.0000 0.9793 0.000 1.000 0.000
#> GSM152915 2 0.0000 0.9793 0.000 1.000 0.000
#> GSM152916 2 0.0000 0.9793 0.000 1.000 0.000
#> GSM152917 2 0.0000 0.9793 0.000 1.000 0.000
#> GSM152918 2 0.0000 0.9793 0.000 1.000 0.000
#> GSM152919 2 0.0000 0.9793 0.000 1.000 0.000
#> GSM152920 2 0.0000 0.9793 0.000 1.000 0.000
#> GSM152921 2 0.0000 0.9793 0.000 1.000 0.000
#> GSM152922 2 0.0000 0.9793 0.000 1.000 0.000
#> GSM152923 2 0.0000 0.9793 0.000 1.000 0.000
#> GSM152924 2 0.4047 0.8150 0.004 0.848 0.148
#> GSM152925 2 0.0237 0.9757 0.004 0.996 0.000
#> GSM152926 2 0.4931 0.7974 0.140 0.828 0.032
#> GSM152927 2 0.0000 0.9793 0.000 1.000 0.000
#> GSM152928 2 0.4059 0.8393 0.012 0.860 0.128
#> GSM152929 2 0.0000 0.9793 0.000 1.000 0.000
#> GSM152930 2 0.0000 0.9793 0.000 1.000 0.000
cbind(get_classes(res, k = 4), get_membership(res, k = 4))
#> class entropy silhouette p1 p2 p3 p4
#> GSM152839 1 0.6890 0.54177 0.580 0.000 0.152 0.268
#> GSM152840 4 0.6650 0.37210 0.200 0.000 0.176 0.624
#> GSM152841 1 0.6885 0.54009 0.588 0.000 0.164 0.248
#> GSM152842 1 0.7441 0.40013 0.468 0.000 0.352 0.180
#> GSM152843 1 0.3383 0.69451 0.872 0.000 0.052 0.076
#> GSM152844 4 0.6315 0.17322 0.064 0.000 0.396 0.540
#> GSM152845 4 0.4405 0.48326 0.048 0.000 0.152 0.800
#> GSM152846 4 0.6587 0.25346 0.100 0.000 0.324 0.576
#> GSM152847 1 0.3278 0.69251 0.864 0.000 0.020 0.116
#> GSM152848 4 0.7196 0.23562 0.212 0.000 0.236 0.552
#> GSM152849 4 0.3999 0.52738 0.140 0.000 0.036 0.824
#> GSM152850 1 0.6264 0.50502 0.560 0.000 0.064 0.376
#> GSM152851 4 0.4245 0.52550 0.064 0.000 0.116 0.820
#> GSM152852 4 0.3335 0.52766 0.020 0.000 0.120 0.860
#> GSM152853 4 0.6823 0.36090 0.196 0.000 0.200 0.604
#> GSM152854 4 0.4108 0.53396 0.052 0.012 0.092 0.844
#> GSM152855 4 0.2089 0.52298 0.020 0.000 0.048 0.932
#> GSM153238 1 0.5404 0.65206 0.700 0.000 0.248 0.052
#> GSM153239 4 0.7472 0.20331 0.264 0.000 0.232 0.504
#> GSM153240 4 0.5632 0.30290 0.340 0.000 0.036 0.624
#> GSM153241 4 0.6118 0.39051 0.208 0.000 0.120 0.672
#> GSM153242 4 0.5910 0.32361 0.244 0.000 0.084 0.672
#> GSM153243 1 0.6245 0.61438 0.668 0.000 0.164 0.168
#> GSM153244 4 0.3745 0.52883 0.088 0.000 0.060 0.852
#> GSM153245 4 0.7846 -0.01527 0.336 0.000 0.272 0.392
#> GSM153246 4 0.7869 -0.08537 0.276 0.000 0.356 0.368
#> GSM153247 1 0.2813 0.66723 0.896 0.000 0.080 0.024
#> GSM153248 1 0.6513 0.64696 0.656 0.008 0.212 0.124
#> GSM153249 1 0.4630 0.64949 0.768 0.000 0.196 0.036
#> GSM153250 1 0.1661 0.66528 0.944 0.000 0.004 0.052
#> GSM153251 1 0.5759 0.61649 0.688 0.000 0.080 0.232
#> GSM153252 1 0.7093 0.59827 0.568 0.000 0.220 0.212
#> GSM153253 4 0.7128 0.27248 0.184 0.000 0.260 0.556
#> GSM153254 4 0.6346 0.41670 0.192 0.000 0.152 0.656
#> GSM153255 1 0.5427 0.67591 0.736 0.000 0.100 0.164
#> GSM153256 1 0.4636 0.69522 0.792 0.000 0.140 0.068
#> GSM153257 1 0.1724 0.66324 0.948 0.000 0.020 0.032
#> GSM153258 4 0.6135 0.16151 0.376 0.000 0.056 0.568
#> GSM153259 4 0.7388 0.16966 0.304 0.000 0.192 0.504
#> GSM153260 4 0.7550 0.15435 0.324 0.016 0.140 0.520
#> GSM153261 4 0.5195 0.42423 0.032 0.000 0.276 0.692
#> GSM153262 4 0.5891 0.44361 0.168 0.000 0.132 0.700
#> GSM153263 4 0.6435 0.34265 0.224 0.000 0.136 0.640
#> GSM153264 4 0.7079 0.24088 0.276 0.000 0.168 0.556
#> GSM153265 4 0.2593 0.52229 0.016 0.000 0.080 0.904
#> GSM153266 1 0.7054 0.56120 0.536 0.000 0.320 0.144
#> GSM153267 1 0.6917 0.56518 0.568 0.000 0.144 0.288
#> GSM153268 4 0.6056 0.42906 0.092 0.000 0.248 0.660
#> GSM153269 1 0.5106 0.66221 0.720 0.000 0.040 0.240
#> GSM153270 1 0.4153 0.66733 0.820 0.000 0.132 0.048
#> GSM153271 1 0.1706 0.65484 0.948 0.000 0.016 0.036
#> GSM153272 1 0.7002 0.57624 0.568 0.000 0.164 0.268
#> GSM153273 1 0.6871 0.59315 0.592 0.000 0.240 0.168
#> GSM153274 1 0.5346 0.67407 0.732 0.000 0.076 0.192
#> GSM153275 4 0.5995 0.33772 0.256 0.000 0.084 0.660
#> GSM153276 1 0.6079 0.61898 0.628 0.000 0.072 0.300
#> GSM153277 4 0.3497 0.52268 0.024 0.000 0.124 0.852
#> GSM153278 4 0.6784 0.11740 0.368 0.000 0.104 0.528
#> GSM153279 4 0.7520 0.09880 0.280 0.000 0.228 0.492
#> GSM153280 4 0.3732 0.53159 0.092 0.000 0.056 0.852
#> GSM153281 1 0.7629 0.16906 0.404 0.000 0.204 0.392
#> GSM153282 4 0.5857 0.34516 0.056 0.000 0.308 0.636
#> GSM153283 1 0.7397 0.54243 0.508 0.000 0.292 0.200
#> GSM153284 1 0.7324 0.52691 0.532 0.000 0.228 0.240
#> GSM153285 4 0.7584 0.06174 0.348 0.000 0.204 0.448
#> GSM153286 1 0.4387 0.69256 0.804 0.000 0.052 0.144
#> GSM153287 1 0.5619 0.62686 0.676 0.000 0.268 0.056
#> GSM153288 1 0.7619 0.08964 0.436 0.000 0.208 0.356
#> GSM153289 4 0.2489 0.52228 0.020 0.000 0.068 0.912
#> GSM153290 4 0.3082 0.53932 0.032 0.000 0.084 0.884
#> GSM153291 4 0.3542 0.51007 0.028 0.000 0.120 0.852
#> GSM153292 4 0.7212 0.16440 0.160 0.000 0.324 0.516
#> GSM153293 4 0.6946 0.30003 0.200 0.000 0.212 0.588
#> GSM153294 1 0.6219 0.65641 0.724 0.044 0.084 0.148
#> GSM153295 4 0.1902 0.53480 0.004 0.000 0.064 0.932
#> GSM153054 1 0.2402 0.65243 0.912 0.000 0.076 0.012
#> GSM153055 4 0.5058 0.50583 0.104 0.000 0.128 0.768
#> GSM153056 1 0.6309 0.54376 0.588 0.000 0.076 0.336
#> GSM153057 4 0.2227 0.53630 0.036 0.000 0.036 0.928
#> GSM153058 1 0.5830 0.36737 0.620 0.000 0.048 0.332
#> GSM153059 4 0.6324 0.41253 0.168 0.000 0.172 0.660
#> GSM153060 1 0.5021 0.65280 0.756 0.000 0.180 0.064
#> GSM153061 3 0.6928 -0.22056 0.108 0.000 0.456 0.436
#> GSM153062 3 0.8578 0.36175 0.144 0.128 0.540 0.188
#> GSM153063 1 0.5851 0.61861 0.680 0.000 0.236 0.084
#> GSM153064 1 0.7384 0.53702 0.476 0.000 0.352 0.172
#> GSM153065 4 0.6714 0.33670 0.044 0.064 0.236 0.656
#> GSM153066 3 0.9649 0.30225 0.204 0.152 0.352 0.292
#> GSM153067 1 0.5351 0.67984 0.744 0.000 0.152 0.104
#> GSM153068 4 0.7808 -0.00300 0.272 0.000 0.312 0.416
#> GSM153069 1 0.7805 0.29043 0.420 0.000 0.280 0.300
#> GSM153070 1 0.3694 0.68396 0.844 0.000 0.032 0.124
#> GSM153071 1 0.6091 0.55846 0.596 0.000 0.344 0.060
#> GSM153072 1 0.3962 0.69665 0.844 0.004 0.052 0.100
#> GSM153073 1 0.2111 0.66984 0.932 0.000 0.044 0.024
#> GSM153074 1 0.6314 0.40165 0.560 0.000 0.068 0.372
#> GSM153075 4 0.2002 0.52890 0.020 0.000 0.044 0.936
#> GSM153076 1 0.4605 0.69253 0.796 0.000 0.072 0.132
#> GSM153077 1 0.5410 0.67332 0.728 0.000 0.192 0.080
#> GSM153078 4 0.5375 0.45974 0.140 0.000 0.116 0.744
#> GSM153079 4 0.2412 0.51347 0.008 0.000 0.084 0.908
#> GSM153080 4 0.6435 0.37498 0.136 0.000 0.224 0.640
#> GSM153081 4 0.3013 0.51628 0.032 0.000 0.080 0.888
#> GSM153082 4 0.8050 0.09077 0.128 0.044 0.336 0.492
#> GSM153083 1 0.5501 0.68055 0.748 0.020 0.056 0.176
#> GSM153084 4 0.8475 0.18716 0.240 0.076 0.164 0.520
#> GSM153085 1 0.6761 0.60394 0.608 0.000 0.168 0.224
#> GSM153086 1 0.6036 0.64173 0.692 0.012 0.076 0.220
#> GSM153087 1 0.4626 0.69633 0.804 0.004 0.120 0.072
#> GSM153088 1 0.1978 0.67230 0.928 0.000 0.004 0.068
#> GSM153089 4 0.4364 0.44416 0.016 0.000 0.220 0.764
#> GSM153090 1 0.3674 0.69073 0.848 0.000 0.036 0.116
#> GSM153091 1 0.5255 0.64844 0.788 0.064 0.112 0.036
#> GSM153092 4 0.7095 0.15867 0.260 0.000 0.180 0.560
#> GSM153093 1 0.3634 0.68687 0.856 0.000 0.048 0.096
#> GSM153094 4 0.7523 -0.07994 0.392 0.008 0.144 0.456
#> GSM153095 1 0.7102 0.32386 0.548 0.000 0.164 0.288
#> GSM153096 4 0.7290 0.11458 0.328 0.000 0.168 0.504
#> GSM153097 1 0.7427 0.54382 0.568 0.012 0.204 0.216
#> GSM153098 1 0.7340 0.49144 0.580 0.012 0.208 0.200
#> GSM153099 1 0.6980 0.30785 0.484 0.000 0.116 0.400
#> GSM153100 4 0.4940 0.51945 0.096 0.000 0.128 0.776
#> GSM153101 4 0.3708 0.47718 0.020 0.000 0.148 0.832
#> GSM153102 4 0.2401 0.51048 0.004 0.000 0.092 0.904
#> GSM153103 1 0.5010 0.68092 0.772 0.000 0.108 0.120
#> GSM153104 1 0.6428 0.38798 0.624 0.000 0.112 0.264
#> GSM153106 4 0.1576 0.51708 0.004 0.000 0.048 0.948
#> GSM153107 4 0.1767 0.52509 0.012 0.000 0.044 0.944
#> GSM153108 4 0.5369 0.50778 0.112 0.000 0.144 0.744
#> GSM153109 4 0.7179 0.28916 0.224 0.072 0.068 0.636
#> GSM153110 1 0.3768 0.65174 0.848 0.008 0.120 0.024
#> GSM153111 1 0.7087 0.61655 0.588 0.008 0.256 0.148
#> GSM153112 1 0.8567 0.42509 0.468 0.048 0.236 0.248
#> GSM153113 4 0.9558 -0.18968 0.316 0.128 0.216 0.340
#> GSM153114 4 0.0707 0.52042 0.000 0.000 0.020 0.980
#> GSM187532 4 0.8362 -0.00506 0.120 0.172 0.144 0.564
#> GSM187533 4 0.4241 0.43735 0.012 0.124 0.036 0.828
#> GSM187534 4 0.6907 -0.13799 0.008 0.376 0.088 0.528
#> GSM187535 4 0.2405 0.52416 0.020 0.016 0.036 0.928
#> GSM152906 2 0.1302 0.93266 0.000 0.956 0.044 0.000
#> GSM152907 2 0.0000 0.93736 0.000 1.000 0.000 0.000
#> GSM152908 2 0.2281 0.91332 0.000 0.904 0.096 0.000
#> GSM152909 2 0.2868 0.90804 0.000 0.864 0.136 0.000
#> GSM152910 2 0.2281 0.91332 0.000 0.904 0.096 0.000
#> GSM152911 2 0.0000 0.93736 0.000 1.000 0.000 0.000
#> GSM152912 2 0.2281 0.91332 0.000 0.904 0.096 0.000
#> GSM152913 2 0.1302 0.93694 0.000 0.956 0.044 0.000
#> GSM152914 2 0.0000 0.93736 0.000 1.000 0.000 0.000
#> GSM152915 2 0.0000 0.93736 0.000 1.000 0.000 0.000
#> GSM152916 2 0.1557 0.93371 0.000 0.944 0.056 0.000
#> GSM152917 2 0.0000 0.93736 0.000 1.000 0.000 0.000
#> GSM152918 2 0.0000 0.93736 0.000 1.000 0.000 0.000
#> GSM152919 2 0.0000 0.93736 0.000 1.000 0.000 0.000
#> GSM152920 2 0.2281 0.91332 0.000 0.904 0.096 0.000
#> GSM152921 2 0.2281 0.91332 0.000 0.904 0.096 0.000
#> GSM152922 2 0.2704 0.91387 0.000 0.876 0.124 0.000
#> GSM152923 2 0.1302 0.93266 0.000 0.956 0.044 0.000
#> GSM152924 2 0.4387 0.75670 0.000 0.804 0.052 0.144
#> GSM152925 2 0.1389 0.93155 0.000 0.952 0.048 0.000
#> GSM152926 2 0.5432 0.74418 0.136 0.768 0.072 0.024
#> GSM152927 2 0.0817 0.93613 0.000 0.976 0.024 0.000
#> GSM152928 2 0.4683 0.78343 0.008 0.808 0.084 0.100
#> GSM152929 2 0.1302 0.93266 0.000 0.956 0.044 0.000
#> GSM152930 2 0.1302 0.93266 0.000 0.956 0.044 0.000
cbind(get_classes(res, k = 5), get_membership(res, k = 5))
#> class entropy silhouette p1 p2 p3 p4 p5
#> GSM152839 1 0.7447 0.4512 0.504 0.000 0.152 0.252 0.092
#> GSM152840 4 0.6381 0.3522 0.180 0.000 0.160 0.620 0.040
#> GSM152841 1 0.6434 0.4737 0.556 0.000 0.180 0.252 0.012
#> GSM152842 1 0.6637 0.3336 0.452 0.000 0.368 0.172 0.008
#> GSM152843 1 0.3859 0.6732 0.836 0.000 0.060 0.068 0.036
#> GSM152844 4 0.5526 0.2068 0.044 0.000 0.404 0.540 0.012
#> GSM152845 4 0.4516 0.4877 0.024 0.000 0.144 0.776 0.056
#> GSM152846 4 0.5943 0.2704 0.088 0.000 0.336 0.564 0.012
#> GSM152847 1 0.2908 0.6664 0.868 0.000 0.008 0.108 0.016
#> GSM152848 4 0.7396 0.1102 0.184 0.000 0.232 0.508 0.076
#> GSM152849 4 0.4482 0.5266 0.112 0.000 0.048 0.792 0.048
#> GSM152850 1 0.6742 0.4627 0.516 0.000 0.084 0.340 0.060
#> GSM152851 4 0.4253 0.5201 0.052 0.000 0.112 0.804 0.032
#> GSM152852 4 0.3550 0.5234 0.020 0.000 0.100 0.844 0.036
#> GSM152853 4 0.6394 0.3595 0.188 0.000 0.192 0.596 0.024
#> GSM152854 4 0.4665 0.5263 0.036 0.008 0.096 0.792 0.068
#> GSM152855 4 0.1934 0.5192 0.016 0.000 0.052 0.928 0.004
#> GSM153238 1 0.4750 0.6155 0.692 0.000 0.260 0.044 0.004
#> GSM153239 4 0.7521 0.1788 0.224 0.000 0.196 0.496 0.084
#> GSM153240 4 0.5662 0.2878 0.324 0.000 0.056 0.600 0.020
#> GSM153241 4 0.5887 0.3973 0.188 0.000 0.124 0.660 0.028
#> GSM153242 4 0.5509 0.3459 0.228 0.000 0.088 0.668 0.016
#> GSM153243 1 0.5496 0.5895 0.668 0.000 0.168 0.160 0.004
#> GSM153244 4 0.3281 0.5300 0.092 0.000 0.060 0.848 0.000
#> GSM153245 4 0.7096 -0.1300 0.332 0.000 0.276 0.380 0.012
#> GSM153246 3 0.7284 0.4016 0.160 0.000 0.536 0.216 0.088
#> GSM153247 1 0.2786 0.6463 0.884 0.000 0.084 0.020 0.012
#> GSM153248 1 0.6659 0.5944 0.604 0.000 0.212 0.100 0.084
#> GSM153249 1 0.4285 0.6196 0.752 0.000 0.208 0.032 0.008
#> GSM153250 1 0.1830 0.6433 0.932 0.000 0.000 0.040 0.028
#> GSM153251 1 0.5802 0.5661 0.664 0.000 0.080 0.216 0.040
#> GSM153252 1 0.6708 0.5485 0.532 0.000 0.256 0.192 0.020
#> GSM153253 4 0.6867 0.2307 0.180 0.000 0.244 0.540 0.036
#> GSM153254 4 0.5682 0.4166 0.172 0.000 0.164 0.656 0.008
#> GSM153255 1 0.5082 0.6549 0.732 0.000 0.096 0.152 0.020
#> GSM153256 1 0.4680 0.6688 0.772 0.000 0.132 0.064 0.032
#> GSM153257 1 0.1623 0.6395 0.948 0.000 0.016 0.020 0.016
#> GSM153258 4 0.5508 0.1330 0.384 0.000 0.060 0.552 0.004
#> GSM153259 4 0.7748 0.1213 0.228 0.000 0.204 0.468 0.100
#> GSM153260 4 0.7949 0.0590 0.304 0.008 0.128 0.440 0.120
#> GSM153261 4 0.4987 0.4081 0.024 0.000 0.280 0.672 0.024
#> GSM153262 4 0.5778 0.4256 0.140 0.000 0.140 0.684 0.036
#> GSM153263 4 0.7089 0.2414 0.204 0.000 0.156 0.560 0.080
#> GSM153264 4 0.7710 0.0962 0.248 0.000 0.164 0.476 0.112
#> GSM153265 4 0.2642 0.5247 0.008 0.000 0.104 0.880 0.008
#> GSM153266 1 0.7224 0.4865 0.492 0.000 0.312 0.120 0.076
#> GSM153267 1 0.6619 0.5131 0.548 0.000 0.144 0.280 0.028
#> GSM153268 4 0.5649 0.4416 0.068 0.000 0.252 0.652 0.028
#> GSM153269 1 0.4583 0.6412 0.740 0.000 0.044 0.204 0.012
#> GSM153270 1 0.3478 0.6452 0.844 0.000 0.108 0.032 0.016
#> GSM153271 1 0.1405 0.6280 0.956 0.000 0.016 0.020 0.008
#> GSM153272 1 0.7096 0.5362 0.536 0.000 0.164 0.240 0.060
#> GSM153273 1 0.6374 0.5501 0.560 0.000 0.264 0.164 0.012
#> GSM153274 1 0.4940 0.6504 0.732 0.000 0.088 0.168 0.012
#> GSM153275 4 0.5795 0.3431 0.236 0.000 0.100 0.644 0.020
#> GSM153276 1 0.5891 0.5953 0.616 0.000 0.052 0.288 0.044
#> GSM153277 4 0.3547 0.5199 0.016 0.000 0.144 0.824 0.016
#> GSM153278 4 0.6302 0.1451 0.356 0.000 0.108 0.520 0.016
#> GSM153279 4 0.6944 0.0732 0.260 0.000 0.232 0.488 0.020
#> GSM153280 4 0.3631 0.5287 0.080 0.000 0.068 0.840 0.012
#> GSM153281 1 0.7006 0.0805 0.380 0.000 0.232 0.376 0.012
#> GSM153282 4 0.4941 0.3533 0.044 0.000 0.328 0.628 0.000
#> GSM153283 1 0.7748 0.4618 0.460 0.000 0.264 0.172 0.104
#> GSM153284 1 0.7334 0.4856 0.500 0.000 0.204 0.236 0.060
#> GSM153285 4 0.7073 -0.0222 0.324 0.000 0.220 0.436 0.020
#> GSM153286 1 0.4236 0.6710 0.796 0.000 0.040 0.136 0.028
#> GSM153287 1 0.4797 0.5919 0.660 0.000 0.296 0.044 0.000
#> GSM153288 1 0.7370 -0.0139 0.408 0.000 0.204 0.348 0.040
#> GSM153289 4 0.2568 0.5175 0.016 0.000 0.092 0.888 0.004
#> GSM153290 4 0.3369 0.5385 0.028 0.000 0.092 0.856 0.024
#> GSM153291 4 0.3694 0.5121 0.020 0.000 0.132 0.824 0.024
#> GSM153292 4 0.6380 0.0814 0.156 0.000 0.344 0.496 0.004
#> GSM153293 4 0.6197 0.2395 0.192 0.000 0.232 0.572 0.004
#> GSM153294 1 0.5991 0.6324 0.716 0.056 0.072 0.120 0.036
#> GSM153295 4 0.1831 0.5345 0.000 0.000 0.076 0.920 0.004
#> GSM153054 1 0.2266 0.6341 0.912 0.000 0.064 0.008 0.016
#> GSM153055 4 0.5249 0.5066 0.088 0.000 0.120 0.740 0.052
#> GSM153056 1 0.6152 0.5009 0.572 0.000 0.076 0.320 0.032
#> GSM153057 4 0.3086 0.5341 0.016 0.000 0.048 0.876 0.060
#> GSM153058 1 0.5976 0.3055 0.584 0.000 0.052 0.324 0.040
#> GSM153059 4 0.6454 0.4132 0.092 0.000 0.160 0.640 0.108
#> GSM153060 1 0.4964 0.6224 0.728 0.000 0.192 0.056 0.024
#> GSM153061 3 0.6628 -0.1020 0.060 0.000 0.460 0.416 0.064
#> GSM153062 5 0.8307 -0.0802 0.056 0.120 0.312 0.076 0.436
#> GSM153063 1 0.5670 0.5688 0.644 0.000 0.256 0.080 0.020
#> GSM153064 1 0.7289 0.4567 0.436 0.000 0.356 0.156 0.052
#> GSM153065 4 0.6501 0.2920 0.024 0.048 0.248 0.620 0.060
#> GSM153066 3 0.9805 0.3324 0.132 0.216 0.284 0.172 0.196
#> GSM153067 1 0.4964 0.6465 0.736 0.000 0.160 0.088 0.016
#> GSM153068 4 0.7823 -0.1388 0.248 0.000 0.308 0.376 0.068
#> GSM153069 1 0.7410 0.1839 0.396 0.000 0.296 0.276 0.032
#> GSM153070 1 0.3647 0.6626 0.840 0.000 0.028 0.100 0.032
#> GSM153071 1 0.5862 0.5065 0.560 0.000 0.360 0.056 0.024
#> GSM153072 1 0.4128 0.6762 0.816 0.000 0.052 0.096 0.036
#> GSM153073 1 0.2617 0.6505 0.904 0.000 0.036 0.028 0.032
#> GSM153074 1 0.5571 0.3939 0.576 0.000 0.072 0.348 0.004
#> GSM153075 4 0.2897 0.5310 0.020 0.000 0.040 0.888 0.052
#> GSM153076 1 0.4697 0.6693 0.776 0.000 0.064 0.120 0.040
#> GSM153077 1 0.6184 0.6269 0.656 0.000 0.180 0.084 0.080
#> GSM153078 4 0.6069 0.4182 0.112 0.000 0.116 0.680 0.092
#> GSM153079 4 0.2392 0.5116 0.004 0.000 0.104 0.888 0.004
#> GSM153080 4 0.6091 0.3458 0.112 0.000 0.236 0.624 0.028
#> GSM153081 4 0.2947 0.5088 0.020 0.000 0.088 0.876 0.016
#> GSM153082 4 0.7787 -0.0641 0.104 0.032 0.340 0.456 0.068
#> GSM153083 1 0.4548 0.6543 0.752 0.004 0.076 0.168 0.000
#> GSM153084 4 0.7960 0.1660 0.220 0.064 0.188 0.496 0.032
#> GSM153085 1 0.6138 0.5702 0.596 0.000 0.188 0.208 0.008
#> GSM153086 1 0.5730 0.6188 0.680 0.012 0.080 0.208 0.020
#> GSM153087 1 0.5312 0.6684 0.744 0.004 0.112 0.052 0.088
#> GSM153088 1 0.1740 0.6476 0.932 0.000 0.000 0.056 0.012
#> GSM153089 4 0.3888 0.4586 0.008 0.000 0.228 0.756 0.008
#> GSM153090 1 0.3051 0.6619 0.852 0.000 0.028 0.120 0.000
#> GSM153091 1 0.5444 0.6298 0.752 0.048 0.116 0.040 0.044
#> GSM153092 4 0.6876 0.1329 0.264 0.000 0.168 0.532 0.036
#> GSM153093 1 0.4103 0.6661 0.820 0.000 0.036 0.080 0.064
#> GSM153094 4 0.7318 -0.0804 0.360 0.012 0.152 0.444 0.032
#> GSM153095 1 0.6859 0.2762 0.540 0.000 0.176 0.248 0.036
#> GSM153096 4 0.7007 0.0800 0.320 0.000 0.180 0.472 0.028
#> GSM153097 1 0.6888 0.4873 0.536 0.008 0.256 0.180 0.020
#> GSM153098 1 0.6712 0.4525 0.580 0.008 0.200 0.188 0.024
#> GSM153099 1 0.7573 0.2446 0.432 0.000 0.124 0.344 0.100
#> GSM153100 4 0.4814 0.5096 0.076 0.000 0.152 0.752 0.020
#> GSM153101 4 0.4222 0.4708 0.012 0.000 0.156 0.784 0.048
#> GSM153102 4 0.2628 0.5159 0.000 0.000 0.088 0.884 0.028
#> GSM153103 1 0.5782 0.6523 0.704 0.000 0.112 0.100 0.084
#> GSM153104 1 0.5617 0.3579 0.620 0.000 0.124 0.256 0.000
#> GSM153106 4 0.1518 0.5207 0.004 0.000 0.048 0.944 0.004
#> GSM153107 4 0.1740 0.5252 0.012 0.000 0.056 0.932 0.000
#> GSM153108 4 0.5678 0.4949 0.084 0.000 0.148 0.704 0.064
#> GSM153109 4 0.6762 0.2925 0.220 0.068 0.064 0.620 0.028
#> GSM153110 1 0.4466 0.6244 0.788 0.004 0.136 0.028 0.044
#> GSM153111 1 0.6621 0.5769 0.560 0.004 0.272 0.140 0.024
#> GSM153112 1 0.8441 0.3676 0.420 0.016 0.240 0.188 0.136
#> GSM153113 4 0.8901 -0.2596 0.296 0.100 0.232 0.328 0.044
#> GSM153114 4 0.0703 0.5227 0.000 0.000 0.024 0.976 0.000
#> GSM187532 4 0.8361 0.0451 0.116 0.152 0.104 0.524 0.104
#> GSM187533 4 0.4187 0.4462 0.008 0.096 0.044 0.820 0.032
#> GSM187534 4 0.7237 -0.0636 0.004 0.288 0.100 0.520 0.088
#> GSM187535 4 0.2388 0.5213 0.016 0.020 0.044 0.916 0.004
#> GSM152906 2 0.4227 0.6529 0.000 0.580 0.000 0.000 0.420
#> GSM152907 2 0.3928 0.7111 0.000 0.700 0.004 0.000 0.296
#> GSM152908 2 0.0000 0.5522 0.000 1.000 0.000 0.000 0.000
#> GSM152909 2 0.2233 0.5137 0.000 0.904 0.016 0.000 0.080
#> GSM152910 2 0.0000 0.5522 0.000 1.000 0.000 0.000 0.000
#> GSM152911 2 0.3928 0.7111 0.000 0.700 0.004 0.000 0.296
#> GSM152912 2 0.0000 0.5522 0.000 1.000 0.000 0.000 0.000
#> GSM152913 2 0.3766 0.6837 0.000 0.728 0.004 0.000 0.268
#> GSM152914 2 0.3928 0.7111 0.000 0.700 0.004 0.000 0.296
#> GSM152915 2 0.3928 0.7111 0.000 0.700 0.004 0.000 0.296
#> GSM152916 2 0.4138 0.6531 0.000 0.616 0.000 0.000 0.384
#> GSM152917 2 0.3928 0.7111 0.000 0.700 0.004 0.000 0.296
#> GSM152918 2 0.3928 0.7111 0.000 0.700 0.004 0.000 0.296
#> GSM152919 2 0.3928 0.7111 0.000 0.700 0.004 0.000 0.296
#> GSM152920 2 0.0000 0.5522 0.000 1.000 0.000 0.000 0.000
#> GSM152921 2 0.0000 0.5522 0.000 1.000 0.000 0.000 0.000
#> GSM152922 2 0.1732 0.5321 0.000 0.920 0.000 0.000 0.080
#> GSM152923 2 0.4227 0.6529 0.000 0.580 0.000 0.000 0.420
#> GSM152924 2 0.6267 0.3507 0.000 0.496 0.008 0.120 0.376
#> GSM152925 2 0.4489 0.6435 0.000 0.572 0.008 0.000 0.420
#> GSM152926 2 0.6364 0.4214 0.088 0.572 0.008 0.024 0.308
#> GSM152927 2 0.3966 0.6996 0.000 0.664 0.000 0.000 0.336
#> GSM152928 5 0.6049 -0.6429 0.000 0.452 0.024 0.060 0.464
#> GSM152929 2 0.4227 0.6529 0.000 0.580 0.000 0.000 0.420
#> GSM152930 2 0.4227 0.6529 0.000 0.580 0.000 0.000 0.420
cbind(get_classes(res, k = 6), get_membership(res, k = 6))
#> class entropy silhouette p1 p2 p3 p4 p5 p6
#> GSM152839 1 0.7237 0.49671 0.488 0.000 0.148 0.244 0.092 0.028
#> GSM152840 4 0.6232 0.47056 0.172 0.000 0.136 0.612 0.064 0.016
#> GSM152841 1 0.6136 0.51619 0.532 0.000 0.196 0.244 0.028 0.000
#> GSM152842 1 0.6118 0.40580 0.436 0.000 0.392 0.156 0.008 0.008
#> GSM152843 1 0.3685 0.68456 0.832 0.000 0.060 0.068 0.024 0.016
#> GSM152844 4 0.5554 0.33795 0.044 0.000 0.388 0.528 0.028 0.012
#> GSM152845 4 0.4799 0.51572 0.020 0.000 0.176 0.724 0.064 0.016
#> GSM152846 4 0.5816 0.38519 0.084 0.000 0.324 0.556 0.024 0.012
#> GSM152847 1 0.2774 0.67947 0.864 0.000 0.012 0.108 0.008 0.008
#> GSM152848 4 0.7326 0.25540 0.188 0.000 0.244 0.468 0.056 0.044
#> GSM152849 4 0.4277 0.57197 0.104 0.000 0.040 0.788 0.056 0.012
#> GSM152850 1 0.6641 0.49626 0.492 0.000 0.108 0.320 0.068 0.012
#> GSM152851 4 0.4326 0.55782 0.040 0.000 0.112 0.780 0.060 0.008
#> GSM152852 4 0.3925 0.55295 0.008 0.000 0.096 0.796 0.092 0.008
#> GSM152853 4 0.6242 0.45287 0.172 0.000 0.208 0.568 0.048 0.004
#> GSM152854 4 0.4761 0.56024 0.024 0.008 0.108 0.764 0.072 0.024
#> GSM152855 4 0.2367 0.54697 0.012 0.000 0.064 0.900 0.020 0.004
#> GSM153238 1 0.4255 0.63048 0.692 0.000 0.272 0.020 0.004 0.012
#> GSM153239 4 0.7111 0.34630 0.200 0.000 0.196 0.500 0.084 0.020
#> GSM153240 4 0.5852 0.41313 0.288 0.000 0.064 0.584 0.056 0.008
#> GSM153241 4 0.5663 0.47857 0.180 0.000 0.120 0.652 0.036 0.012
#> GSM153242 4 0.5347 0.42637 0.204 0.000 0.108 0.660 0.016 0.012
#> GSM153243 1 0.5497 0.61144 0.640 0.000 0.176 0.160 0.020 0.004
#> GSM153244 4 0.3356 0.56626 0.084 0.000 0.068 0.836 0.004 0.008
#> GSM153245 4 0.6634 0.00569 0.332 0.000 0.260 0.384 0.016 0.008
#> GSM153246 3 0.6129 -0.24842 0.068 0.000 0.628 0.056 0.044 0.204
#> GSM153247 1 0.2670 0.65831 0.880 0.000 0.084 0.012 0.008 0.016
#> GSM153248 1 0.6538 0.60688 0.580 0.000 0.228 0.092 0.056 0.044
#> GSM153249 1 0.3888 0.63429 0.740 0.000 0.224 0.028 0.008 0.000
#> GSM153250 1 0.1722 0.65292 0.936 0.000 0.004 0.036 0.016 0.008
#> GSM153251 1 0.5463 0.59703 0.656 0.000 0.084 0.216 0.012 0.032
#> GSM153252 1 0.6413 0.59356 0.520 0.000 0.256 0.184 0.032 0.008
#> GSM153253 4 0.6486 0.36864 0.172 0.000 0.264 0.520 0.024 0.020
#> GSM153254 4 0.5558 0.47371 0.164 0.000 0.192 0.624 0.004 0.016
#> GSM153255 1 0.5172 0.66451 0.704 0.000 0.108 0.136 0.048 0.004
#> GSM153256 1 0.4966 0.67761 0.728 0.000 0.140 0.060 0.064 0.008
#> GSM153257 1 0.1508 0.64981 0.948 0.000 0.016 0.020 0.012 0.004
#> GSM153258 4 0.5196 0.23098 0.372 0.000 0.072 0.548 0.004 0.004
#> GSM153259 4 0.7552 0.29096 0.196 0.000 0.208 0.460 0.100 0.036
#> GSM153260 4 0.7616 0.21096 0.280 0.000 0.132 0.404 0.164 0.020
#> GSM153261 4 0.4927 0.48128 0.020 0.000 0.276 0.656 0.036 0.012
#> GSM153262 4 0.5795 0.49414 0.120 0.000 0.128 0.664 0.076 0.012
#> GSM153263 4 0.7079 0.30875 0.180 0.000 0.184 0.500 0.128 0.008
#> GSM153264 4 0.7491 0.22703 0.236 0.000 0.192 0.440 0.112 0.020
#> GSM153265 4 0.2935 0.55704 0.004 0.000 0.112 0.852 0.028 0.004
#> GSM153266 1 0.7077 0.53328 0.480 0.000 0.300 0.116 0.064 0.040
#> GSM153267 1 0.6374 0.53572 0.524 0.000 0.148 0.284 0.032 0.012
#> GSM153268 4 0.5666 0.51304 0.064 0.000 0.240 0.632 0.052 0.012
#> GSM153269 1 0.4741 0.65796 0.708 0.000 0.048 0.200 0.044 0.000
#> GSM153270 1 0.3510 0.65597 0.824 0.000 0.120 0.032 0.016 0.008
#> GSM153271 1 0.1148 0.63846 0.960 0.000 0.020 0.016 0.000 0.004
#> GSM153272 1 0.6971 0.57261 0.516 0.000 0.164 0.216 0.088 0.016
#> GSM153273 1 0.5899 0.59841 0.560 0.000 0.284 0.128 0.004 0.024
#> GSM153274 1 0.4810 0.66613 0.712 0.000 0.088 0.176 0.020 0.004
#> GSM153275 4 0.5726 0.43776 0.228 0.000 0.116 0.620 0.024 0.012
#> GSM153276 1 0.5370 0.62883 0.616 0.000 0.044 0.288 0.048 0.004
#> GSM153277 4 0.3350 0.55532 0.012 0.000 0.156 0.812 0.004 0.016
#> GSM153278 4 0.5895 0.29032 0.348 0.000 0.120 0.512 0.008 0.012
#> GSM153279 4 0.6461 0.19976 0.240 0.000 0.272 0.464 0.008 0.016
#> GSM153280 4 0.3975 0.55955 0.068 0.000 0.064 0.812 0.048 0.008
#> GSM153281 4 0.6641 -0.12597 0.364 0.000 0.240 0.368 0.024 0.004
#> GSM153282 4 0.4708 0.41902 0.040 0.000 0.356 0.596 0.008 0.000
#> GSM153283 1 0.7706 0.47781 0.412 0.000 0.288 0.168 0.076 0.056
#> GSM153284 1 0.7097 0.54420 0.492 0.000 0.196 0.228 0.040 0.044
#> GSM153285 4 0.6571 0.16608 0.308 0.000 0.236 0.424 0.032 0.000
#> GSM153286 1 0.4249 0.68367 0.776 0.000 0.048 0.116 0.060 0.000
#> GSM153287 1 0.4776 0.61042 0.636 0.000 0.300 0.052 0.012 0.000
#> GSM153288 1 0.7077 0.07786 0.388 0.000 0.208 0.344 0.040 0.020
#> GSM153289 4 0.2715 0.54594 0.012 0.000 0.104 0.868 0.012 0.004
#> GSM153290 4 0.3580 0.57064 0.016 0.000 0.096 0.824 0.060 0.004
#> GSM153291 4 0.3964 0.54192 0.020 0.000 0.136 0.792 0.044 0.008
#> GSM153292 4 0.5933 0.28365 0.152 0.000 0.344 0.492 0.008 0.004
#> GSM153293 4 0.6046 0.35078 0.188 0.000 0.236 0.552 0.020 0.004
#> GSM153294 1 0.5847 0.65496 0.704 0.044 0.076 0.108 0.024 0.044
#> GSM153295 4 0.1757 0.56642 0.000 0.000 0.076 0.916 0.008 0.000
#> GSM153054 1 0.2412 0.64448 0.892 0.000 0.080 0.004 0.012 0.012
#> GSM153055 4 0.5100 0.54348 0.072 0.000 0.132 0.716 0.076 0.004
#> GSM153056 1 0.6294 0.51809 0.532 0.000 0.084 0.316 0.052 0.016
#> GSM153057 4 0.3469 0.56661 0.008 0.000 0.064 0.844 0.032 0.052
#> GSM153058 1 0.5676 0.37033 0.572 0.000 0.064 0.324 0.020 0.020
#> GSM153059 4 0.6329 0.48568 0.076 0.000 0.164 0.632 0.060 0.068
#> GSM153060 1 0.5392 0.60874 0.668 0.000 0.216 0.052 0.016 0.048
#> GSM153061 3 0.6104 -0.28904 0.052 0.000 0.484 0.388 0.008 0.068
#> GSM153062 5 0.4554 0.00000 0.040 0.104 0.040 0.016 0.784 0.016
#> GSM153063 1 0.6052 0.57172 0.600 0.000 0.244 0.088 0.016 0.052
#> GSM153064 1 0.7342 0.49199 0.408 0.000 0.348 0.140 0.056 0.048
#> GSM153065 4 0.6187 0.38740 0.016 0.036 0.276 0.592 0.044 0.036
#> GSM153066 3 0.9168 0.20558 0.120 0.116 0.308 0.124 0.056 0.276
#> GSM153067 1 0.5139 0.65712 0.708 0.000 0.156 0.080 0.048 0.008
#> GSM153068 4 0.7149 0.03850 0.256 0.000 0.344 0.344 0.020 0.036
#> GSM153069 1 0.7370 0.26748 0.356 0.000 0.312 0.252 0.064 0.016
#> GSM153070 1 0.3169 0.67317 0.852 0.000 0.024 0.096 0.020 0.008
#> GSM153071 1 0.5731 0.53833 0.544 0.000 0.356 0.044 0.044 0.012
#> GSM153072 1 0.3920 0.69028 0.804 0.000 0.052 0.092 0.052 0.000
#> GSM153073 1 0.2946 0.66405 0.880 0.000 0.044 0.024 0.032 0.020
#> GSM153074 1 0.5117 0.45858 0.580 0.000 0.076 0.336 0.008 0.000
#> GSM153075 4 0.3065 0.56261 0.012 0.000 0.048 0.852 0.088 0.000
#> GSM153076 1 0.4633 0.68343 0.768 0.000 0.060 0.108 0.040 0.024
#> GSM153077 1 0.5931 0.64607 0.648 0.000 0.188 0.076 0.056 0.032
#> GSM153078 4 0.6217 0.47484 0.120 0.000 0.120 0.644 0.080 0.036
#> GSM153079 4 0.2519 0.54063 0.004 0.000 0.124 0.864 0.004 0.004
#> GSM153080 4 0.5669 0.43448 0.104 0.000 0.264 0.600 0.028 0.004
#> GSM153081 4 0.3447 0.53262 0.016 0.000 0.112 0.832 0.028 0.012
#> GSM153082 4 0.7455 0.09970 0.100 0.044 0.368 0.416 0.024 0.048
#> GSM153083 1 0.4724 0.66851 0.716 0.000 0.100 0.168 0.008 0.008
#> GSM153084 4 0.7235 0.33494 0.216 0.060 0.204 0.488 0.004 0.028
#> GSM153085 1 0.5577 0.59157 0.572 0.000 0.212 0.212 0.000 0.004
#> GSM153086 1 0.5806 0.63808 0.656 0.012 0.100 0.188 0.028 0.016
#> GSM153087 1 0.5445 0.67788 0.720 0.004 0.116 0.052 0.044 0.064
#> GSM153088 1 0.1686 0.65769 0.932 0.000 0.004 0.052 0.004 0.008
#> GSM153089 4 0.3938 0.49463 0.008 0.000 0.244 0.728 0.008 0.012
#> GSM153090 1 0.3024 0.67576 0.844 0.000 0.032 0.116 0.008 0.000
#> GSM153091 1 0.5352 0.64966 0.732 0.044 0.116 0.040 0.056 0.012
#> GSM153092 4 0.6508 0.27785 0.252 0.000 0.168 0.528 0.040 0.012
#> GSM153093 1 0.3898 0.67889 0.808 0.000 0.028 0.076 0.084 0.004
#> GSM153094 4 0.6854 -0.09527 0.356 0.012 0.168 0.428 0.016 0.020
#> GSM153095 1 0.6614 0.37401 0.532 0.000 0.180 0.228 0.016 0.044
#> GSM153096 4 0.6500 0.24718 0.312 0.000 0.192 0.464 0.024 0.008
#> GSM153097 1 0.6536 0.53353 0.512 0.012 0.268 0.172 0.000 0.036
#> GSM153098 1 0.6607 0.48752 0.560 0.008 0.196 0.184 0.028 0.024
#> GSM153099 1 0.7396 0.25649 0.396 0.000 0.124 0.340 0.120 0.020
#> GSM153100 4 0.4895 0.54777 0.060 0.000 0.160 0.716 0.064 0.000
#> GSM153101 4 0.3777 0.52153 0.008 0.000 0.164 0.784 0.040 0.004
#> GSM153102 4 0.2833 0.54426 0.000 0.000 0.104 0.860 0.012 0.024
#> GSM153103 1 0.5636 0.67077 0.696 0.000 0.112 0.092 0.068 0.032
#> GSM153104 1 0.5348 0.41623 0.608 0.000 0.136 0.248 0.008 0.000
#> GSM153106 4 0.1719 0.54949 0.000 0.000 0.056 0.928 0.008 0.008
#> GSM153107 4 0.1668 0.55495 0.008 0.000 0.060 0.928 0.000 0.004
#> GSM153108 4 0.5779 0.52876 0.072 0.000 0.164 0.672 0.052 0.040
#> GSM153109 4 0.6479 0.40477 0.212 0.068 0.080 0.604 0.024 0.012
#> GSM153110 1 0.4115 0.64002 0.784 0.000 0.140 0.024 0.012 0.040
#> GSM153111 1 0.6140 0.61056 0.552 0.004 0.272 0.144 0.020 0.008
#> GSM153112 1 0.8271 0.44036 0.396 0.016 0.256 0.164 0.116 0.052
#> GSM153113 4 0.8155 -0.19272 0.276 0.104 0.256 0.324 0.020 0.020
#> GSM153114 4 0.0858 0.55162 0.000 0.000 0.028 0.968 0.000 0.004
#> GSM187532 4 0.8040 0.14240 0.104 0.164 0.112 0.504 0.032 0.084
#> GSM187533 4 0.3627 0.50334 0.004 0.116 0.048 0.816 0.016 0.000
#> GSM187534 4 0.6044 0.00105 0.004 0.344 0.124 0.504 0.000 0.024
#> GSM187535 4 0.2695 0.54932 0.012 0.016 0.056 0.892 0.020 0.004
#> GSM152906 2 0.3109 0.55550 0.000 0.772 0.004 0.000 0.000 0.224
#> GSM152907 2 0.0000 0.56409 0.000 1.000 0.000 0.000 0.000 0.000
#> GSM152908 2 0.3868 -0.75302 0.000 0.508 0.000 0.000 0.000 0.492
#> GSM152909 6 0.4317 0.87508 0.000 0.408 0.016 0.000 0.004 0.572
#> GSM152910 2 0.3868 -0.75935 0.000 0.504 0.000 0.000 0.000 0.496
#> GSM152911 2 0.0000 0.56409 0.000 1.000 0.000 0.000 0.000 0.000
#> GSM152912 2 0.3868 -0.75302 0.000 0.508 0.000 0.000 0.000 0.492
#> GSM152913 2 0.2793 0.46577 0.000 0.800 0.000 0.000 0.000 0.200
#> GSM152914 2 0.0000 0.56409 0.000 1.000 0.000 0.000 0.000 0.000
#> GSM152915 2 0.0000 0.56409 0.000 1.000 0.000 0.000 0.000 0.000
#> GSM152916 2 0.3136 0.53813 0.000 0.768 0.004 0.000 0.000 0.228
#> GSM152917 2 0.0000 0.56409 0.000 1.000 0.000 0.000 0.000 0.000
#> GSM152918 2 0.0000 0.56409 0.000 1.000 0.000 0.000 0.000 0.000
#> GSM152919 2 0.0000 0.56409 0.000 1.000 0.000 0.000 0.000 0.000
#> GSM152920 2 0.3868 -0.75302 0.000 0.508 0.000 0.000 0.000 0.492
#> GSM152921 2 0.3868 -0.75302 0.000 0.508 0.000 0.000 0.000 0.492
#> GSM152922 6 0.3737 0.87321 0.000 0.392 0.000 0.000 0.000 0.608
#> GSM152923 2 0.3136 0.55407 0.000 0.768 0.004 0.000 0.000 0.228
#> GSM152924 2 0.5125 0.41832 0.000 0.648 0.016 0.100 0.000 0.236
#> GSM152925 2 0.3109 0.55550 0.000 0.772 0.004 0.000 0.000 0.224
#> GSM152926 2 0.5423 0.36635 0.068 0.640 0.016 0.016 0.004 0.256
#> GSM152927 2 0.1471 0.57367 0.000 0.932 0.004 0.000 0.000 0.064
#> GSM152928 2 0.4680 0.49252 0.004 0.696 0.024 0.032 0.004 0.240
#> GSM152929 2 0.3109 0.55550 0.000 0.772 0.004 0.000 0.000 0.224
#> GSM152930 2 0.3023 0.55966 0.000 0.784 0.004 0.000 0.000 0.212
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 tissue(p) k
#> CV:pam 162 6.78e-35 2
#> CV:pam 138 7.78e-28 3
#> CV:pam 104 7.81e-21 4
#> CV:pam 92 4.76e-19 5
#> CV:pam 95 1.12e-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", "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 12013 rows and 164 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 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 0.996 0.949 0.966 0.3165 0.707 0.707
#> 3 3 0.477 0.724 0.801 0.8186 0.738 0.634
#> 4 4 0.622 0.693 0.798 0.2058 0.815 0.615
#> 5 5 0.565 0.548 0.738 0.0656 0.905 0.727
#> 6 6 0.637 0.713 0.804 0.0267 0.941 0.809
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
#> GSM152839 1 0.1414 0.957 0.980 0.020
#> GSM152840 1 0.4022 0.940 0.920 0.080
#> GSM152841 1 0.0000 0.960 1.000 0.000
#> GSM152842 1 0.4022 0.940 0.920 0.080
#> GSM152843 1 0.4022 0.940 0.920 0.080
#> GSM152844 1 0.4022 0.940 0.920 0.080
#> GSM152845 1 0.5059 0.915 0.888 0.112
#> GSM152846 1 0.4022 0.940 0.920 0.080
#> GSM152847 1 0.4022 0.940 0.920 0.080
#> GSM152848 1 0.0000 0.960 1.000 0.000
#> GSM152849 1 0.4022 0.940 0.920 0.080
#> GSM152850 1 0.3879 0.941 0.924 0.076
#> GSM152851 1 0.3274 0.947 0.940 0.060
#> GSM152852 1 0.4022 0.940 0.920 0.080
#> GSM152853 1 0.4022 0.940 0.920 0.080
#> GSM152854 1 0.4022 0.940 0.920 0.080
#> GSM152855 1 0.0000 0.960 1.000 0.000
#> GSM153238 1 0.4022 0.940 0.920 0.080
#> GSM153239 1 0.4022 0.940 0.920 0.080
#> GSM153240 1 0.0000 0.960 1.000 0.000
#> GSM153241 1 0.4022 0.940 0.920 0.080
#> GSM153242 1 0.4022 0.940 0.920 0.080
#> GSM153243 1 0.4022 0.940 0.920 0.080
#> GSM153244 1 0.0000 0.960 1.000 0.000
#> GSM153245 1 0.4022 0.940 0.920 0.080
#> GSM153246 1 0.4022 0.940 0.920 0.080
#> GSM153247 1 0.4022 0.940 0.920 0.080
#> GSM153248 1 0.0000 0.960 1.000 0.000
#> GSM153249 1 0.0000 0.960 1.000 0.000
#> GSM153250 1 0.0000 0.960 1.000 0.000
#> GSM153251 1 0.4022 0.940 0.920 0.080
#> GSM153252 1 0.0000 0.960 1.000 0.000
#> GSM153253 1 0.0000 0.960 1.000 0.000
#> GSM153254 1 0.0376 0.960 0.996 0.004
#> GSM153255 1 0.0000 0.960 1.000 0.000
#> GSM153256 1 0.0000 0.960 1.000 0.000
#> GSM153257 1 0.0000 0.960 1.000 0.000
#> GSM153258 1 0.0000 0.960 1.000 0.000
#> GSM153259 1 0.0000 0.960 1.000 0.000
#> GSM153260 1 0.4022 0.940 0.920 0.080
#> GSM153261 1 0.4022 0.940 0.920 0.080
#> GSM153262 1 0.0000 0.960 1.000 0.000
#> GSM153263 1 0.0000 0.960 1.000 0.000
#> GSM153264 1 0.0000 0.960 1.000 0.000
#> GSM153265 1 0.0000 0.960 1.000 0.000
#> GSM153266 1 0.0000 0.960 1.000 0.000
#> GSM153267 1 0.0000 0.960 1.000 0.000
#> GSM153268 1 0.0376 0.960 0.996 0.004
#> GSM153269 1 0.0000 0.960 1.000 0.000
#> GSM153270 1 0.0000 0.960 1.000 0.000
#> GSM153271 1 0.0000 0.960 1.000 0.000
#> GSM153272 1 0.0000 0.960 1.000 0.000
#> GSM153273 1 0.0938 0.959 0.988 0.012
#> GSM153274 1 0.0000 0.960 1.000 0.000
#> GSM153275 1 0.0000 0.960 1.000 0.000
#> GSM153276 1 0.0000 0.960 1.000 0.000
#> GSM153277 1 0.0000 0.960 1.000 0.000
#> GSM153278 1 0.4022 0.940 0.920 0.080
#> GSM153279 1 0.0000 0.960 1.000 0.000
#> GSM153280 1 0.0000 0.960 1.000 0.000
#> GSM153281 1 0.0000 0.960 1.000 0.000
#> GSM153282 1 0.0000 0.960 1.000 0.000
#> GSM153283 1 0.0000 0.960 1.000 0.000
#> GSM153284 1 0.0000 0.960 1.000 0.000
#> GSM153285 1 0.0000 0.960 1.000 0.000
#> GSM153286 1 0.0000 0.960 1.000 0.000
#> GSM153287 1 0.0000 0.960 1.000 0.000
#> GSM153288 1 0.0000 0.960 1.000 0.000
#> GSM153289 1 0.0000 0.960 1.000 0.000
#> GSM153290 1 0.0000 0.960 1.000 0.000
#> GSM153291 1 0.0000 0.960 1.000 0.000
#> GSM153292 1 0.0000 0.960 1.000 0.000
#> GSM153293 1 0.0000 0.960 1.000 0.000
#> GSM153294 1 0.0000 0.960 1.000 0.000
#> GSM153295 1 0.3879 0.941 0.924 0.076
#> GSM153054 1 0.3584 0.944 0.932 0.068
#> GSM153055 1 0.0000 0.960 1.000 0.000
#> GSM153056 1 0.4022 0.940 0.920 0.080
#> GSM153057 1 0.0376 0.960 0.996 0.004
#> GSM153058 1 0.4022 0.940 0.920 0.080
#> GSM153059 1 0.3274 0.947 0.940 0.060
#> GSM153060 1 0.4022 0.940 0.920 0.080
#> GSM153061 1 0.4022 0.940 0.920 0.080
#> GSM153062 1 0.4022 0.940 0.920 0.080
#> GSM153063 1 0.4022 0.940 0.920 0.080
#> GSM153064 1 0.0000 0.960 1.000 0.000
#> GSM153065 1 0.4022 0.940 0.920 0.080
#> GSM153066 1 0.9608 0.468 0.616 0.384
#> GSM153067 1 0.0000 0.960 1.000 0.000
#> GSM153068 1 0.4022 0.940 0.920 0.080
#> GSM153069 1 0.0000 0.960 1.000 0.000
#> GSM153070 1 0.0000 0.960 1.000 0.000
#> GSM153071 1 0.4022 0.940 0.920 0.080
#> GSM153072 1 0.3879 0.941 0.924 0.076
#> GSM153073 1 0.0000 0.960 1.000 0.000
#> GSM153074 1 0.0000 0.960 1.000 0.000
#> GSM153075 1 0.0000 0.960 1.000 0.000
#> GSM153076 1 0.0000 0.960 1.000 0.000
#> GSM153077 1 0.0376 0.960 0.996 0.004
#> GSM153078 1 0.3274 0.947 0.940 0.060
#> GSM153079 1 0.0000 0.960 1.000 0.000
#> GSM153080 1 0.4022 0.940 0.920 0.080
#> GSM153081 1 0.0000 0.960 1.000 0.000
#> GSM153082 1 0.5059 0.914 0.888 0.112
#> GSM153083 1 0.3733 0.943 0.928 0.072
#> GSM153084 1 0.8713 0.667 0.708 0.292
#> GSM153085 1 0.2948 0.949 0.948 0.052
#> GSM153086 1 0.3879 0.942 0.924 0.076
#> GSM153087 1 0.0000 0.960 1.000 0.000
#> GSM153088 1 0.0000 0.960 1.000 0.000
#> GSM153089 1 0.4022 0.940 0.920 0.080
#> GSM153090 1 0.0000 0.960 1.000 0.000
#> GSM153091 1 0.2778 0.951 0.952 0.048
#> GSM153092 1 0.0000 0.960 1.000 0.000
#> GSM153093 1 0.0000 0.960 1.000 0.000
#> GSM153094 1 0.4815 0.920 0.896 0.104
#> GSM153095 1 0.4298 0.934 0.912 0.088
#> GSM153096 1 0.0000 0.960 1.000 0.000
#> GSM153097 1 0.0938 0.959 0.988 0.012
#> GSM153098 1 0.0376 0.960 0.996 0.004
#> GSM153099 1 0.0000 0.960 1.000 0.000
#> GSM153100 1 0.0000 0.960 1.000 0.000
#> GSM153101 1 0.4022 0.940 0.920 0.080
#> GSM153102 1 0.1414 0.957 0.980 0.020
#> GSM153103 1 0.3584 0.944 0.932 0.068
#> GSM153104 1 0.0000 0.960 1.000 0.000
#> GSM153106 1 0.0000 0.960 1.000 0.000
#> GSM153107 1 0.0000 0.960 1.000 0.000
#> GSM153108 1 0.0000 0.960 1.000 0.000
#> GSM153109 1 0.5737 0.891 0.864 0.136
#> GSM153110 1 0.1184 0.958 0.984 0.016
#> GSM153111 1 0.2778 0.951 0.952 0.048
#> GSM153112 1 0.0376 0.959 0.996 0.004
#> GSM153113 1 0.9833 0.367 0.576 0.424
#> GSM153114 1 0.0000 0.960 1.000 0.000
#> GSM187532 2 0.3431 0.930 0.064 0.936
#> GSM187533 2 0.0376 0.988 0.004 0.996
#> GSM187534 2 0.0672 0.985 0.008 0.992
#> GSM187535 2 0.4815 0.879 0.104 0.896
#> GSM152906 2 0.0000 0.991 0.000 1.000
#> GSM152907 2 0.0000 0.991 0.000 1.000
#> GSM152908 2 0.0000 0.991 0.000 1.000
#> GSM152909 2 0.0000 0.991 0.000 1.000
#> GSM152910 2 0.0000 0.991 0.000 1.000
#> GSM152911 2 0.0000 0.991 0.000 1.000
#> GSM152912 2 0.0000 0.991 0.000 1.000
#> GSM152913 2 0.0000 0.991 0.000 1.000
#> GSM152914 2 0.0000 0.991 0.000 1.000
#> GSM152915 2 0.0000 0.991 0.000 1.000
#> GSM152916 2 0.0000 0.991 0.000 1.000
#> GSM152917 2 0.0000 0.991 0.000 1.000
#> GSM152918 2 0.0000 0.991 0.000 1.000
#> GSM152919 2 0.0000 0.991 0.000 1.000
#> GSM152920 2 0.0000 0.991 0.000 1.000
#> GSM152921 2 0.0000 0.991 0.000 1.000
#> GSM152922 2 0.0000 0.991 0.000 1.000
#> GSM152923 2 0.0000 0.991 0.000 1.000
#> GSM152924 2 0.0000 0.991 0.000 1.000
#> GSM152925 2 0.0000 0.991 0.000 1.000
#> GSM152926 2 0.0000 0.991 0.000 1.000
#> GSM152927 2 0.0000 0.991 0.000 1.000
#> GSM152928 2 0.2778 0.947 0.048 0.952
#> GSM152929 2 0.0000 0.991 0.000 1.000
#> GSM152930 2 0.0000 0.991 0.000 1.000
cbind(get_classes(res, k = 3), get_membership(res, k = 3))
#> class entropy silhouette p1 p2 p3
#> GSM152839 1 0.4555 0.5830 0.800 0.000 0.200
#> GSM152840 3 0.1989 0.6898 0.048 0.004 0.948
#> GSM152841 1 0.6111 0.6529 0.604 0.000 0.396
#> GSM152842 3 0.5905 0.7559 0.352 0.000 0.648
#> GSM152843 3 0.6154 0.7123 0.408 0.000 0.592
#> GSM152844 3 0.1989 0.6898 0.048 0.004 0.948
#> GSM152845 3 0.3043 0.7033 0.084 0.008 0.908
#> GSM152846 3 0.1989 0.6898 0.048 0.004 0.948
#> GSM152847 3 0.6045 0.7422 0.380 0.000 0.620
#> GSM152848 1 0.1753 0.7040 0.952 0.000 0.048
#> GSM152849 3 0.6008 0.7484 0.372 0.000 0.628
#> GSM152850 1 0.6291 -0.4685 0.532 0.000 0.468
#> GSM152851 1 0.6252 0.6115 0.556 0.000 0.444
#> GSM152852 3 0.2400 0.6778 0.064 0.004 0.932
#> GSM152853 3 0.1989 0.6898 0.048 0.004 0.948
#> GSM152854 3 0.2496 0.6994 0.068 0.004 0.928
#> GSM152855 1 0.5291 0.7273 0.732 0.000 0.268
#> GSM153238 3 0.5905 0.7559 0.352 0.000 0.648
#> GSM153239 3 0.1989 0.6898 0.048 0.004 0.948
#> GSM153240 1 0.5968 0.6748 0.636 0.000 0.364
#> GSM153241 3 0.5988 0.7468 0.368 0.000 0.632
#> GSM153242 3 0.1989 0.6898 0.048 0.004 0.948
#> GSM153243 3 0.6235 0.6727 0.436 0.000 0.564
#> GSM153244 1 0.6386 0.6472 0.584 0.004 0.412
#> GSM153245 3 0.2096 0.6918 0.052 0.004 0.944
#> GSM153246 3 0.6954 0.7509 0.352 0.028 0.620
#> GSM153247 3 0.6008 0.7491 0.372 0.000 0.628
#> GSM153248 1 0.1411 0.7028 0.964 0.000 0.036
#> GSM153249 1 0.5926 0.6753 0.644 0.000 0.356
#> GSM153250 1 0.1860 0.7377 0.948 0.000 0.052
#> GSM153251 3 0.2772 0.6999 0.080 0.004 0.916
#> GSM153252 1 0.5016 0.7472 0.760 0.000 0.240
#> GSM153253 1 0.6026 0.6654 0.624 0.000 0.376
#> GSM153254 1 0.6169 0.6831 0.636 0.004 0.360
#> GSM153255 1 0.5882 0.6794 0.652 0.000 0.348
#> GSM153256 1 0.4235 0.7539 0.824 0.000 0.176
#> GSM153257 1 0.4974 0.7421 0.764 0.000 0.236
#> GSM153258 1 0.3941 0.7554 0.844 0.000 0.156
#> GSM153259 1 0.0892 0.7118 0.980 0.000 0.020
#> GSM153260 3 0.5948 0.7548 0.360 0.000 0.640
#> GSM153261 3 0.5785 0.7561 0.332 0.000 0.668
#> GSM153262 1 0.5733 0.7044 0.676 0.000 0.324
#> GSM153263 1 0.2066 0.7355 0.940 0.000 0.060
#> GSM153264 1 0.2066 0.6876 0.940 0.000 0.060
#> GSM153265 1 0.6079 0.6622 0.612 0.000 0.388
#> GSM153266 1 0.2448 0.6823 0.924 0.000 0.076
#> GSM153267 1 0.4235 0.7537 0.824 0.000 0.176
#> GSM153268 1 0.6225 0.6221 0.568 0.000 0.432
#> GSM153269 1 0.3752 0.7545 0.856 0.000 0.144
#> GSM153270 1 0.4452 0.7542 0.808 0.000 0.192
#> GSM153271 1 0.4062 0.7543 0.836 0.000 0.164
#> GSM153272 1 0.5560 0.7126 0.700 0.000 0.300
#> GSM153273 1 0.1163 0.7171 0.972 0.000 0.028
#> GSM153274 1 0.3340 0.7532 0.880 0.000 0.120
#> GSM153275 1 0.4605 0.7508 0.796 0.000 0.204
#> GSM153276 1 0.4750 0.7496 0.784 0.000 0.216
#> GSM153277 1 0.5988 0.6712 0.632 0.000 0.368
#> GSM153278 1 0.6225 -0.3487 0.568 0.000 0.432
#> GSM153279 1 0.6111 0.6689 0.604 0.000 0.396
#> GSM153280 1 0.6154 0.6435 0.592 0.000 0.408
#> GSM153281 1 0.6026 0.6655 0.624 0.000 0.376
#> GSM153282 1 0.6154 0.6435 0.592 0.000 0.408
#> GSM153283 1 0.1529 0.7108 0.960 0.000 0.040
#> GSM153284 1 0.4931 0.7434 0.768 0.000 0.232
#> GSM153285 1 0.6008 0.6675 0.628 0.000 0.372
#> GSM153286 1 0.5678 0.7009 0.684 0.000 0.316
#> GSM153287 1 0.5968 0.6732 0.636 0.000 0.364
#> GSM153288 1 0.5058 0.7375 0.756 0.000 0.244
#> GSM153289 1 0.4555 0.7506 0.800 0.000 0.200
#> GSM153290 1 0.6079 0.6576 0.612 0.000 0.388
#> GSM153291 1 0.5882 0.6794 0.652 0.000 0.348
#> GSM153292 1 0.6008 0.6675 0.628 0.000 0.372
#> GSM153293 1 0.4178 0.7542 0.828 0.000 0.172
#> GSM153294 1 0.2165 0.7217 0.936 0.000 0.064
#> GSM153295 1 0.4121 0.5567 0.832 0.000 0.168
#> GSM153054 1 0.3412 0.6335 0.876 0.000 0.124
#> GSM153055 1 0.4796 0.7480 0.780 0.000 0.220
#> GSM153056 3 0.6280 0.6285 0.460 0.000 0.540
#> GSM153057 1 0.5016 0.6748 0.760 0.000 0.240
#> GSM153058 3 0.5254 0.7429 0.264 0.000 0.736
#> GSM153059 1 0.5722 0.6347 0.704 0.004 0.292
#> GSM153060 3 0.6448 0.7556 0.352 0.012 0.636
#> GSM153061 3 0.6587 0.7548 0.352 0.016 0.632
#> GSM153062 3 0.6978 0.7549 0.336 0.032 0.632
#> GSM153063 3 0.4629 0.7271 0.188 0.004 0.808
#> GSM153064 1 0.1964 0.7364 0.944 0.000 0.056
#> GSM153065 3 0.6126 0.7562 0.352 0.004 0.644
#> GSM153066 3 0.7665 0.6188 0.456 0.044 0.500
#> GSM153067 1 0.5785 0.6894 0.668 0.000 0.332
#> GSM153068 3 0.6297 0.7560 0.352 0.008 0.640
#> GSM153069 1 0.5968 0.6732 0.636 0.000 0.364
#> GSM153070 1 0.3482 0.7548 0.872 0.000 0.128
#> GSM153071 1 0.5560 0.2105 0.700 0.000 0.300
#> GSM153072 1 0.3752 0.5912 0.856 0.000 0.144
#> GSM153073 1 0.0592 0.7197 0.988 0.000 0.012
#> GSM153074 1 0.5733 0.6952 0.676 0.000 0.324
#> GSM153075 1 0.5859 0.6900 0.656 0.000 0.344
#> GSM153076 1 0.0747 0.7259 0.984 0.000 0.016
#> GSM153077 1 0.1964 0.6912 0.944 0.000 0.056
#> GSM153078 1 0.3340 0.6425 0.880 0.000 0.120
#> GSM153079 1 0.2066 0.6860 0.940 0.000 0.060
#> GSM153080 3 0.5070 0.6168 0.224 0.004 0.772
#> GSM153081 1 0.2261 0.6869 0.932 0.000 0.068
#> GSM153082 1 0.1964 0.6887 0.944 0.000 0.056
#> GSM153083 1 0.2066 0.6866 0.940 0.000 0.060
#> GSM153084 1 0.3539 0.6490 0.888 0.012 0.100
#> GSM153085 1 0.2878 0.6618 0.904 0.000 0.096
#> GSM153086 1 0.2165 0.6827 0.936 0.000 0.064
#> GSM153087 1 0.4702 0.7514 0.788 0.000 0.212
#> GSM153088 1 0.0892 0.7156 0.980 0.000 0.020
#> GSM153089 3 0.2096 0.6920 0.052 0.004 0.944
#> GSM153090 1 0.0747 0.7214 0.984 0.000 0.016
#> GSM153091 1 0.1964 0.6887 0.944 0.000 0.056
#> GSM153092 1 0.4452 0.7535 0.808 0.000 0.192
#> GSM153093 1 0.5397 0.7244 0.720 0.000 0.280
#> GSM153094 1 0.1964 0.6887 0.944 0.000 0.056
#> GSM153095 1 0.2878 0.6810 0.904 0.000 0.096
#> GSM153096 1 0.1753 0.7248 0.952 0.000 0.048
#> GSM153097 1 0.1964 0.6887 0.944 0.000 0.056
#> GSM153098 1 0.3412 0.7485 0.876 0.000 0.124
#> GSM153099 1 0.4750 0.7499 0.784 0.000 0.216
#> GSM153100 1 0.4504 0.7524 0.804 0.000 0.196
#> GSM153101 1 0.3816 0.6037 0.852 0.000 0.148
#> GSM153102 1 0.5588 0.7237 0.720 0.004 0.276
#> GSM153103 1 0.2878 0.6627 0.904 0.000 0.096
#> GSM153104 1 0.5968 0.6748 0.636 0.000 0.364
#> GSM153106 1 0.4974 0.7467 0.764 0.000 0.236
#> GSM153107 1 0.4235 0.7540 0.824 0.000 0.176
#> GSM153108 1 0.5591 0.7192 0.696 0.000 0.304
#> GSM153109 1 0.2448 0.7095 0.924 0.000 0.076
#> GSM153110 1 0.1529 0.6993 0.960 0.000 0.040
#> GSM153111 1 0.1964 0.6887 0.944 0.000 0.056
#> GSM153112 1 0.2625 0.7305 0.916 0.000 0.084
#> GSM153113 1 0.3129 0.6595 0.904 0.008 0.088
#> GSM153114 1 0.5678 0.7003 0.684 0.000 0.316
#> GSM187532 2 0.5236 0.7515 0.028 0.804 0.168
#> GSM187533 2 0.1129 0.9526 0.020 0.976 0.004
#> GSM187534 2 0.1453 0.9433 0.024 0.968 0.008
#> GSM187535 1 0.7851 -0.0511 0.532 0.412 0.056
#> GSM152906 2 0.0000 0.9786 0.000 1.000 0.000
#> GSM152907 2 0.0000 0.9786 0.000 1.000 0.000
#> GSM152908 2 0.0000 0.9786 0.000 1.000 0.000
#> GSM152909 2 0.0000 0.9786 0.000 1.000 0.000
#> GSM152910 2 0.0000 0.9786 0.000 1.000 0.000
#> GSM152911 2 0.0000 0.9786 0.000 1.000 0.000
#> GSM152912 2 0.0000 0.9786 0.000 1.000 0.000
#> GSM152913 2 0.0000 0.9786 0.000 1.000 0.000
#> GSM152914 2 0.0000 0.9786 0.000 1.000 0.000
#> GSM152915 2 0.0000 0.9786 0.000 1.000 0.000
#> GSM152916 2 0.0000 0.9786 0.000 1.000 0.000
#> GSM152917 2 0.0000 0.9786 0.000 1.000 0.000
#> GSM152918 2 0.0000 0.9786 0.000 1.000 0.000
#> GSM152919 2 0.0000 0.9786 0.000 1.000 0.000
#> GSM152920 2 0.0000 0.9786 0.000 1.000 0.000
#> GSM152921 2 0.0000 0.9786 0.000 1.000 0.000
#> GSM152922 2 0.0000 0.9786 0.000 1.000 0.000
#> GSM152923 2 0.0000 0.9786 0.000 1.000 0.000
#> GSM152924 2 0.0000 0.9786 0.000 1.000 0.000
#> GSM152925 2 0.0000 0.9786 0.000 1.000 0.000
#> GSM152926 2 0.0000 0.9786 0.000 1.000 0.000
#> GSM152927 2 0.0000 0.9786 0.000 1.000 0.000
#> GSM152928 2 0.5987 0.6287 0.208 0.756 0.036
#> GSM152929 2 0.0000 0.9786 0.000 1.000 0.000
#> GSM152930 2 0.0000 0.9786 0.000 1.000 0.000
cbind(get_classes(res, k = 4), get_membership(res, k = 4))
#> class entropy silhouette p1 p2 p3 p4
#> GSM152839 1 0.5320 0.3699 0.572 0.000 0.416 0.012
#> GSM152840 3 0.4543 0.7829 0.000 0.000 0.676 0.324
#> GSM152841 4 0.4331 0.9111 0.288 0.000 0.000 0.712
#> GSM152842 3 0.0707 0.8166 0.000 0.000 0.980 0.020
#> GSM152843 3 0.1256 0.8148 0.028 0.000 0.964 0.008
#> GSM152844 3 0.4543 0.7829 0.000 0.000 0.676 0.324
#> GSM152845 3 0.4477 0.7863 0.000 0.000 0.688 0.312
#> GSM152846 3 0.4543 0.7829 0.000 0.000 0.676 0.324
#> GSM152847 3 0.1174 0.8152 0.020 0.000 0.968 0.012
#> GSM152848 1 0.3108 0.6964 0.872 0.000 0.112 0.016
#> GSM152849 3 0.1406 0.8169 0.024 0.000 0.960 0.016
#> GSM152850 3 0.2271 0.7767 0.076 0.000 0.916 0.008
#> GSM152851 3 0.7327 0.1608 0.320 0.000 0.504 0.176
#> GSM152852 3 0.4543 0.7829 0.000 0.000 0.676 0.324
#> GSM152853 3 0.4543 0.7829 0.000 0.000 0.676 0.324
#> GSM152854 3 0.4522 0.7839 0.000 0.000 0.680 0.320
#> GSM152855 1 0.3400 0.5868 0.820 0.000 0.000 0.180
#> GSM153238 3 0.0592 0.8161 0.000 0.000 0.984 0.016
#> GSM153239 3 0.4543 0.7829 0.000 0.000 0.676 0.324
#> GSM153240 4 0.4585 0.9065 0.332 0.000 0.000 0.668
#> GSM153241 3 0.1733 0.8187 0.028 0.000 0.948 0.024
#> GSM153242 3 0.4543 0.7829 0.000 0.000 0.676 0.324
#> GSM153243 3 0.1151 0.8140 0.024 0.000 0.968 0.008
#> GSM153244 1 0.6168 -0.2631 0.556 0.000 0.056 0.388
#> GSM153245 3 0.4655 0.7866 0.004 0.000 0.684 0.312
#> GSM153246 3 0.2081 0.8191 0.000 0.000 0.916 0.084
#> GSM153247 3 0.1406 0.8147 0.024 0.000 0.960 0.016
#> GSM153248 1 0.1488 0.7349 0.956 0.000 0.032 0.012
#> GSM153249 4 0.4992 0.6027 0.476 0.000 0.000 0.524
#> GSM153250 1 0.1004 0.7300 0.972 0.000 0.004 0.024
#> GSM153251 3 0.4814 0.7858 0.008 0.000 0.676 0.316
#> GSM153252 1 0.4522 0.2381 0.680 0.000 0.000 0.320
#> GSM153253 4 0.4406 0.9207 0.300 0.000 0.000 0.700
#> GSM153254 1 0.6946 0.1148 0.588 0.000 0.200 0.212
#> GSM153255 4 0.4761 0.8436 0.372 0.000 0.000 0.628
#> GSM153256 1 0.2589 0.6663 0.884 0.000 0.000 0.116
#> GSM153257 1 0.4277 0.3713 0.720 0.000 0.000 0.280
#> GSM153258 1 0.0469 0.7325 0.988 0.000 0.000 0.012
#> GSM153259 1 0.0469 0.7323 0.988 0.000 0.000 0.012
#> GSM153260 3 0.0524 0.8145 0.008 0.000 0.988 0.004
#> GSM153261 3 0.2522 0.8246 0.016 0.000 0.908 0.076
#> GSM153262 1 0.4776 -0.0221 0.624 0.000 0.000 0.376
#> GSM153263 1 0.1174 0.7343 0.968 0.000 0.012 0.020
#> GSM153264 1 0.1042 0.7337 0.972 0.000 0.020 0.008
#> GSM153265 4 0.4356 0.9139 0.292 0.000 0.000 0.708
#> GSM153266 1 0.2814 0.6900 0.868 0.000 0.132 0.000
#> GSM153267 1 0.2921 0.6396 0.860 0.000 0.000 0.140
#> GSM153268 4 0.6138 0.7707 0.260 0.000 0.092 0.648
#> GSM153269 1 0.1474 0.7155 0.948 0.000 0.000 0.052
#> GSM153270 1 0.2216 0.6901 0.908 0.000 0.000 0.092
#> GSM153271 1 0.2530 0.6709 0.888 0.000 0.000 0.112
#> GSM153272 4 0.4999 0.5478 0.492 0.000 0.000 0.508
#> GSM153273 1 0.0672 0.7342 0.984 0.000 0.008 0.008
#> GSM153274 1 0.1792 0.7070 0.932 0.000 0.000 0.068
#> GSM153275 1 0.3764 0.5258 0.784 0.000 0.000 0.216
#> GSM153276 1 0.3266 0.6089 0.832 0.000 0.000 0.168
#> GSM153277 4 0.4477 0.9232 0.312 0.000 0.000 0.688
#> GSM153278 3 0.1890 0.7984 0.056 0.000 0.936 0.008
#> GSM153279 1 0.6276 -0.5360 0.480 0.000 0.056 0.464
#> GSM153280 4 0.4304 0.9076 0.284 0.000 0.000 0.716
#> GSM153281 4 0.4477 0.9232 0.312 0.000 0.000 0.688
#> GSM153282 4 0.4250 0.8972 0.276 0.000 0.000 0.724
#> GSM153283 1 0.1411 0.7340 0.960 0.000 0.020 0.020
#> GSM153284 1 0.3907 0.4939 0.768 0.000 0.000 0.232
#> GSM153285 4 0.4431 0.9222 0.304 0.000 0.000 0.696
#> GSM153286 1 0.4933 -0.3382 0.568 0.000 0.000 0.432
#> GSM153287 4 0.4477 0.9232 0.312 0.000 0.000 0.688
#> GSM153288 1 0.3764 0.5284 0.784 0.000 0.000 0.216
#> GSM153289 1 0.1902 0.7177 0.932 0.000 0.004 0.064
#> GSM153290 4 0.4356 0.9145 0.292 0.000 0.000 0.708
#> GSM153291 4 0.4643 0.8905 0.344 0.000 0.000 0.656
#> GSM153292 4 0.4477 0.9232 0.312 0.000 0.000 0.688
#> GSM153293 1 0.3024 0.6308 0.852 0.000 0.000 0.148
#> GSM153294 1 0.1767 0.7271 0.944 0.000 0.012 0.044
#> GSM153295 3 0.5256 0.2846 0.392 0.000 0.596 0.012
#> GSM153054 1 0.5016 0.4298 0.600 0.000 0.396 0.004
#> GSM153055 1 0.0707 0.7300 0.980 0.000 0.000 0.020
#> GSM153056 3 0.1388 0.8154 0.028 0.000 0.960 0.012
#> GSM153057 1 0.5564 0.3032 0.544 0.000 0.436 0.020
#> GSM153058 3 0.4538 0.8108 0.024 0.000 0.760 0.216
#> GSM153059 3 0.6494 0.4026 0.340 0.000 0.572 0.088
#> GSM153060 3 0.2011 0.8196 0.000 0.000 0.920 0.080
#> GSM153061 3 0.1211 0.8192 0.000 0.000 0.960 0.040
#> GSM153062 3 0.2647 0.8162 0.000 0.000 0.880 0.120
#> GSM153063 3 0.4706 0.8038 0.020 0.000 0.732 0.248
#> GSM153064 1 0.1557 0.7134 0.944 0.000 0.000 0.056
#> GSM153065 3 0.0592 0.8143 0.000 0.000 0.984 0.016
#> GSM153066 3 0.1593 0.8153 0.004 0.016 0.956 0.024
#> GSM153067 1 0.4925 -0.2749 0.572 0.000 0.000 0.428
#> GSM153068 3 0.1389 0.8199 0.000 0.000 0.952 0.048
#> GSM153069 4 0.4477 0.9232 0.312 0.000 0.000 0.688
#> GSM153070 1 0.0469 0.7305 0.988 0.000 0.000 0.012
#> GSM153071 3 0.5088 0.0985 0.424 0.000 0.572 0.004
#> GSM153072 1 0.4776 0.4769 0.624 0.000 0.376 0.000
#> GSM153073 1 0.0779 0.7319 0.980 0.000 0.004 0.016
#> GSM153074 1 0.4888 -0.1946 0.588 0.000 0.000 0.412
#> GSM153075 1 0.4608 0.2763 0.692 0.000 0.004 0.304
#> GSM153076 1 0.1004 0.7301 0.972 0.000 0.004 0.024
#> GSM153077 1 0.1284 0.7347 0.964 0.000 0.024 0.012
#> GSM153078 1 0.4718 0.5668 0.708 0.000 0.280 0.012
#> GSM153079 1 0.3718 0.6633 0.820 0.000 0.168 0.012
#> GSM153080 3 0.5693 0.7729 0.072 0.000 0.688 0.240
#> GSM153081 1 0.1767 0.7288 0.944 0.000 0.044 0.012
#> GSM153082 1 0.4472 0.6268 0.760 0.000 0.220 0.020
#> GSM153083 1 0.3591 0.6620 0.824 0.000 0.168 0.008
#> GSM153084 3 0.5945 0.0202 0.428 0.024 0.540 0.008
#> GSM153085 1 0.4560 0.5617 0.700 0.000 0.296 0.004
#> GSM153086 1 0.3249 0.6824 0.852 0.000 0.140 0.008
#> GSM153087 1 0.4008 0.4670 0.756 0.000 0.000 0.244
#> GSM153088 1 0.1510 0.7343 0.956 0.000 0.016 0.028
#> GSM153089 3 0.4543 0.7829 0.000 0.000 0.676 0.324
#> GSM153090 1 0.0592 0.7317 0.984 0.000 0.000 0.016
#> GSM153091 1 0.4011 0.6338 0.784 0.000 0.208 0.008
#> GSM153092 1 0.1059 0.7353 0.972 0.000 0.012 0.016
#> GSM153093 1 0.4134 0.4160 0.740 0.000 0.000 0.260
#> GSM153094 1 0.3718 0.6621 0.820 0.000 0.168 0.012
#> GSM153095 1 0.5167 0.5109 0.644 0.000 0.340 0.016
#> GSM153096 1 0.0336 0.7336 0.992 0.000 0.008 0.000
#> GSM153097 1 0.3402 0.6672 0.832 0.000 0.164 0.004
#> GSM153098 1 0.1042 0.7328 0.972 0.000 0.008 0.020
#> GSM153099 1 0.4252 0.4502 0.744 0.000 0.004 0.252
#> GSM153100 1 0.0336 0.7318 0.992 0.000 0.000 0.008
#> GSM153101 1 0.4978 0.5277 0.664 0.000 0.324 0.012
#> GSM153102 1 0.1059 0.7349 0.972 0.000 0.016 0.012
#> GSM153103 1 0.4319 0.6142 0.760 0.000 0.228 0.012
#> GSM153104 4 0.4477 0.9224 0.312 0.000 0.000 0.688
#> GSM153106 1 0.1854 0.7274 0.940 0.000 0.012 0.048
#> GSM153107 1 0.0779 0.7327 0.980 0.000 0.004 0.016
#> GSM153108 1 0.2760 0.6553 0.872 0.000 0.000 0.128
#> GSM153109 1 0.3428 0.6768 0.844 0.000 0.144 0.012
#> GSM153110 1 0.1545 0.7307 0.952 0.000 0.040 0.008
#> GSM153111 1 0.3978 0.6405 0.796 0.000 0.192 0.012
#> GSM153112 1 0.1706 0.7346 0.948 0.000 0.036 0.016
#> GSM153113 1 0.4822 0.6122 0.756 0.024 0.212 0.008
#> GSM153114 1 0.4382 0.2861 0.704 0.000 0.000 0.296
#> GSM187532 2 0.5038 0.4378 0.000 0.652 0.336 0.012
#> GSM187533 2 0.1082 0.9374 0.020 0.972 0.004 0.004
#> GSM187534 2 0.1082 0.9373 0.020 0.972 0.004 0.004
#> GSM187535 2 0.7543 0.3766 0.272 0.540 0.176 0.012
#> GSM152906 2 0.0000 0.9555 0.000 1.000 0.000 0.000
#> GSM152907 2 0.0000 0.9555 0.000 1.000 0.000 0.000
#> GSM152908 2 0.0000 0.9555 0.000 1.000 0.000 0.000
#> GSM152909 2 0.1706 0.9201 0.000 0.948 0.036 0.016
#> GSM152910 2 0.0000 0.9555 0.000 1.000 0.000 0.000
#> GSM152911 2 0.0000 0.9555 0.000 1.000 0.000 0.000
#> GSM152912 2 0.0000 0.9555 0.000 1.000 0.000 0.000
#> GSM152913 2 0.1488 0.9264 0.000 0.956 0.032 0.012
#> GSM152914 2 0.0000 0.9555 0.000 1.000 0.000 0.000
#> GSM152915 2 0.0000 0.9555 0.000 1.000 0.000 0.000
#> GSM152916 2 0.0000 0.9555 0.000 1.000 0.000 0.000
#> GSM152917 2 0.0000 0.9555 0.000 1.000 0.000 0.000
#> GSM152918 2 0.0000 0.9555 0.000 1.000 0.000 0.000
#> GSM152919 2 0.0000 0.9555 0.000 1.000 0.000 0.000
#> GSM152920 2 0.0000 0.9555 0.000 1.000 0.000 0.000
#> GSM152921 2 0.0000 0.9555 0.000 1.000 0.000 0.000
#> GSM152922 2 0.0000 0.9555 0.000 1.000 0.000 0.000
#> GSM152923 2 0.0000 0.9555 0.000 1.000 0.000 0.000
#> GSM152924 2 0.0000 0.9555 0.000 1.000 0.000 0.000
#> GSM152925 2 0.0000 0.9555 0.000 1.000 0.000 0.000
#> GSM152926 2 0.0188 0.9532 0.000 0.996 0.004 0.000
#> GSM152927 2 0.0817 0.9388 0.000 0.976 0.024 0.000
#> GSM152928 2 0.4470 0.7533 0.032 0.792 0.172 0.004
#> GSM152929 2 0.0000 0.9555 0.000 1.000 0.000 0.000
#> GSM152930 2 0.0000 0.9555 0.000 1.000 0.000 0.000
cbind(get_classes(res, k = 5), get_membership(res, k = 5))
#> class entropy silhouette p1 p2 p3 p4 p5
#> GSM152839 1 0.4910 0.49065 0.672 0.000 0.276 0.004 0.048
#> GSM152840 5 0.4304 0.98766 0.000 0.000 0.484 0.000 0.516
#> GSM152841 4 0.0992 0.78364 0.008 0.000 0.000 0.968 0.024
#> GSM152842 3 0.0794 0.21897 0.000 0.000 0.972 0.000 0.028
#> GSM152843 3 0.4525 0.29973 0.360 0.000 0.624 0.000 0.016
#> GSM152844 5 0.4305 0.98416 0.000 0.000 0.488 0.000 0.512
#> GSM152845 3 0.4219 -0.73851 0.000 0.000 0.584 0.000 0.416
#> GSM152846 3 0.4294 -0.86479 0.000 0.000 0.532 0.000 0.468
#> GSM152847 3 0.2233 0.27214 0.080 0.000 0.904 0.000 0.016
#> GSM152848 1 0.3814 0.75155 0.784 0.000 0.012 0.012 0.192
#> GSM152849 3 0.4384 0.31448 0.324 0.000 0.660 0.000 0.016
#> GSM152850 3 0.5288 0.27198 0.404 0.000 0.544 0.000 0.052
#> GSM152851 4 0.5626 -0.02599 0.036 0.000 0.448 0.496 0.020
#> GSM152852 3 0.4452 -0.94847 0.000 0.000 0.500 0.004 0.496
#> GSM152853 5 0.4302 0.98410 0.000 0.000 0.480 0.000 0.520
#> GSM152854 3 0.4242 -0.75447 0.000 0.000 0.572 0.000 0.428
#> GSM152855 1 0.6771 0.19014 0.396 0.000 0.000 0.292 0.312
#> GSM153238 3 0.0290 0.23332 0.000 0.000 0.992 0.000 0.008
#> GSM153239 3 0.4306 -0.93080 0.000 0.000 0.508 0.000 0.492
#> GSM153240 4 0.1914 0.78679 0.016 0.000 0.000 0.924 0.060
#> GSM153241 3 0.4400 0.31352 0.308 0.000 0.672 0.000 0.020
#> GSM153242 3 0.4291 -0.83344 0.000 0.000 0.536 0.000 0.464
#> GSM153243 3 0.4135 0.31410 0.340 0.000 0.656 0.000 0.004
#> GSM153244 4 0.6189 0.60763 0.192 0.000 0.144 0.632 0.032
#> GSM153245 3 0.4551 -0.75897 0.004 0.000 0.556 0.004 0.436
#> GSM153246 3 0.1608 0.20321 0.000 0.000 0.928 0.000 0.072
#> GSM153247 3 0.4697 0.30757 0.304 0.000 0.660 0.000 0.036
#> GSM153248 1 0.2291 0.74280 0.908 0.000 0.008 0.012 0.072
#> GSM153249 4 0.4994 0.67897 0.096 0.000 0.000 0.696 0.208
#> GSM153250 1 0.4697 0.70143 0.660 0.000 0.000 0.036 0.304
#> GSM153251 3 0.4273 -0.78100 0.000 0.000 0.552 0.000 0.448
#> GSM153252 1 0.6815 0.31635 0.424 0.000 0.004 0.324 0.248
#> GSM153253 4 0.0693 0.77944 0.008 0.000 0.000 0.980 0.012
#> GSM153254 1 0.7000 0.08940 0.396 0.000 0.232 0.360 0.012
#> GSM153255 4 0.3409 0.76094 0.032 0.000 0.000 0.824 0.144
#> GSM153256 1 0.5811 0.63092 0.568 0.000 0.000 0.116 0.316
#> GSM153257 1 0.6767 0.24134 0.392 0.000 0.000 0.328 0.280
#> GSM153258 1 0.3940 0.73909 0.756 0.000 0.000 0.024 0.220
#> GSM153259 1 0.3438 0.75396 0.808 0.000 0.000 0.020 0.172
#> GSM153260 3 0.1117 0.24536 0.016 0.000 0.964 0.000 0.020
#> GSM153261 3 0.1836 0.24675 0.036 0.000 0.932 0.000 0.032
#> GSM153262 4 0.6634 0.26469 0.260 0.000 0.000 0.452 0.288
#> GSM153263 1 0.3757 0.74616 0.772 0.000 0.000 0.020 0.208
#> GSM153264 1 0.2199 0.73191 0.916 0.000 0.016 0.008 0.060
#> GSM153265 4 0.0510 0.78581 0.016 0.000 0.000 0.984 0.000
#> GSM153266 1 0.3145 0.75624 0.844 0.000 0.012 0.008 0.136
#> GSM153267 1 0.5831 0.64699 0.580 0.000 0.000 0.128 0.292
#> GSM153268 4 0.1306 0.77048 0.008 0.000 0.016 0.960 0.016
#> GSM153269 1 0.5197 0.67439 0.620 0.000 0.000 0.064 0.316
#> GSM153270 1 0.4998 0.71669 0.700 0.000 0.000 0.104 0.196
#> GSM153271 1 0.5452 0.67147 0.616 0.000 0.000 0.092 0.292
#> GSM153272 4 0.5672 0.55002 0.188 0.000 0.000 0.632 0.180
#> GSM153273 1 0.3203 0.75455 0.820 0.000 0.000 0.012 0.168
#> GSM153274 1 0.5218 0.71268 0.672 0.000 0.004 0.084 0.240
#> GSM153275 1 0.6301 0.55287 0.512 0.000 0.000 0.180 0.308
#> GSM153276 1 0.6555 0.56159 0.512 0.000 0.008 0.188 0.292
#> GSM153277 4 0.1648 0.78844 0.020 0.000 0.000 0.940 0.040
#> GSM153278 3 0.5171 0.17829 0.456 0.000 0.504 0.000 0.040
#> GSM153279 4 0.6041 0.53082 0.188 0.000 0.180 0.620 0.012
#> GSM153280 4 0.0693 0.77914 0.008 0.000 0.000 0.980 0.012
#> GSM153281 4 0.0451 0.78237 0.008 0.000 0.000 0.988 0.004
#> GSM153282 4 0.0798 0.77706 0.008 0.000 0.000 0.976 0.016
#> GSM153283 1 0.3829 0.74531 0.776 0.000 0.000 0.028 0.196
#> GSM153284 1 0.6645 0.41716 0.448 0.000 0.000 0.260 0.292
#> GSM153285 4 0.0451 0.78237 0.008 0.000 0.000 0.988 0.004
#> GSM153286 4 0.5931 0.57933 0.164 0.000 0.000 0.588 0.248
#> GSM153287 4 0.0798 0.78642 0.016 0.000 0.000 0.976 0.008
#> GSM153288 1 0.6680 0.37500 0.428 0.000 0.000 0.252 0.320
#> GSM153289 1 0.5180 0.67958 0.624 0.000 0.000 0.064 0.312
#> GSM153290 4 0.1195 0.78610 0.012 0.000 0.000 0.960 0.028
#> GSM153291 4 0.3060 0.77169 0.024 0.000 0.000 0.848 0.128
#> GSM153292 4 0.0290 0.78369 0.008 0.000 0.000 0.992 0.000
#> GSM153293 1 0.5873 0.61997 0.564 0.000 0.000 0.124 0.312
#> GSM153294 1 0.4272 0.74443 0.780 0.000 0.008 0.060 0.152
#> GSM153295 1 0.5494 -0.02305 0.496 0.000 0.456 0.020 0.028
#> GSM153054 1 0.4163 0.60680 0.776 0.000 0.176 0.008 0.040
#> GSM153055 1 0.4400 0.73323 0.744 0.000 0.000 0.060 0.196
#> GSM153056 3 0.4594 0.29737 0.364 0.000 0.620 0.004 0.012
#> GSM153057 1 0.4297 0.58081 0.756 0.000 0.200 0.008 0.036
#> GSM153058 3 0.3847 -0.05105 0.036 0.000 0.784 0.000 0.180
#> GSM153059 1 0.4924 0.29847 0.608 0.000 0.360 0.004 0.028
#> GSM153060 3 0.1608 0.20321 0.000 0.000 0.928 0.000 0.072
#> GSM153061 3 0.1544 0.20452 0.000 0.000 0.932 0.000 0.068
#> GSM153062 3 0.1608 0.20321 0.000 0.000 0.928 0.000 0.072
#> GSM153063 3 0.5929 -0.03571 0.156 0.000 0.584 0.000 0.260
#> GSM153064 1 0.4967 0.69777 0.660 0.000 0.000 0.060 0.280
#> GSM153065 3 0.0794 0.21897 0.000 0.000 0.972 0.000 0.028
#> GSM153066 3 0.2079 0.25454 0.064 0.000 0.916 0.000 0.020
#> GSM153067 4 0.5816 0.57277 0.164 0.000 0.000 0.608 0.228
#> GSM153068 3 0.1043 0.21049 0.000 0.000 0.960 0.000 0.040
#> GSM153069 4 0.0807 0.78774 0.012 0.000 0.000 0.976 0.012
#> GSM153070 1 0.4420 0.71447 0.692 0.000 0.000 0.028 0.280
#> GSM153071 1 0.4853 0.44100 0.664 0.000 0.296 0.008 0.032
#> GSM153072 1 0.4109 0.62300 0.788 0.000 0.148 0.004 0.060
#> GSM153073 1 0.3730 0.75647 0.808 0.000 0.004 0.036 0.152
#> GSM153074 4 0.6176 0.49144 0.184 0.000 0.000 0.548 0.268
#> GSM153075 4 0.6624 0.25703 0.280 0.000 0.000 0.456 0.264
#> GSM153076 1 0.4276 0.72673 0.724 0.000 0.000 0.032 0.244
#> GSM153077 1 0.2364 0.71198 0.908 0.000 0.020 0.008 0.064
#> GSM153078 1 0.3327 0.67926 0.852 0.000 0.084 0.004 0.060
#> GSM153079 1 0.2208 0.70953 0.916 0.000 0.012 0.012 0.060
#> GSM153080 3 0.6468 0.25133 0.288 0.000 0.576 0.076 0.060
#> GSM153081 1 0.3046 0.73578 0.876 0.000 0.028 0.020 0.076
#> GSM153082 1 0.2523 0.73000 0.908 0.004 0.012 0.024 0.052
#> GSM153083 1 0.1934 0.70903 0.928 0.000 0.016 0.004 0.052
#> GSM153084 1 0.5026 0.60198 0.752 0.028 0.164 0.020 0.036
#> GSM153085 1 0.3631 0.68009 0.840 0.000 0.080 0.012 0.068
#> GSM153086 1 0.2144 0.70204 0.912 0.000 0.020 0.000 0.068
#> GSM153087 1 0.6463 0.48616 0.496 0.000 0.000 0.276 0.228
#> GSM153088 1 0.3696 0.74711 0.772 0.000 0.000 0.016 0.212
#> GSM153089 3 0.4283 -0.81368 0.000 0.000 0.544 0.000 0.456
#> GSM153090 1 0.3999 0.73240 0.740 0.000 0.000 0.020 0.240
#> GSM153091 1 0.1492 0.72854 0.948 0.000 0.008 0.004 0.040
#> GSM153092 1 0.3648 0.75213 0.812 0.000 0.008 0.024 0.156
#> GSM153093 1 0.6808 0.14067 0.368 0.000 0.000 0.324 0.308
#> GSM153094 1 0.1857 0.73194 0.928 0.000 0.008 0.004 0.060
#> GSM153095 1 0.4142 0.67348 0.812 0.000 0.108 0.044 0.036
#> GSM153096 1 0.2574 0.75485 0.876 0.000 0.000 0.012 0.112
#> GSM153097 1 0.1444 0.71740 0.948 0.000 0.012 0.000 0.040
#> GSM153098 1 0.3954 0.74552 0.772 0.000 0.000 0.036 0.192
#> GSM153099 1 0.6577 0.53116 0.516 0.000 0.008 0.272 0.204
#> GSM153100 1 0.4318 0.73713 0.736 0.000 0.004 0.032 0.228
#> GSM153101 1 0.3520 0.66716 0.840 0.000 0.076 0.004 0.080
#> GSM153102 1 0.3007 0.73462 0.884 0.000 0.028 0.044 0.044
#> GSM153103 1 0.3053 0.69041 0.872 0.000 0.044 0.008 0.076
#> GSM153104 4 0.1444 0.78880 0.012 0.000 0.000 0.948 0.040
#> GSM153106 1 0.5549 0.65786 0.632 0.000 0.000 0.124 0.244
#> GSM153107 1 0.3112 0.75246 0.856 0.000 0.000 0.044 0.100
#> GSM153108 1 0.6640 0.39286 0.484 0.000 0.004 0.280 0.232
#> GSM153109 1 0.1969 0.72354 0.932 0.008 0.012 0.004 0.044
#> GSM153110 1 0.1788 0.73972 0.932 0.000 0.008 0.004 0.056
#> GSM153111 1 0.1670 0.71353 0.936 0.000 0.012 0.000 0.052
#> GSM153112 1 0.3689 0.75219 0.816 0.000 0.008 0.032 0.144
#> GSM153113 1 0.2724 0.71674 0.900 0.020 0.024 0.004 0.052
#> GSM153114 4 0.6586 0.38020 0.244 0.000 0.000 0.464 0.292
#> GSM187532 2 0.4605 0.58944 0.004 0.708 0.248 0.000 0.040
#> GSM187533 2 0.1554 0.92981 0.012 0.952 0.004 0.008 0.024
#> GSM187534 2 0.1932 0.91950 0.020 0.936 0.004 0.008 0.032
#> GSM187535 2 0.5910 -0.00251 0.436 0.500 0.024 0.012 0.028
#> GSM152906 2 0.0000 0.94689 0.000 1.000 0.000 0.000 0.000
#> GSM152907 2 0.0290 0.94346 0.008 0.992 0.000 0.000 0.000
#> GSM152908 2 0.0000 0.94689 0.000 1.000 0.000 0.000 0.000
#> GSM152909 2 0.2139 0.89597 0.000 0.916 0.052 0.000 0.032
#> GSM152910 2 0.0703 0.94074 0.000 0.976 0.000 0.000 0.024
#> GSM152911 2 0.0000 0.94689 0.000 1.000 0.000 0.000 0.000
#> GSM152912 2 0.0000 0.94689 0.000 1.000 0.000 0.000 0.000
#> GSM152913 2 0.2209 0.89188 0.000 0.912 0.056 0.000 0.032
#> GSM152914 2 0.0000 0.94689 0.000 1.000 0.000 0.000 0.000
#> GSM152915 2 0.0000 0.94689 0.000 1.000 0.000 0.000 0.000
#> GSM152916 2 0.0703 0.94074 0.000 0.976 0.000 0.000 0.024
#> GSM152917 2 0.0000 0.94689 0.000 1.000 0.000 0.000 0.000
#> GSM152918 2 0.0000 0.94689 0.000 1.000 0.000 0.000 0.000
#> GSM152919 2 0.0000 0.94689 0.000 1.000 0.000 0.000 0.000
#> GSM152920 2 0.0000 0.94689 0.000 1.000 0.000 0.000 0.000
#> GSM152921 2 0.0000 0.94689 0.000 1.000 0.000 0.000 0.000
#> GSM152922 2 0.0000 0.94689 0.000 1.000 0.000 0.000 0.000
#> GSM152923 2 0.0000 0.94689 0.000 1.000 0.000 0.000 0.000
#> GSM152924 2 0.0703 0.94074 0.000 0.976 0.000 0.000 0.024
#> GSM152925 2 0.0703 0.94074 0.000 0.976 0.000 0.000 0.024
#> GSM152926 2 0.0451 0.94348 0.008 0.988 0.000 0.000 0.004
#> GSM152927 2 0.1211 0.93264 0.000 0.960 0.016 0.000 0.024
#> GSM152928 2 0.4303 0.79373 0.072 0.808 0.080 0.000 0.040
#> GSM152929 2 0.0000 0.94689 0.000 1.000 0.000 0.000 0.000
#> GSM152930 2 0.0000 0.94689 0.000 1.000 0.000 0.000 0.000
cbind(get_classes(res, k = 6), get_membership(res, k = 6))
#> class entropy silhouette p1 p2 p3 p4 p5 p6
#> GSM152839 1 0.5069 0.5003 0.644 0.000 0.280 0.008 0.032 0.036
#> GSM152840 6 0.2416 0.8516 0.000 0.000 0.156 0.000 0.000 0.844
#> GSM152841 4 0.1477 0.7358 0.008 0.000 0.000 0.940 0.048 0.004
#> GSM152842 3 0.1908 0.5616 0.000 0.000 0.916 0.000 0.056 0.028
#> GSM152843 3 0.2925 0.6945 0.148 0.000 0.832 0.000 0.004 0.016
#> GSM152844 6 0.2491 0.8587 0.000 0.000 0.164 0.000 0.000 0.836
#> GSM152845 6 0.4045 0.8043 0.000 0.000 0.312 0.000 0.024 0.664
#> GSM152846 6 0.2941 0.8868 0.000 0.000 0.220 0.000 0.000 0.780
#> GSM152847 3 0.1065 0.6532 0.020 0.000 0.964 0.000 0.008 0.008
#> GSM152848 1 0.2345 0.7886 0.908 0.000 0.020 0.008 0.044 0.020
#> GSM152849 3 0.2703 0.7064 0.116 0.000 0.860 0.000 0.008 0.016
#> GSM152850 3 0.3873 0.6219 0.176 0.000 0.772 0.000 0.020 0.032
#> GSM152851 4 0.5683 0.4515 0.064 0.000 0.188 0.648 0.004 0.096
#> GSM152852 6 0.2631 0.8671 0.000 0.000 0.180 0.000 0.000 0.820
#> GSM152853 6 0.2416 0.8516 0.000 0.000 0.156 0.000 0.000 0.844
#> GSM152854 6 0.3672 0.7384 0.000 0.000 0.368 0.000 0.000 0.632
#> GSM152855 1 0.5268 0.6075 0.656 0.000 0.004 0.152 0.176 0.012
#> GSM153238 3 0.0632 0.6193 0.000 0.000 0.976 0.000 0.024 0.000
#> GSM153239 6 0.2912 0.8859 0.000 0.000 0.216 0.000 0.000 0.784
#> GSM153240 4 0.2752 0.7358 0.036 0.000 0.000 0.856 0.108 0.000
#> GSM153241 3 0.2667 0.7060 0.128 0.000 0.852 0.000 0.000 0.020
#> GSM153242 6 0.3023 0.8833 0.000 0.000 0.232 0.000 0.000 0.768
#> GSM153243 3 0.3293 0.6835 0.128 0.000 0.824 0.000 0.040 0.008
#> GSM153244 4 0.4765 0.6767 0.136 0.000 0.036 0.752 0.040 0.036
#> GSM153245 6 0.3515 0.8151 0.000 0.000 0.324 0.000 0.000 0.676
#> GSM153246 5 0.4575 0.9805 0.000 0.000 0.352 0.000 0.600 0.048
#> GSM153247 3 0.3355 0.6996 0.116 0.000 0.828 0.000 0.016 0.040
#> GSM153248 1 0.2302 0.7764 0.900 0.000 0.012 0.012 0.072 0.004
#> GSM153249 4 0.4102 0.6956 0.116 0.000 0.000 0.760 0.120 0.004
#> GSM153250 1 0.3124 0.7662 0.848 0.000 0.000 0.040 0.096 0.016
#> GSM153251 6 0.3565 0.8245 0.000 0.000 0.304 0.000 0.004 0.692
#> GSM153252 1 0.5323 0.5725 0.628 0.000 0.004 0.204 0.160 0.004
#> GSM153253 4 0.1503 0.7287 0.008 0.000 0.000 0.944 0.032 0.016
#> GSM153254 4 0.6737 0.1635 0.396 0.000 0.076 0.436 0.052 0.040
#> GSM153255 4 0.3434 0.7198 0.048 0.000 0.000 0.808 0.140 0.004
#> GSM153256 1 0.4747 0.6611 0.688 0.000 0.000 0.100 0.204 0.008
#> GSM153257 1 0.5308 0.5648 0.616 0.000 0.000 0.200 0.180 0.004
#> GSM153258 1 0.2507 0.7869 0.892 0.000 0.000 0.020 0.060 0.028
#> GSM153259 1 0.1722 0.7886 0.936 0.000 0.008 0.004 0.036 0.016
#> GSM153260 3 0.1426 0.6243 0.008 0.000 0.948 0.000 0.028 0.016
#> GSM153261 3 0.1477 0.6254 0.004 0.000 0.940 0.000 0.008 0.048
#> GSM153262 1 0.5694 0.2791 0.504 0.000 0.000 0.312 0.184 0.000
#> GSM153263 1 0.2793 0.7872 0.876 0.000 0.000 0.020 0.060 0.044
#> GSM153264 1 0.2959 0.7678 0.872 0.000 0.028 0.004 0.060 0.036
#> GSM153265 4 0.1251 0.7385 0.012 0.000 0.000 0.956 0.024 0.008
#> GSM153266 1 0.1764 0.7862 0.936 0.000 0.024 0.012 0.024 0.004
#> GSM153267 1 0.4508 0.6929 0.716 0.000 0.000 0.116 0.164 0.004
#> GSM153268 4 0.1426 0.7290 0.008 0.000 0.000 0.948 0.028 0.016
#> GSM153269 1 0.4041 0.7140 0.764 0.000 0.000 0.060 0.164 0.012
#> GSM153270 1 0.3732 0.7571 0.808 0.000 0.020 0.068 0.104 0.000
#> GSM153271 1 0.3772 0.7409 0.792 0.000 0.000 0.072 0.128 0.008
#> GSM153272 4 0.5595 0.1529 0.392 0.000 0.000 0.464 0.144 0.000
#> GSM153273 1 0.1699 0.7875 0.936 0.000 0.008 0.012 0.040 0.004
#> GSM153274 1 0.3600 0.7696 0.828 0.000 0.008 0.064 0.084 0.016
#> GSM153275 1 0.4991 0.6206 0.656 0.000 0.000 0.136 0.204 0.004
#> GSM153276 1 0.5082 0.6525 0.680 0.000 0.008 0.136 0.168 0.008
#> GSM153277 4 0.2106 0.7450 0.032 0.000 0.000 0.904 0.064 0.000
#> GSM153278 3 0.3771 0.6532 0.172 0.000 0.780 0.000 0.024 0.024
#> GSM153279 4 0.5841 0.5824 0.240 0.000 0.048 0.628 0.044 0.040
#> GSM153280 4 0.1332 0.7316 0.008 0.000 0.000 0.952 0.028 0.012
#> GSM153281 4 0.1173 0.7416 0.008 0.000 0.000 0.960 0.016 0.016
#> GSM153282 4 0.1409 0.7305 0.008 0.000 0.000 0.948 0.032 0.012
#> GSM153283 1 0.2315 0.7891 0.908 0.000 0.004 0.040 0.032 0.016
#> GSM153284 1 0.5197 0.5878 0.632 0.000 0.000 0.168 0.196 0.004
#> GSM153285 4 0.1346 0.7326 0.008 0.000 0.000 0.952 0.024 0.016
#> GSM153286 4 0.5783 0.2409 0.372 0.000 0.000 0.448 0.180 0.000
#> GSM153287 4 0.1346 0.7469 0.016 0.000 0.000 0.952 0.024 0.008
#> GSM153288 1 0.4845 0.6200 0.660 0.000 0.000 0.132 0.208 0.000
#> GSM153289 1 0.4279 0.7176 0.756 0.000 0.000 0.064 0.156 0.024
#> GSM153290 4 0.1552 0.7373 0.020 0.000 0.000 0.940 0.036 0.004
#> GSM153291 4 0.3275 0.7224 0.036 0.000 0.000 0.816 0.144 0.004
#> GSM153292 4 0.1268 0.7364 0.008 0.000 0.000 0.952 0.036 0.004
#> GSM153293 1 0.4776 0.6530 0.688 0.000 0.000 0.108 0.196 0.008
#> GSM153294 1 0.2670 0.7882 0.880 0.000 0.004 0.048 0.064 0.004
#> GSM153295 1 0.5122 0.5602 0.636 0.000 0.288 0.012 0.040 0.024
#> GSM153054 1 0.4940 0.4690 0.632 0.000 0.300 0.004 0.048 0.016
#> GSM153055 1 0.3471 0.7712 0.824 0.000 0.004 0.056 0.108 0.008
#> GSM153056 3 0.3168 0.6782 0.172 0.000 0.804 0.000 0.000 0.024
#> GSM153057 1 0.5438 -0.0784 0.480 0.000 0.448 0.012 0.036 0.024
#> GSM153058 3 0.3213 0.5306 0.008 0.000 0.784 0.000 0.004 0.204
#> GSM153059 3 0.5429 0.4150 0.300 0.000 0.600 0.004 0.068 0.028
#> GSM153060 5 0.4707 0.9790 0.000 0.000 0.360 0.000 0.584 0.056
#> GSM153061 5 0.4563 0.9722 0.000 0.000 0.368 0.000 0.588 0.044
#> GSM153062 5 0.4619 0.9809 0.000 0.000 0.348 0.000 0.600 0.052
#> GSM153063 3 0.4507 -0.1715 0.012 0.000 0.544 0.004 0.008 0.432
#> GSM153064 1 0.2866 0.7724 0.860 0.000 0.000 0.052 0.084 0.004
#> GSM153065 3 0.1908 0.5633 0.000 0.000 0.916 0.000 0.056 0.028
#> GSM153066 3 0.2955 0.6569 0.036 0.016 0.876 0.000 0.056 0.016
#> GSM153067 4 0.5743 0.4302 0.308 0.000 0.004 0.532 0.152 0.004
#> GSM153068 3 0.4400 -0.4591 0.000 0.000 0.592 0.000 0.376 0.032
#> GSM153069 4 0.1442 0.7444 0.012 0.000 0.000 0.944 0.040 0.004
#> GSM153070 1 0.2237 0.7797 0.896 0.000 0.000 0.020 0.080 0.004
#> GSM153071 1 0.4313 0.0565 0.504 0.000 0.480 0.000 0.012 0.004
#> GSM153072 1 0.5061 0.5953 0.668 0.000 0.212 0.000 0.100 0.020
#> GSM153073 1 0.1857 0.7875 0.928 0.000 0.012 0.032 0.028 0.000
#> GSM153074 4 0.5804 0.3379 0.332 0.000 0.000 0.492 0.172 0.004
#> GSM153075 1 0.5715 0.0425 0.468 0.000 0.004 0.384 0.144 0.000
#> GSM153076 1 0.2445 0.7839 0.896 0.000 0.000 0.028 0.056 0.020
#> GSM153077 1 0.3432 0.7592 0.840 0.000 0.032 0.008 0.092 0.028
#> GSM153078 1 0.4701 0.6532 0.728 0.000 0.180 0.008 0.052 0.032
#> GSM153079 1 0.3306 0.7548 0.840 0.000 0.020 0.004 0.104 0.032
#> GSM153080 3 0.6000 0.5088 0.128 0.000 0.640 0.032 0.036 0.164
#> GSM153081 1 0.2701 0.7790 0.892 0.000 0.024 0.012 0.036 0.036
#> GSM153082 1 0.3032 0.7656 0.860 0.004 0.020 0.016 0.096 0.004
#> GSM153083 1 0.3278 0.7520 0.840 0.000 0.020 0.004 0.108 0.028
#> GSM153084 1 0.5560 0.6385 0.684 0.032 0.164 0.016 0.096 0.008
#> GSM153085 1 0.4732 0.7048 0.744 0.000 0.116 0.012 0.104 0.024
#> GSM153086 1 0.3600 0.7435 0.820 0.000 0.028 0.004 0.116 0.032
#> GSM153087 1 0.5084 0.5704 0.644 0.000 0.000 0.232 0.116 0.008
#> GSM153088 1 0.2317 0.7896 0.908 0.000 0.004 0.016 0.036 0.036
#> GSM153089 6 0.3126 0.8792 0.000 0.000 0.248 0.000 0.000 0.752
#> GSM153090 1 0.2537 0.7829 0.888 0.000 0.000 0.028 0.068 0.016
#> GSM153091 1 0.2518 0.7670 0.880 0.000 0.012 0.008 0.096 0.004
#> GSM153092 1 0.2574 0.7878 0.884 0.000 0.008 0.024 0.080 0.004
#> GSM153093 1 0.5173 0.5582 0.620 0.000 0.000 0.180 0.200 0.000
#> GSM153094 1 0.2426 0.7679 0.884 0.000 0.012 0.000 0.092 0.012
#> GSM153095 1 0.4756 0.7273 0.748 0.000 0.100 0.060 0.088 0.004
#> GSM153096 1 0.1553 0.7877 0.944 0.000 0.008 0.012 0.032 0.004
#> GSM153097 1 0.2443 0.7625 0.880 0.000 0.020 0.000 0.096 0.004
#> GSM153098 1 0.2618 0.7817 0.876 0.000 0.004 0.024 0.092 0.004
#> GSM153099 1 0.5162 0.5325 0.620 0.000 0.004 0.272 0.100 0.004
#> GSM153100 1 0.2504 0.7782 0.876 0.000 0.004 0.012 0.104 0.004
#> GSM153101 1 0.5578 0.4868 0.620 0.000 0.252 0.004 0.088 0.036
#> GSM153102 1 0.3713 0.7647 0.832 0.000 0.044 0.048 0.064 0.012
#> GSM153103 1 0.3765 0.7373 0.808 0.000 0.044 0.000 0.112 0.036
#> GSM153104 4 0.2207 0.7430 0.008 0.000 0.000 0.900 0.076 0.016
#> GSM153106 1 0.4434 0.7215 0.756 0.000 0.004 0.092 0.128 0.020
#> GSM153107 1 0.2745 0.7871 0.888 0.000 0.008 0.044 0.032 0.028
#> GSM153108 1 0.4996 0.5751 0.652 0.000 0.000 0.216 0.128 0.004
#> GSM153109 1 0.2982 0.7593 0.856 0.000 0.032 0.000 0.096 0.016
#> GSM153110 1 0.1644 0.7771 0.932 0.000 0.012 0.000 0.052 0.004
#> GSM153111 1 0.2894 0.7567 0.860 0.000 0.020 0.004 0.104 0.012
#> GSM153112 1 0.2574 0.7897 0.884 0.000 0.008 0.024 0.080 0.004
#> GSM153113 1 0.3635 0.7565 0.832 0.008 0.032 0.016 0.100 0.012
#> GSM153114 4 0.6108 0.3376 0.352 0.000 0.000 0.468 0.160 0.020
#> GSM187532 2 0.4017 0.7367 0.004 0.776 0.152 0.000 0.012 0.056
#> GSM187533 2 0.1904 0.9390 0.004 0.924 0.000 0.004 0.020 0.048
#> GSM187534 2 0.2051 0.9337 0.012 0.920 0.000 0.004 0.020 0.044
#> GSM187535 1 0.5428 0.5832 0.652 0.240 0.028 0.004 0.064 0.012
#> GSM152906 2 0.0000 0.9645 0.000 1.000 0.000 0.000 0.000 0.000
#> GSM152907 2 0.0837 0.9515 0.004 0.972 0.020 0.000 0.000 0.004
#> GSM152908 2 0.0146 0.9643 0.000 0.996 0.000 0.000 0.000 0.004
#> GSM152909 2 0.1391 0.9498 0.000 0.944 0.000 0.000 0.016 0.040
#> GSM152910 2 0.1245 0.9531 0.000 0.952 0.000 0.000 0.016 0.032
#> GSM152911 2 0.0000 0.9645 0.000 1.000 0.000 0.000 0.000 0.000
#> GSM152912 2 0.0146 0.9643 0.000 0.996 0.000 0.000 0.000 0.004
#> GSM152913 2 0.1391 0.9498 0.000 0.944 0.000 0.000 0.016 0.040
#> GSM152914 2 0.0146 0.9643 0.000 0.996 0.000 0.000 0.000 0.004
#> GSM152915 2 0.0146 0.9643 0.000 0.996 0.000 0.000 0.000 0.004
#> GSM152916 2 0.1245 0.9531 0.000 0.952 0.000 0.000 0.016 0.032
#> GSM152917 2 0.0146 0.9643 0.000 0.996 0.000 0.000 0.000 0.004
#> GSM152918 2 0.0146 0.9643 0.000 0.996 0.000 0.000 0.000 0.004
#> GSM152919 2 0.0000 0.9645 0.000 1.000 0.000 0.000 0.000 0.000
#> GSM152920 2 0.0146 0.9643 0.000 0.996 0.000 0.000 0.000 0.004
#> GSM152921 2 0.0146 0.9643 0.000 0.996 0.000 0.000 0.000 0.004
#> GSM152922 2 0.0000 0.9645 0.000 1.000 0.000 0.000 0.000 0.000
#> GSM152923 2 0.0000 0.9645 0.000 1.000 0.000 0.000 0.000 0.000
#> GSM152924 2 0.1245 0.9531 0.000 0.952 0.000 0.000 0.016 0.032
#> GSM152925 2 0.1245 0.9531 0.000 0.952 0.000 0.000 0.016 0.032
#> GSM152926 2 0.0837 0.9530 0.004 0.972 0.020 0.000 0.004 0.000
#> GSM152927 2 0.1245 0.9531 0.000 0.952 0.000 0.000 0.016 0.032
#> GSM152928 2 0.4574 0.7800 0.048 0.784 0.064 0.000 0.048 0.056
#> GSM152929 2 0.0000 0.9645 0.000 1.000 0.000 0.000 0.000 0.000
#> GSM152930 2 0.0000 0.9645 0.000 1.000 0.000 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 tissue(p) k
#> CV:mclust 162 2.11e-29 2
#> CV:mclust 160 1.60e-32 3
#> CV:mclust 138 1.65e-31 4
#> CV:mclust 113 1.86e-35 5
#> CV:mclust 148 2.16e-32 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 12013 rows and 164 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 0.734 0.862 0.942 0.4318 0.569 0.569
#> 3 3 0.631 0.811 0.898 0.4756 0.709 0.523
#> 4 4 0.496 0.583 0.751 0.1590 0.850 0.609
#> 5 5 0.509 0.472 0.640 0.0668 0.896 0.646
#> 6 6 0.527 0.420 0.608 0.0425 0.929 0.713
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
#> GSM152839 1 0.0000 0.9489 1.000 0.000
#> GSM152840 1 0.0000 0.9489 1.000 0.000
#> GSM152841 1 0.0000 0.9489 1.000 0.000
#> GSM152842 1 0.0000 0.9489 1.000 0.000
#> GSM152843 1 0.0000 0.9489 1.000 0.000
#> GSM152844 1 0.0000 0.9489 1.000 0.000
#> GSM152845 2 0.9795 0.3465 0.416 0.584
#> GSM152846 1 0.0000 0.9489 1.000 0.000
#> GSM152847 1 0.0000 0.9489 1.000 0.000
#> GSM152848 1 0.0000 0.9489 1.000 0.000
#> GSM152849 1 0.0000 0.9489 1.000 0.000
#> GSM152850 1 0.0000 0.9489 1.000 0.000
#> GSM152851 1 0.0376 0.9466 0.996 0.004
#> GSM152852 1 0.0000 0.9489 1.000 0.000
#> GSM152853 1 0.0000 0.9489 1.000 0.000
#> GSM152854 1 0.0000 0.9489 1.000 0.000
#> GSM152855 1 0.0000 0.9489 1.000 0.000
#> GSM153238 1 0.7950 0.6737 0.760 0.240
#> GSM153239 1 0.0000 0.9489 1.000 0.000
#> GSM153240 1 0.0000 0.9489 1.000 0.000
#> GSM153241 1 0.0000 0.9489 1.000 0.000
#> GSM153242 1 0.3879 0.8878 0.924 0.076
#> GSM153243 1 0.8016 0.6700 0.756 0.244
#> GSM153244 1 0.9988 0.0195 0.520 0.480
#> GSM153245 1 0.0000 0.9489 1.000 0.000
#> GSM153246 1 0.0000 0.9489 1.000 0.000
#> GSM153247 1 0.2778 0.9154 0.952 0.048
#> GSM153248 2 0.9608 0.4077 0.384 0.616
#> GSM153249 1 0.0000 0.9489 1.000 0.000
#> GSM153250 1 0.0000 0.9489 1.000 0.000
#> GSM153251 1 0.8955 0.5321 0.688 0.312
#> GSM153252 1 0.0000 0.9489 1.000 0.000
#> GSM153253 1 0.0000 0.9489 1.000 0.000
#> GSM153254 1 0.3879 0.8908 0.924 0.076
#> GSM153255 1 0.0000 0.9489 1.000 0.000
#> GSM153256 1 0.0376 0.9466 0.996 0.004
#> GSM153257 1 0.0000 0.9489 1.000 0.000
#> GSM153258 1 0.0000 0.9489 1.000 0.000
#> GSM153259 1 0.6438 0.7844 0.836 0.164
#> GSM153260 1 0.5408 0.8372 0.876 0.124
#> GSM153261 1 0.0672 0.9440 0.992 0.008
#> GSM153262 1 0.0000 0.9489 1.000 0.000
#> GSM153263 1 0.0000 0.9489 1.000 0.000
#> GSM153264 1 0.0000 0.9489 1.000 0.000
#> GSM153265 1 0.0000 0.9489 1.000 0.000
#> GSM153266 1 0.0000 0.9489 1.000 0.000
#> GSM153267 1 0.0000 0.9489 1.000 0.000
#> GSM153268 1 0.0000 0.9489 1.000 0.000
#> GSM153269 1 0.0000 0.9489 1.000 0.000
#> GSM153270 1 0.0000 0.9489 1.000 0.000
#> GSM153271 1 0.0000 0.9489 1.000 0.000
#> GSM153272 1 0.0000 0.9489 1.000 0.000
#> GSM153273 1 0.8327 0.6306 0.736 0.264
#> GSM153274 1 0.0000 0.9489 1.000 0.000
#> GSM153275 1 0.0000 0.9489 1.000 0.000
#> GSM153276 1 0.0000 0.9489 1.000 0.000
#> GSM153277 1 0.0000 0.9489 1.000 0.000
#> GSM153278 1 0.0000 0.9489 1.000 0.000
#> GSM153279 1 0.0000 0.9489 1.000 0.000
#> GSM153280 1 0.0000 0.9489 1.000 0.000
#> GSM153281 1 0.0000 0.9489 1.000 0.000
#> GSM153282 1 0.0000 0.9489 1.000 0.000
#> GSM153283 1 0.0000 0.9489 1.000 0.000
#> GSM153284 1 0.0376 0.9466 0.996 0.004
#> GSM153285 1 0.0000 0.9489 1.000 0.000
#> GSM153286 1 0.0000 0.9489 1.000 0.000
#> GSM153287 1 0.0000 0.9489 1.000 0.000
#> GSM153288 1 0.0000 0.9489 1.000 0.000
#> GSM153289 1 0.0000 0.9489 1.000 0.000
#> GSM153290 1 0.0000 0.9489 1.000 0.000
#> GSM153291 1 0.0000 0.9489 1.000 0.000
#> GSM153292 1 0.0000 0.9489 1.000 0.000
#> GSM153293 1 0.0000 0.9489 1.000 0.000
#> GSM153294 2 0.9427 0.4623 0.360 0.640
#> GSM153295 1 0.0000 0.9489 1.000 0.000
#> GSM153054 1 0.0000 0.9489 1.000 0.000
#> GSM153055 1 0.2236 0.9248 0.964 0.036
#> GSM153056 1 0.0000 0.9489 1.000 0.000
#> GSM153057 1 0.1184 0.9393 0.984 0.016
#> GSM153058 1 0.0000 0.9489 1.000 0.000
#> GSM153059 2 0.9944 0.2277 0.456 0.544
#> GSM153060 1 0.0000 0.9489 1.000 0.000
#> GSM153061 1 0.0000 0.9489 1.000 0.000
#> GSM153062 1 0.8661 0.5826 0.712 0.288
#> GSM153063 1 0.0376 0.9466 0.996 0.004
#> GSM153064 1 0.3431 0.8995 0.936 0.064
#> GSM153065 2 0.9963 0.2031 0.464 0.536
#> GSM153066 2 0.6048 0.7912 0.148 0.852
#> GSM153067 1 0.1843 0.9303 0.972 0.028
#> GSM153068 1 0.6343 0.7930 0.840 0.160
#> GSM153069 1 0.0000 0.9489 1.000 0.000
#> GSM153070 1 0.0000 0.9489 1.000 0.000
#> GSM153071 1 0.0000 0.9489 1.000 0.000
#> GSM153072 1 0.3274 0.9030 0.940 0.060
#> GSM153073 1 0.0376 0.9466 0.996 0.004
#> GSM153074 1 0.0672 0.9443 0.992 0.008
#> GSM153075 1 0.1414 0.9363 0.980 0.020
#> GSM153076 1 0.0000 0.9489 1.000 0.000
#> GSM153077 1 0.3733 0.8930 0.928 0.072
#> GSM153078 1 0.0000 0.9489 1.000 0.000
#> GSM153079 2 0.7299 0.7303 0.204 0.796
#> GSM153080 1 0.0000 0.9489 1.000 0.000
#> GSM153081 1 0.0000 0.9489 1.000 0.000
#> GSM153082 2 0.0376 0.9025 0.004 0.996
#> GSM153083 2 0.0672 0.9007 0.008 0.992
#> GSM153084 2 0.0672 0.9006 0.008 0.992
#> GSM153085 2 0.9954 0.2167 0.460 0.540
#> GSM153086 2 0.5946 0.7958 0.144 0.856
#> GSM153087 1 0.0000 0.9489 1.000 0.000
#> GSM153088 1 0.0000 0.9489 1.000 0.000
#> GSM153089 1 0.7528 0.7138 0.784 0.216
#> GSM153090 1 0.0000 0.9489 1.000 0.000
#> GSM153091 2 0.0000 0.9043 0.000 1.000
#> GSM153092 1 0.9248 0.4703 0.660 0.340
#> GSM153093 1 0.0000 0.9489 1.000 0.000
#> GSM153094 2 0.0000 0.9043 0.000 1.000
#> GSM153095 2 0.9866 0.2797 0.432 0.568
#> GSM153096 1 0.6438 0.7916 0.836 0.164
#> GSM153097 2 0.1633 0.8914 0.024 0.976
#> GSM153098 1 0.9552 0.3741 0.624 0.376
#> GSM153099 1 0.0000 0.9489 1.000 0.000
#> GSM153100 1 0.9170 0.4897 0.668 0.332
#> GSM153101 1 0.5294 0.8444 0.880 0.120
#> GSM153102 2 0.6048 0.7928 0.148 0.852
#> GSM153103 2 0.9896 0.2695 0.440 0.560
#> GSM153104 1 0.0000 0.9489 1.000 0.000
#> GSM153106 1 0.6712 0.7805 0.824 0.176
#> GSM153107 1 0.7883 0.6838 0.764 0.236
#> GSM153108 1 0.3431 0.9005 0.936 0.064
#> GSM153109 2 0.0000 0.9043 0.000 1.000
#> GSM153110 1 0.8661 0.5869 0.712 0.288
#> GSM153111 2 0.1843 0.8888 0.028 0.972
#> GSM153112 2 0.9044 0.5475 0.320 0.680
#> GSM153113 2 0.0000 0.9043 0.000 1.000
#> GSM153114 1 0.0000 0.9489 1.000 0.000
#> GSM187532 2 0.0672 0.9006 0.008 0.992
#> GSM187533 2 0.0000 0.9043 0.000 1.000
#> GSM187534 2 0.0000 0.9043 0.000 1.000
#> GSM187535 2 0.0000 0.9043 0.000 1.000
#> GSM152906 2 0.0000 0.9043 0.000 1.000
#> GSM152907 2 0.0000 0.9043 0.000 1.000
#> GSM152908 2 0.0000 0.9043 0.000 1.000
#> GSM152909 2 0.0000 0.9043 0.000 1.000
#> GSM152910 2 0.0000 0.9043 0.000 1.000
#> GSM152911 2 0.0000 0.9043 0.000 1.000
#> GSM152912 2 0.0000 0.9043 0.000 1.000
#> GSM152913 2 0.0000 0.9043 0.000 1.000
#> GSM152914 2 0.0000 0.9043 0.000 1.000
#> GSM152915 2 0.0000 0.9043 0.000 1.000
#> GSM152916 2 0.0000 0.9043 0.000 1.000
#> GSM152917 2 0.0000 0.9043 0.000 1.000
#> GSM152918 2 0.0000 0.9043 0.000 1.000
#> GSM152919 2 0.0000 0.9043 0.000 1.000
#> GSM152920 2 0.0000 0.9043 0.000 1.000
#> GSM152921 2 0.0000 0.9043 0.000 1.000
#> GSM152922 2 0.0000 0.9043 0.000 1.000
#> GSM152923 2 0.0000 0.9043 0.000 1.000
#> GSM152924 2 0.0000 0.9043 0.000 1.000
#> GSM152925 2 0.0000 0.9043 0.000 1.000
#> GSM152926 2 0.0000 0.9043 0.000 1.000
#> GSM152927 2 0.0000 0.9043 0.000 1.000
#> GSM152928 2 0.0000 0.9043 0.000 1.000
#> GSM152929 2 0.0000 0.9043 0.000 1.000
#> GSM152930 2 0.0000 0.9043 0.000 1.000
cbind(get_classes(res, k = 3), get_membership(res, k = 3))
#> class entropy silhouette p1 p2 p3
#> GSM152839 3 0.6192 0.3392 0.420 0.000 0.580
#> GSM152840 3 0.4235 0.7930 0.176 0.000 0.824
#> GSM152841 1 0.0592 0.9095 0.988 0.000 0.012
#> GSM152842 3 0.1031 0.8563 0.024 0.000 0.976
#> GSM152843 3 0.4931 0.7309 0.232 0.000 0.768
#> GSM152844 3 0.1411 0.8567 0.036 0.000 0.964
#> GSM152845 3 0.1163 0.8321 0.000 0.028 0.972
#> GSM152846 3 0.0592 0.8544 0.012 0.000 0.988
#> GSM152847 3 0.3752 0.8173 0.144 0.000 0.856
#> GSM152848 1 0.3941 0.8125 0.844 0.000 0.156
#> GSM152849 3 0.2261 0.8516 0.068 0.000 0.932
#> GSM152850 3 0.2878 0.8439 0.096 0.000 0.904
#> GSM152851 3 0.6045 0.4541 0.380 0.000 0.620
#> GSM152852 3 0.0892 0.8559 0.020 0.000 0.980
#> GSM152853 3 0.3116 0.8389 0.108 0.000 0.892
#> GSM152854 3 0.0424 0.8532 0.008 0.000 0.992
#> GSM152855 1 0.0983 0.9030 0.980 0.016 0.004
#> GSM153238 3 0.0237 0.8496 0.000 0.004 0.996
#> GSM153239 3 0.2711 0.8471 0.088 0.000 0.912
#> GSM153240 1 0.0747 0.9091 0.984 0.000 0.016
#> GSM153241 3 0.3192 0.8370 0.112 0.000 0.888
#> GSM153242 3 0.0237 0.8518 0.004 0.000 0.996
#> GSM153243 3 0.0983 0.8438 0.004 0.016 0.980
#> GSM153244 1 0.5894 0.7077 0.752 0.220 0.028
#> GSM153245 3 0.2625 0.8484 0.084 0.000 0.916
#> GSM153246 3 0.0237 0.8518 0.004 0.000 0.996
#> GSM153247 3 0.0592 0.8544 0.012 0.000 0.988
#> GSM153248 1 0.6247 0.4472 0.620 0.376 0.004
#> GSM153249 1 0.0829 0.9049 0.984 0.012 0.004
#> GSM153250 1 0.0661 0.9057 0.988 0.008 0.004
#> GSM153251 3 0.0747 0.8426 0.000 0.016 0.984
#> GSM153252 1 0.1411 0.9047 0.964 0.000 0.036
#> GSM153253 1 0.0892 0.9086 0.980 0.000 0.020
#> GSM153254 3 0.6318 0.5043 0.356 0.008 0.636
#> GSM153255 1 0.0475 0.9070 0.992 0.004 0.004
#> GSM153256 1 0.0475 0.9097 0.992 0.004 0.004
#> GSM153257 1 0.0592 0.9095 0.988 0.000 0.012
#> GSM153258 1 0.0592 0.9104 0.988 0.000 0.012
#> GSM153259 1 0.3784 0.8379 0.864 0.132 0.004
#> GSM153260 3 0.0424 0.8475 0.000 0.008 0.992
#> GSM153261 3 0.0237 0.8518 0.004 0.000 0.996
#> GSM153262 1 0.2165 0.8927 0.936 0.000 0.064
#> GSM153263 1 0.0000 0.9086 1.000 0.000 0.000
#> GSM153264 1 0.3412 0.8468 0.876 0.000 0.124
#> GSM153265 1 0.4842 0.7184 0.776 0.000 0.224
#> GSM153266 1 0.5363 0.6280 0.724 0.000 0.276
#> GSM153267 1 0.0237 0.9079 0.996 0.000 0.004
#> GSM153268 1 0.3551 0.8334 0.868 0.000 0.132
#> GSM153269 1 0.0000 0.9086 1.000 0.000 0.000
#> GSM153270 1 0.2625 0.8786 0.916 0.000 0.084
#> GSM153271 1 0.0829 0.9044 0.984 0.012 0.004
#> GSM153272 1 0.0237 0.9093 0.996 0.000 0.004
#> GSM153273 1 0.3500 0.8506 0.880 0.116 0.004
#> GSM153274 1 0.2537 0.8829 0.920 0.000 0.080
#> GSM153275 1 0.0747 0.9091 0.984 0.000 0.016
#> GSM153276 1 0.3116 0.8611 0.892 0.000 0.108
#> GSM153277 1 0.2066 0.8956 0.940 0.000 0.060
#> GSM153278 3 0.2537 0.8489 0.080 0.000 0.920
#> GSM153279 1 0.5650 0.5321 0.688 0.000 0.312
#> GSM153280 1 0.1529 0.9037 0.960 0.000 0.040
#> GSM153281 1 0.1860 0.8988 0.948 0.000 0.052
#> GSM153282 1 0.1643 0.9026 0.956 0.000 0.044
#> GSM153283 1 0.0592 0.9095 0.988 0.000 0.012
#> GSM153284 1 0.0237 0.9093 0.996 0.000 0.004
#> GSM153285 1 0.1529 0.9037 0.960 0.000 0.040
#> GSM153286 1 0.0000 0.9086 1.000 0.000 0.000
#> GSM153287 1 0.0592 0.9095 0.988 0.000 0.012
#> GSM153288 1 0.0237 0.9080 0.996 0.004 0.000
#> GSM153289 1 0.1399 0.8977 0.968 0.028 0.004
#> GSM153290 1 0.1163 0.9067 0.972 0.000 0.028
#> GSM153291 1 0.0237 0.9079 0.996 0.000 0.004
#> GSM153292 1 0.0424 0.9095 0.992 0.000 0.008
#> GSM153293 1 0.0661 0.9064 0.988 0.008 0.004
#> GSM153294 1 0.6330 0.4116 0.600 0.396 0.004
#> GSM153295 1 0.2878 0.8705 0.904 0.000 0.096
#> GSM153054 3 0.6309 0.0439 0.496 0.000 0.504
#> GSM153055 1 0.3340 0.8505 0.880 0.000 0.120
#> GSM153056 3 0.4654 0.7646 0.208 0.000 0.792
#> GSM153057 3 0.4233 0.8075 0.160 0.004 0.836
#> GSM153058 3 0.1289 0.8568 0.032 0.000 0.968
#> GSM153059 3 0.1399 0.8365 0.004 0.028 0.968
#> GSM153060 3 0.0592 0.8548 0.012 0.000 0.988
#> GSM153061 3 0.0475 0.8519 0.004 0.004 0.992
#> GSM153062 3 0.0747 0.8426 0.000 0.016 0.984
#> GSM153063 3 0.1031 0.8567 0.024 0.000 0.976
#> GSM153064 1 0.0983 0.9058 0.980 0.016 0.004
#> GSM153065 3 0.1031 0.8355 0.000 0.024 0.976
#> GSM153066 3 0.4121 0.6718 0.000 0.168 0.832
#> GSM153067 1 0.1647 0.8934 0.960 0.036 0.004
#> GSM153068 3 0.0592 0.8451 0.000 0.012 0.988
#> GSM153069 1 0.0237 0.9093 0.996 0.000 0.004
#> GSM153070 1 0.0747 0.9091 0.984 0.000 0.016
#> GSM153071 1 0.6307 -0.0103 0.512 0.000 0.488
#> GSM153072 1 0.7245 0.3494 0.596 0.036 0.368
#> GSM153073 1 0.0848 0.9077 0.984 0.008 0.008
#> GSM153074 1 0.0661 0.9057 0.988 0.008 0.004
#> GSM153075 1 0.0892 0.9086 0.980 0.000 0.020
#> GSM153076 1 0.0475 0.9093 0.992 0.004 0.004
#> GSM153077 1 0.5092 0.7726 0.804 0.020 0.176
#> GSM153078 3 0.4654 0.7639 0.208 0.000 0.792
#> GSM153079 2 0.6794 0.5057 0.324 0.648 0.028
#> GSM153080 3 0.3619 0.8223 0.136 0.000 0.864
#> GSM153081 1 0.1753 0.9010 0.952 0.000 0.048
#> GSM153082 2 0.1267 0.8693 0.024 0.972 0.004
#> GSM153083 2 0.3482 0.8521 0.000 0.872 0.128
#> GSM153084 2 0.5882 0.6211 0.000 0.652 0.348
#> GSM153085 3 0.4966 0.7882 0.060 0.100 0.840
#> GSM153086 2 0.8887 0.2413 0.124 0.488 0.388
#> GSM153087 1 0.1163 0.9067 0.972 0.000 0.028
#> GSM153088 1 0.0747 0.9104 0.984 0.000 0.016
#> GSM153089 3 0.0592 0.8449 0.000 0.012 0.988
#> GSM153090 1 0.0892 0.9086 0.980 0.000 0.020
#> GSM153091 2 0.1989 0.8551 0.048 0.948 0.004
#> GSM153092 1 0.3826 0.8380 0.868 0.124 0.008
#> GSM153093 1 0.0592 0.9095 0.988 0.000 0.012
#> GSM153094 2 0.2031 0.8698 0.032 0.952 0.016
#> GSM153095 3 0.8821 0.5220 0.232 0.188 0.580
#> GSM153096 1 0.1989 0.8957 0.948 0.048 0.004
#> GSM153097 2 0.2486 0.8520 0.060 0.932 0.008
#> GSM153098 1 0.4110 0.8154 0.844 0.152 0.004
#> GSM153099 1 0.3340 0.8511 0.880 0.000 0.120
#> GSM153100 1 0.3112 0.8620 0.900 0.096 0.004
#> GSM153101 3 0.4755 0.7826 0.184 0.008 0.808
#> GSM153102 2 0.7983 0.5601 0.108 0.636 0.256
#> GSM153103 3 0.6322 0.7483 0.108 0.120 0.772
#> GSM153104 1 0.1860 0.8995 0.948 0.000 0.052
#> GSM153106 1 0.3918 0.8174 0.856 0.140 0.004
#> GSM153107 1 0.2860 0.8664 0.912 0.084 0.004
#> GSM153108 1 0.2564 0.8996 0.936 0.036 0.028
#> GSM153109 2 0.0829 0.8776 0.012 0.984 0.004
#> GSM153110 1 0.6054 0.7506 0.768 0.180 0.052
#> GSM153111 2 0.3850 0.8505 0.028 0.884 0.088
#> GSM153112 1 0.6282 0.4303 0.612 0.384 0.004
#> GSM153113 2 0.2066 0.8809 0.000 0.940 0.060
#> GSM153114 1 0.0983 0.9030 0.980 0.016 0.004
#> GSM187532 3 0.5363 0.4575 0.000 0.276 0.724
#> GSM187533 2 0.3619 0.8524 0.000 0.864 0.136
#> GSM187534 2 0.2537 0.8753 0.000 0.920 0.080
#> GSM187535 2 0.0829 0.8745 0.012 0.984 0.004
#> GSM152906 2 0.0747 0.8837 0.000 0.984 0.016
#> GSM152907 2 0.0237 0.8808 0.000 0.996 0.004
#> GSM152908 2 0.1031 0.8841 0.000 0.976 0.024
#> GSM152909 2 0.6299 0.3376 0.000 0.524 0.476
#> GSM152910 2 0.5621 0.6867 0.000 0.692 0.308
#> GSM152911 2 0.2066 0.8802 0.000 0.940 0.060
#> GSM152912 2 0.2165 0.8791 0.000 0.936 0.064
#> GSM152913 2 0.5497 0.7078 0.000 0.708 0.292
#> GSM152914 2 0.1163 0.8842 0.000 0.972 0.028
#> GSM152915 2 0.0592 0.8828 0.000 0.988 0.012
#> GSM152916 2 0.4291 0.8232 0.000 0.820 0.180
#> GSM152917 2 0.0424 0.8817 0.000 0.992 0.008
#> GSM152918 2 0.0475 0.8772 0.004 0.992 0.004
#> GSM152919 2 0.0747 0.8837 0.000 0.984 0.016
#> GSM152920 2 0.1031 0.8841 0.000 0.976 0.024
#> GSM152921 2 0.0592 0.8828 0.000 0.988 0.012
#> GSM152922 2 0.2878 0.8693 0.000 0.904 0.096
#> GSM152923 2 0.1031 0.8843 0.000 0.976 0.024
#> GSM152924 2 0.3752 0.8470 0.000 0.856 0.144
#> GSM152925 2 0.4346 0.8205 0.000 0.816 0.184
#> GSM152926 2 0.0475 0.8799 0.004 0.992 0.004
#> GSM152927 2 0.5650 0.6811 0.000 0.688 0.312
#> GSM152928 2 0.4702 0.7954 0.000 0.788 0.212
#> GSM152929 2 0.0747 0.8837 0.000 0.984 0.016
#> GSM152930 2 0.0747 0.8837 0.000 0.984 0.016
cbind(get_classes(res, k = 4), get_membership(res, k = 4))
#> class entropy silhouette p1 p2 p3 p4
#> GSM152839 3 0.7045 0.3788 0.308 0.000 0.544 0.148
#> GSM152840 3 0.6329 0.4245 0.064 0.004 0.588 0.344
#> GSM152841 4 0.2360 0.6842 0.020 0.004 0.052 0.924
#> GSM152842 3 0.3791 0.7255 0.200 0.000 0.796 0.004
#> GSM152843 3 0.5267 0.7062 0.184 0.000 0.740 0.076
#> GSM152844 3 0.5543 0.6276 0.048 0.012 0.720 0.220
#> GSM152845 3 0.4542 0.7156 0.092 0.052 0.828 0.028
#> GSM152846 3 0.5601 0.6794 0.092 0.020 0.756 0.132
#> GSM152847 3 0.4538 0.7084 0.216 0.000 0.760 0.024
#> GSM152848 1 0.6586 0.2959 0.544 0.000 0.088 0.368
#> GSM152849 3 0.2773 0.7577 0.116 0.000 0.880 0.004
#> GSM152850 3 0.5161 0.3089 0.476 0.000 0.520 0.004
#> GSM152851 4 0.6947 0.0110 0.056 0.024 0.428 0.492
#> GSM152852 3 0.6045 0.6306 0.076 0.020 0.708 0.196
#> GSM152853 3 0.5930 0.4951 0.040 0.008 0.632 0.320
#> GSM152854 3 0.4475 0.7139 0.076 0.016 0.828 0.080
#> GSM152855 4 0.5161 0.4271 0.400 0.008 0.000 0.592
#> GSM153238 3 0.3636 0.7376 0.172 0.008 0.820 0.000
#> GSM153239 3 0.5643 0.6301 0.048 0.012 0.708 0.232
#> GSM153240 4 0.0895 0.7037 0.020 0.000 0.004 0.976
#> GSM153241 3 0.4046 0.7619 0.124 0.000 0.828 0.048
#> GSM153242 3 0.5437 0.6862 0.068 0.036 0.776 0.120
#> GSM153243 3 0.4054 0.7258 0.188 0.016 0.796 0.000
#> GSM153244 4 0.7041 0.5065 0.080 0.144 0.100 0.676
#> GSM153245 3 0.4375 0.6821 0.032 0.000 0.788 0.180
#> GSM153246 3 0.2530 0.7550 0.100 0.004 0.896 0.000
#> GSM153247 3 0.3901 0.7436 0.168 0.004 0.816 0.012
#> GSM153248 1 0.5823 0.5754 0.704 0.176 0.000 0.120
#> GSM153249 4 0.1970 0.7055 0.060 0.000 0.008 0.932
#> GSM153250 4 0.4948 0.1529 0.440 0.000 0.000 0.560
#> GSM153251 3 0.4277 0.7198 0.028 0.052 0.844 0.076
#> GSM153252 4 0.3377 0.6875 0.140 0.000 0.012 0.848
#> GSM153253 4 0.2174 0.6879 0.020 0.000 0.052 0.928
#> GSM153254 4 0.8010 0.0530 0.092 0.060 0.376 0.472
#> GSM153255 4 0.1637 0.7014 0.060 0.000 0.000 0.940
#> GSM153256 4 0.4343 0.5635 0.264 0.000 0.004 0.732
#> GSM153257 4 0.3105 0.6836 0.140 0.000 0.004 0.856
#> GSM153258 4 0.5201 0.3135 0.400 0.004 0.004 0.592
#> GSM153259 1 0.5486 0.5169 0.696 0.044 0.004 0.256
#> GSM153260 3 0.4360 0.7001 0.248 0.008 0.744 0.000
#> GSM153261 3 0.2654 0.7562 0.108 0.004 0.888 0.000
#> GSM153262 4 0.4589 0.6906 0.168 0.000 0.048 0.784
#> GSM153263 1 0.5313 0.3447 0.608 0.000 0.016 0.376
#> GSM153264 1 0.4901 0.5967 0.780 0.000 0.112 0.108
#> GSM153265 4 0.5632 0.5346 0.092 0.000 0.196 0.712
#> GSM153266 1 0.6732 0.5251 0.612 0.000 0.220 0.168
#> GSM153267 4 0.4283 0.5694 0.256 0.000 0.004 0.740
#> GSM153268 4 0.4237 0.6150 0.040 0.000 0.152 0.808
#> GSM153269 4 0.4713 0.4075 0.360 0.000 0.000 0.640
#> GSM153270 4 0.5956 0.5486 0.220 0.000 0.100 0.680
#> GSM153271 4 0.5419 0.3277 0.384 0.008 0.008 0.600
#> GSM153272 4 0.2861 0.7088 0.096 0.000 0.016 0.888
#> GSM153273 1 0.6412 0.4626 0.616 0.084 0.004 0.296
#> GSM153274 4 0.6465 0.1694 0.412 0.000 0.072 0.516
#> GSM153275 4 0.3172 0.6693 0.160 0.000 0.000 0.840
#> GSM153276 4 0.3919 0.7015 0.104 0.000 0.056 0.840
#> GSM153277 4 0.4093 0.6575 0.096 0.000 0.072 0.832
#> GSM153278 3 0.3402 0.7411 0.164 0.000 0.832 0.004
#> GSM153279 4 0.4883 0.4797 0.016 0.000 0.288 0.696
#> GSM153280 4 0.5149 0.5974 0.092 0.008 0.124 0.776
#> GSM153281 4 0.2563 0.6845 0.020 0.000 0.072 0.908
#> GSM153282 4 0.3840 0.6449 0.052 0.000 0.104 0.844
#> GSM153283 1 0.4964 0.3521 0.616 0.000 0.004 0.380
#> GSM153284 4 0.2921 0.6877 0.140 0.000 0.000 0.860
#> GSM153285 4 0.3486 0.6606 0.044 0.000 0.092 0.864
#> GSM153286 4 0.2345 0.6949 0.100 0.000 0.000 0.900
#> GSM153287 4 0.1284 0.7042 0.024 0.000 0.012 0.964
#> GSM153288 4 0.2647 0.6869 0.120 0.000 0.000 0.880
#> GSM153289 4 0.5290 0.2056 0.476 0.008 0.000 0.516
#> GSM153290 4 0.3833 0.6494 0.072 0.000 0.080 0.848
#> GSM153291 4 0.2149 0.7041 0.088 0.000 0.000 0.912
#> GSM153292 4 0.2500 0.6857 0.044 0.000 0.040 0.916
#> GSM153293 4 0.4277 0.5378 0.280 0.000 0.000 0.720
#> GSM153294 1 0.7742 0.4087 0.480 0.264 0.004 0.252
#> GSM153295 4 0.6292 0.1375 0.416 0.000 0.060 0.524
#> GSM153054 1 0.5903 0.2872 0.616 0.000 0.332 0.052
#> GSM153055 4 0.5591 0.6289 0.172 0.008 0.084 0.736
#> GSM153056 3 0.5113 0.7272 0.152 0.000 0.760 0.088
#> GSM153057 3 0.4986 0.6825 0.216 0.000 0.740 0.044
#> GSM153058 3 0.3060 0.7621 0.088 0.008 0.888 0.016
#> GSM153059 3 0.3862 0.7568 0.080 0.044 0.860 0.016
#> GSM153060 3 0.3253 0.7599 0.100 0.008 0.876 0.016
#> GSM153061 3 0.3208 0.7426 0.148 0.004 0.848 0.000
#> GSM153062 3 0.1938 0.7563 0.052 0.012 0.936 0.000
#> GSM153063 3 0.4085 0.7403 0.040 0.020 0.848 0.092
#> GSM153064 4 0.5163 0.0411 0.480 0.004 0.000 0.516
#> GSM153065 3 0.4019 0.7221 0.196 0.012 0.792 0.000
#> GSM153066 3 0.5361 0.6753 0.208 0.068 0.724 0.000
#> GSM153067 4 0.2654 0.6945 0.108 0.000 0.004 0.888
#> GSM153068 3 0.2714 0.7521 0.112 0.004 0.884 0.000
#> GSM153069 4 0.0707 0.7038 0.020 0.000 0.000 0.980
#> GSM153070 4 0.5097 0.1935 0.428 0.000 0.004 0.568
#> GSM153071 1 0.7147 0.0901 0.508 0.008 0.376 0.108
#> GSM153072 1 0.5670 0.4604 0.704 0.008 0.232 0.056
#> GSM153073 1 0.5085 0.4937 0.692 0.008 0.012 0.288
#> GSM153074 4 0.1978 0.7012 0.068 0.000 0.004 0.928
#> GSM153075 4 0.4647 0.6594 0.180 0.004 0.036 0.780
#> GSM153076 1 0.4990 0.4072 0.640 0.000 0.008 0.352
#> GSM153077 1 0.5309 0.5603 0.776 0.032 0.140 0.052
#> GSM153078 3 0.4978 0.4718 0.384 0.000 0.612 0.004
#> GSM153079 1 0.5906 0.5584 0.748 0.136 0.056 0.060
#> GSM153080 3 0.3913 0.7080 0.028 0.000 0.824 0.148
#> GSM153081 1 0.5029 0.5725 0.768 0.004 0.064 0.164
#> GSM153082 1 0.5407 -0.1170 0.504 0.484 0.012 0.000
#> GSM153083 1 0.5665 0.4774 0.716 0.176 0.108 0.000
#> GSM153084 2 0.7583 0.3763 0.240 0.480 0.280 0.000
#> GSM153085 3 0.6002 0.2996 0.440 0.032 0.524 0.004
#> GSM153086 1 0.5532 0.4046 0.704 0.068 0.228 0.000
#> GSM153087 4 0.4199 0.6768 0.164 0.000 0.032 0.804
#> GSM153088 1 0.5186 0.4211 0.640 0.000 0.016 0.344
#> GSM153089 3 0.5093 0.7048 0.068 0.048 0.804 0.080
#> GSM153090 1 0.5070 0.3691 0.620 0.000 0.008 0.372
#> GSM153091 1 0.5526 0.1567 0.564 0.416 0.000 0.020
#> GSM153092 4 0.6587 0.4008 0.304 0.084 0.008 0.604
#> GSM153093 4 0.3583 0.6680 0.180 0.000 0.004 0.816
#> GSM153094 2 0.4786 0.6067 0.304 0.688 0.004 0.004
#> GSM153095 3 0.7891 0.1746 0.420 0.100 0.436 0.044
#> GSM153096 1 0.5649 0.2749 0.580 0.028 0.000 0.392
#> GSM153097 1 0.5084 0.5347 0.764 0.180 0.044 0.012
#> GSM153098 1 0.6921 0.0541 0.456 0.092 0.004 0.448
#> GSM153099 4 0.4542 0.6795 0.088 0.000 0.108 0.804
#> GSM153100 4 0.5695 0.4249 0.336 0.040 0.000 0.624
#> GSM153101 1 0.4950 0.0785 0.620 0.000 0.376 0.004
#> GSM153102 2 0.9221 0.3608 0.264 0.432 0.188 0.116
#> GSM153103 1 0.5741 -0.1540 0.536 0.020 0.440 0.004
#> GSM153104 4 0.3015 0.6738 0.024 0.000 0.092 0.884
#> GSM153106 4 0.6318 0.3346 0.408 0.052 0.004 0.536
#> GSM153107 1 0.5974 0.2197 0.608 0.036 0.008 0.348
#> GSM153108 4 0.4476 0.6739 0.104 0.028 0.040 0.828
#> GSM153109 2 0.5032 0.7590 0.220 0.744 0.020 0.016
#> GSM153110 1 0.5656 0.6075 0.760 0.100 0.028 0.112
#> GSM153111 1 0.5778 0.4271 0.684 0.256 0.052 0.008
#> GSM153112 1 0.7783 0.2724 0.432 0.208 0.004 0.356
#> GSM153113 2 0.4635 0.7726 0.216 0.756 0.028 0.000
#> GSM153114 4 0.5026 0.5560 0.312 0.016 0.000 0.672
#> GSM187532 3 0.6990 0.3221 0.124 0.312 0.560 0.004
#> GSM187533 2 0.5160 0.7750 0.180 0.748 0.072 0.000
#> GSM187534 2 0.4244 0.8099 0.160 0.804 0.036 0.000
#> GSM187535 2 0.4746 0.7059 0.276 0.712 0.008 0.004
#> GSM152906 2 0.2647 0.8330 0.120 0.880 0.000 0.000
#> GSM152907 2 0.0779 0.8561 0.016 0.980 0.004 0.000
#> GSM152908 2 0.0376 0.8564 0.004 0.992 0.004 0.000
#> GSM152909 2 0.5806 0.6289 0.052 0.680 0.260 0.008
#> GSM152910 2 0.3659 0.8007 0.024 0.840 0.136 0.000
#> GSM152911 2 0.0524 0.8564 0.004 0.988 0.008 0.000
#> GSM152912 2 0.0672 0.8560 0.008 0.984 0.008 0.000
#> GSM152913 2 0.4916 0.7668 0.068 0.780 0.148 0.004
#> GSM152914 2 0.0927 0.8585 0.016 0.976 0.008 0.000
#> GSM152915 2 0.1042 0.8582 0.020 0.972 0.008 0.000
#> GSM152916 2 0.2660 0.8503 0.036 0.908 0.056 0.000
#> GSM152917 2 0.1489 0.8540 0.044 0.952 0.004 0.000
#> GSM152918 2 0.1902 0.8500 0.064 0.932 0.004 0.000
#> GSM152919 2 0.1474 0.8549 0.052 0.948 0.000 0.000
#> GSM152920 2 0.0657 0.8572 0.012 0.984 0.004 0.000
#> GSM152921 2 0.0592 0.8571 0.016 0.984 0.000 0.000
#> GSM152922 2 0.1798 0.8487 0.016 0.944 0.040 0.000
#> GSM152923 2 0.2048 0.8563 0.064 0.928 0.008 0.000
#> GSM152924 2 0.3421 0.8465 0.088 0.868 0.044 0.000
#> GSM152925 2 0.3687 0.8366 0.080 0.856 0.064 0.000
#> GSM152926 2 0.1824 0.8522 0.060 0.936 0.004 0.000
#> GSM152927 2 0.4920 0.7700 0.068 0.768 0.164 0.000
#> GSM152928 2 0.6504 0.6644 0.216 0.636 0.148 0.000
#> GSM152929 2 0.2081 0.8473 0.084 0.916 0.000 0.000
#> GSM152930 2 0.2081 0.8505 0.084 0.916 0.000 0.000
cbind(get_classes(res, k = 5), get_membership(res, k = 5))
#> class entropy silhouette p1 p2 p3 p4 p5
#> GSM152839 3 0.6906 0.3110 0.360 0.000 0.460 0.028 0.152
#> GSM152840 4 0.6059 -0.1131 0.004 0.000 0.412 0.480 0.104
#> GSM152841 4 0.1461 0.6530 0.016 0.000 0.004 0.952 0.028
#> GSM152842 3 0.4444 0.6222 0.180 0.000 0.748 0.000 0.072
#> GSM152843 3 0.5808 0.6101 0.188 0.000 0.680 0.060 0.072
#> GSM152844 3 0.6195 0.3469 0.004 0.000 0.508 0.360 0.128
#> GSM152845 3 0.5902 0.3928 0.000 0.024 0.544 0.056 0.376
#> GSM152846 3 0.6416 0.4423 0.000 0.008 0.552 0.212 0.228
#> GSM152847 3 0.5309 0.5857 0.236 0.000 0.676 0.012 0.076
#> GSM152848 1 0.7004 0.3990 0.564 0.000 0.076 0.140 0.220
#> GSM152849 3 0.5029 0.6250 0.104 0.000 0.728 0.012 0.156
#> GSM152850 3 0.5919 0.2416 0.416 0.000 0.480 0.000 0.104
#> GSM152851 4 0.6093 0.2577 0.012 0.008 0.284 0.600 0.096
#> GSM152852 3 0.6699 0.3462 0.004 0.000 0.472 0.256 0.268
#> GSM152853 4 0.6207 -0.1676 0.004 0.000 0.420 0.456 0.120
#> GSM152854 3 0.5749 0.4967 0.004 0.000 0.616 0.120 0.260
#> GSM152855 5 0.6804 0.2742 0.304 0.012 0.000 0.208 0.476
#> GSM153238 3 0.4680 0.6342 0.132 0.004 0.764 0.008 0.092
#> GSM153239 3 0.6712 0.3851 0.040 0.000 0.508 0.344 0.108
#> GSM153240 4 0.3130 0.6615 0.096 0.000 0.000 0.856 0.048
#> GSM153241 3 0.4184 0.6511 0.068 0.000 0.816 0.040 0.076
#> GSM153242 3 0.6057 0.4818 0.000 0.016 0.616 0.232 0.136
#> GSM153243 3 0.5439 0.5906 0.204 0.016 0.692 0.004 0.084
#> GSM153244 4 0.6775 0.4522 0.052 0.080 0.052 0.648 0.168
#> GSM153245 3 0.5404 0.5096 0.008 0.000 0.652 0.260 0.080
#> GSM153246 3 0.2940 0.6461 0.048 0.000 0.876 0.004 0.072
#> GSM153247 3 0.5880 0.6039 0.140 0.012 0.692 0.028 0.128
#> GSM153248 1 0.4698 0.4957 0.796 0.092 0.024 0.024 0.064
#> GSM153249 4 0.3370 0.6452 0.148 0.000 0.000 0.824 0.028
#> GSM153250 1 0.5068 0.2407 0.592 0.000 0.000 0.364 0.044
#> GSM153251 3 0.6049 0.5201 0.016 0.016 0.656 0.204 0.108
#> GSM153252 4 0.4960 0.5648 0.264 0.000 0.008 0.680 0.048
#> GSM153253 4 0.2444 0.6587 0.036 0.000 0.024 0.912 0.028
#> GSM153254 4 0.6940 0.2077 0.008 0.028 0.252 0.544 0.168
#> GSM153255 4 0.3355 0.6287 0.184 0.000 0.000 0.804 0.012
#> GSM153256 4 0.5291 0.1871 0.456 0.000 0.000 0.496 0.048
#> GSM153257 4 0.4734 0.5243 0.312 0.000 0.000 0.652 0.036
#> GSM153258 1 0.6557 0.3416 0.564 0.004 0.020 0.268 0.144
#> GSM153259 1 0.5583 0.4118 0.696 0.028 0.012 0.060 0.204
#> GSM153260 3 0.6120 0.5587 0.196 0.004 0.604 0.004 0.192
#> GSM153261 3 0.5148 0.5028 0.032 0.000 0.616 0.012 0.340
#> GSM153262 4 0.6685 0.4591 0.240 0.000 0.024 0.548 0.188
#> GSM153263 1 0.4396 0.5014 0.772 0.000 0.008 0.152 0.068
#> GSM153264 1 0.4711 0.4380 0.736 0.000 0.148 0.000 0.116
#> GSM153265 4 0.4417 0.5358 0.000 0.000 0.148 0.760 0.092
#> GSM153266 1 0.6438 0.3721 0.596 0.000 0.236 0.036 0.132
#> GSM153267 4 0.5234 0.1629 0.460 0.000 0.000 0.496 0.044
#> GSM153268 4 0.3384 0.5996 0.008 0.000 0.084 0.852 0.056
#> GSM153269 1 0.5294 0.1178 0.564 0.000 0.000 0.380 0.056
#> GSM153270 4 0.6869 0.2524 0.380 0.004 0.080 0.480 0.056
#> GSM153271 1 0.5302 0.1148 0.564 0.012 0.000 0.392 0.032
#> GSM153272 4 0.3847 0.6315 0.180 0.000 0.000 0.784 0.036
#> GSM153273 1 0.5444 0.5198 0.748 0.092 0.016 0.092 0.052
#> GSM153274 1 0.6534 0.3743 0.596 0.004 0.080 0.260 0.060
#> GSM153275 4 0.5114 0.3745 0.404 0.000 0.004 0.560 0.032
#> GSM153276 4 0.5561 0.5993 0.204 0.000 0.064 0.688 0.044
#> GSM153277 4 0.4892 0.5696 0.044 0.000 0.024 0.724 0.208
#> GSM153278 3 0.5587 0.6039 0.188 0.000 0.656 0.004 0.152
#> GSM153279 4 0.4756 0.5597 0.040 0.000 0.164 0.756 0.040
#> GSM153280 4 0.4366 0.5497 0.004 0.004 0.072 0.780 0.140
#> GSM153281 4 0.2765 0.6530 0.036 0.000 0.044 0.896 0.024
#> GSM153282 4 0.2664 0.6130 0.004 0.000 0.064 0.892 0.040
#> GSM153283 1 0.4038 0.5278 0.800 0.000 0.008 0.136 0.056
#> GSM153284 4 0.5518 0.4990 0.304 0.004 0.016 0.628 0.048
#> GSM153285 4 0.2618 0.6321 0.012 0.000 0.052 0.900 0.036
#> GSM153286 4 0.4572 0.5426 0.280 0.000 0.000 0.684 0.036
#> GSM153287 4 0.2548 0.6611 0.072 0.000 0.004 0.896 0.028
#> GSM153288 4 0.4712 0.5382 0.268 0.000 0.000 0.684 0.048
#> GSM153289 5 0.6767 0.1441 0.368 0.008 0.000 0.196 0.428
#> GSM153290 4 0.2965 0.6266 0.012 0.000 0.028 0.876 0.084
#> GSM153291 4 0.4926 0.5819 0.176 0.000 0.000 0.712 0.112
#> GSM153292 4 0.1731 0.6486 0.008 0.000 0.012 0.940 0.040
#> GSM153293 4 0.5830 0.1324 0.436 0.004 0.000 0.480 0.080
#> GSM153294 1 0.7599 0.2732 0.476 0.280 0.000 0.120 0.124
#> GSM153295 1 0.7107 0.3144 0.524 0.000 0.048 0.204 0.224
#> GSM153054 1 0.6667 0.1333 0.532 0.020 0.328 0.012 0.108
#> GSM153055 4 0.7319 0.2420 0.380 0.024 0.056 0.460 0.080
#> GSM153056 3 0.5719 0.6394 0.144 0.000 0.700 0.056 0.100
#> GSM153057 3 0.6291 0.5197 0.172 0.000 0.580 0.012 0.236
#> GSM153058 3 0.4673 0.6404 0.100 0.000 0.776 0.028 0.096
#> GSM153059 3 0.6050 0.5950 0.072 0.032 0.692 0.036 0.168
#> GSM153060 3 0.3791 0.6457 0.080 0.000 0.836 0.024 0.060
#> GSM153061 3 0.3479 0.6423 0.084 0.000 0.836 0.000 0.080
#> GSM153062 3 0.2434 0.6347 0.012 0.004 0.908 0.012 0.064
#> GSM153063 3 0.6039 0.5226 0.016 0.008 0.636 0.232 0.108
#> GSM153064 1 0.5587 0.4128 0.644 0.008 0.012 0.276 0.060
#> GSM153065 3 0.5599 0.5828 0.144 0.008 0.664 0.000 0.184
#> GSM153066 3 0.5764 0.5958 0.136 0.024 0.672 0.000 0.168
#> GSM153067 4 0.4224 0.6082 0.216 0.000 0.000 0.744 0.040
#> GSM153068 3 0.2592 0.6461 0.056 0.000 0.892 0.000 0.052
#> GSM153069 4 0.2777 0.6563 0.120 0.000 0.000 0.864 0.016
#> GSM153070 1 0.6426 0.3684 0.564 0.008 0.016 0.300 0.112
#> GSM153071 1 0.7777 -0.0858 0.408 0.024 0.380 0.056 0.132
#> GSM153072 1 0.5820 0.2693 0.628 0.024 0.268 0.000 0.080
#> GSM153073 1 0.4324 0.5398 0.824 0.024 0.040 0.072 0.040
#> GSM153074 4 0.3882 0.5935 0.224 0.000 0.000 0.756 0.020
#> GSM153075 4 0.6348 0.1613 0.128 0.000 0.008 0.480 0.384
#> GSM153076 1 0.3222 0.5310 0.852 0.000 0.004 0.108 0.036
#> GSM153077 1 0.4221 0.4655 0.780 0.008 0.160 0.000 0.052
#> GSM153078 3 0.5928 0.3453 0.388 0.000 0.520 0.008 0.084
#> GSM153079 5 0.6796 0.3776 0.292 0.060 0.072 0.012 0.564
#> GSM153080 3 0.5726 0.5076 0.016 0.000 0.632 0.264 0.088
#> GSM153081 1 0.6581 -0.0984 0.456 0.012 0.076 0.024 0.432
#> GSM153082 1 0.7737 0.0899 0.424 0.340 0.068 0.008 0.160
#> GSM153083 1 0.6808 0.3325 0.604 0.092 0.164 0.000 0.140
#> GSM153084 2 0.8714 0.0135 0.164 0.328 0.308 0.016 0.184
#> GSM153085 3 0.7074 0.2376 0.380 0.036 0.456 0.008 0.120
#> GSM153086 1 0.6116 0.2604 0.608 0.036 0.272 0.000 0.084
#> GSM153087 4 0.6154 0.5495 0.184 0.008 0.060 0.668 0.080
#> GSM153088 1 0.3943 0.5318 0.832 0.000 0.044 0.068 0.056
#> GSM153089 3 0.6566 0.4813 0.008 0.024 0.600 0.172 0.196
#> GSM153090 1 0.4732 0.5164 0.776 0.004 0.024 0.112 0.084
#> GSM153091 1 0.5791 0.2882 0.600 0.308 0.008 0.004 0.080
#> GSM153092 1 0.7772 0.1330 0.408 0.068 0.004 0.332 0.188
#> GSM153093 4 0.5068 0.4174 0.388 0.000 0.000 0.572 0.040
#> GSM153094 2 0.5425 0.4478 0.276 0.648 0.008 0.004 0.064
#> GSM153095 3 0.8946 0.1789 0.296 0.084 0.360 0.072 0.188
#> GSM153096 1 0.6067 0.4508 0.664 0.036 0.004 0.168 0.128
#> GSM153097 1 0.5619 0.4252 0.716 0.072 0.108 0.000 0.104
#> GSM153098 1 0.6499 0.4387 0.624 0.080 0.000 0.196 0.100
#> GSM153099 4 0.5191 0.6316 0.168 0.000 0.064 0.728 0.040
#> GSM153100 1 0.7393 0.1956 0.428 0.040 0.000 0.308 0.224
#> GSM153101 1 0.6835 -0.0276 0.436 0.004 0.348 0.004 0.208
#> GSM153102 5 0.6769 0.4077 0.024 0.160 0.112 0.064 0.640
#> GSM153103 3 0.6902 0.1450 0.396 0.008 0.400 0.004 0.192
#> GSM153104 4 0.2418 0.6529 0.020 0.000 0.044 0.912 0.024
#> GSM153106 5 0.6825 0.5048 0.164 0.084 0.004 0.136 0.612
#> GSM153107 5 0.6296 0.4748 0.232 0.052 0.016 0.060 0.640
#> GSM153108 4 0.6011 0.5844 0.116 0.012 0.028 0.676 0.168
#> GSM153109 2 0.6564 0.0869 0.096 0.476 0.004 0.024 0.400
#> GSM153110 1 0.4490 0.4944 0.804 0.032 0.052 0.012 0.100
#> GSM153111 1 0.6861 0.3020 0.592 0.192 0.088 0.000 0.128
#> GSM153112 1 0.7347 0.3176 0.500 0.260 0.000 0.172 0.068
#> GSM153113 2 0.6277 0.6315 0.108 0.656 0.040 0.012 0.184
#> GSM153114 5 0.6672 0.3651 0.188 0.012 0.004 0.260 0.536
#> GSM187532 5 0.6730 -0.0331 0.008 0.164 0.368 0.004 0.456
#> GSM187533 5 0.5859 0.0791 0.012 0.356 0.076 0.000 0.556
#> GSM187534 2 0.5438 0.3945 0.024 0.576 0.028 0.000 0.372
#> GSM187535 5 0.6405 0.1699 0.124 0.380 0.000 0.012 0.484
#> GSM152906 2 0.2819 0.7761 0.052 0.884 0.000 0.004 0.060
#> GSM152907 2 0.2095 0.7916 0.008 0.920 0.000 0.012 0.060
#> GSM152908 2 0.1671 0.7842 0.000 0.924 0.000 0.000 0.076
#> GSM152909 2 0.6978 0.3261 0.004 0.520 0.212 0.024 0.240
#> GSM152910 2 0.4641 0.6932 0.008 0.760 0.116 0.000 0.116
#> GSM152911 2 0.1410 0.7878 0.000 0.940 0.000 0.000 0.060
#> GSM152912 2 0.2052 0.7824 0.004 0.912 0.004 0.000 0.080
#> GSM152913 2 0.5737 0.6411 0.012 0.696 0.156 0.020 0.116
#> GSM152914 2 0.1124 0.7914 0.004 0.960 0.000 0.000 0.036
#> GSM152915 2 0.1644 0.7909 0.004 0.940 0.000 0.008 0.048
#> GSM152916 2 0.2562 0.7894 0.008 0.900 0.032 0.000 0.060
#> GSM152917 2 0.0932 0.7921 0.004 0.972 0.000 0.004 0.020
#> GSM152918 2 0.1267 0.7912 0.012 0.960 0.000 0.004 0.024
#> GSM152919 2 0.1661 0.7928 0.024 0.940 0.000 0.000 0.036
#> GSM152920 2 0.1952 0.7799 0.004 0.912 0.000 0.000 0.084
#> GSM152921 2 0.1571 0.7848 0.004 0.936 0.000 0.000 0.060
#> GSM152922 2 0.3052 0.7535 0.004 0.856 0.008 0.008 0.124
#> GSM152923 2 0.1485 0.7909 0.020 0.948 0.000 0.000 0.032
#> GSM152924 2 0.4017 0.7619 0.036 0.820 0.040 0.000 0.104
#> GSM152925 2 0.4447 0.7435 0.036 0.792 0.056 0.000 0.116
#> GSM152926 2 0.3008 0.7673 0.036 0.868 0.000 0.004 0.092
#> GSM152927 2 0.5445 0.6589 0.036 0.712 0.156 0.000 0.096
#> GSM152928 2 0.7269 0.4593 0.108 0.544 0.132 0.000 0.216
#> GSM152929 2 0.2628 0.7755 0.028 0.884 0.000 0.000 0.088
#> GSM152930 2 0.1626 0.7913 0.016 0.940 0.000 0.000 0.044
cbind(get_classes(res, k = 6), get_membership(res, k = 6))
#> class entropy silhouette p1 p2 p3 p4 p5 p6
#> GSM152839 1 0.710 0.05570 0.480 0.000 0.284 0.044 0.048 0.144
#> GSM152840 4 0.669 -0.13918 0.012 0.000 0.392 0.424 0.112 0.060
#> GSM152841 4 0.343 0.66321 0.024 0.000 0.056 0.852 0.044 0.024
#> GSM152842 3 0.543 0.42520 0.244 0.000 0.636 0.004 0.084 0.032
#> GSM152843 3 0.622 0.38294 0.308 0.000 0.552 0.044 0.064 0.032
#> GSM152844 3 0.685 0.39432 0.012 0.004 0.512 0.268 0.132 0.072
#> GSM152845 3 0.658 0.40519 0.004 0.020 0.504 0.024 0.148 0.300
#> GSM152846 3 0.671 0.47331 0.000 0.016 0.572 0.128 0.144 0.140
#> GSM152847 3 0.629 0.34732 0.324 0.000 0.528 0.016 0.068 0.064
#> GSM152848 1 0.693 0.40084 0.564 0.000 0.092 0.080 0.064 0.200
#> GSM152849 3 0.662 0.49601 0.148 0.000 0.568 0.008 0.120 0.156
#> GSM152850 1 0.619 0.05577 0.532 0.000 0.320 0.008 0.060 0.080
#> GSM152851 4 0.627 0.33042 0.012 0.016 0.260 0.584 0.092 0.036
#> GSM152852 3 0.764 0.41275 0.016 0.008 0.460 0.152 0.184 0.180
#> GSM152853 3 0.703 0.18852 0.020 0.004 0.428 0.360 0.132 0.056
#> GSM152854 3 0.669 0.51126 0.028 0.008 0.600 0.076 0.156 0.132
#> GSM152855 6 0.468 0.51210 0.132 0.004 0.000 0.128 0.012 0.724
#> GSM153238 3 0.602 0.32725 0.116 0.000 0.548 0.008 0.300 0.028
#> GSM153239 3 0.658 0.42826 0.060 0.000 0.548 0.276 0.076 0.040
#> GSM153240 4 0.524 0.64484 0.128 0.000 0.028 0.720 0.044 0.080
#> GSM153241 3 0.531 0.54393 0.088 0.000 0.724 0.036 0.100 0.052
#> GSM153242 3 0.650 0.50573 0.016 0.016 0.620 0.140 0.136 0.072
#> GSM153243 3 0.650 0.34167 0.300 0.012 0.512 0.004 0.140 0.032
#> GSM153244 4 0.812 0.36714 0.048 0.128 0.092 0.500 0.068 0.164
#> GSM153245 3 0.609 0.47081 0.024 0.000 0.608 0.196 0.144 0.028
#> GSM153246 3 0.441 0.52021 0.064 0.000 0.756 0.008 0.152 0.020
#> GSM153247 3 0.635 0.28304 0.100 0.004 0.540 0.052 0.296 0.008
#> GSM153248 1 0.642 0.33343 0.592 0.072 0.000 0.044 0.228 0.064
#> GSM153249 4 0.367 0.65849 0.064 0.008 0.000 0.832 0.056 0.040
#> GSM153250 1 0.545 0.39511 0.620 0.004 0.008 0.284 0.028 0.056
#> GSM153251 3 0.596 0.52206 0.012 0.032 0.668 0.116 0.140 0.032
#> GSM153252 4 0.588 0.57724 0.180 0.000 0.016 0.648 0.084 0.072
#> GSM153253 4 0.332 0.67473 0.044 0.000 0.044 0.860 0.024 0.028
#> GSM153254 4 0.871 -0.07209 0.028 0.076 0.272 0.344 0.172 0.108
#> GSM153255 4 0.344 0.64340 0.124 0.000 0.000 0.816 0.008 0.052
#> GSM153256 1 0.541 -0.00285 0.488 0.000 0.000 0.424 0.016 0.072
#> GSM153257 4 0.467 0.53511 0.256 0.000 0.000 0.676 0.048 0.020
#> GSM153258 1 0.687 0.44296 0.556 0.008 0.016 0.160 0.076 0.184
#> GSM153259 1 0.647 0.36116 0.524 0.008 0.004 0.032 0.164 0.268
#> GSM153260 3 0.699 0.38616 0.220 0.000 0.504 0.008 0.112 0.156
#> GSM153261 3 0.675 0.39189 0.040 0.000 0.492 0.016 0.188 0.264
#> GSM153262 4 0.693 0.41575 0.100 0.000 0.024 0.532 0.116 0.228
#> GSM153263 1 0.499 0.51348 0.704 0.000 0.000 0.112 0.036 0.148
#> GSM153264 1 0.404 0.45129 0.788 0.000 0.056 0.000 0.036 0.120
#> GSM153265 4 0.564 0.55107 0.012 0.000 0.148 0.676 0.076 0.088
#> GSM153266 1 0.603 0.41812 0.656 0.000 0.120 0.032 0.064 0.128
#> GSM153267 4 0.571 0.07052 0.432 0.000 0.004 0.468 0.028 0.068
#> GSM153268 4 0.476 0.60175 0.024 0.000 0.116 0.756 0.068 0.036
#> GSM153269 1 0.545 0.32602 0.588 0.000 0.000 0.288 0.016 0.108
#> GSM153270 1 0.717 0.04783 0.428 0.000 0.084 0.348 0.112 0.028
#> GSM153271 1 0.545 0.23555 0.556 0.004 0.008 0.360 0.060 0.012
#> GSM153272 4 0.362 0.65145 0.124 0.000 0.000 0.812 0.028 0.036
#> GSM153273 1 0.599 0.47775 0.672 0.032 0.008 0.096 0.136 0.056
#> GSM153274 1 0.635 0.38447 0.580 0.000 0.080 0.228 0.100 0.012
#> GSM153275 4 0.566 0.18285 0.408 0.000 0.000 0.492 0.056 0.044
#> GSM153276 4 0.714 0.41481 0.252 0.000 0.100 0.512 0.088 0.048
#> GSM153277 4 0.621 0.50359 0.020 0.000 0.076 0.612 0.088 0.204
#> GSM153278 3 0.651 0.34467 0.296 0.000 0.504 0.000 0.100 0.100
#> GSM153279 4 0.563 0.60567 0.028 0.000 0.164 0.676 0.092 0.040
#> GSM153280 4 0.516 0.57229 0.004 0.000 0.100 0.712 0.064 0.120
#> GSM153281 4 0.312 0.67411 0.040 0.000 0.056 0.864 0.036 0.004
#> GSM153282 4 0.280 0.65285 0.000 0.000 0.064 0.876 0.036 0.024
#> GSM153283 1 0.470 0.52209 0.748 0.000 0.008 0.056 0.052 0.136
#> GSM153284 4 0.565 0.36412 0.332 0.004 0.004 0.568 0.056 0.036
#> GSM153285 4 0.369 0.66631 0.016 0.000 0.048 0.832 0.076 0.028
#> GSM153286 4 0.544 0.56122 0.228 0.000 0.004 0.648 0.048 0.072
#> GSM153287 4 0.278 0.66833 0.044 0.000 0.000 0.880 0.044 0.032
#> GSM153288 4 0.536 0.52122 0.248 0.000 0.000 0.632 0.032 0.088
#> GSM153289 6 0.503 0.43017 0.196 0.000 0.000 0.124 0.012 0.668
#> GSM153290 4 0.420 0.63720 0.008 0.000 0.036 0.788 0.056 0.112
#> GSM153291 4 0.476 0.61585 0.096 0.000 0.000 0.708 0.020 0.176
#> GSM153292 4 0.177 0.67104 0.000 0.000 0.012 0.932 0.036 0.020
#> GSM153293 4 0.618 0.17961 0.360 0.000 0.000 0.464 0.028 0.148
#> GSM153294 5 0.808 0.10181 0.272 0.188 0.004 0.156 0.352 0.028
#> GSM153295 1 0.736 0.16714 0.412 0.000 0.040 0.148 0.064 0.336
#> GSM153054 1 0.608 -0.02810 0.488 0.004 0.180 0.004 0.320 0.004
#> GSM153055 4 0.829 0.05808 0.336 0.048 0.104 0.368 0.096 0.048
#> GSM153056 3 0.637 0.47685 0.172 0.000 0.620 0.040 0.100 0.068
#> GSM153057 3 0.743 0.29900 0.192 0.008 0.476 0.008 0.156 0.160
#> GSM153058 3 0.505 0.54094 0.144 0.000 0.716 0.024 0.100 0.016
#> GSM153059 3 0.741 0.46702 0.088 0.024 0.520 0.024 0.216 0.128
#> GSM153060 3 0.497 0.48671 0.096 0.000 0.712 0.012 0.160 0.020
#> GSM153061 3 0.502 0.46339 0.108 0.000 0.700 0.000 0.156 0.036
#> GSM153062 3 0.315 0.52765 0.044 0.000 0.844 0.000 0.100 0.012
#> GSM153063 3 0.617 0.45721 0.040 0.004 0.604 0.140 0.200 0.012
#> GSM153064 1 0.637 0.46052 0.560 0.000 0.000 0.188 0.176 0.076
#> GSM153065 3 0.618 0.46260 0.188 0.004 0.580 0.000 0.048 0.180
#> GSM153066 3 0.719 0.24415 0.092 0.040 0.500 0.000 0.256 0.112
#> GSM153067 4 0.503 0.61540 0.128 0.016 0.000 0.732 0.068 0.056
#> GSM153068 3 0.477 0.51493 0.104 0.000 0.736 0.000 0.108 0.052
#> GSM153069 4 0.266 0.67365 0.040 0.000 0.000 0.884 0.020 0.056
#> GSM153070 1 0.651 0.48656 0.608 0.008 0.016 0.168 0.092 0.108
#> GSM153071 5 0.786 0.25738 0.280 0.008 0.260 0.076 0.348 0.028
#> GSM153072 1 0.604 0.01843 0.556 0.004 0.164 0.016 0.256 0.004
#> GSM153073 1 0.437 0.47186 0.788 0.016 0.016 0.060 0.108 0.012
#> GSM153074 4 0.417 0.62933 0.148 0.000 0.000 0.768 0.028 0.056
#> GSM153075 6 0.727 0.10242 0.088 0.012 0.024 0.316 0.096 0.464
#> GSM153076 1 0.464 0.51599 0.748 0.000 0.000 0.112 0.056 0.084
#> GSM153077 1 0.537 0.33602 0.716 0.012 0.116 0.008 0.092 0.056
#> GSM153078 1 0.696 0.05991 0.496 0.016 0.316 0.020 0.076 0.076
#> GSM153079 6 0.490 0.50857 0.200 0.036 0.012 0.004 0.036 0.712
#> GSM153080 3 0.611 0.50332 0.020 0.000 0.616 0.176 0.148 0.040
#> GSM153081 6 0.488 0.24087 0.376 0.000 0.016 0.004 0.028 0.576
#> GSM153082 5 0.827 0.40532 0.272 0.248 0.068 0.020 0.340 0.052
#> GSM153083 1 0.712 0.21364 0.528 0.056 0.056 0.000 0.196 0.164
#> GSM153084 5 0.882 0.32520 0.116 0.236 0.172 0.024 0.352 0.100
#> GSM153085 5 0.724 0.22824 0.284 0.012 0.300 0.008 0.360 0.036
#> GSM153086 1 0.622 0.17830 0.612 0.012 0.136 0.000 0.168 0.072
#> GSM153087 4 0.683 0.46147 0.192 0.016 0.080 0.580 0.112 0.020
#> GSM153088 1 0.335 0.49921 0.856 0.000 0.020 0.044 0.024 0.056
#> GSM153089 3 0.685 0.48122 0.008 0.028 0.580 0.088 0.180 0.116
#> GSM153090 1 0.468 0.51591 0.752 0.000 0.016 0.092 0.024 0.116
#> GSM153091 1 0.586 0.18578 0.584 0.236 0.000 0.016 0.156 0.008
#> GSM153092 1 0.883 0.23545 0.364 0.096 0.024 0.200 0.128 0.188
#> GSM153093 4 0.515 0.44825 0.328 0.000 0.000 0.596 0.036 0.040
#> GSM153094 2 0.680 0.16233 0.264 0.512 0.004 0.004 0.112 0.104
#> GSM153095 5 0.794 0.35355 0.132 0.048 0.212 0.080 0.488 0.040
#> GSM153096 1 0.671 0.47656 0.588 0.032 0.004 0.100 0.088 0.188
#> GSM153097 1 0.587 0.30153 0.608 0.032 0.028 0.000 0.260 0.072
#> GSM153098 1 0.798 0.21764 0.364 0.080 0.000 0.284 0.208 0.064
#> GSM153099 4 0.567 0.61960 0.140 0.000 0.048 0.688 0.084 0.040
#> GSM153100 1 0.763 0.15385 0.332 0.032 0.000 0.272 0.064 0.300
#> GSM153101 6 0.773 -0.16595 0.288 0.000 0.176 0.004 0.228 0.304
#> GSM153102 6 0.729 0.31754 0.012 0.084 0.124 0.048 0.184 0.548
#> GSM153103 1 0.736 0.08965 0.456 0.000 0.184 0.008 0.180 0.172
#> GSM153104 4 0.331 0.66870 0.008 0.000 0.040 0.852 0.072 0.028
#> GSM153106 6 0.440 0.56359 0.096 0.024 0.000 0.068 0.028 0.784
#> GSM153107 6 0.366 0.54979 0.108 0.028 0.000 0.016 0.024 0.824
#> GSM153108 4 0.708 0.51029 0.052 0.020 0.032 0.548 0.128 0.220
#> GSM153109 6 0.782 0.20839 0.108 0.336 0.032 0.012 0.128 0.384
#> GSM153110 1 0.584 0.43538 0.672 0.020 0.036 0.012 0.148 0.112
#> GSM153111 1 0.695 0.16070 0.516 0.112 0.024 0.000 0.256 0.092
#> GSM153112 1 0.821 0.17722 0.368 0.168 0.000 0.192 0.220 0.052
#> GSM153113 2 0.712 0.18248 0.036 0.444 0.040 0.012 0.356 0.112
#> GSM153114 6 0.451 0.51666 0.108 0.000 0.000 0.140 0.016 0.736
#> GSM187532 6 0.753 0.00285 0.008 0.168 0.284 0.000 0.152 0.388
#> GSM187533 6 0.607 0.30799 0.004 0.252 0.056 0.000 0.108 0.580
#> GSM187534 2 0.604 0.04115 0.004 0.440 0.024 0.000 0.112 0.420
#> GSM187535 6 0.548 0.41776 0.052 0.216 0.000 0.004 0.076 0.652
#> GSM152906 2 0.464 0.60773 0.056 0.672 0.000 0.000 0.260 0.012
#> GSM152907 2 0.281 0.70661 0.000 0.840 0.000 0.008 0.144 0.008
#> GSM152908 2 0.101 0.71045 0.000 0.960 0.000 0.000 0.036 0.004
#> GSM152909 2 0.743 0.21673 0.008 0.484 0.196 0.012 0.152 0.148
#> GSM152910 2 0.430 0.62391 0.004 0.784 0.072 0.000 0.088 0.052
#> GSM152911 2 0.218 0.70881 0.004 0.912 0.012 0.000 0.052 0.020
#> GSM152912 2 0.193 0.70160 0.000 0.920 0.004 0.000 0.044 0.032
#> GSM152913 2 0.509 0.57670 0.000 0.732 0.092 0.024 0.112 0.040
#> GSM152914 2 0.137 0.71947 0.000 0.944 0.000 0.000 0.044 0.012
#> GSM152915 2 0.108 0.71773 0.000 0.956 0.000 0.000 0.040 0.004
#> GSM152916 2 0.454 0.64150 0.000 0.696 0.040 0.000 0.240 0.024
#> GSM152917 2 0.153 0.71589 0.004 0.928 0.000 0.000 0.068 0.000
#> GSM152918 2 0.252 0.71025 0.012 0.872 0.000 0.000 0.108 0.008
#> GSM152919 2 0.211 0.71570 0.004 0.900 0.000 0.000 0.084 0.012
#> GSM152920 2 0.214 0.70088 0.000 0.904 0.000 0.000 0.048 0.048
#> GSM152921 2 0.149 0.71215 0.000 0.940 0.000 0.000 0.036 0.024
#> GSM152922 2 0.316 0.67389 0.000 0.852 0.020 0.004 0.092 0.032
#> GSM152923 2 0.383 0.66729 0.012 0.744 0.000 0.000 0.224 0.020
#> GSM152924 2 0.568 0.47296 0.008 0.528 0.036 0.000 0.376 0.052
#> GSM152925 2 0.568 0.41948 0.020 0.532 0.048 0.000 0.376 0.024
#> GSM152926 2 0.440 0.60130 0.028 0.660 0.000 0.000 0.300 0.012
#> GSM152927 2 0.599 0.43553 0.020 0.528 0.096 0.000 0.340 0.016
#> GSM152928 5 0.769 0.12678 0.064 0.240 0.092 0.004 0.472 0.128
#> GSM152929 2 0.414 0.62360 0.024 0.688 0.000 0.000 0.280 0.008
#> GSM152930 2 0.404 0.67531 0.024 0.752 0.000 0.000 0.196 0.028
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 tissue(p) k
#> CV:NMF 152 9.03e-20 2
#> CV:NMF 153 3.86e-23 3
#> CV:NMF 115 5.29e-20 4
#> CV:NMF 88 1.27e-15 5
#> CV:NMF 66 1.16e-12 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 12013 rows and 164 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 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 0.639 0.824 0.911 0.143 0.988 0.988
#> 3 3 0.479 0.863 0.843 0.911 0.707 0.703
#> 4 4 0.380 0.849 0.893 0.367 1.000 1.000
#> 5 5 0.571 0.732 0.881 0.180 0.971 0.958
#> 6 6 0.444 0.761 0.864 0.135 0.909 0.863
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
#> GSM152839 1 0.0938 0.900 0.988 0.012
#> GSM152840 1 0.3879 0.875 0.924 0.076
#> GSM152841 1 0.0672 0.899 0.992 0.008
#> GSM152842 1 0.7056 0.716 0.808 0.192
#> GSM152843 1 0.1184 0.896 0.984 0.016
#> GSM152844 1 0.3733 0.876 0.928 0.072
#> GSM152845 1 0.5178 0.841 0.884 0.116
#> GSM152846 1 0.4298 0.864 0.912 0.088
#> GSM152847 1 0.2043 0.897 0.968 0.032
#> GSM152848 1 0.0672 0.900 0.992 0.008
#> GSM152849 1 0.1843 0.901 0.972 0.028
#> GSM152850 1 0.1633 0.902 0.976 0.024
#> GSM152851 1 0.1184 0.900 0.984 0.016
#> GSM152852 1 0.3584 0.879 0.932 0.068
#> GSM152853 1 0.3584 0.877 0.932 0.068
#> GSM152854 1 0.3733 0.880 0.928 0.072
#> GSM152855 1 0.1633 0.901 0.976 0.024
#> GSM153238 1 0.3584 0.883 0.932 0.068
#> GSM153239 1 0.3431 0.884 0.936 0.064
#> GSM153240 1 0.0938 0.901 0.988 0.012
#> GSM153241 1 0.2948 0.892 0.948 0.052
#> GSM153242 1 0.4690 0.860 0.900 0.100
#> GSM153243 1 0.1414 0.902 0.980 0.020
#> GSM153244 1 0.1184 0.902 0.984 0.016
#> GSM153245 1 0.3274 0.883 0.940 0.060
#> GSM153246 1 0.9954 -0.187 0.540 0.460
#> GSM153247 1 0.3879 0.877 0.924 0.076
#> GSM153248 1 0.1184 0.901 0.984 0.016
#> GSM153249 1 0.0938 0.899 0.988 0.012
#> GSM153250 1 0.0000 0.899 1.000 0.000
#> GSM153251 1 0.5294 0.842 0.880 0.120
#> GSM153252 1 0.0672 0.899 0.992 0.008
#> GSM153253 1 0.1184 0.900 0.984 0.016
#> GSM153254 1 0.1184 0.902 0.984 0.016
#> GSM153255 1 0.1184 0.901 0.984 0.016
#> GSM153256 1 0.0672 0.900 0.992 0.008
#> GSM153257 1 0.0938 0.901 0.988 0.012
#> GSM153258 1 0.1633 0.902 0.976 0.024
#> GSM153259 1 0.1414 0.900 0.980 0.020
#> GSM153260 1 0.2603 0.893 0.956 0.044
#> GSM153261 1 0.1414 0.902 0.980 0.020
#> GSM153262 1 0.0672 0.899 0.992 0.008
#> GSM153263 1 0.1184 0.901 0.984 0.016
#> GSM153264 1 0.0672 0.899 0.992 0.008
#> GSM153265 1 0.0672 0.899 0.992 0.008
#> GSM153266 1 0.1184 0.900 0.984 0.016
#> GSM153267 1 0.0672 0.901 0.992 0.008
#> GSM153268 1 0.1414 0.900 0.980 0.020
#> GSM153269 1 0.0000 0.899 1.000 0.000
#> GSM153270 1 0.0938 0.901 0.988 0.012
#> GSM153271 1 0.0376 0.900 0.996 0.004
#> GSM153272 1 0.1184 0.901 0.984 0.016
#> GSM153273 1 0.1633 0.900 0.976 0.024
#> GSM153274 1 0.0672 0.899 0.992 0.008
#> GSM153275 1 0.1184 0.901 0.984 0.016
#> GSM153276 1 0.1414 0.901 0.980 0.020
#> GSM153277 1 0.0938 0.899 0.988 0.012
#> GSM153278 1 0.1843 0.901 0.972 0.028
#> GSM153279 1 0.1184 0.901 0.984 0.016
#> GSM153280 1 0.0672 0.899 0.992 0.008
#> GSM153281 1 0.0938 0.900 0.988 0.012
#> GSM153282 1 0.0672 0.899 0.992 0.008
#> GSM153283 1 0.1184 0.900 0.984 0.016
#> GSM153284 1 0.0938 0.900 0.988 0.012
#> GSM153285 1 0.0938 0.900 0.988 0.012
#> GSM153286 1 0.0938 0.901 0.988 0.012
#> GSM153287 1 0.0672 0.899 0.992 0.008
#> GSM153288 1 0.1184 0.901 0.984 0.016
#> GSM153289 1 0.1633 0.901 0.976 0.024
#> GSM153290 1 0.0938 0.900 0.988 0.012
#> GSM153291 1 0.1184 0.901 0.984 0.016
#> GSM153292 1 0.0938 0.899 0.988 0.012
#> GSM153293 1 0.1414 0.901 0.980 0.020
#> GSM153294 1 0.1184 0.902 0.984 0.016
#> GSM153295 1 0.1184 0.896 0.984 0.016
#> GSM153054 1 0.2236 0.898 0.964 0.036
#> GSM153055 1 0.0938 0.902 0.988 0.012
#> GSM153056 1 0.1633 0.902 0.976 0.024
#> GSM153057 1 0.3114 0.893 0.944 0.056
#> GSM153058 1 0.3431 0.887 0.936 0.064
#> GSM153059 1 0.3431 0.887 0.936 0.064
#> GSM153060 1 0.9044 0.404 0.680 0.320
#> GSM153061 1 0.8813 0.456 0.700 0.300
#> GSM153062 2 0.7056 0.000 0.192 0.808
#> GSM153063 1 0.3274 0.888 0.940 0.060
#> GSM153064 1 0.1414 0.900 0.980 0.020
#> GSM153065 1 0.4161 0.871 0.916 0.084
#> GSM153066 1 0.4022 0.874 0.920 0.080
#> GSM153067 1 0.0938 0.901 0.988 0.012
#> GSM153068 1 0.4939 0.833 0.892 0.108
#> GSM153069 1 0.0672 0.901 0.992 0.008
#> GSM153070 1 0.0938 0.902 0.988 0.012
#> GSM153071 1 0.2423 0.898 0.960 0.040
#> GSM153072 1 0.2043 0.897 0.968 0.032
#> GSM153073 1 0.0672 0.901 0.992 0.008
#> GSM153074 1 0.0672 0.900 0.992 0.008
#> GSM153075 1 0.1414 0.902 0.980 0.020
#> GSM153076 1 0.0672 0.901 0.992 0.008
#> GSM153077 1 0.0376 0.898 0.996 0.004
#> GSM153078 1 0.0672 0.900 0.992 0.008
#> GSM153079 1 0.1633 0.900 0.976 0.024
#> GSM153080 1 0.1843 0.900 0.972 0.028
#> GSM153081 1 0.0672 0.898 0.992 0.008
#> GSM153082 1 0.3114 0.890 0.944 0.056
#> GSM153083 1 0.1633 0.899 0.976 0.024
#> GSM153084 1 0.3879 0.875 0.924 0.076
#> GSM153085 1 0.2236 0.899 0.964 0.036
#> GSM153086 1 0.2043 0.899 0.968 0.032
#> GSM153087 1 0.0938 0.900 0.988 0.012
#> GSM153088 1 0.0672 0.901 0.992 0.008
#> GSM153089 1 0.3274 0.886 0.940 0.060
#> GSM153090 1 0.0000 0.899 1.000 0.000
#> GSM153091 1 0.1414 0.900 0.980 0.020
#> GSM153092 1 0.1414 0.901 0.980 0.020
#> GSM153093 1 0.0938 0.899 0.988 0.012
#> GSM153094 1 0.1633 0.900 0.976 0.024
#> GSM153095 1 0.1633 0.899 0.976 0.024
#> GSM153096 1 0.1414 0.900 0.980 0.020
#> GSM153097 1 0.2043 0.898 0.968 0.032
#> GSM153098 1 0.0672 0.899 0.992 0.008
#> GSM153099 1 0.1184 0.900 0.984 0.016
#> GSM153100 1 0.1633 0.902 0.976 0.024
#> GSM153101 1 0.3733 0.883 0.928 0.072
#> GSM153102 1 0.2423 0.897 0.960 0.040
#> GSM153103 1 0.2236 0.897 0.964 0.036
#> GSM153104 1 0.0672 0.899 0.992 0.008
#> GSM153106 1 0.1414 0.900 0.980 0.020
#> GSM153107 1 0.1414 0.900 0.980 0.020
#> GSM153108 1 0.0672 0.899 0.992 0.008
#> GSM153109 1 0.2423 0.896 0.960 0.040
#> GSM153110 1 0.1633 0.900 0.976 0.024
#> GSM153111 1 0.1843 0.900 0.972 0.028
#> GSM153112 1 0.1414 0.900 0.980 0.020
#> GSM153113 1 0.5737 0.825 0.864 0.136
#> GSM153114 1 0.1633 0.901 0.976 0.024
#> GSM187532 1 0.8661 0.652 0.712 0.288
#> GSM187533 1 0.8955 0.616 0.688 0.312
#> GSM187534 1 0.8861 0.626 0.696 0.304
#> GSM187535 1 0.3431 0.883 0.936 0.064
#> GSM152906 1 0.9209 0.579 0.664 0.336
#> GSM152907 1 0.9170 0.585 0.668 0.332
#> GSM152908 1 0.9209 0.579 0.664 0.336
#> GSM152909 1 0.9044 0.603 0.680 0.320
#> GSM152910 1 0.9209 0.579 0.664 0.336
#> GSM152911 1 0.9209 0.579 0.664 0.336
#> GSM152912 1 0.9209 0.579 0.664 0.336
#> GSM152913 1 0.9209 0.579 0.664 0.336
#> GSM152914 1 0.9209 0.579 0.664 0.336
#> GSM152915 1 0.9209 0.579 0.664 0.336
#> GSM152916 1 0.9209 0.579 0.664 0.336
#> GSM152917 1 0.9209 0.579 0.664 0.336
#> GSM152918 1 0.9209 0.579 0.664 0.336
#> GSM152919 1 0.9209 0.579 0.664 0.336
#> GSM152920 1 0.9209 0.579 0.664 0.336
#> GSM152921 1 0.9209 0.579 0.664 0.336
#> GSM152922 1 0.9209 0.579 0.664 0.336
#> GSM152923 1 0.9209 0.579 0.664 0.336
#> GSM152924 1 0.9170 0.585 0.668 0.332
#> GSM152925 1 0.9209 0.579 0.664 0.336
#> GSM152926 1 0.9209 0.579 0.664 0.336
#> GSM152927 1 0.9209 0.579 0.664 0.336
#> GSM152928 1 0.7745 0.727 0.772 0.228
#> GSM152929 1 0.9209 0.579 0.664 0.336
#> GSM152930 1 0.9209 0.579 0.664 0.336
cbind(get_classes(res, k = 3), get_membership(res, k = 3))
#> class entropy silhouette p1 p2 p3
#> GSM152839 1 0.1170 0.913 0.976 0.016 0.008
#> GSM152840 1 0.5637 0.653 0.788 0.172 0.040
#> GSM152841 1 0.1129 0.912 0.976 0.020 0.004
#> GSM152842 1 0.6422 0.386 0.660 0.016 0.324
#> GSM152843 1 0.2743 0.892 0.928 0.020 0.052
#> GSM152844 1 0.5455 0.635 0.788 0.184 0.028
#> GSM152845 1 0.6501 0.167 0.664 0.316 0.020
#> GSM152846 1 0.6542 0.482 0.736 0.204 0.060
#> GSM152847 1 0.3237 0.882 0.912 0.032 0.056
#> GSM152848 1 0.1337 0.914 0.972 0.012 0.016
#> GSM152849 1 0.2187 0.908 0.948 0.024 0.028
#> GSM152850 1 0.2176 0.910 0.948 0.032 0.020
#> GSM152851 1 0.1636 0.911 0.964 0.016 0.020
#> GSM152852 1 0.4861 0.647 0.800 0.192 0.008
#> GSM152853 1 0.5062 0.652 0.800 0.184 0.016
#> GSM152854 1 0.5277 0.668 0.796 0.180 0.024
#> GSM152855 1 0.1751 0.913 0.960 0.028 0.012
#> GSM153238 1 0.3983 0.834 0.884 0.068 0.048
#> GSM153239 1 0.5581 0.658 0.792 0.168 0.040
#> GSM153240 1 0.0983 0.913 0.980 0.016 0.004
#> GSM153241 1 0.3791 0.861 0.892 0.060 0.048
#> GSM153242 1 0.6295 0.465 0.728 0.236 0.036
#> GSM153243 1 0.2176 0.904 0.948 0.032 0.020
#> GSM153244 1 0.1585 0.913 0.964 0.028 0.008
#> GSM153245 1 0.6191 0.636 0.776 0.140 0.084
#> GSM153246 3 0.7697 0.473 0.272 0.084 0.644
#> GSM153247 1 0.3875 0.842 0.888 0.044 0.068
#> GSM153248 1 0.1482 0.913 0.968 0.020 0.012
#> GSM153249 1 0.0829 0.911 0.984 0.012 0.004
#> GSM153250 1 0.0661 0.913 0.988 0.008 0.004
#> GSM153251 1 0.5812 0.427 0.724 0.264 0.012
#> GSM153252 1 0.0747 0.912 0.984 0.016 0.000
#> GSM153253 1 0.1482 0.910 0.968 0.020 0.012
#> GSM153254 1 0.1999 0.902 0.952 0.036 0.012
#> GSM153255 1 0.0983 0.913 0.980 0.016 0.004
#> GSM153256 1 0.1015 0.913 0.980 0.012 0.008
#> GSM153257 1 0.0983 0.914 0.980 0.016 0.004
#> GSM153258 1 0.1620 0.916 0.964 0.024 0.012
#> GSM153259 1 0.1482 0.911 0.968 0.020 0.012
#> GSM153260 1 0.4206 0.819 0.872 0.088 0.040
#> GSM153261 1 0.2564 0.896 0.936 0.036 0.028
#> GSM153262 1 0.0747 0.912 0.984 0.016 0.000
#> GSM153263 1 0.0747 0.914 0.984 0.016 0.000
#> GSM153264 1 0.0848 0.914 0.984 0.008 0.008
#> GSM153265 1 0.1129 0.912 0.976 0.020 0.004
#> GSM153266 1 0.1315 0.915 0.972 0.020 0.008
#> GSM153267 1 0.0661 0.913 0.988 0.008 0.004
#> GSM153268 1 0.1999 0.900 0.952 0.036 0.012
#> GSM153269 1 0.0475 0.912 0.992 0.004 0.004
#> GSM153270 1 0.0892 0.913 0.980 0.020 0.000
#> GSM153271 1 0.0829 0.913 0.984 0.012 0.004
#> GSM153272 1 0.0983 0.913 0.980 0.016 0.004
#> GSM153273 1 0.1482 0.911 0.968 0.020 0.012
#> GSM153274 1 0.0848 0.912 0.984 0.008 0.008
#> GSM153275 1 0.1170 0.914 0.976 0.016 0.008
#> GSM153276 1 0.1482 0.915 0.968 0.020 0.012
#> GSM153277 1 0.0983 0.914 0.980 0.016 0.004
#> GSM153278 1 0.1636 0.914 0.964 0.020 0.016
#> GSM153279 1 0.1267 0.914 0.972 0.024 0.004
#> GSM153280 1 0.1267 0.912 0.972 0.024 0.004
#> GSM153281 1 0.1182 0.912 0.976 0.012 0.012
#> GSM153282 1 0.0983 0.911 0.980 0.016 0.004
#> GSM153283 1 0.1482 0.914 0.968 0.020 0.012
#> GSM153284 1 0.0592 0.912 0.988 0.012 0.000
#> GSM153285 1 0.1129 0.911 0.976 0.020 0.004
#> GSM153286 1 0.1170 0.915 0.976 0.016 0.008
#> GSM153287 1 0.0661 0.910 0.988 0.008 0.004
#> GSM153288 1 0.0983 0.913 0.980 0.016 0.004
#> GSM153289 1 0.1751 0.913 0.960 0.028 0.012
#> GSM153290 1 0.1525 0.911 0.964 0.032 0.004
#> GSM153291 1 0.0747 0.914 0.984 0.016 0.000
#> GSM153292 1 0.0829 0.911 0.984 0.012 0.004
#> GSM153293 1 0.1315 0.914 0.972 0.020 0.008
#> GSM153294 1 0.1482 0.914 0.968 0.020 0.012
#> GSM153295 1 0.2414 0.896 0.940 0.020 0.040
#> GSM153054 1 0.3481 0.868 0.904 0.052 0.044
#> GSM153055 1 0.0592 0.914 0.988 0.012 0.000
#> GSM153056 1 0.2564 0.902 0.936 0.028 0.036
#> GSM153057 1 0.3637 0.848 0.892 0.084 0.024
#> GSM153058 1 0.5036 0.687 0.808 0.172 0.020
#> GSM153059 1 0.3454 0.834 0.888 0.104 0.008
#> GSM153060 1 0.6678 -0.117 0.512 0.008 0.480
#> GSM153061 1 0.6713 0.128 0.572 0.012 0.416
#> GSM153062 3 0.6501 0.542 0.020 0.316 0.664
#> GSM153063 1 0.4742 0.783 0.848 0.104 0.048
#> GSM153064 1 0.1482 0.911 0.968 0.020 0.012
#> GSM153065 1 0.5618 0.671 0.796 0.156 0.048
#> GSM153066 1 0.4665 0.785 0.852 0.100 0.048
#> GSM153067 1 0.0829 0.913 0.984 0.012 0.004
#> GSM153068 1 0.6128 0.651 0.780 0.084 0.136
#> GSM153069 1 0.0661 0.912 0.988 0.008 0.004
#> GSM153070 1 0.1129 0.915 0.976 0.020 0.004
#> GSM153071 1 0.2383 0.901 0.940 0.044 0.016
#> GSM153072 1 0.2297 0.903 0.944 0.020 0.036
#> GSM153073 1 0.0892 0.914 0.980 0.020 0.000
#> GSM153074 1 0.0661 0.912 0.988 0.008 0.004
#> GSM153075 1 0.1399 0.915 0.968 0.028 0.004
#> GSM153076 1 0.0747 0.914 0.984 0.016 0.000
#> GSM153077 1 0.0983 0.914 0.980 0.004 0.016
#> GSM153078 1 0.1267 0.912 0.972 0.004 0.024
#> GSM153079 1 0.1620 0.912 0.964 0.024 0.012
#> GSM153080 1 0.1832 0.908 0.956 0.036 0.008
#> GSM153081 1 0.1015 0.913 0.980 0.008 0.012
#> GSM153082 1 0.2599 0.895 0.932 0.052 0.016
#> GSM153083 1 0.1620 0.911 0.964 0.024 0.012
#> GSM153084 1 0.3528 0.844 0.892 0.092 0.016
#> GSM153085 1 0.2313 0.904 0.944 0.032 0.024
#> GSM153086 1 0.1751 0.911 0.960 0.028 0.012
#> GSM153087 1 0.1170 0.915 0.976 0.016 0.008
#> GSM153088 1 0.0592 0.914 0.988 0.012 0.000
#> GSM153089 1 0.4802 0.718 0.824 0.156 0.020
#> GSM153090 1 0.0237 0.912 0.996 0.004 0.000
#> GSM153091 1 0.1315 0.912 0.972 0.020 0.008
#> GSM153092 1 0.1482 0.914 0.968 0.020 0.012
#> GSM153093 1 0.0829 0.911 0.984 0.012 0.004
#> GSM153094 1 0.1774 0.911 0.960 0.024 0.016
#> GSM153095 1 0.2313 0.907 0.944 0.032 0.024
#> GSM153096 1 0.1636 0.912 0.964 0.020 0.016
#> GSM153097 1 0.1905 0.908 0.956 0.028 0.016
#> GSM153098 1 0.0829 0.912 0.984 0.004 0.012
#> GSM153099 1 0.1031 0.913 0.976 0.024 0.000
#> GSM153100 1 0.1620 0.914 0.964 0.024 0.012
#> GSM153101 1 0.3850 0.847 0.884 0.088 0.028
#> GSM153102 1 0.2116 0.903 0.948 0.040 0.012
#> GSM153103 1 0.1999 0.905 0.952 0.036 0.012
#> GSM153104 1 0.0983 0.911 0.980 0.016 0.004
#> GSM153106 1 0.1620 0.912 0.964 0.024 0.012
#> GSM153107 1 0.1620 0.912 0.964 0.024 0.012
#> GSM153108 1 0.1315 0.915 0.972 0.020 0.008
#> GSM153109 1 0.2269 0.903 0.944 0.040 0.016
#> GSM153110 1 0.1774 0.911 0.960 0.024 0.016
#> GSM153111 1 0.1751 0.911 0.960 0.028 0.012
#> GSM153112 1 0.1482 0.911 0.968 0.020 0.012
#> GSM153113 1 0.4953 0.692 0.808 0.176 0.016
#> GSM153114 1 0.1751 0.913 0.960 0.028 0.012
#> GSM187532 2 0.6373 0.861 0.408 0.588 0.004
#> GSM187533 2 0.6026 0.920 0.376 0.624 0.000
#> GSM187534 2 0.6062 0.907 0.384 0.616 0.000
#> GSM187535 1 0.2939 0.879 0.916 0.072 0.012
#> GSM152906 2 0.5810 0.974 0.336 0.664 0.000
#> GSM152907 2 0.5882 0.960 0.348 0.652 0.000
#> GSM152908 2 0.5810 0.974 0.336 0.664 0.000
#> GSM152909 2 0.6126 0.954 0.352 0.644 0.004
#> GSM152910 2 0.5810 0.974 0.336 0.664 0.000
#> GSM152911 2 0.5810 0.974 0.336 0.664 0.000
#> GSM152912 2 0.5810 0.974 0.336 0.664 0.000
#> GSM152913 2 0.5810 0.974 0.336 0.664 0.000
#> GSM152914 2 0.5810 0.974 0.336 0.664 0.000
#> GSM152915 2 0.5810 0.974 0.336 0.664 0.000
#> GSM152916 2 0.5810 0.974 0.336 0.664 0.000
#> GSM152917 2 0.5810 0.974 0.336 0.664 0.000
#> GSM152918 2 0.5810 0.974 0.336 0.664 0.000
#> GSM152919 2 0.5810 0.974 0.336 0.664 0.000
#> GSM152920 2 0.5810 0.974 0.336 0.664 0.000
#> GSM152921 2 0.5810 0.974 0.336 0.664 0.000
#> GSM152922 2 0.5810 0.974 0.336 0.664 0.000
#> GSM152923 2 0.5810 0.974 0.336 0.664 0.000
#> GSM152924 2 0.5835 0.970 0.340 0.660 0.000
#> GSM152925 2 0.5835 0.970 0.340 0.660 0.000
#> GSM152926 2 0.5810 0.974 0.336 0.664 0.000
#> GSM152927 2 0.5810 0.974 0.336 0.664 0.000
#> GSM152928 2 0.6954 0.671 0.484 0.500 0.016
#> GSM152929 2 0.5810 0.974 0.336 0.664 0.000
#> GSM152930 2 0.5810 0.974 0.336 0.664 0.000
cbind(get_classes(res, k = 4), get_membership(res, k = 4))
#> class entropy silhouette p1 p2 p3 p4
#> GSM152839 1 0.1593 0.91040 0.956 0.024 0.004 0.016
#> GSM152840 1 0.6072 0.57846 0.664 0.272 0.020 0.044
#> GSM152841 1 0.1356 0.90752 0.960 0.032 0.000 0.008
#> GSM152842 1 0.7457 0.49534 0.612 0.048 0.120 0.220
#> GSM152843 1 0.2936 0.89341 0.908 0.036 0.032 0.024
#> GSM152844 1 0.5852 0.56402 0.664 0.284 0.012 0.040
#> GSM152845 1 0.6619 0.10593 0.492 0.440 0.008 0.060
#> GSM152846 1 0.6979 0.39895 0.576 0.316 0.016 0.092
#> GSM152847 1 0.3900 0.86248 0.860 0.060 0.016 0.064
#> GSM152848 1 0.1406 0.91067 0.960 0.024 0.000 0.016
#> GSM152849 1 0.2870 0.89485 0.908 0.044 0.012 0.036
#> GSM152850 1 0.2814 0.89939 0.908 0.052 0.008 0.032
#> GSM152851 1 0.2310 0.90641 0.932 0.032 0.016 0.020
#> GSM152852 1 0.5745 0.55546 0.656 0.296 0.004 0.044
#> GSM152853 1 0.5594 0.57978 0.672 0.284 0.004 0.040
#> GSM152854 1 0.6067 0.60475 0.668 0.264 0.016 0.052
#> GSM152855 1 0.1284 0.90841 0.964 0.024 0.000 0.012
#> GSM153238 1 0.4412 0.83177 0.828 0.104 0.016 0.052
#> GSM153239 1 0.5982 0.59259 0.668 0.268 0.012 0.052
#> GSM153240 1 0.1543 0.90923 0.956 0.032 0.004 0.008
#> GSM153241 1 0.4462 0.84986 0.828 0.100 0.020 0.052
#> GSM153242 1 0.6722 0.38758 0.576 0.344 0.020 0.060
#> GSM153243 1 0.2775 0.89837 0.912 0.044 0.012 0.032
#> GSM153244 1 0.1888 0.90897 0.940 0.044 0.000 0.016
#> GSM153245 1 0.6687 0.56363 0.648 0.240 0.024 0.088
#> GSM153246 4 0.1970 0.00000 0.008 0.000 0.060 0.932
#> GSM153247 1 0.4227 0.84533 0.844 0.076 0.020 0.060
#> GSM153248 1 0.1677 0.90766 0.948 0.040 0.000 0.012
#> GSM153249 1 0.1042 0.90811 0.972 0.020 0.000 0.008
#> GSM153250 1 0.1042 0.90963 0.972 0.020 0.000 0.008
#> GSM153251 1 0.6109 0.33929 0.568 0.388 0.008 0.036
#> GSM153252 1 0.1151 0.90947 0.968 0.024 0.000 0.008
#> GSM153253 1 0.1958 0.90437 0.944 0.028 0.008 0.020
#> GSM153254 1 0.3120 0.89544 0.896 0.056 0.012 0.036
#> GSM153255 1 0.1004 0.90909 0.972 0.024 0.000 0.004
#> GSM153256 1 0.1004 0.90973 0.972 0.024 0.000 0.004
#> GSM153257 1 0.1356 0.91027 0.960 0.032 0.000 0.008
#> GSM153258 1 0.1356 0.91153 0.960 0.032 0.000 0.008
#> GSM153259 1 0.1798 0.90505 0.944 0.040 0.000 0.016
#> GSM153260 1 0.4879 0.81094 0.796 0.124 0.012 0.068
#> GSM153261 1 0.3424 0.87869 0.880 0.072 0.012 0.036
#> GSM153262 1 0.1042 0.90957 0.972 0.020 0.000 0.008
#> GSM153263 1 0.1593 0.91097 0.956 0.024 0.004 0.016
#> GSM153264 1 0.1247 0.91008 0.968 0.012 0.004 0.016
#> GSM153265 1 0.1209 0.90805 0.964 0.032 0.000 0.004
#> GSM153266 1 0.1174 0.91065 0.968 0.020 0.000 0.012
#> GSM153267 1 0.0817 0.90848 0.976 0.024 0.000 0.000
#> GSM153268 1 0.2587 0.88990 0.916 0.056 0.008 0.020
#> GSM153269 1 0.0895 0.90841 0.976 0.020 0.000 0.004
#> GSM153270 1 0.1452 0.90929 0.956 0.036 0.000 0.008
#> GSM153271 1 0.1004 0.91006 0.972 0.024 0.000 0.004
#> GSM153272 1 0.1151 0.90871 0.968 0.024 0.000 0.008
#> GSM153273 1 0.1798 0.90471 0.944 0.040 0.000 0.016
#> GSM153274 1 0.1042 0.90898 0.972 0.020 0.000 0.008
#> GSM153275 1 0.0921 0.90950 0.972 0.028 0.000 0.000
#> GSM153276 1 0.1297 0.91045 0.964 0.020 0.000 0.016
#> GSM153277 1 0.0895 0.90953 0.976 0.020 0.000 0.004
#> GSM153278 1 0.2499 0.90358 0.924 0.032 0.012 0.032
#> GSM153279 1 0.1639 0.91066 0.952 0.036 0.004 0.008
#> GSM153280 1 0.1209 0.90825 0.964 0.032 0.000 0.004
#> GSM153281 1 0.1484 0.90723 0.960 0.020 0.004 0.016
#> GSM153282 1 0.1284 0.90762 0.964 0.024 0.000 0.012
#> GSM153283 1 0.1411 0.91095 0.960 0.020 0.000 0.020
#> GSM153284 1 0.1174 0.90917 0.968 0.020 0.000 0.012
#> GSM153285 1 0.1388 0.90746 0.960 0.028 0.000 0.012
#> GSM153286 1 0.1305 0.91067 0.960 0.036 0.000 0.004
#> GSM153287 1 0.0927 0.90666 0.976 0.016 0.000 0.008
#> GSM153288 1 0.1151 0.90871 0.968 0.024 0.000 0.008
#> GSM153289 1 0.1284 0.90841 0.964 0.024 0.000 0.012
#> GSM153290 1 0.1545 0.90741 0.952 0.040 0.000 0.008
#> GSM153291 1 0.1151 0.91002 0.968 0.024 0.000 0.008
#> GSM153292 1 0.1042 0.90796 0.972 0.020 0.000 0.008
#> GSM153293 1 0.1022 0.90995 0.968 0.032 0.000 0.000
#> GSM153294 1 0.1488 0.90869 0.956 0.032 0.000 0.012
#> GSM153295 1 0.2466 0.89319 0.916 0.028 0.000 0.056
#> GSM153054 1 0.3798 0.86472 0.860 0.072 0.008 0.060
#> GSM153055 1 0.1471 0.91117 0.960 0.024 0.004 0.012
#> GSM153056 1 0.3135 0.89265 0.896 0.048 0.012 0.044
#> GSM153057 1 0.3647 0.86099 0.860 0.096 0.004 0.040
#> GSM153058 1 0.5542 0.62086 0.684 0.276 0.012 0.028
#> GSM153059 1 0.3869 0.84402 0.844 0.120 0.008 0.028
#> GSM153060 1 0.8919 0.00908 0.464 0.084 0.232 0.220
#> GSM153061 1 0.8578 0.20482 0.516 0.080 0.192 0.212
#> GSM153062 3 0.0376 0.00000 0.004 0.004 0.992 0.000
#> GSM153063 1 0.5351 0.75650 0.756 0.172 0.016 0.056
#> GSM153064 1 0.1888 0.90666 0.940 0.044 0.000 0.016
#> GSM153065 1 0.5833 0.67593 0.712 0.204 0.012 0.072
#> GSM153066 1 0.5052 0.77468 0.772 0.160 0.008 0.060
#> GSM153067 1 0.1109 0.90906 0.968 0.028 0.000 0.004
#> GSM153068 1 0.6636 0.68859 0.704 0.124 0.060 0.112
#> GSM153069 1 0.1151 0.90827 0.968 0.024 0.000 0.008
#> GSM153070 1 0.1706 0.91185 0.948 0.036 0.000 0.016
#> GSM153071 1 0.2613 0.90008 0.916 0.052 0.008 0.024
#> GSM153072 1 0.2676 0.90018 0.916 0.028 0.012 0.044
#> GSM153073 1 0.1545 0.91175 0.952 0.040 0.000 0.008
#> GSM153074 1 0.1151 0.90796 0.968 0.024 0.000 0.008
#> GSM153075 1 0.1706 0.91213 0.948 0.036 0.000 0.016
#> GSM153076 1 0.1443 0.91060 0.960 0.028 0.004 0.008
#> GSM153077 1 0.1362 0.90980 0.964 0.012 0.004 0.020
#> GSM153078 1 0.2089 0.90622 0.940 0.020 0.012 0.028
#> GSM153079 1 0.1624 0.90779 0.952 0.028 0.000 0.020
#> GSM153080 1 0.2231 0.90823 0.932 0.044 0.012 0.012
#> GSM153081 1 0.1059 0.90920 0.972 0.016 0.000 0.012
#> GSM153082 1 0.2563 0.89260 0.908 0.072 0.000 0.020
#> GSM153083 1 0.1706 0.90564 0.948 0.036 0.000 0.016
#> GSM153084 1 0.3781 0.84459 0.844 0.124 0.004 0.028
#> GSM153085 1 0.2589 0.90142 0.912 0.044 0.000 0.044
#> GSM153086 1 0.2099 0.90418 0.936 0.040 0.004 0.020
#> GSM153087 1 0.1151 0.91047 0.968 0.024 0.000 0.008
#> GSM153088 1 0.1191 0.90993 0.968 0.024 0.004 0.004
#> GSM153089 1 0.5871 0.65258 0.684 0.252 0.012 0.052
#> GSM153090 1 0.1362 0.91035 0.964 0.020 0.004 0.012
#> GSM153091 1 0.1706 0.90784 0.948 0.036 0.000 0.016
#> GSM153092 1 0.1510 0.91068 0.956 0.028 0.000 0.016
#> GSM153093 1 0.1042 0.90711 0.972 0.020 0.000 0.008
#> GSM153094 1 0.1913 0.90566 0.940 0.040 0.000 0.020
#> GSM153095 1 0.2282 0.90267 0.924 0.052 0.000 0.024
#> GSM153096 1 0.1545 0.90628 0.952 0.040 0.000 0.008
#> GSM153097 1 0.2111 0.90331 0.932 0.044 0.000 0.024
#> GSM153098 1 0.0895 0.90801 0.976 0.020 0.000 0.004
#> GSM153099 1 0.1305 0.90982 0.960 0.036 0.000 0.004
#> GSM153100 1 0.1706 0.91081 0.948 0.036 0.000 0.016
#> GSM153101 1 0.3612 0.85872 0.856 0.100 0.000 0.044
#> GSM153102 1 0.2669 0.89749 0.912 0.052 0.004 0.032
#> GSM153103 1 0.2669 0.89723 0.912 0.052 0.004 0.032
#> GSM153104 1 0.1151 0.90675 0.968 0.024 0.000 0.008
#> GSM153106 1 0.1388 0.90765 0.960 0.028 0.000 0.012
#> GSM153107 1 0.1388 0.90765 0.960 0.028 0.000 0.012
#> GSM153108 1 0.1209 0.91151 0.964 0.032 0.000 0.004
#> GSM153109 1 0.2282 0.90057 0.924 0.052 0.000 0.024
#> GSM153110 1 0.1767 0.90477 0.944 0.044 0.000 0.012
#> GSM153111 1 0.1913 0.90484 0.940 0.040 0.000 0.020
#> GSM153112 1 0.1798 0.90505 0.944 0.040 0.000 0.016
#> GSM153113 1 0.4361 0.74827 0.772 0.208 0.000 0.020
#> GSM153114 1 0.1284 0.90841 0.964 0.024 0.000 0.012
#> GSM187532 2 0.4018 0.83868 0.168 0.812 0.004 0.016
#> GSM187533 2 0.3280 0.91320 0.124 0.860 0.000 0.016
#> GSM187534 2 0.3390 0.90129 0.132 0.852 0.000 0.016
#> GSM187535 1 0.2271 0.89609 0.916 0.076 0.000 0.008
#> GSM152906 2 0.2216 0.97003 0.092 0.908 0.000 0.000
#> GSM152907 2 0.2408 0.95898 0.104 0.896 0.000 0.000
#> GSM152908 2 0.2216 0.97003 0.092 0.908 0.000 0.000
#> GSM152909 2 0.2928 0.94753 0.108 0.880 0.000 0.012
#> GSM152910 2 0.2216 0.97003 0.092 0.908 0.000 0.000
#> GSM152911 2 0.2281 0.96939 0.096 0.904 0.000 0.000
#> GSM152912 2 0.2216 0.97003 0.092 0.908 0.000 0.000
#> GSM152913 2 0.2216 0.97003 0.092 0.908 0.000 0.000
#> GSM152914 2 0.2281 0.96939 0.096 0.904 0.000 0.000
#> GSM152915 2 0.2281 0.96939 0.096 0.904 0.000 0.000
#> GSM152916 2 0.2216 0.97003 0.092 0.908 0.000 0.000
#> GSM152917 2 0.2281 0.96939 0.096 0.904 0.000 0.000
#> GSM152918 2 0.2281 0.96939 0.096 0.904 0.000 0.000
#> GSM152919 2 0.2281 0.96939 0.096 0.904 0.000 0.000
#> GSM152920 2 0.2216 0.97003 0.092 0.908 0.000 0.000
#> GSM152921 2 0.2216 0.97003 0.092 0.908 0.000 0.000
#> GSM152922 2 0.2216 0.97003 0.092 0.908 0.000 0.000
#> GSM152923 2 0.2216 0.97003 0.092 0.908 0.000 0.000
#> GSM152924 2 0.2281 0.96830 0.096 0.904 0.000 0.000
#> GSM152925 2 0.2345 0.96460 0.100 0.900 0.000 0.000
#> GSM152926 2 0.2216 0.97003 0.092 0.908 0.000 0.000
#> GSM152927 2 0.2216 0.97003 0.092 0.908 0.000 0.000
#> GSM152928 2 0.4922 0.70819 0.228 0.736 0.000 0.036
#> GSM152929 2 0.2216 0.97003 0.092 0.908 0.000 0.000
#> GSM152930 2 0.2216 0.97003 0.092 0.908 0.000 0.000
cbind(get_classes(res, k = 5), get_membership(res, k = 5))
#> class entropy silhouette p1 p2 p3 p4 p5
#> GSM152839 1 0.2130 0.8425 0.920 0.012 0.060 0.004 0.004
#> GSM152840 1 0.5811 -0.2443 0.516 0.052 0.416 0.012 0.004
#> GSM152841 1 0.1557 0.8388 0.940 0.008 0.052 0.000 0.000
#> GSM152842 1 0.7192 -0.1512 0.568 0.008 0.152 0.072 0.200
#> GSM152843 1 0.3241 0.8020 0.872 0.012 0.076 0.012 0.028
#> GSM152844 1 0.5843 -0.3620 0.476 0.052 0.456 0.012 0.004
#> GSM152845 3 0.6433 0.4092 0.340 0.188 0.472 0.000 0.000
#> GSM152846 1 0.7141 -0.4331 0.448 0.092 0.400 0.016 0.044
#> GSM152847 1 0.4217 0.6489 0.772 0.012 0.188 0.004 0.024
#> GSM152848 1 0.2095 0.8408 0.920 0.012 0.060 0.000 0.008
#> GSM152849 1 0.3250 0.7948 0.856 0.008 0.112 0.012 0.012
#> GSM152850 1 0.3471 0.7804 0.840 0.020 0.124 0.004 0.012
#> GSM152851 1 0.2197 0.8337 0.916 0.004 0.064 0.004 0.012
#> GSM152852 1 0.5501 -0.2993 0.492 0.064 0.444 0.000 0.000
#> GSM152853 1 0.5493 -0.3148 0.488 0.052 0.456 0.004 0.000
#> GSM152854 1 0.5559 -0.0928 0.548 0.052 0.392 0.004 0.004
#> GSM152855 1 0.1300 0.8447 0.956 0.016 0.028 0.000 0.000
#> GSM153238 1 0.5195 0.5866 0.740 0.080 0.144 0.004 0.032
#> GSM153239 1 0.6403 0.0190 0.576 0.080 0.304 0.008 0.032
#> GSM153240 1 0.1372 0.8473 0.956 0.016 0.024 0.004 0.000
#> GSM153241 1 0.4544 0.6548 0.764 0.020 0.180 0.008 0.028
#> GSM153242 1 0.6890 -0.3947 0.460 0.144 0.372 0.008 0.016
#> GSM153243 1 0.3275 0.8077 0.864 0.024 0.092 0.012 0.008
#> GSM153244 1 0.2012 0.8445 0.920 0.020 0.060 0.000 0.000
#> GSM153245 1 0.6817 -0.1507 0.544 0.048 0.320 0.016 0.072
#> GSM153246 5 0.0162 0.0000 0.000 0.000 0.000 0.004 0.996
#> GSM153247 1 0.4549 0.6786 0.796 0.056 0.108 0.008 0.032
#> GSM153248 1 0.1469 0.8440 0.948 0.016 0.036 0.000 0.000
#> GSM153249 1 0.0898 0.8443 0.972 0.008 0.020 0.000 0.000
#> GSM153250 1 0.1195 0.8484 0.960 0.012 0.028 0.000 0.000
#> GSM153251 1 0.7030 -0.4169 0.456 0.228 0.300 0.004 0.012
#> GSM153252 1 0.0992 0.8465 0.968 0.008 0.024 0.000 0.000
#> GSM153253 1 0.2212 0.8221 0.908 0.004 0.080 0.004 0.004
#> GSM153254 1 0.3416 0.8062 0.860 0.028 0.088 0.012 0.012
#> GSM153255 1 0.0992 0.8461 0.968 0.008 0.024 0.000 0.000
#> GSM153256 1 0.0898 0.8467 0.972 0.008 0.020 0.000 0.000
#> GSM153257 1 0.1386 0.8483 0.952 0.016 0.032 0.000 0.000
#> GSM153258 1 0.1630 0.8514 0.944 0.016 0.036 0.000 0.004
#> GSM153259 1 0.1872 0.8380 0.928 0.020 0.052 0.000 0.000
#> GSM153260 1 0.5116 0.5305 0.712 0.048 0.216 0.008 0.016
#> GSM153261 1 0.3934 0.7516 0.828 0.036 0.108 0.008 0.020
#> GSM153262 1 0.0955 0.8459 0.968 0.004 0.028 0.000 0.000
#> GSM153263 1 0.1547 0.8494 0.948 0.016 0.032 0.004 0.000
#> GSM153264 1 0.1517 0.8490 0.952 0.012 0.028 0.004 0.004
#> GSM153265 1 0.1168 0.8442 0.960 0.008 0.032 0.000 0.000
#> GSM153266 1 0.1356 0.8491 0.956 0.012 0.028 0.000 0.004
#> GSM153267 1 0.0912 0.8464 0.972 0.012 0.016 0.000 0.000
#> GSM153268 1 0.2676 0.7937 0.880 0.008 0.104 0.004 0.004
#> GSM153269 1 0.1082 0.8471 0.964 0.008 0.028 0.000 0.000
#> GSM153270 1 0.1399 0.8490 0.952 0.020 0.028 0.000 0.000
#> GSM153271 1 0.1117 0.8492 0.964 0.016 0.020 0.000 0.000
#> GSM153272 1 0.0898 0.8451 0.972 0.008 0.020 0.000 0.000
#> GSM153273 1 0.1965 0.8366 0.924 0.024 0.052 0.000 0.000
#> GSM153274 1 0.1251 0.8495 0.956 0.008 0.036 0.000 0.000
#> GSM153275 1 0.1012 0.8472 0.968 0.012 0.020 0.000 0.000
#> GSM153276 1 0.1518 0.8477 0.944 0.004 0.048 0.000 0.004
#> GSM153277 1 0.0955 0.8473 0.968 0.004 0.028 0.000 0.000
#> GSM153278 1 0.2728 0.8283 0.896 0.016 0.068 0.012 0.008
#> GSM153279 1 0.1605 0.8483 0.944 0.012 0.040 0.004 0.000
#> GSM153280 1 0.1205 0.8448 0.956 0.004 0.040 0.000 0.000
#> GSM153281 1 0.1365 0.8423 0.952 0.004 0.040 0.000 0.004
#> GSM153282 1 0.1124 0.8423 0.960 0.004 0.036 0.000 0.000
#> GSM153283 1 0.1442 0.8491 0.952 0.012 0.032 0.000 0.004
#> GSM153284 1 0.1041 0.8464 0.964 0.004 0.032 0.000 0.000
#> GSM153285 1 0.1205 0.8413 0.956 0.004 0.040 0.000 0.000
#> GSM153286 1 0.1106 0.8476 0.964 0.012 0.024 0.000 0.000
#> GSM153287 1 0.0865 0.8426 0.972 0.004 0.024 0.000 0.000
#> GSM153288 1 0.0898 0.8451 0.972 0.008 0.020 0.000 0.000
#> GSM153289 1 0.1300 0.8447 0.956 0.016 0.028 0.000 0.000
#> GSM153290 1 0.1331 0.8439 0.952 0.008 0.040 0.000 0.000
#> GSM153291 1 0.0912 0.8469 0.972 0.012 0.016 0.000 0.000
#> GSM153292 1 0.0898 0.8440 0.972 0.008 0.020 0.000 0.000
#> GSM153293 1 0.0912 0.8465 0.972 0.012 0.016 0.000 0.000
#> GSM153294 1 0.1331 0.8456 0.952 0.008 0.040 0.000 0.000
#> GSM153295 1 0.2846 0.8069 0.884 0.012 0.076 0.000 0.028
#> GSM153054 1 0.4345 0.7173 0.804 0.056 0.108 0.004 0.028
#> GSM153055 1 0.1630 0.8503 0.944 0.016 0.036 0.004 0.000
#> GSM153056 1 0.3464 0.7925 0.856 0.020 0.088 0.004 0.032
#> GSM153057 1 0.4151 0.7404 0.816 0.040 0.112 0.008 0.024
#> GSM153058 1 0.6169 0.1689 0.608 0.116 0.256 0.008 0.012
#> GSM153059 1 0.4264 0.7119 0.796 0.072 0.120 0.008 0.004
#> GSM153060 3 0.8319 0.4332 0.288 0.008 0.392 0.128 0.184
#> GSM153061 3 0.7996 0.5551 0.348 0.008 0.388 0.088 0.168
#> GSM153062 4 0.0290 0.0000 0.000 0.000 0.000 0.992 0.008
#> GSM153063 1 0.5837 0.3546 0.652 0.060 0.252 0.016 0.020
#> GSM153064 1 0.1872 0.8408 0.928 0.020 0.052 0.000 0.000
#> GSM153065 1 0.6478 0.1521 0.612 0.116 0.232 0.012 0.028
#> GSM153066 1 0.5429 0.5253 0.724 0.124 0.104 0.000 0.048
#> GSM153067 1 0.0912 0.8452 0.972 0.016 0.012 0.000 0.000
#> GSM153068 1 0.6786 0.1650 0.620 0.060 0.216 0.028 0.076
#> GSM153069 1 0.1082 0.8457 0.964 0.008 0.028 0.000 0.000
#> GSM153070 1 0.1710 0.8502 0.940 0.016 0.040 0.000 0.004
#> GSM153071 1 0.2901 0.8236 0.888 0.044 0.048 0.000 0.020
#> GSM153072 1 0.2727 0.8260 0.896 0.024 0.056 0.000 0.024
#> GSM153073 1 0.1399 0.8503 0.952 0.020 0.028 0.000 0.000
#> GSM153074 1 0.0912 0.8439 0.972 0.012 0.016 0.000 0.000
#> GSM153075 1 0.1701 0.8509 0.936 0.016 0.048 0.000 0.000
#> GSM153076 1 0.1377 0.8486 0.956 0.020 0.020 0.004 0.000
#> GSM153077 1 0.1455 0.8491 0.952 0.008 0.032 0.000 0.008
#> GSM153078 1 0.2447 0.8323 0.908 0.008 0.064 0.012 0.008
#> GSM153079 1 0.1725 0.8436 0.936 0.020 0.044 0.000 0.000
#> GSM153080 1 0.2579 0.8354 0.900 0.028 0.064 0.004 0.004
#> GSM153081 1 0.1484 0.8484 0.944 0.008 0.048 0.000 0.000
#> GSM153082 1 0.2987 0.8085 0.880 0.056 0.052 0.000 0.012
#> GSM153083 1 0.1943 0.8373 0.924 0.020 0.056 0.000 0.000
#> GSM153084 1 0.4658 0.6793 0.776 0.092 0.112 0.004 0.016
#> GSM153085 1 0.2958 0.8223 0.880 0.024 0.076 0.000 0.020
#> GSM153086 1 0.2304 0.8304 0.908 0.020 0.068 0.004 0.000
#> GSM153087 1 0.1173 0.8479 0.964 0.012 0.020 0.000 0.004
#> GSM153088 1 0.1267 0.8488 0.960 0.012 0.024 0.004 0.000
#> GSM153089 1 0.6226 0.0934 0.580 0.148 0.260 0.012 0.000
#> GSM153090 1 0.1173 0.8486 0.964 0.012 0.020 0.004 0.000
#> GSM153091 1 0.1774 0.8440 0.932 0.016 0.052 0.000 0.000
#> GSM153092 1 0.1628 0.8500 0.936 0.008 0.056 0.000 0.000
#> GSM153093 1 0.0798 0.8427 0.976 0.008 0.016 0.000 0.000
#> GSM153094 1 0.2103 0.8406 0.920 0.020 0.056 0.000 0.004
#> GSM153095 1 0.2784 0.8189 0.888 0.028 0.072 0.000 0.012
#> GSM153096 1 0.1648 0.8413 0.940 0.020 0.040 0.000 0.000
#> GSM153097 1 0.2331 0.8319 0.908 0.024 0.064 0.000 0.004
#> GSM153098 1 0.0912 0.8456 0.972 0.012 0.016 0.000 0.000
#> GSM153099 1 0.1281 0.8487 0.956 0.012 0.032 0.000 0.000
#> GSM153100 1 0.1628 0.8489 0.936 0.008 0.056 0.000 0.000
#> GSM153101 1 0.3922 0.7405 0.820 0.076 0.092 0.000 0.012
#> GSM153102 1 0.2829 0.8188 0.884 0.028 0.080 0.004 0.004
#> GSM153103 1 0.2977 0.8155 0.880 0.032 0.076 0.004 0.008
#> GSM153104 1 0.1041 0.8412 0.964 0.004 0.032 0.000 0.000
#> GSM153106 1 0.1399 0.8434 0.952 0.020 0.028 0.000 0.000
#> GSM153107 1 0.1399 0.8434 0.952 0.020 0.028 0.000 0.000
#> GSM153108 1 0.1082 0.8498 0.964 0.008 0.028 0.000 0.000
#> GSM153109 1 0.2548 0.8247 0.896 0.028 0.072 0.000 0.004
#> GSM153110 1 0.1893 0.8373 0.928 0.024 0.048 0.000 0.000
#> GSM153111 1 0.2144 0.8325 0.912 0.020 0.068 0.000 0.000
#> GSM153112 1 0.1800 0.8387 0.932 0.020 0.048 0.000 0.000
#> GSM153113 1 0.4510 0.5901 0.752 0.184 0.056 0.000 0.008
#> GSM153114 1 0.1300 0.8447 0.956 0.016 0.028 0.000 0.000
#> GSM187532 2 0.2813 0.8484 0.064 0.884 0.048 0.004 0.000
#> GSM187533 2 0.2142 0.8965 0.048 0.920 0.028 0.000 0.004
#> GSM187534 2 0.2299 0.8873 0.052 0.912 0.032 0.000 0.004
#> GSM187535 1 0.2236 0.8268 0.908 0.068 0.024 0.000 0.000
#> GSM152906 2 0.0404 0.9670 0.012 0.988 0.000 0.000 0.000
#> GSM152907 2 0.0992 0.9507 0.024 0.968 0.008 0.000 0.000
#> GSM152908 2 0.0290 0.9632 0.008 0.992 0.000 0.000 0.000
#> GSM152909 2 0.1525 0.9391 0.012 0.948 0.036 0.000 0.004
#> GSM152910 2 0.0290 0.9632 0.008 0.992 0.000 0.000 0.000
#> GSM152911 2 0.0510 0.9663 0.016 0.984 0.000 0.000 0.000
#> GSM152912 2 0.0290 0.9632 0.008 0.992 0.000 0.000 0.000
#> GSM152913 2 0.0290 0.9632 0.008 0.992 0.000 0.000 0.000
#> GSM152914 2 0.0510 0.9663 0.016 0.984 0.000 0.000 0.000
#> GSM152915 2 0.0510 0.9663 0.016 0.984 0.000 0.000 0.000
#> GSM152916 2 0.0404 0.9670 0.012 0.988 0.000 0.000 0.000
#> GSM152917 2 0.0510 0.9663 0.016 0.984 0.000 0.000 0.000
#> GSM152918 2 0.0510 0.9663 0.016 0.984 0.000 0.000 0.000
#> GSM152919 2 0.0510 0.9663 0.016 0.984 0.000 0.000 0.000
#> GSM152920 2 0.0290 0.9632 0.008 0.992 0.000 0.000 0.000
#> GSM152921 2 0.0290 0.9632 0.008 0.992 0.000 0.000 0.000
#> GSM152922 2 0.0290 0.9632 0.008 0.992 0.000 0.000 0.000
#> GSM152923 2 0.0404 0.9670 0.012 0.988 0.000 0.000 0.000
#> GSM152924 2 0.0510 0.9654 0.016 0.984 0.000 0.000 0.000
#> GSM152925 2 0.0609 0.9613 0.020 0.980 0.000 0.000 0.000
#> GSM152926 2 0.0404 0.9670 0.012 0.988 0.000 0.000 0.000
#> GSM152927 2 0.0404 0.9670 0.012 0.988 0.000 0.000 0.000
#> GSM152928 2 0.3895 0.6922 0.132 0.812 0.044 0.000 0.012
#> GSM152929 2 0.0404 0.9670 0.012 0.988 0.000 0.000 0.000
#> GSM152930 2 0.0404 0.9670 0.012 0.988 0.000 0.000 0.000
cbind(get_classes(res, k = 6), get_membership(res, k = 6))
#> class entropy silhouette p1 p2 p3 p4 p5 p6
#> GSM152839 1 0.2383 0.850 0.880 0.000 0.024 0.096 0.000 0.000
#> GSM152840 4 0.4866 0.660 0.336 0.000 0.028 0.612 0.008 0.016
#> GSM152841 1 0.2121 0.836 0.892 0.000 0.012 0.096 0.000 0.000
#> GSM152842 1 0.6863 -0.144 0.504 0.000 0.304 0.068 0.044 0.080
#> GSM152843 1 0.3698 0.784 0.812 0.000 0.064 0.108 0.008 0.008
#> GSM152844 4 0.4268 0.619 0.240 0.000 0.016 0.716 0.008 0.020
#> GSM152845 4 0.5783 0.272 0.132 0.080 0.052 0.692 0.008 0.036
#> GSM152846 4 0.5430 0.545 0.216 0.020 0.072 0.668 0.008 0.016
#> GSM152847 1 0.4903 0.580 0.704 0.000 0.116 0.160 0.004 0.016
#> GSM152848 1 0.2480 0.844 0.872 0.000 0.024 0.104 0.000 0.000
#> GSM152849 1 0.3953 0.769 0.784 0.004 0.064 0.140 0.004 0.004
#> GSM152850 1 0.4022 0.749 0.772 0.004 0.056 0.160 0.004 0.004
#> GSM152851 1 0.2728 0.826 0.864 0.000 0.032 0.100 0.000 0.004
#> GSM152852 4 0.4144 0.647 0.252 0.000 0.020 0.712 0.004 0.012
#> GSM152853 4 0.3809 0.632 0.240 0.000 0.024 0.732 0.000 0.004
#> GSM152854 4 0.5385 0.594 0.404 0.004 0.056 0.520 0.004 0.012
#> GSM152855 1 0.1851 0.853 0.924 0.004 0.012 0.056 0.004 0.000
#> GSM153238 1 0.5926 0.501 0.664 0.052 0.056 0.184 0.012 0.032
#> GSM153239 4 0.5902 0.608 0.404 0.020 0.064 0.492 0.004 0.016
#> GSM153240 1 0.1411 0.860 0.936 0.000 0.004 0.060 0.000 0.000
#> GSM153241 1 0.5040 0.466 0.656 0.000 0.092 0.236 0.000 0.016
#> GSM153242 4 0.6502 0.574 0.264 0.060 0.092 0.560 0.004 0.020
#> GSM153243 1 0.3583 0.797 0.820 0.016 0.032 0.124 0.004 0.004
#> GSM153244 1 0.2361 0.847 0.880 0.000 0.012 0.104 0.004 0.000
#> GSM153245 4 0.5897 0.605 0.388 0.000 0.084 0.492 0.004 0.032
#> GSM153246 6 0.1075 0.000 0.000 0.000 0.048 0.000 0.000 0.952
#> GSM153247 1 0.5064 0.625 0.736 0.040 0.092 0.112 0.004 0.016
#> GSM153248 1 0.1699 0.856 0.928 0.004 0.004 0.060 0.004 0.000
#> GSM153249 1 0.1524 0.855 0.932 0.000 0.008 0.060 0.000 0.000
#> GSM153250 1 0.1265 0.861 0.948 0.000 0.008 0.044 0.000 0.000
#> GSM153251 4 0.6982 0.526 0.328 0.148 0.064 0.444 0.000 0.016
#> GSM153252 1 0.1444 0.855 0.928 0.000 0.000 0.072 0.000 0.000
#> GSM153253 1 0.2809 0.803 0.848 0.000 0.020 0.128 0.000 0.004
#> GSM153254 1 0.3560 0.807 0.824 0.012 0.032 0.120 0.004 0.008
#> GSM153255 1 0.1265 0.857 0.948 0.000 0.008 0.044 0.000 0.000
#> GSM153256 1 0.1124 0.858 0.956 0.000 0.008 0.036 0.000 0.000
#> GSM153257 1 0.1829 0.857 0.920 0.000 0.012 0.064 0.004 0.000
#> GSM153258 1 0.1672 0.866 0.932 0.004 0.016 0.048 0.000 0.000
#> GSM153259 1 0.1988 0.850 0.912 0.004 0.008 0.072 0.004 0.000
#> GSM153260 1 0.5785 0.194 0.584 0.016 0.092 0.288 0.000 0.020
#> GSM153261 1 0.4445 0.714 0.764 0.024 0.036 0.156 0.008 0.012
#> GSM153262 1 0.1531 0.859 0.928 0.000 0.004 0.068 0.000 0.000
#> GSM153263 1 0.1826 0.865 0.924 0.004 0.020 0.052 0.000 0.000
#> GSM153264 1 0.1528 0.862 0.936 0.000 0.016 0.048 0.000 0.000
#> GSM153265 1 0.1951 0.844 0.908 0.000 0.016 0.076 0.000 0.000
#> GSM153266 1 0.1500 0.863 0.936 0.000 0.012 0.052 0.000 0.000
#> GSM153267 1 0.0937 0.860 0.960 0.000 0.000 0.040 0.000 0.000
#> GSM153268 1 0.3158 0.751 0.812 0.000 0.020 0.164 0.000 0.004
#> GSM153269 1 0.1049 0.859 0.960 0.000 0.008 0.032 0.000 0.000
#> GSM153270 1 0.2056 0.864 0.904 0.000 0.012 0.080 0.004 0.000
#> GSM153271 1 0.1082 0.862 0.956 0.000 0.004 0.040 0.000 0.000
#> GSM153272 1 0.1082 0.857 0.956 0.000 0.004 0.040 0.000 0.000
#> GSM153273 1 0.2099 0.845 0.904 0.004 0.008 0.080 0.004 0.000
#> GSM153274 1 0.1584 0.863 0.928 0.000 0.008 0.064 0.000 0.000
#> GSM153275 1 0.1219 0.861 0.948 0.004 0.000 0.048 0.000 0.000
#> GSM153276 1 0.1719 0.858 0.924 0.000 0.016 0.060 0.000 0.000
#> GSM153277 1 0.1196 0.861 0.952 0.000 0.008 0.040 0.000 0.000
#> GSM153278 1 0.3152 0.823 0.844 0.004 0.032 0.112 0.004 0.004
#> GSM153279 1 0.1967 0.856 0.904 0.000 0.012 0.084 0.000 0.000
#> GSM153280 1 0.1895 0.848 0.912 0.000 0.016 0.072 0.000 0.000
#> GSM153281 1 0.2002 0.845 0.908 0.000 0.012 0.076 0.000 0.004
#> GSM153282 1 0.1643 0.848 0.924 0.000 0.008 0.068 0.000 0.000
#> GSM153283 1 0.1511 0.862 0.940 0.000 0.012 0.044 0.000 0.004
#> GSM153284 1 0.1349 0.858 0.940 0.000 0.004 0.056 0.000 0.000
#> GSM153285 1 0.1866 0.842 0.908 0.000 0.008 0.084 0.000 0.000
#> GSM153286 1 0.1285 0.860 0.944 0.000 0.004 0.052 0.000 0.000
#> GSM153287 1 0.1398 0.853 0.940 0.000 0.008 0.052 0.000 0.000
#> GSM153288 1 0.1124 0.857 0.956 0.000 0.008 0.036 0.000 0.000
#> GSM153289 1 0.1851 0.853 0.924 0.004 0.012 0.056 0.004 0.000
#> GSM153290 1 0.1829 0.852 0.920 0.004 0.012 0.064 0.000 0.000
#> GSM153291 1 0.1367 0.861 0.944 0.000 0.012 0.044 0.000 0.000
#> GSM153292 1 0.1524 0.851 0.932 0.000 0.008 0.060 0.000 0.000
#> GSM153293 1 0.1141 0.862 0.948 0.000 0.000 0.052 0.000 0.000
#> GSM153294 1 0.1732 0.860 0.920 0.000 0.004 0.072 0.004 0.000
#> GSM153295 1 0.3128 0.819 0.844 0.000 0.052 0.096 0.000 0.008
#> GSM153054 1 0.4363 0.724 0.772 0.040 0.040 0.136 0.000 0.012
#> GSM153055 1 0.1838 0.865 0.916 0.000 0.016 0.068 0.000 0.000
#> GSM153056 1 0.3719 0.770 0.800 0.000 0.064 0.124 0.000 0.012
#> GSM153057 1 0.4110 0.670 0.764 0.008 0.052 0.168 0.000 0.008
#> GSM153058 1 0.6044 -0.501 0.468 0.036 0.072 0.412 0.000 0.012
#> GSM153059 1 0.4611 0.659 0.744 0.036 0.048 0.164 0.004 0.004
#> GSM153060 3 0.4278 -0.191 0.044 0.000 0.784 0.004 0.084 0.084
#> GSM153061 3 0.6243 0.290 0.188 0.000 0.628 0.056 0.056 0.072
#> GSM153062 5 0.0363 0.000 0.000 0.000 0.012 0.000 0.988 0.000
#> GSM153063 1 0.5430 -0.120 0.556 0.008 0.080 0.348 0.000 0.008
#> GSM153064 1 0.1932 0.855 0.912 0.004 0.004 0.076 0.004 0.000
#> GSM153065 1 0.7061 -0.387 0.456 0.068 0.096 0.344 0.004 0.032
#> GSM153066 1 0.6179 0.421 0.648 0.100 0.052 0.160 0.008 0.032
#> GSM153067 1 0.1364 0.861 0.944 0.004 0.004 0.048 0.000 0.000
#> GSM153068 1 0.6877 -0.118 0.524 0.032 0.176 0.232 0.008 0.028
#> GSM153069 1 0.1219 0.856 0.948 0.000 0.004 0.048 0.000 0.000
#> GSM153070 1 0.1807 0.865 0.920 0.000 0.020 0.060 0.000 0.000
#> GSM153071 1 0.3246 0.836 0.860 0.024 0.020 0.076 0.004 0.016
#> GSM153072 1 0.3059 0.838 0.868 0.016 0.032 0.068 0.000 0.016
#> GSM153073 1 0.1413 0.864 0.948 0.004 0.008 0.036 0.004 0.000
#> GSM153074 1 0.1152 0.856 0.952 0.000 0.004 0.044 0.000 0.000
#> GSM153075 1 0.2207 0.862 0.900 0.008 0.016 0.076 0.000 0.000
#> GSM153076 1 0.1440 0.862 0.944 0.004 0.004 0.044 0.004 0.000
#> GSM153077 1 0.1624 0.862 0.936 0.000 0.020 0.040 0.000 0.004
#> GSM153078 1 0.3029 0.831 0.852 0.000 0.032 0.104 0.004 0.008
#> GSM153079 1 0.2032 0.851 0.912 0.004 0.012 0.068 0.004 0.000
#> GSM153080 1 0.2830 0.849 0.868 0.012 0.024 0.092 0.004 0.000
#> GSM153081 1 0.1901 0.857 0.912 0.000 0.008 0.076 0.004 0.000
#> GSM153082 1 0.3192 0.820 0.852 0.028 0.016 0.096 0.004 0.004
#> GSM153083 1 0.2253 0.845 0.896 0.004 0.012 0.084 0.004 0.000
#> GSM153084 1 0.5091 0.640 0.716 0.080 0.024 0.160 0.004 0.016
#> GSM153085 1 0.3377 0.820 0.836 0.008 0.024 0.116 0.008 0.008
#> GSM153086 1 0.2662 0.832 0.868 0.008 0.012 0.108 0.004 0.000
#> GSM153087 1 0.1615 0.858 0.928 0.000 0.004 0.064 0.000 0.004
#> GSM153088 1 0.1152 0.862 0.952 0.000 0.004 0.044 0.000 0.000
#> GSM153089 1 0.6685 -0.423 0.460 0.084 0.072 0.368 0.004 0.012
#> GSM153090 1 0.1082 0.863 0.956 0.000 0.004 0.040 0.000 0.000
#> GSM153091 1 0.1699 0.858 0.928 0.004 0.004 0.060 0.004 0.000
#> GSM153092 1 0.1745 0.865 0.920 0.000 0.012 0.068 0.000 0.000
#> GSM153093 1 0.1411 0.856 0.936 0.000 0.004 0.060 0.000 0.000
#> GSM153094 1 0.2182 0.851 0.904 0.004 0.016 0.072 0.004 0.000
#> GSM153095 1 0.3328 0.821 0.840 0.020 0.020 0.108 0.000 0.012
#> GSM153096 1 0.1812 0.852 0.924 0.004 0.008 0.060 0.004 0.000
#> GSM153097 1 0.2417 0.840 0.888 0.008 0.012 0.088 0.004 0.000
#> GSM153098 1 0.1082 0.864 0.956 0.000 0.004 0.040 0.000 0.000
#> GSM153099 1 0.1644 0.865 0.920 0.000 0.004 0.076 0.000 0.000
#> GSM153100 1 0.1913 0.864 0.908 0.000 0.012 0.080 0.000 0.000
#> GSM153101 1 0.4374 0.730 0.768 0.044 0.028 0.148 0.004 0.008
#> GSM153102 1 0.3032 0.830 0.852 0.016 0.020 0.108 0.004 0.000
#> GSM153103 1 0.3123 0.818 0.844 0.016 0.020 0.116 0.004 0.000
#> GSM153104 1 0.1584 0.847 0.928 0.000 0.008 0.064 0.000 0.000
#> GSM153106 1 0.1788 0.852 0.928 0.004 0.012 0.052 0.004 0.000
#> GSM153107 1 0.1788 0.852 0.928 0.004 0.012 0.052 0.004 0.000
#> GSM153108 1 0.1644 0.864 0.932 0.004 0.012 0.052 0.000 0.000
#> GSM153109 1 0.2846 0.836 0.864 0.012 0.020 0.100 0.004 0.000
#> GSM153110 1 0.2099 0.844 0.904 0.004 0.008 0.080 0.004 0.000
#> GSM153111 1 0.2417 0.838 0.888 0.008 0.012 0.088 0.004 0.000
#> GSM153112 1 0.1872 0.853 0.920 0.004 0.008 0.064 0.004 0.000
#> GSM153113 1 0.4938 0.580 0.708 0.160 0.024 0.104 0.000 0.004
#> GSM153114 1 0.1851 0.853 0.924 0.004 0.012 0.056 0.004 0.000
#> GSM187532 2 0.2769 0.859 0.036 0.880 0.032 0.052 0.000 0.000
#> GSM187533 2 0.2244 0.894 0.036 0.912 0.016 0.032 0.000 0.004
#> GSM187534 2 0.2388 0.884 0.040 0.904 0.016 0.036 0.000 0.004
#> GSM187535 1 0.2662 0.839 0.884 0.056 0.008 0.048 0.004 0.000
#> GSM152906 2 0.0291 0.965 0.004 0.992 0.000 0.004 0.000 0.000
#> GSM152907 2 0.0820 0.948 0.016 0.972 0.000 0.012 0.000 0.000
#> GSM152908 2 0.0000 0.962 0.000 1.000 0.000 0.000 0.000 0.000
#> GSM152909 2 0.1630 0.930 0.000 0.940 0.020 0.024 0.000 0.016
#> GSM152910 2 0.0146 0.962 0.000 0.996 0.000 0.000 0.000 0.004
#> GSM152911 2 0.0436 0.965 0.004 0.988 0.004 0.004 0.000 0.000
#> GSM152912 2 0.0000 0.962 0.000 1.000 0.000 0.000 0.000 0.000
#> GSM152913 2 0.0146 0.962 0.000 0.996 0.000 0.004 0.000 0.000
#> GSM152914 2 0.0436 0.965 0.004 0.988 0.004 0.004 0.000 0.000
#> GSM152915 2 0.0436 0.965 0.004 0.988 0.004 0.004 0.000 0.000
#> GSM152916 2 0.0582 0.963 0.004 0.984 0.000 0.004 0.004 0.004
#> GSM152917 2 0.0436 0.965 0.004 0.988 0.004 0.004 0.000 0.000
#> GSM152918 2 0.0436 0.965 0.004 0.988 0.004 0.004 0.000 0.000
#> GSM152919 2 0.0436 0.965 0.004 0.988 0.004 0.004 0.000 0.000
#> GSM152920 2 0.0000 0.962 0.000 1.000 0.000 0.000 0.000 0.000
#> GSM152921 2 0.0000 0.962 0.000 1.000 0.000 0.000 0.000 0.000
#> GSM152922 2 0.0000 0.962 0.000 1.000 0.000 0.000 0.000 0.000
#> GSM152923 2 0.0291 0.965 0.004 0.992 0.000 0.004 0.000 0.000
#> GSM152924 2 0.0696 0.961 0.004 0.980 0.000 0.008 0.004 0.004
#> GSM152925 2 0.0912 0.959 0.008 0.972 0.000 0.012 0.004 0.004
#> GSM152926 2 0.0291 0.965 0.004 0.992 0.000 0.004 0.000 0.000
#> GSM152927 2 0.0696 0.962 0.004 0.980 0.000 0.008 0.004 0.004
#> GSM152928 2 0.4038 0.695 0.104 0.800 0.024 0.064 0.004 0.004
#> GSM152929 2 0.0291 0.965 0.004 0.992 0.000 0.004 0.000 0.000
#> GSM152930 2 0.0291 0.965 0.004 0.992 0.000 0.004 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 tissue(p) k
#> MAD:hclust 160 NA 2
#> MAD:hclust 156 2.63e-27 3
#> MAD:hclust 155 3.15e-29 4
#> MAD:hclust 144 4.87e-25 5
#> MAD:hclust 150 2.74e-32 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 12013 rows and 164 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 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 0.490 0.860 0.892 0.3277 0.707 0.707
#> 3 3 0.902 0.913 0.954 0.7788 0.712 0.592
#> 4 4 0.635 0.663 0.789 0.1860 0.852 0.649
#> 5 5 0.592 0.658 0.783 0.0830 0.876 0.613
#> 6 6 0.650 0.687 0.770 0.0433 0.978 0.908
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
#> GSM152839 1 0.8016 0.773 0.756 0.244
#> GSM152840 1 0.8267 0.765 0.740 0.260
#> GSM152841 1 0.0000 0.892 1.000 0.000
#> GSM152842 1 0.8267 0.765 0.740 0.260
#> GSM152843 1 0.8267 0.765 0.740 0.260
#> GSM152844 1 0.8267 0.765 0.740 0.260
#> GSM152845 1 0.8267 0.765 0.740 0.260
#> GSM152846 1 0.8267 0.765 0.740 0.260
#> GSM152847 1 0.8267 0.765 0.740 0.260
#> GSM152848 1 0.2603 0.879 0.956 0.044
#> GSM152849 1 0.8267 0.765 0.740 0.260
#> GSM152850 1 0.8267 0.765 0.740 0.260
#> GSM152851 1 0.7883 0.779 0.764 0.236
#> GSM152852 1 0.8267 0.765 0.740 0.260
#> GSM152853 1 0.8267 0.765 0.740 0.260
#> GSM152854 1 0.8267 0.765 0.740 0.260
#> GSM152855 1 0.0000 0.892 1.000 0.000
#> GSM153238 1 0.8267 0.765 0.740 0.260
#> GSM153239 1 0.8267 0.765 0.740 0.260
#> GSM153240 1 0.0000 0.892 1.000 0.000
#> GSM153241 1 0.8267 0.765 0.740 0.260
#> GSM153242 1 0.8267 0.765 0.740 0.260
#> GSM153243 1 0.8267 0.765 0.740 0.260
#> GSM153244 1 0.3431 0.869 0.936 0.064
#> GSM153245 1 0.8267 0.765 0.740 0.260
#> GSM153246 1 0.8267 0.765 0.740 0.260
#> GSM153247 1 0.8267 0.765 0.740 0.260
#> GSM153248 1 0.0000 0.892 1.000 0.000
#> GSM153249 1 0.0000 0.892 1.000 0.000
#> GSM153250 1 0.0000 0.892 1.000 0.000
#> GSM153251 1 0.8267 0.765 0.740 0.260
#> GSM153252 1 0.0376 0.892 0.996 0.004
#> GSM153253 1 0.1184 0.889 0.984 0.016
#> GSM153254 1 0.7139 0.801 0.804 0.196
#> GSM153255 1 0.0000 0.892 1.000 0.000
#> GSM153256 1 0.0000 0.892 1.000 0.000
#> GSM153257 1 0.0000 0.892 1.000 0.000
#> GSM153258 1 0.0000 0.892 1.000 0.000
#> GSM153259 1 0.0000 0.892 1.000 0.000
#> GSM153260 1 0.8267 0.765 0.740 0.260
#> GSM153261 1 0.8267 0.765 0.740 0.260
#> GSM153262 1 0.0376 0.892 0.996 0.004
#> GSM153263 1 0.0000 0.892 1.000 0.000
#> GSM153264 1 0.0000 0.892 1.000 0.000
#> GSM153265 1 0.0376 0.892 0.996 0.004
#> GSM153266 1 0.0000 0.892 1.000 0.000
#> GSM153267 1 0.0000 0.892 1.000 0.000
#> GSM153268 1 0.5842 0.831 0.860 0.140
#> GSM153269 1 0.0000 0.892 1.000 0.000
#> GSM153270 1 0.0000 0.892 1.000 0.000
#> GSM153271 1 0.0000 0.892 1.000 0.000
#> GSM153272 1 0.0000 0.892 1.000 0.000
#> GSM153273 1 0.0000 0.892 1.000 0.000
#> GSM153274 1 0.0000 0.892 1.000 0.000
#> GSM153275 1 0.0000 0.892 1.000 0.000
#> GSM153276 1 0.0000 0.892 1.000 0.000
#> GSM153277 1 0.0376 0.892 0.996 0.004
#> GSM153278 1 0.8207 0.767 0.744 0.256
#> GSM153279 1 0.2778 0.878 0.952 0.048
#> GSM153280 1 0.0376 0.892 0.996 0.004
#> GSM153281 1 0.0672 0.891 0.992 0.008
#> GSM153282 1 0.1184 0.889 0.984 0.016
#> GSM153283 1 0.0000 0.892 1.000 0.000
#> GSM153284 1 0.0000 0.892 1.000 0.000
#> GSM153285 1 0.0000 0.892 1.000 0.000
#> GSM153286 1 0.0000 0.892 1.000 0.000
#> GSM153287 1 0.0000 0.892 1.000 0.000
#> GSM153288 1 0.0000 0.892 1.000 0.000
#> GSM153289 1 0.0000 0.892 1.000 0.000
#> GSM153290 1 0.1414 0.888 0.980 0.020
#> GSM153291 1 0.0000 0.892 1.000 0.000
#> GSM153292 1 0.0000 0.892 1.000 0.000
#> GSM153293 1 0.0000 0.892 1.000 0.000
#> GSM153294 1 0.0000 0.892 1.000 0.000
#> GSM153295 1 0.1184 0.889 0.984 0.016
#> GSM153054 1 0.2423 0.880 0.960 0.040
#> GSM153055 1 0.0000 0.892 1.000 0.000
#> GSM153056 1 0.8267 0.765 0.740 0.260
#> GSM153057 1 0.8267 0.765 0.740 0.260
#> GSM153058 1 0.8267 0.765 0.740 0.260
#> GSM153059 1 0.8207 0.767 0.744 0.256
#> GSM153060 1 0.8267 0.765 0.740 0.260
#> GSM153061 1 0.8267 0.765 0.740 0.260
#> GSM153062 1 0.8267 0.765 0.740 0.260
#> GSM153063 1 0.8267 0.765 0.740 0.260
#> GSM153064 1 0.0000 0.892 1.000 0.000
#> GSM153065 1 0.8267 0.765 0.740 0.260
#> GSM153066 1 0.9795 0.517 0.584 0.416
#> GSM153067 1 0.0000 0.892 1.000 0.000
#> GSM153068 1 0.8267 0.765 0.740 0.260
#> GSM153069 1 0.0000 0.892 1.000 0.000
#> GSM153070 1 0.0000 0.892 1.000 0.000
#> GSM153071 1 0.4815 0.851 0.896 0.104
#> GSM153072 1 0.2423 0.881 0.960 0.040
#> GSM153073 1 0.0000 0.892 1.000 0.000
#> GSM153074 1 0.0000 0.892 1.000 0.000
#> GSM153075 1 0.1184 0.889 0.984 0.016
#> GSM153076 1 0.0000 0.892 1.000 0.000
#> GSM153077 1 0.0000 0.892 1.000 0.000
#> GSM153078 1 0.4690 0.853 0.900 0.100
#> GSM153079 1 0.0000 0.892 1.000 0.000
#> GSM153080 1 0.8267 0.765 0.740 0.260
#> GSM153081 1 0.0000 0.892 1.000 0.000
#> GSM153082 1 0.4562 0.784 0.904 0.096
#> GSM153083 1 0.0000 0.892 1.000 0.000
#> GSM153084 1 0.2423 0.880 0.960 0.040
#> GSM153085 1 0.1633 0.886 0.976 0.024
#> GSM153086 1 0.0938 0.890 0.988 0.012
#> GSM153087 1 0.0000 0.892 1.000 0.000
#> GSM153088 1 0.0000 0.892 1.000 0.000
#> GSM153089 1 0.8267 0.765 0.740 0.260
#> GSM153090 1 0.0000 0.892 1.000 0.000
#> GSM153091 1 0.0000 0.892 1.000 0.000
#> GSM153092 1 0.0000 0.892 1.000 0.000
#> GSM153093 1 0.0000 0.892 1.000 0.000
#> GSM153094 1 0.0000 0.892 1.000 0.000
#> GSM153095 1 0.0938 0.890 0.988 0.012
#> GSM153096 1 0.0000 0.892 1.000 0.000
#> GSM153097 1 0.0000 0.892 1.000 0.000
#> GSM153098 1 0.0000 0.892 1.000 0.000
#> GSM153099 1 0.0000 0.892 1.000 0.000
#> GSM153100 1 0.0000 0.892 1.000 0.000
#> GSM153101 1 0.0376 0.892 0.996 0.004
#> GSM153102 1 0.0672 0.891 0.992 0.008
#> GSM153103 1 0.0938 0.890 0.988 0.012
#> GSM153104 1 0.1184 0.889 0.984 0.016
#> GSM153106 1 0.0000 0.892 1.000 0.000
#> GSM153107 1 0.0000 0.892 1.000 0.000
#> GSM153108 1 0.0000 0.892 1.000 0.000
#> GSM153109 1 0.0000 0.892 1.000 0.000
#> GSM153110 1 0.0000 0.892 1.000 0.000
#> GSM153111 1 0.0000 0.892 1.000 0.000
#> GSM153112 1 0.0000 0.892 1.000 0.000
#> GSM153113 1 0.5842 0.715 0.860 0.140
#> GSM153114 1 0.0000 0.892 1.000 0.000
#> GSM187532 2 0.0938 0.744 0.012 0.988
#> GSM187533 2 0.8081 0.936 0.248 0.752
#> GSM187534 2 0.8267 0.940 0.260 0.740
#> GSM187535 2 0.8327 0.936 0.264 0.736
#> GSM152906 2 0.8267 0.940 0.260 0.740
#> GSM152907 2 0.8267 0.940 0.260 0.740
#> GSM152908 2 0.8267 0.940 0.260 0.740
#> GSM152909 2 0.1414 0.752 0.020 0.980
#> GSM152910 2 0.5737 0.858 0.136 0.864
#> GSM152911 2 0.8267 0.940 0.260 0.740
#> GSM152912 2 0.8267 0.940 0.260 0.740
#> GSM152913 2 0.1633 0.756 0.024 0.976
#> GSM152914 2 0.8267 0.940 0.260 0.740
#> GSM152915 2 0.8267 0.940 0.260 0.740
#> GSM152916 2 0.7453 0.920 0.212 0.788
#> GSM152917 2 0.8267 0.940 0.260 0.740
#> GSM152918 2 0.8267 0.940 0.260 0.740
#> GSM152919 2 0.8267 0.940 0.260 0.740
#> GSM152920 2 0.8267 0.940 0.260 0.740
#> GSM152921 2 0.8267 0.940 0.260 0.740
#> GSM152922 2 0.7376 0.917 0.208 0.792
#> GSM152923 2 0.8267 0.940 0.260 0.740
#> GSM152924 2 0.7674 0.926 0.224 0.776
#> GSM152925 2 0.7453 0.920 0.212 0.788
#> GSM152926 2 0.8267 0.940 0.260 0.740
#> GSM152927 2 0.4431 0.819 0.092 0.908
#> GSM152928 2 0.7139 0.909 0.196 0.804
#> GSM152929 2 0.8267 0.940 0.260 0.740
#> GSM152930 2 0.8267 0.940 0.260 0.740
cbind(get_classes(res, k = 3), get_membership(res, k = 3))
#> class entropy silhouette p1 p2 p3
#> GSM152839 3 0.4842 0.728 0.224 0.000 0.776
#> GSM152840 3 0.1529 0.947 0.040 0.000 0.960
#> GSM152841 1 0.0424 0.951 0.992 0.000 0.008
#> GSM152842 3 0.1163 0.955 0.028 0.000 0.972
#> GSM152843 3 0.1163 0.955 0.028 0.000 0.972
#> GSM152844 3 0.1163 0.954 0.028 0.000 0.972
#> GSM152845 3 0.1031 0.951 0.024 0.000 0.976
#> GSM152846 3 0.1163 0.954 0.028 0.000 0.972
#> GSM152847 3 0.1163 0.955 0.028 0.000 0.972
#> GSM152848 1 0.2066 0.914 0.940 0.000 0.060
#> GSM152849 3 0.1163 0.955 0.028 0.000 0.972
#> GSM152850 3 0.1163 0.955 0.028 0.000 0.972
#> GSM152851 3 0.3192 0.872 0.112 0.000 0.888
#> GSM152852 3 0.1163 0.954 0.028 0.000 0.972
#> GSM152853 3 0.1163 0.954 0.028 0.000 0.972
#> GSM152854 3 0.1163 0.954 0.028 0.000 0.972
#> GSM152855 1 0.0424 0.951 0.992 0.000 0.008
#> GSM153238 3 0.1163 0.955 0.028 0.000 0.972
#> GSM153239 3 0.1163 0.954 0.028 0.000 0.972
#> GSM153240 1 0.0424 0.951 0.992 0.000 0.008
#> GSM153241 3 0.1163 0.955 0.028 0.000 0.972
#> GSM153242 3 0.1163 0.954 0.028 0.000 0.972
#> GSM153243 3 0.1163 0.955 0.028 0.000 0.972
#> GSM153244 1 0.6180 0.286 0.584 0.000 0.416
#> GSM153245 3 0.1163 0.954 0.028 0.000 0.972
#> GSM153246 3 0.1585 0.954 0.028 0.008 0.964
#> GSM153247 3 0.1163 0.955 0.028 0.000 0.972
#> GSM153248 1 0.0424 0.950 0.992 0.000 0.008
#> GSM153249 1 0.0424 0.951 0.992 0.000 0.008
#> GSM153250 1 0.0424 0.950 0.992 0.000 0.008
#> GSM153251 3 0.1163 0.954 0.028 0.000 0.972
#> GSM153252 1 0.0424 0.951 0.992 0.000 0.008
#> GSM153253 1 0.0424 0.951 0.992 0.000 0.008
#> GSM153254 3 0.4235 0.788 0.176 0.000 0.824
#> GSM153255 1 0.0424 0.951 0.992 0.000 0.008
#> GSM153256 1 0.0237 0.951 0.996 0.000 0.004
#> GSM153257 1 0.0424 0.951 0.992 0.000 0.008
#> GSM153258 1 0.0424 0.950 0.992 0.000 0.008
#> GSM153259 1 0.0424 0.950 0.992 0.000 0.008
#> GSM153260 3 0.1163 0.955 0.028 0.000 0.972
#> GSM153261 3 0.1163 0.955 0.028 0.000 0.972
#> GSM153262 1 0.0424 0.951 0.992 0.000 0.008
#> GSM153263 1 0.0424 0.950 0.992 0.000 0.008
#> GSM153264 1 0.0424 0.950 0.992 0.000 0.008
#> GSM153265 1 0.0424 0.951 0.992 0.000 0.008
#> GSM153266 1 0.0424 0.950 0.992 0.000 0.008
#> GSM153267 1 0.0237 0.951 0.996 0.000 0.004
#> GSM153268 1 0.2165 0.911 0.936 0.000 0.064
#> GSM153269 1 0.0237 0.951 0.996 0.000 0.004
#> GSM153270 1 0.0424 0.951 0.992 0.000 0.008
#> GSM153271 1 0.0424 0.950 0.992 0.000 0.008
#> GSM153272 1 0.0424 0.951 0.992 0.000 0.008
#> GSM153273 1 0.0424 0.950 0.992 0.000 0.008
#> GSM153274 1 0.0237 0.951 0.996 0.000 0.004
#> GSM153275 1 0.0424 0.951 0.992 0.000 0.008
#> GSM153276 1 0.0424 0.951 0.992 0.000 0.008
#> GSM153277 1 0.0424 0.951 0.992 0.000 0.008
#> GSM153278 3 0.2878 0.890 0.096 0.000 0.904
#> GSM153279 1 0.3686 0.835 0.860 0.000 0.140
#> GSM153280 1 0.0424 0.951 0.992 0.000 0.008
#> GSM153281 1 0.0424 0.951 0.992 0.000 0.008
#> GSM153282 1 0.0424 0.951 0.992 0.000 0.008
#> GSM153283 1 0.0424 0.950 0.992 0.000 0.008
#> GSM153284 1 0.0424 0.951 0.992 0.000 0.008
#> GSM153285 1 0.0424 0.951 0.992 0.000 0.008
#> GSM153286 1 0.0424 0.951 0.992 0.000 0.008
#> GSM153287 1 0.0424 0.951 0.992 0.000 0.008
#> GSM153288 1 0.0424 0.951 0.992 0.000 0.008
#> GSM153289 1 0.0000 0.951 1.000 0.000 0.000
#> GSM153290 1 0.0424 0.951 0.992 0.000 0.008
#> GSM153291 1 0.0424 0.951 0.992 0.000 0.008
#> GSM153292 1 0.0424 0.951 0.992 0.000 0.008
#> GSM153293 1 0.0000 0.951 1.000 0.000 0.000
#> GSM153294 1 0.0424 0.950 0.992 0.000 0.008
#> GSM153295 1 0.0237 0.951 0.996 0.000 0.004
#> GSM153054 1 0.5650 0.567 0.688 0.000 0.312
#> GSM153055 1 0.0424 0.951 0.992 0.000 0.008
#> GSM153056 3 0.1163 0.955 0.028 0.000 0.972
#> GSM153057 3 0.1163 0.955 0.028 0.000 0.972
#> GSM153058 3 0.1163 0.954 0.028 0.000 0.972
#> GSM153059 3 0.1163 0.955 0.028 0.000 0.972
#> GSM153060 3 0.1267 0.954 0.024 0.004 0.972
#> GSM153061 3 0.1399 0.954 0.028 0.004 0.968
#> GSM153062 3 0.1453 0.954 0.024 0.008 0.968
#> GSM153063 3 0.1163 0.954 0.028 0.000 0.972
#> GSM153064 1 0.0424 0.950 0.992 0.000 0.008
#> GSM153065 3 0.1163 0.955 0.028 0.000 0.972
#> GSM153066 3 0.1620 0.948 0.024 0.012 0.964
#> GSM153067 1 0.0424 0.951 0.992 0.000 0.008
#> GSM153068 3 0.1163 0.955 0.028 0.000 0.972
#> GSM153069 1 0.0424 0.951 0.992 0.000 0.008
#> GSM153070 1 0.0424 0.950 0.992 0.000 0.008
#> GSM153071 3 0.6286 0.113 0.464 0.000 0.536
#> GSM153072 1 0.6215 0.271 0.572 0.000 0.428
#> GSM153073 1 0.0424 0.950 0.992 0.000 0.008
#> GSM153074 1 0.0424 0.951 0.992 0.000 0.008
#> GSM153075 1 0.2261 0.908 0.932 0.000 0.068
#> GSM153076 1 0.0424 0.950 0.992 0.000 0.008
#> GSM153077 1 0.0424 0.950 0.992 0.000 0.008
#> GSM153078 1 0.6295 0.111 0.528 0.000 0.472
#> GSM153079 1 0.0592 0.949 0.988 0.000 0.012
#> GSM153080 3 0.3340 0.862 0.120 0.000 0.880
#> GSM153081 1 0.0424 0.950 0.992 0.000 0.008
#> GSM153082 1 0.2550 0.908 0.932 0.056 0.012
#> GSM153083 1 0.0592 0.949 0.988 0.000 0.012
#> GSM153084 1 0.6225 0.258 0.568 0.000 0.432
#> GSM153085 1 0.4504 0.763 0.804 0.000 0.196
#> GSM153086 1 0.4504 0.763 0.804 0.000 0.196
#> GSM153087 1 0.0424 0.951 0.992 0.000 0.008
#> GSM153088 1 0.0424 0.950 0.992 0.000 0.008
#> GSM153089 3 0.1163 0.954 0.028 0.000 0.972
#> GSM153090 1 0.0424 0.950 0.992 0.000 0.008
#> GSM153091 1 0.0424 0.950 0.992 0.000 0.008
#> GSM153092 1 0.0424 0.950 0.992 0.000 0.008
#> GSM153093 1 0.0424 0.951 0.992 0.000 0.008
#> GSM153094 1 0.0424 0.950 0.992 0.000 0.008
#> GSM153095 1 0.4504 0.763 0.804 0.000 0.196
#> GSM153096 1 0.0424 0.950 0.992 0.000 0.008
#> GSM153097 1 0.0424 0.950 0.992 0.000 0.008
#> GSM153098 1 0.0237 0.950 0.996 0.000 0.004
#> GSM153099 1 0.0424 0.951 0.992 0.000 0.008
#> GSM153100 1 0.0424 0.950 0.992 0.000 0.008
#> GSM153101 1 0.1647 0.933 0.960 0.004 0.036
#> GSM153102 1 0.4235 0.789 0.824 0.000 0.176
#> GSM153103 1 0.5327 0.642 0.728 0.000 0.272
#> GSM153104 1 0.0424 0.951 0.992 0.000 0.008
#> GSM153106 1 0.0237 0.950 0.996 0.000 0.004
#> GSM153107 1 0.0424 0.950 0.992 0.000 0.008
#> GSM153108 1 0.0592 0.950 0.988 0.000 0.012
#> GSM153109 1 0.2796 0.884 0.908 0.000 0.092
#> GSM153110 1 0.0424 0.950 0.992 0.000 0.008
#> GSM153111 1 0.0592 0.949 0.988 0.000 0.012
#> GSM153112 1 0.0424 0.950 0.992 0.000 0.008
#> GSM153113 1 0.5062 0.762 0.800 0.184 0.016
#> GSM153114 1 0.0424 0.951 0.992 0.000 0.008
#> GSM187532 2 0.2066 0.928 0.000 0.940 0.060
#> GSM187533 2 0.0848 0.975 0.008 0.984 0.008
#> GSM187534 2 0.0661 0.975 0.008 0.988 0.004
#> GSM187535 2 0.6189 0.411 0.364 0.632 0.004
#> GSM152906 2 0.0848 0.975 0.008 0.984 0.008
#> GSM152907 2 0.0848 0.975 0.008 0.984 0.008
#> GSM152908 2 0.0848 0.975 0.008 0.984 0.008
#> GSM152909 2 0.0892 0.968 0.000 0.980 0.020
#> GSM152910 2 0.0829 0.973 0.004 0.984 0.012
#> GSM152911 2 0.0848 0.975 0.008 0.984 0.008
#> GSM152912 2 0.0848 0.975 0.008 0.984 0.008
#> GSM152913 2 0.0747 0.969 0.000 0.984 0.016
#> GSM152914 2 0.0848 0.975 0.008 0.984 0.008
#> GSM152915 2 0.0848 0.975 0.008 0.984 0.008
#> GSM152916 2 0.0848 0.975 0.008 0.984 0.008
#> GSM152917 2 0.0848 0.975 0.008 0.984 0.008
#> GSM152918 2 0.0848 0.975 0.008 0.984 0.008
#> GSM152919 2 0.0848 0.975 0.008 0.984 0.008
#> GSM152920 2 0.1015 0.974 0.008 0.980 0.012
#> GSM152921 2 0.0848 0.975 0.008 0.984 0.008
#> GSM152922 2 0.0848 0.975 0.008 0.984 0.008
#> GSM152923 2 0.0848 0.975 0.008 0.984 0.008
#> GSM152924 2 0.0848 0.975 0.008 0.984 0.008
#> GSM152925 2 0.0848 0.975 0.008 0.984 0.008
#> GSM152926 2 0.0848 0.975 0.008 0.984 0.008
#> GSM152927 2 0.0829 0.973 0.004 0.984 0.012
#> GSM152928 2 0.1170 0.970 0.008 0.976 0.016
#> GSM152929 2 0.0848 0.975 0.008 0.984 0.008
#> GSM152930 2 0.0848 0.975 0.008 0.984 0.008
cbind(get_classes(res, k = 4), get_membership(res, k = 4))
#> class entropy silhouette p1 p2 p3 p4
#> GSM152839 3 0.6162 0.5089 0.304 0.000 0.620 0.076
#> GSM152840 3 0.5050 0.7686 0.176 0.000 0.756 0.068
#> GSM152841 4 0.2198 0.7181 0.072 0.000 0.008 0.920
#> GSM152842 3 0.2216 0.8279 0.092 0.000 0.908 0.000
#> GSM152843 3 0.0817 0.8342 0.024 0.000 0.976 0.000
#> GSM152844 3 0.4238 0.7920 0.176 0.000 0.796 0.028
#> GSM152845 3 0.3074 0.8216 0.152 0.000 0.848 0.000
#> GSM152846 3 0.3444 0.8073 0.184 0.000 0.816 0.000
#> GSM152847 3 0.1118 0.8350 0.036 0.000 0.964 0.000
#> GSM152848 4 0.7006 -0.5250 0.428 0.000 0.116 0.456
#> GSM152849 3 0.0707 0.8344 0.020 0.000 0.980 0.000
#> GSM152850 3 0.3074 0.7927 0.152 0.000 0.848 0.000
#> GSM152851 3 0.6712 0.4627 0.104 0.000 0.552 0.344
#> GSM152852 3 0.3881 0.8002 0.172 0.000 0.812 0.016
#> GSM152853 3 0.4332 0.7897 0.176 0.000 0.792 0.032
#> GSM152854 3 0.2216 0.8334 0.092 0.000 0.908 0.000
#> GSM152855 4 0.1118 0.7578 0.036 0.000 0.000 0.964
#> GSM153238 3 0.4661 0.6196 0.348 0.000 0.652 0.000
#> GSM153239 3 0.3937 0.7989 0.188 0.000 0.800 0.012
#> GSM153240 4 0.0921 0.7527 0.028 0.000 0.000 0.972
#> GSM153241 3 0.1389 0.8354 0.048 0.000 0.952 0.000
#> GSM153242 3 0.2921 0.8202 0.140 0.000 0.860 0.000
#> GSM153243 3 0.4008 0.7205 0.244 0.000 0.756 0.000
#> GSM153244 4 0.5732 0.3660 0.064 0.000 0.264 0.672
#> GSM153245 3 0.4136 0.7952 0.196 0.000 0.788 0.016
#> GSM153246 3 0.3837 0.7935 0.224 0.000 0.776 0.000
#> GSM153247 3 0.3837 0.7604 0.224 0.000 0.776 0.000
#> GSM153248 1 0.4916 0.7289 0.576 0.000 0.000 0.424
#> GSM153249 4 0.0817 0.7556 0.024 0.000 0.000 0.976
#> GSM153250 4 0.3311 0.6046 0.172 0.000 0.000 0.828
#> GSM153251 3 0.1557 0.8368 0.056 0.000 0.944 0.000
#> GSM153252 4 0.0469 0.7586 0.012 0.000 0.000 0.988
#> GSM153253 4 0.2773 0.6967 0.072 0.000 0.028 0.900
#> GSM153254 3 0.5825 0.6481 0.268 0.000 0.664 0.068
#> GSM153255 4 0.0592 0.7568 0.016 0.000 0.000 0.984
#> GSM153256 4 0.1302 0.7523 0.044 0.000 0.000 0.956
#> GSM153257 4 0.0336 0.7601 0.008 0.000 0.000 0.992
#> GSM153258 4 0.4804 -0.1175 0.384 0.000 0.000 0.616
#> GSM153259 1 0.4961 0.6935 0.552 0.000 0.000 0.448
#> GSM153260 3 0.4967 0.3926 0.452 0.000 0.548 0.000
#> GSM153261 3 0.4222 0.6881 0.272 0.000 0.728 0.000
#> GSM153262 4 0.1118 0.7510 0.036 0.000 0.000 0.964
#> GSM153263 4 0.4072 0.4263 0.252 0.000 0.000 0.748
#> GSM153264 4 0.5165 -0.5378 0.484 0.000 0.004 0.512
#> GSM153265 4 0.1867 0.7251 0.072 0.000 0.000 0.928
#> GSM153266 4 0.4996 -0.5351 0.484 0.000 0.000 0.516
#> GSM153267 4 0.1211 0.7543 0.040 0.000 0.000 0.960
#> GSM153268 4 0.4931 0.5311 0.132 0.000 0.092 0.776
#> GSM153269 4 0.1940 0.7296 0.076 0.000 0.000 0.924
#> GSM153270 4 0.1389 0.7505 0.048 0.000 0.000 0.952
#> GSM153271 4 0.3356 0.5979 0.176 0.000 0.000 0.824
#> GSM153272 4 0.0707 0.7558 0.020 0.000 0.000 0.980
#> GSM153273 1 0.4948 0.7085 0.560 0.000 0.000 0.440
#> GSM153274 4 0.2469 0.6977 0.108 0.000 0.000 0.892
#> GSM153275 4 0.1389 0.7505 0.048 0.000 0.000 0.952
#> GSM153276 4 0.1637 0.7469 0.060 0.000 0.000 0.940
#> GSM153277 4 0.1302 0.7463 0.044 0.000 0.000 0.956
#> GSM153278 3 0.5331 0.5474 0.332 0.000 0.644 0.024
#> GSM153279 4 0.3398 0.6653 0.068 0.000 0.060 0.872
#> GSM153280 4 0.2522 0.7066 0.076 0.000 0.016 0.908
#> GSM153281 4 0.1557 0.7354 0.056 0.000 0.000 0.944
#> GSM153282 4 0.2198 0.7179 0.072 0.000 0.008 0.920
#> GSM153283 4 0.4746 -0.0305 0.368 0.000 0.000 0.632
#> GSM153284 4 0.1211 0.7540 0.040 0.000 0.000 0.960
#> GSM153285 4 0.1940 0.7221 0.076 0.000 0.000 0.924
#> GSM153286 4 0.0921 0.7601 0.028 0.000 0.000 0.972
#> GSM153287 4 0.1118 0.7504 0.036 0.000 0.000 0.964
#> GSM153288 4 0.0592 0.7601 0.016 0.000 0.000 0.984
#> GSM153289 4 0.1302 0.7555 0.044 0.000 0.000 0.956
#> GSM153290 4 0.2742 0.6975 0.076 0.000 0.024 0.900
#> GSM153291 4 0.0188 0.7596 0.004 0.000 0.000 0.996
#> GSM153292 4 0.1302 0.7462 0.044 0.000 0.000 0.956
#> GSM153293 4 0.1211 0.7543 0.040 0.000 0.000 0.960
#> GSM153294 1 0.4955 0.7020 0.556 0.000 0.000 0.444
#> GSM153295 4 0.1022 0.7606 0.032 0.000 0.000 0.968
#> GSM153054 1 0.7319 0.6249 0.532 0.000 0.220 0.248
#> GSM153055 4 0.2589 0.6927 0.116 0.000 0.000 0.884
#> GSM153056 3 0.2589 0.8147 0.116 0.000 0.884 0.000
#> GSM153057 3 0.3105 0.8024 0.140 0.000 0.856 0.004
#> GSM153058 3 0.1940 0.8366 0.076 0.000 0.924 0.000
#> GSM153059 3 0.4356 0.6666 0.292 0.000 0.708 0.000
#> GSM153060 3 0.3024 0.8116 0.148 0.000 0.852 0.000
#> GSM153061 3 0.2973 0.8135 0.144 0.000 0.856 0.000
#> GSM153062 3 0.3837 0.7895 0.224 0.000 0.776 0.000
#> GSM153063 3 0.1792 0.8379 0.068 0.000 0.932 0.000
#> GSM153064 1 0.4961 0.6940 0.552 0.000 0.000 0.448
#> GSM153065 3 0.1302 0.8348 0.044 0.000 0.956 0.000
#> GSM153066 1 0.4994 -0.2649 0.520 0.000 0.480 0.000
#> GSM153067 4 0.0336 0.7591 0.008 0.000 0.000 0.992
#> GSM153068 3 0.2345 0.8279 0.100 0.000 0.900 0.000
#> GSM153069 4 0.1022 0.7509 0.032 0.000 0.000 0.968
#> GSM153070 4 0.4855 -0.1944 0.400 0.000 0.000 0.600
#> GSM153071 1 0.7091 0.3064 0.508 0.000 0.356 0.136
#> GSM153072 1 0.6982 0.5582 0.576 0.000 0.252 0.172
#> GSM153073 1 0.5000 0.5771 0.504 0.000 0.000 0.496
#> GSM153074 4 0.0817 0.7588 0.024 0.000 0.000 0.976
#> GSM153075 4 0.2002 0.7547 0.044 0.000 0.020 0.936
#> GSM153076 4 0.4222 0.3680 0.272 0.000 0.000 0.728
#> GSM153077 4 0.4989 -0.4950 0.472 0.000 0.000 0.528
#> GSM153078 1 0.7332 0.3784 0.480 0.000 0.356 0.164
#> GSM153079 1 0.5050 0.7395 0.588 0.000 0.004 0.408
#> GSM153080 3 0.5359 0.6738 0.288 0.000 0.676 0.036
#> GSM153081 1 0.4989 0.6343 0.528 0.000 0.000 0.472
#> GSM153082 1 0.5329 0.7262 0.568 0.012 0.000 0.420
#> GSM153083 1 0.5060 0.7384 0.584 0.000 0.004 0.412
#> GSM153084 1 0.6808 0.4376 0.572 0.000 0.300 0.128
#> GSM153085 1 0.6792 0.6882 0.588 0.000 0.140 0.272
#> GSM153086 1 0.6295 0.7364 0.580 0.000 0.072 0.348
#> GSM153087 4 0.0707 0.7606 0.020 0.000 0.000 0.980
#> GSM153088 4 0.3528 0.5675 0.192 0.000 0.000 0.808
#> GSM153089 3 0.2081 0.8382 0.084 0.000 0.916 0.000
#> GSM153090 4 0.2868 0.6620 0.136 0.000 0.000 0.864
#> GSM153091 1 0.4948 0.7129 0.560 0.000 0.000 0.440
#> GSM153092 4 0.4992 -0.4981 0.476 0.000 0.000 0.524
#> GSM153093 4 0.0817 0.7592 0.024 0.000 0.000 0.976
#> GSM153094 1 0.4925 0.7250 0.572 0.000 0.000 0.428
#> GSM153095 1 0.6616 0.7064 0.584 0.000 0.108 0.308
#> GSM153096 1 0.4925 0.7250 0.572 0.000 0.000 0.428
#> GSM153097 1 0.5290 0.7415 0.584 0.000 0.012 0.404
#> GSM153098 4 0.4790 -0.0696 0.380 0.000 0.000 0.620
#> GSM153099 4 0.1302 0.7523 0.044 0.000 0.000 0.956
#> GSM153100 4 0.4992 -0.4907 0.476 0.000 0.000 0.524
#> GSM153101 1 0.5913 0.7395 0.600 0.000 0.048 0.352
#> GSM153102 1 0.6340 0.7317 0.580 0.000 0.076 0.344
#> GSM153103 1 0.6814 0.6929 0.584 0.000 0.140 0.276
#> GSM153104 4 0.1302 0.7463 0.044 0.000 0.000 0.956
#> GSM153106 4 0.4730 0.0110 0.364 0.000 0.000 0.636
#> GSM153107 4 0.4888 -0.2248 0.412 0.000 0.000 0.588
#> GSM153108 4 0.2408 0.7023 0.104 0.000 0.000 0.896
#> GSM153109 1 0.5699 0.7436 0.588 0.000 0.032 0.380
#> GSM153110 1 0.4955 0.7020 0.556 0.000 0.000 0.444
#> GSM153111 1 0.5060 0.7384 0.584 0.000 0.004 0.412
#> GSM153112 4 0.4961 -0.3727 0.448 0.000 0.000 0.552
#> GSM153113 1 0.6626 0.7240 0.580 0.048 0.024 0.348
#> GSM153114 4 0.1118 0.7578 0.036 0.000 0.000 0.964
#> GSM187532 2 0.3056 0.8989 0.072 0.888 0.040 0.000
#> GSM187533 2 0.1118 0.9542 0.036 0.964 0.000 0.000
#> GSM187534 2 0.1118 0.9542 0.036 0.964 0.000 0.000
#> GSM187535 2 0.7415 0.1273 0.236 0.516 0.000 0.248
#> GSM152906 2 0.1389 0.9513 0.048 0.952 0.000 0.000
#> GSM152907 2 0.1389 0.9513 0.048 0.952 0.000 0.000
#> GSM152908 2 0.0921 0.9508 0.028 0.972 0.000 0.000
#> GSM152909 2 0.1211 0.9488 0.040 0.960 0.000 0.000
#> GSM152910 2 0.0921 0.9508 0.028 0.972 0.000 0.000
#> GSM152911 2 0.0188 0.9551 0.004 0.996 0.000 0.000
#> GSM152912 2 0.0921 0.9508 0.028 0.972 0.000 0.000
#> GSM152913 2 0.0592 0.9551 0.016 0.984 0.000 0.000
#> GSM152914 2 0.0188 0.9551 0.004 0.996 0.000 0.000
#> GSM152915 2 0.0188 0.9551 0.004 0.996 0.000 0.000
#> GSM152916 2 0.1474 0.9507 0.052 0.948 0.000 0.000
#> GSM152917 2 0.0188 0.9551 0.004 0.996 0.000 0.000
#> GSM152918 2 0.0188 0.9551 0.004 0.996 0.000 0.000
#> GSM152919 2 0.0188 0.9551 0.004 0.996 0.000 0.000
#> GSM152920 2 0.1022 0.9499 0.032 0.968 0.000 0.000
#> GSM152921 2 0.0921 0.9508 0.028 0.972 0.000 0.000
#> GSM152922 2 0.0921 0.9508 0.028 0.972 0.000 0.000
#> GSM152923 2 0.1389 0.9513 0.048 0.952 0.000 0.000
#> GSM152924 2 0.1474 0.9507 0.052 0.948 0.000 0.000
#> GSM152925 2 0.1474 0.9507 0.052 0.948 0.000 0.000
#> GSM152926 2 0.1389 0.9513 0.048 0.952 0.000 0.000
#> GSM152927 2 0.1474 0.9507 0.052 0.948 0.000 0.000
#> GSM152928 2 0.2469 0.9113 0.108 0.892 0.000 0.000
#> GSM152929 2 0.1389 0.9513 0.048 0.952 0.000 0.000
#> GSM152930 2 0.1389 0.9513 0.048 0.952 0.000 0.000
cbind(get_classes(res, k = 5), get_membership(res, k = 5))
#> class entropy silhouette p1 p2 p3 p4 p5
#> GSM152839 3 0.4839 0.4469 0.304 0.000 0.660 0.024 0.012
#> GSM152840 5 0.5870 0.6991 0.008 0.000 0.296 0.104 0.592
#> GSM152841 4 0.2352 0.7978 0.004 0.000 0.008 0.896 0.092
#> GSM152842 3 0.3919 0.3295 0.036 0.000 0.776 0.000 0.188
#> GSM152843 3 0.3374 0.4223 0.044 0.000 0.844 0.004 0.108
#> GSM152844 5 0.5186 0.7787 0.004 0.000 0.320 0.052 0.624
#> GSM152845 5 0.4980 0.5512 0.028 0.000 0.484 0.000 0.488
#> GSM152846 5 0.4594 0.7519 0.004 0.000 0.364 0.012 0.620
#> GSM152847 3 0.3086 0.4322 0.040 0.000 0.864 0.004 0.092
#> GSM152848 1 0.6560 0.5503 0.548 0.000 0.248 0.188 0.016
#> GSM152849 3 0.3152 0.3704 0.024 0.000 0.840 0.000 0.136
#> GSM152850 3 0.3495 0.5204 0.152 0.000 0.816 0.000 0.032
#> GSM152851 4 0.7157 -0.2833 0.020 0.000 0.284 0.428 0.268
#> GSM152852 5 0.5375 0.7543 0.008 0.000 0.380 0.044 0.568
#> GSM152853 5 0.5249 0.7791 0.004 0.000 0.336 0.052 0.608
#> GSM152854 3 0.4610 -0.3577 0.016 0.000 0.596 0.000 0.388
#> GSM152855 4 0.2351 0.8235 0.088 0.000 0.000 0.896 0.016
#> GSM153238 3 0.4546 0.4824 0.304 0.000 0.668 0.000 0.028
#> GSM153239 5 0.4973 0.7601 0.004 0.000 0.376 0.028 0.592
#> GSM153240 4 0.0451 0.8436 0.008 0.000 0.000 0.988 0.004
#> GSM153241 3 0.3002 0.3793 0.028 0.000 0.856 0.000 0.116
#> GSM153242 3 0.4802 -0.6168 0.012 0.000 0.504 0.004 0.480
#> GSM153243 3 0.4203 0.5165 0.188 0.000 0.760 0.000 0.052
#> GSM153244 4 0.6225 0.4217 0.040 0.000 0.204 0.632 0.124
#> GSM153245 5 0.5524 0.7120 0.008 0.000 0.428 0.048 0.516
#> GSM153246 3 0.5534 -0.1963 0.068 0.000 0.508 0.000 0.424
#> GSM153247 3 0.3710 0.5123 0.144 0.000 0.808 0.000 0.048
#> GSM153248 1 0.2970 0.8012 0.828 0.000 0.000 0.168 0.004
#> GSM153249 4 0.1082 0.8384 0.008 0.000 0.000 0.964 0.028
#> GSM153250 4 0.4306 0.3842 0.328 0.000 0.000 0.660 0.012
#> GSM153251 3 0.4603 -0.0132 0.032 0.000 0.668 0.000 0.300
#> GSM153252 4 0.1216 0.8427 0.020 0.000 0.000 0.960 0.020
#> GSM153253 4 0.2789 0.7852 0.008 0.000 0.020 0.880 0.092
#> GSM153254 3 0.6982 0.3485 0.192 0.000 0.580 0.092 0.136
#> GSM153255 4 0.0798 0.8419 0.008 0.000 0.000 0.976 0.016
#> GSM153256 4 0.2011 0.8243 0.088 0.000 0.000 0.908 0.004
#> GSM153257 4 0.1012 0.8432 0.020 0.000 0.000 0.968 0.012
#> GSM153258 1 0.5036 0.6010 0.592 0.000 0.016 0.376 0.016
#> GSM153259 1 0.3086 0.8005 0.816 0.000 0.000 0.180 0.004
#> GSM153260 3 0.4682 0.4535 0.356 0.000 0.620 0.000 0.024
#> GSM153261 3 0.3835 0.5157 0.244 0.000 0.744 0.000 0.012
#> GSM153262 4 0.1116 0.8364 0.004 0.000 0.004 0.964 0.028
#> GSM153263 4 0.4787 -0.1597 0.456 0.000 0.004 0.528 0.012
#> GSM153264 1 0.4976 0.7179 0.660 0.000 0.028 0.296 0.016
#> GSM153265 4 0.2237 0.8038 0.004 0.000 0.008 0.904 0.084
#> GSM153266 1 0.4560 0.7194 0.672 0.000 0.008 0.304 0.016
#> GSM153267 4 0.2233 0.8148 0.104 0.000 0.000 0.892 0.004
#> GSM153268 4 0.3648 0.7132 0.008 0.000 0.024 0.812 0.156
#> GSM153269 4 0.3213 0.7617 0.144 0.000 0.004 0.836 0.016
#> GSM153270 4 0.2646 0.7968 0.124 0.000 0.004 0.868 0.004
#> GSM153271 4 0.4218 0.3848 0.332 0.000 0.000 0.660 0.008
#> GSM153272 4 0.0912 0.8427 0.012 0.000 0.000 0.972 0.016
#> GSM153273 1 0.3048 0.8016 0.820 0.000 0.000 0.176 0.004
#> GSM153274 4 0.3399 0.7297 0.172 0.000 0.004 0.812 0.012
#> GSM153275 4 0.2338 0.8095 0.112 0.000 0.000 0.884 0.004
#> GSM153276 4 0.2694 0.8059 0.108 0.000 0.008 0.876 0.008
#> GSM153277 4 0.1469 0.8391 0.016 0.000 0.000 0.948 0.036
#> GSM153278 3 0.4536 0.4642 0.324 0.000 0.656 0.004 0.016
#> GSM153279 4 0.3013 0.7913 0.016 0.000 0.044 0.880 0.060
#> GSM153280 4 0.2588 0.7896 0.008 0.000 0.008 0.884 0.100
#> GSM153281 4 0.1484 0.8249 0.000 0.000 0.008 0.944 0.048
#> GSM153282 4 0.2295 0.8008 0.004 0.000 0.008 0.900 0.088
#> GSM153283 1 0.4658 0.5403 0.576 0.000 0.000 0.408 0.016
#> GSM153284 4 0.2179 0.8178 0.100 0.000 0.000 0.896 0.004
#> GSM153285 4 0.2533 0.7924 0.008 0.000 0.008 0.888 0.096
#> GSM153286 4 0.1831 0.8299 0.076 0.000 0.000 0.920 0.004
#> GSM153287 4 0.0955 0.8372 0.004 0.000 0.000 0.968 0.028
#> GSM153288 4 0.1704 0.8335 0.068 0.000 0.000 0.928 0.004
#> GSM153289 4 0.2825 0.7920 0.124 0.000 0.000 0.860 0.016
#> GSM153290 4 0.2588 0.7898 0.008 0.000 0.008 0.884 0.100
#> GSM153291 4 0.1216 0.8425 0.020 0.000 0.000 0.960 0.020
#> GSM153292 4 0.1124 0.8346 0.004 0.000 0.000 0.960 0.036
#> GSM153293 4 0.1831 0.8294 0.076 0.000 0.000 0.920 0.004
#> GSM153294 1 0.3455 0.7906 0.784 0.000 0.000 0.208 0.008
#> GSM153295 4 0.1697 0.8356 0.060 0.000 0.000 0.932 0.008
#> GSM153054 1 0.5234 0.5686 0.708 0.000 0.200 0.064 0.028
#> GSM153055 4 0.4479 0.6604 0.200 0.000 0.040 0.748 0.012
#> GSM153056 3 0.3421 0.4799 0.080 0.000 0.840 0.000 0.080
#> GSM153057 3 0.4648 0.4837 0.156 0.000 0.740 0.000 0.104
#> GSM153058 3 0.4506 -0.0370 0.028 0.000 0.676 0.000 0.296
#> GSM153059 3 0.5037 0.4906 0.228 0.000 0.684 0.000 0.088
#> GSM153060 3 0.5240 0.0121 0.056 0.000 0.584 0.000 0.360
#> GSM153061 3 0.5160 0.0623 0.056 0.000 0.608 0.000 0.336
#> GSM153062 5 0.5371 0.3165 0.056 0.000 0.420 0.000 0.524
#> GSM153063 3 0.4605 0.1013 0.032 0.000 0.692 0.004 0.272
#> GSM153064 1 0.3266 0.7930 0.796 0.000 0.000 0.200 0.004
#> GSM153065 3 0.3565 0.3778 0.040 0.000 0.816 0.000 0.144
#> GSM153066 3 0.5315 0.3618 0.456 0.004 0.500 0.000 0.040
#> GSM153067 4 0.1568 0.8433 0.036 0.000 0.000 0.944 0.020
#> GSM153068 3 0.4054 0.3254 0.036 0.000 0.760 0.000 0.204
#> GSM153069 4 0.0963 0.8358 0.000 0.000 0.000 0.964 0.036
#> GSM153070 1 0.5212 0.4943 0.548 0.000 0.020 0.416 0.016
#> GSM153071 3 0.5166 0.3440 0.444 0.000 0.524 0.016 0.016
#> GSM153072 1 0.4721 0.3121 0.672 0.000 0.296 0.016 0.016
#> GSM153073 1 0.4265 0.7599 0.712 0.000 0.008 0.268 0.012
#> GSM153074 4 0.1894 0.8360 0.072 0.000 0.000 0.920 0.008
#> GSM153075 4 0.2005 0.8413 0.056 0.000 0.016 0.924 0.004
#> GSM153076 1 0.4659 0.2853 0.500 0.000 0.000 0.488 0.012
#> GSM153077 1 0.4915 0.7165 0.660 0.000 0.024 0.300 0.016
#> GSM153078 1 0.6015 -0.1233 0.468 0.000 0.452 0.052 0.028
#> GSM153079 1 0.3554 0.7905 0.828 0.000 0.016 0.136 0.020
#> GSM153080 3 0.5352 0.4959 0.220 0.000 0.692 0.036 0.052
#> GSM153081 1 0.4684 0.7699 0.712 0.000 0.020 0.244 0.024
#> GSM153082 1 0.3362 0.7985 0.824 0.008 0.000 0.156 0.012
#> GSM153083 1 0.2865 0.7862 0.856 0.000 0.008 0.132 0.004
#> GSM153084 1 0.4704 0.3385 0.696 0.000 0.264 0.012 0.028
#> GSM153085 1 0.5097 0.6713 0.728 0.000 0.148 0.108 0.016
#> GSM153086 1 0.3523 0.7648 0.832 0.000 0.044 0.120 0.004
#> GSM153087 4 0.1901 0.8417 0.056 0.000 0.004 0.928 0.012
#> GSM153088 4 0.4893 0.2407 0.360 0.000 0.012 0.612 0.016
#> GSM153089 3 0.4977 0.0785 0.040 0.000 0.660 0.008 0.292
#> GSM153090 4 0.4033 0.6124 0.236 0.000 0.004 0.744 0.016
#> GSM153091 1 0.3086 0.8017 0.816 0.000 0.000 0.180 0.004
#> GSM153092 1 0.3838 0.7472 0.716 0.000 0.000 0.280 0.004
#> GSM153093 4 0.1430 0.8391 0.052 0.000 0.000 0.944 0.004
#> GSM153094 1 0.2732 0.7996 0.840 0.000 0.000 0.160 0.000
#> GSM153095 1 0.4810 0.5786 0.732 0.000 0.192 0.064 0.012
#> GSM153096 1 0.2852 0.8024 0.828 0.000 0.000 0.172 0.000
#> GSM153097 1 0.3031 0.7805 0.852 0.000 0.016 0.128 0.004
#> GSM153098 1 0.4135 0.6627 0.656 0.000 0.000 0.340 0.004
#> GSM153099 4 0.2179 0.8173 0.100 0.000 0.000 0.896 0.004
#> GSM153100 1 0.3790 0.7482 0.724 0.000 0.000 0.272 0.004
#> GSM153101 1 0.3749 0.7547 0.828 0.000 0.052 0.108 0.012
#> GSM153102 1 0.4519 0.7123 0.764 0.000 0.112 0.120 0.004
#> GSM153103 1 0.4469 0.6725 0.776 0.000 0.132 0.080 0.012
#> GSM153104 4 0.1329 0.8335 0.008 0.000 0.004 0.956 0.032
#> GSM153106 1 0.4588 0.6033 0.604 0.000 0.000 0.380 0.016
#> GSM153107 1 0.4467 0.6684 0.640 0.000 0.000 0.344 0.016
#> GSM153108 4 0.3575 0.7201 0.180 0.000 0.004 0.800 0.016
#> GSM153109 1 0.3985 0.7471 0.804 0.000 0.072 0.120 0.004
#> GSM153110 1 0.2929 0.8012 0.820 0.000 0.000 0.180 0.000
#> GSM153111 1 0.2865 0.7864 0.856 0.000 0.008 0.132 0.004
#> GSM153112 1 0.3766 0.7457 0.728 0.000 0.000 0.268 0.004
#> GSM153113 1 0.4971 0.7350 0.776 0.032 0.052 0.116 0.024
#> GSM153114 4 0.2293 0.8276 0.084 0.000 0.000 0.900 0.016
#> GSM187532 2 0.5054 0.8113 0.076 0.760 0.072 0.000 0.092
#> GSM187533 2 0.2511 0.9302 0.028 0.892 0.000 0.000 0.080
#> GSM187534 2 0.2388 0.9320 0.028 0.900 0.000 0.000 0.072
#> GSM187535 1 0.7104 0.2070 0.448 0.376 0.000 0.120 0.056
#> GSM152906 2 0.2388 0.9296 0.028 0.900 0.000 0.000 0.072
#> GSM152907 2 0.2388 0.9296 0.028 0.900 0.000 0.000 0.072
#> GSM152908 2 0.1626 0.9300 0.016 0.940 0.000 0.000 0.044
#> GSM152909 2 0.2609 0.9170 0.028 0.896 0.008 0.000 0.068
#> GSM152910 2 0.1701 0.9291 0.016 0.936 0.000 0.000 0.048
#> GSM152911 2 0.0404 0.9379 0.000 0.988 0.000 0.000 0.012
#> GSM152912 2 0.1626 0.9300 0.016 0.940 0.000 0.000 0.044
#> GSM152913 2 0.1121 0.9366 0.000 0.956 0.000 0.000 0.044
#> GSM152914 2 0.0290 0.9384 0.000 0.992 0.000 0.000 0.008
#> GSM152915 2 0.0290 0.9384 0.000 0.992 0.000 0.000 0.008
#> GSM152916 2 0.2676 0.9260 0.036 0.884 0.000 0.000 0.080
#> GSM152917 2 0.0290 0.9384 0.000 0.992 0.000 0.000 0.008
#> GSM152918 2 0.0290 0.9384 0.000 0.992 0.000 0.000 0.008
#> GSM152919 2 0.0290 0.9384 0.000 0.992 0.000 0.000 0.008
#> GSM152920 2 0.1626 0.9300 0.016 0.940 0.000 0.000 0.044
#> GSM152921 2 0.1626 0.9300 0.016 0.940 0.000 0.000 0.044
#> GSM152922 2 0.1701 0.9291 0.016 0.936 0.000 0.000 0.048
#> GSM152923 2 0.2473 0.9290 0.032 0.896 0.000 0.000 0.072
#> GSM152924 2 0.2793 0.9250 0.036 0.876 0.000 0.000 0.088
#> GSM152925 2 0.2735 0.9251 0.036 0.880 0.000 0.000 0.084
#> GSM152926 2 0.2473 0.9290 0.032 0.896 0.000 0.000 0.072
#> GSM152927 2 0.2735 0.9259 0.036 0.880 0.000 0.000 0.084
#> GSM152928 2 0.3859 0.8839 0.084 0.816 0.004 0.000 0.096
#> GSM152929 2 0.2473 0.9290 0.032 0.896 0.000 0.000 0.072
#> GSM152930 2 0.2388 0.9296 0.028 0.900 0.000 0.000 0.072
cbind(get_classes(res, k = 6), get_membership(res, k = 6))
#> class entropy silhouette p1 p2 p3 p4 p5 p6
#> GSM152839 3 0.5124 0.5138 0.196 0.000 0.700 0.032 0.040 0.032
#> GSM152840 6 0.3571 0.6989 0.000 0.000 0.084 0.068 0.024 0.824
#> GSM152841 4 0.3185 0.7718 0.000 0.000 0.004 0.832 0.048 0.116
#> GSM152842 3 0.4749 0.0950 0.004 0.000 0.656 0.000 0.260 0.080
#> GSM152843 3 0.4272 0.4950 0.020 0.000 0.772 0.004 0.096 0.108
#> GSM152844 6 0.2505 0.7786 0.000 0.000 0.092 0.020 0.008 0.880
#> GSM152845 6 0.4109 0.6947 0.012 0.000 0.212 0.000 0.040 0.736
#> GSM152846 6 0.3017 0.7565 0.000 0.000 0.096 0.004 0.052 0.848
#> GSM152847 3 0.4088 0.5042 0.020 0.000 0.788 0.004 0.096 0.092
#> GSM152848 3 0.6869 -0.0883 0.364 0.000 0.388 0.196 0.044 0.008
#> GSM152849 3 0.4153 0.5056 0.024 0.000 0.756 0.000 0.044 0.176
#> GSM152850 3 0.3726 0.5719 0.080 0.000 0.816 0.000 0.072 0.032
#> GSM152851 4 0.6854 -0.1398 0.004 0.000 0.184 0.408 0.056 0.348
#> GSM152852 6 0.2678 0.7857 0.000 0.000 0.116 0.020 0.004 0.860
#> GSM152853 6 0.2402 0.7776 0.000 0.000 0.084 0.020 0.008 0.888
#> GSM152854 6 0.4323 0.5254 0.004 0.000 0.376 0.000 0.020 0.600
#> GSM152855 4 0.2914 0.7992 0.084 0.000 0.000 0.860 0.048 0.008
#> GSM153238 3 0.5186 0.4895 0.248 0.000 0.640 0.000 0.092 0.020
#> GSM153239 6 0.3496 0.7539 0.000 0.000 0.140 0.004 0.052 0.804
#> GSM153240 4 0.1176 0.8286 0.024 0.000 0.000 0.956 0.020 0.000
#> GSM153241 3 0.3984 0.4477 0.008 0.000 0.776 0.000 0.124 0.092
#> GSM153242 6 0.4407 0.6403 0.004 0.000 0.264 0.000 0.052 0.680
#> GSM153243 3 0.3427 0.6024 0.100 0.000 0.828 0.000 0.016 0.056
#> GSM153244 4 0.6323 0.4080 0.024 0.000 0.240 0.576 0.040 0.120
#> GSM153245 6 0.4429 0.7082 0.000 0.000 0.168 0.016 0.080 0.736
#> GSM153246 5 0.5011 0.7943 0.000 0.000 0.180 0.000 0.644 0.176
#> GSM153247 3 0.4494 0.5477 0.108 0.000 0.752 0.000 0.108 0.032
#> GSM153248 1 0.1701 0.7858 0.920 0.000 0.000 0.072 0.008 0.000
#> GSM153249 4 0.2450 0.8250 0.016 0.000 0.004 0.900 0.048 0.032
#> GSM153250 4 0.5092 0.2393 0.356 0.000 0.024 0.576 0.044 0.000
#> GSM153251 3 0.5064 0.1506 0.004 0.000 0.552 0.000 0.072 0.372
#> GSM153252 4 0.1862 0.8330 0.016 0.000 0.004 0.928 0.044 0.008
#> GSM153253 4 0.3441 0.7530 0.000 0.000 0.008 0.812 0.044 0.136
#> GSM153254 3 0.5296 0.5387 0.080 0.000 0.696 0.040 0.016 0.168
#> GSM153255 4 0.1442 0.8312 0.004 0.000 0.000 0.944 0.040 0.012
#> GSM153256 4 0.1951 0.8119 0.076 0.000 0.000 0.908 0.016 0.000
#> GSM153257 4 0.1988 0.8331 0.024 0.000 0.004 0.920 0.048 0.004
#> GSM153258 1 0.5421 0.5246 0.568 0.000 0.044 0.340 0.048 0.000
#> GSM153259 1 0.1714 0.7864 0.908 0.000 0.000 0.092 0.000 0.000
#> GSM153260 3 0.4125 0.5752 0.208 0.000 0.740 0.000 0.024 0.028
#> GSM153261 3 0.4684 0.5811 0.184 0.000 0.720 0.000 0.052 0.044
#> GSM153262 4 0.1988 0.8262 0.004 0.000 0.004 0.920 0.048 0.024
#> GSM153263 4 0.5017 -0.1625 0.460 0.000 0.012 0.484 0.044 0.000
#> GSM153264 1 0.5683 0.6386 0.616 0.000 0.112 0.228 0.044 0.000
#> GSM153265 4 0.2750 0.7987 0.000 0.000 0.004 0.868 0.048 0.080
#> GSM153266 1 0.4871 0.6774 0.668 0.000 0.032 0.252 0.048 0.000
#> GSM153267 4 0.1913 0.8135 0.080 0.000 0.000 0.908 0.012 0.000
#> GSM153268 4 0.3931 0.6840 0.000 0.000 0.008 0.756 0.044 0.192
#> GSM153269 4 0.3608 0.7384 0.132 0.000 0.020 0.808 0.040 0.000
#> GSM153270 4 0.2339 0.8131 0.072 0.000 0.012 0.896 0.020 0.000
#> GSM153271 4 0.4985 0.2836 0.344 0.000 0.020 0.592 0.044 0.000
#> GSM153272 4 0.0508 0.8330 0.004 0.000 0.000 0.984 0.012 0.000
#> GSM153273 1 0.1663 0.7866 0.912 0.000 0.000 0.088 0.000 0.000
#> GSM153274 4 0.3798 0.7357 0.128 0.000 0.032 0.800 0.040 0.000
#> GSM153275 4 0.2170 0.8036 0.100 0.000 0.000 0.888 0.012 0.000
#> GSM153276 4 0.3637 0.7620 0.080 0.000 0.056 0.824 0.040 0.000
#> GSM153277 4 0.2475 0.8239 0.012 0.000 0.000 0.892 0.036 0.060
#> GSM153278 3 0.4117 0.5871 0.164 0.000 0.772 0.012 0.032 0.020
#> GSM153279 4 0.3665 0.7762 0.004 0.000 0.040 0.828 0.052 0.076
#> GSM153280 4 0.3229 0.7688 0.000 0.000 0.004 0.828 0.048 0.120
#> GSM153281 4 0.2471 0.8139 0.000 0.000 0.004 0.888 0.056 0.052
#> GSM153282 4 0.2750 0.7953 0.000 0.000 0.004 0.868 0.048 0.080
#> GSM153283 1 0.4883 0.5151 0.588 0.000 0.016 0.356 0.040 0.000
#> GSM153284 4 0.1858 0.8134 0.076 0.000 0.000 0.912 0.012 0.000
#> GSM153285 4 0.3096 0.7774 0.000 0.000 0.004 0.840 0.048 0.108
#> GSM153286 4 0.2034 0.8153 0.060 0.000 0.004 0.912 0.024 0.000
#> GSM153287 4 0.2279 0.8132 0.000 0.000 0.004 0.900 0.048 0.048
#> GSM153288 4 0.1297 0.8267 0.040 0.000 0.000 0.948 0.012 0.000
#> GSM153289 4 0.3527 0.7488 0.132 0.000 0.000 0.808 0.052 0.008
#> GSM153290 4 0.3049 0.7808 0.000 0.000 0.004 0.844 0.048 0.104
#> GSM153291 4 0.1974 0.8319 0.020 0.000 0.000 0.920 0.048 0.012
#> GSM153292 4 0.2727 0.8042 0.004 0.000 0.004 0.876 0.048 0.068
#> GSM153293 4 0.1327 0.8213 0.064 0.000 0.000 0.936 0.000 0.000
#> GSM153294 1 0.1814 0.7858 0.900 0.000 0.000 0.100 0.000 0.000
#> GSM153295 4 0.2314 0.8127 0.056 0.000 0.008 0.900 0.036 0.000
#> GSM153054 1 0.4835 0.5731 0.716 0.000 0.192 0.020 0.052 0.020
#> GSM153055 4 0.4834 0.6668 0.128 0.000 0.108 0.724 0.040 0.000
#> GSM153056 3 0.3953 0.5413 0.048 0.000 0.800 0.000 0.100 0.052
#> GSM153057 3 0.3648 0.5918 0.068 0.000 0.820 0.000 0.028 0.084
#> GSM153058 3 0.4957 0.2064 0.004 0.000 0.580 0.000 0.068 0.348
#> GSM153059 3 0.4702 0.5845 0.120 0.000 0.740 0.000 0.048 0.092
#> GSM153060 5 0.5404 0.8053 0.000 0.000 0.312 0.000 0.548 0.140
#> GSM153061 5 0.5475 0.7793 0.000 0.000 0.316 0.000 0.536 0.148
#> GSM153062 5 0.5092 0.7333 0.000 0.000 0.144 0.000 0.624 0.232
#> GSM153063 3 0.5663 0.1904 0.012 0.000 0.532 0.008 0.092 0.356
#> GSM153064 1 0.1863 0.7851 0.896 0.000 0.000 0.104 0.000 0.000
#> GSM153065 3 0.4994 0.3960 0.012 0.000 0.676 0.000 0.136 0.176
#> GSM153066 3 0.5566 0.3507 0.388 0.000 0.500 0.000 0.100 0.012
#> GSM153067 4 0.2231 0.8321 0.028 0.000 0.000 0.908 0.048 0.016
#> GSM153068 3 0.4770 0.1233 0.004 0.000 0.652 0.000 0.264 0.080
#> GSM153069 4 0.2136 0.8152 0.000 0.000 0.000 0.904 0.048 0.048
#> GSM153070 1 0.5726 0.3831 0.504 0.000 0.064 0.388 0.044 0.000
#> GSM153071 3 0.5185 0.4805 0.288 0.000 0.624 0.004 0.064 0.020
#> GSM153072 1 0.4952 0.1476 0.568 0.000 0.376 0.004 0.044 0.008
#> GSM153073 1 0.5076 0.6840 0.672 0.000 0.056 0.224 0.048 0.000
#> GSM153074 4 0.1349 0.8266 0.056 0.000 0.000 0.940 0.004 0.000
#> GSM153075 4 0.2288 0.8265 0.040 0.000 0.048 0.904 0.004 0.004
#> GSM153076 1 0.5099 0.2991 0.508 0.000 0.020 0.432 0.040 0.000
#> GSM153077 1 0.5311 0.6532 0.640 0.000 0.068 0.248 0.044 0.000
#> GSM153078 3 0.5473 0.4432 0.284 0.000 0.616 0.056 0.032 0.012
#> GSM153079 1 0.3192 0.7605 0.864 0.000 0.032 0.040 0.052 0.012
#> GSM153080 3 0.4689 0.5945 0.116 0.000 0.764 0.032 0.040 0.048
#> GSM153081 1 0.5580 0.6877 0.672 0.000 0.072 0.164 0.084 0.008
#> GSM153082 1 0.2095 0.7778 0.916 0.000 0.016 0.052 0.012 0.004
#> GSM153083 1 0.2217 0.7713 0.908 0.000 0.036 0.048 0.004 0.004
#> GSM153084 1 0.5032 0.3981 0.656 0.000 0.256 0.004 0.064 0.020
#> GSM153085 1 0.4469 0.5955 0.712 0.000 0.228 0.032 0.024 0.004
#> GSM153086 1 0.2557 0.7492 0.892 0.000 0.056 0.036 0.012 0.004
#> GSM153087 4 0.2430 0.8342 0.036 0.000 0.004 0.900 0.048 0.012
#> GSM153088 4 0.5443 0.2151 0.348 0.000 0.048 0.560 0.044 0.000
#> GSM153089 3 0.5296 0.1450 0.008 0.000 0.532 0.008 0.060 0.392
#> GSM153090 4 0.4493 0.6337 0.192 0.000 0.036 0.728 0.044 0.000
#> GSM153091 1 0.1501 0.7865 0.924 0.000 0.000 0.076 0.000 0.000
#> GSM153092 1 0.3582 0.7082 0.732 0.000 0.000 0.252 0.016 0.000
#> GSM153093 4 0.1682 0.8216 0.052 0.000 0.000 0.928 0.020 0.000
#> GSM153094 1 0.1732 0.7858 0.920 0.000 0.004 0.072 0.004 0.000
#> GSM153095 1 0.3909 0.6910 0.808 0.000 0.112 0.036 0.032 0.012
#> GSM153096 1 0.1643 0.7851 0.924 0.000 0.000 0.068 0.008 0.000
#> GSM153097 1 0.2150 0.7691 0.912 0.000 0.036 0.044 0.004 0.004
#> GSM153098 1 0.2912 0.7306 0.784 0.000 0.000 0.216 0.000 0.000
#> GSM153099 4 0.2060 0.8087 0.084 0.000 0.000 0.900 0.016 0.000
#> GSM153100 1 0.2595 0.7671 0.836 0.000 0.000 0.160 0.004 0.000
#> GSM153101 1 0.2640 0.7573 0.892 0.000 0.040 0.032 0.032 0.004
#> GSM153102 1 0.3560 0.7272 0.836 0.000 0.084 0.044 0.012 0.024
#> GSM153103 1 0.3495 0.7077 0.820 0.000 0.128 0.028 0.020 0.004
#> GSM153104 4 0.2074 0.8191 0.000 0.000 0.004 0.912 0.048 0.036
#> GSM153106 1 0.4704 0.6618 0.660 0.000 0.000 0.272 0.056 0.012
#> GSM153107 1 0.4562 0.6994 0.692 0.000 0.000 0.236 0.060 0.012
#> GSM153108 4 0.3529 0.7417 0.176 0.000 0.000 0.788 0.028 0.008
#> GSM153109 1 0.2868 0.7520 0.876 0.000 0.060 0.044 0.012 0.008
#> GSM153110 1 0.1501 0.7865 0.924 0.000 0.000 0.076 0.000 0.000
#> GSM153111 1 0.2214 0.7713 0.912 0.000 0.028 0.044 0.012 0.004
#> GSM153112 1 0.2416 0.7677 0.844 0.000 0.000 0.156 0.000 0.000
#> GSM153113 1 0.3611 0.7187 0.840 0.008 0.064 0.032 0.052 0.004
#> GSM153114 4 0.2808 0.8033 0.076 0.000 0.000 0.868 0.048 0.008
#> GSM187532 2 0.5924 0.6797 0.020 0.644 0.120 0.000 0.168 0.048
#> GSM187533 2 0.3819 0.8582 0.028 0.784 0.000 0.000 0.160 0.028
#> GSM187534 2 0.3707 0.8622 0.024 0.792 0.000 0.000 0.156 0.028
#> GSM187535 1 0.6587 0.4218 0.564 0.220 0.000 0.068 0.128 0.020
#> GSM152906 2 0.2195 0.9095 0.012 0.904 0.000 0.000 0.068 0.016
#> GSM152907 2 0.2195 0.9095 0.012 0.904 0.000 0.000 0.068 0.016
#> GSM152908 2 0.1608 0.9022 0.016 0.940 0.004 0.000 0.036 0.004
#> GSM152909 2 0.3632 0.8690 0.020 0.824 0.020 0.000 0.112 0.024
#> GSM152910 2 0.1608 0.9022 0.016 0.940 0.004 0.000 0.036 0.004
#> GSM152911 2 0.0405 0.9144 0.000 0.988 0.000 0.000 0.008 0.004
#> GSM152912 2 0.1608 0.9022 0.016 0.940 0.004 0.000 0.036 0.004
#> GSM152913 2 0.1500 0.9107 0.000 0.936 0.000 0.000 0.052 0.012
#> GSM152914 2 0.0291 0.9147 0.000 0.992 0.000 0.000 0.004 0.004
#> GSM152915 2 0.0520 0.9139 0.000 0.984 0.000 0.000 0.008 0.008
#> GSM152916 2 0.2704 0.9015 0.012 0.868 0.000 0.000 0.100 0.020
#> GSM152917 2 0.0291 0.9147 0.000 0.992 0.000 0.000 0.004 0.004
#> GSM152918 2 0.0291 0.9147 0.000 0.992 0.000 0.000 0.004 0.004
#> GSM152919 2 0.0291 0.9147 0.000 0.992 0.000 0.000 0.004 0.004
#> GSM152920 2 0.1608 0.9022 0.016 0.940 0.004 0.000 0.036 0.004
#> GSM152921 2 0.1608 0.9022 0.016 0.940 0.004 0.000 0.036 0.004
#> GSM152922 2 0.1608 0.9022 0.016 0.940 0.004 0.000 0.036 0.004
#> GSM152923 2 0.2195 0.9095 0.012 0.904 0.000 0.000 0.068 0.016
#> GSM152924 2 0.2844 0.8989 0.016 0.860 0.000 0.000 0.104 0.020
#> GSM152925 2 0.2981 0.8943 0.016 0.848 0.000 0.000 0.116 0.020
#> GSM152926 2 0.2252 0.9089 0.012 0.900 0.000 0.000 0.072 0.016
#> GSM152927 2 0.2844 0.8989 0.016 0.860 0.000 0.000 0.104 0.020
#> GSM152928 2 0.4563 0.8139 0.096 0.756 0.012 0.000 0.116 0.020
#> GSM152929 2 0.2195 0.9095 0.012 0.904 0.000 0.000 0.068 0.016
#> GSM152930 2 0.2195 0.9095 0.012 0.904 0.000 0.000 0.068 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 tissue(p) k
#> MAD:kmeans 164 9.07e-30 2
#> MAD:kmeans 158 1.15e-33 3
#> MAD:kmeans 141 1.39e-34 4
#> MAD:kmeans 124 1.20e-34 5
#> MAD:kmeans 139 4.66e-36 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 12013 rows and 164 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 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 0.647 0.839 0.928 0.4902 0.508 0.508
#> 3 3 0.683 0.831 0.916 0.3379 0.762 0.565
#> 4 4 0.516 0.623 0.780 0.1405 0.846 0.591
#> 5 5 0.487 0.441 0.644 0.0643 0.957 0.836
#> 6 6 0.506 0.323 0.580 0.0404 0.912 0.665
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
#> GSM152839 1 0.0000 0.9347 1.000 0.000
#> GSM152840 1 0.0000 0.9347 1.000 0.000
#> GSM152841 1 0.0000 0.9347 1.000 0.000
#> GSM152842 1 0.8861 0.5517 0.696 0.304
#> GSM152843 1 0.0376 0.9328 0.996 0.004
#> GSM152844 1 0.2778 0.9075 0.952 0.048
#> GSM152845 2 0.0000 0.9004 0.000 1.000
#> GSM152846 2 0.9998 0.1028 0.492 0.508
#> GSM152847 1 0.0000 0.9347 1.000 0.000
#> GSM152848 1 0.0000 0.9347 1.000 0.000
#> GSM152849 1 0.8713 0.5777 0.708 0.292
#> GSM152850 1 0.5737 0.8270 0.864 0.136
#> GSM152851 1 0.7299 0.7397 0.796 0.204
#> GSM152852 1 0.7674 0.7084 0.776 0.224
#> GSM152853 1 0.1633 0.9230 0.976 0.024
#> GSM152854 2 0.9775 0.3704 0.412 0.588
#> GSM152855 1 0.0000 0.9347 1.000 0.000
#> GSM153238 2 0.0672 0.8984 0.008 0.992
#> GSM153239 1 0.3274 0.8987 0.940 0.060
#> GSM153240 1 0.0000 0.9347 1.000 0.000
#> GSM153241 1 0.3733 0.8898 0.928 0.072
#> GSM153242 2 0.7528 0.7396 0.216 0.784
#> GSM153243 2 0.0376 0.8995 0.004 0.996
#> GSM153244 2 0.9661 0.4303 0.392 0.608
#> GSM153245 1 0.2948 0.9053 0.948 0.052
#> GSM153246 2 0.6438 0.7963 0.164 0.836
#> GSM153247 2 0.8499 0.6578 0.276 0.724
#> GSM153248 1 0.9996 -0.0130 0.512 0.488
#> GSM153249 1 0.0000 0.9347 1.000 0.000
#> GSM153250 1 0.0000 0.9347 1.000 0.000
#> GSM153251 2 0.5059 0.8418 0.112 0.888
#> GSM153252 1 0.0000 0.9347 1.000 0.000
#> GSM153253 1 0.0000 0.9347 1.000 0.000
#> GSM153254 2 0.9954 0.2197 0.460 0.540
#> GSM153255 1 0.0000 0.9347 1.000 0.000
#> GSM153256 1 0.0000 0.9347 1.000 0.000
#> GSM153257 1 0.0000 0.9347 1.000 0.000
#> GSM153258 1 0.0376 0.9329 0.996 0.004
#> GSM153259 1 0.3114 0.9005 0.944 0.056
#> GSM153260 2 0.3114 0.8815 0.056 0.944
#> GSM153261 2 0.9850 0.3037 0.428 0.572
#> GSM153262 1 0.0000 0.9347 1.000 0.000
#> GSM153263 1 0.0000 0.9347 1.000 0.000
#> GSM153264 1 0.0000 0.9347 1.000 0.000
#> GSM153265 1 0.0000 0.9347 1.000 0.000
#> GSM153266 1 0.0000 0.9347 1.000 0.000
#> GSM153267 1 0.0000 0.9347 1.000 0.000
#> GSM153268 1 0.0000 0.9347 1.000 0.000
#> GSM153269 1 0.0000 0.9347 1.000 0.000
#> GSM153270 1 0.0000 0.9347 1.000 0.000
#> GSM153271 1 0.0000 0.9347 1.000 0.000
#> GSM153272 1 0.0000 0.9347 1.000 0.000
#> GSM153273 1 0.6247 0.8075 0.844 0.156
#> GSM153274 1 0.0000 0.9347 1.000 0.000
#> GSM153275 1 0.0000 0.9347 1.000 0.000
#> GSM153276 1 0.0000 0.9347 1.000 0.000
#> GSM153277 1 0.0000 0.9347 1.000 0.000
#> GSM153278 1 0.7056 0.7601 0.808 0.192
#> GSM153279 1 0.2603 0.9113 0.956 0.044
#> GSM153280 1 0.0000 0.9347 1.000 0.000
#> GSM153281 1 0.0000 0.9347 1.000 0.000
#> GSM153282 1 0.0000 0.9347 1.000 0.000
#> GSM153283 1 0.0000 0.9347 1.000 0.000
#> GSM153284 1 0.0000 0.9347 1.000 0.000
#> GSM153285 1 0.0000 0.9347 1.000 0.000
#> GSM153286 1 0.0000 0.9347 1.000 0.000
#> GSM153287 1 0.0000 0.9347 1.000 0.000
#> GSM153288 1 0.0000 0.9347 1.000 0.000
#> GSM153289 1 0.0000 0.9347 1.000 0.000
#> GSM153290 1 0.0000 0.9347 1.000 0.000
#> GSM153291 1 0.0000 0.9347 1.000 0.000
#> GSM153292 1 0.0000 0.9347 1.000 0.000
#> GSM153293 1 0.0000 0.9347 1.000 0.000
#> GSM153294 1 0.8386 0.6373 0.732 0.268
#> GSM153295 1 0.0000 0.9347 1.000 0.000
#> GSM153054 1 0.9996 -0.0393 0.512 0.488
#> GSM153055 1 0.0000 0.9347 1.000 0.000
#> GSM153056 1 0.0672 0.9309 0.992 0.008
#> GSM153057 2 0.8207 0.6907 0.256 0.744
#> GSM153058 2 0.9427 0.5014 0.360 0.640
#> GSM153059 2 0.0376 0.8995 0.004 0.996
#> GSM153060 2 0.9909 0.2786 0.444 0.556
#> GSM153061 2 0.2236 0.8890 0.036 0.964
#> GSM153062 2 0.1414 0.8946 0.020 0.980
#> GSM153063 1 0.9977 0.0261 0.528 0.472
#> GSM153064 1 0.3114 0.9012 0.944 0.056
#> GSM153065 2 0.0000 0.9004 0.000 1.000
#> GSM153066 2 0.0000 0.9004 0.000 1.000
#> GSM153067 1 0.0000 0.9347 1.000 0.000
#> GSM153068 2 0.1843 0.8915 0.028 0.972
#> GSM153069 1 0.0000 0.9347 1.000 0.000
#> GSM153070 1 0.1414 0.9254 0.980 0.020
#> GSM153071 2 0.9850 0.3286 0.428 0.572
#> GSM153072 2 0.5629 0.8292 0.132 0.868
#> GSM153073 1 0.1414 0.9254 0.980 0.020
#> GSM153074 1 0.0000 0.9347 1.000 0.000
#> GSM153075 1 0.0376 0.9329 0.996 0.004
#> GSM153076 1 0.0000 0.9347 1.000 0.000
#> GSM153077 1 0.3274 0.9008 0.940 0.060
#> GSM153078 1 0.7602 0.7187 0.780 0.220
#> GSM153079 2 0.8144 0.6846 0.252 0.748
#> GSM153080 1 0.7815 0.6941 0.768 0.232
#> GSM153081 1 0.0000 0.9347 1.000 0.000
#> GSM153082 2 0.2603 0.8855 0.044 0.956
#> GSM153083 2 0.0672 0.8985 0.008 0.992
#> GSM153084 2 0.0000 0.9004 0.000 1.000
#> GSM153085 2 0.2778 0.8859 0.048 0.952
#> GSM153086 2 0.6531 0.7917 0.168 0.832
#> GSM153087 1 0.0000 0.9347 1.000 0.000
#> GSM153088 1 0.0000 0.9347 1.000 0.000
#> GSM153089 2 0.4562 0.8562 0.096 0.904
#> GSM153090 1 0.0000 0.9347 1.000 0.000
#> GSM153091 2 0.7139 0.7603 0.196 0.804
#> GSM153092 1 0.4431 0.8762 0.908 0.092
#> GSM153093 1 0.0000 0.9347 1.000 0.000
#> GSM153094 2 0.5294 0.8349 0.120 0.880
#> GSM153095 2 0.8608 0.6393 0.284 0.716
#> GSM153096 1 0.6712 0.7833 0.824 0.176
#> GSM153097 2 0.2603 0.8860 0.044 0.956
#> GSM153098 1 0.4298 0.8762 0.912 0.088
#> GSM153099 1 0.0000 0.9347 1.000 0.000
#> GSM153100 1 0.2603 0.9112 0.956 0.044
#> GSM153101 2 0.7056 0.7658 0.192 0.808
#> GSM153102 2 0.3879 0.8679 0.076 0.924
#> GSM153103 2 0.2948 0.8822 0.052 0.948
#> GSM153104 1 0.0000 0.9347 1.000 0.000
#> GSM153106 1 0.6712 0.7828 0.824 0.176
#> GSM153107 1 0.6343 0.8027 0.840 0.160
#> GSM153108 1 0.1843 0.9212 0.972 0.028
#> GSM153109 2 0.0000 0.9004 0.000 1.000
#> GSM153110 1 0.8386 0.6381 0.732 0.268
#> GSM153111 2 0.4431 0.8575 0.092 0.908
#> GSM153112 1 0.7376 0.7398 0.792 0.208
#> GSM153113 2 0.0000 0.9004 0.000 1.000
#> GSM153114 1 0.0000 0.9347 1.000 0.000
#> GSM187532 2 0.0000 0.9004 0.000 1.000
#> GSM187533 2 0.0000 0.9004 0.000 1.000
#> GSM187534 2 0.0000 0.9004 0.000 1.000
#> GSM187535 2 0.0938 0.8973 0.012 0.988
#> GSM152906 2 0.0000 0.9004 0.000 1.000
#> GSM152907 2 0.0000 0.9004 0.000 1.000
#> GSM152908 2 0.0000 0.9004 0.000 1.000
#> GSM152909 2 0.0000 0.9004 0.000 1.000
#> GSM152910 2 0.0000 0.9004 0.000 1.000
#> GSM152911 2 0.0000 0.9004 0.000 1.000
#> GSM152912 2 0.0000 0.9004 0.000 1.000
#> GSM152913 2 0.0000 0.9004 0.000 1.000
#> GSM152914 2 0.0000 0.9004 0.000 1.000
#> GSM152915 2 0.0000 0.9004 0.000 1.000
#> GSM152916 2 0.0000 0.9004 0.000 1.000
#> GSM152917 2 0.0000 0.9004 0.000 1.000
#> GSM152918 2 0.0000 0.9004 0.000 1.000
#> GSM152919 2 0.0000 0.9004 0.000 1.000
#> GSM152920 2 0.0000 0.9004 0.000 1.000
#> GSM152921 2 0.0000 0.9004 0.000 1.000
#> GSM152922 2 0.0000 0.9004 0.000 1.000
#> GSM152923 2 0.0000 0.9004 0.000 1.000
#> GSM152924 2 0.0000 0.9004 0.000 1.000
#> GSM152925 2 0.0000 0.9004 0.000 1.000
#> GSM152926 2 0.0000 0.9004 0.000 1.000
#> GSM152927 2 0.0000 0.9004 0.000 1.000
#> GSM152928 2 0.0000 0.9004 0.000 1.000
#> GSM152929 2 0.0000 0.9004 0.000 1.000
#> GSM152930 2 0.0000 0.9004 0.000 1.000
cbind(get_classes(res, k = 3), get_membership(res, k = 3))
#> class entropy silhouette p1 p2 p3
#> GSM152839 3 0.4291 0.76319 0.180 0.000 0.820
#> GSM152840 3 0.2537 0.86197 0.080 0.000 0.920
#> GSM152841 1 0.1529 0.90955 0.960 0.000 0.040
#> GSM152842 3 0.0237 0.91042 0.004 0.000 0.996
#> GSM152843 3 0.0237 0.91119 0.004 0.000 0.996
#> GSM152844 3 0.0000 0.91149 0.000 0.000 1.000
#> GSM152845 3 0.0592 0.90918 0.000 0.012 0.988
#> GSM152846 3 0.0000 0.91149 0.000 0.000 1.000
#> GSM152847 3 0.0237 0.91042 0.004 0.000 0.996
#> GSM152848 1 0.6305 0.07772 0.516 0.000 0.484
#> GSM152849 3 0.0000 0.91149 0.000 0.000 1.000
#> GSM152850 3 0.0592 0.90969 0.012 0.000 0.988
#> GSM152851 3 0.3500 0.83178 0.116 0.004 0.880
#> GSM152852 3 0.0000 0.91149 0.000 0.000 1.000
#> GSM152853 3 0.0000 0.91149 0.000 0.000 1.000
#> GSM152854 3 0.0000 0.91149 0.000 0.000 1.000
#> GSM152855 1 0.0237 0.91551 0.996 0.000 0.004
#> GSM153238 3 0.2165 0.87892 0.000 0.064 0.936
#> GSM153239 3 0.0000 0.91149 0.000 0.000 1.000
#> GSM153240 1 0.0424 0.91528 0.992 0.000 0.008
#> GSM153241 3 0.0000 0.91149 0.000 0.000 1.000
#> GSM153242 3 0.0000 0.91149 0.000 0.000 1.000
#> GSM153243 3 0.1964 0.88483 0.000 0.056 0.944
#> GSM153244 3 0.8858 0.31083 0.136 0.332 0.532
#> GSM153245 3 0.0237 0.91093 0.004 0.000 0.996
#> GSM153246 3 0.0000 0.91149 0.000 0.000 1.000
#> GSM153247 3 0.2152 0.89460 0.016 0.036 0.948
#> GSM153248 1 0.6577 0.27075 0.572 0.420 0.008
#> GSM153249 1 0.0237 0.91551 0.996 0.000 0.004
#> GSM153250 1 0.0000 0.91503 1.000 0.000 0.000
#> GSM153251 3 0.0237 0.91125 0.000 0.004 0.996
#> GSM153252 1 0.0747 0.91492 0.984 0.000 0.016
#> GSM153253 1 0.3816 0.84069 0.852 0.000 0.148
#> GSM153254 3 0.5042 0.81328 0.060 0.104 0.836
#> GSM153255 1 0.0237 0.91551 0.996 0.000 0.004
#> GSM153256 1 0.0000 0.91503 1.000 0.000 0.000
#> GSM153257 1 0.0237 0.91551 0.996 0.000 0.004
#> GSM153258 1 0.1647 0.90989 0.960 0.004 0.036
#> GSM153259 1 0.0983 0.91257 0.980 0.016 0.004
#> GSM153260 3 0.1267 0.90339 0.004 0.024 0.972
#> GSM153261 3 0.0237 0.91049 0.000 0.004 0.996
#> GSM153262 1 0.1529 0.91080 0.960 0.000 0.040
#> GSM153263 1 0.0000 0.91503 1.000 0.000 0.000
#> GSM153264 1 0.3551 0.85125 0.868 0.000 0.132
#> GSM153265 1 0.1643 0.90881 0.956 0.000 0.044
#> GSM153266 1 0.3816 0.83856 0.852 0.000 0.148
#> GSM153267 1 0.0000 0.91503 1.000 0.000 0.000
#> GSM153268 1 0.5733 0.57403 0.676 0.000 0.324
#> GSM153269 1 0.0000 0.91503 1.000 0.000 0.000
#> GSM153270 1 0.4062 0.82420 0.836 0.000 0.164
#> GSM153271 1 0.0000 0.91503 1.000 0.000 0.000
#> GSM153272 1 0.0237 0.91551 0.996 0.000 0.004
#> GSM153273 1 0.4349 0.83128 0.852 0.128 0.020
#> GSM153274 1 0.2796 0.88442 0.908 0.000 0.092
#> GSM153275 1 0.0237 0.91551 0.996 0.000 0.004
#> GSM153276 1 0.4002 0.82866 0.840 0.000 0.160
#> GSM153277 1 0.1753 0.90759 0.952 0.000 0.048
#> GSM153278 3 0.1163 0.90319 0.028 0.000 0.972
#> GSM153279 3 0.6659 0.07719 0.460 0.008 0.532
#> GSM153280 1 0.3340 0.86514 0.880 0.000 0.120
#> GSM153281 1 0.1031 0.91342 0.976 0.000 0.024
#> GSM153282 1 0.2959 0.87960 0.900 0.000 0.100
#> GSM153283 1 0.0000 0.91503 1.000 0.000 0.000
#> GSM153284 1 0.0237 0.91551 0.996 0.000 0.004
#> GSM153285 1 0.1860 0.90503 0.948 0.000 0.052
#> GSM153286 1 0.0000 0.91503 1.000 0.000 0.000
#> GSM153287 1 0.0237 0.91551 0.996 0.000 0.004
#> GSM153288 1 0.0237 0.91551 0.996 0.000 0.004
#> GSM153289 1 0.0237 0.91551 0.996 0.000 0.004
#> GSM153290 1 0.4931 0.73479 0.768 0.000 0.232
#> GSM153291 1 0.0237 0.91551 0.996 0.000 0.004
#> GSM153292 1 0.0237 0.91551 0.996 0.000 0.004
#> GSM153293 1 0.0000 0.91503 1.000 0.000 0.000
#> GSM153294 1 0.3879 0.81472 0.848 0.152 0.000
#> GSM153295 1 0.0592 0.91537 0.988 0.000 0.012
#> GSM153054 3 0.7930 0.61705 0.168 0.168 0.664
#> GSM153055 1 0.5072 0.77545 0.792 0.012 0.196
#> GSM153056 3 0.0892 0.90536 0.020 0.000 0.980
#> GSM153057 3 0.2703 0.88041 0.016 0.056 0.928
#> GSM153058 3 0.0000 0.91149 0.000 0.000 1.000
#> GSM153059 3 0.4654 0.72039 0.000 0.208 0.792
#> GSM153060 3 0.0000 0.91149 0.000 0.000 1.000
#> GSM153061 3 0.0000 0.91149 0.000 0.000 1.000
#> GSM153062 3 0.0237 0.91049 0.000 0.004 0.996
#> GSM153063 3 0.0237 0.91093 0.004 0.000 0.996
#> GSM153064 1 0.0000 0.91503 1.000 0.000 0.000
#> GSM153065 3 0.1289 0.89999 0.000 0.032 0.968
#> GSM153066 2 0.5835 0.48309 0.000 0.660 0.340
#> GSM153067 1 0.0237 0.91551 0.996 0.000 0.004
#> GSM153068 3 0.0237 0.91049 0.000 0.004 0.996
#> GSM153069 1 0.0237 0.91551 0.996 0.000 0.004
#> GSM153070 1 0.5117 0.83493 0.832 0.060 0.108
#> GSM153071 3 0.6389 0.74988 0.124 0.108 0.768
#> GSM153072 3 0.7421 0.59200 0.084 0.240 0.676
#> GSM153073 1 0.2804 0.89561 0.924 0.016 0.060
#> GSM153074 1 0.0237 0.91551 0.996 0.000 0.004
#> GSM153075 1 0.5138 0.69364 0.748 0.000 0.252
#> GSM153076 1 0.0000 0.91503 1.000 0.000 0.000
#> GSM153077 1 0.5848 0.79812 0.796 0.080 0.124
#> GSM153078 3 0.5346 0.77940 0.152 0.040 0.808
#> GSM153079 2 0.9118 0.42774 0.232 0.548 0.220
#> GSM153080 3 0.0892 0.90547 0.020 0.000 0.980
#> GSM153081 1 0.4047 0.83256 0.848 0.004 0.148
#> GSM153082 2 0.3192 0.82181 0.112 0.888 0.000
#> GSM153083 2 0.0237 0.90337 0.004 0.996 0.000
#> GSM153084 2 0.3116 0.82238 0.000 0.892 0.108
#> GSM153085 2 0.8784 0.37234 0.136 0.548 0.316
#> GSM153086 2 0.9267 0.15801 0.160 0.460 0.380
#> GSM153087 1 0.3207 0.88762 0.904 0.012 0.084
#> GSM153088 1 0.0000 0.91503 1.000 0.000 0.000
#> GSM153089 3 0.0747 0.90804 0.000 0.016 0.984
#> GSM153090 1 0.0000 0.91503 1.000 0.000 0.000
#> GSM153091 2 0.5397 0.59908 0.280 0.720 0.000
#> GSM153092 1 0.4745 0.85183 0.852 0.080 0.068
#> GSM153093 1 0.0237 0.91551 0.996 0.000 0.004
#> GSM153094 2 0.2878 0.83695 0.096 0.904 0.000
#> GSM153095 3 0.9369 -0.00826 0.168 0.408 0.424
#> GSM153096 1 0.6302 0.70011 0.744 0.208 0.048
#> GSM153097 2 0.3415 0.84353 0.080 0.900 0.020
#> GSM153098 1 0.0983 0.91373 0.980 0.016 0.004
#> GSM153099 1 0.1289 0.91174 0.968 0.000 0.032
#> GSM153100 1 0.1643 0.90260 0.956 0.044 0.000
#> GSM153101 2 0.9207 0.30494 0.172 0.508 0.320
#> GSM153102 2 0.9117 0.30204 0.160 0.512 0.328
#> GSM153103 2 0.8457 0.22602 0.092 0.512 0.396
#> GSM153104 1 0.2625 0.88971 0.916 0.000 0.084
#> GSM153106 1 0.2860 0.87912 0.912 0.084 0.004
#> GSM153107 1 0.3918 0.82982 0.856 0.140 0.004
#> GSM153108 1 0.3921 0.85874 0.872 0.016 0.112
#> GSM153109 2 0.0892 0.89415 0.000 0.980 0.020
#> GSM153110 1 0.8109 0.50383 0.620 0.272 0.108
#> GSM153111 2 0.2945 0.84272 0.088 0.908 0.004
#> GSM153112 1 0.4555 0.75468 0.800 0.200 0.000
#> GSM153113 2 0.0000 0.90583 0.000 1.000 0.000
#> GSM153114 1 0.0237 0.91551 0.996 0.000 0.004
#> GSM187532 2 0.1031 0.89124 0.000 0.976 0.024
#> GSM187533 2 0.0000 0.90583 0.000 1.000 0.000
#> GSM187534 2 0.0000 0.90583 0.000 1.000 0.000
#> GSM187535 2 0.0000 0.90583 0.000 1.000 0.000
#> GSM152906 2 0.0000 0.90583 0.000 1.000 0.000
#> GSM152907 2 0.0000 0.90583 0.000 1.000 0.000
#> GSM152908 2 0.0000 0.90583 0.000 1.000 0.000
#> GSM152909 2 0.0000 0.90583 0.000 1.000 0.000
#> GSM152910 2 0.0000 0.90583 0.000 1.000 0.000
#> GSM152911 2 0.0000 0.90583 0.000 1.000 0.000
#> GSM152912 2 0.0000 0.90583 0.000 1.000 0.000
#> GSM152913 2 0.0000 0.90583 0.000 1.000 0.000
#> GSM152914 2 0.0000 0.90583 0.000 1.000 0.000
#> GSM152915 2 0.0000 0.90583 0.000 1.000 0.000
#> GSM152916 2 0.0000 0.90583 0.000 1.000 0.000
#> GSM152917 2 0.0000 0.90583 0.000 1.000 0.000
#> GSM152918 2 0.0000 0.90583 0.000 1.000 0.000
#> GSM152919 2 0.0000 0.90583 0.000 1.000 0.000
#> GSM152920 2 0.0000 0.90583 0.000 1.000 0.000
#> GSM152921 2 0.0000 0.90583 0.000 1.000 0.000
#> GSM152922 2 0.0000 0.90583 0.000 1.000 0.000
#> GSM152923 2 0.0000 0.90583 0.000 1.000 0.000
#> GSM152924 2 0.0000 0.90583 0.000 1.000 0.000
#> GSM152925 2 0.0000 0.90583 0.000 1.000 0.000
#> GSM152926 2 0.0000 0.90583 0.000 1.000 0.000
#> GSM152927 2 0.0000 0.90583 0.000 1.000 0.000
#> GSM152928 2 0.0000 0.90583 0.000 1.000 0.000
#> GSM152929 2 0.0000 0.90583 0.000 1.000 0.000
#> GSM152930 2 0.0000 0.90583 0.000 1.000 0.000
cbind(get_classes(res, k = 4), get_membership(res, k = 4))
#> class entropy silhouette p1 p2 p3 p4
#> GSM152839 3 0.7128 0.3318 0.320 0.000 0.528 0.152
#> GSM152840 3 0.5088 0.6004 0.024 0.000 0.688 0.288
#> GSM152841 4 0.1488 0.7176 0.032 0.000 0.012 0.956
#> GSM152842 3 0.0657 0.8149 0.012 0.000 0.984 0.004
#> GSM152843 3 0.3004 0.8074 0.060 0.000 0.892 0.048
#> GSM152844 3 0.2473 0.8080 0.012 0.000 0.908 0.080
#> GSM152845 3 0.1884 0.8177 0.016 0.020 0.948 0.016
#> GSM152846 3 0.0804 0.8144 0.008 0.000 0.980 0.012
#> GSM152847 3 0.2563 0.8123 0.072 0.000 0.908 0.020
#> GSM152848 1 0.7450 0.3189 0.504 0.000 0.280 0.216
#> GSM152849 3 0.1256 0.8176 0.028 0.000 0.964 0.008
#> GSM152850 3 0.3718 0.7552 0.168 0.000 0.820 0.012
#> GSM152851 3 0.5709 0.4257 0.024 0.004 0.588 0.384
#> GSM152852 3 0.2255 0.8116 0.012 0.000 0.920 0.068
#> GSM152853 3 0.3428 0.7705 0.012 0.000 0.844 0.144
#> GSM152854 3 0.1042 0.8171 0.020 0.000 0.972 0.008
#> GSM152855 4 0.4356 0.6446 0.292 0.000 0.000 0.708
#> GSM153238 3 0.4359 0.7571 0.100 0.084 0.816 0.000
#> GSM153239 3 0.2450 0.8112 0.016 0.000 0.912 0.072
#> GSM153240 4 0.4019 0.7209 0.196 0.000 0.012 0.792
#> GSM153241 3 0.2060 0.8173 0.052 0.000 0.932 0.016
#> GSM153242 3 0.0524 0.8137 0.004 0.000 0.988 0.008
#> GSM153243 3 0.3486 0.7885 0.092 0.044 0.864 0.000
#> GSM153244 3 0.9371 0.0463 0.100 0.276 0.376 0.248
#> GSM153245 3 0.1902 0.8145 0.004 0.000 0.932 0.064
#> GSM153246 3 0.0000 0.8116 0.000 0.000 1.000 0.000
#> GSM153247 3 0.6681 0.6748 0.088 0.128 0.704 0.080
#> GSM153248 1 0.4300 0.5521 0.820 0.092 0.000 0.088
#> GSM153249 4 0.2408 0.7255 0.104 0.000 0.000 0.896
#> GSM153250 1 0.4961 -0.0267 0.552 0.000 0.000 0.448
#> GSM153251 3 0.1059 0.8160 0.000 0.016 0.972 0.012
#> GSM153252 4 0.3306 0.7242 0.156 0.000 0.004 0.840
#> GSM153253 4 0.2500 0.7129 0.040 0.000 0.044 0.916
#> GSM153254 3 0.8107 0.5221 0.144 0.136 0.592 0.128
#> GSM153255 4 0.2469 0.7272 0.108 0.000 0.000 0.892
#> GSM153256 4 0.4843 0.4716 0.396 0.000 0.000 0.604
#> GSM153257 4 0.3311 0.7250 0.172 0.000 0.000 0.828
#> GSM153258 1 0.5557 0.3586 0.652 0.000 0.040 0.308
#> GSM153259 1 0.3266 0.5101 0.832 0.000 0.000 0.168
#> GSM153260 3 0.4648 0.7072 0.216 0.016 0.760 0.008
#> GSM153261 3 0.2597 0.8110 0.084 0.004 0.904 0.008
#> GSM153262 4 0.2730 0.7342 0.088 0.000 0.016 0.896
#> GSM153263 1 0.4955 0.0509 0.556 0.000 0.000 0.444
#> GSM153264 1 0.5371 0.4846 0.732 0.000 0.080 0.188
#> GSM153265 4 0.2797 0.7213 0.068 0.000 0.032 0.900
#> GSM153266 1 0.6525 0.4257 0.612 0.000 0.116 0.272
#> GSM153267 4 0.4643 0.5709 0.344 0.000 0.000 0.656
#> GSM153268 4 0.3946 0.6041 0.020 0.000 0.168 0.812
#> GSM153269 4 0.5132 0.3568 0.448 0.000 0.004 0.548
#> GSM153270 4 0.6664 0.4796 0.308 0.000 0.112 0.580
#> GSM153271 1 0.4961 0.0242 0.552 0.000 0.000 0.448
#> GSM153272 4 0.3219 0.7209 0.164 0.000 0.000 0.836
#> GSM153273 1 0.4801 0.5324 0.764 0.048 0.000 0.188
#> GSM153274 4 0.6514 0.2687 0.408 0.000 0.076 0.516
#> GSM153275 4 0.4889 0.5228 0.360 0.000 0.004 0.636
#> GSM153276 4 0.6681 0.4785 0.292 0.000 0.120 0.588
#> GSM153277 4 0.5810 0.5643 0.256 0.000 0.072 0.672
#> GSM153278 3 0.4957 0.7046 0.204 0.000 0.748 0.048
#> GSM153279 4 0.6646 0.3162 0.112 0.000 0.304 0.584
#> GSM153280 4 0.2111 0.7162 0.044 0.000 0.024 0.932
#> GSM153281 4 0.2775 0.7316 0.084 0.000 0.020 0.896
#> GSM153282 4 0.1936 0.7150 0.032 0.000 0.028 0.940
#> GSM153283 1 0.4746 0.2612 0.632 0.000 0.000 0.368
#> GSM153284 4 0.3942 0.6802 0.236 0.000 0.000 0.764
#> GSM153285 4 0.1389 0.7187 0.048 0.000 0.000 0.952
#> GSM153286 4 0.4277 0.6462 0.280 0.000 0.000 0.720
#> GSM153287 4 0.1118 0.7168 0.036 0.000 0.000 0.964
#> GSM153288 4 0.3569 0.7129 0.196 0.000 0.000 0.804
#> GSM153289 4 0.4746 0.5301 0.368 0.000 0.000 0.632
#> GSM153290 4 0.3301 0.6908 0.048 0.000 0.076 0.876
#> GSM153291 4 0.2281 0.7279 0.096 0.000 0.000 0.904
#> GSM153292 4 0.1557 0.7182 0.056 0.000 0.000 0.944
#> GSM153293 4 0.4277 0.6265 0.280 0.000 0.000 0.720
#> GSM153294 1 0.6259 0.4189 0.616 0.084 0.000 0.300
#> GSM153295 4 0.5062 0.6269 0.284 0.000 0.024 0.692
#> GSM153054 3 0.8385 -0.0771 0.408 0.076 0.412 0.104
#> GSM153055 4 0.7533 0.2678 0.308 0.012 0.156 0.524
#> GSM153056 3 0.4410 0.7631 0.128 0.000 0.808 0.064
#> GSM153057 3 0.6105 0.7185 0.104 0.084 0.744 0.068
#> GSM153058 3 0.0336 0.8134 0.008 0.000 0.992 0.000
#> GSM153059 3 0.6077 0.6011 0.096 0.220 0.680 0.004
#> GSM153060 3 0.0000 0.8116 0.000 0.000 1.000 0.000
#> GSM153061 3 0.0000 0.8116 0.000 0.000 1.000 0.000
#> GSM153062 3 0.0188 0.8121 0.000 0.000 0.996 0.004
#> GSM153063 3 0.2466 0.8155 0.028 0.000 0.916 0.056
#> GSM153064 1 0.4008 0.4701 0.756 0.000 0.000 0.244
#> GSM153065 3 0.1936 0.8130 0.028 0.032 0.940 0.000
#> GSM153066 2 0.6275 0.3682 0.076 0.596 0.328 0.000
#> GSM153067 4 0.3837 0.6996 0.224 0.000 0.000 0.776
#> GSM153068 3 0.0000 0.8116 0.000 0.000 1.000 0.000
#> GSM153069 4 0.1940 0.7250 0.076 0.000 0.000 0.924
#> GSM153070 1 0.6971 0.3369 0.588 0.020 0.088 0.304
#> GSM153071 3 0.8413 0.4252 0.136 0.120 0.556 0.188
#> GSM153072 3 0.9236 -0.0501 0.304 0.240 0.372 0.084
#> GSM153073 1 0.5775 0.4221 0.660 0.004 0.048 0.288
#> GSM153074 4 0.4008 0.6852 0.244 0.000 0.000 0.756
#> GSM153075 4 0.6349 0.5629 0.164 0.008 0.148 0.680
#> GSM153076 1 0.4661 0.3119 0.652 0.000 0.000 0.348
#> GSM153077 1 0.6145 0.4795 0.692 0.016 0.080 0.212
#> GSM153078 3 0.7164 0.5173 0.244 0.032 0.616 0.108
#> GSM153079 1 0.7540 0.5230 0.628 0.188 0.088 0.096
#> GSM153080 3 0.5140 0.7165 0.096 0.000 0.760 0.144
#> GSM153081 1 0.4990 0.5045 0.756 0.000 0.060 0.184
#> GSM153082 2 0.6544 0.2460 0.352 0.576 0.012 0.060
#> GSM153083 1 0.5702 0.2718 0.572 0.404 0.008 0.016
#> GSM153084 2 0.6416 0.5125 0.152 0.648 0.200 0.000
#> GSM153085 1 0.9302 0.2484 0.344 0.308 0.264 0.084
#> GSM153086 1 0.7291 0.5108 0.636 0.148 0.172 0.044
#> GSM153087 4 0.5397 0.6493 0.220 0.000 0.064 0.716
#> GSM153088 1 0.4888 0.1093 0.588 0.000 0.000 0.412
#> GSM153089 3 0.3495 0.8066 0.036 0.048 0.884 0.032
#> GSM153090 1 0.5163 -0.1409 0.516 0.000 0.004 0.480
#> GSM153091 1 0.6027 0.5251 0.660 0.252 0.000 0.088
#> GSM153092 1 0.6415 0.4516 0.664 0.032 0.056 0.248
#> GSM153093 4 0.3688 0.7073 0.208 0.000 0.000 0.792
#> GSM153094 1 0.6061 0.2955 0.552 0.400 0.000 0.048
#> GSM153095 1 0.9847 0.2929 0.320 0.232 0.268 0.180
#> GSM153096 1 0.5281 0.5397 0.756 0.048 0.016 0.180
#> GSM153097 1 0.6412 0.4065 0.604 0.332 0.024 0.040
#> GSM153098 4 0.5992 0.1871 0.444 0.040 0.000 0.516
#> GSM153099 4 0.5866 0.5252 0.324 0.000 0.052 0.624
#> GSM153100 1 0.5933 0.0379 0.516 0.028 0.004 0.452
#> GSM153101 1 0.9203 0.4293 0.460 0.220 0.172 0.148
#> GSM153102 1 0.9586 0.3136 0.348 0.300 0.220 0.132
#> GSM153103 1 0.8027 0.3864 0.500 0.296 0.176 0.028
#> GSM153104 4 0.4163 0.6879 0.096 0.000 0.076 0.828
#> GSM153106 4 0.6652 0.1466 0.396 0.088 0.000 0.516
#> GSM153107 1 0.6597 0.2766 0.540 0.088 0.000 0.372
#> GSM153108 4 0.6521 0.5628 0.192 0.024 0.104 0.680
#> GSM153109 2 0.5924 0.5686 0.240 0.692 0.048 0.020
#> GSM153110 1 0.4760 0.5497 0.816 0.060 0.028 0.096
#> GSM153111 1 0.5859 0.3631 0.588 0.376 0.004 0.032
#> GSM153112 1 0.6575 0.3463 0.560 0.092 0.000 0.348
#> GSM153113 2 0.2647 0.8337 0.120 0.880 0.000 0.000
#> GSM153114 4 0.3528 0.7019 0.192 0.000 0.000 0.808
#> GSM187532 2 0.1867 0.8695 0.000 0.928 0.072 0.000
#> GSM187533 2 0.0000 0.9402 0.000 1.000 0.000 0.000
#> GSM187534 2 0.0188 0.9370 0.004 0.996 0.000 0.000
#> GSM187535 2 0.2413 0.8692 0.064 0.916 0.000 0.020
#> GSM152906 2 0.0000 0.9402 0.000 1.000 0.000 0.000
#> GSM152907 2 0.0000 0.9402 0.000 1.000 0.000 0.000
#> GSM152908 2 0.0000 0.9402 0.000 1.000 0.000 0.000
#> GSM152909 2 0.0188 0.9368 0.000 0.996 0.004 0.000
#> GSM152910 2 0.0000 0.9402 0.000 1.000 0.000 0.000
#> GSM152911 2 0.0000 0.9402 0.000 1.000 0.000 0.000
#> GSM152912 2 0.0000 0.9402 0.000 1.000 0.000 0.000
#> GSM152913 2 0.0000 0.9402 0.000 1.000 0.000 0.000
#> GSM152914 2 0.0000 0.9402 0.000 1.000 0.000 0.000
#> GSM152915 2 0.0000 0.9402 0.000 1.000 0.000 0.000
#> GSM152916 2 0.0000 0.9402 0.000 1.000 0.000 0.000
#> GSM152917 2 0.0000 0.9402 0.000 1.000 0.000 0.000
#> GSM152918 2 0.0000 0.9402 0.000 1.000 0.000 0.000
#> GSM152919 2 0.0000 0.9402 0.000 1.000 0.000 0.000
#> GSM152920 2 0.0000 0.9402 0.000 1.000 0.000 0.000
#> GSM152921 2 0.0000 0.9402 0.000 1.000 0.000 0.000
#> GSM152922 2 0.0000 0.9402 0.000 1.000 0.000 0.000
#> GSM152923 2 0.0000 0.9402 0.000 1.000 0.000 0.000
#> GSM152924 2 0.0000 0.9402 0.000 1.000 0.000 0.000
#> GSM152925 2 0.0000 0.9402 0.000 1.000 0.000 0.000
#> GSM152926 2 0.0000 0.9402 0.000 1.000 0.000 0.000
#> GSM152927 2 0.0000 0.9402 0.000 1.000 0.000 0.000
#> GSM152928 2 0.0188 0.9367 0.000 0.996 0.004 0.000
#> GSM152929 2 0.0000 0.9402 0.000 1.000 0.000 0.000
#> GSM152930 2 0.0000 0.9402 0.000 1.000 0.000 0.000
cbind(get_classes(res, k = 5), get_membership(res, k = 5))
#> class entropy silhouette p1 p2 p3 p4 p5
#> GSM152839 3 0.8058 0.17039 0.216 0.000 0.408 0.116 0.260
#> GSM152840 3 0.6626 0.31536 0.016 0.000 0.476 0.364 0.144
#> GSM152841 4 0.3591 0.54976 0.020 0.000 0.028 0.836 0.116
#> GSM152842 3 0.3127 0.70213 0.020 0.000 0.848 0.004 0.128
#> GSM152843 3 0.5772 0.61639 0.040 0.000 0.656 0.068 0.236
#> GSM152844 3 0.4111 0.68406 0.000 0.000 0.788 0.120 0.092
#> GSM152845 3 0.3598 0.70342 0.008 0.056 0.844 0.004 0.088
#> GSM152846 3 0.3008 0.70243 0.004 0.000 0.868 0.036 0.092
#> GSM152847 3 0.5614 0.67085 0.084 0.000 0.696 0.044 0.176
#> GSM152848 5 0.8140 0.22943 0.228 0.000 0.252 0.124 0.396
#> GSM152849 3 0.3888 0.70212 0.032 0.000 0.788 0.004 0.176
#> GSM152850 3 0.6188 0.57758 0.120 0.000 0.592 0.020 0.268
#> GSM152851 3 0.7540 0.09853 0.044 0.008 0.388 0.388 0.172
#> GSM152852 3 0.4507 0.68566 0.012 0.000 0.776 0.112 0.100
#> GSM152853 3 0.5225 0.61744 0.004 0.000 0.692 0.188 0.116
#> GSM152854 3 0.3031 0.70908 0.004 0.000 0.856 0.020 0.120
#> GSM152855 4 0.6296 0.29691 0.200 0.000 0.000 0.528 0.272
#> GSM153238 3 0.6546 0.61195 0.156 0.060 0.632 0.004 0.148
#> GSM153239 3 0.4499 0.69344 0.004 0.000 0.764 0.096 0.136
#> GSM153240 4 0.6022 0.47621 0.112 0.000 0.020 0.616 0.252
#> GSM153241 3 0.4461 0.69670 0.020 0.000 0.760 0.036 0.184
#> GSM153242 3 0.2351 0.70469 0.000 0.000 0.896 0.016 0.088
#> GSM153243 3 0.5955 0.64933 0.076 0.060 0.664 0.000 0.200
#> GSM153244 3 0.9623 -0.10617 0.076 0.216 0.244 0.240 0.224
#> GSM153245 3 0.5070 0.65943 0.004 0.000 0.712 0.160 0.124
#> GSM153246 3 0.1764 0.69680 0.008 0.000 0.928 0.000 0.064
#> GSM153247 3 0.7605 0.57287 0.104 0.076 0.572 0.052 0.196
#> GSM153248 1 0.5160 0.17499 0.740 0.048 0.000 0.068 0.144
#> GSM153249 4 0.3692 0.55631 0.136 0.000 0.000 0.812 0.052
#> GSM153250 4 0.6801 -0.25416 0.292 0.000 0.000 0.360 0.348
#> GSM153251 3 0.3937 0.71099 0.012 0.024 0.828 0.024 0.112
#> GSM153252 4 0.5169 0.53900 0.116 0.000 0.012 0.716 0.156
#> GSM153253 4 0.4397 0.52507 0.020 0.000 0.068 0.788 0.124
#> GSM153254 3 0.9119 0.31929 0.092 0.120 0.400 0.152 0.236
#> GSM153255 4 0.4123 0.55110 0.104 0.000 0.000 0.788 0.108
#> GSM153256 4 0.6452 0.17936 0.220 0.000 0.000 0.496 0.284
#> GSM153257 4 0.5691 0.49980 0.124 0.000 0.008 0.644 0.224
#> GSM153258 5 0.7906 0.39479 0.348 0.004 0.076 0.196 0.376
#> GSM153259 1 0.4781 0.06257 0.728 0.000 0.000 0.112 0.160
#> GSM153260 3 0.6281 0.60320 0.152 0.040 0.632 0.000 0.176
#> GSM153261 3 0.5651 0.66862 0.096 0.004 0.680 0.020 0.200
#> GSM153262 4 0.5108 0.55503 0.076 0.000 0.020 0.720 0.184
#> GSM153263 1 0.7096 -0.37244 0.380 0.000 0.012 0.332 0.276
#> GSM153264 5 0.7373 0.41140 0.380 0.000 0.068 0.136 0.416
#> GSM153265 4 0.5496 0.52792 0.064 0.000 0.056 0.708 0.172
#> GSM153266 1 0.7635 -0.32823 0.432 0.000 0.096 0.140 0.332
#> GSM153267 4 0.7107 -0.06237 0.268 0.000 0.016 0.420 0.296
#> GSM153268 4 0.4863 0.47214 0.008 0.000 0.116 0.740 0.136
#> GSM153269 4 0.6824 -0.10428 0.240 0.000 0.004 0.404 0.352
#> GSM153270 4 0.8068 0.14300 0.208 0.000 0.132 0.424 0.236
#> GSM153271 4 0.6771 -0.13799 0.312 0.000 0.000 0.396 0.292
#> GSM153272 4 0.5045 0.49925 0.108 0.000 0.000 0.696 0.196
#> GSM153273 1 0.5595 0.05874 0.668 0.004 0.004 0.184 0.140
#> GSM153274 4 0.7987 -0.15704 0.284 0.000 0.080 0.348 0.288
#> GSM153275 4 0.6389 0.28851 0.284 0.000 0.004 0.528 0.184
#> GSM153276 4 0.7634 0.14059 0.148 0.000 0.096 0.452 0.304
#> GSM153277 4 0.7089 0.41712 0.136 0.000 0.072 0.540 0.252
#> GSM153278 3 0.6980 0.51411 0.156 0.000 0.548 0.056 0.240
#> GSM153279 4 0.7341 0.24883 0.064 0.000 0.196 0.504 0.236
#> GSM153280 4 0.4392 0.52773 0.024 0.000 0.068 0.792 0.116
#> GSM153281 4 0.4675 0.55655 0.072 0.000 0.020 0.764 0.144
#> GSM153282 4 0.3989 0.54353 0.008 0.000 0.048 0.800 0.144
#> GSM153283 1 0.6748 -0.36289 0.456 0.000 0.004 0.252 0.288
#> GSM153284 4 0.5877 0.45117 0.196 0.000 0.000 0.604 0.200
#> GSM153285 4 0.3763 0.55539 0.044 0.000 0.036 0.840 0.080
#> GSM153286 4 0.5848 0.43442 0.192 0.000 0.000 0.608 0.200
#> GSM153287 4 0.2124 0.55705 0.028 0.000 0.000 0.916 0.056
#> GSM153288 4 0.5184 0.51227 0.136 0.000 0.000 0.688 0.176
#> GSM153289 4 0.6556 0.15103 0.260 0.000 0.000 0.476 0.264
#> GSM153290 4 0.4845 0.51177 0.020 0.000 0.084 0.752 0.144
#> GSM153291 4 0.3857 0.55699 0.084 0.000 0.000 0.808 0.108
#> GSM153292 4 0.3256 0.56262 0.064 0.000 0.012 0.864 0.060
#> GSM153293 4 0.6128 0.35454 0.252 0.000 0.000 0.560 0.188
#> GSM153294 1 0.6798 0.05457 0.556 0.040 0.000 0.240 0.164
#> GSM153295 4 0.7294 0.24096 0.172 0.000 0.056 0.484 0.288
#> GSM153054 3 0.8871 -0.03958 0.288 0.048 0.352 0.096 0.216
#> GSM153055 4 0.8151 -0.10198 0.212 0.004 0.104 0.392 0.288
#> GSM153056 3 0.6358 0.59634 0.076 0.000 0.612 0.068 0.244
#> GSM153057 3 0.6970 0.62477 0.092 0.060 0.640 0.056 0.152
#> GSM153058 3 0.3573 0.70973 0.012 0.000 0.816 0.016 0.156
#> GSM153059 3 0.7564 0.47677 0.116 0.152 0.528 0.004 0.200
#> GSM153060 3 0.1851 0.69982 0.000 0.000 0.912 0.000 0.088
#> GSM153061 3 0.2570 0.70249 0.028 0.000 0.888 0.000 0.084
#> GSM153062 3 0.1502 0.69399 0.004 0.000 0.940 0.000 0.056
#> GSM153063 3 0.5337 0.68317 0.036 0.000 0.724 0.100 0.140
#> GSM153064 1 0.4967 0.07515 0.704 0.000 0.000 0.192 0.104
#> GSM153065 3 0.4113 0.69843 0.024 0.048 0.808 0.000 0.120
#> GSM153066 2 0.7310 0.19184 0.140 0.520 0.252 0.000 0.088
#> GSM153067 4 0.4797 0.52764 0.172 0.000 0.000 0.724 0.104
#> GSM153068 3 0.1831 0.70020 0.004 0.000 0.920 0.000 0.076
#> GSM153069 4 0.2871 0.55753 0.040 0.000 0.000 0.872 0.088
#> GSM153070 5 0.7753 0.44713 0.324 0.012 0.048 0.196 0.420
#> GSM153071 3 0.9193 0.22260 0.204 0.076 0.388 0.140 0.192
#> GSM153072 3 0.9277 0.02463 0.264 0.108 0.336 0.084 0.208
#> GSM153073 5 0.7517 0.39409 0.348 0.000 0.040 0.248 0.364
#> GSM153074 4 0.5610 0.49995 0.180 0.000 0.000 0.640 0.180
#> GSM153075 4 0.7427 0.25559 0.124 0.000 0.096 0.484 0.296
#> GSM153076 1 0.6450 -0.33552 0.492 0.000 0.000 0.296 0.212
#> GSM153077 5 0.7856 0.42435 0.372 0.012 0.056 0.188 0.372
#> GSM153078 3 0.8396 0.05053 0.224 0.016 0.360 0.092 0.308
#> GSM153079 1 0.8356 0.19663 0.480 0.156 0.088 0.052 0.224
#> GSM153080 3 0.7159 0.54529 0.092 0.000 0.560 0.164 0.184
#> GSM153081 1 0.6816 -0.27906 0.468 0.000 0.040 0.112 0.380
#> GSM153082 1 0.7792 0.24877 0.400 0.392 0.028 0.056 0.124
#> GSM153083 1 0.6384 0.28338 0.532 0.340 0.024 0.000 0.104
#> GSM153084 2 0.7777 0.17168 0.216 0.516 0.132 0.012 0.124
#> GSM153085 1 0.9538 0.15014 0.324 0.184 0.184 0.088 0.220
#> GSM153086 1 0.7389 0.20114 0.588 0.076 0.136 0.032 0.168
#> GSM153087 4 0.6932 0.39062 0.184 0.004 0.048 0.572 0.192
#> GSM153088 5 0.7132 0.35472 0.344 0.000 0.012 0.296 0.348
#> GSM153089 3 0.6923 0.64794 0.048 0.092 0.644 0.068 0.148
#> GSM153090 4 0.6911 -0.14604 0.296 0.000 0.004 0.392 0.308
#> GSM153091 1 0.6512 0.21132 0.612 0.160 0.000 0.048 0.180
#> GSM153092 1 0.8347 -0.24632 0.420 0.040 0.064 0.192 0.284
#> GSM153093 4 0.5969 0.46695 0.132 0.000 0.016 0.628 0.224
#> GSM153094 1 0.6698 0.29355 0.536 0.320 0.008 0.028 0.108
#> GSM153095 1 0.9580 0.15231 0.344 0.184 0.192 0.116 0.164
#> GSM153096 1 0.6290 0.11414 0.664 0.032 0.020 0.160 0.124
#> GSM153097 1 0.5994 0.30493 0.644 0.216 0.020 0.004 0.116
#> GSM153098 1 0.6616 -0.06002 0.488 0.024 0.004 0.380 0.104
#> GSM153099 4 0.7784 0.00266 0.276 0.000 0.064 0.388 0.272
#> GSM153100 1 0.7406 -0.14790 0.464 0.024 0.012 0.244 0.256
#> GSM153101 1 0.9221 0.20428 0.404 0.180 0.160 0.092 0.164
#> GSM153102 1 0.9785 0.17180 0.276 0.228 0.212 0.132 0.152
#> GSM153103 1 0.9080 0.20647 0.372 0.196 0.160 0.048 0.224
#> GSM153104 4 0.5314 0.53121 0.060 0.000 0.068 0.732 0.140
#> GSM153106 4 0.8079 -0.10744 0.328 0.068 0.008 0.348 0.248
#> GSM153107 1 0.7214 -0.09887 0.464 0.032 0.000 0.252 0.252
#> GSM153108 4 0.7622 0.24014 0.212 0.000 0.076 0.464 0.248
#> GSM153109 2 0.7720 0.12310 0.264 0.516 0.072 0.032 0.116
#> GSM153110 1 0.5210 0.20092 0.752 0.032 0.012 0.080 0.124
#> GSM153111 1 0.6717 0.30709 0.612 0.216 0.024 0.032 0.116
#> GSM153112 1 0.7602 0.03114 0.496 0.104 0.008 0.280 0.112
#> GSM153113 2 0.5344 0.57491 0.192 0.696 0.008 0.004 0.100
#> GSM153114 4 0.5900 0.39190 0.188 0.000 0.000 0.600 0.212
#> GSM187532 2 0.2494 0.85602 0.016 0.908 0.044 0.000 0.032
#> GSM187533 2 0.1018 0.90781 0.016 0.968 0.000 0.000 0.016
#> GSM187534 2 0.1117 0.90758 0.020 0.964 0.000 0.000 0.016
#> GSM187535 2 0.4422 0.70517 0.116 0.788 0.000 0.020 0.076
#> GSM152906 2 0.0324 0.92178 0.004 0.992 0.000 0.000 0.004
#> GSM152907 2 0.0324 0.92178 0.004 0.992 0.000 0.000 0.004
#> GSM152908 2 0.0162 0.92214 0.000 0.996 0.000 0.000 0.004
#> GSM152909 2 0.0451 0.91863 0.000 0.988 0.004 0.000 0.008
#> GSM152910 2 0.0162 0.92214 0.000 0.996 0.000 0.000 0.004
#> GSM152911 2 0.0000 0.92231 0.000 1.000 0.000 0.000 0.000
#> GSM152912 2 0.0162 0.92214 0.000 0.996 0.000 0.000 0.004
#> GSM152913 2 0.0324 0.92079 0.000 0.992 0.004 0.000 0.004
#> GSM152914 2 0.0000 0.92231 0.000 1.000 0.000 0.000 0.000
#> GSM152915 2 0.0000 0.92231 0.000 1.000 0.000 0.000 0.000
#> GSM152916 2 0.0290 0.92160 0.000 0.992 0.000 0.000 0.008
#> GSM152917 2 0.0000 0.92231 0.000 1.000 0.000 0.000 0.000
#> GSM152918 2 0.0000 0.92231 0.000 1.000 0.000 0.000 0.000
#> GSM152919 2 0.0000 0.92231 0.000 1.000 0.000 0.000 0.000
#> GSM152920 2 0.0162 0.92214 0.000 0.996 0.000 0.000 0.004
#> GSM152921 2 0.0162 0.92214 0.000 0.996 0.000 0.000 0.004
#> GSM152922 2 0.0162 0.92214 0.000 0.996 0.000 0.000 0.004
#> GSM152923 2 0.0451 0.92063 0.004 0.988 0.000 0.000 0.008
#> GSM152924 2 0.0579 0.91975 0.008 0.984 0.000 0.000 0.008
#> GSM152925 2 0.0290 0.92160 0.000 0.992 0.000 0.000 0.008
#> GSM152926 2 0.0324 0.92178 0.004 0.992 0.000 0.000 0.004
#> GSM152927 2 0.0693 0.91888 0.008 0.980 0.000 0.000 0.012
#> GSM152928 2 0.1471 0.90102 0.024 0.952 0.004 0.000 0.020
#> GSM152929 2 0.0324 0.92178 0.004 0.992 0.000 0.000 0.004
#> GSM152930 2 0.0324 0.92178 0.004 0.992 0.000 0.000 0.004
cbind(get_classes(res, k = 6), get_membership(res, k = 6))
#> class entropy silhouette p1 p2 p3 p4 p5 p6
#> GSM152839 3 0.8595 -0.08030 0.204 0.000 0.300 0.088 0.244 0.164
#> GSM152840 3 0.6854 0.18326 0.032 0.000 0.416 0.380 0.140 0.032
#> GSM152841 4 0.4838 0.47120 0.068 0.000 0.052 0.764 0.076 0.040
#> GSM152842 3 0.4950 0.53348 0.060 0.000 0.680 0.008 0.232 0.020
#> GSM152843 3 0.6972 0.41017 0.144 0.000 0.552 0.088 0.180 0.036
#> GSM152844 3 0.5480 0.50613 0.024 0.000 0.656 0.176 0.136 0.008
#> GSM152845 3 0.4784 0.51917 0.004 0.052 0.740 0.004 0.148 0.052
#> GSM152846 3 0.4140 0.55794 0.004 0.000 0.776 0.072 0.132 0.016
#> GSM152847 3 0.7082 0.37020 0.156 0.000 0.524 0.040 0.212 0.068
#> GSM152848 1 0.8497 -0.00171 0.348 0.000 0.228 0.100 0.180 0.144
#> GSM152849 3 0.5287 0.54291 0.048 0.000 0.668 0.016 0.228 0.040
#> GSM152850 3 0.6968 0.33151 0.152 0.000 0.496 0.028 0.268 0.056
#> GSM152851 3 0.8119 0.07371 0.084 0.016 0.364 0.340 0.128 0.068
#> GSM152852 3 0.5594 0.52729 0.012 0.000 0.664 0.136 0.152 0.036
#> GSM152853 3 0.5298 0.48338 0.004 0.000 0.632 0.200 0.160 0.004
#> GSM152854 3 0.4755 0.56136 0.032 0.004 0.736 0.032 0.176 0.020
#> GSM152855 4 0.6894 0.07553 0.252 0.000 0.000 0.360 0.052 0.336
#> GSM153238 3 0.7282 0.32276 0.048 0.072 0.548 0.024 0.216 0.092
#> GSM153239 3 0.5643 0.53426 0.040 0.000 0.668 0.140 0.136 0.016
#> GSM153240 4 0.6483 0.29261 0.276 0.000 0.016 0.544 0.092 0.072
#> GSM153241 3 0.5989 0.50407 0.084 0.000 0.632 0.036 0.208 0.040
#> GSM153242 3 0.3956 0.56187 0.004 0.000 0.776 0.056 0.156 0.008
#> GSM153243 3 0.7398 0.30476 0.080 0.064 0.492 0.004 0.264 0.096
#> GSM153244 2 0.9869 -0.60008 0.148 0.216 0.164 0.192 0.176 0.104
#> GSM153245 3 0.5655 0.50120 0.020 0.000 0.644 0.172 0.148 0.016
#> GSM153246 3 0.3077 0.55458 0.008 0.000 0.836 0.012 0.136 0.008
#> GSM153247 3 0.7717 0.27393 0.060 0.040 0.472 0.068 0.288 0.072
#> GSM153248 6 0.7465 0.14531 0.272 0.056 0.016 0.048 0.124 0.484
#> GSM153249 4 0.5052 0.42412 0.148 0.000 0.000 0.708 0.064 0.080
#> GSM153250 1 0.5776 0.39773 0.608 0.000 0.000 0.236 0.056 0.100
#> GSM153251 3 0.4813 0.54837 0.012 0.024 0.736 0.032 0.176 0.020
#> GSM153252 4 0.6883 0.36083 0.152 0.000 0.040 0.572 0.092 0.144
#> GSM153253 4 0.5163 0.46249 0.052 0.000 0.076 0.736 0.100 0.036
#> GSM153254 3 0.9445 -0.09033 0.088 0.108 0.304 0.148 0.232 0.120
#> GSM153255 4 0.5006 0.40904 0.184 0.000 0.000 0.696 0.044 0.076
#> GSM153256 1 0.6456 0.08465 0.436 0.000 0.000 0.388 0.092 0.084
#> GSM153257 4 0.6080 0.36049 0.240 0.000 0.004 0.580 0.128 0.048
#> GSM153258 1 0.7842 0.29088 0.444 0.000 0.056 0.132 0.148 0.220
#> GSM153259 6 0.6814 0.00801 0.352 0.000 0.004 0.116 0.092 0.436
#> GSM153260 3 0.7907 0.19016 0.100 0.036 0.448 0.024 0.260 0.132
#> GSM153261 3 0.6682 0.40583 0.064 0.004 0.540 0.020 0.268 0.104
#> GSM153262 4 0.6989 0.37125 0.124 0.000 0.048 0.564 0.096 0.168
#> GSM153263 1 0.7051 0.23499 0.420 0.000 0.004 0.312 0.080 0.184
#> GSM153264 1 0.7503 0.26551 0.508 0.000 0.080 0.080 0.164 0.168
#> GSM153265 4 0.6220 0.42986 0.140 0.000 0.068 0.648 0.088 0.056
#> GSM153266 1 0.8013 0.29301 0.432 0.000 0.064 0.176 0.148 0.180
#> GSM153267 1 0.6950 0.25162 0.452 0.000 0.004 0.308 0.100 0.136
#> GSM153268 4 0.5798 0.39198 0.064 0.000 0.160 0.664 0.092 0.020
#> GSM153269 1 0.6600 0.25698 0.508 0.000 0.004 0.288 0.084 0.116
#> GSM153270 4 0.8403 -0.07016 0.304 0.000 0.112 0.312 0.168 0.104
#> GSM153271 1 0.5460 0.27365 0.560 0.000 0.000 0.324 0.012 0.104
#> GSM153272 4 0.6088 0.31041 0.280 0.000 0.012 0.572 0.084 0.052
#> GSM153273 6 0.7687 0.11145 0.296 0.016 0.004 0.140 0.152 0.392
#> GSM153274 1 0.8252 0.24914 0.352 0.000 0.080 0.288 0.136 0.144
#> GSM153275 4 0.7127 0.02116 0.364 0.000 0.020 0.404 0.072 0.140
#> GSM153276 1 0.7724 0.12654 0.360 0.000 0.068 0.352 0.156 0.064
#> GSM153277 4 0.7842 0.26790 0.188 0.000 0.072 0.464 0.124 0.152
#> GSM153278 3 0.8067 0.11299 0.136 0.000 0.372 0.068 0.296 0.128
#> GSM153279 4 0.8218 0.11616 0.108 0.000 0.196 0.384 0.228 0.084
#> GSM153280 4 0.6115 0.44286 0.056 0.000 0.084 0.664 0.108 0.088
#> GSM153281 4 0.5490 0.45682 0.148 0.000 0.040 0.700 0.060 0.052
#> GSM153282 4 0.5201 0.46938 0.096 0.000 0.056 0.728 0.096 0.024
#> GSM153283 1 0.6819 0.35018 0.512 0.000 0.004 0.212 0.092 0.180
#> GSM153284 4 0.7053 0.06821 0.360 0.000 0.016 0.420 0.096 0.108
#> GSM153285 4 0.5681 0.46687 0.096 0.000 0.072 0.700 0.084 0.048
#> GSM153286 4 0.6691 0.11313 0.340 0.000 0.008 0.464 0.068 0.120
#> GSM153287 4 0.3273 0.47081 0.072 0.000 0.000 0.848 0.044 0.036
#> GSM153288 4 0.6197 0.31858 0.256 0.000 0.004 0.568 0.068 0.104
#> GSM153289 6 0.7190 -0.25192 0.300 0.000 0.000 0.292 0.080 0.328
#> GSM153290 4 0.6572 0.42583 0.068 0.000 0.096 0.620 0.136 0.080
#> GSM153291 4 0.5951 0.39602 0.156 0.000 0.004 0.620 0.056 0.164
#> GSM153292 4 0.4005 0.47648 0.080 0.000 0.008 0.808 0.040 0.064
#> GSM153293 4 0.6771 0.00399 0.360 0.000 0.004 0.404 0.048 0.184
#> GSM153294 6 0.8213 0.03560 0.288 0.048 0.004 0.204 0.120 0.336
#> GSM153295 4 0.7996 -0.01070 0.304 0.000 0.068 0.372 0.100 0.156
#> GSM153054 6 0.9235 -0.28373 0.184 0.036 0.240 0.084 0.212 0.244
#> GSM153055 1 0.8369 0.24868 0.344 0.000 0.076 0.248 0.196 0.136
#> GSM153056 3 0.7737 0.29599 0.128 0.000 0.424 0.096 0.288 0.064
#> GSM153057 3 0.8158 0.22977 0.096 0.036 0.452 0.060 0.244 0.112
#> GSM153058 3 0.4276 0.56185 0.036 0.000 0.764 0.016 0.164 0.020
#> GSM153059 3 0.8555 -0.07317 0.080 0.176 0.368 0.016 0.248 0.112
#> GSM153060 3 0.3057 0.55655 0.008 0.000 0.852 0.016 0.108 0.016
#> GSM153061 3 0.3304 0.54618 0.008 0.000 0.804 0.000 0.168 0.020
#> GSM153062 3 0.2243 0.54938 0.000 0.004 0.880 0.004 0.112 0.000
#> GSM153063 3 0.6388 0.48249 0.044 0.000 0.624 0.100 0.160 0.072
#> GSM153064 6 0.7236 0.06559 0.300 0.000 0.004 0.192 0.100 0.404
#> GSM153065 3 0.5222 0.49280 0.012 0.056 0.700 0.000 0.172 0.060
#> GSM153066 2 0.7562 -0.23560 0.016 0.432 0.208 0.000 0.204 0.140
#> GSM153067 4 0.5565 0.39557 0.192 0.000 0.000 0.648 0.060 0.100
#> GSM153068 3 0.3799 0.54685 0.028 0.004 0.776 0.000 0.180 0.012
#> GSM153069 4 0.4205 0.46553 0.136 0.000 0.012 0.780 0.048 0.024
#> GSM153070 1 0.7222 0.36371 0.556 0.004 0.052 0.136 0.112 0.140
#> GSM153071 3 0.9038 -0.24863 0.132 0.052 0.316 0.104 0.288 0.108
#> GSM153072 5 0.9592 0.33563 0.164 0.088 0.204 0.084 0.236 0.224
#> GSM153073 1 0.8247 0.30089 0.388 0.000 0.068 0.192 0.164 0.188
#> GSM153074 4 0.6558 0.25152 0.268 0.000 0.000 0.500 0.064 0.168
#> GSM153075 4 0.8547 0.03553 0.164 0.000 0.084 0.308 0.192 0.252
#> GSM153076 1 0.6533 0.35648 0.516 0.000 0.000 0.232 0.064 0.188
#> GSM153077 1 0.7482 0.31895 0.520 0.008 0.040 0.128 0.132 0.172
#> GSM153078 3 0.8706 -0.10736 0.228 0.016 0.320 0.064 0.228 0.144
#> GSM153079 6 0.7835 0.04281 0.168 0.116 0.040 0.036 0.128 0.512
#> GSM153080 3 0.7949 0.15327 0.060 0.000 0.408 0.192 0.240 0.100
#> GSM153081 1 0.7622 0.12654 0.364 0.000 0.040 0.080 0.168 0.348
#> GSM153082 2 0.8693 -0.43487 0.176 0.344 0.016 0.084 0.128 0.252
#> GSM153083 6 0.8194 -0.07473 0.164 0.260 0.040 0.008 0.152 0.376
#> GSM153084 2 0.8561 -0.37828 0.064 0.380 0.140 0.020 0.228 0.168
#> GSM153085 5 0.9690 0.33096 0.160 0.148 0.148 0.080 0.256 0.208
#> GSM153086 6 0.8148 -0.11262 0.208 0.052 0.088 0.020 0.204 0.428
#> GSM153087 4 0.7644 0.15589 0.252 0.004 0.048 0.452 0.168 0.076
#> GSM153088 1 0.6902 0.42275 0.528 0.000 0.016 0.216 0.092 0.148
#> GSM153089 3 0.7424 0.39434 0.036 0.068 0.544 0.068 0.216 0.068
#> GSM153090 1 0.6292 0.39338 0.572 0.000 0.020 0.264 0.064 0.080
#> GSM153091 6 0.8363 0.02895 0.304 0.216 0.008 0.060 0.104 0.308
#> GSM153092 1 0.8249 0.08372 0.384 0.028 0.040 0.116 0.136 0.296
#> GSM153093 4 0.6473 0.33652 0.260 0.000 0.024 0.560 0.092 0.064
#> GSM153094 6 0.8214 -0.03865 0.192 0.312 0.008 0.056 0.096 0.336
#> GSM153095 5 0.9596 0.31501 0.148 0.136 0.152 0.076 0.280 0.208
#> GSM153096 6 0.7811 0.11231 0.268 0.020 0.016 0.112 0.160 0.424
#> GSM153097 6 0.8130 -0.03696 0.176 0.168 0.012 0.036 0.188 0.420
#> GSM153098 4 0.7976 -0.06386 0.220 0.028 0.004 0.364 0.120 0.264
#> GSM153099 1 0.8128 0.22118 0.372 0.000 0.060 0.272 0.148 0.148
#> GSM153100 6 0.7810 -0.17595 0.304 0.012 0.004 0.220 0.128 0.332
#> GSM153101 6 0.9652 -0.32197 0.112 0.140 0.152 0.104 0.220 0.272
#> GSM153102 6 0.9631 -0.22536 0.100 0.164 0.160 0.096 0.208 0.272
#> GSM153103 6 0.8894 -0.22546 0.136 0.120 0.108 0.032 0.260 0.344
#> GSM153104 4 0.6733 0.39575 0.116 0.000 0.092 0.596 0.148 0.048
#> GSM153106 6 0.7678 -0.04587 0.188 0.032 0.008 0.224 0.092 0.456
#> GSM153107 6 0.7026 -0.03775 0.256 0.020 0.000 0.136 0.088 0.500
#> GSM153108 4 0.8422 0.10136 0.140 0.004 0.080 0.376 0.180 0.220
#> GSM153109 2 0.8478 -0.31298 0.076 0.392 0.088 0.028 0.160 0.256
#> GSM153110 6 0.7214 0.19915 0.276 0.028 0.012 0.080 0.104 0.500
#> GSM153111 6 0.8652 -0.02251 0.204 0.216 0.032 0.052 0.128 0.368
#> GSM153112 6 0.8573 0.06034 0.244 0.080 0.004 0.196 0.148 0.328
#> GSM153113 2 0.6790 0.19170 0.072 0.560 0.020 0.016 0.088 0.244
#> GSM153114 4 0.7125 0.06838 0.224 0.000 0.000 0.364 0.084 0.328
#> GSM187532 2 0.4380 0.59695 0.000 0.756 0.124 0.000 0.096 0.024
#> GSM187533 2 0.1528 0.80567 0.000 0.936 0.000 0.000 0.016 0.048
#> GSM187534 2 0.1644 0.80793 0.000 0.932 0.000 0.000 0.028 0.040
#> GSM187535 2 0.5752 0.37186 0.052 0.624 0.000 0.024 0.048 0.252
#> GSM152906 2 0.0717 0.83262 0.000 0.976 0.000 0.000 0.016 0.008
#> GSM152907 2 0.0520 0.83387 0.000 0.984 0.000 0.000 0.008 0.008
#> GSM152908 2 0.0000 0.83473 0.000 1.000 0.000 0.000 0.000 0.000
#> GSM152909 2 0.1364 0.81685 0.000 0.952 0.016 0.000 0.020 0.012
#> GSM152910 2 0.0291 0.83357 0.000 0.992 0.000 0.000 0.004 0.004
#> GSM152911 2 0.0000 0.83473 0.000 1.000 0.000 0.000 0.000 0.000
#> GSM152912 2 0.0000 0.83473 0.000 1.000 0.000 0.000 0.000 0.000
#> GSM152913 2 0.1369 0.82176 0.000 0.952 0.016 0.000 0.016 0.016
#> GSM152914 2 0.0146 0.83471 0.000 0.996 0.000 0.000 0.000 0.004
#> GSM152915 2 0.0000 0.83473 0.000 1.000 0.000 0.000 0.000 0.000
#> GSM152916 2 0.0717 0.83317 0.000 0.976 0.000 0.000 0.016 0.008
#> GSM152917 2 0.0291 0.83461 0.000 0.992 0.000 0.000 0.004 0.004
#> GSM152918 2 0.0146 0.83471 0.000 0.996 0.000 0.000 0.004 0.000
#> GSM152919 2 0.0000 0.83473 0.000 1.000 0.000 0.000 0.000 0.000
#> GSM152920 2 0.0000 0.83473 0.000 1.000 0.000 0.000 0.000 0.000
#> GSM152921 2 0.0146 0.83471 0.000 0.996 0.000 0.000 0.004 0.000
#> GSM152922 2 0.0000 0.83473 0.000 1.000 0.000 0.000 0.000 0.000
#> GSM152923 2 0.0622 0.83344 0.000 0.980 0.000 0.000 0.012 0.008
#> GSM152924 2 0.1151 0.82910 0.000 0.956 0.000 0.000 0.032 0.012
#> GSM152925 2 0.1708 0.81824 0.000 0.932 0.004 0.000 0.040 0.024
#> GSM152926 2 0.0806 0.83193 0.000 0.972 0.000 0.000 0.020 0.008
#> GSM152927 2 0.1116 0.82968 0.000 0.960 0.004 0.000 0.028 0.008
#> GSM152928 2 0.2842 0.76720 0.000 0.872 0.020 0.000 0.068 0.040
#> GSM152929 2 0.0717 0.83262 0.000 0.976 0.000 0.000 0.016 0.008
#> GSM152930 2 0.0717 0.83262 0.000 0.976 0.000 0.000 0.016 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 tissue(p) k
#> MAD:skmeans 154 1.42e-13 2
#> MAD:skmeans 152 4.40e-25 3
#> MAD:skmeans 118 1.91e-20 4
#> MAD:skmeans 83 1.50e-15 5
#> MAD:skmeans 46 2.66e-08 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 12013 rows and 164 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 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 0.908 0.936 0.969 0.3278 0.684 0.684
#> 3 3 0.342 0.722 0.817 0.9089 0.687 0.547
#> 4 4 0.387 0.556 0.746 0.1382 0.870 0.675
#> 5 5 0.407 0.520 0.708 0.0450 0.974 0.913
#> 6 6 0.416 0.534 0.687 0.0255 0.983 0.942
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
#> GSM152839 1 0.0000 0.9731 1.000 0.000
#> GSM152840 1 0.0376 0.9732 0.996 0.004
#> GSM152841 1 0.0000 0.9731 1.000 0.000
#> GSM152842 1 0.0376 0.9732 0.996 0.004
#> GSM152843 1 0.0376 0.9732 0.996 0.004
#> GSM152844 1 0.0376 0.9732 0.996 0.004
#> GSM152845 1 0.0000 0.9731 1.000 0.000
#> GSM152846 1 0.0376 0.9732 0.996 0.004
#> GSM152847 1 0.0376 0.9732 0.996 0.004
#> GSM152848 1 0.0376 0.9732 0.996 0.004
#> GSM152849 1 0.0376 0.9732 0.996 0.004
#> GSM152850 1 0.0376 0.9732 0.996 0.004
#> GSM152851 1 0.0000 0.9731 1.000 0.000
#> GSM152852 1 0.0000 0.9731 1.000 0.000
#> GSM152853 1 0.0000 0.9731 1.000 0.000
#> GSM152854 1 0.4939 0.8814 0.892 0.108
#> GSM152855 1 0.0000 0.9731 1.000 0.000
#> GSM153238 1 0.3584 0.9242 0.932 0.068
#> GSM153239 1 0.0376 0.9732 0.996 0.004
#> GSM153240 1 0.0000 0.9731 1.000 0.000
#> GSM153241 1 0.0376 0.9732 0.996 0.004
#> GSM153242 1 0.0376 0.9719 0.996 0.004
#> GSM153243 1 0.5059 0.8783 0.888 0.112
#> GSM153244 1 0.3114 0.9354 0.944 0.056
#> GSM153245 1 0.0376 0.9732 0.996 0.004
#> GSM153246 1 0.2778 0.9433 0.952 0.048
#> GSM153247 1 0.2043 0.9556 0.968 0.032
#> GSM153248 1 0.2236 0.9529 0.964 0.036
#> GSM153249 1 0.0376 0.9720 0.996 0.004
#> GSM153250 1 0.0376 0.9732 0.996 0.004
#> GSM153251 1 0.0672 0.9718 0.992 0.008
#> GSM153252 1 0.0000 0.9731 1.000 0.000
#> GSM153253 1 0.0376 0.9732 0.996 0.004
#> GSM153254 1 0.0000 0.9731 1.000 0.000
#> GSM153255 1 0.0000 0.9731 1.000 0.000
#> GSM153256 1 0.0376 0.9732 0.996 0.004
#> GSM153257 1 0.0000 0.9731 1.000 0.000
#> GSM153258 1 0.0376 0.9732 0.996 0.004
#> GSM153259 1 0.0376 0.9732 0.996 0.004
#> GSM153260 1 0.0672 0.9717 0.992 0.008
#> GSM153261 1 0.0376 0.9732 0.996 0.004
#> GSM153262 1 0.0000 0.9731 1.000 0.000
#> GSM153263 1 0.0376 0.9732 0.996 0.004
#> GSM153264 1 0.0376 0.9732 0.996 0.004
#> GSM153265 1 0.0376 0.9732 0.996 0.004
#> GSM153266 1 0.0376 0.9732 0.996 0.004
#> GSM153267 1 0.0000 0.9731 1.000 0.000
#> GSM153268 1 0.0000 0.9731 1.000 0.000
#> GSM153269 1 0.0376 0.9732 0.996 0.004
#> GSM153270 1 0.0376 0.9732 0.996 0.004
#> GSM153271 1 0.0376 0.9732 0.996 0.004
#> GSM153272 1 0.0000 0.9731 1.000 0.000
#> GSM153273 1 0.0376 0.9720 0.996 0.004
#> GSM153274 1 0.0376 0.9732 0.996 0.004
#> GSM153275 1 0.0000 0.9731 1.000 0.000
#> GSM153276 1 0.0376 0.9732 0.996 0.004
#> GSM153277 1 0.0000 0.9731 1.000 0.000
#> GSM153278 1 0.0376 0.9732 0.996 0.004
#> GSM153279 1 0.0000 0.9731 1.000 0.000
#> GSM153280 1 0.0000 0.9731 1.000 0.000
#> GSM153281 1 0.0000 0.9731 1.000 0.000
#> GSM153282 1 0.0000 0.9731 1.000 0.000
#> GSM153283 1 0.0000 0.9731 1.000 0.000
#> GSM153284 1 0.0000 0.9731 1.000 0.000
#> GSM153285 1 0.0000 0.9731 1.000 0.000
#> GSM153286 1 0.0000 0.9731 1.000 0.000
#> GSM153287 1 0.0000 0.9731 1.000 0.000
#> GSM153288 1 0.0000 0.9731 1.000 0.000
#> GSM153289 1 0.0000 0.9731 1.000 0.000
#> GSM153290 1 0.0000 0.9731 1.000 0.000
#> GSM153291 1 0.0000 0.9731 1.000 0.000
#> GSM153292 1 0.0000 0.9731 1.000 0.000
#> GSM153293 1 0.0000 0.9731 1.000 0.000
#> GSM153294 1 0.8267 0.6567 0.740 0.260
#> GSM153295 1 0.0376 0.9732 0.996 0.004
#> GSM153054 1 0.0672 0.9718 0.992 0.008
#> GSM153055 1 0.0376 0.9719 0.996 0.004
#> GSM153056 1 0.0000 0.9731 1.000 0.000
#> GSM153057 1 0.1843 0.9586 0.972 0.028
#> GSM153058 1 0.0376 0.9732 0.996 0.004
#> GSM153059 1 0.0376 0.9732 0.996 0.004
#> GSM153060 1 0.0000 0.9731 1.000 0.000
#> GSM153061 1 0.0672 0.9717 0.992 0.008
#> GSM153062 1 0.3274 0.9326 0.940 0.060
#> GSM153063 1 0.0000 0.9731 1.000 0.000
#> GSM153064 1 0.0376 0.9732 0.996 0.004
#> GSM153065 1 0.3274 0.9310 0.940 0.060
#> GSM153066 2 0.6623 0.8017 0.172 0.828
#> GSM153067 1 0.0376 0.9718 0.996 0.004
#> GSM153068 1 0.0376 0.9732 0.996 0.004
#> GSM153069 1 0.0000 0.9731 1.000 0.000
#> GSM153070 1 0.0376 0.9732 0.996 0.004
#> GSM153071 1 0.0938 0.9696 0.988 0.012
#> GSM153072 1 0.7299 0.7521 0.796 0.204
#> GSM153073 1 0.1184 0.9672 0.984 0.016
#> GSM153074 1 0.0000 0.9731 1.000 0.000
#> GSM153075 1 0.0000 0.9731 1.000 0.000
#> GSM153076 1 0.0376 0.9720 0.996 0.004
#> GSM153077 1 0.0376 0.9732 0.996 0.004
#> GSM153078 1 0.0376 0.9732 0.996 0.004
#> GSM153079 1 0.0672 0.9717 0.992 0.008
#> GSM153080 1 0.0376 0.9732 0.996 0.004
#> GSM153081 1 0.0376 0.9732 0.996 0.004
#> GSM153082 2 0.9427 0.4592 0.360 0.640
#> GSM153083 1 0.7883 0.7083 0.764 0.236
#> GSM153084 1 0.7674 0.7280 0.776 0.224
#> GSM153085 1 0.1843 0.9586 0.972 0.028
#> GSM153086 1 0.4022 0.9129 0.920 0.080
#> GSM153087 1 0.0376 0.9732 0.996 0.004
#> GSM153088 1 0.0376 0.9732 0.996 0.004
#> GSM153089 1 0.2043 0.9547 0.968 0.032
#> GSM153090 1 0.0376 0.9732 0.996 0.004
#> GSM153091 1 0.8763 0.5980 0.704 0.296
#> GSM153092 1 0.1184 0.9672 0.984 0.016
#> GSM153093 1 0.0376 0.9732 0.996 0.004
#> GSM153094 1 0.6712 0.7968 0.824 0.176
#> GSM153095 1 0.1184 0.9647 0.984 0.016
#> GSM153096 1 0.0000 0.9731 1.000 0.000
#> GSM153097 1 0.7950 0.6987 0.760 0.240
#> GSM153098 1 0.0000 0.9731 1.000 0.000
#> GSM153099 1 0.0376 0.9732 0.996 0.004
#> GSM153100 1 0.0000 0.9731 1.000 0.000
#> GSM153101 1 0.0376 0.9732 0.996 0.004
#> GSM153102 1 0.3584 0.9175 0.932 0.068
#> GSM153103 1 0.1414 0.9647 0.980 0.020
#> GSM153104 1 0.0000 0.9731 1.000 0.000
#> GSM153106 1 0.0000 0.9731 1.000 0.000
#> GSM153107 1 0.0000 0.9731 1.000 0.000
#> GSM153108 1 0.0376 0.9732 0.996 0.004
#> GSM153109 1 0.9996 0.0279 0.512 0.488
#> GSM153110 1 0.2603 0.9460 0.956 0.044
#> GSM153111 1 0.4562 0.8957 0.904 0.096
#> GSM153112 1 0.3274 0.9323 0.940 0.060
#> GSM153113 2 0.7139 0.7741 0.196 0.804
#> GSM153114 1 0.0000 0.9731 1.000 0.000
#> GSM187532 2 0.2948 0.9176 0.052 0.948
#> GSM187533 2 0.7453 0.7488 0.212 0.788
#> GSM187534 2 0.5519 0.8512 0.128 0.872
#> GSM187535 2 0.9427 0.4900 0.360 0.640
#> GSM152906 2 0.0000 0.9486 0.000 1.000
#> GSM152907 2 0.0000 0.9486 0.000 1.000
#> GSM152908 2 0.0000 0.9486 0.000 1.000
#> GSM152909 2 0.0000 0.9486 0.000 1.000
#> GSM152910 2 0.0000 0.9486 0.000 1.000
#> GSM152911 2 0.0000 0.9486 0.000 1.000
#> GSM152912 2 0.0000 0.9486 0.000 1.000
#> GSM152913 2 0.0000 0.9486 0.000 1.000
#> GSM152914 2 0.0000 0.9486 0.000 1.000
#> GSM152915 2 0.0000 0.9486 0.000 1.000
#> GSM152916 2 0.0000 0.9486 0.000 1.000
#> GSM152917 2 0.0000 0.9486 0.000 1.000
#> GSM152918 2 0.0000 0.9486 0.000 1.000
#> GSM152919 2 0.0000 0.9486 0.000 1.000
#> GSM152920 2 0.0000 0.9486 0.000 1.000
#> GSM152921 2 0.0000 0.9486 0.000 1.000
#> GSM152922 2 0.0000 0.9486 0.000 1.000
#> GSM152923 2 0.0000 0.9486 0.000 1.000
#> GSM152924 2 0.0000 0.9486 0.000 1.000
#> GSM152925 2 0.0376 0.9458 0.004 0.996
#> GSM152926 2 0.1843 0.9348 0.028 0.972
#> GSM152927 2 0.0000 0.9486 0.000 1.000
#> GSM152928 2 0.2423 0.9259 0.040 0.960
#> GSM152929 2 0.0000 0.9486 0.000 1.000
#> GSM152930 2 0.0000 0.9486 0.000 1.000
cbind(get_classes(res, k = 3), get_membership(res, k = 3))
#> class entropy silhouette p1 p2 p3
#> GSM152839 1 0.5497 0.551 0.708 0.000 0.292
#> GSM152840 3 0.5733 0.659 0.324 0.000 0.676
#> GSM152841 3 0.6111 0.480 0.396 0.000 0.604
#> GSM152842 1 0.3267 0.795 0.884 0.000 0.116
#> GSM152843 1 0.1860 0.784 0.948 0.000 0.052
#> GSM152844 3 0.5905 0.605 0.352 0.000 0.648
#> GSM152845 3 0.2796 0.802 0.092 0.000 0.908
#> GSM152846 3 0.5138 0.761 0.252 0.000 0.748
#> GSM152847 1 0.3619 0.780 0.864 0.000 0.136
#> GSM152848 1 0.6274 0.308 0.544 0.000 0.456
#> GSM152849 3 0.5835 0.504 0.340 0.000 0.660
#> GSM152850 1 0.5785 0.633 0.668 0.000 0.332
#> GSM152851 3 0.2878 0.801 0.096 0.000 0.904
#> GSM152852 3 0.2537 0.803 0.080 0.000 0.920
#> GSM152853 3 0.5882 0.582 0.348 0.000 0.652
#> GSM152854 3 0.5147 0.765 0.180 0.020 0.800
#> GSM152855 3 0.0592 0.788 0.012 0.000 0.988
#> GSM153238 1 0.2564 0.783 0.936 0.036 0.028
#> GSM153239 1 0.5810 0.511 0.664 0.000 0.336
#> GSM153240 3 0.6267 0.243 0.452 0.000 0.548
#> GSM153241 1 0.6111 0.506 0.604 0.000 0.396
#> GSM153242 1 0.5988 0.499 0.632 0.000 0.368
#> GSM153243 1 0.2590 0.783 0.924 0.004 0.072
#> GSM153244 3 0.3482 0.792 0.128 0.000 0.872
#> GSM153245 1 0.6062 0.439 0.616 0.000 0.384
#> GSM153246 1 0.2116 0.789 0.948 0.012 0.040
#> GSM153247 1 0.2066 0.784 0.940 0.000 0.060
#> GSM153248 1 0.4346 0.785 0.816 0.000 0.184
#> GSM153249 1 0.3752 0.767 0.856 0.000 0.144
#> GSM153250 1 0.2448 0.787 0.924 0.000 0.076
#> GSM153251 1 0.5465 0.567 0.712 0.000 0.288
#> GSM153252 1 0.6062 0.580 0.616 0.000 0.384
#> GSM153253 1 0.6168 0.278 0.588 0.000 0.412
#> GSM153254 3 0.5560 0.680 0.300 0.000 0.700
#> GSM153255 1 0.5397 0.720 0.720 0.000 0.280
#> GSM153256 1 0.2165 0.790 0.936 0.000 0.064
#> GSM153257 1 0.2959 0.786 0.900 0.000 0.100
#> GSM153258 1 0.4605 0.757 0.796 0.000 0.204
#> GSM153259 1 0.4504 0.769 0.804 0.000 0.196
#> GSM153260 1 0.3686 0.788 0.860 0.000 0.140
#> GSM153261 3 0.2066 0.795 0.060 0.000 0.940
#> GSM153262 3 0.4178 0.775 0.172 0.000 0.828
#> GSM153263 3 0.4399 0.760 0.188 0.000 0.812
#> GSM153264 1 0.6280 0.248 0.540 0.000 0.460
#> GSM153265 3 0.3340 0.791 0.120 0.000 0.880
#> GSM153266 1 0.4062 0.777 0.836 0.000 0.164
#> GSM153267 3 0.6168 0.202 0.412 0.000 0.588
#> GSM153268 3 0.4974 0.743 0.236 0.000 0.764
#> GSM153269 1 0.5733 0.661 0.676 0.000 0.324
#> GSM153270 1 0.2711 0.791 0.912 0.000 0.088
#> GSM153271 1 0.2261 0.788 0.932 0.000 0.068
#> GSM153272 1 0.5098 0.736 0.752 0.000 0.248
#> GSM153273 1 0.5138 0.732 0.748 0.000 0.252
#> GSM153274 1 0.5216 0.716 0.740 0.000 0.260
#> GSM153275 1 0.6215 0.495 0.572 0.000 0.428
#> GSM153276 1 0.4931 0.764 0.768 0.000 0.232
#> GSM153277 3 0.2959 0.787 0.100 0.000 0.900
#> GSM153278 1 0.4931 0.737 0.768 0.000 0.232
#> GSM153279 1 0.5254 0.689 0.736 0.000 0.264
#> GSM153280 3 0.2796 0.801 0.092 0.000 0.908
#> GSM153281 1 0.5016 0.733 0.760 0.000 0.240
#> GSM153282 3 0.4291 0.784 0.180 0.000 0.820
#> GSM153283 1 0.5497 0.672 0.708 0.000 0.292
#> GSM153284 1 0.3116 0.790 0.892 0.000 0.108
#> GSM153285 3 0.6140 0.447 0.404 0.000 0.596
#> GSM153286 1 0.2796 0.784 0.908 0.000 0.092
#> GSM153287 1 0.4062 0.771 0.836 0.000 0.164
#> GSM153288 1 0.6180 0.379 0.584 0.000 0.416
#> GSM153289 3 0.0592 0.788 0.012 0.000 0.988
#> GSM153290 3 0.2711 0.795 0.088 0.000 0.912
#> GSM153291 3 0.2261 0.802 0.068 0.000 0.932
#> GSM153292 1 0.5988 0.582 0.632 0.000 0.368
#> GSM153293 3 0.5363 0.639 0.276 0.000 0.724
#> GSM153294 1 0.3637 0.767 0.892 0.084 0.024
#> GSM153295 3 0.2356 0.801 0.072 0.000 0.928
#> GSM153054 1 0.2301 0.783 0.936 0.004 0.060
#> GSM153055 3 0.5650 0.603 0.312 0.000 0.688
#> GSM153056 1 0.4931 0.737 0.768 0.000 0.232
#> GSM153057 3 0.2261 0.789 0.068 0.000 0.932
#> GSM153058 1 0.6168 0.243 0.588 0.000 0.412
#> GSM153059 3 0.5497 0.646 0.292 0.000 0.708
#> GSM153060 1 0.2448 0.793 0.924 0.000 0.076
#> GSM153061 3 0.6126 0.533 0.400 0.000 0.600
#> GSM153062 1 0.5028 0.774 0.828 0.040 0.132
#> GSM153063 1 0.6267 0.257 0.548 0.000 0.452
#> GSM153064 1 0.4842 0.765 0.776 0.000 0.224
#> GSM153065 3 0.4249 0.793 0.108 0.028 0.864
#> GSM153066 2 0.6079 0.738 0.128 0.784 0.088
#> GSM153067 1 0.2711 0.783 0.912 0.000 0.088
#> GSM153068 1 0.5098 0.726 0.752 0.000 0.248
#> GSM153069 3 0.5733 0.666 0.324 0.000 0.676
#> GSM153070 1 0.1411 0.783 0.964 0.000 0.036
#> GSM153071 1 0.3551 0.783 0.868 0.000 0.132
#> GSM153072 1 0.5407 0.780 0.804 0.040 0.156
#> GSM153073 1 0.1163 0.778 0.972 0.000 0.028
#> GSM153074 3 0.5621 0.684 0.308 0.000 0.692
#> GSM153075 3 0.2165 0.801 0.064 0.000 0.936
#> GSM153076 1 0.3267 0.788 0.884 0.000 0.116
#> GSM153077 1 0.2711 0.794 0.912 0.000 0.088
#> GSM153078 1 0.6045 0.605 0.620 0.000 0.380
#> GSM153079 3 0.1860 0.786 0.052 0.000 0.948
#> GSM153080 3 0.6291 0.174 0.468 0.000 0.532
#> GSM153081 3 0.2261 0.794 0.068 0.000 0.932
#> GSM153082 2 0.7671 0.184 0.048 0.544 0.408
#> GSM153083 1 0.4683 0.729 0.836 0.140 0.024
#> GSM153084 1 0.9203 0.120 0.476 0.156 0.368
#> GSM153085 1 0.3826 0.798 0.868 0.008 0.124
#> GSM153086 1 0.2959 0.794 0.900 0.000 0.100
#> GSM153087 1 0.2537 0.790 0.920 0.000 0.080
#> GSM153088 1 0.3412 0.784 0.876 0.000 0.124
#> GSM153089 3 0.4346 0.789 0.184 0.000 0.816
#> GSM153090 1 0.3038 0.784 0.896 0.000 0.104
#> GSM153091 1 0.3846 0.750 0.876 0.108 0.016
#> GSM153092 1 0.3112 0.796 0.900 0.004 0.096
#> GSM153093 1 0.3267 0.790 0.884 0.000 0.116
#> GSM153094 1 0.8222 0.439 0.592 0.100 0.308
#> GSM153095 1 0.5378 0.714 0.756 0.008 0.236
#> GSM153096 1 0.5905 0.516 0.648 0.000 0.352
#> GSM153097 1 0.8371 0.579 0.624 0.164 0.212
#> GSM153098 1 0.3551 0.792 0.868 0.000 0.132
#> GSM153099 1 0.2537 0.795 0.920 0.000 0.080
#> GSM153100 3 0.5254 0.681 0.264 0.000 0.736
#> GSM153101 3 0.3619 0.801 0.136 0.000 0.864
#> GSM153102 3 0.3965 0.787 0.132 0.008 0.860
#> GSM153103 1 0.2537 0.787 0.920 0.000 0.080
#> GSM153104 1 0.2878 0.784 0.904 0.000 0.096
#> GSM153106 3 0.0592 0.788 0.012 0.000 0.988
#> GSM153107 3 0.0747 0.788 0.016 0.000 0.984
#> GSM153108 3 0.3340 0.796 0.120 0.000 0.880
#> GSM153109 1 0.9120 0.363 0.504 0.340 0.156
#> GSM153110 1 0.3618 0.776 0.884 0.012 0.104
#> GSM153111 1 0.3765 0.784 0.888 0.028 0.084
#> GSM153112 1 0.5223 0.779 0.800 0.024 0.176
#> GSM153113 2 0.7339 0.629 0.144 0.708 0.148
#> GSM153114 3 0.0892 0.788 0.020 0.000 0.980
#> GSM187532 2 0.5610 0.734 0.028 0.776 0.196
#> GSM187533 3 0.5138 0.586 0.000 0.252 0.748
#> GSM187534 2 0.6473 0.501 0.016 0.652 0.332
#> GSM187535 3 0.1878 0.775 0.004 0.044 0.952
#> GSM152906 2 0.0000 0.943 0.000 1.000 0.000
#> GSM152907 2 0.0000 0.943 0.000 1.000 0.000
#> GSM152908 2 0.0000 0.943 0.000 1.000 0.000
#> GSM152909 2 0.0000 0.943 0.000 1.000 0.000
#> GSM152910 2 0.0000 0.943 0.000 1.000 0.000
#> GSM152911 2 0.0000 0.943 0.000 1.000 0.000
#> GSM152912 2 0.0000 0.943 0.000 1.000 0.000
#> GSM152913 2 0.0000 0.943 0.000 1.000 0.000
#> GSM152914 2 0.0000 0.943 0.000 1.000 0.000
#> GSM152915 2 0.0000 0.943 0.000 1.000 0.000
#> GSM152916 2 0.0000 0.943 0.000 1.000 0.000
#> GSM152917 2 0.0000 0.943 0.000 1.000 0.000
#> GSM152918 2 0.0000 0.943 0.000 1.000 0.000
#> GSM152919 2 0.0000 0.943 0.000 1.000 0.000
#> GSM152920 2 0.0000 0.943 0.000 1.000 0.000
#> GSM152921 2 0.0000 0.943 0.000 1.000 0.000
#> GSM152922 2 0.0237 0.940 0.004 0.996 0.000
#> GSM152923 2 0.0000 0.943 0.000 1.000 0.000
#> GSM152924 2 0.0747 0.932 0.000 0.984 0.016
#> GSM152925 2 0.0000 0.943 0.000 1.000 0.000
#> GSM152926 2 0.0892 0.929 0.020 0.980 0.000
#> GSM152927 2 0.0000 0.943 0.000 1.000 0.000
#> GSM152928 2 0.1999 0.909 0.036 0.952 0.012
#> GSM152929 2 0.0000 0.943 0.000 1.000 0.000
#> GSM152930 2 0.0000 0.943 0.000 1.000 0.000
cbind(get_classes(res, k = 4), get_membership(res, k = 4))
#> class entropy silhouette p1 p2 p3 p4
#> GSM152839 1 0.6054 0.46006 0.656 0.000 0.256 0.088
#> GSM152840 4 0.5833 0.55236 0.096 0.000 0.212 0.692
#> GSM152841 4 0.7232 0.41654 0.164 0.000 0.320 0.516
#> GSM152842 4 0.6042 0.35784 0.368 0.000 0.052 0.580
#> GSM152843 1 0.1890 0.68680 0.936 0.000 0.008 0.056
#> GSM152844 4 0.5392 0.43873 0.040 0.000 0.280 0.680
#> GSM152845 3 0.3731 0.64224 0.036 0.000 0.844 0.120
#> GSM152846 3 0.6652 0.37988 0.108 0.000 0.576 0.316
#> GSM152847 1 0.3198 0.69771 0.880 0.000 0.080 0.040
#> GSM152848 1 0.7332 0.08558 0.448 0.000 0.396 0.156
#> GSM152849 3 0.4790 0.32305 0.380 0.000 0.620 0.000
#> GSM152850 1 0.5936 0.49785 0.620 0.000 0.324 0.056
#> GSM152851 3 0.6009 0.02216 0.040 0.000 0.492 0.468
#> GSM152852 3 0.3978 0.60972 0.012 0.000 0.796 0.192
#> GSM152853 4 0.6681 0.48667 0.120 0.000 0.292 0.588
#> GSM152854 3 0.5253 0.61109 0.132 0.012 0.772 0.084
#> GSM152855 3 0.0188 0.66277 0.000 0.000 0.996 0.004
#> GSM153238 1 0.4178 0.67931 0.824 0.020 0.016 0.140
#> GSM153239 4 0.6674 0.57834 0.300 0.000 0.116 0.584
#> GSM153240 3 0.7715 -0.06494 0.324 0.000 0.436 0.240
#> GSM153241 1 0.6678 0.28578 0.500 0.000 0.412 0.088
#> GSM153242 1 0.7743 -0.09193 0.436 0.000 0.256 0.308
#> GSM153243 1 0.2623 0.69227 0.908 0.000 0.028 0.064
#> GSM153244 3 0.3598 0.63530 0.124 0.000 0.848 0.028
#> GSM153245 4 0.5511 0.62207 0.196 0.000 0.084 0.720
#> GSM153246 1 0.5085 0.59534 0.716 0.008 0.020 0.256
#> GSM153247 1 0.3384 0.68762 0.860 0.000 0.024 0.116
#> GSM153248 1 0.4127 0.68799 0.824 0.000 0.124 0.052
#> GSM153249 4 0.6253 0.41877 0.372 0.000 0.064 0.564
#> GSM153250 1 0.1629 0.68612 0.952 0.000 0.024 0.024
#> GSM153251 1 0.7377 0.20020 0.520 0.000 0.216 0.264
#> GSM153252 4 0.7575 0.40020 0.356 0.000 0.200 0.444
#> GSM153253 4 0.6635 0.54716 0.152 0.000 0.228 0.620
#> GSM153254 3 0.7228 0.13857 0.156 0.000 0.504 0.340
#> GSM153255 4 0.7220 0.35502 0.384 0.000 0.144 0.472
#> GSM153256 1 0.5106 0.56349 0.720 0.000 0.040 0.240
#> GSM153257 1 0.4055 0.68992 0.832 0.000 0.060 0.108
#> GSM153258 1 0.3945 0.66107 0.780 0.000 0.216 0.004
#> GSM153259 1 0.4285 0.68569 0.820 0.000 0.076 0.104
#> GSM153260 1 0.4462 0.67585 0.804 0.000 0.064 0.132
#> GSM153261 3 0.2408 0.67035 0.044 0.000 0.920 0.036
#> GSM153262 3 0.4459 0.60731 0.032 0.000 0.780 0.188
#> GSM153263 3 0.4740 0.62034 0.080 0.000 0.788 0.132
#> GSM153264 1 0.7098 0.19039 0.472 0.000 0.400 0.128
#> GSM153265 4 0.5167 -0.01066 0.004 0.000 0.488 0.508
#> GSM153266 1 0.6357 0.53658 0.644 0.000 0.124 0.232
#> GSM153267 3 0.5708 0.11807 0.416 0.000 0.556 0.028
#> GSM153268 4 0.4993 0.45906 0.028 0.000 0.260 0.712
#> GSM153269 1 0.4983 0.60095 0.704 0.000 0.272 0.024
#> GSM153270 1 0.3962 0.68732 0.820 0.000 0.028 0.152
#> GSM153271 1 0.1677 0.68529 0.948 0.000 0.012 0.040
#> GSM153272 4 0.7253 0.17448 0.428 0.000 0.144 0.428
#> GSM153273 1 0.6404 0.54543 0.644 0.000 0.136 0.220
#> GSM153274 1 0.6835 0.36352 0.592 0.000 0.156 0.252
#> GSM153275 1 0.7576 0.09118 0.464 0.000 0.324 0.212
#> GSM153276 1 0.4669 0.67053 0.780 0.000 0.168 0.052
#> GSM153277 3 0.4907 0.26268 0.000 0.000 0.580 0.420
#> GSM153278 1 0.6075 0.59877 0.680 0.000 0.192 0.128
#> GSM153279 4 0.6828 0.51346 0.264 0.000 0.148 0.588
#> GSM153280 3 0.4579 0.58383 0.032 0.000 0.768 0.200
#> GSM153281 4 0.6015 0.55575 0.268 0.000 0.080 0.652
#> GSM153282 4 0.5366 0.42632 0.040 0.000 0.276 0.684
#> GSM153283 1 0.6714 0.50029 0.612 0.000 0.228 0.160
#> GSM153284 1 0.4677 0.61147 0.768 0.000 0.040 0.192
#> GSM153285 4 0.5906 0.45453 0.064 0.000 0.292 0.644
#> GSM153286 1 0.4284 0.66113 0.780 0.000 0.020 0.200
#> GSM153287 4 0.4453 0.54771 0.244 0.000 0.012 0.744
#> GSM153288 4 0.6840 0.59658 0.220 0.000 0.180 0.600
#> GSM153289 3 0.0336 0.66239 0.000 0.000 0.992 0.008
#> GSM153290 4 0.4866 0.24065 0.000 0.000 0.404 0.596
#> GSM153291 3 0.4874 0.56852 0.056 0.000 0.764 0.180
#> GSM153292 4 0.7463 0.54099 0.272 0.000 0.224 0.504
#> GSM153293 3 0.6490 0.43101 0.204 0.000 0.640 0.156
#> GSM153294 1 0.3104 0.68746 0.892 0.044 0.004 0.060
#> GSM153295 3 0.2928 0.65621 0.012 0.000 0.880 0.108
#> GSM153054 1 0.3221 0.69348 0.876 0.004 0.020 0.100
#> GSM153055 3 0.7647 -0.07536 0.220 0.000 0.444 0.336
#> GSM153056 1 0.6407 0.57362 0.648 0.000 0.204 0.148
#> GSM153057 3 0.1398 0.66685 0.040 0.000 0.956 0.004
#> GSM153058 1 0.7392 0.04952 0.472 0.000 0.356 0.172
#> GSM153059 3 0.7084 0.32661 0.264 0.000 0.560 0.176
#> GSM153060 1 0.5383 0.53830 0.672 0.000 0.036 0.292
#> GSM153061 3 0.7640 0.11492 0.252 0.000 0.468 0.280
#> GSM153062 4 0.7625 -0.18879 0.424 0.048 0.072 0.456
#> GSM153063 4 0.7901 0.35055 0.312 0.000 0.316 0.372
#> GSM153064 1 0.6432 0.54094 0.636 0.000 0.128 0.236
#> GSM153065 3 0.4316 0.64942 0.100 0.024 0.836 0.040
#> GSM153066 2 0.6627 0.64485 0.124 0.708 0.092 0.076
#> GSM153067 4 0.5244 0.36559 0.388 0.000 0.012 0.600
#> GSM153068 1 0.6353 0.54444 0.652 0.000 0.140 0.208
#> GSM153069 4 0.5031 0.50401 0.048 0.000 0.212 0.740
#> GSM153070 1 0.0921 0.68136 0.972 0.000 0.000 0.028
#> GSM153071 1 0.6570 0.50949 0.604 0.000 0.116 0.280
#> GSM153072 1 0.4037 0.69286 0.848 0.024 0.100 0.028
#> GSM153073 1 0.1867 0.68558 0.928 0.000 0.000 0.072
#> GSM153074 3 0.7076 0.04503 0.124 0.000 0.460 0.416
#> GSM153075 3 0.2861 0.65720 0.016 0.000 0.888 0.096
#> GSM153076 1 0.2882 0.68638 0.892 0.000 0.024 0.084
#> GSM153077 1 0.2840 0.69717 0.900 0.000 0.056 0.044
#> GSM153078 1 0.5613 0.46750 0.592 0.000 0.380 0.028
#> GSM153079 3 0.0469 0.66282 0.012 0.000 0.988 0.000
#> GSM153080 4 0.7036 0.54529 0.212 0.000 0.212 0.576
#> GSM153081 3 0.1557 0.66417 0.056 0.000 0.944 0.000
#> GSM153082 2 0.7834 -0.06369 0.052 0.452 0.412 0.084
#> GSM153083 1 0.3316 0.68051 0.888 0.064 0.028 0.020
#> GSM153084 1 0.8843 0.07019 0.416 0.128 0.356 0.100
#> GSM153085 1 0.5649 0.66380 0.728 0.004 0.100 0.168
#> GSM153086 1 0.4296 0.69526 0.824 0.004 0.060 0.112
#> GSM153087 1 0.4655 0.65055 0.760 0.000 0.032 0.208
#> GSM153088 1 0.1629 0.68485 0.952 0.000 0.024 0.024
#> GSM153089 4 0.6991 0.31770 0.128 0.000 0.348 0.524
#> GSM153090 1 0.2048 0.68960 0.928 0.000 0.064 0.008
#> GSM153091 1 0.1631 0.68492 0.956 0.020 0.008 0.016
#> GSM153092 1 0.2300 0.69595 0.924 0.000 0.048 0.028
#> GSM153093 1 0.5787 0.50152 0.680 0.000 0.076 0.244
#> GSM153094 1 0.5963 0.46360 0.660 0.040 0.284 0.016
#> GSM153095 1 0.7027 0.40739 0.576 0.004 0.144 0.276
#> GSM153096 1 0.7344 0.28884 0.524 0.000 0.268 0.208
#> GSM153097 1 0.7544 0.51850 0.624 0.112 0.192 0.072
#> GSM153098 1 0.5750 0.62682 0.696 0.000 0.088 0.216
#> GSM153099 1 0.4123 0.68713 0.820 0.000 0.044 0.136
#> GSM153100 3 0.7456 0.00257 0.196 0.000 0.488 0.316
#> GSM153101 3 0.6274 0.43153 0.088 0.000 0.620 0.292
#> GSM153102 3 0.6179 0.35041 0.060 0.004 0.612 0.324
#> GSM153103 1 0.3694 0.67816 0.844 0.000 0.032 0.124
#> GSM153104 1 0.5901 0.09174 0.532 0.000 0.036 0.432
#> GSM153106 3 0.0188 0.66277 0.000 0.000 0.996 0.004
#> GSM153107 3 0.0188 0.66277 0.000 0.000 0.996 0.004
#> GSM153108 3 0.5337 0.51966 0.044 0.000 0.696 0.260
#> GSM153109 1 0.7557 0.32201 0.556 0.300 0.108 0.036
#> GSM153110 1 0.2131 0.68740 0.932 0.000 0.032 0.036
#> GSM153111 1 0.3313 0.69913 0.880 0.008 0.028 0.084
#> GSM153112 1 0.7013 0.44473 0.604 0.016 0.116 0.264
#> GSM153113 2 0.7567 0.51207 0.148 0.636 0.124 0.092
#> GSM153114 3 0.0188 0.66277 0.000 0.000 0.996 0.004
#> GSM187532 2 0.5166 0.71520 0.044 0.756 0.188 0.012
#> GSM187533 3 0.3764 0.52211 0.000 0.216 0.784 0.000
#> GSM187534 2 0.5220 0.45941 0.016 0.632 0.352 0.000
#> GSM187535 3 0.0336 0.66124 0.000 0.008 0.992 0.000
#> GSM152906 2 0.0000 0.92903 0.000 1.000 0.000 0.000
#> GSM152907 2 0.0000 0.92903 0.000 1.000 0.000 0.000
#> GSM152908 2 0.0592 0.92657 0.000 0.984 0.000 0.016
#> GSM152909 2 0.0592 0.92657 0.000 0.984 0.000 0.016
#> GSM152910 2 0.0592 0.92657 0.000 0.984 0.000 0.016
#> GSM152911 2 0.0000 0.92903 0.000 1.000 0.000 0.000
#> GSM152912 2 0.0592 0.92657 0.000 0.984 0.000 0.016
#> GSM152913 2 0.0188 0.92854 0.000 0.996 0.000 0.004
#> GSM152914 2 0.0000 0.92903 0.000 1.000 0.000 0.000
#> GSM152915 2 0.0000 0.92903 0.000 1.000 0.000 0.000
#> GSM152916 2 0.0376 0.92754 0.004 0.992 0.000 0.004
#> GSM152917 2 0.0000 0.92903 0.000 1.000 0.000 0.000
#> GSM152918 2 0.0000 0.92903 0.000 1.000 0.000 0.000
#> GSM152919 2 0.0000 0.92903 0.000 1.000 0.000 0.000
#> GSM152920 2 0.0592 0.92657 0.000 0.984 0.000 0.016
#> GSM152921 2 0.0592 0.92657 0.000 0.984 0.000 0.016
#> GSM152922 2 0.0779 0.92496 0.004 0.980 0.000 0.016
#> GSM152923 2 0.0000 0.92903 0.000 1.000 0.000 0.000
#> GSM152924 2 0.0817 0.91703 0.000 0.976 0.024 0.000
#> GSM152925 2 0.0000 0.92903 0.000 1.000 0.000 0.000
#> GSM152926 2 0.1938 0.89018 0.052 0.936 0.000 0.012
#> GSM152927 2 0.0000 0.92903 0.000 1.000 0.000 0.000
#> GSM152928 2 0.2032 0.89021 0.036 0.936 0.000 0.028
#> GSM152929 2 0.0000 0.92903 0.000 1.000 0.000 0.000
#> GSM152930 2 0.0000 0.92903 0.000 1.000 0.000 0.000
cbind(get_classes(res, k = 5), get_membership(res, k = 5))
#> class entropy silhouette p1 p2 p3 p4 p5
#> GSM152839 1 0.7066 0.39663 0.540 0.000 0.240 0.060 0.160
#> GSM152840 4 0.5328 0.57608 0.084 0.000 0.160 0.720 0.036
#> GSM152841 4 0.6366 0.45516 0.124 0.000 0.300 0.556 0.020
#> GSM152842 4 0.5748 0.40609 0.300 0.000 0.036 0.616 0.048
#> GSM152843 1 0.2075 0.64387 0.924 0.000 0.004 0.040 0.032
#> GSM152844 4 0.5049 0.51503 0.020 0.000 0.232 0.700 0.048
#> GSM152845 3 0.4848 0.60527 0.016 0.000 0.752 0.116 0.116
#> GSM152846 3 0.6834 0.32465 0.088 0.000 0.524 0.320 0.068
#> GSM152847 1 0.3546 0.65385 0.852 0.000 0.060 0.024 0.064
#> GSM152848 1 0.7837 0.17335 0.400 0.000 0.340 0.112 0.148
#> GSM152849 3 0.5278 0.31518 0.344 0.000 0.600 0.004 0.052
#> GSM152850 1 0.5680 0.47464 0.612 0.000 0.308 0.056 0.024
#> GSM152851 4 0.6326 0.14726 0.016 0.000 0.436 0.448 0.100
#> GSM152852 3 0.4062 0.59472 0.016 0.000 0.796 0.152 0.036
#> GSM152853 4 0.5659 0.56362 0.084 0.000 0.232 0.660 0.024
#> GSM152854 3 0.4952 0.60038 0.128 0.008 0.764 0.072 0.028
#> GSM152855 3 0.0000 0.64148 0.000 0.000 1.000 0.000 0.000
#> GSM153238 1 0.5475 0.62035 0.704 0.016 0.004 0.148 0.128
#> GSM153239 4 0.6341 0.54070 0.208 0.000 0.084 0.632 0.076
#> GSM153240 3 0.7152 0.04039 0.296 0.000 0.444 0.236 0.024
#> GSM153241 1 0.6582 0.31000 0.476 0.000 0.400 0.080 0.044
#> GSM153242 1 0.7569 -0.04183 0.400 0.000 0.240 0.312 0.048
#> GSM153243 1 0.3934 0.64591 0.824 0.000 0.020 0.064 0.092
#> GSM153244 3 0.3919 0.62131 0.108 0.000 0.820 0.016 0.056
#> GSM153245 4 0.4361 0.56305 0.144 0.000 0.052 0.784 0.020
#> GSM153246 1 0.6267 0.29050 0.556 0.008 0.012 0.328 0.096
#> GSM153247 1 0.3753 0.64807 0.832 0.000 0.012 0.080 0.076
#> GSM153248 1 0.5599 0.61304 0.680 0.000 0.080 0.032 0.208
#> GSM153249 4 0.7095 0.40424 0.272 0.000 0.056 0.520 0.152
#> GSM153250 1 0.0981 0.63450 0.972 0.000 0.012 0.008 0.008
#> GSM153251 1 0.7925 0.24162 0.444 0.000 0.204 0.236 0.116
#> GSM153252 4 0.7726 0.40911 0.292 0.000 0.140 0.452 0.116
#> GSM153253 4 0.5435 0.56102 0.112 0.000 0.180 0.692 0.016
#> GSM153254 3 0.7332 0.00014 0.140 0.000 0.440 0.356 0.064
#> GSM153255 4 0.7408 0.40993 0.316 0.000 0.120 0.472 0.092
#> GSM153256 1 0.5657 0.51130 0.664 0.000 0.032 0.232 0.072
#> GSM153257 1 0.3126 0.64638 0.868 0.000 0.028 0.088 0.016
#> GSM153258 1 0.3421 0.62284 0.788 0.000 0.204 0.000 0.008
#> GSM153259 1 0.5843 0.58809 0.672 0.000 0.040 0.100 0.188
#> GSM153260 1 0.5105 0.62735 0.748 0.000 0.040 0.104 0.108
#> GSM153261 3 0.2897 0.64911 0.024 0.000 0.884 0.020 0.072
#> GSM153262 3 0.3650 0.59482 0.028 0.000 0.796 0.176 0.000
#> GSM153263 3 0.4155 0.60694 0.048 0.000 0.796 0.140 0.016
#> GSM153264 1 0.7197 0.23120 0.456 0.000 0.364 0.100 0.080
#> GSM153265 4 0.4833 0.26218 0.000 0.000 0.412 0.564 0.024
#> GSM153266 1 0.6942 0.53456 0.588 0.000 0.092 0.172 0.148
#> GSM153267 3 0.5096 0.13253 0.400 0.000 0.568 0.016 0.016
#> GSM153268 4 0.3719 0.53491 0.004 0.000 0.208 0.776 0.012
#> GSM153269 1 0.4798 0.57098 0.684 0.000 0.272 0.008 0.036
#> GSM153270 1 0.3996 0.64152 0.808 0.000 0.016 0.132 0.044
#> GSM153271 1 0.1243 0.63405 0.960 0.000 0.004 0.008 0.028
#> GSM153272 1 0.7378 -0.14095 0.400 0.000 0.136 0.396 0.068
#> GSM153273 1 0.7235 0.49677 0.492 0.000 0.060 0.152 0.296
#> GSM153274 1 0.7075 0.39117 0.564 0.000 0.140 0.208 0.088
#> GSM153275 1 0.8112 0.03858 0.388 0.000 0.276 0.220 0.116
#> GSM153276 1 0.4325 0.62920 0.776 0.000 0.168 0.032 0.024
#> GSM153277 3 0.6202 0.04352 0.004 0.000 0.464 0.412 0.120
#> GSM153278 1 0.6103 0.55772 0.652 0.000 0.184 0.120 0.044
#> GSM153279 4 0.6412 0.47065 0.212 0.000 0.124 0.616 0.048
#> GSM153280 3 0.4520 0.54871 0.032 0.000 0.760 0.180 0.028
#> GSM153281 4 0.5299 0.50935 0.232 0.000 0.064 0.684 0.020
#> GSM153282 4 0.5437 0.53815 0.012 0.000 0.204 0.680 0.104
#> GSM153283 1 0.7648 0.46334 0.508 0.000 0.188 0.148 0.156
#> GSM153284 1 0.5472 0.56013 0.696 0.000 0.024 0.180 0.100
#> GSM153285 4 0.5898 0.55437 0.044 0.000 0.228 0.652 0.076
#> GSM153286 1 0.4290 0.62724 0.768 0.000 0.016 0.184 0.032
#> GSM153287 4 0.4550 0.52816 0.188 0.000 0.004 0.744 0.064
#> GSM153288 4 0.6967 0.54013 0.168 0.000 0.144 0.588 0.100
#> GSM153289 3 0.0290 0.64208 0.000 0.000 0.992 0.000 0.008
#> GSM153290 4 0.4620 0.43052 0.000 0.000 0.320 0.652 0.028
#> GSM153291 3 0.5231 0.52138 0.036 0.000 0.716 0.188 0.060
#> GSM153292 4 0.7569 0.47915 0.212 0.000 0.180 0.504 0.104
#> GSM153293 3 0.6724 0.43798 0.164 0.000 0.612 0.136 0.088
#> GSM153294 1 0.3753 0.64196 0.832 0.020 0.000 0.044 0.104
#> GSM153295 3 0.2907 0.63153 0.008 0.000 0.864 0.116 0.012
#> GSM153054 1 0.3823 0.64998 0.808 0.004 0.000 0.048 0.140
#> GSM153055 3 0.8016 -0.15901 0.188 0.000 0.388 0.312 0.112
#> GSM153056 1 0.5661 0.55696 0.644 0.000 0.208 0.144 0.004
#> GSM153057 3 0.1822 0.64973 0.024 0.000 0.936 0.004 0.036
#> GSM153058 1 0.7411 0.04532 0.428 0.000 0.352 0.160 0.060
#> GSM153059 3 0.7733 0.30655 0.192 0.000 0.484 0.116 0.208
#> GSM153060 1 0.6333 0.53714 0.592 0.000 0.024 0.244 0.140
#> GSM153061 3 0.8338 0.13776 0.208 0.000 0.380 0.232 0.180
#> GSM153062 5 0.7806 0.00000 0.176 0.048 0.048 0.200 0.528
#> GSM153063 4 0.7623 0.31120 0.276 0.000 0.288 0.388 0.048
#> GSM153064 1 0.6950 0.50666 0.512 0.000 0.048 0.132 0.308
#> GSM153065 3 0.5316 0.59988 0.080 0.012 0.752 0.048 0.108
#> GSM153066 2 0.7374 0.34137 0.088 0.560 0.068 0.036 0.248
#> GSM153067 4 0.5437 0.44138 0.324 0.000 0.008 0.608 0.060
#> GSM153068 1 0.7047 0.50763 0.584 0.000 0.124 0.156 0.136
#> GSM153069 4 0.4413 0.56025 0.032 0.000 0.160 0.776 0.032
#> GSM153070 1 0.0579 0.62814 0.984 0.000 0.000 0.008 0.008
#> GSM153071 1 0.6837 0.47354 0.552 0.000 0.088 0.280 0.080
#> GSM153072 1 0.3768 0.64509 0.840 0.020 0.048 0.004 0.088
#> GSM153073 1 0.1331 0.63658 0.952 0.000 0.000 0.040 0.008
#> GSM153074 3 0.7270 -0.05341 0.088 0.000 0.420 0.396 0.096
#> GSM153075 3 0.2990 0.63394 0.012 0.000 0.876 0.080 0.032
#> GSM153076 1 0.2459 0.63990 0.904 0.000 0.004 0.052 0.040
#> GSM153077 1 0.2086 0.64618 0.924 0.000 0.048 0.008 0.020
#> GSM153078 1 0.5029 0.46664 0.592 0.000 0.376 0.012 0.020
#> GSM153079 3 0.1205 0.64428 0.000 0.000 0.956 0.004 0.040
#> GSM153080 4 0.7572 0.45505 0.168 0.000 0.200 0.512 0.120
#> GSM153081 3 0.1872 0.64599 0.052 0.000 0.928 0.000 0.020
#> GSM153082 3 0.8121 0.00301 0.032 0.356 0.392 0.060 0.160
#> GSM153083 1 0.3346 0.63417 0.856 0.036 0.004 0.008 0.096
#> GSM153084 1 0.8955 0.00235 0.348 0.088 0.328 0.084 0.152
#> GSM153085 1 0.5627 0.62938 0.696 0.000 0.096 0.168 0.040
#> GSM153086 1 0.5309 0.62631 0.724 0.000 0.040 0.080 0.156
#> GSM153087 1 0.4858 0.62561 0.740 0.000 0.032 0.184 0.044
#> GSM153088 1 0.1186 0.63381 0.964 0.000 0.008 0.008 0.020
#> GSM153089 4 0.7381 0.41191 0.096 0.000 0.264 0.508 0.132
#> GSM153090 1 0.1205 0.63717 0.956 0.000 0.040 0.004 0.000
#> GSM153091 1 0.3421 0.64306 0.824 0.016 0.000 0.008 0.152
#> GSM153092 1 0.3938 0.63120 0.796 0.000 0.016 0.024 0.164
#> GSM153093 1 0.6049 0.45802 0.636 0.000 0.072 0.240 0.052
#> GSM153094 1 0.5103 0.41699 0.668 0.008 0.284 0.016 0.024
#> GSM153095 1 0.7805 0.34263 0.464 0.000 0.120 0.168 0.248
#> GSM153096 1 0.8025 0.30344 0.440 0.000 0.236 0.168 0.156
#> GSM153097 1 0.7676 0.45162 0.556 0.056 0.160 0.048 0.180
#> GSM153098 1 0.6786 0.58040 0.588 0.000 0.060 0.168 0.184
#> GSM153099 1 0.4600 0.64761 0.776 0.000 0.020 0.108 0.096
#> GSM153100 3 0.7837 -0.17066 0.112 0.000 0.400 0.340 0.148
#> GSM153101 3 0.7637 0.20040 0.064 0.000 0.432 0.284 0.220
#> GSM153102 3 0.7255 0.21044 0.036 0.004 0.480 0.292 0.188
#> GSM153103 1 0.4353 0.63303 0.792 0.000 0.016 0.100 0.092
#> GSM153104 4 0.5844 0.11775 0.464 0.000 0.028 0.468 0.040
#> GSM153106 3 0.1041 0.64345 0.000 0.000 0.964 0.004 0.032
#> GSM153107 3 0.0404 0.64270 0.000 0.000 0.988 0.000 0.012
#> GSM153108 3 0.5832 0.47536 0.008 0.000 0.624 0.240 0.128
#> GSM153109 1 0.7414 0.22915 0.560 0.240 0.080 0.032 0.088
#> GSM153110 1 0.3759 0.61681 0.792 0.000 0.004 0.024 0.180
#> GSM153111 1 0.4472 0.64532 0.776 0.004 0.012 0.056 0.152
#> GSM153112 1 0.7706 0.36185 0.444 0.008 0.052 0.216 0.280
#> GSM153113 2 0.7938 0.18085 0.116 0.568 0.116 0.080 0.120
#> GSM153114 3 0.0000 0.64148 0.000 0.000 1.000 0.000 0.000
#> GSM187532 2 0.6164 0.57658 0.068 0.672 0.156 0.004 0.100
#> GSM187533 3 0.3912 0.49428 0.000 0.208 0.768 0.004 0.020
#> GSM187534 2 0.5355 0.39240 0.016 0.624 0.316 0.000 0.044
#> GSM187535 3 0.0000 0.64148 0.000 0.000 1.000 0.000 0.000
#> GSM152906 2 0.0290 0.88238 0.000 0.992 0.000 0.000 0.008
#> GSM152907 2 0.0000 0.88301 0.000 1.000 0.000 0.000 0.000
#> GSM152908 2 0.2773 0.82680 0.000 0.836 0.000 0.000 0.164
#> GSM152909 2 0.2732 0.82869 0.000 0.840 0.000 0.000 0.160
#> GSM152910 2 0.2773 0.82680 0.000 0.836 0.000 0.000 0.164
#> GSM152911 2 0.0000 0.88301 0.000 1.000 0.000 0.000 0.000
#> GSM152912 2 0.2813 0.82684 0.000 0.832 0.000 0.000 0.168
#> GSM152913 2 0.0609 0.88227 0.000 0.980 0.000 0.000 0.020
#> GSM152914 2 0.0000 0.88301 0.000 1.000 0.000 0.000 0.000
#> GSM152915 2 0.0000 0.88301 0.000 1.000 0.000 0.000 0.000
#> GSM152916 2 0.1124 0.87813 0.004 0.960 0.000 0.000 0.036
#> GSM152917 2 0.0000 0.88301 0.000 1.000 0.000 0.000 0.000
#> GSM152918 2 0.0000 0.88301 0.000 1.000 0.000 0.000 0.000
#> GSM152919 2 0.0000 0.88301 0.000 1.000 0.000 0.000 0.000
#> GSM152920 2 0.2773 0.82680 0.000 0.836 0.000 0.000 0.164
#> GSM152921 2 0.2773 0.82680 0.000 0.836 0.000 0.000 0.164
#> GSM152922 2 0.2852 0.82692 0.000 0.828 0.000 0.000 0.172
#> GSM152923 2 0.0290 0.88238 0.000 0.992 0.000 0.000 0.008
#> GSM152924 2 0.0833 0.87502 0.004 0.976 0.016 0.000 0.004
#> GSM152925 2 0.0290 0.88238 0.000 0.992 0.000 0.000 0.008
#> GSM152926 2 0.2554 0.83240 0.036 0.892 0.000 0.000 0.072
#> GSM152927 2 0.0290 0.88238 0.000 0.992 0.000 0.000 0.008
#> GSM152928 2 0.2699 0.80899 0.012 0.880 0.000 0.008 0.100
#> GSM152929 2 0.0290 0.88238 0.000 0.992 0.000 0.000 0.008
#> GSM152930 2 0.0290 0.88238 0.000 0.992 0.000 0.000 0.008
cbind(get_classes(res, k = 6), get_membership(res, k = 6))
#> class entropy silhouette p1 p2 p3 p4 p5 p6
#> GSM152839 1 0.6769 0.4719 0.520 0.000 0.244 0.040 NA 0.168
#> GSM152840 4 0.4107 0.6294 0.056 0.000 0.120 0.788 NA 0.032
#> GSM152841 4 0.5437 0.5279 0.092 0.000 0.256 0.624 NA 0.024
#> GSM152842 4 0.5155 0.4948 0.268 0.000 0.028 0.636 NA 0.068
#> GSM152843 1 0.1931 0.6798 0.924 0.000 0.004 0.028 NA 0.040
#> GSM152844 4 0.4564 0.5927 0.020 0.000 0.168 0.744 NA 0.052
#> GSM152845 3 0.4698 0.6192 0.012 0.000 0.740 0.120 NA 0.112
#> GSM152846 3 0.6470 0.2904 0.084 0.000 0.492 0.348 NA 0.060
#> GSM152847 1 0.3456 0.6892 0.844 0.000 0.064 0.020 NA 0.060
#> GSM152848 1 0.7473 0.2085 0.396 0.000 0.336 0.100 NA 0.140
#> GSM152849 3 0.4897 0.3120 0.344 0.000 0.588 0.000 NA 0.064
#> GSM152850 1 0.5200 0.5584 0.628 0.000 0.292 0.044 NA 0.024
#> GSM152851 4 0.6288 0.2798 0.008 0.000 0.384 0.464 NA 0.104
#> GSM152852 3 0.4026 0.6034 0.008 0.000 0.784 0.148 NA 0.036
#> GSM152853 4 0.4617 0.6113 0.052 0.000 0.188 0.728 NA 0.024
#> GSM152854 3 0.4607 0.6202 0.128 0.008 0.760 0.076 NA 0.016
#> GSM152855 3 0.0000 0.6590 0.000 0.000 1.000 0.000 NA 0.000
#> GSM153238 1 0.5452 0.6488 0.676 0.016 0.004 0.152 NA 0.136
#> GSM153239 4 0.5187 0.6261 0.156 0.000 0.048 0.704 NA 0.084
#> GSM153240 3 0.6791 0.1154 0.288 0.000 0.432 0.240 NA 0.028
#> GSM153241 1 0.6191 0.3760 0.472 0.000 0.384 0.092 NA 0.048
#> GSM153242 1 0.6973 0.0897 0.404 0.000 0.228 0.308 NA 0.056
#> GSM153243 1 0.3809 0.6874 0.820 0.000 0.016 0.056 NA 0.088
#> GSM153244 3 0.3870 0.6391 0.104 0.000 0.808 0.020 NA 0.060
#> GSM153245 4 0.3044 0.6239 0.088 0.000 0.032 0.860 NA 0.012
#> GSM153246 1 0.7365 -0.2589 0.352 0.000 0.004 0.224 NA 0.100
#> GSM153247 1 0.3726 0.6858 0.824 0.000 0.012 0.084 NA 0.060
#> GSM153248 1 0.5463 0.6554 0.640 0.000 0.084 0.024 NA 0.240
#> GSM153249 4 0.6631 0.5023 0.220 0.000 0.024 0.536 NA 0.184
#> GSM153250 1 0.1129 0.6761 0.964 0.000 0.012 0.004 NA 0.012
#> GSM153251 1 0.7449 0.2774 0.432 0.000 0.196 0.236 NA 0.124
#> GSM153252 4 0.7271 0.5569 0.224 0.000 0.120 0.508 NA 0.108
#> GSM153253 4 0.4381 0.6279 0.096 0.000 0.108 0.768 NA 0.020
#> GSM153254 3 0.7332 -0.1100 0.120 0.000 0.396 0.368 NA 0.076
#> GSM153255 4 0.7153 0.5603 0.240 0.000 0.104 0.516 NA 0.096
#> GSM153256 1 0.5631 0.3836 0.592 0.000 0.032 0.296 NA 0.072
#> GSM153257 1 0.3017 0.6789 0.872 0.000 0.024 0.064 NA 0.024
#> GSM153258 1 0.3110 0.6718 0.792 0.000 0.196 0.000 NA 0.012
#> GSM153259 1 0.5481 0.6271 0.644 0.000 0.028 0.116 NA 0.208
#> GSM153260 1 0.4640 0.6760 0.752 0.000 0.032 0.088 NA 0.120
#> GSM153261 3 0.2865 0.6651 0.032 0.000 0.868 0.020 NA 0.080
#> GSM153262 3 0.3550 0.6079 0.024 0.000 0.788 0.176 NA 0.000
#> GSM153263 3 0.3929 0.6275 0.036 0.000 0.796 0.136 NA 0.020
#> GSM153264 1 0.6685 0.2334 0.448 0.000 0.376 0.080 NA 0.080
#> GSM153265 4 0.4365 0.4445 0.000 0.000 0.332 0.636 NA 0.024
#> GSM153266 1 0.6795 0.5675 0.556 0.000 0.104 0.168 NA 0.156
#> GSM153267 3 0.4804 0.1369 0.396 0.000 0.564 0.016 NA 0.016
#> GSM153268 4 0.2680 0.5966 0.000 0.000 0.124 0.856 NA 0.016
#> GSM153269 1 0.4605 0.6190 0.672 0.000 0.272 0.012 NA 0.040
#> GSM153270 1 0.3785 0.6749 0.800 0.000 0.016 0.140 NA 0.036
#> GSM153271 1 0.1307 0.6737 0.952 0.000 0.000 0.008 NA 0.032
#> GSM153272 4 0.7350 0.1789 0.356 0.000 0.132 0.400 NA 0.076
#> GSM153273 1 0.6635 0.5388 0.480 0.000 0.044 0.120 NA 0.336
#> GSM153274 1 0.6985 0.3939 0.536 0.000 0.128 0.204 NA 0.108
#> GSM153275 1 0.7823 -0.0677 0.352 0.000 0.240 0.260 NA 0.128
#> GSM153276 1 0.4242 0.6750 0.768 0.000 0.160 0.036 NA 0.016
#> GSM153277 4 0.6009 0.0955 0.000 0.000 0.400 0.444 NA 0.136
#> GSM153278 1 0.5574 0.6385 0.660 0.000 0.180 0.096 NA 0.060
#> GSM153279 4 0.5447 0.5842 0.164 0.000 0.104 0.680 NA 0.040
#> GSM153280 3 0.4889 0.5202 0.028 0.000 0.716 0.192 NA 0.028
#> GSM153281 4 0.4424 0.6179 0.176 0.000 0.044 0.748 NA 0.016
#> GSM153282 4 0.4960 0.6036 0.008 0.000 0.116 0.728 NA 0.108
#> GSM153283 1 0.7567 0.4299 0.456 0.000 0.200 0.156 NA 0.164
#> GSM153284 1 0.5756 0.5154 0.644 0.000 0.016 0.192 NA 0.112
#> GSM153285 4 0.5511 0.6214 0.028 0.000 0.160 0.688 NA 0.084
#> GSM153286 1 0.4179 0.6490 0.756 0.000 0.012 0.184 NA 0.036
#> GSM153287 4 0.4061 0.6226 0.104 0.000 0.004 0.796 NA 0.060
#> GSM153288 4 0.6612 0.6175 0.144 0.000 0.100 0.608 NA 0.104
#> GSM153289 3 0.0551 0.6603 0.000 0.000 0.984 0.004 NA 0.008
#> GSM153290 4 0.3719 0.5517 0.000 0.000 0.248 0.728 NA 0.024
#> GSM153291 3 0.5196 0.4947 0.032 0.000 0.680 0.216 NA 0.056
#> GSM153292 4 0.7118 0.5738 0.176 0.000 0.132 0.540 NA 0.116
#> GSM153293 3 0.6315 0.4736 0.160 0.000 0.608 0.128 NA 0.092
#> GSM153294 1 0.3471 0.6848 0.832 0.016 0.000 0.040 NA 0.104
#> GSM153295 3 0.2466 0.6507 0.008 0.000 0.872 0.112 NA 0.008
#> GSM153054 1 0.3845 0.6903 0.800 0.000 0.000 0.048 NA 0.120
#> GSM153055 3 0.7907 -0.2346 0.176 0.000 0.340 0.328 NA 0.116
#> GSM153056 1 0.5464 0.5893 0.628 0.000 0.200 0.156 NA 0.004
#> GSM153057 3 0.1899 0.6680 0.028 0.000 0.928 0.008 NA 0.032
#> GSM153058 1 0.7022 0.1031 0.416 0.000 0.332 0.176 NA 0.068
#> GSM153059 3 0.7362 0.3891 0.188 0.000 0.468 0.096 NA 0.224
#> GSM153060 1 0.6116 0.5692 0.588 0.000 0.020 0.220 NA 0.148
#> GSM153061 3 0.7834 0.2223 0.200 0.000 0.376 0.216 NA 0.192
#> GSM153062 6 0.6572 0.0000 0.060 0.036 0.024 0.108 NA 0.636
#> GSM153063 4 0.7115 0.3686 0.236 0.000 0.264 0.432 NA 0.052
#> GSM153064 1 0.6331 0.5345 0.476 0.000 0.032 0.116 NA 0.364
#> GSM153065 3 0.5252 0.6104 0.084 0.008 0.720 0.044 NA 0.132
#> GSM153066 2 0.8047 0.2727 0.088 0.496 0.076 0.032 NA 0.136
#> GSM153067 4 0.4907 0.5750 0.244 0.000 0.000 0.668 NA 0.064
#> GSM153068 1 0.6619 0.5659 0.584 0.000 0.128 0.132 NA 0.140
#> GSM153069 4 0.3441 0.6103 0.020 0.000 0.100 0.836 NA 0.036
#> GSM153070 1 0.0665 0.6705 0.980 0.000 0.000 0.008 NA 0.004
#> GSM153071 1 0.6472 0.4578 0.524 0.000 0.088 0.296 NA 0.084
#> GSM153072 1 0.3754 0.6894 0.832 0.020 0.052 0.012 NA 0.076
#> GSM153073 1 0.1074 0.6743 0.960 0.000 0.000 0.028 NA 0.000
#> GSM153074 3 0.6960 -0.0587 0.080 0.000 0.400 0.392 NA 0.112
#> GSM153075 3 0.3129 0.6499 0.008 0.000 0.864 0.064 NA 0.036
#> GSM153076 1 0.2415 0.6758 0.904 0.000 0.004 0.036 NA 0.032
#> GSM153077 1 0.2309 0.6880 0.908 0.000 0.052 0.012 NA 0.016
#> GSM153078 1 0.4992 0.5234 0.580 0.000 0.368 0.016 NA 0.020
#> GSM153079 3 0.1555 0.6599 0.000 0.000 0.940 0.008 NA 0.040
#> GSM153080 4 0.6900 0.5540 0.144 0.000 0.164 0.552 NA 0.120
#> GSM153081 3 0.1718 0.6659 0.044 0.000 0.932 0.000 NA 0.016
#> GSM153082 3 0.7472 0.0424 0.032 0.360 0.384 0.056 NA 0.160
#> GSM153083 1 0.3243 0.6870 0.844 0.036 0.004 0.008 NA 0.104
#> GSM153084 1 0.8628 0.0983 0.340 0.076 0.308 0.080 NA 0.156
#> GSM153085 1 0.5053 0.6644 0.700 0.000 0.096 0.160 NA 0.044
#> GSM153086 1 0.5014 0.6687 0.712 0.000 0.040 0.072 NA 0.168
#> GSM153087 1 0.4671 0.6471 0.724 0.000 0.032 0.192 NA 0.044
#> GSM153088 1 0.1381 0.6731 0.952 0.000 0.004 0.004 NA 0.020
#> GSM153089 4 0.6486 0.5404 0.084 0.000 0.192 0.572 NA 0.144
#> GSM153090 1 0.0713 0.6756 0.972 0.000 0.028 0.000 NA 0.000
#> GSM153091 1 0.3087 0.6866 0.808 0.012 0.000 0.004 NA 0.176
#> GSM153092 1 0.4076 0.6754 0.768 0.000 0.016 0.024 NA 0.176
#> GSM153093 1 0.5643 0.4189 0.608 0.000 0.060 0.276 NA 0.048
#> GSM153094 1 0.4593 0.4943 0.672 0.004 0.280 0.008 NA 0.028
#> GSM153095 1 0.7326 0.4241 0.444 0.000 0.104 0.164 NA 0.272
#> GSM153096 1 0.7730 0.3804 0.436 0.000 0.232 0.136 NA 0.160
#> GSM153097 1 0.7180 0.5409 0.532 0.064 0.148 0.048 NA 0.204
#> GSM153098 1 0.6337 0.6120 0.560 0.000 0.060 0.148 NA 0.228
#> GSM153099 1 0.4686 0.6825 0.756 0.000 0.020 0.104 NA 0.096
#> GSM153100 4 0.7368 0.3281 0.092 0.000 0.332 0.400 NA 0.156
#> GSM153101 3 0.7092 0.1282 0.056 0.000 0.392 0.308 NA 0.236
#> GSM153102 3 0.6858 0.1755 0.024 0.008 0.448 0.300 NA 0.208
#> GSM153103 1 0.4015 0.6774 0.796 0.000 0.008 0.084 NA 0.096
#> GSM153104 4 0.5531 0.3549 0.384 0.000 0.024 0.536 NA 0.032
#> GSM153106 3 0.1194 0.6597 0.000 0.000 0.956 0.004 NA 0.032
#> GSM153107 3 0.0363 0.6602 0.000 0.000 0.988 0.000 NA 0.012
#> GSM153108 3 0.5583 0.4933 0.008 0.000 0.612 0.236 NA 0.132
#> GSM153109 1 0.7129 0.3881 0.544 0.240 0.084 0.032 NA 0.076
#> GSM153110 1 0.3430 0.6665 0.772 0.000 0.004 0.016 NA 0.208
#> GSM153111 1 0.4348 0.6857 0.772 0.004 0.016 0.048 NA 0.144
#> GSM153112 1 0.7260 0.3083 0.392 0.012 0.056 0.220 NA 0.316
#> GSM153113 2 0.7471 0.1512 0.116 0.548 0.112 0.084 NA 0.132
#> GSM153114 3 0.0000 0.6590 0.000 0.000 1.000 0.000 NA 0.000
#> GSM187532 2 0.6332 0.5471 0.056 0.636 0.128 0.004 NA 0.040
#> GSM187533 3 0.4110 0.5097 0.000 0.208 0.744 0.004 NA 0.020
#> GSM187534 2 0.5734 0.3765 0.004 0.572 0.280 0.000 NA 0.016
#> GSM187535 3 0.0000 0.6590 0.000 0.000 1.000 0.000 NA 0.000
#> GSM152906 2 0.1327 0.7811 0.000 0.936 0.000 0.000 NA 0.000
#> GSM152907 2 0.0713 0.7845 0.000 0.972 0.000 0.000 NA 0.000
#> GSM152908 2 0.3747 0.5887 0.000 0.604 0.000 0.000 NA 0.000
#> GSM152909 2 0.3684 0.6074 0.000 0.628 0.000 0.000 NA 0.000
#> GSM152910 2 0.3727 0.5907 0.000 0.612 0.000 0.000 NA 0.000
#> GSM152911 2 0.0260 0.7838 0.000 0.992 0.000 0.000 NA 0.000
#> GSM152912 2 0.3756 0.5905 0.000 0.600 0.000 0.000 NA 0.000
#> GSM152913 2 0.1267 0.7855 0.000 0.940 0.000 0.000 NA 0.000
#> GSM152914 2 0.0260 0.7838 0.000 0.992 0.000 0.000 NA 0.000
#> GSM152915 2 0.0260 0.7838 0.000 0.992 0.000 0.000 NA 0.000
#> GSM152916 2 0.2378 0.7724 0.000 0.848 0.000 0.000 NA 0.000
#> GSM152917 2 0.0260 0.7838 0.000 0.992 0.000 0.000 NA 0.000
#> GSM152918 2 0.0260 0.7838 0.000 0.992 0.000 0.000 NA 0.000
#> GSM152919 2 0.0260 0.7838 0.000 0.992 0.000 0.000 NA 0.000
#> GSM152920 2 0.3747 0.5887 0.000 0.604 0.000 0.000 NA 0.000
#> GSM152921 2 0.3747 0.5902 0.000 0.604 0.000 0.000 NA 0.000
#> GSM152922 2 0.3817 0.5866 0.000 0.568 0.000 0.000 NA 0.000
#> GSM152923 2 0.1814 0.7708 0.000 0.900 0.000 0.000 NA 0.000
#> GSM152924 2 0.1657 0.7785 0.000 0.928 0.016 0.000 NA 0.000
#> GSM152925 2 0.1957 0.7769 0.000 0.888 0.000 0.000 NA 0.000
#> GSM152926 2 0.3300 0.7562 0.012 0.816 0.000 0.000 NA 0.024
#> GSM152927 2 0.1814 0.7701 0.000 0.900 0.000 0.000 NA 0.000
#> GSM152928 2 0.3291 0.7388 0.004 0.828 0.000 0.000 NA 0.064
#> GSM152929 2 0.1910 0.7750 0.000 0.892 0.000 0.000 NA 0.000
#> GSM152930 2 0.2003 0.7732 0.000 0.884 0.000 0.000 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 tissue(p) k
#> MAD:pam 161 3.77e-28 2
#> MAD:pam 146 9.94e-26 3
#> MAD:pam 112 4.41e-19 4
#> MAD:pam 104 3.14e-20 5
#> MAD:pam 117 1.59e-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 12013 rows and 164 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 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 0.973 0.988 0.3155 0.692 0.692
#> 3 3 0.546 0.676 0.808 0.8429 0.696 0.569
#> 4 4 0.647 0.767 0.856 0.2293 0.789 0.530
#> 5 5 0.730 0.743 0.855 0.0536 0.955 0.841
#> 6 6 0.732 0.687 0.839 0.0616 0.907 0.652
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
#> GSM152839 1 0.0376 0.988 0.996 0.004
#> GSM152840 1 0.0376 0.988 0.996 0.004
#> GSM152841 1 0.0000 0.988 1.000 0.000
#> GSM152842 1 0.0376 0.988 0.996 0.004
#> GSM152843 1 0.0376 0.988 0.996 0.004
#> GSM152844 1 0.0376 0.988 0.996 0.004
#> GSM152845 1 0.3274 0.934 0.940 0.060
#> GSM152846 1 0.0376 0.988 0.996 0.004
#> GSM152847 1 0.0376 0.988 0.996 0.004
#> GSM152848 1 0.0000 0.988 1.000 0.000
#> GSM152849 1 0.0376 0.988 0.996 0.004
#> GSM152850 1 0.0376 0.988 0.996 0.004
#> GSM152851 1 0.0376 0.988 0.996 0.004
#> GSM152852 1 0.0376 0.988 0.996 0.004
#> GSM152853 1 0.0376 0.988 0.996 0.004
#> GSM152854 1 0.0376 0.988 0.996 0.004
#> GSM152855 1 0.0000 0.988 1.000 0.000
#> GSM153238 1 0.1414 0.975 0.980 0.020
#> GSM153239 1 0.0376 0.988 0.996 0.004
#> GSM153240 1 0.0000 0.988 1.000 0.000
#> GSM153241 1 0.0376 0.988 0.996 0.004
#> GSM153242 1 0.0376 0.988 0.996 0.004
#> GSM153243 1 0.0376 0.988 0.996 0.004
#> GSM153244 1 0.0376 0.988 0.996 0.004
#> GSM153245 1 0.0376 0.988 0.996 0.004
#> GSM153246 1 0.0376 0.988 0.996 0.004
#> GSM153247 1 0.0376 0.988 0.996 0.004
#> GSM153248 1 0.0000 0.988 1.000 0.000
#> GSM153249 1 0.0000 0.988 1.000 0.000
#> GSM153250 1 0.0000 0.988 1.000 0.000
#> GSM153251 1 0.0376 0.988 0.996 0.004
#> GSM153252 1 0.0000 0.988 1.000 0.000
#> GSM153253 1 0.0000 0.988 1.000 0.000
#> GSM153254 1 0.0376 0.988 0.996 0.004
#> GSM153255 1 0.0000 0.988 1.000 0.000
#> GSM153256 1 0.0000 0.988 1.000 0.000
#> GSM153257 1 0.0000 0.988 1.000 0.000
#> GSM153258 1 0.0000 0.988 1.000 0.000
#> GSM153259 1 0.0000 0.988 1.000 0.000
#> GSM153260 1 0.0376 0.988 0.996 0.004
#> GSM153261 1 0.0376 0.988 0.996 0.004
#> GSM153262 1 0.0000 0.988 1.000 0.000
#> GSM153263 1 0.0000 0.988 1.000 0.000
#> GSM153264 1 0.0000 0.988 1.000 0.000
#> GSM153265 1 0.0000 0.988 1.000 0.000
#> GSM153266 1 0.0000 0.988 1.000 0.000
#> GSM153267 1 0.0000 0.988 1.000 0.000
#> GSM153268 1 0.0000 0.988 1.000 0.000
#> GSM153269 1 0.0000 0.988 1.000 0.000
#> GSM153270 1 0.0000 0.988 1.000 0.000
#> GSM153271 1 0.0000 0.988 1.000 0.000
#> GSM153272 1 0.0000 0.988 1.000 0.000
#> GSM153273 1 0.0000 0.988 1.000 0.000
#> GSM153274 1 0.0000 0.988 1.000 0.000
#> GSM153275 1 0.0000 0.988 1.000 0.000
#> GSM153276 1 0.0000 0.988 1.000 0.000
#> GSM153277 1 0.0000 0.988 1.000 0.000
#> GSM153278 1 0.0376 0.988 0.996 0.004
#> GSM153279 1 0.0000 0.988 1.000 0.000
#> GSM153280 1 0.0000 0.988 1.000 0.000
#> GSM153281 1 0.0000 0.988 1.000 0.000
#> GSM153282 1 0.0000 0.988 1.000 0.000
#> GSM153283 1 0.0000 0.988 1.000 0.000
#> GSM153284 1 0.0000 0.988 1.000 0.000
#> GSM153285 1 0.0000 0.988 1.000 0.000
#> GSM153286 1 0.0000 0.988 1.000 0.000
#> GSM153287 1 0.0000 0.988 1.000 0.000
#> GSM153288 1 0.0000 0.988 1.000 0.000
#> GSM153289 1 0.0000 0.988 1.000 0.000
#> GSM153290 1 0.0000 0.988 1.000 0.000
#> GSM153291 1 0.0000 0.988 1.000 0.000
#> GSM153292 1 0.0000 0.988 1.000 0.000
#> GSM153293 1 0.0000 0.988 1.000 0.000
#> GSM153294 1 0.0000 0.988 1.000 0.000
#> GSM153295 1 0.0376 0.988 0.996 0.004
#> GSM153054 1 0.0376 0.988 0.996 0.004
#> GSM153055 1 0.0000 0.988 1.000 0.000
#> GSM153056 1 0.0376 0.988 0.996 0.004
#> GSM153057 1 0.0376 0.988 0.996 0.004
#> GSM153058 1 0.0376 0.988 0.996 0.004
#> GSM153059 1 0.0376 0.988 0.996 0.004
#> GSM153060 1 0.0376 0.988 0.996 0.004
#> GSM153061 1 0.0376 0.988 0.996 0.004
#> GSM153062 1 0.0376 0.988 0.996 0.004
#> GSM153063 1 0.0376 0.988 0.996 0.004
#> GSM153064 1 0.0000 0.988 1.000 0.000
#> GSM153065 1 0.0376 0.988 0.996 0.004
#> GSM153066 1 0.9087 0.523 0.676 0.324
#> GSM153067 1 0.0000 0.988 1.000 0.000
#> GSM153068 1 0.0376 0.988 0.996 0.004
#> GSM153069 1 0.0000 0.988 1.000 0.000
#> GSM153070 1 0.0000 0.988 1.000 0.000
#> GSM153071 1 0.0376 0.988 0.996 0.004
#> GSM153072 1 0.0376 0.988 0.996 0.004
#> GSM153073 1 0.0000 0.988 1.000 0.000
#> GSM153074 1 0.0000 0.988 1.000 0.000
#> GSM153075 1 0.0000 0.988 1.000 0.000
#> GSM153076 1 0.0000 0.988 1.000 0.000
#> GSM153077 1 0.0000 0.988 1.000 0.000
#> GSM153078 1 0.0376 0.988 0.996 0.004
#> GSM153079 1 0.0376 0.988 0.996 0.004
#> GSM153080 1 0.0376 0.988 0.996 0.004
#> GSM153081 1 0.0000 0.988 1.000 0.000
#> GSM153082 1 0.7139 0.760 0.804 0.196
#> GSM153083 1 0.2778 0.948 0.952 0.048
#> GSM153084 1 0.9850 0.254 0.572 0.428
#> GSM153085 1 0.0672 0.985 0.992 0.008
#> GSM153086 1 0.0000 0.988 1.000 0.000
#> GSM153087 1 0.0000 0.988 1.000 0.000
#> GSM153088 1 0.0000 0.988 1.000 0.000
#> GSM153089 1 0.0376 0.988 0.996 0.004
#> GSM153090 1 0.0000 0.988 1.000 0.000
#> GSM153091 1 0.3274 0.933 0.940 0.060
#> GSM153092 1 0.0000 0.988 1.000 0.000
#> GSM153093 1 0.0000 0.988 1.000 0.000
#> GSM153094 1 0.4690 0.890 0.900 0.100
#> GSM153095 1 0.0376 0.988 0.996 0.004
#> GSM153096 1 0.0000 0.988 1.000 0.000
#> GSM153097 1 0.2423 0.953 0.960 0.040
#> GSM153098 1 0.0000 0.988 1.000 0.000
#> GSM153099 1 0.0000 0.988 1.000 0.000
#> GSM153100 1 0.0000 0.988 1.000 0.000
#> GSM153101 1 0.0376 0.988 0.996 0.004
#> GSM153102 1 0.0376 0.988 0.996 0.004
#> GSM153103 1 0.0672 0.985 0.992 0.008
#> GSM153104 1 0.0000 0.988 1.000 0.000
#> GSM153106 1 0.0000 0.988 1.000 0.000
#> GSM153107 1 0.0000 0.988 1.000 0.000
#> GSM153108 1 0.0000 0.988 1.000 0.000
#> GSM153109 2 0.8207 0.662 0.256 0.744
#> GSM153110 1 0.0000 0.988 1.000 0.000
#> GSM153111 1 0.2778 0.945 0.952 0.048
#> GSM153112 1 0.0000 0.988 1.000 0.000
#> GSM153113 2 0.6343 0.811 0.160 0.840
#> GSM153114 1 0.0000 0.988 1.000 0.000
#> GSM187532 2 0.1414 0.968 0.020 0.980
#> GSM187533 2 0.0000 0.983 0.000 1.000
#> GSM187534 2 0.0000 0.983 0.000 1.000
#> GSM187535 2 0.2603 0.946 0.044 0.956
#> GSM152906 2 0.0000 0.983 0.000 1.000
#> GSM152907 2 0.0000 0.983 0.000 1.000
#> GSM152908 2 0.0000 0.983 0.000 1.000
#> GSM152909 2 0.0000 0.983 0.000 1.000
#> GSM152910 2 0.0000 0.983 0.000 1.000
#> GSM152911 2 0.0000 0.983 0.000 1.000
#> GSM152912 2 0.0000 0.983 0.000 1.000
#> GSM152913 2 0.0000 0.983 0.000 1.000
#> GSM152914 2 0.0000 0.983 0.000 1.000
#> GSM152915 2 0.0000 0.983 0.000 1.000
#> GSM152916 2 0.0000 0.983 0.000 1.000
#> GSM152917 2 0.0000 0.983 0.000 1.000
#> GSM152918 2 0.0000 0.983 0.000 1.000
#> GSM152919 2 0.0000 0.983 0.000 1.000
#> GSM152920 2 0.0000 0.983 0.000 1.000
#> GSM152921 2 0.0000 0.983 0.000 1.000
#> GSM152922 2 0.0000 0.983 0.000 1.000
#> GSM152923 2 0.0000 0.983 0.000 1.000
#> GSM152924 2 0.0000 0.983 0.000 1.000
#> GSM152925 2 0.0000 0.983 0.000 1.000
#> GSM152926 2 0.0000 0.983 0.000 1.000
#> GSM152927 2 0.0000 0.983 0.000 1.000
#> GSM152928 2 0.1633 0.965 0.024 0.976
#> GSM152929 2 0.0000 0.983 0.000 1.000
#> GSM152930 2 0.0000 0.983 0.000 1.000
cbind(get_classes(res, k = 3), get_membership(res, k = 3))
#> class entropy silhouette p1 p2 p3
#> GSM152839 3 0.5497 0.1393 0.292 0.000 0.708
#> GSM152840 3 0.6095 0.5283 0.392 0.000 0.608
#> GSM152841 1 0.1529 0.6107 0.960 0.000 0.040
#> GSM152842 3 0.0237 0.7292 0.004 0.000 0.996
#> GSM152843 3 0.0892 0.7241 0.020 0.000 0.980
#> GSM152844 3 0.5988 0.5445 0.368 0.000 0.632
#> GSM152845 3 0.3784 0.6865 0.132 0.004 0.864
#> GSM152846 3 0.5948 0.5480 0.360 0.000 0.640
#> GSM152847 3 0.0592 0.7278 0.012 0.000 0.988
#> GSM152848 1 0.6215 0.6854 0.572 0.000 0.428
#> GSM152849 3 0.0000 0.7287 0.000 0.000 1.000
#> GSM152850 3 0.1163 0.7187 0.028 0.000 0.972
#> GSM152851 1 0.5706 0.0407 0.680 0.000 0.320
#> GSM152852 3 0.5988 0.5449 0.368 0.000 0.632
#> GSM152853 3 0.5988 0.5445 0.368 0.000 0.632
#> GSM152854 3 0.2165 0.7206 0.064 0.000 0.936
#> GSM152855 1 0.3686 0.6971 0.860 0.000 0.140
#> GSM153238 3 0.0000 0.7287 0.000 0.000 1.000
#> GSM153239 3 0.5988 0.5445 0.368 0.000 0.632
#> GSM153240 1 0.1163 0.6296 0.972 0.000 0.028
#> GSM153241 3 0.0237 0.7292 0.004 0.000 0.996
#> GSM153242 3 0.5859 0.5591 0.344 0.000 0.656
#> GSM153243 3 0.0000 0.7287 0.000 0.000 1.000
#> GSM153244 1 0.3412 0.5696 0.876 0.000 0.124
#> GSM153245 3 0.5988 0.5445 0.368 0.000 0.632
#> GSM153246 3 0.1289 0.7284 0.032 0.000 0.968
#> GSM153247 3 0.1411 0.7254 0.036 0.000 0.964
#> GSM153248 1 0.6079 0.7156 0.612 0.000 0.388
#> GSM153249 1 0.0592 0.6262 0.988 0.000 0.012
#> GSM153250 1 0.5968 0.7225 0.636 0.000 0.364
#> GSM153251 3 0.4796 0.6398 0.220 0.000 0.780
#> GSM153252 1 0.1753 0.6538 0.952 0.000 0.048
#> GSM153253 1 0.1753 0.6048 0.952 0.000 0.048
#> GSM153254 1 0.6095 0.4718 0.608 0.000 0.392
#> GSM153255 1 0.0747 0.6296 0.984 0.000 0.016
#> GSM153256 1 0.4931 0.7204 0.768 0.000 0.232
#> GSM153257 1 0.2066 0.6616 0.940 0.000 0.060
#> GSM153258 1 0.5988 0.7214 0.632 0.000 0.368
#> GSM153259 1 0.5988 0.7212 0.632 0.000 0.368
#> GSM153260 3 0.0237 0.7276 0.004 0.000 0.996
#> GSM153261 3 0.0000 0.7287 0.000 0.000 1.000
#> GSM153262 1 0.1529 0.6420 0.960 0.000 0.040
#> GSM153263 1 0.5968 0.7225 0.636 0.000 0.364
#> GSM153264 1 0.6062 0.7193 0.616 0.000 0.384
#> GSM153265 1 0.1411 0.6132 0.964 0.000 0.036
#> GSM153266 1 0.6008 0.7233 0.628 0.000 0.372
#> GSM153267 1 0.5905 0.7265 0.648 0.000 0.352
#> GSM153268 1 0.2448 0.5802 0.924 0.000 0.076
#> GSM153269 1 0.5760 0.7297 0.672 0.000 0.328
#> GSM153270 1 0.4750 0.7137 0.784 0.000 0.216
#> GSM153271 1 0.5968 0.7225 0.636 0.000 0.364
#> GSM153272 1 0.0892 0.6329 0.980 0.000 0.020
#> GSM153273 1 0.6045 0.7181 0.620 0.000 0.380
#> GSM153274 1 0.5810 0.7303 0.664 0.000 0.336
#> GSM153275 1 0.4178 0.7061 0.828 0.000 0.172
#> GSM153276 1 0.5178 0.7237 0.744 0.000 0.256
#> GSM153277 1 0.1031 0.6210 0.976 0.000 0.024
#> GSM153278 3 0.1753 0.6918 0.048 0.000 0.952
#> GSM153279 1 0.2959 0.5665 0.900 0.000 0.100
#> GSM153280 1 0.1964 0.5996 0.944 0.000 0.056
#> GSM153281 1 0.1411 0.6132 0.964 0.000 0.036
#> GSM153282 1 0.2066 0.5958 0.940 0.000 0.060
#> GSM153283 1 0.5968 0.7225 0.636 0.000 0.364
#> GSM153284 1 0.3192 0.6866 0.888 0.000 0.112
#> GSM153285 1 0.1529 0.6107 0.960 0.000 0.040
#> GSM153286 1 0.2796 0.6812 0.908 0.000 0.092
#> GSM153287 1 0.0592 0.6262 0.988 0.000 0.012
#> GSM153288 1 0.2625 0.6773 0.916 0.000 0.084
#> GSM153289 1 0.5291 0.7259 0.732 0.000 0.268
#> GSM153290 1 0.2356 0.5872 0.928 0.000 0.072
#> GSM153291 1 0.0892 0.6346 0.980 0.000 0.020
#> GSM153292 1 0.1031 0.6203 0.976 0.000 0.024
#> GSM153293 1 0.4121 0.7070 0.832 0.000 0.168
#> GSM153294 1 0.6079 0.7174 0.612 0.000 0.388
#> GSM153295 1 0.5733 0.7282 0.676 0.000 0.324
#> GSM153054 3 0.6307 -0.5596 0.488 0.000 0.512
#> GSM153055 1 0.5968 0.7264 0.636 0.000 0.364
#> GSM153056 3 0.1163 0.7186 0.028 0.000 0.972
#> GSM153057 3 0.4931 0.3520 0.232 0.000 0.768
#> GSM153058 3 0.0592 0.7300 0.012 0.000 0.988
#> GSM153059 3 0.3752 0.5434 0.144 0.000 0.856
#> GSM153060 3 0.2537 0.7128 0.080 0.000 0.920
#> GSM153061 3 0.0000 0.7287 0.000 0.000 1.000
#> GSM153062 3 0.1860 0.7241 0.052 0.000 0.948
#> GSM153063 3 0.5327 0.6071 0.272 0.000 0.728
#> GSM153064 1 0.6026 0.7201 0.624 0.000 0.376
#> GSM153065 3 0.0000 0.7287 0.000 0.000 1.000
#> GSM153066 3 0.6348 0.3438 0.212 0.048 0.740
#> GSM153067 1 0.0747 0.6296 0.984 0.000 0.016
#> GSM153068 3 0.0000 0.7287 0.000 0.000 1.000
#> GSM153069 1 0.0747 0.6244 0.984 0.000 0.016
#> GSM153070 1 0.6045 0.7217 0.620 0.000 0.380
#> GSM153071 3 0.6267 -0.4756 0.452 0.000 0.548
#> GSM153072 1 0.6291 0.6294 0.532 0.000 0.468
#> GSM153073 1 0.6026 0.7179 0.624 0.000 0.376
#> GSM153074 1 0.2796 0.6806 0.908 0.000 0.092
#> GSM153075 1 0.1964 0.6381 0.944 0.000 0.056
#> GSM153076 1 0.5968 0.7225 0.636 0.000 0.364
#> GSM153077 1 0.6079 0.7156 0.612 0.000 0.388
#> GSM153078 3 0.6286 -0.5059 0.464 0.000 0.536
#> GSM153079 1 0.6154 0.7016 0.592 0.000 0.408
#> GSM153080 3 0.3267 0.6829 0.116 0.000 0.884
#> GSM153081 1 0.6062 0.7193 0.616 0.000 0.384
#> GSM153082 1 0.6848 0.6832 0.568 0.016 0.416
#> GSM153083 1 0.6192 0.6900 0.580 0.000 0.420
#> GSM153084 3 0.7657 -0.4965 0.448 0.044 0.508
#> GSM153085 1 0.6252 0.6629 0.556 0.000 0.444
#> GSM153086 1 0.6215 0.6833 0.572 0.000 0.428
#> GSM153087 1 0.2959 0.6751 0.900 0.000 0.100
#> GSM153088 1 0.5988 0.7231 0.632 0.000 0.368
#> GSM153089 3 0.4605 0.6531 0.204 0.000 0.796
#> GSM153090 1 0.5968 0.7225 0.636 0.000 0.364
#> GSM153091 1 0.6140 0.7053 0.596 0.000 0.404
#> GSM153092 1 0.6095 0.7128 0.608 0.000 0.392
#> GSM153093 1 0.2261 0.6688 0.932 0.000 0.068
#> GSM153094 1 0.6192 0.6900 0.580 0.000 0.420
#> GSM153095 1 0.6215 0.6743 0.572 0.000 0.428
#> GSM153096 1 0.6062 0.7183 0.616 0.000 0.384
#> GSM153097 1 0.6154 0.7021 0.592 0.000 0.408
#> GSM153098 1 0.5968 0.7274 0.636 0.000 0.364
#> GSM153099 1 0.5835 0.7289 0.660 0.000 0.340
#> GSM153100 1 0.6026 0.7227 0.624 0.000 0.376
#> GSM153101 1 0.6295 0.6249 0.528 0.000 0.472
#> GSM153102 1 0.6215 0.6830 0.572 0.000 0.428
#> GSM153103 1 0.6244 0.6674 0.560 0.000 0.440
#> GSM153104 1 0.1529 0.6116 0.960 0.000 0.040
#> GSM153106 1 0.5706 0.7296 0.680 0.000 0.320
#> GSM153107 1 0.6008 0.7198 0.628 0.000 0.372
#> GSM153108 1 0.3879 0.6943 0.848 0.000 0.152
#> GSM153109 1 0.7542 0.6392 0.528 0.040 0.432
#> GSM153110 1 0.6079 0.7156 0.612 0.000 0.388
#> GSM153111 1 0.6154 0.7024 0.592 0.000 0.408
#> GSM153112 1 0.6079 0.7174 0.612 0.000 0.388
#> GSM153113 1 0.9263 0.5172 0.476 0.164 0.360
#> GSM153114 1 0.3192 0.6873 0.888 0.000 0.112
#> GSM187532 2 0.2537 0.8886 0.000 0.920 0.080
#> GSM187533 2 0.0000 0.9661 0.000 1.000 0.000
#> GSM187534 2 0.0000 0.9661 0.000 1.000 0.000
#> GSM187535 2 0.9878 -0.2518 0.264 0.396 0.340
#> GSM152906 2 0.0000 0.9661 0.000 1.000 0.000
#> GSM152907 2 0.0000 0.9661 0.000 1.000 0.000
#> GSM152908 2 0.0000 0.9661 0.000 1.000 0.000
#> GSM152909 2 0.0000 0.9661 0.000 1.000 0.000
#> GSM152910 2 0.0000 0.9661 0.000 1.000 0.000
#> GSM152911 2 0.0000 0.9661 0.000 1.000 0.000
#> GSM152912 2 0.0000 0.9661 0.000 1.000 0.000
#> GSM152913 2 0.0000 0.9661 0.000 1.000 0.000
#> GSM152914 2 0.0000 0.9661 0.000 1.000 0.000
#> GSM152915 2 0.0000 0.9661 0.000 1.000 0.000
#> GSM152916 2 0.0000 0.9661 0.000 1.000 0.000
#> GSM152917 2 0.0000 0.9661 0.000 1.000 0.000
#> GSM152918 2 0.0000 0.9661 0.000 1.000 0.000
#> GSM152919 2 0.0000 0.9661 0.000 1.000 0.000
#> GSM152920 2 0.0000 0.9661 0.000 1.000 0.000
#> GSM152921 2 0.0000 0.9661 0.000 1.000 0.000
#> GSM152922 2 0.0000 0.9661 0.000 1.000 0.000
#> GSM152923 2 0.0000 0.9661 0.000 1.000 0.000
#> GSM152924 2 0.0000 0.9661 0.000 1.000 0.000
#> GSM152925 2 0.0000 0.9661 0.000 1.000 0.000
#> GSM152926 2 0.0000 0.9661 0.000 1.000 0.000
#> GSM152927 2 0.0000 0.9661 0.000 1.000 0.000
#> GSM152928 2 0.3377 0.8417 0.012 0.896 0.092
#> GSM152929 2 0.0000 0.9661 0.000 1.000 0.000
#> GSM152930 2 0.0000 0.9661 0.000 1.000 0.000
cbind(get_classes(res, k = 4), get_membership(res, k = 4))
#> class entropy silhouette p1 p2 p3 p4
#> GSM152839 1 0.5483 -0.0970 0.536 0.000 0.448 0.016
#> GSM152840 3 0.4193 0.6696 0.000 0.000 0.732 0.268
#> GSM152841 4 0.0000 0.8196 0.000 0.000 0.000 1.000
#> GSM152842 3 0.2973 0.8924 0.144 0.000 0.856 0.000
#> GSM152843 3 0.3444 0.8801 0.184 0.000 0.816 0.000
#> GSM152844 3 0.2469 0.8293 0.000 0.000 0.892 0.108
#> GSM152845 3 0.1284 0.8696 0.012 0.000 0.964 0.024
#> GSM152846 3 0.1557 0.8579 0.000 0.000 0.944 0.056
#> GSM152847 3 0.3444 0.8814 0.184 0.000 0.816 0.000
#> GSM152848 1 0.3691 0.7513 0.856 0.000 0.068 0.076
#> GSM152849 3 0.2973 0.8924 0.144 0.000 0.856 0.000
#> GSM152850 3 0.3801 0.8533 0.220 0.000 0.780 0.000
#> GSM152851 3 0.3400 0.7813 0.000 0.000 0.820 0.180
#> GSM152852 3 0.2408 0.8322 0.000 0.000 0.896 0.104
#> GSM152853 3 0.2704 0.8197 0.000 0.000 0.876 0.124
#> GSM152854 3 0.1297 0.8732 0.020 0.000 0.964 0.016
#> GSM152855 4 0.5159 0.4574 0.364 0.000 0.012 0.624
#> GSM153238 3 0.3123 0.8909 0.156 0.000 0.844 0.000
#> GSM153239 3 0.2469 0.8312 0.000 0.000 0.892 0.108
#> GSM153240 4 0.1716 0.8228 0.064 0.000 0.000 0.936
#> GSM153241 3 0.3356 0.8859 0.176 0.000 0.824 0.000
#> GSM153242 3 0.1356 0.8664 0.008 0.000 0.960 0.032
#> GSM153243 3 0.3123 0.8909 0.156 0.000 0.844 0.000
#> GSM153244 3 0.5943 0.4433 0.048 0.000 0.592 0.360
#> GSM153245 3 0.2868 0.8117 0.000 0.000 0.864 0.136
#> GSM153246 3 0.2973 0.8924 0.144 0.000 0.856 0.000
#> GSM153247 3 0.3494 0.8896 0.172 0.000 0.824 0.004
#> GSM153248 1 0.3486 0.7712 0.864 0.000 0.044 0.092
#> GSM153249 4 0.0817 0.8292 0.024 0.000 0.000 0.976
#> GSM153250 1 0.3870 0.7346 0.788 0.000 0.004 0.208
#> GSM153251 3 0.1388 0.8684 0.012 0.000 0.960 0.028
#> GSM153252 4 0.4917 0.4995 0.336 0.000 0.008 0.656
#> GSM153253 4 0.0000 0.8196 0.000 0.000 0.000 1.000
#> GSM153254 3 0.3435 0.8555 0.100 0.000 0.864 0.036
#> GSM153255 4 0.0921 0.8297 0.028 0.000 0.000 0.972
#> GSM153256 1 0.5075 0.5304 0.644 0.000 0.012 0.344
#> GSM153257 4 0.4222 0.6400 0.272 0.000 0.000 0.728
#> GSM153258 1 0.2921 0.7709 0.860 0.000 0.000 0.140
#> GSM153259 1 0.3545 0.7679 0.828 0.000 0.008 0.164
#> GSM153260 3 0.3444 0.8819 0.184 0.000 0.816 0.000
#> GSM153261 3 0.3219 0.8902 0.164 0.000 0.836 0.000
#> GSM153262 4 0.3498 0.7630 0.160 0.000 0.008 0.832
#> GSM153263 1 0.3688 0.7375 0.792 0.000 0.000 0.208
#> GSM153264 1 0.4206 0.7768 0.816 0.000 0.048 0.136
#> GSM153265 4 0.0469 0.8250 0.012 0.000 0.000 0.988
#> GSM153266 1 0.3768 0.7584 0.808 0.000 0.008 0.184
#> GSM153267 1 0.4485 0.6901 0.740 0.000 0.012 0.248
#> GSM153268 4 0.1389 0.7892 0.000 0.000 0.048 0.952
#> GSM153269 1 0.4647 0.6361 0.704 0.000 0.008 0.288
#> GSM153270 1 0.5244 0.2807 0.556 0.000 0.008 0.436
#> GSM153271 1 0.4353 0.7073 0.756 0.000 0.012 0.232
#> GSM153272 4 0.2530 0.7992 0.112 0.000 0.000 0.888
#> GSM153273 1 0.2999 0.7734 0.864 0.000 0.004 0.132
#> GSM153274 1 0.4372 0.6702 0.728 0.000 0.004 0.268
#> GSM153275 4 0.5407 -0.0100 0.484 0.000 0.012 0.504
#> GSM153276 1 0.4936 0.4726 0.624 0.000 0.004 0.372
#> GSM153277 4 0.1302 0.8284 0.044 0.000 0.000 0.956
#> GSM153278 3 0.4277 0.7732 0.280 0.000 0.720 0.000
#> GSM153279 4 0.3271 0.7317 0.012 0.000 0.132 0.856
#> GSM153280 4 0.0000 0.8196 0.000 0.000 0.000 1.000
#> GSM153281 4 0.0921 0.8297 0.028 0.000 0.000 0.972
#> GSM153282 4 0.0000 0.8196 0.000 0.000 0.000 1.000
#> GSM153283 1 0.3852 0.7497 0.800 0.000 0.008 0.192
#> GSM153284 4 0.4761 0.5385 0.332 0.000 0.004 0.664
#> GSM153285 4 0.0000 0.8196 0.000 0.000 0.000 1.000
#> GSM153286 4 0.5402 0.0403 0.472 0.000 0.012 0.516
#> GSM153287 4 0.0921 0.8297 0.028 0.000 0.000 0.972
#> GSM153288 1 0.5407 0.0817 0.504 0.000 0.012 0.484
#> GSM153289 1 0.4795 0.6279 0.696 0.000 0.012 0.292
#> GSM153290 4 0.0000 0.8196 0.000 0.000 0.000 1.000
#> GSM153291 4 0.1211 0.8290 0.040 0.000 0.000 0.960
#> GSM153292 4 0.0592 0.8271 0.016 0.000 0.000 0.984
#> GSM153293 1 0.5268 0.4160 0.592 0.000 0.012 0.396
#> GSM153294 1 0.3597 0.7759 0.836 0.000 0.016 0.148
#> GSM153295 1 0.5972 0.6465 0.640 0.000 0.068 0.292
#> GSM153054 1 0.3257 0.6551 0.844 0.000 0.152 0.004
#> GSM153055 1 0.3945 0.7350 0.780 0.000 0.004 0.216
#> GSM153056 3 0.3444 0.8806 0.184 0.000 0.816 0.000
#> GSM153057 3 0.4122 0.8358 0.236 0.000 0.760 0.004
#> GSM153058 3 0.2412 0.8900 0.084 0.000 0.908 0.008
#> GSM153059 3 0.3626 0.8840 0.184 0.000 0.812 0.004
#> GSM153060 3 0.2814 0.8932 0.132 0.000 0.868 0.000
#> GSM153061 3 0.2973 0.8924 0.144 0.000 0.856 0.000
#> GSM153062 3 0.1356 0.8789 0.032 0.000 0.960 0.008
#> GSM153063 3 0.1388 0.8682 0.012 0.000 0.960 0.028
#> GSM153064 1 0.3400 0.7585 0.820 0.000 0.000 0.180
#> GSM153065 3 0.2973 0.8924 0.144 0.000 0.856 0.000
#> GSM153066 3 0.3539 0.8857 0.176 0.004 0.820 0.000
#> GSM153067 4 0.2053 0.8181 0.072 0.000 0.004 0.924
#> GSM153068 3 0.2973 0.8924 0.144 0.000 0.856 0.000
#> GSM153069 4 0.0921 0.8297 0.028 0.000 0.000 0.972
#> GSM153070 1 0.3969 0.7636 0.804 0.000 0.016 0.180
#> GSM153071 1 0.4500 0.3311 0.684 0.000 0.316 0.000
#> GSM153072 1 0.2589 0.6871 0.884 0.000 0.116 0.000
#> GSM153073 1 0.2999 0.7734 0.864 0.000 0.004 0.132
#> GSM153074 4 0.4891 0.5788 0.308 0.000 0.012 0.680
#> GSM153075 4 0.3731 0.7697 0.120 0.000 0.036 0.844
#> GSM153076 1 0.4049 0.7285 0.780 0.000 0.008 0.212
#> GSM153077 1 0.4070 0.7768 0.824 0.000 0.044 0.132
#> GSM153078 1 0.3831 0.5873 0.792 0.000 0.204 0.004
#> GSM153079 1 0.2300 0.7477 0.924 0.000 0.048 0.028
#> GSM153080 3 0.3441 0.8809 0.120 0.000 0.856 0.024
#> GSM153081 1 0.4123 0.7770 0.820 0.000 0.044 0.136
#> GSM153082 1 0.1576 0.7307 0.948 0.004 0.048 0.000
#> GSM153083 1 0.1722 0.7368 0.944 0.000 0.048 0.008
#> GSM153084 1 0.5444 -0.1052 0.560 0.016 0.424 0.000
#> GSM153085 1 0.2011 0.7142 0.920 0.000 0.080 0.000
#> GSM153086 1 0.3617 0.7632 0.860 0.000 0.064 0.076
#> GSM153087 4 0.5085 0.5436 0.304 0.000 0.020 0.676
#> GSM153088 1 0.3751 0.7490 0.800 0.000 0.004 0.196
#> GSM153089 3 0.1388 0.8684 0.012 0.000 0.960 0.028
#> GSM153090 1 0.3945 0.7344 0.780 0.000 0.004 0.216
#> GSM153091 1 0.2111 0.7472 0.932 0.000 0.044 0.024
#> GSM153092 1 0.3856 0.7783 0.832 0.000 0.032 0.136
#> GSM153093 4 0.4663 0.6366 0.272 0.000 0.012 0.716
#> GSM153094 1 0.1302 0.7333 0.956 0.000 0.044 0.000
#> GSM153095 1 0.2988 0.6923 0.876 0.000 0.112 0.012
#> GSM153096 1 0.3032 0.7769 0.868 0.000 0.008 0.124
#> GSM153097 1 0.1975 0.7414 0.936 0.000 0.048 0.016
#> GSM153098 1 0.3852 0.7577 0.800 0.000 0.008 0.192
#> GSM153099 1 0.4746 0.6162 0.688 0.000 0.008 0.304
#> GSM153100 1 0.3123 0.7655 0.844 0.000 0.000 0.156
#> GSM153101 1 0.2011 0.7155 0.920 0.000 0.080 0.000
#> GSM153102 1 0.3464 0.7066 0.860 0.000 0.108 0.032
#> GSM153103 1 0.1867 0.7195 0.928 0.000 0.072 0.000
#> GSM153104 4 0.0817 0.8293 0.024 0.000 0.000 0.976
#> GSM153106 1 0.3768 0.7626 0.808 0.000 0.008 0.184
#> GSM153107 1 0.2704 0.7738 0.876 0.000 0.000 0.124
#> GSM153108 1 0.5906 0.3380 0.528 0.000 0.036 0.436
#> GSM153109 1 0.1978 0.7224 0.928 0.004 0.068 0.000
#> GSM153110 1 0.3205 0.7767 0.872 0.000 0.024 0.104
#> GSM153111 1 0.3081 0.7623 0.888 0.000 0.048 0.064
#> GSM153112 1 0.3913 0.7769 0.824 0.000 0.028 0.148
#> GSM153113 1 0.3697 0.6685 0.852 0.100 0.048 0.000
#> GSM153114 4 0.4914 0.5724 0.312 0.000 0.012 0.676
#> GSM187532 2 0.4883 0.5321 0.016 0.696 0.288 0.000
#> GSM187533 2 0.0000 0.9835 0.000 1.000 0.000 0.000
#> GSM187534 2 0.0000 0.9835 0.000 1.000 0.000 0.000
#> GSM187535 1 0.4356 0.6330 0.812 0.140 0.044 0.004
#> GSM152906 2 0.0000 0.9835 0.000 1.000 0.000 0.000
#> GSM152907 2 0.0000 0.9835 0.000 1.000 0.000 0.000
#> GSM152908 2 0.0000 0.9835 0.000 1.000 0.000 0.000
#> GSM152909 2 0.0336 0.9757 0.000 0.992 0.008 0.000
#> GSM152910 2 0.0000 0.9835 0.000 1.000 0.000 0.000
#> GSM152911 2 0.0000 0.9835 0.000 1.000 0.000 0.000
#> GSM152912 2 0.0000 0.9835 0.000 1.000 0.000 0.000
#> GSM152913 2 0.0000 0.9835 0.000 1.000 0.000 0.000
#> GSM152914 2 0.0000 0.9835 0.000 1.000 0.000 0.000
#> GSM152915 2 0.0000 0.9835 0.000 1.000 0.000 0.000
#> GSM152916 2 0.0000 0.9835 0.000 1.000 0.000 0.000
#> GSM152917 2 0.0000 0.9835 0.000 1.000 0.000 0.000
#> GSM152918 2 0.0000 0.9835 0.000 1.000 0.000 0.000
#> GSM152919 2 0.0000 0.9835 0.000 1.000 0.000 0.000
#> GSM152920 2 0.0000 0.9835 0.000 1.000 0.000 0.000
#> GSM152921 2 0.0000 0.9835 0.000 1.000 0.000 0.000
#> GSM152922 2 0.0000 0.9835 0.000 1.000 0.000 0.000
#> GSM152923 2 0.0000 0.9835 0.000 1.000 0.000 0.000
#> GSM152924 2 0.0000 0.9835 0.000 1.000 0.000 0.000
#> GSM152925 2 0.0000 0.9835 0.000 1.000 0.000 0.000
#> GSM152926 2 0.0000 0.9835 0.000 1.000 0.000 0.000
#> GSM152927 2 0.0000 0.9835 0.000 1.000 0.000 0.000
#> GSM152928 2 0.2926 0.8762 0.048 0.896 0.056 0.000
#> GSM152929 2 0.0000 0.9835 0.000 1.000 0.000 0.000
#> GSM152930 2 0.0000 0.9835 0.000 1.000 0.000 0.000
cbind(get_classes(res, k = 5), get_membership(res, k = 5))
#> class entropy silhouette p1 p2 p3 p4 p5
#> GSM152839 1 0.4537 0.3474 0.592 0.000 0.396 0.000 0.012
#> GSM152840 5 0.5813 0.7773 0.000 0.000 0.328 0.112 0.560
#> GSM152841 4 0.3612 0.6255 0.000 0.000 0.000 0.732 0.268
#> GSM152842 3 0.0162 0.8027 0.004 0.000 0.996 0.000 0.000
#> GSM152843 3 0.0510 0.8014 0.016 0.000 0.984 0.000 0.000
#> GSM152844 5 0.4451 0.8855 0.000 0.000 0.340 0.016 0.644
#> GSM152845 5 0.4287 0.7571 0.000 0.000 0.460 0.000 0.540
#> GSM152846 5 0.4211 0.8852 0.000 0.000 0.360 0.004 0.636
#> GSM152847 3 0.0510 0.8014 0.016 0.000 0.984 0.000 0.000
#> GSM152848 1 0.1173 0.8580 0.964 0.000 0.004 0.020 0.012
#> GSM152849 3 0.0162 0.8027 0.004 0.000 0.996 0.000 0.000
#> GSM152850 3 0.0693 0.8008 0.012 0.000 0.980 0.000 0.008
#> GSM152851 5 0.6923 0.4767 0.004 0.000 0.340 0.284 0.372
#> GSM152852 5 0.4430 0.8856 0.000 0.000 0.360 0.012 0.628
#> GSM152853 5 0.4451 0.8855 0.000 0.000 0.340 0.016 0.644
#> GSM152854 3 0.3999 -0.1545 0.000 0.000 0.656 0.000 0.344
#> GSM152855 4 0.4946 0.4193 0.368 0.000 0.000 0.596 0.036
#> GSM153238 3 0.0451 0.7990 0.004 0.000 0.988 0.000 0.008
#> GSM153239 5 0.4467 0.8872 0.000 0.000 0.344 0.016 0.640
#> GSM153240 4 0.1211 0.7340 0.024 0.000 0.000 0.960 0.016
#> GSM153241 3 0.0290 0.8038 0.008 0.000 0.992 0.000 0.000
#> GSM153242 5 0.4088 0.8813 0.000 0.000 0.368 0.000 0.632
#> GSM153243 3 0.0566 0.8006 0.004 0.000 0.984 0.000 0.012
#> GSM153244 4 0.5071 0.2092 0.040 0.000 0.340 0.616 0.004
#> GSM153245 5 0.4555 0.8867 0.000 0.000 0.344 0.020 0.636
#> GSM153246 3 0.2329 0.6291 0.000 0.000 0.876 0.000 0.124
#> GSM153247 3 0.1281 0.7803 0.012 0.000 0.956 0.000 0.032
#> GSM153248 1 0.1357 0.8510 0.948 0.000 0.004 0.000 0.048
#> GSM153249 4 0.0162 0.7309 0.000 0.000 0.000 0.996 0.004
#> GSM153250 1 0.1485 0.8493 0.948 0.000 0.000 0.032 0.020
#> GSM153251 5 0.4171 0.8630 0.000 0.000 0.396 0.000 0.604
#> GSM153252 4 0.4540 0.4692 0.340 0.000 0.000 0.640 0.020
#> GSM153253 4 0.3612 0.6255 0.000 0.000 0.000 0.732 0.268
#> GSM153254 3 0.6452 0.1059 0.192 0.000 0.540 0.260 0.008
#> GSM153255 4 0.0451 0.7322 0.008 0.000 0.000 0.988 0.004
#> GSM153256 1 0.4657 0.5344 0.668 0.000 0.000 0.296 0.036
#> GSM153257 4 0.3910 0.5958 0.272 0.000 0.000 0.720 0.008
#> GSM153258 1 0.0865 0.8558 0.972 0.000 0.000 0.024 0.004
#> GSM153259 1 0.1012 0.8581 0.968 0.000 0.000 0.020 0.012
#> GSM153260 3 0.0566 0.8007 0.004 0.000 0.984 0.000 0.012
#> GSM153261 3 0.0290 0.8038 0.008 0.000 0.992 0.000 0.000
#> GSM153262 4 0.3039 0.7064 0.152 0.000 0.000 0.836 0.012
#> GSM153263 1 0.1041 0.8522 0.964 0.000 0.000 0.032 0.004
#> GSM153264 1 0.0912 0.8574 0.972 0.000 0.012 0.000 0.016
#> GSM153265 4 0.1704 0.7172 0.004 0.000 0.000 0.928 0.068
#> GSM153266 1 0.1082 0.8556 0.964 0.000 0.000 0.028 0.008
#> GSM153267 1 0.3615 0.7465 0.808 0.000 0.000 0.156 0.036
#> GSM153268 4 0.3967 0.6178 0.000 0.000 0.012 0.724 0.264
#> GSM153269 1 0.4197 0.6283 0.728 0.000 0.000 0.244 0.028
#> GSM153270 1 0.4752 0.2523 0.568 0.000 0.000 0.412 0.020
#> GSM153271 1 0.1830 0.8453 0.932 0.000 0.000 0.040 0.028
#> GSM153272 4 0.2513 0.7170 0.116 0.000 0.000 0.876 0.008
#> GSM153273 1 0.0609 0.8583 0.980 0.000 0.000 0.000 0.020
#> GSM153274 1 0.3438 0.7383 0.808 0.000 0.000 0.172 0.020
#> GSM153275 1 0.5096 0.1035 0.520 0.000 0.000 0.444 0.036
#> GSM153276 1 0.4422 0.5016 0.664 0.000 0.004 0.320 0.012
#> GSM153277 4 0.0854 0.7325 0.012 0.000 0.008 0.976 0.004
#> GSM153278 3 0.3280 0.5347 0.176 0.000 0.812 0.000 0.012
#> GSM153279 4 0.4303 0.4942 0.020 0.000 0.216 0.748 0.016
#> GSM153280 4 0.3612 0.6255 0.000 0.000 0.000 0.732 0.268
#> GSM153281 4 0.0671 0.7304 0.004 0.000 0.000 0.980 0.016
#> GSM153282 4 0.3612 0.6255 0.000 0.000 0.000 0.732 0.268
#> GSM153283 1 0.1168 0.8515 0.960 0.000 0.000 0.032 0.008
#> GSM153284 4 0.4697 0.5141 0.320 0.000 0.000 0.648 0.032
#> GSM153285 4 0.3534 0.6337 0.000 0.000 0.000 0.744 0.256
#> GSM153286 4 0.4979 0.0196 0.480 0.000 0.000 0.492 0.028
#> GSM153287 4 0.0510 0.7286 0.000 0.000 0.000 0.984 0.016
#> GSM153288 1 0.5111 0.0418 0.500 0.000 0.000 0.464 0.036
#> GSM153289 1 0.4404 0.5935 0.704 0.000 0.000 0.264 0.032
#> GSM153290 4 0.3612 0.6255 0.000 0.000 0.000 0.732 0.268
#> GSM153291 4 0.0807 0.7335 0.012 0.000 0.000 0.976 0.012
#> GSM153292 4 0.3480 0.6371 0.000 0.000 0.000 0.752 0.248
#> GSM153293 1 0.4851 0.4510 0.624 0.000 0.000 0.340 0.036
#> GSM153294 1 0.1211 0.8579 0.960 0.000 0.000 0.016 0.024
#> GSM153295 1 0.3780 0.7808 0.812 0.000 0.072 0.116 0.000
#> GSM153054 1 0.3733 0.7534 0.804 0.000 0.160 0.004 0.032
#> GSM153055 1 0.2536 0.7963 0.868 0.000 0.000 0.128 0.004
#> GSM153056 3 0.0609 0.7989 0.020 0.000 0.980 0.000 0.000
#> GSM153057 3 0.3551 0.4553 0.220 0.000 0.772 0.000 0.008
#> GSM153058 3 0.2763 0.5990 0.004 0.000 0.848 0.000 0.148
#> GSM153059 3 0.0807 0.7978 0.012 0.000 0.976 0.000 0.012
#> GSM153060 3 0.2561 0.5864 0.000 0.000 0.856 0.000 0.144
#> GSM153061 3 0.0162 0.8027 0.004 0.000 0.996 0.000 0.000
#> GSM153062 3 0.4302 -0.6397 0.000 0.000 0.520 0.000 0.480
#> GSM153063 5 0.4425 0.7623 0.000 0.000 0.452 0.004 0.544
#> GSM153064 1 0.1485 0.8514 0.948 0.000 0.000 0.032 0.020
#> GSM153065 3 0.0162 0.8027 0.004 0.000 0.996 0.000 0.000
#> GSM153066 3 0.0771 0.7956 0.004 0.000 0.976 0.000 0.020
#> GSM153067 4 0.1282 0.7312 0.044 0.000 0.000 0.952 0.004
#> GSM153068 3 0.0162 0.8027 0.004 0.000 0.996 0.000 0.000
#> GSM153069 4 0.0609 0.7279 0.000 0.000 0.000 0.980 0.020
#> GSM153070 1 0.1300 0.8573 0.956 0.000 0.000 0.028 0.016
#> GSM153071 1 0.4691 0.5874 0.680 0.000 0.276 0.000 0.044
#> GSM153072 1 0.3201 0.8064 0.852 0.000 0.096 0.000 0.052
#> GSM153073 1 0.0162 0.8578 0.996 0.000 0.000 0.004 0.000
#> GSM153074 4 0.4541 0.5734 0.288 0.000 0.000 0.680 0.032
#> GSM153075 4 0.2835 0.7177 0.112 0.000 0.016 0.868 0.004
#> GSM153076 1 0.1485 0.8493 0.948 0.000 0.000 0.032 0.020
#> GSM153077 1 0.1205 0.8532 0.956 0.000 0.004 0.000 0.040
#> GSM153078 1 0.4114 0.6146 0.712 0.000 0.272 0.000 0.016
#> GSM153079 1 0.1430 0.8498 0.944 0.000 0.004 0.000 0.052
#> GSM153080 3 0.4829 0.4176 0.200 0.000 0.724 0.008 0.068
#> GSM153081 1 0.0960 0.8584 0.972 0.000 0.008 0.004 0.016
#> GSM153082 1 0.1787 0.8497 0.936 0.016 0.004 0.000 0.044
#> GSM153083 1 0.1430 0.8498 0.944 0.000 0.004 0.000 0.052
#> GSM153084 1 0.5177 0.6032 0.676 0.024 0.260 0.000 0.040
#> GSM153085 1 0.2221 0.8414 0.912 0.000 0.036 0.000 0.052
#> GSM153086 1 0.3437 0.7825 0.832 0.000 0.120 0.000 0.048
#> GSM153087 4 0.4416 0.4285 0.356 0.000 0.000 0.632 0.012
#> GSM153088 1 0.1041 0.8522 0.964 0.000 0.000 0.032 0.004
#> GSM153089 5 0.4161 0.8687 0.000 0.000 0.392 0.000 0.608
#> GSM153090 1 0.1043 0.8512 0.960 0.000 0.000 0.040 0.000
#> GSM153091 1 0.1357 0.8508 0.948 0.000 0.004 0.000 0.048
#> GSM153092 1 0.1074 0.8597 0.968 0.000 0.004 0.016 0.012
#> GSM153093 4 0.4315 0.5918 0.276 0.000 0.000 0.700 0.024
#> GSM153094 1 0.1430 0.8498 0.944 0.000 0.004 0.000 0.052
#> GSM153095 1 0.3445 0.8165 0.856 0.000 0.072 0.020 0.052
#> GSM153096 1 0.0290 0.8580 0.992 0.000 0.000 0.000 0.008
#> GSM153097 1 0.1430 0.8498 0.944 0.000 0.004 0.000 0.052
#> GSM153098 1 0.2351 0.8267 0.896 0.000 0.000 0.088 0.016
#> GSM153099 1 0.3476 0.7409 0.804 0.000 0.000 0.176 0.020
#> GSM153100 1 0.1281 0.8564 0.956 0.000 0.000 0.032 0.012
#> GSM153101 1 0.1484 0.8503 0.944 0.000 0.008 0.000 0.048
#> GSM153102 1 0.3089 0.8202 0.872 0.000 0.076 0.012 0.040
#> GSM153103 1 0.2522 0.8323 0.896 0.000 0.052 0.000 0.052
#> GSM153104 4 0.0324 0.7316 0.004 0.000 0.000 0.992 0.004
#> GSM153106 1 0.2915 0.7950 0.860 0.000 0.000 0.116 0.024
#> GSM153107 1 0.0865 0.8588 0.972 0.000 0.000 0.004 0.024
#> GSM153108 4 0.4994 0.0487 0.464 0.000 0.016 0.512 0.008
#> GSM153109 1 0.2339 0.8464 0.912 0.008 0.028 0.000 0.052
#> GSM153110 1 0.1041 0.8564 0.964 0.000 0.004 0.000 0.032
#> GSM153111 1 0.1430 0.8498 0.944 0.000 0.004 0.000 0.052
#> GSM153112 1 0.1442 0.8595 0.952 0.000 0.004 0.012 0.032
#> GSM153113 1 0.3570 0.7755 0.828 0.124 0.004 0.000 0.044
#> GSM153114 4 0.4616 0.5820 0.288 0.000 0.000 0.676 0.036
#> GSM187532 2 0.3809 0.6176 0.000 0.736 0.256 0.000 0.008
#> GSM187533 2 0.0000 0.9852 0.000 1.000 0.000 0.000 0.000
#> GSM187534 2 0.0000 0.9852 0.000 1.000 0.000 0.000 0.000
#> GSM187535 1 0.2952 0.8194 0.872 0.088 0.004 0.000 0.036
#> GSM152906 2 0.0000 0.9852 0.000 1.000 0.000 0.000 0.000
#> GSM152907 2 0.0000 0.9852 0.000 1.000 0.000 0.000 0.000
#> GSM152908 2 0.0000 0.9852 0.000 1.000 0.000 0.000 0.000
#> GSM152909 2 0.0162 0.9806 0.000 0.996 0.004 0.000 0.000
#> GSM152910 2 0.0000 0.9852 0.000 1.000 0.000 0.000 0.000
#> GSM152911 2 0.0000 0.9852 0.000 1.000 0.000 0.000 0.000
#> GSM152912 2 0.0000 0.9852 0.000 1.000 0.000 0.000 0.000
#> GSM152913 2 0.0000 0.9852 0.000 1.000 0.000 0.000 0.000
#> GSM152914 2 0.0000 0.9852 0.000 1.000 0.000 0.000 0.000
#> GSM152915 2 0.0000 0.9852 0.000 1.000 0.000 0.000 0.000
#> GSM152916 2 0.0000 0.9852 0.000 1.000 0.000 0.000 0.000
#> GSM152917 2 0.0000 0.9852 0.000 1.000 0.000 0.000 0.000
#> GSM152918 2 0.0000 0.9852 0.000 1.000 0.000 0.000 0.000
#> GSM152919 2 0.0000 0.9852 0.000 1.000 0.000 0.000 0.000
#> GSM152920 2 0.0000 0.9852 0.000 1.000 0.000 0.000 0.000
#> GSM152921 2 0.0000 0.9852 0.000 1.000 0.000 0.000 0.000
#> GSM152922 2 0.0000 0.9852 0.000 1.000 0.000 0.000 0.000
#> GSM152923 2 0.0000 0.9852 0.000 1.000 0.000 0.000 0.000
#> GSM152924 2 0.0000 0.9852 0.000 1.000 0.000 0.000 0.000
#> GSM152925 2 0.0000 0.9852 0.000 1.000 0.000 0.000 0.000
#> GSM152926 2 0.0000 0.9852 0.000 1.000 0.000 0.000 0.000
#> GSM152927 2 0.0000 0.9852 0.000 1.000 0.000 0.000 0.000
#> GSM152928 2 0.2291 0.8884 0.008 0.908 0.072 0.000 0.012
#> GSM152929 2 0.0000 0.9852 0.000 1.000 0.000 0.000 0.000
#> GSM152930 2 0.0000 0.9852 0.000 1.000 0.000 0.000 0.000
cbind(get_classes(res, k = 6), get_membership(res, k = 6))
#> class entropy silhouette p1 p2 p3 p4 p5 p6
#> GSM152839 3 0.5423 0.0590 0.392 0.000 0.488 0.120 0.000 0.000
#> GSM152840 6 0.2520 0.6619 0.000 0.000 0.000 0.004 0.152 0.844
#> GSM152841 5 0.0363 0.7030 0.000 0.000 0.000 0.012 0.988 0.000
#> GSM152842 3 0.0291 0.8292 0.000 0.000 0.992 0.004 0.000 0.004
#> GSM152843 3 0.0820 0.8252 0.012 0.000 0.972 0.016 0.000 0.000
#> GSM152844 6 0.0458 0.7771 0.000 0.000 0.000 0.000 0.016 0.984
#> GSM152845 6 0.3607 0.5629 0.000 0.000 0.348 0.000 0.000 0.652
#> GSM152846 6 0.0937 0.8058 0.000 0.000 0.040 0.000 0.000 0.960
#> GSM152847 3 0.0146 0.8306 0.000 0.000 0.996 0.004 0.000 0.000
#> GSM152848 1 0.2841 0.7889 0.824 0.000 0.012 0.164 0.000 0.000
#> GSM152849 3 0.0405 0.8305 0.000 0.000 0.988 0.008 0.000 0.004
#> GSM152850 3 0.0291 0.8313 0.004 0.000 0.992 0.004 0.000 0.000
#> GSM152851 6 0.4982 0.6824 0.000 0.000 0.172 0.000 0.180 0.648
#> GSM152852 6 0.1461 0.8039 0.000 0.000 0.044 0.000 0.016 0.940
#> GSM152853 6 0.0632 0.7751 0.000 0.000 0.000 0.000 0.024 0.976
#> GSM152854 3 0.3847 -0.0780 0.000 0.000 0.544 0.000 0.000 0.456
#> GSM152855 4 0.1257 0.6990 0.028 0.000 0.000 0.952 0.020 0.000
#> GSM153238 3 0.0870 0.8296 0.012 0.000 0.972 0.000 0.004 0.012
#> GSM153239 6 0.1657 0.8106 0.000 0.000 0.056 0.000 0.016 0.928
#> GSM153240 4 0.3874 0.2401 0.008 0.000 0.000 0.636 0.356 0.000
#> GSM153241 3 0.0146 0.8306 0.000 0.000 0.996 0.004 0.000 0.000
#> GSM153242 6 0.1556 0.8039 0.000 0.000 0.080 0.000 0.000 0.920
#> GSM153243 3 0.0777 0.8281 0.024 0.000 0.972 0.000 0.000 0.004
#> GSM153244 5 0.7363 -0.1799 0.024 0.000 0.184 0.068 0.368 0.356
#> GSM153245 6 0.1829 0.8094 0.000 0.000 0.056 0.000 0.024 0.920
#> GSM153246 3 0.2981 0.6914 0.000 0.000 0.820 0.020 0.000 0.160
#> GSM153247 3 0.2316 0.8011 0.028 0.000 0.900 0.004 0.004 0.064
#> GSM153248 1 0.0935 0.7891 0.964 0.000 0.004 0.032 0.000 0.000
#> GSM153249 5 0.3857 0.2942 0.000 0.000 0.000 0.468 0.532 0.000
#> GSM153250 1 0.3830 0.6371 0.620 0.000 0.000 0.376 0.004 0.000
#> GSM153251 6 0.2912 0.7329 0.000 0.000 0.216 0.000 0.000 0.784
#> GSM153252 4 0.1829 0.6994 0.024 0.000 0.000 0.920 0.056 0.000
#> GSM153253 5 0.0363 0.7030 0.000 0.000 0.000 0.012 0.988 0.000
#> GSM153254 3 0.6701 0.0593 0.092 0.000 0.492 0.044 0.040 0.332
#> GSM153255 4 0.3774 0.0434 0.000 0.000 0.000 0.592 0.408 0.000
#> GSM153256 4 0.1075 0.6954 0.048 0.000 0.000 0.952 0.000 0.000
#> GSM153257 4 0.2538 0.6686 0.016 0.000 0.000 0.860 0.124 0.000
#> GSM153258 1 0.2996 0.7634 0.772 0.000 0.000 0.228 0.000 0.000
#> GSM153259 1 0.2738 0.7851 0.820 0.000 0.004 0.176 0.000 0.000
#> GSM153260 3 0.0260 0.8309 0.008 0.000 0.992 0.000 0.000 0.000
#> GSM153261 3 0.0000 0.8293 0.000 0.000 1.000 0.000 0.000 0.000
#> GSM153262 4 0.3487 0.5657 0.020 0.000 0.000 0.756 0.224 0.000
#> GSM153263 1 0.3547 0.6788 0.668 0.000 0.000 0.332 0.000 0.000
#> GSM153264 1 0.2355 0.7942 0.876 0.000 0.008 0.112 0.004 0.000
#> GSM153265 5 0.3578 0.4987 0.000 0.000 0.000 0.340 0.660 0.000
#> GSM153266 1 0.3052 0.7709 0.780 0.000 0.004 0.216 0.000 0.000
#> GSM153267 4 0.3563 0.1429 0.336 0.000 0.000 0.664 0.000 0.000
#> GSM153268 5 0.0725 0.6978 0.000 0.000 0.000 0.012 0.976 0.012
#> GSM153269 4 0.2491 0.6396 0.164 0.000 0.000 0.836 0.000 0.000
#> GSM153270 4 0.2573 0.6723 0.112 0.000 0.000 0.864 0.024 0.000
#> GSM153271 1 0.3944 0.5725 0.568 0.000 0.000 0.428 0.004 0.000
#> GSM153272 4 0.3163 0.5308 0.004 0.000 0.000 0.764 0.232 0.000
#> GSM153273 1 0.3101 0.7624 0.756 0.000 0.000 0.244 0.000 0.000
#> GSM153274 4 0.3620 0.2217 0.352 0.000 0.000 0.648 0.000 0.000
#> GSM153275 4 0.0993 0.7012 0.024 0.000 0.000 0.964 0.012 0.000
#> GSM153276 4 0.2879 0.6388 0.176 0.000 0.004 0.816 0.004 0.000
#> GSM153277 4 0.3838 -0.0760 0.000 0.000 0.000 0.552 0.448 0.000
#> GSM153278 3 0.2066 0.7816 0.072 0.000 0.904 0.024 0.000 0.000
#> GSM153279 5 0.6169 0.2458 0.000 0.000 0.044 0.416 0.432 0.108
#> GSM153280 5 0.0363 0.7030 0.000 0.000 0.000 0.012 0.988 0.000
#> GSM153281 5 0.3857 0.2822 0.000 0.000 0.000 0.468 0.532 0.000
#> GSM153282 5 0.0363 0.7030 0.000 0.000 0.000 0.012 0.988 0.000
#> GSM153283 1 0.3646 0.7295 0.700 0.000 0.004 0.292 0.004 0.000
#> GSM153284 4 0.1657 0.6954 0.016 0.000 0.000 0.928 0.056 0.000
#> GSM153285 5 0.0713 0.7068 0.000 0.000 0.000 0.028 0.972 0.000
#> GSM153286 4 0.1408 0.7030 0.036 0.000 0.000 0.944 0.020 0.000
#> GSM153287 5 0.3817 0.3702 0.000 0.000 0.000 0.432 0.568 0.000
#> GSM153288 4 0.0858 0.6995 0.028 0.000 0.000 0.968 0.004 0.000
#> GSM153289 4 0.1700 0.6849 0.080 0.000 0.000 0.916 0.004 0.000
#> GSM153290 5 0.0363 0.7030 0.000 0.000 0.000 0.012 0.988 0.000
#> GSM153291 4 0.3672 0.1635 0.000 0.000 0.000 0.632 0.368 0.000
#> GSM153292 5 0.1444 0.6984 0.000 0.000 0.000 0.072 0.928 0.000
#> GSM153293 4 0.0972 0.7009 0.028 0.000 0.000 0.964 0.008 0.000
#> GSM153294 1 0.3925 0.6963 0.656 0.000 0.008 0.332 0.004 0.000
#> GSM153295 1 0.5241 0.4146 0.492 0.000 0.028 0.440 0.040 0.000
#> GSM153054 1 0.3831 0.7254 0.776 0.000 0.168 0.048 0.004 0.004
#> GSM153055 1 0.4080 0.3713 0.536 0.000 0.008 0.456 0.000 0.000
#> GSM153056 3 0.1461 0.8045 0.016 0.000 0.940 0.044 0.000 0.000
#> GSM153057 3 0.3766 0.6667 0.188 0.000 0.772 0.028 0.004 0.008
#> GSM153058 3 0.2527 0.7005 0.000 0.000 0.832 0.000 0.000 0.168
#> GSM153059 3 0.2734 0.7399 0.148 0.000 0.840 0.000 0.004 0.008
#> GSM153060 3 0.3253 0.6484 0.000 0.000 0.788 0.020 0.000 0.192
#> GSM153061 3 0.0622 0.8278 0.000 0.000 0.980 0.012 0.000 0.008
#> GSM153062 6 0.4338 0.1497 0.000 0.000 0.488 0.020 0.000 0.492
#> GSM153063 6 0.3547 0.6441 0.000 0.000 0.300 0.000 0.004 0.696
#> GSM153064 1 0.3756 0.6707 0.644 0.000 0.000 0.352 0.004 0.000
#> GSM153065 3 0.0291 0.8292 0.000 0.000 0.992 0.004 0.000 0.004
#> GSM153066 3 0.2504 0.7523 0.136 0.004 0.856 0.000 0.004 0.000
#> GSM153067 4 0.3330 0.4481 0.000 0.000 0.000 0.716 0.284 0.000
#> GSM153068 3 0.0692 0.8269 0.000 0.000 0.976 0.020 0.000 0.004
#> GSM153069 5 0.3797 0.3912 0.000 0.000 0.000 0.420 0.580 0.000
#> GSM153070 1 0.3012 0.7793 0.796 0.000 0.008 0.196 0.000 0.000
#> GSM153071 1 0.4311 0.5718 0.692 0.000 0.268 0.024 0.004 0.012
#> GSM153072 1 0.1908 0.7507 0.900 0.000 0.096 0.000 0.004 0.000
#> GSM153073 1 0.2631 0.7855 0.820 0.000 0.000 0.180 0.000 0.000
#> GSM153074 4 0.1657 0.6921 0.016 0.000 0.000 0.928 0.056 0.000
#> GSM153075 4 0.4278 0.2579 0.016 0.000 0.008 0.624 0.352 0.000
#> GSM153076 1 0.3852 0.6228 0.612 0.000 0.000 0.384 0.004 0.000
#> GSM153077 1 0.0935 0.7907 0.964 0.000 0.004 0.032 0.000 0.000
#> GSM153078 1 0.3727 0.6798 0.748 0.000 0.216 0.036 0.000 0.000
#> GSM153079 1 0.0260 0.7819 0.992 0.000 0.008 0.000 0.000 0.000
#> GSM153080 3 0.5132 0.5822 0.032 0.000 0.696 0.112 0.004 0.156
#> GSM153081 1 0.2355 0.7942 0.876 0.000 0.008 0.112 0.004 0.000
#> GSM153082 1 0.1065 0.7817 0.964 0.020 0.008 0.008 0.000 0.000
#> GSM153083 1 0.0260 0.7819 0.992 0.000 0.008 0.000 0.000 0.000
#> GSM153084 1 0.3909 0.4414 0.688 0.008 0.296 0.004 0.004 0.000
#> GSM153085 1 0.1285 0.7710 0.944 0.000 0.052 0.000 0.004 0.000
#> GSM153086 1 0.1471 0.7667 0.932 0.000 0.064 0.000 0.004 0.000
#> GSM153087 4 0.3042 0.6685 0.032 0.000 0.004 0.836 0.128 0.000
#> GSM153088 1 0.3360 0.7468 0.732 0.000 0.004 0.264 0.000 0.000
#> GSM153089 6 0.3288 0.6690 0.000 0.000 0.276 0.000 0.000 0.724
#> GSM153090 1 0.3371 0.7190 0.708 0.000 0.000 0.292 0.000 0.000
#> GSM153091 1 0.0622 0.7845 0.980 0.000 0.008 0.012 0.000 0.000
#> GSM153092 1 0.2697 0.7849 0.812 0.000 0.000 0.188 0.000 0.000
#> GSM153093 4 0.2019 0.6862 0.012 0.000 0.000 0.900 0.088 0.000
#> GSM153094 1 0.0405 0.7831 0.988 0.000 0.008 0.004 0.000 0.000
#> GSM153095 1 0.2575 0.7600 0.888 0.000 0.072 0.020 0.016 0.004
#> GSM153096 1 0.2980 0.7818 0.800 0.000 0.008 0.192 0.000 0.000
#> GSM153097 1 0.0260 0.7819 0.992 0.000 0.008 0.000 0.000 0.000
#> GSM153098 1 0.4338 0.3804 0.492 0.000 0.000 0.488 0.020 0.000
#> GSM153099 4 0.4131 0.1555 0.356 0.000 0.000 0.624 0.020 0.000
#> GSM153100 1 0.3499 0.6993 0.680 0.000 0.000 0.320 0.000 0.000
#> GSM153101 1 0.0458 0.7797 0.984 0.000 0.016 0.000 0.000 0.000
#> GSM153102 1 0.2350 0.7673 0.896 0.000 0.076 0.016 0.008 0.004
#> GSM153103 1 0.1082 0.7730 0.956 0.000 0.040 0.000 0.004 0.000
#> GSM153104 4 0.3869 -0.2580 0.000 0.000 0.000 0.500 0.500 0.000
#> GSM153106 4 0.3838 -0.2034 0.448 0.000 0.000 0.552 0.000 0.000
#> GSM153107 1 0.3330 0.7335 0.716 0.000 0.000 0.284 0.000 0.000
#> GSM153108 4 0.3198 0.6826 0.060 0.000 0.012 0.844 0.084 0.000
#> GSM153109 1 0.1293 0.7788 0.956 0.016 0.020 0.004 0.004 0.000
#> GSM153110 1 0.2100 0.7963 0.884 0.000 0.004 0.112 0.000 0.000
#> GSM153111 1 0.0405 0.7810 0.988 0.000 0.008 0.000 0.004 0.000
#> GSM153112 1 0.3595 0.7392 0.704 0.000 0.008 0.288 0.000 0.000
#> GSM153113 1 0.2544 0.7066 0.852 0.140 0.000 0.004 0.004 0.000
#> GSM153114 4 0.3101 0.6217 0.032 0.000 0.000 0.820 0.148 0.000
#> GSM187532 2 0.3337 0.7281 0.004 0.796 0.184 0.004 0.004 0.008
#> GSM187533 2 0.0146 0.9850 0.000 0.996 0.000 0.004 0.000 0.000
#> GSM187534 2 0.0146 0.9850 0.000 0.996 0.000 0.004 0.000 0.000
#> GSM187535 1 0.4550 0.5702 0.676 0.240 0.000 0.084 0.000 0.000
#> GSM152906 2 0.0000 0.9859 0.000 1.000 0.000 0.000 0.000 0.000
#> GSM152907 2 0.0000 0.9859 0.000 1.000 0.000 0.000 0.000 0.000
#> GSM152908 2 0.0000 0.9859 0.000 1.000 0.000 0.000 0.000 0.000
#> GSM152909 2 0.0291 0.9816 0.000 0.992 0.004 0.004 0.000 0.000
#> GSM152910 2 0.0146 0.9850 0.000 0.996 0.000 0.004 0.000 0.000
#> GSM152911 2 0.0000 0.9859 0.000 1.000 0.000 0.000 0.000 0.000
#> GSM152912 2 0.0000 0.9859 0.000 1.000 0.000 0.000 0.000 0.000
#> GSM152913 2 0.0146 0.9850 0.000 0.996 0.000 0.004 0.000 0.000
#> GSM152914 2 0.0000 0.9859 0.000 1.000 0.000 0.000 0.000 0.000
#> GSM152915 2 0.0000 0.9859 0.000 1.000 0.000 0.000 0.000 0.000
#> GSM152916 2 0.0146 0.9850 0.000 0.996 0.000 0.004 0.000 0.000
#> GSM152917 2 0.0000 0.9859 0.000 1.000 0.000 0.000 0.000 0.000
#> GSM152918 2 0.0000 0.9859 0.000 1.000 0.000 0.000 0.000 0.000
#> GSM152919 2 0.0000 0.9859 0.000 1.000 0.000 0.000 0.000 0.000
#> GSM152920 2 0.0000 0.9859 0.000 1.000 0.000 0.000 0.000 0.000
#> GSM152921 2 0.0000 0.9859 0.000 1.000 0.000 0.000 0.000 0.000
#> GSM152922 2 0.0146 0.9850 0.000 0.996 0.000 0.004 0.000 0.000
#> GSM152923 2 0.0000 0.9859 0.000 1.000 0.000 0.000 0.000 0.000
#> GSM152924 2 0.0146 0.9850 0.000 0.996 0.000 0.004 0.000 0.000
#> GSM152925 2 0.0146 0.9850 0.000 0.996 0.000 0.004 0.000 0.000
#> GSM152926 2 0.0000 0.9859 0.000 1.000 0.000 0.000 0.000 0.000
#> GSM152927 2 0.0146 0.9850 0.000 0.996 0.000 0.004 0.000 0.000
#> GSM152928 2 0.2340 0.8800 0.044 0.896 0.056 0.004 0.000 0.000
#> GSM152929 2 0.0000 0.9859 0.000 1.000 0.000 0.000 0.000 0.000
#> GSM152930 2 0.0000 0.9859 0.000 1.000 0.000 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)
#> Error in mat[ceiling(1:nr/h_ratio), ceiling(1:nc/w_ratio), drop = FALSE]: subscript out of bounds
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 tissue(p) k
#> MAD:mclust 163 1.65e-27 2
#> MAD:mclust 154 1.31e-32 3
#> MAD:mclust 151 1.96e-33 4
#> MAD:mclust 146 4.05e-32 5
#> MAD:mclust 138 7.04e-31 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 12013 rows and 164 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 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 0.788 0.877 0.948 0.4513 0.548 0.548
#> 3 3 0.626 0.783 0.884 0.4216 0.720 0.525
#> 4 4 0.543 0.642 0.799 0.1619 0.808 0.517
#> 5 5 0.536 0.507 0.707 0.0610 0.933 0.754
#> 6 6 0.555 0.441 0.652 0.0401 0.952 0.797
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
#> GSM152839 1 0.0000 0.9537 1.000 0.000
#> GSM152840 1 0.0000 0.9537 1.000 0.000
#> GSM152841 1 0.0000 0.9537 1.000 0.000
#> GSM152842 1 0.0000 0.9537 1.000 0.000
#> GSM152843 1 0.0000 0.9537 1.000 0.000
#> GSM152844 1 0.0000 0.9537 1.000 0.000
#> GSM152845 2 0.3584 0.8804 0.068 0.932
#> GSM152846 1 0.0672 0.9493 0.992 0.008
#> GSM152847 1 0.0000 0.9537 1.000 0.000
#> GSM152848 1 0.0000 0.9537 1.000 0.000
#> GSM152849 1 0.0000 0.9537 1.000 0.000
#> GSM152850 1 0.0000 0.9537 1.000 0.000
#> GSM152851 1 0.0376 0.9516 0.996 0.004
#> GSM152852 1 0.0000 0.9537 1.000 0.000
#> GSM152853 1 0.0000 0.9537 1.000 0.000
#> GSM152854 1 0.2778 0.9202 0.952 0.048
#> GSM152855 1 0.0000 0.9537 1.000 0.000
#> GSM153238 2 0.9248 0.5174 0.340 0.660
#> GSM153239 1 0.0000 0.9537 1.000 0.000
#> GSM153240 1 0.0000 0.9537 1.000 0.000
#> GSM153241 1 0.0000 0.9537 1.000 0.000
#> GSM153242 1 0.6247 0.8015 0.844 0.156
#> GSM153243 2 0.2043 0.9049 0.032 0.968
#> GSM153244 2 0.8327 0.6595 0.264 0.736
#> GSM153245 1 0.0000 0.9537 1.000 0.000
#> GSM153246 1 0.0938 0.9471 0.988 0.012
#> GSM153247 1 0.7674 0.7072 0.776 0.224
#> GSM153248 2 0.9732 0.3638 0.404 0.596
#> GSM153249 1 0.0000 0.9537 1.000 0.000
#> GSM153250 1 0.0000 0.9537 1.000 0.000
#> GSM153251 2 0.8909 0.5870 0.308 0.692
#> GSM153252 1 0.0000 0.9537 1.000 0.000
#> GSM153253 1 0.0000 0.9537 1.000 0.000
#> GSM153254 1 0.8713 0.5772 0.708 0.292
#> GSM153255 1 0.0000 0.9537 1.000 0.000
#> GSM153256 1 0.0000 0.9537 1.000 0.000
#> GSM153257 1 0.0000 0.9537 1.000 0.000
#> GSM153258 1 0.0000 0.9537 1.000 0.000
#> GSM153259 1 0.0376 0.9516 0.996 0.004
#> GSM153260 1 0.7815 0.6916 0.768 0.232
#> GSM153261 1 0.2423 0.9251 0.960 0.040
#> GSM153262 1 0.0000 0.9537 1.000 0.000
#> GSM153263 1 0.0000 0.9537 1.000 0.000
#> GSM153264 1 0.0000 0.9537 1.000 0.000
#> GSM153265 1 0.0000 0.9537 1.000 0.000
#> GSM153266 1 0.0000 0.9537 1.000 0.000
#> GSM153267 1 0.0000 0.9537 1.000 0.000
#> GSM153268 1 0.0000 0.9537 1.000 0.000
#> GSM153269 1 0.0000 0.9537 1.000 0.000
#> GSM153270 1 0.0000 0.9537 1.000 0.000
#> GSM153271 1 0.0000 0.9537 1.000 0.000
#> GSM153272 1 0.0000 0.9537 1.000 0.000
#> GSM153273 1 0.4022 0.8897 0.920 0.080
#> GSM153274 1 0.0000 0.9537 1.000 0.000
#> GSM153275 1 0.0000 0.9537 1.000 0.000
#> GSM153276 1 0.0000 0.9537 1.000 0.000
#> GSM153277 1 0.0000 0.9537 1.000 0.000
#> GSM153278 1 0.0000 0.9537 1.000 0.000
#> GSM153279 1 0.0000 0.9537 1.000 0.000
#> GSM153280 1 0.0000 0.9537 1.000 0.000
#> GSM153281 1 0.0000 0.9537 1.000 0.000
#> GSM153282 1 0.0000 0.9537 1.000 0.000
#> GSM153283 1 0.0000 0.9537 1.000 0.000
#> GSM153284 1 0.0000 0.9537 1.000 0.000
#> GSM153285 1 0.0000 0.9537 1.000 0.000
#> GSM153286 1 0.0000 0.9537 1.000 0.000
#> GSM153287 1 0.0000 0.9537 1.000 0.000
#> GSM153288 1 0.0000 0.9537 1.000 0.000
#> GSM153289 1 0.0000 0.9537 1.000 0.000
#> GSM153290 1 0.0000 0.9537 1.000 0.000
#> GSM153291 1 0.0000 0.9537 1.000 0.000
#> GSM153292 1 0.0000 0.9537 1.000 0.000
#> GSM153293 1 0.0000 0.9537 1.000 0.000
#> GSM153294 1 0.9248 0.4840 0.660 0.340
#> GSM153295 1 0.0000 0.9537 1.000 0.000
#> GSM153054 1 0.2423 0.9269 0.960 0.040
#> GSM153055 1 0.0672 0.9497 0.992 0.008
#> GSM153056 1 0.0000 0.9537 1.000 0.000
#> GSM153057 1 0.8861 0.5602 0.696 0.304
#> GSM153058 1 0.1414 0.9419 0.980 0.020
#> GSM153059 2 0.1633 0.9097 0.024 0.976
#> GSM153060 1 0.0000 0.9537 1.000 0.000
#> GSM153061 1 0.1843 0.9359 0.972 0.028
#> GSM153062 2 0.6247 0.8032 0.156 0.844
#> GSM153063 1 0.0672 0.9494 0.992 0.008
#> GSM153064 1 0.0376 0.9516 0.996 0.004
#> GSM153065 2 0.4562 0.8587 0.096 0.904
#> GSM153066 2 0.0000 0.9224 0.000 1.000
#> GSM153067 1 0.0000 0.9537 1.000 0.000
#> GSM153068 2 0.9850 0.3109 0.428 0.572
#> GSM153069 1 0.0000 0.9537 1.000 0.000
#> GSM153070 1 0.1184 0.9441 0.984 0.016
#> GSM153071 1 0.8081 0.6697 0.752 0.248
#> GSM153072 1 0.9833 0.2314 0.576 0.424
#> GSM153073 1 0.1414 0.9419 0.980 0.020
#> GSM153074 1 0.0000 0.9537 1.000 0.000
#> GSM153075 1 0.0000 0.9537 1.000 0.000
#> GSM153076 1 0.0000 0.9537 1.000 0.000
#> GSM153077 1 0.1843 0.9362 0.972 0.028
#> GSM153078 1 0.0376 0.9515 0.996 0.004
#> GSM153079 2 0.6801 0.7787 0.180 0.820
#> GSM153080 1 0.0000 0.9537 1.000 0.000
#> GSM153081 1 0.0000 0.9537 1.000 0.000
#> GSM153082 2 0.0000 0.9224 0.000 1.000
#> GSM153083 2 0.0000 0.9224 0.000 1.000
#> GSM153084 2 0.0000 0.9224 0.000 1.000
#> GSM153085 2 0.6712 0.7805 0.176 0.824
#> GSM153086 2 0.9686 0.3899 0.396 0.604
#> GSM153087 1 0.0000 0.9537 1.000 0.000
#> GSM153088 1 0.0000 0.9537 1.000 0.000
#> GSM153089 2 0.9754 0.3644 0.408 0.592
#> GSM153090 1 0.0000 0.9537 1.000 0.000
#> GSM153091 2 0.0000 0.9224 0.000 1.000
#> GSM153092 1 0.5946 0.8193 0.856 0.144
#> GSM153093 1 0.0000 0.9537 1.000 0.000
#> GSM153094 2 0.0000 0.9224 0.000 1.000
#> GSM153095 1 1.0000 -0.0605 0.500 0.500
#> GSM153096 1 0.2043 0.9331 0.968 0.032
#> GSM153097 2 0.0376 0.9203 0.004 0.996
#> GSM153098 1 0.3733 0.8981 0.928 0.072
#> GSM153099 1 0.0000 0.9537 1.000 0.000
#> GSM153100 1 0.3114 0.9131 0.944 0.056
#> GSM153101 2 0.9954 0.1889 0.460 0.540
#> GSM153102 2 0.6973 0.7697 0.188 0.812
#> GSM153103 2 0.3879 0.8739 0.076 0.924
#> GSM153104 1 0.0000 0.9537 1.000 0.000
#> GSM153106 1 0.9635 0.3396 0.612 0.388
#> GSM153107 1 0.7453 0.7232 0.788 0.212
#> GSM153108 1 0.0938 0.9469 0.988 0.012
#> GSM153109 2 0.0000 0.9224 0.000 1.000
#> GSM153110 1 0.5178 0.8521 0.884 0.116
#> GSM153111 2 0.0000 0.9224 0.000 1.000
#> GSM153112 1 0.9896 0.1927 0.560 0.440
#> GSM153113 2 0.0000 0.9224 0.000 1.000
#> GSM153114 1 0.0000 0.9537 1.000 0.000
#> GSM187532 2 0.0000 0.9224 0.000 1.000
#> GSM187533 2 0.0000 0.9224 0.000 1.000
#> GSM187534 2 0.0000 0.9224 0.000 1.000
#> GSM187535 2 0.0000 0.9224 0.000 1.000
#> GSM152906 2 0.0000 0.9224 0.000 1.000
#> GSM152907 2 0.0000 0.9224 0.000 1.000
#> GSM152908 2 0.0000 0.9224 0.000 1.000
#> GSM152909 2 0.0000 0.9224 0.000 1.000
#> GSM152910 2 0.0000 0.9224 0.000 1.000
#> GSM152911 2 0.0000 0.9224 0.000 1.000
#> GSM152912 2 0.0000 0.9224 0.000 1.000
#> GSM152913 2 0.0000 0.9224 0.000 1.000
#> GSM152914 2 0.0000 0.9224 0.000 1.000
#> GSM152915 2 0.0000 0.9224 0.000 1.000
#> GSM152916 2 0.0000 0.9224 0.000 1.000
#> GSM152917 2 0.0000 0.9224 0.000 1.000
#> GSM152918 2 0.0000 0.9224 0.000 1.000
#> GSM152919 2 0.0000 0.9224 0.000 1.000
#> GSM152920 2 0.0000 0.9224 0.000 1.000
#> GSM152921 2 0.0000 0.9224 0.000 1.000
#> GSM152922 2 0.0000 0.9224 0.000 1.000
#> GSM152923 2 0.0000 0.9224 0.000 1.000
#> GSM152924 2 0.0000 0.9224 0.000 1.000
#> GSM152925 2 0.0000 0.9224 0.000 1.000
#> GSM152926 2 0.0000 0.9224 0.000 1.000
#> GSM152927 2 0.0000 0.9224 0.000 1.000
#> GSM152928 2 0.0000 0.9224 0.000 1.000
#> GSM152929 2 0.0000 0.9224 0.000 1.000
#> GSM152930 2 0.0000 0.9224 0.000 1.000
cbind(get_classes(res, k = 3), get_membership(res, k = 3))
#> class entropy silhouette p1 p2 p3
#> GSM152839 3 0.6140 0.3427 0.404 0.000 0.596
#> GSM152840 3 0.4796 0.7243 0.220 0.000 0.780
#> GSM152841 1 0.1643 0.9051 0.956 0.000 0.044
#> GSM152842 3 0.1643 0.8359 0.044 0.000 0.956
#> GSM152843 3 0.4555 0.7497 0.200 0.000 0.800
#> GSM152844 3 0.1529 0.8361 0.040 0.000 0.960
#> GSM152845 3 0.2796 0.7733 0.000 0.092 0.908
#> GSM152846 3 0.1315 0.8330 0.020 0.008 0.972
#> GSM152847 3 0.4555 0.7504 0.200 0.000 0.800
#> GSM152848 1 0.5465 0.6299 0.712 0.000 0.288
#> GSM152849 3 0.1411 0.8356 0.036 0.000 0.964
#> GSM152850 3 0.2537 0.8280 0.080 0.000 0.920
#> GSM152851 3 0.3116 0.8168 0.108 0.000 0.892
#> GSM152852 3 0.1163 0.8347 0.028 0.000 0.972
#> GSM152853 3 0.1964 0.8350 0.056 0.000 0.944
#> GSM152854 3 0.1315 0.8287 0.008 0.020 0.972
#> GSM152855 1 0.1170 0.8947 0.976 0.008 0.016
#> GSM153238 3 0.2165 0.7969 0.000 0.064 0.936
#> GSM153239 3 0.2066 0.8342 0.060 0.000 0.940
#> GSM153240 1 0.2165 0.9000 0.936 0.000 0.064
#> GSM153241 3 0.2625 0.8266 0.084 0.000 0.916
#> GSM153242 3 0.1711 0.8196 0.008 0.032 0.960
#> GSM153243 3 0.2448 0.7867 0.000 0.076 0.924
#> GSM153244 3 0.8969 0.3437 0.140 0.348 0.512
#> GSM153245 3 0.3116 0.8164 0.108 0.000 0.892
#> GSM153246 3 0.1182 0.8311 0.012 0.012 0.976
#> GSM153247 3 0.1482 0.8330 0.020 0.012 0.968
#> GSM153248 2 0.7188 0.0175 0.484 0.492 0.024
#> GSM153249 1 0.1129 0.8945 0.976 0.004 0.020
#> GSM153250 1 0.0983 0.9004 0.980 0.004 0.016
#> GSM153251 3 0.1860 0.8056 0.000 0.052 0.948
#> GSM153252 1 0.2066 0.9012 0.940 0.000 0.060
#> GSM153253 1 0.3038 0.8787 0.896 0.000 0.104
#> GSM153254 3 0.2902 0.8341 0.064 0.016 0.920
#> GSM153255 1 0.0592 0.9034 0.988 0.000 0.012
#> GSM153256 1 0.0592 0.9031 0.988 0.000 0.012
#> GSM153257 1 0.1163 0.9072 0.972 0.000 0.028
#> GSM153258 1 0.1411 0.9077 0.964 0.000 0.036
#> GSM153259 1 0.1015 0.9041 0.980 0.008 0.012
#> GSM153260 3 0.1182 0.8311 0.012 0.012 0.976
#> GSM153261 3 0.1267 0.8346 0.024 0.004 0.972
#> GSM153262 1 0.2537 0.8939 0.920 0.000 0.080
#> GSM153263 1 0.0592 0.9064 0.988 0.000 0.012
#> GSM153264 1 0.2796 0.8869 0.908 0.000 0.092
#> GSM153265 1 0.3686 0.8507 0.860 0.000 0.140
#> GSM153266 1 0.3619 0.8560 0.864 0.000 0.136
#> GSM153267 1 0.1031 0.9068 0.976 0.000 0.024
#> GSM153268 1 0.5560 0.6039 0.700 0.000 0.300
#> GSM153269 1 0.0592 0.9064 0.988 0.000 0.012
#> GSM153270 1 0.3752 0.8451 0.856 0.000 0.144
#> GSM153271 1 0.1129 0.8945 0.976 0.004 0.020
#> GSM153272 1 0.1031 0.9076 0.976 0.000 0.024
#> GSM153273 1 0.1877 0.8895 0.956 0.032 0.012
#> GSM153274 1 0.2261 0.8995 0.932 0.000 0.068
#> GSM153275 1 0.1411 0.9067 0.964 0.000 0.036
#> GSM153276 1 0.3267 0.8722 0.884 0.000 0.116
#> GSM153277 1 0.4002 0.8310 0.840 0.000 0.160
#> GSM153278 3 0.4002 0.7856 0.160 0.000 0.840
#> GSM153279 1 0.6260 0.1923 0.552 0.000 0.448
#> GSM153280 1 0.3551 0.8568 0.868 0.000 0.132
#> GSM153281 1 0.2537 0.8930 0.920 0.000 0.080
#> GSM153282 1 0.3482 0.8605 0.872 0.000 0.128
#> GSM153283 1 0.0747 0.9066 0.984 0.000 0.016
#> GSM153284 1 0.1163 0.9076 0.972 0.000 0.028
#> GSM153285 1 0.2625 0.8916 0.916 0.000 0.084
#> GSM153286 1 0.0747 0.9066 0.984 0.000 0.016
#> GSM153287 1 0.1031 0.9071 0.976 0.000 0.024
#> GSM153288 1 0.0592 0.9053 0.988 0.000 0.012
#> GSM153289 1 0.1129 0.8945 0.976 0.004 0.020
#> GSM153290 1 0.3879 0.8372 0.848 0.000 0.152
#> GSM153291 1 0.0592 0.9062 0.988 0.000 0.012
#> GSM153292 1 0.1163 0.9078 0.972 0.000 0.028
#> GSM153293 1 0.0237 0.9030 0.996 0.000 0.004
#> GSM153294 1 0.6673 0.4351 0.636 0.344 0.020
#> GSM153295 1 0.2711 0.8902 0.912 0.000 0.088
#> GSM153054 3 0.5431 0.6251 0.284 0.000 0.716
#> GSM153055 1 0.4110 0.8353 0.844 0.004 0.152
#> GSM153056 3 0.4555 0.7501 0.200 0.000 0.800
#> GSM153057 3 0.1774 0.8347 0.024 0.016 0.960
#> GSM153058 3 0.1315 0.8330 0.020 0.008 0.972
#> GSM153059 3 0.3038 0.7607 0.000 0.104 0.896
#> GSM153060 3 0.0892 0.8339 0.020 0.000 0.980
#> GSM153061 3 0.1482 0.8314 0.020 0.012 0.968
#> GSM153062 3 0.1860 0.8056 0.000 0.052 0.948
#> GSM153063 3 0.1860 0.8351 0.052 0.000 0.948
#> GSM153064 1 0.0983 0.8970 0.980 0.004 0.016
#> GSM153065 3 0.2537 0.7836 0.000 0.080 0.920
#> GSM153066 3 0.6280 -0.0410 0.000 0.460 0.540
#> GSM153067 1 0.1129 0.8945 0.976 0.004 0.020
#> GSM153068 3 0.1643 0.8105 0.000 0.044 0.956
#> GSM153069 1 0.1031 0.9071 0.976 0.000 0.024
#> GSM153070 1 0.3183 0.8927 0.908 0.016 0.076
#> GSM153071 3 0.5455 0.7478 0.204 0.020 0.776
#> GSM153072 3 0.8223 0.5644 0.288 0.108 0.604
#> GSM153073 1 0.1781 0.9003 0.960 0.020 0.020
#> GSM153074 1 0.0829 0.8985 0.984 0.004 0.012
#> GSM153075 1 0.3941 0.8350 0.844 0.000 0.156
#> GSM153076 1 0.0592 0.9002 0.988 0.000 0.012
#> GSM153077 1 0.1905 0.9063 0.956 0.016 0.028
#> GSM153078 3 0.4555 0.7534 0.200 0.000 0.800
#> GSM153079 2 0.7003 0.5947 0.248 0.692 0.060
#> GSM153080 3 0.3686 0.7969 0.140 0.000 0.860
#> GSM153081 1 0.2165 0.9009 0.936 0.000 0.064
#> GSM153082 2 0.2651 0.8328 0.060 0.928 0.012
#> GSM153083 2 0.1170 0.8635 0.008 0.976 0.016
#> GSM153084 2 0.5465 0.6586 0.000 0.712 0.288
#> GSM153085 3 0.8311 0.4669 0.112 0.292 0.596
#> GSM153086 1 0.9910 -0.0748 0.384 0.344 0.272
#> GSM153087 1 0.1529 0.9057 0.960 0.000 0.040
#> GSM153088 1 0.0892 0.9074 0.980 0.000 0.020
#> GSM153089 3 0.1643 0.8105 0.000 0.044 0.956
#> GSM153090 1 0.1411 0.9071 0.964 0.000 0.036
#> GSM153091 2 0.4663 0.7447 0.156 0.828 0.016
#> GSM153092 1 0.4830 0.8434 0.848 0.084 0.068
#> GSM153093 1 0.1411 0.9067 0.964 0.000 0.036
#> GSM153094 2 0.2584 0.8336 0.064 0.928 0.008
#> GSM153095 3 0.9810 0.2041 0.372 0.240 0.388
#> GSM153096 1 0.1267 0.9020 0.972 0.024 0.004
#> GSM153097 2 0.2804 0.8365 0.060 0.924 0.016
#> GSM153098 1 0.3141 0.8578 0.912 0.068 0.020
#> GSM153099 1 0.2537 0.8935 0.920 0.000 0.080
#> GSM153100 1 0.1711 0.8958 0.960 0.032 0.008
#> GSM153101 3 0.9319 0.4627 0.296 0.196 0.508
#> GSM153102 2 0.7533 0.4060 0.052 0.600 0.348
#> GSM153103 2 0.8069 0.0579 0.064 0.476 0.460
#> GSM153104 1 0.3192 0.8751 0.888 0.000 0.112
#> GSM153106 1 0.6255 0.4832 0.668 0.320 0.012
#> GSM153107 1 0.5147 0.7297 0.800 0.180 0.020
#> GSM153108 1 0.3112 0.8822 0.900 0.004 0.096
#> GSM153109 2 0.1753 0.8561 0.000 0.952 0.048
#> GSM153110 1 0.1999 0.8974 0.952 0.036 0.012
#> GSM153111 2 0.3295 0.8066 0.096 0.896 0.008
#> GSM153112 1 0.6814 0.3656 0.608 0.372 0.020
#> GSM153113 2 0.0848 0.8595 0.008 0.984 0.008
#> GSM153114 1 0.0661 0.9032 0.988 0.004 0.008
#> GSM187532 3 0.6295 -0.0853 0.000 0.472 0.528
#> GSM187533 2 0.2537 0.8454 0.000 0.920 0.080
#> GSM187534 2 0.0592 0.8662 0.000 0.988 0.012
#> GSM187535 2 0.2297 0.8425 0.036 0.944 0.020
#> GSM152906 2 0.0000 0.8643 0.000 1.000 0.000
#> GSM152907 2 0.0829 0.8649 0.004 0.984 0.012
#> GSM152908 2 0.0592 0.8661 0.000 0.988 0.012
#> GSM152909 2 0.6140 0.4318 0.000 0.596 0.404
#> GSM152910 2 0.5178 0.7044 0.000 0.744 0.256
#> GSM152911 2 0.1753 0.8580 0.000 0.952 0.048
#> GSM152912 2 0.1163 0.8634 0.000 0.972 0.028
#> GSM152913 2 0.5650 0.6205 0.000 0.688 0.312
#> GSM152914 2 0.0592 0.8661 0.000 0.988 0.012
#> GSM152915 2 0.0424 0.8659 0.000 0.992 0.008
#> GSM152916 2 0.4291 0.7818 0.000 0.820 0.180
#> GSM152917 2 0.0424 0.8659 0.000 0.992 0.008
#> GSM152918 2 0.0475 0.8625 0.004 0.992 0.004
#> GSM152919 2 0.0424 0.8659 0.000 0.992 0.008
#> GSM152920 2 0.0747 0.8657 0.000 0.984 0.016
#> GSM152921 2 0.0424 0.8659 0.000 0.992 0.008
#> GSM152922 2 0.3619 0.8147 0.000 0.864 0.136
#> GSM152923 2 0.0592 0.8662 0.000 0.988 0.012
#> GSM152924 2 0.4002 0.7980 0.000 0.840 0.160
#> GSM152925 2 0.4178 0.7882 0.000 0.828 0.172
#> GSM152926 2 0.0000 0.8643 0.000 1.000 0.000
#> GSM152927 2 0.5138 0.7079 0.000 0.748 0.252
#> GSM152928 2 0.4931 0.7318 0.000 0.768 0.232
#> GSM152929 2 0.0424 0.8659 0.000 0.992 0.008
#> GSM152930 2 0.0424 0.8659 0.000 0.992 0.008
cbind(get_classes(res, k = 4), get_membership(res, k = 4))
#> class entropy silhouette p1 p2 p3 p4
#> GSM152839 3 0.6038 0.2845 0.424 0.000 0.532 0.044
#> GSM152840 4 0.5060 0.2533 0.000 0.004 0.412 0.584
#> GSM152841 4 0.2076 0.7858 0.004 0.008 0.056 0.932
#> GSM152842 3 0.4304 0.5661 0.284 0.000 0.716 0.000
#> GSM152843 3 0.4655 0.6561 0.208 0.000 0.760 0.032
#> GSM152844 3 0.4936 0.4373 0.000 0.008 0.652 0.340
#> GSM152845 3 0.4174 0.6419 0.000 0.140 0.816 0.044
#> GSM152846 3 0.4761 0.6381 0.000 0.044 0.764 0.192
#> GSM152847 3 0.5284 0.4201 0.368 0.000 0.616 0.016
#> GSM152848 1 0.5256 0.6014 0.732 0.000 0.204 0.064
#> GSM152849 3 0.2412 0.7218 0.084 0.000 0.908 0.008
#> GSM152850 1 0.5168 -0.0952 0.504 0.000 0.492 0.004
#> GSM152851 4 0.6314 -0.0260 0.004 0.048 0.464 0.484
#> GSM152852 3 0.5453 0.4603 0.000 0.032 0.648 0.320
#> GSM152853 3 0.5203 0.2532 0.000 0.008 0.576 0.416
#> GSM152854 3 0.3436 0.7096 0.008 0.036 0.876 0.080
#> GSM152855 4 0.4318 0.6821 0.208 0.012 0.004 0.776
#> GSM153238 3 0.4158 0.6369 0.224 0.008 0.768 0.000
#> GSM153239 3 0.4387 0.6042 0.000 0.012 0.752 0.236
#> GSM153240 4 0.1624 0.7995 0.028 0.000 0.020 0.952
#> GSM153241 3 0.3166 0.7131 0.116 0.000 0.868 0.016
#> GSM153242 3 0.5003 0.6521 0.000 0.084 0.768 0.148
#> GSM153243 3 0.4348 0.6593 0.196 0.024 0.780 0.000
#> GSM153244 4 0.8133 0.0825 0.012 0.276 0.280 0.432
#> GSM153245 3 0.4722 0.5128 0.000 0.008 0.692 0.300
#> GSM153246 3 0.1792 0.7225 0.068 0.000 0.932 0.000
#> GSM153247 3 0.3445 0.7174 0.112 0.012 0.864 0.012
#> GSM153248 1 0.1635 0.7245 0.948 0.044 0.008 0.000
#> GSM153249 4 0.1305 0.7973 0.036 0.000 0.004 0.960
#> GSM153250 1 0.4153 0.6518 0.784 0.008 0.004 0.204
#> GSM153251 3 0.4610 0.6607 0.000 0.100 0.800 0.100
#> GSM153252 4 0.3547 0.7572 0.144 0.000 0.016 0.840
#> GSM153253 4 0.2839 0.7574 0.004 0.004 0.108 0.884
#> GSM153254 3 0.7146 0.5658 0.028 0.128 0.624 0.220
#> GSM153255 4 0.1302 0.7965 0.044 0.000 0.000 0.956
#> GSM153256 4 0.4624 0.5007 0.340 0.000 0.000 0.660
#> GSM153257 4 0.2737 0.7866 0.104 0.000 0.008 0.888
#> GSM153258 1 0.4018 0.6940 0.812 0.004 0.016 0.168
#> GSM153259 1 0.2222 0.7368 0.928 0.008 0.008 0.056
#> GSM153260 3 0.5097 0.2834 0.428 0.004 0.568 0.000
#> GSM153261 3 0.3074 0.6954 0.152 0.000 0.848 0.000
#> GSM153262 4 0.1798 0.8011 0.040 0.000 0.016 0.944
#> GSM153263 1 0.3937 0.6715 0.800 0.000 0.012 0.188
#> GSM153264 1 0.3301 0.6999 0.876 0.004 0.092 0.028
#> GSM153265 4 0.2281 0.7713 0.000 0.000 0.096 0.904
#> GSM153266 1 0.4608 0.7127 0.800 0.000 0.096 0.104
#> GSM153267 4 0.5269 0.2640 0.428 0.004 0.004 0.564
#> GSM153268 4 0.3249 0.7381 0.008 0.000 0.140 0.852
#> GSM153269 4 0.5161 0.1427 0.476 0.004 0.000 0.520
#> GSM153270 4 0.3653 0.7704 0.128 0.000 0.028 0.844
#> GSM153271 1 0.4875 0.5100 0.692 0.008 0.004 0.296
#> GSM153272 4 0.2053 0.7940 0.072 0.000 0.004 0.924
#> GSM153273 1 0.3557 0.7248 0.856 0.036 0.000 0.108
#> GSM153274 1 0.5590 0.0774 0.524 0.000 0.020 0.456
#> GSM153275 4 0.3494 0.7347 0.172 0.000 0.004 0.824
#> GSM153276 4 0.4057 0.7571 0.152 0.000 0.032 0.816
#> GSM153277 4 0.2334 0.7789 0.004 0.000 0.088 0.908
#> GSM153278 3 0.4914 0.5174 0.312 0.000 0.676 0.012
#> GSM153279 4 0.3907 0.6255 0.000 0.000 0.232 0.768
#> GSM153280 4 0.3161 0.7428 0.000 0.012 0.124 0.864
#> GSM153281 4 0.1833 0.7975 0.024 0.000 0.032 0.944
#> GSM153282 4 0.2408 0.7655 0.000 0.000 0.104 0.896
#> GSM153283 1 0.3278 0.7331 0.864 0.000 0.020 0.116
#> GSM153284 4 0.1940 0.7942 0.076 0.000 0.000 0.924
#> GSM153285 4 0.2401 0.7720 0.004 0.000 0.092 0.904
#> GSM153286 4 0.3266 0.7335 0.168 0.000 0.000 0.832
#> GSM153287 4 0.0895 0.7981 0.020 0.000 0.004 0.976
#> GSM153288 4 0.3355 0.7364 0.160 0.004 0.000 0.836
#> GSM153289 4 0.5349 0.4199 0.368 0.012 0.004 0.616
#> GSM153290 4 0.3375 0.7488 0.008 0.012 0.116 0.864
#> GSM153291 4 0.1398 0.7997 0.040 0.000 0.004 0.956
#> GSM153292 4 0.1661 0.7891 0.004 0.000 0.052 0.944
#> GSM153293 4 0.4509 0.5819 0.288 0.004 0.000 0.708
#> GSM153294 1 0.6140 0.6209 0.684 0.196 0.004 0.116
#> GSM153295 1 0.6120 0.1939 0.520 0.000 0.048 0.432
#> GSM153054 1 0.4995 0.3727 0.648 0.004 0.344 0.004
#> GSM153055 4 0.6187 0.3440 0.388 0.008 0.040 0.564
#> GSM153056 3 0.4781 0.6464 0.212 0.000 0.752 0.036
#> GSM153057 3 0.2909 0.7259 0.052 0.036 0.904 0.008
#> GSM153058 3 0.2708 0.7263 0.076 0.004 0.904 0.016
#> GSM153059 3 0.3555 0.7143 0.048 0.080 0.868 0.004
#> GSM153060 3 0.1958 0.7259 0.028 0.008 0.944 0.020
#> GSM153061 3 0.3219 0.6860 0.164 0.000 0.836 0.000
#> GSM153062 3 0.2153 0.7185 0.008 0.036 0.936 0.020
#> GSM153063 3 0.4267 0.6504 0.000 0.024 0.788 0.188
#> GSM153064 1 0.4082 0.6836 0.812 0.020 0.004 0.164
#> GSM153065 3 0.3925 0.6778 0.176 0.016 0.808 0.000
#> GSM153066 3 0.6140 0.5522 0.252 0.096 0.652 0.000
#> GSM153067 4 0.1902 0.7946 0.064 0.000 0.004 0.932
#> GSM153068 3 0.2271 0.7203 0.076 0.008 0.916 0.000
#> GSM153069 4 0.1059 0.7978 0.016 0.000 0.012 0.972
#> GSM153070 1 0.4613 0.7070 0.792 0.008 0.036 0.164
#> GSM153071 3 0.5281 0.1682 0.464 0.008 0.528 0.000
#> GSM153072 1 0.4963 0.4813 0.696 0.020 0.284 0.000
#> GSM153073 1 0.2096 0.7337 0.940 0.016 0.016 0.028
#> GSM153074 4 0.2281 0.7840 0.096 0.000 0.000 0.904
#> GSM153075 4 0.2597 0.7798 0.008 0.004 0.084 0.904
#> GSM153076 1 0.2976 0.7194 0.872 0.000 0.008 0.120
#> GSM153077 1 0.2474 0.7148 0.920 0.008 0.056 0.016
#> GSM153078 3 0.5615 0.2666 0.424 0.004 0.556 0.016
#> GSM153079 1 0.4108 0.7056 0.848 0.080 0.056 0.016
#> GSM153080 3 0.3447 0.7023 0.020 0.000 0.852 0.128
#> GSM153081 1 0.3056 0.7128 0.888 0.000 0.072 0.040
#> GSM153082 1 0.5159 0.3869 0.624 0.364 0.012 0.000
#> GSM153083 1 0.4856 0.6523 0.780 0.136 0.084 0.000
#> GSM153084 1 0.8080 -0.0679 0.336 0.324 0.336 0.004
#> GSM153085 1 0.5548 0.3603 0.628 0.032 0.340 0.000
#> GSM153086 1 0.3969 0.6215 0.804 0.016 0.180 0.000
#> GSM153087 4 0.2011 0.7927 0.080 0.000 0.000 0.920
#> GSM153088 1 0.2775 0.7359 0.896 0.000 0.020 0.084
#> GSM153089 3 0.4300 0.6744 0.000 0.088 0.820 0.092
#> GSM153090 1 0.3048 0.7329 0.876 0.000 0.016 0.108
#> GSM153091 1 0.3583 0.6703 0.816 0.180 0.004 0.000
#> GSM153092 1 0.6516 0.5433 0.644 0.092 0.012 0.252
#> GSM153093 4 0.2466 0.7877 0.096 0.000 0.004 0.900
#> GSM153094 2 0.5446 0.4298 0.340 0.636 0.020 0.004
#> GSM153095 1 0.6908 0.3490 0.576 0.052 0.336 0.036
#> GSM153096 1 0.2915 0.7362 0.892 0.016 0.004 0.088
#> GSM153097 1 0.3805 0.6897 0.856 0.072 0.068 0.004
#> GSM153098 4 0.6719 0.0980 0.440 0.076 0.004 0.480
#> GSM153099 4 0.4776 0.6272 0.244 0.000 0.024 0.732
#> GSM153100 1 0.6028 0.3379 0.596 0.044 0.004 0.356
#> GSM153101 1 0.5005 0.5032 0.712 0.020 0.264 0.004
#> GSM153102 2 0.7431 0.4084 0.052 0.552 0.328 0.068
#> GSM153103 1 0.5291 0.4069 0.652 0.024 0.324 0.000
#> GSM153104 4 0.1902 0.7883 0.004 0.000 0.064 0.932
#> GSM153106 4 0.7688 0.2639 0.252 0.252 0.004 0.492
#> GSM153107 1 0.6414 0.5619 0.648 0.112 0.004 0.236
#> GSM153108 4 0.3150 0.7951 0.036 0.004 0.072 0.888
#> GSM153109 2 0.3414 0.8623 0.048 0.876 0.072 0.004
#> GSM153110 1 0.2188 0.7329 0.936 0.012 0.020 0.032
#> GSM153111 1 0.3587 0.6938 0.856 0.104 0.040 0.000
#> GSM153112 1 0.7566 0.3536 0.488 0.324 0.004 0.184
#> GSM153113 2 0.4192 0.7038 0.208 0.780 0.008 0.004
#> GSM153114 4 0.2311 0.7939 0.076 0.004 0.004 0.916
#> GSM187532 3 0.5925 -0.0428 0.036 0.452 0.512 0.000
#> GSM187533 2 0.2707 0.8770 0.016 0.908 0.068 0.008
#> GSM187534 2 0.1520 0.8872 0.024 0.956 0.020 0.000
#> GSM187535 2 0.3172 0.8231 0.112 0.872 0.004 0.012
#> GSM152906 2 0.1474 0.8715 0.052 0.948 0.000 0.000
#> GSM152907 2 0.1509 0.8827 0.008 0.960 0.020 0.012
#> GSM152908 2 0.0657 0.8862 0.004 0.984 0.012 0.000
#> GSM152909 2 0.5386 0.5470 0.008 0.636 0.344 0.012
#> GSM152910 2 0.3836 0.8025 0.016 0.816 0.168 0.000
#> GSM152911 2 0.1398 0.8832 0.004 0.956 0.040 0.000
#> GSM152912 2 0.1042 0.8857 0.008 0.972 0.020 0.000
#> GSM152913 2 0.4770 0.6524 0.000 0.700 0.288 0.012
#> GSM152914 2 0.0657 0.8866 0.004 0.984 0.012 0.000
#> GSM152915 2 0.0188 0.8859 0.000 0.996 0.004 0.000
#> GSM152916 2 0.2928 0.8595 0.012 0.880 0.108 0.000
#> GSM152917 2 0.0707 0.8844 0.020 0.980 0.000 0.000
#> GSM152918 2 0.1489 0.8733 0.044 0.952 0.004 0.000
#> GSM152919 2 0.0707 0.8844 0.020 0.980 0.000 0.000
#> GSM152920 2 0.0927 0.8858 0.008 0.976 0.016 0.000
#> GSM152921 2 0.0376 0.8860 0.004 0.992 0.004 0.000
#> GSM152922 2 0.2731 0.8624 0.008 0.896 0.092 0.004
#> GSM152923 2 0.1284 0.8864 0.024 0.964 0.012 0.000
#> GSM152924 2 0.3292 0.8572 0.016 0.868 0.112 0.004
#> GSM152925 2 0.3224 0.8535 0.016 0.864 0.120 0.000
#> GSM152926 2 0.1492 0.8809 0.036 0.956 0.004 0.004
#> GSM152927 2 0.4284 0.7554 0.012 0.764 0.224 0.000
#> GSM152928 2 0.5252 0.7451 0.052 0.736 0.208 0.004
#> GSM152929 2 0.1389 0.8764 0.048 0.952 0.000 0.000
#> GSM152930 2 0.1004 0.8854 0.024 0.972 0.004 0.000
cbind(get_classes(res, k = 5), get_membership(res, k = 5))
#> class entropy silhouette p1 p2 p3 p4 p5
#> GSM152839 1 0.5496 -0.0711 0.472 0.000 0.472 0.004 0.052
#> GSM152840 4 0.5351 0.2860 0.000 0.000 0.380 0.560 0.060
#> GSM152841 4 0.2446 0.7101 0.000 0.000 0.056 0.900 0.044
#> GSM152842 3 0.4623 0.4813 0.304 0.000 0.664 0.000 0.032
#> GSM152843 3 0.4935 0.5873 0.212 0.000 0.720 0.028 0.040
#> GSM152844 3 0.5701 0.4388 0.000 0.000 0.604 0.272 0.124
#> GSM152845 3 0.5661 0.4530 0.000 0.032 0.600 0.040 0.328
#> GSM152846 3 0.5647 0.5359 0.000 0.012 0.668 0.156 0.164
#> GSM152847 3 0.5033 0.3244 0.400 0.000 0.568 0.004 0.028
#> GSM152848 1 0.4580 0.5384 0.772 0.000 0.144 0.024 0.060
#> GSM152849 3 0.4055 0.6541 0.108 0.004 0.808 0.004 0.076
#> GSM152850 1 0.5151 0.1155 0.560 0.000 0.396 0.000 0.044
#> GSM152851 4 0.6010 0.2181 0.000 0.028 0.392 0.524 0.056
#> GSM152852 3 0.6846 0.3322 0.000 0.012 0.476 0.232 0.280
#> GSM152853 3 0.5853 0.0470 0.000 0.000 0.472 0.432 0.096
#> GSM152854 3 0.5271 0.6058 0.024 0.008 0.728 0.072 0.168
#> GSM152855 5 0.6593 0.2722 0.216 0.000 0.000 0.352 0.432
#> GSM153238 3 0.5457 0.5553 0.172 0.004 0.672 0.000 0.152
#> GSM153239 3 0.4477 0.5141 0.000 0.000 0.708 0.252 0.040
#> GSM153240 4 0.3267 0.7228 0.064 0.000 0.024 0.868 0.044
#> GSM153241 3 0.3975 0.6576 0.116 0.000 0.816 0.020 0.048
#> GSM153242 3 0.4761 0.5890 0.000 0.020 0.760 0.136 0.084
#> GSM153243 3 0.5223 0.5559 0.240 0.012 0.680 0.000 0.068
#> GSM153244 4 0.7567 0.2972 0.000 0.168 0.244 0.492 0.096
#> GSM153245 3 0.4735 0.4598 0.000 0.000 0.672 0.284 0.044
#> GSM153246 3 0.3002 0.6539 0.048 0.004 0.872 0.000 0.076
#> GSM153247 3 0.5183 0.6117 0.136 0.008 0.728 0.008 0.120
#> GSM153248 1 0.4733 0.5391 0.720 0.020 0.012 0.012 0.236
#> GSM153249 4 0.2171 0.7213 0.024 0.000 0.000 0.912 0.064
#> GSM153250 1 0.3488 0.5199 0.808 0.000 0.000 0.168 0.024
#> GSM153251 3 0.3981 0.6118 0.000 0.028 0.820 0.108 0.044
#> GSM153252 4 0.4544 0.6726 0.156 0.000 0.012 0.764 0.068
#> GSM153253 4 0.2795 0.6980 0.000 0.000 0.100 0.872 0.028
#> GSM153254 3 0.8149 0.2978 0.028 0.056 0.428 0.224 0.264
#> GSM153255 4 0.2130 0.7163 0.080 0.000 0.000 0.908 0.012
#> GSM153256 4 0.4930 0.3195 0.388 0.000 0.000 0.580 0.032
#> GSM153257 4 0.4480 0.6807 0.128 0.000 0.012 0.776 0.084
#> GSM153258 1 0.5293 0.4698 0.692 0.000 0.016 0.080 0.212
#> GSM153259 1 0.4961 0.4465 0.660 0.004 0.004 0.036 0.296
#> GSM153260 3 0.6557 0.0922 0.404 0.004 0.420 0.000 0.172
#> GSM153261 3 0.6176 0.4606 0.128 0.004 0.560 0.004 0.304
#> GSM153262 4 0.4147 0.6954 0.064 0.000 0.016 0.804 0.116
#> GSM153263 1 0.4548 0.5339 0.752 0.000 0.000 0.120 0.128
#> GSM153264 1 0.2888 0.5667 0.880 0.000 0.056 0.004 0.060
#> GSM153265 4 0.3526 0.6829 0.000 0.000 0.096 0.832 0.072
#> GSM153266 1 0.4220 0.5639 0.808 0.000 0.056 0.032 0.104
#> GSM153267 1 0.4980 -0.0777 0.488 0.000 0.000 0.484 0.028
#> GSM153268 4 0.4199 0.6308 0.000 0.000 0.180 0.764 0.056
#> GSM153269 1 0.5107 0.3238 0.620 0.000 0.004 0.332 0.044
#> GSM153270 4 0.5380 0.6448 0.188 0.000 0.048 0.708 0.056
#> GSM153271 1 0.4736 0.4664 0.712 0.000 0.000 0.216 0.072
#> GSM153272 4 0.2678 0.7120 0.100 0.000 0.004 0.880 0.016
#> GSM153273 1 0.5234 0.5437 0.728 0.028 0.004 0.072 0.168
#> GSM153274 1 0.5956 0.2531 0.560 0.000 0.044 0.356 0.040
#> GSM153275 4 0.4197 0.5863 0.244 0.000 0.000 0.728 0.028
#> GSM153276 4 0.5776 0.5318 0.280 0.000 0.056 0.628 0.036
#> GSM153277 4 0.5532 0.5408 0.016 0.000 0.092 0.668 0.224
#> GSM153278 3 0.6074 0.3255 0.340 0.004 0.536 0.000 0.120
#> GSM153279 4 0.4750 0.5665 0.000 0.004 0.260 0.692 0.044
#> GSM153280 4 0.4743 0.6209 0.000 0.004 0.136 0.744 0.116
#> GSM153281 4 0.1787 0.7268 0.016 0.000 0.032 0.940 0.012
#> GSM153282 4 0.3141 0.6914 0.000 0.000 0.108 0.852 0.040
#> GSM153283 1 0.3424 0.5752 0.856 0.000 0.016 0.064 0.064
#> GSM153284 4 0.3497 0.7139 0.108 0.000 0.008 0.840 0.044
#> GSM153285 4 0.2905 0.7035 0.000 0.000 0.096 0.868 0.036
#> GSM153286 4 0.4254 0.5947 0.220 0.000 0.000 0.740 0.040
#> GSM153287 4 0.1731 0.7243 0.008 0.000 0.012 0.940 0.040
#> GSM153288 4 0.3841 0.6349 0.188 0.000 0.000 0.780 0.032
#> GSM153289 5 0.6703 0.1211 0.360 0.000 0.000 0.244 0.396
#> GSM153290 4 0.4183 0.6477 0.000 0.000 0.136 0.780 0.084
#> GSM153291 4 0.3559 0.6963 0.064 0.000 0.004 0.836 0.096
#> GSM153292 4 0.2067 0.7183 0.000 0.004 0.044 0.924 0.028
#> GSM153293 4 0.5639 0.3243 0.340 0.000 0.000 0.568 0.092
#> GSM153294 1 0.7890 0.2343 0.440 0.176 0.000 0.116 0.268
#> GSM153295 1 0.5524 0.3665 0.608 0.000 0.012 0.320 0.060
#> GSM153054 1 0.7032 0.2846 0.504 0.016 0.288 0.012 0.180
#> GSM153055 1 0.6805 0.1932 0.500 0.004 0.068 0.364 0.064
#> GSM153056 3 0.5166 0.5560 0.256 0.000 0.680 0.032 0.032
#> GSM153057 3 0.4406 0.6511 0.072 0.016 0.804 0.012 0.096
#> GSM153058 3 0.3171 0.6610 0.072 0.008 0.876 0.016 0.028
#> GSM153059 3 0.5382 0.6219 0.056 0.056 0.736 0.008 0.144
#> GSM153060 3 0.3912 0.6547 0.080 0.008 0.832 0.012 0.068
#> GSM153061 3 0.3734 0.6338 0.128 0.000 0.812 0.000 0.060
#> GSM153062 3 0.1969 0.6510 0.004 0.008 0.932 0.012 0.044
#> GSM153063 3 0.4581 0.5667 0.004 0.004 0.744 0.196 0.052
#> GSM153064 1 0.5546 0.4971 0.656 0.008 0.000 0.108 0.228
#> GSM153065 3 0.4965 0.6149 0.112 0.012 0.736 0.000 0.140
#> GSM153066 3 0.7056 0.4550 0.156 0.060 0.540 0.000 0.244
#> GSM153067 4 0.3968 0.6930 0.076 0.016 0.000 0.820 0.088
#> GSM153068 3 0.3372 0.6534 0.088 0.008 0.852 0.000 0.052
#> GSM153069 4 0.0740 0.7238 0.008 0.000 0.004 0.980 0.008
#> GSM153070 1 0.4677 0.5607 0.788 0.008 0.032 0.108 0.064
#> GSM153071 3 0.7499 0.1496 0.348 0.020 0.428 0.024 0.180
#> GSM153072 1 0.6769 0.3236 0.540 0.024 0.276 0.004 0.156
#> GSM153073 1 0.4320 0.5697 0.804 0.016 0.040 0.016 0.124
#> GSM153074 4 0.3152 0.6890 0.136 0.000 0.000 0.840 0.024
#> GSM153075 4 0.6341 0.4020 0.016 0.012 0.096 0.580 0.296
#> GSM153076 1 0.3375 0.5499 0.840 0.000 0.000 0.104 0.056
#> GSM153077 1 0.2149 0.5740 0.916 0.000 0.048 0.000 0.036
#> GSM153078 1 0.6295 0.0544 0.508 0.012 0.392 0.012 0.076
#> GSM153079 5 0.6093 -0.0840 0.448 0.028 0.040 0.008 0.476
#> GSM153080 3 0.4264 0.6173 0.020 0.000 0.788 0.148 0.044
#> GSM153081 1 0.4739 0.3736 0.652 0.000 0.016 0.012 0.320
#> GSM153082 1 0.7042 0.0818 0.392 0.348 0.012 0.000 0.248
#> GSM153083 1 0.6142 0.4414 0.612 0.048 0.072 0.000 0.268
#> GSM153084 3 0.8577 -0.0141 0.264 0.208 0.280 0.000 0.248
#> GSM153085 1 0.6490 0.2563 0.540 0.024 0.312 0.000 0.124
#> GSM153086 1 0.5504 0.5099 0.676 0.008 0.168 0.000 0.148
#> GSM153087 4 0.5417 0.6651 0.112 0.008 0.048 0.740 0.092
#> GSM153088 1 0.2507 0.5797 0.908 0.000 0.028 0.044 0.020
#> GSM153089 3 0.4982 0.5859 0.000 0.024 0.748 0.116 0.112
#> GSM153090 1 0.3084 0.5765 0.880 0.004 0.016 0.064 0.036
#> GSM153091 1 0.5189 0.5154 0.720 0.124 0.008 0.004 0.144
#> GSM153092 1 0.7162 0.1846 0.516 0.028 0.024 0.124 0.308
#> GSM153093 4 0.3037 0.7076 0.100 0.000 0.000 0.860 0.040
#> GSM153094 2 0.6999 -0.1686 0.340 0.424 0.008 0.004 0.224
#> GSM153095 1 0.7995 0.3062 0.420 0.044 0.232 0.024 0.280
#> GSM153096 1 0.4558 0.5258 0.740 0.000 0.000 0.080 0.180
#> GSM153097 1 0.5173 0.5295 0.708 0.028 0.056 0.000 0.208
#> GSM153098 4 0.7886 0.0722 0.268 0.084 0.000 0.408 0.240
#> GSM153099 4 0.5819 0.4072 0.336 0.000 0.048 0.584 0.032
#> GSM153100 1 0.6924 0.2285 0.456 0.012 0.000 0.248 0.284
#> GSM153101 1 0.6756 0.2962 0.448 0.008 0.200 0.000 0.344
#> GSM153102 5 0.6851 0.3565 0.024 0.148 0.164 0.044 0.620
#> GSM153103 1 0.6691 0.3789 0.540 0.020 0.228 0.000 0.212
#> GSM153104 4 0.2554 0.7183 0.000 0.000 0.072 0.892 0.036
#> GSM153106 5 0.6708 0.4889 0.136 0.080 0.004 0.156 0.624
#> GSM153107 5 0.6196 0.3554 0.268 0.028 0.004 0.092 0.608
#> GSM153108 4 0.5081 0.6316 0.036 0.000 0.064 0.736 0.164
#> GSM153109 5 0.6109 0.0434 0.036 0.432 0.040 0.004 0.488
#> GSM153110 1 0.4534 0.5312 0.728 0.008 0.012 0.016 0.236
#> GSM153111 1 0.4971 0.5314 0.716 0.036 0.032 0.000 0.216
#> GSM153112 1 0.8407 0.1214 0.356 0.208 0.000 0.184 0.252
#> GSM153113 2 0.4983 0.5263 0.064 0.664 0.000 0.000 0.272
#> GSM153114 5 0.6138 0.1021 0.112 0.004 0.000 0.420 0.464
#> GSM187532 3 0.7140 0.0164 0.016 0.252 0.372 0.000 0.360
#> GSM187533 5 0.5324 0.0318 0.008 0.420 0.036 0.000 0.536
#> GSM187534 2 0.4360 0.5232 0.020 0.680 0.000 0.000 0.300
#> GSM187535 5 0.5630 0.1076 0.044 0.412 0.000 0.016 0.528
#> GSM152906 2 0.2331 0.8008 0.020 0.900 0.000 0.000 0.080
#> GSM152907 2 0.1571 0.8148 0.000 0.936 0.004 0.000 0.060
#> GSM152908 2 0.1410 0.8085 0.000 0.940 0.000 0.000 0.060
#> GSM152909 2 0.6476 0.2923 0.000 0.524 0.240 0.004 0.232
#> GSM152910 2 0.3620 0.7532 0.000 0.824 0.068 0.000 0.108
#> GSM152911 2 0.1557 0.8095 0.000 0.940 0.008 0.000 0.052
#> GSM152912 2 0.1952 0.7993 0.000 0.912 0.004 0.000 0.084
#> GSM152913 2 0.4231 0.6846 0.000 0.776 0.160 0.004 0.060
#> GSM152914 2 0.0162 0.8164 0.000 0.996 0.000 0.000 0.004
#> GSM152915 2 0.0794 0.8153 0.000 0.972 0.000 0.000 0.028
#> GSM152916 2 0.1997 0.8127 0.000 0.924 0.036 0.000 0.040
#> GSM152917 2 0.1168 0.8155 0.008 0.960 0.000 0.000 0.032
#> GSM152918 2 0.1211 0.8140 0.016 0.960 0.000 0.000 0.024
#> GSM152919 2 0.0898 0.8170 0.008 0.972 0.000 0.000 0.020
#> GSM152920 2 0.1892 0.8013 0.000 0.916 0.004 0.000 0.080
#> GSM152921 2 0.1410 0.8082 0.000 0.940 0.000 0.000 0.060
#> GSM152922 2 0.2722 0.7827 0.000 0.872 0.020 0.000 0.108
#> GSM152923 2 0.1522 0.8168 0.012 0.944 0.000 0.000 0.044
#> GSM152924 2 0.3735 0.7624 0.004 0.816 0.048 0.000 0.132
#> GSM152925 2 0.4152 0.7323 0.000 0.772 0.060 0.000 0.168
#> GSM152926 2 0.3421 0.7447 0.016 0.816 0.000 0.004 0.164
#> GSM152927 2 0.4866 0.6976 0.004 0.732 0.116 0.000 0.148
#> GSM152928 2 0.6741 0.4804 0.048 0.564 0.132 0.000 0.256
#> GSM152929 2 0.2669 0.7846 0.020 0.876 0.000 0.000 0.104
#> GSM152930 2 0.1597 0.8134 0.012 0.940 0.000 0.000 0.048
cbind(get_classes(res, k = 6), get_membership(res, k = 6))
#> class entropy silhouette p1 p2 p3 p4 p5 p6
#> GSM152839 1 0.602 0.07996 0.492 0.000 0.372 0.000 0.084 0.052
#> GSM152840 4 0.533 0.35323 0.000 0.000 0.328 0.584 0.044 0.044
#> GSM152841 4 0.157 0.71207 0.004 0.000 0.016 0.944 0.008 0.028
#> GSM152842 3 0.532 0.44344 0.244 0.000 0.632 0.000 0.100 0.024
#> GSM152843 3 0.568 0.52895 0.180 0.000 0.668 0.024 0.076 0.052
#> GSM152844 3 0.649 0.28642 0.000 0.000 0.520 0.260 0.072 0.148
#> GSM152845 6 0.579 0.02682 0.000 0.020 0.360 0.016 0.072 0.532
#> GSM152846 3 0.582 0.37828 0.000 0.004 0.620 0.108 0.052 0.216
#> GSM152847 3 0.601 0.30833 0.368 0.000 0.512 0.016 0.072 0.032
#> GSM152848 1 0.586 0.47197 0.652 0.000 0.144 0.008 0.088 0.108
#> GSM152849 3 0.649 0.42770 0.104 0.008 0.564 0.000 0.100 0.224
#> GSM152850 1 0.594 0.06843 0.508 0.004 0.364 0.000 0.092 0.032
#> GSM152851 4 0.602 0.27302 0.004 0.004 0.332 0.540 0.048 0.072
#> GSM152852 6 0.636 0.02710 0.000 0.000 0.360 0.120 0.056 0.464
#> GSM152853 3 0.653 0.20245 0.004 0.000 0.464 0.328 0.040 0.164
#> GSM152854 3 0.633 0.34745 0.016 0.040 0.568 0.024 0.060 0.292
#> GSM152855 6 0.655 0.31464 0.164 0.004 0.000 0.220 0.072 0.540
#> GSM153238 3 0.673 0.28009 0.124 0.012 0.480 0.004 0.328 0.052
#> GSM153239 3 0.460 0.47904 0.016 0.000 0.724 0.204 0.024 0.032
#> GSM153240 4 0.522 0.68623 0.144 0.000 0.044 0.716 0.024 0.072
#> GSM153241 3 0.466 0.58000 0.084 0.000 0.772 0.028 0.072 0.044
#> GSM153242 3 0.569 0.44083 0.000 0.028 0.676 0.092 0.048 0.156
#> GSM153243 3 0.736 0.40252 0.176 0.044 0.516 0.000 0.124 0.140
#> GSM153244 4 0.815 0.10707 0.000 0.192 0.232 0.388 0.068 0.120
#> GSM153245 3 0.542 0.42344 0.004 0.000 0.612 0.260 0.112 0.012
#> GSM153246 3 0.434 0.53797 0.024 0.008 0.756 0.004 0.176 0.032
#> GSM153247 3 0.562 0.40774 0.068 0.004 0.612 0.020 0.280 0.016
#> GSM153248 1 0.494 0.32349 0.612 0.004 0.004 0.000 0.316 0.064
#> GSM153249 4 0.297 0.71720 0.040 0.000 0.008 0.868 0.072 0.012
#> GSM153250 1 0.318 0.54238 0.844 0.008 0.008 0.116 0.004 0.020
#> GSM153251 3 0.543 0.49275 0.000 0.032 0.716 0.076 0.080 0.096
#> GSM153252 4 0.483 0.68685 0.100 0.000 0.048 0.748 0.092 0.012
#> GSM153253 4 0.261 0.69214 0.000 0.000 0.092 0.876 0.020 0.012
#> GSM153254 6 0.809 -0.06175 0.020 0.076 0.344 0.112 0.076 0.372
#> GSM153255 4 0.225 0.71617 0.092 0.000 0.000 0.888 0.000 0.020
#> GSM153256 4 0.459 0.17172 0.480 0.000 0.000 0.484 0.000 0.036
#> GSM153257 4 0.461 0.69870 0.108 0.000 0.036 0.752 0.100 0.004
#> GSM153258 1 0.698 0.39364 0.540 0.032 0.044 0.024 0.100 0.260
#> GSM153259 1 0.543 0.44886 0.624 0.000 0.004 0.012 0.132 0.228
#> GSM153260 3 0.739 0.16396 0.316 0.000 0.340 0.000 0.128 0.216
#> GSM153261 6 0.669 -0.06700 0.048 0.004 0.380 0.000 0.164 0.404
#> GSM153262 4 0.596 0.61247 0.064 0.000 0.028 0.660 0.124 0.124
#> GSM153263 1 0.435 0.54675 0.784 0.000 0.008 0.088 0.052 0.068
#> GSM153264 1 0.298 0.55466 0.868 0.000 0.044 0.000 0.052 0.036
#> GSM153265 4 0.337 0.69796 0.000 0.000 0.048 0.840 0.032 0.080
#> GSM153266 1 0.439 0.56699 0.784 0.004 0.040 0.016 0.040 0.116
#> GSM153267 1 0.514 0.04513 0.544 0.004 0.004 0.400 0.028 0.020
#> GSM153268 4 0.327 0.66895 0.000 0.000 0.128 0.828 0.016 0.028
#> GSM153269 1 0.486 0.45192 0.692 0.000 0.016 0.228 0.016 0.048
#> GSM153270 4 0.670 0.55357 0.220 0.000 0.060 0.568 0.108 0.044
#> GSM153271 1 0.438 0.50766 0.756 0.012 0.008 0.176 0.032 0.016
#> GSM153272 4 0.320 0.70645 0.148 0.000 0.008 0.824 0.012 0.008
#> GSM153273 1 0.483 0.50946 0.736 0.012 0.004 0.056 0.160 0.032
#> GSM153274 1 0.561 0.25237 0.580 0.000 0.048 0.324 0.028 0.020
#> GSM153275 4 0.489 0.51434 0.328 0.000 0.000 0.612 0.028 0.032
#> GSM153276 4 0.700 0.23841 0.372 0.000 0.084 0.432 0.036 0.076
#> GSM153277 4 0.679 0.31205 0.040 0.000 0.096 0.484 0.048 0.332
#> GSM153278 3 0.697 0.23206 0.320 0.000 0.424 0.004 0.072 0.180
#> GSM153279 4 0.465 0.62462 0.000 0.000 0.152 0.736 0.064 0.048
#> GSM153280 4 0.443 0.63982 0.004 0.000 0.076 0.752 0.020 0.148
#> GSM153281 4 0.267 0.72508 0.064 0.000 0.020 0.888 0.016 0.012
#> GSM153282 4 0.262 0.69728 0.000 0.000 0.068 0.884 0.020 0.028
#> GSM153283 1 0.288 0.57077 0.884 0.000 0.024 0.024 0.028 0.040
#> GSM153284 4 0.492 0.68029 0.164 0.000 0.020 0.728 0.044 0.044
#> GSM153285 4 0.252 0.70557 0.000 0.000 0.068 0.888 0.032 0.012
#> GSM153286 4 0.489 0.51077 0.304 0.000 0.004 0.624 0.004 0.064
#> GSM153287 4 0.207 0.72136 0.024 0.000 0.012 0.920 0.040 0.004
#> GSM153288 4 0.399 0.63270 0.240 0.000 0.000 0.724 0.008 0.028
#> GSM153289 6 0.695 0.17021 0.268 0.004 0.000 0.192 0.076 0.460
#> GSM153290 4 0.380 0.66366 0.000 0.004 0.080 0.800 0.008 0.108
#> GSM153291 4 0.379 0.69831 0.044 0.000 0.004 0.816 0.040 0.096
#> GSM153292 4 0.168 0.71417 0.000 0.000 0.016 0.936 0.036 0.012
#> GSM153293 4 0.564 0.35448 0.352 0.000 0.000 0.536 0.028 0.084
#> GSM153294 5 0.680 0.25241 0.288 0.072 0.000 0.080 0.520 0.040
#> GSM153295 1 0.675 0.38406 0.564 0.000 0.044 0.224 0.096 0.072
#> GSM153054 1 0.705 0.00540 0.388 0.012 0.248 0.004 0.316 0.032
#> GSM153055 1 0.745 0.34871 0.528 0.020 0.092 0.224 0.072 0.064
#> GSM153056 3 0.596 0.44243 0.292 0.000 0.576 0.012 0.064 0.056
#> GSM153057 3 0.621 0.49102 0.064 0.040 0.648 0.008 0.072 0.168
#> GSM153058 3 0.348 0.57659 0.064 0.004 0.852 0.020 0.032 0.028
#> GSM153059 3 0.746 0.29394 0.036 0.108 0.480 0.004 0.120 0.252
#> GSM153060 3 0.489 0.55705 0.044 0.008 0.752 0.040 0.132 0.024
#> GSM153061 3 0.515 0.52182 0.068 0.008 0.704 0.000 0.168 0.052
#> GSM153062 3 0.341 0.56992 0.008 0.008 0.848 0.016 0.084 0.036
#> GSM153063 3 0.540 0.43731 0.000 0.000 0.624 0.224 0.136 0.016
#> GSM153064 1 0.569 0.42889 0.620 0.000 0.000 0.056 0.228 0.096
#> GSM153065 3 0.620 0.43535 0.068 0.008 0.584 0.000 0.104 0.236
#> GSM153066 3 0.749 -0.00663 0.044 0.048 0.356 0.000 0.348 0.204
#> GSM153067 4 0.344 0.71191 0.068 0.004 0.000 0.824 0.100 0.004
#> GSM153068 3 0.418 0.57369 0.040 0.008 0.792 0.000 0.104 0.056
#> GSM153069 4 0.118 0.72138 0.024 0.000 0.004 0.960 0.008 0.004
#> GSM153070 1 0.590 0.51728 0.700 0.040 0.084 0.016 0.080 0.080
#> GSM153071 3 0.730 0.05850 0.152 0.020 0.392 0.036 0.376 0.024
#> GSM153072 1 0.682 -0.08200 0.392 0.008 0.236 0.000 0.332 0.032
#> GSM153073 1 0.522 0.51611 0.752 0.052 0.060 0.028 0.084 0.024
#> GSM153074 4 0.356 0.68648 0.180 0.000 0.000 0.784 0.008 0.028
#> GSM153075 4 0.623 0.20058 0.028 0.004 0.056 0.456 0.032 0.424
#> GSM153076 1 0.240 0.56087 0.900 0.000 0.000 0.048 0.028 0.024
#> GSM153077 1 0.374 0.53018 0.820 0.000 0.068 0.008 0.084 0.020
#> GSM153078 1 0.763 -0.01326 0.396 0.024 0.320 0.004 0.112 0.144
#> GSM153079 6 0.559 0.14941 0.316 0.008 0.020 0.000 0.080 0.576
#> GSM153080 3 0.549 0.52665 0.012 0.000 0.668 0.132 0.160 0.028
#> GSM153081 1 0.546 0.34322 0.544 0.000 0.016 0.000 0.088 0.352
#> GSM153082 5 0.631 0.37010 0.200 0.256 0.016 0.000 0.516 0.012
#> GSM153083 1 0.701 0.35711 0.504 0.044 0.040 0.000 0.240 0.172
#> GSM153084 5 0.836 0.19673 0.088 0.124 0.208 0.000 0.364 0.216
#> GSM153085 5 0.737 0.06433 0.312 0.016 0.276 0.000 0.336 0.060
#> GSM153086 1 0.585 0.38316 0.620 0.000 0.088 0.000 0.204 0.088
#> GSM153087 4 0.504 0.67552 0.108 0.000 0.096 0.728 0.060 0.008
#> GSM153088 1 0.225 0.56071 0.916 0.004 0.028 0.020 0.028 0.004
#> GSM153089 3 0.676 0.37901 0.000 0.028 0.560 0.068 0.156 0.188
#> GSM153090 1 0.241 0.56052 0.900 0.000 0.024 0.044 0.032 0.000
#> GSM153091 1 0.512 0.47109 0.712 0.108 0.008 0.000 0.132 0.040
#> GSM153092 1 0.737 0.31833 0.492 0.048 0.032 0.044 0.092 0.292
#> GSM153093 4 0.341 0.71579 0.128 0.000 0.000 0.820 0.036 0.016
#> GSM153094 1 0.711 0.13291 0.420 0.276 0.008 0.000 0.064 0.232
#> GSM153095 5 0.633 0.38539 0.176 0.008 0.160 0.012 0.600 0.044
#> GSM153096 1 0.492 0.53418 0.720 0.008 0.004 0.024 0.076 0.168
#> GSM153097 1 0.563 0.44507 0.640 0.012 0.044 0.000 0.228 0.076
#> GSM153098 5 0.756 0.11770 0.224 0.056 0.000 0.304 0.376 0.040
#> GSM153099 4 0.607 0.30922 0.380 0.000 0.036 0.500 0.064 0.020
#> GSM153100 1 0.734 0.30653 0.456 0.012 0.000 0.140 0.152 0.240
#> GSM153101 5 0.738 0.23047 0.212 0.004 0.124 0.000 0.408 0.252
#> GSM153102 6 0.504 0.41052 0.024 0.024 0.100 0.028 0.068 0.756
#> GSM153103 1 0.695 0.25677 0.484 0.000 0.140 0.000 0.144 0.232
#> GSM153104 4 0.377 0.70419 0.016 0.000 0.060 0.824 0.080 0.020
#> GSM153106 6 0.510 0.41341 0.092 0.028 0.000 0.076 0.064 0.740
#> GSM153107 6 0.588 0.36691 0.112 0.028 0.000 0.064 0.128 0.668
#> GSM153108 4 0.623 0.48108 0.044 0.004 0.032 0.580 0.064 0.276
#> GSM153109 6 0.577 0.33470 0.028 0.168 0.040 0.008 0.080 0.676
#> GSM153110 1 0.534 0.47329 0.648 0.000 0.008 0.008 0.184 0.152
#> GSM153111 1 0.587 0.42332 0.620 0.008 0.044 0.000 0.212 0.116
#> GSM153112 1 0.810 -0.04732 0.352 0.124 0.000 0.144 0.312 0.068
#> GSM153113 5 0.673 0.18092 0.032 0.308 0.008 0.004 0.460 0.188
#> GSM153114 6 0.588 0.35808 0.080 0.012 0.000 0.244 0.052 0.612
#> GSM187532 6 0.708 0.20163 0.000 0.172 0.284 0.000 0.112 0.432
#> GSM187533 6 0.621 0.20975 0.004 0.248 0.032 0.000 0.172 0.544
#> GSM187534 2 0.644 0.09764 0.000 0.424 0.016 0.004 0.224 0.332
#> GSM187535 6 0.721 0.05907 0.048 0.212 0.000 0.032 0.256 0.452
#> GSM152906 2 0.379 0.70327 0.012 0.772 0.004 0.000 0.188 0.024
#> GSM152907 2 0.304 0.74757 0.000 0.836 0.000 0.008 0.132 0.024
#> GSM152908 2 0.123 0.75168 0.000 0.956 0.004 0.000 0.024 0.016
#> GSM152909 2 0.700 0.05661 0.000 0.424 0.164 0.000 0.100 0.312
#> GSM152910 2 0.396 0.66997 0.000 0.804 0.064 0.000 0.064 0.068
#> GSM152911 2 0.158 0.75394 0.004 0.944 0.008 0.000 0.020 0.024
#> GSM152912 2 0.233 0.73515 0.000 0.900 0.008 0.000 0.044 0.048
#> GSM152913 2 0.486 0.64599 0.000 0.720 0.100 0.000 0.140 0.040
#> GSM152914 2 0.169 0.76072 0.000 0.924 0.000 0.000 0.064 0.012
#> GSM152915 2 0.141 0.75786 0.000 0.944 0.000 0.000 0.036 0.020
#> GSM152916 2 0.392 0.70519 0.000 0.748 0.016 0.000 0.212 0.024
#> GSM152917 2 0.127 0.75922 0.000 0.940 0.000 0.000 0.060 0.000
#> GSM152918 2 0.159 0.75703 0.004 0.924 0.000 0.000 0.072 0.000
#> GSM152919 2 0.141 0.76063 0.000 0.936 0.000 0.000 0.060 0.004
#> GSM152920 2 0.222 0.73673 0.004 0.908 0.004 0.000 0.040 0.044
#> GSM152921 2 0.161 0.75461 0.000 0.936 0.004 0.000 0.044 0.016
#> GSM152922 2 0.342 0.70046 0.000 0.840 0.040 0.000 0.056 0.064
#> GSM152923 2 0.333 0.71629 0.004 0.792 0.004 0.000 0.188 0.012
#> GSM152924 2 0.528 0.42880 0.004 0.516 0.024 0.000 0.416 0.040
#> GSM152925 2 0.519 0.35703 0.004 0.496 0.048 0.000 0.440 0.012
#> GSM152926 2 0.427 0.56251 0.012 0.628 0.000 0.000 0.348 0.012
#> GSM152927 2 0.530 0.50301 0.004 0.560 0.048 0.000 0.364 0.024
#> GSM152928 5 0.604 -0.13907 0.008 0.360 0.076 0.000 0.512 0.044
#> GSM152929 2 0.389 0.62878 0.004 0.692 0.008 0.000 0.292 0.004
#> GSM152930 2 0.293 0.73873 0.008 0.844 0.004 0.000 0.132 0.012
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 tissue(p) k
#> MAD:NMF 154 6.80e-16 2
#> MAD:NMF 148 3.75e-23 3
#> MAD:NMF 132 4.45e-23 4
#> MAD:NMF 103 2.76e-20 5
#> MAD:NMF 75 1.15e-15 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 12013 rows and 164 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 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 0.983 0.992 0.3082 0.699 0.699
#> 3 3 1.000 0.977 0.990 0.0262 0.996 0.994
#> 4 4 0.884 0.933 0.953 0.1131 1.000 1.000
#> 5 5 0.518 0.743 0.856 0.2990 0.952 0.931
#> 6 6 0.460 0.565 0.806 0.1128 0.863 0.789
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
#> GSM152839 1 0.0000 0.991 1.000 0.000
#> GSM152840 1 0.2603 0.955 0.956 0.044
#> GSM152841 1 0.0376 0.989 0.996 0.004
#> GSM152842 1 0.0000 0.991 1.000 0.000
#> GSM152843 1 0.0000 0.991 1.000 0.000
#> GSM152844 1 0.2603 0.955 0.956 0.044
#> GSM152845 2 0.3114 0.938 0.056 0.944
#> GSM152846 1 0.8207 0.669 0.744 0.256
#> GSM152847 1 0.0000 0.991 1.000 0.000
#> GSM152848 1 0.0000 0.991 1.000 0.000
#> GSM152849 1 0.0000 0.991 1.000 0.000
#> GSM152850 1 0.0000 0.991 1.000 0.000
#> GSM152851 1 0.0000 0.991 1.000 0.000
#> GSM152852 1 0.7376 0.749 0.792 0.208
#> GSM152853 1 0.2603 0.955 0.956 0.044
#> GSM152854 1 0.1414 0.976 0.980 0.020
#> GSM152855 1 0.0000 0.991 1.000 0.000
#> GSM153238 1 0.0000 0.991 1.000 0.000
#> GSM153239 1 0.0000 0.991 1.000 0.000
#> GSM153240 1 0.0000 0.991 1.000 0.000
#> GSM153241 1 0.0000 0.991 1.000 0.000
#> GSM153242 1 0.3114 0.944 0.944 0.056
#> GSM153243 1 0.0672 0.986 0.992 0.008
#> GSM153244 1 0.2043 0.967 0.968 0.032
#> GSM153245 1 0.0000 0.991 1.000 0.000
#> GSM153246 1 0.0000 0.991 1.000 0.000
#> GSM153247 1 0.0000 0.991 1.000 0.000
#> GSM153248 1 0.0000 0.991 1.000 0.000
#> GSM153249 1 0.0000 0.991 1.000 0.000
#> GSM153250 1 0.0000 0.991 1.000 0.000
#> GSM153251 1 0.2236 0.963 0.964 0.036
#> GSM153252 1 0.0000 0.991 1.000 0.000
#> GSM153253 1 0.0376 0.989 0.996 0.004
#> GSM153254 1 0.0000 0.991 1.000 0.000
#> GSM153255 1 0.0000 0.991 1.000 0.000
#> GSM153256 1 0.0000 0.991 1.000 0.000
#> GSM153257 1 0.0000 0.991 1.000 0.000
#> GSM153258 1 0.0000 0.991 1.000 0.000
#> GSM153259 1 0.0000 0.991 1.000 0.000
#> GSM153260 1 0.0000 0.991 1.000 0.000
#> GSM153261 1 0.0000 0.991 1.000 0.000
#> GSM153262 1 0.0000 0.991 1.000 0.000
#> GSM153263 1 0.0000 0.991 1.000 0.000
#> GSM153264 1 0.0000 0.991 1.000 0.000
#> GSM153265 1 0.0000 0.991 1.000 0.000
#> GSM153266 1 0.0000 0.991 1.000 0.000
#> GSM153267 1 0.0000 0.991 1.000 0.000
#> GSM153268 1 0.0376 0.989 0.996 0.004
#> GSM153269 1 0.0000 0.991 1.000 0.000
#> GSM153270 1 0.0000 0.991 1.000 0.000
#> GSM153271 1 0.0000 0.991 1.000 0.000
#> GSM153272 1 0.0000 0.991 1.000 0.000
#> GSM153273 1 0.0000 0.991 1.000 0.000
#> GSM153274 1 0.0000 0.991 1.000 0.000
#> GSM153275 1 0.0000 0.991 1.000 0.000
#> GSM153276 1 0.0000 0.991 1.000 0.000
#> GSM153277 1 0.0000 0.991 1.000 0.000
#> GSM153278 1 0.0000 0.991 1.000 0.000
#> GSM153279 1 0.0000 0.991 1.000 0.000
#> GSM153280 1 0.0000 0.991 1.000 0.000
#> GSM153281 1 0.0000 0.991 1.000 0.000
#> GSM153282 1 0.0376 0.989 0.996 0.004
#> GSM153283 1 0.0000 0.991 1.000 0.000
#> GSM153284 1 0.0000 0.991 1.000 0.000
#> GSM153285 1 0.0000 0.991 1.000 0.000
#> GSM153286 1 0.0000 0.991 1.000 0.000
#> GSM153287 1 0.0000 0.991 1.000 0.000
#> GSM153288 1 0.0000 0.991 1.000 0.000
#> GSM153289 1 0.0000 0.991 1.000 0.000
#> GSM153290 1 0.0000 0.991 1.000 0.000
#> GSM153291 1 0.0000 0.991 1.000 0.000
#> GSM153292 1 0.0000 0.991 1.000 0.000
#> GSM153293 1 0.0000 0.991 1.000 0.000
#> GSM153294 1 0.0000 0.991 1.000 0.000
#> GSM153295 1 0.0000 0.991 1.000 0.000
#> GSM153054 1 0.0000 0.991 1.000 0.000
#> GSM153055 1 0.0000 0.991 1.000 0.000
#> GSM153056 1 0.0000 0.991 1.000 0.000
#> GSM153057 1 0.2043 0.967 0.968 0.032
#> GSM153058 1 0.2236 0.963 0.964 0.036
#> GSM153059 1 0.2043 0.967 0.968 0.032
#> GSM153060 1 0.2043 0.966 0.968 0.032
#> GSM153061 1 0.0000 0.991 1.000 0.000
#> GSM153062 2 0.6148 0.823 0.152 0.848
#> GSM153063 1 0.0000 0.991 1.000 0.000
#> GSM153064 1 0.0000 0.991 1.000 0.000
#> GSM153065 1 0.0000 0.991 1.000 0.000
#> GSM153066 1 0.4298 0.907 0.912 0.088
#> GSM153067 1 0.0000 0.991 1.000 0.000
#> GSM153068 1 0.0672 0.986 0.992 0.008
#> GSM153069 1 0.0000 0.991 1.000 0.000
#> GSM153070 1 0.0000 0.991 1.000 0.000
#> GSM153071 1 0.0000 0.991 1.000 0.000
#> GSM153072 1 0.0000 0.991 1.000 0.000
#> GSM153073 1 0.0000 0.991 1.000 0.000
#> GSM153074 1 0.0000 0.991 1.000 0.000
#> GSM153075 1 0.0000 0.991 1.000 0.000
#> GSM153076 1 0.0000 0.991 1.000 0.000
#> GSM153077 1 0.0000 0.991 1.000 0.000
#> GSM153078 1 0.0000 0.991 1.000 0.000
#> GSM153079 1 0.0000 0.991 1.000 0.000
#> GSM153080 1 0.0000 0.991 1.000 0.000
#> GSM153081 1 0.0000 0.991 1.000 0.000
#> GSM153082 1 0.0938 0.983 0.988 0.012
#> GSM153083 1 0.0000 0.991 1.000 0.000
#> GSM153084 1 0.2236 0.962 0.964 0.036
#> GSM153085 1 0.0376 0.989 0.996 0.004
#> GSM153086 1 0.0000 0.991 1.000 0.000
#> GSM153087 1 0.0000 0.991 1.000 0.000
#> GSM153088 1 0.0000 0.991 1.000 0.000
#> GSM153089 1 0.2236 0.963 0.964 0.036
#> GSM153090 1 0.0000 0.991 1.000 0.000
#> GSM153091 1 0.0000 0.991 1.000 0.000
#> GSM153092 1 0.0000 0.991 1.000 0.000
#> GSM153093 1 0.0000 0.991 1.000 0.000
#> GSM153094 1 0.0000 0.991 1.000 0.000
#> GSM153095 1 0.0000 0.991 1.000 0.000
#> GSM153096 1 0.0000 0.991 1.000 0.000
#> GSM153097 1 0.0000 0.991 1.000 0.000
#> GSM153098 1 0.0000 0.991 1.000 0.000
#> GSM153099 1 0.0000 0.991 1.000 0.000
#> GSM153100 1 0.0000 0.991 1.000 0.000
#> GSM153101 1 0.0000 0.991 1.000 0.000
#> GSM153102 1 0.0672 0.986 0.992 0.008
#> GSM153103 1 0.0376 0.989 0.996 0.004
#> GSM153104 1 0.0000 0.991 1.000 0.000
#> GSM153106 1 0.0000 0.991 1.000 0.000
#> GSM153107 1 0.0000 0.991 1.000 0.000
#> GSM153108 1 0.0000 0.991 1.000 0.000
#> GSM153109 1 0.0672 0.986 0.992 0.008
#> GSM153110 1 0.0000 0.991 1.000 0.000
#> GSM153111 1 0.0000 0.991 1.000 0.000
#> GSM153112 1 0.0000 0.991 1.000 0.000
#> GSM153113 1 0.2236 0.963 0.964 0.036
#> GSM153114 1 0.0000 0.991 1.000 0.000
#> GSM187532 2 0.0000 0.993 0.000 1.000
#> GSM187533 2 0.0000 0.993 0.000 1.000
#> GSM187534 2 0.0000 0.993 0.000 1.000
#> GSM187535 1 0.2236 0.963 0.964 0.036
#> GSM152906 2 0.0000 0.993 0.000 1.000
#> GSM152907 2 0.0000 0.993 0.000 1.000
#> GSM152908 2 0.0000 0.993 0.000 1.000
#> GSM152909 2 0.0000 0.993 0.000 1.000
#> GSM152910 2 0.0000 0.993 0.000 1.000
#> GSM152911 2 0.0000 0.993 0.000 1.000
#> GSM152912 2 0.0000 0.993 0.000 1.000
#> GSM152913 2 0.0000 0.993 0.000 1.000
#> GSM152914 2 0.0000 0.993 0.000 1.000
#> GSM152915 2 0.0000 0.993 0.000 1.000
#> GSM152916 2 0.0000 0.993 0.000 1.000
#> GSM152917 2 0.0000 0.993 0.000 1.000
#> GSM152918 2 0.0000 0.993 0.000 1.000
#> GSM152919 2 0.0000 0.993 0.000 1.000
#> GSM152920 2 0.0000 0.993 0.000 1.000
#> GSM152921 2 0.0000 0.993 0.000 1.000
#> GSM152922 2 0.0000 0.993 0.000 1.000
#> GSM152923 2 0.0000 0.993 0.000 1.000
#> GSM152924 2 0.0000 0.993 0.000 1.000
#> GSM152925 2 0.0000 0.993 0.000 1.000
#> GSM152926 2 0.0000 0.993 0.000 1.000
#> GSM152927 2 0.0000 0.993 0.000 1.000
#> GSM152928 2 0.0000 0.993 0.000 1.000
#> GSM152929 2 0.0000 0.993 0.000 1.000
#> GSM152930 2 0.0000 0.993 0.000 1.000
cbind(get_classes(res, k = 3), get_membership(res, k = 3))
#> class entropy silhouette p1 p2 p3
#> GSM152839 1 0.0000 0.990 1.000 0.000 0.000
#> GSM152840 1 0.1643 0.952 0.956 0.000 0.044
#> GSM152841 1 0.0237 0.988 0.996 0.000 0.004
#> GSM152842 1 0.0000 0.990 1.000 0.000 0.000
#> GSM152843 1 0.0000 0.990 1.000 0.000 0.000
#> GSM152844 1 0.1860 0.944 0.948 0.000 0.052
#> GSM152845 3 0.0237 0.802 0.000 0.004 0.996
#> GSM152846 1 0.5397 0.607 0.720 0.000 0.280
#> GSM152847 1 0.0000 0.990 1.000 0.000 0.000
#> GSM152848 1 0.0000 0.990 1.000 0.000 0.000
#> GSM152849 1 0.0000 0.990 1.000 0.000 0.000
#> GSM152850 1 0.0000 0.990 1.000 0.000 0.000
#> GSM152851 1 0.0000 0.990 1.000 0.000 0.000
#> GSM152852 1 0.4931 0.697 0.768 0.000 0.232
#> GSM152853 1 0.1643 0.952 0.956 0.000 0.044
#> GSM152854 1 0.0892 0.975 0.980 0.000 0.020
#> GSM152855 1 0.0000 0.990 1.000 0.000 0.000
#> GSM153238 1 0.0000 0.990 1.000 0.000 0.000
#> GSM153239 1 0.0000 0.990 1.000 0.000 0.000
#> GSM153240 1 0.0000 0.990 1.000 0.000 0.000
#> GSM153241 1 0.0000 0.990 1.000 0.000 0.000
#> GSM153242 1 0.1964 0.942 0.944 0.000 0.056
#> GSM153243 1 0.0424 0.985 0.992 0.000 0.008
#> GSM153244 1 0.1289 0.965 0.968 0.000 0.032
#> GSM153245 1 0.0000 0.990 1.000 0.000 0.000
#> GSM153246 1 0.0000 0.990 1.000 0.000 0.000
#> GSM153247 1 0.0000 0.990 1.000 0.000 0.000
#> GSM153248 1 0.0000 0.990 1.000 0.000 0.000
#> GSM153249 1 0.0000 0.990 1.000 0.000 0.000
#> GSM153250 1 0.0000 0.990 1.000 0.000 0.000
#> GSM153251 1 0.1411 0.961 0.964 0.000 0.036
#> GSM153252 1 0.0000 0.990 1.000 0.000 0.000
#> GSM153253 1 0.0237 0.988 0.996 0.000 0.004
#> GSM153254 1 0.0000 0.990 1.000 0.000 0.000
#> GSM153255 1 0.0000 0.990 1.000 0.000 0.000
#> GSM153256 1 0.0000 0.990 1.000 0.000 0.000
#> GSM153257 1 0.0000 0.990 1.000 0.000 0.000
#> GSM153258 1 0.0000 0.990 1.000 0.000 0.000
#> GSM153259 1 0.0000 0.990 1.000 0.000 0.000
#> GSM153260 1 0.0000 0.990 1.000 0.000 0.000
#> GSM153261 1 0.0000 0.990 1.000 0.000 0.000
#> GSM153262 1 0.0000 0.990 1.000 0.000 0.000
#> GSM153263 1 0.0000 0.990 1.000 0.000 0.000
#> GSM153264 1 0.0000 0.990 1.000 0.000 0.000
#> GSM153265 1 0.0000 0.990 1.000 0.000 0.000
#> GSM153266 1 0.0000 0.990 1.000 0.000 0.000
#> GSM153267 1 0.0000 0.990 1.000 0.000 0.000
#> GSM153268 1 0.0237 0.988 0.996 0.000 0.004
#> GSM153269 1 0.0000 0.990 1.000 0.000 0.000
#> GSM153270 1 0.0000 0.990 1.000 0.000 0.000
#> GSM153271 1 0.0000 0.990 1.000 0.000 0.000
#> GSM153272 1 0.0000 0.990 1.000 0.000 0.000
#> GSM153273 1 0.0000 0.990 1.000 0.000 0.000
#> GSM153274 1 0.0000 0.990 1.000 0.000 0.000
#> GSM153275 1 0.0000 0.990 1.000 0.000 0.000
#> GSM153276 1 0.0000 0.990 1.000 0.000 0.000
#> GSM153277 1 0.0000 0.990 1.000 0.000 0.000
#> GSM153278 1 0.0000 0.990 1.000 0.000 0.000
#> GSM153279 1 0.0000 0.990 1.000 0.000 0.000
#> GSM153280 1 0.0000 0.990 1.000 0.000 0.000
#> GSM153281 1 0.0000 0.990 1.000 0.000 0.000
#> GSM153282 1 0.0237 0.988 0.996 0.000 0.004
#> GSM153283 1 0.0000 0.990 1.000 0.000 0.000
#> GSM153284 1 0.0000 0.990 1.000 0.000 0.000
#> GSM153285 1 0.0000 0.990 1.000 0.000 0.000
#> GSM153286 1 0.0000 0.990 1.000 0.000 0.000
#> GSM153287 1 0.0000 0.990 1.000 0.000 0.000
#> GSM153288 1 0.0000 0.990 1.000 0.000 0.000
#> GSM153289 1 0.0000 0.990 1.000 0.000 0.000
#> GSM153290 1 0.0000 0.990 1.000 0.000 0.000
#> GSM153291 1 0.0000 0.990 1.000 0.000 0.000
#> GSM153292 1 0.0000 0.990 1.000 0.000 0.000
#> GSM153293 1 0.0000 0.990 1.000 0.000 0.000
#> GSM153294 1 0.0000 0.990 1.000 0.000 0.000
#> GSM153295 1 0.0000 0.990 1.000 0.000 0.000
#> GSM153054 1 0.0000 0.990 1.000 0.000 0.000
#> GSM153055 1 0.0000 0.990 1.000 0.000 0.000
#> GSM153056 1 0.0000 0.990 1.000 0.000 0.000
#> GSM153057 1 0.1289 0.965 0.968 0.000 0.032
#> GSM153058 1 0.1411 0.961 0.964 0.000 0.036
#> GSM153059 1 0.1289 0.965 0.968 0.000 0.032
#> GSM153060 1 0.1289 0.964 0.968 0.000 0.032
#> GSM153061 1 0.0000 0.990 1.000 0.000 0.000
#> GSM153062 3 0.2796 0.807 0.092 0.000 0.908
#> GSM153063 1 0.0000 0.990 1.000 0.000 0.000
#> GSM153064 1 0.0000 0.990 1.000 0.000 0.000
#> GSM153065 1 0.0000 0.990 1.000 0.000 0.000
#> GSM153066 1 0.2860 0.893 0.912 0.084 0.004
#> GSM153067 1 0.0000 0.990 1.000 0.000 0.000
#> GSM153068 1 0.0424 0.985 0.992 0.000 0.008
#> GSM153069 1 0.0000 0.990 1.000 0.000 0.000
#> GSM153070 1 0.0000 0.990 1.000 0.000 0.000
#> GSM153071 1 0.0000 0.990 1.000 0.000 0.000
#> GSM153072 1 0.0000 0.990 1.000 0.000 0.000
#> GSM153073 1 0.0000 0.990 1.000 0.000 0.000
#> GSM153074 1 0.0000 0.990 1.000 0.000 0.000
#> GSM153075 1 0.0000 0.990 1.000 0.000 0.000
#> GSM153076 1 0.0000 0.990 1.000 0.000 0.000
#> GSM153077 1 0.0000 0.990 1.000 0.000 0.000
#> GSM153078 1 0.0000 0.990 1.000 0.000 0.000
#> GSM153079 1 0.0000 0.990 1.000 0.000 0.000
#> GSM153080 1 0.0000 0.990 1.000 0.000 0.000
#> GSM153081 1 0.0000 0.990 1.000 0.000 0.000
#> GSM153082 1 0.0592 0.980 0.988 0.012 0.000
#> GSM153083 1 0.0000 0.990 1.000 0.000 0.000
#> GSM153084 1 0.1525 0.957 0.964 0.032 0.004
#> GSM153085 1 0.0237 0.987 0.996 0.000 0.004
#> GSM153086 1 0.0000 0.990 1.000 0.000 0.000
#> GSM153087 1 0.0000 0.990 1.000 0.000 0.000
#> GSM153088 1 0.0000 0.990 1.000 0.000 0.000
#> GSM153089 1 0.1411 0.961 0.964 0.000 0.036
#> GSM153090 1 0.0000 0.990 1.000 0.000 0.000
#> GSM153091 1 0.0000 0.990 1.000 0.000 0.000
#> GSM153092 1 0.0000 0.990 1.000 0.000 0.000
#> GSM153093 1 0.0000 0.990 1.000 0.000 0.000
#> GSM153094 1 0.0000 0.990 1.000 0.000 0.000
#> GSM153095 1 0.0000 0.990 1.000 0.000 0.000
#> GSM153096 1 0.0000 0.990 1.000 0.000 0.000
#> GSM153097 1 0.0000 0.990 1.000 0.000 0.000
#> GSM153098 1 0.0000 0.990 1.000 0.000 0.000
#> GSM153099 1 0.0000 0.990 1.000 0.000 0.000
#> GSM153100 1 0.0000 0.990 1.000 0.000 0.000
#> GSM153101 1 0.0000 0.990 1.000 0.000 0.000
#> GSM153102 1 0.0475 0.984 0.992 0.004 0.004
#> GSM153103 1 0.0237 0.987 0.996 0.000 0.004
#> GSM153104 1 0.0000 0.990 1.000 0.000 0.000
#> GSM153106 1 0.0000 0.990 1.000 0.000 0.000
#> GSM153107 1 0.0000 0.990 1.000 0.000 0.000
#> GSM153108 1 0.0000 0.990 1.000 0.000 0.000
#> GSM153109 1 0.0475 0.984 0.992 0.004 0.004
#> GSM153110 1 0.0000 0.990 1.000 0.000 0.000
#> GSM153111 1 0.0000 0.990 1.000 0.000 0.000
#> GSM153112 1 0.0000 0.990 1.000 0.000 0.000
#> GSM153113 1 0.1525 0.957 0.964 0.032 0.004
#> GSM153114 1 0.0000 0.990 1.000 0.000 0.000
#> GSM187532 2 0.3879 0.832 0.000 0.848 0.152
#> GSM187533 2 0.0000 0.987 0.000 1.000 0.000
#> GSM187534 2 0.0000 0.987 0.000 1.000 0.000
#> GSM187535 1 0.1525 0.957 0.964 0.032 0.004
#> GSM152906 2 0.0237 0.985 0.000 0.996 0.004
#> GSM152907 2 0.0237 0.985 0.000 0.996 0.004
#> GSM152908 2 0.0000 0.987 0.000 1.000 0.000
#> GSM152909 2 0.3879 0.832 0.000 0.848 0.152
#> GSM152910 2 0.0000 0.987 0.000 1.000 0.000
#> GSM152911 2 0.0000 0.987 0.000 1.000 0.000
#> GSM152912 2 0.0000 0.987 0.000 1.000 0.000
#> GSM152913 2 0.1031 0.967 0.000 0.976 0.024
#> GSM152914 2 0.0000 0.987 0.000 1.000 0.000
#> GSM152915 2 0.0000 0.987 0.000 1.000 0.000
#> GSM152916 2 0.0000 0.987 0.000 1.000 0.000
#> GSM152917 2 0.0000 0.987 0.000 1.000 0.000
#> GSM152918 2 0.0000 0.987 0.000 1.000 0.000
#> GSM152919 2 0.0000 0.987 0.000 1.000 0.000
#> GSM152920 2 0.0000 0.987 0.000 1.000 0.000
#> GSM152921 2 0.0000 0.987 0.000 1.000 0.000
#> GSM152922 2 0.0000 0.987 0.000 1.000 0.000
#> GSM152923 2 0.0000 0.987 0.000 1.000 0.000
#> GSM152924 2 0.0000 0.987 0.000 1.000 0.000
#> GSM152925 2 0.0000 0.987 0.000 1.000 0.000
#> GSM152926 2 0.0237 0.985 0.000 0.996 0.004
#> GSM152927 2 0.0000 0.987 0.000 1.000 0.000
#> GSM152928 2 0.0237 0.985 0.000 0.996 0.004
#> GSM152929 2 0.0237 0.985 0.000 0.996 0.004
#> GSM152930 2 0.0237 0.985 0.000 0.996 0.004
cbind(get_classes(res, k = 4), get_membership(res, k = 4))
#> class entropy silhouette p1 p2 p3 p4
#> GSM152839 1 0.0921 0.956 0.972 0.000 0.028 0.000
#> GSM152840 1 0.3164 0.900 0.884 0.000 0.064 0.052
#> GSM152841 1 0.1902 0.937 0.932 0.000 0.064 0.004
#> GSM152842 1 0.0921 0.956 0.972 0.000 0.028 0.000
#> GSM152843 1 0.0921 0.956 0.972 0.000 0.028 0.000
#> GSM152844 1 0.3400 0.888 0.872 0.000 0.064 0.064
#> GSM152845 4 0.0469 0.000 0.000 0.000 0.012 0.988
#> GSM152846 1 0.5546 0.577 0.664 0.000 0.044 0.292
#> GSM152847 1 0.0921 0.956 0.972 0.000 0.028 0.000
#> GSM152848 1 0.0921 0.956 0.972 0.000 0.028 0.000
#> GSM152849 1 0.0921 0.956 0.972 0.000 0.028 0.000
#> GSM152850 1 0.0921 0.956 0.972 0.000 0.028 0.000
#> GSM152851 1 0.1474 0.946 0.948 0.000 0.052 0.000
#> GSM152852 1 0.5374 0.658 0.704 0.000 0.052 0.244
#> GSM152853 1 0.3164 0.900 0.884 0.000 0.064 0.052
#> GSM152854 1 0.2011 0.931 0.920 0.000 0.080 0.000
#> GSM152855 1 0.0921 0.953 0.972 0.000 0.028 0.000
#> GSM153238 1 0.1389 0.952 0.952 0.000 0.048 0.000
#> GSM153239 1 0.1637 0.941 0.940 0.000 0.060 0.000
#> GSM153240 1 0.1118 0.951 0.964 0.000 0.036 0.000
#> GSM153241 1 0.0921 0.959 0.972 0.000 0.028 0.000
#> GSM153242 1 0.2949 0.905 0.888 0.000 0.088 0.024
#> GSM153243 1 0.1743 0.949 0.940 0.000 0.056 0.004
#> GSM153244 1 0.2197 0.933 0.916 0.000 0.080 0.004
#> GSM153245 1 0.1637 0.941 0.940 0.000 0.060 0.000
#> GSM153246 1 0.1022 0.953 0.968 0.000 0.032 0.000
#> GSM153247 1 0.1302 0.953 0.956 0.000 0.044 0.000
#> GSM153248 1 0.1211 0.954 0.960 0.000 0.040 0.000
#> GSM153249 1 0.1389 0.946 0.952 0.000 0.048 0.000
#> GSM153250 1 0.0592 0.958 0.984 0.000 0.016 0.000
#> GSM153251 1 0.2401 0.920 0.904 0.000 0.092 0.004
#> GSM153252 1 0.0817 0.954 0.976 0.000 0.024 0.000
#> GSM153253 1 0.1902 0.937 0.932 0.000 0.064 0.004
#> GSM153254 1 0.1474 0.946 0.948 0.000 0.052 0.000
#> GSM153255 1 0.1118 0.951 0.964 0.000 0.036 0.000
#> GSM153256 1 0.0336 0.958 0.992 0.000 0.008 0.000
#> GSM153257 1 0.0921 0.953 0.972 0.000 0.028 0.000
#> GSM153258 1 0.0707 0.958 0.980 0.000 0.020 0.000
#> GSM153259 1 0.1557 0.950 0.944 0.000 0.056 0.000
#> GSM153260 1 0.1389 0.953 0.952 0.000 0.048 0.000
#> GSM153261 1 0.1389 0.953 0.952 0.000 0.048 0.000
#> GSM153262 1 0.1474 0.945 0.948 0.000 0.052 0.000
#> GSM153263 1 0.0817 0.958 0.976 0.000 0.024 0.000
#> GSM153264 1 0.1022 0.956 0.968 0.000 0.032 0.000
#> GSM153265 1 0.1637 0.941 0.940 0.000 0.060 0.000
#> GSM153266 1 0.0817 0.957 0.976 0.000 0.024 0.000
#> GSM153267 1 0.0592 0.957 0.984 0.000 0.016 0.000
#> GSM153268 1 0.1902 0.937 0.932 0.000 0.064 0.004
#> GSM153269 1 0.0469 0.958 0.988 0.000 0.012 0.000
#> GSM153270 1 0.0469 0.957 0.988 0.000 0.012 0.000
#> GSM153271 1 0.0592 0.958 0.984 0.000 0.016 0.000
#> GSM153272 1 0.0336 0.958 0.992 0.000 0.008 0.000
#> GSM153273 1 0.1211 0.954 0.960 0.000 0.040 0.000
#> GSM153274 1 0.0707 0.955 0.980 0.000 0.020 0.000
#> GSM153275 1 0.0817 0.955 0.976 0.000 0.024 0.000
#> GSM153276 1 0.0469 0.958 0.988 0.000 0.012 0.000
#> GSM153277 1 0.0921 0.953 0.972 0.000 0.028 0.000
#> GSM153278 1 0.1557 0.950 0.944 0.000 0.056 0.000
#> GSM153279 1 0.1474 0.946 0.948 0.000 0.052 0.000
#> GSM153280 1 0.1637 0.941 0.940 0.000 0.060 0.000
#> GSM153281 1 0.1118 0.951 0.964 0.000 0.036 0.000
#> GSM153282 1 0.1902 0.937 0.932 0.000 0.064 0.004
#> GSM153283 1 0.1022 0.956 0.968 0.000 0.032 0.000
#> GSM153284 1 0.0592 0.958 0.984 0.000 0.016 0.000
#> GSM153285 1 0.1211 0.949 0.960 0.000 0.040 0.000
#> GSM153286 1 0.0469 0.958 0.988 0.000 0.012 0.000
#> GSM153287 1 0.1118 0.951 0.964 0.000 0.036 0.000
#> GSM153288 1 0.0817 0.954 0.976 0.000 0.024 0.000
#> GSM153289 1 0.0707 0.955 0.980 0.000 0.020 0.000
#> GSM153290 1 0.1637 0.941 0.940 0.000 0.060 0.000
#> GSM153291 1 0.0817 0.954 0.976 0.000 0.024 0.000
#> GSM153292 1 0.1302 0.949 0.956 0.000 0.044 0.000
#> GSM153293 1 0.0469 0.958 0.988 0.000 0.012 0.000
#> GSM153294 1 0.1211 0.954 0.960 0.000 0.040 0.000
#> GSM153295 1 0.1022 0.956 0.968 0.000 0.032 0.000
#> GSM153054 1 0.1389 0.952 0.952 0.000 0.048 0.000
#> GSM153055 1 0.0707 0.958 0.980 0.000 0.020 0.000
#> GSM153056 1 0.0921 0.959 0.972 0.000 0.028 0.000
#> GSM153057 1 0.2197 0.933 0.916 0.000 0.080 0.004
#> GSM153058 1 0.2401 0.920 0.904 0.000 0.092 0.004
#> GSM153059 1 0.2197 0.939 0.916 0.000 0.080 0.004
#> GSM153060 1 0.2216 0.923 0.908 0.000 0.092 0.000
#> GSM153061 1 0.1474 0.952 0.948 0.000 0.052 0.000
#> GSM153062 3 0.3444 0.000 0.000 0.000 0.816 0.184
#> GSM153063 1 0.1474 0.946 0.948 0.000 0.052 0.000
#> GSM153064 1 0.1557 0.950 0.944 0.000 0.056 0.000
#> GSM153065 1 0.1637 0.948 0.940 0.000 0.060 0.000
#> GSM153066 1 0.3697 0.872 0.852 0.048 0.100 0.000
#> GSM153067 1 0.1302 0.949 0.956 0.000 0.044 0.000
#> GSM153068 1 0.1792 0.952 0.932 0.000 0.068 0.000
#> GSM153069 1 0.1118 0.951 0.964 0.000 0.036 0.000
#> GSM153070 1 0.0817 0.957 0.976 0.000 0.024 0.000
#> GSM153071 1 0.1302 0.953 0.956 0.000 0.044 0.000
#> GSM153072 1 0.1302 0.953 0.956 0.000 0.044 0.000
#> GSM153073 1 0.1302 0.953 0.956 0.000 0.044 0.000
#> GSM153074 1 0.1022 0.952 0.968 0.000 0.032 0.000
#> GSM153075 1 0.0469 0.957 0.988 0.000 0.012 0.000
#> GSM153076 1 0.0592 0.958 0.984 0.000 0.016 0.000
#> GSM153077 1 0.1022 0.956 0.968 0.000 0.032 0.000
#> GSM153078 1 0.0921 0.956 0.972 0.000 0.028 0.000
#> GSM153079 1 0.1474 0.950 0.948 0.000 0.052 0.000
#> GSM153080 1 0.1118 0.959 0.964 0.000 0.036 0.000
#> GSM153081 1 0.1022 0.956 0.968 0.000 0.032 0.000
#> GSM153082 1 0.1637 0.948 0.940 0.000 0.060 0.000
#> GSM153083 1 0.1557 0.950 0.944 0.000 0.056 0.000
#> GSM153084 1 0.2281 0.925 0.904 0.000 0.096 0.000
#> GSM153085 1 0.1637 0.948 0.940 0.000 0.060 0.000
#> GSM153086 1 0.1557 0.950 0.944 0.000 0.056 0.000
#> GSM153087 1 0.1302 0.950 0.956 0.000 0.044 0.000
#> GSM153088 1 0.0592 0.958 0.984 0.000 0.016 0.000
#> GSM153089 1 0.2401 0.920 0.904 0.000 0.092 0.004
#> GSM153090 1 0.0469 0.958 0.988 0.000 0.012 0.000
#> GSM153091 1 0.1557 0.950 0.944 0.000 0.056 0.000
#> GSM153092 1 0.0592 0.958 0.984 0.000 0.016 0.000
#> GSM153093 1 0.1118 0.951 0.964 0.000 0.036 0.000
#> GSM153094 1 0.1557 0.950 0.944 0.000 0.056 0.000
#> GSM153095 1 0.1474 0.951 0.948 0.000 0.052 0.000
#> GSM153096 1 0.1211 0.954 0.960 0.000 0.040 0.000
#> GSM153097 1 0.1557 0.950 0.944 0.000 0.056 0.000
#> GSM153098 1 0.0921 0.957 0.972 0.000 0.028 0.000
#> GSM153099 1 0.0336 0.958 0.992 0.000 0.008 0.000
#> GSM153100 1 0.1211 0.954 0.960 0.000 0.040 0.000
#> GSM153101 1 0.1211 0.954 0.960 0.000 0.040 0.000
#> GSM153102 1 0.1792 0.944 0.932 0.000 0.068 0.000
#> GSM153103 1 0.1637 0.948 0.940 0.000 0.060 0.000
#> GSM153104 1 0.1302 0.949 0.956 0.000 0.044 0.000
#> GSM153106 1 0.1211 0.954 0.960 0.000 0.040 0.000
#> GSM153107 1 0.1211 0.954 0.960 0.000 0.040 0.000
#> GSM153108 1 0.0921 0.957 0.972 0.000 0.028 0.000
#> GSM153109 1 0.1792 0.944 0.932 0.000 0.068 0.000
#> GSM153110 1 0.1557 0.950 0.944 0.000 0.056 0.000
#> GSM153111 1 0.1557 0.950 0.944 0.000 0.056 0.000
#> GSM153112 1 0.1211 0.954 0.960 0.000 0.040 0.000
#> GSM153113 1 0.2401 0.925 0.904 0.004 0.092 0.000
#> GSM153114 1 0.1022 0.952 0.968 0.000 0.032 0.000
#> GSM187532 2 0.3647 0.808 0.000 0.832 0.016 0.152
#> GSM187533 2 0.0188 0.970 0.000 0.996 0.004 0.000
#> GSM187534 2 0.0188 0.971 0.000 0.996 0.004 0.000
#> GSM187535 1 0.2281 0.925 0.904 0.000 0.096 0.000
#> GSM152906 2 0.1389 0.957 0.000 0.952 0.048 0.000
#> GSM152907 2 0.1389 0.957 0.000 0.952 0.048 0.000
#> GSM152908 2 0.0000 0.971 0.000 1.000 0.000 0.000
#> GSM152909 2 0.3647 0.808 0.000 0.832 0.016 0.152
#> GSM152910 2 0.0000 0.971 0.000 1.000 0.000 0.000
#> GSM152911 2 0.0000 0.971 0.000 1.000 0.000 0.000
#> GSM152912 2 0.0000 0.971 0.000 1.000 0.000 0.000
#> GSM152913 2 0.0817 0.958 0.000 0.976 0.000 0.024
#> GSM152914 2 0.0000 0.971 0.000 1.000 0.000 0.000
#> GSM152915 2 0.0000 0.971 0.000 1.000 0.000 0.000
#> GSM152916 2 0.0817 0.967 0.000 0.976 0.024 0.000
#> GSM152917 2 0.0000 0.971 0.000 1.000 0.000 0.000
#> GSM152918 2 0.0000 0.971 0.000 1.000 0.000 0.000
#> GSM152919 2 0.0000 0.971 0.000 1.000 0.000 0.000
#> GSM152920 2 0.0000 0.971 0.000 1.000 0.000 0.000
#> GSM152921 2 0.0000 0.971 0.000 1.000 0.000 0.000
#> GSM152922 2 0.0000 0.971 0.000 1.000 0.000 0.000
#> GSM152923 2 0.0921 0.966 0.000 0.972 0.028 0.000
#> GSM152924 2 0.0817 0.967 0.000 0.976 0.024 0.000
#> GSM152925 2 0.0817 0.967 0.000 0.976 0.024 0.000
#> GSM152926 2 0.1389 0.957 0.000 0.952 0.048 0.000
#> GSM152927 2 0.0817 0.967 0.000 0.976 0.024 0.000
#> GSM152928 2 0.1389 0.957 0.000 0.952 0.048 0.000
#> GSM152929 2 0.1389 0.957 0.000 0.952 0.048 0.000
#> GSM152930 2 0.1389 0.957 0.000 0.952 0.048 0.000
cbind(get_classes(res, k = 5), get_membership(res, k = 5))
#> class entropy silhouette p1 p2 p3 p4 p5
#> GSM152839 1 0.0404 0.810 0.988 0.000 0.000 0.012 0.000
#> GSM152840 4 0.3857 0.786 0.312 0.000 0.000 0.688 0.000
#> GSM152841 1 0.4138 0.411 0.616 0.000 0.000 0.384 0.000
#> GSM152842 1 0.0290 0.809 0.992 0.000 0.000 0.008 0.000
#> GSM152843 1 0.0290 0.809 0.992 0.000 0.000 0.008 0.000
#> GSM152844 4 0.3752 0.792 0.292 0.000 0.000 0.708 0.000
#> GSM152845 5 0.3527 0.000 0.000 0.000 0.056 0.116 0.828
#> GSM152846 4 0.4799 0.445 0.120 0.000 0.016 0.756 0.108
#> GSM152847 1 0.0404 0.810 0.988 0.000 0.000 0.012 0.000
#> GSM152848 1 0.0290 0.809 0.992 0.000 0.000 0.008 0.000
#> GSM152849 1 0.0404 0.810 0.988 0.000 0.000 0.012 0.000
#> GSM152850 1 0.0404 0.810 0.988 0.000 0.000 0.012 0.000
#> GSM152851 1 0.3949 0.553 0.668 0.000 0.000 0.332 0.000
#> GSM152852 4 0.4604 0.593 0.156 0.000 0.012 0.760 0.072
#> GSM152853 4 0.3857 0.786 0.312 0.000 0.000 0.688 0.000
#> GSM152854 1 0.4341 0.358 0.592 0.000 0.004 0.404 0.000
#> GSM152855 1 0.3210 0.724 0.788 0.000 0.000 0.212 0.000
#> GSM153238 1 0.1251 0.794 0.956 0.000 0.008 0.036 0.000
#> GSM153239 1 0.4074 0.468 0.636 0.000 0.000 0.364 0.000
#> GSM153240 1 0.3242 0.719 0.784 0.000 0.000 0.216 0.000
#> GSM153241 1 0.1851 0.805 0.912 0.000 0.000 0.088 0.000
#> GSM153242 1 0.4706 -0.135 0.496 0.000 0.008 0.492 0.004
#> GSM153243 1 0.3396 0.744 0.832 0.000 0.028 0.136 0.004
#> GSM153244 1 0.3928 0.621 0.700 0.000 0.004 0.296 0.000
#> GSM153245 1 0.4074 0.468 0.636 0.000 0.000 0.364 0.000
#> GSM153246 1 0.3662 0.668 0.744 0.000 0.000 0.252 0.004
#> GSM153247 1 0.1106 0.799 0.964 0.000 0.012 0.024 0.000
#> GSM153248 1 0.1106 0.798 0.964 0.000 0.012 0.024 0.000
#> GSM153249 1 0.3480 0.683 0.752 0.000 0.000 0.248 0.000
#> GSM153250 1 0.0703 0.811 0.976 0.000 0.000 0.024 0.000
#> GSM153251 1 0.4341 0.355 0.592 0.000 0.004 0.404 0.000
#> GSM153252 1 0.2891 0.754 0.824 0.000 0.000 0.176 0.000
#> GSM153253 1 0.4126 0.424 0.620 0.000 0.000 0.380 0.000
#> GSM153254 1 0.3816 0.609 0.696 0.000 0.000 0.304 0.000
#> GSM153255 1 0.3586 0.661 0.736 0.000 0.000 0.264 0.000
#> GSM153256 1 0.1544 0.807 0.932 0.000 0.000 0.068 0.000
#> GSM153257 1 0.2891 0.754 0.824 0.000 0.000 0.176 0.000
#> GSM153258 1 0.1197 0.813 0.952 0.000 0.000 0.048 0.000
#> GSM153259 1 0.1522 0.789 0.944 0.000 0.012 0.044 0.000
#> GSM153260 1 0.2450 0.784 0.896 0.000 0.028 0.076 0.000
#> GSM153261 1 0.2450 0.784 0.896 0.000 0.028 0.076 0.000
#> GSM153262 1 0.3796 0.605 0.700 0.000 0.000 0.300 0.000
#> GSM153263 1 0.1270 0.815 0.948 0.000 0.000 0.052 0.000
#> GSM153264 1 0.0510 0.808 0.984 0.000 0.000 0.016 0.000
#> GSM153265 1 0.4030 0.497 0.648 0.000 0.000 0.352 0.000
#> GSM153266 1 0.0880 0.812 0.968 0.000 0.000 0.032 0.000
#> GSM153267 1 0.2074 0.796 0.896 0.000 0.000 0.104 0.000
#> GSM153268 1 0.4235 0.270 0.576 0.000 0.000 0.424 0.000
#> GSM153269 1 0.2127 0.794 0.892 0.000 0.000 0.108 0.000
#> GSM153270 1 0.2471 0.786 0.864 0.000 0.000 0.136 0.000
#> GSM153271 1 0.0703 0.811 0.976 0.000 0.000 0.024 0.000
#> GSM153272 1 0.1478 0.808 0.936 0.000 0.000 0.064 0.000
#> GSM153273 1 0.1106 0.798 0.964 0.000 0.012 0.024 0.000
#> GSM153274 1 0.2127 0.794 0.892 0.000 0.000 0.108 0.000
#> GSM153275 1 0.2891 0.756 0.824 0.000 0.000 0.176 0.000
#> GSM153276 1 0.2127 0.794 0.892 0.000 0.000 0.108 0.000
#> GSM153277 1 0.3074 0.741 0.804 0.000 0.000 0.196 0.000
#> GSM153278 1 0.1626 0.798 0.940 0.000 0.016 0.044 0.000
#> GSM153279 1 0.3876 0.576 0.684 0.000 0.000 0.316 0.000
#> GSM153280 1 0.4045 0.487 0.644 0.000 0.000 0.356 0.000
#> GSM153281 1 0.3242 0.719 0.784 0.000 0.000 0.216 0.000
#> GSM153282 1 0.4126 0.423 0.620 0.000 0.000 0.380 0.000
#> GSM153283 1 0.0510 0.808 0.984 0.000 0.000 0.016 0.000
#> GSM153284 1 0.2377 0.787 0.872 0.000 0.000 0.128 0.000
#> GSM153285 1 0.3774 0.612 0.704 0.000 0.000 0.296 0.000
#> GSM153286 1 0.1608 0.807 0.928 0.000 0.000 0.072 0.000
#> GSM153287 1 0.3586 0.661 0.736 0.000 0.000 0.264 0.000
#> GSM153288 1 0.2813 0.760 0.832 0.000 0.000 0.168 0.000
#> GSM153289 1 0.2852 0.757 0.828 0.000 0.000 0.172 0.000
#> GSM153290 1 0.4045 0.487 0.644 0.000 0.000 0.356 0.000
#> GSM153291 1 0.2891 0.754 0.824 0.000 0.000 0.176 0.000
#> GSM153292 1 0.3636 0.654 0.728 0.000 0.000 0.272 0.000
#> GSM153293 1 0.1270 0.810 0.948 0.000 0.000 0.052 0.000
#> GSM153294 1 0.1106 0.798 0.964 0.000 0.012 0.024 0.000
#> GSM153295 1 0.2516 0.778 0.860 0.000 0.000 0.140 0.000
#> GSM153054 1 0.1251 0.794 0.956 0.000 0.008 0.036 0.000
#> GSM153055 1 0.1792 0.807 0.916 0.000 0.000 0.084 0.000
#> GSM153056 1 0.1851 0.805 0.912 0.000 0.000 0.088 0.000
#> GSM153057 1 0.3715 0.680 0.736 0.000 0.004 0.260 0.000
#> GSM153058 1 0.4375 0.295 0.576 0.000 0.004 0.420 0.000
#> GSM153059 1 0.3700 0.699 0.752 0.000 0.008 0.240 0.000
#> GSM153060 1 0.4225 0.480 0.632 0.000 0.004 0.364 0.000
#> GSM153061 1 0.1830 0.783 0.932 0.000 0.028 0.040 0.000
#> GSM153062 3 0.0794 0.000 0.000 0.000 0.972 0.028 0.000
#> GSM153063 1 0.3684 0.648 0.720 0.000 0.000 0.280 0.000
#> GSM153064 1 0.1522 0.789 0.944 0.000 0.012 0.044 0.000
#> GSM153065 1 0.1981 0.775 0.924 0.000 0.028 0.048 0.000
#> GSM153066 1 0.4005 0.672 0.836 0.048 0.028 0.076 0.012
#> GSM153067 1 0.3636 0.654 0.728 0.000 0.000 0.272 0.000
#> GSM153068 1 0.2873 0.787 0.860 0.000 0.020 0.120 0.000
#> GSM153069 1 0.3586 0.661 0.736 0.000 0.000 0.264 0.000
#> GSM153070 1 0.0609 0.811 0.980 0.000 0.000 0.020 0.000
#> GSM153071 1 0.0898 0.801 0.972 0.000 0.008 0.020 0.000
#> GSM153072 1 0.1106 0.799 0.964 0.000 0.012 0.024 0.000
#> GSM153073 1 0.0898 0.801 0.972 0.000 0.008 0.020 0.000
#> GSM153074 1 0.2929 0.752 0.820 0.000 0.000 0.180 0.000
#> GSM153075 1 0.2561 0.783 0.856 0.000 0.000 0.144 0.000
#> GSM153076 1 0.1043 0.812 0.960 0.000 0.000 0.040 0.000
#> GSM153077 1 0.0510 0.808 0.984 0.000 0.000 0.016 0.000
#> GSM153078 1 0.0404 0.810 0.988 0.000 0.000 0.012 0.000
#> GSM153079 1 0.1818 0.787 0.932 0.000 0.024 0.044 0.000
#> GSM153080 1 0.2127 0.801 0.892 0.000 0.000 0.108 0.000
#> GSM153081 1 0.0510 0.810 0.984 0.000 0.000 0.016 0.000
#> GSM153082 1 0.1854 0.786 0.936 0.000 0.020 0.036 0.008
#> GSM153083 1 0.1626 0.787 0.940 0.000 0.016 0.044 0.000
#> GSM153084 1 0.2784 0.740 0.888 0.000 0.028 0.072 0.012
#> GSM153085 1 0.1978 0.779 0.928 0.000 0.024 0.044 0.004
#> GSM153086 1 0.1522 0.789 0.944 0.000 0.012 0.044 0.000
#> GSM153087 1 0.3452 0.691 0.756 0.000 0.000 0.244 0.000
#> GSM153088 1 0.0703 0.811 0.976 0.000 0.000 0.024 0.000
#> GSM153089 1 0.4341 0.355 0.592 0.000 0.004 0.404 0.000
#> GSM153090 1 0.1608 0.807 0.928 0.000 0.000 0.072 0.000
#> GSM153091 1 0.1626 0.787 0.940 0.000 0.016 0.044 0.000
#> GSM153092 1 0.1544 0.811 0.932 0.000 0.000 0.068 0.000
#> GSM153093 1 0.3074 0.739 0.804 0.000 0.000 0.196 0.000
#> GSM153094 1 0.1626 0.787 0.940 0.000 0.016 0.044 0.000
#> GSM153095 1 0.1648 0.793 0.940 0.000 0.020 0.040 0.000
#> GSM153096 1 0.1106 0.798 0.964 0.000 0.012 0.024 0.000
#> GSM153097 1 0.1626 0.787 0.940 0.000 0.016 0.044 0.000
#> GSM153098 1 0.2249 0.807 0.896 0.000 0.008 0.096 0.000
#> GSM153099 1 0.1544 0.807 0.932 0.000 0.000 0.068 0.000
#> GSM153100 1 0.1281 0.803 0.956 0.000 0.012 0.032 0.000
#> GSM153101 1 0.1399 0.802 0.952 0.000 0.020 0.028 0.000
#> GSM153102 1 0.2214 0.769 0.916 0.000 0.028 0.052 0.004
#> GSM153103 1 0.1978 0.779 0.928 0.000 0.024 0.044 0.004
#> GSM153104 1 0.3636 0.654 0.728 0.000 0.000 0.272 0.000
#> GSM153106 1 0.1106 0.803 0.964 0.000 0.012 0.024 0.000
#> GSM153107 1 0.1106 0.803 0.964 0.000 0.012 0.024 0.000
#> GSM153108 1 0.2136 0.809 0.904 0.000 0.008 0.088 0.000
#> GSM153109 1 0.2214 0.769 0.916 0.000 0.028 0.052 0.004
#> GSM153110 1 0.1522 0.789 0.944 0.000 0.012 0.044 0.000
#> GSM153111 1 0.1626 0.787 0.940 0.000 0.016 0.044 0.000
#> GSM153112 1 0.1281 0.803 0.956 0.000 0.012 0.032 0.000
#> GSM153113 1 0.2880 0.742 0.888 0.004 0.028 0.068 0.012
#> GSM153114 1 0.3274 0.716 0.780 0.000 0.000 0.220 0.000
#> GSM187532 2 0.3796 0.638 0.000 0.700 0.000 0.000 0.300
#> GSM187533 2 0.2377 0.859 0.000 0.872 0.000 0.000 0.128
#> GSM187534 2 0.2488 0.863 0.000 0.872 0.000 0.004 0.124
#> GSM187535 1 0.2790 0.748 0.892 0.000 0.028 0.060 0.020
#> GSM152906 2 0.1399 0.939 0.000 0.952 0.000 0.028 0.020
#> GSM152907 2 0.1399 0.939 0.000 0.952 0.000 0.028 0.020
#> GSM152908 2 0.0290 0.950 0.000 0.992 0.000 0.000 0.008
#> GSM152909 2 0.3796 0.638 0.000 0.700 0.000 0.000 0.300
#> GSM152910 2 0.0290 0.950 0.000 0.992 0.000 0.000 0.008
#> GSM152911 2 0.0000 0.951 0.000 1.000 0.000 0.000 0.000
#> GSM152912 2 0.0290 0.950 0.000 0.992 0.000 0.000 0.008
#> GSM152913 2 0.0794 0.941 0.000 0.972 0.000 0.000 0.028
#> GSM152914 2 0.0000 0.951 0.000 1.000 0.000 0.000 0.000
#> GSM152915 2 0.0000 0.951 0.000 1.000 0.000 0.000 0.000
#> GSM152916 2 0.0798 0.948 0.000 0.976 0.000 0.016 0.008
#> GSM152917 2 0.0000 0.951 0.000 1.000 0.000 0.000 0.000
#> GSM152918 2 0.0000 0.951 0.000 1.000 0.000 0.000 0.000
#> GSM152919 2 0.0000 0.951 0.000 1.000 0.000 0.000 0.000
#> GSM152920 2 0.0290 0.950 0.000 0.992 0.000 0.000 0.008
#> GSM152921 2 0.0290 0.950 0.000 0.992 0.000 0.000 0.008
#> GSM152922 2 0.0290 0.950 0.000 0.992 0.000 0.000 0.008
#> GSM152923 2 0.0912 0.947 0.000 0.972 0.000 0.016 0.012
#> GSM152924 2 0.0798 0.948 0.000 0.976 0.000 0.016 0.008
#> GSM152925 2 0.0798 0.948 0.000 0.976 0.000 0.016 0.008
#> GSM152926 2 0.1399 0.939 0.000 0.952 0.000 0.028 0.020
#> GSM152927 2 0.0798 0.948 0.000 0.976 0.000 0.016 0.008
#> GSM152928 2 0.1399 0.939 0.000 0.952 0.000 0.028 0.020
#> GSM152929 2 0.1399 0.939 0.000 0.952 0.000 0.028 0.020
#> GSM152930 2 0.1399 0.939 0.000 0.952 0.000 0.028 0.020
cbind(get_classes(res, k = 6), get_membership(res, k = 6))
#> class entropy silhouette p1 p2 p3 p4 p5 p6
#> GSM152839 1 0.1049 0.7318 0.960 0.000 0.000 0.032 0.008 0.000
#> GSM152840 4 0.2815 0.2683 0.120 0.000 0.000 0.848 0.032 0.000
#> GSM152841 4 0.3979 0.5530 0.456 0.000 0.000 0.540 0.004 0.000
#> GSM152842 1 0.0972 0.7312 0.964 0.000 0.000 0.028 0.008 0.000
#> GSM152843 1 0.0972 0.7312 0.964 0.000 0.000 0.028 0.008 0.000
#> GSM152844 4 0.2609 0.1853 0.096 0.000 0.000 0.868 0.036 0.000
#> GSM152845 5 0.1444 0.0000 0.000 0.000 0.000 0.000 0.928 0.072
#> GSM152846 4 0.3886 -0.4097 0.028 0.000 0.000 0.708 0.264 0.000
#> GSM152847 1 0.1196 0.7311 0.952 0.000 0.000 0.040 0.008 0.000
#> GSM152848 1 0.0972 0.7312 0.964 0.000 0.000 0.028 0.008 0.000
#> GSM152849 1 0.1049 0.7318 0.960 0.000 0.000 0.032 0.008 0.000
#> GSM152850 1 0.1049 0.7318 0.960 0.000 0.000 0.032 0.008 0.000
#> GSM152851 1 0.3862 -0.3715 0.524 0.000 0.000 0.476 0.000 0.000
#> GSM152852 4 0.3980 -0.3128 0.052 0.000 0.000 0.732 0.216 0.000
#> GSM152853 4 0.2815 0.2683 0.120 0.000 0.000 0.848 0.032 0.000
#> GSM152854 4 0.4488 0.5644 0.432 0.000 0.004 0.544 0.016 0.004
#> GSM152855 1 0.3578 0.3068 0.660 0.000 0.000 0.340 0.000 0.000
#> GSM153238 1 0.0881 0.7230 0.972 0.000 0.000 0.008 0.008 0.012
#> GSM153239 4 0.3860 0.5208 0.472 0.000 0.000 0.528 0.000 0.000
#> GSM153240 1 0.3620 0.2655 0.648 0.000 0.000 0.352 0.000 0.000
#> GSM153241 1 0.2558 0.6750 0.840 0.000 0.000 0.156 0.004 0.000
#> GSM153242 4 0.4528 0.5543 0.340 0.000 0.008 0.624 0.024 0.004
#> GSM153243 1 0.3582 0.6299 0.812 0.000 0.020 0.140 0.012 0.016
#> GSM153244 1 0.4371 -0.0530 0.576 0.000 0.008 0.404 0.008 0.004
#> GSM153245 4 0.3860 0.5208 0.472 0.000 0.000 0.528 0.000 0.000
#> GSM153246 1 0.6178 -0.1843 0.492 0.000 0.000 0.308 0.024 0.176
#> GSM153247 1 0.0810 0.7285 0.976 0.000 0.004 0.004 0.008 0.008
#> GSM153248 1 0.0798 0.7268 0.976 0.000 0.004 0.004 0.012 0.004
#> GSM153249 1 0.3727 0.1030 0.612 0.000 0.000 0.388 0.000 0.000
#> GSM153250 1 0.1643 0.7245 0.924 0.000 0.000 0.068 0.008 0.000
#> GSM153251 4 0.4598 0.5300 0.440 0.000 0.008 0.532 0.016 0.004
#> GSM153252 1 0.3508 0.4422 0.704 0.000 0.000 0.292 0.004 0.000
#> GSM153253 4 0.3982 0.5478 0.460 0.000 0.000 0.536 0.004 0.000
#> GSM153254 1 0.3833 -0.2196 0.556 0.000 0.000 0.444 0.000 0.000
#> GSM153255 1 0.3737 0.0791 0.608 0.000 0.000 0.392 0.000 0.000
#> GSM153256 1 0.2513 0.6812 0.852 0.000 0.000 0.140 0.008 0.000
#> GSM153257 1 0.3508 0.4403 0.704 0.000 0.000 0.292 0.004 0.000
#> GSM153258 1 0.1663 0.7204 0.912 0.000 0.000 0.088 0.000 0.000
#> GSM153259 1 0.1223 0.7174 0.960 0.000 0.004 0.016 0.008 0.012
#> GSM153260 1 0.2459 0.7012 0.900 0.000 0.020 0.056 0.012 0.012
#> GSM153261 1 0.2459 0.7012 0.900 0.000 0.020 0.056 0.012 0.012
#> GSM153262 1 0.3950 -0.1553 0.564 0.000 0.000 0.432 0.004 0.000
#> GSM153263 1 0.2165 0.7121 0.884 0.000 0.000 0.108 0.008 0.000
#> GSM153264 1 0.0972 0.7321 0.964 0.000 0.000 0.028 0.008 0.000
#> GSM153265 4 0.3866 0.4848 0.484 0.000 0.000 0.516 0.000 0.000
#> GSM153266 1 0.1531 0.7255 0.928 0.000 0.000 0.068 0.004 0.000
#> GSM153267 1 0.2871 0.6257 0.804 0.000 0.000 0.192 0.004 0.000
#> GSM153268 4 0.3907 0.5804 0.408 0.000 0.000 0.588 0.004 0.000
#> GSM153269 1 0.3023 0.5972 0.784 0.000 0.000 0.212 0.004 0.000
#> GSM153270 1 0.3050 0.5619 0.764 0.000 0.000 0.236 0.000 0.000
#> GSM153271 1 0.1643 0.7245 0.924 0.000 0.000 0.068 0.008 0.000
#> GSM153272 1 0.2473 0.6847 0.856 0.000 0.000 0.136 0.008 0.000
#> GSM153273 1 0.0798 0.7268 0.976 0.000 0.004 0.004 0.012 0.004
#> GSM153274 1 0.2964 0.6092 0.792 0.000 0.000 0.204 0.004 0.000
#> GSM153275 1 0.3547 0.4265 0.696 0.000 0.000 0.300 0.004 0.000
#> GSM153276 1 0.3023 0.5972 0.784 0.000 0.000 0.212 0.004 0.000
#> GSM153277 1 0.3531 0.3557 0.672 0.000 0.000 0.328 0.000 0.000
#> GSM153278 1 0.1476 0.7308 0.948 0.000 0.008 0.028 0.012 0.004
#> GSM153279 1 0.3854 -0.3045 0.536 0.000 0.000 0.464 0.000 0.000
#> GSM153280 4 0.3864 0.4991 0.480 0.000 0.000 0.520 0.000 0.000
#> GSM153281 1 0.3647 0.2364 0.640 0.000 0.000 0.360 0.000 0.000
#> GSM153282 4 0.3982 0.5479 0.460 0.000 0.000 0.536 0.004 0.000
#> GSM153283 1 0.0972 0.7321 0.964 0.000 0.000 0.028 0.008 0.000
#> GSM153284 1 0.3163 0.5707 0.764 0.000 0.000 0.232 0.004 0.000
#> GSM153285 1 0.3810 -0.1273 0.572 0.000 0.000 0.428 0.000 0.000
#> GSM153286 1 0.2553 0.6790 0.848 0.000 0.000 0.144 0.008 0.000
#> GSM153287 1 0.3737 0.0791 0.608 0.000 0.000 0.392 0.000 0.000
#> GSM153288 1 0.3426 0.4798 0.720 0.000 0.000 0.276 0.004 0.000
#> GSM153289 1 0.3489 0.4529 0.708 0.000 0.000 0.288 0.004 0.000
#> GSM153290 4 0.3864 0.4991 0.480 0.000 0.000 0.520 0.000 0.000
#> GSM153291 1 0.3390 0.4370 0.704 0.000 0.000 0.296 0.000 0.000
#> GSM153292 1 0.3756 0.0504 0.600 0.000 0.000 0.400 0.000 0.000
#> GSM153293 1 0.2346 0.6948 0.868 0.000 0.000 0.124 0.008 0.000
#> GSM153294 1 0.0798 0.7268 0.976 0.000 0.004 0.004 0.012 0.004
#> GSM153295 1 0.3314 0.5220 0.740 0.000 0.000 0.256 0.004 0.000
#> GSM153054 1 0.0881 0.7230 0.972 0.000 0.000 0.008 0.008 0.012
#> GSM153055 1 0.2378 0.6743 0.848 0.000 0.000 0.152 0.000 0.000
#> GSM153056 1 0.2558 0.6750 0.840 0.000 0.000 0.156 0.004 0.000
#> GSM153057 1 0.4316 0.2261 0.628 0.000 0.008 0.348 0.012 0.004
#> GSM153058 4 0.4589 0.5287 0.432 0.000 0.008 0.540 0.016 0.004
#> GSM153059 1 0.4291 0.3154 0.656 0.000 0.012 0.316 0.012 0.004
#> GSM153060 4 0.4354 0.4656 0.476 0.000 0.008 0.508 0.004 0.004
#> GSM153061 1 0.1895 0.7107 0.932 0.000 0.020 0.024 0.012 0.012
#> GSM153062 3 0.0547 0.0000 0.000 0.000 0.980 0.020 0.000 0.000
#> GSM153063 1 0.3797 -0.0838 0.580 0.000 0.000 0.420 0.000 0.000
#> GSM153064 1 0.1223 0.7174 0.960 0.000 0.004 0.016 0.008 0.012
#> GSM153065 1 0.1723 0.7023 0.940 0.000 0.020 0.016 0.012 0.012
#> GSM153066 1 0.3480 0.6151 0.852 0.028 0.020 0.016 0.012 0.072
#> GSM153067 1 0.3756 0.0504 0.600 0.000 0.000 0.400 0.000 0.000
#> GSM153068 1 0.3193 0.6696 0.836 0.000 0.012 0.128 0.012 0.012
#> GSM153069 1 0.3737 0.0791 0.608 0.000 0.000 0.392 0.000 0.000
#> GSM153070 1 0.1462 0.7284 0.936 0.000 0.000 0.056 0.008 0.000
#> GSM153071 1 0.0551 0.7306 0.984 0.000 0.000 0.004 0.004 0.008
#> GSM153072 1 0.0810 0.7285 0.976 0.000 0.004 0.004 0.008 0.008
#> GSM153073 1 0.0551 0.7306 0.984 0.000 0.000 0.004 0.004 0.008
#> GSM153074 1 0.3565 0.4145 0.692 0.000 0.000 0.304 0.004 0.000
#> GSM153075 1 0.3101 0.5519 0.756 0.000 0.000 0.244 0.000 0.000
#> GSM153076 1 0.1970 0.7145 0.900 0.000 0.000 0.092 0.008 0.000
#> GSM153077 1 0.0972 0.7321 0.964 0.000 0.000 0.028 0.008 0.000
#> GSM153078 1 0.1124 0.7312 0.956 0.000 0.000 0.036 0.008 0.000
#> GSM153079 1 0.1533 0.7142 0.948 0.000 0.016 0.016 0.008 0.012
#> GSM153080 1 0.2703 0.6601 0.824 0.000 0.000 0.172 0.004 0.000
#> GSM153081 1 0.1124 0.7325 0.956 0.000 0.000 0.036 0.008 0.000
#> GSM153082 1 0.1414 0.7192 0.952 0.000 0.012 0.004 0.012 0.020
#> GSM153083 1 0.1337 0.7150 0.956 0.000 0.008 0.016 0.008 0.012
#> GSM153084 1 0.2425 0.6841 0.904 0.000 0.020 0.016 0.012 0.048
#> GSM153085 1 0.1627 0.7083 0.944 0.000 0.016 0.016 0.008 0.016
#> GSM153086 1 0.1223 0.7174 0.960 0.000 0.004 0.016 0.008 0.012
#> GSM153087 1 0.3684 0.1801 0.628 0.000 0.000 0.372 0.000 0.000
#> GSM153088 1 0.1643 0.7245 0.924 0.000 0.000 0.068 0.008 0.000
#> GSM153089 4 0.4598 0.5300 0.440 0.000 0.008 0.532 0.016 0.004
#> GSM153090 1 0.2558 0.6683 0.840 0.000 0.000 0.156 0.004 0.000
#> GSM153091 1 0.1337 0.7146 0.956 0.000 0.008 0.016 0.008 0.012
#> GSM153092 1 0.1957 0.7071 0.888 0.000 0.000 0.112 0.000 0.000
#> GSM153093 1 0.3547 0.3407 0.668 0.000 0.000 0.332 0.000 0.000
#> GSM153094 1 0.1337 0.7146 0.956 0.000 0.008 0.016 0.008 0.012
#> GSM153095 1 0.1242 0.7235 0.960 0.000 0.012 0.008 0.008 0.012
#> GSM153096 1 0.0798 0.7268 0.976 0.000 0.004 0.004 0.012 0.004
#> GSM153097 1 0.1337 0.7146 0.956 0.000 0.008 0.016 0.008 0.012
#> GSM153098 1 0.2504 0.6775 0.856 0.000 0.000 0.136 0.004 0.004
#> GSM153099 1 0.2593 0.6759 0.844 0.000 0.000 0.148 0.008 0.000
#> GSM153100 1 0.1015 0.7303 0.968 0.000 0.004 0.012 0.012 0.004
#> GSM153101 1 0.1026 0.7287 0.968 0.000 0.012 0.008 0.008 0.004
#> GSM153102 1 0.1905 0.7017 0.932 0.000 0.020 0.016 0.012 0.020
#> GSM153103 1 0.1627 0.7083 0.944 0.000 0.016 0.016 0.008 0.016
#> GSM153104 1 0.3756 0.0504 0.600 0.000 0.000 0.400 0.000 0.000
#> GSM153106 1 0.0696 0.7301 0.980 0.000 0.004 0.004 0.008 0.004
#> GSM153107 1 0.0696 0.7301 0.980 0.000 0.004 0.004 0.008 0.004
#> GSM153108 1 0.2420 0.6863 0.864 0.000 0.000 0.128 0.004 0.004
#> GSM153109 1 0.1905 0.7017 0.932 0.000 0.020 0.016 0.012 0.020
#> GSM153110 1 0.1223 0.7174 0.960 0.000 0.004 0.016 0.008 0.012
#> GSM153111 1 0.1337 0.7146 0.956 0.000 0.008 0.016 0.008 0.012
#> GSM153112 1 0.1015 0.7303 0.968 0.000 0.004 0.012 0.012 0.004
#> GSM153113 1 0.2502 0.6842 0.904 0.004 0.020 0.016 0.012 0.044
#> GSM153114 1 0.3634 0.2508 0.644 0.000 0.000 0.356 0.000 0.000
#> GSM187532 6 0.3198 1.0000 0.000 0.260 0.000 0.000 0.000 0.740
#> GSM187533 2 0.3862 -0.3975 0.000 0.524 0.000 0.000 0.000 0.476
#> GSM187534 2 0.3862 -0.3831 0.000 0.524 0.000 0.000 0.000 0.476
#> GSM187535 1 0.2332 0.6910 0.908 0.000 0.020 0.012 0.012 0.048
#> GSM152906 2 0.1387 0.8758 0.000 0.932 0.000 0.000 0.000 0.068
#> GSM152907 2 0.1387 0.8758 0.000 0.932 0.000 0.000 0.000 0.068
#> GSM152908 2 0.1141 0.8649 0.000 0.948 0.000 0.000 0.000 0.052
#> GSM152909 6 0.3198 1.0000 0.000 0.260 0.000 0.000 0.000 0.740
#> GSM152910 2 0.1141 0.8649 0.000 0.948 0.000 0.000 0.000 0.052
#> GSM152911 2 0.0000 0.8885 0.000 1.000 0.000 0.000 0.000 0.000
#> GSM152912 2 0.1141 0.8649 0.000 0.948 0.000 0.000 0.000 0.052
#> GSM152913 2 0.1910 0.8023 0.000 0.892 0.000 0.000 0.000 0.108
#> GSM152914 2 0.0000 0.8885 0.000 1.000 0.000 0.000 0.000 0.000
#> GSM152915 2 0.0000 0.8885 0.000 1.000 0.000 0.000 0.000 0.000
#> GSM152916 2 0.1007 0.8867 0.000 0.956 0.000 0.000 0.000 0.044
#> GSM152917 2 0.0000 0.8885 0.000 1.000 0.000 0.000 0.000 0.000
#> GSM152918 2 0.0000 0.8885 0.000 1.000 0.000 0.000 0.000 0.000
#> GSM152919 2 0.0000 0.8885 0.000 1.000 0.000 0.000 0.000 0.000
#> GSM152920 2 0.1141 0.8649 0.000 0.948 0.000 0.000 0.000 0.052
#> GSM152921 2 0.1141 0.8649 0.000 0.948 0.000 0.000 0.000 0.052
#> GSM152922 2 0.1141 0.8649 0.000 0.948 0.000 0.000 0.000 0.052
#> GSM152923 2 0.1075 0.8853 0.000 0.952 0.000 0.000 0.000 0.048
#> GSM152924 2 0.1007 0.8867 0.000 0.956 0.000 0.000 0.000 0.044
#> GSM152925 2 0.1007 0.8867 0.000 0.956 0.000 0.000 0.000 0.044
#> GSM152926 2 0.1387 0.8758 0.000 0.932 0.000 0.000 0.000 0.068
#> GSM152927 2 0.1007 0.8867 0.000 0.956 0.000 0.000 0.000 0.044
#> GSM152928 2 0.1387 0.8758 0.000 0.932 0.000 0.000 0.000 0.068
#> GSM152929 2 0.1387 0.8758 0.000 0.932 0.000 0.000 0.000 0.068
#> GSM152930 2 0.1387 0.8758 0.000 0.932 0.000 0.000 0.000 0.068
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 tissue(p) k
#> ATC:hclust 164 1.48e-28 2
#> ATC:hclust 164 2.47e-29 3
#> ATC:hclust 162 1.39e-30 4
#> ATC:hclust 146 7.83e-34 5
#> ATC:hclust 120 1.33e-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["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 12013 rows and 164 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 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 0.999 1.000 0.2942 0.707 0.707
#> 3 3 0.544 0.809 0.870 0.8955 0.715 0.598
#> 4 4 0.596 0.776 0.847 0.2241 0.761 0.507
#> 5 5 0.705 0.553 0.795 0.0901 0.991 0.971
#> 6 6 0.702 0.623 0.712 0.0502 0.831 0.495
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
#> GSM152839 1 0.0000 0.999 1.000 0.000
#> GSM152840 1 0.0000 0.999 1.000 0.000
#> GSM152841 1 0.0000 0.999 1.000 0.000
#> GSM152842 1 0.0000 0.999 1.000 0.000
#> GSM152843 1 0.0000 0.999 1.000 0.000
#> GSM152844 1 0.0000 0.999 1.000 0.000
#> GSM152845 2 0.0000 1.000 0.000 1.000
#> GSM152846 1 0.0000 0.999 1.000 0.000
#> GSM152847 1 0.0000 0.999 1.000 0.000
#> GSM152848 1 0.0000 0.999 1.000 0.000
#> GSM152849 1 0.0000 0.999 1.000 0.000
#> GSM152850 1 0.0000 0.999 1.000 0.000
#> GSM152851 1 0.0000 0.999 1.000 0.000
#> GSM152852 1 0.0000 0.999 1.000 0.000
#> GSM152853 1 0.0000 0.999 1.000 0.000
#> GSM152854 1 0.0000 0.999 1.000 0.000
#> GSM152855 1 0.0000 0.999 1.000 0.000
#> GSM153238 1 0.0000 0.999 1.000 0.000
#> GSM153239 1 0.0000 0.999 1.000 0.000
#> GSM153240 1 0.0000 0.999 1.000 0.000
#> GSM153241 1 0.0000 0.999 1.000 0.000
#> GSM153242 1 0.0000 0.999 1.000 0.000
#> GSM153243 1 0.0000 0.999 1.000 0.000
#> GSM153244 1 0.0000 0.999 1.000 0.000
#> GSM153245 1 0.0000 0.999 1.000 0.000
#> GSM153246 1 0.0000 0.999 1.000 0.000
#> GSM153247 1 0.0000 0.999 1.000 0.000
#> GSM153248 1 0.0000 0.999 1.000 0.000
#> GSM153249 1 0.0000 0.999 1.000 0.000
#> GSM153250 1 0.0000 0.999 1.000 0.000
#> GSM153251 1 0.0000 0.999 1.000 0.000
#> GSM153252 1 0.0000 0.999 1.000 0.000
#> GSM153253 1 0.0000 0.999 1.000 0.000
#> GSM153254 1 0.0000 0.999 1.000 0.000
#> GSM153255 1 0.0000 0.999 1.000 0.000
#> GSM153256 1 0.0000 0.999 1.000 0.000
#> GSM153257 1 0.0000 0.999 1.000 0.000
#> GSM153258 1 0.0000 0.999 1.000 0.000
#> GSM153259 1 0.0000 0.999 1.000 0.000
#> GSM153260 1 0.0000 0.999 1.000 0.000
#> GSM153261 1 0.0000 0.999 1.000 0.000
#> GSM153262 1 0.0000 0.999 1.000 0.000
#> GSM153263 1 0.0000 0.999 1.000 0.000
#> GSM153264 1 0.0000 0.999 1.000 0.000
#> GSM153265 1 0.0000 0.999 1.000 0.000
#> GSM153266 1 0.0000 0.999 1.000 0.000
#> GSM153267 1 0.0000 0.999 1.000 0.000
#> GSM153268 1 0.0000 0.999 1.000 0.000
#> GSM153269 1 0.0000 0.999 1.000 0.000
#> GSM153270 1 0.0000 0.999 1.000 0.000
#> GSM153271 1 0.0000 0.999 1.000 0.000
#> GSM153272 1 0.0000 0.999 1.000 0.000
#> GSM153273 1 0.0000 0.999 1.000 0.000
#> GSM153274 1 0.0000 0.999 1.000 0.000
#> GSM153275 1 0.0000 0.999 1.000 0.000
#> GSM153276 1 0.0000 0.999 1.000 0.000
#> GSM153277 1 0.0000 0.999 1.000 0.000
#> GSM153278 1 0.0000 0.999 1.000 0.000
#> GSM153279 1 0.0000 0.999 1.000 0.000
#> GSM153280 1 0.0000 0.999 1.000 0.000
#> GSM153281 1 0.0000 0.999 1.000 0.000
#> GSM153282 1 0.0000 0.999 1.000 0.000
#> GSM153283 1 0.0000 0.999 1.000 0.000
#> GSM153284 1 0.0000 0.999 1.000 0.000
#> GSM153285 1 0.0000 0.999 1.000 0.000
#> GSM153286 1 0.0000 0.999 1.000 0.000
#> GSM153287 1 0.0000 0.999 1.000 0.000
#> GSM153288 1 0.0000 0.999 1.000 0.000
#> GSM153289 1 0.0000 0.999 1.000 0.000
#> GSM153290 1 0.0000 0.999 1.000 0.000
#> GSM153291 1 0.0000 0.999 1.000 0.000
#> GSM153292 1 0.0000 0.999 1.000 0.000
#> GSM153293 1 0.0000 0.999 1.000 0.000
#> GSM153294 1 0.0000 0.999 1.000 0.000
#> GSM153295 1 0.0000 0.999 1.000 0.000
#> GSM153054 1 0.0000 0.999 1.000 0.000
#> GSM153055 1 0.0000 0.999 1.000 0.000
#> GSM153056 1 0.0000 0.999 1.000 0.000
#> GSM153057 1 0.0000 0.999 1.000 0.000
#> GSM153058 1 0.0000 0.999 1.000 0.000
#> GSM153059 1 0.0000 0.999 1.000 0.000
#> GSM153060 1 0.0000 0.999 1.000 0.000
#> GSM153061 1 0.0000 0.999 1.000 0.000
#> GSM153062 1 0.3879 0.918 0.924 0.076
#> GSM153063 1 0.0000 0.999 1.000 0.000
#> GSM153064 1 0.0000 0.999 1.000 0.000
#> GSM153065 1 0.0000 0.999 1.000 0.000
#> GSM153066 1 0.0376 0.995 0.996 0.004
#> GSM153067 1 0.0000 0.999 1.000 0.000
#> GSM153068 1 0.0000 0.999 1.000 0.000
#> GSM153069 1 0.0000 0.999 1.000 0.000
#> GSM153070 1 0.0000 0.999 1.000 0.000
#> GSM153071 1 0.0000 0.999 1.000 0.000
#> GSM153072 1 0.0000 0.999 1.000 0.000
#> GSM153073 1 0.0000 0.999 1.000 0.000
#> GSM153074 1 0.0000 0.999 1.000 0.000
#> GSM153075 1 0.0000 0.999 1.000 0.000
#> GSM153076 1 0.0000 0.999 1.000 0.000
#> GSM153077 1 0.0000 0.999 1.000 0.000
#> GSM153078 1 0.0000 0.999 1.000 0.000
#> GSM153079 1 0.0000 0.999 1.000 0.000
#> GSM153080 1 0.0000 0.999 1.000 0.000
#> GSM153081 1 0.0000 0.999 1.000 0.000
#> GSM153082 1 0.0000 0.999 1.000 0.000
#> GSM153083 1 0.0000 0.999 1.000 0.000
#> GSM153084 1 0.0000 0.999 1.000 0.000
#> GSM153085 1 0.0000 0.999 1.000 0.000
#> GSM153086 1 0.0000 0.999 1.000 0.000
#> GSM153087 1 0.0000 0.999 1.000 0.000
#> GSM153088 1 0.0000 0.999 1.000 0.000
#> GSM153089 1 0.0000 0.999 1.000 0.000
#> GSM153090 1 0.0000 0.999 1.000 0.000
#> GSM153091 1 0.0000 0.999 1.000 0.000
#> GSM153092 1 0.0000 0.999 1.000 0.000
#> GSM153093 1 0.0000 0.999 1.000 0.000
#> GSM153094 1 0.0000 0.999 1.000 0.000
#> GSM153095 1 0.0000 0.999 1.000 0.000
#> GSM153096 1 0.0000 0.999 1.000 0.000
#> GSM153097 1 0.0000 0.999 1.000 0.000
#> GSM153098 1 0.0000 0.999 1.000 0.000
#> GSM153099 1 0.0000 0.999 1.000 0.000
#> GSM153100 1 0.0000 0.999 1.000 0.000
#> GSM153101 1 0.0000 0.999 1.000 0.000
#> GSM153102 1 0.0000 0.999 1.000 0.000
#> GSM153103 1 0.0000 0.999 1.000 0.000
#> GSM153104 1 0.0000 0.999 1.000 0.000
#> GSM153106 1 0.0000 0.999 1.000 0.000
#> GSM153107 1 0.0000 0.999 1.000 0.000
#> GSM153108 1 0.0000 0.999 1.000 0.000
#> GSM153109 1 0.0000 0.999 1.000 0.000
#> GSM153110 1 0.0000 0.999 1.000 0.000
#> GSM153111 1 0.0000 0.999 1.000 0.000
#> GSM153112 1 0.0000 0.999 1.000 0.000
#> GSM153113 1 0.0000 0.999 1.000 0.000
#> GSM153114 1 0.0000 0.999 1.000 0.000
#> GSM187532 2 0.0000 1.000 0.000 1.000
#> GSM187533 2 0.0000 1.000 0.000 1.000
#> GSM187534 2 0.0000 1.000 0.000 1.000
#> GSM187535 1 0.0000 0.999 1.000 0.000
#> GSM152906 2 0.0000 1.000 0.000 1.000
#> GSM152907 2 0.0000 1.000 0.000 1.000
#> GSM152908 2 0.0000 1.000 0.000 1.000
#> GSM152909 2 0.0000 1.000 0.000 1.000
#> GSM152910 2 0.0000 1.000 0.000 1.000
#> GSM152911 2 0.0000 1.000 0.000 1.000
#> GSM152912 2 0.0000 1.000 0.000 1.000
#> GSM152913 2 0.0000 1.000 0.000 1.000
#> GSM152914 2 0.0000 1.000 0.000 1.000
#> GSM152915 2 0.0000 1.000 0.000 1.000
#> GSM152916 2 0.0000 1.000 0.000 1.000
#> GSM152917 2 0.0000 1.000 0.000 1.000
#> GSM152918 2 0.0000 1.000 0.000 1.000
#> GSM152919 2 0.0000 1.000 0.000 1.000
#> GSM152920 2 0.0000 1.000 0.000 1.000
#> GSM152921 2 0.0000 1.000 0.000 1.000
#> GSM152922 2 0.0000 1.000 0.000 1.000
#> GSM152923 2 0.0000 1.000 0.000 1.000
#> GSM152924 2 0.0000 1.000 0.000 1.000
#> GSM152925 2 0.0000 1.000 0.000 1.000
#> GSM152926 2 0.0000 1.000 0.000 1.000
#> GSM152927 2 0.0000 1.000 0.000 1.000
#> GSM152928 2 0.0000 1.000 0.000 1.000
#> GSM152929 2 0.0000 1.000 0.000 1.000
#> GSM152930 2 0.0000 1.000 0.000 1.000
cbind(get_classes(res, k = 3), get_membership(res, k = 3))
#> class entropy silhouette p1 p2 p3
#> GSM152839 1 0.1031 0.865 0.976 0.000 0.024
#> GSM152840 3 0.3941 0.833 0.156 0.000 0.844
#> GSM152841 3 0.5363 0.779 0.276 0.000 0.724
#> GSM152842 1 0.0000 0.868 1.000 0.000 0.000
#> GSM152843 1 0.0747 0.867 0.984 0.000 0.016
#> GSM152844 3 0.3941 0.833 0.156 0.000 0.844
#> GSM152845 3 0.4784 0.427 0.004 0.200 0.796
#> GSM152846 3 0.2796 0.824 0.092 0.000 0.908
#> GSM152847 1 0.0237 0.868 0.996 0.000 0.004
#> GSM152848 1 0.0892 0.866 0.980 0.000 0.020
#> GSM152849 1 0.1643 0.861 0.956 0.000 0.044
#> GSM152850 1 0.0000 0.868 1.000 0.000 0.000
#> GSM152851 3 0.5178 0.796 0.256 0.000 0.744
#> GSM152852 3 0.2796 0.824 0.092 0.000 0.908
#> GSM152853 3 0.3941 0.833 0.156 0.000 0.844
#> GSM152854 3 0.2959 0.826 0.100 0.000 0.900
#> GSM152855 1 0.5016 0.650 0.760 0.000 0.240
#> GSM153238 1 0.1964 0.848 0.944 0.000 0.056
#> GSM153239 3 0.3941 0.833 0.156 0.000 0.844
#> GSM153240 1 0.5882 0.395 0.652 0.000 0.348
#> GSM153241 1 0.4750 0.701 0.784 0.000 0.216
#> GSM153242 3 0.2796 0.824 0.092 0.000 0.908
#> GSM153243 1 0.4452 0.695 0.808 0.000 0.192
#> GSM153244 3 0.2711 0.824 0.088 0.000 0.912
#> GSM153245 3 0.3941 0.833 0.156 0.000 0.844
#> GSM153246 3 0.3192 0.822 0.112 0.000 0.888
#> GSM153247 1 0.0237 0.867 0.996 0.000 0.004
#> GSM153248 1 0.0237 0.867 0.996 0.000 0.004
#> GSM153249 3 0.6192 0.528 0.420 0.000 0.580
#> GSM153250 1 0.0892 0.866 0.980 0.000 0.020
#> GSM153251 3 0.2796 0.824 0.092 0.000 0.908
#> GSM153252 1 0.3752 0.788 0.856 0.000 0.144
#> GSM153253 3 0.5397 0.775 0.280 0.000 0.720
#> GSM153254 3 0.2878 0.826 0.096 0.000 0.904
#> GSM153255 1 0.5621 0.504 0.692 0.000 0.308
#> GSM153256 1 0.3038 0.822 0.896 0.000 0.104
#> GSM153257 1 0.3752 0.788 0.856 0.000 0.144
#> GSM153258 1 0.0237 0.867 0.996 0.000 0.004
#> GSM153259 1 0.0892 0.863 0.980 0.000 0.020
#> GSM153260 1 0.4931 0.633 0.768 0.000 0.232
#> GSM153261 3 0.5733 0.592 0.324 0.000 0.676
#> GSM153262 3 0.5678 0.731 0.316 0.000 0.684
#> GSM153263 1 0.0892 0.866 0.980 0.000 0.020
#> GSM153264 1 0.0000 0.868 1.000 0.000 0.000
#> GSM153265 3 0.5529 0.758 0.296 0.000 0.704
#> GSM153266 1 0.0000 0.868 1.000 0.000 0.000
#> GSM153267 1 0.2448 0.841 0.924 0.000 0.076
#> GSM153268 3 0.3941 0.833 0.156 0.000 0.844
#> GSM153269 1 0.3752 0.788 0.856 0.000 0.144
#> GSM153270 1 0.5678 0.486 0.684 0.000 0.316
#> GSM153271 1 0.0892 0.866 0.980 0.000 0.020
#> GSM153272 1 0.3752 0.788 0.856 0.000 0.144
#> GSM153273 1 0.0237 0.867 0.996 0.000 0.004
#> GSM153274 1 0.3752 0.788 0.856 0.000 0.144
#> GSM153275 1 0.3752 0.788 0.856 0.000 0.144
#> GSM153276 1 0.3816 0.784 0.852 0.000 0.148
#> GSM153277 3 0.5621 0.743 0.308 0.000 0.692
#> GSM153278 1 0.2448 0.835 0.924 0.000 0.076
#> GSM153279 3 0.5291 0.787 0.268 0.000 0.732
#> GSM153280 3 0.4702 0.819 0.212 0.000 0.788
#> GSM153281 3 0.6168 0.548 0.412 0.000 0.588
#> GSM153282 3 0.5216 0.793 0.260 0.000 0.740
#> GSM153283 1 0.0000 0.868 1.000 0.000 0.000
#> GSM153284 1 0.3752 0.788 0.856 0.000 0.144
#> GSM153285 3 0.6180 0.539 0.416 0.000 0.584
#> GSM153286 1 0.3752 0.788 0.856 0.000 0.144
#> GSM153287 1 0.5882 0.394 0.652 0.000 0.348
#> GSM153288 1 0.3752 0.788 0.856 0.000 0.144
#> GSM153289 1 0.3340 0.809 0.880 0.000 0.120
#> GSM153290 3 0.5138 0.799 0.252 0.000 0.748
#> GSM153291 1 0.5529 0.533 0.704 0.000 0.296
#> GSM153292 3 0.6168 0.549 0.412 0.000 0.588
#> GSM153293 1 0.2537 0.838 0.920 0.000 0.080
#> GSM153294 1 0.0237 0.867 0.996 0.000 0.004
#> GSM153295 1 0.3412 0.806 0.876 0.000 0.124
#> GSM153054 1 0.0237 0.867 0.996 0.000 0.004
#> GSM153055 1 0.1964 0.852 0.944 0.000 0.056
#> GSM153056 1 0.4887 0.674 0.772 0.000 0.228
#> GSM153057 3 0.2796 0.824 0.092 0.000 0.908
#> GSM153058 3 0.2796 0.824 0.092 0.000 0.908
#> GSM153059 3 0.4887 0.719 0.228 0.000 0.772
#> GSM153060 3 0.2796 0.824 0.092 0.000 0.908
#> GSM153061 1 0.4931 0.633 0.768 0.000 0.232
#> GSM153062 3 0.2806 0.695 0.040 0.032 0.928
#> GSM153063 3 0.4346 0.829 0.184 0.000 0.816
#> GSM153064 1 0.0000 0.868 1.000 0.000 0.000
#> GSM153065 1 0.4931 0.633 0.768 0.000 0.232
#> GSM153066 1 0.4288 0.783 0.872 0.060 0.068
#> GSM153067 1 0.4178 0.755 0.828 0.000 0.172
#> GSM153068 3 0.5138 0.693 0.252 0.000 0.748
#> GSM153069 1 0.5988 0.328 0.632 0.000 0.368
#> GSM153070 1 0.0424 0.868 0.992 0.000 0.008
#> GSM153071 1 0.0892 0.866 0.980 0.000 0.020
#> GSM153072 1 0.0892 0.863 0.980 0.000 0.020
#> GSM153073 1 0.0592 0.867 0.988 0.000 0.012
#> GSM153074 1 0.5810 0.429 0.664 0.000 0.336
#> GSM153075 3 0.6215 0.504 0.428 0.000 0.572
#> GSM153076 1 0.0892 0.866 0.980 0.000 0.020
#> GSM153077 1 0.0000 0.868 1.000 0.000 0.000
#> GSM153078 1 0.0000 0.868 1.000 0.000 0.000
#> GSM153079 1 0.2261 0.839 0.932 0.000 0.068
#> GSM153080 1 0.4346 0.775 0.816 0.000 0.184
#> GSM153081 1 0.0237 0.867 0.996 0.000 0.004
#> GSM153082 1 0.1964 0.848 0.944 0.000 0.056
#> GSM153083 1 0.1964 0.848 0.944 0.000 0.056
#> GSM153084 1 0.2261 0.839 0.932 0.000 0.068
#> GSM153085 1 0.2261 0.839 0.932 0.000 0.068
#> GSM153086 1 0.1964 0.848 0.944 0.000 0.056
#> GSM153087 1 0.5882 0.394 0.652 0.000 0.348
#> GSM153088 1 0.0892 0.866 0.980 0.000 0.020
#> GSM153089 3 0.3116 0.815 0.108 0.000 0.892
#> GSM153090 1 0.2959 0.825 0.900 0.000 0.100
#> GSM153091 1 0.1964 0.848 0.944 0.000 0.056
#> GSM153092 1 0.1860 0.850 0.948 0.000 0.052
#> GSM153093 1 0.5905 0.382 0.648 0.000 0.352
#> GSM153094 1 0.1964 0.848 0.944 0.000 0.056
#> GSM153095 1 0.1860 0.850 0.948 0.000 0.052
#> GSM153096 1 0.0237 0.867 0.996 0.000 0.004
#> GSM153097 1 0.1964 0.848 0.944 0.000 0.056
#> GSM153098 1 0.1031 0.865 0.976 0.000 0.024
#> GSM153099 1 0.3038 0.822 0.896 0.000 0.104
#> GSM153100 1 0.0237 0.867 0.996 0.000 0.004
#> GSM153101 1 0.1964 0.848 0.944 0.000 0.056
#> GSM153102 1 0.2261 0.839 0.932 0.000 0.068
#> GSM153103 1 0.1964 0.848 0.944 0.000 0.056
#> GSM153104 1 0.5948 0.356 0.640 0.000 0.360
#> GSM153106 1 0.2066 0.845 0.940 0.000 0.060
#> GSM153107 1 0.0592 0.866 0.988 0.000 0.012
#> GSM153108 1 0.0237 0.867 0.996 0.000 0.004
#> GSM153109 1 0.2261 0.839 0.932 0.000 0.068
#> GSM153110 1 0.0747 0.865 0.984 0.000 0.016
#> GSM153111 1 0.1964 0.848 0.944 0.000 0.056
#> GSM153112 1 0.0424 0.868 0.992 0.000 0.008
#> GSM153113 1 0.2261 0.839 0.932 0.000 0.068
#> GSM153114 3 0.5591 0.748 0.304 0.000 0.696
#> GSM187532 2 0.2261 0.966 0.000 0.932 0.068
#> GSM187533 2 0.2261 0.966 0.000 0.932 0.068
#> GSM187534 2 0.0000 0.976 0.000 1.000 0.000
#> GSM187535 1 0.3899 0.799 0.888 0.056 0.056
#> GSM152906 2 0.0747 0.975 0.000 0.984 0.016
#> GSM152907 2 0.0747 0.975 0.000 0.984 0.016
#> GSM152908 2 0.2356 0.966 0.000 0.928 0.072
#> GSM152909 2 0.2356 0.966 0.000 0.928 0.072
#> GSM152910 2 0.2356 0.966 0.000 0.928 0.072
#> GSM152911 2 0.1753 0.971 0.000 0.952 0.048
#> GSM152912 2 0.2356 0.966 0.000 0.928 0.072
#> GSM152913 2 0.2356 0.966 0.000 0.928 0.072
#> GSM152914 2 0.0237 0.976 0.000 0.996 0.004
#> GSM152915 2 0.0592 0.976 0.000 0.988 0.012
#> GSM152916 2 0.0747 0.975 0.000 0.984 0.016
#> GSM152917 2 0.0237 0.976 0.000 0.996 0.004
#> GSM152918 2 0.0237 0.976 0.000 0.996 0.004
#> GSM152919 2 0.0237 0.976 0.000 0.996 0.004
#> GSM152920 2 0.2356 0.966 0.000 0.928 0.072
#> GSM152921 2 0.2356 0.966 0.000 0.928 0.072
#> GSM152922 2 0.2356 0.966 0.000 0.928 0.072
#> GSM152923 2 0.0747 0.975 0.000 0.984 0.016
#> GSM152924 2 0.0747 0.975 0.000 0.984 0.016
#> GSM152925 2 0.0747 0.975 0.000 0.984 0.016
#> GSM152926 2 0.0747 0.975 0.000 0.984 0.016
#> GSM152927 2 0.0747 0.975 0.000 0.984 0.016
#> GSM152928 2 0.0747 0.975 0.000 0.984 0.016
#> GSM152929 2 0.0747 0.975 0.000 0.984 0.016
#> GSM152930 2 0.0747 0.975 0.000 0.984 0.016
cbind(get_classes(res, k = 4), get_membership(res, k = 4))
#> class entropy silhouette p1 p2 p3 p4
#> GSM152839 1 0.4500 0.7909 0.776 0.000 0.032 0.192
#> GSM152840 4 0.3982 0.4951 0.004 0.000 0.220 0.776
#> GSM152841 4 0.3679 0.6958 0.060 0.000 0.084 0.856
#> GSM152842 1 0.4105 0.8253 0.812 0.000 0.032 0.156
#> GSM152843 1 0.4323 0.7997 0.788 0.000 0.028 0.184
#> GSM152844 4 0.5155 -0.2457 0.004 0.000 0.468 0.528
#> GSM152845 3 0.3229 0.7760 0.000 0.048 0.880 0.072
#> GSM152846 3 0.3810 0.9191 0.008 0.000 0.804 0.188
#> GSM152847 1 0.4152 0.8223 0.808 0.000 0.032 0.160
#> GSM152848 1 0.3539 0.8001 0.820 0.000 0.004 0.176
#> GSM152849 1 0.4579 0.7812 0.768 0.000 0.032 0.200
#> GSM152850 1 0.3907 0.8367 0.828 0.000 0.032 0.140
#> GSM152851 4 0.4378 0.6003 0.040 0.000 0.164 0.796
#> GSM152852 3 0.3810 0.9191 0.008 0.000 0.804 0.188
#> GSM152853 4 0.5119 -0.1465 0.004 0.000 0.440 0.556
#> GSM152854 3 0.3831 0.9138 0.004 0.000 0.792 0.204
#> GSM152855 4 0.3172 0.7765 0.160 0.000 0.000 0.840
#> GSM153238 1 0.1305 0.8630 0.960 0.000 0.036 0.004
#> GSM153239 4 0.4837 0.1929 0.004 0.000 0.348 0.648
#> GSM153240 4 0.2921 0.7773 0.140 0.000 0.000 0.860
#> GSM153241 1 0.5337 0.6977 0.696 0.000 0.044 0.260
#> GSM153242 3 0.3810 0.9191 0.008 0.000 0.804 0.188
#> GSM153243 1 0.4401 0.5689 0.724 0.000 0.272 0.004
#> GSM153244 3 0.4594 0.8173 0.008 0.000 0.712 0.280
#> GSM153245 4 0.3583 0.5583 0.004 0.000 0.180 0.816
#> GSM153246 3 0.3681 0.9068 0.008 0.000 0.816 0.176
#> GSM153247 1 0.1837 0.8746 0.944 0.000 0.028 0.028
#> GSM153248 1 0.0469 0.8783 0.988 0.000 0.000 0.012
#> GSM153249 4 0.3793 0.7597 0.112 0.000 0.044 0.844
#> GSM153250 1 0.3583 0.7958 0.816 0.000 0.004 0.180
#> GSM153251 3 0.3893 0.9182 0.008 0.000 0.796 0.196
#> GSM153252 4 0.3982 0.7596 0.220 0.000 0.004 0.776
#> GSM153253 4 0.3400 0.7131 0.064 0.000 0.064 0.872
#> GSM153254 4 0.5204 0.0815 0.012 0.000 0.376 0.612
#> GSM153255 4 0.2868 0.7773 0.136 0.000 0.000 0.864
#> GSM153256 4 0.4477 0.6602 0.312 0.000 0.000 0.688
#> GSM153257 4 0.3982 0.7596 0.220 0.000 0.004 0.776
#> GSM153258 1 0.2216 0.8581 0.908 0.000 0.000 0.092
#> GSM153259 1 0.0188 0.8781 0.996 0.000 0.000 0.004
#> GSM153260 1 0.5229 0.1887 0.564 0.000 0.428 0.008
#> GSM153261 3 0.5608 0.6503 0.256 0.000 0.684 0.060
#> GSM153262 4 0.3421 0.7453 0.088 0.000 0.044 0.868
#> GSM153263 1 0.3583 0.7958 0.816 0.000 0.004 0.180
#> GSM153264 1 0.3105 0.8304 0.856 0.000 0.004 0.140
#> GSM153265 4 0.3761 0.7037 0.068 0.000 0.080 0.852
#> GSM153266 1 0.2647 0.8442 0.880 0.000 0.000 0.120
#> GSM153267 4 0.4543 0.6405 0.324 0.000 0.000 0.676
#> GSM153268 4 0.3831 0.5164 0.004 0.000 0.204 0.792
#> GSM153269 4 0.4193 0.7206 0.268 0.000 0.000 0.732
#> GSM153270 4 0.3710 0.7724 0.192 0.000 0.004 0.804
#> GSM153271 1 0.3668 0.7862 0.808 0.000 0.004 0.188
#> GSM153272 4 0.3907 0.7537 0.232 0.000 0.000 0.768
#> GSM153273 1 0.0592 0.8781 0.984 0.000 0.000 0.016
#> GSM153274 4 0.4193 0.7206 0.268 0.000 0.000 0.732
#> GSM153275 4 0.3907 0.7537 0.232 0.000 0.000 0.768
#> GSM153276 4 0.4193 0.7206 0.268 0.000 0.000 0.732
#> GSM153277 4 0.3156 0.7278 0.068 0.000 0.048 0.884
#> GSM153278 1 0.1305 0.8610 0.960 0.000 0.036 0.004
#> GSM153279 4 0.4415 0.6366 0.056 0.000 0.140 0.804
#> GSM153280 4 0.4225 0.5649 0.024 0.000 0.184 0.792
#> GSM153281 4 0.3734 0.7580 0.108 0.000 0.044 0.848
#> GSM153282 4 0.4123 0.6374 0.044 0.000 0.136 0.820
#> GSM153283 1 0.3257 0.8213 0.844 0.000 0.004 0.152
#> GSM153284 4 0.3837 0.7590 0.224 0.000 0.000 0.776
#> GSM153285 4 0.3734 0.7580 0.108 0.000 0.044 0.848
#> GSM153286 4 0.3975 0.7472 0.240 0.000 0.000 0.760
#> GSM153287 4 0.2814 0.7768 0.132 0.000 0.000 0.868
#> GSM153288 4 0.3942 0.7507 0.236 0.000 0.000 0.764
#> GSM153289 4 0.4222 0.7162 0.272 0.000 0.000 0.728
#> GSM153290 4 0.4332 0.6060 0.040 0.000 0.160 0.800
#> GSM153291 4 0.2973 0.7774 0.144 0.000 0.000 0.856
#> GSM153292 4 0.3734 0.7580 0.108 0.000 0.044 0.848
#> GSM153293 4 0.4500 0.6538 0.316 0.000 0.000 0.684
#> GSM153294 1 0.1302 0.8739 0.956 0.000 0.000 0.044
#> GSM153295 4 0.4401 0.7119 0.272 0.000 0.004 0.724
#> GSM153054 1 0.1209 0.8766 0.964 0.000 0.004 0.032
#> GSM153055 4 0.4761 0.5434 0.372 0.000 0.000 0.628
#> GSM153056 4 0.5659 0.4549 0.368 0.000 0.032 0.600
#> GSM153057 3 0.3893 0.9182 0.008 0.000 0.796 0.196
#> GSM153058 3 0.3893 0.9182 0.008 0.000 0.796 0.196
#> GSM153059 3 0.4969 0.8612 0.088 0.000 0.772 0.140
#> GSM153060 3 0.3636 0.9121 0.008 0.000 0.820 0.172
#> GSM153061 1 0.5290 0.2577 0.584 0.000 0.404 0.012
#> GSM153062 3 0.3324 0.8962 0.012 0.000 0.852 0.136
#> GSM153063 4 0.4121 0.5628 0.020 0.000 0.184 0.796
#> GSM153064 1 0.1716 0.8688 0.936 0.000 0.000 0.064
#> GSM153065 1 0.5203 0.2239 0.576 0.000 0.416 0.008
#> GSM153066 1 0.1585 0.8579 0.952 0.004 0.040 0.004
#> GSM153067 4 0.3444 0.7727 0.184 0.000 0.000 0.816
#> GSM153068 3 0.4840 0.8218 0.116 0.000 0.784 0.100
#> GSM153069 4 0.2814 0.7768 0.132 0.000 0.000 0.868
#> GSM153070 1 0.3266 0.8082 0.832 0.000 0.000 0.168
#> GSM153071 1 0.3539 0.8003 0.820 0.000 0.004 0.176
#> GSM153072 1 0.0524 0.8781 0.988 0.000 0.008 0.004
#> GSM153073 1 0.3448 0.8079 0.828 0.000 0.004 0.168
#> GSM153074 4 0.2868 0.7773 0.136 0.000 0.000 0.864
#> GSM153075 4 0.4401 0.7435 0.112 0.000 0.076 0.812
#> GSM153076 1 0.3583 0.7958 0.816 0.000 0.004 0.180
#> GSM153077 1 0.2714 0.8484 0.884 0.000 0.004 0.112
#> GSM153078 1 0.3749 0.8423 0.840 0.000 0.032 0.128
#> GSM153079 1 0.1209 0.8634 0.964 0.000 0.032 0.004
#> GSM153080 1 0.3919 0.7869 0.840 0.000 0.056 0.104
#> GSM153081 1 0.2197 0.8734 0.928 0.000 0.024 0.048
#> GSM153082 1 0.0376 0.8760 0.992 0.000 0.004 0.004
#> GSM153083 1 0.0188 0.8770 0.996 0.000 0.004 0.000
#> GSM153084 1 0.1489 0.8583 0.952 0.000 0.044 0.004
#> GSM153085 1 0.0779 0.8717 0.980 0.000 0.016 0.004
#> GSM153086 1 0.0188 0.8770 0.996 0.000 0.004 0.000
#> GSM153087 4 0.4070 0.7680 0.132 0.000 0.044 0.824
#> GSM153088 1 0.3668 0.7862 0.808 0.000 0.004 0.188
#> GSM153089 3 0.3852 0.9189 0.008 0.000 0.800 0.192
#> GSM153090 4 0.4624 0.6126 0.340 0.000 0.000 0.660
#> GSM153091 1 0.0188 0.8770 0.996 0.000 0.004 0.000
#> GSM153092 1 0.0376 0.8760 0.992 0.000 0.004 0.004
#> GSM153093 4 0.2868 0.7773 0.136 0.000 0.000 0.864
#> GSM153094 1 0.0188 0.8770 0.996 0.000 0.004 0.000
#> GSM153095 1 0.0524 0.8752 0.988 0.000 0.008 0.004
#> GSM153096 1 0.0469 0.8783 0.988 0.000 0.000 0.012
#> GSM153097 1 0.0188 0.8770 0.996 0.000 0.004 0.000
#> GSM153098 4 0.4761 0.5433 0.372 0.000 0.000 0.628
#> GSM153099 4 0.4679 0.5891 0.352 0.000 0.000 0.648
#> GSM153100 1 0.1716 0.8693 0.936 0.000 0.000 0.064
#> GSM153101 1 0.0376 0.8760 0.992 0.000 0.004 0.004
#> GSM153102 1 0.0779 0.8723 0.980 0.000 0.016 0.004
#> GSM153103 1 0.0469 0.8756 0.988 0.000 0.012 0.000
#> GSM153104 4 0.4070 0.7680 0.132 0.000 0.044 0.824
#> GSM153106 1 0.0672 0.8746 0.984 0.000 0.008 0.008
#> GSM153107 1 0.0188 0.8781 0.996 0.000 0.000 0.004
#> GSM153108 1 0.4866 0.2515 0.596 0.000 0.000 0.404
#> GSM153109 1 0.0524 0.8744 0.988 0.000 0.008 0.004
#> GSM153110 1 0.0188 0.8781 0.996 0.000 0.000 0.004
#> GSM153111 1 0.0188 0.8770 0.996 0.000 0.004 0.000
#> GSM153112 1 0.1474 0.8727 0.948 0.000 0.000 0.052
#> GSM153113 1 0.0524 0.8744 0.988 0.000 0.008 0.004
#> GSM153114 4 0.4022 0.6900 0.068 0.000 0.096 0.836
#> GSM187532 2 0.4224 0.8916 0.000 0.812 0.144 0.044
#> GSM187533 2 0.4017 0.8997 0.000 0.828 0.128 0.044
#> GSM187534 2 0.1004 0.9344 0.000 0.972 0.024 0.004
#> GSM187535 1 0.0712 0.8728 0.984 0.004 0.008 0.004
#> GSM152906 2 0.1182 0.9345 0.000 0.968 0.016 0.016
#> GSM152907 2 0.1182 0.9345 0.000 0.968 0.016 0.016
#> GSM152908 2 0.4017 0.8997 0.000 0.828 0.128 0.044
#> GSM152909 2 0.4224 0.8916 0.000 0.812 0.144 0.044
#> GSM152910 2 0.4017 0.8997 0.000 0.828 0.128 0.044
#> GSM152911 2 0.1807 0.9291 0.000 0.940 0.052 0.008
#> GSM152912 2 0.4017 0.8997 0.000 0.828 0.128 0.044
#> GSM152913 2 0.2859 0.9148 0.000 0.880 0.112 0.008
#> GSM152914 2 0.0524 0.9359 0.000 0.988 0.008 0.004
#> GSM152915 2 0.0524 0.9359 0.000 0.988 0.008 0.004
#> GSM152916 2 0.1182 0.9345 0.000 0.968 0.016 0.016
#> GSM152917 2 0.0000 0.9363 0.000 1.000 0.000 0.000
#> GSM152918 2 0.0000 0.9363 0.000 1.000 0.000 0.000
#> GSM152919 2 0.0000 0.9363 0.000 1.000 0.000 0.000
#> GSM152920 2 0.4017 0.8997 0.000 0.828 0.128 0.044
#> GSM152921 2 0.4017 0.8997 0.000 0.828 0.128 0.044
#> GSM152922 2 0.4017 0.8997 0.000 0.828 0.128 0.044
#> GSM152923 2 0.1182 0.9345 0.000 0.968 0.016 0.016
#> GSM152924 2 0.1182 0.9345 0.000 0.968 0.016 0.016
#> GSM152925 2 0.1182 0.9345 0.000 0.968 0.016 0.016
#> GSM152926 2 0.1182 0.9345 0.000 0.968 0.016 0.016
#> GSM152927 2 0.1182 0.9345 0.000 0.968 0.016 0.016
#> GSM152928 2 0.1182 0.9345 0.000 0.968 0.016 0.016
#> GSM152929 2 0.1182 0.9345 0.000 0.968 0.016 0.016
#> GSM152930 2 0.1182 0.9345 0.000 0.968 0.016 0.016
cbind(get_classes(res, k = 5), get_membership(res, k = 5))
#> class entropy silhouette p1 p2 p3 p4 p5
#> GSM152839 1 0.6031 -0.2828 0.480 0.000 0.012 0.080 0.428
#> GSM152840 4 0.5054 0.4988 0.004 0.000 0.184 0.708 0.104
#> GSM152841 4 0.1990 0.6979 0.008 0.000 0.068 0.920 0.004
#> GSM152842 1 0.5891 -0.2336 0.492 0.000 0.012 0.068 0.428
#> GSM152843 1 0.5721 -0.1939 0.492 0.000 0.000 0.084 0.424
#> GSM152844 4 0.6265 -0.0897 0.004 0.000 0.380 0.484 0.132
#> GSM152845 3 0.3274 0.8270 0.000 0.000 0.780 0.000 0.220
#> GSM152846 3 0.3224 0.8576 0.000 0.000 0.824 0.016 0.160
#> GSM152847 1 0.5979 -0.2473 0.488 0.000 0.016 0.068 0.428
#> GSM152848 1 0.5779 -0.1129 0.508 0.000 0.000 0.092 0.400
#> GSM152849 1 0.6523 -0.3793 0.452 0.000 0.036 0.084 0.428
#> GSM152850 1 0.5841 -0.2194 0.496 0.000 0.012 0.064 0.428
#> GSM152851 4 0.2575 0.6759 0.012 0.000 0.100 0.884 0.004
#> GSM152852 3 0.3224 0.8576 0.000 0.000 0.824 0.016 0.160
#> GSM152853 4 0.6203 -0.0198 0.004 0.000 0.364 0.504 0.128
#> GSM152854 3 0.1369 0.8986 0.008 0.000 0.956 0.028 0.008
#> GSM152855 4 0.1211 0.7119 0.016 0.000 0.000 0.960 0.024
#> GSM153238 1 0.2179 0.5927 0.896 0.000 0.000 0.004 0.100
#> GSM153239 4 0.4775 0.3316 0.008 0.000 0.332 0.640 0.020
#> GSM153240 4 0.4090 0.5301 0.016 0.000 0.000 0.716 0.268
#> GSM153241 5 0.7156 0.0765 0.400 0.000 0.088 0.084 0.428
#> GSM153242 3 0.2172 0.8844 0.000 0.000 0.908 0.016 0.076
#> GSM153243 1 0.5018 0.3110 0.664 0.000 0.268 0.000 0.068
#> GSM153244 3 0.3353 0.7416 0.008 0.000 0.796 0.196 0.000
#> GSM153245 4 0.3474 0.6257 0.008 0.000 0.148 0.824 0.020
#> GSM153246 3 0.3639 0.8474 0.016 0.000 0.828 0.028 0.128
#> GSM153247 1 0.2723 0.5835 0.864 0.000 0.000 0.012 0.124
#> GSM153248 1 0.1018 0.6409 0.968 0.000 0.000 0.016 0.016
#> GSM153249 4 0.1018 0.7164 0.016 0.000 0.016 0.968 0.000
#> GSM153250 1 0.5672 0.1036 0.584 0.000 0.000 0.104 0.312
#> GSM153251 3 0.1483 0.8990 0.008 0.000 0.952 0.028 0.012
#> GSM153252 4 0.4326 0.5202 0.028 0.000 0.000 0.708 0.264
#> GSM153253 4 0.1788 0.7034 0.008 0.000 0.056 0.932 0.004
#> GSM153254 4 0.4664 0.1444 0.008 0.000 0.436 0.552 0.004
#> GSM153255 4 0.1018 0.7141 0.016 0.000 0.000 0.968 0.016
#> GSM153256 4 0.5086 0.3773 0.060 0.000 0.000 0.636 0.304
#> GSM153257 4 0.4374 0.5105 0.028 0.000 0.000 0.700 0.272
#> GSM153258 1 0.5409 0.1679 0.604 0.000 0.000 0.080 0.316
#> GSM153259 1 0.0912 0.6419 0.972 0.000 0.000 0.016 0.012
#> GSM153260 1 0.5648 -0.1426 0.476 0.000 0.448 0.000 0.076
#> GSM153261 3 0.4736 0.6742 0.216 0.000 0.712 0.000 0.072
#> GSM153262 4 0.1356 0.7134 0.012 0.000 0.028 0.956 0.004
#> GSM153263 1 0.5568 0.1363 0.596 0.000 0.000 0.096 0.308
#> GSM153264 1 0.5393 0.1756 0.608 0.000 0.000 0.080 0.312
#> GSM153265 4 0.1901 0.7043 0.012 0.000 0.056 0.928 0.004
#> GSM153266 1 0.5443 0.1645 0.604 0.000 0.000 0.084 0.312
#> GSM153267 4 0.5005 0.4332 0.064 0.000 0.000 0.660 0.276
#> GSM153268 4 0.3513 0.6309 0.004 0.000 0.132 0.828 0.036
#> GSM153269 4 0.4668 0.4860 0.044 0.000 0.000 0.684 0.272
#> GSM153270 4 0.4292 0.5173 0.024 0.000 0.000 0.704 0.272
#> GSM153271 1 0.6036 -0.0407 0.548 0.000 0.000 0.144 0.308
#> GSM153272 4 0.4527 0.4996 0.036 0.000 0.000 0.692 0.272
#> GSM153273 1 0.1211 0.6393 0.960 0.000 0.000 0.016 0.024
#> GSM153274 4 0.4668 0.4860 0.044 0.000 0.000 0.684 0.272
#> GSM153275 4 0.4452 0.5059 0.032 0.000 0.000 0.696 0.272
#> GSM153276 4 0.4668 0.4860 0.044 0.000 0.000 0.684 0.272
#> GSM153277 4 0.1356 0.7155 0.012 0.000 0.028 0.956 0.004
#> GSM153278 1 0.4430 0.4572 0.752 0.000 0.076 0.000 0.172
#> GSM153279 4 0.2407 0.6889 0.012 0.000 0.088 0.896 0.004
#> GSM153280 4 0.2575 0.6812 0.012 0.000 0.100 0.884 0.004
#> GSM153281 4 0.0912 0.7167 0.016 0.000 0.012 0.972 0.000
#> GSM153282 4 0.2054 0.6958 0.008 0.000 0.072 0.916 0.004
#> GSM153283 1 0.5491 0.1523 0.600 0.000 0.000 0.088 0.312
#> GSM153284 4 0.4397 0.5054 0.028 0.000 0.000 0.696 0.276
#> GSM153285 4 0.0960 0.7167 0.016 0.000 0.008 0.972 0.004
#> GSM153286 4 0.4599 0.4936 0.040 0.000 0.000 0.688 0.272
#> GSM153287 4 0.0912 0.7147 0.016 0.000 0.000 0.972 0.012
#> GSM153288 4 0.4452 0.5058 0.032 0.000 0.000 0.696 0.272
#> GSM153289 4 0.4758 0.4701 0.048 0.000 0.000 0.676 0.276
#> GSM153290 4 0.2520 0.6837 0.012 0.000 0.096 0.888 0.004
#> GSM153291 4 0.1117 0.7131 0.016 0.000 0.000 0.964 0.020
#> GSM153292 4 0.1117 0.7157 0.016 0.000 0.020 0.964 0.000
#> GSM153293 4 0.5200 0.3533 0.068 0.000 0.000 0.628 0.304
#> GSM153294 1 0.2491 0.6071 0.896 0.000 0.000 0.036 0.068
#> GSM153295 4 0.4969 0.4178 0.056 0.000 0.000 0.652 0.292
#> GSM153054 1 0.3229 0.5687 0.840 0.000 0.000 0.032 0.128
#> GSM153055 4 0.5325 0.3636 0.088 0.000 0.000 0.636 0.276
#> GSM153056 5 0.7223 0.2864 0.172 0.000 0.040 0.360 0.428
#> GSM153057 3 0.2170 0.8938 0.020 0.000 0.924 0.036 0.020
#> GSM153058 3 0.0992 0.8991 0.008 0.000 0.968 0.024 0.000
#> GSM153059 3 0.2313 0.8861 0.040 0.000 0.916 0.012 0.032
#> GSM153060 3 0.2333 0.8925 0.016 0.000 0.916 0.028 0.040
#> GSM153061 1 0.5965 0.1600 0.544 0.000 0.328 0.000 0.128
#> GSM153062 3 0.2660 0.8703 0.000 0.000 0.864 0.008 0.128
#> GSM153063 4 0.2497 0.6676 0.004 0.000 0.112 0.880 0.004
#> GSM153064 1 0.4548 0.3874 0.716 0.000 0.000 0.052 0.232
#> GSM153065 1 0.5569 0.1294 0.556 0.000 0.364 0.000 0.080
#> GSM153066 1 0.1300 0.6175 0.956 0.000 0.016 0.000 0.028
#> GSM153067 4 0.1216 0.7111 0.020 0.000 0.000 0.960 0.020
#> GSM153068 3 0.3021 0.8583 0.060 0.000 0.872 0.004 0.064
#> GSM153069 4 0.0798 0.7153 0.016 0.000 0.000 0.976 0.008
#> GSM153070 1 0.5644 0.1069 0.584 0.000 0.000 0.100 0.316
#> GSM153071 1 0.5748 0.1064 0.584 0.000 0.000 0.116 0.300
#> GSM153072 1 0.1018 0.6420 0.968 0.000 0.000 0.016 0.016
#> GSM153073 1 0.5697 0.0175 0.548 0.000 0.000 0.092 0.360
#> GSM153074 4 0.1211 0.7119 0.016 0.000 0.000 0.960 0.024
#> GSM153075 4 0.1787 0.7164 0.016 0.000 0.032 0.940 0.012
#> GSM153076 1 0.5896 0.0254 0.564 0.000 0.000 0.128 0.308
#> GSM153077 1 0.5393 0.1756 0.608 0.000 0.000 0.080 0.312
#> GSM153078 1 0.5770 -0.1419 0.516 0.000 0.012 0.060 0.412
#> GSM153079 1 0.0981 0.6346 0.972 0.000 0.012 0.008 0.008
#> GSM153080 1 0.3429 0.5427 0.848 0.000 0.040 0.100 0.012
#> GSM153081 1 0.4467 0.2351 0.640 0.000 0.000 0.016 0.344
#> GSM153082 1 0.1087 0.6395 0.968 0.000 0.008 0.016 0.008
#> GSM153083 1 0.0671 0.6419 0.980 0.000 0.000 0.016 0.004
#> GSM153084 1 0.2054 0.5876 0.920 0.000 0.052 0.000 0.028
#> GSM153085 1 0.1405 0.6272 0.956 0.000 0.016 0.008 0.020
#> GSM153086 1 0.0510 0.6423 0.984 0.000 0.000 0.016 0.000
#> GSM153087 4 0.1179 0.7161 0.016 0.000 0.004 0.964 0.016
#> GSM153088 1 0.5982 -0.0180 0.552 0.000 0.000 0.136 0.312
#> GSM153089 3 0.1982 0.8985 0.012 0.000 0.932 0.028 0.028
#> GSM153090 4 0.5144 0.3642 0.064 0.000 0.000 0.632 0.304
#> GSM153091 1 0.0671 0.6419 0.980 0.000 0.000 0.016 0.004
#> GSM153092 1 0.1960 0.6285 0.928 0.000 0.004 0.020 0.048
#> GSM153093 4 0.1018 0.7141 0.016 0.000 0.000 0.968 0.016
#> GSM153094 1 0.0833 0.6411 0.976 0.000 0.004 0.016 0.004
#> GSM153095 1 0.0854 0.6421 0.976 0.000 0.004 0.012 0.008
#> GSM153096 1 0.1117 0.6402 0.964 0.000 0.000 0.016 0.020
#> GSM153097 1 0.0510 0.6423 0.984 0.000 0.000 0.016 0.000
#> GSM153098 4 0.5607 0.2889 0.228 0.000 0.000 0.632 0.140
#> GSM153099 4 0.5359 0.3102 0.080 0.000 0.000 0.616 0.304
#> GSM153100 1 0.3339 0.5516 0.836 0.000 0.000 0.040 0.124
#> GSM153101 1 0.1074 0.6394 0.968 0.000 0.004 0.016 0.012
#> GSM153102 1 0.1419 0.6344 0.956 0.000 0.012 0.016 0.016
#> GSM153103 1 0.0290 0.6409 0.992 0.000 0.000 0.008 0.000
#> GSM153104 4 0.0912 0.7168 0.016 0.000 0.012 0.972 0.000
#> GSM153106 1 0.1518 0.6330 0.952 0.000 0.012 0.020 0.016
#> GSM153107 1 0.0510 0.6423 0.984 0.000 0.000 0.016 0.000
#> GSM153108 1 0.5962 -0.3006 0.468 0.000 0.000 0.424 0.108
#> GSM153109 1 0.1419 0.6344 0.956 0.000 0.012 0.016 0.016
#> GSM153110 1 0.0912 0.6419 0.972 0.000 0.000 0.016 0.012
#> GSM153111 1 0.0510 0.6423 0.984 0.000 0.000 0.016 0.000
#> GSM153112 1 0.2782 0.5918 0.880 0.000 0.000 0.048 0.072
#> GSM153113 1 0.1716 0.6290 0.944 0.000 0.016 0.016 0.024
#> GSM153114 4 0.1877 0.7028 0.012 0.000 0.064 0.924 0.000
#> GSM187532 2 0.4365 0.7960 0.000 0.676 0.012 0.004 0.308
#> GSM187533 2 0.3895 0.8293 0.000 0.728 0.004 0.004 0.264
#> GSM187534 2 0.2474 0.8782 0.000 0.896 0.008 0.012 0.084
#> GSM187535 1 0.1405 0.6351 0.956 0.000 0.008 0.016 0.020
#> GSM152906 2 0.1608 0.8776 0.000 0.928 0.000 0.000 0.072
#> GSM152907 2 0.1608 0.8776 0.000 0.928 0.000 0.000 0.072
#> GSM152908 2 0.3452 0.8415 0.000 0.756 0.000 0.000 0.244
#> GSM152909 2 0.4251 0.7924 0.000 0.672 0.012 0.000 0.316
#> GSM152910 2 0.3452 0.8415 0.000 0.756 0.000 0.000 0.244
#> GSM152911 2 0.3362 0.8637 0.000 0.824 0.008 0.012 0.156
#> GSM152912 2 0.3452 0.8415 0.000 0.756 0.000 0.000 0.244
#> GSM152913 2 0.3443 0.8618 0.000 0.816 0.008 0.012 0.164
#> GSM152914 2 0.1569 0.8830 0.000 0.948 0.008 0.012 0.032
#> GSM152915 2 0.1731 0.8827 0.000 0.940 0.008 0.012 0.040
#> GSM152916 2 0.1608 0.8776 0.000 0.928 0.000 0.000 0.072
#> GSM152917 2 0.0693 0.8837 0.000 0.980 0.008 0.012 0.000
#> GSM152918 2 0.0693 0.8837 0.000 0.980 0.008 0.012 0.000
#> GSM152919 2 0.0693 0.8837 0.000 0.980 0.008 0.012 0.000
#> GSM152920 2 0.3452 0.8415 0.000 0.756 0.000 0.000 0.244
#> GSM152921 2 0.3452 0.8415 0.000 0.756 0.000 0.000 0.244
#> GSM152922 2 0.3452 0.8415 0.000 0.756 0.000 0.000 0.244
#> GSM152923 2 0.1608 0.8776 0.000 0.928 0.000 0.000 0.072
#> GSM152924 2 0.1608 0.8776 0.000 0.928 0.000 0.000 0.072
#> GSM152925 2 0.1608 0.8776 0.000 0.928 0.000 0.000 0.072
#> GSM152926 2 0.1608 0.8776 0.000 0.928 0.000 0.000 0.072
#> GSM152927 2 0.1608 0.8776 0.000 0.928 0.000 0.000 0.072
#> GSM152928 2 0.1608 0.8776 0.000 0.928 0.000 0.000 0.072
#> GSM152929 2 0.1608 0.8776 0.000 0.928 0.000 0.000 0.072
#> GSM152930 2 0.1608 0.8776 0.000 0.928 0.000 0.000 0.072
cbind(get_classes(res, k = 6), get_membership(res, k = 6))
#> class entropy silhouette p1 p2 p3 p4 p5 p6
#> GSM152839 6 0.5598 0.4140 0.248 0.000 0.024 0.004 NA 0.612
#> GSM152840 4 0.5692 0.4300 0.000 0.000 0.080 0.636 NA 0.084
#> GSM152841 4 0.1672 0.7996 0.004 0.000 0.016 0.932 NA 0.000
#> GSM152842 6 0.5560 0.4137 0.248 0.000 0.024 0.004 NA 0.616
#> GSM152843 6 0.5127 0.4411 0.252 0.000 0.004 0.008 NA 0.640
#> GSM152844 4 0.6212 0.3114 0.000 0.000 0.120 0.580 NA 0.088
#> GSM152845 3 0.5486 0.5903 0.000 0.000 0.496 0.000 NA 0.132
#> GSM152846 3 0.5830 0.6029 0.000 0.000 0.508 0.016 NA 0.132
#> GSM152847 6 0.5674 0.4109 0.236 0.000 0.032 0.004 NA 0.616
#> GSM152848 6 0.4912 0.4657 0.272 0.000 0.000 0.012 NA 0.644
#> GSM152849 6 0.5717 0.4118 0.232 0.000 0.036 0.004 NA 0.616
#> GSM152850 6 0.5385 0.4240 0.252 0.000 0.020 0.004 NA 0.628
#> GSM152851 4 0.1777 0.7975 0.004 0.000 0.024 0.928 NA 0.000
#> GSM152852 3 0.5828 0.6025 0.000 0.000 0.508 0.020 NA 0.120
#> GSM152853 4 0.6147 0.3277 0.000 0.000 0.120 0.588 NA 0.084
#> GSM152854 3 0.2798 0.7509 0.000 0.000 0.876 0.048 NA 0.020
#> GSM152855 4 0.2662 0.7135 0.004 0.000 0.000 0.840 NA 0.152
#> GSM153238 1 0.3725 0.7005 0.776 0.000 0.004 0.000 NA 0.172
#> GSM153239 4 0.4647 0.5579 0.000 0.000 0.172 0.724 NA 0.028
#> GSM153240 4 0.4225 -0.2374 0.004 0.000 0.000 0.508 NA 0.480
#> GSM153241 6 0.6375 0.3969 0.136 0.000 0.120 0.016 NA 0.612
#> GSM153242 3 0.3382 0.7265 0.000 0.000 0.820 0.008 NA 0.048
#> GSM153243 1 0.4985 -0.1881 0.476 0.000 0.464 0.000 NA 0.056
#> GSM153244 3 0.3187 0.6778 0.004 0.000 0.796 0.188 NA 0.000
#> GSM153245 4 0.3094 0.7400 0.000 0.000 0.048 0.860 NA 0.032
#> GSM153246 3 0.4638 0.6778 0.000 0.000 0.708 0.008 NA 0.172
#> GSM153247 1 0.3494 0.7215 0.792 0.000 0.000 0.004 NA 0.168
#> GSM153248 1 0.1411 0.8266 0.936 0.000 0.000 0.000 NA 0.060
#> GSM153249 4 0.0922 0.8043 0.004 0.000 0.000 0.968 NA 0.024
#> GSM153250 6 0.4141 0.4574 0.388 0.000 0.000 0.016 NA 0.596
#> GSM153251 3 0.2293 0.7496 0.004 0.000 0.896 0.080 NA 0.004
#> GSM153252 4 0.4264 -0.2821 0.016 0.000 0.000 0.500 NA 0.484
#> GSM153253 4 0.1536 0.8019 0.004 0.000 0.016 0.940 NA 0.000
#> GSM153254 3 0.4597 0.0537 0.004 0.000 0.488 0.484 NA 0.004
#> GSM153255 4 0.2234 0.7447 0.004 0.000 0.000 0.872 NA 0.124
#> GSM153256 6 0.4787 0.3929 0.052 0.000 0.000 0.432 NA 0.516
#> GSM153257 6 0.4264 0.2777 0.016 0.000 0.000 0.488 NA 0.496
#> GSM153258 6 0.4614 0.4164 0.400 0.000 0.008 0.004 NA 0.568
#> GSM153259 1 0.1010 0.8403 0.960 0.000 0.000 0.000 NA 0.036
#> GSM153260 3 0.5365 0.4868 0.308 0.000 0.596 0.000 NA 0.056
#> GSM153261 3 0.4518 0.6755 0.164 0.000 0.740 0.000 NA 0.056
#> GSM153262 4 0.1155 0.8057 0.004 0.000 0.004 0.956 NA 0.000
#> GSM153263 6 0.4310 0.4346 0.404 0.000 0.000 0.016 NA 0.576
#> GSM153264 6 0.4351 0.4077 0.416 0.000 0.000 0.008 NA 0.564
#> GSM153265 4 0.1413 0.8051 0.004 0.000 0.008 0.948 NA 0.004
#> GSM153266 6 0.4724 0.4129 0.404 0.000 0.008 0.008 NA 0.560
#> GSM153267 6 0.5101 0.3989 0.068 0.000 0.000 0.424 NA 0.504
#> GSM153268 4 0.3869 0.6755 0.000 0.000 0.040 0.796 NA 0.036
#> GSM153269 6 0.4927 0.3525 0.044 0.000 0.000 0.452 NA 0.496
#> GSM153270 6 0.4967 0.2866 0.020 0.000 0.012 0.472 NA 0.484
#> GSM153271 6 0.4389 0.4764 0.372 0.000 0.000 0.032 NA 0.596
#> GSM153272 6 0.4591 0.3388 0.036 0.000 0.000 0.464 NA 0.500
#> GSM153273 1 0.1644 0.8146 0.920 0.000 0.000 0.000 NA 0.076
#> GSM153274 6 0.4927 0.3525 0.044 0.000 0.000 0.452 NA 0.496
#> GSM153275 6 0.4492 0.2795 0.016 0.000 0.000 0.480 NA 0.496
#> GSM153276 6 0.4874 0.3438 0.040 0.000 0.000 0.456 NA 0.496
#> GSM153277 4 0.1931 0.7875 0.004 0.000 0.004 0.916 NA 0.068
#> GSM153278 1 0.6862 0.2071 0.452 0.000 0.156 0.000 NA 0.300
#> GSM153279 4 0.1663 0.8059 0.004 0.000 0.024 0.940 NA 0.008
#> GSM153280 4 0.1844 0.7953 0.000 0.000 0.024 0.924 NA 0.004
#> GSM153281 4 0.1226 0.8017 0.004 0.000 0.000 0.952 NA 0.040
#> GSM153282 4 0.1536 0.8019 0.004 0.000 0.016 0.940 NA 0.000
#> GSM153283 6 0.4419 0.4292 0.404 0.000 0.000 0.012 NA 0.572
#> GSM153284 6 0.4097 0.2619 0.008 0.000 0.000 0.492 NA 0.500
#> GSM153285 4 0.1194 0.8068 0.004 0.000 0.000 0.956 NA 0.008
#> GSM153286 6 0.4591 0.3388 0.036 0.000 0.000 0.464 NA 0.500
#> GSM153287 4 0.1668 0.7927 0.004 0.000 0.000 0.928 NA 0.060
#> GSM153288 6 0.4532 0.3297 0.032 0.000 0.000 0.468 NA 0.500
#> GSM153289 6 0.4751 0.3642 0.048 0.000 0.000 0.452 NA 0.500
#> GSM153290 4 0.1768 0.8005 0.004 0.000 0.020 0.932 NA 0.004
#> GSM153291 4 0.2278 0.7405 0.004 0.000 0.000 0.868 NA 0.128
#> GSM153292 4 0.1194 0.8032 0.004 0.000 0.000 0.956 NA 0.032
#> GSM153293 6 0.4878 0.4040 0.060 0.000 0.000 0.424 NA 0.516
#> GSM153294 1 0.2400 0.7632 0.872 0.000 0.000 0.008 NA 0.116
#> GSM153295 6 0.4695 0.3690 0.044 0.000 0.000 0.448 NA 0.508
#> GSM153054 1 0.3168 0.7094 0.804 0.000 0.000 0.000 NA 0.172
#> GSM153055 6 0.5283 0.4028 0.076 0.000 0.000 0.420 NA 0.496
#> GSM153056 6 0.6340 0.4698 0.080 0.000 0.044 0.124 NA 0.636
#> GSM153057 3 0.1870 0.7567 0.012 0.000 0.928 0.044 NA 0.012
#> GSM153058 3 0.0862 0.7551 0.004 0.000 0.972 0.016 NA 0.000
#> GSM153059 3 0.1370 0.7519 0.036 0.000 0.948 0.004 NA 0.012
#> GSM153060 3 0.2537 0.7509 0.000 0.000 0.888 0.016 NA 0.068
#> GSM153061 3 0.6983 0.3120 0.336 0.000 0.412 0.000 NA 0.144
#> GSM153062 3 0.4764 0.6692 0.000 0.000 0.660 0.000 NA 0.108
#> GSM153063 4 0.1693 0.8016 0.000 0.000 0.044 0.932 NA 0.004
#> GSM153064 1 0.3918 0.2450 0.632 0.000 0.000 0.004 NA 0.360
#> GSM153065 3 0.5168 0.2292 0.440 0.000 0.488 0.000 NA 0.064
#> GSM153066 1 0.1624 0.8268 0.936 0.000 0.044 0.000 NA 0.012
#> GSM153067 4 0.2595 0.7012 0.004 0.000 0.000 0.836 NA 0.160
#> GSM153068 3 0.2245 0.7465 0.040 0.000 0.908 0.000 NA 0.036
#> GSM153069 4 0.1668 0.7927 0.004 0.000 0.000 0.928 NA 0.060
#> GSM153070 6 0.4486 0.4415 0.396 0.000 0.000 0.016 NA 0.576
#> GSM153071 6 0.4814 0.4267 0.412 0.000 0.000 0.056 NA 0.532
#> GSM153072 1 0.1010 0.8394 0.960 0.000 0.000 0.004 NA 0.036
#> GSM153073 6 0.4512 0.4585 0.348 0.000 0.000 0.012 NA 0.616
#> GSM153074 4 0.2573 0.7362 0.004 0.000 0.000 0.856 NA 0.132
#> GSM153075 4 0.2609 0.7585 0.004 0.000 0.008 0.868 NA 0.112
#> GSM153076 6 0.4273 0.4679 0.380 0.000 0.000 0.024 NA 0.596
#> GSM153077 6 0.4357 0.4028 0.420 0.000 0.000 0.008 NA 0.560
#> GSM153078 6 0.5588 0.4055 0.276 0.000 0.028 0.000 NA 0.592
#> GSM153079 1 0.1003 0.8404 0.964 0.000 0.028 0.000 NA 0.004
#> GSM153080 1 0.4826 0.6075 0.716 0.000 0.068 0.184 NA 0.012
#> GSM153081 6 0.5523 0.2717 0.420 0.000 0.020 0.000 NA 0.484
#> GSM153082 1 0.0291 0.8492 0.992 0.000 0.000 0.000 NA 0.004
#> GSM153083 1 0.0260 0.8491 0.992 0.000 0.000 0.000 NA 0.008
#> GSM153084 1 0.2466 0.7561 0.872 0.000 0.112 0.000 NA 0.008
#> GSM153085 1 0.1542 0.8264 0.936 0.000 0.052 0.000 NA 0.004
#> GSM153086 1 0.0363 0.8482 0.988 0.000 0.000 0.000 NA 0.012
#> GSM153087 4 0.2531 0.7398 0.004 0.000 0.000 0.860 NA 0.128
#> GSM153088 6 0.4333 0.4726 0.376 0.000 0.000 0.028 NA 0.596
#> GSM153089 3 0.2358 0.7511 0.012 0.000 0.896 0.076 NA 0.004
#> GSM153090 6 0.4921 0.4057 0.064 0.000 0.000 0.420 NA 0.516
#> GSM153091 1 0.0260 0.8487 0.992 0.000 0.000 0.000 NA 0.008
#> GSM153092 1 0.3567 0.6662 0.796 0.000 0.016 0.008 NA 0.168
#> GSM153093 4 0.2420 0.7429 0.004 0.000 0.000 0.864 NA 0.128
#> GSM153094 1 0.0000 0.8487 1.000 0.000 0.000 0.000 NA 0.000
#> GSM153095 1 0.0508 0.8496 0.984 0.000 0.000 0.000 NA 0.004
#> GSM153096 1 0.1349 0.8294 0.940 0.000 0.000 0.000 NA 0.056
#> GSM153097 1 0.0363 0.8482 0.988 0.000 0.000 0.000 NA 0.012
#> GSM153098 4 0.5990 -0.1761 0.264 0.000 0.000 0.440 NA 0.296
#> GSM153099 6 0.4916 0.4101 0.064 0.000 0.000 0.416 NA 0.520
#> GSM153100 1 0.3430 0.6112 0.772 0.000 0.000 0.016 NA 0.208
#> GSM153101 1 0.0000 0.8487 1.000 0.000 0.000 0.000 NA 0.000
#> GSM153102 1 0.1285 0.8286 0.944 0.000 0.052 0.000 NA 0.004
#> GSM153103 1 0.0260 0.8491 0.992 0.000 0.000 0.000 NA 0.008
#> GSM153104 4 0.1080 0.8025 0.004 0.000 0.000 0.960 NA 0.032
#> GSM153106 1 0.1265 0.8318 0.948 0.000 0.044 0.000 NA 0.008
#> GSM153107 1 0.0405 0.8493 0.988 0.000 0.000 0.000 NA 0.008
#> GSM153108 1 0.6214 -0.2375 0.428 0.000 0.000 0.308 NA 0.256
#> GSM153109 1 0.1152 0.8330 0.952 0.000 0.044 0.000 NA 0.004
#> GSM153110 1 0.0935 0.8415 0.964 0.000 0.000 0.000 NA 0.032
#> GSM153111 1 0.0363 0.8482 0.988 0.000 0.000 0.000 NA 0.012
#> GSM153112 1 0.3361 0.6491 0.788 0.000 0.000 0.020 NA 0.188
#> GSM153113 1 0.1340 0.8323 0.948 0.000 0.040 0.000 NA 0.004
#> GSM153114 4 0.1690 0.8080 0.004 0.000 0.016 0.940 NA 0.020
#> GSM187532 2 0.4570 0.7076 0.000 0.588 0.008 0.000 NA 0.028
#> GSM187533 2 0.4230 0.7525 0.000 0.648 0.004 0.000 NA 0.024
#> GSM187534 2 0.2575 0.8313 0.000 0.872 0.004 0.000 NA 0.024
#> GSM187535 1 0.0603 0.8451 0.980 0.000 0.016 0.000 NA 0.000
#> GSM152906 2 0.2221 0.8302 0.000 0.896 0.000 0.000 NA 0.032
#> GSM152907 2 0.2221 0.8302 0.000 0.896 0.000 0.000 NA 0.032
#> GSM152908 2 0.3482 0.7721 0.000 0.684 0.000 0.000 NA 0.000
#> GSM152909 2 0.4455 0.7050 0.000 0.584 0.008 0.000 NA 0.020
#> GSM152910 2 0.3482 0.7721 0.000 0.684 0.000 0.000 NA 0.000
#> GSM152911 2 0.2848 0.8208 0.000 0.828 0.000 0.004 NA 0.008
#> GSM152912 2 0.3482 0.7721 0.000 0.684 0.000 0.000 NA 0.000
#> GSM152913 2 0.3056 0.8155 0.000 0.804 0.000 0.004 NA 0.008
#> GSM152914 2 0.1477 0.8388 0.000 0.940 0.000 0.004 NA 0.008
#> GSM152915 2 0.1728 0.8377 0.000 0.924 0.000 0.004 NA 0.008
#> GSM152916 2 0.2277 0.8297 0.000 0.892 0.000 0.000 NA 0.032
#> GSM152917 2 0.0436 0.8406 0.000 0.988 0.000 0.004 NA 0.004
#> GSM152918 2 0.0436 0.8406 0.000 0.988 0.000 0.004 NA 0.004
#> GSM152919 2 0.0436 0.8406 0.000 0.988 0.000 0.004 NA 0.004
#> GSM152920 2 0.3482 0.7721 0.000 0.684 0.000 0.000 NA 0.000
#> GSM152921 2 0.3482 0.7721 0.000 0.684 0.000 0.000 NA 0.000
#> GSM152922 2 0.3482 0.7721 0.000 0.684 0.000 0.000 NA 0.000
#> GSM152923 2 0.2221 0.8302 0.000 0.896 0.000 0.000 NA 0.032
#> GSM152924 2 0.2277 0.8297 0.000 0.892 0.000 0.000 NA 0.032
#> GSM152925 2 0.2277 0.8297 0.000 0.892 0.000 0.000 NA 0.032
#> GSM152926 2 0.2221 0.8302 0.000 0.896 0.000 0.000 NA 0.032
#> GSM152927 2 0.2277 0.8297 0.000 0.892 0.000 0.000 NA 0.032
#> GSM152928 2 0.2221 0.8302 0.000 0.896 0.000 0.000 NA 0.032
#> GSM152929 2 0.2221 0.8302 0.000 0.896 0.000 0.000 NA 0.032
#> GSM152930 2 0.2221 0.8302 0.000 0.896 0.000 0.000 NA 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 tissue(p) k
#> ATC:kmeans 164 1.08e-29 2
#> ATC:kmeans 155 5.49e-29 3
#> ATC:kmeans 154 2.31e-30 4
#> ATC:kmeans 114 2.22e-25 5
#> ATC:kmeans 108 1.03e-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["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 12013 rows and 164 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 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 0.936 0.914 0.967 0.4549 0.556 0.556
#> 3 3 0.835 0.867 0.943 0.4552 0.710 0.511
#> 4 4 0.745 0.830 0.901 0.1143 0.791 0.484
#> 5 5 0.825 0.844 0.913 0.0761 0.834 0.475
#> 6 6 0.762 0.689 0.777 0.0371 0.955 0.786
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
#> GSM152839 1 0.0000 0.9611 1.000 0.000
#> GSM152840 1 0.0000 0.9611 1.000 0.000
#> GSM152841 1 0.0000 0.9611 1.000 0.000
#> GSM152842 1 0.0000 0.9611 1.000 0.000
#> GSM152843 1 0.0000 0.9611 1.000 0.000
#> GSM152844 1 0.0000 0.9611 1.000 0.000
#> GSM152845 2 0.0000 0.9716 0.000 1.000
#> GSM152846 2 0.0938 0.9614 0.012 0.988
#> GSM152847 1 0.0000 0.9611 1.000 0.000
#> GSM152848 1 0.0000 0.9611 1.000 0.000
#> GSM152849 1 0.0000 0.9611 1.000 0.000
#> GSM152850 1 0.0000 0.9611 1.000 0.000
#> GSM152851 1 0.0000 0.9611 1.000 0.000
#> GSM152852 2 0.8661 0.5879 0.288 0.712
#> GSM152853 1 0.0000 0.9611 1.000 0.000
#> GSM152854 1 0.9866 0.2154 0.568 0.432
#> GSM152855 1 0.0000 0.9611 1.000 0.000
#> GSM153238 1 0.0000 0.9611 1.000 0.000
#> GSM153239 1 0.0000 0.9611 1.000 0.000
#> GSM153240 1 0.0000 0.9611 1.000 0.000
#> GSM153241 1 0.0000 0.9611 1.000 0.000
#> GSM153242 2 0.0000 0.9716 0.000 1.000
#> GSM153243 2 0.0000 0.9716 0.000 1.000
#> GSM153244 2 0.3584 0.9071 0.068 0.932
#> GSM153245 1 0.0000 0.9611 1.000 0.000
#> GSM153246 1 0.2043 0.9319 0.968 0.032
#> GSM153247 1 0.0000 0.9611 1.000 0.000
#> GSM153248 1 0.0000 0.9611 1.000 0.000
#> GSM153249 1 0.0000 0.9611 1.000 0.000
#> GSM153250 1 0.0000 0.9611 1.000 0.000
#> GSM153251 2 0.0000 0.9716 0.000 1.000
#> GSM153252 1 0.0000 0.9611 1.000 0.000
#> GSM153253 1 0.0000 0.9611 1.000 0.000
#> GSM153254 2 0.9393 0.4437 0.356 0.644
#> GSM153255 1 0.0000 0.9611 1.000 0.000
#> GSM153256 1 0.0000 0.9611 1.000 0.000
#> GSM153257 1 0.0000 0.9611 1.000 0.000
#> GSM153258 1 0.0000 0.9611 1.000 0.000
#> GSM153259 1 0.0000 0.9611 1.000 0.000
#> GSM153260 2 0.0000 0.9716 0.000 1.000
#> GSM153261 2 0.0000 0.9716 0.000 1.000
#> GSM153262 1 0.0000 0.9611 1.000 0.000
#> GSM153263 1 0.0000 0.9611 1.000 0.000
#> GSM153264 1 0.0000 0.9611 1.000 0.000
#> GSM153265 1 0.0000 0.9611 1.000 0.000
#> GSM153266 1 0.0000 0.9611 1.000 0.000
#> GSM153267 1 0.0000 0.9611 1.000 0.000
#> GSM153268 1 0.0000 0.9611 1.000 0.000
#> GSM153269 1 0.0000 0.9611 1.000 0.000
#> GSM153270 1 0.0000 0.9611 1.000 0.000
#> GSM153271 1 0.0000 0.9611 1.000 0.000
#> GSM153272 1 0.0000 0.9611 1.000 0.000
#> GSM153273 1 0.0000 0.9611 1.000 0.000
#> GSM153274 1 0.0000 0.9611 1.000 0.000
#> GSM153275 1 0.0000 0.9611 1.000 0.000
#> GSM153276 1 0.0000 0.9611 1.000 0.000
#> GSM153277 1 0.0000 0.9611 1.000 0.000
#> GSM153278 1 0.0000 0.9611 1.000 0.000
#> GSM153279 1 0.0000 0.9611 1.000 0.000
#> GSM153280 1 0.0000 0.9611 1.000 0.000
#> GSM153281 1 0.0000 0.9611 1.000 0.000
#> GSM153282 1 0.0000 0.9611 1.000 0.000
#> GSM153283 1 0.0000 0.9611 1.000 0.000
#> GSM153284 1 0.0000 0.9611 1.000 0.000
#> GSM153285 1 0.0000 0.9611 1.000 0.000
#> GSM153286 1 0.0000 0.9611 1.000 0.000
#> GSM153287 1 0.0000 0.9611 1.000 0.000
#> GSM153288 1 0.0000 0.9611 1.000 0.000
#> GSM153289 1 0.0000 0.9611 1.000 0.000
#> GSM153290 1 0.0000 0.9611 1.000 0.000
#> GSM153291 1 0.0000 0.9611 1.000 0.000
#> GSM153292 1 0.0000 0.9611 1.000 0.000
#> GSM153293 1 0.0000 0.9611 1.000 0.000
#> GSM153294 1 0.0000 0.9611 1.000 0.000
#> GSM153295 1 0.0000 0.9611 1.000 0.000
#> GSM153054 1 0.0000 0.9611 1.000 0.000
#> GSM153055 1 0.0000 0.9611 1.000 0.000
#> GSM153056 1 0.0000 0.9611 1.000 0.000
#> GSM153057 2 0.2603 0.9316 0.044 0.956
#> GSM153058 2 0.0000 0.9716 0.000 1.000
#> GSM153059 2 0.0000 0.9716 0.000 1.000
#> GSM153060 1 1.0000 -0.0126 0.504 0.496
#> GSM153061 2 0.6531 0.7868 0.168 0.832
#> GSM153062 2 0.0000 0.9716 0.000 1.000
#> GSM153063 1 0.0000 0.9611 1.000 0.000
#> GSM153064 1 0.0000 0.9611 1.000 0.000
#> GSM153065 2 0.0000 0.9716 0.000 1.000
#> GSM153066 2 0.0000 0.9716 0.000 1.000
#> GSM153067 1 0.0000 0.9611 1.000 0.000
#> GSM153068 2 0.0000 0.9716 0.000 1.000
#> GSM153069 1 0.0000 0.9611 1.000 0.000
#> GSM153070 1 0.0000 0.9611 1.000 0.000
#> GSM153071 1 0.0000 0.9611 1.000 0.000
#> GSM153072 1 0.0000 0.9611 1.000 0.000
#> GSM153073 1 0.0000 0.9611 1.000 0.000
#> GSM153074 1 0.0000 0.9611 1.000 0.000
#> GSM153075 1 0.0000 0.9611 1.000 0.000
#> GSM153076 1 0.0000 0.9611 1.000 0.000
#> GSM153077 1 0.0000 0.9611 1.000 0.000
#> GSM153078 1 0.0000 0.9611 1.000 0.000
#> GSM153079 1 0.8713 0.5927 0.708 0.292
#> GSM153080 1 0.0000 0.9611 1.000 0.000
#> GSM153081 1 0.0000 0.9611 1.000 0.000
#> GSM153082 2 0.9988 0.0104 0.480 0.520
#> GSM153083 1 0.9815 0.3075 0.580 0.420
#> GSM153084 2 0.0000 0.9716 0.000 1.000
#> GSM153085 2 0.0000 0.9716 0.000 1.000
#> GSM153086 1 0.4431 0.8726 0.908 0.092
#> GSM153087 1 0.0000 0.9611 1.000 0.000
#> GSM153088 1 0.0000 0.9611 1.000 0.000
#> GSM153089 2 0.0000 0.9716 0.000 1.000
#> GSM153090 1 0.0000 0.9611 1.000 0.000
#> GSM153091 1 0.9608 0.4011 0.616 0.384
#> GSM153092 1 0.0000 0.9611 1.000 0.000
#> GSM153093 1 0.0000 0.9611 1.000 0.000
#> GSM153094 1 0.9896 0.2496 0.560 0.440
#> GSM153095 1 0.0000 0.9611 1.000 0.000
#> GSM153096 1 0.0000 0.9611 1.000 0.000
#> GSM153097 1 0.9393 0.4656 0.644 0.356
#> GSM153098 1 0.0000 0.9611 1.000 0.000
#> GSM153099 1 0.0000 0.9611 1.000 0.000
#> GSM153100 1 0.0000 0.9611 1.000 0.000
#> GSM153101 1 0.2948 0.9135 0.948 0.052
#> GSM153102 2 0.0000 0.9716 0.000 1.000
#> GSM153103 1 0.9427 0.4568 0.640 0.360
#> GSM153104 1 0.0000 0.9611 1.000 0.000
#> GSM153106 1 0.8608 0.6085 0.716 0.284
#> GSM153107 1 0.0000 0.9611 1.000 0.000
#> GSM153108 1 0.0000 0.9611 1.000 0.000
#> GSM153109 2 0.0000 0.9716 0.000 1.000
#> GSM153110 1 0.0000 0.9611 1.000 0.000
#> GSM153111 1 0.9608 0.4012 0.616 0.384
#> GSM153112 1 0.0000 0.9611 1.000 0.000
#> GSM153113 2 0.0000 0.9716 0.000 1.000
#> GSM153114 1 0.0000 0.9611 1.000 0.000
#> GSM187532 2 0.0000 0.9716 0.000 1.000
#> GSM187533 2 0.0000 0.9716 0.000 1.000
#> GSM187534 2 0.0000 0.9716 0.000 1.000
#> GSM187535 2 0.0000 0.9716 0.000 1.000
#> GSM152906 2 0.0000 0.9716 0.000 1.000
#> GSM152907 2 0.0000 0.9716 0.000 1.000
#> GSM152908 2 0.0000 0.9716 0.000 1.000
#> GSM152909 2 0.0000 0.9716 0.000 1.000
#> GSM152910 2 0.0000 0.9716 0.000 1.000
#> GSM152911 2 0.0000 0.9716 0.000 1.000
#> GSM152912 2 0.0000 0.9716 0.000 1.000
#> GSM152913 2 0.0000 0.9716 0.000 1.000
#> GSM152914 2 0.0000 0.9716 0.000 1.000
#> GSM152915 2 0.0000 0.9716 0.000 1.000
#> GSM152916 2 0.0000 0.9716 0.000 1.000
#> GSM152917 2 0.0000 0.9716 0.000 1.000
#> GSM152918 2 0.0000 0.9716 0.000 1.000
#> GSM152919 2 0.0000 0.9716 0.000 1.000
#> GSM152920 2 0.0000 0.9716 0.000 1.000
#> GSM152921 2 0.0000 0.9716 0.000 1.000
#> GSM152922 2 0.0000 0.9716 0.000 1.000
#> GSM152923 2 0.0000 0.9716 0.000 1.000
#> GSM152924 2 0.0000 0.9716 0.000 1.000
#> GSM152925 2 0.0000 0.9716 0.000 1.000
#> GSM152926 2 0.0000 0.9716 0.000 1.000
#> GSM152927 2 0.0000 0.9716 0.000 1.000
#> GSM152928 2 0.0000 0.9716 0.000 1.000
#> GSM152929 2 0.0000 0.9716 0.000 1.000
#> GSM152930 2 0.0000 0.9716 0.000 1.000
cbind(get_classes(res, k = 3), get_membership(res, k = 3))
#> class entropy silhouette p1 p2 p3
#> GSM152839 1 0.0424 0.897 0.992 0.000 0.008
#> GSM152840 3 0.0000 0.946 0.000 0.000 1.000
#> GSM152841 3 0.0000 0.946 0.000 0.000 1.000
#> GSM152842 1 0.0000 0.901 1.000 0.000 0.000
#> GSM152843 1 0.0000 0.901 1.000 0.000 0.000
#> GSM152844 3 0.0000 0.946 0.000 0.000 1.000
#> GSM152845 2 0.0000 0.981 0.000 1.000 0.000
#> GSM152846 3 0.0237 0.943 0.000 0.004 0.996
#> GSM152847 1 0.0000 0.901 1.000 0.000 0.000
#> GSM152848 1 0.0000 0.901 1.000 0.000 0.000
#> GSM152849 1 0.0424 0.897 0.992 0.000 0.008
#> GSM152850 1 0.0000 0.901 1.000 0.000 0.000
#> GSM152851 3 0.0000 0.946 0.000 0.000 1.000
#> GSM152852 3 0.0000 0.946 0.000 0.000 1.000
#> GSM152853 3 0.0000 0.946 0.000 0.000 1.000
#> GSM152854 3 0.0000 0.946 0.000 0.000 1.000
#> GSM152855 3 0.0237 0.943 0.004 0.000 0.996
#> GSM153238 1 0.0000 0.901 1.000 0.000 0.000
#> GSM153239 3 0.0000 0.946 0.000 0.000 1.000
#> GSM153240 3 0.0000 0.946 0.000 0.000 1.000
#> GSM153241 3 0.3619 0.814 0.136 0.000 0.864
#> GSM153242 3 0.4654 0.714 0.000 0.208 0.792
#> GSM153243 2 0.0000 0.981 0.000 1.000 0.000
#> GSM153244 3 0.0592 0.937 0.000 0.012 0.988
#> GSM153245 3 0.0000 0.946 0.000 0.000 1.000
#> GSM153246 3 0.1964 0.898 0.056 0.000 0.944
#> GSM153247 1 0.0000 0.901 1.000 0.000 0.000
#> GSM153248 1 0.0000 0.901 1.000 0.000 0.000
#> GSM153249 3 0.0000 0.946 0.000 0.000 1.000
#> GSM153250 1 0.0000 0.901 1.000 0.000 0.000
#> GSM153251 3 0.6180 0.265 0.000 0.416 0.584
#> GSM153252 1 0.6308 0.201 0.508 0.000 0.492
#> GSM153253 3 0.0000 0.946 0.000 0.000 1.000
#> GSM153254 3 0.0000 0.946 0.000 0.000 1.000
#> GSM153255 3 0.0000 0.946 0.000 0.000 1.000
#> GSM153256 1 0.4974 0.704 0.764 0.000 0.236
#> GSM153257 1 0.6215 0.385 0.572 0.000 0.428
#> GSM153258 1 0.0000 0.901 1.000 0.000 0.000
#> GSM153259 1 0.0000 0.901 1.000 0.000 0.000
#> GSM153260 2 0.2448 0.914 0.076 0.924 0.000
#> GSM153261 2 0.7338 0.528 0.060 0.652 0.288
#> GSM153262 3 0.0000 0.946 0.000 0.000 1.000
#> GSM153263 1 0.0000 0.901 1.000 0.000 0.000
#> GSM153264 1 0.0000 0.901 1.000 0.000 0.000
#> GSM153265 3 0.0000 0.946 0.000 0.000 1.000
#> GSM153266 1 0.0000 0.901 1.000 0.000 0.000
#> GSM153267 1 0.5810 0.566 0.664 0.000 0.336
#> GSM153268 3 0.0000 0.946 0.000 0.000 1.000
#> GSM153269 1 0.6286 0.289 0.536 0.000 0.464
#> GSM153270 3 0.0000 0.946 0.000 0.000 1.000
#> GSM153271 1 0.0000 0.901 1.000 0.000 0.000
#> GSM153272 1 0.6204 0.395 0.576 0.000 0.424
#> GSM153273 1 0.0000 0.901 1.000 0.000 0.000
#> GSM153274 3 0.3879 0.775 0.152 0.000 0.848
#> GSM153275 3 0.4750 0.668 0.216 0.000 0.784
#> GSM153276 3 0.3412 0.815 0.124 0.000 0.876
#> GSM153277 3 0.0000 0.946 0.000 0.000 1.000
#> GSM153278 1 0.0424 0.896 0.992 0.000 0.008
#> GSM153279 3 0.0000 0.946 0.000 0.000 1.000
#> GSM153280 3 0.0000 0.946 0.000 0.000 1.000
#> GSM153281 3 0.0000 0.946 0.000 0.000 1.000
#> GSM153282 3 0.0000 0.946 0.000 0.000 1.000
#> GSM153283 1 0.0000 0.901 1.000 0.000 0.000
#> GSM153284 3 0.6307 -0.159 0.488 0.000 0.512
#> GSM153285 3 0.0000 0.946 0.000 0.000 1.000
#> GSM153286 1 0.6192 0.404 0.580 0.000 0.420
#> GSM153287 3 0.0000 0.946 0.000 0.000 1.000
#> GSM153288 1 0.6267 0.323 0.548 0.000 0.452
#> GSM153289 1 0.6180 0.413 0.584 0.000 0.416
#> GSM153290 3 0.0000 0.946 0.000 0.000 1.000
#> GSM153291 3 0.0000 0.946 0.000 0.000 1.000
#> GSM153292 3 0.0000 0.946 0.000 0.000 1.000
#> GSM153293 1 0.4002 0.783 0.840 0.000 0.160
#> GSM153294 1 0.0000 0.901 1.000 0.000 0.000
#> GSM153295 1 0.5733 0.581 0.676 0.000 0.324
#> GSM153054 1 0.0000 0.901 1.000 0.000 0.000
#> GSM153055 1 0.6154 0.431 0.592 0.000 0.408
#> GSM153056 3 0.1529 0.916 0.040 0.000 0.960
#> GSM153057 3 0.4121 0.772 0.000 0.168 0.832
#> GSM153058 3 0.6192 0.253 0.000 0.420 0.580
#> GSM153059 2 0.0000 0.981 0.000 1.000 0.000
#> GSM153060 3 0.0424 0.940 0.000 0.008 0.992
#> GSM153061 1 0.3192 0.798 0.888 0.112 0.000
#> GSM153062 2 0.0000 0.981 0.000 1.000 0.000
#> GSM153063 3 0.0000 0.946 0.000 0.000 1.000
#> GSM153064 1 0.0000 0.901 1.000 0.000 0.000
#> GSM153065 2 0.0237 0.978 0.004 0.996 0.000
#> GSM153066 2 0.0000 0.981 0.000 1.000 0.000
#> GSM153067 3 0.1031 0.927 0.024 0.000 0.976
#> GSM153068 2 0.0000 0.981 0.000 1.000 0.000
#> GSM153069 3 0.0000 0.946 0.000 0.000 1.000
#> GSM153070 1 0.0000 0.901 1.000 0.000 0.000
#> GSM153071 1 0.0000 0.901 1.000 0.000 0.000
#> GSM153072 1 0.0000 0.901 1.000 0.000 0.000
#> GSM153073 1 0.0000 0.901 1.000 0.000 0.000
#> GSM153074 3 0.0000 0.946 0.000 0.000 1.000
#> GSM153075 3 0.0000 0.946 0.000 0.000 1.000
#> GSM153076 1 0.0000 0.901 1.000 0.000 0.000
#> GSM153077 1 0.0000 0.901 1.000 0.000 0.000
#> GSM153078 1 0.0000 0.901 1.000 0.000 0.000
#> GSM153079 1 0.0000 0.901 1.000 0.000 0.000
#> GSM153080 3 0.0592 0.937 0.012 0.000 0.988
#> GSM153081 1 0.0000 0.901 1.000 0.000 0.000
#> GSM153082 1 0.0000 0.901 1.000 0.000 0.000
#> GSM153083 1 0.0000 0.901 1.000 0.000 0.000
#> GSM153084 2 0.0000 0.981 0.000 1.000 0.000
#> GSM153085 2 0.5016 0.697 0.240 0.760 0.000
#> GSM153086 1 0.0000 0.901 1.000 0.000 0.000
#> GSM153087 3 0.0000 0.946 0.000 0.000 1.000
#> GSM153088 1 0.0000 0.901 1.000 0.000 0.000
#> GSM153089 2 0.0892 0.964 0.000 0.980 0.020
#> GSM153090 1 0.5529 0.622 0.704 0.000 0.296
#> GSM153091 1 0.0000 0.901 1.000 0.000 0.000
#> GSM153092 1 0.0000 0.901 1.000 0.000 0.000
#> GSM153093 3 0.0000 0.946 0.000 0.000 1.000
#> GSM153094 1 0.0000 0.901 1.000 0.000 0.000
#> GSM153095 1 0.0000 0.901 1.000 0.000 0.000
#> GSM153096 1 0.0000 0.901 1.000 0.000 0.000
#> GSM153097 1 0.0000 0.901 1.000 0.000 0.000
#> GSM153098 1 0.4931 0.711 0.768 0.000 0.232
#> GSM153099 1 0.5431 0.640 0.716 0.000 0.284
#> GSM153100 1 0.0000 0.901 1.000 0.000 0.000
#> GSM153101 1 0.0000 0.901 1.000 0.000 0.000
#> GSM153102 2 0.2066 0.929 0.060 0.940 0.000
#> GSM153103 1 0.0000 0.901 1.000 0.000 0.000
#> GSM153104 3 0.0000 0.946 0.000 0.000 1.000
#> GSM153106 1 0.7083 0.401 0.592 0.028 0.380
#> GSM153107 1 0.0000 0.901 1.000 0.000 0.000
#> GSM153108 1 0.4399 0.757 0.812 0.000 0.188
#> GSM153109 2 0.2165 0.926 0.064 0.936 0.000
#> GSM153110 1 0.0000 0.901 1.000 0.000 0.000
#> GSM153111 1 0.0000 0.901 1.000 0.000 0.000
#> GSM153112 1 0.0000 0.901 1.000 0.000 0.000
#> GSM153113 2 0.0000 0.981 0.000 1.000 0.000
#> GSM153114 3 0.0000 0.946 0.000 0.000 1.000
#> GSM187532 2 0.0000 0.981 0.000 1.000 0.000
#> GSM187533 2 0.0000 0.981 0.000 1.000 0.000
#> GSM187534 2 0.0000 0.981 0.000 1.000 0.000
#> GSM187535 2 0.0000 0.981 0.000 1.000 0.000
#> GSM152906 2 0.0000 0.981 0.000 1.000 0.000
#> GSM152907 2 0.0000 0.981 0.000 1.000 0.000
#> GSM152908 2 0.0000 0.981 0.000 1.000 0.000
#> GSM152909 2 0.0000 0.981 0.000 1.000 0.000
#> GSM152910 2 0.0000 0.981 0.000 1.000 0.000
#> GSM152911 2 0.0000 0.981 0.000 1.000 0.000
#> GSM152912 2 0.0000 0.981 0.000 1.000 0.000
#> GSM152913 2 0.0000 0.981 0.000 1.000 0.000
#> GSM152914 2 0.0000 0.981 0.000 1.000 0.000
#> GSM152915 2 0.0000 0.981 0.000 1.000 0.000
#> GSM152916 2 0.0000 0.981 0.000 1.000 0.000
#> GSM152917 2 0.0000 0.981 0.000 1.000 0.000
#> GSM152918 2 0.0000 0.981 0.000 1.000 0.000
#> GSM152919 2 0.0000 0.981 0.000 1.000 0.000
#> GSM152920 2 0.0000 0.981 0.000 1.000 0.000
#> GSM152921 2 0.0000 0.981 0.000 1.000 0.000
#> GSM152922 2 0.0000 0.981 0.000 1.000 0.000
#> GSM152923 2 0.0000 0.981 0.000 1.000 0.000
#> GSM152924 2 0.0000 0.981 0.000 1.000 0.000
#> GSM152925 2 0.0000 0.981 0.000 1.000 0.000
#> GSM152926 2 0.0000 0.981 0.000 1.000 0.000
#> GSM152927 2 0.0000 0.981 0.000 1.000 0.000
#> GSM152928 2 0.0000 0.981 0.000 1.000 0.000
#> GSM152929 2 0.0000 0.981 0.000 1.000 0.000
#> GSM152930 2 0.0000 0.981 0.000 1.000 0.000
cbind(get_classes(res, k = 4), get_membership(res, k = 4))
#> class entropy silhouette p1 p2 p3 p4
#> GSM152839 1 0.4996 0.8261 0.752 0.000 0.056 0.192
#> GSM152840 4 0.4585 0.6406 0.000 0.000 0.332 0.668
#> GSM152841 4 0.3356 0.8274 0.000 0.000 0.176 0.824
#> GSM152842 1 0.3991 0.8703 0.808 0.000 0.020 0.172
#> GSM152843 1 0.3356 0.8766 0.824 0.000 0.000 0.176
#> GSM152844 3 0.4454 0.3968 0.000 0.000 0.692 0.308
#> GSM152845 3 0.3172 0.7418 0.000 0.160 0.840 0.000
#> GSM152846 3 0.0000 0.8147 0.000 0.000 1.000 0.000
#> GSM152847 1 0.4633 0.8509 0.780 0.000 0.048 0.172
#> GSM152848 1 0.3400 0.8748 0.820 0.000 0.000 0.180
#> GSM152849 1 0.7475 0.2548 0.448 0.000 0.372 0.180
#> GSM152850 1 0.3636 0.8764 0.820 0.000 0.008 0.172
#> GSM152851 4 0.3764 0.7973 0.000 0.000 0.216 0.784
#> GSM152852 3 0.0000 0.8147 0.000 0.000 1.000 0.000
#> GSM152853 3 0.4746 0.2388 0.000 0.000 0.632 0.368
#> GSM152854 3 0.0000 0.8147 0.000 0.000 1.000 0.000
#> GSM152855 4 0.0817 0.8625 0.000 0.000 0.024 0.976
#> GSM153238 1 0.0000 0.8766 1.000 0.000 0.000 0.000
#> GSM153239 3 0.4643 0.3085 0.000 0.000 0.656 0.344
#> GSM153240 4 0.0188 0.8596 0.000 0.000 0.004 0.996
#> GSM153241 3 0.5228 0.5658 0.024 0.000 0.664 0.312
#> GSM153242 3 0.0000 0.8147 0.000 0.000 1.000 0.000
#> GSM153243 3 0.4956 0.7412 0.108 0.116 0.776 0.000
#> GSM153244 3 0.0188 0.8127 0.000 0.000 0.996 0.004
#> GSM153245 4 0.4855 0.5029 0.000 0.000 0.400 0.600
#> GSM153246 3 0.1302 0.8044 0.000 0.000 0.956 0.044
#> GSM153247 1 0.3448 0.8790 0.828 0.000 0.004 0.168
#> GSM153248 1 0.0188 0.8776 0.996 0.000 0.000 0.004
#> GSM153249 4 0.3172 0.8357 0.000 0.000 0.160 0.840
#> GSM153250 1 0.3400 0.8748 0.820 0.000 0.000 0.180
#> GSM153251 3 0.0000 0.8147 0.000 0.000 1.000 0.000
#> GSM153252 4 0.0000 0.8583 0.000 0.000 0.000 1.000
#> GSM153253 4 0.3311 0.8294 0.000 0.000 0.172 0.828
#> GSM153254 3 0.0000 0.8147 0.000 0.000 1.000 0.000
#> GSM153255 4 0.0592 0.8618 0.000 0.000 0.016 0.984
#> GSM153256 4 0.1211 0.8343 0.040 0.000 0.000 0.960
#> GSM153257 4 0.0188 0.8576 0.004 0.000 0.000 0.996
#> GSM153258 1 0.3123 0.8823 0.844 0.000 0.000 0.156
#> GSM153259 1 0.0000 0.8766 1.000 0.000 0.000 0.000
#> GSM153260 3 0.3636 0.7561 0.172 0.008 0.820 0.000
#> GSM153261 3 0.2868 0.7804 0.136 0.000 0.864 0.000
#> GSM153262 4 0.3311 0.8294 0.000 0.000 0.172 0.828
#> GSM153263 1 0.3400 0.8748 0.820 0.000 0.000 0.180
#> GSM153264 1 0.3311 0.8782 0.828 0.000 0.000 0.172
#> GSM153265 4 0.3356 0.8274 0.000 0.000 0.176 0.824
#> GSM153266 1 0.3024 0.8836 0.852 0.000 0.000 0.148
#> GSM153267 4 0.0469 0.8536 0.012 0.000 0.000 0.988
#> GSM153268 4 0.3444 0.8224 0.000 0.000 0.184 0.816
#> GSM153269 4 0.0188 0.8576 0.004 0.000 0.000 0.996
#> GSM153270 4 0.2814 0.8467 0.000 0.000 0.132 0.868
#> GSM153271 1 0.3400 0.8748 0.820 0.000 0.000 0.180
#> GSM153272 4 0.0188 0.8576 0.004 0.000 0.000 0.996
#> GSM153273 1 0.0000 0.8766 1.000 0.000 0.000 0.000
#> GSM153274 4 0.0000 0.8583 0.000 0.000 0.000 1.000
#> GSM153275 4 0.0188 0.8576 0.004 0.000 0.000 0.996
#> GSM153276 4 0.0188 0.8576 0.004 0.000 0.000 0.996
#> GSM153277 4 0.3356 0.8274 0.000 0.000 0.176 0.824
#> GSM153278 3 0.4319 0.7056 0.228 0.000 0.760 0.012
#> GSM153279 4 0.3444 0.8226 0.000 0.000 0.184 0.816
#> GSM153280 4 0.3400 0.8248 0.000 0.000 0.180 0.820
#> GSM153281 4 0.3172 0.8357 0.000 0.000 0.160 0.840
#> GSM153282 4 0.3400 0.8248 0.000 0.000 0.180 0.820
#> GSM153283 1 0.3311 0.8782 0.828 0.000 0.000 0.172
#> GSM153284 4 0.0188 0.8576 0.004 0.000 0.000 0.996
#> GSM153285 4 0.3074 0.8387 0.000 0.000 0.152 0.848
#> GSM153286 4 0.0188 0.8576 0.004 0.000 0.000 0.996
#> GSM153287 4 0.0707 0.8623 0.000 0.000 0.020 0.980
#> GSM153288 4 0.0188 0.8576 0.004 0.000 0.000 0.996
#> GSM153289 4 0.0188 0.8576 0.004 0.000 0.000 0.996
#> GSM153290 4 0.3400 0.8248 0.000 0.000 0.180 0.820
#> GSM153291 4 0.0707 0.8623 0.000 0.000 0.020 0.980
#> GSM153292 4 0.3172 0.8357 0.000 0.000 0.160 0.840
#> GSM153293 4 0.1389 0.8276 0.048 0.000 0.000 0.952
#> GSM153294 1 0.2760 0.8845 0.872 0.000 0.000 0.128
#> GSM153295 4 0.1118 0.8381 0.036 0.000 0.000 0.964
#> GSM153054 1 0.0817 0.8815 0.976 0.000 0.000 0.024
#> GSM153055 4 0.0592 0.8515 0.016 0.000 0.000 0.984
#> GSM153056 4 0.5263 -0.0553 0.008 0.000 0.448 0.544
#> GSM153057 3 0.0000 0.8147 0.000 0.000 1.000 0.000
#> GSM153058 3 0.0188 0.8149 0.000 0.004 0.996 0.000
#> GSM153059 3 0.3219 0.7380 0.000 0.164 0.836 0.000
#> GSM153060 3 0.0000 0.8147 0.000 0.000 1.000 0.000
#> GSM153061 3 0.3610 0.7390 0.200 0.000 0.800 0.000
#> GSM153062 3 0.3172 0.7418 0.000 0.160 0.840 0.000
#> GSM153063 4 0.4134 0.7497 0.000 0.000 0.260 0.740
#> GSM153064 1 0.0592 0.8801 0.984 0.000 0.000 0.016
#> GSM153065 3 0.4849 0.7449 0.164 0.064 0.772 0.000
#> GSM153066 2 0.0000 0.9874 0.000 1.000 0.000 0.000
#> GSM153067 4 0.0592 0.8618 0.000 0.000 0.016 0.984
#> GSM153068 3 0.3172 0.7418 0.000 0.160 0.840 0.000
#> GSM153069 4 0.1022 0.8625 0.000 0.000 0.032 0.968
#> GSM153070 1 0.3356 0.8766 0.824 0.000 0.000 0.176
#> GSM153071 1 0.3486 0.8690 0.812 0.000 0.000 0.188
#> GSM153072 1 0.0707 0.8805 0.980 0.000 0.000 0.020
#> GSM153073 1 0.3400 0.8748 0.820 0.000 0.000 0.180
#> GSM153074 4 0.1557 0.8607 0.000 0.000 0.056 0.944
#> GSM153075 4 0.3400 0.8248 0.000 0.000 0.180 0.820
#> GSM153076 1 0.3400 0.8748 0.820 0.000 0.000 0.180
#> GSM153077 1 0.3311 0.8782 0.828 0.000 0.000 0.172
#> GSM153078 1 0.3836 0.8745 0.816 0.000 0.016 0.168
#> GSM153079 1 0.0000 0.8766 1.000 0.000 0.000 0.000
#> GSM153080 3 0.5582 0.0946 0.024 0.000 0.576 0.400
#> GSM153081 1 0.1302 0.8832 0.956 0.000 0.000 0.044
#> GSM153082 1 0.0336 0.8719 0.992 0.008 0.000 0.000
#> GSM153083 1 0.0000 0.8766 1.000 0.000 0.000 0.000
#> GSM153084 2 0.0000 0.9874 0.000 1.000 0.000 0.000
#> GSM153085 1 0.4018 0.6317 0.772 0.224 0.004 0.000
#> GSM153086 1 0.0000 0.8766 1.000 0.000 0.000 0.000
#> GSM153087 4 0.3123 0.8374 0.000 0.000 0.156 0.844
#> GSM153088 1 0.3400 0.8748 0.820 0.000 0.000 0.180
#> GSM153089 3 0.3688 0.6965 0.000 0.208 0.792 0.000
#> GSM153090 4 0.1557 0.8204 0.056 0.000 0.000 0.944
#> GSM153091 1 0.0000 0.8766 1.000 0.000 0.000 0.000
#> GSM153092 1 0.3142 0.8287 0.860 0.000 0.008 0.132
#> GSM153093 4 0.1389 0.8616 0.000 0.000 0.048 0.952
#> GSM153094 1 0.0000 0.8766 1.000 0.000 0.000 0.000
#> GSM153095 1 0.0000 0.8766 1.000 0.000 0.000 0.000
#> GSM153096 1 0.0000 0.8766 1.000 0.000 0.000 0.000
#> GSM153097 1 0.0000 0.8766 1.000 0.000 0.000 0.000
#> GSM153098 4 0.1474 0.8219 0.052 0.000 0.000 0.948
#> GSM153099 4 0.2530 0.7566 0.112 0.000 0.000 0.888
#> GSM153100 1 0.3172 0.8814 0.840 0.000 0.000 0.160
#> GSM153101 1 0.0188 0.8740 0.996 0.004 0.000 0.000
#> GSM153102 3 0.7904 0.1901 0.308 0.324 0.368 0.000
#> GSM153103 1 0.0000 0.8766 1.000 0.000 0.000 0.000
#> GSM153104 4 0.3219 0.8337 0.000 0.000 0.164 0.836
#> GSM153106 4 0.7659 0.1075 0.296 0.000 0.244 0.460
#> GSM153107 1 0.0000 0.8766 1.000 0.000 0.000 0.000
#> GSM153108 4 0.2469 0.7934 0.108 0.000 0.000 0.892
#> GSM153109 2 0.4643 0.5165 0.344 0.656 0.000 0.000
#> GSM153110 1 0.0000 0.8766 1.000 0.000 0.000 0.000
#> GSM153111 1 0.0000 0.8766 1.000 0.000 0.000 0.000
#> GSM153112 1 0.2216 0.8856 0.908 0.000 0.000 0.092
#> GSM153113 2 0.0000 0.9874 0.000 1.000 0.000 0.000
#> GSM153114 4 0.3400 0.8248 0.000 0.000 0.180 0.820
#> GSM187532 2 0.0000 0.9874 0.000 1.000 0.000 0.000
#> GSM187533 2 0.0000 0.9874 0.000 1.000 0.000 0.000
#> GSM187534 2 0.0000 0.9874 0.000 1.000 0.000 0.000
#> GSM187535 2 0.0000 0.9874 0.000 1.000 0.000 0.000
#> GSM152906 2 0.0000 0.9874 0.000 1.000 0.000 0.000
#> GSM152907 2 0.0000 0.9874 0.000 1.000 0.000 0.000
#> GSM152908 2 0.0000 0.9874 0.000 1.000 0.000 0.000
#> GSM152909 2 0.0000 0.9874 0.000 1.000 0.000 0.000
#> GSM152910 2 0.0000 0.9874 0.000 1.000 0.000 0.000
#> GSM152911 2 0.0000 0.9874 0.000 1.000 0.000 0.000
#> GSM152912 2 0.0000 0.9874 0.000 1.000 0.000 0.000
#> GSM152913 2 0.0000 0.9874 0.000 1.000 0.000 0.000
#> GSM152914 2 0.0000 0.9874 0.000 1.000 0.000 0.000
#> GSM152915 2 0.0000 0.9874 0.000 1.000 0.000 0.000
#> GSM152916 2 0.0000 0.9874 0.000 1.000 0.000 0.000
#> GSM152917 2 0.0000 0.9874 0.000 1.000 0.000 0.000
#> GSM152918 2 0.0000 0.9874 0.000 1.000 0.000 0.000
#> GSM152919 2 0.0000 0.9874 0.000 1.000 0.000 0.000
#> GSM152920 2 0.0000 0.9874 0.000 1.000 0.000 0.000
#> GSM152921 2 0.0000 0.9874 0.000 1.000 0.000 0.000
#> GSM152922 2 0.0000 0.9874 0.000 1.000 0.000 0.000
#> GSM152923 2 0.0000 0.9874 0.000 1.000 0.000 0.000
#> GSM152924 2 0.0000 0.9874 0.000 1.000 0.000 0.000
#> GSM152925 2 0.0000 0.9874 0.000 1.000 0.000 0.000
#> GSM152926 2 0.0000 0.9874 0.000 1.000 0.000 0.000
#> GSM152927 2 0.0000 0.9874 0.000 1.000 0.000 0.000
#> GSM152928 2 0.0000 0.9874 0.000 1.000 0.000 0.000
#> GSM152929 2 0.0000 0.9874 0.000 1.000 0.000 0.000
#> GSM152930 2 0.0000 0.9874 0.000 1.000 0.000 0.000
cbind(get_classes(res, k = 5), get_membership(res, k = 5))
#> class entropy silhouette p1 p2 p3 p4 p5
#> GSM152839 1 0.0404 0.8379 0.988 0.000 0.012 0.000 0.000
#> GSM152840 4 0.2127 0.8475 0.000 0.000 0.108 0.892 0.000
#> GSM152841 4 0.0510 0.9020 0.000 0.000 0.016 0.984 0.000
#> GSM152842 1 0.0579 0.8381 0.984 0.000 0.008 0.000 0.008
#> GSM152843 1 0.0451 0.8390 0.988 0.000 0.004 0.000 0.008
#> GSM152844 4 0.3707 0.6252 0.000 0.000 0.284 0.716 0.000
#> GSM152845 3 0.0451 0.9269 0.000 0.008 0.988 0.004 0.000
#> GSM152846 3 0.0162 0.9276 0.000 0.000 0.996 0.004 0.000
#> GSM152847 1 0.0566 0.8370 0.984 0.000 0.012 0.000 0.004
#> GSM152848 1 0.0290 0.8401 0.992 0.000 0.000 0.000 0.008
#> GSM152849 1 0.1671 0.8085 0.924 0.000 0.076 0.000 0.000
#> GSM152850 1 0.0579 0.8381 0.984 0.000 0.008 0.000 0.008
#> GSM152851 4 0.1671 0.8734 0.000 0.000 0.076 0.924 0.000
#> GSM152852 3 0.0162 0.9276 0.000 0.000 0.996 0.004 0.000
#> GSM152853 4 0.3143 0.7405 0.000 0.000 0.204 0.796 0.000
#> GSM152854 3 0.0162 0.9276 0.000 0.000 0.996 0.004 0.000
#> GSM152855 4 0.0404 0.9007 0.012 0.000 0.000 0.988 0.000
#> GSM153238 5 0.3452 0.7692 0.244 0.000 0.000 0.000 0.756
#> GSM153239 4 0.4074 0.4736 0.000 0.000 0.364 0.636 0.000
#> GSM153240 1 0.4283 0.3986 0.544 0.000 0.000 0.456 0.000
#> GSM153241 1 0.4014 0.5998 0.728 0.000 0.256 0.016 0.000
#> GSM153242 3 0.0162 0.9276 0.000 0.000 0.996 0.004 0.000
#> GSM153243 3 0.5490 0.7487 0.036 0.128 0.712 0.000 0.124
#> GSM153244 3 0.1270 0.8986 0.000 0.000 0.948 0.052 0.000
#> GSM153245 4 0.2424 0.8251 0.000 0.000 0.132 0.868 0.000
#> GSM153246 3 0.0880 0.9159 0.032 0.000 0.968 0.000 0.000
#> GSM153247 1 0.4201 0.0713 0.592 0.000 0.000 0.000 0.408
#> GSM153248 5 0.2127 0.8665 0.108 0.000 0.000 0.000 0.892
#> GSM153249 4 0.0162 0.9030 0.004 0.000 0.000 0.996 0.000
#> GSM153250 1 0.0798 0.8417 0.976 0.000 0.000 0.008 0.016
#> GSM153251 3 0.0404 0.9245 0.000 0.000 0.988 0.012 0.000
#> GSM153252 4 0.4305 -0.2476 0.488 0.000 0.000 0.512 0.000
#> GSM153253 4 0.0290 0.9032 0.000 0.000 0.008 0.992 0.000
#> GSM153254 3 0.2280 0.8284 0.000 0.000 0.880 0.120 0.000
#> GSM153255 4 0.0510 0.8987 0.016 0.000 0.000 0.984 0.000
#> GSM153256 1 0.2690 0.8189 0.844 0.000 0.000 0.156 0.000
#> GSM153257 1 0.3752 0.7136 0.708 0.000 0.000 0.292 0.000
#> GSM153258 1 0.1768 0.8174 0.924 0.000 0.004 0.000 0.072
#> GSM153259 5 0.0404 0.8929 0.012 0.000 0.000 0.000 0.988
#> GSM153260 3 0.3400 0.8462 0.040 0.004 0.840 0.000 0.116
#> GSM153261 3 0.1469 0.9099 0.016 0.000 0.948 0.000 0.036
#> GSM153262 4 0.0451 0.9036 0.004 0.000 0.008 0.988 0.000
#> GSM153263 1 0.1168 0.8375 0.960 0.000 0.000 0.008 0.032
#> GSM153264 1 0.0510 0.8398 0.984 0.000 0.000 0.000 0.016
#> GSM153265 4 0.0162 0.9033 0.000 0.000 0.004 0.996 0.000
#> GSM153266 1 0.1952 0.8126 0.912 0.000 0.004 0.000 0.084
#> GSM153267 1 0.3177 0.7892 0.792 0.000 0.000 0.208 0.000
#> GSM153268 4 0.1671 0.8733 0.000 0.000 0.076 0.924 0.000
#> GSM153269 1 0.3480 0.7582 0.752 0.000 0.000 0.248 0.000
#> GSM153270 4 0.5142 0.4941 0.244 0.000 0.088 0.668 0.000
#> GSM153271 1 0.0912 0.8421 0.972 0.000 0.000 0.012 0.016
#> GSM153272 1 0.3274 0.7788 0.780 0.000 0.000 0.220 0.000
#> GSM153273 5 0.1965 0.8715 0.096 0.000 0.000 0.000 0.904
#> GSM153274 1 0.4227 0.4896 0.580 0.000 0.000 0.420 0.000
#> GSM153275 1 0.4192 0.5236 0.596 0.000 0.000 0.404 0.000
#> GSM153276 1 0.3636 0.7328 0.728 0.000 0.000 0.272 0.000
#> GSM153277 4 0.0510 0.9024 0.000 0.000 0.016 0.984 0.000
#> GSM153278 3 0.5519 0.6514 0.204 0.000 0.648 0.000 0.148
#> GSM153279 4 0.1270 0.8881 0.000 0.000 0.052 0.948 0.000
#> GSM153280 4 0.1341 0.8862 0.000 0.000 0.056 0.944 0.000
#> GSM153281 4 0.0162 0.9030 0.004 0.000 0.000 0.996 0.000
#> GSM153282 4 0.0963 0.8959 0.000 0.000 0.036 0.964 0.000
#> GSM153283 1 0.0510 0.8398 0.984 0.000 0.000 0.000 0.016
#> GSM153284 1 0.3837 0.6901 0.692 0.000 0.000 0.308 0.000
#> GSM153285 4 0.0162 0.9030 0.004 0.000 0.000 0.996 0.000
#> GSM153286 1 0.3336 0.7734 0.772 0.000 0.000 0.228 0.000
#> GSM153287 4 0.0290 0.9022 0.008 0.000 0.000 0.992 0.000
#> GSM153288 1 0.3752 0.7137 0.708 0.000 0.000 0.292 0.000
#> GSM153289 1 0.3661 0.7312 0.724 0.000 0.000 0.276 0.000
#> GSM153290 4 0.0963 0.8960 0.000 0.000 0.036 0.964 0.000
#> GSM153291 4 0.0510 0.8984 0.016 0.000 0.000 0.984 0.000
#> GSM153292 4 0.0162 0.9030 0.004 0.000 0.000 0.996 0.000
#> GSM153293 1 0.2732 0.8170 0.840 0.000 0.000 0.160 0.000
#> GSM153294 5 0.3039 0.8113 0.192 0.000 0.000 0.000 0.808
#> GSM153295 1 0.2690 0.8203 0.844 0.000 0.000 0.156 0.000
#> GSM153054 5 0.3661 0.7242 0.276 0.000 0.000 0.000 0.724
#> GSM153055 1 0.3752 0.7127 0.708 0.000 0.000 0.292 0.000
#> GSM153056 1 0.2426 0.8202 0.900 0.000 0.064 0.036 0.000
#> GSM153057 3 0.0162 0.9276 0.000 0.000 0.996 0.004 0.000
#> GSM153058 3 0.0162 0.9276 0.000 0.000 0.996 0.004 0.000
#> GSM153059 3 0.0566 0.9256 0.000 0.012 0.984 0.004 0.000
#> GSM153060 3 0.0451 0.9269 0.008 0.000 0.988 0.004 0.000
#> GSM153061 3 0.4136 0.7696 0.048 0.000 0.764 0.000 0.188
#> GSM153062 3 0.0451 0.9269 0.000 0.008 0.988 0.004 0.000
#> GSM153063 4 0.2230 0.8439 0.000 0.000 0.116 0.884 0.000
#> GSM153064 5 0.2929 0.8239 0.180 0.000 0.000 0.000 0.820
#> GSM153065 3 0.5128 0.7238 0.020 0.064 0.708 0.000 0.208
#> GSM153066 2 0.0880 0.9621 0.000 0.968 0.000 0.000 0.032
#> GSM153067 4 0.0404 0.9007 0.012 0.000 0.000 0.988 0.000
#> GSM153068 3 0.0566 0.9245 0.012 0.004 0.984 0.000 0.000
#> GSM153069 4 0.0290 0.9022 0.008 0.000 0.000 0.992 0.000
#> GSM153070 1 0.0404 0.8408 0.988 0.000 0.000 0.000 0.012
#> GSM153071 1 0.1399 0.8413 0.952 0.000 0.000 0.028 0.020
#> GSM153072 5 0.2605 0.8459 0.148 0.000 0.000 0.000 0.852
#> GSM153073 1 0.0404 0.8402 0.988 0.000 0.000 0.000 0.012
#> GSM153074 4 0.0404 0.9009 0.012 0.000 0.000 0.988 0.000
#> GSM153075 4 0.0703 0.9013 0.000 0.000 0.024 0.976 0.000
#> GSM153076 1 0.1012 0.8414 0.968 0.000 0.000 0.012 0.020
#> GSM153077 1 0.0510 0.8398 0.984 0.000 0.000 0.000 0.016
#> GSM153078 1 0.0992 0.8346 0.968 0.000 0.008 0.000 0.024
#> GSM153079 5 0.0290 0.8883 0.008 0.000 0.000 0.000 0.992
#> GSM153080 4 0.5532 0.6165 0.048 0.000 0.216 0.684 0.052
#> GSM153081 1 0.2068 0.8041 0.904 0.000 0.004 0.000 0.092
#> GSM153082 5 0.0510 0.8919 0.016 0.000 0.000 0.000 0.984
#> GSM153083 5 0.0000 0.8907 0.000 0.000 0.000 0.000 1.000
#> GSM153084 2 0.0963 0.9602 0.000 0.964 0.000 0.000 0.036
#> GSM153085 5 0.0566 0.8856 0.004 0.012 0.000 0.000 0.984
#> GSM153086 5 0.0000 0.8907 0.000 0.000 0.000 0.000 1.000
#> GSM153087 4 0.0290 0.9025 0.008 0.000 0.000 0.992 0.000
#> GSM153088 1 0.0798 0.8417 0.976 0.000 0.000 0.008 0.016
#> GSM153089 3 0.1168 0.9144 0.000 0.032 0.960 0.008 0.000
#> GSM153090 1 0.2516 0.8264 0.860 0.000 0.000 0.140 0.000
#> GSM153091 5 0.0000 0.8907 0.000 0.000 0.000 0.000 1.000
#> GSM153092 5 0.4675 0.2927 0.380 0.000 0.000 0.020 0.600
#> GSM153093 4 0.0290 0.9023 0.008 0.000 0.000 0.992 0.000
#> GSM153094 5 0.0000 0.8907 0.000 0.000 0.000 0.000 1.000
#> GSM153095 5 0.1965 0.8754 0.096 0.000 0.000 0.000 0.904
#> GSM153096 5 0.1732 0.8771 0.080 0.000 0.000 0.000 0.920
#> GSM153097 5 0.0290 0.8926 0.008 0.000 0.000 0.000 0.992
#> GSM153098 4 0.4998 0.5686 0.196 0.000 0.000 0.700 0.104
#> GSM153099 1 0.2074 0.8363 0.896 0.000 0.000 0.104 0.000
#> GSM153100 5 0.3884 0.6527 0.288 0.000 0.000 0.004 0.708
#> GSM153101 5 0.0290 0.8923 0.008 0.000 0.000 0.000 0.992
#> GSM153102 5 0.0451 0.8862 0.000 0.004 0.008 0.000 0.988
#> GSM153103 5 0.0290 0.8924 0.008 0.000 0.000 0.000 0.992
#> GSM153104 4 0.0162 0.9030 0.004 0.000 0.000 0.996 0.000
#> GSM153106 5 0.0798 0.8810 0.000 0.000 0.008 0.016 0.976
#> GSM153107 5 0.0000 0.8907 0.000 0.000 0.000 0.000 1.000
#> GSM153108 5 0.6290 0.3180 0.168 0.000 0.000 0.332 0.500
#> GSM153109 5 0.0290 0.8871 0.000 0.008 0.000 0.000 0.992
#> GSM153110 5 0.0510 0.8923 0.016 0.000 0.000 0.000 0.984
#> GSM153111 5 0.0290 0.8927 0.008 0.000 0.000 0.000 0.992
#> GSM153112 5 0.2424 0.8530 0.132 0.000 0.000 0.000 0.868
#> GSM153113 2 0.2516 0.8366 0.000 0.860 0.000 0.000 0.140
#> GSM153114 4 0.0609 0.9012 0.000 0.000 0.020 0.980 0.000
#> GSM187532 2 0.0000 0.9928 0.000 1.000 0.000 0.000 0.000
#> GSM187533 2 0.0000 0.9928 0.000 1.000 0.000 0.000 0.000
#> GSM187534 2 0.0000 0.9928 0.000 1.000 0.000 0.000 0.000
#> GSM187535 2 0.0000 0.9928 0.000 1.000 0.000 0.000 0.000
#> GSM152906 2 0.0000 0.9928 0.000 1.000 0.000 0.000 0.000
#> GSM152907 2 0.0000 0.9928 0.000 1.000 0.000 0.000 0.000
#> GSM152908 2 0.0000 0.9928 0.000 1.000 0.000 0.000 0.000
#> GSM152909 2 0.0000 0.9928 0.000 1.000 0.000 0.000 0.000
#> GSM152910 2 0.0000 0.9928 0.000 1.000 0.000 0.000 0.000
#> GSM152911 2 0.0000 0.9928 0.000 1.000 0.000 0.000 0.000
#> GSM152912 2 0.0000 0.9928 0.000 1.000 0.000 0.000 0.000
#> GSM152913 2 0.0000 0.9928 0.000 1.000 0.000 0.000 0.000
#> GSM152914 2 0.0000 0.9928 0.000 1.000 0.000 0.000 0.000
#> GSM152915 2 0.0000 0.9928 0.000 1.000 0.000 0.000 0.000
#> GSM152916 2 0.0000 0.9928 0.000 1.000 0.000 0.000 0.000
#> GSM152917 2 0.0000 0.9928 0.000 1.000 0.000 0.000 0.000
#> GSM152918 2 0.0000 0.9928 0.000 1.000 0.000 0.000 0.000
#> GSM152919 2 0.0000 0.9928 0.000 1.000 0.000 0.000 0.000
#> GSM152920 2 0.0000 0.9928 0.000 1.000 0.000 0.000 0.000
#> GSM152921 2 0.0000 0.9928 0.000 1.000 0.000 0.000 0.000
#> GSM152922 2 0.0000 0.9928 0.000 1.000 0.000 0.000 0.000
#> GSM152923 2 0.0000 0.9928 0.000 1.000 0.000 0.000 0.000
#> GSM152924 2 0.0000 0.9928 0.000 1.000 0.000 0.000 0.000
#> GSM152925 2 0.0000 0.9928 0.000 1.000 0.000 0.000 0.000
#> GSM152926 2 0.0000 0.9928 0.000 1.000 0.000 0.000 0.000
#> GSM152927 2 0.0000 0.9928 0.000 1.000 0.000 0.000 0.000
#> GSM152928 2 0.0000 0.9928 0.000 1.000 0.000 0.000 0.000
#> GSM152929 2 0.0000 0.9928 0.000 1.000 0.000 0.000 0.000
#> GSM152930 2 0.0000 0.9928 0.000 1.000 0.000 0.000 0.000
cbind(get_classes(res, k = 6), get_membership(res, k = 6))
#> class entropy silhouette p1 p2 p3 p4 p5 p6
#> GSM152839 6 0.0692 0.57746 0.000 0.000 0.004 0.000 0.020 0.976
#> GSM152840 4 0.1866 0.77731 0.000 0.000 0.084 0.908 0.008 0.000
#> GSM152841 4 0.0622 0.80160 0.000 0.000 0.012 0.980 0.008 0.000
#> GSM152842 6 0.0937 0.58395 0.000 0.000 0.000 0.000 0.040 0.960
#> GSM152843 6 0.1814 0.57560 0.000 0.000 0.000 0.000 0.100 0.900
#> GSM152844 4 0.3642 0.61014 0.000 0.000 0.236 0.744 0.012 0.008
#> GSM152845 3 0.0767 0.86493 0.000 0.008 0.976 0.004 0.012 0.000
#> GSM152846 3 0.1434 0.85787 0.000 0.000 0.940 0.048 0.012 0.000
#> GSM152847 6 0.0777 0.57650 0.000 0.000 0.004 0.000 0.024 0.972
#> GSM152848 6 0.2402 0.55723 0.004 0.000 0.000 0.000 0.140 0.856
#> GSM152849 6 0.1572 0.56110 0.000 0.000 0.036 0.000 0.028 0.936
#> GSM152850 6 0.0790 0.58548 0.000 0.000 0.000 0.000 0.032 0.968
#> GSM152851 4 0.1838 0.78426 0.000 0.000 0.068 0.916 0.016 0.000
#> GSM152852 3 0.1779 0.85288 0.000 0.000 0.920 0.064 0.016 0.000
#> GSM152853 4 0.2946 0.69284 0.000 0.000 0.176 0.812 0.012 0.000
#> GSM152854 3 0.1555 0.86004 0.000 0.000 0.940 0.040 0.012 0.008
#> GSM152855 4 0.3371 0.66067 0.000 0.000 0.000 0.708 0.292 0.000
#> GSM153238 1 0.5549 0.45519 0.484 0.000 0.000 0.000 0.140 0.376
#> GSM153239 4 0.4636 0.39761 0.000 0.000 0.336 0.620 0.024 0.020
#> GSM153240 5 0.6069 0.48390 0.000 0.000 0.000 0.308 0.404 0.288
#> GSM153241 6 0.3660 0.43025 0.000 0.000 0.160 0.000 0.060 0.780
#> GSM153242 3 0.0520 0.86434 0.000 0.000 0.984 0.008 0.008 0.000
#> GSM153243 3 0.7122 0.50724 0.236 0.060 0.516 0.000 0.136 0.052
#> GSM153244 3 0.1780 0.85543 0.000 0.000 0.924 0.048 0.028 0.000
#> GSM153245 4 0.2358 0.75837 0.000 0.000 0.108 0.876 0.016 0.000
#> GSM153246 3 0.3280 0.78926 0.000 0.000 0.808 0.004 0.028 0.160
#> GSM153247 6 0.6186 0.18648 0.248 0.000 0.004 0.004 0.292 0.452
#> GSM153248 1 0.3815 0.77415 0.776 0.000 0.000 0.000 0.132 0.092
#> GSM153249 4 0.1444 0.79703 0.000 0.000 0.000 0.928 0.072 0.000
#> GSM153250 6 0.3954 0.25543 0.012 0.000 0.000 0.000 0.352 0.636
#> GSM153251 3 0.1863 0.85488 0.000 0.000 0.920 0.044 0.036 0.000
#> GSM153252 5 0.5899 0.49212 0.000 0.000 0.000 0.360 0.432 0.208
#> GSM153253 4 0.0717 0.80226 0.000 0.000 0.008 0.976 0.016 0.000
#> GSM153254 3 0.3727 0.71058 0.000 0.000 0.768 0.188 0.040 0.004
#> GSM153255 4 0.3288 0.63692 0.000 0.000 0.000 0.724 0.276 0.000
#> GSM153256 5 0.5194 0.55015 0.004 0.000 0.000 0.076 0.488 0.432
#> GSM153257 5 0.5779 0.62515 0.000 0.000 0.000 0.188 0.472 0.340
#> GSM153258 6 0.4280 0.46046 0.056 0.000 0.000 0.004 0.232 0.708
#> GSM153259 1 0.1890 0.82272 0.916 0.000 0.000 0.000 0.024 0.060
#> GSM153260 3 0.6445 0.61463 0.120 0.000 0.564 0.000 0.188 0.128
#> GSM153261 3 0.5150 0.72702 0.048 0.000 0.688 0.000 0.176 0.088
#> GSM153262 4 0.0717 0.80279 0.000 0.000 0.008 0.976 0.016 0.000
#> GSM153263 6 0.4658 0.19931 0.040 0.000 0.000 0.004 0.376 0.580
#> GSM153264 6 0.3566 0.49131 0.020 0.000 0.000 0.000 0.236 0.744
#> GSM153265 4 0.1082 0.80410 0.000 0.000 0.004 0.956 0.040 0.000
#> GSM153266 6 0.4616 0.45197 0.080 0.000 0.000 0.004 0.236 0.680
#> GSM153267 5 0.4899 0.54928 0.000 0.000 0.000 0.064 0.532 0.404
#> GSM153268 4 0.1391 0.79573 0.000 0.000 0.040 0.944 0.016 0.000
#> GSM153269 5 0.5300 0.59085 0.000 0.000 0.000 0.108 0.516 0.376
#> GSM153270 4 0.6799 -0.00983 0.000 0.000 0.068 0.412 0.348 0.172
#> GSM153271 6 0.4093 0.06632 0.012 0.000 0.000 0.000 0.404 0.584
#> GSM153272 5 0.5205 0.58716 0.000 0.000 0.000 0.092 0.496 0.412
#> GSM153273 1 0.3072 0.80044 0.840 0.000 0.000 0.000 0.076 0.084
#> GSM153274 5 0.5837 0.58593 0.000 0.000 0.000 0.224 0.484 0.292
#> GSM153275 5 0.5816 0.58161 0.000 0.000 0.000 0.212 0.484 0.304
#> GSM153276 5 0.5495 0.55811 0.000 0.000 0.000 0.128 0.468 0.404
#> GSM153277 4 0.2734 0.76291 0.000 0.000 0.008 0.840 0.148 0.004
#> GSM153278 6 0.7069 -0.10195 0.096 0.000 0.232 0.000 0.236 0.436
#> GSM153279 4 0.1498 0.79761 0.000 0.000 0.032 0.940 0.028 0.000
#> GSM153280 4 0.1257 0.79924 0.000 0.000 0.028 0.952 0.020 0.000
#> GSM153281 4 0.2053 0.79209 0.000 0.000 0.004 0.888 0.108 0.000
#> GSM153282 4 0.0603 0.80102 0.000 0.000 0.016 0.980 0.004 0.000
#> GSM153283 6 0.3558 0.47719 0.016 0.000 0.000 0.000 0.248 0.736
#> GSM153284 5 0.5861 0.63772 0.000 0.000 0.000 0.220 0.472 0.308
#> GSM153285 4 0.1556 0.79486 0.000 0.000 0.000 0.920 0.080 0.000
#> GSM153286 5 0.5175 0.57752 0.000 0.000 0.000 0.088 0.492 0.420
#> GSM153287 4 0.2912 0.70459 0.000 0.000 0.000 0.784 0.216 0.000
#> GSM153288 5 0.5818 0.63992 0.000 0.000 0.000 0.192 0.456 0.352
#> GSM153289 5 0.5916 0.62813 0.004 0.000 0.000 0.196 0.476 0.324
#> GSM153290 4 0.1088 0.80022 0.000 0.000 0.024 0.960 0.016 0.000
#> GSM153291 4 0.3198 0.65617 0.000 0.000 0.000 0.740 0.260 0.000
#> GSM153292 4 0.2003 0.78015 0.000 0.000 0.000 0.884 0.116 0.000
#> GSM153293 5 0.5136 0.57384 0.000 0.000 0.000 0.084 0.496 0.420
#> GSM153294 1 0.4863 0.63673 0.624 0.000 0.000 0.000 0.284 0.092
#> GSM153295 5 0.5203 0.49979 0.004 0.000 0.000 0.076 0.464 0.456
#> GSM153054 1 0.5498 0.46544 0.528 0.000 0.000 0.000 0.148 0.324
#> GSM153055 5 0.5668 0.61621 0.004 0.000 0.000 0.152 0.516 0.328
#> GSM153056 6 0.2257 0.53791 0.000 0.000 0.048 0.008 0.040 0.904
#> GSM153057 3 0.0146 0.86478 0.000 0.000 0.996 0.000 0.004 0.000
#> GSM153058 3 0.0146 0.86478 0.000 0.000 0.996 0.000 0.004 0.000
#> GSM153059 3 0.0520 0.86371 0.000 0.008 0.984 0.000 0.008 0.000
#> GSM153060 3 0.1092 0.86300 0.000 0.000 0.960 0.000 0.020 0.020
#> GSM153061 3 0.6903 0.53532 0.128 0.000 0.488 0.000 0.148 0.236
#> GSM153062 3 0.0520 0.86365 0.000 0.008 0.984 0.000 0.008 0.000
#> GSM153063 4 0.2489 0.76235 0.000 0.000 0.128 0.860 0.012 0.000
#> GSM153064 1 0.4396 0.66574 0.704 0.000 0.000 0.000 0.088 0.208
#> GSM153065 3 0.6731 0.51284 0.252 0.032 0.540 0.000 0.120 0.056
#> GSM153066 2 0.2712 0.87511 0.048 0.864 0.000 0.000 0.088 0.000
#> GSM153067 4 0.3601 0.56580 0.000 0.000 0.000 0.684 0.312 0.004
#> GSM153068 3 0.1552 0.85851 0.000 0.004 0.940 0.000 0.036 0.020
#> GSM153069 4 0.2597 0.74086 0.000 0.000 0.000 0.824 0.176 0.000
#> GSM153070 6 0.3240 0.47935 0.004 0.000 0.000 0.000 0.244 0.752
#> GSM153071 5 0.5163 -0.06855 0.056 0.000 0.000 0.012 0.488 0.444
#> GSM153072 1 0.4443 0.72695 0.704 0.000 0.000 0.004 0.216 0.076
#> GSM153073 6 0.3634 0.42595 0.008 0.000 0.000 0.000 0.296 0.696
#> GSM153074 4 0.3288 0.67965 0.000 0.000 0.000 0.724 0.276 0.000
#> GSM153075 4 0.3874 0.72255 0.000 0.000 0.028 0.752 0.208 0.012
#> GSM153076 6 0.4452 0.12500 0.024 0.000 0.000 0.004 0.400 0.572
#> GSM153077 6 0.3688 0.47995 0.020 0.000 0.000 0.000 0.256 0.724
#> GSM153078 6 0.1462 0.57348 0.000 0.000 0.008 0.000 0.056 0.936
#> GSM153079 1 0.2494 0.79001 0.864 0.000 0.000 0.000 0.120 0.016
#> GSM153080 4 0.6211 0.53824 0.028 0.000 0.124 0.640 0.120 0.088
#> GSM153081 6 0.4166 0.49620 0.088 0.000 0.004 0.000 0.160 0.748
#> GSM153082 1 0.2588 0.80873 0.860 0.004 0.000 0.000 0.124 0.012
#> GSM153083 1 0.1327 0.81099 0.936 0.000 0.000 0.000 0.064 0.000
#> GSM153084 2 0.2888 0.87949 0.068 0.860 0.004 0.000 0.068 0.000
#> GSM153085 1 0.3385 0.75963 0.816 0.016 0.008 0.000 0.148 0.012
#> GSM153086 1 0.0291 0.82070 0.992 0.000 0.000 0.000 0.004 0.004
#> GSM153087 4 0.3245 0.69927 0.000 0.000 0.000 0.764 0.228 0.008
#> GSM153088 6 0.3979 0.22536 0.012 0.000 0.000 0.000 0.360 0.628
#> GSM153089 3 0.2316 0.85214 0.000 0.016 0.904 0.040 0.040 0.000
#> GSM153090 5 0.4855 0.48371 0.000 0.000 0.000 0.056 0.484 0.460
#> GSM153091 1 0.0865 0.81594 0.964 0.000 0.000 0.000 0.036 0.000
#> GSM153092 1 0.6243 0.30453 0.448 0.000 0.004 0.016 0.360 0.172
#> GSM153093 4 0.3076 0.70257 0.000 0.000 0.000 0.760 0.240 0.000
#> GSM153094 1 0.1007 0.82121 0.956 0.000 0.000 0.000 0.044 0.000
#> GSM153095 1 0.4318 0.76269 0.728 0.000 0.000 0.000 0.132 0.140
#> GSM153096 1 0.2554 0.81176 0.876 0.000 0.000 0.000 0.048 0.076
#> GSM153097 1 0.0777 0.82078 0.972 0.000 0.000 0.000 0.024 0.004
#> GSM153098 4 0.6546 -0.05838 0.112 0.000 0.000 0.412 0.400 0.076
#> GSM153099 6 0.4723 -0.44286 0.004 0.000 0.000 0.036 0.476 0.484
#> GSM153100 1 0.5349 0.52455 0.608 0.000 0.000 0.004 0.216 0.172
#> GSM153101 1 0.2714 0.80394 0.848 0.004 0.000 0.000 0.136 0.012
#> GSM153102 1 0.2531 0.78121 0.856 0.000 0.012 0.000 0.132 0.000
#> GSM153103 1 0.1462 0.81406 0.936 0.000 0.000 0.000 0.056 0.008
#> GSM153104 4 0.1863 0.78669 0.000 0.000 0.000 0.896 0.104 0.000
#> GSM153106 1 0.3296 0.74806 0.792 0.000 0.012 0.008 0.188 0.000
#> GSM153107 1 0.1643 0.82055 0.924 0.000 0.000 0.000 0.068 0.008
#> GSM153108 5 0.7029 0.15660 0.276 0.000 0.000 0.296 0.364 0.064
#> GSM153109 1 0.1765 0.80026 0.904 0.000 0.000 0.000 0.096 0.000
#> GSM153110 1 0.1049 0.82263 0.960 0.000 0.000 0.000 0.008 0.032
#> GSM153111 1 0.0692 0.82147 0.976 0.000 0.000 0.000 0.020 0.004
#> GSM153112 1 0.4293 0.69845 0.716 0.000 0.000 0.000 0.200 0.084
#> GSM153113 2 0.4094 0.70890 0.168 0.744 0.000 0.000 0.088 0.000
#> GSM153114 4 0.2312 0.78102 0.000 0.000 0.012 0.876 0.112 0.000
#> GSM187532 2 0.0790 0.96213 0.000 0.968 0.000 0.000 0.032 0.000
#> GSM187533 2 0.0790 0.96357 0.000 0.968 0.000 0.000 0.032 0.000
#> GSM187534 2 0.0547 0.96551 0.000 0.980 0.000 0.000 0.020 0.000
#> GSM187535 2 0.0713 0.96447 0.000 0.972 0.000 0.000 0.028 0.000
#> GSM152906 2 0.0713 0.96447 0.000 0.972 0.000 0.000 0.028 0.000
#> GSM152907 2 0.0547 0.96519 0.000 0.980 0.000 0.000 0.020 0.000
#> GSM152908 2 0.0865 0.96113 0.000 0.964 0.000 0.000 0.036 0.000
#> GSM152909 2 0.0865 0.96113 0.000 0.964 0.000 0.000 0.036 0.000
#> GSM152910 2 0.0865 0.96113 0.000 0.964 0.000 0.000 0.036 0.000
#> GSM152911 2 0.0458 0.96506 0.000 0.984 0.000 0.000 0.016 0.000
#> GSM152912 2 0.0865 0.96113 0.000 0.964 0.000 0.000 0.036 0.000
#> GSM152913 2 0.0547 0.96455 0.000 0.980 0.000 0.000 0.020 0.000
#> GSM152914 2 0.0000 0.96658 0.000 1.000 0.000 0.000 0.000 0.000
#> GSM152915 2 0.0000 0.96658 0.000 1.000 0.000 0.000 0.000 0.000
#> GSM152916 2 0.0713 0.96447 0.000 0.972 0.000 0.000 0.028 0.000
#> GSM152917 2 0.0000 0.96658 0.000 1.000 0.000 0.000 0.000 0.000
#> GSM152918 2 0.0000 0.96658 0.000 1.000 0.000 0.000 0.000 0.000
#> GSM152919 2 0.0000 0.96658 0.000 1.000 0.000 0.000 0.000 0.000
#> GSM152920 2 0.0865 0.96113 0.000 0.964 0.000 0.000 0.036 0.000
#> GSM152921 2 0.0865 0.96113 0.000 0.964 0.000 0.000 0.036 0.000
#> GSM152922 2 0.0865 0.96113 0.000 0.964 0.000 0.000 0.036 0.000
#> GSM152923 2 0.0713 0.96447 0.000 0.972 0.000 0.000 0.028 0.000
#> GSM152924 2 0.0713 0.96447 0.000 0.972 0.000 0.000 0.028 0.000
#> GSM152925 2 0.0713 0.96447 0.000 0.972 0.000 0.000 0.028 0.000
#> GSM152926 2 0.0713 0.96447 0.000 0.972 0.000 0.000 0.028 0.000
#> GSM152927 2 0.0713 0.96447 0.000 0.972 0.000 0.000 0.028 0.000
#> GSM152928 2 0.0713 0.96447 0.000 0.972 0.000 0.000 0.028 0.000
#> GSM152929 2 0.0713 0.96447 0.000 0.972 0.000 0.000 0.028 0.000
#> GSM152930 2 0.0713 0.96447 0.000 0.972 0.000 0.000 0.028 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 tissue(p) k
#> ATC:skmeans 154 6.47e-14 2
#> ATC:skmeans 152 1.74e-17 3
#> ATC:skmeans 156 2.10e-24 4
#> ATC:skmeans 156 7.48e-25 5
#> ATC:skmeans 135 2.30e-30 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 12013 rows and 164 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 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 0.989 0.995 0.2867 0.715 0.715
#> 3 3 0.689 0.885 0.923 1.0854 0.664 0.535
#> 4 4 0.676 0.846 0.914 0.0456 0.973 0.933
#> 5 5 0.703 0.811 0.879 0.1712 0.819 0.553
#> 6 6 0.813 0.830 0.919 0.0317 0.986 0.944
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
#> GSM152839 1 0.0000 0.997 1.000 0.000
#> GSM152840 1 0.0000 0.997 1.000 0.000
#> GSM152841 1 0.0000 0.997 1.000 0.000
#> GSM152842 1 0.0000 0.997 1.000 0.000
#> GSM152843 1 0.0000 0.997 1.000 0.000
#> GSM152844 1 0.0000 0.997 1.000 0.000
#> GSM152845 1 0.9775 0.283 0.588 0.412
#> GSM152846 1 0.0000 0.997 1.000 0.000
#> GSM152847 1 0.0000 0.997 1.000 0.000
#> GSM152848 1 0.0000 0.997 1.000 0.000
#> GSM152849 1 0.0000 0.997 1.000 0.000
#> GSM152850 1 0.0000 0.997 1.000 0.000
#> GSM152851 1 0.0000 0.997 1.000 0.000
#> GSM152852 1 0.0000 0.997 1.000 0.000
#> GSM152853 1 0.0000 0.997 1.000 0.000
#> GSM152854 1 0.0000 0.997 1.000 0.000
#> GSM152855 1 0.0000 0.997 1.000 0.000
#> GSM153238 1 0.0000 0.997 1.000 0.000
#> GSM153239 1 0.0000 0.997 1.000 0.000
#> GSM153240 1 0.0000 0.997 1.000 0.000
#> GSM153241 1 0.0000 0.997 1.000 0.000
#> GSM153242 1 0.0000 0.997 1.000 0.000
#> GSM153243 1 0.0000 0.997 1.000 0.000
#> GSM153244 1 0.0000 0.997 1.000 0.000
#> GSM153245 1 0.0000 0.997 1.000 0.000
#> GSM153246 1 0.0000 0.997 1.000 0.000
#> GSM153247 1 0.0000 0.997 1.000 0.000
#> GSM153248 1 0.0000 0.997 1.000 0.000
#> GSM153249 1 0.0000 0.997 1.000 0.000
#> GSM153250 1 0.0000 0.997 1.000 0.000
#> GSM153251 1 0.0000 0.997 1.000 0.000
#> GSM153252 1 0.0000 0.997 1.000 0.000
#> GSM153253 1 0.0000 0.997 1.000 0.000
#> GSM153254 1 0.0000 0.997 1.000 0.000
#> GSM153255 1 0.0000 0.997 1.000 0.000
#> GSM153256 1 0.0000 0.997 1.000 0.000
#> GSM153257 1 0.0000 0.997 1.000 0.000
#> GSM153258 1 0.0000 0.997 1.000 0.000
#> GSM153259 1 0.0000 0.997 1.000 0.000
#> GSM153260 1 0.0000 0.997 1.000 0.000
#> GSM153261 1 0.0000 0.997 1.000 0.000
#> GSM153262 1 0.0000 0.997 1.000 0.000
#> GSM153263 1 0.0000 0.997 1.000 0.000
#> GSM153264 1 0.0000 0.997 1.000 0.000
#> GSM153265 1 0.0000 0.997 1.000 0.000
#> GSM153266 1 0.0000 0.997 1.000 0.000
#> GSM153267 1 0.0000 0.997 1.000 0.000
#> GSM153268 1 0.0000 0.997 1.000 0.000
#> GSM153269 1 0.0000 0.997 1.000 0.000
#> GSM153270 1 0.0000 0.997 1.000 0.000
#> GSM153271 1 0.0000 0.997 1.000 0.000
#> GSM153272 1 0.0000 0.997 1.000 0.000
#> GSM153273 1 0.0000 0.997 1.000 0.000
#> GSM153274 1 0.0000 0.997 1.000 0.000
#> GSM153275 1 0.0000 0.997 1.000 0.000
#> GSM153276 1 0.0000 0.997 1.000 0.000
#> GSM153277 1 0.0000 0.997 1.000 0.000
#> GSM153278 1 0.0000 0.997 1.000 0.000
#> GSM153279 1 0.0000 0.997 1.000 0.000
#> GSM153280 1 0.0000 0.997 1.000 0.000
#> GSM153281 1 0.0000 0.997 1.000 0.000
#> GSM153282 1 0.0000 0.997 1.000 0.000
#> GSM153283 1 0.0000 0.997 1.000 0.000
#> GSM153284 1 0.0000 0.997 1.000 0.000
#> GSM153285 1 0.0000 0.997 1.000 0.000
#> GSM153286 1 0.0000 0.997 1.000 0.000
#> GSM153287 1 0.0000 0.997 1.000 0.000
#> GSM153288 1 0.0000 0.997 1.000 0.000
#> GSM153289 1 0.0000 0.997 1.000 0.000
#> GSM153290 1 0.0000 0.997 1.000 0.000
#> GSM153291 1 0.0000 0.997 1.000 0.000
#> GSM153292 1 0.0000 0.997 1.000 0.000
#> GSM153293 1 0.0000 0.997 1.000 0.000
#> GSM153294 1 0.0000 0.997 1.000 0.000
#> GSM153295 1 0.0000 0.997 1.000 0.000
#> GSM153054 1 0.0000 0.997 1.000 0.000
#> GSM153055 1 0.0000 0.997 1.000 0.000
#> GSM153056 1 0.0000 0.997 1.000 0.000
#> GSM153057 1 0.0000 0.997 1.000 0.000
#> GSM153058 1 0.0000 0.997 1.000 0.000
#> GSM153059 1 0.0000 0.997 1.000 0.000
#> GSM153060 1 0.0000 0.997 1.000 0.000
#> GSM153061 1 0.0000 0.997 1.000 0.000
#> GSM153062 1 0.0000 0.997 1.000 0.000
#> GSM153063 1 0.0000 0.997 1.000 0.000
#> GSM153064 1 0.0000 0.997 1.000 0.000
#> GSM153065 1 0.0000 0.997 1.000 0.000
#> GSM153066 1 0.1414 0.977 0.980 0.020
#> GSM153067 1 0.0000 0.997 1.000 0.000
#> GSM153068 1 0.0000 0.997 1.000 0.000
#> GSM153069 1 0.0000 0.997 1.000 0.000
#> GSM153070 1 0.0000 0.997 1.000 0.000
#> GSM153071 1 0.0000 0.997 1.000 0.000
#> GSM153072 1 0.0000 0.997 1.000 0.000
#> GSM153073 1 0.0000 0.997 1.000 0.000
#> GSM153074 1 0.0000 0.997 1.000 0.000
#> GSM153075 1 0.0000 0.997 1.000 0.000
#> GSM153076 1 0.0000 0.997 1.000 0.000
#> GSM153077 1 0.0000 0.997 1.000 0.000
#> GSM153078 1 0.0000 0.997 1.000 0.000
#> GSM153079 1 0.0000 0.997 1.000 0.000
#> GSM153080 1 0.0000 0.997 1.000 0.000
#> GSM153081 1 0.0000 0.997 1.000 0.000
#> GSM153082 1 0.0000 0.997 1.000 0.000
#> GSM153083 1 0.0000 0.997 1.000 0.000
#> GSM153084 1 0.0000 0.997 1.000 0.000
#> GSM153085 1 0.0000 0.997 1.000 0.000
#> GSM153086 1 0.0000 0.997 1.000 0.000
#> GSM153087 1 0.0000 0.997 1.000 0.000
#> GSM153088 1 0.0000 0.997 1.000 0.000
#> GSM153089 1 0.0000 0.997 1.000 0.000
#> GSM153090 1 0.0000 0.997 1.000 0.000
#> GSM153091 1 0.0000 0.997 1.000 0.000
#> GSM153092 1 0.0000 0.997 1.000 0.000
#> GSM153093 1 0.0000 0.997 1.000 0.000
#> GSM153094 1 0.0000 0.997 1.000 0.000
#> GSM153095 1 0.0000 0.997 1.000 0.000
#> GSM153096 1 0.0000 0.997 1.000 0.000
#> GSM153097 1 0.0000 0.997 1.000 0.000
#> GSM153098 1 0.0000 0.997 1.000 0.000
#> GSM153099 1 0.0000 0.997 1.000 0.000
#> GSM153100 1 0.0000 0.997 1.000 0.000
#> GSM153101 1 0.0000 0.997 1.000 0.000
#> GSM153102 1 0.0000 0.997 1.000 0.000
#> GSM153103 1 0.0000 0.997 1.000 0.000
#> GSM153104 1 0.0000 0.997 1.000 0.000
#> GSM153106 1 0.0000 0.997 1.000 0.000
#> GSM153107 1 0.0000 0.997 1.000 0.000
#> GSM153108 1 0.0000 0.997 1.000 0.000
#> GSM153109 1 0.0000 0.997 1.000 0.000
#> GSM153110 1 0.0000 0.997 1.000 0.000
#> GSM153111 1 0.0000 0.997 1.000 0.000
#> GSM153112 1 0.0000 0.997 1.000 0.000
#> GSM153113 1 0.0376 0.993 0.996 0.004
#> GSM153114 1 0.0000 0.997 1.000 0.000
#> GSM187532 2 0.0000 0.989 0.000 1.000
#> GSM187533 2 0.0000 0.989 0.000 1.000
#> GSM187534 2 0.0000 0.989 0.000 1.000
#> GSM187535 1 0.1184 0.981 0.984 0.016
#> GSM152906 2 0.0000 0.989 0.000 1.000
#> GSM152907 2 0.0000 0.989 0.000 1.000
#> GSM152908 2 0.0000 0.989 0.000 1.000
#> GSM152909 2 0.0000 0.989 0.000 1.000
#> GSM152910 2 0.0000 0.989 0.000 1.000
#> GSM152911 2 0.0000 0.989 0.000 1.000
#> GSM152912 2 0.0000 0.989 0.000 1.000
#> GSM152913 2 0.0000 0.989 0.000 1.000
#> GSM152914 2 0.0000 0.989 0.000 1.000
#> GSM152915 2 0.0000 0.989 0.000 1.000
#> GSM152916 2 0.0000 0.989 0.000 1.000
#> GSM152917 2 0.0000 0.989 0.000 1.000
#> GSM152918 2 0.0000 0.989 0.000 1.000
#> GSM152919 2 0.0000 0.989 0.000 1.000
#> GSM152920 2 0.0000 0.989 0.000 1.000
#> GSM152921 2 0.0000 0.989 0.000 1.000
#> GSM152922 2 0.0000 0.989 0.000 1.000
#> GSM152923 2 0.0000 0.989 0.000 1.000
#> GSM152924 2 0.0000 0.989 0.000 1.000
#> GSM152925 2 0.0000 0.989 0.000 1.000
#> GSM152926 2 0.7139 0.760 0.196 0.804
#> GSM152927 2 0.0000 0.989 0.000 1.000
#> GSM152928 2 0.4939 0.879 0.108 0.892
#> GSM152929 2 0.0000 0.989 0.000 1.000
#> GSM152930 2 0.0000 0.989 0.000 1.000
cbind(get_classes(res, k = 3), get_membership(res, k = 3))
#> class entropy silhouette p1 p2 p3
#> GSM152839 1 0.4062 0.844 0.836 0.000 0.164
#> GSM152840 1 0.0000 0.919 1.000 0.000 0.000
#> GSM152841 1 0.0000 0.919 1.000 0.000 0.000
#> GSM152842 1 0.5058 0.774 0.756 0.000 0.244
#> GSM152843 1 0.5016 0.778 0.760 0.000 0.240
#> GSM152844 1 0.0000 0.919 1.000 0.000 0.000
#> GSM152845 3 0.5944 0.711 0.064 0.152 0.784
#> GSM152846 1 0.1411 0.915 0.964 0.000 0.036
#> GSM152847 1 0.4887 0.790 0.772 0.000 0.228
#> GSM152848 1 0.4654 0.805 0.792 0.000 0.208
#> GSM152849 1 0.5058 0.774 0.756 0.000 0.244
#> GSM152850 1 0.5529 0.697 0.704 0.000 0.296
#> GSM152851 1 0.1411 0.916 0.964 0.000 0.036
#> GSM152852 1 0.0747 0.921 0.984 0.000 0.016
#> GSM152853 1 0.0000 0.919 1.000 0.000 0.000
#> GSM152854 1 0.1411 0.916 0.964 0.000 0.036
#> GSM152855 1 0.0237 0.920 0.996 0.000 0.004
#> GSM153238 3 0.1289 0.906 0.032 0.000 0.968
#> GSM153239 1 0.0424 0.921 0.992 0.000 0.008
#> GSM153240 1 0.0000 0.919 1.000 0.000 0.000
#> GSM153241 1 0.3619 0.872 0.864 0.000 0.136
#> GSM153242 1 0.0237 0.920 0.996 0.000 0.004
#> GSM153243 3 0.1411 0.907 0.036 0.000 0.964
#> GSM153244 1 0.0892 0.920 0.980 0.000 0.020
#> GSM153245 1 0.0237 0.920 0.996 0.000 0.004
#> GSM153246 1 0.2066 0.918 0.940 0.000 0.060
#> GSM153247 3 0.1860 0.905 0.052 0.000 0.948
#> GSM153248 3 0.1411 0.906 0.036 0.000 0.964
#> GSM153249 1 0.0000 0.919 1.000 0.000 0.000
#> GSM153250 1 0.4605 0.807 0.796 0.000 0.204
#> GSM153251 1 0.4555 0.733 0.800 0.000 0.200
#> GSM153252 1 0.0424 0.921 0.992 0.000 0.008
#> GSM153253 1 0.0000 0.919 1.000 0.000 0.000
#> GSM153254 1 0.2261 0.899 0.932 0.000 0.068
#> GSM153255 1 0.0892 0.920 0.980 0.000 0.020
#> GSM153256 1 0.2261 0.911 0.932 0.000 0.068
#> GSM153257 1 0.2448 0.905 0.924 0.000 0.076
#> GSM153258 3 0.2448 0.901 0.076 0.000 0.924
#> GSM153259 3 0.4346 0.782 0.184 0.000 0.816
#> GSM153260 3 0.2066 0.903 0.060 0.000 0.940
#> GSM153261 3 0.3267 0.881 0.116 0.000 0.884
#> GSM153262 1 0.0000 0.919 1.000 0.000 0.000
#> GSM153263 1 0.5058 0.774 0.756 0.000 0.244
#> GSM153264 3 0.4121 0.807 0.168 0.000 0.832
#> GSM153265 1 0.0000 0.919 1.000 0.000 0.000
#> GSM153266 3 0.2711 0.897 0.088 0.000 0.912
#> GSM153267 1 0.2711 0.906 0.912 0.000 0.088
#> GSM153268 1 0.0000 0.919 1.000 0.000 0.000
#> GSM153269 1 0.1964 0.914 0.944 0.000 0.056
#> GSM153270 1 0.1643 0.914 0.956 0.000 0.044
#> GSM153271 1 0.4555 0.810 0.800 0.000 0.200
#> GSM153272 1 0.1860 0.914 0.948 0.000 0.052
#> GSM153273 3 0.1289 0.906 0.032 0.000 0.968
#> GSM153274 1 0.0892 0.922 0.980 0.000 0.020
#> GSM153275 1 0.0237 0.920 0.996 0.000 0.004
#> GSM153276 1 0.2066 0.915 0.940 0.000 0.060
#> GSM153277 1 0.0237 0.920 0.996 0.000 0.004
#> GSM153278 3 0.2537 0.901 0.080 0.000 0.920
#> GSM153279 1 0.1163 0.918 0.972 0.000 0.028
#> GSM153280 1 0.0000 0.919 1.000 0.000 0.000
#> GSM153281 1 0.0000 0.919 1.000 0.000 0.000
#> GSM153282 1 0.0000 0.919 1.000 0.000 0.000
#> GSM153283 3 0.5859 0.454 0.344 0.000 0.656
#> GSM153284 1 0.1411 0.919 0.964 0.000 0.036
#> GSM153285 1 0.0237 0.920 0.996 0.000 0.004
#> GSM153286 1 0.1860 0.914 0.948 0.000 0.052
#> GSM153287 1 0.1163 0.919 0.972 0.000 0.028
#> GSM153288 1 0.1163 0.919 0.972 0.000 0.028
#> GSM153289 1 0.1411 0.919 0.964 0.000 0.036
#> GSM153290 1 0.0000 0.919 1.000 0.000 0.000
#> GSM153291 1 0.0424 0.921 0.992 0.000 0.008
#> GSM153292 1 0.0000 0.919 1.000 0.000 0.000
#> GSM153293 1 0.4452 0.817 0.808 0.000 0.192
#> GSM153294 3 0.1529 0.906 0.040 0.000 0.960
#> GSM153295 1 0.2711 0.898 0.912 0.000 0.088
#> GSM153054 3 0.5591 0.552 0.304 0.000 0.696
#> GSM153055 1 0.2878 0.893 0.904 0.000 0.096
#> GSM153056 1 0.2165 0.914 0.936 0.000 0.064
#> GSM153057 1 0.3192 0.862 0.888 0.000 0.112
#> GSM153058 1 0.1163 0.918 0.972 0.000 0.028
#> GSM153059 3 0.4796 0.789 0.220 0.000 0.780
#> GSM153060 1 0.1860 0.917 0.948 0.000 0.052
#> GSM153061 3 0.1289 0.906 0.032 0.000 0.968
#> GSM153062 3 0.4887 0.782 0.228 0.000 0.772
#> GSM153063 1 0.0747 0.920 0.984 0.000 0.016
#> GSM153064 1 0.5178 0.759 0.744 0.000 0.256
#> GSM153065 3 0.1753 0.907 0.048 0.000 0.952
#> GSM153066 3 0.1289 0.906 0.032 0.000 0.968
#> GSM153067 1 0.1163 0.919 0.972 0.000 0.028
#> GSM153068 3 0.4452 0.816 0.192 0.000 0.808
#> GSM153069 1 0.0000 0.919 1.000 0.000 0.000
#> GSM153070 1 0.5138 0.764 0.748 0.000 0.252
#> GSM153071 1 0.4887 0.791 0.772 0.000 0.228
#> GSM153072 3 0.1289 0.906 0.032 0.000 0.968
#> GSM153073 1 0.4842 0.794 0.776 0.000 0.224
#> GSM153074 1 0.0237 0.920 0.996 0.000 0.004
#> GSM153075 1 0.1529 0.914 0.960 0.000 0.040
#> GSM153076 1 0.4452 0.817 0.808 0.000 0.192
#> GSM153077 3 0.1860 0.903 0.052 0.000 0.948
#> GSM153078 3 0.2711 0.883 0.088 0.000 0.912
#> GSM153079 3 0.2066 0.903 0.060 0.000 0.940
#> GSM153080 3 0.5016 0.779 0.240 0.000 0.760
#> GSM153081 3 0.2066 0.900 0.060 0.000 0.940
#> GSM153082 3 0.1529 0.908 0.040 0.000 0.960
#> GSM153083 3 0.1289 0.906 0.032 0.000 0.968
#> GSM153084 3 0.2066 0.903 0.060 0.000 0.940
#> GSM153085 3 0.1753 0.907 0.048 0.000 0.952
#> GSM153086 3 0.1289 0.906 0.032 0.000 0.968
#> GSM153087 1 0.1289 0.921 0.968 0.000 0.032
#> GSM153088 1 0.4555 0.810 0.800 0.000 0.200
#> GSM153089 3 0.4887 0.782 0.228 0.000 0.772
#> GSM153090 1 0.2625 0.907 0.916 0.000 0.084
#> GSM153091 3 0.1529 0.908 0.040 0.000 0.960
#> GSM153092 3 0.5497 0.714 0.292 0.000 0.708
#> GSM153093 1 0.0424 0.921 0.992 0.000 0.008
#> GSM153094 3 0.1411 0.907 0.036 0.000 0.964
#> GSM153095 3 0.1529 0.908 0.040 0.000 0.960
#> GSM153096 3 0.1289 0.906 0.032 0.000 0.968
#> GSM153097 3 0.1289 0.906 0.032 0.000 0.968
#> GSM153098 1 0.2878 0.901 0.904 0.000 0.096
#> GSM153099 1 0.2625 0.908 0.916 0.000 0.084
#> GSM153100 3 0.4750 0.767 0.216 0.000 0.784
#> GSM153101 3 0.3192 0.878 0.112 0.000 0.888
#> GSM153102 3 0.4796 0.789 0.220 0.000 0.780
#> GSM153103 3 0.1289 0.906 0.032 0.000 0.968
#> GSM153104 1 0.0424 0.921 0.992 0.000 0.008
#> GSM153106 3 0.4796 0.789 0.220 0.000 0.780
#> GSM153107 3 0.2448 0.902 0.076 0.000 0.924
#> GSM153108 1 0.1860 0.910 0.948 0.000 0.052
#> GSM153109 3 0.1753 0.907 0.048 0.000 0.952
#> GSM153110 3 0.1289 0.906 0.032 0.000 0.968
#> GSM153111 3 0.1289 0.906 0.032 0.000 0.968
#> GSM153112 1 0.6154 0.429 0.592 0.000 0.408
#> GSM153113 3 0.1529 0.908 0.040 0.000 0.960
#> GSM153114 1 0.0000 0.919 1.000 0.000 0.000
#> GSM187532 2 0.0424 0.980 0.000 0.992 0.008
#> GSM187533 2 0.0592 0.979 0.000 0.988 0.012
#> GSM187534 2 0.0237 0.980 0.000 0.996 0.004
#> GSM187535 3 0.1964 0.904 0.056 0.000 0.944
#> GSM152906 2 0.2448 0.931 0.000 0.924 0.076
#> GSM152907 2 0.1031 0.976 0.000 0.976 0.024
#> GSM152908 2 0.0424 0.980 0.000 0.992 0.008
#> GSM152909 2 0.0424 0.980 0.000 0.992 0.008
#> GSM152910 2 0.0424 0.980 0.000 0.992 0.008
#> GSM152911 2 0.0424 0.980 0.000 0.992 0.008
#> GSM152912 2 0.0424 0.980 0.000 0.992 0.008
#> GSM152913 2 0.0237 0.981 0.000 0.996 0.004
#> GSM152914 2 0.0000 0.981 0.000 1.000 0.000
#> GSM152915 2 0.0000 0.981 0.000 1.000 0.000
#> GSM152916 2 0.1031 0.976 0.000 0.976 0.024
#> GSM152917 2 0.0000 0.981 0.000 1.000 0.000
#> GSM152918 2 0.0237 0.980 0.000 0.996 0.004
#> GSM152919 2 0.0237 0.980 0.000 0.996 0.004
#> GSM152920 2 0.0424 0.980 0.000 0.992 0.008
#> GSM152921 2 0.0424 0.980 0.000 0.992 0.008
#> GSM152922 2 0.0424 0.980 0.000 0.992 0.008
#> GSM152923 2 0.1031 0.976 0.000 0.976 0.024
#> GSM152924 2 0.1031 0.976 0.000 0.976 0.024
#> GSM152925 2 0.1031 0.976 0.000 0.976 0.024
#> GSM152926 3 0.4504 0.685 0.000 0.196 0.804
#> GSM152927 2 0.1031 0.976 0.000 0.976 0.024
#> GSM152928 3 0.4346 0.705 0.000 0.184 0.816
#> GSM152929 2 0.5216 0.675 0.000 0.740 0.260
#> GSM152930 2 0.1031 0.976 0.000 0.976 0.024
cbind(get_classes(res, k = 4), get_membership(res, k = 4))
#> class entropy silhouette p1 p2 p3 p4
#> GSM152839 4 0.3873 0.777 0.228 0.000 0.000 0.772
#> GSM152840 4 0.0000 0.893 0.000 0.000 0.000 1.000
#> GSM152841 4 0.0000 0.893 0.000 0.000 0.000 1.000
#> GSM152842 4 0.4564 0.676 0.328 0.000 0.000 0.672
#> GSM152843 4 0.4500 0.690 0.316 0.000 0.000 0.684
#> GSM152844 4 0.0000 0.893 0.000 0.000 0.000 1.000
#> GSM152845 1 0.7596 0.504 0.616 0.200 0.116 0.068
#> GSM152846 4 0.1118 0.895 0.036 0.000 0.000 0.964
#> GSM152847 4 0.4406 0.709 0.300 0.000 0.000 0.700
#> GSM152848 4 0.4304 0.723 0.284 0.000 0.000 0.716
#> GSM152849 4 0.4522 0.685 0.320 0.000 0.000 0.680
#> GSM152850 4 0.4730 0.612 0.364 0.000 0.000 0.636
#> GSM152851 4 0.1211 0.894 0.040 0.000 0.000 0.960
#> GSM152852 4 0.0817 0.897 0.024 0.000 0.000 0.976
#> GSM152853 4 0.0000 0.893 0.000 0.000 0.000 1.000
#> GSM152854 4 0.1389 0.892 0.048 0.000 0.000 0.952
#> GSM152855 4 0.0469 0.896 0.012 0.000 0.000 0.988
#> GSM153238 1 0.0000 0.884 1.000 0.000 0.000 0.000
#> GSM153239 4 0.0336 0.895 0.008 0.000 0.000 0.992
#> GSM153240 4 0.0000 0.893 0.000 0.000 0.000 1.000
#> GSM153241 4 0.3444 0.824 0.184 0.000 0.000 0.816
#> GSM153242 4 0.0469 0.896 0.012 0.000 0.000 0.988
#> GSM153243 1 0.0188 0.885 0.996 0.000 0.000 0.004
#> GSM153244 4 0.0921 0.896 0.028 0.000 0.000 0.972
#> GSM153245 4 0.0188 0.894 0.004 0.000 0.000 0.996
#> GSM153246 4 0.2216 0.887 0.092 0.000 0.000 0.908
#> GSM153247 1 0.0817 0.883 0.976 0.000 0.000 0.024
#> GSM153248 1 0.0188 0.885 0.996 0.000 0.000 0.004
#> GSM153249 4 0.0000 0.893 0.000 0.000 0.000 1.000
#> GSM153250 4 0.4277 0.726 0.280 0.000 0.000 0.720
#> GSM153251 4 0.3444 0.756 0.184 0.000 0.000 0.816
#> GSM153252 4 0.0469 0.896 0.012 0.000 0.000 0.988
#> GSM153253 4 0.0000 0.893 0.000 0.000 0.000 1.000
#> GSM153254 4 0.1940 0.879 0.076 0.000 0.000 0.924
#> GSM153255 4 0.0707 0.895 0.020 0.000 0.000 0.980
#> GSM153256 4 0.2149 0.884 0.088 0.000 0.000 0.912
#> GSM153257 4 0.2408 0.872 0.104 0.000 0.000 0.896
#> GSM153258 1 0.1211 0.883 0.960 0.000 0.000 0.040
#> GSM153259 1 0.2868 0.771 0.864 0.000 0.000 0.136
#> GSM153260 1 0.1211 0.880 0.960 0.000 0.000 0.040
#> GSM153261 1 0.2281 0.849 0.904 0.000 0.000 0.096
#> GSM153262 4 0.0000 0.893 0.000 0.000 0.000 1.000
#> GSM153263 4 0.4564 0.676 0.328 0.000 0.000 0.672
#> GSM153264 1 0.2760 0.788 0.872 0.000 0.000 0.128
#> GSM153265 4 0.0000 0.893 0.000 0.000 0.000 1.000
#> GSM153266 1 0.1474 0.879 0.948 0.000 0.000 0.052
#> GSM153267 4 0.2647 0.873 0.120 0.000 0.000 0.880
#> GSM153268 4 0.0000 0.893 0.000 0.000 0.000 1.000
#> GSM153269 4 0.1867 0.890 0.072 0.000 0.000 0.928
#> GSM153270 4 0.1867 0.885 0.072 0.000 0.000 0.928
#> GSM153271 4 0.4250 0.730 0.276 0.000 0.000 0.724
#> GSM153272 4 0.1637 0.889 0.060 0.000 0.000 0.940
#> GSM153273 1 0.0188 0.885 0.996 0.000 0.000 0.004
#> GSM153274 4 0.0921 0.898 0.028 0.000 0.000 0.972
#> GSM153275 4 0.0469 0.896 0.012 0.000 0.000 0.988
#> GSM153276 4 0.2081 0.889 0.084 0.000 0.000 0.916
#> GSM153277 4 0.0469 0.896 0.012 0.000 0.000 0.988
#> GSM153278 1 0.1389 0.879 0.952 0.000 0.000 0.048
#> GSM153279 4 0.1118 0.895 0.036 0.000 0.000 0.964
#> GSM153280 4 0.0000 0.893 0.000 0.000 0.000 1.000
#> GSM153281 4 0.0000 0.893 0.000 0.000 0.000 1.000
#> GSM153282 4 0.0000 0.893 0.000 0.000 0.000 1.000
#> GSM153283 1 0.4406 0.485 0.700 0.000 0.000 0.300
#> GSM153284 4 0.1389 0.895 0.048 0.000 0.000 0.952
#> GSM153285 4 0.0188 0.894 0.004 0.000 0.000 0.996
#> GSM153286 4 0.1637 0.889 0.060 0.000 0.000 0.940
#> GSM153287 4 0.1022 0.893 0.032 0.000 0.000 0.968
#> GSM153288 4 0.1022 0.893 0.032 0.000 0.000 0.968
#> GSM153289 4 0.1637 0.894 0.060 0.000 0.000 0.940
#> GSM153290 4 0.0336 0.895 0.008 0.000 0.000 0.992
#> GSM153291 4 0.0336 0.895 0.008 0.000 0.000 0.992
#> GSM153292 4 0.0000 0.893 0.000 0.000 0.000 1.000
#> GSM153293 4 0.3975 0.765 0.240 0.000 0.000 0.760
#> GSM153294 1 0.0336 0.885 0.992 0.000 0.000 0.008
#> GSM153295 4 0.2589 0.865 0.116 0.000 0.000 0.884
#> GSM153054 1 0.4193 0.554 0.732 0.000 0.000 0.268
#> GSM153055 4 0.2760 0.858 0.128 0.000 0.000 0.872
#> GSM153056 4 0.2281 0.883 0.096 0.000 0.000 0.904
#> GSM153057 4 0.2469 0.856 0.108 0.000 0.000 0.892
#> GSM153058 4 0.1118 0.895 0.036 0.000 0.000 0.964
#> GSM153059 1 0.3907 0.707 0.768 0.000 0.000 0.232
#> GSM153060 4 0.1637 0.895 0.060 0.000 0.000 0.940
#> GSM153061 1 0.0000 0.884 1.000 0.000 0.000 0.000
#> GSM153062 1 0.4222 0.658 0.728 0.000 0.000 0.272
#> GSM153063 4 0.0817 0.896 0.024 0.000 0.000 0.976
#> GSM153064 4 0.4605 0.663 0.336 0.000 0.000 0.664
#> GSM153065 1 0.0592 0.885 0.984 0.000 0.000 0.016
#> GSM153066 1 0.0336 0.883 0.992 0.008 0.000 0.000
#> GSM153067 4 0.1022 0.893 0.032 0.000 0.000 0.968
#> GSM153068 1 0.3649 0.742 0.796 0.000 0.000 0.204
#> GSM153069 4 0.0000 0.893 0.000 0.000 0.000 1.000
#> GSM153070 4 0.4564 0.673 0.328 0.000 0.000 0.672
#> GSM153071 4 0.4277 0.734 0.280 0.000 0.000 0.720
#> GSM153072 1 0.0000 0.884 1.000 0.000 0.000 0.000
#> GSM153073 4 0.4382 0.714 0.296 0.000 0.000 0.704
#> GSM153074 4 0.0469 0.896 0.012 0.000 0.000 0.988
#> GSM153075 4 0.1302 0.894 0.044 0.000 0.000 0.956
#> GSM153076 4 0.4072 0.754 0.252 0.000 0.000 0.748
#> GSM153077 1 0.0592 0.884 0.984 0.000 0.000 0.016
#> GSM153078 1 0.1389 0.866 0.952 0.000 0.000 0.048
#> GSM153079 1 0.1022 0.880 0.968 0.000 0.000 0.032
#> GSM153080 1 0.4008 0.701 0.756 0.000 0.000 0.244
#> GSM153081 1 0.0817 0.881 0.976 0.000 0.000 0.024
#> GSM153082 1 0.0336 0.886 0.992 0.000 0.000 0.008
#> GSM153083 1 0.0000 0.884 1.000 0.000 0.000 0.000
#> GSM153084 1 0.1022 0.880 0.968 0.000 0.000 0.032
#> GSM153085 1 0.0921 0.885 0.972 0.000 0.000 0.028
#> GSM153086 1 0.0000 0.884 1.000 0.000 0.000 0.000
#> GSM153087 4 0.1302 0.897 0.044 0.000 0.000 0.956
#> GSM153088 4 0.4250 0.730 0.276 0.000 0.000 0.724
#> GSM153089 1 0.4250 0.656 0.724 0.000 0.000 0.276
#> GSM153090 4 0.2973 0.859 0.144 0.000 0.000 0.856
#> GSM153091 1 0.0336 0.886 0.992 0.000 0.000 0.008
#> GSM153092 1 0.4331 0.659 0.712 0.000 0.000 0.288
#> GSM153093 4 0.0592 0.897 0.016 0.000 0.000 0.984
#> GSM153094 1 0.0188 0.885 0.996 0.000 0.000 0.004
#> GSM153095 1 0.0469 0.887 0.988 0.000 0.000 0.012
#> GSM153096 1 0.0000 0.884 1.000 0.000 0.000 0.000
#> GSM153097 1 0.0000 0.884 1.000 0.000 0.000 0.000
#> GSM153098 4 0.2704 0.873 0.124 0.000 0.000 0.876
#> GSM153099 4 0.3074 0.854 0.152 0.000 0.000 0.848
#> GSM153100 1 0.3311 0.759 0.828 0.000 0.000 0.172
#> GSM153101 1 0.2469 0.834 0.892 0.000 0.000 0.108
#> GSM153102 1 0.3873 0.709 0.772 0.000 0.000 0.228
#> GSM153103 1 0.0000 0.884 1.000 0.000 0.000 0.000
#> GSM153104 4 0.0336 0.895 0.008 0.000 0.000 0.992
#> GSM153106 1 0.3907 0.707 0.768 0.000 0.000 0.232
#> GSM153107 1 0.0921 0.884 0.972 0.000 0.000 0.028
#> GSM153108 4 0.2011 0.883 0.080 0.000 0.000 0.920
#> GSM153109 1 0.0707 0.885 0.980 0.000 0.000 0.020
#> GSM153110 1 0.0000 0.884 1.000 0.000 0.000 0.000
#> GSM153111 1 0.0000 0.884 1.000 0.000 0.000 0.000
#> GSM153112 4 0.4977 0.368 0.460 0.000 0.000 0.540
#> GSM153113 1 0.0336 0.886 0.992 0.000 0.000 0.008
#> GSM153114 4 0.0336 0.895 0.008 0.000 0.000 0.992
#> GSM187532 3 0.0188 0.965 0.000 0.004 0.996 0.000
#> GSM187533 3 0.2760 0.779 0.128 0.000 0.872 0.000
#> GSM187534 1 0.6158 0.404 0.628 0.080 0.292 0.000
#> GSM187535 1 0.0921 0.882 0.972 0.000 0.000 0.028
#> GSM152906 2 0.0000 0.930 0.000 1.000 0.000 0.000
#> GSM152907 2 0.0000 0.930 0.000 1.000 0.000 0.000
#> GSM152908 3 0.0000 0.967 0.000 0.000 1.000 0.000
#> GSM152909 3 0.0000 0.967 0.000 0.000 1.000 0.000
#> GSM152910 3 0.0000 0.967 0.000 0.000 1.000 0.000
#> GSM152911 3 0.0188 0.965 0.000 0.004 0.996 0.000
#> GSM152912 3 0.0000 0.967 0.000 0.000 1.000 0.000
#> GSM152913 3 0.1557 0.923 0.000 0.056 0.944 0.000
#> GSM152914 2 0.3975 0.735 0.000 0.760 0.240 0.000
#> GSM152915 3 0.1867 0.906 0.000 0.072 0.928 0.000
#> GSM152916 2 0.0000 0.930 0.000 1.000 0.000 0.000
#> GSM152917 2 0.3837 0.757 0.000 0.776 0.224 0.000
#> GSM152918 2 0.3688 0.775 0.000 0.792 0.208 0.000
#> GSM152919 2 0.3688 0.775 0.000 0.792 0.208 0.000
#> GSM152920 3 0.0000 0.967 0.000 0.000 1.000 0.000
#> GSM152921 3 0.0000 0.967 0.000 0.000 1.000 0.000
#> GSM152922 3 0.0000 0.967 0.000 0.000 1.000 0.000
#> GSM152923 2 0.0000 0.930 0.000 1.000 0.000 0.000
#> GSM152924 2 0.0000 0.930 0.000 1.000 0.000 0.000
#> GSM152925 2 0.0000 0.930 0.000 1.000 0.000 0.000
#> GSM152926 2 0.0000 0.930 0.000 1.000 0.000 0.000
#> GSM152927 2 0.0000 0.930 0.000 1.000 0.000 0.000
#> GSM152928 2 0.0000 0.930 0.000 1.000 0.000 0.000
#> GSM152929 2 0.0000 0.930 0.000 1.000 0.000 0.000
#> GSM152930 2 0.0000 0.930 0.000 1.000 0.000 0.000
cbind(get_classes(res, k = 5), get_membership(res, k = 5))
#> class entropy silhouette p1 p2 p3 p4 p5
#> GSM152839 1 0.5583 0.5528 0.564 0.000 0.084 0.352 0.000
#> GSM152840 4 0.0162 0.9110 0.004 0.000 0.000 0.996 0.000
#> GSM152841 4 0.0162 0.9110 0.004 0.000 0.000 0.996 0.000
#> GSM152842 1 0.3375 0.8359 0.840 0.000 0.104 0.056 0.000
#> GSM152843 1 0.3323 0.8367 0.844 0.000 0.100 0.056 0.000
#> GSM152844 4 0.0162 0.9110 0.004 0.000 0.000 0.996 0.000
#> GSM152845 3 0.6448 0.5010 0.000 0.160 0.616 0.044 0.180
#> GSM152846 4 0.1211 0.9055 0.016 0.000 0.024 0.960 0.000
#> GSM152847 1 0.3362 0.8369 0.844 0.000 0.080 0.076 0.000
#> GSM152848 1 0.3354 0.8339 0.844 0.000 0.068 0.088 0.000
#> GSM152849 1 0.3336 0.8373 0.844 0.000 0.096 0.060 0.000
#> GSM152850 1 0.3323 0.8368 0.844 0.000 0.100 0.056 0.000
#> GSM152851 4 0.1106 0.9055 0.012 0.000 0.024 0.964 0.000
#> GSM152852 4 0.0912 0.9095 0.012 0.000 0.016 0.972 0.000
#> GSM152853 4 0.0162 0.9110 0.004 0.000 0.000 0.996 0.000
#> GSM152854 4 0.1469 0.8981 0.016 0.000 0.036 0.948 0.000
#> GSM152855 4 0.0609 0.9114 0.020 0.000 0.000 0.980 0.000
#> GSM153238 3 0.3534 0.5677 0.256 0.000 0.744 0.000 0.000
#> GSM153239 4 0.0609 0.9121 0.020 0.000 0.000 0.980 0.000
#> GSM153240 4 0.0609 0.9121 0.020 0.000 0.000 0.980 0.000
#> GSM153241 4 0.5591 0.0273 0.396 0.000 0.076 0.528 0.000
#> GSM153242 4 0.0566 0.9116 0.012 0.000 0.004 0.984 0.000
#> GSM153243 3 0.0000 0.8884 0.000 0.000 1.000 0.000 0.000
#> GSM153244 4 0.1018 0.9090 0.016 0.000 0.016 0.968 0.000
#> GSM153245 4 0.0162 0.9110 0.004 0.000 0.000 0.996 0.000
#> GSM153246 4 0.3309 0.8135 0.128 0.000 0.036 0.836 0.000
#> GSM153247 1 0.4904 0.2639 0.504 0.000 0.472 0.024 0.000
#> GSM153248 1 0.4088 0.5374 0.632 0.000 0.368 0.000 0.000
#> GSM153249 4 0.0290 0.9116 0.008 0.000 0.000 0.992 0.000
#> GSM153250 1 0.3359 0.8351 0.844 0.000 0.072 0.084 0.000
#> GSM153251 4 0.3039 0.7833 0.012 0.000 0.152 0.836 0.000
#> GSM153252 4 0.1331 0.8979 0.040 0.000 0.008 0.952 0.000
#> GSM153253 4 0.0162 0.9110 0.004 0.000 0.000 0.996 0.000
#> GSM153254 4 0.1981 0.8815 0.016 0.000 0.064 0.920 0.000
#> GSM153255 4 0.1792 0.8679 0.084 0.000 0.000 0.916 0.000
#> GSM153256 1 0.3596 0.7693 0.784 0.000 0.016 0.200 0.000
#> GSM153257 4 0.4714 0.4329 0.324 0.000 0.032 0.644 0.000
#> GSM153258 1 0.5638 0.6851 0.632 0.000 0.152 0.216 0.000
#> GSM153259 1 0.3074 0.7756 0.804 0.000 0.196 0.000 0.000
#> GSM153260 3 0.0451 0.8883 0.008 0.000 0.988 0.004 0.000
#> GSM153261 3 0.1701 0.8641 0.016 0.000 0.936 0.048 0.000
#> GSM153262 4 0.0162 0.9110 0.004 0.000 0.000 0.996 0.000
#> GSM153263 1 0.3442 0.8371 0.836 0.000 0.104 0.060 0.000
#> GSM153264 1 0.2953 0.8108 0.844 0.000 0.144 0.012 0.000
#> GSM153265 4 0.0162 0.9110 0.004 0.000 0.000 0.996 0.000
#> GSM153266 1 0.6111 0.5780 0.560 0.000 0.260 0.180 0.000
#> GSM153267 1 0.4876 0.4699 0.576 0.000 0.028 0.396 0.000
#> GSM153268 4 0.0162 0.9110 0.004 0.000 0.000 0.996 0.000
#> GSM153269 1 0.3177 0.7629 0.792 0.000 0.000 0.208 0.000
#> GSM153270 4 0.2426 0.8740 0.064 0.000 0.036 0.900 0.000
#> GSM153271 1 0.3346 0.8322 0.844 0.000 0.064 0.092 0.000
#> GSM153272 1 0.2929 0.7770 0.820 0.000 0.000 0.180 0.000
#> GSM153273 3 0.0963 0.8785 0.036 0.000 0.964 0.000 0.000
#> GSM153274 4 0.2966 0.7562 0.184 0.000 0.000 0.816 0.000
#> GSM153275 4 0.0703 0.9106 0.024 0.000 0.000 0.976 0.000
#> GSM153276 1 0.4084 0.6191 0.668 0.000 0.004 0.328 0.000
#> GSM153277 4 0.0703 0.9106 0.024 0.000 0.000 0.976 0.000
#> GSM153278 3 0.4370 0.6367 0.040 0.000 0.724 0.236 0.000
#> GSM153279 4 0.1018 0.9087 0.016 0.000 0.016 0.968 0.000
#> GSM153280 4 0.0290 0.9118 0.008 0.000 0.000 0.992 0.000
#> GSM153281 4 0.0404 0.9114 0.012 0.000 0.000 0.988 0.000
#> GSM153282 4 0.0162 0.9110 0.004 0.000 0.000 0.996 0.000
#> GSM153283 1 0.3061 0.8169 0.844 0.000 0.136 0.020 0.000
#> GSM153284 4 0.3636 0.6458 0.272 0.000 0.000 0.728 0.000
#> GSM153285 4 0.0162 0.9110 0.004 0.000 0.000 0.996 0.000
#> GSM153286 1 0.3949 0.5827 0.668 0.000 0.000 0.332 0.000
#> GSM153287 4 0.3003 0.7511 0.188 0.000 0.000 0.812 0.000
#> GSM153288 4 0.3480 0.6655 0.248 0.000 0.000 0.752 0.000
#> GSM153289 4 0.3621 0.7259 0.192 0.000 0.020 0.788 0.000
#> GSM153290 4 0.0290 0.9118 0.008 0.000 0.000 0.992 0.000
#> GSM153291 4 0.0703 0.9088 0.024 0.000 0.000 0.976 0.000
#> GSM153292 4 0.0290 0.9116 0.008 0.000 0.000 0.992 0.000
#> GSM153293 1 0.3875 0.8007 0.792 0.000 0.048 0.160 0.000
#> GSM153294 1 0.3752 0.6767 0.708 0.000 0.292 0.000 0.000
#> GSM153295 1 0.5047 0.1714 0.496 0.000 0.032 0.472 0.000
#> GSM153054 1 0.3123 0.7895 0.812 0.000 0.184 0.004 0.000
#> GSM153055 4 0.2304 0.8747 0.044 0.000 0.048 0.908 0.000
#> GSM153056 4 0.3732 0.7317 0.176 0.000 0.032 0.792 0.000
#> GSM153057 4 0.2473 0.8662 0.032 0.000 0.072 0.896 0.000
#> GSM153058 4 0.1117 0.9076 0.016 0.000 0.020 0.964 0.000
#> GSM153059 3 0.1357 0.8600 0.004 0.000 0.948 0.048 0.000
#> GSM153060 4 0.2079 0.8859 0.064 0.000 0.020 0.916 0.000
#> GSM153061 3 0.0510 0.8869 0.016 0.000 0.984 0.000 0.000
#> GSM153062 3 0.3123 0.7352 0.004 0.000 0.812 0.184 0.000
#> GSM153063 4 0.0992 0.9097 0.024 0.000 0.008 0.968 0.000
#> GSM153064 1 0.3375 0.8359 0.840 0.000 0.104 0.056 0.000
#> GSM153065 3 0.0162 0.8885 0.004 0.000 0.996 0.000 0.000
#> GSM153066 3 0.0290 0.8888 0.008 0.000 0.992 0.000 0.000
#> GSM153067 4 0.2929 0.7627 0.180 0.000 0.000 0.820 0.000
#> GSM153068 3 0.1282 0.8654 0.004 0.000 0.952 0.044 0.000
#> GSM153069 4 0.0290 0.9116 0.008 0.000 0.000 0.992 0.000
#> GSM153070 1 0.3346 0.8377 0.844 0.000 0.092 0.064 0.000
#> GSM153071 1 0.3749 0.8320 0.816 0.000 0.080 0.104 0.000
#> GSM153072 1 0.4015 0.6011 0.652 0.000 0.348 0.000 0.000
#> GSM153073 1 0.3359 0.8355 0.844 0.000 0.072 0.084 0.000
#> GSM153074 4 0.0703 0.9106 0.024 0.000 0.000 0.976 0.000
#> GSM153075 4 0.1579 0.9007 0.024 0.000 0.032 0.944 0.000
#> GSM153076 1 0.3307 0.8262 0.844 0.000 0.052 0.104 0.000
#> GSM153077 1 0.2806 0.8037 0.844 0.000 0.152 0.004 0.000
#> GSM153078 1 0.2997 0.8102 0.840 0.000 0.148 0.012 0.000
#> GSM153079 3 0.0510 0.8869 0.016 0.000 0.984 0.000 0.000
#> GSM153080 3 0.4141 0.6510 0.028 0.000 0.736 0.236 0.000
#> GSM153081 1 0.2886 0.8071 0.844 0.000 0.148 0.008 0.000
#> GSM153082 3 0.0290 0.8888 0.008 0.000 0.992 0.000 0.000
#> GSM153083 3 0.0510 0.8869 0.016 0.000 0.984 0.000 0.000
#> GSM153084 3 0.0000 0.8884 0.000 0.000 1.000 0.000 0.000
#> GSM153085 3 0.0451 0.8871 0.004 0.000 0.988 0.008 0.000
#> GSM153086 3 0.0404 0.8877 0.012 0.000 0.988 0.000 0.000
#> GSM153087 4 0.4045 0.3563 0.356 0.000 0.000 0.644 0.000
#> GSM153088 1 0.3346 0.8322 0.844 0.000 0.064 0.092 0.000
#> GSM153089 3 0.2763 0.7766 0.004 0.000 0.848 0.148 0.000
#> GSM153090 1 0.3507 0.8226 0.828 0.000 0.052 0.120 0.000
#> GSM153091 3 0.0162 0.8877 0.000 0.000 0.996 0.004 0.000
#> GSM153092 3 0.5696 0.4060 0.096 0.000 0.560 0.344 0.000
#> GSM153093 4 0.0609 0.9114 0.020 0.000 0.000 0.980 0.000
#> GSM153094 3 0.0000 0.8884 0.000 0.000 1.000 0.000 0.000
#> GSM153095 3 0.0794 0.8834 0.028 0.000 0.972 0.000 0.000
#> GSM153096 3 0.0290 0.8888 0.008 0.000 0.992 0.000 0.000
#> GSM153097 3 0.0290 0.8888 0.008 0.000 0.992 0.000 0.000
#> GSM153098 4 0.3847 0.7530 0.180 0.000 0.036 0.784 0.000
#> GSM153099 1 0.4885 0.6952 0.668 0.000 0.056 0.276 0.000
#> GSM153100 3 0.4827 0.6372 0.116 0.000 0.724 0.160 0.000
#> GSM153101 3 0.0798 0.8839 0.008 0.000 0.976 0.016 0.000
#> GSM153102 3 0.1197 0.8606 0.000 0.000 0.952 0.048 0.000
#> GSM153103 3 0.0290 0.8888 0.008 0.000 0.992 0.000 0.000
#> GSM153104 4 0.0290 0.9116 0.008 0.000 0.000 0.992 0.000
#> GSM153106 3 0.1270 0.8594 0.000 0.000 0.948 0.052 0.000
#> GSM153107 3 0.2914 0.8203 0.076 0.000 0.872 0.052 0.000
#> GSM153108 4 0.2300 0.8770 0.040 0.000 0.052 0.908 0.000
#> GSM153109 3 0.0000 0.8884 0.000 0.000 1.000 0.000 0.000
#> GSM153110 3 0.0794 0.8830 0.028 0.000 0.972 0.000 0.000
#> GSM153111 3 0.3305 0.6283 0.224 0.000 0.776 0.000 0.000
#> GSM153112 1 0.4509 0.8127 0.752 0.000 0.152 0.096 0.000
#> GSM153113 3 0.0000 0.8884 0.000 0.000 1.000 0.000 0.000
#> GSM153114 4 0.0290 0.9118 0.008 0.000 0.000 0.992 0.000
#> GSM187532 5 0.2389 0.8855 0.116 0.004 0.000 0.000 0.880
#> GSM187533 5 0.5126 0.7054 0.152 0.000 0.152 0.000 0.696
#> GSM187534 3 0.6148 0.4753 0.152 0.040 0.648 0.000 0.160
#> GSM187535 3 0.0290 0.8888 0.008 0.000 0.992 0.000 0.000
#> GSM152906 2 0.0000 0.9065 0.000 1.000 0.000 0.000 0.000
#> GSM152907 2 0.0000 0.9065 0.000 1.000 0.000 0.000 0.000
#> GSM152908 5 0.0000 0.9175 0.000 0.000 0.000 0.000 1.000
#> GSM152909 5 0.0000 0.9175 0.000 0.000 0.000 0.000 1.000
#> GSM152910 5 0.0000 0.9175 0.000 0.000 0.000 0.000 1.000
#> GSM152911 5 0.2806 0.8686 0.152 0.004 0.000 0.000 0.844
#> GSM152912 5 0.0000 0.9175 0.000 0.000 0.000 0.000 1.000
#> GSM152913 5 0.3723 0.8426 0.152 0.044 0.000 0.000 0.804
#> GSM152914 2 0.5372 0.6432 0.152 0.668 0.000 0.000 0.180
#> GSM152915 5 0.3995 0.8273 0.152 0.060 0.000 0.000 0.788
#> GSM152916 2 0.0000 0.9065 0.000 1.000 0.000 0.000 0.000
#> GSM152917 2 0.5271 0.6619 0.152 0.680 0.000 0.000 0.168
#> GSM152918 2 0.5163 0.6768 0.152 0.692 0.000 0.000 0.156
#> GSM152919 2 0.5163 0.6768 0.152 0.692 0.000 0.000 0.156
#> GSM152920 5 0.0000 0.9175 0.000 0.000 0.000 0.000 1.000
#> GSM152921 5 0.0000 0.9175 0.000 0.000 0.000 0.000 1.000
#> GSM152922 5 0.0000 0.9175 0.000 0.000 0.000 0.000 1.000
#> GSM152923 2 0.0000 0.9065 0.000 1.000 0.000 0.000 0.000
#> GSM152924 2 0.0000 0.9065 0.000 1.000 0.000 0.000 0.000
#> GSM152925 2 0.0000 0.9065 0.000 1.000 0.000 0.000 0.000
#> GSM152926 2 0.0000 0.9065 0.000 1.000 0.000 0.000 0.000
#> GSM152927 2 0.0000 0.9065 0.000 1.000 0.000 0.000 0.000
#> GSM152928 2 0.0000 0.9065 0.000 1.000 0.000 0.000 0.000
#> GSM152929 2 0.0000 0.9065 0.000 1.000 0.000 0.000 0.000
#> GSM152930 2 0.0000 0.9065 0.000 1.000 0.000 0.000 0.000
cbind(get_classes(res, k = 6), get_membership(res, k = 6))
#> class entropy silhouette p1 p2 p3 p4 p5 p6
#> GSM152839 1 0.4026 0.417 0.612 0.0 0.012 0.376 0.000 0.000
#> GSM152840 4 0.0508 0.901 0.012 0.0 0.000 0.984 0.004 0.000
#> GSM152841 4 0.0508 0.901 0.012 0.0 0.000 0.984 0.004 0.000
#> GSM152842 1 0.0547 0.854 0.980 0.0 0.020 0.000 0.000 0.000
#> GSM152843 1 0.0458 0.856 0.984 0.0 0.016 0.000 0.000 0.000
#> GSM152844 4 0.0603 0.902 0.016 0.0 0.000 0.980 0.004 0.000
#> GSM152845 5 0.5419 0.141 0.000 0.1 0.428 0.004 0.468 0.000
#> GSM152846 4 0.1003 0.900 0.016 0.0 0.020 0.964 0.000 0.000
#> GSM152847 1 0.0363 0.858 0.988 0.0 0.012 0.000 0.000 0.000
#> GSM152848 1 0.0363 0.858 0.988 0.0 0.012 0.000 0.000 0.000
#> GSM152849 1 0.0508 0.858 0.984 0.0 0.012 0.004 0.000 0.000
#> GSM152850 1 0.0363 0.858 0.988 0.0 0.012 0.000 0.000 0.000
#> GSM152851 4 0.0725 0.903 0.012 0.0 0.012 0.976 0.000 0.000
#> GSM152852 4 0.0820 0.902 0.012 0.0 0.016 0.972 0.000 0.000
#> GSM152853 4 0.0508 0.901 0.012 0.0 0.000 0.984 0.004 0.000
#> GSM152854 4 0.1003 0.900 0.016 0.0 0.020 0.964 0.000 0.000
#> GSM152855 4 0.0777 0.905 0.024 0.0 0.004 0.972 0.000 0.000
#> GSM153238 3 0.3221 0.596 0.264 0.0 0.736 0.000 0.000 0.000
#> GSM153239 4 0.0858 0.906 0.028 0.0 0.004 0.968 0.000 0.000
#> GSM153240 4 0.0713 0.906 0.028 0.0 0.000 0.972 0.000 0.000
#> GSM153241 4 0.4361 0.219 0.424 0.0 0.024 0.552 0.000 0.000
#> GSM153242 4 0.0622 0.904 0.012 0.0 0.008 0.980 0.000 0.000
#> GSM153243 3 0.0146 0.895 0.004 0.0 0.996 0.000 0.000 0.000
#> GSM153244 4 0.1003 0.900 0.016 0.0 0.020 0.964 0.000 0.000
#> GSM153245 4 0.0603 0.902 0.016 0.0 0.000 0.980 0.004 0.000
#> GSM153246 4 0.2553 0.830 0.144 0.0 0.008 0.848 0.000 0.000
#> GSM153247 1 0.4242 0.211 0.536 0.0 0.448 0.016 0.000 0.000
#> GSM153248 1 0.3482 0.535 0.684 0.0 0.316 0.000 0.000 0.000
#> GSM153249 4 0.0405 0.905 0.008 0.0 0.000 0.988 0.004 0.000
#> GSM153250 1 0.0363 0.858 0.988 0.0 0.012 0.000 0.000 0.000
#> GSM153251 4 0.2692 0.778 0.012 0.0 0.148 0.840 0.000 0.000
#> GSM153252 4 0.1411 0.888 0.060 0.0 0.000 0.936 0.004 0.000
#> GSM153253 4 0.0603 0.902 0.016 0.0 0.000 0.980 0.004 0.000
#> GSM153254 4 0.1391 0.893 0.016 0.0 0.040 0.944 0.000 0.000
#> GSM153255 4 0.2100 0.847 0.112 0.0 0.000 0.884 0.004 0.000
#> GSM153256 1 0.1714 0.803 0.908 0.0 0.000 0.092 0.000 0.000
#> GSM153257 4 0.3899 0.382 0.404 0.0 0.000 0.592 0.004 0.000
#> GSM153258 1 0.3629 0.599 0.712 0.0 0.012 0.276 0.000 0.000
#> GSM153259 1 0.1204 0.837 0.944 0.0 0.056 0.000 0.000 0.000
#> GSM153260 3 0.0547 0.893 0.020 0.0 0.980 0.000 0.000 0.000
#> GSM153261 3 0.1807 0.842 0.020 0.0 0.920 0.060 0.000 0.000
#> GSM153262 4 0.0603 0.902 0.016 0.0 0.000 0.980 0.004 0.000
#> GSM153263 1 0.0777 0.855 0.972 0.0 0.024 0.004 0.000 0.000
#> GSM153264 1 0.0363 0.858 0.988 0.0 0.012 0.000 0.000 0.000
#> GSM153265 4 0.0291 0.904 0.004 0.0 0.000 0.992 0.004 0.000
#> GSM153266 1 0.5309 0.493 0.596 0.0 0.176 0.228 0.000 0.000
#> GSM153267 1 0.3923 0.423 0.620 0.0 0.008 0.372 0.000 0.000
#> GSM153268 4 0.0508 0.901 0.012 0.0 0.000 0.984 0.004 0.000
#> GSM153269 1 0.1588 0.825 0.924 0.0 0.004 0.072 0.000 0.000
#> GSM153270 4 0.1913 0.879 0.080 0.0 0.012 0.908 0.000 0.000
#> GSM153271 1 0.0363 0.858 0.988 0.0 0.012 0.000 0.000 0.000
#> GSM153272 1 0.0937 0.834 0.960 0.0 0.000 0.040 0.000 0.000
#> GSM153273 3 0.0937 0.882 0.040 0.0 0.960 0.000 0.000 0.000
#> GSM153274 4 0.3023 0.728 0.212 0.0 0.004 0.784 0.000 0.000
#> GSM153275 4 0.0858 0.904 0.028 0.0 0.004 0.968 0.000 0.000
#> GSM153276 1 0.3081 0.691 0.776 0.0 0.004 0.220 0.000 0.000
#> GSM153277 4 0.0777 0.904 0.024 0.0 0.004 0.972 0.000 0.000
#> GSM153278 3 0.4386 0.491 0.048 0.0 0.652 0.300 0.000 0.000
#> GSM153279 4 0.0820 0.903 0.016 0.0 0.012 0.972 0.000 0.000
#> GSM153280 4 0.0405 0.904 0.008 0.0 0.004 0.988 0.000 0.000
#> GSM153281 4 0.0603 0.906 0.016 0.0 0.000 0.980 0.004 0.000
#> GSM153282 4 0.0508 0.901 0.012 0.0 0.000 0.984 0.004 0.000
#> GSM153283 1 0.0363 0.858 0.988 0.0 0.012 0.000 0.000 0.000
#> GSM153284 4 0.3578 0.555 0.340 0.0 0.000 0.660 0.000 0.000
#> GSM153285 4 0.0603 0.902 0.016 0.0 0.000 0.980 0.004 0.000
#> GSM153286 1 0.3109 0.656 0.772 0.0 0.000 0.224 0.004 0.000
#> GSM153287 4 0.3360 0.662 0.264 0.0 0.000 0.732 0.004 0.000
#> GSM153288 4 0.3515 0.567 0.324 0.0 0.000 0.676 0.000 0.000
#> GSM153289 4 0.3360 0.663 0.264 0.0 0.000 0.732 0.004 0.000
#> GSM153290 4 0.0405 0.904 0.008 0.0 0.004 0.988 0.000 0.000
#> GSM153291 4 0.1010 0.900 0.036 0.0 0.000 0.960 0.004 0.000
#> GSM153292 4 0.0692 0.903 0.020 0.0 0.000 0.976 0.004 0.000
#> GSM153293 1 0.1500 0.837 0.936 0.0 0.012 0.052 0.000 0.000
#> GSM153294 1 0.2730 0.718 0.808 0.0 0.192 0.000 0.000 0.000
#> GSM153295 1 0.3756 0.268 0.600 0.0 0.000 0.400 0.000 0.000
#> GSM153054 1 0.1007 0.846 0.956 0.0 0.044 0.000 0.000 0.000
#> GSM153055 4 0.1349 0.895 0.056 0.0 0.004 0.940 0.000 0.000
#> GSM153056 4 0.2703 0.787 0.172 0.0 0.004 0.824 0.000 0.000
#> GSM153057 4 0.1789 0.885 0.032 0.0 0.044 0.924 0.000 0.000
#> GSM153058 4 0.0914 0.902 0.016 0.0 0.016 0.968 0.000 0.000
#> GSM153059 3 0.0508 0.886 0.004 0.0 0.984 0.012 0.000 0.000
#> GSM153060 4 0.1745 0.886 0.068 0.0 0.012 0.920 0.000 0.000
#> GSM153061 3 0.0632 0.892 0.024 0.0 0.976 0.000 0.000 0.000
#> GSM153062 3 0.2915 0.691 0.008 0.0 0.808 0.184 0.000 0.000
#> GSM153063 4 0.0972 0.904 0.028 0.0 0.008 0.964 0.000 0.000
#> GSM153064 1 0.0547 0.854 0.980 0.0 0.020 0.000 0.000 0.000
#> GSM153065 3 0.0260 0.895 0.008 0.0 0.992 0.000 0.000 0.000
#> GSM153066 3 0.0363 0.895 0.012 0.0 0.988 0.000 0.000 0.000
#> GSM153067 4 0.3314 0.675 0.256 0.0 0.000 0.740 0.004 0.000
#> GSM153068 3 0.0520 0.888 0.008 0.0 0.984 0.008 0.000 0.000
#> GSM153069 4 0.0692 0.903 0.020 0.0 0.000 0.976 0.004 0.000
#> GSM153070 1 0.0458 0.857 0.984 0.0 0.016 0.000 0.000 0.000
#> GSM153071 1 0.1088 0.851 0.960 0.0 0.016 0.024 0.000 0.000
#> GSM153072 1 0.3023 0.676 0.768 0.0 0.232 0.000 0.000 0.000
#> GSM153073 1 0.0363 0.858 0.988 0.0 0.012 0.000 0.000 0.000
#> GSM153074 4 0.0858 0.904 0.028 0.0 0.004 0.968 0.000 0.000
#> GSM153075 4 0.1088 0.902 0.024 0.0 0.016 0.960 0.000 0.000
#> GSM153076 1 0.0363 0.858 0.988 0.0 0.012 0.000 0.000 0.000
#> GSM153077 1 0.0458 0.857 0.984 0.0 0.016 0.000 0.000 0.000
#> GSM153078 1 0.0458 0.858 0.984 0.0 0.016 0.000 0.000 0.000
#> GSM153079 3 0.0632 0.892 0.024 0.0 0.976 0.000 0.000 0.000
#> GSM153080 3 0.3745 0.592 0.028 0.0 0.732 0.240 0.000 0.000
#> GSM153081 1 0.0363 0.858 0.988 0.0 0.012 0.000 0.000 0.000
#> GSM153082 3 0.0363 0.895 0.012 0.0 0.988 0.000 0.000 0.000
#> GSM153083 3 0.0632 0.892 0.024 0.0 0.976 0.000 0.000 0.000
#> GSM153084 3 0.0146 0.895 0.004 0.0 0.996 0.000 0.000 0.000
#> GSM153085 3 0.0260 0.892 0.008 0.0 0.992 0.000 0.000 0.000
#> GSM153086 3 0.0458 0.894 0.016 0.0 0.984 0.000 0.000 0.000
#> GSM153087 4 0.3862 0.333 0.388 0.0 0.004 0.608 0.000 0.000
#> GSM153088 1 0.0363 0.858 0.988 0.0 0.012 0.000 0.000 0.000
#> GSM153089 3 0.2070 0.805 0.008 0.0 0.892 0.100 0.000 0.000
#> GSM153090 1 0.1010 0.843 0.960 0.0 0.004 0.036 0.000 0.000
#> GSM153091 3 0.0146 0.895 0.004 0.0 0.996 0.000 0.000 0.000
#> GSM153092 3 0.5182 0.315 0.096 0.0 0.532 0.372 0.000 0.000
#> GSM153093 4 0.0777 0.905 0.024 0.0 0.004 0.972 0.000 0.000
#> GSM153094 3 0.0146 0.895 0.004 0.0 0.996 0.000 0.000 0.000
#> GSM153095 3 0.0865 0.887 0.036 0.0 0.964 0.000 0.000 0.000
#> GSM153096 3 0.0363 0.895 0.012 0.0 0.988 0.000 0.000 0.000
#> GSM153097 3 0.0363 0.895 0.012 0.0 0.988 0.000 0.000 0.000
#> GSM153098 4 0.3534 0.697 0.244 0.0 0.016 0.740 0.000 0.000
#> GSM153099 1 0.3189 0.676 0.760 0.0 0.004 0.236 0.000 0.000
#> GSM153100 3 0.4416 0.597 0.124 0.0 0.716 0.160 0.000 0.000
#> GSM153101 3 0.0363 0.895 0.012 0.0 0.988 0.000 0.000 0.000
#> GSM153102 3 0.0363 0.886 0.000 0.0 0.988 0.012 0.000 0.000
#> GSM153103 3 0.0363 0.895 0.012 0.0 0.988 0.000 0.000 0.000
#> GSM153104 4 0.0692 0.903 0.020 0.0 0.000 0.976 0.004 0.000
#> GSM153106 3 0.0508 0.886 0.004 0.0 0.984 0.012 0.000 0.000
#> GSM153107 3 0.2956 0.786 0.088 0.0 0.848 0.064 0.000 0.000
#> GSM153108 4 0.1528 0.895 0.048 0.0 0.016 0.936 0.000 0.000
#> GSM153109 3 0.0146 0.895 0.004 0.0 0.996 0.000 0.000 0.000
#> GSM153110 3 0.0865 0.886 0.036 0.0 0.964 0.000 0.000 0.000
#> GSM153111 3 0.3023 0.645 0.232 0.0 0.768 0.000 0.000 0.000
#> GSM153112 1 0.2384 0.818 0.888 0.0 0.048 0.064 0.000 0.000
#> GSM153113 3 0.0146 0.895 0.004 0.0 0.996 0.000 0.000 0.000
#> GSM153114 4 0.0405 0.904 0.008 0.0 0.004 0.988 0.000 0.000
#> GSM187532 6 0.1663 0.903 0.000 0.0 0.000 0.000 0.088 0.912
#> GSM187533 6 0.0146 0.986 0.000 0.0 0.000 0.000 0.004 0.996
#> GSM187534 6 0.0146 0.984 0.000 0.0 0.004 0.000 0.000 0.996
#> GSM187535 3 0.0363 0.895 0.012 0.0 0.988 0.000 0.000 0.000
#> GSM152906 2 0.0000 1.000 0.000 1.0 0.000 0.000 0.000 0.000
#> GSM152907 2 0.0000 1.000 0.000 1.0 0.000 0.000 0.000 0.000
#> GSM152908 5 0.0146 0.897 0.000 0.0 0.000 0.000 0.996 0.004
#> GSM152909 5 0.0146 0.897 0.000 0.0 0.000 0.000 0.996 0.004
#> GSM152910 5 0.0146 0.897 0.000 0.0 0.000 0.000 0.996 0.004
#> GSM152911 6 0.0000 0.989 0.000 0.0 0.000 0.000 0.000 1.000
#> GSM152912 5 0.0146 0.897 0.000 0.0 0.000 0.000 0.996 0.004
#> GSM152913 6 0.0000 0.989 0.000 0.0 0.000 0.000 0.000 1.000
#> GSM152914 6 0.0000 0.989 0.000 0.0 0.000 0.000 0.000 1.000
#> GSM152915 6 0.0000 0.989 0.000 0.0 0.000 0.000 0.000 1.000
#> GSM152916 2 0.0000 1.000 0.000 1.0 0.000 0.000 0.000 0.000
#> GSM152917 6 0.0000 0.989 0.000 0.0 0.000 0.000 0.000 1.000
#> GSM152918 6 0.0000 0.989 0.000 0.0 0.000 0.000 0.000 1.000
#> GSM152919 6 0.0000 0.989 0.000 0.0 0.000 0.000 0.000 1.000
#> GSM152920 5 0.0146 0.897 0.000 0.0 0.000 0.000 0.996 0.004
#> GSM152921 5 0.0146 0.897 0.000 0.0 0.000 0.000 0.996 0.004
#> GSM152922 5 0.0146 0.897 0.000 0.0 0.000 0.000 0.996 0.004
#> GSM152923 2 0.0000 1.000 0.000 1.0 0.000 0.000 0.000 0.000
#> GSM152924 2 0.0000 1.000 0.000 1.0 0.000 0.000 0.000 0.000
#> GSM152925 2 0.0000 1.000 0.000 1.0 0.000 0.000 0.000 0.000
#> GSM152926 2 0.0000 1.000 0.000 1.0 0.000 0.000 0.000 0.000
#> GSM152927 2 0.0000 1.000 0.000 1.0 0.000 0.000 0.000 0.000
#> GSM152928 2 0.0000 1.000 0.000 1.0 0.000 0.000 0.000 0.000
#> GSM152929 2 0.0000 1.000 0.000 1.0 0.000 0.000 0.000 0.000
#> GSM152930 2 0.0000 1.000 0.000 1.0 0.000 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)
#> Error in mat[ceiling(1:nr/h_ratio), ceiling(1:nc/w_ratio), drop = FALSE]: subscript out of bounds
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 tissue(p) k
#> ATC:pam 163 8.95e-31 2
#> ATC:pam 162 2.66e-31 3
#> ATC:pam 161 8.41e-34 4
#> ATC:pam 156 1.57e-31 5
#> ATC:pam 153 1.45e-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["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 12013 rows and 164 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 0.986 0.994 0.3016 0.692 0.692
#> 3 3 0.424 0.536 0.731 0.8756 0.648 0.502
#> 4 4 0.660 0.684 0.867 0.2097 0.851 0.641
#> 5 5 0.656 0.593 0.811 0.0848 0.830 0.552
#> 6 6 0.696 0.704 0.806 0.0414 0.874 0.619
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
#> GSM152839 1 0.000 1.000 1.000 0.000
#> GSM152840 1 0.000 1.000 1.000 0.000
#> GSM152841 1 0.000 1.000 1.000 0.000
#> GSM152842 1 0.000 1.000 1.000 0.000
#> GSM152843 1 0.000 1.000 1.000 0.000
#> GSM152844 1 0.000 1.000 1.000 0.000
#> GSM152845 1 0.000 1.000 1.000 0.000
#> GSM152846 1 0.000 1.000 1.000 0.000
#> GSM152847 1 0.000 1.000 1.000 0.000
#> GSM152848 1 0.000 1.000 1.000 0.000
#> GSM152849 1 0.000 1.000 1.000 0.000
#> GSM152850 1 0.000 1.000 1.000 0.000
#> GSM152851 1 0.000 1.000 1.000 0.000
#> GSM152852 1 0.000 1.000 1.000 0.000
#> GSM152853 1 0.000 1.000 1.000 0.000
#> GSM152854 1 0.000 1.000 1.000 0.000
#> GSM152855 1 0.000 1.000 1.000 0.000
#> GSM153238 1 0.000 1.000 1.000 0.000
#> GSM153239 1 0.000 1.000 1.000 0.000
#> GSM153240 1 0.000 1.000 1.000 0.000
#> GSM153241 1 0.000 1.000 1.000 0.000
#> GSM153242 1 0.000 1.000 1.000 0.000
#> GSM153243 1 0.000 1.000 1.000 0.000
#> GSM153244 1 0.000 1.000 1.000 0.000
#> GSM153245 1 0.000 1.000 1.000 0.000
#> GSM153246 1 0.000 1.000 1.000 0.000
#> GSM153247 1 0.000 1.000 1.000 0.000
#> GSM153248 1 0.000 1.000 1.000 0.000
#> GSM153249 1 0.000 1.000 1.000 0.000
#> GSM153250 1 0.000 1.000 1.000 0.000
#> GSM153251 1 0.000 1.000 1.000 0.000
#> GSM153252 1 0.000 1.000 1.000 0.000
#> GSM153253 1 0.000 1.000 1.000 0.000
#> GSM153254 1 0.000 1.000 1.000 0.000
#> GSM153255 1 0.000 1.000 1.000 0.000
#> GSM153256 1 0.000 1.000 1.000 0.000
#> GSM153257 1 0.000 1.000 1.000 0.000
#> GSM153258 1 0.000 1.000 1.000 0.000
#> GSM153259 1 0.000 1.000 1.000 0.000
#> GSM153260 1 0.000 1.000 1.000 0.000
#> GSM153261 1 0.000 1.000 1.000 0.000
#> GSM153262 1 0.000 1.000 1.000 0.000
#> GSM153263 1 0.000 1.000 1.000 0.000
#> GSM153264 1 0.000 1.000 1.000 0.000
#> GSM153265 1 0.000 1.000 1.000 0.000
#> GSM153266 1 0.000 1.000 1.000 0.000
#> GSM153267 1 0.000 1.000 1.000 0.000
#> GSM153268 1 0.000 1.000 1.000 0.000
#> GSM153269 1 0.000 1.000 1.000 0.000
#> GSM153270 1 0.000 1.000 1.000 0.000
#> GSM153271 1 0.000 1.000 1.000 0.000
#> GSM153272 1 0.000 1.000 1.000 0.000
#> GSM153273 1 0.000 1.000 1.000 0.000
#> GSM153274 1 0.000 1.000 1.000 0.000
#> GSM153275 1 0.000 1.000 1.000 0.000
#> GSM153276 1 0.000 1.000 1.000 0.000
#> GSM153277 1 0.000 1.000 1.000 0.000
#> GSM153278 1 0.000 1.000 1.000 0.000
#> GSM153279 1 0.000 1.000 1.000 0.000
#> GSM153280 1 0.000 1.000 1.000 0.000
#> GSM153281 1 0.000 1.000 1.000 0.000
#> GSM153282 1 0.000 1.000 1.000 0.000
#> GSM153283 1 0.000 1.000 1.000 0.000
#> GSM153284 1 0.000 1.000 1.000 0.000
#> GSM153285 1 0.000 1.000 1.000 0.000
#> GSM153286 1 0.000 1.000 1.000 0.000
#> GSM153287 1 0.000 1.000 1.000 0.000
#> GSM153288 1 0.000 1.000 1.000 0.000
#> GSM153289 1 0.000 1.000 1.000 0.000
#> GSM153290 1 0.000 1.000 1.000 0.000
#> GSM153291 1 0.000 1.000 1.000 0.000
#> GSM153292 1 0.000 1.000 1.000 0.000
#> GSM153293 1 0.000 1.000 1.000 0.000
#> GSM153294 1 0.000 1.000 1.000 0.000
#> GSM153295 1 0.000 1.000 1.000 0.000
#> GSM153054 1 0.000 1.000 1.000 0.000
#> GSM153055 1 0.000 1.000 1.000 0.000
#> GSM153056 1 0.000 1.000 1.000 0.000
#> GSM153057 1 0.000 1.000 1.000 0.000
#> GSM153058 1 0.000 1.000 1.000 0.000
#> GSM153059 1 0.000 1.000 1.000 0.000
#> GSM153060 1 0.000 1.000 1.000 0.000
#> GSM153061 1 0.000 1.000 1.000 0.000
#> GSM153062 1 0.000 1.000 1.000 0.000
#> GSM153063 1 0.000 1.000 1.000 0.000
#> GSM153064 1 0.000 1.000 1.000 0.000
#> GSM153065 1 0.000 1.000 1.000 0.000
#> GSM153066 2 0.983 0.298 0.424 0.576
#> GSM153067 1 0.000 1.000 1.000 0.000
#> GSM153068 1 0.000 1.000 1.000 0.000
#> GSM153069 1 0.000 1.000 1.000 0.000
#> GSM153070 1 0.000 1.000 1.000 0.000
#> GSM153071 1 0.000 1.000 1.000 0.000
#> GSM153072 1 0.000 1.000 1.000 0.000
#> GSM153073 1 0.000 1.000 1.000 0.000
#> GSM153074 1 0.000 1.000 1.000 0.000
#> GSM153075 1 0.000 1.000 1.000 0.000
#> GSM153076 1 0.000 1.000 1.000 0.000
#> GSM153077 1 0.000 1.000 1.000 0.000
#> GSM153078 1 0.000 1.000 1.000 0.000
#> GSM153079 1 0.000 1.000 1.000 0.000
#> GSM153080 1 0.000 1.000 1.000 0.000
#> GSM153081 1 0.000 1.000 1.000 0.000
#> GSM153082 1 0.000 1.000 1.000 0.000
#> GSM153083 1 0.000 1.000 1.000 0.000
#> GSM153084 1 0.000 1.000 1.000 0.000
#> GSM153085 1 0.000 1.000 1.000 0.000
#> GSM153086 1 0.000 1.000 1.000 0.000
#> GSM153087 1 0.000 1.000 1.000 0.000
#> GSM153088 1 0.000 1.000 1.000 0.000
#> GSM153089 1 0.000 1.000 1.000 0.000
#> GSM153090 1 0.000 1.000 1.000 0.000
#> GSM153091 1 0.000 1.000 1.000 0.000
#> GSM153092 1 0.000 1.000 1.000 0.000
#> GSM153093 1 0.000 1.000 1.000 0.000
#> GSM153094 1 0.000 1.000 1.000 0.000
#> GSM153095 1 0.000 1.000 1.000 0.000
#> GSM153096 1 0.000 1.000 1.000 0.000
#> GSM153097 1 0.000 1.000 1.000 0.000
#> GSM153098 1 0.000 1.000 1.000 0.000
#> GSM153099 1 0.000 1.000 1.000 0.000
#> GSM153100 1 0.000 1.000 1.000 0.000
#> GSM153101 1 0.000 1.000 1.000 0.000
#> GSM153102 1 0.000 1.000 1.000 0.000
#> GSM153103 1 0.000 1.000 1.000 0.000
#> GSM153104 1 0.000 1.000 1.000 0.000
#> GSM153106 1 0.000 1.000 1.000 0.000
#> GSM153107 1 0.000 1.000 1.000 0.000
#> GSM153108 1 0.000 1.000 1.000 0.000
#> GSM153109 1 0.000 1.000 1.000 0.000
#> GSM153110 1 0.000 1.000 1.000 0.000
#> GSM153111 1 0.000 1.000 1.000 0.000
#> GSM153112 1 0.000 1.000 1.000 0.000
#> GSM153113 2 0.891 0.576 0.308 0.692
#> GSM153114 1 0.000 1.000 1.000 0.000
#> GSM187532 2 0.000 0.968 0.000 1.000
#> GSM187533 2 0.000 0.968 0.000 1.000
#> GSM187534 2 0.000 0.968 0.000 1.000
#> GSM187535 2 0.788 0.700 0.236 0.764
#> GSM152906 2 0.000 0.968 0.000 1.000
#> GSM152907 2 0.000 0.968 0.000 1.000
#> GSM152908 2 0.000 0.968 0.000 1.000
#> GSM152909 2 0.000 0.968 0.000 1.000
#> GSM152910 2 0.000 0.968 0.000 1.000
#> GSM152911 2 0.000 0.968 0.000 1.000
#> GSM152912 2 0.000 0.968 0.000 1.000
#> GSM152913 2 0.000 0.968 0.000 1.000
#> GSM152914 2 0.000 0.968 0.000 1.000
#> GSM152915 2 0.000 0.968 0.000 1.000
#> GSM152916 2 0.000 0.968 0.000 1.000
#> GSM152917 2 0.000 0.968 0.000 1.000
#> GSM152918 2 0.000 0.968 0.000 1.000
#> GSM152919 2 0.000 0.968 0.000 1.000
#> GSM152920 2 0.000 0.968 0.000 1.000
#> GSM152921 2 0.000 0.968 0.000 1.000
#> GSM152922 2 0.000 0.968 0.000 1.000
#> GSM152923 2 0.000 0.968 0.000 1.000
#> GSM152924 2 0.000 0.968 0.000 1.000
#> GSM152925 2 0.000 0.968 0.000 1.000
#> GSM152926 2 0.000 0.968 0.000 1.000
#> GSM152927 2 0.000 0.968 0.000 1.000
#> GSM152928 2 0.000 0.968 0.000 1.000
#> GSM152929 2 0.000 0.968 0.000 1.000
#> GSM152930 2 0.000 0.968 0.000 1.000
cbind(get_classes(res, k = 3), get_membership(res, k = 3))
#> class entropy silhouette p1 p2 p3
#> GSM152839 3 0.6244 0.5775 0.440 0.000 0.560
#> GSM152840 1 0.3879 0.5754 0.848 0.000 0.152
#> GSM152841 1 0.2537 0.6466 0.920 0.000 0.080
#> GSM152842 3 0.4887 0.5600 0.228 0.000 0.772
#> GSM152843 3 0.6286 0.5425 0.464 0.000 0.536
#> GSM152844 1 0.6140 0.2964 0.596 0.000 0.404
#> GSM152845 3 0.5138 0.1669 0.252 0.000 0.748
#> GSM152846 3 0.6235 -0.1519 0.436 0.000 0.564
#> GSM152847 3 0.3412 0.4857 0.124 0.000 0.876
#> GSM152848 3 0.6302 0.5200 0.480 0.000 0.520
#> GSM152849 3 0.4887 0.4148 0.228 0.000 0.772
#> GSM152850 3 0.6192 0.6036 0.420 0.000 0.580
#> GSM152851 1 0.2878 0.6476 0.904 0.000 0.096
#> GSM152852 3 0.6235 -0.1519 0.436 0.000 0.564
#> GSM152853 1 0.4002 0.5660 0.840 0.000 0.160
#> GSM152854 1 0.6295 0.1940 0.528 0.000 0.472
#> GSM152855 1 0.1031 0.6496 0.976 0.000 0.024
#> GSM153238 3 0.6026 0.6312 0.376 0.000 0.624
#> GSM153239 1 0.3038 0.6255 0.896 0.000 0.104
#> GSM153240 1 0.2537 0.6519 0.920 0.000 0.080
#> GSM153241 3 0.6154 0.3044 0.408 0.000 0.592
#> GSM153242 3 0.6235 -0.1519 0.436 0.000 0.564
#> GSM153243 3 0.6111 0.4188 0.396 0.000 0.604
#> GSM153244 1 0.5431 0.3982 0.716 0.000 0.284
#> GSM153245 1 0.2537 0.6466 0.920 0.000 0.080
#> GSM153246 3 0.4842 0.3189 0.224 0.000 0.776
#> GSM153247 3 0.6267 0.5583 0.452 0.000 0.548
#> GSM153248 3 0.6215 0.5920 0.428 0.000 0.572
#> GSM153249 1 0.1643 0.6554 0.956 0.000 0.044
#> GSM153250 3 0.6305 0.5123 0.484 0.000 0.516
#> GSM153251 1 0.5560 0.3952 0.700 0.000 0.300
#> GSM153252 1 0.2959 0.5911 0.900 0.000 0.100
#> GSM153253 1 0.2448 0.6484 0.924 0.000 0.076
#> GSM153254 1 0.5835 0.2634 0.660 0.000 0.340
#> GSM153255 1 0.0892 0.6515 0.980 0.000 0.020
#> GSM153256 1 0.4702 0.4400 0.788 0.000 0.212
#> GSM153257 1 0.1643 0.6390 0.956 0.000 0.044
#> GSM153258 3 0.6095 0.6268 0.392 0.000 0.608
#> GSM153259 3 0.6026 0.6312 0.376 0.000 0.624
#> GSM153260 3 0.5098 0.3511 0.248 0.000 0.752
#> GSM153261 3 0.4796 0.2658 0.220 0.000 0.780
#> GSM153262 1 0.2448 0.6484 0.924 0.000 0.076
#> GSM153263 3 0.6309 0.4846 0.496 0.000 0.504
#> GSM153264 3 0.6267 0.5583 0.452 0.000 0.548
#> GSM153265 1 0.2537 0.6466 0.920 0.000 0.080
#> GSM153266 3 0.6111 0.6243 0.396 0.000 0.604
#> GSM153267 1 0.6235 -0.3144 0.564 0.000 0.436
#> GSM153268 1 0.3752 0.5851 0.856 0.000 0.144
#> GSM153269 1 0.5216 0.3327 0.740 0.000 0.260
#> GSM153270 1 0.6280 -0.1850 0.540 0.000 0.460
#> GSM153271 1 0.6302 -0.4396 0.520 0.000 0.480
#> GSM153272 1 0.3412 0.5658 0.876 0.000 0.124
#> GSM153273 3 0.6260 0.5648 0.448 0.000 0.552
#> GSM153274 1 0.6045 -0.1226 0.620 0.000 0.380
#> GSM153275 1 0.4002 0.5266 0.840 0.000 0.160
#> GSM153276 1 0.4121 0.5043 0.832 0.000 0.168
#> GSM153277 1 0.2537 0.6466 0.920 0.000 0.080
#> GSM153278 3 0.4796 0.3425 0.220 0.000 0.780
#> GSM153279 1 0.2625 0.6473 0.916 0.000 0.084
#> GSM153280 1 0.2537 0.6466 0.920 0.000 0.080
#> GSM153281 1 0.2165 0.6522 0.936 0.000 0.064
#> GSM153282 1 0.2537 0.6466 0.920 0.000 0.080
#> GSM153283 3 0.6260 0.5648 0.448 0.000 0.552
#> GSM153284 1 0.3686 0.5474 0.860 0.000 0.140
#> GSM153285 1 0.0000 0.6554 1.000 0.000 0.000
#> GSM153286 1 0.4062 0.5117 0.836 0.000 0.164
#> GSM153287 1 0.0237 0.6554 0.996 0.000 0.004
#> GSM153288 1 0.3619 0.5507 0.864 0.000 0.136
#> GSM153289 1 0.4702 0.4403 0.788 0.000 0.212
#> GSM153290 1 0.2537 0.6466 0.920 0.000 0.080
#> GSM153291 1 0.0892 0.6515 0.980 0.000 0.020
#> GSM153292 1 0.1753 0.6550 0.952 0.000 0.048
#> GSM153293 1 0.4931 0.4000 0.768 0.000 0.232
#> GSM153294 3 0.6267 0.5583 0.452 0.000 0.548
#> GSM153295 1 0.5591 0.3113 0.696 0.000 0.304
#> GSM153054 3 0.6154 0.6129 0.408 0.000 0.592
#> GSM153055 1 0.6286 -0.3993 0.536 0.000 0.464
#> GSM153056 3 0.5835 0.3254 0.340 0.000 0.660
#> GSM153057 1 0.6295 -0.1927 0.528 0.000 0.472
#> GSM153058 3 0.5431 0.1443 0.284 0.000 0.716
#> GSM153059 3 0.6252 0.2271 0.444 0.000 0.556
#> GSM153060 3 0.5926 0.1860 0.356 0.000 0.644
#> GSM153061 3 0.5098 0.3589 0.248 0.000 0.752
#> GSM153062 3 0.5138 0.1669 0.252 0.000 0.748
#> GSM153063 1 0.2537 0.6466 0.920 0.000 0.080
#> GSM153064 3 0.6140 0.6197 0.404 0.000 0.596
#> GSM153065 3 0.5733 0.3902 0.324 0.000 0.676
#> GSM153066 3 0.7804 0.5347 0.216 0.120 0.664
#> GSM153067 1 0.2711 0.6054 0.912 0.000 0.088
#> GSM153068 3 0.5859 0.2388 0.344 0.000 0.656
#> GSM153069 1 0.0000 0.6554 1.000 0.000 0.000
#> GSM153070 3 0.6299 0.5273 0.476 0.000 0.524
#> GSM153071 3 0.6299 0.5247 0.476 0.000 0.524
#> GSM153072 3 0.6204 0.5963 0.424 0.000 0.576
#> GSM153073 3 0.6305 0.5123 0.484 0.000 0.516
#> GSM153074 1 0.0747 0.6525 0.984 0.000 0.016
#> GSM153075 1 0.4121 0.5811 0.832 0.000 0.168
#> GSM153076 1 0.6252 -0.3883 0.556 0.000 0.444
#> GSM153077 3 0.6267 0.5583 0.452 0.000 0.548
#> GSM153078 3 0.6111 0.6252 0.396 0.000 0.604
#> GSM153079 3 0.5760 0.6122 0.328 0.000 0.672
#> GSM153080 1 0.6140 -0.0785 0.596 0.000 0.404
#> GSM153081 3 0.5178 0.5737 0.256 0.000 0.744
#> GSM153082 3 0.5948 0.6308 0.360 0.000 0.640
#> GSM153083 3 0.6008 0.6317 0.372 0.000 0.628
#> GSM153084 3 0.5621 0.5744 0.308 0.000 0.692
#> GSM153085 3 0.5785 0.6115 0.332 0.000 0.668
#> GSM153086 3 0.5988 0.6316 0.368 0.000 0.632
#> GSM153087 1 0.1529 0.6478 0.960 0.000 0.040
#> GSM153088 1 0.6309 -0.4897 0.500 0.000 0.500
#> GSM153089 1 0.6244 -0.0341 0.560 0.000 0.440
#> GSM153090 1 0.6225 -0.3001 0.568 0.000 0.432
#> GSM153091 3 0.5988 0.6316 0.368 0.000 0.632
#> GSM153092 3 0.6299 0.5046 0.476 0.000 0.524
#> GSM153093 1 0.0424 0.6544 0.992 0.000 0.008
#> GSM153094 3 0.5988 0.6316 0.368 0.000 0.632
#> GSM153095 3 0.6045 0.6303 0.380 0.000 0.620
#> GSM153096 3 0.6126 0.6195 0.400 0.000 0.600
#> GSM153097 3 0.5988 0.6316 0.368 0.000 0.632
#> GSM153098 1 0.4974 0.4045 0.764 0.000 0.236
#> GSM153099 1 0.6008 -0.0777 0.628 0.000 0.372
#> GSM153100 3 0.6295 0.5339 0.472 0.000 0.528
#> GSM153101 3 0.6062 0.6267 0.384 0.000 0.616
#> GSM153102 3 0.6215 0.4015 0.428 0.000 0.572
#> GSM153103 3 0.6008 0.6317 0.372 0.000 0.628
#> GSM153104 1 0.0592 0.6546 0.988 0.000 0.012
#> GSM153106 3 0.6291 0.3400 0.468 0.000 0.532
#> GSM153107 3 0.6095 0.6248 0.392 0.000 0.608
#> GSM153108 1 0.6305 -0.4539 0.516 0.000 0.484
#> GSM153109 3 0.5650 0.5981 0.312 0.000 0.688
#> GSM153110 3 0.6026 0.6312 0.376 0.000 0.624
#> GSM153111 3 0.5988 0.6316 0.368 0.000 0.632
#> GSM153112 3 0.6267 0.5583 0.452 0.000 0.548
#> GSM153113 3 0.7865 0.5359 0.216 0.124 0.660
#> GSM153114 1 0.2537 0.6466 0.920 0.000 0.080
#> GSM187532 2 0.0000 0.9996 0.000 1.000 0.000
#> GSM187533 2 0.0000 0.9996 0.000 1.000 0.000
#> GSM187534 2 0.0000 0.9996 0.000 1.000 0.000
#> GSM187535 3 0.7796 0.4242 0.112 0.228 0.660
#> GSM152906 2 0.0000 0.9996 0.000 1.000 0.000
#> GSM152907 2 0.0747 0.9893 0.000 0.984 0.016
#> GSM152908 2 0.0000 0.9996 0.000 1.000 0.000
#> GSM152909 2 0.0000 0.9996 0.000 1.000 0.000
#> GSM152910 2 0.0000 0.9996 0.000 1.000 0.000
#> GSM152911 2 0.0000 0.9996 0.000 1.000 0.000
#> GSM152912 2 0.0000 0.9996 0.000 1.000 0.000
#> GSM152913 2 0.0000 0.9996 0.000 1.000 0.000
#> GSM152914 2 0.0000 0.9996 0.000 1.000 0.000
#> GSM152915 2 0.0000 0.9996 0.000 1.000 0.000
#> GSM152916 2 0.0000 0.9996 0.000 1.000 0.000
#> GSM152917 2 0.0000 0.9996 0.000 1.000 0.000
#> GSM152918 2 0.0000 0.9996 0.000 1.000 0.000
#> GSM152919 2 0.0000 0.9996 0.000 1.000 0.000
#> GSM152920 2 0.0000 0.9996 0.000 1.000 0.000
#> GSM152921 2 0.0000 0.9996 0.000 1.000 0.000
#> GSM152922 2 0.0000 0.9996 0.000 1.000 0.000
#> GSM152923 2 0.0000 0.9996 0.000 1.000 0.000
#> GSM152924 2 0.0000 0.9996 0.000 1.000 0.000
#> GSM152925 2 0.0000 0.9996 0.000 1.000 0.000
#> GSM152926 2 0.0000 0.9996 0.000 1.000 0.000
#> GSM152927 2 0.0000 0.9996 0.000 1.000 0.000
#> GSM152928 2 0.0000 0.9996 0.000 1.000 0.000
#> GSM152929 2 0.0000 0.9996 0.000 1.000 0.000
#> GSM152930 2 0.0000 0.9996 0.000 1.000 0.000
cbind(get_classes(res, k = 4), get_membership(res, k = 4))
#> class entropy silhouette p1 p2 p3 p4
#> GSM152839 1 0.1022 0.7355 0.968 0 0.000 0.032
#> GSM152840 4 0.3444 0.6682 0.000 0 0.184 0.816
#> GSM152841 4 0.0000 0.8438 0.000 0 0.000 1.000
#> GSM152842 1 0.0336 0.7220 0.992 0 0.008 0.000
#> GSM152843 1 0.1867 0.7241 0.928 0 0.000 0.072
#> GSM152844 4 0.4843 0.3227 0.000 0 0.396 0.604
#> GSM152845 3 0.0000 0.6095 0.000 0 1.000 0.000
#> GSM152846 3 0.0000 0.6095 0.000 0 1.000 0.000
#> GSM152847 1 0.3024 0.5768 0.852 0 0.148 0.000
#> GSM152848 1 0.1940 0.7232 0.924 0 0.000 0.076
#> GSM152849 1 0.4516 0.4578 0.736 0 0.252 0.012
#> GSM152850 1 0.0592 0.7338 0.984 0 0.000 0.016
#> GSM152851 4 0.0188 0.8426 0.000 0 0.004 0.996
#> GSM152852 3 0.0000 0.6095 0.000 0 1.000 0.000
#> GSM152853 4 0.3444 0.6682 0.000 0 0.184 0.816
#> GSM152854 3 0.5080 0.1037 0.004 0 0.576 0.420
#> GSM152855 4 0.0000 0.8438 0.000 0 0.000 1.000
#> GSM153238 1 0.0000 0.7242 1.000 0 0.000 0.000
#> GSM153239 4 0.3311 0.6810 0.000 0 0.172 0.828
#> GSM153240 4 0.0657 0.8388 0.012 0 0.004 0.984
#> GSM153241 1 0.5297 0.3669 0.676 0 0.292 0.032
#> GSM153242 3 0.0336 0.6092 0.000 0 0.992 0.008
#> GSM153243 1 0.6970 0.2233 0.576 0 0.256 0.168
#> GSM153244 4 0.4250 0.5729 0.000 0 0.276 0.724
#> GSM153245 4 0.1557 0.8045 0.000 0 0.056 0.944
#> GSM153246 3 0.5132 0.4749 0.448 0 0.548 0.004
#> GSM153247 1 0.2589 0.6987 0.884 0 0.000 0.116
#> GSM153248 1 0.0336 0.7300 0.992 0 0.000 0.008
#> GSM153249 4 0.0000 0.8438 0.000 0 0.000 1.000
#> GSM153250 1 0.4304 0.5804 0.716 0 0.000 0.284
#> GSM153251 4 0.4304 0.5617 0.000 0 0.284 0.716
#> GSM153252 4 0.0000 0.8438 0.000 0 0.000 1.000
#> GSM153253 4 0.0000 0.8438 0.000 0 0.000 1.000
#> GSM153254 4 0.4868 0.5710 0.024 0 0.256 0.720
#> GSM153255 4 0.0000 0.8438 0.000 0 0.000 1.000
#> GSM153256 4 0.3942 0.6019 0.236 0 0.000 0.764
#> GSM153257 4 0.0000 0.8438 0.000 0 0.000 1.000
#> GSM153258 1 0.0817 0.7360 0.976 0 0.000 0.024
#> GSM153259 1 0.0469 0.7321 0.988 0 0.000 0.012
#> GSM153260 3 0.4967 0.4743 0.452 0 0.548 0.000
#> GSM153261 3 0.4967 0.4743 0.452 0 0.548 0.000
#> GSM153262 4 0.0188 0.8426 0.000 0 0.004 0.996
#> GSM153263 1 0.4382 0.5689 0.704 0 0.000 0.296
#> GSM153264 1 0.0921 0.7355 0.972 0 0.000 0.028
#> GSM153265 4 0.0000 0.8438 0.000 0 0.000 1.000
#> GSM153266 1 0.0817 0.7354 0.976 0 0.000 0.024
#> GSM153267 1 0.4855 0.4346 0.600 0 0.000 0.400
#> GSM153268 4 0.3266 0.6888 0.000 0 0.168 0.832
#> GSM153269 4 0.4967 0.0296 0.452 0 0.000 0.548
#> GSM153270 1 0.4624 0.4986 0.660 0 0.000 0.340
#> GSM153271 1 0.4888 0.4203 0.588 0 0.000 0.412
#> GSM153272 4 0.0000 0.8438 0.000 0 0.000 1.000
#> GSM153273 1 0.0336 0.7300 0.992 0 0.000 0.008
#> GSM153274 4 0.4996 -0.0962 0.484 0 0.000 0.516
#> GSM153275 4 0.4356 0.5138 0.292 0 0.000 0.708
#> GSM153276 4 0.4925 0.1303 0.428 0 0.000 0.572
#> GSM153277 4 0.1109 0.8290 0.028 0 0.004 0.968
#> GSM153278 3 0.4967 0.4743 0.452 0 0.548 0.000
#> GSM153279 4 0.0188 0.8426 0.000 0 0.004 0.996
#> GSM153280 4 0.0188 0.8426 0.000 0 0.004 0.996
#> GSM153281 4 0.0188 0.8426 0.000 0 0.004 0.996
#> GSM153282 4 0.0000 0.8438 0.000 0 0.000 1.000
#> GSM153283 1 0.0921 0.7355 0.972 0 0.000 0.028
#> GSM153284 4 0.0336 0.8405 0.008 0 0.000 0.992
#> GSM153285 4 0.0000 0.8438 0.000 0 0.000 1.000
#> GSM153286 4 0.0592 0.8362 0.016 0 0.000 0.984
#> GSM153287 4 0.0000 0.8438 0.000 0 0.000 1.000
#> GSM153288 4 0.0000 0.8438 0.000 0 0.000 1.000
#> GSM153289 4 0.3024 0.7182 0.148 0 0.000 0.852
#> GSM153290 4 0.0188 0.8426 0.000 0 0.004 0.996
#> GSM153291 4 0.0000 0.8438 0.000 0 0.000 1.000
#> GSM153292 4 0.0000 0.8438 0.000 0 0.000 1.000
#> GSM153293 4 0.4585 0.3847 0.332 0 0.000 0.668
#> GSM153294 1 0.1940 0.7137 0.924 0 0.000 0.076
#> GSM153295 4 0.5151 0.1240 0.464 0 0.004 0.532
#> GSM153054 1 0.0707 0.7352 0.980 0 0.000 0.020
#> GSM153055 1 0.4898 0.3974 0.584 0 0.000 0.416
#> GSM153056 1 0.5590 0.4423 0.692 0 0.244 0.064
#> GSM153057 4 0.7519 0.1086 0.248 0 0.256 0.496
#> GSM153058 3 0.3554 0.5641 0.020 0 0.844 0.136
#> GSM153059 1 0.7752 0.0218 0.436 0 0.264 0.300
#> GSM153060 3 0.6851 0.5129 0.300 0 0.568 0.132
#> GSM153061 3 0.4967 0.4743 0.452 0 0.548 0.000
#> GSM153062 3 0.0000 0.6095 0.000 0 1.000 0.000
#> GSM153063 4 0.0000 0.8438 0.000 0 0.000 1.000
#> GSM153064 1 0.1211 0.7353 0.960 0 0.000 0.040
#> GSM153065 3 0.4967 0.4743 0.452 0 0.548 0.000
#> GSM153066 1 0.4072 0.3732 0.748 0 0.252 0.000
#> GSM153067 4 0.0376 0.8418 0.004 0 0.004 0.992
#> GSM153068 3 0.5257 0.4746 0.444 0 0.548 0.008
#> GSM153069 4 0.0000 0.8438 0.000 0 0.000 1.000
#> GSM153070 1 0.1716 0.7300 0.936 0 0.000 0.064
#> GSM153071 1 0.3726 0.6417 0.788 0 0.000 0.212
#> GSM153072 1 0.1389 0.7274 0.952 0 0.000 0.048
#> GSM153073 1 0.4134 0.6011 0.740 0 0.000 0.260
#> GSM153074 4 0.0000 0.8438 0.000 0 0.000 1.000
#> GSM153075 4 0.3907 0.6340 0.232 0 0.000 0.768
#> GSM153076 1 0.4866 0.4319 0.596 0 0.000 0.404
#> GSM153077 1 0.0817 0.7360 0.976 0 0.000 0.024
#> GSM153078 1 0.0592 0.7337 0.984 0 0.000 0.016
#> GSM153079 1 0.4008 0.3916 0.756 0 0.244 0.000
#> GSM153080 1 0.5105 0.3451 0.564 0 0.004 0.432
#> GSM153081 1 0.0707 0.7156 0.980 0 0.020 0.000
#> GSM153082 1 0.1182 0.7270 0.968 0 0.016 0.016
#> GSM153083 1 0.3172 0.5554 0.840 0 0.160 0.000
#> GSM153084 1 0.4072 0.3732 0.748 0 0.252 0.000
#> GSM153085 1 0.3764 0.4496 0.784 0 0.216 0.000
#> GSM153086 1 0.0672 0.7281 0.984 0 0.008 0.008
#> GSM153087 4 0.0188 0.8426 0.000 0 0.004 0.996
#> GSM153088 1 0.4382 0.5689 0.704 0 0.000 0.296
#> GSM153089 4 0.5497 0.4952 0.044 0 0.284 0.672
#> GSM153090 1 0.4981 0.2561 0.536 0 0.000 0.464
#> GSM153091 1 0.0469 0.7200 0.988 0 0.012 0.000
#> GSM153092 1 0.3837 0.6204 0.776 0 0.000 0.224
#> GSM153093 4 0.0000 0.8438 0.000 0 0.000 1.000
#> GSM153094 1 0.0592 0.7180 0.984 0 0.016 0.000
#> GSM153095 1 0.0336 0.7300 0.992 0 0.000 0.008
#> GSM153096 1 0.0469 0.7321 0.988 0 0.000 0.012
#> GSM153097 1 0.0188 0.7230 0.996 0 0.004 0.000
#> GSM153098 4 0.4819 0.4042 0.344 0 0.004 0.652
#> GSM153099 1 0.4898 0.3937 0.584 0 0.000 0.416
#> GSM153100 1 0.3801 0.6337 0.780 0 0.000 0.220
#> GSM153101 1 0.0707 0.7355 0.980 0 0.000 0.020
#> GSM153102 1 0.7672 0.0482 0.460 0 0.256 0.284
#> GSM153103 1 0.1302 0.6967 0.956 0 0.044 0.000
#> GSM153104 4 0.0000 0.8438 0.000 0 0.000 1.000
#> GSM153106 1 0.5090 0.4990 0.660 0 0.016 0.324
#> GSM153107 1 0.0817 0.7360 0.976 0 0.000 0.024
#> GSM153108 1 0.4746 0.4848 0.632 0 0.000 0.368
#> GSM153109 1 0.4072 0.3732 0.748 0 0.252 0.000
#> GSM153110 1 0.0921 0.7355 0.972 0 0.000 0.028
#> GSM153111 1 0.0707 0.7156 0.980 0 0.020 0.000
#> GSM153112 1 0.1940 0.7224 0.924 0 0.000 0.076
#> GSM153113 1 0.4072 0.3732 0.748 0 0.252 0.000
#> GSM153114 4 0.0000 0.8438 0.000 0 0.000 1.000
#> GSM187532 2 0.0000 1.0000 0.000 1 0.000 0.000
#> GSM187533 2 0.0000 1.0000 0.000 1 0.000 0.000
#> GSM187534 2 0.0000 1.0000 0.000 1 0.000 0.000
#> GSM187535 1 0.4072 0.3732 0.748 0 0.252 0.000
#> GSM152906 2 0.0000 1.0000 0.000 1 0.000 0.000
#> GSM152907 2 0.0000 1.0000 0.000 1 0.000 0.000
#> GSM152908 2 0.0000 1.0000 0.000 1 0.000 0.000
#> GSM152909 2 0.0000 1.0000 0.000 1 0.000 0.000
#> GSM152910 2 0.0000 1.0000 0.000 1 0.000 0.000
#> GSM152911 2 0.0000 1.0000 0.000 1 0.000 0.000
#> GSM152912 2 0.0000 1.0000 0.000 1 0.000 0.000
#> GSM152913 2 0.0000 1.0000 0.000 1 0.000 0.000
#> GSM152914 2 0.0000 1.0000 0.000 1 0.000 0.000
#> GSM152915 2 0.0000 1.0000 0.000 1 0.000 0.000
#> GSM152916 2 0.0000 1.0000 0.000 1 0.000 0.000
#> GSM152917 2 0.0000 1.0000 0.000 1 0.000 0.000
#> GSM152918 2 0.0000 1.0000 0.000 1 0.000 0.000
#> GSM152919 2 0.0000 1.0000 0.000 1 0.000 0.000
#> GSM152920 2 0.0000 1.0000 0.000 1 0.000 0.000
#> GSM152921 2 0.0000 1.0000 0.000 1 0.000 0.000
#> GSM152922 2 0.0000 1.0000 0.000 1 0.000 0.000
#> GSM152923 2 0.0000 1.0000 0.000 1 0.000 0.000
#> GSM152924 2 0.0000 1.0000 0.000 1 0.000 0.000
#> GSM152925 2 0.0000 1.0000 0.000 1 0.000 0.000
#> GSM152926 2 0.0000 1.0000 0.000 1 0.000 0.000
#> GSM152927 2 0.0000 1.0000 0.000 1 0.000 0.000
#> GSM152928 2 0.0000 1.0000 0.000 1 0.000 0.000
#> GSM152929 2 0.0000 1.0000 0.000 1 0.000 0.000
#> GSM152930 2 0.0000 1.0000 0.000 1 0.000 0.000
cbind(get_classes(res, k = 5), get_membership(res, k = 5))
#> class entropy silhouette p1 p2 p3 p4 p5
#> GSM152839 1 0.1357 0.67356 0.948 0.000 0.048 0.000 0.004
#> GSM152840 4 0.0000 0.82554 0.000 0.000 0.000 1.000 0.000
#> GSM152841 4 0.0000 0.82554 0.000 0.000 0.000 1.000 0.000
#> GSM152842 1 0.3635 0.52435 0.748 0.000 0.248 0.000 0.004
#> GSM152843 1 0.0404 0.67981 0.988 0.000 0.012 0.000 0.000
#> GSM152844 4 0.3809 0.54917 0.000 0.000 0.256 0.736 0.008
#> GSM152845 5 0.4126 0.46004 0.000 0.000 0.380 0.000 0.620
#> GSM152846 5 0.4126 0.46004 0.000 0.000 0.380 0.000 0.620
#> GSM152847 1 0.4473 0.23162 0.580 0.000 0.412 0.000 0.008
#> GSM152848 1 0.1121 0.67837 0.956 0.000 0.000 0.000 0.044
#> GSM152849 1 0.3783 0.50401 0.740 0.000 0.252 0.000 0.008
#> GSM152850 1 0.0510 0.67649 0.984 0.000 0.016 0.000 0.000
#> GSM152851 4 0.0000 0.82554 0.000 0.000 0.000 1.000 0.000
#> GSM152852 5 0.4126 0.46004 0.000 0.000 0.380 0.000 0.620
#> GSM152853 4 0.0000 0.82554 0.000 0.000 0.000 1.000 0.000
#> GSM152854 4 0.7366 -0.01995 0.160 0.000 0.356 0.428 0.056
#> GSM152855 4 0.6805 -0.10995 0.296 0.000 0.000 0.360 0.344
#> GSM153238 1 0.3336 0.42241 0.772 0.000 0.228 0.000 0.000
#> GSM153239 4 0.0963 0.80207 0.000 0.000 0.036 0.964 0.000
#> GSM153240 4 0.6357 0.21199 0.276 0.000 0.004 0.536 0.184
#> GSM153241 1 0.3196 0.57066 0.804 0.000 0.192 0.000 0.004
#> GSM153242 5 0.4276 0.45827 0.000 0.000 0.380 0.004 0.616
#> GSM153243 3 0.2773 0.64156 0.164 0.000 0.836 0.000 0.000
#> GSM153244 4 0.3890 0.54911 0.012 0.000 0.252 0.736 0.000
#> GSM153245 4 0.0000 0.82554 0.000 0.000 0.000 1.000 0.000
#> GSM153246 1 0.5246 0.04451 0.512 0.000 0.448 0.004 0.036
#> GSM153247 1 0.0162 0.67894 0.996 0.000 0.004 0.000 0.000
#> GSM153248 1 0.1851 0.62739 0.912 0.000 0.088 0.000 0.000
#> GSM153249 4 0.0000 0.82554 0.000 0.000 0.000 1.000 0.000
#> GSM153250 1 0.1851 0.66790 0.912 0.000 0.000 0.000 0.088
#> GSM153251 4 0.4283 0.48313 0.004 0.000 0.292 0.692 0.012
#> GSM153252 5 0.6738 -0.03662 0.256 0.000 0.000 0.364 0.380
#> GSM153253 4 0.0000 0.82554 0.000 0.000 0.000 1.000 0.000
#> GSM153254 4 0.6987 -0.06612 0.316 0.000 0.276 0.400 0.008
#> GSM153255 4 0.1106 0.80899 0.012 0.000 0.000 0.964 0.024
#> GSM153256 1 0.4980 0.43634 0.584 0.000 0.000 0.036 0.380
#> GSM153257 4 0.6407 0.18127 0.204 0.000 0.000 0.500 0.296
#> GSM153258 1 0.0794 0.67587 0.972 0.000 0.028 0.000 0.000
#> GSM153259 1 0.0963 0.67550 0.964 0.000 0.036 0.000 0.000
#> GSM153260 3 0.2006 0.55208 0.072 0.000 0.916 0.000 0.012
#> GSM153261 3 0.4866 0.37167 0.344 0.000 0.620 0.000 0.036
#> GSM153262 4 0.0000 0.82554 0.000 0.000 0.000 1.000 0.000
#> GSM153263 1 0.2970 0.63373 0.828 0.000 0.000 0.004 0.168
#> GSM153264 1 0.0510 0.67649 0.984 0.000 0.016 0.000 0.000
#> GSM153265 4 0.0000 0.82554 0.000 0.000 0.000 1.000 0.000
#> GSM153266 1 0.0963 0.67620 0.964 0.000 0.036 0.000 0.000
#> GSM153267 1 0.4608 0.50371 0.640 0.000 0.000 0.024 0.336
#> GSM153268 4 0.0000 0.82554 0.000 0.000 0.000 1.000 0.000
#> GSM153269 1 0.4921 0.46163 0.604 0.000 0.000 0.036 0.360
#> GSM153270 1 0.3007 0.63327 0.864 0.000 0.104 0.028 0.004
#> GSM153271 1 0.3086 0.62786 0.816 0.000 0.000 0.004 0.180
#> GSM153272 5 0.6790 -0.00939 0.352 0.000 0.000 0.284 0.364
#> GSM153273 1 0.0703 0.67481 0.976 0.000 0.024 0.000 0.000
#> GSM153274 1 0.4498 0.54976 0.688 0.000 0.000 0.032 0.280
#> GSM153275 1 0.5316 0.43935 0.588 0.000 0.000 0.064 0.348
#> GSM153276 1 0.5218 0.46009 0.604 0.000 0.000 0.060 0.336
#> GSM153277 4 0.1943 0.77271 0.056 0.000 0.000 0.924 0.020
#> GSM153278 3 0.4444 0.36743 0.364 0.000 0.624 0.000 0.012
#> GSM153279 4 0.0000 0.82554 0.000 0.000 0.000 1.000 0.000
#> GSM153280 4 0.0000 0.82554 0.000 0.000 0.000 1.000 0.000
#> GSM153281 4 0.0162 0.82379 0.004 0.000 0.000 0.996 0.000
#> GSM153282 4 0.0000 0.82554 0.000 0.000 0.000 1.000 0.000
#> GSM153283 1 0.0794 0.67709 0.972 0.000 0.028 0.000 0.000
#> GSM153284 1 0.6377 0.16425 0.452 0.000 0.000 0.168 0.380
#> GSM153285 4 0.0000 0.82554 0.000 0.000 0.000 1.000 0.000
#> GSM153286 1 0.5868 0.31423 0.516 0.000 0.000 0.104 0.380
#> GSM153287 4 0.0162 0.82379 0.004 0.000 0.000 0.996 0.000
#> GSM153288 5 0.6719 -0.06564 0.372 0.000 0.000 0.248 0.380
#> GSM153289 1 0.5386 0.40130 0.564 0.000 0.000 0.064 0.372
#> GSM153290 4 0.0000 0.82554 0.000 0.000 0.000 1.000 0.000
#> GSM153291 4 0.4158 0.63819 0.092 0.000 0.000 0.784 0.124
#> GSM153292 4 0.0000 0.82554 0.000 0.000 0.000 1.000 0.000
#> GSM153293 1 0.5048 0.43178 0.580 0.000 0.000 0.040 0.380
#> GSM153294 1 0.1981 0.65588 0.920 0.000 0.064 0.000 0.016
#> GSM153295 1 0.6659 0.47191 0.612 0.000 0.144 0.072 0.172
#> GSM153054 1 0.0609 0.67606 0.980 0.000 0.020 0.000 0.000
#> GSM153055 1 0.3098 0.64193 0.836 0.000 0.000 0.016 0.148
#> GSM153056 1 0.3578 0.55661 0.784 0.000 0.204 0.004 0.008
#> GSM153057 1 0.6840 -0.14123 0.444 0.000 0.320 0.228 0.008
#> GSM153058 5 0.4759 0.43684 0.004 0.000 0.388 0.016 0.592
#> GSM153059 3 0.3146 0.61213 0.128 0.000 0.844 0.000 0.028
#> GSM153060 3 0.7258 0.12761 0.376 0.000 0.400 0.188 0.036
#> GSM153061 3 0.4130 0.44663 0.292 0.000 0.696 0.000 0.012
#> GSM153062 5 0.4126 0.46004 0.000 0.000 0.380 0.000 0.620
#> GSM153063 4 0.0451 0.81994 0.008 0.000 0.000 0.988 0.004
#> GSM153064 1 0.0609 0.67606 0.980 0.000 0.020 0.000 0.000
#> GSM153065 3 0.1628 0.54509 0.056 0.000 0.936 0.000 0.008
#> GSM153066 3 0.3353 0.64406 0.196 0.008 0.796 0.000 0.000
#> GSM153067 4 0.2953 0.65756 0.144 0.000 0.000 0.844 0.012
#> GSM153068 3 0.3656 0.53077 0.168 0.000 0.800 0.000 0.032
#> GSM153069 4 0.0162 0.82379 0.004 0.000 0.000 0.996 0.000
#> GSM153070 1 0.0290 0.67862 0.992 0.000 0.008 0.000 0.000
#> GSM153071 1 0.1430 0.67749 0.944 0.000 0.004 0.000 0.052
#> GSM153072 1 0.3336 0.42590 0.772 0.000 0.228 0.000 0.000
#> GSM153073 1 0.1952 0.66865 0.912 0.000 0.004 0.000 0.084
#> GSM153074 4 0.5491 0.43640 0.104 0.000 0.000 0.624 0.272
#> GSM153075 1 0.5408 0.11676 0.516 0.000 0.020 0.440 0.024
#> GSM153076 1 0.3010 0.63180 0.824 0.000 0.000 0.004 0.172
#> GSM153077 1 0.0609 0.67606 0.980 0.000 0.020 0.000 0.000
#> GSM153078 1 0.1121 0.67399 0.956 0.000 0.044 0.000 0.000
#> GSM153079 3 0.4434 0.33264 0.460 0.000 0.536 0.000 0.004
#> GSM153080 1 0.1243 0.67831 0.960 0.000 0.004 0.028 0.008
#> GSM153081 1 0.3689 0.51456 0.740 0.000 0.256 0.000 0.004
#> GSM153082 1 0.4171 -0.00305 0.604 0.000 0.396 0.000 0.000
#> GSM153083 1 0.4306 -0.26146 0.508 0.000 0.492 0.000 0.000
#> GSM153084 3 0.3242 0.64150 0.216 0.000 0.784 0.000 0.000
#> GSM153085 3 0.4307 0.24096 0.496 0.000 0.504 0.000 0.000
#> GSM153086 1 0.4304 -0.24360 0.516 0.000 0.484 0.000 0.000
#> GSM153087 4 0.6172 0.21677 0.280 0.000 0.000 0.544 0.176
#> GSM153088 1 0.2890 0.63797 0.836 0.000 0.000 0.004 0.160
#> GSM153089 3 0.5653 0.20972 0.088 0.000 0.632 0.268 0.012
#> GSM153090 1 0.4774 0.47237 0.612 0.000 0.000 0.028 0.360
#> GSM153091 1 0.4305 -0.25263 0.512 0.000 0.488 0.000 0.000
#> GSM153092 1 0.0609 0.67523 0.980 0.000 0.020 0.000 0.000
#> GSM153093 4 0.0798 0.81554 0.008 0.000 0.000 0.976 0.016
#> GSM153094 1 0.4305 -0.25263 0.512 0.000 0.488 0.000 0.000
#> GSM153095 1 0.1544 0.64608 0.932 0.000 0.068 0.000 0.000
#> GSM153096 1 0.0609 0.67606 0.980 0.000 0.020 0.000 0.000
#> GSM153097 1 0.4304 -0.24360 0.516 0.000 0.484 0.000 0.000
#> GSM153098 1 0.5468 0.35754 0.608 0.000 0.016 0.328 0.048
#> GSM153099 1 0.4774 0.47237 0.612 0.000 0.000 0.028 0.360
#> GSM153100 1 0.0324 0.67942 0.992 0.000 0.004 0.000 0.004
#> GSM153101 1 0.2020 0.61675 0.900 0.000 0.100 0.000 0.000
#> GSM153102 3 0.3534 0.62720 0.256 0.000 0.744 0.000 0.000
#> GSM153103 1 0.4305 -0.25219 0.512 0.000 0.488 0.000 0.000
#> GSM153104 4 0.0000 0.82554 0.000 0.000 0.000 1.000 0.000
#> GSM153106 1 0.3109 0.45562 0.800 0.000 0.200 0.000 0.000
#> GSM153107 1 0.0609 0.67606 0.980 0.000 0.020 0.000 0.000
#> GSM153108 1 0.3282 0.62730 0.804 0.000 0.000 0.008 0.188
#> GSM153109 3 0.3336 0.64208 0.228 0.000 0.772 0.000 0.000
#> GSM153110 1 0.0963 0.66835 0.964 0.000 0.036 0.000 0.000
#> GSM153111 1 0.4306 -0.26146 0.508 0.000 0.492 0.000 0.000
#> GSM153112 1 0.0566 0.67898 0.984 0.000 0.012 0.000 0.004
#> GSM153113 3 0.4096 0.61181 0.144 0.072 0.784 0.000 0.000
#> GSM153114 4 0.0000 0.82554 0.000 0.000 0.000 1.000 0.000
#> GSM187532 2 0.0000 0.99829 0.000 1.000 0.000 0.000 0.000
#> GSM187533 2 0.0000 0.99829 0.000 1.000 0.000 0.000 0.000
#> GSM187534 2 0.0000 0.99829 0.000 1.000 0.000 0.000 0.000
#> GSM187535 3 0.4210 0.58510 0.124 0.096 0.780 0.000 0.000
#> GSM152906 2 0.0000 0.99829 0.000 1.000 0.000 0.000 0.000
#> GSM152907 2 0.0609 0.98123 0.000 0.980 0.020 0.000 0.000
#> GSM152908 2 0.0000 0.99829 0.000 1.000 0.000 0.000 0.000
#> GSM152909 2 0.0000 0.99829 0.000 1.000 0.000 0.000 0.000
#> GSM152910 2 0.0000 0.99829 0.000 1.000 0.000 0.000 0.000
#> GSM152911 2 0.0000 0.99829 0.000 1.000 0.000 0.000 0.000
#> GSM152912 2 0.0000 0.99829 0.000 1.000 0.000 0.000 0.000
#> GSM152913 2 0.0000 0.99829 0.000 1.000 0.000 0.000 0.000
#> GSM152914 2 0.0000 0.99829 0.000 1.000 0.000 0.000 0.000
#> GSM152915 2 0.0000 0.99829 0.000 1.000 0.000 0.000 0.000
#> GSM152916 2 0.0000 0.99829 0.000 1.000 0.000 0.000 0.000
#> GSM152917 2 0.0000 0.99829 0.000 1.000 0.000 0.000 0.000
#> GSM152918 2 0.0000 0.99829 0.000 1.000 0.000 0.000 0.000
#> GSM152919 2 0.0000 0.99829 0.000 1.000 0.000 0.000 0.000
#> GSM152920 2 0.0000 0.99829 0.000 1.000 0.000 0.000 0.000
#> GSM152921 2 0.0000 0.99829 0.000 1.000 0.000 0.000 0.000
#> GSM152922 2 0.0000 0.99829 0.000 1.000 0.000 0.000 0.000
#> GSM152923 2 0.0000 0.99829 0.000 1.000 0.000 0.000 0.000
#> GSM152924 2 0.0000 0.99829 0.000 1.000 0.000 0.000 0.000
#> GSM152925 2 0.0000 0.99829 0.000 1.000 0.000 0.000 0.000
#> GSM152926 2 0.0609 0.98123 0.000 0.980 0.020 0.000 0.000
#> GSM152927 2 0.0000 0.99829 0.000 1.000 0.000 0.000 0.000
#> GSM152928 2 0.0290 0.99241 0.000 0.992 0.008 0.000 0.000
#> GSM152929 2 0.0000 0.99829 0.000 1.000 0.000 0.000 0.000
#> GSM152930 2 0.0000 0.99829 0.000 1.000 0.000 0.000 0.000
cbind(get_classes(res, k = 6), get_membership(res, k = 6))
#> class entropy silhouette p1 p2 p3 p4 p5 p6
#> GSM152839 1 0.2765 0.6883 0.840 0.000 0.004 0.004 0.148 0.004
#> GSM152840 4 0.0458 0.8734 0.000 0.000 0.000 0.984 0.000 0.016
#> GSM152841 4 0.1082 0.8747 0.000 0.000 0.004 0.956 0.000 0.040
#> GSM152842 3 0.6394 0.4503 0.352 0.000 0.420 0.000 0.204 0.024
#> GSM152843 1 0.2001 0.6985 0.900 0.000 0.004 0.004 0.092 0.000
#> GSM152844 4 0.2350 0.7882 0.000 0.000 0.000 0.880 0.020 0.100
#> GSM152845 6 0.2066 0.8260 0.000 0.000 0.052 0.000 0.040 0.908
#> GSM152846 6 0.1267 0.8460 0.000 0.000 0.000 0.000 0.060 0.940
#> GSM152847 3 0.6244 0.6842 0.156 0.000 0.500 0.000 0.308 0.036
#> GSM152848 1 0.1668 0.7000 0.928 0.000 0.008 0.004 0.060 0.000
#> GSM152849 1 0.6612 -0.4641 0.360 0.000 0.360 0.004 0.256 0.020
#> GSM152850 1 0.2070 0.6918 0.896 0.000 0.012 0.000 0.092 0.000
#> GSM152851 4 0.0291 0.8749 0.000 0.000 0.004 0.992 0.000 0.004
#> GSM152852 6 0.1267 0.8460 0.000 0.000 0.000 0.000 0.060 0.940
#> GSM152853 4 0.0458 0.8734 0.000 0.000 0.000 0.984 0.000 0.016
#> GSM152854 6 0.6818 0.3569 0.176 0.000 0.000 0.200 0.116 0.508
#> GSM152855 1 0.5633 0.5168 0.532 0.000 0.272 0.196 0.000 0.000
#> GSM153238 1 0.3872 0.0134 0.604 0.000 0.004 0.000 0.392 0.000
#> GSM153239 4 0.0146 0.8768 0.000 0.000 0.000 0.996 0.000 0.004
#> GSM153240 1 0.5174 0.3846 0.536 0.000 0.096 0.368 0.000 0.000
#> GSM153241 1 0.3993 0.6447 0.764 0.000 0.012 0.012 0.188 0.024
#> GSM153242 6 0.1890 0.8412 0.000 0.000 0.000 0.024 0.060 0.916
#> GSM153243 5 0.3948 0.6192 0.124 0.000 0.052 0.000 0.792 0.032
#> GSM153244 4 0.3350 0.7315 0.008 0.000 0.004 0.836 0.064 0.088
#> GSM153245 4 0.0000 0.8771 0.000 0.000 0.000 1.000 0.000 0.000
#> GSM153246 3 0.6010 0.7539 0.056 0.000 0.496 0.008 0.384 0.056
#> GSM153247 1 0.0547 0.7046 0.980 0.000 0.000 0.000 0.020 0.000
#> GSM153248 1 0.3531 0.1976 0.672 0.000 0.000 0.000 0.328 0.000
#> GSM153249 4 0.1297 0.8738 0.000 0.000 0.012 0.948 0.000 0.040
#> GSM153250 1 0.1370 0.7083 0.948 0.000 0.012 0.004 0.036 0.000
#> GSM153251 4 0.4390 0.5766 0.000 0.000 0.004 0.724 0.096 0.176
#> GSM153252 1 0.4958 0.5698 0.560 0.000 0.364 0.076 0.000 0.000
#> GSM153253 4 0.1082 0.8747 0.000 0.000 0.004 0.956 0.000 0.040
#> GSM153254 1 0.6511 0.3824 0.504 0.000 0.004 0.304 0.120 0.068
#> GSM153255 4 0.2212 0.8167 0.008 0.000 0.112 0.880 0.000 0.000
#> GSM153256 1 0.3756 0.6323 0.644 0.000 0.352 0.004 0.000 0.000
#> GSM153257 4 0.6089 0.0144 0.308 0.000 0.300 0.392 0.000 0.000
#> GSM153258 1 0.1625 0.6895 0.928 0.000 0.012 0.000 0.060 0.000
#> GSM153259 1 0.2499 0.6619 0.880 0.000 0.048 0.000 0.072 0.000
#> GSM153260 3 0.4776 0.7569 0.004 0.000 0.496 0.000 0.460 0.040
#> GSM153261 3 0.4974 0.7527 0.004 0.000 0.500 0.000 0.440 0.056
#> GSM153262 4 0.0547 0.8775 0.000 0.000 0.020 0.980 0.000 0.000
#> GSM153263 1 0.0935 0.7152 0.964 0.000 0.032 0.004 0.000 0.000
#> GSM153264 1 0.1643 0.6872 0.924 0.000 0.008 0.000 0.068 0.000
#> GSM153265 4 0.0146 0.8778 0.000 0.000 0.004 0.996 0.000 0.000
#> GSM153266 1 0.2491 0.6846 0.868 0.000 0.020 0.000 0.112 0.000
#> GSM153267 1 0.3215 0.6814 0.756 0.000 0.240 0.004 0.000 0.000
#> GSM153268 4 0.0458 0.8734 0.000 0.000 0.000 0.984 0.000 0.016
#> GSM153269 1 0.3684 0.6424 0.664 0.000 0.332 0.004 0.000 0.000
#> GSM153270 1 0.4345 0.6422 0.740 0.000 0.000 0.180 0.060 0.020
#> GSM153271 1 0.1411 0.7169 0.936 0.000 0.060 0.004 0.000 0.000
#> GSM153272 1 0.5042 0.5831 0.576 0.000 0.332 0.092 0.000 0.000
#> GSM153273 1 0.2362 0.6178 0.860 0.000 0.004 0.000 0.136 0.000
#> GSM153274 1 0.3766 0.6788 0.736 0.000 0.232 0.032 0.000 0.000
#> GSM153275 1 0.3778 0.6596 0.696 0.000 0.288 0.016 0.000 0.000
#> GSM153276 1 0.4495 0.6429 0.660 0.000 0.276 0.064 0.000 0.000
#> GSM153277 4 0.3817 0.0502 0.432 0.000 0.000 0.568 0.000 0.000
#> GSM153278 3 0.5399 0.7688 0.044 0.000 0.504 0.000 0.416 0.036
#> GSM153279 4 0.0146 0.8756 0.000 0.000 0.004 0.996 0.000 0.000
#> GSM153280 4 0.0000 0.8771 0.000 0.000 0.000 1.000 0.000 0.000
#> GSM153281 4 0.1219 0.8661 0.004 0.000 0.048 0.948 0.000 0.000
#> GSM153282 4 0.0000 0.8771 0.000 0.000 0.000 1.000 0.000 0.000
#> GSM153283 1 0.1643 0.6872 0.924 0.000 0.008 0.000 0.068 0.000
#> GSM153284 1 0.3899 0.6240 0.628 0.000 0.364 0.008 0.000 0.000
#> GSM153285 4 0.1297 0.8738 0.000 0.000 0.012 0.948 0.000 0.040
#> GSM153286 1 0.4230 0.6131 0.612 0.000 0.364 0.024 0.000 0.000
#> GSM153287 4 0.1297 0.8738 0.000 0.000 0.012 0.948 0.000 0.040
#> GSM153288 1 0.4664 0.5920 0.584 0.000 0.364 0.052 0.000 0.000
#> GSM153289 1 0.3742 0.6347 0.648 0.000 0.348 0.004 0.000 0.000
#> GSM153290 4 0.0000 0.8771 0.000 0.000 0.000 1.000 0.000 0.000
#> GSM153291 4 0.3506 0.7248 0.052 0.000 0.156 0.792 0.000 0.000
#> GSM153292 4 0.1082 0.8747 0.000 0.000 0.004 0.956 0.000 0.040
#> GSM153293 1 0.3714 0.6398 0.656 0.000 0.340 0.004 0.000 0.000
#> GSM153294 1 0.3109 0.4599 0.772 0.000 0.004 0.000 0.224 0.000
#> GSM153295 1 0.5367 0.6634 0.712 0.000 0.104 0.100 0.064 0.020
#> GSM153054 1 0.2402 0.6360 0.856 0.000 0.004 0.000 0.140 0.000
#> GSM153055 1 0.2520 0.7089 0.844 0.000 0.152 0.004 0.000 0.000
#> GSM153056 1 0.4538 0.6345 0.728 0.000 0.012 0.040 0.200 0.020
#> GSM153057 1 0.6669 0.4020 0.524 0.000 0.004 0.232 0.160 0.080
#> GSM153058 6 0.3337 0.7731 0.000 0.000 0.004 0.064 0.108 0.824
#> GSM153059 5 0.4534 0.2261 0.072 0.000 0.096 0.000 0.760 0.072
#> GSM153060 1 0.8310 -0.2707 0.336 0.000 0.204 0.088 0.272 0.100
#> GSM153061 3 0.4775 0.7572 0.004 0.000 0.500 0.000 0.456 0.040
#> GSM153062 6 0.2066 0.8288 0.000 0.000 0.052 0.000 0.040 0.908
#> GSM153063 4 0.0547 0.8711 0.020 0.000 0.000 0.980 0.000 0.000
#> GSM153064 1 0.1588 0.6864 0.924 0.000 0.004 0.000 0.072 0.000
#> GSM153065 3 0.4779 0.7546 0.004 0.000 0.488 0.000 0.468 0.040
#> GSM153066 5 0.4386 0.6743 0.124 0.016 0.068 0.000 0.772 0.020
#> GSM153067 4 0.2190 0.8551 0.008 0.000 0.044 0.908 0.000 0.040
#> GSM153068 3 0.5904 0.6868 0.064 0.000 0.504 0.000 0.372 0.060
#> GSM153069 4 0.1297 0.8738 0.000 0.000 0.012 0.948 0.000 0.040
#> GSM153070 1 0.0291 0.7067 0.992 0.000 0.004 0.000 0.004 0.000
#> GSM153071 1 0.0622 0.7105 0.980 0.000 0.012 0.000 0.008 0.000
#> GSM153072 1 0.3864 -0.4334 0.520 0.000 0.000 0.000 0.480 0.000
#> GSM153073 1 0.0603 0.7114 0.980 0.000 0.016 0.000 0.004 0.000
#> GSM153074 4 0.5839 0.2350 0.276 0.000 0.236 0.488 0.000 0.000
#> GSM153075 1 0.4436 0.5208 0.632 0.000 0.000 0.332 0.028 0.008
#> GSM153076 1 0.1219 0.7166 0.948 0.000 0.048 0.004 0.000 0.000
#> GSM153077 1 0.1349 0.6934 0.940 0.000 0.004 0.000 0.056 0.000
#> GSM153078 1 0.3381 0.6481 0.800 0.000 0.044 0.000 0.156 0.000
#> GSM153079 3 0.6404 0.3765 0.204 0.000 0.452 0.000 0.316 0.028
#> GSM153080 1 0.2728 0.7059 0.864 0.000 0.004 0.100 0.032 0.000
#> GSM153081 3 0.6296 0.6037 0.240 0.000 0.500 0.000 0.232 0.028
#> GSM153082 5 0.3659 0.6803 0.364 0.000 0.000 0.000 0.636 0.000
#> GSM153083 5 0.3109 0.7497 0.224 0.000 0.004 0.000 0.772 0.000
#> GSM153084 5 0.3455 0.7074 0.200 0.000 0.004 0.000 0.776 0.020
#> GSM153085 5 0.3175 0.7432 0.256 0.000 0.000 0.000 0.744 0.000
#> GSM153086 5 0.3309 0.7311 0.280 0.000 0.000 0.000 0.720 0.000
#> GSM153087 1 0.5777 0.4667 0.500 0.000 0.216 0.284 0.000 0.000
#> GSM153088 1 0.1194 0.7161 0.956 0.000 0.032 0.004 0.008 0.000
#> GSM153089 1 0.7236 0.2543 0.440 0.000 0.004 0.228 0.216 0.112
#> GSM153090 1 0.3668 0.6447 0.668 0.000 0.328 0.004 0.000 0.000
#> GSM153091 5 0.3371 0.7435 0.292 0.000 0.000 0.000 0.708 0.000
#> GSM153092 1 0.1285 0.7061 0.944 0.000 0.004 0.000 0.052 0.000
#> GSM153093 4 0.2480 0.8080 0.024 0.000 0.104 0.872 0.000 0.000
#> GSM153094 5 0.3499 0.7338 0.320 0.000 0.000 0.000 0.680 0.000
#> GSM153095 1 0.1957 0.6392 0.888 0.000 0.000 0.000 0.112 0.000
#> GSM153096 1 0.2703 0.5934 0.824 0.000 0.004 0.000 0.172 0.000
#> GSM153097 5 0.3482 0.6976 0.316 0.000 0.000 0.000 0.684 0.000
#> GSM153098 1 0.4373 0.6592 0.736 0.000 0.080 0.172 0.000 0.012
#> GSM153099 1 0.3668 0.6447 0.668 0.000 0.328 0.004 0.000 0.000
#> GSM153100 1 0.0260 0.7056 0.992 0.000 0.000 0.000 0.008 0.000
#> GSM153101 1 0.2219 0.6347 0.864 0.000 0.000 0.000 0.136 0.000
#> GSM153102 5 0.3593 0.7149 0.208 0.000 0.004 0.000 0.764 0.024
#> GSM153103 5 0.3314 0.7445 0.256 0.000 0.004 0.000 0.740 0.000
#> GSM153104 4 0.1075 0.8682 0.000 0.000 0.048 0.952 0.000 0.000
#> GSM153106 1 0.3078 0.6076 0.796 0.000 0.000 0.000 0.192 0.012
#> GSM153107 1 0.1285 0.6962 0.944 0.000 0.004 0.000 0.052 0.000
#> GSM153108 1 0.2772 0.7018 0.816 0.000 0.180 0.004 0.000 0.000
#> GSM153109 5 0.2830 0.7060 0.144 0.000 0.000 0.000 0.836 0.020
#> GSM153110 1 0.4449 0.4182 0.712 0.000 0.088 0.000 0.196 0.004
#> GSM153111 5 0.3198 0.7447 0.260 0.000 0.000 0.000 0.740 0.000
#> GSM153112 1 0.0363 0.7053 0.988 0.000 0.000 0.000 0.012 0.000
#> GSM153113 5 0.4426 0.5019 0.016 0.128 0.068 0.000 0.768 0.020
#> GSM153114 4 0.0000 0.8771 0.000 0.000 0.000 1.000 0.000 0.000
#> GSM187532 2 0.0363 0.9694 0.000 0.988 0.012 0.000 0.000 0.000
#> GSM187533 2 0.0363 0.9694 0.000 0.988 0.012 0.000 0.000 0.000
#> GSM187534 2 0.0146 0.9702 0.000 0.996 0.000 0.000 0.004 0.000
#> GSM187535 5 0.4376 0.4938 0.012 0.132 0.068 0.000 0.768 0.020
#> GSM152906 2 0.1471 0.9543 0.000 0.932 0.064 0.000 0.004 0.000
#> GSM152907 2 0.0146 0.9701 0.000 0.996 0.000 0.000 0.004 0.000
#> GSM152908 2 0.0363 0.9694 0.000 0.988 0.012 0.000 0.000 0.000
#> GSM152909 2 0.0622 0.9675 0.000 0.980 0.012 0.000 0.000 0.008
#> GSM152910 2 0.0363 0.9694 0.000 0.988 0.012 0.000 0.000 0.000
#> GSM152911 2 0.0363 0.9694 0.000 0.988 0.012 0.000 0.000 0.000
#> GSM152912 2 0.0363 0.9694 0.000 0.988 0.012 0.000 0.000 0.000
#> GSM152913 2 0.0363 0.9694 0.000 0.988 0.012 0.000 0.000 0.000
#> GSM152914 2 0.0146 0.9702 0.000 0.996 0.000 0.000 0.004 0.000
#> GSM152915 2 0.0146 0.9703 0.000 0.996 0.004 0.000 0.000 0.000
#> GSM152916 2 0.0146 0.9703 0.000 0.996 0.004 0.000 0.000 0.000
#> GSM152917 2 0.0603 0.9676 0.000 0.980 0.016 0.000 0.004 0.000
#> GSM152918 2 0.1471 0.9543 0.000 0.932 0.064 0.000 0.004 0.000
#> GSM152919 2 0.1471 0.9543 0.000 0.932 0.064 0.000 0.004 0.000
#> GSM152920 2 0.0146 0.9703 0.000 0.996 0.004 0.000 0.000 0.000
#> GSM152921 2 0.0363 0.9694 0.000 0.988 0.012 0.000 0.000 0.000
#> GSM152922 2 0.0363 0.9694 0.000 0.988 0.012 0.000 0.000 0.000
#> GSM152923 2 0.1471 0.9543 0.000 0.932 0.064 0.000 0.004 0.000
#> GSM152924 2 0.1471 0.9543 0.000 0.932 0.064 0.000 0.004 0.000
#> GSM152925 2 0.0146 0.9702 0.000 0.996 0.000 0.000 0.004 0.000
#> GSM152926 2 0.1584 0.9521 0.000 0.928 0.064 0.000 0.008 0.000
#> GSM152927 2 0.1471 0.9543 0.000 0.932 0.064 0.000 0.004 0.000
#> GSM152928 2 0.1643 0.9497 0.000 0.924 0.068 0.000 0.008 0.000
#> GSM152929 2 0.1471 0.9543 0.000 0.932 0.064 0.000 0.004 0.000
#> GSM152930 2 0.1471 0.9543 0.000 0.932 0.064 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)
#> Error in mat[ceiling(1:nr/h_ratio), ceiling(1:nc/w_ratio), drop = FALSE]: subscript out of bounds
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 tissue(p) k
#> ATC:mclust 163 1.69e-28 2
#> ATC:mclust 116 2.03e-24 3
#> ATC:mclust 124 4.61e-25 4
#> ATC:mclust 113 6.43e-21 5
#> ATC:mclust 144 5.57e-27 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 12013 rows and 164 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 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 0.949 0.950 0.978 0.3744 0.629 0.629
#> 3 3 0.585 0.759 0.878 0.6662 0.648 0.476
#> 4 4 0.654 0.728 0.851 0.1191 0.851 0.636
#> 5 5 0.584 0.671 0.792 0.0507 0.947 0.841
#> 6 6 0.581 0.592 0.737 0.0519 0.967 0.894
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
#> GSM152839 1 0.0000 0.982 1.000 0.000
#> GSM152840 1 0.0000 0.982 1.000 0.000
#> GSM152841 1 0.0000 0.982 1.000 0.000
#> GSM152842 1 0.0000 0.982 1.000 0.000
#> GSM152843 1 0.0000 0.982 1.000 0.000
#> GSM152844 1 0.0000 0.982 1.000 0.000
#> GSM152845 2 0.0000 0.962 0.000 1.000
#> GSM152846 1 0.1633 0.962 0.976 0.024
#> GSM152847 1 0.0000 0.982 1.000 0.000
#> GSM152848 1 0.0000 0.982 1.000 0.000
#> GSM152849 1 0.0000 0.982 1.000 0.000
#> GSM152850 1 0.0000 0.982 1.000 0.000
#> GSM152851 1 0.0000 0.982 1.000 0.000
#> GSM152852 1 0.0000 0.982 1.000 0.000
#> GSM152853 1 0.0000 0.982 1.000 0.000
#> GSM152854 1 0.0000 0.982 1.000 0.000
#> GSM152855 1 0.0000 0.982 1.000 0.000
#> GSM153238 1 0.0000 0.982 1.000 0.000
#> GSM153239 1 0.0000 0.982 1.000 0.000
#> GSM153240 1 0.0000 0.982 1.000 0.000
#> GSM153241 1 0.0000 0.982 1.000 0.000
#> GSM153242 1 0.9866 0.219 0.568 0.432
#> GSM153243 2 0.8327 0.663 0.264 0.736
#> GSM153244 1 0.5294 0.857 0.880 0.120
#> GSM153245 1 0.0000 0.982 1.000 0.000
#> GSM153246 1 0.0000 0.982 1.000 0.000
#> GSM153247 1 0.0000 0.982 1.000 0.000
#> GSM153248 1 0.0000 0.982 1.000 0.000
#> GSM153249 1 0.0000 0.982 1.000 0.000
#> GSM153250 1 0.0000 0.982 1.000 0.000
#> GSM153251 2 0.8955 0.572 0.312 0.688
#> GSM153252 1 0.0000 0.982 1.000 0.000
#> GSM153253 1 0.0000 0.982 1.000 0.000
#> GSM153254 1 0.1184 0.969 0.984 0.016
#> GSM153255 1 0.0000 0.982 1.000 0.000
#> GSM153256 1 0.0000 0.982 1.000 0.000
#> GSM153257 1 0.0000 0.982 1.000 0.000
#> GSM153258 1 0.0000 0.982 1.000 0.000
#> GSM153259 1 0.0000 0.982 1.000 0.000
#> GSM153260 1 0.6438 0.799 0.836 0.164
#> GSM153261 1 0.0672 0.975 0.992 0.008
#> GSM153262 1 0.0000 0.982 1.000 0.000
#> GSM153263 1 0.0000 0.982 1.000 0.000
#> GSM153264 1 0.0000 0.982 1.000 0.000
#> GSM153265 1 0.0000 0.982 1.000 0.000
#> GSM153266 1 0.0000 0.982 1.000 0.000
#> GSM153267 1 0.0000 0.982 1.000 0.000
#> GSM153268 1 0.0000 0.982 1.000 0.000
#> GSM153269 1 0.0000 0.982 1.000 0.000
#> GSM153270 1 0.0000 0.982 1.000 0.000
#> GSM153271 1 0.0000 0.982 1.000 0.000
#> GSM153272 1 0.0000 0.982 1.000 0.000
#> GSM153273 1 0.0000 0.982 1.000 0.000
#> GSM153274 1 0.0000 0.982 1.000 0.000
#> GSM153275 1 0.0000 0.982 1.000 0.000
#> GSM153276 1 0.0000 0.982 1.000 0.000
#> GSM153277 1 0.0000 0.982 1.000 0.000
#> GSM153278 1 0.0000 0.982 1.000 0.000
#> GSM153279 1 0.0000 0.982 1.000 0.000
#> GSM153280 1 0.0000 0.982 1.000 0.000
#> GSM153281 1 0.0000 0.982 1.000 0.000
#> GSM153282 1 0.0000 0.982 1.000 0.000
#> GSM153283 1 0.0000 0.982 1.000 0.000
#> GSM153284 1 0.0000 0.982 1.000 0.000
#> GSM153285 1 0.0000 0.982 1.000 0.000
#> GSM153286 1 0.0000 0.982 1.000 0.000
#> GSM153287 1 0.0000 0.982 1.000 0.000
#> GSM153288 1 0.0000 0.982 1.000 0.000
#> GSM153289 1 0.0000 0.982 1.000 0.000
#> GSM153290 1 0.0000 0.982 1.000 0.000
#> GSM153291 1 0.0000 0.982 1.000 0.000
#> GSM153292 1 0.0000 0.982 1.000 0.000
#> GSM153293 1 0.0000 0.982 1.000 0.000
#> GSM153294 1 0.0000 0.982 1.000 0.000
#> GSM153295 1 0.0000 0.982 1.000 0.000
#> GSM153054 1 0.0000 0.982 1.000 0.000
#> GSM153055 1 0.0000 0.982 1.000 0.000
#> GSM153056 1 0.0000 0.982 1.000 0.000
#> GSM153057 1 0.2778 0.938 0.952 0.048
#> GSM153058 1 0.8499 0.615 0.724 0.276
#> GSM153059 2 0.6438 0.806 0.164 0.836
#> GSM153060 1 0.0000 0.982 1.000 0.000
#> GSM153061 1 0.0000 0.982 1.000 0.000
#> GSM153062 2 0.0000 0.962 0.000 1.000
#> GSM153063 1 0.0000 0.982 1.000 0.000
#> GSM153064 1 0.0000 0.982 1.000 0.000
#> GSM153065 2 0.8861 0.589 0.304 0.696
#> GSM153066 2 0.0000 0.962 0.000 1.000
#> GSM153067 1 0.0000 0.982 1.000 0.000
#> GSM153068 1 0.9635 0.353 0.612 0.388
#> GSM153069 1 0.0000 0.982 1.000 0.000
#> GSM153070 1 0.0000 0.982 1.000 0.000
#> GSM153071 1 0.0000 0.982 1.000 0.000
#> GSM153072 1 0.0000 0.982 1.000 0.000
#> GSM153073 1 0.0000 0.982 1.000 0.000
#> GSM153074 1 0.0000 0.982 1.000 0.000
#> GSM153075 1 0.0000 0.982 1.000 0.000
#> GSM153076 1 0.0000 0.982 1.000 0.000
#> GSM153077 1 0.0000 0.982 1.000 0.000
#> GSM153078 1 0.0000 0.982 1.000 0.000
#> GSM153079 1 0.0000 0.982 1.000 0.000
#> GSM153080 1 0.0000 0.982 1.000 0.000
#> GSM153081 1 0.0000 0.982 1.000 0.000
#> GSM153082 1 0.1843 0.958 0.972 0.028
#> GSM153083 1 0.1633 0.962 0.976 0.024
#> GSM153084 2 0.0000 0.962 0.000 1.000
#> GSM153085 1 0.8207 0.652 0.744 0.256
#> GSM153086 1 0.0000 0.982 1.000 0.000
#> GSM153087 1 0.0000 0.982 1.000 0.000
#> GSM153088 1 0.0000 0.982 1.000 0.000
#> GSM153089 2 0.7815 0.714 0.232 0.768
#> GSM153090 1 0.0000 0.982 1.000 0.000
#> GSM153091 1 0.2236 0.950 0.964 0.036
#> GSM153092 1 0.0000 0.982 1.000 0.000
#> GSM153093 1 0.0000 0.982 1.000 0.000
#> GSM153094 1 0.3274 0.926 0.940 0.060
#> GSM153095 1 0.0000 0.982 1.000 0.000
#> GSM153096 1 0.0000 0.982 1.000 0.000
#> GSM153097 1 0.0376 0.979 0.996 0.004
#> GSM153098 1 0.0000 0.982 1.000 0.000
#> GSM153099 1 0.0000 0.982 1.000 0.000
#> GSM153100 1 0.0000 0.982 1.000 0.000
#> GSM153101 1 0.0000 0.982 1.000 0.000
#> GSM153102 1 0.7674 0.708 0.776 0.224
#> GSM153103 1 0.0000 0.982 1.000 0.000
#> GSM153104 1 0.0000 0.982 1.000 0.000
#> GSM153106 1 0.0000 0.982 1.000 0.000
#> GSM153107 1 0.0000 0.982 1.000 0.000
#> GSM153108 1 0.0000 0.982 1.000 0.000
#> GSM153109 2 0.6048 0.825 0.148 0.852
#> GSM153110 1 0.0000 0.982 1.000 0.000
#> GSM153111 1 0.1184 0.969 0.984 0.016
#> GSM153112 1 0.0000 0.982 1.000 0.000
#> GSM153113 2 0.0000 0.962 0.000 1.000
#> GSM153114 1 0.0000 0.982 1.000 0.000
#> GSM187532 2 0.0000 0.962 0.000 1.000
#> GSM187533 2 0.0000 0.962 0.000 1.000
#> GSM187534 2 0.0000 0.962 0.000 1.000
#> GSM187535 2 0.0000 0.962 0.000 1.000
#> GSM152906 2 0.0000 0.962 0.000 1.000
#> GSM152907 2 0.0000 0.962 0.000 1.000
#> GSM152908 2 0.0000 0.962 0.000 1.000
#> GSM152909 2 0.0000 0.962 0.000 1.000
#> GSM152910 2 0.0000 0.962 0.000 1.000
#> GSM152911 2 0.0000 0.962 0.000 1.000
#> GSM152912 2 0.0000 0.962 0.000 1.000
#> GSM152913 2 0.0000 0.962 0.000 1.000
#> GSM152914 2 0.0000 0.962 0.000 1.000
#> GSM152915 2 0.0000 0.962 0.000 1.000
#> GSM152916 2 0.0000 0.962 0.000 1.000
#> GSM152917 2 0.0000 0.962 0.000 1.000
#> GSM152918 2 0.0000 0.962 0.000 1.000
#> GSM152919 2 0.0000 0.962 0.000 1.000
#> GSM152920 2 0.0000 0.962 0.000 1.000
#> GSM152921 2 0.0000 0.962 0.000 1.000
#> GSM152922 2 0.0000 0.962 0.000 1.000
#> GSM152923 2 0.0000 0.962 0.000 1.000
#> GSM152924 2 0.0000 0.962 0.000 1.000
#> GSM152925 2 0.0000 0.962 0.000 1.000
#> GSM152926 2 0.0000 0.962 0.000 1.000
#> GSM152927 2 0.0000 0.962 0.000 1.000
#> GSM152928 2 0.0000 0.962 0.000 1.000
#> GSM152929 2 0.0000 0.962 0.000 1.000
#> GSM152930 2 0.0000 0.962 0.000 1.000
cbind(get_classes(res, k = 3), get_membership(res, k = 3))
#> class entropy silhouette p1 p2 p3
#> GSM152839 1 0.6305 -0.0532 0.516 0.000 0.484
#> GSM152840 3 0.1031 0.8414 0.024 0.000 0.976
#> GSM152841 3 0.1753 0.8490 0.048 0.000 0.952
#> GSM152842 1 0.1753 0.8523 0.952 0.000 0.048
#> GSM152843 1 0.1964 0.8479 0.944 0.000 0.056
#> GSM152844 3 0.0424 0.8334 0.008 0.000 0.992
#> GSM152845 2 0.6204 0.3754 0.000 0.576 0.424
#> GSM152846 3 0.1860 0.7915 0.000 0.052 0.948
#> GSM152847 1 0.4555 0.7105 0.800 0.000 0.200
#> GSM152848 1 0.2165 0.8432 0.936 0.000 0.064
#> GSM152849 3 0.5621 0.6501 0.308 0.000 0.692
#> GSM152850 1 0.1411 0.8573 0.964 0.000 0.036
#> GSM152851 3 0.0829 0.8341 0.012 0.004 0.984
#> GSM152852 3 0.1529 0.8001 0.000 0.040 0.960
#> GSM152853 3 0.0000 0.8285 0.000 0.000 1.000
#> GSM152854 3 0.0892 0.8148 0.000 0.020 0.980
#> GSM152855 3 0.4235 0.8133 0.176 0.000 0.824
#> GSM153238 1 0.0000 0.8559 1.000 0.000 0.000
#> GSM153239 3 0.1031 0.8414 0.024 0.000 0.976
#> GSM153240 3 0.3816 0.8315 0.148 0.000 0.852
#> GSM153241 3 0.4605 0.7866 0.204 0.000 0.796
#> GSM153242 3 0.3267 0.7297 0.000 0.116 0.884
#> GSM153243 1 0.3941 0.7133 0.844 0.156 0.000
#> GSM153244 3 0.2066 0.7854 0.000 0.060 0.940
#> GSM153245 3 0.1163 0.8431 0.028 0.000 0.972
#> GSM153246 3 0.2261 0.8518 0.068 0.000 0.932
#> GSM153247 1 0.1411 0.8581 0.964 0.000 0.036
#> GSM153248 1 0.0592 0.8508 0.988 0.012 0.000
#> GSM153249 3 0.3038 0.8479 0.104 0.000 0.896
#> GSM153250 1 0.1289 0.8575 0.968 0.000 0.032
#> GSM153251 3 0.4504 0.6226 0.000 0.196 0.804
#> GSM153252 3 0.5560 0.6660 0.300 0.000 0.700
#> GSM153253 3 0.1964 0.8500 0.056 0.000 0.944
#> GSM153254 3 0.0424 0.8235 0.000 0.008 0.992
#> GSM153255 3 0.4002 0.8248 0.160 0.000 0.840
#> GSM153256 1 0.5810 0.4460 0.664 0.000 0.336
#> GSM153257 3 0.6252 0.3309 0.444 0.000 0.556
#> GSM153258 1 0.1643 0.8542 0.956 0.000 0.044
#> GSM153259 1 0.0424 0.8581 0.992 0.000 0.008
#> GSM153260 1 0.1647 0.8575 0.960 0.004 0.036
#> GSM153261 3 0.2878 0.8468 0.096 0.000 0.904
#> GSM153262 3 0.2796 0.8498 0.092 0.000 0.908
#> GSM153263 1 0.1643 0.8540 0.956 0.000 0.044
#> GSM153264 1 0.0892 0.8587 0.980 0.000 0.020
#> GSM153265 3 0.1860 0.8496 0.052 0.000 0.948
#> GSM153266 1 0.2625 0.8290 0.916 0.000 0.084
#> GSM153267 1 0.6095 0.2952 0.608 0.000 0.392
#> GSM153268 3 0.0424 0.8334 0.008 0.000 0.992
#> GSM153269 3 0.5968 0.5413 0.364 0.000 0.636
#> GSM153270 3 0.3686 0.8362 0.140 0.000 0.860
#> GSM153271 1 0.1411 0.8567 0.964 0.000 0.036
#> GSM153272 3 0.6252 0.3294 0.444 0.000 0.556
#> GSM153273 1 0.0424 0.8528 0.992 0.008 0.000
#> GSM153274 3 0.5706 0.6325 0.320 0.000 0.680
#> GSM153275 3 0.5138 0.7331 0.252 0.000 0.748
#> GSM153276 3 0.4796 0.7710 0.220 0.000 0.780
#> GSM153277 3 0.2448 0.8508 0.076 0.000 0.924
#> GSM153278 1 0.6140 0.2777 0.596 0.000 0.404
#> GSM153279 3 0.1529 0.8473 0.040 0.000 0.960
#> GSM153280 3 0.0892 0.8148 0.000 0.020 0.980
#> GSM153281 3 0.2959 0.8485 0.100 0.000 0.900
#> GSM153282 3 0.1289 0.8447 0.032 0.000 0.968
#> GSM153283 1 0.1411 0.8567 0.964 0.000 0.036
#> GSM153284 3 0.5591 0.6591 0.304 0.000 0.696
#> GSM153285 3 0.3116 0.8468 0.108 0.000 0.892
#> GSM153286 3 0.6026 0.5139 0.376 0.000 0.624
#> GSM153287 3 0.3686 0.8357 0.140 0.000 0.860
#> GSM153288 3 0.5835 0.5952 0.340 0.000 0.660
#> GSM153289 1 0.6309 -0.1287 0.504 0.000 0.496
#> GSM153290 3 0.0592 0.8356 0.012 0.000 0.988
#> GSM153291 3 0.4002 0.8245 0.160 0.000 0.840
#> GSM153292 3 0.2711 0.8503 0.088 0.000 0.912
#> GSM153293 1 0.4605 0.6972 0.796 0.000 0.204
#> GSM153294 1 0.0592 0.8508 0.988 0.012 0.000
#> GSM153295 1 0.6302 -0.0519 0.520 0.000 0.480
#> GSM153054 1 0.0000 0.8559 1.000 0.000 0.000
#> GSM153055 3 0.6295 0.2219 0.472 0.000 0.528
#> GSM153056 3 0.4121 0.8188 0.168 0.000 0.832
#> GSM153057 3 0.0661 0.8266 0.004 0.008 0.988
#> GSM153058 3 0.2796 0.7564 0.000 0.092 0.908
#> GSM153059 2 0.6299 0.2099 0.000 0.524 0.476
#> GSM153060 3 0.0237 0.8316 0.004 0.000 0.996
#> GSM153061 1 0.3482 0.7941 0.872 0.000 0.128
#> GSM153062 3 0.5706 0.3827 0.000 0.320 0.680
#> GSM153063 3 0.1964 0.8503 0.056 0.000 0.944
#> GSM153064 1 0.0747 0.8589 0.984 0.000 0.016
#> GSM153065 1 0.4062 0.7107 0.836 0.164 0.000
#> GSM153066 1 0.5216 0.5381 0.740 0.260 0.000
#> GSM153067 3 0.5397 0.6989 0.280 0.000 0.720
#> GSM153068 3 0.4324 0.7537 0.028 0.112 0.860
#> GSM153069 3 0.3482 0.8408 0.128 0.000 0.872
#> GSM153070 1 0.2261 0.8409 0.932 0.000 0.068
#> GSM153071 1 0.1860 0.8515 0.948 0.000 0.052
#> GSM153072 1 0.1031 0.8435 0.976 0.024 0.000
#> GSM153073 1 0.0892 0.8587 0.980 0.000 0.020
#> GSM153074 3 0.3941 0.8269 0.156 0.000 0.844
#> GSM153075 3 0.2878 0.8493 0.096 0.000 0.904
#> GSM153076 1 0.1529 0.8555 0.960 0.000 0.040
#> GSM153077 1 0.0237 0.8545 0.996 0.004 0.000
#> GSM153078 1 0.3482 0.7912 0.872 0.000 0.128
#> GSM153079 1 0.0592 0.8508 0.988 0.012 0.000
#> GSM153080 3 0.4842 0.7665 0.224 0.000 0.776
#> GSM153081 1 0.1289 0.8578 0.968 0.000 0.032
#> GSM153082 1 0.1643 0.8297 0.956 0.044 0.000
#> GSM153083 1 0.1860 0.8231 0.948 0.052 0.000
#> GSM153084 2 0.6280 0.2400 0.460 0.540 0.000
#> GSM153085 1 0.1860 0.8234 0.948 0.052 0.000
#> GSM153086 1 0.1411 0.8354 0.964 0.036 0.000
#> GSM153087 3 0.4062 0.8219 0.164 0.000 0.836
#> GSM153088 1 0.1529 0.8555 0.960 0.000 0.040
#> GSM153089 3 0.5431 0.4680 0.000 0.284 0.716
#> GSM153090 1 0.6154 0.2383 0.592 0.000 0.408
#> GSM153091 1 0.1860 0.8231 0.948 0.052 0.000
#> GSM153092 1 0.4750 0.6808 0.784 0.000 0.216
#> GSM153093 3 0.3551 0.8392 0.132 0.000 0.868
#> GSM153094 1 0.1753 0.8265 0.952 0.048 0.000
#> GSM153095 1 0.0237 0.8545 0.996 0.004 0.000
#> GSM153096 1 0.0237 0.8545 0.996 0.004 0.000
#> GSM153097 1 0.1860 0.8231 0.948 0.052 0.000
#> GSM153098 1 0.3879 0.7625 0.848 0.000 0.152
#> GSM153099 1 0.6140 0.2572 0.596 0.000 0.404
#> GSM153100 1 0.1529 0.8566 0.960 0.000 0.040
#> GSM153101 1 0.0424 0.8581 0.992 0.000 0.008
#> GSM153102 1 0.1989 0.8494 0.948 0.004 0.048
#> GSM153103 1 0.1753 0.8265 0.952 0.048 0.000
#> GSM153104 3 0.3482 0.8409 0.128 0.000 0.872
#> GSM153106 1 0.6111 0.2842 0.604 0.000 0.396
#> GSM153107 1 0.0747 0.8589 0.984 0.000 0.016
#> GSM153108 1 0.5098 0.6280 0.752 0.000 0.248
#> GSM153109 1 0.3340 0.7475 0.880 0.120 0.000
#> GSM153110 1 0.0237 0.8545 0.996 0.004 0.000
#> GSM153111 1 0.1860 0.8231 0.948 0.052 0.000
#> GSM153112 1 0.0747 0.8589 0.984 0.000 0.016
#> GSM153113 1 0.5760 0.3887 0.672 0.328 0.000
#> GSM153114 3 0.2066 0.8504 0.060 0.000 0.940
#> GSM187532 2 0.1529 0.8934 0.000 0.960 0.040
#> GSM187533 2 0.0475 0.9102 0.004 0.992 0.004
#> GSM187534 2 0.1163 0.9117 0.028 0.972 0.000
#> GSM187535 1 0.4750 0.6124 0.784 0.216 0.000
#> GSM152906 2 0.3551 0.8526 0.132 0.868 0.000
#> GSM152907 2 0.0424 0.9087 0.000 0.992 0.008
#> GSM152908 2 0.0237 0.9091 0.000 0.996 0.004
#> GSM152909 2 0.2448 0.8699 0.000 0.924 0.076
#> GSM152910 2 0.0892 0.9037 0.000 0.980 0.020
#> GSM152911 2 0.0592 0.9115 0.012 0.988 0.000
#> GSM152912 2 0.1031 0.9020 0.000 0.976 0.024
#> GSM152913 2 0.1163 0.9000 0.000 0.972 0.028
#> GSM152914 2 0.1289 0.9112 0.032 0.968 0.000
#> GSM152915 2 0.0892 0.9118 0.020 0.980 0.000
#> GSM152916 2 0.1031 0.9119 0.024 0.976 0.000
#> GSM152917 2 0.1860 0.9050 0.052 0.948 0.000
#> GSM152918 2 0.3482 0.8562 0.128 0.872 0.000
#> GSM152919 2 0.2625 0.8890 0.084 0.916 0.000
#> GSM152920 2 0.0000 0.9099 0.000 1.000 0.000
#> GSM152921 2 0.0237 0.9091 0.000 0.996 0.004
#> GSM152922 2 0.1031 0.9020 0.000 0.976 0.024
#> GSM152923 2 0.2356 0.8961 0.072 0.928 0.000
#> GSM152924 2 0.1411 0.9103 0.036 0.964 0.000
#> GSM152925 2 0.1163 0.9117 0.028 0.972 0.000
#> GSM152926 2 0.3038 0.8753 0.104 0.896 0.000
#> GSM152927 2 0.1289 0.9112 0.032 0.968 0.000
#> GSM152928 2 0.4346 0.7977 0.184 0.816 0.000
#> GSM152929 2 0.4178 0.8117 0.172 0.828 0.000
#> GSM152930 2 0.2261 0.8982 0.068 0.932 0.000
cbind(get_classes(res, k = 4), get_membership(res, k = 4))
#> class entropy silhouette p1 p2 p3 p4
#> GSM152839 1 0.2761 0.83605 0.904 0.000 0.048 0.048
#> GSM152840 4 0.1022 0.81979 0.000 0.000 0.032 0.968
#> GSM152841 4 0.0707 0.82543 0.000 0.000 0.020 0.980
#> GSM152842 1 0.1389 0.85264 0.952 0.000 0.048 0.000
#> GSM152843 1 0.1109 0.86035 0.968 0.000 0.028 0.004
#> GSM152844 4 0.2704 0.73581 0.000 0.000 0.124 0.876
#> GSM152845 3 0.4071 0.56867 0.000 0.104 0.832 0.064
#> GSM152846 3 0.5161 0.51411 0.000 0.008 0.592 0.400
#> GSM152847 1 0.1867 0.84440 0.928 0.000 0.072 0.000
#> GSM152848 1 0.1297 0.86041 0.964 0.000 0.016 0.020
#> GSM152849 1 0.4916 0.68590 0.760 0.000 0.184 0.056
#> GSM152850 1 0.1109 0.85681 0.968 0.000 0.028 0.004
#> GSM152851 4 0.0817 0.82531 0.000 0.000 0.024 0.976
#> GSM152852 3 0.4888 0.48862 0.000 0.000 0.588 0.412
#> GSM152853 4 0.2081 0.77753 0.000 0.000 0.084 0.916
#> GSM152854 3 0.4837 0.59670 0.004 0.000 0.648 0.348
#> GSM152855 4 0.1209 0.82270 0.032 0.000 0.004 0.964
#> GSM153238 1 0.1022 0.85779 0.968 0.000 0.032 0.000
#> GSM153239 4 0.2921 0.71884 0.000 0.000 0.140 0.860
#> GSM153240 4 0.1284 0.82598 0.012 0.000 0.024 0.964
#> GSM153241 1 0.6134 0.57972 0.668 0.000 0.216 0.116
#> GSM153242 3 0.4933 0.65241 0.000 0.016 0.688 0.296
#> GSM153243 1 0.3105 0.79867 0.856 0.004 0.140 0.000
#> GSM153244 4 0.2466 0.76463 0.000 0.004 0.096 0.900
#> GSM153245 4 0.1211 0.81668 0.000 0.000 0.040 0.960
#> GSM153246 3 0.7180 0.35328 0.348 0.000 0.504 0.148
#> GSM153247 1 0.5193 0.72382 0.772 0.024 0.044 0.160
#> GSM153248 1 0.1975 0.84714 0.936 0.016 0.048 0.000
#> GSM153249 4 0.0657 0.82667 0.004 0.000 0.012 0.984
#> GSM153250 1 0.1443 0.85611 0.960 0.004 0.008 0.028
#> GSM153251 4 0.5856 -0.01784 0.000 0.036 0.408 0.556
#> GSM153252 4 0.2021 0.80700 0.056 0.000 0.012 0.932
#> GSM153253 4 0.0921 0.82518 0.000 0.000 0.028 0.972
#> GSM153254 4 0.3982 0.58554 0.000 0.004 0.220 0.776
#> GSM153255 4 0.1182 0.82700 0.016 0.000 0.016 0.968
#> GSM153256 4 0.5222 0.51804 0.280 0.000 0.032 0.688
#> GSM153257 4 0.2521 0.79653 0.064 0.000 0.024 0.912
#> GSM153258 1 0.0779 0.85782 0.980 0.000 0.016 0.004
#> GSM153259 1 0.1302 0.85262 0.956 0.000 0.044 0.000
#> GSM153260 1 0.4428 0.62328 0.720 0.000 0.276 0.004
#> GSM153261 3 0.5990 0.39506 0.336 0.000 0.608 0.056
#> GSM153262 4 0.0707 0.82431 0.000 0.000 0.020 0.980
#> GSM153263 1 0.2174 0.84570 0.928 0.000 0.020 0.052
#> GSM153264 1 0.0524 0.85867 0.988 0.000 0.008 0.004
#> GSM153265 4 0.0592 0.82493 0.000 0.000 0.016 0.984
#> GSM153266 1 0.0817 0.85664 0.976 0.000 0.024 0.000
#> GSM153267 1 0.5174 0.42830 0.620 0.000 0.012 0.368
#> GSM153268 4 0.1302 0.81088 0.000 0.000 0.044 0.956
#> GSM153269 4 0.5161 0.06355 0.476 0.000 0.004 0.520
#> GSM153270 4 0.7505 0.09845 0.324 0.000 0.200 0.476
#> GSM153271 1 0.3940 0.80152 0.848 0.008 0.044 0.100
#> GSM153272 4 0.2563 0.79216 0.072 0.000 0.020 0.908
#> GSM153273 1 0.1004 0.85735 0.972 0.004 0.024 0.000
#> GSM153274 4 0.3908 0.64144 0.212 0.000 0.004 0.784
#> GSM153275 4 0.3108 0.76323 0.112 0.000 0.016 0.872
#> GSM153276 4 0.5936 0.32776 0.380 0.000 0.044 0.576
#> GSM153277 4 0.1389 0.81298 0.000 0.000 0.048 0.952
#> GSM153278 1 0.4214 0.70938 0.780 0.000 0.204 0.016
#> GSM153279 4 0.0592 0.82589 0.000 0.000 0.016 0.984
#> GSM153280 4 0.0921 0.82138 0.000 0.000 0.028 0.972
#> GSM153281 4 0.0592 0.82493 0.000 0.000 0.016 0.984
#> GSM153282 4 0.0592 0.82493 0.000 0.000 0.016 0.984
#> GSM153283 1 0.0779 0.85782 0.980 0.000 0.016 0.004
#> GSM153284 4 0.1722 0.81883 0.048 0.000 0.008 0.944
#> GSM153285 4 0.0707 0.82550 0.000 0.000 0.020 0.980
#> GSM153286 4 0.2999 0.74211 0.132 0.000 0.004 0.864
#> GSM153287 4 0.1406 0.82196 0.016 0.000 0.024 0.960
#> GSM153288 4 0.2522 0.79197 0.076 0.000 0.016 0.908
#> GSM153289 4 0.3925 0.68245 0.176 0.000 0.016 0.808
#> GSM153290 4 0.0817 0.82305 0.000 0.000 0.024 0.976
#> GSM153291 4 0.1388 0.82197 0.028 0.000 0.012 0.960
#> GSM153292 4 0.0817 0.82431 0.000 0.000 0.024 0.976
#> GSM153293 4 0.5790 0.41261 0.340 0.000 0.044 0.616
#> GSM153294 1 0.7394 0.59605 0.644 0.172 0.096 0.088
#> GSM153295 4 0.5273 0.13217 0.456 0.000 0.008 0.536
#> GSM153054 1 0.3117 0.82113 0.880 0.028 0.092 0.000
#> GSM153055 1 0.5119 0.22024 0.556 0.000 0.004 0.440
#> GSM153056 1 0.7062 0.38310 0.572 0.000 0.204 0.224
#> GSM153057 3 0.5030 0.69396 0.024 0.008 0.732 0.236
#> GSM153058 3 0.4595 0.66984 0.000 0.040 0.776 0.184
#> GSM153059 3 0.4352 0.58040 0.020 0.088 0.836 0.056
#> GSM153060 3 0.6065 0.64658 0.080 0.000 0.644 0.276
#> GSM153061 1 0.3257 0.78268 0.844 0.004 0.152 0.000
#> GSM153062 3 0.3970 0.59496 0.000 0.084 0.840 0.076
#> GSM153063 4 0.0707 0.82543 0.000 0.000 0.020 0.980
#> GSM153064 1 0.1489 0.85559 0.952 0.004 0.044 0.000
#> GSM153065 1 0.3831 0.73814 0.792 0.004 0.204 0.000
#> GSM153066 1 0.4990 0.68898 0.756 0.184 0.060 0.000
#> GSM153067 4 0.2214 0.80735 0.044 0.000 0.028 0.928
#> GSM153068 3 0.5803 0.58241 0.216 0.012 0.708 0.064
#> GSM153069 4 0.0657 0.82682 0.004 0.000 0.012 0.984
#> GSM153070 1 0.1182 0.85792 0.968 0.000 0.016 0.016
#> GSM153071 1 0.7511 0.47923 0.584 0.064 0.076 0.276
#> GSM153072 1 0.6556 0.64302 0.692 0.176 0.092 0.040
#> GSM153073 1 0.1811 0.85448 0.948 0.004 0.020 0.028
#> GSM153074 4 0.1042 0.82734 0.020 0.000 0.008 0.972
#> GSM153075 4 0.1824 0.80789 0.004 0.000 0.060 0.936
#> GSM153076 1 0.3156 0.82748 0.884 0.000 0.048 0.068
#> GSM153077 1 0.0564 0.85866 0.988 0.004 0.004 0.004
#> GSM153078 1 0.1209 0.85655 0.964 0.000 0.032 0.004
#> GSM153079 1 0.1389 0.85252 0.952 0.000 0.048 0.000
#> GSM153080 4 0.4986 0.59411 0.216 0.000 0.044 0.740
#> GSM153081 1 0.1022 0.85566 0.968 0.000 0.032 0.000
#> GSM153082 1 0.3970 0.81193 0.856 0.084 0.036 0.024
#> GSM153083 1 0.0707 0.85815 0.980 0.000 0.020 0.000
#> GSM153084 1 0.4237 0.73761 0.808 0.152 0.040 0.000
#> GSM153085 1 0.0712 0.85910 0.984 0.004 0.008 0.004
#> GSM153086 1 0.1661 0.85310 0.944 0.004 0.052 0.000
#> GSM153087 4 0.1209 0.82496 0.032 0.000 0.004 0.964
#> GSM153088 1 0.1305 0.85432 0.960 0.004 0.000 0.036
#> GSM153089 4 0.6732 -0.00336 0.000 0.108 0.336 0.556
#> GSM153090 1 0.4836 0.53351 0.672 0.000 0.008 0.320
#> GSM153091 1 0.0804 0.85890 0.980 0.012 0.008 0.000
#> GSM153092 1 0.1837 0.85490 0.944 0.000 0.028 0.028
#> GSM153093 4 0.0336 0.82815 0.008 0.000 0.000 0.992
#> GSM153094 1 0.0859 0.85874 0.980 0.008 0.008 0.004
#> GSM153095 1 0.1674 0.85471 0.952 0.012 0.032 0.004
#> GSM153096 1 0.1305 0.85690 0.960 0.004 0.036 0.000
#> GSM153097 1 0.0657 0.85861 0.984 0.004 0.012 0.000
#> GSM153098 4 0.6428 0.60913 0.100 0.080 0.096 0.724
#> GSM153099 1 0.4836 0.53635 0.672 0.000 0.008 0.320
#> GSM153100 1 0.3540 0.81857 0.872 0.012 0.032 0.084
#> GSM153101 1 0.5873 0.74125 0.760 0.076 0.088 0.076
#> GSM153102 1 0.2674 0.84420 0.908 0.004 0.068 0.020
#> GSM153103 1 0.0707 0.85795 0.980 0.000 0.020 0.000
#> GSM153104 4 0.1182 0.82463 0.016 0.000 0.016 0.968
#> GSM153106 1 0.4271 0.76904 0.816 0.004 0.040 0.140
#> GSM153107 1 0.0469 0.85825 0.988 0.000 0.012 0.000
#> GSM153108 1 0.6211 0.07681 0.488 0.000 0.052 0.460
#> GSM153109 1 0.1767 0.85432 0.944 0.012 0.044 0.000
#> GSM153110 1 0.1557 0.84995 0.944 0.000 0.056 0.000
#> GSM153111 1 0.1824 0.85161 0.936 0.004 0.060 0.000
#> GSM153112 1 0.4191 0.81127 0.848 0.024 0.060 0.068
#> GSM153113 2 0.4874 0.65527 0.172 0.776 0.044 0.008
#> GSM153114 4 0.0921 0.82233 0.000 0.000 0.028 0.972
#> GSM187532 2 0.4992 0.41967 0.000 0.524 0.476 0.000
#> GSM187533 2 0.4072 0.77762 0.000 0.748 0.252 0.000
#> GSM187534 2 0.2814 0.83832 0.000 0.868 0.132 0.000
#> GSM187535 2 0.4227 0.75190 0.060 0.820 0.120 0.000
#> GSM152906 2 0.3266 0.79747 0.024 0.868 0.108 0.000
#> GSM152907 2 0.1792 0.84973 0.000 0.932 0.068 0.000
#> GSM152908 2 0.3610 0.81390 0.000 0.800 0.200 0.000
#> GSM152909 3 0.4989 -0.35998 0.000 0.472 0.528 0.000
#> GSM152910 2 0.4193 0.76361 0.000 0.732 0.268 0.000
#> GSM152911 2 0.3219 0.82709 0.000 0.836 0.164 0.000
#> GSM152912 2 0.4277 0.75107 0.000 0.720 0.280 0.000
#> GSM152913 2 0.3801 0.80029 0.000 0.780 0.220 0.000
#> GSM152914 2 0.1867 0.84870 0.000 0.928 0.072 0.000
#> GSM152915 2 0.2281 0.84580 0.000 0.904 0.096 0.000
#> GSM152916 2 0.2345 0.84562 0.000 0.900 0.100 0.000
#> GSM152917 2 0.1488 0.84335 0.012 0.956 0.032 0.000
#> GSM152918 2 0.2060 0.83023 0.016 0.932 0.052 0.000
#> GSM152919 2 0.1388 0.83816 0.012 0.960 0.028 0.000
#> GSM152920 2 0.3764 0.80788 0.000 0.784 0.216 0.000
#> GSM152921 2 0.3873 0.79801 0.000 0.772 0.228 0.000
#> GSM152922 2 0.4134 0.77301 0.000 0.740 0.260 0.000
#> GSM152923 2 0.1807 0.83392 0.008 0.940 0.052 0.000
#> GSM152924 2 0.1557 0.84446 0.000 0.944 0.056 0.000
#> GSM152925 2 0.0817 0.84826 0.000 0.976 0.024 0.000
#> GSM152926 2 0.3280 0.79315 0.016 0.860 0.124 0.000
#> GSM152927 2 0.1118 0.84754 0.000 0.964 0.036 0.000
#> GSM152928 2 0.3616 0.78587 0.036 0.852 0.112 0.000
#> GSM152929 2 0.3160 0.79997 0.020 0.872 0.108 0.000
#> GSM152930 2 0.1890 0.83242 0.008 0.936 0.056 0.000
cbind(get_classes(res, k = 5), get_membership(res, k = 5))
#> class entropy silhouette p1 p2 p3 p4 p5
#> GSM152839 1 0.3689 0.7666 0.836 0.000 0.068 0.012 0.084
#> GSM152840 4 0.2921 0.7467 0.000 0.000 0.124 0.856 0.020
#> GSM152841 4 0.1386 0.8073 0.000 0.000 0.032 0.952 0.016
#> GSM152842 1 0.3608 0.7521 0.812 0.000 0.040 0.000 0.148
#> GSM152843 1 0.3774 0.7607 0.804 0.000 0.028 0.008 0.160
#> GSM152844 4 0.3795 0.6620 0.000 0.000 0.192 0.780 0.028
#> GSM152845 3 0.4719 0.6337 0.000 0.168 0.756 0.040 0.036
#> GSM152846 3 0.4240 0.6786 0.000 0.004 0.732 0.240 0.024
#> GSM152847 1 0.3569 0.7539 0.828 0.000 0.068 0.000 0.104
#> GSM152848 1 0.2864 0.7796 0.864 0.000 0.024 0.000 0.112
#> GSM152849 1 0.5086 0.6252 0.688 0.000 0.228 0.004 0.080
#> GSM152850 1 0.2932 0.7752 0.864 0.000 0.032 0.000 0.104
#> GSM152851 4 0.1300 0.8076 0.000 0.000 0.028 0.956 0.016
#> GSM152852 3 0.4725 0.6238 0.000 0.004 0.680 0.280 0.036
#> GSM152853 4 0.3197 0.7279 0.000 0.000 0.140 0.836 0.024
#> GSM152854 3 0.3981 0.6869 0.004 0.008 0.748 0.236 0.004
#> GSM152855 4 0.3256 0.7639 0.084 0.000 0.024 0.864 0.028
#> GSM153238 1 0.3016 0.7712 0.848 0.000 0.020 0.000 0.132
#> GSM153239 4 0.3844 0.6808 0.000 0.000 0.164 0.792 0.044
#> GSM153240 4 0.2378 0.8043 0.048 0.000 0.048 0.904 0.000
#> GSM153241 1 0.4488 0.6893 0.748 0.000 0.188 0.004 0.060
#> GSM153242 3 0.4132 0.6941 0.000 0.032 0.760 0.204 0.004
#> GSM153243 1 0.5336 0.5309 0.648 0.000 0.252 0.000 0.100
#> GSM153244 4 0.3292 0.7405 0.000 0.004 0.120 0.844 0.032
#> GSM153245 4 0.3141 0.7458 0.000 0.000 0.108 0.852 0.040
#> GSM153246 3 0.6909 0.4613 0.292 0.000 0.536 0.068 0.104
#> GSM153247 1 0.7054 0.5770 0.584 0.000 0.128 0.140 0.148
#> GSM153248 1 0.2047 0.8038 0.928 0.000 0.020 0.012 0.040
#> GSM153249 4 0.0290 0.8154 0.000 0.000 0.008 0.992 0.000
#> GSM153250 1 0.1393 0.8013 0.956 0.000 0.008 0.024 0.012
#> GSM153251 4 0.7087 -0.0369 0.000 0.264 0.244 0.468 0.024
#> GSM153252 4 0.2437 0.7917 0.032 0.000 0.060 0.904 0.004
#> GSM153253 4 0.1211 0.8095 0.000 0.000 0.024 0.960 0.016
#> GSM153254 4 0.4492 0.6290 0.000 0.052 0.204 0.740 0.004
#> GSM153255 4 0.0798 0.8148 0.016 0.000 0.008 0.976 0.000
#> GSM153256 4 0.5759 0.3336 0.344 0.000 0.064 0.576 0.016
#> GSM153257 4 0.2173 0.7996 0.016 0.000 0.052 0.920 0.012
#> GSM153258 1 0.2060 0.8012 0.928 0.000 0.012 0.024 0.036
#> GSM153259 1 0.2297 0.8030 0.912 0.000 0.020 0.008 0.060
#> GSM153260 1 0.5001 0.6525 0.700 0.004 0.216 0.000 0.080
#> GSM153261 3 0.5633 0.4164 0.316 0.016 0.612 0.004 0.052
#> GSM153262 4 0.1041 0.8111 0.000 0.000 0.032 0.964 0.004
#> GSM153263 1 0.1764 0.8016 0.940 0.000 0.012 0.036 0.012
#> GSM153264 1 0.0798 0.7980 0.976 0.000 0.008 0.000 0.016
#> GSM153265 4 0.1329 0.8142 0.008 0.000 0.032 0.956 0.004
#> GSM153266 1 0.1617 0.8013 0.948 0.000 0.012 0.020 0.020
#> GSM153267 1 0.4691 0.6943 0.740 0.000 0.028 0.200 0.032
#> GSM153268 4 0.2130 0.7840 0.000 0.000 0.080 0.908 0.012
#> GSM153269 1 0.4873 0.6080 0.676 0.000 0.012 0.280 0.032
#> GSM153270 1 0.5681 0.6633 0.696 0.004 0.048 0.184 0.068
#> GSM153271 1 0.4053 0.7595 0.816 0.000 0.056 0.104 0.024
#> GSM153272 4 0.3257 0.7676 0.052 0.000 0.080 0.860 0.008
#> GSM153273 1 0.1569 0.8033 0.944 0.000 0.004 0.008 0.044
#> GSM153274 4 0.5975 0.2008 0.384 0.004 0.036 0.540 0.036
#> GSM153275 4 0.4766 0.5427 0.272 0.000 0.016 0.688 0.024
#> GSM153276 1 0.4883 0.6542 0.712 0.000 0.020 0.228 0.040
#> GSM153277 4 0.3893 0.7701 0.048 0.000 0.084 0.832 0.036
#> GSM153278 1 0.4549 0.6728 0.728 0.000 0.220 0.004 0.048
#> GSM153279 4 0.0771 0.8159 0.000 0.000 0.020 0.976 0.004
#> GSM153280 4 0.1717 0.8063 0.004 0.000 0.052 0.936 0.008
#> GSM153281 4 0.0955 0.8116 0.000 0.000 0.028 0.968 0.004
#> GSM153282 4 0.1740 0.7968 0.000 0.000 0.056 0.932 0.012
#> GSM153283 1 0.0854 0.7993 0.976 0.000 0.008 0.004 0.012
#> GSM153284 4 0.1106 0.8164 0.024 0.000 0.012 0.964 0.000
#> GSM153285 4 0.1300 0.8117 0.000 0.000 0.028 0.956 0.016
#> GSM153286 4 0.4552 0.6398 0.184 0.000 0.052 0.752 0.012
#> GSM153287 4 0.1356 0.8122 0.004 0.000 0.028 0.956 0.012
#> GSM153288 4 0.3727 0.7314 0.104 0.000 0.068 0.824 0.004
#> GSM153289 4 0.5700 0.5282 0.236 0.000 0.092 0.652 0.020
#> GSM153290 4 0.1041 0.8124 0.000 0.000 0.032 0.964 0.004
#> GSM153291 4 0.1399 0.8097 0.020 0.000 0.028 0.952 0.000
#> GSM153292 4 0.0693 0.8147 0.000 0.000 0.012 0.980 0.008
#> GSM153293 4 0.5881 0.2874 0.356 0.000 0.064 0.560 0.020
#> GSM153294 1 0.7002 0.5970 0.616 0.016 0.144 0.140 0.084
#> GSM153295 1 0.5325 0.2381 0.524 0.000 0.020 0.436 0.020
#> GSM153054 1 0.5014 0.4351 0.540 0.000 0.024 0.004 0.432
#> GSM153055 1 0.5118 0.6894 0.724 0.004 0.036 0.196 0.040
#> GSM153056 1 0.5987 0.6046 0.664 0.000 0.196 0.072 0.068
#> GSM153057 3 0.7233 0.6563 0.048 0.160 0.588 0.172 0.032
#> GSM153058 3 0.4308 0.6777 0.000 0.128 0.788 0.072 0.012
#> GSM153059 3 0.4600 0.5796 0.036 0.212 0.736 0.000 0.016
#> GSM153060 3 0.6392 0.6807 0.112 0.004 0.652 0.160 0.072
#> GSM153061 1 0.4876 0.6212 0.700 0.000 0.220 0.000 0.080
#> GSM153062 3 0.4198 0.6381 0.000 0.172 0.780 0.024 0.024
#> GSM153063 4 0.1965 0.7950 0.000 0.000 0.052 0.924 0.024
#> GSM153064 1 0.2331 0.8021 0.908 0.000 0.016 0.008 0.068
#> GSM153065 1 0.5073 0.6146 0.688 0.000 0.212 0.000 0.100
#> GSM153066 1 0.7203 0.2214 0.464 0.148 0.052 0.000 0.336
#> GSM153067 4 0.2644 0.7811 0.012 0.000 0.088 0.888 0.012
#> GSM153068 3 0.5591 0.5560 0.256 0.040 0.656 0.000 0.048
#> GSM153069 4 0.0451 0.8149 0.000 0.000 0.004 0.988 0.008
#> GSM153070 1 0.1026 0.8004 0.968 0.000 0.004 0.004 0.024
#> GSM153071 1 0.7725 0.3756 0.476 0.000 0.136 0.252 0.136
#> GSM153072 1 0.7159 0.5423 0.560 0.004 0.120 0.088 0.228
#> GSM153073 1 0.3632 0.7856 0.836 0.000 0.028 0.024 0.112
#> GSM153074 4 0.2677 0.7845 0.064 0.000 0.020 0.896 0.020
#> GSM153075 4 0.4786 0.7057 0.132 0.004 0.056 0.772 0.036
#> GSM153076 1 0.3454 0.7812 0.856 0.000 0.044 0.076 0.024
#> GSM153077 1 0.1329 0.7993 0.956 0.000 0.008 0.004 0.032
#> GSM153078 1 0.1915 0.7918 0.928 0.000 0.040 0.000 0.032
#> GSM153079 1 0.2074 0.7996 0.920 0.000 0.044 0.000 0.036
#> GSM153080 4 0.5450 0.2389 0.392 0.004 0.032 0.560 0.012
#> GSM153081 1 0.1836 0.7999 0.932 0.000 0.032 0.000 0.036
#> GSM153082 1 0.5545 0.7337 0.740 0.016 0.112 0.072 0.060
#> GSM153083 1 0.1300 0.8013 0.956 0.000 0.016 0.000 0.028
#> GSM153084 1 0.6143 0.4421 0.576 0.320 0.044 0.000 0.060
#> GSM153085 1 0.3012 0.7924 0.880 0.004 0.040 0.008 0.068
#> GSM153086 1 0.2448 0.7964 0.892 0.000 0.020 0.000 0.088
#> GSM153087 4 0.1612 0.8127 0.016 0.000 0.024 0.948 0.012
#> GSM153088 1 0.1588 0.8017 0.948 0.000 0.016 0.028 0.008
#> GSM153089 4 0.6882 0.0303 0.000 0.240 0.256 0.488 0.016
#> GSM153090 1 0.4219 0.7167 0.772 0.000 0.020 0.184 0.024
#> GSM153091 1 0.2680 0.7993 0.904 0.008 0.016 0.024 0.048
#> GSM153092 1 0.3762 0.7840 0.848 0.008 0.044 0.028 0.072
#> GSM153093 4 0.0510 0.8158 0.016 0.000 0.000 0.984 0.000
#> GSM153094 1 0.2404 0.7983 0.916 0.004 0.024 0.016 0.040
#> GSM153095 1 0.3053 0.8037 0.872 0.000 0.044 0.008 0.076
#> GSM153096 1 0.2304 0.8010 0.908 0.000 0.020 0.004 0.068
#> GSM153097 1 0.0771 0.8006 0.976 0.000 0.000 0.004 0.020
#> GSM153098 4 0.4541 0.7025 0.056 0.004 0.140 0.780 0.020
#> GSM153099 1 0.4208 0.7032 0.760 0.000 0.020 0.204 0.016
#> GSM153100 1 0.4111 0.7687 0.824 0.004 0.044 0.088 0.040
#> GSM153101 1 0.6741 0.6268 0.636 0.008 0.120 0.124 0.112
#> GSM153102 1 0.6591 0.5111 0.592 0.020 0.256 0.020 0.112
#> GSM153103 1 0.1012 0.7975 0.968 0.000 0.012 0.000 0.020
#> GSM153104 4 0.1168 0.8116 0.000 0.000 0.032 0.960 0.008
#> GSM153106 1 0.6369 0.7091 0.696 0.044 0.088 0.080 0.092
#> GSM153107 1 0.3172 0.7939 0.876 0.004 0.028 0.024 0.068
#> GSM153108 1 0.6860 0.3259 0.496 0.008 0.100 0.360 0.036
#> GSM153109 1 0.3415 0.7865 0.848 0.012 0.024 0.004 0.112
#> GSM153110 1 0.2208 0.7965 0.908 0.000 0.020 0.000 0.072
#> GSM153111 1 0.2777 0.7869 0.864 0.000 0.016 0.000 0.120
#> GSM153112 1 0.5031 0.7424 0.768 0.004 0.072 0.092 0.064
#> GSM153113 2 0.6003 0.4400 0.072 0.712 0.124 0.028 0.064
#> GSM153114 4 0.3310 0.7902 0.036 0.000 0.056 0.868 0.040
#> GSM187532 2 0.4163 0.5542 0.000 0.740 0.228 0.000 0.032
#> GSM187533 2 0.2054 0.7135 0.000 0.920 0.052 0.000 0.028
#> GSM187534 2 0.2104 0.7019 0.000 0.916 0.024 0.000 0.060
#> GSM187535 5 0.4347 0.8051 0.024 0.256 0.004 0.000 0.716
#> GSM152906 5 0.3630 0.7904 0.016 0.204 0.000 0.000 0.780
#> GSM152907 2 0.4679 -0.1168 0.000 0.596 0.008 0.008 0.388
#> GSM152908 2 0.0807 0.7174 0.000 0.976 0.012 0.000 0.012
#> GSM152909 2 0.3596 0.5656 0.000 0.776 0.212 0.000 0.012
#> GSM152910 2 0.0955 0.7160 0.000 0.968 0.028 0.000 0.004
#> GSM152911 2 0.2006 0.6997 0.000 0.916 0.012 0.000 0.072
#> GSM152912 2 0.1282 0.7084 0.000 0.952 0.044 0.000 0.004
#> GSM152913 2 0.2685 0.6825 0.000 0.880 0.028 0.000 0.092
#> GSM152914 2 0.3884 0.3223 0.000 0.708 0.004 0.000 0.288
#> GSM152915 2 0.3143 0.5307 0.000 0.796 0.000 0.000 0.204
#> GSM152916 5 0.4659 0.4688 0.000 0.488 0.012 0.000 0.500
#> GSM152917 2 0.4415 -0.3208 0.000 0.552 0.004 0.000 0.444
#> GSM152918 5 0.4448 0.4902 0.000 0.480 0.004 0.000 0.516
#> GSM152919 2 0.4452 -0.4987 0.000 0.500 0.004 0.000 0.496
#> GSM152920 2 0.1522 0.7070 0.000 0.944 0.044 0.000 0.012
#> GSM152921 2 0.0671 0.7186 0.000 0.980 0.016 0.000 0.004
#> GSM152922 2 0.0880 0.7168 0.000 0.968 0.032 0.000 0.000
#> GSM152923 5 0.3838 0.8266 0.000 0.280 0.004 0.000 0.716
#> GSM152924 5 0.4088 0.8133 0.000 0.304 0.008 0.000 0.688
#> GSM152925 5 0.4510 0.6286 0.000 0.432 0.008 0.000 0.560
#> GSM152926 5 0.3579 0.8203 0.004 0.240 0.000 0.000 0.756
#> GSM152927 5 0.4251 0.7993 0.000 0.316 0.012 0.000 0.672
#> GSM152928 5 0.3280 0.7622 0.012 0.176 0.000 0.000 0.812
#> GSM152929 5 0.3596 0.8026 0.012 0.212 0.000 0.000 0.776
#> GSM152930 5 0.3684 0.8263 0.000 0.280 0.000 0.000 0.720
cbind(get_classes(res, k = 6), get_membership(res, k = 6))
#> class entropy silhouette p1 p2 p3 p4 p5 p6
#> GSM152839 1 0.4046 0.6027 0.748 0.000 0.036 0.016 NA 0.000
#> GSM152840 4 0.2909 0.7011 0.000 0.000 0.136 0.836 NA 0.000
#> GSM152841 4 0.1461 0.7715 0.000 0.000 0.044 0.940 NA 0.000
#> GSM152842 1 0.4552 0.5283 0.668 0.000 0.024 0.000 NA 0.028
#> GSM152843 1 0.4620 0.5422 0.664 0.004 0.016 0.000 NA 0.032
#> GSM152844 4 0.3978 0.5438 0.000 0.000 0.268 0.700 NA 0.000
#> GSM152845 3 0.4094 0.5511 0.000 0.076 0.780 0.024 NA 0.000
#> GSM152846 3 0.2911 0.6111 0.000 0.008 0.856 0.100 NA 0.000
#> GSM152847 1 0.4460 0.5535 0.700 0.000 0.040 0.000 NA 0.020
#> GSM152848 1 0.4080 0.5896 0.704 0.000 0.016 0.000 NA 0.016
#> GSM152849 1 0.5711 0.3798 0.544 0.000 0.204 0.000 NA 0.004
#> GSM152850 1 0.3812 0.5685 0.712 0.000 0.016 0.000 NA 0.004
#> GSM152851 4 0.1682 0.7688 0.000 0.000 0.052 0.928 NA 0.000
#> GSM152852 3 0.3382 0.6062 0.000 0.004 0.820 0.112 NA 0.000
#> GSM152853 4 0.2988 0.6929 0.000 0.000 0.144 0.828 NA 0.000
#> GSM152854 3 0.4366 0.5762 0.000 0.012 0.708 0.232 NA 0.000
#> GSM152855 4 0.3887 0.7007 0.104 0.000 0.004 0.780 NA 0.000
#> GSM153238 1 0.4452 0.5481 0.664 0.000 0.028 0.000 NA 0.016
#> GSM153239 4 0.4982 0.4641 0.008 0.000 0.228 0.656 NA 0.000
#> GSM153240 4 0.2743 0.7741 0.060 0.000 0.028 0.880 NA 0.000
#> GSM153241 1 0.5360 0.4708 0.604 0.000 0.116 0.012 NA 0.000
#> GSM153242 3 0.4383 0.5925 0.000 0.028 0.732 0.196 NA 0.000
#> GSM153243 1 0.6484 0.3561 0.536 0.000 0.208 0.000 NA 0.072
#> GSM153244 4 0.4234 0.6522 0.000 0.048 0.132 0.772 NA 0.000
#> GSM153245 4 0.3946 0.6333 0.004 0.000 0.152 0.768 NA 0.000
#> GSM153246 1 0.7136 -0.1441 0.332 0.008 0.328 0.032 NA 0.008
#> GSM153247 1 0.6493 0.4219 0.504 0.024 0.028 0.084 NA 0.012
#> GSM153248 1 0.3718 0.6651 0.800 0.000 0.008 0.028 NA 0.016
#> GSM153249 4 0.1251 0.7897 0.008 0.000 0.012 0.956 NA 0.000
#> GSM153250 1 0.2147 0.6855 0.912 0.000 0.012 0.032 NA 0.000
#> GSM153251 4 0.6880 -0.0626 0.000 0.372 0.128 0.408 NA 0.004
#> GSM153252 4 0.2307 0.7816 0.024 0.000 0.012 0.900 NA 0.000
#> GSM153253 4 0.1320 0.7744 0.000 0.000 0.036 0.948 NA 0.000
#> GSM153254 4 0.5031 0.5450 0.004 0.180 0.132 0.676 NA 0.000
#> GSM153255 4 0.0951 0.7886 0.008 0.000 0.004 0.968 NA 0.000
#> GSM153256 4 0.5248 0.4494 0.292 0.000 0.004 0.600 NA 0.004
#> GSM153257 4 0.1921 0.7836 0.012 0.000 0.012 0.920 NA 0.000
#> GSM153258 1 0.2468 0.6848 0.884 0.000 0.008 0.012 NA 0.004
#> GSM153259 1 0.3434 0.6695 0.808 0.000 0.004 0.000 NA 0.048
#> GSM153260 1 0.5727 0.4033 0.520 0.020 0.108 0.000 NA 0.000
#> GSM153261 3 0.6525 0.3139 0.264 0.020 0.436 0.004 NA 0.000
#> GSM153262 4 0.1793 0.7874 0.004 0.000 0.032 0.928 NA 0.000
#> GSM153263 1 0.3282 0.6814 0.844 0.000 0.008 0.052 NA 0.008
#> GSM153264 1 0.0858 0.6803 0.968 0.000 0.000 0.000 NA 0.004
#> GSM153265 4 0.1405 0.7857 0.004 0.000 0.024 0.948 NA 0.000
#> GSM153266 1 0.1956 0.6797 0.908 0.000 0.000 0.008 NA 0.004
#> GSM153267 1 0.5322 0.5021 0.604 0.000 0.004 0.244 NA 0.000
#> GSM153268 4 0.2039 0.7531 0.000 0.000 0.076 0.904 NA 0.000
#> GSM153269 1 0.5540 0.3291 0.520 0.000 0.004 0.348 NA 0.000
#> GSM153270 1 0.6813 0.3896 0.496 0.004 0.076 0.236 NA 0.000
#> GSM153271 1 0.4262 0.6611 0.768 0.004 0.016 0.088 NA 0.000
#> GSM153272 4 0.2577 0.7758 0.040 0.000 0.016 0.888 NA 0.000
#> GSM153273 1 0.1976 0.6834 0.920 0.000 0.008 0.008 NA 0.008
#> GSM153274 4 0.5751 0.3020 0.312 0.000 0.008 0.524 NA 0.000
#> GSM153275 4 0.4777 0.5443 0.240 0.000 0.004 0.664 NA 0.000
#> GSM153276 1 0.5081 0.4740 0.608 0.000 0.008 0.300 NA 0.000
#> GSM153277 4 0.4871 0.6853 0.080 0.000 0.108 0.732 NA 0.000
#> GSM153278 1 0.5286 0.5256 0.620 0.000 0.136 0.000 NA 0.008
#> GSM153279 4 0.2285 0.7872 0.008 0.000 0.028 0.900 NA 0.000
#> GSM153280 4 0.1793 0.7844 0.004 0.000 0.036 0.928 NA 0.000
#> GSM153281 4 0.0922 0.7845 0.004 0.000 0.024 0.968 NA 0.000
#> GSM153282 4 0.1367 0.7731 0.000 0.000 0.044 0.944 NA 0.000
#> GSM153283 1 0.1333 0.6792 0.944 0.000 0.000 0.008 NA 0.000
#> GSM153284 4 0.2547 0.7728 0.036 0.000 0.000 0.880 NA 0.004
#> GSM153285 4 0.1549 0.7725 0.000 0.000 0.044 0.936 NA 0.000
#> GSM153286 4 0.4400 0.6525 0.164 0.000 0.008 0.732 NA 0.000
#> GSM153287 4 0.1555 0.7858 0.008 0.000 0.012 0.940 NA 0.000
#> GSM153288 4 0.3475 0.7400 0.084 0.000 0.012 0.824 NA 0.000
#> GSM153289 4 0.6041 0.4696 0.216 0.004 0.024 0.564 NA 0.000
#> GSM153290 4 0.1138 0.7843 0.004 0.000 0.024 0.960 NA 0.000
#> GSM153291 4 0.1767 0.7847 0.020 0.000 0.012 0.932 NA 0.000
#> GSM153292 4 0.0665 0.7883 0.004 0.000 0.008 0.980 NA 0.000
#> GSM153293 4 0.5667 0.4093 0.284 0.000 0.012 0.572 NA 0.004
#> GSM153294 1 0.6105 0.5493 0.564 0.008 0.024 0.100 NA 0.012
#> GSM153295 4 0.5370 0.0564 0.428 0.000 0.008 0.480 NA 0.000
#> GSM153054 1 0.5914 0.3873 0.524 0.004 0.004 0.000 NA 0.260
#> GSM153055 1 0.5731 0.4655 0.556 0.000 0.008 0.240 NA 0.000
#> GSM153056 1 0.6431 0.3826 0.544 0.000 0.172 0.072 NA 0.000
#> GSM153057 3 0.7835 0.4740 0.036 0.208 0.420 0.200 NA 0.000
#> GSM153058 3 0.5771 0.5942 0.012 0.128 0.664 0.068 NA 0.000
#> GSM153059 3 0.4584 0.5337 0.036 0.160 0.736 0.000 NA 0.000
#> GSM153060 3 0.7896 0.4299 0.184 0.028 0.352 0.140 NA 0.000
#> GSM153061 1 0.5626 0.4305 0.592 0.004 0.140 0.000 NA 0.012
#> GSM153062 3 0.4780 0.5738 0.000 0.128 0.708 0.016 NA 0.000
#> GSM153063 4 0.2641 0.7499 0.004 0.000 0.072 0.876 NA 0.000
#> GSM153064 1 0.3705 0.6718 0.816 0.000 0.008 0.012 NA 0.064
#> GSM153065 1 0.5452 0.4748 0.616 0.000 0.140 0.000 NA 0.016
#> GSM153066 1 0.7738 0.1465 0.376 0.144 0.016 0.000 NA 0.200
#> GSM153067 4 0.2230 0.7787 0.016 0.000 0.016 0.904 NA 0.000
#> GSM153068 3 0.6967 0.3712 0.252 0.068 0.412 0.000 NA 0.000
#> GSM153069 4 0.0551 0.7871 0.004 0.000 0.008 0.984 NA 0.000
#> GSM153070 1 0.2679 0.6698 0.872 0.000 0.008 0.012 NA 0.008
#> GSM153071 1 0.6978 0.3337 0.444 0.020 0.020 0.192 NA 0.012
#> GSM153072 1 0.6366 0.5198 0.548 0.008 0.024 0.044 NA 0.068
#> GSM153073 1 0.4264 0.5783 0.688 0.004 0.012 0.004 NA 0.012
#> GSM153074 4 0.3052 0.7466 0.068 0.000 0.004 0.848 NA 0.000
#> GSM153075 4 0.4392 0.6869 0.120 0.000 0.032 0.760 NA 0.000
#> GSM153076 1 0.3175 0.6819 0.852 0.000 0.012 0.056 NA 0.004
#> GSM153077 1 0.3122 0.6584 0.816 0.000 0.004 0.020 NA 0.000
#> GSM153078 1 0.2692 0.6472 0.840 0.000 0.012 0.000 NA 0.000
#> GSM153079 1 0.3845 0.6427 0.756 0.000 0.028 0.000 NA 0.012
#> GSM153080 4 0.6690 0.2149 0.244 0.012 0.032 0.480 NA 0.000
#> GSM153081 1 0.2377 0.6768 0.868 0.000 0.004 0.004 NA 0.000
#> GSM153082 1 0.5496 0.5529 0.604 0.008 0.024 0.060 NA 0.004
#> GSM153083 1 0.2376 0.6794 0.884 0.000 0.008 0.000 NA 0.012
#> GSM153084 2 0.6083 0.1135 0.316 0.476 0.012 0.000 NA 0.000
#> GSM153085 1 0.5148 0.5478 0.612 0.024 0.024 0.020 NA 0.000
#> GSM153086 1 0.3624 0.6636 0.812 0.000 0.016 0.000 NA 0.060
#> GSM153087 4 0.1873 0.7863 0.008 0.000 0.020 0.924 NA 0.000
#> GSM153088 1 0.2715 0.6784 0.872 0.000 0.012 0.028 NA 0.000
#> GSM153089 4 0.8137 -0.1252 0.000 0.240 0.160 0.372 NA 0.048
#> GSM153090 1 0.5228 0.5138 0.620 0.000 0.008 0.252 NA 0.000
#> GSM153091 1 0.3505 0.6660 0.816 0.004 0.004 0.024 NA 0.012
#> GSM153092 1 0.5252 0.5663 0.640 0.008 0.032 0.052 NA 0.000
#> GSM153093 4 0.1088 0.7880 0.016 0.000 0.000 0.960 NA 0.000
#> GSM153094 1 0.3657 0.6419 0.768 0.000 0.012 0.012 NA 0.004
#> GSM153095 1 0.5364 0.5528 0.608 0.004 0.020 0.016 NA 0.040
#> GSM153096 1 0.2775 0.6805 0.876 0.000 0.012 0.004 NA 0.032
#> GSM153097 1 0.1453 0.6811 0.944 0.000 0.008 0.000 NA 0.008
#> GSM153098 4 0.5082 0.6296 0.052 0.004 0.036 0.696 NA 0.008
#> GSM153099 1 0.4663 0.5399 0.664 0.000 0.000 0.244 NA 0.000
#> GSM153100 1 0.4552 0.6022 0.700 0.000 0.000 0.128 NA 0.000
#> GSM153101 1 0.7201 0.3989 0.448 0.012 0.024 0.096 NA 0.076
#> GSM153102 3 0.6985 0.2174 0.256 0.020 0.380 0.012 NA 0.008
#> GSM153103 1 0.1644 0.6782 0.920 0.000 0.000 0.000 NA 0.004
#> GSM153104 4 0.1577 0.7870 0.008 0.000 0.016 0.940 NA 0.000
#> GSM153106 1 0.6664 0.3073 0.420 0.028 0.060 0.076 NA 0.000
#> GSM153107 1 0.4837 0.5930 0.656 0.004 0.020 0.032 NA 0.004
#> GSM153108 1 0.6772 0.1899 0.368 0.004 0.020 0.304 NA 0.004
#> GSM153109 1 0.5451 0.5374 0.612 0.016 0.056 0.004 NA 0.016
#> GSM153110 1 0.2803 0.6767 0.864 0.000 0.004 0.000 NA 0.048
#> GSM153111 1 0.3127 0.6697 0.840 0.000 0.004 0.000 NA 0.100
#> GSM153112 1 0.6037 0.5332 0.592 0.004 0.020 0.148 NA 0.012
#> GSM153113 2 0.7198 0.3653 0.116 0.480 0.020 0.012 NA 0.076
#> GSM153114 4 0.3716 0.7491 0.044 0.000 0.068 0.820 NA 0.000
#> GSM187532 2 0.5373 0.5934 0.000 0.672 0.176 0.000 NA 0.064
#> GSM187533 2 0.4192 0.6877 0.000 0.776 0.028 0.000 NA 0.088
#> GSM187534 2 0.5126 0.6131 0.000 0.668 0.016 0.000 NA 0.152
#> GSM187535 6 0.2106 0.8097 0.000 0.064 0.000 0.000 NA 0.904
#> GSM152906 6 0.1049 0.8048 0.000 0.008 0.000 0.000 NA 0.960
#> GSM152907 6 0.3607 0.5652 0.000 0.348 0.000 0.000 NA 0.652
#> GSM152908 2 0.1737 0.7270 0.000 0.932 0.008 0.000 NA 0.040
#> GSM152909 2 0.3300 0.6788 0.000 0.832 0.116 0.000 NA 0.020
#> GSM152910 2 0.1074 0.7298 0.000 0.960 0.000 0.000 NA 0.028
#> GSM152911 2 0.2669 0.6659 0.000 0.836 0.000 0.000 NA 0.156
#> GSM152912 2 0.1074 0.7298 0.000 0.960 0.000 0.000 NA 0.028
#> GSM152913 2 0.3692 0.5613 0.000 0.736 0.012 0.000 NA 0.244
#> GSM152914 2 0.4183 -0.1309 0.000 0.508 0.000 0.000 NA 0.480
#> GSM152915 2 0.3911 0.2847 0.000 0.624 0.000 0.000 NA 0.368
#> GSM152916 6 0.3394 0.7134 0.000 0.236 0.000 0.000 NA 0.752
#> GSM152917 6 0.3965 0.4700 0.000 0.388 0.000 0.000 NA 0.604
#> GSM152918 6 0.3508 0.6554 0.000 0.292 0.000 0.000 NA 0.704
#> GSM152919 6 0.3390 0.6524 0.000 0.296 0.000 0.000 NA 0.704
#> GSM152920 2 0.2245 0.7205 0.000 0.908 0.016 0.000 NA 0.036
#> GSM152921 2 0.1901 0.7260 0.000 0.924 0.008 0.000 NA 0.040
#> GSM152922 2 0.1116 0.7294 0.000 0.960 0.004 0.000 NA 0.028
#> GSM152923 6 0.0790 0.8244 0.000 0.032 0.000 0.000 NA 0.968
#> GSM152924 6 0.1007 0.8243 0.000 0.044 0.000 0.000 NA 0.956
#> GSM152925 6 0.3133 0.7398 0.000 0.212 0.000 0.000 NA 0.780
#> GSM152926 6 0.1003 0.8148 0.000 0.016 0.000 0.000 NA 0.964
#> GSM152927 6 0.0937 0.8244 0.000 0.040 0.000 0.000 NA 0.960
#> GSM152928 6 0.0547 0.8027 0.000 0.000 0.000 0.000 NA 0.980
#> GSM152929 6 0.0717 0.8113 0.000 0.008 0.000 0.000 NA 0.976
#> GSM152930 6 0.1151 0.8228 0.000 0.032 0.000 0.000 NA 0.956
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 tissue(p) k
#> ATC:NMF 162 2.59e-20 2
#> ATC:NMF 146 1.08e-29 3
#> ATC:NMF 147 9.00e-28 4
#> ATC:NMF 143 3.75e-24 5
#> ATC:NMF 126 2.60e-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.
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