Date: 2019-12-25 21:21:31 CET, cola version: 1.3.2
Document is loading...
All available functions which can be applied to this res_list object:
res_list
#> A 'ConsensusPartitionList' object with 24 methods.
#> On a matrix with 51776 rows and 143 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] 51776 143
The density distribution for each sample is visualized as in one column in the following heatmap. The clustering is based on the distance which is the Kolmogorov-Smirnov statistic between two distributions.
library(ComplexHeatmap)
densityHeatmap(mat, top_annotation = HeatmapAnnotation(df = get_anno(res_list),
col = get_anno_col(res_list)), ylab = "value", cluster_columns = TRUE, show_column_names = FALSE,
mc.cores = 4)
Folowing table shows the best k (number of partitions) for each combination
of top-value methods and partition methods. Clicking on the method name in
the table goes to the section for a single combination of methods.
The cola vignette explains the definition of the metrics used for determining the best number of partitions.
suggest_best_k(res_list)
| The best k | 1-PAC | Mean silhouette | Concordance | Optional k | ||
|---|---|---|---|---|---|---|
| ATC:kmeans | 4 | 1.000 | 0.950 | 0.969 | ** | 2 |
| ATC:pam | 4 | 0.972 | 0.962 | 0.983 | ** | 2 |
| ATC:mclust | 2 | 0.941 | 0.950 | 0.978 | * | |
| ATC:skmeans | 5 | 0.929 | 0.871 | 0.941 | * | 2,3,4 |
| CV:pam | 2 | 0.917 | 0.935 | 0.957 | * | |
| ATC:NMF | 2 | 0.914 | 0.943 | 0.975 | * | |
| CV:NMF | 3 | 0.911 | 0.910 | 0.961 | * | |
| MAD:mclust | 4 | 0.848 | 0.851 | 0.921 | ||
| MAD:NMF | 3 | 0.825 | 0.877 | 0.948 | ||
| MAD:skmeans | 3 | 0.822 | 0.835 | 0.930 | ||
| CV:skmeans | 3 | 0.792 | 0.846 | 0.932 | ||
| SD:NMF | 3 | 0.790 | 0.846 | 0.938 | ||
| CV:kmeans | 3 | 0.719 | 0.852 | 0.913 | ||
| CV:mclust | 2 | 0.681 | 0.880 | 0.937 | ||
| ATC:hclust | 3 | 0.620 | 0.828 | 0.900 | ||
| SD:mclust | 2 | 0.612 | 0.776 | 0.899 | ||
| MAD:kmeans | 2 | 0.551 | 0.900 | 0.898 | ||
| SD:kmeans | 2 | 0.505 | 0.866 | 0.885 | ||
| SD:skmeans | 2 | 0.503 | 0.848 | 0.898 | ||
| MAD:pam | 2 | 0.494 | 0.811 | 0.913 | ||
| SD:pam | 2 | 0.378 | 0.843 | 0.887 | ||
| SD:hclust | 3 | 0.304 | 0.601 | 0.802 | ||
| CV:hclust | 3 | 0.211 | 0.491 | 0.697 | ||
| MAD:hclust | 2 | 0.203 | 0.699 | 0.818 |
**: 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 0.501 0.822 0.902 0.473 0.514 0.514
#> CV:NMF 2 0.591 0.825 0.922 0.445 0.576 0.576
#> MAD:NMF 2 0.553 0.822 0.912 0.496 0.505 0.505
#> ATC:NMF 2 0.914 0.943 0.975 0.280 0.719 0.719
#> SD:skmeans 2 0.503 0.848 0.898 0.498 0.498 0.498
#> CV:skmeans 2 0.551 0.671 0.856 0.492 0.510 0.510
#> MAD:skmeans 2 0.493 0.881 0.906 0.500 0.498 0.498
#> ATC:skmeans 2 1.000 0.974 0.989 0.483 0.514 0.514
#> SD:mclust 2 0.612 0.776 0.899 0.433 0.523 0.523
#> CV:mclust 2 0.681 0.880 0.937 0.468 0.527 0.527
#> MAD:mclust 2 0.558 0.724 0.881 0.430 0.571 0.571
#> ATC:mclust 2 0.941 0.950 0.978 0.389 0.628 0.628
#> SD:kmeans 2 0.505 0.866 0.885 0.442 0.556 0.556
#> CV:kmeans 2 0.484 0.810 0.894 0.426 0.582 0.582
#> MAD:kmeans 2 0.551 0.900 0.898 0.466 0.538 0.538
#> ATC:kmeans 2 1.000 0.964 0.987 0.445 0.561 0.561
#> SD:pam 2 0.378 0.843 0.887 0.459 0.534 0.534
#> CV:pam 2 0.917 0.935 0.957 0.423 0.582 0.582
#> MAD:pam 2 0.494 0.811 0.913 0.463 0.527 0.527
#> ATC:pam 2 1.000 0.972 0.990 0.452 0.546 0.546
#> SD:hclust 2 0.174 0.490 0.704 0.397 0.501 0.501
#> CV:hclust 2 0.631 0.774 0.907 0.282 0.728 0.728
#> MAD:hclust 2 0.203 0.699 0.818 0.441 0.502 0.502
#> ATC:hclust 2 0.767 0.928 0.962 0.293 0.738 0.738
get_stats(res_list, k = 3)
#> k 1-PAC mean_silhouette concordance area_increased Rand Jaccard
#> SD:NMF 3 0.790 0.846 0.938 0.327 0.723 0.524
#> CV:NMF 3 0.911 0.910 0.961 0.465 0.676 0.480
#> MAD:NMF 3 0.825 0.877 0.948 0.267 0.798 0.628
#> ATC:NMF 3 0.423 0.626 0.807 1.011 0.614 0.481
#> SD:skmeans 3 0.691 0.812 0.914 0.324 0.767 0.567
#> CV:skmeans 3 0.792 0.846 0.932 0.354 0.705 0.479
#> MAD:skmeans 3 0.822 0.835 0.930 0.315 0.778 0.582
#> ATC:skmeans 3 1.000 0.963 0.985 0.240 0.883 0.773
#> SD:mclust 3 0.409 0.643 0.809 0.244 0.634 0.463
#> CV:mclust 3 0.253 0.455 0.657 0.275 0.733 0.567
#> MAD:mclust 3 0.292 0.365 0.649 0.257 0.654 0.465
#> ATC:mclust 3 0.393 0.687 0.783 0.480 0.731 0.581
#> SD:kmeans 3 0.573 0.715 0.859 0.402 0.732 0.554
#> CV:kmeans 3 0.719 0.852 0.913 0.489 0.677 0.494
#> MAD:kmeans 3 0.501 0.643 0.809 0.355 0.685 0.478
#> ATC:kmeans 3 0.745 0.906 0.947 0.399 0.679 0.492
#> SD:pam 3 0.693 0.809 0.914 0.414 0.762 0.576
#> CV:pam 3 0.456 0.679 0.836 0.550 0.722 0.535
#> MAD:pam 3 0.518 0.738 0.864 0.401 0.675 0.455
#> ATC:pam 3 0.551 0.796 0.870 0.362 0.609 0.409
#> SD:hclust 3 0.304 0.601 0.802 0.384 0.695 0.507
#> CV:hclust 3 0.211 0.491 0.697 0.972 0.617 0.487
#> MAD:hclust 3 0.362 0.694 0.836 0.273 0.909 0.821
#> ATC:hclust 3 0.620 0.828 0.900 1.071 0.640 0.512
get_stats(res_list, k = 4)
#> k 1-PAC mean_silhouette concordance area_increased Rand Jaccard
#> SD:NMF 4 0.707 0.772 0.890 0.1615 0.791 0.510
#> CV:NMF 4 0.517 0.624 0.795 0.1180 0.875 0.664
#> MAD:NMF 4 0.777 0.819 0.915 0.1568 0.780 0.495
#> ATC:NMF 4 0.328 0.584 0.749 0.0675 0.819 0.646
#> SD:skmeans 4 0.698 0.740 0.835 0.1252 0.865 0.635
#> CV:skmeans 4 0.740 0.727 0.854 0.1221 0.825 0.533
#> MAD:skmeans 4 0.737 0.793 0.892 0.1270 0.855 0.611
#> ATC:skmeans 4 0.919 0.858 0.940 0.0659 0.940 0.853
#> SD:mclust 4 0.372 0.388 0.655 0.2247 0.702 0.462
#> CV:mclust 4 0.455 0.607 0.771 0.1281 0.707 0.450
#> MAD:mclust 4 0.848 0.851 0.921 0.3044 0.727 0.423
#> ATC:mclust 4 0.345 0.511 0.664 0.1289 0.811 0.576
#> SD:kmeans 4 0.516 0.380 0.642 0.1461 0.851 0.638
#> CV:kmeans 4 0.567 0.520 0.757 0.1466 0.736 0.410
#> MAD:kmeans 4 0.553 0.581 0.782 0.1405 0.780 0.479
#> ATC:kmeans 4 1.000 0.950 0.969 0.1436 0.725 0.414
#> SD:pam 4 0.704 0.817 0.899 0.1459 0.867 0.643
#> CV:pam 4 0.481 0.441 0.688 0.1274 0.817 0.533
#> MAD:pam 4 0.626 0.734 0.863 0.1437 0.809 0.514
#> ATC:pam 4 0.972 0.962 0.983 0.1420 0.715 0.414
#> SD:hclust 4 0.331 0.575 0.775 0.1131 0.943 0.868
#> CV:hclust 4 0.287 0.299 0.601 0.1671 0.758 0.512
#> MAD:hclust 4 0.399 0.614 0.771 0.1178 0.969 0.928
#> ATC:hclust 4 0.628 0.750 0.874 0.0510 0.983 0.955
get_stats(res_list, k = 5)
#> k 1-PAC mean_silhouette concordance area_increased Rand Jaccard
#> SD:NMF 5 0.630 0.626 0.812 0.0705 0.839 0.498
#> CV:NMF 5 0.513 0.501 0.702 0.0797 0.858 0.547
#> MAD:NMF 5 0.659 0.609 0.815 0.0724 0.863 0.557
#> ATC:NMF 5 0.339 0.422 0.693 0.1350 0.740 0.521
#> SD:skmeans 5 0.785 0.752 0.871 0.0628 0.861 0.548
#> CV:skmeans 5 0.644 0.582 0.771 0.0533 0.941 0.778
#> MAD:skmeans 5 0.718 0.645 0.815 0.0636 0.861 0.549
#> ATC:skmeans 5 0.929 0.871 0.941 0.0447 0.977 0.936
#> SD:mclust 5 0.614 0.714 0.832 0.1009 0.699 0.346
#> CV:mclust 5 0.444 0.639 0.757 0.0654 0.796 0.496
#> MAD:mclust 5 0.659 0.720 0.842 0.0694 0.918 0.738
#> ATC:mclust 5 0.422 0.454 0.727 0.0358 0.842 0.593
#> SD:kmeans 5 0.651 0.749 0.823 0.0806 0.791 0.440
#> CV:kmeans 5 0.621 0.516 0.688 0.0690 0.829 0.494
#> MAD:kmeans 5 0.628 0.625 0.778 0.0790 0.884 0.621
#> ATC:kmeans 5 0.784 0.806 0.835 0.0748 0.853 0.540
#> SD:pam 5 0.718 0.802 0.904 0.0237 0.979 0.921
#> CV:pam 5 0.554 0.519 0.692 0.0680 0.853 0.525
#> MAD:pam 5 0.625 0.505 0.717 0.0432 0.886 0.607
#> ATC:pam 5 0.733 0.463 0.761 0.0916 0.937 0.797
#> SD:hclust 5 0.403 0.486 0.701 0.1254 0.869 0.675
#> CV:hclust 5 0.366 0.447 0.662 0.0750 0.787 0.504
#> MAD:hclust 5 0.432 0.494 0.701 0.1303 0.856 0.651
#> ATC:hclust 5 0.662 0.764 0.841 0.1000 0.915 0.770
get_stats(res_list, k = 6)
#> k 1-PAC mean_silhouette concordance area_increased Rand Jaccard
#> SD:NMF 6 0.687 0.608 0.788 0.0495 0.929 0.696
#> CV:NMF 6 0.602 0.494 0.707 0.0494 0.902 0.597
#> MAD:NMF 6 0.722 0.646 0.813 0.0531 0.886 0.540
#> ATC:NMF 6 0.420 0.450 0.698 0.0873 0.818 0.563
#> SD:skmeans 6 0.793 0.698 0.850 0.0377 0.961 0.822
#> CV:skmeans 6 0.655 0.577 0.728 0.0375 0.928 0.707
#> MAD:skmeans 6 0.780 0.665 0.845 0.0396 0.953 0.797
#> ATC:skmeans 6 0.839 0.837 0.904 0.0454 0.987 0.963
#> SD:mclust 6 0.707 0.702 0.858 0.0861 0.800 0.424
#> CV:mclust 6 0.472 0.471 0.660 0.0597 0.823 0.465
#> MAD:mclust 6 0.765 0.756 0.883 0.0602 0.904 0.643
#> ATC:mclust 6 0.505 0.398 0.700 0.1009 0.867 0.620
#> SD:kmeans 6 0.684 0.606 0.769 0.0558 0.931 0.721
#> CV:kmeans 6 0.670 0.612 0.760 0.0471 0.869 0.530
#> MAD:kmeans 6 0.689 0.542 0.755 0.0500 0.890 0.573
#> ATC:kmeans 6 0.758 0.753 0.857 0.0417 0.984 0.927
#> SD:pam 6 0.713 0.728 0.839 0.0526 0.953 0.807
#> CV:pam 6 0.551 0.446 0.650 0.0331 0.961 0.822
#> MAD:pam 6 0.700 0.739 0.846 0.0399 0.895 0.589
#> ATC:pam 6 0.825 0.797 0.892 0.0618 0.866 0.532
#> SD:hclust 6 0.431 0.434 0.674 0.0676 0.938 0.806
#> CV:hclust 6 0.416 0.396 0.626 0.0471 0.972 0.901
#> MAD:hclust 6 0.489 0.433 0.642 0.0711 0.870 0.589
#> ATC:hclust 6 0.720 0.769 0.875 0.0267 0.990 0.964
Following heatmap plots the partition for each combination of methods and the lightness correspond to the silhouette scores for samples in each method. On top the consensus subgroup is inferred from all methods by taking the mean silhouette scores as weight.
collect_stats(res_list, k = 2)
collect_stats(res_list, k = 3)
collect_stats(res_list, k = 4)
collect_stats(res_list, k = 5)
collect_stats(res_list, k = 6)
Collect partitions from all methods:
collect_classes(res_list, k = 2)
collect_classes(res_list, k = 3)
collect_classes(res_list, k = 4)
collect_classes(res_list, k = 5)
collect_classes(res_list, k = 6)
Overlap of top rows from different top-row methods:
top_rows_overlap(res_list, top_n = 1000, method = "euler")
top_rows_overlap(res_list, top_n = 2000, method = "euler")
top_rows_overlap(res_list, top_n = 3000, method = "euler")
top_rows_overlap(res_list, top_n = 4000, method = "euler")
top_rows_overlap(res_list, top_n = 5000, method = "euler")
Also visualize the correspondance of rankings between different top-row methods:
top_rows_overlap(res_list, top_n = 1000, method = "correspondance")
top_rows_overlap(res_list, top_n = 2000, method = "correspondance")
top_rows_overlap(res_list, top_n = 3000, method = "correspondance")
top_rows_overlap(res_list, top_n = 4000, method = "correspondance")
top_rows_overlap(res_list, top_n = 5000, method = "correspondance")
Heatmaps of the top rows:
top_rows_heatmap(res_list, top_n = 1000)
top_rows_heatmap(res_list, top_n = 2000)
top_rows_heatmap(res_list, top_n = 3000)
top_rows_heatmap(res_list, top_n = 4000)
top_rows_heatmap(res_list, top_n = 5000)
Test correlation between subgroups and known annotations. If the known annotation is numeric, one-way ANOVA test is applied, and if the known annotation is discrete, chi-squared contingency table test is applied.
test_to_known_factors(res_list, k = 2)
#> n disease.state(p) k
#> SD:NMF 133 6.11e-04 2
#> CV:NMF 133 2.90e-01 2
#> MAD:NMF 133 2.19e-04 2
#> ATC:NMF 139 4.58e-03 2
#> SD:skmeans 141 4.17e-05 2
#> CV:skmeans 134 6.01e-01 2
#> MAD:skmeans 143 4.87e-05 2
#> ATC:skmeans 141 8.61e-04 2
#> SD:mclust 121 4.87e-01 2
#> CV:mclust 139 2.60e-02 2
#> MAD:mclust 117 3.18e-01 2
#> ATC:mclust 141 8.73e-01 2
#> SD:kmeans 143 9.79e-04 2
#> CV:kmeans 139 5.53e-01 2
#> MAD:kmeans 142 4.74e-04 2
#> ATC:kmeans 139 2.55e-03 2
#> SD:pam 142 2.16e-03 2
#> CV:pam 140 7.36e-01 2
#> MAD:pam 134 9.38e-05 2
#> ATC:pam 141 1.97e-03 2
#> SD:hclust 98 1.18e-04 2
#> CV:hclust 126 4.58e-01 2
#> MAD:hclust 127 4.37e-04 2
#> ATC:hclust 142 2.81e-03 2
test_to_known_factors(res_list, k = 3)
#> n disease.state(p) k
#> SD:NMF 133 4.18e-04 3
#> CV:NMF 139 3.80e-04 3
#> MAD:NMF 135 2.08e-04 3
#> ATC:NMF 112 1.71e-05 3
#> SD:skmeans 131 2.01e-04 3
#> CV:skmeans 136 2.66e-03 3
#> MAD:skmeans 129 1.18e-04 3
#> ATC:skmeans 142 1.42e-04 3
#> SD:mclust 119 1.23e-01 3
#> CV:mclust 90 1.89e-02 3
#> MAD:mclust 63 1.94e-03 3
#> ATC:mclust 129 3.15e-01 3
#> SD:kmeans 124 1.16e-03 3
#> CV:kmeans 141 6.81e-03 3
#> MAD:kmeans 110 2.04e-04 3
#> ATC:kmeans 140 6.25e-05 3
#> SD:pam 129 4.20e-03 3
#> CV:pam 120 1.09e-03 3
#> MAD:pam 128 2.76e-04 3
#> ATC:pam 143 1.51e-07 3
#> SD:hclust 111 2.86e-03 3
#> CV:hclust 89 2.43e-05 3
#> MAD:hclust 126 1.35e-02 3
#> ATC:hclust 138 2.21e-06 3
test_to_known_factors(res_list, k = 4)
#> n disease.state(p) k
#> SD:NMF 129 9.87e-05 4
#> CV:NMF 110 1.15e-04 4
#> MAD:NMF 133 3.83e-05 4
#> ATC:NMF 106 1.42e-03 4
#> SD:skmeans 128 5.43e-06 4
#> CV:skmeans 125 1.43e-05 4
#> MAD:skmeans 135 6.00e-06 4
#> ATC:skmeans 125 1.65e-05 4
#> SD:mclust 67 6.17e-02 4
#> CV:mclust 111 1.33e-01 4
#> MAD:mclust 135 8.43e-04 4
#> ATC:mclust 99 4.28e-02 4
#> SD:kmeans 55 7.21e-02 4
#> CV:kmeans 82 1.27e-02 4
#> MAD:kmeans 103 6.34e-06 4
#> ATC:kmeans 140 3.61e-06 4
#> SD:pam 137 1.83e-05 4
#> CV:pam 63 8.34e-04 4
#> MAD:pam 133 2.93e-05 4
#> ATC:pam 142 1.52e-05 4
#> SD:hclust 111 3.30e-03 4
#> CV:hclust 33 2.46e-01 4
#> MAD:hclust 112 2.41e-04 4
#> ATC:hclust 133 9.04e-06 4
test_to_known_factors(res_list, k = 5)
#> n disease.state(p) k
#> SD:NMF 109 3.96e-05 5
#> CV:NMF 83 1.68e-03 5
#> MAD:NMF 96 1.17e-04 5
#> ATC:NMF 64 1.96e-03 5
#> SD:skmeans 129 1.87e-04 5
#> CV:skmeans 103 2.14e-06 5
#> MAD:skmeans 114 2.04e-05 5
#> ATC:skmeans 133 2.10e-04 5
#> SD:mclust 132 5.68e-04 5
#> CV:mclust 119 6.12e-02 5
#> MAD:mclust 130 8.54e-04 5
#> ATC:mclust 80 6.82e-02 5
#> SD:kmeans 133 3.10e-04 5
#> CV:kmeans 89 4.87e-03 5
#> MAD:kmeans 119 6.34e-05 5
#> ATC:kmeans 127 1.22e-05 5
#> SD:pam 137 4.24e-05 5
#> CV:pam 78 3.86e-04 5
#> MAD:pam 86 1.60e-05 5
#> ATC:pam 79 2.33e-05 5
#> SD:hclust 69 1.05e-03 5
#> CV:hclust 75 8.58e-04 5
#> MAD:hclust 91 9.78e-06 5
#> ATC:hclust 133 8.78e-06 5
test_to_known_factors(res_list, k = 6)
#> n disease.state(p) k
#> SD:NMF 105 3.09e-05 6
#> CV:NMF 85 5.49e-05 6
#> MAD:NMF 111 3.40e-04 6
#> ATC:NMF 83 3.88e-06 6
#> SD:skmeans 114 5.18e-05 6
#> CV:skmeans 105 3.52e-05 6
#> MAD:skmeans 114 1.08e-04 6
#> ATC:skmeans 136 6.10e-05 6
#> SD:mclust 121 3.29e-05 6
#> CV:mclust 84 7.43e-04 6
#> MAD:mclust 128 1.04e-03 6
#> ATC:mclust 67 5.01e-02 6
#> SD:kmeans 90 5.88e-04 6
#> CV:kmeans 104 1.38e-06 6
#> MAD:kmeans 79 6.33e-06 6
#> ATC:kmeans 131 9.91e-06 6
#> SD:pam 131 1.45e-04 6
#> CV:pam 71 7.49e-04 6
#> MAD:pam 127 3.22e-05 6
#> ATC:pam 135 2.03e-04 6
#> SD:hclust 62 2.88e-04 6
#> CV:hclust 58 7.13e-03 6
#> MAD:hclust 71 5.32e-04 6
#> ATC:hclust 135 1.23e-05 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 51776 rows and 143 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 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 0.174 0.490 0.704 0.3966 0.501 0.501
#> 3 3 0.304 0.601 0.802 0.3838 0.695 0.507
#> 4 4 0.331 0.575 0.775 0.1131 0.943 0.868
#> 5 5 0.403 0.486 0.701 0.1254 0.869 0.675
#> 6 6 0.431 0.434 0.674 0.0676 0.938 0.806
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
#> GSM550785 1 0.1414 0.63334 0.980 0.020
#> GSM550786 2 0.9993 0.33123 0.484 0.516
#> GSM550788 2 0.9732 0.73712 0.404 0.596
#> GSM550789 2 0.9710 0.73851 0.400 0.600
#> GSM550790 1 0.1184 0.63241 0.984 0.016
#> GSM550791 1 0.2603 0.63447 0.956 0.044
#> GSM550792 1 0.9944 -0.46246 0.544 0.456
#> GSM550796 2 0.9710 0.73851 0.400 0.600
#> GSM550797 2 0.9710 0.73851 0.400 0.600
#> GSM550799 2 0.6343 0.38293 0.160 0.840
#> GSM550800 1 0.9988 -0.54695 0.520 0.480
#> GSM550801 2 0.9710 0.73851 0.400 0.600
#> GSM550804 2 0.9933 0.70170 0.452 0.548
#> GSM550806 2 0.8608 0.35641 0.284 0.716
#> GSM550807 2 0.9710 0.73851 0.400 0.600
#> GSM550808 2 0.9522 0.73478 0.372 0.628
#> GSM550809 1 0.4690 0.61667 0.900 0.100
#> GSM550810 2 0.9522 0.73478 0.372 0.628
#> GSM550811 1 0.5737 0.58516 0.864 0.136
#> GSM550813 2 0.9909 0.71093 0.444 0.556
#> GSM550814 2 0.9881 0.71892 0.436 0.564
#> GSM550815 2 0.9710 0.73851 0.400 0.600
#> GSM550816 2 0.9970 0.66401 0.468 0.532
#> GSM550817 2 0.6343 0.29054 0.160 0.840
#> GSM550818 2 0.6247 0.28676 0.156 0.844
#> GSM550819 2 0.9977 0.63590 0.472 0.528
#> GSM550820 1 0.4022 0.62791 0.920 0.080
#> GSM550821 2 0.9686 0.65517 0.396 0.604
#> GSM550822 2 0.9710 0.73851 0.400 0.600
#> GSM550826 1 0.7056 0.57845 0.808 0.192
#> GSM550832 2 0.9580 0.73690 0.380 0.620
#> GSM550833 2 0.9732 0.73742 0.404 0.596
#> GSM550835 2 0.8763 0.67727 0.296 0.704
#> GSM550836 1 0.9710 0.34045 0.600 0.400
#> GSM550837 2 0.9323 0.72077 0.348 0.652
#> GSM550838 1 0.4690 0.61667 0.900 0.100
#> GSM550841 2 0.5842 0.32745 0.140 0.860
#> GSM550842 2 0.8713 0.67575 0.292 0.708
#> GSM550846 1 0.9323 -0.00831 0.652 0.348
#> GSM550849 1 0.7299 0.49464 0.796 0.204
#> GSM550850 1 0.0938 0.63333 0.988 0.012
#> GSM550851 2 0.9323 0.72077 0.348 0.652
#> GSM550852 1 0.9944 -0.46246 0.544 0.456
#> GSM550853 2 0.9896 0.71679 0.440 0.560
#> GSM550855 2 0.9896 0.71679 0.440 0.560
#> GSM550856 2 0.9909 0.71309 0.444 0.556
#> GSM550861 2 0.9815 0.73070 0.420 0.580
#> GSM550863 1 0.6247 0.54955 0.844 0.156
#> GSM550864 2 0.9896 0.71620 0.440 0.560
#> GSM550866 2 0.9909 0.71309 0.444 0.556
#> GSM550867 1 0.1184 0.62818 0.984 0.016
#> GSM550885 1 0.1184 0.62818 0.984 0.016
#> GSM550886 2 0.9044 0.55861 0.320 0.680
#> GSM550887 2 0.9710 0.73851 0.400 0.600
#> GSM550889 1 0.8909 0.17157 0.692 0.308
#> GSM550894 2 0.9522 0.73478 0.372 0.628
#> GSM550897 1 0.4161 0.62586 0.916 0.084
#> GSM550903 2 0.9850 0.72607 0.428 0.572
#> GSM550905 2 0.9323 0.72119 0.348 0.652
#> GSM550906 2 0.9710 0.73851 0.400 0.600
#> GSM550907 2 0.7139 0.19109 0.196 0.804
#> GSM550909 2 0.9850 0.71905 0.428 0.572
#> GSM550911 2 0.7139 0.17010 0.196 0.804
#> GSM550913 2 0.9710 0.73851 0.400 0.600
#> GSM550915 1 0.6531 0.53535 0.832 0.168
#> GSM550917 2 0.9933 0.70170 0.452 0.548
#> GSM550919 1 0.6148 0.55934 0.848 0.152
#> GSM550921 1 0.9710 0.34045 0.600 0.400
#> GSM550924 2 0.9608 0.58510 0.384 0.616
#> GSM550926 2 0.9896 0.71679 0.440 0.560
#> GSM550927 2 0.9710 0.73851 0.400 0.600
#> GSM550787 1 0.5842 0.58545 0.860 0.140
#> GSM550793 1 0.7745 0.48349 0.772 0.228
#> GSM550794 1 0.9944 -0.46246 0.544 0.456
#> GSM550795 1 0.5059 0.60029 0.888 0.112
#> GSM550798 1 0.4431 0.58200 0.908 0.092
#> GSM550803 1 0.1184 0.62818 0.984 0.016
#> GSM550805 1 0.4161 0.62858 0.916 0.084
#> GSM550823 1 0.9209 0.04521 0.664 0.336
#> GSM550824 1 0.1184 0.62818 0.984 0.016
#> GSM550825 1 0.5946 0.54937 0.856 0.144
#> GSM550827 1 0.9522 -0.16232 0.628 0.372
#> GSM550828 1 0.3879 0.62797 0.924 0.076
#> GSM550829 1 0.5946 0.54937 0.856 0.144
#> GSM550830 1 0.9209 0.04521 0.664 0.336
#> GSM550834 1 0.1414 0.63504 0.980 0.020
#> GSM550839 2 0.8763 0.50591 0.296 0.704
#> GSM550840 1 0.4022 0.63030 0.920 0.080
#> GSM550843 2 0.8144 0.46008 0.252 0.748
#> GSM550844 1 0.4161 0.62858 0.916 0.084
#> GSM550845 2 0.9933 0.70055 0.452 0.548
#> GSM550848 1 0.6148 0.55934 0.848 0.152
#> GSM550854 1 0.1184 0.62818 0.984 0.016
#> GSM550857 1 0.9710 0.34045 0.600 0.400
#> GSM550858 1 0.3431 0.63537 0.936 0.064
#> GSM550859 1 0.1184 0.62818 0.984 0.016
#> GSM550862 1 0.3431 0.63537 0.936 0.064
#> GSM550865 1 0.6247 0.54955 0.844 0.156
#> GSM550868 1 0.9170 0.06177 0.668 0.332
#> GSM550869 1 0.9754 0.32744 0.592 0.408
#> GSM550870 2 0.9933 0.70055 0.452 0.548
#> GSM550871 2 0.8763 0.50591 0.296 0.704
#> GSM550872 1 0.6247 0.54955 0.844 0.156
#> GSM550873 1 0.9944 -0.46246 0.544 0.456
#> GSM550874 2 0.9896 0.71679 0.440 0.560
#> GSM550876 2 0.8499 0.39393 0.276 0.724
#> GSM550877 2 0.9896 0.71679 0.440 0.560
#> GSM550878 2 0.7056 0.32386 0.192 0.808
#> GSM550879 1 0.4022 0.62298 0.920 0.080
#> GSM550882 1 0.8909 0.42111 0.692 0.308
#> GSM550888 1 0.9710 0.34045 0.600 0.400
#> GSM550890 1 0.9323 -0.00831 0.652 0.348
#> GSM550891 1 0.9850 0.33606 0.572 0.428
#> GSM550892 1 0.6148 0.55505 0.848 0.152
#> GSM550893 1 0.9896 -0.40713 0.560 0.440
#> GSM550895 1 0.9552 -0.15165 0.624 0.376
#> GSM550896 1 0.9815 -0.33599 0.580 0.420
#> GSM550898 1 0.1184 0.62818 0.984 0.016
#> GSM550899 2 0.9933 0.70057 0.452 0.548
#> GSM550900 1 0.9427 -0.07752 0.640 0.360
#> GSM550901 1 0.6048 0.56464 0.852 0.148
#> GSM550902 1 0.7745 0.48349 0.772 0.228
#> GSM550904 1 0.4022 0.62791 0.920 0.080
#> GSM550908 1 0.9710 0.34045 0.600 0.400
#> GSM550912 2 0.9909 0.71093 0.444 0.556
#> GSM550914 1 0.9323 -0.00831 0.652 0.348
#> GSM550918 2 0.9933 0.70170 0.452 0.548
#> GSM550922 2 0.8207 0.62714 0.256 0.744
#> GSM550923 1 0.2043 0.61986 0.968 0.032
#> GSM550925 1 0.4815 0.61120 0.896 0.104
#> GSM550802 2 0.9993 0.61048 0.484 0.516
#> GSM550812 2 0.9993 0.61048 0.484 0.516
#> GSM550831 1 0.1414 0.63504 0.980 0.020
#> GSM550847 1 0.1184 0.62818 0.984 0.016
#> GSM550860 1 0.9933 0.23200 0.548 0.452
#> GSM550875 1 0.4161 0.62858 0.916 0.084
#> GSM550880 1 0.7602 0.43730 0.780 0.220
#> GSM550881 1 0.9087 0.40296 0.676 0.324
#> GSM550883 1 0.9087 0.40296 0.676 0.324
#> GSM550884 1 0.9881 -0.38630 0.564 0.436
#> GSM550910 2 0.8386 0.31440 0.268 0.732
#> GSM550916 1 0.2603 0.63461 0.956 0.044
#> GSM550920 2 0.9209 0.54606 0.336 0.664
cbind(get_classes(res, k = 3), get_membership(res, k = 3))
#> class entropy silhouette p1 p2 p3
#> GSM550785 1 0.2096 0.716984 0.944 0.052 0.004
#> GSM550786 2 0.8233 0.483565 0.272 0.612 0.116
#> GSM550788 2 0.0237 0.775810 0.004 0.996 0.000
#> GSM550789 2 0.0000 0.774381 0.000 1.000 0.000
#> GSM550790 1 0.0829 0.694535 0.984 0.012 0.004
#> GSM550791 1 0.5656 0.694813 0.728 0.264 0.008
#> GSM550792 2 0.5536 0.646544 0.236 0.752 0.012
#> GSM550796 2 0.0000 0.774381 0.000 1.000 0.000
#> GSM550797 2 0.0000 0.774381 0.000 1.000 0.000
#> GSM550799 2 0.6442 0.122806 0.004 0.564 0.432
#> GSM550800 2 0.4172 0.711270 0.156 0.840 0.004
#> GSM550801 2 0.0237 0.775472 0.004 0.996 0.000
#> GSM550804 2 0.2165 0.781340 0.064 0.936 0.000
#> GSM550806 2 0.8384 0.163844 0.088 0.520 0.392
#> GSM550807 2 0.0237 0.775472 0.004 0.996 0.000
#> GSM550808 2 0.1399 0.769256 0.004 0.968 0.028
#> GSM550809 1 0.4353 0.742001 0.836 0.156 0.008
#> GSM550810 2 0.1399 0.769256 0.004 0.968 0.028
#> GSM550811 1 0.5012 0.728534 0.788 0.204 0.008
#> GSM550813 2 0.1989 0.784027 0.048 0.948 0.004
#> GSM550814 2 0.2492 0.785258 0.048 0.936 0.016
#> GSM550815 2 0.0000 0.774381 0.000 1.000 0.000
#> GSM550816 2 0.2796 0.768443 0.092 0.908 0.000
#> GSM550817 3 0.6299 0.118759 0.000 0.476 0.524
#> GSM550818 3 0.6295 0.129295 0.000 0.472 0.528
#> GSM550819 2 0.5036 0.715568 0.172 0.808 0.020
#> GSM550820 1 0.4099 0.743606 0.852 0.140 0.008
#> GSM550821 2 0.5650 0.731270 0.108 0.808 0.084
#> GSM550822 2 0.0000 0.774381 0.000 1.000 0.000
#> GSM550826 1 0.6853 0.687553 0.712 0.224 0.064
#> GSM550832 2 0.1129 0.771857 0.004 0.976 0.020
#> GSM550833 2 0.0237 0.776004 0.004 0.996 0.000
#> GSM550835 2 0.3755 0.713572 0.008 0.872 0.120
#> GSM550836 3 0.1411 0.661484 0.036 0.000 0.964
#> GSM550837 2 0.2384 0.757813 0.008 0.936 0.056
#> GSM550838 1 0.4353 0.742001 0.836 0.156 0.008
#> GSM550841 2 0.6307 -0.072389 0.000 0.512 0.488
#> GSM550842 2 0.3619 0.695848 0.000 0.864 0.136
#> GSM550846 2 0.6274 0.046846 0.456 0.544 0.000
#> GSM550849 1 0.6869 0.412360 0.560 0.424 0.016
#> GSM550850 1 0.1129 0.700432 0.976 0.020 0.004
#> GSM550851 2 0.2384 0.757813 0.008 0.936 0.056
#> GSM550852 2 0.5493 0.650537 0.232 0.756 0.012
#> GSM550853 2 0.1529 0.782889 0.040 0.960 0.000
#> GSM550855 2 0.1529 0.782889 0.040 0.960 0.000
#> GSM550856 2 0.2356 0.778236 0.072 0.928 0.000
#> GSM550861 2 0.0892 0.779977 0.020 0.980 0.000
#> GSM550863 1 0.5810 0.622085 0.664 0.336 0.000
#> GSM550864 2 0.1860 0.783892 0.052 0.948 0.000
#> GSM550866 2 0.2356 0.778236 0.072 0.928 0.000
#> GSM550867 1 0.0237 0.681505 0.996 0.000 0.004
#> GSM550885 1 0.0829 0.689420 0.984 0.012 0.004
#> GSM550886 2 0.6968 0.607756 0.080 0.716 0.204
#> GSM550887 2 0.0000 0.774381 0.000 1.000 0.000
#> GSM550889 2 0.6126 0.332922 0.352 0.644 0.004
#> GSM550894 2 0.1163 0.767562 0.000 0.972 0.028
#> GSM550897 1 0.5785 0.676194 0.696 0.300 0.004
#> GSM550903 2 0.1289 0.783128 0.032 0.968 0.000
#> GSM550905 2 0.2384 0.758009 0.008 0.936 0.056
#> GSM550906 2 0.0000 0.774381 0.000 1.000 0.000
#> GSM550907 3 0.6126 0.321054 0.000 0.400 0.600
#> GSM550909 2 0.4015 0.764526 0.096 0.876 0.028
#> GSM550911 3 0.6062 0.355158 0.000 0.384 0.616
#> GSM550913 2 0.0000 0.774381 0.000 1.000 0.000
#> GSM550915 1 0.6168 0.497860 0.588 0.412 0.000
#> GSM550917 2 0.2066 0.781921 0.060 0.940 0.000
#> GSM550919 1 0.6062 0.559703 0.616 0.384 0.000
#> GSM550921 3 0.1289 0.660733 0.032 0.000 0.968
#> GSM550924 2 0.6679 0.659657 0.100 0.748 0.152
#> GSM550926 2 0.1529 0.782889 0.040 0.960 0.000
#> GSM550927 2 0.0000 0.774381 0.000 1.000 0.000
#> GSM550787 1 0.6796 0.575303 0.632 0.344 0.024
#> GSM550793 3 0.7396 0.126518 0.480 0.032 0.488
#> GSM550794 2 0.5578 0.641531 0.240 0.748 0.012
#> GSM550795 1 0.4978 0.733055 0.780 0.216 0.004
#> GSM550798 1 0.2537 0.643351 0.920 0.000 0.080
#> GSM550803 1 0.0237 0.681505 0.996 0.000 0.004
#> GSM550805 1 0.5896 0.678878 0.700 0.292 0.008
#> GSM550823 2 0.6081 0.379835 0.344 0.652 0.004
#> GSM550824 1 0.0237 0.681505 0.996 0.000 0.004
#> GSM550825 1 0.5335 0.457787 0.760 0.008 0.232
#> GSM550827 2 0.6267 0.119981 0.452 0.548 0.000
#> GSM550828 1 0.3816 0.747002 0.852 0.148 0.000
#> GSM550829 1 0.5335 0.457787 0.760 0.008 0.232
#> GSM550830 2 0.6081 0.379835 0.344 0.652 0.004
#> GSM550834 1 0.2682 0.730372 0.920 0.076 0.004
#> GSM550839 2 0.8042 0.503352 0.116 0.636 0.248
#> GSM550840 1 0.5797 0.690848 0.712 0.280 0.008
#> GSM550843 2 0.8311 0.417497 0.112 0.596 0.292
#> GSM550844 1 0.5896 0.678878 0.700 0.292 0.008
#> GSM550845 2 0.2165 0.780923 0.064 0.936 0.000
#> GSM550848 1 0.6062 0.559703 0.616 0.384 0.000
#> GSM550854 1 0.0237 0.681505 0.996 0.000 0.004
#> GSM550857 3 0.1411 0.661484 0.036 0.000 0.964
#> GSM550858 1 0.3030 0.735906 0.904 0.092 0.004
#> GSM550859 1 0.0237 0.681505 0.996 0.000 0.004
#> GSM550862 1 0.3030 0.735906 0.904 0.092 0.004
#> GSM550865 1 0.5810 0.622085 0.664 0.336 0.000
#> GSM550868 2 0.6489 0.046108 0.456 0.540 0.004
#> GSM550869 1 0.9758 0.194944 0.412 0.356 0.232
#> GSM550870 2 0.2165 0.780923 0.064 0.936 0.000
#> GSM550871 2 0.8042 0.503352 0.116 0.636 0.248
#> GSM550872 1 0.5785 0.627144 0.668 0.332 0.000
#> GSM550873 2 0.5493 0.650537 0.232 0.756 0.012
#> GSM550874 2 0.1529 0.782889 0.040 0.960 0.000
#> GSM550876 2 0.7996 0.218933 0.068 0.552 0.380
#> GSM550877 2 0.1529 0.782889 0.040 0.960 0.000
#> GSM550878 2 0.7665 -0.000992 0.044 0.500 0.456
#> GSM550879 1 0.4121 0.745594 0.832 0.168 0.000
#> GSM550882 3 0.8155 0.378053 0.332 0.088 0.580
#> GSM550888 3 0.1411 0.661484 0.036 0.000 0.964
#> GSM550890 2 0.6274 0.046846 0.456 0.544 0.000
#> GSM550891 3 0.0237 0.653374 0.004 0.000 0.996
#> GSM550892 1 0.5760 0.633631 0.672 0.328 0.000
#> GSM550893 2 0.4883 0.645863 0.208 0.788 0.004
#> GSM550895 2 0.5690 0.511717 0.288 0.708 0.004
#> GSM550896 2 0.5158 0.612256 0.232 0.764 0.004
#> GSM550898 1 0.0237 0.681505 0.996 0.000 0.004
#> GSM550899 2 0.2066 0.781648 0.060 0.940 0.000
#> GSM550900 2 0.5929 0.446893 0.320 0.676 0.004
#> GSM550901 1 0.6045 0.567540 0.620 0.380 0.000
#> GSM550902 3 0.7396 0.126518 0.480 0.032 0.488
#> GSM550904 1 0.4033 0.742697 0.856 0.136 0.008
#> GSM550908 3 0.1411 0.661484 0.036 0.000 0.964
#> GSM550912 2 0.1989 0.784027 0.048 0.948 0.004
#> GSM550914 2 0.6274 0.046846 0.456 0.544 0.000
#> GSM550918 2 0.2165 0.781340 0.064 0.936 0.000
#> GSM550922 2 0.4465 0.660213 0.004 0.820 0.176
#> GSM550923 1 0.0892 0.674005 0.980 0.000 0.020
#> GSM550925 1 0.6129 0.635645 0.668 0.324 0.008
#> GSM550802 2 0.5486 0.691773 0.196 0.780 0.024
#> GSM550812 2 0.5536 0.688086 0.200 0.776 0.024
#> GSM550831 1 0.2682 0.730372 0.920 0.076 0.004
#> GSM550847 1 0.0237 0.681505 0.996 0.000 0.004
#> GSM550860 2 0.9857 -0.092946 0.368 0.380 0.252
#> GSM550875 1 0.5896 0.678878 0.700 0.292 0.008
#> GSM550880 1 0.6111 0.506382 0.604 0.396 0.000
#> GSM550881 3 0.6587 0.421866 0.352 0.016 0.632
#> GSM550883 3 0.6587 0.421866 0.352 0.016 0.632
#> GSM550884 2 0.6096 0.584021 0.280 0.704 0.016
#> GSM550910 2 0.7169 0.043549 0.024 0.520 0.456
#> GSM550916 1 0.2096 0.718637 0.944 0.052 0.004
#> GSM550920 2 0.7153 0.601658 0.092 0.708 0.200
cbind(get_classes(res, k = 4), get_membership(res, k = 4))
#> class entropy silhouette p1 p2 p3 p4
#> GSM550785 1 0.3107 0.6792 0.884 0.080 0.000 0.036
#> GSM550786 2 0.7768 0.3161 0.260 0.524 0.016 0.200
#> GSM550788 2 0.0817 0.7425 0.000 0.976 0.000 0.024
#> GSM550789 2 0.1118 0.7389 0.000 0.964 0.000 0.036
#> GSM550790 1 0.2463 0.6531 0.924 0.036 0.008 0.032
#> GSM550791 1 0.5623 0.6491 0.676 0.276 0.004 0.044
#> GSM550792 2 0.5430 0.6386 0.204 0.732 0.008 0.056
#> GSM550796 2 0.1118 0.7389 0.000 0.964 0.000 0.036
#> GSM550797 2 0.1118 0.7389 0.000 0.964 0.000 0.036
#> GSM550799 4 0.6775 0.5718 0.012 0.348 0.076 0.564
#> GSM550800 2 0.3280 0.6951 0.124 0.860 0.000 0.016
#> GSM550801 2 0.1209 0.7415 0.004 0.964 0.000 0.032
#> GSM550804 2 0.1118 0.7487 0.036 0.964 0.000 0.000
#> GSM550806 4 0.7279 0.5789 0.068 0.308 0.048 0.576
#> GSM550807 2 0.1209 0.7415 0.004 0.964 0.000 0.032
#> GSM550808 2 0.3355 0.6674 0.004 0.836 0.000 0.160
#> GSM550809 1 0.4400 0.6984 0.816 0.136 0.012 0.036
#> GSM550810 2 0.3355 0.6674 0.004 0.836 0.000 0.160
#> GSM550811 1 0.5083 0.6886 0.760 0.188 0.012 0.040
#> GSM550813 2 0.1297 0.7499 0.016 0.964 0.000 0.020
#> GSM550814 2 0.2222 0.7416 0.016 0.924 0.000 0.060
#> GSM550815 2 0.1118 0.7389 0.000 0.964 0.000 0.036
#> GSM550816 2 0.4362 0.7167 0.088 0.816 0.000 0.096
#> GSM550817 4 0.5226 0.5642 0.000 0.116 0.128 0.756
#> GSM550818 4 0.5222 0.5593 0.000 0.112 0.132 0.756
#> GSM550819 2 0.5370 0.6661 0.152 0.756 0.008 0.084
#> GSM550820 1 0.3965 0.7009 0.840 0.120 0.008 0.032
#> GSM550821 2 0.6109 0.5669 0.096 0.676 0.004 0.224
#> GSM550822 2 0.1118 0.7389 0.000 0.964 0.000 0.036
#> GSM550826 1 0.6422 0.6486 0.684 0.192 0.020 0.104
#> GSM550832 2 0.2334 0.7210 0.004 0.908 0.000 0.088
#> GSM550833 2 0.1118 0.7403 0.000 0.964 0.000 0.036
#> GSM550835 2 0.4509 0.4854 0.004 0.708 0.000 0.288
#> GSM550836 3 0.0817 0.6153 0.000 0.000 0.976 0.024
#> GSM550837 2 0.4018 0.5899 0.004 0.772 0.000 0.224
#> GSM550838 1 0.4400 0.6984 0.816 0.136 0.012 0.036
#> GSM550841 4 0.5361 0.5896 0.000 0.148 0.108 0.744
#> GSM550842 2 0.4564 0.4050 0.000 0.672 0.000 0.328
#> GSM550846 2 0.5643 0.0614 0.428 0.548 0.000 0.024
#> GSM550849 1 0.6597 0.3569 0.512 0.420 0.008 0.060
#> GSM550850 1 0.2364 0.6558 0.928 0.036 0.008 0.028
#> GSM550851 2 0.4018 0.5899 0.004 0.772 0.000 0.224
#> GSM550852 2 0.5466 0.6402 0.200 0.732 0.008 0.060
#> GSM550853 2 0.0524 0.7470 0.008 0.988 0.000 0.004
#> GSM550855 2 0.0524 0.7470 0.008 0.988 0.000 0.004
#> GSM550856 2 0.1398 0.7461 0.040 0.956 0.000 0.004
#> GSM550861 2 0.0779 0.7450 0.004 0.980 0.000 0.016
#> GSM550863 1 0.5403 0.5794 0.628 0.348 0.000 0.024
#> GSM550864 2 0.0817 0.7491 0.024 0.976 0.000 0.000
#> GSM550866 2 0.1398 0.7461 0.040 0.956 0.000 0.004
#> GSM550867 1 0.1743 0.6142 0.940 0.000 0.004 0.056
#> GSM550885 1 0.2207 0.6218 0.928 0.012 0.004 0.056
#> GSM550886 2 0.6890 0.3066 0.076 0.580 0.020 0.324
#> GSM550887 2 0.1118 0.7389 0.000 0.964 0.000 0.036
#> GSM550889 2 0.5173 0.3564 0.320 0.660 0.000 0.020
#> GSM550894 2 0.2345 0.7106 0.000 0.900 0.000 0.100
#> GSM550897 1 0.5980 0.6339 0.644 0.300 0.008 0.048
#> GSM550903 2 0.1059 0.7496 0.012 0.972 0.000 0.016
#> GSM550905 2 0.3870 0.6112 0.004 0.788 0.000 0.208
#> GSM550906 2 0.1118 0.7389 0.000 0.964 0.000 0.036
#> GSM550907 4 0.4105 0.3951 0.000 0.032 0.156 0.812
#> GSM550909 2 0.5986 0.5794 0.092 0.688 0.004 0.216
#> GSM550911 4 0.4149 0.3688 0.000 0.028 0.168 0.804
#> GSM550913 2 0.1118 0.7389 0.000 0.964 0.000 0.036
#> GSM550915 1 0.5476 0.4892 0.584 0.396 0.000 0.020
#> GSM550917 2 0.1022 0.7488 0.032 0.968 0.000 0.000
#> GSM550919 1 0.5284 0.5500 0.616 0.368 0.000 0.016
#> GSM550921 3 0.0921 0.6133 0.000 0.000 0.972 0.028
#> GSM550924 2 0.6722 0.4056 0.088 0.604 0.012 0.296
#> GSM550926 2 0.0524 0.7470 0.008 0.988 0.000 0.004
#> GSM550927 2 0.1118 0.7389 0.000 0.964 0.000 0.036
#> GSM550787 1 0.6751 0.5346 0.576 0.328 0.008 0.088
#> GSM550793 3 0.7407 0.3480 0.424 0.008 0.440 0.128
#> GSM550794 2 0.5539 0.6328 0.208 0.724 0.008 0.060
#> GSM550795 1 0.4627 0.6981 0.772 0.196 0.004 0.028
#> GSM550798 1 0.3873 0.5505 0.844 0.000 0.096 0.060
#> GSM550803 1 0.2300 0.6067 0.920 0.000 0.016 0.064
#> GSM550805 1 0.6031 0.6293 0.644 0.296 0.008 0.052
#> GSM550823 2 0.5228 0.3929 0.312 0.664 0.000 0.024
#> GSM550824 1 0.1743 0.6142 0.940 0.000 0.004 0.056
#> GSM550825 1 0.5696 0.3130 0.692 0.000 0.232 0.076
#> GSM550827 2 0.5535 0.1415 0.420 0.560 0.000 0.020
#> GSM550828 1 0.4038 0.7053 0.828 0.136 0.004 0.032
#> GSM550829 1 0.5696 0.3130 0.692 0.000 0.232 0.076
#> GSM550830 2 0.5228 0.3929 0.312 0.664 0.000 0.024
#> GSM550834 1 0.3013 0.6858 0.888 0.080 0.000 0.032
#> GSM550839 2 0.7553 0.0799 0.096 0.508 0.032 0.364
#> GSM550840 1 0.5911 0.6420 0.656 0.288 0.008 0.048
#> GSM550843 2 0.8026 0.0205 0.096 0.504 0.064 0.336
#> GSM550844 1 0.6031 0.6293 0.644 0.296 0.008 0.052
#> GSM550845 2 0.1118 0.7482 0.036 0.964 0.000 0.000
#> GSM550848 1 0.5284 0.5500 0.616 0.368 0.000 0.016
#> GSM550854 1 0.1743 0.6142 0.940 0.000 0.004 0.056
#> GSM550857 3 0.0817 0.6153 0.000 0.000 0.976 0.024
#> GSM550858 1 0.3435 0.6944 0.864 0.100 0.000 0.036
#> GSM550859 1 0.1743 0.6142 0.940 0.000 0.004 0.056
#> GSM550862 1 0.3435 0.6944 0.864 0.100 0.000 0.036
#> GSM550865 1 0.5403 0.5794 0.628 0.348 0.000 0.024
#> GSM550868 2 0.5716 0.0778 0.420 0.552 0.000 0.028
#> GSM550869 1 0.8727 0.1089 0.364 0.296 0.036 0.304
#> GSM550870 2 0.1118 0.7482 0.036 0.964 0.000 0.000
#> GSM550871 2 0.7553 0.0799 0.096 0.508 0.032 0.364
#> GSM550872 1 0.5386 0.5837 0.632 0.344 0.000 0.024
#> GSM550873 2 0.5466 0.6402 0.200 0.732 0.008 0.060
#> GSM550874 2 0.0524 0.7470 0.008 0.988 0.000 0.004
#> GSM550876 4 0.6989 0.5559 0.056 0.320 0.040 0.584
#> GSM550877 2 0.0524 0.7470 0.008 0.988 0.000 0.004
#> GSM550878 4 0.7630 0.6035 0.044 0.304 0.100 0.552
#> GSM550879 1 0.3940 0.7063 0.824 0.152 0.004 0.020
#> GSM550882 3 0.8357 0.3555 0.280 0.020 0.412 0.288
#> GSM550888 3 0.0817 0.6153 0.000 0.000 0.976 0.024
#> GSM550890 2 0.5643 0.0614 0.428 0.548 0.000 0.024
#> GSM550891 3 0.3942 0.4260 0.000 0.000 0.764 0.236
#> GSM550892 1 0.5368 0.5907 0.636 0.340 0.000 0.024
#> GSM550893 2 0.3925 0.6526 0.176 0.808 0.000 0.016
#> GSM550895 2 0.4767 0.5219 0.256 0.724 0.000 0.020
#> GSM550896 2 0.4284 0.6157 0.200 0.780 0.000 0.020
#> GSM550898 1 0.1743 0.6142 0.940 0.000 0.004 0.056
#> GSM550899 2 0.1209 0.7494 0.032 0.964 0.000 0.004
#> GSM550900 2 0.5088 0.4566 0.288 0.688 0.000 0.024
#> GSM550901 1 0.5269 0.5574 0.620 0.364 0.000 0.016
#> GSM550902 3 0.7407 0.3480 0.424 0.008 0.440 0.128
#> GSM550904 1 0.4001 0.6984 0.840 0.116 0.008 0.036
#> GSM550908 3 0.0817 0.6153 0.000 0.000 0.976 0.024
#> GSM550912 2 0.1297 0.7499 0.016 0.964 0.000 0.020
#> GSM550914 2 0.5643 0.0614 0.428 0.548 0.000 0.024
#> GSM550918 2 0.1118 0.7487 0.036 0.964 0.000 0.000
#> GSM550922 2 0.5018 0.3616 0.000 0.656 0.012 0.332
#> GSM550923 1 0.2739 0.5927 0.904 0.000 0.036 0.060
#> GSM550925 1 0.6120 0.5882 0.616 0.328 0.008 0.048
#> GSM550802 2 0.5735 0.6403 0.180 0.724 0.008 0.088
#> GSM550812 2 0.5774 0.6370 0.184 0.720 0.008 0.088
#> GSM550831 1 0.3013 0.6858 0.888 0.080 0.000 0.032
#> GSM550847 1 0.1661 0.6140 0.944 0.000 0.004 0.052
#> GSM550860 4 0.8871 -0.0325 0.324 0.300 0.044 0.332
#> GSM550875 1 0.6031 0.6293 0.644 0.296 0.008 0.052
#> GSM550880 1 0.5398 0.4719 0.580 0.404 0.000 0.016
#> GSM550881 3 0.6497 0.5420 0.304 0.000 0.596 0.100
#> GSM550883 3 0.6497 0.5420 0.304 0.000 0.596 0.100
#> GSM550884 2 0.5904 0.5837 0.244 0.684 0.008 0.064
#> GSM550910 4 0.5757 0.5677 0.020 0.180 0.068 0.732
#> GSM550916 1 0.3272 0.6797 0.884 0.076 0.008 0.032
#> GSM550920 2 0.7131 0.2886 0.080 0.568 0.028 0.324
cbind(get_classes(res, k = 5), get_membership(res, k = 5))
#> class entropy silhouette p1 p2 p3 p4 p5
#> GSM550785 1 0.4855 0.3512 0.552 0.024 0.000 0.424 0.000
#> GSM550786 2 0.7297 0.0378 0.048 0.412 0.008 0.408 0.124
#> GSM550788 2 0.0794 0.7357 0.000 0.972 0.000 0.028 0.000
#> GSM550789 2 0.0162 0.7344 0.000 0.996 0.000 0.004 0.000
#> GSM550790 1 0.4359 0.4301 0.584 0.000 0.004 0.412 0.000
#> GSM550791 4 0.6669 0.3651 0.308 0.220 0.000 0.468 0.004
#> GSM550792 2 0.5190 0.3589 0.020 0.560 0.000 0.404 0.016
#> GSM550796 2 0.0162 0.7344 0.000 0.996 0.000 0.004 0.000
#> GSM550797 2 0.0162 0.7344 0.000 0.996 0.000 0.004 0.000
#> GSM550799 5 0.5825 0.5291 0.000 0.348 0.016 0.068 0.568
#> GSM550800 2 0.3534 0.5247 0.000 0.744 0.000 0.256 0.000
#> GSM550801 2 0.0510 0.7359 0.000 0.984 0.000 0.016 0.000
#> GSM550804 2 0.2179 0.7187 0.004 0.896 0.000 0.100 0.000
#> GSM550806 5 0.6861 0.5380 0.000 0.280 0.024 0.188 0.508
#> GSM550807 2 0.0510 0.7359 0.000 0.984 0.000 0.016 0.000
#> GSM550808 2 0.3454 0.6630 0.000 0.836 0.000 0.064 0.100
#> GSM550809 1 0.5056 0.2218 0.500 0.012 0.004 0.476 0.008
#> GSM550810 2 0.3454 0.6630 0.000 0.836 0.000 0.064 0.100
#> GSM550811 4 0.5494 -0.0460 0.396 0.040 0.004 0.552 0.008
#> GSM550813 2 0.2361 0.7317 0.000 0.892 0.000 0.096 0.012
#> GSM550814 2 0.3365 0.7236 0.000 0.836 0.000 0.120 0.044
#> GSM550815 2 0.0162 0.7344 0.000 0.996 0.000 0.004 0.000
#> GSM550816 2 0.4368 0.6561 0.012 0.772 0.000 0.164 0.052
#> GSM550817 5 0.3093 0.6088 0.000 0.080 0.032 0.016 0.872
#> GSM550818 5 0.3033 0.6051 0.000 0.076 0.032 0.016 0.876
#> GSM550819 2 0.5181 0.4817 0.016 0.612 0.000 0.344 0.028
#> GSM550820 4 0.4849 -0.2606 0.480 0.004 0.004 0.504 0.008
#> GSM550821 2 0.5715 0.5165 0.000 0.620 0.000 0.228 0.152
#> GSM550822 2 0.0162 0.7344 0.000 0.996 0.000 0.004 0.000
#> GSM550826 4 0.6380 0.0558 0.328 0.048 0.008 0.564 0.052
#> GSM550832 2 0.2149 0.7243 0.000 0.916 0.000 0.048 0.036
#> GSM550833 2 0.0404 0.7371 0.000 0.988 0.000 0.012 0.000
#> GSM550835 2 0.4822 0.4850 0.000 0.704 0.000 0.076 0.220
#> GSM550836 3 0.0290 0.6658 0.000 0.000 0.992 0.000 0.008
#> GSM550837 2 0.4277 0.5901 0.000 0.768 0.000 0.076 0.156
#> GSM550838 1 0.5056 0.2218 0.500 0.012 0.004 0.476 0.008
#> GSM550841 5 0.3544 0.6215 0.000 0.120 0.028 0.016 0.836
#> GSM550842 2 0.4960 0.3977 0.000 0.668 0.000 0.064 0.268
#> GSM550846 4 0.5855 0.4785 0.108 0.356 0.000 0.536 0.000
#> GSM550849 4 0.5660 0.5417 0.100 0.244 0.000 0.644 0.012
#> GSM550850 1 0.4375 0.4211 0.576 0.000 0.004 0.420 0.000
#> GSM550851 2 0.4277 0.5901 0.000 0.768 0.000 0.076 0.156
#> GSM550852 2 0.5112 0.3640 0.016 0.560 0.000 0.408 0.016
#> GSM550853 2 0.1410 0.7296 0.000 0.940 0.000 0.060 0.000
#> GSM550855 2 0.1410 0.7296 0.000 0.940 0.000 0.060 0.000
#> GSM550856 2 0.2020 0.7156 0.000 0.900 0.000 0.100 0.000
#> GSM550861 2 0.0794 0.7351 0.000 0.972 0.000 0.028 0.000
#> GSM550863 4 0.5462 0.4749 0.212 0.136 0.000 0.652 0.000
#> GSM550864 2 0.1704 0.7300 0.004 0.928 0.000 0.068 0.000
#> GSM550866 2 0.2020 0.7156 0.000 0.900 0.000 0.100 0.000
#> GSM550867 1 0.0290 0.6440 0.992 0.000 0.000 0.008 0.000
#> GSM550885 1 0.0703 0.6413 0.976 0.000 0.000 0.024 0.000
#> GSM550886 2 0.6481 0.2547 0.000 0.516 0.004 0.204 0.276
#> GSM550887 2 0.0162 0.7344 0.000 0.996 0.000 0.004 0.000
#> GSM550889 4 0.4656 0.2229 0.012 0.480 0.000 0.508 0.000
#> GSM550894 2 0.2228 0.7155 0.000 0.912 0.000 0.040 0.048
#> GSM550897 4 0.6241 0.4633 0.240 0.192 0.004 0.564 0.000
#> GSM550903 2 0.1270 0.7367 0.000 0.948 0.000 0.052 0.000
#> GSM550905 2 0.4212 0.6074 0.000 0.776 0.000 0.080 0.144
#> GSM550906 2 0.0290 0.7342 0.000 0.992 0.000 0.008 0.000
#> GSM550907 5 0.1818 0.4638 0.000 0.000 0.044 0.024 0.932
#> GSM550909 2 0.5914 0.5329 0.016 0.644 0.000 0.176 0.164
#> GSM550911 5 0.2446 0.4384 0.000 0.000 0.044 0.056 0.900
#> GSM550913 2 0.0162 0.7344 0.000 0.996 0.000 0.004 0.000
#> GSM550915 4 0.6510 0.4868 0.252 0.260 0.000 0.488 0.000
#> GSM550917 2 0.2020 0.7200 0.000 0.900 0.000 0.100 0.000
#> GSM550919 4 0.6581 0.4470 0.296 0.240 0.000 0.464 0.000
#> GSM550921 3 0.0404 0.6638 0.000 0.000 0.988 0.000 0.012
#> GSM550924 2 0.6648 0.3420 0.004 0.532 0.008 0.240 0.216
#> GSM550926 2 0.1410 0.7296 0.000 0.940 0.000 0.060 0.000
#> GSM550927 2 0.0162 0.7344 0.000 0.996 0.000 0.004 0.000
#> GSM550787 4 0.6794 0.4321 0.192 0.228 0.004 0.552 0.024
#> GSM550793 3 0.7557 0.3992 0.180 0.000 0.416 0.340 0.064
#> GSM550794 2 0.5278 0.3479 0.024 0.552 0.000 0.408 0.016
#> GSM550795 4 0.5394 0.0619 0.384 0.052 0.000 0.560 0.004
#> GSM550798 1 0.3620 0.5374 0.824 0.000 0.068 0.108 0.000
#> GSM550803 1 0.1502 0.6223 0.940 0.000 0.004 0.056 0.000
#> GSM550805 4 0.6175 0.4674 0.228 0.192 0.004 0.576 0.000
#> GSM550823 4 0.4980 0.1927 0.028 0.484 0.000 0.488 0.000
#> GSM550824 1 0.0290 0.6440 0.992 0.000 0.000 0.008 0.000
#> GSM550825 1 0.6297 0.3072 0.572 0.000 0.204 0.216 0.008
#> GSM550827 4 0.6321 0.4181 0.160 0.376 0.000 0.464 0.000
#> GSM550828 1 0.4966 0.3012 0.564 0.032 0.000 0.404 0.000
#> GSM550829 1 0.6297 0.3072 0.572 0.000 0.204 0.216 0.008
#> GSM550830 4 0.4980 0.1927 0.028 0.484 0.000 0.488 0.000
#> GSM550834 1 0.4807 0.3397 0.532 0.020 0.000 0.448 0.000
#> GSM550839 2 0.7063 -0.0308 0.000 0.408 0.012 0.288 0.292
#> GSM550840 4 0.6256 0.4453 0.248 0.188 0.004 0.560 0.000
#> GSM550843 2 0.7237 -0.0771 0.000 0.412 0.024 0.248 0.316
#> GSM550844 4 0.6175 0.4674 0.228 0.192 0.004 0.576 0.000
#> GSM550845 2 0.2124 0.7204 0.004 0.900 0.000 0.096 0.000
#> GSM550848 4 0.6581 0.4470 0.296 0.240 0.000 0.464 0.000
#> GSM550854 1 0.0290 0.6440 0.992 0.000 0.000 0.008 0.000
#> GSM550857 3 0.0290 0.6658 0.000 0.000 0.992 0.000 0.008
#> GSM550858 1 0.4526 0.4918 0.672 0.028 0.000 0.300 0.000
#> GSM550859 1 0.0290 0.6440 0.992 0.000 0.000 0.008 0.000
#> GSM550862 1 0.4526 0.4918 0.672 0.028 0.000 0.300 0.000
#> GSM550865 4 0.5462 0.4749 0.212 0.136 0.000 0.652 0.000
#> GSM550868 4 0.5894 0.4727 0.112 0.356 0.000 0.532 0.000
#> GSM550869 4 0.7377 0.2874 0.048 0.156 0.020 0.540 0.236
#> GSM550870 2 0.2011 0.7231 0.004 0.908 0.000 0.088 0.000
#> GSM550871 2 0.7063 -0.0308 0.000 0.408 0.012 0.288 0.292
#> GSM550872 4 0.5450 0.4698 0.216 0.132 0.000 0.652 0.000
#> GSM550873 2 0.5112 0.3640 0.016 0.560 0.000 0.408 0.016
#> GSM550874 2 0.1410 0.7296 0.000 0.940 0.000 0.060 0.000
#> GSM550876 5 0.6788 0.5127 0.000 0.304 0.020 0.176 0.500
#> GSM550877 2 0.1410 0.7296 0.000 0.940 0.000 0.060 0.000
#> GSM550878 5 0.6468 0.5876 0.000 0.300 0.036 0.104 0.560
#> GSM550879 1 0.5049 0.1742 0.488 0.032 0.000 0.480 0.000
#> GSM550882 3 0.8119 0.4000 0.120 0.000 0.396 0.260 0.224
#> GSM550888 3 0.0290 0.6658 0.000 0.000 0.992 0.000 0.008
#> GSM550890 4 0.5855 0.4785 0.108 0.356 0.000 0.536 0.000
#> GSM550891 3 0.4441 0.4444 0.000 0.000 0.720 0.044 0.236
#> GSM550892 4 0.5410 0.4643 0.216 0.128 0.000 0.656 0.000
#> GSM550893 2 0.3949 0.3743 0.000 0.668 0.000 0.332 0.000
#> GSM550895 2 0.4522 0.0154 0.008 0.552 0.000 0.440 0.000
#> GSM550896 2 0.4150 0.2337 0.000 0.612 0.000 0.388 0.000
#> GSM550898 1 0.0290 0.6440 0.992 0.000 0.000 0.008 0.000
#> GSM550899 2 0.1792 0.7267 0.000 0.916 0.000 0.084 0.000
#> GSM550900 2 0.4902 -0.1390 0.024 0.508 0.000 0.468 0.000
#> GSM550901 4 0.6592 0.4413 0.300 0.240 0.000 0.460 0.000
#> GSM550902 3 0.7557 0.3992 0.180 0.000 0.416 0.340 0.064
#> GSM550904 4 0.4851 -0.2738 0.488 0.004 0.004 0.496 0.008
#> GSM550908 3 0.0290 0.6658 0.000 0.000 0.992 0.000 0.008
#> GSM550912 2 0.2361 0.7317 0.000 0.892 0.000 0.096 0.012
#> GSM550914 4 0.5855 0.4785 0.108 0.356 0.000 0.536 0.000
#> GSM550918 2 0.2179 0.7187 0.004 0.896 0.000 0.100 0.000
#> GSM550922 2 0.5192 0.3716 0.000 0.644 0.000 0.076 0.280
#> GSM550923 1 0.2361 0.5963 0.892 0.000 0.012 0.096 0.000
#> GSM550925 4 0.6178 0.4735 0.196 0.224 0.004 0.576 0.000
#> GSM550802 2 0.5357 0.4305 0.020 0.580 0.000 0.372 0.028
#> GSM550812 2 0.5357 0.4301 0.020 0.580 0.000 0.372 0.028
#> GSM550831 1 0.4807 0.3397 0.532 0.020 0.000 0.448 0.000
#> GSM550847 1 0.0609 0.6439 0.980 0.000 0.000 0.020 0.000
#> GSM550860 4 0.7643 0.1406 0.040 0.176 0.028 0.500 0.256
#> GSM550875 4 0.6175 0.4674 0.228 0.192 0.004 0.576 0.000
#> GSM550880 4 0.6102 0.4947 0.232 0.200 0.000 0.568 0.000
#> GSM550881 3 0.6768 0.5720 0.140 0.000 0.572 0.236 0.052
#> GSM550883 3 0.6768 0.5720 0.140 0.000 0.572 0.236 0.052
#> GSM550884 2 0.5478 0.2628 0.028 0.516 0.000 0.436 0.020
#> GSM550910 5 0.4117 0.5706 0.000 0.116 0.000 0.096 0.788
#> GSM550916 1 0.4449 0.3314 0.512 0.000 0.004 0.484 0.000
#> GSM550920 2 0.6648 0.2356 0.000 0.504 0.008 0.220 0.268
cbind(get_classes(res, k = 6), get_membership(res, k = 6))
#> class entropy silhouette p1 p2 p3 p4 p5 p6
#> GSM550785 6 0.5611 -0.2289 0.420 0.008 0.000 0.112 0.000 0.460
#> GSM550786 2 0.7286 -0.1139 0.012 0.356 0.000 0.292 0.060 0.280
#> GSM550788 2 0.0820 0.7219 0.000 0.972 0.000 0.016 0.000 0.012
#> GSM550789 2 0.0458 0.7170 0.000 0.984 0.000 0.016 0.000 0.000
#> GSM550790 1 0.5319 0.3177 0.520 0.000 0.000 0.112 0.000 0.368
#> GSM550791 6 0.7341 0.2707 0.240 0.188 0.000 0.160 0.000 0.412
#> GSM550792 2 0.5756 0.3618 0.004 0.492 0.000 0.160 0.000 0.344
#> GSM550796 2 0.0458 0.7170 0.000 0.984 0.000 0.016 0.000 0.000
#> GSM550797 2 0.0458 0.7170 0.000 0.984 0.000 0.016 0.000 0.000
#> GSM550799 5 0.6261 0.0536 0.000 0.276 0.000 0.268 0.444 0.012
#> GSM550800 2 0.3558 0.5526 0.000 0.736 0.000 0.016 0.000 0.248
#> GSM550801 2 0.0914 0.7208 0.000 0.968 0.000 0.016 0.000 0.016
#> GSM550804 2 0.2266 0.7126 0.000 0.880 0.000 0.012 0.000 0.108
#> GSM550806 4 0.6760 -0.1051 0.000 0.208 0.004 0.400 0.348 0.040
#> GSM550807 2 0.0914 0.7208 0.000 0.968 0.000 0.016 0.000 0.016
#> GSM550808 2 0.3837 0.6010 0.000 0.752 0.000 0.212 0.016 0.020
#> GSM550809 6 0.5938 0.1588 0.280 0.000 0.000 0.260 0.000 0.460
#> GSM550810 2 0.3837 0.6010 0.000 0.752 0.000 0.212 0.016 0.020
#> GSM550811 6 0.6162 0.2607 0.212 0.020 0.000 0.264 0.000 0.504
#> GSM550813 2 0.2554 0.7215 0.000 0.876 0.000 0.048 0.000 0.076
#> GSM550814 2 0.3785 0.6891 0.000 0.788 0.000 0.120 0.004 0.088
#> GSM550815 2 0.0458 0.7170 0.000 0.984 0.000 0.016 0.000 0.000
#> GSM550816 2 0.4995 0.5998 0.000 0.684 0.000 0.148 0.016 0.152
#> GSM550817 5 0.3072 0.6544 0.000 0.036 0.004 0.124 0.836 0.000
#> GSM550818 5 0.3000 0.6538 0.000 0.032 0.004 0.124 0.840 0.000
#> GSM550819 2 0.5771 0.4080 0.004 0.524 0.000 0.192 0.000 0.280
#> GSM550820 6 0.5829 0.1777 0.268 0.000 0.000 0.240 0.000 0.492
#> GSM550821 2 0.6287 0.3726 0.000 0.532 0.000 0.272 0.056 0.140
#> GSM550822 2 0.0458 0.7170 0.000 0.984 0.000 0.016 0.000 0.000
#> GSM550826 6 0.6739 0.2633 0.176 0.024 0.000 0.320 0.024 0.456
#> GSM550832 2 0.2201 0.6939 0.000 0.896 0.000 0.076 0.000 0.028
#> GSM550833 2 0.0790 0.7195 0.000 0.968 0.000 0.032 0.000 0.000
#> GSM550835 2 0.5272 0.4241 0.000 0.624 0.000 0.256 0.104 0.016
#> GSM550836 3 0.0000 0.8121 0.000 0.000 1.000 0.000 0.000 0.000
#> GSM550837 2 0.4607 0.5215 0.000 0.684 0.000 0.248 0.052 0.016
#> GSM550838 6 0.5938 0.1588 0.280 0.000 0.000 0.260 0.000 0.460
#> GSM550841 5 0.3766 0.6339 0.000 0.068 0.004 0.144 0.784 0.000
#> GSM550842 2 0.5650 0.3401 0.000 0.584 0.000 0.248 0.152 0.016
#> GSM550846 6 0.4164 0.4418 0.016 0.280 0.000 0.016 0.000 0.688
#> GSM550849 6 0.5888 0.4027 0.024 0.196 0.000 0.208 0.000 0.572
#> GSM550850 1 0.5361 0.3071 0.512 0.000 0.000 0.116 0.000 0.372
#> GSM550851 2 0.4607 0.5215 0.000 0.684 0.000 0.248 0.052 0.016
#> GSM550852 2 0.5773 0.3645 0.004 0.492 0.000 0.164 0.000 0.340
#> GSM550853 2 0.1500 0.7206 0.000 0.936 0.000 0.012 0.000 0.052
#> GSM550855 2 0.1500 0.7206 0.000 0.936 0.000 0.012 0.000 0.052
#> GSM550856 2 0.2121 0.7147 0.000 0.892 0.000 0.012 0.000 0.096
#> GSM550861 2 0.0692 0.7227 0.000 0.976 0.000 0.004 0.000 0.020
#> GSM550863 6 0.2683 0.4553 0.052 0.056 0.000 0.012 0.000 0.880
#> GSM550864 2 0.1812 0.7209 0.000 0.912 0.000 0.008 0.000 0.080
#> GSM550866 2 0.2121 0.7147 0.000 0.892 0.000 0.012 0.000 0.096
#> GSM550867 1 0.1387 0.7377 0.932 0.000 0.000 0.000 0.000 0.068
#> GSM550885 1 0.1714 0.7270 0.908 0.000 0.000 0.000 0.000 0.092
#> GSM550886 2 0.6775 -0.0391 0.000 0.428 0.000 0.348 0.140 0.084
#> GSM550887 2 0.0458 0.7170 0.000 0.984 0.000 0.016 0.000 0.000
#> GSM550889 6 0.4434 0.1518 0.000 0.428 0.000 0.028 0.000 0.544
#> GSM550894 2 0.2112 0.6863 0.000 0.896 0.000 0.088 0.000 0.016
#> GSM550897 6 0.6909 0.4001 0.152 0.168 0.000 0.156 0.004 0.520
#> GSM550903 2 0.1367 0.7261 0.000 0.944 0.000 0.012 0.000 0.044
#> GSM550905 2 0.4402 0.5371 0.000 0.700 0.000 0.244 0.040 0.016
#> GSM550906 2 0.0260 0.7181 0.000 0.992 0.000 0.008 0.000 0.000
#> GSM550907 5 0.0820 0.5709 0.000 0.000 0.016 0.012 0.972 0.000
#> GSM550909 2 0.6611 0.4125 0.004 0.548 0.000 0.212 0.112 0.124
#> GSM550911 5 0.2405 0.4922 0.000 0.000 0.016 0.100 0.880 0.004
#> GSM550913 2 0.0458 0.7170 0.000 0.984 0.000 0.016 0.000 0.000
#> GSM550915 6 0.6275 0.4677 0.084 0.196 0.000 0.144 0.000 0.576
#> GSM550917 2 0.2070 0.7178 0.000 0.896 0.000 0.012 0.000 0.092
#> GSM550919 6 0.6819 0.4491 0.128 0.196 0.000 0.164 0.000 0.512
#> GSM550921 3 0.0547 0.8039 0.000 0.000 0.980 0.020 0.000 0.000
#> GSM550924 2 0.6782 0.0178 0.000 0.432 0.000 0.348 0.104 0.116
#> GSM550926 2 0.1563 0.7205 0.000 0.932 0.000 0.012 0.000 0.056
#> GSM550927 2 0.0458 0.7170 0.000 0.984 0.000 0.016 0.000 0.000
#> GSM550787 6 0.7496 0.2887 0.164 0.176 0.000 0.264 0.004 0.392
#> GSM550793 4 0.6711 -0.3112 0.060 0.000 0.384 0.428 0.012 0.116
#> GSM550794 2 0.5771 0.3513 0.004 0.484 0.000 0.160 0.000 0.352
#> GSM550795 6 0.5197 0.3114 0.172 0.012 0.000 0.164 0.000 0.652
#> GSM550798 1 0.3689 0.6403 0.824 0.000 0.048 0.088 0.004 0.036
#> GSM550803 1 0.1863 0.7238 0.920 0.000 0.000 0.044 0.000 0.036
#> GSM550805 6 0.6908 0.3950 0.148 0.168 0.000 0.160 0.004 0.520
#> GSM550823 6 0.4555 0.1601 0.004 0.420 0.000 0.028 0.000 0.548
#> GSM550824 1 0.1387 0.7377 0.932 0.000 0.000 0.000 0.000 0.068
#> GSM550825 1 0.6446 0.3344 0.528 0.000 0.176 0.244 0.004 0.048
#> GSM550827 6 0.5796 0.3372 0.072 0.328 0.000 0.052 0.000 0.548
#> GSM550828 6 0.6319 0.0830 0.324 0.024 0.000 0.196 0.000 0.456
#> GSM550829 1 0.6446 0.3344 0.528 0.000 0.176 0.244 0.004 0.048
#> GSM550830 6 0.4555 0.1601 0.004 0.420 0.000 0.028 0.000 0.548
#> GSM550834 6 0.5619 -0.1559 0.392 0.008 0.000 0.116 0.000 0.484
#> GSM550839 4 0.7367 0.1946 0.000 0.336 0.000 0.344 0.160 0.160
#> GSM550840 6 0.7085 0.3756 0.160 0.164 0.000 0.180 0.004 0.492
#> GSM550843 2 0.7520 -0.3049 0.000 0.344 0.000 0.276 0.224 0.156
#> GSM550844 6 0.6908 0.3950 0.148 0.168 0.000 0.160 0.004 0.520
#> GSM550845 2 0.2218 0.7144 0.000 0.884 0.000 0.012 0.000 0.104
#> GSM550848 6 0.6819 0.4491 0.128 0.196 0.000 0.164 0.000 0.512
#> GSM550854 1 0.1387 0.7377 0.932 0.000 0.000 0.000 0.000 0.068
#> GSM550857 3 0.0000 0.8121 0.000 0.000 1.000 0.000 0.000 0.000
#> GSM550858 1 0.5005 0.3591 0.544 0.012 0.000 0.048 0.000 0.396
#> GSM550859 1 0.1387 0.7377 0.932 0.000 0.000 0.000 0.000 0.068
#> GSM550862 1 0.5005 0.3591 0.544 0.012 0.000 0.048 0.000 0.396
#> GSM550865 6 0.2683 0.4553 0.052 0.056 0.000 0.012 0.000 0.880
#> GSM550868 6 0.4601 0.4100 0.032 0.292 0.000 0.020 0.000 0.656
#> GSM550869 6 0.6926 0.0158 0.008 0.100 0.000 0.336 0.112 0.444
#> GSM550870 2 0.2121 0.7164 0.000 0.892 0.000 0.012 0.000 0.096
#> GSM550871 4 0.7367 0.1946 0.000 0.336 0.000 0.344 0.160 0.160
#> GSM550872 6 0.2621 0.4529 0.052 0.052 0.000 0.012 0.000 0.884
#> GSM550873 2 0.5773 0.3645 0.004 0.492 0.000 0.164 0.000 0.340
#> GSM550874 2 0.1563 0.7205 0.000 0.932 0.000 0.012 0.000 0.056
#> GSM550876 4 0.6465 -0.0866 0.000 0.228 0.000 0.412 0.336 0.024
#> GSM550877 2 0.1500 0.7206 0.000 0.936 0.000 0.012 0.000 0.052
#> GSM550878 5 0.6315 0.0967 0.000 0.228 0.004 0.300 0.456 0.012
#> GSM550879 6 0.6151 0.1943 0.256 0.020 0.000 0.216 0.000 0.508
#> GSM550882 4 0.6151 -0.2509 0.000 0.000 0.376 0.476 0.092 0.056
#> GSM550888 3 0.0000 0.8121 0.000 0.000 1.000 0.000 0.000 0.000
#> GSM550890 6 0.4164 0.4418 0.016 0.280 0.000 0.016 0.000 0.688
#> GSM550891 3 0.5116 0.5232 0.004 0.000 0.656 0.144 0.192 0.004
#> GSM550892 6 0.2736 0.4502 0.052 0.048 0.000 0.020 0.000 0.880
#> GSM550893 2 0.4193 0.3711 0.000 0.624 0.000 0.024 0.000 0.352
#> GSM550895 2 0.4472 0.0376 0.000 0.496 0.000 0.028 0.000 0.476
#> GSM550896 2 0.4326 0.2513 0.000 0.572 0.000 0.024 0.000 0.404
#> GSM550898 1 0.1387 0.7377 0.932 0.000 0.000 0.000 0.000 0.068
#> GSM550899 2 0.1951 0.7214 0.000 0.908 0.000 0.016 0.000 0.076
#> GSM550900 6 0.4588 0.0678 0.004 0.448 0.000 0.028 0.000 0.520
#> GSM550901 6 0.6849 0.4459 0.132 0.196 0.000 0.164 0.000 0.508
#> GSM550902 4 0.6711 -0.3112 0.060 0.000 0.384 0.428 0.012 0.116
#> GSM550904 6 0.5870 0.1635 0.276 0.000 0.000 0.244 0.000 0.480
#> GSM550908 3 0.0000 0.8121 0.000 0.000 1.000 0.000 0.000 0.000
#> GSM550912 2 0.2554 0.7215 0.000 0.876 0.000 0.048 0.000 0.076
#> GSM550914 6 0.4164 0.4418 0.016 0.280 0.000 0.016 0.000 0.688
#> GSM550918 2 0.2266 0.7126 0.000 0.880 0.000 0.012 0.000 0.108
#> GSM550922 2 0.5700 0.3117 0.000 0.568 0.000 0.252 0.168 0.012
#> GSM550923 1 0.2046 0.6950 0.908 0.000 0.000 0.060 0.000 0.032
#> GSM550925 6 0.7243 0.3475 0.164 0.184 0.000 0.184 0.004 0.464
#> GSM550802 2 0.5898 0.3552 0.004 0.488 0.000 0.200 0.000 0.308
#> GSM550812 2 0.5898 0.3525 0.004 0.488 0.000 0.200 0.000 0.308
#> GSM550831 6 0.5619 -0.1559 0.392 0.008 0.000 0.116 0.000 0.484
#> GSM550847 1 0.1444 0.7361 0.928 0.000 0.000 0.000 0.000 0.072
#> GSM550860 6 0.7204 -0.1465 0.004 0.108 0.008 0.376 0.120 0.384
#> GSM550875 6 0.6908 0.3950 0.148 0.168 0.000 0.160 0.004 0.520
#> GSM550880 6 0.4294 0.4627 0.080 0.120 0.000 0.032 0.000 0.768
#> GSM550881 3 0.5389 0.4289 0.032 0.000 0.552 0.368 0.004 0.044
#> GSM550883 3 0.5389 0.4289 0.032 0.000 0.552 0.368 0.004 0.044
#> GSM550884 2 0.5797 0.2730 0.004 0.448 0.000 0.156 0.000 0.392
#> GSM550910 5 0.4811 0.5097 0.000 0.088 0.000 0.136 0.728 0.048
#> GSM550916 1 0.5411 0.2240 0.472 0.000 0.000 0.116 0.000 0.412
#> GSM550920 2 0.6855 -0.1051 0.000 0.408 0.000 0.360 0.140 0.092
Heatmaps for the consensus matrix. It visualizes the probability of two samples to be in a same group.
consensus_heatmap(res, k = 2)
consensus_heatmap(res, k = 3)
consensus_heatmap(res, k = 4)
consensus_heatmap(res, k = 5)
consensus_heatmap(res, k = 6)
Heatmaps for the membership of samples in all partitions to see how consistent they are:
membership_heatmap(res, k = 2)
membership_heatmap(res, k = 3)
membership_heatmap(res, k = 4)
membership_heatmap(res, k = 5)
membership_heatmap(res, k = 6)
As soon as we have had the classes for columns, we can look for signatures which are significantly different between classes which can be candidate marks for certain classes. Following are the heatmaps for signatures.
Signature heatmaps where rows are scaled:
get_signatures(res, k = 2)
get_signatures(res, k = 3)
get_signatures(res, k = 4)
get_signatures(res, k = 5)
get_signatures(res, k = 6)
Signature heatmaps where rows are not scaled:
get_signatures(res, k = 2, scale_rows = FALSE)
get_signatures(res, k = 3, scale_rows = FALSE)
get_signatures(res, k = 4, scale_rows = FALSE)
get_signatures(res, k = 5, scale_rows = FALSE)
get_signatures(res, k = 6, scale_rows = FALSE)
Compare the overlap of signatures from different k:
compare_signatures(res)
get_signature() returns a data frame invisibly. TO get the list of signatures, the function
call should be assigned to a variable explicitly. In following code, if plot argument is set
to FALSE, no heatmap is plotted while only the differential analysis is performed.
# code only for demonstration
tb = get_signature(res, k = ..., plot = FALSE)
An example of the output of tb is:
#> which_row fdr mean_1 mean_2 scaled_mean_1 scaled_mean_2 km
#> 1 38 0.042760348 8.373488 9.131774 -0.5533452 0.5164555 1
#> 2 40 0.018707592 7.106213 8.469186 -0.6173731 0.5762149 1
#> 3 55 0.019134737 10.221463 11.207825 -0.6159697 0.5749050 1
#> 4 59 0.006059896 5.921854 7.869574 -0.6899429 0.6439467 1
#> 5 60 0.018055526 8.928898 10.211722 -0.6204761 0.5791110 1
#> 6 98 0.009384629 15.714769 14.887706 0.6635654 -0.6193277 2
...
The columns in tb are:
which_row: row indices corresponding to the input matrix.fdr: FDR for the differential test. mean_x: The mean value in group x.scaled_mean_x: The mean value in group x after rows are scaled.km: Row groups if k-means clustering is applied to rows.UMAP plot which shows how samples are separated.
dimension_reduction(res, k = 2, method = "UMAP")
dimension_reduction(res, k = 3, method = "UMAP")
dimension_reduction(res, k = 4, method = "UMAP")
dimension_reduction(res, k = 5, method = "UMAP")
dimension_reduction(res, k = 6, method = "UMAP")
Following heatmap shows how subgroups are split when increasing k:
collect_classes(res)
Test correlation between subgroups and known annotations. If the known annotation is numeric, one-way ANOVA test is applied, and if the known annotation is discrete, chi-squared contingency table test is applied.
test_to_known_factors(res)
#> n disease.state(p) k
#> SD:hclust 98 0.000118 2
#> SD:hclust 111 0.002862 3
#> SD:hclust 111 0.003299 4
#> SD:hclust 69 0.001046 5
#> SD:hclust 62 0.000288 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 51776 rows and 143 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 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 0.505 0.866 0.885 0.4416 0.556 0.556
#> 3 3 0.573 0.715 0.859 0.4018 0.732 0.554
#> 4 4 0.516 0.380 0.642 0.1461 0.851 0.638
#> 5 5 0.651 0.749 0.823 0.0806 0.791 0.440
#> 6 6 0.684 0.606 0.769 0.0558 0.931 0.721
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
#> GSM550785 1 0.7815 0.882 0.768 0.232
#> GSM550786 2 0.7815 0.770 0.232 0.768
#> GSM550788 2 0.0000 0.915 0.000 1.000
#> GSM550789 2 0.0000 0.915 0.000 1.000
#> GSM550790 1 0.7815 0.882 0.768 0.232
#> GSM550791 1 0.7815 0.882 0.768 0.232
#> GSM550792 2 0.0000 0.915 0.000 1.000
#> GSM550796 2 0.0376 0.914 0.004 0.996
#> GSM550797 2 0.0000 0.915 0.000 1.000
#> GSM550799 2 0.7815 0.770 0.232 0.768
#> GSM550800 2 0.0000 0.915 0.000 1.000
#> GSM550801 2 0.0000 0.915 0.000 1.000
#> GSM550804 2 0.0000 0.915 0.000 1.000
#> GSM550806 2 0.7950 0.764 0.240 0.760
#> GSM550807 2 0.0000 0.915 0.000 1.000
#> GSM550808 2 0.5737 0.841 0.136 0.864
#> GSM550809 1 0.7815 0.882 0.768 0.232
#> GSM550810 2 0.0376 0.914 0.004 0.996
#> GSM550811 2 0.7883 0.570 0.236 0.764
#> GSM550813 2 0.0000 0.915 0.000 1.000
#> GSM550814 2 0.0000 0.915 0.000 1.000
#> GSM550815 2 0.0376 0.914 0.004 0.996
#> GSM550816 2 0.0000 0.915 0.000 1.000
#> GSM550817 2 0.7815 0.770 0.232 0.768
#> GSM550818 2 0.7815 0.770 0.232 0.768
#> GSM550819 2 0.0000 0.915 0.000 1.000
#> GSM550820 1 0.7815 0.882 0.768 0.232
#> GSM550821 2 0.6623 0.817 0.172 0.828
#> GSM550822 2 0.0376 0.914 0.004 0.996
#> GSM550826 1 0.0938 0.824 0.988 0.012
#> GSM550832 2 0.0000 0.915 0.000 1.000
#> GSM550833 2 0.0000 0.915 0.000 1.000
#> GSM550835 2 0.7602 0.780 0.220 0.780
#> GSM550836 1 0.0376 0.821 0.996 0.004
#> GSM550837 2 0.6623 0.817 0.172 0.828
#> GSM550838 1 0.5059 0.855 0.888 0.112
#> GSM550841 2 0.7815 0.770 0.232 0.768
#> GSM550842 2 0.6712 0.814 0.176 0.824
#> GSM550846 2 0.1633 0.901 0.024 0.976
#> GSM550849 2 0.0672 0.911 0.008 0.992
#> GSM550850 1 0.7815 0.882 0.768 0.232
#> GSM550851 2 0.6712 0.814 0.176 0.824
#> GSM550852 2 0.0000 0.915 0.000 1.000
#> GSM550853 2 0.0000 0.915 0.000 1.000
#> GSM550855 2 0.0000 0.915 0.000 1.000
#> GSM550856 2 0.0000 0.915 0.000 1.000
#> GSM550861 2 0.0000 0.915 0.000 1.000
#> GSM550863 2 0.1843 0.899 0.028 0.972
#> GSM550864 2 0.0000 0.915 0.000 1.000
#> GSM550866 2 0.0000 0.915 0.000 1.000
#> GSM550867 1 0.7815 0.882 0.768 0.232
#> GSM550885 1 0.7815 0.882 0.768 0.232
#> GSM550886 2 0.7745 0.773 0.228 0.772
#> GSM550887 2 0.0376 0.914 0.004 0.996
#> GSM550889 2 0.0000 0.915 0.000 1.000
#> GSM550894 2 0.0376 0.914 0.004 0.996
#> GSM550897 1 0.7815 0.882 0.768 0.232
#> GSM550903 2 0.0000 0.915 0.000 1.000
#> GSM550905 2 0.6623 0.817 0.172 0.828
#> GSM550906 2 0.0000 0.915 0.000 1.000
#> GSM550907 2 0.7883 0.767 0.236 0.764
#> GSM550909 2 0.1414 0.908 0.020 0.980
#> GSM550911 2 0.7883 0.767 0.236 0.764
#> GSM550913 2 0.0000 0.915 0.000 1.000
#> GSM550915 2 0.1843 0.899 0.028 0.972
#> GSM550917 2 0.0000 0.915 0.000 1.000
#> GSM550919 2 0.1843 0.899 0.028 0.972
#> GSM550921 1 0.0376 0.821 0.996 0.004
#> GSM550924 2 0.6531 0.819 0.168 0.832
#> GSM550926 2 0.0000 0.915 0.000 1.000
#> GSM550927 2 0.0000 0.915 0.000 1.000
#> GSM550787 2 0.7950 0.765 0.240 0.760
#> GSM550793 1 0.0376 0.821 0.996 0.004
#> GSM550794 2 0.0376 0.913 0.004 0.996
#> GSM550795 1 0.7815 0.882 0.768 0.232
#> GSM550798 1 0.0376 0.823 0.996 0.004
#> GSM550803 1 0.7602 0.879 0.780 0.220
#> GSM550805 2 0.4562 0.824 0.096 0.904
#> GSM550823 2 0.0000 0.915 0.000 1.000
#> GSM550824 1 0.7815 0.882 0.768 0.232
#> GSM550825 1 0.0000 0.821 1.000 0.000
#> GSM550827 2 0.1843 0.899 0.028 0.972
#> GSM550828 1 0.7815 0.882 0.768 0.232
#> GSM550829 1 0.0376 0.823 0.996 0.004
#> GSM550830 2 0.0000 0.915 0.000 1.000
#> GSM550834 1 0.7815 0.882 0.768 0.232
#> GSM550839 2 0.7674 0.777 0.224 0.776
#> GSM550840 1 0.7815 0.882 0.768 0.232
#> GSM550843 2 0.7815 0.770 0.232 0.768
#> GSM550844 1 0.7815 0.882 0.768 0.232
#> GSM550845 2 0.0000 0.915 0.000 1.000
#> GSM550848 2 0.1843 0.899 0.028 0.972
#> GSM550854 1 0.7815 0.882 0.768 0.232
#> GSM550857 1 0.0000 0.821 1.000 0.000
#> GSM550858 1 0.7815 0.882 0.768 0.232
#> GSM550859 1 0.7815 0.882 0.768 0.232
#> GSM550862 1 0.7815 0.882 0.768 0.232
#> GSM550865 2 0.1843 0.899 0.028 0.972
#> GSM550868 2 0.1843 0.899 0.028 0.972
#> GSM550869 2 0.5408 0.850 0.124 0.876
#> GSM550870 2 0.0000 0.915 0.000 1.000
#> GSM550871 2 0.7674 0.777 0.224 0.776
#> GSM550872 2 0.1843 0.899 0.028 0.972
#> GSM550873 2 0.0000 0.915 0.000 1.000
#> GSM550874 2 0.0000 0.915 0.000 1.000
#> GSM550876 2 0.7815 0.770 0.232 0.768
#> GSM550877 2 0.0000 0.915 0.000 1.000
#> GSM550878 2 0.7883 0.767 0.236 0.764
#> GSM550879 1 0.7815 0.882 0.768 0.232
#> GSM550882 1 0.1843 0.809 0.972 0.028
#> GSM550888 1 0.0376 0.821 0.996 0.004
#> GSM550890 2 0.1843 0.899 0.028 0.972
#> GSM550891 1 0.1843 0.809 0.972 0.028
#> GSM550892 1 0.7815 0.882 0.768 0.232
#> GSM550893 2 0.0000 0.915 0.000 1.000
#> GSM550895 2 0.0000 0.915 0.000 1.000
#> GSM550896 2 0.0000 0.915 0.000 1.000
#> GSM550898 1 0.7815 0.882 0.768 0.232
#> GSM550899 2 0.0000 0.915 0.000 1.000
#> GSM550900 2 0.1843 0.899 0.028 0.972
#> GSM550901 2 0.4939 0.813 0.108 0.892
#> GSM550902 1 0.0938 0.824 0.988 0.012
#> GSM550904 1 0.6343 0.866 0.840 0.160
#> GSM550908 1 0.0376 0.821 0.996 0.004
#> GSM550912 2 0.0000 0.915 0.000 1.000
#> GSM550914 2 0.1843 0.899 0.028 0.972
#> GSM550918 2 0.0000 0.915 0.000 1.000
#> GSM550922 2 0.7815 0.770 0.232 0.768
#> GSM550923 1 0.0672 0.825 0.992 0.008
#> GSM550925 1 0.8713 0.808 0.708 0.292
#> GSM550802 2 0.0000 0.915 0.000 1.000
#> GSM550812 2 0.0000 0.915 0.000 1.000
#> GSM550831 1 0.7815 0.882 0.768 0.232
#> GSM550847 1 0.7815 0.882 0.768 0.232
#> GSM550860 1 0.2043 0.808 0.968 0.032
#> GSM550875 1 0.7883 0.879 0.764 0.236
#> GSM550880 2 0.2236 0.892 0.036 0.964
#> GSM550881 1 0.1184 0.816 0.984 0.016
#> GSM550883 1 0.0376 0.821 0.996 0.004
#> GSM550884 2 0.0000 0.915 0.000 1.000
#> GSM550910 2 0.7815 0.770 0.232 0.768
#> GSM550916 1 0.7815 0.882 0.768 0.232
#> GSM550920 2 0.7815 0.770 0.232 0.768
cbind(get_classes(res, k = 3), get_membership(res, k = 3))
#> class entropy silhouette p1 p2 p3
#> GSM550785 1 0.0237 0.8874 0.996 0.004 0.000
#> GSM550786 3 0.6018 0.5863 0.008 0.308 0.684
#> GSM550788 2 0.1860 0.8054 0.000 0.948 0.052
#> GSM550789 2 0.1964 0.8040 0.000 0.944 0.056
#> GSM550790 1 0.0475 0.8868 0.992 0.004 0.004
#> GSM550791 1 0.0661 0.8863 0.988 0.008 0.004
#> GSM550792 2 0.6253 0.6374 0.232 0.732 0.036
#> GSM550796 2 0.2878 0.7786 0.000 0.904 0.096
#> GSM550797 2 0.1964 0.8040 0.000 0.944 0.056
#> GSM550799 3 0.5397 0.6519 0.000 0.280 0.720
#> GSM550800 2 0.0000 0.8138 0.000 1.000 0.000
#> GSM550801 2 0.1860 0.8054 0.000 0.948 0.052
#> GSM550804 2 0.0000 0.8138 0.000 1.000 0.000
#> GSM550806 3 0.3528 0.7403 0.016 0.092 0.892
#> GSM550807 2 0.1163 0.8114 0.000 0.972 0.028
#> GSM550808 2 0.3573 0.7576 0.004 0.876 0.120
#> GSM550809 1 0.0237 0.8866 0.996 0.000 0.004
#> GSM550810 2 0.3112 0.7769 0.004 0.900 0.096
#> GSM550811 1 0.6632 0.5601 0.692 0.272 0.036
#> GSM550813 2 0.0000 0.8138 0.000 1.000 0.000
#> GSM550814 2 0.0661 0.8132 0.004 0.988 0.008
#> GSM550815 2 0.2878 0.7786 0.000 0.904 0.096
#> GSM550816 2 0.1964 0.8040 0.000 0.944 0.056
#> GSM550817 3 0.4796 0.6969 0.000 0.220 0.780
#> GSM550818 3 0.2400 0.7563 0.004 0.064 0.932
#> GSM550819 2 0.2297 0.7946 0.020 0.944 0.036
#> GSM550820 1 0.0000 0.8868 1.000 0.000 0.000
#> GSM550821 2 0.3851 0.7562 0.004 0.860 0.136
#> GSM550822 2 0.2878 0.7786 0.000 0.904 0.096
#> GSM550826 1 0.0592 0.8843 0.988 0.000 0.012
#> GSM550832 2 0.2200 0.8029 0.004 0.940 0.056
#> GSM550833 2 0.1964 0.8040 0.000 0.944 0.056
#> GSM550835 2 0.6169 0.3829 0.004 0.636 0.360
#> GSM550836 3 0.3941 0.6913 0.156 0.000 0.844
#> GSM550837 2 0.3500 0.7612 0.004 0.880 0.116
#> GSM550838 1 0.0237 0.8866 0.996 0.000 0.004
#> GSM550841 3 0.5431 0.6472 0.000 0.284 0.716
#> GSM550842 2 0.3644 0.7539 0.004 0.872 0.124
#> GSM550846 2 0.6526 0.6052 0.260 0.704 0.036
#> GSM550849 1 0.7245 0.3223 0.596 0.368 0.036
#> GSM550850 1 0.0475 0.8868 0.992 0.004 0.004
#> GSM550851 2 0.3644 0.7539 0.004 0.872 0.124
#> GSM550852 2 0.1525 0.8027 0.004 0.964 0.032
#> GSM550853 2 0.1163 0.8114 0.000 0.972 0.028
#> GSM550855 2 0.1163 0.8114 0.000 0.972 0.028
#> GSM550856 2 0.0000 0.8138 0.000 1.000 0.000
#> GSM550861 2 0.1964 0.8040 0.000 0.944 0.056
#> GSM550863 2 0.7476 0.1934 0.452 0.512 0.036
#> GSM550864 2 0.0000 0.8138 0.000 1.000 0.000
#> GSM550866 2 0.0000 0.8138 0.000 1.000 0.000
#> GSM550867 1 0.2096 0.8647 0.944 0.004 0.052
#> GSM550885 1 0.2096 0.8647 0.944 0.004 0.052
#> GSM550886 3 0.6330 0.3991 0.004 0.396 0.600
#> GSM550887 2 0.2356 0.7954 0.000 0.928 0.072
#> GSM550889 2 0.6295 0.6190 0.236 0.728 0.036
#> GSM550894 2 0.2200 0.8029 0.004 0.940 0.056
#> GSM550897 1 0.3083 0.8435 0.916 0.060 0.024
#> GSM550903 2 0.1964 0.8040 0.000 0.944 0.056
#> GSM550905 2 0.3573 0.7576 0.004 0.876 0.120
#> GSM550906 2 0.1964 0.8040 0.000 0.944 0.056
#> GSM550907 3 0.1989 0.7546 0.004 0.048 0.948
#> GSM550909 2 0.4110 0.7536 0.004 0.844 0.152
#> GSM550911 3 0.1989 0.7546 0.004 0.048 0.948
#> GSM550913 2 0.1964 0.8040 0.000 0.944 0.056
#> GSM550915 2 0.7471 0.2063 0.448 0.516 0.036
#> GSM550917 2 0.0000 0.8138 0.000 1.000 0.000
#> GSM550919 2 0.7353 0.3522 0.396 0.568 0.036
#> GSM550921 3 0.3551 0.7034 0.132 0.000 0.868
#> GSM550924 2 0.7495 0.4974 0.084 0.668 0.248
#> GSM550926 2 0.0000 0.8138 0.000 1.000 0.000
#> GSM550927 2 0.1964 0.8040 0.000 0.944 0.056
#> GSM550787 1 0.9502 0.2503 0.492 0.272 0.236
#> GSM550793 3 0.5810 0.4917 0.336 0.000 0.664
#> GSM550794 2 0.6962 0.5341 0.316 0.648 0.036
#> GSM550795 1 0.0475 0.8870 0.992 0.004 0.004
#> GSM550798 1 0.1860 0.8631 0.948 0.000 0.052
#> GSM550803 1 0.2096 0.8647 0.944 0.004 0.052
#> GSM550805 1 0.6335 0.6211 0.724 0.240 0.036
#> GSM550823 2 0.4708 0.7300 0.120 0.844 0.036
#> GSM550824 1 0.2096 0.8647 0.944 0.004 0.052
#> GSM550825 3 0.5058 0.6073 0.244 0.000 0.756
#> GSM550827 2 0.7460 0.2303 0.440 0.524 0.036
#> GSM550828 1 0.0237 0.8874 0.996 0.004 0.000
#> GSM550829 1 0.5058 0.5754 0.756 0.000 0.244
#> GSM550830 2 0.7013 0.4934 0.324 0.640 0.036
#> GSM550834 1 0.2947 0.8461 0.920 0.060 0.020
#> GSM550839 3 0.6608 0.3752 0.008 0.432 0.560
#> GSM550840 1 0.3083 0.8435 0.916 0.060 0.024
#> GSM550843 3 0.4931 0.6998 0.004 0.212 0.784
#> GSM550844 1 0.0237 0.8866 0.996 0.000 0.004
#> GSM550845 2 0.0000 0.8138 0.000 1.000 0.000
#> GSM550848 2 0.6852 0.5547 0.300 0.664 0.036
#> GSM550854 1 0.2096 0.8647 0.944 0.004 0.052
#> GSM550857 3 0.4002 0.6883 0.160 0.000 0.840
#> GSM550858 1 0.0475 0.8868 0.992 0.004 0.004
#> GSM550859 1 0.2096 0.8647 0.944 0.004 0.052
#> GSM550862 1 0.0237 0.8874 0.996 0.004 0.000
#> GSM550865 2 0.7484 0.1655 0.460 0.504 0.036
#> GSM550868 2 0.7484 0.1655 0.460 0.504 0.036
#> GSM550869 2 0.8801 0.4243 0.292 0.560 0.148
#> GSM550870 2 0.0000 0.8138 0.000 1.000 0.000
#> GSM550871 3 0.7069 0.2820 0.020 0.472 0.508
#> GSM550872 1 0.7480 -0.0184 0.508 0.456 0.036
#> GSM550873 2 0.1525 0.8027 0.004 0.964 0.032
#> GSM550874 2 0.0000 0.8138 0.000 1.000 0.000
#> GSM550876 3 0.5988 0.6411 0.008 0.304 0.688
#> GSM550877 2 0.0000 0.8138 0.000 1.000 0.000
#> GSM550878 3 0.1989 0.7546 0.004 0.048 0.948
#> GSM550879 1 0.0475 0.8870 0.992 0.004 0.004
#> GSM550882 3 0.2959 0.7166 0.100 0.000 0.900
#> GSM550888 3 0.3941 0.6913 0.156 0.000 0.844
#> GSM550890 2 0.7311 0.3853 0.384 0.580 0.036
#> GSM550891 3 0.1964 0.7279 0.056 0.000 0.944
#> GSM550892 1 0.0661 0.8863 0.988 0.008 0.004
#> GSM550893 2 0.0000 0.8138 0.000 1.000 0.000
#> GSM550895 2 0.3310 0.7720 0.064 0.908 0.028
#> GSM550896 2 0.0000 0.8138 0.000 1.000 0.000
#> GSM550898 1 0.2096 0.8647 0.944 0.004 0.052
#> GSM550899 2 0.0000 0.8138 0.000 1.000 0.000
#> GSM550900 2 0.7471 0.2067 0.448 0.516 0.036
#> GSM550901 1 0.4413 0.7934 0.860 0.104 0.036
#> GSM550902 1 0.0747 0.8832 0.984 0.000 0.016
#> GSM550904 1 0.0000 0.8868 1.000 0.000 0.000
#> GSM550908 3 0.3941 0.6913 0.156 0.000 0.844
#> GSM550912 2 0.0892 0.8078 0.000 0.980 0.020
#> GSM550914 2 0.6597 0.5981 0.268 0.696 0.036
#> GSM550918 2 0.0000 0.8138 0.000 1.000 0.000
#> GSM550922 3 0.6081 0.5503 0.004 0.344 0.652
#> GSM550923 1 0.1860 0.8631 0.948 0.000 0.052
#> GSM550925 1 0.3722 0.8198 0.888 0.088 0.024
#> GSM550802 2 0.2152 0.7950 0.016 0.948 0.036
#> GSM550812 2 0.5413 0.6955 0.164 0.800 0.036
#> GSM550831 1 0.0237 0.8874 0.996 0.004 0.000
#> GSM550847 1 0.1647 0.8733 0.960 0.004 0.036
#> GSM550860 3 0.6254 0.6361 0.188 0.056 0.756
#> GSM550875 1 0.3237 0.8371 0.912 0.056 0.032
#> GSM550880 1 0.5689 0.7010 0.780 0.184 0.036
#> GSM550881 3 0.3816 0.6946 0.148 0.000 0.852
#> GSM550883 3 0.3941 0.6913 0.156 0.000 0.844
#> GSM550884 2 0.5891 0.6665 0.200 0.764 0.036
#> GSM550910 3 0.5443 0.6595 0.004 0.260 0.736
#> GSM550916 1 0.0475 0.8868 0.992 0.004 0.004
#> GSM550920 3 0.5580 0.6615 0.008 0.256 0.736
cbind(get_classes(res, k = 4), get_membership(res, k = 4))
#> class entropy silhouette p1 p2 p3 p4
#> GSM550785 1 0.1302 7.68e-01 0.956 0.000 0.000 0.044
#> GSM550786 3 0.5470 4.00e-01 0.000 0.100 0.732 0.168
#> GSM550788 2 0.4053 3.85e-01 0.000 0.768 0.228 0.004
#> GSM550789 2 0.4040 3.62e-01 0.000 0.752 0.248 0.000
#> GSM550790 1 0.0707 7.63e-01 0.980 0.000 0.000 0.020
#> GSM550791 1 0.4222 6.73e-01 0.728 0.000 0.000 0.272
#> GSM550792 2 0.8054 9.31e-02 0.040 0.428 0.124 0.408
#> GSM550796 2 0.4608 2.64e-01 0.000 0.692 0.304 0.004
#> GSM550797 2 0.3975 3.73e-01 0.000 0.760 0.240 0.000
#> GSM550799 3 0.3278 5.96e-01 0.000 0.116 0.864 0.020
#> GSM550800 2 0.0524 5.22e-01 0.000 0.988 0.008 0.004
#> GSM550801 2 0.3837 3.89e-01 0.000 0.776 0.224 0.000
#> GSM550804 2 0.0000 5.25e-01 0.000 1.000 0.000 0.000
#> GSM550806 3 0.5055 1.28e-01 0.000 0.008 0.624 0.368
#> GSM550807 2 0.3751 4.11e-01 0.000 0.800 0.196 0.004
#> GSM550808 3 0.4888 3.68e-01 0.000 0.412 0.588 0.000
#> GSM550809 1 0.4776 6.05e-01 0.624 0.000 0.000 0.376
#> GSM550810 2 0.4679 1.69e-01 0.000 0.648 0.352 0.000
#> GSM550811 4 0.9172 1.09e-01 0.144 0.316 0.128 0.412
#> GSM550813 2 0.0336 5.27e-01 0.000 0.992 0.000 0.008
#> GSM550814 2 0.2999 4.53e-01 0.000 0.864 0.132 0.004
#> GSM550815 2 0.4608 2.64e-01 0.000 0.692 0.304 0.004
#> GSM550816 2 0.5279 3.74e-01 0.000 0.716 0.232 0.052
#> GSM550817 3 0.3149 5.76e-01 0.000 0.088 0.880 0.032
#> GSM550818 3 0.3196 4.29e-01 0.000 0.008 0.856 0.136
#> GSM550819 2 0.7569 1.07e-01 0.008 0.432 0.148 0.412
#> GSM550820 1 0.4746 6.13e-01 0.632 0.000 0.000 0.368
#> GSM550821 3 0.6179 4.23e-01 0.000 0.320 0.608 0.072
#> GSM550822 2 0.4632 2.55e-01 0.000 0.688 0.308 0.004
#> GSM550826 1 0.6949 4.14e-01 0.480 0.000 0.112 0.408
#> GSM550832 2 0.4164 3.48e-01 0.000 0.736 0.264 0.000
#> GSM550833 2 0.4155 3.73e-01 0.000 0.756 0.240 0.004
#> GSM550835 3 0.4560 5.08e-01 0.000 0.296 0.700 0.004
#> GSM550836 4 0.5997 1.58e-01 0.048 0.000 0.376 0.576
#> GSM550837 3 0.5060 3.61e-01 0.000 0.412 0.584 0.004
#> GSM550838 1 0.5204 5.96e-01 0.612 0.000 0.012 0.376
#> GSM550841 3 0.3271 6.04e-01 0.000 0.132 0.856 0.012
#> GSM550842 3 0.5039 3.74e-01 0.000 0.404 0.592 0.004
#> GSM550846 2 0.7837 1.27e-01 0.084 0.448 0.052 0.416
#> GSM550849 4 0.9198 1.15e-01 0.144 0.312 0.132 0.412
#> GSM550850 1 0.1211 7.68e-01 0.960 0.000 0.000 0.040
#> GSM550851 3 0.4898 3.61e-01 0.000 0.416 0.584 0.000
#> GSM550852 2 0.5339 4.13e-01 0.000 0.744 0.100 0.156
#> GSM550853 2 0.3870 4.02e-01 0.000 0.788 0.208 0.004
#> GSM550855 2 0.3870 4.02e-01 0.000 0.788 0.208 0.004
#> GSM550856 2 0.0469 5.26e-01 0.000 0.988 0.000 0.012
#> GSM550861 2 0.3975 3.73e-01 0.000 0.760 0.240 0.000
#> GSM550863 2 0.7305 1.38e-01 0.132 0.460 0.004 0.404
#> GSM550864 2 0.0592 5.27e-01 0.000 0.984 0.000 0.016
#> GSM550866 2 0.0921 5.26e-01 0.000 0.972 0.000 0.028
#> GSM550867 1 0.0000 7.57e-01 1.000 0.000 0.000 0.000
#> GSM550885 1 0.0000 7.57e-01 1.000 0.000 0.000 0.000
#> GSM550886 3 0.3757 6.08e-01 0.000 0.152 0.828 0.020
#> GSM550887 2 0.4608 2.64e-01 0.000 0.692 0.304 0.004
#> GSM550889 2 0.5580 2.70e-01 0.016 0.572 0.004 0.408
#> GSM550894 2 0.4222 3.37e-01 0.000 0.728 0.272 0.000
#> GSM550897 4 0.7681 -1.10e-01 0.380 0.216 0.000 0.404
#> GSM550903 2 0.3975 3.73e-01 0.000 0.760 0.240 0.000
#> GSM550905 3 0.4888 3.68e-01 0.000 0.412 0.588 0.000
#> GSM550906 2 0.4155 3.73e-01 0.000 0.756 0.240 0.004
#> GSM550907 3 0.4730 1.47e-01 0.000 0.000 0.636 0.364
#> GSM550909 3 0.6731 4.35e-01 0.000 0.236 0.608 0.156
#> GSM550911 3 0.4730 1.47e-01 0.000 0.000 0.636 0.364
#> GSM550913 2 0.3975 3.73e-01 0.000 0.760 0.240 0.000
#> GSM550915 2 0.7276 1.37e-01 0.128 0.456 0.004 0.412
#> GSM550917 2 0.0000 5.25e-01 0.000 1.000 0.000 0.000
#> GSM550919 2 0.7115 1.60e-01 0.112 0.476 0.004 0.408
#> GSM550921 4 0.5805 1.52e-01 0.036 0.000 0.388 0.576
#> GSM550924 4 0.7816 5.73e-02 0.000 0.316 0.272 0.412
#> GSM550926 2 0.1004 5.25e-01 0.000 0.972 0.004 0.024
#> GSM550927 2 0.4220 3.62e-01 0.000 0.748 0.248 0.004
#> GSM550787 4 0.9296 1.57e-01 0.088 0.276 0.264 0.372
#> GSM550793 4 0.7534 7.06e-02 0.188 0.000 0.380 0.432
#> GSM550794 2 0.8270 7.45e-02 0.056 0.416 0.120 0.408
#> GSM550795 1 0.4761 6.02e-01 0.628 0.000 0.000 0.372
#> GSM550798 1 0.1474 7.12e-01 0.948 0.000 0.000 0.052
#> GSM550803 1 0.0000 7.57e-01 1.000 0.000 0.000 0.000
#> GSM550805 4 0.9303 1.51e-01 0.172 0.288 0.128 0.412
#> GSM550823 2 0.7239 1.80e-01 0.020 0.480 0.084 0.416
#> GSM550824 1 0.0000 7.57e-01 1.000 0.000 0.000 0.000
#> GSM550825 4 0.7169 1.38e-01 0.152 0.000 0.332 0.516
#> GSM550827 2 0.7235 1.46e-01 0.124 0.464 0.004 0.408
#> GSM550828 1 0.1474 7.66e-01 0.948 0.000 0.000 0.052
#> GSM550829 1 0.4667 5.68e-01 0.796 0.000 0.096 0.108
#> GSM550830 2 0.5955 2.50e-01 0.032 0.552 0.004 0.412
#> GSM550834 1 0.5004 5.69e-01 0.604 0.004 0.000 0.392
#> GSM550839 3 0.6147 4.06e-01 0.000 0.224 0.664 0.112
#> GSM550840 1 0.5279 5.43e-01 0.588 0.012 0.000 0.400
#> GSM550843 3 0.5121 4.77e-01 0.000 0.120 0.764 0.116
#> GSM550844 1 0.4776 6.06e-01 0.624 0.000 0.000 0.376
#> GSM550845 2 0.1389 5.20e-01 0.000 0.952 0.000 0.048
#> GSM550848 2 0.7157 1.55e-01 0.116 0.472 0.004 0.408
#> GSM550854 1 0.0000 7.57e-01 1.000 0.000 0.000 0.000
#> GSM550857 4 0.6150 1.59e-01 0.060 0.000 0.360 0.580
#> GSM550858 1 0.1211 7.68e-01 0.960 0.000 0.000 0.040
#> GSM550859 1 0.0000 7.57e-01 1.000 0.000 0.000 0.000
#> GSM550862 1 0.1302 7.68e-01 0.956 0.000 0.000 0.044
#> GSM550865 2 0.7305 1.38e-01 0.132 0.460 0.004 0.404
#> GSM550868 2 0.7305 1.38e-01 0.132 0.460 0.004 0.404
#> GSM550869 4 0.7979 -5.17e-03 0.008 0.352 0.224 0.416
#> GSM550870 2 0.0000 5.25e-01 0.000 1.000 0.000 0.000
#> GSM550871 3 0.7626 3.61e-05 0.000 0.304 0.464 0.232
#> GSM550872 2 0.7305 1.38e-01 0.132 0.460 0.004 0.404
#> GSM550873 2 0.5998 3.10e-01 0.000 0.684 0.200 0.116
#> GSM550874 2 0.0779 5.26e-01 0.000 0.980 0.004 0.016
#> GSM550876 3 0.5520 4.23e-01 0.000 0.244 0.696 0.060
#> GSM550877 2 0.0336 5.26e-01 0.000 0.992 0.000 0.008
#> GSM550878 3 0.4746 1.41e-01 0.000 0.000 0.632 0.368
#> GSM550879 1 0.4730 6.09e-01 0.636 0.000 0.000 0.364
#> GSM550882 4 0.5105 1.03e-01 0.004 0.000 0.432 0.564
#> GSM550888 4 0.5997 1.58e-01 0.048 0.000 0.376 0.576
#> GSM550890 2 0.7309 1.36e-01 0.132 0.456 0.004 0.408
#> GSM550891 4 0.5080 1.18e-01 0.004 0.000 0.420 0.576
#> GSM550892 1 0.4406 6.51e-01 0.700 0.000 0.000 0.300
#> GSM550893 2 0.0469 5.27e-01 0.000 0.988 0.000 0.012
#> GSM550895 2 0.5201 2.89e-01 0.004 0.592 0.004 0.400
#> GSM550896 2 0.0336 5.26e-01 0.000 0.992 0.000 0.008
#> GSM550898 1 0.0000 7.57e-01 1.000 0.000 0.000 0.000
#> GSM550899 2 0.0469 5.27e-01 0.000 0.988 0.000 0.012
#> GSM550900 2 0.7341 1.31e-01 0.136 0.456 0.004 0.404
#> GSM550901 4 0.7665 -1.17e-01 0.384 0.212 0.000 0.404
#> GSM550902 1 0.7379 3.93e-01 0.472 0.020 0.096 0.412
#> GSM550904 1 0.4920 6.12e-01 0.628 0.000 0.004 0.368
#> GSM550908 4 0.5936 1.56e-01 0.044 0.000 0.380 0.576
#> GSM550912 2 0.1109 5.23e-01 0.000 0.968 0.004 0.028
#> GSM550914 2 0.7115 1.65e-01 0.112 0.476 0.004 0.408
#> GSM550918 2 0.0188 5.26e-01 0.000 0.996 0.000 0.004
#> GSM550922 3 0.3123 6.07e-01 0.000 0.156 0.844 0.000
#> GSM550923 1 0.0336 7.54e-01 0.992 0.000 0.000 0.008
#> GSM550925 4 0.7785 -4.01e-02 0.348 0.248 0.000 0.404
#> GSM550802 2 0.7070 1.82e-01 0.008 0.484 0.096 0.412
#> GSM550812 2 0.7836 9.43e-02 0.020 0.428 0.144 0.408
#> GSM550831 1 0.1302 7.68e-01 0.956 0.000 0.000 0.044
#> GSM550847 1 0.0000 7.57e-01 1.000 0.000 0.000 0.000
#> GSM550860 3 0.8639 -7.32e-03 0.052 0.224 0.460 0.264
#> GSM550875 4 0.9151 1.21e-02 0.292 0.204 0.092 0.412
#> GSM550880 4 0.7990 8.09e-02 0.276 0.316 0.004 0.404
#> GSM550881 4 0.5805 1.52e-01 0.036 0.000 0.388 0.576
#> GSM550883 4 0.5984 1.59e-01 0.048 0.000 0.372 0.580
#> GSM550884 2 0.7868 8.03e-02 0.020 0.420 0.148 0.412
#> GSM550910 3 0.3335 6.02e-01 0.000 0.120 0.860 0.020
#> GSM550916 1 0.1211 7.68e-01 0.960 0.000 0.000 0.040
#> GSM550920 3 0.4731 5.16e-01 0.000 0.160 0.780 0.060
cbind(get_classes(res, k = 5), get_membership(res, k = 5))
#> class entropy silhouette p1 p2 p3 p4 p5
#> GSM550785 1 0.1443 0.9343 0.948 0.000 0.004 0.044 0.004
#> GSM550786 5 0.2756 0.7270 0.000 0.004 0.024 0.092 0.880
#> GSM550788 2 0.1901 0.8041 0.000 0.932 0.004 0.024 0.040
#> GSM550789 2 0.2249 0.7923 0.000 0.896 0.000 0.008 0.096
#> GSM550790 1 0.0912 0.9467 0.972 0.000 0.012 0.016 0.000
#> GSM550791 4 0.5730 0.2022 0.464 0.004 0.012 0.476 0.044
#> GSM550792 4 0.3839 0.7710 0.004 0.064 0.008 0.828 0.096
#> GSM550796 2 0.2280 0.7757 0.000 0.880 0.000 0.000 0.120
#> GSM550797 2 0.2193 0.7933 0.000 0.900 0.000 0.008 0.092
#> GSM550799 5 0.2514 0.7714 0.000 0.044 0.060 0.000 0.896
#> GSM550800 2 0.2206 0.7990 0.000 0.912 0.016 0.068 0.004
#> GSM550801 2 0.2069 0.7994 0.000 0.912 0.000 0.012 0.076
#> GSM550804 2 0.3594 0.7851 0.000 0.804 0.004 0.172 0.020
#> GSM550806 5 0.3993 0.6343 0.000 0.000 0.216 0.028 0.756
#> GSM550807 2 0.0955 0.8092 0.000 0.968 0.000 0.004 0.028
#> GSM550808 5 0.3980 0.6487 0.000 0.284 0.000 0.008 0.708
#> GSM550809 4 0.5416 0.6300 0.256 0.000 0.024 0.664 0.056
#> GSM550810 2 0.2329 0.7739 0.000 0.876 0.000 0.000 0.124
#> GSM550811 4 0.3971 0.7672 0.024 0.028 0.016 0.832 0.100
#> GSM550813 2 0.3427 0.7804 0.000 0.796 0.000 0.192 0.012
#> GSM550814 2 0.3194 0.7949 0.000 0.832 0.000 0.148 0.020
#> GSM550815 2 0.2280 0.7757 0.000 0.880 0.000 0.000 0.120
#> GSM550816 2 0.4559 0.7224 0.000 0.748 0.000 0.152 0.100
#> GSM550817 5 0.2569 0.7690 0.000 0.040 0.068 0.000 0.892
#> GSM550818 5 0.2969 0.7351 0.000 0.020 0.128 0.000 0.852
#> GSM550819 4 0.3924 0.7662 0.000 0.096 0.020 0.824 0.060
#> GSM550820 4 0.5567 0.6055 0.280 0.000 0.028 0.640 0.052
#> GSM550821 5 0.2522 0.7575 0.000 0.108 0.000 0.012 0.880
#> GSM550822 2 0.2280 0.7757 0.000 0.880 0.000 0.000 0.120
#> GSM550826 4 0.5712 0.6638 0.188 0.000 0.028 0.676 0.108
#> GSM550832 2 0.2233 0.7893 0.000 0.892 0.000 0.004 0.104
#> GSM550833 2 0.2020 0.7904 0.000 0.900 0.000 0.000 0.100
#> GSM550835 5 0.2911 0.7539 0.000 0.136 0.004 0.008 0.852
#> GSM550836 3 0.1270 0.9065 0.000 0.000 0.948 0.000 0.052
#> GSM550837 5 0.4415 0.4644 0.000 0.388 0.000 0.008 0.604
#> GSM550838 4 0.5615 0.6273 0.256 0.000 0.028 0.652 0.064
#> GSM550841 5 0.2446 0.7726 0.000 0.044 0.056 0.000 0.900
#> GSM550842 5 0.3612 0.6624 0.000 0.268 0.000 0.000 0.732
#> GSM550846 4 0.3952 0.7749 0.012 0.084 0.012 0.832 0.060
#> GSM550849 4 0.4104 0.7587 0.024 0.028 0.008 0.812 0.128
#> GSM550850 1 0.1682 0.9321 0.940 0.000 0.012 0.044 0.004
#> GSM550851 5 0.4415 0.4644 0.000 0.388 0.000 0.008 0.604
#> GSM550852 4 0.5509 0.3323 0.000 0.360 0.000 0.564 0.076
#> GSM550853 2 0.1012 0.8078 0.000 0.968 0.000 0.012 0.020
#> GSM550855 2 0.1018 0.8076 0.000 0.968 0.000 0.016 0.016
#> GSM550856 2 0.3527 0.7722 0.000 0.792 0.016 0.192 0.000
#> GSM550861 2 0.2249 0.7923 0.000 0.896 0.000 0.008 0.096
#> GSM550863 4 0.3983 0.7728 0.048 0.104 0.020 0.824 0.004
#> GSM550864 2 0.3419 0.7850 0.000 0.804 0.000 0.180 0.016
#> GSM550866 2 0.3596 0.7657 0.000 0.784 0.016 0.200 0.000
#> GSM550867 1 0.1082 0.9497 0.964 0.000 0.028 0.008 0.000
#> GSM550885 1 0.1082 0.9497 0.964 0.000 0.028 0.008 0.000
#> GSM550886 5 0.2673 0.7680 0.000 0.028 0.024 0.048 0.900
#> GSM550887 2 0.2280 0.7757 0.000 0.880 0.000 0.000 0.120
#> GSM550889 4 0.3984 0.7216 0.004 0.184 0.020 0.784 0.008
#> GSM550894 2 0.2127 0.7872 0.000 0.892 0.000 0.000 0.108
#> GSM550897 4 0.3751 0.7737 0.104 0.016 0.024 0.840 0.016
#> GSM550903 2 0.2249 0.7923 0.000 0.896 0.000 0.008 0.096
#> GSM550905 5 0.3388 0.7130 0.000 0.200 0.000 0.008 0.792
#> GSM550906 2 0.1965 0.7921 0.000 0.904 0.000 0.000 0.096
#> GSM550907 5 0.4166 0.4418 0.000 0.000 0.348 0.004 0.648
#> GSM550909 5 0.3743 0.7245 0.000 0.076 0.004 0.096 0.824
#> GSM550911 5 0.4166 0.4418 0.000 0.000 0.348 0.004 0.648
#> GSM550913 2 0.2249 0.7923 0.000 0.896 0.000 0.008 0.096
#> GSM550915 4 0.4381 0.7719 0.040 0.076 0.012 0.816 0.056
#> GSM550917 2 0.3264 0.7911 0.000 0.820 0.000 0.164 0.016
#> GSM550919 4 0.4319 0.7730 0.040 0.084 0.008 0.816 0.052
#> GSM550921 3 0.1341 0.9050 0.000 0.000 0.944 0.000 0.056
#> GSM550924 4 0.5444 0.5332 0.004 0.044 0.012 0.616 0.324
#> GSM550926 2 0.3752 0.7632 0.000 0.780 0.016 0.200 0.004
#> GSM550927 2 0.2020 0.7904 0.000 0.900 0.000 0.000 0.100
#> GSM550787 4 0.5274 0.5250 0.020 0.012 0.020 0.652 0.296
#> GSM550793 3 0.7538 0.1872 0.100 0.000 0.452 0.324 0.124
#> GSM550794 4 0.3487 0.7723 0.008 0.056 0.008 0.856 0.072
#> GSM550795 4 0.4926 0.6258 0.276 0.000 0.012 0.676 0.036
#> GSM550798 1 0.1877 0.9163 0.924 0.000 0.064 0.012 0.000
#> GSM550803 1 0.0794 0.9459 0.972 0.000 0.028 0.000 0.000
#> GSM550805 4 0.3488 0.7596 0.024 0.012 0.016 0.856 0.092
#> GSM550823 4 0.3387 0.7665 0.000 0.100 0.020 0.852 0.028
#> GSM550824 1 0.1082 0.9497 0.964 0.000 0.028 0.008 0.000
#> GSM550825 3 0.2754 0.8322 0.080 0.000 0.884 0.004 0.032
#> GSM550827 4 0.4395 0.7708 0.040 0.100 0.008 0.808 0.044
#> GSM550828 1 0.2037 0.9088 0.920 0.000 0.004 0.064 0.012
#> GSM550829 1 0.4254 0.7520 0.768 0.000 0.188 0.024 0.020
#> GSM550830 4 0.3203 0.7611 0.000 0.124 0.020 0.848 0.008
#> GSM550834 4 0.4508 0.6509 0.256 0.000 0.004 0.708 0.032
#> GSM550839 5 0.4344 0.6656 0.000 0.068 0.024 0.112 0.796
#> GSM550840 4 0.5096 0.6536 0.264 0.012 0.024 0.684 0.016
#> GSM550843 5 0.3171 0.7520 0.000 0.008 0.084 0.044 0.864
#> GSM550844 4 0.5330 0.6080 0.296 0.000 0.016 0.640 0.048
#> GSM550845 2 0.4061 0.7171 0.000 0.740 0.016 0.240 0.004
#> GSM550848 4 0.4483 0.7708 0.040 0.096 0.008 0.804 0.052
#> GSM550854 1 0.1082 0.9497 0.964 0.000 0.028 0.008 0.000
#> GSM550857 3 0.1251 0.8975 0.008 0.000 0.956 0.000 0.036
#> GSM550858 1 0.1116 0.9413 0.964 0.000 0.004 0.028 0.004
#> GSM550859 1 0.1082 0.9497 0.964 0.000 0.028 0.008 0.000
#> GSM550862 1 0.1285 0.9381 0.956 0.000 0.004 0.036 0.004
#> GSM550865 4 0.3720 0.7709 0.048 0.096 0.020 0.836 0.000
#> GSM550868 4 0.3678 0.7701 0.048 0.100 0.016 0.836 0.000
#> GSM550869 4 0.5549 0.6585 0.020 0.048 0.028 0.704 0.200
#> GSM550870 2 0.3318 0.7856 0.000 0.808 0.000 0.180 0.012
#> GSM550871 4 0.6002 0.3747 0.000 0.064 0.024 0.540 0.372
#> GSM550872 4 0.3720 0.7709 0.048 0.096 0.020 0.836 0.000
#> GSM550873 2 0.6770 0.0846 0.000 0.384 0.000 0.340 0.276
#> GSM550874 2 0.3596 0.7657 0.000 0.784 0.016 0.200 0.000
#> GSM550876 5 0.4349 0.6788 0.000 0.064 0.032 0.104 0.800
#> GSM550877 2 0.3527 0.7722 0.000 0.792 0.016 0.192 0.000
#> GSM550878 5 0.4402 0.4326 0.000 0.000 0.352 0.012 0.636
#> GSM550879 4 0.5136 0.6157 0.284 0.000 0.016 0.660 0.040
#> GSM550882 3 0.2722 0.8467 0.000 0.000 0.872 0.020 0.108
#> GSM550888 3 0.1270 0.9065 0.000 0.000 0.948 0.000 0.052
#> GSM550890 4 0.4679 0.7709 0.044 0.092 0.012 0.796 0.056
#> GSM550891 3 0.1831 0.8899 0.000 0.000 0.920 0.004 0.076
#> GSM550892 4 0.4774 0.5788 0.328 0.000 0.012 0.644 0.016
#> GSM550893 2 0.3752 0.7632 0.000 0.780 0.016 0.200 0.004
#> GSM550895 4 0.3622 0.7347 0.000 0.172 0.016 0.804 0.008
#> GSM550896 2 0.3562 0.7706 0.000 0.788 0.016 0.196 0.000
#> GSM550898 1 0.1082 0.9497 0.964 0.000 0.028 0.008 0.000
#> GSM550899 2 0.3419 0.7850 0.000 0.804 0.000 0.180 0.016
#> GSM550900 4 0.3960 0.7679 0.040 0.104 0.020 0.828 0.008
#> GSM550901 4 0.4504 0.7684 0.096 0.024 0.016 0.804 0.060
#> GSM550902 4 0.5667 0.6683 0.192 0.000 0.020 0.672 0.116
#> GSM550904 4 0.5646 0.6121 0.272 0.000 0.028 0.640 0.060
#> GSM550908 3 0.1270 0.9065 0.000 0.000 0.948 0.000 0.052
#> GSM550912 2 0.3596 0.7727 0.000 0.784 0.000 0.200 0.016
#> GSM550914 4 0.4830 0.7690 0.036 0.100 0.020 0.788 0.056
#> GSM550918 2 0.3670 0.7820 0.000 0.796 0.004 0.180 0.020
#> GSM550922 5 0.2171 0.7755 0.000 0.064 0.024 0.000 0.912
#> GSM550923 1 0.1364 0.9384 0.952 0.000 0.036 0.012 0.000
#> GSM550925 4 0.3972 0.7736 0.108 0.028 0.024 0.828 0.012
#> GSM550802 4 0.3735 0.7646 0.000 0.116 0.016 0.828 0.040
#> GSM550812 4 0.3869 0.7698 0.000 0.084 0.012 0.824 0.080
#> GSM550831 1 0.2095 0.9163 0.920 0.000 0.012 0.060 0.008
#> GSM550847 1 0.0693 0.9493 0.980 0.000 0.012 0.008 0.000
#> GSM550860 4 0.5492 0.5901 0.016 0.036 0.020 0.668 0.260
#> GSM550875 4 0.4509 0.7473 0.080 0.012 0.020 0.800 0.088
#> GSM550880 4 0.3335 0.7774 0.072 0.016 0.008 0.868 0.036
#> GSM550881 3 0.1740 0.9012 0.000 0.000 0.932 0.012 0.056
#> GSM550883 3 0.1197 0.9052 0.000 0.000 0.952 0.000 0.048
#> GSM550884 4 0.3810 0.7687 0.000 0.076 0.012 0.828 0.084
#> GSM550910 5 0.2040 0.7750 0.000 0.032 0.032 0.008 0.928
#> GSM550916 1 0.1106 0.9433 0.964 0.000 0.012 0.024 0.000
#> GSM550920 5 0.3114 0.7519 0.000 0.016 0.036 0.076 0.872
cbind(get_classes(res, k = 6), get_membership(res, k = 6))
#> class entropy silhouette p1 p2 p3 p4 p5 p6
#> GSM550785 1 0.2752 0.8370 0.864 0.000 0.000 0.036 0.004 0.096
#> GSM550786 5 0.2237 0.8038 0.000 0.004 0.000 0.080 0.896 0.020
#> GSM550788 2 0.0790 0.8123 0.000 0.968 0.000 0.032 0.000 0.000
#> GSM550789 2 0.1003 0.8042 0.000 0.964 0.000 0.020 0.016 0.000
#> GSM550790 1 0.1116 0.8831 0.960 0.000 0.000 0.028 0.004 0.008
#> GSM550791 6 0.6328 0.2344 0.296 0.004 0.000 0.260 0.008 0.432
#> GSM550792 4 0.4961 0.1863 0.000 0.016 0.004 0.564 0.032 0.384
#> GSM550796 2 0.1421 0.7933 0.000 0.944 0.000 0.028 0.028 0.000
#> GSM550797 2 0.0603 0.8094 0.000 0.980 0.000 0.004 0.016 0.000
#> GSM550799 5 0.2240 0.8146 0.000 0.032 0.008 0.056 0.904 0.000
#> GSM550800 2 0.2266 0.7954 0.000 0.880 0.000 0.108 0.000 0.012
#> GSM550801 2 0.0717 0.8101 0.000 0.976 0.000 0.008 0.016 0.000
#> GSM550804 2 0.4870 0.7280 0.000 0.716 0.004 0.152 0.024 0.104
#> GSM550806 5 0.3743 0.7622 0.000 0.000 0.052 0.144 0.792 0.012
#> GSM550807 2 0.0520 0.8125 0.000 0.984 0.000 0.008 0.008 0.000
#> GSM550808 5 0.4219 0.6161 0.000 0.320 0.000 0.032 0.648 0.000
#> GSM550809 6 0.4733 0.4545 0.120 0.000 0.000 0.188 0.004 0.688
#> GSM550810 2 0.1341 0.7935 0.000 0.948 0.000 0.024 0.028 0.000
#> GSM550811 6 0.3240 0.3901 0.000 0.000 0.000 0.244 0.004 0.752
#> GSM550813 2 0.4816 0.7306 0.000 0.720 0.004 0.156 0.024 0.096
#> GSM550814 2 0.4056 0.7408 0.000 0.732 0.000 0.224 0.012 0.032
#> GSM550815 2 0.1421 0.7933 0.000 0.944 0.000 0.028 0.028 0.000
#> GSM550816 2 0.4106 0.7377 0.000 0.788 0.004 0.064 0.028 0.116
#> GSM550817 5 0.1622 0.8071 0.000 0.028 0.016 0.016 0.940 0.000
#> GSM550818 5 0.1426 0.8034 0.000 0.008 0.028 0.016 0.948 0.000
#> GSM550819 4 0.3197 0.4336 0.000 0.012 0.000 0.804 0.008 0.176
#> GSM550820 6 0.4742 0.4548 0.124 0.000 0.000 0.184 0.004 0.688
#> GSM550821 5 0.2065 0.8134 0.000 0.052 0.004 0.032 0.912 0.000
#> GSM550822 2 0.1421 0.7933 0.000 0.944 0.000 0.028 0.028 0.000
#> GSM550826 6 0.4703 0.4373 0.096 0.000 0.000 0.204 0.008 0.692
#> GSM550832 2 0.0777 0.8094 0.000 0.972 0.000 0.004 0.024 0.000
#> GSM550833 2 0.1092 0.8028 0.000 0.960 0.000 0.020 0.020 0.000
#> GSM550835 5 0.3252 0.7960 0.000 0.108 0.000 0.068 0.824 0.000
#> GSM550836 3 0.0260 0.9586 0.000 0.000 0.992 0.000 0.008 0.000
#> GSM550837 5 0.4417 0.4843 0.000 0.416 0.000 0.028 0.556 0.000
#> GSM550838 6 0.4762 0.4526 0.120 0.000 0.000 0.192 0.004 0.684
#> GSM550841 5 0.1478 0.8090 0.000 0.032 0.004 0.020 0.944 0.000
#> GSM550842 5 0.4020 0.6588 0.000 0.276 0.000 0.032 0.692 0.000
#> GSM550846 6 0.4422 0.2817 0.000 0.008 0.008 0.288 0.024 0.672
#> GSM550849 6 0.4591 0.0537 0.000 0.000 0.004 0.452 0.028 0.516
#> GSM550850 1 0.3141 0.8143 0.832 0.000 0.000 0.040 0.004 0.124
#> GSM550851 5 0.4403 0.5008 0.000 0.408 0.000 0.028 0.564 0.000
#> GSM550852 4 0.6532 0.1966 0.000 0.244 0.004 0.500 0.040 0.212
#> GSM550853 2 0.0632 0.8126 0.000 0.976 0.000 0.024 0.000 0.000
#> GSM550855 2 0.0632 0.8126 0.000 0.976 0.000 0.024 0.000 0.000
#> GSM550856 2 0.4464 0.6963 0.000 0.676 0.000 0.264 0.004 0.056
#> GSM550861 2 0.0603 0.8094 0.000 0.980 0.000 0.004 0.016 0.000
#> GSM550863 6 0.4322 -0.1040 0.008 0.008 0.000 0.472 0.000 0.512
#> GSM550864 2 0.4826 0.7306 0.000 0.720 0.004 0.152 0.024 0.100
#> GSM550866 2 0.4408 0.6826 0.000 0.664 0.000 0.280 0.000 0.056
#> GSM550867 1 0.0000 0.8920 1.000 0.000 0.000 0.000 0.000 0.000
#> GSM550885 1 0.0000 0.8920 1.000 0.000 0.000 0.000 0.000 0.000
#> GSM550886 5 0.1843 0.8072 0.000 0.004 0.000 0.080 0.912 0.004
#> GSM550887 2 0.1257 0.7990 0.000 0.952 0.000 0.028 0.020 0.000
#> GSM550889 4 0.3974 0.3680 0.000 0.024 0.000 0.680 0.000 0.296
#> GSM550894 2 0.0692 0.8086 0.000 0.976 0.000 0.004 0.020 0.000
#> GSM550897 4 0.4556 0.2020 0.020 0.000 0.000 0.516 0.008 0.456
#> GSM550903 2 0.0603 0.8094 0.000 0.980 0.000 0.004 0.016 0.000
#> GSM550905 5 0.3171 0.7325 0.000 0.204 0.000 0.012 0.784 0.000
#> GSM550906 2 0.0692 0.8079 0.000 0.976 0.000 0.004 0.020 0.000
#> GSM550907 5 0.3394 0.6612 0.000 0.000 0.200 0.024 0.776 0.000
#> GSM550909 5 0.4057 0.6773 0.000 0.016 0.004 0.160 0.772 0.048
#> GSM550911 5 0.3394 0.6612 0.000 0.000 0.200 0.024 0.776 0.000
#> GSM550913 2 0.0603 0.8094 0.000 0.980 0.000 0.004 0.016 0.000
#> GSM550915 6 0.4015 0.3388 0.004 0.016 0.008 0.184 0.020 0.768
#> GSM550917 2 0.4791 0.7333 0.000 0.724 0.004 0.148 0.024 0.100
#> GSM550919 6 0.4346 0.2995 0.000 0.024 0.004 0.220 0.028 0.724
#> GSM550921 3 0.0260 0.9586 0.000 0.000 0.992 0.000 0.008 0.000
#> GSM550924 4 0.6142 0.1924 0.000 0.016 0.004 0.520 0.200 0.260
#> GSM550926 2 0.4792 0.6498 0.000 0.632 0.000 0.300 0.008 0.060
#> GSM550927 2 0.1168 0.8027 0.000 0.956 0.000 0.028 0.016 0.000
#> GSM550787 4 0.5452 0.2791 0.000 0.008 0.004 0.620 0.160 0.208
#> GSM550793 4 0.6986 -0.0166 0.028 0.000 0.312 0.372 0.016 0.272
#> GSM550794 4 0.4581 0.3520 0.000 0.016 0.004 0.672 0.032 0.276
#> GSM550795 6 0.3517 0.4674 0.136 0.000 0.000 0.056 0.004 0.804
#> GSM550798 1 0.0260 0.8896 0.992 0.000 0.000 0.000 0.000 0.008
#> GSM550803 1 0.0260 0.8896 0.992 0.000 0.000 0.000 0.000 0.008
#> GSM550805 4 0.3835 0.2469 0.000 0.000 0.000 0.668 0.012 0.320
#> GSM550823 4 0.2664 0.4431 0.000 0.016 0.000 0.848 0.000 0.136
#> GSM550824 1 0.0000 0.8920 1.000 0.000 0.000 0.000 0.000 0.000
#> GSM550825 3 0.2996 0.8856 0.072 0.000 0.868 0.016 0.008 0.036
#> GSM550827 6 0.4994 0.1296 0.004 0.024 0.004 0.320 0.028 0.620
#> GSM550828 1 0.4286 0.5871 0.648 0.000 0.000 0.028 0.004 0.320
#> GSM550829 1 0.5630 0.6068 0.664 0.000 0.056 0.164 0.008 0.108
#> GSM550830 4 0.3871 0.3688 0.000 0.016 0.000 0.676 0.000 0.308
#> GSM550834 6 0.4252 0.4481 0.120 0.000 0.000 0.120 0.008 0.752
#> GSM550839 5 0.3370 0.7233 0.000 0.012 0.000 0.212 0.772 0.004
#> GSM550840 4 0.5176 0.1304 0.076 0.000 0.000 0.508 0.004 0.412
#> GSM550843 5 0.1913 0.8079 0.000 0.000 0.012 0.080 0.908 0.000
#> GSM550844 4 0.5760 -0.1697 0.120 0.000 0.000 0.436 0.012 0.432
#> GSM550845 2 0.6180 0.3010 0.000 0.448 0.000 0.328 0.012 0.212
#> GSM550848 6 0.4635 0.2685 0.004 0.028 0.004 0.232 0.028 0.704
#> GSM550854 1 0.0000 0.8920 1.000 0.000 0.000 0.000 0.000 0.000
#> GSM550857 3 0.0405 0.9575 0.000 0.000 0.988 0.000 0.008 0.004
#> GSM550858 1 0.3517 0.7631 0.780 0.000 0.000 0.028 0.004 0.188
#> GSM550859 1 0.0000 0.8920 1.000 0.000 0.000 0.000 0.000 0.000
#> GSM550862 1 0.4031 0.7312 0.748 0.000 0.000 0.060 0.004 0.188
#> GSM550865 4 0.4419 0.2365 0.008 0.016 0.000 0.568 0.000 0.408
#> GSM550868 4 0.4387 0.2584 0.008 0.016 0.000 0.584 0.000 0.392
#> GSM550869 4 0.3800 0.3952 0.000 0.012 0.000 0.780 0.044 0.164
#> GSM550870 2 0.4816 0.7306 0.000 0.720 0.004 0.156 0.024 0.096
#> GSM550871 4 0.4582 0.3128 0.000 0.012 0.000 0.652 0.296 0.040
#> GSM550872 4 0.4419 0.2365 0.008 0.016 0.000 0.568 0.000 0.408
#> GSM550873 4 0.6745 0.2274 0.000 0.216 0.004 0.528 0.148 0.104
#> GSM550874 2 0.4579 0.6590 0.000 0.644 0.000 0.300 0.004 0.052
#> GSM550876 5 0.3087 0.7536 0.000 0.012 0.000 0.176 0.808 0.004
#> GSM550877 2 0.4428 0.6956 0.000 0.676 0.000 0.268 0.004 0.052
#> GSM550878 5 0.4195 0.6729 0.000 0.000 0.200 0.076 0.724 0.000
#> GSM550879 6 0.3331 0.4698 0.136 0.000 0.000 0.044 0.004 0.816
#> GSM550882 3 0.3779 0.8312 0.000 0.000 0.812 0.080 0.076 0.032
#> GSM550888 3 0.0260 0.9586 0.000 0.000 0.992 0.000 0.008 0.000
#> GSM550890 6 0.4376 0.3036 0.008 0.012 0.008 0.220 0.024 0.728
#> GSM550891 3 0.0405 0.9574 0.000 0.000 0.988 0.004 0.008 0.000
#> GSM550892 6 0.5551 0.1065 0.144 0.000 0.000 0.360 0.000 0.496
#> GSM550893 2 0.4612 0.6488 0.000 0.636 0.000 0.308 0.004 0.052
#> GSM550895 4 0.4445 0.3511 0.000 0.056 0.000 0.656 0.000 0.288
#> GSM550896 2 0.4488 0.6866 0.000 0.664 0.000 0.280 0.004 0.052
#> GSM550898 1 0.0000 0.8920 1.000 0.000 0.000 0.000 0.000 0.000
#> GSM550899 2 0.4826 0.7306 0.000 0.720 0.004 0.152 0.024 0.100
#> GSM550900 4 0.4008 0.3657 0.004 0.016 0.000 0.672 0.000 0.308
#> GSM550901 6 0.3320 0.4012 0.008 0.012 0.004 0.112 0.024 0.840
#> GSM550902 6 0.4684 0.3403 0.052 0.000 0.000 0.300 0.008 0.640
#> GSM550904 6 0.4762 0.4526 0.120 0.000 0.000 0.192 0.004 0.684
#> GSM550908 3 0.0260 0.9586 0.000 0.000 0.992 0.000 0.008 0.000
#> GSM550912 2 0.5107 0.7075 0.000 0.692 0.004 0.172 0.028 0.104
#> GSM550914 6 0.4596 0.2564 0.008 0.012 0.008 0.256 0.024 0.692
#> GSM550918 2 0.4904 0.7261 0.000 0.712 0.004 0.156 0.024 0.104
#> GSM550922 5 0.1320 0.8102 0.000 0.036 0.000 0.016 0.948 0.000
#> GSM550923 1 0.0260 0.8896 0.992 0.000 0.000 0.000 0.000 0.008
#> GSM550925 4 0.4525 0.2511 0.004 0.012 0.000 0.528 0.008 0.448
#> GSM550802 4 0.3604 0.4127 0.000 0.012 0.000 0.760 0.012 0.216
#> GSM550812 4 0.4464 0.3474 0.000 0.012 0.004 0.672 0.028 0.284
#> GSM550831 1 0.3960 0.7157 0.736 0.000 0.000 0.040 0.004 0.220
#> GSM550847 1 0.0000 0.8920 1.000 0.000 0.000 0.000 0.000 0.000
#> GSM550860 4 0.4817 0.3505 0.000 0.008 0.000 0.684 0.112 0.196
#> GSM550875 4 0.3867 0.2291 0.000 0.000 0.000 0.660 0.012 0.328
#> GSM550880 6 0.3560 0.2918 0.008 0.004 0.000 0.256 0.000 0.732
#> GSM550881 3 0.2113 0.9252 0.000 0.000 0.912 0.048 0.008 0.032
#> GSM550883 3 0.1149 0.9499 0.000 0.000 0.960 0.008 0.008 0.024
#> GSM550884 4 0.4612 0.3455 0.000 0.020 0.004 0.668 0.028 0.280
#> GSM550910 5 0.0964 0.8105 0.000 0.016 0.000 0.012 0.968 0.004
#> GSM550916 1 0.1442 0.8778 0.944 0.000 0.000 0.040 0.004 0.012
#> GSM550920 5 0.1897 0.8063 0.000 0.004 0.000 0.084 0.908 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)
get_signatures(res, k = 3)
get_signatures(res, k = 4)
get_signatures(res, k = 5)
get_signatures(res, k = 6)
Signature heatmaps where rows are not scaled:
get_signatures(res, k = 2, scale_rows = FALSE)
get_signatures(res, k = 3, scale_rows = FALSE)
get_signatures(res, k = 4, scale_rows = FALSE)
get_signatures(res, k = 5, scale_rows = FALSE)
get_signatures(res, k = 6, scale_rows = FALSE)
Compare the overlap of signatures from different k:
compare_signatures(res)
get_signature() returns a data frame invisibly. TO get the list of signatures, the function
call should be assigned to a variable explicitly. In following code, if plot argument is set
to FALSE, no heatmap is plotted while only the differential analysis is performed.
# code only for demonstration
tb = get_signature(res, k = ..., plot = FALSE)
An example of the output of tb is:
#> which_row fdr mean_1 mean_2 scaled_mean_1 scaled_mean_2 km
#> 1 38 0.042760348 8.373488 9.131774 -0.5533452 0.5164555 1
#> 2 40 0.018707592 7.106213 8.469186 -0.6173731 0.5762149 1
#> 3 55 0.019134737 10.221463 11.207825 -0.6159697 0.5749050 1
#> 4 59 0.006059896 5.921854 7.869574 -0.6899429 0.6439467 1
#> 5 60 0.018055526 8.928898 10.211722 -0.6204761 0.5791110 1
#> 6 98 0.009384629 15.714769 14.887706 0.6635654 -0.6193277 2
...
The columns in tb are:
which_row: row indices corresponding to the input matrix.fdr: FDR for the differential test. mean_x: The mean value in group x.scaled_mean_x: The mean value in group x after rows are scaled.km: Row groups if k-means clustering is applied to rows.UMAP plot which shows how samples are separated.
dimension_reduction(res, k = 2, method = "UMAP")
dimension_reduction(res, k = 3, method = "UMAP")
dimension_reduction(res, k = 4, method = "UMAP")
dimension_reduction(res, k = 5, method = "UMAP")
dimension_reduction(res, k = 6, method = "UMAP")
Following heatmap shows how subgroups are split when increasing k:
collect_classes(res)
Test correlation between subgroups and known annotations. If the known annotation is numeric, one-way ANOVA test is applied, and if the known annotation is discrete, chi-squared contingency table test is applied.
test_to_known_factors(res)
#> n disease.state(p) k
#> SD:kmeans 143 0.000979 2
#> SD:kmeans 124 0.001159 3
#> SD:kmeans 55 0.072108 4
#> SD:kmeans 133 0.000310 5
#> SD:kmeans 90 0.000588 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 51776 rows and 143 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 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 0.503 0.848 0.898 0.4979 0.498 0.498
#> 3 3 0.691 0.812 0.914 0.3237 0.767 0.567
#> 4 4 0.698 0.740 0.835 0.1252 0.865 0.635
#> 5 5 0.785 0.752 0.871 0.0628 0.861 0.548
#> 6 6 0.793 0.698 0.850 0.0377 0.961 0.822
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
#> GSM550785 1 0.000 0.863 1.000 0.000
#> GSM550786 2 0.000 0.835 0.000 1.000
#> GSM550788 2 0.722 0.900 0.200 0.800
#> GSM550789 2 0.722 0.900 0.200 0.800
#> GSM550790 1 0.000 0.863 1.000 0.000
#> GSM550791 1 0.000 0.863 1.000 0.000
#> GSM550792 2 0.730 0.897 0.204 0.796
#> GSM550796 2 0.722 0.900 0.200 0.800
#> GSM550797 2 0.722 0.900 0.200 0.800
#> GSM550799 2 0.000 0.835 0.000 1.000
#> GSM550800 2 0.722 0.900 0.200 0.800
#> GSM550801 2 0.722 0.900 0.200 0.800
#> GSM550804 2 0.722 0.900 0.200 0.800
#> GSM550806 1 0.900 0.743 0.684 0.316
#> GSM550807 2 0.722 0.900 0.200 0.800
#> GSM550808 2 0.000 0.835 0.000 1.000
#> GSM550809 1 0.722 0.848 0.800 0.200
#> GSM550810 2 0.722 0.900 0.200 0.800
#> GSM550811 1 0.722 0.848 0.800 0.200
#> GSM550813 2 0.722 0.900 0.200 0.800
#> GSM550814 2 0.722 0.900 0.200 0.800
#> GSM550815 2 0.722 0.900 0.200 0.800
#> GSM550816 2 0.722 0.900 0.200 0.800
#> GSM550817 2 0.000 0.835 0.000 1.000
#> GSM550818 2 0.000 0.835 0.000 1.000
#> GSM550819 2 0.595 0.883 0.144 0.856
#> GSM550820 1 0.722 0.848 0.800 0.200
#> GSM550821 2 0.000 0.835 0.000 1.000
#> GSM550822 2 0.722 0.900 0.200 0.800
#> GSM550826 1 0.722 0.848 0.800 0.200
#> GSM550832 2 0.722 0.900 0.200 0.800
#> GSM550833 2 0.722 0.900 0.200 0.800
#> GSM550835 2 0.000 0.835 0.000 1.000
#> GSM550836 1 0.722 0.848 0.800 0.200
#> GSM550837 2 0.000 0.835 0.000 1.000
#> GSM550838 1 0.722 0.848 0.800 0.200
#> GSM550841 2 0.000 0.835 0.000 1.000
#> GSM550842 2 0.000 0.835 0.000 1.000
#> GSM550846 2 0.722 0.900 0.200 0.800
#> GSM550849 1 0.722 0.848 0.800 0.200
#> GSM550850 1 0.000 0.863 1.000 0.000
#> GSM550851 2 0.000 0.835 0.000 1.000
#> GSM550852 2 0.722 0.900 0.200 0.800
#> GSM550853 2 0.722 0.900 0.200 0.800
#> GSM550855 2 0.722 0.900 0.200 0.800
#> GSM550856 2 0.722 0.900 0.200 0.800
#> GSM550861 2 0.722 0.900 0.200 0.800
#> GSM550863 1 0.000 0.863 1.000 0.000
#> GSM550864 2 0.722 0.900 0.200 0.800
#> GSM550866 2 0.722 0.900 0.200 0.800
#> GSM550867 1 0.000 0.863 1.000 0.000
#> GSM550885 1 0.000 0.863 1.000 0.000
#> GSM550886 2 0.000 0.835 0.000 1.000
#> GSM550887 2 0.722 0.900 0.200 0.800
#> GSM550889 1 0.000 0.863 1.000 0.000
#> GSM550894 2 0.722 0.900 0.200 0.800
#> GSM550897 1 0.000 0.863 1.000 0.000
#> GSM550903 2 0.722 0.900 0.200 0.800
#> GSM550905 2 0.000 0.835 0.000 1.000
#> GSM550906 2 0.722 0.900 0.200 0.800
#> GSM550907 2 0.000 0.835 0.000 1.000
#> GSM550909 2 0.000 0.835 0.000 1.000
#> GSM550911 2 0.000 0.835 0.000 1.000
#> GSM550913 2 0.722 0.900 0.200 0.800
#> GSM550915 1 0.430 0.775 0.912 0.088
#> GSM550917 2 0.722 0.900 0.200 0.800
#> GSM550919 1 0.995 -0.268 0.540 0.460
#> GSM550921 1 0.722 0.848 0.800 0.200
#> GSM550924 2 0.000 0.835 0.000 1.000
#> GSM550926 2 0.722 0.900 0.200 0.800
#> GSM550927 2 0.722 0.900 0.200 0.800
#> GSM550787 1 0.722 0.848 0.800 0.200
#> GSM550793 1 0.722 0.848 0.800 0.200
#> GSM550794 2 0.971 0.628 0.400 0.600
#> GSM550795 1 0.000 0.863 1.000 0.000
#> GSM550798 1 0.722 0.848 0.800 0.200
#> GSM550803 1 0.722 0.848 0.800 0.200
#> GSM550805 1 0.722 0.848 0.800 0.200
#> GSM550823 1 0.416 0.784 0.916 0.084
#> GSM550824 1 0.000 0.863 1.000 0.000
#> GSM550825 1 0.722 0.848 0.800 0.200
#> GSM550827 1 0.224 0.833 0.964 0.036
#> GSM550828 1 0.000 0.863 1.000 0.000
#> GSM550829 1 0.722 0.848 0.800 0.200
#> GSM550830 1 0.000 0.863 1.000 0.000
#> GSM550834 1 0.000 0.863 1.000 0.000
#> GSM550839 2 0.000 0.835 0.000 1.000
#> GSM550840 1 0.000 0.863 1.000 0.000
#> GSM550843 2 0.000 0.835 0.000 1.000
#> GSM550844 1 0.722 0.848 0.800 0.200
#> GSM550845 2 0.722 0.900 0.200 0.800
#> GSM550848 2 0.814 0.852 0.252 0.748
#> GSM550854 1 0.000 0.863 1.000 0.000
#> GSM550857 1 0.722 0.848 0.800 0.200
#> GSM550858 1 0.000 0.863 1.000 0.000
#> GSM550859 1 0.000 0.863 1.000 0.000
#> GSM550862 1 0.000 0.863 1.000 0.000
#> GSM550865 1 0.000 0.863 1.000 0.000
#> GSM550868 1 0.000 0.863 1.000 0.000
#> GSM550869 1 0.722 0.848 0.800 0.200
#> GSM550870 2 0.722 0.900 0.200 0.800
#> GSM550871 2 0.000 0.835 0.000 1.000
#> GSM550872 1 0.000 0.863 1.000 0.000
#> GSM550873 2 0.000 0.835 0.000 1.000
#> GSM550874 2 0.722 0.900 0.200 0.800
#> GSM550876 2 0.000 0.835 0.000 1.000
#> GSM550877 2 0.722 0.900 0.200 0.800
#> GSM550878 2 0.000 0.835 0.000 1.000
#> GSM550879 1 0.000 0.863 1.000 0.000
#> GSM550882 1 0.722 0.848 0.800 0.200
#> GSM550888 1 0.722 0.848 0.800 0.200
#> GSM550890 1 0.980 -0.105 0.584 0.416
#> GSM550891 1 0.722 0.848 0.800 0.200
#> GSM550892 1 0.000 0.863 1.000 0.000
#> GSM550893 2 0.722 0.900 0.200 0.800
#> GSM550895 2 0.722 0.900 0.200 0.800
#> GSM550896 2 0.722 0.900 0.200 0.800
#> GSM550898 1 0.000 0.863 1.000 0.000
#> GSM550899 2 0.722 0.900 0.200 0.800
#> GSM550900 1 0.000 0.863 1.000 0.000
#> GSM550901 1 0.000 0.863 1.000 0.000
#> GSM550902 1 0.722 0.848 0.800 0.200
#> GSM550904 1 0.722 0.848 0.800 0.200
#> GSM550908 1 0.722 0.848 0.800 0.200
#> GSM550912 2 0.722 0.900 0.200 0.800
#> GSM550914 2 0.753 0.887 0.216 0.784
#> GSM550918 2 0.722 0.900 0.200 0.800
#> GSM550922 2 0.000 0.835 0.000 1.000
#> GSM550923 1 0.722 0.848 0.800 0.200
#> GSM550925 1 0.000 0.863 1.000 0.000
#> GSM550802 2 0.722 0.900 0.200 0.800
#> GSM550812 2 0.000 0.835 0.000 1.000
#> GSM550831 1 0.000 0.863 1.000 0.000
#> GSM550847 1 0.000 0.863 1.000 0.000
#> GSM550860 1 0.722 0.848 0.800 0.200
#> GSM550875 1 0.722 0.848 0.800 0.200
#> GSM550880 1 0.000 0.863 1.000 0.000
#> GSM550881 1 0.722 0.848 0.800 0.200
#> GSM550883 1 0.722 0.848 0.800 0.200
#> GSM550884 2 0.000 0.835 0.000 1.000
#> GSM550910 2 0.000 0.835 0.000 1.000
#> GSM550916 1 0.000 0.863 1.000 0.000
#> GSM550920 2 0.000 0.835 0.000 1.000
cbind(get_classes(res, k = 3), get_membership(res, k = 3))
#> class entropy silhouette p1 p2 p3
#> GSM550785 1 0.0000 0.876 1.000 0.000 0.000
#> GSM550786 3 0.0000 0.915 0.000 0.000 1.000
#> GSM550788 2 0.0000 0.913 0.000 1.000 0.000
#> GSM550789 2 0.0000 0.913 0.000 1.000 0.000
#> GSM550790 1 0.0000 0.876 1.000 0.000 0.000
#> GSM550791 1 0.0000 0.876 1.000 0.000 0.000
#> GSM550792 2 0.5138 0.635 0.252 0.748 0.000
#> GSM550796 2 0.0000 0.913 0.000 1.000 0.000
#> GSM550797 2 0.0000 0.913 0.000 1.000 0.000
#> GSM550799 3 0.0000 0.915 0.000 0.000 1.000
#> GSM550800 2 0.0000 0.913 0.000 1.000 0.000
#> GSM550801 2 0.0000 0.913 0.000 1.000 0.000
#> GSM550804 2 0.0000 0.913 0.000 1.000 0.000
#> GSM550806 3 0.0000 0.915 0.000 0.000 1.000
#> GSM550807 2 0.0000 0.913 0.000 1.000 0.000
#> GSM550808 2 0.5591 0.621 0.000 0.696 0.304
#> GSM550809 1 0.0000 0.876 1.000 0.000 0.000
#> GSM550810 2 0.0000 0.913 0.000 1.000 0.000
#> GSM550811 1 0.3116 0.777 0.892 0.000 0.108
#> GSM550813 2 0.0000 0.913 0.000 1.000 0.000
#> GSM550814 2 0.0000 0.913 0.000 1.000 0.000
#> GSM550815 2 0.0000 0.913 0.000 1.000 0.000
#> GSM550816 2 0.0000 0.913 0.000 1.000 0.000
#> GSM550817 3 0.0000 0.915 0.000 0.000 1.000
#> GSM550818 3 0.0000 0.915 0.000 0.000 1.000
#> GSM550819 2 0.3551 0.808 0.000 0.868 0.132
#> GSM550820 1 0.0000 0.876 1.000 0.000 0.000
#> GSM550821 2 0.5988 0.515 0.000 0.632 0.368
#> GSM550822 2 0.0000 0.913 0.000 1.000 0.000
#> GSM550826 1 0.6126 0.236 0.600 0.000 0.400
#> GSM550832 2 0.0000 0.913 0.000 1.000 0.000
#> GSM550833 2 0.0000 0.913 0.000 1.000 0.000
#> GSM550835 3 0.0747 0.903 0.000 0.016 0.984
#> GSM550836 3 0.3816 0.861 0.148 0.000 0.852
#> GSM550837 2 0.5859 0.559 0.000 0.656 0.344
#> GSM550838 1 0.0000 0.876 1.000 0.000 0.000
#> GSM550841 3 0.0000 0.915 0.000 0.000 1.000
#> GSM550842 2 0.5882 0.553 0.000 0.652 0.348
#> GSM550846 2 0.8825 0.376 0.336 0.532 0.132
#> GSM550849 1 0.5650 0.460 0.688 0.000 0.312
#> GSM550850 1 0.0000 0.876 1.000 0.000 0.000
#> GSM550851 2 0.5926 0.538 0.000 0.644 0.356
#> GSM550852 2 0.0000 0.913 0.000 1.000 0.000
#> GSM550853 2 0.0000 0.913 0.000 1.000 0.000
#> GSM550855 2 0.0000 0.913 0.000 1.000 0.000
#> GSM550856 2 0.0000 0.913 0.000 1.000 0.000
#> GSM550861 2 0.0000 0.913 0.000 1.000 0.000
#> GSM550863 1 0.4121 0.767 0.832 0.168 0.000
#> GSM550864 2 0.0000 0.913 0.000 1.000 0.000
#> GSM550866 2 0.0000 0.913 0.000 1.000 0.000
#> GSM550867 1 0.0000 0.876 1.000 0.000 0.000
#> GSM550885 1 0.0000 0.876 1.000 0.000 0.000
#> GSM550886 3 0.0000 0.915 0.000 0.000 1.000
#> GSM550887 2 0.0000 0.913 0.000 1.000 0.000
#> GSM550889 1 0.6140 0.413 0.596 0.404 0.000
#> GSM550894 2 0.0000 0.913 0.000 1.000 0.000
#> GSM550897 1 0.0000 0.876 1.000 0.000 0.000
#> GSM550903 2 0.0000 0.913 0.000 1.000 0.000
#> GSM550905 2 0.5882 0.553 0.000 0.652 0.348
#> GSM550906 2 0.0000 0.913 0.000 1.000 0.000
#> GSM550907 3 0.0000 0.915 0.000 0.000 1.000
#> GSM550909 2 0.5988 0.515 0.000 0.632 0.368
#> GSM550911 3 0.0000 0.915 0.000 0.000 1.000
#> GSM550913 2 0.0000 0.913 0.000 1.000 0.000
#> GSM550915 1 0.4062 0.771 0.836 0.164 0.000
#> GSM550917 2 0.0000 0.913 0.000 1.000 0.000
#> GSM550919 1 0.4399 0.745 0.812 0.188 0.000
#> GSM550921 3 0.3686 0.865 0.140 0.000 0.860
#> GSM550924 3 0.0000 0.915 0.000 0.000 1.000
#> GSM550926 2 0.0000 0.913 0.000 1.000 0.000
#> GSM550927 2 0.0000 0.913 0.000 1.000 0.000
#> GSM550787 3 0.4062 0.847 0.164 0.000 0.836
#> GSM550793 3 0.5016 0.760 0.240 0.000 0.760
#> GSM550794 1 0.6225 0.241 0.568 0.432 0.000
#> GSM550795 1 0.0000 0.876 1.000 0.000 0.000
#> GSM550798 1 0.0000 0.876 1.000 0.000 0.000
#> GSM550803 1 0.0000 0.876 1.000 0.000 0.000
#> GSM550805 1 0.6168 0.198 0.588 0.000 0.412
#> GSM550823 2 0.2066 0.863 0.060 0.940 0.000
#> GSM550824 1 0.0000 0.876 1.000 0.000 0.000
#> GSM550825 3 0.5016 0.760 0.240 0.000 0.760
#> GSM550827 1 0.4555 0.731 0.800 0.200 0.000
#> GSM550828 1 0.0000 0.876 1.000 0.000 0.000
#> GSM550829 1 0.6095 0.260 0.608 0.000 0.392
#> GSM550830 1 0.6026 0.476 0.624 0.376 0.000
#> GSM550834 1 0.0000 0.876 1.000 0.000 0.000
#> GSM550839 3 0.0000 0.915 0.000 0.000 1.000
#> GSM550840 1 0.0000 0.876 1.000 0.000 0.000
#> GSM550843 3 0.0000 0.915 0.000 0.000 1.000
#> GSM550844 1 0.0000 0.876 1.000 0.000 0.000
#> GSM550845 2 0.0000 0.913 0.000 1.000 0.000
#> GSM550848 2 0.6204 0.253 0.424 0.576 0.000
#> GSM550854 1 0.0000 0.876 1.000 0.000 0.000
#> GSM550857 3 0.5016 0.760 0.240 0.000 0.760
#> GSM550858 1 0.0000 0.876 1.000 0.000 0.000
#> GSM550859 1 0.0000 0.876 1.000 0.000 0.000
#> GSM550862 1 0.0000 0.876 1.000 0.000 0.000
#> GSM550865 1 0.3941 0.776 0.844 0.156 0.000
#> GSM550868 1 0.3941 0.776 0.844 0.156 0.000
#> GSM550869 3 0.3816 0.861 0.148 0.000 0.852
#> GSM550870 2 0.0000 0.913 0.000 1.000 0.000
#> GSM550871 3 0.0000 0.915 0.000 0.000 1.000
#> GSM550872 1 0.3941 0.776 0.844 0.156 0.000
#> GSM550873 2 0.5785 0.574 0.000 0.668 0.332
#> GSM550874 2 0.0000 0.913 0.000 1.000 0.000
#> GSM550876 3 0.0000 0.915 0.000 0.000 1.000
#> GSM550877 2 0.0000 0.913 0.000 1.000 0.000
#> GSM550878 3 0.0000 0.915 0.000 0.000 1.000
#> GSM550879 1 0.0000 0.876 1.000 0.000 0.000
#> GSM550882 3 0.3686 0.865 0.140 0.000 0.860
#> GSM550888 3 0.3816 0.861 0.148 0.000 0.852
#> GSM550890 1 0.4887 0.693 0.772 0.228 0.000
#> GSM550891 3 0.0000 0.915 0.000 0.000 1.000
#> GSM550892 1 0.0000 0.876 1.000 0.000 0.000
#> GSM550893 2 0.0000 0.913 0.000 1.000 0.000
#> GSM550895 2 0.0000 0.913 0.000 1.000 0.000
#> GSM550896 2 0.0000 0.913 0.000 1.000 0.000
#> GSM550898 1 0.0000 0.876 1.000 0.000 0.000
#> GSM550899 2 0.0000 0.913 0.000 1.000 0.000
#> GSM550900 1 0.4291 0.754 0.820 0.180 0.000
#> GSM550901 1 0.0000 0.876 1.000 0.000 0.000
#> GSM550902 1 0.6126 0.236 0.600 0.000 0.400
#> GSM550904 1 0.0000 0.876 1.000 0.000 0.000
#> GSM550908 3 0.3816 0.861 0.148 0.000 0.852
#> GSM550912 2 0.0000 0.913 0.000 1.000 0.000
#> GSM550914 2 0.5926 0.435 0.356 0.644 0.000
#> GSM550918 2 0.0000 0.913 0.000 1.000 0.000
#> GSM550922 3 0.0000 0.915 0.000 0.000 1.000
#> GSM550923 1 0.0000 0.876 1.000 0.000 0.000
#> GSM550925 1 0.0000 0.876 1.000 0.000 0.000
#> GSM550802 2 0.0000 0.913 0.000 1.000 0.000
#> GSM550812 2 0.6023 0.754 0.092 0.788 0.120
#> GSM550831 1 0.0000 0.876 1.000 0.000 0.000
#> GSM550847 1 0.0000 0.876 1.000 0.000 0.000
#> GSM550860 3 0.3816 0.861 0.148 0.000 0.852
#> GSM550875 1 0.5810 0.405 0.664 0.000 0.336
#> GSM550880 1 0.0000 0.876 1.000 0.000 0.000
#> GSM550881 3 0.3816 0.861 0.148 0.000 0.852
#> GSM550883 3 0.4291 0.832 0.180 0.000 0.820
#> GSM550884 3 0.5327 0.609 0.000 0.272 0.728
#> GSM550910 3 0.0000 0.915 0.000 0.000 1.000
#> GSM550916 1 0.0000 0.876 1.000 0.000 0.000
#> GSM550920 3 0.0000 0.915 0.000 0.000 1.000
cbind(get_classes(res, k = 4), get_membership(res, k = 4))
#> class entropy silhouette p1 p2 p3 p4
#> GSM550785 1 0.3486 0.848 0.812 0.000 0.000 0.188
#> GSM550786 3 0.0469 0.878 0.000 0.000 0.988 0.012
#> GSM550788 2 0.0336 0.851 0.000 0.992 0.000 0.008
#> GSM550789 2 0.0000 0.853 0.000 1.000 0.000 0.000
#> GSM550790 1 0.3486 0.848 0.812 0.000 0.000 0.188
#> GSM550791 1 0.3486 0.848 0.812 0.000 0.000 0.188
#> GSM550792 2 0.5332 0.590 0.128 0.748 0.000 0.124
#> GSM550796 2 0.0000 0.853 0.000 1.000 0.000 0.000
#> GSM550797 2 0.0000 0.853 0.000 1.000 0.000 0.000
#> GSM550799 3 0.0779 0.875 0.000 0.004 0.980 0.016
#> GSM550800 2 0.2973 0.727 0.000 0.856 0.000 0.144
#> GSM550801 2 0.0000 0.853 0.000 1.000 0.000 0.000
#> GSM550804 2 0.0188 0.852 0.000 0.996 0.000 0.004
#> GSM550806 3 0.2926 0.856 0.056 0.000 0.896 0.048
#> GSM550807 2 0.0000 0.853 0.000 1.000 0.000 0.000
#> GSM550808 2 0.4737 0.642 0.000 0.728 0.252 0.020
#> GSM550809 1 0.2081 0.787 0.916 0.000 0.000 0.084
#> GSM550810 2 0.1042 0.841 0.000 0.972 0.008 0.020
#> GSM550811 1 0.2882 0.753 0.892 0.000 0.024 0.084
#> GSM550813 2 0.0592 0.847 0.000 0.984 0.000 0.016
#> GSM550814 2 0.0000 0.853 0.000 1.000 0.000 0.000
#> GSM550815 2 0.0000 0.853 0.000 1.000 0.000 0.000
#> GSM550816 2 0.0188 0.852 0.000 0.996 0.004 0.000
#> GSM550817 3 0.0469 0.878 0.000 0.000 0.988 0.012
#> GSM550818 3 0.0469 0.878 0.000 0.000 0.988 0.012
#> GSM550819 4 0.5328 0.631 0.000 0.064 0.212 0.724
#> GSM550820 1 0.1792 0.803 0.932 0.000 0.000 0.068
#> GSM550821 2 0.5173 0.544 0.000 0.660 0.320 0.020
#> GSM550822 2 0.0188 0.852 0.000 0.996 0.004 0.000
#> GSM550826 1 0.3674 0.675 0.852 0.000 0.104 0.044
#> GSM550832 2 0.0707 0.845 0.000 0.980 0.000 0.020
#> GSM550833 2 0.0000 0.853 0.000 1.000 0.000 0.000
#> GSM550835 3 0.3853 0.726 0.000 0.160 0.820 0.020
#> GSM550836 3 0.4919 0.771 0.200 0.000 0.752 0.048
#> GSM550837 2 0.4855 0.626 0.000 0.712 0.268 0.020
#> GSM550838 1 0.1584 0.757 0.952 0.000 0.012 0.036
#> GSM550841 3 0.2089 0.845 0.000 0.048 0.932 0.020
#> GSM550842 2 0.4855 0.626 0.000 0.712 0.268 0.020
#> GSM550846 4 0.5173 0.737 0.028 0.100 0.080 0.792
#> GSM550849 1 0.1635 0.758 0.948 0.000 0.008 0.044
#> GSM550850 1 0.3486 0.848 0.812 0.000 0.000 0.188
#> GSM550851 2 0.4855 0.626 0.000 0.712 0.268 0.020
#> GSM550852 2 0.0592 0.847 0.000 0.984 0.000 0.016
#> GSM550853 2 0.0336 0.851 0.000 0.992 0.000 0.008
#> GSM550855 2 0.0336 0.851 0.000 0.992 0.000 0.008
#> GSM550856 2 0.4843 0.264 0.000 0.604 0.000 0.396
#> GSM550861 2 0.0000 0.853 0.000 1.000 0.000 0.000
#> GSM550863 4 0.2089 0.772 0.048 0.020 0.000 0.932
#> GSM550864 2 0.0817 0.841 0.000 0.976 0.000 0.024
#> GSM550866 2 0.4907 0.190 0.000 0.580 0.000 0.420
#> GSM550867 1 0.3486 0.848 0.812 0.000 0.000 0.188
#> GSM550885 1 0.3528 0.846 0.808 0.000 0.000 0.192
#> GSM550886 3 0.1798 0.853 0.000 0.040 0.944 0.016
#> GSM550887 2 0.0000 0.853 0.000 1.000 0.000 0.000
#> GSM550889 4 0.4761 0.709 0.044 0.192 0.000 0.764
#> GSM550894 2 0.0707 0.845 0.000 0.980 0.000 0.020
#> GSM550897 1 0.3610 0.842 0.800 0.000 0.000 0.200
#> GSM550903 2 0.0000 0.853 0.000 1.000 0.000 0.000
#> GSM550905 2 0.4882 0.621 0.000 0.708 0.272 0.020
#> GSM550906 2 0.0000 0.853 0.000 1.000 0.000 0.000
#> GSM550907 3 0.0000 0.880 0.000 0.000 1.000 0.000
#> GSM550909 2 0.5323 0.482 0.000 0.628 0.352 0.020
#> GSM550911 3 0.0000 0.880 0.000 0.000 1.000 0.000
#> GSM550913 2 0.0000 0.853 0.000 1.000 0.000 0.000
#> GSM550915 4 0.3653 0.700 0.128 0.028 0.000 0.844
#> GSM550917 2 0.0469 0.849 0.000 0.988 0.000 0.012
#> GSM550919 4 0.7239 0.386 0.248 0.208 0.000 0.544
#> GSM550921 3 0.4842 0.776 0.192 0.000 0.760 0.048
#> GSM550924 3 0.0707 0.875 0.000 0.000 0.980 0.020
#> GSM550926 2 0.4855 0.253 0.000 0.600 0.000 0.400
#> GSM550927 2 0.0000 0.853 0.000 1.000 0.000 0.000
#> GSM550787 3 0.5760 0.176 0.448 0.000 0.524 0.028
#> GSM550793 1 0.5712 0.275 0.644 0.000 0.308 0.048
#> GSM550794 4 0.4858 0.599 0.216 0.024 0.008 0.752
#> GSM550795 1 0.3873 0.820 0.772 0.000 0.000 0.228
#> GSM550798 1 0.1042 0.765 0.972 0.000 0.020 0.008
#> GSM550803 1 0.3486 0.848 0.812 0.000 0.000 0.188
#> GSM550805 1 0.2489 0.732 0.912 0.000 0.068 0.020
#> GSM550823 4 0.4706 0.674 0.028 0.224 0.000 0.748
#> GSM550824 1 0.3486 0.848 0.812 0.000 0.000 0.188
#> GSM550825 1 0.5599 0.330 0.664 0.000 0.288 0.048
#> GSM550827 4 0.2282 0.771 0.052 0.024 0.000 0.924
#> GSM550828 1 0.3486 0.848 0.812 0.000 0.000 0.188
#> GSM550829 1 0.2759 0.720 0.904 0.000 0.052 0.044
#> GSM550830 4 0.3818 0.773 0.048 0.108 0.000 0.844
#> GSM550834 1 0.3569 0.843 0.804 0.000 0.000 0.196
#> GSM550839 3 0.0524 0.878 0.000 0.004 0.988 0.008
#> GSM550840 1 0.3486 0.848 0.812 0.000 0.000 0.188
#> GSM550843 3 0.0000 0.880 0.000 0.000 1.000 0.000
#> GSM550844 1 0.3172 0.841 0.840 0.000 0.000 0.160
#> GSM550845 4 0.4477 0.558 0.000 0.312 0.000 0.688
#> GSM550848 4 0.3581 0.761 0.032 0.116 0.000 0.852
#> GSM550854 1 0.3486 0.848 0.812 0.000 0.000 0.188
#> GSM550857 1 0.5599 0.330 0.664 0.000 0.288 0.048
#> GSM550858 1 0.3486 0.848 0.812 0.000 0.000 0.188
#> GSM550859 1 0.3486 0.848 0.812 0.000 0.000 0.188
#> GSM550862 1 0.3486 0.848 0.812 0.000 0.000 0.188
#> GSM550865 4 0.1902 0.762 0.064 0.004 0.000 0.932
#> GSM550868 4 0.1902 0.762 0.064 0.004 0.000 0.932
#> GSM550869 3 0.3198 0.851 0.080 0.000 0.880 0.040
#> GSM550870 2 0.0592 0.847 0.000 0.984 0.000 0.016
#> GSM550871 3 0.0188 0.880 0.000 0.000 0.996 0.004
#> GSM550872 4 0.1902 0.762 0.064 0.004 0.000 0.932
#> GSM550873 2 0.4797 0.635 0.000 0.720 0.260 0.020
#> GSM550874 2 0.4855 0.253 0.000 0.600 0.000 0.400
#> GSM550876 3 0.0188 0.880 0.000 0.000 0.996 0.004
#> GSM550877 2 0.4855 0.253 0.000 0.600 0.000 0.400
#> GSM550878 3 0.0188 0.880 0.000 0.000 0.996 0.004
#> GSM550879 1 0.3649 0.839 0.796 0.000 0.000 0.204
#> GSM550882 3 0.3081 0.853 0.064 0.000 0.888 0.048
#> GSM550888 3 0.4919 0.771 0.200 0.000 0.752 0.048
#> GSM550890 4 0.2385 0.773 0.052 0.028 0.000 0.920
#> GSM550891 3 0.3004 0.855 0.060 0.000 0.892 0.048
#> GSM550892 1 0.4994 0.377 0.520 0.000 0.000 0.480
#> GSM550893 2 0.4661 0.383 0.000 0.652 0.000 0.348
#> GSM550895 4 0.4134 0.631 0.000 0.260 0.000 0.740
#> GSM550896 4 0.4925 0.296 0.000 0.428 0.000 0.572
#> GSM550898 1 0.3486 0.848 0.812 0.000 0.000 0.188
#> GSM550899 2 0.0469 0.849 0.000 0.988 0.000 0.012
#> GSM550900 4 0.2048 0.764 0.064 0.008 0.000 0.928
#> GSM550901 1 0.3486 0.848 0.812 0.000 0.000 0.188
#> GSM550902 1 0.4633 0.573 0.780 0.000 0.172 0.048
#> GSM550904 1 0.1545 0.770 0.952 0.000 0.008 0.040
#> GSM550908 3 0.4881 0.774 0.196 0.000 0.756 0.048
#> GSM550912 2 0.0469 0.849 0.000 0.988 0.000 0.012
#> GSM550914 4 0.2443 0.780 0.024 0.060 0.000 0.916
#> GSM550918 2 0.0592 0.847 0.000 0.984 0.000 0.016
#> GSM550922 3 0.2775 0.812 0.000 0.084 0.896 0.020
#> GSM550923 1 0.1305 0.794 0.960 0.000 0.004 0.036
#> GSM550925 1 0.3486 0.848 0.812 0.000 0.000 0.188
#> GSM550802 4 0.4804 0.613 0.000 0.276 0.016 0.708
#> GSM550812 4 0.5682 0.660 0.112 0.020 0.116 0.752
#> GSM550831 1 0.3486 0.848 0.812 0.000 0.000 0.188
#> GSM550847 1 0.3486 0.848 0.812 0.000 0.000 0.188
#> GSM550860 3 0.3570 0.841 0.092 0.000 0.860 0.048
#> GSM550875 1 0.2021 0.748 0.936 0.000 0.040 0.024
#> GSM550880 4 0.4948 -0.157 0.440 0.000 0.000 0.560
#> GSM550881 3 0.4881 0.774 0.196 0.000 0.756 0.048
#> GSM550883 3 0.5997 0.521 0.376 0.000 0.576 0.048
#> GSM550884 4 0.6132 0.628 0.100 0.020 0.168 0.712
#> GSM550910 3 0.0469 0.878 0.000 0.000 0.988 0.012
#> GSM550916 1 0.3486 0.848 0.812 0.000 0.000 0.188
#> GSM550920 3 0.0469 0.878 0.000 0.000 0.988 0.012
cbind(get_classes(res, k = 5), get_membership(res, k = 5))
#> class entropy silhouette p1 p2 p3 p4 p5
#> GSM550785 1 0.0290 0.83533 0.992 0.000 0.000 0.008 0.000
#> GSM550786 5 0.0703 0.89633 0.000 0.000 0.024 0.000 0.976
#> GSM550788 2 0.1408 0.90079 0.000 0.948 0.000 0.044 0.008
#> GSM550789 2 0.0290 0.91229 0.000 0.992 0.000 0.000 0.008
#> GSM550790 1 0.0000 0.83488 1.000 0.000 0.000 0.000 0.000
#> GSM550791 1 0.0324 0.83282 0.992 0.004 0.000 0.004 0.000
#> GSM550792 2 0.7495 0.35165 0.244 0.552 0.072 0.096 0.036
#> GSM550796 2 0.0671 0.91140 0.000 0.980 0.000 0.004 0.016
#> GSM550797 2 0.0162 0.91243 0.000 0.996 0.000 0.000 0.004
#> GSM550799 5 0.0404 0.89676 0.000 0.000 0.012 0.000 0.988
#> GSM550800 2 0.2929 0.80370 0.000 0.820 0.000 0.180 0.000
#> GSM550801 2 0.0162 0.91243 0.000 0.996 0.000 0.000 0.004
#> GSM550804 2 0.0955 0.90424 0.000 0.968 0.028 0.004 0.000
#> GSM550806 3 0.3966 0.53020 0.000 0.000 0.664 0.000 0.336
#> GSM550807 2 0.0162 0.91243 0.000 0.996 0.000 0.000 0.004
#> GSM550808 5 0.2424 0.83042 0.000 0.132 0.000 0.000 0.868
#> GSM550809 1 0.5876 0.14568 0.488 0.000 0.412 0.100 0.000
#> GSM550810 2 0.1357 0.89738 0.000 0.948 0.000 0.004 0.048
#> GSM550811 3 0.6638 -0.00289 0.400 0.000 0.464 0.104 0.032
#> GSM550813 2 0.0609 0.90805 0.000 0.980 0.020 0.000 0.000
#> GSM550814 2 0.0955 0.90791 0.000 0.968 0.000 0.004 0.028
#> GSM550815 2 0.0566 0.91183 0.000 0.984 0.000 0.004 0.012
#> GSM550816 2 0.1630 0.89502 0.000 0.944 0.004 0.036 0.016
#> GSM550817 5 0.0703 0.89633 0.000 0.000 0.024 0.000 0.976
#> GSM550818 5 0.0794 0.89481 0.000 0.000 0.028 0.000 0.972
#> GSM550819 4 0.3612 0.64346 0.000 0.008 0.000 0.764 0.228
#> GSM550820 1 0.3906 0.71981 0.800 0.000 0.132 0.068 0.000
#> GSM550821 5 0.1792 0.86617 0.000 0.084 0.000 0.000 0.916
#> GSM550822 2 0.0771 0.91050 0.000 0.976 0.000 0.004 0.020
#> GSM550826 3 0.3904 0.61421 0.216 0.000 0.764 0.008 0.012
#> GSM550832 2 0.0794 0.90610 0.000 0.972 0.000 0.000 0.028
#> GSM550833 2 0.0566 0.91183 0.000 0.984 0.000 0.004 0.012
#> GSM550835 5 0.1121 0.88734 0.000 0.044 0.000 0.000 0.956
#> GSM550836 3 0.1908 0.81360 0.000 0.000 0.908 0.000 0.092
#> GSM550837 5 0.2966 0.77582 0.000 0.184 0.000 0.000 0.816
#> GSM550838 3 0.5556 -0.06835 0.456 0.000 0.476 0.068 0.000
#> GSM550841 5 0.0671 0.89517 0.000 0.016 0.004 0.000 0.980
#> GSM550842 5 0.1908 0.86054 0.000 0.092 0.000 0.000 0.908
#> GSM550846 4 0.6003 0.67188 0.028 0.024 0.092 0.688 0.168
#> GSM550849 1 0.5053 0.64681 0.744 0.004 0.144 0.020 0.088
#> GSM550850 1 0.0000 0.83488 1.000 0.000 0.000 0.000 0.000
#> GSM550851 5 0.2732 0.80320 0.000 0.160 0.000 0.000 0.840
#> GSM550852 2 0.1686 0.89937 0.000 0.944 0.020 0.008 0.028
#> GSM550853 2 0.1282 0.90165 0.000 0.952 0.000 0.044 0.004
#> GSM550855 2 0.1041 0.90657 0.000 0.964 0.000 0.032 0.004
#> GSM550856 2 0.2929 0.80365 0.000 0.820 0.000 0.180 0.000
#> GSM550861 2 0.0290 0.91229 0.000 0.992 0.000 0.000 0.008
#> GSM550863 4 0.1568 0.81696 0.036 0.000 0.020 0.944 0.000
#> GSM550864 2 0.0703 0.90697 0.000 0.976 0.024 0.000 0.000
#> GSM550866 2 0.3177 0.77564 0.000 0.792 0.000 0.208 0.000
#> GSM550867 1 0.0290 0.83533 0.992 0.000 0.000 0.008 0.000
#> GSM550885 1 0.0609 0.83141 0.980 0.000 0.000 0.020 0.000
#> GSM550886 5 0.1117 0.89805 0.000 0.016 0.020 0.000 0.964
#> GSM550887 2 0.0671 0.91140 0.000 0.980 0.000 0.004 0.016
#> GSM550889 4 0.2645 0.80066 0.044 0.068 0.000 0.888 0.000
#> GSM550894 2 0.0963 0.90417 0.000 0.964 0.000 0.000 0.036
#> GSM550897 1 0.0404 0.83234 0.988 0.000 0.000 0.012 0.000
#> GSM550903 2 0.0290 0.91229 0.000 0.992 0.000 0.000 0.008
#> GSM550905 5 0.2074 0.85281 0.000 0.104 0.000 0.000 0.896
#> GSM550906 2 0.0566 0.91183 0.000 0.984 0.000 0.004 0.012
#> GSM550907 5 0.1121 0.88767 0.000 0.000 0.044 0.000 0.956
#> GSM550909 5 0.2526 0.86377 0.000 0.080 0.012 0.012 0.896
#> GSM550911 5 0.1121 0.88767 0.000 0.000 0.044 0.000 0.956
#> GSM550913 2 0.0162 0.91243 0.000 0.996 0.000 0.000 0.004
#> GSM550915 4 0.5940 0.53113 0.272 0.024 0.088 0.616 0.000
#> GSM550917 2 0.0703 0.90697 0.000 0.976 0.024 0.000 0.000
#> GSM550919 1 0.7909 -0.01616 0.396 0.300 0.088 0.216 0.000
#> GSM550921 3 0.1908 0.81360 0.000 0.000 0.908 0.000 0.092
#> GSM550924 5 0.1408 0.88921 0.000 0.008 0.044 0.000 0.948
#> GSM550926 2 0.3336 0.75341 0.000 0.772 0.000 0.228 0.000
#> GSM550927 2 0.0566 0.91183 0.000 0.984 0.000 0.004 0.012
#> GSM550787 1 0.6366 -0.15134 0.440 0.000 0.396 0.000 0.164
#> GSM550793 3 0.2300 0.80489 0.052 0.000 0.908 0.000 0.040
#> GSM550794 1 0.6139 -0.17925 0.468 0.024 0.056 0.448 0.004
#> GSM550795 1 0.4769 0.56720 0.688 0.000 0.056 0.256 0.000
#> GSM550798 1 0.2929 0.69885 0.820 0.000 0.180 0.000 0.000
#> GSM550803 1 0.0000 0.83488 1.000 0.000 0.000 0.000 0.000
#> GSM550805 1 0.4798 0.12113 0.540 0.000 0.440 0.000 0.020
#> GSM550823 4 0.2610 0.79600 0.028 0.076 0.004 0.892 0.000
#> GSM550824 1 0.0290 0.83533 0.992 0.000 0.000 0.008 0.000
#> GSM550825 3 0.2300 0.80530 0.052 0.000 0.908 0.000 0.040
#> GSM550827 4 0.3947 0.78586 0.072 0.020 0.084 0.824 0.000
#> GSM550828 1 0.0290 0.83533 0.992 0.000 0.000 0.008 0.000
#> GSM550829 3 0.4425 0.30162 0.392 0.000 0.600 0.000 0.008
#> GSM550830 4 0.2511 0.81132 0.080 0.028 0.000 0.892 0.000
#> GSM550834 1 0.0992 0.82680 0.968 0.000 0.008 0.024 0.000
#> GSM550839 5 0.1168 0.89339 0.000 0.000 0.032 0.008 0.960
#> GSM550840 1 0.0000 0.83488 1.000 0.000 0.000 0.000 0.000
#> GSM550843 5 0.1121 0.88767 0.000 0.000 0.044 0.000 0.956
#> GSM550844 1 0.0000 0.83488 1.000 0.000 0.000 0.000 0.000
#> GSM550845 2 0.4760 0.35993 0.000 0.564 0.020 0.416 0.000
#> GSM550848 4 0.6957 0.57719 0.104 0.248 0.088 0.560 0.000
#> GSM550854 1 0.0290 0.83533 0.992 0.000 0.000 0.008 0.000
#> GSM550857 3 0.2304 0.80651 0.048 0.000 0.908 0.000 0.044
#> GSM550858 1 0.0290 0.83533 0.992 0.000 0.000 0.008 0.000
#> GSM550859 1 0.0290 0.83533 0.992 0.000 0.000 0.008 0.000
#> GSM550862 1 0.0290 0.83533 0.992 0.000 0.000 0.008 0.000
#> GSM550865 4 0.1410 0.81935 0.060 0.000 0.000 0.940 0.000
#> GSM550868 4 0.1341 0.81951 0.056 0.000 0.000 0.944 0.000
#> GSM550869 3 0.5456 0.66203 0.048 0.000 0.684 0.044 0.224
#> GSM550870 2 0.0510 0.90919 0.000 0.984 0.016 0.000 0.000
#> GSM550871 5 0.4465 0.64660 0.000 0.000 0.204 0.060 0.736
#> GSM550872 4 0.1410 0.81935 0.060 0.000 0.000 0.940 0.000
#> GSM550873 5 0.4691 0.51694 0.000 0.340 0.020 0.004 0.636
#> GSM550874 2 0.3366 0.74851 0.000 0.768 0.000 0.232 0.000
#> GSM550876 5 0.2124 0.84849 0.000 0.000 0.096 0.004 0.900
#> GSM550877 2 0.3336 0.75341 0.000 0.772 0.000 0.228 0.000
#> GSM550878 5 0.1908 0.85163 0.000 0.000 0.092 0.000 0.908
#> GSM550879 1 0.2793 0.77264 0.876 0.000 0.036 0.088 0.000
#> GSM550882 3 0.3039 0.74622 0.000 0.000 0.808 0.000 0.192
#> GSM550888 3 0.1908 0.81360 0.000 0.000 0.908 0.000 0.092
#> GSM550890 4 0.3653 0.79009 0.056 0.016 0.088 0.840 0.000
#> GSM550891 3 0.3109 0.73771 0.000 0.000 0.800 0.000 0.200
#> GSM550892 4 0.4306 0.05295 0.492 0.000 0.000 0.508 0.000
#> GSM550893 2 0.3305 0.75802 0.000 0.776 0.000 0.224 0.000
#> GSM550895 4 0.2179 0.78025 0.004 0.100 0.000 0.896 0.000
#> GSM550896 2 0.3913 0.61135 0.000 0.676 0.000 0.324 0.000
#> GSM550898 1 0.0162 0.83528 0.996 0.000 0.000 0.004 0.000
#> GSM550899 2 0.0865 0.90586 0.000 0.972 0.024 0.004 0.000
#> GSM550900 4 0.1965 0.80892 0.096 0.000 0.000 0.904 0.000
#> GSM550901 1 0.2227 0.79643 0.916 0.004 0.048 0.032 0.000
#> GSM550902 3 0.2300 0.78716 0.072 0.000 0.904 0.000 0.024
#> GSM550904 1 0.5284 0.32735 0.568 0.000 0.376 0.056 0.000
#> GSM550908 3 0.1908 0.81360 0.000 0.000 0.908 0.000 0.092
#> GSM550912 2 0.0794 0.90565 0.000 0.972 0.028 0.000 0.000
#> GSM550914 4 0.3477 0.79618 0.036 0.024 0.088 0.852 0.000
#> GSM550918 2 0.0955 0.90424 0.000 0.968 0.028 0.004 0.000
#> GSM550922 5 0.1041 0.89185 0.000 0.032 0.004 0.000 0.964
#> GSM550923 1 0.1851 0.77766 0.912 0.000 0.088 0.000 0.000
#> GSM550925 1 0.0162 0.83451 0.996 0.000 0.000 0.004 0.000
#> GSM550802 4 0.2971 0.72554 0.000 0.156 0.000 0.836 0.008
#> GSM550812 4 0.2605 0.79389 0.000 0.004 0.044 0.896 0.056
#> GSM550831 1 0.0162 0.83528 0.996 0.000 0.000 0.004 0.000
#> GSM550847 1 0.0000 0.83488 1.000 0.000 0.000 0.000 0.000
#> GSM550860 3 0.2719 0.78663 0.000 0.000 0.852 0.004 0.144
#> GSM550875 1 0.4538 0.11648 0.540 0.000 0.452 0.000 0.008
#> GSM550880 1 0.4793 0.10263 0.544 0.000 0.020 0.436 0.000
#> GSM550881 3 0.1908 0.81360 0.000 0.000 0.908 0.000 0.092
#> GSM550883 3 0.2172 0.81339 0.016 0.000 0.908 0.000 0.076
#> GSM550884 4 0.4177 0.71265 0.000 0.004 0.168 0.776 0.052
#> GSM550910 5 0.0703 0.89633 0.000 0.000 0.024 0.000 0.976
#> GSM550916 1 0.0000 0.83488 1.000 0.000 0.000 0.000 0.000
#> GSM550920 5 0.0880 0.89301 0.000 0.000 0.032 0.000 0.968
cbind(get_classes(res, k = 6), get_membership(res, k = 6))
#> class entropy silhouette p1 p2 p3 p4 p5 p6
#> GSM550785 1 0.0436 0.8319 0.988 0.000 0.004 0.004 0.000 0.004
#> GSM550786 5 0.1075 0.8783 0.000 0.000 0.048 0.000 0.952 0.000
#> GSM550788 2 0.3066 0.7810 0.000 0.828 0.004 0.148 0.016 0.004
#> GSM550789 2 0.0405 0.8549 0.000 0.988 0.000 0.000 0.004 0.008
#> GSM550790 1 0.0508 0.8295 0.984 0.000 0.004 0.000 0.000 0.012
#> GSM550791 1 0.0858 0.8251 0.968 0.000 0.004 0.000 0.000 0.028
#> GSM550792 6 0.5244 0.3626 0.040 0.300 0.000 0.012 0.028 0.620
#> GSM550796 2 0.0982 0.8539 0.000 0.968 0.004 0.004 0.020 0.004
#> GSM550797 2 0.0508 0.8546 0.000 0.984 0.000 0.000 0.004 0.012
#> GSM550799 5 0.0632 0.8775 0.000 0.000 0.024 0.000 0.976 0.000
#> GSM550800 2 0.3807 0.5301 0.000 0.628 0.004 0.368 0.000 0.000
#> GSM550801 2 0.0363 0.8545 0.000 0.988 0.000 0.000 0.000 0.012
#> GSM550804 2 0.2664 0.7413 0.000 0.816 0.000 0.000 0.000 0.184
#> GSM550806 3 0.3103 0.6867 0.000 0.000 0.784 0.000 0.208 0.008
#> GSM550807 2 0.0000 0.8556 0.000 1.000 0.000 0.000 0.000 0.000
#> GSM550808 5 0.2489 0.7868 0.000 0.128 0.000 0.000 0.860 0.012
#> GSM550809 6 0.6407 0.3200 0.304 0.000 0.272 0.016 0.000 0.408
#> GSM550810 2 0.1769 0.8368 0.000 0.924 0.000 0.004 0.060 0.012
#> GSM550811 6 0.5273 0.4569 0.124 0.000 0.236 0.012 0.000 0.628
#> GSM550813 2 0.0865 0.8499 0.000 0.964 0.000 0.000 0.000 0.036
#> GSM550814 2 0.1973 0.8465 0.000 0.924 0.004 0.036 0.028 0.008
#> GSM550815 2 0.1096 0.8536 0.000 0.964 0.004 0.008 0.020 0.004
#> GSM550816 2 0.2556 0.7912 0.000 0.864 0.000 0.008 0.008 0.120
#> GSM550817 5 0.1007 0.8778 0.000 0.000 0.044 0.000 0.956 0.000
#> GSM550818 5 0.1007 0.8778 0.000 0.000 0.044 0.000 0.956 0.000
#> GSM550819 4 0.1511 0.7436 0.000 0.000 0.004 0.940 0.044 0.012
#> GSM550820 1 0.5492 0.0829 0.508 0.000 0.092 0.012 0.000 0.388
#> GSM550821 5 0.0508 0.8675 0.000 0.012 0.000 0.000 0.984 0.004
#> GSM550822 2 0.1096 0.8536 0.000 0.964 0.004 0.008 0.020 0.004
#> GSM550826 3 0.5049 0.3375 0.104 0.000 0.624 0.004 0.000 0.268
#> GSM550832 2 0.1549 0.8445 0.000 0.936 0.000 0.000 0.044 0.020
#> GSM550833 2 0.1204 0.8532 0.000 0.960 0.004 0.016 0.016 0.004
#> GSM550835 5 0.0972 0.8701 0.000 0.028 0.008 0.000 0.964 0.000
#> GSM550836 3 0.0458 0.8647 0.000 0.000 0.984 0.000 0.016 0.000
#> GSM550837 5 0.3273 0.6885 0.000 0.212 0.004 0.000 0.776 0.008
#> GSM550838 6 0.6395 0.2541 0.288 0.000 0.336 0.012 0.000 0.364
#> GSM550841 5 0.0508 0.8752 0.000 0.004 0.012 0.000 0.984 0.000
#> GSM550842 5 0.1542 0.8471 0.000 0.052 0.004 0.000 0.936 0.008
#> GSM550846 6 0.1876 0.5889 0.004 0.004 0.000 0.072 0.004 0.916
#> GSM550849 1 0.6131 0.4803 0.620 0.008 0.084 0.004 0.088 0.196
#> GSM550850 1 0.0603 0.8295 0.980 0.000 0.004 0.000 0.000 0.016
#> GSM550851 5 0.2948 0.7232 0.000 0.188 0.000 0.000 0.804 0.008
#> GSM550852 2 0.2456 0.8200 0.000 0.888 0.000 0.008 0.028 0.076
#> GSM550853 2 0.2333 0.8070 0.000 0.872 0.004 0.120 0.004 0.000
#> GSM550855 2 0.2400 0.8082 0.000 0.872 0.004 0.116 0.008 0.000
#> GSM550856 2 0.3942 0.5271 0.000 0.624 0.004 0.368 0.000 0.004
#> GSM550861 2 0.0405 0.8549 0.000 0.988 0.000 0.000 0.004 0.008
#> GSM550863 4 0.2848 0.6477 0.008 0.000 0.000 0.816 0.000 0.176
#> GSM550864 2 0.1204 0.8434 0.000 0.944 0.000 0.000 0.000 0.056
#> GSM550866 2 0.4015 0.4769 0.000 0.596 0.004 0.396 0.000 0.004
#> GSM550867 1 0.0146 0.8328 0.996 0.000 0.000 0.004 0.000 0.000
#> GSM550885 1 0.1152 0.8111 0.952 0.000 0.000 0.004 0.000 0.044
#> GSM550886 5 0.0935 0.8788 0.000 0.004 0.032 0.000 0.964 0.000
#> GSM550887 2 0.1096 0.8536 0.000 0.964 0.004 0.008 0.020 0.004
#> GSM550889 4 0.0508 0.7652 0.004 0.012 0.000 0.984 0.000 0.000
#> GSM550894 2 0.1528 0.8431 0.000 0.936 0.000 0.000 0.048 0.016
#> GSM550897 1 0.1643 0.7963 0.924 0.000 0.000 0.068 0.000 0.008
#> GSM550903 2 0.0508 0.8546 0.000 0.984 0.000 0.000 0.004 0.012
#> GSM550905 5 0.1866 0.8273 0.000 0.084 0.000 0.000 0.908 0.008
#> GSM550906 2 0.1007 0.8543 0.000 0.968 0.004 0.008 0.016 0.004
#> GSM550907 5 0.1765 0.8556 0.000 0.000 0.096 0.000 0.904 0.000
#> GSM550909 5 0.1901 0.8560 0.000 0.012 0.004 0.008 0.924 0.052
#> GSM550911 5 0.1765 0.8556 0.000 0.000 0.096 0.000 0.904 0.000
#> GSM550913 2 0.0260 0.8549 0.000 0.992 0.000 0.000 0.000 0.008
#> GSM550915 6 0.3125 0.6065 0.056 0.016 0.000 0.076 0.000 0.852
#> GSM550917 2 0.1327 0.8403 0.000 0.936 0.000 0.000 0.000 0.064
#> GSM550919 6 0.3462 0.5905 0.080 0.100 0.000 0.004 0.000 0.816
#> GSM550921 3 0.0458 0.8647 0.000 0.000 0.984 0.000 0.016 0.000
#> GSM550924 5 0.3388 0.7778 0.000 0.004 0.036 0.000 0.804 0.156
#> GSM550926 2 0.3986 0.4993 0.000 0.608 0.004 0.384 0.000 0.004
#> GSM550927 2 0.1198 0.8533 0.000 0.960 0.004 0.020 0.012 0.004
#> GSM550787 1 0.5994 0.2692 0.528 0.000 0.336 0.004 0.092 0.040
#> GSM550793 3 0.0405 0.8594 0.008 0.000 0.988 0.000 0.004 0.000
#> GSM550794 6 0.5380 0.1179 0.432 0.008 0.004 0.072 0.000 0.484
#> GSM550795 1 0.5894 0.0651 0.496 0.000 0.028 0.108 0.000 0.368
#> GSM550798 1 0.1957 0.7589 0.888 0.000 0.112 0.000 0.000 0.000
#> GSM550803 1 0.0000 0.8324 1.000 0.000 0.000 0.000 0.000 0.000
#> GSM550805 1 0.4948 0.4441 0.612 0.000 0.328 0.012 0.008 0.040
#> GSM550823 4 0.0405 0.7658 0.004 0.008 0.000 0.988 0.000 0.000
#> GSM550824 1 0.0146 0.8328 0.996 0.000 0.000 0.004 0.000 0.000
#> GSM550825 3 0.0622 0.8607 0.012 0.000 0.980 0.000 0.008 0.000
#> GSM550827 6 0.4196 0.5231 0.044 0.028 0.000 0.172 0.000 0.756
#> GSM550828 1 0.0146 0.8328 0.996 0.000 0.000 0.004 0.000 0.000
#> GSM550829 3 0.3872 0.2673 0.392 0.000 0.604 0.000 0.004 0.000
#> GSM550830 4 0.0520 0.7659 0.008 0.008 0.000 0.984 0.000 0.000
#> GSM550834 1 0.1843 0.7854 0.912 0.000 0.004 0.004 0.000 0.080
#> GSM550839 5 0.2326 0.8522 0.000 0.000 0.092 0.012 0.888 0.008
#> GSM550840 1 0.0951 0.8254 0.968 0.000 0.004 0.008 0.000 0.020
#> GSM550843 5 0.1610 0.8624 0.000 0.000 0.084 0.000 0.916 0.000
#> GSM550844 1 0.0146 0.8323 0.996 0.000 0.000 0.000 0.000 0.004
#> GSM550845 2 0.4642 0.2427 0.000 0.508 0.000 0.452 0.000 0.040
#> GSM550848 6 0.3431 0.6064 0.060 0.052 0.000 0.048 0.000 0.840
#> GSM550854 1 0.0146 0.8328 0.996 0.000 0.000 0.004 0.000 0.000
#> GSM550857 3 0.0405 0.8594 0.008 0.000 0.988 0.000 0.004 0.000
#> GSM550858 1 0.0146 0.8328 0.996 0.000 0.000 0.004 0.000 0.000
#> GSM550859 1 0.0146 0.8328 0.996 0.000 0.000 0.004 0.000 0.000
#> GSM550862 1 0.0146 0.8328 0.996 0.000 0.000 0.004 0.000 0.000
#> GSM550865 4 0.1584 0.7529 0.008 0.000 0.000 0.928 0.000 0.064
#> GSM550868 4 0.1686 0.7513 0.012 0.000 0.000 0.924 0.000 0.064
#> GSM550869 3 0.5511 0.5332 0.008 0.000 0.616 0.256 0.104 0.016
#> GSM550870 2 0.0937 0.8486 0.000 0.960 0.000 0.000 0.000 0.040
#> GSM550871 5 0.5354 0.4630 0.000 0.000 0.288 0.116 0.588 0.008
#> GSM550872 4 0.1462 0.7551 0.008 0.000 0.000 0.936 0.000 0.056
#> GSM550873 5 0.4853 0.3103 0.000 0.388 0.000 0.004 0.556 0.052
#> GSM550874 2 0.4033 0.4607 0.000 0.588 0.004 0.404 0.004 0.000
#> GSM550876 5 0.2669 0.8018 0.000 0.000 0.156 0.000 0.836 0.008
#> GSM550877 2 0.4041 0.4525 0.000 0.584 0.004 0.408 0.000 0.004
#> GSM550878 5 0.2668 0.7929 0.000 0.000 0.168 0.000 0.828 0.004
#> GSM550879 1 0.4591 0.2555 0.592 0.000 0.016 0.020 0.000 0.372
#> GSM550882 3 0.1701 0.8323 0.000 0.000 0.920 0.000 0.072 0.008
#> GSM550888 3 0.0458 0.8647 0.000 0.000 0.984 0.000 0.016 0.000
#> GSM550890 6 0.2765 0.5754 0.016 0.004 0.000 0.132 0.000 0.848
#> GSM550891 3 0.1714 0.8197 0.000 0.000 0.908 0.000 0.092 0.000
#> GSM550892 4 0.4856 -0.0889 0.468 0.000 0.000 0.476 0.000 0.056
#> GSM550893 2 0.4149 0.4744 0.000 0.592 0.004 0.396 0.004 0.004
#> GSM550895 4 0.0820 0.7647 0.000 0.016 0.000 0.972 0.000 0.012
#> GSM550896 4 0.3996 -0.2519 0.000 0.484 0.000 0.512 0.000 0.004
#> GSM550898 1 0.0146 0.8328 0.996 0.000 0.000 0.004 0.000 0.000
#> GSM550899 2 0.1444 0.8369 0.000 0.928 0.000 0.000 0.000 0.072
#> GSM550900 4 0.0692 0.7631 0.020 0.000 0.000 0.976 0.000 0.004
#> GSM550901 1 0.3954 0.3032 0.620 0.004 0.004 0.000 0.000 0.372
#> GSM550902 3 0.1951 0.7934 0.020 0.000 0.916 0.004 0.000 0.060
#> GSM550904 6 0.6222 0.2047 0.372 0.000 0.236 0.008 0.000 0.384
#> GSM550908 3 0.0458 0.8647 0.000 0.000 0.984 0.000 0.016 0.000
#> GSM550912 2 0.1765 0.8224 0.000 0.904 0.000 0.000 0.000 0.096
#> GSM550914 6 0.2755 0.5686 0.012 0.004 0.000 0.140 0.000 0.844
#> GSM550918 2 0.2527 0.7612 0.000 0.832 0.000 0.000 0.000 0.168
#> GSM550922 5 0.0405 0.8739 0.000 0.004 0.008 0.000 0.988 0.000
#> GSM550923 1 0.1007 0.8120 0.956 0.000 0.044 0.000 0.000 0.000
#> GSM550925 1 0.1232 0.8201 0.956 0.000 0.004 0.016 0.000 0.024
#> GSM550802 4 0.2970 0.6950 0.000 0.072 0.004 0.860 0.004 0.060
#> GSM550812 4 0.4921 0.4456 0.000 0.008 0.000 0.608 0.064 0.320
#> GSM550831 1 0.0653 0.8309 0.980 0.000 0.004 0.004 0.000 0.012
#> GSM550847 1 0.0000 0.8324 1.000 0.000 0.000 0.000 0.000 0.000
#> GSM550860 3 0.1655 0.8445 0.000 0.000 0.932 0.008 0.052 0.008
#> GSM550875 1 0.4500 0.4551 0.632 0.000 0.332 0.008 0.004 0.024
#> GSM550880 1 0.5942 0.1055 0.492 0.000 0.004 0.268 0.000 0.236
#> GSM550881 3 0.0632 0.8625 0.000 0.000 0.976 0.000 0.024 0.000
#> GSM550883 3 0.0405 0.8623 0.004 0.000 0.988 0.000 0.008 0.000
#> GSM550884 4 0.5635 0.1557 0.000 0.000 0.080 0.472 0.024 0.424
#> GSM550910 5 0.0937 0.8786 0.000 0.000 0.040 0.000 0.960 0.000
#> GSM550916 1 0.0692 0.8279 0.976 0.000 0.004 0.000 0.000 0.020
#> GSM550920 5 0.1007 0.8781 0.000 0.000 0.044 0.000 0.956 0.000
Heatmaps for the consensus matrix. It visualizes the probability of two samples to be in a same group.
consensus_heatmap(res, k = 2)
consensus_heatmap(res, k = 3)
consensus_heatmap(res, k = 4)
consensus_heatmap(res, k = 5)
consensus_heatmap(res, k = 6)
Heatmaps for the membership of samples in all partitions to see how consistent they are:
membership_heatmap(res, k = 2)
membership_heatmap(res, k = 3)
membership_heatmap(res, k = 4)
membership_heatmap(res, k = 5)
membership_heatmap(res, k = 6)
As soon as we have had the classes for columns, we can look for signatures which are significantly different between classes which can be candidate marks for certain classes. Following are the heatmaps for signatures.
Signature heatmaps where rows are scaled:
get_signatures(res, k = 2)
get_signatures(res, k = 3)
get_signatures(res, k = 4)
get_signatures(res, k = 5)
get_signatures(res, k = 6)
Signature heatmaps where rows are not scaled:
get_signatures(res, k = 2, scale_rows = FALSE)
get_signatures(res, k = 3, scale_rows = FALSE)
get_signatures(res, k = 4, scale_rows = FALSE)
get_signatures(res, k = 5, scale_rows = FALSE)
get_signatures(res, k = 6, scale_rows = FALSE)
Compare the overlap of signatures from different k:
compare_signatures(res)
get_signature() returns a data frame invisibly. TO get the list of signatures, the function
call should be assigned to a variable explicitly. In following code, if plot argument is set
to FALSE, no heatmap is plotted while only the differential analysis is performed.
# code only for demonstration
tb = get_signature(res, k = ..., plot = FALSE)
An example of the output of tb is:
#> which_row fdr mean_1 mean_2 scaled_mean_1 scaled_mean_2 km
#> 1 38 0.042760348 8.373488 9.131774 -0.5533452 0.5164555 1
#> 2 40 0.018707592 7.106213 8.469186 -0.6173731 0.5762149 1
#> 3 55 0.019134737 10.221463 11.207825 -0.6159697 0.5749050 1
#> 4 59 0.006059896 5.921854 7.869574 -0.6899429 0.6439467 1
#> 5 60 0.018055526 8.928898 10.211722 -0.6204761 0.5791110 1
#> 6 98 0.009384629 15.714769 14.887706 0.6635654 -0.6193277 2
...
The columns in tb are:
which_row: row indices corresponding to the input matrix.fdr: FDR for the differential test. mean_x: The mean value in group x.scaled_mean_x: The mean value in group x after rows are scaled.km: Row groups if k-means clustering is applied to rows.UMAP plot which shows how samples are separated.
dimension_reduction(res, k = 2, method = "UMAP")
dimension_reduction(res, k = 3, method = "UMAP")
dimension_reduction(res, k = 4, method = "UMAP")
dimension_reduction(res, k = 5, method = "UMAP")
dimension_reduction(res, k = 6, method = "UMAP")
Following heatmap shows how subgroups are split when increasing k:
collect_classes(res)
Test correlation between subgroups and known annotations. If the known annotation is numeric, one-way ANOVA test is applied, and if the known annotation is discrete, chi-squared contingency table test is applied.
test_to_known_factors(res)
#> n disease.state(p) k
#> SD:skmeans 141 4.17e-05 2
#> SD:skmeans 131 2.01e-04 3
#> SD:skmeans 128 5.43e-06 4
#> SD:skmeans 129 1.87e-04 5
#> SD:skmeans 114 5.18e-05 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 51776 rows and 143 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 0.378 0.843 0.887 0.4592 0.534 0.534
#> 3 3 0.693 0.809 0.914 0.4135 0.762 0.576
#> 4 4 0.704 0.817 0.899 0.1459 0.867 0.643
#> 5 5 0.718 0.802 0.904 0.0237 0.979 0.921
#> 6 6 0.713 0.728 0.839 0.0526 0.953 0.807
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
#> GSM550785 1 0.722 0.904 0.800 0.200
#> GSM550786 1 0.541 0.721 0.876 0.124
#> GSM550788 2 0.000 0.891 0.000 1.000
#> GSM550789 2 0.000 0.891 0.000 1.000
#> GSM550790 1 0.722 0.904 0.800 0.200
#> GSM550791 1 0.738 0.896 0.792 0.208
#> GSM550792 2 0.615 0.779 0.152 0.848
#> GSM550796 2 0.000 0.891 0.000 1.000
#> GSM550797 2 0.000 0.891 0.000 1.000
#> GSM550799 2 0.722 0.775 0.200 0.800
#> GSM550800 2 0.000 0.891 0.000 1.000
#> GSM550801 2 0.000 0.891 0.000 1.000
#> GSM550804 2 0.000 0.891 0.000 1.000
#> GSM550806 2 0.904 0.710 0.320 0.680
#> GSM550807 2 0.000 0.891 0.000 1.000
#> GSM550808 2 0.416 0.853 0.084 0.916
#> GSM550809 1 0.722 0.904 0.800 0.200
#> GSM550810 2 0.000 0.891 0.000 1.000
#> GSM550811 1 0.904 0.749 0.680 0.320
#> GSM550813 2 0.000 0.891 0.000 1.000
#> GSM550814 2 0.000 0.891 0.000 1.000
#> GSM550815 2 0.000 0.891 0.000 1.000
#> GSM550816 2 0.000 0.891 0.000 1.000
#> GSM550817 2 0.722 0.775 0.200 0.800
#> GSM550818 2 0.730 0.774 0.204 0.796
#> GSM550819 2 0.000 0.891 0.000 1.000
#> GSM550820 1 0.722 0.904 0.800 0.200
#> GSM550821 2 0.552 0.826 0.128 0.872
#> GSM550822 2 0.000 0.891 0.000 1.000
#> GSM550826 1 0.373 0.853 0.928 0.072
#> GSM550832 2 0.000 0.891 0.000 1.000
#> GSM550833 2 0.000 0.891 0.000 1.000
#> GSM550835 2 0.722 0.775 0.200 0.800
#> GSM550836 1 0.000 0.815 1.000 0.000
#> GSM550837 2 0.722 0.775 0.200 0.800
#> GSM550838 1 0.260 0.840 0.956 0.044
#> GSM550841 2 0.722 0.775 0.200 0.800
#> GSM550842 2 0.722 0.775 0.200 0.800
#> GSM550846 2 0.000 0.891 0.000 1.000
#> GSM550849 1 0.909 0.742 0.676 0.324
#> GSM550850 1 0.722 0.904 0.800 0.200
#> GSM550851 2 0.722 0.775 0.200 0.800
#> GSM550852 2 0.000 0.891 0.000 1.000
#> GSM550853 2 0.000 0.891 0.000 1.000
#> GSM550855 2 0.000 0.891 0.000 1.000
#> GSM550856 2 0.000 0.891 0.000 1.000
#> GSM550861 2 0.000 0.891 0.000 1.000
#> GSM550863 2 0.506 0.821 0.112 0.888
#> GSM550864 2 0.000 0.891 0.000 1.000
#> GSM550866 2 0.000 0.891 0.000 1.000
#> GSM550867 1 0.722 0.904 0.800 0.200
#> GSM550885 1 0.722 0.904 0.800 0.200
#> GSM550886 2 0.722 0.775 0.200 0.800
#> GSM550887 2 0.000 0.891 0.000 1.000
#> GSM550889 2 0.788 0.646 0.236 0.764
#> GSM550894 2 0.000 0.891 0.000 1.000
#> GSM550897 1 0.722 0.904 0.800 0.200
#> GSM550903 2 0.000 0.891 0.000 1.000
#> GSM550905 2 0.529 0.831 0.120 0.880
#> GSM550906 2 0.000 0.891 0.000 1.000
#> GSM550907 2 0.978 0.568 0.412 0.588
#> GSM550909 2 0.416 0.853 0.084 0.916
#> GSM550911 2 0.722 0.775 0.200 0.800
#> GSM550913 2 0.000 0.891 0.000 1.000
#> GSM550915 2 0.506 0.821 0.112 0.888
#> GSM550917 2 0.000 0.891 0.000 1.000
#> GSM550919 2 0.552 0.807 0.128 0.872
#> GSM550921 1 0.000 0.815 1.000 0.000
#> GSM550924 2 0.738 0.790 0.208 0.792
#> GSM550926 2 0.000 0.891 0.000 1.000
#> GSM550927 2 0.000 0.891 0.000 1.000
#> GSM550787 1 0.634 0.891 0.840 0.160
#> GSM550793 1 0.184 0.831 0.972 0.028
#> GSM550794 2 0.506 0.821 0.112 0.888
#> GSM550795 1 0.722 0.904 0.800 0.200
#> GSM550798 1 0.000 0.815 1.000 0.000
#> GSM550803 1 0.722 0.904 0.800 0.200
#> GSM550805 1 0.722 0.904 0.800 0.200
#> GSM550823 2 0.506 0.821 0.112 0.888
#> GSM550824 1 0.722 0.904 0.800 0.200
#> GSM550825 1 0.000 0.815 1.000 0.000
#> GSM550827 2 0.506 0.821 0.112 0.888
#> GSM550828 1 0.722 0.904 0.800 0.200
#> GSM550829 1 0.000 0.815 1.000 0.000
#> GSM550830 2 0.738 0.694 0.208 0.792
#> GSM550834 1 0.722 0.904 0.800 0.200
#> GSM550839 2 0.722 0.775 0.200 0.800
#> GSM550840 1 0.722 0.904 0.800 0.200
#> GSM550843 2 0.881 0.728 0.300 0.700
#> GSM550844 1 0.722 0.904 0.800 0.200
#> GSM550845 2 0.000 0.891 0.000 1.000
#> GSM550848 2 0.506 0.821 0.112 0.888
#> GSM550854 1 0.722 0.904 0.800 0.200
#> GSM550857 1 0.000 0.815 1.000 0.000
#> GSM550858 1 0.722 0.904 0.800 0.200
#> GSM550859 1 0.722 0.904 0.800 0.200
#> GSM550862 1 0.722 0.904 0.800 0.200
#> GSM550865 2 0.506 0.821 0.112 0.888
#> GSM550868 2 0.541 0.811 0.124 0.876
#> GSM550869 2 0.891 0.484 0.308 0.692
#> GSM550870 2 0.000 0.891 0.000 1.000
#> GSM550871 2 0.895 0.718 0.312 0.688
#> GSM550872 2 0.529 0.815 0.120 0.880
#> GSM550873 2 0.000 0.891 0.000 1.000
#> GSM550874 2 0.000 0.891 0.000 1.000
#> GSM550876 2 0.775 0.769 0.228 0.772
#> GSM550877 2 0.000 0.891 0.000 1.000
#> GSM550878 2 0.904 0.710 0.320 0.680
#> GSM550879 1 0.722 0.904 0.800 0.200
#> GSM550882 1 0.000 0.815 1.000 0.000
#> GSM550888 1 0.000 0.815 1.000 0.000
#> GSM550890 2 0.456 0.834 0.096 0.904
#> GSM550891 1 0.141 0.808 0.980 0.020
#> GSM550892 1 0.722 0.904 0.800 0.200
#> GSM550893 2 0.000 0.891 0.000 1.000
#> GSM550895 2 0.000 0.891 0.000 1.000
#> GSM550896 2 0.000 0.891 0.000 1.000
#> GSM550898 1 0.722 0.904 0.800 0.200
#> GSM550899 2 0.000 0.891 0.000 1.000
#> GSM550900 2 0.529 0.815 0.120 0.880
#> GSM550901 1 0.722 0.904 0.800 0.200
#> GSM550902 1 0.373 0.853 0.928 0.072
#> GSM550904 1 0.722 0.904 0.800 0.200
#> GSM550908 1 0.000 0.815 1.000 0.000
#> GSM550912 2 0.000 0.891 0.000 1.000
#> GSM550914 2 0.000 0.891 0.000 1.000
#> GSM550918 2 0.000 0.891 0.000 1.000
#> GSM550922 2 0.722 0.775 0.200 0.800
#> GSM550923 1 0.625 0.889 0.844 0.156
#> GSM550925 1 0.866 0.796 0.712 0.288
#> GSM550802 2 0.000 0.891 0.000 1.000
#> GSM550812 2 0.000 0.891 0.000 1.000
#> GSM550831 1 0.722 0.904 0.800 0.200
#> GSM550847 1 0.722 0.904 0.800 0.200
#> GSM550860 2 0.987 0.539 0.432 0.568
#> GSM550875 1 0.722 0.904 0.800 0.200
#> GSM550880 2 0.529 0.815 0.120 0.880
#> GSM550881 1 0.000 0.815 1.000 0.000
#> GSM550883 1 0.000 0.815 1.000 0.000
#> GSM550884 2 0.506 0.821 0.112 0.888
#> GSM550910 2 0.767 0.770 0.224 0.776
#> GSM550916 1 0.722 0.904 0.800 0.200
#> GSM550920 2 0.971 0.594 0.400 0.600
cbind(get_classes(res, k = 3), get_membership(res, k = 3))
#> class entropy silhouette p1 p2 p3
#> GSM550785 1 0.0000 0.9015 1.000 0.000 0.000
#> GSM550786 3 0.0592 0.9288 0.012 0.000 0.988
#> GSM550788 2 0.0000 0.8872 0.000 1.000 0.000
#> GSM550789 2 0.0592 0.8829 0.000 0.988 0.012
#> GSM550790 1 0.0000 0.9015 1.000 0.000 0.000
#> GSM550791 1 0.1860 0.8802 0.948 0.052 0.000
#> GSM550792 2 0.4452 0.7401 0.192 0.808 0.000
#> GSM550796 2 0.0592 0.8829 0.000 0.988 0.012
#> GSM550797 2 0.0592 0.8829 0.000 0.988 0.012
#> GSM550799 3 0.0000 0.9308 0.000 0.000 1.000
#> GSM550800 2 0.0000 0.8872 0.000 1.000 0.000
#> GSM550801 2 0.0592 0.8829 0.000 0.988 0.012
#> GSM550804 2 0.0000 0.8872 0.000 1.000 0.000
#> GSM550806 3 0.0592 0.9309 0.000 0.012 0.988
#> GSM550807 2 0.0000 0.8872 0.000 1.000 0.000
#> GSM550808 2 0.6267 0.0554 0.000 0.548 0.452
#> GSM550809 1 0.1163 0.8923 0.972 0.028 0.000
#> GSM550810 2 0.0592 0.8829 0.000 0.988 0.012
#> GSM550811 1 0.4062 0.7854 0.836 0.164 0.000
#> GSM550813 2 0.0000 0.8872 0.000 1.000 0.000
#> GSM550814 2 0.0000 0.8872 0.000 1.000 0.000
#> GSM550815 2 0.0592 0.8829 0.000 0.988 0.012
#> GSM550816 2 0.0592 0.8829 0.000 0.988 0.012
#> GSM550817 3 0.0000 0.9308 0.000 0.000 1.000
#> GSM550818 3 0.0000 0.9308 0.000 0.000 1.000
#> GSM550819 3 0.5894 0.7024 0.028 0.220 0.752
#> GSM550820 1 0.1031 0.8939 0.976 0.024 0.000
#> GSM550821 3 0.1031 0.9218 0.000 0.024 0.976
#> GSM550822 2 0.0592 0.8829 0.000 0.988 0.012
#> GSM550826 1 0.4618 0.8151 0.840 0.024 0.136
#> GSM550832 2 0.0000 0.8872 0.000 1.000 0.000
#> GSM550833 2 0.0592 0.8829 0.000 0.988 0.012
#> GSM550835 3 0.1163 0.9213 0.000 0.028 0.972
#> GSM550836 3 0.0592 0.9288 0.012 0.000 0.988
#> GSM550837 3 0.5497 0.6169 0.000 0.292 0.708
#> GSM550838 1 0.4261 0.8161 0.848 0.012 0.140
#> GSM550841 3 0.0000 0.9308 0.000 0.000 1.000
#> GSM550842 3 0.4121 0.8035 0.000 0.168 0.832
#> GSM550846 2 0.3415 0.8273 0.020 0.900 0.080
#> GSM550849 1 0.4002 0.7896 0.840 0.160 0.000
#> GSM550850 1 0.0000 0.9015 1.000 0.000 0.000
#> GSM550851 3 0.0892 0.9254 0.000 0.020 0.980
#> GSM550852 2 0.0000 0.8872 0.000 1.000 0.000
#> GSM550853 2 0.0000 0.8872 0.000 1.000 0.000
#> GSM550855 2 0.0000 0.8872 0.000 1.000 0.000
#> GSM550856 2 0.0000 0.8872 0.000 1.000 0.000
#> GSM550861 2 0.0000 0.8872 0.000 1.000 0.000
#> GSM550863 2 0.4974 0.7030 0.236 0.764 0.000
#> GSM550864 2 0.0000 0.8872 0.000 1.000 0.000
#> GSM550866 2 0.0000 0.8872 0.000 1.000 0.000
#> GSM550867 1 0.0000 0.9015 1.000 0.000 0.000
#> GSM550885 1 0.0000 0.9015 1.000 0.000 0.000
#> GSM550886 3 0.1860 0.9076 0.000 0.052 0.948
#> GSM550887 2 0.0592 0.8829 0.000 0.988 0.012
#> GSM550889 2 0.5650 0.5663 0.312 0.688 0.000
#> GSM550894 2 0.0000 0.8872 0.000 1.000 0.000
#> GSM550897 1 0.0424 0.8994 0.992 0.008 0.000
#> GSM550903 2 0.0000 0.8872 0.000 1.000 0.000
#> GSM550905 3 0.4887 0.7185 0.000 0.228 0.772
#> GSM550906 2 0.0000 0.8872 0.000 1.000 0.000
#> GSM550907 3 0.0000 0.9308 0.000 0.000 1.000
#> GSM550909 3 0.5016 0.6881 0.000 0.240 0.760
#> GSM550911 3 0.0000 0.9308 0.000 0.000 1.000
#> GSM550913 2 0.0000 0.8872 0.000 1.000 0.000
#> GSM550915 2 0.5178 0.6438 0.256 0.744 0.000
#> GSM550917 2 0.0000 0.8872 0.000 1.000 0.000
#> GSM550919 2 0.5905 0.4739 0.352 0.648 0.000
#> GSM550921 3 0.0592 0.9288 0.012 0.000 0.988
#> GSM550924 2 0.8291 0.4239 0.100 0.580 0.320
#> GSM550926 2 0.0000 0.8872 0.000 1.000 0.000
#> GSM550927 2 0.0000 0.8872 0.000 1.000 0.000
#> GSM550787 1 0.4859 0.8225 0.840 0.044 0.116
#> GSM550793 1 0.4291 0.8062 0.840 0.008 0.152
#> GSM550794 2 0.4291 0.7509 0.180 0.820 0.000
#> GSM550795 1 0.0000 0.9015 1.000 0.000 0.000
#> GSM550798 1 0.0000 0.9015 1.000 0.000 0.000
#> GSM550803 1 0.0000 0.9015 1.000 0.000 0.000
#> GSM550805 1 0.4002 0.7896 0.840 0.160 0.000
#> GSM550823 2 0.6045 0.4124 0.380 0.620 0.000
#> GSM550824 1 0.0000 0.9015 1.000 0.000 0.000
#> GSM550825 1 0.4555 0.7564 0.800 0.000 0.200
#> GSM550827 2 0.5968 0.4472 0.364 0.636 0.000
#> GSM550828 1 0.0000 0.9015 1.000 0.000 0.000
#> GSM550829 1 0.4002 0.8003 0.840 0.000 0.160
#> GSM550830 2 0.5859 0.4853 0.344 0.656 0.000
#> GSM550834 1 0.0000 0.9015 1.000 0.000 0.000
#> GSM550839 3 0.0592 0.9309 0.000 0.012 0.988
#> GSM550840 1 0.0000 0.9015 1.000 0.000 0.000
#> GSM550843 3 0.0592 0.9309 0.000 0.012 0.988
#> GSM550844 1 0.0747 0.8969 0.984 0.016 0.000
#> GSM550845 2 0.0000 0.8872 0.000 1.000 0.000
#> GSM550848 2 0.1753 0.8623 0.048 0.952 0.000
#> GSM550854 1 0.0000 0.9015 1.000 0.000 0.000
#> GSM550857 1 0.6008 0.4740 0.628 0.000 0.372
#> GSM550858 1 0.0000 0.9015 1.000 0.000 0.000
#> GSM550859 1 0.0000 0.9015 1.000 0.000 0.000
#> GSM550862 1 0.0000 0.9015 1.000 0.000 0.000
#> GSM550865 1 0.6309 -0.1624 0.504 0.496 0.000
#> GSM550868 2 0.6309 0.1531 0.500 0.500 0.000
#> GSM550869 2 0.6483 0.2019 0.452 0.544 0.004
#> GSM550870 2 0.0000 0.8872 0.000 1.000 0.000
#> GSM550871 3 0.0592 0.9309 0.000 0.012 0.988
#> GSM550872 2 0.6079 0.4634 0.388 0.612 0.000
#> GSM550873 2 0.0000 0.8872 0.000 1.000 0.000
#> GSM550874 2 0.0000 0.8872 0.000 1.000 0.000
#> GSM550876 3 0.2711 0.8782 0.000 0.088 0.912
#> GSM550877 2 0.0000 0.8872 0.000 1.000 0.000
#> GSM550878 3 0.0592 0.9309 0.000 0.012 0.988
#> GSM550879 1 0.0000 0.9015 1.000 0.000 0.000
#> GSM550882 3 0.0592 0.9288 0.012 0.000 0.988
#> GSM550888 3 0.0592 0.9288 0.012 0.000 0.988
#> GSM550890 2 0.4346 0.7567 0.184 0.816 0.000
#> GSM550891 3 0.0661 0.9304 0.008 0.004 0.988
#> GSM550892 1 0.0000 0.9015 1.000 0.000 0.000
#> GSM550893 2 0.0000 0.8872 0.000 1.000 0.000
#> GSM550895 2 0.1031 0.8742 0.024 0.976 0.000
#> GSM550896 2 0.0000 0.8872 0.000 1.000 0.000
#> GSM550898 1 0.0000 0.9015 1.000 0.000 0.000
#> GSM550899 2 0.0000 0.8872 0.000 1.000 0.000
#> GSM550900 1 0.6307 -0.1413 0.512 0.488 0.000
#> GSM550901 1 0.3941 0.7939 0.844 0.156 0.000
#> GSM550902 1 0.4618 0.8151 0.840 0.024 0.136
#> GSM550904 1 0.1031 0.8939 0.976 0.024 0.000
#> GSM550908 3 0.0592 0.9288 0.012 0.000 0.988
#> GSM550912 2 0.0000 0.8872 0.000 1.000 0.000
#> GSM550914 2 0.3619 0.7907 0.136 0.864 0.000
#> GSM550918 2 0.0000 0.8872 0.000 1.000 0.000
#> GSM550922 3 0.0000 0.9308 0.000 0.000 1.000
#> GSM550923 1 0.0000 0.9015 1.000 0.000 0.000
#> GSM550925 1 0.5254 0.6275 0.736 0.264 0.000
#> GSM550802 2 0.0424 0.8843 0.008 0.992 0.000
#> GSM550812 2 0.6890 0.4398 0.028 0.632 0.340
#> GSM550831 1 0.0000 0.9015 1.000 0.000 0.000
#> GSM550847 1 0.0000 0.9015 1.000 0.000 0.000
#> GSM550860 3 0.4291 0.7717 0.000 0.180 0.820
#> GSM550875 1 0.2537 0.8629 0.920 0.080 0.000
#> GSM550880 2 0.5178 0.6807 0.256 0.744 0.000
#> GSM550881 3 0.4605 0.7068 0.204 0.000 0.796
#> GSM550883 1 0.5465 0.6346 0.712 0.000 0.288
#> GSM550884 2 0.6796 0.4613 0.024 0.632 0.344
#> GSM550910 3 0.0000 0.9308 0.000 0.000 1.000
#> GSM550916 1 0.0000 0.9015 1.000 0.000 0.000
#> GSM550920 3 0.0592 0.9309 0.000 0.012 0.988
cbind(get_classes(res, k = 4), get_membership(res, k = 4))
#> class entropy silhouette p1 p2 p3 p4
#> GSM550785 1 0.0000 0.8941 1.000 0.000 0.000 0.000
#> GSM550786 3 0.0188 0.9278 0.004 0.000 0.996 0.000
#> GSM550788 2 0.2081 0.8482 0.000 0.916 0.000 0.084
#> GSM550789 2 0.0336 0.9028 0.000 0.992 0.000 0.008
#> GSM550790 1 0.0000 0.8941 1.000 0.000 0.000 0.000
#> GSM550791 1 0.3610 0.8206 0.800 0.000 0.000 0.200
#> GSM550792 4 0.3383 0.7689 0.076 0.052 0.000 0.872
#> GSM550796 2 0.0336 0.9028 0.000 0.992 0.000 0.008
#> GSM550797 2 0.0336 0.9028 0.000 0.992 0.000 0.008
#> GSM550799 3 0.0188 0.9286 0.000 0.004 0.996 0.000
#> GSM550800 2 0.1022 0.8924 0.000 0.968 0.000 0.032
#> GSM550801 2 0.0336 0.9028 0.000 0.992 0.000 0.008
#> GSM550804 4 0.1940 0.8015 0.000 0.076 0.000 0.924
#> GSM550806 3 0.0188 0.9286 0.000 0.000 0.996 0.004
#> GSM550807 2 0.0469 0.9024 0.000 0.988 0.000 0.012
#> GSM550808 2 0.3681 0.7610 0.000 0.816 0.008 0.176
#> GSM550809 1 0.3610 0.8206 0.800 0.000 0.000 0.200
#> GSM550810 2 0.3486 0.7557 0.000 0.812 0.000 0.188
#> GSM550811 1 0.3610 0.8206 0.800 0.000 0.000 0.200
#> GSM550813 4 0.0469 0.8268 0.000 0.012 0.000 0.988
#> GSM550814 2 0.4522 0.6068 0.000 0.680 0.000 0.320
#> GSM550815 2 0.0336 0.9028 0.000 0.992 0.000 0.008
#> GSM550816 2 0.3688 0.7312 0.000 0.792 0.000 0.208
#> GSM550817 3 0.0188 0.9286 0.000 0.004 0.996 0.000
#> GSM550818 3 0.0188 0.9286 0.000 0.004 0.996 0.000
#> GSM550819 3 0.4283 0.6696 0.000 0.004 0.740 0.256
#> GSM550820 1 0.3569 0.8231 0.804 0.000 0.000 0.196
#> GSM550821 3 0.3751 0.7335 0.000 0.004 0.800 0.196
#> GSM550822 2 0.0336 0.9028 0.000 0.992 0.000 0.008
#> GSM550826 1 0.3937 0.8239 0.800 0.000 0.012 0.188
#> GSM550832 4 0.1940 0.8015 0.000 0.076 0.000 0.924
#> GSM550833 2 0.0336 0.9028 0.000 0.992 0.000 0.008
#> GSM550835 2 0.4277 0.6102 0.000 0.720 0.280 0.000
#> GSM550836 3 0.0524 0.9251 0.004 0.008 0.988 0.000
#> GSM550837 2 0.1792 0.8662 0.000 0.932 0.068 0.000
#> GSM550838 1 0.4364 0.8081 0.808 0.000 0.136 0.056
#> GSM550841 3 0.0188 0.9286 0.000 0.004 0.996 0.000
#> GSM550842 2 0.0817 0.8924 0.000 0.976 0.024 0.000
#> GSM550846 4 0.0188 0.8273 0.000 0.004 0.000 0.996
#> GSM550849 1 0.3610 0.8206 0.800 0.000 0.000 0.200
#> GSM550850 1 0.0000 0.8941 1.000 0.000 0.000 0.000
#> GSM550851 2 0.4888 0.3353 0.000 0.588 0.412 0.000
#> GSM550852 4 0.4989 -0.0434 0.000 0.472 0.000 0.528
#> GSM550853 4 0.4898 0.4314 0.000 0.416 0.000 0.584
#> GSM550855 4 0.4564 0.6139 0.000 0.328 0.000 0.672
#> GSM550856 4 0.3649 0.7619 0.000 0.204 0.000 0.796
#> GSM550861 2 0.0469 0.9024 0.000 0.988 0.000 0.012
#> GSM550863 4 0.3610 0.7693 0.200 0.000 0.000 0.800
#> GSM550864 2 0.3074 0.7600 0.000 0.848 0.000 0.152
#> GSM550866 4 0.3649 0.7619 0.000 0.204 0.000 0.796
#> GSM550867 1 0.0000 0.8941 1.000 0.000 0.000 0.000
#> GSM550885 1 0.0000 0.8941 1.000 0.000 0.000 0.000
#> GSM550886 3 0.2149 0.8619 0.000 0.000 0.912 0.088
#> GSM550887 2 0.0336 0.9028 0.000 0.992 0.000 0.008
#> GSM550889 4 0.3610 0.7693 0.200 0.000 0.000 0.800
#> GSM550894 4 0.0707 0.8271 0.000 0.020 0.000 0.980
#> GSM550897 1 0.0000 0.8941 1.000 0.000 0.000 0.000
#> GSM550903 2 0.0707 0.9003 0.000 0.980 0.000 0.020
#> GSM550905 2 0.5291 0.7295 0.000 0.740 0.080 0.180
#> GSM550906 2 0.0817 0.8972 0.000 0.976 0.000 0.024
#> GSM550907 3 0.0188 0.9286 0.000 0.004 0.996 0.000
#> GSM550909 3 0.5627 0.6277 0.000 0.068 0.692 0.240
#> GSM550911 3 0.0188 0.9286 0.000 0.004 0.996 0.000
#> GSM550913 2 0.0469 0.9024 0.000 0.988 0.000 0.012
#> GSM550915 4 0.0000 0.8273 0.000 0.000 0.000 1.000
#> GSM550917 4 0.3400 0.7825 0.000 0.180 0.000 0.820
#> GSM550919 4 0.0188 0.8272 0.004 0.000 0.000 0.996
#> GSM550921 3 0.0336 0.9266 0.000 0.008 0.992 0.000
#> GSM550924 4 0.1109 0.8198 0.028 0.000 0.004 0.968
#> GSM550926 4 0.3649 0.7619 0.000 0.204 0.000 0.796
#> GSM550927 2 0.0469 0.9024 0.000 0.988 0.000 0.012
#> GSM550787 1 0.3610 0.8206 0.800 0.000 0.000 0.200
#> GSM550793 1 0.4608 0.8205 0.800 0.000 0.096 0.104
#> GSM550794 4 0.0188 0.8272 0.004 0.000 0.000 0.996
#> GSM550795 1 0.0188 0.8923 0.996 0.000 0.000 0.004
#> GSM550798 1 0.0000 0.8941 1.000 0.000 0.000 0.000
#> GSM550803 1 0.0000 0.8941 1.000 0.000 0.000 0.000
#> GSM550805 1 0.3610 0.8206 0.800 0.000 0.000 0.200
#> GSM550823 4 0.0000 0.8273 0.000 0.000 0.000 1.000
#> GSM550824 1 0.0000 0.8941 1.000 0.000 0.000 0.000
#> GSM550825 1 0.3610 0.7611 0.800 0.000 0.200 0.000
#> GSM550827 4 0.0188 0.8274 0.004 0.000 0.000 0.996
#> GSM550828 1 0.0000 0.8941 1.000 0.000 0.000 0.000
#> GSM550829 1 0.3610 0.7611 0.800 0.000 0.200 0.000
#> GSM550830 4 0.4079 0.7754 0.020 0.180 0.000 0.800
#> GSM550834 1 0.0469 0.8920 0.988 0.000 0.000 0.012
#> GSM550839 3 0.0188 0.9286 0.000 0.000 0.996 0.004
#> GSM550840 1 0.0000 0.8941 1.000 0.000 0.000 0.000
#> GSM550843 3 0.0188 0.9286 0.000 0.000 0.996 0.004
#> GSM550844 1 0.2760 0.8556 0.872 0.000 0.000 0.128
#> GSM550845 4 0.0000 0.8273 0.000 0.000 0.000 1.000
#> GSM550848 4 0.0188 0.8275 0.000 0.004 0.000 0.996
#> GSM550854 1 0.0000 0.8941 1.000 0.000 0.000 0.000
#> GSM550857 1 0.5055 0.4839 0.624 0.008 0.368 0.000
#> GSM550858 1 0.0000 0.8941 1.000 0.000 0.000 0.000
#> GSM550859 1 0.0000 0.8941 1.000 0.000 0.000 0.000
#> GSM550862 1 0.0000 0.8941 1.000 0.000 0.000 0.000
#> GSM550865 4 0.3610 0.7693 0.200 0.000 0.000 0.800
#> GSM550868 4 0.3610 0.7693 0.200 0.000 0.000 0.800
#> GSM550869 4 0.2704 0.7499 0.124 0.000 0.000 0.876
#> GSM550870 4 0.2973 0.7499 0.000 0.144 0.000 0.856
#> GSM550871 3 0.0188 0.9286 0.000 0.000 0.996 0.004
#> GSM550872 4 0.3610 0.7693 0.200 0.000 0.000 0.800
#> GSM550873 4 0.0188 0.8273 0.000 0.004 0.000 0.996
#> GSM550874 4 0.3649 0.7619 0.000 0.204 0.000 0.796
#> GSM550876 3 0.2868 0.8134 0.000 0.000 0.864 0.136
#> GSM550877 4 0.3649 0.7619 0.000 0.204 0.000 0.796
#> GSM550878 3 0.0188 0.9286 0.000 0.000 0.996 0.004
#> GSM550879 1 0.0188 0.8923 0.996 0.000 0.000 0.004
#> GSM550882 3 0.0188 0.9278 0.004 0.000 0.996 0.000
#> GSM550888 3 0.0336 0.9266 0.000 0.008 0.992 0.000
#> GSM550890 4 0.3528 0.7738 0.192 0.000 0.000 0.808
#> GSM550891 3 0.0336 0.9266 0.000 0.008 0.992 0.000
#> GSM550892 1 0.0188 0.8923 0.996 0.000 0.000 0.004
#> GSM550893 4 0.3649 0.7619 0.000 0.204 0.000 0.796
#> GSM550895 4 0.3610 0.7632 0.000 0.200 0.000 0.800
#> GSM550896 4 0.3610 0.7632 0.000 0.200 0.000 0.800
#> GSM550898 1 0.0000 0.8941 1.000 0.000 0.000 0.000
#> GSM550899 2 0.0469 0.9024 0.000 0.988 0.000 0.012
#> GSM550900 4 0.3610 0.7693 0.200 0.000 0.000 0.800
#> GSM550901 1 0.3610 0.8206 0.800 0.000 0.000 0.200
#> GSM550902 1 0.3610 0.8206 0.800 0.000 0.000 0.200
#> GSM550904 1 0.3610 0.8206 0.800 0.000 0.000 0.200
#> GSM550908 3 0.0336 0.9266 0.000 0.008 0.992 0.000
#> GSM550912 4 0.0188 0.8273 0.000 0.004 0.000 0.996
#> GSM550914 4 0.3610 0.7693 0.200 0.000 0.000 0.800
#> GSM550918 4 0.1474 0.8129 0.000 0.052 0.000 0.948
#> GSM550922 3 0.0188 0.9286 0.000 0.004 0.996 0.000
#> GSM550923 1 0.0000 0.8941 1.000 0.000 0.000 0.000
#> GSM550925 1 0.2973 0.7583 0.856 0.000 0.000 0.144
#> GSM550802 4 0.2868 0.7438 0.000 0.136 0.000 0.864
#> GSM550812 4 0.4697 0.3527 0.000 0.000 0.356 0.644
#> GSM550831 1 0.0000 0.8941 1.000 0.000 0.000 0.000
#> GSM550847 1 0.0000 0.8941 1.000 0.000 0.000 0.000
#> GSM550860 3 0.4624 0.4614 0.000 0.000 0.660 0.340
#> GSM550875 1 0.3610 0.8206 0.800 0.000 0.000 0.200
#> GSM550880 4 0.3610 0.7693 0.200 0.000 0.000 0.800
#> GSM550881 3 0.3649 0.7005 0.204 0.000 0.796 0.000
#> GSM550883 1 0.4621 0.6428 0.708 0.008 0.284 0.000
#> GSM550884 4 0.0000 0.8273 0.000 0.000 0.000 1.000
#> GSM550910 3 0.0188 0.9286 0.000 0.004 0.996 0.000
#> GSM550916 1 0.0000 0.8941 1.000 0.000 0.000 0.000
#> GSM550920 3 0.0188 0.9286 0.000 0.000 0.996 0.004
cbind(get_classes(res, k = 5), get_membership(res, k = 5))
#> class entropy silhouette p1 p2 p3 p4 p5
#> GSM550785 1 0.0000 0.884 1.000 0.000 0.000 0.000 0.000
#> GSM550786 5 0.0000 0.899 0.000 0.000 0.000 0.000 1.000
#> GSM550788 2 0.1608 0.834 0.000 0.928 0.000 0.072 0.000
#> GSM550789 2 0.0000 0.891 0.000 1.000 0.000 0.000 0.000
#> GSM550790 1 0.0000 0.884 1.000 0.000 0.000 0.000 0.000
#> GSM550791 1 0.3109 0.796 0.800 0.000 0.000 0.200 0.000
#> GSM550792 4 0.2914 0.753 0.076 0.052 0.000 0.872 0.000
#> GSM550796 2 0.0000 0.891 0.000 1.000 0.000 0.000 0.000
#> GSM550797 2 0.0000 0.891 0.000 1.000 0.000 0.000 0.000
#> GSM550799 5 0.0000 0.899 0.000 0.000 0.000 0.000 1.000
#> GSM550800 2 0.0609 0.880 0.000 0.980 0.000 0.020 0.000
#> GSM550801 2 0.0000 0.891 0.000 1.000 0.000 0.000 0.000
#> GSM550804 4 0.1671 0.793 0.000 0.076 0.000 0.924 0.000
#> GSM550806 5 0.0000 0.899 0.000 0.000 0.000 0.000 1.000
#> GSM550807 2 0.0000 0.891 0.000 1.000 0.000 0.000 0.000
#> GSM550808 2 0.2891 0.730 0.000 0.824 0.000 0.176 0.000
#> GSM550809 1 0.3109 0.796 0.800 0.000 0.000 0.200 0.000
#> GSM550810 2 0.2929 0.725 0.000 0.820 0.000 0.180 0.000
#> GSM550811 1 0.3109 0.796 0.800 0.000 0.000 0.200 0.000
#> GSM550813 4 0.0404 0.817 0.000 0.012 0.000 0.988 0.000
#> GSM550814 2 0.3876 0.605 0.000 0.684 0.000 0.316 0.000
#> GSM550815 2 0.0000 0.891 0.000 1.000 0.000 0.000 0.000
#> GSM550816 2 0.3109 0.698 0.000 0.800 0.000 0.200 0.000
#> GSM550817 5 0.0000 0.899 0.000 0.000 0.000 0.000 1.000
#> GSM550818 5 0.0000 0.899 0.000 0.000 0.000 0.000 1.000
#> GSM550819 5 0.3662 0.617 0.000 0.004 0.000 0.252 0.744
#> GSM550820 1 0.3074 0.799 0.804 0.000 0.000 0.196 0.000
#> GSM550821 5 0.3074 0.680 0.000 0.000 0.000 0.196 0.804
#> GSM550822 2 0.0000 0.891 0.000 1.000 0.000 0.000 0.000
#> GSM550826 1 0.3391 0.798 0.800 0.000 0.000 0.188 0.012
#> GSM550832 4 0.1671 0.793 0.000 0.076 0.000 0.924 0.000
#> GSM550833 2 0.0000 0.891 0.000 1.000 0.000 0.000 0.000
#> GSM550835 2 0.3636 0.621 0.000 0.728 0.000 0.000 0.272
#> GSM550836 3 0.0000 0.921 0.000 0.000 1.000 0.000 0.000
#> GSM550837 2 0.1410 0.853 0.000 0.940 0.000 0.000 0.060
#> GSM550838 1 0.3759 0.783 0.808 0.000 0.000 0.056 0.136
#> GSM550841 5 0.0000 0.899 0.000 0.000 0.000 0.000 1.000
#> GSM550842 2 0.0510 0.884 0.000 0.984 0.000 0.000 0.016
#> GSM550846 4 0.0162 0.817 0.000 0.004 0.000 0.996 0.000
#> GSM550849 1 0.3109 0.796 0.800 0.000 0.000 0.200 0.000
#> GSM550850 1 0.0000 0.884 1.000 0.000 0.000 0.000 0.000
#> GSM550851 2 0.4210 0.350 0.000 0.588 0.000 0.000 0.412
#> GSM550852 4 0.4300 -0.042 0.000 0.476 0.000 0.524 0.000
#> GSM550853 4 0.4219 0.440 0.000 0.416 0.000 0.584 0.000
#> GSM550855 4 0.3949 0.612 0.000 0.332 0.000 0.668 0.000
#> GSM550856 4 0.3143 0.764 0.000 0.204 0.000 0.796 0.000
#> GSM550861 2 0.0000 0.891 0.000 1.000 0.000 0.000 0.000
#> GSM550863 4 0.3109 0.745 0.200 0.000 0.000 0.800 0.000
#> GSM550864 2 0.2561 0.747 0.000 0.856 0.000 0.144 0.000
#> GSM550866 4 0.3143 0.764 0.000 0.204 0.000 0.796 0.000
#> GSM550867 1 0.0000 0.884 1.000 0.000 0.000 0.000 0.000
#> GSM550885 1 0.0000 0.884 1.000 0.000 0.000 0.000 0.000
#> GSM550886 5 0.1851 0.820 0.000 0.000 0.000 0.088 0.912
#> GSM550887 2 0.0000 0.891 0.000 1.000 0.000 0.000 0.000
#> GSM550889 4 0.3109 0.745 0.200 0.000 0.000 0.800 0.000
#> GSM550894 4 0.0609 0.818 0.000 0.020 0.000 0.980 0.000
#> GSM550897 1 0.0000 0.884 1.000 0.000 0.000 0.000 0.000
#> GSM550903 2 0.0290 0.888 0.000 0.992 0.000 0.008 0.000
#> GSM550905 2 0.4444 0.690 0.000 0.748 0.000 0.180 0.072
#> GSM550906 2 0.0404 0.885 0.000 0.988 0.000 0.012 0.000
#> GSM550907 5 0.0000 0.899 0.000 0.000 0.000 0.000 1.000
#> GSM550909 5 0.4788 0.574 0.000 0.064 0.000 0.240 0.696
#> GSM550911 5 0.0000 0.899 0.000 0.000 0.000 0.000 1.000
#> GSM550913 2 0.0000 0.891 0.000 1.000 0.000 0.000 0.000
#> GSM550915 4 0.0000 0.816 0.000 0.000 0.000 1.000 0.000
#> GSM550917 4 0.2929 0.783 0.000 0.180 0.000 0.820 0.000
#> GSM550919 4 0.0162 0.816 0.004 0.000 0.000 0.996 0.000
#> GSM550921 3 0.0000 0.921 0.000 0.000 1.000 0.000 0.000
#> GSM550924 4 0.0955 0.807 0.028 0.000 0.000 0.968 0.004
#> GSM550926 4 0.3143 0.764 0.000 0.204 0.000 0.796 0.000
#> GSM550927 2 0.0000 0.891 0.000 1.000 0.000 0.000 0.000
#> GSM550787 1 0.3109 0.796 0.800 0.000 0.000 0.200 0.000
#> GSM550793 1 0.3970 0.794 0.800 0.000 0.000 0.104 0.096
#> GSM550794 4 0.0162 0.816 0.004 0.000 0.000 0.996 0.000
#> GSM550795 1 0.0162 0.882 0.996 0.000 0.000 0.004 0.000
#> GSM550798 1 0.0000 0.884 1.000 0.000 0.000 0.000 0.000
#> GSM550803 1 0.0000 0.884 1.000 0.000 0.000 0.000 0.000
#> GSM550805 1 0.3109 0.796 0.800 0.000 0.000 0.200 0.000
#> GSM550823 4 0.0000 0.816 0.000 0.000 0.000 1.000 0.000
#> GSM550824 1 0.0000 0.884 1.000 0.000 0.000 0.000 0.000
#> GSM550825 1 0.3109 0.735 0.800 0.000 0.000 0.000 0.200
#> GSM550827 4 0.0162 0.816 0.004 0.000 0.000 0.996 0.000
#> GSM550828 1 0.0000 0.884 1.000 0.000 0.000 0.000 0.000
#> GSM550829 1 0.3109 0.735 0.800 0.000 0.000 0.000 0.200
#> GSM550830 4 0.3513 0.775 0.020 0.180 0.000 0.800 0.000
#> GSM550834 1 0.0404 0.881 0.988 0.000 0.000 0.012 0.000
#> GSM550839 5 0.0000 0.899 0.000 0.000 0.000 0.000 1.000
#> GSM550840 1 0.0000 0.884 1.000 0.000 0.000 0.000 0.000
#> GSM550843 5 0.0000 0.899 0.000 0.000 0.000 0.000 1.000
#> GSM550844 1 0.2377 0.836 0.872 0.000 0.000 0.128 0.000
#> GSM550845 4 0.0000 0.816 0.000 0.000 0.000 1.000 0.000
#> GSM550848 4 0.0162 0.817 0.000 0.004 0.000 0.996 0.000
#> GSM550854 1 0.0000 0.884 1.000 0.000 0.000 0.000 0.000
#> GSM550857 3 0.0000 0.921 0.000 0.000 1.000 0.000 0.000
#> GSM550858 1 0.0000 0.884 1.000 0.000 0.000 0.000 0.000
#> GSM550859 1 0.0000 0.884 1.000 0.000 0.000 0.000 0.000
#> GSM550862 1 0.0000 0.884 1.000 0.000 0.000 0.000 0.000
#> GSM550865 4 0.3109 0.745 0.200 0.000 0.000 0.800 0.000
#> GSM550868 4 0.3109 0.745 0.200 0.000 0.000 0.800 0.000
#> GSM550869 4 0.2329 0.727 0.124 0.000 0.000 0.876 0.000
#> GSM550870 4 0.2561 0.748 0.000 0.144 0.000 0.856 0.000
#> GSM550871 5 0.0000 0.899 0.000 0.000 0.000 0.000 1.000
#> GSM550872 4 0.3109 0.745 0.200 0.000 0.000 0.800 0.000
#> GSM550873 4 0.0162 0.817 0.000 0.004 0.000 0.996 0.000
#> GSM550874 4 0.3143 0.764 0.000 0.204 0.000 0.796 0.000
#> GSM550876 5 0.2471 0.764 0.000 0.000 0.000 0.136 0.864
#> GSM550877 4 0.3143 0.764 0.000 0.204 0.000 0.796 0.000
#> GSM550878 5 0.0000 0.899 0.000 0.000 0.000 0.000 1.000
#> GSM550879 1 0.0162 0.882 0.996 0.000 0.000 0.004 0.000
#> GSM550882 5 0.0000 0.899 0.000 0.000 0.000 0.000 1.000
#> GSM550888 3 0.0000 0.921 0.000 0.000 1.000 0.000 0.000
#> GSM550890 4 0.3039 0.750 0.192 0.000 0.000 0.808 0.000
#> GSM550891 3 0.0000 0.921 0.000 0.000 1.000 0.000 0.000
#> GSM550892 1 0.0162 0.882 0.996 0.000 0.000 0.004 0.000
#> GSM550893 4 0.3143 0.764 0.000 0.204 0.000 0.796 0.000
#> GSM550895 4 0.3109 0.765 0.000 0.200 0.000 0.800 0.000
#> GSM550896 4 0.3109 0.765 0.000 0.200 0.000 0.800 0.000
#> GSM550898 1 0.0000 0.884 1.000 0.000 0.000 0.000 0.000
#> GSM550899 2 0.0000 0.891 0.000 1.000 0.000 0.000 0.000
#> GSM550900 4 0.3109 0.745 0.200 0.000 0.000 0.800 0.000
#> GSM550901 1 0.3109 0.796 0.800 0.000 0.000 0.200 0.000
#> GSM550902 1 0.3109 0.796 0.800 0.000 0.000 0.200 0.000
#> GSM550904 1 0.3109 0.796 0.800 0.000 0.000 0.200 0.000
#> GSM550908 3 0.0000 0.921 0.000 0.000 1.000 0.000 0.000
#> GSM550912 4 0.0162 0.817 0.000 0.004 0.000 0.996 0.000
#> GSM550914 4 0.3109 0.745 0.200 0.000 0.000 0.800 0.000
#> GSM550918 4 0.1270 0.804 0.000 0.052 0.000 0.948 0.000
#> GSM550922 5 0.0000 0.899 0.000 0.000 0.000 0.000 1.000
#> GSM550923 1 0.0000 0.884 1.000 0.000 0.000 0.000 0.000
#> GSM550925 1 0.2561 0.727 0.856 0.000 0.000 0.144 0.000
#> GSM550802 4 0.2516 0.740 0.000 0.140 0.000 0.860 0.000
#> GSM550812 4 0.4060 0.329 0.000 0.000 0.000 0.640 0.360
#> GSM550831 1 0.0000 0.884 1.000 0.000 0.000 0.000 0.000
#> GSM550847 1 0.0000 0.884 1.000 0.000 0.000 0.000 0.000
#> GSM550860 5 0.3983 0.455 0.000 0.000 0.000 0.340 0.660
#> GSM550875 1 0.3109 0.796 0.800 0.000 0.000 0.200 0.000
#> GSM550880 4 0.3109 0.745 0.200 0.000 0.000 0.800 0.000
#> GSM550881 5 0.3143 0.629 0.204 0.000 0.000 0.000 0.796
#> GSM550883 3 0.3999 0.405 0.344 0.000 0.656 0.000 0.000
#> GSM550884 4 0.0000 0.816 0.000 0.000 0.000 1.000 0.000
#> GSM550910 5 0.0000 0.899 0.000 0.000 0.000 0.000 1.000
#> GSM550916 1 0.0000 0.884 1.000 0.000 0.000 0.000 0.000
#> GSM550920 5 0.0000 0.899 0.000 0.000 0.000 0.000 1.000
cbind(get_classes(res, k = 6), get_membership(res, k = 6))
#> class entropy silhouette p1 p2 p3 p4 p5 p6
#> GSM550785 6 0.2969 0.6751 0.224 0.000 0.000 0.000 0.000 0.776
#> GSM550786 5 0.0000 0.9024 0.000 0.000 0.000 0.000 1.000 0.000
#> GSM550788 2 0.0937 0.8099 0.000 0.960 0.000 0.040 0.000 0.000
#> GSM550789 2 0.0000 0.8283 0.000 1.000 0.000 0.000 0.000 0.000
#> GSM550790 1 0.3684 0.7633 0.628 0.000 0.000 0.000 0.000 0.372
#> GSM550791 6 0.3175 0.6406 0.000 0.000 0.000 0.256 0.000 0.744
#> GSM550792 4 0.2934 0.7335 0.064 0.024 0.000 0.868 0.000 0.044
#> GSM550796 2 0.0000 0.8283 0.000 1.000 0.000 0.000 0.000 0.000
#> GSM550797 2 0.0000 0.8283 0.000 1.000 0.000 0.000 0.000 0.000
#> GSM550799 5 0.0000 0.9024 0.000 0.000 0.000 0.000 1.000 0.000
#> GSM550800 2 0.0458 0.8233 0.000 0.984 0.000 0.016 0.000 0.000
#> GSM550801 2 0.2135 0.7716 0.000 0.872 0.000 0.128 0.000 0.000
#> GSM550804 4 0.1152 0.7284 0.000 0.044 0.000 0.952 0.000 0.004
#> GSM550806 5 0.0000 0.9024 0.000 0.000 0.000 0.000 1.000 0.000
#> GSM550807 2 0.0000 0.8283 0.000 1.000 0.000 0.000 0.000 0.000
#> GSM550808 2 0.2703 0.7152 0.000 0.824 0.000 0.172 0.000 0.004
#> GSM550809 6 0.1267 0.7994 0.000 0.000 0.000 0.060 0.000 0.940
#> GSM550810 2 0.2738 0.7114 0.000 0.820 0.000 0.176 0.000 0.004
#> GSM550811 6 0.3351 0.5987 0.000 0.000 0.000 0.288 0.000 0.712
#> GSM550813 4 0.0858 0.7433 0.000 0.028 0.000 0.968 0.000 0.004
#> GSM550814 2 0.3652 0.5546 0.000 0.672 0.000 0.324 0.000 0.004
#> GSM550815 2 0.0000 0.8283 0.000 1.000 0.000 0.000 0.000 0.000
#> GSM550816 2 0.3769 0.5189 0.000 0.640 0.000 0.356 0.000 0.004
#> GSM550817 5 0.0000 0.9024 0.000 0.000 0.000 0.000 1.000 0.000
#> GSM550818 5 0.0000 0.9024 0.000 0.000 0.000 0.000 1.000 0.000
#> GSM550819 5 0.3919 0.6274 0.016 0.004 0.000 0.244 0.728 0.008
#> GSM550820 6 0.0692 0.7965 0.020 0.000 0.000 0.004 0.000 0.976
#> GSM550821 5 0.3081 0.6714 0.000 0.000 0.000 0.220 0.776 0.004
#> GSM550822 2 0.0000 0.8283 0.000 1.000 0.000 0.000 0.000 0.000
#> GSM550826 6 0.1480 0.7934 0.000 0.000 0.000 0.020 0.040 0.940
#> GSM550832 4 0.1265 0.7284 0.000 0.044 0.000 0.948 0.000 0.008
#> GSM550833 2 0.0000 0.8283 0.000 1.000 0.000 0.000 0.000 0.000
#> GSM550835 2 0.3101 0.6163 0.000 0.756 0.000 0.000 0.244 0.000
#> GSM550836 3 0.0000 0.9169 0.000 0.000 1.000 0.000 0.000 0.000
#> GSM550837 2 0.0865 0.8133 0.000 0.964 0.000 0.000 0.036 0.000
#> GSM550838 6 0.1563 0.7835 0.000 0.000 0.000 0.012 0.056 0.932
#> GSM550841 5 0.0000 0.9024 0.000 0.000 0.000 0.000 1.000 0.000
#> GSM550842 2 0.0458 0.8222 0.000 0.984 0.000 0.000 0.016 0.000
#> GSM550846 4 0.2432 0.7323 0.000 0.016 0.000 0.892 0.072 0.020
#> GSM550849 6 0.3351 0.5987 0.000 0.000 0.000 0.288 0.000 0.712
#> GSM550850 6 0.1267 0.7795 0.060 0.000 0.000 0.000 0.000 0.940
#> GSM550851 2 0.3955 0.3682 0.000 0.608 0.000 0.008 0.384 0.000
#> GSM550852 4 0.3975 0.1245 0.000 0.392 0.000 0.600 0.000 0.008
#> GSM550853 2 0.3756 0.0791 0.000 0.600 0.000 0.400 0.000 0.000
#> GSM550855 2 0.3868 -0.2724 0.000 0.508 0.000 0.492 0.000 0.000
#> GSM550856 4 0.3944 0.4411 0.000 0.428 0.000 0.568 0.000 0.004
#> GSM550861 2 0.0000 0.8283 0.000 1.000 0.000 0.000 0.000 0.000
#> GSM550863 4 0.4543 0.6453 0.384 0.000 0.000 0.576 0.000 0.040
#> GSM550864 2 0.3198 0.6394 0.000 0.740 0.000 0.260 0.000 0.000
#> GSM550866 4 0.4703 0.5071 0.052 0.380 0.000 0.568 0.000 0.000
#> GSM550867 1 0.2697 0.8916 0.812 0.000 0.000 0.000 0.000 0.188
#> GSM550885 1 0.2631 0.8741 0.820 0.000 0.000 0.000 0.000 0.180
#> GSM550886 5 0.1588 0.8377 0.000 0.000 0.000 0.072 0.924 0.004
#> GSM550887 2 0.0000 0.8283 0.000 1.000 0.000 0.000 0.000 0.000
#> GSM550889 4 0.4543 0.6453 0.384 0.000 0.000 0.576 0.000 0.040
#> GSM550894 4 0.2053 0.7243 0.000 0.108 0.000 0.888 0.000 0.004
#> GSM550897 6 0.2848 0.7091 0.176 0.000 0.000 0.008 0.000 0.816
#> GSM550903 2 0.2416 0.7583 0.000 0.844 0.000 0.156 0.000 0.000
#> GSM550905 2 0.3695 0.6939 0.000 0.776 0.000 0.176 0.044 0.004
#> GSM550906 2 0.0146 0.8273 0.000 0.996 0.000 0.004 0.000 0.000
#> GSM550907 5 0.0000 0.9024 0.000 0.000 0.000 0.000 1.000 0.000
#> GSM550909 5 0.4569 0.4836 0.000 0.036 0.000 0.332 0.624 0.008
#> GSM550911 5 0.0000 0.9024 0.000 0.000 0.000 0.000 1.000 0.000
#> GSM550913 2 0.2003 0.7771 0.000 0.884 0.000 0.116 0.000 0.000
#> GSM550915 4 0.0547 0.7433 0.000 0.000 0.000 0.980 0.000 0.020
#> GSM550917 4 0.2454 0.6955 0.000 0.160 0.000 0.840 0.000 0.000
#> GSM550919 4 0.1334 0.7505 0.020 0.000 0.000 0.948 0.000 0.032
#> GSM550921 3 0.0000 0.9169 0.000 0.000 1.000 0.000 0.000 0.000
#> GSM550924 4 0.0972 0.7374 0.000 0.000 0.000 0.964 0.008 0.028
#> GSM550926 4 0.3833 0.5950 0.016 0.272 0.000 0.708 0.000 0.004
#> GSM550927 2 0.0000 0.8283 0.000 1.000 0.000 0.000 0.000 0.000
#> GSM550787 6 0.1204 0.8011 0.000 0.000 0.000 0.056 0.000 0.944
#> GSM550793 6 0.1480 0.8011 0.000 0.000 0.000 0.040 0.020 0.940
#> GSM550794 4 0.2373 0.7458 0.084 0.004 0.000 0.888 0.000 0.024
#> GSM550795 6 0.3807 0.4807 0.368 0.000 0.000 0.004 0.000 0.628
#> GSM550798 1 0.3684 0.7633 0.628 0.000 0.000 0.000 0.000 0.372
#> GSM550803 1 0.3409 0.8304 0.700 0.000 0.000 0.000 0.000 0.300
#> GSM550805 6 0.1204 0.8011 0.000 0.000 0.000 0.056 0.000 0.944
#> GSM550823 4 0.3776 0.7311 0.188 0.000 0.000 0.760 0.000 0.052
#> GSM550824 1 0.2730 0.8927 0.808 0.000 0.000 0.000 0.000 0.192
#> GSM550825 6 0.3101 0.6024 0.000 0.000 0.000 0.000 0.244 0.756
#> GSM550827 4 0.3408 0.7399 0.152 0.000 0.000 0.800 0.000 0.048
#> GSM550828 6 0.2793 0.6797 0.200 0.000 0.000 0.000 0.000 0.800
#> GSM550829 6 0.1408 0.7857 0.036 0.000 0.000 0.000 0.020 0.944
#> GSM550830 4 0.6333 0.6772 0.188 0.132 0.000 0.576 0.000 0.104
#> GSM550834 6 0.0547 0.7932 0.020 0.000 0.000 0.000 0.000 0.980
#> GSM550839 5 0.0000 0.9024 0.000 0.000 0.000 0.000 1.000 0.000
#> GSM550840 6 0.1176 0.7996 0.024 0.000 0.000 0.020 0.000 0.956
#> GSM550843 5 0.0000 0.9024 0.000 0.000 0.000 0.000 1.000 0.000
#> GSM550844 6 0.1421 0.7985 0.028 0.000 0.000 0.028 0.000 0.944
#> GSM550845 4 0.1858 0.7476 0.092 0.004 0.000 0.904 0.000 0.000
#> GSM550848 4 0.1718 0.7508 0.016 0.008 0.000 0.932 0.000 0.044
#> GSM550854 1 0.2697 0.8916 0.812 0.000 0.000 0.000 0.000 0.188
#> GSM550857 3 0.0000 0.9169 0.000 0.000 1.000 0.000 0.000 0.000
#> GSM550858 6 0.2941 0.6766 0.220 0.000 0.000 0.000 0.000 0.780
#> GSM550859 1 0.2730 0.8927 0.808 0.000 0.000 0.000 0.000 0.192
#> GSM550862 6 0.2969 0.6750 0.224 0.000 0.000 0.000 0.000 0.776
#> GSM550865 4 0.4543 0.6453 0.384 0.000 0.000 0.576 0.000 0.040
#> GSM550868 4 0.4543 0.6453 0.384 0.000 0.000 0.576 0.000 0.040
#> GSM550869 4 0.4410 0.6623 0.120 0.000 0.000 0.716 0.000 0.164
#> GSM550870 4 0.1858 0.6939 0.000 0.092 0.000 0.904 0.000 0.004
#> GSM550871 5 0.0291 0.8975 0.004 0.000 0.000 0.004 0.992 0.000
#> GSM550872 4 0.4543 0.6453 0.384 0.000 0.000 0.576 0.000 0.040
#> GSM550873 4 0.0405 0.7397 0.000 0.004 0.000 0.988 0.000 0.008
#> GSM550874 4 0.3817 0.4351 0.000 0.432 0.000 0.568 0.000 0.000
#> GSM550876 5 0.2446 0.7757 0.012 0.000 0.000 0.124 0.864 0.000
#> GSM550877 4 0.4002 0.4703 0.008 0.404 0.000 0.588 0.000 0.000
#> GSM550878 5 0.0000 0.9024 0.000 0.000 0.000 0.000 1.000 0.000
#> GSM550879 6 0.2969 0.6610 0.224 0.000 0.000 0.000 0.000 0.776
#> GSM550882 5 0.0000 0.9024 0.000 0.000 0.000 0.000 1.000 0.000
#> GSM550888 3 0.0000 0.9169 0.000 0.000 1.000 0.000 0.000 0.000
#> GSM550890 4 0.4606 0.6659 0.344 0.000 0.000 0.604 0.000 0.052
#> GSM550891 3 0.0000 0.9169 0.000 0.000 1.000 0.000 0.000 0.000
#> GSM550892 6 0.3911 0.4780 0.368 0.000 0.000 0.008 0.000 0.624
#> GSM550893 4 0.4107 0.5868 0.028 0.280 0.000 0.688 0.000 0.004
#> GSM550895 4 0.6028 0.6519 0.188 0.196 0.000 0.576 0.000 0.040
#> GSM550896 4 0.5738 0.6545 0.144 0.200 0.000 0.616 0.000 0.040
#> GSM550898 1 0.2730 0.8927 0.808 0.000 0.000 0.000 0.000 0.192
#> GSM550899 2 0.2562 0.7459 0.000 0.828 0.000 0.172 0.000 0.000
#> GSM550900 4 0.4543 0.6453 0.384 0.000 0.000 0.576 0.000 0.040
#> GSM550901 6 0.1141 0.8009 0.000 0.000 0.000 0.052 0.000 0.948
#> GSM550902 6 0.2883 0.6867 0.000 0.000 0.000 0.212 0.000 0.788
#> GSM550904 6 0.1267 0.7993 0.000 0.000 0.000 0.060 0.000 0.940
#> GSM550908 3 0.0000 0.9169 0.000 0.000 1.000 0.000 0.000 0.000
#> GSM550912 4 0.0405 0.7397 0.000 0.004 0.000 0.988 0.000 0.008
#> GSM550914 4 0.4619 0.6608 0.348 0.000 0.000 0.600 0.000 0.052
#> GSM550918 4 0.1168 0.7367 0.000 0.028 0.000 0.956 0.000 0.016
#> GSM550922 5 0.0000 0.9024 0.000 0.000 0.000 0.000 1.000 0.000
#> GSM550923 1 0.3684 0.7633 0.628 0.000 0.000 0.000 0.000 0.372
#> GSM550925 6 0.2398 0.7028 0.020 0.000 0.000 0.104 0.000 0.876
#> GSM550802 4 0.3481 0.6024 0.012 0.228 0.000 0.756 0.000 0.004
#> GSM550812 4 0.5354 0.4744 0.132 0.000 0.000 0.604 0.256 0.008
#> GSM550831 6 0.1556 0.7800 0.080 0.000 0.000 0.000 0.000 0.920
#> GSM550847 1 0.2697 0.8916 0.812 0.000 0.000 0.000 0.000 0.188
#> GSM550860 5 0.3629 0.5743 0.016 0.000 0.000 0.260 0.724 0.000
#> GSM550875 6 0.1267 0.8014 0.000 0.000 0.000 0.060 0.000 0.940
#> GSM550880 4 0.4737 0.6511 0.372 0.000 0.000 0.572 0.000 0.056
#> GSM550881 5 0.2823 0.6540 0.000 0.000 0.000 0.000 0.796 0.204
#> GSM550883 3 0.3592 0.3721 0.000 0.000 0.656 0.000 0.000 0.344
#> GSM550884 4 0.2320 0.7414 0.132 0.000 0.000 0.864 0.000 0.004
#> GSM550910 5 0.0000 0.9024 0.000 0.000 0.000 0.000 1.000 0.000
#> GSM550916 6 0.1714 0.7561 0.092 0.000 0.000 0.000 0.000 0.908
#> GSM550920 5 0.0000 0.9024 0.000 0.000 0.000 0.000 1.000 0.000
Heatmaps for the consensus matrix. It visualizes the probability of two samples to be in a same group.
consensus_heatmap(res, k = 2)
consensus_heatmap(res, k = 3)
consensus_heatmap(res, k = 4)
consensus_heatmap(res, k = 5)
consensus_heatmap(res, k = 6)
Heatmaps for the membership of samples in all partitions to see how consistent they are:
membership_heatmap(res, k = 2)
membership_heatmap(res, k = 3)
membership_heatmap(res, k = 4)
membership_heatmap(res, k = 5)
membership_heatmap(res, k = 6)
As soon as we have had the classes for columns, we can look for signatures which are significantly different between classes which can be candidate marks for certain classes. Following are the heatmaps for signatures.
Signature heatmaps where rows are scaled:
get_signatures(res, k = 2)
get_signatures(res, k = 3)
get_signatures(res, k = 4)
get_signatures(res, k = 5)
get_signatures(res, k = 6)
Signature heatmaps where rows are not scaled:
get_signatures(res, k = 2, scale_rows = FALSE)
get_signatures(res, k = 3, scale_rows = FALSE)
get_signatures(res, k = 4, scale_rows = FALSE)
get_signatures(res, k = 5, scale_rows = FALSE)
get_signatures(res, k = 6, scale_rows = FALSE)
Compare the overlap of signatures from different k:
compare_signatures(res)
get_signature() returns a data frame invisibly. TO get the list of signatures, the function
call should be assigned to a variable explicitly. In following code, if plot argument is set
to FALSE, no heatmap is plotted while only the differential analysis is performed.
# code only for demonstration
tb = get_signature(res, k = ..., plot = FALSE)
An example of the output of tb is:
#> which_row fdr mean_1 mean_2 scaled_mean_1 scaled_mean_2 km
#> 1 38 0.042760348 8.373488 9.131774 -0.5533452 0.5164555 1
#> 2 40 0.018707592 7.106213 8.469186 -0.6173731 0.5762149 1
#> 3 55 0.019134737 10.221463 11.207825 -0.6159697 0.5749050 1
#> 4 59 0.006059896 5.921854 7.869574 -0.6899429 0.6439467 1
#> 5 60 0.018055526 8.928898 10.211722 -0.6204761 0.5791110 1
#> 6 98 0.009384629 15.714769 14.887706 0.6635654 -0.6193277 2
...
The columns in tb are:
which_row: row indices corresponding to the input matrix.fdr: FDR for the differential test. mean_x: The mean value in group x.scaled_mean_x: The mean value in group x after rows are scaled.km: Row groups if k-means clustering is applied to rows.UMAP plot which shows how samples are separated.
dimension_reduction(res, k = 2, method = "UMAP")
dimension_reduction(res, k = 3, method = "UMAP")
dimension_reduction(res, k = 4, method = "UMAP")
dimension_reduction(res, k = 5, method = "UMAP")
dimension_reduction(res, k = 6, method = "UMAP")
Following heatmap shows how subgroups are split when increasing k:
collect_classes(res)
Test correlation between subgroups and known annotations. If the known annotation is numeric, one-way ANOVA test is applied, and if the known annotation is discrete, chi-squared contingency table test is applied.
test_to_known_factors(res)
#> n disease.state(p) k
#> SD:pam 142 2.16e-03 2
#> SD:pam 129 4.20e-03 3
#> SD:pam 137 1.83e-05 4
#> SD:pam 137 4.24e-05 5
#> SD:pam 131 1.45e-04 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 51776 rows and 143 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 0.612 0.776 0.899 0.4328 0.523 0.523
#> 3 3 0.409 0.643 0.809 0.2443 0.634 0.463
#> 4 4 0.372 0.388 0.655 0.2247 0.702 0.462
#> 5 5 0.614 0.714 0.832 0.1009 0.699 0.346
#> 6 6 0.707 0.702 0.858 0.0861 0.800 0.424
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
#> GSM550785 2 0.0938 0.9306 0.012 0.988
#> GSM550786 1 0.6247 0.7320 0.844 0.156
#> GSM550788 2 0.0938 0.9306 0.012 0.988
#> GSM550789 2 0.0000 0.9282 0.000 1.000
#> GSM550790 2 0.0938 0.9306 0.012 0.988
#> GSM550791 2 0.3733 0.8736 0.072 0.928
#> GSM550792 2 0.7299 0.6860 0.204 0.796
#> GSM550796 2 0.0000 0.9282 0.000 1.000
#> GSM550797 2 0.0000 0.9282 0.000 1.000
#> GSM550799 1 0.0000 0.7890 1.000 0.000
#> GSM550800 2 0.0000 0.9282 0.000 1.000
#> GSM550801 2 0.0000 0.9282 0.000 1.000
#> GSM550804 2 0.0000 0.9282 0.000 1.000
#> GSM550806 1 0.0000 0.7890 1.000 0.000
#> GSM550807 2 0.0000 0.9282 0.000 1.000
#> GSM550808 1 0.8909 0.6270 0.692 0.308
#> GSM550809 1 0.9850 0.4750 0.572 0.428
#> GSM550810 2 0.9393 0.2774 0.356 0.644
#> GSM550811 1 0.9881 0.4563 0.564 0.436
#> GSM550813 2 0.0000 0.9282 0.000 1.000
#> GSM550814 2 0.9358 0.2879 0.352 0.648
#> GSM550815 2 0.0000 0.9282 0.000 1.000
#> GSM550816 2 0.0938 0.9306 0.012 0.988
#> GSM550817 1 0.0000 0.7890 1.000 0.000
#> GSM550818 1 0.0000 0.7890 1.000 0.000
#> GSM550819 2 0.9993 -0.2248 0.484 0.516
#> GSM550820 1 0.9850 0.4750 0.572 0.428
#> GSM550821 1 0.9635 0.5361 0.612 0.388
#> GSM550822 2 0.0000 0.9282 0.000 1.000
#> GSM550826 1 0.9833 0.4833 0.576 0.424
#> GSM550832 2 0.6887 0.7057 0.184 0.816
#> GSM550833 2 0.0000 0.9282 0.000 1.000
#> GSM550835 1 0.1184 0.7871 0.984 0.016
#> GSM550836 1 0.0000 0.7890 1.000 0.000
#> GSM550837 1 0.7139 0.7150 0.804 0.196
#> GSM550838 1 0.9833 0.4833 0.576 0.424
#> GSM550841 1 0.0000 0.7890 1.000 0.000
#> GSM550842 1 0.1414 0.7856 0.980 0.020
#> GSM550846 1 0.9933 0.4157 0.548 0.452
#> GSM550849 1 0.9977 0.3557 0.528 0.472
#> GSM550850 2 0.3114 0.8908 0.056 0.944
#> GSM550851 1 0.7745 0.6917 0.772 0.228
#> GSM550852 2 0.6712 0.7191 0.176 0.824
#> GSM550853 2 0.0000 0.9282 0.000 1.000
#> GSM550855 2 0.0000 0.9282 0.000 1.000
#> GSM550856 2 0.0000 0.9282 0.000 1.000
#> GSM550861 2 0.0000 0.9282 0.000 1.000
#> GSM550863 2 0.0938 0.9306 0.012 0.988
#> GSM550864 2 0.0000 0.9282 0.000 1.000
#> GSM550866 2 0.0000 0.9282 0.000 1.000
#> GSM550867 2 0.0938 0.9306 0.012 0.988
#> GSM550885 2 0.0938 0.9306 0.012 0.988
#> GSM550886 1 0.0376 0.7889 0.996 0.004
#> GSM550887 2 0.0000 0.9282 0.000 1.000
#> GSM550889 2 0.0938 0.9306 0.012 0.988
#> GSM550894 2 0.9087 0.3793 0.324 0.676
#> GSM550897 2 0.0938 0.9306 0.012 0.988
#> GSM550903 2 0.0000 0.9282 0.000 1.000
#> GSM550905 1 0.5946 0.7384 0.856 0.144
#> GSM550906 2 0.0000 0.9282 0.000 1.000
#> GSM550907 1 0.0000 0.7890 1.000 0.000
#> GSM550909 1 0.9635 0.5360 0.612 0.388
#> GSM550911 1 0.0000 0.7890 1.000 0.000
#> GSM550913 2 0.0000 0.9282 0.000 1.000
#> GSM550915 2 0.0938 0.9306 0.012 0.988
#> GSM550917 2 0.0000 0.9282 0.000 1.000
#> GSM550919 2 0.0938 0.9306 0.012 0.988
#> GSM550921 1 0.0000 0.7890 1.000 0.000
#> GSM550924 1 0.9833 0.4833 0.576 0.424
#> GSM550926 2 0.0000 0.9282 0.000 1.000
#> GSM550927 2 0.0000 0.9282 0.000 1.000
#> GSM550787 1 0.9815 0.4900 0.580 0.420
#> GSM550793 1 0.0938 0.7881 0.988 0.012
#> GSM550794 2 0.7139 0.7002 0.196 0.804
#> GSM550795 2 0.0938 0.9306 0.012 0.988
#> GSM550798 1 0.9775 0.5006 0.588 0.412
#> GSM550803 2 0.8144 0.5896 0.252 0.748
#> GSM550805 1 0.9909 0.4359 0.556 0.444
#> GSM550823 2 0.6623 0.7399 0.172 0.828
#> GSM550824 2 0.0938 0.9306 0.012 0.988
#> GSM550825 1 0.0000 0.7890 1.000 0.000
#> GSM550827 2 0.0938 0.9306 0.012 0.988
#> GSM550828 2 0.0938 0.9306 0.012 0.988
#> GSM550829 1 0.9775 0.5006 0.588 0.412
#> GSM550830 2 0.0938 0.9306 0.012 0.988
#> GSM550834 2 0.0938 0.9306 0.012 0.988
#> GSM550839 1 0.0938 0.7881 0.988 0.012
#> GSM550840 2 0.0938 0.9306 0.012 0.988
#> GSM550843 1 0.0000 0.7890 1.000 0.000
#> GSM550844 2 0.9129 0.3946 0.328 0.672
#> GSM550845 2 0.0000 0.9282 0.000 1.000
#> GSM550848 2 0.0938 0.9306 0.012 0.988
#> GSM550854 2 0.0938 0.9306 0.012 0.988
#> GSM550857 1 0.0000 0.7890 1.000 0.000
#> GSM550858 2 0.0938 0.9306 0.012 0.988
#> GSM550859 2 0.0938 0.9306 0.012 0.988
#> GSM550862 2 0.0938 0.9306 0.012 0.988
#> GSM550865 2 0.0938 0.9306 0.012 0.988
#> GSM550868 2 0.0938 0.9306 0.012 0.988
#> GSM550869 1 0.9635 0.5360 0.612 0.388
#> GSM550870 2 0.0000 0.9282 0.000 1.000
#> GSM550871 1 0.1633 0.7849 0.976 0.024
#> GSM550872 2 0.0938 0.9306 0.012 0.988
#> GSM550873 2 0.9996 -0.2740 0.488 0.512
#> GSM550874 2 0.0376 0.9290 0.004 0.996
#> GSM550876 1 0.0000 0.7890 1.000 0.000
#> GSM550877 2 0.0000 0.9282 0.000 1.000
#> GSM550878 1 0.0000 0.7890 1.000 0.000
#> GSM550879 2 0.0938 0.9306 0.012 0.988
#> GSM550882 1 0.0000 0.7890 1.000 0.000
#> GSM550888 1 0.0000 0.7890 1.000 0.000
#> GSM550890 2 0.0938 0.9306 0.012 0.988
#> GSM550891 1 0.0000 0.7890 1.000 0.000
#> GSM550892 2 0.0938 0.9306 0.012 0.988
#> GSM550893 2 0.0938 0.9306 0.012 0.988
#> GSM550895 2 0.0938 0.9306 0.012 0.988
#> GSM550896 2 0.0938 0.9306 0.012 0.988
#> GSM550898 2 0.0938 0.9306 0.012 0.988
#> GSM550899 2 0.0000 0.9282 0.000 1.000
#> GSM550900 2 0.0938 0.9306 0.012 0.988
#> GSM550901 2 0.0938 0.9306 0.012 0.988
#> GSM550902 1 0.9833 0.4833 0.576 0.424
#> GSM550904 1 0.9833 0.4833 0.576 0.424
#> GSM550908 1 0.0000 0.7890 1.000 0.000
#> GSM550912 2 0.0000 0.9282 0.000 1.000
#> GSM550914 2 0.0938 0.9306 0.012 0.988
#> GSM550918 2 0.0000 0.9282 0.000 1.000
#> GSM550922 1 0.0000 0.7890 1.000 0.000
#> GSM550923 1 0.9833 0.4833 0.576 0.424
#> GSM550925 2 0.0938 0.9306 0.012 0.988
#> GSM550802 2 0.5946 0.7690 0.144 0.856
#> GSM550812 2 0.9775 0.0891 0.412 0.588
#> GSM550831 2 0.1184 0.9280 0.016 0.984
#> GSM550847 2 0.0938 0.9306 0.012 0.988
#> GSM550860 1 0.0938 0.7881 0.988 0.012
#> GSM550875 1 0.9866 0.4657 0.568 0.432
#> GSM550880 2 0.0938 0.9306 0.012 0.988
#> GSM550881 1 0.0000 0.7890 1.000 0.000
#> GSM550883 1 0.0000 0.7890 1.000 0.000
#> GSM550884 1 1.0000 0.2756 0.504 0.496
#> GSM550910 1 0.0376 0.7889 0.996 0.004
#> GSM550916 2 0.3733 0.8736 0.072 0.928
#> GSM550920 1 0.0000 0.7890 1.000 0.000
cbind(get_classes(res, k = 3), get_membership(res, k = 3))
#> class entropy silhouette p1 p2 p3
#> GSM550785 1 0.3879 0.7228 0.848 0.152 0.000
#> GSM550786 2 0.6208 0.6710 0.076 0.772 0.152
#> GSM550788 2 0.2356 0.7828 0.072 0.928 0.000
#> GSM550789 2 0.1643 0.7908 0.044 0.956 0.000
#> GSM550790 1 0.3879 0.7228 0.848 0.152 0.000
#> GSM550791 2 0.7145 -0.1623 0.440 0.536 0.024
#> GSM550792 2 0.4288 0.7547 0.068 0.872 0.060
#> GSM550796 2 0.0892 0.7942 0.020 0.980 0.000
#> GSM550797 2 0.1860 0.7893 0.052 0.948 0.000
#> GSM550799 3 0.0237 0.8526 0.000 0.004 0.996
#> GSM550800 2 0.1964 0.7856 0.056 0.944 0.000
#> GSM550801 2 0.1289 0.7919 0.032 0.968 0.000
#> GSM550804 2 0.1753 0.7898 0.048 0.952 0.000
#> GSM550806 3 0.1643 0.8253 0.044 0.000 0.956
#> GSM550807 2 0.1643 0.7889 0.044 0.956 0.000
#> GSM550808 2 0.5174 0.7303 0.076 0.832 0.092
#> GSM550809 1 0.8391 0.2943 0.484 0.432 0.084
#> GSM550810 2 0.3623 0.7700 0.032 0.896 0.072
#> GSM550811 2 0.8337 -0.1907 0.444 0.476 0.080
#> GSM550813 2 0.1163 0.7906 0.028 0.972 0.000
#> GSM550814 2 0.3764 0.7723 0.040 0.892 0.068
#> GSM550815 2 0.0892 0.7938 0.020 0.980 0.000
#> GSM550816 2 0.4842 0.5420 0.224 0.776 0.000
#> GSM550817 3 0.2187 0.8425 0.024 0.028 0.948
#> GSM550818 3 0.3042 0.8285 0.040 0.040 0.920
#> GSM550819 2 0.4379 0.7657 0.060 0.868 0.072
#> GSM550820 1 0.8054 0.5229 0.580 0.340 0.080
#> GSM550821 2 0.5174 0.7303 0.076 0.832 0.092
#> GSM550822 2 0.1620 0.7944 0.024 0.964 0.012
#> GSM550826 2 0.8464 -0.2107 0.448 0.464 0.088
#> GSM550832 2 0.4288 0.7547 0.068 0.872 0.060
#> GSM550833 2 0.0592 0.7948 0.012 0.988 0.000
#> GSM550835 3 0.7610 0.2358 0.044 0.420 0.536
#> GSM550836 3 0.0424 0.8520 0.008 0.000 0.992
#> GSM550837 2 0.5036 0.7274 0.048 0.832 0.120
#> GSM550838 1 0.8454 0.2829 0.480 0.432 0.088
#> GSM550841 3 0.3155 0.8271 0.044 0.040 0.916
#> GSM550842 2 0.7610 0.2214 0.048 0.564 0.388
#> GSM550846 2 0.8288 -0.0369 0.408 0.512 0.080
#> GSM550849 2 0.5010 0.7411 0.084 0.840 0.076
#> GSM550850 1 0.6647 0.5491 0.592 0.396 0.012
#> GSM550851 2 0.5253 0.7275 0.076 0.828 0.096
#> GSM550852 2 0.3791 0.7652 0.048 0.892 0.060
#> GSM550853 2 0.1964 0.7868 0.056 0.944 0.000
#> GSM550855 2 0.1964 0.7868 0.056 0.944 0.000
#> GSM550856 2 0.2448 0.7829 0.076 0.924 0.000
#> GSM550861 2 0.0424 0.7934 0.008 0.992 0.000
#> GSM550863 2 0.2878 0.7654 0.096 0.904 0.000
#> GSM550864 2 0.2261 0.7898 0.068 0.932 0.000
#> GSM550866 2 0.2356 0.7834 0.072 0.928 0.000
#> GSM550867 1 0.3816 0.7202 0.852 0.148 0.000
#> GSM550885 1 0.4002 0.7213 0.840 0.160 0.000
#> GSM550886 3 0.7851 0.2498 0.056 0.412 0.532
#> GSM550887 2 0.1411 0.7958 0.036 0.964 0.000
#> GSM550889 2 0.2356 0.7828 0.072 0.928 0.000
#> GSM550894 2 0.3572 0.7687 0.040 0.900 0.060
#> GSM550897 2 0.2537 0.7839 0.080 0.920 0.000
#> GSM550903 2 0.1289 0.7922 0.032 0.968 0.000
#> GSM550905 2 0.5174 0.7303 0.076 0.832 0.092
#> GSM550906 2 0.1289 0.7915 0.032 0.968 0.000
#> GSM550907 3 0.1774 0.8460 0.016 0.024 0.960
#> GSM550909 2 0.5174 0.7303 0.076 0.832 0.092
#> GSM550911 3 0.0848 0.8517 0.008 0.008 0.984
#> GSM550913 2 0.1989 0.7892 0.048 0.948 0.004
#> GSM550915 2 0.6225 -0.1448 0.432 0.568 0.000
#> GSM550917 2 0.1643 0.7905 0.044 0.956 0.000
#> GSM550919 2 0.6225 -0.1448 0.432 0.568 0.000
#> GSM550921 3 0.0424 0.8520 0.008 0.000 0.992
#> GSM550924 2 0.4914 0.7380 0.068 0.844 0.088
#> GSM550926 2 0.2356 0.7828 0.072 0.928 0.000
#> GSM550927 2 0.1289 0.7914 0.032 0.968 0.000
#> GSM550787 2 0.5815 0.7376 0.096 0.800 0.104
#> GSM550793 3 0.7395 0.2017 0.040 0.380 0.580
#> GSM550794 2 0.4658 0.7696 0.076 0.856 0.068
#> GSM550795 1 0.6280 0.4768 0.540 0.460 0.000
#> GSM550798 1 0.8694 0.5599 0.580 0.268 0.152
#> GSM550803 1 0.4768 0.6012 0.848 0.052 0.100
#> GSM550805 2 0.5603 0.7379 0.060 0.804 0.136
#> GSM550823 2 0.3690 0.7844 0.100 0.884 0.016
#> GSM550824 1 0.3879 0.7228 0.848 0.152 0.000
#> GSM550825 3 0.0592 0.8500 0.012 0.000 0.988
#> GSM550827 2 0.4002 0.6717 0.160 0.840 0.000
#> GSM550828 1 0.4062 0.7195 0.836 0.164 0.000
#> GSM550829 1 0.9465 0.4202 0.472 0.332 0.196
#> GSM550830 2 0.2356 0.7828 0.072 0.928 0.000
#> GSM550834 2 0.6260 -0.2405 0.448 0.552 0.000
#> GSM550839 2 0.6984 0.5348 0.040 0.656 0.304
#> GSM550840 2 0.2537 0.7839 0.080 0.920 0.000
#> GSM550843 3 0.2031 0.8438 0.016 0.032 0.952
#> GSM550844 2 0.8190 -0.1153 0.432 0.496 0.072
#> GSM550845 2 0.1964 0.7883 0.056 0.944 0.000
#> GSM550848 2 0.6432 -0.1461 0.428 0.568 0.004
#> GSM550854 1 0.3551 0.7135 0.868 0.132 0.000
#> GSM550857 3 0.1289 0.8477 0.032 0.000 0.968
#> GSM550858 1 0.3619 0.7159 0.864 0.136 0.000
#> GSM550859 1 0.3816 0.7202 0.852 0.148 0.000
#> GSM550862 1 0.5138 0.6948 0.748 0.252 0.000
#> GSM550865 2 0.2537 0.7820 0.080 0.920 0.000
#> GSM550868 2 0.2878 0.7736 0.096 0.904 0.000
#> GSM550869 2 0.5892 0.7342 0.100 0.796 0.104
#> GSM550870 2 0.1163 0.7916 0.028 0.972 0.000
#> GSM550871 2 0.5875 0.7192 0.056 0.784 0.160
#> GSM550872 2 0.3551 0.7454 0.132 0.868 0.000
#> GSM550873 2 0.4477 0.7503 0.068 0.864 0.068
#> GSM550874 2 0.2356 0.7828 0.072 0.928 0.000
#> GSM550876 3 0.2200 0.8376 0.056 0.004 0.940
#> GSM550877 2 0.2066 0.7851 0.060 0.940 0.000
#> GSM550878 3 0.0237 0.8521 0.004 0.000 0.996
#> GSM550879 1 0.6180 0.5306 0.584 0.416 0.000
#> GSM550882 3 0.1643 0.8253 0.044 0.000 0.956
#> GSM550888 3 0.0424 0.8520 0.008 0.000 0.992
#> GSM550890 2 0.6225 -0.1467 0.432 0.568 0.000
#> GSM550891 3 0.0424 0.8520 0.008 0.000 0.992
#> GSM550892 2 0.5785 0.4014 0.332 0.668 0.000
#> GSM550893 2 0.3038 0.7830 0.104 0.896 0.000
#> GSM550895 2 0.2165 0.7845 0.064 0.936 0.000
#> GSM550896 2 0.2796 0.7862 0.092 0.908 0.000
#> GSM550898 1 0.3551 0.7135 0.868 0.132 0.000
#> GSM550899 2 0.2066 0.7876 0.060 0.940 0.000
#> GSM550900 2 0.2448 0.7835 0.076 0.924 0.000
#> GSM550901 2 0.6267 -0.1991 0.452 0.548 0.000
#> GSM550902 2 0.4887 0.7368 0.060 0.844 0.096
#> GSM550904 1 0.8295 0.4317 0.532 0.384 0.084
#> GSM550908 3 0.0892 0.8510 0.020 0.000 0.980
#> GSM550912 2 0.1031 0.7939 0.024 0.976 0.000
#> GSM550914 2 0.5678 0.2810 0.316 0.684 0.000
#> GSM550918 2 0.1753 0.7889 0.048 0.952 0.000
#> GSM550922 3 0.4565 0.7907 0.076 0.064 0.860
#> GSM550923 1 0.8520 0.5592 0.588 0.280 0.132
#> GSM550925 2 0.2448 0.7835 0.076 0.924 0.000
#> GSM550802 2 0.3148 0.7889 0.036 0.916 0.048
#> GSM550812 2 0.3764 0.7645 0.040 0.892 0.068
#> GSM550831 1 0.6973 0.5359 0.564 0.416 0.020
#> GSM550847 1 0.3551 0.7135 0.868 0.132 0.000
#> GSM550860 3 0.8425 0.1820 0.096 0.364 0.540
#> GSM550875 2 0.5538 0.7400 0.060 0.808 0.132
#> GSM550880 2 0.6244 -0.1585 0.440 0.560 0.000
#> GSM550881 3 0.0424 0.8520 0.008 0.000 0.992
#> GSM550883 3 0.0424 0.8520 0.008 0.000 0.992
#> GSM550884 2 0.4558 0.7452 0.044 0.856 0.100
#> GSM550910 3 0.4290 0.8007 0.064 0.064 0.872
#> GSM550916 2 0.4978 0.6190 0.216 0.780 0.004
#> GSM550920 3 0.7248 0.5528 0.068 0.256 0.676
cbind(get_classes(res, k = 4), get_membership(res, k = 4))
#> class entropy silhouette p1 p2 p3 p4
#> GSM550785 1 0.7453 0.5121 0.484 0.192 0.000 0.324
#> GSM550786 3 0.6206 0.3021 0.280 0.088 0.632 0.000
#> GSM550788 2 0.0188 0.6152 0.004 0.996 0.000 0.000
#> GSM550789 2 0.6806 0.6052 0.336 0.560 0.004 0.100
#> GSM550790 1 0.7453 0.5121 0.484 0.192 0.000 0.324
#> GSM550791 1 0.7110 0.5036 0.608 0.176 0.012 0.204
#> GSM550792 1 0.6270 -0.3895 0.536 0.404 0.060 0.000
#> GSM550796 2 0.7290 0.5867 0.348 0.536 0.024 0.092
#> GSM550797 2 0.6770 0.6057 0.340 0.560 0.004 0.096
#> GSM550799 3 0.3636 0.2125 0.008 0.000 0.820 0.172
#> GSM550800 2 0.0188 0.6153 0.004 0.996 0.000 0.000
#> GSM550801 2 0.6770 0.6057 0.340 0.560 0.004 0.096
#> GSM550804 2 0.5689 0.5593 0.412 0.564 0.004 0.020
#> GSM550806 3 0.4661 0.1153 0.008 0.004 0.724 0.264
#> GSM550807 2 0.6666 0.6068 0.340 0.568 0.004 0.088
#> GSM550808 1 0.7591 -0.3400 0.432 0.368 0.200 0.000
#> GSM550809 1 0.4361 0.4737 0.772 0.000 0.020 0.208
#> GSM550810 1 0.7909 -0.3743 0.428 0.388 0.168 0.016
#> GSM550811 1 0.5912 0.4109 0.732 0.100 0.020 0.148
#> GSM550813 2 0.6545 0.6206 0.300 0.604 0.004 0.092
#> GSM550814 2 0.7684 0.3765 0.408 0.420 0.164 0.008
#> GSM550815 2 0.6733 0.6000 0.344 0.560 0.004 0.092
#> GSM550816 2 0.5655 0.5320 0.432 0.548 0.012 0.008
#> GSM550817 3 0.0592 0.4639 0.016 0.000 0.984 0.000
#> GSM550818 3 0.0469 0.4638 0.012 0.000 0.988 0.000
#> GSM550819 1 0.7476 -0.4096 0.432 0.424 0.136 0.008
#> GSM550820 1 0.4507 0.4705 0.756 0.000 0.020 0.224
#> GSM550821 1 0.7591 -0.3390 0.432 0.368 0.200 0.000
#> GSM550822 2 0.8932 0.4310 0.344 0.412 0.152 0.092
#> GSM550826 1 0.4630 0.4667 0.768 0.000 0.036 0.196
#> GSM550832 1 0.7704 -0.3761 0.432 0.392 0.168 0.008
#> GSM550833 2 0.7393 0.5922 0.328 0.548 0.032 0.092
#> GSM550835 3 0.4163 0.4814 0.076 0.096 0.828 0.000
#> GSM550836 4 0.4941 0.9924 0.000 0.000 0.436 0.564
#> GSM550837 1 0.7650 -0.3337 0.424 0.364 0.212 0.000
#> GSM550838 1 0.4638 0.4601 0.776 0.000 0.044 0.180
#> GSM550841 3 0.0921 0.4738 0.028 0.000 0.972 0.000
#> GSM550842 3 0.5527 0.3312 0.168 0.104 0.728 0.000
#> GSM550846 1 0.4173 0.1099 0.804 0.172 0.020 0.004
#> GSM550849 1 0.5414 -0.3467 0.604 0.376 0.020 0.000
#> GSM550850 1 0.7617 0.5191 0.516 0.196 0.008 0.280
#> GSM550851 1 0.7660 -0.3278 0.428 0.356 0.216 0.000
#> GSM550852 1 0.7655 -0.3905 0.428 0.404 0.160 0.008
#> GSM550853 2 0.4012 0.6412 0.204 0.788 0.004 0.004
#> GSM550855 2 0.4053 0.6405 0.228 0.768 0.004 0.000
#> GSM550856 2 0.2311 0.6335 0.076 0.916 0.004 0.004
#> GSM550861 2 0.6704 0.6034 0.336 0.568 0.004 0.092
#> GSM550863 2 0.6650 0.4711 0.272 0.612 0.004 0.112
#> GSM550864 2 0.6654 0.6026 0.352 0.560 0.004 0.084
#> GSM550866 2 0.1082 0.6203 0.020 0.972 0.004 0.004
#> GSM550867 1 0.7453 0.5121 0.484 0.192 0.000 0.324
#> GSM550885 1 0.7386 0.5144 0.496 0.184 0.000 0.320
#> GSM550886 3 0.4292 0.4734 0.080 0.100 0.820 0.000
#> GSM550887 2 0.8368 0.4272 0.380 0.424 0.148 0.048
#> GSM550889 2 0.0188 0.6152 0.004 0.996 0.000 0.000
#> GSM550894 1 0.7815 -0.3727 0.424 0.396 0.168 0.012
#> GSM550897 2 0.0707 0.6112 0.020 0.980 0.000 0.000
#> GSM550903 2 0.6719 0.6024 0.340 0.564 0.004 0.092
#> GSM550905 1 0.7613 -0.3376 0.428 0.368 0.204 0.000
#> GSM550906 2 0.6753 0.6212 0.292 0.608 0.016 0.084
#> GSM550907 3 0.4454 -0.3202 0.000 0.000 0.692 0.308
#> GSM550909 1 0.7485 -0.3530 0.440 0.380 0.180 0.000
#> GSM550911 3 0.4907 -0.7031 0.000 0.000 0.580 0.420
#> GSM550913 2 0.6770 0.6057 0.340 0.560 0.004 0.096
#> GSM550915 1 0.7373 0.4078 0.516 0.280 0.000 0.204
#> GSM550917 2 0.6756 0.6070 0.336 0.564 0.004 0.096
#> GSM550919 1 0.7133 0.3783 0.548 0.280 0.000 0.172
#> GSM550921 4 0.4941 0.9924 0.000 0.000 0.436 0.564
#> GSM550924 1 0.5957 -0.3330 0.588 0.364 0.048 0.000
#> GSM550926 2 0.0336 0.6177 0.008 0.992 0.000 0.000
#> GSM550927 2 0.6674 0.6155 0.316 0.584 0.004 0.096
#> GSM550787 2 0.6057 0.4131 0.288 0.648 0.056 0.008
#> GSM550793 3 0.6987 0.3975 0.124 0.096 0.684 0.096
#> GSM550794 2 0.5989 0.4800 0.472 0.496 0.024 0.008
#> GSM550795 1 0.7358 0.5155 0.564 0.196 0.008 0.232
#> GSM550798 1 0.6858 0.2954 0.588 0.004 0.124 0.284
#> GSM550803 1 0.7430 0.5064 0.540 0.120 0.020 0.320
#> GSM550805 2 0.5821 0.4295 0.432 0.536 0.032 0.000
#> GSM550823 2 0.1262 0.6137 0.016 0.968 0.008 0.008
#> GSM550824 1 0.7441 0.5131 0.488 0.192 0.000 0.320
#> GSM550825 3 0.4697 0.0139 0.008 0.000 0.696 0.296
#> GSM550827 2 0.7011 0.3715 0.300 0.552 0.000 0.148
#> GSM550828 1 0.7315 0.5161 0.512 0.180 0.000 0.308
#> GSM550829 1 0.6910 0.2464 0.584 0.000 0.164 0.252
#> GSM550830 2 0.0188 0.6152 0.004 0.996 0.000 0.000
#> GSM550834 1 0.6917 0.5032 0.592 0.200 0.000 0.208
#> GSM550839 3 0.6389 0.4154 0.172 0.116 0.692 0.020
#> GSM550840 2 0.1302 0.6006 0.044 0.956 0.000 0.000
#> GSM550843 3 0.1271 0.4609 0.012 0.012 0.968 0.008
#> GSM550844 1 0.6437 0.4993 0.672 0.088 0.020 0.220
#> GSM550845 2 0.3072 0.6130 0.124 0.868 0.004 0.004
#> GSM550848 1 0.7085 0.3249 0.544 0.300 0.000 0.156
#> GSM550854 1 0.7479 0.5104 0.480 0.196 0.000 0.324
#> GSM550857 4 0.4941 0.9924 0.000 0.000 0.436 0.564
#> GSM550858 1 0.7553 0.5041 0.476 0.216 0.000 0.308
#> GSM550859 1 0.7453 0.5121 0.484 0.192 0.000 0.324
#> GSM550862 1 0.7627 0.4871 0.472 0.256 0.000 0.272
#> GSM550865 2 0.1398 0.6148 0.040 0.956 0.000 0.004
#> GSM550868 2 0.2197 0.6071 0.080 0.916 0.000 0.004
#> GSM550869 2 0.5708 0.4281 0.288 0.668 0.032 0.012
#> GSM550870 2 0.6514 0.6241 0.284 0.616 0.004 0.096
#> GSM550871 3 0.7486 0.3258 0.248 0.172 0.564 0.016
#> GSM550872 2 0.1209 0.6079 0.032 0.964 0.000 0.004
#> GSM550873 1 0.7701 -0.3706 0.436 0.388 0.168 0.008
#> GSM550874 2 0.0336 0.6177 0.008 0.992 0.000 0.000
#> GSM550876 3 0.6406 0.3538 0.024 0.116 0.696 0.164
#> GSM550877 2 0.0469 0.6218 0.012 0.988 0.000 0.000
#> GSM550878 3 0.4134 0.0869 0.000 0.000 0.740 0.260
#> GSM550879 1 0.6958 0.5099 0.584 0.184 0.000 0.232
#> GSM550882 3 0.4539 0.0925 0.008 0.000 0.720 0.272
#> GSM550888 4 0.4941 0.9924 0.000 0.000 0.436 0.564
#> GSM550890 1 0.6916 0.3589 0.572 0.280 0.000 0.148
#> GSM550891 4 0.4967 0.9612 0.000 0.000 0.452 0.548
#> GSM550892 2 0.5863 0.3273 0.180 0.700 0.000 0.120
#> GSM550893 2 0.0188 0.6149 0.000 0.996 0.000 0.004
#> GSM550895 2 0.0188 0.6152 0.004 0.996 0.000 0.000
#> GSM550896 2 0.0992 0.6167 0.012 0.976 0.008 0.004
#> GSM550898 1 0.7479 0.5104 0.480 0.196 0.000 0.324
#> GSM550899 2 0.6545 0.5923 0.372 0.552 0.004 0.072
#> GSM550900 2 0.0336 0.6125 0.008 0.992 0.000 0.000
#> GSM550901 1 0.7036 0.4829 0.576 0.212 0.000 0.212
#> GSM550902 1 0.7323 0.3835 0.628 0.148 0.040 0.184
#> GSM550904 1 0.4472 0.4716 0.760 0.000 0.020 0.220
#> GSM550908 4 0.4941 0.9924 0.000 0.000 0.436 0.564
#> GSM550912 2 0.6937 0.4846 0.424 0.484 0.084 0.008
#> GSM550914 2 0.5682 0.4728 0.456 0.520 0.000 0.024
#> GSM550918 2 0.6770 0.6057 0.340 0.560 0.004 0.096
#> GSM550922 3 0.1792 0.4843 0.068 0.000 0.932 0.000
#> GSM550923 1 0.5769 0.4287 0.668 0.012 0.036 0.284
#> GSM550925 2 0.0336 0.6170 0.008 0.992 0.000 0.000
#> GSM550802 2 0.7641 0.4314 0.364 0.464 0.164 0.008
#> GSM550812 1 0.6474 -0.3677 0.536 0.388 0.076 0.000
#> GSM550831 1 0.7666 0.5206 0.524 0.192 0.012 0.272
#> GSM550847 1 0.7518 0.5071 0.476 0.204 0.000 0.320
#> GSM550860 3 0.7231 0.3762 0.100 0.140 0.664 0.096
#> GSM550875 2 0.5359 0.4334 0.288 0.676 0.036 0.000
#> GSM550880 1 0.7203 0.3717 0.524 0.312 0.000 0.164
#> GSM550881 3 0.4567 0.0846 0.008 0.000 0.716 0.276
#> GSM550883 3 0.4697 0.0139 0.008 0.000 0.696 0.296
#> GSM550884 1 0.5738 -0.3905 0.540 0.432 0.028 0.000
#> GSM550910 3 0.1557 0.4872 0.056 0.000 0.944 0.000
#> GSM550916 2 0.4842 0.3981 0.192 0.760 0.000 0.048
#> GSM550920 3 0.3308 0.4953 0.036 0.092 0.872 0.000
cbind(get_classes(res, k = 5), get_membership(res, k = 5))
#> class entropy silhouette p1 p2 p3 p4 p5
#> GSM550785 4 0.2329 0.6580 0.124 0.000 0.000 0.876 0.000
#> GSM550786 5 0.4305 0.5956 0.000 0.200 0.000 0.052 0.748
#> GSM550788 2 0.5244 0.6871 0.192 0.704 0.088 0.016 0.000
#> GSM550789 2 0.0162 0.8173 0.000 0.996 0.004 0.000 0.000
#> GSM550790 1 0.4045 0.7372 0.644 0.000 0.000 0.356 0.000
#> GSM550791 4 0.0671 0.7169 0.000 0.016 0.004 0.980 0.000
#> GSM550792 4 0.3774 0.6743 0.000 0.296 0.000 0.704 0.000
#> GSM550796 2 0.0162 0.8173 0.000 0.996 0.000 0.004 0.000
#> GSM550797 2 0.0162 0.8173 0.000 0.996 0.004 0.000 0.000
#> GSM550799 5 0.3885 0.5986 0.040 0.000 0.176 0.000 0.784
#> GSM550800 2 0.5211 0.6898 0.188 0.708 0.088 0.016 0.000
#> GSM550801 2 0.0162 0.8173 0.000 0.996 0.004 0.000 0.000
#> GSM550804 2 0.1205 0.8064 0.000 0.956 0.004 0.040 0.000
#> GSM550806 5 0.3907 0.5703 0.016 0.000 0.204 0.008 0.772
#> GSM550807 2 0.0000 0.8177 0.000 1.000 0.000 0.000 0.000
#> GSM550808 2 0.2519 0.7601 0.000 0.884 0.000 0.016 0.100
#> GSM550809 4 0.0510 0.7178 0.000 0.016 0.000 0.984 0.000
#> GSM550810 2 0.0290 0.8156 0.000 0.992 0.000 0.008 0.000
#> GSM550811 4 0.1270 0.7261 0.000 0.052 0.000 0.948 0.000
#> GSM550813 2 0.2929 0.7531 0.180 0.820 0.000 0.000 0.000
#> GSM550814 2 0.3160 0.7481 0.188 0.808 0.000 0.004 0.000
#> GSM550815 2 0.0162 0.8173 0.000 0.996 0.000 0.004 0.000
#> GSM550816 2 0.2286 0.7671 0.000 0.888 0.004 0.108 0.000
#> GSM550817 5 0.0000 0.7059 0.000 0.000 0.000 0.000 1.000
#> GSM550818 5 0.0000 0.7059 0.000 0.000 0.000 0.000 1.000
#> GSM550819 2 0.3895 0.4304 0.000 0.680 0.000 0.320 0.000
#> GSM550820 4 0.0510 0.7178 0.000 0.016 0.000 0.984 0.000
#> GSM550821 2 0.3942 0.5913 0.000 0.748 0.000 0.020 0.232
#> GSM550822 2 0.0162 0.8173 0.000 0.996 0.000 0.004 0.000
#> GSM550826 4 0.0510 0.7178 0.000 0.016 0.000 0.984 0.000
#> GSM550832 2 0.0162 0.8172 0.000 0.996 0.000 0.004 0.000
#> GSM550833 2 0.0000 0.8177 0.000 1.000 0.000 0.000 0.000
#> GSM550835 5 0.5639 0.4830 0.076 0.320 0.000 0.008 0.596
#> GSM550836 3 0.1965 0.9076 0.000 0.000 0.904 0.000 0.096
#> GSM550837 2 0.3353 0.6534 0.000 0.796 0.000 0.008 0.196
#> GSM550838 4 0.0510 0.7178 0.000 0.016 0.000 0.984 0.000
#> GSM550841 5 0.0000 0.7059 0.000 0.000 0.000 0.000 1.000
#> GSM550842 2 0.3980 0.5169 0.000 0.708 0.000 0.008 0.284
#> GSM550846 4 0.3452 0.6784 0.000 0.244 0.000 0.756 0.000
#> GSM550849 4 0.3586 0.6867 0.000 0.264 0.000 0.736 0.000
#> GSM550850 4 0.2605 0.6286 0.148 0.000 0.000 0.852 0.000
#> GSM550851 2 0.3861 0.5510 0.000 0.728 0.000 0.008 0.264
#> GSM550852 2 0.1671 0.7819 0.000 0.924 0.000 0.076 0.000
#> GSM550853 2 0.3907 0.7408 0.180 0.788 0.016 0.016 0.000
#> GSM550855 2 0.3849 0.7505 0.164 0.800 0.020 0.016 0.000
#> GSM550856 2 0.4925 0.7090 0.180 0.732 0.072 0.016 0.000
#> GSM550861 2 0.0162 0.8173 0.000 0.996 0.004 0.000 0.000
#> GSM550863 4 0.4559 0.7559 0.152 0.100 0.000 0.748 0.000
#> GSM550864 2 0.0566 0.8147 0.000 0.984 0.004 0.012 0.000
#> GSM550866 2 0.5211 0.6898 0.188 0.708 0.088 0.016 0.000
#> GSM550867 1 0.3143 0.9349 0.796 0.000 0.000 0.204 0.000
#> GSM550885 1 0.3274 0.9276 0.780 0.000 0.000 0.220 0.000
#> GSM550886 5 0.6140 0.4928 0.192 0.204 0.000 0.008 0.596
#> GSM550887 2 0.0162 0.8173 0.000 0.996 0.000 0.004 0.000
#> GSM550889 4 0.5335 0.7360 0.192 0.020 0.088 0.700 0.000
#> GSM550894 2 0.2077 0.7991 0.084 0.908 0.000 0.008 0.000
#> GSM550897 4 0.5389 0.7366 0.188 0.024 0.088 0.700 0.000
#> GSM550903 2 0.0162 0.8173 0.000 0.996 0.004 0.000 0.000
#> GSM550905 2 0.3789 0.6299 0.000 0.768 0.000 0.020 0.212
#> GSM550906 2 0.3003 0.7478 0.188 0.812 0.000 0.000 0.000
#> GSM550907 5 0.0794 0.6978 0.000 0.000 0.028 0.000 0.972
#> GSM550909 2 0.4467 0.6354 0.000 0.752 0.000 0.164 0.084
#> GSM550911 5 0.0880 0.6955 0.000 0.000 0.032 0.000 0.968
#> GSM550913 2 0.0162 0.8173 0.000 0.996 0.004 0.000 0.000
#> GSM550915 4 0.0898 0.7182 0.000 0.020 0.008 0.972 0.000
#> GSM550917 2 0.0162 0.8173 0.000 0.996 0.004 0.000 0.000
#> GSM550919 4 0.3421 0.7038 0.000 0.204 0.008 0.788 0.000
#> GSM550921 3 0.1965 0.9076 0.000 0.000 0.904 0.000 0.096
#> GSM550924 4 0.5316 0.6288 0.000 0.284 0.000 0.632 0.084
#> GSM550926 2 0.5211 0.6898 0.188 0.708 0.088 0.016 0.000
#> GSM550927 2 0.0000 0.8177 0.000 1.000 0.000 0.000 0.000
#> GSM550787 4 0.6866 0.6640 0.192 0.012 0.072 0.612 0.112
#> GSM550793 4 0.6679 0.4865 0.204 0.000 0.016 0.528 0.252
#> GSM550794 4 0.4063 0.6825 0.000 0.280 0.012 0.708 0.000
#> GSM550795 4 0.1469 0.7095 0.036 0.016 0.000 0.948 0.000
#> GSM550798 1 0.4264 0.8905 0.744 0.000 0.000 0.212 0.044
#> GSM550803 1 0.3177 0.9338 0.792 0.000 0.000 0.208 0.000
#> GSM550805 4 0.5429 0.7386 0.188 0.016 0.076 0.708 0.012
#> GSM550823 4 0.5335 0.7360 0.192 0.020 0.088 0.700 0.000
#> GSM550824 1 0.3242 0.9304 0.784 0.000 0.000 0.216 0.000
#> GSM550825 3 0.2464 0.9002 0.012 0.000 0.892 0.004 0.092
#> GSM550827 4 0.3783 0.7111 0.012 0.216 0.004 0.768 0.000
#> GSM550828 4 0.2233 0.6902 0.080 0.016 0.000 0.904 0.000
#> GSM550829 1 0.7543 0.6163 0.492 0.000 0.180 0.240 0.088
#> GSM550830 4 0.5389 0.7366 0.188 0.024 0.088 0.700 0.000
#> GSM550834 4 0.0960 0.7148 0.008 0.016 0.004 0.972 0.000
#> GSM550839 5 0.6598 0.4806 0.204 0.192 0.016 0.008 0.580
#> GSM550840 4 0.5389 0.7366 0.188 0.024 0.088 0.700 0.000
#> GSM550843 5 0.3317 0.6265 0.000 0.188 0.004 0.004 0.804
#> GSM550844 4 0.2213 0.6968 0.072 0.008 0.004 0.912 0.004
#> GSM550845 2 0.3586 0.7392 0.188 0.792 0.020 0.000 0.000
#> GSM550848 4 0.3421 0.7038 0.000 0.204 0.008 0.788 0.000
#> GSM550854 1 0.3143 0.9349 0.796 0.000 0.000 0.204 0.000
#> GSM550857 3 0.1965 0.9076 0.000 0.000 0.904 0.000 0.096
#> GSM550858 4 0.3983 0.1752 0.340 0.000 0.000 0.660 0.000
#> GSM550859 1 0.3143 0.9349 0.796 0.000 0.000 0.204 0.000
#> GSM550862 4 0.4430 0.6876 0.360 0.012 0.000 0.628 0.000
#> GSM550865 4 0.5389 0.7366 0.188 0.024 0.088 0.700 0.000
#> GSM550868 4 0.5369 0.7374 0.192 0.024 0.084 0.700 0.000
#> GSM550869 4 0.5313 0.7379 0.192 0.012 0.080 0.708 0.008
#> GSM550870 2 0.3086 0.7538 0.180 0.816 0.004 0.000 0.000
#> GSM550871 4 0.7680 0.1180 0.204 0.032 0.016 0.384 0.364
#> GSM550872 4 0.5389 0.7366 0.188 0.024 0.088 0.700 0.000
#> GSM550873 2 0.1121 0.8042 0.000 0.956 0.000 0.044 0.000
#> GSM550874 2 0.5211 0.6898 0.188 0.708 0.088 0.016 0.000
#> GSM550876 5 0.6024 0.5260 0.204 0.136 0.016 0.004 0.640
#> GSM550877 2 0.4686 0.7135 0.188 0.744 0.052 0.016 0.000
#> GSM550878 5 0.3563 0.5666 0.012 0.000 0.208 0.000 0.780
#> GSM550879 4 0.0833 0.7154 0.004 0.016 0.004 0.976 0.000
#> GSM550882 3 0.4658 0.1205 0.012 0.000 0.504 0.000 0.484
#> GSM550888 3 0.1965 0.9076 0.000 0.000 0.904 0.000 0.096
#> GSM550890 4 0.3421 0.7038 0.000 0.204 0.008 0.788 0.000
#> GSM550891 3 0.2020 0.9060 0.000 0.000 0.900 0.000 0.100
#> GSM550892 4 0.4535 0.7351 0.288 0.024 0.004 0.684 0.000
#> GSM550893 2 0.5244 0.6871 0.192 0.704 0.088 0.016 0.000
#> GSM550895 2 0.7837 0.0399 0.188 0.392 0.088 0.332 0.000
#> GSM550896 2 0.5211 0.6898 0.188 0.708 0.088 0.016 0.000
#> GSM550898 1 0.3143 0.9349 0.796 0.000 0.000 0.204 0.000
#> GSM550899 2 0.0771 0.8127 0.000 0.976 0.004 0.020 0.000
#> GSM550900 4 0.5389 0.7366 0.188 0.024 0.088 0.700 0.000
#> GSM550901 4 0.0798 0.7163 0.000 0.016 0.008 0.976 0.000
#> GSM550902 4 0.2300 0.7093 0.000 0.024 0.000 0.904 0.072
#> GSM550904 4 0.0510 0.7178 0.000 0.016 0.000 0.984 0.000
#> GSM550908 3 0.1965 0.9076 0.000 0.000 0.904 0.000 0.096
#> GSM550912 2 0.0000 0.8177 0.000 1.000 0.000 0.000 0.000
#> GSM550914 4 0.3689 0.6785 0.000 0.256 0.004 0.740 0.000
#> GSM550918 2 0.0162 0.8173 0.000 0.996 0.004 0.000 0.000
#> GSM550922 5 0.0162 0.7064 0.000 0.000 0.000 0.004 0.996
#> GSM550923 1 0.3696 0.9223 0.772 0.000 0.000 0.212 0.016
#> GSM550925 4 0.5389 0.7366 0.188 0.024 0.088 0.700 0.000
#> GSM550802 2 0.3878 0.6007 0.000 0.748 0.016 0.236 0.000
#> GSM550812 4 0.4294 0.3411 0.000 0.468 0.000 0.532 0.000
#> GSM550831 4 0.1571 0.6948 0.060 0.000 0.004 0.936 0.000
#> GSM550847 1 0.3143 0.9349 0.796 0.000 0.000 0.204 0.000
#> GSM550860 4 0.6679 0.4865 0.204 0.000 0.016 0.528 0.252
#> GSM550875 4 0.5312 0.7384 0.188 0.016 0.084 0.708 0.004
#> GSM550880 4 0.3670 0.7175 0.020 0.180 0.004 0.796 0.000
#> GSM550881 3 0.3992 0.6656 0.012 0.000 0.720 0.000 0.268
#> GSM550883 3 0.2361 0.9028 0.012 0.000 0.892 0.000 0.096
#> GSM550884 4 0.4981 0.7380 0.188 0.108 0.000 0.704 0.000
#> GSM550910 5 0.0290 0.7062 0.000 0.000 0.000 0.008 0.992
#> GSM550916 4 0.5514 0.7381 0.204 0.024 0.088 0.684 0.000
#> GSM550920 5 0.3509 0.6225 0.004 0.196 0.000 0.008 0.792
cbind(get_classes(res, k = 6), get_membership(res, k = 6))
#> class entropy silhouette p1 p2 p3 p4 p5 p6
#> GSM550785 1 0.4012 0.7093 0.752 0.000 0.000 0.084 0.000 0.164
#> GSM550786 5 0.4389 0.4392 0.000 0.372 0.000 0.000 0.596 0.032
#> GSM550788 4 0.3446 0.6249 0.000 0.308 0.000 0.692 0.000 0.000
#> GSM550789 2 0.0000 0.8375 0.000 1.000 0.000 0.000 0.000 0.000
#> GSM550790 1 0.1588 0.8195 0.924 0.000 0.000 0.072 0.000 0.004
#> GSM550791 6 0.1908 0.9013 0.000 0.004 0.000 0.096 0.000 0.900
#> GSM550792 2 0.4831 0.3470 0.000 0.548 0.000 0.060 0.000 0.392
#> GSM550796 2 0.0000 0.8375 0.000 1.000 0.000 0.000 0.000 0.000
#> GSM550797 2 0.0000 0.8375 0.000 1.000 0.000 0.000 0.000 0.000
#> GSM550799 5 0.3782 0.2359 0.000 0.000 0.004 0.360 0.636 0.000
#> GSM550800 4 0.3464 0.6164 0.000 0.312 0.000 0.688 0.000 0.000
#> GSM550801 2 0.0000 0.8375 0.000 1.000 0.000 0.000 0.000 0.000
#> GSM550804 2 0.0260 0.8375 0.000 0.992 0.000 0.008 0.000 0.000
#> GSM550806 3 0.5309 0.2768 0.000 0.000 0.488 0.104 0.408 0.000
#> GSM550807 2 0.0000 0.8375 0.000 1.000 0.000 0.000 0.000 0.000
#> GSM550808 2 0.0935 0.8243 0.000 0.964 0.000 0.000 0.032 0.004
#> GSM550809 6 0.0000 0.8936 0.000 0.000 0.000 0.000 0.000 1.000
#> GSM550810 2 0.0000 0.8375 0.000 1.000 0.000 0.000 0.000 0.000
#> GSM550811 6 0.0000 0.8936 0.000 0.000 0.000 0.000 0.000 1.000
#> GSM550813 2 0.2941 0.6239 0.000 0.780 0.000 0.220 0.000 0.000
#> GSM550814 2 0.3198 0.5390 0.000 0.740 0.000 0.260 0.000 0.000
#> GSM550815 2 0.0146 0.8374 0.000 0.996 0.000 0.004 0.000 0.000
#> GSM550816 2 0.2969 0.6582 0.000 0.776 0.000 0.000 0.000 0.224
#> GSM550817 5 0.0146 0.6620 0.000 0.000 0.004 0.000 0.996 0.000
#> GSM550818 5 0.0146 0.6646 0.000 0.000 0.000 0.000 0.996 0.004
#> GSM550819 2 0.3862 0.6994 0.000 0.772 0.000 0.132 0.000 0.096
#> GSM550820 6 0.0000 0.8936 0.000 0.000 0.000 0.000 0.000 1.000
#> GSM550821 2 0.2747 0.7590 0.000 0.860 0.000 0.000 0.044 0.096
#> GSM550822 2 0.0000 0.8375 0.000 1.000 0.000 0.000 0.000 0.000
#> GSM550826 6 0.0000 0.8936 0.000 0.000 0.000 0.000 0.000 1.000
#> GSM550832 2 0.0000 0.8375 0.000 1.000 0.000 0.000 0.000 0.000
#> GSM550833 2 0.0146 0.8374 0.000 0.996 0.000 0.004 0.000 0.000
#> GSM550835 2 0.5157 -0.1287 0.000 0.484 0.000 0.072 0.440 0.004
#> GSM550836 3 0.0000 0.8312 0.000 0.000 1.000 0.000 0.000 0.000
#> GSM550837 2 0.0405 0.8350 0.000 0.988 0.000 0.000 0.008 0.004
#> GSM550838 6 0.0000 0.8936 0.000 0.000 0.000 0.000 0.000 1.000
#> GSM550841 5 0.0146 0.6646 0.000 0.000 0.000 0.000 0.996 0.004
#> GSM550842 2 0.3426 0.5315 0.000 0.720 0.000 0.000 0.276 0.004
#> GSM550846 6 0.0405 0.8908 0.000 0.004 0.000 0.008 0.000 0.988
#> GSM550849 6 0.0622 0.8850 0.000 0.008 0.000 0.012 0.000 0.980
#> GSM550850 1 0.4768 0.2417 0.532 0.000 0.000 0.052 0.000 0.416
#> GSM550851 2 0.2362 0.7318 0.000 0.860 0.000 0.000 0.136 0.004
#> GSM550852 2 0.0508 0.8358 0.000 0.984 0.000 0.012 0.000 0.004
#> GSM550853 2 0.2300 0.7340 0.000 0.856 0.000 0.144 0.000 0.000
#> GSM550855 2 0.1556 0.7942 0.000 0.920 0.000 0.080 0.000 0.000
#> GSM550856 2 0.3126 0.6306 0.000 0.752 0.000 0.248 0.000 0.000
#> GSM550861 2 0.0000 0.8375 0.000 1.000 0.000 0.000 0.000 0.000
#> GSM550863 4 0.5941 -0.0562 0.000 0.376 0.000 0.408 0.000 0.216
#> GSM550864 2 0.0458 0.8361 0.000 0.984 0.000 0.016 0.000 0.000
#> GSM550866 4 0.3390 0.6311 0.000 0.296 0.000 0.704 0.000 0.000
#> GSM550867 1 0.0000 0.8497 1.000 0.000 0.000 0.000 0.000 0.000
#> GSM550885 1 0.0000 0.8497 1.000 0.000 0.000 0.000 0.000 0.000
#> GSM550886 5 0.6068 0.2907 0.000 0.332 0.000 0.228 0.436 0.004
#> GSM550887 2 0.0146 0.8374 0.000 0.996 0.000 0.004 0.000 0.000
#> GSM550889 4 0.0146 0.7500 0.000 0.000 0.000 0.996 0.000 0.004
#> GSM550894 2 0.0632 0.8295 0.000 0.976 0.000 0.024 0.000 0.000
#> GSM550897 4 0.0363 0.7465 0.000 0.000 0.000 0.988 0.000 0.012
#> GSM550903 2 0.0146 0.8376 0.000 0.996 0.000 0.004 0.000 0.000
#> GSM550905 2 0.1265 0.8164 0.000 0.948 0.000 0.000 0.044 0.008
#> GSM550906 2 0.3578 0.3241 0.000 0.660 0.000 0.340 0.000 0.000
#> GSM550907 5 0.0260 0.6591 0.000 0.000 0.008 0.000 0.992 0.000
#> GSM550909 2 0.2814 0.7250 0.000 0.820 0.000 0.000 0.008 0.172
#> GSM550911 5 0.0363 0.6548 0.000 0.000 0.012 0.000 0.988 0.000
#> GSM550913 2 0.0000 0.8375 0.000 1.000 0.000 0.000 0.000 0.000
#> GSM550915 6 0.1908 0.9013 0.000 0.004 0.000 0.096 0.000 0.900
#> GSM550917 2 0.0260 0.8375 0.000 0.992 0.000 0.008 0.000 0.000
#> GSM550919 6 0.2006 0.8994 0.000 0.004 0.000 0.104 0.000 0.892
#> GSM550921 3 0.0000 0.8312 0.000 0.000 1.000 0.000 0.000 0.000
#> GSM550924 2 0.4728 0.3657 0.000 0.556 0.000 0.052 0.000 0.392
#> GSM550926 4 0.3371 0.6336 0.000 0.292 0.000 0.708 0.000 0.000
#> GSM550927 2 0.0146 0.8374 0.000 0.996 0.000 0.004 0.000 0.000
#> GSM550787 4 0.2020 0.7225 0.000 0.000 0.000 0.896 0.008 0.096
#> GSM550793 4 0.6016 0.2955 0.000 0.000 0.252 0.472 0.004 0.272
#> GSM550794 2 0.4859 0.4131 0.000 0.584 0.000 0.344 0.000 0.072
#> GSM550795 6 0.2383 0.8908 0.024 0.000 0.000 0.096 0.000 0.880
#> GSM550798 1 0.0146 0.8480 0.996 0.000 0.000 0.000 0.000 0.004
#> GSM550803 1 0.0000 0.8497 1.000 0.000 0.000 0.000 0.000 0.000
#> GSM550805 4 0.1814 0.7244 0.000 0.000 0.000 0.900 0.000 0.100
#> GSM550823 4 0.0146 0.7500 0.000 0.000 0.000 0.996 0.000 0.004
#> GSM550824 1 0.0000 0.8497 1.000 0.000 0.000 0.000 0.000 0.000
#> GSM550825 3 0.0000 0.8312 0.000 0.000 1.000 0.000 0.000 0.000
#> GSM550827 2 0.5675 -0.0133 0.000 0.444 0.000 0.156 0.000 0.400
#> GSM550828 1 0.5150 0.4435 0.588 0.004 0.000 0.096 0.000 0.312
#> GSM550829 1 0.4085 0.7036 0.748 0.000 0.096 0.000 0.000 0.156
#> GSM550830 4 0.0146 0.7500 0.000 0.000 0.000 0.996 0.000 0.004
#> GSM550834 6 0.1908 0.9013 0.000 0.004 0.000 0.096 0.000 0.900
#> GSM550839 4 0.3890 0.3369 0.000 0.004 0.000 0.596 0.400 0.000
#> GSM550840 4 0.0363 0.7465 0.000 0.000 0.000 0.988 0.000 0.012
#> GSM550843 5 0.3565 0.5113 0.000 0.304 0.000 0.000 0.692 0.004
#> GSM550844 1 0.5388 0.5376 0.584 0.000 0.000 0.188 0.000 0.228
#> GSM550845 4 0.3578 0.5746 0.000 0.340 0.000 0.660 0.000 0.000
#> GSM550848 6 0.2146 0.8933 0.000 0.004 0.000 0.116 0.000 0.880
#> GSM550854 1 0.0000 0.8497 1.000 0.000 0.000 0.000 0.000 0.000
#> GSM550857 3 0.0000 0.8312 0.000 0.000 1.000 0.000 0.000 0.000
#> GSM550858 1 0.2214 0.8022 0.888 0.000 0.000 0.096 0.000 0.016
#> GSM550859 1 0.0000 0.8497 1.000 0.000 0.000 0.000 0.000 0.000
#> GSM550862 1 0.3420 0.6656 0.748 0.000 0.000 0.240 0.000 0.012
#> GSM550865 4 0.0146 0.7500 0.000 0.000 0.000 0.996 0.000 0.004
#> GSM550868 4 0.0146 0.7500 0.000 0.000 0.000 0.996 0.000 0.004
#> GSM550869 4 0.1958 0.7235 0.000 0.000 0.000 0.896 0.004 0.100
#> GSM550870 2 0.2793 0.6546 0.000 0.800 0.000 0.200 0.000 0.000
#> GSM550871 4 0.3690 0.4962 0.000 0.000 0.000 0.684 0.308 0.008
#> GSM550872 4 0.0146 0.7500 0.000 0.000 0.000 0.996 0.000 0.004
#> GSM550873 2 0.2170 0.7793 0.000 0.888 0.000 0.012 0.000 0.100
#> GSM550874 4 0.3464 0.6192 0.000 0.312 0.000 0.688 0.000 0.000
#> GSM550876 4 0.3737 0.3580 0.000 0.000 0.000 0.608 0.392 0.000
#> GSM550877 4 0.3672 0.5331 0.000 0.368 0.000 0.632 0.000 0.000
#> GSM550878 3 0.3765 0.4449 0.000 0.000 0.596 0.000 0.404 0.000
#> GSM550879 6 0.1908 0.9013 0.000 0.004 0.000 0.096 0.000 0.900
#> GSM550882 3 0.4209 0.4654 0.000 0.000 0.596 0.020 0.384 0.000
#> GSM550888 3 0.0000 0.8312 0.000 0.000 1.000 0.000 0.000 0.000
#> GSM550890 6 0.1958 0.9007 0.000 0.004 0.000 0.100 0.000 0.896
#> GSM550891 3 0.1957 0.7810 0.000 0.000 0.888 0.000 0.112 0.000
#> GSM550892 4 0.2709 0.6691 0.132 0.000 0.000 0.848 0.000 0.020
#> GSM550893 4 0.3371 0.6336 0.000 0.292 0.000 0.708 0.000 0.000
#> GSM550895 4 0.0291 0.7504 0.000 0.004 0.000 0.992 0.000 0.004
#> GSM550896 4 0.3409 0.6283 0.000 0.300 0.000 0.700 0.000 0.000
#> GSM550898 1 0.0000 0.8497 1.000 0.000 0.000 0.000 0.000 0.000
#> GSM550899 2 0.0363 0.8370 0.000 0.988 0.000 0.012 0.000 0.000
#> GSM550900 4 0.0146 0.7500 0.000 0.000 0.000 0.996 0.000 0.004
#> GSM550901 6 0.1908 0.9013 0.000 0.004 0.000 0.096 0.000 0.900
#> GSM550902 6 0.0000 0.8936 0.000 0.000 0.000 0.000 0.000 1.000
#> GSM550904 6 0.0000 0.8936 0.000 0.000 0.000 0.000 0.000 1.000
#> GSM550908 3 0.0000 0.8312 0.000 0.000 1.000 0.000 0.000 0.000
#> GSM550912 2 0.0603 0.8346 0.000 0.980 0.000 0.016 0.000 0.004
#> GSM550914 6 0.5100 0.4945 0.000 0.284 0.000 0.116 0.000 0.600
#> GSM550918 2 0.0363 0.8370 0.000 0.988 0.000 0.012 0.000 0.000
#> GSM550922 5 0.0146 0.6646 0.000 0.000 0.000 0.000 0.996 0.004
#> GSM550923 1 0.0146 0.8480 0.996 0.000 0.000 0.000 0.000 0.004
#> GSM550925 4 0.0146 0.7500 0.000 0.000 0.000 0.996 0.000 0.004
#> GSM550802 2 0.2234 0.7709 0.000 0.872 0.000 0.124 0.000 0.004
#> GSM550812 2 0.4887 0.4346 0.000 0.596 0.000 0.080 0.000 0.324
#> GSM550831 6 0.3518 0.7984 0.104 0.000 0.000 0.092 0.000 0.804
#> GSM550847 1 0.0000 0.8497 1.000 0.000 0.000 0.000 0.000 0.000
#> GSM550860 4 0.2221 0.7149 0.000 0.000 0.000 0.896 0.072 0.032
#> GSM550875 4 0.1863 0.7252 0.000 0.000 0.000 0.896 0.000 0.104
#> GSM550880 6 0.2048 0.8898 0.000 0.000 0.000 0.120 0.000 0.880
#> GSM550881 3 0.2762 0.7176 0.000 0.000 0.804 0.000 0.196 0.000
#> GSM550883 3 0.0000 0.8312 0.000 0.000 1.000 0.000 0.000 0.000
#> GSM550884 4 0.4668 0.5805 0.000 0.116 0.000 0.680 0.000 0.204
#> GSM550910 5 0.0146 0.6646 0.000 0.000 0.000 0.000 0.996 0.004
#> GSM550916 4 0.2896 0.6514 0.160 0.000 0.000 0.824 0.000 0.016
#> GSM550920 5 0.3930 0.3438 0.000 0.420 0.000 0.000 0.576 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)
get_signatures(res, k = 3)
get_signatures(res, k = 4)
get_signatures(res, k = 5)
get_signatures(res, k = 6)
Signature heatmaps where rows are not scaled:
get_signatures(res, k = 2, scale_rows = FALSE)
get_signatures(res, k = 3, scale_rows = FALSE)
get_signatures(res, k = 4, scale_rows = FALSE)
get_signatures(res, k = 5, scale_rows = FALSE)
get_signatures(res, k = 6, scale_rows = FALSE)
Compare the overlap of signatures from different k:
compare_signatures(res)
get_signature() returns a data frame invisibly. TO get the list of signatures, the function
call should be assigned to a variable explicitly. In following code, if plot argument is set
to FALSE, no heatmap is plotted while only the differential analysis is performed.
# code only for demonstration
tb = get_signature(res, k = ..., plot = FALSE)
An example of the output of tb is:
#> which_row fdr mean_1 mean_2 scaled_mean_1 scaled_mean_2 km
#> 1 38 0.042760348 8.373488 9.131774 -0.5533452 0.5164555 1
#> 2 40 0.018707592 7.106213 8.469186 -0.6173731 0.5762149 1
#> 3 55 0.019134737 10.221463 11.207825 -0.6159697 0.5749050 1
#> 4 59 0.006059896 5.921854 7.869574 -0.6899429 0.6439467 1
#> 5 60 0.018055526 8.928898 10.211722 -0.6204761 0.5791110 1
#> 6 98 0.009384629 15.714769 14.887706 0.6635654 -0.6193277 2
...
The columns in tb are:
which_row: row indices corresponding to the input matrix.fdr: FDR for the differential test. mean_x: The mean value in group x.scaled_mean_x: The mean value in group x after rows are scaled.km: Row groups if k-means clustering is applied to rows.UMAP plot which shows how samples are separated.
dimension_reduction(res, k = 2, method = "UMAP")
dimension_reduction(res, k = 3, method = "UMAP")
dimension_reduction(res, k = 4, method = "UMAP")
dimension_reduction(res, k = 5, method = "UMAP")
dimension_reduction(res, k = 6, method = "UMAP")
Following heatmap shows how subgroups are split when increasing k:
collect_classes(res)
Test correlation between subgroups and known annotations. If the known annotation is numeric, one-way ANOVA test is applied, and if the known annotation is discrete, chi-squared contingency table test is applied.
test_to_known_factors(res)
#> n disease.state(p) k
#> SD:mclust 121 4.87e-01 2
#> SD:mclust 119 1.23e-01 3
#> SD:mclust 67 6.17e-02 4
#> SD:mclust 132 5.68e-04 5
#> SD:mclust 121 3.29e-05 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 51776 rows and 143 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 0.501 0.822 0.902 0.4729 0.514 0.514
#> 3 3 0.790 0.846 0.938 0.3273 0.723 0.524
#> 4 4 0.707 0.772 0.890 0.1615 0.791 0.510
#> 5 5 0.630 0.626 0.812 0.0705 0.839 0.498
#> 6 6 0.687 0.608 0.788 0.0495 0.929 0.696
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
#> GSM550785 1 0.7219 0.8454 0.800 0.200
#> GSM550786 2 0.9795 0.4182 0.416 0.584
#> GSM550788 2 0.0000 0.9206 0.000 1.000
#> GSM550789 2 0.0000 0.9206 0.000 1.000
#> GSM550790 1 0.7219 0.8454 0.800 0.200
#> GSM550791 1 0.7299 0.8425 0.796 0.204
#> GSM550792 2 0.0376 0.9178 0.004 0.996
#> GSM550796 2 0.0000 0.9206 0.000 1.000
#> GSM550797 2 0.0000 0.9206 0.000 1.000
#> GSM550799 2 0.7219 0.7387 0.200 0.800
#> GSM550800 2 0.0000 0.9206 0.000 1.000
#> GSM550801 2 0.0000 0.9206 0.000 1.000
#> GSM550804 2 0.0000 0.9206 0.000 1.000
#> GSM550806 1 0.0000 0.8262 1.000 0.000
#> GSM550807 2 0.0000 0.9206 0.000 1.000
#> GSM550808 2 0.0000 0.9206 0.000 1.000
#> GSM550809 1 0.0000 0.8262 1.000 0.000
#> GSM550810 2 0.0000 0.9206 0.000 1.000
#> GSM550811 1 0.7299 0.8425 0.796 0.204
#> GSM550813 2 0.0000 0.9206 0.000 1.000
#> GSM550814 2 0.0000 0.9206 0.000 1.000
#> GSM550815 2 0.0000 0.9206 0.000 1.000
#> GSM550816 2 0.0000 0.9206 0.000 1.000
#> GSM550817 2 0.8813 0.6305 0.300 0.700
#> GSM550818 2 0.9710 0.4523 0.400 0.600
#> GSM550819 2 0.0000 0.9206 0.000 1.000
#> GSM550820 1 0.0000 0.8262 1.000 0.000
#> GSM550821 2 0.0376 0.9180 0.004 0.996
#> GSM550822 2 0.0000 0.9206 0.000 1.000
#> GSM550826 1 0.0000 0.8262 1.000 0.000
#> GSM550832 2 0.0000 0.9206 0.000 1.000
#> GSM550833 2 0.0000 0.9206 0.000 1.000
#> GSM550835 2 0.7056 0.7473 0.192 0.808
#> GSM550836 1 0.0000 0.8262 1.000 0.000
#> GSM550837 2 0.0000 0.9206 0.000 1.000
#> GSM550838 1 0.0000 0.8262 1.000 0.000
#> GSM550841 2 0.7219 0.7387 0.200 0.800
#> GSM550842 2 0.0000 0.9206 0.000 1.000
#> GSM550846 2 0.0000 0.9206 0.000 1.000
#> GSM550849 1 0.8267 0.7826 0.740 0.260
#> GSM550850 1 0.7219 0.8454 0.800 0.200
#> GSM550851 2 0.0672 0.9153 0.008 0.992
#> GSM550852 2 0.0000 0.9206 0.000 1.000
#> GSM550853 2 0.0000 0.9206 0.000 1.000
#> GSM550855 2 0.0000 0.9206 0.000 1.000
#> GSM550856 2 0.0000 0.9206 0.000 1.000
#> GSM550861 2 0.0000 0.9206 0.000 1.000
#> GSM550863 2 0.0000 0.9206 0.000 1.000
#> GSM550864 2 0.0000 0.9206 0.000 1.000
#> GSM550866 2 0.0000 0.9206 0.000 1.000
#> GSM550867 1 0.7219 0.8454 0.800 0.200
#> GSM550885 1 0.7219 0.8454 0.800 0.200
#> GSM550886 2 0.7299 0.7357 0.204 0.796
#> GSM550887 2 0.0000 0.9206 0.000 1.000
#> GSM550889 2 0.7219 0.6619 0.200 0.800
#> GSM550894 2 0.0000 0.9206 0.000 1.000
#> GSM550897 1 0.7299 0.8425 0.796 0.204
#> GSM550903 2 0.0000 0.9206 0.000 1.000
#> GSM550905 2 0.0000 0.9206 0.000 1.000
#> GSM550906 2 0.0000 0.9206 0.000 1.000
#> GSM550907 1 0.9866 0.0566 0.568 0.432
#> GSM550909 2 0.7056 0.7473 0.192 0.808
#> GSM550911 1 0.9998 -0.1722 0.508 0.492
#> GSM550913 2 0.0000 0.9206 0.000 1.000
#> GSM550915 2 0.4939 0.8106 0.108 0.892
#> GSM550917 2 0.0000 0.9206 0.000 1.000
#> GSM550919 2 0.0000 0.9206 0.000 1.000
#> GSM550921 1 0.0000 0.8262 1.000 0.000
#> GSM550924 2 0.9795 0.3697 0.416 0.584
#> GSM550926 2 0.0000 0.9206 0.000 1.000
#> GSM550927 2 0.0000 0.9206 0.000 1.000
#> GSM550787 1 0.7299 0.8427 0.796 0.204
#> GSM550793 1 0.0000 0.8262 1.000 0.000
#> GSM550794 2 0.1184 0.9088 0.016 0.984
#> GSM550795 1 0.7219 0.8454 0.800 0.200
#> GSM550798 1 0.0000 0.8262 1.000 0.000
#> GSM550803 1 0.0000 0.8262 1.000 0.000
#> GSM550805 1 0.7299 0.8425 0.796 0.204
#> GSM550823 2 0.0000 0.9206 0.000 1.000
#> GSM550824 1 0.7219 0.8454 0.800 0.200
#> GSM550825 1 0.0000 0.8262 1.000 0.000
#> GSM550827 2 0.0000 0.9206 0.000 1.000
#> GSM550828 1 0.7219 0.8454 0.800 0.200
#> GSM550829 1 0.0000 0.8262 1.000 0.000
#> GSM550830 2 0.4431 0.8299 0.092 0.908
#> GSM550834 1 0.7299 0.8425 0.796 0.204
#> GSM550839 2 0.8144 0.6911 0.252 0.748
#> GSM550840 1 0.7219 0.8454 0.800 0.200
#> GSM550843 2 0.9896 0.3598 0.440 0.560
#> GSM550844 1 0.7219 0.8454 0.800 0.200
#> GSM550845 2 0.0000 0.9206 0.000 1.000
#> GSM550848 2 0.0000 0.9206 0.000 1.000
#> GSM550854 1 0.7219 0.8454 0.800 0.200
#> GSM550857 1 0.0000 0.8262 1.000 0.000
#> GSM550858 1 0.7219 0.8454 0.800 0.200
#> GSM550859 1 0.7219 0.8454 0.800 0.200
#> GSM550862 1 0.7219 0.8454 0.800 0.200
#> GSM550865 2 0.6623 0.7145 0.172 0.828
#> GSM550868 2 0.5294 0.7943 0.120 0.880
#> GSM550869 1 0.7528 0.8309 0.784 0.216
#> GSM550870 2 0.0000 0.9206 0.000 1.000
#> GSM550871 2 0.9815 0.4089 0.420 0.580
#> GSM550872 2 0.4431 0.8309 0.092 0.908
#> GSM550873 2 0.0000 0.9206 0.000 1.000
#> GSM550874 2 0.0000 0.9206 0.000 1.000
#> GSM550876 2 0.8813 0.6308 0.300 0.700
#> GSM550877 2 0.0000 0.9206 0.000 1.000
#> GSM550878 1 0.8813 0.4505 0.700 0.300
#> GSM550879 1 0.7219 0.8454 0.800 0.200
#> GSM550882 1 0.0000 0.8262 1.000 0.000
#> GSM550888 1 0.0000 0.8262 1.000 0.000
#> GSM550890 2 0.0000 0.9206 0.000 1.000
#> GSM550891 1 0.0000 0.8262 1.000 0.000
#> GSM550892 1 0.7219 0.8454 0.800 0.200
#> GSM550893 2 0.0000 0.9206 0.000 1.000
#> GSM550895 2 0.0000 0.9206 0.000 1.000
#> GSM550896 2 0.0000 0.9206 0.000 1.000
#> GSM550898 1 0.7219 0.8454 0.800 0.200
#> GSM550899 2 0.0000 0.9206 0.000 1.000
#> GSM550900 2 0.0376 0.9178 0.004 0.996
#> GSM550901 1 0.9635 0.5690 0.612 0.388
#> GSM550902 1 0.0000 0.8262 1.000 0.000
#> GSM550904 1 0.0000 0.8262 1.000 0.000
#> GSM550908 1 0.0000 0.8262 1.000 0.000
#> GSM550912 2 0.0000 0.9206 0.000 1.000
#> GSM550914 2 0.0000 0.9206 0.000 1.000
#> GSM550918 2 0.0000 0.9206 0.000 1.000
#> GSM550922 2 0.7219 0.7387 0.200 0.800
#> GSM550923 1 0.0000 0.8262 1.000 0.000
#> GSM550925 1 0.8763 0.7301 0.704 0.296
#> GSM550802 2 0.0000 0.9206 0.000 1.000
#> GSM550812 2 0.0000 0.9206 0.000 1.000
#> GSM550831 1 0.7219 0.8454 0.800 0.200
#> GSM550847 1 0.7219 0.8454 0.800 0.200
#> GSM550860 1 0.0000 0.8262 1.000 0.000
#> GSM550875 1 0.7219 0.8454 0.800 0.200
#> GSM550880 1 0.9933 0.4236 0.548 0.452
#> GSM550881 1 0.0000 0.8262 1.000 0.000
#> GSM550883 1 0.0000 0.8262 1.000 0.000
#> GSM550884 2 0.1843 0.9029 0.028 0.972
#> GSM550910 2 0.8327 0.6774 0.264 0.736
#> GSM550916 1 0.7219 0.8454 0.800 0.200
#> GSM550920 2 0.9909 0.3492 0.444 0.556
cbind(get_classes(res, k = 3), get_membership(res, k = 3))
#> class entropy silhouette p1 p2 p3
#> GSM550785 1 0.0000 0.9219 1.000 0.000 0.000
#> GSM550786 3 0.5650 0.5280 0.000 0.312 0.688
#> GSM550788 2 0.0000 0.9359 0.000 1.000 0.000
#> GSM550789 2 0.0000 0.9359 0.000 1.000 0.000
#> GSM550790 1 0.0000 0.9219 1.000 0.000 0.000
#> GSM550791 1 0.0000 0.9219 1.000 0.000 0.000
#> GSM550792 2 0.0237 0.9327 0.004 0.996 0.000
#> GSM550796 2 0.0000 0.9359 0.000 1.000 0.000
#> GSM550797 2 0.0000 0.9359 0.000 1.000 0.000
#> GSM550799 3 0.1529 0.8848 0.000 0.040 0.960
#> GSM550800 2 0.0000 0.9359 0.000 1.000 0.000
#> GSM550801 2 0.0000 0.9359 0.000 1.000 0.000
#> GSM550804 2 0.0000 0.9359 0.000 1.000 0.000
#> GSM550806 3 0.0000 0.9079 0.000 0.000 1.000
#> GSM550807 2 0.0000 0.9359 0.000 1.000 0.000
#> GSM550808 2 0.0000 0.9359 0.000 1.000 0.000
#> GSM550809 1 0.3340 0.8197 0.880 0.000 0.120
#> GSM550810 2 0.0000 0.9359 0.000 1.000 0.000
#> GSM550811 1 0.7338 0.5455 0.652 0.288 0.060
#> GSM550813 2 0.0000 0.9359 0.000 1.000 0.000
#> GSM550814 2 0.0000 0.9359 0.000 1.000 0.000
#> GSM550815 2 0.0000 0.9359 0.000 1.000 0.000
#> GSM550816 2 0.0000 0.9359 0.000 1.000 0.000
#> GSM550817 3 0.0000 0.9079 0.000 0.000 1.000
#> GSM550818 3 0.0000 0.9079 0.000 0.000 1.000
#> GSM550819 2 0.0000 0.9359 0.000 1.000 0.000
#> GSM550820 1 0.0000 0.9219 1.000 0.000 0.000
#> GSM550821 2 0.0237 0.9330 0.000 0.996 0.004
#> GSM550822 2 0.0000 0.9359 0.000 1.000 0.000
#> GSM550826 1 0.5138 0.6515 0.748 0.000 0.252
#> GSM550832 2 0.0000 0.9359 0.000 1.000 0.000
#> GSM550833 2 0.0000 0.9359 0.000 1.000 0.000
#> GSM550835 2 0.3686 0.8023 0.000 0.860 0.140
#> GSM550836 3 0.0000 0.9079 0.000 0.000 1.000
#> GSM550837 2 0.0000 0.9359 0.000 1.000 0.000
#> GSM550838 1 0.4654 0.7170 0.792 0.000 0.208
#> GSM550841 3 0.0237 0.9059 0.000 0.004 0.996
#> GSM550842 2 0.0000 0.9359 0.000 1.000 0.000
#> GSM550846 2 0.0000 0.9359 0.000 1.000 0.000
#> GSM550849 2 0.6518 -0.0257 0.484 0.512 0.004
#> GSM550850 1 0.0000 0.9219 1.000 0.000 0.000
#> GSM550851 2 0.0000 0.9359 0.000 1.000 0.000
#> GSM550852 2 0.0000 0.9359 0.000 1.000 0.000
#> GSM550853 2 0.0000 0.9359 0.000 1.000 0.000
#> GSM550855 2 0.0000 0.9359 0.000 1.000 0.000
#> GSM550856 2 0.0000 0.9359 0.000 1.000 0.000
#> GSM550861 2 0.0000 0.9359 0.000 1.000 0.000
#> GSM550863 1 0.1753 0.8813 0.952 0.048 0.000
#> GSM550864 2 0.0000 0.9359 0.000 1.000 0.000
#> GSM550866 2 0.0000 0.9359 0.000 1.000 0.000
#> GSM550867 1 0.0000 0.9219 1.000 0.000 0.000
#> GSM550885 1 0.0000 0.9219 1.000 0.000 0.000
#> GSM550886 2 0.5859 0.4656 0.000 0.656 0.344
#> GSM550887 2 0.0000 0.9359 0.000 1.000 0.000
#> GSM550889 1 0.6126 0.3902 0.600 0.400 0.000
#> GSM550894 2 0.0000 0.9359 0.000 1.000 0.000
#> GSM550897 1 0.0000 0.9219 1.000 0.000 0.000
#> GSM550903 2 0.0000 0.9359 0.000 1.000 0.000
#> GSM550905 2 0.0000 0.9359 0.000 1.000 0.000
#> GSM550906 2 0.0000 0.9359 0.000 1.000 0.000
#> GSM550907 3 0.0000 0.9079 0.000 0.000 1.000
#> GSM550909 2 0.3752 0.7972 0.000 0.856 0.144
#> GSM550911 3 0.0000 0.9079 0.000 0.000 1.000
#> GSM550913 2 0.0000 0.9359 0.000 1.000 0.000
#> GSM550915 1 0.0424 0.9165 0.992 0.008 0.000
#> GSM550917 2 0.0000 0.9359 0.000 1.000 0.000
#> GSM550919 1 0.4654 0.7109 0.792 0.208 0.000
#> GSM550921 3 0.0000 0.9079 0.000 0.000 1.000
#> GSM550924 2 0.4605 0.7172 0.000 0.796 0.204
#> GSM550926 2 0.0000 0.9359 0.000 1.000 0.000
#> GSM550927 2 0.0000 0.9359 0.000 1.000 0.000
#> GSM550787 1 0.7108 0.6497 0.716 0.184 0.100
#> GSM550793 3 0.6309 -0.0753 0.500 0.000 0.500
#> GSM550794 2 0.5216 0.6544 0.260 0.740 0.000
#> GSM550795 1 0.0000 0.9219 1.000 0.000 0.000
#> GSM550798 1 0.0000 0.9219 1.000 0.000 0.000
#> GSM550803 1 0.0000 0.9219 1.000 0.000 0.000
#> GSM550805 1 0.0592 0.9138 0.988 0.012 0.000
#> GSM550823 2 0.0424 0.9293 0.008 0.992 0.000
#> GSM550824 1 0.0000 0.9219 1.000 0.000 0.000
#> GSM550825 1 0.5948 0.4454 0.640 0.000 0.360
#> GSM550827 1 0.1643 0.8856 0.956 0.044 0.000
#> GSM550828 1 0.0000 0.9219 1.000 0.000 0.000
#> GSM550829 1 0.4399 0.7419 0.812 0.000 0.188
#> GSM550830 1 0.5988 0.4666 0.632 0.368 0.000
#> GSM550834 1 0.0000 0.9219 1.000 0.000 0.000
#> GSM550839 2 0.5706 0.5179 0.000 0.680 0.320
#> GSM550840 1 0.0000 0.9219 1.000 0.000 0.000
#> GSM550843 3 0.0000 0.9079 0.000 0.000 1.000
#> GSM550844 1 0.0000 0.9219 1.000 0.000 0.000
#> GSM550845 2 0.0000 0.9359 0.000 1.000 0.000
#> GSM550848 2 0.6204 0.3019 0.424 0.576 0.000
#> GSM550854 1 0.0000 0.9219 1.000 0.000 0.000
#> GSM550857 3 0.0000 0.9079 0.000 0.000 1.000
#> GSM550858 1 0.0000 0.9219 1.000 0.000 0.000
#> GSM550859 1 0.0000 0.9219 1.000 0.000 0.000
#> GSM550862 1 0.0000 0.9219 1.000 0.000 0.000
#> GSM550865 1 0.0000 0.9219 1.000 0.000 0.000
#> GSM550868 1 0.0000 0.9219 1.000 0.000 0.000
#> GSM550869 2 0.8834 0.3164 0.316 0.544 0.140
#> GSM550870 2 0.0000 0.9359 0.000 1.000 0.000
#> GSM550871 2 0.5591 0.5507 0.000 0.696 0.304
#> GSM550872 1 0.0000 0.9219 1.000 0.000 0.000
#> GSM550873 2 0.0000 0.9359 0.000 1.000 0.000
#> GSM550874 2 0.0000 0.9359 0.000 1.000 0.000
#> GSM550876 3 0.6295 0.0821 0.000 0.472 0.528
#> GSM550877 2 0.0000 0.9359 0.000 1.000 0.000
#> GSM550878 3 0.0000 0.9079 0.000 0.000 1.000
#> GSM550879 1 0.0000 0.9219 1.000 0.000 0.000
#> GSM550882 3 0.0000 0.9079 0.000 0.000 1.000
#> GSM550888 3 0.0000 0.9079 0.000 0.000 1.000
#> GSM550890 2 0.5905 0.4841 0.352 0.648 0.000
#> GSM550891 3 0.0000 0.9079 0.000 0.000 1.000
#> GSM550892 1 0.0000 0.9219 1.000 0.000 0.000
#> GSM550893 2 0.0000 0.9359 0.000 1.000 0.000
#> GSM550895 2 0.0000 0.9359 0.000 1.000 0.000
#> GSM550896 2 0.0000 0.9359 0.000 1.000 0.000
#> GSM550898 1 0.0000 0.9219 1.000 0.000 0.000
#> GSM550899 2 0.0000 0.9359 0.000 1.000 0.000
#> GSM550900 1 0.4887 0.6593 0.772 0.228 0.000
#> GSM550901 1 0.0000 0.9219 1.000 0.000 0.000
#> GSM550902 1 0.4504 0.7313 0.804 0.000 0.196
#> GSM550904 1 0.0237 0.9194 0.996 0.000 0.004
#> GSM550908 3 0.0000 0.9079 0.000 0.000 1.000
#> GSM550912 2 0.0000 0.9359 0.000 1.000 0.000
#> GSM550914 2 0.3752 0.7973 0.144 0.856 0.000
#> GSM550918 2 0.0000 0.9359 0.000 1.000 0.000
#> GSM550922 3 0.4062 0.7692 0.000 0.164 0.836
#> GSM550923 1 0.0000 0.9219 1.000 0.000 0.000
#> GSM550925 1 0.0000 0.9219 1.000 0.000 0.000
#> GSM550802 2 0.0000 0.9359 0.000 1.000 0.000
#> GSM550812 2 0.0237 0.9329 0.000 0.996 0.004
#> GSM550831 1 0.0000 0.9219 1.000 0.000 0.000
#> GSM550847 1 0.0000 0.9219 1.000 0.000 0.000
#> GSM550860 3 0.5465 0.5380 0.288 0.000 0.712
#> GSM550875 1 0.0000 0.9219 1.000 0.000 0.000
#> GSM550880 1 0.0000 0.9219 1.000 0.000 0.000
#> GSM550881 3 0.0000 0.9079 0.000 0.000 1.000
#> GSM550883 3 0.0000 0.9079 0.000 0.000 1.000
#> GSM550884 2 0.3192 0.8328 0.000 0.888 0.112
#> GSM550910 3 0.1753 0.8787 0.000 0.048 0.952
#> GSM550916 1 0.0000 0.9219 1.000 0.000 0.000
#> GSM550920 3 0.2796 0.8447 0.000 0.092 0.908
cbind(get_classes(res, k = 4), get_membership(res, k = 4))
#> class entropy silhouette p1 p2 p3 p4
#> GSM550785 1 0.0469 0.9059 0.988 0.000 0.000 0.012
#> GSM550786 2 0.4295 0.6153 0.008 0.752 0.240 0.000
#> GSM550788 4 0.2814 0.7986 0.000 0.132 0.000 0.868
#> GSM550789 2 0.0469 0.8625 0.000 0.988 0.000 0.012
#> GSM550790 1 0.0188 0.9069 0.996 0.000 0.000 0.004
#> GSM550791 1 0.0657 0.9036 0.984 0.012 0.000 0.004
#> GSM550792 2 0.2401 0.8052 0.092 0.904 0.000 0.004
#> GSM550796 2 0.0707 0.8629 0.000 0.980 0.000 0.020
#> GSM550797 2 0.0336 0.8619 0.000 0.992 0.000 0.008
#> GSM550799 3 0.0524 0.8901 0.000 0.008 0.988 0.004
#> GSM550800 4 0.2345 0.8151 0.000 0.100 0.000 0.900
#> GSM550801 2 0.0817 0.8626 0.000 0.976 0.000 0.024
#> GSM550804 2 0.0188 0.8581 0.004 0.996 0.000 0.000
#> GSM550806 3 0.2647 0.7925 0.000 0.000 0.880 0.120
#> GSM550807 2 0.1637 0.8530 0.000 0.940 0.000 0.060
#> GSM550808 2 0.0188 0.8581 0.004 0.996 0.000 0.000
#> GSM550809 1 0.0817 0.8958 0.976 0.024 0.000 0.000
#> GSM550810 2 0.0592 0.8629 0.000 0.984 0.000 0.016
#> GSM550811 1 0.4843 0.4291 0.604 0.396 0.000 0.000
#> GSM550813 2 0.2408 0.8246 0.000 0.896 0.000 0.104
#> GSM550814 2 0.4543 0.5272 0.000 0.676 0.000 0.324
#> GSM550815 2 0.0592 0.8629 0.000 0.984 0.000 0.016
#> GSM550816 2 0.0336 0.8567 0.008 0.992 0.000 0.000
#> GSM550817 3 0.1474 0.8716 0.000 0.052 0.948 0.000
#> GSM550818 3 0.1398 0.8779 0.004 0.040 0.956 0.000
#> GSM550819 2 0.4985 0.2551 0.000 0.532 0.000 0.468
#> GSM550820 1 0.0336 0.9033 0.992 0.008 0.000 0.000
#> GSM550821 2 0.0376 0.8577 0.004 0.992 0.004 0.000
#> GSM550822 2 0.0000 0.8595 0.000 1.000 0.000 0.000
#> GSM550826 1 0.4406 0.7015 0.780 0.028 0.192 0.000
#> GSM550832 2 0.0469 0.8625 0.000 0.988 0.000 0.012
#> GSM550833 2 0.1867 0.8472 0.000 0.928 0.000 0.072
#> GSM550835 2 0.6380 0.1678 0.000 0.500 0.436 0.064
#> GSM550836 3 0.0000 0.8948 0.000 0.000 1.000 0.000
#> GSM550837 2 0.1211 0.8605 0.000 0.960 0.000 0.040
#> GSM550838 1 0.3708 0.7655 0.832 0.020 0.148 0.000
#> GSM550841 3 0.4331 0.6033 0.000 0.288 0.712 0.000
#> GSM550842 2 0.0469 0.8627 0.000 0.988 0.000 0.012
#> GSM550846 2 0.0592 0.8540 0.016 0.984 0.000 0.000
#> GSM550849 1 0.4500 0.5801 0.684 0.316 0.000 0.000
#> GSM550850 1 0.0188 0.9069 0.996 0.000 0.000 0.004
#> GSM550851 2 0.0336 0.8619 0.000 0.992 0.000 0.008
#> GSM550852 2 0.0524 0.8615 0.004 0.988 0.000 0.008
#> GSM550853 2 0.4697 0.4848 0.000 0.644 0.000 0.356
#> GSM550855 2 0.4661 0.4900 0.000 0.652 0.000 0.348
#> GSM550856 2 0.4804 0.4113 0.000 0.616 0.000 0.384
#> GSM550861 2 0.1022 0.8613 0.000 0.968 0.000 0.032
#> GSM550863 4 0.1545 0.8391 0.040 0.008 0.000 0.952
#> GSM550864 2 0.0707 0.8630 0.000 0.980 0.000 0.020
#> GSM550866 4 0.3726 0.7199 0.000 0.212 0.000 0.788
#> GSM550867 1 0.0188 0.9069 0.996 0.000 0.000 0.004
#> GSM550885 1 0.0336 0.9065 0.992 0.000 0.000 0.008
#> GSM550886 3 0.6125 0.0529 0.000 0.436 0.516 0.048
#> GSM550887 2 0.1716 0.8517 0.000 0.936 0.000 0.064
#> GSM550889 4 0.0188 0.8445 0.000 0.004 0.000 0.996
#> GSM550894 2 0.1792 0.8493 0.000 0.932 0.000 0.068
#> GSM550897 4 0.0921 0.8378 0.028 0.000 0.000 0.972
#> GSM550903 2 0.0336 0.8619 0.000 0.992 0.000 0.008
#> GSM550905 2 0.0188 0.8581 0.004 0.996 0.000 0.000
#> GSM550906 2 0.2868 0.7964 0.000 0.864 0.000 0.136
#> GSM550907 3 0.0188 0.8941 0.000 0.004 0.996 0.000
#> GSM550909 2 0.1576 0.8348 0.004 0.948 0.048 0.000
#> GSM550911 3 0.0188 0.8941 0.000 0.004 0.996 0.000
#> GSM550913 2 0.0707 0.8630 0.000 0.980 0.000 0.020
#> GSM550915 1 0.3764 0.7218 0.784 0.216 0.000 0.000
#> GSM550917 2 0.1211 0.8597 0.000 0.960 0.000 0.040
#> GSM550919 1 0.4250 0.6441 0.724 0.276 0.000 0.000
#> GSM550921 3 0.0000 0.8948 0.000 0.000 1.000 0.000
#> GSM550924 2 0.3427 0.7652 0.028 0.860 0.112 0.000
#> GSM550926 4 0.4193 0.6455 0.000 0.268 0.000 0.732
#> GSM550927 2 0.1557 0.8561 0.000 0.944 0.000 0.056
#> GSM550787 1 0.9671 0.0594 0.380 0.200 0.180 0.240
#> GSM550793 3 0.3877 0.7819 0.048 0.000 0.840 0.112
#> GSM550794 2 0.4800 0.5002 0.340 0.656 0.000 0.004
#> GSM550795 1 0.1389 0.8846 0.952 0.000 0.000 0.048
#> GSM550798 1 0.0336 0.9065 0.992 0.000 0.000 0.008
#> GSM550803 1 0.0469 0.9059 0.988 0.000 0.000 0.012
#> GSM550805 4 0.7143 0.6412 0.228 0.072 0.064 0.636
#> GSM550823 4 0.0336 0.8446 0.000 0.008 0.000 0.992
#> GSM550824 1 0.0188 0.9069 0.996 0.000 0.000 0.004
#> GSM550825 3 0.3653 0.7844 0.128 0.000 0.844 0.028
#> GSM550827 1 0.2944 0.8042 0.868 0.128 0.000 0.004
#> GSM550828 1 0.0188 0.9069 0.996 0.000 0.000 0.004
#> GSM550829 1 0.1489 0.8818 0.952 0.000 0.044 0.004
#> GSM550830 4 0.0188 0.8449 0.000 0.004 0.000 0.996
#> GSM550834 1 0.0000 0.9062 1.000 0.000 0.000 0.000
#> GSM550839 4 0.5256 0.6229 0.000 0.040 0.260 0.700
#> GSM550840 4 0.2469 0.7993 0.108 0.000 0.000 0.892
#> GSM550843 3 0.0000 0.8948 0.000 0.000 1.000 0.000
#> GSM550844 1 0.0336 0.9065 0.992 0.000 0.000 0.008
#> GSM550845 4 0.4222 0.6315 0.000 0.272 0.000 0.728
#> GSM550848 2 0.4981 0.0852 0.464 0.536 0.000 0.000
#> GSM550854 1 0.0592 0.9046 0.984 0.000 0.000 0.016
#> GSM550857 3 0.1637 0.8592 0.060 0.000 0.940 0.000
#> GSM550858 1 0.0469 0.9059 0.988 0.000 0.000 0.012
#> GSM550859 1 0.0469 0.9059 0.988 0.000 0.000 0.012
#> GSM550862 4 0.3801 0.6863 0.220 0.000 0.000 0.780
#> GSM550865 4 0.0592 0.8418 0.016 0.000 0.000 0.984
#> GSM550868 4 0.0336 0.8438 0.008 0.000 0.000 0.992
#> GSM550869 4 0.0336 0.8446 0.000 0.008 0.000 0.992
#> GSM550870 2 0.2345 0.8277 0.000 0.900 0.000 0.100
#> GSM550871 4 0.3978 0.7159 0.000 0.012 0.192 0.796
#> GSM550872 4 0.0336 0.8438 0.008 0.000 0.000 0.992
#> GSM550873 2 0.0657 0.8624 0.004 0.984 0.000 0.012
#> GSM550874 4 0.2216 0.8246 0.000 0.092 0.000 0.908
#> GSM550876 4 0.3479 0.7668 0.000 0.012 0.148 0.840
#> GSM550877 4 0.2814 0.7946 0.000 0.132 0.000 0.868
#> GSM550878 3 0.0000 0.8948 0.000 0.000 1.000 0.000
#> GSM550879 1 0.0188 0.9069 0.996 0.000 0.000 0.004
#> GSM550882 4 0.4500 0.5611 0.000 0.000 0.316 0.684
#> GSM550888 3 0.0000 0.8948 0.000 0.000 1.000 0.000
#> GSM550890 2 0.4830 0.3268 0.392 0.608 0.000 0.000
#> GSM550891 3 0.0000 0.8948 0.000 0.000 1.000 0.000
#> GSM550892 4 0.2281 0.8018 0.096 0.000 0.000 0.904
#> GSM550893 4 0.2281 0.8221 0.000 0.096 0.000 0.904
#> GSM550895 4 0.0336 0.8446 0.000 0.008 0.000 0.992
#> GSM550896 4 0.1302 0.8387 0.000 0.044 0.000 0.956
#> GSM550898 1 0.0592 0.9046 0.984 0.000 0.000 0.016
#> GSM550899 2 0.0524 0.8585 0.008 0.988 0.000 0.004
#> GSM550900 4 0.0188 0.8445 0.000 0.004 0.000 0.996
#> GSM550901 1 0.2081 0.8522 0.916 0.084 0.000 0.000
#> GSM550902 1 0.4086 0.6804 0.776 0.000 0.216 0.008
#> GSM550904 1 0.0000 0.9062 1.000 0.000 0.000 0.000
#> GSM550908 3 0.0000 0.8948 0.000 0.000 1.000 0.000
#> GSM550912 2 0.1557 0.8548 0.000 0.944 0.000 0.056
#> GSM550914 2 0.3913 0.7686 0.028 0.824 0.000 0.148
#> GSM550918 2 0.0707 0.8630 0.000 0.980 0.000 0.020
#> GSM550922 2 0.3907 0.6392 0.000 0.768 0.232 0.000
#> GSM550923 1 0.0188 0.9069 0.996 0.000 0.000 0.004
#> GSM550925 4 0.3837 0.7142 0.224 0.000 0.000 0.776
#> GSM550802 2 0.4866 0.4254 0.000 0.596 0.000 0.404
#> GSM550812 2 0.3798 0.7974 0.008 0.860 0.072 0.060
#> GSM550831 1 0.0000 0.9062 1.000 0.000 0.000 0.000
#> GSM550847 1 0.0592 0.9046 0.984 0.000 0.000 0.016
#> GSM550860 4 0.0895 0.8396 0.004 0.000 0.020 0.976
#> GSM550875 4 0.1389 0.8339 0.048 0.000 0.000 0.952
#> GSM550880 1 0.0672 0.9028 0.984 0.008 0.000 0.008
#> GSM550881 3 0.0000 0.8948 0.000 0.000 1.000 0.000
#> GSM550883 3 0.0188 0.8936 0.004 0.000 0.996 0.000
#> GSM550884 4 0.6783 0.5713 0.004 0.168 0.204 0.624
#> GSM550910 2 0.5016 0.2883 0.004 0.600 0.396 0.000
#> GSM550916 4 0.4994 0.1267 0.480 0.000 0.000 0.520
#> GSM550920 3 0.4746 0.3907 0.000 0.368 0.632 0.000
cbind(get_classes(res, k = 5), get_membership(res, k = 5))
#> class entropy silhouette p1 p2 p3 p4 p5
#> GSM550785 1 0.0963 0.7882 0.964 0.000 0.000 0.000 0.036
#> GSM550786 5 0.6327 0.4396 0.000 0.280 0.200 0.000 0.520
#> GSM550788 2 0.4666 0.1916 0.000 0.572 0.000 0.412 0.016
#> GSM550789 2 0.0000 0.8046 0.000 1.000 0.000 0.000 0.000
#> GSM550790 1 0.0162 0.7935 0.996 0.000 0.000 0.000 0.004
#> GSM550791 1 0.1270 0.7802 0.948 0.000 0.000 0.000 0.052
#> GSM550792 2 0.4617 0.5072 0.224 0.716 0.000 0.000 0.060
#> GSM550796 2 0.0510 0.8057 0.000 0.984 0.000 0.000 0.016
#> GSM550797 2 0.0000 0.8046 0.000 1.000 0.000 0.000 0.000
#> GSM550799 3 0.2308 0.7852 0.000 0.048 0.912 0.004 0.036
#> GSM550800 4 0.3991 0.7108 0.000 0.172 0.000 0.780 0.048
#> GSM550801 2 0.0324 0.8050 0.000 0.992 0.000 0.004 0.004
#> GSM550804 2 0.4060 0.3480 0.000 0.640 0.000 0.000 0.360
#> GSM550806 3 0.2612 0.7467 0.000 0.000 0.868 0.124 0.008
#> GSM550807 2 0.0807 0.8059 0.000 0.976 0.000 0.012 0.012
#> GSM550808 2 0.1792 0.7704 0.000 0.916 0.000 0.000 0.084
#> GSM550809 5 0.2976 0.5726 0.132 0.004 0.012 0.000 0.852
#> GSM550810 2 0.0794 0.8031 0.000 0.972 0.000 0.000 0.028
#> GSM550811 5 0.4028 0.6061 0.104 0.080 0.008 0.000 0.808
#> GSM550813 2 0.1997 0.7905 0.000 0.924 0.000 0.036 0.040
#> GSM550814 2 0.4856 0.2446 0.000 0.584 0.000 0.388 0.028
#> GSM550815 2 0.1410 0.7933 0.000 0.940 0.000 0.000 0.060
#> GSM550816 5 0.4192 0.4072 0.000 0.404 0.000 0.000 0.596
#> GSM550817 3 0.3578 0.7299 0.000 0.048 0.820 0.000 0.132
#> GSM550818 3 0.4025 0.5563 0.000 0.008 0.700 0.000 0.292
#> GSM550819 5 0.5264 0.5046 0.000 0.128 0.000 0.196 0.676
#> GSM550820 5 0.4297 -0.0118 0.472 0.000 0.000 0.000 0.528
#> GSM550821 5 0.4434 0.1976 0.000 0.460 0.004 0.000 0.536
#> GSM550822 2 0.4045 0.3595 0.000 0.644 0.000 0.000 0.356
#> GSM550826 5 0.4095 0.5006 0.220 0.000 0.024 0.004 0.752
#> GSM550832 2 0.0671 0.8033 0.000 0.980 0.000 0.004 0.016
#> GSM550833 2 0.0912 0.8061 0.000 0.972 0.000 0.012 0.016
#> GSM550835 2 0.4265 0.6151 0.000 0.744 0.224 0.020 0.012
#> GSM550836 3 0.0290 0.8172 0.000 0.000 0.992 0.000 0.008
#> GSM550837 2 0.2362 0.7831 0.000 0.900 0.008 0.008 0.084
#> GSM550838 5 0.3035 0.5776 0.112 0.000 0.032 0.000 0.856
#> GSM550841 3 0.5808 0.4359 0.000 0.232 0.608 0.000 0.160
#> GSM550842 2 0.2727 0.7461 0.000 0.868 0.016 0.000 0.116
#> GSM550846 5 0.4252 0.5663 0.020 0.280 0.000 0.000 0.700
#> GSM550849 1 0.3146 0.6949 0.844 0.128 0.000 0.000 0.028
#> GSM550850 1 0.1124 0.7885 0.960 0.000 0.000 0.004 0.036
#> GSM550851 2 0.1522 0.7965 0.000 0.944 0.012 0.000 0.044
#> GSM550852 2 0.2843 0.7142 0.008 0.848 0.000 0.000 0.144
#> GSM550853 2 0.5850 0.1129 0.000 0.476 0.000 0.428 0.096
#> GSM550855 2 0.3053 0.6826 0.000 0.828 0.000 0.164 0.008
#> GSM550856 2 0.3596 0.6324 0.000 0.776 0.000 0.212 0.012
#> GSM550861 2 0.0290 0.8052 0.000 0.992 0.000 0.008 0.000
#> GSM550863 5 0.3934 0.4309 0.016 0.000 0.000 0.244 0.740
#> GSM550864 2 0.1740 0.8011 0.000 0.932 0.000 0.012 0.056
#> GSM550866 4 0.4252 0.5265 0.000 0.340 0.000 0.652 0.008
#> GSM550867 1 0.1124 0.7899 0.960 0.000 0.000 0.004 0.036
#> GSM550885 1 0.3766 0.5820 0.728 0.000 0.000 0.004 0.268
#> GSM550886 2 0.5402 0.3123 0.000 0.564 0.388 0.024 0.024
#> GSM550887 2 0.1597 0.7987 0.000 0.940 0.000 0.012 0.048
#> GSM550889 4 0.0162 0.8188 0.000 0.004 0.000 0.996 0.000
#> GSM550894 2 0.1012 0.8033 0.000 0.968 0.000 0.020 0.012
#> GSM550897 4 0.1981 0.8079 0.028 0.000 0.000 0.924 0.048
#> GSM550903 2 0.1043 0.7976 0.000 0.960 0.000 0.000 0.040
#> GSM550905 2 0.2930 0.7011 0.000 0.832 0.004 0.000 0.164
#> GSM550906 2 0.1992 0.7950 0.000 0.924 0.000 0.032 0.044
#> GSM550907 3 0.0510 0.8155 0.000 0.000 0.984 0.000 0.016
#> GSM550909 5 0.6097 0.2263 0.000 0.420 0.124 0.000 0.456
#> GSM550911 3 0.1121 0.8091 0.000 0.000 0.956 0.000 0.044
#> GSM550913 2 0.0451 0.8057 0.000 0.988 0.000 0.004 0.008
#> GSM550915 5 0.4593 0.6273 0.124 0.128 0.000 0.000 0.748
#> GSM550917 2 0.1281 0.8005 0.000 0.956 0.000 0.012 0.032
#> GSM550919 1 0.4748 0.3660 0.660 0.300 0.000 0.000 0.040
#> GSM550921 3 0.0290 0.8172 0.000 0.000 0.992 0.000 0.008
#> GSM550924 2 0.6184 0.2956 0.332 0.564 0.044 0.000 0.060
#> GSM550926 4 0.4787 0.4591 0.000 0.364 0.000 0.608 0.028
#> GSM550927 2 0.1628 0.7968 0.000 0.936 0.000 0.008 0.056
#> GSM550787 1 0.6794 0.1033 0.468 0.404 0.044 0.008 0.076
#> GSM550793 3 0.3867 0.7554 0.012 0.000 0.824 0.076 0.088
#> GSM550794 1 0.6624 0.2253 0.532 0.196 0.004 0.008 0.260
#> GSM550795 5 0.5862 0.4331 0.208 0.016 0.000 0.132 0.644
#> GSM550798 1 0.0992 0.7905 0.968 0.000 0.008 0.000 0.024
#> GSM550803 1 0.0290 0.7938 0.992 0.000 0.000 0.000 0.008
#> GSM550805 1 0.6891 0.4347 0.600 0.136 0.020 0.204 0.040
#> GSM550823 4 0.0451 0.8198 0.000 0.004 0.000 0.988 0.008
#> GSM550824 1 0.0963 0.7903 0.964 0.000 0.000 0.000 0.036
#> GSM550825 3 0.4250 0.5818 0.252 0.000 0.720 0.000 0.028
#> GSM550827 5 0.6976 0.3999 0.304 0.280 0.000 0.008 0.408
#> GSM550828 1 0.1270 0.7889 0.948 0.000 0.000 0.000 0.052
#> GSM550829 1 0.2588 0.7552 0.892 0.000 0.060 0.000 0.048
#> GSM550830 4 0.1012 0.8199 0.000 0.020 0.000 0.968 0.012
#> GSM550834 1 0.3519 0.6729 0.776 0.008 0.000 0.000 0.216
#> GSM550839 4 0.4137 0.6435 0.000 0.008 0.248 0.732 0.012
#> GSM550840 1 0.4620 0.3347 0.592 0.000 0.000 0.392 0.016
#> GSM550843 3 0.1197 0.8111 0.000 0.000 0.952 0.000 0.048
#> GSM550844 1 0.2843 0.7327 0.848 0.000 0.000 0.008 0.144
#> GSM550845 4 0.4648 0.7211 0.004 0.108 0.000 0.752 0.136
#> GSM550848 1 0.6816 -0.3394 0.360 0.320 0.000 0.000 0.320
#> GSM550854 1 0.1082 0.7934 0.964 0.000 0.000 0.008 0.028
#> GSM550857 3 0.3888 0.7263 0.072 0.000 0.812 0.004 0.112
#> GSM550858 1 0.2124 0.7666 0.900 0.000 0.000 0.004 0.096
#> GSM550859 1 0.1124 0.7906 0.960 0.000 0.000 0.004 0.036
#> GSM550862 4 0.2740 0.7681 0.096 0.000 0.000 0.876 0.028
#> GSM550865 4 0.1478 0.8085 0.000 0.000 0.000 0.936 0.064
#> GSM550868 4 0.2067 0.8134 0.012 0.028 0.000 0.928 0.032
#> GSM550869 4 0.1710 0.8196 0.000 0.020 0.012 0.944 0.024
#> GSM550870 2 0.2359 0.7920 0.000 0.904 0.000 0.036 0.060
#> GSM550871 4 0.3742 0.7118 0.000 0.004 0.188 0.788 0.020
#> GSM550872 4 0.0404 0.8175 0.000 0.000 0.000 0.988 0.012
#> GSM550873 2 0.1644 0.7927 0.004 0.940 0.000 0.008 0.048
#> GSM550874 4 0.2920 0.7762 0.000 0.132 0.000 0.852 0.016
#> GSM550876 4 0.3828 0.6808 0.000 0.008 0.220 0.764 0.008
#> GSM550877 4 0.3861 0.7553 0.000 0.068 0.000 0.804 0.128
#> GSM550878 3 0.0000 0.8170 0.000 0.000 1.000 0.000 0.000
#> GSM550879 5 0.4182 0.3203 0.352 0.000 0.000 0.004 0.644
#> GSM550882 3 0.4617 0.1116 0.000 0.000 0.552 0.436 0.012
#> GSM550888 3 0.0290 0.8172 0.000 0.000 0.992 0.000 0.008
#> GSM550890 5 0.4028 0.6339 0.048 0.176 0.000 0.000 0.776
#> GSM550891 3 0.0000 0.8170 0.000 0.000 1.000 0.000 0.000
#> GSM550892 4 0.1168 0.8095 0.008 0.000 0.000 0.960 0.032
#> GSM550893 2 0.4906 -0.0859 0.000 0.496 0.000 0.480 0.024
#> GSM550895 4 0.0324 0.8192 0.000 0.004 0.000 0.992 0.004
#> GSM550896 4 0.3916 0.6557 0.000 0.256 0.000 0.732 0.012
#> GSM550898 1 0.0324 0.7938 0.992 0.000 0.000 0.004 0.004
#> GSM550899 2 0.2020 0.7596 0.000 0.900 0.000 0.000 0.100
#> GSM550900 4 0.0451 0.8198 0.000 0.008 0.000 0.988 0.004
#> GSM550901 1 0.0807 0.7916 0.976 0.012 0.000 0.000 0.012
#> GSM550902 5 0.4612 0.5031 0.204 0.000 0.052 0.008 0.736
#> GSM550904 5 0.4449 -0.0630 0.484 0.000 0.000 0.004 0.512
#> GSM550908 3 0.0290 0.8172 0.000 0.000 0.992 0.000 0.008
#> GSM550912 2 0.1830 0.7923 0.004 0.932 0.000 0.012 0.052
#> GSM550914 5 0.4268 0.5531 0.016 0.272 0.000 0.004 0.708
#> GSM550918 2 0.1732 0.7886 0.000 0.920 0.000 0.000 0.080
#> GSM550922 3 0.4392 0.3587 0.000 0.380 0.612 0.000 0.008
#> GSM550923 1 0.0000 0.7937 1.000 0.000 0.000 0.000 0.000
#> GSM550925 1 0.5141 0.6031 0.732 0.068 0.000 0.164 0.036
#> GSM550802 5 0.6303 0.4063 0.000 0.196 0.000 0.280 0.524
#> GSM550812 5 0.5358 0.5415 0.020 0.296 0.012 0.024 0.648
#> GSM550831 1 0.1357 0.7816 0.948 0.000 0.000 0.004 0.048
#> GSM550847 1 0.0162 0.7936 0.996 0.000 0.000 0.004 0.000
#> GSM550860 4 0.1041 0.8174 0.000 0.000 0.032 0.964 0.004
#> GSM550875 4 0.5841 0.2126 0.400 0.044 0.004 0.532 0.020
#> GSM550880 1 0.6186 0.1014 0.500 0.044 0.000 0.048 0.408
#> GSM550881 3 0.0510 0.8170 0.000 0.000 0.984 0.000 0.016
#> GSM550883 3 0.2077 0.7944 0.000 0.000 0.908 0.008 0.084
#> GSM550884 4 0.7163 0.4086 0.016 0.064 0.088 0.532 0.300
#> GSM550910 3 0.6687 0.0341 0.000 0.248 0.420 0.000 0.332
#> GSM550916 1 0.1670 0.7764 0.936 0.000 0.000 0.052 0.012
#> GSM550920 2 0.4582 0.2665 0.000 0.572 0.416 0.000 0.012
cbind(get_classes(res, k = 6), get_membership(res, k = 6))
#> class entropy silhouette p1 p2 p3 p4 p5 p6
#> GSM550785 1 0.0790 0.8302 0.968 0.000 0.000 0.000 0.000 0.032
#> GSM550786 6 0.5848 0.4788 0.000 0.072 0.188 0.000 0.116 0.624
#> GSM550788 2 0.4844 -0.0495 0.000 0.500 0.000 0.456 0.012 0.032
#> GSM550789 2 0.0603 0.7935 0.000 0.980 0.000 0.004 0.016 0.000
#> GSM550790 1 0.0363 0.8286 0.988 0.000 0.000 0.000 0.000 0.012
#> GSM550791 1 0.1327 0.8285 0.936 0.000 0.000 0.000 0.000 0.064
#> GSM550792 2 0.6920 0.1064 0.348 0.416 0.000 0.004 0.156 0.076
#> GSM550796 2 0.0547 0.7929 0.000 0.980 0.000 0.000 0.020 0.000
#> GSM550797 2 0.0458 0.7936 0.000 0.984 0.000 0.000 0.016 0.000
#> GSM550799 3 0.2536 0.6911 0.000 0.116 0.864 0.000 0.000 0.020
#> GSM550800 4 0.4818 0.0692 0.000 0.460 0.000 0.496 0.008 0.036
#> GSM550801 2 0.1059 0.7934 0.000 0.964 0.000 0.004 0.016 0.016
#> GSM550804 2 0.5892 0.0584 0.004 0.460 0.000 0.000 0.356 0.180
#> GSM550806 3 0.1434 0.7288 0.000 0.000 0.940 0.048 0.000 0.012
#> GSM550807 2 0.1218 0.7938 0.000 0.956 0.000 0.004 0.028 0.012
#> GSM550808 2 0.4644 0.0961 0.000 0.524 0.000 0.004 0.440 0.032
#> GSM550809 6 0.3647 0.5525 0.000 0.000 0.000 0.000 0.360 0.640
#> GSM550810 2 0.3473 0.6827 0.000 0.780 0.000 0.004 0.192 0.024
#> GSM550811 6 0.3819 0.5498 0.004 0.000 0.000 0.000 0.372 0.624
#> GSM550813 2 0.3198 0.7536 0.000 0.844 0.000 0.012 0.084 0.060
#> GSM550814 2 0.6356 0.3959 0.000 0.540 0.000 0.236 0.164 0.060
#> GSM550815 2 0.1334 0.7883 0.000 0.948 0.000 0.000 0.032 0.020
#> GSM550816 5 0.2794 0.5659 0.000 0.080 0.000 0.000 0.860 0.060
#> GSM550817 3 0.5034 0.3916 0.000 0.032 0.584 0.000 0.352 0.032
#> GSM550818 5 0.4167 0.2726 0.000 0.000 0.368 0.000 0.612 0.020
#> GSM550819 5 0.4716 0.4960 0.000 0.020 0.000 0.084 0.708 0.188
#> GSM550820 6 0.5604 0.4061 0.144 0.000 0.000 0.000 0.404 0.452
#> GSM550821 5 0.4689 0.5292 0.000 0.128 0.004 0.000 0.696 0.172
#> GSM550822 5 0.5404 0.3770 0.000 0.312 0.000 0.000 0.548 0.140
#> GSM550826 6 0.4147 0.6683 0.044 0.000 0.044 0.000 0.136 0.776
#> GSM550832 2 0.1321 0.7895 0.000 0.952 0.000 0.004 0.024 0.020
#> GSM550833 2 0.0777 0.7924 0.000 0.972 0.000 0.004 0.024 0.000
#> GSM550835 2 0.3198 0.5562 0.000 0.740 0.260 0.000 0.000 0.000
#> GSM550836 3 0.0000 0.7466 0.000 0.000 1.000 0.000 0.000 0.000
#> GSM550837 2 0.2573 0.7515 0.000 0.864 0.000 0.000 0.024 0.112
#> GSM550838 6 0.3742 0.5674 0.000 0.000 0.004 0.000 0.348 0.648
#> GSM550841 3 0.5761 0.3133 0.000 0.080 0.536 0.000 0.344 0.040
#> GSM550842 2 0.4640 0.0807 0.000 0.528 0.004 0.000 0.436 0.032
#> GSM550846 5 0.3352 0.5266 0.000 0.032 0.000 0.000 0.792 0.176
#> GSM550849 1 0.2825 0.7917 0.880 0.056 0.000 0.004 0.032 0.028
#> GSM550850 1 0.1934 0.8115 0.916 0.000 0.000 0.000 0.044 0.040
#> GSM550851 2 0.1003 0.7909 0.000 0.964 0.000 0.000 0.016 0.020
#> GSM550852 2 0.5587 0.1177 0.016 0.472 0.000 0.004 0.432 0.076
#> GSM550853 2 0.5958 0.0116 0.000 0.452 0.000 0.392 0.016 0.140
#> GSM550855 2 0.2069 0.7694 0.000 0.908 0.000 0.068 0.020 0.004
#> GSM550856 2 0.2203 0.7604 0.000 0.896 0.000 0.084 0.016 0.004
#> GSM550861 2 0.0291 0.7941 0.000 0.992 0.000 0.004 0.000 0.004
#> GSM550863 5 0.6004 0.0920 0.000 0.000 0.000 0.244 0.416 0.340
#> GSM550864 2 0.1564 0.7904 0.000 0.936 0.000 0.000 0.024 0.040
#> GSM550866 2 0.3841 0.2963 0.000 0.616 0.000 0.380 0.004 0.000
#> GSM550867 1 0.1863 0.8050 0.896 0.000 0.000 0.000 0.000 0.104
#> GSM550885 6 0.3756 0.2276 0.400 0.000 0.000 0.000 0.000 0.600
#> GSM550886 3 0.6139 0.2103 0.000 0.380 0.492 0.012 0.056 0.060
#> GSM550887 2 0.1003 0.7912 0.000 0.964 0.000 0.000 0.016 0.020
#> GSM550889 4 0.0291 0.8033 0.000 0.000 0.000 0.992 0.004 0.004
#> GSM550894 2 0.1599 0.7875 0.000 0.940 0.000 0.008 0.024 0.028
#> GSM550897 4 0.3021 0.7914 0.044 0.020 0.000 0.860 0.000 0.076
#> GSM550903 2 0.0891 0.7924 0.000 0.968 0.000 0.000 0.008 0.024
#> GSM550905 2 0.3441 0.7037 0.000 0.812 0.008 0.000 0.044 0.136
#> GSM550906 2 0.1065 0.7927 0.000 0.964 0.000 0.008 0.008 0.020
#> GSM550907 3 0.1765 0.7278 0.000 0.000 0.924 0.000 0.052 0.024
#> GSM550909 5 0.2796 0.5524 0.000 0.064 0.004 0.004 0.872 0.056
#> GSM550911 3 0.2979 0.6889 0.000 0.000 0.840 0.000 0.116 0.044
#> GSM550913 2 0.0291 0.7949 0.000 0.992 0.000 0.000 0.004 0.004
#> GSM550915 5 0.3565 0.3998 0.004 0.004 0.000 0.000 0.716 0.276
#> GSM550917 2 0.2213 0.7761 0.000 0.904 0.000 0.004 0.048 0.044
#> GSM550919 1 0.6266 0.2285 0.488 0.360 0.000 0.004 0.060 0.088
#> GSM550921 3 0.0000 0.7466 0.000 0.000 1.000 0.000 0.000 0.000
#> GSM550924 1 0.6999 0.4752 0.592 0.120 0.112 0.004 0.088 0.084
#> GSM550926 4 0.5211 0.6366 0.000 0.196 0.000 0.676 0.076 0.052
#> GSM550927 2 0.1341 0.7892 0.000 0.948 0.000 0.000 0.028 0.024
#> GSM550787 1 0.3465 0.7531 0.828 0.084 0.008 0.000 0.004 0.076
#> GSM550793 3 0.4479 0.3970 0.000 0.000 0.600 0.024 0.008 0.368
#> GSM550794 1 0.6445 0.4085 0.540 0.044 0.000 0.028 0.292 0.096
#> GSM550795 6 0.5154 0.5571 0.028 0.000 0.000 0.080 0.240 0.652
#> GSM550798 1 0.1141 0.8270 0.948 0.000 0.000 0.000 0.000 0.052
#> GSM550803 1 0.0865 0.8296 0.964 0.000 0.000 0.000 0.000 0.036
#> GSM550805 1 0.6319 0.6188 0.676 0.032 0.076 0.096 0.052 0.068
#> GSM550823 4 0.0405 0.8030 0.000 0.000 0.000 0.988 0.004 0.008
#> GSM550824 1 0.1204 0.8263 0.944 0.000 0.000 0.000 0.000 0.056
#> GSM550825 3 0.3695 0.5042 0.272 0.000 0.712 0.000 0.000 0.016
#> GSM550827 5 0.6207 0.3372 0.032 0.232 0.000 0.008 0.560 0.168
#> GSM550828 1 0.1204 0.8291 0.944 0.000 0.000 0.000 0.000 0.056
#> GSM550829 1 0.2501 0.7989 0.872 0.000 0.016 0.000 0.004 0.108
#> GSM550830 4 0.0862 0.8052 0.000 0.016 0.000 0.972 0.004 0.008
#> GSM550834 1 0.4976 0.4351 0.592 0.012 0.000 0.000 0.340 0.056
#> GSM550839 4 0.4514 0.5842 0.000 0.000 0.264 0.680 0.040 0.016
#> GSM550840 1 0.4794 0.5822 0.676 0.000 0.000 0.248 0.036 0.040
#> GSM550843 3 0.0603 0.7428 0.000 0.000 0.980 0.000 0.004 0.016
#> GSM550844 1 0.3426 0.6080 0.720 0.000 0.000 0.004 0.000 0.276
#> GSM550845 4 0.6426 0.4516 0.000 0.216 0.000 0.508 0.044 0.232
#> GSM550848 5 0.6052 0.3623 0.180 0.140 0.000 0.000 0.604 0.076
#> GSM550854 1 0.1327 0.8242 0.936 0.000 0.000 0.000 0.000 0.064
#> GSM550857 3 0.4988 0.0852 0.068 0.000 0.484 0.000 0.000 0.448
#> GSM550858 1 0.2996 0.6852 0.772 0.000 0.000 0.000 0.000 0.228
#> GSM550859 1 0.1765 0.8112 0.904 0.000 0.000 0.000 0.000 0.096
#> GSM550862 4 0.3593 0.7288 0.132 0.000 0.000 0.800 0.004 0.064
#> GSM550865 4 0.2848 0.7434 0.000 0.000 0.000 0.816 0.008 0.176
#> GSM550868 4 0.3600 0.7622 0.012 0.008 0.000 0.824 0.096 0.060
#> GSM550869 4 0.2789 0.7787 0.000 0.016 0.012 0.884 0.032 0.056
#> GSM550870 2 0.2322 0.7827 0.000 0.896 0.000 0.008 0.024 0.072
#> GSM550871 4 0.4233 0.6894 0.000 0.008 0.192 0.748 0.016 0.036
#> GSM550872 4 0.1225 0.8020 0.000 0.000 0.000 0.952 0.012 0.036
#> GSM550873 2 0.3900 0.7134 0.020 0.796 0.000 0.004 0.128 0.052
#> GSM550874 4 0.1320 0.8064 0.000 0.036 0.000 0.948 0.000 0.016
#> GSM550876 4 0.4244 0.6350 0.000 0.008 0.236 0.716 0.004 0.036
#> GSM550877 4 0.3954 0.7257 0.000 0.056 0.000 0.764 0.008 0.172
#> GSM550878 3 0.0146 0.7464 0.000 0.000 0.996 0.000 0.000 0.004
#> GSM550879 6 0.3767 0.6609 0.088 0.000 0.000 0.000 0.132 0.780
#> GSM550882 3 0.3922 0.3906 0.000 0.000 0.664 0.320 0.000 0.016
#> GSM550888 3 0.0000 0.7466 0.000 0.000 1.000 0.000 0.000 0.000
#> GSM550890 5 0.3766 0.4904 0.000 0.032 0.000 0.000 0.736 0.232
#> GSM550891 3 0.0000 0.7466 0.000 0.000 1.000 0.000 0.000 0.000
#> GSM550892 4 0.1814 0.7917 0.000 0.000 0.000 0.900 0.000 0.100
#> GSM550893 4 0.4583 0.4997 0.000 0.336 0.000 0.620 0.008 0.036
#> GSM550895 4 0.1194 0.8052 0.000 0.008 0.000 0.956 0.004 0.032
#> GSM550896 4 0.3031 0.7728 0.000 0.100 0.000 0.852 0.016 0.032
#> GSM550898 1 0.0260 0.8309 0.992 0.000 0.000 0.000 0.000 0.008
#> GSM550899 2 0.2350 0.7734 0.000 0.888 0.000 0.000 0.076 0.036
#> GSM550900 4 0.0777 0.8013 0.000 0.000 0.000 0.972 0.004 0.024
#> GSM550901 1 0.0862 0.8304 0.972 0.008 0.000 0.000 0.004 0.016
#> GSM550902 6 0.3904 0.6417 0.028 0.000 0.076 0.008 0.076 0.812
#> GSM550904 5 0.4941 -0.3074 0.064 0.000 0.000 0.000 0.492 0.444
#> GSM550908 3 0.0146 0.7462 0.000 0.000 0.996 0.000 0.000 0.004
#> GSM550912 2 0.4124 0.7002 0.008 0.772 0.000 0.008 0.144 0.068
#> GSM550914 5 0.3858 0.5134 0.000 0.044 0.000 0.000 0.740 0.216
#> GSM550918 2 0.4231 0.6996 0.016 0.768 0.000 0.004 0.076 0.136
#> GSM550922 3 0.4209 0.3463 0.000 0.384 0.596 0.000 0.020 0.000
#> GSM550923 1 0.0000 0.8304 1.000 0.000 0.000 0.000 0.000 0.000
#> GSM550925 1 0.3232 0.7825 0.860 0.044 0.000 0.036 0.008 0.052
#> GSM550802 5 0.3325 0.5456 0.000 0.036 0.000 0.092 0.840 0.032
#> GSM550812 5 0.1321 0.5561 0.000 0.024 0.000 0.004 0.952 0.020
#> GSM550831 1 0.2843 0.7815 0.848 0.000 0.000 0.000 0.116 0.036
#> GSM550847 1 0.0000 0.8304 1.000 0.000 0.000 0.000 0.000 0.000
#> GSM550860 4 0.1564 0.8030 0.000 0.000 0.040 0.936 0.000 0.024
#> GSM550875 4 0.5042 0.6458 0.204 0.024 0.016 0.708 0.024 0.024
#> GSM550880 5 0.5777 0.4102 0.120 0.028 0.000 0.120 0.676 0.056
#> GSM550881 3 0.1010 0.7376 0.000 0.000 0.960 0.000 0.004 0.036
#> GSM550883 3 0.3808 0.5349 0.000 0.000 0.700 0.012 0.004 0.284
#> GSM550884 5 0.6098 0.1255 0.000 0.028 0.000 0.344 0.488 0.140
#> GSM550910 5 0.5732 0.4487 0.000 0.048 0.152 0.000 0.628 0.172
#> GSM550916 1 0.1168 0.8260 0.956 0.000 0.000 0.016 0.000 0.028
#> GSM550920 3 0.4459 0.5386 0.008 0.268 0.688 0.004 0.008 0.024
Heatmaps for the consensus matrix. It visualizes the probability of two samples to be in a same group.
consensus_heatmap(res, k = 2)
consensus_heatmap(res, k = 3)
consensus_heatmap(res, k = 4)
consensus_heatmap(res, k = 5)
consensus_heatmap(res, k = 6)
Heatmaps for the membership of samples in all partitions to see how consistent they are:
membership_heatmap(res, k = 2)
membership_heatmap(res, k = 3)
membership_heatmap(res, k = 4)
membership_heatmap(res, k = 5)
membership_heatmap(res, k = 6)
As soon as we have had the classes for columns, we can look for signatures which are significantly different between classes which can be candidate marks for certain classes. Following are the heatmaps for signatures.
Signature heatmaps where rows are scaled:
get_signatures(res, k = 2)
get_signatures(res, k = 3)
get_signatures(res, k = 4)
get_signatures(res, k = 5)
get_signatures(res, k = 6)
Signature heatmaps where rows are not scaled:
get_signatures(res, k = 2, scale_rows = FALSE)
get_signatures(res, k = 3, scale_rows = FALSE)
get_signatures(res, k = 4, scale_rows = FALSE)
get_signatures(res, k = 5, scale_rows = FALSE)
get_signatures(res, k = 6, scale_rows = FALSE)
Compare the overlap of signatures from different k:
compare_signatures(res)
get_signature() returns a data frame invisibly. TO get the list of signatures, the function
call should be assigned to a variable explicitly. In following code, if plot argument is set
to FALSE, no heatmap is plotted while only the differential analysis is performed.
# code only for demonstration
tb = get_signature(res, k = ..., plot = FALSE)
An example of the output of tb is:
#> which_row fdr mean_1 mean_2 scaled_mean_1 scaled_mean_2 km
#> 1 38 0.042760348 8.373488 9.131774 -0.5533452 0.5164555 1
#> 2 40 0.018707592 7.106213 8.469186 -0.6173731 0.5762149 1
#> 3 55 0.019134737 10.221463 11.207825 -0.6159697 0.5749050 1
#> 4 59 0.006059896 5.921854 7.869574 -0.6899429 0.6439467 1
#> 5 60 0.018055526 8.928898 10.211722 -0.6204761 0.5791110 1
#> 6 98 0.009384629 15.714769 14.887706 0.6635654 -0.6193277 2
...
The columns in tb are:
which_row: row indices corresponding to the input matrix.fdr: FDR for the differential test. mean_x: The mean value in group x.scaled_mean_x: The mean value in group x after rows are scaled.km: Row groups if k-means clustering is applied to rows.UMAP plot which shows how samples are separated.
dimension_reduction(res, k = 2, method = "UMAP")
dimension_reduction(res, k = 3, method = "UMAP")
dimension_reduction(res, k = 4, method = "UMAP")
dimension_reduction(res, k = 5, method = "UMAP")
dimension_reduction(res, k = 6, method = "UMAP")
Following heatmap shows how subgroups are split when increasing k:
collect_classes(res)
Test correlation between subgroups and known annotations. If the known annotation is numeric, one-way ANOVA test is applied, and if the known annotation is discrete, chi-squared contingency table test is applied.
test_to_known_factors(res)
#> n disease.state(p) k
#> SD:NMF 133 6.11e-04 2
#> SD:NMF 133 4.18e-04 3
#> SD:NMF 129 9.87e-05 4
#> SD:NMF 109 3.96e-05 5
#> SD:NMF 105 3.09e-05 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 51776 rows and 143 columns.
#> Top rows (1000, 2000, 3000, 4000, 5000) are extracted by 'CV' method.
#> Subgroups are detected by 'hclust' method.
#> Performed in total 1250 partitions by row resampling.
#> Best k for subgroups seems to be 3.
#>
#> Following methods can be applied to this 'ConsensusPartition' object:
#> [1] "cola_report" "collect_classes" "collect_plots"
#> [4] "collect_stats" "colnames" "compare_signatures"
#> [7] "consensus_heatmap" "dimension_reduction" "functional_enrichment"
#> [10] "get_anno_col" "get_anno" "get_classes"
#> [13] "get_consensus" "get_matrix" "get_membership"
#> [16] "get_param" "get_signatures" "get_stats"
#> [19] "is_best_k" "is_stable_k" "membership_heatmap"
#> [22] "ncol" "nrow" "plot_ecdf"
#> [25] "rownames" "select_partition_number" "show"
#> [28] "suggest_best_k" "test_to_known_factors"
collect_plots() function collects all the plots made from res for all k (number of partitions)
into one single page to provide an easy and fast comparison between different k.
collect_plots(res)
The plots are:
k and the heatmap of
predicted classes for each k.k.k.k.All the plots in panels can be made by individual functions and they are plotted later in this section.
select_partition_number() produces several plots showing different
statistics for choosing “optimized” k. There are following statistics:
k;k, the area increased is defined as \(A_k - A_{k-1}\).The detailed explanations of these statistics can be found in the cola vignette.
Generally speaking, lower PAC score, higher mean silhouette score or higher
concordance corresponds to better partition. Rand index and Jaccard index
measure how similar the current partition is compared to partition with k-1.
If they are too similar, we won't accept k is better than k-1.
select_partition_number(res)
The numeric values for all these statistics can be obtained by get_stats().
get_stats(res)
#> k 1-PAC mean_silhouette concordance area_increased Rand Jaccard
#> 2 2 0.631 0.774 0.907 0.2824 0.728 0.728
#> 3 3 0.211 0.491 0.697 0.9720 0.617 0.487
#> 4 4 0.287 0.299 0.601 0.1671 0.758 0.512
#> 5 5 0.366 0.447 0.662 0.0750 0.787 0.504
#> 6 6 0.416 0.396 0.626 0.0471 0.972 0.901
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
#> GSM550785 2 0.0000 0.91096 0.000 1.000
#> GSM550786 2 0.9732 0.08719 0.404 0.596
#> GSM550788 2 0.0000 0.91096 0.000 1.000
#> GSM550789 2 0.0000 0.91096 0.000 1.000
#> GSM550790 2 0.0000 0.91096 0.000 1.000
#> GSM550791 2 0.0000 0.91096 0.000 1.000
#> GSM550792 2 0.2948 0.87947 0.052 0.948
#> GSM550796 2 0.0376 0.90932 0.004 0.996
#> GSM550797 2 0.0000 0.91096 0.000 1.000
#> GSM550799 2 0.9988 -0.24967 0.480 0.520
#> GSM550800 2 0.0000 0.91096 0.000 1.000
#> GSM550801 2 0.0000 0.91096 0.000 1.000
#> GSM550804 2 0.0000 0.91096 0.000 1.000
#> GSM550806 1 0.9323 0.66200 0.652 0.348
#> GSM550807 2 0.0000 0.91096 0.000 1.000
#> GSM550808 2 0.5178 0.81200 0.116 0.884
#> GSM550809 2 0.0938 0.90564 0.012 0.988
#> GSM550810 2 0.2778 0.88387 0.048 0.952
#> GSM550811 2 0.2423 0.88841 0.040 0.960
#> GSM550813 2 0.0376 0.90920 0.004 0.996
#> GSM550814 2 0.1633 0.89869 0.024 0.976
#> GSM550815 2 0.0000 0.91096 0.000 1.000
#> GSM550816 2 0.0672 0.90765 0.008 0.992
#> GSM550817 1 0.9358 0.65137 0.648 0.352
#> GSM550818 1 0.9358 0.65137 0.648 0.352
#> GSM550819 2 0.5519 0.79347 0.128 0.872
#> GSM550820 2 0.2423 0.88966 0.040 0.960
#> GSM550821 2 0.7528 0.64963 0.216 0.784
#> GSM550822 2 0.0000 0.91096 0.000 1.000
#> GSM550826 2 0.8327 0.55507 0.264 0.736
#> GSM550832 2 0.3584 0.86602 0.068 0.932
#> GSM550833 2 0.0000 0.91096 0.000 1.000
#> GSM550835 2 0.9754 0.06653 0.408 0.592
#> GSM550836 1 0.0000 0.73026 1.000 0.000
#> GSM550837 2 0.9815 0.00925 0.420 0.580
#> GSM550838 2 0.0938 0.90564 0.012 0.988
#> GSM550841 1 0.9491 0.62704 0.632 0.368
#> GSM550842 2 0.9286 0.32032 0.344 0.656
#> GSM550846 2 0.0000 0.91096 0.000 1.000
#> GSM550849 2 0.1843 0.89716 0.028 0.972
#> GSM550850 2 0.0000 0.91096 0.000 1.000
#> GSM550851 2 0.9522 0.22060 0.372 0.628
#> GSM550852 2 0.3431 0.87043 0.064 0.936
#> GSM550853 2 0.0000 0.91096 0.000 1.000
#> GSM550855 2 0.0000 0.91096 0.000 1.000
#> GSM550856 2 0.0000 0.91096 0.000 1.000
#> GSM550861 2 0.0000 0.91096 0.000 1.000
#> GSM550863 2 0.0000 0.91096 0.000 1.000
#> GSM550864 2 0.0000 0.91096 0.000 1.000
#> GSM550866 2 0.0000 0.91096 0.000 1.000
#> GSM550867 2 0.0000 0.91096 0.000 1.000
#> GSM550885 2 0.0000 0.91096 0.000 1.000
#> GSM550886 2 0.9909 -0.09155 0.444 0.556
#> GSM550887 2 0.0000 0.91096 0.000 1.000
#> GSM550889 2 0.0000 0.91096 0.000 1.000
#> GSM550894 2 0.3733 0.86218 0.072 0.928
#> GSM550897 2 0.0376 0.90921 0.004 0.996
#> GSM550903 2 0.0000 0.91096 0.000 1.000
#> GSM550905 2 0.8661 0.49069 0.288 0.712
#> GSM550906 2 0.0000 0.91096 0.000 1.000
#> GSM550907 1 0.0000 0.73026 1.000 0.000
#> GSM550909 2 0.4161 0.85220 0.084 0.916
#> GSM550911 1 0.0000 0.73026 1.000 0.000
#> GSM550913 2 0.0000 0.91096 0.000 1.000
#> GSM550915 2 0.0000 0.91096 0.000 1.000
#> GSM550917 2 0.0000 0.91096 0.000 1.000
#> GSM550919 2 0.0000 0.91096 0.000 1.000
#> GSM550921 1 0.0000 0.73026 1.000 0.000
#> GSM550924 2 0.7883 0.62130 0.236 0.764
#> GSM550926 2 0.0376 0.90932 0.004 0.996
#> GSM550927 2 0.0000 0.91096 0.000 1.000
#> GSM550787 2 0.7299 0.67574 0.204 0.796
#> GSM550793 2 0.9970 -0.19887 0.468 0.532
#> GSM550794 2 0.2778 0.88245 0.048 0.952
#> GSM550795 2 0.0000 0.91096 0.000 1.000
#> GSM550798 2 0.7056 0.69324 0.192 0.808
#> GSM550803 2 0.1184 0.90362 0.016 0.984
#> GSM550805 2 0.3733 0.86281 0.072 0.928
#> GSM550823 2 0.0672 0.90770 0.008 0.992
#> GSM550824 2 0.0000 0.91096 0.000 1.000
#> GSM550825 1 0.9963 0.40873 0.536 0.464
#> GSM550827 2 0.0376 0.90920 0.004 0.996
#> GSM550828 2 0.0000 0.91096 0.000 1.000
#> GSM550829 2 0.9996 -0.27538 0.488 0.512
#> GSM550830 2 0.0000 0.91096 0.000 1.000
#> GSM550834 2 0.0000 0.91096 0.000 1.000
#> GSM550839 1 0.9909 0.48119 0.556 0.444
#> GSM550840 2 0.0000 0.91096 0.000 1.000
#> GSM550843 1 0.9358 0.65769 0.648 0.352
#> GSM550844 2 0.3879 0.85898 0.076 0.924
#> GSM550845 2 0.0000 0.91096 0.000 1.000
#> GSM550848 2 0.0000 0.91096 0.000 1.000
#> GSM550854 2 0.0000 0.91096 0.000 1.000
#> GSM550857 1 0.0000 0.73026 1.000 0.000
#> GSM550858 2 0.0000 0.91096 0.000 1.000
#> GSM550859 2 0.0000 0.91096 0.000 1.000
#> GSM550862 2 0.0000 0.91096 0.000 1.000
#> GSM550865 2 0.0000 0.91096 0.000 1.000
#> GSM550868 2 0.0000 0.91096 0.000 1.000
#> GSM550869 2 0.5737 0.79133 0.136 0.864
#> GSM550870 2 0.0000 0.91096 0.000 1.000
#> GSM550871 1 0.9909 0.48119 0.556 0.444
#> GSM550872 2 0.0000 0.91096 0.000 1.000
#> GSM550873 2 0.4690 0.83330 0.100 0.900
#> GSM550874 2 0.0000 0.91096 0.000 1.000
#> GSM550876 1 0.8861 0.70289 0.696 0.304
#> GSM550877 2 0.0000 0.91096 0.000 1.000
#> GSM550878 1 0.8555 0.71548 0.720 0.280
#> GSM550879 2 0.0000 0.91096 0.000 1.000
#> GSM550882 1 0.8713 0.70793 0.708 0.292
#> GSM550888 1 0.0000 0.73026 1.000 0.000
#> GSM550890 2 0.0000 0.91096 0.000 1.000
#> GSM550891 1 0.0000 0.73026 1.000 0.000
#> GSM550892 2 0.0000 0.91096 0.000 1.000
#> GSM550893 2 0.0376 0.90932 0.004 0.996
#> GSM550895 2 0.0000 0.91096 0.000 1.000
#> GSM550896 2 0.0000 0.91096 0.000 1.000
#> GSM550898 2 0.0000 0.91096 0.000 1.000
#> GSM550899 2 0.0000 0.91096 0.000 1.000
#> GSM550900 2 0.0000 0.91096 0.000 1.000
#> GSM550901 2 0.0000 0.91096 0.000 1.000
#> GSM550902 2 0.9248 0.35215 0.340 0.660
#> GSM550904 2 0.2948 0.88033 0.052 0.948
#> GSM550908 1 0.0000 0.73026 1.000 0.000
#> GSM550912 2 0.0376 0.90920 0.004 0.996
#> GSM550914 2 0.0000 0.91096 0.000 1.000
#> GSM550918 2 0.0000 0.91096 0.000 1.000
#> GSM550922 1 0.9983 0.37430 0.524 0.476
#> GSM550923 2 0.2778 0.88196 0.048 0.952
#> GSM550925 2 0.0000 0.91096 0.000 1.000
#> GSM550802 2 0.2603 0.88552 0.044 0.956
#> GSM550812 2 0.2778 0.88308 0.048 0.952
#> GSM550831 2 0.0000 0.91096 0.000 1.000
#> GSM550847 2 0.0000 0.91096 0.000 1.000
#> GSM550860 2 0.9661 0.15474 0.392 0.608
#> GSM550875 2 0.3879 0.85898 0.076 0.924
#> GSM550880 2 0.0000 0.91096 0.000 1.000
#> GSM550881 1 0.8713 0.70810 0.708 0.292
#> GSM550883 1 0.8713 0.70793 0.708 0.292
#> GSM550884 2 0.4161 0.85122 0.084 0.916
#> GSM550910 1 0.3431 0.73052 0.936 0.064
#> GSM550916 2 0.1843 0.89641 0.028 0.972
#> GSM550920 2 0.9993 -0.25964 0.484 0.516
cbind(get_classes(res, k = 3), get_membership(res, k = 3))
#> class entropy silhouette p1 p2 p3
#> GSM550785 1 0.2959 0.6726 0.900 0.100 0.000
#> GSM550786 2 0.7157 0.1490 0.056 0.668 0.276
#> GSM550788 2 0.4399 0.6505 0.188 0.812 0.000
#> GSM550789 2 0.4399 0.6503 0.188 0.812 0.000
#> GSM550790 1 0.1753 0.6584 0.952 0.048 0.000
#> GSM550791 1 0.2625 0.6639 0.916 0.084 0.000
#> GSM550792 1 0.7169 0.3341 0.520 0.456 0.024
#> GSM550796 2 0.4178 0.6498 0.172 0.828 0.000
#> GSM550797 2 0.4399 0.6503 0.188 0.812 0.000
#> GSM550799 2 0.5835 -0.0545 0.000 0.660 0.340
#> GSM550800 2 0.6168 0.2283 0.412 0.588 0.000
#> GSM550801 2 0.4399 0.6503 0.188 0.812 0.000
#> GSM550804 2 0.5905 0.4451 0.352 0.648 0.000
#> GSM550806 3 0.8227 0.5427 0.080 0.384 0.536
#> GSM550807 2 0.4504 0.6479 0.196 0.804 0.000
#> GSM550808 2 0.4665 0.5991 0.100 0.852 0.048
#> GSM550809 1 0.4575 0.6506 0.812 0.184 0.004
#> GSM550810 2 0.3573 0.6244 0.120 0.876 0.004
#> GSM550811 1 0.6879 0.4077 0.556 0.428 0.016
#> GSM550813 2 0.5810 0.4477 0.336 0.664 0.000
#> GSM550814 2 0.5982 0.3966 0.328 0.668 0.004
#> GSM550815 2 0.4399 0.6503 0.188 0.812 0.000
#> GSM550816 2 0.4842 0.6125 0.224 0.776 0.000
#> GSM550817 3 0.6260 0.4367 0.000 0.448 0.552
#> GSM550818 3 0.6252 0.4414 0.000 0.444 0.556
#> GSM550819 2 0.7141 0.0804 0.368 0.600 0.032
#> GSM550820 1 0.5450 0.6277 0.760 0.228 0.012
#> GSM550821 2 0.6383 0.5013 0.128 0.768 0.104
#> GSM550822 2 0.4399 0.6503 0.188 0.812 0.000
#> GSM550826 1 0.9105 0.3042 0.500 0.348 0.152
#> GSM550832 2 0.4326 0.6343 0.144 0.844 0.012
#> GSM550833 2 0.4399 0.6502 0.188 0.812 0.000
#> GSM550835 2 0.5919 0.1585 0.012 0.712 0.276
#> GSM550836 3 0.0000 0.7265 0.000 0.000 1.000
#> GSM550837 2 0.5656 0.1257 0.004 0.712 0.284
#> GSM550838 1 0.4575 0.6506 0.812 0.184 0.004
#> GSM550841 3 0.6308 0.4142 0.000 0.492 0.508
#> GSM550842 2 0.4605 0.2956 0.000 0.796 0.204
#> GSM550846 1 0.5706 0.5830 0.680 0.320 0.000
#> GSM550849 1 0.6521 0.0948 0.500 0.496 0.004
#> GSM550850 1 0.1860 0.6602 0.948 0.052 0.000
#> GSM550851 2 0.5201 0.2399 0.004 0.760 0.236
#> GSM550852 2 0.6917 0.2191 0.368 0.608 0.024
#> GSM550853 2 0.4555 0.6465 0.200 0.800 0.000
#> GSM550855 2 0.4605 0.6467 0.204 0.796 0.000
#> GSM550856 2 0.4605 0.6467 0.204 0.796 0.000
#> GSM550861 2 0.4842 0.6277 0.224 0.776 0.000
#> GSM550863 1 0.5363 0.6268 0.724 0.276 0.000
#> GSM550864 2 0.5138 0.6017 0.252 0.748 0.000
#> GSM550866 2 0.6180 0.2258 0.416 0.584 0.000
#> GSM550867 1 0.1031 0.6480 0.976 0.024 0.000
#> GSM550885 1 0.1289 0.6504 0.968 0.032 0.000
#> GSM550886 2 0.7084 0.0626 0.036 0.628 0.336
#> GSM550887 2 0.4399 0.6503 0.188 0.812 0.000
#> GSM550889 1 0.5926 0.5403 0.644 0.356 0.000
#> GSM550894 2 0.4261 0.6326 0.140 0.848 0.012
#> GSM550897 1 0.5254 0.6494 0.736 0.264 0.000
#> GSM550903 2 0.4750 0.6348 0.216 0.784 0.000
#> GSM550905 2 0.5734 0.4111 0.048 0.788 0.164
#> GSM550906 2 0.4399 0.6503 0.188 0.812 0.000
#> GSM550907 3 0.0592 0.7262 0.000 0.012 0.988
#> GSM550909 2 0.6772 0.3991 0.304 0.664 0.032
#> GSM550911 3 0.0000 0.7265 0.000 0.000 1.000
#> GSM550913 2 0.4399 0.6503 0.188 0.812 0.000
#> GSM550915 1 0.5706 0.5834 0.680 0.320 0.000
#> GSM550917 2 0.5835 0.4644 0.340 0.660 0.000
#> GSM550919 1 0.5327 0.6340 0.728 0.272 0.000
#> GSM550921 3 0.0000 0.7265 0.000 0.000 1.000
#> GSM550924 2 0.8386 0.4451 0.204 0.624 0.172
#> GSM550926 2 0.4750 0.6394 0.216 0.784 0.000
#> GSM550927 2 0.4452 0.6494 0.192 0.808 0.000
#> GSM550787 1 0.7478 0.3962 0.692 0.192 0.116
#> GSM550793 3 0.9909 0.2144 0.364 0.268 0.368
#> GSM550794 1 0.7102 0.3901 0.556 0.420 0.024
#> GSM550795 1 0.2066 0.6617 0.940 0.060 0.000
#> GSM550798 1 0.6486 0.3786 0.760 0.144 0.096
#> GSM550803 1 0.1289 0.6261 0.968 0.032 0.000
#> GSM550805 1 0.7295 0.4720 0.584 0.380 0.036
#> GSM550823 1 0.6126 0.4821 0.600 0.400 0.000
#> GSM550824 1 0.1031 0.6480 0.976 0.024 0.000
#> GSM550825 3 0.9264 0.3620 0.412 0.156 0.432
#> GSM550827 1 0.5760 0.5788 0.672 0.328 0.000
#> GSM550828 1 0.4399 0.6663 0.812 0.188 0.000
#> GSM550829 1 0.9274 -0.3058 0.456 0.160 0.384
#> GSM550830 1 0.6302 0.2343 0.520 0.480 0.000
#> GSM550834 1 0.1860 0.6602 0.948 0.052 0.000
#> GSM550839 2 0.8128 -0.3727 0.068 0.492 0.440
#> GSM550840 1 0.4702 0.6625 0.788 0.212 0.000
#> GSM550843 3 0.8362 0.5327 0.088 0.384 0.528
#> GSM550844 1 0.7245 0.4970 0.596 0.368 0.036
#> GSM550845 2 0.6192 0.2391 0.420 0.580 0.000
#> GSM550848 1 0.5431 0.6231 0.716 0.284 0.000
#> GSM550854 1 0.1031 0.6480 0.976 0.024 0.000
#> GSM550857 3 0.0000 0.7265 0.000 0.000 1.000
#> GSM550858 1 0.2796 0.6682 0.908 0.092 0.000
#> GSM550859 1 0.1031 0.6480 0.976 0.024 0.000
#> GSM550862 1 0.5058 0.6466 0.756 0.244 0.000
#> GSM550865 1 0.5560 0.6089 0.700 0.300 0.000
#> GSM550868 1 0.6126 0.4535 0.600 0.400 0.000
#> GSM550869 1 0.8355 0.3249 0.508 0.408 0.084
#> GSM550870 2 0.6180 0.2499 0.416 0.584 0.000
#> GSM550871 2 0.8128 -0.3727 0.068 0.492 0.440
#> GSM550872 1 0.5760 0.5808 0.672 0.328 0.000
#> GSM550873 2 0.7306 0.2581 0.340 0.616 0.044
#> GSM550874 2 0.4654 0.6426 0.208 0.792 0.000
#> GSM550876 3 0.8019 0.5895 0.076 0.348 0.576
#> GSM550877 2 0.4702 0.6393 0.212 0.788 0.000
#> GSM550878 3 0.7637 0.6145 0.076 0.284 0.640
#> GSM550879 1 0.4399 0.6674 0.812 0.188 0.000
#> GSM550882 3 0.8016 0.6061 0.260 0.108 0.632
#> GSM550888 3 0.0000 0.7265 0.000 0.000 1.000
#> GSM550890 1 0.5733 0.5800 0.676 0.324 0.000
#> GSM550891 3 0.0000 0.7265 0.000 0.000 1.000
#> GSM550892 1 0.5397 0.6249 0.720 0.280 0.000
#> GSM550893 1 0.6045 0.5195 0.620 0.380 0.000
#> GSM550895 1 0.6111 0.4604 0.604 0.396 0.000
#> GSM550896 1 0.6126 0.4535 0.600 0.400 0.000
#> GSM550898 1 0.1031 0.6480 0.976 0.024 0.000
#> GSM550899 2 0.5650 0.5234 0.312 0.688 0.000
#> GSM550900 1 0.6008 0.5143 0.628 0.372 0.000
#> GSM550901 1 0.5327 0.6340 0.728 0.272 0.000
#> GSM550902 1 0.9677 0.1410 0.452 0.312 0.236
#> GSM550904 1 0.6126 0.5974 0.712 0.268 0.020
#> GSM550908 3 0.0000 0.7265 0.000 0.000 1.000
#> GSM550912 2 0.5810 0.4489 0.336 0.664 0.000
#> GSM550914 1 0.5733 0.5800 0.676 0.324 0.000
#> GSM550918 2 0.5905 0.4451 0.352 0.648 0.000
#> GSM550922 2 0.6962 -0.2200 0.020 0.568 0.412
#> GSM550923 1 0.2955 0.5873 0.912 0.080 0.008
#> GSM550925 1 0.5785 0.5728 0.668 0.332 0.000
#> GSM550802 1 0.7043 0.3236 0.532 0.448 0.020
#> GSM550812 1 0.6919 0.3766 0.536 0.448 0.016
#> GSM550831 1 0.1860 0.6602 0.948 0.052 0.000
#> GSM550847 1 0.1031 0.6480 0.976 0.024 0.000
#> GSM550860 2 0.9948 -0.1465 0.352 0.364 0.284
#> GSM550875 1 0.7378 0.4322 0.560 0.404 0.036
#> GSM550880 1 0.3038 0.6702 0.896 0.104 0.000
#> GSM550881 3 0.7745 0.6079 0.260 0.092 0.648
#> GSM550883 3 0.8016 0.6061 0.260 0.108 0.632
#> GSM550884 2 0.7420 -0.0368 0.420 0.544 0.036
#> GSM550910 3 0.4233 0.7106 0.004 0.160 0.836
#> GSM550916 1 0.2743 0.6265 0.928 0.052 0.020
#> GSM550920 2 0.7379 -0.0755 0.040 0.584 0.376
cbind(get_classes(res, k = 4), get_membership(res, k = 4))
#> class entropy silhouette p1 p2 p3 p4
#> GSM550785 4 0.4382 0.25429 0.296 0.000 0.000 0.704
#> GSM550786 2 0.6979 0.16856 0.268 0.620 0.040 0.072
#> GSM550788 2 0.4855 0.45951 0.000 0.600 0.000 0.400
#> GSM550789 2 0.4843 0.46545 0.000 0.604 0.000 0.396
#> GSM550790 4 0.5320 0.04537 0.416 0.012 0.000 0.572
#> GSM550791 4 0.5835 0.13060 0.372 0.040 0.000 0.588
#> GSM550792 4 0.7146 0.32059 0.212 0.228 0.000 0.560
#> GSM550796 2 0.5364 0.46683 0.016 0.592 0.000 0.392
#> GSM550797 2 0.4843 0.46545 0.000 0.604 0.000 0.396
#> GSM550799 2 0.6080 0.06763 0.292 0.644 0.056 0.008
#> GSM550800 4 0.4730 0.08619 0.000 0.364 0.000 0.636
#> GSM550801 2 0.4843 0.46545 0.000 0.604 0.000 0.396
#> GSM550804 4 0.4855 -0.05593 0.000 0.400 0.000 0.600
#> GSM550806 2 0.8877 -0.34031 0.316 0.368 0.268 0.048
#> GSM550807 2 0.4877 0.45627 0.000 0.592 0.000 0.408
#> GSM550808 2 0.7193 0.42785 0.140 0.580 0.012 0.268
#> GSM550809 4 0.6599 0.16059 0.340 0.096 0.000 0.564
#> GSM550810 2 0.6415 0.43192 0.100 0.612 0.000 0.288
#> GSM550811 4 0.6948 0.34546 0.204 0.208 0.000 0.588
#> GSM550813 4 0.5731 -0.10105 0.028 0.428 0.000 0.544
#> GSM550814 4 0.6299 -0.03858 0.060 0.420 0.000 0.520
#> GSM550815 2 0.4843 0.46545 0.000 0.604 0.000 0.396
#> GSM550816 2 0.6182 0.31887 0.052 0.520 0.000 0.428
#> GSM550817 2 0.7542 -0.28025 0.232 0.488 0.280 0.000
#> GSM550818 2 0.7551 -0.28890 0.228 0.484 0.288 0.000
#> GSM550819 4 0.6991 0.20806 0.136 0.324 0.000 0.540
#> GSM550820 4 0.6725 0.09697 0.348 0.104 0.000 0.548
#> GSM550821 2 0.7200 0.31793 0.228 0.552 0.000 0.220
#> GSM550822 2 0.4843 0.46545 0.000 0.604 0.000 0.396
#> GSM550826 1 0.8645 0.42215 0.408 0.212 0.044 0.336
#> GSM550832 2 0.6391 0.45525 0.084 0.588 0.000 0.328
#> GSM550833 2 0.5112 0.46476 0.008 0.608 0.000 0.384
#> GSM550835 2 0.6383 0.18815 0.276 0.648 0.040 0.036
#> GSM550836 3 0.0188 0.75446 0.004 0.000 0.996 0.000
#> GSM550837 2 0.6301 0.18053 0.276 0.652 0.036 0.036
#> GSM550838 4 0.6599 0.16059 0.340 0.096 0.000 0.564
#> GSM550841 2 0.7408 -0.22953 0.276 0.512 0.212 0.000
#> GSM550842 2 0.6075 0.27853 0.216 0.700 0.028 0.056
#> GSM550846 4 0.1151 0.54325 0.008 0.024 0.000 0.968
#> GSM550849 2 0.7919 -0.15866 0.316 0.348 0.000 0.336
#> GSM550850 4 0.5244 0.13976 0.388 0.012 0.000 0.600
#> GSM550851 2 0.6309 0.24760 0.232 0.680 0.036 0.052
#> GSM550852 4 0.7468 0.11179 0.184 0.352 0.000 0.464
#> GSM550853 2 0.4907 0.44645 0.000 0.580 0.000 0.420
#> GSM550855 2 0.5080 0.44425 0.004 0.576 0.000 0.420
#> GSM550856 2 0.5080 0.44425 0.004 0.576 0.000 0.420
#> GSM550861 2 0.4941 0.41816 0.000 0.564 0.000 0.436
#> GSM550863 4 0.1389 0.52064 0.048 0.000 0.000 0.952
#> GSM550864 2 0.4992 0.35165 0.000 0.524 0.000 0.476
#> GSM550866 4 0.4564 0.16292 0.000 0.328 0.000 0.672
#> GSM550867 4 0.4933 0.05591 0.432 0.000 0.000 0.568
#> GSM550885 4 0.4907 0.07995 0.420 0.000 0.000 0.580
#> GSM550886 2 0.8873 0.22678 0.200 0.504 0.168 0.128
#> GSM550887 2 0.4855 0.46331 0.000 0.600 0.000 0.400
#> GSM550889 4 0.2197 0.53996 0.004 0.080 0.000 0.916
#> GSM550894 2 0.6462 0.45366 0.088 0.580 0.000 0.332
#> GSM550897 4 0.3674 0.50690 0.104 0.044 0.000 0.852
#> GSM550903 2 0.4941 0.41844 0.000 0.564 0.000 0.436
#> GSM550905 2 0.6577 0.31782 0.220 0.648 0.008 0.124
#> GSM550906 2 0.4855 0.46331 0.000 0.600 0.000 0.400
#> GSM550907 3 0.4188 0.72115 0.112 0.064 0.824 0.000
#> GSM550909 2 0.7665 0.08810 0.216 0.424 0.000 0.360
#> GSM550911 3 0.3051 0.73929 0.088 0.028 0.884 0.000
#> GSM550913 2 0.4855 0.46331 0.000 0.600 0.000 0.400
#> GSM550915 4 0.1004 0.54156 0.004 0.024 0.000 0.972
#> GSM550917 4 0.4925 -0.12733 0.000 0.428 0.000 0.572
#> GSM550919 4 0.2443 0.52120 0.060 0.024 0.000 0.916
#> GSM550921 3 0.0188 0.75380 0.000 0.004 0.996 0.000
#> GSM550924 2 0.8382 0.16070 0.264 0.496 0.048 0.192
#> GSM550926 2 0.5244 0.42355 0.008 0.556 0.000 0.436
#> GSM550927 2 0.4866 0.45969 0.000 0.596 0.000 0.404
#> GSM550787 1 0.7215 0.57053 0.576 0.140 0.012 0.272
#> GSM550793 1 0.9731 0.32286 0.372 0.208 0.224 0.196
#> GSM550794 4 0.6915 0.36492 0.196 0.212 0.000 0.592
#> GSM550795 4 0.5313 0.14743 0.376 0.016 0.000 0.608
#> GSM550798 1 0.7249 0.55944 0.600 0.072 0.052 0.276
#> GSM550803 1 0.5279 0.32754 0.588 0.012 0.000 0.400
#> GSM550805 4 0.6915 0.31150 0.212 0.196 0.000 0.592
#> GSM550823 4 0.3485 0.53471 0.028 0.116 0.000 0.856
#> GSM550824 4 0.4933 0.05591 0.432 0.000 0.000 0.568
#> GSM550825 1 0.8958 0.11835 0.464 0.124 0.276 0.136
#> GSM550827 4 0.2830 0.53796 0.040 0.060 0.000 0.900
#> GSM550828 4 0.3577 0.43739 0.156 0.012 0.000 0.832
#> GSM550829 1 0.8856 0.23554 0.492 0.116 0.240 0.152
#> GSM550830 4 0.3801 0.40275 0.000 0.220 0.000 0.780
#> GSM550834 4 0.5244 0.13976 0.388 0.012 0.000 0.600
#> GSM550839 2 0.8725 -0.13697 0.308 0.440 0.192 0.060
#> GSM550840 4 0.5288 0.40106 0.200 0.068 0.000 0.732
#> GSM550843 2 0.9074 -0.32522 0.328 0.352 0.256 0.064
#> GSM550844 4 0.6991 0.25065 0.232 0.188 0.000 0.580
#> GSM550845 4 0.4643 0.11055 0.000 0.344 0.000 0.656
#> GSM550848 4 0.2214 0.52724 0.044 0.028 0.000 0.928
#> GSM550854 4 0.4925 0.06652 0.428 0.000 0.000 0.572
#> GSM550857 3 0.0188 0.75446 0.004 0.000 0.996 0.000
#> GSM550858 4 0.4564 0.22812 0.328 0.000 0.000 0.672
#> GSM550859 4 0.4933 0.05591 0.432 0.000 0.000 0.568
#> GSM550862 4 0.2408 0.48740 0.104 0.000 0.000 0.896
#> GSM550865 4 0.1297 0.53744 0.020 0.016 0.000 0.964
#> GSM550868 4 0.2647 0.52025 0.000 0.120 0.000 0.880
#> GSM550869 4 0.8315 0.00705 0.260 0.232 0.032 0.476
#> GSM550870 4 0.4679 0.09486 0.000 0.352 0.000 0.648
#> GSM550871 2 0.8725 -0.13697 0.308 0.440 0.192 0.060
#> GSM550872 4 0.1724 0.54201 0.020 0.032 0.000 0.948
#> GSM550873 4 0.7501 0.04906 0.184 0.372 0.000 0.444
#> GSM550874 2 0.5408 0.43292 0.016 0.576 0.000 0.408
#> GSM550876 2 0.8966 -0.39476 0.288 0.348 0.312 0.052
#> GSM550877 2 0.4948 0.42453 0.000 0.560 0.000 0.440
#> GSM550878 3 0.8887 0.30674 0.252 0.312 0.384 0.052
#> GSM550879 4 0.3074 0.43334 0.152 0.000 0.000 0.848
#> GSM550882 3 0.8526 0.32889 0.332 0.100 0.468 0.100
#> GSM550888 3 0.0188 0.75446 0.004 0.000 0.996 0.000
#> GSM550890 4 0.0817 0.54262 0.000 0.024 0.000 0.976
#> GSM550891 3 0.0188 0.75380 0.000 0.004 0.996 0.000
#> GSM550892 4 0.1118 0.52578 0.036 0.000 0.000 0.964
#> GSM550893 4 0.2741 0.53789 0.012 0.096 0.000 0.892
#> GSM550895 4 0.2589 0.52335 0.000 0.116 0.000 0.884
#> GSM550896 4 0.2704 0.51812 0.000 0.124 0.000 0.876
#> GSM550898 4 0.4933 0.05591 0.432 0.000 0.000 0.568
#> GSM550899 4 0.4972 -0.22342 0.000 0.456 0.000 0.544
#> GSM550900 4 0.2466 0.53895 0.004 0.096 0.000 0.900
#> GSM550901 4 0.2443 0.52120 0.060 0.024 0.000 0.916
#> GSM550902 1 0.9276 0.52138 0.408 0.240 0.100 0.252
#> GSM550904 4 0.7019 0.06797 0.344 0.132 0.000 0.524
#> GSM550908 3 0.0000 0.75421 0.000 0.000 1.000 0.000
#> GSM550912 4 0.5815 -0.09719 0.032 0.428 0.000 0.540
#> GSM550914 4 0.0817 0.54262 0.000 0.024 0.000 0.976
#> GSM550918 4 0.4855 -0.05593 0.000 0.400 0.000 0.600
#> GSM550922 2 0.7498 -0.00981 0.236 0.580 0.160 0.024
#> GSM550923 1 0.5746 0.41762 0.600 0.028 0.004 0.368
#> GSM550925 4 0.2443 0.54374 0.024 0.060 0.000 0.916
#> GSM550802 4 0.6958 0.37150 0.184 0.232 0.000 0.584
#> GSM550812 4 0.7064 0.32454 0.208 0.220 0.000 0.572
#> GSM550831 4 0.5244 0.13976 0.388 0.012 0.000 0.600
#> GSM550847 4 0.4933 0.06141 0.432 0.000 0.000 0.568
#> GSM550860 1 0.9751 0.42926 0.304 0.248 0.148 0.300
#> GSM550875 4 0.7147 0.26810 0.224 0.216 0.000 0.560
#> GSM550880 4 0.4891 0.26895 0.308 0.012 0.000 0.680
#> GSM550881 3 0.8423 0.35227 0.328 0.092 0.480 0.100
#> GSM550883 3 0.8526 0.32889 0.332 0.100 0.468 0.100
#> GSM550884 4 0.7541 0.22889 0.192 0.300 0.004 0.504
#> GSM550910 3 0.6949 0.59369 0.216 0.176 0.604 0.004
#> GSM550916 1 0.5815 0.31842 0.540 0.032 0.000 0.428
#> GSM550920 2 0.8886 0.16939 0.216 0.492 0.184 0.108
cbind(get_classes(res, k = 5), get_membership(res, k = 5))
#> class entropy silhouette p1 p2 p3 p4 p5
#> GSM550785 1 0.3791 0.4464 0.812 0.076 0.000 0.112 0.000
#> GSM550786 5 0.5615 0.6002 0.028 0.252 0.008 0.048 0.664
#> GSM550788 2 0.1503 0.7383 0.020 0.952 0.000 0.008 0.020
#> GSM550789 2 0.0566 0.7360 0.000 0.984 0.000 0.004 0.012
#> GSM550790 1 0.4326 0.2458 0.708 0.028 0.000 0.264 0.000
#> GSM550791 1 0.4527 0.3343 0.732 0.064 0.000 0.204 0.000
#> GSM550792 1 0.7747 0.1966 0.376 0.332 0.000 0.228 0.064
#> GSM550796 2 0.0807 0.7344 0.000 0.976 0.000 0.012 0.012
#> GSM550797 2 0.0566 0.7360 0.000 0.984 0.000 0.004 0.012
#> GSM550799 5 0.3282 0.6327 0.000 0.188 0.008 0.000 0.804
#> GSM550800 2 0.3635 0.4912 0.248 0.748 0.000 0.004 0.000
#> GSM550801 2 0.0566 0.7360 0.000 0.984 0.000 0.004 0.012
#> GSM550804 2 0.3242 0.5740 0.216 0.784 0.000 0.000 0.000
#> GSM550806 5 0.7497 0.4711 0.036 0.080 0.176 0.128 0.580
#> GSM550807 2 0.0162 0.7396 0.000 0.996 0.000 0.004 0.000
#> GSM550808 2 0.5311 0.4469 0.012 0.692 0.000 0.096 0.200
#> GSM550809 1 0.6205 0.2360 0.596 0.128 0.000 0.256 0.020
#> GSM550810 2 0.4745 0.5533 0.012 0.756 0.000 0.108 0.124
#> GSM550811 1 0.7572 0.2626 0.408 0.316 0.000 0.224 0.052
#> GSM550813 2 0.4187 0.5991 0.196 0.764 0.000 0.032 0.008
#> GSM550814 2 0.5415 0.5245 0.212 0.688 0.000 0.076 0.024
#> GSM550815 2 0.0404 0.7350 0.000 0.988 0.000 0.000 0.012
#> GSM550816 2 0.5494 0.6267 0.124 0.724 0.000 0.080 0.072
#> GSM550817 5 0.5700 0.5283 0.000 0.120 0.180 0.024 0.676
#> GSM550818 5 0.5764 0.5265 0.000 0.120 0.188 0.024 0.668
#> GSM550819 2 0.7920 0.0489 0.316 0.400 0.000 0.104 0.180
#> GSM550820 1 0.6683 0.1762 0.536 0.148 0.000 0.288 0.028
#> GSM550821 2 0.7137 -0.1051 0.064 0.468 0.000 0.116 0.352
#> GSM550822 2 0.0404 0.7350 0.000 0.988 0.000 0.000 0.012
#> GSM550826 1 0.8823 -0.3913 0.340 0.136 0.024 0.264 0.236
#> GSM550832 2 0.4037 0.5983 0.020 0.796 0.000 0.028 0.156
#> GSM550833 2 0.1612 0.7337 0.016 0.948 0.000 0.012 0.024
#> GSM550835 5 0.4216 0.6240 0.000 0.260 0.008 0.012 0.720
#> GSM550836 3 0.0566 0.7257 0.000 0.000 0.984 0.012 0.004
#> GSM550837 5 0.3508 0.6246 0.000 0.252 0.000 0.000 0.748
#> GSM550838 1 0.6205 0.2360 0.596 0.128 0.000 0.256 0.020
#> GSM550841 5 0.4764 0.5624 0.000 0.112 0.080 0.036 0.772
#> GSM550842 5 0.4551 0.5408 0.000 0.368 0.000 0.016 0.616
#> GSM550846 1 0.4313 0.5074 0.636 0.356 0.000 0.008 0.000
#> GSM550849 4 0.7288 0.1127 0.124 0.384 0.000 0.424 0.068
#> GSM550850 1 0.3012 0.3733 0.852 0.024 0.000 0.124 0.000
#> GSM550851 5 0.3895 0.5855 0.000 0.320 0.000 0.000 0.680
#> GSM550852 2 0.7928 0.2252 0.228 0.452 0.000 0.192 0.128
#> GSM550853 2 0.0404 0.7402 0.012 0.988 0.000 0.000 0.000
#> GSM550855 2 0.0794 0.7402 0.028 0.972 0.000 0.000 0.000
#> GSM550856 2 0.0794 0.7402 0.028 0.972 0.000 0.000 0.000
#> GSM550861 2 0.1041 0.7362 0.032 0.964 0.000 0.000 0.004
#> GSM550863 1 0.4161 0.5662 0.704 0.280 0.000 0.016 0.000
#> GSM550864 2 0.1831 0.7172 0.076 0.920 0.000 0.000 0.004
#> GSM550866 2 0.3913 0.3533 0.324 0.676 0.000 0.000 0.000
#> GSM550867 1 0.2813 0.3040 0.832 0.000 0.000 0.168 0.000
#> GSM550885 1 0.3053 0.3170 0.828 0.008 0.000 0.164 0.000
#> GSM550886 5 0.7612 0.5006 0.016 0.348 0.128 0.060 0.448
#> GSM550887 2 0.0290 0.7360 0.000 0.992 0.000 0.000 0.008
#> GSM550889 1 0.4350 0.4353 0.588 0.408 0.000 0.004 0.000
#> GSM550894 2 0.4037 0.5993 0.020 0.796 0.000 0.028 0.156
#> GSM550897 1 0.4622 0.5770 0.684 0.276 0.000 0.040 0.000
#> GSM550903 2 0.1124 0.7365 0.036 0.960 0.000 0.000 0.004
#> GSM550905 5 0.6030 0.3516 0.016 0.432 0.000 0.072 0.480
#> GSM550906 2 0.0290 0.7360 0.000 0.992 0.000 0.000 0.008
#> GSM550907 3 0.6147 0.5239 0.000 0.000 0.544 0.168 0.288
#> GSM550909 2 0.8171 0.1761 0.160 0.416 0.000 0.224 0.200
#> GSM550911 3 0.5798 0.5811 0.000 0.000 0.608 0.156 0.236
#> GSM550913 2 0.0290 0.7360 0.000 0.992 0.000 0.000 0.008
#> GSM550915 1 0.4298 0.5121 0.640 0.352 0.000 0.008 0.000
#> GSM550917 2 0.2966 0.6112 0.184 0.816 0.000 0.000 0.000
#> GSM550919 1 0.4465 0.5582 0.672 0.304 0.000 0.024 0.000
#> GSM550921 3 0.0579 0.7196 0.000 0.000 0.984 0.008 0.008
#> GSM550924 2 0.8088 -0.3166 0.052 0.364 0.020 0.224 0.340
#> GSM550926 2 0.1282 0.7365 0.044 0.952 0.000 0.004 0.000
#> GSM550927 2 0.0807 0.7398 0.012 0.976 0.000 0.000 0.012
#> GSM550787 4 0.6980 0.5280 0.272 0.044 0.000 0.524 0.160
#> GSM550793 4 0.9311 0.2264 0.156 0.080 0.160 0.356 0.248
#> GSM550794 1 0.7512 0.2237 0.392 0.348 0.000 0.212 0.048
#> GSM550795 1 0.3182 0.3836 0.844 0.032 0.000 0.124 0.000
#> GSM550798 4 0.6341 0.5162 0.284 0.000 0.028 0.576 0.112
#> GSM550803 4 0.4397 0.4267 0.432 0.004 0.000 0.564 0.000
#> GSM550805 1 0.7693 0.2727 0.424 0.288 0.000 0.220 0.068
#> GSM550823 1 0.5107 0.3375 0.520 0.448 0.000 0.028 0.004
#> GSM550824 1 0.2813 0.3040 0.832 0.000 0.000 0.168 0.000
#> GSM550825 4 0.7688 0.1040 0.096 0.004 0.204 0.500 0.196
#> GSM550827 1 0.4585 0.5122 0.628 0.352 0.000 0.020 0.000
#> GSM550828 1 0.4617 0.5607 0.716 0.224 0.000 0.060 0.000
#> GSM550829 4 0.7450 0.2016 0.100 0.004 0.168 0.540 0.188
#> GSM550830 2 0.4517 -0.0726 0.436 0.556 0.000 0.008 0.000
#> GSM550834 1 0.3012 0.3733 0.852 0.024 0.000 0.124 0.000
#> GSM550839 5 0.7370 0.5911 0.032 0.144 0.112 0.112 0.600
#> GSM550840 1 0.5040 0.5172 0.712 0.192 0.000 0.088 0.008
#> GSM550843 5 0.7423 0.4853 0.044 0.076 0.156 0.128 0.596
#> GSM550844 1 0.7698 0.2337 0.440 0.240 0.000 0.248 0.072
#> GSM550845 2 0.3766 0.4832 0.268 0.728 0.000 0.004 0.000
#> GSM550848 1 0.4473 0.5418 0.656 0.324 0.000 0.020 0.000
#> GSM550854 1 0.2773 0.3082 0.836 0.000 0.000 0.164 0.000
#> GSM550857 3 0.0566 0.7257 0.000 0.000 0.984 0.012 0.004
#> GSM550858 1 0.3840 0.4321 0.808 0.076 0.000 0.116 0.000
#> GSM550859 1 0.2813 0.3040 0.832 0.000 0.000 0.168 0.000
#> GSM550862 1 0.4325 0.5803 0.724 0.240 0.000 0.036 0.000
#> GSM550865 1 0.4323 0.5326 0.656 0.332 0.000 0.012 0.000
#> GSM550868 1 0.4425 0.3470 0.544 0.452 0.000 0.004 0.000
#> GSM550869 1 0.8786 -0.0790 0.320 0.228 0.016 0.280 0.156
#> GSM550870 2 0.3689 0.4976 0.256 0.740 0.000 0.004 0.000
#> GSM550871 5 0.7370 0.5911 0.032 0.144 0.112 0.112 0.600
#> GSM550872 1 0.4235 0.5301 0.656 0.336 0.000 0.008 0.000
#> GSM550873 2 0.8002 0.2386 0.224 0.448 0.000 0.164 0.164
#> GSM550874 2 0.1960 0.7341 0.048 0.928 0.000 0.020 0.004
#> GSM550876 5 0.7603 0.4242 0.040 0.068 0.204 0.128 0.560
#> GSM550877 2 0.1043 0.7363 0.040 0.960 0.000 0.000 0.000
#> GSM550878 5 0.7934 0.3218 0.040 0.068 0.280 0.124 0.488
#> GSM550879 1 0.3841 0.5591 0.780 0.188 0.000 0.032 0.000
#> GSM550882 3 0.7740 0.2270 0.060 0.004 0.380 0.360 0.196
#> GSM550888 3 0.0566 0.7257 0.000 0.000 0.984 0.012 0.004
#> GSM550890 1 0.4196 0.5073 0.640 0.356 0.000 0.004 0.000
#> GSM550891 3 0.0992 0.7170 0.000 0.000 0.968 0.008 0.024
#> GSM550892 1 0.4109 0.5612 0.700 0.288 0.000 0.012 0.000
#> GSM550893 1 0.4610 0.3919 0.556 0.432 0.000 0.012 0.000
#> GSM550895 1 0.4420 0.3542 0.548 0.448 0.000 0.004 0.000
#> GSM550896 1 0.4430 0.3401 0.540 0.456 0.000 0.004 0.000
#> GSM550898 1 0.2813 0.3040 0.832 0.000 0.000 0.168 0.000
#> GSM550899 2 0.2848 0.6505 0.156 0.840 0.000 0.000 0.004
#> GSM550900 1 0.4604 0.3968 0.560 0.428 0.000 0.012 0.000
#> GSM550901 1 0.4465 0.5582 0.672 0.304 0.000 0.024 0.000
#> GSM550902 4 0.9120 0.3303 0.240 0.112 0.060 0.344 0.244
#> GSM550904 1 0.7127 0.1266 0.496 0.160 0.000 0.296 0.048
#> GSM550908 3 0.0693 0.7255 0.000 0.000 0.980 0.012 0.008
#> GSM550912 2 0.4264 0.5969 0.196 0.760 0.000 0.036 0.008
#> GSM550914 1 0.4196 0.5073 0.640 0.356 0.000 0.004 0.000
#> GSM550918 2 0.3242 0.5740 0.216 0.784 0.000 0.000 0.000
#> GSM550922 5 0.6116 0.6364 0.012 0.200 0.096 0.032 0.660
#> GSM550923 4 0.4196 0.5103 0.356 0.000 0.000 0.640 0.004
#> GSM550925 1 0.4564 0.4911 0.612 0.372 0.000 0.016 0.000
#> GSM550802 2 0.7491 -0.1962 0.372 0.376 0.000 0.204 0.048
#> GSM550812 1 0.7692 0.2424 0.396 0.312 0.000 0.232 0.060
#> GSM550831 1 0.3012 0.3733 0.852 0.024 0.000 0.124 0.000
#> GSM550847 1 0.2813 0.3045 0.832 0.000 0.000 0.168 0.000
#> GSM550860 5 0.9578 -0.2517 0.220 0.136 0.104 0.232 0.308
#> GSM550875 1 0.7792 0.2211 0.408 0.280 0.000 0.240 0.072
#> GSM550880 1 0.3593 0.4526 0.828 0.084 0.000 0.088 0.000
#> GSM550881 3 0.7719 0.2526 0.060 0.004 0.392 0.352 0.192
#> GSM550883 3 0.7740 0.2270 0.060 0.004 0.380 0.360 0.196
#> GSM550884 2 0.8256 0.0253 0.280 0.364 0.000 0.220 0.136
#> GSM550910 5 0.6602 -0.2552 0.000 0.008 0.324 0.180 0.488
#> GSM550916 4 0.4731 0.4085 0.456 0.016 0.000 0.528 0.000
#> GSM550920 5 0.7686 0.5419 0.020 0.296 0.136 0.064 0.484
cbind(get_classes(res, k = 6), get_membership(res, k = 6))
#> class entropy silhouette p1 p2 p3 p4 p5 p6
#> GSM550785 6 0.4253 0.37540 0.136 0.060 0.000 0.028 0.004 0.772
#> GSM550786 5 0.5027 0.58333 0.056 0.200 0.000 0.020 0.700 0.024
#> GSM550788 2 0.1787 0.74559 0.020 0.932 0.000 0.000 0.016 0.032
#> GSM550789 2 0.0520 0.74347 0.008 0.984 0.000 0.000 0.008 0.000
#> GSM550790 6 0.5172 0.10972 0.304 0.016 0.000 0.064 0.004 0.612
#> GSM550791 6 0.5159 0.21737 0.256 0.040 0.000 0.048 0.004 0.652
#> GSM550792 6 0.7148 0.14602 0.324 0.260 0.000 0.004 0.064 0.348
#> GSM550796 2 0.0779 0.74137 0.008 0.976 0.000 0.008 0.008 0.000
#> GSM550797 2 0.0520 0.74347 0.008 0.984 0.000 0.000 0.008 0.000
#> GSM550799 5 0.2988 0.57200 0.000 0.152 0.000 0.024 0.824 0.000
#> GSM550800 2 0.3244 0.51086 0.000 0.732 0.000 0.000 0.000 0.268
#> GSM550801 2 0.0520 0.74347 0.008 0.984 0.000 0.000 0.008 0.000
#> GSM550804 2 0.3050 0.58714 0.000 0.764 0.000 0.000 0.000 0.236
#> GSM550806 5 0.6583 0.35088 0.036 0.052 0.108 0.160 0.624 0.020
#> GSM550807 2 0.0405 0.74975 0.004 0.988 0.000 0.000 0.000 0.008
#> GSM550808 2 0.5110 0.37628 0.160 0.644 0.000 0.004 0.192 0.000
#> GSM550809 6 0.5608 0.08037 0.396 0.064 0.000 0.012 0.016 0.512
#> GSM550810 2 0.4563 0.50313 0.176 0.708 0.000 0.004 0.112 0.000
#> GSM550811 6 0.6941 0.18300 0.320 0.240 0.000 0.000 0.060 0.380
#> GSM550813 2 0.4117 0.61433 0.064 0.740 0.000 0.000 0.004 0.192
#> GSM550814 2 0.5214 0.53814 0.104 0.664 0.000 0.004 0.020 0.208
#> GSM550815 2 0.0405 0.74268 0.004 0.988 0.000 0.000 0.008 0.000
#> GSM550816 2 0.5282 0.60343 0.120 0.692 0.000 0.000 0.068 0.120
#> GSM550817 5 0.5561 0.43409 0.000 0.088 0.116 0.128 0.668 0.000
#> GSM550818 5 0.5637 0.43427 0.000 0.088 0.124 0.128 0.660 0.000
#> GSM550819 2 0.7598 0.01322 0.136 0.364 0.000 0.012 0.176 0.312
#> GSM550820 6 0.6017 0.04231 0.400 0.096 0.000 0.016 0.016 0.472
#> GSM550821 2 0.6889 -0.22859 0.160 0.408 0.000 0.008 0.364 0.060
#> GSM550822 2 0.0405 0.74268 0.004 0.988 0.000 0.000 0.008 0.000
#> GSM550826 6 0.8486 -0.41728 0.280 0.104 0.024 0.040 0.268 0.284
#> GSM550832 2 0.4018 0.56518 0.036 0.768 0.000 0.008 0.176 0.012
#> GSM550833 2 0.1602 0.74086 0.016 0.944 0.000 0.004 0.020 0.016
#> GSM550835 5 0.3914 0.58561 0.016 0.228 0.004 0.012 0.740 0.000
#> GSM550836 3 0.0291 0.56211 0.000 0.000 0.992 0.004 0.004 0.000
#> GSM550837 5 0.3287 0.57988 0.000 0.220 0.000 0.012 0.768 0.000
#> GSM550838 6 0.5608 0.08037 0.396 0.064 0.000 0.012 0.016 0.512
#> GSM550841 5 0.4865 0.44910 0.000 0.088 0.040 0.156 0.716 0.000
#> GSM550842 5 0.4499 0.50344 0.012 0.344 0.000 0.024 0.620 0.000
#> GSM550846 6 0.3922 0.47461 0.016 0.320 0.000 0.000 0.000 0.664
#> GSM550849 1 0.7231 0.18166 0.508 0.220 0.000 0.128 0.112 0.032
#> GSM550850 6 0.3766 0.27491 0.224 0.004 0.000 0.020 0.004 0.748
#> GSM550851 5 0.3753 0.54763 0.004 0.292 0.000 0.008 0.696 0.000
#> GSM550852 2 0.7378 0.17778 0.268 0.404 0.000 0.004 0.124 0.200
#> GSM550853 2 0.0547 0.75107 0.000 0.980 0.000 0.000 0.000 0.020
#> GSM550855 2 0.1010 0.75096 0.004 0.960 0.000 0.000 0.000 0.036
#> GSM550856 2 0.1010 0.75096 0.004 0.960 0.000 0.000 0.000 0.036
#> GSM550861 2 0.0790 0.74875 0.000 0.968 0.000 0.000 0.000 0.032
#> GSM550863 6 0.3373 0.53358 0.008 0.248 0.000 0.000 0.000 0.744
#> GSM550864 2 0.1501 0.73305 0.000 0.924 0.000 0.000 0.000 0.076
#> GSM550866 2 0.3699 0.38442 0.004 0.660 0.000 0.000 0.000 0.336
#> GSM550867 6 0.4094 0.20027 0.252 0.000 0.000 0.036 0.004 0.708
#> GSM550885 6 0.3858 0.21535 0.248 0.000 0.000 0.024 0.004 0.724
#> GSM550886 5 0.7647 0.47935 0.068 0.300 0.088 0.088 0.448 0.008
#> GSM550887 2 0.0291 0.74372 0.004 0.992 0.000 0.000 0.004 0.000
#> GSM550889 6 0.3934 0.39939 0.008 0.376 0.000 0.000 0.000 0.616
#> GSM550894 2 0.4052 0.56787 0.040 0.768 0.000 0.008 0.172 0.012
#> GSM550897 6 0.4507 0.54192 0.040 0.248 0.000 0.020 0.000 0.692
#> GSM550903 2 0.0865 0.74912 0.000 0.964 0.000 0.000 0.000 0.036
#> GSM550905 5 0.5982 0.40523 0.104 0.388 0.000 0.008 0.480 0.020
#> GSM550906 2 0.0291 0.74372 0.004 0.992 0.000 0.000 0.004 0.000
#> GSM550907 4 0.5042 0.23659 0.000 0.000 0.308 0.592 0.100 0.000
#> GSM550909 2 0.7403 -0.01213 0.320 0.344 0.000 0.000 0.196 0.140
#> GSM550911 4 0.5109 0.16049 0.004 0.000 0.372 0.548 0.076 0.000
#> GSM550913 2 0.0146 0.74502 0.000 0.996 0.000 0.000 0.004 0.000
#> GSM550915 6 0.3741 0.47894 0.008 0.320 0.000 0.000 0.000 0.672
#> GSM550917 2 0.2793 0.62575 0.000 0.800 0.000 0.000 0.000 0.200
#> GSM550919 6 0.3746 0.52557 0.012 0.272 0.000 0.004 0.000 0.712
#> GSM550921 3 0.1531 0.52355 0.004 0.000 0.928 0.068 0.000 0.000
#> GSM550924 5 0.7345 0.24514 0.288 0.288 0.004 0.036 0.360 0.024
#> GSM550926 2 0.1398 0.74758 0.008 0.940 0.000 0.000 0.000 0.052
#> GSM550927 2 0.0767 0.74731 0.004 0.976 0.000 0.000 0.008 0.012
#> GSM550787 1 0.7824 0.31209 0.424 0.036 0.000 0.212 0.140 0.188
#> GSM550793 1 0.9131 -0.00197 0.296 0.036 0.100 0.192 0.248 0.128
#> GSM550794 6 0.7067 0.20351 0.304 0.268 0.000 0.004 0.056 0.368
#> GSM550795 6 0.3970 0.28962 0.224 0.012 0.000 0.020 0.004 0.740
#> GSM550798 1 0.7196 0.30046 0.476 0.000 0.028 0.252 0.068 0.176
#> GSM550803 1 0.5896 0.41217 0.548 0.000 0.000 0.132 0.028 0.292
#> GSM550805 6 0.7060 0.16647 0.332 0.208 0.000 0.004 0.068 0.388
#> GSM550823 6 0.4752 0.30293 0.032 0.420 0.000 0.004 0.004 0.540
#> GSM550824 6 0.4159 0.19689 0.252 0.000 0.000 0.040 0.004 0.704
#> GSM550825 4 0.7972 0.18509 0.308 0.000 0.152 0.336 0.172 0.032
#> GSM550827 6 0.4058 0.47836 0.016 0.320 0.000 0.004 0.000 0.660
#> GSM550828 6 0.4239 0.51663 0.056 0.196 0.000 0.012 0.000 0.736
#> GSM550829 4 0.7875 0.15941 0.332 0.000 0.124 0.340 0.168 0.036
#> GSM550830 2 0.4089 -0.05596 0.008 0.524 0.000 0.000 0.000 0.468
#> GSM550834 6 0.3766 0.27491 0.224 0.004 0.000 0.020 0.004 0.748
#> GSM550839 5 0.6549 0.48993 0.036 0.104 0.064 0.132 0.640 0.024
#> GSM550840 6 0.5143 0.43689 0.144 0.144 0.000 0.012 0.012 0.688
#> GSM550843 5 0.6355 0.35991 0.040 0.044 0.096 0.144 0.652 0.024
#> GSM550844 6 0.7035 0.12487 0.344 0.176 0.000 0.008 0.068 0.404
#> GSM550845 2 0.3351 0.50616 0.000 0.712 0.000 0.000 0.000 0.288
#> GSM550848 6 0.3710 0.51039 0.012 0.292 0.000 0.000 0.000 0.696
#> GSM550854 6 0.4071 0.20529 0.248 0.000 0.000 0.036 0.004 0.712
#> GSM550857 3 0.0405 0.56053 0.000 0.000 0.988 0.004 0.008 0.000
#> GSM550858 6 0.4278 0.35319 0.188 0.060 0.000 0.008 0.004 0.740
#> GSM550859 6 0.4094 0.20027 0.252 0.000 0.000 0.036 0.004 0.708
#> GSM550862 6 0.3777 0.53969 0.028 0.208 0.000 0.008 0.000 0.756
#> GSM550865 6 0.3547 0.49818 0.004 0.300 0.000 0.000 0.000 0.696
#> GSM550868 6 0.3930 0.32084 0.004 0.420 0.000 0.000 0.000 0.576
#> GSM550869 1 0.8244 0.09440 0.340 0.160 0.004 0.048 0.156 0.292
#> GSM550870 2 0.3288 0.51973 0.000 0.724 0.000 0.000 0.000 0.276
#> GSM550871 5 0.6549 0.48993 0.036 0.104 0.064 0.132 0.640 0.024
#> GSM550872 6 0.3565 0.49688 0.004 0.304 0.000 0.000 0.000 0.692
#> GSM550873 2 0.7387 0.19398 0.232 0.404 0.000 0.000 0.164 0.200
#> GSM550874 2 0.2154 0.74213 0.020 0.908 0.000 0.004 0.004 0.064
#> GSM550876 5 0.6630 0.28967 0.036 0.036 0.120 0.184 0.604 0.020
#> GSM550877 2 0.1075 0.74820 0.000 0.952 0.000 0.000 0.000 0.048
#> GSM550878 5 0.7153 0.18199 0.036 0.036 0.192 0.184 0.532 0.020
#> GSM550879 6 0.3494 0.51951 0.036 0.168 0.000 0.004 0.000 0.792
#> GSM550882 3 0.8212 -0.16409 0.212 0.000 0.296 0.260 0.200 0.032
#> GSM550888 3 0.0291 0.56211 0.000 0.000 0.992 0.004 0.004 0.000
#> GSM550890 6 0.3652 0.47327 0.004 0.324 0.000 0.000 0.000 0.672
#> GSM550891 3 0.2009 0.50766 0.004 0.000 0.904 0.084 0.008 0.000
#> GSM550892 6 0.3314 0.52833 0.004 0.256 0.000 0.000 0.000 0.740
#> GSM550893 6 0.4168 0.35452 0.016 0.400 0.000 0.000 0.000 0.584
#> GSM550895 6 0.3923 0.32866 0.004 0.416 0.000 0.000 0.000 0.580
#> GSM550896 6 0.3937 0.31257 0.004 0.424 0.000 0.000 0.000 0.572
#> GSM550898 6 0.4094 0.20027 0.252 0.000 0.000 0.036 0.004 0.708
#> GSM550899 2 0.2491 0.66546 0.000 0.836 0.000 0.000 0.000 0.164
#> GSM550900 6 0.4362 0.37166 0.020 0.392 0.000 0.004 0.000 0.584
#> GSM550901 6 0.3746 0.52557 0.012 0.272 0.000 0.004 0.000 0.712
#> GSM550902 1 0.8698 0.25085 0.340 0.060 0.024 0.132 0.244 0.200
#> GSM550904 6 0.6330 -0.00548 0.416 0.108 0.000 0.016 0.028 0.432
#> GSM550908 3 0.0508 0.55867 0.000 0.000 0.984 0.012 0.004 0.000
#> GSM550912 2 0.4141 0.61604 0.068 0.740 0.000 0.000 0.004 0.188
#> GSM550914 6 0.3652 0.47327 0.004 0.324 0.000 0.000 0.000 0.672
#> GSM550918 2 0.3050 0.58714 0.000 0.764 0.000 0.000 0.000 0.236
#> GSM550922 5 0.5670 0.56896 0.024 0.160 0.064 0.056 0.688 0.008
#> GSM550923 1 0.6018 0.40669 0.564 0.000 0.000 0.188 0.032 0.216
#> GSM550925 6 0.4134 0.45502 0.016 0.340 0.000 0.004 0.000 0.640
#> GSM550802 6 0.7014 0.20465 0.292 0.304 0.000 0.004 0.048 0.352
#> GSM550812 6 0.6977 0.16467 0.328 0.236 0.000 0.000 0.064 0.372
#> GSM550831 6 0.3766 0.27491 0.224 0.004 0.000 0.020 0.004 0.748
#> GSM550847 6 0.4117 0.19830 0.256 0.000 0.000 0.036 0.004 0.704
#> GSM550860 5 0.9400 -0.23535 0.240 0.096 0.064 0.136 0.276 0.188
#> GSM550875 6 0.7095 0.10763 0.352 0.204 0.000 0.004 0.072 0.368
#> GSM550880 6 0.4236 0.37042 0.164 0.064 0.000 0.012 0.004 0.756
#> GSM550881 3 0.8221 -0.16810 0.212 0.000 0.292 0.260 0.204 0.032
#> GSM550883 3 0.8212 -0.16409 0.212 0.000 0.296 0.260 0.200 0.032
#> GSM550884 2 0.7590 -0.03697 0.300 0.304 0.000 0.004 0.128 0.264
#> GSM550910 4 0.5783 0.29205 0.020 0.008 0.108 0.572 0.292 0.000
#> GSM550916 1 0.6405 0.43942 0.468 0.012 0.000 0.136 0.028 0.356
#> GSM550920 5 0.7713 0.49944 0.072 0.244 0.088 0.100 0.484 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 disease.state(p) k
#> CV:hclust 126 4.58e-01 2
#> CV:hclust 89 2.43e-05 3
#> CV:hclust 33 2.46e-01 4
#> CV:hclust 75 8.58e-04 5
#> CV:hclust 58 7.13e-03 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 51776 rows and 143 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 0.484 0.810 0.894 0.4264 0.582 0.582
#> 3 3 0.719 0.852 0.913 0.4892 0.677 0.494
#> 4 4 0.567 0.520 0.757 0.1466 0.736 0.410
#> 5 5 0.621 0.516 0.688 0.0690 0.829 0.494
#> 6 6 0.670 0.612 0.760 0.0471 0.869 0.530
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
#> GSM550785 2 0.7883 0.7754 0.236 0.764
#> GSM550786 1 0.6438 0.8146 0.836 0.164
#> GSM550788 2 0.0000 0.8842 0.000 1.000
#> GSM550789 2 0.0000 0.8842 0.000 1.000
#> GSM550790 2 0.8016 0.7702 0.244 0.756
#> GSM550791 2 0.8016 0.7702 0.244 0.756
#> GSM550792 2 0.0000 0.8842 0.000 1.000
#> GSM550796 2 0.0000 0.8842 0.000 1.000
#> GSM550797 2 0.0000 0.8842 0.000 1.000
#> GSM550799 1 0.7056 0.8002 0.808 0.192
#> GSM550800 2 0.0000 0.8842 0.000 1.000
#> GSM550801 2 0.0000 0.8842 0.000 1.000
#> GSM550804 2 0.0000 0.8842 0.000 1.000
#> GSM550806 1 0.0938 0.8357 0.988 0.012
#> GSM550807 2 0.0000 0.8842 0.000 1.000
#> GSM550808 2 0.5519 0.7425 0.128 0.872
#> GSM550809 2 0.8016 0.7702 0.244 0.756
#> GSM550810 2 0.0000 0.8842 0.000 1.000
#> GSM550811 2 0.8016 0.7702 0.244 0.756
#> GSM550813 2 0.0000 0.8842 0.000 1.000
#> GSM550814 2 0.0000 0.8842 0.000 1.000
#> GSM550815 2 0.0000 0.8842 0.000 1.000
#> GSM550816 2 0.0000 0.8842 0.000 1.000
#> GSM550817 1 0.6623 0.8112 0.828 0.172
#> GSM550818 1 0.2948 0.8361 0.948 0.052
#> GSM550819 2 0.0000 0.8842 0.000 1.000
#> GSM550820 2 0.8016 0.7702 0.244 0.756
#> GSM550821 1 0.9608 0.6203 0.616 0.384
#> GSM550822 2 0.0000 0.8842 0.000 1.000
#> GSM550826 1 0.4815 0.7773 0.896 0.104
#> GSM550832 2 0.0000 0.8842 0.000 1.000
#> GSM550833 2 0.0000 0.8842 0.000 1.000
#> GSM550835 1 0.8016 0.7607 0.756 0.244
#> GSM550836 1 0.0000 0.8333 1.000 0.000
#> GSM550837 1 0.9775 0.5722 0.588 0.412
#> GSM550838 2 0.9087 0.6641 0.324 0.676
#> GSM550841 1 0.7056 0.8002 0.808 0.192
#> GSM550842 1 0.9393 0.6587 0.644 0.356
#> GSM550846 2 0.0376 0.8835 0.004 0.996
#> GSM550849 2 0.7950 0.7713 0.240 0.760
#> GSM550850 2 0.8016 0.7702 0.244 0.756
#> GSM550851 1 0.9580 0.6263 0.620 0.380
#> GSM550852 2 0.0000 0.8842 0.000 1.000
#> GSM550853 2 0.0000 0.8842 0.000 1.000
#> GSM550855 2 0.0000 0.8842 0.000 1.000
#> GSM550856 2 0.0000 0.8842 0.000 1.000
#> GSM550861 2 0.0000 0.8842 0.000 1.000
#> GSM550863 2 0.0938 0.8820 0.012 0.988
#> GSM550864 2 0.0000 0.8842 0.000 1.000
#> GSM550866 2 0.0000 0.8842 0.000 1.000
#> GSM550867 2 0.8016 0.7702 0.244 0.756
#> GSM550885 2 0.8016 0.7702 0.244 0.756
#> GSM550886 1 0.7883 0.7642 0.764 0.236
#> GSM550887 2 0.0000 0.8842 0.000 1.000
#> GSM550889 2 0.0938 0.8820 0.012 0.988
#> GSM550894 2 0.0000 0.8842 0.000 1.000
#> GSM550897 2 0.7883 0.7754 0.236 0.764
#> GSM550903 2 0.0000 0.8842 0.000 1.000
#> GSM550905 1 0.9922 0.4976 0.552 0.448
#> GSM550906 2 0.0000 0.8842 0.000 1.000
#> GSM550907 1 0.0938 0.8357 0.988 0.012
#> GSM550909 2 0.5737 0.7303 0.136 0.864
#> GSM550911 1 0.0938 0.8357 0.988 0.012
#> GSM550913 2 0.0000 0.8842 0.000 1.000
#> GSM550915 2 0.0938 0.8820 0.012 0.988
#> GSM550917 2 0.0000 0.8842 0.000 1.000
#> GSM550919 2 0.0938 0.8820 0.012 0.988
#> GSM550921 1 0.0376 0.8346 0.996 0.004
#> GSM550924 2 0.9850 0.0452 0.428 0.572
#> GSM550926 2 0.0000 0.8842 0.000 1.000
#> GSM550927 2 0.0000 0.8842 0.000 1.000
#> GSM550787 1 0.6623 0.7198 0.828 0.172
#> GSM550793 1 0.0000 0.8333 1.000 0.000
#> GSM550794 2 0.0000 0.8842 0.000 1.000
#> GSM550795 2 0.8016 0.7702 0.244 0.756
#> GSM550798 1 0.0000 0.8333 1.000 0.000
#> GSM550803 2 0.8016 0.7702 0.244 0.756
#> GSM550805 2 0.7950 0.7713 0.240 0.760
#> GSM550823 2 0.0000 0.8842 0.000 1.000
#> GSM550824 2 0.8016 0.7702 0.244 0.756
#> GSM550825 1 0.0000 0.8333 1.000 0.000
#> GSM550827 2 0.0938 0.8820 0.012 0.988
#> GSM550828 2 0.7883 0.7754 0.236 0.764
#> GSM550829 1 0.0000 0.8333 1.000 0.000
#> GSM550830 2 0.0376 0.8833 0.004 0.996
#> GSM550834 2 0.8016 0.7702 0.244 0.756
#> GSM550839 1 0.7219 0.7979 0.800 0.200
#> GSM550840 2 0.8016 0.7702 0.244 0.756
#> GSM550843 1 0.6148 0.8182 0.848 0.152
#> GSM550844 2 0.8016 0.7702 0.244 0.756
#> GSM550845 2 0.0000 0.8842 0.000 1.000
#> GSM550848 2 0.0938 0.8820 0.012 0.988
#> GSM550854 2 0.8016 0.7702 0.244 0.756
#> GSM550857 1 0.0000 0.8333 1.000 0.000
#> GSM550858 2 0.7950 0.7729 0.240 0.760
#> GSM550859 2 0.8016 0.7702 0.244 0.756
#> GSM550862 2 0.7883 0.7754 0.236 0.764
#> GSM550865 2 0.0938 0.8820 0.012 0.988
#> GSM550868 2 0.0938 0.8820 0.012 0.988
#> GSM550869 1 0.9710 0.2037 0.600 0.400
#> GSM550870 2 0.0000 0.8842 0.000 1.000
#> GSM550871 1 0.8016 0.7732 0.756 0.244
#> GSM550872 2 0.0938 0.8820 0.012 0.988
#> GSM550873 2 0.0000 0.8842 0.000 1.000
#> GSM550874 2 0.0000 0.8842 0.000 1.000
#> GSM550876 1 0.7056 0.8002 0.808 0.192
#> GSM550877 2 0.0000 0.8842 0.000 1.000
#> GSM550878 1 0.2948 0.8361 0.948 0.052
#> GSM550879 2 0.7883 0.7754 0.236 0.764
#> GSM550882 1 0.0672 0.8353 0.992 0.008
#> GSM550888 1 0.0000 0.8333 1.000 0.000
#> GSM550890 2 0.0938 0.8820 0.012 0.988
#> GSM550891 1 0.0672 0.8353 0.992 0.008
#> GSM550892 2 0.7602 0.7839 0.220 0.780
#> GSM550893 2 0.0000 0.8842 0.000 1.000
#> GSM550895 2 0.0000 0.8842 0.000 1.000
#> GSM550896 2 0.0000 0.8842 0.000 1.000
#> GSM550898 2 0.8016 0.7702 0.244 0.756
#> GSM550899 2 0.0000 0.8842 0.000 1.000
#> GSM550900 2 0.0938 0.8820 0.012 0.988
#> GSM550901 2 0.5408 0.8329 0.124 0.876
#> GSM550902 1 0.8081 0.5842 0.752 0.248
#> GSM550904 2 0.8016 0.7702 0.244 0.756
#> GSM550908 1 0.0000 0.8333 1.000 0.000
#> GSM550912 2 0.0000 0.8842 0.000 1.000
#> GSM550914 2 0.0938 0.8820 0.012 0.988
#> GSM550918 2 0.0000 0.8842 0.000 1.000
#> GSM550922 1 0.7883 0.7642 0.764 0.236
#> GSM550923 1 0.9460 0.2807 0.636 0.364
#> GSM550925 2 0.7453 0.7878 0.212 0.788
#> GSM550802 2 0.0000 0.8842 0.000 1.000
#> GSM550812 2 0.0000 0.8842 0.000 1.000
#> GSM550831 2 0.8016 0.7702 0.244 0.756
#> GSM550847 2 0.8016 0.7702 0.244 0.756
#> GSM550860 1 0.0376 0.8346 0.996 0.004
#> GSM550875 2 0.8016 0.7702 0.244 0.756
#> GSM550880 2 0.7883 0.7754 0.236 0.764
#> GSM550881 1 0.0376 0.8346 0.996 0.004
#> GSM550883 1 0.0000 0.8333 1.000 0.000
#> GSM550884 2 0.0000 0.8842 0.000 1.000
#> GSM550910 1 0.6623 0.8112 0.828 0.172
#> GSM550916 2 0.8016 0.7702 0.244 0.756
#> GSM550920 1 0.6438 0.8146 0.836 0.164
cbind(get_classes(res, k = 3), get_membership(res, k = 3))
#> class entropy silhouette p1 p2 p3
#> GSM550785 1 0.2448 0.925 0.924 0.076 0.000
#> GSM550786 3 0.2356 0.933 0.072 0.000 0.928
#> GSM550788 2 0.0000 0.881 0.000 1.000 0.000
#> GSM550789 2 0.0000 0.881 0.000 1.000 0.000
#> GSM550790 1 0.2165 0.925 0.936 0.064 0.000
#> GSM550791 1 0.2066 0.924 0.940 0.060 0.000
#> GSM550792 2 0.5098 0.756 0.248 0.752 0.000
#> GSM550796 2 0.0000 0.881 0.000 1.000 0.000
#> GSM550797 2 0.0000 0.881 0.000 1.000 0.000
#> GSM550799 3 0.0237 0.965 0.004 0.000 0.996
#> GSM550800 2 0.0000 0.881 0.000 1.000 0.000
#> GSM550801 2 0.0000 0.881 0.000 1.000 0.000
#> GSM550804 2 0.0000 0.881 0.000 1.000 0.000
#> GSM550806 3 0.0237 0.965 0.004 0.000 0.996
#> GSM550807 2 0.0000 0.881 0.000 1.000 0.000
#> GSM550808 2 0.2448 0.847 0.076 0.924 0.000
#> GSM550809 1 0.0000 0.895 1.000 0.000 0.000
#> GSM550810 2 0.2448 0.847 0.076 0.924 0.000
#> GSM550811 1 0.3038 0.835 0.896 0.104 0.000
#> GSM550813 2 0.0000 0.881 0.000 1.000 0.000
#> GSM550814 2 0.2165 0.853 0.064 0.936 0.000
#> GSM550815 2 0.0000 0.881 0.000 1.000 0.000
#> GSM550816 2 0.0000 0.881 0.000 1.000 0.000
#> GSM550817 3 0.0237 0.965 0.004 0.000 0.996
#> GSM550818 3 0.0237 0.965 0.004 0.000 0.996
#> GSM550819 2 0.3192 0.845 0.112 0.888 0.000
#> GSM550820 1 0.0237 0.898 0.996 0.004 0.000
#> GSM550821 2 0.7106 0.624 0.076 0.700 0.224
#> GSM550822 2 0.0000 0.881 0.000 1.000 0.000
#> GSM550826 1 0.4702 0.684 0.788 0.000 0.212
#> GSM550832 2 0.2165 0.853 0.064 0.936 0.000
#> GSM550833 2 0.0000 0.881 0.000 1.000 0.000
#> GSM550835 3 0.5319 0.830 0.072 0.104 0.824
#> GSM550836 3 0.0000 0.965 0.000 0.000 1.000
#> GSM550837 2 0.5331 0.779 0.076 0.824 0.100
#> GSM550838 1 0.0000 0.895 1.000 0.000 0.000
#> GSM550841 3 0.0237 0.965 0.004 0.000 0.996
#> GSM550842 2 0.7184 0.602 0.072 0.688 0.240
#> GSM550846 2 0.5560 0.640 0.300 0.700 0.000
#> GSM550849 1 0.1411 0.883 0.964 0.036 0.000
#> GSM550850 1 0.2066 0.924 0.940 0.060 0.000
#> GSM550851 2 0.7222 0.595 0.072 0.684 0.244
#> GSM550852 2 0.2356 0.849 0.072 0.928 0.000
#> GSM550853 2 0.0000 0.881 0.000 1.000 0.000
#> GSM550855 2 0.0000 0.881 0.000 1.000 0.000
#> GSM550856 2 0.0000 0.881 0.000 1.000 0.000
#> GSM550861 2 0.0000 0.881 0.000 1.000 0.000
#> GSM550863 2 0.5785 0.581 0.332 0.668 0.000
#> GSM550864 2 0.0000 0.881 0.000 1.000 0.000
#> GSM550866 2 0.0000 0.881 0.000 1.000 0.000
#> GSM550867 1 0.2448 0.925 0.924 0.076 0.000
#> GSM550885 1 0.2448 0.925 0.924 0.076 0.000
#> GSM550886 3 0.2400 0.936 0.064 0.004 0.932
#> GSM550887 2 0.0000 0.881 0.000 1.000 0.000
#> GSM550889 2 0.5291 0.672 0.268 0.732 0.000
#> GSM550894 2 0.2261 0.851 0.068 0.932 0.000
#> GSM550897 1 0.2448 0.925 0.924 0.076 0.000
#> GSM550903 2 0.0000 0.881 0.000 1.000 0.000
#> GSM550905 2 0.4565 0.809 0.076 0.860 0.064
#> GSM550906 2 0.0000 0.881 0.000 1.000 0.000
#> GSM550907 3 0.0000 0.965 0.000 0.000 1.000
#> GSM550909 2 0.5000 0.814 0.124 0.832 0.044
#> GSM550911 3 0.0000 0.965 0.000 0.000 1.000
#> GSM550913 2 0.0000 0.881 0.000 1.000 0.000
#> GSM550915 2 0.5591 0.627 0.304 0.696 0.000
#> GSM550917 2 0.0000 0.881 0.000 1.000 0.000
#> GSM550919 2 0.5465 0.649 0.288 0.712 0.000
#> GSM550921 3 0.0000 0.965 0.000 0.000 1.000
#> GSM550924 2 0.9281 0.480 0.276 0.520 0.204
#> GSM550926 2 0.0000 0.881 0.000 1.000 0.000
#> GSM550927 2 0.0000 0.881 0.000 1.000 0.000
#> GSM550787 1 0.5497 0.539 0.708 0.000 0.292
#> GSM550793 3 0.2356 0.933 0.072 0.000 0.928
#> GSM550794 2 0.5835 0.650 0.340 0.660 0.000
#> GSM550795 1 0.2165 0.925 0.936 0.064 0.000
#> GSM550798 1 0.3038 0.812 0.896 0.000 0.104
#> GSM550803 1 0.1289 0.913 0.968 0.032 0.000
#> GSM550805 1 0.1753 0.879 0.952 0.048 0.000
#> GSM550823 2 0.3412 0.832 0.124 0.876 0.000
#> GSM550824 1 0.2448 0.925 0.924 0.076 0.000
#> GSM550825 3 0.0000 0.965 0.000 0.000 1.000
#> GSM550827 2 0.5560 0.634 0.300 0.700 0.000
#> GSM550828 1 0.2448 0.925 0.924 0.076 0.000
#> GSM550829 1 0.5948 0.378 0.640 0.000 0.360
#> GSM550830 2 0.4399 0.760 0.188 0.812 0.000
#> GSM550834 1 0.2165 0.925 0.936 0.064 0.000
#> GSM550839 3 0.5319 0.830 0.072 0.104 0.824
#> GSM550840 1 0.2165 0.925 0.936 0.064 0.000
#> GSM550843 3 0.0237 0.965 0.004 0.000 0.996
#> GSM550844 1 0.0237 0.898 0.996 0.004 0.000
#> GSM550845 2 0.0000 0.881 0.000 1.000 0.000
#> GSM550848 2 0.5497 0.643 0.292 0.708 0.000
#> GSM550854 1 0.2448 0.925 0.924 0.076 0.000
#> GSM550857 3 0.0000 0.965 0.000 0.000 1.000
#> GSM550858 1 0.2448 0.925 0.924 0.076 0.000
#> GSM550859 1 0.2448 0.925 0.924 0.076 0.000
#> GSM550862 1 0.2448 0.925 0.924 0.076 0.000
#> GSM550865 2 0.5529 0.638 0.296 0.704 0.000
#> GSM550868 2 0.5706 0.602 0.320 0.680 0.000
#> GSM550869 1 0.6595 0.667 0.744 0.076 0.180
#> GSM550870 2 0.0000 0.881 0.000 1.000 0.000
#> GSM550871 3 0.5481 0.822 0.076 0.108 0.816
#> GSM550872 2 0.5926 0.532 0.356 0.644 0.000
#> GSM550873 2 0.2448 0.847 0.076 0.924 0.000
#> GSM550874 2 0.0000 0.881 0.000 1.000 0.000
#> GSM550876 3 0.1529 0.952 0.040 0.000 0.960
#> GSM550877 2 0.0000 0.881 0.000 1.000 0.000
#> GSM550878 3 0.0000 0.965 0.000 0.000 1.000
#> GSM550879 1 0.2448 0.925 0.924 0.076 0.000
#> GSM550882 3 0.0000 0.965 0.000 0.000 1.000
#> GSM550888 3 0.0000 0.965 0.000 0.000 1.000
#> GSM550890 2 0.5650 0.615 0.312 0.688 0.000
#> GSM550891 3 0.0000 0.965 0.000 0.000 1.000
#> GSM550892 1 0.2448 0.925 0.924 0.076 0.000
#> GSM550893 2 0.0000 0.881 0.000 1.000 0.000
#> GSM550895 2 0.0000 0.881 0.000 1.000 0.000
#> GSM550896 2 0.0000 0.881 0.000 1.000 0.000
#> GSM550898 1 0.2448 0.925 0.924 0.076 0.000
#> GSM550899 2 0.0000 0.881 0.000 1.000 0.000
#> GSM550900 2 0.5733 0.597 0.324 0.676 0.000
#> GSM550901 1 0.2448 0.925 0.924 0.076 0.000
#> GSM550902 1 0.4605 0.696 0.796 0.000 0.204
#> GSM550904 1 0.0000 0.895 1.000 0.000 0.000
#> GSM550908 3 0.0000 0.965 0.000 0.000 1.000
#> GSM550912 2 0.0000 0.881 0.000 1.000 0.000
#> GSM550914 2 0.5497 0.645 0.292 0.708 0.000
#> GSM550918 2 0.0000 0.881 0.000 1.000 0.000
#> GSM550922 3 0.1529 0.952 0.040 0.000 0.960
#> GSM550923 1 0.0000 0.895 1.000 0.000 0.000
#> GSM550925 1 0.2448 0.925 0.924 0.076 0.000
#> GSM550802 2 0.3686 0.834 0.140 0.860 0.000
#> GSM550812 2 0.4555 0.798 0.200 0.800 0.000
#> GSM550831 1 0.2066 0.924 0.940 0.060 0.000
#> GSM550847 1 0.2448 0.925 0.924 0.076 0.000
#> GSM550860 3 0.2356 0.933 0.072 0.000 0.928
#> GSM550875 1 0.0747 0.892 0.984 0.016 0.000
#> GSM550880 1 0.2448 0.925 0.924 0.076 0.000
#> GSM550881 3 0.0000 0.965 0.000 0.000 1.000
#> GSM550883 3 0.0000 0.965 0.000 0.000 1.000
#> GSM550884 2 0.4452 0.804 0.192 0.808 0.000
#> GSM550910 3 0.1289 0.956 0.032 0.000 0.968
#> GSM550916 1 0.2261 0.925 0.932 0.068 0.000
#> GSM550920 3 0.1643 0.950 0.044 0.000 0.956
cbind(get_classes(res, k = 4), get_membership(res, k = 4))
#> class entropy silhouette p1 p2 p3 p4
#> GSM550785 1 0.4406 0.56831 0.700 0.000 0.000 0.300
#> GSM550786 4 0.5957 0.02932 0.000 0.048 0.364 0.588
#> GSM550788 2 0.0000 0.83807 0.000 1.000 0.000 0.000
#> GSM550789 2 0.0000 0.83807 0.000 1.000 0.000 0.000
#> GSM550790 1 0.4585 0.55739 0.668 0.000 0.000 0.332
#> GSM550791 1 0.4994 0.48458 0.520 0.000 0.000 0.480
#> GSM550792 4 0.7028 0.51013 0.196 0.228 0.000 0.576
#> GSM550796 2 0.0000 0.83807 0.000 1.000 0.000 0.000
#> GSM550797 2 0.0000 0.83807 0.000 1.000 0.000 0.000
#> GSM550799 3 0.4564 0.64028 0.000 0.000 0.672 0.328
#> GSM550800 2 0.0469 0.83777 0.012 0.988 0.000 0.000
#> GSM550801 2 0.0000 0.83807 0.000 1.000 0.000 0.000
#> GSM550804 2 0.3569 0.80146 0.196 0.804 0.000 0.000
#> GSM550806 3 0.3873 0.72663 0.000 0.000 0.772 0.228
#> GSM550807 2 0.0000 0.83807 0.000 1.000 0.000 0.000
#> GSM550808 4 0.4898 0.43709 0.000 0.416 0.000 0.584
#> GSM550809 4 0.4977 -0.28625 0.460 0.000 0.000 0.540
#> GSM550810 2 0.3942 0.47504 0.000 0.764 0.000 0.236
#> GSM550811 4 0.4539 0.40994 0.272 0.008 0.000 0.720
#> GSM550813 2 0.2973 0.81715 0.144 0.856 0.000 0.000
#> GSM550814 2 0.2256 0.79455 0.020 0.924 0.000 0.056
#> GSM550815 2 0.0000 0.83807 0.000 1.000 0.000 0.000
#> GSM550816 2 0.2345 0.82636 0.100 0.900 0.000 0.000
#> GSM550817 3 0.4008 0.71615 0.000 0.000 0.756 0.244
#> GSM550818 3 0.3907 0.72438 0.000 0.000 0.768 0.232
#> GSM550819 4 0.7665 0.30978 0.304 0.240 0.000 0.456
#> GSM550820 1 0.4843 0.40050 0.604 0.000 0.000 0.396
#> GSM550821 4 0.6276 0.45769 0.048 0.368 0.008 0.576
#> GSM550822 2 0.0000 0.83807 0.000 1.000 0.000 0.000
#> GSM550826 4 0.4630 0.49252 0.196 0.000 0.036 0.768
#> GSM550832 2 0.1637 0.78083 0.000 0.940 0.000 0.060
#> GSM550833 2 0.0188 0.83536 0.000 0.996 0.000 0.004
#> GSM550835 4 0.6964 0.32124 0.000 0.228 0.188 0.584
#> GSM550836 3 0.0000 0.80632 0.000 0.000 1.000 0.000
#> GSM550837 4 0.4866 0.45119 0.000 0.404 0.000 0.596
#> GSM550838 4 0.4477 -0.12512 0.312 0.000 0.000 0.688
#> GSM550841 3 0.4564 0.64028 0.000 0.000 0.672 0.328
#> GSM550842 4 0.5846 0.37235 0.000 0.452 0.032 0.516
#> GSM550846 1 0.7070 0.00518 0.516 0.348 0.000 0.136
#> GSM550849 4 0.3123 0.36103 0.156 0.000 0.000 0.844
#> GSM550850 1 0.4985 0.48933 0.532 0.000 0.000 0.468
#> GSM550851 4 0.5827 0.39994 0.000 0.436 0.032 0.532
#> GSM550852 2 0.4817 0.02521 0.000 0.612 0.000 0.388
#> GSM550853 2 0.0000 0.83807 0.000 1.000 0.000 0.000
#> GSM550855 2 0.0000 0.83807 0.000 1.000 0.000 0.000
#> GSM550856 2 0.3486 0.80480 0.188 0.812 0.000 0.000
#> GSM550861 2 0.0000 0.83807 0.000 1.000 0.000 0.000
#> GSM550863 1 0.5769 0.05688 0.588 0.376 0.000 0.036
#> GSM550864 2 0.3528 0.80343 0.192 0.808 0.000 0.000
#> GSM550866 2 0.3528 0.80343 0.192 0.808 0.000 0.000
#> GSM550867 1 0.4431 0.56802 0.696 0.000 0.000 0.304
#> GSM550885 1 0.4406 0.56831 0.700 0.000 0.000 0.300
#> GSM550886 4 0.6140 -0.22918 0.000 0.048 0.452 0.500
#> GSM550887 2 0.0000 0.83807 0.000 1.000 0.000 0.000
#> GSM550889 1 0.5935 -0.22274 0.496 0.468 0.000 0.036
#> GSM550894 2 0.1716 0.77590 0.000 0.936 0.000 0.064
#> GSM550897 1 0.1398 0.45816 0.956 0.004 0.000 0.040
#> GSM550903 2 0.0000 0.83807 0.000 1.000 0.000 0.000
#> GSM550905 4 0.4941 0.40851 0.000 0.436 0.000 0.564
#> GSM550906 2 0.0000 0.83807 0.000 1.000 0.000 0.000
#> GSM550907 3 0.0000 0.80632 0.000 0.000 1.000 0.000
#> GSM550909 4 0.6323 0.54040 0.164 0.176 0.000 0.660
#> GSM550911 3 0.0000 0.80632 0.000 0.000 1.000 0.000
#> GSM550913 2 0.0000 0.83807 0.000 1.000 0.000 0.000
#> GSM550915 1 0.5805 0.02698 0.576 0.388 0.000 0.036
#> GSM550917 2 0.3569 0.80146 0.196 0.804 0.000 0.000
#> GSM550919 1 0.5847 -0.02248 0.560 0.404 0.000 0.036
#> GSM550921 3 0.0000 0.80632 0.000 0.000 1.000 0.000
#> GSM550924 4 0.5979 0.51275 0.292 0.044 0.012 0.652
#> GSM550926 2 0.3528 0.80329 0.192 0.808 0.000 0.000
#> GSM550927 2 0.0000 0.83807 0.000 1.000 0.000 0.000
#> GSM550787 4 0.4037 0.50451 0.112 0.000 0.056 0.832
#> GSM550793 4 0.6189 0.06514 0.060 0.000 0.372 0.568
#> GSM550794 4 0.7001 0.42428 0.316 0.140 0.000 0.544
#> GSM550795 1 0.4994 0.48657 0.520 0.000 0.000 0.480
#> GSM550798 4 0.5281 -0.36705 0.464 0.000 0.008 0.528
#> GSM550803 1 0.4730 0.54043 0.636 0.000 0.000 0.364
#> GSM550805 4 0.4040 0.48430 0.248 0.000 0.000 0.752
#> GSM550823 2 0.7519 0.35046 0.312 0.480 0.000 0.208
#> GSM550824 1 0.4431 0.56802 0.696 0.000 0.000 0.304
#> GSM550825 3 0.0000 0.80632 0.000 0.000 1.000 0.000
#> GSM550827 1 0.5781 0.04712 0.584 0.380 0.000 0.036
#> GSM550828 1 0.3688 0.54857 0.792 0.000 0.000 0.208
#> GSM550829 4 0.6717 -0.01110 0.332 0.000 0.108 0.560
#> GSM550830 2 0.6785 0.42681 0.352 0.540 0.000 0.108
#> GSM550834 1 0.4985 0.49750 0.532 0.000 0.000 0.468
#> GSM550839 4 0.6307 0.08645 0.012 0.048 0.344 0.596
#> GSM550840 1 0.4994 0.48657 0.520 0.000 0.000 0.480
#> GSM550843 3 0.4564 0.64028 0.000 0.000 0.672 0.328
#> GSM550844 1 0.4624 0.37708 0.660 0.000 0.000 0.340
#> GSM550845 2 0.3908 0.78324 0.212 0.784 0.000 0.004
#> GSM550848 1 0.5816 0.01509 0.572 0.392 0.000 0.036
#> GSM550854 1 0.4431 0.56802 0.696 0.000 0.000 0.304
#> GSM550857 3 0.0000 0.80632 0.000 0.000 1.000 0.000
#> GSM550858 1 0.4406 0.56831 0.700 0.000 0.000 0.300
#> GSM550859 1 0.4431 0.56802 0.696 0.000 0.000 0.304
#> GSM550862 1 0.4406 0.56831 0.700 0.000 0.000 0.300
#> GSM550865 1 0.5888 -0.08765 0.540 0.424 0.000 0.036
#> GSM550868 1 0.5769 0.05688 0.588 0.376 0.000 0.036
#> GSM550869 4 0.4436 0.52979 0.216 0.000 0.020 0.764
#> GSM550870 2 0.3569 0.80146 0.196 0.804 0.000 0.000
#> GSM550871 4 0.6870 0.17435 0.044 0.048 0.308 0.600
#> GSM550872 1 0.6309 0.11796 0.588 0.336 0.000 0.076
#> GSM550873 4 0.5476 0.44925 0.020 0.396 0.000 0.584
#> GSM550874 2 0.0188 0.83812 0.004 0.996 0.000 0.000
#> GSM550876 3 0.4941 0.45775 0.000 0.000 0.564 0.436
#> GSM550877 2 0.3569 0.80146 0.196 0.804 0.000 0.000
#> GSM550878 3 0.1302 0.79592 0.000 0.000 0.956 0.044
#> GSM550879 1 0.3356 0.51595 0.824 0.000 0.000 0.176
#> GSM550882 3 0.0000 0.80632 0.000 0.000 1.000 0.000
#> GSM550888 3 0.0000 0.80632 0.000 0.000 1.000 0.000
#> GSM550890 1 0.5805 0.02698 0.576 0.388 0.000 0.036
#> GSM550891 3 0.0000 0.80632 0.000 0.000 1.000 0.000
#> GSM550892 1 0.0707 0.46705 0.980 0.000 0.000 0.020
#> GSM550893 2 0.4123 0.77001 0.220 0.772 0.000 0.008
#> GSM550895 2 0.5432 0.59857 0.316 0.652 0.000 0.032
#> GSM550896 2 0.3569 0.80146 0.196 0.804 0.000 0.000
#> GSM550898 1 0.4431 0.56802 0.696 0.000 0.000 0.304
#> GSM550899 2 0.3569 0.80146 0.196 0.804 0.000 0.000
#> GSM550900 1 0.5713 0.09030 0.604 0.360 0.000 0.036
#> GSM550901 1 0.1716 0.47193 0.936 0.000 0.000 0.064
#> GSM550902 4 0.5339 0.40384 0.356 0.000 0.020 0.624
#> GSM550904 1 0.4981 0.21350 0.536 0.000 0.000 0.464
#> GSM550908 3 0.0000 0.80632 0.000 0.000 1.000 0.000
#> GSM550912 2 0.4228 0.75605 0.232 0.760 0.000 0.008
#> GSM550914 1 0.5805 0.02698 0.576 0.388 0.000 0.036
#> GSM550918 2 0.3569 0.80146 0.196 0.804 0.000 0.000
#> GSM550922 3 0.6137 0.33273 0.000 0.048 0.504 0.448
#> GSM550923 1 0.4888 0.50081 0.588 0.000 0.000 0.412
#> GSM550925 1 0.1211 0.45985 0.960 0.000 0.000 0.040
#> GSM550802 4 0.7211 0.50069 0.192 0.264 0.000 0.544
#> GSM550812 4 0.7137 0.44852 0.288 0.168 0.000 0.544
#> GSM550831 1 0.4985 0.48933 0.532 0.000 0.000 0.468
#> GSM550847 1 0.4431 0.56802 0.696 0.000 0.000 0.304
#> GSM550860 4 0.5792 -0.10046 0.032 0.000 0.416 0.552
#> GSM550875 4 0.4222 0.41396 0.272 0.000 0.000 0.728
#> GSM550880 1 0.4804 0.54222 0.616 0.000 0.000 0.384
#> GSM550881 3 0.0000 0.80632 0.000 0.000 1.000 0.000
#> GSM550883 3 0.0000 0.80632 0.000 0.000 1.000 0.000
#> GSM550884 4 0.7506 0.36818 0.308 0.208 0.000 0.484
#> GSM550910 3 0.4866 0.52122 0.000 0.000 0.596 0.404
#> GSM550916 1 0.4431 0.56802 0.696 0.000 0.000 0.304
#> GSM550920 3 0.4941 0.45706 0.000 0.000 0.564 0.436
cbind(get_classes(res, k = 5), get_membership(res, k = 5))
#> class entropy silhouette p1 p2 p3 p4 p5
#> GSM550785 1 0.0162 0.6825 0.996 0.000 0.004 0.000 0.000
#> GSM550786 5 0.4651 0.5238 0.000 0.000 0.020 0.372 0.608
#> GSM550788 2 0.4183 0.6367 0.000 0.668 0.324 0.008 0.000
#> GSM550789 2 0.3990 0.6404 0.000 0.688 0.308 0.004 0.000
#> GSM550790 1 0.1704 0.6585 0.928 0.000 0.004 0.068 0.000
#> GSM550791 1 0.4540 0.4949 0.656 0.000 0.024 0.320 0.000
#> GSM550792 4 0.3343 0.5991 0.004 0.068 0.012 0.864 0.052
#> GSM550796 2 0.4009 0.6385 0.000 0.684 0.312 0.004 0.000
#> GSM550797 2 0.3990 0.6404 0.000 0.688 0.308 0.004 0.000
#> GSM550799 5 0.2411 0.5752 0.000 0.000 0.008 0.108 0.884
#> GSM550800 2 0.4046 0.6459 0.000 0.696 0.296 0.008 0.000
#> GSM550801 2 0.3949 0.6436 0.000 0.696 0.300 0.004 0.000
#> GSM550804 2 0.1872 0.6211 0.000 0.928 0.052 0.020 0.000
#> GSM550806 5 0.3476 0.4201 0.000 0.000 0.076 0.088 0.836
#> GSM550807 2 0.3949 0.6436 0.000 0.696 0.300 0.004 0.000
#> GSM550808 5 0.7117 0.4380 0.000 0.032 0.280 0.208 0.480
#> GSM550809 4 0.4565 0.2555 0.308 0.000 0.028 0.664 0.000
#> GSM550810 2 0.6397 0.5217 0.000 0.540 0.312 0.132 0.016
#> GSM550811 4 0.3205 0.5898 0.052 0.004 0.020 0.876 0.048
#> GSM550813 2 0.2074 0.6499 0.000 0.896 0.104 0.000 0.000
#> GSM550814 2 0.5105 0.6098 0.000 0.660 0.264 0.076 0.000
#> GSM550815 2 0.4009 0.6400 0.000 0.684 0.312 0.004 0.000
#> GSM550816 2 0.3596 0.6495 0.000 0.776 0.212 0.012 0.000
#> GSM550817 5 0.3239 0.3981 0.000 0.000 0.080 0.068 0.852
#> GSM550818 5 0.3719 0.3202 0.000 0.000 0.116 0.068 0.816
#> GSM550819 4 0.6136 0.2707 0.000 0.364 0.024 0.536 0.076
#> GSM550820 4 0.4702 0.1027 0.432 0.000 0.016 0.552 0.000
#> GSM550821 5 0.6437 0.5534 0.000 0.028 0.120 0.288 0.564
#> GSM550822 2 0.4029 0.6381 0.000 0.680 0.316 0.004 0.000
#> GSM550826 4 0.4775 0.3749 0.036 0.008 0.000 0.688 0.268
#> GSM550832 2 0.5122 0.6027 0.000 0.628 0.312 0.060 0.000
#> GSM550833 2 0.4127 0.6365 0.000 0.680 0.312 0.008 0.000
#> GSM550835 5 0.6427 0.5585 0.000 0.020 0.136 0.288 0.556
#> GSM550836 3 0.5059 0.9751 0.000 0.000 0.548 0.036 0.416
#> GSM550837 5 0.6836 0.4798 0.000 0.024 0.280 0.184 0.512
#> GSM550838 4 0.5152 0.0933 0.392 0.000 0.024 0.572 0.012
#> GSM550841 5 0.1952 0.5601 0.000 0.000 0.004 0.084 0.912
#> GSM550842 5 0.6651 0.4835 0.000 0.028 0.280 0.148 0.544
#> GSM550846 2 0.7328 0.0602 0.096 0.428 0.080 0.392 0.004
#> GSM550849 4 0.5342 0.4542 0.176 0.000 0.032 0.712 0.080
#> GSM550850 1 0.4503 0.5050 0.664 0.000 0.024 0.312 0.000
#> GSM550851 5 0.6803 0.4849 0.000 0.028 0.280 0.168 0.524
#> GSM550852 2 0.7530 0.2739 0.000 0.388 0.292 0.280 0.040
#> GSM550853 2 0.4047 0.6420 0.000 0.676 0.320 0.004 0.000
#> GSM550855 2 0.3969 0.6440 0.000 0.692 0.304 0.004 0.000
#> GSM550856 2 0.1331 0.6430 0.000 0.952 0.040 0.008 0.000
#> GSM550861 2 0.3796 0.6445 0.000 0.700 0.300 0.000 0.000
#> GSM550863 2 0.7574 0.2451 0.156 0.488 0.100 0.256 0.000
#> GSM550864 2 0.0912 0.6409 0.000 0.972 0.016 0.012 0.000
#> GSM550866 2 0.1211 0.6363 0.000 0.960 0.024 0.016 0.000
#> GSM550867 1 0.0000 0.6833 1.000 0.000 0.000 0.000 0.000
#> GSM550885 1 0.0880 0.6742 0.968 0.000 0.032 0.000 0.000
#> GSM550886 5 0.4243 0.6152 0.000 0.000 0.024 0.264 0.712
#> GSM550887 2 0.4029 0.6381 0.000 0.680 0.316 0.004 0.000
#> GSM550889 2 0.7226 0.2835 0.128 0.528 0.088 0.256 0.000
#> GSM550894 2 0.5272 0.6001 0.000 0.624 0.312 0.060 0.004
#> GSM550897 1 0.8085 0.0945 0.336 0.300 0.092 0.272 0.000
#> GSM550903 2 0.3816 0.6443 0.000 0.696 0.304 0.000 0.000
#> GSM550905 5 0.6635 0.5554 0.000 0.032 0.148 0.260 0.560
#> GSM550906 2 0.4029 0.6381 0.000 0.680 0.316 0.004 0.000
#> GSM550907 3 0.4897 0.9558 0.000 0.000 0.516 0.024 0.460
#> GSM550909 4 0.5103 -0.2857 0.000 0.000 0.036 0.512 0.452
#> GSM550911 3 0.4894 0.9583 0.000 0.000 0.520 0.024 0.456
#> GSM550913 2 0.3774 0.6452 0.000 0.704 0.296 0.000 0.000
#> GSM550915 2 0.7390 0.2592 0.160 0.504 0.080 0.256 0.000
#> GSM550917 2 0.0671 0.6431 0.000 0.980 0.016 0.004 0.000
#> GSM550919 2 0.7161 0.2833 0.156 0.532 0.068 0.244 0.000
#> GSM550921 3 0.5059 0.9751 0.000 0.000 0.548 0.036 0.416
#> GSM550924 4 0.5669 0.1816 0.000 0.076 0.008 0.588 0.328
#> GSM550926 2 0.1195 0.6366 0.000 0.960 0.012 0.028 0.000
#> GSM550927 2 0.3796 0.6451 0.000 0.700 0.300 0.000 0.000
#> GSM550787 5 0.5146 0.2831 0.008 0.016 0.004 0.480 0.492
#> GSM550793 4 0.4581 0.1423 0.012 0.000 0.004 0.624 0.360
#> GSM550794 4 0.3184 0.5850 0.000 0.100 0.000 0.852 0.048
#> GSM550795 1 0.4747 0.4858 0.636 0.000 0.032 0.332 0.000
#> GSM550798 1 0.4777 0.4670 0.708 0.000 0.012 0.240 0.040
#> GSM550803 1 0.2011 0.6480 0.908 0.000 0.004 0.088 0.000
#> GSM550805 4 0.3218 0.5764 0.016 0.020 0.000 0.856 0.108
#> GSM550823 2 0.5096 0.1111 0.000 0.520 0.036 0.444 0.000
#> GSM550824 1 0.0000 0.6833 1.000 0.000 0.000 0.000 0.000
#> GSM550825 3 0.5092 0.9491 0.000 0.000 0.524 0.036 0.440
#> GSM550827 2 0.7384 0.2545 0.164 0.508 0.080 0.248 0.000
#> GSM550828 1 0.5097 0.4629 0.712 0.020 0.064 0.204 0.000
#> GSM550829 1 0.6924 -0.1639 0.444 0.000 0.024 0.368 0.164
#> GSM550830 2 0.5302 0.3142 0.008 0.608 0.048 0.336 0.000
#> GSM550834 1 0.4655 0.4896 0.644 0.000 0.028 0.328 0.000
#> GSM550839 5 0.4717 0.5039 0.000 0.000 0.020 0.396 0.584
#> GSM550840 1 0.4671 0.4852 0.640 0.000 0.028 0.332 0.000
#> GSM550843 5 0.2389 0.5818 0.000 0.000 0.004 0.116 0.880
#> GSM550844 4 0.4874 0.1691 0.388 0.008 0.016 0.588 0.000
#> GSM550845 2 0.2863 0.5937 0.000 0.876 0.060 0.064 0.000
#> GSM550848 2 0.7169 0.2835 0.148 0.532 0.072 0.248 0.000
#> GSM550854 1 0.0000 0.6833 1.000 0.000 0.000 0.000 0.000
#> GSM550857 3 0.5052 0.9741 0.000 0.000 0.552 0.036 0.412
#> GSM550858 1 0.1408 0.6660 0.948 0.000 0.044 0.008 0.000
#> GSM550859 1 0.0000 0.6833 1.000 0.000 0.000 0.000 0.000
#> GSM550862 1 0.3504 0.5954 0.840 0.004 0.064 0.092 0.000
#> GSM550865 2 0.7413 0.2670 0.140 0.508 0.096 0.256 0.000
#> GSM550868 2 0.7534 0.2466 0.156 0.492 0.096 0.256 0.000
#> GSM550869 4 0.4029 0.4020 0.000 0.024 0.000 0.744 0.232
#> GSM550870 2 0.0579 0.6402 0.000 0.984 0.008 0.008 0.000
#> GSM550871 5 0.4851 0.4559 0.000 0.012 0.008 0.420 0.560
#> GSM550872 2 0.7762 0.1436 0.168 0.432 0.096 0.304 0.000
#> GSM550873 5 0.6902 0.4096 0.000 0.036 0.128 0.396 0.440
#> GSM550874 2 0.4086 0.6459 0.000 0.704 0.284 0.012 0.000
#> GSM550876 5 0.3109 0.6330 0.000 0.000 0.000 0.200 0.800
#> GSM550877 2 0.1300 0.6340 0.000 0.956 0.028 0.016 0.000
#> GSM550878 5 0.4774 -0.7784 0.000 0.000 0.424 0.020 0.556
#> GSM550879 1 0.7249 0.2823 0.524 0.152 0.076 0.248 0.000
#> GSM550882 3 0.4965 0.9413 0.000 0.000 0.520 0.028 0.452
#> GSM550888 3 0.5059 0.9751 0.000 0.000 0.548 0.036 0.416
#> GSM550890 2 0.7479 0.2552 0.160 0.496 0.088 0.256 0.000
#> GSM550891 3 0.5059 0.9751 0.000 0.000 0.548 0.036 0.416
#> GSM550892 1 0.7939 0.1604 0.400 0.264 0.088 0.248 0.000
#> GSM550893 2 0.1469 0.6291 0.000 0.948 0.016 0.036 0.000
#> GSM550895 2 0.4769 0.4195 0.000 0.688 0.056 0.256 0.000
#> GSM550896 2 0.1300 0.6333 0.000 0.956 0.028 0.016 0.000
#> GSM550898 1 0.0000 0.6833 1.000 0.000 0.000 0.000 0.000
#> GSM550899 2 0.0566 0.6382 0.000 0.984 0.004 0.012 0.000
#> GSM550900 2 0.7549 0.2405 0.164 0.488 0.092 0.256 0.000
#> GSM550901 1 0.7673 0.1907 0.428 0.264 0.064 0.244 0.000
#> GSM550902 4 0.5432 0.5273 0.116 0.012 0.012 0.716 0.144
#> GSM550904 4 0.4565 0.3097 0.352 0.000 0.008 0.632 0.008
#> GSM550908 3 0.5059 0.9751 0.000 0.000 0.548 0.036 0.416
#> GSM550912 2 0.1386 0.6339 0.000 0.952 0.016 0.032 0.000
#> GSM550914 2 0.7479 0.2552 0.160 0.496 0.088 0.256 0.000
#> GSM550918 2 0.1597 0.6263 0.000 0.940 0.048 0.012 0.000
#> GSM550922 5 0.3639 0.6395 0.000 0.000 0.024 0.184 0.792
#> GSM550923 1 0.2522 0.6293 0.880 0.000 0.012 0.108 0.000
#> GSM550925 1 0.7674 0.1701 0.412 0.288 0.060 0.240 0.000
#> GSM550802 4 0.3597 0.5915 0.000 0.076 0.024 0.848 0.052
#> GSM550812 4 0.3346 0.5891 0.000 0.092 0.000 0.844 0.064
#> GSM550831 1 0.4584 0.5026 0.660 0.000 0.028 0.312 0.000
#> GSM550847 1 0.0000 0.6833 1.000 0.000 0.000 0.000 0.000
#> GSM550860 5 0.4538 0.3287 0.000 0.000 0.008 0.452 0.540
#> GSM550875 4 0.3291 0.5838 0.028 0.016 0.000 0.856 0.100
#> GSM550880 1 0.4527 0.5468 0.700 0.000 0.040 0.260 0.000
#> GSM550881 3 0.5083 0.9582 0.000 0.000 0.532 0.036 0.432
#> GSM550883 3 0.5182 0.9723 0.000 0.000 0.544 0.044 0.412
#> GSM550884 4 0.6236 0.3696 0.012 0.332 0.008 0.556 0.092
#> GSM550910 5 0.2561 0.6297 0.000 0.000 0.000 0.144 0.856
#> GSM550916 1 0.0000 0.6833 1.000 0.000 0.000 0.000 0.000
#> GSM550920 5 0.3177 0.6310 0.000 0.000 0.000 0.208 0.792
cbind(get_classes(res, k = 6), get_membership(res, k = 6))
#> class entropy silhouette p1 p2 p3 p4 p5 p6
#> GSM550785 1 0.2178 0.817019 0.868 0.000 0.000 0.132 0.000 0.000
#> GSM550786 5 0.2848 0.701781 0.000 0.000 0.008 0.004 0.828 0.160
#> GSM550788 2 0.1262 0.772739 0.000 0.956 0.000 0.020 0.008 0.016
#> GSM550789 2 0.0653 0.775815 0.000 0.980 0.000 0.004 0.004 0.012
#> GSM550790 1 0.1492 0.744292 0.940 0.000 0.000 0.024 0.000 0.036
#> GSM550791 6 0.4305 0.224616 0.436 0.000 0.000 0.020 0.000 0.544
#> GSM550792 6 0.3441 0.575362 0.004 0.012 0.000 0.060 0.092 0.832
#> GSM550796 2 0.0909 0.772713 0.000 0.968 0.000 0.000 0.020 0.012
#> GSM550797 2 0.0653 0.775815 0.000 0.980 0.000 0.004 0.004 0.012
#> GSM550799 5 0.3053 0.708219 0.000 0.000 0.144 0.004 0.828 0.024
#> GSM550800 2 0.2320 0.738987 0.000 0.864 0.000 0.132 0.000 0.004
#> GSM550801 2 0.0146 0.776695 0.000 0.996 0.000 0.004 0.000 0.000
#> GSM550804 4 0.5669 -0.082888 0.000 0.436 0.000 0.464 0.060 0.040
#> GSM550806 5 0.4053 0.639503 0.000 0.000 0.200 0.008 0.744 0.048
#> GSM550807 2 0.0260 0.777156 0.000 0.992 0.000 0.008 0.000 0.000
#> GSM550808 5 0.5143 0.529391 0.004 0.280 0.000 0.000 0.608 0.108
#> GSM550809 6 0.4004 0.544854 0.172 0.000 0.008 0.032 0.016 0.772
#> GSM550810 2 0.2988 0.692252 0.000 0.852 0.000 0.004 0.060 0.084
#> GSM550811 6 0.2973 0.582032 0.016 0.000 0.000 0.040 0.084 0.860
#> GSM550813 2 0.3487 0.656195 0.000 0.776 0.000 0.200 0.012 0.012
#> GSM550814 2 0.3821 0.710626 0.000 0.808 0.000 0.092 0.032 0.068
#> GSM550815 2 0.1180 0.774741 0.000 0.960 0.000 0.012 0.012 0.016
#> GSM550816 2 0.3563 0.691785 0.000 0.808 0.000 0.132 0.048 0.012
#> GSM550817 5 0.3711 0.607783 0.020 0.000 0.216 0.004 0.756 0.004
#> GSM550818 5 0.4053 0.529463 0.020 0.000 0.272 0.004 0.700 0.004
#> GSM550819 4 0.4927 0.420584 0.004 0.020 0.000 0.640 0.044 0.292
#> GSM550820 6 0.6458 0.389257 0.280 0.000 0.008 0.188 0.028 0.496
#> GSM550821 5 0.2920 0.725131 0.016 0.040 0.000 0.000 0.864 0.080
#> GSM550822 2 0.1173 0.773797 0.000 0.960 0.000 0.008 0.016 0.016
#> GSM550826 6 0.6110 0.199700 0.020 0.000 0.008 0.124 0.364 0.484
#> GSM550832 2 0.1716 0.753666 0.000 0.932 0.000 0.004 0.028 0.036
#> GSM550833 2 0.0976 0.773962 0.000 0.968 0.000 0.008 0.008 0.016
#> GSM550835 5 0.3367 0.710028 0.000 0.080 0.000 0.000 0.816 0.104
#> GSM550836 3 0.0260 0.924070 0.000 0.000 0.992 0.000 0.008 0.000
#> GSM550837 5 0.4332 0.574058 0.000 0.276 0.000 0.000 0.672 0.052
#> GSM550838 6 0.4275 0.501562 0.228 0.000 0.008 0.020 0.020 0.724
#> GSM550841 5 0.3223 0.687819 0.020 0.000 0.144 0.008 0.824 0.004
#> GSM550842 5 0.4086 0.593204 0.008 0.256 0.000 0.000 0.708 0.028
#> GSM550846 4 0.5204 0.690583 0.016 0.036 0.000 0.696 0.068 0.184
#> GSM550849 6 0.3590 0.577755 0.112 0.000 0.000 0.012 0.064 0.812
#> GSM550850 6 0.4403 0.159592 0.468 0.000 0.000 0.024 0.000 0.508
#> GSM550851 5 0.4310 0.581412 0.000 0.268 0.000 0.004 0.684 0.044
#> GSM550852 2 0.5045 0.348578 0.004 0.624 0.000 0.008 0.072 0.292
#> GSM550853 2 0.1370 0.774121 0.000 0.948 0.000 0.036 0.004 0.012
#> GSM550855 2 0.0790 0.775050 0.000 0.968 0.000 0.032 0.000 0.000
#> GSM550856 2 0.3699 0.553491 0.000 0.660 0.000 0.336 0.000 0.004
#> GSM550861 2 0.0291 0.776694 0.000 0.992 0.000 0.000 0.004 0.004
#> GSM550863 4 0.1913 0.775858 0.016 0.044 0.000 0.924 0.000 0.016
#> GSM550864 2 0.5106 0.402105 0.000 0.572 0.000 0.356 0.056 0.016
#> GSM550866 2 0.3975 0.366526 0.000 0.544 0.000 0.452 0.000 0.004
#> GSM550867 1 0.1957 0.824596 0.888 0.000 0.000 0.112 0.000 0.000
#> GSM550885 1 0.2378 0.805648 0.848 0.000 0.000 0.152 0.000 0.000
#> GSM550886 5 0.2765 0.737044 0.008 0.000 0.056 0.000 0.872 0.064
#> GSM550887 2 0.1262 0.772545 0.000 0.956 0.000 0.008 0.020 0.016
#> GSM550889 4 0.1914 0.775034 0.008 0.056 0.000 0.920 0.000 0.016
#> GSM550894 2 0.1867 0.747894 0.000 0.924 0.000 0.004 0.036 0.036
#> GSM550897 4 0.1909 0.754485 0.052 0.000 0.000 0.920 0.004 0.024
#> GSM550903 2 0.0665 0.776383 0.000 0.980 0.000 0.008 0.004 0.008
#> GSM550905 5 0.3301 0.709446 0.004 0.100 0.000 0.000 0.828 0.068
#> GSM550906 2 0.0665 0.776748 0.000 0.980 0.000 0.004 0.008 0.008
#> GSM550907 3 0.2643 0.878603 0.016 0.000 0.868 0.004 0.108 0.004
#> GSM550909 5 0.4303 0.351235 0.012 0.000 0.000 0.008 0.588 0.392
#> GSM550911 3 0.2346 0.892045 0.016 0.000 0.892 0.004 0.084 0.004
#> GSM550913 2 0.0551 0.776508 0.000 0.984 0.000 0.004 0.004 0.008
#> GSM550915 4 0.4433 0.761810 0.036 0.056 0.000 0.792 0.068 0.048
#> GSM550917 2 0.5172 0.473661 0.000 0.608 0.000 0.308 0.056 0.028
#> GSM550919 4 0.4438 0.762500 0.040 0.056 0.000 0.792 0.068 0.044
#> GSM550921 3 0.0551 0.923499 0.004 0.000 0.984 0.000 0.008 0.004
#> GSM550924 5 0.5945 -0.000081 0.012 0.000 0.000 0.152 0.456 0.380
#> GSM550926 2 0.3975 0.464341 0.000 0.600 0.000 0.392 0.000 0.008
#> GSM550927 2 0.0748 0.777051 0.000 0.976 0.000 0.016 0.004 0.004
#> GSM550787 5 0.5189 0.412349 0.040 0.000 0.000 0.032 0.564 0.364
#> GSM550793 6 0.5147 0.146411 0.012 0.000 0.028 0.020 0.376 0.564
#> GSM550794 6 0.5280 0.455532 0.008 0.008 0.000 0.280 0.088 0.616
#> GSM550795 6 0.4521 0.200508 0.448 0.004 0.000 0.024 0.000 0.524
#> GSM550798 1 0.4593 0.392172 0.708 0.000 0.012 0.020 0.032 0.228
#> GSM550803 1 0.1858 0.700545 0.912 0.000 0.000 0.012 0.000 0.076
#> GSM550805 6 0.4422 0.509569 0.004 0.000 0.000 0.096 0.180 0.720
#> GSM550823 4 0.4822 0.516788 0.000 0.060 0.000 0.668 0.020 0.252
#> GSM550824 1 0.1957 0.824596 0.888 0.000 0.000 0.112 0.000 0.000
#> GSM550825 3 0.3280 0.870247 0.020 0.000 0.860 0.024 0.056 0.040
#> GSM550827 4 0.4179 0.772277 0.040 0.060 0.000 0.808 0.060 0.032
#> GSM550828 1 0.5126 0.262485 0.496 0.000 0.000 0.444 0.032 0.028
#> GSM550829 6 0.6663 0.278122 0.384 0.000 0.024 0.020 0.160 0.412
#> GSM550830 4 0.4120 0.645983 0.000 0.160 0.000 0.744 0.000 0.096
#> GSM550834 6 0.4524 0.193413 0.452 0.004 0.000 0.024 0.000 0.520
#> GSM550839 5 0.3109 0.695000 0.000 0.000 0.004 0.016 0.812 0.168
#> GSM550840 6 0.4389 0.200911 0.448 0.000 0.000 0.024 0.000 0.528
#> GSM550843 5 0.3043 0.707960 0.000 0.000 0.132 0.008 0.836 0.024
#> GSM550844 6 0.6457 0.421256 0.204 0.000 0.008 0.240 0.032 0.516
#> GSM550845 4 0.4047 0.087447 0.000 0.384 0.000 0.604 0.000 0.012
#> GSM550848 4 0.4428 0.763652 0.036 0.060 0.000 0.792 0.068 0.044
#> GSM550854 1 0.1957 0.824596 0.888 0.000 0.000 0.112 0.000 0.000
#> GSM550857 3 0.0146 0.920771 0.000 0.000 0.996 0.000 0.000 0.004
#> GSM550858 1 0.2823 0.763456 0.796 0.000 0.000 0.204 0.000 0.000
#> GSM550859 1 0.1957 0.824596 0.888 0.000 0.000 0.112 0.000 0.000
#> GSM550862 1 0.3668 0.623276 0.668 0.000 0.000 0.328 0.000 0.004
#> GSM550865 4 0.1913 0.775858 0.016 0.044 0.000 0.924 0.000 0.016
#> GSM550868 4 0.1793 0.777217 0.012 0.048 0.000 0.928 0.000 0.012
#> GSM550869 6 0.4949 0.411118 0.004 0.000 0.000 0.104 0.248 0.644
#> GSM550870 2 0.4924 0.408549 0.000 0.572 0.000 0.372 0.040 0.016
#> GSM550871 5 0.3488 0.658616 0.000 0.000 0.004 0.016 0.764 0.216
#> GSM550872 4 0.1962 0.771538 0.020 0.028 0.000 0.924 0.000 0.028
#> GSM550873 5 0.5655 0.386942 0.000 0.120 0.000 0.012 0.524 0.344
#> GSM550874 2 0.1918 0.755941 0.000 0.904 0.000 0.088 0.000 0.008
#> GSM550876 5 0.2968 0.734512 0.000 0.000 0.092 0.004 0.852 0.052
#> GSM550877 2 0.4152 0.393766 0.000 0.548 0.000 0.440 0.000 0.012
#> GSM550878 3 0.4053 0.643314 0.004 0.000 0.700 0.004 0.272 0.020
#> GSM550879 4 0.5087 0.527103 0.208 0.000 0.000 0.680 0.060 0.052
#> GSM550882 3 0.2890 0.869314 0.000 0.000 0.860 0.012 0.096 0.032
#> GSM550888 3 0.0260 0.924070 0.000 0.000 0.992 0.000 0.008 0.000
#> GSM550890 4 0.4303 0.763278 0.032 0.052 0.000 0.800 0.068 0.048
#> GSM550891 3 0.0551 0.923499 0.004 0.000 0.984 0.000 0.008 0.004
#> GSM550892 4 0.3010 0.675480 0.148 0.000 0.000 0.828 0.004 0.020
#> GSM550893 2 0.4083 0.331111 0.000 0.532 0.000 0.460 0.000 0.008
#> GSM550895 4 0.3290 0.603100 0.000 0.208 0.000 0.776 0.000 0.016
#> GSM550896 2 0.4093 0.308304 0.000 0.516 0.000 0.476 0.000 0.008
#> GSM550898 1 0.1957 0.824596 0.888 0.000 0.000 0.112 0.000 0.000
#> GSM550899 2 0.5467 0.338620 0.000 0.540 0.000 0.368 0.060 0.032
#> GSM550900 4 0.1922 0.774655 0.012 0.040 0.000 0.924 0.000 0.024
#> GSM550901 4 0.4480 0.696835 0.116 0.008 0.000 0.768 0.068 0.040
#> GSM550902 6 0.6492 0.356834 0.024 0.000 0.008 0.236 0.244 0.488
#> GSM550904 6 0.6565 0.456431 0.212 0.000 0.008 0.196 0.052 0.532
#> GSM550908 3 0.0405 0.923727 0.000 0.000 0.988 0.000 0.008 0.004
#> GSM550912 2 0.5439 0.383094 0.000 0.560 0.000 0.348 0.052 0.040
#> GSM550914 4 0.4303 0.763278 0.032 0.052 0.000 0.800 0.068 0.048
#> GSM550918 2 0.5654 0.211157 0.000 0.488 0.000 0.412 0.060 0.040
#> GSM550922 5 0.2202 0.740187 0.008 0.004 0.072 0.000 0.904 0.012
#> GSM550923 1 0.2501 0.653964 0.872 0.000 0.000 0.016 0.004 0.108
#> GSM550925 4 0.4097 0.731098 0.092 0.012 0.000 0.800 0.068 0.028
#> GSM550802 6 0.4099 0.567242 0.004 0.028 0.000 0.084 0.092 0.792
#> GSM550812 6 0.5138 0.505860 0.000 0.012 0.000 0.232 0.112 0.644
#> GSM550831 6 0.4403 0.159592 0.468 0.000 0.000 0.024 0.000 0.508
#> GSM550847 1 0.1957 0.824596 0.888 0.000 0.000 0.112 0.000 0.000
#> GSM550860 5 0.6209 0.434050 0.016 0.000 0.040 0.108 0.564 0.272
#> GSM550875 6 0.4403 0.514750 0.004 0.000 0.000 0.100 0.172 0.724
#> GSM550880 1 0.5635 0.040321 0.432 0.000 0.000 0.148 0.000 0.420
#> GSM550881 3 0.2177 0.903038 0.000 0.000 0.908 0.008 0.052 0.032
#> GSM550883 3 0.0858 0.916786 0.000 0.000 0.968 0.004 0.000 0.028
#> GSM550884 4 0.5862 0.251548 0.004 0.012 0.000 0.524 0.136 0.324
#> GSM550910 5 0.3388 0.716176 0.028 0.000 0.108 0.008 0.836 0.020
#> GSM550916 1 0.1970 0.812740 0.900 0.000 0.000 0.092 0.000 0.008
#> GSM550920 5 0.2554 0.739602 0.000 0.000 0.076 0.000 0.876 0.048
Heatmaps for the consensus matrix. It visualizes the probability of two samples to be in a same group.
consensus_heatmap(res, k = 2)
consensus_heatmap(res, k = 3)
consensus_heatmap(res, k = 4)
consensus_heatmap(res, k = 5)
consensus_heatmap(res, k = 6)
Heatmaps for the membership of samples in all partitions to see how consistent they are:
membership_heatmap(res, k = 2)
membership_heatmap(res, k = 3)
membership_heatmap(res, k = 4)
membership_heatmap(res, k = 5)
membership_heatmap(res, k = 6)
As soon as we have had the classes for columns, we can look for signatures which are significantly different between classes which can be candidate marks for certain classes. Following are the heatmaps for signatures.
Signature heatmaps where rows are scaled:
get_signatures(res, k = 2)
get_signatures(res, k = 3)
get_signatures(res, k = 4)
get_signatures(res, k = 5)
get_signatures(res, k = 6)
Signature heatmaps where rows are not scaled:
get_signatures(res, k = 2, scale_rows = FALSE)
get_signatures(res, k = 3, scale_rows = FALSE)
get_signatures(res, k = 4, scale_rows = FALSE)
get_signatures(res, k = 5, scale_rows = FALSE)
get_signatures(res, k = 6, scale_rows = FALSE)
Compare the overlap of signatures from different k:
compare_signatures(res)
get_signature() returns a data frame invisibly. TO get the list of signatures, the function
call should be assigned to a variable explicitly. In following code, if plot argument is set
to FALSE, no heatmap is plotted while only the differential analysis is performed.
# code only for demonstration
tb = get_signature(res, k = ..., plot = FALSE)
An example of the output of tb is:
#> which_row fdr mean_1 mean_2 scaled_mean_1 scaled_mean_2 km
#> 1 38 0.042760348 8.373488 9.131774 -0.5533452 0.5164555 1
#> 2 40 0.018707592 7.106213 8.469186 -0.6173731 0.5762149 1
#> 3 55 0.019134737 10.221463 11.207825 -0.6159697 0.5749050 1
#> 4 59 0.006059896 5.921854 7.869574 -0.6899429 0.6439467 1
#> 5 60 0.018055526 8.928898 10.211722 -0.6204761 0.5791110 1
#> 6 98 0.009384629 15.714769 14.887706 0.6635654 -0.6193277 2
...
The columns in tb are:
which_row: row indices corresponding to the input matrix.fdr: FDR for the differential test. mean_x: The mean value in group x.scaled_mean_x: The mean value in group x after rows are scaled.km: Row groups if k-means clustering is applied to rows.UMAP plot which shows how samples are separated.
dimension_reduction(res, k = 2, method = "UMAP")
dimension_reduction(res, k = 3, method = "UMAP")
dimension_reduction(res, k = 4, method = "UMAP")
dimension_reduction(res, k = 5, method = "UMAP")
dimension_reduction(res, k = 6, method = "UMAP")
Following heatmap shows how subgroups are split when increasing k:
collect_classes(res)
Test correlation between subgroups and known annotations. If the known annotation is numeric, one-way ANOVA test is applied, and if the known annotation is discrete, chi-squared contingency table test is applied.
test_to_known_factors(res)
#> n disease.state(p) k
#> CV:kmeans 139 5.53e-01 2
#> CV:kmeans 141 6.81e-03 3
#> CV:kmeans 82 1.27e-02 4
#> CV:kmeans 89 4.87e-03 5
#> CV:kmeans 104 1.38e-06 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 51776 rows and 143 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 0.551 0.671 0.856 0.4923 0.510 0.510
#> 3 3 0.792 0.846 0.932 0.3542 0.705 0.479
#> 4 4 0.740 0.727 0.854 0.1221 0.825 0.533
#> 5 5 0.644 0.582 0.771 0.0533 0.941 0.778
#> 6 6 0.655 0.577 0.728 0.0375 0.928 0.707
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
#> GSM550785 2 0.0000 0.531 0.000 1.000
#> GSM550786 1 0.9580 0.802 0.620 0.380
#> GSM550788 2 0.9608 0.822 0.384 0.616
#> GSM550789 2 0.9608 0.822 0.384 0.616
#> GSM550790 2 0.0000 0.531 0.000 1.000
#> GSM550791 2 0.0376 0.525 0.004 0.996
#> GSM550792 1 0.9993 -0.674 0.516 0.484
#> GSM550796 2 0.9608 0.822 0.384 0.616
#> GSM550797 2 0.9608 0.822 0.384 0.616
#> GSM550799 1 0.6887 0.681 0.816 0.184
#> GSM550800 2 0.9608 0.822 0.384 0.616
#> GSM550801 2 0.9608 0.822 0.384 0.616
#> GSM550804 2 0.9608 0.822 0.384 0.616
#> GSM550806 1 0.9608 0.802 0.616 0.384
#> GSM550807 2 0.9608 0.822 0.384 0.616
#> GSM550808 1 0.0000 0.501 1.000 0.000
#> GSM550809 1 0.9608 0.802 0.616 0.384
#> GSM550810 1 0.9686 -0.523 0.604 0.396
#> GSM550811 1 0.9608 0.802 0.616 0.384
#> GSM550813 2 0.9608 0.822 0.384 0.616
#> GSM550814 2 0.9608 0.822 0.384 0.616
#> GSM550815 2 0.9608 0.822 0.384 0.616
#> GSM550816 2 0.9608 0.822 0.384 0.616
#> GSM550817 1 0.9580 0.802 0.620 0.380
#> GSM550818 1 0.9580 0.802 0.620 0.380
#> GSM550819 1 0.9998 -0.687 0.508 0.492
#> GSM550820 1 0.9608 0.802 0.616 0.384
#> GSM550821 1 0.0000 0.501 1.000 0.000
#> GSM550822 2 0.9608 0.822 0.384 0.616
#> GSM550826 1 0.9608 0.802 0.616 0.384
#> GSM550832 2 0.9963 0.736 0.464 0.536
#> GSM550833 2 0.9608 0.822 0.384 0.616
#> GSM550835 1 0.0376 0.506 0.996 0.004
#> GSM550836 1 0.9608 0.802 0.616 0.384
#> GSM550837 1 0.0000 0.501 1.000 0.000
#> GSM550838 1 0.9608 0.802 0.616 0.384
#> GSM550841 1 0.6887 0.681 0.816 0.184
#> GSM550842 1 0.0000 0.501 1.000 0.000
#> GSM550846 2 0.9608 0.822 0.384 0.616
#> GSM550849 1 0.9608 0.802 0.616 0.384
#> GSM550850 2 0.3733 0.391 0.072 0.928
#> GSM550851 1 0.0000 0.501 1.000 0.000
#> GSM550852 2 0.9608 0.822 0.384 0.616
#> GSM550853 2 0.9608 0.822 0.384 0.616
#> GSM550855 2 0.9608 0.822 0.384 0.616
#> GSM550856 2 0.9608 0.822 0.384 0.616
#> GSM550861 2 0.9608 0.822 0.384 0.616
#> GSM550863 2 0.9580 0.821 0.380 0.620
#> GSM550864 2 0.9608 0.822 0.384 0.616
#> GSM550866 2 0.9608 0.822 0.384 0.616
#> GSM550867 2 0.0000 0.531 0.000 1.000
#> GSM550885 2 0.0000 0.531 0.000 1.000
#> GSM550886 1 0.0672 0.510 0.992 0.008
#> GSM550887 2 0.9608 0.822 0.384 0.616
#> GSM550889 2 0.9580 0.821 0.380 0.620
#> GSM550894 1 0.9608 -0.499 0.616 0.384
#> GSM550897 2 0.0000 0.531 0.000 1.000
#> GSM550903 2 0.9608 0.822 0.384 0.616
#> GSM550905 1 0.0000 0.501 1.000 0.000
#> GSM550906 2 0.9608 0.822 0.384 0.616
#> GSM550907 1 0.9580 0.802 0.620 0.380
#> GSM550909 1 0.0000 0.501 1.000 0.000
#> GSM550911 1 0.9608 0.802 0.616 0.384
#> GSM550913 2 0.9608 0.822 0.384 0.616
#> GSM550915 2 0.9580 0.821 0.380 0.620
#> GSM550917 2 0.9608 0.822 0.384 0.616
#> GSM550919 2 0.9608 0.822 0.384 0.616
#> GSM550921 1 0.9608 0.802 0.616 0.384
#> GSM550924 1 0.9580 0.802 0.620 0.380
#> GSM550926 2 0.9608 0.822 0.384 0.616
#> GSM550927 2 0.9608 0.822 0.384 0.616
#> GSM550787 1 0.9608 0.802 0.616 0.384
#> GSM550793 1 0.9608 0.802 0.616 0.384
#> GSM550794 2 0.9608 0.822 0.384 0.616
#> GSM550795 2 0.0376 0.525 0.004 0.996
#> GSM550798 1 0.9608 0.802 0.616 0.384
#> GSM550803 2 0.9522 -0.476 0.372 0.628
#> GSM550805 1 0.9608 0.802 0.616 0.384
#> GSM550823 2 0.9608 0.822 0.384 0.616
#> GSM550824 2 0.0000 0.531 0.000 1.000
#> GSM550825 1 0.9608 0.802 0.616 0.384
#> GSM550827 2 0.9608 0.822 0.384 0.616
#> GSM550828 2 0.0000 0.531 0.000 1.000
#> GSM550829 1 0.9608 0.802 0.616 0.384
#> GSM550830 2 0.9580 0.821 0.380 0.620
#> GSM550834 2 0.0000 0.531 0.000 1.000
#> GSM550839 1 0.6887 0.681 0.816 0.184
#> GSM550840 2 0.0000 0.531 0.000 1.000
#> GSM550843 1 0.9580 0.802 0.620 0.380
#> GSM550844 2 0.8909 -0.329 0.308 0.692
#> GSM550845 2 0.9608 0.822 0.384 0.616
#> GSM550848 2 0.9608 0.822 0.384 0.616
#> GSM550854 2 0.0000 0.531 0.000 1.000
#> GSM550857 1 0.9608 0.802 0.616 0.384
#> GSM550858 2 0.0000 0.531 0.000 1.000
#> GSM550859 2 0.0000 0.531 0.000 1.000
#> GSM550862 2 0.0000 0.531 0.000 1.000
#> GSM550865 2 0.9580 0.821 0.380 0.620
#> GSM550868 2 0.9580 0.821 0.380 0.620
#> GSM550869 1 0.9608 0.802 0.616 0.384
#> GSM550870 2 0.9608 0.822 0.384 0.616
#> GSM550871 1 0.6887 0.681 0.816 0.184
#> GSM550872 2 0.9580 0.821 0.380 0.620
#> GSM550873 1 0.0000 0.501 1.000 0.000
#> GSM550874 2 0.9608 0.822 0.384 0.616
#> GSM550876 1 0.6887 0.681 0.816 0.184
#> GSM550877 2 0.9608 0.822 0.384 0.616
#> GSM550878 1 0.9580 0.802 0.620 0.380
#> GSM550879 2 0.0000 0.531 0.000 1.000
#> GSM550882 1 0.9608 0.802 0.616 0.384
#> GSM550888 1 0.9608 0.802 0.616 0.384
#> GSM550890 2 0.9580 0.821 0.380 0.620
#> GSM550891 1 0.9608 0.802 0.616 0.384
#> GSM550892 2 0.0376 0.535 0.004 0.996
#> GSM550893 2 0.9608 0.822 0.384 0.616
#> GSM550895 2 0.9608 0.822 0.384 0.616
#> GSM550896 2 0.9608 0.822 0.384 0.616
#> GSM550898 2 0.0000 0.531 0.000 1.000
#> GSM550899 2 0.9608 0.822 0.384 0.616
#> GSM550900 2 0.9580 0.821 0.380 0.620
#> GSM550901 2 0.5629 0.642 0.132 0.868
#> GSM550902 1 0.9608 0.802 0.616 0.384
#> GSM550904 1 0.9608 0.802 0.616 0.384
#> GSM550908 1 0.9608 0.802 0.616 0.384
#> GSM550912 2 0.9608 0.822 0.384 0.616
#> GSM550914 2 0.9608 0.822 0.384 0.616
#> GSM550918 2 0.9608 0.822 0.384 0.616
#> GSM550922 1 0.0000 0.501 1.000 0.000
#> GSM550923 1 0.9608 0.802 0.616 0.384
#> GSM550925 2 0.1633 0.552 0.024 0.976
#> GSM550802 2 0.9635 0.819 0.388 0.612
#> GSM550812 1 0.6531 0.120 0.832 0.168
#> GSM550831 2 0.1184 0.504 0.016 0.984
#> GSM550847 2 0.0000 0.531 0.000 1.000
#> GSM550860 1 0.9608 0.802 0.616 0.384
#> GSM550875 1 0.9608 0.802 0.616 0.384
#> GSM550880 2 0.0000 0.531 0.000 1.000
#> GSM550881 1 0.9608 0.802 0.616 0.384
#> GSM550883 1 0.9608 0.802 0.616 0.384
#> GSM550884 1 0.1184 0.476 0.984 0.016
#> GSM550910 1 0.9580 0.802 0.620 0.380
#> GSM550916 2 0.0000 0.531 0.000 1.000
#> GSM550920 1 0.9580 0.802 0.620 0.380
cbind(get_classes(res, k = 3), get_membership(res, k = 3))
#> class entropy silhouette p1 p2 p3
#> GSM550785 1 0.0000 0.8782 1.000 0.000 0.000
#> GSM550786 3 0.0000 0.9337 0.000 0.000 1.000
#> GSM550788 2 0.0000 0.9564 0.000 1.000 0.000
#> GSM550789 2 0.0000 0.9564 0.000 1.000 0.000
#> GSM550790 1 0.0000 0.8782 1.000 0.000 0.000
#> GSM550791 1 0.0000 0.8782 1.000 0.000 0.000
#> GSM550792 2 0.6126 0.4135 0.352 0.644 0.004
#> GSM550796 2 0.0000 0.9564 0.000 1.000 0.000
#> GSM550797 2 0.0000 0.9564 0.000 1.000 0.000
#> GSM550799 3 0.0000 0.9337 0.000 0.000 1.000
#> GSM550800 2 0.0000 0.9564 0.000 1.000 0.000
#> GSM550801 2 0.0000 0.9564 0.000 1.000 0.000
#> GSM550804 2 0.0000 0.9564 0.000 1.000 0.000
#> GSM550806 3 0.0000 0.9337 0.000 0.000 1.000
#> GSM550807 2 0.0000 0.9564 0.000 1.000 0.000
#> GSM550808 2 0.6307 -0.0188 0.000 0.512 0.488
#> GSM550809 1 0.0000 0.8782 1.000 0.000 0.000
#> GSM550810 2 0.0000 0.9564 0.000 1.000 0.000
#> GSM550811 1 0.0592 0.8701 0.988 0.000 0.012
#> GSM550813 2 0.0000 0.9564 0.000 1.000 0.000
#> GSM550814 2 0.0000 0.9564 0.000 1.000 0.000
#> GSM550815 2 0.0000 0.9564 0.000 1.000 0.000
#> GSM550816 2 0.0424 0.9495 0.008 0.992 0.000
#> GSM550817 3 0.0000 0.9337 0.000 0.000 1.000
#> GSM550818 3 0.0000 0.9337 0.000 0.000 1.000
#> GSM550819 2 0.1163 0.9309 0.000 0.972 0.028
#> GSM550820 1 0.0000 0.8782 1.000 0.000 0.000
#> GSM550821 3 0.0747 0.9227 0.000 0.016 0.984
#> GSM550822 2 0.0000 0.9564 0.000 1.000 0.000
#> GSM550826 3 0.1031 0.9174 0.024 0.000 0.976
#> GSM550832 2 0.0000 0.9564 0.000 1.000 0.000
#> GSM550833 2 0.0000 0.9564 0.000 1.000 0.000
#> GSM550835 3 0.0000 0.9337 0.000 0.000 1.000
#> GSM550836 3 0.0000 0.9337 0.000 0.000 1.000
#> GSM550837 3 0.6140 0.3418 0.000 0.404 0.596
#> GSM550838 1 0.4842 0.6262 0.776 0.000 0.224
#> GSM550841 3 0.0000 0.9337 0.000 0.000 1.000
#> GSM550842 3 0.5810 0.5057 0.000 0.336 0.664
#> GSM550846 1 0.6297 0.5601 0.640 0.352 0.008
#> GSM550849 3 0.5905 0.5050 0.352 0.000 0.648
#> GSM550850 1 0.0000 0.8782 1.000 0.000 0.000
#> GSM550851 3 0.5706 0.5382 0.000 0.320 0.680
#> GSM550852 2 0.0000 0.9564 0.000 1.000 0.000
#> GSM550853 2 0.0000 0.9564 0.000 1.000 0.000
#> GSM550855 2 0.0000 0.9564 0.000 1.000 0.000
#> GSM550856 2 0.0000 0.9564 0.000 1.000 0.000
#> GSM550861 2 0.0000 0.9564 0.000 1.000 0.000
#> GSM550863 1 0.5431 0.6692 0.716 0.284 0.000
#> GSM550864 2 0.0000 0.9564 0.000 1.000 0.000
#> GSM550866 2 0.0000 0.9564 0.000 1.000 0.000
#> GSM550867 1 0.0000 0.8782 1.000 0.000 0.000
#> GSM550885 1 0.0000 0.8782 1.000 0.000 0.000
#> GSM550886 3 0.0000 0.9337 0.000 0.000 1.000
#> GSM550887 2 0.0000 0.9564 0.000 1.000 0.000
#> GSM550889 1 0.6299 0.2790 0.524 0.476 0.000
#> GSM550894 2 0.0000 0.9564 0.000 1.000 0.000
#> GSM550897 1 0.0000 0.8782 1.000 0.000 0.000
#> GSM550903 2 0.0000 0.9564 0.000 1.000 0.000
#> GSM550905 3 0.3267 0.8360 0.000 0.116 0.884
#> GSM550906 2 0.0000 0.9564 0.000 1.000 0.000
#> GSM550907 3 0.0000 0.9337 0.000 0.000 1.000
#> GSM550909 3 0.0000 0.9337 0.000 0.000 1.000
#> GSM550911 3 0.0000 0.9337 0.000 0.000 1.000
#> GSM550913 2 0.0000 0.9564 0.000 1.000 0.000
#> GSM550915 1 0.5254 0.6909 0.736 0.264 0.000
#> GSM550917 2 0.0000 0.9564 0.000 1.000 0.000
#> GSM550919 1 0.5560 0.6510 0.700 0.300 0.000
#> GSM550921 3 0.0000 0.9337 0.000 0.000 1.000
#> GSM550924 3 0.0000 0.9337 0.000 0.000 1.000
#> GSM550926 2 0.0000 0.9564 0.000 1.000 0.000
#> GSM550927 2 0.0000 0.9564 0.000 1.000 0.000
#> GSM550787 3 0.0237 0.9313 0.004 0.000 0.996
#> GSM550793 3 0.0237 0.9313 0.004 0.000 0.996
#> GSM550794 1 0.5291 0.6654 0.732 0.268 0.000
#> GSM550795 1 0.0000 0.8782 1.000 0.000 0.000
#> GSM550798 1 0.5178 0.5701 0.744 0.000 0.256
#> GSM550803 1 0.0000 0.8782 1.000 0.000 0.000
#> GSM550805 3 0.5431 0.6259 0.284 0.000 0.716
#> GSM550823 2 0.0424 0.9489 0.008 0.992 0.000
#> GSM550824 1 0.0000 0.8782 1.000 0.000 0.000
#> GSM550825 3 0.0000 0.9337 0.000 0.000 1.000
#> GSM550827 1 0.5835 0.5889 0.660 0.340 0.000
#> GSM550828 1 0.0000 0.8782 1.000 0.000 0.000
#> GSM550829 3 0.4796 0.7207 0.220 0.000 0.780
#> GSM550830 2 0.5650 0.4380 0.312 0.688 0.000
#> GSM550834 1 0.0000 0.8782 1.000 0.000 0.000
#> GSM550839 3 0.0000 0.9337 0.000 0.000 1.000
#> GSM550840 1 0.0000 0.8782 1.000 0.000 0.000
#> GSM550843 3 0.0000 0.9337 0.000 0.000 1.000
#> GSM550844 1 0.0000 0.8782 1.000 0.000 0.000
#> GSM550845 2 0.0000 0.9564 0.000 1.000 0.000
#> GSM550848 1 0.5785 0.6038 0.668 0.332 0.000
#> GSM550854 1 0.0000 0.8782 1.000 0.000 0.000
#> GSM550857 3 0.0000 0.9337 0.000 0.000 1.000
#> GSM550858 1 0.0000 0.8782 1.000 0.000 0.000
#> GSM550859 1 0.0000 0.8782 1.000 0.000 0.000
#> GSM550862 1 0.0000 0.8782 1.000 0.000 0.000
#> GSM550865 1 0.6062 0.5119 0.616 0.384 0.000
#> GSM550868 1 0.5465 0.6645 0.712 0.288 0.000
#> GSM550869 3 0.0000 0.9337 0.000 0.000 1.000
#> GSM550870 2 0.0000 0.9564 0.000 1.000 0.000
#> GSM550871 3 0.0000 0.9337 0.000 0.000 1.000
#> GSM550872 1 0.5431 0.6692 0.716 0.284 0.000
#> GSM550873 2 0.6204 0.2099 0.000 0.576 0.424
#> GSM550874 2 0.0000 0.9564 0.000 1.000 0.000
#> GSM550876 3 0.0000 0.9337 0.000 0.000 1.000
#> GSM550877 2 0.0000 0.9564 0.000 1.000 0.000
#> GSM550878 3 0.0000 0.9337 0.000 0.000 1.000
#> GSM550879 1 0.0000 0.8782 1.000 0.000 0.000
#> GSM550882 3 0.0000 0.9337 0.000 0.000 1.000
#> GSM550888 3 0.0000 0.9337 0.000 0.000 1.000
#> GSM550890 1 0.5397 0.6739 0.720 0.280 0.000
#> GSM550891 3 0.0000 0.9337 0.000 0.000 1.000
#> GSM550892 1 0.0000 0.8782 1.000 0.000 0.000
#> GSM550893 2 0.0000 0.9564 0.000 1.000 0.000
#> GSM550895 2 0.0000 0.9564 0.000 1.000 0.000
#> GSM550896 2 0.0000 0.9564 0.000 1.000 0.000
#> GSM550898 1 0.0000 0.8782 1.000 0.000 0.000
#> GSM550899 2 0.0000 0.9564 0.000 1.000 0.000
#> GSM550900 1 0.5497 0.6599 0.708 0.292 0.000
#> GSM550901 1 0.0000 0.8782 1.000 0.000 0.000
#> GSM550902 3 0.2959 0.8530 0.100 0.000 0.900
#> GSM550904 1 0.3412 0.7652 0.876 0.000 0.124
#> GSM550908 3 0.0000 0.9337 0.000 0.000 1.000
#> GSM550912 2 0.0000 0.9564 0.000 1.000 0.000
#> GSM550914 1 0.5882 0.5742 0.652 0.348 0.000
#> GSM550918 2 0.0000 0.9564 0.000 1.000 0.000
#> GSM550922 3 0.0000 0.9337 0.000 0.000 1.000
#> GSM550923 1 0.1031 0.8609 0.976 0.000 0.024
#> GSM550925 1 0.0000 0.8782 1.000 0.000 0.000
#> GSM550802 2 0.2356 0.8833 0.072 0.928 0.000
#> GSM550812 2 0.3886 0.8404 0.096 0.880 0.024
#> GSM550831 1 0.0000 0.8782 1.000 0.000 0.000
#> GSM550847 1 0.0000 0.8782 1.000 0.000 0.000
#> GSM550860 3 0.0000 0.9337 0.000 0.000 1.000
#> GSM550875 3 0.6235 0.3067 0.436 0.000 0.564
#> GSM550880 1 0.0000 0.8782 1.000 0.000 0.000
#> GSM550881 3 0.0000 0.9337 0.000 0.000 1.000
#> GSM550883 3 0.0000 0.9337 0.000 0.000 1.000
#> GSM550884 3 0.4605 0.7266 0.000 0.204 0.796
#> GSM550910 3 0.0000 0.9337 0.000 0.000 1.000
#> GSM550916 1 0.0000 0.8782 1.000 0.000 0.000
#> GSM550920 3 0.0000 0.9337 0.000 0.000 1.000
cbind(get_classes(res, k = 4), get_membership(res, k = 4))
#> class entropy silhouette p1 p2 p3 p4
#> GSM550785 1 0.4164 0.7983 0.736 0.000 0.000 0.264
#> GSM550786 3 0.0188 0.9513 0.000 0.000 0.996 0.004
#> GSM550788 2 0.0000 0.8102 0.000 1.000 0.000 0.000
#> GSM550789 2 0.0188 0.8105 0.000 0.996 0.000 0.004
#> GSM550790 1 0.2011 0.8227 0.920 0.000 0.000 0.080
#> GSM550791 1 0.1118 0.8161 0.964 0.000 0.000 0.036
#> GSM550792 2 0.6242 0.2064 0.456 0.496 0.004 0.044
#> GSM550796 2 0.0188 0.8105 0.000 0.996 0.000 0.004
#> GSM550797 2 0.0188 0.8105 0.000 0.996 0.000 0.004
#> GSM550799 3 0.0376 0.9496 0.000 0.004 0.992 0.004
#> GSM550800 2 0.1867 0.7670 0.000 0.928 0.000 0.072
#> GSM550801 2 0.0188 0.8105 0.000 0.996 0.000 0.004
#> GSM550804 4 0.4804 0.5387 0.000 0.384 0.000 0.616
#> GSM550806 3 0.0376 0.9523 0.004 0.000 0.992 0.004
#> GSM550807 2 0.0188 0.8105 0.000 0.996 0.000 0.004
#> GSM550808 2 0.5170 0.6299 0.020 0.756 0.192 0.032
#> GSM550809 1 0.0469 0.8047 0.988 0.000 0.000 0.012
#> GSM550810 2 0.1388 0.7938 0.012 0.960 0.000 0.028
#> GSM550811 1 0.2002 0.7747 0.936 0.020 0.000 0.044
#> GSM550813 2 0.3444 0.6001 0.000 0.816 0.000 0.184
#> GSM550814 2 0.1022 0.8026 0.000 0.968 0.000 0.032
#> GSM550815 2 0.0336 0.8105 0.000 0.992 0.000 0.008
#> GSM550816 2 0.3356 0.6451 0.000 0.824 0.000 0.176
#> GSM550817 3 0.0000 0.9524 0.000 0.000 1.000 0.000
#> GSM550818 3 0.0000 0.9524 0.000 0.000 1.000 0.000
#> GSM550819 4 0.4441 0.7095 0.020 0.136 0.028 0.816
#> GSM550820 1 0.3528 0.8165 0.808 0.000 0.000 0.192
#> GSM550821 3 0.1940 0.8894 0.000 0.076 0.924 0.000
#> GSM550822 2 0.0336 0.8105 0.000 0.992 0.000 0.008
#> GSM550826 3 0.2053 0.9015 0.072 0.000 0.924 0.004
#> GSM550832 2 0.0707 0.8071 0.000 0.980 0.000 0.020
#> GSM550833 2 0.0336 0.8084 0.000 0.992 0.000 0.008
#> GSM550835 3 0.4319 0.6738 0.000 0.228 0.760 0.012
#> GSM550836 3 0.0524 0.9520 0.008 0.000 0.988 0.004
#> GSM550837 2 0.5348 0.4777 0.012 0.664 0.312 0.012
#> GSM550838 1 0.1362 0.7883 0.964 0.004 0.020 0.012
#> GSM550841 3 0.0000 0.9524 0.000 0.000 1.000 0.000
#> GSM550842 2 0.5093 0.4190 0.000 0.640 0.348 0.012
#> GSM550846 4 0.1674 0.7139 0.032 0.012 0.004 0.952
#> GSM550849 1 0.3982 0.6927 0.824 0.012 0.152 0.012
#> GSM550850 1 0.1109 0.8127 0.968 0.004 0.000 0.028
#> GSM550851 2 0.5143 0.3910 0.000 0.628 0.360 0.012
#> GSM550852 2 0.2483 0.7670 0.052 0.916 0.000 0.032
#> GSM550853 2 0.0469 0.8096 0.000 0.988 0.000 0.012
#> GSM550855 2 0.0707 0.8057 0.000 0.980 0.000 0.020
#> GSM550856 2 0.4888 -0.0219 0.000 0.588 0.000 0.412
#> GSM550861 2 0.0469 0.8081 0.000 0.988 0.000 0.012
#> GSM550863 4 0.1256 0.7147 0.028 0.008 0.000 0.964
#> GSM550864 4 0.4961 0.4316 0.000 0.448 0.000 0.552
#> GSM550866 4 0.4776 0.5604 0.000 0.376 0.000 0.624
#> GSM550867 1 0.4134 0.8007 0.740 0.000 0.000 0.260
#> GSM550885 1 0.4193 0.7956 0.732 0.000 0.000 0.268
#> GSM550886 3 0.0000 0.9524 0.000 0.000 1.000 0.000
#> GSM550887 2 0.0336 0.8105 0.000 0.992 0.000 0.008
#> GSM550889 4 0.2300 0.7333 0.016 0.064 0.000 0.920
#> GSM550894 2 0.0469 0.8095 0.000 0.988 0.000 0.012
#> GSM550897 4 0.4406 0.1976 0.300 0.000 0.000 0.700
#> GSM550903 2 0.0817 0.8043 0.000 0.976 0.000 0.024
#> GSM550905 3 0.5161 0.0523 0.000 0.476 0.520 0.004
#> GSM550906 2 0.0336 0.8105 0.000 0.992 0.000 0.008
#> GSM550907 3 0.0000 0.9524 0.000 0.000 1.000 0.000
#> GSM550909 3 0.3302 0.8498 0.020 0.096 0.876 0.008
#> GSM550911 3 0.0188 0.9524 0.000 0.000 0.996 0.004
#> GSM550913 2 0.0469 0.8081 0.000 0.988 0.000 0.012
#> GSM550915 4 0.1584 0.7115 0.036 0.012 0.000 0.952
#> GSM550917 4 0.5000 0.3023 0.000 0.500 0.000 0.500
#> GSM550919 4 0.1929 0.7153 0.036 0.024 0.000 0.940
#> GSM550921 3 0.0524 0.9520 0.008 0.000 0.988 0.004
#> GSM550924 3 0.0376 0.9519 0.004 0.000 0.992 0.004
#> GSM550926 4 0.4916 0.4799 0.000 0.424 0.000 0.576
#> GSM550927 2 0.1792 0.7689 0.000 0.932 0.000 0.068
#> GSM550787 3 0.1824 0.9123 0.060 0.000 0.936 0.004
#> GSM550793 3 0.0524 0.9520 0.008 0.000 0.988 0.004
#> GSM550794 1 0.7250 0.2594 0.552 0.168 0.004 0.276
#> GSM550795 1 0.0895 0.8076 0.976 0.004 0.000 0.020
#> GSM550798 1 0.1867 0.7774 0.928 0.000 0.072 0.000
#> GSM550803 1 0.1302 0.8174 0.956 0.000 0.000 0.044
#> GSM550805 1 0.5200 0.5115 0.704 0.004 0.264 0.028
#> GSM550823 4 0.3982 0.6814 0.004 0.220 0.000 0.776
#> GSM550824 1 0.4134 0.8007 0.740 0.000 0.000 0.260
#> GSM550825 3 0.0524 0.9520 0.008 0.000 0.988 0.004
#> GSM550827 4 0.1629 0.7206 0.024 0.024 0.000 0.952
#> GSM550828 1 0.4585 0.7370 0.668 0.000 0.000 0.332
#> GSM550829 3 0.5028 0.3023 0.400 0.000 0.596 0.004
#> GSM550830 4 0.4776 0.7033 0.060 0.164 0.000 0.776
#> GSM550834 1 0.1209 0.8124 0.964 0.004 0.000 0.032
#> GSM550839 3 0.0804 0.9431 0.000 0.008 0.980 0.012
#> GSM550840 1 0.1109 0.8110 0.968 0.004 0.000 0.028
#> GSM550843 3 0.0000 0.9524 0.000 0.000 1.000 0.000
#> GSM550844 1 0.2921 0.8222 0.860 0.000 0.000 0.140
#> GSM550845 4 0.4500 0.6149 0.000 0.316 0.000 0.684
#> GSM550848 4 0.1629 0.7206 0.024 0.024 0.000 0.952
#> GSM550854 1 0.4134 0.8007 0.740 0.000 0.000 0.260
#> GSM550857 3 0.0524 0.9520 0.008 0.000 0.988 0.004
#> GSM550858 1 0.4406 0.7693 0.700 0.000 0.000 0.300
#> GSM550859 1 0.4134 0.8007 0.740 0.000 0.000 0.260
#> GSM550862 1 0.4605 0.7374 0.664 0.000 0.000 0.336
#> GSM550865 4 0.1913 0.7283 0.020 0.040 0.000 0.940
#> GSM550868 4 0.1388 0.7157 0.028 0.012 0.000 0.960
#> GSM550869 3 0.1151 0.9421 0.024 0.000 0.968 0.008
#> GSM550870 2 0.4994 -0.2626 0.000 0.520 0.000 0.480
#> GSM550871 3 0.0188 0.9513 0.000 0.000 0.996 0.004
#> GSM550872 4 0.1398 0.7083 0.040 0.004 0.000 0.956
#> GSM550873 2 0.5487 0.5890 0.016 0.712 0.240 0.032
#> GSM550874 2 0.0469 0.8103 0.000 0.988 0.000 0.012
#> GSM550876 3 0.0000 0.9524 0.000 0.000 1.000 0.000
#> GSM550877 4 0.4746 0.5646 0.000 0.368 0.000 0.632
#> GSM550878 3 0.0000 0.9524 0.000 0.000 1.000 0.000
#> GSM550879 1 0.4697 0.7117 0.644 0.000 0.000 0.356
#> GSM550882 3 0.0524 0.9520 0.008 0.000 0.988 0.004
#> GSM550888 3 0.0524 0.9520 0.008 0.000 0.988 0.004
#> GSM550890 4 0.1356 0.7134 0.032 0.008 0.000 0.960
#> GSM550891 3 0.0524 0.9520 0.008 0.000 0.988 0.004
#> GSM550892 4 0.3311 0.5164 0.172 0.000 0.000 0.828
#> GSM550893 4 0.4697 0.5819 0.000 0.356 0.000 0.644
#> GSM550895 4 0.4250 0.6496 0.000 0.276 0.000 0.724
#> GSM550896 4 0.4624 0.5976 0.000 0.340 0.000 0.660
#> GSM550898 1 0.4134 0.8007 0.740 0.000 0.000 0.260
#> GSM550899 4 0.4948 0.4473 0.000 0.440 0.000 0.560
#> GSM550900 4 0.1356 0.7125 0.032 0.008 0.000 0.960
#> GSM550901 1 0.4977 0.5164 0.540 0.000 0.000 0.460
#> GSM550902 3 0.1890 0.9144 0.056 0.000 0.936 0.008
#> GSM550904 1 0.3015 0.8176 0.884 0.000 0.024 0.092
#> GSM550908 3 0.0524 0.9520 0.008 0.000 0.988 0.004
#> GSM550912 2 0.4992 -0.2709 0.000 0.524 0.000 0.476
#> GSM550914 4 0.1388 0.7168 0.028 0.012 0.000 0.960
#> GSM550918 4 0.4776 0.5554 0.000 0.376 0.000 0.624
#> GSM550922 3 0.0000 0.9524 0.000 0.000 1.000 0.000
#> GSM550923 1 0.1890 0.8207 0.936 0.000 0.008 0.056
#> GSM550925 4 0.4500 0.1704 0.316 0.000 0.000 0.684
#> GSM550802 2 0.6250 0.5315 0.268 0.644 0.004 0.084
#> GSM550812 2 0.8224 0.2289 0.308 0.424 0.016 0.252
#> GSM550831 1 0.1109 0.8127 0.968 0.004 0.000 0.028
#> GSM550847 1 0.4134 0.8007 0.740 0.000 0.000 0.260
#> GSM550860 3 0.0524 0.9520 0.008 0.000 0.988 0.004
#> GSM550875 1 0.3428 0.7058 0.844 0.000 0.144 0.012
#> GSM550880 1 0.3801 0.8108 0.780 0.000 0.000 0.220
#> GSM550881 3 0.0524 0.9520 0.008 0.000 0.988 0.004
#> GSM550883 3 0.0524 0.9520 0.008 0.000 0.988 0.004
#> GSM550884 4 0.5317 0.3576 0.008 0.008 0.356 0.628
#> GSM550910 3 0.0000 0.9524 0.000 0.000 1.000 0.000
#> GSM550916 1 0.4134 0.8007 0.740 0.000 0.000 0.260
#> GSM550920 3 0.0000 0.9524 0.000 0.000 1.000 0.000
cbind(get_classes(res, k = 5), get_membership(res, k = 5))
#> class entropy silhouette p1 p2 p3 p4 p5
#> GSM550785 1 0.2848 0.6638 0.840 0.000 0.000 0.156 0.004
#> GSM550786 3 0.3280 0.8384 0.000 0.000 0.812 0.012 0.176
#> GSM550788 2 0.1818 0.7462 0.000 0.932 0.000 0.024 0.044
#> GSM550789 2 0.0771 0.7499 0.000 0.976 0.000 0.004 0.020
#> GSM550790 1 0.2236 0.5978 0.908 0.000 0.000 0.024 0.068
#> GSM550791 1 0.4464 0.1602 0.632 0.004 0.000 0.008 0.356
#> GSM550792 5 0.5470 0.6441 0.160 0.152 0.000 0.008 0.680
#> GSM550796 2 0.0880 0.7487 0.000 0.968 0.000 0.000 0.032
#> GSM550797 2 0.0898 0.7506 0.000 0.972 0.000 0.008 0.020
#> GSM550799 3 0.3750 0.8060 0.000 0.000 0.756 0.012 0.232
#> GSM550800 2 0.3488 0.6634 0.000 0.808 0.000 0.168 0.024
#> GSM550801 2 0.1117 0.7500 0.000 0.964 0.000 0.016 0.020
#> GSM550804 4 0.6070 0.2152 0.004 0.428 0.000 0.464 0.104
#> GSM550806 3 0.1557 0.8643 0.000 0.000 0.940 0.008 0.052
#> GSM550807 2 0.1168 0.7507 0.000 0.960 0.000 0.008 0.032
#> GSM550808 2 0.5764 0.2147 0.000 0.508 0.052 0.016 0.424
#> GSM550809 1 0.4508 0.2125 0.648 0.000 0.000 0.020 0.332
#> GSM550810 2 0.3612 0.6002 0.000 0.764 0.000 0.008 0.228
#> GSM550811 5 0.5051 0.4705 0.356 0.012 0.008 0.012 0.612
#> GSM550813 2 0.2983 0.6878 0.000 0.864 0.000 0.096 0.040
#> GSM550814 2 0.2554 0.7417 0.000 0.892 0.000 0.036 0.072
#> GSM550815 2 0.1012 0.7501 0.000 0.968 0.000 0.012 0.020
#> GSM550816 2 0.4782 0.5109 0.004 0.700 0.000 0.244 0.052
#> GSM550817 3 0.3319 0.8410 0.000 0.000 0.820 0.020 0.160
#> GSM550818 3 0.2864 0.8536 0.000 0.000 0.852 0.012 0.136
#> GSM550819 4 0.4008 0.6059 0.012 0.060 0.008 0.824 0.096
#> GSM550820 1 0.2927 0.6510 0.868 0.000 0.000 0.092 0.040
#> GSM550821 3 0.5432 0.7474 0.000 0.084 0.692 0.024 0.200
#> GSM550822 2 0.0992 0.7497 0.000 0.968 0.000 0.008 0.024
#> GSM550826 3 0.3152 0.7789 0.084 0.000 0.868 0.016 0.032
#> GSM550832 2 0.1942 0.7451 0.000 0.920 0.000 0.012 0.068
#> GSM550833 2 0.1430 0.7472 0.000 0.944 0.000 0.004 0.052
#> GSM550835 3 0.6413 0.5299 0.000 0.120 0.536 0.020 0.324
#> GSM550836 3 0.0000 0.8571 0.000 0.000 1.000 0.000 0.000
#> GSM550837 2 0.6662 0.1404 0.000 0.468 0.148 0.016 0.368
#> GSM550838 1 0.5631 -0.0884 0.540 0.000 0.040 0.020 0.400
#> GSM550841 3 0.3476 0.8330 0.000 0.000 0.804 0.020 0.176
#> GSM550842 2 0.7109 0.1401 0.000 0.456 0.228 0.024 0.292
#> GSM550846 4 0.5858 0.5976 0.116 0.044 0.000 0.680 0.160
#> GSM550849 5 0.6276 0.4732 0.340 0.012 0.104 0.004 0.540
#> GSM550850 1 0.4392 0.1107 0.612 0.000 0.000 0.008 0.380
#> GSM550851 2 0.7093 0.1173 0.000 0.444 0.240 0.020 0.296
#> GSM550852 2 0.4025 0.5336 0.000 0.700 0.000 0.008 0.292
#> GSM550853 2 0.2054 0.7428 0.000 0.920 0.000 0.052 0.028
#> GSM550855 2 0.2511 0.7259 0.000 0.892 0.000 0.080 0.028
#> GSM550856 2 0.4538 0.3142 0.000 0.620 0.000 0.364 0.016
#> GSM550861 2 0.0693 0.7464 0.000 0.980 0.000 0.008 0.012
#> GSM550863 4 0.2199 0.6537 0.060 0.008 0.000 0.916 0.016
#> GSM550864 2 0.5418 0.1548 0.000 0.568 0.000 0.364 0.068
#> GSM550866 4 0.4905 0.1213 0.000 0.476 0.000 0.500 0.024
#> GSM550867 1 0.2280 0.6710 0.880 0.000 0.000 0.120 0.000
#> GSM550885 1 0.2813 0.6607 0.832 0.000 0.000 0.168 0.000
#> GSM550886 3 0.3151 0.8482 0.000 0.000 0.836 0.020 0.144
#> GSM550887 2 0.0992 0.7502 0.000 0.968 0.000 0.008 0.024
#> GSM550889 4 0.3191 0.6588 0.040 0.064 0.000 0.872 0.024
#> GSM550894 2 0.2046 0.7418 0.000 0.916 0.000 0.016 0.068
#> GSM550897 1 0.5109 0.2356 0.504 0.000 0.000 0.460 0.036
#> GSM550903 2 0.1493 0.7410 0.000 0.948 0.000 0.028 0.024
#> GSM550905 3 0.7137 0.2945 0.000 0.316 0.424 0.020 0.240
#> GSM550906 2 0.0912 0.7492 0.000 0.972 0.000 0.012 0.016
#> GSM550907 3 0.2305 0.8617 0.000 0.000 0.896 0.012 0.092
#> GSM550909 3 0.6104 0.6348 0.008 0.076 0.596 0.020 0.300
#> GSM550911 3 0.1571 0.8645 0.000 0.000 0.936 0.004 0.060
#> GSM550913 2 0.1216 0.7412 0.000 0.960 0.000 0.020 0.020
#> GSM550915 4 0.5329 0.6009 0.144 0.024 0.000 0.716 0.116
#> GSM550917 2 0.5088 0.4006 0.000 0.668 0.000 0.252 0.080
#> GSM550919 4 0.6853 0.5219 0.224 0.080 0.000 0.580 0.116
#> GSM550921 3 0.0000 0.8571 0.000 0.000 1.000 0.000 0.000
#> GSM550924 3 0.3981 0.8306 0.024 0.004 0.816 0.028 0.128
#> GSM550926 2 0.5028 0.1663 0.000 0.564 0.000 0.400 0.036
#> GSM550927 2 0.2248 0.7126 0.000 0.900 0.000 0.088 0.012
#> GSM550787 3 0.3854 0.7860 0.080 0.000 0.816 0.004 0.100
#> GSM550793 3 0.1124 0.8443 0.004 0.000 0.960 0.000 0.036
#> GSM550794 5 0.6878 0.5787 0.216 0.056 0.000 0.160 0.568
#> GSM550795 1 0.4640 0.0455 0.584 0.000 0.000 0.016 0.400
#> GSM550798 1 0.5295 0.3329 0.704 0.000 0.160 0.012 0.124
#> GSM550803 1 0.2068 0.5544 0.904 0.000 0.000 0.004 0.092
#> GSM550805 5 0.6680 0.4529 0.332 0.004 0.184 0.004 0.476
#> GSM550823 4 0.4622 0.6258 0.024 0.148 0.000 0.768 0.060
#> GSM550824 1 0.2280 0.6710 0.880 0.000 0.000 0.120 0.000
#> GSM550825 3 0.0324 0.8552 0.000 0.000 0.992 0.004 0.004
#> GSM550827 4 0.4201 0.6460 0.096 0.024 0.000 0.808 0.072
#> GSM550828 1 0.3123 0.6443 0.812 0.000 0.000 0.184 0.004
#> GSM550829 3 0.4929 0.3792 0.312 0.000 0.648 0.008 0.032
#> GSM550830 4 0.6358 0.4888 0.060 0.144 0.000 0.640 0.156
#> GSM550834 1 0.4527 0.0750 0.596 0.000 0.000 0.012 0.392
#> GSM550839 3 0.4380 0.7409 0.000 0.012 0.692 0.008 0.288
#> GSM550840 1 0.4707 0.0986 0.588 0.000 0.000 0.020 0.392
#> GSM550843 3 0.2873 0.8546 0.000 0.000 0.856 0.016 0.128
#> GSM550844 1 0.2740 0.6497 0.876 0.000 0.000 0.096 0.028
#> GSM550845 4 0.4206 0.5352 0.000 0.272 0.000 0.708 0.020
#> GSM550848 4 0.5897 0.6063 0.148 0.056 0.000 0.684 0.112
#> GSM550854 1 0.2179 0.6702 0.888 0.000 0.000 0.112 0.000
#> GSM550857 3 0.0000 0.8571 0.000 0.000 1.000 0.000 0.000
#> GSM550858 1 0.2891 0.6575 0.824 0.000 0.000 0.176 0.000
#> GSM550859 1 0.2280 0.6710 0.880 0.000 0.000 0.120 0.000
#> GSM550862 1 0.3491 0.6220 0.768 0.000 0.000 0.228 0.004
#> GSM550865 4 0.2321 0.6561 0.044 0.016 0.000 0.916 0.024
#> GSM550868 4 0.2456 0.6480 0.064 0.008 0.000 0.904 0.024
#> GSM550869 3 0.2452 0.8115 0.016 0.000 0.896 0.004 0.084
#> GSM550870 2 0.5329 0.2615 0.000 0.596 0.000 0.336 0.068
#> GSM550871 3 0.2843 0.8499 0.000 0.000 0.848 0.008 0.144
#> GSM550872 4 0.3463 0.6013 0.072 0.008 0.000 0.848 0.072
#> GSM550873 2 0.6010 0.2518 0.000 0.512 0.060 0.024 0.404
#> GSM550874 2 0.3898 0.6779 0.000 0.804 0.000 0.116 0.080
#> GSM550876 3 0.2011 0.8635 0.000 0.000 0.908 0.004 0.088
#> GSM550877 4 0.4861 0.2312 0.000 0.428 0.000 0.548 0.024
#> GSM550878 3 0.1956 0.8634 0.000 0.000 0.916 0.008 0.076
#> GSM550879 1 0.4429 0.5736 0.712 0.004 0.000 0.256 0.028
#> GSM550882 3 0.0000 0.8571 0.000 0.000 1.000 0.000 0.000
#> GSM550888 3 0.0000 0.8571 0.000 0.000 1.000 0.000 0.000
#> GSM550890 4 0.4498 0.6214 0.112 0.008 0.000 0.772 0.108
#> GSM550891 3 0.0000 0.8571 0.000 0.000 1.000 0.000 0.000
#> GSM550892 4 0.4574 0.0520 0.412 0.000 0.000 0.576 0.012
#> GSM550893 4 0.4666 0.2940 0.000 0.412 0.000 0.572 0.016
#> GSM550895 4 0.3935 0.6108 0.004 0.200 0.000 0.772 0.024
#> GSM550896 4 0.4696 0.3869 0.000 0.360 0.000 0.616 0.024
#> GSM550898 1 0.2280 0.6710 0.880 0.000 0.000 0.120 0.000
#> GSM550899 2 0.5589 0.0973 0.000 0.548 0.000 0.372 0.080
#> GSM550900 4 0.2673 0.6442 0.072 0.008 0.000 0.892 0.028
#> GSM550901 1 0.5496 0.4702 0.628 0.004 0.000 0.280 0.088
#> GSM550902 3 0.3792 0.6665 0.180 0.000 0.792 0.008 0.020
#> GSM550904 1 0.4686 0.5365 0.780 0.000 0.112 0.052 0.056
#> GSM550908 3 0.0000 0.8571 0.000 0.000 1.000 0.000 0.000
#> GSM550912 2 0.5575 0.3052 0.000 0.612 0.000 0.280 0.108
#> GSM550914 4 0.4667 0.6364 0.088 0.028 0.000 0.776 0.108
#> GSM550918 4 0.6001 0.2044 0.000 0.432 0.000 0.456 0.112
#> GSM550922 3 0.3513 0.8310 0.000 0.000 0.800 0.020 0.180
#> GSM550923 1 0.2523 0.5992 0.908 0.000 0.024 0.028 0.040
#> GSM550925 1 0.5448 0.4462 0.624 0.008 0.000 0.300 0.068
#> GSM550802 5 0.6606 0.6374 0.100 0.152 0.000 0.120 0.628
#> GSM550812 5 0.6573 0.5331 0.056 0.160 0.000 0.172 0.612
#> GSM550831 1 0.4403 0.0998 0.608 0.000 0.000 0.008 0.384
#> GSM550847 1 0.2280 0.6710 0.880 0.000 0.000 0.120 0.000
#> GSM550860 3 0.0000 0.8571 0.000 0.000 1.000 0.000 0.000
#> GSM550875 1 0.7065 -0.2996 0.396 0.000 0.264 0.012 0.328
#> GSM550880 1 0.5190 0.4503 0.668 0.000 0.000 0.096 0.236
#> GSM550881 3 0.0000 0.8571 0.000 0.000 1.000 0.000 0.000
#> GSM550883 3 0.0000 0.8571 0.000 0.000 1.000 0.000 0.000
#> GSM550884 4 0.6543 0.2927 0.012 0.016 0.268 0.576 0.128
#> GSM550910 3 0.2969 0.8542 0.000 0.000 0.852 0.020 0.128
#> GSM550916 1 0.2329 0.6704 0.876 0.000 0.000 0.124 0.000
#> GSM550920 3 0.2723 0.8576 0.000 0.000 0.864 0.012 0.124
cbind(get_classes(res, k = 6), get_membership(res, k = 6))
#> class entropy silhouette p1 p2 p3 p4 p5 p6
#> GSM550785 1 0.0976 0.7743 0.968 0.000 0.016 0.008 0.000 0.008
#> GSM550786 5 0.4444 0.5748 0.000 0.000 0.316 0.008 0.644 0.032
#> GSM550788 2 0.3263 0.6927 0.000 0.848 0.064 0.060 0.000 0.028
#> GSM550789 2 0.1196 0.7138 0.000 0.952 0.040 0.008 0.000 0.000
#> GSM550790 1 0.3314 0.4691 0.740 0.000 0.004 0.000 0.000 0.256
#> GSM550791 6 0.3833 0.6124 0.344 0.000 0.008 0.000 0.000 0.648
#> GSM550792 6 0.4797 0.5824 0.032 0.080 0.136 0.012 0.000 0.740
#> GSM550796 2 0.1444 0.6975 0.000 0.928 0.072 0.000 0.000 0.000
#> GSM550797 2 0.1151 0.7222 0.000 0.956 0.032 0.012 0.000 0.000
#> GSM550799 5 0.4306 0.5744 0.000 0.000 0.308 0.004 0.656 0.032
#> GSM550800 2 0.4204 0.6078 0.000 0.692 0.020 0.272 0.000 0.016
#> GSM550801 2 0.1564 0.7327 0.000 0.936 0.040 0.024 0.000 0.000
#> GSM550804 2 0.6951 0.1003 0.012 0.420 0.208 0.316 0.000 0.044
#> GSM550806 5 0.1411 0.7613 0.000 0.000 0.060 0.004 0.936 0.000
#> GSM550807 2 0.1713 0.7331 0.000 0.928 0.028 0.044 0.000 0.000
#> GSM550808 3 0.5821 0.5510 0.000 0.392 0.492 0.000 0.044 0.072
#> GSM550809 6 0.5455 0.5452 0.332 0.000 0.056 0.032 0.004 0.576
#> GSM550810 2 0.3975 0.4122 0.000 0.716 0.244 0.000 0.000 0.040
#> GSM550811 6 0.4688 0.6826 0.104 0.008 0.080 0.036 0.008 0.764
#> GSM550813 2 0.3852 0.7049 0.000 0.796 0.080 0.108 0.000 0.016
#> GSM550814 2 0.4909 0.6745 0.000 0.716 0.136 0.108 0.000 0.040
#> GSM550815 2 0.1391 0.7142 0.000 0.944 0.040 0.016 0.000 0.000
#> GSM550816 2 0.4993 0.6438 0.008 0.704 0.136 0.136 0.000 0.016
#> GSM550817 5 0.3288 0.6699 0.000 0.000 0.276 0.000 0.724 0.000
#> GSM550818 5 0.3076 0.6995 0.000 0.000 0.240 0.000 0.760 0.000
#> GSM550819 4 0.5278 0.5361 0.032 0.044 0.172 0.708 0.004 0.040
#> GSM550820 1 0.4203 0.6767 0.788 0.000 0.072 0.040 0.004 0.096
#> GSM550821 5 0.5043 0.1625 0.000 0.040 0.468 0.000 0.476 0.016
#> GSM550822 2 0.1719 0.7152 0.000 0.924 0.060 0.016 0.000 0.000
#> GSM550826 5 0.3988 0.6629 0.040 0.000 0.076 0.020 0.816 0.048
#> GSM550832 2 0.2806 0.6710 0.000 0.844 0.136 0.016 0.000 0.004
#> GSM550833 2 0.2449 0.6731 0.000 0.888 0.080 0.012 0.000 0.020
#> GSM550835 3 0.6488 0.2110 0.000 0.092 0.436 0.008 0.400 0.064
#> GSM550836 5 0.0146 0.7585 0.000 0.000 0.000 0.004 0.996 0.000
#> GSM550837 3 0.6831 0.6719 0.000 0.348 0.440 0.008 0.132 0.072
#> GSM550838 6 0.5260 0.6720 0.220 0.000 0.064 0.028 0.016 0.672
#> GSM550841 5 0.3695 0.5482 0.000 0.000 0.376 0.000 0.624 0.000
#> GSM550842 3 0.5888 0.7093 0.000 0.320 0.508 0.000 0.160 0.012
#> GSM550846 4 0.7794 0.4544 0.200 0.032 0.280 0.380 0.000 0.108
#> GSM550849 6 0.6134 0.6464 0.176 0.000 0.108 0.004 0.100 0.612
#> GSM550850 6 0.3446 0.6545 0.308 0.000 0.000 0.000 0.000 0.692
#> GSM550851 3 0.6392 0.7055 0.000 0.340 0.448 0.000 0.180 0.032
#> GSM550852 2 0.5723 0.0971 0.000 0.568 0.264 0.016 0.000 0.152
#> GSM550853 2 0.2937 0.7124 0.000 0.848 0.056 0.096 0.000 0.000
#> GSM550855 2 0.3001 0.7254 0.000 0.840 0.024 0.128 0.000 0.008
#> GSM550856 2 0.4750 0.4758 0.000 0.608 0.040 0.340 0.000 0.012
#> GSM550861 2 0.1485 0.7335 0.000 0.944 0.028 0.024 0.000 0.004
#> GSM550863 4 0.4482 0.5998 0.160 0.004 0.072 0.744 0.000 0.020
#> GSM550864 2 0.5726 0.4277 0.000 0.572 0.140 0.268 0.000 0.020
#> GSM550866 4 0.4822 -0.1966 0.000 0.476 0.036 0.480 0.000 0.008
#> GSM550867 1 0.0291 0.7741 0.992 0.000 0.000 0.004 0.000 0.004
#> GSM550885 1 0.1053 0.7729 0.964 0.000 0.020 0.012 0.000 0.004
#> GSM550886 5 0.3772 0.6477 0.000 0.000 0.296 0.004 0.692 0.008
#> GSM550887 2 0.2145 0.7121 0.000 0.900 0.072 0.028 0.000 0.000
#> GSM550889 4 0.3024 0.6097 0.128 0.016 0.000 0.840 0.000 0.016
#> GSM550894 2 0.2964 0.6865 0.000 0.836 0.140 0.012 0.000 0.012
#> GSM550897 1 0.4724 0.4402 0.628 0.000 0.028 0.320 0.000 0.024
#> GSM550903 2 0.2772 0.7322 0.000 0.876 0.060 0.048 0.000 0.016
#> GSM550905 3 0.6067 0.5773 0.000 0.208 0.512 0.000 0.264 0.016
#> GSM550906 2 0.1765 0.7306 0.000 0.924 0.052 0.024 0.000 0.000
#> GSM550907 5 0.2454 0.7433 0.000 0.000 0.160 0.000 0.840 0.000
#> GSM550909 3 0.6401 0.0664 0.000 0.036 0.484 0.028 0.368 0.084
#> GSM550911 5 0.2092 0.7546 0.000 0.000 0.124 0.000 0.876 0.000
#> GSM550913 2 0.2314 0.7333 0.000 0.900 0.056 0.036 0.000 0.008
#> GSM550915 4 0.7620 0.4331 0.280 0.028 0.232 0.380 0.000 0.080
#> GSM550917 2 0.5979 0.4611 0.000 0.588 0.168 0.200 0.000 0.044
#> GSM550919 4 0.7959 0.3660 0.316 0.056 0.236 0.316 0.000 0.076
#> GSM550921 5 0.0000 0.7590 0.000 0.000 0.000 0.000 1.000 0.000
#> GSM550924 5 0.5451 0.5562 0.016 0.004 0.244 0.036 0.652 0.048
#> GSM550926 2 0.5541 0.3668 0.000 0.548 0.064 0.352 0.000 0.036
#> GSM550927 2 0.2979 0.7271 0.000 0.848 0.032 0.112 0.000 0.008
#> GSM550787 5 0.5219 0.6194 0.072 0.000 0.128 0.008 0.712 0.080
#> GSM550793 5 0.1767 0.7287 0.000 0.000 0.036 0.012 0.932 0.020
#> GSM550794 6 0.7157 0.4217 0.088 0.024 0.192 0.192 0.000 0.504
#> GSM550795 6 0.3764 0.6871 0.256 0.000 0.012 0.008 0.000 0.724
#> GSM550798 1 0.6540 0.1350 0.544 0.000 0.044 0.020 0.144 0.248
#> GSM550803 1 0.3081 0.5335 0.776 0.000 0.004 0.000 0.000 0.220
#> GSM550805 6 0.6181 0.5928 0.136 0.000 0.072 0.016 0.152 0.624
#> GSM550823 4 0.4370 0.5693 0.036 0.068 0.044 0.796 0.000 0.056
#> GSM550824 1 0.0146 0.7738 0.996 0.000 0.000 0.000 0.000 0.004
#> GSM550825 5 0.1413 0.7402 0.004 0.000 0.036 0.008 0.948 0.004
#> GSM550827 4 0.7231 0.5391 0.220 0.036 0.192 0.488 0.000 0.064
#> GSM550828 1 0.2467 0.7488 0.896 0.000 0.036 0.048 0.000 0.020
#> GSM550829 5 0.5522 0.2883 0.312 0.000 0.036 0.020 0.596 0.036
#> GSM550830 4 0.5751 0.4853 0.064 0.084 0.024 0.672 0.000 0.156
#> GSM550834 6 0.3288 0.6787 0.276 0.000 0.000 0.000 0.000 0.724
#> GSM550839 5 0.5325 0.4548 0.000 0.016 0.304 0.008 0.604 0.068
#> GSM550840 6 0.3508 0.6690 0.292 0.000 0.004 0.000 0.000 0.704
#> GSM550843 5 0.2871 0.7283 0.000 0.000 0.192 0.004 0.804 0.000
#> GSM550844 1 0.3278 0.7224 0.848 0.000 0.032 0.056 0.000 0.064
#> GSM550845 4 0.5478 0.3354 0.000 0.276 0.100 0.600 0.000 0.024
#> GSM550848 4 0.8041 0.4870 0.232 0.072 0.240 0.376 0.000 0.080
#> GSM550854 1 0.0508 0.7725 0.984 0.000 0.000 0.004 0.000 0.012
#> GSM550857 5 0.0806 0.7492 0.000 0.000 0.020 0.008 0.972 0.000
#> GSM550858 1 0.1391 0.7678 0.944 0.000 0.016 0.040 0.000 0.000
#> GSM550859 1 0.0291 0.7741 0.992 0.000 0.000 0.004 0.000 0.004
#> GSM550862 1 0.2547 0.7349 0.868 0.000 0.016 0.112 0.000 0.004
#> GSM550865 4 0.3706 0.6090 0.156 0.004 0.040 0.792 0.000 0.008
#> GSM550868 4 0.3569 0.6119 0.152 0.004 0.016 0.804 0.000 0.024
#> GSM550869 5 0.5025 0.6130 0.036 0.000 0.076 0.052 0.748 0.088
#> GSM550870 2 0.5626 0.4780 0.000 0.588 0.132 0.260 0.000 0.020
#> GSM550871 5 0.4053 0.6831 0.000 0.000 0.204 0.012 0.744 0.040
#> GSM550872 4 0.4625 0.5565 0.144 0.000 0.032 0.736 0.000 0.088
#> GSM550873 3 0.6513 0.5621 0.000 0.328 0.504 0.016 0.064 0.088
#> GSM550874 2 0.4489 0.6760 0.000 0.744 0.044 0.160 0.000 0.052
#> GSM550876 5 0.2738 0.7407 0.000 0.000 0.176 0.004 0.820 0.000
#> GSM550877 4 0.5169 -0.0464 0.000 0.416 0.052 0.516 0.000 0.016
#> GSM550878 5 0.2178 0.7502 0.000 0.000 0.132 0.000 0.868 0.000
#> GSM550879 1 0.4095 0.6891 0.784 0.000 0.060 0.120 0.000 0.036
#> GSM550882 5 0.0458 0.7607 0.000 0.000 0.016 0.000 0.984 0.000
#> GSM550888 5 0.0405 0.7558 0.000 0.000 0.008 0.004 0.988 0.000
#> GSM550890 4 0.7334 0.4937 0.228 0.016 0.236 0.436 0.000 0.084
#> GSM550891 5 0.0363 0.7605 0.000 0.000 0.012 0.000 0.988 0.000
#> GSM550892 1 0.4601 0.3018 0.588 0.000 0.020 0.376 0.000 0.016
#> GSM550893 4 0.5011 0.0358 0.000 0.400 0.028 0.544 0.000 0.028
#> GSM550895 4 0.3354 0.5549 0.020 0.128 0.000 0.824 0.000 0.028
#> GSM550896 4 0.4588 0.2043 0.000 0.344 0.020 0.616 0.000 0.020
#> GSM550898 1 0.0291 0.7731 0.992 0.000 0.004 0.000 0.000 0.004
#> GSM550899 2 0.6283 0.3411 0.000 0.520 0.200 0.244 0.000 0.036
#> GSM550900 4 0.3653 0.5937 0.132 0.000 0.016 0.804 0.000 0.048
#> GSM550901 1 0.4807 0.6024 0.732 0.000 0.132 0.068 0.000 0.068
#> GSM550902 5 0.5058 0.4984 0.156 0.000 0.052 0.040 0.724 0.028
#> GSM550904 1 0.6131 0.5377 0.664 0.000 0.092 0.060 0.100 0.084
#> GSM550908 5 0.0146 0.7585 0.000 0.000 0.000 0.004 0.996 0.000
#> GSM550912 2 0.6432 0.3327 0.000 0.516 0.184 0.248 0.000 0.052
#> GSM550914 4 0.7266 0.5064 0.220 0.016 0.236 0.448 0.000 0.080
#> GSM550918 2 0.6848 0.1363 0.004 0.432 0.208 0.304 0.000 0.052
#> GSM550922 5 0.3634 0.5767 0.000 0.000 0.356 0.000 0.644 0.000
#> GSM550923 1 0.4460 0.6189 0.784 0.000 0.048 0.028 0.044 0.096
#> GSM550925 1 0.4154 0.6560 0.772 0.000 0.048 0.144 0.000 0.036
#> GSM550802 6 0.5752 0.4795 0.004 0.100 0.124 0.112 0.000 0.660
#> GSM550812 6 0.6872 0.2949 0.000 0.092 0.224 0.204 0.000 0.480
#> GSM550831 6 0.3330 0.6737 0.284 0.000 0.000 0.000 0.000 0.716
#> GSM550847 1 0.0146 0.7738 0.996 0.000 0.000 0.000 0.000 0.004
#> GSM550860 5 0.0692 0.7569 0.000 0.000 0.020 0.004 0.976 0.000
#> GSM550875 6 0.7862 0.3864 0.224 0.000 0.080 0.052 0.260 0.384
#> GSM550880 1 0.5493 -0.1716 0.496 0.000 0.032 0.056 0.000 0.416
#> GSM550881 5 0.0291 0.7573 0.000 0.000 0.004 0.004 0.992 0.000
#> GSM550883 5 0.0291 0.7573 0.000 0.000 0.004 0.004 0.992 0.000
#> GSM550884 4 0.7308 0.2286 0.012 0.004 0.216 0.456 0.228 0.084
#> GSM550910 5 0.3351 0.6682 0.000 0.000 0.288 0.000 0.712 0.000
#> GSM550916 1 0.0603 0.7707 0.980 0.000 0.004 0.000 0.000 0.016
#> GSM550920 5 0.3244 0.6843 0.000 0.000 0.268 0.000 0.732 0.000
Heatmaps for the consensus matrix. It visualizes the probability of two samples to be in a same group.
consensus_heatmap(res, k = 2)
consensus_heatmap(res, k = 3)
consensus_heatmap(res, k = 4)
consensus_heatmap(res, k = 5)
consensus_heatmap(res, k = 6)
Heatmaps for the membership of samples in all partitions to see how consistent they are:
membership_heatmap(res, k = 2)
membership_heatmap(res, k = 3)
membership_heatmap(res, k = 4)
membership_heatmap(res, k = 5)
membership_heatmap(res, k = 6)
As soon as we have had the classes for columns, we can look for signatures which are significantly different between classes which can be candidate marks for certain classes. Following are the heatmaps for signatures.
Signature heatmaps where rows are scaled:
get_signatures(res, k = 2)
get_signatures(res, k = 3)
get_signatures(res, k = 4)
get_signatures(res, k = 5)
get_signatures(res, k = 6)
Signature heatmaps where rows are not scaled:
get_signatures(res, k = 2, scale_rows = FALSE)
get_signatures(res, k = 3, scale_rows = FALSE)
get_signatures(res, k = 4, scale_rows = FALSE)
get_signatures(res, k = 5, scale_rows = FALSE)
get_signatures(res, k = 6, scale_rows = FALSE)
Compare the overlap of signatures from different k:
compare_signatures(res)
get_signature() returns a data frame invisibly. TO get the list of signatures, the function
call should be assigned to a variable explicitly. In following code, if plot argument is set
to FALSE, no heatmap is plotted while only the differential analysis is performed.
# code only for demonstration
tb = get_signature(res, k = ..., plot = FALSE)
An example of the output of tb is:
#> which_row fdr mean_1 mean_2 scaled_mean_1 scaled_mean_2 km
#> 1 38 0.042760348 8.373488 9.131774 -0.5533452 0.5164555 1
#> 2 40 0.018707592 7.106213 8.469186 -0.6173731 0.5762149 1
#> 3 55 0.019134737 10.221463 11.207825 -0.6159697 0.5749050 1
#> 4 59 0.006059896 5.921854 7.869574 -0.6899429 0.6439467 1
#> 5 60 0.018055526 8.928898 10.211722 -0.6204761 0.5791110 1
#> 6 98 0.009384629 15.714769 14.887706 0.6635654 -0.6193277 2
...
The columns in tb are:
which_row: row indices corresponding to the input matrix.fdr: FDR for the differential test. mean_x: The mean value in group x.scaled_mean_x: The mean value in group x after rows are scaled.km: Row groups if k-means clustering is applied to rows.UMAP plot which shows how samples are separated.
dimension_reduction(res, k = 2, method = "UMAP")
dimension_reduction(res, k = 3, method = "UMAP")
dimension_reduction(res, k = 4, method = "UMAP")
dimension_reduction(res, k = 5, method = "UMAP")
dimension_reduction(res, k = 6, method = "UMAP")
Following heatmap shows how subgroups are split when increasing k:
collect_classes(res)
Test correlation between subgroups and known annotations. If the known annotation is numeric, one-way ANOVA test is applied, and if the known annotation is discrete, chi-squared contingency table test is applied.
test_to_known_factors(res)
#> n disease.state(p) k
#> CV:skmeans 134 6.01e-01 2
#> CV:skmeans 136 2.66e-03 3
#> CV:skmeans 125 1.43e-05 4
#> CV:skmeans 103 2.14e-06 5
#> CV:skmeans 105 3.52e-05 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 51776 rows and 143 columns.
#> Top rows (1000, 2000, 3000, 4000, 5000) are extracted by 'CV' method.
#> Subgroups are detected by 'pam' method.
#> Performed in total 1250 partitions by row resampling.
#> Best k for subgroups seems to be 2.
#>
#> Following methods can be applied to this 'ConsensusPartition' object:
#> [1] "cola_report" "collect_classes" "collect_plots"
#> [4] "collect_stats" "colnames" "compare_signatures"
#> [7] "consensus_heatmap" "dimension_reduction" "functional_enrichment"
#> [10] "get_anno_col" "get_anno" "get_classes"
#> [13] "get_consensus" "get_matrix" "get_membership"
#> [16] "get_param" "get_signatures" "get_stats"
#> [19] "is_best_k" "is_stable_k" "membership_heatmap"
#> [22] "ncol" "nrow" "plot_ecdf"
#> [25] "rownames" "select_partition_number" "show"
#> [28] "suggest_best_k" "test_to_known_factors"
collect_plots() function collects all the plots made from res for all k (number of partitions)
into one single page to provide an easy and fast comparison between different k.
collect_plots(res)
The plots are:
k and the heatmap of
predicted classes for each k.k.k.k.All the plots in panels can be made by individual functions and they are plotted later in this section.
select_partition_number() produces several plots showing different
statistics for choosing “optimized” k. There are following statistics:
k;k, the area increased is defined as \(A_k - A_{k-1}\).The detailed explanations of these statistics can be found in the cola vignette.
Generally speaking, lower PAC score, higher mean silhouette score or higher
concordance corresponds to better partition. Rand index and Jaccard index
measure how similar the current partition is compared to partition with k-1.
If they are too similar, we won't accept k is better than k-1.
select_partition_number(res)
The numeric values for all these statistics can be obtained by get_stats().
get_stats(res)
#> k 1-PAC mean_silhouette concordance area_increased Rand Jaccard
#> 2 2 0.917 0.935 0.957 0.4227 0.582 0.582
#> 3 3 0.456 0.679 0.836 0.5499 0.722 0.535
#> 4 4 0.481 0.441 0.688 0.1274 0.817 0.533
#> 5 5 0.554 0.519 0.692 0.0680 0.853 0.525
#> 6 6 0.551 0.446 0.650 0.0331 0.961 0.822
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
#> GSM550785 2 0.1843 0.963 0.028 0.972
#> GSM550786 1 0.0672 0.950 0.992 0.008
#> GSM550788 2 0.0938 0.962 0.012 0.988
#> GSM550789 2 0.1414 0.960 0.020 0.980
#> GSM550790 2 0.2236 0.962 0.036 0.964
#> GSM550791 2 0.2948 0.960 0.052 0.948
#> GSM550792 2 0.2603 0.952 0.044 0.956
#> GSM550796 2 0.3584 0.928 0.068 0.932
#> GSM550797 2 0.1414 0.960 0.020 0.980
#> GSM550799 1 0.1414 0.947 0.980 0.020
#> GSM550800 2 0.0000 0.965 0.000 1.000
#> GSM550801 2 0.1184 0.960 0.016 0.984
#> GSM550804 2 0.1184 0.963 0.016 0.984
#> GSM550806 1 0.1843 0.952 0.972 0.028
#> GSM550807 2 0.1414 0.960 0.020 0.980
#> GSM550808 1 0.9522 0.462 0.628 0.372
#> GSM550809 2 0.4298 0.931 0.088 0.912
#> GSM550810 2 0.3114 0.944 0.056 0.944
#> GSM550811 2 0.2778 0.959 0.048 0.952
#> GSM550813 2 0.0000 0.965 0.000 1.000
#> GSM550814 2 0.0000 0.965 0.000 1.000
#> GSM550815 2 0.1184 0.960 0.016 0.984
#> GSM550816 2 0.1414 0.961 0.020 0.980
#> GSM550817 1 0.0672 0.950 0.992 0.008
#> GSM550818 1 0.0672 0.950 0.992 0.008
#> GSM550819 2 0.6801 0.805 0.180 0.820
#> GSM550820 2 0.3879 0.937 0.076 0.924
#> GSM550821 1 0.2043 0.945 0.968 0.032
#> GSM550822 2 0.4298 0.909 0.088 0.912
#> GSM550826 1 0.3584 0.924 0.932 0.068
#> GSM550832 2 0.1633 0.959 0.024 0.976
#> GSM550833 2 0.1414 0.960 0.020 0.980
#> GSM550835 1 0.3879 0.923 0.924 0.076
#> GSM550836 1 0.0000 0.949 1.000 0.000
#> GSM550837 1 0.2778 0.941 0.952 0.048
#> GSM550838 2 0.9608 0.432 0.384 0.616
#> GSM550841 1 0.1414 0.947 0.980 0.020
#> GSM550842 1 0.2423 0.944 0.960 0.040
#> GSM550846 2 0.2236 0.962 0.036 0.964
#> GSM550849 2 0.4815 0.925 0.104 0.896
#> GSM550850 2 0.2603 0.962 0.044 0.956
#> GSM550851 1 0.2236 0.944 0.964 0.036
#> GSM550852 2 0.1184 0.964 0.016 0.984
#> GSM550853 2 0.0672 0.963 0.008 0.992
#> GSM550855 2 0.0000 0.965 0.000 1.000
#> GSM550856 2 0.0000 0.965 0.000 1.000
#> GSM550861 2 0.1184 0.960 0.016 0.984
#> GSM550863 2 0.0672 0.966 0.008 0.992
#> GSM550864 2 0.0000 0.965 0.000 1.000
#> GSM550866 2 0.0000 0.965 0.000 1.000
#> GSM550867 2 0.2043 0.963 0.032 0.968
#> GSM550885 2 0.2043 0.963 0.032 0.968
#> GSM550886 1 0.3114 0.940 0.944 0.056
#> GSM550887 2 0.3431 0.932 0.064 0.936
#> GSM550889 2 0.1633 0.964 0.024 0.976
#> GSM550894 2 0.3584 0.928 0.068 0.932
#> GSM550897 2 0.1843 0.963 0.028 0.972
#> GSM550903 2 0.1414 0.961 0.020 0.980
#> GSM550905 1 0.4298 0.912 0.912 0.088
#> GSM550906 2 0.0000 0.965 0.000 1.000
#> GSM550907 1 0.0938 0.950 0.988 0.012
#> GSM550909 1 0.6801 0.815 0.820 0.180
#> GSM550911 1 0.0938 0.950 0.988 0.012
#> GSM550913 2 0.1184 0.960 0.016 0.984
#> GSM550915 2 0.1184 0.966 0.016 0.984
#> GSM550917 2 0.0000 0.965 0.000 1.000
#> GSM550919 2 0.1414 0.965 0.020 0.980
#> GSM550921 1 0.0000 0.949 1.000 0.000
#> GSM550924 1 0.9209 0.528 0.664 0.336
#> GSM550926 2 0.0000 0.965 0.000 1.000
#> GSM550927 2 0.0000 0.965 0.000 1.000
#> GSM550787 2 0.9491 0.457 0.368 0.632
#> GSM550793 1 0.2236 0.945 0.964 0.036
#> GSM550794 2 0.1184 0.966 0.016 0.984
#> GSM550795 2 0.2043 0.965 0.032 0.968
#> GSM550798 1 0.7815 0.708 0.768 0.232
#> GSM550803 2 0.2236 0.962 0.036 0.964
#> GSM550805 2 0.3274 0.948 0.060 0.940
#> GSM550823 2 0.1633 0.965 0.024 0.976
#> GSM550824 2 0.2236 0.962 0.036 0.964
#> GSM550825 1 0.1414 0.950 0.980 0.020
#> GSM550827 2 0.0938 0.966 0.012 0.988
#> GSM550828 2 0.1843 0.963 0.028 0.972
#> GSM550829 1 0.1184 0.950 0.984 0.016
#> GSM550830 2 0.1633 0.964 0.024 0.976
#> GSM550834 2 0.2423 0.962 0.040 0.960
#> GSM550839 1 0.1633 0.950 0.976 0.024
#> GSM550840 2 0.1843 0.964 0.028 0.972
#> GSM550843 1 0.1843 0.952 0.972 0.028
#> GSM550844 2 0.2043 0.963 0.032 0.968
#> GSM550845 2 0.0000 0.965 0.000 1.000
#> GSM550848 2 0.0672 0.966 0.008 0.992
#> GSM550854 2 0.1633 0.964 0.024 0.976
#> GSM550857 1 0.1184 0.950 0.984 0.016
#> GSM550858 2 0.1633 0.964 0.024 0.976
#> GSM550859 2 0.2043 0.963 0.032 0.968
#> GSM550862 2 0.1843 0.963 0.028 0.972
#> GSM550865 2 0.1184 0.965 0.016 0.984
#> GSM550868 2 0.1184 0.965 0.016 0.984
#> GSM550869 2 0.5842 0.856 0.140 0.860
#> GSM550870 2 0.0000 0.965 0.000 1.000
#> GSM550871 1 0.3274 0.940 0.940 0.060
#> GSM550872 2 0.1184 0.966 0.016 0.984
#> GSM550873 2 0.4939 0.892 0.108 0.892
#> GSM550874 2 0.0000 0.965 0.000 1.000
#> GSM550876 1 0.1843 0.952 0.972 0.028
#> GSM550877 2 0.0000 0.965 0.000 1.000
#> GSM550878 1 0.1843 0.952 0.972 0.028
#> GSM550879 2 0.2043 0.963 0.032 0.968
#> GSM550882 1 0.1843 0.952 0.972 0.028
#> GSM550888 1 0.1184 0.950 0.984 0.016
#> GSM550890 2 0.0672 0.966 0.008 0.992
#> GSM550891 1 0.1184 0.950 0.984 0.016
#> GSM550892 2 0.1633 0.964 0.024 0.976
#> GSM550893 2 0.0672 0.966 0.008 0.992
#> GSM550895 2 0.0000 0.965 0.000 1.000
#> GSM550896 2 0.0000 0.965 0.000 1.000
#> GSM550898 2 0.1843 0.963 0.028 0.972
#> GSM550899 2 0.0376 0.965 0.004 0.996
#> GSM550900 2 0.1843 0.963 0.028 0.972
#> GSM550901 2 0.2043 0.963 0.032 0.968
#> GSM550902 1 0.5737 0.857 0.864 0.136
#> GSM550904 2 0.5178 0.900 0.116 0.884
#> GSM550908 1 0.1184 0.950 0.984 0.016
#> GSM550912 2 0.0938 0.964 0.012 0.988
#> GSM550914 2 0.0000 0.965 0.000 1.000
#> GSM550918 2 0.0376 0.965 0.004 0.996
#> GSM550922 1 0.1414 0.947 0.980 0.020
#> GSM550923 2 0.7139 0.797 0.196 0.804
#> GSM550925 2 0.2043 0.963 0.032 0.968
#> GSM550802 2 0.0000 0.965 0.000 1.000
#> GSM550812 2 0.2043 0.960 0.032 0.968
#> GSM550831 2 0.2778 0.961 0.048 0.952
#> GSM550847 2 0.1843 0.963 0.028 0.972
#> GSM550860 1 0.1414 0.950 0.980 0.020
#> GSM550875 2 0.3114 0.951 0.056 0.944
#> GSM550880 2 0.1633 0.965 0.024 0.976
#> GSM550881 1 0.1414 0.950 0.980 0.020
#> GSM550883 1 0.1184 0.950 0.984 0.016
#> GSM550884 2 0.4298 0.919 0.088 0.912
#> GSM550910 1 0.1414 0.951 0.980 0.020
#> GSM550916 2 0.2043 0.963 0.032 0.968
#> GSM550920 1 0.0672 0.950 0.992 0.008
cbind(get_classes(res, k = 3), get_membership(res, k = 3))
#> class entropy silhouette p1 p2 p3
#> GSM550785 1 0.3267 0.7437 0.884 0.116 0.000
#> GSM550786 3 0.0237 0.9120 0.004 0.000 0.996
#> GSM550788 2 0.5058 0.6346 0.244 0.756 0.000
#> GSM550789 2 0.0000 0.7609 0.000 1.000 0.000
#> GSM550790 1 0.1289 0.7483 0.968 0.032 0.000
#> GSM550791 1 0.5098 0.6038 0.752 0.248 0.000
#> GSM550792 2 0.6307 0.1772 0.488 0.512 0.000
#> GSM550796 2 0.1753 0.7564 0.048 0.952 0.000
#> GSM550797 2 0.3941 0.7307 0.156 0.844 0.000
#> GSM550799 3 0.0000 0.9132 0.000 0.000 1.000
#> GSM550800 2 0.5465 0.5725 0.288 0.712 0.000
#> GSM550801 2 0.2537 0.7610 0.080 0.920 0.000
#> GSM550804 2 0.2165 0.7691 0.064 0.936 0.000
#> GSM550806 3 0.0000 0.9132 0.000 0.000 1.000
#> GSM550807 2 0.2878 0.7515 0.096 0.904 0.000
#> GSM550808 2 0.8129 0.4743 0.124 0.632 0.244
#> GSM550809 1 0.2383 0.7487 0.940 0.044 0.016
#> GSM550810 2 0.3879 0.7132 0.152 0.848 0.000
#> GSM550811 1 0.4605 0.6829 0.796 0.204 0.000
#> GSM550813 2 0.2878 0.7594 0.096 0.904 0.000
#> GSM550814 2 0.5254 0.6175 0.264 0.736 0.000
#> GSM550815 2 0.0000 0.7609 0.000 1.000 0.000
#> GSM550816 2 0.3192 0.7648 0.112 0.888 0.000
#> GSM550817 3 0.0000 0.9132 0.000 0.000 1.000
#> GSM550818 3 0.0000 0.9132 0.000 0.000 1.000
#> GSM550819 1 0.7770 0.3038 0.560 0.056 0.384
#> GSM550820 1 0.1529 0.7536 0.960 0.040 0.000
#> GSM550821 3 0.1182 0.9062 0.012 0.012 0.976
#> GSM550822 2 0.0892 0.7626 0.020 0.980 0.000
#> GSM550826 3 0.8814 0.1311 0.404 0.116 0.480
#> GSM550832 2 0.2625 0.7485 0.084 0.916 0.000
#> GSM550833 2 0.5497 0.5721 0.292 0.708 0.000
#> GSM550835 3 0.5004 0.8061 0.088 0.072 0.840
#> GSM550836 3 0.0000 0.9132 0.000 0.000 1.000
#> GSM550837 3 0.7622 0.4316 0.060 0.332 0.608
#> GSM550838 1 0.5639 0.5900 0.752 0.016 0.232
#> GSM550841 3 0.0000 0.9132 0.000 0.000 1.000
#> GSM550842 3 0.1170 0.9048 0.008 0.016 0.976
#> GSM550846 1 0.6026 0.4085 0.624 0.376 0.000
#> GSM550849 1 0.5058 0.6179 0.756 0.244 0.000
#> GSM550850 1 0.1860 0.7375 0.948 0.052 0.000
#> GSM550851 3 0.1919 0.8944 0.024 0.020 0.956
#> GSM550852 2 0.5706 0.5469 0.320 0.680 0.000
#> GSM550853 2 0.0747 0.7651 0.016 0.984 0.000
#> GSM550855 2 0.4842 0.6453 0.224 0.776 0.000
#> GSM550856 2 0.2878 0.7666 0.096 0.904 0.000
#> GSM550861 2 0.0000 0.7609 0.000 1.000 0.000
#> GSM550863 1 0.6140 0.3198 0.596 0.404 0.000
#> GSM550864 2 0.2537 0.7594 0.080 0.920 0.000
#> GSM550866 2 0.5835 0.5207 0.340 0.660 0.000
#> GSM550867 1 0.3116 0.7379 0.892 0.108 0.000
#> GSM550885 1 0.4062 0.7134 0.836 0.164 0.000
#> GSM550886 3 0.4277 0.7978 0.016 0.132 0.852
#> GSM550887 2 0.1753 0.7614 0.048 0.952 0.000
#> GSM550889 1 0.5465 0.5875 0.712 0.288 0.000
#> GSM550894 2 0.2959 0.7307 0.100 0.900 0.000
#> GSM550897 1 0.4178 0.7249 0.828 0.172 0.000
#> GSM550903 2 0.1753 0.7654 0.048 0.952 0.000
#> GSM550905 3 0.4982 0.8072 0.064 0.096 0.840
#> GSM550906 2 0.2625 0.7667 0.084 0.916 0.000
#> GSM550907 3 0.0000 0.9132 0.000 0.000 1.000
#> GSM550909 3 0.9422 0.3046 0.216 0.284 0.500
#> GSM550911 3 0.0000 0.9132 0.000 0.000 1.000
#> GSM550913 2 0.0000 0.7609 0.000 1.000 0.000
#> GSM550915 2 0.5733 0.4736 0.324 0.676 0.000
#> GSM550917 2 0.1529 0.7642 0.040 0.960 0.000
#> GSM550919 2 0.5968 0.3255 0.364 0.636 0.000
#> GSM550921 3 0.0000 0.9132 0.000 0.000 1.000
#> GSM550924 1 0.9641 0.2680 0.464 0.296 0.240
#> GSM550926 2 0.4654 0.6795 0.208 0.792 0.000
#> GSM550927 2 0.0747 0.7589 0.016 0.984 0.000
#> GSM550787 1 0.6301 0.5649 0.712 0.028 0.260
#> GSM550793 3 0.4453 0.7859 0.152 0.012 0.836
#> GSM550794 1 0.5591 0.4602 0.696 0.304 0.000
#> GSM550795 1 0.3482 0.7312 0.872 0.128 0.000
#> GSM550798 1 0.6309 -0.0961 0.500 0.000 0.500
#> GSM550803 1 0.0592 0.7434 0.988 0.012 0.000
#> GSM550805 1 0.3682 0.7279 0.876 0.116 0.008
#> GSM550823 1 0.4062 0.7197 0.836 0.164 0.000
#> GSM550824 1 0.1031 0.7463 0.976 0.024 0.000
#> GSM550825 3 0.2066 0.8734 0.060 0.000 0.940
#> GSM550827 2 0.6308 0.0871 0.492 0.508 0.000
#> GSM550828 1 0.3116 0.7392 0.892 0.108 0.000
#> GSM550829 3 0.5948 0.4444 0.360 0.000 0.640
#> GSM550830 1 0.5291 0.6014 0.732 0.268 0.000
#> GSM550834 1 0.5363 0.5747 0.724 0.276 0.000
#> GSM550839 3 0.0892 0.9066 0.020 0.000 0.980
#> GSM550840 1 0.3038 0.7434 0.896 0.104 0.000
#> GSM550843 3 0.0000 0.9132 0.000 0.000 1.000
#> GSM550844 1 0.1860 0.7486 0.948 0.052 0.000
#> GSM550845 2 0.4750 0.6705 0.216 0.784 0.000
#> GSM550848 2 0.4750 0.6595 0.216 0.784 0.000
#> GSM550854 1 0.3116 0.7379 0.892 0.108 0.000
#> GSM550857 3 0.0000 0.9132 0.000 0.000 1.000
#> GSM550858 1 0.5138 0.6479 0.748 0.252 0.000
#> GSM550859 1 0.3116 0.7395 0.892 0.108 0.000
#> GSM550862 1 0.2959 0.7447 0.900 0.100 0.000
#> GSM550865 1 0.5465 0.5855 0.712 0.288 0.000
#> GSM550868 1 0.5926 0.4206 0.644 0.356 0.000
#> GSM550869 1 0.2804 0.7474 0.924 0.060 0.016
#> GSM550870 2 0.4062 0.7404 0.164 0.836 0.000
#> GSM550871 3 0.3359 0.8530 0.084 0.016 0.900
#> GSM550872 2 0.6305 0.1690 0.484 0.516 0.000
#> GSM550873 1 0.6617 0.2987 0.600 0.388 0.012
#> GSM550874 2 0.5397 0.5905 0.280 0.720 0.000
#> GSM550876 3 0.0000 0.9132 0.000 0.000 1.000
#> GSM550877 2 0.4887 0.6596 0.228 0.772 0.000
#> GSM550878 3 0.0000 0.9132 0.000 0.000 1.000
#> GSM550879 1 0.4750 0.6847 0.784 0.216 0.000
#> GSM550882 3 0.0000 0.9132 0.000 0.000 1.000
#> GSM550888 3 0.0000 0.9132 0.000 0.000 1.000
#> GSM550890 2 0.5254 0.6076 0.264 0.736 0.000
#> GSM550891 3 0.0000 0.9132 0.000 0.000 1.000
#> GSM550892 1 0.4796 0.6863 0.780 0.220 0.000
#> GSM550893 2 0.5650 0.5673 0.312 0.688 0.000
#> GSM550895 2 0.6299 0.1900 0.476 0.524 0.000
#> GSM550896 2 0.5363 0.6161 0.276 0.724 0.000
#> GSM550898 1 0.2537 0.7450 0.920 0.080 0.000
#> GSM550899 2 0.1860 0.7624 0.052 0.948 0.000
#> GSM550900 1 0.4235 0.7230 0.824 0.176 0.000
#> GSM550901 1 0.5291 0.6307 0.732 0.268 0.000
#> GSM550902 3 0.7029 0.2222 0.440 0.020 0.540
#> GSM550904 1 0.4121 0.7053 0.832 0.168 0.000
#> GSM550908 3 0.0000 0.9132 0.000 0.000 1.000
#> GSM550912 2 0.2165 0.7688 0.064 0.936 0.000
#> GSM550914 2 0.4346 0.6879 0.184 0.816 0.000
#> GSM550918 2 0.1860 0.7585 0.052 0.948 0.000
#> GSM550922 3 0.0237 0.9120 0.000 0.004 0.996
#> GSM550923 1 0.2050 0.7419 0.952 0.020 0.028
#> GSM550925 1 0.5098 0.6812 0.752 0.248 0.000
#> GSM550802 2 0.6299 0.2147 0.476 0.524 0.000
#> GSM550812 1 0.5926 0.3187 0.644 0.356 0.000
#> GSM550831 1 0.2959 0.7421 0.900 0.100 0.000
#> GSM550847 1 0.2796 0.7431 0.908 0.092 0.000
#> GSM550860 3 0.1031 0.9048 0.024 0.000 0.976
#> GSM550875 1 0.2165 0.7475 0.936 0.064 0.000
#> GSM550880 1 0.6291 -0.0888 0.532 0.468 0.000
#> GSM550881 3 0.0000 0.9132 0.000 0.000 1.000
#> GSM550883 3 0.0000 0.9132 0.000 0.000 1.000
#> GSM550884 1 0.5756 0.6613 0.764 0.208 0.028
#> GSM550910 3 0.1289 0.8960 0.000 0.032 0.968
#> GSM550916 1 0.1860 0.7535 0.948 0.052 0.000
#> GSM550920 3 0.0237 0.9121 0.000 0.004 0.996
cbind(get_classes(res, k = 4), get_membership(res, k = 4))
#> class entropy silhouette p1 p2 p3 p4
#> GSM550785 1 0.2480 0.73065 0.904 0.008 0.000 0.088
#> GSM550786 3 0.0524 0.88254 0.000 0.004 0.988 0.008
#> GSM550788 2 0.4086 0.45049 0.008 0.776 0.000 0.216
#> GSM550789 2 0.0592 0.58219 0.000 0.984 0.000 0.016
#> GSM550790 1 0.3266 0.66480 0.832 0.000 0.000 0.168
#> GSM550791 4 0.7120 0.09568 0.368 0.136 0.000 0.496
#> GSM550792 2 0.5781 0.08026 0.028 0.488 0.000 0.484
#> GSM550796 2 0.2973 0.53946 0.000 0.856 0.000 0.144
#> GSM550797 2 0.3219 0.53032 0.000 0.836 0.000 0.164
#> GSM550799 3 0.0000 0.88566 0.000 0.000 1.000 0.000
#> GSM550800 2 0.4194 0.46661 0.028 0.800 0.000 0.172
#> GSM550801 2 0.2469 0.57618 0.000 0.892 0.000 0.108
#> GSM550804 2 0.5901 0.41655 0.036 0.532 0.000 0.432
#> GSM550806 3 0.0000 0.88566 0.000 0.000 1.000 0.000
#> GSM550807 2 0.2198 0.56352 0.008 0.920 0.000 0.072
#> GSM550808 2 0.5384 0.43075 0.000 0.728 0.076 0.196
#> GSM550809 4 0.6140 0.07001 0.372 0.008 0.040 0.580
#> GSM550810 2 0.3688 0.49527 0.000 0.792 0.000 0.208
#> GSM550811 4 0.6223 0.16279 0.060 0.384 0.000 0.556
#> GSM550813 2 0.5039 0.50473 0.004 0.592 0.000 0.404
#> GSM550814 2 0.5016 0.46375 0.004 0.600 0.000 0.396
#> GSM550815 2 0.0188 0.58087 0.000 0.996 0.000 0.004
#> GSM550816 2 0.5510 0.44494 0.024 0.600 0.000 0.376
#> GSM550817 3 0.0000 0.88566 0.000 0.000 1.000 0.000
#> GSM550818 3 0.0000 0.88566 0.000 0.000 1.000 0.000
#> GSM550819 4 0.6926 0.19478 0.068 0.020 0.368 0.544
#> GSM550820 4 0.5292 -0.10726 0.480 0.008 0.000 0.512
#> GSM550821 3 0.1256 0.87378 0.000 0.008 0.964 0.028
#> GSM550822 2 0.2216 0.58306 0.000 0.908 0.000 0.092
#> GSM550826 3 0.8909 -0.16312 0.332 0.052 0.364 0.252
#> GSM550832 4 0.5143 -0.37340 0.004 0.456 0.000 0.540
#> GSM550833 2 0.3725 0.47867 0.008 0.812 0.000 0.180
#> GSM550835 3 0.7789 0.05789 0.000 0.352 0.400 0.248
#> GSM550836 3 0.0000 0.88566 0.000 0.000 1.000 0.000
#> GSM550837 2 0.6603 0.20786 0.000 0.572 0.328 0.100
#> GSM550838 4 0.7783 -0.00517 0.332 0.004 0.216 0.448
#> GSM550841 3 0.0000 0.88566 0.000 0.000 1.000 0.000
#> GSM550842 3 0.3088 0.82605 0.000 0.060 0.888 0.052
#> GSM550846 4 0.4415 0.26157 0.056 0.140 0.000 0.804
#> GSM550849 4 0.7525 0.25238 0.232 0.276 0.000 0.492
#> GSM550850 4 0.7702 0.06859 0.360 0.224 0.000 0.416
#> GSM550851 3 0.4072 0.76844 0.000 0.120 0.828 0.052
#> GSM550852 2 0.4522 0.41215 0.000 0.680 0.000 0.320
#> GSM550853 2 0.3257 0.57472 0.004 0.844 0.000 0.152
#> GSM550855 2 0.4897 0.40854 0.008 0.660 0.000 0.332
#> GSM550856 2 0.4988 0.50963 0.020 0.692 0.000 0.288
#> GSM550861 2 0.1389 0.58837 0.000 0.952 0.000 0.048
#> GSM550863 4 0.7325 0.26049 0.264 0.208 0.000 0.528
#> GSM550864 2 0.5460 0.45850 0.028 0.632 0.000 0.340
#> GSM550866 2 0.6443 0.17532 0.072 0.528 0.000 0.400
#> GSM550867 1 0.1637 0.73494 0.940 0.000 0.000 0.060
#> GSM550885 1 0.3099 0.69798 0.876 0.020 0.000 0.104
#> GSM550886 3 0.5057 0.63563 0.004 0.044 0.748 0.204
#> GSM550887 2 0.1474 0.58637 0.000 0.948 0.000 0.052
#> GSM550889 4 0.7017 0.34012 0.236 0.188 0.000 0.576
#> GSM550894 2 0.4999 0.43403 0.000 0.508 0.000 0.492
#> GSM550897 4 0.7252 0.05954 0.420 0.144 0.000 0.436
#> GSM550903 2 0.4978 0.49645 0.004 0.612 0.000 0.384
#> GSM550905 3 0.6435 0.53258 0.000 0.224 0.640 0.136
#> GSM550906 2 0.3837 0.55183 0.000 0.776 0.000 0.224
#> GSM550907 3 0.0000 0.88566 0.000 0.000 1.000 0.000
#> GSM550909 4 0.7514 0.15268 0.024 0.108 0.360 0.508
#> GSM550911 3 0.0000 0.88566 0.000 0.000 1.000 0.000
#> GSM550913 2 0.4741 0.47894 0.004 0.668 0.000 0.328
#> GSM550915 4 0.6435 -0.09601 0.072 0.396 0.000 0.532
#> GSM550917 2 0.5271 0.46162 0.020 0.640 0.000 0.340
#> GSM550919 4 0.7221 -0.15084 0.140 0.424 0.000 0.436
#> GSM550921 3 0.0000 0.88566 0.000 0.000 1.000 0.000
#> GSM550924 4 0.8360 0.24285 0.200 0.104 0.140 0.556
#> GSM550926 4 0.5511 0.03413 0.028 0.352 0.000 0.620
#> GSM550927 2 0.4382 0.50265 0.000 0.704 0.000 0.296
#> GSM550787 4 0.7907 -0.11033 0.376 0.004 0.232 0.388
#> GSM550793 3 0.6031 0.59753 0.144 0.000 0.688 0.168
#> GSM550794 4 0.5998 0.34723 0.200 0.116 0.000 0.684
#> GSM550795 4 0.7019 0.20812 0.132 0.344 0.000 0.524
#> GSM550798 1 0.6104 0.51007 0.680 0.000 0.180 0.140
#> GSM550803 1 0.2589 0.70731 0.884 0.000 0.000 0.116
#> GSM550805 4 0.5614 0.15851 0.336 0.036 0.000 0.628
#> GSM550823 4 0.4833 0.35834 0.228 0.032 0.000 0.740
#> GSM550824 1 0.0000 0.74840 1.000 0.000 0.000 0.000
#> GSM550825 3 0.2081 0.82834 0.084 0.000 0.916 0.000
#> GSM550827 4 0.5803 0.23700 0.104 0.196 0.000 0.700
#> GSM550828 1 0.4904 0.54058 0.744 0.040 0.000 0.216
#> GSM550829 3 0.5090 0.45732 0.324 0.000 0.660 0.016
#> GSM550830 4 0.6928 0.14569 0.108 0.436 0.000 0.456
#> GSM550834 4 0.7151 0.16262 0.132 0.420 0.000 0.448
#> GSM550839 3 0.1722 0.86136 0.000 0.008 0.944 0.048
#> GSM550840 4 0.7402 0.25880 0.220 0.264 0.000 0.516
#> GSM550843 3 0.0000 0.88566 0.000 0.000 1.000 0.000
#> GSM550844 4 0.5132 -0.01173 0.448 0.004 0.000 0.548
#> GSM550845 4 0.6532 -0.11188 0.076 0.420 0.000 0.504
#> GSM550848 2 0.6595 0.21471 0.080 0.492 0.000 0.428
#> GSM550854 1 0.0657 0.75180 0.984 0.004 0.000 0.012
#> GSM550857 3 0.0000 0.88566 0.000 0.000 1.000 0.000
#> GSM550858 1 0.4731 0.58283 0.780 0.160 0.000 0.060
#> GSM550859 1 0.0592 0.74883 0.984 0.000 0.000 0.016
#> GSM550862 1 0.4248 0.59542 0.768 0.012 0.000 0.220
#> GSM550865 4 0.7205 0.25205 0.296 0.172 0.000 0.532
#> GSM550868 4 0.7443 0.24328 0.312 0.196 0.000 0.492
#> GSM550869 4 0.5250 0.19415 0.316 0.000 0.024 0.660
#> GSM550870 2 0.5313 0.49600 0.016 0.608 0.000 0.376
#> GSM550871 3 0.3973 0.72362 0.004 0.004 0.792 0.200
#> GSM550872 4 0.7210 0.25031 0.184 0.276 0.000 0.540
#> GSM550873 4 0.6272 0.33124 0.132 0.152 0.016 0.700
#> GSM550874 2 0.5281 0.24878 0.008 0.528 0.000 0.464
#> GSM550876 3 0.0188 0.88440 0.000 0.000 0.996 0.004
#> GSM550877 4 0.6286 -0.03687 0.064 0.384 0.000 0.552
#> GSM550878 3 0.0000 0.88566 0.000 0.000 1.000 0.000
#> GSM550879 1 0.7015 0.21787 0.568 0.168 0.000 0.264
#> GSM550882 3 0.0000 0.88566 0.000 0.000 1.000 0.000
#> GSM550888 3 0.0000 0.88566 0.000 0.000 1.000 0.000
#> GSM550890 4 0.6669 0.03164 0.104 0.332 0.000 0.564
#> GSM550891 3 0.0000 0.88566 0.000 0.000 1.000 0.000
#> GSM550892 1 0.6580 0.11867 0.504 0.080 0.000 0.416
#> GSM550893 4 0.5497 0.13927 0.044 0.284 0.000 0.672
#> GSM550895 4 0.6627 0.15646 0.096 0.348 0.000 0.556
#> GSM550896 4 0.6659 -0.10073 0.088 0.400 0.000 0.512
#> GSM550898 1 0.0336 0.75017 0.992 0.000 0.000 0.008
#> GSM550899 2 0.5233 0.46961 0.020 0.648 0.000 0.332
#> GSM550900 4 0.5964 0.35162 0.208 0.108 0.000 0.684
#> GSM550901 1 0.7200 0.07632 0.484 0.144 0.000 0.372
#> GSM550902 3 0.7366 0.08219 0.344 0.000 0.484 0.172
#> GSM550904 4 0.6253 0.08400 0.396 0.060 0.000 0.544
#> GSM550908 3 0.0000 0.88566 0.000 0.000 1.000 0.000
#> GSM550912 2 0.5498 0.43093 0.020 0.576 0.000 0.404
#> GSM550914 4 0.6817 -0.11155 0.100 0.408 0.000 0.492
#> GSM550918 2 0.5543 0.43158 0.028 0.612 0.000 0.360
#> GSM550922 3 0.0376 0.88362 0.000 0.004 0.992 0.004
#> GSM550923 1 0.2715 0.71083 0.892 0.004 0.004 0.100
#> GSM550925 4 0.7069 0.08547 0.408 0.124 0.000 0.468
#> GSM550802 4 0.5155 0.00264 0.004 0.468 0.000 0.528
#> GSM550812 4 0.3601 0.41340 0.084 0.056 0.000 0.860
#> GSM550831 4 0.7537 0.22566 0.196 0.348 0.000 0.456
#> GSM550847 1 0.0592 0.75057 0.984 0.000 0.000 0.016
#> GSM550860 3 0.2174 0.85425 0.020 0.000 0.928 0.052
#> GSM550875 4 0.5285 0.14611 0.352 0.004 0.012 0.632
#> GSM550880 2 0.7012 -0.00361 0.124 0.504 0.000 0.372
#> GSM550881 3 0.0336 0.88356 0.000 0.000 0.992 0.008
#> GSM550883 3 0.0000 0.88566 0.000 0.000 1.000 0.000
#> GSM550884 4 0.5644 0.37887 0.180 0.056 0.024 0.740
#> GSM550910 3 0.2124 0.83817 0.000 0.008 0.924 0.068
#> GSM550916 1 0.2973 0.69304 0.856 0.000 0.000 0.144
#> GSM550920 3 0.0336 0.88373 0.000 0.000 0.992 0.008
cbind(get_classes(res, k = 5), get_membership(res, k = 5))
#> class entropy silhouette p1 p2 p3 p4 p5
#> GSM550785 1 0.3339 0.75593 0.840 0.000 0.000 0.048 0.112
#> GSM550786 3 0.0693 0.87976 0.000 0.008 0.980 0.012 0.000
#> GSM550788 2 0.5076 0.57172 0.000 0.692 0.000 0.108 0.200
#> GSM550789 2 0.1331 0.64971 0.000 0.952 0.000 0.008 0.040
#> GSM550790 1 0.3508 0.63368 0.748 0.000 0.000 0.252 0.000
#> GSM550791 4 0.6389 0.44431 0.164 0.084 0.000 0.644 0.108
#> GSM550792 4 0.5068 0.17697 0.004 0.384 0.000 0.580 0.032
#> GSM550796 2 0.2171 0.66507 0.000 0.912 0.000 0.064 0.024
#> GSM550797 2 0.1877 0.66313 0.000 0.924 0.000 0.064 0.012
#> GSM550799 3 0.0162 0.88248 0.000 0.004 0.996 0.000 0.000
#> GSM550800 2 0.4599 0.55570 0.004 0.752 0.000 0.156 0.088
#> GSM550801 2 0.2362 0.64245 0.000 0.900 0.000 0.024 0.076
#> GSM550804 5 0.5240 0.42835 0.004 0.372 0.000 0.044 0.580
#> GSM550806 3 0.0000 0.88274 0.000 0.000 1.000 0.000 0.000
#> GSM550807 2 0.1981 0.65042 0.000 0.924 0.000 0.028 0.048
#> GSM550808 2 0.2329 0.65312 0.000 0.876 0.000 0.124 0.000
#> GSM550809 4 0.3408 0.56760 0.088 0.028 0.008 0.860 0.016
#> GSM550810 2 0.2660 0.65316 0.000 0.864 0.000 0.128 0.008
#> GSM550811 4 0.5101 0.25631 0.012 0.348 0.000 0.612 0.028
#> GSM550813 2 0.5773 -0.09949 0.000 0.476 0.000 0.088 0.436
#> GSM550814 2 0.6129 0.41871 0.004 0.548 0.000 0.136 0.312
#> GSM550815 2 0.1270 0.64239 0.000 0.948 0.000 0.000 0.052
#> GSM550816 5 0.6355 0.36179 0.004 0.408 0.000 0.140 0.448
#> GSM550817 3 0.0000 0.88274 0.000 0.000 1.000 0.000 0.000
#> GSM550818 3 0.0162 0.88287 0.000 0.000 0.996 0.004 0.000
#> GSM550819 4 0.6654 0.44038 0.012 0.024 0.208 0.596 0.160
#> GSM550820 4 0.5049 0.48148 0.200 0.012 0.000 0.712 0.076
#> GSM550821 3 0.1836 0.86656 0.000 0.008 0.936 0.016 0.040
#> GSM550822 2 0.3573 0.64463 0.000 0.812 0.000 0.036 0.152
#> GSM550826 3 0.8753 -0.11088 0.112 0.028 0.348 0.276 0.236
#> GSM550832 5 0.6120 0.39028 0.000 0.256 0.000 0.184 0.560
#> GSM550833 2 0.2900 0.66837 0.000 0.864 0.000 0.108 0.028
#> GSM550835 2 0.6354 0.28104 0.000 0.520 0.216 0.264 0.000
#> GSM550836 3 0.1752 0.86357 0.004 0.004 0.936 0.052 0.004
#> GSM550837 2 0.5016 0.52712 0.000 0.704 0.204 0.088 0.004
#> GSM550838 4 0.5683 0.45404 0.064 0.044 0.200 0.688 0.004
#> GSM550841 3 0.0000 0.88274 0.000 0.000 1.000 0.000 0.000
#> GSM550842 3 0.3272 0.80268 0.000 0.100 0.856 0.032 0.012
#> GSM550846 5 0.5719 0.21348 0.016 0.064 0.000 0.332 0.588
#> GSM550849 4 0.6138 -0.00219 0.068 0.428 0.000 0.480 0.024
#> GSM550850 4 0.5506 0.39356 0.220 0.120 0.000 0.656 0.004
#> GSM550851 3 0.3759 0.72394 0.000 0.180 0.792 0.024 0.004
#> GSM550852 2 0.3849 0.59043 0.000 0.752 0.000 0.232 0.016
#> GSM550853 2 0.3988 0.56025 0.000 0.768 0.000 0.036 0.196
#> GSM550855 2 0.5037 0.39771 0.000 0.616 0.000 0.048 0.336
#> GSM550856 5 0.6036 0.14516 0.000 0.432 0.000 0.116 0.452
#> GSM550861 2 0.2179 0.60489 0.000 0.888 0.000 0.000 0.112
#> GSM550863 5 0.7612 0.04322 0.228 0.064 0.000 0.264 0.444
#> GSM550864 5 0.4590 0.41850 0.000 0.420 0.000 0.012 0.568
#> GSM550866 2 0.6868 -0.09766 0.008 0.428 0.000 0.228 0.336
#> GSM550867 1 0.1251 0.80738 0.956 0.000 0.000 0.036 0.008
#> GSM550885 1 0.3898 0.74432 0.804 0.000 0.000 0.080 0.116
#> GSM550886 3 0.5446 0.49103 0.000 0.000 0.628 0.100 0.272
#> GSM550887 2 0.2563 0.64486 0.000 0.872 0.000 0.008 0.120
#> GSM550889 4 0.6143 0.12631 0.008 0.100 0.000 0.460 0.432
#> GSM550894 5 0.5681 0.36079 0.000 0.268 0.000 0.124 0.608
#> GSM550897 4 0.7374 0.25293 0.140 0.068 0.000 0.440 0.352
#> GSM550903 5 0.4917 0.38431 0.000 0.416 0.000 0.028 0.556
#> GSM550905 3 0.6842 0.21345 0.000 0.340 0.504 0.104 0.052
#> GSM550906 2 0.4728 0.45435 0.000 0.700 0.000 0.060 0.240
#> GSM550907 3 0.0324 0.88302 0.004 0.004 0.992 0.000 0.000
#> GSM550909 4 0.7676 0.20838 0.004 0.064 0.304 0.440 0.188
#> GSM550911 3 0.0162 0.88300 0.004 0.000 0.996 0.000 0.000
#> GSM550913 5 0.4641 0.37534 0.000 0.456 0.000 0.012 0.532
#> GSM550915 5 0.4704 0.52859 0.016 0.104 0.000 0.116 0.764
#> GSM550917 5 0.4682 0.41537 0.000 0.420 0.000 0.016 0.564
#> GSM550919 5 0.3542 0.55123 0.020 0.112 0.000 0.028 0.840
#> GSM550921 3 0.0486 0.88262 0.004 0.004 0.988 0.000 0.004
#> GSM550924 5 0.7268 -0.10221 0.040 0.028 0.088 0.400 0.444
#> GSM550926 5 0.5394 0.38628 0.000 0.132 0.000 0.208 0.660
#> GSM550927 5 0.4410 0.38024 0.000 0.440 0.000 0.004 0.556
#> GSM550787 4 0.7479 0.43465 0.144 0.016 0.188 0.560 0.092
#> GSM550793 3 0.5344 0.61218 0.060 0.032 0.696 0.212 0.000
#> GSM550794 4 0.4600 0.55273 0.020 0.108 0.000 0.776 0.096
#> GSM550795 4 0.4774 0.24239 0.012 0.328 0.000 0.644 0.016
#> GSM550798 1 0.6084 0.50684 0.612 0.000 0.108 0.256 0.024
#> GSM550803 1 0.1732 0.79327 0.920 0.000 0.000 0.080 0.000
#> GSM550805 4 0.4087 0.57292 0.100 0.028 0.000 0.816 0.056
#> GSM550823 4 0.4834 0.42224 0.008 0.028 0.000 0.656 0.308
#> GSM550824 1 0.0162 0.81456 0.996 0.000 0.000 0.004 0.000
#> GSM550825 3 0.1341 0.85851 0.056 0.000 0.944 0.000 0.000
#> GSM550827 5 0.6018 -0.05675 0.008 0.088 0.000 0.424 0.480
#> GSM550828 1 0.6697 0.14498 0.500 0.024 0.000 0.336 0.140
#> GSM550829 3 0.3867 0.77872 0.108 0.004 0.828 0.044 0.016
#> GSM550830 4 0.6599 0.41205 0.028 0.292 0.000 0.544 0.136
#> GSM550834 2 0.5967 0.19880 0.068 0.500 0.000 0.416 0.016
#> GSM550839 3 0.1682 0.86400 0.000 0.012 0.940 0.044 0.004
#> GSM550840 4 0.4794 0.50918 0.080 0.164 0.000 0.744 0.012
#> GSM550843 3 0.0000 0.88274 0.000 0.000 1.000 0.000 0.000
#> GSM550844 4 0.4761 0.53770 0.168 0.000 0.000 0.728 0.104
#> GSM550845 5 0.3779 0.54752 0.004 0.136 0.000 0.048 0.812
#> GSM550848 5 0.4295 0.53280 0.004 0.248 0.000 0.024 0.724
#> GSM550854 1 0.0566 0.81535 0.984 0.000 0.000 0.012 0.004
#> GSM550857 3 0.0324 0.88286 0.000 0.004 0.992 0.000 0.004
#> GSM550858 1 0.5307 0.63088 0.708 0.056 0.000 0.040 0.196
#> GSM550859 1 0.0290 0.81433 0.992 0.000 0.000 0.008 0.000
#> GSM550862 1 0.5740 0.50582 0.644 0.008 0.000 0.208 0.140
#> GSM550865 5 0.7726 -0.04428 0.232 0.064 0.000 0.304 0.400
#> GSM550868 4 0.7680 0.21427 0.164 0.092 0.000 0.448 0.296
#> GSM550869 4 0.4473 0.54835 0.040 0.008 0.012 0.772 0.168
#> GSM550870 5 0.5931 0.31451 0.000 0.436 0.000 0.104 0.460
#> GSM550871 3 0.5103 0.58266 0.000 0.024 0.688 0.248 0.040
#> GSM550872 4 0.6964 0.18534 0.092 0.064 0.000 0.456 0.388
#> GSM550873 4 0.5842 0.46936 0.020 0.116 0.000 0.648 0.216
#> GSM550874 2 0.6145 0.43067 0.000 0.532 0.000 0.156 0.312
#> GSM550876 3 0.0290 0.88226 0.000 0.000 0.992 0.000 0.008
#> GSM550877 5 0.4149 0.45654 0.004 0.080 0.000 0.124 0.792
#> GSM550878 3 0.0000 0.88274 0.000 0.000 1.000 0.000 0.000
#> GSM550879 5 0.7419 -0.01891 0.316 0.036 0.000 0.244 0.404
#> GSM550882 3 0.0000 0.88274 0.000 0.000 1.000 0.000 0.000
#> GSM550888 3 0.0486 0.88262 0.004 0.004 0.988 0.000 0.004
#> GSM550890 5 0.3080 0.52661 0.008 0.060 0.000 0.060 0.872
#> GSM550891 3 0.0486 0.88262 0.004 0.004 0.988 0.000 0.004
#> GSM550892 5 0.6957 -0.14423 0.320 0.004 0.000 0.328 0.348
#> GSM550893 5 0.5421 0.27354 0.000 0.096 0.000 0.276 0.628
#> GSM550895 4 0.6403 0.17093 0.004 0.148 0.000 0.452 0.396
#> GSM550896 5 0.6293 0.43225 0.004 0.240 0.000 0.200 0.556
#> GSM550898 1 0.0162 0.81456 0.996 0.000 0.000 0.004 0.000
#> GSM550899 5 0.4702 0.40591 0.000 0.432 0.000 0.016 0.552
#> GSM550900 4 0.5070 0.46860 0.012 0.056 0.000 0.688 0.244
#> GSM550901 5 0.6232 0.30855 0.176 0.028 0.000 0.172 0.624
#> GSM550902 3 0.7044 0.18481 0.116 0.000 0.492 0.332 0.060
#> GSM550904 4 0.5833 0.48989 0.164 0.020 0.000 0.660 0.156
#> GSM550908 3 0.0486 0.88262 0.004 0.004 0.988 0.000 0.004
#> GSM550912 5 0.4597 0.49132 0.000 0.260 0.000 0.044 0.696
#> GSM550914 5 0.3008 0.55530 0.004 0.092 0.000 0.036 0.868
#> GSM550918 5 0.4220 0.49382 0.004 0.300 0.000 0.008 0.688
#> GSM550922 3 0.1471 0.87348 0.000 0.004 0.952 0.020 0.024
#> GSM550923 1 0.1845 0.79968 0.928 0.000 0.000 0.056 0.016
#> GSM550925 5 0.6853 0.17349 0.156 0.040 0.000 0.264 0.540
#> GSM550802 2 0.5046 0.10902 0.000 0.500 0.000 0.468 0.032
#> GSM550812 4 0.2953 0.56644 0.004 0.028 0.000 0.868 0.100
#> GSM550831 4 0.5644 0.41332 0.136 0.200 0.000 0.656 0.008
#> GSM550847 1 0.0290 0.81495 0.992 0.000 0.000 0.008 0.000
#> GSM550860 3 0.4112 0.73475 0.016 0.000 0.800 0.136 0.048
#> GSM550875 4 0.4781 0.56806 0.092 0.020 0.000 0.760 0.128
#> GSM550880 4 0.6616 0.24827 0.036 0.332 0.000 0.524 0.108
#> GSM550881 3 0.1300 0.87537 0.000 0.000 0.956 0.016 0.028
#> GSM550883 3 0.1372 0.87551 0.004 0.000 0.956 0.016 0.024
#> GSM550884 4 0.5495 0.30972 0.012 0.032 0.004 0.536 0.416
#> GSM550910 3 0.2856 0.80941 0.000 0.008 0.872 0.016 0.104
#> GSM550916 1 0.2771 0.74068 0.860 0.000 0.000 0.128 0.012
#> GSM550920 3 0.1310 0.87380 0.000 0.000 0.956 0.024 0.020
cbind(get_classes(res, k = 6), get_membership(res, k = 6))
#> class entropy silhouette p1 p2 p3 p4 p5 p6
#> GSM550785 1 0.3465 0.7304 0.820 0.000 0.016 0.044 0.000 0.120
#> GSM550786 5 0.0665 0.6224 0.000 0.004 0.008 0.008 0.980 0.000
#> GSM550788 2 0.5448 0.5513 0.000 0.668 0.056 0.124 0.000 0.152
#> GSM550789 2 0.0891 0.6263 0.000 0.968 0.000 0.008 0.000 0.024
#> GSM550790 1 0.3823 0.6410 0.760 0.000 0.044 0.192 0.000 0.004
#> GSM550791 4 0.7029 0.3997 0.144 0.036 0.204 0.536 0.000 0.080
#> GSM550792 4 0.5693 0.2088 0.000 0.320 0.080 0.560 0.000 0.040
#> GSM550796 2 0.1921 0.6425 0.000 0.920 0.012 0.056 0.000 0.012
#> GSM550797 2 0.1606 0.6395 0.000 0.932 0.004 0.056 0.000 0.008
#> GSM550799 5 0.0622 0.6187 0.000 0.008 0.012 0.000 0.980 0.000
#> GSM550800 2 0.3826 0.5689 0.000 0.784 0.004 0.124 0.000 0.088
#> GSM550801 2 0.1657 0.6179 0.000 0.928 0.000 0.016 0.000 0.056
#> GSM550804 6 0.4672 0.4827 0.000 0.312 0.016 0.036 0.000 0.636
#> GSM550806 5 0.0964 0.6123 0.000 0.000 0.004 0.016 0.968 0.012
#> GSM550807 2 0.1334 0.6270 0.000 0.948 0.000 0.020 0.000 0.032
#> GSM550808 2 0.2826 0.6282 0.000 0.844 0.028 0.128 0.000 0.000
#> GSM550809 4 0.4142 0.5271 0.056 0.008 0.144 0.776 0.000 0.016
#> GSM550810 2 0.2959 0.6283 0.000 0.844 0.024 0.124 0.000 0.008
#> GSM550811 4 0.6093 0.3189 0.000 0.256 0.144 0.556 0.000 0.044
#> GSM550813 2 0.6554 -0.1771 0.000 0.408 0.108 0.080 0.000 0.404
#> GSM550814 2 0.6971 0.3878 0.004 0.488 0.100 0.184 0.000 0.224
#> GSM550815 2 0.0937 0.6253 0.000 0.960 0.000 0.000 0.000 0.040
#> GSM550816 6 0.5991 0.4010 0.000 0.392 0.028 0.116 0.000 0.464
#> GSM550817 5 0.0291 0.6165 0.000 0.004 0.004 0.000 0.992 0.000
#> GSM550818 5 0.1226 0.6148 0.000 0.004 0.040 0.000 0.952 0.004
#> GSM550819 4 0.5962 0.4443 0.012 0.012 0.016 0.620 0.192 0.148
#> GSM550820 4 0.6273 0.4467 0.144 0.012 0.128 0.616 0.000 0.100
#> GSM550821 5 0.2168 0.6165 0.000 0.004 0.016 0.036 0.916 0.028
#> GSM550822 2 0.3603 0.6250 0.000 0.816 0.036 0.032 0.000 0.116
#> GSM550826 5 0.8940 -0.1026 0.092 0.016 0.200 0.236 0.296 0.160
#> GSM550832 6 0.7105 0.3687 0.000 0.184 0.136 0.192 0.004 0.484
#> GSM550833 2 0.2174 0.6472 0.000 0.896 0.008 0.088 0.000 0.008
#> GSM550835 2 0.6272 0.3257 0.000 0.524 0.036 0.208 0.232 0.000
#> GSM550836 3 0.3782 0.8657 0.000 0.000 0.588 0.000 0.412 0.000
#> GSM550837 2 0.4739 0.5335 0.000 0.700 0.016 0.088 0.196 0.000
#> GSM550838 4 0.6173 0.4648 0.044 0.024 0.208 0.608 0.116 0.000
#> GSM550841 5 0.0146 0.6164 0.000 0.004 0.000 0.000 0.996 0.000
#> GSM550842 5 0.3151 0.5440 0.000 0.088 0.024 0.024 0.856 0.008
#> GSM550846 6 0.5826 0.2094 0.004 0.032 0.084 0.304 0.004 0.572
#> GSM550849 4 0.6841 0.0870 0.060 0.348 0.140 0.440 0.000 0.012
#> GSM550850 4 0.6166 0.3604 0.188 0.048 0.200 0.564 0.000 0.000
#> GSM550851 5 0.4030 0.3674 0.000 0.196 0.020 0.032 0.752 0.000
#> GSM550852 2 0.3946 0.5766 0.000 0.736 0.016 0.228 0.000 0.020
#> GSM550853 2 0.4894 0.5179 0.000 0.716 0.088 0.044 0.000 0.152
#> GSM550855 2 0.5974 0.3770 0.000 0.592 0.112 0.064 0.000 0.232
#> GSM550856 2 0.6918 -0.1609 0.000 0.384 0.116 0.120 0.000 0.380
#> GSM550861 2 0.1908 0.5826 0.000 0.900 0.004 0.000 0.000 0.096
#> GSM550863 6 0.7730 -0.0101 0.188 0.060 0.072 0.256 0.000 0.424
#> GSM550864 6 0.4070 0.4497 0.000 0.424 0.004 0.004 0.000 0.568
#> GSM550866 2 0.7027 -0.0653 0.000 0.420 0.080 0.240 0.000 0.260
#> GSM550867 1 0.1218 0.7954 0.956 0.000 0.004 0.028 0.000 0.012
#> GSM550885 1 0.4381 0.7068 0.760 0.000 0.036 0.072 0.000 0.132
#> GSM550886 5 0.6929 0.1069 0.000 0.000 0.196 0.124 0.492 0.188
#> GSM550887 2 0.2844 0.6161 0.000 0.856 0.020 0.012 0.000 0.112
#> GSM550889 4 0.6681 0.2027 0.000 0.112 0.108 0.484 0.000 0.296
#> GSM550894 6 0.7163 0.3496 0.000 0.164 0.196 0.112 0.020 0.508
#> GSM550897 4 0.7601 0.3123 0.112 0.076 0.096 0.476 0.000 0.240
#> GSM550903 6 0.4601 0.4379 0.000 0.376 0.016 0.020 0.000 0.588
#> GSM550905 5 0.7053 0.0797 0.000 0.316 0.072 0.092 0.476 0.044
#> GSM550906 2 0.4908 0.3638 0.000 0.644 0.020 0.056 0.000 0.280
#> GSM550907 5 0.3351 -0.1524 0.000 0.000 0.288 0.000 0.712 0.000
#> GSM550909 4 0.7558 0.1741 0.000 0.052 0.072 0.416 0.312 0.148
#> GSM550911 5 0.1444 0.5739 0.000 0.000 0.072 0.000 0.928 0.000
#> GSM550913 6 0.4393 0.4184 0.000 0.448 0.008 0.012 0.000 0.532
#> GSM550915 6 0.4272 0.5371 0.008 0.084 0.024 0.104 0.000 0.780
#> GSM550917 6 0.4159 0.4636 0.000 0.396 0.000 0.016 0.000 0.588
#> GSM550919 6 0.3807 0.5538 0.012 0.084 0.060 0.024 0.000 0.820
#> GSM550921 3 0.3860 0.9502 0.000 0.000 0.528 0.000 0.472 0.000
#> GSM550924 4 0.7703 0.0389 0.028 0.024 0.144 0.376 0.064 0.364
#> GSM550926 6 0.6771 0.2885 0.000 0.136 0.124 0.232 0.000 0.508
#> GSM550927 6 0.4441 0.4242 0.000 0.416 0.012 0.012 0.000 0.560
#> GSM550787 4 0.7395 0.4412 0.120 0.016 0.100 0.556 0.152 0.056
#> GSM550793 5 0.6145 0.2670 0.056 0.020 0.100 0.192 0.628 0.004
#> GSM550794 4 0.3935 0.5333 0.016 0.080 0.020 0.812 0.000 0.072
#> GSM550795 4 0.6161 0.3026 0.004 0.232 0.212 0.532 0.000 0.020
#> GSM550798 1 0.6541 0.4512 0.548 0.000 0.140 0.200 0.112 0.000
#> GSM550803 1 0.1858 0.7792 0.912 0.000 0.012 0.076 0.000 0.000
#> GSM550805 4 0.4172 0.5482 0.084 0.024 0.048 0.804 0.000 0.040
#> GSM550823 4 0.5024 0.4299 0.000 0.020 0.104 0.676 0.000 0.200
#> GSM550824 1 0.0000 0.8016 1.000 0.000 0.000 0.000 0.000 0.000
#> GSM550825 5 0.1890 0.5796 0.060 0.000 0.024 0.000 0.916 0.000
#> GSM550827 4 0.6546 0.0940 0.004 0.096 0.076 0.428 0.000 0.396
#> GSM550828 1 0.7199 0.1262 0.444 0.036 0.048 0.300 0.000 0.172
#> GSM550829 5 0.4166 0.5022 0.092 0.000 0.068 0.044 0.792 0.004
#> GSM550830 4 0.6029 0.3638 0.020 0.288 0.032 0.572 0.000 0.088
#> GSM550834 2 0.6892 0.1063 0.056 0.428 0.156 0.348 0.000 0.012
#> GSM550839 5 0.2469 0.6035 0.000 0.028 0.020 0.036 0.904 0.012
#> GSM550840 4 0.5239 0.4985 0.044 0.088 0.164 0.696 0.000 0.008
#> GSM550843 5 0.0146 0.6139 0.000 0.000 0.004 0.000 0.996 0.000
#> GSM550844 4 0.4783 0.5161 0.148 0.000 0.052 0.728 0.000 0.072
#> GSM550845 6 0.4220 0.5566 0.000 0.104 0.044 0.072 0.000 0.780
#> GSM550848 6 0.4067 0.5644 0.000 0.200 0.024 0.028 0.000 0.748
#> GSM550854 1 0.0436 0.8018 0.988 0.000 0.004 0.004 0.000 0.004
#> GSM550857 5 0.3857 -0.8493 0.000 0.000 0.468 0.000 0.532 0.000
#> GSM550858 1 0.5879 0.5874 0.656 0.068 0.052 0.040 0.000 0.184
#> GSM550859 1 0.0146 0.8009 0.996 0.000 0.000 0.004 0.000 0.000
#> GSM550862 1 0.5945 0.4442 0.600 0.004 0.040 0.212 0.000 0.144
#> GSM550865 6 0.7923 -0.1375 0.192 0.060 0.080 0.320 0.000 0.348
#> GSM550868 4 0.7500 0.2322 0.120 0.100 0.048 0.456 0.000 0.276
#> GSM550869 4 0.4316 0.5334 0.036 0.008 0.056 0.792 0.008 0.100
#> GSM550870 6 0.5520 0.4090 0.000 0.368 0.024 0.076 0.000 0.532
#> GSM550871 5 0.4421 0.3296 0.000 0.008 0.012 0.284 0.676 0.020
#> GSM550872 4 0.7307 0.2300 0.052 0.076 0.104 0.448 0.000 0.320
#> GSM550873 4 0.6023 0.4621 0.020 0.068 0.108 0.656 0.004 0.144
#> GSM550874 2 0.6633 0.4273 0.000 0.528 0.104 0.148 0.000 0.220
#> GSM550876 5 0.1269 0.6171 0.000 0.000 0.012 0.020 0.956 0.012
#> GSM550877 6 0.5784 0.4104 0.000 0.092 0.120 0.144 0.000 0.644
#> GSM550878 5 0.0713 0.6118 0.000 0.000 0.028 0.000 0.972 0.000
#> GSM550879 6 0.7006 0.0690 0.240 0.012 0.084 0.172 0.000 0.492
#> GSM550882 5 0.1116 0.6023 0.000 0.000 0.028 0.008 0.960 0.004
#> GSM550888 3 0.3866 0.9376 0.000 0.000 0.516 0.000 0.484 0.000
#> GSM550890 6 0.3095 0.5059 0.000 0.020 0.052 0.072 0.000 0.856
#> GSM550891 3 0.3857 0.9332 0.000 0.000 0.532 0.000 0.468 0.000
#> GSM550892 4 0.7144 0.1253 0.280 0.000 0.076 0.348 0.000 0.296
#> GSM550893 6 0.6906 0.1619 0.000 0.104 0.148 0.296 0.000 0.452
#> GSM550895 4 0.6814 0.2418 0.000 0.144 0.104 0.480 0.000 0.272
#> GSM550896 6 0.6741 0.3275 0.000 0.244 0.056 0.244 0.000 0.456
#> GSM550898 1 0.0000 0.8016 1.000 0.000 0.000 0.000 0.000 0.000
#> GSM550899 6 0.4351 0.4488 0.000 0.416 0.012 0.008 0.000 0.564
#> GSM550900 4 0.4940 0.4792 0.008 0.056 0.056 0.724 0.000 0.156
#> GSM550901 6 0.5727 0.3902 0.140 0.024 0.040 0.128 0.000 0.668
#> GSM550902 5 0.6915 0.1117 0.092 0.000 0.068 0.356 0.452 0.032
#> GSM550904 4 0.6718 0.4455 0.124 0.016 0.132 0.584 0.004 0.140
#> GSM550908 3 0.3860 0.9502 0.000 0.000 0.528 0.000 0.472 0.000
#> GSM550912 6 0.5051 0.5185 0.000 0.192 0.080 0.040 0.000 0.688
#> GSM550914 6 0.2565 0.5415 0.000 0.032 0.032 0.044 0.000 0.892
#> GSM550918 6 0.4082 0.5443 0.000 0.228 0.032 0.012 0.000 0.728
#> GSM550922 5 0.2597 0.6045 0.000 0.008 0.088 0.020 0.880 0.004
#> GSM550923 1 0.2074 0.7770 0.912 0.000 0.048 0.036 0.000 0.004
#> GSM550925 6 0.7588 0.1440 0.128 0.044 0.116 0.260 0.000 0.452
#> GSM550802 2 0.4413 0.1589 0.000 0.496 0.008 0.484 0.000 0.012
#> GSM550812 4 0.3097 0.5479 0.000 0.012 0.064 0.852 0.000 0.072
#> GSM550831 4 0.6710 0.4005 0.128 0.108 0.196 0.556 0.000 0.012
#> GSM550847 1 0.0000 0.8016 1.000 0.000 0.000 0.000 0.000 0.000
#> GSM550860 5 0.3850 0.4470 0.012 0.000 0.012 0.180 0.776 0.020
#> GSM550875 4 0.3844 0.5475 0.084 0.004 0.028 0.812 0.000 0.072
#> GSM550880 4 0.7362 0.3026 0.016 0.264 0.204 0.428 0.000 0.088
#> GSM550881 5 0.3124 0.5775 0.008 0.000 0.116 0.024 0.844 0.008
#> GSM550883 5 0.3053 0.5165 0.012 0.000 0.172 0.000 0.812 0.004
#> GSM550884 4 0.6703 0.2901 0.008 0.028 0.196 0.488 0.008 0.272
#> GSM550910 5 0.3832 0.5064 0.000 0.004 0.072 0.036 0.816 0.072
#> GSM550916 1 0.2048 0.7426 0.880 0.000 0.000 0.120 0.000 0.000
#> GSM550920 5 0.2554 0.5961 0.000 0.000 0.092 0.028 0.876 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)
get_signatures(res, k = 3)
get_signatures(res, k = 4)
get_signatures(res, k = 5)
get_signatures(res, k = 6)
Signature heatmaps where rows are not scaled:
get_signatures(res, k = 2, scale_rows = FALSE)
get_signatures(res, k = 3, scale_rows = FALSE)
get_signatures(res, k = 4, scale_rows = FALSE)
get_signatures(res, k = 5, scale_rows = FALSE)
get_signatures(res, k = 6, scale_rows = FALSE)
Compare the overlap of signatures from different k:
compare_signatures(res)
get_signature() returns a data frame invisibly. TO get the list of signatures, the function
call should be assigned to a variable explicitly. In following code, if plot argument is set
to FALSE, no heatmap is plotted while only the differential analysis is performed.
# code only for demonstration
tb = get_signature(res, k = ..., plot = FALSE)
An example of the output of tb is:
#> which_row fdr mean_1 mean_2 scaled_mean_1 scaled_mean_2 km
#> 1 38 0.042760348 8.373488 9.131774 -0.5533452 0.5164555 1
#> 2 40 0.018707592 7.106213 8.469186 -0.6173731 0.5762149 1
#> 3 55 0.019134737 10.221463 11.207825 -0.6159697 0.5749050 1
#> 4 59 0.006059896 5.921854 7.869574 -0.6899429 0.6439467 1
#> 5 60 0.018055526 8.928898 10.211722 -0.6204761 0.5791110 1
#> 6 98 0.009384629 15.714769 14.887706 0.6635654 -0.6193277 2
...
The columns in tb are:
which_row: row indices corresponding to the input matrix.fdr: FDR for the differential test. mean_x: The mean value in group x.scaled_mean_x: The mean value in group x after rows are scaled.km: Row groups if k-means clustering is applied to rows.UMAP plot which shows how samples are separated.
dimension_reduction(res, k = 2, method = "UMAP")
dimension_reduction(res, k = 3, method = "UMAP")
dimension_reduction(res, k = 4, method = "UMAP")
dimension_reduction(res, k = 5, method = "UMAP")
dimension_reduction(res, k = 6, method = "UMAP")
Following heatmap shows how subgroups are split when increasing k:
collect_classes(res)
Test correlation between subgroups and known annotations. If the known annotation is numeric, one-way ANOVA test is applied, and if the known annotation is discrete, chi-squared contingency table test is applied.
test_to_known_factors(res)
#> n disease.state(p) k
#> CV:pam 140 0.736229 2
#> CV:pam 120 0.001094 3
#> CV:pam 63 0.000834 4
#> CV:pam 78 0.000386 5
#> CV:pam 71 0.000749 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 51776 rows and 143 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 0.681 0.880 0.937 0.4681 0.527 0.527
#> 3 3 0.253 0.455 0.657 0.2751 0.733 0.567
#> 4 4 0.455 0.607 0.771 0.1281 0.707 0.450
#> 5 5 0.444 0.639 0.757 0.0654 0.796 0.496
#> 6 6 0.472 0.471 0.660 0.0597 0.823 0.465
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
#> GSM550785 2 0.1633 0.907 0.024 0.976
#> GSM550786 1 0.0672 0.941 0.992 0.008
#> GSM550788 1 0.2603 0.932 0.956 0.044
#> GSM550789 1 0.7139 0.783 0.804 0.196
#> GSM550790 1 0.5519 0.863 0.872 0.128
#> GSM550791 1 0.2236 0.940 0.964 0.036
#> GSM550792 1 0.1633 0.942 0.976 0.024
#> GSM550796 1 0.7056 0.786 0.808 0.192
#> GSM550797 1 0.7056 0.789 0.808 0.192
#> GSM550799 1 0.0672 0.941 0.992 0.008
#> GSM550800 1 0.8267 0.700 0.740 0.260
#> GSM550801 1 0.7219 0.779 0.800 0.200
#> GSM550804 2 0.0000 0.915 0.000 1.000
#> GSM550806 1 0.0672 0.941 0.992 0.008
#> GSM550807 1 0.8499 0.662 0.724 0.276
#> GSM550808 1 0.1184 0.944 0.984 0.016
#> GSM550809 1 0.1633 0.942 0.976 0.024
#> GSM550810 1 0.1633 0.942 0.976 0.024
#> GSM550811 1 0.1633 0.942 0.976 0.024
#> GSM550813 2 0.0938 0.916 0.012 0.988
#> GSM550814 1 0.7602 0.723 0.780 0.220
#> GSM550815 1 0.8763 0.637 0.704 0.296
#> GSM550816 2 0.5408 0.840 0.124 0.876
#> GSM550817 1 0.0000 0.942 1.000 0.000
#> GSM550818 1 0.0000 0.942 1.000 0.000
#> GSM550819 1 0.2423 0.939 0.960 0.040
#> GSM550820 1 0.1843 0.940 0.972 0.028
#> GSM550821 1 0.1633 0.943 0.976 0.024
#> GSM550822 2 0.9323 0.503 0.348 0.652
#> GSM550826 1 0.1633 0.943 0.976 0.024
#> GSM550832 2 0.9833 0.359 0.424 0.576
#> GSM550833 1 0.3274 0.922 0.940 0.060
#> GSM550835 1 0.0000 0.942 1.000 0.000
#> GSM550836 1 0.0000 0.942 1.000 0.000
#> GSM550837 1 0.1633 0.943 0.976 0.024
#> GSM550838 1 0.1633 0.943 0.976 0.024
#> GSM550841 1 0.0672 0.941 0.992 0.008
#> GSM550842 1 0.0000 0.942 1.000 0.000
#> GSM550846 1 0.5178 0.869 0.884 0.116
#> GSM550849 1 0.1184 0.944 0.984 0.016
#> GSM550850 1 0.2778 0.929 0.952 0.048
#> GSM550851 1 0.0938 0.942 0.988 0.012
#> GSM550852 1 0.1633 0.942 0.976 0.024
#> GSM550853 1 0.8386 0.687 0.732 0.268
#> GSM550855 2 0.7139 0.758 0.196 0.804
#> GSM550856 2 0.4562 0.865 0.096 0.904
#> GSM550861 2 0.1184 0.915 0.016 0.984
#> GSM550863 2 0.0000 0.915 0.000 1.000
#> GSM550864 2 0.0672 0.917 0.008 0.992
#> GSM550866 2 0.9522 0.469 0.372 0.628
#> GSM550867 2 0.8207 0.668 0.256 0.744
#> GSM550885 2 0.4431 0.861 0.092 0.908
#> GSM550886 1 0.0000 0.942 1.000 0.000
#> GSM550887 1 0.7453 0.753 0.788 0.212
#> GSM550889 2 0.0376 0.916 0.004 0.996
#> GSM550894 1 0.5842 0.836 0.860 0.140
#> GSM550897 2 0.7602 0.733 0.220 0.780
#> GSM550903 2 0.3584 0.882 0.068 0.932
#> GSM550905 1 0.1633 0.943 0.976 0.024
#> GSM550906 2 0.6887 0.782 0.184 0.816
#> GSM550907 1 0.0000 0.942 1.000 0.000
#> GSM550909 1 0.1184 0.944 0.984 0.016
#> GSM550911 1 0.0000 0.942 1.000 0.000
#> GSM550913 2 0.0938 0.916 0.012 0.988
#> GSM550915 2 0.0672 0.917 0.008 0.992
#> GSM550917 2 0.0672 0.917 0.008 0.992
#> GSM550919 2 0.0672 0.917 0.008 0.992
#> GSM550921 1 0.0000 0.942 1.000 0.000
#> GSM550924 1 0.1184 0.944 0.984 0.016
#> GSM550926 2 0.6247 0.815 0.156 0.844
#> GSM550927 2 0.0000 0.915 0.000 1.000
#> GSM550787 1 0.1633 0.943 0.976 0.024
#> GSM550793 1 0.0000 0.942 1.000 0.000
#> GSM550794 1 0.1633 0.942 0.976 0.024
#> GSM550795 1 0.3114 0.924 0.944 0.056
#> GSM550798 1 0.0672 0.941 0.992 0.008
#> GSM550803 1 0.1633 0.942 0.976 0.024
#> GSM550805 1 0.1184 0.944 0.984 0.016
#> GSM550823 2 0.9686 0.434 0.396 0.604
#> GSM550824 2 0.0672 0.917 0.008 0.992
#> GSM550825 1 0.0672 0.941 0.992 0.008
#> GSM550827 2 0.0672 0.917 0.008 0.992
#> GSM550828 2 0.0672 0.917 0.008 0.992
#> GSM550829 1 0.0672 0.941 0.992 0.008
#> GSM550830 1 0.4939 0.882 0.892 0.108
#> GSM550834 1 0.3274 0.922 0.940 0.060
#> GSM550839 1 0.0000 0.942 1.000 0.000
#> GSM550840 1 0.2778 0.929 0.952 0.048
#> GSM550843 1 0.0672 0.941 0.992 0.008
#> GSM550844 1 0.8763 0.561 0.704 0.296
#> GSM550845 2 0.0000 0.915 0.000 1.000
#> GSM550848 2 0.0672 0.917 0.008 0.992
#> GSM550854 2 0.7815 0.707 0.232 0.768
#> GSM550857 1 0.0672 0.941 0.992 0.008
#> GSM550858 2 0.0000 0.915 0.000 1.000
#> GSM550859 2 0.0672 0.917 0.008 0.992
#> GSM550862 2 0.0000 0.915 0.000 1.000
#> GSM550865 2 0.0000 0.915 0.000 1.000
#> GSM550868 2 0.1184 0.915 0.016 0.984
#> GSM550869 1 0.1184 0.944 0.984 0.016
#> GSM550870 2 0.0000 0.915 0.000 1.000
#> GSM550871 1 0.0000 0.942 1.000 0.000
#> GSM550872 1 0.8443 0.680 0.728 0.272
#> GSM550873 1 0.1184 0.944 0.984 0.016
#> GSM550874 1 0.2778 0.929 0.952 0.048
#> GSM550876 1 0.0000 0.942 1.000 0.000
#> GSM550877 2 0.0000 0.915 0.000 1.000
#> GSM550878 1 0.0000 0.942 1.000 0.000
#> GSM550879 2 0.0000 0.915 0.000 1.000
#> GSM550882 1 0.0672 0.941 0.992 0.008
#> GSM550888 1 0.0672 0.941 0.992 0.008
#> GSM550890 2 0.0000 0.915 0.000 1.000
#> GSM550891 1 0.0000 0.942 1.000 0.000
#> GSM550892 2 0.0000 0.915 0.000 1.000
#> GSM550893 2 0.6148 0.818 0.152 0.848
#> GSM550895 2 0.0672 0.917 0.008 0.992
#> GSM550896 2 0.1633 0.912 0.024 0.976
#> GSM550898 2 0.0672 0.917 0.008 0.992
#> GSM550899 2 0.0672 0.917 0.008 0.992
#> GSM550900 2 0.0672 0.917 0.008 0.992
#> GSM550901 2 0.0672 0.917 0.008 0.992
#> GSM550902 1 0.1633 0.943 0.976 0.024
#> GSM550904 1 0.1184 0.944 0.984 0.016
#> GSM550908 1 0.0672 0.941 0.992 0.008
#> GSM550912 2 0.6712 0.795 0.176 0.824
#> GSM550914 2 0.0000 0.915 0.000 1.000
#> GSM550918 2 0.0000 0.915 0.000 1.000
#> GSM550922 1 0.0000 0.942 1.000 0.000
#> GSM550923 1 0.1184 0.944 0.984 0.016
#> GSM550925 2 0.3114 0.894 0.056 0.944
#> GSM550802 1 0.1633 0.942 0.976 0.024
#> GSM550812 1 0.1633 0.942 0.976 0.024
#> GSM550831 1 0.2778 0.929 0.952 0.048
#> GSM550847 2 0.0672 0.917 0.008 0.992
#> GSM550860 1 0.0672 0.941 0.992 0.008
#> GSM550875 1 0.1184 0.944 0.984 0.016
#> GSM550880 1 0.8443 0.669 0.728 0.272
#> GSM550881 1 0.0000 0.942 1.000 0.000
#> GSM550883 1 0.0000 0.942 1.000 0.000
#> GSM550884 1 0.1184 0.944 0.984 0.016
#> GSM550910 1 0.0672 0.941 0.992 0.008
#> GSM550916 2 0.9850 0.342 0.428 0.572
#> GSM550920 1 0.0000 0.942 1.000 0.000
cbind(get_classes(res, k = 3), get_membership(res, k = 3))
#> class entropy silhouette p1 p2 p3
#> GSM550785 1 0.9501 0.8811 0.472 0.324 0.204
#> GSM550786 3 0.7309 0.6890 0.124 0.168 0.708
#> GSM550788 2 0.6126 0.3306 0.000 0.600 0.400
#> GSM550789 2 0.6102 0.4471 0.008 0.672 0.320
#> GSM550790 3 0.2261 0.6364 0.000 0.068 0.932
#> GSM550791 3 0.1453 0.6549 0.008 0.024 0.968
#> GSM550792 3 0.4887 0.5849 0.000 0.228 0.772
#> GSM550796 2 0.6045 0.3651 0.000 0.620 0.380
#> GSM550797 2 0.5956 0.4405 0.004 0.672 0.324
#> GSM550799 3 0.5843 0.6957 0.252 0.016 0.732
#> GSM550800 2 0.5659 0.5036 0.012 0.740 0.248
#> GSM550801 2 0.5958 0.4656 0.008 0.692 0.300
#> GSM550804 2 0.6168 -0.2621 0.412 0.588 0.000
#> GSM550806 3 0.6398 0.6685 0.416 0.004 0.580
#> GSM550807 2 0.5656 0.4972 0.008 0.728 0.264
#> GSM550808 3 0.5220 0.6168 0.012 0.208 0.780
#> GSM550809 3 0.0747 0.6550 0.000 0.016 0.984
#> GSM550810 2 0.6745 0.2399 0.012 0.560 0.428
#> GSM550811 3 0.4291 0.6348 0.000 0.180 0.820
#> GSM550813 2 0.4645 0.5235 0.008 0.816 0.176
#> GSM550814 2 0.7222 0.2846 0.032 0.580 0.388
#> GSM550815 2 0.5461 0.5052 0.008 0.748 0.244
#> GSM550816 2 0.4840 0.5179 0.016 0.816 0.168
#> GSM550817 3 0.6305 0.6390 0.484 0.000 0.516
#> GSM550818 3 0.6244 0.6573 0.440 0.000 0.560
#> GSM550819 3 0.8955 0.4983 0.144 0.332 0.524
#> GSM550820 3 0.4994 0.6778 0.160 0.024 0.816
#> GSM550821 3 0.8670 0.6922 0.240 0.168 0.592
#> GSM550822 2 0.5455 0.5302 0.020 0.776 0.204
#> GSM550826 3 0.8532 0.6938 0.224 0.168 0.608
#> GSM550832 2 0.7770 0.3693 0.080 0.628 0.292
#> GSM550833 2 0.6111 0.3415 0.000 0.604 0.396
#> GSM550835 3 0.5932 0.6741 0.056 0.164 0.780
#> GSM550836 3 0.5138 0.6929 0.252 0.000 0.748
#> GSM550837 3 0.5412 0.6595 0.032 0.172 0.796
#> GSM550838 3 0.1337 0.6642 0.016 0.012 0.972
#> GSM550841 3 0.6625 0.6582 0.440 0.008 0.552
#> GSM550842 3 0.6544 0.6826 0.084 0.164 0.752
#> GSM550846 3 0.8470 0.4662 0.104 0.344 0.552
#> GSM550849 3 0.4121 0.6436 0.000 0.168 0.832
#> GSM550850 3 0.1411 0.6484 0.000 0.036 0.964
#> GSM550851 3 0.6138 0.6718 0.060 0.172 0.768
#> GSM550852 2 0.6252 0.2389 0.000 0.556 0.444
#> GSM550853 2 0.5722 0.4624 0.004 0.704 0.292
#> GSM550855 2 0.4551 0.4996 0.020 0.840 0.140
#> GSM550856 2 0.2866 0.4320 0.008 0.916 0.076
#> GSM550861 2 0.4589 0.5217 0.008 0.820 0.172
#> GSM550863 2 0.6244 -0.3071 0.440 0.560 0.000
#> GSM550864 2 0.6451 -0.2094 0.384 0.608 0.008
#> GSM550866 2 0.4784 0.5237 0.004 0.796 0.200
#> GSM550867 3 0.9647 -0.4586 0.264 0.268 0.468
#> GSM550885 1 0.9613 0.8444 0.464 0.308 0.228
#> GSM550886 3 0.8843 0.6871 0.276 0.160 0.564
#> GSM550887 2 0.7214 0.3784 0.044 0.632 0.324
#> GSM550889 2 0.6421 -0.2764 0.424 0.572 0.004
#> GSM550894 2 0.8097 0.1704 0.072 0.540 0.388
#> GSM550897 3 0.9120 0.4865 0.156 0.340 0.504
#> GSM550903 2 0.5277 0.5283 0.024 0.796 0.180
#> GSM550905 3 0.7097 0.6829 0.108 0.172 0.720
#> GSM550906 2 0.6049 0.5196 0.040 0.756 0.204
#> GSM550907 3 0.6305 0.6390 0.484 0.000 0.516
#> GSM550909 3 0.7027 0.6795 0.104 0.172 0.724
#> GSM550911 3 0.6305 0.6390 0.484 0.000 0.516
#> GSM550913 2 0.6341 -0.0812 0.312 0.672 0.016
#> GSM550915 2 0.6410 -0.2830 0.420 0.576 0.004
#> GSM550917 2 0.6617 -0.2113 0.388 0.600 0.012
#> GSM550919 2 0.6587 -0.2784 0.424 0.568 0.008
#> GSM550921 3 0.6305 0.6390 0.484 0.000 0.516
#> GSM550924 3 0.8532 0.6907 0.224 0.168 0.608
#> GSM550926 2 0.6201 0.5168 0.044 0.748 0.208
#> GSM550927 2 0.6079 -0.2248 0.388 0.612 0.000
#> GSM550787 3 0.6677 0.6818 0.088 0.168 0.744
#> GSM550793 3 0.3112 0.6894 0.096 0.004 0.900
#> GSM550794 3 0.5591 0.4708 0.000 0.304 0.696
#> GSM550795 3 0.1643 0.6457 0.000 0.044 0.956
#> GSM550798 3 0.2200 0.6783 0.056 0.004 0.940
#> GSM550803 3 0.1031 0.6521 0.000 0.024 0.976
#> GSM550805 3 0.4178 0.6407 0.000 0.172 0.828
#> GSM550823 3 0.7777 0.3746 0.060 0.364 0.576
#> GSM550824 1 0.9167 0.9104 0.512 0.320 0.168
#> GSM550825 3 0.6520 0.6373 0.488 0.004 0.508
#> GSM550827 2 0.6421 -0.2918 0.424 0.572 0.004
#> GSM550828 1 0.9335 0.8667 0.456 0.376 0.168
#> GSM550829 3 0.5797 0.6607 0.280 0.008 0.712
#> GSM550830 3 0.5882 0.3945 0.000 0.348 0.652
#> GSM550834 3 0.1753 0.6430 0.000 0.048 0.952
#> GSM550839 3 0.6208 0.6781 0.068 0.164 0.768
#> GSM550840 3 0.1411 0.6484 0.000 0.036 0.964
#> GSM550843 3 0.7063 0.6488 0.464 0.020 0.516
#> GSM550844 3 0.4551 0.6778 0.132 0.024 0.844
#> GSM550845 2 0.6154 -0.2565 0.408 0.592 0.000
#> GSM550848 2 0.6701 -0.2522 0.412 0.576 0.012
#> GSM550854 1 0.9928 0.5952 0.372 0.276 0.352
#> GSM550857 3 0.6520 0.6373 0.488 0.004 0.508
#> GSM550858 1 0.9229 0.9068 0.496 0.336 0.168
#> GSM550859 1 0.9167 0.9104 0.512 0.320 0.168
#> GSM550862 1 0.9215 0.9085 0.500 0.332 0.168
#> GSM550865 2 0.6180 -0.2709 0.416 0.584 0.000
#> GSM550868 2 0.9001 -0.0920 0.280 0.548 0.172
#> GSM550869 3 0.4921 0.6578 0.020 0.164 0.816
#> GSM550870 2 0.3434 0.4385 0.032 0.904 0.064
#> GSM550871 3 0.6848 0.6874 0.100 0.164 0.736
#> GSM550872 3 0.6205 0.5081 0.008 0.336 0.656
#> GSM550873 3 0.6769 0.4450 0.028 0.320 0.652
#> GSM550874 2 0.6079 0.3522 0.000 0.612 0.388
#> GSM550876 3 0.8848 0.6865 0.284 0.156 0.560
#> GSM550877 2 0.2152 0.4087 0.016 0.948 0.036
#> GSM550878 3 0.6305 0.6390 0.484 0.000 0.516
#> GSM550879 2 0.9361 -0.8092 0.396 0.436 0.168
#> GSM550882 3 0.6520 0.6373 0.488 0.004 0.508
#> GSM550888 3 0.6520 0.6373 0.488 0.004 0.508
#> GSM550890 2 0.6192 -0.2765 0.420 0.580 0.000
#> GSM550891 3 0.6305 0.6390 0.484 0.000 0.516
#> GSM550892 1 0.9298 0.8689 0.460 0.376 0.164
#> GSM550893 2 0.6306 0.5174 0.052 0.748 0.200
#> GSM550895 2 0.6754 -0.2766 0.432 0.556 0.012
#> GSM550896 2 0.5253 0.1583 0.188 0.792 0.020
#> GSM550898 1 0.9167 0.9104 0.512 0.320 0.168
#> GSM550899 2 0.6600 -0.2034 0.384 0.604 0.012
#> GSM550900 2 0.7741 -0.1740 0.376 0.568 0.056
#> GSM550901 2 0.6824 -0.2553 0.408 0.576 0.016
#> GSM550902 3 0.8576 0.6948 0.240 0.160 0.600
#> GSM550904 3 0.5072 0.6778 0.196 0.012 0.792
#> GSM550908 3 0.6520 0.6373 0.488 0.004 0.508
#> GSM550912 2 0.6141 0.5040 0.032 0.736 0.232
#> GSM550914 2 0.6180 -0.2709 0.416 0.584 0.000
#> GSM550918 2 0.6079 -0.2220 0.388 0.612 0.000
#> GSM550922 3 0.8528 0.6961 0.240 0.156 0.604
#> GSM550923 3 0.4409 0.6813 0.172 0.004 0.824
#> GSM550925 2 0.9581 0.1171 0.236 0.476 0.288
#> GSM550802 3 0.5560 0.4752 0.000 0.300 0.700
#> GSM550812 3 0.5560 0.4784 0.000 0.300 0.700
#> GSM550831 3 0.1411 0.6484 0.000 0.036 0.964
#> GSM550847 1 0.9299 0.9076 0.496 0.324 0.180
#> GSM550860 3 0.8914 0.6861 0.280 0.164 0.556
#> GSM550875 3 0.4235 0.6377 0.000 0.176 0.824
#> GSM550880 3 0.5235 0.5223 0.036 0.152 0.812
#> GSM550881 3 0.6305 0.6390 0.484 0.000 0.516
#> GSM550883 3 0.6299 0.6414 0.476 0.000 0.524
#> GSM550884 3 0.8309 0.6839 0.188 0.180 0.632
#> GSM550910 3 0.8752 0.6913 0.292 0.144 0.564
#> GSM550916 3 0.5932 0.6521 0.164 0.056 0.780
#> GSM550920 3 0.8334 0.7035 0.248 0.136 0.616
cbind(get_classes(res, k = 4), get_membership(res, k = 4))
#> class entropy silhouette p1 p2 p3 p4
#> GSM550785 1 0.3004 0.89769 0.892 0.048 0.000 0.060
#> GSM550786 2 0.3893 0.57091 0.008 0.796 0.196 0.000
#> GSM550788 2 0.4372 0.57429 0.000 0.728 0.004 0.268
#> GSM550789 2 0.4632 0.54155 0.000 0.688 0.004 0.308
#> GSM550790 2 0.4826 0.57244 0.264 0.716 0.000 0.020
#> GSM550791 2 0.4803 0.59006 0.248 0.732 0.008 0.012
#> GSM550792 2 0.4011 0.61253 0.008 0.784 0.000 0.208
#> GSM550796 2 0.4720 0.52933 0.000 0.672 0.004 0.324
#> GSM550797 2 0.4655 0.53880 0.000 0.684 0.004 0.312
#> GSM550799 3 0.5548 0.55212 0.024 0.388 0.588 0.000
#> GSM550800 2 0.4741 0.53414 0.000 0.668 0.004 0.328
#> GSM550801 2 0.4677 0.53472 0.000 0.680 0.004 0.316
#> GSM550804 4 0.2670 0.71453 0.040 0.052 0.000 0.908
#> GSM550806 3 0.1256 0.88362 0.008 0.028 0.964 0.000
#> GSM550807 2 0.4655 0.53880 0.000 0.684 0.004 0.312
#> GSM550808 2 0.1677 0.67268 0.000 0.948 0.040 0.012
#> GSM550809 2 0.4540 0.59117 0.248 0.740 0.008 0.004
#> GSM550810 2 0.4283 0.58087 0.000 0.740 0.004 0.256
#> GSM550811 2 0.4226 0.67562 0.084 0.836 0.008 0.072
#> GSM550813 4 0.3326 0.70526 0.008 0.132 0.004 0.856
#> GSM550814 2 0.5746 0.40088 0.000 0.572 0.032 0.396
#> GSM550815 2 0.4720 0.53616 0.000 0.672 0.004 0.324
#> GSM550816 4 0.5433 -0.00865 0.008 0.448 0.004 0.540
#> GSM550817 3 0.0817 0.88381 0.000 0.024 0.976 0.000
#> GSM550818 3 0.1211 0.87773 0.000 0.040 0.960 0.000
#> GSM550819 2 0.7293 0.41426 0.000 0.496 0.164 0.340
#> GSM550820 2 0.8113 0.46093 0.272 0.488 0.216 0.024
#> GSM550821 2 0.5723 0.45676 0.008 0.648 0.312 0.032
#> GSM550822 4 0.5168 -0.19979 0.000 0.496 0.004 0.500
#> GSM550826 2 0.6391 0.46603 0.056 0.636 0.288 0.020
#> GSM550832 2 0.6495 0.27093 0.000 0.492 0.072 0.436
#> GSM550833 2 0.4462 0.58142 0.004 0.736 0.004 0.256
#> GSM550835 2 0.3495 0.60711 0.016 0.844 0.140 0.000
#> GSM550836 3 0.5019 0.63479 0.044 0.200 0.752 0.004
#> GSM550837 2 0.2927 0.66471 0.024 0.900 0.068 0.008
#> GSM550838 2 0.3647 0.64933 0.152 0.832 0.016 0.000
#> GSM550841 3 0.3196 0.83581 0.008 0.136 0.856 0.000
#> GSM550842 2 0.4050 0.60675 0.000 0.808 0.168 0.024
#> GSM550846 2 0.6702 0.30861 0.000 0.512 0.092 0.396
#> GSM550849 2 0.2353 0.67416 0.056 0.924 0.008 0.012
#> GSM550850 2 0.4647 0.57995 0.288 0.704 0.008 0.000
#> GSM550851 2 0.2271 0.67045 0.008 0.928 0.052 0.012
#> GSM550852 2 0.4164 0.58005 0.000 0.736 0.000 0.264
#> GSM550853 2 0.4741 0.53292 0.000 0.668 0.004 0.328
#> GSM550855 4 0.5457 -0.09405 0.008 0.472 0.004 0.516
#> GSM550856 4 0.3737 0.71066 0.020 0.136 0.004 0.840
#> GSM550861 4 0.5438 -0.01962 0.008 0.452 0.004 0.536
#> GSM550863 4 0.4579 0.48897 0.200 0.032 0.000 0.768
#> GSM550864 4 0.2722 0.71865 0.032 0.064 0.000 0.904
#> GSM550866 4 0.3232 0.71677 0.016 0.108 0.004 0.872
#> GSM550867 1 0.2742 0.88022 0.900 0.076 0.000 0.024
#> GSM550885 1 0.2761 0.89559 0.904 0.048 0.000 0.048
#> GSM550886 2 0.5337 0.22811 0.000 0.564 0.424 0.012
#> GSM550887 2 0.5337 0.36717 0.000 0.564 0.012 0.424
#> GSM550889 4 0.2871 0.67591 0.072 0.032 0.000 0.896
#> GSM550894 2 0.7181 0.43125 0.000 0.512 0.152 0.336
#> GSM550897 4 0.8986 0.01119 0.252 0.304 0.060 0.384
#> GSM550903 4 0.3074 0.68758 0.000 0.152 0.000 0.848
#> GSM550905 2 0.3544 0.67250 0.008 0.872 0.076 0.044
#> GSM550906 4 0.5158 -0.12422 0.000 0.472 0.004 0.524
#> GSM550907 3 0.0188 0.88500 0.000 0.004 0.996 0.000
#> GSM550909 2 0.4793 0.60149 0.000 0.756 0.204 0.040
#> GSM550911 3 0.0188 0.88500 0.000 0.004 0.996 0.000
#> GSM550913 4 0.5578 0.45592 0.040 0.312 0.000 0.648
#> GSM550915 4 0.3224 0.65099 0.120 0.016 0.000 0.864
#> GSM550917 4 0.2996 0.71775 0.044 0.064 0.000 0.892
#> GSM550919 4 0.3286 0.67842 0.080 0.044 0.000 0.876
#> GSM550921 3 0.0712 0.88351 0.004 0.008 0.984 0.004
#> GSM550924 2 0.5496 0.47253 0.000 0.652 0.312 0.036
#> GSM550926 4 0.2589 0.71390 0.000 0.116 0.000 0.884
#> GSM550927 4 0.5821 0.28056 0.040 0.368 0.000 0.592
#> GSM550787 2 0.4889 0.63245 0.028 0.788 0.156 0.028
#> GSM550793 2 0.3428 0.61903 0.012 0.844 0.144 0.000
#> GSM550794 2 0.4245 0.61436 0.020 0.784 0.000 0.196
#> GSM550795 2 0.4647 0.57995 0.288 0.704 0.008 0.000
#> GSM550798 2 0.3634 0.65544 0.096 0.856 0.048 0.000
#> GSM550803 2 0.4164 0.57784 0.264 0.736 0.000 0.000
#> GSM550805 2 0.2245 0.67851 0.040 0.932 0.008 0.020
#> GSM550823 2 0.6392 0.30859 0.000 0.528 0.068 0.404
#> GSM550824 1 0.2411 0.90007 0.920 0.040 0.000 0.040
#> GSM550825 3 0.0992 0.88351 0.012 0.008 0.976 0.004
#> GSM550827 4 0.3695 0.60646 0.156 0.016 0.000 0.828
#> GSM550828 1 0.4849 0.79052 0.772 0.064 0.000 0.164
#> GSM550829 2 0.6265 0.40287 0.072 0.588 0.340 0.000
#> GSM550830 2 0.4134 0.57859 0.000 0.740 0.000 0.260
#> GSM550834 2 0.4647 0.57995 0.288 0.704 0.008 0.000
#> GSM550839 2 0.2921 0.62308 0.000 0.860 0.140 0.000
#> GSM550840 2 0.4540 0.59117 0.248 0.740 0.008 0.004
#> GSM550843 3 0.3196 0.83016 0.008 0.136 0.856 0.000
#> GSM550844 2 0.8156 0.49545 0.256 0.512 0.196 0.036
#> GSM550845 4 0.2928 0.71273 0.052 0.052 0.000 0.896
#> GSM550848 4 0.2593 0.68041 0.080 0.016 0.000 0.904
#> GSM550854 1 0.2670 0.88180 0.904 0.072 0.000 0.024
#> GSM550857 3 0.0992 0.88351 0.012 0.008 0.976 0.004
#> GSM550858 1 0.3082 0.89136 0.884 0.032 0.000 0.084
#> GSM550859 1 0.2411 0.90007 0.920 0.040 0.000 0.040
#> GSM550862 1 0.3013 0.89388 0.888 0.032 0.000 0.080
#> GSM550865 4 0.2401 0.66859 0.092 0.004 0.000 0.904
#> GSM550868 4 0.5364 0.46326 0.204 0.060 0.004 0.732
#> GSM550869 2 0.2807 0.67797 0.032 0.912 0.040 0.016
#> GSM550870 4 0.2860 0.71332 0.008 0.100 0.004 0.888
#> GSM550871 2 0.4826 0.53573 0.000 0.716 0.264 0.020
#> GSM550872 2 0.5874 0.62121 0.192 0.696 0.000 0.112
#> GSM550873 2 0.3745 0.66838 0.000 0.852 0.060 0.088
#> GSM550874 2 0.4509 0.56072 0.000 0.708 0.004 0.288
#> GSM550876 3 0.4134 0.72784 0.000 0.260 0.740 0.000
#> GSM550877 4 0.2281 0.71525 0.000 0.096 0.000 0.904
#> GSM550878 3 0.0188 0.88500 0.000 0.004 0.996 0.000
#> GSM550879 1 0.6491 0.33844 0.496 0.060 0.004 0.440
#> GSM550882 3 0.1256 0.88250 0.008 0.028 0.964 0.000
#> GSM550888 3 0.0992 0.88351 0.012 0.008 0.976 0.004
#> GSM550890 4 0.2799 0.64755 0.108 0.008 0.000 0.884
#> GSM550891 3 0.0712 0.88351 0.004 0.008 0.984 0.004
#> GSM550892 1 0.5906 0.63536 0.644 0.064 0.000 0.292
#> GSM550893 4 0.2530 0.71510 0.000 0.112 0.000 0.888
#> GSM550895 4 0.3323 0.71451 0.060 0.064 0.000 0.876
#> GSM550896 4 0.2413 0.71861 0.020 0.064 0.000 0.916
#> GSM550898 1 0.2411 0.90007 0.920 0.040 0.000 0.040
#> GSM550899 4 0.2816 0.71850 0.036 0.064 0.000 0.900
#> GSM550900 4 0.4728 0.43518 0.216 0.032 0.000 0.752
#> GSM550901 4 0.5312 0.28762 0.268 0.040 0.000 0.692
#> GSM550902 2 0.6481 0.47202 0.064 0.636 0.280 0.020
#> GSM550904 2 0.7888 0.50231 0.196 0.528 0.252 0.024
#> GSM550908 3 0.0992 0.88351 0.012 0.008 0.976 0.004
#> GSM550912 4 0.4222 0.51736 0.000 0.272 0.000 0.728
#> GSM550914 4 0.2530 0.66300 0.100 0.004 0.000 0.896
#> GSM550918 4 0.2282 0.71578 0.024 0.052 0.000 0.924
#> GSM550922 3 0.4040 0.74636 0.000 0.248 0.752 0.000
#> GSM550923 2 0.8100 0.44365 0.264 0.464 0.256 0.016
#> GSM550925 4 0.6998 0.22741 0.232 0.084 0.044 0.640
#> GSM550802 2 0.3801 0.60115 0.000 0.780 0.000 0.220
#> GSM550812 2 0.3486 0.62695 0.000 0.812 0.000 0.188
#> GSM550831 2 0.4647 0.57995 0.288 0.704 0.008 0.000
#> GSM550847 1 0.2670 0.90001 0.908 0.040 0.000 0.052
#> GSM550860 2 0.5577 0.37438 0.008 0.612 0.364 0.016
#> GSM550875 2 0.2660 0.66901 0.072 0.908 0.008 0.012
#> GSM550880 2 0.5251 0.58262 0.252 0.712 0.008 0.028
#> GSM550881 3 0.0188 0.88500 0.000 0.004 0.996 0.000
#> GSM550883 3 0.0712 0.88351 0.004 0.008 0.984 0.004
#> GSM550884 2 0.5520 0.56154 0.000 0.696 0.244 0.060
#> GSM550910 3 0.4086 0.77186 0.008 0.216 0.776 0.000
#> GSM550916 2 0.8607 0.44793 0.272 0.476 0.192 0.060
#> GSM550920 3 0.4661 0.54633 0.000 0.348 0.652 0.000
cbind(get_classes(res, k = 5), get_membership(res, k = 5))
#> class entropy silhouette p1 p2 p3 p4 p5
#> GSM550785 1 0.3546 0.69364 0.840 0.024 0.000 0.024 0.112
#> GSM550786 4 0.2972 0.69852 0.004 0.000 0.084 0.872 0.040
#> GSM550788 4 0.4225 0.13185 0.000 0.364 0.000 0.632 0.004
#> GSM550789 2 0.4967 0.42174 0.004 0.512 0.000 0.464 0.020
#> GSM550790 1 0.4639 0.47689 0.636 0.008 0.000 0.344 0.012
#> GSM550791 4 0.5433 0.63962 0.144 0.012 0.020 0.724 0.100
#> GSM550792 4 0.3227 0.69752 0.020 0.072 0.000 0.868 0.040
#> GSM550796 2 0.4219 0.54489 0.000 0.584 0.000 0.416 0.000
#> GSM550797 2 0.4811 0.45248 0.000 0.528 0.000 0.452 0.020
#> GSM550799 4 0.5216 0.27359 0.000 0.004 0.344 0.604 0.048
#> GSM550800 2 0.5061 0.59402 0.012 0.580 0.000 0.388 0.020
#> GSM550801 2 0.4651 0.61600 0.000 0.608 0.000 0.372 0.020
#> GSM550804 2 0.0798 0.70373 0.016 0.976 0.000 0.000 0.008
#> GSM550806 3 0.4276 0.62666 0.000 0.000 0.716 0.256 0.028
#> GSM550807 2 0.4626 0.62676 0.000 0.616 0.000 0.364 0.020
#> GSM550808 4 0.2193 0.70789 0.000 0.028 0.008 0.920 0.044
#> GSM550809 4 0.4767 0.66041 0.128 0.020 0.020 0.780 0.052
#> GSM550810 4 0.3491 0.53834 0.000 0.228 0.000 0.768 0.004
#> GSM550811 4 0.3748 0.69666 0.064 0.036 0.004 0.848 0.048
#> GSM550813 2 0.1282 0.75189 0.000 0.952 0.000 0.044 0.004
#> GSM550814 2 0.3861 0.66422 0.000 0.712 0.000 0.284 0.004
#> GSM550815 4 0.4800 -0.33454 0.012 0.476 0.000 0.508 0.004
#> GSM550816 2 0.2798 0.77132 0.000 0.852 0.000 0.140 0.008
#> GSM550817 3 0.4276 0.60645 0.000 0.000 0.716 0.256 0.028
#> GSM550818 3 0.2230 0.79535 0.000 0.000 0.884 0.116 0.000
#> GSM550819 4 0.4777 0.51412 0.004 0.316 0.012 0.656 0.012
#> GSM550820 4 0.7629 0.27382 0.300 0.104 0.008 0.480 0.108
#> GSM550821 4 0.5258 0.67914 0.004 0.112 0.100 0.744 0.040
#> GSM550822 2 0.3652 0.74516 0.004 0.784 0.000 0.200 0.012
#> GSM550826 4 0.6090 0.65117 0.064 0.096 0.136 0.692 0.012
#> GSM550832 2 0.3870 0.68221 0.000 0.732 0.004 0.260 0.004
#> GSM550833 4 0.3656 0.60630 0.000 0.196 0.000 0.784 0.020
#> GSM550835 4 0.2798 0.70582 0.000 0.008 0.044 0.888 0.060
#> GSM550836 3 0.3812 0.68848 0.000 0.000 0.812 0.096 0.092
#> GSM550837 4 0.2416 0.70838 0.000 0.016 0.016 0.908 0.060
#> GSM550838 4 0.4908 0.65770 0.092 0.000 0.028 0.756 0.124
#> GSM550841 3 0.4898 0.47505 0.004 0.000 0.632 0.332 0.032
#> GSM550842 4 0.3319 0.71151 0.000 0.040 0.052 0.868 0.040
#> GSM550846 4 0.5061 0.52204 0.024 0.312 0.000 0.644 0.020
#> GSM550849 4 0.3229 0.70485 0.044 0.016 0.016 0.880 0.044
#> GSM550850 4 0.6209 0.57530 0.140 0.008 0.020 0.636 0.196
#> GSM550851 4 0.1949 0.70667 0.000 0.012 0.016 0.932 0.040
#> GSM550852 4 0.3607 0.50288 0.000 0.244 0.000 0.752 0.004
#> GSM550853 2 0.4747 0.62174 0.008 0.604 0.000 0.376 0.012
#> GSM550855 2 0.2690 0.76726 0.000 0.844 0.000 0.156 0.000
#> GSM550856 2 0.0955 0.74172 0.004 0.968 0.000 0.028 0.000
#> GSM550861 2 0.2719 0.76997 0.000 0.852 0.000 0.144 0.004
#> GSM550863 5 0.5371 0.82381 0.096 0.208 0.000 0.012 0.684
#> GSM550864 2 0.0451 0.70970 0.008 0.988 0.000 0.000 0.004
#> GSM550866 2 0.1270 0.74909 0.000 0.948 0.000 0.052 0.000
#> GSM550867 1 0.2522 0.70151 0.880 0.012 0.000 0.108 0.000
#> GSM550885 1 0.2295 0.70736 0.900 0.004 0.000 0.088 0.008
#> GSM550886 4 0.5929 0.51674 0.000 0.068 0.276 0.620 0.036
#> GSM550887 2 0.3427 0.75271 0.000 0.796 0.000 0.192 0.012
#> GSM550889 5 0.4518 0.81312 0.016 0.320 0.000 0.004 0.660
#> GSM550894 2 0.4770 0.42209 0.000 0.596 0.012 0.384 0.008
#> GSM550897 4 0.7974 0.39761 0.200 0.168 0.004 0.476 0.152
#> GSM550903 2 0.2005 0.75703 0.004 0.924 0.000 0.056 0.016
#> GSM550905 4 0.3113 0.71886 0.000 0.080 0.008 0.868 0.044
#> GSM550906 2 0.3399 0.76135 0.004 0.812 0.000 0.172 0.012
#> GSM550907 3 0.0000 0.85843 0.000 0.000 1.000 0.000 0.000
#> GSM550909 4 0.3635 0.70576 0.000 0.132 0.036 0.824 0.008
#> GSM550911 3 0.0000 0.85843 0.000 0.000 1.000 0.000 0.000
#> GSM550913 2 0.3006 0.76804 0.004 0.836 0.000 0.156 0.004
#> GSM550915 5 0.4329 0.86600 0.032 0.252 0.000 0.000 0.716
#> GSM550917 2 0.0613 0.71469 0.008 0.984 0.000 0.004 0.004
#> GSM550919 5 0.5169 0.82218 0.024 0.300 0.000 0.028 0.648
#> GSM550921 3 0.0000 0.85843 0.000 0.000 1.000 0.000 0.000
#> GSM550924 4 0.4857 0.68452 0.004 0.116 0.112 0.756 0.012
#> GSM550926 2 0.2136 0.76604 0.000 0.904 0.000 0.088 0.008
#> GSM550927 2 0.2997 0.76958 0.012 0.840 0.000 0.148 0.000
#> GSM550787 4 0.3792 0.72124 0.016 0.096 0.036 0.840 0.012
#> GSM550793 4 0.4191 0.70251 0.028 0.032 0.104 0.820 0.016
#> GSM550794 4 0.4192 0.69907 0.028 0.132 0.000 0.800 0.040
#> GSM550795 4 0.6209 0.57530 0.140 0.008 0.020 0.636 0.196
#> GSM550798 4 0.5425 0.62759 0.172 0.000 0.048 0.712 0.068
#> GSM550803 1 0.5343 0.38295 0.580 0.008 0.000 0.368 0.044
#> GSM550805 4 0.3299 0.70870 0.044 0.032 0.008 0.876 0.040
#> GSM550823 4 0.4419 0.49691 0.008 0.344 0.000 0.644 0.004
#> GSM550824 1 0.0566 0.69418 0.984 0.012 0.000 0.004 0.000
#> GSM550825 3 0.1074 0.85384 0.004 0.000 0.968 0.016 0.012
#> GSM550827 5 0.4370 0.86373 0.040 0.236 0.000 0.000 0.724
#> GSM550828 1 0.5164 0.56941 0.708 0.112 0.000 0.008 0.172
#> GSM550829 4 0.5816 0.59264 0.140 0.000 0.204 0.644 0.012
#> GSM550830 4 0.3718 0.64195 0.016 0.196 0.000 0.784 0.004
#> GSM550834 4 0.6209 0.57530 0.140 0.008 0.020 0.636 0.196
#> GSM550839 4 0.2424 0.70489 0.000 0.008 0.052 0.908 0.032
#> GSM550840 4 0.5199 0.64387 0.140 0.012 0.016 0.740 0.092
#> GSM550843 3 0.5083 0.39235 0.004 0.000 0.596 0.364 0.036
#> GSM550844 4 0.7144 0.54661 0.180 0.108 0.008 0.588 0.116
#> GSM550845 2 0.0798 0.70373 0.016 0.976 0.000 0.000 0.008
#> GSM550848 5 0.3885 0.85719 0.008 0.268 0.000 0.000 0.724
#> GSM550854 1 0.2470 0.70342 0.884 0.012 0.000 0.104 0.000
#> GSM550857 3 0.0486 0.85650 0.004 0.000 0.988 0.004 0.004
#> GSM550858 1 0.4125 0.64636 0.780 0.040 0.000 0.008 0.172
#> GSM550859 1 0.0566 0.69418 0.984 0.012 0.000 0.004 0.000
#> GSM550862 1 0.3918 0.66232 0.804 0.044 0.000 0.008 0.144
#> GSM550865 5 0.4138 0.84792 0.016 0.276 0.000 0.000 0.708
#> GSM550868 5 0.8413 0.23963 0.148 0.268 0.000 0.280 0.304
#> GSM550869 4 0.3343 0.72392 0.012 0.076 0.016 0.868 0.028
#> GSM550870 2 0.1281 0.74205 0.012 0.956 0.000 0.032 0.000
#> GSM550871 4 0.4456 0.70952 0.000 0.080 0.088 0.796 0.036
#> GSM550872 4 0.5593 0.61530 0.176 0.064 0.000 0.700 0.060
#> GSM550873 4 0.3597 0.67923 0.000 0.180 0.012 0.800 0.008
#> GSM550874 2 0.4434 0.47797 0.000 0.536 0.000 0.460 0.004
#> GSM550876 4 0.5234 0.17239 0.000 0.004 0.436 0.524 0.036
#> GSM550877 2 0.1281 0.74345 0.012 0.956 0.000 0.032 0.000
#> GSM550878 3 0.0162 0.85874 0.000 0.000 0.996 0.004 0.000
#> GSM550879 1 0.5874 0.46021 0.640 0.156 0.000 0.012 0.192
#> GSM550882 3 0.2104 0.83296 0.000 0.000 0.916 0.060 0.024
#> GSM550888 3 0.0486 0.85650 0.004 0.000 0.988 0.004 0.004
#> GSM550890 5 0.4384 0.85833 0.044 0.228 0.000 0.000 0.728
#> GSM550891 3 0.0000 0.85843 0.000 0.000 1.000 0.000 0.000
#> GSM550892 1 0.5830 0.48602 0.652 0.144 0.000 0.016 0.188
#> GSM550893 2 0.1430 0.75692 0.000 0.944 0.000 0.052 0.004
#> GSM550895 2 0.0955 0.69397 0.004 0.968 0.000 0.000 0.028
#> GSM550896 2 0.0324 0.71229 0.004 0.992 0.000 0.000 0.004
#> GSM550898 1 0.0566 0.69418 0.984 0.012 0.000 0.004 0.000
#> GSM550899 2 0.0451 0.70970 0.008 0.988 0.000 0.000 0.004
#> GSM550900 5 0.5197 0.84607 0.068 0.236 0.000 0.012 0.684
#> GSM550901 5 0.6011 0.76699 0.112 0.192 0.000 0.040 0.656
#> GSM550902 4 0.6312 0.64447 0.088 0.096 0.136 0.672 0.008
#> GSM550904 4 0.7522 0.57051 0.184 0.104 0.076 0.584 0.052
#> GSM550908 3 0.0486 0.85650 0.004 0.000 0.988 0.004 0.004
#> GSM550912 2 0.2707 0.77013 0.000 0.860 0.000 0.132 0.008
#> GSM550914 5 0.4355 0.85611 0.044 0.224 0.000 0.000 0.732
#> GSM550918 2 0.0912 0.69628 0.016 0.972 0.000 0.000 0.012
#> GSM550922 4 0.5299 0.14224 0.000 0.004 0.436 0.520 0.040
#> GSM550923 1 0.6163 -0.00803 0.464 0.008 0.032 0.456 0.040
#> GSM550925 4 0.8414 0.20233 0.192 0.208 0.004 0.396 0.200
#> GSM550802 4 0.3412 0.69156 0.012 0.088 0.000 0.852 0.048
#> GSM550812 4 0.3433 0.70016 0.004 0.132 0.000 0.832 0.032
#> GSM550831 4 0.6209 0.57530 0.140 0.008 0.020 0.636 0.196
#> GSM550847 1 0.2653 0.71113 0.900 0.020 0.000 0.028 0.052
#> GSM550860 4 0.5781 0.58577 0.012 0.060 0.232 0.668 0.028
#> GSM550875 4 0.5082 0.69425 0.088 0.092 0.012 0.768 0.040
#> GSM550880 4 0.4537 0.64345 0.192 0.032 0.008 0.756 0.012
#> GSM550881 3 0.0324 0.85881 0.000 0.000 0.992 0.004 0.004
#> GSM550883 3 0.0324 0.85881 0.000 0.000 0.992 0.004 0.004
#> GSM550884 4 0.4377 0.66202 0.004 0.188 0.044 0.760 0.004
#> GSM550910 4 0.5320 0.00843 0.004 0.000 0.468 0.488 0.040
#> GSM550916 1 0.6992 0.46448 0.584 0.104 0.008 0.224 0.080
#> GSM550920 4 0.5218 0.21028 0.000 0.004 0.424 0.536 0.036
cbind(get_classes(res, k = 6), get_membership(res, k = 6))
#> class entropy silhouette p1 p2 p3 p4 p5 p6
#> GSM550785 1 0.5403 0.6679 0.608 0.000 0.008 0.156 0.000 0.228
#> GSM550786 5 0.5336 0.3581 0.000 0.168 0.000 0.000 0.588 0.244
#> GSM550788 2 0.2738 0.6179 0.000 0.820 0.004 0.000 0.000 0.176
#> GSM550789 2 0.2923 0.6756 0.000 0.848 0.052 0.000 0.000 0.100
#> GSM550790 6 0.4724 -0.0693 0.468 0.020 0.004 0.004 0.004 0.500
#> GSM550791 6 0.3009 0.6390 0.008 0.136 0.004 0.004 0.008 0.840
#> GSM550792 6 0.5233 0.6357 0.000 0.212 0.000 0.084 0.040 0.664
#> GSM550796 2 0.2191 0.6732 0.000 0.876 0.000 0.000 0.004 0.120
#> GSM550797 2 0.3006 0.6762 0.000 0.844 0.064 0.000 0.000 0.092
#> GSM550799 5 0.3461 0.2938 0.000 0.008 0.036 0.000 0.804 0.152
#> GSM550800 2 0.3052 0.6842 0.000 0.852 0.064 0.008 0.000 0.076
#> GSM550801 2 0.3098 0.6808 0.000 0.844 0.064 0.004 0.000 0.088
#> GSM550804 2 0.6531 0.4670 0.072 0.520 0.244 0.164 0.000 0.000
#> GSM550806 5 0.2278 -0.1909 0.000 0.000 0.128 0.000 0.868 0.004
#> GSM550807 2 0.2956 0.6790 0.000 0.848 0.064 0.000 0.000 0.088
#> GSM550808 5 0.6314 0.1267 0.000 0.296 0.008 0.000 0.376 0.320
#> GSM550809 6 0.3273 0.6486 0.008 0.180 0.000 0.004 0.008 0.800
#> GSM550810 2 0.3473 0.5721 0.000 0.780 0.004 0.000 0.024 0.192
#> GSM550811 6 0.3328 0.6464 0.000 0.192 0.000 0.008 0.012 0.788
#> GSM550813 2 0.5559 0.6060 0.044 0.664 0.188 0.092 0.000 0.012
#> GSM550814 2 0.2264 0.6824 0.000 0.888 0.000 0.012 0.004 0.096
#> GSM550815 2 0.2357 0.6705 0.000 0.872 0.012 0.000 0.000 0.116
#> GSM550816 2 0.3948 0.7046 0.036 0.824 0.052 0.048 0.000 0.040
#> GSM550817 5 0.2146 -0.1226 0.000 0.000 0.116 0.000 0.880 0.004
#> GSM550818 5 0.3109 -0.3938 0.000 0.000 0.224 0.000 0.772 0.004
#> GSM550819 2 0.6584 -0.2613 0.000 0.460 0.008 0.088 0.080 0.364
#> GSM550820 6 0.5756 0.3722 0.272 0.032 0.004 0.072 0.012 0.608
#> GSM550821 5 0.6047 0.3001 0.000 0.244 0.000 0.016 0.520 0.220
#> GSM550822 2 0.1429 0.7041 0.000 0.940 0.004 0.000 0.004 0.052
#> GSM550826 6 0.7029 0.4086 0.000 0.196 0.004 0.080 0.276 0.444
#> GSM550832 2 0.1970 0.6859 0.000 0.900 0.000 0.008 0.000 0.092
#> GSM550833 2 0.3452 0.4589 0.000 0.736 0.004 0.000 0.004 0.256
#> GSM550835 5 0.6229 0.2674 0.000 0.224 0.016 0.000 0.468 0.292
#> GSM550836 3 0.4573 0.8834 0.000 0.000 0.584 0.000 0.372 0.044
#> GSM550837 5 0.6366 0.1752 0.000 0.292 0.012 0.000 0.396 0.300
#> GSM550838 6 0.3010 0.6373 0.000 0.132 0.004 0.000 0.028 0.836
#> GSM550841 5 0.1426 0.1360 0.000 0.008 0.028 0.000 0.948 0.016
#> GSM550842 5 0.5826 0.3145 0.000 0.272 0.000 0.000 0.492 0.236
#> GSM550846 6 0.6341 0.5561 0.000 0.316 0.004 0.132 0.044 0.504
#> GSM550849 6 0.4230 0.6191 0.000 0.196 0.004 0.004 0.060 0.736
#> GSM550850 6 0.2452 0.4136 0.028 0.000 0.084 0.004 0.000 0.884
#> GSM550851 5 0.6167 0.2064 0.000 0.292 0.004 0.000 0.416 0.288
#> GSM550852 2 0.3646 0.4091 0.000 0.700 0.000 0.004 0.004 0.292
#> GSM550853 2 0.2474 0.6863 0.000 0.880 0.040 0.000 0.000 0.080
#> GSM550855 2 0.1464 0.7118 0.000 0.944 0.004 0.016 0.000 0.036
#> GSM550856 2 0.5605 0.6125 0.048 0.664 0.180 0.096 0.000 0.012
#> GSM550861 2 0.0935 0.7120 0.000 0.964 0.004 0.000 0.000 0.032
#> GSM550863 4 0.2408 0.7563 0.004 0.024 0.004 0.892 0.000 0.076
#> GSM550864 2 0.6682 0.4886 0.072 0.524 0.244 0.152 0.000 0.008
#> GSM550866 2 0.5516 0.6487 0.044 0.696 0.104 0.128 0.000 0.028
#> GSM550867 1 0.2288 0.7730 0.876 0.000 0.004 0.004 0.000 0.116
#> GSM550885 1 0.2633 0.7769 0.864 0.000 0.004 0.020 0.000 0.112
#> GSM550886 5 0.4548 0.4749 0.000 0.156 0.008 0.000 0.720 0.116
#> GSM550887 2 0.1285 0.7051 0.000 0.944 0.004 0.000 0.000 0.052
#> GSM550889 4 0.3099 0.6943 0.004 0.120 0.004 0.840 0.000 0.032
#> GSM550894 2 0.4132 0.5424 0.000 0.756 0.000 0.004 0.104 0.136
#> GSM550897 6 0.7027 0.2873 0.060 0.144 0.008 0.376 0.008 0.404
#> GSM550903 2 0.4774 0.6155 0.048 0.708 0.196 0.048 0.000 0.000
#> GSM550905 5 0.6044 0.1980 0.000 0.308 0.000 0.000 0.416 0.276
#> GSM550906 2 0.0858 0.7099 0.000 0.968 0.004 0.000 0.000 0.028
#> GSM550907 5 0.3833 -0.8007 0.000 0.000 0.444 0.000 0.556 0.000
#> GSM550909 5 0.6967 -0.0529 0.000 0.232 0.000 0.064 0.376 0.328
#> GSM550911 5 0.3823 -0.7912 0.000 0.000 0.436 0.000 0.564 0.000
#> GSM550913 2 0.0862 0.7142 0.000 0.972 0.004 0.016 0.000 0.008
#> GSM550915 4 0.0767 0.7730 0.000 0.012 0.004 0.976 0.000 0.008
#> GSM550917 2 0.6534 0.5104 0.072 0.544 0.244 0.132 0.000 0.008
#> GSM550919 4 0.2322 0.7641 0.000 0.036 0.004 0.896 0.000 0.064
#> GSM550921 3 0.3782 0.9543 0.000 0.000 0.588 0.000 0.412 0.000
#> GSM550924 6 0.7137 0.3543 0.000 0.204 0.004 0.084 0.292 0.416
#> GSM550926 2 0.4824 0.6668 0.052 0.756 0.076 0.096 0.000 0.020
#> GSM550927 2 0.0260 0.7116 0.000 0.992 0.008 0.000 0.000 0.000
#> GSM550787 6 0.7025 0.4018 0.000 0.200 0.004 0.080 0.268 0.448
#> GSM550793 5 0.4699 -0.0324 0.000 0.028 0.008 0.000 0.496 0.468
#> GSM550794 6 0.4907 0.6455 0.000 0.204 0.000 0.084 0.024 0.688
#> GSM550795 6 0.2290 0.4257 0.020 0.000 0.084 0.004 0.000 0.892
#> GSM550798 6 0.5503 0.4959 0.124 0.028 0.004 0.004 0.180 0.660
#> GSM550803 6 0.4786 0.0625 0.424 0.020 0.004 0.004 0.008 0.540
#> GSM550805 6 0.5496 0.6243 0.000 0.200 0.000 0.084 0.064 0.652
#> GSM550823 6 0.5613 0.5160 0.000 0.368 0.000 0.092 0.020 0.520
#> GSM550824 1 0.1501 0.7719 0.924 0.000 0.000 0.000 0.000 0.076
#> GSM550825 3 0.4702 0.8701 0.000 0.000 0.496 0.000 0.460 0.044
#> GSM550827 4 0.0767 0.7730 0.000 0.012 0.004 0.976 0.000 0.008
#> GSM550828 1 0.5881 0.5522 0.504 0.000 0.004 0.276 0.000 0.216
#> GSM550829 6 0.5747 0.2475 0.096 0.024 0.000 0.000 0.384 0.496
#> GSM550830 6 0.5278 0.6032 0.004 0.284 0.000 0.096 0.008 0.608
#> GSM550834 6 0.2290 0.4257 0.020 0.000 0.084 0.004 0.000 0.892
#> GSM550839 5 0.5925 0.3053 0.000 0.168 0.016 0.000 0.528 0.288
#> GSM550840 6 0.3611 0.6419 0.020 0.148 0.012 0.004 0.008 0.808
#> GSM550843 5 0.0820 0.1848 0.000 0.016 0.000 0.000 0.972 0.012
#> GSM550844 6 0.6043 0.4991 0.172 0.044 0.004 0.140 0.012 0.628
#> GSM550845 2 0.6505 0.4748 0.072 0.524 0.244 0.160 0.000 0.000
#> GSM550848 4 0.0767 0.7730 0.000 0.012 0.004 0.976 0.000 0.008
#> GSM550854 1 0.2243 0.7736 0.880 0.000 0.004 0.004 0.000 0.112
#> GSM550857 3 0.3797 0.9564 0.000 0.000 0.580 0.000 0.420 0.000
#> GSM550858 1 0.5758 0.6261 0.552 0.000 0.008 0.236 0.000 0.204
#> GSM550859 1 0.1444 0.7707 0.928 0.000 0.000 0.000 0.000 0.072
#> GSM550862 1 0.5437 0.6728 0.608 0.000 0.008 0.180 0.000 0.204
#> GSM550865 4 0.1621 0.7600 0.004 0.048 0.004 0.936 0.000 0.008
#> GSM550868 4 0.6252 0.2190 0.040 0.132 0.000 0.520 0.004 0.304
#> GSM550869 6 0.6292 0.5722 0.000 0.200 0.004 0.080 0.132 0.584
#> GSM550870 2 0.5724 0.5997 0.056 0.648 0.188 0.100 0.000 0.008
#> GSM550871 5 0.6270 0.2242 0.000 0.176 0.000 0.036 0.512 0.276
#> GSM550872 6 0.6256 0.6152 0.024 0.208 0.004 0.196 0.008 0.560
#> GSM550873 2 0.6740 -0.0714 0.000 0.456 0.000 0.056 0.236 0.252
#> GSM550874 2 0.2700 0.6437 0.000 0.836 0.004 0.004 0.000 0.156
#> GSM550876 5 0.3109 0.3930 0.000 0.068 0.008 0.000 0.848 0.076
#> GSM550877 2 0.5505 0.5834 0.056 0.648 0.204 0.092 0.000 0.000
#> GSM550878 5 0.3765 -0.7540 0.000 0.000 0.404 0.000 0.596 0.000
#> GSM550879 4 0.6331 -0.3016 0.344 0.004 0.008 0.408 0.000 0.236
#> GSM550882 5 0.2883 -0.4243 0.000 0.000 0.212 0.000 0.788 0.000
#> GSM550888 3 0.3797 0.9564 0.000 0.000 0.580 0.000 0.420 0.000
#> GSM550890 4 0.0551 0.7674 0.000 0.008 0.004 0.984 0.000 0.004
#> GSM550891 3 0.3782 0.9543 0.000 0.000 0.588 0.000 0.412 0.000
#> GSM550892 1 0.6176 0.3053 0.392 0.000 0.008 0.380 0.000 0.220
#> GSM550893 2 0.5172 0.6467 0.056 0.720 0.108 0.104 0.000 0.012
#> GSM550895 2 0.6446 0.5117 0.056 0.556 0.212 0.168 0.000 0.008
#> GSM550896 2 0.6463 0.5183 0.068 0.556 0.232 0.136 0.000 0.008
#> GSM550898 1 0.1444 0.7707 0.928 0.000 0.000 0.000 0.000 0.072
#> GSM550899 2 0.6761 0.4746 0.072 0.512 0.244 0.164 0.000 0.008
#> GSM550900 4 0.2136 0.7664 0.012 0.016 0.000 0.908 0.000 0.064
#> GSM550901 4 0.2205 0.7457 0.004 0.008 0.000 0.896 0.004 0.088
#> GSM550902 6 0.6774 0.5182 0.000 0.176 0.004 0.084 0.224 0.512
#> GSM550904 6 0.5811 0.4836 0.228 0.040 0.000 0.024 0.076 0.632
#> GSM550908 3 0.3797 0.9564 0.000 0.000 0.580 0.000 0.420 0.000
#> GSM550912 2 0.4687 0.6761 0.048 0.768 0.048 0.104 0.000 0.032
#> GSM550914 4 0.0653 0.7664 0.004 0.012 0.004 0.980 0.000 0.000
#> GSM550918 2 0.6673 0.4304 0.072 0.496 0.244 0.188 0.000 0.000
#> GSM550922 5 0.3621 0.4413 0.000 0.124 0.008 0.000 0.804 0.064
#> GSM550923 6 0.5031 0.2644 0.352 0.028 0.000 0.000 0.036 0.584
#> GSM550925 4 0.6530 0.0947 0.100 0.064 0.004 0.480 0.004 0.348
#> GSM550802 6 0.4755 0.5597 0.000 0.304 0.000 0.008 0.056 0.632
#> GSM550812 6 0.5597 0.6141 0.000 0.216 0.000 0.084 0.064 0.636
#> GSM550831 6 0.2373 0.4200 0.024 0.000 0.084 0.004 0.000 0.888
#> GSM550847 1 0.2420 0.7727 0.884 0.000 0.000 0.040 0.000 0.076
#> GSM550860 5 0.6476 0.0952 0.000 0.116 0.004 0.064 0.496 0.320
#> GSM550875 6 0.4823 0.6514 0.000 0.192 0.000 0.084 0.024 0.700
#> GSM550880 6 0.5368 0.6571 0.036 0.192 0.000 0.092 0.008 0.672
#> GSM550881 5 0.4410 -0.7816 0.000 0.000 0.412 0.000 0.560 0.028
#> GSM550883 3 0.3843 0.9327 0.000 0.000 0.548 0.000 0.452 0.000
#> GSM550884 6 0.6779 0.5311 0.000 0.220 0.004 0.084 0.180 0.512
#> GSM550910 5 0.2129 0.3203 0.000 0.040 0.000 0.000 0.904 0.056
#> GSM550916 6 0.5794 -0.1230 0.432 0.028 0.004 0.064 0.004 0.468
#> GSM550920 5 0.3646 0.4443 0.000 0.116 0.008 0.000 0.804 0.072
Heatmaps for the consensus matrix. It visualizes the probability of two samples to be in a same group.
consensus_heatmap(res, k = 2)
consensus_heatmap(res, k = 3)
consensus_heatmap(res, k = 4)
consensus_heatmap(res, k = 5)
consensus_heatmap(res, k = 6)
Heatmaps for the membership of samples in all partitions to see how consistent they are:
membership_heatmap(res, k = 2)
membership_heatmap(res, k = 3)
membership_heatmap(res, k = 4)
membership_heatmap(res, k = 5)
membership_heatmap(res, k = 6)
As soon as we have had the classes for columns, we can look for signatures which are significantly different between classes which can be candidate marks for certain classes. Following are the heatmaps for signatures.
Signature heatmaps where rows are scaled:
get_signatures(res, k = 2)
get_signatures(res, k = 3)
get_signatures(res, k = 4)
get_signatures(res, k = 5)
get_signatures(res, k = 6)
Signature heatmaps where rows are not scaled:
get_signatures(res, k = 2, scale_rows = FALSE)
get_signatures(res, k = 3, scale_rows = FALSE)
get_signatures(res, k = 4, scale_rows = FALSE)
get_signatures(res, k = 5, scale_rows = FALSE)
get_signatures(res, k = 6, scale_rows = FALSE)
Compare the overlap of signatures from different k:
compare_signatures(res)
get_signature() returns a data frame invisibly. TO get the list of signatures, the function
call should be assigned to a variable explicitly. In following code, if plot argument is set
to FALSE, no heatmap is plotted while only the differential analysis is performed.
# code only for demonstration
tb = get_signature(res, k = ..., plot = FALSE)
An example of the output of tb is:
#> which_row fdr mean_1 mean_2 scaled_mean_1 scaled_mean_2 km
#> 1 38 0.042760348 8.373488 9.131774 -0.5533452 0.5164555 1
#> 2 40 0.018707592 7.106213 8.469186 -0.6173731 0.5762149 1
#> 3 55 0.019134737 10.221463 11.207825 -0.6159697 0.5749050 1
#> 4 59 0.006059896 5.921854 7.869574 -0.6899429 0.6439467 1
#> 5 60 0.018055526 8.928898 10.211722 -0.6204761 0.5791110 1
#> 6 98 0.009384629 15.714769 14.887706 0.6635654 -0.6193277 2
...
The columns in tb are:
which_row: row indices corresponding to the input matrix.fdr: FDR for the differential test. mean_x: The mean value in group x.scaled_mean_x: The mean value in group x after rows are scaled.km: Row groups if k-means clustering is applied to rows.UMAP plot which shows how samples are separated.
dimension_reduction(res, k = 2, method = "UMAP")
dimension_reduction(res, k = 3, method = "UMAP")
dimension_reduction(res, k = 4, method = "UMAP")
dimension_reduction(res, k = 5, method = "UMAP")
dimension_reduction(res, k = 6, method = "UMAP")
Following heatmap shows how subgroups are split when increasing k:
collect_classes(res)
Test correlation between subgroups and known annotations. If the known annotation is numeric, one-way ANOVA test is applied, and if the known annotation is discrete, chi-squared contingency table test is applied.
test_to_known_factors(res)
#> n disease.state(p) k
#> CV:mclust 139 0.026000 2
#> CV:mclust 90 0.018854 3
#> CV:mclust 111 0.133308 4
#> CV:mclust 119 0.061234 5
#> CV:mclust 84 0.000743 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 51776 rows and 143 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 0.591 0.825 0.922 0.4449 0.576 0.576
#> 3 3 0.911 0.910 0.961 0.4645 0.676 0.480
#> 4 4 0.517 0.624 0.795 0.1180 0.875 0.664
#> 5 5 0.513 0.501 0.702 0.0797 0.858 0.547
#> 6 6 0.602 0.494 0.707 0.0494 0.902 0.597
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
#> GSM550785 2 0.3879 0.8645 0.076 0.924
#> GSM550786 1 0.0000 0.9272 1.000 0.000
#> GSM550788 2 0.0000 0.9028 0.000 1.000
#> GSM550789 2 0.0000 0.9028 0.000 1.000
#> GSM550790 2 0.7299 0.7713 0.204 0.796
#> GSM550791 2 0.7139 0.7786 0.196 0.804
#> GSM550792 2 0.0000 0.9028 0.000 1.000
#> GSM550796 2 0.0000 0.9028 0.000 1.000
#> GSM550797 2 0.0000 0.9028 0.000 1.000
#> GSM550799 1 0.0376 0.9252 0.996 0.004
#> GSM550800 2 0.0000 0.9028 0.000 1.000
#> GSM550801 2 0.0000 0.9028 0.000 1.000
#> GSM550804 2 0.0000 0.9028 0.000 1.000
#> GSM550806 1 0.0000 0.9272 1.000 0.000
#> GSM550807 2 0.0000 0.9028 0.000 1.000
#> GSM550808 2 0.9795 0.2085 0.416 0.584
#> GSM550809 2 0.8267 0.7062 0.260 0.740
#> GSM550810 2 0.0000 0.9028 0.000 1.000
#> GSM550811 2 0.9850 0.3796 0.428 0.572
#> GSM550813 2 0.0000 0.9028 0.000 1.000
#> GSM550814 2 0.0000 0.9028 0.000 1.000
#> GSM550815 2 0.0000 0.9028 0.000 1.000
#> GSM550816 2 0.0000 0.9028 0.000 1.000
#> GSM550817 1 0.0000 0.9272 1.000 0.000
#> GSM550818 1 0.0000 0.9272 1.000 0.000
#> GSM550819 2 0.0376 0.9006 0.004 0.996
#> GSM550820 2 0.9323 0.5663 0.348 0.652
#> GSM550821 1 0.9922 0.2674 0.552 0.448
#> GSM550822 2 0.0000 0.9028 0.000 1.000
#> GSM550826 1 0.0000 0.9272 1.000 0.000
#> GSM550832 2 0.0000 0.9028 0.000 1.000
#> GSM550833 2 0.0000 0.9028 0.000 1.000
#> GSM550835 1 0.6801 0.7564 0.820 0.180
#> GSM550836 1 0.0000 0.9272 1.000 0.000
#> GSM550837 2 0.9608 0.3088 0.384 0.616
#> GSM550838 1 0.0000 0.9272 1.000 0.000
#> GSM550841 1 0.1184 0.9183 0.984 0.016
#> GSM550842 2 0.9944 0.0623 0.456 0.544
#> GSM550846 2 0.0000 0.9028 0.000 1.000
#> GSM550849 2 0.6247 0.8114 0.156 0.844
#> GSM550850 2 0.7299 0.7713 0.204 0.796
#> GSM550851 2 0.9815 0.1949 0.420 0.580
#> GSM550852 2 0.0000 0.9028 0.000 1.000
#> GSM550853 2 0.0000 0.9028 0.000 1.000
#> GSM550855 2 0.0000 0.9028 0.000 1.000
#> GSM550856 2 0.0000 0.9028 0.000 1.000
#> GSM550861 2 0.0000 0.9028 0.000 1.000
#> GSM550863 2 0.0000 0.9028 0.000 1.000
#> GSM550864 2 0.0000 0.9028 0.000 1.000
#> GSM550866 2 0.0000 0.9028 0.000 1.000
#> GSM550867 2 0.7299 0.7713 0.204 0.796
#> GSM550885 2 0.7299 0.7713 0.204 0.796
#> GSM550886 1 0.5629 0.8138 0.868 0.132
#> GSM550887 2 0.0000 0.9028 0.000 1.000
#> GSM550889 2 0.0000 0.9028 0.000 1.000
#> GSM550894 2 0.0000 0.9028 0.000 1.000
#> GSM550897 2 0.5178 0.8400 0.116 0.884
#> GSM550903 2 0.0000 0.9028 0.000 1.000
#> GSM550905 1 0.9970 0.2039 0.532 0.468
#> GSM550906 2 0.0000 0.9028 0.000 1.000
#> GSM550907 1 0.0000 0.9272 1.000 0.000
#> GSM550909 2 0.9954 0.0460 0.460 0.540
#> GSM550911 1 0.0000 0.9272 1.000 0.000
#> GSM550913 2 0.0000 0.9028 0.000 1.000
#> GSM550915 2 0.0000 0.9028 0.000 1.000
#> GSM550917 2 0.0000 0.9028 0.000 1.000
#> GSM550919 2 0.0000 0.9028 0.000 1.000
#> GSM550921 1 0.0000 0.9272 1.000 0.000
#> GSM550924 1 0.6531 0.7503 0.832 0.168
#> GSM550926 2 0.0000 0.9028 0.000 1.000
#> GSM550927 2 0.0000 0.9028 0.000 1.000
#> GSM550787 1 0.7528 0.6749 0.784 0.216
#> GSM550793 1 0.0000 0.9272 1.000 0.000
#> GSM550794 2 0.0000 0.9028 0.000 1.000
#> GSM550795 2 0.7299 0.7713 0.204 0.796
#> GSM550798 1 0.0000 0.9272 1.000 0.000
#> GSM550803 2 0.9044 0.6076 0.320 0.680
#> GSM550805 1 0.9954 -0.0118 0.540 0.460
#> GSM550823 2 0.0000 0.9028 0.000 1.000
#> GSM550824 2 0.7299 0.7713 0.204 0.796
#> GSM550825 1 0.0000 0.9272 1.000 0.000
#> GSM550827 2 0.0000 0.9028 0.000 1.000
#> GSM550828 2 0.4562 0.8526 0.096 0.904
#> GSM550829 1 0.0000 0.9272 1.000 0.000
#> GSM550830 2 0.0000 0.9028 0.000 1.000
#> GSM550834 2 0.6343 0.8085 0.160 0.840
#> GSM550839 1 0.3584 0.8770 0.932 0.068
#> GSM550840 2 0.5294 0.8374 0.120 0.880
#> GSM550843 1 0.0000 0.9272 1.000 0.000
#> GSM550844 2 0.7299 0.7713 0.204 0.796
#> GSM550845 2 0.0000 0.9028 0.000 1.000
#> GSM550848 2 0.0000 0.9028 0.000 1.000
#> GSM550854 2 0.7299 0.7713 0.204 0.796
#> GSM550857 1 0.0000 0.9272 1.000 0.000
#> GSM550858 2 0.7219 0.7750 0.200 0.800
#> GSM550859 2 0.7299 0.7713 0.204 0.796
#> GSM550862 2 0.7056 0.7823 0.192 0.808
#> GSM550865 2 0.0000 0.9028 0.000 1.000
#> GSM550868 2 0.0000 0.9028 0.000 1.000
#> GSM550869 1 0.8608 0.5424 0.716 0.284
#> GSM550870 2 0.0000 0.9028 0.000 1.000
#> GSM550871 1 0.2603 0.8973 0.956 0.044
#> GSM550872 2 0.0000 0.9028 0.000 1.000
#> GSM550873 2 0.6148 0.7706 0.152 0.848
#> GSM550874 2 0.0000 0.9028 0.000 1.000
#> GSM550876 1 0.0938 0.9208 0.988 0.012
#> GSM550877 2 0.0000 0.9028 0.000 1.000
#> GSM550878 1 0.0000 0.9272 1.000 0.000
#> GSM550879 2 0.6801 0.7925 0.180 0.820
#> GSM550882 1 0.0000 0.9272 1.000 0.000
#> GSM550888 1 0.0000 0.9272 1.000 0.000
#> GSM550890 2 0.0000 0.9028 0.000 1.000
#> GSM550891 1 0.0000 0.9272 1.000 0.000
#> GSM550892 2 0.1184 0.8959 0.016 0.984
#> GSM550893 2 0.0000 0.9028 0.000 1.000
#> GSM550895 2 0.0000 0.9028 0.000 1.000
#> GSM550896 2 0.0000 0.9028 0.000 1.000
#> GSM550898 2 0.7299 0.7713 0.204 0.796
#> GSM550899 2 0.0000 0.9028 0.000 1.000
#> GSM550900 2 0.0000 0.9028 0.000 1.000
#> GSM550901 2 0.0000 0.9028 0.000 1.000
#> GSM550902 1 0.0000 0.9272 1.000 0.000
#> GSM550904 1 0.0672 0.9224 0.992 0.008
#> GSM550908 1 0.0000 0.9272 1.000 0.000
#> GSM550912 2 0.0000 0.9028 0.000 1.000
#> GSM550914 2 0.0000 0.9028 0.000 1.000
#> GSM550918 2 0.0000 0.9028 0.000 1.000
#> GSM550922 1 0.6247 0.7865 0.844 0.156
#> GSM550923 1 0.0000 0.9272 1.000 0.000
#> GSM550925 2 0.0376 0.9011 0.004 0.996
#> GSM550802 2 0.0000 0.9028 0.000 1.000
#> GSM550812 2 0.3879 0.8494 0.076 0.924
#> GSM550831 2 0.7299 0.7713 0.204 0.796
#> GSM550847 2 0.7299 0.7713 0.204 0.796
#> GSM550860 1 0.0000 0.9272 1.000 0.000
#> GSM550875 2 0.9754 0.4315 0.408 0.592
#> GSM550880 2 0.0672 0.8995 0.008 0.992
#> GSM550881 1 0.0000 0.9272 1.000 0.000
#> GSM550883 1 0.0000 0.9272 1.000 0.000
#> GSM550884 2 0.6343 0.7606 0.160 0.840
#> GSM550910 1 0.0672 0.9232 0.992 0.008
#> GSM550916 2 0.7299 0.7713 0.204 0.796
#> GSM550920 1 0.0000 0.9272 1.000 0.000
cbind(get_classes(res, k = 3), get_membership(res, k = 3))
#> class entropy silhouette p1 p2 p3
#> GSM550785 1 0.0000 0.94940 1.000 0.000 0.000
#> GSM550786 3 0.0000 0.92489 0.000 0.000 1.000
#> GSM550788 2 0.0000 0.98277 0.000 1.000 0.000
#> GSM550789 2 0.0000 0.98277 0.000 1.000 0.000
#> GSM550790 1 0.0000 0.94940 1.000 0.000 0.000
#> GSM550791 1 0.0000 0.94940 1.000 0.000 0.000
#> GSM550792 2 0.0892 0.96446 0.020 0.980 0.000
#> GSM550796 2 0.0000 0.98277 0.000 1.000 0.000
#> GSM550797 2 0.0000 0.98277 0.000 1.000 0.000
#> GSM550799 3 0.0000 0.92489 0.000 0.000 1.000
#> GSM550800 2 0.0000 0.98277 0.000 1.000 0.000
#> GSM550801 2 0.0000 0.98277 0.000 1.000 0.000
#> GSM550804 2 0.0000 0.98277 0.000 1.000 0.000
#> GSM550806 3 0.0000 0.92489 0.000 0.000 1.000
#> GSM550807 2 0.0000 0.98277 0.000 1.000 0.000
#> GSM550808 2 0.0000 0.98277 0.000 1.000 0.000
#> GSM550809 1 0.0000 0.94940 1.000 0.000 0.000
#> GSM550810 2 0.0000 0.98277 0.000 1.000 0.000
#> GSM550811 1 0.7133 0.64534 0.712 0.096 0.192
#> GSM550813 2 0.0000 0.98277 0.000 1.000 0.000
#> GSM550814 2 0.0000 0.98277 0.000 1.000 0.000
#> GSM550815 2 0.0000 0.98277 0.000 1.000 0.000
#> GSM550816 2 0.0000 0.98277 0.000 1.000 0.000
#> GSM550817 3 0.0000 0.92489 0.000 0.000 1.000
#> GSM550818 3 0.0000 0.92489 0.000 0.000 1.000
#> GSM550819 2 0.0237 0.97961 0.000 0.996 0.004
#> GSM550820 1 0.0000 0.94940 1.000 0.000 0.000
#> GSM550821 2 0.1031 0.96179 0.000 0.976 0.024
#> GSM550822 2 0.0000 0.98277 0.000 1.000 0.000
#> GSM550826 1 0.6309 -0.00132 0.500 0.000 0.500
#> GSM550832 2 0.0000 0.98277 0.000 1.000 0.000
#> GSM550833 2 0.0000 0.98277 0.000 1.000 0.000
#> GSM550835 3 0.5760 0.55366 0.000 0.328 0.672
#> GSM550836 3 0.0000 0.92489 0.000 0.000 1.000
#> GSM550837 2 0.0000 0.98277 0.000 1.000 0.000
#> GSM550838 1 0.0000 0.94940 1.000 0.000 0.000
#> GSM550841 3 0.0000 0.92489 0.000 0.000 1.000
#> GSM550842 2 0.0000 0.98277 0.000 1.000 0.000
#> GSM550846 2 0.4452 0.75535 0.192 0.808 0.000
#> GSM550849 1 0.1860 0.90850 0.948 0.052 0.000
#> GSM550850 1 0.0000 0.94940 1.000 0.000 0.000
#> GSM550851 2 0.0000 0.98277 0.000 1.000 0.000
#> GSM550852 2 0.0000 0.98277 0.000 1.000 0.000
#> GSM550853 2 0.0000 0.98277 0.000 1.000 0.000
#> GSM550855 2 0.0000 0.98277 0.000 1.000 0.000
#> GSM550856 2 0.0000 0.98277 0.000 1.000 0.000
#> GSM550861 2 0.0000 0.98277 0.000 1.000 0.000
#> GSM550863 1 0.0000 0.94940 1.000 0.000 0.000
#> GSM550864 2 0.0000 0.98277 0.000 1.000 0.000
#> GSM550866 2 0.0237 0.97947 0.004 0.996 0.000
#> GSM550867 1 0.0000 0.94940 1.000 0.000 0.000
#> GSM550885 1 0.0000 0.94940 1.000 0.000 0.000
#> GSM550886 3 0.4842 0.72377 0.000 0.224 0.776
#> GSM550887 2 0.0000 0.98277 0.000 1.000 0.000
#> GSM550889 1 0.2165 0.89719 0.936 0.064 0.000
#> GSM550894 2 0.0000 0.98277 0.000 1.000 0.000
#> GSM550897 1 0.0000 0.94940 1.000 0.000 0.000
#> GSM550903 2 0.0000 0.98277 0.000 1.000 0.000
#> GSM550905 2 0.0000 0.98277 0.000 1.000 0.000
#> GSM550906 2 0.0000 0.98277 0.000 1.000 0.000
#> GSM550907 3 0.0000 0.92489 0.000 0.000 1.000
#> GSM550909 2 0.4002 0.79135 0.000 0.840 0.160
#> GSM550911 3 0.0000 0.92489 0.000 0.000 1.000
#> GSM550913 2 0.0000 0.98277 0.000 1.000 0.000
#> GSM550915 1 0.0237 0.94681 0.996 0.004 0.000
#> GSM550917 2 0.0000 0.98277 0.000 1.000 0.000
#> GSM550919 1 0.2537 0.88069 0.920 0.080 0.000
#> GSM550921 3 0.0000 0.92489 0.000 0.000 1.000
#> GSM550924 3 0.5650 0.58663 0.000 0.312 0.688
#> GSM550926 2 0.0000 0.98277 0.000 1.000 0.000
#> GSM550927 2 0.0000 0.98277 0.000 1.000 0.000
#> GSM550787 3 0.8188 0.31721 0.372 0.080 0.548
#> GSM550793 3 0.0747 0.91349 0.016 0.000 0.984
#> GSM550794 2 0.5465 0.59923 0.288 0.712 0.000
#> GSM550795 1 0.0000 0.94940 1.000 0.000 0.000
#> GSM550798 1 0.0237 0.94686 0.996 0.000 0.004
#> GSM550803 1 0.0000 0.94940 1.000 0.000 0.000
#> GSM550805 1 0.4994 0.76860 0.816 0.024 0.160
#> GSM550823 2 0.1964 0.92642 0.056 0.944 0.000
#> GSM550824 1 0.0000 0.94940 1.000 0.000 0.000
#> GSM550825 3 0.2796 0.84713 0.092 0.000 0.908
#> GSM550827 1 0.1031 0.93160 0.976 0.024 0.000
#> GSM550828 1 0.0000 0.94940 1.000 0.000 0.000
#> GSM550829 1 0.5968 0.42112 0.636 0.000 0.364
#> GSM550830 1 0.5650 0.56095 0.688 0.312 0.000
#> GSM550834 1 0.0000 0.94940 1.000 0.000 0.000
#> GSM550839 3 0.4062 0.79372 0.000 0.164 0.836
#> GSM550840 1 0.0000 0.94940 1.000 0.000 0.000
#> GSM550843 3 0.0000 0.92489 0.000 0.000 1.000
#> GSM550844 1 0.0000 0.94940 1.000 0.000 0.000
#> GSM550845 2 0.0000 0.98277 0.000 1.000 0.000
#> GSM550848 1 0.1529 0.91915 0.960 0.040 0.000
#> GSM550854 1 0.0000 0.94940 1.000 0.000 0.000
#> GSM550857 3 0.0000 0.92489 0.000 0.000 1.000
#> GSM550858 1 0.0000 0.94940 1.000 0.000 0.000
#> GSM550859 1 0.0000 0.94940 1.000 0.000 0.000
#> GSM550862 1 0.0000 0.94940 1.000 0.000 0.000
#> GSM550865 1 0.1031 0.93260 0.976 0.024 0.000
#> GSM550868 1 0.0000 0.94940 1.000 0.000 0.000
#> GSM550869 3 0.9046 0.34622 0.332 0.152 0.516
#> GSM550870 2 0.0000 0.98277 0.000 1.000 0.000
#> GSM550871 3 0.5254 0.66775 0.000 0.264 0.736
#> GSM550872 1 0.0000 0.94940 1.000 0.000 0.000
#> GSM550873 2 0.0000 0.98277 0.000 1.000 0.000
#> GSM550874 2 0.0000 0.98277 0.000 1.000 0.000
#> GSM550876 3 0.0000 0.92489 0.000 0.000 1.000
#> GSM550877 2 0.0000 0.98277 0.000 1.000 0.000
#> GSM550878 3 0.0000 0.92489 0.000 0.000 1.000
#> GSM550879 1 0.0000 0.94940 1.000 0.000 0.000
#> GSM550882 3 0.0000 0.92489 0.000 0.000 1.000
#> GSM550888 3 0.0000 0.92489 0.000 0.000 1.000
#> GSM550890 1 0.0000 0.94940 1.000 0.000 0.000
#> GSM550891 3 0.0000 0.92489 0.000 0.000 1.000
#> GSM550892 1 0.0000 0.94940 1.000 0.000 0.000
#> GSM550893 2 0.0000 0.98277 0.000 1.000 0.000
#> GSM550895 2 0.0747 0.96868 0.016 0.984 0.000
#> GSM550896 2 0.0000 0.98277 0.000 1.000 0.000
#> GSM550898 1 0.0000 0.94940 1.000 0.000 0.000
#> GSM550899 2 0.0000 0.98277 0.000 1.000 0.000
#> GSM550900 1 0.0237 0.94681 0.996 0.004 0.000
#> GSM550901 1 0.0000 0.94940 1.000 0.000 0.000
#> GSM550902 1 0.5678 0.53294 0.684 0.000 0.316
#> GSM550904 1 0.0000 0.94940 1.000 0.000 0.000
#> GSM550908 3 0.0000 0.92489 0.000 0.000 1.000
#> GSM550912 2 0.0000 0.98277 0.000 1.000 0.000
#> GSM550914 1 0.3619 0.80814 0.864 0.136 0.000
#> GSM550918 2 0.0000 0.98277 0.000 1.000 0.000
#> GSM550922 3 0.0000 0.92489 0.000 0.000 1.000
#> GSM550923 1 0.0000 0.94940 1.000 0.000 0.000
#> GSM550925 1 0.0000 0.94940 1.000 0.000 0.000
#> GSM550802 2 0.0000 0.98277 0.000 1.000 0.000
#> GSM550812 2 0.1031 0.96184 0.000 0.976 0.024
#> GSM550831 1 0.0000 0.94940 1.000 0.000 0.000
#> GSM550847 1 0.0000 0.94940 1.000 0.000 0.000
#> GSM550860 3 0.0000 0.92489 0.000 0.000 1.000
#> GSM550875 1 0.0424 0.94411 0.992 0.000 0.008
#> GSM550880 1 0.0000 0.94940 1.000 0.000 0.000
#> GSM550881 3 0.0000 0.92489 0.000 0.000 1.000
#> GSM550883 3 0.0000 0.92489 0.000 0.000 1.000
#> GSM550884 2 0.2200 0.92589 0.004 0.940 0.056
#> GSM550910 3 0.0237 0.92254 0.000 0.004 0.996
#> GSM550916 1 0.0000 0.94940 1.000 0.000 0.000
#> GSM550920 3 0.0000 0.92489 0.000 0.000 1.000
cbind(get_classes(res, k = 4), get_membership(res, k = 4))
#> class entropy silhouette p1 p2 p3 p4
#> GSM550785 4 0.4431 0.4941 0.304 0.000 0.000 0.696
#> GSM550786 3 0.4054 0.7649 0.000 0.016 0.796 0.188
#> GSM550788 2 0.4770 0.6025 0.288 0.700 0.000 0.012
#> GSM550789 2 0.3726 0.6823 0.212 0.788 0.000 0.000
#> GSM550790 1 0.4356 0.3333 0.708 0.000 0.000 0.292
#> GSM550791 1 0.4382 0.4647 0.704 0.000 0.000 0.296
#> GSM550792 1 0.3668 0.5249 0.808 0.188 0.000 0.004
#> GSM550796 2 0.0707 0.7933 0.020 0.980 0.000 0.000
#> GSM550797 2 0.4250 0.6173 0.276 0.724 0.000 0.000
#> GSM550799 3 0.4648 0.8013 0.088 0.020 0.820 0.072
#> GSM550800 2 0.6546 0.6521 0.172 0.636 0.000 0.192
#> GSM550801 2 0.1792 0.7846 0.068 0.932 0.000 0.000
#> GSM550804 2 0.4356 0.7037 0.000 0.708 0.000 0.292
#> GSM550806 3 0.1389 0.8747 0.000 0.000 0.952 0.048
#> GSM550807 2 0.2647 0.7609 0.120 0.880 0.000 0.000
#> GSM550808 2 0.4222 0.6157 0.272 0.728 0.000 0.000
#> GSM550809 1 0.3873 0.4464 0.772 0.000 0.000 0.228
#> GSM550810 2 0.1474 0.7871 0.052 0.948 0.000 0.000
#> GSM550811 1 0.2081 0.5897 0.916 0.084 0.000 0.000
#> GSM550813 2 0.2805 0.7782 0.100 0.888 0.000 0.012
#> GSM550814 2 0.1174 0.7980 0.012 0.968 0.000 0.020
#> GSM550815 2 0.3243 0.7766 0.036 0.876 0.000 0.088
#> GSM550816 2 0.2888 0.7714 0.124 0.872 0.000 0.004
#> GSM550817 3 0.0000 0.8859 0.000 0.000 1.000 0.000
#> GSM550818 3 0.0000 0.8859 0.000 0.000 1.000 0.000
#> GSM550819 2 0.4866 0.5862 0.000 0.596 0.000 0.404
#> GSM550820 4 0.4454 0.6117 0.308 0.000 0.000 0.692
#> GSM550821 2 0.4222 0.7175 0.000 0.728 0.000 0.272
#> GSM550822 2 0.2401 0.7811 0.004 0.904 0.000 0.092
#> GSM550826 4 0.3436 0.5837 0.036 0.008 0.080 0.876
#> GSM550832 2 0.1042 0.7977 0.008 0.972 0.000 0.020
#> GSM550833 2 0.4679 0.4922 0.352 0.648 0.000 0.000
#> GSM550835 2 0.7466 0.1797 0.388 0.436 0.176 0.000
#> GSM550836 3 0.2345 0.8302 0.100 0.000 0.900 0.000
#> GSM550837 2 0.6943 0.4476 0.348 0.540 0.004 0.108
#> GSM550838 1 0.4328 0.4947 0.748 0.000 0.008 0.244
#> GSM550841 3 0.2198 0.8599 0.000 0.008 0.920 0.072
#> GSM550842 2 0.0657 0.7946 0.012 0.984 0.004 0.000
#> GSM550846 2 0.6928 0.2728 0.116 0.512 0.000 0.372
#> GSM550849 1 0.2266 0.5911 0.912 0.084 0.000 0.004
#> GSM550850 1 0.1389 0.6062 0.952 0.000 0.000 0.048
#> GSM550851 2 0.4239 0.7633 0.032 0.812 0.004 0.152
#> GSM550852 2 0.4008 0.7097 0.244 0.756 0.000 0.000
#> GSM550853 2 0.4423 0.7560 0.040 0.792 0.000 0.168
#> GSM550855 2 0.0657 0.7949 0.012 0.984 0.000 0.004
#> GSM550856 2 0.2266 0.7878 0.084 0.912 0.000 0.004
#> GSM550861 2 0.0376 0.7958 0.004 0.992 0.000 0.004
#> GSM550863 4 0.1109 0.6324 0.028 0.004 0.000 0.968
#> GSM550864 2 0.1722 0.7992 0.008 0.944 0.000 0.048
#> GSM550866 2 0.1929 0.8017 0.024 0.940 0.000 0.036
#> GSM550867 1 0.4925 -0.0715 0.572 0.000 0.000 0.428
#> GSM550885 4 0.4713 0.4075 0.360 0.000 0.000 0.640
#> GSM550886 3 0.5371 0.4152 0.000 0.364 0.616 0.020
#> GSM550887 2 0.2216 0.7806 0.000 0.908 0.000 0.092
#> GSM550889 4 0.5142 0.6283 0.192 0.064 0.000 0.744
#> GSM550894 2 0.1211 0.7969 0.000 0.960 0.000 0.040
#> GSM550897 4 0.0592 0.6317 0.016 0.000 0.000 0.984
#> GSM550903 2 0.3649 0.7460 0.000 0.796 0.000 0.204
#> GSM550905 2 0.3479 0.7675 0.012 0.840 0.000 0.148
#> GSM550906 2 0.2469 0.7800 0.000 0.892 0.000 0.108
#> GSM550907 3 0.0000 0.8859 0.000 0.000 1.000 0.000
#> GSM550909 2 0.3840 0.7639 0.116 0.848 0.012 0.024
#> GSM550911 3 0.0000 0.8859 0.000 0.000 1.000 0.000
#> GSM550913 2 0.0592 0.7967 0.000 0.984 0.000 0.016
#> GSM550915 4 0.4635 0.6232 0.124 0.080 0.000 0.796
#> GSM550917 2 0.3037 0.7836 0.076 0.888 0.000 0.036
#> GSM550919 4 0.5067 0.5942 0.116 0.116 0.000 0.768
#> GSM550921 3 0.0000 0.8859 0.000 0.000 1.000 0.000
#> GSM550924 4 0.8639 0.3033 0.112 0.228 0.140 0.520
#> GSM550926 2 0.4030 0.7639 0.072 0.836 0.000 0.092
#> GSM550927 2 0.2469 0.7808 0.000 0.892 0.000 0.108
#> GSM550787 4 0.7416 0.3024 0.060 0.112 0.200 0.628
#> GSM550793 3 0.1792 0.8518 0.068 0.000 0.932 0.000
#> GSM550794 2 0.6317 0.4948 0.280 0.624 0.000 0.096
#> GSM550795 1 0.0469 0.6112 0.988 0.000 0.000 0.012
#> GSM550798 1 0.5143 0.1028 0.540 0.000 0.004 0.456
#> GSM550803 1 0.4804 0.1076 0.616 0.000 0.000 0.384
#> GSM550805 1 0.4667 0.5778 0.796 0.096 0.000 0.108
#> GSM550823 2 0.7020 0.2303 0.124 0.500 0.000 0.376
#> GSM550824 4 0.4907 0.4586 0.420 0.000 0.000 0.580
#> GSM550825 4 0.5143 0.1200 0.004 0.000 0.456 0.540
#> GSM550827 4 0.4888 0.6131 0.124 0.096 0.000 0.780
#> GSM550828 4 0.4134 0.6453 0.260 0.000 0.000 0.740
#> GSM550829 4 0.6613 0.4086 0.172 0.000 0.200 0.628
#> GSM550830 1 0.6238 0.4768 0.652 0.236 0.000 0.112
#> GSM550834 1 0.0000 0.6088 1.000 0.000 0.000 0.000
#> GSM550839 1 0.7884 -0.0318 0.360 0.284 0.356 0.000
#> GSM550840 1 0.1118 0.6105 0.964 0.000 0.000 0.036
#> GSM550843 3 0.2149 0.8547 0.000 0.000 0.912 0.088
#> GSM550844 4 0.4277 0.6340 0.280 0.000 0.000 0.720
#> GSM550845 2 0.4730 0.6343 0.000 0.636 0.000 0.364
#> GSM550848 4 0.4700 0.6210 0.124 0.084 0.000 0.792
#> GSM550854 1 0.4985 -0.1789 0.532 0.000 0.000 0.468
#> GSM550857 3 0.1389 0.8714 0.000 0.000 0.952 0.048
#> GSM550858 4 0.4008 0.5621 0.244 0.000 0.000 0.756
#> GSM550859 4 0.4866 0.4893 0.404 0.000 0.000 0.596
#> GSM550862 4 0.3444 0.6296 0.184 0.000 0.000 0.816
#> GSM550865 4 0.0657 0.6223 0.004 0.012 0.000 0.984
#> GSM550868 4 0.5712 0.5397 0.308 0.048 0.000 0.644
#> GSM550869 1 0.9552 0.2352 0.388 0.236 0.140 0.236
#> GSM550870 2 0.3649 0.7445 0.000 0.796 0.000 0.204
#> GSM550871 3 0.6575 0.2981 0.092 0.348 0.560 0.000
#> GSM550872 1 0.5288 0.2309 0.520 0.008 0.000 0.472
#> GSM550873 2 0.2799 0.7744 0.108 0.884 0.000 0.008
#> GSM550874 2 0.4356 0.6515 0.292 0.708 0.000 0.000
#> GSM550876 3 0.2973 0.8238 0.000 0.096 0.884 0.020
#> GSM550877 2 0.4277 0.7102 0.000 0.720 0.000 0.280
#> GSM550878 3 0.0000 0.8859 0.000 0.000 1.000 0.000
#> GSM550879 4 0.2011 0.6388 0.080 0.000 0.000 0.920
#> GSM550882 3 0.0000 0.8859 0.000 0.000 1.000 0.000
#> GSM550888 3 0.1302 0.8733 0.000 0.000 0.956 0.044
#> GSM550890 4 0.0921 0.6117 0.000 0.028 0.000 0.972
#> GSM550891 3 0.0000 0.8859 0.000 0.000 1.000 0.000
#> GSM550892 4 0.1637 0.6487 0.060 0.000 0.000 0.940
#> GSM550893 2 0.3958 0.7624 0.052 0.836 0.000 0.112
#> GSM550895 2 0.5018 0.7266 0.144 0.768 0.000 0.088
#> GSM550896 2 0.3176 0.7827 0.084 0.880 0.000 0.036
#> GSM550898 4 0.4776 0.5300 0.376 0.000 0.000 0.624
#> GSM550899 2 0.3308 0.7823 0.036 0.872 0.000 0.092
#> GSM550900 4 0.4728 0.6547 0.216 0.032 0.000 0.752
#> GSM550901 4 0.3972 0.6577 0.204 0.008 0.000 0.788
#> GSM550902 4 0.0844 0.6272 0.004 0.004 0.012 0.980
#> GSM550904 4 0.4155 0.6516 0.240 0.004 0.000 0.756
#> GSM550908 3 0.0000 0.8859 0.000 0.000 1.000 0.000
#> GSM550912 2 0.4245 0.7502 0.116 0.820 0.000 0.064
#> GSM550914 4 0.1302 0.5992 0.000 0.044 0.000 0.956
#> GSM550918 2 0.4746 0.6313 0.000 0.632 0.000 0.368
#> GSM550922 3 0.2773 0.8091 0.000 0.116 0.880 0.004
#> GSM550923 4 0.4925 0.4482 0.428 0.000 0.000 0.572
#> GSM550925 4 0.4595 0.6466 0.176 0.044 0.000 0.780
#> GSM550802 1 0.4800 0.1894 0.656 0.340 0.000 0.004
#> GSM550812 2 0.4295 0.7052 0.240 0.752 0.000 0.008
#> GSM550831 1 0.0817 0.6113 0.976 0.000 0.000 0.024
#> GSM550847 4 0.4898 0.4678 0.416 0.000 0.000 0.584
#> GSM550860 3 0.4454 0.6520 0.000 0.000 0.692 0.308
#> GSM550875 1 0.6454 0.1231 0.544 0.076 0.000 0.380
#> GSM550880 1 0.3024 0.5435 0.852 0.000 0.000 0.148
#> GSM550881 3 0.0188 0.8851 0.000 0.000 0.996 0.004
#> GSM550883 3 0.0000 0.8859 0.000 0.000 1.000 0.000
#> GSM550884 4 0.7122 0.1862 0.116 0.384 0.004 0.496
#> GSM550910 3 0.6780 0.5633 0.000 0.164 0.604 0.232
#> GSM550916 4 0.4193 0.6405 0.268 0.000 0.000 0.732
#> GSM550920 3 0.0657 0.8818 0.000 0.012 0.984 0.004
cbind(get_classes(res, k = 5), get_membership(res, k = 5))
#> class entropy silhouette p1 p2 p3 p4 p5
#> GSM550785 1 0.5599 0.5330 0.620 0.000 0.000 0.260 0.120
#> GSM550786 3 0.5990 0.4574 0.004 0.148 0.592 0.256 0.000
#> GSM550788 5 0.6763 -0.2308 0.000 0.280 0.000 0.324 0.396
#> GSM550789 2 0.3016 0.6809 0.000 0.848 0.000 0.020 0.132
#> GSM550790 5 0.4557 0.0640 0.476 0.000 0.000 0.008 0.516
#> GSM550791 5 0.6663 0.2201 0.244 0.012 0.000 0.224 0.520
#> GSM550792 5 0.6079 0.4158 0.196 0.208 0.000 0.004 0.592
#> GSM550796 2 0.1082 0.7063 0.000 0.964 0.000 0.028 0.008
#> GSM550797 2 0.3280 0.6741 0.004 0.824 0.000 0.012 0.160
#> GSM550799 3 0.5541 0.6050 0.000 0.024 0.696 0.132 0.148
#> GSM550800 4 0.6452 0.3018 0.000 0.232 0.000 0.500 0.268
#> GSM550801 2 0.2359 0.7030 0.000 0.904 0.000 0.036 0.060
#> GSM550804 2 0.5396 0.5286 0.080 0.636 0.000 0.280 0.004
#> GSM550806 3 0.1121 0.8055 0.000 0.000 0.956 0.044 0.000
#> GSM550807 2 0.3875 0.6508 0.000 0.792 0.000 0.048 0.160
#> GSM550808 2 0.3246 0.6619 0.000 0.808 0.000 0.008 0.184
#> GSM550809 5 0.4924 0.1650 0.420 0.000 0.000 0.028 0.552
#> GSM550810 2 0.2046 0.7055 0.000 0.916 0.000 0.016 0.068
#> GSM550811 5 0.4943 0.5305 0.200 0.076 0.000 0.008 0.716
#> GSM550813 2 0.5439 0.6352 0.136 0.716 0.000 0.112 0.036
#> GSM550814 2 0.4338 0.6086 0.036 0.760 0.000 0.192 0.012
#> GSM550815 2 0.3521 0.6716 0.000 0.820 0.000 0.140 0.040
#> GSM550816 2 0.4437 0.6699 0.148 0.780 0.000 0.044 0.028
#> GSM550817 3 0.1173 0.8085 0.004 0.020 0.964 0.012 0.000
#> GSM550818 3 0.1372 0.8053 0.004 0.024 0.956 0.016 0.000
#> GSM550819 4 0.5030 0.3170 0.072 0.236 0.004 0.688 0.000
#> GSM550820 1 0.3072 0.6216 0.872 0.004 0.004 0.040 0.080
#> GSM550821 2 0.5389 0.5578 0.056 0.656 0.012 0.272 0.004
#> GSM550822 2 0.3218 0.6798 0.024 0.844 0.000 0.128 0.004
#> GSM550826 1 0.6097 0.5005 0.596 0.052 0.016 0.312 0.024
#> GSM550832 2 0.3076 0.7031 0.088 0.868 0.000 0.036 0.008
#> GSM550833 2 0.5264 0.3494 0.000 0.556 0.000 0.052 0.392
#> GSM550835 5 0.7734 0.1213 0.000 0.260 0.252 0.068 0.420
#> GSM550836 3 0.3074 0.6682 0.000 0.000 0.804 0.000 0.196
#> GSM550837 2 0.6507 0.2202 0.000 0.432 0.000 0.192 0.376
#> GSM550838 5 0.5791 0.3542 0.196 0.000 0.000 0.188 0.616
#> GSM550841 3 0.5389 0.5240 0.004 0.260 0.648 0.088 0.000
#> GSM550842 2 0.0740 0.7106 0.008 0.980 0.000 0.008 0.004
#> GSM550846 2 0.6422 0.2198 0.428 0.468 0.004 0.068 0.032
#> GSM550849 5 0.5203 0.4678 0.264 0.072 0.000 0.004 0.660
#> GSM550850 5 0.2674 0.5651 0.140 0.000 0.000 0.004 0.856
#> GSM550851 2 0.3759 0.6458 0.000 0.764 0.000 0.220 0.016
#> GSM550852 2 0.5798 0.6098 0.088 0.684 0.000 0.052 0.176
#> GSM550853 2 0.6288 0.2327 0.000 0.472 0.000 0.372 0.156
#> GSM550855 2 0.4100 0.6325 0.008 0.792 0.000 0.148 0.052
#> GSM550856 2 0.5683 0.5847 0.064 0.700 0.000 0.160 0.076
#> GSM550861 2 0.1743 0.7121 0.028 0.940 0.000 0.028 0.004
#> GSM550863 4 0.3209 0.4281 0.180 0.000 0.000 0.812 0.008
#> GSM550864 2 0.1525 0.7111 0.036 0.948 0.000 0.012 0.004
#> GSM550866 4 0.6170 0.3037 0.004 0.384 0.000 0.492 0.120
#> GSM550867 1 0.4551 0.2888 0.616 0.000 0.000 0.016 0.368
#> GSM550885 1 0.5687 0.5273 0.628 0.000 0.000 0.208 0.164
#> GSM550886 3 0.6047 0.1611 0.080 0.376 0.528 0.016 0.000
#> GSM550887 2 0.3171 0.6735 0.000 0.816 0.000 0.176 0.008
#> GSM550889 4 0.5816 0.5005 0.160 0.012 0.000 0.648 0.180
#> GSM550894 2 0.3120 0.7015 0.084 0.864 0.000 0.048 0.004
#> GSM550897 4 0.3280 0.4515 0.184 0.004 0.000 0.808 0.004
#> GSM550903 2 0.4178 0.6181 0.028 0.748 0.000 0.220 0.004
#> GSM550905 2 0.5003 0.5992 0.036 0.700 0.012 0.244 0.008
#> GSM550906 2 0.3750 0.6463 0.000 0.756 0.000 0.232 0.012
#> GSM550907 3 0.0324 0.8140 0.004 0.000 0.992 0.004 0.000
#> GSM550909 2 0.5524 0.6189 0.200 0.704 0.016 0.052 0.028
#> GSM550911 3 0.0290 0.8139 0.000 0.000 0.992 0.008 0.000
#> GSM550913 2 0.1757 0.7098 0.048 0.936 0.000 0.012 0.004
#> GSM550915 1 0.4697 0.5256 0.764 0.152 0.000 0.052 0.032
#> GSM550917 2 0.4141 0.6736 0.152 0.788 0.000 0.052 0.008
#> GSM550919 1 0.4271 0.5222 0.768 0.180 0.000 0.044 0.008
#> GSM550921 3 0.0000 0.8132 0.000 0.000 1.000 0.000 0.000
#> GSM550924 1 0.6348 0.2688 0.580 0.304 0.064 0.048 0.004
#> GSM550926 2 0.6442 0.0525 0.156 0.460 0.000 0.380 0.004
#> GSM550927 2 0.3264 0.6751 0.020 0.836 0.000 0.140 0.004
#> GSM550787 4 0.7816 0.0163 0.188 0.048 0.336 0.412 0.016
#> GSM550793 3 0.1911 0.7882 0.028 0.000 0.932 0.004 0.036
#> GSM550794 2 0.7417 0.3214 0.248 0.476 0.000 0.056 0.220
#> GSM550795 5 0.1124 0.5672 0.036 0.000 0.000 0.004 0.960
#> GSM550798 5 0.6361 -0.1128 0.424 0.000 0.004 0.140 0.432
#> GSM550803 1 0.4815 0.0633 0.524 0.000 0.000 0.020 0.456
#> GSM550805 5 0.6766 0.3566 0.188 0.068 0.004 0.132 0.608
#> GSM550823 4 0.6475 0.4993 0.192 0.096 0.000 0.628 0.084
#> GSM550824 1 0.3531 0.6025 0.816 0.000 0.000 0.036 0.148
#> GSM550825 3 0.5949 0.3906 0.172 0.000 0.588 0.240 0.000
#> GSM550827 1 0.4985 0.4857 0.744 0.124 0.000 0.112 0.020
#> GSM550828 1 0.1582 0.6390 0.944 0.000 0.000 0.028 0.028
#> GSM550829 1 0.5538 0.5738 0.688 0.000 0.024 0.188 0.100
#> GSM550830 4 0.6539 0.2707 0.080 0.040 0.000 0.460 0.420
#> GSM550834 5 0.1410 0.5803 0.060 0.000 0.000 0.000 0.940
#> GSM550839 5 0.7660 -0.0771 0.000 0.052 0.344 0.244 0.360
#> GSM550840 5 0.2291 0.5358 0.036 0.000 0.000 0.056 0.908
#> GSM550843 3 0.1732 0.7846 0.000 0.000 0.920 0.080 0.000
#> GSM550844 1 0.3827 0.6006 0.816 0.004 0.000 0.112 0.068
#> GSM550845 4 0.3639 0.5145 0.044 0.144 0.000 0.812 0.000
#> GSM550848 1 0.4513 0.4999 0.744 0.200 0.000 0.048 0.008
#> GSM550854 1 0.4747 0.3300 0.620 0.000 0.000 0.028 0.352
#> GSM550857 3 0.2208 0.7715 0.020 0.000 0.908 0.072 0.000
#> GSM550858 1 0.5158 0.5541 0.656 0.000 0.000 0.264 0.080
#> GSM550859 1 0.3452 0.6020 0.820 0.000 0.000 0.032 0.148
#> GSM550862 4 0.5237 -0.2224 0.468 0.000 0.000 0.488 0.044
#> GSM550865 4 0.2722 0.4956 0.120 0.004 0.000 0.868 0.008
#> GSM550868 4 0.6604 0.4432 0.276 0.036 0.000 0.560 0.128
#> GSM550869 4 0.7599 0.4162 0.144 0.028 0.064 0.540 0.224
#> GSM550870 2 0.4341 0.5324 0.000 0.628 0.000 0.364 0.008
#> GSM550871 4 0.7839 0.4154 0.048 0.096 0.228 0.536 0.092
#> GSM550872 4 0.4977 0.4179 0.052 0.008 0.000 0.684 0.256
#> GSM550873 2 0.4643 0.6695 0.144 0.768 0.000 0.064 0.024
#> GSM550874 4 0.6901 0.2227 0.004 0.268 0.000 0.364 0.364
#> GSM550876 3 0.5184 0.0692 0.004 0.032 0.508 0.456 0.000
#> GSM550877 4 0.3519 0.4435 0.008 0.216 0.000 0.776 0.000
#> GSM550878 3 0.0162 0.8128 0.000 0.000 0.996 0.004 0.000
#> GSM550879 1 0.4284 0.5887 0.736 0.000 0.000 0.224 0.040
#> GSM550882 3 0.3395 0.5943 0.000 0.000 0.764 0.236 0.000
#> GSM550888 3 0.0290 0.8139 0.000 0.000 0.992 0.008 0.000
#> GSM550890 1 0.5640 0.4671 0.592 0.104 0.000 0.304 0.000
#> GSM550891 3 0.0000 0.8132 0.000 0.000 1.000 0.000 0.000
#> GSM550892 4 0.4109 0.3481 0.288 0.000 0.000 0.700 0.012
#> GSM550893 4 0.6038 0.3662 0.120 0.328 0.000 0.548 0.004
#> GSM550895 4 0.6941 0.4836 0.144 0.140 0.000 0.596 0.120
#> GSM550896 4 0.6618 0.3103 0.112 0.344 0.000 0.512 0.032
#> GSM550898 1 0.3339 0.6107 0.836 0.000 0.000 0.040 0.124
#> GSM550899 2 0.3648 0.6770 0.156 0.812 0.000 0.024 0.008
#> GSM550900 4 0.5878 0.4841 0.244 0.012 0.000 0.624 0.120
#> GSM550901 1 0.2703 0.6156 0.896 0.060 0.000 0.024 0.020
#> GSM550902 1 0.4791 0.4566 0.616 0.008 0.016 0.360 0.000
#> GSM550904 1 0.1818 0.6333 0.932 0.000 0.000 0.044 0.024
#> GSM550908 3 0.0162 0.8141 0.000 0.000 0.996 0.004 0.000
#> GSM550912 2 0.4610 0.6496 0.176 0.752 0.000 0.060 0.012
#> GSM550914 1 0.6366 0.2360 0.440 0.164 0.000 0.396 0.000
#> GSM550918 2 0.5828 0.4944 0.128 0.608 0.000 0.260 0.004
#> GSM550922 2 0.5144 0.1216 0.024 0.520 0.448 0.008 0.000
#> GSM550923 1 0.3284 0.5972 0.828 0.000 0.000 0.024 0.148
#> GSM550925 1 0.4660 0.5148 0.752 0.044 0.000 0.180 0.024
#> GSM550802 5 0.4059 0.3871 0.008 0.072 0.000 0.116 0.804
#> GSM550812 2 0.7595 0.3616 0.160 0.472 0.000 0.092 0.276
#> GSM550831 5 0.2020 0.5795 0.100 0.000 0.000 0.000 0.900
#> GSM550847 1 0.3970 0.5890 0.788 0.000 0.000 0.056 0.156
#> GSM550860 4 0.3496 0.4933 0.040 0.000 0.124 0.832 0.004
#> GSM550875 4 0.7231 0.2873 0.196 0.028 0.004 0.456 0.316
#> GSM550880 5 0.4423 0.4311 0.296 0.012 0.000 0.008 0.684
#> GSM550881 3 0.0324 0.8137 0.004 0.000 0.992 0.004 0.000
#> GSM550883 3 0.0162 0.8128 0.000 0.000 0.996 0.004 0.000
#> GSM550884 4 0.6902 0.2993 0.404 0.136 0.000 0.428 0.032
#> GSM550910 3 0.7835 0.1077 0.056 0.300 0.384 0.256 0.004
#> GSM550916 1 0.3692 0.6010 0.812 0.000 0.000 0.136 0.052
#> GSM550920 3 0.1200 0.8051 0.008 0.016 0.964 0.012 0.000
cbind(get_classes(res, k = 6), get_membership(res, k = 6))
#> class entropy silhouette p1 p2 p3 p4 p5 p6
#> GSM550785 1 0.4674 0.5486 0.684 0.000 0.000 0.008 0.228 0.080
#> GSM550786 3 0.6010 0.2686 0.004 0.108 0.544 0.016 0.316 0.012
#> GSM550788 4 0.6222 0.2244 0.000 0.268 0.000 0.476 0.016 0.240
#> GSM550789 2 0.2313 0.6689 0.000 0.884 0.000 0.004 0.012 0.100
#> GSM550790 1 0.3620 0.4533 0.648 0.000 0.000 0.000 0.000 0.352
#> GSM550791 6 0.5948 -0.0979 0.392 0.004 0.000 0.008 0.144 0.452
#> GSM550792 6 0.6549 0.2200 0.172 0.372 0.004 0.008 0.020 0.424
#> GSM550796 2 0.1390 0.6726 0.000 0.948 0.000 0.032 0.016 0.004
#> GSM550797 2 0.2489 0.6617 0.000 0.860 0.000 0.000 0.012 0.128
#> GSM550799 3 0.4280 0.7106 0.000 0.032 0.792 0.020 0.096 0.060
#> GSM550800 4 0.6756 0.4022 0.000 0.152 0.000 0.524 0.188 0.136
#> GSM550801 2 0.1462 0.6763 0.000 0.936 0.000 0.008 0.000 0.056
#> GSM550804 5 0.4362 0.1221 0.020 0.392 0.000 0.004 0.584 0.000
#> GSM550806 3 0.0993 0.8131 0.000 0.000 0.964 0.012 0.024 0.000
#> GSM550807 2 0.2972 0.6641 0.000 0.852 0.000 0.024 0.016 0.108
#> GSM550808 2 0.4002 0.5614 0.000 0.704 0.000 0.000 0.036 0.260
#> GSM550809 6 0.5571 0.4104 0.140 0.004 0.000 0.004 0.284 0.568
#> GSM550810 2 0.2340 0.6756 0.000 0.896 0.000 0.004 0.044 0.056
#> GSM550811 6 0.3641 0.6523 0.048 0.048 0.008 0.004 0.052 0.840
#> GSM550813 2 0.5506 0.5816 0.116 0.708 0.000 0.080 0.056 0.040
#> GSM550814 2 0.5741 0.4835 0.060 0.624 0.000 0.252 0.040 0.024
#> GSM550815 2 0.4438 0.5793 0.000 0.720 0.000 0.020 0.208 0.052
#> GSM550816 2 0.5617 0.1641 0.032 0.500 0.000 0.008 0.412 0.048
#> GSM550817 3 0.2196 0.7835 0.000 0.004 0.884 0.004 0.108 0.000
#> GSM550818 3 0.1843 0.7994 0.000 0.004 0.912 0.004 0.080 0.000
#> GSM550819 5 0.4341 0.2316 0.016 0.024 0.000 0.284 0.676 0.000
#> GSM550820 1 0.5386 0.4902 0.600 0.012 0.000 0.004 0.288 0.096
#> GSM550821 5 0.3968 0.3241 0.008 0.280 0.004 0.004 0.700 0.004
#> GSM550822 2 0.4377 0.2277 0.000 0.540 0.000 0.024 0.436 0.000
#> GSM550826 5 0.4141 0.3794 0.228 0.004 0.016 0.004 0.732 0.016
#> GSM550832 2 0.3525 0.6406 0.076 0.836 0.000 0.032 0.052 0.004
#> GSM550833 2 0.5117 0.1731 0.000 0.508 0.000 0.032 0.028 0.432
#> GSM550835 6 0.6823 0.2074 0.000 0.288 0.212 0.032 0.016 0.452
#> GSM550836 3 0.3409 0.5559 0.000 0.000 0.700 0.000 0.000 0.300
#> GSM550837 2 0.6410 0.1441 0.000 0.448 0.004 0.036 0.144 0.368
#> GSM550838 6 0.4867 0.5098 0.080 0.004 0.004 0.004 0.232 0.676
#> GSM550841 5 0.5877 0.1134 0.000 0.172 0.380 0.004 0.444 0.000
#> GSM550842 2 0.3421 0.6302 0.004 0.804 0.004 0.028 0.160 0.000
#> GSM550846 5 0.6458 0.3626 0.172 0.132 0.000 0.040 0.604 0.052
#> GSM550849 6 0.3708 0.5699 0.172 0.032 0.000 0.008 0.004 0.784
#> GSM550850 6 0.1958 0.6342 0.100 0.000 0.000 0.000 0.004 0.896
#> GSM550851 2 0.3616 0.6092 0.000 0.780 0.000 0.024 0.184 0.012
#> GSM550852 2 0.4829 0.6169 0.020 0.744 0.000 0.064 0.036 0.136
#> GSM550853 2 0.7092 0.2293 0.000 0.416 0.000 0.216 0.276 0.092
#> GSM550855 2 0.5165 0.5621 0.040 0.676 0.000 0.228 0.040 0.016
#> GSM550856 2 0.5821 0.5030 0.060 0.620 0.000 0.248 0.020 0.052
#> GSM550861 2 0.1312 0.6744 0.012 0.956 0.000 0.008 0.020 0.004
#> GSM550863 5 0.4869 -0.2501 0.040 0.000 0.000 0.448 0.504 0.008
#> GSM550864 2 0.2846 0.6539 0.016 0.856 0.000 0.008 0.116 0.004
#> GSM550866 4 0.3086 0.6398 0.000 0.076 0.000 0.856 0.020 0.048
#> GSM550867 1 0.3833 0.5513 0.708 0.000 0.000 0.004 0.016 0.272
#> GSM550885 1 0.5828 0.4235 0.512 0.000 0.000 0.012 0.328 0.148
#> GSM550886 3 0.6752 0.3444 0.072 0.252 0.556 0.040 0.076 0.004
#> GSM550887 2 0.3694 0.5743 0.000 0.740 0.000 0.028 0.232 0.000
#> GSM550889 4 0.2151 0.6466 0.048 0.000 0.000 0.912 0.016 0.024
#> GSM550894 2 0.4147 0.6290 0.068 0.800 0.000 0.052 0.072 0.008
#> GSM550897 4 0.4764 0.5228 0.108 0.000 0.000 0.660 0.232 0.000
#> GSM550903 2 0.3627 0.5711 0.004 0.752 0.000 0.020 0.224 0.000
#> GSM550905 5 0.4225 -0.1415 0.000 0.480 0.000 0.008 0.508 0.004
#> GSM550906 2 0.4095 0.5715 0.000 0.724 0.000 0.060 0.216 0.000
#> GSM550907 3 0.1349 0.8112 0.000 0.000 0.940 0.004 0.056 0.000
#> GSM550909 5 0.7549 0.0783 0.104 0.308 0.020 0.040 0.456 0.072
#> GSM550911 3 0.1858 0.7954 0.000 0.000 0.904 0.004 0.092 0.000
#> GSM550913 2 0.1261 0.6737 0.008 0.956 0.000 0.004 0.028 0.004
#> GSM550915 5 0.5727 0.0880 0.396 0.076 0.000 0.008 0.500 0.020
#> GSM550917 2 0.4533 0.5938 0.128 0.756 0.000 0.036 0.076 0.004
#> GSM550919 1 0.4963 0.4937 0.716 0.128 0.000 0.024 0.124 0.008
#> GSM550921 3 0.0260 0.8151 0.000 0.000 0.992 0.000 0.008 0.000
#> GSM550924 1 0.6637 0.3802 0.608 0.132 0.072 0.040 0.144 0.004
#> GSM550926 4 0.7033 0.1615 0.120 0.356 0.000 0.424 0.084 0.016
#> GSM550927 2 0.4544 0.2539 0.000 0.548 0.000 0.036 0.416 0.000
#> GSM550787 1 0.6620 0.3117 0.532 0.064 0.028 0.028 0.316 0.032
#> GSM550793 3 0.1338 0.8120 0.008 0.000 0.952 0.004 0.004 0.032
#> GSM550794 1 0.7815 -0.0745 0.364 0.308 0.000 0.080 0.048 0.200
#> GSM550795 6 0.1518 0.6597 0.024 0.000 0.000 0.024 0.008 0.944
#> GSM550798 1 0.5632 0.3574 0.536 0.000 0.008 0.008 0.100 0.348
#> GSM550803 1 0.4034 0.4329 0.624 0.000 0.000 0.004 0.008 0.364
#> GSM550805 6 0.8021 0.1641 0.324 0.180 0.016 0.108 0.024 0.348
#> GSM550823 4 0.2594 0.6522 0.072 0.020 0.000 0.888 0.008 0.012
#> GSM550824 1 0.3072 0.6454 0.836 0.000 0.000 0.004 0.036 0.124
#> GSM550825 3 0.5497 0.4647 0.204 0.000 0.628 0.024 0.144 0.000
#> GSM550827 1 0.7166 0.2449 0.508 0.132 0.000 0.104 0.228 0.028
#> GSM550828 1 0.2881 0.6585 0.872 0.012 0.000 0.004 0.064 0.048
#> GSM550829 1 0.5245 0.5653 0.688 0.000 0.052 0.008 0.188 0.064
#> GSM550830 4 0.3569 0.6061 0.020 0.020 0.000 0.812 0.008 0.140
#> GSM550834 6 0.1138 0.6600 0.024 0.000 0.000 0.012 0.004 0.960
#> GSM550839 3 0.7054 -0.1691 0.000 0.036 0.332 0.328 0.012 0.292
#> GSM550840 6 0.2888 0.6420 0.068 0.000 0.000 0.068 0.004 0.860
#> GSM550843 3 0.1327 0.8003 0.000 0.000 0.936 0.000 0.064 0.000
#> GSM550844 1 0.2848 0.6254 0.880 0.024 0.000 0.064 0.016 0.016
#> GSM550845 4 0.5024 0.4697 0.020 0.044 0.000 0.616 0.316 0.004
#> GSM550848 1 0.5378 0.4359 0.672 0.112 0.000 0.024 0.180 0.012
#> GSM550854 1 0.3970 0.5572 0.712 0.000 0.000 0.012 0.016 0.260
#> GSM550857 3 0.2689 0.7654 0.036 0.000 0.876 0.004 0.080 0.004
#> GSM550858 1 0.4901 0.4666 0.632 0.000 0.000 0.024 0.300 0.044
#> GSM550859 1 0.2968 0.6559 0.852 0.000 0.000 0.004 0.052 0.092
#> GSM550862 4 0.6302 0.2264 0.284 0.000 0.000 0.428 0.276 0.012
#> GSM550865 4 0.3710 0.5220 0.012 0.000 0.000 0.696 0.292 0.000
#> GSM550868 4 0.5116 0.5963 0.160 0.048 0.000 0.712 0.012 0.068
#> GSM550869 4 0.4364 0.6373 0.056 0.028 0.016 0.796 0.012 0.092
#> GSM550870 2 0.4787 0.4788 0.000 0.624 0.000 0.056 0.312 0.008
#> GSM550871 4 0.5180 0.5344 0.024 0.048 0.248 0.664 0.004 0.012
#> GSM550872 4 0.4303 0.6033 0.028 0.000 0.000 0.764 0.128 0.080
#> GSM550873 2 0.4402 0.6308 0.108 0.784 0.000 0.040 0.040 0.028
#> GSM550874 4 0.5422 0.4206 0.000 0.164 0.000 0.592 0.004 0.240
#> GSM550876 4 0.4603 0.3419 0.012 0.008 0.364 0.604 0.004 0.008
#> GSM550877 4 0.4842 0.4350 0.008 0.040 0.000 0.592 0.356 0.004
#> GSM550878 3 0.0146 0.8148 0.000 0.000 0.996 0.000 0.004 0.000
#> GSM550879 5 0.4642 -0.1231 0.452 0.000 0.000 0.012 0.516 0.020
#> GSM550882 3 0.3426 0.5140 0.000 0.000 0.720 0.276 0.000 0.004
#> GSM550888 3 0.0508 0.8160 0.000 0.000 0.984 0.004 0.012 0.000
#> GSM550890 5 0.2946 0.5077 0.120 0.024 0.000 0.004 0.848 0.004
#> GSM550891 3 0.0405 0.8154 0.000 0.000 0.988 0.004 0.008 0.000
#> GSM550892 4 0.4736 0.4684 0.072 0.000 0.000 0.620 0.308 0.000
#> GSM550893 4 0.5984 0.4979 0.128 0.224 0.000 0.600 0.040 0.008
#> GSM550895 4 0.1931 0.6539 0.028 0.040 0.000 0.924 0.004 0.004
#> GSM550896 4 0.5469 0.5348 0.100 0.204 0.000 0.656 0.032 0.008
#> GSM550898 1 0.2114 0.6565 0.904 0.000 0.000 0.008 0.012 0.076
#> GSM550899 2 0.5958 0.4156 0.124 0.600 0.000 0.032 0.232 0.012
#> GSM550900 4 0.2015 0.6496 0.056 0.000 0.000 0.916 0.012 0.016
#> GSM550901 1 0.2529 0.6422 0.892 0.028 0.000 0.004 0.064 0.012
#> GSM550902 5 0.4364 0.4109 0.216 0.000 0.016 0.040 0.724 0.004
#> GSM550904 1 0.4586 0.5100 0.704 0.016 0.000 0.020 0.236 0.024
#> GSM550908 3 0.0363 0.8161 0.000 0.000 0.988 0.000 0.012 0.000
#> GSM550912 2 0.5776 0.5303 0.136 0.668 0.000 0.056 0.120 0.020
#> GSM550914 5 0.2743 0.5363 0.060 0.032 0.000 0.028 0.880 0.000
#> GSM550918 2 0.5302 0.1975 0.068 0.520 0.000 0.008 0.400 0.004
#> GSM550922 3 0.4349 0.5275 0.000 0.264 0.684 0.004 0.048 0.000
#> GSM550923 1 0.2302 0.6477 0.872 0.000 0.000 0.000 0.008 0.120
#> GSM550925 1 0.3387 0.5994 0.852 0.056 0.000 0.048 0.032 0.012
#> GSM550802 6 0.4606 0.4884 0.004 0.056 0.000 0.204 0.020 0.716
#> GSM550812 6 0.8529 0.1154 0.132 0.228 0.000 0.128 0.160 0.352
#> GSM550831 6 0.1230 0.6591 0.028 0.000 0.000 0.008 0.008 0.956
#> GSM550847 1 0.2425 0.6519 0.880 0.000 0.000 0.012 0.008 0.100
#> GSM550860 4 0.4572 0.5832 0.024 0.000 0.076 0.728 0.172 0.000
#> GSM550875 4 0.7207 0.2642 0.316 0.064 0.004 0.440 0.020 0.156
#> GSM550880 6 0.4413 0.6216 0.104 0.020 0.000 0.020 0.080 0.776
#> GSM550881 3 0.0653 0.8167 0.004 0.000 0.980 0.000 0.012 0.004
#> GSM550883 3 0.0291 0.8154 0.000 0.000 0.992 0.000 0.004 0.004
#> GSM550884 4 0.7902 0.3383 0.236 0.096 0.036 0.452 0.160 0.020
#> GSM550910 5 0.4617 0.4808 0.004 0.104 0.176 0.004 0.712 0.000
#> GSM550916 1 0.1952 0.6449 0.920 0.000 0.000 0.052 0.012 0.016
#> GSM550920 3 0.2244 0.7798 0.008 0.072 0.904 0.004 0.008 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)
get_signatures(res, k = 3)
get_signatures(res, k = 4)
get_signatures(res, k = 5)
get_signatures(res, k = 6)
Signature heatmaps where rows are not scaled:
get_signatures(res, k = 2, scale_rows = FALSE)
get_signatures(res, k = 3, scale_rows = FALSE)
get_signatures(res, k = 4, scale_rows = FALSE)
get_signatures(res, k = 5, scale_rows = FALSE)
get_signatures(res, k = 6, scale_rows = FALSE)
Compare the overlap of signatures from different k:
compare_signatures(res)
get_signature() returns a data frame invisibly. TO get the list of signatures, the function
call should be assigned to a variable explicitly. In following code, if plot argument is set
to FALSE, no heatmap is plotted while only the differential analysis is performed.
# code only for demonstration
tb = get_signature(res, k = ..., plot = FALSE)
An example of the output of tb is:
#> which_row fdr mean_1 mean_2 scaled_mean_1 scaled_mean_2 km
#> 1 38 0.042760348 8.373488 9.131774 -0.5533452 0.5164555 1
#> 2 40 0.018707592 7.106213 8.469186 -0.6173731 0.5762149 1
#> 3 55 0.019134737 10.221463 11.207825 -0.6159697 0.5749050 1
#> 4 59 0.006059896 5.921854 7.869574 -0.6899429 0.6439467 1
#> 5 60 0.018055526 8.928898 10.211722 -0.6204761 0.5791110 1
#> 6 98 0.009384629 15.714769 14.887706 0.6635654 -0.6193277 2
...
The columns in tb are:
which_row: row indices corresponding to the input matrix.fdr: FDR for the differential test. mean_x: The mean value in group x.scaled_mean_x: The mean value in group x after rows are scaled.km: Row groups if k-means clustering is applied to rows.UMAP plot which shows how samples are separated.
dimension_reduction(res, k = 2, method = "UMAP")
dimension_reduction(res, k = 3, method = "UMAP")
dimension_reduction(res, k = 4, method = "UMAP")
dimension_reduction(res, k = 5, method = "UMAP")
dimension_reduction(res, k = 6, method = "UMAP")
Following heatmap shows how subgroups are split when increasing k:
collect_classes(res)
Test correlation between subgroups and known annotations. If the known annotation is numeric, one-way ANOVA test is applied, and if the known annotation is discrete, chi-squared contingency table test is applied.
test_to_known_factors(res)
#> n disease.state(p) k
#> CV:NMF 133 2.90e-01 2
#> CV:NMF 139 3.80e-04 3
#> CV:NMF 110 1.15e-04 4
#> CV:NMF 83 1.68e-03 5
#> CV:NMF 85 5.49e-05 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 51776 rows and 143 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 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 0.203 0.699 0.818 0.4410 0.502 0.502
#> 3 3 0.362 0.694 0.836 0.2730 0.909 0.821
#> 4 4 0.399 0.614 0.771 0.1178 0.969 0.928
#> 5 5 0.432 0.494 0.701 0.1303 0.856 0.651
#> 6 6 0.489 0.433 0.642 0.0711 0.870 0.589
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
#> GSM550785 1 0.7950 0.78191 0.760 0.240
#> GSM550786 2 0.8327 0.67383 0.264 0.736
#> GSM550788 2 0.0000 0.83215 0.000 1.000
#> GSM550789 2 0.0000 0.83215 0.000 1.000
#> GSM550790 1 0.7950 0.78191 0.760 0.240
#> GSM550791 1 0.8207 0.77480 0.744 0.256
#> GSM550792 2 0.5178 0.80020 0.116 0.884
#> GSM550796 2 0.0000 0.83215 0.000 1.000
#> GSM550797 2 0.0000 0.83215 0.000 1.000
#> GSM550799 2 0.8861 0.57859 0.304 0.696
#> GSM550800 2 0.5408 0.79121 0.124 0.876
#> GSM550801 2 0.0938 0.83724 0.012 0.988
#> GSM550804 2 0.2423 0.83827 0.040 0.960
#> GSM550806 2 0.9988 0.28132 0.480 0.520
#> GSM550807 2 0.0938 0.83724 0.012 0.988
#> GSM550808 2 0.0376 0.83144 0.004 0.996
#> GSM550809 1 0.7602 0.78598 0.780 0.220
#> GSM550810 2 0.0376 0.83144 0.004 0.996
#> GSM550811 1 0.7674 0.78559 0.776 0.224
#> GSM550813 2 0.1843 0.83927 0.028 0.972
#> GSM550814 2 0.2948 0.83697 0.052 0.948
#> GSM550815 2 0.0000 0.83215 0.000 1.000
#> GSM550816 2 0.2423 0.83777 0.040 0.960
#> GSM550817 1 0.9323 0.29557 0.652 0.348
#> GSM550818 1 0.9323 0.29557 0.652 0.348
#> GSM550819 2 0.5946 0.77853 0.144 0.856
#> GSM550820 1 0.7674 0.78603 0.776 0.224
#> GSM550821 2 0.3431 0.83532 0.064 0.936
#> GSM550822 2 0.0000 0.83215 0.000 1.000
#> GSM550826 1 0.7674 0.78594 0.776 0.224
#> GSM550832 2 0.0376 0.83144 0.004 0.996
#> GSM550833 2 0.0000 0.83215 0.000 1.000
#> GSM550835 2 0.4690 0.78841 0.100 0.900
#> GSM550836 1 0.0000 0.67749 1.000 0.000
#> GSM550837 2 0.4562 0.79189 0.096 0.904
#> GSM550838 1 0.7602 0.78598 0.780 0.220
#> GSM550841 1 0.9988 -0.08107 0.520 0.480
#> GSM550842 2 0.3274 0.79640 0.060 0.940
#> GSM550846 2 0.7528 0.67269 0.216 0.784
#> GSM550849 2 0.9815 -0.00986 0.420 0.580
#> GSM550850 1 0.8016 0.78019 0.756 0.244
#> GSM550851 2 0.4298 0.79531 0.088 0.912
#> GSM550852 2 0.5178 0.80020 0.116 0.884
#> GSM550853 2 0.1633 0.83891 0.024 0.976
#> GSM550855 2 0.1633 0.83891 0.024 0.976
#> GSM550856 2 0.2603 0.83814 0.044 0.956
#> GSM550861 2 0.0938 0.83660 0.012 0.988
#> GSM550863 1 0.9933 0.48909 0.548 0.452
#> GSM550864 2 0.1843 0.83927 0.028 0.972
#> GSM550866 2 0.2603 0.83826 0.044 0.956
#> GSM550867 1 0.7219 0.78473 0.800 0.200
#> GSM550885 1 0.7219 0.78473 0.800 0.200
#> GSM550886 2 0.8327 0.67308 0.264 0.736
#> GSM550887 2 0.0000 0.83215 0.000 1.000
#> GSM550889 2 0.7950 0.62667 0.240 0.760
#> GSM550894 2 0.0376 0.83144 0.004 0.996
#> GSM550897 1 0.8608 0.75043 0.716 0.284
#> GSM550903 2 0.1843 0.83927 0.028 0.972
#> GSM550905 2 0.4022 0.80565 0.080 0.920
#> GSM550906 2 0.0000 0.83215 0.000 1.000
#> GSM550907 1 0.9170 0.32969 0.668 0.332
#> GSM550909 2 0.3114 0.83501 0.056 0.944
#> GSM550911 1 0.8813 0.39850 0.700 0.300
#> GSM550913 2 0.0000 0.83215 0.000 1.000
#> GSM550915 1 0.9933 0.49874 0.548 0.452
#> GSM550917 2 0.2423 0.83827 0.040 0.960
#> GSM550919 1 0.9795 0.58396 0.584 0.416
#> GSM550921 1 0.0000 0.67749 1.000 0.000
#> GSM550924 2 0.8267 0.69087 0.260 0.740
#> GSM550926 2 0.1633 0.83891 0.024 0.976
#> GSM550927 2 0.0000 0.83215 0.000 1.000
#> GSM550787 1 0.9933 0.47519 0.548 0.452
#> GSM550793 1 0.3733 0.73167 0.928 0.072
#> GSM550794 2 0.5294 0.79775 0.120 0.880
#> GSM550795 1 0.8016 0.77906 0.756 0.244
#> GSM550798 1 0.5294 0.75756 0.880 0.120
#> GSM550803 1 0.7056 0.78382 0.808 0.192
#> GSM550805 1 0.9129 0.71116 0.672 0.328
#> GSM550823 2 0.8081 0.61652 0.248 0.752
#> GSM550824 1 0.7219 0.78473 0.800 0.200
#> GSM550825 1 0.4431 0.74340 0.908 0.092
#> GSM550827 2 0.8016 0.62649 0.244 0.756
#> GSM550828 1 0.7950 0.77952 0.760 0.240
#> GSM550829 1 0.4431 0.74340 0.908 0.092
#> GSM550830 2 0.8081 0.61652 0.248 0.752
#> GSM550834 1 0.7745 0.78497 0.772 0.228
#> GSM550839 2 0.9358 0.57152 0.352 0.648
#> GSM550840 1 0.9087 0.71455 0.676 0.324
#> GSM550843 2 0.9580 0.53419 0.380 0.620
#> GSM550844 1 0.9129 0.71116 0.672 0.328
#> GSM550845 2 0.2423 0.83827 0.040 0.960
#> GSM550848 1 0.9815 0.57620 0.580 0.420
#> GSM550854 1 0.7219 0.78473 0.800 0.200
#> GSM550857 1 0.0000 0.67749 1.000 0.000
#> GSM550858 1 0.7883 0.78125 0.764 0.236
#> GSM550859 1 0.7219 0.78473 0.800 0.200
#> GSM550862 1 0.7883 0.78125 0.764 0.236
#> GSM550865 1 0.9896 0.51945 0.560 0.440
#> GSM550868 2 0.8327 0.57868 0.264 0.736
#> GSM550869 2 0.9988 0.21977 0.480 0.520
#> GSM550870 2 0.2423 0.83827 0.040 0.960
#> GSM550871 2 0.9323 0.57686 0.348 0.652
#> GSM550872 1 0.9922 0.49935 0.552 0.448
#> GSM550873 2 0.5178 0.80020 0.116 0.884
#> GSM550874 2 0.1633 0.83891 0.024 0.976
#> GSM550876 2 0.9850 0.40257 0.428 0.572
#> GSM550877 2 0.1633 0.83891 0.024 0.976
#> GSM550878 2 0.9922 0.36822 0.448 0.552
#> GSM550879 1 0.7883 0.78046 0.764 0.236
#> GSM550882 1 0.5737 0.68122 0.864 0.136
#> GSM550888 1 0.0000 0.67749 1.000 0.000
#> GSM550890 2 0.7528 0.67269 0.216 0.784
#> GSM550891 1 0.2236 0.68423 0.964 0.036
#> GSM550892 1 0.9815 0.56160 0.580 0.420
#> GSM550893 2 0.7815 0.64188 0.232 0.768
#> GSM550895 2 0.7219 0.69728 0.200 0.800
#> GSM550896 2 0.6438 0.74724 0.164 0.836
#> GSM550898 1 0.7219 0.78473 0.800 0.200
#> GSM550899 2 0.1843 0.83927 0.028 0.972
#> GSM550900 2 0.7950 0.63245 0.240 0.760
#> GSM550901 1 0.9795 0.58396 0.584 0.416
#> GSM550902 1 0.3733 0.73167 0.928 0.072
#> GSM550904 1 0.7745 0.78503 0.772 0.228
#> GSM550908 1 0.0000 0.67749 1.000 0.000
#> GSM550912 2 0.1843 0.83927 0.028 0.972
#> GSM550914 2 0.7528 0.67269 0.216 0.784
#> GSM550918 2 0.2423 0.83827 0.040 0.960
#> GSM550922 2 0.8909 0.57432 0.308 0.692
#> GSM550923 1 0.5737 0.76490 0.864 0.136
#> GSM550925 1 0.9795 0.56398 0.584 0.416
#> GSM550802 2 0.5629 0.78735 0.132 0.868
#> GSM550812 2 0.5629 0.78735 0.132 0.868
#> GSM550831 1 0.7745 0.78497 0.772 0.228
#> GSM550847 1 0.7219 0.78473 0.800 0.200
#> GSM550860 1 1.0000 -0.21579 0.500 0.500
#> GSM550875 1 0.9129 0.71116 0.672 0.328
#> GSM550880 1 0.9866 0.53847 0.568 0.432
#> GSM550881 1 0.3431 0.72648 0.936 0.064
#> GSM550883 1 0.3431 0.72648 0.936 0.064
#> GSM550884 2 0.5737 0.78446 0.136 0.864
#> GSM550910 1 0.9833 0.24735 0.576 0.424
#> GSM550916 1 0.9686 0.59853 0.604 0.396
#> GSM550920 2 0.8267 0.69087 0.260 0.740
cbind(get_classes(res, k = 3), get_membership(res, k = 3))
#> class entropy silhouette p1 p2 p3
#> GSM550785 1 0.1529 0.8085 0.960 0.040 0.000
#> GSM550786 2 0.7493 0.6517 0.136 0.696 0.168
#> GSM550788 2 0.0000 0.8048 0.000 1.000 0.000
#> GSM550789 2 0.0000 0.8048 0.000 1.000 0.000
#> GSM550790 1 0.1529 0.8085 0.960 0.040 0.000
#> GSM550791 1 0.4399 0.7627 0.812 0.188 0.000
#> GSM550792 2 0.4589 0.7688 0.172 0.820 0.008
#> GSM550796 2 0.0000 0.8048 0.000 1.000 0.000
#> GSM550797 2 0.0000 0.8048 0.000 1.000 0.000
#> GSM550799 2 0.5760 0.4568 0.000 0.672 0.328
#> GSM550800 2 0.3412 0.7884 0.124 0.876 0.000
#> GSM550801 2 0.1163 0.8132 0.028 0.972 0.000
#> GSM550804 2 0.2066 0.8132 0.060 0.940 0.000
#> GSM550806 2 0.8925 0.2517 0.132 0.504 0.364
#> GSM550807 2 0.1163 0.8132 0.028 0.972 0.000
#> GSM550808 2 0.0237 0.8046 0.000 0.996 0.004
#> GSM550809 1 0.2804 0.8115 0.924 0.060 0.016
#> GSM550810 2 0.0237 0.8046 0.000 0.996 0.004
#> GSM550811 1 0.2902 0.8112 0.920 0.064 0.016
#> GSM550813 2 0.1529 0.8147 0.040 0.960 0.000
#> GSM550814 2 0.2313 0.8129 0.032 0.944 0.024
#> GSM550815 2 0.0000 0.8048 0.000 1.000 0.000
#> GSM550816 2 0.3112 0.8026 0.096 0.900 0.004
#> GSM550817 3 0.5706 0.5450 0.000 0.320 0.680
#> GSM550818 3 0.5706 0.5450 0.000 0.320 0.680
#> GSM550819 2 0.6067 0.7135 0.236 0.736 0.028
#> GSM550820 1 0.2902 0.8127 0.920 0.064 0.016
#> GSM550821 2 0.3805 0.8007 0.092 0.884 0.024
#> GSM550822 2 0.0000 0.8048 0.000 1.000 0.000
#> GSM550826 1 0.3183 0.8104 0.908 0.076 0.016
#> GSM550832 2 0.0237 0.8046 0.000 0.996 0.004
#> GSM550833 2 0.0237 0.8037 0.000 0.996 0.004
#> GSM550835 2 0.3116 0.7566 0.000 0.892 0.108
#> GSM550836 3 0.1411 0.7152 0.036 0.000 0.964
#> GSM550837 2 0.3038 0.7603 0.000 0.896 0.104
#> GSM550838 1 0.2804 0.8115 0.924 0.060 0.016
#> GSM550841 3 0.6274 0.2169 0.000 0.456 0.544
#> GSM550842 2 0.2165 0.7860 0.000 0.936 0.064
#> GSM550846 2 0.6026 0.4899 0.376 0.624 0.000
#> GSM550849 2 0.6816 0.0434 0.472 0.516 0.012
#> GSM550850 1 0.1643 0.8094 0.956 0.044 0.000
#> GSM550851 2 0.2796 0.7679 0.000 0.908 0.092
#> GSM550852 2 0.4589 0.7688 0.172 0.820 0.008
#> GSM550853 2 0.1031 0.8127 0.024 0.976 0.000
#> GSM550855 2 0.1031 0.8127 0.024 0.976 0.000
#> GSM550856 2 0.1753 0.8150 0.048 0.952 0.000
#> GSM550861 2 0.0592 0.8097 0.012 0.988 0.000
#> GSM550863 1 0.5560 0.6255 0.700 0.300 0.000
#> GSM550864 2 0.1289 0.8143 0.032 0.968 0.000
#> GSM550866 2 0.1753 0.8151 0.048 0.952 0.000
#> GSM550867 1 0.0000 0.7884 1.000 0.000 0.000
#> GSM550885 1 0.0000 0.7884 1.000 0.000 0.000
#> GSM550886 2 0.6756 0.6270 0.056 0.712 0.232
#> GSM550887 2 0.0000 0.8048 0.000 1.000 0.000
#> GSM550889 2 0.5138 0.6590 0.252 0.748 0.000
#> GSM550894 2 0.0237 0.8046 0.000 0.996 0.004
#> GSM550897 1 0.4733 0.7582 0.800 0.196 0.004
#> GSM550903 2 0.1163 0.8135 0.028 0.972 0.000
#> GSM550905 2 0.2625 0.7735 0.000 0.916 0.084
#> GSM550906 2 0.0000 0.8048 0.000 1.000 0.000
#> GSM550907 3 0.5591 0.5674 0.000 0.304 0.696
#> GSM550909 2 0.4443 0.7880 0.084 0.864 0.052
#> GSM550911 3 0.5254 0.6143 0.000 0.264 0.736
#> GSM550913 2 0.0000 0.8048 0.000 1.000 0.000
#> GSM550915 1 0.5968 0.5216 0.636 0.364 0.000
#> GSM550917 2 0.1964 0.8136 0.056 0.944 0.000
#> GSM550919 1 0.5760 0.6078 0.672 0.328 0.000
#> GSM550921 3 0.1411 0.7152 0.036 0.000 0.964
#> GSM550924 2 0.7180 0.6603 0.096 0.708 0.196
#> GSM550926 2 0.1163 0.8136 0.028 0.972 0.000
#> GSM550927 2 0.0000 0.8048 0.000 1.000 0.000
#> GSM550787 1 0.6899 0.4764 0.612 0.364 0.024
#> GSM550793 3 0.5859 0.4935 0.344 0.000 0.656
#> GSM550794 2 0.4645 0.7664 0.176 0.816 0.008
#> GSM550795 1 0.2945 0.8077 0.908 0.088 0.004
#> GSM550798 1 0.2537 0.7421 0.920 0.000 0.080
#> GSM550803 1 0.0424 0.7871 0.992 0.000 0.008
#> GSM550805 1 0.5578 0.7216 0.748 0.240 0.012
#> GSM550823 2 0.5882 0.5275 0.348 0.652 0.000
#> GSM550824 1 0.0000 0.7884 1.000 0.000 0.000
#> GSM550825 1 0.4291 0.6384 0.820 0.000 0.180
#> GSM550827 2 0.5882 0.5285 0.348 0.652 0.000
#> GSM550828 1 0.1753 0.8123 0.952 0.048 0.000
#> GSM550829 1 0.4291 0.6384 0.820 0.000 0.180
#> GSM550830 2 0.5882 0.5275 0.348 0.652 0.000
#> GSM550834 1 0.1163 0.8053 0.972 0.028 0.000
#> GSM550839 2 0.8079 0.5458 0.112 0.628 0.260
#> GSM550840 1 0.5378 0.7262 0.756 0.236 0.008
#> GSM550843 2 0.8160 0.5047 0.104 0.608 0.288
#> GSM550844 1 0.5578 0.7216 0.748 0.240 0.012
#> GSM550845 2 0.2066 0.8132 0.060 0.940 0.000
#> GSM550848 1 0.5785 0.6001 0.668 0.332 0.000
#> GSM550854 1 0.0000 0.7884 1.000 0.000 0.000
#> GSM550857 3 0.1411 0.7152 0.036 0.000 0.964
#> GSM550858 1 0.1529 0.8112 0.960 0.040 0.000
#> GSM550859 1 0.0000 0.7884 1.000 0.000 0.000
#> GSM550862 1 0.1529 0.8112 0.960 0.040 0.000
#> GSM550865 1 0.5465 0.6488 0.712 0.288 0.000
#> GSM550868 2 0.6192 0.3718 0.420 0.580 0.000
#> GSM550869 2 0.9431 0.3240 0.220 0.500 0.280
#> GSM550870 2 0.2066 0.8132 0.060 0.940 0.000
#> GSM550871 2 0.8047 0.5535 0.112 0.632 0.256
#> GSM550872 1 0.5529 0.6338 0.704 0.296 0.000
#> GSM550873 2 0.4589 0.7688 0.172 0.820 0.008
#> GSM550874 2 0.1163 0.8136 0.028 0.972 0.000
#> GSM550876 2 0.8486 0.3411 0.104 0.548 0.348
#> GSM550877 2 0.1031 0.8127 0.024 0.976 0.000
#> GSM550878 2 0.8295 0.2665 0.084 0.532 0.384
#> GSM550879 1 0.1643 0.8116 0.956 0.044 0.000
#> GSM550882 3 0.7372 0.6314 0.168 0.128 0.704
#> GSM550888 3 0.1411 0.7152 0.036 0.000 0.964
#> GSM550890 2 0.6026 0.4899 0.376 0.624 0.000
#> GSM550891 3 0.0000 0.7082 0.000 0.000 1.000
#> GSM550892 1 0.5291 0.6778 0.732 0.268 0.000
#> GSM550893 2 0.4974 0.6795 0.236 0.764 0.000
#> GSM550895 2 0.4702 0.7137 0.212 0.788 0.000
#> GSM550896 2 0.4235 0.7540 0.176 0.824 0.000
#> GSM550898 1 0.0000 0.7884 1.000 0.000 0.000
#> GSM550899 2 0.1163 0.8135 0.028 0.972 0.000
#> GSM550900 2 0.5810 0.5496 0.336 0.664 0.000
#> GSM550901 1 0.5760 0.6078 0.672 0.328 0.000
#> GSM550902 3 0.5859 0.4935 0.344 0.000 0.656
#> GSM550904 1 0.2998 0.8121 0.916 0.068 0.016
#> GSM550908 3 0.1411 0.7152 0.036 0.000 0.964
#> GSM550912 2 0.1529 0.8147 0.040 0.960 0.000
#> GSM550914 2 0.6026 0.4899 0.376 0.624 0.000
#> GSM550918 2 0.2066 0.8132 0.060 0.940 0.000
#> GSM550922 2 0.5733 0.4614 0.000 0.676 0.324
#> GSM550923 1 0.2165 0.7561 0.936 0.000 0.064
#> GSM550925 1 0.6129 0.5907 0.668 0.324 0.008
#> GSM550802 2 0.5402 0.7604 0.180 0.792 0.028
#> GSM550812 2 0.5402 0.7604 0.180 0.792 0.028
#> GSM550831 1 0.1163 0.8053 0.972 0.028 0.000
#> GSM550847 1 0.0000 0.7884 1.000 0.000 0.000
#> GSM550860 2 0.9488 0.2613 0.208 0.480 0.312
#> GSM550875 1 0.5578 0.7216 0.748 0.240 0.012
#> GSM550880 1 0.5397 0.6620 0.720 0.280 0.000
#> GSM550881 3 0.5760 0.5206 0.328 0.000 0.672
#> GSM550883 3 0.5760 0.5206 0.328 0.000 0.672
#> GSM550884 2 0.5012 0.7512 0.204 0.788 0.008
#> GSM550910 3 0.6467 0.4066 0.008 0.388 0.604
#> GSM550916 1 0.5247 0.7075 0.768 0.224 0.008
#> GSM550920 2 0.7180 0.6603 0.096 0.708 0.196
cbind(get_classes(res, k = 4), get_membership(res, k = 4))
#> class entropy silhouette p1 p2 p3 p4
#> GSM550785 1 0.2360 0.7922 0.924 0.052 0.020 0.004
#> GSM550786 2 0.7577 0.3743 0.120 0.556 0.032 0.292
#> GSM550788 2 0.1732 0.7264 0.004 0.948 0.008 0.040
#> GSM550789 2 0.1890 0.7165 0.000 0.936 0.008 0.056
#> GSM550790 1 0.2360 0.7922 0.924 0.052 0.020 0.004
#> GSM550791 1 0.5051 0.7517 0.776 0.164 0.040 0.020
#> GSM550792 2 0.5579 0.6555 0.140 0.760 0.028 0.072
#> GSM550796 2 0.1890 0.7165 0.000 0.936 0.008 0.056
#> GSM550797 2 0.1890 0.7165 0.000 0.936 0.008 0.056
#> GSM550799 2 0.5604 0.0153 0.000 0.504 0.020 0.476
#> GSM550800 2 0.4010 0.6838 0.100 0.848 0.016 0.036
#> GSM550801 2 0.2484 0.7316 0.024 0.924 0.012 0.040
#> GSM550804 2 0.1892 0.7312 0.036 0.944 0.016 0.004
#> GSM550806 4 0.8301 0.1548 0.096 0.404 0.076 0.424
#> GSM550807 2 0.2484 0.7316 0.024 0.924 0.012 0.040
#> GSM550808 2 0.2593 0.7071 0.000 0.892 0.004 0.104
#> GSM550809 1 0.2990 0.7920 0.900 0.036 0.056 0.008
#> GSM550810 2 0.2593 0.7071 0.000 0.892 0.004 0.104
#> GSM550811 1 0.3082 0.7924 0.896 0.040 0.056 0.008
#> GSM550813 2 0.0927 0.7346 0.016 0.976 0.000 0.008
#> GSM550814 2 0.1576 0.7292 0.004 0.948 0.000 0.048
#> GSM550815 2 0.1890 0.7165 0.000 0.936 0.008 0.056
#> GSM550816 2 0.5164 0.6932 0.096 0.788 0.020 0.096
#> GSM550817 4 0.3342 0.4715 0.000 0.032 0.100 0.868
#> GSM550818 4 0.3342 0.4715 0.000 0.032 0.100 0.868
#> GSM550819 2 0.6577 0.5747 0.216 0.660 0.016 0.108
#> GSM550820 1 0.3000 0.7949 0.900 0.040 0.052 0.008
#> GSM550821 2 0.5384 0.6843 0.088 0.772 0.020 0.120
#> GSM550822 2 0.1743 0.7163 0.000 0.940 0.004 0.056
#> GSM550826 1 0.3536 0.7921 0.880 0.052 0.048 0.020
#> GSM550832 2 0.2053 0.7144 0.000 0.924 0.004 0.072
#> GSM550833 2 0.1940 0.7164 0.000 0.924 0.000 0.076
#> GSM550835 2 0.4283 0.5734 0.000 0.740 0.004 0.256
#> GSM550836 3 0.2675 0.7143 0.008 0.000 0.892 0.100
#> GSM550837 2 0.4134 0.5752 0.000 0.740 0.000 0.260
#> GSM550838 1 0.2990 0.7920 0.900 0.036 0.056 0.008
#> GSM550841 4 0.4874 0.4919 0.000 0.180 0.056 0.764
#> GSM550842 2 0.3583 0.6579 0.000 0.816 0.004 0.180
#> GSM550846 2 0.7333 0.3660 0.356 0.536 0.060 0.048
#> GSM550849 2 0.7270 -0.0405 0.444 0.460 0.040 0.056
#> GSM550850 1 0.2505 0.7920 0.920 0.052 0.020 0.008
#> GSM550851 2 0.4040 0.5902 0.000 0.752 0.000 0.248
#> GSM550852 2 0.5579 0.6555 0.140 0.760 0.028 0.072
#> GSM550853 2 0.0564 0.7313 0.004 0.988 0.004 0.004
#> GSM550855 2 0.0712 0.7319 0.008 0.984 0.004 0.004
#> GSM550856 2 0.1639 0.7323 0.036 0.952 0.008 0.004
#> GSM550861 2 0.1635 0.7218 0.000 0.948 0.008 0.044
#> GSM550863 1 0.6402 0.6558 0.680 0.224 0.056 0.040
#> GSM550864 2 0.1394 0.7332 0.008 0.964 0.012 0.016
#> GSM550866 2 0.1639 0.7325 0.036 0.952 0.008 0.004
#> GSM550867 1 0.0921 0.7721 0.972 0.000 0.028 0.000
#> GSM550885 1 0.0921 0.7721 0.972 0.000 0.028 0.000
#> GSM550886 2 0.6441 0.3287 0.036 0.580 0.024 0.360
#> GSM550887 2 0.1890 0.7165 0.000 0.936 0.008 0.056
#> GSM550889 2 0.6503 0.5315 0.236 0.668 0.044 0.052
#> GSM550894 2 0.2053 0.7144 0.000 0.924 0.004 0.072
#> GSM550897 1 0.4917 0.7424 0.776 0.176 0.024 0.024
#> GSM550903 2 0.1362 0.7313 0.004 0.964 0.012 0.020
#> GSM550905 2 0.3975 0.5996 0.000 0.760 0.000 0.240
#> GSM550906 2 0.1807 0.7177 0.000 0.940 0.008 0.052
#> GSM550907 4 0.3047 0.4339 0.000 0.012 0.116 0.872
#> GSM550909 2 0.6027 0.6260 0.084 0.708 0.016 0.192
#> GSM550911 4 0.2921 0.3558 0.000 0.000 0.140 0.860
#> GSM550913 2 0.1890 0.7165 0.000 0.936 0.008 0.056
#> GSM550915 1 0.6256 0.5667 0.636 0.300 0.040 0.024
#> GSM550917 2 0.1796 0.7316 0.032 0.948 0.016 0.004
#> GSM550919 1 0.5770 0.6336 0.672 0.280 0.032 0.016
#> GSM550921 3 0.2675 0.7143 0.008 0.000 0.892 0.100
#> GSM550924 2 0.6859 0.3791 0.060 0.596 0.032 0.312
#> GSM550926 2 0.0844 0.7328 0.012 0.980 0.004 0.004
#> GSM550927 2 0.1890 0.7165 0.000 0.936 0.008 0.056
#> GSM550787 1 0.6860 0.4836 0.580 0.332 0.028 0.060
#> GSM550793 3 0.5801 0.6466 0.280 0.004 0.664 0.052
#> GSM550794 2 0.5627 0.6526 0.144 0.756 0.028 0.072
#> GSM550795 1 0.3170 0.7925 0.892 0.056 0.044 0.008
#> GSM550798 1 0.3142 0.7059 0.860 0.000 0.132 0.008
#> GSM550803 1 0.1661 0.7640 0.944 0.000 0.052 0.004
#> GSM550805 1 0.5717 0.7032 0.716 0.220 0.032 0.032
#> GSM550823 2 0.7157 0.4035 0.324 0.572 0.052 0.052
#> GSM550824 1 0.0921 0.7721 0.972 0.000 0.028 0.000
#> GSM550825 1 0.4507 0.5819 0.756 0.000 0.224 0.020
#> GSM550827 2 0.6032 0.4846 0.328 0.624 0.032 0.016
#> GSM550828 1 0.1878 0.7979 0.944 0.040 0.008 0.008
#> GSM550829 1 0.4507 0.5819 0.756 0.000 0.224 0.020
#> GSM550830 2 0.7157 0.4035 0.324 0.572 0.052 0.052
#> GSM550834 1 0.1892 0.7917 0.944 0.036 0.016 0.004
#> GSM550839 2 0.7363 0.2532 0.076 0.548 0.040 0.336
#> GSM550840 1 0.5591 0.7075 0.724 0.216 0.032 0.028
#> GSM550843 2 0.7622 0.2162 0.072 0.540 0.060 0.328
#> GSM550844 1 0.5717 0.7032 0.716 0.220 0.032 0.032
#> GSM550845 2 0.1892 0.7312 0.036 0.944 0.016 0.004
#> GSM550848 1 0.5795 0.6263 0.668 0.284 0.032 0.016
#> GSM550854 1 0.0921 0.7721 0.972 0.000 0.028 0.000
#> GSM550857 3 0.2675 0.7143 0.008 0.000 0.892 0.100
#> GSM550858 1 0.2010 0.7970 0.940 0.040 0.012 0.008
#> GSM550859 1 0.0921 0.7721 0.972 0.000 0.028 0.000
#> GSM550862 1 0.2010 0.7970 0.940 0.040 0.012 0.008
#> GSM550865 1 0.6303 0.6698 0.692 0.212 0.056 0.040
#> GSM550868 2 0.7304 0.2297 0.400 0.500 0.052 0.048
#> GSM550869 2 0.8724 -0.0656 0.180 0.416 0.060 0.344
#> GSM550870 2 0.1892 0.7312 0.036 0.944 0.016 0.004
#> GSM550871 2 0.7286 0.2625 0.076 0.552 0.036 0.336
#> GSM550872 1 0.6370 0.6607 0.684 0.220 0.056 0.040
#> GSM550873 2 0.5579 0.6555 0.140 0.760 0.028 0.072
#> GSM550874 2 0.0844 0.7328 0.012 0.980 0.004 0.004
#> GSM550876 4 0.7588 0.0993 0.060 0.440 0.056 0.444
#> GSM550877 2 0.0564 0.7313 0.004 0.988 0.004 0.004
#> GSM550878 4 0.7507 0.1671 0.044 0.428 0.068 0.460
#> GSM550879 1 0.1543 0.7969 0.956 0.032 0.004 0.008
#> GSM550882 3 0.8496 0.3577 0.128 0.100 0.524 0.248
#> GSM550888 3 0.2675 0.7143 0.008 0.000 0.892 0.100
#> GSM550890 2 0.7333 0.3660 0.356 0.536 0.060 0.048
#> GSM550891 3 0.4431 0.5058 0.000 0.000 0.696 0.304
#> GSM550892 1 0.6085 0.6873 0.716 0.188 0.056 0.040
#> GSM550893 2 0.6297 0.5516 0.220 0.688 0.040 0.052
#> GSM550895 2 0.6170 0.5736 0.196 0.708 0.048 0.048
#> GSM550896 2 0.5805 0.6120 0.160 0.744 0.048 0.048
#> GSM550898 1 0.0921 0.7721 0.972 0.000 0.028 0.000
#> GSM550899 2 0.1631 0.7338 0.008 0.956 0.016 0.020
#> GSM550900 2 0.7105 0.4281 0.312 0.584 0.052 0.052
#> GSM550901 1 0.5770 0.6336 0.672 0.280 0.032 0.016
#> GSM550902 3 0.5801 0.6466 0.280 0.004 0.664 0.052
#> GSM550904 1 0.3170 0.7941 0.892 0.044 0.056 0.008
#> GSM550908 3 0.2675 0.7143 0.008 0.000 0.892 0.100
#> GSM550912 2 0.0927 0.7346 0.016 0.976 0.000 0.008
#> GSM550914 2 0.7333 0.3660 0.356 0.536 0.060 0.048
#> GSM550918 2 0.1892 0.7312 0.036 0.944 0.016 0.004
#> GSM550922 2 0.5888 0.1373 0.000 0.540 0.036 0.424
#> GSM550923 1 0.2918 0.7214 0.876 0.000 0.116 0.008
#> GSM550925 1 0.6418 0.5910 0.632 0.296 0.036 0.036
#> GSM550802 2 0.6221 0.6222 0.156 0.708 0.020 0.116
#> GSM550812 2 0.6221 0.6222 0.156 0.708 0.020 0.116
#> GSM550831 1 0.1892 0.7917 0.944 0.036 0.016 0.004
#> GSM550847 1 0.1022 0.7711 0.968 0.000 0.032 0.000
#> GSM550860 2 0.8733 -0.1677 0.168 0.388 0.064 0.380
#> GSM550875 1 0.5717 0.7032 0.716 0.220 0.032 0.032
#> GSM550880 1 0.6233 0.6772 0.700 0.204 0.056 0.040
#> GSM550881 3 0.5796 0.6590 0.268 0.004 0.672 0.056
#> GSM550883 3 0.5796 0.6590 0.268 0.004 0.672 0.056
#> GSM550884 2 0.5850 0.6392 0.176 0.728 0.020 0.076
#> GSM550910 4 0.4036 0.4755 0.000 0.076 0.088 0.836
#> GSM550916 1 0.5230 0.6880 0.736 0.220 0.028 0.016
#> GSM550920 2 0.6859 0.3791 0.060 0.596 0.032 0.312
cbind(get_classes(res, k = 5), get_membership(res, k = 5))
#> class entropy silhouette p1 p2 p3 p4 p5
#> GSM550785 1 0.3730 6.12e-01 0.712 0.000 0.000 0.288 0.000
#> GSM550786 2 0.7484 2.24e-01 0.064 0.476 0.000 0.216 0.244
#> GSM550788 2 0.2280 6.95e-01 0.000 0.880 0.000 0.120 0.000
#> GSM550789 2 0.0609 6.90e-01 0.000 0.980 0.000 0.020 0.000
#> GSM550790 1 0.3707 6.13e-01 0.716 0.000 0.000 0.284 0.000
#> GSM550791 1 0.5786 4.32e-01 0.532 0.072 0.000 0.388 0.008
#> GSM550792 2 0.6017 3.55e-01 0.032 0.528 0.000 0.388 0.052
#> GSM550796 2 0.0703 6.86e-01 0.000 0.976 0.000 0.024 0.000
#> GSM550797 2 0.0609 6.90e-01 0.000 0.980 0.000 0.020 0.000
#> GSM550799 2 0.6415 -1.10e-01 0.000 0.424 0.004 0.148 0.424
#> GSM550800 2 0.4210 3.21e-01 0.000 0.588 0.000 0.412 0.000
#> GSM550801 2 0.2286 6.98e-01 0.004 0.888 0.000 0.108 0.000
#> GSM550804 2 0.3582 6.40e-01 0.008 0.768 0.000 0.224 0.000
#> GSM550806 5 0.7886 2.38e-01 0.008 0.196 0.064 0.352 0.380
#> GSM550807 2 0.2338 6.98e-01 0.004 0.884 0.000 0.112 0.000
#> GSM550808 2 0.2300 6.84e-01 0.000 0.908 0.000 0.052 0.040
#> GSM550809 1 0.3527 7.04e-01 0.792 0.000 0.016 0.192 0.000
#> GSM550810 2 0.2228 6.84e-01 0.000 0.912 0.000 0.048 0.040
#> GSM550811 1 0.3851 7.01e-01 0.768 0.004 0.016 0.212 0.000
#> GSM550813 2 0.3086 6.80e-01 0.004 0.816 0.000 0.180 0.000
#> GSM550814 2 0.3574 6.94e-01 0.000 0.804 0.000 0.168 0.028
#> GSM550815 2 0.0703 6.86e-01 0.000 0.976 0.000 0.024 0.000
#> GSM550816 2 0.5398 5.82e-01 0.028 0.676 0.000 0.240 0.056
#> GSM550817 5 0.1485 5.90e-01 0.000 0.032 0.020 0.000 0.948
#> GSM550818 5 0.1485 5.90e-01 0.000 0.032 0.020 0.000 0.948
#> GSM550819 2 0.7094 1.38e-01 0.080 0.428 0.004 0.416 0.072
#> GSM550820 1 0.3759 7.04e-01 0.764 0.000 0.016 0.220 0.000
#> GSM550821 2 0.5554 5.80e-01 0.024 0.672 0.000 0.224 0.080
#> GSM550822 2 0.0703 6.87e-01 0.000 0.976 0.000 0.024 0.000
#> GSM550826 1 0.4423 6.95e-01 0.752 0.016 0.016 0.208 0.008
#> GSM550832 2 0.1310 6.98e-01 0.000 0.956 0.000 0.024 0.020
#> GSM550833 2 0.1965 7.00e-01 0.000 0.924 0.000 0.052 0.024
#> GSM550835 2 0.5104 5.43e-01 0.000 0.692 0.000 0.116 0.192
#> GSM550836 3 0.0404 7.39e-01 0.000 0.000 0.988 0.000 0.012
#> GSM550837 2 0.5072 5.45e-01 0.000 0.696 0.000 0.116 0.188
#> GSM550838 1 0.3527 7.04e-01 0.792 0.000 0.016 0.192 0.000
#> GSM550841 5 0.4196 5.53e-01 0.000 0.176 0.012 0.036 0.776
#> GSM550842 2 0.3216 6.53e-01 0.000 0.848 0.000 0.044 0.108
#> GSM550846 4 0.6012 4.37e-01 0.132 0.332 0.000 0.536 0.000
#> GSM550849 4 0.6673 4.26e-01 0.196 0.228 0.000 0.552 0.024
#> GSM550850 1 0.3730 6.14e-01 0.712 0.000 0.000 0.288 0.000
#> GSM550851 2 0.4971 5.61e-01 0.000 0.708 0.000 0.116 0.176
#> GSM550852 2 0.6017 3.55e-01 0.032 0.528 0.000 0.388 0.052
#> GSM550853 2 0.2605 6.91e-01 0.000 0.852 0.000 0.148 0.000
#> GSM550855 2 0.2732 6.87e-01 0.000 0.840 0.000 0.160 0.000
#> GSM550856 2 0.3366 6.58e-01 0.004 0.784 0.000 0.212 0.000
#> GSM550861 2 0.0963 7.02e-01 0.000 0.964 0.000 0.036 0.000
#> GSM550863 4 0.4760 -5.82e-03 0.416 0.020 0.000 0.564 0.000
#> GSM550864 2 0.2561 6.93e-01 0.000 0.856 0.000 0.144 0.000
#> GSM550866 2 0.3366 6.55e-01 0.004 0.784 0.000 0.212 0.000
#> GSM550867 1 0.0162 7.13e-01 0.996 0.000 0.000 0.004 0.000
#> GSM550885 1 0.0162 7.13e-01 0.996 0.000 0.000 0.004 0.000
#> GSM550886 2 0.7075 1.57e-01 0.004 0.440 0.012 0.232 0.312
#> GSM550887 2 0.0703 6.86e-01 0.000 0.976 0.000 0.024 0.000
#> GSM550889 4 0.4046 4.19e-01 0.008 0.296 0.000 0.696 0.000
#> GSM550894 2 0.1310 6.98e-01 0.000 0.956 0.000 0.024 0.020
#> GSM550897 1 0.5533 4.70e-01 0.540 0.060 0.000 0.396 0.004
#> GSM550903 2 0.2127 7.01e-01 0.000 0.892 0.000 0.108 0.000
#> GSM550905 2 0.4936 5.68e-01 0.000 0.712 0.000 0.116 0.172
#> GSM550906 2 0.0609 6.94e-01 0.000 0.980 0.000 0.020 0.000
#> GSM550907 5 0.1195 5.67e-01 0.000 0.012 0.028 0.000 0.960
#> GSM550909 2 0.6160 5.42e-01 0.028 0.632 0.000 0.184 0.156
#> GSM550911 5 0.1493 5.14e-01 0.000 0.000 0.028 0.024 0.948
#> GSM550913 2 0.0703 6.86e-01 0.000 0.976 0.000 0.024 0.000
#> GSM550915 1 0.6399 1.83e-01 0.492 0.192 0.000 0.316 0.000
#> GSM550917 2 0.3398 6.50e-01 0.004 0.780 0.000 0.216 0.000
#> GSM550919 1 0.6148 2.96e-01 0.536 0.160 0.000 0.304 0.000
#> GSM550921 3 0.0404 7.39e-01 0.000 0.000 0.988 0.000 0.012
#> GSM550924 2 0.7250 1.76e-01 0.004 0.416 0.016 0.288 0.276
#> GSM550926 2 0.2890 6.86e-01 0.004 0.836 0.000 0.160 0.000
#> GSM550927 2 0.0703 6.86e-01 0.000 0.976 0.000 0.024 0.000
#> GSM550787 4 0.6018 1.41e-01 0.272 0.088 0.000 0.612 0.028
#> GSM550793 3 0.5565 6.73e-01 0.244 0.000 0.652 0.092 0.012
#> GSM550794 2 0.6032 3.46e-01 0.032 0.520 0.000 0.396 0.052
#> GSM550795 1 0.3352 6.88e-01 0.800 0.004 0.004 0.192 0.000
#> GSM550798 1 0.3234 6.53e-01 0.852 0.000 0.064 0.084 0.000
#> GSM550803 1 0.1557 7.03e-01 0.940 0.000 0.008 0.052 0.000
#> GSM550805 1 0.5901 3.38e-01 0.476 0.064 0.008 0.448 0.004
#> GSM550823 4 0.5032 5.20e-01 0.092 0.220 0.000 0.688 0.000
#> GSM550824 1 0.0162 7.13e-01 0.996 0.000 0.000 0.004 0.000
#> GSM550825 1 0.5099 5.29e-01 0.708 0.000 0.168 0.120 0.004
#> GSM550827 4 0.6472 2.25e-01 0.184 0.384 0.000 0.432 0.000
#> GSM550828 1 0.2424 7.17e-01 0.868 0.000 0.000 0.132 0.000
#> GSM550829 1 0.5099 5.29e-01 0.708 0.000 0.168 0.120 0.004
#> GSM550830 4 0.5032 5.20e-01 0.092 0.220 0.000 0.688 0.000
#> GSM550834 1 0.3177 6.87e-01 0.792 0.000 0.000 0.208 0.000
#> GSM550839 4 0.7530 -1.16e-01 0.000 0.328 0.036 0.344 0.292
#> GSM550840 1 0.5652 3.46e-01 0.468 0.064 0.000 0.464 0.004
#> GSM550843 2 0.7690 -4.83e-02 0.000 0.328 0.048 0.324 0.300
#> GSM550844 1 0.5901 3.38e-01 0.476 0.064 0.008 0.448 0.004
#> GSM550845 2 0.3582 6.40e-01 0.008 0.768 0.000 0.224 0.000
#> GSM550848 1 0.6162 2.85e-01 0.532 0.160 0.000 0.308 0.000
#> GSM550854 1 0.0162 7.13e-01 0.996 0.000 0.000 0.004 0.000
#> GSM550857 3 0.0404 7.39e-01 0.000 0.000 0.988 0.000 0.012
#> GSM550858 1 0.3109 6.91e-01 0.800 0.000 0.000 0.200 0.000
#> GSM550859 1 0.0162 7.13e-01 0.996 0.000 0.000 0.004 0.000
#> GSM550862 1 0.3109 6.91e-01 0.800 0.000 0.000 0.200 0.000
#> GSM550865 4 0.4510 -6.03e-02 0.432 0.008 0.000 0.560 0.000
#> GSM550868 4 0.5379 5.24e-01 0.168 0.164 0.000 0.668 0.000
#> GSM550869 4 0.8224 -1.26e-01 0.048 0.172 0.052 0.436 0.292
#> GSM550870 2 0.3551 6.43e-01 0.008 0.772 0.000 0.220 0.000
#> GSM550871 4 0.7525 -1.06e-01 0.000 0.328 0.036 0.348 0.288
#> GSM550872 4 0.4689 -2.83e-02 0.424 0.016 0.000 0.560 0.000
#> GSM550873 2 0.6017 3.55e-01 0.032 0.528 0.000 0.388 0.052
#> GSM550874 2 0.2890 6.86e-01 0.004 0.836 0.000 0.160 0.000
#> GSM550876 5 0.7587 2.53e-01 0.000 0.244 0.048 0.316 0.392
#> GSM550877 2 0.2605 6.91e-01 0.000 0.852 0.000 0.148 0.000
#> GSM550878 5 0.7558 3.03e-01 0.000 0.244 0.052 0.276 0.428
#> GSM550879 1 0.2377 7.18e-01 0.872 0.000 0.000 0.128 0.000
#> GSM550882 3 0.7447 3.97e-01 0.064 0.012 0.536 0.180 0.208
#> GSM550888 3 0.0404 7.39e-01 0.000 0.000 0.988 0.000 0.012
#> GSM550890 4 0.6012 4.37e-01 0.132 0.332 0.000 0.536 0.000
#> GSM550891 3 0.4540 4.35e-01 0.000 0.000 0.656 0.024 0.320
#> GSM550892 4 0.4559 -1.86e-01 0.480 0.008 0.000 0.512 0.000
#> GSM550893 4 0.4084 3.69e-01 0.004 0.328 0.000 0.668 0.000
#> GSM550895 4 0.4298 3.29e-01 0.008 0.352 0.000 0.640 0.000
#> GSM550896 4 0.4341 1.98e-01 0.004 0.404 0.000 0.592 0.000
#> GSM550898 1 0.0162 7.13e-01 0.996 0.000 0.000 0.004 0.000
#> GSM550899 2 0.2561 6.94e-01 0.000 0.856 0.000 0.144 0.000
#> GSM550900 4 0.4879 5.09e-01 0.076 0.228 0.000 0.696 0.000
#> GSM550901 1 0.6148 2.96e-01 0.536 0.160 0.000 0.304 0.000
#> GSM550902 3 0.5565 6.73e-01 0.244 0.000 0.652 0.092 0.012
#> GSM550904 1 0.3759 6.99e-01 0.764 0.000 0.016 0.220 0.000
#> GSM550908 3 0.0404 7.39e-01 0.000 0.000 0.988 0.000 0.012
#> GSM550912 2 0.3086 6.80e-01 0.004 0.816 0.000 0.180 0.000
#> GSM550914 4 0.6012 4.37e-01 0.132 0.332 0.000 0.536 0.000
#> GSM550918 2 0.3612 6.37e-01 0.008 0.764 0.000 0.228 0.000
#> GSM550922 2 0.6247 7.03e-02 0.000 0.488 0.012 0.104 0.396
#> GSM550923 1 0.3019 6.63e-01 0.864 0.000 0.048 0.088 0.000
#> GSM550925 4 0.5418 -7.29e-05 0.320 0.068 0.000 0.608 0.004
#> GSM550802 2 0.6578 3.05e-01 0.040 0.480 0.004 0.404 0.072
#> GSM550812 2 0.6586 2.89e-01 0.040 0.472 0.004 0.412 0.072
#> GSM550831 1 0.3177 6.87e-01 0.792 0.000 0.000 0.208 0.000
#> GSM550847 1 0.0000 7.13e-01 1.000 0.000 0.000 0.000 0.000
#> GSM550860 4 0.8269 -2.09e-01 0.048 0.152 0.060 0.416 0.324
#> GSM550875 1 0.5901 3.38e-01 0.476 0.064 0.008 0.448 0.004
#> GSM550880 4 0.4723 -1.03e-01 0.448 0.016 0.000 0.536 0.000
#> GSM550881 3 0.5439 6.86e-01 0.232 0.000 0.668 0.088 0.012
#> GSM550883 3 0.5439 6.86e-01 0.232 0.000 0.668 0.088 0.012
#> GSM550884 2 0.6425 3.09e-01 0.052 0.504 0.004 0.392 0.048
#> GSM550910 5 0.2260 5.84e-01 0.000 0.064 0.000 0.028 0.908
#> GSM550916 4 0.4415 -2.44e-01 0.444 0.004 0.000 0.552 0.000
#> GSM550920 2 0.7250 1.76e-01 0.004 0.416 0.016 0.288 0.276
cbind(get_classes(res, k = 6), get_membership(res, k = 6))
#> class entropy silhouette p1 p2 p3 p4 p5 p6
#> GSM550785 1 0.5003 0.32745 0.588 0.000 0.000 0.092 0.000 0.320
#> GSM550786 4 0.6940 0.26761 0.036 0.312 0.000 0.480 0.120 0.052
#> GSM550788 2 0.2631 0.66208 0.000 0.840 0.000 0.152 0.000 0.008
#> GSM550789 2 0.0260 0.68375 0.000 0.992 0.000 0.008 0.000 0.000
#> GSM550790 1 0.4975 0.33232 0.596 0.000 0.000 0.092 0.000 0.312
#> GSM550791 1 0.6573 -0.02732 0.404 0.036 0.000 0.204 0.000 0.356
#> GSM550792 4 0.5710 0.15004 0.012 0.372 0.000 0.496 0.000 0.120
#> GSM550796 2 0.0260 0.67739 0.000 0.992 0.000 0.008 0.000 0.000
#> GSM550797 2 0.0260 0.68375 0.000 0.992 0.000 0.008 0.000 0.000
#> GSM550799 4 0.6260 0.18610 0.000 0.264 0.000 0.444 0.280 0.012
#> GSM550800 2 0.5723 0.16816 0.000 0.508 0.000 0.292 0.000 0.200
#> GSM550801 2 0.2662 0.68070 0.000 0.856 0.000 0.120 0.000 0.024
#> GSM550804 2 0.4312 0.57774 0.000 0.676 0.000 0.272 0.000 0.052
#> GSM550806 4 0.6209 0.15366 0.000 0.044 0.036 0.604 0.228 0.088
#> GSM550807 2 0.2784 0.67781 0.000 0.848 0.000 0.124 0.000 0.028
#> GSM550808 2 0.2678 0.62899 0.000 0.860 0.000 0.116 0.020 0.004
#> GSM550809 1 0.4728 0.52889 0.660 0.000 0.000 0.080 0.004 0.256
#> GSM550810 2 0.2633 0.63130 0.000 0.864 0.000 0.112 0.020 0.004
#> GSM550811 1 0.4810 0.51952 0.624 0.000 0.000 0.084 0.000 0.292
#> GSM550813 2 0.3998 0.63585 0.000 0.712 0.000 0.248 0.000 0.040
#> GSM550814 2 0.3936 0.63046 0.000 0.700 0.000 0.276 0.004 0.020
#> GSM550815 2 0.0260 0.67739 0.000 0.992 0.000 0.008 0.000 0.000
#> GSM550816 2 0.5535 0.20307 0.004 0.520 0.000 0.384 0.016 0.076
#> GSM550817 5 0.1524 0.87828 0.000 0.008 0.000 0.060 0.932 0.000
#> GSM550818 5 0.1524 0.87828 0.000 0.008 0.000 0.060 0.932 0.000
#> GSM550819 4 0.5995 0.35884 0.052 0.284 0.000 0.568 0.004 0.092
#> GSM550820 1 0.4871 0.51729 0.616 0.000 0.000 0.088 0.000 0.296
#> GSM550821 2 0.5636 0.17617 0.000 0.512 0.000 0.384 0.032 0.072
#> GSM550822 2 0.0458 0.67806 0.000 0.984 0.000 0.016 0.000 0.000
#> GSM550826 1 0.5202 0.51238 0.616 0.004 0.000 0.104 0.004 0.272
#> GSM550832 2 0.1956 0.67978 0.000 0.908 0.000 0.080 0.008 0.004
#> GSM550833 2 0.2755 0.66996 0.000 0.844 0.000 0.140 0.012 0.004
#> GSM550835 2 0.5097 0.24843 0.000 0.544 0.000 0.384 0.064 0.008
#> GSM550836 3 0.0000 0.72352 0.000 0.000 1.000 0.000 0.000 0.000
#> GSM550837 2 0.5049 0.25326 0.000 0.548 0.000 0.384 0.060 0.008
#> GSM550838 1 0.4728 0.52889 0.660 0.000 0.000 0.080 0.004 0.256
#> GSM550841 5 0.4356 0.69546 0.000 0.140 0.000 0.136 0.724 0.000
#> GSM550842 2 0.3530 0.54884 0.000 0.792 0.000 0.152 0.056 0.000
#> GSM550846 6 0.7194 0.08955 0.092 0.320 0.000 0.228 0.000 0.360
#> GSM550849 4 0.6581 -0.04092 0.088 0.112 0.000 0.472 0.000 0.328
#> GSM550850 1 0.4989 0.32958 0.592 0.000 0.000 0.092 0.000 0.316
#> GSM550851 2 0.4990 0.26851 0.000 0.556 0.000 0.380 0.056 0.008
#> GSM550852 4 0.5710 0.15004 0.012 0.372 0.000 0.496 0.000 0.120
#> GSM550853 2 0.3261 0.66150 0.000 0.780 0.000 0.204 0.000 0.016
#> GSM550855 2 0.3403 0.65591 0.000 0.768 0.000 0.212 0.000 0.020
#> GSM550856 2 0.4085 0.60357 0.000 0.704 0.000 0.252 0.000 0.044
#> GSM550861 2 0.1267 0.69688 0.000 0.940 0.000 0.060 0.000 0.000
#> GSM550863 6 0.6246 0.29436 0.352 0.008 0.000 0.248 0.000 0.392
#> GSM550864 2 0.3315 0.67028 0.000 0.780 0.000 0.200 0.000 0.020
#> GSM550866 2 0.4061 0.60344 0.000 0.708 0.000 0.248 0.000 0.044
#> GSM550867 1 0.0146 0.59599 0.996 0.000 0.000 0.000 0.004 0.000
#> GSM550885 1 0.0405 0.59606 0.988 0.000 0.000 0.000 0.004 0.008
#> GSM550886 4 0.5989 0.31924 0.000 0.272 0.000 0.524 0.188 0.016
#> GSM550887 2 0.0458 0.67814 0.000 0.984 0.000 0.016 0.000 0.000
#> GSM550889 4 0.5928 0.16052 0.000 0.220 0.000 0.436 0.000 0.344
#> GSM550894 2 0.1956 0.67978 0.000 0.908 0.000 0.080 0.008 0.004
#> GSM550897 6 0.6244 0.11548 0.340 0.028 0.000 0.164 0.000 0.468
#> GSM550903 2 0.2805 0.68767 0.000 0.828 0.000 0.160 0.000 0.012
#> GSM550905 2 0.4990 0.27110 0.000 0.556 0.000 0.380 0.056 0.008
#> GSM550906 2 0.0790 0.68918 0.000 0.968 0.000 0.032 0.000 0.000
#> GSM550907 5 0.1340 0.86298 0.000 0.000 0.008 0.040 0.948 0.004
#> GSM550909 2 0.6385 0.10947 0.004 0.484 0.000 0.344 0.116 0.052
#> GSM550911 5 0.1010 0.80934 0.000 0.000 0.000 0.004 0.960 0.036
#> GSM550913 2 0.0260 0.67739 0.000 0.992 0.000 0.008 0.000 0.000
#> GSM550915 1 0.7324 0.00167 0.404 0.144 0.000 0.192 0.000 0.260
#> GSM550917 2 0.4190 0.59507 0.000 0.692 0.000 0.260 0.000 0.048
#> GSM550919 1 0.7123 0.08358 0.436 0.116 0.000 0.188 0.000 0.260
#> GSM550921 3 0.0146 0.72184 0.000 0.000 0.996 0.000 0.000 0.004
#> GSM550924 4 0.5939 0.36578 0.000 0.240 0.004 0.584 0.140 0.032
#> GSM550926 2 0.3432 0.65465 0.000 0.764 0.000 0.216 0.000 0.020
#> GSM550927 2 0.0363 0.67996 0.000 0.988 0.000 0.012 0.000 0.000
#> GSM550787 6 0.5991 0.33378 0.100 0.036 0.000 0.328 0.004 0.532
#> GSM550793 3 0.5985 0.66253 0.168 0.000 0.604 0.044 0.004 0.180
#> GSM550794 4 0.5735 0.16047 0.012 0.368 0.000 0.496 0.000 0.124
#> GSM550795 1 0.4616 0.51643 0.704 0.004 0.000 0.088 0.004 0.200
#> GSM550798 1 0.4023 0.51933 0.748 0.000 0.040 0.012 0.000 0.200
#> GSM550803 1 0.2482 0.56556 0.848 0.000 0.000 0.004 0.000 0.148
#> GSM550805 6 0.6636 0.29035 0.288 0.028 0.004 0.248 0.000 0.432
#> GSM550823 4 0.6715 0.04726 0.068 0.156 0.000 0.428 0.000 0.348
#> GSM550824 1 0.0146 0.59599 0.996 0.000 0.000 0.000 0.004 0.000
#> GSM550825 1 0.5831 0.37813 0.556 0.000 0.136 0.024 0.000 0.284
#> GSM550827 4 0.7346 0.21082 0.148 0.284 0.000 0.388 0.000 0.180
#> GSM550828 1 0.3612 0.56745 0.764 0.000 0.000 0.036 0.000 0.200
#> GSM550829 1 0.5831 0.37813 0.556 0.000 0.136 0.024 0.000 0.284
#> GSM550830 4 0.6715 0.04726 0.068 0.156 0.000 0.428 0.000 0.348
#> GSM550834 1 0.4427 0.45983 0.660 0.000 0.000 0.056 0.000 0.284
#> GSM550839 4 0.5974 0.41229 0.000 0.172 0.012 0.616 0.164 0.036
#> GSM550840 6 0.6455 0.27192 0.288 0.028 0.000 0.232 0.000 0.452
#> GSM550843 4 0.6176 0.39754 0.000 0.172 0.020 0.584 0.200 0.024
#> GSM550844 6 0.6636 0.29035 0.288 0.028 0.004 0.248 0.000 0.432
#> GSM550845 2 0.4332 0.57275 0.000 0.672 0.000 0.276 0.000 0.052
#> GSM550848 1 0.7130 0.07400 0.436 0.116 0.000 0.192 0.000 0.256
#> GSM550854 1 0.0146 0.59599 0.996 0.000 0.000 0.000 0.004 0.000
#> GSM550857 3 0.0000 0.72352 0.000 0.000 1.000 0.000 0.000 0.000
#> GSM550858 1 0.4452 0.43025 0.636 0.000 0.000 0.048 0.000 0.316
#> GSM550859 1 0.0146 0.59599 0.996 0.000 0.000 0.000 0.004 0.000
#> GSM550862 1 0.4452 0.43025 0.636 0.000 0.000 0.048 0.000 0.316
#> GSM550865 6 0.6125 0.28025 0.364 0.004 0.000 0.236 0.000 0.396
#> GSM550868 4 0.6909 -0.12913 0.128 0.108 0.000 0.400 0.000 0.364
#> GSM550869 4 0.6375 0.21201 0.024 0.028 0.024 0.624 0.156 0.144
#> GSM550870 2 0.4254 0.58180 0.000 0.680 0.000 0.272 0.000 0.048
#> GSM550871 4 0.5944 0.41643 0.000 0.172 0.012 0.620 0.160 0.036
#> GSM550872 6 0.6146 0.28788 0.360 0.004 0.000 0.244 0.000 0.392
#> GSM550873 4 0.5710 0.15004 0.012 0.372 0.000 0.496 0.000 0.120
#> GSM550874 2 0.3432 0.65465 0.000 0.764 0.000 0.216 0.000 0.020
#> GSM550876 4 0.6056 0.20405 0.000 0.080 0.020 0.608 0.236 0.056
#> GSM550877 2 0.3261 0.66150 0.000 0.780 0.000 0.204 0.000 0.016
#> GSM550878 4 0.6014 0.15390 0.000 0.080 0.024 0.588 0.272 0.036
#> GSM550879 1 0.3551 0.56891 0.772 0.000 0.000 0.036 0.000 0.192
#> GSM550882 3 0.7100 0.38447 0.012 0.004 0.512 0.220 0.136 0.116
#> GSM550888 3 0.0000 0.72352 0.000 0.000 1.000 0.000 0.000 0.000
#> GSM550890 6 0.7194 0.08955 0.092 0.320 0.000 0.228 0.000 0.360
#> GSM550891 3 0.5174 0.33354 0.000 0.000 0.600 0.032 0.320 0.048
#> GSM550892 6 0.6042 0.19524 0.392 0.004 0.000 0.208 0.000 0.396
#> GSM550893 4 0.6023 0.19015 0.000 0.252 0.000 0.412 0.000 0.336
#> GSM550895 4 0.6050 0.21698 0.000 0.276 0.000 0.412 0.000 0.312
#> GSM550896 4 0.6093 0.22339 0.000 0.328 0.000 0.384 0.000 0.288
#> GSM550898 1 0.0146 0.59599 0.996 0.000 0.000 0.000 0.004 0.000
#> GSM550899 2 0.3364 0.67192 0.000 0.780 0.000 0.196 0.000 0.024
#> GSM550900 4 0.6629 0.06830 0.056 0.164 0.000 0.432 0.000 0.348
#> GSM550901 1 0.7123 0.08358 0.436 0.116 0.000 0.188 0.000 0.260
#> GSM550902 3 0.5985 0.66253 0.168 0.000 0.604 0.044 0.004 0.180
#> GSM550904 1 0.4819 0.51751 0.628 0.000 0.000 0.088 0.000 0.284
#> GSM550908 3 0.0000 0.72352 0.000 0.000 1.000 0.000 0.000 0.000
#> GSM550912 2 0.3998 0.63585 0.000 0.712 0.000 0.248 0.000 0.040
#> GSM550914 6 0.7194 0.08955 0.092 0.320 0.000 0.228 0.000 0.360
#> GSM550918 2 0.4388 0.56826 0.000 0.668 0.000 0.276 0.000 0.056
#> GSM550922 2 0.6223 -0.12628 0.000 0.380 0.000 0.300 0.316 0.004
#> GSM550923 1 0.3799 0.52372 0.756 0.000 0.024 0.012 0.000 0.208
#> GSM550925 6 0.5867 0.34917 0.132 0.028 0.000 0.284 0.000 0.556
#> GSM550802 4 0.5237 0.29908 0.016 0.308 0.000 0.604 0.004 0.068
#> GSM550812 4 0.5206 0.31473 0.016 0.300 0.000 0.612 0.004 0.068
#> GSM550831 1 0.4427 0.45983 0.660 0.000 0.000 0.056 0.000 0.284
#> GSM550847 1 0.0405 0.59622 0.988 0.000 0.000 0.000 0.004 0.008
#> GSM550860 4 0.6176 0.15765 0.020 0.012 0.032 0.628 0.176 0.132
#> GSM550875 6 0.6636 0.29035 0.288 0.028 0.004 0.248 0.000 0.432
#> GSM550880 6 0.6188 0.24740 0.380 0.008 0.000 0.224 0.000 0.388
#> GSM550881 3 0.5865 0.67218 0.152 0.000 0.620 0.044 0.004 0.180
#> GSM550883 3 0.5865 0.67218 0.152 0.000 0.620 0.044 0.004 0.180
#> GSM550884 4 0.6010 0.19089 0.028 0.360 0.000 0.500 0.004 0.108
#> GSM550910 5 0.3161 0.81667 0.000 0.028 0.000 0.136 0.828 0.008
#> GSM550916 6 0.5760 0.24127 0.268 0.000 0.000 0.224 0.000 0.508
#> GSM550920 4 0.5939 0.36578 0.000 0.240 0.004 0.584 0.140 0.032
Heatmaps for the consensus matrix. It visualizes the probability of two samples to be in a same group.
consensus_heatmap(res, k = 2)
consensus_heatmap(res, k = 3)
consensus_heatmap(res, k = 4)
consensus_heatmap(res, k = 5)
consensus_heatmap(res, k = 6)
Heatmaps for the membership of samples in all partitions to see how consistent they are:
membership_heatmap(res, k = 2)
membership_heatmap(res, k = 3)
membership_heatmap(res, k = 4)
membership_heatmap(res, k = 5)
membership_heatmap(res, k = 6)
As soon as we have had the classes for columns, we can look for signatures which are significantly different between classes which can be candidate marks for certain classes. Following are the heatmaps for signatures.
Signature heatmaps where rows are scaled:
get_signatures(res, k = 2)
get_signatures(res, k = 3)
get_signatures(res, k = 4)
get_signatures(res, k = 5)
get_signatures(res, k = 6)
Signature heatmaps where rows are not scaled:
get_signatures(res, k = 2, scale_rows = FALSE)
get_signatures(res, k = 3, scale_rows = FALSE)
get_signatures(res, k = 4, scale_rows = FALSE)
get_signatures(res, k = 5, scale_rows = FALSE)
get_signatures(res, k = 6, scale_rows = FALSE)
Compare the overlap of signatures from different k:
compare_signatures(res)
get_signature() returns a data frame invisibly. TO get the list of signatures, the function
call should be assigned to a variable explicitly. In following code, if plot argument is set
to FALSE, no heatmap is plotted while only the differential analysis is performed.
# code only for demonstration
tb = get_signature(res, k = ..., plot = FALSE)
An example of the output of tb is:
#> which_row fdr mean_1 mean_2 scaled_mean_1 scaled_mean_2 km
#> 1 38 0.042760348 8.373488 9.131774 -0.5533452 0.5164555 1
#> 2 40 0.018707592 7.106213 8.469186 -0.6173731 0.5762149 1
#> 3 55 0.019134737 10.221463 11.207825 -0.6159697 0.5749050 1
#> 4 59 0.006059896 5.921854 7.869574 -0.6899429 0.6439467 1
#> 5 60 0.018055526 8.928898 10.211722 -0.6204761 0.5791110 1
#> 6 98 0.009384629 15.714769 14.887706 0.6635654 -0.6193277 2
...
The columns in tb are:
which_row: row indices corresponding to the input matrix.fdr: FDR for the differential test. mean_x: The mean value in group x.scaled_mean_x: The mean value in group x after rows are scaled.km: Row groups if k-means clustering is applied to rows.UMAP plot which shows how samples are separated.
dimension_reduction(res, k = 2, method = "UMAP")
dimension_reduction(res, k = 3, method = "UMAP")
dimension_reduction(res, k = 4, method = "UMAP")
dimension_reduction(res, k = 5, method = "UMAP")
dimension_reduction(res, k = 6, method = "UMAP")
Following heatmap shows how subgroups are split when increasing k:
collect_classes(res)
Test correlation between subgroups and known annotations. If the known annotation is numeric, one-way ANOVA test is applied, and if the known annotation is discrete, chi-squared contingency table test is applied.
test_to_known_factors(res)
#> n disease.state(p) k
#> MAD:hclust 127 4.37e-04 2
#> MAD:hclust 126 1.35e-02 3
#> MAD:hclust 112 2.41e-04 4
#> MAD:hclust 91 9.78e-06 5
#> MAD:hclust 71 5.32e-04 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 51776 rows and 143 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 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 0.551 0.900 0.898 0.466 0.538 0.538
#> 3 3 0.501 0.643 0.809 0.355 0.685 0.478
#> 4 4 0.553 0.581 0.782 0.141 0.780 0.479
#> 5 5 0.628 0.625 0.778 0.079 0.884 0.621
#> 6 6 0.689 0.542 0.755 0.050 0.890 0.573
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
#> GSM550785 1 0.5059 0.935 0.888 0.112
#> GSM550786 2 0.6887 0.854 0.184 0.816
#> GSM550788 2 0.0376 0.927 0.004 0.996
#> GSM550789 2 0.0000 0.928 0.000 1.000
#> GSM550790 1 0.5059 0.935 0.888 0.112
#> GSM550791 1 0.5059 0.935 0.888 0.112
#> GSM550792 2 0.3431 0.906 0.064 0.936
#> GSM550796 2 0.0376 0.927 0.004 0.996
#> GSM550797 2 0.0000 0.928 0.000 1.000
#> GSM550799 2 0.5737 0.875 0.136 0.864
#> GSM550800 2 0.0000 0.928 0.000 1.000
#> GSM550801 2 0.0000 0.928 0.000 1.000
#> GSM550804 2 0.0000 0.928 0.000 1.000
#> GSM550806 2 0.8207 0.788 0.256 0.744
#> GSM550807 2 0.0000 0.928 0.000 1.000
#> GSM550808 2 0.4431 0.893 0.092 0.908
#> GSM550809 1 0.4562 0.934 0.904 0.096
#> GSM550810 2 0.0376 0.927 0.004 0.996
#> GSM550811 1 0.5408 0.927 0.876 0.124
#> GSM550813 2 0.0000 0.928 0.000 1.000
#> GSM550814 2 0.0376 0.927 0.004 0.996
#> GSM550815 2 0.0376 0.927 0.004 0.996
#> GSM550816 2 0.0000 0.928 0.000 1.000
#> GSM550817 2 0.6887 0.854 0.184 0.816
#> GSM550818 2 0.6887 0.854 0.184 0.816
#> GSM550819 2 0.1184 0.924 0.016 0.984
#> GSM550820 1 0.4562 0.934 0.904 0.096
#> GSM550821 2 0.4815 0.891 0.104 0.896
#> GSM550822 2 0.0376 0.927 0.004 0.996
#> GSM550826 1 0.0376 0.909 0.996 0.004
#> GSM550832 2 0.0376 0.927 0.004 0.996
#> GSM550833 2 0.0000 0.928 0.000 1.000
#> GSM550835 2 0.5294 0.879 0.120 0.880
#> GSM550836 1 0.0000 0.907 1.000 0.000
#> GSM550837 2 0.4431 0.893 0.092 0.908
#> GSM550838 1 0.0376 0.909 0.996 0.004
#> GSM550841 2 0.6247 0.867 0.156 0.844
#> GSM550842 2 0.4431 0.893 0.092 0.908
#> GSM550846 2 0.2948 0.908 0.052 0.948
#> GSM550849 2 0.4431 0.890 0.092 0.908
#> GSM550850 1 0.5059 0.935 0.888 0.112
#> GSM550851 2 0.4431 0.893 0.092 0.908
#> GSM550852 2 0.0000 0.928 0.000 1.000
#> GSM550853 2 0.0000 0.928 0.000 1.000
#> GSM550855 2 0.0000 0.928 0.000 1.000
#> GSM550856 2 0.0000 0.928 0.000 1.000
#> GSM550861 2 0.0000 0.928 0.000 1.000
#> GSM550863 2 0.5178 0.853 0.116 0.884
#> GSM550864 2 0.0000 0.928 0.000 1.000
#> GSM550866 2 0.0000 0.928 0.000 1.000
#> GSM550867 1 0.5059 0.935 0.888 0.112
#> GSM550885 1 0.5059 0.935 0.888 0.112
#> GSM550886 2 0.6887 0.854 0.184 0.816
#> GSM550887 2 0.0376 0.927 0.004 0.996
#> GSM550889 2 0.4298 0.874 0.088 0.912
#> GSM550894 2 0.0376 0.927 0.004 0.996
#> GSM550897 1 0.5178 0.933 0.884 0.116
#> GSM550903 2 0.0000 0.928 0.000 1.000
#> GSM550905 2 0.4431 0.893 0.092 0.908
#> GSM550906 2 0.0376 0.927 0.004 0.996
#> GSM550907 2 0.6887 0.854 0.184 0.816
#> GSM550909 2 0.5519 0.886 0.128 0.872
#> GSM550911 2 0.6887 0.854 0.184 0.816
#> GSM550913 2 0.0000 0.928 0.000 1.000
#> GSM550915 2 0.3879 0.884 0.076 0.924
#> GSM550917 2 0.0000 0.928 0.000 1.000
#> GSM550919 2 0.2423 0.909 0.040 0.960
#> GSM550921 1 0.0000 0.907 1.000 0.000
#> GSM550924 2 0.6531 0.865 0.168 0.832
#> GSM550926 2 0.0000 0.928 0.000 1.000
#> GSM550927 2 0.0000 0.928 0.000 1.000
#> GSM550787 2 0.7453 0.833 0.212 0.788
#> GSM550793 1 0.0000 0.907 1.000 0.000
#> GSM550794 2 0.4022 0.898 0.080 0.920
#> GSM550795 1 0.5059 0.935 0.888 0.112
#> GSM550798 1 0.0376 0.909 0.996 0.004
#> GSM550803 1 0.4562 0.933 0.904 0.096
#> GSM550805 1 0.5408 0.926 0.876 0.124
#> GSM550823 2 0.1633 0.922 0.024 0.976
#> GSM550824 1 0.5059 0.935 0.888 0.112
#> GSM550825 1 0.0000 0.907 1.000 0.000
#> GSM550827 2 0.4298 0.879 0.088 0.912
#> GSM550828 1 0.5059 0.935 0.888 0.112
#> GSM550829 1 0.0376 0.909 0.996 0.004
#> GSM550830 2 0.5178 0.851 0.116 0.884
#> GSM550834 1 0.5408 0.926 0.876 0.124
#> GSM550839 2 0.6887 0.854 0.184 0.816
#> GSM550840 1 0.5059 0.935 0.888 0.112
#> GSM550843 2 0.6887 0.854 0.184 0.816
#> GSM550844 1 0.5059 0.935 0.888 0.112
#> GSM550845 2 0.0000 0.928 0.000 1.000
#> GSM550848 2 0.2236 0.911 0.036 0.964
#> GSM550854 1 0.5059 0.935 0.888 0.112
#> GSM550857 1 0.0000 0.907 1.000 0.000
#> GSM550858 1 0.5294 0.930 0.880 0.120
#> GSM550859 1 0.5059 0.935 0.888 0.112
#> GSM550862 1 0.5059 0.935 0.888 0.112
#> GSM550865 2 0.6973 0.761 0.188 0.812
#> GSM550868 2 0.6973 0.761 0.188 0.812
#> GSM550869 2 0.8499 0.755 0.276 0.724
#> GSM550870 2 0.0000 0.928 0.000 1.000
#> GSM550871 2 0.6887 0.854 0.184 0.816
#> GSM550872 2 0.6973 0.761 0.188 0.812
#> GSM550873 2 0.0672 0.927 0.008 0.992
#> GSM550874 2 0.0000 0.928 0.000 1.000
#> GSM550876 2 0.6887 0.854 0.184 0.816
#> GSM550877 2 0.0000 0.928 0.000 1.000
#> GSM550878 2 0.6887 0.854 0.184 0.816
#> GSM550879 1 0.5059 0.935 0.888 0.112
#> GSM550882 1 0.2236 0.888 0.964 0.036
#> GSM550888 1 0.0000 0.907 1.000 0.000
#> GSM550890 2 0.4298 0.879 0.088 0.912
#> GSM550891 1 0.2603 0.883 0.956 0.044
#> GSM550892 1 0.5294 0.930 0.880 0.120
#> GSM550893 2 0.0000 0.928 0.000 1.000
#> GSM550895 2 0.0000 0.928 0.000 1.000
#> GSM550896 2 0.0000 0.928 0.000 1.000
#> GSM550898 1 0.5059 0.935 0.888 0.112
#> GSM550899 2 0.0000 0.928 0.000 1.000
#> GSM550900 2 0.4562 0.874 0.096 0.904
#> GSM550901 1 0.6531 0.883 0.832 0.168
#> GSM550902 1 0.0376 0.909 0.996 0.004
#> GSM550904 1 0.0376 0.909 0.996 0.004
#> GSM550908 1 0.0000 0.907 1.000 0.000
#> GSM550912 2 0.0000 0.928 0.000 1.000
#> GSM550914 2 0.2236 0.911 0.036 0.964
#> GSM550918 2 0.0000 0.928 0.000 1.000
#> GSM550922 2 0.5737 0.875 0.136 0.864
#> GSM550923 1 0.0376 0.909 0.996 0.004
#> GSM550925 1 0.6531 0.883 0.832 0.168
#> GSM550802 2 0.0376 0.927 0.004 0.996
#> GSM550812 2 0.3431 0.906 0.064 0.936
#> GSM550831 1 0.5059 0.935 0.888 0.112
#> GSM550847 1 0.5059 0.935 0.888 0.112
#> GSM550860 1 0.2236 0.888 0.964 0.036
#> GSM550875 1 0.4161 0.932 0.916 0.084
#> GSM550880 1 0.9933 0.328 0.548 0.452
#> GSM550881 1 0.0000 0.907 1.000 0.000
#> GSM550883 1 0.0000 0.907 1.000 0.000
#> GSM550884 2 0.4022 0.900 0.080 0.920
#> GSM550910 2 0.6887 0.854 0.184 0.816
#> GSM550916 1 0.5059 0.935 0.888 0.112
#> GSM550920 2 0.6887 0.854 0.184 0.816
cbind(get_classes(res, k = 3), get_membership(res, k = 3))
#> class entropy silhouette p1 p2 p3
#> GSM550785 1 0.0000 0.792265 1.000 0.000 0.000
#> GSM550786 3 0.5529 0.556501 0.000 0.296 0.704
#> GSM550788 2 0.2261 0.792350 0.000 0.932 0.068
#> GSM550789 2 0.3482 0.776403 0.000 0.872 0.128
#> GSM550790 1 0.0000 0.792265 1.000 0.000 0.000
#> GSM550791 1 0.0000 0.792265 1.000 0.000 0.000
#> GSM550792 2 0.7492 0.297908 0.340 0.608 0.052
#> GSM550796 2 0.4346 0.736530 0.000 0.816 0.184
#> GSM550797 2 0.3340 0.780013 0.000 0.880 0.120
#> GSM550799 3 0.5591 0.495568 0.000 0.304 0.696
#> GSM550800 2 0.0237 0.793942 0.000 0.996 0.004
#> GSM550801 2 0.3116 0.783821 0.000 0.892 0.108
#> GSM550804 2 0.0424 0.794658 0.000 0.992 0.008
#> GSM550806 3 0.4731 0.656078 0.032 0.128 0.840
#> GSM550807 2 0.2165 0.792751 0.000 0.936 0.064
#> GSM550808 2 0.4654 0.714524 0.000 0.792 0.208
#> GSM550809 1 0.1031 0.785970 0.976 0.000 0.024
#> GSM550810 2 0.4346 0.736530 0.000 0.816 0.184
#> GSM550811 1 0.3791 0.740104 0.892 0.060 0.048
#> GSM550813 2 0.0237 0.792237 0.000 0.996 0.004
#> GSM550814 2 0.0424 0.793870 0.000 0.992 0.008
#> GSM550815 2 0.4346 0.736530 0.000 0.816 0.184
#> GSM550816 2 0.3412 0.778644 0.000 0.876 0.124
#> GSM550817 3 0.4842 0.582883 0.000 0.224 0.776
#> GSM550818 3 0.3686 0.643876 0.000 0.140 0.860
#> GSM550819 2 0.5138 0.657691 0.120 0.828 0.052
#> GSM550820 1 0.1031 0.785970 0.976 0.000 0.024
#> GSM550821 2 0.5098 0.693944 0.000 0.752 0.248
#> GSM550822 2 0.4346 0.736530 0.000 0.816 0.184
#> GSM550826 1 0.3340 0.679239 0.880 0.000 0.120
#> GSM550832 2 0.3412 0.778742 0.000 0.876 0.124
#> GSM550833 2 0.3412 0.778742 0.000 0.876 0.124
#> GSM550835 2 0.6308 0.087583 0.000 0.508 0.492
#> GSM550836 3 0.5216 0.575423 0.260 0.000 0.740
#> GSM550837 2 0.4654 0.714524 0.000 0.792 0.208
#> GSM550838 1 0.1031 0.785970 0.976 0.000 0.024
#> GSM550841 3 0.5591 0.495568 0.000 0.304 0.696
#> GSM550842 2 0.4654 0.714524 0.000 0.792 0.208
#> GSM550846 2 0.7327 0.373314 0.312 0.636 0.052
#> GSM550849 1 0.8195 0.251673 0.492 0.436 0.072
#> GSM550850 1 0.0000 0.792265 1.000 0.000 0.000
#> GSM550851 2 0.4654 0.714524 0.000 0.792 0.208
#> GSM550852 2 0.1643 0.769872 0.000 0.956 0.044
#> GSM550853 2 0.2261 0.792350 0.000 0.932 0.068
#> GSM550855 2 0.1964 0.793207 0.000 0.944 0.056
#> GSM550856 2 0.0000 0.793598 0.000 1.000 0.000
#> GSM550861 2 0.3412 0.778742 0.000 0.876 0.124
#> GSM550863 1 0.7757 0.372224 0.540 0.408 0.052
#> GSM550864 2 0.0000 0.793598 0.000 1.000 0.000
#> GSM550866 2 0.0829 0.786915 0.012 0.984 0.004
#> GSM550867 1 0.1411 0.780522 0.964 0.000 0.036
#> GSM550885 1 0.1411 0.780522 0.964 0.000 0.036
#> GSM550886 3 0.5810 0.404690 0.000 0.336 0.664
#> GSM550887 2 0.4346 0.736530 0.000 0.816 0.184
#> GSM550889 2 0.6781 0.497455 0.244 0.704 0.052
#> GSM550894 2 0.4178 0.746463 0.000 0.828 0.172
#> GSM550897 1 0.1453 0.781461 0.968 0.024 0.008
#> GSM550903 2 0.3412 0.778742 0.000 0.876 0.124
#> GSM550905 2 0.4654 0.714524 0.000 0.792 0.208
#> GSM550906 2 0.3412 0.778742 0.000 0.876 0.124
#> GSM550907 3 0.1529 0.670859 0.000 0.040 0.960
#> GSM550909 2 0.5497 0.651198 0.000 0.708 0.292
#> GSM550911 3 0.1529 0.670859 0.000 0.040 0.960
#> GSM550913 2 0.3412 0.778742 0.000 0.876 0.124
#> GSM550915 1 0.7671 0.377367 0.544 0.408 0.048
#> GSM550917 2 0.0592 0.794627 0.000 0.988 0.012
#> GSM550919 1 0.7708 0.339610 0.528 0.424 0.048
#> GSM550921 3 0.4974 0.592182 0.236 0.000 0.764
#> GSM550924 2 0.8135 -0.227657 0.068 0.484 0.448
#> GSM550926 2 0.1031 0.782602 0.000 0.976 0.024
#> GSM550927 2 0.3482 0.776403 0.000 0.872 0.128
#> GSM550787 3 0.9059 0.306591 0.136 0.408 0.456
#> GSM550793 3 0.6062 0.433663 0.384 0.000 0.616
#> GSM550794 2 0.7589 0.236871 0.360 0.588 0.052
#> GSM550795 1 0.0000 0.792265 1.000 0.000 0.000
#> GSM550798 1 0.1411 0.780522 0.964 0.000 0.036
#> GSM550803 1 0.1411 0.780522 0.964 0.000 0.036
#> GSM550805 1 0.5835 0.664750 0.784 0.164 0.052
#> GSM550823 2 0.7065 0.449424 0.276 0.672 0.052
#> GSM550824 1 0.1411 0.780522 0.964 0.000 0.036
#> GSM550825 3 0.5859 0.484621 0.344 0.000 0.656
#> GSM550827 1 0.7699 0.349084 0.532 0.420 0.048
#> GSM550828 1 0.0000 0.792265 1.000 0.000 0.000
#> GSM550829 1 0.4931 0.482725 0.768 0.000 0.232
#> GSM550830 1 0.7832 0.263247 0.496 0.452 0.052
#> GSM550834 1 0.1015 0.786786 0.980 0.012 0.008
#> GSM550839 3 0.6260 0.355563 0.000 0.448 0.552
#> GSM550840 1 0.3921 0.735557 0.884 0.080 0.036
#> GSM550843 3 0.4750 0.631395 0.000 0.216 0.784
#> GSM550844 1 0.0000 0.792265 1.000 0.000 0.000
#> GSM550845 2 0.0237 0.792237 0.000 0.996 0.004
#> GSM550848 2 0.7708 -0.000823 0.424 0.528 0.048
#> GSM550854 1 0.1411 0.780522 0.964 0.000 0.036
#> GSM550857 3 0.5859 0.484621 0.344 0.000 0.656
#> GSM550858 1 0.0000 0.792265 1.000 0.000 0.000
#> GSM550859 1 0.1411 0.780522 0.964 0.000 0.036
#> GSM550862 1 0.0000 0.792265 1.000 0.000 0.000
#> GSM550865 1 0.7757 0.372224 0.540 0.408 0.052
#> GSM550868 1 0.7757 0.372224 0.540 0.408 0.052
#> GSM550869 3 0.9623 0.348060 0.216 0.336 0.448
#> GSM550870 2 0.0000 0.793598 0.000 1.000 0.000
#> GSM550871 3 0.7394 0.278184 0.032 0.472 0.496
#> GSM550872 1 0.7757 0.372224 0.540 0.408 0.052
#> GSM550873 2 0.1753 0.767658 0.000 0.952 0.048
#> GSM550874 2 0.0237 0.792237 0.000 0.996 0.004
#> GSM550876 3 0.5968 0.522004 0.000 0.364 0.636
#> GSM550877 2 0.0000 0.793598 0.000 1.000 0.000
#> GSM550878 3 0.2625 0.676789 0.000 0.084 0.916
#> GSM550879 1 0.0000 0.792265 1.000 0.000 0.000
#> GSM550882 3 0.5119 0.625504 0.160 0.028 0.812
#> GSM550888 3 0.5216 0.575423 0.260 0.000 0.740
#> GSM550890 1 0.7819 0.287036 0.508 0.440 0.052
#> GSM550891 3 0.3272 0.654824 0.104 0.004 0.892
#> GSM550892 1 0.0000 0.792265 1.000 0.000 0.000
#> GSM550893 2 0.0747 0.786982 0.000 0.984 0.016
#> GSM550895 2 0.3375 0.734637 0.044 0.908 0.048
#> GSM550896 2 0.0000 0.793598 0.000 1.000 0.000
#> GSM550898 1 0.1411 0.780522 0.964 0.000 0.036
#> GSM550899 2 0.0000 0.793598 0.000 1.000 0.000
#> GSM550900 1 0.7785 0.342775 0.528 0.420 0.052
#> GSM550901 1 0.5905 0.656020 0.772 0.184 0.044
#> GSM550902 1 0.1964 0.760605 0.944 0.000 0.056
#> GSM550904 1 0.1031 0.785970 0.976 0.000 0.024
#> GSM550908 3 0.5216 0.575423 0.260 0.000 0.740
#> GSM550912 2 0.1529 0.772323 0.000 0.960 0.040
#> GSM550914 2 0.7181 0.397564 0.304 0.648 0.048
#> GSM550918 2 0.0000 0.793598 0.000 1.000 0.000
#> GSM550922 3 0.5650 0.481525 0.000 0.312 0.688
#> GSM550923 1 0.1411 0.780522 0.964 0.000 0.036
#> GSM550925 1 0.5905 0.656020 0.772 0.184 0.044
#> GSM550802 2 0.4443 0.697182 0.084 0.864 0.052
#> GSM550812 2 0.6742 0.512687 0.240 0.708 0.052
#> GSM550831 1 0.0000 0.792265 1.000 0.000 0.000
#> GSM550847 1 0.1163 0.784393 0.972 0.000 0.028
#> GSM550860 3 0.6856 0.609828 0.132 0.128 0.740
#> GSM550875 1 0.2663 0.761911 0.932 0.024 0.044
#> GSM550880 1 0.6258 0.639460 0.752 0.196 0.052
#> GSM550881 3 0.5216 0.575423 0.260 0.000 0.740
#> GSM550883 3 0.5733 0.511049 0.324 0.000 0.676
#> GSM550884 2 0.7065 0.457330 0.276 0.672 0.052
#> GSM550910 3 0.5098 0.558505 0.000 0.248 0.752
#> GSM550916 1 0.0000 0.792265 1.000 0.000 0.000
#> GSM550920 3 0.5497 0.561485 0.000 0.292 0.708
cbind(get_classes(res, k = 4), get_membership(res, k = 4))
#> class entropy silhouette p1 p2 p3 p4
#> GSM550785 1 0.1557 0.8523 0.944 0.000 0.000 0.056
#> GSM550786 4 0.7052 -0.1591 0.000 0.128 0.372 0.500
#> GSM550788 2 0.1902 0.6726 0.000 0.932 0.004 0.064
#> GSM550789 2 0.0336 0.6853 0.000 0.992 0.000 0.008
#> GSM550790 1 0.1389 0.8515 0.952 0.000 0.000 0.048
#> GSM550791 1 0.3610 0.8084 0.800 0.000 0.000 0.200
#> GSM550792 4 0.3810 0.7260 0.092 0.060 0.000 0.848
#> GSM550796 2 0.0188 0.6800 0.000 0.996 0.004 0.000
#> GSM550797 2 0.0336 0.6853 0.000 0.992 0.000 0.008
#> GSM550799 2 0.7775 -0.2855 0.000 0.384 0.376 0.240
#> GSM550800 2 0.4837 0.4323 0.000 0.648 0.004 0.348
#> GSM550801 2 0.0469 0.6855 0.000 0.988 0.000 0.012
#> GSM550804 2 0.4624 0.4401 0.000 0.660 0.000 0.340
#> GSM550806 3 0.3486 0.7274 0.000 0.000 0.812 0.188
#> GSM550807 2 0.1389 0.6768 0.000 0.952 0.000 0.048
#> GSM550808 2 0.3831 0.5341 0.000 0.792 0.004 0.204
#> GSM550809 1 0.3448 0.8179 0.828 0.000 0.004 0.168
#> GSM550810 2 0.0376 0.6772 0.000 0.992 0.004 0.004
#> GSM550811 4 0.4103 0.5643 0.256 0.000 0.000 0.744
#> GSM550813 2 0.4679 0.4247 0.000 0.648 0.000 0.352
#> GSM550814 2 0.4837 0.4602 0.000 0.648 0.004 0.348
#> GSM550815 2 0.0188 0.6800 0.000 0.996 0.004 0.000
#> GSM550816 2 0.2654 0.6398 0.000 0.888 0.004 0.108
#> GSM550817 3 0.7772 0.2648 0.000 0.368 0.392 0.240
#> GSM550818 3 0.7521 0.4241 0.000 0.292 0.488 0.220
#> GSM550819 4 0.2982 0.7090 0.032 0.068 0.004 0.896
#> GSM550820 1 0.3208 0.8278 0.848 0.000 0.004 0.148
#> GSM550821 2 0.5898 0.3599 0.000 0.628 0.056 0.316
#> GSM550822 2 0.0188 0.6800 0.000 0.996 0.004 0.000
#> GSM550826 1 0.4194 0.7741 0.764 0.000 0.008 0.228
#> GSM550832 2 0.0336 0.6853 0.000 0.992 0.000 0.008
#> GSM550833 2 0.0336 0.6853 0.000 0.992 0.000 0.008
#> GSM550835 2 0.6797 0.2382 0.000 0.600 0.160 0.240
#> GSM550836 3 0.2011 0.7857 0.080 0.000 0.920 0.000
#> GSM550837 2 0.3831 0.5341 0.000 0.792 0.004 0.204
#> GSM550838 1 0.3448 0.8179 0.828 0.000 0.004 0.168
#> GSM550841 2 0.7774 -0.2783 0.000 0.388 0.372 0.240
#> GSM550842 2 0.4214 0.5216 0.000 0.780 0.016 0.204
#> GSM550846 4 0.4756 0.7187 0.144 0.072 0.000 0.784
#> GSM550849 4 0.2401 0.7011 0.092 0.004 0.000 0.904
#> GSM550850 1 0.1474 0.8525 0.948 0.000 0.000 0.052
#> GSM550851 2 0.3831 0.5341 0.000 0.792 0.004 0.204
#> GSM550852 4 0.4643 0.2913 0.000 0.344 0.000 0.656
#> GSM550853 2 0.1637 0.6743 0.000 0.940 0.000 0.060
#> GSM550855 2 0.1792 0.6708 0.000 0.932 0.000 0.068
#> GSM550856 2 0.5070 0.3170 0.000 0.580 0.004 0.416
#> GSM550861 2 0.0336 0.6853 0.000 0.992 0.000 0.008
#> GSM550863 4 0.5212 0.6900 0.192 0.068 0.000 0.740
#> GSM550864 2 0.4697 0.4183 0.000 0.644 0.000 0.356
#> GSM550866 2 0.5080 0.3077 0.000 0.576 0.004 0.420
#> GSM550867 1 0.0188 0.8356 0.996 0.000 0.004 0.000
#> GSM550885 1 0.0376 0.8366 0.992 0.000 0.004 0.004
#> GSM550886 2 0.7789 -0.2444 0.000 0.400 0.352 0.248
#> GSM550887 2 0.0188 0.6800 0.000 0.996 0.004 0.000
#> GSM550889 4 0.5458 0.5860 0.052 0.232 0.004 0.712
#> GSM550894 2 0.0000 0.6813 0.000 1.000 0.000 0.000
#> GSM550897 1 0.4978 0.5164 0.612 0.000 0.004 0.384
#> GSM550903 2 0.0336 0.6853 0.000 0.992 0.000 0.008
#> GSM550905 2 0.4468 0.4918 0.000 0.752 0.016 0.232
#> GSM550906 2 0.0336 0.6853 0.000 0.992 0.000 0.008
#> GSM550907 3 0.4452 0.7300 0.000 0.048 0.796 0.156
#> GSM550909 2 0.6549 0.2097 0.000 0.488 0.076 0.436
#> GSM550911 3 0.4452 0.7300 0.000 0.048 0.796 0.156
#> GSM550913 2 0.0336 0.6853 0.000 0.992 0.000 0.008
#> GSM550915 4 0.5392 0.6862 0.204 0.072 0.000 0.724
#> GSM550917 2 0.4543 0.4583 0.000 0.676 0.000 0.324
#> GSM550919 4 0.5392 0.6862 0.204 0.072 0.000 0.724
#> GSM550921 3 0.1474 0.7905 0.052 0.000 0.948 0.000
#> GSM550924 4 0.1722 0.6440 0.008 0.000 0.048 0.944
#> GSM550926 2 0.5163 0.1393 0.000 0.516 0.004 0.480
#> GSM550927 2 0.0336 0.6853 0.000 0.992 0.000 0.008
#> GSM550787 4 0.3109 0.6116 0.016 0.004 0.100 0.880
#> GSM550793 3 0.4546 0.6141 0.256 0.000 0.732 0.012
#> GSM550794 4 0.3542 0.7249 0.076 0.060 0.000 0.864
#> GSM550795 1 0.3726 0.7894 0.788 0.000 0.000 0.212
#> GSM550798 1 0.2402 0.7606 0.912 0.000 0.076 0.012
#> GSM550803 1 0.0376 0.8347 0.992 0.000 0.004 0.004
#> GSM550805 4 0.3448 0.6739 0.168 0.000 0.004 0.828
#> GSM550823 4 0.3979 0.7124 0.056 0.096 0.004 0.844
#> GSM550824 1 0.0188 0.8356 0.996 0.000 0.004 0.000
#> GSM550825 3 0.3907 0.6558 0.232 0.000 0.768 0.000
#> GSM550827 4 0.5429 0.6821 0.208 0.072 0.000 0.720
#> GSM550828 1 0.1474 0.8531 0.948 0.000 0.000 0.052
#> GSM550829 1 0.4284 0.5683 0.764 0.000 0.224 0.012
#> GSM550830 4 0.5555 0.7028 0.140 0.116 0.004 0.740
#> GSM550834 1 0.4331 0.6962 0.712 0.000 0.000 0.288
#> GSM550839 4 0.5022 0.3461 0.000 0.028 0.264 0.708
#> GSM550840 1 0.4800 0.5812 0.656 0.000 0.004 0.340
#> GSM550843 4 0.6840 -0.2402 0.000 0.100 0.432 0.468
#> GSM550844 1 0.3123 0.8292 0.844 0.000 0.000 0.156
#> GSM550845 4 0.4999 -0.0998 0.000 0.492 0.000 0.508
#> GSM550848 4 0.5473 0.6932 0.192 0.084 0.000 0.724
#> GSM550854 1 0.0188 0.8356 0.996 0.000 0.004 0.000
#> GSM550857 3 0.3024 0.7373 0.148 0.000 0.852 0.000
#> GSM550858 1 0.1474 0.8531 0.948 0.000 0.000 0.052
#> GSM550859 1 0.0188 0.8356 0.996 0.000 0.004 0.000
#> GSM550862 1 0.1474 0.8531 0.948 0.000 0.000 0.052
#> GSM550865 4 0.5352 0.6926 0.188 0.068 0.004 0.740
#> GSM550868 4 0.5352 0.6926 0.188 0.068 0.004 0.740
#> GSM550869 4 0.1124 0.6747 0.012 0.004 0.012 0.972
#> GSM550870 2 0.4643 0.4364 0.000 0.656 0.000 0.344
#> GSM550871 4 0.3791 0.4885 0.000 0.004 0.200 0.796
#> GSM550872 4 0.5352 0.6926 0.188 0.068 0.004 0.740
#> GSM550873 4 0.4661 0.1579 0.000 0.348 0.000 0.652
#> GSM550874 2 0.5070 0.3170 0.000 0.580 0.004 0.416
#> GSM550876 4 0.5649 0.0498 0.000 0.028 0.392 0.580
#> GSM550877 2 0.5060 0.3255 0.000 0.584 0.004 0.412
#> GSM550878 3 0.3625 0.7397 0.000 0.012 0.828 0.160
#> GSM550879 1 0.3528 0.8055 0.808 0.000 0.000 0.192
#> GSM550882 3 0.0336 0.7836 0.000 0.000 0.992 0.008
#> GSM550888 3 0.2011 0.7857 0.080 0.000 0.920 0.000
#> GSM550890 4 0.5356 0.6888 0.200 0.072 0.000 0.728
#> GSM550891 3 0.0188 0.7836 0.000 0.000 0.996 0.004
#> GSM550892 1 0.3569 0.7970 0.804 0.000 0.000 0.196
#> GSM550893 2 0.5070 0.3170 0.000 0.580 0.004 0.416
#> GSM550895 4 0.4456 0.5115 0.000 0.280 0.004 0.716
#> GSM550896 2 0.5039 0.3415 0.000 0.592 0.004 0.404
#> GSM550898 1 0.0188 0.8356 0.996 0.000 0.004 0.000
#> GSM550899 2 0.4643 0.4346 0.000 0.656 0.000 0.344
#> GSM550900 4 0.5312 0.6958 0.184 0.068 0.004 0.744
#> GSM550901 1 0.4985 0.2548 0.532 0.000 0.000 0.468
#> GSM550902 1 0.4175 0.7968 0.784 0.000 0.016 0.200
#> GSM550904 1 0.3448 0.8179 0.828 0.000 0.004 0.168
#> GSM550908 3 0.1792 0.7898 0.068 0.000 0.932 0.000
#> GSM550912 2 0.4961 0.2217 0.000 0.552 0.000 0.448
#> GSM550914 4 0.5380 0.7054 0.136 0.120 0.000 0.744
#> GSM550918 2 0.4624 0.4401 0.000 0.660 0.000 0.340
#> GSM550922 2 0.7756 -0.2297 0.000 0.412 0.348 0.240
#> GSM550923 1 0.0657 0.8333 0.984 0.000 0.004 0.012
#> GSM550925 4 0.4699 0.5405 0.320 0.000 0.004 0.676
#> GSM550802 4 0.3198 0.7074 0.032 0.080 0.004 0.884
#> GSM550812 4 0.2983 0.7126 0.040 0.068 0.000 0.892
#> GSM550831 1 0.1474 0.8531 0.948 0.000 0.000 0.052
#> GSM550847 1 0.0592 0.8417 0.984 0.000 0.000 0.016
#> GSM550860 4 0.4690 0.3713 0.012 0.000 0.276 0.712
#> GSM550875 1 0.5168 0.3113 0.504 0.000 0.004 0.492
#> GSM550880 4 0.4277 0.5730 0.280 0.000 0.000 0.720
#> GSM550881 3 0.1792 0.7898 0.068 0.000 0.932 0.000
#> GSM550883 3 0.2704 0.7577 0.124 0.000 0.876 0.000
#> GSM550884 4 0.2983 0.7126 0.040 0.068 0.000 0.892
#> GSM550910 3 0.7811 0.2542 0.000 0.368 0.380 0.252
#> GSM550916 1 0.1557 0.8523 0.944 0.000 0.000 0.056
#> GSM550920 4 0.7226 -0.2050 0.000 0.144 0.388 0.468
cbind(get_classes(res, k = 5), get_membership(res, k = 5))
#> class entropy silhouette p1 p2 p3 p4 p5
#> GSM550785 1 0.1153 0.79991 0.964 0.000 0.004 0.008 0.024
#> GSM550786 5 0.3688 0.66871 0.000 0.020 0.124 0.028 0.828
#> GSM550788 2 0.2891 0.67602 0.000 0.824 0.000 0.176 0.000
#> GSM550789 2 0.0162 0.71639 0.000 0.996 0.000 0.004 0.000
#> GSM550790 1 0.1106 0.79962 0.964 0.000 0.012 0.000 0.024
#> GSM550791 1 0.6083 0.62043 0.608 0.004 0.004 0.176 0.208
#> GSM550792 4 0.4370 0.70873 0.012 0.004 0.004 0.700 0.280
#> GSM550796 2 0.0162 0.71651 0.000 0.996 0.000 0.004 0.000
#> GSM550797 2 0.0162 0.71639 0.000 0.996 0.000 0.004 0.000
#> GSM550799 5 0.5354 0.72010 0.000 0.208 0.128 0.000 0.664
#> GSM550800 2 0.3707 0.60536 0.000 0.716 0.000 0.284 0.000
#> GSM550801 2 0.0324 0.71654 0.000 0.992 0.000 0.004 0.004
#> GSM550804 2 0.5555 0.54846 0.000 0.644 0.000 0.204 0.152
#> GSM550806 5 0.5228 0.53208 0.000 0.000 0.356 0.056 0.588
#> GSM550807 2 0.0566 0.71838 0.000 0.984 0.000 0.012 0.004
#> GSM550808 2 0.4300 -0.30951 0.000 0.524 0.000 0.000 0.476
#> GSM550809 1 0.5987 0.63816 0.620 0.000 0.012 0.224 0.144
#> GSM550810 2 0.0000 0.71653 0.000 1.000 0.000 0.000 0.000
#> GSM550811 4 0.4964 0.68483 0.032 0.004 0.004 0.648 0.312
#> GSM550813 2 0.5733 0.49661 0.000 0.608 0.000 0.256 0.136
#> GSM550814 2 0.5016 0.49519 0.000 0.608 0.000 0.348 0.044
#> GSM550815 2 0.0290 0.71616 0.000 0.992 0.000 0.008 0.000
#> GSM550816 2 0.4630 0.58316 0.000 0.744 0.000 0.116 0.140
#> GSM550817 5 0.5392 0.72045 0.000 0.192 0.144 0.000 0.664
#> GSM550818 5 0.4901 0.71067 0.000 0.096 0.196 0.000 0.708
#> GSM550819 4 0.1041 0.73175 0.000 0.004 0.000 0.964 0.032
#> GSM550820 1 0.5605 0.68459 0.672 0.000 0.012 0.172 0.144
#> GSM550821 5 0.3883 0.67852 0.000 0.216 0.004 0.016 0.764
#> GSM550822 2 0.0290 0.71616 0.000 0.992 0.000 0.008 0.000
#> GSM550826 1 0.6567 0.58144 0.560 0.000 0.020 0.228 0.192
#> GSM550832 2 0.0162 0.71639 0.000 0.996 0.000 0.004 0.000
#> GSM550833 2 0.0290 0.71616 0.000 0.992 0.000 0.008 0.000
#> GSM550835 5 0.5221 0.53600 0.000 0.400 0.048 0.000 0.552
#> GSM550836 3 0.0510 0.94404 0.016 0.000 0.984 0.000 0.000
#> GSM550837 2 0.4114 -0.01295 0.000 0.624 0.000 0.000 0.376
#> GSM550838 1 0.6082 0.63755 0.616 0.000 0.016 0.224 0.144
#> GSM550841 5 0.5354 0.72010 0.000 0.208 0.128 0.000 0.664
#> GSM550842 2 0.4302 -0.31936 0.000 0.520 0.000 0.000 0.480
#> GSM550846 4 0.4788 0.69837 0.024 0.004 0.004 0.660 0.308
#> GSM550849 4 0.4783 0.68080 0.016 0.004 0.004 0.628 0.348
#> GSM550850 1 0.1153 0.79991 0.964 0.000 0.004 0.008 0.024
#> GSM550851 2 0.4150 -0.05391 0.000 0.612 0.000 0.000 0.388
#> GSM550852 4 0.5477 0.62627 0.000 0.132 0.000 0.648 0.220
#> GSM550853 2 0.1908 0.70583 0.000 0.908 0.000 0.092 0.000
#> GSM550855 2 0.2074 0.70340 0.000 0.896 0.000 0.104 0.000
#> GSM550856 2 0.4632 0.38573 0.000 0.540 0.000 0.448 0.012
#> GSM550861 2 0.0162 0.71639 0.000 0.996 0.000 0.004 0.000
#> GSM550863 4 0.2054 0.73978 0.028 0.000 0.000 0.920 0.052
#> GSM550864 2 0.5762 0.49969 0.000 0.608 0.000 0.248 0.144
#> GSM550866 2 0.4650 0.34153 0.000 0.520 0.000 0.468 0.012
#> GSM550867 1 0.0794 0.79951 0.972 0.000 0.028 0.000 0.000
#> GSM550885 1 0.0794 0.79951 0.972 0.000 0.028 0.000 0.000
#> GSM550886 5 0.5176 0.73452 0.000 0.152 0.120 0.012 0.716
#> GSM550887 2 0.0290 0.71616 0.000 0.992 0.000 0.008 0.000
#> GSM550889 4 0.2189 0.67808 0.012 0.084 0.000 0.904 0.000
#> GSM550894 2 0.0000 0.71653 0.000 1.000 0.000 0.000 0.000
#> GSM550897 4 0.5018 0.45397 0.252 0.000 0.004 0.680 0.064
#> GSM550903 2 0.0162 0.71639 0.000 0.996 0.000 0.004 0.000
#> GSM550905 5 0.4126 0.55325 0.000 0.380 0.000 0.000 0.620
#> GSM550906 2 0.0162 0.71651 0.000 0.996 0.000 0.004 0.000
#> GSM550907 5 0.4415 0.51580 0.000 0.008 0.388 0.000 0.604
#> GSM550909 5 0.4696 0.65818 0.000 0.184 0.008 0.068 0.740
#> GSM550911 5 0.4403 0.52227 0.000 0.008 0.384 0.000 0.608
#> GSM550913 2 0.0162 0.71639 0.000 0.996 0.000 0.004 0.000
#> GSM550915 4 0.5320 0.68090 0.052 0.004 0.004 0.624 0.316
#> GSM550917 2 0.4096 0.66269 0.000 0.784 0.000 0.072 0.144
#> GSM550919 4 0.5411 0.68283 0.044 0.012 0.004 0.624 0.316
#> GSM550921 3 0.0794 0.92254 0.000 0.000 0.972 0.000 0.028
#> GSM550924 5 0.4321 -0.29059 0.000 0.000 0.004 0.396 0.600
#> GSM550926 4 0.4760 -0.10152 0.000 0.416 0.000 0.564 0.020
#> GSM550927 2 0.0290 0.71616 0.000 0.992 0.000 0.008 0.000
#> GSM550787 4 0.5545 0.45501 0.016 0.000 0.052 0.600 0.332
#> GSM550793 3 0.3688 0.79742 0.124 0.000 0.828 0.020 0.028
#> GSM550794 4 0.3889 0.72240 0.004 0.004 0.004 0.748 0.240
#> GSM550795 1 0.5927 0.58535 0.592 0.000 0.004 0.272 0.132
#> GSM550798 1 0.1341 0.78207 0.944 0.000 0.056 0.000 0.000
#> GSM550803 1 0.0794 0.79951 0.972 0.000 0.028 0.000 0.000
#> GSM550805 4 0.4003 0.72283 0.036 0.000 0.004 0.780 0.180
#> GSM550823 4 0.0854 0.72773 0.012 0.008 0.000 0.976 0.004
#> GSM550824 1 0.0794 0.79951 0.972 0.000 0.028 0.000 0.000
#> GSM550825 3 0.2020 0.87128 0.100 0.000 0.900 0.000 0.000
#> GSM550827 4 0.4888 0.70838 0.048 0.004 0.000 0.676 0.272
#> GSM550828 1 0.0486 0.80492 0.988 0.000 0.004 0.004 0.004
#> GSM550829 1 0.3424 0.62004 0.760 0.000 0.240 0.000 0.000
#> GSM550830 4 0.0807 0.72773 0.012 0.012 0.000 0.976 0.000
#> GSM550834 1 0.6536 0.33499 0.480 0.000 0.004 0.332 0.184
#> GSM550839 5 0.5492 0.40090 0.000 0.000 0.068 0.396 0.536
#> GSM550840 4 0.5363 0.23990 0.372 0.000 0.004 0.572 0.052
#> GSM550843 5 0.5364 0.69540 0.000 0.040 0.188 0.064 0.708
#> GSM550844 1 0.4455 0.71648 0.744 0.000 0.000 0.188 0.068
#> GSM550845 4 0.5113 -0.00375 0.000 0.380 0.000 0.576 0.044
#> GSM550848 4 0.5243 0.69968 0.048 0.008 0.004 0.652 0.288
#> GSM550854 1 0.0955 0.79917 0.968 0.000 0.028 0.004 0.000
#> GSM550857 3 0.1043 0.92719 0.040 0.000 0.960 0.000 0.000
#> GSM550858 1 0.0162 0.80402 0.996 0.000 0.000 0.004 0.000
#> GSM550859 1 0.0955 0.79917 0.968 0.000 0.028 0.004 0.000
#> GSM550862 1 0.0510 0.80390 0.984 0.000 0.000 0.016 0.000
#> GSM550865 4 0.1626 0.73240 0.044 0.000 0.000 0.940 0.016
#> GSM550868 4 0.1701 0.73157 0.048 0.000 0.000 0.936 0.016
#> GSM550869 4 0.2929 0.67431 0.008 0.000 0.000 0.840 0.152
#> GSM550870 2 0.5644 0.52881 0.000 0.628 0.000 0.228 0.144
#> GSM550871 4 0.4495 0.52663 0.000 0.000 0.064 0.736 0.200
#> GSM550872 4 0.1701 0.73157 0.048 0.000 0.000 0.936 0.016
#> GSM550873 4 0.6387 0.32351 0.000 0.168 0.000 0.440 0.392
#> GSM550874 4 0.4659 -0.30863 0.000 0.492 0.000 0.496 0.012
#> GSM550876 5 0.5470 0.55715 0.000 0.000 0.092 0.296 0.612
#> GSM550877 2 0.4644 0.36310 0.000 0.528 0.000 0.460 0.012
#> GSM550878 5 0.4161 0.50816 0.000 0.000 0.392 0.000 0.608
#> GSM550879 1 0.5748 0.66298 0.652 0.000 0.012 0.200 0.136
#> GSM550882 3 0.1386 0.91452 0.000 0.000 0.952 0.016 0.032
#> GSM550888 3 0.0510 0.94404 0.016 0.000 0.984 0.000 0.000
#> GSM550890 4 0.5060 0.69891 0.044 0.004 0.004 0.660 0.288
#> GSM550891 3 0.1121 0.90682 0.000 0.000 0.956 0.000 0.044
#> GSM550892 1 0.4354 0.66605 0.712 0.000 0.000 0.256 0.032
#> GSM550893 2 0.4659 0.28393 0.000 0.496 0.000 0.492 0.012
#> GSM550895 4 0.2068 0.67232 0.004 0.092 0.000 0.904 0.000
#> GSM550896 2 0.4622 0.41018 0.000 0.548 0.000 0.440 0.012
#> GSM550898 1 0.0955 0.79917 0.968 0.000 0.028 0.004 0.000
#> GSM550899 2 0.5693 0.51605 0.000 0.620 0.000 0.236 0.144
#> GSM550900 4 0.1043 0.72944 0.040 0.000 0.000 0.960 0.000
#> GSM550901 4 0.6656 0.48205 0.180 0.004 0.004 0.480 0.332
#> GSM550902 1 0.6568 0.55601 0.556 0.000 0.028 0.276 0.140
#> GSM550904 1 0.5890 0.66240 0.644 0.000 0.016 0.196 0.144
#> GSM550908 3 0.0671 0.94376 0.016 0.000 0.980 0.000 0.004
#> GSM550912 2 0.6254 0.21606 0.000 0.480 0.000 0.368 0.152
#> GSM550914 4 0.4661 0.71413 0.032 0.004 0.004 0.704 0.256
#> GSM550918 2 0.5555 0.54846 0.000 0.644 0.000 0.204 0.152
#> GSM550922 5 0.5295 0.71479 0.000 0.224 0.112 0.000 0.664
#> GSM550923 1 0.0880 0.79799 0.968 0.000 0.032 0.000 0.000
#> GSM550925 4 0.4219 0.71073 0.112 0.004 0.004 0.796 0.084
#> GSM550802 4 0.1124 0.73347 0.000 0.004 0.000 0.960 0.036
#> GSM550812 4 0.2732 0.73425 0.000 0.000 0.000 0.840 0.160
#> GSM550831 1 0.1717 0.79722 0.936 0.000 0.004 0.008 0.052
#> GSM550847 1 0.0671 0.80095 0.980 0.000 0.016 0.004 0.000
#> GSM550860 4 0.4427 0.60777 0.008 0.000 0.088 0.776 0.128
#> GSM550875 4 0.5272 0.50409 0.212 0.000 0.004 0.680 0.104
#> GSM550880 4 0.4801 0.68913 0.084 0.000 0.004 0.728 0.184
#> GSM550881 3 0.0798 0.94256 0.016 0.000 0.976 0.000 0.008
#> GSM550883 3 0.0510 0.94404 0.016 0.000 0.984 0.000 0.000
#> GSM550884 4 0.3074 0.72857 0.000 0.000 0.000 0.804 0.196
#> GSM550910 5 0.5084 0.73250 0.000 0.144 0.140 0.004 0.712
#> GSM550916 1 0.1507 0.79694 0.952 0.000 0.012 0.012 0.024
#> GSM550920 5 0.4614 0.69907 0.000 0.048 0.136 0.040 0.776
cbind(get_classes(res, k = 6), get_membership(res, k = 6))
#> class entropy silhouette p1 p2 p3 p4 p5 p6
#> GSM550785 1 0.3874 0.9116 0.636 0.000 0.000 0.000 0.008 0.356
#> GSM550786 5 0.2483 0.7445 0.020 0.004 0.004 0.016 0.900 0.056
#> GSM550788 2 0.2871 0.6197 0.004 0.804 0.000 0.192 0.000 0.000
#> GSM550789 2 0.0146 0.7546 0.004 0.996 0.000 0.000 0.000 0.000
#> GSM550790 1 0.3804 0.8988 0.656 0.000 0.000 0.000 0.008 0.336
#> GSM550791 6 0.4964 0.3922 0.224 0.008 0.004 0.040 0.032 0.692
#> GSM550792 6 0.7419 0.2352 0.256 0.004 0.008 0.308 0.072 0.352
#> GSM550796 2 0.0508 0.7538 0.004 0.984 0.000 0.012 0.000 0.000
#> GSM550797 2 0.0146 0.7546 0.004 0.996 0.000 0.000 0.000 0.000
#> GSM550799 5 0.1829 0.7616 0.012 0.064 0.004 0.000 0.920 0.000
#> GSM550800 2 0.3955 0.1912 0.004 0.560 0.000 0.436 0.000 0.000
#> GSM550801 2 0.0260 0.7543 0.000 0.992 0.000 0.008 0.000 0.000
#> GSM550804 2 0.6789 0.4128 0.224 0.544 0.008 0.160 0.040 0.024
#> GSM550806 5 0.5767 0.5348 0.052 0.000 0.124 0.204 0.620 0.000
#> GSM550807 2 0.1082 0.7440 0.004 0.956 0.000 0.040 0.000 0.000
#> GSM550808 2 0.4098 -0.2385 0.008 0.496 0.000 0.000 0.496 0.000
#> GSM550809 6 0.1693 0.4044 0.020 0.000 0.004 0.044 0.000 0.932
#> GSM550810 2 0.0291 0.7535 0.004 0.992 0.000 0.000 0.004 0.000
#> GSM550811 6 0.5698 0.4623 0.228 0.000 0.004 0.144 0.020 0.604
#> GSM550813 2 0.6237 0.4444 0.184 0.584 0.008 0.184 0.036 0.004
#> GSM550814 2 0.4782 0.2167 0.008 0.544 0.000 0.416 0.028 0.004
#> GSM550815 2 0.0508 0.7538 0.004 0.984 0.000 0.012 0.000 0.000
#> GSM550816 2 0.6760 0.4366 0.164 0.588 0.008 0.056 0.036 0.148
#> GSM550817 5 0.2173 0.7578 0.028 0.064 0.004 0.000 0.904 0.000
#> GSM550818 5 0.2038 0.7567 0.028 0.032 0.020 0.000 0.920 0.000
#> GSM550819 4 0.2206 0.5693 0.008 0.000 0.000 0.904 0.024 0.064
#> GSM550820 6 0.1826 0.3571 0.052 0.000 0.004 0.020 0.000 0.924
#> GSM550821 5 0.2251 0.7598 0.016 0.052 0.008 0.008 0.912 0.004
#> GSM550822 2 0.0653 0.7528 0.004 0.980 0.000 0.012 0.004 0.000
#> GSM550826 6 0.1692 0.4350 0.000 0.000 0.012 0.048 0.008 0.932
#> GSM550832 2 0.0000 0.7550 0.000 1.000 0.000 0.000 0.000 0.000
#> GSM550833 2 0.0508 0.7538 0.004 0.984 0.000 0.012 0.000 0.000
#> GSM550835 5 0.4185 0.5197 0.020 0.332 0.000 0.004 0.644 0.000
#> GSM550836 3 0.0458 0.9404 0.000 0.000 0.984 0.000 0.016 0.000
#> GSM550837 2 0.3993 0.0505 0.008 0.592 0.000 0.000 0.400 0.000
#> GSM550838 6 0.1737 0.4027 0.020 0.000 0.008 0.040 0.000 0.932
#> GSM550841 5 0.2094 0.7578 0.024 0.064 0.004 0.000 0.908 0.000
#> GSM550842 5 0.3966 0.3179 0.004 0.444 0.000 0.000 0.552 0.000
#> GSM550846 6 0.6748 0.3788 0.236 0.000 0.012 0.256 0.032 0.464
#> GSM550849 6 0.6977 0.3679 0.300 0.000 0.004 0.160 0.088 0.448
#> GSM550850 1 0.4089 0.8808 0.632 0.000 0.000 0.004 0.012 0.352
#> GSM550851 2 0.4032 -0.0141 0.008 0.572 0.000 0.000 0.420 0.000
#> GSM550852 4 0.8614 0.0135 0.232 0.204 0.008 0.316 0.060 0.180
#> GSM550853 2 0.1958 0.7100 0.004 0.896 0.000 0.100 0.000 0.000
#> GSM550855 2 0.1908 0.7129 0.004 0.900 0.000 0.096 0.000 0.000
#> GSM550856 4 0.4161 0.0702 0.012 0.448 0.000 0.540 0.000 0.000
#> GSM550861 2 0.0000 0.7550 0.000 1.000 0.000 0.000 0.000 0.000
#> GSM550863 4 0.3782 0.4327 0.036 0.000 0.000 0.740 0.000 0.224
#> GSM550864 2 0.6335 0.4286 0.200 0.568 0.008 0.184 0.036 0.004
#> GSM550866 4 0.4152 0.0951 0.012 0.440 0.000 0.548 0.000 0.000
#> GSM550867 1 0.4211 0.9419 0.616 0.000 0.016 0.000 0.004 0.364
#> GSM550885 1 0.4245 0.9367 0.604 0.000 0.016 0.000 0.004 0.376
#> GSM550886 5 0.2076 0.7623 0.020 0.040 0.004 0.016 0.920 0.000
#> GSM550887 2 0.0508 0.7538 0.004 0.984 0.000 0.012 0.000 0.000
#> GSM550889 4 0.1844 0.5815 0.028 0.024 0.000 0.932 0.004 0.012
#> GSM550894 2 0.0000 0.7550 0.000 1.000 0.000 0.000 0.000 0.000
#> GSM550897 4 0.5524 0.3000 0.112 0.000 0.004 0.616 0.020 0.248
#> GSM550903 2 0.0291 0.7537 0.004 0.992 0.000 0.000 0.004 0.000
#> GSM550905 5 0.3023 0.6808 0.004 0.212 0.000 0.000 0.784 0.000
#> GSM550906 2 0.0363 0.7538 0.000 0.988 0.000 0.012 0.000 0.000
#> GSM550907 5 0.3447 0.6761 0.036 0.000 0.136 0.008 0.816 0.004
#> GSM550909 5 0.4500 0.6922 0.048 0.036 0.008 0.024 0.788 0.096
#> GSM550911 5 0.3447 0.6761 0.036 0.000 0.136 0.008 0.816 0.004
#> GSM550913 2 0.0146 0.7546 0.004 0.996 0.000 0.000 0.000 0.000
#> GSM550915 6 0.6803 0.4081 0.244 0.004 0.012 0.228 0.032 0.480
#> GSM550917 2 0.5588 0.5424 0.180 0.664 0.008 0.108 0.036 0.004
#> GSM550919 6 0.6997 0.4065 0.248 0.012 0.008 0.220 0.040 0.472
#> GSM550921 3 0.0632 0.9376 0.000 0.000 0.976 0.000 0.024 0.000
#> GSM550924 5 0.7240 0.0475 0.272 0.000 0.004 0.108 0.424 0.192
#> GSM550926 4 0.4341 0.2696 0.024 0.356 0.004 0.616 0.000 0.000
#> GSM550927 2 0.0508 0.7538 0.004 0.984 0.000 0.012 0.000 0.000
#> GSM550787 4 0.6796 0.3354 0.152 0.000 0.004 0.500 0.256 0.088
#> GSM550793 3 0.5030 0.6479 0.036 0.000 0.676 0.044 0.008 0.236
#> GSM550794 4 0.6780 0.1247 0.244 0.000 0.004 0.492 0.068 0.192
#> GSM550795 6 0.2680 0.4397 0.032 0.000 0.000 0.108 0.000 0.860
#> GSM550798 1 0.4553 0.9170 0.580 0.000 0.032 0.000 0.004 0.384
#> GSM550803 1 0.4211 0.9419 0.616 0.000 0.016 0.000 0.004 0.364
#> GSM550805 4 0.6433 0.3166 0.148 0.000 0.004 0.552 0.068 0.228
#> GSM550823 4 0.1890 0.5751 0.024 0.000 0.000 0.924 0.008 0.044
#> GSM550824 1 0.4211 0.9419 0.616 0.000 0.016 0.000 0.004 0.364
#> GSM550825 3 0.2557 0.8816 0.032 0.000 0.892 0.008 0.008 0.060
#> GSM550827 6 0.6919 0.3126 0.244 0.000 0.008 0.304 0.040 0.404
#> GSM550828 1 0.3782 0.9137 0.588 0.000 0.000 0.000 0.000 0.412
#> GSM550829 6 0.6205 -0.6058 0.340 0.000 0.228 0.004 0.004 0.424
#> GSM550830 4 0.1777 0.5744 0.024 0.000 0.000 0.928 0.004 0.044
#> GSM550834 6 0.4216 0.4462 0.084 0.000 0.000 0.148 0.012 0.756
#> GSM550839 5 0.4919 0.1866 0.044 0.000 0.000 0.440 0.508 0.008
#> GSM550840 4 0.6238 0.1570 0.224 0.000 0.004 0.516 0.020 0.236
#> GSM550843 5 0.1999 0.7578 0.020 0.016 0.016 0.020 0.928 0.000
#> GSM550844 6 0.5389 -0.1561 0.220 0.000 0.004 0.132 0.012 0.632
#> GSM550845 4 0.5839 0.2389 0.132 0.312 0.004 0.540 0.004 0.008
#> GSM550848 6 0.7200 0.3561 0.244 0.012 0.008 0.268 0.044 0.424
#> GSM550854 1 0.4211 0.9419 0.616 0.000 0.016 0.000 0.004 0.364
#> GSM550857 3 0.0622 0.9372 0.000 0.000 0.980 0.000 0.008 0.012
#> GSM550858 1 0.3695 0.9353 0.624 0.000 0.000 0.000 0.000 0.376
#> GSM550859 1 0.4211 0.9419 0.616 0.000 0.016 0.000 0.004 0.364
#> GSM550862 1 0.4037 0.9254 0.608 0.000 0.000 0.012 0.000 0.380
#> GSM550865 4 0.2747 0.5442 0.028 0.000 0.000 0.860 0.004 0.108
#> GSM550868 4 0.2605 0.5437 0.028 0.000 0.000 0.864 0.000 0.108
#> GSM550869 4 0.4424 0.5236 0.080 0.000 0.004 0.776 0.076 0.064
#> GSM550870 2 0.6184 0.4542 0.180 0.592 0.008 0.180 0.036 0.004
#> GSM550871 4 0.4811 0.4031 0.044 0.000 0.000 0.672 0.252 0.032
#> GSM550872 4 0.2747 0.5442 0.028 0.000 0.000 0.860 0.004 0.108
#> GSM550873 5 0.8721 -0.1074 0.236 0.192 0.008 0.224 0.276 0.064
#> GSM550874 4 0.4047 0.2307 0.012 0.384 0.000 0.604 0.000 0.000
#> GSM550876 5 0.4563 0.4090 0.048 0.000 0.000 0.348 0.604 0.000
#> GSM550877 4 0.4157 0.0815 0.012 0.444 0.000 0.544 0.000 0.000
#> GSM550878 5 0.3178 0.6901 0.028 0.000 0.128 0.012 0.832 0.000
#> GSM550879 6 0.2136 0.3725 0.048 0.000 0.000 0.048 0.000 0.904
#> GSM550882 3 0.2966 0.8862 0.044 0.000 0.876 0.036 0.036 0.008
#> GSM550888 3 0.0458 0.9404 0.000 0.000 0.984 0.000 0.016 0.000
#> GSM550890 6 0.6790 0.3774 0.244 0.000 0.012 0.260 0.032 0.452
#> GSM550891 3 0.1526 0.9242 0.008 0.000 0.944 0.008 0.036 0.004
#> GSM550892 6 0.6094 -0.0994 0.248 0.000 0.000 0.308 0.004 0.440
#> GSM550893 4 0.4110 0.2549 0.016 0.376 0.000 0.608 0.000 0.000
#> GSM550895 4 0.1578 0.5801 0.012 0.028 0.000 0.944 0.004 0.012
#> GSM550896 4 0.4157 0.0797 0.012 0.444 0.000 0.544 0.000 0.000
#> GSM550898 1 0.4211 0.9419 0.616 0.000 0.016 0.000 0.004 0.364
#> GSM550899 2 0.6495 0.4353 0.208 0.564 0.008 0.172 0.036 0.012
#> GSM550900 4 0.1719 0.5734 0.032 0.000 0.000 0.932 0.004 0.032
#> GSM550901 6 0.6241 0.4747 0.292 0.012 0.000 0.100 0.048 0.548
#> GSM550902 6 0.2806 0.4533 0.028 0.000 0.012 0.084 0.004 0.872
#> GSM550904 6 0.1434 0.3980 0.024 0.000 0.008 0.020 0.000 0.948
#> GSM550908 3 0.0458 0.9404 0.000 0.000 0.984 0.000 0.016 0.000
#> GSM550912 2 0.7156 0.3141 0.228 0.488 0.008 0.208 0.036 0.032
#> GSM550914 6 0.6905 0.2939 0.240 0.000 0.012 0.320 0.032 0.396
#> GSM550918 2 0.6622 0.4352 0.212 0.560 0.008 0.164 0.036 0.020
#> GSM550922 5 0.2094 0.7578 0.024 0.064 0.004 0.000 0.908 0.000
#> GSM550923 1 0.4323 0.9320 0.600 0.000 0.020 0.000 0.004 0.376
#> GSM550925 4 0.5282 0.4462 0.192 0.000 0.004 0.672 0.032 0.100
#> GSM550802 4 0.3206 0.5539 0.052 0.000 0.004 0.856 0.024 0.064
#> GSM550812 4 0.5463 0.3443 0.096 0.000 0.004 0.648 0.036 0.216
#> GSM550831 1 0.4303 0.7341 0.524 0.000 0.000 0.004 0.012 0.460
#> GSM550847 1 0.4127 0.9406 0.620 0.000 0.012 0.000 0.004 0.364
#> GSM550860 4 0.5173 0.4993 0.068 0.000 0.020 0.724 0.128 0.060
#> GSM550875 4 0.6233 0.2793 0.104 0.000 0.004 0.552 0.064 0.276
#> GSM550880 4 0.5968 -0.1308 0.140 0.000 0.000 0.432 0.016 0.412
#> GSM550881 3 0.1180 0.9373 0.004 0.000 0.960 0.004 0.024 0.008
#> GSM550883 3 0.0820 0.9382 0.000 0.000 0.972 0.000 0.012 0.016
#> GSM550884 4 0.5914 0.2640 0.132 0.000 0.008 0.600 0.032 0.228
#> GSM550910 5 0.1788 0.7608 0.028 0.040 0.004 0.000 0.928 0.000
#> GSM550916 1 0.4214 0.8868 0.656 0.000 0.004 0.012 0.008 0.320
#> GSM550920 5 0.1816 0.7541 0.028 0.012 0.004 0.016 0.936 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)
get_signatures(res, k = 3)
get_signatures(res, k = 4)
get_signatures(res, k = 5)
get_signatures(res, k = 6)
Signature heatmaps where rows are not scaled:
get_signatures(res, k = 2, scale_rows = FALSE)
get_signatures(res, k = 3, scale_rows = FALSE)
get_signatures(res, k = 4, scale_rows = FALSE)
get_signatures(res, k = 5, scale_rows = FALSE)
get_signatures(res, k = 6, scale_rows = FALSE)
Compare the overlap of signatures from different k:
compare_signatures(res)
get_signature() returns a data frame invisibly. TO get the list of signatures, the function
call should be assigned to a variable explicitly. In following code, if plot argument is set
to FALSE, no heatmap is plotted while only the differential analysis is performed.
# code only for demonstration
tb = get_signature(res, k = ..., plot = FALSE)
An example of the output of tb is:
#> which_row fdr mean_1 mean_2 scaled_mean_1 scaled_mean_2 km
#> 1 38 0.042760348 8.373488 9.131774 -0.5533452 0.5164555 1
#> 2 40 0.018707592 7.106213 8.469186 -0.6173731 0.5762149 1
#> 3 55 0.019134737 10.221463 11.207825 -0.6159697 0.5749050 1
#> 4 59 0.006059896 5.921854 7.869574 -0.6899429 0.6439467 1
#> 5 60 0.018055526 8.928898 10.211722 -0.6204761 0.5791110 1
#> 6 98 0.009384629 15.714769 14.887706 0.6635654 -0.6193277 2
...
The columns in tb are:
which_row: row indices corresponding to the input matrix.fdr: FDR for the differential test. mean_x: The mean value in group x.scaled_mean_x: The mean value in group x after rows are scaled.km: Row groups if k-means clustering is applied to rows.UMAP plot which shows how samples are separated.
dimension_reduction(res, k = 2, method = "UMAP")
dimension_reduction(res, k = 3, method = "UMAP")
dimension_reduction(res, k = 4, method = "UMAP")
dimension_reduction(res, k = 5, method = "UMAP")
dimension_reduction(res, k = 6, method = "UMAP")
Following heatmap shows how subgroups are split when increasing k:
collect_classes(res)
Test correlation between subgroups and known annotations. If the known annotation is numeric, one-way ANOVA test is applied, and if the known annotation is discrete, chi-squared contingency table test is applied.
test_to_known_factors(res)
#> n disease.state(p) k
#> MAD:kmeans 142 4.74e-04 2
#> MAD:kmeans 110 2.04e-04 3
#> MAD:kmeans 103 6.34e-06 4
#> MAD:kmeans 119 6.34e-05 5
#> MAD:kmeans 79 6.33e-06 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 51776 rows and 143 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 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 0.493 0.881 0.906 0.4999 0.498 0.498
#> 3 3 0.822 0.835 0.930 0.3146 0.778 0.582
#> 4 4 0.737 0.793 0.892 0.1270 0.855 0.611
#> 5 5 0.718 0.645 0.815 0.0636 0.861 0.549
#> 6 6 0.780 0.665 0.845 0.0396 0.953 0.797
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
#> GSM550785 1 0.6712 0.892 0.824 0.176
#> GSM550786 2 0.7139 0.850 0.196 0.804
#> GSM550788 2 0.0000 0.908 0.000 1.000
#> GSM550789 2 0.0000 0.908 0.000 1.000
#> GSM550790 1 0.6712 0.892 0.824 0.176
#> GSM550791 1 0.6712 0.892 0.824 0.176
#> GSM550792 2 0.5059 0.880 0.112 0.888
#> GSM550796 2 0.0000 0.908 0.000 1.000
#> GSM550797 2 0.0000 0.908 0.000 1.000
#> GSM550799 2 0.6712 0.858 0.176 0.824
#> GSM550800 2 0.0000 0.908 0.000 1.000
#> GSM550801 2 0.0000 0.908 0.000 1.000
#> GSM550804 2 0.0000 0.908 0.000 1.000
#> GSM550806 1 0.2423 0.849 0.960 0.040
#> GSM550807 2 0.0000 0.908 0.000 1.000
#> GSM550808 2 0.6712 0.858 0.176 0.824
#> GSM550809 1 0.0000 0.875 1.000 0.000
#> GSM550810 2 0.0000 0.908 0.000 1.000
#> GSM550811 1 0.0000 0.875 1.000 0.000
#> GSM550813 2 0.0000 0.908 0.000 1.000
#> GSM550814 2 0.0376 0.907 0.004 0.996
#> GSM550815 2 0.0000 0.908 0.000 1.000
#> GSM550816 2 0.0000 0.908 0.000 1.000
#> GSM550817 2 0.7139 0.850 0.196 0.804
#> GSM550818 2 0.7139 0.850 0.196 0.804
#> GSM550819 2 0.6712 0.859 0.176 0.824
#> GSM550820 1 0.0000 0.875 1.000 0.000
#> GSM550821 2 0.6712 0.858 0.176 0.824
#> GSM550822 2 0.0000 0.908 0.000 1.000
#> GSM550826 1 0.0000 0.875 1.000 0.000
#> GSM550832 2 0.0000 0.908 0.000 1.000
#> GSM550833 2 0.0000 0.908 0.000 1.000
#> GSM550835 2 0.6712 0.858 0.176 0.824
#> GSM550836 1 0.0000 0.875 1.000 0.000
#> GSM550837 2 0.6712 0.858 0.176 0.824
#> GSM550838 1 0.0000 0.875 1.000 0.000
#> GSM550841 2 0.6973 0.853 0.188 0.812
#> GSM550842 2 0.6712 0.858 0.176 0.824
#> GSM550846 2 0.1843 0.887 0.028 0.972
#> GSM550849 1 0.0000 0.875 1.000 0.000
#> GSM550850 1 0.6712 0.892 0.824 0.176
#> GSM550851 2 0.6712 0.858 0.176 0.824
#> GSM550852 2 0.0000 0.908 0.000 1.000
#> GSM550853 2 0.0000 0.908 0.000 1.000
#> GSM550855 2 0.0000 0.908 0.000 1.000
#> GSM550856 2 0.0000 0.908 0.000 1.000
#> GSM550861 2 0.0000 0.908 0.000 1.000
#> GSM550863 1 0.7139 0.881 0.804 0.196
#> GSM550864 2 0.0000 0.908 0.000 1.000
#> GSM550866 2 0.0000 0.908 0.000 1.000
#> GSM550867 1 0.6712 0.892 0.824 0.176
#> GSM550885 1 0.6712 0.892 0.824 0.176
#> GSM550886 2 0.7139 0.850 0.196 0.804
#> GSM550887 2 0.0000 0.908 0.000 1.000
#> GSM550889 1 0.7528 0.868 0.784 0.216
#> GSM550894 2 0.0000 0.908 0.000 1.000
#> GSM550897 1 0.6712 0.892 0.824 0.176
#> GSM550903 2 0.0000 0.908 0.000 1.000
#> GSM550905 2 0.6712 0.858 0.176 0.824
#> GSM550906 2 0.0000 0.908 0.000 1.000
#> GSM550907 2 0.7139 0.850 0.196 0.804
#> GSM550909 2 0.6712 0.858 0.176 0.824
#> GSM550911 2 0.7139 0.850 0.196 0.804
#> GSM550913 2 0.0000 0.908 0.000 1.000
#> GSM550915 1 0.7139 0.881 0.804 0.196
#> GSM550917 2 0.0000 0.908 0.000 1.000
#> GSM550919 1 0.7299 0.876 0.796 0.204
#> GSM550921 1 0.0000 0.875 1.000 0.000
#> GSM550924 2 0.7219 0.848 0.200 0.800
#> GSM550926 2 0.0000 0.908 0.000 1.000
#> GSM550927 2 0.0000 0.908 0.000 1.000
#> GSM550787 1 0.1184 0.866 0.984 0.016
#> GSM550793 1 0.0000 0.875 1.000 0.000
#> GSM550794 2 0.7056 0.686 0.192 0.808
#> GSM550795 1 0.6712 0.892 0.824 0.176
#> GSM550798 1 0.0000 0.875 1.000 0.000
#> GSM550803 1 0.0000 0.875 1.000 0.000
#> GSM550805 1 0.0000 0.875 1.000 0.000
#> GSM550823 1 0.7745 0.858 0.772 0.228
#> GSM550824 1 0.6712 0.892 0.824 0.176
#> GSM550825 1 0.0000 0.875 1.000 0.000
#> GSM550827 1 0.7139 0.881 0.804 0.196
#> GSM550828 1 0.6712 0.892 0.824 0.176
#> GSM550829 1 0.0000 0.875 1.000 0.000
#> GSM550830 1 0.7139 0.881 0.804 0.196
#> GSM550834 1 0.6712 0.892 0.824 0.176
#> GSM550839 2 0.7139 0.850 0.196 0.804
#> GSM550840 1 0.6712 0.892 0.824 0.176
#> GSM550843 2 0.7139 0.850 0.196 0.804
#> GSM550844 1 0.0000 0.875 1.000 0.000
#> GSM550845 2 0.0000 0.908 0.000 1.000
#> GSM550848 2 0.3114 0.861 0.056 0.944
#> GSM550854 1 0.6712 0.892 0.824 0.176
#> GSM550857 1 0.0000 0.875 1.000 0.000
#> GSM550858 1 0.6712 0.892 0.824 0.176
#> GSM550859 1 0.6712 0.892 0.824 0.176
#> GSM550862 1 0.6712 0.892 0.824 0.176
#> GSM550865 1 0.7139 0.881 0.804 0.196
#> GSM550868 1 0.7139 0.881 0.804 0.196
#> GSM550869 1 0.0376 0.873 0.996 0.004
#> GSM550870 2 0.0000 0.908 0.000 1.000
#> GSM550871 2 0.7139 0.850 0.196 0.804
#> GSM550872 1 0.7139 0.881 0.804 0.196
#> GSM550873 2 0.6712 0.858 0.176 0.824
#> GSM550874 2 0.0000 0.908 0.000 1.000
#> GSM550876 2 0.7139 0.850 0.196 0.804
#> GSM550877 2 0.0000 0.908 0.000 1.000
#> GSM550878 2 0.7139 0.850 0.196 0.804
#> GSM550879 1 0.6712 0.892 0.824 0.176
#> GSM550882 1 0.0376 0.873 0.996 0.004
#> GSM550888 1 0.0000 0.875 1.000 0.000
#> GSM550890 1 0.9044 0.735 0.680 0.320
#> GSM550891 1 0.1184 0.866 0.984 0.016
#> GSM550892 1 0.6712 0.892 0.824 0.176
#> GSM550893 2 0.0000 0.908 0.000 1.000
#> GSM550895 2 0.0000 0.908 0.000 1.000
#> GSM550896 2 0.0000 0.908 0.000 1.000
#> GSM550898 1 0.6712 0.892 0.824 0.176
#> GSM550899 2 0.0000 0.908 0.000 1.000
#> GSM550900 1 0.7139 0.881 0.804 0.196
#> GSM550901 1 0.6887 0.888 0.816 0.184
#> GSM550902 1 0.0000 0.875 1.000 0.000
#> GSM550904 1 0.0000 0.875 1.000 0.000
#> GSM550908 1 0.0000 0.875 1.000 0.000
#> GSM550912 2 0.0000 0.908 0.000 1.000
#> GSM550914 2 0.1843 0.887 0.028 0.972
#> GSM550918 2 0.0000 0.908 0.000 1.000
#> GSM550922 2 0.6712 0.858 0.176 0.824
#> GSM550923 1 0.0000 0.875 1.000 0.000
#> GSM550925 1 0.7056 0.884 0.808 0.192
#> GSM550802 2 0.0000 0.908 0.000 1.000
#> GSM550812 2 0.7219 0.848 0.200 0.800
#> GSM550831 1 0.6712 0.892 0.824 0.176
#> GSM550847 1 0.6712 0.892 0.824 0.176
#> GSM550860 1 0.0000 0.875 1.000 0.000
#> GSM550875 1 0.0000 0.875 1.000 0.000
#> GSM550880 1 0.7139 0.881 0.804 0.196
#> GSM550881 1 0.0000 0.875 1.000 0.000
#> GSM550883 1 0.0000 0.875 1.000 0.000
#> GSM550884 2 0.7219 0.848 0.200 0.800
#> GSM550910 2 0.7139 0.850 0.196 0.804
#> GSM550916 1 0.6712 0.892 0.824 0.176
#> GSM550920 2 0.7139 0.850 0.196 0.804
cbind(get_classes(res, k = 3), get_membership(res, k = 3))
#> class entropy silhouette p1 p2 p3
#> GSM550785 1 0.0000 0.90222 1.000 0.000 0.000
#> GSM550786 3 0.0000 0.91442 0.000 0.000 1.000
#> GSM550788 2 0.0000 0.93776 0.000 1.000 0.000
#> GSM550789 2 0.0000 0.93776 0.000 1.000 0.000
#> GSM550790 1 0.0000 0.90222 1.000 0.000 0.000
#> GSM550791 1 0.0000 0.90222 1.000 0.000 0.000
#> GSM550792 2 0.6654 0.17448 0.456 0.536 0.008
#> GSM550796 2 0.0000 0.93776 0.000 1.000 0.000
#> GSM550797 2 0.0000 0.93776 0.000 1.000 0.000
#> GSM550799 3 0.0424 0.91155 0.000 0.008 0.992
#> GSM550800 2 0.0000 0.93776 0.000 1.000 0.000
#> GSM550801 2 0.0000 0.93776 0.000 1.000 0.000
#> GSM550804 2 0.0000 0.93776 0.000 1.000 0.000
#> GSM550806 3 0.0000 0.91442 0.000 0.000 1.000
#> GSM550807 2 0.0000 0.93776 0.000 1.000 0.000
#> GSM550808 2 0.2261 0.89198 0.000 0.932 0.068
#> GSM550809 1 0.0000 0.90222 1.000 0.000 0.000
#> GSM550810 2 0.0424 0.93296 0.000 0.992 0.008
#> GSM550811 1 0.3340 0.79671 0.880 0.000 0.120
#> GSM550813 2 0.0000 0.93776 0.000 1.000 0.000
#> GSM550814 2 0.0000 0.93776 0.000 1.000 0.000
#> GSM550815 2 0.0000 0.93776 0.000 1.000 0.000
#> GSM550816 2 0.0000 0.93776 0.000 1.000 0.000
#> GSM550817 3 0.0000 0.91442 0.000 0.000 1.000
#> GSM550818 3 0.0000 0.91442 0.000 0.000 1.000
#> GSM550819 2 0.4121 0.79390 0.000 0.832 0.168
#> GSM550820 1 0.0000 0.90222 1.000 0.000 0.000
#> GSM550821 2 0.5327 0.64426 0.000 0.728 0.272
#> GSM550822 2 0.0000 0.93776 0.000 1.000 0.000
#> GSM550826 1 0.5397 0.56813 0.720 0.000 0.280
#> GSM550832 2 0.0000 0.93776 0.000 1.000 0.000
#> GSM550833 2 0.0000 0.93776 0.000 1.000 0.000
#> GSM550835 3 0.5591 0.51044 0.000 0.304 0.696
#> GSM550836 3 0.2261 0.89112 0.068 0.000 0.932
#> GSM550837 2 0.2261 0.89198 0.000 0.932 0.068
#> GSM550838 1 0.1860 0.86392 0.948 0.000 0.052
#> GSM550841 3 0.1163 0.90084 0.000 0.028 0.972
#> GSM550842 2 0.2261 0.89198 0.000 0.932 0.068
#> GSM550846 2 0.7794 0.38437 0.368 0.572 0.060
#> GSM550849 1 0.5706 0.49506 0.680 0.000 0.320
#> GSM550850 1 0.0000 0.90222 1.000 0.000 0.000
#> GSM550851 2 0.2959 0.86724 0.000 0.900 0.100
#> GSM550852 2 0.0000 0.93776 0.000 1.000 0.000
#> GSM550853 2 0.0000 0.93776 0.000 1.000 0.000
#> GSM550855 2 0.0000 0.93776 0.000 1.000 0.000
#> GSM550856 2 0.0000 0.93776 0.000 1.000 0.000
#> GSM550861 2 0.0000 0.93776 0.000 1.000 0.000
#> GSM550863 1 0.2066 0.86440 0.940 0.060 0.000
#> GSM550864 2 0.0000 0.93776 0.000 1.000 0.000
#> GSM550866 2 0.0000 0.93776 0.000 1.000 0.000
#> GSM550867 1 0.0000 0.90222 1.000 0.000 0.000
#> GSM550885 1 0.0000 0.90222 1.000 0.000 0.000
#> GSM550886 3 0.1411 0.89572 0.000 0.036 0.964
#> GSM550887 2 0.0000 0.93776 0.000 1.000 0.000
#> GSM550889 1 0.6260 0.26218 0.552 0.448 0.000
#> GSM550894 2 0.0000 0.93776 0.000 1.000 0.000
#> GSM550897 1 0.0000 0.90222 1.000 0.000 0.000
#> GSM550903 2 0.0000 0.93776 0.000 1.000 0.000
#> GSM550905 2 0.2625 0.88051 0.000 0.916 0.084
#> GSM550906 2 0.0000 0.93776 0.000 1.000 0.000
#> GSM550907 3 0.0000 0.91442 0.000 0.000 1.000
#> GSM550909 2 0.5327 0.64426 0.000 0.728 0.272
#> GSM550911 3 0.0000 0.91442 0.000 0.000 1.000
#> GSM550913 2 0.0000 0.93776 0.000 1.000 0.000
#> GSM550915 1 0.1289 0.88443 0.968 0.032 0.000
#> GSM550917 2 0.0000 0.93776 0.000 1.000 0.000
#> GSM550919 1 0.2711 0.84185 0.912 0.088 0.000
#> GSM550921 3 0.1411 0.90496 0.036 0.000 0.964
#> GSM550924 3 0.0000 0.91442 0.000 0.000 1.000
#> GSM550926 2 0.0000 0.93776 0.000 1.000 0.000
#> GSM550927 2 0.0000 0.93776 0.000 1.000 0.000
#> GSM550787 3 0.2165 0.89395 0.064 0.000 0.936
#> GSM550793 3 0.6045 0.43139 0.380 0.000 0.620
#> GSM550794 2 0.6955 0.04508 0.492 0.492 0.016
#> GSM550795 1 0.0000 0.90222 1.000 0.000 0.000
#> GSM550798 1 0.0000 0.90222 1.000 0.000 0.000
#> GSM550803 1 0.0000 0.90222 1.000 0.000 0.000
#> GSM550805 1 0.6045 0.34112 0.620 0.000 0.380
#> GSM550823 1 0.6299 0.17784 0.524 0.476 0.000
#> GSM550824 1 0.0000 0.90222 1.000 0.000 0.000
#> GSM550825 3 0.6045 0.43139 0.380 0.000 0.620
#> GSM550827 1 0.2711 0.84171 0.912 0.088 0.000
#> GSM550828 1 0.0000 0.90222 1.000 0.000 0.000
#> GSM550829 1 0.5465 0.55344 0.712 0.000 0.288
#> GSM550830 1 0.3619 0.79430 0.864 0.136 0.000
#> GSM550834 1 0.0000 0.90222 1.000 0.000 0.000
#> GSM550839 3 0.0424 0.91155 0.000 0.008 0.992
#> GSM550840 1 0.0000 0.90222 1.000 0.000 0.000
#> GSM550843 3 0.0000 0.91442 0.000 0.000 1.000
#> GSM550844 1 0.0000 0.90222 1.000 0.000 0.000
#> GSM550845 2 0.0000 0.93776 0.000 1.000 0.000
#> GSM550848 1 0.6305 0.00056 0.516 0.484 0.000
#> GSM550854 1 0.0000 0.90222 1.000 0.000 0.000
#> GSM550857 3 0.6045 0.43139 0.380 0.000 0.620
#> GSM550858 1 0.0000 0.90222 1.000 0.000 0.000
#> GSM550859 1 0.0000 0.90222 1.000 0.000 0.000
#> GSM550862 1 0.0000 0.90222 1.000 0.000 0.000
#> GSM550865 1 0.0747 0.89373 0.984 0.016 0.000
#> GSM550868 1 0.2066 0.86440 0.940 0.060 0.000
#> GSM550869 3 0.2165 0.89351 0.064 0.000 0.936
#> GSM550870 2 0.0000 0.93776 0.000 1.000 0.000
#> GSM550871 3 0.0000 0.91442 0.000 0.000 1.000
#> GSM550872 1 0.1860 0.87030 0.948 0.052 0.000
#> GSM550873 2 0.3267 0.84692 0.000 0.884 0.116
#> GSM550874 2 0.0000 0.93776 0.000 1.000 0.000
#> GSM550876 3 0.0000 0.91442 0.000 0.000 1.000
#> GSM550877 2 0.0000 0.93776 0.000 1.000 0.000
#> GSM550878 3 0.0000 0.91442 0.000 0.000 1.000
#> GSM550879 1 0.0000 0.90222 1.000 0.000 0.000
#> GSM550882 3 0.1964 0.89728 0.056 0.000 0.944
#> GSM550888 3 0.2261 0.89112 0.068 0.000 0.932
#> GSM550890 1 0.4062 0.76102 0.836 0.164 0.000
#> GSM550891 3 0.0000 0.91442 0.000 0.000 1.000
#> GSM550892 1 0.0000 0.90222 1.000 0.000 0.000
#> GSM550893 2 0.0000 0.93776 0.000 1.000 0.000
#> GSM550895 2 0.0000 0.93776 0.000 1.000 0.000
#> GSM550896 2 0.0000 0.93776 0.000 1.000 0.000
#> GSM550898 1 0.0000 0.90222 1.000 0.000 0.000
#> GSM550899 2 0.0000 0.93776 0.000 1.000 0.000
#> GSM550900 1 0.2066 0.86440 0.940 0.060 0.000
#> GSM550901 1 0.0000 0.90222 1.000 0.000 0.000
#> GSM550902 1 0.5678 0.49875 0.684 0.000 0.316
#> GSM550904 1 0.0000 0.90222 1.000 0.000 0.000
#> GSM550908 3 0.2261 0.89112 0.068 0.000 0.932
#> GSM550912 2 0.0000 0.93776 0.000 1.000 0.000
#> GSM550914 2 0.5926 0.45645 0.356 0.644 0.000
#> GSM550918 2 0.0000 0.93776 0.000 1.000 0.000
#> GSM550922 3 0.1411 0.89557 0.000 0.036 0.964
#> GSM550923 1 0.0000 0.90222 1.000 0.000 0.000
#> GSM550925 1 0.0000 0.90222 1.000 0.000 0.000
#> GSM550802 2 0.0424 0.93301 0.000 0.992 0.008
#> GSM550812 2 0.5939 0.68965 0.028 0.748 0.224
#> GSM550831 1 0.0000 0.90222 1.000 0.000 0.000
#> GSM550847 1 0.0000 0.90222 1.000 0.000 0.000
#> GSM550860 3 0.2165 0.89351 0.064 0.000 0.936
#> GSM550875 1 0.5785 0.46200 0.668 0.000 0.332
#> GSM550880 1 0.0000 0.90222 1.000 0.000 0.000
#> GSM550881 3 0.2261 0.89112 0.068 0.000 0.932
#> GSM550883 3 0.5882 0.50164 0.348 0.000 0.652
#> GSM550884 3 0.2878 0.85624 0.000 0.096 0.904
#> GSM550910 3 0.0000 0.91442 0.000 0.000 1.000
#> GSM550916 1 0.0000 0.90222 1.000 0.000 0.000
#> GSM550920 3 0.0000 0.91442 0.000 0.000 1.000
cbind(get_classes(res, k = 4), get_membership(res, k = 4))
#> class entropy silhouette p1 p2 p3 p4
#> GSM550785 1 0.0000 0.88175 1.000 0.000 0.000 0.000
#> GSM550786 3 0.0188 0.88245 0.000 0.000 0.996 0.004
#> GSM550788 2 0.3172 0.75508 0.000 0.840 0.000 0.160
#> GSM550789 2 0.0000 0.92354 0.000 1.000 0.000 0.000
#> GSM550790 1 0.0000 0.88175 1.000 0.000 0.000 0.000
#> GSM550791 1 0.0000 0.88175 1.000 0.000 0.000 0.000
#> GSM550792 2 0.5664 0.57225 0.228 0.696 0.000 0.076
#> GSM550796 2 0.0000 0.92354 0.000 1.000 0.000 0.000
#> GSM550797 2 0.0000 0.92354 0.000 1.000 0.000 0.000
#> GSM550799 3 0.1398 0.86247 0.000 0.040 0.956 0.004
#> GSM550800 4 0.4907 0.44832 0.000 0.420 0.000 0.580
#> GSM550801 2 0.0000 0.92354 0.000 1.000 0.000 0.000
#> GSM550804 2 0.0000 0.92354 0.000 1.000 0.000 0.000
#> GSM550806 3 0.0469 0.88146 0.000 0.000 0.988 0.012
#> GSM550807 2 0.0000 0.92354 0.000 1.000 0.000 0.000
#> GSM550808 2 0.2714 0.84147 0.000 0.884 0.112 0.004
#> GSM550809 1 0.2081 0.85702 0.916 0.000 0.000 0.084
#> GSM550810 2 0.0188 0.92187 0.000 0.996 0.000 0.004
#> GSM550811 1 0.2216 0.85404 0.908 0.000 0.000 0.092
#> GSM550813 2 0.0000 0.92354 0.000 1.000 0.000 0.000
#> GSM550814 2 0.0000 0.92354 0.000 1.000 0.000 0.000
#> GSM550815 2 0.0000 0.92354 0.000 1.000 0.000 0.000
#> GSM550816 2 0.0000 0.92354 0.000 1.000 0.000 0.000
#> GSM550817 3 0.0188 0.88245 0.000 0.000 0.996 0.004
#> GSM550818 3 0.0188 0.88245 0.000 0.000 0.996 0.004
#> GSM550819 4 0.2530 0.75930 0.000 0.000 0.112 0.888
#> GSM550820 1 0.2011 0.85856 0.920 0.000 0.000 0.080
#> GSM550821 2 0.4122 0.70442 0.000 0.760 0.236 0.004
#> GSM550822 2 0.0000 0.92354 0.000 1.000 0.000 0.000
#> GSM550826 1 0.4931 0.74706 0.776 0.000 0.132 0.092
#> GSM550832 2 0.0188 0.92187 0.000 0.996 0.000 0.004
#> GSM550833 2 0.0000 0.92354 0.000 1.000 0.000 0.000
#> GSM550835 3 0.5112 0.18390 0.000 0.436 0.560 0.004
#> GSM550836 3 0.4030 0.80651 0.072 0.000 0.836 0.092
#> GSM550837 2 0.2654 0.84456 0.000 0.888 0.108 0.004
#> GSM550838 1 0.2401 0.85166 0.904 0.000 0.004 0.092
#> GSM550841 3 0.3306 0.76141 0.000 0.156 0.840 0.004
#> GSM550842 2 0.2831 0.83423 0.000 0.876 0.120 0.004
#> GSM550846 2 0.8754 -0.14595 0.240 0.384 0.044 0.332
#> GSM550849 1 0.4958 0.79898 0.808 0.036 0.064 0.092
#> GSM550850 1 0.0000 0.88175 1.000 0.000 0.000 0.000
#> GSM550851 2 0.2714 0.84141 0.000 0.884 0.112 0.004
#> GSM550852 2 0.0188 0.92187 0.000 0.996 0.000 0.004
#> GSM550853 2 0.2469 0.82433 0.000 0.892 0.000 0.108
#> GSM550855 2 0.2408 0.82884 0.000 0.896 0.000 0.104
#> GSM550856 4 0.4431 0.68414 0.000 0.304 0.000 0.696
#> GSM550861 2 0.0000 0.92354 0.000 1.000 0.000 0.000
#> GSM550863 4 0.2408 0.80018 0.104 0.000 0.000 0.896
#> GSM550864 2 0.0188 0.92064 0.000 0.996 0.000 0.004
#> GSM550866 4 0.4250 0.72000 0.000 0.276 0.000 0.724
#> GSM550867 1 0.0000 0.88175 1.000 0.000 0.000 0.000
#> GSM550885 1 0.0000 0.88175 1.000 0.000 0.000 0.000
#> GSM550886 3 0.3157 0.77556 0.000 0.144 0.852 0.004
#> GSM550887 2 0.0000 0.92354 0.000 1.000 0.000 0.000
#> GSM550889 4 0.2480 0.81635 0.008 0.088 0.000 0.904
#> GSM550894 2 0.0188 0.92187 0.000 0.996 0.000 0.004
#> GSM550897 1 0.2081 0.83301 0.916 0.000 0.000 0.084
#> GSM550903 2 0.0000 0.92354 0.000 1.000 0.000 0.000
#> GSM550905 2 0.3105 0.81476 0.000 0.856 0.140 0.004
#> GSM550906 2 0.0000 0.92354 0.000 1.000 0.000 0.000
#> GSM550907 3 0.0000 0.88281 0.000 0.000 1.000 0.000
#> GSM550909 2 0.4655 0.57126 0.000 0.684 0.312 0.004
#> GSM550911 3 0.0000 0.88281 0.000 0.000 1.000 0.000
#> GSM550913 2 0.0000 0.92354 0.000 1.000 0.000 0.000
#> GSM550915 1 0.3791 0.66883 0.796 0.004 0.000 0.200
#> GSM550917 2 0.0000 0.92354 0.000 1.000 0.000 0.000
#> GSM550919 1 0.3037 0.79438 0.888 0.076 0.000 0.036
#> GSM550921 3 0.2546 0.84561 0.008 0.000 0.900 0.092
#> GSM550924 3 0.0376 0.88148 0.000 0.004 0.992 0.004
#> GSM550926 4 0.4277 0.71601 0.000 0.280 0.000 0.720
#> GSM550927 2 0.0000 0.92354 0.000 1.000 0.000 0.000
#> GSM550787 3 0.2300 0.85812 0.064 0.000 0.920 0.016
#> GSM550793 1 0.6737 0.16103 0.488 0.000 0.420 0.092
#> GSM550794 4 0.4564 0.56392 0.328 0.000 0.000 0.672
#> GSM550795 1 0.0336 0.87881 0.992 0.000 0.000 0.008
#> GSM550798 1 0.2401 0.85166 0.904 0.000 0.004 0.092
#> GSM550803 1 0.0000 0.88175 1.000 0.000 0.000 0.000
#> GSM550805 1 0.5705 0.65258 0.704 0.000 0.204 0.092
#> GSM550823 4 0.2480 0.81635 0.008 0.088 0.000 0.904
#> GSM550824 1 0.0000 0.88175 1.000 0.000 0.000 0.000
#> GSM550825 1 0.6737 0.16103 0.488 0.000 0.420 0.092
#> GSM550827 4 0.4697 0.50555 0.356 0.000 0.000 0.644
#> GSM550828 1 0.0000 0.88175 1.000 0.000 0.000 0.000
#> GSM550829 1 0.4931 0.74706 0.776 0.000 0.132 0.092
#> GSM550830 4 0.2670 0.81056 0.072 0.024 0.000 0.904
#> GSM550834 1 0.0000 0.88175 1.000 0.000 0.000 0.000
#> GSM550839 3 0.2530 0.81314 0.000 0.000 0.888 0.112
#> GSM550840 1 0.0000 0.88175 1.000 0.000 0.000 0.000
#> GSM550843 3 0.0000 0.88281 0.000 0.000 1.000 0.000
#> GSM550844 1 0.1637 0.86557 0.940 0.000 0.000 0.060
#> GSM550845 4 0.3569 0.77960 0.000 0.196 0.000 0.804
#> GSM550848 1 0.7795 -0.15434 0.420 0.268 0.000 0.312
#> GSM550854 1 0.0000 0.88175 1.000 0.000 0.000 0.000
#> GSM550857 1 0.6737 0.16103 0.488 0.000 0.420 0.092
#> GSM550858 1 0.0000 0.88175 1.000 0.000 0.000 0.000
#> GSM550859 1 0.0000 0.88175 1.000 0.000 0.000 0.000
#> GSM550862 1 0.0000 0.88175 1.000 0.000 0.000 0.000
#> GSM550865 4 0.2281 0.80309 0.096 0.000 0.000 0.904
#> GSM550868 4 0.2281 0.80309 0.096 0.000 0.000 0.904
#> GSM550869 3 0.2813 0.85267 0.024 0.000 0.896 0.080
#> GSM550870 2 0.0000 0.92354 0.000 1.000 0.000 0.000
#> GSM550871 3 0.3074 0.78027 0.000 0.000 0.848 0.152
#> GSM550872 4 0.2281 0.80309 0.096 0.000 0.000 0.904
#> GSM550873 2 0.2466 0.85352 0.000 0.900 0.096 0.004
#> GSM550874 4 0.4304 0.71152 0.000 0.284 0.000 0.716
#> GSM550876 3 0.0000 0.88281 0.000 0.000 1.000 0.000
#> GSM550877 4 0.4304 0.71152 0.000 0.284 0.000 0.716
#> GSM550878 3 0.0000 0.88281 0.000 0.000 1.000 0.000
#> GSM550879 1 0.0000 0.88175 1.000 0.000 0.000 0.000
#> GSM550882 3 0.1629 0.87257 0.024 0.000 0.952 0.024
#> GSM550888 3 0.4030 0.80651 0.072 0.000 0.836 0.092
#> GSM550890 4 0.4193 0.65045 0.268 0.000 0.000 0.732
#> GSM550891 3 0.0592 0.88067 0.000 0.000 0.984 0.016
#> GSM550892 1 0.2760 0.79136 0.872 0.000 0.000 0.128
#> GSM550893 4 0.4356 0.70168 0.000 0.292 0.000 0.708
#> GSM550895 4 0.2281 0.81471 0.000 0.096 0.000 0.904
#> GSM550896 4 0.3801 0.76471 0.000 0.220 0.000 0.780
#> GSM550898 1 0.0000 0.88175 1.000 0.000 0.000 0.000
#> GSM550899 2 0.0000 0.92354 0.000 1.000 0.000 0.000
#> GSM550900 4 0.2281 0.80309 0.096 0.000 0.000 0.904
#> GSM550901 1 0.0000 0.88175 1.000 0.000 0.000 0.000
#> GSM550902 1 0.5265 0.71638 0.748 0.000 0.160 0.092
#> GSM550904 1 0.2149 0.85531 0.912 0.000 0.000 0.088
#> GSM550908 3 0.3959 0.80960 0.068 0.000 0.840 0.092
#> GSM550912 2 0.0000 0.92354 0.000 1.000 0.000 0.000
#> GSM550914 4 0.3577 0.77250 0.156 0.012 0.000 0.832
#> GSM550918 2 0.0000 0.92354 0.000 1.000 0.000 0.000
#> GSM550922 3 0.4509 0.56068 0.000 0.288 0.708 0.004
#> GSM550923 1 0.2011 0.85856 0.920 0.000 0.000 0.080
#> GSM550925 1 0.0336 0.87887 0.992 0.000 0.000 0.008
#> GSM550802 4 0.2408 0.81446 0.000 0.104 0.000 0.896
#> GSM550812 4 0.1545 0.77841 0.008 0.000 0.040 0.952
#> GSM550831 1 0.0000 0.88175 1.000 0.000 0.000 0.000
#> GSM550847 1 0.0000 0.88175 1.000 0.000 0.000 0.000
#> GSM550860 3 0.2699 0.85853 0.028 0.000 0.904 0.068
#> GSM550875 1 0.5265 0.71370 0.748 0.000 0.160 0.092
#> GSM550880 1 0.2704 0.79562 0.876 0.000 0.000 0.124
#> GSM550881 3 0.3959 0.80960 0.068 0.000 0.840 0.092
#> GSM550883 3 0.6745 0.00917 0.428 0.000 0.480 0.092
#> GSM550884 4 0.3400 0.63209 0.000 0.000 0.180 0.820
#> GSM550910 3 0.0188 0.88245 0.000 0.000 0.996 0.004
#> GSM550916 1 0.0000 0.88175 1.000 0.000 0.000 0.000
#> GSM550920 3 0.0188 0.88245 0.000 0.000 0.996 0.004
cbind(get_classes(res, k = 5), get_membership(res, k = 5))
#> class entropy silhouette p1 p2 p3 p4 p5
#> GSM550785 1 0.0000 0.8166 1.000 0.000 0.000 0.000 0.000
#> GSM550786 5 0.2891 0.7671 0.000 0.000 0.176 0.000 0.824
#> GSM550788 2 0.3242 0.6845 0.000 0.784 0.000 0.216 0.000
#> GSM550789 2 0.0000 0.8184 0.000 1.000 0.000 0.000 0.000
#> GSM550790 1 0.0000 0.8166 1.000 0.000 0.000 0.000 0.000
#> GSM550791 1 0.0290 0.8151 0.992 0.008 0.000 0.000 0.000
#> GSM550792 2 0.8290 0.0903 0.288 0.400 0.064 0.028 0.220
#> GSM550796 2 0.0693 0.8171 0.000 0.980 0.000 0.008 0.012
#> GSM550797 2 0.0000 0.8184 0.000 1.000 0.000 0.000 0.000
#> GSM550799 5 0.3327 0.7771 0.000 0.028 0.144 0.000 0.828
#> GSM550800 2 0.4161 0.4439 0.000 0.608 0.000 0.392 0.000
#> GSM550801 2 0.0162 0.8181 0.000 0.996 0.000 0.000 0.004
#> GSM550804 2 0.2409 0.7801 0.000 0.900 0.032 0.000 0.068
#> GSM550806 3 0.3395 0.5274 0.000 0.000 0.764 0.000 0.236
#> GSM550807 2 0.0451 0.8187 0.000 0.988 0.000 0.008 0.004
#> GSM550808 5 0.4171 0.4453 0.000 0.396 0.000 0.000 0.604
#> GSM550809 1 0.6328 0.3893 0.560 0.000 0.316 0.032 0.092
#> GSM550810 2 0.1124 0.8078 0.000 0.960 0.000 0.004 0.036
#> GSM550811 1 0.7053 0.2275 0.456 0.000 0.352 0.036 0.156
#> GSM550813 2 0.0671 0.8152 0.000 0.980 0.004 0.000 0.016
#> GSM550814 2 0.0798 0.8169 0.000 0.976 0.000 0.016 0.008
#> GSM550815 2 0.0807 0.8170 0.000 0.976 0.000 0.012 0.012
#> GSM550816 2 0.2416 0.7920 0.000 0.908 0.016 0.016 0.060
#> GSM550817 5 0.3123 0.7742 0.000 0.012 0.160 0.000 0.828
#> GSM550818 5 0.2852 0.7685 0.000 0.000 0.172 0.000 0.828
#> GSM550819 4 0.2074 0.7708 0.000 0.000 0.000 0.896 0.104
#> GSM550820 1 0.4801 0.7003 0.768 0.000 0.108 0.032 0.092
#> GSM550821 5 0.3734 0.7414 0.000 0.128 0.060 0.000 0.812
#> GSM550822 2 0.0807 0.8170 0.000 0.976 0.000 0.012 0.012
#> GSM550826 3 0.5997 0.0991 0.404 0.000 0.500 0.008 0.088
#> GSM550832 2 0.0162 0.8180 0.000 0.996 0.000 0.000 0.004
#> GSM550833 2 0.0807 0.8170 0.000 0.976 0.000 0.012 0.012
#> GSM550835 5 0.5137 0.6668 0.000 0.228 0.096 0.000 0.676
#> GSM550836 3 0.1740 0.7575 0.056 0.000 0.932 0.000 0.012
#> GSM550837 2 0.4305 -0.1776 0.000 0.512 0.000 0.000 0.488
#> GSM550838 1 0.6415 0.3237 0.532 0.000 0.344 0.032 0.092
#> GSM550841 5 0.3507 0.7747 0.000 0.052 0.120 0.000 0.828
#> GSM550842 5 0.3774 0.6141 0.000 0.296 0.000 0.000 0.704
#> GSM550846 5 0.7971 -0.2538 0.072 0.068 0.068 0.348 0.444
#> GSM550849 1 0.6006 0.5702 0.668 0.024 0.144 0.008 0.156
#> GSM550850 1 0.0000 0.8166 1.000 0.000 0.000 0.000 0.000
#> GSM550851 5 0.4305 0.2088 0.000 0.488 0.000 0.000 0.512
#> GSM550852 2 0.1644 0.8044 0.000 0.940 0.008 0.004 0.048
#> GSM550853 2 0.2891 0.7235 0.000 0.824 0.000 0.176 0.000
#> GSM550855 2 0.2852 0.7261 0.000 0.828 0.000 0.172 0.000
#> GSM550856 2 0.4268 0.3422 0.000 0.556 0.000 0.444 0.000
#> GSM550861 2 0.0000 0.8184 0.000 1.000 0.000 0.000 0.000
#> GSM550863 4 0.2362 0.7916 0.024 0.000 0.000 0.900 0.076
#> GSM550864 2 0.1597 0.8022 0.000 0.940 0.012 0.000 0.048
#> GSM550866 2 0.4287 0.3067 0.000 0.540 0.000 0.460 0.000
#> GSM550867 1 0.0290 0.8172 0.992 0.000 0.008 0.000 0.000
#> GSM550885 1 0.2364 0.7864 0.908 0.000 0.008 0.020 0.064
#> GSM550886 5 0.3366 0.7774 0.000 0.032 0.140 0.000 0.828
#> GSM550887 2 0.0807 0.8170 0.000 0.976 0.000 0.012 0.012
#> GSM550889 4 0.1082 0.8193 0.008 0.028 0.000 0.964 0.000
#> GSM550894 2 0.0404 0.8172 0.000 0.988 0.000 0.000 0.012
#> GSM550897 1 0.1444 0.8030 0.948 0.000 0.012 0.040 0.000
#> GSM550903 2 0.0000 0.8184 0.000 1.000 0.000 0.000 0.000
#> GSM550905 5 0.3966 0.5561 0.000 0.336 0.000 0.000 0.664
#> GSM550906 2 0.0579 0.8179 0.000 0.984 0.000 0.008 0.008
#> GSM550907 5 0.3336 0.7286 0.000 0.000 0.228 0.000 0.772
#> GSM550909 5 0.3323 0.7508 0.000 0.100 0.056 0.000 0.844
#> GSM550911 5 0.3366 0.7245 0.000 0.000 0.232 0.000 0.768
#> GSM550913 2 0.0000 0.8184 0.000 1.000 0.000 0.000 0.000
#> GSM550915 1 0.7772 0.4211 0.536 0.032 0.072 0.188 0.172
#> GSM550917 2 0.1774 0.7987 0.000 0.932 0.016 0.000 0.052
#> GSM550919 1 0.6548 0.6101 0.664 0.048 0.068 0.052 0.168
#> GSM550921 3 0.1671 0.7123 0.000 0.000 0.924 0.000 0.076
#> GSM550924 5 0.2921 0.7473 0.004 0.004 0.148 0.000 0.844
#> GSM550926 2 0.4297 0.2791 0.000 0.528 0.000 0.472 0.000
#> GSM550927 2 0.0807 0.8170 0.000 0.976 0.000 0.012 0.012
#> GSM550787 3 0.6483 0.4334 0.296 0.000 0.508 0.004 0.192
#> GSM550793 3 0.2127 0.7542 0.108 0.000 0.892 0.000 0.000
#> GSM550794 1 0.7465 -0.1878 0.412 0.016 0.060 0.408 0.104
#> GSM550795 1 0.5467 0.6637 0.712 0.000 0.040 0.156 0.092
#> GSM550798 1 0.2329 0.7434 0.876 0.000 0.124 0.000 0.000
#> GSM550803 1 0.0290 0.8172 0.992 0.000 0.008 0.000 0.000
#> GSM550805 1 0.4262 0.0622 0.560 0.000 0.440 0.000 0.000
#> GSM550823 4 0.1179 0.8226 0.016 0.016 0.004 0.964 0.000
#> GSM550824 1 0.0290 0.8172 0.992 0.000 0.008 0.000 0.000
#> GSM550825 3 0.2280 0.7509 0.120 0.000 0.880 0.000 0.000
#> GSM550827 4 0.7891 0.4099 0.236 0.028 0.068 0.500 0.168
#> GSM550828 1 0.0290 0.8172 0.992 0.000 0.008 0.000 0.000
#> GSM550829 3 0.4302 0.0834 0.480 0.000 0.520 0.000 0.000
#> GSM550830 4 0.1082 0.8234 0.028 0.008 0.000 0.964 0.000
#> GSM550834 1 0.0451 0.8149 0.988 0.000 0.008 0.000 0.004
#> GSM550839 5 0.5646 0.6142 0.000 0.000 0.212 0.156 0.632
#> GSM550840 1 0.0404 0.8145 0.988 0.000 0.000 0.012 0.000
#> GSM550843 5 0.3039 0.7579 0.000 0.000 0.192 0.000 0.808
#> GSM550844 1 0.0609 0.8131 0.980 0.000 0.020 0.000 0.000
#> GSM550845 2 0.4596 0.1803 0.000 0.500 0.004 0.492 0.004
#> GSM550848 1 0.9382 -0.0220 0.332 0.228 0.068 0.204 0.168
#> GSM550854 1 0.0290 0.8172 0.992 0.000 0.008 0.000 0.000
#> GSM550857 3 0.2127 0.7542 0.108 0.000 0.892 0.000 0.000
#> GSM550858 1 0.0290 0.8172 0.992 0.000 0.008 0.000 0.000
#> GSM550859 1 0.0290 0.8172 0.992 0.000 0.008 0.000 0.000
#> GSM550862 1 0.0693 0.8154 0.980 0.000 0.008 0.012 0.000
#> GSM550865 4 0.0794 0.8266 0.028 0.000 0.000 0.972 0.000
#> GSM550868 4 0.0794 0.8266 0.028 0.000 0.000 0.972 0.000
#> GSM550869 3 0.5462 0.5766 0.028 0.000 0.704 0.164 0.104
#> GSM550870 2 0.0833 0.8151 0.000 0.976 0.004 0.004 0.016
#> GSM550871 3 0.6744 -0.0959 0.000 0.000 0.400 0.268 0.332
#> GSM550872 4 0.0794 0.8266 0.028 0.000 0.000 0.972 0.000
#> GSM550873 2 0.4367 0.1947 0.000 0.620 0.008 0.000 0.372
#> GSM550874 2 0.4302 0.2596 0.000 0.520 0.000 0.480 0.000
#> GSM550876 5 0.4763 0.5526 0.000 0.000 0.336 0.032 0.632
#> GSM550877 2 0.4300 0.2697 0.000 0.524 0.000 0.476 0.000
#> GSM550878 5 0.3876 0.6189 0.000 0.000 0.316 0.000 0.684
#> GSM550879 1 0.3305 0.7603 0.860 0.000 0.020 0.032 0.088
#> GSM550882 3 0.2389 0.6863 0.004 0.000 0.880 0.000 0.116
#> GSM550888 3 0.1740 0.7575 0.056 0.000 0.932 0.000 0.012
#> GSM550890 4 0.7005 0.5896 0.128 0.020 0.068 0.612 0.172
#> GSM550891 3 0.3003 0.6047 0.000 0.000 0.812 0.000 0.188
#> GSM550892 1 0.4387 0.5070 0.652 0.000 0.008 0.336 0.004
#> GSM550893 2 0.4302 0.2612 0.000 0.520 0.000 0.480 0.000
#> GSM550895 4 0.0963 0.8145 0.000 0.036 0.000 0.964 0.000
#> GSM550896 4 0.4297 -0.1858 0.000 0.472 0.000 0.528 0.000
#> GSM550898 1 0.0290 0.8172 0.992 0.000 0.008 0.000 0.000
#> GSM550899 2 0.1893 0.7966 0.000 0.928 0.024 0.000 0.048
#> GSM550900 4 0.1197 0.8196 0.048 0.000 0.000 0.952 0.000
#> GSM550901 1 0.3853 0.7271 0.836 0.008 0.068 0.012 0.076
#> GSM550902 3 0.3304 0.7048 0.168 0.000 0.816 0.000 0.016
#> GSM550904 1 0.6216 0.4465 0.588 0.000 0.288 0.032 0.092
#> GSM550908 3 0.1800 0.7542 0.048 0.000 0.932 0.000 0.020
#> GSM550912 2 0.2012 0.7923 0.000 0.920 0.020 0.000 0.060
#> GSM550914 4 0.6417 0.6647 0.048 0.044 0.068 0.672 0.168
#> GSM550918 2 0.2569 0.7747 0.000 0.892 0.040 0.000 0.068
#> GSM550922 5 0.3569 0.7705 0.000 0.068 0.104 0.000 0.828
#> GSM550923 1 0.1197 0.7986 0.952 0.000 0.048 0.000 0.000
#> GSM550925 1 0.0404 0.8145 0.988 0.000 0.000 0.012 0.000
#> GSM550802 4 0.1485 0.8158 0.000 0.032 0.000 0.948 0.020
#> GSM550812 4 0.3152 0.7656 0.000 0.000 0.024 0.840 0.136
#> GSM550831 1 0.0000 0.8166 1.000 0.000 0.000 0.000 0.000
#> GSM550847 1 0.0290 0.8172 0.992 0.000 0.008 0.000 0.000
#> GSM550860 3 0.2859 0.6987 0.000 0.000 0.876 0.068 0.056
#> GSM550875 3 0.4201 0.3348 0.408 0.000 0.592 0.000 0.000
#> GSM550880 1 0.4631 0.6429 0.728 0.000 0.024 0.224 0.024
#> GSM550881 3 0.1774 0.7562 0.052 0.000 0.932 0.000 0.016
#> GSM550883 3 0.1908 0.7574 0.092 0.000 0.908 0.000 0.000
#> GSM550884 4 0.4680 0.6670 0.000 0.000 0.132 0.740 0.128
#> GSM550910 5 0.3123 0.7742 0.000 0.012 0.160 0.000 0.828
#> GSM550916 1 0.0162 0.8161 0.996 0.000 0.000 0.004 0.000
#> GSM550920 5 0.2891 0.7667 0.000 0.000 0.176 0.000 0.824
cbind(get_classes(res, k = 6), get_membership(res, k = 6))
#> class entropy silhouette p1 p2 p3 p4 p5 p6
#> GSM550785 1 0.0146 0.80732 0.996 0.000 0.000 0.000 0.000 0.004
#> GSM550786 5 0.1010 0.84167 0.000 0.000 0.036 0.000 0.960 0.004
#> GSM550788 2 0.3023 0.67214 0.000 0.768 0.000 0.232 0.000 0.000
#> GSM550789 2 0.0146 0.81983 0.000 0.996 0.000 0.000 0.004 0.000
#> GSM550790 1 0.0260 0.80656 0.992 0.000 0.000 0.000 0.000 0.008
#> GSM550791 1 0.0632 0.80254 0.976 0.000 0.000 0.000 0.000 0.024
#> GSM550792 6 0.4213 0.65491 0.040 0.164 0.004 0.008 0.016 0.768
#> GSM550796 2 0.0363 0.81944 0.000 0.988 0.000 0.000 0.012 0.000
#> GSM550797 2 0.0000 0.81968 0.000 1.000 0.000 0.000 0.000 0.000
#> GSM550799 5 0.0405 0.84446 0.000 0.008 0.004 0.000 0.988 0.000
#> GSM550800 2 0.3810 0.38393 0.000 0.572 0.000 0.428 0.000 0.000
#> GSM550801 2 0.0000 0.81968 0.000 1.000 0.000 0.000 0.000 0.000
#> GSM550804 2 0.3351 0.59101 0.000 0.712 0.000 0.000 0.000 0.288
#> GSM550806 3 0.3147 0.69874 0.000 0.000 0.816 0.008 0.160 0.016
#> GSM550807 2 0.0000 0.81968 0.000 1.000 0.000 0.000 0.000 0.000
#> GSM550808 5 0.3076 0.69108 0.000 0.240 0.000 0.000 0.760 0.000
#> GSM550809 1 0.6226 0.04264 0.372 0.000 0.332 0.000 0.004 0.292
#> GSM550810 2 0.1141 0.80480 0.000 0.948 0.000 0.000 0.052 0.000
#> GSM550811 6 0.5924 0.24215 0.212 0.000 0.296 0.000 0.004 0.488
#> GSM550813 2 0.1204 0.80421 0.000 0.944 0.000 0.000 0.000 0.056
#> GSM550814 2 0.0891 0.81704 0.000 0.968 0.000 0.008 0.024 0.000
#> GSM550815 2 0.0622 0.81935 0.000 0.980 0.000 0.008 0.012 0.000
#> GSM550816 2 0.3136 0.67755 0.000 0.796 0.000 0.000 0.016 0.188
#> GSM550817 5 0.0692 0.84525 0.000 0.004 0.020 0.000 0.976 0.000
#> GSM550818 5 0.0790 0.84282 0.000 0.000 0.032 0.000 0.968 0.000
#> GSM550819 4 0.1082 0.80598 0.000 0.000 0.000 0.956 0.040 0.004
#> GSM550820 1 0.5544 0.37358 0.556 0.000 0.152 0.000 0.004 0.288
#> GSM550821 5 0.0790 0.83751 0.000 0.032 0.000 0.000 0.968 0.000
#> GSM550822 2 0.0622 0.81935 0.000 0.980 0.000 0.008 0.012 0.000
#> GSM550826 3 0.5823 0.16277 0.216 0.000 0.520 0.000 0.004 0.260
#> GSM550832 2 0.0937 0.81086 0.000 0.960 0.000 0.000 0.040 0.000
#> GSM550833 2 0.0622 0.81935 0.000 0.980 0.000 0.008 0.012 0.000
#> GSM550835 5 0.2527 0.76166 0.000 0.168 0.000 0.000 0.832 0.000
#> GSM550836 3 0.0260 0.81872 0.000 0.000 0.992 0.000 0.008 0.000
#> GSM550837 5 0.3620 0.52375 0.000 0.352 0.000 0.000 0.648 0.000
#> GSM550838 1 0.6219 0.04686 0.372 0.000 0.340 0.000 0.004 0.284
#> GSM550841 5 0.0363 0.84310 0.000 0.012 0.000 0.000 0.988 0.000
#> GSM550842 5 0.2697 0.74383 0.000 0.188 0.000 0.000 0.812 0.000
#> GSM550846 6 0.1198 0.79004 0.004 0.000 0.004 0.012 0.020 0.960
#> GSM550849 1 0.7135 0.17459 0.472 0.012 0.068 0.004 0.200 0.244
#> GSM550850 1 0.0260 0.80656 0.992 0.000 0.000 0.000 0.000 0.008
#> GSM550851 5 0.3482 0.59492 0.000 0.316 0.000 0.000 0.684 0.000
#> GSM550852 2 0.2882 0.74656 0.000 0.848 0.000 0.004 0.028 0.120
#> GSM550853 2 0.2260 0.75556 0.000 0.860 0.000 0.140 0.000 0.000
#> GSM550855 2 0.2300 0.75253 0.000 0.856 0.000 0.144 0.000 0.000
#> GSM550856 2 0.3847 0.32729 0.000 0.544 0.000 0.456 0.000 0.000
#> GSM550861 2 0.0146 0.81983 0.000 0.996 0.000 0.000 0.004 0.000
#> GSM550863 4 0.3245 0.58864 0.008 0.000 0.000 0.764 0.000 0.228
#> GSM550864 2 0.1714 0.78839 0.000 0.908 0.000 0.000 0.000 0.092
#> GSM550866 2 0.3982 0.31338 0.000 0.536 0.000 0.460 0.000 0.004
#> GSM550867 1 0.0146 0.80821 0.996 0.000 0.004 0.000 0.000 0.000
#> GSM550885 1 0.2402 0.72091 0.856 0.000 0.004 0.000 0.000 0.140
#> GSM550886 5 0.0806 0.84584 0.000 0.008 0.020 0.000 0.972 0.000
#> GSM550887 2 0.0622 0.81935 0.000 0.980 0.000 0.008 0.012 0.000
#> GSM550889 4 0.0260 0.82598 0.008 0.000 0.000 0.992 0.000 0.000
#> GSM550894 2 0.0865 0.81276 0.000 0.964 0.000 0.000 0.036 0.000
#> GSM550897 1 0.1151 0.79489 0.956 0.000 0.000 0.032 0.000 0.012
#> GSM550903 2 0.0000 0.81968 0.000 1.000 0.000 0.000 0.000 0.000
#> GSM550905 5 0.2664 0.74488 0.000 0.184 0.000 0.000 0.816 0.000
#> GSM550906 2 0.0363 0.81944 0.000 0.988 0.000 0.000 0.012 0.000
#> GSM550907 5 0.1910 0.80200 0.000 0.000 0.108 0.000 0.892 0.000
#> GSM550909 5 0.0767 0.84204 0.000 0.012 0.004 0.000 0.976 0.008
#> GSM550911 5 0.2048 0.79201 0.000 0.000 0.120 0.000 0.880 0.000
#> GSM550913 2 0.0000 0.81968 0.000 1.000 0.000 0.000 0.000 0.000
#> GSM550915 6 0.1155 0.79549 0.036 0.004 0.000 0.004 0.000 0.956
#> GSM550917 2 0.1714 0.78761 0.000 0.908 0.000 0.000 0.000 0.092
#> GSM550919 6 0.1865 0.78550 0.040 0.040 0.000 0.000 0.000 0.920
#> GSM550921 3 0.0363 0.81861 0.000 0.000 0.988 0.000 0.012 0.000
#> GSM550924 5 0.3086 0.73812 0.000 0.000 0.020 0.004 0.820 0.156
#> GSM550926 2 0.3989 0.29476 0.000 0.528 0.000 0.468 0.000 0.004
#> GSM550927 2 0.0547 0.81822 0.000 0.980 0.000 0.020 0.000 0.000
#> GSM550787 1 0.6469 -0.08806 0.428 0.000 0.380 0.004 0.152 0.036
#> GSM550793 3 0.0146 0.81568 0.000 0.000 0.996 0.000 0.000 0.004
#> GSM550794 6 0.5413 0.41785 0.320 0.004 0.000 0.096 0.008 0.572
#> GSM550795 1 0.5442 0.46730 0.620 0.000 0.068 0.036 0.004 0.272
#> GSM550798 1 0.1806 0.76722 0.908 0.000 0.088 0.000 0.000 0.004
#> GSM550803 1 0.0146 0.80821 0.996 0.000 0.004 0.000 0.000 0.000
#> GSM550805 1 0.4617 0.37486 0.624 0.000 0.328 0.008 0.000 0.040
#> GSM550823 4 0.0291 0.82411 0.004 0.000 0.000 0.992 0.000 0.004
#> GSM550824 1 0.0146 0.80821 0.996 0.000 0.004 0.000 0.000 0.000
#> GSM550825 3 0.0665 0.81612 0.008 0.000 0.980 0.000 0.004 0.008
#> GSM550827 6 0.1515 0.79611 0.020 0.008 0.000 0.028 0.000 0.944
#> GSM550828 1 0.0291 0.80776 0.992 0.000 0.004 0.000 0.000 0.004
#> GSM550829 3 0.3966 0.08516 0.444 0.000 0.552 0.000 0.000 0.004
#> GSM550830 4 0.0260 0.82598 0.008 0.000 0.000 0.992 0.000 0.000
#> GSM550834 1 0.0935 0.79611 0.964 0.000 0.000 0.000 0.004 0.032
#> GSM550839 5 0.5335 0.56691 0.000 0.000 0.140 0.208 0.636 0.016
#> GSM550840 1 0.0603 0.80393 0.980 0.000 0.000 0.004 0.000 0.016
#> GSM550843 5 0.1141 0.83605 0.000 0.000 0.052 0.000 0.948 0.000
#> GSM550844 1 0.0520 0.80737 0.984 0.000 0.008 0.000 0.000 0.008
#> GSM550845 2 0.4684 0.41158 0.000 0.576 0.000 0.372 0.000 0.052
#> GSM550848 6 0.1313 0.79683 0.028 0.016 0.000 0.004 0.000 0.952
#> GSM550854 1 0.0146 0.80821 0.996 0.000 0.004 0.000 0.000 0.000
#> GSM550857 3 0.0146 0.81568 0.000 0.000 0.996 0.000 0.000 0.004
#> GSM550858 1 0.0146 0.80821 0.996 0.000 0.004 0.000 0.000 0.000
#> GSM550859 1 0.0146 0.80821 0.996 0.000 0.004 0.000 0.000 0.000
#> GSM550862 1 0.0405 0.80748 0.988 0.000 0.004 0.008 0.000 0.000
#> GSM550865 4 0.0993 0.82032 0.012 0.000 0.000 0.964 0.000 0.024
#> GSM550868 4 0.0993 0.82080 0.012 0.000 0.000 0.964 0.000 0.024
#> GSM550869 3 0.5579 0.31898 0.008 0.000 0.552 0.352 0.064 0.024
#> GSM550870 2 0.1007 0.80851 0.000 0.956 0.000 0.000 0.000 0.044
#> GSM550871 4 0.6363 -0.00811 0.000 0.000 0.332 0.412 0.240 0.016
#> GSM550872 4 0.0909 0.82185 0.012 0.000 0.000 0.968 0.000 0.020
#> GSM550873 2 0.4778 -0.06891 0.000 0.492 0.000 0.004 0.464 0.040
#> GSM550874 2 0.3860 0.29040 0.000 0.528 0.000 0.472 0.000 0.000
#> GSM550876 5 0.5169 0.53182 0.000 0.000 0.244 0.100 0.640 0.016
#> GSM550877 2 0.3986 0.30479 0.000 0.532 0.000 0.464 0.000 0.004
#> GSM550878 5 0.3076 0.65989 0.000 0.000 0.240 0.000 0.760 0.000
#> GSM550879 1 0.4306 0.49445 0.656 0.000 0.032 0.000 0.004 0.308
#> GSM550882 3 0.1605 0.79681 0.000 0.000 0.936 0.004 0.044 0.016
#> GSM550888 3 0.0363 0.81861 0.000 0.000 0.988 0.000 0.012 0.000
#> GSM550890 6 0.1074 0.79353 0.012 0.000 0.000 0.028 0.000 0.960
#> GSM550891 3 0.2320 0.73798 0.000 0.000 0.864 0.000 0.132 0.004
#> GSM550892 1 0.4270 0.49148 0.652 0.000 0.004 0.316 0.000 0.028
#> GSM550893 2 0.3866 0.25481 0.000 0.516 0.000 0.484 0.000 0.000
#> GSM550895 4 0.0405 0.82306 0.000 0.008 0.000 0.988 0.000 0.004
#> GSM550896 4 0.3817 -0.07301 0.000 0.432 0.000 0.568 0.000 0.000
#> GSM550898 1 0.0000 0.80775 1.000 0.000 0.000 0.000 0.000 0.000
#> GSM550899 2 0.1957 0.77677 0.000 0.888 0.000 0.000 0.000 0.112
#> GSM550900 4 0.0363 0.82521 0.012 0.000 0.000 0.988 0.000 0.000
#> GSM550901 1 0.3998 -0.01884 0.504 0.004 0.000 0.000 0.000 0.492
#> GSM550902 3 0.0717 0.80433 0.016 0.000 0.976 0.000 0.000 0.008
#> GSM550904 1 0.6230 0.02445 0.372 0.000 0.300 0.000 0.004 0.324
#> GSM550908 3 0.0260 0.81872 0.000 0.000 0.992 0.000 0.008 0.000
#> GSM550912 2 0.2416 0.74440 0.000 0.844 0.000 0.000 0.000 0.156
#> GSM550914 6 0.1155 0.78893 0.004 0.004 0.000 0.036 0.000 0.956
#> GSM550918 2 0.3175 0.63894 0.000 0.744 0.000 0.000 0.000 0.256
#> GSM550922 5 0.0363 0.84310 0.000 0.012 0.000 0.000 0.988 0.000
#> GSM550923 1 0.0508 0.80549 0.984 0.000 0.012 0.000 0.000 0.004
#> GSM550925 1 0.1059 0.79765 0.964 0.000 0.004 0.016 0.000 0.016
#> GSM550802 4 0.1832 0.78866 0.000 0.032 0.000 0.928 0.008 0.032
#> GSM550812 4 0.4037 0.53624 0.000 0.000 0.008 0.724 0.032 0.236
#> GSM550831 1 0.0146 0.80793 0.996 0.000 0.000 0.000 0.004 0.000
#> GSM550847 1 0.0000 0.80775 1.000 0.000 0.000 0.000 0.000 0.000
#> GSM550860 3 0.2765 0.76555 0.000 0.000 0.876 0.064 0.044 0.016
#> GSM550875 3 0.4787 -0.00562 0.476 0.000 0.484 0.012 0.000 0.028
#> GSM550880 1 0.4020 0.64733 0.764 0.000 0.000 0.160 0.008 0.068
#> GSM550881 3 0.0363 0.81861 0.000 0.000 0.988 0.000 0.012 0.000
#> GSM550883 3 0.0146 0.81568 0.000 0.000 0.996 0.000 0.000 0.004
#> GSM550884 6 0.5310 0.02286 0.000 0.000 0.040 0.456 0.032 0.472
#> GSM550910 5 0.0692 0.84493 0.000 0.004 0.020 0.000 0.976 0.000
#> GSM550916 1 0.0508 0.80483 0.984 0.000 0.000 0.004 0.000 0.012
#> GSM550920 5 0.0632 0.84383 0.000 0.000 0.024 0.000 0.976 0.000
Heatmaps for the consensus matrix. It visualizes the probability of two samples to be in a same group.
consensus_heatmap(res, k = 2)
consensus_heatmap(res, k = 3)
consensus_heatmap(res, k = 4)
consensus_heatmap(res, k = 5)
consensus_heatmap(res, k = 6)
Heatmaps for the membership of samples in all partitions to see how consistent they are:
membership_heatmap(res, k = 2)
membership_heatmap(res, k = 3)
membership_heatmap(res, k = 4)
membership_heatmap(res, k = 5)
membership_heatmap(res, k = 6)
As soon as we have had the classes for columns, we can look for signatures which are significantly different between classes which can be candidate marks for certain classes. Following are the heatmaps for signatures.
Signature heatmaps where rows are scaled:
get_signatures(res, k = 2)
get_signatures(res, k = 3)
get_signatures(res, k = 4)
get_signatures(res, k = 5)
get_signatures(res, k = 6)
Signature heatmaps where rows are not scaled:
get_signatures(res, k = 2, scale_rows = FALSE)
get_signatures(res, k = 3, scale_rows = FALSE)
get_signatures(res, k = 4, scale_rows = FALSE)
get_signatures(res, k = 5, scale_rows = FALSE)
get_signatures(res, k = 6, scale_rows = FALSE)
Compare the overlap of signatures from different k:
compare_signatures(res)
get_signature() returns a data frame invisibly. TO get the list of signatures, the function
call should be assigned to a variable explicitly. In following code, if plot argument is set
to FALSE, no heatmap is plotted while only the differential analysis is performed.
# code only for demonstration
tb = get_signature(res, k = ..., plot = FALSE)
An example of the output of tb is:
#> which_row fdr mean_1 mean_2 scaled_mean_1 scaled_mean_2 km
#> 1 38 0.042760348 8.373488 9.131774 -0.5533452 0.5164555 1
#> 2 40 0.018707592 7.106213 8.469186 -0.6173731 0.5762149 1
#> 3 55 0.019134737 10.221463 11.207825 -0.6159697 0.5749050 1
#> 4 59 0.006059896 5.921854 7.869574 -0.6899429 0.6439467 1
#> 5 60 0.018055526 8.928898 10.211722 -0.6204761 0.5791110 1
#> 6 98 0.009384629 15.714769 14.887706 0.6635654 -0.6193277 2
...
The columns in tb are:
which_row: row indices corresponding to the input matrix.fdr: FDR for the differential test. mean_x: The mean value in group x.scaled_mean_x: The mean value in group x after rows are scaled.km: Row groups if k-means clustering is applied to rows.UMAP plot which shows how samples are separated.
dimension_reduction(res, k = 2, method = "UMAP")
dimension_reduction(res, k = 3, method = "UMAP")
dimension_reduction(res, k = 4, method = "UMAP")
dimension_reduction(res, k = 5, method = "UMAP")
dimension_reduction(res, k = 6, method = "UMAP")
Following heatmap shows how subgroups are split when increasing k:
collect_classes(res)
Test correlation between subgroups and known annotations. If the known annotation is numeric, one-way ANOVA test is applied, and if the known annotation is discrete, chi-squared contingency table test is applied.
test_to_known_factors(res)
#> n disease.state(p) k
#> MAD:skmeans 143 4.87e-05 2
#> MAD:skmeans 129 1.18e-04 3
#> MAD:skmeans 135 6.00e-06 4
#> MAD:skmeans 114 2.04e-05 5
#> MAD:skmeans 114 1.08e-04 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 51776 rows and 143 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 0.494 0.811 0.913 0.4634 0.527 0.527
#> 3 3 0.518 0.738 0.864 0.4007 0.675 0.455
#> 4 4 0.626 0.734 0.863 0.1437 0.809 0.514
#> 5 5 0.625 0.505 0.717 0.0432 0.886 0.607
#> 6 6 0.700 0.739 0.846 0.0399 0.895 0.589
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
#> GSM550785 1 0.0000 0.877 1.000 0.000
#> GSM550786 2 0.9909 0.192 0.444 0.556
#> GSM550788 2 0.0000 0.908 0.000 1.000
#> GSM550789 2 0.0000 0.908 0.000 1.000
#> GSM550790 1 0.0000 0.877 1.000 0.000
#> GSM550791 1 0.9944 0.202 0.544 0.456
#> GSM550792 2 0.6887 0.757 0.184 0.816
#> GSM550796 2 0.0000 0.908 0.000 1.000
#> GSM550797 2 0.0000 0.908 0.000 1.000
#> GSM550799 2 0.0000 0.908 0.000 1.000
#> GSM550800 2 0.0000 0.908 0.000 1.000
#> GSM550801 2 0.0000 0.908 0.000 1.000
#> GSM550804 2 0.0000 0.908 0.000 1.000
#> GSM550806 2 0.7376 0.728 0.208 0.792
#> GSM550807 2 0.0000 0.908 0.000 1.000
#> GSM550808 2 0.0000 0.908 0.000 1.000
#> GSM550809 1 0.6148 0.834 0.848 0.152
#> GSM550810 2 0.0000 0.908 0.000 1.000
#> GSM550811 2 0.9933 0.161 0.452 0.548
#> GSM550813 2 0.0000 0.908 0.000 1.000
#> GSM550814 2 0.0000 0.908 0.000 1.000
#> GSM550815 2 0.0000 0.908 0.000 1.000
#> GSM550816 2 0.0000 0.908 0.000 1.000
#> GSM550817 2 0.0000 0.908 0.000 1.000
#> GSM550818 2 0.0000 0.908 0.000 1.000
#> GSM550819 2 0.0000 0.908 0.000 1.000
#> GSM550820 1 0.5178 0.851 0.884 0.116
#> GSM550821 2 0.0000 0.908 0.000 1.000
#> GSM550822 2 0.0000 0.908 0.000 1.000
#> GSM550826 1 0.6247 0.830 0.844 0.156
#> GSM550832 2 0.0000 0.908 0.000 1.000
#> GSM550833 2 0.0000 0.908 0.000 1.000
#> GSM550835 2 0.0000 0.908 0.000 1.000
#> GSM550836 1 0.5946 0.840 0.856 0.144
#> GSM550837 2 0.0000 0.908 0.000 1.000
#> GSM550838 1 0.5946 0.840 0.856 0.144
#> GSM550841 2 0.0000 0.908 0.000 1.000
#> GSM550842 2 0.0000 0.908 0.000 1.000
#> GSM550846 2 0.0938 0.901 0.012 0.988
#> GSM550849 2 0.9909 0.192 0.444 0.556
#> GSM550850 1 0.0000 0.877 1.000 0.000
#> GSM550851 2 0.0000 0.908 0.000 1.000
#> GSM550852 2 0.0000 0.908 0.000 1.000
#> GSM550853 2 0.0000 0.908 0.000 1.000
#> GSM550855 2 0.0000 0.908 0.000 1.000
#> GSM550856 2 0.0000 0.908 0.000 1.000
#> GSM550861 2 0.0000 0.908 0.000 1.000
#> GSM550863 2 0.9491 0.506 0.368 0.632
#> GSM550864 2 0.0000 0.908 0.000 1.000
#> GSM550866 2 0.0000 0.908 0.000 1.000
#> GSM550867 1 0.0000 0.877 1.000 0.000
#> GSM550885 1 0.0000 0.877 1.000 0.000
#> GSM550886 2 0.0000 0.908 0.000 1.000
#> GSM550887 2 0.0000 0.908 0.000 1.000
#> GSM550889 1 0.8555 0.584 0.720 0.280
#> GSM550894 2 0.0000 0.908 0.000 1.000
#> GSM550897 1 0.0000 0.877 1.000 0.000
#> GSM550903 2 0.0000 0.908 0.000 1.000
#> GSM550905 2 0.0000 0.908 0.000 1.000
#> GSM550906 2 0.0000 0.908 0.000 1.000
#> GSM550907 2 0.7453 0.728 0.212 0.788
#> GSM550909 2 0.0000 0.908 0.000 1.000
#> GSM550911 2 0.0000 0.908 0.000 1.000
#> GSM550913 2 0.0000 0.908 0.000 1.000
#> GSM550915 2 0.7376 0.728 0.208 0.792
#> GSM550917 2 0.0000 0.908 0.000 1.000
#> GSM550919 2 0.8016 0.679 0.244 0.756
#> GSM550921 1 0.5946 0.840 0.856 0.144
#> GSM550924 2 0.7376 0.728 0.208 0.792
#> GSM550926 2 0.0000 0.908 0.000 1.000
#> GSM550927 2 0.0000 0.908 0.000 1.000
#> GSM550787 1 0.8555 0.667 0.720 0.280
#> GSM550793 1 0.6148 0.834 0.848 0.152
#> GSM550794 2 0.7376 0.728 0.208 0.792
#> GSM550795 1 0.2603 0.863 0.956 0.044
#> GSM550798 1 0.0000 0.877 1.000 0.000
#> GSM550803 1 0.0000 0.877 1.000 0.000
#> GSM550805 1 0.5946 0.840 0.856 0.144
#> GSM550823 2 0.8861 0.575 0.304 0.696
#> GSM550824 1 0.0000 0.877 1.000 0.000
#> GSM550825 1 0.0000 0.877 1.000 0.000
#> GSM550827 2 0.7602 0.714 0.220 0.780
#> GSM550828 1 0.0000 0.877 1.000 0.000
#> GSM550829 1 0.1414 0.875 0.980 0.020
#> GSM550830 1 0.8016 0.678 0.756 0.244
#> GSM550834 1 0.0000 0.877 1.000 0.000
#> GSM550839 2 0.0000 0.908 0.000 1.000
#> GSM550840 1 0.0000 0.877 1.000 0.000
#> GSM550843 2 0.6531 0.774 0.168 0.832
#> GSM550844 1 0.0000 0.877 1.000 0.000
#> GSM550845 2 0.0000 0.908 0.000 1.000
#> GSM550848 2 0.7376 0.728 0.208 0.792
#> GSM550854 1 0.0000 0.877 1.000 0.000
#> GSM550857 1 0.1414 0.875 0.980 0.020
#> GSM550858 1 0.0000 0.877 1.000 0.000
#> GSM550859 1 0.0000 0.877 1.000 0.000
#> GSM550862 1 0.0000 0.877 1.000 0.000
#> GSM550865 2 0.9358 0.539 0.352 0.648
#> GSM550868 2 0.9996 0.155 0.488 0.512
#> GSM550869 1 0.9732 0.404 0.596 0.404
#> GSM550870 2 0.0000 0.908 0.000 1.000
#> GSM550871 2 0.5946 0.797 0.144 0.856
#> GSM550872 1 0.9998 -0.102 0.508 0.492
#> GSM550873 2 0.0000 0.908 0.000 1.000
#> GSM550874 2 0.0000 0.908 0.000 1.000
#> GSM550876 2 0.0000 0.908 0.000 1.000
#> GSM550877 2 0.0000 0.908 0.000 1.000
#> GSM550878 2 0.7299 0.733 0.204 0.796
#> GSM550879 1 0.0000 0.877 1.000 0.000
#> GSM550882 1 0.5946 0.840 0.856 0.144
#> GSM550888 1 0.5842 0.842 0.860 0.140
#> GSM550890 2 0.7056 0.750 0.192 0.808
#> GSM550891 1 0.9460 0.507 0.636 0.364
#> GSM550892 1 0.0000 0.877 1.000 0.000
#> GSM550893 2 0.0000 0.908 0.000 1.000
#> GSM550895 2 0.5946 0.768 0.144 0.856
#> GSM550896 2 0.0000 0.908 0.000 1.000
#> GSM550898 1 0.0000 0.877 1.000 0.000
#> GSM550899 2 0.0000 0.908 0.000 1.000
#> GSM550900 2 0.9933 0.284 0.452 0.548
#> GSM550901 1 0.5946 0.840 0.856 0.144
#> GSM550902 1 0.5946 0.840 0.856 0.144
#> GSM550904 1 0.5946 0.840 0.856 0.144
#> GSM550908 1 0.5946 0.840 0.856 0.144
#> GSM550912 2 0.0000 0.908 0.000 1.000
#> GSM550914 2 0.2778 0.870 0.048 0.952
#> GSM550918 2 0.0000 0.908 0.000 1.000
#> GSM550922 2 0.0000 0.908 0.000 1.000
#> GSM550923 1 0.0000 0.877 1.000 0.000
#> GSM550925 1 0.5519 0.799 0.872 0.128
#> GSM550802 2 0.0000 0.908 0.000 1.000
#> GSM550812 2 0.0000 0.908 0.000 1.000
#> GSM550831 1 0.0000 0.877 1.000 0.000
#> GSM550847 1 0.0000 0.877 1.000 0.000
#> GSM550860 1 0.9686 0.426 0.604 0.396
#> GSM550875 1 0.5946 0.840 0.856 0.144
#> GSM550880 2 0.9393 0.532 0.356 0.644
#> GSM550881 1 0.6148 0.834 0.848 0.152
#> GSM550883 1 0.5946 0.840 0.856 0.144
#> GSM550884 2 0.7376 0.728 0.208 0.792
#> GSM550910 2 0.3114 0.871 0.056 0.944
#> GSM550916 1 0.0000 0.877 1.000 0.000
#> GSM550920 2 0.7139 0.745 0.196 0.804
cbind(get_classes(res, k = 3), get_membership(res, k = 3))
#> class entropy silhouette p1 p2 p3
#> GSM550785 1 0.0000 0.8351 1.000 0.000 0.000
#> GSM550786 3 0.4514 0.7361 0.156 0.012 0.832
#> GSM550788 2 0.0000 0.8773 0.000 1.000 0.000
#> GSM550789 2 0.3941 0.7718 0.000 0.844 0.156
#> GSM550790 1 0.0000 0.8351 1.000 0.000 0.000
#> GSM550791 1 0.3528 0.8110 0.892 0.092 0.016
#> GSM550792 2 0.7764 0.2848 0.328 0.604 0.068
#> GSM550796 2 0.3941 0.7718 0.000 0.844 0.156
#> GSM550797 2 0.3941 0.7718 0.000 0.844 0.156
#> GSM550799 3 0.0892 0.7807 0.000 0.020 0.980
#> GSM550800 2 0.0000 0.8773 0.000 1.000 0.000
#> GSM550801 2 0.3941 0.7718 0.000 0.844 0.156
#> GSM550804 2 0.0892 0.8730 0.000 0.980 0.020
#> GSM550806 3 0.3941 0.7913 0.000 0.156 0.844
#> GSM550807 2 0.0000 0.8773 0.000 1.000 0.000
#> GSM550808 2 0.5706 0.5195 0.000 0.680 0.320
#> GSM550809 1 0.3183 0.8165 0.908 0.076 0.016
#> GSM550810 2 0.3941 0.7718 0.000 0.844 0.156
#> GSM550811 1 0.5426 0.7782 0.820 0.088 0.092
#> GSM550813 2 0.0892 0.8730 0.000 0.980 0.020
#> GSM550814 2 0.0892 0.8730 0.000 0.980 0.020
#> GSM550815 2 0.3941 0.7718 0.000 0.844 0.156
#> GSM550816 2 0.4346 0.7687 0.000 0.816 0.184
#> GSM550817 3 0.0892 0.7807 0.000 0.020 0.980
#> GSM550818 3 0.0000 0.7843 0.000 0.000 1.000
#> GSM550819 3 0.5848 0.6908 0.012 0.268 0.720
#> GSM550820 1 0.2356 0.8206 0.928 0.072 0.000
#> GSM550821 3 0.2448 0.7689 0.000 0.076 0.924
#> GSM550822 2 0.3941 0.7718 0.000 0.844 0.156
#> GSM550826 1 0.4937 0.7546 0.824 0.028 0.148
#> GSM550832 2 0.0892 0.8730 0.000 0.980 0.020
#> GSM550833 2 0.3941 0.7718 0.000 0.844 0.156
#> GSM550835 3 0.5178 0.5887 0.000 0.256 0.744
#> GSM550836 3 0.4399 0.7059 0.188 0.000 0.812
#> GSM550837 3 0.6225 0.1905 0.000 0.432 0.568
#> GSM550838 1 0.4326 0.7612 0.844 0.012 0.144
#> GSM550841 3 0.0592 0.7826 0.000 0.012 0.988
#> GSM550842 3 0.6302 0.0267 0.000 0.480 0.520
#> GSM550846 2 0.7652 -0.1088 0.044 0.512 0.444
#> GSM550849 1 0.4934 0.7710 0.820 0.156 0.024
#> GSM550850 1 0.0000 0.8351 1.000 0.000 0.000
#> GSM550851 3 0.5138 0.5887 0.000 0.252 0.748
#> GSM550852 2 0.0892 0.8730 0.000 0.980 0.020
#> GSM550853 2 0.0000 0.8773 0.000 1.000 0.000
#> GSM550855 2 0.0000 0.8773 0.000 1.000 0.000
#> GSM550856 2 0.0000 0.8773 0.000 1.000 0.000
#> GSM550861 2 0.0000 0.8773 0.000 1.000 0.000
#> GSM550863 1 0.7268 0.2298 0.524 0.448 0.028
#> GSM550864 2 0.0424 0.8760 0.000 0.992 0.008
#> GSM550866 2 0.0000 0.8773 0.000 1.000 0.000
#> GSM550867 1 0.0000 0.8351 1.000 0.000 0.000
#> GSM550885 1 0.0000 0.8351 1.000 0.000 0.000
#> GSM550886 3 0.3941 0.7913 0.000 0.156 0.844
#> GSM550887 2 0.3941 0.7718 0.000 0.844 0.156
#> GSM550889 1 0.6062 0.4715 0.616 0.384 0.000
#> GSM550894 2 0.0237 0.8767 0.000 0.996 0.004
#> GSM550897 1 0.0892 0.8328 0.980 0.020 0.000
#> GSM550903 2 0.1964 0.8470 0.000 0.944 0.056
#> GSM550905 3 0.5760 0.4783 0.000 0.328 0.672
#> GSM550906 2 0.0000 0.8773 0.000 1.000 0.000
#> GSM550907 3 0.0000 0.7843 0.000 0.000 1.000
#> GSM550909 3 0.2959 0.7579 0.000 0.100 0.900
#> GSM550911 3 0.0892 0.7807 0.000 0.020 0.980
#> GSM550913 2 0.0000 0.8773 0.000 1.000 0.000
#> GSM550915 1 0.7063 0.3079 0.516 0.464 0.020
#> GSM550917 2 0.0892 0.8730 0.000 0.980 0.020
#> GSM550919 1 0.6869 0.4190 0.560 0.424 0.016
#> GSM550921 3 0.4235 0.7178 0.176 0.000 0.824
#> GSM550924 3 0.8390 0.4753 0.100 0.340 0.560
#> GSM550926 2 0.0892 0.8730 0.000 0.980 0.020
#> GSM550927 2 0.0000 0.8773 0.000 1.000 0.000
#> GSM550787 1 0.5913 0.7610 0.788 0.144 0.068
#> GSM550793 1 0.5010 0.7827 0.840 0.076 0.084
#> GSM550794 2 0.9528 0.1407 0.272 0.488 0.240
#> GSM550795 1 0.0000 0.8351 1.000 0.000 0.000
#> GSM550798 1 0.0000 0.8351 1.000 0.000 0.000
#> GSM550803 1 0.0000 0.8351 1.000 0.000 0.000
#> GSM550805 1 0.3272 0.8102 0.892 0.104 0.004
#> GSM550823 1 0.7462 0.5182 0.600 0.352 0.048
#> GSM550824 1 0.0000 0.8351 1.000 0.000 0.000
#> GSM550825 1 0.4002 0.7520 0.840 0.000 0.160
#> GSM550827 1 0.6881 0.4682 0.592 0.388 0.020
#> GSM550828 1 0.0000 0.8351 1.000 0.000 0.000
#> GSM550829 1 0.3752 0.7636 0.856 0.000 0.144
#> GSM550830 1 0.5138 0.6951 0.748 0.252 0.000
#> GSM550834 1 0.0424 0.8347 0.992 0.008 0.000
#> GSM550839 3 0.4121 0.7878 0.000 0.168 0.832
#> GSM550840 1 0.0000 0.8351 1.000 0.000 0.000
#> GSM550843 3 0.3941 0.7913 0.000 0.156 0.844
#> GSM550844 1 0.0000 0.8351 1.000 0.000 0.000
#> GSM550845 2 0.1129 0.8715 0.004 0.976 0.020
#> GSM550848 2 0.5899 0.5652 0.244 0.736 0.020
#> GSM550854 1 0.0000 0.8351 1.000 0.000 0.000
#> GSM550857 1 0.4555 0.7128 0.800 0.000 0.200
#> GSM550858 1 0.0000 0.8351 1.000 0.000 0.000
#> GSM550859 1 0.0000 0.8351 1.000 0.000 0.000
#> GSM550862 1 0.0000 0.8351 1.000 0.000 0.000
#> GSM550865 1 0.6126 0.6319 0.712 0.268 0.020
#> GSM550868 1 0.6255 0.5952 0.684 0.300 0.016
#> GSM550869 1 0.9642 0.2732 0.440 0.344 0.216
#> GSM550870 2 0.0892 0.8730 0.000 0.980 0.020
#> GSM550871 3 0.4121 0.7878 0.000 0.168 0.832
#> GSM550872 1 0.6501 0.5652 0.664 0.316 0.020
#> GSM550873 2 0.3192 0.7899 0.000 0.888 0.112
#> GSM550874 2 0.0000 0.8773 0.000 1.000 0.000
#> GSM550876 3 0.4235 0.7799 0.000 0.176 0.824
#> GSM550877 2 0.0000 0.8773 0.000 1.000 0.000
#> GSM550878 3 0.3941 0.7913 0.000 0.156 0.844
#> GSM550879 1 0.0000 0.8351 1.000 0.000 0.000
#> GSM550882 3 0.4235 0.7178 0.176 0.000 0.824
#> GSM550888 3 0.4291 0.7141 0.180 0.000 0.820
#> GSM550890 2 0.5899 0.5763 0.244 0.736 0.020
#> GSM550891 3 0.4802 0.7920 0.020 0.156 0.824
#> GSM550892 1 0.0000 0.8351 1.000 0.000 0.000
#> GSM550893 2 0.0000 0.8773 0.000 1.000 0.000
#> GSM550895 2 0.2625 0.8064 0.084 0.916 0.000
#> GSM550896 2 0.0000 0.8773 0.000 1.000 0.000
#> GSM550898 1 0.0000 0.8351 1.000 0.000 0.000
#> GSM550899 2 0.0892 0.8730 0.000 0.980 0.020
#> GSM550900 1 0.6326 0.6015 0.688 0.292 0.020
#> GSM550901 1 0.3116 0.8079 0.892 0.108 0.000
#> GSM550902 1 0.4925 0.7857 0.844 0.076 0.080
#> GSM550904 1 0.3461 0.8141 0.900 0.076 0.024
#> GSM550908 3 0.4235 0.7178 0.176 0.000 0.824
#> GSM550912 2 0.0892 0.8730 0.000 0.980 0.020
#> GSM550914 2 0.2297 0.8528 0.036 0.944 0.020
#> GSM550918 2 0.0892 0.8730 0.000 0.980 0.020
#> GSM550922 3 0.0892 0.7807 0.000 0.020 0.980
#> GSM550923 1 0.0000 0.8351 1.000 0.000 0.000
#> GSM550925 1 0.3879 0.7722 0.848 0.152 0.000
#> GSM550802 2 0.5024 0.6160 0.004 0.776 0.220
#> GSM550812 3 0.5291 0.6834 0.000 0.268 0.732
#> GSM550831 1 0.0000 0.8351 1.000 0.000 0.000
#> GSM550847 1 0.0000 0.8351 1.000 0.000 0.000
#> GSM550860 3 0.5200 0.7830 0.020 0.184 0.796
#> GSM550875 1 0.2945 0.8166 0.908 0.088 0.004
#> GSM550880 1 0.6881 0.4206 0.592 0.388 0.020
#> GSM550881 1 0.6079 0.3808 0.612 0.000 0.388
#> GSM550883 1 0.4399 0.7252 0.812 0.000 0.188
#> GSM550884 3 0.5905 0.5547 0.000 0.352 0.648
#> GSM550910 3 0.4002 0.7920 0.000 0.160 0.840
#> GSM550916 1 0.0000 0.8351 1.000 0.000 0.000
#> GSM550920 3 0.3941 0.7913 0.000 0.156 0.844
cbind(get_classes(res, k = 4), get_membership(res, k = 4))
#> class entropy silhouette p1 p2 p3 p4
#> GSM550785 1 0.0000 0.8777 1.000 0.000 0.000 0.000
#> GSM550786 3 0.3257 0.7915 0.004 0.000 0.844 0.152
#> GSM550788 2 0.3400 0.6724 0.000 0.820 0.000 0.180
#> GSM550789 2 0.0000 0.8301 0.000 1.000 0.000 0.000
#> GSM550790 1 0.0000 0.8777 1.000 0.000 0.000 0.000
#> GSM550791 1 0.4605 0.6236 0.664 0.000 0.000 0.336
#> GSM550792 4 0.4300 0.6688 0.020 0.112 0.036 0.832
#> GSM550796 2 0.0000 0.8301 0.000 1.000 0.000 0.000
#> GSM550797 2 0.0000 0.8301 0.000 1.000 0.000 0.000
#> GSM550799 3 0.0188 0.8604 0.000 0.004 0.996 0.000
#> GSM550800 2 0.2589 0.7502 0.000 0.884 0.000 0.116
#> GSM550801 2 0.0000 0.8301 0.000 1.000 0.000 0.000
#> GSM550804 4 0.3726 0.6180 0.000 0.212 0.000 0.788
#> GSM550806 3 0.0188 0.8606 0.000 0.000 0.996 0.004
#> GSM550807 2 0.0188 0.8297 0.000 0.996 0.000 0.004
#> GSM550808 2 0.3569 0.6848 0.000 0.804 0.000 0.196
#> GSM550809 1 0.3649 0.7796 0.796 0.000 0.000 0.204
#> GSM550810 2 0.3726 0.6697 0.000 0.788 0.000 0.212
#> GSM550811 1 0.4624 0.6175 0.660 0.000 0.000 0.340
#> GSM550813 4 0.2469 0.7156 0.000 0.108 0.000 0.892
#> GSM550814 2 0.4855 0.4633 0.000 0.600 0.000 0.400
#> GSM550815 2 0.0000 0.8301 0.000 1.000 0.000 0.000
#> GSM550816 2 0.4624 0.5106 0.000 0.660 0.000 0.340
#> GSM550817 3 0.0188 0.8604 0.000 0.004 0.996 0.000
#> GSM550818 3 0.0188 0.8604 0.000 0.004 0.996 0.000
#> GSM550819 3 0.4328 0.6922 0.000 0.008 0.748 0.244
#> GSM550820 1 0.3266 0.8043 0.832 0.000 0.000 0.168
#> GSM550821 3 0.4313 0.6786 0.000 0.004 0.736 0.260
#> GSM550822 2 0.0000 0.8301 0.000 1.000 0.000 0.000
#> GSM550826 1 0.4655 0.7967 0.796 0.000 0.088 0.116
#> GSM550832 4 0.3726 0.6180 0.000 0.212 0.000 0.788
#> GSM550833 2 0.0000 0.8301 0.000 1.000 0.000 0.000
#> GSM550835 2 0.3975 0.6442 0.000 0.760 0.240 0.000
#> GSM550836 3 0.2011 0.8035 0.080 0.000 0.920 0.000
#> GSM550837 2 0.2011 0.7920 0.000 0.920 0.080 0.000
#> GSM550838 1 0.4669 0.7939 0.796 0.000 0.100 0.104
#> GSM550841 3 0.0188 0.8604 0.000 0.004 0.996 0.000
#> GSM550842 2 0.1302 0.8131 0.000 0.956 0.044 0.000
#> GSM550846 4 0.0592 0.7503 0.000 0.000 0.016 0.984
#> GSM550849 1 0.4624 0.6175 0.660 0.000 0.000 0.340
#> GSM550850 1 0.0000 0.8777 1.000 0.000 0.000 0.000
#> GSM550851 2 0.7023 0.4685 0.000 0.564 0.272 0.164
#> GSM550852 2 0.4817 0.4496 0.000 0.612 0.000 0.388
#> GSM550853 2 0.4500 0.4128 0.000 0.684 0.000 0.316
#> GSM550855 4 0.4790 0.5014 0.000 0.380 0.000 0.620
#> GSM550856 4 0.4776 0.5081 0.000 0.376 0.000 0.624
#> GSM550861 2 0.0188 0.8297 0.000 0.996 0.000 0.004
#> GSM550863 4 0.3726 0.6809 0.212 0.000 0.000 0.788
#> GSM550864 2 0.1389 0.8067 0.000 0.952 0.000 0.048
#> GSM550866 4 0.4730 0.5206 0.000 0.364 0.000 0.636
#> GSM550867 1 0.0000 0.8777 1.000 0.000 0.000 0.000
#> GSM550885 1 0.0188 0.8760 0.996 0.000 0.000 0.004
#> GSM550886 3 0.3219 0.7338 0.000 0.000 0.836 0.164
#> GSM550887 2 0.0000 0.8301 0.000 1.000 0.000 0.000
#> GSM550889 4 0.5090 0.5947 0.324 0.016 0.000 0.660
#> GSM550894 4 0.3942 0.6435 0.000 0.236 0.000 0.764
#> GSM550897 1 0.0000 0.8777 1.000 0.000 0.000 0.000
#> GSM550903 2 0.2216 0.7904 0.000 0.908 0.000 0.092
#> GSM550905 2 0.6650 0.5842 0.000 0.624 0.176 0.200
#> GSM550906 2 0.0188 0.8297 0.000 0.996 0.000 0.004
#> GSM550907 3 0.0188 0.8604 0.000 0.004 0.996 0.000
#> GSM550909 3 0.6547 0.4792 0.000 0.092 0.568 0.340
#> GSM550911 3 0.0188 0.8604 0.000 0.004 0.996 0.000
#> GSM550913 2 0.0188 0.8297 0.000 0.996 0.000 0.004
#> GSM550915 4 0.0000 0.7510 0.000 0.000 0.000 1.000
#> GSM550917 4 0.3726 0.6180 0.000 0.212 0.000 0.788
#> GSM550919 4 0.1302 0.7469 0.044 0.000 0.000 0.956
#> GSM550921 3 0.0000 0.8603 0.000 0.000 1.000 0.000
#> GSM550924 4 0.1256 0.7479 0.008 0.000 0.028 0.964
#> GSM550926 4 0.4193 0.6210 0.000 0.268 0.000 0.732
#> GSM550927 2 0.0188 0.8297 0.000 0.996 0.000 0.004
#> GSM550787 1 0.4072 0.7364 0.748 0.000 0.000 0.252
#> GSM550793 1 0.3649 0.7796 0.796 0.000 0.000 0.204
#> GSM550794 4 0.1297 0.7493 0.020 0.000 0.016 0.964
#> GSM550795 1 0.1302 0.8556 0.956 0.000 0.000 0.044
#> GSM550798 1 0.0000 0.8777 1.000 0.000 0.000 0.000
#> GSM550803 1 0.0000 0.8777 1.000 0.000 0.000 0.000
#> GSM550805 1 0.3649 0.7796 0.796 0.000 0.000 0.204
#> GSM550823 4 0.2011 0.7411 0.080 0.000 0.000 0.920
#> GSM550824 1 0.0000 0.8777 1.000 0.000 0.000 0.000
#> GSM550825 1 0.3649 0.7579 0.796 0.000 0.204 0.000
#> GSM550827 4 0.0000 0.7510 0.000 0.000 0.000 1.000
#> GSM550828 1 0.0000 0.8777 1.000 0.000 0.000 0.000
#> GSM550829 1 0.2805 0.8327 0.888 0.000 0.100 0.012
#> GSM550830 4 0.7315 0.4625 0.308 0.180 0.000 0.512
#> GSM550834 1 0.0469 0.8748 0.988 0.000 0.000 0.012
#> GSM550839 3 0.3123 0.7908 0.000 0.000 0.844 0.156
#> GSM550840 1 0.0000 0.8777 1.000 0.000 0.000 0.000
#> GSM550843 3 0.0188 0.8606 0.000 0.000 0.996 0.004
#> GSM550844 1 0.0000 0.8777 1.000 0.000 0.000 0.000
#> GSM550845 4 0.0000 0.7510 0.000 0.000 0.000 1.000
#> GSM550848 4 0.1118 0.7457 0.000 0.036 0.000 0.964
#> GSM550854 1 0.0000 0.8777 1.000 0.000 0.000 0.000
#> GSM550857 1 0.3688 0.7556 0.792 0.000 0.208 0.000
#> GSM550858 1 0.0000 0.8777 1.000 0.000 0.000 0.000
#> GSM550859 1 0.0000 0.8777 1.000 0.000 0.000 0.000
#> GSM550862 1 0.0000 0.8777 1.000 0.000 0.000 0.000
#> GSM550865 4 0.3649 0.6833 0.204 0.000 0.000 0.796
#> GSM550868 4 0.4454 0.6196 0.308 0.000 0.000 0.692
#> GSM550869 4 0.3311 0.6855 0.172 0.000 0.000 0.828
#> GSM550870 2 0.4804 0.4445 0.000 0.616 0.000 0.384
#> GSM550871 3 0.3123 0.7908 0.000 0.000 0.844 0.156
#> GSM550872 4 0.4564 0.5931 0.328 0.000 0.000 0.672
#> GSM550873 4 0.1356 0.7464 0.000 0.008 0.032 0.960
#> GSM550874 4 0.4776 0.5081 0.000 0.376 0.000 0.624
#> GSM550876 3 0.4998 -0.0419 0.000 0.000 0.512 0.488
#> GSM550877 4 0.4776 0.5081 0.000 0.376 0.000 0.624
#> GSM550878 3 0.0188 0.8606 0.000 0.000 0.996 0.004
#> GSM550879 1 0.0000 0.8777 1.000 0.000 0.000 0.000
#> GSM550882 3 0.0188 0.8598 0.004 0.000 0.996 0.000
#> GSM550888 3 0.0188 0.8592 0.004 0.000 0.996 0.000
#> GSM550890 4 0.0188 0.7521 0.004 0.000 0.000 0.996
#> GSM550891 3 0.0000 0.8603 0.000 0.000 1.000 0.000
#> GSM550892 1 0.1118 0.8585 0.964 0.000 0.000 0.036
#> GSM550893 4 0.4713 0.5242 0.000 0.360 0.000 0.640
#> GSM550895 4 0.4624 0.5404 0.000 0.340 0.000 0.660
#> GSM550896 4 0.4624 0.5404 0.000 0.340 0.000 0.660
#> GSM550898 1 0.0000 0.8777 1.000 0.000 0.000 0.000
#> GSM550899 2 0.2589 0.7661 0.000 0.884 0.000 0.116
#> GSM550900 4 0.4356 0.6366 0.292 0.000 0.000 0.708
#> GSM550901 1 0.3649 0.7796 0.796 0.000 0.000 0.204
#> GSM550902 1 0.3649 0.7796 0.796 0.000 0.000 0.204
#> GSM550904 1 0.3649 0.7796 0.796 0.000 0.000 0.204
#> GSM550908 3 0.0000 0.8603 0.000 0.000 1.000 0.000
#> GSM550912 4 0.1118 0.7447 0.000 0.036 0.000 0.964
#> GSM550914 4 0.1716 0.7492 0.064 0.000 0.000 0.936
#> GSM550918 4 0.3400 0.6445 0.000 0.180 0.000 0.820
#> GSM550922 3 0.0469 0.8572 0.000 0.012 0.988 0.000
#> GSM550923 1 0.0000 0.8777 1.000 0.000 0.000 0.000
#> GSM550925 1 0.3873 0.5955 0.772 0.000 0.000 0.228
#> GSM550802 4 0.3074 0.6621 0.000 0.152 0.000 0.848
#> GSM550812 3 0.4830 0.5121 0.000 0.000 0.608 0.392
#> GSM550831 1 0.0592 0.8703 0.984 0.000 0.000 0.016
#> GSM550847 1 0.0000 0.8777 1.000 0.000 0.000 0.000
#> GSM550860 3 0.6147 0.1299 0.048 0.000 0.488 0.464
#> GSM550875 1 0.3649 0.7796 0.796 0.000 0.000 0.204
#> GSM550880 4 0.3726 0.6807 0.212 0.000 0.000 0.788
#> GSM550881 1 0.4830 0.4591 0.608 0.000 0.392 0.000
#> GSM550883 1 0.3649 0.7579 0.796 0.000 0.204 0.000
#> GSM550884 4 0.0592 0.7506 0.000 0.000 0.016 0.984
#> GSM550910 3 0.3257 0.7920 0.000 0.004 0.844 0.152
#> GSM550916 1 0.0000 0.8777 1.000 0.000 0.000 0.000
#> GSM550920 3 0.0188 0.8606 0.000 0.000 0.996 0.004
cbind(get_classes(res, k = 5), get_membership(res, k = 5))
#> class entropy silhouette p1 p2 p3 p4 p5
#> GSM550785 1 0.0000 0.85332 1.000 0.000 0.000 0.000 0.000
#> GSM550786 5 0.2068 0.81401 0.004 0.092 0.000 0.000 0.904
#> GSM550788 3 0.6574 0.58615 0.000 0.288 0.468 0.244 0.000
#> GSM550789 3 0.6315 0.66304 0.000 0.372 0.468 0.160 0.000
#> GSM550790 1 0.0000 0.85332 1.000 0.000 0.000 0.000 0.000
#> GSM550791 1 0.4287 0.37132 0.540 0.460 0.000 0.000 0.000
#> GSM550792 2 0.4402 0.39665 0.008 0.688 0.000 0.292 0.012
#> GSM550796 3 0.6315 0.66304 0.000 0.372 0.468 0.160 0.000
#> GSM550797 3 0.6315 0.66304 0.000 0.372 0.468 0.160 0.000
#> GSM550799 5 0.0162 0.85888 0.000 0.000 0.004 0.000 0.996
#> GSM550800 3 0.6506 0.62445 0.000 0.324 0.468 0.208 0.000
#> GSM550801 2 0.6330 -0.60599 0.000 0.456 0.384 0.160 0.000
#> GSM550804 2 0.3636 0.41822 0.000 0.728 0.000 0.272 0.000
#> GSM550806 5 0.0162 0.85911 0.000 0.000 0.000 0.004 0.996
#> GSM550807 3 0.6315 0.66304 0.000 0.372 0.468 0.160 0.000
#> GSM550808 2 0.4390 -0.33379 0.000 0.568 0.428 0.004 0.000
#> GSM550809 1 0.3074 0.76422 0.804 0.196 0.000 0.000 0.000
#> GSM550810 2 0.4219 -0.30169 0.000 0.584 0.416 0.000 0.000
#> GSM550811 1 0.4307 0.28831 0.504 0.496 0.000 0.000 0.000
#> GSM550813 2 0.5762 0.30653 0.000 0.548 0.100 0.352 0.000
#> GSM550814 2 0.5459 0.00621 0.000 0.600 0.316 0.084 0.000
#> GSM550815 3 0.6315 0.66304 0.000 0.372 0.468 0.160 0.000
#> GSM550816 2 0.0609 0.39769 0.000 0.980 0.020 0.000 0.000
#> GSM550817 5 0.0162 0.85888 0.000 0.000 0.004 0.000 0.996
#> GSM550818 5 0.0162 0.86035 0.000 0.004 0.000 0.000 0.996
#> GSM550819 5 0.5510 0.57856 0.000 0.184 0.000 0.164 0.652
#> GSM550820 1 0.2848 0.79246 0.840 0.156 0.000 0.004 0.000
#> GSM550821 5 0.3932 0.48993 0.000 0.328 0.000 0.000 0.672
#> GSM550822 3 0.6315 0.66304 0.000 0.372 0.468 0.160 0.000
#> GSM550826 1 0.3795 0.77801 0.808 0.044 0.000 0.004 0.144
#> GSM550832 2 0.3636 0.41822 0.000 0.728 0.000 0.272 0.000
#> GSM550833 3 0.6315 0.66304 0.000 0.372 0.468 0.160 0.000
#> GSM550835 3 0.7518 0.51897 0.000 0.288 0.464 0.072 0.176
#> GSM550836 3 0.4949 -0.45160 0.020 0.000 0.532 0.004 0.444
#> GSM550837 3 0.6725 0.65430 0.000 0.356 0.468 0.160 0.016
#> GSM550838 1 0.3461 0.76523 0.812 0.016 0.000 0.004 0.168
#> GSM550841 5 0.0162 0.86035 0.000 0.004 0.000 0.000 0.996
#> GSM550842 3 0.6315 0.66304 0.000 0.372 0.468 0.160 0.000
#> GSM550846 2 0.5043 0.34688 0.000 0.600 0.000 0.356 0.044
#> GSM550849 1 0.4307 0.28831 0.504 0.496 0.000 0.000 0.000
#> GSM550850 1 0.0000 0.85332 1.000 0.000 0.000 0.000 0.000
#> GSM550851 2 0.6647 -0.24704 0.000 0.444 0.304 0.000 0.252
#> GSM550852 2 0.0898 0.40026 0.000 0.972 0.020 0.008 0.000
#> GSM550853 3 0.6426 0.41960 0.000 0.184 0.468 0.348 0.000
#> GSM550855 4 0.4824 0.02647 0.000 0.020 0.468 0.512 0.000
#> GSM550856 4 0.4740 0.04001 0.000 0.016 0.468 0.516 0.000
#> GSM550861 3 0.6315 0.66304 0.000 0.372 0.468 0.160 0.000
#> GSM550863 4 0.3010 0.56630 0.172 0.004 0.000 0.824 0.000
#> GSM550864 3 0.6517 0.60290 0.000 0.392 0.416 0.192 0.000
#> GSM550866 4 0.4264 0.25392 0.000 0.004 0.376 0.620 0.000
#> GSM550867 1 0.0404 0.85104 0.988 0.000 0.000 0.012 0.000
#> GSM550885 1 0.0880 0.84514 0.968 0.000 0.000 0.032 0.000
#> GSM550886 5 0.2843 0.73989 0.000 0.008 0.000 0.144 0.848
#> GSM550887 3 0.6315 0.66304 0.000 0.372 0.468 0.160 0.000
#> GSM550889 4 0.2813 0.56677 0.168 0.000 0.000 0.832 0.000
#> GSM550894 3 0.6820 -0.34280 0.000 0.332 0.352 0.316 0.000
#> GSM550897 1 0.0609 0.85071 0.980 0.000 0.000 0.020 0.000
#> GSM550903 2 0.5932 -0.44014 0.000 0.560 0.308 0.132 0.000
#> GSM550905 2 0.5725 -0.29576 0.000 0.488 0.428 0.000 0.084
#> GSM550906 3 0.6315 0.66304 0.000 0.372 0.468 0.160 0.000
#> GSM550907 5 0.0162 0.86035 0.000 0.004 0.000 0.000 0.996
#> GSM550909 2 0.4060 0.20015 0.000 0.640 0.000 0.000 0.360
#> GSM550911 5 0.0162 0.85888 0.000 0.000 0.004 0.000 0.996
#> GSM550913 3 0.6349 0.63022 0.000 0.412 0.428 0.160 0.000
#> GSM550915 2 0.4114 0.34676 0.000 0.624 0.000 0.376 0.000
#> GSM550917 2 0.3636 0.41822 0.000 0.728 0.000 0.272 0.000
#> GSM550919 2 0.4613 0.34951 0.020 0.620 0.000 0.360 0.000
#> GSM550921 3 0.4437 -0.46605 0.000 0.000 0.532 0.004 0.464
#> GSM550924 2 0.4511 0.36091 0.000 0.628 0.000 0.356 0.016
#> GSM550926 4 0.5141 0.27017 0.000 0.236 0.092 0.672 0.000
#> GSM550927 3 0.6315 0.66304 0.000 0.372 0.468 0.160 0.000
#> GSM550787 1 0.4619 0.69489 0.720 0.216 0.000 0.064 0.000
#> GSM550793 1 0.3606 0.78052 0.808 0.164 0.024 0.004 0.000
#> GSM550794 2 0.4734 0.34388 0.000 0.604 0.000 0.372 0.024
#> GSM550795 1 0.4147 0.52993 0.676 0.008 0.000 0.316 0.000
#> GSM550798 1 0.1571 0.83987 0.936 0.000 0.060 0.004 0.000
#> GSM550803 1 0.0000 0.85332 1.000 0.000 0.000 0.000 0.000
#> GSM550805 1 0.3343 0.77667 0.812 0.172 0.000 0.016 0.000
#> GSM550823 4 0.3081 0.44689 0.012 0.156 0.000 0.832 0.000
#> GSM550824 1 0.0000 0.85332 1.000 0.000 0.000 0.000 0.000
#> GSM550825 1 0.3845 0.78031 0.812 0.000 0.060 0.004 0.124
#> GSM550827 4 0.4304 -0.13983 0.000 0.484 0.000 0.516 0.000
#> GSM550828 1 0.0000 0.85332 1.000 0.000 0.000 0.000 0.000
#> GSM550829 1 0.3715 0.78840 0.824 0.000 0.064 0.004 0.108
#> GSM550830 4 0.2439 0.51359 0.120 0.000 0.004 0.876 0.000
#> GSM550834 1 0.1205 0.84200 0.956 0.004 0.000 0.040 0.000
#> GSM550839 5 0.2376 0.82983 0.000 0.044 0.000 0.052 0.904
#> GSM550840 1 0.0404 0.85159 0.988 0.000 0.000 0.012 0.000
#> GSM550843 5 0.0162 0.86035 0.000 0.004 0.000 0.000 0.996
#> GSM550844 1 0.0162 0.85298 0.996 0.000 0.000 0.004 0.000
#> GSM550845 2 0.4192 0.31252 0.000 0.596 0.000 0.404 0.000
#> GSM550848 2 0.4088 0.35527 0.000 0.632 0.000 0.368 0.000
#> GSM550854 1 0.0000 0.85332 1.000 0.000 0.000 0.000 0.000
#> GSM550857 3 0.5390 -0.37971 0.420 0.000 0.532 0.008 0.040
#> GSM550858 1 0.0000 0.85332 1.000 0.000 0.000 0.000 0.000
#> GSM550859 1 0.0404 0.85104 0.988 0.000 0.000 0.012 0.000
#> GSM550862 1 0.0510 0.84994 0.984 0.000 0.000 0.016 0.000
#> GSM550865 4 0.3010 0.56630 0.172 0.004 0.000 0.824 0.000
#> GSM550868 4 0.2891 0.56577 0.176 0.000 0.000 0.824 0.000
#> GSM550869 4 0.5578 0.32235 0.180 0.176 0.000 0.644 0.000
#> GSM550870 2 0.0609 0.40468 0.000 0.980 0.000 0.020 0.000
#> GSM550871 5 0.3565 0.76468 0.000 0.040 0.000 0.144 0.816
#> GSM550872 4 0.2891 0.56577 0.176 0.000 0.000 0.824 0.000
#> GSM550873 2 0.4497 0.36559 0.000 0.632 0.000 0.352 0.016
#> GSM550874 4 0.4740 0.04001 0.000 0.016 0.468 0.516 0.000
#> GSM550876 5 0.4302 0.16931 0.000 0.000 0.000 0.480 0.520
#> GSM550877 4 0.4511 0.25938 0.000 0.016 0.356 0.628 0.000
#> GSM550878 5 0.0162 0.86035 0.000 0.004 0.000 0.000 0.996
#> GSM550879 1 0.0955 0.84742 0.968 0.004 0.000 0.028 0.000
#> GSM550882 5 0.0992 0.85080 0.000 0.000 0.024 0.008 0.968
#> GSM550888 3 0.4580 -0.46303 0.004 0.000 0.532 0.004 0.460
#> GSM550890 4 0.4118 0.22161 0.004 0.336 0.000 0.660 0.000
#> GSM550891 5 0.4450 0.46554 0.000 0.000 0.488 0.004 0.508
#> GSM550892 1 0.3876 0.53276 0.684 0.000 0.000 0.316 0.000
#> GSM550893 4 0.3656 0.42501 0.000 0.020 0.196 0.784 0.000
#> GSM550895 4 0.0290 0.53454 0.000 0.000 0.008 0.992 0.000
#> GSM550896 4 0.0510 0.53278 0.000 0.000 0.016 0.984 0.000
#> GSM550898 1 0.0000 0.85332 1.000 0.000 0.000 0.000 0.000
#> GSM550899 2 0.4535 -0.02874 0.000 0.748 0.092 0.160 0.000
#> GSM550900 4 0.2813 0.56677 0.168 0.000 0.000 0.832 0.000
#> GSM550901 1 0.3003 0.76976 0.812 0.188 0.000 0.000 0.000
#> GSM550902 1 0.3243 0.77407 0.812 0.180 0.004 0.004 0.000
#> GSM550904 1 0.3123 0.77191 0.812 0.184 0.000 0.004 0.000
#> GSM550908 3 0.4437 -0.46605 0.000 0.000 0.532 0.004 0.464
#> GSM550912 2 0.4045 0.36542 0.000 0.644 0.000 0.356 0.000
#> GSM550914 4 0.4967 0.32756 0.060 0.280 0.000 0.660 0.000
#> GSM550918 2 0.3707 0.41341 0.000 0.716 0.000 0.284 0.000
#> GSM550922 5 0.0510 0.85375 0.000 0.000 0.016 0.000 0.984
#> GSM550923 1 0.0162 0.85320 0.996 0.000 0.000 0.004 0.000
#> GSM550925 1 0.2813 0.70411 0.832 0.000 0.000 0.168 0.000
#> GSM550802 2 0.5375 0.30276 0.000 0.604 0.076 0.320 0.000
#> GSM550812 2 0.6202 0.12753 0.000 0.496 0.000 0.148 0.356
#> GSM550831 1 0.1341 0.82921 0.944 0.000 0.000 0.056 0.000
#> GSM550847 1 0.0000 0.85332 1.000 0.000 0.000 0.000 0.000
#> GSM550860 5 0.5199 0.33080 0.036 0.004 0.000 0.412 0.548
#> GSM550875 1 0.3343 0.77667 0.812 0.172 0.000 0.016 0.000
#> GSM550880 4 0.3171 0.56379 0.176 0.008 0.000 0.816 0.000
#> GSM550881 1 0.4800 0.45861 0.604 0.000 0.028 0.000 0.368
#> GSM550883 1 0.3895 0.77726 0.796 0.000 0.164 0.008 0.032
#> GSM550884 4 0.4306 -0.18774 0.000 0.492 0.000 0.508 0.000
#> GSM550910 5 0.1908 0.81534 0.000 0.092 0.000 0.000 0.908
#> GSM550916 1 0.0000 0.85332 1.000 0.000 0.000 0.000 0.000
#> GSM550920 5 0.0162 0.86035 0.000 0.004 0.000 0.000 0.996
cbind(get_classes(res, k = 6), get_membership(res, k = 6))
#> class entropy silhouette p1 p2 p3 p4 p5 p6
#> GSM550785 1 0.1088 0.8430 0.960 0.000 0.024 0.016 0.000 0.000
#> GSM550786 5 0.0937 0.8608 0.000 0.000 0.000 0.000 0.960 0.040
#> GSM550788 2 0.0865 0.8397 0.000 0.964 0.000 0.000 0.000 0.036
#> GSM550789 2 0.0000 0.8494 0.000 1.000 0.000 0.000 0.000 0.000
#> GSM550790 1 0.2573 0.8222 0.864 0.000 0.024 0.112 0.000 0.000
#> GSM550791 6 0.3986 0.0924 0.464 0.000 0.000 0.004 0.000 0.532
#> GSM550792 6 0.2457 0.7445 0.000 0.036 0.000 0.084 0.000 0.880
#> GSM550796 2 0.0000 0.8494 0.000 1.000 0.000 0.000 0.000 0.000
#> GSM550797 2 0.0363 0.8465 0.000 0.988 0.000 0.012 0.000 0.000
#> GSM550799 5 0.0000 0.8820 0.000 0.000 0.000 0.000 1.000 0.000
#> GSM550800 2 0.0713 0.8428 0.000 0.972 0.000 0.000 0.000 0.028
#> GSM550801 2 0.3078 0.7328 0.000 0.796 0.000 0.012 0.000 0.192
#> GSM550804 6 0.1225 0.7652 0.000 0.036 0.000 0.012 0.000 0.952
#> GSM550806 5 0.0000 0.8820 0.000 0.000 0.000 0.000 1.000 0.000
#> GSM550807 2 0.0000 0.8494 0.000 1.000 0.000 0.000 0.000 0.000
#> GSM550808 2 0.2762 0.7003 0.000 0.804 0.000 0.000 0.000 0.196
#> GSM550809 1 0.3163 0.7865 0.820 0.000 0.000 0.040 0.000 0.140
#> GSM550810 2 0.2883 0.6802 0.000 0.788 0.000 0.000 0.000 0.212
#> GSM550811 6 0.3899 0.3923 0.364 0.000 0.000 0.008 0.000 0.628
#> GSM550813 6 0.2340 0.6841 0.000 0.148 0.000 0.000 0.000 0.852
#> GSM550814 2 0.3838 0.2049 0.000 0.552 0.000 0.000 0.000 0.448
#> GSM550815 2 0.0000 0.8494 0.000 1.000 0.000 0.000 0.000 0.000
#> GSM550816 6 0.3141 0.6931 0.000 0.200 0.000 0.012 0.000 0.788
#> GSM550817 5 0.0000 0.8820 0.000 0.000 0.000 0.000 1.000 0.000
#> GSM550818 5 0.0000 0.8820 0.000 0.000 0.000 0.000 1.000 0.000
#> GSM550819 5 0.4791 0.6014 0.000 0.000 0.000 0.244 0.652 0.104
#> GSM550820 1 0.3194 0.8069 0.840 0.000 0.012 0.044 0.000 0.104
#> GSM550821 5 0.3446 0.5221 0.000 0.000 0.000 0.000 0.692 0.308
#> GSM550822 2 0.0000 0.8494 0.000 1.000 0.000 0.000 0.000 0.000
#> GSM550826 1 0.3783 0.7967 0.812 0.000 0.008 0.032 0.116 0.032
#> GSM550832 6 0.0865 0.7659 0.000 0.036 0.000 0.000 0.000 0.964
#> GSM550833 2 0.0000 0.8494 0.000 1.000 0.000 0.000 0.000 0.000
#> GSM550835 2 0.2219 0.7660 0.000 0.864 0.000 0.000 0.136 0.000
#> GSM550836 3 0.0865 0.9807 0.000 0.000 0.964 0.000 0.036 0.000
#> GSM550837 2 0.0146 0.8482 0.000 0.996 0.000 0.000 0.004 0.000
#> GSM550838 1 0.3336 0.7926 0.824 0.000 0.008 0.032 0.132 0.004
#> GSM550841 5 0.0000 0.8820 0.000 0.000 0.000 0.000 1.000 0.000
#> GSM550842 2 0.0000 0.8494 0.000 1.000 0.000 0.000 0.000 0.000
#> GSM550846 6 0.2218 0.7251 0.000 0.000 0.000 0.012 0.104 0.884
#> GSM550849 6 0.3647 0.4101 0.360 0.000 0.000 0.000 0.000 0.640
#> GSM550850 1 0.0508 0.8439 0.984 0.000 0.012 0.004 0.000 0.000
#> GSM550851 2 0.5186 0.5285 0.000 0.616 0.000 0.000 0.216 0.168
#> GSM550852 6 0.2730 0.6989 0.000 0.192 0.000 0.000 0.000 0.808
#> GSM550853 2 0.1444 0.8266 0.000 0.928 0.000 0.000 0.000 0.072
#> GSM550855 2 0.1910 0.8014 0.000 0.892 0.000 0.000 0.000 0.108
#> GSM550856 2 0.1910 0.8014 0.000 0.892 0.000 0.000 0.000 0.108
#> GSM550861 2 0.0000 0.8494 0.000 1.000 0.000 0.000 0.000 0.000
#> GSM550863 4 0.4148 0.7539 0.148 0.000 0.000 0.744 0.000 0.108
#> GSM550864 2 0.2805 0.7779 0.000 0.828 0.000 0.012 0.000 0.160
#> GSM550866 2 0.4953 0.3964 0.000 0.624 0.000 0.268 0.000 0.108
#> GSM550867 1 0.2706 0.8185 0.852 0.000 0.024 0.124 0.000 0.000
#> GSM550885 1 0.3098 0.8072 0.812 0.000 0.024 0.164 0.000 0.000
#> GSM550886 5 0.1714 0.8083 0.000 0.000 0.000 0.000 0.908 0.092
#> GSM550887 2 0.0000 0.8494 0.000 1.000 0.000 0.000 0.000 0.000
#> GSM550889 4 0.3078 0.7561 0.056 0.000 0.000 0.836 0.000 0.108
#> GSM550894 2 0.3843 0.3613 0.000 0.548 0.000 0.000 0.000 0.452
#> GSM550897 1 0.1863 0.8236 0.896 0.000 0.000 0.104 0.000 0.000
#> GSM550903 2 0.3690 0.6117 0.000 0.700 0.000 0.012 0.000 0.288
#> GSM550905 2 0.3612 0.6848 0.000 0.764 0.000 0.000 0.036 0.200
#> GSM550906 2 0.0000 0.8494 0.000 1.000 0.000 0.000 0.000 0.000
#> GSM550907 5 0.0000 0.8820 0.000 0.000 0.000 0.000 1.000 0.000
#> GSM550909 6 0.3794 0.6020 0.000 0.028 0.000 0.000 0.248 0.724
#> GSM550911 5 0.0000 0.8820 0.000 0.000 0.000 0.000 1.000 0.000
#> GSM550913 2 0.2003 0.7973 0.000 0.884 0.000 0.000 0.000 0.116
#> GSM550915 6 0.1584 0.7499 0.008 0.000 0.000 0.064 0.000 0.928
#> GSM550917 6 0.1225 0.7652 0.000 0.036 0.000 0.012 0.000 0.952
#> GSM550919 6 0.1176 0.7597 0.020 0.000 0.000 0.024 0.000 0.956
#> GSM550921 3 0.0865 0.9807 0.000 0.000 0.964 0.000 0.036 0.000
#> GSM550924 6 0.0000 0.7643 0.000 0.000 0.000 0.000 0.000 1.000
#> GSM550926 6 0.5520 0.2480 0.000 0.240 0.000 0.200 0.000 0.560
#> GSM550927 2 0.0000 0.8494 0.000 1.000 0.000 0.000 0.000 0.000
#> GSM550787 1 0.4418 0.6709 0.704 0.000 0.008 0.060 0.000 0.228
#> GSM550793 1 0.3139 0.7753 0.812 0.000 0.028 0.000 0.000 0.160
#> GSM550794 6 0.1829 0.7420 0.000 0.000 0.000 0.056 0.024 0.920
#> GSM550795 4 0.3789 0.4284 0.416 0.000 0.000 0.584 0.000 0.000
#> GSM550798 1 0.3845 0.8090 0.772 0.000 0.088 0.140 0.000 0.000
#> GSM550803 1 0.2651 0.8225 0.860 0.000 0.028 0.112 0.000 0.000
#> GSM550805 1 0.3372 0.7898 0.816 0.000 0.000 0.084 0.000 0.100
#> GSM550823 4 0.2597 0.7210 0.000 0.000 0.000 0.824 0.000 0.176
#> GSM550824 1 0.2988 0.8225 0.828 0.000 0.028 0.144 0.000 0.000
#> GSM550825 1 0.3341 0.7905 0.816 0.000 0.068 0.000 0.116 0.000
#> GSM550827 6 0.3244 0.5109 0.000 0.000 0.000 0.268 0.000 0.732
#> GSM550828 1 0.0260 0.8433 0.992 0.000 0.000 0.008 0.000 0.000
#> GSM550829 1 0.3671 0.8005 0.820 0.000 0.068 0.032 0.080 0.000
#> GSM550830 4 0.3557 0.7299 0.032 0.060 0.000 0.828 0.000 0.080
#> GSM550834 1 0.1444 0.8288 0.928 0.000 0.000 0.072 0.000 0.000
#> GSM550839 5 0.1074 0.8681 0.000 0.000 0.000 0.028 0.960 0.012
#> GSM550840 1 0.0458 0.8421 0.984 0.000 0.000 0.016 0.000 0.000
#> GSM550843 5 0.0000 0.8820 0.000 0.000 0.000 0.000 1.000 0.000
#> GSM550844 1 0.0260 0.8425 0.992 0.000 0.000 0.008 0.000 0.000
#> GSM550845 6 0.2178 0.7021 0.000 0.000 0.000 0.132 0.000 0.868
#> GSM550848 6 0.0777 0.7608 0.004 0.000 0.000 0.024 0.000 0.972
#> GSM550854 1 0.2662 0.8197 0.856 0.000 0.024 0.120 0.000 0.000
#> GSM550857 3 0.0692 0.9488 0.020 0.000 0.976 0.000 0.004 0.000
#> GSM550858 1 0.0363 0.8424 0.988 0.000 0.000 0.012 0.000 0.000
#> GSM550859 1 0.2706 0.8185 0.852 0.000 0.024 0.124 0.000 0.000
#> GSM550862 1 0.0632 0.8415 0.976 0.000 0.000 0.024 0.000 0.000
#> GSM550865 4 0.4148 0.7539 0.148 0.000 0.000 0.744 0.000 0.108
#> GSM550868 4 0.4036 0.7583 0.136 0.000 0.000 0.756 0.000 0.108
#> GSM550869 4 0.5546 0.5371 0.228 0.000 0.000 0.576 0.004 0.192
#> GSM550870 6 0.2170 0.7335 0.000 0.100 0.000 0.012 0.000 0.888
#> GSM550871 5 0.3314 0.7140 0.000 0.000 0.000 0.224 0.764 0.012
#> GSM550872 4 0.3792 0.7622 0.112 0.000 0.000 0.780 0.000 0.108
#> GSM550873 6 0.0000 0.7643 0.000 0.000 0.000 0.000 0.000 1.000
#> GSM550874 2 0.1910 0.8014 0.000 0.892 0.000 0.000 0.000 0.108
#> GSM550876 5 0.4875 0.5245 0.000 0.000 0.000 0.260 0.636 0.104
#> GSM550877 2 0.3876 0.6805 0.000 0.772 0.000 0.120 0.000 0.108
#> GSM550878 5 0.0000 0.8820 0.000 0.000 0.000 0.000 1.000 0.000
#> GSM550879 1 0.1700 0.8395 0.916 0.000 0.000 0.080 0.000 0.004
#> GSM550882 5 0.0692 0.8703 0.000 0.000 0.020 0.004 0.976 0.000
#> GSM550888 3 0.0865 0.9807 0.000 0.000 0.964 0.000 0.036 0.000
#> GSM550890 4 0.3955 0.4305 0.008 0.000 0.000 0.608 0.000 0.384
#> GSM550891 3 0.1556 0.9401 0.000 0.000 0.920 0.000 0.080 0.000
#> GSM550892 4 0.3789 0.4311 0.416 0.000 0.000 0.584 0.000 0.000
#> GSM550893 4 0.5768 0.3147 0.000 0.316 0.000 0.488 0.000 0.196
#> GSM550895 4 0.3252 0.7262 0.000 0.068 0.000 0.824 0.000 0.108
#> GSM550896 4 0.3501 0.7202 0.000 0.080 0.000 0.804 0.000 0.116
#> GSM550898 1 0.2662 0.8197 0.856 0.000 0.024 0.120 0.000 0.000
#> GSM550899 6 0.3954 0.3989 0.000 0.352 0.000 0.012 0.000 0.636
#> GSM550900 4 0.3078 0.7561 0.056 0.000 0.000 0.836 0.000 0.108
#> GSM550901 1 0.3025 0.7724 0.820 0.000 0.000 0.024 0.000 0.156
#> GSM550902 1 0.3275 0.7878 0.820 0.000 0.008 0.032 0.000 0.140
#> GSM550904 1 0.3164 0.7885 0.824 0.000 0.004 0.032 0.000 0.140
#> GSM550908 3 0.0865 0.9807 0.000 0.000 0.964 0.000 0.036 0.000
#> GSM550912 6 0.0000 0.7643 0.000 0.000 0.000 0.000 0.000 1.000
#> GSM550914 4 0.4445 0.4382 0.032 0.000 0.000 0.572 0.000 0.396
#> GSM550918 6 0.1341 0.7650 0.000 0.028 0.000 0.024 0.000 0.948
#> GSM550922 5 0.0146 0.8800 0.000 0.004 0.000 0.000 0.996 0.000
#> GSM550923 1 0.3094 0.8238 0.824 0.000 0.036 0.140 0.000 0.000
#> GSM550925 1 0.3159 0.7828 0.832 0.000 0.000 0.100 0.000 0.068
#> GSM550802 6 0.4801 0.5625 0.000 0.196 0.000 0.136 0.000 0.668
#> GSM550812 6 0.4934 0.5395 0.000 0.000 0.000 0.264 0.108 0.628
#> GSM550831 1 0.2402 0.8105 0.868 0.000 0.012 0.120 0.000 0.000
#> GSM550847 1 0.2662 0.8197 0.856 0.000 0.024 0.120 0.000 0.000
#> GSM550860 5 0.5421 0.4043 0.012 0.000 0.000 0.312 0.572 0.104
#> GSM550875 1 0.3372 0.7900 0.816 0.000 0.000 0.100 0.000 0.084
#> GSM550880 4 0.4308 0.7496 0.152 0.000 0.000 0.728 0.000 0.120
#> GSM550881 1 0.4230 0.4971 0.612 0.000 0.024 0.000 0.364 0.000
#> GSM550883 1 0.3955 0.4786 0.608 0.000 0.384 0.000 0.008 0.000
#> GSM550884 6 0.3534 0.5140 0.000 0.000 0.000 0.276 0.008 0.716
#> GSM550910 5 0.0937 0.8608 0.000 0.000 0.000 0.000 0.960 0.040
#> GSM550916 1 0.2311 0.8286 0.880 0.000 0.016 0.104 0.000 0.000
#> GSM550920 5 0.0000 0.8820 0.000 0.000 0.000 0.000 1.000 0.000
Heatmaps for the consensus matrix. It visualizes the probability of two samples to be in a same group.
consensus_heatmap(res, k = 2)
consensus_heatmap(res, k = 3)
consensus_heatmap(res, k = 4)
consensus_heatmap(res, k = 5)
consensus_heatmap(res, k = 6)
Heatmaps for the membership of samples in all partitions to see how consistent they are:
membership_heatmap(res, k = 2)
membership_heatmap(res, k = 3)
membership_heatmap(res, k = 4)
membership_heatmap(res, k = 5)
membership_heatmap(res, k = 6)
As soon as we have had the classes for columns, we can look for signatures which are significantly different between classes which can be candidate marks for certain classes. Following are the heatmaps for signatures.
Signature heatmaps where rows are scaled:
get_signatures(res, k = 2)
get_signatures(res, k = 3)
get_signatures(res, k = 4)
get_signatures(res, k = 5)
get_signatures(res, k = 6)
Signature heatmaps where rows are not scaled:
get_signatures(res, k = 2, scale_rows = FALSE)
get_signatures(res, k = 3, scale_rows = FALSE)
get_signatures(res, k = 4, scale_rows = FALSE)
get_signatures(res, k = 5, scale_rows = FALSE)
get_signatures(res, k = 6, scale_rows = FALSE)
Compare the overlap of signatures from different k:
compare_signatures(res)
get_signature() returns a data frame invisibly. TO get the list of signatures, the function
call should be assigned to a variable explicitly. In following code, if plot argument is set
to FALSE, no heatmap is plotted while only the differential analysis is performed.
# code only for demonstration
tb = get_signature(res, k = ..., plot = FALSE)
An example of the output of tb is:
#> which_row fdr mean_1 mean_2 scaled_mean_1 scaled_mean_2 km
#> 1 38 0.042760348 8.373488 9.131774 -0.5533452 0.5164555 1
#> 2 40 0.018707592 7.106213 8.469186 -0.6173731 0.5762149 1
#> 3 55 0.019134737 10.221463 11.207825 -0.6159697 0.5749050 1
#> 4 59 0.006059896 5.921854 7.869574 -0.6899429 0.6439467 1
#> 5 60 0.018055526 8.928898 10.211722 -0.6204761 0.5791110 1
#> 6 98 0.009384629 15.714769 14.887706 0.6635654 -0.6193277 2
...
The columns in tb are:
which_row: row indices corresponding to the input matrix.fdr: FDR for the differential test. mean_x: The mean value in group x.scaled_mean_x: The mean value in group x after rows are scaled.km: Row groups if k-means clustering is applied to rows.UMAP plot which shows how samples are separated.
dimension_reduction(res, k = 2, method = "UMAP")
dimension_reduction(res, k = 3, method = "UMAP")
dimension_reduction(res, k = 4, method = "UMAP")
dimension_reduction(res, k = 5, method = "UMAP")
dimension_reduction(res, k = 6, method = "UMAP")
Following heatmap shows how subgroups are split when increasing k:
collect_classes(res)
Test correlation between subgroups and known annotations. If the known annotation is numeric, one-way ANOVA test is applied, and if the known annotation is discrete, chi-squared contingency table test is applied.
test_to_known_factors(res)
#> n disease.state(p) k
#> MAD:pam 134 9.38e-05 2
#> MAD:pam 128 2.76e-04 3
#> MAD:pam 133 2.93e-05 4
#> MAD:pam 86 1.60e-05 5
#> MAD:pam 127 3.22e-05 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 51776 rows and 143 columns.
#> Top rows (1000, 2000, 3000, 4000, 5000) are extracted by 'MAD' method.
#> Subgroups are detected by 'mclust' method.
#> Performed in total 1250 partitions by row resampling.
#> Best k for subgroups seems to be 4.
#>
#> Following methods can be applied to this 'ConsensusPartition' object:
#> [1] "cola_report" "collect_classes" "collect_plots"
#> [4] "collect_stats" "colnames" "compare_signatures"
#> [7] "consensus_heatmap" "dimension_reduction" "functional_enrichment"
#> [10] "get_anno_col" "get_anno" "get_classes"
#> [13] "get_consensus" "get_matrix" "get_membership"
#> [16] "get_param" "get_signatures" "get_stats"
#> [19] "is_best_k" "is_stable_k" "membership_heatmap"
#> [22] "ncol" "nrow" "plot_ecdf"
#> [25] "rownames" "select_partition_number" "show"
#> [28] "suggest_best_k" "test_to_known_factors"
collect_plots() function collects all the plots made from res for all k (number of partitions)
into one single page to provide an easy and fast comparison between different k.
collect_plots(res)
The plots are:
k and the heatmap of
predicted classes for each k.k.k.k.All the plots in panels can be made by individual functions and they are plotted later in this section.
select_partition_number() produces several plots showing different
statistics for choosing “optimized” k. There are following statistics:
k;k, the area increased is defined as \(A_k - A_{k-1}\).The detailed explanations of these statistics can be found in the cola vignette.
Generally speaking, lower PAC score, higher mean silhouette score or higher
concordance corresponds to better partition. Rand index and Jaccard index
measure how similar the current partition is compared to partition with k-1.
If they are too similar, we won't accept k is better than k-1.
select_partition_number(res)
The numeric values for all these statistics can be obtained by get_stats().
get_stats(res)
#> k 1-PAC mean_silhouette concordance area_increased Rand Jaccard
#> 2 2 0.558 0.724 0.881 0.4295 0.571 0.571
#> 3 3 0.292 0.365 0.649 0.2568 0.654 0.465
#> 4 4 0.848 0.851 0.921 0.3044 0.727 0.423
#> 5 5 0.659 0.720 0.842 0.0694 0.918 0.738
#> 6 6 0.765 0.756 0.883 0.0602 0.904 0.643
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
#> GSM550785 2 0.2043 0.86136 0.032 0.968
#> GSM550786 1 0.3584 0.82353 0.932 0.068
#> GSM550788 2 0.0376 0.86410 0.004 0.996
#> GSM550789 2 0.3114 0.85592 0.056 0.944
#> GSM550790 2 0.2043 0.86136 0.032 0.968
#> GSM550791 2 0.4690 0.83178 0.100 0.900
#> GSM550792 2 0.8016 0.68191 0.244 0.756
#> GSM550796 2 0.6148 0.79103 0.152 0.848
#> GSM550797 2 0.2423 0.85892 0.040 0.960
#> GSM550799 1 0.1633 0.84911 0.976 0.024
#> GSM550800 2 0.0000 0.86289 0.000 1.000
#> GSM550801 2 0.2236 0.85883 0.036 0.964
#> GSM550804 2 0.2043 0.85819 0.032 0.968
#> GSM550806 1 0.2043 0.84957 0.968 0.032
#> GSM550807 2 0.1843 0.85982 0.028 0.972
#> GSM550808 1 0.6247 0.74560 0.844 0.156
#> GSM550809 2 1.0000 0.08831 0.496 0.504
#> GSM550810 1 0.9944 0.08336 0.544 0.456
#> GSM550811 2 0.9996 0.12153 0.488 0.512
#> GSM550813 2 0.1843 0.85982 0.028 0.972
#> GSM550814 2 0.9522 0.44655 0.372 0.628
#> GSM550815 2 0.5408 0.81760 0.124 0.876
#> GSM550816 2 0.2603 0.86077 0.044 0.956
#> GSM550817 1 0.0376 0.84296 0.996 0.004
#> GSM550818 1 0.0376 0.84296 0.996 0.004
#> GSM550819 2 0.9710 0.32877 0.400 0.600
#> GSM550820 2 0.9732 0.38229 0.404 0.596
#> GSM550821 1 0.9686 0.28297 0.604 0.396
#> GSM550822 2 0.7745 0.70531 0.228 0.772
#> GSM550826 1 0.9993 -0.04394 0.516 0.484
#> GSM550832 2 0.7453 0.73210 0.212 0.788
#> GSM550833 2 0.2043 0.86064 0.032 0.968
#> GSM550835 1 0.2236 0.83941 0.964 0.036
#> GSM550836 1 0.2043 0.84957 0.968 0.032
#> GSM550837 1 0.5178 0.78710 0.884 0.116
#> GSM550838 1 1.0000 -0.08818 0.504 0.496
#> GSM550841 1 0.0376 0.84296 0.996 0.004
#> GSM550842 1 0.2603 0.83540 0.956 0.044
#> GSM550846 2 0.9815 0.33602 0.420 0.580
#> GSM550849 2 0.9954 0.22294 0.460 0.540
#> GSM550850 2 0.1843 0.86231 0.028 0.972
#> GSM550851 1 0.5294 0.78350 0.880 0.120
#> GSM550852 2 0.7745 0.70587 0.228 0.772
#> GSM550853 2 0.0000 0.86289 0.000 1.000
#> GSM550855 2 0.0000 0.86289 0.000 1.000
#> GSM550856 2 0.0000 0.86289 0.000 1.000
#> GSM550861 2 0.2603 0.85866 0.044 0.956
#> GSM550863 2 0.0376 0.86374 0.004 0.996
#> GSM550864 2 0.2043 0.85819 0.032 0.968
#> GSM550866 2 0.0000 0.86289 0.000 1.000
#> GSM550867 2 0.2043 0.86136 0.032 0.968
#> GSM550885 2 0.2043 0.86136 0.032 0.968
#> GSM550886 1 0.1184 0.84454 0.984 0.016
#> GSM550887 2 0.5946 0.79862 0.144 0.856
#> GSM550889 2 0.0376 0.86374 0.004 0.996
#> GSM550894 2 0.9393 0.49832 0.356 0.644
#> GSM550897 2 0.0376 0.86374 0.004 0.996
#> GSM550903 2 0.2948 0.85714 0.052 0.948
#> GSM550905 1 0.6148 0.75027 0.848 0.152
#> GSM550906 2 0.2948 0.85914 0.052 0.948
#> GSM550907 1 0.0938 0.84614 0.988 0.012
#> GSM550909 1 0.9427 0.38261 0.640 0.360
#> GSM550911 1 0.2043 0.84957 0.968 0.032
#> GSM550913 2 0.3114 0.85592 0.056 0.944
#> GSM550915 2 0.2043 0.86116 0.032 0.968
#> GSM550917 2 0.2043 0.85819 0.032 0.968
#> GSM550919 2 0.2043 0.86116 0.032 0.968
#> GSM550921 1 0.2043 0.84957 0.968 0.032
#> GSM550924 1 1.0000 -0.10285 0.500 0.500
#> GSM550926 2 0.0000 0.86289 0.000 1.000
#> GSM550927 2 0.1843 0.85982 0.028 0.972
#> GSM550787 2 0.9922 0.17593 0.448 0.552
#> GSM550793 1 0.2423 0.84936 0.960 0.040
#> GSM550794 2 0.6148 0.76061 0.152 0.848
#> GSM550795 2 0.1633 0.86312 0.024 0.976
#> GSM550798 1 0.9996 0.03289 0.512 0.488
#> GSM550803 2 0.8499 0.58869 0.276 0.724
#> GSM550805 2 0.9850 0.24313 0.428 0.572
#> GSM550823 2 0.4022 0.82604 0.080 0.920
#> GSM550824 2 0.2043 0.86136 0.032 0.968
#> GSM550825 1 0.2043 0.84957 0.968 0.032
#> GSM550827 2 0.2043 0.86116 0.032 0.968
#> GSM550828 2 0.2043 0.86136 0.032 0.968
#> GSM550829 1 0.9993 0.04836 0.516 0.484
#> GSM550830 2 0.0376 0.86374 0.004 0.996
#> GSM550834 2 0.0376 0.86374 0.004 0.996
#> GSM550839 1 0.2778 0.84797 0.952 0.048
#> GSM550840 2 0.0376 0.86374 0.004 0.996
#> GSM550843 1 0.1633 0.84912 0.976 0.024
#> GSM550844 2 0.8327 0.61673 0.264 0.736
#> GSM550845 2 0.0000 0.86289 0.000 1.000
#> GSM550848 2 0.2043 0.86116 0.032 0.968
#> GSM550854 2 0.2043 0.86136 0.032 0.968
#> GSM550857 1 0.2043 0.84957 0.968 0.032
#> GSM550858 2 0.2043 0.86136 0.032 0.968
#> GSM550859 2 0.2043 0.86136 0.032 0.968
#> GSM550862 2 0.1843 0.86231 0.028 0.972
#> GSM550865 2 0.0376 0.86374 0.004 0.996
#> GSM550868 2 0.0672 0.86403 0.008 0.992
#> GSM550869 1 0.9522 0.41883 0.628 0.372
#> GSM550870 2 0.1843 0.85982 0.028 0.972
#> GSM550871 1 0.5408 0.80416 0.876 0.124
#> GSM550872 2 0.0376 0.86374 0.004 0.996
#> GSM550873 2 0.9850 0.32236 0.428 0.572
#> GSM550874 2 0.0000 0.86289 0.000 1.000
#> GSM550876 1 0.2423 0.84942 0.960 0.040
#> GSM550877 2 0.0000 0.86289 0.000 1.000
#> GSM550878 1 0.2043 0.84957 0.968 0.032
#> GSM550879 2 0.2778 0.86232 0.048 0.952
#> GSM550882 1 0.2043 0.84957 0.968 0.032
#> GSM550888 1 0.2043 0.84957 0.968 0.032
#> GSM550890 2 0.2043 0.86116 0.032 0.968
#> GSM550891 1 0.2043 0.84957 0.968 0.032
#> GSM550892 2 0.1843 0.86231 0.028 0.972
#> GSM550893 2 0.0000 0.86289 0.000 1.000
#> GSM550895 2 0.0376 0.86374 0.004 0.996
#> GSM550896 2 0.0000 0.86289 0.000 1.000
#> GSM550898 2 0.2043 0.86136 0.032 0.968
#> GSM550899 2 0.2043 0.85819 0.032 0.968
#> GSM550900 2 0.0376 0.86374 0.004 0.996
#> GSM550901 2 0.2043 0.86116 0.032 0.968
#> GSM550902 2 1.0000 -0.00812 0.496 0.504
#> GSM550904 2 0.9988 0.15210 0.480 0.520
#> GSM550908 1 0.2043 0.84957 0.968 0.032
#> GSM550912 2 0.2948 0.85909 0.052 0.948
#> GSM550914 2 0.2043 0.86116 0.032 0.968
#> GSM550918 2 0.2043 0.85819 0.032 0.968
#> GSM550922 1 0.0938 0.84449 0.988 0.012
#> GSM550923 2 0.9983 0.08725 0.476 0.524
#> GSM550925 2 0.0376 0.86374 0.004 0.996
#> GSM550802 2 0.6247 0.75332 0.156 0.844
#> GSM550812 2 0.9580 0.39007 0.380 0.620
#> GSM550831 2 0.1843 0.86231 0.028 0.972
#> GSM550847 2 0.2043 0.86136 0.032 0.968
#> GSM550860 1 0.4431 0.82660 0.908 0.092
#> GSM550875 2 0.9896 0.20323 0.440 0.560
#> GSM550880 2 0.0376 0.86374 0.004 0.996
#> GSM550881 1 0.2043 0.84957 0.968 0.032
#> GSM550883 1 0.2043 0.84957 0.968 0.032
#> GSM550884 2 0.9754 0.30470 0.408 0.592
#> GSM550910 1 0.0938 0.84449 0.988 0.012
#> GSM550916 2 0.1633 0.86397 0.024 0.976
#> GSM550920 1 0.0672 0.84421 0.992 0.008
cbind(get_classes(res, k = 3), get_membership(res, k = 3))
#> class entropy silhouette p1 p2 p3
#> GSM550785 1 0.4452 4.21e-01 0.808 0.192 0.000
#> GSM550786 2 0.8029 3.45e-01 0.172 0.656 0.172
#> GSM550788 1 0.6260 -3.26e-01 0.552 0.448 0.000
#> GSM550789 2 0.6291 6.20e-01 0.468 0.532 0.000
#> GSM550790 1 0.4452 4.21e-01 0.808 0.192 0.000
#> GSM550791 1 0.4235 3.54e-01 0.824 0.176 0.000
#> GSM550792 2 0.5968 6.46e-01 0.364 0.636 0.000
#> GSM550796 2 0.6192 6.47e-01 0.420 0.580 0.000
#> GSM550797 2 0.6291 6.20e-01 0.468 0.532 0.000
#> GSM550799 3 0.4796 7.91e-01 0.000 0.220 0.780
#> GSM550800 1 0.6260 -3.26e-01 0.552 0.448 0.000
#> GSM550801 2 0.6291 6.20e-01 0.468 0.532 0.000
#> GSM550804 2 0.6291 6.20e-01 0.468 0.532 0.000
#> GSM550806 3 0.0892 8.35e-01 0.000 0.020 0.980
#> GSM550807 2 0.6308 5.70e-01 0.492 0.508 0.000
#> GSM550808 2 0.4842 5.60e-01 0.224 0.776 0.000
#> GSM550809 1 0.5178 3.04e-01 0.744 0.256 0.000
#> GSM550810 2 0.5058 5.74e-01 0.244 0.756 0.000
#> GSM550811 1 0.6204 1.33e-02 0.576 0.424 0.000
#> GSM550813 2 0.6299 5.93e-01 0.476 0.524 0.000
#> GSM550814 2 0.6140 6.49e-01 0.404 0.596 0.000
#> GSM550815 2 0.6295 6.17e-01 0.472 0.528 0.000
#> GSM550816 2 0.6295 6.16e-01 0.472 0.528 0.000
#> GSM550817 3 0.6192 6.91e-01 0.000 0.420 0.580
#> GSM550818 3 0.6045 7.20e-01 0.000 0.380 0.620
#> GSM550819 2 0.7571 5.26e-01 0.452 0.508 0.040
#> GSM550820 1 0.5016 3.15e-01 0.760 0.240 0.000
#> GSM550821 2 0.4842 5.60e-01 0.224 0.776 0.000
#> GSM550822 2 0.5810 6.37e-01 0.336 0.664 0.000
#> GSM550826 1 0.5327 2.93e-01 0.728 0.272 0.000
#> GSM550832 2 0.6026 6.50e-01 0.376 0.624 0.000
#> GSM550833 2 0.6299 5.96e-01 0.476 0.524 0.000
#> GSM550835 2 0.7016 3.81e-01 0.116 0.728 0.156
#> GSM550836 3 0.0424 8.36e-01 0.000 0.008 0.992
#> GSM550837 2 0.5247 5.61e-01 0.224 0.768 0.008
#> GSM550838 1 0.5254 2.99e-01 0.736 0.264 0.000
#> GSM550841 3 0.6215 6.83e-01 0.000 0.428 0.572
#> GSM550842 2 0.5951 3.09e-01 0.040 0.764 0.196
#> GSM550846 1 0.6225 -5.31e-05 0.568 0.432 0.000
#> GSM550849 2 0.5905 5.81e-01 0.352 0.648 0.000
#> GSM550850 1 0.0747 4.37e-01 0.984 0.016 0.000
#> GSM550851 2 0.4842 5.60e-01 0.224 0.776 0.000
#> GSM550852 2 0.6026 6.50e-01 0.376 0.624 0.000
#> GSM550853 1 0.6252 -3.32e-01 0.556 0.444 0.000
#> GSM550855 1 0.6260 -3.26e-01 0.552 0.448 0.000
#> GSM550856 1 0.6252 -3.32e-01 0.556 0.444 0.000
#> GSM550861 2 0.6291 6.20e-01 0.468 0.532 0.000
#> GSM550863 1 0.5678 -3.34e-02 0.684 0.316 0.000
#> GSM550864 2 0.6299 6.05e-01 0.476 0.524 0.000
#> GSM550866 1 0.6260 -3.26e-01 0.552 0.448 0.000
#> GSM550867 1 0.4452 4.21e-01 0.808 0.192 0.000
#> GSM550885 1 0.4452 4.21e-01 0.808 0.192 0.000
#> GSM550886 2 0.8196 2.68e-01 0.124 0.624 0.252
#> GSM550887 2 0.6274 6.27e-01 0.456 0.544 0.000
#> GSM550889 1 0.6295 -3.42e-01 0.528 0.472 0.000
#> GSM550894 2 0.5926 6.52e-01 0.356 0.644 0.000
#> GSM550897 1 0.5431 1.16e-01 0.716 0.284 0.000
#> GSM550903 2 0.6280 6.27e-01 0.460 0.540 0.000
#> GSM550905 2 0.4654 5.42e-01 0.208 0.792 0.000
#> GSM550906 2 0.6302 5.86e-01 0.480 0.520 0.000
#> GSM550907 3 0.4887 7.96e-01 0.000 0.228 0.772
#> GSM550909 2 0.4842 5.60e-01 0.224 0.776 0.000
#> GSM550911 3 0.3267 8.24e-01 0.000 0.116 0.884
#> GSM550913 2 0.6291 6.20e-01 0.468 0.532 0.000
#> GSM550915 1 0.4235 3.18e-01 0.824 0.176 0.000
#> GSM550917 2 0.6291 6.20e-01 0.468 0.532 0.000
#> GSM550919 1 0.5363 1.18e-01 0.724 0.276 0.000
#> GSM550921 3 0.0424 8.36e-01 0.000 0.008 0.992
#> GSM550924 2 0.5650 6.14e-01 0.312 0.688 0.000
#> GSM550926 1 0.6260 -3.26e-01 0.552 0.448 0.000
#> GSM550927 1 0.6291 -4.70e-01 0.532 0.468 0.000
#> GSM550787 2 0.9496 4.37e-01 0.372 0.440 0.188
#> GSM550793 3 0.5578 5.99e-01 0.240 0.012 0.748
#> GSM550794 2 0.6521 4.97e-01 0.492 0.504 0.004
#> GSM550795 1 0.0237 4.35e-01 0.996 0.004 0.000
#> GSM550798 1 0.6693 3.39e-01 0.748 0.148 0.104
#> GSM550803 1 0.5508 4.09e-01 0.784 0.188 0.028
#> GSM550805 1 0.9172 -2.55e-01 0.488 0.356 0.156
#> GSM550823 1 0.6509 -3.48e-01 0.524 0.472 0.004
#> GSM550824 1 0.4452 4.21e-01 0.808 0.192 0.000
#> GSM550825 3 0.0000 8.36e-01 0.000 0.000 1.000
#> GSM550827 1 0.5058 1.74e-01 0.756 0.244 0.000
#> GSM550828 1 0.4452 4.21e-01 0.808 0.192 0.000
#> GSM550829 1 0.8052 2.72e-01 0.652 0.152 0.196
#> GSM550830 1 0.6260 -3.26e-01 0.552 0.448 0.000
#> GSM550834 1 0.0237 4.35e-01 0.996 0.004 0.000
#> GSM550839 3 0.9465 -2.42e-02 0.184 0.372 0.444
#> GSM550840 1 0.5363 1.29e-01 0.724 0.276 0.000
#> GSM550843 3 0.5988 7.29e-01 0.000 0.368 0.632
#> GSM550844 1 0.3692 4.15e-01 0.896 0.048 0.056
#> GSM550845 1 0.6260 -3.64e-01 0.552 0.448 0.000
#> GSM550848 1 0.4504 2.94e-01 0.804 0.196 0.000
#> GSM550854 1 0.4399 4.20e-01 0.812 0.188 0.000
#> GSM550857 3 0.0424 8.36e-01 0.000 0.008 0.992
#> GSM550858 1 0.4399 4.20e-01 0.812 0.188 0.000
#> GSM550859 1 0.4452 4.21e-01 0.808 0.192 0.000
#> GSM550862 1 0.1753 4.40e-01 0.952 0.048 0.000
#> GSM550865 1 0.5926 -9.37e-02 0.644 0.356 0.000
#> GSM550868 1 0.5678 2.84e-02 0.684 0.316 0.000
#> GSM550869 2 0.9544 3.98e-01 0.328 0.464 0.208
#> GSM550870 2 0.6299 6.00e-01 0.476 0.524 0.000
#> GSM550871 2 0.9982 2.46e-01 0.308 0.360 0.332
#> GSM550872 1 0.5621 5.38e-02 0.692 0.308 0.000
#> GSM550873 2 0.5835 6.41e-01 0.340 0.660 0.000
#> GSM550874 1 0.6260 -3.26e-01 0.552 0.448 0.000
#> GSM550876 3 0.3752 8.09e-01 0.020 0.096 0.884
#> GSM550877 1 0.6260 -3.26e-01 0.552 0.448 0.000
#> GSM550878 3 0.1031 8.35e-01 0.000 0.024 0.976
#> GSM550879 1 0.1289 4.29e-01 0.968 0.032 0.000
#> GSM550882 3 0.0892 8.35e-01 0.000 0.020 0.980
#> GSM550888 3 0.0000 8.36e-01 0.000 0.000 1.000
#> GSM550890 1 0.3941 3.42e-01 0.844 0.156 0.000
#> GSM550891 3 0.0000 8.36e-01 0.000 0.000 1.000
#> GSM550892 1 0.5254 1.89e-01 0.736 0.264 0.000
#> GSM550893 1 0.6267 -3.29e-01 0.548 0.452 0.000
#> GSM550895 1 0.6267 -3.29e-01 0.548 0.452 0.000
#> GSM550896 1 0.6260 -3.26e-01 0.552 0.448 0.000
#> GSM550898 1 0.4399 4.20e-01 0.812 0.188 0.000
#> GSM550899 2 0.6299 6.11e-01 0.476 0.524 0.000
#> GSM550900 1 0.5948 -1.06e-01 0.640 0.360 0.000
#> GSM550901 1 0.2796 3.97e-01 0.908 0.092 0.000
#> GSM550902 1 0.8264 -1.58e-01 0.488 0.436 0.076
#> GSM550904 1 0.5138 3.07e-01 0.748 0.252 0.000
#> GSM550908 3 0.0424 8.36e-01 0.000 0.008 0.992
#> GSM550912 2 0.6168 6.49e-01 0.412 0.588 0.000
#> GSM550914 1 0.5926 -1.72e-01 0.644 0.356 0.000
#> GSM550918 2 0.6291 6.20e-01 0.468 0.532 0.000
#> GSM550922 3 0.6225 6.79e-01 0.000 0.432 0.568
#> GSM550923 1 0.6363 3.51e-01 0.768 0.136 0.096
#> GSM550925 1 0.5760 -5.47e-03 0.672 0.328 0.000
#> GSM550802 1 0.6476 -3.79e-01 0.548 0.448 0.004
#> GSM550812 2 0.7050 6.34e-01 0.372 0.600 0.028
#> GSM550831 1 0.1031 4.37e-01 0.976 0.024 0.000
#> GSM550847 1 0.4399 4.20e-01 0.812 0.188 0.000
#> GSM550860 3 0.7909 4.35e-01 0.240 0.112 0.648
#> GSM550875 1 0.9112 -2.34e-02 0.540 0.272 0.188
#> GSM550880 1 0.1411 4.22e-01 0.964 0.036 0.000
#> GSM550881 3 0.0000 8.36e-01 0.000 0.000 1.000
#> GSM550883 3 0.0000 8.36e-01 0.000 0.000 1.000
#> GSM550884 2 0.7279 6.37e-01 0.376 0.588 0.036
#> GSM550910 3 0.6260 6.59e-01 0.000 0.448 0.552
#> GSM550916 1 0.5443 1.59e-01 0.736 0.260 0.004
#> GSM550920 2 0.7536 -3.49e-02 0.064 0.632 0.304
cbind(get_classes(res, k = 4), get_membership(res, k = 4))
#> class entropy silhouette p1 p2 p3 p4
#> GSM550785 1 0.0336 0.9401 0.992 0.000 0.000 0.008
#> GSM550786 2 0.1721 0.9074 0.028 0.952 0.008 0.012
#> GSM550788 4 0.1510 0.9260 0.028 0.016 0.000 0.956
#> GSM550789 2 0.0000 0.9088 0.000 1.000 0.000 0.000
#> GSM550790 1 0.0592 0.9390 0.984 0.000 0.000 0.016
#> GSM550791 1 0.3123 0.8135 0.844 0.156 0.000 0.000
#> GSM550792 2 0.0921 0.9101 0.028 0.972 0.000 0.000
#> GSM550796 2 0.0336 0.9081 0.000 0.992 0.000 0.008
#> GSM550797 2 0.0000 0.9088 0.000 1.000 0.000 0.000
#> GSM550799 4 0.8008 -0.1297 0.008 0.228 0.364 0.400
#> GSM550800 4 0.1510 0.9260 0.028 0.016 0.000 0.956
#> GSM550801 2 0.0000 0.9088 0.000 1.000 0.000 0.000
#> GSM550804 2 0.0188 0.9098 0.004 0.996 0.000 0.000
#> GSM550806 3 0.4994 0.2063 0.000 0.000 0.520 0.480
#> GSM550807 2 0.1151 0.9000 0.024 0.968 0.000 0.008
#> GSM550808 2 0.1004 0.9111 0.024 0.972 0.000 0.004
#> GSM550809 1 0.1978 0.9044 0.928 0.068 0.004 0.000
#> GSM550810 2 0.0707 0.9109 0.020 0.980 0.000 0.000
#> GSM550811 2 0.5321 0.1088 0.464 0.528 0.004 0.004
#> GSM550813 2 0.3444 0.7454 0.000 0.816 0.000 0.184
#> GSM550814 4 0.5620 0.2516 0.024 0.416 0.000 0.560
#> GSM550815 2 0.0524 0.9077 0.004 0.988 0.000 0.008
#> GSM550816 2 0.0707 0.9109 0.020 0.980 0.000 0.000
#> GSM550817 2 0.4068 0.7865 0.008 0.816 0.160 0.016
#> GSM550818 2 0.3257 0.8449 0.008 0.872 0.108 0.012
#> GSM550819 2 0.5538 0.5215 0.036 0.644 0.000 0.320
#> GSM550820 1 0.1474 0.9171 0.948 0.052 0.000 0.000
#> GSM550821 2 0.1256 0.9104 0.028 0.964 0.000 0.008
#> GSM550822 2 0.0336 0.9081 0.000 0.992 0.000 0.008
#> GSM550826 1 0.3182 0.8294 0.860 0.132 0.004 0.004
#> GSM550832 2 0.0707 0.9109 0.020 0.980 0.000 0.000
#> GSM550833 2 0.1406 0.8961 0.024 0.960 0.000 0.016
#> GSM550835 2 0.2762 0.8931 0.028 0.912 0.012 0.048
#> GSM550836 3 0.0000 0.8882 0.000 0.000 1.000 0.000
#> GSM550837 2 0.1443 0.9105 0.028 0.960 0.008 0.004
#> GSM550838 1 0.1762 0.9125 0.944 0.048 0.004 0.004
#> GSM550841 2 0.2631 0.8794 0.008 0.912 0.064 0.016
#> GSM550842 2 0.1721 0.9083 0.028 0.952 0.008 0.012
#> GSM550846 2 0.0921 0.9101 0.028 0.972 0.000 0.000
#> GSM550849 2 0.1004 0.9105 0.024 0.972 0.000 0.004
#> GSM550850 1 0.0592 0.9390 0.984 0.000 0.000 0.016
#> GSM550851 2 0.1256 0.9104 0.028 0.964 0.000 0.008
#> GSM550852 2 0.0707 0.9109 0.020 0.980 0.000 0.000
#> GSM550853 4 0.1837 0.9211 0.028 0.028 0.000 0.944
#> GSM550855 4 0.1624 0.9249 0.028 0.020 0.000 0.952
#> GSM550856 4 0.1936 0.9207 0.032 0.028 0.000 0.940
#> GSM550861 2 0.0000 0.9088 0.000 1.000 0.000 0.000
#> GSM550863 4 0.3969 0.7819 0.180 0.016 0.000 0.804
#> GSM550864 2 0.0000 0.9088 0.000 1.000 0.000 0.000
#> GSM550866 4 0.1610 0.9256 0.032 0.016 0.000 0.952
#> GSM550867 1 0.0336 0.9401 0.992 0.000 0.000 0.008
#> GSM550885 1 0.0336 0.9401 0.992 0.000 0.000 0.008
#> GSM550886 2 0.3975 0.8477 0.028 0.852 0.024 0.096
#> GSM550887 2 0.0927 0.9046 0.008 0.976 0.000 0.016
#> GSM550889 4 0.1510 0.9260 0.028 0.016 0.000 0.956
#> GSM550894 2 0.1174 0.9104 0.020 0.968 0.000 0.012
#> GSM550897 4 0.1637 0.9198 0.060 0.000 0.000 0.940
#> GSM550903 2 0.0000 0.9088 0.000 1.000 0.000 0.000
#> GSM550905 2 0.1256 0.9104 0.028 0.964 0.000 0.008
#> GSM550906 2 0.5476 0.2709 0.020 0.584 0.000 0.396
#> GSM550907 3 0.1362 0.8711 0.004 0.020 0.964 0.012
#> GSM550909 2 0.1443 0.9095 0.028 0.960 0.004 0.008
#> GSM550911 3 0.0592 0.8871 0.000 0.000 0.984 0.016
#> GSM550913 2 0.0000 0.9088 0.000 1.000 0.000 0.000
#> GSM550915 1 0.3982 0.7204 0.776 0.220 0.000 0.004
#> GSM550917 2 0.0000 0.9088 0.000 1.000 0.000 0.000
#> GSM550919 2 0.2654 0.8566 0.108 0.888 0.000 0.004
#> GSM550921 3 0.0000 0.8882 0.000 0.000 1.000 0.000
#> GSM550924 2 0.1575 0.9083 0.028 0.956 0.004 0.012
#> GSM550926 4 0.1510 0.9260 0.028 0.016 0.000 0.956
#> GSM550927 2 0.1929 0.8831 0.024 0.940 0.000 0.036
#> GSM550787 4 0.1174 0.9061 0.020 0.000 0.012 0.968
#> GSM550793 3 0.4907 0.3212 0.000 0.000 0.580 0.420
#> GSM550794 2 0.2142 0.8937 0.056 0.928 0.000 0.016
#> GSM550795 1 0.0592 0.9390 0.984 0.000 0.000 0.016
#> GSM550798 1 0.1978 0.8988 0.928 0.000 0.068 0.004
#> GSM550803 1 0.0592 0.9390 0.984 0.000 0.000 0.016
#> GSM550805 4 0.1388 0.9088 0.028 0.000 0.012 0.960
#> GSM550823 4 0.1388 0.9185 0.028 0.012 0.000 0.960
#> GSM550824 1 0.0336 0.9401 0.992 0.000 0.000 0.008
#> GSM550825 3 0.0817 0.8833 0.000 0.000 0.976 0.024
#> GSM550827 2 0.4837 0.5076 0.348 0.648 0.000 0.004
#> GSM550828 1 0.0336 0.9401 0.992 0.000 0.000 0.008
#> GSM550829 1 0.1792 0.8966 0.932 0.000 0.068 0.000
#> GSM550830 4 0.1510 0.9260 0.028 0.016 0.000 0.956
#> GSM550834 1 0.0592 0.9390 0.984 0.000 0.000 0.016
#> GSM550839 4 0.1975 0.8803 0.016 0.000 0.048 0.936
#> GSM550840 4 0.1716 0.9189 0.064 0.000 0.000 0.936
#> GSM550843 2 0.4727 0.7413 0.008 0.772 0.192 0.028
#> GSM550844 1 0.0895 0.9375 0.976 0.000 0.004 0.020
#> GSM550845 4 0.2965 0.8797 0.036 0.072 0.000 0.892
#> GSM550848 2 0.2334 0.8743 0.088 0.908 0.000 0.004
#> GSM550854 1 0.0336 0.9401 0.992 0.000 0.000 0.008
#> GSM550857 3 0.0000 0.8882 0.000 0.000 1.000 0.000
#> GSM550858 1 0.0336 0.9401 0.992 0.000 0.000 0.008
#> GSM550859 1 0.0336 0.9401 0.992 0.000 0.000 0.008
#> GSM550862 4 0.1792 0.9184 0.068 0.000 0.000 0.932
#> GSM550865 4 0.1389 0.9221 0.048 0.000 0.000 0.952
#> GSM550868 4 0.1743 0.9237 0.056 0.004 0.000 0.940
#> GSM550869 4 0.1362 0.9083 0.020 0.004 0.012 0.964
#> GSM550870 2 0.3486 0.7390 0.000 0.812 0.000 0.188
#> GSM550871 4 0.1297 0.9035 0.020 0.000 0.016 0.964
#> GSM550872 4 0.1389 0.9221 0.048 0.000 0.000 0.952
#> GSM550873 2 0.0895 0.9110 0.020 0.976 0.000 0.004
#> GSM550874 4 0.1510 0.9260 0.028 0.016 0.000 0.956
#> GSM550876 4 0.1978 0.8633 0.004 0.000 0.068 0.928
#> GSM550877 4 0.1510 0.9260 0.028 0.016 0.000 0.956
#> GSM550878 3 0.0469 0.8871 0.000 0.000 0.988 0.012
#> GSM550879 1 0.0592 0.9367 0.984 0.016 0.000 0.000
#> GSM550882 3 0.4925 0.3474 0.000 0.000 0.572 0.428
#> GSM550888 3 0.0817 0.8833 0.000 0.000 0.976 0.024
#> GSM550890 2 0.3710 0.7671 0.192 0.804 0.000 0.004
#> GSM550891 3 0.0592 0.8875 0.000 0.000 0.984 0.016
#> GSM550892 4 0.1867 0.9174 0.072 0.000 0.000 0.928
#> GSM550893 4 0.1510 0.9260 0.028 0.016 0.000 0.956
#> GSM550895 4 0.1510 0.9260 0.028 0.016 0.000 0.956
#> GSM550896 4 0.1610 0.9256 0.032 0.016 0.000 0.952
#> GSM550898 1 0.0336 0.9401 0.992 0.000 0.000 0.008
#> GSM550899 2 0.0000 0.9088 0.000 1.000 0.000 0.000
#> GSM550900 4 0.1302 0.9226 0.044 0.000 0.000 0.956
#> GSM550901 1 0.2593 0.8706 0.892 0.104 0.000 0.004
#> GSM550902 1 0.2262 0.9135 0.932 0.012 0.040 0.016
#> GSM550904 1 0.1576 0.9165 0.948 0.048 0.004 0.000
#> GSM550908 3 0.0000 0.8882 0.000 0.000 1.000 0.000
#> GSM550912 2 0.1042 0.9110 0.020 0.972 0.000 0.008
#> GSM550914 2 0.1661 0.9044 0.052 0.944 0.000 0.004
#> GSM550918 2 0.0000 0.9088 0.000 1.000 0.000 0.000
#> GSM550922 2 0.2107 0.9021 0.020 0.940 0.024 0.016
#> GSM550923 1 0.1545 0.9222 0.952 0.000 0.040 0.008
#> GSM550925 4 0.1637 0.9210 0.060 0.000 0.000 0.940
#> GSM550802 2 0.5102 0.6750 0.048 0.732 0.000 0.220
#> GSM550812 2 0.1871 0.9084 0.024 0.948 0.016 0.012
#> GSM550831 1 0.0592 0.9390 0.984 0.000 0.000 0.016
#> GSM550847 1 0.0592 0.9379 0.984 0.000 0.000 0.016
#> GSM550860 4 0.1635 0.8852 0.008 0.000 0.044 0.948
#> GSM550875 4 0.1488 0.9097 0.032 0.000 0.012 0.956
#> GSM550880 1 0.5332 0.6638 0.736 0.184 0.000 0.080
#> GSM550881 3 0.0188 0.8881 0.000 0.000 0.996 0.004
#> GSM550883 3 0.0000 0.8882 0.000 0.000 1.000 0.000
#> GSM550884 2 0.6184 0.0638 0.028 0.496 0.012 0.464
#> GSM550910 2 0.2210 0.9023 0.028 0.936 0.020 0.016
#> GSM550916 4 0.1716 0.9189 0.064 0.000 0.000 0.936
#> GSM550920 2 0.2643 0.8870 0.016 0.916 0.052 0.016
cbind(get_classes(res, k = 5), get_membership(res, k = 5))
#> class entropy silhouette p1 p2 p3 p4 p5
#> GSM550785 1 0.0000 0.836 1.000 0.000 0.000 0.000 0.000
#> GSM550786 5 0.5367 0.230 0.004 0.452 0.008 0.028 0.508
#> GSM550788 4 0.3336 0.739 0.000 0.228 0.000 0.772 0.000
#> GSM550789 2 0.0000 0.793 0.000 1.000 0.000 0.000 0.000
#> GSM550790 1 0.0162 0.837 0.996 0.000 0.000 0.004 0.000
#> GSM550791 1 0.6126 0.727 0.644 0.040 0.000 0.196 0.120
#> GSM550792 2 0.5253 0.606 0.008 0.684 0.000 0.220 0.088
#> GSM550796 2 0.0162 0.793 0.000 0.996 0.000 0.000 0.004
#> GSM550797 2 0.0000 0.793 0.000 1.000 0.000 0.000 0.000
#> GSM550799 5 0.5698 0.582 0.000 0.084 0.068 0.144 0.704
#> GSM550800 4 0.3305 0.743 0.000 0.224 0.000 0.776 0.000
#> GSM550801 2 0.0000 0.793 0.000 1.000 0.000 0.000 0.000
#> GSM550804 2 0.1608 0.769 0.000 0.928 0.000 0.000 0.072
#> GSM550806 3 0.4933 0.657 0.000 0.000 0.704 0.096 0.200
#> GSM550807 2 0.0162 0.793 0.000 0.996 0.000 0.000 0.004
#> GSM550808 2 0.1205 0.770 0.004 0.956 0.000 0.000 0.040
#> GSM550809 1 0.4697 0.809 0.776 0.040 0.000 0.064 0.120
#> GSM550810 2 0.0162 0.793 0.004 0.996 0.000 0.000 0.000
#> GSM550811 1 0.6279 0.711 0.628 0.044 0.000 0.208 0.120
#> GSM550813 2 0.1892 0.759 0.004 0.916 0.000 0.080 0.000
#> GSM550814 2 0.4166 0.284 0.004 0.648 0.000 0.348 0.000
#> GSM550815 2 0.0162 0.793 0.000 0.996 0.000 0.000 0.004
#> GSM550816 2 0.1952 0.762 0.004 0.912 0.000 0.000 0.084
#> GSM550817 5 0.2727 0.744 0.000 0.116 0.016 0.000 0.868
#> GSM550818 5 0.2293 0.717 0.000 0.084 0.016 0.000 0.900
#> GSM550819 2 0.4300 0.372 0.000 0.524 0.000 0.476 0.000
#> GSM550820 1 0.4503 0.812 0.788 0.040 0.000 0.052 0.120
#> GSM550821 2 0.1704 0.756 0.004 0.928 0.000 0.000 0.068
#> GSM550822 2 0.0162 0.793 0.000 0.996 0.000 0.000 0.004
#> GSM550826 1 0.5937 0.747 0.668 0.040 0.000 0.172 0.120
#> GSM550832 2 0.0162 0.793 0.004 0.996 0.000 0.000 0.000
#> GSM550833 2 0.0162 0.793 0.000 0.996 0.000 0.000 0.004
#> GSM550835 2 0.4538 0.217 0.000 0.620 0.016 0.000 0.364
#> GSM550836 3 0.0000 0.861 0.000 0.000 1.000 0.000 0.000
#> GSM550837 2 0.1205 0.770 0.004 0.956 0.000 0.000 0.040
#> GSM550838 1 0.4634 0.810 0.780 0.040 0.000 0.060 0.120
#> GSM550841 5 0.2727 0.744 0.000 0.116 0.016 0.000 0.868
#> GSM550842 2 0.4333 0.246 0.004 0.640 0.004 0.000 0.352
#> GSM550846 2 0.5913 0.571 0.024 0.648 0.000 0.208 0.120
#> GSM550849 2 0.5657 0.581 0.012 0.656 0.000 0.216 0.116
#> GSM550850 1 0.0162 0.837 0.996 0.000 0.000 0.000 0.004
#> GSM550851 2 0.3086 0.637 0.004 0.816 0.000 0.000 0.180
#> GSM550852 2 0.3300 0.673 0.004 0.792 0.000 0.204 0.000
#> GSM550853 4 0.3796 0.664 0.000 0.300 0.000 0.700 0.000
#> GSM550855 4 0.3480 0.724 0.000 0.248 0.000 0.752 0.000
#> GSM550856 4 0.3210 0.756 0.000 0.212 0.000 0.788 0.000
#> GSM550861 2 0.0000 0.793 0.000 1.000 0.000 0.000 0.000
#> GSM550863 4 0.2722 0.750 0.108 0.020 0.000 0.872 0.000
#> GSM550864 2 0.1992 0.779 0.000 0.924 0.000 0.032 0.044
#> GSM550866 4 0.3074 0.764 0.000 0.196 0.000 0.804 0.000
#> GSM550867 1 0.0290 0.834 0.992 0.000 0.000 0.000 0.008
#> GSM550885 1 0.0404 0.838 0.988 0.000 0.000 0.000 0.012
#> GSM550886 2 0.5259 0.152 0.000 0.588 0.016 0.028 0.368
#> GSM550887 2 0.0162 0.793 0.000 0.996 0.000 0.000 0.004
#> GSM550889 4 0.0000 0.819 0.000 0.000 0.000 1.000 0.000
#> GSM550894 2 0.0324 0.793 0.004 0.992 0.000 0.004 0.000
#> GSM550897 4 0.0000 0.819 0.000 0.000 0.000 1.000 0.000
#> GSM550903 2 0.0000 0.793 0.000 1.000 0.000 0.000 0.000
#> GSM550905 2 0.1205 0.773 0.004 0.956 0.000 0.000 0.040
#> GSM550906 2 0.3491 0.535 0.000 0.768 0.000 0.228 0.004
#> GSM550907 5 0.2471 0.583 0.000 0.000 0.136 0.000 0.864
#> GSM550909 2 0.1830 0.775 0.004 0.932 0.000 0.052 0.012
#> GSM550911 5 0.3561 0.386 0.000 0.000 0.260 0.000 0.740
#> GSM550913 2 0.0000 0.793 0.000 1.000 0.000 0.000 0.000
#> GSM550915 1 0.6212 0.714 0.632 0.040 0.000 0.208 0.120
#> GSM550917 2 0.0000 0.793 0.000 1.000 0.000 0.000 0.000
#> GSM550919 1 0.7745 0.508 0.484 0.188 0.000 0.208 0.120
#> GSM550921 3 0.0000 0.861 0.000 0.000 1.000 0.000 0.000
#> GSM550924 2 0.4316 0.646 0.004 0.748 0.000 0.208 0.040
#> GSM550926 4 0.3074 0.765 0.000 0.196 0.000 0.804 0.000
#> GSM550927 2 0.0162 0.793 0.000 0.996 0.000 0.000 0.004
#> GSM550787 4 0.0566 0.816 0.000 0.000 0.004 0.984 0.012
#> GSM550793 3 0.5805 0.427 0.032 0.000 0.588 0.332 0.048
#> GSM550794 2 0.3949 0.607 0.004 0.696 0.000 0.300 0.000
#> GSM550795 1 0.2286 0.827 0.888 0.000 0.000 0.108 0.004
#> GSM550798 1 0.0404 0.833 0.988 0.000 0.012 0.000 0.000
#> GSM550803 1 0.0000 0.836 1.000 0.000 0.000 0.000 0.000
#> GSM550805 4 0.0162 0.818 0.004 0.000 0.000 0.996 0.000
#> GSM550823 4 0.0000 0.819 0.000 0.000 0.000 1.000 0.000
#> GSM550824 1 0.0000 0.836 1.000 0.000 0.000 0.000 0.000
#> GSM550825 3 0.0000 0.861 0.000 0.000 1.000 0.000 0.000
#> GSM550827 2 0.7149 0.459 0.124 0.560 0.000 0.208 0.108
#> GSM550828 1 0.0609 0.838 0.980 0.000 0.000 0.000 0.020
#> GSM550829 1 0.3911 0.790 0.812 0.004 0.100 0.000 0.084
#> GSM550830 4 0.0000 0.819 0.000 0.000 0.000 1.000 0.000
#> GSM550834 1 0.4087 0.762 0.756 0.000 0.000 0.208 0.036
#> GSM550839 4 0.4370 0.651 0.000 0.000 0.056 0.744 0.200
#> GSM550840 4 0.0000 0.819 0.000 0.000 0.000 1.000 0.000
#> GSM550843 5 0.4847 0.640 0.000 0.216 0.080 0.000 0.704
#> GSM550844 1 0.2690 0.810 0.844 0.000 0.000 0.156 0.000
#> GSM550845 4 0.2813 0.780 0.000 0.168 0.000 0.832 0.000
#> GSM550848 2 0.7026 0.478 0.100 0.572 0.000 0.208 0.120
#> GSM550854 1 0.0290 0.834 0.992 0.000 0.000 0.000 0.008
#> GSM550857 3 0.0000 0.861 0.000 0.000 1.000 0.000 0.000
#> GSM550858 1 0.1331 0.839 0.952 0.000 0.000 0.040 0.008
#> GSM550859 1 0.0290 0.834 0.992 0.000 0.000 0.000 0.008
#> GSM550862 4 0.4030 0.568 0.352 0.000 0.000 0.648 0.000
#> GSM550865 4 0.0000 0.819 0.000 0.000 0.000 1.000 0.000
#> GSM550868 4 0.0609 0.813 0.020 0.000 0.000 0.980 0.000
#> GSM550869 4 0.0000 0.819 0.000 0.000 0.000 1.000 0.000
#> GSM550870 2 0.1430 0.772 0.004 0.944 0.000 0.052 0.000
#> GSM550871 4 0.2708 0.774 0.000 0.000 0.044 0.884 0.072
#> GSM550872 4 0.0162 0.818 0.004 0.000 0.000 0.996 0.000
#> GSM550873 2 0.1282 0.787 0.004 0.952 0.000 0.044 0.000
#> GSM550874 4 0.3143 0.759 0.000 0.204 0.000 0.796 0.000
#> GSM550876 4 0.4433 0.647 0.000 0.000 0.060 0.740 0.200
#> GSM550877 4 0.3305 0.743 0.000 0.224 0.000 0.776 0.000
#> GSM550878 3 0.3336 0.702 0.000 0.000 0.772 0.000 0.228
#> GSM550879 1 0.4503 0.812 0.788 0.040 0.000 0.052 0.120
#> GSM550882 3 0.4555 0.691 0.000 0.000 0.732 0.068 0.200
#> GSM550888 3 0.0000 0.861 0.000 0.000 1.000 0.000 0.000
#> GSM550890 2 0.8056 0.150 0.260 0.412 0.000 0.208 0.120
#> GSM550891 3 0.2424 0.793 0.000 0.000 0.868 0.000 0.132
#> GSM550892 4 0.3895 0.606 0.320 0.000 0.000 0.680 0.000
#> GSM550893 4 0.3109 0.762 0.000 0.200 0.000 0.800 0.000
#> GSM550895 4 0.0162 0.820 0.000 0.004 0.000 0.996 0.000
#> GSM550896 4 0.3305 0.743 0.000 0.224 0.000 0.776 0.000
#> GSM550898 1 0.0290 0.834 0.992 0.000 0.000 0.000 0.008
#> GSM550899 2 0.2104 0.773 0.000 0.916 0.000 0.024 0.060
#> GSM550900 4 0.0000 0.819 0.000 0.000 0.000 1.000 0.000
#> GSM550901 1 0.6212 0.714 0.632 0.040 0.000 0.208 0.120
#> GSM550902 1 0.5934 0.748 0.680 0.040 0.008 0.184 0.088
#> GSM550904 1 0.4503 0.812 0.788 0.040 0.000 0.052 0.120
#> GSM550908 3 0.0000 0.861 0.000 0.000 1.000 0.000 0.000
#> GSM550912 2 0.2068 0.762 0.004 0.904 0.000 0.092 0.000
#> GSM550914 2 0.5457 0.595 0.012 0.672 0.000 0.220 0.096
#> GSM550918 2 0.1205 0.784 0.000 0.956 0.000 0.004 0.040
#> GSM550922 5 0.2783 0.742 0.004 0.116 0.012 0.000 0.868
#> GSM550923 1 0.0162 0.834 0.996 0.000 0.004 0.000 0.000
#> GSM550925 4 0.0000 0.819 0.000 0.000 0.000 1.000 0.000
#> GSM550802 2 0.4171 0.502 0.000 0.604 0.000 0.396 0.000
#> GSM550812 2 0.3521 0.651 0.004 0.764 0.000 0.232 0.000
#> GSM550831 1 0.1907 0.839 0.928 0.000 0.000 0.044 0.028
#> GSM550847 1 0.0451 0.832 0.988 0.000 0.000 0.004 0.008
#> GSM550860 4 0.2853 0.768 0.000 0.000 0.052 0.876 0.072
#> GSM550875 4 0.0000 0.819 0.000 0.000 0.000 1.000 0.000
#> GSM550880 1 0.5290 0.703 0.676 0.036 0.000 0.252 0.036
#> GSM550881 3 0.1341 0.839 0.000 0.000 0.944 0.000 0.056
#> GSM550883 3 0.0000 0.861 0.000 0.000 1.000 0.000 0.000
#> GSM550884 4 0.4084 0.382 0.004 0.328 0.000 0.668 0.000
#> GSM550910 5 0.2727 0.744 0.000 0.116 0.016 0.000 0.868
#> GSM550916 4 0.3534 0.668 0.256 0.000 0.000 0.744 0.000
#> GSM550920 5 0.5328 0.210 0.000 0.468 0.012 0.028 0.492
cbind(get_classes(res, k = 6), get_membership(res, k = 6))
#> class entropy silhouette p1 p2 p3 p4 p5 p6
#> GSM550785 1 0.0632 0.8649 0.976 0.000 0.000 0.000 0.000 0.024
#> GSM550786 5 0.4151 0.5555 0.000 0.044 0.000 0.000 0.692 0.264
#> GSM550788 4 0.2558 0.8225 0.000 0.156 0.004 0.840 0.000 0.000
#> GSM550789 2 0.0000 0.8646 0.000 1.000 0.000 0.000 0.000 0.000
#> GSM550790 1 0.0865 0.8618 0.964 0.000 0.000 0.000 0.000 0.036
#> GSM550791 6 0.0820 0.8773 0.012 0.016 0.000 0.000 0.000 0.972
#> GSM550792 6 0.3652 0.5250 0.000 0.324 0.000 0.004 0.000 0.672
#> GSM550796 2 0.0146 0.8646 0.000 0.996 0.000 0.000 0.004 0.000
#> GSM550797 2 0.0146 0.8647 0.000 0.996 0.000 0.000 0.000 0.004
#> GSM550799 5 0.3352 0.5593 0.000 0.008 0.008 0.208 0.776 0.000
#> GSM550800 4 0.2520 0.8250 0.000 0.152 0.004 0.844 0.000 0.000
#> GSM550801 2 0.0146 0.8647 0.000 0.996 0.000 0.000 0.000 0.004
#> GSM550804 2 0.0363 0.8630 0.000 0.988 0.000 0.000 0.000 0.012
#> GSM550806 3 0.4377 0.7139 0.008 0.000 0.736 0.100 0.156 0.000
#> GSM550807 2 0.0291 0.8645 0.000 0.992 0.000 0.004 0.004 0.000
#> GSM550808 2 0.1349 0.8336 0.000 0.940 0.000 0.000 0.056 0.004
#> GSM550809 6 0.0914 0.8768 0.016 0.016 0.000 0.000 0.000 0.968
#> GSM550810 2 0.0146 0.8645 0.000 0.996 0.000 0.000 0.000 0.004
#> GSM550811 6 0.0820 0.8773 0.012 0.016 0.000 0.000 0.000 0.972
#> GSM550813 2 0.1524 0.8207 0.000 0.932 0.000 0.060 0.000 0.008
#> GSM550814 2 0.3742 0.3417 0.000 0.648 0.000 0.348 0.000 0.004
#> GSM550815 2 0.0146 0.8646 0.000 0.996 0.000 0.000 0.004 0.000
#> GSM550816 2 0.1556 0.8227 0.000 0.920 0.000 0.000 0.000 0.080
#> GSM550817 5 0.0405 0.7555 0.000 0.008 0.004 0.000 0.988 0.000
#> GSM550818 5 0.0405 0.7555 0.000 0.008 0.004 0.000 0.988 0.000
#> GSM550819 4 0.4407 -0.1526 0.000 0.480 0.000 0.496 0.000 0.024
#> GSM550820 6 0.0820 0.8746 0.016 0.012 0.000 0.000 0.000 0.972
#> GSM550821 2 0.3405 0.5599 0.000 0.724 0.000 0.000 0.272 0.004
#> GSM550822 2 0.0146 0.8646 0.000 0.996 0.000 0.000 0.004 0.000
#> GSM550826 6 0.0914 0.8768 0.016 0.016 0.000 0.000 0.000 0.968
#> GSM550832 2 0.0146 0.8645 0.000 0.996 0.000 0.000 0.000 0.004
#> GSM550833 2 0.0146 0.8646 0.000 0.996 0.000 0.000 0.004 0.000
#> GSM550835 2 0.4279 0.1436 0.000 0.548 0.004 0.012 0.436 0.000
#> GSM550836 3 0.0291 0.8906 0.000 0.000 0.992 0.000 0.004 0.004
#> GSM550837 2 0.0603 0.8552 0.000 0.980 0.004 0.000 0.016 0.000
#> GSM550838 6 0.0820 0.8746 0.016 0.012 0.000 0.000 0.000 0.972
#> GSM550841 5 0.0405 0.7555 0.000 0.008 0.004 0.000 0.988 0.000
#> GSM550842 2 0.3890 0.2813 0.000 0.596 0.004 0.000 0.400 0.000
#> GSM550846 6 0.1082 0.8686 0.000 0.040 0.000 0.004 0.000 0.956
#> GSM550849 6 0.1082 0.8686 0.000 0.040 0.000 0.004 0.000 0.956
#> GSM550850 1 0.3765 0.3669 0.596 0.000 0.000 0.000 0.000 0.404
#> GSM550851 2 0.3807 0.3715 0.000 0.628 0.000 0.000 0.368 0.004
#> GSM550852 2 0.2146 0.7774 0.000 0.880 0.000 0.004 0.000 0.116
#> GSM550853 2 0.3923 0.1770 0.000 0.580 0.004 0.416 0.000 0.000
#> GSM550855 4 0.3426 0.6829 0.000 0.276 0.004 0.720 0.000 0.000
#> GSM550856 4 0.2668 0.8141 0.000 0.168 0.004 0.828 0.000 0.000
#> GSM550861 2 0.0000 0.8646 0.000 1.000 0.000 0.000 0.000 0.000
#> GSM550863 4 0.2026 0.8374 0.028 0.020 0.000 0.924 0.004 0.024
#> GSM550864 2 0.0508 0.8623 0.000 0.984 0.000 0.004 0.000 0.012
#> GSM550866 4 0.2482 0.8273 0.000 0.148 0.004 0.848 0.000 0.000
#> GSM550867 1 0.0458 0.8650 0.984 0.000 0.000 0.000 0.000 0.016
#> GSM550885 1 0.0632 0.8648 0.976 0.000 0.000 0.000 0.000 0.024
#> GSM550886 5 0.4779 0.0262 0.000 0.468 0.004 0.040 0.488 0.000
#> GSM550887 2 0.0146 0.8646 0.000 0.996 0.000 0.000 0.004 0.000
#> GSM550889 4 0.0520 0.8532 0.008 0.000 0.000 0.984 0.000 0.008
#> GSM550894 2 0.0146 0.8645 0.000 0.996 0.000 0.000 0.000 0.004
#> GSM550897 4 0.0405 0.8535 0.004 0.000 0.000 0.988 0.000 0.008
#> GSM550903 2 0.0146 0.8647 0.000 0.996 0.000 0.000 0.000 0.004
#> GSM550905 2 0.2994 0.6734 0.000 0.788 0.000 0.000 0.208 0.004
#> GSM550906 2 0.2964 0.6313 0.000 0.792 0.000 0.204 0.004 0.000
#> GSM550907 5 0.0458 0.7451 0.000 0.000 0.016 0.000 0.984 0.000
#> GSM550909 2 0.2778 0.7138 0.000 0.824 0.000 0.000 0.008 0.168
#> GSM550911 5 0.2996 0.4495 0.000 0.000 0.228 0.000 0.772 0.000
#> GSM550913 2 0.0000 0.8646 0.000 1.000 0.000 0.000 0.000 0.000
#> GSM550915 6 0.0806 0.8776 0.008 0.020 0.000 0.000 0.000 0.972
#> GSM550917 2 0.0146 0.8647 0.000 0.996 0.000 0.000 0.000 0.004
#> GSM550919 6 0.0858 0.8751 0.000 0.028 0.000 0.004 0.000 0.968
#> GSM550921 3 0.0291 0.8906 0.000 0.000 0.992 0.000 0.004 0.004
#> GSM550924 6 0.3665 0.5665 0.000 0.296 0.000 0.004 0.004 0.696
#> GSM550926 4 0.2482 0.8276 0.000 0.148 0.004 0.848 0.000 0.000
#> GSM550927 2 0.0291 0.8645 0.000 0.992 0.000 0.004 0.004 0.000
#> GSM550787 4 0.2373 0.8259 0.000 0.000 0.004 0.888 0.084 0.024
#> GSM550793 3 0.4893 0.6950 0.012 0.000 0.736 0.124 0.036 0.092
#> GSM550794 2 0.4173 0.5787 0.000 0.688 0.000 0.044 0.000 0.268
#> GSM550795 1 0.3717 0.4379 0.616 0.000 0.000 0.000 0.000 0.384
#> GSM550798 1 0.2011 0.8257 0.912 0.000 0.064 0.000 0.004 0.020
#> GSM550803 1 0.0363 0.8652 0.988 0.000 0.000 0.000 0.000 0.012
#> GSM550805 4 0.2504 0.7915 0.000 0.000 0.004 0.856 0.004 0.136
#> GSM550823 4 0.0291 0.8537 0.004 0.000 0.000 0.992 0.000 0.004
#> GSM550824 1 0.0632 0.8648 0.976 0.000 0.000 0.000 0.000 0.024
#> GSM550825 3 0.0405 0.8886 0.008 0.000 0.988 0.000 0.004 0.000
#> GSM550827 6 0.2994 0.6877 0.000 0.208 0.000 0.004 0.000 0.788
#> GSM550828 1 0.1610 0.8340 0.916 0.000 0.000 0.000 0.000 0.084
#> GSM550829 1 0.5871 0.1458 0.416 0.000 0.168 0.000 0.004 0.412
#> GSM550830 4 0.0146 0.8537 0.004 0.000 0.000 0.996 0.000 0.000
#> GSM550834 6 0.1007 0.8464 0.044 0.000 0.000 0.000 0.000 0.956
#> GSM550839 4 0.3277 0.7704 0.008 0.000 0.024 0.812 0.156 0.000
#> GSM550840 4 0.0862 0.8503 0.008 0.000 0.000 0.972 0.004 0.016
#> GSM550843 5 0.2902 0.6472 0.000 0.196 0.004 0.000 0.800 0.000
#> GSM550844 1 0.3221 0.7162 0.792 0.000 0.000 0.020 0.000 0.188
#> GSM550845 4 0.2562 0.8123 0.000 0.172 0.000 0.828 0.000 0.000
#> GSM550848 6 0.0935 0.8735 0.000 0.032 0.000 0.004 0.000 0.964
#> GSM550854 1 0.0363 0.8652 0.988 0.000 0.000 0.000 0.000 0.012
#> GSM550857 3 0.0291 0.8906 0.000 0.000 0.992 0.000 0.004 0.004
#> GSM550858 1 0.0622 0.8632 0.980 0.000 0.000 0.000 0.008 0.012
#> GSM550859 1 0.0363 0.8652 0.988 0.000 0.000 0.000 0.000 0.012
#> GSM550862 1 0.3955 0.3597 0.648 0.000 0.000 0.340 0.008 0.004
#> GSM550865 4 0.0291 0.8537 0.004 0.000 0.000 0.992 0.000 0.004
#> GSM550868 4 0.0717 0.8514 0.016 0.000 0.000 0.976 0.008 0.000
#> GSM550869 4 0.0146 0.8541 0.000 0.000 0.004 0.996 0.000 0.000
#> GSM550870 2 0.0972 0.8500 0.000 0.964 0.000 0.028 0.000 0.008
#> GSM550871 4 0.3073 0.7791 0.008 0.000 0.016 0.824 0.152 0.000
#> GSM550872 4 0.0767 0.8519 0.012 0.000 0.000 0.976 0.004 0.008
#> GSM550873 2 0.1152 0.8409 0.000 0.952 0.000 0.004 0.000 0.044
#> GSM550874 4 0.2482 0.8273 0.000 0.148 0.004 0.848 0.000 0.000
#> GSM550876 4 0.3239 0.7743 0.008 0.000 0.024 0.816 0.152 0.000
#> GSM550877 4 0.2558 0.8225 0.000 0.156 0.004 0.840 0.000 0.000
#> GSM550878 3 0.2597 0.7970 0.000 0.000 0.824 0.000 0.176 0.000
#> GSM550879 6 0.0909 0.8727 0.020 0.012 0.000 0.000 0.000 0.968
#> GSM550882 3 0.3196 0.8018 0.008 0.000 0.816 0.020 0.156 0.000
#> GSM550888 3 0.0291 0.8906 0.000 0.000 0.992 0.000 0.004 0.004
#> GSM550890 6 0.0935 0.8735 0.000 0.032 0.000 0.004 0.000 0.964
#> GSM550891 3 0.2595 0.8100 0.000 0.000 0.836 0.000 0.160 0.004
#> GSM550892 4 0.3323 0.7478 0.204 0.000 0.000 0.780 0.008 0.008
#> GSM550893 4 0.2442 0.8293 0.000 0.144 0.004 0.852 0.000 0.000
#> GSM550895 4 0.0405 0.8535 0.004 0.000 0.000 0.988 0.000 0.008
#> GSM550896 4 0.2100 0.8413 0.000 0.112 0.004 0.884 0.000 0.000
#> GSM550898 1 0.0363 0.8652 0.988 0.000 0.000 0.000 0.000 0.012
#> GSM550899 2 0.0508 0.8623 0.000 0.984 0.000 0.004 0.000 0.012
#> GSM550900 4 0.0520 0.8532 0.008 0.000 0.000 0.984 0.000 0.008
#> GSM550901 6 0.0806 0.8776 0.008 0.020 0.000 0.000 0.000 0.972
#> GSM550902 6 0.0964 0.8736 0.016 0.012 0.000 0.000 0.004 0.968
#> GSM550904 6 0.0914 0.8768 0.016 0.016 0.000 0.000 0.000 0.968
#> GSM550908 3 0.0291 0.8906 0.000 0.000 0.992 0.000 0.004 0.004
#> GSM550912 2 0.0508 0.8628 0.000 0.984 0.000 0.004 0.000 0.012
#> GSM550914 6 0.4072 0.1830 0.000 0.448 0.000 0.008 0.000 0.544
#> GSM550918 2 0.0260 0.8638 0.000 0.992 0.000 0.000 0.000 0.008
#> GSM550922 5 0.0405 0.7555 0.000 0.008 0.004 0.000 0.988 0.000
#> GSM550923 1 0.0692 0.8638 0.976 0.000 0.004 0.000 0.000 0.020
#> GSM550925 4 0.0146 0.8537 0.004 0.000 0.000 0.996 0.000 0.000
#> GSM550802 2 0.3774 0.4188 0.000 0.592 0.000 0.408 0.000 0.000
#> GSM550812 2 0.3351 0.7087 0.000 0.800 0.000 0.028 0.004 0.168
#> GSM550831 6 0.3050 0.5827 0.236 0.000 0.000 0.000 0.000 0.764
#> GSM550847 1 0.0622 0.8632 0.980 0.000 0.000 0.000 0.008 0.012
#> GSM550860 4 0.3073 0.7792 0.008 0.000 0.016 0.824 0.152 0.000
#> GSM550875 4 0.0748 0.8529 0.004 0.000 0.004 0.976 0.000 0.016
#> GSM550880 6 0.4259 0.6031 0.040 0.004 0.000 0.228 0.008 0.720
#> GSM550881 3 0.1387 0.8707 0.000 0.000 0.932 0.000 0.068 0.000
#> GSM550883 3 0.0146 0.8902 0.000 0.000 0.996 0.000 0.004 0.000
#> GSM550884 4 0.5173 0.5779 0.000 0.188 0.000 0.636 0.004 0.172
#> GSM550910 5 0.0405 0.7555 0.000 0.008 0.004 0.000 0.988 0.000
#> GSM550916 4 0.3418 0.7574 0.192 0.000 0.000 0.784 0.008 0.016
#> GSM550920 5 0.3805 0.4781 0.000 0.328 0.004 0.004 0.664 0.000
Heatmaps for the consensus matrix. It visualizes the probability of two samples to be in a same group.
consensus_heatmap(res, k = 2)
consensus_heatmap(res, k = 3)
consensus_heatmap(res, k = 4)
consensus_heatmap(res, k = 5)
consensus_heatmap(res, k = 6)
Heatmaps for the membership of samples in all partitions to see how consistent they are:
membership_heatmap(res, k = 2)
membership_heatmap(res, k = 3)
membership_heatmap(res, k = 4)
membership_heatmap(res, k = 5)
membership_heatmap(res, k = 6)
As soon as we have had the classes for columns, we can look for signatures which are significantly different between classes which can be candidate marks for certain classes. Following are the heatmaps for signatures.
Signature heatmaps where rows are scaled:
get_signatures(res, k = 2)
get_signatures(res, k = 3)
get_signatures(res, k = 4)
get_signatures(res, k = 5)
get_signatures(res, k = 6)
Signature heatmaps where rows are not scaled:
get_signatures(res, k = 2, scale_rows = FALSE)
get_signatures(res, k = 3, scale_rows = FALSE)
get_signatures(res, k = 4, scale_rows = FALSE)
get_signatures(res, k = 5, scale_rows = FALSE)
get_signatures(res, k = 6, scale_rows = FALSE)
Compare the overlap of signatures from different k:
compare_signatures(res)
get_signature() returns a data frame invisibly. TO get the list of signatures, the function
call should be assigned to a variable explicitly. In following code, if plot argument is set
to FALSE, no heatmap is plotted while only the differential analysis is performed.
# code only for demonstration
tb = get_signature(res, k = ..., plot = FALSE)
An example of the output of tb is:
#> which_row fdr mean_1 mean_2 scaled_mean_1 scaled_mean_2 km
#> 1 38 0.042760348 8.373488 9.131774 -0.5533452 0.5164555 1
#> 2 40 0.018707592 7.106213 8.469186 -0.6173731 0.5762149 1
#> 3 55 0.019134737 10.221463 11.207825 -0.6159697 0.5749050 1
#> 4 59 0.006059896 5.921854 7.869574 -0.6899429 0.6439467 1
#> 5 60 0.018055526 8.928898 10.211722 -0.6204761 0.5791110 1
#> 6 98 0.009384629 15.714769 14.887706 0.6635654 -0.6193277 2
...
The columns in tb are:
which_row: row indices corresponding to the input matrix.fdr: FDR for the differential test. mean_x: The mean value in group x.scaled_mean_x: The mean value in group x after rows are scaled.km: Row groups if k-means clustering is applied to rows.UMAP plot which shows how samples are separated.
dimension_reduction(res, k = 2, method = "UMAP")
dimension_reduction(res, k = 3, method = "UMAP")
dimension_reduction(res, k = 4, method = "UMAP")
dimension_reduction(res, k = 5, method = "UMAP")
dimension_reduction(res, k = 6, method = "UMAP")
Following heatmap shows how subgroups are split when increasing k:
collect_classes(res)
Test correlation between subgroups and known annotations. If the known annotation is numeric, one-way ANOVA test is applied, and if the known annotation is discrete, chi-squared contingency table test is applied.
test_to_known_factors(res)
#> n disease.state(p) k
#> MAD:mclust 117 0.318243 2
#> MAD:mclust 63 0.001944 3
#> MAD:mclust 135 0.000843 4
#> MAD:mclust 130 0.000854 5
#> MAD:mclust 128 0.001035 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 51776 rows and 143 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 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 0.553 0.822 0.912 0.4963 0.505 0.505
#> 3 3 0.825 0.877 0.948 0.2672 0.798 0.628
#> 4 4 0.777 0.819 0.915 0.1568 0.780 0.495
#> 5 5 0.659 0.609 0.815 0.0724 0.863 0.557
#> 6 6 0.722 0.646 0.813 0.0531 0.886 0.540
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
#> GSM550785 1 0.5737 0.84911 0.864 0.136
#> GSM550786 2 0.9988 0.28465 0.480 0.520
#> GSM550788 2 0.0000 0.89437 0.000 1.000
#> GSM550789 2 0.0000 0.89437 0.000 1.000
#> GSM550790 1 0.2423 0.90705 0.960 0.040
#> GSM550791 1 0.7056 0.80385 0.808 0.192
#> GSM550792 2 0.6623 0.75635 0.172 0.828
#> GSM550796 2 0.0000 0.89437 0.000 1.000
#> GSM550797 2 0.0000 0.89437 0.000 1.000
#> GSM550799 2 0.5629 0.81762 0.132 0.868
#> GSM550800 2 0.0000 0.89437 0.000 1.000
#> GSM550801 2 0.0000 0.89437 0.000 1.000
#> GSM550804 2 0.0000 0.89437 0.000 1.000
#> GSM550806 1 0.0376 0.90932 0.996 0.004
#> GSM550807 2 0.0000 0.89437 0.000 1.000
#> GSM550808 2 0.0000 0.89437 0.000 1.000
#> GSM550809 1 0.0000 0.90910 1.000 0.000
#> GSM550810 2 0.0000 0.89437 0.000 1.000
#> GSM550811 1 0.0938 0.91107 0.988 0.012
#> GSM550813 2 0.0000 0.89437 0.000 1.000
#> GSM550814 2 0.0000 0.89437 0.000 1.000
#> GSM550815 2 0.0000 0.89437 0.000 1.000
#> GSM550816 2 0.0000 0.89437 0.000 1.000
#> GSM550817 2 0.7139 0.76413 0.196 0.804
#> GSM550818 2 0.8144 0.71336 0.252 0.748
#> GSM550819 2 0.0000 0.89437 0.000 1.000
#> GSM550820 1 0.0000 0.90910 1.000 0.000
#> GSM550821 2 0.0000 0.89437 0.000 1.000
#> GSM550822 2 0.0000 0.89437 0.000 1.000
#> GSM550826 1 0.0376 0.90932 0.996 0.004
#> GSM550832 2 0.0000 0.89437 0.000 1.000
#> GSM550833 2 0.0000 0.89437 0.000 1.000
#> GSM550835 2 0.1633 0.88155 0.024 0.976
#> GSM550836 1 0.0376 0.90932 0.996 0.004
#> GSM550837 2 0.0000 0.89437 0.000 1.000
#> GSM550838 1 0.0000 0.90910 1.000 0.000
#> GSM550841 2 0.7056 0.76790 0.192 0.808
#> GSM550842 2 0.0000 0.89437 0.000 1.000
#> GSM550846 2 0.3431 0.86122 0.064 0.936
#> GSM550849 1 0.6531 0.82609 0.832 0.168
#> GSM550850 1 0.1633 0.91294 0.976 0.024
#> GSM550851 2 0.0000 0.89437 0.000 1.000
#> GSM550852 2 0.0000 0.89437 0.000 1.000
#> GSM550853 2 0.0000 0.89437 0.000 1.000
#> GSM550855 2 0.0000 0.89437 0.000 1.000
#> GSM550856 2 0.0000 0.89437 0.000 1.000
#> GSM550861 2 0.0000 0.89437 0.000 1.000
#> GSM550863 1 0.9044 0.62594 0.680 0.320
#> GSM550864 2 0.0000 0.89437 0.000 1.000
#> GSM550866 2 0.0376 0.89198 0.004 0.996
#> GSM550867 1 0.1633 0.91294 0.976 0.024
#> GSM550885 1 0.1633 0.91294 0.976 0.024
#> GSM550886 2 0.7139 0.76413 0.196 0.804
#> GSM550887 2 0.0000 0.89437 0.000 1.000
#> GSM550889 2 0.9954 -0.00922 0.460 0.540
#> GSM550894 2 0.0000 0.89437 0.000 1.000
#> GSM550897 1 0.7056 0.80385 0.808 0.192
#> GSM550903 2 0.0000 0.89437 0.000 1.000
#> GSM550905 2 0.0000 0.89437 0.000 1.000
#> GSM550906 2 0.0000 0.89437 0.000 1.000
#> GSM550907 2 0.9686 0.49076 0.396 0.604
#> GSM550909 2 0.6801 0.77873 0.180 0.820
#> GSM550911 2 0.9491 0.54606 0.368 0.632
#> GSM550913 2 0.0000 0.89437 0.000 1.000
#> GSM550915 1 0.9209 0.59365 0.664 0.336
#> GSM550917 2 0.0000 0.89437 0.000 1.000
#> GSM550919 2 0.9129 0.44907 0.328 0.672
#> GSM550921 1 0.0376 0.90932 0.996 0.004
#> GSM550924 2 1.0000 0.21705 0.496 0.504
#> GSM550926 2 0.0000 0.89437 0.000 1.000
#> GSM550927 2 0.0000 0.89437 0.000 1.000
#> GSM550787 1 0.4690 0.86905 0.900 0.100
#> GSM550793 1 0.0376 0.90932 0.996 0.004
#> GSM550794 2 0.5629 0.79642 0.132 0.868
#> GSM550795 1 0.1633 0.91294 0.976 0.024
#> GSM550798 1 0.0000 0.90910 1.000 0.000
#> GSM550803 1 0.0000 0.90910 1.000 0.000
#> GSM550805 1 0.1843 0.91227 0.972 0.028
#> GSM550823 2 0.9087 0.45559 0.324 0.676
#> GSM550824 1 0.1414 0.91270 0.980 0.020
#> GSM550825 1 0.0000 0.90910 1.000 0.000
#> GSM550827 2 0.9608 0.30791 0.384 0.616
#> GSM550828 1 0.3274 0.89733 0.940 0.060
#> GSM550829 1 0.0000 0.90910 1.000 0.000
#> GSM550830 1 0.9580 0.49849 0.620 0.380
#> GSM550834 1 0.7139 0.79987 0.804 0.196
#> GSM550839 2 0.7139 0.76413 0.196 0.804
#> GSM550840 1 0.7056 0.80385 0.808 0.192
#> GSM550843 2 0.9358 0.57495 0.352 0.648
#> GSM550844 1 0.1633 0.91294 0.976 0.024
#> GSM550845 2 0.0000 0.89437 0.000 1.000
#> GSM550848 2 0.0376 0.89198 0.004 0.996
#> GSM550854 1 0.1843 0.91183 0.972 0.028
#> GSM550857 1 0.0376 0.90932 0.996 0.004
#> GSM550858 1 0.7056 0.80385 0.808 0.192
#> GSM550859 1 0.1633 0.91294 0.976 0.024
#> GSM550862 1 0.4022 0.88610 0.920 0.080
#> GSM550865 1 0.7219 0.79605 0.800 0.200
#> GSM550868 1 0.7883 0.75302 0.764 0.236
#> GSM550869 1 0.2043 0.91151 0.968 0.032
#> GSM550870 2 0.0000 0.89437 0.000 1.000
#> GSM550871 2 0.9286 0.59146 0.344 0.656
#> GSM550872 1 0.7219 0.79605 0.800 0.200
#> GSM550873 2 0.0000 0.89437 0.000 1.000
#> GSM550874 2 0.0000 0.89437 0.000 1.000
#> GSM550876 2 0.7056 0.76790 0.192 0.808
#> GSM550877 2 0.0000 0.89437 0.000 1.000
#> GSM550878 2 0.9983 0.29583 0.476 0.524
#> GSM550879 1 0.1633 0.91294 0.976 0.024
#> GSM550882 1 0.0376 0.90932 0.996 0.004
#> GSM550888 1 0.0376 0.90932 0.996 0.004
#> GSM550890 2 0.8955 0.50432 0.312 0.688
#> GSM550891 1 0.0376 0.90932 0.996 0.004
#> GSM550892 1 0.6343 0.83082 0.840 0.160
#> GSM550893 2 0.0000 0.89437 0.000 1.000
#> GSM550895 2 0.0376 0.89198 0.004 0.996
#> GSM550896 2 0.0000 0.89437 0.000 1.000
#> GSM550898 1 0.1633 0.91294 0.976 0.024
#> GSM550899 2 0.0000 0.89437 0.000 1.000
#> GSM550900 1 0.9983 0.20597 0.524 0.476
#> GSM550901 1 0.7139 0.79987 0.804 0.196
#> GSM550902 1 0.0376 0.90932 0.996 0.004
#> GSM550904 1 0.0000 0.90910 1.000 0.000
#> GSM550908 1 0.0376 0.90932 0.996 0.004
#> GSM550912 2 0.0000 0.89437 0.000 1.000
#> GSM550914 2 0.0376 0.89198 0.004 0.996
#> GSM550918 2 0.0376 0.89198 0.004 0.996
#> GSM550922 2 0.6048 0.80534 0.148 0.852
#> GSM550923 1 0.0000 0.90910 1.000 0.000
#> GSM550925 1 0.7139 0.79987 0.804 0.196
#> GSM550802 2 0.0000 0.89437 0.000 1.000
#> GSM550812 2 0.4939 0.83051 0.108 0.892
#> GSM550831 1 0.1633 0.91294 0.976 0.024
#> GSM550847 1 0.1633 0.91294 0.976 0.024
#> GSM550860 1 0.0376 0.90932 0.996 0.004
#> GSM550875 1 0.1633 0.91294 0.976 0.024
#> GSM550880 1 0.7139 0.79987 0.804 0.196
#> GSM550881 1 0.0376 0.90932 0.996 0.004
#> GSM550883 1 0.0376 0.90932 0.996 0.004
#> GSM550884 2 0.8555 0.68081 0.280 0.720
#> GSM550910 2 0.7219 0.76143 0.200 0.800
#> GSM550916 1 0.1633 0.91294 0.976 0.024
#> GSM550920 2 0.8661 0.67209 0.288 0.712
cbind(get_classes(res, k = 3), get_membership(res, k = 3))
#> class entropy silhouette p1 p2 p3
#> GSM550785 1 0.0000 0.928 1.000 0.000 0.000
#> GSM550786 3 0.3116 0.874 0.000 0.108 0.892
#> GSM550788 2 0.0000 0.945 0.000 1.000 0.000
#> GSM550789 2 0.0000 0.945 0.000 1.000 0.000
#> GSM550790 1 0.0000 0.928 1.000 0.000 0.000
#> GSM550791 1 0.0000 0.928 1.000 0.000 0.000
#> GSM550792 2 0.2165 0.888 0.064 0.936 0.000
#> GSM550796 2 0.0000 0.945 0.000 1.000 0.000
#> GSM550797 2 0.0000 0.945 0.000 1.000 0.000
#> GSM550799 3 0.5926 0.428 0.000 0.356 0.644
#> GSM550800 2 0.0000 0.945 0.000 1.000 0.000
#> GSM550801 2 0.0000 0.945 0.000 1.000 0.000
#> GSM550804 2 0.0000 0.945 0.000 1.000 0.000
#> GSM550806 3 0.0000 0.958 0.000 0.000 1.000
#> GSM550807 2 0.0000 0.945 0.000 1.000 0.000
#> GSM550808 2 0.0000 0.945 0.000 1.000 0.000
#> GSM550809 1 0.0424 0.923 0.992 0.000 0.008
#> GSM550810 2 0.0000 0.945 0.000 1.000 0.000
#> GSM550811 1 0.5092 0.759 0.804 0.020 0.176
#> GSM550813 2 0.0000 0.945 0.000 1.000 0.000
#> GSM550814 2 0.0000 0.945 0.000 1.000 0.000
#> GSM550815 2 0.0000 0.945 0.000 1.000 0.000
#> GSM550816 2 0.0000 0.945 0.000 1.000 0.000
#> GSM550817 3 0.0000 0.958 0.000 0.000 1.000
#> GSM550818 3 0.0000 0.958 0.000 0.000 1.000
#> GSM550819 2 0.0000 0.945 0.000 1.000 0.000
#> GSM550820 1 0.0000 0.928 1.000 0.000 0.000
#> GSM550821 2 0.0000 0.945 0.000 1.000 0.000
#> GSM550822 2 0.0000 0.945 0.000 1.000 0.000
#> GSM550826 1 0.4931 0.702 0.768 0.000 0.232
#> GSM550832 2 0.0000 0.945 0.000 1.000 0.000
#> GSM550833 2 0.0000 0.945 0.000 1.000 0.000
#> GSM550835 2 0.2356 0.886 0.000 0.928 0.072
#> GSM550836 3 0.0000 0.958 0.000 0.000 1.000
#> GSM550837 2 0.0000 0.945 0.000 1.000 0.000
#> GSM550838 1 0.3340 0.834 0.880 0.000 0.120
#> GSM550841 3 0.0424 0.954 0.000 0.008 0.992
#> GSM550842 2 0.0000 0.945 0.000 1.000 0.000
#> GSM550846 2 0.2165 0.890 0.064 0.936 0.000
#> GSM550849 1 0.6192 0.318 0.580 0.420 0.000
#> GSM550850 1 0.0000 0.928 1.000 0.000 0.000
#> GSM550851 2 0.0000 0.945 0.000 1.000 0.000
#> GSM550852 2 0.0000 0.945 0.000 1.000 0.000
#> GSM550853 2 0.0000 0.945 0.000 1.000 0.000
#> GSM550855 2 0.0000 0.945 0.000 1.000 0.000
#> GSM550856 2 0.0000 0.945 0.000 1.000 0.000
#> GSM550861 2 0.0000 0.945 0.000 1.000 0.000
#> GSM550863 1 0.0000 0.928 1.000 0.000 0.000
#> GSM550864 2 0.0000 0.945 0.000 1.000 0.000
#> GSM550866 2 0.0000 0.945 0.000 1.000 0.000
#> GSM550867 1 0.0000 0.928 1.000 0.000 0.000
#> GSM550885 1 0.0000 0.928 1.000 0.000 0.000
#> GSM550886 2 0.5835 0.497 0.000 0.660 0.340
#> GSM550887 2 0.0000 0.945 0.000 1.000 0.000
#> GSM550889 1 0.5363 0.631 0.724 0.276 0.000
#> GSM550894 2 0.0000 0.945 0.000 1.000 0.000
#> GSM550897 1 0.0000 0.928 1.000 0.000 0.000
#> GSM550903 2 0.0000 0.945 0.000 1.000 0.000
#> GSM550905 2 0.0000 0.945 0.000 1.000 0.000
#> GSM550906 2 0.0000 0.945 0.000 1.000 0.000
#> GSM550907 3 0.0000 0.958 0.000 0.000 1.000
#> GSM550909 2 0.4235 0.771 0.000 0.824 0.176
#> GSM550911 3 0.0000 0.958 0.000 0.000 1.000
#> GSM550913 2 0.0000 0.945 0.000 1.000 0.000
#> GSM550915 1 0.0000 0.928 1.000 0.000 0.000
#> GSM550917 2 0.0000 0.945 0.000 1.000 0.000
#> GSM550919 1 0.1163 0.909 0.972 0.028 0.000
#> GSM550921 3 0.0000 0.958 0.000 0.000 1.000
#> GSM550924 2 0.4504 0.745 0.000 0.804 0.196
#> GSM550926 2 0.0000 0.945 0.000 1.000 0.000
#> GSM550927 2 0.0000 0.945 0.000 1.000 0.000
#> GSM550787 1 0.6701 0.296 0.576 0.412 0.012
#> GSM550793 1 0.5968 0.469 0.636 0.000 0.364
#> GSM550794 2 0.5591 0.586 0.304 0.696 0.000
#> GSM550795 1 0.0000 0.928 1.000 0.000 0.000
#> GSM550798 1 0.0000 0.928 1.000 0.000 0.000
#> GSM550803 1 0.0000 0.928 1.000 0.000 0.000
#> GSM550805 1 0.0000 0.928 1.000 0.000 0.000
#> GSM550823 2 0.6260 0.116 0.448 0.552 0.000
#> GSM550824 1 0.0000 0.928 1.000 0.000 0.000
#> GSM550825 1 0.4931 0.705 0.768 0.000 0.232
#> GSM550827 1 0.0237 0.925 0.996 0.004 0.000
#> GSM550828 1 0.0000 0.928 1.000 0.000 0.000
#> GSM550829 1 0.3412 0.830 0.876 0.000 0.124
#> GSM550830 1 0.1411 0.902 0.964 0.036 0.000
#> GSM550834 1 0.0000 0.928 1.000 0.000 0.000
#> GSM550839 2 0.5560 0.579 0.000 0.700 0.300
#> GSM550840 1 0.0000 0.928 1.000 0.000 0.000
#> GSM550843 3 0.0000 0.958 0.000 0.000 1.000
#> GSM550844 1 0.0000 0.928 1.000 0.000 0.000
#> GSM550845 2 0.0000 0.945 0.000 1.000 0.000
#> GSM550848 1 0.4555 0.709 0.800 0.200 0.000
#> GSM550854 1 0.0000 0.928 1.000 0.000 0.000
#> GSM550857 3 0.0237 0.955 0.004 0.000 0.996
#> GSM550858 1 0.0000 0.928 1.000 0.000 0.000
#> GSM550859 1 0.0000 0.928 1.000 0.000 0.000
#> GSM550862 1 0.0000 0.928 1.000 0.000 0.000
#> GSM550865 1 0.0000 0.928 1.000 0.000 0.000
#> GSM550868 1 0.0000 0.928 1.000 0.000 0.000
#> GSM550869 1 0.5851 0.751 0.792 0.140 0.068
#> GSM550870 2 0.0000 0.945 0.000 1.000 0.000
#> GSM550871 2 0.5254 0.643 0.000 0.736 0.264
#> GSM550872 1 0.0000 0.928 1.000 0.000 0.000
#> GSM550873 2 0.0000 0.945 0.000 1.000 0.000
#> GSM550874 2 0.0000 0.945 0.000 1.000 0.000
#> GSM550876 2 0.6180 0.305 0.000 0.584 0.416
#> GSM550877 2 0.0000 0.945 0.000 1.000 0.000
#> GSM550878 3 0.0000 0.958 0.000 0.000 1.000
#> GSM550879 1 0.0000 0.928 1.000 0.000 0.000
#> GSM550882 3 0.0000 0.958 0.000 0.000 1.000
#> GSM550888 3 0.0000 0.958 0.000 0.000 1.000
#> GSM550890 1 0.2066 0.876 0.940 0.060 0.000
#> GSM550891 3 0.0000 0.958 0.000 0.000 1.000
#> GSM550892 1 0.0000 0.928 1.000 0.000 0.000
#> GSM550893 2 0.0000 0.945 0.000 1.000 0.000
#> GSM550895 2 0.0000 0.945 0.000 1.000 0.000
#> GSM550896 2 0.0000 0.945 0.000 1.000 0.000
#> GSM550898 1 0.0000 0.928 1.000 0.000 0.000
#> GSM550899 2 0.0000 0.945 0.000 1.000 0.000
#> GSM550900 1 0.0424 0.922 0.992 0.008 0.000
#> GSM550901 1 0.0000 0.928 1.000 0.000 0.000
#> GSM550902 1 0.4178 0.778 0.828 0.000 0.172
#> GSM550904 1 0.0000 0.928 1.000 0.000 0.000
#> GSM550908 3 0.0000 0.958 0.000 0.000 1.000
#> GSM550912 2 0.0000 0.945 0.000 1.000 0.000
#> GSM550914 2 0.4504 0.739 0.196 0.804 0.000
#> GSM550918 2 0.0000 0.945 0.000 1.000 0.000
#> GSM550922 3 0.3038 0.879 0.000 0.104 0.896
#> GSM550923 1 0.0000 0.928 1.000 0.000 0.000
#> GSM550925 1 0.0000 0.928 1.000 0.000 0.000
#> GSM550802 2 0.0000 0.945 0.000 1.000 0.000
#> GSM550812 2 0.1411 0.918 0.000 0.964 0.036
#> GSM550831 1 0.0000 0.928 1.000 0.000 0.000
#> GSM550847 1 0.0000 0.928 1.000 0.000 0.000
#> GSM550860 1 0.6305 0.140 0.516 0.000 0.484
#> GSM550875 1 0.0000 0.928 1.000 0.000 0.000
#> GSM550880 1 0.0000 0.928 1.000 0.000 0.000
#> GSM550881 3 0.0000 0.958 0.000 0.000 1.000
#> GSM550883 3 0.1643 0.920 0.044 0.000 0.956
#> GSM550884 2 0.4235 0.771 0.000 0.824 0.176
#> GSM550910 3 0.1411 0.936 0.000 0.036 0.964
#> GSM550916 1 0.0000 0.928 1.000 0.000 0.000
#> GSM550920 3 0.3192 0.870 0.000 0.112 0.888
cbind(get_classes(res, k = 4), get_membership(res, k = 4))
#> class entropy silhouette p1 p2 p3 p4
#> GSM550785 1 0.0000 0.969 1.000 0.000 0.000 0.000
#> GSM550786 2 0.4452 0.639 0.008 0.732 0.260 0.000
#> GSM550788 4 0.2281 0.814 0.000 0.096 0.000 0.904
#> GSM550789 2 0.0000 0.882 0.000 1.000 0.000 0.000
#> GSM550790 1 0.0000 0.969 1.000 0.000 0.000 0.000
#> GSM550791 1 0.0469 0.963 0.988 0.012 0.000 0.000
#> GSM550792 2 0.4605 0.507 0.336 0.664 0.000 0.000
#> GSM550796 2 0.0336 0.883 0.000 0.992 0.000 0.008
#> GSM550797 2 0.0000 0.882 0.000 1.000 0.000 0.000
#> GSM550799 3 0.1854 0.858 0.000 0.048 0.940 0.012
#> GSM550800 4 0.2011 0.826 0.000 0.080 0.000 0.920
#> GSM550801 2 0.0188 0.883 0.000 0.996 0.000 0.004
#> GSM550804 2 0.0188 0.881 0.004 0.996 0.000 0.000
#> GSM550806 3 0.4916 0.225 0.000 0.000 0.576 0.424
#> GSM550807 2 0.0592 0.881 0.000 0.984 0.000 0.016
#> GSM550808 2 0.0000 0.882 0.000 1.000 0.000 0.000
#> GSM550809 1 0.0188 0.967 0.996 0.004 0.000 0.000
#> GSM550810 2 0.0336 0.883 0.000 0.992 0.000 0.008
#> GSM550811 1 0.1637 0.923 0.940 0.060 0.000 0.000
#> GSM550813 2 0.1389 0.865 0.000 0.952 0.000 0.048
#> GSM550814 2 0.4072 0.645 0.000 0.748 0.000 0.252
#> GSM550815 2 0.0469 0.882 0.000 0.988 0.000 0.012
#> GSM550816 2 0.0188 0.881 0.004 0.996 0.000 0.000
#> GSM550817 3 0.0921 0.883 0.000 0.028 0.972 0.000
#> GSM550818 3 0.0707 0.889 0.000 0.020 0.980 0.000
#> GSM550819 4 0.4817 0.292 0.000 0.388 0.000 0.612
#> GSM550820 1 0.0000 0.969 1.000 0.000 0.000 0.000
#> GSM550821 2 0.0000 0.882 0.000 1.000 0.000 0.000
#> GSM550822 2 0.0188 0.883 0.000 0.996 0.000 0.004
#> GSM550826 1 0.0927 0.956 0.976 0.008 0.016 0.000
#> GSM550832 2 0.0188 0.883 0.000 0.996 0.000 0.004
#> GSM550833 2 0.1022 0.874 0.000 0.968 0.000 0.032
#> GSM550835 2 0.4872 0.672 0.000 0.728 0.244 0.028
#> GSM550836 3 0.0000 0.898 0.000 0.000 1.000 0.000
#> GSM550837 2 0.0469 0.882 0.000 0.988 0.000 0.012
#> GSM550838 1 0.0000 0.969 1.000 0.000 0.000 0.000
#> GSM550841 3 0.4222 0.579 0.000 0.272 0.728 0.000
#> GSM550842 2 0.0336 0.883 0.000 0.992 0.000 0.008
#> GSM550846 2 0.3569 0.722 0.196 0.804 0.000 0.000
#> GSM550849 1 0.3726 0.726 0.788 0.212 0.000 0.000
#> GSM550850 1 0.0000 0.969 1.000 0.000 0.000 0.000
#> GSM550851 2 0.0000 0.882 0.000 1.000 0.000 0.000
#> GSM550852 2 0.0000 0.882 0.000 1.000 0.000 0.000
#> GSM550853 2 0.4008 0.662 0.000 0.756 0.000 0.244
#> GSM550855 2 0.4277 0.604 0.000 0.720 0.000 0.280
#> GSM550856 2 0.4454 0.560 0.000 0.692 0.000 0.308
#> GSM550861 2 0.0188 0.883 0.000 0.996 0.000 0.004
#> GSM550863 4 0.1118 0.845 0.036 0.000 0.000 0.964
#> GSM550864 2 0.0188 0.883 0.000 0.996 0.000 0.004
#> GSM550866 4 0.3024 0.772 0.000 0.148 0.000 0.852
#> GSM550867 1 0.0188 0.968 0.996 0.000 0.000 0.004
#> GSM550885 1 0.0000 0.969 1.000 0.000 0.000 0.000
#> GSM550886 2 0.5592 0.379 0.000 0.572 0.404 0.024
#> GSM550887 2 0.0707 0.880 0.000 0.980 0.000 0.020
#> GSM550889 4 0.0000 0.855 0.000 0.000 0.000 1.000
#> GSM550894 2 0.0817 0.878 0.000 0.976 0.000 0.024
#> GSM550897 4 0.0707 0.851 0.020 0.000 0.000 0.980
#> GSM550903 2 0.0000 0.882 0.000 1.000 0.000 0.000
#> GSM550905 2 0.0000 0.882 0.000 1.000 0.000 0.000
#> GSM550906 2 0.1557 0.861 0.000 0.944 0.000 0.056
#> GSM550907 3 0.0000 0.898 0.000 0.000 1.000 0.000
#> GSM550909 2 0.1474 0.857 0.000 0.948 0.052 0.000
#> GSM550911 3 0.0000 0.898 0.000 0.000 1.000 0.000
#> GSM550913 2 0.0188 0.883 0.000 0.996 0.000 0.004
#> GSM550915 1 0.1302 0.937 0.956 0.044 0.000 0.000
#> GSM550917 2 0.0188 0.883 0.000 0.996 0.000 0.004
#> GSM550919 1 0.2216 0.888 0.908 0.092 0.000 0.000
#> GSM550921 3 0.0000 0.898 0.000 0.000 1.000 0.000
#> GSM550924 2 0.2654 0.808 0.108 0.888 0.004 0.000
#> GSM550926 4 0.4134 0.649 0.000 0.260 0.000 0.740
#> GSM550927 2 0.0592 0.881 0.000 0.984 0.000 0.016
#> GSM550787 2 0.8137 0.393 0.216 0.528 0.040 0.216
#> GSM550793 3 0.5208 0.729 0.172 0.000 0.748 0.080
#> GSM550794 2 0.4454 0.595 0.308 0.692 0.000 0.000
#> GSM550795 1 0.0592 0.961 0.984 0.000 0.000 0.016
#> GSM550798 1 0.0188 0.968 0.996 0.000 0.000 0.004
#> GSM550803 1 0.0188 0.968 0.996 0.000 0.000 0.004
#> GSM550805 4 0.5137 0.222 0.452 0.004 0.000 0.544
#> GSM550823 4 0.0000 0.855 0.000 0.000 0.000 1.000
#> GSM550824 1 0.0188 0.968 0.996 0.000 0.000 0.004
#> GSM550825 3 0.5902 0.677 0.184 0.000 0.696 0.120
#> GSM550827 1 0.0921 0.950 0.972 0.028 0.000 0.000
#> GSM550828 1 0.0000 0.969 1.000 0.000 0.000 0.000
#> GSM550829 1 0.0000 0.969 1.000 0.000 0.000 0.000
#> GSM550830 4 0.0000 0.855 0.000 0.000 0.000 1.000
#> GSM550834 1 0.0000 0.969 1.000 0.000 0.000 0.000
#> GSM550839 4 0.4012 0.705 0.000 0.016 0.184 0.800
#> GSM550840 4 0.1211 0.841 0.040 0.000 0.000 0.960
#> GSM550843 3 0.0000 0.898 0.000 0.000 1.000 0.000
#> GSM550844 1 0.0188 0.968 0.996 0.000 0.000 0.004
#> GSM550845 4 0.4941 0.259 0.000 0.436 0.000 0.564
#> GSM550848 1 0.3837 0.701 0.776 0.224 0.000 0.000
#> GSM550854 1 0.0188 0.968 0.996 0.000 0.000 0.004
#> GSM550857 3 0.4741 0.524 0.328 0.000 0.668 0.004
#> GSM550858 1 0.0188 0.968 0.996 0.000 0.000 0.004
#> GSM550859 1 0.0188 0.968 0.996 0.000 0.000 0.004
#> GSM550862 4 0.3074 0.749 0.152 0.000 0.000 0.848
#> GSM550865 4 0.0336 0.854 0.008 0.000 0.000 0.992
#> GSM550868 4 0.0336 0.854 0.008 0.000 0.000 0.992
#> GSM550869 4 0.0000 0.855 0.000 0.000 0.000 1.000
#> GSM550870 2 0.1211 0.869 0.000 0.960 0.000 0.040
#> GSM550871 4 0.2125 0.817 0.000 0.004 0.076 0.920
#> GSM550872 4 0.0188 0.855 0.004 0.000 0.000 0.996
#> GSM550873 2 0.0000 0.882 0.000 1.000 0.000 0.000
#> GSM550874 4 0.1557 0.841 0.000 0.056 0.000 0.944
#> GSM550876 4 0.0188 0.855 0.000 0.004 0.000 0.996
#> GSM550877 4 0.2760 0.793 0.000 0.128 0.000 0.872
#> GSM550878 3 0.0000 0.898 0.000 0.000 1.000 0.000
#> GSM550879 1 0.0000 0.969 1.000 0.000 0.000 0.000
#> GSM550882 4 0.3942 0.644 0.000 0.000 0.236 0.764
#> GSM550888 3 0.0000 0.898 0.000 0.000 1.000 0.000
#> GSM550890 1 0.2216 0.885 0.908 0.092 0.000 0.000
#> GSM550891 3 0.0000 0.898 0.000 0.000 1.000 0.000
#> GSM550892 4 0.1867 0.821 0.072 0.000 0.000 0.928
#> GSM550893 4 0.0817 0.852 0.000 0.024 0.000 0.976
#> GSM550895 4 0.0188 0.855 0.000 0.004 0.000 0.996
#> GSM550896 4 0.1302 0.844 0.000 0.044 0.000 0.956
#> GSM550898 1 0.0188 0.968 0.996 0.000 0.000 0.004
#> GSM550899 2 0.0188 0.881 0.004 0.996 0.000 0.000
#> GSM550900 4 0.0188 0.855 0.004 0.000 0.000 0.996
#> GSM550901 1 0.0592 0.960 0.984 0.016 0.000 0.000
#> GSM550902 1 0.1109 0.947 0.968 0.000 0.028 0.004
#> GSM550904 1 0.0000 0.969 1.000 0.000 0.000 0.000
#> GSM550908 3 0.0000 0.898 0.000 0.000 1.000 0.000
#> GSM550912 2 0.0469 0.882 0.000 0.988 0.000 0.012
#> GSM550914 2 0.2345 0.823 0.100 0.900 0.000 0.000
#> GSM550918 2 0.0000 0.882 0.000 1.000 0.000 0.000
#> GSM550922 2 0.3444 0.742 0.000 0.816 0.184 0.000
#> GSM550923 1 0.0188 0.968 0.996 0.000 0.000 0.004
#> GSM550925 4 0.3801 0.682 0.220 0.000 0.000 0.780
#> GSM550802 2 0.4981 0.215 0.000 0.536 0.000 0.464
#> GSM550812 2 0.5209 0.723 0.000 0.756 0.104 0.140
#> GSM550831 1 0.0000 0.969 1.000 0.000 0.000 0.000
#> GSM550847 1 0.0336 0.966 0.992 0.000 0.000 0.008
#> GSM550860 4 0.0188 0.854 0.000 0.000 0.004 0.996
#> GSM550875 4 0.0707 0.851 0.020 0.000 0.000 0.980
#> GSM550880 1 0.0921 0.950 0.972 0.000 0.000 0.028
#> GSM550881 3 0.0000 0.898 0.000 0.000 1.000 0.000
#> GSM550883 3 0.0524 0.893 0.008 0.000 0.988 0.004
#> GSM550884 4 0.6948 0.461 0.000 0.204 0.208 0.588
#> GSM550910 2 0.4843 0.397 0.000 0.604 0.396 0.000
#> GSM550916 4 0.3610 0.702 0.200 0.000 0.000 0.800
#> GSM550920 2 0.4730 0.470 0.000 0.636 0.364 0.000
cbind(get_classes(res, k = 5), get_membership(res, k = 5))
#> class entropy silhouette p1 p2 p3 p4 p5
#> GSM550785 1 0.0000 0.8005 1.000 0.000 0.000 0.000 0.000
#> GSM550786 3 0.7009 0.2991 0.024 0.244 0.488 0.000 0.244
#> GSM550788 2 0.4829 -0.0828 0.000 0.500 0.000 0.480 0.020
#> GSM550789 2 0.0162 0.8328 0.000 0.996 0.000 0.000 0.004
#> GSM550790 1 0.0162 0.7996 0.996 0.000 0.000 0.000 0.004
#> GSM550791 1 0.0162 0.7995 0.996 0.000 0.000 0.000 0.004
#> GSM550792 1 0.4654 0.2803 0.628 0.348 0.000 0.000 0.024
#> GSM550796 2 0.0000 0.8333 0.000 1.000 0.000 0.000 0.000
#> GSM550797 2 0.0162 0.8328 0.000 0.996 0.000 0.000 0.004
#> GSM550799 3 0.3365 0.6299 0.000 0.180 0.808 0.004 0.008
#> GSM550800 4 0.2813 0.7414 0.000 0.168 0.000 0.832 0.000
#> GSM550801 2 0.0162 0.8337 0.000 0.996 0.000 0.000 0.004
#> GSM550804 2 0.4045 0.3247 0.000 0.644 0.000 0.000 0.356
#> GSM550806 3 0.3707 0.4553 0.000 0.000 0.716 0.284 0.000
#> GSM550807 2 0.0324 0.8340 0.000 0.992 0.000 0.004 0.004
#> GSM550808 2 0.1671 0.7892 0.000 0.924 0.000 0.000 0.076
#> GSM550809 5 0.2329 0.4792 0.124 0.000 0.000 0.000 0.876
#> GSM550810 2 0.0703 0.8284 0.000 0.976 0.000 0.000 0.024
#> GSM550811 5 0.3551 0.3750 0.220 0.008 0.000 0.000 0.772
#> GSM550813 2 0.1012 0.8289 0.000 0.968 0.000 0.012 0.020
#> GSM550814 2 0.5975 0.2556 0.000 0.532 0.000 0.344 0.124
#> GSM550815 2 0.0162 0.8330 0.000 0.996 0.000 0.000 0.004
#> GSM550816 5 0.4235 0.3074 0.000 0.424 0.000 0.000 0.576
#> GSM550817 3 0.3578 0.6696 0.000 0.048 0.820 0.000 0.132
#> GSM550818 3 0.4321 0.3759 0.000 0.004 0.600 0.000 0.396
#> GSM550819 5 0.6063 0.3028 0.000 0.144 0.000 0.316 0.540
#> GSM550820 5 0.4307 -0.2828 0.496 0.000 0.000 0.000 0.504
#> GSM550821 5 0.4268 0.2496 0.000 0.444 0.000 0.000 0.556
#> GSM550822 2 0.3876 0.4105 0.000 0.684 0.000 0.000 0.316
#> GSM550826 5 0.5185 -0.0361 0.384 0.000 0.048 0.000 0.568
#> GSM550832 2 0.0609 0.8320 0.000 0.980 0.000 0.000 0.020
#> GSM550833 2 0.0162 0.8333 0.000 0.996 0.000 0.004 0.000
#> GSM550835 2 0.3579 0.5869 0.000 0.756 0.240 0.004 0.000
#> GSM550836 3 0.0000 0.7434 0.000 0.000 1.000 0.000 0.000
#> GSM550837 2 0.1205 0.8175 0.000 0.956 0.000 0.004 0.040
#> GSM550838 5 0.2563 0.4792 0.120 0.000 0.008 0.000 0.872
#> GSM550841 3 0.5475 0.3935 0.000 0.308 0.604 0.000 0.088
#> GSM550842 2 0.2179 0.7531 0.000 0.888 0.000 0.000 0.112
#> GSM550846 5 0.3884 0.5008 0.004 0.288 0.000 0.000 0.708
#> GSM550849 1 0.2305 0.7383 0.896 0.092 0.000 0.000 0.012
#> GSM550850 1 0.0671 0.7968 0.980 0.000 0.000 0.004 0.016
#> GSM550851 2 0.0162 0.8328 0.000 0.996 0.000 0.000 0.004
#> GSM550852 2 0.3876 0.4184 0.000 0.684 0.000 0.000 0.316
#> GSM550853 2 0.4808 0.3069 0.000 0.576 0.000 0.400 0.024
#> GSM550855 2 0.2813 0.6699 0.000 0.832 0.000 0.168 0.000
#> GSM550856 2 0.2966 0.6547 0.000 0.816 0.000 0.184 0.000
#> GSM550861 2 0.0404 0.8331 0.000 0.988 0.000 0.000 0.012
#> GSM550863 5 0.3177 0.4302 0.000 0.000 0.000 0.208 0.792
#> GSM550864 2 0.0510 0.8332 0.000 0.984 0.000 0.000 0.016
#> GSM550866 4 0.4108 0.5790 0.000 0.308 0.000 0.684 0.008
#> GSM550867 1 0.2536 0.7664 0.868 0.000 0.000 0.004 0.128
#> GSM550885 1 0.4151 0.5514 0.652 0.000 0.000 0.004 0.344
#> GSM550886 2 0.5557 0.1008 0.000 0.520 0.424 0.012 0.044
#> GSM550887 2 0.0162 0.8333 0.000 0.996 0.000 0.004 0.000
#> GSM550889 4 0.0162 0.8396 0.000 0.004 0.000 0.996 0.000
#> GSM550894 2 0.0771 0.8318 0.000 0.976 0.000 0.004 0.020
#> GSM550897 4 0.0865 0.8329 0.024 0.000 0.000 0.972 0.004
#> GSM550903 2 0.0404 0.8336 0.000 0.988 0.000 0.000 0.012
#> GSM550905 2 0.1043 0.8173 0.000 0.960 0.000 0.000 0.040
#> GSM550906 2 0.0693 0.8311 0.000 0.980 0.000 0.008 0.012
#> GSM550907 3 0.0510 0.7411 0.000 0.000 0.984 0.000 0.016
#> GSM550909 5 0.4744 0.2981 0.000 0.408 0.020 0.000 0.572
#> GSM550911 3 0.0880 0.7380 0.000 0.000 0.968 0.000 0.032
#> GSM550913 2 0.0404 0.8331 0.000 0.988 0.000 0.000 0.012
#> GSM550915 5 0.2504 0.5200 0.064 0.040 0.000 0.000 0.896
#> GSM550917 2 0.1041 0.8267 0.004 0.964 0.000 0.000 0.032
#> GSM550919 1 0.4642 0.3449 0.660 0.308 0.000 0.000 0.032
#> GSM550921 3 0.0000 0.7434 0.000 0.000 1.000 0.000 0.000
#> GSM550924 1 0.5946 0.4450 0.668 0.188 0.092 0.000 0.052
#> GSM550926 4 0.3381 0.7278 0.000 0.176 0.000 0.808 0.016
#> GSM550927 2 0.0000 0.8333 0.000 1.000 0.000 0.000 0.000
#> GSM550787 2 0.5482 0.1217 0.448 0.500 0.000 0.008 0.044
#> GSM550793 3 0.6569 0.3282 0.264 0.000 0.532 0.012 0.192
#> GSM550794 5 0.5717 0.3114 0.368 0.092 0.000 0.000 0.540
#> GSM550795 5 0.5868 0.1303 0.292 0.000 0.000 0.132 0.576
#> GSM550798 1 0.0566 0.8021 0.984 0.000 0.000 0.004 0.012
#> GSM550803 1 0.0566 0.8021 0.984 0.000 0.000 0.004 0.012
#> GSM550805 1 0.3146 0.7134 0.844 0.000 0.000 0.128 0.028
#> GSM550823 4 0.0162 0.8396 0.000 0.004 0.000 0.996 0.000
#> GSM550824 1 0.1124 0.8005 0.960 0.000 0.000 0.004 0.036
#> GSM550825 3 0.4387 0.3901 0.348 0.000 0.640 0.012 0.000
#> GSM550827 5 0.6749 0.4089 0.304 0.288 0.000 0.000 0.408
#> GSM550828 1 0.1571 0.7969 0.936 0.000 0.000 0.004 0.060
#> GSM550829 1 0.1990 0.7938 0.920 0.000 0.008 0.004 0.068
#> GSM550830 4 0.0000 0.8394 0.000 0.000 0.000 1.000 0.000
#> GSM550834 1 0.4225 0.5180 0.632 0.000 0.000 0.004 0.364
#> GSM550839 4 0.2964 0.7360 0.000 0.004 0.152 0.840 0.004
#> GSM550840 4 0.4576 0.3890 0.376 0.000 0.000 0.608 0.016
#> GSM550843 3 0.1205 0.7331 0.000 0.004 0.956 0.000 0.040
#> GSM550844 1 0.3521 0.6818 0.764 0.000 0.000 0.004 0.232
#> GSM550845 4 0.3659 0.6811 0.000 0.220 0.000 0.768 0.012
#> GSM550848 5 0.6551 0.4643 0.228 0.304 0.000 0.000 0.468
#> GSM550854 1 0.2233 0.7797 0.892 0.000 0.000 0.004 0.104
#> GSM550857 3 0.6801 0.1104 0.316 0.000 0.432 0.004 0.248
#> GSM550858 1 0.3086 0.7295 0.816 0.000 0.000 0.004 0.180
#> GSM550859 1 0.2179 0.7818 0.896 0.000 0.000 0.004 0.100
#> GSM550862 4 0.3596 0.6799 0.200 0.000 0.000 0.784 0.016
#> GSM550865 4 0.0404 0.8384 0.000 0.000 0.000 0.988 0.012
#> GSM550868 4 0.0404 0.8391 0.000 0.000 0.000 0.988 0.012
#> GSM550869 4 0.0566 0.8395 0.000 0.004 0.000 0.984 0.012
#> GSM550870 2 0.1012 0.8289 0.000 0.968 0.000 0.012 0.020
#> GSM550871 4 0.1731 0.8192 0.000 0.004 0.060 0.932 0.004
#> GSM550872 4 0.0162 0.8391 0.000 0.000 0.000 0.996 0.004
#> GSM550873 2 0.0794 0.8296 0.000 0.972 0.000 0.000 0.028
#> GSM550874 4 0.0671 0.8386 0.000 0.016 0.000 0.980 0.004
#> GSM550876 4 0.1924 0.8168 0.000 0.004 0.064 0.924 0.008
#> GSM550877 4 0.1168 0.8332 0.000 0.032 0.000 0.960 0.008
#> GSM550878 3 0.0000 0.7434 0.000 0.000 1.000 0.000 0.000
#> GSM550879 1 0.4341 0.4570 0.592 0.000 0.000 0.004 0.404
#> GSM550882 4 0.4481 0.2909 0.000 0.000 0.416 0.576 0.008
#> GSM550888 3 0.0162 0.7427 0.000 0.000 0.996 0.004 0.000
#> GSM550890 5 0.3616 0.5450 0.032 0.164 0.000 0.000 0.804
#> GSM550891 3 0.0000 0.7434 0.000 0.000 1.000 0.000 0.000
#> GSM550892 4 0.0880 0.8290 0.000 0.000 0.000 0.968 0.032
#> GSM550893 4 0.4886 0.4169 0.000 0.372 0.000 0.596 0.032
#> GSM550895 4 0.0324 0.8397 0.000 0.004 0.000 0.992 0.004
#> GSM550896 4 0.1408 0.8283 0.000 0.044 0.000 0.948 0.008
#> GSM550898 1 0.0162 0.8010 0.996 0.000 0.000 0.004 0.000
#> GSM550899 2 0.1043 0.8189 0.000 0.960 0.000 0.000 0.040
#> GSM550900 4 0.0451 0.8398 0.000 0.004 0.000 0.988 0.008
#> GSM550901 1 0.0566 0.7995 0.984 0.004 0.000 0.000 0.012
#> GSM550902 1 0.6480 0.2392 0.444 0.000 0.160 0.004 0.392
#> GSM550904 5 0.4273 -0.1680 0.448 0.000 0.000 0.000 0.552
#> GSM550908 3 0.0000 0.7434 0.000 0.000 1.000 0.000 0.000
#> GSM550912 2 0.0880 0.8284 0.000 0.968 0.000 0.000 0.032
#> GSM550914 5 0.4182 0.4262 0.000 0.352 0.000 0.004 0.644
#> GSM550918 2 0.1041 0.8267 0.004 0.964 0.000 0.000 0.032
#> GSM550922 3 0.4449 0.0662 0.000 0.484 0.512 0.000 0.004
#> GSM550923 1 0.0000 0.8005 1.000 0.000 0.000 0.000 0.000
#> GSM550925 1 0.4756 0.6105 0.752 0.040 0.000 0.172 0.036
#> GSM550802 5 0.6108 0.4166 0.000 0.188 0.000 0.248 0.564
#> GSM550812 5 0.5144 0.4624 0.000 0.304 0.000 0.064 0.632
#> GSM550831 1 0.1041 0.7997 0.964 0.000 0.000 0.004 0.032
#> GSM550847 1 0.0162 0.8010 0.996 0.000 0.000 0.004 0.000
#> GSM550860 4 0.0000 0.8394 0.000 0.000 0.000 1.000 0.000
#> GSM550875 4 0.4101 0.4591 0.332 0.000 0.000 0.664 0.004
#> GSM550880 1 0.6558 0.1433 0.504 0.004 0.000 0.224 0.268
#> GSM550881 3 0.0000 0.7434 0.000 0.000 1.000 0.000 0.000
#> GSM550883 3 0.2970 0.6647 0.000 0.000 0.828 0.004 0.168
#> GSM550884 4 0.6029 0.1119 0.000 0.048 0.032 0.464 0.456
#> GSM550910 3 0.6616 0.1962 0.000 0.252 0.456 0.000 0.292
#> GSM550916 1 0.2233 0.7416 0.904 0.000 0.000 0.080 0.016
#> GSM550920 2 0.5647 0.0785 0.016 0.516 0.424 0.000 0.044
cbind(get_classes(res, k = 6), get_membership(res, k = 6))
#> class entropy silhouette p1 p2 p3 p4 p5 p6
#> GSM550785 1 0.0363 0.7605 0.988 0.000 0.000 0.000 0.000 0.012
#> GSM550786 6 0.5679 0.5500 0.028 0.052 0.216 0.000 0.052 0.652
#> GSM550788 2 0.4195 0.1598 0.000 0.548 0.000 0.440 0.004 0.008
#> GSM550789 2 0.0363 0.8580 0.000 0.988 0.000 0.000 0.012 0.000
#> GSM550790 1 0.0146 0.7595 0.996 0.000 0.000 0.000 0.000 0.004
#> GSM550791 1 0.1007 0.7550 0.956 0.000 0.000 0.000 0.000 0.044
#> GSM550792 1 0.5757 0.4518 0.620 0.216 0.000 0.000 0.104 0.060
#> GSM550796 2 0.0508 0.8579 0.000 0.984 0.000 0.004 0.012 0.000
#> GSM550797 2 0.0363 0.8580 0.000 0.988 0.000 0.000 0.012 0.000
#> GSM550799 3 0.3371 0.5515 0.000 0.292 0.708 0.000 0.000 0.000
#> GSM550800 4 0.4397 0.1202 0.000 0.452 0.000 0.528 0.012 0.008
#> GSM550801 2 0.1007 0.8549 0.000 0.956 0.000 0.000 0.044 0.000
#> GSM550804 5 0.3373 0.6156 0.000 0.248 0.000 0.000 0.744 0.008
#> GSM550806 3 0.3343 0.6383 0.000 0.000 0.796 0.176 0.004 0.024
#> GSM550807 2 0.1080 0.8577 0.000 0.960 0.000 0.004 0.032 0.004
#> GSM550808 5 0.5068 0.1574 0.000 0.460 0.024 0.000 0.484 0.032
#> GSM550809 6 0.2988 0.6562 0.024 0.000 0.000 0.000 0.152 0.824
#> GSM550810 2 0.3499 0.7065 0.000 0.780 0.008 0.004 0.196 0.012
#> GSM550811 6 0.3802 0.6203 0.044 0.000 0.000 0.000 0.208 0.748
#> GSM550813 2 0.1515 0.8483 0.000 0.944 0.000 0.008 0.028 0.020
#> GSM550814 2 0.5893 0.4633 0.000 0.604 0.000 0.216 0.124 0.056
#> GSM550815 2 0.1036 0.8537 0.000 0.964 0.000 0.004 0.024 0.008
#> GSM550816 5 0.2672 0.7058 0.000 0.052 0.000 0.000 0.868 0.080
#> GSM550817 3 0.5257 0.3538 0.000 0.016 0.572 0.000 0.340 0.072
#> GSM550818 5 0.4289 0.4977 0.000 0.004 0.264 0.000 0.688 0.044
#> GSM550819 5 0.5254 0.5775 0.000 0.012 0.000 0.220 0.636 0.132
#> GSM550820 6 0.4243 0.6787 0.164 0.000 0.000 0.000 0.104 0.732
#> GSM550821 5 0.2545 0.7102 0.000 0.068 0.020 0.000 0.888 0.024
#> GSM550822 5 0.4933 0.4849 0.000 0.340 0.000 0.004 0.588 0.068
#> GSM550826 6 0.3316 0.7220 0.072 0.000 0.028 0.000 0.056 0.844
#> GSM550832 2 0.1268 0.8502 0.004 0.952 0.000 0.000 0.036 0.008
#> GSM550833 2 0.0862 0.8559 0.000 0.972 0.000 0.004 0.016 0.008
#> GSM550835 2 0.2723 0.7650 0.000 0.852 0.128 0.000 0.004 0.016
#> GSM550836 3 0.0713 0.7565 0.000 0.000 0.972 0.000 0.000 0.028
#> GSM550837 2 0.1864 0.8389 0.000 0.924 0.000 0.004 0.040 0.032
#> GSM550838 6 0.2973 0.6693 0.024 0.000 0.004 0.000 0.136 0.836
#> GSM550841 3 0.5744 0.3321 0.000 0.060 0.556 0.000 0.324 0.060
#> GSM550842 2 0.5463 -0.0826 0.000 0.500 0.028 0.004 0.420 0.048
#> GSM550846 5 0.2798 0.6994 0.000 0.036 0.000 0.000 0.852 0.112
#> GSM550849 1 0.2803 0.7226 0.876 0.028 0.000 0.000 0.064 0.032
#> GSM550850 1 0.1176 0.7577 0.956 0.000 0.000 0.000 0.020 0.024
#> GSM550851 2 0.0363 0.8580 0.000 0.988 0.000 0.000 0.012 0.000
#> GSM550852 5 0.4393 0.4521 0.000 0.316 0.000 0.000 0.640 0.044
#> GSM550853 4 0.4382 0.6049 0.000 0.248 0.000 0.700 0.024 0.028
#> GSM550855 2 0.1477 0.8377 0.000 0.940 0.000 0.048 0.004 0.008
#> GSM550856 2 0.1942 0.8239 0.000 0.916 0.000 0.064 0.008 0.012
#> GSM550861 2 0.0146 0.8580 0.000 0.996 0.000 0.000 0.004 0.000
#> GSM550863 5 0.5731 0.4330 0.000 0.000 0.000 0.260 0.516 0.224
#> GSM550864 2 0.0717 0.8583 0.000 0.976 0.000 0.000 0.008 0.016
#> GSM550866 2 0.3817 0.2052 0.000 0.568 0.000 0.432 0.000 0.000
#> GSM550867 1 0.3864 -0.0411 0.520 0.000 0.000 0.000 0.000 0.480
#> GSM550885 6 0.3175 0.5959 0.256 0.000 0.000 0.000 0.000 0.744
#> GSM550886 3 0.5980 0.2779 0.004 0.376 0.504 0.008 0.084 0.024
#> GSM550887 2 0.0653 0.8575 0.000 0.980 0.000 0.004 0.012 0.004
#> GSM550889 4 0.0146 0.8593 0.000 0.000 0.000 0.996 0.000 0.004
#> GSM550894 2 0.1204 0.8524 0.004 0.960 0.000 0.004 0.016 0.016
#> GSM550897 4 0.1906 0.8409 0.036 0.008 0.000 0.924 0.000 0.032
#> GSM550903 2 0.0146 0.8580 0.000 0.996 0.000 0.000 0.004 0.000
#> GSM550905 2 0.1408 0.8496 0.000 0.944 0.000 0.000 0.020 0.036
#> GSM550906 2 0.0260 0.8571 0.000 0.992 0.000 0.008 0.000 0.000
#> GSM550907 3 0.0806 0.7537 0.000 0.000 0.972 0.000 0.020 0.008
#> GSM550909 5 0.3029 0.7012 0.000 0.040 0.028 0.004 0.868 0.060
#> GSM550911 3 0.1908 0.7396 0.000 0.000 0.916 0.000 0.056 0.028
#> GSM550913 2 0.0260 0.8579 0.000 0.992 0.000 0.000 0.008 0.000
#> GSM550915 5 0.2595 0.6621 0.000 0.004 0.000 0.000 0.836 0.160
#> GSM550917 2 0.2933 0.7873 0.008 0.852 0.000 0.000 0.108 0.032
#> GSM550919 1 0.6356 0.2982 0.532 0.236 0.000 0.000 0.052 0.180
#> GSM550921 3 0.0713 0.7565 0.000 0.000 0.972 0.000 0.000 0.028
#> GSM550924 1 0.4474 0.6191 0.764 0.012 0.032 0.000 0.136 0.056
#> GSM550926 4 0.2649 0.8233 0.000 0.064 0.000 0.884 0.024 0.028
#> GSM550927 2 0.0767 0.8570 0.000 0.976 0.000 0.004 0.012 0.008
#> GSM550787 1 0.3139 0.6814 0.852 0.100 0.024 0.000 0.012 0.012
#> GSM550793 6 0.4975 0.4148 0.040 0.000 0.336 0.008 0.012 0.604
#> GSM550794 1 0.5398 0.2803 0.536 0.000 0.024 0.008 0.388 0.044
#> GSM550795 6 0.3345 0.6956 0.052 0.000 0.000 0.068 0.036 0.844
#> GSM550798 1 0.1531 0.7453 0.928 0.000 0.000 0.000 0.004 0.068
#> GSM550803 1 0.1411 0.7491 0.936 0.000 0.000 0.000 0.004 0.060
#> GSM550805 1 0.1698 0.7546 0.940 0.008 0.012 0.032 0.004 0.004
#> GSM550823 4 0.0000 0.8594 0.000 0.000 0.000 1.000 0.000 0.000
#> GSM550824 1 0.2668 0.6705 0.828 0.000 0.000 0.000 0.004 0.168
#> GSM550825 3 0.4421 0.4194 0.328 0.000 0.636 0.008 0.000 0.028
#> GSM550827 5 0.4999 0.6127 0.036 0.088 0.000 0.012 0.724 0.140
#> GSM550828 1 0.2442 0.6932 0.852 0.000 0.000 0.000 0.004 0.144
#> GSM550829 1 0.4234 0.3870 0.644 0.000 0.032 0.000 0.000 0.324
#> GSM550830 4 0.0291 0.8589 0.000 0.000 0.000 0.992 0.004 0.004
#> GSM550834 1 0.6100 -0.1056 0.364 0.000 0.000 0.000 0.284 0.352
#> GSM550839 4 0.3892 0.7296 0.000 0.000 0.160 0.780 0.032 0.028
#> GSM550840 1 0.4424 0.5035 0.676 0.000 0.000 0.276 0.012 0.036
#> GSM550843 3 0.3190 0.6930 0.000 0.000 0.820 0.000 0.136 0.044
#> GSM550844 6 0.3817 0.2734 0.432 0.000 0.000 0.000 0.000 0.568
#> GSM550845 4 0.5625 0.6077 0.004 0.144 0.000 0.664 0.124 0.064
#> GSM550848 5 0.3977 0.6567 0.092 0.060 0.000 0.000 0.800 0.048
#> GSM550854 1 0.3446 0.4636 0.692 0.000 0.000 0.000 0.000 0.308
#> GSM550857 6 0.4668 0.6379 0.116 0.000 0.204 0.000 0.000 0.680
#> GSM550858 6 0.3847 0.1763 0.456 0.000 0.000 0.000 0.000 0.544
#> GSM550859 1 0.3737 0.2607 0.608 0.000 0.000 0.000 0.000 0.392
#> GSM550862 4 0.2726 0.7883 0.112 0.000 0.000 0.856 0.000 0.032
#> GSM550865 4 0.0777 0.8595 0.000 0.000 0.000 0.972 0.004 0.024
#> GSM550868 4 0.1088 0.8580 0.000 0.000 0.000 0.960 0.016 0.024
#> GSM550869 4 0.1448 0.8502 0.000 0.000 0.016 0.948 0.012 0.024
#> GSM550870 2 0.2017 0.8380 0.008 0.920 0.000 0.004 0.048 0.020
#> GSM550871 4 0.1728 0.8396 0.000 0.000 0.064 0.924 0.004 0.008
#> GSM550872 4 0.0603 0.8580 0.000 0.000 0.000 0.980 0.016 0.004
#> GSM550873 2 0.4420 0.6805 0.016 0.744 0.008 0.000 0.176 0.056
#> GSM550874 4 0.0520 0.8609 0.000 0.008 0.000 0.984 0.000 0.008
#> GSM550876 4 0.1753 0.8315 0.000 0.000 0.084 0.912 0.000 0.004
#> GSM550877 4 0.1053 0.8587 0.000 0.004 0.000 0.964 0.012 0.020
#> GSM550878 3 0.0000 0.7576 0.000 0.000 1.000 0.000 0.000 0.000
#> GSM550879 6 0.3134 0.6809 0.168 0.000 0.000 0.000 0.024 0.808
#> GSM550882 4 0.4983 0.0196 0.000 0.000 0.460 0.484 0.008 0.048
#> GSM550888 3 0.1007 0.7531 0.000 0.000 0.956 0.000 0.000 0.044
#> GSM550890 5 0.2726 0.6959 0.000 0.032 0.000 0.000 0.856 0.112
#> GSM550891 3 0.0547 0.7579 0.000 0.000 0.980 0.000 0.000 0.020
#> GSM550892 4 0.1007 0.8554 0.000 0.000 0.000 0.956 0.000 0.044
#> GSM550893 4 0.3833 0.6218 0.000 0.272 0.000 0.708 0.004 0.016
#> GSM550895 4 0.0260 0.8601 0.000 0.000 0.000 0.992 0.000 0.008
#> GSM550896 4 0.1524 0.8395 0.000 0.060 0.000 0.932 0.000 0.008
#> GSM550898 1 0.0632 0.7592 0.976 0.000 0.000 0.000 0.000 0.024
#> GSM550899 2 0.1421 0.8506 0.000 0.944 0.000 0.000 0.028 0.028
#> GSM550900 4 0.1053 0.8560 0.004 0.000 0.000 0.964 0.012 0.020
#> GSM550901 1 0.0914 0.7617 0.968 0.000 0.000 0.000 0.016 0.016
#> GSM550902 6 0.3613 0.7068 0.096 0.000 0.096 0.004 0.000 0.804
#> GSM550904 6 0.4774 0.3212 0.052 0.000 0.000 0.000 0.420 0.528
#> GSM550908 3 0.1007 0.7525 0.000 0.000 0.956 0.000 0.000 0.044
#> GSM550912 2 0.3390 0.7639 0.004 0.820 0.000 0.004 0.128 0.044
#> GSM550914 5 0.2579 0.7024 0.000 0.040 0.000 0.000 0.872 0.088
#> GSM550918 2 0.5243 0.5563 0.084 0.656 0.000 0.000 0.224 0.036
#> GSM550922 2 0.4676 0.1462 0.000 0.552 0.412 0.000 0.016 0.020
#> GSM550923 1 0.0458 0.7600 0.984 0.000 0.000 0.000 0.000 0.016
#> GSM550925 1 0.2869 0.7203 0.880 0.024 0.000 0.052 0.008 0.036
#> GSM550802 5 0.3673 0.6767 0.000 0.008 0.000 0.088 0.804 0.100
#> GSM550812 5 0.2624 0.7056 0.000 0.024 0.000 0.016 0.880 0.080
#> GSM550831 1 0.2740 0.7237 0.864 0.000 0.000 0.000 0.076 0.060
#> GSM550847 1 0.0260 0.7602 0.992 0.000 0.000 0.000 0.000 0.008
#> GSM550860 4 0.0363 0.8593 0.000 0.000 0.000 0.988 0.000 0.012
#> GSM550875 4 0.3896 0.7106 0.156 0.008 0.000 0.780 0.004 0.052
#> GSM550880 5 0.6750 0.3703 0.168 0.000 0.000 0.288 0.468 0.076
#> GSM550881 3 0.2632 0.6613 0.000 0.000 0.832 0.000 0.004 0.164
#> GSM550883 6 0.4220 0.0974 0.000 0.000 0.468 0.008 0.004 0.520
#> GSM550884 5 0.5301 0.3903 0.000 0.008 0.004 0.300 0.596 0.092
#> GSM550910 5 0.5563 0.3633 0.004 0.028 0.300 0.004 0.596 0.068
#> GSM550916 1 0.1321 0.7487 0.952 0.000 0.000 0.024 0.004 0.020
#> GSM550920 3 0.5996 0.5475 0.124 0.184 0.628 0.000 0.048 0.016
Heatmaps for the consensus matrix. It visualizes the probability of two samples to be in a same group.
consensus_heatmap(res, k = 2)
consensus_heatmap(res, k = 3)
consensus_heatmap(res, k = 4)
consensus_heatmap(res, k = 5)
consensus_heatmap(res, k = 6)
Heatmaps for the membership of samples in all partitions to see how consistent they are:
membership_heatmap(res, k = 2)
membership_heatmap(res, k = 3)
membership_heatmap(res, k = 4)
membership_heatmap(res, k = 5)
membership_heatmap(res, k = 6)
As soon as we have had the classes for columns, we can look for signatures which are significantly different between classes which can be candidate marks for certain classes. Following are the heatmaps for signatures.
Signature heatmaps where rows are scaled:
get_signatures(res, k = 2)
get_signatures(res, k = 3)
get_signatures(res, k = 4)
get_signatures(res, k = 5)
get_signatures(res, k = 6)
Signature heatmaps where rows are not scaled:
get_signatures(res, k = 2, scale_rows = FALSE)
get_signatures(res, k = 3, scale_rows = FALSE)
get_signatures(res, k = 4, scale_rows = FALSE)
get_signatures(res, k = 5, scale_rows = FALSE)
get_signatures(res, k = 6, scale_rows = FALSE)
Compare the overlap of signatures from different k:
compare_signatures(res)
get_signature() returns a data frame invisibly. TO get the list of signatures, the function
call should be assigned to a variable explicitly. In following code, if plot argument is set
to FALSE, no heatmap is plotted while only the differential analysis is performed.
# code only for demonstration
tb = get_signature(res, k = ..., plot = FALSE)
An example of the output of tb is:
#> which_row fdr mean_1 mean_2 scaled_mean_1 scaled_mean_2 km
#> 1 38 0.042760348 8.373488 9.131774 -0.5533452 0.5164555 1
#> 2 40 0.018707592 7.106213 8.469186 -0.6173731 0.5762149 1
#> 3 55 0.019134737 10.221463 11.207825 -0.6159697 0.5749050 1
#> 4 59 0.006059896 5.921854 7.869574 -0.6899429 0.6439467 1
#> 5 60 0.018055526 8.928898 10.211722 -0.6204761 0.5791110 1
#> 6 98 0.009384629 15.714769 14.887706 0.6635654 -0.6193277 2
...
The columns in tb are:
which_row: row indices corresponding to the input matrix.fdr: FDR for the differential test. mean_x: The mean value in group x.scaled_mean_x: The mean value in group x after rows are scaled.km: Row groups if k-means clustering is applied to rows.UMAP plot which shows how samples are separated.
dimension_reduction(res, k = 2, method = "UMAP")
dimension_reduction(res, k = 3, method = "UMAP")
dimension_reduction(res, k = 4, method = "UMAP")
dimension_reduction(res, k = 5, method = "UMAP")
dimension_reduction(res, k = 6, method = "UMAP")
Following heatmap shows how subgroups are split when increasing k:
collect_classes(res)
Test correlation between subgroups and known annotations. If the known annotation is numeric, one-way ANOVA test is applied, and if the known annotation is discrete, chi-squared contingency table test is applied.
test_to_known_factors(res)
#> n disease.state(p) k
#> MAD:NMF 133 2.19e-04 2
#> MAD:NMF 135 2.08e-04 3
#> MAD:NMF 133 3.83e-05 4
#> MAD:NMF 96 1.17e-04 5
#> MAD:NMF 111 3.40e-04 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 51776 rows and 143 columns.
#> Top rows (1000, 2000, 3000, 4000, 5000) are extracted by 'ATC' method.
#> Subgroups are detected by 'hclust' method.
#> Performed in total 1250 partitions by row resampling.
#> Best k for subgroups seems to be 3.
#>
#> Following methods can be applied to this 'ConsensusPartition' object:
#> [1] "cola_report" "collect_classes" "collect_plots"
#> [4] "collect_stats" "colnames" "compare_signatures"
#> [7] "consensus_heatmap" "dimension_reduction" "functional_enrichment"
#> [10] "get_anno_col" "get_anno" "get_classes"
#> [13] "get_consensus" "get_matrix" "get_membership"
#> [16] "get_param" "get_signatures" "get_stats"
#> [19] "is_best_k" "is_stable_k" "membership_heatmap"
#> [22] "ncol" "nrow" "plot_ecdf"
#> [25] "rownames" "select_partition_number" "show"
#> [28] "suggest_best_k" "test_to_known_factors"
collect_plots() function collects all the plots made from res for all k (number of partitions)
into one single page to provide an easy and fast comparison between different k.
collect_plots(res)
The plots are:
k and the heatmap of
predicted classes for each k.k.k.k.All the plots in panels can be made by individual functions and they are plotted later in this section.
select_partition_number() produces several plots showing different
statistics for choosing “optimized” k. There are following statistics:
k;k, the area increased is defined as \(A_k - A_{k-1}\).The detailed explanations of these statistics can be found in the cola vignette.
Generally speaking, lower PAC score, higher mean silhouette score or higher
concordance corresponds to better partition. Rand index and Jaccard index
measure how similar the current partition is compared to partition with k-1.
If they are too similar, we won't accept k is better than k-1.
select_partition_number(res)
The numeric values for all these statistics can be obtained by get_stats().
get_stats(res)
#> k 1-PAC mean_silhouette concordance area_increased Rand Jaccard
#> 2 2 0.767 0.928 0.962 0.2928 0.738 0.738
#> 3 3 0.620 0.828 0.900 1.0713 0.640 0.512
#> 4 4 0.628 0.750 0.874 0.0510 0.983 0.955
#> 5 5 0.662 0.764 0.841 0.1000 0.915 0.770
#> 6 6 0.720 0.769 0.875 0.0267 0.990 0.964
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
#> GSM550785 2 0.5737 0.860 0.136 0.864
#> GSM550786 2 0.0000 0.959 0.000 1.000
#> GSM550788 2 0.0000 0.959 0.000 1.000
#> GSM550789 2 0.0000 0.959 0.000 1.000
#> GSM550790 2 0.6801 0.818 0.180 0.820
#> GSM550791 2 0.3584 0.917 0.068 0.932
#> GSM550792 2 0.0376 0.957 0.004 0.996
#> GSM550796 2 0.0000 0.959 0.000 1.000
#> GSM550797 2 0.0000 0.959 0.000 1.000
#> GSM550799 2 0.0000 0.959 0.000 1.000
#> GSM550800 2 0.0000 0.959 0.000 1.000
#> GSM550801 2 0.0000 0.959 0.000 1.000
#> GSM550804 2 0.0000 0.959 0.000 1.000
#> GSM550806 2 0.0672 0.956 0.008 0.992
#> GSM550807 2 0.0000 0.959 0.000 1.000
#> GSM550808 2 0.0000 0.959 0.000 1.000
#> GSM550809 2 0.4022 0.909 0.080 0.920
#> GSM550810 2 0.0000 0.959 0.000 1.000
#> GSM550811 2 0.3733 0.914 0.072 0.928
#> GSM550813 2 0.0000 0.959 0.000 1.000
#> GSM550814 2 0.0000 0.959 0.000 1.000
#> GSM550815 2 0.0000 0.959 0.000 1.000
#> GSM550816 2 0.0000 0.959 0.000 1.000
#> GSM550817 2 0.0000 0.959 0.000 1.000
#> GSM550818 2 0.0000 0.959 0.000 1.000
#> GSM550819 2 0.0000 0.959 0.000 1.000
#> GSM550820 2 0.7139 0.798 0.196 0.804
#> GSM550821 2 0.0000 0.959 0.000 1.000
#> GSM550822 2 0.0000 0.959 0.000 1.000
#> GSM550826 2 0.7139 0.798 0.196 0.804
#> GSM550832 2 0.0000 0.959 0.000 1.000
#> GSM550833 2 0.0000 0.959 0.000 1.000
#> GSM550835 2 0.0000 0.959 0.000 1.000
#> GSM550836 1 0.0000 0.970 1.000 0.000
#> GSM550837 2 0.0000 0.959 0.000 1.000
#> GSM550838 2 0.4022 0.909 0.080 0.920
#> GSM550841 2 0.0000 0.959 0.000 1.000
#> GSM550842 2 0.0000 0.959 0.000 1.000
#> GSM550846 2 0.0376 0.957 0.004 0.996
#> GSM550849 2 0.2043 0.941 0.032 0.968
#> GSM550850 2 0.6343 0.838 0.160 0.840
#> GSM550851 2 0.0000 0.959 0.000 1.000
#> GSM550852 2 0.0000 0.959 0.000 1.000
#> GSM550853 2 0.0000 0.959 0.000 1.000
#> GSM550855 2 0.0000 0.959 0.000 1.000
#> GSM550856 2 0.0000 0.959 0.000 1.000
#> GSM550861 2 0.0000 0.959 0.000 1.000
#> GSM550863 2 0.0376 0.957 0.004 0.996
#> GSM550864 2 0.0000 0.959 0.000 1.000
#> GSM550866 2 0.0000 0.959 0.000 1.000
#> GSM550867 1 0.0000 0.970 1.000 0.000
#> GSM550885 1 0.0000 0.970 1.000 0.000
#> GSM550886 2 0.0000 0.959 0.000 1.000
#> GSM550887 2 0.0000 0.959 0.000 1.000
#> GSM550889 2 0.7376 0.783 0.208 0.792
#> GSM550894 2 0.0000 0.959 0.000 1.000
#> GSM550897 2 0.6343 0.838 0.160 0.840
#> GSM550903 2 0.0000 0.959 0.000 1.000
#> GSM550905 2 0.0000 0.959 0.000 1.000
#> GSM550906 2 0.0000 0.959 0.000 1.000
#> GSM550907 2 0.0000 0.959 0.000 1.000
#> GSM550909 2 0.0000 0.959 0.000 1.000
#> GSM550911 2 0.0000 0.959 0.000 1.000
#> GSM550913 2 0.0000 0.959 0.000 1.000
#> GSM550915 2 0.0376 0.957 0.004 0.996
#> GSM550917 2 0.0000 0.959 0.000 1.000
#> GSM550919 2 0.0672 0.956 0.008 0.992
#> GSM550921 1 0.0000 0.970 1.000 0.000
#> GSM550924 2 0.0672 0.956 0.008 0.992
#> GSM550926 2 0.0000 0.959 0.000 1.000
#> GSM550927 2 0.0000 0.959 0.000 1.000
#> GSM550787 2 0.0938 0.954 0.012 0.988
#> GSM550793 2 0.9970 0.206 0.468 0.532
#> GSM550794 2 0.0000 0.959 0.000 1.000
#> GSM550795 2 0.7299 0.788 0.204 0.796
#> GSM550798 1 0.0000 0.970 1.000 0.000
#> GSM550803 1 0.0000 0.970 1.000 0.000
#> GSM550805 2 0.0672 0.956 0.008 0.992
#> GSM550823 2 0.0672 0.956 0.008 0.992
#> GSM550824 1 0.0000 0.970 1.000 0.000
#> GSM550825 1 0.0000 0.970 1.000 0.000
#> GSM550827 2 0.0376 0.957 0.004 0.996
#> GSM550828 2 0.7219 0.793 0.200 0.800
#> GSM550829 1 0.0000 0.970 1.000 0.000
#> GSM550830 2 0.0672 0.956 0.008 0.992
#> GSM550834 2 0.3584 0.917 0.068 0.932
#> GSM550839 2 0.0000 0.959 0.000 1.000
#> GSM550840 2 0.3584 0.917 0.068 0.932
#> GSM550843 2 0.0000 0.959 0.000 1.000
#> GSM550844 2 0.7139 0.798 0.196 0.804
#> GSM550845 2 0.0000 0.959 0.000 1.000
#> GSM550848 2 0.0376 0.957 0.004 0.996
#> GSM550854 1 0.0000 0.970 1.000 0.000
#> GSM550857 1 0.0000 0.970 1.000 0.000
#> GSM550858 1 0.7056 0.761 0.808 0.192
#> GSM550859 1 0.0000 0.970 1.000 0.000
#> GSM550862 1 0.7056 0.761 0.808 0.192
#> GSM550865 2 0.3431 0.921 0.064 0.936
#> GSM550868 2 0.0376 0.957 0.004 0.996
#> GSM550869 2 0.0672 0.956 0.008 0.992
#> GSM550870 2 0.0000 0.959 0.000 1.000
#> GSM550871 2 0.0000 0.959 0.000 1.000
#> GSM550872 2 0.0000 0.959 0.000 1.000
#> GSM550873 2 0.0000 0.959 0.000 1.000
#> GSM550874 2 0.0000 0.959 0.000 1.000
#> GSM550876 2 0.0000 0.959 0.000 1.000
#> GSM550877 2 0.0000 0.959 0.000 1.000
#> GSM550878 2 0.0000 0.959 0.000 1.000
#> GSM550879 2 0.6343 0.838 0.160 0.840
#> GSM550882 2 0.7376 0.783 0.208 0.792
#> GSM550888 1 0.0000 0.970 1.000 0.000
#> GSM550890 2 0.0376 0.957 0.004 0.996
#> GSM550891 1 0.0000 0.970 1.000 0.000
#> GSM550892 2 0.7376 0.783 0.208 0.792
#> GSM550893 2 0.0000 0.959 0.000 1.000
#> GSM550895 2 0.0000 0.959 0.000 1.000
#> GSM550896 2 0.0000 0.959 0.000 1.000
#> GSM550898 1 0.0000 0.970 1.000 0.000
#> GSM550899 2 0.0000 0.959 0.000 1.000
#> GSM550900 2 0.0000 0.959 0.000 1.000
#> GSM550901 2 0.0672 0.956 0.008 0.992
#> GSM550902 2 0.6343 0.838 0.160 0.840
#> GSM550904 1 0.7139 0.754 0.804 0.196
#> GSM550908 1 0.0000 0.970 1.000 0.000
#> GSM550912 2 0.0000 0.959 0.000 1.000
#> GSM550914 2 0.0672 0.956 0.008 0.992
#> GSM550918 2 0.0000 0.959 0.000 1.000
#> GSM550922 2 0.0000 0.959 0.000 1.000
#> GSM550923 1 0.0000 0.970 1.000 0.000
#> GSM550925 2 0.7376 0.783 0.208 0.792
#> GSM550802 2 0.0000 0.959 0.000 1.000
#> GSM550812 2 0.0000 0.959 0.000 1.000
#> GSM550831 2 0.6343 0.838 0.160 0.840
#> GSM550847 1 0.0000 0.970 1.000 0.000
#> GSM550860 2 0.6048 0.850 0.148 0.852
#> GSM550875 2 0.6343 0.838 0.160 0.840
#> GSM550880 2 0.0672 0.956 0.008 0.992
#> GSM550881 2 0.7815 0.750 0.232 0.768
#> GSM550883 1 0.0000 0.970 1.000 0.000
#> GSM550884 2 0.0376 0.957 0.004 0.996
#> GSM550910 2 0.0000 0.959 0.000 1.000
#> GSM550916 2 0.6801 0.818 0.180 0.820
#> GSM550920 2 0.0376 0.957 0.004 0.996
cbind(get_classes(res, k = 3), get_membership(res, k = 3))
#> class entropy silhouette p1 p2 p3
#> GSM550785 1 0.2356 0.8660 0.928 0.000 0.072
#> GSM550786 1 0.6295 -0.0896 0.528 0.472 0.000
#> GSM550788 2 0.1289 0.8630 0.032 0.968 0.000
#> GSM550789 2 0.0000 0.8560 0.000 1.000 0.000
#> GSM550790 1 0.3267 0.8472 0.884 0.000 0.116
#> GSM550791 1 0.1919 0.8860 0.956 0.020 0.024
#> GSM550792 1 0.2165 0.8882 0.936 0.064 0.000
#> GSM550796 2 0.0000 0.8560 0.000 1.000 0.000
#> GSM550797 2 0.0000 0.8560 0.000 1.000 0.000
#> GSM550799 2 0.4931 0.7677 0.232 0.768 0.000
#> GSM550800 2 0.1163 0.8630 0.028 0.972 0.000
#> GSM550801 2 0.0000 0.8560 0.000 1.000 0.000
#> GSM550804 2 0.1163 0.8630 0.028 0.972 0.000
#> GSM550806 1 0.1964 0.8916 0.944 0.056 0.000
#> GSM550807 2 0.1163 0.8630 0.028 0.972 0.000
#> GSM550808 2 0.0000 0.8560 0.000 1.000 0.000
#> GSM550809 1 0.0747 0.8790 0.984 0.000 0.016
#> GSM550810 2 0.0000 0.8560 0.000 1.000 0.000
#> GSM550811 1 0.2050 0.8856 0.952 0.020 0.028
#> GSM550813 2 0.5905 0.6057 0.352 0.648 0.000
#> GSM550814 2 0.4974 0.7649 0.236 0.764 0.000
#> GSM550815 2 0.0000 0.8560 0.000 1.000 0.000
#> GSM550816 2 0.0000 0.8560 0.000 1.000 0.000
#> GSM550817 2 0.0237 0.8574 0.004 0.996 0.000
#> GSM550818 2 0.1289 0.8626 0.032 0.968 0.000
#> GSM550819 2 0.5058 0.7574 0.244 0.756 0.000
#> GSM550820 1 0.3551 0.8365 0.868 0.000 0.132
#> GSM550821 2 0.1163 0.8630 0.028 0.972 0.000
#> GSM550822 2 0.0000 0.8560 0.000 1.000 0.000
#> GSM550826 1 0.3551 0.8365 0.868 0.000 0.132
#> GSM550832 2 0.1163 0.8630 0.028 0.972 0.000
#> GSM550833 2 0.0000 0.8560 0.000 1.000 0.000
#> GSM550835 2 0.4974 0.7649 0.236 0.764 0.000
#> GSM550836 3 0.0000 0.9655 0.000 0.000 1.000
#> GSM550837 2 0.0000 0.8560 0.000 1.000 0.000
#> GSM550838 1 0.0747 0.8790 0.984 0.000 0.016
#> GSM550841 2 0.0000 0.8560 0.000 1.000 0.000
#> GSM550842 2 0.0000 0.8560 0.000 1.000 0.000
#> GSM550846 1 0.2066 0.8903 0.940 0.060 0.000
#> GSM550849 1 0.1289 0.8894 0.968 0.032 0.000
#> GSM550850 1 0.2878 0.8581 0.904 0.000 0.096
#> GSM550851 2 0.0000 0.8560 0.000 1.000 0.000
#> GSM550852 2 0.6140 0.4858 0.404 0.596 0.000
#> GSM550853 2 0.0000 0.8560 0.000 1.000 0.000
#> GSM550855 2 0.1163 0.8630 0.028 0.972 0.000
#> GSM550856 2 0.5016 0.7613 0.240 0.760 0.000
#> GSM550861 2 0.1643 0.8628 0.044 0.956 0.000
#> GSM550863 1 0.2066 0.8900 0.940 0.060 0.000
#> GSM550864 2 0.5905 0.6057 0.352 0.648 0.000
#> GSM550866 2 0.5905 0.6057 0.352 0.648 0.000
#> GSM550867 3 0.0000 0.9655 0.000 0.000 1.000
#> GSM550885 3 0.0000 0.9655 0.000 0.000 1.000
#> GSM550886 2 0.4178 0.8107 0.172 0.828 0.000
#> GSM550887 2 0.0000 0.8560 0.000 1.000 0.000
#> GSM550889 1 0.3752 0.8267 0.856 0.000 0.144
#> GSM550894 2 0.0237 0.8575 0.004 0.996 0.000
#> GSM550897 1 0.2878 0.8580 0.904 0.000 0.096
#> GSM550903 2 0.1643 0.8628 0.044 0.956 0.000
#> GSM550905 2 0.2165 0.8599 0.064 0.936 0.000
#> GSM550906 2 0.1289 0.8630 0.032 0.968 0.000
#> GSM550907 2 0.3038 0.8479 0.104 0.896 0.000
#> GSM550909 2 0.0000 0.8560 0.000 1.000 0.000
#> GSM550911 1 0.5431 0.5469 0.716 0.284 0.000
#> GSM550913 2 0.0000 0.8560 0.000 1.000 0.000
#> GSM550915 1 0.2066 0.8903 0.940 0.060 0.000
#> GSM550917 2 0.5016 0.7613 0.240 0.760 0.000
#> GSM550919 1 0.1964 0.8916 0.944 0.056 0.000
#> GSM550921 3 0.0000 0.9655 0.000 0.000 1.000
#> GSM550924 1 0.1964 0.8916 0.944 0.056 0.000
#> GSM550926 2 0.5016 0.7613 0.240 0.760 0.000
#> GSM550927 2 0.0000 0.8560 0.000 1.000 0.000
#> GSM550787 1 0.1860 0.8919 0.948 0.052 0.000
#> GSM550793 1 0.6140 0.3647 0.596 0.000 0.404
#> GSM550794 1 0.5621 0.5087 0.692 0.308 0.000
#> GSM550795 1 0.3686 0.8300 0.860 0.000 0.140
#> GSM550798 3 0.0000 0.9655 0.000 0.000 1.000
#> GSM550803 3 0.0000 0.9655 0.000 0.000 1.000
#> GSM550805 1 0.1964 0.8916 0.944 0.056 0.000
#> GSM550823 1 0.1964 0.8916 0.944 0.056 0.000
#> GSM550824 3 0.0000 0.9655 0.000 0.000 1.000
#> GSM550825 3 0.0000 0.9655 0.000 0.000 1.000
#> GSM550827 1 0.2066 0.8900 0.940 0.060 0.000
#> GSM550828 1 0.3619 0.8339 0.864 0.000 0.136
#> GSM550829 3 0.0000 0.9655 0.000 0.000 1.000
#> GSM550830 1 0.1964 0.8916 0.944 0.056 0.000
#> GSM550834 1 0.1919 0.8860 0.956 0.020 0.024
#> GSM550839 2 0.3551 0.8349 0.132 0.868 0.000
#> GSM550840 1 0.1919 0.8860 0.956 0.020 0.024
#> GSM550843 2 0.5926 0.5900 0.356 0.644 0.000
#> GSM550844 1 0.3551 0.8365 0.868 0.000 0.132
#> GSM550845 2 0.5733 0.6490 0.324 0.676 0.000
#> GSM550848 1 0.3412 0.8283 0.876 0.124 0.000
#> GSM550854 3 0.0000 0.9655 0.000 0.000 1.000
#> GSM550857 3 0.0000 0.9655 0.000 0.000 1.000
#> GSM550858 3 0.4842 0.7225 0.224 0.000 0.776
#> GSM550859 3 0.0000 0.9655 0.000 0.000 1.000
#> GSM550862 3 0.4842 0.7225 0.224 0.000 0.776
#> GSM550865 1 0.1781 0.8878 0.960 0.020 0.020
#> GSM550868 1 0.2066 0.8900 0.940 0.060 0.000
#> GSM550869 1 0.1964 0.8916 0.944 0.056 0.000
#> GSM550870 2 0.5138 0.7488 0.252 0.748 0.000
#> GSM550871 1 0.5138 0.6372 0.748 0.252 0.000
#> GSM550872 1 0.2537 0.8797 0.920 0.080 0.000
#> GSM550873 2 0.6192 0.4457 0.420 0.580 0.000
#> GSM550874 2 0.5733 0.6490 0.324 0.676 0.000
#> GSM550876 1 0.2711 0.8726 0.912 0.088 0.000
#> GSM550877 2 0.5016 0.7613 0.240 0.760 0.000
#> GSM550878 1 0.2537 0.8797 0.920 0.080 0.000
#> GSM550879 1 0.2878 0.8580 0.904 0.000 0.096
#> GSM550882 1 0.3752 0.8267 0.856 0.000 0.144
#> GSM550888 3 0.0000 0.9655 0.000 0.000 1.000
#> GSM550890 1 0.2066 0.8903 0.940 0.060 0.000
#> GSM550891 3 0.0000 0.9655 0.000 0.000 1.000
#> GSM550892 1 0.3752 0.8267 0.856 0.000 0.144
#> GSM550893 2 0.4931 0.7677 0.232 0.768 0.000
#> GSM550895 1 0.2537 0.8797 0.920 0.080 0.000
#> GSM550896 2 0.0237 0.8575 0.004 0.996 0.000
#> GSM550898 3 0.0000 0.9655 0.000 0.000 1.000
#> GSM550899 2 0.5678 0.6674 0.316 0.684 0.000
#> GSM550900 1 0.2537 0.8797 0.920 0.080 0.000
#> GSM550901 1 0.1964 0.8916 0.944 0.056 0.000
#> GSM550902 1 0.2878 0.8580 0.904 0.000 0.096
#> GSM550904 3 0.4887 0.7149 0.228 0.000 0.772
#> GSM550908 3 0.0000 0.9655 0.000 0.000 1.000
#> GSM550912 2 0.6305 0.2439 0.484 0.516 0.000
#> GSM550914 1 0.1964 0.8918 0.944 0.056 0.000
#> GSM550918 2 0.5016 0.7613 0.240 0.760 0.000
#> GSM550922 2 0.1643 0.8628 0.044 0.956 0.000
#> GSM550923 3 0.0000 0.9655 0.000 0.000 1.000
#> GSM550925 1 0.3752 0.8267 0.856 0.000 0.144
#> GSM550802 2 0.3551 0.8349 0.132 0.868 0.000
#> GSM550812 2 0.3551 0.8349 0.132 0.868 0.000
#> GSM550831 1 0.2878 0.8581 0.904 0.000 0.096
#> GSM550847 3 0.0000 0.9655 0.000 0.000 1.000
#> GSM550860 1 0.2625 0.8627 0.916 0.000 0.084
#> GSM550875 1 0.2878 0.8580 0.904 0.000 0.096
#> GSM550880 1 0.1964 0.8918 0.944 0.056 0.000
#> GSM550881 1 0.4121 0.8005 0.832 0.000 0.168
#> GSM550883 3 0.0000 0.9655 0.000 0.000 1.000
#> GSM550884 1 0.2066 0.8900 0.940 0.060 0.000
#> GSM550910 2 0.3116 0.8464 0.108 0.892 0.000
#> GSM550916 1 0.3267 0.8472 0.884 0.000 0.116
#> GSM550920 1 0.2066 0.8903 0.940 0.060 0.000
cbind(get_classes(res, k = 4), get_membership(res, k = 4))
#> class entropy silhouette p1 p2 p3 p4
#> GSM550785 4 0.3400 0.7898 0.000 0.000 0.180 0.820
#> GSM550786 4 0.4916 -0.0536 0.000 0.424 0.000 0.576
#> GSM550788 2 0.1389 0.8143 0.000 0.952 0.000 0.048
#> GSM550789 2 0.0592 0.7995 0.000 0.984 0.016 0.000
#> GSM550790 4 0.4123 0.7686 0.008 0.000 0.220 0.772
#> GSM550791 4 0.2714 0.8085 0.000 0.004 0.112 0.884
#> GSM550792 4 0.0592 0.8076 0.000 0.016 0.000 0.984
#> GSM550796 2 0.0592 0.7995 0.000 0.984 0.016 0.000
#> GSM550797 2 0.0592 0.7995 0.000 0.984 0.016 0.000
#> GSM550799 2 0.4164 0.7114 0.000 0.736 0.000 0.264
#> GSM550800 2 0.1474 0.8143 0.000 0.948 0.000 0.052
#> GSM550801 2 0.0592 0.7995 0.000 0.984 0.016 0.000
#> GSM550804 2 0.1474 0.8143 0.000 0.948 0.000 0.052
#> GSM550806 4 0.0188 0.8133 0.000 0.004 0.000 0.996
#> GSM550807 2 0.1474 0.8143 0.000 0.948 0.000 0.052
#> GSM550808 2 0.0592 0.7995 0.000 0.984 0.016 0.000
#> GSM550809 4 0.2760 0.8025 0.000 0.000 0.128 0.872
#> GSM550810 2 0.0592 0.7995 0.000 0.984 0.016 0.000
#> GSM550811 4 0.2773 0.8082 0.000 0.004 0.116 0.880
#> GSM550813 2 0.4830 0.5424 0.000 0.608 0.000 0.392
#> GSM550814 2 0.4193 0.7085 0.000 0.732 0.000 0.268
#> GSM550815 2 0.0592 0.7995 0.000 0.984 0.016 0.000
#> GSM550816 2 0.0592 0.7995 0.000 0.984 0.016 0.000
#> GSM550817 2 0.0657 0.8025 0.000 0.984 0.012 0.004
#> GSM550818 2 0.1767 0.8095 0.000 0.944 0.012 0.044
#> GSM550819 2 0.4250 0.7009 0.000 0.724 0.000 0.276
#> GSM550820 4 0.4262 0.7586 0.008 0.000 0.236 0.756
#> GSM550821 2 0.1474 0.8143 0.000 0.948 0.000 0.052
#> GSM550822 2 0.0592 0.7995 0.000 0.984 0.016 0.000
#> GSM550826 4 0.4262 0.7586 0.008 0.000 0.236 0.756
#> GSM550832 2 0.1474 0.8143 0.000 0.948 0.000 0.052
#> GSM550833 2 0.0592 0.7995 0.000 0.984 0.016 0.000
#> GSM550835 2 0.4193 0.7085 0.000 0.732 0.000 0.268
#> GSM550836 1 0.0000 0.8986 1.000 0.000 0.000 0.000
#> GSM550837 2 0.0592 0.7995 0.000 0.984 0.016 0.000
#> GSM550838 4 0.2760 0.8025 0.000 0.000 0.128 0.872
#> GSM550841 2 0.0592 0.7995 0.000 0.984 0.016 0.000
#> GSM550842 2 0.0592 0.7995 0.000 0.984 0.016 0.000
#> GSM550846 4 0.0469 0.8098 0.000 0.012 0.000 0.988
#> GSM550849 4 0.1576 0.8126 0.000 0.004 0.048 0.948
#> GSM550850 4 0.3688 0.7799 0.000 0.000 0.208 0.792
#> GSM550851 2 0.0592 0.7995 0.000 0.984 0.016 0.000
#> GSM550852 2 0.4941 0.4319 0.000 0.564 0.000 0.436
#> GSM550853 2 0.0927 0.8025 0.000 0.976 0.016 0.008
#> GSM550855 2 0.1474 0.8143 0.000 0.948 0.000 0.052
#> GSM550856 2 0.4222 0.7050 0.000 0.728 0.000 0.272
#> GSM550861 2 0.1792 0.8121 0.000 0.932 0.000 0.068
#> GSM550863 4 0.0469 0.8097 0.000 0.012 0.000 0.988
#> GSM550864 2 0.4830 0.5424 0.000 0.608 0.000 0.392
#> GSM550866 2 0.4830 0.5424 0.000 0.608 0.000 0.392
#> GSM550867 1 0.0000 0.8986 1.000 0.000 0.000 0.000
#> GSM550885 1 0.0000 0.8986 1.000 0.000 0.000 0.000
#> GSM550886 2 0.3569 0.7578 0.000 0.804 0.000 0.196
#> GSM550887 2 0.0592 0.7995 0.000 0.984 0.016 0.000
#> GSM550889 4 0.4535 0.7485 0.016 0.000 0.240 0.744
#> GSM550894 2 0.1004 0.8098 0.000 0.972 0.004 0.024
#> GSM550897 4 0.3649 0.7821 0.000 0.000 0.204 0.796
#> GSM550903 2 0.1792 0.8121 0.000 0.932 0.000 0.068
#> GSM550905 2 0.2149 0.8072 0.000 0.912 0.000 0.088
#> GSM550906 2 0.1389 0.8143 0.000 0.952 0.000 0.048
#> GSM550907 2 0.2868 0.7927 0.000 0.864 0.000 0.136
#> GSM550909 2 0.0592 0.7995 0.000 0.984 0.016 0.000
#> GSM550911 3 0.4535 0.0000 0.000 0.016 0.744 0.240
#> GSM550913 2 0.0592 0.7995 0.000 0.984 0.016 0.000
#> GSM550915 4 0.0469 0.8098 0.000 0.012 0.000 0.988
#> GSM550917 2 0.4222 0.7050 0.000 0.728 0.000 0.272
#> GSM550919 4 0.0188 0.8133 0.000 0.004 0.000 0.996
#> GSM550921 1 0.0000 0.8986 1.000 0.000 0.000 0.000
#> GSM550924 4 0.0188 0.8133 0.000 0.004 0.000 0.996
#> GSM550926 2 0.4222 0.7050 0.000 0.728 0.000 0.272
#> GSM550927 2 0.0592 0.7995 0.000 0.984 0.016 0.000
#> GSM550787 4 0.0524 0.8143 0.000 0.004 0.008 0.988
#> GSM550793 4 0.7480 0.2920 0.276 0.000 0.224 0.500
#> GSM550794 4 0.4134 0.4200 0.000 0.260 0.000 0.740
#> GSM550795 4 0.4502 0.7519 0.016 0.000 0.236 0.748
#> GSM550798 1 0.0000 0.8986 1.000 0.000 0.000 0.000
#> GSM550803 1 0.0000 0.8986 1.000 0.000 0.000 0.000
#> GSM550805 4 0.0188 0.8133 0.000 0.004 0.000 0.996
#> GSM550823 4 0.0188 0.8133 0.000 0.004 0.000 0.996
#> GSM550824 1 0.0000 0.8986 1.000 0.000 0.000 0.000
#> GSM550825 1 0.2704 0.8206 0.876 0.000 0.124 0.000
#> GSM550827 4 0.0469 0.8097 0.000 0.012 0.000 0.988
#> GSM550828 4 0.4387 0.7559 0.012 0.000 0.236 0.752
#> GSM550829 1 0.2704 0.8206 0.876 0.000 0.124 0.000
#> GSM550830 4 0.0188 0.8133 0.000 0.004 0.000 0.996
#> GSM550834 4 0.2714 0.8085 0.000 0.004 0.112 0.884
#> GSM550839 2 0.3123 0.7777 0.000 0.844 0.000 0.156
#> GSM550840 4 0.2714 0.8085 0.000 0.004 0.112 0.884
#> GSM550843 2 0.4843 0.5234 0.000 0.604 0.000 0.396
#> GSM550844 4 0.4262 0.7586 0.008 0.000 0.236 0.756
#> GSM550845 2 0.4730 0.5805 0.000 0.636 0.000 0.364
#> GSM550848 4 0.1940 0.7333 0.000 0.076 0.000 0.924
#> GSM550854 1 0.0000 0.8986 1.000 0.000 0.000 0.000
#> GSM550857 1 0.0000 0.8986 1.000 0.000 0.000 0.000
#> GSM550858 1 0.6429 0.4631 0.648 0.000 0.160 0.192
#> GSM550859 1 0.0000 0.8986 1.000 0.000 0.000 0.000
#> GSM550862 1 0.6429 0.4631 0.648 0.000 0.160 0.192
#> GSM550865 4 0.2216 0.8141 0.000 0.000 0.092 0.908
#> GSM550868 4 0.0469 0.8097 0.000 0.012 0.000 0.988
#> GSM550869 4 0.0376 0.8141 0.000 0.004 0.004 0.992
#> GSM550870 2 0.4356 0.6831 0.000 0.708 0.000 0.292
#> GSM550871 4 0.3649 0.5325 0.000 0.204 0.000 0.796
#> GSM550872 4 0.0921 0.8029 0.000 0.028 0.000 0.972
#> GSM550873 2 0.4977 0.3937 0.000 0.540 0.000 0.460
#> GSM550874 2 0.4730 0.5805 0.000 0.636 0.000 0.364
#> GSM550876 4 0.1211 0.7907 0.000 0.040 0.000 0.960
#> GSM550877 2 0.4222 0.7050 0.000 0.728 0.000 0.272
#> GSM550878 4 0.1022 0.7994 0.000 0.032 0.000 0.968
#> GSM550879 4 0.3649 0.7821 0.000 0.000 0.204 0.796
#> GSM550882 4 0.4535 0.7485 0.016 0.000 0.240 0.744
#> GSM550888 1 0.0000 0.8986 1.000 0.000 0.000 0.000
#> GSM550890 4 0.0469 0.8098 0.000 0.012 0.000 0.988
#> GSM550891 1 0.2081 0.8500 0.916 0.000 0.084 0.000
#> GSM550892 4 0.4535 0.7485 0.016 0.000 0.240 0.744
#> GSM550893 2 0.4164 0.7114 0.000 0.736 0.000 0.264
#> GSM550895 4 0.1022 0.7994 0.000 0.032 0.000 0.968
#> GSM550896 2 0.1109 0.8107 0.000 0.968 0.004 0.028
#> GSM550898 1 0.0000 0.8986 1.000 0.000 0.000 0.000
#> GSM550899 2 0.4697 0.6010 0.000 0.644 0.000 0.356
#> GSM550900 4 0.1022 0.7994 0.000 0.032 0.000 0.968
#> GSM550901 4 0.0188 0.8133 0.000 0.004 0.000 0.996
#> GSM550902 4 0.3649 0.7821 0.000 0.000 0.204 0.796
#> GSM550904 1 0.6463 0.4529 0.644 0.000 0.160 0.196
#> GSM550908 1 0.0000 0.8986 1.000 0.000 0.000 0.000
#> GSM550912 4 0.4989 -0.2404 0.000 0.472 0.000 0.528
#> GSM550914 4 0.0657 0.8120 0.000 0.012 0.004 0.984
#> GSM550918 2 0.4222 0.7050 0.000 0.728 0.000 0.272
#> GSM550922 2 0.1792 0.8121 0.000 0.932 0.000 0.068
#> GSM550923 1 0.0000 0.8986 1.000 0.000 0.000 0.000
#> GSM550925 4 0.4535 0.7485 0.016 0.000 0.240 0.744
#> GSM550802 2 0.3123 0.7777 0.000 0.844 0.000 0.156
#> GSM550812 2 0.3123 0.7777 0.000 0.844 0.000 0.156
#> GSM550831 4 0.3688 0.7799 0.000 0.000 0.208 0.792
#> GSM550847 1 0.2704 0.8206 0.876 0.000 0.124 0.000
#> GSM550860 4 0.3768 0.7865 0.008 0.000 0.184 0.808
#> GSM550875 4 0.3649 0.7821 0.000 0.000 0.204 0.796
#> GSM550880 4 0.0657 0.8120 0.000 0.012 0.004 0.984
#> GSM550881 4 0.5123 0.7232 0.044 0.000 0.232 0.724
#> GSM550883 1 0.0188 0.8966 0.996 0.000 0.004 0.000
#> GSM550884 4 0.0469 0.8097 0.000 0.012 0.000 0.988
#> GSM550910 2 0.2868 0.7925 0.000 0.864 0.000 0.136
#> GSM550916 4 0.4123 0.7686 0.008 0.000 0.220 0.772
#> GSM550920 4 0.0469 0.8098 0.000 0.012 0.000 0.988
cbind(get_classes(res, k = 5), get_membership(res, k = 5))
#> class entropy silhouette p1 p2 p3 p4 p5
#> GSM550785 1 0.3452 0.84772 0.756 0.000 0.000 0.244 0.000
#> GSM550786 4 0.4201 0.00699 0.000 0.408 0.000 0.592 0.000
#> GSM550788 2 0.1478 0.84047 0.000 0.936 0.000 0.064 0.000
#> GSM550789 2 0.0000 0.82260 0.000 1.000 0.000 0.000 0.000
#> GSM550790 1 0.3048 0.85125 0.820 0.000 0.004 0.176 0.000
#> GSM550791 1 0.4659 0.52617 0.500 0.000 0.000 0.488 0.012
#> GSM550792 4 0.0324 0.88207 0.004 0.004 0.000 0.992 0.000
#> GSM550796 2 0.0000 0.82260 0.000 1.000 0.000 0.000 0.000
#> GSM550797 2 0.0000 0.82260 0.000 1.000 0.000 0.000 0.000
#> GSM550799 2 0.3684 0.74516 0.000 0.720 0.000 0.280 0.000
#> GSM550800 2 0.1544 0.84072 0.000 0.932 0.000 0.068 0.000
#> GSM550801 2 0.0000 0.82260 0.000 1.000 0.000 0.000 0.000
#> GSM550804 2 0.1544 0.84072 0.000 0.932 0.000 0.068 0.000
#> GSM550806 4 0.0798 0.87378 0.016 0.000 0.000 0.976 0.008
#> GSM550807 2 0.1544 0.84072 0.000 0.932 0.000 0.068 0.000
#> GSM550808 2 0.0000 0.82260 0.000 1.000 0.000 0.000 0.000
#> GSM550809 1 0.3942 0.82609 0.728 0.000 0.000 0.260 0.012
#> GSM550810 2 0.0000 0.82260 0.000 1.000 0.000 0.000 0.000
#> GSM550811 1 0.4658 0.53436 0.504 0.000 0.000 0.484 0.012
#> GSM550813 2 0.4201 0.56233 0.000 0.592 0.000 0.408 0.000
#> GSM550814 2 0.3707 0.74178 0.000 0.716 0.000 0.284 0.000
#> GSM550815 2 0.0000 0.82260 0.000 1.000 0.000 0.000 0.000
#> GSM550816 2 0.0000 0.82260 0.000 1.000 0.000 0.000 0.000
#> GSM550817 2 0.0290 0.82568 0.000 0.992 0.000 0.008 0.000
#> GSM550818 2 0.1197 0.83445 0.000 0.952 0.000 0.048 0.000
#> GSM550819 2 0.3752 0.73475 0.000 0.708 0.000 0.292 0.000
#> GSM550820 1 0.2690 0.84604 0.844 0.000 0.000 0.156 0.000
#> GSM550821 2 0.1544 0.84072 0.000 0.932 0.000 0.068 0.000
#> GSM550822 2 0.0000 0.82260 0.000 1.000 0.000 0.000 0.000
#> GSM550826 1 0.2732 0.84819 0.840 0.000 0.000 0.160 0.000
#> GSM550832 2 0.1544 0.84072 0.000 0.932 0.000 0.068 0.000
#> GSM550833 2 0.0000 0.82260 0.000 1.000 0.000 0.000 0.000
#> GSM550835 2 0.3707 0.74178 0.000 0.716 0.000 0.284 0.000
#> GSM550836 3 0.0000 0.85792 0.000 0.000 1.000 0.000 0.000
#> GSM550837 2 0.0000 0.82260 0.000 1.000 0.000 0.000 0.000
#> GSM550838 1 0.3942 0.82609 0.728 0.000 0.000 0.260 0.012
#> GSM550841 2 0.0000 0.82260 0.000 1.000 0.000 0.000 0.000
#> GSM550842 2 0.0000 0.82260 0.000 1.000 0.000 0.000 0.000
#> GSM550846 4 0.0162 0.88231 0.004 0.000 0.000 0.996 0.000
#> GSM550849 4 0.4401 0.04343 0.328 0.000 0.000 0.656 0.016
#> GSM550850 1 0.3333 0.85437 0.788 0.000 0.000 0.208 0.004
#> GSM550851 2 0.0000 0.82260 0.000 1.000 0.000 0.000 0.000
#> GSM550852 2 0.4278 0.44448 0.000 0.548 0.000 0.452 0.000
#> GSM550853 2 0.0290 0.82595 0.000 0.992 0.000 0.008 0.000
#> GSM550855 2 0.1544 0.84072 0.000 0.932 0.000 0.068 0.000
#> GSM550856 2 0.3730 0.73832 0.000 0.712 0.000 0.288 0.000
#> GSM550861 2 0.1792 0.84004 0.000 0.916 0.000 0.084 0.000
#> GSM550863 4 0.0162 0.88258 0.004 0.000 0.000 0.996 0.000
#> GSM550864 2 0.4201 0.56233 0.000 0.592 0.000 0.408 0.000
#> GSM550866 2 0.4201 0.56233 0.000 0.592 0.000 0.408 0.000
#> GSM550867 3 0.0000 0.85792 0.000 0.000 1.000 0.000 0.000
#> GSM550885 3 0.0000 0.85792 0.000 0.000 1.000 0.000 0.000
#> GSM550886 2 0.3210 0.79339 0.000 0.788 0.000 0.212 0.000
#> GSM550887 2 0.0000 0.82260 0.000 1.000 0.000 0.000 0.000
#> GSM550889 1 0.2763 0.84020 0.848 0.000 0.004 0.148 0.000
#> GSM550894 2 0.0963 0.83447 0.000 0.964 0.000 0.036 0.000
#> GSM550897 1 0.3635 0.84486 0.748 0.000 0.000 0.248 0.004
#> GSM550903 2 0.1792 0.84004 0.000 0.916 0.000 0.084 0.000
#> GSM550905 2 0.2074 0.83689 0.000 0.896 0.000 0.104 0.000
#> GSM550906 2 0.1478 0.84047 0.000 0.936 0.000 0.064 0.000
#> GSM550907 2 0.2648 0.82592 0.000 0.848 0.000 0.152 0.000
#> GSM550909 2 0.0000 0.82260 0.000 1.000 0.000 0.000 0.000
#> GSM550911 5 0.0162 0.00000 0.000 0.000 0.000 0.004 0.996
#> GSM550913 2 0.0000 0.82260 0.000 1.000 0.000 0.000 0.000
#> GSM550915 4 0.0162 0.88231 0.004 0.000 0.000 0.996 0.000
#> GSM550917 2 0.3730 0.73832 0.000 0.712 0.000 0.288 0.000
#> GSM550919 4 0.0798 0.87378 0.016 0.000 0.000 0.976 0.008
#> GSM550921 3 0.0000 0.85792 0.000 0.000 1.000 0.000 0.000
#> GSM550924 4 0.0798 0.87378 0.016 0.000 0.000 0.976 0.008
#> GSM550926 2 0.3730 0.73832 0.000 0.712 0.000 0.288 0.000
#> GSM550927 2 0.0000 0.82260 0.000 1.000 0.000 0.000 0.000
#> GSM550787 4 0.1670 0.82453 0.052 0.000 0.000 0.936 0.012
#> GSM550793 1 0.3914 0.48944 0.788 0.000 0.164 0.048 0.000
#> GSM550794 4 0.3452 0.54351 0.000 0.244 0.000 0.756 0.000
#> GSM550795 1 0.2806 0.84326 0.844 0.000 0.004 0.152 0.000
#> GSM550798 3 0.0000 0.85792 0.000 0.000 1.000 0.000 0.000
#> GSM550803 3 0.0000 0.85792 0.000 0.000 1.000 0.000 0.000
#> GSM550805 4 0.0798 0.87378 0.016 0.000 0.000 0.976 0.008
#> GSM550823 4 0.0798 0.87378 0.016 0.000 0.000 0.976 0.008
#> GSM550824 3 0.0000 0.85792 0.000 0.000 1.000 0.000 0.000
#> GSM550825 3 0.3561 0.70176 0.260 0.000 0.740 0.000 0.000
#> GSM550827 4 0.0162 0.88258 0.004 0.000 0.000 0.996 0.000
#> GSM550828 1 0.2848 0.84585 0.840 0.000 0.004 0.156 0.000
#> GSM550829 3 0.3561 0.70176 0.260 0.000 0.740 0.000 0.000
#> GSM550830 4 0.0798 0.87378 0.016 0.000 0.000 0.976 0.008
#> GSM550834 1 0.4659 0.52617 0.500 0.000 0.000 0.488 0.012
#> GSM550839 2 0.2852 0.81345 0.000 0.828 0.000 0.172 0.000
#> GSM550840 1 0.4656 0.54276 0.508 0.000 0.000 0.480 0.012
#> GSM550843 2 0.4210 0.54920 0.000 0.588 0.000 0.412 0.000
#> GSM550844 1 0.2732 0.84819 0.840 0.000 0.000 0.160 0.000
#> GSM550845 2 0.4126 0.61239 0.000 0.620 0.000 0.380 0.000
#> GSM550848 4 0.1638 0.82316 0.004 0.064 0.000 0.932 0.000
#> GSM550854 3 0.0000 0.85792 0.000 0.000 1.000 0.000 0.000
#> GSM550857 3 0.0000 0.85792 0.000 0.000 1.000 0.000 0.000
#> GSM550858 3 0.4821 0.40442 0.464 0.000 0.516 0.020 0.000
#> GSM550859 3 0.0000 0.85792 0.000 0.000 1.000 0.000 0.000
#> GSM550862 3 0.4821 0.40442 0.464 0.000 0.516 0.020 0.000
#> GSM550865 1 0.4648 0.52192 0.524 0.000 0.000 0.464 0.012
#> GSM550868 4 0.0162 0.88258 0.004 0.000 0.000 0.996 0.000
#> GSM550869 4 0.1484 0.84084 0.048 0.000 0.000 0.944 0.008
#> GSM550870 2 0.3837 0.71631 0.000 0.692 0.000 0.308 0.000
#> GSM550871 4 0.3003 0.64936 0.000 0.188 0.000 0.812 0.000
#> GSM550872 4 0.0960 0.87734 0.004 0.016 0.000 0.972 0.008
#> GSM550873 2 0.4300 0.38877 0.000 0.524 0.000 0.476 0.000
#> GSM550874 2 0.4126 0.61239 0.000 0.620 0.000 0.380 0.000
#> GSM550876 4 0.0703 0.86737 0.000 0.024 0.000 0.976 0.000
#> GSM550877 2 0.3730 0.73832 0.000 0.712 0.000 0.288 0.000
#> GSM550878 4 0.0510 0.87435 0.000 0.016 0.000 0.984 0.000
#> GSM550879 1 0.3635 0.84486 0.748 0.000 0.000 0.248 0.004
#> GSM550882 1 0.2763 0.84020 0.848 0.000 0.004 0.148 0.000
#> GSM550888 3 0.0000 0.85792 0.000 0.000 1.000 0.000 0.000
#> GSM550890 4 0.0162 0.88231 0.004 0.000 0.000 0.996 0.000
#> GSM550891 3 0.3452 0.71718 0.244 0.000 0.756 0.000 0.000
#> GSM550892 1 0.2763 0.84020 0.848 0.000 0.004 0.148 0.000
#> GSM550893 2 0.3684 0.74516 0.000 0.720 0.000 0.280 0.000
#> GSM550895 4 0.0510 0.87435 0.000 0.016 0.000 0.984 0.000
#> GSM550896 2 0.1043 0.83556 0.000 0.960 0.000 0.040 0.000
#> GSM550898 3 0.0000 0.85792 0.000 0.000 1.000 0.000 0.000
#> GSM550899 2 0.4101 0.62703 0.000 0.628 0.000 0.372 0.000
#> GSM550900 4 0.0510 0.87435 0.000 0.016 0.000 0.984 0.000
#> GSM550901 4 0.0798 0.87378 0.016 0.000 0.000 0.976 0.008
#> GSM550902 1 0.3635 0.84486 0.748 0.000 0.000 0.248 0.004
#> GSM550904 3 0.4897 0.39946 0.460 0.000 0.516 0.024 0.000
#> GSM550908 3 0.0000 0.85792 0.000 0.000 1.000 0.000 0.000
#> GSM550912 4 0.4283 -0.19238 0.000 0.456 0.000 0.544 0.000
#> GSM550914 4 0.0324 0.88115 0.004 0.000 0.000 0.992 0.004
#> GSM550918 2 0.3730 0.73832 0.000 0.712 0.000 0.288 0.000
#> GSM550922 2 0.1792 0.84004 0.000 0.916 0.000 0.084 0.000
#> GSM550923 3 0.0000 0.85792 0.000 0.000 1.000 0.000 0.000
#> GSM550925 1 0.2763 0.84020 0.848 0.000 0.004 0.148 0.000
#> GSM550802 2 0.2852 0.81345 0.000 0.828 0.000 0.172 0.000
#> GSM550812 2 0.2852 0.81345 0.000 0.828 0.000 0.172 0.000
#> GSM550831 1 0.3333 0.85437 0.788 0.000 0.000 0.208 0.004
#> GSM550847 3 0.3561 0.70176 0.260 0.000 0.740 0.000 0.000
#> GSM550860 1 0.3635 0.84703 0.748 0.000 0.004 0.248 0.000
#> GSM550875 1 0.3635 0.84486 0.748 0.000 0.000 0.248 0.004
#> GSM550880 4 0.0324 0.88115 0.004 0.000 0.000 0.992 0.004
#> GSM550881 1 0.3495 0.82602 0.816 0.000 0.032 0.152 0.000
#> GSM550883 3 0.0510 0.85076 0.016 0.000 0.984 0.000 0.000
#> GSM550884 4 0.0162 0.88258 0.004 0.000 0.000 0.996 0.000
#> GSM550910 2 0.2648 0.82583 0.000 0.848 0.000 0.152 0.000
#> GSM550916 1 0.3048 0.85125 0.820 0.000 0.004 0.176 0.000
#> GSM550920 4 0.0162 0.88231 0.004 0.000 0.000 0.996 0.000
cbind(get_classes(res, k = 6), get_membership(res, k = 6))
#> class entropy silhouette p1 p2 p3 p4 p5 p6
#> GSM550785 6 0.1584 0.8161 0.000 0.000 0.008 0.064 0 0.928
#> GSM550786 4 0.3774 0.0414 0.000 0.408 0.000 0.592 0 0.000
#> GSM550788 2 0.1327 0.8413 0.000 0.936 0.000 0.064 0 0.000
#> GSM550789 2 0.0000 0.8234 0.000 1.000 0.000 0.000 0 0.000
#> GSM550790 6 0.0363 0.8195 0.000 0.000 0.012 0.000 0 0.988
#> GSM550791 6 0.4118 0.5095 0.000 0.000 0.020 0.352 0 0.628
#> GSM550792 4 0.0291 0.8779 0.000 0.004 0.000 0.992 0 0.004
#> GSM550796 2 0.0000 0.8234 0.000 1.000 0.000 0.000 0 0.000
#> GSM550797 2 0.0000 0.8234 0.000 1.000 0.000 0.000 0 0.000
#> GSM550799 2 0.3309 0.7400 0.000 0.720 0.000 0.280 0 0.000
#> GSM550800 2 0.1387 0.8415 0.000 0.932 0.000 0.068 0 0.000
#> GSM550801 2 0.0000 0.8234 0.000 1.000 0.000 0.000 0 0.000
#> GSM550804 2 0.1387 0.8415 0.000 0.932 0.000 0.068 0 0.000
#> GSM550806 4 0.0820 0.8691 0.000 0.000 0.012 0.972 0 0.016
#> GSM550807 2 0.1387 0.8415 0.000 0.932 0.000 0.068 0 0.000
#> GSM550808 2 0.0000 0.8234 0.000 1.000 0.000 0.000 0 0.000
#> GSM550809 6 0.2001 0.7989 0.000 0.000 0.048 0.040 0 0.912
#> GSM550810 2 0.0000 0.8234 0.000 1.000 0.000 0.000 0 0.000
#> GSM550811 6 0.4039 0.5111 0.000 0.000 0.016 0.352 0 0.632
#> GSM550813 2 0.3774 0.5543 0.000 0.592 0.000 0.408 0 0.000
#> GSM550814 2 0.3330 0.7370 0.000 0.716 0.000 0.284 0 0.000
#> GSM550815 2 0.0000 0.8234 0.000 1.000 0.000 0.000 0 0.000
#> GSM550816 2 0.0000 0.8234 0.000 1.000 0.000 0.000 0 0.000
#> GSM550817 2 0.0260 0.8265 0.000 0.992 0.000 0.008 0 0.000
#> GSM550818 2 0.1075 0.8353 0.000 0.952 0.000 0.048 0 0.000
#> GSM550819 2 0.3371 0.7298 0.000 0.708 0.000 0.292 0 0.000
#> GSM550820 6 0.0713 0.8191 0.000 0.000 0.028 0.000 0 0.972
#> GSM550821 2 0.1387 0.8415 0.000 0.932 0.000 0.068 0 0.000
#> GSM550822 2 0.0000 0.8234 0.000 1.000 0.000 0.000 0 0.000
#> GSM550826 6 0.0858 0.8214 0.000 0.000 0.028 0.004 0 0.968
#> GSM550832 2 0.1387 0.8415 0.000 0.932 0.000 0.068 0 0.000
#> GSM550833 2 0.0000 0.8234 0.000 1.000 0.000 0.000 0 0.000
#> GSM550835 2 0.3330 0.7370 0.000 0.716 0.000 0.284 0 0.000
#> GSM550836 1 0.0000 0.9907 1.000 0.000 0.000 0.000 0 0.000
#> GSM550837 2 0.0000 0.8234 0.000 1.000 0.000 0.000 0 0.000
#> GSM550838 6 0.2001 0.7989 0.000 0.000 0.048 0.040 0 0.912
#> GSM550841 2 0.0000 0.8234 0.000 1.000 0.000 0.000 0 0.000
#> GSM550842 2 0.0000 0.8234 0.000 1.000 0.000 0.000 0 0.000
#> GSM550846 4 0.0508 0.8758 0.000 0.000 0.012 0.984 0 0.004
#> GSM550849 4 0.4751 -0.1420 0.000 0.000 0.048 0.500 0 0.452
#> GSM550850 6 0.0806 0.8241 0.000 0.000 0.008 0.020 0 0.972
#> GSM550851 2 0.0000 0.8234 0.000 1.000 0.000 0.000 0 0.000
#> GSM550852 2 0.3843 0.4290 0.000 0.548 0.000 0.452 0 0.000
#> GSM550853 2 0.0260 0.8267 0.000 0.992 0.000 0.008 0 0.000
#> GSM550855 2 0.1387 0.8415 0.000 0.932 0.000 0.068 0 0.000
#> GSM550856 2 0.3351 0.7334 0.000 0.712 0.000 0.288 0 0.000
#> GSM550861 2 0.1610 0.8409 0.000 0.916 0.000 0.084 0 0.000
#> GSM550863 4 0.0146 0.8777 0.000 0.000 0.000 0.996 0 0.004
#> GSM550864 2 0.3774 0.5543 0.000 0.592 0.000 0.408 0 0.000
#> GSM550866 2 0.3774 0.5543 0.000 0.592 0.000 0.408 0 0.000
#> GSM550867 1 0.0000 0.9907 1.000 0.000 0.000 0.000 0 0.000
#> GSM550885 1 0.0000 0.9907 1.000 0.000 0.000 0.000 0 0.000
#> GSM550886 2 0.2883 0.7899 0.000 0.788 0.000 0.212 0 0.000
#> GSM550887 2 0.0000 0.8234 0.000 1.000 0.000 0.000 0 0.000
#> GSM550889 6 0.0937 0.8163 0.000 0.000 0.040 0.000 0 0.960
#> GSM550894 2 0.0865 0.8353 0.000 0.964 0.000 0.036 0 0.000
#> GSM550897 6 0.2412 0.8054 0.000 0.000 0.028 0.092 0 0.880
#> GSM550903 2 0.1610 0.8409 0.000 0.916 0.000 0.084 0 0.000
#> GSM550905 2 0.1863 0.8377 0.000 0.896 0.000 0.104 0 0.000
#> GSM550906 2 0.1327 0.8413 0.000 0.936 0.000 0.064 0 0.000
#> GSM550907 2 0.2378 0.8258 0.000 0.848 0.000 0.152 0 0.000
#> GSM550909 2 0.0000 0.8234 0.000 1.000 0.000 0.000 0 0.000
#> GSM550911 5 0.0000 0.0000 0.000 0.000 0.000 0.000 1 0.000
#> GSM550913 2 0.0000 0.8234 0.000 1.000 0.000 0.000 0 0.000
#> GSM550915 4 0.0508 0.8758 0.000 0.000 0.012 0.984 0 0.004
#> GSM550917 2 0.3351 0.7334 0.000 0.712 0.000 0.288 0 0.000
#> GSM550919 4 0.0820 0.8691 0.000 0.000 0.012 0.972 0 0.016
#> GSM550921 1 0.0000 0.9907 1.000 0.000 0.000 0.000 0 0.000
#> GSM550924 4 0.0820 0.8691 0.000 0.000 0.012 0.972 0 0.016
#> GSM550926 2 0.3351 0.7334 0.000 0.712 0.000 0.288 0 0.000
#> GSM550927 2 0.0000 0.8234 0.000 1.000 0.000 0.000 0 0.000
#> GSM550787 4 0.2358 0.7747 0.000 0.000 0.016 0.876 0 0.108
#> GSM550793 6 0.3690 0.4250 0.012 0.000 0.288 0.000 0 0.700
#> GSM550794 4 0.3101 0.5583 0.000 0.244 0.000 0.756 0 0.000
#> GSM550795 6 0.0865 0.8171 0.000 0.000 0.036 0.000 0 0.964
#> GSM550798 1 0.0000 0.9907 1.000 0.000 0.000 0.000 0 0.000
#> GSM550803 1 0.0000 0.9907 1.000 0.000 0.000 0.000 0 0.000
#> GSM550805 4 0.0820 0.8691 0.000 0.000 0.012 0.972 0 0.016
#> GSM550823 4 0.0820 0.8691 0.000 0.000 0.012 0.972 0 0.016
#> GSM550824 1 0.0000 0.9907 1.000 0.000 0.000 0.000 0 0.000
#> GSM550825 3 0.5254 0.6388 0.392 0.000 0.508 0.000 0 0.100
#> GSM550827 4 0.0146 0.8777 0.000 0.000 0.000 0.996 0 0.004
#> GSM550828 6 0.0790 0.8185 0.000 0.000 0.032 0.000 0 0.968
#> GSM550829 3 0.5254 0.6388 0.392 0.000 0.508 0.000 0 0.100
#> GSM550830 4 0.0820 0.8691 0.000 0.000 0.012 0.972 0 0.016
#> GSM550834 6 0.4118 0.5095 0.000 0.000 0.020 0.352 0 0.628
#> GSM550839 2 0.2562 0.8124 0.000 0.828 0.000 0.172 0 0.000
#> GSM550840 6 0.4092 0.5192 0.000 0.000 0.020 0.344 0 0.636
#> GSM550843 2 0.3782 0.5401 0.000 0.588 0.000 0.412 0 0.000
#> GSM550844 6 0.0858 0.8214 0.000 0.000 0.028 0.004 0 0.968
#> GSM550845 2 0.3706 0.6043 0.000 0.620 0.000 0.380 0 0.000
#> GSM550848 4 0.1471 0.8216 0.000 0.064 0.000 0.932 0 0.004
#> GSM550854 1 0.0000 0.9907 1.000 0.000 0.000 0.000 0 0.000
#> GSM550857 1 0.0000 0.9907 1.000 0.000 0.000 0.000 0 0.000
#> GSM550858 3 0.5711 0.6615 0.180 0.000 0.492 0.000 0 0.328
#> GSM550859 1 0.0000 0.9907 1.000 0.000 0.000 0.000 0 0.000
#> GSM550862 3 0.5711 0.6615 0.180 0.000 0.492 0.000 0 0.328
#> GSM550865 6 0.3835 0.5319 0.000 0.000 0.016 0.300 0 0.684
#> GSM550868 4 0.0146 0.8777 0.000 0.000 0.000 0.996 0 0.004
#> GSM550869 4 0.1625 0.8309 0.000 0.000 0.012 0.928 0 0.060
#> GSM550870 2 0.3446 0.7109 0.000 0.692 0.000 0.308 0 0.000
#> GSM550871 4 0.2697 0.6635 0.000 0.188 0.000 0.812 0 0.000
#> GSM550872 4 0.0862 0.8750 0.000 0.016 0.008 0.972 0 0.004
#> GSM550873 2 0.3862 0.3716 0.000 0.524 0.000 0.476 0 0.000
#> GSM550874 2 0.3706 0.6043 0.000 0.620 0.000 0.380 0 0.000
#> GSM550876 4 0.0632 0.8651 0.000 0.024 0.000 0.976 0 0.000
#> GSM550877 2 0.3351 0.7334 0.000 0.712 0.000 0.288 0 0.000
#> GSM550878 4 0.0458 0.8715 0.000 0.016 0.000 0.984 0 0.000
#> GSM550879 6 0.2412 0.8054 0.000 0.000 0.028 0.092 0 0.880
#> GSM550882 6 0.0937 0.8163 0.000 0.000 0.040 0.000 0 0.960
#> GSM550888 1 0.0000 0.9907 1.000 0.000 0.000 0.000 0 0.000
#> GSM550890 4 0.0508 0.8758 0.000 0.000 0.012 0.984 0 0.004
#> GSM550891 3 0.1564 0.1180 0.024 0.000 0.936 0.000 0 0.040
#> GSM550892 6 0.0937 0.8163 0.000 0.000 0.040 0.000 0 0.960
#> GSM550893 2 0.3309 0.7400 0.000 0.720 0.000 0.280 0 0.000
#> GSM550895 4 0.0458 0.8715 0.000 0.016 0.000 0.984 0 0.000
#> GSM550896 2 0.0937 0.8363 0.000 0.960 0.000 0.040 0 0.000
#> GSM550898 1 0.0000 0.9907 1.000 0.000 0.000 0.000 0 0.000
#> GSM550899 2 0.3684 0.6209 0.000 0.628 0.000 0.372 0 0.000
#> GSM550900 4 0.0458 0.8715 0.000 0.016 0.000 0.984 0 0.000
#> GSM550901 4 0.0820 0.8691 0.000 0.000 0.012 0.972 0 0.016
#> GSM550902 6 0.2412 0.8054 0.000 0.000 0.028 0.092 0 0.880
#> GSM550904 3 0.5720 0.6533 0.180 0.000 0.488 0.000 0 0.332
#> GSM550908 1 0.0000 0.9907 1.000 0.000 0.000 0.000 0 0.000
#> GSM550912 4 0.3847 -0.1898 0.000 0.456 0.000 0.544 0 0.000
#> GSM550914 4 0.0603 0.8747 0.000 0.000 0.016 0.980 0 0.004
#> GSM550918 2 0.3351 0.7334 0.000 0.712 0.000 0.288 0 0.000
#> GSM550922 2 0.1610 0.8409 0.000 0.916 0.000 0.084 0 0.000
#> GSM550923 1 0.0000 0.9907 1.000 0.000 0.000 0.000 0 0.000
#> GSM550925 6 0.0937 0.8163 0.000 0.000 0.040 0.000 0 0.960
#> GSM550802 2 0.2562 0.8124 0.000 0.828 0.000 0.172 0 0.000
#> GSM550812 2 0.2562 0.8124 0.000 0.828 0.000 0.172 0 0.000
#> GSM550831 6 0.0806 0.8241 0.000 0.000 0.008 0.020 0 0.972
#> GSM550847 3 0.5254 0.6388 0.392 0.000 0.508 0.000 0 0.100
#> GSM550860 6 0.1858 0.8126 0.000 0.000 0.012 0.076 0 0.912
#> GSM550875 6 0.2412 0.8054 0.000 0.000 0.028 0.092 0 0.880
#> GSM550880 4 0.0603 0.8747 0.000 0.000 0.016 0.980 0 0.004
#> GSM550881 6 0.1327 0.7970 0.000 0.000 0.064 0.000 0 0.936
#> GSM550883 1 0.1858 0.8534 0.904 0.000 0.092 0.000 0 0.004
#> GSM550884 4 0.0146 0.8777 0.000 0.000 0.000 0.996 0 0.004
#> GSM550910 2 0.2378 0.8258 0.000 0.848 0.000 0.152 0 0.000
#> GSM550916 6 0.0363 0.8195 0.000 0.000 0.012 0.000 0 0.988
#> GSM550920 4 0.0508 0.8758 0.000 0.000 0.012 0.984 0 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)
get_signatures(res, k = 3)
get_signatures(res, k = 4)
get_signatures(res, k = 5)
get_signatures(res, k = 6)
Signature heatmaps where rows are not scaled:
get_signatures(res, k = 2, scale_rows = FALSE)
get_signatures(res, k = 3, scale_rows = FALSE)
get_signatures(res, k = 4, scale_rows = FALSE)
get_signatures(res, k = 5, scale_rows = FALSE)
get_signatures(res, k = 6, scale_rows = FALSE)
Compare the overlap of signatures from different k:
compare_signatures(res)
get_signature() returns a data frame invisibly. TO get the list of signatures, the function
call should be assigned to a variable explicitly. In following code, if plot argument is set
to FALSE, no heatmap is plotted while only the differential analysis is performed.
# code only for demonstration
tb = get_signature(res, k = ..., plot = FALSE)
An example of the output of tb is:
#> which_row fdr mean_1 mean_2 scaled_mean_1 scaled_mean_2 km
#> 1 38 0.042760348 8.373488 9.131774 -0.5533452 0.5164555 1
#> 2 40 0.018707592 7.106213 8.469186 -0.6173731 0.5762149 1
#> 3 55 0.019134737 10.221463 11.207825 -0.6159697 0.5749050 1
#> 4 59 0.006059896 5.921854 7.869574 -0.6899429 0.6439467 1
#> 5 60 0.018055526 8.928898 10.211722 -0.6204761 0.5791110 1
#> 6 98 0.009384629 15.714769 14.887706 0.6635654 -0.6193277 2
...
The columns in tb are:
which_row: row indices corresponding to the input matrix.fdr: FDR for the differential test. mean_x: The mean value in group x.scaled_mean_x: The mean value in group x after rows are scaled.km: Row groups if k-means clustering is applied to rows.UMAP plot which shows how samples are separated.
dimension_reduction(res, k = 2, method = "UMAP")
dimension_reduction(res, k = 3, method = "UMAP")
dimension_reduction(res, k = 4, method = "UMAP")
dimension_reduction(res, k = 5, method = "UMAP")
dimension_reduction(res, k = 6, method = "UMAP")
Following heatmap shows how subgroups are split when increasing k:
collect_classes(res)
Test correlation between subgroups and known annotations. If the known annotation is numeric, one-way ANOVA test is applied, and if the known annotation is discrete, chi-squared contingency table test is applied.
test_to_known_factors(res)
#> n disease.state(p) k
#> ATC:hclust 142 2.81e-03 2
#> ATC:hclust 138 2.21e-06 3
#> ATC:hclust 133 9.04e-06 4
#> ATC:hclust 133 8.78e-06 5
#> ATC:hclust 135 1.23e-05 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 51776 rows and 143 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 4.
#>
#> Following methods can be applied to this 'ConsensusPartition' object:
#> [1] "cola_report" "collect_classes" "collect_plots"
#> [4] "collect_stats" "colnames" "compare_signatures"
#> [7] "consensus_heatmap" "dimension_reduction" "functional_enrichment"
#> [10] "get_anno_col" "get_anno" "get_classes"
#> [13] "get_consensus" "get_matrix" "get_membership"
#> [16] "get_param" "get_signatures" "get_stats"
#> [19] "is_best_k" "is_stable_k" "membership_heatmap"
#> [22] "ncol" "nrow" "plot_ecdf"
#> [25] "rownames" "select_partition_number" "show"
#> [28] "suggest_best_k" "test_to_known_factors"
collect_plots() function collects all the plots made from res for all k (number of partitions)
into one single page to provide an easy and fast comparison between different k.
collect_plots(res)
The plots are:
k and the heatmap of
predicted classes for each k.k.k.k.All the plots in panels can be made by individual functions and they are plotted later in this section.
select_partition_number() produces several plots showing different
statistics for choosing “optimized” k. There are following statistics:
k;k, the area increased is defined as \(A_k - A_{k-1}\).The detailed explanations of these statistics can be found in the cola vignette.
Generally speaking, lower PAC score, higher mean silhouette score or higher
concordance corresponds to better partition. Rand index and Jaccard index
measure how similar the current partition is compared to partition with k-1.
If they are too similar, we won't accept k is better than k-1.
select_partition_number(res)
The numeric values for all these statistics can be obtained by get_stats().
get_stats(res)
#> k 1-PAC mean_silhouette concordance area_increased Rand Jaccard
#> 2 2 1.000 0.964 0.987 0.4452 0.561 0.561
#> 3 3 0.745 0.906 0.947 0.3991 0.679 0.492
#> 4 4 1.000 0.950 0.969 0.1436 0.725 0.414
#> 5 5 0.784 0.806 0.835 0.0748 0.853 0.540
#> 6 6 0.758 0.753 0.857 0.0417 0.984 0.927
suggest_best_k() suggests the best \(k\) based on these statistics. The rules are as follows:
suggest_best_k(res)
#> [1] 4
#> attr(,"optional")
#> [1] 2
There is also optional best \(k\) = 2 that is worth to check.
Following shows the table of the partitions (You need to click the show/hide
code output link to see it). The membership matrix (columns with name p*)
is inferred by
clue::cl_consensus()
function with the SE method. Basically the value in the membership matrix
represents the probability to belong to a certain group. The finall class
label for an item is determined with the group with highest probability it
belongs to.
In get_classes() function, the entropy is calculated from the membership
matrix and the silhouette score is calculated from the consensus matrix.
cbind(get_classes(res, k = 2), get_membership(res, k = 2))
#> class entropy silhouette p1 p2
#> GSM550785 1 0.000 0.991 1.000 0.000
#> GSM550786 2 0.000 0.984 0.000 1.000
#> GSM550788 2 0.000 0.984 0.000 1.000
#> GSM550789 2 0.000 0.984 0.000 1.000
#> GSM550790 1 0.000 0.991 1.000 0.000
#> GSM550791 1 0.971 0.312 0.600 0.400
#> GSM550792 2 0.000 0.984 0.000 1.000
#> GSM550796 2 0.000 0.984 0.000 1.000
#> GSM550797 2 0.000 0.984 0.000 1.000
#> GSM550799 2 0.000 0.984 0.000 1.000
#> GSM550800 2 0.000 0.984 0.000 1.000
#> GSM550801 2 0.000 0.984 0.000 1.000
#> GSM550804 2 0.000 0.984 0.000 1.000
#> GSM550806 2 0.000 0.984 0.000 1.000
#> GSM550807 2 0.000 0.984 0.000 1.000
#> GSM550808 2 0.000 0.984 0.000 1.000
#> GSM550809 1 0.000 0.991 1.000 0.000
#> GSM550810 2 0.000 0.984 0.000 1.000
#> GSM550811 2 0.961 0.378 0.384 0.616
#> GSM550813 2 0.000 0.984 0.000 1.000
#> GSM550814 2 0.000 0.984 0.000 1.000
#> GSM550815 2 0.000 0.984 0.000 1.000
#> GSM550816 2 0.000 0.984 0.000 1.000
#> GSM550817 2 0.000 0.984 0.000 1.000
#> GSM550818 2 0.000 0.984 0.000 1.000
#> GSM550819 2 0.000 0.984 0.000 1.000
#> GSM550820 1 0.000 0.991 1.000 0.000
#> GSM550821 2 0.000 0.984 0.000 1.000
#> GSM550822 2 0.000 0.984 0.000 1.000
#> GSM550826 1 0.000 0.991 1.000 0.000
#> GSM550832 2 0.000 0.984 0.000 1.000
#> GSM550833 2 0.000 0.984 0.000 1.000
#> GSM550835 2 0.000 0.984 0.000 1.000
#> GSM550836 1 0.000 0.991 1.000 0.000
#> GSM550837 2 0.000 0.984 0.000 1.000
#> GSM550838 1 0.000 0.991 1.000 0.000
#> GSM550841 2 0.000 0.984 0.000 1.000
#> GSM550842 2 0.000 0.984 0.000 1.000
#> GSM550846 2 0.000 0.984 0.000 1.000
#> GSM550849 2 0.000 0.984 0.000 1.000
#> GSM550850 1 0.000 0.991 1.000 0.000
#> GSM550851 2 0.000 0.984 0.000 1.000
#> GSM550852 2 0.000 0.984 0.000 1.000
#> GSM550853 2 0.000 0.984 0.000 1.000
#> GSM550855 2 0.000 0.984 0.000 1.000
#> GSM550856 2 0.000 0.984 0.000 1.000
#> GSM550861 2 0.000 0.984 0.000 1.000
#> GSM550863 2 0.000 0.984 0.000 1.000
#> GSM550864 2 0.000 0.984 0.000 1.000
#> GSM550866 2 0.000 0.984 0.000 1.000
#> GSM550867 1 0.000 0.991 1.000 0.000
#> GSM550885 1 0.000 0.991 1.000 0.000
#> GSM550886 2 0.000 0.984 0.000 1.000
#> GSM550887 2 0.000 0.984 0.000 1.000
#> GSM550889 1 0.000 0.991 1.000 0.000
#> GSM550894 2 0.000 0.984 0.000 1.000
#> GSM550897 1 0.000 0.991 1.000 0.000
#> GSM550903 2 0.000 0.984 0.000 1.000
#> GSM550905 2 0.000 0.984 0.000 1.000
#> GSM550906 2 0.000 0.984 0.000 1.000
#> GSM550907 2 0.000 0.984 0.000 1.000
#> GSM550909 2 0.000 0.984 0.000 1.000
#> GSM550911 2 0.000 0.984 0.000 1.000
#> GSM550913 2 0.000 0.984 0.000 1.000
#> GSM550915 2 0.000 0.984 0.000 1.000
#> GSM550917 2 0.000 0.984 0.000 1.000
#> GSM550919 2 0.000 0.984 0.000 1.000
#> GSM550921 1 0.000 0.991 1.000 0.000
#> GSM550924 2 0.000 0.984 0.000 1.000
#> GSM550926 2 0.000 0.984 0.000 1.000
#> GSM550927 2 0.000 0.984 0.000 1.000
#> GSM550787 2 0.000 0.984 0.000 1.000
#> GSM550793 1 0.000 0.991 1.000 0.000
#> GSM550794 2 0.000 0.984 0.000 1.000
#> GSM550795 1 0.000 0.991 1.000 0.000
#> GSM550798 1 0.000 0.991 1.000 0.000
#> GSM550803 1 0.000 0.991 1.000 0.000
#> GSM550805 2 0.000 0.984 0.000 1.000
#> GSM550823 2 0.000 0.984 0.000 1.000
#> GSM550824 1 0.000 0.991 1.000 0.000
#> GSM550825 1 0.000 0.991 1.000 0.000
#> GSM550827 2 0.000 0.984 0.000 1.000
#> GSM550828 1 0.000 0.991 1.000 0.000
#> GSM550829 1 0.000 0.991 1.000 0.000
#> GSM550830 2 0.000 0.984 0.000 1.000
#> GSM550834 2 0.988 0.231 0.436 0.564
#> GSM550839 2 0.000 0.984 0.000 1.000
#> GSM550840 2 0.993 0.180 0.452 0.548
#> GSM550843 2 0.000 0.984 0.000 1.000
#> GSM550844 1 0.000 0.991 1.000 0.000
#> GSM550845 2 0.000 0.984 0.000 1.000
#> GSM550848 2 0.000 0.984 0.000 1.000
#> GSM550854 1 0.000 0.991 1.000 0.000
#> GSM550857 1 0.000 0.991 1.000 0.000
#> GSM550858 1 0.000 0.991 1.000 0.000
#> GSM550859 1 0.000 0.991 1.000 0.000
#> GSM550862 1 0.000 0.991 1.000 0.000
#> GSM550865 2 0.781 0.693 0.232 0.768
#> GSM550868 2 0.000 0.984 0.000 1.000
#> GSM550869 2 0.000 0.984 0.000 1.000
#> GSM550870 2 0.000 0.984 0.000 1.000
#> GSM550871 2 0.000 0.984 0.000 1.000
#> GSM550872 2 0.000 0.984 0.000 1.000
#> GSM550873 2 0.000 0.984 0.000 1.000
#> GSM550874 2 0.000 0.984 0.000 1.000
#> GSM550876 2 0.000 0.984 0.000 1.000
#> GSM550877 2 0.000 0.984 0.000 1.000
#> GSM550878 2 0.000 0.984 0.000 1.000
#> GSM550879 1 0.000 0.991 1.000 0.000
#> GSM550882 1 0.000 0.991 1.000 0.000
#> GSM550888 1 0.000 0.991 1.000 0.000
#> GSM550890 2 0.000 0.984 0.000 1.000
#> GSM550891 1 0.000 0.991 1.000 0.000
#> GSM550892 1 0.000 0.991 1.000 0.000
#> GSM550893 2 0.000 0.984 0.000 1.000
#> GSM550895 2 0.000 0.984 0.000 1.000
#> GSM550896 2 0.000 0.984 0.000 1.000
#> GSM550898 1 0.000 0.991 1.000 0.000
#> GSM550899 2 0.000 0.984 0.000 1.000
#> GSM550900 2 0.000 0.984 0.000 1.000
#> GSM550901 2 0.000 0.984 0.000 1.000
#> GSM550902 1 0.000 0.991 1.000 0.000
#> GSM550904 1 0.000 0.991 1.000 0.000
#> GSM550908 1 0.000 0.991 1.000 0.000
#> GSM550912 2 0.000 0.984 0.000 1.000
#> GSM550914 2 0.000 0.984 0.000 1.000
#> GSM550918 2 0.000 0.984 0.000 1.000
#> GSM550922 2 0.000 0.984 0.000 1.000
#> GSM550923 1 0.000 0.991 1.000 0.000
#> GSM550925 1 0.000 0.991 1.000 0.000
#> GSM550802 2 0.000 0.984 0.000 1.000
#> GSM550812 2 0.000 0.984 0.000 1.000
#> GSM550831 1 0.000 0.991 1.000 0.000
#> GSM550847 1 0.000 0.991 1.000 0.000
#> GSM550860 1 0.000 0.991 1.000 0.000
#> GSM550875 1 0.000 0.991 1.000 0.000
#> GSM550880 2 0.000 0.984 0.000 1.000
#> GSM550881 1 0.000 0.991 1.000 0.000
#> GSM550883 1 0.000 0.991 1.000 0.000
#> GSM550884 2 0.000 0.984 0.000 1.000
#> GSM550910 2 0.000 0.984 0.000 1.000
#> GSM550916 1 0.000 0.991 1.000 0.000
#> GSM550920 2 0.000 0.984 0.000 1.000
cbind(get_classes(res, k = 3), get_membership(res, k = 3))
#> class entropy silhouette p1 p2 p3
#> GSM550785 1 0.3619 0.860 0.864 0.000 0.136
#> GSM550786 2 0.3482 0.905 0.128 0.872 0.000
#> GSM550788 2 0.0000 0.954 0.000 1.000 0.000
#> GSM550789 2 0.0000 0.954 0.000 1.000 0.000
#> GSM550790 1 0.6299 0.207 0.524 0.000 0.476
#> GSM550791 1 0.0424 0.906 0.992 0.000 0.008
#> GSM550792 1 0.2796 0.829 0.908 0.092 0.000
#> GSM550796 2 0.0000 0.954 0.000 1.000 0.000
#> GSM550797 2 0.0000 0.954 0.000 1.000 0.000
#> GSM550799 2 0.0592 0.952 0.012 0.988 0.000
#> GSM550800 2 0.0000 0.954 0.000 1.000 0.000
#> GSM550801 2 0.0000 0.954 0.000 1.000 0.000
#> GSM550804 2 0.0000 0.954 0.000 1.000 0.000
#> GSM550806 1 0.0424 0.906 0.992 0.008 0.000
#> GSM550807 2 0.0000 0.954 0.000 1.000 0.000
#> GSM550808 2 0.0000 0.954 0.000 1.000 0.000
#> GSM550809 1 0.3619 0.860 0.864 0.000 0.136
#> GSM550810 2 0.0000 0.954 0.000 1.000 0.000
#> GSM550811 1 0.0424 0.906 0.992 0.000 0.008
#> GSM550813 2 0.3482 0.905 0.128 0.872 0.000
#> GSM550814 2 0.2878 0.921 0.096 0.904 0.000
#> GSM550815 2 0.0000 0.954 0.000 1.000 0.000
#> GSM550816 2 0.0000 0.954 0.000 1.000 0.000
#> GSM550817 2 0.0000 0.954 0.000 1.000 0.000
#> GSM550818 2 0.3482 0.905 0.128 0.872 0.000
#> GSM550819 2 0.2959 0.919 0.100 0.900 0.000
#> GSM550820 1 0.3619 0.860 0.864 0.000 0.136
#> GSM550821 2 0.0000 0.954 0.000 1.000 0.000
#> GSM550822 2 0.0000 0.954 0.000 1.000 0.000
#> GSM550826 1 0.3619 0.860 0.864 0.000 0.136
#> GSM550832 2 0.0000 0.954 0.000 1.000 0.000
#> GSM550833 2 0.0000 0.954 0.000 1.000 0.000
#> GSM550835 2 0.1411 0.945 0.036 0.964 0.000
#> GSM550836 3 0.0000 0.970 0.000 0.000 1.000
#> GSM550837 2 0.0000 0.954 0.000 1.000 0.000
#> GSM550838 1 0.3619 0.860 0.864 0.000 0.136
#> GSM550841 2 0.0000 0.954 0.000 1.000 0.000
#> GSM550842 2 0.0000 0.954 0.000 1.000 0.000
#> GSM550846 1 0.0747 0.902 0.984 0.016 0.000
#> GSM550849 1 0.0424 0.906 0.992 0.008 0.000
#> GSM550850 1 0.3619 0.860 0.864 0.000 0.136
#> GSM550851 2 0.0000 0.954 0.000 1.000 0.000
#> GSM550852 2 0.0000 0.954 0.000 1.000 0.000
#> GSM550853 2 0.0000 0.954 0.000 1.000 0.000
#> GSM550855 2 0.0000 0.954 0.000 1.000 0.000
#> GSM550856 2 0.1031 0.948 0.024 0.976 0.000
#> GSM550861 2 0.0000 0.954 0.000 1.000 0.000
#> GSM550863 1 0.1529 0.883 0.960 0.040 0.000
#> GSM550864 2 0.3482 0.905 0.128 0.872 0.000
#> GSM550866 2 0.3482 0.905 0.128 0.872 0.000
#> GSM550867 3 0.0000 0.970 0.000 0.000 1.000
#> GSM550885 3 0.0000 0.970 0.000 0.000 1.000
#> GSM550886 2 0.0424 0.952 0.008 0.992 0.000
#> GSM550887 2 0.0000 0.954 0.000 1.000 0.000
#> GSM550889 1 0.3619 0.860 0.864 0.000 0.136
#> GSM550894 2 0.0000 0.954 0.000 1.000 0.000
#> GSM550897 1 0.3038 0.875 0.896 0.000 0.104
#> GSM550903 2 0.0000 0.954 0.000 1.000 0.000
#> GSM550905 2 0.0000 0.954 0.000 1.000 0.000
#> GSM550906 2 0.0000 0.954 0.000 1.000 0.000
#> GSM550907 2 0.2878 0.921 0.096 0.904 0.000
#> GSM550909 2 0.0000 0.954 0.000 1.000 0.000
#> GSM550911 1 0.1643 0.876 0.956 0.044 0.000
#> GSM550913 2 0.0000 0.954 0.000 1.000 0.000
#> GSM550915 1 0.0424 0.906 0.992 0.008 0.000
#> GSM550917 2 0.0000 0.954 0.000 1.000 0.000
#> GSM550919 1 0.0424 0.906 0.992 0.008 0.000
#> GSM550921 3 0.0000 0.970 0.000 0.000 1.000
#> GSM550924 1 0.0424 0.906 0.992 0.008 0.000
#> GSM550926 2 0.3482 0.905 0.128 0.872 0.000
#> GSM550927 2 0.0000 0.954 0.000 1.000 0.000
#> GSM550787 1 0.0424 0.906 0.992 0.008 0.000
#> GSM550793 3 0.2625 0.890 0.084 0.000 0.916
#> GSM550794 2 0.3482 0.905 0.128 0.872 0.000
#> GSM550795 1 0.3619 0.860 0.864 0.000 0.136
#> GSM550798 3 0.0000 0.970 0.000 0.000 1.000
#> GSM550803 3 0.0000 0.970 0.000 0.000 1.000
#> GSM550805 1 0.0424 0.906 0.992 0.008 0.000
#> GSM550823 1 0.0424 0.906 0.992 0.008 0.000
#> GSM550824 3 0.0000 0.970 0.000 0.000 1.000
#> GSM550825 3 0.0000 0.970 0.000 0.000 1.000
#> GSM550827 1 0.1529 0.883 0.960 0.040 0.000
#> GSM550828 1 0.3619 0.860 0.864 0.000 0.136
#> GSM550829 3 0.0000 0.970 0.000 0.000 1.000
#> GSM550830 1 0.0424 0.906 0.992 0.008 0.000
#> GSM550834 1 0.0424 0.906 0.992 0.000 0.008
#> GSM550839 2 0.0000 0.954 0.000 1.000 0.000
#> GSM550840 1 0.0424 0.906 0.992 0.000 0.008
#> GSM550843 2 0.3482 0.905 0.128 0.872 0.000
#> GSM550844 1 0.3619 0.860 0.864 0.000 0.136
#> GSM550845 2 0.3482 0.905 0.128 0.872 0.000
#> GSM550848 2 0.3482 0.905 0.128 0.872 0.000
#> GSM550854 3 0.0000 0.970 0.000 0.000 1.000
#> GSM550857 3 0.0000 0.970 0.000 0.000 1.000
#> GSM550858 3 0.6079 0.266 0.388 0.000 0.612
#> GSM550859 3 0.0000 0.970 0.000 0.000 1.000
#> GSM550862 1 0.6225 0.344 0.568 0.000 0.432
#> GSM550865 1 0.0475 0.906 0.992 0.004 0.004
#> GSM550868 1 0.0424 0.906 0.992 0.008 0.000
#> GSM550869 1 0.0424 0.906 0.992 0.008 0.000
#> GSM550870 2 0.3482 0.905 0.128 0.872 0.000
#> GSM550871 1 0.4887 0.640 0.772 0.228 0.000
#> GSM550872 1 0.0424 0.906 0.992 0.008 0.000
#> GSM550873 2 0.3412 0.907 0.124 0.876 0.000
#> GSM550874 2 0.3482 0.905 0.128 0.872 0.000
#> GSM550876 2 0.3482 0.905 0.128 0.872 0.000
#> GSM550877 2 0.1289 0.946 0.032 0.968 0.000
#> GSM550878 1 0.0747 0.902 0.984 0.016 0.000
#> GSM550879 1 0.3038 0.875 0.896 0.000 0.104
#> GSM550882 1 0.3619 0.860 0.864 0.000 0.136
#> GSM550888 3 0.0000 0.970 0.000 0.000 1.000
#> GSM550890 1 0.0424 0.906 0.992 0.008 0.000
#> GSM550891 3 0.0000 0.970 0.000 0.000 1.000
#> GSM550892 1 0.3619 0.860 0.864 0.000 0.136
#> GSM550893 2 0.3482 0.905 0.128 0.872 0.000
#> GSM550895 2 0.3482 0.905 0.128 0.872 0.000
#> GSM550896 2 0.0000 0.954 0.000 1.000 0.000
#> GSM550898 3 0.0000 0.970 0.000 0.000 1.000
#> GSM550899 2 0.3482 0.905 0.128 0.872 0.000
#> GSM550900 1 0.2796 0.829 0.908 0.092 0.000
#> GSM550901 1 0.0424 0.906 0.992 0.008 0.000
#> GSM550902 1 0.0592 0.905 0.988 0.000 0.012
#> GSM550904 3 0.2625 0.890 0.084 0.000 0.916
#> GSM550908 3 0.0000 0.970 0.000 0.000 1.000
#> GSM550912 2 0.3482 0.905 0.128 0.872 0.000
#> GSM550914 1 0.0424 0.906 0.992 0.008 0.000
#> GSM550918 2 0.2878 0.921 0.096 0.904 0.000
#> GSM550922 2 0.0000 0.954 0.000 1.000 0.000
#> GSM550923 3 0.0000 0.970 0.000 0.000 1.000
#> GSM550925 1 0.3619 0.860 0.864 0.000 0.136
#> GSM550802 2 0.0237 0.953 0.004 0.996 0.000
#> GSM550812 2 0.0000 0.954 0.000 1.000 0.000
#> GSM550831 1 0.3619 0.860 0.864 0.000 0.136
#> GSM550847 3 0.0000 0.970 0.000 0.000 1.000
#> GSM550860 1 0.3038 0.875 0.896 0.000 0.104
#> GSM550875 1 0.0424 0.906 0.992 0.000 0.008
#> GSM550880 1 0.0424 0.906 0.992 0.008 0.000
#> GSM550881 1 0.3619 0.860 0.864 0.000 0.136
#> GSM550883 3 0.0000 0.970 0.000 0.000 1.000
#> GSM550884 1 0.0424 0.906 0.992 0.008 0.000
#> GSM550910 2 0.1860 0.939 0.052 0.948 0.000
#> GSM550916 1 0.3619 0.860 0.864 0.000 0.136
#> GSM550920 1 0.2796 0.829 0.908 0.092 0.000
cbind(get_classes(res, k = 4), get_membership(res, k = 4))
#> class entropy silhouette p1 p2 p3 p4
#> GSM550785 1 0.0000 0.99373 1.000 0.000 0.000 0.000
#> GSM550786 4 0.1118 0.96429 0.000 0.036 0.000 0.964
#> GSM550788 2 0.0469 0.96392 0.000 0.988 0.000 0.012
#> GSM550789 2 0.0469 0.96392 0.000 0.988 0.000 0.012
#> GSM550790 1 0.0592 0.97973 0.984 0.000 0.016 0.000
#> GSM550791 1 0.0000 0.99373 1.000 0.000 0.000 0.000
#> GSM550792 4 0.1209 0.95993 0.032 0.004 0.000 0.964
#> GSM550796 2 0.0469 0.96392 0.000 0.988 0.000 0.012
#> GSM550797 2 0.0469 0.96392 0.000 0.988 0.000 0.012
#> GSM550799 4 0.1118 0.96429 0.000 0.036 0.000 0.964
#> GSM550800 2 0.0469 0.96392 0.000 0.988 0.000 0.012
#> GSM550801 2 0.0469 0.96392 0.000 0.988 0.000 0.012
#> GSM550804 2 0.0469 0.96392 0.000 0.988 0.000 0.012
#> GSM550806 4 0.1389 0.95348 0.048 0.000 0.000 0.952
#> GSM550807 2 0.0469 0.96392 0.000 0.988 0.000 0.012
#> GSM550808 2 0.0469 0.96392 0.000 0.988 0.000 0.012
#> GSM550809 1 0.0188 0.99125 0.996 0.000 0.000 0.004
#> GSM550810 2 0.0469 0.96392 0.000 0.988 0.000 0.012
#> GSM550811 1 0.0000 0.99373 1.000 0.000 0.000 0.000
#> GSM550813 4 0.1118 0.96429 0.000 0.036 0.000 0.964
#> GSM550814 4 0.1118 0.96429 0.000 0.036 0.000 0.964
#> GSM550815 2 0.0469 0.96392 0.000 0.988 0.000 0.012
#> GSM550816 2 0.0469 0.96392 0.000 0.988 0.000 0.012
#> GSM550817 2 0.0469 0.96392 0.000 0.988 0.000 0.012
#> GSM550818 4 0.1118 0.96429 0.000 0.036 0.000 0.964
#> GSM550819 4 0.1118 0.96429 0.000 0.036 0.000 0.964
#> GSM550820 1 0.0000 0.99373 1.000 0.000 0.000 0.000
#> GSM550821 2 0.0469 0.96392 0.000 0.988 0.000 0.012
#> GSM550822 2 0.0469 0.96392 0.000 0.988 0.000 0.012
#> GSM550826 1 0.0000 0.99373 1.000 0.000 0.000 0.000
#> GSM550832 2 0.0469 0.96392 0.000 0.988 0.000 0.012
#> GSM550833 2 0.0469 0.96392 0.000 0.988 0.000 0.012
#> GSM550835 4 0.1118 0.96429 0.000 0.036 0.000 0.964
#> GSM550836 3 0.0000 0.99305 0.000 0.000 1.000 0.000
#> GSM550837 2 0.0469 0.96392 0.000 0.988 0.000 0.012
#> GSM550838 1 0.0188 0.99125 0.996 0.000 0.000 0.004
#> GSM550841 2 0.0469 0.96392 0.000 0.988 0.000 0.012
#> GSM550842 2 0.0469 0.96392 0.000 0.988 0.000 0.012
#> GSM550846 4 0.1118 0.95878 0.036 0.000 0.000 0.964
#> GSM550849 4 0.1389 0.95348 0.048 0.000 0.000 0.952
#> GSM550850 1 0.0000 0.99373 1.000 0.000 0.000 0.000
#> GSM550851 2 0.0469 0.96392 0.000 0.988 0.000 0.012
#> GSM550852 4 0.2216 0.91360 0.000 0.092 0.000 0.908
#> GSM550853 2 0.0469 0.96392 0.000 0.988 0.000 0.012
#> GSM550855 2 0.0469 0.96392 0.000 0.988 0.000 0.012
#> GSM550856 4 0.1118 0.96429 0.000 0.036 0.000 0.964
#> GSM550861 2 0.0469 0.96392 0.000 0.988 0.000 0.012
#> GSM550863 4 0.1118 0.95878 0.036 0.000 0.000 0.964
#> GSM550864 4 0.1118 0.96429 0.000 0.036 0.000 0.964
#> GSM550866 4 0.1118 0.96429 0.000 0.036 0.000 0.964
#> GSM550867 3 0.0000 0.99305 0.000 0.000 1.000 0.000
#> GSM550885 3 0.0000 0.99305 0.000 0.000 1.000 0.000
#> GSM550886 4 0.1118 0.96429 0.000 0.036 0.000 0.964
#> GSM550887 2 0.0469 0.96392 0.000 0.988 0.000 0.012
#> GSM550889 1 0.0000 0.99373 1.000 0.000 0.000 0.000
#> GSM550894 2 0.0469 0.96392 0.000 0.988 0.000 0.012
#> GSM550897 1 0.0000 0.99373 1.000 0.000 0.000 0.000
#> GSM550903 2 0.0469 0.96392 0.000 0.988 0.000 0.012
#> GSM550905 2 0.4999 0.00215 0.000 0.508 0.000 0.492
#> GSM550906 2 0.0469 0.96392 0.000 0.988 0.000 0.012
#> GSM550907 4 0.1118 0.96429 0.000 0.036 0.000 0.964
#> GSM550909 2 0.0469 0.96392 0.000 0.988 0.000 0.012
#> GSM550911 4 0.0469 0.94696 0.000 0.012 0.000 0.988
#> GSM550913 2 0.0469 0.96392 0.000 0.988 0.000 0.012
#> GSM550915 4 0.1389 0.95348 0.048 0.000 0.000 0.952
#> GSM550917 2 0.4999 0.00215 0.000 0.508 0.000 0.492
#> GSM550919 4 0.1389 0.95348 0.048 0.000 0.000 0.952
#> GSM550921 3 0.0000 0.99305 0.000 0.000 1.000 0.000
#> GSM550924 4 0.1389 0.95348 0.048 0.000 0.000 0.952
#> GSM550926 4 0.1118 0.96429 0.000 0.036 0.000 0.964
#> GSM550927 2 0.0469 0.96392 0.000 0.988 0.000 0.012
#> GSM550787 4 0.1389 0.95348 0.048 0.000 0.000 0.952
#> GSM550793 1 0.1022 0.96224 0.968 0.000 0.032 0.000
#> GSM550794 4 0.1118 0.96429 0.000 0.036 0.000 0.964
#> GSM550795 1 0.0000 0.99373 1.000 0.000 0.000 0.000
#> GSM550798 3 0.0000 0.99305 0.000 0.000 1.000 0.000
#> GSM550803 3 0.0000 0.99305 0.000 0.000 1.000 0.000
#> GSM550805 4 0.1389 0.95348 0.048 0.000 0.000 0.952
#> GSM550823 4 0.1389 0.95348 0.048 0.000 0.000 0.952
#> GSM550824 3 0.0000 0.99305 0.000 0.000 1.000 0.000
#> GSM550825 3 0.0592 0.97920 0.016 0.000 0.984 0.000
#> GSM550827 4 0.1118 0.95878 0.036 0.000 0.000 0.964
#> GSM550828 1 0.0000 0.99373 1.000 0.000 0.000 0.000
#> GSM550829 3 0.0000 0.99305 0.000 0.000 1.000 0.000
#> GSM550830 4 0.1389 0.95348 0.048 0.000 0.000 0.952
#> GSM550834 1 0.1211 0.94409 0.960 0.000 0.000 0.040
#> GSM550839 2 0.0469 0.96392 0.000 0.988 0.000 0.012
#> GSM550840 1 0.0000 0.99373 1.000 0.000 0.000 0.000
#> GSM550843 4 0.1118 0.96429 0.000 0.036 0.000 0.964
#> GSM550844 1 0.0000 0.99373 1.000 0.000 0.000 0.000
#> GSM550845 4 0.1118 0.96429 0.000 0.036 0.000 0.964
#> GSM550848 4 0.1118 0.96429 0.000 0.036 0.000 0.964
#> GSM550854 3 0.0000 0.99305 0.000 0.000 1.000 0.000
#> GSM550857 3 0.0000 0.99305 0.000 0.000 1.000 0.000
#> GSM550858 1 0.0707 0.97566 0.980 0.000 0.020 0.000
#> GSM550859 3 0.0000 0.99305 0.000 0.000 1.000 0.000
#> GSM550862 1 0.0188 0.99074 0.996 0.000 0.004 0.000
#> GSM550865 1 0.0000 0.99373 1.000 0.000 0.000 0.000
#> GSM550868 4 0.1389 0.95348 0.048 0.000 0.000 0.952
#> GSM550869 4 0.1389 0.95348 0.048 0.000 0.000 0.952
#> GSM550870 4 0.1118 0.96429 0.000 0.036 0.000 0.964
#> GSM550871 4 0.1297 0.96263 0.016 0.020 0.000 0.964
#> GSM550872 4 0.1389 0.95348 0.048 0.000 0.000 0.952
#> GSM550873 4 0.1118 0.96429 0.000 0.036 0.000 0.964
#> GSM550874 4 0.1118 0.96429 0.000 0.036 0.000 0.964
#> GSM550876 4 0.1118 0.96429 0.000 0.036 0.000 0.964
#> GSM550877 4 0.1118 0.96429 0.000 0.036 0.000 0.964
#> GSM550878 4 0.1118 0.95878 0.036 0.000 0.000 0.964
#> GSM550879 1 0.0000 0.99373 1.000 0.000 0.000 0.000
#> GSM550882 1 0.0000 0.99373 1.000 0.000 0.000 0.000
#> GSM550888 3 0.0000 0.99305 0.000 0.000 1.000 0.000
#> GSM550890 4 0.1389 0.95348 0.048 0.000 0.000 0.952
#> GSM550891 3 0.2469 0.87939 0.108 0.000 0.892 0.000
#> GSM550892 1 0.0000 0.99373 1.000 0.000 0.000 0.000
#> GSM550893 4 0.1118 0.96429 0.000 0.036 0.000 0.964
#> GSM550895 4 0.1118 0.96429 0.000 0.036 0.000 0.964
#> GSM550896 2 0.0469 0.96392 0.000 0.988 0.000 0.012
#> GSM550898 3 0.0000 0.99305 0.000 0.000 1.000 0.000
#> GSM550899 4 0.1118 0.96429 0.000 0.036 0.000 0.964
#> GSM550900 4 0.1209 0.95993 0.032 0.004 0.000 0.964
#> GSM550901 4 0.1389 0.95348 0.048 0.000 0.000 0.952
#> GSM550902 1 0.0000 0.99373 1.000 0.000 0.000 0.000
#> GSM550904 1 0.1022 0.96224 0.968 0.000 0.032 0.000
#> GSM550908 3 0.0000 0.99305 0.000 0.000 1.000 0.000
#> GSM550912 4 0.1118 0.96429 0.000 0.036 0.000 0.964
#> GSM550914 4 0.1389 0.95348 0.048 0.000 0.000 0.952
#> GSM550918 4 0.1118 0.96429 0.000 0.036 0.000 0.964
#> GSM550922 2 0.0469 0.96392 0.000 0.988 0.000 0.012
#> GSM550923 3 0.0000 0.99305 0.000 0.000 1.000 0.000
#> GSM550925 1 0.0000 0.99373 1.000 0.000 0.000 0.000
#> GSM550802 4 0.1940 0.93008 0.000 0.076 0.000 0.924
#> GSM550812 4 0.4998 0.03883 0.000 0.488 0.000 0.512
#> GSM550831 1 0.0000 0.99373 1.000 0.000 0.000 0.000
#> GSM550847 3 0.0000 0.99305 0.000 0.000 1.000 0.000
#> GSM550860 1 0.0000 0.99373 1.000 0.000 0.000 0.000
#> GSM550875 1 0.0000 0.99373 1.000 0.000 0.000 0.000
#> GSM550880 4 0.1474 0.95077 0.052 0.000 0.000 0.948
#> GSM550881 1 0.0000 0.99373 1.000 0.000 0.000 0.000
#> GSM550883 3 0.0000 0.99305 0.000 0.000 1.000 0.000
#> GSM550884 4 0.1389 0.95348 0.048 0.000 0.000 0.952
#> GSM550910 4 0.1118 0.96429 0.000 0.036 0.000 0.964
#> GSM550916 1 0.0000 0.99373 1.000 0.000 0.000 0.000
#> GSM550920 4 0.1209 0.95993 0.032 0.004 0.000 0.964
cbind(get_classes(res, k = 5), get_membership(res, k = 5))
#> class entropy silhouette p1 p2 p3 p4 p5
#> GSM550785 1 0.0510 0.906 0.984 0.016 0.000 0.000 0.000
#> GSM550786 2 0.4219 0.681 0.000 0.584 0.000 0.416 0.000
#> GSM550788 2 0.4227 0.433 0.000 0.580 0.000 0.000 0.420
#> GSM550789 5 0.0000 0.998 0.000 0.000 0.000 0.000 1.000
#> GSM550790 1 0.2127 0.865 0.892 0.108 0.000 0.000 0.000
#> GSM550791 1 0.4333 0.728 0.752 0.060 0.000 0.188 0.000
#> GSM550792 4 0.0290 0.929 0.000 0.008 0.000 0.992 0.000
#> GSM550796 5 0.0000 0.998 0.000 0.000 0.000 0.000 1.000
#> GSM550797 5 0.0000 0.998 0.000 0.000 0.000 0.000 1.000
#> GSM550799 2 0.4201 0.687 0.000 0.592 0.000 0.408 0.000
#> GSM550800 2 0.4227 0.433 0.000 0.580 0.000 0.000 0.420
#> GSM550801 5 0.0000 0.998 0.000 0.000 0.000 0.000 1.000
#> GSM550804 2 0.4227 0.433 0.000 0.580 0.000 0.000 0.420
#> GSM550806 4 0.0609 0.920 0.000 0.020 0.000 0.980 0.000
#> GSM550807 2 0.4227 0.433 0.000 0.580 0.000 0.000 0.420
#> GSM550808 5 0.0000 0.998 0.000 0.000 0.000 0.000 1.000
#> GSM550809 1 0.1732 0.887 0.920 0.080 0.000 0.000 0.000
#> GSM550810 5 0.0000 0.998 0.000 0.000 0.000 0.000 1.000
#> GSM550811 1 0.5285 0.491 0.584 0.060 0.000 0.356 0.000
#> GSM550813 2 0.4273 0.625 0.000 0.552 0.000 0.448 0.000
#> GSM550814 2 0.4210 0.686 0.000 0.588 0.000 0.412 0.000
#> GSM550815 5 0.0000 0.998 0.000 0.000 0.000 0.000 1.000
#> GSM550816 5 0.0000 0.998 0.000 0.000 0.000 0.000 1.000
#> GSM550817 5 0.0794 0.972 0.000 0.028 0.000 0.000 0.972
#> GSM550818 2 0.4150 0.682 0.000 0.612 0.000 0.388 0.000
#> GSM550819 2 0.4192 0.687 0.000 0.596 0.000 0.404 0.000
#> GSM550820 1 0.0703 0.906 0.976 0.024 0.000 0.000 0.000
#> GSM550821 2 0.4227 0.433 0.000 0.580 0.000 0.000 0.420
#> GSM550822 5 0.0000 0.998 0.000 0.000 0.000 0.000 1.000
#> GSM550826 1 0.0510 0.906 0.984 0.016 0.000 0.000 0.000
#> GSM550832 2 0.4227 0.433 0.000 0.580 0.000 0.000 0.420
#> GSM550833 5 0.0000 0.998 0.000 0.000 0.000 0.000 1.000
#> GSM550835 2 0.4210 0.686 0.000 0.588 0.000 0.412 0.000
#> GSM550836 3 0.0000 0.942 0.000 0.000 1.000 0.000 0.000
#> GSM550837 5 0.0000 0.998 0.000 0.000 0.000 0.000 1.000
#> GSM550838 1 0.1043 0.903 0.960 0.040 0.000 0.000 0.000
#> GSM550841 5 0.0000 0.998 0.000 0.000 0.000 0.000 1.000
#> GSM550842 5 0.0000 0.998 0.000 0.000 0.000 0.000 1.000
#> GSM550846 4 0.0290 0.926 0.000 0.008 0.000 0.992 0.000
#> GSM550849 4 0.1892 0.858 0.004 0.080 0.000 0.916 0.000
#> GSM550850 1 0.1732 0.888 0.920 0.080 0.000 0.000 0.000
#> GSM550851 5 0.0000 0.998 0.000 0.000 0.000 0.000 1.000
#> GSM550852 2 0.4824 0.691 0.000 0.596 0.000 0.376 0.028
#> GSM550853 5 0.0000 0.998 0.000 0.000 0.000 0.000 1.000
#> GSM550855 2 0.4249 0.408 0.000 0.568 0.000 0.000 0.432
#> GSM550856 2 0.4210 0.686 0.000 0.588 0.000 0.412 0.000
#> GSM550861 2 0.4227 0.433 0.000 0.580 0.000 0.000 0.420
#> GSM550863 4 0.0290 0.929 0.000 0.008 0.000 0.992 0.000
#> GSM550864 2 0.4305 0.537 0.000 0.512 0.000 0.488 0.000
#> GSM550866 4 0.4302 -0.480 0.000 0.480 0.000 0.520 0.000
#> GSM550867 3 0.0000 0.942 0.000 0.000 1.000 0.000 0.000
#> GSM550885 3 0.0000 0.942 0.000 0.000 1.000 0.000 0.000
#> GSM550886 2 0.4210 0.686 0.000 0.588 0.000 0.412 0.000
#> GSM550887 5 0.0000 0.998 0.000 0.000 0.000 0.000 1.000
#> GSM550889 1 0.0609 0.905 0.980 0.020 0.000 0.000 0.000
#> GSM550894 5 0.0162 0.994 0.000 0.004 0.000 0.000 0.996
#> GSM550897 1 0.0000 0.907 1.000 0.000 0.000 0.000 0.000
#> GSM550903 2 0.4227 0.433 0.000 0.580 0.000 0.000 0.420
#> GSM550905 2 0.5908 0.674 0.000 0.588 0.000 0.256 0.156
#> GSM550906 2 0.4227 0.433 0.000 0.580 0.000 0.000 0.420
#> GSM550907 2 0.4138 0.686 0.000 0.616 0.000 0.384 0.000
#> GSM550909 5 0.0000 0.998 0.000 0.000 0.000 0.000 1.000
#> GSM550911 4 0.3752 0.613 0.000 0.292 0.000 0.708 0.000
#> GSM550913 5 0.0000 0.998 0.000 0.000 0.000 0.000 1.000
#> GSM550915 4 0.0794 0.915 0.000 0.028 0.000 0.972 0.000
#> GSM550917 2 0.5908 0.674 0.000 0.588 0.000 0.256 0.156
#> GSM550919 4 0.0000 0.928 0.000 0.000 0.000 1.000 0.000
#> GSM550921 3 0.0000 0.942 0.000 0.000 1.000 0.000 0.000
#> GSM550924 4 0.0000 0.928 0.000 0.000 0.000 1.000 0.000
#> GSM550926 2 0.4210 0.686 0.000 0.588 0.000 0.412 0.000
#> GSM550927 5 0.0000 0.998 0.000 0.000 0.000 0.000 1.000
#> GSM550787 4 0.0703 0.917 0.000 0.024 0.000 0.976 0.000
#> GSM550793 1 0.2074 0.866 0.896 0.104 0.000 0.000 0.000
#> GSM550794 4 0.1671 0.848 0.000 0.076 0.000 0.924 0.000
#> GSM550795 1 0.0609 0.906 0.980 0.020 0.000 0.000 0.000
#> GSM550798 3 0.0000 0.942 0.000 0.000 1.000 0.000 0.000
#> GSM550803 3 0.0000 0.942 0.000 0.000 1.000 0.000 0.000
#> GSM550805 4 0.0703 0.917 0.000 0.024 0.000 0.976 0.000
#> GSM550823 4 0.0290 0.929 0.000 0.008 0.000 0.992 0.000
#> GSM550824 3 0.0000 0.942 0.000 0.000 1.000 0.000 0.000
#> GSM550825 3 0.5382 0.604 0.252 0.104 0.644 0.000 0.000
#> GSM550827 4 0.0290 0.929 0.000 0.008 0.000 0.992 0.000
#> GSM550828 1 0.0510 0.906 0.984 0.016 0.000 0.000 0.000
#> GSM550829 3 0.4901 0.708 0.184 0.104 0.712 0.000 0.000
#> GSM550830 4 0.0290 0.929 0.000 0.008 0.000 0.992 0.000
#> GSM550834 1 0.5252 0.559 0.616 0.068 0.000 0.316 0.000
#> GSM550839 2 0.4436 0.458 0.000 0.596 0.000 0.008 0.396
#> GSM550840 1 0.4850 0.682 0.700 0.076 0.000 0.224 0.000
#> GSM550843 2 0.4210 0.686 0.000 0.588 0.000 0.412 0.000
#> GSM550844 1 0.0162 0.907 0.996 0.004 0.000 0.000 0.000
#> GSM550845 2 0.4210 0.686 0.000 0.588 0.000 0.412 0.000
#> GSM550848 4 0.0290 0.929 0.000 0.008 0.000 0.992 0.000
#> GSM550854 3 0.0000 0.942 0.000 0.000 1.000 0.000 0.000
#> GSM550857 3 0.0000 0.942 0.000 0.000 1.000 0.000 0.000
#> GSM550858 1 0.2074 0.866 0.896 0.104 0.000 0.000 0.000
#> GSM550859 3 0.0000 0.942 0.000 0.000 1.000 0.000 0.000
#> GSM550862 1 0.2074 0.866 0.896 0.104 0.000 0.000 0.000
#> GSM550865 1 0.4851 0.524 0.624 0.036 0.000 0.340 0.000
#> GSM550868 4 0.0290 0.929 0.000 0.008 0.000 0.992 0.000
#> GSM550869 4 0.0794 0.915 0.000 0.028 0.000 0.972 0.000
#> GSM550870 2 0.4210 0.686 0.000 0.588 0.000 0.412 0.000
#> GSM550871 4 0.0290 0.929 0.000 0.008 0.000 0.992 0.000
#> GSM550872 4 0.0290 0.929 0.000 0.008 0.000 0.992 0.000
#> GSM550873 2 0.4210 0.686 0.000 0.588 0.000 0.412 0.000
#> GSM550874 2 0.4210 0.686 0.000 0.588 0.000 0.412 0.000
#> GSM550876 4 0.1608 0.854 0.000 0.072 0.000 0.928 0.000
#> GSM550877 2 0.4210 0.686 0.000 0.588 0.000 0.412 0.000
#> GSM550878 4 0.0290 0.929 0.000 0.008 0.000 0.992 0.000
#> GSM550879 1 0.0510 0.906 0.984 0.016 0.000 0.000 0.000
#> GSM550882 1 0.0609 0.905 0.980 0.020 0.000 0.000 0.000
#> GSM550888 3 0.0000 0.942 0.000 0.000 1.000 0.000 0.000
#> GSM550890 4 0.0290 0.926 0.000 0.008 0.000 0.992 0.000
#> GSM550891 3 0.5788 0.494 0.300 0.120 0.580 0.000 0.000
#> GSM550892 1 0.0404 0.906 0.988 0.012 0.000 0.000 0.000
#> GSM550893 2 0.4210 0.686 0.000 0.588 0.000 0.412 0.000
#> GSM550895 4 0.2732 0.685 0.000 0.160 0.000 0.840 0.000
#> GSM550896 2 0.4227 0.433 0.000 0.580 0.000 0.000 0.420
#> GSM550898 3 0.0000 0.942 0.000 0.000 1.000 0.000 0.000
#> GSM550899 2 0.4210 0.686 0.000 0.588 0.000 0.412 0.000
#> GSM550900 4 0.0290 0.929 0.000 0.008 0.000 0.992 0.000
#> GSM550901 4 0.0703 0.917 0.000 0.024 0.000 0.976 0.000
#> GSM550902 1 0.0510 0.906 0.984 0.016 0.000 0.000 0.000
#> GSM550904 1 0.2074 0.866 0.896 0.104 0.000 0.000 0.000
#> GSM550908 3 0.0000 0.942 0.000 0.000 1.000 0.000 0.000
#> GSM550912 4 0.1043 0.896 0.000 0.040 0.000 0.960 0.000
#> GSM550914 4 0.0510 0.923 0.000 0.016 0.000 0.984 0.000
#> GSM550918 2 0.4210 0.686 0.000 0.588 0.000 0.412 0.000
#> GSM550922 2 0.4227 0.433 0.000 0.580 0.000 0.000 0.420
#> GSM550923 3 0.0000 0.942 0.000 0.000 1.000 0.000 0.000
#> GSM550925 1 0.0609 0.905 0.980 0.020 0.000 0.000 0.000
#> GSM550802 2 0.4757 0.692 0.000 0.596 0.000 0.380 0.024
#> GSM550812 2 0.5759 0.668 0.000 0.616 0.000 0.224 0.160
#> GSM550831 1 0.1732 0.888 0.920 0.080 0.000 0.000 0.000
#> GSM550847 3 0.1732 0.903 0.000 0.080 0.920 0.000 0.000
#> GSM550860 1 0.0162 0.907 0.996 0.004 0.000 0.000 0.000
#> GSM550875 1 0.0963 0.900 0.964 0.036 0.000 0.000 0.000
#> GSM550880 4 0.1915 0.867 0.040 0.032 0.000 0.928 0.000
#> GSM550881 1 0.0510 0.905 0.984 0.016 0.000 0.000 0.000
#> GSM550883 3 0.0963 0.926 0.000 0.036 0.964 0.000 0.000
#> GSM550884 4 0.0290 0.929 0.000 0.008 0.000 0.992 0.000
#> GSM550910 2 0.4138 0.686 0.000 0.616 0.000 0.384 0.000
#> GSM550916 1 0.0510 0.906 0.984 0.016 0.000 0.000 0.000
#> GSM550920 4 0.0290 0.929 0.000 0.008 0.000 0.992 0.000
cbind(get_classes(res, k = 6), get_membership(res, k = 6))
#> class entropy silhouette p1 p2 p3 p4 p5 p6
#> GSM550785 6 0.0806 0.8291 0.000 0.000 0.020 0.008 0.000 0.972
#> GSM550786 2 0.2778 0.7642 0.000 0.824 0.008 0.168 0.000 0.000
#> GSM550788 2 0.4892 0.6755 0.000 0.660 0.176 0.000 0.164 0.000
#> GSM550789 5 0.1814 0.9137 0.000 0.000 0.100 0.000 0.900 0.000
#> GSM550790 6 0.2883 0.7597 0.000 0.000 0.212 0.000 0.000 0.788
#> GSM550791 6 0.5098 0.4126 0.000 0.004 0.124 0.240 0.000 0.632
#> GSM550792 4 0.1644 0.8066 0.000 0.076 0.004 0.920 0.000 0.000
#> GSM550796 5 0.0146 0.9178 0.000 0.000 0.004 0.000 0.996 0.000
#> GSM550797 5 0.2768 0.8844 0.000 0.012 0.156 0.000 0.832 0.000
#> GSM550799 2 0.2536 0.8104 0.000 0.864 0.020 0.116 0.000 0.000
#> GSM550800 2 0.4830 0.6813 0.000 0.668 0.172 0.000 0.160 0.000
#> GSM550801 5 0.2378 0.8941 0.000 0.000 0.152 0.000 0.848 0.000
#> GSM550804 2 0.4830 0.6813 0.000 0.668 0.172 0.000 0.160 0.000
#> GSM550806 4 0.0993 0.7981 0.000 0.024 0.012 0.964 0.000 0.000
#> GSM550807 2 0.4830 0.6813 0.000 0.668 0.172 0.000 0.160 0.000
#> GSM550808 5 0.0363 0.9168 0.000 0.000 0.012 0.000 0.988 0.000
#> GSM550809 6 0.3358 0.7529 0.000 0.024 0.128 0.024 0.000 0.824
#> GSM550810 5 0.0146 0.9178 0.000 0.000 0.004 0.000 0.996 0.000
#> GSM550811 6 0.5417 -0.1286 0.000 0.004 0.100 0.424 0.000 0.472
#> GSM550813 2 0.3405 0.6197 0.000 0.724 0.004 0.272 0.000 0.000
#> GSM550814 2 0.2003 0.8075 0.000 0.884 0.000 0.116 0.000 0.000
#> GSM550815 5 0.0260 0.9166 0.000 0.000 0.008 0.000 0.992 0.000
#> GSM550816 5 0.0547 0.9185 0.000 0.000 0.020 0.000 0.980 0.000
#> GSM550817 5 0.1010 0.9177 0.000 0.004 0.036 0.000 0.960 0.000
#> GSM550818 2 0.3211 0.7744 0.000 0.824 0.056 0.120 0.000 0.000
#> GSM550819 2 0.2003 0.8075 0.000 0.884 0.000 0.116 0.000 0.000
#> GSM550820 6 0.0806 0.8291 0.000 0.000 0.020 0.008 0.000 0.972
#> GSM550821 2 0.4830 0.6813 0.000 0.668 0.172 0.000 0.160 0.000
#> GSM550822 5 0.0260 0.9166 0.000 0.000 0.008 0.000 0.992 0.000
#> GSM550826 6 0.0806 0.8291 0.000 0.000 0.020 0.008 0.000 0.972
#> GSM550832 2 0.4830 0.6813 0.000 0.668 0.172 0.000 0.160 0.000
#> GSM550833 5 0.2491 0.8883 0.000 0.000 0.164 0.000 0.836 0.000
#> GSM550835 2 0.2536 0.8104 0.000 0.864 0.020 0.116 0.000 0.000
#> GSM550836 1 0.0000 0.8882 1.000 0.000 0.000 0.000 0.000 0.000
#> GSM550837 5 0.1957 0.9124 0.000 0.000 0.112 0.000 0.888 0.000
#> GSM550838 6 0.2652 0.7914 0.000 0.020 0.104 0.008 0.000 0.868
#> GSM550841 5 0.0363 0.9168 0.000 0.000 0.012 0.000 0.988 0.000
#> GSM550842 5 0.0146 0.9178 0.000 0.000 0.004 0.000 0.996 0.000
#> GSM550846 4 0.2230 0.7314 0.000 0.024 0.084 0.892 0.000 0.000
#> GSM550849 4 0.3098 0.5223 0.000 0.040 0.120 0.836 0.000 0.004
#> GSM550850 6 0.3358 0.7529 0.000 0.024 0.128 0.024 0.000 0.824
#> GSM550851 5 0.2416 0.8938 0.000 0.000 0.156 0.000 0.844 0.000
#> GSM550852 2 0.3141 0.8059 0.000 0.836 0.048 0.112 0.004 0.000
#> GSM550853 5 0.2416 0.8938 0.000 0.000 0.156 0.000 0.844 0.000
#> GSM550855 2 0.4862 0.6767 0.000 0.664 0.172 0.000 0.164 0.000
#> GSM550856 2 0.2536 0.8100 0.000 0.864 0.020 0.116 0.000 0.000
#> GSM550861 2 0.4830 0.6813 0.000 0.668 0.172 0.000 0.160 0.000
#> GSM550863 4 0.1588 0.8095 0.000 0.072 0.004 0.924 0.000 0.000
#> GSM550864 2 0.3819 0.4112 0.000 0.624 0.004 0.372 0.000 0.000
#> GSM550866 2 0.3890 0.3289 0.000 0.596 0.004 0.400 0.000 0.000
#> GSM550867 1 0.0000 0.8882 1.000 0.000 0.000 0.000 0.000 0.000
#> GSM550885 1 0.0000 0.8882 1.000 0.000 0.000 0.000 0.000 0.000
#> GSM550886 2 0.2536 0.8100 0.000 0.864 0.020 0.116 0.000 0.000
#> GSM550887 5 0.0547 0.9223 0.000 0.000 0.020 0.000 0.980 0.000
#> GSM550889 6 0.1858 0.8231 0.000 0.004 0.092 0.000 0.000 0.904
#> GSM550894 5 0.2932 0.8693 0.000 0.016 0.164 0.000 0.820 0.000
#> GSM550897 6 0.0291 0.8324 0.000 0.000 0.004 0.004 0.000 0.992
#> GSM550903 2 0.4671 0.6910 0.000 0.688 0.152 0.000 0.160 0.000
#> GSM550905 2 0.4613 0.7600 0.000 0.744 0.136 0.072 0.048 0.000
#> GSM550906 2 0.4830 0.6813 0.000 0.668 0.172 0.000 0.160 0.000
#> GSM550907 2 0.2212 0.8096 0.000 0.880 0.008 0.112 0.000 0.000
#> GSM550909 5 0.1501 0.9187 0.000 0.000 0.076 0.000 0.924 0.000
#> GSM550911 3 0.5182 0.0000 0.000 0.096 0.532 0.372 0.000 0.000
#> GSM550913 5 0.0547 0.9223 0.000 0.000 0.020 0.000 0.980 0.000
#> GSM550915 4 0.1866 0.7087 0.000 0.008 0.084 0.908 0.000 0.000
#> GSM550917 2 0.4032 0.7829 0.000 0.796 0.088 0.072 0.044 0.000
#> GSM550919 4 0.1196 0.8117 0.000 0.040 0.008 0.952 0.000 0.000
#> GSM550921 1 0.0260 0.8844 0.992 0.000 0.008 0.000 0.000 0.000
#> GSM550924 4 0.0937 0.8153 0.000 0.040 0.000 0.960 0.000 0.000
#> GSM550926 2 0.2320 0.7986 0.000 0.864 0.004 0.132 0.000 0.000
#> GSM550927 5 0.1957 0.9104 0.000 0.000 0.112 0.000 0.888 0.000
#> GSM550787 4 0.1092 0.7881 0.000 0.020 0.020 0.960 0.000 0.000
#> GSM550793 6 0.2941 0.7542 0.000 0.000 0.220 0.000 0.000 0.780
#> GSM550794 4 0.3349 0.5724 0.000 0.244 0.008 0.748 0.000 0.000
#> GSM550795 6 0.0547 0.8317 0.000 0.000 0.020 0.000 0.000 0.980
#> GSM550798 1 0.0000 0.8882 1.000 0.000 0.000 0.000 0.000 0.000
#> GSM550803 1 0.0000 0.8882 1.000 0.000 0.000 0.000 0.000 0.000
#> GSM550805 4 0.1148 0.7772 0.000 0.016 0.020 0.960 0.000 0.004
#> GSM550823 4 0.1007 0.8168 0.000 0.044 0.000 0.956 0.000 0.000
#> GSM550824 1 0.0000 0.8882 1.000 0.000 0.000 0.000 0.000 0.000
#> GSM550825 1 0.5837 0.3396 0.484 0.000 0.224 0.000 0.000 0.292
#> GSM550827 4 0.1588 0.8095 0.000 0.072 0.004 0.924 0.000 0.000
#> GSM550828 6 0.1501 0.8275 0.000 0.000 0.076 0.000 0.000 0.924
#> GSM550829 1 0.5648 0.4262 0.536 0.000 0.224 0.000 0.000 0.240
#> GSM550830 4 0.1007 0.8168 0.000 0.044 0.000 0.956 0.000 0.000
#> GSM550834 6 0.5603 -0.0507 0.000 0.004 0.128 0.384 0.000 0.484
#> GSM550839 2 0.3681 0.7309 0.000 0.780 0.064 0.000 0.156 0.000
#> GSM550840 6 0.5732 0.3234 0.000 0.024 0.136 0.260 0.000 0.580
#> GSM550843 2 0.2320 0.7986 0.000 0.864 0.004 0.132 0.000 0.000
#> GSM550844 6 0.0363 0.8330 0.000 0.000 0.012 0.000 0.000 0.988
#> GSM550845 2 0.2320 0.7986 0.000 0.864 0.004 0.132 0.000 0.000
#> GSM550848 4 0.3109 0.6103 0.000 0.224 0.004 0.772 0.000 0.000
#> GSM550854 1 0.0000 0.8882 1.000 0.000 0.000 0.000 0.000 0.000
#> GSM550857 1 0.0000 0.8882 1.000 0.000 0.000 0.000 0.000 0.000
#> GSM550858 6 0.2883 0.7597 0.000 0.000 0.212 0.000 0.000 0.788
#> GSM550859 1 0.0000 0.8882 1.000 0.000 0.000 0.000 0.000 0.000
#> GSM550862 6 0.2883 0.7597 0.000 0.000 0.212 0.000 0.000 0.788
#> GSM550865 4 0.4305 -0.2616 0.000 0.000 0.020 0.544 0.000 0.436
#> GSM550868 4 0.1007 0.8168 0.000 0.044 0.000 0.956 0.000 0.000
#> GSM550869 4 0.1176 0.7832 0.000 0.024 0.020 0.956 0.000 0.000
#> GSM550870 2 0.2191 0.8049 0.000 0.876 0.004 0.120 0.000 0.000
#> GSM550871 4 0.2118 0.7742 0.000 0.104 0.008 0.888 0.000 0.000
#> GSM550872 4 0.1204 0.8179 0.000 0.056 0.000 0.944 0.000 0.000
#> GSM550873 2 0.2346 0.8026 0.000 0.868 0.008 0.124 0.000 0.000
#> GSM550874 2 0.2346 0.8026 0.000 0.868 0.008 0.124 0.000 0.000
#> GSM550876 4 0.3323 0.5790 0.000 0.240 0.008 0.752 0.000 0.000
#> GSM550877 2 0.2146 0.8085 0.000 0.880 0.004 0.116 0.000 0.000
#> GSM550878 4 0.1204 0.8176 0.000 0.056 0.000 0.944 0.000 0.000
#> GSM550879 6 0.0891 0.8279 0.000 0.000 0.024 0.008 0.000 0.968
#> GSM550882 6 0.1858 0.8231 0.000 0.004 0.092 0.000 0.000 0.904
#> GSM550888 1 0.0000 0.8882 1.000 0.000 0.000 0.000 0.000 0.000
#> GSM550890 4 0.2230 0.7314 0.000 0.024 0.084 0.892 0.000 0.000
#> GSM550891 1 0.6699 0.1975 0.404 0.040 0.236 0.000 0.000 0.320
#> GSM550892 6 0.1663 0.8252 0.000 0.000 0.088 0.000 0.000 0.912
#> GSM550893 2 0.2146 0.8085 0.000 0.880 0.004 0.116 0.000 0.000
#> GSM550895 4 0.3508 0.4818 0.000 0.292 0.004 0.704 0.000 0.000
#> GSM550896 2 0.4862 0.6772 0.000 0.664 0.172 0.000 0.164 0.000
#> GSM550898 1 0.0000 0.8882 1.000 0.000 0.000 0.000 0.000 0.000
#> GSM550899 2 0.2362 0.7956 0.000 0.860 0.004 0.136 0.000 0.000
#> GSM550900 4 0.1588 0.8095 0.000 0.072 0.004 0.924 0.000 0.000
#> GSM550901 4 0.1003 0.7907 0.000 0.020 0.016 0.964 0.000 0.000
#> GSM550902 6 0.0891 0.8279 0.000 0.000 0.024 0.008 0.000 0.968
#> GSM550904 6 0.2941 0.7542 0.000 0.000 0.220 0.000 0.000 0.780
#> GSM550908 1 0.0260 0.8844 0.992 0.000 0.008 0.000 0.000 0.000
#> GSM550912 4 0.3265 0.5714 0.000 0.248 0.004 0.748 0.000 0.000
#> GSM550914 4 0.2230 0.7314 0.000 0.024 0.084 0.892 0.000 0.000
#> GSM550918 2 0.2257 0.8092 0.000 0.876 0.008 0.116 0.000 0.000
#> GSM550922 2 0.4671 0.6910 0.000 0.688 0.152 0.000 0.160 0.000
#> GSM550923 1 0.0000 0.8882 1.000 0.000 0.000 0.000 0.000 0.000
#> GSM550925 6 0.1858 0.8231 0.000 0.004 0.092 0.000 0.000 0.904
#> GSM550802 2 0.3141 0.8059 0.000 0.836 0.048 0.112 0.004 0.000
#> GSM550812 2 0.3666 0.7814 0.000 0.824 0.060 0.048 0.068 0.000
#> GSM550831 6 0.3358 0.7529 0.000 0.024 0.128 0.024 0.000 0.824
#> GSM550847 1 0.2178 0.7972 0.868 0.000 0.132 0.000 0.000 0.000
#> GSM550860 6 0.0547 0.8331 0.000 0.000 0.020 0.000 0.000 0.980
#> GSM550875 6 0.1921 0.8035 0.000 0.000 0.032 0.052 0.000 0.916
#> GSM550880 4 0.1542 0.6544 0.000 0.004 0.008 0.936 0.000 0.052
#> GSM550881 6 0.1714 0.8239 0.000 0.000 0.092 0.000 0.000 0.908
#> GSM550883 1 0.1387 0.8464 0.932 0.000 0.068 0.000 0.000 0.000
#> GSM550884 4 0.1204 0.8176 0.000 0.056 0.000 0.944 0.000 0.000
#> GSM550910 2 0.2212 0.8096 0.000 0.880 0.008 0.112 0.000 0.000
#> GSM550916 6 0.1714 0.8239 0.000 0.000 0.092 0.000 0.000 0.908
#> GSM550920 4 0.1411 0.8171 0.000 0.060 0.004 0.936 0.000 0.000
Heatmaps for the consensus matrix. It visualizes the probability of two samples to be in a same group.
consensus_heatmap(res, k = 2)
consensus_heatmap(res, k = 3)
consensus_heatmap(res, k = 4)
consensus_heatmap(res, k = 5)
consensus_heatmap(res, k = 6)
Heatmaps for the membership of samples in all partitions to see how consistent they are:
membership_heatmap(res, k = 2)
membership_heatmap(res, k = 3)
membership_heatmap(res, k = 4)
membership_heatmap(res, k = 5)
membership_heatmap(res, k = 6)
As soon as we have had the classes for columns, we can look for signatures which are significantly different between classes which can be candidate marks for certain classes. Following are the heatmaps for signatures.
Signature heatmaps where rows are scaled:
get_signatures(res, k = 2)
get_signatures(res, k = 3)
get_signatures(res, k = 4)
get_signatures(res, k = 5)
get_signatures(res, k = 6)
Signature heatmaps where rows are not scaled:
get_signatures(res, k = 2, scale_rows = FALSE)
get_signatures(res, k = 3, scale_rows = FALSE)
get_signatures(res, k = 4, scale_rows = FALSE)
get_signatures(res, k = 5, scale_rows = FALSE)
get_signatures(res, k = 6, scale_rows = FALSE)
Compare the overlap of signatures from different k:
compare_signatures(res)
get_signature() returns a data frame invisibly. TO get the list of signatures, the function
call should be assigned to a variable explicitly. In following code, if plot argument is set
to FALSE, no heatmap is plotted while only the differential analysis is performed.
# code only for demonstration
tb = get_signature(res, k = ..., plot = FALSE)
An example of the output of tb is:
#> which_row fdr mean_1 mean_2 scaled_mean_1 scaled_mean_2 km
#> 1 38 0.042760348 8.373488 9.131774 -0.5533452 0.5164555 1
#> 2 40 0.018707592 7.106213 8.469186 -0.6173731 0.5762149 1
#> 3 55 0.019134737 10.221463 11.207825 -0.6159697 0.5749050 1
#> 4 59 0.006059896 5.921854 7.869574 -0.6899429 0.6439467 1
#> 5 60 0.018055526 8.928898 10.211722 -0.6204761 0.5791110 1
#> 6 98 0.009384629 15.714769 14.887706 0.6635654 -0.6193277 2
...
The columns in tb are:
which_row: row indices corresponding to the input matrix.fdr: FDR for the differential test. mean_x: The mean value in group x.scaled_mean_x: The mean value in group x after rows are scaled.km: Row groups if k-means clustering is applied to rows.UMAP plot which shows how samples are separated.
dimension_reduction(res, k = 2, method = "UMAP")
dimension_reduction(res, k = 3, method = "UMAP")
dimension_reduction(res, k = 4, method = "UMAP")
dimension_reduction(res, k = 5, method = "UMAP")
dimension_reduction(res, k = 6, method = "UMAP")
Following heatmap shows how subgroups are split when increasing k:
collect_classes(res)
Test correlation between subgroups and known annotations. If the known annotation is numeric, one-way ANOVA test is applied, and if the known annotation is discrete, chi-squared contingency table test is applied.
test_to_known_factors(res)
#> n disease.state(p) k
#> ATC:kmeans 139 2.55e-03 2
#> ATC:kmeans 140 6.25e-05 3
#> ATC:kmeans 140 3.61e-06 4
#> ATC:kmeans 127 1.22e-05 5
#> ATC:kmeans 131 9.91e-06 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 51776 rows and 143 columns.
#> Top rows (1000, 2000, 3000, 4000, 5000) are extracted by 'ATC' method.
#> Subgroups are detected by 'skmeans' method.
#> Performed in total 1250 partitions by row resampling.
#> Best k for subgroups seems to be 5.
#>
#> Following methods can be applied to this 'ConsensusPartition' object:
#> [1] "cola_report" "collect_classes" "collect_plots"
#> [4] "collect_stats" "colnames" "compare_signatures"
#> [7] "consensus_heatmap" "dimension_reduction" "functional_enrichment"
#> [10] "get_anno_col" "get_anno" "get_classes"
#> [13] "get_consensus" "get_matrix" "get_membership"
#> [16] "get_param" "get_signatures" "get_stats"
#> [19] "is_best_k" "is_stable_k" "membership_heatmap"
#> [22] "ncol" "nrow" "plot_ecdf"
#> [25] "rownames" "select_partition_number" "show"
#> [28] "suggest_best_k" "test_to_known_factors"
collect_plots() function collects all the plots made from res for all k (number of partitions)
into one single page to provide an easy and fast comparison between different k.
collect_plots(res)
The plots are:
k and the heatmap of
predicted classes for each k.k.k.k.All the plots in panels can be made by individual functions and they are plotted later in this section.
select_partition_number() produces several plots showing different
statistics for choosing “optimized” k. There are following statistics:
k;k, the area increased is defined as \(A_k - A_{k-1}\).The detailed explanations of these statistics can be found in the cola vignette.
Generally speaking, lower PAC score, higher mean silhouette score or higher
concordance corresponds to better partition. Rand index and Jaccard index
measure how similar the current partition is compared to partition with k-1.
If they are too similar, we won't accept k is better than k-1.
select_partition_number(res)
The numeric values for all these statistics can be obtained by get_stats().
get_stats(res)
#> k 1-PAC mean_silhouette concordance area_increased Rand Jaccard
#> 2 2 1.000 0.974 0.989 0.4835 0.514 0.514
#> 3 3 1.000 0.963 0.985 0.2400 0.883 0.773
#> 4 4 0.919 0.858 0.940 0.0659 0.940 0.853
#> 5 5 0.929 0.871 0.941 0.0447 0.977 0.936
#> 6 6 0.839 0.837 0.904 0.0454 0.987 0.963
suggest_best_k() suggests the best \(k\) based on these statistics. The rules are as follows:
suggest_best_k(res)
#> [1] 5
#> attr(,"optional")
#> [1] 2 3 4
There is also optional best \(k\) = 2 3 4 that is worth to check.
Following shows the table of the partitions (You need to click the show/hide
code output link to see it). The membership matrix (columns with name p*)
is inferred by
clue::cl_consensus()
function with the SE method. Basically the value in the membership matrix
represents the probability to belong to a certain group. The finall class
label for an item is determined with the group with highest probability it
belongs to.
In get_classes() function, the entropy is calculated from the membership
matrix and the silhouette score is calculated from the consensus matrix.
cbind(get_classes(res, k = 2), get_membership(res, k = 2))
#> class entropy silhouette p1 p2
#> GSM550785 1 0.000 0.979 1.000 0.000
#> GSM550786 2 0.000 0.996 0.000 1.000
#> GSM550788 2 0.000 0.996 0.000 1.000
#> GSM550789 2 0.000 0.996 0.000 1.000
#> GSM550790 1 0.000 0.979 1.000 0.000
#> GSM550791 1 0.000 0.979 1.000 0.000
#> GSM550792 2 0.000 0.996 0.000 1.000
#> GSM550796 2 0.000 0.996 0.000 1.000
#> GSM550797 2 0.000 0.996 0.000 1.000
#> GSM550799 2 0.000 0.996 0.000 1.000
#> GSM550800 2 0.000 0.996 0.000 1.000
#> GSM550801 2 0.000 0.996 0.000 1.000
#> GSM550804 2 0.000 0.996 0.000 1.000
#> GSM550806 1 0.000 0.979 1.000 0.000
#> GSM550807 2 0.000 0.996 0.000 1.000
#> GSM550808 2 0.000 0.996 0.000 1.000
#> GSM550809 1 0.000 0.979 1.000 0.000
#> GSM550810 2 0.000 0.996 0.000 1.000
#> GSM550811 1 0.000 0.979 1.000 0.000
#> GSM550813 2 0.000 0.996 0.000 1.000
#> GSM550814 2 0.000 0.996 0.000 1.000
#> GSM550815 2 0.000 0.996 0.000 1.000
#> GSM550816 2 0.000 0.996 0.000 1.000
#> GSM550817 2 0.000 0.996 0.000 1.000
#> GSM550818 2 0.000 0.996 0.000 1.000
#> GSM550819 2 0.000 0.996 0.000 1.000
#> GSM550820 1 0.000 0.979 1.000 0.000
#> GSM550821 2 0.000 0.996 0.000 1.000
#> GSM550822 2 0.000 0.996 0.000 1.000
#> GSM550826 1 0.000 0.979 1.000 0.000
#> GSM550832 2 0.000 0.996 0.000 1.000
#> GSM550833 2 0.000 0.996 0.000 1.000
#> GSM550835 2 0.000 0.996 0.000 1.000
#> GSM550836 1 0.000 0.979 1.000 0.000
#> GSM550837 2 0.000 0.996 0.000 1.000
#> GSM550838 1 0.000 0.979 1.000 0.000
#> GSM550841 2 0.000 0.996 0.000 1.000
#> GSM550842 2 0.000 0.996 0.000 1.000
#> GSM550846 2 0.000 0.996 0.000 1.000
#> GSM550849 1 0.714 0.758 0.804 0.196
#> GSM550850 1 0.000 0.979 1.000 0.000
#> GSM550851 2 0.000 0.996 0.000 1.000
#> GSM550852 2 0.000 0.996 0.000 1.000
#> GSM550853 2 0.000 0.996 0.000 1.000
#> GSM550855 2 0.000 0.996 0.000 1.000
#> GSM550856 2 0.000 0.996 0.000 1.000
#> GSM550861 2 0.000 0.996 0.000 1.000
#> GSM550863 2 0.000 0.996 0.000 1.000
#> GSM550864 2 0.000 0.996 0.000 1.000
#> GSM550866 2 0.000 0.996 0.000 1.000
#> GSM550867 1 0.000 0.979 1.000 0.000
#> GSM550885 1 0.000 0.979 1.000 0.000
#> GSM550886 2 0.000 0.996 0.000 1.000
#> GSM550887 2 0.000 0.996 0.000 1.000
#> GSM550889 1 0.000 0.979 1.000 0.000
#> GSM550894 2 0.000 0.996 0.000 1.000
#> GSM550897 1 0.000 0.979 1.000 0.000
#> GSM550903 2 0.000 0.996 0.000 1.000
#> GSM550905 2 0.000 0.996 0.000 1.000
#> GSM550906 2 0.000 0.996 0.000 1.000
#> GSM550907 2 0.000 0.996 0.000 1.000
#> GSM550909 2 0.000 0.996 0.000 1.000
#> GSM550911 2 0.000 0.996 0.000 1.000
#> GSM550913 2 0.000 0.996 0.000 1.000
#> GSM550915 1 0.946 0.450 0.636 0.364
#> GSM550917 2 0.000 0.996 0.000 1.000
#> GSM550919 2 0.000 0.996 0.000 1.000
#> GSM550921 1 0.000 0.979 1.000 0.000
#> GSM550924 2 0.000 0.996 0.000 1.000
#> GSM550926 2 0.000 0.996 0.000 1.000
#> GSM550927 2 0.000 0.996 0.000 1.000
#> GSM550787 1 0.000 0.979 1.000 0.000
#> GSM550793 1 0.000 0.979 1.000 0.000
#> GSM550794 2 0.000 0.996 0.000 1.000
#> GSM550795 1 0.000 0.979 1.000 0.000
#> GSM550798 1 0.000 0.979 1.000 0.000
#> GSM550803 1 0.000 0.979 1.000 0.000
#> GSM550805 1 0.000 0.979 1.000 0.000
#> GSM550823 2 0.000 0.996 0.000 1.000
#> GSM550824 1 0.000 0.979 1.000 0.000
#> GSM550825 1 0.000 0.979 1.000 0.000
#> GSM550827 2 0.000 0.996 0.000 1.000
#> GSM550828 1 0.000 0.979 1.000 0.000
#> GSM550829 1 0.000 0.979 1.000 0.000
#> GSM550830 2 0.000 0.996 0.000 1.000
#> GSM550834 1 0.000 0.979 1.000 0.000
#> GSM550839 2 0.000 0.996 0.000 1.000
#> GSM550840 1 0.000 0.979 1.000 0.000
#> GSM550843 2 0.000 0.996 0.000 1.000
#> GSM550844 1 0.000 0.979 1.000 0.000
#> GSM550845 2 0.000 0.996 0.000 1.000
#> GSM550848 2 0.000 0.996 0.000 1.000
#> GSM550854 1 0.000 0.979 1.000 0.000
#> GSM550857 1 0.000 0.979 1.000 0.000
#> GSM550858 1 0.000 0.979 1.000 0.000
#> GSM550859 1 0.000 0.979 1.000 0.000
#> GSM550862 1 0.000 0.979 1.000 0.000
#> GSM550865 1 0.000 0.979 1.000 0.000
#> GSM550868 2 0.000 0.996 0.000 1.000
#> GSM550869 1 0.781 0.704 0.768 0.232
#> GSM550870 2 0.000 0.996 0.000 1.000
#> GSM550871 2 0.000 0.996 0.000 1.000
#> GSM550872 2 0.000 0.996 0.000 1.000
#> GSM550873 2 0.000 0.996 0.000 1.000
#> GSM550874 2 0.000 0.996 0.000 1.000
#> GSM550876 2 0.000 0.996 0.000 1.000
#> GSM550877 2 0.000 0.996 0.000 1.000
#> GSM550878 2 0.000 0.996 0.000 1.000
#> GSM550879 1 0.000 0.979 1.000 0.000
#> GSM550882 1 0.000 0.979 1.000 0.000
#> GSM550888 1 0.000 0.979 1.000 0.000
#> GSM550890 2 0.000 0.996 0.000 1.000
#> GSM550891 1 0.000 0.979 1.000 0.000
#> GSM550892 1 0.000 0.979 1.000 0.000
#> GSM550893 2 0.000 0.996 0.000 1.000
#> GSM550895 2 0.000 0.996 0.000 1.000
#> GSM550896 2 0.000 0.996 0.000 1.000
#> GSM550898 1 0.000 0.979 1.000 0.000
#> GSM550899 2 0.000 0.996 0.000 1.000
#> GSM550900 2 0.000 0.996 0.000 1.000
#> GSM550901 1 0.978 0.327 0.588 0.412
#> GSM550902 1 0.000 0.979 1.000 0.000
#> GSM550904 1 0.000 0.979 1.000 0.000
#> GSM550908 1 0.000 0.979 1.000 0.000
#> GSM550912 2 0.000 0.996 0.000 1.000
#> GSM550914 2 0.881 0.561 0.300 0.700
#> GSM550918 2 0.000 0.996 0.000 1.000
#> GSM550922 2 0.000 0.996 0.000 1.000
#> GSM550923 1 0.000 0.979 1.000 0.000
#> GSM550925 1 0.000 0.979 1.000 0.000
#> GSM550802 2 0.000 0.996 0.000 1.000
#> GSM550812 2 0.000 0.996 0.000 1.000
#> GSM550831 1 0.000 0.979 1.000 0.000
#> GSM550847 1 0.000 0.979 1.000 0.000
#> GSM550860 1 0.000 0.979 1.000 0.000
#> GSM550875 1 0.000 0.979 1.000 0.000
#> GSM550880 1 0.000 0.979 1.000 0.000
#> GSM550881 1 0.000 0.979 1.000 0.000
#> GSM550883 1 0.000 0.979 1.000 0.000
#> GSM550884 2 0.000 0.996 0.000 1.000
#> GSM550910 2 0.000 0.996 0.000 1.000
#> GSM550916 1 0.000 0.979 1.000 0.000
#> GSM550920 2 0.000 0.996 0.000 1.000
cbind(get_classes(res, k = 3), get_membership(res, k = 3))
#> class entropy silhouette p1 p2 p3
#> GSM550785 1 0.0000 0.9780 1.000 0.000 0.000
#> GSM550786 2 0.0000 0.9891 0.000 1.000 0.000
#> GSM550788 2 0.0000 0.9891 0.000 1.000 0.000
#> GSM550789 2 0.0000 0.9891 0.000 1.000 0.000
#> GSM550790 1 0.0000 0.9780 1.000 0.000 0.000
#> GSM550791 1 0.0000 0.9780 1.000 0.000 0.000
#> GSM550792 2 0.2878 0.8909 0.000 0.904 0.096
#> GSM550796 2 0.0000 0.9891 0.000 1.000 0.000
#> GSM550797 2 0.0000 0.9891 0.000 1.000 0.000
#> GSM550799 2 0.0000 0.9891 0.000 1.000 0.000
#> GSM550800 2 0.0000 0.9891 0.000 1.000 0.000
#> GSM550801 2 0.0000 0.9891 0.000 1.000 0.000
#> GSM550804 2 0.0000 0.9891 0.000 1.000 0.000
#> GSM550806 1 0.0000 0.9780 1.000 0.000 0.000
#> GSM550807 2 0.0000 0.9891 0.000 1.000 0.000
#> GSM550808 2 0.0000 0.9891 0.000 1.000 0.000
#> GSM550809 1 0.0000 0.9780 1.000 0.000 0.000
#> GSM550810 2 0.0000 0.9891 0.000 1.000 0.000
#> GSM550811 1 0.0000 0.9780 1.000 0.000 0.000
#> GSM550813 2 0.0000 0.9891 0.000 1.000 0.000
#> GSM550814 2 0.0000 0.9891 0.000 1.000 0.000
#> GSM550815 2 0.0000 0.9891 0.000 1.000 0.000
#> GSM550816 2 0.0000 0.9891 0.000 1.000 0.000
#> GSM550817 2 0.0000 0.9891 0.000 1.000 0.000
#> GSM550818 2 0.0000 0.9891 0.000 1.000 0.000
#> GSM550819 2 0.0000 0.9891 0.000 1.000 0.000
#> GSM550820 1 0.0000 0.9780 1.000 0.000 0.000
#> GSM550821 2 0.0000 0.9891 0.000 1.000 0.000
#> GSM550822 2 0.0000 0.9891 0.000 1.000 0.000
#> GSM550826 1 0.0000 0.9780 1.000 0.000 0.000
#> GSM550832 2 0.0000 0.9891 0.000 1.000 0.000
#> GSM550833 2 0.0000 0.9891 0.000 1.000 0.000
#> GSM550835 2 0.0000 0.9891 0.000 1.000 0.000
#> GSM550836 1 0.0000 0.9780 1.000 0.000 0.000
#> GSM550837 2 0.0000 0.9891 0.000 1.000 0.000
#> GSM550838 1 0.0000 0.9780 1.000 0.000 0.000
#> GSM550841 2 0.0000 0.9891 0.000 1.000 0.000
#> GSM550842 2 0.0000 0.9891 0.000 1.000 0.000
#> GSM550846 3 0.0000 0.9760 0.000 0.000 1.000
#> GSM550849 1 0.4931 0.6460 0.768 0.232 0.000
#> GSM550850 1 0.0000 0.9780 1.000 0.000 0.000
#> GSM550851 2 0.0000 0.9891 0.000 1.000 0.000
#> GSM550852 2 0.0000 0.9891 0.000 1.000 0.000
#> GSM550853 2 0.0000 0.9891 0.000 1.000 0.000
#> GSM550855 2 0.0000 0.9891 0.000 1.000 0.000
#> GSM550856 2 0.0000 0.9891 0.000 1.000 0.000
#> GSM550861 2 0.0000 0.9891 0.000 1.000 0.000
#> GSM550863 3 0.1031 0.9584 0.000 0.024 0.976
#> GSM550864 2 0.0000 0.9891 0.000 1.000 0.000
#> GSM550866 2 0.0000 0.9891 0.000 1.000 0.000
#> GSM550867 1 0.0000 0.9780 1.000 0.000 0.000
#> GSM550885 1 0.0000 0.9780 1.000 0.000 0.000
#> GSM550886 2 0.0000 0.9891 0.000 1.000 0.000
#> GSM550887 2 0.0000 0.9891 0.000 1.000 0.000
#> GSM550889 1 0.0000 0.9780 1.000 0.000 0.000
#> GSM550894 2 0.0000 0.9891 0.000 1.000 0.000
#> GSM550897 1 0.0000 0.9780 1.000 0.000 0.000
#> GSM550903 2 0.0000 0.9891 0.000 1.000 0.000
#> GSM550905 2 0.0000 0.9891 0.000 1.000 0.000
#> GSM550906 2 0.0000 0.9891 0.000 1.000 0.000
#> GSM550907 2 0.0000 0.9891 0.000 1.000 0.000
#> GSM550909 2 0.0000 0.9891 0.000 1.000 0.000
#> GSM550911 2 0.0000 0.9891 0.000 1.000 0.000
#> GSM550913 2 0.0000 0.9891 0.000 1.000 0.000
#> GSM550915 3 0.0000 0.9760 0.000 0.000 1.000
#> GSM550917 2 0.0000 0.9891 0.000 1.000 0.000
#> GSM550919 3 0.0000 0.9760 0.000 0.000 1.000
#> GSM550921 1 0.0000 0.9780 1.000 0.000 0.000
#> GSM550924 3 0.0000 0.9760 0.000 0.000 1.000
#> GSM550926 2 0.0000 0.9891 0.000 1.000 0.000
#> GSM550927 2 0.0000 0.9891 0.000 1.000 0.000
#> GSM550787 1 0.0892 0.9541 0.980 0.020 0.000
#> GSM550793 1 0.0000 0.9780 1.000 0.000 0.000
#> GSM550794 2 0.0000 0.9891 0.000 1.000 0.000
#> GSM550795 1 0.0000 0.9780 1.000 0.000 0.000
#> GSM550798 1 0.0000 0.9780 1.000 0.000 0.000
#> GSM550803 1 0.0000 0.9780 1.000 0.000 0.000
#> GSM550805 1 0.0000 0.9780 1.000 0.000 0.000
#> GSM550823 2 0.5138 0.6665 0.000 0.748 0.252
#> GSM550824 1 0.0000 0.9780 1.000 0.000 0.000
#> GSM550825 1 0.0000 0.9780 1.000 0.000 0.000
#> GSM550827 3 0.5216 0.6429 0.000 0.260 0.740
#> GSM550828 1 0.0000 0.9780 1.000 0.000 0.000
#> GSM550829 1 0.0000 0.9780 1.000 0.000 0.000
#> GSM550830 3 0.0000 0.9760 0.000 0.000 1.000
#> GSM550834 1 0.0000 0.9780 1.000 0.000 0.000
#> GSM550839 2 0.0000 0.9891 0.000 1.000 0.000
#> GSM550840 1 0.0000 0.9780 1.000 0.000 0.000
#> GSM550843 2 0.0000 0.9891 0.000 1.000 0.000
#> GSM550844 1 0.0000 0.9780 1.000 0.000 0.000
#> GSM550845 2 0.0000 0.9891 0.000 1.000 0.000
#> GSM550848 2 0.4002 0.8112 0.000 0.840 0.160
#> GSM550854 1 0.0000 0.9780 1.000 0.000 0.000
#> GSM550857 1 0.0000 0.9780 1.000 0.000 0.000
#> GSM550858 1 0.0000 0.9780 1.000 0.000 0.000
#> GSM550859 1 0.0000 0.9780 1.000 0.000 0.000
#> GSM550862 1 0.0000 0.9780 1.000 0.000 0.000
#> GSM550865 1 0.0000 0.9780 1.000 0.000 0.000
#> GSM550868 3 0.0000 0.9760 0.000 0.000 1.000
#> GSM550869 1 0.5178 0.6061 0.744 0.256 0.000
#> GSM550870 2 0.0000 0.9891 0.000 1.000 0.000
#> GSM550871 2 0.4796 0.7228 0.000 0.780 0.220
#> GSM550872 3 0.0000 0.9760 0.000 0.000 1.000
#> GSM550873 2 0.0000 0.9891 0.000 1.000 0.000
#> GSM550874 2 0.0000 0.9891 0.000 1.000 0.000
#> GSM550876 2 0.0424 0.9816 0.000 0.992 0.008
#> GSM550877 2 0.0000 0.9891 0.000 1.000 0.000
#> GSM550878 3 0.0892 0.9632 0.000 0.020 0.980
#> GSM550879 1 0.0000 0.9780 1.000 0.000 0.000
#> GSM550882 1 0.0000 0.9780 1.000 0.000 0.000
#> GSM550888 1 0.0000 0.9780 1.000 0.000 0.000
#> GSM550890 3 0.0000 0.9760 0.000 0.000 1.000
#> GSM550891 1 0.0000 0.9780 1.000 0.000 0.000
#> GSM550892 1 0.0000 0.9780 1.000 0.000 0.000
#> GSM550893 2 0.0000 0.9891 0.000 1.000 0.000
#> GSM550895 3 0.0000 0.9760 0.000 0.000 1.000
#> GSM550896 2 0.0000 0.9891 0.000 1.000 0.000
#> GSM550898 1 0.0000 0.9780 1.000 0.000 0.000
#> GSM550899 2 0.0000 0.9891 0.000 1.000 0.000
#> GSM550900 3 0.0000 0.9760 0.000 0.000 1.000
#> GSM550901 1 0.9457 0.0573 0.468 0.192 0.340
#> GSM550902 1 0.0000 0.9780 1.000 0.000 0.000
#> GSM550904 1 0.0000 0.9780 1.000 0.000 0.000
#> GSM550908 1 0.0000 0.9780 1.000 0.000 0.000
#> GSM550912 2 0.0000 0.9891 0.000 1.000 0.000
#> GSM550914 3 0.0000 0.9760 0.000 0.000 1.000
#> GSM550918 2 0.0000 0.9891 0.000 1.000 0.000
#> GSM550922 2 0.0000 0.9891 0.000 1.000 0.000
#> GSM550923 1 0.0000 0.9780 1.000 0.000 0.000
#> GSM550925 1 0.0000 0.9780 1.000 0.000 0.000
#> GSM550802 2 0.0000 0.9891 0.000 1.000 0.000
#> GSM550812 2 0.0000 0.9891 0.000 1.000 0.000
#> GSM550831 1 0.0000 0.9780 1.000 0.000 0.000
#> GSM550847 1 0.0000 0.9780 1.000 0.000 0.000
#> GSM550860 1 0.0000 0.9780 1.000 0.000 0.000
#> GSM550875 1 0.0000 0.9780 1.000 0.000 0.000
#> GSM550880 3 0.1031 0.9564 0.024 0.000 0.976
#> GSM550881 1 0.0000 0.9780 1.000 0.000 0.000
#> GSM550883 1 0.0000 0.9780 1.000 0.000 0.000
#> GSM550884 3 0.0000 0.9760 0.000 0.000 1.000
#> GSM550910 2 0.0000 0.9891 0.000 1.000 0.000
#> GSM550916 1 0.0000 0.9780 1.000 0.000 0.000
#> GSM550920 3 0.0747 0.9661 0.000 0.016 0.984
cbind(get_classes(res, k = 4), get_membership(res, k = 4))
#> class entropy silhouette p1 p2 p3 p4
#> GSM550785 1 0.0000 0.97126 1.000 0.000 0.000 0.000
#> GSM550786 2 0.0000 0.98720 0.000 1.000 0.000 0.000
#> GSM550788 2 0.0000 0.98720 0.000 1.000 0.000 0.000
#> GSM550789 2 0.0000 0.98720 0.000 1.000 0.000 0.000
#> GSM550790 1 0.0000 0.97126 1.000 0.000 0.000 0.000
#> GSM550791 1 0.2345 0.88170 0.900 0.000 0.100 0.000
#> GSM550792 4 0.4888 0.25029 0.000 0.412 0.000 0.588
#> GSM550796 2 0.0000 0.98720 0.000 1.000 0.000 0.000
#> GSM550797 2 0.0000 0.98720 0.000 1.000 0.000 0.000
#> GSM550799 2 0.0000 0.98720 0.000 1.000 0.000 0.000
#> GSM550800 2 0.0000 0.98720 0.000 1.000 0.000 0.000
#> GSM550801 2 0.0000 0.98720 0.000 1.000 0.000 0.000
#> GSM550804 2 0.0000 0.98720 0.000 1.000 0.000 0.000
#> GSM550806 4 0.7827 -0.00949 0.276 0.000 0.316 0.408
#> GSM550807 2 0.0000 0.98720 0.000 1.000 0.000 0.000
#> GSM550808 2 0.0000 0.98720 0.000 1.000 0.000 0.000
#> GSM550809 1 0.1792 0.91238 0.932 0.000 0.068 0.000
#> GSM550810 2 0.0000 0.98720 0.000 1.000 0.000 0.000
#> GSM550811 1 0.0000 0.97126 1.000 0.000 0.000 0.000
#> GSM550813 2 0.0000 0.98720 0.000 1.000 0.000 0.000
#> GSM550814 2 0.0000 0.98720 0.000 1.000 0.000 0.000
#> GSM550815 2 0.0000 0.98720 0.000 1.000 0.000 0.000
#> GSM550816 2 0.0000 0.98720 0.000 1.000 0.000 0.000
#> GSM550817 2 0.0000 0.98720 0.000 1.000 0.000 0.000
#> GSM550818 2 0.1118 0.95158 0.000 0.964 0.036 0.000
#> GSM550819 2 0.0000 0.98720 0.000 1.000 0.000 0.000
#> GSM550820 1 0.0000 0.97126 1.000 0.000 0.000 0.000
#> GSM550821 2 0.0000 0.98720 0.000 1.000 0.000 0.000
#> GSM550822 2 0.0000 0.98720 0.000 1.000 0.000 0.000
#> GSM550826 1 0.0000 0.97126 1.000 0.000 0.000 0.000
#> GSM550832 2 0.0000 0.98720 0.000 1.000 0.000 0.000
#> GSM550833 2 0.0000 0.98720 0.000 1.000 0.000 0.000
#> GSM550835 2 0.0000 0.98720 0.000 1.000 0.000 0.000
#> GSM550836 1 0.0000 0.97126 1.000 0.000 0.000 0.000
#> GSM550837 2 0.0000 0.98720 0.000 1.000 0.000 0.000
#> GSM550838 1 0.0000 0.97126 1.000 0.000 0.000 0.000
#> GSM550841 2 0.0000 0.98720 0.000 1.000 0.000 0.000
#> GSM550842 2 0.0000 0.98720 0.000 1.000 0.000 0.000
#> GSM550846 3 0.4500 0.42661 0.000 0.000 0.684 0.316
#> GSM550849 3 0.6633 0.12781 0.416 0.084 0.500 0.000
#> GSM550850 1 0.2345 0.88161 0.900 0.000 0.100 0.000
#> GSM550851 2 0.0000 0.98720 0.000 1.000 0.000 0.000
#> GSM550852 2 0.0000 0.98720 0.000 1.000 0.000 0.000
#> GSM550853 2 0.0000 0.98720 0.000 1.000 0.000 0.000
#> GSM550855 2 0.0000 0.98720 0.000 1.000 0.000 0.000
#> GSM550856 2 0.0000 0.98720 0.000 1.000 0.000 0.000
#> GSM550861 2 0.0000 0.98720 0.000 1.000 0.000 0.000
#> GSM550863 4 0.1004 0.63785 0.000 0.024 0.004 0.972
#> GSM550864 2 0.0336 0.97933 0.000 0.992 0.000 0.008
#> GSM550866 2 0.0000 0.98720 0.000 1.000 0.000 0.000
#> GSM550867 1 0.0000 0.97126 1.000 0.000 0.000 0.000
#> GSM550885 1 0.0000 0.97126 1.000 0.000 0.000 0.000
#> GSM550886 2 0.0000 0.98720 0.000 1.000 0.000 0.000
#> GSM550887 2 0.0000 0.98720 0.000 1.000 0.000 0.000
#> GSM550889 1 0.0000 0.97126 1.000 0.000 0.000 0.000
#> GSM550894 2 0.0000 0.98720 0.000 1.000 0.000 0.000
#> GSM550897 1 0.0000 0.97126 1.000 0.000 0.000 0.000
#> GSM550903 2 0.0000 0.98720 0.000 1.000 0.000 0.000
#> GSM550905 2 0.0000 0.98720 0.000 1.000 0.000 0.000
#> GSM550906 2 0.0000 0.98720 0.000 1.000 0.000 0.000
#> GSM550907 2 0.0000 0.98720 0.000 1.000 0.000 0.000
#> GSM550909 2 0.0000 0.98720 0.000 1.000 0.000 0.000
#> GSM550911 3 0.4331 0.15669 0.000 0.288 0.712 0.000
#> GSM550913 2 0.0000 0.98720 0.000 1.000 0.000 0.000
#> GSM550915 3 0.4655 0.42730 0.004 0.000 0.684 0.312
#> GSM550917 2 0.0000 0.98720 0.000 1.000 0.000 0.000
#> GSM550919 3 0.4855 0.27957 0.000 0.000 0.600 0.400
#> GSM550921 1 0.0000 0.97126 1.000 0.000 0.000 0.000
#> GSM550924 4 0.5279 0.11137 0.000 0.012 0.400 0.588
#> GSM550926 2 0.0000 0.98720 0.000 1.000 0.000 0.000
#> GSM550927 2 0.0000 0.98720 0.000 1.000 0.000 0.000
#> GSM550787 1 0.4925 0.29293 0.572 0.000 0.428 0.000
#> GSM550793 1 0.0000 0.97126 1.000 0.000 0.000 0.000
#> GSM550794 2 0.0000 0.98720 0.000 1.000 0.000 0.000
#> GSM550795 1 0.0000 0.97126 1.000 0.000 0.000 0.000
#> GSM550798 1 0.0000 0.97126 1.000 0.000 0.000 0.000
#> GSM550803 1 0.0000 0.97126 1.000 0.000 0.000 0.000
#> GSM550805 1 0.4500 0.55990 0.684 0.000 0.316 0.000
#> GSM550823 4 0.5383 0.51846 0.000 0.128 0.128 0.744
#> GSM550824 1 0.0000 0.97126 1.000 0.000 0.000 0.000
#> GSM550825 1 0.0000 0.97126 1.000 0.000 0.000 0.000
#> GSM550827 4 0.3870 0.48293 0.000 0.208 0.004 0.788
#> GSM550828 1 0.0000 0.97126 1.000 0.000 0.000 0.000
#> GSM550829 1 0.0000 0.97126 1.000 0.000 0.000 0.000
#> GSM550830 4 0.2589 0.58864 0.000 0.000 0.116 0.884
#> GSM550834 1 0.2408 0.87773 0.896 0.000 0.104 0.000
#> GSM550839 2 0.0000 0.98720 0.000 1.000 0.000 0.000
#> GSM550840 1 0.3123 0.81622 0.844 0.000 0.156 0.000
#> GSM550843 2 0.0000 0.98720 0.000 1.000 0.000 0.000
#> GSM550844 1 0.0000 0.97126 1.000 0.000 0.000 0.000
#> GSM550845 2 0.4406 0.52464 0.000 0.700 0.000 0.300
#> GSM550848 2 0.1489 0.93579 0.000 0.952 0.004 0.044
#> GSM550854 1 0.0000 0.97126 1.000 0.000 0.000 0.000
#> GSM550857 1 0.0000 0.97126 1.000 0.000 0.000 0.000
#> GSM550858 1 0.0000 0.97126 1.000 0.000 0.000 0.000
#> GSM550859 1 0.0000 0.97126 1.000 0.000 0.000 0.000
#> GSM550862 1 0.0000 0.97126 1.000 0.000 0.000 0.000
#> GSM550865 1 0.0000 0.97126 1.000 0.000 0.000 0.000
#> GSM550868 4 0.0188 0.63799 0.000 0.000 0.004 0.996
#> GSM550869 3 0.6416 0.09961 0.428 0.056 0.512 0.004
#> GSM550870 2 0.0000 0.98720 0.000 1.000 0.000 0.000
#> GSM550871 4 0.4008 0.44651 0.000 0.244 0.000 0.756
#> GSM550872 4 0.0000 0.63875 0.000 0.000 0.000 1.000
#> GSM550873 2 0.0000 0.98720 0.000 1.000 0.000 0.000
#> GSM550874 2 0.0000 0.98720 0.000 1.000 0.000 0.000
#> GSM550876 2 0.4889 0.35957 0.000 0.636 0.004 0.360
#> GSM550877 2 0.0000 0.98720 0.000 1.000 0.000 0.000
#> GSM550878 4 0.2892 0.59745 0.000 0.068 0.036 0.896
#> GSM550879 1 0.0000 0.97126 1.000 0.000 0.000 0.000
#> GSM550882 1 0.0000 0.97126 1.000 0.000 0.000 0.000
#> GSM550888 1 0.0000 0.97126 1.000 0.000 0.000 0.000
#> GSM550890 3 0.4500 0.42661 0.000 0.000 0.684 0.316
#> GSM550891 1 0.0000 0.97126 1.000 0.000 0.000 0.000
#> GSM550892 1 0.0000 0.97126 1.000 0.000 0.000 0.000
#> GSM550893 2 0.0000 0.98720 0.000 1.000 0.000 0.000
#> GSM550895 4 0.0000 0.63875 0.000 0.000 0.000 1.000
#> GSM550896 2 0.0000 0.98720 0.000 1.000 0.000 0.000
#> GSM550898 1 0.0000 0.97126 1.000 0.000 0.000 0.000
#> GSM550899 2 0.0000 0.98720 0.000 1.000 0.000 0.000
#> GSM550900 4 0.0000 0.63875 0.000 0.000 0.000 1.000
#> GSM550901 3 0.2074 0.38527 0.016 0.012 0.940 0.032
#> GSM550902 1 0.0000 0.97126 1.000 0.000 0.000 0.000
#> GSM550904 1 0.0000 0.97126 1.000 0.000 0.000 0.000
#> GSM550908 1 0.0000 0.97126 1.000 0.000 0.000 0.000
#> GSM550912 2 0.0000 0.98720 0.000 1.000 0.000 0.000
#> GSM550914 3 0.4500 0.42661 0.000 0.000 0.684 0.316
#> GSM550918 2 0.0000 0.98720 0.000 1.000 0.000 0.000
#> GSM550922 2 0.0000 0.98720 0.000 1.000 0.000 0.000
#> GSM550923 1 0.0000 0.97126 1.000 0.000 0.000 0.000
#> GSM550925 1 0.0000 0.97126 1.000 0.000 0.000 0.000
#> GSM550802 2 0.0000 0.98720 0.000 1.000 0.000 0.000
#> GSM550812 2 0.0000 0.98720 0.000 1.000 0.000 0.000
#> GSM550831 1 0.2216 0.88946 0.908 0.000 0.092 0.000
#> GSM550847 1 0.0000 0.97126 1.000 0.000 0.000 0.000
#> GSM550860 1 0.0000 0.97126 1.000 0.000 0.000 0.000
#> GSM550875 1 0.0000 0.97126 1.000 0.000 0.000 0.000
#> GSM550880 4 0.5784 0.03867 0.032 0.000 0.412 0.556
#> GSM550881 1 0.0000 0.97126 1.000 0.000 0.000 0.000
#> GSM550883 1 0.0000 0.97126 1.000 0.000 0.000 0.000
#> GSM550884 4 0.0188 0.63799 0.000 0.000 0.004 0.996
#> GSM550910 2 0.0000 0.98720 0.000 1.000 0.000 0.000
#> GSM550916 1 0.0000 0.97126 1.000 0.000 0.000 0.000
#> GSM550920 4 0.5137 0.32436 0.000 0.024 0.296 0.680
cbind(get_classes(res, k = 5), get_membership(res, k = 5))
#> class entropy silhouette p1 p2 p3 p4 p5
#> GSM550785 1 0.0000 0.971 1.000 0.000 0.000 0.000 0.000
#> GSM550786 2 0.0290 0.967 0.000 0.992 0.008 0.000 0.000
#> GSM550788 2 0.0404 0.967 0.000 0.988 0.012 0.000 0.000
#> GSM550789 2 0.0162 0.967 0.000 0.996 0.004 0.000 0.000
#> GSM550790 1 0.0000 0.971 1.000 0.000 0.000 0.000 0.000
#> GSM550791 1 0.3586 0.599 0.736 0.000 0.264 0.000 0.000
#> GSM550792 4 0.3550 0.435 0.000 0.236 0.004 0.760 0.000
#> GSM550796 2 0.0290 0.967 0.000 0.992 0.008 0.000 0.000
#> GSM550797 2 0.0290 0.967 0.000 0.992 0.008 0.000 0.000
#> GSM550799 2 0.0865 0.964 0.000 0.972 0.024 0.000 0.004
#> GSM550800 2 0.0290 0.967 0.000 0.992 0.008 0.000 0.000
#> GSM550801 2 0.0162 0.967 0.000 0.996 0.000 0.000 0.004
#> GSM550804 2 0.0324 0.967 0.000 0.992 0.004 0.000 0.004
#> GSM550806 3 0.3612 0.511 0.016 0.000 0.796 0.184 0.004
#> GSM550807 2 0.0671 0.965 0.000 0.980 0.016 0.000 0.004
#> GSM550808 2 0.0290 0.967 0.000 0.992 0.008 0.000 0.000
#> GSM550809 1 0.2377 0.822 0.872 0.000 0.128 0.000 0.000
#> GSM550810 2 0.0290 0.967 0.000 0.992 0.008 0.000 0.000
#> GSM550811 1 0.0000 0.971 1.000 0.000 0.000 0.000 0.000
#> GSM550813 2 0.1082 0.963 0.000 0.964 0.028 0.000 0.008
#> GSM550814 2 0.1082 0.963 0.000 0.964 0.028 0.000 0.008
#> GSM550815 2 0.0290 0.967 0.000 0.992 0.008 0.000 0.000
#> GSM550816 2 0.0290 0.967 0.000 0.992 0.008 0.000 0.000
#> GSM550817 2 0.0290 0.967 0.000 0.992 0.008 0.000 0.000
#> GSM550818 2 0.2660 0.842 0.000 0.864 0.008 0.000 0.128
#> GSM550819 2 0.0290 0.967 0.000 0.992 0.008 0.000 0.000
#> GSM550820 1 0.0000 0.971 1.000 0.000 0.000 0.000 0.000
#> GSM550821 2 0.0324 0.967 0.000 0.992 0.004 0.000 0.004
#> GSM550822 2 0.0290 0.967 0.000 0.992 0.008 0.000 0.000
#> GSM550826 1 0.0000 0.971 1.000 0.000 0.000 0.000 0.000
#> GSM550832 2 0.1082 0.963 0.000 0.964 0.028 0.000 0.008
#> GSM550833 2 0.0290 0.967 0.000 0.992 0.008 0.000 0.000
#> GSM550835 2 0.1082 0.963 0.000 0.964 0.028 0.000 0.008
#> GSM550836 1 0.0000 0.971 1.000 0.000 0.000 0.000 0.000
#> GSM550837 2 0.0290 0.967 0.000 0.992 0.008 0.000 0.000
#> GSM550838 1 0.0000 0.971 1.000 0.000 0.000 0.000 0.000
#> GSM550841 2 0.0290 0.967 0.000 0.992 0.008 0.000 0.000
#> GSM550842 2 0.0290 0.967 0.000 0.992 0.008 0.000 0.000
#> GSM550846 5 0.1121 0.697 0.000 0.000 0.000 0.044 0.956
#> GSM550849 3 0.3784 0.675 0.088 0.016 0.832 0.000 0.064
#> GSM550850 1 0.3895 0.468 0.680 0.000 0.320 0.000 0.000
#> GSM550851 2 0.0290 0.967 0.000 0.992 0.008 0.000 0.000
#> GSM550852 2 0.0290 0.967 0.000 0.992 0.008 0.000 0.000
#> GSM550853 2 0.0290 0.967 0.000 0.992 0.008 0.000 0.000
#> GSM550855 2 0.0162 0.967 0.000 0.996 0.004 0.000 0.000
#> GSM550856 2 0.1082 0.963 0.000 0.964 0.028 0.000 0.008
#> GSM550861 2 0.1082 0.963 0.000 0.964 0.028 0.000 0.008
#> GSM550863 4 0.0404 0.817 0.000 0.000 0.000 0.988 0.012
#> GSM550864 2 0.1369 0.959 0.000 0.956 0.028 0.008 0.008
#> GSM550866 2 0.1082 0.963 0.000 0.964 0.028 0.000 0.008
#> GSM550867 1 0.0000 0.971 1.000 0.000 0.000 0.000 0.000
#> GSM550885 1 0.0000 0.971 1.000 0.000 0.000 0.000 0.000
#> GSM550886 2 0.1082 0.963 0.000 0.964 0.028 0.000 0.008
#> GSM550887 2 0.0162 0.967 0.000 0.996 0.000 0.000 0.004
#> GSM550889 1 0.0000 0.971 1.000 0.000 0.000 0.000 0.000
#> GSM550894 2 0.1082 0.963 0.000 0.964 0.028 0.000 0.008
#> GSM550897 1 0.0000 0.971 1.000 0.000 0.000 0.000 0.000
#> GSM550903 2 0.1082 0.963 0.000 0.964 0.028 0.000 0.008
#> GSM550905 2 0.1082 0.963 0.000 0.964 0.028 0.000 0.008
#> GSM550906 2 0.1082 0.963 0.000 0.964 0.028 0.000 0.008
#> GSM550907 2 0.0451 0.967 0.000 0.988 0.008 0.000 0.004
#> GSM550909 2 0.0290 0.967 0.000 0.992 0.008 0.000 0.000
#> GSM550911 3 0.5215 0.277 0.000 0.052 0.576 0.000 0.372
#> GSM550913 2 0.0566 0.966 0.000 0.984 0.012 0.000 0.004
#> GSM550915 5 0.1121 0.697 0.000 0.000 0.000 0.044 0.956
#> GSM550917 2 0.1082 0.963 0.000 0.964 0.028 0.000 0.008
#> GSM550919 5 0.4986 0.591 0.000 0.000 0.084 0.228 0.688
#> GSM550921 1 0.0000 0.971 1.000 0.000 0.000 0.000 0.000
#> GSM550924 5 0.6242 0.194 0.000 0.000 0.144 0.408 0.448
#> GSM550926 2 0.1082 0.963 0.000 0.964 0.028 0.000 0.008
#> GSM550927 2 0.0992 0.964 0.000 0.968 0.024 0.000 0.008
#> GSM550787 3 0.1205 0.609 0.040 0.000 0.956 0.000 0.004
#> GSM550793 1 0.0000 0.971 1.000 0.000 0.000 0.000 0.000
#> GSM550794 2 0.0451 0.965 0.000 0.988 0.008 0.004 0.000
#> GSM550795 1 0.0000 0.971 1.000 0.000 0.000 0.000 0.000
#> GSM550798 1 0.0000 0.971 1.000 0.000 0.000 0.000 0.000
#> GSM550803 1 0.0000 0.971 1.000 0.000 0.000 0.000 0.000
#> GSM550805 3 0.2605 0.672 0.148 0.000 0.852 0.000 0.000
#> GSM550823 4 0.1173 0.807 0.000 0.012 0.020 0.964 0.004
#> GSM550824 1 0.0000 0.971 1.000 0.000 0.000 0.000 0.000
#> GSM550825 1 0.0000 0.971 1.000 0.000 0.000 0.000 0.000
#> GSM550827 4 0.3307 0.628 0.000 0.116 0.012 0.848 0.024
#> GSM550828 1 0.0000 0.971 1.000 0.000 0.000 0.000 0.000
#> GSM550829 1 0.0000 0.971 1.000 0.000 0.000 0.000 0.000
#> GSM550830 4 0.0566 0.814 0.000 0.000 0.012 0.984 0.004
#> GSM550834 1 0.3586 0.600 0.736 0.000 0.264 0.000 0.000
#> GSM550839 2 0.0290 0.967 0.000 0.992 0.008 0.000 0.000
#> GSM550840 3 0.4045 0.448 0.356 0.000 0.644 0.000 0.000
#> GSM550843 2 0.0000 0.967 0.000 1.000 0.000 0.000 0.000
#> GSM550844 1 0.0000 0.971 1.000 0.000 0.000 0.000 0.000
#> GSM550845 2 0.4548 0.619 0.000 0.708 0.028 0.256 0.008
#> GSM550848 2 0.1954 0.941 0.000 0.932 0.028 0.008 0.032
#> GSM550854 1 0.0000 0.971 1.000 0.000 0.000 0.000 0.000
#> GSM550857 1 0.0000 0.971 1.000 0.000 0.000 0.000 0.000
#> GSM550858 1 0.0000 0.971 1.000 0.000 0.000 0.000 0.000
#> GSM550859 1 0.0000 0.971 1.000 0.000 0.000 0.000 0.000
#> GSM550862 1 0.0000 0.971 1.000 0.000 0.000 0.000 0.000
#> GSM550865 1 0.0000 0.971 1.000 0.000 0.000 0.000 0.000
#> GSM550868 4 0.0404 0.817 0.000 0.000 0.000 0.988 0.012
#> GSM550869 3 0.5546 0.633 0.160 0.016 0.696 0.004 0.124
#> GSM550870 2 0.1082 0.963 0.000 0.964 0.028 0.000 0.008
#> GSM550871 4 0.0404 0.815 0.000 0.012 0.000 0.988 0.000
#> GSM550872 4 0.0000 0.819 0.000 0.000 0.000 1.000 0.000
#> GSM550873 2 0.0290 0.967 0.000 0.992 0.008 0.000 0.000
#> GSM550874 2 0.0510 0.966 0.000 0.984 0.016 0.000 0.000
#> GSM550876 2 0.6547 -0.136 0.000 0.452 0.100 0.420 0.028
#> GSM550877 2 0.1082 0.963 0.000 0.964 0.028 0.000 0.008
#> GSM550878 4 0.6315 0.406 0.000 0.048 0.152 0.636 0.164
#> GSM550879 1 0.0000 0.971 1.000 0.000 0.000 0.000 0.000
#> GSM550882 1 0.0000 0.971 1.000 0.000 0.000 0.000 0.000
#> GSM550888 1 0.0000 0.971 1.000 0.000 0.000 0.000 0.000
#> GSM550890 5 0.1121 0.697 0.000 0.000 0.000 0.044 0.956
#> GSM550891 1 0.0000 0.971 1.000 0.000 0.000 0.000 0.000
#> GSM550892 1 0.0000 0.971 1.000 0.000 0.000 0.000 0.000
#> GSM550893 2 0.1082 0.963 0.000 0.964 0.028 0.000 0.008
#> GSM550895 4 0.0000 0.819 0.000 0.000 0.000 1.000 0.000
#> GSM550896 2 0.0955 0.964 0.000 0.968 0.028 0.000 0.004
#> GSM550898 1 0.0000 0.971 1.000 0.000 0.000 0.000 0.000
#> GSM550899 2 0.1082 0.963 0.000 0.964 0.028 0.000 0.008
#> GSM550900 4 0.0000 0.819 0.000 0.000 0.000 1.000 0.000
#> GSM550901 5 0.5045 0.112 0.012 0.004 0.456 0.008 0.520
#> GSM550902 1 0.0000 0.971 1.000 0.000 0.000 0.000 0.000
#> GSM550904 1 0.0000 0.971 1.000 0.000 0.000 0.000 0.000
#> GSM550908 1 0.0000 0.971 1.000 0.000 0.000 0.000 0.000
#> GSM550912 2 0.1082 0.963 0.000 0.964 0.028 0.000 0.008
#> GSM550914 5 0.1121 0.697 0.000 0.000 0.000 0.044 0.956
#> GSM550918 2 0.1082 0.963 0.000 0.964 0.028 0.000 0.008
#> GSM550922 2 0.1082 0.963 0.000 0.964 0.028 0.000 0.008
#> GSM550923 1 0.0000 0.971 1.000 0.000 0.000 0.000 0.000
#> GSM550925 1 0.0000 0.971 1.000 0.000 0.000 0.000 0.000
#> GSM550802 2 0.0290 0.967 0.000 0.992 0.008 0.000 0.000
#> GSM550812 2 0.0290 0.967 0.000 0.992 0.008 0.000 0.000
#> GSM550831 1 0.3210 0.694 0.788 0.000 0.212 0.000 0.000
#> GSM550847 1 0.0000 0.971 1.000 0.000 0.000 0.000 0.000
#> GSM550860 1 0.0000 0.971 1.000 0.000 0.000 0.000 0.000
#> GSM550875 1 0.0000 0.971 1.000 0.000 0.000 0.000 0.000
#> GSM550880 5 0.6858 0.337 0.032 0.000 0.140 0.344 0.484
#> GSM550881 1 0.0000 0.971 1.000 0.000 0.000 0.000 0.000
#> GSM550883 1 0.0000 0.971 1.000 0.000 0.000 0.000 0.000
#> GSM550884 4 0.0510 0.815 0.000 0.000 0.000 0.984 0.016
#> GSM550910 2 0.0290 0.967 0.000 0.992 0.008 0.000 0.000
#> GSM550916 1 0.0000 0.971 1.000 0.000 0.000 0.000 0.000
#> GSM550920 4 0.6288 -0.142 0.000 0.000 0.156 0.472 0.372
cbind(get_classes(res, k = 6), get_membership(res, k = 6))
#> class entropy silhouette p1 p2 p3 p4 p5 p6
#> GSM550785 1 0.0000 0.965 1.000 0.000 0.000 0.000 0.000 0.000
#> GSM550786 2 0.0767 0.863 0.000 0.976 0.004 0.008 0.012 0.000
#> GSM550788 2 0.0405 0.870 0.000 0.988 0.004 0.000 0.008 0.000
#> GSM550789 2 0.0937 0.875 0.000 0.960 0.000 0.000 0.040 0.000
#> GSM550790 1 0.0000 0.965 1.000 0.000 0.000 0.000 0.000 0.000
#> GSM550791 1 0.4065 0.499 0.672 0.000 0.300 0.000 0.028 0.000
#> GSM550792 4 0.2965 0.733 0.000 0.080 0.000 0.848 0.072 0.000
#> GSM550796 2 0.0146 0.869 0.000 0.996 0.004 0.000 0.000 0.000
#> GSM550797 2 0.0146 0.869 0.000 0.996 0.004 0.000 0.000 0.000
#> GSM550799 2 0.2416 0.862 0.000 0.844 0.000 0.000 0.156 0.000
#> GSM550800 2 0.0146 0.869 0.000 0.996 0.004 0.000 0.000 0.000
#> GSM550801 2 0.1141 0.875 0.000 0.948 0.000 0.000 0.052 0.000
#> GSM550804 2 0.1204 0.875 0.000 0.944 0.000 0.000 0.056 0.000
#> GSM550806 3 0.2179 0.658 0.004 0.000 0.908 0.064 0.016 0.008
#> GSM550807 2 0.2378 0.864 0.000 0.848 0.000 0.000 0.152 0.000
#> GSM550808 2 0.0858 0.859 0.000 0.968 0.004 0.000 0.028 0.000
#> GSM550809 1 0.3042 0.783 0.836 0.000 0.128 0.000 0.032 0.004
#> GSM550810 2 0.0291 0.868 0.000 0.992 0.004 0.000 0.004 0.000
#> GSM550811 1 0.0146 0.962 0.996 0.000 0.000 0.000 0.004 0.000
#> GSM550813 2 0.3050 0.837 0.000 0.764 0.000 0.000 0.236 0.000
#> GSM550814 2 0.2969 0.843 0.000 0.776 0.000 0.000 0.224 0.000
#> GSM550815 2 0.0777 0.861 0.000 0.972 0.004 0.000 0.024 0.000
#> GSM550816 2 0.0858 0.859 0.000 0.968 0.004 0.000 0.028 0.000
#> GSM550817 2 0.0935 0.857 0.000 0.964 0.004 0.000 0.032 0.000
#> GSM550818 2 0.3712 0.628 0.000 0.760 0.004 0.000 0.032 0.204
#> GSM550819 2 0.0865 0.873 0.000 0.964 0.000 0.000 0.036 0.000
#> GSM550820 1 0.0000 0.965 1.000 0.000 0.000 0.000 0.000 0.000
#> GSM550821 2 0.1075 0.875 0.000 0.952 0.000 0.000 0.048 0.000
#> GSM550822 2 0.0858 0.859 0.000 0.968 0.004 0.000 0.028 0.000
#> GSM550826 1 0.0000 0.965 1.000 0.000 0.000 0.000 0.000 0.000
#> GSM550832 2 0.2941 0.844 0.000 0.780 0.000 0.000 0.220 0.000
#> GSM550833 2 0.0146 0.869 0.000 0.996 0.004 0.000 0.000 0.000
#> GSM550835 2 0.2969 0.843 0.000 0.776 0.000 0.000 0.224 0.000
#> GSM550836 1 0.0000 0.965 1.000 0.000 0.000 0.000 0.000 0.000
#> GSM550837 2 0.0146 0.869 0.000 0.996 0.004 0.000 0.000 0.000
#> GSM550838 1 0.0260 0.958 0.992 0.000 0.000 0.000 0.008 0.000
#> GSM550841 2 0.0858 0.859 0.000 0.968 0.004 0.000 0.028 0.000
#> GSM550842 2 0.0291 0.868 0.000 0.992 0.004 0.000 0.004 0.000
#> GSM550846 6 0.0632 0.752 0.000 0.000 0.000 0.024 0.000 0.976
#> GSM550849 3 0.1635 0.695 0.016 0.004 0.944 0.004 0.008 0.024
#> GSM550850 1 0.4578 0.215 0.568 0.000 0.396 0.000 0.032 0.004
#> GSM550851 2 0.0291 0.868 0.000 0.992 0.004 0.000 0.004 0.000
#> GSM550852 2 0.0870 0.861 0.000 0.972 0.004 0.012 0.012 0.000
#> GSM550853 2 0.0146 0.869 0.000 0.996 0.004 0.000 0.000 0.000
#> GSM550855 2 0.0146 0.871 0.000 0.996 0.000 0.000 0.004 0.000
#> GSM550856 2 0.3023 0.839 0.000 0.768 0.000 0.000 0.232 0.000
#> GSM550861 2 0.3023 0.839 0.000 0.768 0.000 0.000 0.232 0.000
#> GSM550863 4 0.0820 0.925 0.000 0.000 0.000 0.972 0.012 0.016
#> GSM550864 2 0.3394 0.829 0.000 0.752 0.000 0.012 0.236 0.000
#> GSM550866 2 0.3050 0.837 0.000 0.764 0.000 0.000 0.236 0.000
#> GSM550867 1 0.0000 0.965 1.000 0.000 0.000 0.000 0.000 0.000
#> GSM550885 1 0.0000 0.965 1.000 0.000 0.000 0.000 0.000 0.000
#> GSM550886 2 0.3023 0.839 0.000 0.768 0.000 0.000 0.232 0.000
#> GSM550887 2 0.1327 0.875 0.000 0.936 0.000 0.000 0.064 0.000
#> GSM550889 1 0.0000 0.965 1.000 0.000 0.000 0.000 0.000 0.000
#> GSM550894 2 0.2996 0.841 0.000 0.772 0.000 0.000 0.228 0.000
#> GSM550897 1 0.0000 0.965 1.000 0.000 0.000 0.000 0.000 0.000
#> GSM550903 2 0.3023 0.839 0.000 0.768 0.000 0.000 0.232 0.000
#> GSM550905 2 0.3050 0.837 0.000 0.764 0.000 0.000 0.236 0.000
#> GSM550906 2 0.2738 0.858 0.000 0.820 0.004 0.000 0.176 0.000
#> GSM550907 2 0.1444 0.871 0.000 0.928 0.000 0.000 0.072 0.000
#> GSM550909 2 0.0858 0.859 0.000 0.968 0.004 0.000 0.028 0.000
#> GSM550911 6 0.6807 -0.058 0.000 0.116 0.388 0.000 0.104 0.392
#> GSM550913 2 0.1663 0.873 0.000 0.912 0.000 0.000 0.088 0.000
#> GSM550915 6 0.0458 0.748 0.000 0.000 0.000 0.016 0.000 0.984
#> GSM550917 2 0.3050 0.837 0.000 0.764 0.000 0.000 0.236 0.000
#> GSM550919 6 0.5955 0.147 0.000 0.000 0.020 0.144 0.328 0.508
#> GSM550921 1 0.0000 0.965 1.000 0.000 0.000 0.000 0.000 0.000
#> GSM550924 5 0.5143 0.626 0.000 0.000 0.032 0.108 0.680 0.180
#> GSM550926 2 0.3050 0.837 0.000 0.764 0.000 0.000 0.236 0.000
#> GSM550927 2 0.2597 0.857 0.000 0.824 0.000 0.000 0.176 0.000
#> GSM550787 3 0.1503 0.698 0.016 0.000 0.944 0.000 0.032 0.008
#> GSM550793 1 0.0000 0.965 1.000 0.000 0.000 0.000 0.000 0.000
#> GSM550794 2 0.0964 0.860 0.000 0.968 0.004 0.016 0.012 0.000
#> GSM550795 1 0.0000 0.965 1.000 0.000 0.000 0.000 0.000 0.000
#> GSM550798 1 0.0000 0.965 1.000 0.000 0.000 0.000 0.000 0.000
#> GSM550803 1 0.0000 0.965 1.000 0.000 0.000 0.000 0.000 0.000
#> GSM550805 3 0.1749 0.710 0.036 0.000 0.932 0.000 0.024 0.008
#> GSM550823 4 0.0810 0.923 0.000 0.004 0.004 0.976 0.008 0.008
#> GSM550824 1 0.0000 0.965 1.000 0.000 0.000 0.000 0.000 0.000
#> GSM550825 1 0.0000 0.965 1.000 0.000 0.000 0.000 0.000 0.000
#> GSM550827 4 0.2903 0.797 0.000 0.036 0.000 0.864 0.084 0.016
#> GSM550828 1 0.0000 0.965 1.000 0.000 0.000 0.000 0.000 0.000
#> GSM550829 1 0.0000 0.965 1.000 0.000 0.000 0.000 0.000 0.000
#> GSM550830 4 0.0976 0.917 0.000 0.000 0.016 0.968 0.008 0.008
#> GSM550834 1 0.4338 0.475 0.660 0.000 0.300 0.000 0.036 0.004
#> GSM550839 2 0.0964 0.860 0.000 0.968 0.004 0.012 0.016 0.000
#> GSM550840 3 0.3852 0.511 0.224 0.000 0.740 0.000 0.032 0.004
#> GSM550843 2 0.0790 0.874 0.000 0.968 0.000 0.000 0.032 0.000
#> GSM550844 1 0.0000 0.965 1.000 0.000 0.000 0.000 0.000 0.000
#> GSM550845 2 0.5478 0.579 0.000 0.568 0.000 0.196 0.236 0.000
#> GSM550848 2 0.3987 0.813 0.000 0.728 0.000 0.012 0.236 0.024
#> GSM550854 1 0.0000 0.965 1.000 0.000 0.000 0.000 0.000 0.000
#> GSM550857 1 0.0000 0.965 1.000 0.000 0.000 0.000 0.000 0.000
#> GSM550858 1 0.0000 0.965 1.000 0.000 0.000 0.000 0.000 0.000
#> GSM550859 1 0.0000 0.965 1.000 0.000 0.000 0.000 0.000 0.000
#> GSM550862 1 0.0000 0.965 1.000 0.000 0.000 0.000 0.000 0.000
#> GSM550865 1 0.0000 0.965 1.000 0.000 0.000 0.000 0.000 0.000
#> GSM550868 4 0.0458 0.926 0.000 0.000 0.000 0.984 0.000 0.016
#> GSM550869 3 0.5526 0.560 0.152 0.008 0.692 0.008 0.076 0.064
#> GSM550870 2 0.3050 0.837 0.000 0.764 0.000 0.000 0.236 0.000
#> GSM550871 4 0.1074 0.904 0.000 0.028 0.000 0.960 0.012 0.000
#> GSM550872 4 0.0000 0.928 0.000 0.000 0.000 1.000 0.000 0.000
#> GSM550873 2 0.0870 0.861 0.000 0.972 0.004 0.012 0.012 0.000
#> GSM550874 2 0.2163 0.870 0.000 0.892 0.004 0.008 0.096 0.000
#> GSM550876 5 0.5522 0.349 0.000 0.260 0.024 0.112 0.604 0.000
#> GSM550877 2 0.3023 0.839 0.000 0.768 0.000 0.000 0.232 0.000
#> GSM550878 5 0.4303 0.618 0.000 0.020 0.028 0.148 0.772 0.032
#> GSM550879 1 0.0000 0.965 1.000 0.000 0.000 0.000 0.000 0.000
#> GSM550882 1 0.0000 0.965 1.000 0.000 0.000 0.000 0.000 0.000
#> GSM550888 1 0.0000 0.965 1.000 0.000 0.000 0.000 0.000 0.000
#> GSM550890 6 0.0632 0.752 0.000 0.000 0.000 0.024 0.000 0.976
#> GSM550891 1 0.0000 0.965 1.000 0.000 0.000 0.000 0.000 0.000
#> GSM550892 1 0.0000 0.965 1.000 0.000 0.000 0.000 0.000 0.000
#> GSM550893 2 0.3050 0.837 0.000 0.764 0.000 0.000 0.236 0.000
#> GSM550895 4 0.0405 0.929 0.000 0.000 0.000 0.988 0.008 0.004
#> GSM550896 2 0.2941 0.844 0.000 0.780 0.000 0.000 0.220 0.000
#> GSM550898 1 0.0000 0.965 1.000 0.000 0.000 0.000 0.000 0.000
#> GSM550899 2 0.3050 0.837 0.000 0.764 0.000 0.000 0.236 0.000
#> GSM550900 4 0.0146 0.928 0.000 0.000 0.000 0.996 0.004 0.000
#> GSM550901 3 0.6494 -0.015 0.012 0.012 0.412 0.000 0.204 0.360
#> GSM550902 1 0.0000 0.965 1.000 0.000 0.000 0.000 0.000 0.000
#> GSM550904 1 0.0000 0.965 1.000 0.000 0.000 0.000 0.000 0.000
#> GSM550908 1 0.0000 0.965 1.000 0.000 0.000 0.000 0.000 0.000
#> GSM550912 2 0.3244 0.813 0.000 0.732 0.000 0.000 0.268 0.000
#> GSM550914 6 0.0632 0.752 0.000 0.000 0.000 0.024 0.000 0.976
#> GSM550918 2 0.3050 0.837 0.000 0.764 0.000 0.000 0.236 0.000
#> GSM550922 2 0.3023 0.839 0.000 0.768 0.000 0.000 0.232 0.000
#> GSM550923 1 0.0000 0.965 1.000 0.000 0.000 0.000 0.000 0.000
#> GSM550925 1 0.0000 0.965 1.000 0.000 0.000 0.000 0.000 0.000
#> GSM550802 2 0.0862 0.862 0.000 0.972 0.004 0.008 0.016 0.000
#> GSM550812 2 0.1442 0.845 0.000 0.944 0.004 0.012 0.040 0.000
#> GSM550831 1 0.3878 0.626 0.736 0.000 0.228 0.000 0.032 0.004
#> GSM550847 1 0.0000 0.965 1.000 0.000 0.000 0.000 0.000 0.000
#> GSM550860 1 0.0000 0.965 1.000 0.000 0.000 0.000 0.000 0.000
#> GSM550875 1 0.0000 0.965 1.000 0.000 0.000 0.000 0.000 0.000
#> GSM550880 5 0.5817 0.554 0.024 0.000 0.036 0.100 0.644 0.196
#> GSM550881 1 0.0000 0.965 1.000 0.000 0.000 0.000 0.000 0.000
#> GSM550883 1 0.0000 0.965 1.000 0.000 0.000 0.000 0.000 0.000
#> GSM550884 4 0.0993 0.922 0.000 0.000 0.000 0.964 0.012 0.024
#> GSM550910 2 0.0858 0.859 0.000 0.968 0.004 0.000 0.028 0.000
#> GSM550916 1 0.0000 0.965 1.000 0.000 0.000 0.000 0.000 0.000
#> GSM550920 5 0.4859 0.657 0.000 0.000 0.032 0.116 0.716 0.136
Heatmaps for the consensus matrix. It visualizes the probability of two samples to be in a same group.
consensus_heatmap(res, k = 2)
consensus_heatmap(res, k = 3)
consensus_heatmap(res, k = 4)
consensus_heatmap(res, k = 5)
consensus_heatmap(res, k = 6)
Heatmaps for the membership of samples in all partitions to see how consistent they are:
membership_heatmap(res, k = 2)
membership_heatmap(res, k = 3)
membership_heatmap(res, k = 4)
membership_heatmap(res, k = 5)
membership_heatmap(res, k = 6)
As soon as we have had the classes for columns, we can look for signatures which are significantly different between classes which can be candidate marks for certain classes. Following are the heatmaps for signatures.
Signature heatmaps where rows are scaled:
get_signatures(res, k = 2)
get_signatures(res, k = 3)
get_signatures(res, k = 4)
get_signatures(res, k = 5)
get_signatures(res, k = 6)
Signature heatmaps where rows are not scaled:
get_signatures(res, k = 2, scale_rows = FALSE)
get_signatures(res, k = 3, scale_rows = FALSE)
get_signatures(res, k = 4, scale_rows = FALSE)
get_signatures(res, k = 5, scale_rows = FALSE)
get_signatures(res, k = 6, scale_rows = FALSE)
Compare the overlap of signatures from different k:
compare_signatures(res)
get_signature() returns a data frame invisibly. TO get the list of signatures, the function
call should be assigned to a variable explicitly. In following code, if plot argument is set
to FALSE, no heatmap is plotted while only the differential analysis is performed.
# code only for demonstration
tb = get_signature(res, k = ..., plot = FALSE)
An example of the output of tb is:
#> which_row fdr mean_1 mean_2 scaled_mean_1 scaled_mean_2 km
#> 1 38 0.042760348 8.373488 9.131774 -0.5533452 0.5164555 1
#> 2 40 0.018707592 7.106213 8.469186 -0.6173731 0.5762149 1
#> 3 55 0.019134737 10.221463 11.207825 -0.6159697 0.5749050 1
#> 4 59 0.006059896 5.921854 7.869574 -0.6899429 0.6439467 1
#> 5 60 0.018055526 8.928898 10.211722 -0.6204761 0.5791110 1
#> 6 98 0.009384629 15.714769 14.887706 0.6635654 -0.6193277 2
...
The columns in tb are:
which_row: row indices corresponding to the input matrix.fdr: FDR for the differential test. mean_x: The mean value in group x.scaled_mean_x: The mean value in group x after rows are scaled.km: Row groups if k-means clustering is applied to rows.UMAP plot which shows how samples are separated.
dimension_reduction(res, k = 2, method = "UMAP")
dimension_reduction(res, k = 3, method = "UMAP")
dimension_reduction(res, k = 4, method = "UMAP")
dimension_reduction(res, k = 5, method = "UMAP")
dimension_reduction(res, k = 6, method = "UMAP")
Following heatmap shows how subgroups are split when increasing k:
collect_classes(res)
Test correlation between subgroups and known annotations. If the known annotation is numeric, one-way ANOVA test is applied, and if the known annotation is discrete, chi-squared contingency table test is applied.
test_to_known_factors(res)
#> n disease.state(p) k
#> ATC:skmeans 141 8.61e-04 2
#> ATC:skmeans 142 1.42e-04 3
#> ATC:skmeans 125 1.65e-05 4
#> ATC:skmeans 133 2.10e-04 5
#> ATC:skmeans 136 6.10e-05 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 51776 rows and 143 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 4.
#>
#> Following methods can be applied to this 'ConsensusPartition' object:
#> [1] "cola_report" "collect_classes" "collect_plots"
#> [4] "collect_stats" "colnames" "compare_signatures"
#> [7] "consensus_heatmap" "dimension_reduction" "functional_enrichment"
#> [10] "get_anno_col" "get_anno" "get_classes"
#> [13] "get_consensus" "get_matrix" "get_membership"
#> [16] "get_param" "get_signatures" "get_stats"
#> [19] "is_best_k" "is_stable_k" "membership_heatmap"
#> [22] "ncol" "nrow" "plot_ecdf"
#> [25] "rownames" "select_partition_number" "show"
#> [28] "suggest_best_k" "test_to_known_factors"
collect_plots() function collects all the plots made from res for all k (number of partitions)
into one single page to provide an easy and fast comparison between different k.
collect_plots(res)
The plots are:
k and the heatmap of
predicted classes for each k.k.k.k.All the plots in panels can be made by individual functions and they are plotted later in this section.
select_partition_number() produces several plots showing different
statistics for choosing “optimized” k. There are following statistics:
k;k, the area increased is defined as \(A_k - A_{k-1}\).The detailed explanations of these statistics can be found in the cola vignette.
Generally speaking, lower PAC score, higher mean silhouette score or higher
concordance corresponds to better partition. Rand index and Jaccard index
measure how similar the current partition is compared to partition with k-1.
If they are too similar, we won't accept k is better than k-1.
select_partition_number(res)
The numeric values for all these statistics can be obtained by get_stats().
get_stats(res)
#> k 1-PAC mean_silhouette concordance area_increased Rand Jaccard
#> 2 2 1.000 0.972 0.990 0.4519 0.546 0.546
#> 3 3 0.551 0.796 0.870 0.3617 0.609 0.409
#> 4 4 0.972 0.962 0.983 0.1420 0.715 0.414
#> 5 5 0.733 0.463 0.761 0.0916 0.937 0.797
#> 6 6 0.825 0.797 0.892 0.0618 0.866 0.532
suggest_best_k() suggests the best \(k\) based on these statistics. The rules are as follows:
suggest_best_k(res)
#> [1] 4
#> attr(,"optional")
#> [1] 2
There is also optional best \(k\) = 2 that is worth to check.
Following shows the table of the partitions (You need to click the show/hide
code output link to see it). The membership matrix (columns with name p*)
is inferred by
clue::cl_consensus()
function with the SE method. Basically the value in the membership matrix
represents the probability to belong to a certain group. The finall class
label for an item is determined with the group with highest probability it
belongs to.
In get_classes() function, the entropy is calculated from the membership
matrix and the silhouette score is calculated from the consensus matrix.
cbind(get_classes(res, k = 2), get_membership(res, k = 2))
#> class entropy silhouette p1 p2
#> GSM550785 1 0.0000 0.9795 1.000 0.000
#> GSM550786 2 0.0000 0.9945 0.000 1.000
#> GSM550788 2 0.0000 0.9945 0.000 1.000
#> GSM550789 2 0.0000 0.9945 0.000 1.000
#> GSM550790 1 0.0000 0.9795 1.000 0.000
#> GSM550791 1 0.3114 0.9267 0.944 0.056
#> GSM550792 2 0.0000 0.9945 0.000 1.000
#> GSM550796 2 0.0000 0.9945 0.000 1.000
#> GSM550797 2 0.0000 0.9945 0.000 1.000
#> GSM550799 2 0.0000 0.9945 0.000 1.000
#> GSM550800 2 0.0000 0.9945 0.000 1.000
#> GSM550801 2 0.0000 0.9945 0.000 1.000
#> GSM550804 2 0.0000 0.9945 0.000 1.000
#> GSM550806 2 0.0000 0.9945 0.000 1.000
#> GSM550807 2 0.0000 0.9945 0.000 1.000
#> GSM550808 2 0.0000 0.9945 0.000 1.000
#> GSM550809 1 0.0000 0.9795 1.000 0.000
#> GSM550810 2 0.0000 0.9945 0.000 1.000
#> GSM550811 2 1.0000 -0.0302 0.496 0.504
#> GSM550813 2 0.0000 0.9945 0.000 1.000
#> GSM550814 2 0.0000 0.9945 0.000 1.000
#> GSM550815 2 0.0000 0.9945 0.000 1.000
#> GSM550816 2 0.0000 0.9945 0.000 1.000
#> GSM550817 2 0.0000 0.9945 0.000 1.000
#> GSM550818 2 0.0000 0.9945 0.000 1.000
#> GSM550819 2 0.0000 0.9945 0.000 1.000
#> GSM550820 1 0.0000 0.9795 1.000 0.000
#> GSM550821 2 0.0000 0.9945 0.000 1.000
#> GSM550822 2 0.0000 0.9945 0.000 1.000
#> GSM550826 1 0.0000 0.9795 1.000 0.000
#> GSM550832 2 0.0000 0.9945 0.000 1.000
#> GSM550833 2 0.0000 0.9945 0.000 1.000
#> GSM550835 2 0.0000 0.9945 0.000 1.000
#> GSM550836 1 0.0000 0.9795 1.000 0.000
#> GSM550837 2 0.0000 0.9945 0.000 1.000
#> GSM550838 1 0.0000 0.9795 1.000 0.000
#> GSM550841 2 0.0000 0.9945 0.000 1.000
#> GSM550842 2 0.0000 0.9945 0.000 1.000
#> GSM550846 2 0.0000 0.9945 0.000 1.000
#> GSM550849 2 0.0000 0.9945 0.000 1.000
#> GSM550850 1 0.0000 0.9795 1.000 0.000
#> GSM550851 2 0.0000 0.9945 0.000 1.000
#> GSM550852 2 0.0000 0.9945 0.000 1.000
#> GSM550853 2 0.0000 0.9945 0.000 1.000
#> GSM550855 2 0.0000 0.9945 0.000 1.000
#> GSM550856 2 0.0000 0.9945 0.000 1.000
#> GSM550861 2 0.0000 0.9945 0.000 1.000
#> GSM550863 2 0.0000 0.9945 0.000 1.000
#> GSM550864 2 0.0000 0.9945 0.000 1.000
#> GSM550866 2 0.0000 0.9945 0.000 1.000
#> GSM550867 1 0.0000 0.9795 1.000 0.000
#> GSM550885 1 0.0000 0.9795 1.000 0.000
#> GSM550886 2 0.0000 0.9945 0.000 1.000
#> GSM550887 2 0.0000 0.9945 0.000 1.000
#> GSM550889 1 0.0000 0.9795 1.000 0.000
#> GSM550894 2 0.0000 0.9945 0.000 1.000
#> GSM550897 1 0.0000 0.9795 1.000 0.000
#> GSM550903 2 0.0000 0.9945 0.000 1.000
#> GSM550905 2 0.0000 0.9945 0.000 1.000
#> GSM550906 2 0.0000 0.9945 0.000 1.000
#> GSM550907 2 0.0000 0.9945 0.000 1.000
#> GSM550909 2 0.0000 0.9945 0.000 1.000
#> GSM550911 2 0.0000 0.9945 0.000 1.000
#> GSM550913 2 0.0000 0.9945 0.000 1.000
#> GSM550915 2 0.0000 0.9945 0.000 1.000
#> GSM550917 2 0.0000 0.9945 0.000 1.000
#> GSM550919 2 0.0000 0.9945 0.000 1.000
#> GSM550921 1 0.0000 0.9795 1.000 0.000
#> GSM550924 2 0.0000 0.9945 0.000 1.000
#> GSM550926 2 0.0000 0.9945 0.000 1.000
#> GSM550927 2 0.0000 0.9945 0.000 1.000
#> GSM550787 2 0.0000 0.9945 0.000 1.000
#> GSM550793 1 0.0000 0.9795 1.000 0.000
#> GSM550794 2 0.0000 0.9945 0.000 1.000
#> GSM550795 1 0.0000 0.9795 1.000 0.000
#> GSM550798 1 0.0000 0.9795 1.000 0.000
#> GSM550803 1 0.0000 0.9795 1.000 0.000
#> GSM550805 2 0.0000 0.9945 0.000 1.000
#> GSM550823 2 0.0000 0.9945 0.000 1.000
#> GSM550824 1 0.0000 0.9795 1.000 0.000
#> GSM550825 1 0.0000 0.9795 1.000 0.000
#> GSM550827 2 0.0000 0.9945 0.000 1.000
#> GSM550828 1 0.0000 0.9795 1.000 0.000
#> GSM550829 1 0.0000 0.9795 1.000 0.000
#> GSM550830 2 0.0000 0.9945 0.000 1.000
#> GSM550834 1 0.9170 0.5153 0.668 0.332
#> GSM550839 2 0.0000 0.9945 0.000 1.000
#> GSM550840 1 0.6438 0.8006 0.836 0.164
#> GSM550843 2 0.0000 0.9945 0.000 1.000
#> GSM550844 1 0.0000 0.9795 1.000 0.000
#> GSM550845 2 0.0000 0.9945 0.000 1.000
#> GSM550848 2 0.0000 0.9945 0.000 1.000
#> GSM550854 1 0.0000 0.9795 1.000 0.000
#> GSM550857 1 0.0000 0.9795 1.000 0.000
#> GSM550858 1 0.0000 0.9795 1.000 0.000
#> GSM550859 1 0.0000 0.9795 1.000 0.000
#> GSM550862 1 0.0000 0.9795 1.000 0.000
#> GSM550865 1 0.9833 0.2752 0.576 0.424
#> GSM550868 2 0.0000 0.9945 0.000 1.000
#> GSM550869 2 0.0000 0.9945 0.000 1.000
#> GSM550870 2 0.0000 0.9945 0.000 1.000
#> GSM550871 2 0.0000 0.9945 0.000 1.000
#> GSM550872 2 0.0000 0.9945 0.000 1.000
#> GSM550873 2 0.0000 0.9945 0.000 1.000
#> GSM550874 2 0.0000 0.9945 0.000 1.000
#> GSM550876 2 0.0000 0.9945 0.000 1.000
#> GSM550877 2 0.0000 0.9945 0.000 1.000
#> GSM550878 2 0.0000 0.9945 0.000 1.000
#> GSM550879 1 0.0000 0.9795 1.000 0.000
#> GSM550882 1 0.0000 0.9795 1.000 0.000
#> GSM550888 1 0.0000 0.9795 1.000 0.000
#> GSM550890 2 0.0000 0.9945 0.000 1.000
#> GSM550891 1 0.0000 0.9795 1.000 0.000
#> GSM550892 1 0.0000 0.9795 1.000 0.000
#> GSM550893 2 0.0000 0.9945 0.000 1.000
#> GSM550895 2 0.0000 0.9945 0.000 1.000
#> GSM550896 2 0.0000 0.9945 0.000 1.000
#> GSM550898 1 0.0000 0.9795 1.000 0.000
#> GSM550899 2 0.0000 0.9945 0.000 1.000
#> GSM550900 2 0.0000 0.9945 0.000 1.000
#> GSM550901 2 0.0000 0.9945 0.000 1.000
#> GSM550902 1 0.0000 0.9795 1.000 0.000
#> GSM550904 1 0.0000 0.9795 1.000 0.000
#> GSM550908 1 0.0000 0.9795 1.000 0.000
#> GSM550912 2 0.0000 0.9945 0.000 1.000
#> GSM550914 2 0.0000 0.9945 0.000 1.000
#> GSM550918 2 0.0000 0.9945 0.000 1.000
#> GSM550922 2 0.0000 0.9945 0.000 1.000
#> GSM550923 1 0.0000 0.9795 1.000 0.000
#> GSM550925 1 0.0000 0.9795 1.000 0.000
#> GSM550802 2 0.0000 0.9945 0.000 1.000
#> GSM550812 2 0.0000 0.9945 0.000 1.000
#> GSM550831 1 0.0000 0.9795 1.000 0.000
#> GSM550847 1 0.0000 0.9795 1.000 0.000
#> GSM550860 1 0.0000 0.9795 1.000 0.000
#> GSM550875 1 0.0000 0.9795 1.000 0.000
#> GSM550880 2 0.0376 0.9904 0.004 0.996
#> GSM550881 1 0.0000 0.9795 1.000 0.000
#> GSM550883 1 0.0000 0.9795 1.000 0.000
#> GSM550884 2 0.0000 0.9945 0.000 1.000
#> GSM550910 2 0.0000 0.9945 0.000 1.000
#> GSM550916 1 0.0000 0.9795 1.000 0.000
#> GSM550920 2 0.0000 0.9945 0.000 1.000
cbind(get_classes(res, k = 3), get_membership(res, k = 3))
#> class entropy silhouette p1 p2 p3
#> GSM550785 1 0.5058 0.640 0.756 0.000 0.244
#> GSM550786 1 0.4291 0.742 0.820 0.180 0.000
#> GSM550788 2 0.0000 0.894 0.000 1.000 0.000
#> GSM550789 2 0.0000 0.894 0.000 1.000 0.000
#> GSM550790 3 0.5810 0.534 0.336 0.000 0.664
#> GSM550791 1 0.4555 0.671 0.800 0.000 0.200
#> GSM550792 1 0.4291 0.742 0.820 0.180 0.000
#> GSM550796 2 0.0000 0.894 0.000 1.000 0.000
#> GSM550797 2 0.0000 0.894 0.000 1.000 0.000
#> GSM550799 2 0.4654 0.822 0.208 0.792 0.000
#> GSM550800 2 0.4605 0.824 0.204 0.796 0.000
#> GSM550801 2 0.0000 0.894 0.000 1.000 0.000
#> GSM550804 2 0.4346 0.833 0.184 0.816 0.000
#> GSM550806 1 0.0892 0.784 0.980 0.020 0.000
#> GSM550807 2 0.0000 0.894 0.000 1.000 0.000
#> GSM550808 2 0.0000 0.894 0.000 1.000 0.000
#> GSM550809 1 0.5058 0.640 0.756 0.000 0.244
#> GSM550810 2 0.0000 0.894 0.000 1.000 0.000
#> GSM550811 1 0.0000 0.776 1.000 0.000 0.000
#> GSM550813 1 0.4291 0.742 0.820 0.180 0.000
#> GSM550814 2 0.5058 0.790 0.244 0.756 0.000
#> GSM550815 2 0.0000 0.894 0.000 1.000 0.000
#> GSM550816 2 0.0000 0.894 0.000 1.000 0.000
#> GSM550817 2 0.4654 0.822 0.208 0.792 0.000
#> GSM550818 1 0.5397 0.587 0.720 0.280 0.000
#> GSM550819 2 0.5058 0.790 0.244 0.756 0.000
#> GSM550820 1 0.5058 0.640 0.756 0.000 0.244
#> GSM550821 2 0.0000 0.894 0.000 1.000 0.000
#> GSM550822 2 0.0000 0.894 0.000 1.000 0.000
#> GSM550826 1 0.5058 0.640 0.756 0.000 0.244
#> GSM550832 2 0.0000 0.894 0.000 1.000 0.000
#> GSM550833 2 0.0000 0.894 0.000 1.000 0.000
#> GSM550835 2 0.5016 0.794 0.240 0.760 0.000
#> GSM550836 3 0.0000 0.952 0.000 0.000 1.000
#> GSM550837 2 0.0000 0.894 0.000 1.000 0.000
#> GSM550838 1 0.5058 0.640 0.756 0.000 0.244
#> GSM550841 2 0.0000 0.894 0.000 1.000 0.000
#> GSM550842 2 0.0000 0.894 0.000 1.000 0.000
#> GSM550846 1 0.4002 0.755 0.840 0.160 0.000
#> GSM550849 1 0.1411 0.787 0.964 0.036 0.000
#> GSM550850 1 0.5058 0.640 0.756 0.000 0.244
#> GSM550851 2 0.0000 0.894 0.000 1.000 0.000
#> GSM550852 2 0.4654 0.822 0.208 0.792 0.000
#> GSM550853 2 0.0000 0.894 0.000 1.000 0.000
#> GSM550855 2 0.1643 0.883 0.044 0.956 0.000
#> GSM550856 2 0.5016 0.794 0.240 0.760 0.000
#> GSM550861 2 0.0000 0.894 0.000 1.000 0.000
#> GSM550863 1 0.4291 0.742 0.820 0.180 0.000
#> GSM550864 1 0.4291 0.742 0.820 0.180 0.000
#> GSM550866 1 0.4291 0.742 0.820 0.180 0.000
#> GSM550867 3 0.0000 0.952 0.000 0.000 1.000
#> GSM550885 3 0.0000 0.952 0.000 0.000 1.000
#> GSM550886 2 0.5058 0.790 0.244 0.756 0.000
#> GSM550887 2 0.0000 0.894 0.000 1.000 0.000
#> GSM550889 1 0.5058 0.640 0.756 0.000 0.244
#> GSM550894 2 0.0000 0.894 0.000 1.000 0.000
#> GSM550897 1 0.5058 0.640 0.756 0.000 0.244
#> GSM550903 2 0.0424 0.892 0.008 0.992 0.000
#> GSM550905 2 0.4654 0.822 0.208 0.792 0.000
#> GSM550906 2 0.0000 0.894 0.000 1.000 0.000
#> GSM550907 2 0.5058 0.790 0.244 0.756 0.000
#> GSM550909 2 0.0000 0.894 0.000 1.000 0.000
#> GSM550911 1 0.3482 0.772 0.872 0.128 0.000
#> GSM550913 2 0.0000 0.894 0.000 1.000 0.000
#> GSM550915 1 0.0892 0.784 0.980 0.020 0.000
#> GSM550917 2 0.4702 0.818 0.212 0.788 0.000
#> GSM550919 1 0.0892 0.784 0.980 0.020 0.000
#> GSM550921 3 0.0000 0.952 0.000 0.000 1.000
#> GSM550924 1 0.3412 0.774 0.876 0.124 0.000
#> GSM550926 1 0.4346 0.738 0.816 0.184 0.000
#> GSM550927 2 0.0000 0.894 0.000 1.000 0.000
#> GSM550787 1 0.0892 0.784 0.980 0.020 0.000
#> GSM550793 3 0.4291 0.814 0.180 0.000 0.820
#> GSM550794 1 0.4291 0.742 0.820 0.180 0.000
#> GSM550795 1 0.5058 0.640 0.756 0.000 0.244
#> GSM550798 3 0.0000 0.952 0.000 0.000 1.000
#> GSM550803 3 0.0000 0.952 0.000 0.000 1.000
#> GSM550805 1 0.0000 0.776 1.000 0.000 0.000
#> GSM550823 1 0.2261 0.788 0.932 0.068 0.000
#> GSM550824 3 0.0000 0.952 0.000 0.000 1.000
#> GSM550825 3 0.1031 0.941 0.024 0.000 0.976
#> GSM550827 1 0.3482 0.772 0.872 0.128 0.000
#> GSM550828 1 0.5058 0.640 0.756 0.000 0.244
#> GSM550829 3 0.0892 0.943 0.020 0.000 0.980
#> GSM550830 1 0.1529 0.787 0.960 0.040 0.000
#> GSM550834 1 0.4291 0.685 0.820 0.000 0.180
#> GSM550839 2 0.4654 0.822 0.208 0.792 0.000
#> GSM550840 1 0.4291 0.685 0.820 0.000 0.180
#> GSM550843 1 0.4291 0.742 0.820 0.180 0.000
#> GSM550844 1 0.5058 0.640 0.756 0.000 0.244
#> GSM550845 1 0.4291 0.742 0.820 0.180 0.000
#> GSM550848 1 0.4291 0.742 0.820 0.180 0.000
#> GSM550854 3 0.0000 0.952 0.000 0.000 1.000
#> GSM550857 3 0.0000 0.952 0.000 0.000 1.000
#> GSM550858 3 0.4796 0.760 0.220 0.000 0.780
#> GSM550859 3 0.0000 0.952 0.000 0.000 1.000
#> GSM550862 1 0.5058 0.640 0.756 0.000 0.244
#> GSM550865 1 0.1163 0.768 0.972 0.000 0.028
#> GSM550868 1 0.1964 0.788 0.944 0.056 0.000
#> GSM550869 1 0.0892 0.784 0.980 0.020 0.000
#> GSM550870 1 0.4654 0.708 0.792 0.208 0.000
#> GSM550871 1 0.4291 0.742 0.820 0.180 0.000
#> GSM550872 1 0.1964 0.788 0.944 0.056 0.000
#> GSM550873 1 0.5621 0.527 0.692 0.308 0.000
#> GSM550874 1 0.4291 0.742 0.820 0.180 0.000
#> GSM550876 1 0.4291 0.742 0.820 0.180 0.000
#> GSM550877 2 0.5016 0.794 0.240 0.760 0.000
#> GSM550878 1 0.2165 0.789 0.936 0.064 0.000
#> GSM550879 1 0.5058 0.640 0.756 0.000 0.244
#> GSM550882 1 0.5058 0.640 0.756 0.000 0.244
#> GSM550888 3 0.0000 0.952 0.000 0.000 1.000
#> GSM550890 1 0.4002 0.755 0.840 0.160 0.000
#> GSM550891 3 0.2165 0.915 0.064 0.000 0.936
#> GSM550892 1 0.5058 0.640 0.756 0.000 0.244
#> GSM550893 1 0.4654 0.708 0.792 0.208 0.000
#> GSM550895 1 0.4291 0.742 0.820 0.180 0.000
#> GSM550896 2 0.0000 0.894 0.000 1.000 0.000
#> GSM550898 3 0.0000 0.952 0.000 0.000 1.000
#> GSM550899 1 0.4605 0.713 0.796 0.204 0.000
#> GSM550900 1 0.4291 0.742 0.820 0.180 0.000
#> GSM550901 1 0.0892 0.784 0.980 0.020 0.000
#> GSM550902 1 0.5058 0.640 0.756 0.000 0.244
#> GSM550904 3 0.4291 0.814 0.180 0.000 0.820
#> GSM550908 3 0.0000 0.952 0.000 0.000 1.000
#> GSM550912 1 0.4291 0.742 0.820 0.180 0.000
#> GSM550914 1 0.0892 0.783 0.980 0.020 0.000
#> GSM550918 2 0.5058 0.790 0.244 0.756 0.000
#> GSM550922 2 0.0000 0.894 0.000 1.000 0.000
#> GSM550923 3 0.0000 0.952 0.000 0.000 1.000
#> GSM550925 1 0.5058 0.640 0.756 0.000 0.244
#> GSM550802 2 0.4654 0.822 0.208 0.792 0.000
#> GSM550812 2 0.4654 0.822 0.208 0.792 0.000
#> GSM550831 1 0.5058 0.640 0.756 0.000 0.244
#> GSM550847 3 0.0000 0.952 0.000 0.000 1.000
#> GSM550860 1 0.5058 0.640 0.756 0.000 0.244
#> GSM550875 1 0.5016 0.643 0.760 0.000 0.240
#> GSM550880 1 0.0000 0.776 1.000 0.000 0.000
#> GSM550881 1 0.5058 0.640 0.756 0.000 0.244
#> GSM550883 3 0.0000 0.952 0.000 0.000 1.000
#> GSM550884 1 0.2711 0.786 0.912 0.088 0.000
#> GSM550910 2 0.5058 0.790 0.244 0.756 0.000
#> GSM550916 1 0.5058 0.640 0.756 0.000 0.244
#> GSM550920 1 0.3412 0.774 0.876 0.124 0.000
cbind(get_classes(res, k = 4), get_membership(res, k = 4))
#> class entropy silhouette p1 p2 p3 p4
#> GSM550785 1 0.0000 0.994 1.000 0.000 0 0.000
#> GSM550786 4 0.0000 0.962 0.000 0.000 0 1.000
#> GSM550788 2 0.0000 0.995 0.000 1.000 0 0.000
#> GSM550789 2 0.0000 0.995 0.000 1.000 0 0.000
#> GSM550790 1 0.0000 0.994 1.000 0.000 0 0.000
#> GSM550791 1 0.0000 0.994 1.000 0.000 0 0.000
#> GSM550792 4 0.0000 0.962 0.000 0.000 0 1.000
#> GSM550796 2 0.0000 0.995 0.000 1.000 0 0.000
#> GSM550797 2 0.0000 0.995 0.000 1.000 0 0.000
#> GSM550799 4 0.3074 0.831 0.000 0.152 0 0.848
#> GSM550800 4 0.3764 0.754 0.000 0.216 0 0.784
#> GSM550801 2 0.0000 0.995 0.000 1.000 0 0.000
#> GSM550804 4 0.4948 0.291 0.000 0.440 0 0.560
#> GSM550806 4 0.0000 0.962 0.000 0.000 0 1.000
#> GSM550807 2 0.0000 0.995 0.000 1.000 0 0.000
#> GSM550808 2 0.0000 0.995 0.000 1.000 0 0.000
#> GSM550809 1 0.0000 0.994 1.000 0.000 0 0.000
#> GSM550810 2 0.0000 0.995 0.000 1.000 0 0.000
#> GSM550811 1 0.0000 0.994 1.000 0.000 0 0.000
#> GSM550813 4 0.0000 0.962 0.000 0.000 0 1.000
#> GSM550814 4 0.0000 0.962 0.000 0.000 0 1.000
#> GSM550815 2 0.0000 0.995 0.000 1.000 0 0.000
#> GSM550816 2 0.0000 0.995 0.000 1.000 0 0.000
#> GSM550817 4 0.4331 0.642 0.000 0.288 0 0.712
#> GSM550818 4 0.0000 0.962 0.000 0.000 0 1.000
#> GSM550819 4 0.0000 0.962 0.000 0.000 0 1.000
#> GSM550820 1 0.0000 0.994 1.000 0.000 0 0.000
#> GSM550821 2 0.0000 0.995 0.000 1.000 0 0.000
#> GSM550822 2 0.0000 0.995 0.000 1.000 0 0.000
#> GSM550826 1 0.0000 0.994 1.000 0.000 0 0.000
#> GSM550832 2 0.0188 0.990 0.000 0.996 0 0.004
#> GSM550833 2 0.0000 0.995 0.000 1.000 0 0.000
#> GSM550835 4 0.0000 0.962 0.000 0.000 0 1.000
#> GSM550836 3 0.0000 1.000 0.000 0.000 1 0.000
#> GSM550837 2 0.0000 0.995 0.000 1.000 0 0.000
#> GSM550838 1 0.0000 0.994 1.000 0.000 0 0.000
#> GSM550841 2 0.0000 0.995 0.000 1.000 0 0.000
#> GSM550842 2 0.0000 0.995 0.000 1.000 0 0.000
#> GSM550846 4 0.0000 0.962 0.000 0.000 0 1.000
#> GSM550849 4 0.0000 0.962 0.000 0.000 0 1.000
#> GSM550850 1 0.0000 0.994 1.000 0.000 0 0.000
#> GSM550851 2 0.0000 0.995 0.000 1.000 0 0.000
#> GSM550852 4 0.3356 0.806 0.000 0.176 0 0.824
#> GSM550853 2 0.0000 0.995 0.000 1.000 0 0.000
#> GSM550855 2 0.1389 0.933 0.000 0.952 0 0.048
#> GSM550856 4 0.0000 0.962 0.000 0.000 0 1.000
#> GSM550861 2 0.0000 0.995 0.000 1.000 0 0.000
#> GSM550863 4 0.0000 0.962 0.000 0.000 0 1.000
#> GSM550864 4 0.0000 0.962 0.000 0.000 0 1.000
#> GSM550866 4 0.0000 0.962 0.000 0.000 0 1.000
#> GSM550867 3 0.0000 1.000 0.000 0.000 1 0.000
#> GSM550885 3 0.0000 1.000 0.000 0.000 1 0.000
#> GSM550886 4 0.0000 0.962 0.000 0.000 0 1.000
#> GSM550887 2 0.0000 0.995 0.000 1.000 0 0.000
#> GSM550889 1 0.0000 0.994 1.000 0.000 0 0.000
#> GSM550894 2 0.0000 0.995 0.000 1.000 0 0.000
#> GSM550897 1 0.0000 0.994 1.000 0.000 0 0.000
#> GSM550903 2 0.0592 0.977 0.000 0.984 0 0.016
#> GSM550905 4 0.3074 0.831 0.000 0.152 0 0.848
#> GSM550906 2 0.0000 0.995 0.000 1.000 0 0.000
#> GSM550907 4 0.0000 0.962 0.000 0.000 0 1.000
#> GSM550909 2 0.0000 0.995 0.000 1.000 0 0.000
#> GSM550911 4 0.0000 0.962 0.000 0.000 0 1.000
#> GSM550913 2 0.0000 0.995 0.000 1.000 0 0.000
#> GSM550915 4 0.0000 0.962 0.000 0.000 0 1.000
#> GSM550917 4 0.2868 0.846 0.000 0.136 0 0.864
#> GSM550919 4 0.0000 0.962 0.000 0.000 0 1.000
#> GSM550921 3 0.0000 1.000 0.000 0.000 1 0.000
#> GSM550924 4 0.0000 0.962 0.000 0.000 0 1.000
#> GSM550926 4 0.0000 0.962 0.000 0.000 0 1.000
#> GSM550927 2 0.0000 0.995 0.000 1.000 0 0.000
#> GSM550787 4 0.0000 0.962 0.000 0.000 0 1.000
#> GSM550793 1 0.0000 0.994 1.000 0.000 0 0.000
#> GSM550794 4 0.0000 0.962 0.000 0.000 0 1.000
#> GSM550795 1 0.0000 0.994 1.000 0.000 0 0.000
#> GSM550798 3 0.0000 1.000 0.000 0.000 1 0.000
#> GSM550803 3 0.0000 1.000 0.000 0.000 1 0.000
#> GSM550805 4 0.0000 0.962 0.000 0.000 0 1.000
#> GSM550823 4 0.0000 0.962 0.000 0.000 0 1.000
#> GSM550824 3 0.0000 1.000 0.000 0.000 1 0.000
#> GSM550825 1 0.0000 0.994 1.000 0.000 0 0.000
#> GSM550827 4 0.0000 0.962 0.000 0.000 0 1.000
#> GSM550828 1 0.0000 0.994 1.000 0.000 0 0.000
#> GSM550829 1 0.0000 0.994 1.000 0.000 0 0.000
#> GSM550830 4 0.0000 0.962 0.000 0.000 0 1.000
#> GSM550834 1 0.3024 0.787 0.852 0.000 0 0.148
#> GSM550839 4 0.3444 0.796 0.000 0.184 0 0.816
#> GSM550840 1 0.0000 0.994 1.000 0.000 0 0.000
#> GSM550843 4 0.0000 0.962 0.000 0.000 0 1.000
#> GSM550844 1 0.0000 0.994 1.000 0.000 0 0.000
#> GSM550845 4 0.0000 0.962 0.000 0.000 0 1.000
#> GSM550848 4 0.0000 0.962 0.000 0.000 0 1.000
#> GSM550854 3 0.0000 1.000 0.000 0.000 1 0.000
#> GSM550857 3 0.0000 1.000 0.000 0.000 1 0.000
#> GSM550858 1 0.0000 0.994 1.000 0.000 0 0.000
#> GSM550859 3 0.0000 1.000 0.000 0.000 1 0.000
#> GSM550862 1 0.0000 0.994 1.000 0.000 0 0.000
#> GSM550865 1 0.0000 0.994 1.000 0.000 0 0.000
#> GSM550868 4 0.0000 0.962 0.000 0.000 0 1.000
#> GSM550869 4 0.0000 0.962 0.000 0.000 0 1.000
#> GSM550870 4 0.0000 0.962 0.000 0.000 0 1.000
#> GSM550871 4 0.0000 0.962 0.000 0.000 0 1.000
#> GSM550872 4 0.0000 0.962 0.000 0.000 0 1.000
#> GSM550873 4 0.0000 0.962 0.000 0.000 0 1.000
#> GSM550874 4 0.0000 0.962 0.000 0.000 0 1.000
#> GSM550876 4 0.0000 0.962 0.000 0.000 0 1.000
#> GSM550877 4 0.0000 0.962 0.000 0.000 0 1.000
#> GSM550878 4 0.0000 0.962 0.000 0.000 0 1.000
#> GSM550879 1 0.0000 0.994 1.000 0.000 0 0.000
#> GSM550882 1 0.0000 0.994 1.000 0.000 0 0.000
#> GSM550888 3 0.0000 1.000 0.000 0.000 1 0.000
#> GSM550890 4 0.0000 0.962 0.000 0.000 0 1.000
#> GSM550891 1 0.0000 0.994 1.000 0.000 0 0.000
#> GSM550892 1 0.0000 0.994 1.000 0.000 0 0.000
#> GSM550893 4 0.0000 0.962 0.000 0.000 0 1.000
#> GSM550895 4 0.0000 0.962 0.000 0.000 0 1.000
#> GSM550896 2 0.0000 0.995 0.000 1.000 0 0.000
#> GSM550898 3 0.0000 1.000 0.000 0.000 1 0.000
#> GSM550899 4 0.0000 0.962 0.000 0.000 0 1.000
#> GSM550900 4 0.0000 0.962 0.000 0.000 0 1.000
#> GSM550901 4 0.0000 0.962 0.000 0.000 0 1.000
#> GSM550902 1 0.0000 0.994 1.000 0.000 0 0.000
#> GSM550904 1 0.0000 0.994 1.000 0.000 0 0.000
#> GSM550908 3 0.0000 1.000 0.000 0.000 1 0.000
#> GSM550912 4 0.0000 0.962 0.000 0.000 0 1.000
#> GSM550914 4 0.0000 0.962 0.000 0.000 0 1.000
#> GSM550918 4 0.0000 0.962 0.000 0.000 0 1.000
#> GSM550922 2 0.1211 0.945 0.000 0.960 0 0.040
#> GSM550923 3 0.0000 1.000 0.000 0.000 1 0.000
#> GSM550925 1 0.0000 0.994 1.000 0.000 0 0.000
#> GSM550802 4 0.3356 0.806 0.000 0.176 0 0.824
#> GSM550812 4 0.3486 0.791 0.000 0.188 0 0.812
#> GSM550831 1 0.0000 0.994 1.000 0.000 0 0.000
#> GSM550847 3 0.0000 1.000 0.000 0.000 1 0.000
#> GSM550860 1 0.0000 0.994 1.000 0.000 0 0.000
#> GSM550875 1 0.0000 0.994 1.000 0.000 0 0.000
#> GSM550880 4 0.1474 0.914 0.052 0.000 0 0.948
#> GSM550881 1 0.0000 0.994 1.000 0.000 0 0.000
#> GSM550883 3 0.0000 1.000 0.000 0.000 1 0.000
#> GSM550884 4 0.0000 0.962 0.000 0.000 0 1.000
#> GSM550910 4 0.0000 0.962 0.000 0.000 0 1.000
#> GSM550916 1 0.0000 0.994 1.000 0.000 0 0.000
#> GSM550920 4 0.0000 0.962 0.000 0.000 0 1.000
cbind(get_classes(res, k = 5), get_membership(res, k = 5))
#> class entropy silhouette p1 p2 p3 p4 p5
#> GSM550785 1 0.0000 0.8176 1.000 0.000 0.000 0.000 0.000
#> GSM550786 4 0.4088 -0.2219 0.000 0.000 0.000 0.632 0.368
#> GSM550788 2 0.2648 0.6826 0.000 0.848 0.000 0.000 0.152
#> GSM550789 2 0.0000 0.7583 0.000 1.000 0.000 0.000 0.000
#> GSM550790 1 0.3424 0.8075 0.760 0.000 0.000 0.000 0.240
#> GSM550791 1 0.3707 0.5607 0.716 0.000 0.000 0.284 0.000
#> GSM550792 4 0.0000 0.4871 0.000 0.000 0.000 1.000 0.000
#> GSM550796 2 0.3586 0.6819 0.000 0.736 0.000 0.000 0.264
#> GSM550797 2 0.0000 0.7583 0.000 1.000 0.000 0.000 0.000
#> GSM550799 5 0.5795 0.7312 0.000 0.092 0.000 0.412 0.496
#> GSM550800 2 0.6625 -0.3288 0.000 0.412 0.000 0.220 0.368
#> GSM550801 2 0.0000 0.7583 0.000 1.000 0.000 0.000 0.000
#> GSM550804 2 0.6478 -0.2251 0.000 0.444 0.000 0.188 0.368
#> GSM550806 4 0.3305 0.3607 0.224 0.000 0.000 0.776 0.000
#> GSM550807 2 0.4060 0.4378 0.000 0.640 0.000 0.000 0.360
#> GSM550808 2 0.3586 0.6819 0.000 0.736 0.000 0.000 0.264
#> GSM550809 1 0.0000 0.8176 1.000 0.000 0.000 0.000 0.000
#> GSM550810 2 0.3586 0.6819 0.000 0.736 0.000 0.000 0.264
#> GSM550811 1 0.4307 0.2600 0.504 0.000 0.000 0.496 0.000
#> GSM550813 4 0.4304 -0.4233 0.000 0.000 0.000 0.516 0.484
#> GSM550814 4 0.4307 -0.4453 0.000 0.000 0.000 0.504 0.496
#> GSM550815 2 0.3586 0.6819 0.000 0.736 0.000 0.000 0.264
#> GSM550816 2 0.3586 0.6819 0.000 0.736 0.000 0.000 0.264
#> GSM550817 5 0.6442 -0.0881 0.000 0.300 0.000 0.208 0.492
#> GSM550818 4 0.4307 -0.4453 0.000 0.000 0.000 0.504 0.496
#> GSM550819 4 0.4307 -0.4453 0.000 0.000 0.000 0.504 0.496
#> GSM550820 1 0.0000 0.8176 1.000 0.000 0.000 0.000 0.000
#> GSM550821 2 0.3707 0.5526 0.000 0.716 0.000 0.000 0.284
#> GSM550822 2 0.3586 0.6819 0.000 0.736 0.000 0.000 0.264
#> GSM550826 1 0.0000 0.8176 1.000 0.000 0.000 0.000 0.000
#> GSM550832 2 0.4470 0.3903 0.000 0.616 0.000 0.012 0.372
#> GSM550833 2 0.0000 0.7583 0.000 1.000 0.000 0.000 0.000
#> GSM550835 5 0.5635 0.7173 0.000 0.076 0.000 0.428 0.496
#> GSM550836 3 0.0000 0.9726 0.000 0.000 1.000 0.000 0.000
#> GSM550837 2 0.0000 0.7583 0.000 1.000 0.000 0.000 0.000
#> GSM550838 1 0.0880 0.8177 0.968 0.000 0.000 0.000 0.032
#> GSM550841 2 0.3586 0.6819 0.000 0.736 0.000 0.000 0.264
#> GSM550842 2 0.3586 0.6819 0.000 0.736 0.000 0.000 0.264
#> GSM550846 4 0.1478 0.4683 0.000 0.000 0.000 0.936 0.064
#> GSM550849 4 0.3242 0.3656 0.216 0.000 0.000 0.784 0.000
#> GSM550850 1 0.0000 0.8176 1.000 0.000 0.000 0.000 0.000
#> GSM550851 2 0.0000 0.7583 0.000 1.000 0.000 0.000 0.000
#> GSM550852 4 0.6272 -0.5388 0.000 0.152 0.000 0.468 0.380
#> GSM550853 2 0.0000 0.7583 0.000 1.000 0.000 0.000 0.000
#> GSM550855 2 0.4735 0.4810 0.000 0.672 0.000 0.044 0.284
#> GSM550856 4 0.4307 -0.4453 0.000 0.000 0.000 0.504 0.496
#> GSM550861 2 0.1270 0.7455 0.000 0.948 0.000 0.000 0.052
#> GSM550863 4 0.0162 0.4868 0.000 0.000 0.000 0.996 0.004
#> GSM550864 4 0.4307 -0.4453 0.000 0.000 0.000 0.504 0.496
#> GSM550866 4 0.4307 -0.4453 0.000 0.000 0.000 0.504 0.496
#> GSM550867 3 0.0000 0.9726 0.000 0.000 1.000 0.000 0.000
#> GSM550885 3 0.0000 0.9726 0.000 0.000 1.000 0.000 0.000
#> GSM550886 4 0.4562 -0.4822 0.000 0.008 0.000 0.496 0.496
#> GSM550887 2 0.1671 0.7385 0.000 0.924 0.000 0.000 0.076
#> GSM550889 1 0.0000 0.8176 1.000 0.000 0.000 0.000 0.000
#> GSM550894 2 0.0000 0.7583 0.000 1.000 0.000 0.000 0.000
#> GSM550897 1 0.0000 0.8176 1.000 0.000 0.000 0.000 0.000
#> GSM550903 2 0.4269 0.5121 0.000 0.684 0.000 0.016 0.300
#> GSM550905 5 0.6025 0.6945 0.000 0.120 0.000 0.384 0.496
#> GSM550906 2 0.0000 0.7583 0.000 1.000 0.000 0.000 0.000
#> GSM550907 4 0.4307 -0.4453 0.000 0.000 0.000 0.504 0.496
#> GSM550909 2 0.0000 0.7583 0.000 1.000 0.000 0.000 0.000
#> GSM550911 4 0.1544 0.4550 0.000 0.000 0.000 0.932 0.068
#> GSM550913 2 0.3508 0.6865 0.000 0.748 0.000 0.000 0.252
#> GSM550915 4 0.1197 0.4758 0.000 0.000 0.000 0.952 0.048
#> GSM550917 5 0.5795 0.7312 0.000 0.092 0.000 0.412 0.496
#> GSM550919 4 0.0000 0.4871 0.000 0.000 0.000 1.000 0.000
#> GSM550921 3 0.0000 0.9726 0.000 0.000 1.000 0.000 0.000
#> GSM550924 4 0.0404 0.4857 0.000 0.000 0.000 0.988 0.012
#> GSM550926 4 0.4307 -0.4453 0.000 0.000 0.000 0.504 0.496
#> GSM550927 2 0.0000 0.7583 0.000 1.000 0.000 0.000 0.000
#> GSM550787 4 0.3336 0.3581 0.228 0.000 0.000 0.772 0.000
#> GSM550793 1 0.3424 0.8075 0.760 0.000 0.000 0.000 0.240
#> GSM550794 4 0.2648 0.3893 0.000 0.000 0.000 0.848 0.152
#> GSM550795 1 0.3424 0.8075 0.760 0.000 0.000 0.000 0.240
#> GSM550798 3 0.0000 0.9726 0.000 0.000 1.000 0.000 0.000
#> GSM550803 3 0.0000 0.9726 0.000 0.000 1.000 0.000 0.000
#> GSM550805 4 0.3336 0.3581 0.228 0.000 0.000 0.772 0.000
#> GSM550823 4 0.0000 0.4871 0.000 0.000 0.000 1.000 0.000
#> GSM550824 3 0.0000 0.9726 0.000 0.000 1.000 0.000 0.000
#> GSM550825 1 0.3424 0.8075 0.760 0.000 0.000 0.000 0.240
#> GSM550827 4 0.2280 0.4303 0.000 0.000 0.000 0.880 0.120
#> GSM550828 1 0.3424 0.8075 0.760 0.000 0.000 0.000 0.240
#> GSM550829 1 0.3424 0.8075 0.760 0.000 0.000 0.000 0.240
#> GSM550830 4 0.0000 0.4871 0.000 0.000 0.000 1.000 0.000
#> GSM550834 1 0.4307 0.2600 0.504 0.000 0.000 0.496 0.000
#> GSM550839 2 0.6646 -0.3694 0.000 0.396 0.000 0.224 0.380
#> GSM550840 1 0.4306 0.2670 0.508 0.000 0.000 0.492 0.000
#> GSM550843 4 0.4307 -0.4453 0.000 0.000 0.000 0.504 0.496
#> GSM550844 1 0.0162 0.8181 0.996 0.000 0.000 0.000 0.004
#> GSM550845 4 0.4307 -0.4453 0.000 0.000 0.000 0.504 0.496
#> GSM550848 4 0.4278 -0.3579 0.000 0.000 0.000 0.548 0.452
#> GSM550854 3 0.0000 0.9726 0.000 0.000 1.000 0.000 0.000
#> GSM550857 3 0.0000 0.9726 0.000 0.000 1.000 0.000 0.000
#> GSM550858 1 0.3424 0.8075 0.760 0.000 0.000 0.000 0.240
#> GSM550859 3 0.0000 0.9726 0.000 0.000 1.000 0.000 0.000
#> GSM550862 1 0.3424 0.8075 0.760 0.000 0.000 0.000 0.240
#> GSM550865 1 0.2648 0.7043 0.848 0.000 0.000 0.152 0.000
#> GSM550868 4 0.0000 0.4871 0.000 0.000 0.000 1.000 0.000
#> GSM550869 4 0.3177 0.3702 0.208 0.000 0.000 0.792 0.000
#> GSM550870 4 0.4307 -0.4453 0.000 0.000 0.000 0.504 0.496
#> GSM550871 4 0.0162 0.4868 0.000 0.000 0.000 0.996 0.004
#> GSM550872 4 0.0000 0.4871 0.000 0.000 0.000 1.000 0.000
#> GSM550873 4 0.4307 -0.4453 0.000 0.000 0.000 0.504 0.496
#> GSM550874 4 0.4307 -0.4453 0.000 0.000 0.000 0.504 0.496
#> GSM550876 4 0.3109 0.3435 0.000 0.000 0.000 0.800 0.200
#> GSM550877 5 0.5635 0.7173 0.000 0.076 0.000 0.428 0.496
#> GSM550878 4 0.1121 0.4773 0.000 0.000 0.000 0.956 0.044
#> GSM550879 1 0.0000 0.8176 1.000 0.000 0.000 0.000 0.000
#> GSM550882 1 0.3305 0.8098 0.776 0.000 0.000 0.000 0.224
#> GSM550888 3 0.0000 0.9726 0.000 0.000 1.000 0.000 0.000
#> GSM550890 4 0.0963 0.4800 0.000 0.000 0.000 0.964 0.036
#> GSM550891 1 0.3424 0.8075 0.760 0.000 0.000 0.000 0.240
#> GSM550892 1 0.3424 0.8075 0.760 0.000 0.000 0.000 0.240
#> GSM550893 4 0.4307 -0.4453 0.000 0.000 0.000 0.504 0.496
#> GSM550895 4 0.4192 -0.2453 0.000 0.000 0.000 0.596 0.404
#> GSM550896 2 0.3707 0.5526 0.000 0.716 0.000 0.000 0.284
#> GSM550898 3 0.0000 0.9726 0.000 0.000 1.000 0.000 0.000
#> GSM550899 4 0.4307 -0.4453 0.000 0.000 0.000 0.504 0.496
#> GSM550900 4 0.0000 0.4871 0.000 0.000 0.000 1.000 0.000
#> GSM550901 4 0.2966 0.3832 0.184 0.000 0.000 0.816 0.000
#> GSM550902 1 0.0000 0.8176 1.000 0.000 0.000 0.000 0.000
#> GSM550904 1 0.3424 0.8075 0.760 0.000 0.000 0.000 0.240
#> GSM550908 3 0.0000 0.9726 0.000 0.000 1.000 0.000 0.000
#> GSM550912 4 0.3366 0.2931 0.000 0.000 0.000 0.768 0.232
#> GSM550914 4 0.2286 0.4399 0.004 0.000 0.000 0.888 0.108
#> GSM550918 5 0.5591 0.7051 0.000 0.072 0.000 0.432 0.496
#> GSM550922 2 0.4470 0.3911 0.000 0.616 0.000 0.012 0.372
#> GSM550923 3 0.0000 0.9726 0.000 0.000 1.000 0.000 0.000
#> GSM550925 1 0.3177 0.8112 0.792 0.000 0.000 0.000 0.208
#> GSM550802 4 0.6248 -0.5435 0.000 0.148 0.000 0.468 0.384
#> GSM550812 4 0.6336 -0.5265 0.000 0.164 0.000 0.468 0.368
#> GSM550831 1 0.0000 0.8176 1.000 0.000 0.000 0.000 0.000
#> GSM550847 3 0.3424 0.7651 0.000 0.000 0.760 0.000 0.240
#> GSM550860 1 0.1908 0.8191 0.908 0.000 0.000 0.000 0.092
#> GSM550875 1 0.0000 0.8176 1.000 0.000 0.000 0.000 0.000
#> GSM550880 4 0.3424 0.3490 0.240 0.000 0.000 0.760 0.000
#> GSM550881 1 0.3305 0.8098 0.776 0.000 0.000 0.000 0.224
#> GSM550883 3 0.3143 0.8011 0.000 0.000 0.796 0.000 0.204
#> GSM550884 4 0.0000 0.4871 0.000 0.000 0.000 1.000 0.000
#> GSM550910 4 0.4307 -0.4453 0.000 0.000 0.000 0.504 0.496
#> GSM550916 1 0.3305 0.8098 0.776 0.000 0.000 0.000 0.224
#> GSM550920 4 0.0000 0.4871 0.000 0.000 0.000 1.000 0.000
cbind(get_classes(res, k = 6), get_membership(res, k = 6))
#> class entropy silhouette p1 p2 p3 p4 p5 p6
#> GSM550785 6 0.2994 0.8556 0.000 0.000 0.004 0.208 0.000 0.788
#> GSM550786 5 0.3151 0.5260 0.000 0.000 0.000 0.252 0.748 0.000
#> GSM550788 2 0.1176 0.9135 0.000 0.956 0.024 0.000 0.020 0.000
#> GSM550789 2 0.0713 0.9093 0.000 0.972 0.028 0.000 0.000 0.000
#> GSM550790 6 0.0713 0.8613 0.000 0.000 0.028 0.000 0.000 0.972
#> GSM550791 6 0.3999 0.3678 0.000 0.000 0.004 0.496 0.000 0.500
#> GSM550792 4 0.2996 0.7676 0.000 0.000 0.000 0.772 0.228 0.000
#> GSM550796 3 0.0790 0.9903 0.000 0.032 0.968 0.000 0.000 0.000
#> GSM550797 2 0.0632 0.9115 0.000 0.976 0.024 0.000 0.000 0.000
#> GSM550799 5 0.2996 0.6662 0.000 0.228 0.000 0.000 0.772 0.000
#> GSM550800 2 0.0790 0.9068 0.000 0.968 0.000 0.000 0.032 0.000
#> GSM550801 2 0.0632 0.9115 0.000 0.976 0.024 0.000 0.000 0.000
#> GSM550804 2 0.0790 0.9068 0.000 0.968 0.000 0.000 0.032 0.000
#> GSM550806 4 0.0146 0.7451 0.000 0.000 0.000 0.996 0.004 0.000
#> GSM550807 2 0.0790 0.9068 0.000 0.968 0.000 0.000 0.032 0.000
#> GSM550808 3 0.0790 0.9903 0.000 0.032 0.968 0.000 0.000 0.000
#> GSM550809 6 0.2994 0.8556 0.000 0.000 0.004 0.208 0.000 0.788
#> GSM550810 3 0.0790 0.9903 0.000 0.032 0.968 0.000 0.000 0.000
#> GSM550811 4 0.0858 0.7252 0.000 0.000 0.004 0.968 0.000 0.028
#> GSM550813 5 0.0000 0.8354 0.000 0.000 0.000 0.000 1.000 0.000
#> GSM550814 5 0.0146 0.8349 0.000 0.004 0.000 0.000 0.996 0.000
#> GSM550815 3 0.0790 0.9903 0.000 0.032 0.968 0.000 0.000 0.000
#> GSM550816 3 0.0865 0.9876 0.000 0.036 0.964 0.000 0.000 0.000
#> GSM550817 3 0.1649 0.9496 0.000 0.036 0.932 0.000 0.032 0.000
#> GSM550818 5 0.0000 0.8354 0.000 0.000 0.000 0.000 1.000 0.000
#> GSM550819 5 0.0000 0.8354 0.000 0.000 0.000 0.000 1.000 0.000
#> GSM550820 6 0.2994 0.8556 0.000 0.000 0.004 0.208 0.000 0.788
#> GSM550821 2 0.0632 0.9104 0.000 0.976 0.000 0.000 0.024 0.000
#> GSM550822 3 0.0790 0.9903 0.000 0.032 0.968 0.000 0.000 0.000
#> GSM550826 6 0.2994 0.8556 0.000 0.000 0.004 0.208 0.000 0.788
#> GSM550832 2 0.3499 0.4985 0.000 0.680 0.000 0.000 0.320 0.000
#> GSM550833 2 0.0632 0.9115 0.000 0.976 0.024 0.000 0.000 0.000
#> GSM550835 5 0.2883 0.6807 0.000 0.212 0.000 0.000 0.788 0.000
#> GSM550836 1 0.0000 0.9675 1.000 0.000 0.000 0.000 0.000 0.000
#> GSM550837 2 0.0713 0.9093 0.000 0.972 0.028 0.000 0.000 0.000
#> GSM550838 6 0.3543 0.8542 0.000 0.000 0.032 0.200 0.000 0.768
#> GSM550841 3 0.0790 0.9903 0.000 0.032 0.968 0.000 0.000 0.000
#> GSM550842 3 0.0790 0.9903 0.000 0.032 0.968 0.000 0.000 0.000
#> GSM550846 5 0.3828 -0.1383 0.000 0.000 0.000 0.440 0.560 0.000
#> GSM550849 4 0.0260 0.7477 0.000 0.000 0.000 0.992 0.008 0.000
#> GSM550850 6 0.2994 0.8556 0.000 0.000 0.004 0.208 0.000 0.788
#> GSM550851 2 0.0632 0.9115 0.000 0.976 0.024 0.000 0.000 0.000
#> GSM550852 5 0.3330 0.5511 0.000 0.284 0.000 0.000 0.716 0.000
#> GSM550853 2 0.0632 0.9115 0.000 0.976 0.024 0.000 0.000 0.000
#> GSM550855 2 0.0632 0.9104 0.000 0.976 0.000 0.000 0.024 0.000
#> GSM550856 5 0.0713 0.8298 0.000 0.028 0.000 0.000 0.972 0.000
#> GSM550861 2 0.0363 0.9124 0.000 0.988 0.000 0.000 0.012 0.000
#> GSM550863 4 0.3634 0.6160 0.000 0.000 0.000 0.644 0.356 0.000
#> GSM550864 5 0.0000 0.8354 0.000 0.000 0.000 0.000 1.000 0.000
#> GSM550866 5 0.0000 0.8354 0.000 0.000 0.000 0.000 1.000 0.000
#> GSM550867 1 0.0000 0.9675 1.000 0.000 0.000 0.000 0.000 0.000
#> GSM550885 1 0.0000 0.9675 1.000 0.000 0.000 0.000 0.000 0.000
#> GSM550886 5 0.0865 0.8272 0.000 0.036 0.000 0.000 0.964 0.000
#> GSM550887 2 0.3717 0.3459 0.000 0.616 0.384 0.000 0.000 0.000
#> GSM550889 6 0.2994 0.8556 0.000 0.000 0.004 0.208 0.000 0.788
#> GSM550894 2 0.0547 0.9121 0.000 0.980 0.020 0.000 0.000 0.000
#> GSM550897 6 0.2994 0.8556 0.000 0.000 0.004 0.208 0.000 0.788
#> GSM550903 2 0.1075 0.8962 0.000 0.952 0.000 0.000 0.048 0.000
#> GSM550905 5 0.3050 0.6543 0.000 0.236 0.000 0.000 0.764 0.000
#> GSM550906 2 0.0000 0.9119 0.000 1.000 0.000 0.000 0.000 0.000
#> GSM550907 5 0.0000 0.8354 0.000 0.000 0.000 0.000 1.000 0.000
#> GSM550909 2 0.0632 0.9115 0.000 0.976 0.024 0.000 0.000 0.000
#> GSM550911 4 0.3659 0.6048 0.000 0.000 0.000 0.636 0.364 0.000
#> GSM550913 3 0.1267 0.9640 0.000 0.060 0.940 0.000 0.000 0.000
#> GSM550915 4 0.3756 0.5485 0.000 0.000 0.000 0.600 0.400 0.000
#> GSM550917 5 0.2996 0.6662 0.000 0.228 0.000 0.000 0.772 0.000
#> GSM550919 4 0.2854 0.7800 0.000 0.000 0.000 0.792 0.208 0.000
#> GSM550921 1 0.0000 0.9675 1.000 0.000 0.000 0.000 0.000 0.000
#> GSM550924 4 0.3428 0.6979 0.000 0.000 0.000 0.696 0.304 0.000
#> GSM550926 5 0.0632 0.8310 0.000 0.024 0.000 0.000 0.976 0.000
#> GSM550927 2 0.0713 0.9093 0.000 0.972 0.028 0.000 0.000 0.000
#> GSM550787 4 0.0146 0.7451 0.000 0.000 0.000 0.996 0.004 0.000
#> GSM550793 6 0.0713 0.8613 0.000 0.000 0.028 0.000 0.000 0.972
#> GSM550794 5 0.2823 0.6207 0.000 0.000 0.000 0.204 0.796 0.000
#> GSM550795 6 0.0713 0.8613 0.000 0.000 0.028 0.000 0.000 0.972
#> GSM550798 1 0.0000 0.9675 1.000 0.000 0.000 0.000 0.000 0.000
#> GSM550803 1 0.0000 0.9675 1.000 0.000 0.000 0.000 0.000 0.000
#> GSM550805 4 0.0146 0.7451 0.000 0.000 0.000 0.996 0.004 0.000
#> GSM550823 4 0.2854 0.7800 0.000 0.000 0.000 0.792 0.208 0.000
#> GSM550824 1 0.0000 0.9675 1.000 0.000 0.000 0.000 0.000 0.000
#> GSM550825 6 0.0713 0.8613 0.000 0.000 0.028 0.000 0.000 0.972
#> GSM550827 5 0.3706 0.1050 0.000 0.000 0.000 0.380 0.620 0.000
#> GSM550828 6 0.0713 0.8613 0.000 0.000 0.028 0.000 0.000 0.972
#> GSM550829 6 0.0713 0.8613 0.000 0.000 0.028 0.000 0.000 0.972
#> GSM550830 4 0.2854 0.7800 0.000 0.000 0.000 0.792 0.208 0.000
#> GSM550834 4 0.0777 0.7277 0.000 0.000 0.004 0.972 0.000 0.024
#> GSM550839 2 0.1714 0.8702 0.000 0.908 0.000 0.000 0.092 0.000
#> GSM550840 4 0.0777 0.7242 0.000 0.000 0.004 0.972 0.000 0.024
#> GSM550843 5 0.0000 0.8354 0.000 0.000 0.000 0.000 1.000 0.000
#> GSM550844 6 0.2964 0.8564 0.000 0.000 0.004 0.204 0.000 0.792
#> GSM550845 5 0.0000 0.8354 0.000 0.000 0.000 0.000 1.000 0.000
#> GSM550848 5 0.0632 0.8203 0.000 0.000 0.000 0.024 0.976 0.000
#> GSM550854 1 0.0000 0.9675 1.000 0.000 0.000 0.000 0.000 0.000
#> GSM550857 1 0.0000 0.9675 1.000 0.000 0.000 0.000 0.000 0.000
#> GSM550858 6 0.0713 0.8613 0.000 0.000 0.028 0.000 0.000 0.972
#> GSM550859 1 0.0000 0.9675 1.000 0.000 0.000 0.000 0.000 0.000
#> GSM550862 6 0.0713 0.8613 0.000 0.000 0.028 0.000 0.000 0.972
#> GSM550865 4 0.3819 -0.0552 0.000 0.000 0.004 0.624 0.000 0.372
#> GSM550868 4 0.2854 0.7800 0.000 0.000 0.000 0.792 0.208 0.000
#> GSM550869 4 0.0260 0.7477 0.000 0.000 0.000 0.992 0.008 0.000
#> GSM550870 5 0.0632 0.8310 0.000 0.024 0.000 0.000 0.976 0.000
#> GSM550871 4 0.3634 0.6160 0.000 0.000 0.000 0.644 0.356 0.000
#> GSM550872 4 0.2854 0.7800 0.000 0.000 0.000 0.792 0.208 0.000
#> GSM550873 5 0.0000 0.8354 0.000 0.000 0.000 0.000 1.000 0.000
#> GSM550874 5 0.0000 0.8354 0.000 0.000 0.000 0.000 1.000 0.000
#> GSM550876 5 0.1714 0.7585 0.000 0.000 0.000 0.092 0.908 0.000
#> GSM550877 5 0.2969 0.6718 0.000 0.224 0.000 0.000 0.776 0.000
#> GSM550878 4 0.3706 0.5858 0.000 0.000 0.000 0.620 0.380 0.000
#> GSM550879 6 0.2994 0.8556 0.000 0.000 0.004 0.208 0.000 0.788
#> GSM550882 6 0.0146 0.8642 0.000 0.000 0.000 0.004 0.000 0.996
#> GSM550888 1 0.0000 0.9675 1.000 0.000 0.000 0.000 0.000 0.000
#> GSM550890 4 0.3747 0.5580 0.000 0.000 0.000 0.604 0.396 0.000
#> GSM550891 6 0.0713 0.8613 0.000 0.000 0.028 0.000 0.000 0.972
#> GSM550892 6 0.0713 0.8613 0.000 0.000 0.028 0.000 0.000 0.972
#> GSM550893 5 0.0632 0.8310 0.000 0.024 0.000 0.000 0.976 0.000
#> GSM550895 5 0.2178 0.7084 0.000 0.000 0.000 0.132 0.868 0.000
#> GSM550896 2 0.0632 0.9104 0.000 0.976 0.000 0.000 0.024 0.000
#> GSM550898 1 0.0000 0.9675 1.000 0.000 0.000 0.000 0.000 0.000
#> GSM550899 5 0.0000 0.8354 0.000 0.000 0.000 0.000 1.000 0.000
#> GSM550900 4 0.2854 0.7800 0.000 0.000 0.000 0.792 0.208 0.000
#> GSM550901 4 0.0632 0.7546 0.000 0.000 0.000 0.976 0.024 0.000
#> GSM550902 6 0.2994 0.8556 0.000 0.000 0.004 0.208 0.000 0.788
#> GSM550904 6 0.0713 0.8613 0.000 0.000 0.028 0.000 0.000 0.972
#> GSM550908 1 0.0000 0.9675 1.000 0.000 0.000 0.000 0.000 0.000
#> GSM550912 5 0.0725 0.8313 0.000 0.012 0.000 0.012 0.976 0.000
#> GSM550914 5 0.3869 -0.3336 0.000 0.000 0.000 0.500 0.500 0.000
#> GSM550918 5 0.2912 0.6810 0.000 0.216 0.000 0.000 0.784 0.000
#> GSM550922 2 0.1267 0.8875 0.000 0.940 0.000 0.000 0.060 0.000
#> GSM550923 1 0.0000 0.9675 1.000 0.000 0.000 0.000 0.000 0.000
#> GSM550925 6 0.0260 0.8644 0.000 0.000 0.000 0.008 0.000 0.992
#> GSM550802 5 0.3266 0.5714 0.000 0.272 0.000 0.000 0.728 0.000
#> GSM550812 2 0.3695 0.3723 0.000 0.624 0.000 0.000 0.376 0.000
#> GSM550831 6 0.2994 0.8556 0.000 0.000 0.004 0.208 0.000 0.788
#> GSM550847 1 0.3558 0.7297 0.760 0.000 0.028 0.000 0.000 0.212
#> GSM550860 6 0.2146 0.8644 0.000 0.000 0.004 0.116 0.000 0.880
#> GSM550875 6 0.2994 0.8556 0.000 0.000 0.004 0.208 0.000 0.788
#> GSM550880 4 0.0291 0.7372 0.000 0.000 0.004 0.992 0.000 0.004
#> GSM550881 6 0.0146 0.8642 0.000 0.000 0.000 0.004 0.000 0.996
#> GSM550883 1 0.2823 0.7674 0.796 0.000 0.000 0.000 0.000 0.204
#> GSM550884 4 0.2912 0.7764 0.000 0.000 0.000 0.784 0.216 0.000
#> GSM550910 5 0.0146 0.8352 0.000 0.004 0.000 0.000 0.996 0.000
#> GSM550916 6 0.0146 0.8642 0.000 0.000 0.000 0.004 0.000 0.996
#> GSM550920 4 0.2883 0.7784 0.000 0.000 0.000 0.788 0.212 0.000
Heatmaps for the consensus matrix. It visualizes the probability of two samples to be in a same group.
consensus_heatmap(res, k = 2)
consensus_heatmap(res, k = 3)
consensus_heatmap(res, k = 4)
consensus_heatmap(res, k = 5)
consensus_heatmap(res, k = 6)
Heatmaps for the membership of samples in all partitions to see how consistent they are:
membership_heatmap(res, k = 2)
membership_heatmap(res, k = 3)
membership_heatmap(res, k = 4)
membership_heatmap(res, k = 5)
membership_heatmap(res, k = 6)
As soon as we have had the classes for columns, we can look for signatures which are significantly different between classes which can be candidate marks for certain classes. Following are the heatmaps for signatures.
Signature heatmaps where rows are scaled:
get_signatures(res, k = 2)
get_signatures(res, k = 3)
get_signatures(res, k = 4)
get_signatures(res, k = 5)
get_signatures(res, k = 6)
Signature heatmaps where rows are not scaled:
get_signatures(res, k = 2, scale_rows = FALSE)
get_signatures(res, k = 3, scale_rows = FALSE)
get_signatures(res, k = 4, scale_rows = FALSE)
get_signatures(res, k = 5, scale_rows = FALSE)
get_signatures(res, k = 6, scale_rows = FALSE)
Compare the overlap of signatures from different k:
compare_signatures(res)
get_signature() returns a data frame invisibly. TO get the list of signatures, the function
call should be assigned to a variable explicitly. In following code, if plot argument is set
to FALSE, no heatmap is plotted while only the differential analysis is performed.
# code only for demonstration
tb = get_signature(res, k = ..., plot = FALSE)
An example of the output of tb is:
#> which_row fdr mean_1 mean_2 scaled_mean_1 scaled_mean_2 km
#> 1 38 0.042760348 8.373488 9.131774 -0.5533452 0.5164555 1
#> 2 40 0.018707592 7.106213 8.469186 -0.6173731 0.5762149 1
#> 3 55 0.019134737 10.221463 11.207825 -0.6159697 0.5749050 1
#> 4 59 0.006059896 5.921854 7.869574 -0.6899429 0.6439467 1
#> 5 60 0.018055526 8.928898 10.211722 -0.6204761 0.5791110 1
#> 6 98 0.009384629 15.714769 14.887706 0.6635654 -0.6193277 2
...
The columns in tb are:
which_row: row indices corresponding to the input matrix.fdr: FDR for the differential test. mean_x: The mean value in group x.scaled_mean_x: The mean value in group x after rows are scaled.km: Row groups if k-means clustering is applied to rows.UMAP plot which shows how samples are separated.
dimension_reduction(res, k = 2, method = "UMAP")
dimension_reduction(res, k = 3, method = "UMAP")
dimension_reduction(res, k = 4, method = "UMAP")
dimension_reduction(res, k = 5, method = "UMAP")
dimension_reduction(res, k = 6, method = "UMAP")
Following heatmap shows how subgroups are split when increasing k:
collect_classes(res)
Test correlation between subgroups and known annotations. If the known annotation is numeric, one-way ANOVA test is applied, and if the known annotation is discrete, chi-squared contingency table test is applied.
test_to_known_factors(res)
#> n disease.state(p) k
#> ATC:pam 141 1.97e-03 2
#> ATC:pam 143 1.51e-07 3
#> ATC:pam 142 1.52e-05 4
#> ATC:pam 79 2.33e-05 5
#> ATC:pam 135 2.03e-04 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 51776 rows and 143 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 0.941 0.950 0.978 0.3894 0.628 0.628
#> 3 3 0.393 0.687 0.783 0.4802 0.731 0.581
#> 4 4 0.345 0.511 0.664 0.1289 0.811 0.576
#> 5 5 0.422 0.454 0.727 0.0358 0.842 0.593
#> 6 6 0.505 0.398 0.700 0.1009 0.867 0.620
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
#> GSM550785 2 0.0000 0.973 0.000 1.000
#> GSM550786 2 0.0000 0.973 0.000 1.000
#> GSM550788 2 0.0000 0.973 0.000 1.000
#> GSM550789 2 0.0000 0.973 0.000 1.000
#> GSM550790 2 0.9608 0.404 0.384 0.616
#> GSM550791 2 0.0376 0.970 0.004 0.996
#> GSM550792 2 0.0000 0.973 0.000 1.000
#> GSM550796 2 0.0000 0.973 0.000 1.000
#> GSM550797 2 0.0000 0.973 0.000 1.000
#> GSM550799 2 0.0000 0.973 0.000 1.000
#> GSM550800 2 0.0000 0.973 0.000 1.000
#> GSM550801 2 0.0000 0.973 0.000 1.000
#> GSM550804 2 0.0000 0.973 0.000 1.000
#> GSM550806 2 0.0000 0.973 0.000 1.000
#> GSM550807 2 0.0000 0.973 0.000 1.000
#> GSM550808 1 0.0000 0.989 1.000 0.000
#> GSM550809 1 0.0000 0.989 1.000 0.000
#> GSM550810 2 0.6973 0.773 0.188 0.812
#> GSM550811 2 0.0000 0.973 0.000 1.000
#> GSM550813 2 0.0000 0.973 0.000 1.000
#> GSM550814 2 0.0000 0.973 0.000 1.000
#> GSM550815 1 0.1633 0.967 0.976 0.024
#> GSM550816 1 0.0000 0.989 1.000 0.000
#> GSM550817 1 0.0000 0.989 1.000 0.000
#> GSM550818 1 0.0000 0.989 1.000 0.000
#> GSM550819 2 0.0000 0.973 0.000 1.000
#> GSM550820 2 0.7602 0.736 0.220 0.780
#> GSM550821 2 0.0000 0.973 0.000 1.000
#> GSM550822 1 0.1184 0.975 0.984 0.016
#> GSM550826 2 0.0000 0.973 0.000 1.000
#> GSM550832 2 0.0000 0.973 0.000 1.000
#> GSM550833 2 0.0000 0.973 0.000 1.000
#> GSM550835 2 0.0000 0.973 0.000 1.000
#> GSM550836 1 0.0000 0.989 1.000 0.000
#> GSM550837 2 0.0000 0.973 0.000 1.000
#> GSM550838 1 0.0000 0.989 1.000 0.000
#> GSM550841 1 0.0000 0.989 1.000 0.000
#> GSM550842 2 0.7219 0.756 0.200 0.800
#> GSM550846 2 0.0000 0.973 0.000 1.000
#> GSM550849 1 0.0000 0.989 1.000 0.000
#> GSM550850 1 0.0000 0.989 1.000 0.000
#> GSM550851 2 0.0000 0.973 0.000 1.000
#> GSM550852 2 0.0000 0.973 0.000 1.000
#> GSM550853 2 0.0000 0.973 0.000 1.000
#> GSM550855 2 0.0000 0.973 0.000 1.000
#> GSM550856 2 0.0000 0.973 0.000 1.000
#> GSM550861 2 0.0000 0.973 0.000 1.000
#> GSM550863 2 0.0000 0.973 0.000 1.000
#> GSM550864 2 0.0000 0.973 0.000 1.000
#> GSM550866 2 0.0000 0.973 0.000 1.000
#> GSM550867 1 0.0000 0.989 1.000 0.000
#> GSM550885 1 0.0000 0.989 1.000 0.000
#> GSM550886 2 0.0000 0.973 0.000 1.000
#> GSM550887 2 0.0000 0.973 0.000 1.000
#> GSM550889 2 0.4562 0.887 0.096 0.904
#> GSM550894 2 0.0000 0.973 0.000 1.000
#> GSM550897 2 0.0000 0.973 0.000 1.000
#> GSM550903 2 0.0000 0.973 0.000 1.000
#> GSM550905 2 0.0000 0.973 0.000 1.000
#> GSM550906 2 0.0000 0.973 0.000 1.000
#> GSM550907 1 0.0000 0.989 1.000 0.000
#> GSM550909 2 0.7139 0.762 0.196 0.804
#> GSM550911 1 0.0000 0.989 1.000 0.000
#> GSM550913 2 0.0000 0.973 0.000 1.000
#> GSM550915 2 0.7376 0.745 0.208 0.792
#> GSM550917 2 0.0000 0.973 0.000 1.000
#> GSM550919 2 0.0000 0.973 0.000 1.000
#> GSM550921 1 0.0000 0.989 1.000 0.000
#> GSM550924 2 0.0000 0.973 0.000 1.000
#> GSM550926 2 0.0000 0.973 0.000 1.000
#> GSM550927 2 0.0000 0.973 0.000 1.000
#> GSM550787 2 0.0000 0.973 0.000 1.000
#> GSM550793 2 0.2423 0.940 0.040 0.960
#> GSM550794 2 0.0000 0.973 0.000 1.000
#> GSM550795 2 0.0000 0.973 0.000 1.000
#> GSM550798 1 0.0000 0.989 1.000 0.000
#> GSM550803 1 0.0000 0.989 1.000 0.000
#> GSM550805 2 0.0000 0.973 0.000 1.000
#> GSM550823 2 0.0000 0.973 0.000 1.000
#> GSM550824 1 0.0000 0.989 1.000 0.000
#> GSM550825 2 0.4022 0.903 0.080 0.920
#> GSM550827 2 0.0000 0.973 0.000 1.000
#> GSM550828 2 0.6973 0.777 0.188 0.812
#> GSM550829 1 0.0376 0.986 0.996 0.004
#> GSM550830 2 0.0000 0.973 0.000 1.000
#> GSM550834 2 0.0000 0.973 0.000 1.000
#> GSM550839 2 0.0000 0.973 0.000 1.000
#> GSM550840 1 0.0000 0.989 1.000 0.000
#> GSM550843 2 0.0000 0.973 0.000 1.000
#> GSM550844 2 0.0000 0.973 0.000 1.000
#> GSM550845 2 0.0000 0.973 0.000 1.000
#> GSM550848 2 0.0000 0.973 0.000 1.000
#> GSM550854 1 0.0000 0.989 1.000 0.000
#> GSM550857 1 0.0000 0.989 1.000 0.000
#> GSM550858 2 0.5408 0.857 0.124 0.876
#> GSM550859 1 0.0000 0.989 1.000 0.000
#> GSM550862 2 0.0000 0.973 0.000 1.000
#> GSM550865 2 0.0000 0.973 0.000 1.000
#> GSM550868 2 0.0000 0.973 0.000 1.000
#> GSM550869 2 0.0000 0.973 0.000 1.000
#> GSM550870 2 0.0000 0.973 0.000 1.000
#> GSM550871 2 0.0000 0.973 0.000 1.000
#> GSM550872 2 0.0000 0.973 0.000 1.000
#> GSM550873 2 0.0000 0.973 0.000 1.000
#> GSM550874 2 0.0000 0.973 0.000 1.000
#> GSM550876 2 0.0000 0.973 0.000 1.000
#> GSM550877 2 0.0000 0.973 0.000 1.000
#> GSM550878 2 0.0000 0.973 0.000 1.000
#> GSM550879 2 0.0000 0.973 0.000 1.000
#> GSM550882 2 0.9323 0.490 0.348 0.652
#> GSM550888 1 0.0000 0.989 1.000 0.000
#> GSM550890 2 0.0000 0.973 0.000 1.000
#> GSM550891 1 0.0000 0.989 1.000 0.000
#> GSM550892 2 0.0000 0.973 0.000 1.000
#> GSM550893 2 0.0000 0.973 0.000 1.000
#> GSM550895 2 0.0000 0.973 0.000 1.000
#> GSM550896 2 0.0000 0.973 0.000 1.000
#> GSM550898 1 0.0000 0.989 1.000 0.000
#> GSM550899 2 0.0000 0.973 0.000 1.000
#> GSM550900 2 0.0000 0.973 0.000 1.000
#> GSM550901 2 0.0000 0.973 0.000 1.000
#> GSM550902 2 0.0000 0.973 0.000 1.000
#> GSM550904 2 0.0000 0.973 0.000 1.000
#> GSM550908 1 0.0000 0.989 1.000 0.000
#> GSM550912 2 0.0000 0.973 0.000 1.000
#> GSM550914 2 0.1184 0.960 0.016 0.984
#> GSM550918 2 0.0000 0.973 0.000 1.000
#> GSM550922 2 0.0000 0.973 0.000 1.000
#> GSM550923 1 0.0000 0.989 1.000 0.000
#> GSM550925 1 0.8661 0.580 0.712 0.288
#> GSM550802 2 0.0000 0.973 0.000 1.000
#> GSM550812 1 0.0000 0.989 1.000 0.000
#> GSM550831 1 0.0000 0.989 1.000 0.000
#> GSM550847 1 0.1843 0.963 0.972 0.028
#> GSM550860 2 0.0000 0.973 0.000 1.000
#> GSM550875 2 0.0000 0.973 0.000 1.000
#> GSM550880 2 0.0376 0.970 0.004 0.996
#> GSM550881 2 0.0000 0.973 0.000 1.000
#> GSM550883 1 0.0000 0.989 1.000 0.000
#> GSM550884 2 0.0000 0.973 0.000 1.000
#> GSM550910 2 0.8144 0.675 0.252 0.748
#> GSM550916 2 0.8499 0.638 0.276 0.724
#> GSM550920 2 0.0000 0.973 0.000 1.000
cbind(get_classes(res, k = 3), get_membership(res, k = 3))
#> class entropy silhouette p1 p2 p3
#> GSM550785 1 0.4974 0.707 0.764 0.236 0.000
#> GSM550786 1 0.0000 0.718 1.000 0.000 0.000
#> GSM550788 1 0.5785 -0.243 0.668 0.332 0.000
#> GSM550789 2 0.6308 0.775 0.492 0.508 0.000
#> GSM550790 1 0.6624 0.671 0.708 0.248 0.044
#> GSM550791 1 0.4682 0.727 0.804 0.192 0.004
#> GSM550792 1 0.0000 0.718 1.000 0.000 0.000
#> GSM550796 1 0.0747 0.705 0.984 0.016 0.000
#> GSM550797 1 0.0000 0.718 1.000 0.000 0.000
#> GSM550799 1 0.6008 -0.327 0.628 0.372 0.000
#> GSM550800 1 0.1031 0.697 0.976 0.024 0.000
#> GSM550801 2 0.6026 0.952 0.376 0.624 0.000
#> GSM550804 1 0.6291 -0.699 0.532 0.468 0.000
#> GSM550806 1 0.0000 0.718 1.000 0.000 0.000
#> GSM550807 2 0.6008 0.954 0.372 0.628 0.000
#> GSM550808 3 0.1765 0.866 0.040 0.004 0.956
#> GSM550809 3 0.0237 0.847 0.000 0.004 0.996
#> GSM550810 1 0.2448 0.705 0.924 0.000 0.076
#> GSM550811 1 0.4062 0.735 0.836 0.164 0.000
#> GSM550813 2 0.6008 0.954 0.372 0.628 0.000
#> GSM550814 2 0.6045 0.950 0.380 0.620 0.000
#> GSM550815 3 0.4629 0.777 0.188 0.004 0.808
#> GSM550816 3 0.1878 0.867 0.044 0.004 0.952
#> GSM550817 3 0.0661 0.849 0.008 0.004 0.988
#> GSM550818 3 0.2590 0.866 0.072 0.004 0.924
#> GSM550819 1 0.1163 0.693 0.972 0.028 0.000
#> GSM550820 1 0.6335 0.686 0.724 0.240 0.036
#> GSM550821 1 0.6062 -0.441 0.616 0.384 0.000
#> GSM550822 3 0.4575 0.782 0.184 0.004 0.812
#> GSM550826 1 0.4974 0.707 0.764 0.236 0.000
#> GSM550832 2 0.6008 0.954 0.372 0.628 0.000
#> GSM550833 1 0.0424 0.712 0.992 0.008 0.000
#> GSM550835 2 0.6008 0.954 0.372 0.628 0.000
#> GSM550836 3 0.7333 0.839 0.136 0.156 0.708
#> GSM550837 1 0.0000 0.718 1.000 0.000 0.000
#> GSM550838 3 0.0000 0.848 0.000 0.000 1.000
#> GSM550841 3 0.1525 0.863 0.032 0.004 0.964
#> GSM550842 1 0.2537 0.703 0.920 0.000 0.080
#> GSM550846 1 0.2261 0.720 0.932 0.068 0.000
#> GSM550849 3 0.5174 0.832 0.076 0.092 0.832
#> GSM550850 3 0.1878 0.867 0.044 0.004 0.952
#> GSM550851 1 0.0000 0.718 1.000 0.000 0.000
#> GSM550852 1 0.0000 0.718 1.000 0.000 0.000
#> GSM550853 1 0.0000 0.718 1.000 0.000 0.000
#> GSM550855 1 0.0424 0.712 0.992 0.008 0.000
#> GSM550856 2 0.6008 0.954 0.372 0.628 0.000
#> GSM550861 2 0.6008 0.954 0.372 0.628 0.000
#> GSM550863 1 0.2959 0.595 0.900 0.100 0.000
#> GSM550864 2 0.6008 0.954 0.372 0.628 0.000
#> GSM550866 2 0.5988 0.950 0.368 0.632 0.000
#> GSM550867 3 0.7975 0.818 0.140 0.204 0.656
#> GSM550885 3 0.7739 0.829 0.136 0.188 0.676
#> GSM550886 2 0.6008 0.954 0.372 0.628 0.000
#> GSM550887 1 0.6168 -0.539 0.588 0.412 0.000
#> GSM550889 1 0.5269 0.727 0.784 0.200 0.016
#> GSM550894 2 0.6008 0.954 0.372 0.628 0.000
#> GSM550897 1 0.4178 0.736 0.828 0.172 0.000
#> GSM550903 2 0.6026 0.952 0.376 0.624 0.000
#> GSM550905 2 0.6079 0.934 0.388 0.612 0.000
#> GSM550906 2 0.6008 0.954 0.372 0.628 0.000
#> GSM550907 3 0.2096 0.865 0.052 0.004 0.944
#> GSM550909 1 0.2796 0.701 0.908 0.000 0.092
#> GSM550911 3 0.0424 0.848 0.000 0.008 0.992
#> GSM550913 2 0.6309 0.758 0.500 0.500 0.000
#> GSM550915 1 0.4413 0.737 0.832 0.160 0.008
#> GSM550917 2 0.6008 0.954 0.372 0.628 0.000
#> GSM550919 2 0.6280 0.845 0.460 0.540 0.000
#> GSM550921 3 0.4316 0.868 0.044 0.088 0.868
#> GSM550924 2 0.6267 0.856 0.452 0.548 0.000
#> GSM550926 2 0.6008 0.954 0.372 0.628 0.000
#> GSM550927 2 0.6008 0.954 0.372 0.628 0.000
#> GSM550787 1 0.0592 0.714 0.988 0.012 0.000
#> GSM550793 1 0.5058 0.702 0.756 0.244 0.000
#> GSM550794 1 0.0000 0.718 1.000 0.000 0.000
#> GSM550795 1 0.5016 0.705 0.760 0.240 0.000
#> GSM550798 3 0.7960 0.820 0.136 0.208 0.656
#> GSM550803 3 0.6488 0.855 0.084 0.160 0.756
#> GSM550805 1 0.3412 0.739 0.876 0.124 0.000
#> GSM550823 1 0.0000 0.718 1.000 0.000 0.000
#> GSM550824 3 0.7441 0.837 0.136 0.164 0.700
#> GSM550825 1 0.5502 0.694 0.744 0.248 0.008
#> GSM550827 2 0.6111 0.937 0.396 0.604 0.000
#> GSM550828 1 0.5578 0.698 0.748 0.240 0.012
#> GSM550829 3 0.9006 0.680 0.188 0.256 0.556
#> GSM550830 1 0.0237 0.715 0.996 0.004 0.000
#> GSM550834 1 0.4654 0.721 0.792 0.208 0.000
#> GSM550839 1 0.0237 0.718 0.996 0.000 0.004
#> GSM550840 3 0.1878 0.867 0.044 0.004 0.952
#> GSM550843 1 0.1289 0.689 0.968 0.032 0.000
#> GSM550844 1 0.4796 0.716 0.780 0.220 0.000
#> GSM550845 2 0.6215 0.897 0.428 0.572 0.000
#> GSM550848 2 0.6308 0.790 0.492 0.508 0.000
#> GSM550854 3 0.7960 0.820 0.136 0.208 0.656
#> GSM550857 3 0.7333 0.839 0.136 0.156 0.708
#> GSM550858 1 0.5480 0.683 0.732 0.264 0.004
#> GSM550859 3 0.7545 0.835 0.136 0.172 0.692
#> GSM550862 1 0.4974 0.707 0.764 0.236 0.000
#> GSM550865 1 0.0237 0.719 0.996 0.004 0.000
#> GSM550868 1 0.6274 -0.670 0.544 0.456 0.000
#> GSM550869 1 0.4047 0.737 0.848 0.148 0.004
#> GSM550870 2 0.6008 0.954 0.372 0.628 0.000
#> GSM550871 1 0.0424 0.720 0.992 0.008 0.000
#> GSM550872 1 0.0424 0.720 0.992 0.008 0.000
#> GSM550873 1 0.0000 0.718 1.000 0.000 0.000
#> GSM550874 1 0.3192 0.575 0.888 0.112 0.000
#> GSM550876 1 0.4504 0.358 0.804 0.196 0.000
#> GSM550877 2 0.6008 0.954 0.372 0.628 0.000
#> GSM550878 2 0.6079 0.940 0.388 0.612 0.000
#> GSM550879 1 0.4504 0.726 0.804 0.196 0.000
#> GSM550882 1 0.7107 0.680 0.712 0.196 0.092
#> GSM550888 3 0.7221 0.840 0.136 0.148 0.716
#> GSM550890 1 0.4235 0.732 0.824 0.176 0.000
#> GSM550891 3 0.0424 0.848 0.000 0.008 0.992
#> GSM550892 1 0.4654 0.722 0.792 0.208 0.000
#> GSM550893 2 0.6215 0.885 0.428 0.572 0.000
#> GSM550895 1 0.6309 -0.771 0.500 0.500 0.000
#> GSM550896 2 0.6008 0.954 0.372 0.628 0.000
#> GSM550898 3 0.7960 0.820 0.136 0.208 0.656
#> GSM550899 2 0.6008 0.954 0.372 0.628 0.000
#> GSM550900 1 0.6302 -0.732 0.520 0.480 0.000
#> GSM550901 1 0.3879 0.736 0.848 0.152 0.000
#> GSM550902 1 0.4555 0.725 0.800 0.200 0.000
#> GSM550904 1 0.4974 0.707 0.764 0.236 0.000
#> GSM550908 3 0.4527 0.868 0.052 0.088 0.860
#> GSM550912 1 0.4842 0.360 0.776 0.224 0.000
#> GSM550914 1 0.4645 0.735 0.816 0.176 0.008
#> GSM550918 2 0.5988 0.950 0.368 0.632 0.000
#> GSM550922 2 0.6045 0.949 0.380 0.620 0.000
#> GSM550923 3 0.7975 0.818 0.140 0.204 0.656
#> GSM550925 1 0.8587 0.550 0.604 0.176 0.220
#> GSM550802 1 0.0000 0.718 1.000 0.000 0.000
#> GSM550812 3 0.1525 0.863 0.032 0.004 0.964
#> GSM550831 3 0.1878 0.867 0.044 0.004 0.952
#> GSM550847 3 0.9612 0.466 0.332 0.216 0.452
#> GSM550860 1 0.4178 0.736 0.828 0.172 0.000
#> GSM550875 1 0.4121 0.734 0.832 0.168 0.000
#> GSM550880 1 0.7534 -0.236 0.584 0.368 0.048
#> GSM550881 1 0.4504 0.732 0.804 0.196 0.000
#> GSM550883 1 0.9481 -0.259 0.432 0.184 0.384
#> GSM550884 2 0.6280 0.849 0.460 0.540 0.000
#> GSM550910 1 0.5741 0.656 0.776 0.036 0.188
#> GSM550916 1 0.5420 0.700 0.752 0.240 0.008
#> GSM550920 1 0.6307 -0.744 0.512 0.488 0.000
cbind(get_classes(res, k = 4), get_membership(res, k = 4))
#> class entropy silhouette p1 p2 p3 p4
#> GSM550785 4 0.8989 0.6274 0.100 0.156 0.312 0.432
#> GSM550786 4 0.3837 0.5208 0.000 0.224 0.000 0.776
#> GSM550788 2 0.4973 0.4641 0.000 0.644 0.008 0.348
#> GSM550789 2 0.5184 0.5483 0.000 0.672 0.024 0.304
#> GSM550790 4 0.8898 0.5089 0.200 0.068 0.316 0.416
#> GSM550791 4 0.7556 0.6407 0.004 0.188 0.312 0.496
#> GSM550792 4 0.4406 0.4776 0.000 0.300 0.000 0.700
#> GSM550796 4 0.5994 0.3761 0.000 0.156 0.152 0.692
#> GSM550797 4 0.4839 0.4791 0.000 0.184 0.052 0.764
#> GSM550799 2 0.3808 0.7153 0.000 0.812 0.012 0.176
#> GSM550800 4 0.4844 0.4484 0.000 0.300 0.012 0.688
#> GSM550801 2 0.2868 0.7763 0.000 0.864 0.000 0.136
#> GSM550804 2 0.5112 0.3749 0.000 0.608 0.008 0.384
#> GSM550806 4 0.7267 0.5770 0.004 0.260 0.180 0.556
#> GSM550807 2 0.0817 0.8344 0.000 0.976 0.000 0.024
#> GSM550808 3 0.7511 0.3771 0.336 0.000 0.468 0.196
#> GSM550809 3 0.5604 0.1507 0.476 0.000 0.504 0.020
#> GSM550810 4 0.5690 0.2111 0.000 0.096 0.196 0.708
#> GSM550811 4 0.7556 0.6407 0.004 0.188 0.312 0.496
#> GSM550813 2 0.0000 0.8292 0.000 1.000 0.000 0.000
#> GSM550814 2 0.0817 0.8342 0.000 0.976 0.000 0.024
#> GSM550815 3 0.7752 0.3695 0.328 0.004 0.456 0.212
#> GSM550816 3 0.7511 0.3771 0.336 0.000 0.468 0.196
#> GSM550817 3 0.6652 0.2594 0.396 0.000 0.516 0.088
#> GSM550818 1 0.7972 -0.2772 0.416 0.012 0.376 0.196
#> GSM550819 4 0.4917 0.4164 0.000 0.336 0.008 0.656
#> GSM550820 4 0.9108 0.5321 0.184 0.092 0.324 0.400
#> GSM550821 2 0.5150 0.3367 0.000 0.596 0.008 0.396
#> GSM550822 3 0.7752 0.3695 0.328 0.004 0.456 0.212
#> GSM550826 4 0.8901 0.6319 0.092 0.156 0.312 0.440
#> GSM550832 2 0.0188 0.8291 0.000 0.996 0.000 0.004
#> GSM550833 4 0.4807 0.4899 0.000 0.248 0.024 0.728
#> GSM550835 2 0.0000 0.8292 0.000 1.000 0.000 0.000
#> GSM550836 1 0.3521 0.5320 0.864 0.000 0.052 0.084
#> GSM550837 4 0.4466 0.4908 0.000 0.180 0.036 0.784
#> GSM550838 1 0.6384 -0.2469 0.496 0.000 0.440 0.064
#> GSM550841 3 0.7511 0.3771 0.336 0.000 0.468 0.196
#> GSM550842 4 0.5763 0.1977 0.000 0.096 0.204 0.700
#> GSM550846 2 0.7922 -0.5148 0.000 0.344 0.320 0.336
#> GSM550849 1 0.7777 -0.2133 0.424 0.004 0.368 0.204
#> GSM550850 1 0.6884 -0.2377 0.500 0.004 0.404 0.092
#> GSM550851 4 0.4332 0.5015 0.000 0.176 0.032 0.792
#> GSM550852 4 0.3444 0.5245 0.000 0.184 0.000 0.816
#> GSM550853 4 0.4728 0.5004 0.000 0.216 0.032 0.752
#> GSM550855 4 0.4542 0.5072 0.000 0.228 0.020 0.752
#> GSM550856 2 0.0000 0.8292 0.000 1.000 0.000 0.000
#> GSM550861 2 0.0000 0.8292 0.000 1.000 0.000 0.000
#> GSM550863 2 0.3907 0.6519 0.000 0.768 0.000 0.232
#> GSM550864 2 0.0336 0.8323 0.000 0.992 0.000 0.008
#> GSM550866 2 0.0000 0.8292 0.000 1.000 0.000 0.000
#> GSM550867 1 0.3448 0.4801 0.828 0.000 0.004 0.168
#> GSM550885 1 0.2081 0.5450 0.916 0.000 0.000 0.084
#> GSM550886 2 0.0336 0.8323 0.000 0.992 0.000 0.008
#> GSM550887 2 0.4718 0.5458 0.000 0.708 0.012 0.280
#> GSM550889 4 0.9535 0.5774 0.128 0.208 0.332 0.332
#> GSM550894 2 0.1209 0.8254 0.000 0.964 0.032 0.004
#> GSM550897 4 0.9215 0.5894 0.080 0.244 0.312 0.364
#> GSM550903 2 0.0188 0.8296 0.000 0.996 0.004 0.000
#> GSM550905 2 0.1305 0.8234 0.000 0.960 0.036 0.004
#> GSM550906 2 0.0000 0.8292 0.000 1.000 0.000 0.000
#> GSM550907 1 0.8735 -0.1723 0.424 0.084 0.356 0.136
#> GSM550909 4 0.6082 0.2677 0.016 0.104 0.168 0.712
#> GSM550911 3 0.5657 0.1497 0.436 0.000 0.540 0.024
#> GSM550913 2 0.4576 0.6135 0.000 0.728 0.012 0.260
#> GSM550915 4 0.8071 0.5789 0.008 0.256 0.328 0.408
#> GSM550917 2 0.0000 0.8292 0.000 1.000 0.000 0.000
#> GSM550919 2 0.2011 0.8162 0.000 0.920 0.000 0.080
#> GSM550921 1 0.4332 0.3943 0.792 0.000 0.176 0.032
#> GSM550924 2 0.1867 0.8209 0.000 0.928 0.000 0.072
#> GSM550926 2 0.0336 0.8323 0.000 0.992 0.000 0.008
#> GSM550927 2 0.1356 0.8328 0.000 0.960 0.008 0.032
#> GSM550787 4 0.7784 0.5735 0.000 0.292 0.280 0.428
#> GSM550793 4 0.9039 0.5969 0.136 0.120 0.316 0.428
#> GSM550794 4 0.4343 0.5125 0.004 0.264 0.000 0.732
#> GSM550795 4 0.9041 0.6081 0.124 0.132 0.316 0.428
#> GSM550798 1 0.2149 0.5448 0.912 0.000 0.000 0.088
#> GSM550803 1 0.2983 0.4797 0.892 0.000 0.068 0.040
#> GSM550805 4 0.7709 0.6329 0.004 0.212 0.312 0.472
#> GSM550823 4 0.4955 0.5181 0.004 0.272 0.016 0.708
#> GSM550824 1 0.2266 0.5446 0.912 0.000 0.004 0.084
#> GSM550825 4 0.9020 0.5841 0.148 0.108 0.316 0.428
#> GSM550827 2 0.1474 0.8276 0.000 0.948 0.000 0.052
#> GSM550828 4 0.9065 0.5537 0.172 0.096 0.316 0.416
#> GSM550829 1 0.6256 0.2761 0.616 0.044 0.016 0.324
#> GSM550830 4 0.4790 0.3642 0.000 0.380 0.000 0.620
#> GSM550834 4 0.7813 0.6447 0.016 0.176 0.312 0.496
#> GSM550839 4 0.3721 0.5187 0.004 0.176 0.004 0.816
#> GSM550840 1 0.7063 -0.2267 0.488 0.004 0.400 0.108
#> GSM550843 4 0.4624 0.4141 0.000 0.340 0.000 0.660
#> GSM550844 4 0.9030 0.6265 0.104 0.156 0.312 0.428
#> GSM550845 2 0.2011 0.8182 0.000 0.920 0.000 0.080
#> GSM550848 2 0.2281 0.8048 0.000 0.904 0.000 0.096
#> GSM550854 1 0.2334 0.5440 0.908 0.000 0.004 0.088
#> GSM550857 1 0.3521 0.5320 0.864 0.000 0.052 0.084
#> GSM550858 4 0.8831 0.5254 0.188 0.068 0.316 0.428
#> GSM550859 1 0.2081 0.5450 0.916 0.000 0.000 0.084
#> GSM550862 4 0.9094 0.6155 0.120 0.144 0.312 0.424
#> GSM550865 2 0.6544 0.2660 0.044 0.604 0.028 0.324
#> GSM550868 2 0.3074 0.7585 0.000 0.848 0.000 0.152
#> GSM550869 4 0.8138 0.5669 0.008 0.280 0.328 0.384
#> GSM550870 2 0.0000 0.8292 0.000 1.000 0.000 0.000
#> GSM550871 4 0.4422 0.5243 0.008 0.256 0.000 0.736
#> GSM550872 4 0.4391 0.5297 0.008 0.252 0.000 0.740
#> GSM550873 4 0.3975 0.5160 0.000 0.240 0.000 0.760
#> GSM550874 2 0.4972 0.1250 0.000 0.544 0.000 0.456
#> GSM550876 2 0.4343 0.5926 0.000 0.732 0.004 0.264
#> GSM550877 2 0.0000 0.8292 0.000 1.000 0.000 0.000
#> GSM550878 2 0.0921 0.8330 0.000 0.972 0.000 0.028
#> GSM550879 4 0.8798 0.6385 0.068 0.184 0.312 0.436
#> GSM550882 3 0.9649 -0.5901 0.148 0.208 0.344 0.300
#> GSM550888 1 0.3611 0.5260 0.860 0.000 0.060 0.080
#> GSM550890 4 0.7883 0.5467 0.000 0.292 0.328 0.380
#> GSM550891 1 0.5392 -0.1320 0.528 0.000 0.460 0.012
#> GSM550892 4 0.9050 0.6214 0.112 0.148 0.312 0.428
#> GSM550893 2 0.1820 0.8241 0.000 0.944 0.036 0.020
#> GSM550895 2 0.2589 0.7930 0.000 0.884 0.000 0.116
#> GSM550896 2 0.0469 0.8323 0.000 0.988 0.000 0.012
#> GSM550898 1 0.2149 0.5448 0.912 0.000 0.000 0.088
#> GSM550899 2 0.0817 0.8320 0.000 0.976 0.000 0.024
#> GSM550900 2 0.2704 0.7880 0.000 0.876 0.000 0.124
#> GSM550901 4 0.7542 0.6331 0.000 0.212 0.312 0.476
#> GSM550902 4 0.8391 0.6469 0.048 0.168 0.312 0.472
#> GSM550904 4 0.9477 0.5919 0.128 0.196 0.312 0.364
#> GSM550908 1 0.3749 0.4420 0.840 0.000 0.128 0.032
#> GSM550912 2 0.3653 0.7470 0.000 0.844 0.028 0.128
#> GSM550914 4 0.7748 0.5794 0.000 0.248 0.324 0.428
#> GSM550918 2 0.1022 0.8254 0.000 0.968 0.032 0.000
#> GSM550922 2 0.1022 0.8254 0.000 0.968 0.032 0.000
#> GSM550923 1 0.2921 0.5091 0.860 0.000 0.000 0.140
#> GSM550925 3 0.9914 -0.3643 0.280 0.208 0.296 0.216
#> GSM550802 4 0.3583 0.5211 0.000 0.180 0.004 0.816
#> GSM550812 1 0.7244 -0.3145 0.452 0.004 0.420 0.124
#> GSM550831 1 0.7187 -0.1922 0.476 0.004 0.400 0.120
#> GSM550847 1 0.7963 0.0484 0.496 0.020 0.196 0.288
#> GSM550860 4 0.9230 0.5842 0.080 0.248 0.316 0.356
#> GSM550875 4 0.8246 0.6421 0.032 0.188 0.312 0.468
#> GSM550880 2 0.5556 0.6598 0.032 0.760 0.060 0.148
#> GSM550881 4 0.9401 0.5966 0.108 0.216 0.316 0.360
#> GSM550883 1 0.8914 -0.0515 0.464 0.128 0.124 0.284
#> GSM550884 2 0.1867 0.8207 0.000 0.928 0.000 0.072
#> GSM550910 4 0.7536 0.5221 0.008 0.144 0.408 0.440
#> GSM550916 4 0.9511 0.5912 0.128 0.204 0.312 0.356
#> GSM550920 2 0.3024 0.7608 0.000 0.852 0.000 0.148
cbind(get_classes(res, k = 5), get_membership(res, k = 5))
#> class entropy silhouette p1 p2 p3 p4 p5
#> GSM550785 1 0.1965 0.41126 0.924 0.052 0.024 0.000 0.000
#> GSM550786 1 0.6676 0.08707 0.568 0.188 0.000 0.212 0.032
#> GSM550788 2 0.4786 0.62364 0.092 0.720 0.000 0.188 0.000
#> GSM550789 2 0.5361 0.55602 0.088 0.668 0.000 0.236 0.008
#> GSM550790 1 0.4431 0.55199 0.732 0.216 0.052 0.000 0.000
#> GSM550791 1 0.3109 0.55684 0.800 0.200 0.000 0.000 0.000
#> GSM550792 1 0.5295 0.06414 0.488 0.464 0.000 0.048 0.000
#> GSM550796 5 0.7041 0.17133 0.056 0.128 0.000 0.312 0.504
#> GSM550797 4 0.8385 -0.03687 0.276 0.148 0.000 0.328 0.248
#> GSM550799 2 0.2520 0.75334 0.048 0.896 0.000 0.056 0.000
#> GSM550800 2 0.5577 0.51527 0.108 0.636 0.000 0.252 0.004
#> GSM550801 2 0.3239 0.71888 0.068 0.852 0.000 0.080 0.000
#> GSM550804 2 0.4376 0.66195 0.092 0.764 0.000 0.144 0.000
#> GSM550806 1 0.4949 0.17057 0.532 0.444 0.000 0.020 0.004
#> GSM550807 2 0.0609 0.76403 0.020 0.980 0.000 0.000 0.000
#> GSM550808 5 0.0404 0.51462 0.000 0.000 0.012 0.000 0.988
#> GSM550809 4 0.6538 -0.21963 0.084 0.000 0.040 0.496 0.380
#> GSM550810 5 0.5960 0.31753 0.028 0.068 0.000 0.316 0.588
#> GSM550811 1 0.3671 0.54090 0.756 0.236 0.000 0.008 0.000
#> GSM550813 2 0.0451 0.76032 0.000 0.988 0.000 0.008 0.004
#> GSM550814 2 0.1153 0.76528 0.024 0.964 0.000 0.008 0.004
#> GSM550815 5 0.1329 0.51917 0.004 0.000 0.008 0.032 0.956
#> GSM550816 5 0.0566 0.51575 0.004 0.000 0.012 0.000 0.984
#> GSM550817 5 0.3848 0.38866 0.000 0.000 0.040 0.172 0.788
#> GSM550818 5 0.4311 0.45855 0.048 0.000 0.036 0.116 0.800
#> GSM550819 2 0.5496 0.57455 0.160 0.668 0.000 0.168 0.004
#> GSM550820 1 0.1808 0.38230 0.936 0.020 0.040 0.004 0.000
#> GSM550821 2 0.4698 0.63034 0.096 0.732 0.000 0.172 0.000
#> GSM550822 5 0.1492 0.51800 0.004 0.000 0.008 0.040 0.948
#> GSM550826 1 0.2540 0.48306 0.888 0.088 0.024 0.000 0.000
#> GSM550832 2 0.0290 0.76213 0.008 0.992 0.000 0.000 0.000
#> GSM550833 2 0.6779 0.33332 0.128 0.528 0.000 0.304 0.040
#> GSM550835 2 0.0290 0.76079 0.000 0.992 0.000 0.008 0.000
#> GSM550836 3 0.0324 0.83748 0.004 0.000 0.992 0.004 0.000
#> GSM550837 1 0.8156 -0.34796 0.360 0.148 0.000 0.328 0.164
#> GSM550838 5 0.7587 -0.00113 0.256 0.000 0.044 0.348 0.352
#> GSM550841 5 0.0404 0.51462 0.000 0.000 0.012 0.000 0.988
#> GSM550842 5 0.5849 0.32644 0.028 0.060 0.000 0.316 0.596
#> GSM550846 2 0.5604 -0.05592 0.460 0.480 0.000 0.052 0.008
#> GSM550849 1 0.6712 -0.39394 0.476 0.008 0.036 0.080 0.400
#> GSM550850 1 0.7228 -0.42910 0.432 0.000 0.052 0.144 0.372
#> GSM550851 1 0.7988 -0.31902 0.396 0.148 0.000 0.320 0.136
#> GSM550852 1 0.7761 -0.28043 0.432 0.148 0.000 0.312 0.108
#> GSM550853 4 0.8341 -0.03486 0.236 0.300 0.000 0.324 0.140
#> GSM550855 2 0.8064 -0.11772 0.100 0.364 0.000 0.308 0.228
#> GSM550856 2 0.0000 0.76080 0.000 1.000 0.000 0.000 0.000
#> GSM550861 2 0.0451 0.76012 0.000 0.988 0.004 0.008 0.000
#> GSM550863 2 0.4015 0.56600 0.264 0.724 0.000 0.008 0.004
#> GSM550864 2 0.0324 0.76105 0.004 0.992 0.000 0.004 0.000
#> GSM550866 2 0.0324 0.76077 0.000 0.992 0.000 0.004 0.004
#> GSM550867 3 0.1270 0.80771 0.052 0.000 0.948 0.000 0.000
#> GSM550885 3 0.0290 0.83929 0.008 0.000 0.992 0.000 0.000
#> GSM550886 2 0.0932 0.76038 0.004 0.972 0.000 0.020 0.004
#> GSM550887 2 0.5394 0.59139 0.072 0.688 0.004 0.220 0.016
#> GSM550889 1 0.6402 0.36016 0.532 0.360 0.064 0.040 0.004
#> GSM550894 2 0.1285 0.75749 0.000 0.956 0.004 0.036 0.004
#> GSM550897 1 0.5409 0.36906 0.568 0.380 0.044 0.004 0.004
#> GSM550903 2 0.1041 0.75881 0.000 0.964 0.004 0.032 0.000
#> GSM550905 2 0.1766 0.75822 0.012 0.940 0.004 0.040 0.004
#> GSM550906 2 0.0566 0.75983 0.000 0.984 0.004 0.012 0.000
#> GSM550907 5 0.7533 0.12016 0.060 0.228 0.028 0.140 0.544
#> GSM550909 5 0.6373 0.30467 0.036 0.072 0.004 0.336 0.552
#> GSM550911 4 0.5102 -0.22333 0.000 0.000 0.044 0.580 0.376
#> GSM550913 2 0.5337 0.59973 0.068 0.692 0.004 0.220 0.016
#> GSM550915 1 0.5915 0.32638 0.544 0.380 0.008 0.056 0.012
#> GSM550917 2 0.0451 0.76012 0.000 0.988 0.004 0.008 0.000
#> GSM550919 2 0.3289 0.67972 0.172 0.816 0.000 0.008 0.004
#> GSM550921 3 0.3053 0.76186 0.008 0.000 0.872 0.044 0.076
#> GSM550924 2 0.3197 0.69403 0.152 0.832 0.000 0.012 0.004
#> GSM550926 2 0.0162 0.76080 0.000 0.996 0.000 0.004 0.000
#> GSM550927 2 0.1652 0.75722 0.008 0.944 0.004 0.040 0.004
#> GSM550787 2 0.4793 0.14227 0.436 0.544 0.000 0.020 0.000
#> GSM550793 1 0.2520 0.44773 0.896 0.056 0.048 0.000 0.000
#> GSM550794 1 0.5942 0.33010 0.580 0.292 0.000 0.124 0.004
#> GSM550795 1 0.1399 0.39153 0.952 0.020 0.028 0.000 0.000
#> GSM550798 3 0.0290 0.83929 0.008 0.000 0.992 0.000 0.000
#> GSM550803 3 0.6740 0.26207 0.364 0.004 0.500 0.040 0.092
#> GSM550805 1 0.4201 0.44197 0.664 0.328 0.000 0.008 0.000
#> GSM550823 1 0.5341 0.32208 0.580 0.364 0.000 0.052 0.004
#> GSM550824 3 0.0290 0.83929 0.008 0.000 0.992 0.000 0.000
#> GSM550825 1 0.5045 0.47387 0.636 0.308 0.056 0.000 0.000
#> GSM550827 2 0.2956 0.70572 0.140 0.848 0.000 0.008 0.004
#> GSM550828 1 0.3134 0.51576 0.848 0.120 0.032 0.000 0.000
#> GSM550829 1 0.4525 -0.07197 0.624 0.016 0.360 0.000 0.000
#> GSM550830 2 0.4808 0.25729 0.400 0.576 0.000 0.024 0.000
#> GSM550834 1 0.3728 0.53597 0.748 0.244 0.000 0.008 0.000
#> GSM550839 1 0.7761 -0.28043 0.432 0.148 0.000 0.312 0.108
#> GSM550840 1 0.7071 -0.41706 0.448 0.004 0.052 0.104 0.392
#> GSM550843 2 0.5275 0.50726 0.276 0.640 0.000 0.084 0.000
#> GSM550844 1 0.3944 0.55843 0.768 0.200 0.032 0.000 0.000
#> GSM550845 2 0.2719 0.71289 0.144 0.852 0.000 0.004 0.000
#> GSM550848 2 0.2956 0.71264 0.140 0.848 0.000 0.008 0.004
#> GSM550854 3 0.1043 0.82468 0.040 0.000 0.960 0.000 0.000
#> GSM550857 3 0.0324 0.83748 0.004 0.000 0.992 0.004 0.000
#> GSM550858 1 0.4433 0.55615 0.740 0.200 0.060 0.000 0.000
#> GSM550859 3 0.0290 0.83929 0.008 0.000 0.992 0.000 0.000
#> GSM550862 1 0.5036 0.46015 0.628 0.320 0.052 0.000 0.000
#> GSM550865 2 0.5133 0.27471 0.380 0.584 0.016 0.020 0.000
#> GSM550868 2 0.4134 0.52574 0.284 0.704 0.000 0.008 0.004
#> GSM550869 1 0.5672 0.33638 0.560 0.380 0.008 0.040 0.012
#> GSM550870 2 0.0000 0.76080 0.000 1.000 0.000 0.000 0.000
#> GSM550871 1 0.6224 0.29329 0.540 0.332 0.000 0.116 0.012
#> GSM550872 1 0.5781 0.34666 0.596 0.292 0.000 0.108 0.004
#> GSM550873 1 0.6403 0.21697 0.576 0.224 0.000 0.184 0.016
#> GSM550874 2 0.4000 0.64158 0.228 0.748 0.000 0.024 0.000
#> GSM550876 2 0.3690 0.63004 0.224 0.764 0.000 0.012 0.000
#> GSM550877 2 0.0290 0.76079 0.000 0.992 0.000 0.008 0.000
#> GSM550878 2 0.2982 0.71330 0.116 0.860 0.000 0.020 0.004
#> GSM550879 1 0.4696 0.40934 0.616 0.360 0.024 0.000 0.000
#> GSM550882 1 0.6746 0.35556 0.512 0.360 0.068 0.052 0.008
#> GSM550888 3 0.0854 0.83138 0.004 0.000 0.976 0.012 0.008
#> GSM550890 1 0.5758 0.26334 0.524 0.404 0.000 0.060 0.012
#> GSM550891 3 0.6291 0.29705 0.004 0.000 0.544 0.172 0.280
#> GSM550892 1 0.3863 0.55879 0.772 0.200 0.028 0.000 0.000
#> GSM550893 2 0.2138 0.74650 0.024 0.924 0.004 0.044 0.004
#> GSM550895 2 0.3010 0.68943 0.172 0.824 0.000 0.004 0.000
#> GSM550896 2 0.0703 0.76018 0.000 0.976 0.000 0.024 0.000
#> GSM550898 3 0.0290 0.83929 0.008 0.000 0.992 0.000 0.000
#> GSM550899 2 0.1059 0.76436 0.020 0.968 0.000 0.008 0.004
#> GSM550900 2 0.3707 0.63133 0.220 0.768 0.000 0.008 0.004
#> GSM550901 1 0.3519 0.55046 0.776 0.216 0.000 0.008 0.000
#> GSM550902 1 0.4106 0.52966 0.724 0.256 0.020 0.000 0.000
#> GSM550904 1 0.5388 0.39832 0.580 0.360 0.056 0.000 0.004
#> GSM550908 3 0.1911 0.80742 0.004 0.000 0.932 0.036 0.028
#> GSM550912 2 0.3709 0.70953 0.068 0.844 0.004 0.068 0.016
#> GSM550914 1 0.5802 0.32370 0.548 0.380 0.004 0.056 0.012
#> GSM550918 2 0.1285 0.75763 0.000 0.956 0.004 0.036 0.004
#> GSM550922 2 0.1365 0.75691 0.000 0.952 0.004 0.040 0.004
#> GSM550923 3 0.0963 0.82311 0.036 0.000 0.964 0.000 0.000
#> GSM550925 1 0.7332 0.34001 0.472 0.360 0.076 0.076 0.016
#> GSM550802 1 0.7761 -0.28043 0.432 0.148 0.000 0.312 0.108
#> GSM550812 5 0.5893 0.13916 0.352 0.004 0.012 0.068 0.564
#> GSM550831 1 0.7146 -0.42481 0.440 0.000 0.052 0.132 0.376
#> GSM550847 3 0.3731 0.64318 0.160 0.040 0.800 0.000 0.000
#> GSM550860 1 0.5468 0.36456 0.564 0.384 0.040 0.008 0.004
#> GSM550875 1 0.3706 0.51644 0.756 0.236 0.004 0.004 0.000
#> GSM550880 2 0.5044 0.32577 0.352 0.608 0.000 0.036 0.004
#> GSM550881 1 0.5490 0.38723 0.576 0.364 0.052 0.004 0.004
#> GSM550883 3 0.6530 -0.07354 0.188 0.320 0.488 0.004 0.000
#> GSM550884 2 0.3211 0.68912 0.164 0.824 0.000 0.008 0.004
#> GSM550910 5 0.7888 0.10144 0.168 0.120 0.000 0.272 0.440
#> GSM550916 1 0.5037 0.37895 0.584 0.376 0.040 0.000 0.000
#> GSM550920 2 0.3662 0.58110 0.252 0.744 0.000 0.004 0.000
cbind(get_classes(res, k = 6), get_membership(res, k = 6))
#> class entropy silhouette p1 p2 p3 p4 p5 p6
#> GSM550785 4 0.2294 0.5439 0.008 0.076 0.020 0.896 0.000 0.000
#> GSM550786 2 0.7757 0.0293 0.000 0.328 0.220 0.240 0.208 0.004
#> GSM550788 2 0.4830 0.4301 0.000 0.672 0.020 0.064 0.244 0.000
#> GSM550789 2 0.5057 0.1706 0.000 0.528 0.016 0.044 0.412 0.000
#> GSM550790 4 0.2340 0.5864 0.056 0.000 0.004 0.896 0.000 0.044
#> GSM550791 4 0.2581 0.5097 0.000 0.000 0.128 0.856 0.000 0.016
#> GSM550792 2 0.6644 0.0443 0.000 0.444 0.220 0.292 0.044 0.000
#> GSM550796 5 0.3023 0.4609 0.000 0.180 0.004 0.008 0.808 0.000
#> GSM550797 5 0.5852 0.3779 0.000 0.308 0.028 0.120 0.544 0.000
#> GSM550799 2 0.3626 0.5139 0.000 0.800 0.020 0.032 0.148 0.000
#> GSM550800 2 0.5677 0.2216 0.000 0.556 0.020 0.116 0.308 0.000
#> GSM550801 2 0.2408 0.5635 0.000 0.876 0.012 0.004 0.108 0.000
#> GSM550804 2 0.4267 0.4722 0.000 0.740 0.016 0.056 0.188 0.000
#> GSM550806 4 0.6625 -0.4245 0.000 0.300 0.220 0.444 0.032 0.004
#> GSM550807 2 0.0937 0.5834 0.000 0.960 0.000 0.000 0.040 0.000
#> GSM550808 5 0.4451 -0.1347 0.000 0.000 0.072 0.000 0.680 0.248
#> GSM550809 6 0.3552 0.6425 0.000 0.000 0.148 0.020 0.028 0.804
#> GSM550810 5 0.1668 0.3429 0.000 0.060 0.000 0.008 0.928 0.004
#> GSM550811 4 0.3607 0.3731 0.000 0.012 0.204 0.768 0.000 0.016
#> GSM550813 2 0.3076 0.5299 0.000 0.760 0.240 0.000 0.000 0.000
#> GSM550814 2 0.0146 0.5841 0.000 0.996 0.000 0.004 0.000 0.000
#> GSM550815 5 0.4272 -0.1103 0.000 0.004 0.052 0.000 0.704 0.240
#> GSM550816 5 0.4451 -0.1347 0.000 0.000 0.072 0.000 0.680 0.248
#> GSM550817 6 0.5729 0.5209 0.000 0.000 0.176 0.000 0.348 0.476
#> GSM550818 5 0.6528 -0.2863 0.000 0.004 0.212 0.024 0.428 0.332
#> GSM550819 2 0.6913 0.2354 0.000 0.468 0.172 0.100 0.260 0.000
#> GSM550820 4 0.2758 0.5763 0.036 0.000 0.012 0.872 0.000 0.080
#> GSM550821 2 0.4511 0.4367 0.000 0.688 0.016 0.044 0.252 0.000
#> GSM550822 5 0.4518 -0.1110 0.000 0.004 0.072 0.000 0.688 0.236
#> GSM550826 4 0.0820 0.5980 0.000 0.000 0.012 0.972 0.000 0.016
#> GSM550832 2 0.0146 0.5828 0.000 0.996 0.000 0.000 0.004 0.000
#> GSM550833 5 0.6012 0.1172 0.000 0.408 0.020 0.136 0.436 0.000
#> GSM550835 2 0.0458 0.5825 0.000 0.984 0.016 0.000 0.000 0.000
#> GSM550836 1 0.0146 0.8661 0.996 0.000 0.000 0.000 0.000 0.004
#> GSM550837 5 0.6268 0.3916 0.000 0.296 0.032 0.140 0.524 0.008
#> GSM550838 6 0.3651 0.6603 0.040 0.000 0.060 0.052 0.012 0.836
#> GSM550841 5 0.4451 -0.1347 0.000 0.000 0.072 0.000 0.680 0.248
#> GSM550842 5 0.1219 0.3183 0.000 0.048 0.000 0.000 0.948 0.004
#> GSM550846 3 0.7439 0.7828 0.000 0.288 0.328 0.280 0.100 0.004
#> GSM550849 6 0.4828 0.6335 0.040 0.000 0.004 0.268 0.024 0.664
#> GSM550850 6 0.4308 0.6723 0.040 0.000 0.004 0.208 0.016 0.732
#> GSM550851 5 0.6439 0.3663 0.000 0.308 0.032 0.160 0.492 0.008
#> GSM550852 5 0.6869 0.2625 0.000 0.328 0.044 0.204 0.416 0.008
#> GSM550853 5 0.5968 0.2676 0.000 0.356 0.024 0.128 0.492 0.000
#> GSM550855 5 0.5238 0.2243 0.000 0.380 0.020 0.056 0.544 0.000
#> GSM550856 2 0.0458 0.5842 0.000 0.984 0.016 0.000 0.000 0.000
#> GSM550861 2 0.0858 0.5775 0.000 0.968 0.028 0.000 0.004 0.000
#> GSM550863 2 0.4670 0.4317 0.000 0.636 0.292 0.072 0.000 0.000
#> GSM550864 2 0.3198 0.5159 0.000 0.740 0.260 0.000 0.000 0.000
#> GSM550866 2 0.2632 0.5595 0.000 0.832 0.164 0.004 0.000 0.000
#> GSM550867 1 0.1285 0.8485 0.944 0.000 0.000 0.052 0.000 0.004
#> GSM550885 1 0.0146 0.8690 0.996 0.000 0.000 0.004 0.000 0.000
#> GSM550886 2 0.0632 0.5766 0.000 0.976 0.024 0.000 0.000 0.000
#> GSM550887 2 0.4089 0.3851 0.000 0.632 0.004 0.012 0.352 0.000
#> GSM550889 4 0.6427 0.2345 0.020 0.156 0.208 0.572 0.044 0.000
#> GSM550894 2 0.2474 0.5506 0.000 0.880 0.040 0.000 0.080 0.000
#> GSM550897 4 0.3913 0.4745 0.012 0.156 0.056 0.776 0.000 0.000
#> GSM550903 2 0.1176 0.5768 0.000 0.956 0.020 0.000 0.024 0.000
#> GSM550905 2 0.2796 0.5386 0.000 0.868 0.044 0.008 0.080 0.000
#> GSM550906 2 0.0891 0.5805 0.000 0.968 0.024 0.000 0.008 0.000
#> GSM550907 6 0.8105 0.2145 0.000 0.084 0.220 0.076 0.252 0.368
#> GSM550909 5 0.4426 0.4054 0.000 0.120 0.104 0.012 0.756 0.008
#> GSM550911 6 0.3969 0.5906 0.004 0.000 0.344 0.000 0.008 0.644
#> GSM550913 2 0.3942 0.3661 0.000 0.624 0.004 0.004 0.368 0.000
#> GSM550915 4 0.7455 -0.7944 0.000 0.212 0.328 0.348 0.104 0.008
#> GSM550917 2 0.0632 0.5774 0.000 0.976 0.024 0.000 0.000 0.000
#> GSM550919 2 0.4361 0.4206 0.000 0.648 0.308 0.044 0.000 0.000
#> GSM550921 1 0.3295 0.7288 0.816 0.000 0.056 0.000 0.000 0.128
#> GSM550924 2 0.4083 0.4515 0.000 0.668 0.304 0.028 0.000 0.000
#> GSM550926 2 0.1863 0.5744 0.000 0.896 0.104 0.000 0.000 0.000
#> GSM550927 2 0.2412 0.5566 0.000 0.880 0.028 0.000 0.092 0.000
#> GSM550787 2 0.6551 -0.1939 0.000 0.428 0.228 0.312 0.032 0.000
#> GSM550793 4 0.1074 0.6048 0.028 0.012 0.000 0.960 0.000 0.000
#> GSM550794 2 0.7329 -0.0297 0.000 0.364 0.212 0.304 0.120 0.000
#> GSM550795 4 0.1074 0.5978 0.000 0.000 0.012 0.960 0.000 0.028
#> GSM550798 1 0.0146 0.8690 0.996 0.000 0.000 0.004 0.000 0.000
#> GSM550803 1 0.4389 0.5801 0.712 0.000 0.000 0.188 0.000 0.100
#> GSM550805 4 0.5506 -0.0925 0.000 0.124 0.224 0.628 0.020 0.004
#> GSM550823 4 0.7100 -0.4075 0.000 0.320 0.212 0.392 0.072 0.004
#> GSM550824 1 0.0146 0.8690 0.996 0.000 0.000 0.004 0.000 0.000
#> GSM550825 4 0.4010 0.5621 0.048 0.084 0.052 0.808 0.000 0.008
#> GSM550827 2 0.3990 0.4817 0.000 0.688 0.284 0.028 0.000 0.000
#> GSM550828 4 0.1082 0.5975 0.004 0.000 0.000 0.956 0.000 0.040
#> GSM550829 4 0.4007 0.4078 0.220 0.000 0.000 0.728 0.000 0.052
#> GSM550830 2 0.6342 0.1440 0.000 0.500 0.228 0.240 0.032 0.000
#> GSM550834 4 0.4135 0.3784 0.008 0.012 0.200 0.748 0.000 0.032
#> GSM550839 5 0.6774 0.3355 0.000 0.316 0.036 0.176 0.456 0.016
#> GSM550840 6 0.4524 0.6647 0.040 0.000 0.004 0.228 0.020 0.708
#> GSM550843 2 0.7102 0.1193 0.000 0.432 0.228 0.240 0.100 0.000
#> GSM550844 4 0.1148 0.6058 0.016 0.020 0.004 0.960 0.000 0.000
#> GSM550845 2 0.4193 0.4773 0.000 0.684 0.272 0.044 0.000 0.000
#> GSM550848 2 0.3840 0.4814 0.000 0.696 0.284 0.020 0.000 0.000
#> GSM550854 1 0.2706 0.7675 0.860 0.000 0.000 0.104 0.000 0.036
#> GSM550857 1 0.0000 0.8674 1.000 0.000 0.000 0.000 0.000 0.000
#> GSM550858 4 0.2258 0.5857 0.060 0.000 0.000 0.896 0.000 0.044
#> GSM550859 1 0.0146 0.8690 0.996 0.000 0.000 0.004 0.000 0.000
#> GSM550862 4 0.2937 0.5757 0.020 0.080 0.036 0.864 0.000 0.000
#> GSM550865 2 0.5335 -0.1977 0.000 0.492 0.108 0.400 0.000 0.000
#> GSM550868 2 0.4735 0.4258 0.000 0.628 0.296 0.076 0.000 0.000
#> GSM550869 4 0.7189 -0.7196 0.000 0.188 0.332 0.392 0.080 0.008
#> GSM550870 2 0.1714 0.5770 0.000 0.908 0.092 0.000 0.000 0.000
#> GSM550871 2 0.7303 -0.0414 0.000 0.368 0.212 0.304 0.116 0.000
#> GSM550872 2 0.7217 -0.0851 0.000 0.352 0.212 0.336 0.100 0.000
#> GSM550873 2 0.7546 0.0680 0.000 0.364 0.216 0.232 0.188 0.000
#> GSM550874 2 0.5917 0.3162 0.000 0.552 0.268 0.156 0.024 0.000
#> GSM550876 2 0.4549 0.4670 0.000 0.676 0.264 0.048 0.012 0.000
#> GSM550877 2 0.0547 0.5789 0.000 0.980 0.020 0.000 0.000 0.000
#> GSM550878 2 0.4319 0.4308 0.000 0.648 0.320 0.024 0.008 0.000
#> GSM550879 4 0.1297 0.6006 0.000 0.040 0.012 0.948 0.000 0.000
#> GSM550882 4 0.6565 0.2143 0.024 0.156 0.220 0.556 0.044 0.000
#> GSM550888 1 0.0806 0.8547 0.972 0.000 0.008 0.000 0.000 0.020
#> GSM550890 3 0.7449 0.7640 0.000 0.248 0.332 0.320 0.092 0.008
#> GSM550891 6 0.5654 0.1730 0.404 0.000 0.152 0.000 0.000 0.444
#> GSM550892 4 0.2655 0.5967 0.020 0.060 0.036 0.884 0.000 0.000
#> GSM550893 2 0.3406 0.5065 0.000 0.840 0.056 0.020 0.080 0.004
#> GSM550895 2 0.4107 0.4804 0.000 0.688 0.280 0.028 0.000 0.004
#> GSM550896 2 0.1003 0.5801 0.000 0.964 0.020 0.000 0.016 0.000
#> GSM550898 1 0.0363 0.8677 0.988 0.000 0.000 0.012 0.000 0.000
#> GSM550899 2 0.2219 0.5759 0.000 0.864 0.136 0.000 0.000 0.000
#> GSM550900 2 0.4481 0.4512 0.000 0.656 0.284 0.060 0.000 0.000
#> GSM550901 4 0.5262 0.1271 0.000 0.060 0.216 0.676 0.028 0.020
#> GSM550902 4 0.0837 0.5947 0.000 0.004 0.020 0.972 0.000 0.004
#> GSM550904 4 0.3997 0.4941 0.024 0.144 0.052 0.780 0.000 0.000
#> GSM550908 1 0.2436 0.7905 0.880 0.000 0.032 0.000 0.000 0.088
#> GSM550912 2 0.6337 -0.1241 0.000 0.544 0.280 0.060 0.108 0.008
#> GSM550914 4 0.7391 -0.8120 0.000 0.208 0.344 0.344 0.096 0.008
#> GSM550918 2 0.2074 0.5605 0.000 0.912 0.036 0.004 0.048 0.000
#> GSM550922 2 0.2474 0.5509 0.000 0.884 0.032 0.004 0.080 0.000
#> GSM550923 1 0.1526 0.8509 0.944 0.008 0.008 0.036 0.000 0.004
#> GSM550925 4 0.7285 0.2228 0.080 0.160 0.156 0.548 0.044 0.012
#> GSM550802 5 0.6794 0.2939 0.000 0.324 0.044 0.188 0.436 0.008
#> GSM550812 6 0.5667 0.4726 0.040 0.000 0.012 0.036 0.424 0.488
#> GSM550831 6 0.4364 0.6702 0.040 0.000 0.004 0.216 0.016 0.724
#> GSM550847 1 0.3960 0.6147 0.736 0.000 0.008 0.224 0.000 0.032
#> GSM550860 4 0.3913 0.4723 0.012 0.156 0.056 0.776 0.000 0.000
#> GSM550875 4 0.3037 0.3476 0.000 0.176 0.016 0.808 0.000 0.000
#> GSM550880 2 0.6461 -0.1575 0.000 0.500 0.268 0.196 0.028 0.008
#> GSM550881 4 0.3913 0.4745 0.012 0.156 0.056 0.776 0.000 0.000
#> GSM550883 1 0.5835 0.4338 0.632 0.156 0.052 0.156 0.000 0.004
#> GSM550884 2 0.3969 0.4599 0.000 0.668 0.312 0.020 0.000 0.000
#> GSM550910 5 0.6960 0.2779 0.000 0.104 0.196 0.088 0.560 0.052
#> GSM550916 4 0.3624 0.5523 0.044 0.100 0.028 0.824 0.000 0.004
#> GSM550920 2 0.4619 0.4152 0.000 0.668 0.244 0.088 0.000 0.000
Heatmaps for the consensus matrix. It visualizes the probability of two samples to be in a same group.
consensus_heatmap(res, k = 2)
consensus_heatmap(res, k = 3)
consensus_heatmap(res, k = 4)
consensus_heatmap(res, k = 5)
consensus_heatmap(res, k = 6)
Heatmaps for the membership of samples in all partitions to see how consistent they are:
membership_heatmap(res, k = 2)
membership_heatmap(res, k = 3)
membership_heatmap(res, k = 4)
membership_heatmap(res, k = 5)
membership_heatmap(res, k = 6)
As soon as we have had the classes for columns, we can look for signatures which are significantly different between classes which can be candidate marks for certain classes. Following are the heatmaps for signatures.
Signature heatmaps where rows are scaled:
get_signatures(res, k = 2)
get_signatures(res, k = 3)
get_signatures(res, k = 4)
get_signatures(res, k = 5)
get_signatures(res, k = 6)
Signature heatmaps where rows are not scaled:
get_signatures(res, k = 2, scale_rows = FALSE)
get_signatures(res, k = 3, scale_rows = FALSE)
get_signatures(res, k = 4, scale_rows = FALSE)
get_signatures(res, k = 5, scale_rows = FALSE)
get_signatures(res, k = 6, scale_rows = FALSE)
Compare the overlap of signatures from different k:
compare_signatures(res)
get_signature() returns a data frame invisibly. TO get the list of signatures, the function
call should be assigned to a variable explicitly. In following code, if plot argument is set
to FALSE, no heatmap is plotted while only the differential analysis is performed.
# code only for demonstration
tb = get_signature(res, k = ..., plot = FALSE)
An example of the output of tb is:
#> which_row fdr mean_1 mean_2 scaled_mean_1 scaled_mean_2 km
#> 1 38 0.042760348 8.373488 9.131774 -0.5533452 0.5164555 1
#> 2 40 0.018707592 7.106213 8.469186 -0.6173731 0.5762149 1
#> 3 55 0.019134737 10.221463 11.207825 -0.6159697 0.5749050 1
#> 4 59 0.006059896 5.921854 7.869574 -0.6899429 0.6439467 1
#> 5 60 0.018055526 8.928898 10.211722 -0.6204761 0.5791110 1
#> 6 98 0.009384629 15.714769 14.887706 0.6635654 -0.6193277 2
...
The columns in tb are:
which_row: row indices corresponding to the input matrix.fdr: FDR for the differential test. mean_x: The mean value in group x.scaled_mean_x: The mean value in group x after rows are scaled.km: Row groups if k-means clustering is applied to rows.UMAP plot which shows how samples are separated.
dimension_reduction(res, k = 2, method = "UMAP")
dimension_reduction(res, k = 3, method = "UMAP")
dimension_reduction(res, k = 4, method = "UMAP")
dimension_reduction(res, k = 5, method = "UMAP")
dimension_reduction(res, k = 6, method = "UMAP")
Following heatmap shows how subgroups are split when increasing k:
collect_classes(res)
Test correlation between subgroups and known annotations. If the known annotation is numeric, one-way ANOVA test is applied, and if the known annotation is discrete, chi-squared contingency table test is applied.
test_to_known_factors(res)
#> n disease.state(p) k
#> ATC:mclust 141 0.8730 2
#> ATC:mclust 129 0.3149 3
#> ATC:mclust 99 0.0428 4
#> ATC:mclust 80 0.0682 5
#> ATC:mclust 67 0.0501 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 51776 rows and 143 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 0.914 0.943 0.975 0.2796 0.719 0.719
#> 3 3 0.423 0.626 0.807 1.0114 0.614 0.481
#> 4 4 0.328 0.584 0.749 0.0675 0.819 0.646
#> 5 5 0.339 0.422 0.693 0.1350 0.740 0.521
#> 6 6 0.420 0.450 0.698 0.0873 0.818 0.563
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
#> GSM550785 2 0.1184 0.969 0.016 0.984
#> GSM550786 2 0.0000 0.983 0.000 1.000
#> GSM550788 2 0.0000 0.983 0.000 1.000
#> GSM550789 2 0.0000 0.983 0.000 1.000
#> GSM550790 1 0.9552 0.473 0.624 0.376
#> GSM550791 2 0.0000 0.983 0.000 1.000
#> GSM550792 2 0.0000 0.983 0.000 1.000
#> GSM550796 2 0.0000 0.983 0.000 1.000
#> GSM550797 2 0.0000 0.983 0.000 1.000
#> GSM550799 2 0.0000 0.983 0.000 1.000
#> GSM550800 2 0.0000 0.983 0.000 1.000
#> GSM550801 2 0.0000 0.983 0.000 1.000
#> GSM550804 2 0.0000 0.983 0.000 1.000
#> GSM550806 2 0.0000 0.983 0.000 1.000
#> GSM550807 2 0.0000 0.983 0.000 1.000
#> GSM550808 2 0.0000 0.983 0.000 1.000
#> GSM550809 2 0.1633 0.962 0.024 0.976
#> GSM550810 2 0.0000 0.983 0.000 1.000
#> GSM550811 2 0.0000 0.983 0.000 1.000
#> GSM550813 2 0.0000 0.983 0.000 1.000
#> GSM550814 2 0.0000 0.983 0.000 1.000
#> GSM550815 2 0.0000 0.983 0.000 1.000
#> GSM550816 2 0.0000 0.983 0.000 1.000
#> GSM550817 2 0.0000 0.983 0.000 1.000
#> GSM550818 2 0.0000 0.983 0.000 1.000
#> GSM550819 2 0.0000 0.983 0.000 1.000
#> GSM550820 2 0.6048 0.819 0.148 0.852
#> GSM550821 2 0.0000 0.983 0.000 1.000
#> GSM550822 2 0.0000 0.983 0.000 1.000
#> GSM550826 2 0.0938 0.973 0.012 0.988
#> GSM550832 2 0.0000 0.983 0.000 1.000
#> GSM550833 2 0.0000 0.983 0.000 1.000
#> GSM550835 2 0.0000 0.983 0.000 1.000
#> GSM550836 1 0.0000 0.918 1.000 0.000
#> GSM550837 2 0.0000 0.983 0.000 1.000
#> GSM550838 2 0.6048 0.819 0.148 0.852
#> GSM550841 2 0.0000 0.983 0.000 1.000
#> GSM550842 2 0.0000 0.983 0.000 1.000
#> GSM550846 2 0.0000 0.983 0.000 1.000
#> GSM550849 2 0.0000 0.983 0.000 1.000
#> GSM550850 2 0.1633 0.962 0.024 0.976
#> GSM550851 2 0.0000 0.983 0.000 1.000
#> GSM550852 2 0.0000 0.983 0.000 1.000
#> GSM550853 2 0.0000 0.983 0.000 1.000
#> GSM550855 2 0.0000 0.983 0.000 1.000
#> GSM550856 2 0.0000 0.983 0.000 1.000
#> GSM550861 2 0.0000 0.983 0.000 1.000
#> GSM550863 2 0.0000 0.983 0.000 1.000
#> GSM550864 2 0.0000 0.983 0.000 1.000
#> GSM550866 2 0.0000 0.983 0.000 1.000
#> GSM550867 1 0.0000 0.918 1.000 0.000
#> GSM550885 1 0.0000 0.918 1.000 0.000
#> GSM550886 2 0.0000 0.983 0.000 1.000
#> GSM550887 2 0.0000 0.983 0.000 1.000
#> GSM550889 2 0.0000 0.983 0.000 1.000
#> GSM550894 2 0.0000 0.983 0.000 1.000
#> GSM550897 2 0.0000 0.983 0.000 1.000
#> GSM550903 2 0.0000 0.983 0.000 1.000
#> GSM550905 2 0.0000 0.983 0.000 1.000
#> GSM550906 2 0.0000 0.983 0.000 1.000
#> GSM550907 2 0.0000 0.983 0.000 1.000
#> GSM550909 2 0.0000 0.983 0.000 1.000
#> GSM550911 2 0.0000 0.983 0.000 1.000
#> GSM550913 2 0.0000 0.983 0.000 1.000
#> GSM550915 2 0.0000 0.983 0.000 1.000
#> GSM550917 2 0.0000 0.983 0.000 1.000
#> GSM550919 2 0.0000 0.983 0.000 1.000
#> GSM550921 1 0.0000 0.918 1.000 0.000
#> GSM550924 2 0.0000 0.983 0.000 1.000
#> GSM550926 2 0.0000 0.983 0.000 1.000
#> GSM550927 2 0.0000 0.983 0.000 1.000
#> GSM550787 2 0.0000 0.983 0.000 1.000
#> GSM550793 1 0.9635 0.443 0.612 0.388
#> GSM550794 2 0.0000 0.983 0.000 1.000
#> GSM550795 2 0.6247 0.808 0.156 0.844
#> GSM550798 1 0.0000 0.918 1.000 0.000
#> GSM550803 1 0.0000 0.918 1.000 0.000
#> GSM550805 2 0.0000 0.983 0.000 1.000
#> GSM550823 2 0.0000 0.983 0.000 1.000
#> GSM550824 1 0.0000 0.918 1.000 0.000
#> GSM550825 1 0.1414 0.908 0.980 0.020
#> GSM550827 2 0.0000 0.983 0.000 1.000
#> GSM550828 2 0.9491 0.370 0.368 0.632
#> GSM550829 1 0.0938 0.912 0.988 0.012
#> GSM550830 2 0.0000 0.983 0.000 1.000
#> GSM550834 2 0.0000 0.983 0.000 1.000
#> GSM550839 2 0.0000 0.983 0.000 1.000
#> GSM550840 2 0.0000 0.983 0.000 1.000
#> GSM550843 2 0.0000 0.983 0.000 1.000
#> GSM550844 2 0.5737 0.835 0.136 0.864
#> GSM550845 2 0.0000 0.983 0.000 1.000
#> GSM550848 2 0.0000 0.983 0.000 1.000
#> GSM550854 1 0.0000 0.918 1.000 0.000
#> GSM550857 1 0.0000 0.918 1.000 0.000
#> GSM550858 1 0.8267 0.680 0.740 0.260
#> GSM550859 1 0.0000 0.918 1.000 0.000
#> GSM550862 1 0.9580 0.463 0.620 0.380
#> GSM550865 2 0.0000 0.983 0.000 1.000
#> GSM550868 2 0.0000 0.983 0.000 1.000
#> GSM550869 2 0.0000 0.983 0.000 1.000
#> GSM550870 2 0.0000 0.983 0.000 1.000
#> GSM550871 2 0.0000 0.983 0.000 1.000
#> GSM550872 2 0.0000 0.983 0.000 1.000
#> GSM550873 2 0.0000 0.983 0.000 1.000
#> GSM550874 2 0.0000 0.983 0.000 1.000
#> GSM550876 2 0.0000 0.983 0.000 1.000
#> GSM550877 2 0.0000 0.983 0.000 1.000
#> GSM550878 2 0.0000 0.983 0.000 1.000
#> GSM550879 2 0.0938 0.973 0.012 0.988
#> GSM550882 2 0.2948 0.934 0.052 0.948
#> GSM550888 1 0.0000 0.918 1.000 0.000
#> GSM550890 2 0.0000 0.983 0.000 1.000
#> GSM550891 1 0.4562 0.854 0.904 0.096
#> GSM550892 2 0.6623 0.785 0.172 0.828
#> GSM550893 2 0.0000 0.983 0.000 1.000
#> GSM550895 2 0.0000 0.983 0.000 1.000
#> GSM550896 2 0.0000 0.983 0.000 1.000
#> GSM550898 1 0.0000 0.918 1.000 0.000
#> GSM550899 2 0.0000 0.983 0.000 1.000
#> GSM550900 2 0.0000 0.983 0.000 1.000
#> GSM550901 2 0.0000 0.983 0.000 1.000
#> GSM550902 2 0.0000 0.983 0.000 1.000
#> GSM550904 1 0.8499 0.657 0.724 0.276
#> GSM550908 1 0.0000 0.918 1.000 0.000
#> GSM550912 2 0.0000 0.983 0.000 1.000
#> GSM550914 2 0.0000 0.983 0.000 1.000
#> GSM550918 2 0.0000 0.983 0.000 1.000
#> GSM550922 2 0.0000 0.983 0.000 1.000
#> GSM550923 1 0.0000 0.918 1.000 0.000
#> GSM550925 2 0.5629 0.840 0.132 0.868
#> GSM550802 2 0.0000 0.983 0.000 1.000
#> GSM550812 2 0.0000 0.983 0.000 1.000
#> GSM550831 2 0.1843 0.958 0.028 0.972
#> GSM550847 1 0.0000 0.918 1.000 0.000
#> GSM550860 2 0.0000 0.983 0.000 1.000
#> GSM550875 2 0.0000 0.983 0.000 1.000
#> GSM550880 2 0.0000 0.983 0.000 1.000
#> GSM550881 2 0.7745 0.692 0.228 0.772
#> GSM550883 1 0.0000 0.918 1.000 0.000
#> GSM550884 2 0.0000 0.983 0.000 1.000
#> GSM550910 2 0.0000 0.983 0.000 1.000
#> GSM550916 2 0.6438 0.796 0.164 0.836
#> GSM550920 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
#> GSM550785 1 0.6936 0.5339 0.672 0.044 0.284
#> GSM550786 2 0.5178 0.6210 0.256 0.744 0.000
#> GSM550788 2 0.6140 0.2799 0.404 0.596 0.000
#> GSM550789 2 0.5678 0.5273 0.316 0.684 0.000
#> GSM550790 3 0.4861 0.7370 0.180 0.012 0.808
#> GSM550791 2 0.8659 0.0301 0.408 0.488 0.104
#> GSM550792 1 0.5016 0.6752 0.760 0.240 0.000
#> GSM550796 2 0.3192 0.7467 0.112 0.888 0.000
#> GSM550797 2 0.2261 0.7578 0.068 0.932 0.000
#> GSM550799 1 0.6305 0.2135 0.516 0.484 0.000
#> GSM550800 2 0.5678 0.5281 0.316 0.684 0.000
#> GSM550801 1 0.6291 0.2769 0.532 0.468 0.000
#> GSM550804 2 0.6225 0.1637 0.432 0.568 0.000
#> GSM550806 1 0.6095 0.4872 0.608 0.392 0.000
#> GSM550807 1 0.6111 0.4813 0.604 0.396 0.000
#> GSM550808 2 0.0424 0.7514 0.008 0.992 0.000
#> GSM550809 2 0.1129 0.7349 0.004 0.976 0.020
#> GSM550810 2 0.1289 0.7586 0.032 0.968 0.000
#> GSM550811 1 0.6286 0.2896 0.536 0.464 0.000
#> GSM550813 1 0.3619 0.7130 0.864 0.136 0.000
#> GSM550814 1 0.6204 0.3979 0.576 0.424 0.000
#> GSM550815 2 0.0747 0.7544 0.016 0.984 0.000
#> GSM550816 2 0.0424 0.7514 0.008 0.992 0.000
#> GSM550817 2 0.0237 0.7491 0.004 0.996 0.000
#> GSM550818 2 0.0424 0.7514 0.008 0.992 0.000
#> GSM550819 2 0.6008 0.3822 0.372 0.628 0.000
#> GSM550820 3 0.8769 0.2014 0.348 0.124 0.528
#> GSM550821 2 0.6026 0.3731 0.376 0.624 0.000
#> GSM550822 2 0.0747 0.7544 0.016 0.984 0.000
#> GSM550826 1 0.9425 0.3804 0.488 0.200 0.312
#> GSM550832 1 0.5968 0.5432 0.636 0.364 0.000
#> GSM550833 2 0.5497 0.5703 0.292 0.708 0.000
#> GSM550835 1 0.5291 0.6549 0.732 0.268 0.000
#> GSM550836 3 0.0000 0.8885 0.000 0.000 1.000
#> GSM550837 2 0.3038 0.7502 0.104 0.896 0.000
#> GSM550838 2 0.2590 0.6840 0.004 0.924 0.072
#> GSM550841 2 0.0424 0.7514 0.008 0.992 0.000
#> GSM550842 2 0.1289 0.7586 0.032 0.968 0.000
#> GSM550846 2 0.6308 -0.1328 0.492 0.508 0.000
#> GSM550849 2 0.0237 0.7491 0.004 0.996 0.000
#> GSM550850 2 0.0983 0.7382 0.004 0.980 0.016
#> GSM550851 2 0.2878 0.7526 0.096 0.904 0.000
#> GSM550852 2 0.3551 0.7354 0.132 0.868 0.000
#> GSM550853 2 0.4235 0.7059 0.176 0.824 0.000
#> GSM550855 2 0.4062 0.7151 0.164 0.836 0.000
#> GSM550856 1 0.5810 0.5856 0.664 0.336 0.000
#> GSM550861 1 0.5431 0.6398 0.716 0.284 0.000
#> GSM550863 1 0.4346 0.7003 0.816 0.184 0.000
#> GSM550864 1 0.1753 0.7152 0.952 0.048 0.000
#> GSM550866 1 0.4842 0.6834 0.776 0.224 0.000
#> GSM550867 3 0.0000 0.8885 0.000 0.000 1.000
#> GSM550885 3 0.0000 0.8885 0.000 0.000 1.000
#> GSM550886 1 0.1031 0.7097 0.976 0.024 0.000
#> GSM550887 2 0.5621 0.5437 0.308 0.692 0.000
#> GSM550889 1 0.0237 0.6962 0.996 0.004 0.000
#> GSM550894 1 0.6111 0.4719 0.604 0.396 0.000
#> GSM550897 1 0.0237 0.7011 0.996 0.004 0.000
#> GSM550903 1 0.6280 0.3056 0.540 0.460 0.000
#> GSM550905 1 0.6111 0.4708 0.604 0.396 0.000
#> GSM550906 1 0.6260 0.3298 0.552 0.448 0.000
#> GSM550907 2 0.1163 0.7577 0.028 0.972 0.000
#> GSM550909 2 0.1411 0.7590 0.036 0.964 0.000
#> GSM550911 2 0.0424 0.7514 0.008 0.992 0.000
#> GSM550913 2 0.5882 0.4564 0.348 0.652 0.000
#> GSM550915 2 0.5098 0.6354 0.248 0.752 0.000
#> GSM550917 1 0.3879 0.7092 0.848 0.152 0.000
#> GSM550919 1 0.1289 0.7117 0.968 0.032 0.000
#> GSM550921 3 0.0000 0.8885 0.000 0.000 1.000
#> GSM550924 1 0.2537 0.7180 0.920 0.080 0.000
#> GSM550926 1 0.1529 0.7136 0.960 0.040 0.000
#> GSM550927 1 0.6204 0.4141 0.576 0.424 0.000
#> GSM550787 1 0.5363 0.6495 0.724 0.276 0.000
#> GSM550793 1 0.3030 0.6469 0.904 0.004 0.092
#> GSM550794 1 0.6291 0.2768 0.532 0.468 0.000
#> GSM550795 1 0.7382 0.1206 0.512 0.032 0.456
#> GSM550798 3 0.0000 0.8885 0.000 0.000 1.000
#> GSM550803 3 0.0237 0.8865 0.000 0.004 0.996
#> GSM550805 1 0.6252 0.3572 0.556 0.444 0.000
#> GSM550823 1 0.6260 0.3445 0.552 0.448 0.000
#> GSM550824 3 0.0000 0.8885 0.000 0.000 1.000
#> GSM550825 3 0.6267 0.4082 0.452 0.000 0.548
#> GSM550827 1 0.0424 0.7026 0.992 0.008 0.000
#> GSM550828 3 0.5763 0.5927 0.276 0.008 0.716
#> GSM550829 3 0.0000 0.8885 0.000 0.000 1.000
#> GSM550830 1 0.2165 0.7169 0.936 0.064 0.000
#> GSM550834 2 0.6148 0.4170 0.356 0.640 0.004
#> GSM550839 2 0.2878 0.7530 0.096 0.904 0.000
#> GSM550840 2 0.0237 0.7491 0.004 0.996 0.000
#> GSM550843 1 0.6225 0.3920 0.568 0.432 0.000
#> GSM550844 1 0.2584 0.6885 0.928 0.008 0.064
#> GSM550845 1 0.0747 0.7062 0.984 0.016 0.000
#> GSM550848 1 0.5098 0.6705 0.752 0.248 0.000
#> GSM550854 3 0.0000 0.8885 0.000 0.000 1.000
#> GSM550857 3 0.0000 0.8885 0.000 0.000 1.000
#> GSM550858 3 0.4682 0.7309 0.192 0.004 0.804
#> GSM550859 3 0.0000 0.8885 0.000 0.000 1.000
#> GSM550862 1 0.3532 0.6357 0.884 0.008 0.108
#> GSM550865 1 0.0237 0.7008 0.996 0.004 0.000
#> GSM550868 1 0.0424 0.7026 0.992 0.008 0.000
#> GSM550869 2 0.5178 0.6256 0.256 0.744 0.000
#> GSM550870 1 0.1643 0.7145 0.956 0.044 0.000
#> GSM550871 1 0.5497 0.6398 0.708 0.292 0.000
#> GSM550872 1 0.5678 0.6099 0.684 0.316 0.000
#> GSM550873 2 0.6252 0.1119 0.444 0.556 0.000
#> GSM550874 1 0.5905 0.5610 0.648 0.352 0.000
#> GSM550876 1 0.5785 0.5899 0.668 0.332 0.000
#> GSM550877 1 0.3551 0.7134 0.868 0.132 0.000
#> GSM550878 1 0.1411 0.7134 0.964 0.036 0.000
#> GSM550879 1 0.5167 0.6312 0.792 0.016 0.192
#> GSM550882 1 0.0475 0.6941 0.992 0.004 0.004
#> GSM550888 3 0.0000 0.8885 0.000 0.000 1.000
#> GSM550890 1 0.6095 0.4840 0.608 0.392 0.000
#> GSM550891 3 0.5378 0.6775 0.008 0.236 0.756
#> GSM550892 1 0.0848 0.6989 0.984 0.008 0.008
#> GSM550893 1 0.5327 0.6456 0.728 0.272 0.000
#> GSM550895 1 0.0000 0.6990 1.000 0.000 0.000
#> GSM550896 1 0.5098 0.6701 0.752 0.248 0.000
#> GSM550898 3 0.0000 0.8885 0.000 0.000 1.000
#> GSM550899 1 0.5835 0.5803 0.660 0.340 0.000
#> GSM550900 1 0.2711 0.7178 0.912 0.088 0.000
#> GSM550901 2 0.6244 0.1249 0.440 0.560 0.000
#> GSM550902 1 0.6719 0.6791 0.744 0.160 0.096
#> GSM550904 1 0.2711 0.6345 0.912 0.000 0.088
#> GSM550908 3 0.0000 0.8885 0.000 0.000 1.000
#> GSM550912 1 0.5968 0.5416 0.636 0.364 0.000
#> GSM550914 2 0.5733 0.5201 0.324 0.676 0.000
#> GSM550918 1 0.4504 0.6950 0.804 0.196 0.000
#> GSM550922 1 0.5926 0.5491 0.644 0.356 0.000
#> GSM550923 3 0.0000 0.8885 0.000 0.000 1.000
#> GSM550925 1 0.0661 0.6915 0.988 0.004 0.008
#> GSM550802 2 0.2711 0.7551 0.088 0.912 0.000
#> GSM550812 2 0.0237 0.7491 0.004 0.996 0.000
#> GSM550831 2 0.1399 0.7288 0.004 0.968 0.028
#> GSM550847 3 0.0000 0.8885 0.000 0.000 1.000
#> GSM550860 1 0.0424 0.7026 0.992 0.008 0.000
#> GSM550875 1 0.1163 0.7104 0.972 0.028 0.000
#> GSM550880 1 0.2796 0.7172 0.908 0.092 0.000
#> GSM550881 1 0.0747 0.6889 0.984 0.000 0.016
#> GSM550883 3 0.0592 0.8834 0.012 0.000 0.988
#> GSM550884 1 0.0000 0.6990 1.000 0.000 0.000
#> GSM550910 2 0.1753 0.7592 0.048 0.952 0.000
#> GSM550916 3 0.6680 0.0506 0.484 0.008 0.508
#> GSM550920 1 0.0000 0.6990 1.000 0.000 0.000
cbind(get_classes(res, k = 4), get_membership(res, k = 4))
#> class entropy silhouette p1 p2 p3 p4
#> GSM550785 4 0.8232 0.4362 0.108 0.100 0.240 0.552
#> GSM550786 2 0.5244 0.2529 0.000 0.600 0.012 0.388
#> GSM550788 4 0.6534 0.5697 0.000 0.220 0.148 0.632
#> GSM550789 4 0.5728 0.4212 0.000 0.364 0.036 0.600
#> GSM550790 1 0.6892 0.3845 0.656 0.028 0.184 0.132
#> GSM550791 4 0.8635 0.2582 0.212 0.280 0.052 0.456
#> GSM550792 4 0.5476 0.6887 0.000 0.144 0.120 0.736
#> GSM550796 2 0.5244 0.3756 0.000 0.600 0.012 0.388
#> GSM550797 2 0.4158 0.7002 0.000 0.768 0.008 0.224
#> GSM550799 4 0.6245 0.6258 0.000 0.164 0.168 0.668
#> GSM550800 4 0.5050 0.3633 0.000 0.408 0.004 0.588
#> GSM550801 4 0.5182 0.5629 0.000 0.288 0.028 0.684
#> GSM550804 4 0.4964 0.4233 0.000 0.380 0.004 0.616
#> GSM550806 4 0.5581 0.6957 0.000 0.132 0.140 0.728
#> GSM550807 4 0.4872 0.6162 0.000 0.244 0.028 0.728
#> GSM550808 2 0.1807 0.7043 0.000 0.940 0.008 0.052
#> GSM550809 2 0.1585 0.6327 0.004 0.952 0.040 0.004
#> GSM550810 2 0.4004 0.7324 0.000 0.812 0.024 0.164
#> GSM550811 4 0.5628 0.3721 0.000 0.420 0.024 0.556
#> GSM550813 4 0.2489 0.7099 0.000 0.020 0.068 0.912
#> GSM550814 4 0.4724 0.6862 0.000 0.136 0.076 0.788
#> GSM550815 2 0.3464 0.7213 0.000 0.860 0.032 0.108
#> GSM550816 2 0.1557 0.7126 0.000 0.944 0.000 0.056
#> GSM550817 2 0.1520 0.6714 0.000 0.956 0.024 0.020
#> GSM550818 2 0.2797 0.7043 0.000 0.900 0.032 0.068
#> GSM550819 4 0.5070 0.3563 0.000 0.416 0.004 0.580
#> GSM550820 2 0.9594 0.1112 0.224 0.400 0.188 0.188
#> GSM550821 4 0.5150 0.3966 0.000 0.396 0.008 0.596
#> GSM550822 2 0.2973 0.7226 0.000 0.884 0.020 0.096
#> GSM550826 4 0.9698 0.1530 0.260 0.208 0.168 0.364
#> GSM550832 4 0.5122 0.6700 0.000 0.164 0.080 0.756
#> GSM550833 4 0.5112 0.2860 0.000 0.436 0.004 0.560
#> GSM550835 4 0.4608 0.6968 0.000 0.096 0.104 0.800
#> GSM550836 1 0.0000 0.7705 1.000 0.000 0.000 0.000
#> GSM550837 2 0.4391 0.6675 0.000 0.740 0.008 0.252
#> GSM550838 2 0.4305 0.5077 0.044 0.816 0.136 0.004
#> GSM550841 2 0.2563 0.7140 0.000 0.908 0.020 0.072
#> GSM550842 2 0.3577 0.7349 0.000 0.832 0.012 0.156
#> GSM550846 4 0.5869 0.4699 0.000 0.360 0.044 0.596
#> GSM550849 2 0.1677 0.7043 0.000 0.948 0.012 0.040
#> GSM550850 2 0.3432 0.6236 0.020 0.872 0.096 0.012
#> GSM550851 2 0.4452 0.6524 0.000 0.732 0.008 0.260
#> GSM550852 2 0.4248 0.6724 0.000 0.768 0.012 0.220
#> GSM550853 2 0.5257 0.1776 0.000 0.548 0.008 0.444
#> GSM550855 2 0.5119 0.1891 0.000 0.556 0.004 0.440
#> GSM550856 4 0.4636 0.6633 0.000 0.188 0.040 0.772
#> GSM550861 4 0.4840 0.6939 0.000 0.100 0.116 0.784
#> GSM550863 4 0.3320 0.7136 0.000 0.068 0.056 0.876
#> GSM550864 4 0.1174 0.7106 0.000 0.012 0.020 0.968
#> GSM550866 4 0.3474 0.7099 0.000 0.064 0.068 0.868
#> GSM550867 1 0.0707 0.7718 0.980 0.000 0.020 0.000
#> GSM550885 1 0.0000 0.7705 1.000 0.000 0.000 0.000
#> GSM550886 4 0.2222 0.7053 0.000 0.016 0.060 0.924
#> GSM550887 4 0.6706 0.4751 0.000 0.288 0.124 0.588
#> GSM550889 4 0.4049 0.6155 0.008 0.000 0.212 0.780
#> GSM550894 4 0.5003 0.6892 0.000 0.084 0.148 0.768
#> GSM550897 4 0.2805 0.6799 0.012 0.000 0.100 0.888
#> GSM550903 4 0.5985 0.6404 0.000 0.168 0.140 0.692
#> GSM550905 4 0.5576 0.6722 0.000 0.096 0.184 0.720
#> GSM550906 4 0.5477 0.6719 0.000 0.092 0.180 0.728
#> GSM550907 2 0.6719 0.5305 0.000 0.608 0.240 0.152
#> GSM550909 2 0.3803 0.7317 0.000 0.836 0.032 0.132
#> GSM550911 2 0.2706 0.6202 0.000 0.900 0.080 0.020
#> GSM550913 4 0.6280 0.4956 0.000 0.304 0.084 0.612
#> GSM550915 4 0.5933 0.1886 0.000 0.464 0.036 0.500
#> GSM550917 4 0.2214 0.7140 0.000 0.044 0.028 0.928
#> GSM550919 4 0.1256 0.7079 0.000 0.008 0.028 0.964
#> GSM550921 1 0.2647 0.6231 0.880 0.000 0.120 0.000
#> GSM550924 4 0.1820 0.7088 0.000 0.020 0.036 0.944
#> GSM550926 4 0.1174 0.7100 0.000 0.012 0.020 0.968
#> GSM550927 4 0.5662 0.6028 0.000 0.236 0.072 0.692
#> GSM550787 4 0.4605 0.7123 0.000 0.072 0.132 0.796
#> GSM550793 4 0.6935 0.3744 0.132 0.012 0.240 0.616
#> GSM550794 4 0.6324 0.4016 0.000 0.400 0.064 0.536
#> GSM550795 4 0.9471 0.1587 0.264 0.124 0.224 0.388
#> GSM550798 1 0.1940 0.7475 0.924 0.000 0.076 0.000
#> GSM550803 1 0.2976 0.7090 0.872 0.008 0.120 0.000
#> GSM550805 4 0.6081 0.6104 0.000 0.260 0.088 0.652
#> GSM550823 4 0.6369 0.4860 0.000 0.352 0.076 0.572
#> GSM550824 1 0.0188 0.7715 0.996 0.000 0.004 0.000
#> GSM550825 1 0.7552 0.0025 0.440 0.004 0.164 0.392
#> GSM550827 4 0.2271 0.6965 0.000 0.008 0.076 0.916
#> GSM550828 1 0.9283 0.0675 0.424 0.112 0.236 0.228
#> GSM550829 1 0.3647 0.6711 0.832 0.016 0.152 0.000
#> GSM550830 4 0.2888 0.6770 0.000 0.004 0.124 0.872
#> GSM550834 2 0.5805 -0.0826 0.012 0.516 0.012 0.460
#> GSM550839 2 0.3626 0.7282 0.000 0.812 0.004 0.184
#> GSM550840 2 0.3485 0.6370 0.000 0.856 0.116 0.028
#> GSM550843 4 0.4973 0.4889 0.000 0.348 0.008 0.644
#> GSM550844 4 0.5697 0.6055 0.064 0.012 0.204 0.720
#> GSM550845 4 0.2197 0.6944 0.000 0.004 0.080 0.916
#> GSM550848 4 0.4224 0.7029 0.000 0.144 0.044 0.812
#> GSM550854 1 0.2530 0.7232 0.888 0.000 0.112 0.000
#> GSM550857 1 0.0000 0.7705 1.000 0.000 0.000 0.000
#> GSM550858 1 0.5170 0.4575 0.764 0.008 0.064 0.164
#> GSM550859 1 0.0188 0.7715 0.996 0.000 0.004 0.000
#> GSM550862 4 0.6405 0.4692 0.132 0.004 0.204 0.660
#> GSM550865 4 0.2408 0.6834 0.000 0.000 0.104 0.896
#> GSM550868 4 0.2918 0.6799 0.000 0.008 0.116 0.876
#> GSM550869 4 0.5950 0.2485 0.000 0.416 0.040 0.544
#> GSM550870 4 0.0779 0.7086 0.000 0.004 0.016 0.980
#> GSM550871 4 0.6071 0.6464 0.000 0.172 0.144 0.684
#> GSM550872 4 0.6509 0.6173 0.000 0.228 0.140 0.632
#> GSM550873 4 0.6261 0.2822 0.000 0.440 0.056 0.504
#> GSM550874 4 0.4410 0.7061 0.000 0.128 0.064 0.808
#> GSM550876 4 0.3647 0.7059 0.000 0.108 0.040 0.852
#> GSM550877 4 0.2402 0.7071 0.000 0.012 0.076 0.912
#> GSM550878 4 0.1940 0.7045 0.000 0.000 0.076 0.924
#> GSM550879 4 0.6050 0.5996 0.176 0.012 0.104 0.708
#> GSM550882 4 0.4364 0.5730 0.016 0.000 0.220 0.764
#> GSM550888 1 0.0000 0.7705 1.000 0.000 0.000 0.000
#> GSM550890 4 0.5050 0.6921 0.000 0.176 0.068 0.756
#> GSM550891 3 0.5684 0.0000 0.252 0.032 0.696 0.020
#> GSM550892 4 0.4426 0.6205 0.020 0.004 0.196 0.780
#> GSM550893 4 0.4842 0.6761 0.000 0.048 0.192 0.760
#> GSM550895 4 0.2149 0.6879 0.000 0.000 0.088 0.912
#> GSM550896 4 0.3399 0.7137 0.000 0.092 0.040 0.868
#> GSM550898 1 0.1118 0.7678 0.964 0.000 0.036 0.000
#> GSM550899 4 0.5109 0.6550 0.000 0.196 0.060 0.744
#> GSM550900 4 0.2198 0.6964 0.000 0.008 0.072 0.920
#> GSM550901 4 0.5488 0.2373 0.000 0.452 0.016 0.532
#> GSM550902 4 0.6555 0.6494 0.076 0.064 0.156 0.704
#> GSM550904 4 0.5849 0.4857 0.164 0.000 0.132 0.704
#> GSM550908 1 0.1389 0.7291 0.952 0.000 0.048 0.000
#> GSM550912 4 0.5006 0.6933 0.000 0.104 0.124 0.772
#> GSM550914 4 0.5898 0.4718 0.000 0.348 0.048 0.604
#> GSM550918 4 0.3758 0.7069 0.000 0.048 0.104 0.848
#> GSM550922 4 0.5719 0.6643 0.000 0.132 0.152 0.716
#> GSM550923 1 0.0469 0.7678 0.988 0.000 0.012 0.000
#> GSM550925 4 0.5218 0.5425 0.064 0.000 0.200 0.736
#> GSM550802 2 0.3626 0.7173 0.000 0.812 0.004 0.184
#> GSM550812 2 0.1356 0.6979 0.000 0.960 0.008 0.032
#> GSM550831 2 0.3232 0.6333 0.028 0.888 0.072 0.012
#> GSM550847 1 0.0921 0.7699 0.972 0.000 0.028 0.000
#> GSM550860 4 0.2973 0.6603 0.000 0.000 0.144 0.856
#> GSM550875 4 0.4644 0.6280 0.004 0.024 0.208 0.764
#> GSM550880 4 0.2335 0.7082 0.000 0.020 0.060 0.920
#> GSM550881 4 0.4542 0.6104 0.088 0.000 0.108 0.804
#> GSM550883 1 0.2546 0.6960 0.912 0.000 0.060 0.028
#> GSM550884 4 0.2149 0.6874 0.000 0.000 0.088 0.912
#> GSM550910 2 0.5578 0.5482 0.000 0.648 0.040 0.312
#> GSM550916 4 0.7329 0.1380 0.416 0.008 0.120 0.456
#> GSM550920 4 0.1302 0.7024 0.000 0.000 0.044 0.956
cbind(get_classes(res, k = 5), get_membership(res, k = 5))
#> class entropy silhouette p1 p2 p3 p4 p5
#> GSM550785 4 0.7932 0.4672 0.044 0.272 0.132 0.492 0.060
#> GSM550786 2 0.4691 0.4106 0.000 0.684 0.008 0.028 0.280
#> GSM550788 2 0.6677 0.2865 0.000 0.624 0.116 0.132 0.128
#> GSM550789 2 0.2352 0.5955 0.000 0.896 0.004 0.008 0.092
#> GSM550790 4 0.6389 -0.2040 0.436 0.016 0.048 0.472 0.028
#> GSM550791 2 0.7727 -0.1808 0.300 0.488 0.052 0.124 0.036
#> GSM550792 2 0.4532 0.4799 0.000 0.672 0.004 0.304 0.020
#> GSM550796 2 0.3737 0.5049 0.000 0.764 0.008 0.004 0.224
#> GSM550797 2 0.4540 0.2916 0.000 0.640 0.000 0.020 0.340
#> GSM550799 2 0.6087 0.3634 0.000 0.672 0.148 0.108 0.072
#> GSM550800 2 0.3388 0.5398 0.000 0.792 0.000 0.008 0.200
#> GSM550801 2 0.1731 0.6014 0.000 0.932 0.004 0.004 0.060
#> GSM550804 2 0.3578 0.6060 0.000 0.820 0.000 0.048 0.132
#> GSM550806 4 0.5579 0.4405 0.000 0.408 0.020 0.536 0.036
#> GSM550807 2 0.1341 0.6035 0.000 0.944 0.000 0.000 0.056
#> GSM550808 5 0.2964 0.6597 0.000 0.152 0.004 0.004 0.840
#> GSM550809 5 0.2157 0.5888 0.000 0.036 0.040 0.004 0.920
#> GSM550810 2 0.4414 0.2418 0.000 0.616 0.004 0.004 0.376
#> GSM550811 2 0.3710 0.6144 0.012 0.840 0.008 0.040 0.100
#> GSM550813 2 0.3649 0.4914 0.000 0.808 0.040 0.152 0.000
#> GSM550814 2 0.2492 0.6075 0.000 0.908 0.024 0.048 0.020
#> GSM550815 5 0.4533 0.2833 0.000 0.448 0.008 0.000 0.544
#> GSM550816 5 0.3087 0.6605 0.000 0.152 0.004 0.008 0.836
#> GSM550817 5 0.1605 0.5874 0.000 0.040 0.012 0.004 0.944
#> GSM550818 5 0.3883 0.6235 0.000 0.244 0.004 0.008 0.744
#> GSM550819 2 0.4670 0.5538 0.000 0.724 0.000 0.076 0.200
#> GSM550820 1 0.9333 0.0357 0.328 0.124 0.096 0.160 0.292
#> GSM550821 2 0.3867 0.5951 0.000 0.804 0.004 0.048 0.144
#> GSM550822 5 0.4473 0.3864 0.000 0.412 0.008 0.000 0.580
#> GSM550826 2 0.8183 -0.1828 0.288 0.464 0.112 0.092 0.044
#> GSM550832 2 0.1978 0.5909 0.000 0.932 0.032 0.024 0.012
#> GSM550833 2 0.3053 0.5652 0.000 0.828 0.000 0.008 0.164
#> GSM550835 2 0.1668 0.5901 0.000 0.940 0.032 0.028 0.000
#> GSM550836 1 0.0000 0.7604 1.000 0.000 0.000 0.000 0.000
#> GSM550837 2 0.4698 0.3395 0.000 0.664 0.004 0.028 0.304
#> GSM550838 5 0.5475 0.4767 0.020 0.048 0.120 0.068 0.744
#> GSM550841 5 0.3690 0.6559 0.000 0.224 0.012 0.000 0.764
#> GSM550842 2 0.4362 0.2714 0.000 0.632 0.004 0.004 0.360
#> GSM550846 2 0.5768 0.3904 0.000 0.560 0.012 0.360 0.068
#> GSM550849 5 0.3631 0.6461 0.000 0.144 0.024 0.012 0.820
#> GSM550850 5 0.5003 0.5307 0.028 0.044 0.084 0.060 0.784
#> GSM550851 2 0.4620 0.2966 0.000 0.652 0.000 0.028 0.320
#> GSM550852 5 0.6508 0.3024 0.000 0.392 0.016 0.124 0.468
#> GSM550853 2 0.4181 0.4177 0.000 0.712 0.000 0.020 0.268
#> GSM550855 2 0.3861 0.4332 0.000 0.712 0.000 0.004 0.284
#> GSM550856 2 0.1915 0.6110 0.000 0.928 0.000 0.032 0.040
#> GSM550861 2 0.1469 0.5951 0.000 0.948 0.036 0.016 0.000
#> GSM550863 2 0.4430 0.4181 0.000 0.628 0.012 0.360 0.000
#> GSM550864 2 0.2787 0.5868 0.000 0.856 0.004 0.136 0.004
#> GSM550866 2 0.2054 0.5816 0.000 0.920 0.028 0.052 0.000
#> GSM550867 1 0.1043 0.7460 0.960 0.000 0.000 0.040 0.000
#> GSM550885 1 0.0000 0.7604 1.000 0.000 0.000 0.000 0.000
#> GSM550886 2 0.4791 0.4128 0.000 0.616 0.008 0.360 0.016
#> GSM550887 2 0.3307 0.6089 0.000 0.844 0.052 0.000 0.104
#> GSM550889 4 0.6195 0.4831 0.012 0.304 0.108 0.572 0.004
#> GSM550894 2 0.3242 0.6015 0.000 0.852 0.076 0.072 0.000
#> GSM550897 4 0.5579 0.5156 0.040 0.348 0.024 0.588 0.000
#> GSM550903 2 0.2158 0.5914 0.000 0.920 0.052 0.020 0.008
#> GSM550905 2 0.4071 0.5815 0.000 0.808 0.072 0.108 0.012
#> GSM550906 2 0.5233 0.3458 0.000 0.696 0.136 0.164 0.004
#> GSM550907 2 0.6538 0.0955 0.000 0.508 0.108 0.028 0.356
#> GSM550909 5 0.5109 0.1237 0.000 0.460 0.000 0.036 0.504
#> GSM550911 5 0.2152 0.5644 0.000 0.032 0.032 0.012 0.924
#> GSM550913 2 0.2928 0.6102 0.000 0.872 0.032 0.004 0.092
#> GSM550915 2 0.6739 0.3681 0.000 0.540 0.032 0.276 0.152
#> GSM550917 2 0.3213 0.5823 0.000 0.836 0.004 0.144 0.016
#> GSM550919 2 0.4313 0.5119 0.000 0.716 0.008 0.260 0.016
#> GSM550921 1 0.3774 0.3407 0.704 0.000 0.296 0.000 0.000
#> GSM550924 2 0.4852 0.3919 0.000 0.596 0.008 0.380 0.016
#> GSM550926 2 0.3783 0.5468 0.000 0.768 0.004 0.216 0.012
#> GSM550927 2 0.2659 0.6125 0.000 0.888 0.000 0.060 0.052
#> GSM550787 4 0.5267 0.4428 0.000 0.428 0.032 0.532 0.008
#> GSM550793 4 0.7519 0.4401 0.088 0.216 0.108 0.560 0.028
#> GSM550794 2 0.6350 0.3262 0.000 0.540 0.004 0.268 0.188
#> GSM550795 1 0.8898 -0.0853 0.388 0.248 0.132 0.188 0.044
#> GSM550798 1 0.0771 0.7571 0.976 0.000 0.020 0.004 0.000
#> GSM550803 1 0.2859 0.7060 0.876 0.000 0.096 0.012 0.016
#> GSM550805 4 0.6023 0.4195 0.000 0.428 0.036 0.492 0.044
#> GSM550823 4 0.5774 0.4506 0.000 0.368 0.004 0.544 0.084
#> GSM550824 1 0.0000 0.7604 1.000 0.000 0.000 0.000 0.000
#> GSM550825 4 0.6706 0.1826 0.276 0.088 0.052 0.576 0.008
#> GSM550827 2 0.3737 0.5472 0.000 0.764 0.008 0.224 0.004
#> GSM550828 1 0.8393 0.1775 0.404 0.044 0.108 0.336 0.108
#> GSM550829 1 0.3716 0.6782 0.836 0.004 0.108 0.036 0.016
#> GSM550830 4 0.4810 0.4768 0.000 0.400 0.012 0.580 0.008
#> GSM550834 2 0.6146 0.3122 0.104 0.620 0.004 0.024 0.248
#> GSM550839 5 0.4253 0.5486 0.000 0.332 0.004 0.004 0.660
#> GSM550840 5 0.6421 0.3360 0.000 0.064 0.124 0.180 0.632
#> GSM550843 2 0.3420 0.6115 0.000 0.840 0.000 0.076 0.084
#> GSM550844 2 0.8630 -0.3933 0.256 0.380 0.128 0.216 0.020
#> GSM550845 2 0.3928 0.4926 0.000 0.700 0.004 0.296 0.000
#> GSM550848 2 0.4846 0.4578 0.000 0.644 0.012 0.324 0.020
#> GSM550854 1 0.3454 0.6870 0.848 0.000 0.100 0.036 0.016
#> GSM550857 1 0.0000 0.7604 1.000 0.000 0.000 0.000 0.000
#> GSM550858 1 0.5271 0.4883 0.728 0.152 0.040 0.080 0.000
#> GSM550859 1 0.0000 0.7604 1.000 0.000 0.000 0.000 0.000
#> GSM550862 4 0.6493 0.2332 0.296 0.108 0.036 0.560 0.000
#> GSM550865 4 0.5140 0.3804 0.000 0.428 0.020 0.540 0.012
#> GSM550868 2 0.4951 0.3206 0.000 0.556 0.012 0.420 0.012
#> GSM550869 2 0.6633 0.1846 0.000 0.548 0.048 0.100 0.304
#> GSM550870 2 0.2574 0.5546 0.000 0.876 0.012 0.112 0.000
#> GSM550871 4 0.6550 0.4057 0.000 0.332 0.084 0.536 0.048
#> GSM550872 2 0.6145 0.3466 0.000 0.564 0.048 0.336 0.052
#> GSM550873 2 0.6152 -0.0626 0.000 0.536 0.012 0.348 0.104
#> GSM550874 2 0.4893 -0.1310 0.000 0.580 0.016 0.396 0.008
#> GSM550876 2 0.5131 0.0603 0.000 0.532 0.024 0.436 0.008
#> GSM550877 2 0.3209 0.5659 0.000 0.848 0.028 0.120 0.004
#> GSM550878 2 0.4477 0.4896 0.000 0.708 0.040 0.252 0.000
#> GSM550879 2 0.6891 0.0865 0.200 0.448 0.008 0.340 0.004
#> GSM550882 4 0.6181 0.3345 0.012 0.208 0.180 0.600 0.000
#> GSM550888 1 0.0000 0.7604 1.000 0.000 0.000 0.000 0.000
#> GSM550890 2 0.6451 0.2412 0.000 0.480 0.044 0.408 0.068
#> GSM550891 3 0.3744 0.0000 0.100 0.012 0.840 0.036 0.012
#> GSM550892 4 0.7789 0.3825 0.128 0.256 0.084 0.508 0.024
#> GSM550893 2 0.6356 0.0745 0.000 0.572 0.232 0.184 0.012
#> GSM550895 2 0.5087 0.2626 0.000 0.516 0.012 0.456 0.016
#> GSM550896 2 0.4065 0.5314 0.000 0.720 0.000 0.264 0.016
#> GSM550898 1 0.0162 0.7603 0.996 0.000 0.004 0.000 0.000
#> GSM550899 2 0.1588 0.5993 0.000 0.948 0.016 0.008 0.028
#> GSM550900 2 0.4645 0.3354 0.000 0.564 0.008 0.424 0.004
#> GSM550901 2 0.4325 0.5383 0.000 0.736 0.000 0.044 0.220
#> GSM550902 2 0.8486 -0.0928 0.192 0.396 0.080 0.296 0.036
#> GSM550904 4 0.6833 -0.0326 0.408 0.144 0.008 0.428 0.012
#> GSM550908 1 0.1544 0.7191 0.932 0.000 0.068 0.000 0.000
#> GSM550912 2 0.3463 0.5637 0.000 0.820 0.016 0.156 0.008
#> GSM550914 2 0.6992 0.3439 0.000 0.492 0.036 0.312 0.160
#> GSM550918 2 0.3256 0.5723 0.000 0.832 0.004 0.148 0.016
#> GSM550922 2 0.2629 0.6059 0.000 0.896 0.032 0.064 0.008
#> GSM550923 1 0.1341 0.7361 0.944 0.000 0.000 0.056 0.000
#> GSM550925 4 0.7596 0.2582 0.028 0.260 0.276 0.424 0.012
#> GSM550802 5 0.4481 0.3681 0.000 0.416 0.000 0.008 0.576
#> GSM550812 5 0.2414 0.6281 0.000 0.080 0.008 0.012 0.900
#> GSM550831 5 0.4193 0.5569 0.032 0.040 0.068 0.028 0.832
#> GSM550847 1 0.1059 0.7556 0.968 0.004 0.008 0.020 0.000
#> GSM550860 4 0.4180 0.4922 0.000 0.220 0.036 0.744 0.000
#> GSM550875 2 0.7028 -0.4365 0.008 0.420 0.128 0.416 0.028
#> GSM550880 2 0.4789 0.4042 0.000 0.608 0.004 0.368 0.020
#> GSM550881 4 0.7777 0.2720 0.292 0.300 0.032 0.364 0.012
#> GSM550883 1 0.5609 0.3059 0.584 0.020 0.024 0.360 0.012
#> GSM550884 4 0.4981 -0.0988 0.000 0.440 0.012 0.536 0.012
#> GSM550910 2 0.4936 0.1678 0.000 0.564 0.012 0.012 0.412
#> GSM550916 4 0.5212 0.2156 0.152 0.064 0.020 0.744 0.020
#> GSM550920 2 0.3944 0.4985 0.000 0.720 0.004 0.272 0.004
cbind(get_classes(res, k = 6), get_membership(res, k = 6))
#> class entropy silhouette p1 p2 p3 p4 p5 p6
#> GSM550785 4 0.4079 0.5657 0.020 0.032 0.020 0.824 0.040 0.064
#> GSM550786 2 0.4044 0.6403 0.000 0.796 0.004 0.076 0.096 0.028
#> GSM550788 2 0.7141 0.2221 0.000 0.468 0.176 0.260 0.016 0.080
#> GSM550789 2 0.2024 0.6677 0.000 0.924 0.008 0.036 0.020 0.012
#> GSM550790 1 0.7358 -0.0326 0.316 0.012 0.004 0.312 0.052 0.304
#> GSM550791 2 0.6910 0.2968 0.224 0.528 0.012 0.176 0.020 0.040
#> GSM550792 2 0.6339 -0.1828 0.000 0.448 0.000 0.224 0.020 0.308
#> GSM550796 2 0.2879 0.6603 0.000 0.872 0.016 0.024 0.080 0.008
#> GSM550797 2 0.4225 0.6123 0.000 0.760 0.012 0.028 0.176 0.024
#> GSM550799 2 0.6528 0.3877 0.000 0.564 0.148 0.212 0.016 0.060
#> GSM550800 2 0.3352 0.6645 0.000 0.840 0.000 0.060 0.076 0.024
#> GSM550801 2 0.1363 0.6670 0.000 0.952 0.004 0.028 0.004 0.012
#> GSM550804 2 0.2655 0.6357 0.000 0.884 0.000 0.020 0.036 0.060
#> GSM550806 4 0.4144 0.6419 0.000 0.156 0.028 0.776 0.016 0.024
#> GSM550807 2 0.0914 0.6627 0.000 0.968 0.000 0.016 0.000 0.016
#> GSM550808 5 0.3771 0.5326 0.000 0.252 0.004 0.004 0.728 0.012
#> GSM550809 5 0.1679 0.5454 0.000 0.012 0.000 0.036 0.936 0.016
#> GSM550810 2 0.3825 0.5992 0.000 0.764 0.008 0.012 0.200 0.016
#> GSM550811 2 0.3932 0.6259 0.036 0.824 0.000 0.032 0.056 0.052
#> GSM550813 2 0.5087 0.5616 0.000 0.688 0.056 0.192 0.000 0.064
#> GSM550814 2 0.2476 0.6654 0.000 0.892 0.004 0.060 0.004 0.040
#> GSM550815 2 0.4329 0.3816 0.000 0.624 0.008 0.004 0.352 0.012
#> GSM550816 5 0.2958 0.5746 0.000 0.160 0.000 0.008 0.824 0.008
#> GSM550817 5 0.1406 0.5447 0.000 0.020 0.008 0.004 0.952 0.016
#> GSM550818 5 0.3533 0.5555 0.000 0.196 0.000 0.008 0.776 0.020
#> GSM550819 2 0.4785 0.5045 0.000 0.712 0.000 0.020 0.120 0.148
#> GSM550820 5 0.9040 -0.1352 0.232 0.124 0.012 0.152 0.264 0.216
#> GSM550821 2 0.3074 0.6283 0.000 0.856 0.000 0.016 0.060 0.068
#> GSM550822 2 0.4409 0.3159 0.000 0.596 0.008 0.004 0.380 0.012
#> GSM550826 2 0.7098 0.0386 0.344 0.448 0.016 0.128 0.044 0.020
#> GSM550832 2 0.2822 0.6558 0.000 0.864 0.004 0.096 0.004 0.032
#> GSM550833 2 0.2895 0.6610 0.000 0.876 0.004 0.044 0.052 0.024
#> GSM550835 2 0.3147 0.6529 0.000 0.844 0.012 0.100 0.000 0.044
#> GSM550836 1 0.0260 0.7268 0.992 0.000 0.008 0.000 0.000 0.000
#> GSM550837 2 0.4708 0.6151 0.000 0.748 0.016 0.056 0.144 0.036
#> GSM550838 5 0.5400 0.4203 0.004 0.060 0.020 0.228 0.664 0.024
#> GSM550841 5 0.4589 0.2776 0.000 0.388 0.008 0.004 0.580 0.020
#> GSM550842 2 0.3622 0.6090 0.000 0.788 0.008 0.020 0.176 0.008
#> GSM550846 6 0.5420 0.4486 0.000 0.396 0.004 0.016 0.064 0.520
#> GSM550849 5 0.4864 0.5321 0.000 0.124 0.012 0.084 0.740 0.040
#> GSM550850 5 0.4099 0.4551 0.020 0.008 0.012 0.104 0.804 0.052
#> GSM550851 2 0.4559 0.6286 0.000 0.768 0.020 0.064 0.116 0.032
#> GSM550852 2 0.6832 -0.2048 0.000 0.352 0.004 0.296 0.316 0.032
#> GSM550853 2 0.4173 0.6434 0.000 0.788 0.008 0.064 0.112 0.028
#> GSM550855 2 0.3856 0.6461 0.000 0.796 0.004 0.052 0.132 0.016
#> GSM550856 2 0.1983 0.6455 0.000 0.908 0.000 0.020 0.000 0.072
#> GSM550861 2 0.2138 0.6618 0.000 0.908 0.004 0.052 0.000 0.036
#> GSM550863 6 0.5253 0.5112 0.000 0.364 0.000 0.060 0.020 0.556
#> GSM550864 2 0.2822 0.6314 0.000 0.852 0.000 0.040 0.000 0.108
#> GSM550866 2 0.3127 0.6495 0.000 0.840 0.004 0.100 0.000 0.056
#> GSM550867 1 0.1693 0.7122 0.932 0.020 0.000 0.004 0.000 0.044
#> GSM550885 1 0.0000 0.7282 1.000 0.000 0.000 0.000 0.000 0.000
#> GSM550886 2 0.4096 -0.1558 0.000 0.508 0.000 0.008 0.000 0.484
#> GSM550887 2 0.1604 0.6667 0.000 0.944 0.024 0.016 0.008 0.008
#> GSM550889 4 0.5563 0.6113 0.008 0.084 0.116 0.684 0.000 0.108
#> GSM550894 2 0.3623 0.6372 0.000 0.820 0.028 0.056 0.000 0.096
#> GSM550897 4 0.6565 0.5946 0.116 0.108 0.016 0.584 0.000 0.176
#> GSM550903 2 0.2508 0.6628 0.000 0.892 0.012 0.068 0.004 0.024
#> GSM550905 2 0.2585 0.6429 0.000 0.880 0.024 0.012 0.000 0.084
#> GSM550906 2 0.6335 0.4161 0.000 0.572 0.140 0.212 0.004 0.072
#> GSM550907 2 0.5652 0.4916 0.000 0.676 0.080 0.012 0.144 0.088
#> GSM550909 2 0.5959 0.0763 0.000 0.432 0.004 0.008 0.412 0.144
#> GSM550911 5 0.2982 0.4977 0.000 0.016 0.036 0.012 0.872 0.064
#> GSM550913 2 0.1353 0.6675 0.000 0.952 0.024 0.012 0.012 0.000
#> GSM550915 6 0.5605 0.4237 0.000 0.392 0.024 0.004 0.068 0.512
#> GSM550917 2 0.2547 0.6290 0.000 0.868 0.004 0.016 0.000 0.112
#> GSM550919 2 0.3582 0.4728 0.000 0.732 0.000 0.016 0.000 0.252
#> GSM550921 1 0.4230 0.2067 0.612 0.000 0.364 0.000 0.000 0.024
#> GSM550924 6 0.4912 0.4163 0.000 0.408 0.004 0.044 0.004 0.540
#> GSM550926 2 0.4212 0.4349 0.000 0.688 0.000 0.048 0.000 0.264
#> GSM550927 2 0.2393 0.6377 0.000 0.884 0.004 0.020 0.000 0.092
#> GSM550787 4 0.5206 0.6133 0.000 0.176 0.036 0.692 0.008 0.088
#> GSM550793 4 0.2741 0.6125 0.032 0.040 0.008 0.892 0.004 0.024
#> GSM550794 4 0.6579 0.3108 0.000 0.208 0.000 0.540 0.108 0.144
#> GSM550795 1 0.8308 0.1682 0.388 0.180 0.020 0.264 0.060 0.088
#> GSM550798 1 0.0291 0.7280 0.992 0.000 0.004 0.004 0.000 0.000
#> GSM550803 1 0.3218 0.6743 0.856 0.000 0.020 0.080 0.032 0.012
#> GSM550805 4 0.3627 0.6631 0.000 0.152 0.000 0.796 0.012 0.040
#> GSM550823 4 0.4430 0.6464 0.000 0.076 0.004 0.772 0.048 0.100
#> GSM550824 1 0.0000 0.7282 1.000 0.000 0.000 0.000 0.000 0.000
#> GSM550825 4 0.4648 0.5068 0.184 0.024 0.004 0.724 0.000 0.064
#> GSM550827 2 0.4460 0.2850 0.000 0.644 0.000 0.052 0.000 0.304
#> GSM550828 1 0.7931 0.0486 0.324 0.000 0.016 0.248 0.168 0.244
#> GSM550829 1 0.2569 0.6978 0.896 0.004 0.016 0.060 0.008 0.016
#> GSM550830 4 0.3757 0.6548 0.000 0.084 0.000 0.780 0.000 0.136
#> GSM550834 2 0.6268 0.4683 0.164 0.620 0.000 0.080 0.116 0.020
#> GSM550839 5 0.5109 0.1834 0.000 0.424 0.000 0.032 0.516 0.028
#> GSM550840 5 0.4803 0.2046 0.000 0.008 0.008 0.408 0.552 0.024
#> GSM550843 2 0.3179 0.6129 0.000 0.848 0.000 0.028 0.032 0.092
#> GSM550844 1 0.7033 0.1042 0.440 0.168 0.016 0.328 0.008 0.040
#> GSM550845 2 0.5703 -0.1973 0.000 0.472 0.000 0.168 0.000 0.360
#> GSM550848 2 0.4238 0.0527 0.000 0.580 0.000 0.008 0.008 0.404
#> GSM550854 1 0.2900 0.6735 0.856 0.000 0.016 0.112 0.004 0.012
#> GSM550857 1 0.0146 0.7277 0.996 0.000 0.004 0.000 0.000 0.000
#> GSM550858 1 0.4219 0.5641 0.764 0.060 0.012 0.156 0.000 0.008
#> GSM550859 1 0.0146 0.7281 0.996 0.000 0.004 0.000 0.000 0.000
#> GSM550862 6 0.6403 -0.1052 0.260 0.016 0.000 0.320 0.000 0.404
#> GSM550865 4 0.4664 0.6365 0.000 0.152 0.012 0.724 0.004 0.108
#> GSM550868 6 0.5068 0.5817 0.000 0.272 0.000 0.104 0.004 0.620
#> GSM550869 2 0.8073 0.0393 0.000 0.404 0.072 0.232 0.184 0.108
#> GSM550870 2 0.4294 0.5831 0.000 0.728 0.004 0.188 0.000 0.080
#> GSM550871 4 0.5485 0.4736 0.000 0.132 0.004 0.676 0.056 0.132
#> GSM550872 2 0.7067 -0.4575 0.000 0.336 0.004 0.300 0.052 0.308
#> GSM550873 4 0.5652 0.3261 0.000 0.380 0.004 0.520 0.068 0.028
#> GSM550874 4 0.5507 0.3209 0.000 0.376 0.044 0.532 0.000 0.048
#> GSM550876 4 0.6371 0.2094 0.000 0.268 0.012 0.472 0.008 0.240
#> GSM550877 2 0.4435 0.5756 0.000 0.720 0.004 0.176 0.000 0.100
#> GSM550878 2 0.6870 0.0281 0.000 0.460 0.076 0.232 0.000 0.232
#> GSM550879 6 0.6786 0.5054 0.252 0.304 0.004 0.016 0.012 0.412
#> GSM550882 4 0.6879 0.3937 0.008 0.064 0.204 0.484 0.000 0.240
#> GSM550888 1 0.0260 0.7268 0.992 0.000 0.008 0.000 0.000 0.000
#> GSM550890 6 0.4743 0.4840 0.000 0.152 0.032 0.000 0.092 0.724
#> GSM550891 3 0.2001 0.0000 0.032 0.000 0.924 0.012 0.004 0.028
#> GSM550892 6 0.7489 0.1831 0.084 0.144 0.016 0.364 0.012 0.380
#> GSM550893 2 0.7322 0.0764 0.000 0.444 0.168 0.220 0.004 0.164
#> GSM550895 6 0.4631 0.5659 0.000 0.200 0.008 0.092 0.000 0.700
#> GSM550896 2 0.4362 0.2893 0.000 0.628 0.004 0.020 0.004 0.344
#> GSM550898 1 0.0000 0.7282 1.000 0.000 0.000 0.000 0.000 0.000
#> GSM550899 2 0.2058 0.6645 0.000 0.908 0.000 0.056 0.000 0.036
#> GSM550900 6 0.5403 0.5626 0.000 0.248 0.004 0.156 0.000 0.592
#> GSM550901 2 0.4042 0.6121 0.004 0.792 0.000 0.024 0.112 0.068
#> GSM550902 6 0.8403 0.3980 0.168 0.236 0.020 0.216 0.024 0.336
#> GSM550904 6 0.5898 0.0479 0.404 0.064 0.000 0.056 0.000 0.476
#> GSM550908 1 0.1444 0.6971 0.928 0.000 0.072 0.000 0.000 0.000
#> GSM550912 2 0.5845 0.3870 0.000 0.588 0.024 0.148 0.004 0.236
#> GSM550914 6 0.6885 0.5306 0.000 0.312 0.044 0.044 0.112 0.488
#> GSM550918 2 0.2930 0.6268 0.000 0.840 0.000 0.036 0.000 0.124
#> GSM550922 2 0.2252 0.6491 0.000 0.900 0.012 0.016 0.000 0.072
#> GSM550923 1 0.2234 0.6769 0.872 0.000 0.000 0.004 0.000 0.124
#> GSM550925 4 0.7665 0.2297 0.016 0.104 0.252 0.344 0.000 0.284
#> GSM550802 5 0.5106 0.1344 0.000 0.440 0.000 0.040 0.500 0.020
#> GSM550812 5 0.1710 0.5582 0.000 0.028 0.000 0.020 0.936 0.016
#> GSM550831 5 0.3406 0.5005 0.016 0.008 0.016 0.044 0.856 0.060
#> GSM550847 1 0.0692 0.7265 0.976 0.000 0.004 0.020 0.000 0.000
#> GSM550860 4 0.4770 0.5520 0.000 0.036 0.032 0.664 0.000 0.268
#> GSM550875 4 0.4916 0.6154 0.040 0.124 0.016 0.756 0.020 0.044
#> GSM550880 6 0.5535 0.3553 0.000 0.424 0.008 0.088 0.004 0.476
#> GSM550881 1 0.7555 -0.1382 0.372 0.168 0.024 0.100 0.000 0.336
#> GSM550883 1 0.4994 0.2749 0.508 0.004 0.008 0.040 0.000 0.440
#> GSM550884 6 0.4706 0.4865 0.000 0.156 0.004 0.144 0.000 0.696
#> GSM550910 2 0.5559 0.4494 0.000 0.584 0.012 0.012 0.304 0.088
#> GSM550916 6 0.6548 -0.2194 0.036 0.000 0.016 0.340 0.132 0.476
#> GSM550920 2 0.5632 -0.0774 0.000 0.496 0.004 0.136 0.000 0.364
Heatmaps for the consensus matrix. It visualizes the probability of two samples to be in a same group.
consensus_heatmap(res, k = 2)
consensus_heatmap(res, k = 3)
consensus_heatmap(res, k = 4)
consensus_heatmap(res, k = 5)
consensus_heatmap(res, k = 6)
Heatmaps for the membership of samples in all partitions to see how consistent they are:
membership_heatmap(res, k = 2)
membership_heatmap(res, k = 3)
membership_heatmap(res, k = 4)
membership_heatmap(res, k = 5)
membership_heatmap(res, k = 6)
As soon as we have had the classes for columns, we can look for signatures which are significantly different between classes which can be candidate marks for certain classes. Following are the heatmaps for signatures.
Signature heatmaps where rows are scaled:
get_signatures(res, k = 2)
get_signatures(res, k = 3)
get_signatures(res, k = 4)
get_signatures(res, k = 5)
get_signatures(res, k = 6)
Signature heatmaps where rows are not scaled:
get_signatures(res, k = 2, scale_rows = FALSE)
get_signatures(res, k = 3, scale_rows = FALSE)
get_signatures(res, k = 4, scale_rows = FALSE)
get_signatures(res, k = 5, scale_rows = FALSE)
get_signatures(res, k = 6, scale_rows = FALSE)
Compare the overlap of signatures from different k:
compare_signatures(res)
get_signature() returns a data frame invisibly. TO get the list of signatures, the function
call should be assigned to a variable explicitly. In following code, if plot argument is set
to FALSE, no heatmap is plotted while only the differential analysis is performed.
# code only for demonstration
tb = get_signature(res, k = ..., plot = FALSE)
An example of the output of tb is:
#> which_row fdr mean_1 mean_2 scaled_mean_1 scaled_mean_2 km
#> 1 38 0.042760348 8.373488 9.131774 -0.5533452 0.5164555 1
#> 2 40 0.018707592 7.106213 8.469186 -0.6173731 0.5762149 1
#> 3 55 0.019134737 10.221463 11.207825 -0.6159697 0.5749050 1
#> 4 59 0.006059896 5.921854 7.869574 -0.6899429 0.6439467 1
#> 5 60 0.018055526 8.928898 10.211722 -0.6204761 0.5791110 1
#> 6 98 0.009384629 15.714769 14.887706 0.6635654 -0.6193277 2
...
The columns in tb are:
which_row: row indices corresponding to the input matrix.fdr: FDR for the differential test. mean_x: The mean value in group x.scaled_mean_x: The mean value in group x after rows are scaled.km: Row groups if k-means clustering is applied to rows.UMAP plot which shows how samples are separated.
dimension_reduction(res, k = 2, method = "UMAP")
dimension_reduction(res, k = 3, method = "UMAP")
dimension_reduction(res, k = 4, method = "UMAP")
dimension_reduction(res, k = 5, method = "UMAP")
dimension_reduction(res, k = 6, method = "UMAP")
Following heatmap shows how subgroups are split when increasing k:
collect_classes(res)
Test correlation between subgroups and known annotations. If the known annotation is numeric, one-way ANOVA test is applied, and if the known annotation is discrete, chi-squared contingency table test is applied.
test_to_known_factors(res)
#> n disease.state(p) k
#> ATC:NMF 139 4.58e-03 2
#> ATC:NMF 112 1.71e-05 3
#> ATC:NMF 106 1.42e-03 4
#> ATC:NMF 64 1.96e-03 5
#> ATC:NMF 83 3.88e-06 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