Date: 2019-12-25 21:19:39 CET, cola version: 1.3.2
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All available functions which can be applied to this res_list object:
res_list
#> A 'ConsensusPartitionList' object with 24 methods.
#> On a matrix with 4537 rows and 166 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] 4537 166
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 | ||
|---|---|---|---|---|---|
| ATC:mclust | 2 | 1.000 | 0.962 | 0.978 | ** |
| MAD:kmeans | 2 | 0.964 | 0.940 | 0.963 | ** |
| ATC:skmeans | 2 | 0.950 | 0.940 | 0.975 | * |
| MAD:mclust | 2 | 0.908 | 0.942 | 0.973 | * |
| ATC:NMF | 3 | 0.905 | 0.890 | 0.956 | * |
| MAD:NMF | 2 | 0.862 | 0.904 | 0.956 | |
| SD:NMF | 2 | 0.807 | 0.902 | 0.958 | |
| ATC:kmeans | 3 | 0.776 | 0.884 | 0.925 | |
| ATC:pam | 3 | 0.731 | 0.817 | 0.917 | |
| CV:NMF | 2 | 0.715 | 0.877 | 0.942 | |
| SD:mclust | 3 | 0.640 | 0.789 | 0.893 | |
| SD:skmeans | 2 | 0.598 | 0.868 | 0.931 | |
| MAD:skmeans | 2 | 0.542 | 0.814 | 0.913 | |
| CV:skmeans | 2 | 0.538 | 0.886 | 0.933 | |
| SD:kmeans | 3 | 0.511 | 0.677 | 0.811 | |
| CV:mclust | 3 | 0.462 | 0.801 | 0.864 | |
| MAD:pam | 2 | 0.385 | 0.717 | 0.857 | |
| CV:pam | 2 | 0.301 | 0.652 | 0.839 | |
| SD:pam | 2 | 0.256 | 0.784 | 0.854 | |
| CV:kmeans | 2 | 0.183 | 0.682 | 0.803 | |
| ATC:hclust | 2 | 0.155 | 0.666 | 0.813 | |
| CV:hclust | 3 | 0.105 | 0.553 | 0.693 | |
| MAD:hclust | 3 | 0.052 | 0.379 | 0.634 | |
| SD:hclust | 2 | 0.024 | 0.493 | 0.683 |
**: 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 0.8066 0.902 0.958 0.461 0.550 0.550
#> CV:NMF 2 0.7154 0.877 0.942 0.460 0.550 0.550
#> MAD:NMF 2 0.8616 0.904 0.956 0.465 0.543 0.543
#> ATC:NMF 2 0.8989 0.926 0.968 0.478 0.523 0.523
#> SD:skmeans 2 0.5981 0.868 0.931 0.485 0.516 0.516
#> CV:skmeans 2 0.5383 0.886 0.933 0.489 0.521 0.521
#> MAD:skmeans 2 0.5420 0.814 0.913 0.475 0.550 0.550
#> ATC:skmeans 2 0.9496 0.940 0.975 0.502 0.498 0.498
#> SD:mclust 2 0.7247 0.890 0.942 0.432 0.586 0.586
#> CV:mclust 2 0.5056 0.819 0.867 0.425 0.608 0.608
#> MAD:mclust 2 0.9083 0.942 0.973 0.402 0.592 0.592
#> ATC:mclust 2 1.0000 0.962 0.978 0.407 0.597 0.597
#> SD:kmeans 2 0.6231 0.921 0.932 0.440 0.576 0.576
#> CV:kmeans 2 0.1829 0.682 0.803 0.447 0.554 0.554
#> MAD:kmeans 2 0.9644 0.940 0.963 0.412 0.581 0.581
#> ATC:kmeans 2 0.6834 0.915 0.941 0.430 0.592 0.592
#> SD:pam 2 0.2563 0.784 0.854 0.493 0.500 0.500
#> CV:pam 2 0.3009 0.652 0.839 0.486 0.511 0.511
#> MAD:pam 2 0.3851 0.717 0.857 0.468 0.529 0.529
#> ATC:pam 2 0.5367 0.675 0.873 0.473 0.497 0.497
#> SD:hclust 2 0.0240 0.493 0.683 0.435 0.501 0.501
#> CV:hclust 2 0.0563 0.707 0.792 0.317 0.845 0.845
#> MAD:hclust 2 0.0469 0.689 0.754 0.363 0.796 0.796
#> ATC:hclust 2 0.1550 0.666 0.813 0.460 0.500 0.500
get_stats(res_list, k = 3)
#> k 1-PAC mean_silhouette concordance area_increased Rand Jaccard
#> SD:NMF 3 0.5732 0.665 0.847 0.442 0.732 0.534
#> CV:NMF 3 0.6437 0.757 0.892 0.448 0.711 0.506
#> MAD:NMF 3 0.5344 0.683 0.837 0.424 0.738 0.539
#> ATC:NMF 3 0.9049 0.890 0.956 0.391 0.739 0.533
#> SD:skmeans 3 0.7203 0.833 0.920 0.373 0.707 0.486
#> CV:skmeans 3 0.7887 0.845 0.928 0.369 0.730 0.519
#> MAD:skmeans 3 0.6520 0.787 0.884 0.402 0.734 0.537
#> ATC:skmeans 3 0.8575 0.886 0.950 0.326 0.751 0.540
#> SD:mclust 3 0.6400 0.789 0.893 0.517 0.743 0.565
#> CV:mclust 3 0.4616 0.801 0.864 0.502 0.722 0.544
#> MAD:mclust 3 0.4435 0.686 0.768 0.511 0.736 0.557
#> ATC:mclust 3 0.6534 0.746 0.886 0.611 0.731 0.552
#> SD:kmeans 3 0.5109 0.677 0.811 0.483 0.756 0.576
#> CV:kmeans 3 0.3240 0.670 0.782 0.413 0.753 0.565
#> MAD:kmeans 3 0.4275 0.623 0.758 0.550 0.752 0.573
#> ATC:kmeans 3 0.7763 0.884 0.925 0.526 0.731 0.552
#> SD:pam 3 0.5522 0.726 0.862 0.338 0.735 0.518
#> CV:pam 3 0.5256 0.638 0.829 0.313 0.791 0.614
#> MAD:pam 3 0.4740 0.703 0.821 0.342 0.773 0.593
#> ATC:pam 3 0.7306 0.817 0.917 0.393 0.724 0.501
#> SD:hclust 3 0.0203 0.347 0.589 0.375 0.906 0.826
#> CV:hclust 3 0.1053 0.553 0.693 0.637 0.648 0.584
#> MAD:hclust 3 0.0521 0.379 0.634 0.573 0.663 0.580
#> ATC:hclust 3 0.2268 0.512 0.734 0.281 0.880 0.763
get_stats(res_list, k = 4)
#> k 1-PAC mean_silhouette concordance area_increased Rand Jaccard
#> SD:NMF 4 0.586 0.568 0.783 0.1150 0.801 0.497
#> CV:NMF 4 0.631 0.579 0.737 0.1228 0.864 0.633
#> MAD:NMF 4 0.523 0.442 0.715 0.1189 0.774 0.452
#> ATC:NMF 4 0.605 0.559 0.760 0.1190 0.821 0.538
#> SD:skmeans 4 0.737 0.707 0.809 0.1252 0.851 0.596
#> CV:skmeans 4 0.679 0.698 0.836 0.1163 0.858 0.608
#> MAD:skmeans 4 0.727 0.693 0.821 0.1210 0.851 0.593
#> ATC:skmeans 4 0.686 0.646 0.811 0.1238 0.859 0.612
#> SD:mclust 4 0.599 0.523 0.787 0.0940 0.946 0.845
#> CV:mclust 4 0.508 0.630 0.756 0.1043 0.941 0.827
#> MAD:mclust 4 0.459 0.627 0.791 0.1223 0.896 0.721
#> ATC:mclust 4 0.649 0.729 0.854 0.0827 0.905 0.737
#> SD:kmeans 4 0.573 0.610 0.762 0.1310 0.895 0.700
#> CV:kmeans 4 0.567 0.668 0.771 0.1374 0.931 0.799
#> MAD:kmeans 4 0.479 0.561 0.671 0.1364 0.858 0.612
#> ATC:kmeans 4 0.615 0.550 0.770 0.1203 0.969 0.909
#> SD:pam 4 0.514 0.476 0.695 0.1245 0.808 0.506
#> CV:pam 4 0.551 0.642 0.779 0.1308 0.810 0.532
#> MAD:pam 4 0.521 0.683 0.808 0.1402 0.874 0.677
#> ATC:pam 4 0.616 0.576 0.767 0.1084 0.908 0.739
#> SD:hclust 4 0.123 0.318 0.525 0.1594 0.756 0.512
#> CV:hclust 4 0.163 0.513 0.655 0.1790 0.906 0.833
#> MAD:hclust 4 0.170 0.429 0.629 0.1504 0.814 0.637
#> ATC:hclust 4 0.290 0.513 0.704 0.1510 0.907 0.773
get_stats(res_list, k = 5)
#> k 1-PAC mean_silhouette concordance area_increased Rand Jaccard
#> SD:NMF 5 0.659 0.613 0.792 0.0691 0.875 0.579
#> CV:NMF 5 0.625 0.454 0.650 0.0626 0.802 0.408
#> MAD:NMF 5 0.681 0.718 0.825 0.0704 0.853 0.524
#> ATC:NMF 5 0.651 0.606 0.759 0.0701 0.813 0.428
#> SD:skmeans 5 0.704 0.631 0.779 0.0656 0.884 0.600
#> CV:skmeans 5 0.725 0.656 0.807 0.0685 0.916 0.692
#> MAD:skmeans 5 0.650 0.481 0.709 0.0650 0.875 0.578
#> ATC:skmeans 5 0.666 0.528 0.721 0.0629 0.937 0.760
#> SD:mclust 5 0.633 0.554 0.747 0.0679 0.903 0.709
#> CV:mclust 5 0.640 0.680 0.795 0.0704 0.915 0.726
#> MAD:mclust 5 0.506 0.535 0.731 0.0944 0.887 0.655
#> ATC:mclust 5 0.720 0.659 0.776 0.0906 0.895 0.661
#> SD:kmeans 5 0.614 0.587 0.704 0.0686 0.886 0.611
#> CV:kmeans 5 0.652 0.660 0.771 0.0773 0.919 0.728
#> MAD:kmeans 5 0.577 0.515 0.658 0.0797 0.863 0.551
#> ATC:kmeans 5 0.621 0.516 0.685 0.0671 0.840 0.526
#> SD:pam 5 0.584 0.445 0.713 0.0739 0.871 0.557
#> CV:pam 5 0.559 0.552 0.725 0.0738 0.937 0.775
#> MAD:pam 5 0.582 0.533 0.742 0.0887 0.895 0.659
#> ATC:pam 5 0.629 0.626 0.779 0.0733 0.889 0.639
#> SD:hclust 5 0.284 0.324 0.542 0.0911 0.831 0.499
#> CV:hclust 5 0.189 0.149 0.553 0.0885 0.939 0.888
#> MAD:hclust 5 0.277 0.412 0.599 0.0905 0.916 0.781
#> ATC:hclust 5 0.396 0.465 0.661 0.1006 0.922 0.765
get_stats(res_list, k = 6)
#> k 1-PAC mean_silhouette concordance area_increased Rand Jaccard
#> SD:NMF 6 0.680 0.585 0.736 0.0482 0.887 0.539
#> CV:NMF 6 0.769 0.706 0.833 0.0455 0.911 0.606
#> MAD:NMF 6 0.711 0.650 0.805 0.0441 0.946 0.750
#> ATC:NMF 6 0.785 0.758 0.843 0.0470 0.901 0.579
#> SD:skmeans 6 0.720 0.619 0.779 0.0435 0.915 0.629
#> CV:skmeans 6 0.745 0.667 0.806 0.0416 0.915 0.632
#> MAD:skmeans 6 0.685 0.531 0.732 0.0456 0.879 0.518
#> ATC:skmeans 6 0.744 0.618 0.801 0.0469 0.884 0.534
#> SD:mclust 6 0.655 0.502 0.711 0.0550 0.913 0.673
#> CV:mclust 6 0.696 0.628 0.794 0.0794 0.895 0.591
#> MAD:mclust 6 0.516 0.472 0.668 0.0523 0.850 0.489
#> ATC:mclust 6 0.753 0.722 0.846 0.0607 0.906 0.617
#> SD:kmeans 6 0.669 0.558 0.707 0.0431 0.920 0.651
#> CV:kmeans 6 0.715 0.605 0.735 0.0417 0.945 0.765
#> MAD:kmeans 6 0.644 0.556 0.709 0.0477 0.905 0.606
#> ATC:kmeans 6 0.662 0.598 0.737 0.0455 0.926 0.673
#> SD:pam 6 0.655 0.438 0.651 0.0407 0.925 0.669
#> CV:pam 6 0.697 0.643 0.788 0.0564 0.878 0.539
#> MAD:pam 6 0.649 0.554 0.738 0.0494 0.927 0.688
#> ATC:pam 6 0.664 0.442 0.684 0.0512 0.896 0.583
#> SD:hclust 6 0.387 0.363 0.543 0.0538 0.890 0.571
#> CV:hclust 6 0.266 0.303 0.554 0.0769 0.802 0.598
#> MAD:hclust 6 0.350 0.360 0.580 0.0634 0.914 0.746
#> ATC:hclust 6 0.493 0.482 0.687 0.0503 0.957 0.837
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 = 454, method = "euler")
top_rows_overlap(res_list, top_n = 908, method = "euler")
top_rows_overlap(res_list, top_n = 1361, method = "euler")
top_rows_overlap(res_list, top_n = 1814, method = "euler")
top_rows_overlap(res_list, top_n = 2268, method = "euler")
Also visualize the correspondance of rankings between different top-row methods:
top_rows_overlap(res_list, top_n = 454, method = "correspondance")
top_rows_overlap(res_list, top_n = 908, method = "correspondance")
top_rows_overlap(res_list, top_n = 1361, method = "correspondance")
top_rows_overlap(res_list, top_n = 1814, method = "correspondance")
top_rows_overlap(res_list, top_n = 2268, method = "correspondance")
Heatmaps of the top rows:
top_rows_heatmap(res_list, top_n = 454)
top_rows_heatmap(res_list, top_n = 908)
top_rows_heatmap(res_list, top_n = 1361)
top_rows_heatmap(res_list, top_n = 1814)
top_rows_heatmap(res_list, top_n = 2268)
Test correlation between subgroups and known annotations. If the known annotation is numeric, one-way ANOVA test is applied, and if the known annotation is discrete, chi-squared contingency table test is applied.
test_to_known_factors(res_list, k = 2)
#> n tissue(p) disease.state(p) agent(p) k
#> SD:NMF 159 3.05e-23 0.74006 0.85578 2
#> CV:NMF 157 1.94e-23 0.56581 0.73506 2
#> MAD:NMF 156 2.47e-21 1.00000 0.98117 2
#> ATC:NMF 161 1.71e-12 0.38803 0.55559 2
#> SD:skmeans 162 1.43e-31 0.96598 0.81680 2
#> CV:skmeans 165 2.25e-31 0.78253 0.75524 2
#> MAD:skmeans 151 4.34e-26 0.34388 0.50729 2
#> ATC:skmeans 162 6.17e-09 0.31434 0.41321 2
#> SD:mclust 162 1.20e-22 0.11902 0.19465 2
#> CV:mclust 165 2.86e-20 0.16191 0.25061 2
#> MAD:mclust 163 2.98e-22 0.06605 0.11675 2
#> ATC:mclust 165 4.98e-20 0.13906 0.22050 2
#> SD:kmeans 166 1.10e-23 0.13103 0.21996 2
#> CV:kmeans 150 6.28e-28 0.27762 0.42918 2
#> MAD:kmeans 163 6.55e-23 0.05445 0.09399 2
#> ATC:kmeans 165 5.52e-21 0.13906 0.22050 2
#> SD:pam 158 1.05e-09 0.27317 0.31062 2
#> CV:pam 133 1.94e-19 1.00000 0.95160 2
#> MAD:pam 141 2.60e-17 1.00000 0.96370 2
#> ATC:pam 127 5.46e-11 0.16389 0.24938 2
#> SD:hclust 108 3.48e-09 0.00982 0.01214 2
#> CV:hclust 161 5.09e-03 0.00731 0.00668 2
#> MAD:hclust 153 8.76e-08 0.57298 0.10539 2
#> ATC:hclust 136 1.97e-10 0.34372 0.51441 2
test_to_known_factors(res_list, k = 3)
#> n tissue(p) disease.state(p) agent(p) k
#> SD:NMF 130 1.33e-34 0.20051 0.4494 3
#> CV:NMF 144 2.23e-37 0.19944 0.4823 3
#> MAD:NMF 134 4.04e-24 0.43920 0.7087 3
#> ATC:NMF 153 5.97e-19 0.25085 0.2672 3
#> SD:skmeans 148 7.19e-45 0.12185 0.3738 3
#> CV:skmeans 155 1.30e-51 0.37855 0.6670 3
#> MAD:skmeans 155 9.83e-47 0.18126 0.4446 3
#> ATC:skmeans 159 1.25e-26 0.22798 0.1806 3
#> SD:mclust 151 3.79e-46 0.46827 0.7377 3
#> CV:mclust 158 9.32e-45 0.11760 0.3426 3
#> MAD:mclust 149 2.78e-32 0.10576 0.3309 3
#> ATC:mclust 138 1.91e-26 0.21382 0.4383 3
#> SD:kmeans 132 4.69e-46 0.77559 0.9636 3
#> CV:kmeans 138 1.70e-43 0.40550 0.7626 3
#> MAD:kmeans 132 8.90e-44 0.13087 0.3786 3
#> ATC:kmeans 161 1.05e-25 0.18521 0.1813 3
#> SD:pam 144 4.40e-39 0.14088 0.3299 3
#> CV:pam 125 7.45e-49 0.76007 0.2918 3
#> MAD:pam 148 6.73e-26 0.89673 0.9056 3
#> ATC:pam 153 1.12e-34 0.24242 0.4565 3
#> SD:hclust 52 5.11e-12 0.94945 0.2473 3
#> CV:hclust 124 3.71e-09 0.00722 0.0260 3
#> MAD:hclust 86 3.22e-14 0.16160 0.0214 3
#> ATC:hclust 112 9.62e-13 0.84749 0.9126 3
test_to_known_factors(res_list, k = 4)
#> n tissue(p) disease.state(p) agent(p) k
#> SD:NMF 114 4.55e-34 3.79e-01 2.52e-01 4
#> CV:NMF 113 4.21e-31 9.03e-03 5.10e-02 4
#> MAD:NMF 76 4.36e-23 2.02e-01 4.33e-01 4
#> ATC:NMF 102 2.52e-19 7.70e-02 1.78e-01 4
#> SD:skmeans 146 1.66e-52 4.30e-07 2.42e-06 4
#> CV:skmeans 121 1.90e-48 4.76e-02 1.64e-01 4
#> MAD:skmeans 128 1.64e-46 5.61e-07 4.24e-06 4
#> ATC:skmeans 123 2.10e-45 1.23e-01 2.09e-01 4
#> SD:mclust 111 1.68e-44 7.19e-01 9.16e-01 4
#> CV:mclust 142 3.37e-40 1.80e-01 2.99e-01 4
#> MAD:mclust 134 9.74e-28 2.17e-01 2.98e-01 4
#> ATC:mclust 144 1.34e-25 5.78e-01 3.32e-01 4
#> SD:kmeans 122 7.85e-50 4.12e-03 1.35e-02 4
#> CV:kmeans 137 3.02e-56 7.99e-03 1.89e-02 4
#> MAD:kmeans 114 2.46e-45 2.29e-07 5.39e-06 4
#> ATC:kmeans 104 9.64e-37 5.78e-01 7.31e-01 4
#> SD:pam 91 3.17e-31 1.47e-01 4.76e-02 4
#> CV:pam 132 9.92e-48 4.28e-01 9.06e-02 4
#> MAD:pam 145 4.13e-24 1.65e-01 4.79e-03 4
#> ATC:pam 119 1.59e-31 4.11e-01 7.55e-01 4
#> SD:hclust 35 3.07e-01 2.74e-01 6.81e-02 4
#> CV:hclust 115 1.20e-06 3.62e-03 7.82e-03 4
#> MAD:hclust 87 7.59e-13 2.24e-01 1.08e-02 4
#> ATC:hclust 125 3.50e-18 5.79e-02 2.50e-02 4
test_to_known_factors(res_list, k = 5)
#> n tissue(p) disease.state(p) agent(p) k
#> SD:NMF 124 1.55e-37 6.30e-02 1.96e-03 5
#> CV:NMF 97 3.59e-39 2.03e-01 1.17e-01 5
#> MAD:NMF 144 3.24e-38 5.05e-01 2.70e-01 5
#> ATC:NMF 134 1.00e-29 3.36e-01 2.39e-01 5
#> SD:skmeans 137 1.39e-54 4.37e-03 5.97e-03 5
#> CV:skmeans 131 1.36e-49 5.61e-03 5.96e-03 5
#> MAD:skmeans 96 9.56e-39 5.25e-01 2.53e-01 5
#> ATC:skmeans 121 1.12e-44 2.27e-01 2.43e-01 5
#> SD:mclust 132 1.78e-35 3.53e-01 3.56e-01 5
#> CV:mclust 145 1.17e-36 1.93e-01 5.51e-02 5
#> MAD:mclust 116 2.56e-33 6.10e-01 1.85e-01 5
#> ATC:mclust 133 1.31e-21 3.10e-01 4.08e-02 5
#> SD:kmeans 127 2.44e-50 7.12e-04 1.55e-03 5
#> CV:kmeans 139 1.24e-52 1.68e-02 4.65e-02 5
#> MAD:kmeans 102 9.17e-40 1.49e-05 8.16e-05 5
#> ATC:kmeans 102 1.14e-36 3.23e-01 4.72e-02 5
#> SD:pam 81 1.03e-29 2.56e-03 9.54e-04 5
#> CV:pam 109 5.37e-19 2.02e-01 9.60e-02 5
#> MAD:pam 118 4.21e-36 3.99e-01 2.82e-03 5
#> ATC:pam 139 2.27e-32 4.22e-01 2.02e-01 5
#> SD:hclust 53 7.56e-03 2.68e-03 1.33e-03 5
#> CV:hclust 21 1.38e-03 3.04e-01 6.44e-01 5
#> MAD:hclust 89 1.56e-13 1.27e-01 3.35e-03 5
#> ATC:hclust 100 3.38e-15 1.25e-01 1.19e-02 5
test_to_known_factors(res_list, k = 6)
#> n tissue(p) disease.state(p) agent(p) k
#> SD:NMF 122 3.01e-44 0.017145 1.09e-03 6
#> CV:NMF 144 3.69e-44 0.100569 4.98e-04 6
#> MAD:NMF 134 2.16e-43 0.122702 4.33e-02 6
#> ATC:NMF 147 7.25e-33 0.208489 5.54e-02 6
#> SD:skmeans 126 2.06e-48 0.009638 6.13e-04 6
#> CV:skmeans 133 5.18e-49 0.001386 2.05e-04 6
#> MAD:skmeans 106 7.24e-39 0.000632 6.80e-05 6
#> ATC:skmeans 120 9.36e-35 0.031199 3.52e-03 6
#> SD:mclust 99 1.50e-37 0.203697 4.27e-02 6
#> CV:mclust 134 3.90e-36 0.192252 3.65e-03 6
#> MAD:mclust 89 1.50e-28 0.936402 3.78e-01 6
#> ATC:mclust 144 2.34e-24 0.561900 2.83e-02 6
#> SD:kmeans 113 5.92e-43 0.003398 2.41e-04 6
#> CV:kmeans 125 2.58e-44 0.031883 7.89e-03 6
#> MAD:kmeans 112 2.24e-41 0.013393 6.18e-04 6
#> ATC:kmeans 129 9.20e-44 0.211896 1.24e-01 6
#> SD:pam 73 1.34e-27 0.011907 1.33e-04 6
#> CV:pam 133 8.10e-45 0.826207 2.84e-03 6
#> MAD:pam 112 1.30e-37 0.868214 4.07e-02 6
#> ATC:pam 75 9.54e-22 0.904120 1.87e-01 6
#> SD:hclust 68 1.07e-10 0.002545 3.09e-04 6
#> CV:hclust 38 7.35e-06 0.024701 2.53e-05 6
#> MAD:hclust 85 5.53e-15 0.210017 1.23e-02 6
#> ATC:hclust 106 1.43e-17 0.109783 3.32e-04 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 4537 rows and 166 columns.
#> Top rows (454, 908, 1361, 1814, 2268) are extracted by 'SD' method.
#> Subgroups are detected by 'hclust' method.
#> Performed in total 1250 partitions by row resampling.
#> Best k for subgroups seems to be 2.
#>
#> Following methods can be applied to this 'ConsensusPartition' object:
#> [1] "cola_report" "collect_classes" "collect_plots"
#> [4] "collect_stats" "colnames" "compare_signatures"
#> [7] "consensus_heatmap" "dimension_reduction" "functional_enrichment"
#> [10] "get_anno_col" "get_anno" "get_classes"
#> [13] "get_consensus" "get_matrix" "get_membership"
#> [16] "get_param" "get_signatures" "get_stats"
#> [19] "is_best_k" "is_stable_k" "membership_heatmap"
#> [22] "ncol" "nrow" "plot_ecdf"
#> [25] "rownames" "select_partition_number" "show"
#> [28] "suggest_best_k" "test_to_known_factors"
collect_plots() function collects all the plots made from res for all k (number of partitions)
into one single page to provide an easy and fast comparison between different k.
collect_plots(res)
The plots are:
k and the heatmap of
predicted classes for each k.k.k.k.All the plots in panels can be made by individual functions and they are plotted later in this section.
select_partition_number() produces several plots showing different
statistics for choosing “optimized” k. There are following statistics:
k;k, the area increased is defined as \(A_k - A_{k-1}\).The detailed explanations of these statistics can be found in the cola vignette.
Generally speaking, lower PAC score, higher mean silhouette score or higher
concordance corresponds to better partition. Rand index and Jaccard index
measure how similar the current partition is compared to partition with k-1.
If they are too similar, we won't accept k is better than k-1.
select_partition_number(res)
The numeric values for all these statistics can be obtained by get_stats().
get_stats(res)
#> k 1-PAC mean_silhouette concordance area_increased Rand Jaccard
#> 2 2 0.0240 0.493 0.683 0.4350 0.501 0.501
#> 3 3 0.0203 0.347 0.589 0.3753 0.906 0.826
#> 4 4 0.1232 0.318 0.525 0.1594 0.756 0.512
#> 5 5 0.2843 0.324 0.542 0.0911 0.831 0.499
#> 6 6 0.3867 0.363 0.543 0.0538 0.890 0.571
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
#> GSM751298 1 0.833 0.6311 0.736 0.264
#> GSM751304 2 0.939 0.4875 0.356 0.644
#> GSM751305 2 0.939 0.4875 0.356 0.644
#> GSM751307 2 0.917 0.5140 0.332 0.668
#> GSM751310 1 0.913 0.5924 0.672 0.328
#> GSM751314 1 0.904 0.5829 0.680 0.320
#> GSM751316 1 0.913 0.5929 0.672 0.328
#> GSM751318 1 0.952 0.4637 0.628 0.372
#> GSM751342 1 0.969 0.4505 0.604 0.396
#> GSM751346 1 0.821 0.6129 0.744 0.256
#> GSM751347 1 0.821 0.6129 0.744 0.256
#> GSM751348 2 0.563 0.6354 0.132 0.868
#> GSM751349 2 0.563 0.6354 0.132 0.868
#> GSM751352 2 0.808 0.5961 0.248 0.752
#> GSM751353 2 0.808 0.5961 0.248 0.752
#> GSM751354 2 0.921 0.4925 0.336 0.664
#> GSM751355 2 0.921 0.4925 0.336 0.664
#> GSM751358 2 0.753 0.6288 0.216 0.784
#> GSM751359 2 0.753 0.6288 0.216 0.784
#> GSM751294 2 1.000 0.0526 0.492 0.508
#> GSM751296 1 0.795 0.6342 0.760 0.240
#> GSM751297 1 0.866 0.6038 0.712 0.288
#> GSM751299 2 0.943 0.4540 0.360 0.640
#> GSM751300 1 0.767 0.6349 0.776 0.224
#> GSM751301 2 0.998 0.2798 0.472 0.528
#> GSM751302 1 0.833 0.6040 0.736 0.264
#> GSM751303 1 0.943 0.5305 0.640 0.360
#> GSM751306 1 0.946 0.5244 0.636 0.364
#> GSM751308 1 0.999 0.1465 0.516 0.484
#> GSM751309 1 0.961 0.4887 0.616 0.384
#> GSM751311 1 0.961 0.4887 0.616 0.384
#> GSM751312 1 0.913 0.5929 0.672 0.328
#> GSM751313 1 0.788 0.6198 0.764 0.236
#> GSM751315 1 0.900 0.6001 0.684 0.316
#> GSM751317 1 0.891 0.6022 0.692 0.308
#> GSM751320 1 0.900 0.5855 0.684 0.316
#> GSM751321 1 0.904 0.5981 0.680 0.320
#> GSM751322 1 0.900 0.5855 0.684 0.316
#> GSM751324 1 0.886 0.5517 0.696 0.304
#> GSM751325 1 0.895 0.5544 0.688 0.312
#> GSM751332 1 0.925 0.5386 0.660 0.340
#> GSM751334 1 0.925 0.5386 0.660 0.340
#> GSM751339 1 0.904 0.5936 0.680 0.320
#> GSM751341 1 0.963 0.4804 0.612 0.388
#> GSM751343 1 0.952 0.4637 0.628 0.372
#> GSM751344 2 0.833 0.5844 0.264 0.736
#> GSM751345 2 0.833 0.5844 0.264 0.736
#> GSM751356 2 0.952 0.4200 0.372 0.628
#> GSM751357 2 0.952 0.4200 0.372 0.628
#> GSM751293 2 0.998 0.2798 0.472 0.528
#> GSM751295 1 0.833 0.6040 0.736 0.264
#> GSM751319 1 0.900 0.6001 0.684 0.316
#> GSM751323 1 0.895 0.6126 0.688 0.312
#> GSM751326 1 0.788 0.6310 0.764 0.236
#> GSM751327 1 0.833 0.6312 0.736 0.264
#> GSM751328 1 0.936 0.5116 0.648 0.352
#> GSM751329 1 0.833 0.6244 0.736 0.264
#> GSM751330 1 0.844 0.6241 0.728 0.272
#> GSM751331 1 0.844 0.5985 0.728 0.272
#> GSM751333 1 0.833 0.6238 0.736 0.264
#> GSM751335 1 0.839 0.6246 0.732 0.268
#> GSM751336 1 0.844 0.5985 0.728 0.272
#> GSM751337 1 0.866 0.6258 0.712 0.288
#> GSM751338 1 0.904 0.5936 0.680 0.320
#> GSM751340 1 0.973 0.3024 0.596 0.404
#> GSM751350 1 0.833 0.6040 0.736 0.264
#> GSM751351 1 0.833 0.6040 0.736 0.264
#> GSM751362 1 0.900 0.5920 0.684 0.316
#> GSM751363 1 0.966 0.4831 0.608 0.392
#> GSM751367 1 0.936 0.4809 0.648 0.352
#> GSM751368 2 0.949 0.3709 0.368 0.632
#> GSM751371 1 0.983 0.4285 0.576 0.424
#> GSM751375 2 0.605 0.6361 0.148 0.852
#> GSM751376 2 0.932 0.4664 0.348 0.652
#> GSM751378 2 0.866 0.5607 0.288 0.712
#> GSM751379 2 0.932 0.4664 0.348 0.652
#> GSM751382 2 0.574 0.6331 0.136 0.864
#> GSM751386 2 0.662 0.6315 0.172 0.828
#> GSM751388 2 0.689 0.6282 0.184 0.816
#> GSM751391 2 1.000 -0.1578 0.496 0.504
#> GSM751410 1 0.939 0.5328 0.644 0.356
#> GSM751414 1 0.969 0.4635 0.604 0.396
#> GSM751361 2 0.921 0.4466 0.336 0.664
#> GSM751365 1 0.952 0.5564 0.628 0.372
#> GSM751366 1 0.932 0.5618 0.652 0.348
#> GSM751369 1 0.991 0.3798 0.556 0.444
#> GSM751370 1 0.900 0.5920 0.684 0.316
#> GSM751372 1 0.969 0.5187 0.604 0.396
#> GSM751373 1 0.955 0.5203 0.624 0.376
#> GSM751374 2 0.932 0.4664 0.348 0.652
#> GSM751377 2 0.900 0.4650 0.316 0.684
#> GSM751380 1 0.855 0.5745 0.720 0.280
#> GSM751381 2 0.653 0.6321 0.168 0.832
#> GSM751383 2 0.697 0.6272 0.188 0.812
#> GSM751384 2 0.671 0.6291 0.176 0.824
#> GSM751385 2 0.802 0.6220 0.244 0.756
#> GSM751387 2 0.697 0.6223 0.188 0.812
#> GSM751389 1 0.839 0.5848 0.732 0.268
#> GSM751393 2 0.936 0.4770 0.352 0.648
#> GSM751394 2 0.653 0.6321 0.168 0.832
#> GSM751395 2 0.936 0.4770 0.352 0.648
#> GSM751397 2 0.615 0.6328 0.152 0.848
#> GSM751398 2 0.644 0.6329 0.164 0.836
#> GSM751404 1 0.917 0.5785 0.668 0.332
#> GSM751406 1 0.795 0.5032 0.760 0.240
#> GSM751411 1 0.955 0.4744 0.624 0.376
#> GSM751413 1 0.999 0.2738 0.516 0.484
#> GSM751415 1 0.839 0.5848 0.732 0.268
#> GSM751416 2 0.999 -0.1567 0.480 0.520
#> GSM751417 2 0.999 -0.1567 0.480 0.520
#> GSM751421 1 0.983 0.4285 0.576 0.424
#> GSM751422 1 0.983 0.4285 0.576 0.424
#> GSM751360 1 1.000 0.2584 0.508 0.492
#> GSM751364 2 0.999 -0.1567 0.480 0.520
#> GSM751390 2 0.738 0.6190 0.208 0.792
#> GSM751392 2 0.634 0.6370 0.160 0.840
#> GSM751396 2 0.653 0.6397 0.168 0.832
#> GSM751399 1 0.904 0.5309 0.680 0.320
#> GSM751400 1 0.788 0.5879 0.764 0.236
#> GSM751401 1 0.788 0.5879 0.764 0.236
#> GSM751402 1 0.788 0.5879 0.764 0.236
#> GSM751403 1 0.795 0.5885 0.760 0.240
#> GSM751405 1 0.795 0.5041 0.760 0.240
#> GSM751407 1 0.788 0.5879 0.764 0.236
#> GSM751408 1 0.833 0.5907 0.736 0.264
#> GSM751409 1 0.866 0.5762 0.712 0.288
#> GSM751412 1 0.833 0.5907 0.736 0.264
#> GSM751418 1 0.981 0.4684 0.580 0.420
#> GSM751419 1 0.981 0.4684 0.580 0.420
#> GSM751420 1 0.881 0.5253 0.700 0.300
#> GSM751425 2 0.625 0.6154 0.156 0.844
#> GSM751429 1 0.808 0.3929 0.752 0.248
#> GSM751430 2 0.900 0.5539 0.316 0.684
#> GSM751433 2 0.866 0.5234 0.288 0.712
#> GSM751437 1 0.808 0.3976 0.752 0.248
#> GSM751448 1 0.767 0.4209 0.776 0.224
#> GSM751451 2 0.861 0.5216 0.284 0.716
#> GSM751423 2 0.993 0.1841 0.452 0.548
#> GSM751424 2 0.844 0.5472 0.272 0.728
#> GSM751428 2 0.995 0.1148 0.460 0.540
#> GSM751431 2 0.866 0.5234 0.288 0.712
#> GSM751432 2 0.900 0.5539 0.316 0.684
#> GSM751434 2 0.900 0.5553 0.316 0.684
#> GSM751435 2 0.999 0.0228 0.480 0.520
#> GSM751436 2 0.866 0.5234 0.288 0.712
#> GSM751440 1 0.996 0.0838 0.536 0.464
#> GSM751444 2 0.900 0.5607 0.316 0.684
#> GSM751446 1 0.998 0.0574 0.524 0.476
#> GSM751449 2 0.833 0.6013 0.264 0.736
#> GSM751450 2 0.992 0.1851 0.448 0.552
#> GSM751452 2 0.844 0.5472 0.272 0.728
#> GSM751426 2 0.866 0.5267 0.288 0.712
#> GSM751427 2 0.995 0.1148 0.460 0.540
#> GSM751438 2 0.943 0.3683 0.360 0.640
#> GSM751439 1 1.000 -0.0309 0.504 0.496
#> GSM751441 2 0.615 0.6239 0.152 0.848
#> GSM751442 2 0.998 0.0563 0.476 0.524
#> GSM751443 1 0.788 0.4152 0.764 0.236
#> GSM751445 2 0.833 0.6013 0.264 0.736
#> GSM751447 2 0.615 0.6239 0.152 0.848
#> GSM751453 2 0.605 0.6256 0.148 0.852
#> GSM751454 2 0.605 0.6256 0.148 0.852
#> GSM751455 2 0.998 0.0563 0.476 0.524
#> GSM751456 2 0.998 0.0563 0.476 0.524
#> GSM751457 2 0.615 0.6210 0.152 0.848
#> GSM751458 2 0.615 0.6210 0.152 0.848
cbind(get_classes(res, k = 3), get_membership(res, k = 3))
#> class entropy silhouette p1 p2 p3
#> GSM751298 1 0.725 0.54281 0.704 0.100 0.196
#> GSM751304 2 0.927 -0.25126 0.156 0.428 0.416
#> GSM751305 2 0.927 -0.25126 0.156 0.428 0.416
#> GSM751307 2 0.943 -0.32792 0.180 0.448 0.372
#> GSM751310 1 0.788 0.52782 0.668 0.160 0.172
#> GSM751314 1 0.821 0.49830 0.636 0.148 0.216
#> GSM751316 1 0.767 0.53368 0.684 0.160 0.156
#> GSM751318 1 0.969 0.29804 0.460 0.268 0.272
#> GSM751342 1 0.967 0.28290 0.460 0.248 0.292
#> GSM751346 1 0.538 0.55627 0.820 0.068 0.112
#> GSM751347 1 0.538 0.55627 0.820 0.068 0.112
#> GSM751348 2 0.432 0.41796 0.088 0.868 0.044
#> GSM751349 2 0.432 0.41796 0.088 0.868 0.044
#> GSM751352 2 0.734 0.19616 0.100 0.696 0.204
#> GSM751353 2 0.734 0.19616 0.100 0.696 0.204
#> GSM751354 2 0.911 -0.24278 0.140 0.432 0.428
#> GSM751355 2 0.911 -0.24278 0.140 0.432 0.428
#> GSM751358 2 0.618 0.36191 0.120 0.780 0.100
#> GSM751359 2 0.618 0.36191 0.120 0.780 0.100
#> GSM751294 2 0.965 0.07498 0.380 0.412 0.208
#> GSM751296 1 0.668 0.55244 0.744 0.088 0.168
#> GSM751297 1 0.639 0.56463 0.768 0.112 0.120
#> GSM751299 2 0.912 0.12553 0.232 0.548 0.220
#> GSM751300 1 0.632 0.55811 0.764 0.076 0.160
#> GSM751301 3 0.992 0.47890 0.272 0.352 0.376
#> GSM751302 1 0.579 0.54809 0.796 0.068 0.136
#> GSM751303 1 0.907 0.42970 0.548 0.192 0.260
#> GSM751306 1 0.910 0.42433 0.544 0.192 0.264
#> GSM751308 1 0.936 0.12831 0.440 0.392 0.168
#> GSM751309 1 0.931 0.38305 0.516 0.208 0.276
#> GSM751311 1 0.931 0.38305 0.516 0.208 0.276
#> GSM751312 1 0.767 0.53368 0.684 0.160 0.156
#> GSM751313 1 0.563 0.56644 0.804 0.064 0.132
#> GSM751315 1 0.744 0.52408 0.700 0.136 0.164
#> GSM751317 1 0.754 0.52486 0.692 0.136 0.172
#> GSM751320 1 0.793 0.51450 0.664 0.176 0.160
#> GSM751321 1 0.749 0.52185 0.696 0.136 0.168
#> GSM751322 1 0.793 0.51450 0.664 0.176 0.160
#> GSM751324 1 0.913 0.41816 0.544 0.204 0.252
#> GSM751325 1 0.905 0.42487 0.552 0.196 0.252
#> GSM751332 1 0.893 0.43734 0.568 0.196 0.236
#> GSM751334 1 0.893 0.43734 0.568 0.196 0.236
#> GSM751339 1 0.798 0.56682 0.660 0.172 0.168
#> GSM751341 1 0.955 0.33307 0.480 0.228 0.292
#> GSM751343 1 0.969 0.29804 0.460 0.268 0.272
#> GSM751344 2 0.855 -0.12211 0.116 0.560 0.324
#> GSM751345 2 0.855 -0.12211 0.116 0.560 0.324
#> GSM751356 2 0.920 0.13665 0.248 0.536 0.216
#> GSM751357 2 0.920 0.13665 0.248 0.536 0.216
#> GSM751293 3 0.992 0.47890 0.272 0.352 0.376
#> GSM751295 1 0.579 0.54809 0.796 0.068 0.136
#> GSM751319 1 0.744 0.52408 0.700 0.136 0.164
#> GSM751323 1 0.728 0.55291 0.712 0.144 0.144
#> GSM751326 1 0.639 0.56061 0.768 0.108 0.124
#> GSM751327 1 0.637 0.56615 0.768 0.100 0.132
#> GSM751328 1 0.919 0.39705 0.536 0.208 0.256
#> GSM751329 1 0.594 0.56392 0.792 0.088 0.120
#> GSM751330 1 0.593 0.56430 0.792 0.084 0.124
#> GSM751331 1 0.605 0.54945 0.784 0.080 0.136
#> GSM751333 1 0.587 0.57081 0.796 0.088 0.116
#> GSM751335 1 0.600 0.56566 0.788 0.084 0.128
#> GSM751336 1 0.605 0.54945 0.784 0.080 0.136
#> GSM751337 1 0.772 0.57082 0.680 0.148 0.172
#> GSM751338 1 0.798 0.56682 0.660 0.172 0.168
#> GSM751340 1 0.937 0.29771 0.504 0.292 0.204
#> GSM751350 1 0.579 0.54809 0.796 0.068 0.136
#> GSM751351 1 0.579 0.54809 0.796 0.068 0.136
#> GSM751362 1 0.784 0.54116 0.664 0.208 0.128
#> GSM751363 1 0.885 0.42463 0.552 0.300 0.148
#> GSM751367 1 0.869 0.47494 0.596 0.196 0.208
#> GSM751368 2 0.918 0.04939 0.324 0.508 0.168
#> GSM751371 1 0.947 0.41364 0.488 0.300 0.212
#> GSM751375 2 0.429 0.40683 0.092 0.868 0.040
#> GSM751376 2 0.966 -0.18330 0.220 0.440 0.340
#> GSM751378 2 0.663 0.37439 0.212 0.728 0.060
#> GSM751379 2 0.966 -0.18330 0.220 0.440 0.340
#> GSM751382 2 0.364 0.41639 0.084 0.892 0.024
#> GSM751386 2 0.517 0.37983 0.092 0.832 0.076
#> GSM751388 2 0.555 0.37451 0.112 0.812 0.076
#> GSM751391 1 0.967 0.14069 0.396 0.392 0.212
#> GSM751410 1 0.873 0.53938 0.588 0.236 0.176
#> GSM751414 1 0.859 0.46063 0.588 0.268 0.144
#> GSM751361 2 0.875 0.12102 0.292 0.564 0.144
#> GSM751365 1 0.861 0.49926 0.596 0.244 0.160
#> GSM751366 1 0.830 0.51849 0.624 0.232 0.144
#> GSM751369 1 0.976 0.34295 0.428 0.332 0.240
#> GSM751370 1 0.784 0.54116 0.664 0.208 0.128
#> GSM751372 1 0.838 0.46712 0.596 0.284 0.120
#> GSM751373 1 0.853 0.49637 0.600 0.252 0.148
#> GSM751374 2 0.966 -0.18330 0.220 0.440 0.340
#> GSM751377 2 0.795 0.21385 0.260 0.636 0.104
#> GSM751380 1 0.859 0.53993 0.604 0.180 0.216
#> GSM751381 2 0.384 0.41622 0.116 0.872 0.012
#> GSM751383 2 0.554 0.37544 0.116 0.812 0.072
#> GSM751384 2 0.392 0.41835 0.120 0.868 0.012
#> GSM751385 2 0.715 0.35893 0.176 0.716 0.108
#> GSM751387 2 0.489 0.39680 0.124 0.836 0.040
#> GSM751389 1 0.797 0.54106 0.660 0.156 0.184
#> GSM751393 2 0.966 -0.18393 0.224 0.444 0.332
#> GSM751394 2 0.498 0.38340 0.096 0.840 0.064
#> GSM751395 2 0.966 -0.18393 0.224 0.444 0.332
#> GSM751397 2 0.448 0.40017 0.096 0.860 0.044
#> GSM751398 2 0.517 0.37926 0.092 0.832 0.076
#> GSM751404 1 0.822 0.53378 0.636 0.212 0.152
#> GSM751406 1 0.841 0.49411 0.616 0.152 0.232
#> GSM751411 1 0.890 0.45242 0.552 0.292 0.156
#> GSM751413 1 0.949 0.24040 0.444 0.368 0.188
#> GSM751415 1 0.797 0.54237 0.660 0.156 0.184
#> GSM751416 1 0.922 0.18786 0.448 0.400 0.152
#> GSM751417 1 0.922 0.18786 0.448 0.400 0.152
#> GSM751421 1 0.947 0.41364 0.488 0.300 0.212
#> GSM751422 1 0.947 0.41364 0.488 0.300 0.212
#> GSM751360 1 0.950 0.24494 0.440 0.372 0.188
#> GSM751364 1 0.922 0.18786 0.448 0.400 0.152
#> GSM751390 2 0.511 0.39943 0.144 0.820 0.036
#> GSM751392 2 0.451 0.39943 0.092 0.860 0.048
#> GSM751396 2 0.490 0.39031 0.092 0.844 0.064
#> GSM751399 1 0.855 0.51136 0.608 0.216 0.176
#> GSM751400 1 0.787 0.52935 0.664 0.136 0.200
#> GSM751401 1 0.787 0.52935 0.664 0.136 0.200
#> GSM751402 1 0.787 0.52935 0.664 0.136 0.200
#> GSM751403 1 0.789 0.53133 0.664 0.140 0.196
#> GSM751405 1 0.842 0.49653 0.616 0.156 0.228
#> GSM751407 1 0.787 0.52935 0.664 0.136 0.200
#> GSM751408 1 0.787 0.54525 0.668 0.156 0.176
#> GSM751409 1 0.826 0.53728 0.636 0.184 0.180
#> GSM751412 1 0.787 0.54525 0.668 0.156 0.176
#> GSM751418 1 0.890 0.45241 0.552 0.292 0.156
#> GSM751419 1 0.890 0.45241 0.552 0.292 0.156
#> GSM751420 1 0.891 0.49617 0.572 0.212 0.216
#> GSM751425 2 0.558 0.39774 0.084 0.812 0.104
#> GSM751429 1 0.856 0.43531 0.596 0.148 0.256
#> GSM751430 3 0.941 0.65374 0.176 0.380 0.444
#> GSM751433 2 0.853 0.18308 0.188 0.612 0.200
#> GSM751437 1 0.861 0.42721 0.592 0.152 0.256
#> GSM751448 1 0.832 0.44763 0.600 0.116 0.284
#> GSM751451 2 0.844 0.19749 0.192 0.620 0.188
#> GSM751423 2 0.899 0.11271 0.392 0.476 0.132
#> GSM751424 2 0.926 -0.19479 0.216 0.528 0.256
#> GSM751428 2 0.915 0.00526 0.424 0.432 0.144
#> GSM751431 2 0.848 0.19423 0.196 0.616 0.188
#> GSM751432 3 0.941 0.65374 0.176 0.380 0.444
#> GSM751434 3 0.931 0.64278 0.164 0.384 0.452
#> GSM751435 1 0.918 0.05332 0.444 0.408 0.148
#> GSM751436 2 0.853 0.18308 0.188 0.612 0.200
#> GSM751440 1 0.903 0.09259 0.476 0.388 0.136
#> GSM751444 2 0.851 0.28775 0.212 0.612 0.176
#> GSM751446 1 0.896 0.08263 0.472 0.400 0.128
#> GSM751449 2 0.767 0.34024 0.168 0.684 0.148
#> GSM751450 2 0.894 0.11176 0.392 0.480 0.128
#> GSM751452 2 0.926 -0.19479 0.216 0.528 0.256
#> GSM751426 2 0.848 0.18890 0.192 0.616 0.192
#> GSM751427 2 0.915 0.00526 0.424 0.432 0.144
#> GSM751438 2 0.890 0.26765 0.232 0.572 0.196
#> GSM751439 2 0.957 0.07423 0.380 0.424 0.196
#> GSM751441 2 0.548 0.39726 0.076 0.816 0.108
#> GSM751442 2 0.968 0.09852 0.368 0.416 0.216
#> GSM751443 1 0.846 0.44159 0.592 0.128 0.280
#> GSM751445 2 0.767 0.34024 0.168 0.684 0.148
#> GSM751447 2 0.548 0.39726 0.076 0.816 0.108
#> GSM751453 2 0.539 0.39813 0.072 0.820 0.108
#> GSM751454 2 0.539 0.39813 0.072 0.820 0.108
#> GSM751455 2 0.968 0.09852 0.368 0.416 0.216
#> GSM751456 2 0.968 0.09852 0.368 0.416 0.216
#> GSM751457 2 0.564 0.39650 0.080 0.808 0.112
#> GSM751458 2 0.564 0.39650 0.080 0.808 0.112
cbind(get_classes(res, k = 4), get_membership(res, k = 4))
#> class entropy silhouette p1 p2 p3 p4
#> GSM751298 1 0.707 0.17936 0.548 0.040 0.360 0.052
#> GSM751304 4 0.757 0.65621 0.084 0.192 0.100 0.624
#> GSM751305 4 0.757 0.65621 0.084 0.192 0.100 0.624
#> GSM751307 4 0.851 0.64346 0.156 0.188 0.112 0.544
#> GSM751310 1 0.687 0.40155 0.668 0.036 0.168 0.128
#> GSM751314 1 0.548 0.47252 0.764 0.032 0.148 0.056
#> GSM751316 1 0.690 0.39305 0.664 0.036 0.176 0.124
#> GSM751318 1 0.776 0.34668 0.612 0.116 0.184 0.088
#> GSM751342 1 0.710 0.38081 0.676 0.104 0.124 0.096
#> GSM751346 3 0.718 0.07518 0.420 0.036 0.488 0.056
#> GSM751347 3 0.718 0.07518 0.420 0.036 0.488 0.056
#> GSM751348 2 0.356 0.54005 0.036 0.880 0.056 0.028
#> GSM751349 2 0.356 0.54005 0.036 0.880 0.056 0.028
#> GSM751352 2 0.708 0.12603 0.020 0.572 0.092 0.316
#> GSM751353 2 0.708 0.12603 0.020 0.572 0.092 0.316
#> GSM751354 4 0.762 0.65582 0.068 0.192 0.124 0.616
#> GSM751355 4 0.762 0.65582 0.068 0.192 0.124 0.616
#> GSM751358 2 0.641 0.50059 0.120 0.716 0.048 0.116
#> GSM751359 2 0.641 0.50059 0.120 0.716 0.048 0.116
#> GSM751294 3 0.948 -0.04140 0.124 0.308 0.364 0.204
#> GSM751296 1 0.663 0.16890 0.568 0.036 0.364 0.032
#> GSM751297 3 0.751 0.05187 0.436 0.068 0.452 0.044
#> GSM751299 2 0.875 -0.13530 0.052 0.424 0.220 0.304
#> GSM751300 1 0.651 0.14011 0.560 0.028 0.380 0.032
#> GSM751301 4 0.911 0.28194 0.368 0.152 0.108 0.372
#> GSM751302 3 0.742 0.07021 0.412 0.040 0.480 0.068
#> GSM751303 1 0.621 0.44827 0.732 0.060 0.132 0.076
#> GSM751306 1 0.627 0.44639 0.728 0.060 0.132 0.080
#> GSM751308 3 0.979 0.10724 0.236 0.260 0.336 0.168
#> GSM751309 1 0.656 0.43571 0.712 0.076 0.128 0.084
#> GSM751311 1 0.656 0.43571 0.712 0.076 0.128 0.084
#> GSM751312 1 0.690 0.39305 0.664 0.036 0.176 0.124
#> GSM751313 1 0.726 0.01574 0.464 0.036 0.440 0.060
#> GSM751315 1 0.583 0.43021 0.736 0.020 0.156 0.088
#> GSM751317 1 0.594 0.45038 0.728 0.028 0.172 0.072
#> GSM751320 1 0.588 0.46248 0.724 0.032 0.192 0.052
#> GSM751321 1 0.589 0.43055 0.732 0.020 0.156 0.092
#> GSM751322 1 0.588 0.46248 0.724 0.032 0.192 0.052
#> GSM751324 1 0.648 0.41995 0.696 0.048 0.184 0.072
#> GSM751325 1 0.635 0.42602 0.704 0.048 0.184 0.064
#> GSM751332 1 0.628 0.41415 0.700 0.044 0.200 0.056
#> GSM751334 1 0.628 0.41415 0.700 0.044 0.200 0.056
#> GSM751339 3 0.808 0.14153 0.328 0.084 0.508 0.080
#> GSM751341 1 0.744 0.38031 0.644 0.100 0.160 0.096
#> GSM751343 1 0.776 0.34668 0.612 0.116 0.184 0.088
#> GSM751344 4 0.820 0.45544 0.076 0.356 0.092 0.476
#> GSM751345 4 0.820 0.45544 0.076 0.356 0.092 0.476
#> GSM751356 2 0.891 -0.08731 0.060 0.412 0.244 0.284
#> GSM751357 2 0.891 -0.08731 0.060 0.412 0.244 0.284
#> GSM751293 4 0.911 0.28194 0.368 0.152 0.108 0.372
#> GSM751295 3 0.742 0.07021 0.412 0.040 0.480 0.068
#> GSM751319 1 0.583 0.43021 0.736 0.020 0.156 0.088
#> GSM751323 1 0.637 0.39544 0.664 0.032 0.252 0.052
#> GSM751326 1 0.614 0.30631 0.632 0.020 0.312 0.036
#> GSM751327 1 0.660 0.29707 0.600 0.024 0.324 0.052
#> GSM751328 1 0.681 0.40799 0.684 0.064 0.168 0.084
#> GSM751329 1 0.689 0.21473 0.564 0.024 0.348 0.064
#> GSM751330 1 0.697 0.20242 0.564 0.028 0.344 0.064
#> GSM751331 3 0.756 0.03909 0.424 0.044 0.460 0.072
#> GSM751333 1 0.741 0.14488 0.528 0.052 0.360 0.060
#> GSM751335 1 0.702 0.18857 0.556 0.032 0.352 0.060
#> GSM751336 3 0.756 0.03909 0.424 0.044 0.460 0.072
#> GSM751337 1 0.737 0.09321 0.456 0.036 0.440 0.068
#> GSM751338 3 0.808 0.14153 0.328 0.084 0.508 0.080
#> GSM751340 3 0.909 0.26991 0.172 0.212 0.476 0.140
#> GSM751350 3 0.742 0.07021 0.412 0.040 0.480 0.068
#> GSM751351 3 0.742 0.07021 0.412 0.040 0.480 0.068
#> GSM751362 1 0.777 0.30846 0.576 0.076 0.260 0.088
#> GSM751363 1 0.812 0.35918 0.584 0.128 0.180 0.108
#> GSM751367 3 0.878 0.02534 0.372 0.068 0.392 0.168
#> GSM751368 2 0.929 0.05208 0.316 0.388 0.184 0.112
#> GSM751371 3 0.902 0.11011 0.308 0.136 0.436 0.120
#> GSM751375 2 0.375 0.53437 0.036 0.872 0.036 0.056
#> GSM751376 4 0.906 0.64491 0.112 0.200 0.220 0.468
#> GSM751378 2 0.619 0.48451 0.056 0.728 0.148 0.068
#> GSM751379 4 0.906 0.64491 0.112 0.200 0.220 0.468
#> GSM751382 2 0.314 0.53771 0.036 0.900 0.032 0.032
#> GSM751386 2 0.542 0.51477 0.092 0.784 0.048 0.076
#> GSM751388 2 0.573 0.52141 0.092 0.768 0.068 0.072
#> GSM751391 3 0.966 0.13758 0.232 0.220 0.380 0.168
#> GSM751410 1 0.860 -0.01595 0.408 0.112 0.392 0.088
#> GSM751414 1 0.838 0.34970 0.528 0.160 0.240 0.072
#> GSM751361 2 0.892 0.25383 0.280 0.460 0.160 0.100
#> GSM751365 1 0.877 0.21900 0.440 0.160 0.324 0.076
#> GSM751366 1 0.807 0.17301 0.448 0.136 0.380 0.036
#> GSM751369 1 0.935 0.00264 0.364 0.136 0.344 0.156
#> GSM751370 1 0.777 0.30846 0.576 0.076 0.260 0.088
#> GSM751372 1 0.847 0.30690 0.528 0.156 0.232 0.084
#> GSM751373 1 0.818 0.19964 0.460 0.156 0.348 0.036
#> GSM751374 4 0.906 0.64491 0.112 0.200 0.220 0.468
#> GSM751377 2 0.790 0.31415 0.312 0.532 0.092 0.064
#> GSM751380 3 0.720 0.35087 0.196 0.080 0.648 0.076
#> GSM751381 2 0.367 0.54451 0.052 0.876 0.040 0.032
#> GSM751383 2 0.553 0.52521 0.088 0.780 0.068 0.064
#> GSM751384 2 0.364 0.54795 0.056 0.876 0.044 0.024
#> GSM751385 2 0.751 0.44726 0.104 0.644 0.120 0.132
#> GSM751387 2 0.462 0.54381 0.076 0.828 0.060 0.036
#> GSM751389 3 0.656 0.35874 0.172 0.084 0.696 0.048
#> GSM751393 4 0.906 0.63895 0.108 0.204 0.224 0.464
#> GSM751394 2 0.523 0.51878 0.096 0.792 0.036 0.076
#> GSM751395 4 0.906 0.63895 0.108 0.204 0.224 0.464
#> GSM751397 2 0.436 0.53488 0.076 0.840 0.028 0.056
#> GSM751398 2 0.532 0.51228 0.092 0.788 0.040 0.080
#> GSM751404 3 0.799 -0.13845 0.416 0.124 0.424 0.036
#> GSM751406 3 0.630 0.40915 0.120 0.060 0.728 0.092
#> GSM751411 1 0.896 0.17157 0.432 0.192 0.296 0.080
#> GSM751413 1 0.871 0.30747 0.524 0.200 0.132 0.144
#> GSM751415 3 0.660 0.36008 0.172 0.092 0.692 0.044
#> GSM751416 1 0.853 0.29539 0.504 0.272 0.140 0.084
#> GSM751417 1 0.853 0.29539 0.504 0.272 0.140 0.084
#> GSM751421 3 0.902 0.11011 0.308 0.136 0.436 0.120
#> GSM751422 3 0.902 0.11011 0.308 0.136 0.436 0.120
#> GSM751360 1 0.869 0.30421 0.524 0.204 0.128 0.144
#> GSM751364 1 0.853 0.29539 0.504 0.272 0.140 0.084
#> GSM751390 2 0.476 0.55341 0.080 0.816 0.080 0.024
#> GSM751392 2 0.409 0.53877 0.036 0.856 0.048 0.060
#> GSM751396 2 0.469 0.52905 0.044 0.824 0.048 0.084
#> GSM751399 3 0.758 0.31642 0.188 0.148 0.612 0.052
#> GSM751400 3 0.585 0.41281 0.128 0.076 0.752 0.044
#> GSM751401 3 0.585 0.41281 0.128 0.076 0.752 0.044
#> GSM751402 3 0.585 0.41281 0.128 0.076 0.752 0.044
#> GSM751403 3 0.586 0.41191 0.124 0.080 0.752 0.044
#> GSM751405 3 0.643 0.40724 0.124 0.064 0.720 0.092
#> GSM751407 3 0.585 0.41281 0.128 0.076 0.752 0.044
#> GSM751408 3 0.648 0.34829 0.180 0.096 0.692 0.032
#> GSM751409 3 0.655 0.36412 0.172 0.100 0.692 0.036
#> GSM751412 3 0.648 0.34829 0.180 0.096 0.692 0.032
#> GSM751418 1 0.857 0.19978 0.424 0.172 0.352 0.052
#> GSM751419 1 0.857 0.19978 0.424 0.172 0.352 0.052
#> GSM751420 3 0.746 0.35110 0.180 0.100 0.636 0.084
#> GSM751425 2 0.526 0.49590 0.060 0.784 0.032 0.124
#> GSM751429 3 0.775 0.31985 0.160 0.084 0.616 0.140
#> GSM751430 4 0.791 0.59248 0.216 0.152 0.056 0.576
#> GSM751433 2 0.878 0.35637 0.284 0.472 0.092 0.152
#> GSM751437 3 0.830 0.30217 0.160 0.120 0.572 0.148
#> GSM751448 3 0.616 0.37291 0.084 0.048 0.732 0.136
#> GSM751451 2 0.878 0.35944 0.280 0.476 0.096 0.148
#> GSM751423 2 0.944 0.08783 0.228 0.372 0.288 0.112
#> GSM751424 2 0.899 0.10475 0.300 0.384 0.060 0.256
#> GSM751428 2 0.943 -0.01321 0.236 0.348 0.312 0.104
#> GSM751431 2 0.878 0.35934 0.280 0.476 0.096 0.148
#> GSM751432 4 0.791 0.59248 0.216 0.152 0.056 0.576
#> GSM751434 4 0.776 0.59300 0.220 0.156 0.044 0.580
#> GSM751435 2 0.951 -0.08026 0.260 0.328 0.304 0.108
#> GSM751436 2 0.878 0.35637 0.284 0.472 0.092 0.152
#> GSM751440 3 0.954 0.07232 0.260 0.296 0.332 0.112
#> GSM751444 2 0.871 0.39401 0.120 0.520 0.208 0.152
#> GSM751446 3 0.950 0.06839 0.256 0.304 0.332 0.108
#> GSM751449 2 0.781 0.44833 0.084 0.608 0.180 0.128
#> GSM751450 2 0.943 0.08746 0.224 0.376 0.288 0.112
#> GSM751452 2 0.899 0.10475 0.300 0.384 0.060 0.256
#> GSM751426 2 0.882 0.35461 0.276 0.472 0.092 0.160
#> GSM751427 2 0.943 -0.01321 0.236 0.348 0.312 0.104
#> GSM751438 2 0.807 0.33307 0.060 0.536 0.280 0.124
#> GSM751439 3 0.907 -0.02112 0.136 0.336 0.408 0.120
#> GSM751441 2 0.538 0.50176 0.056 0.776 0.036 0.132
#> GSM751442 3 0.910 -0.06610 0.124 0.372 0.372 0.132
#> GSM751443 3 0.614 0.37176 0.072 0.060 0.736 0.132
#> GSM751445 2 0.781 0.44833 0.084 0.608 0.180 0.128
#> GSM751447 2 0.538 0.50176 0.056 0.776 0.036 0.132
#> GSM751453 2 0.530 0.50344 0.052 0.780 0.036 0.132
#> GSM751454 2 0.530 0.50344 0.052 0.780 0.036 0.132
#> GSM751455 3 0.910 -0.06610 0.124 0.372 0.372 0.132
#> GSM751456 2 0.910 0.02565 0.124 0.372 0.372 0.132
#> GSM751457 2 0.538 0.49620 0.056 0.776 0.036 0.132
#> GSM751458 2 0.538 0.49620 0.056 0.776 0.036 0.132
cbind(get_classes(res, k = 5), get_membership(res, k = 5))
#> class entropy silhouette p1 p2 p3 p4 p5
#> GSM751298 1 0.605 0.30823 0.616 0.024 0.056 0.288 0.016
#> GSM751304 5 0.613 0.71263 0.112 0.064 0.080 0.036 0.708
#> GSM751305 5 0.613 0.71263 0.112 0.064 0.080 0.036 0.708
#> GSM751307 5 0.706 0.67188 0.168 0.076 0.048 0.080 0.628
#> GSM751310 1 0.646 0.18034 0.536 0.000 0.028 0.328 0.108
#> GSM751314 4 0.545 0.14570 0.380 0.000 0.020 0.568 0.032
#> GSM751316 1 0.643 0.19233 0.548 0.000 0.028 0.316 0.108
#> GSM751318 4 0.550 0.37455 0.100 0.056 0.060 0.752 0.032
#> GSM751342 4 0.485 0.38811 0.092 0.036 0.040 0.792 0.040
#> GSM751346 1 0.250 0.44708 0.912 0.016 0.048 0.012 0.012
#> GSM751347 1 0.250 0.44708 0.912 0.016 0.048 0.012 0.012
#> GSM751348 2 0.432 0.54676 0.024 0.824 0.044 0.036 0.072
#> GSM751349 2 0.432 0.54676 0.024 0.824 0.044 0.036 0.072
#> GSM751352 2 0.684 0.17182 0.096 0.492 0.044 0.004 0.364
#> GSM751353 2 0.684 0.17182 0.096 0.492 0.044 0.004 0.364
#> GSM751354 5 0.604 0.71464 0.112 0.064 0.068 0.040 0.716
#> GSM751355 5 0.604 0.71464 0.112 0.064 0.068 0.040 0.716
#> GSM751358 2 0.623 0.51326 0.008 0.680 0.080 0.116 0.116
#> GSM751359 2 0.623 0.51326 0.008 0.680 0.080 0.116 0.116
#> GSM751294 3 0.968 0.03270 0.140 0.228 0.268 0.112 0.252
#> GSM751296 1 0.551 0.34413 0.664 0.016 0.056 0.256 0.008
#> GSM751297 1 0.492 0.41665 0.788 0.028 0.068 0.080 0.036
#> GSM751299 2 0.878 -0.08232 0.112 0.344 0.164 0.044 0.336
#> GSM751300 1 0.522 0.36383 0.692 0.008 0.060 0.232 0.008
#> GSM751301 4 0.827 -0.11903 0.100 0.092 0.048 0.392 0.368
#> GSM751302 1 0.174 0.45071 0.944 0.008 0.032 0.008 0.008
#> GSM751303 4 0.563 0.30127 0.248 0.012 0.028 0.668 0.044
#> GSM751306 4 0.556 0.30079 0.248 0.012 0.028 0.672 0.040
#> GSM751308 4 0.986 -0.14127 0.144 0.192 0.224 0.268 0.172
#> GSM751309 4 0.532 0.34590 0.204 0.012 0.028 0.712 0.044
#> GSM751311 4 0.532 0.34590 0.204 0.012 0.028 0.712 0.044
#> GSM751312 1 0.643 0.19233 0.548 0.000 0.028 0.316 0.108
#> GSM751313 1 0.324 0.44037 0.868 0.008 0.036 0.080 0.008
#> GSM751315 1 0.582 0.15057 0.536 0.000 0.016 0.388 0.060
#> GSM751317 1 0.569 0.05266 0.508 0.000 0.024 0.432 0.036
#> GSM751320 4 0.525 0.16575 0.392 0.000 0.020 0.568 0.020
#> GSM751321 1 0.583 0.14671 0.532 0.000 0.016 0.392 0.060
#> GSM751322 4 0.525 0.16575 0.392 0.000 0.020 0.568 0.020
#> GSM751324 4 0.550 0.34664 0.192 0.012 0.056 0.708 0.032
#> GSM751325 4 0.541 0.33539 0.216 0.012 0.044 0.700 0.028
#> GSM751332 4 0.550 0.25228 0.308 0.024 0.024 0.632 0.012
#> GSM751334 4 0.550 0.25228 0.308 0.024 0.024 0.632 0.012
#> GSM751339 1 0.827 -0.25481 0.368 0.016 0.284 0.260 0.072
#> GSM751341 4 0.551 0.36342 0.156 0.040 0.036 0.732 0.036
#> GSM751343 4 0.550 0.37455 0.100 0.056 0.060 0.752 0.032
#> GSM751344 5 0.715 0.46876 0.108 0.248 0.024 0.052 0.568
#> GSM751345 5 0.715 0.46876 0.108 0.248 0.024 0.052 0.568
#> GSM751356 2 0.910 -0.04426 0.100 0.320 0.192 0.072 0.316
#> GSM751357 2 0.910 -0.04426 0.100 0.320 0.192 0.072 0.316
#> GSM751293 4 0.827 -0.11903 0.100 0.092 0.048 0.392 0.368
#> GSM751295 1 0.174 0.45071 0.944 0.008 0.032 0.008 0.008
#> GSM751319 1 0.582 0.15057 0.536 0.000 0.016 0.388 0.060
#> GSM751323 1 0.549 0.01767 0.492 0.004 0.016 0.464 0.024
#> GSM751326 1 0.523 0.17792 0.572 0.008 0.020 0.392 0.008
#> GSM751327 1 0.534 0.20088 0.596 0.008 0.020 0.360 0.016
#> GSM751328 4 0.581 0.30441 0.256 0.036 0.024 0.656 0.028
#> GSM751329 1 0.435 0.36751 0.744 0.012 0.008 0.224 0.012
#> GSM751330 1 0.419 0.38041 0.764 0.012 0.008 0.204 0.012
#> GSM751331 1 0.148 0.45074 0.956 0.012 0.004 0.016 0.012
#> GSM751333 1 0.362 0.40810 0.816 0.016 0.004 0.156 0.008
#> GSM751335 1 0.402 0.38431 0.776 0.012 0.008 0.196 0.008
#> GSM751336 1 0.148 0.45074 0.956 0.012 0.004 0.016 0.012
#> GSM751337 4 0.752 0.08730 0.344 0.012 0.244 0.380 0.020
#> GSM751338 1 0.827 -0.25481 0.368 0.016 0.284 0.260 0.072
#> GSM751340 3 0.965 0.29342 0.216 0.136 0.324 0.136 0.188
#> GSM751350 1 0.186 0.45126 0.940 0.008 0.032 0.012 0.008
#> GSM751351 1 0.186 0.45126 0.940 0.008 0.032 0.012 0.008
#> GSM751362 1 0.772 0.17101 0.532 0.072 0.048 0.252 0.096
#> GSM751363 1 0.866 -0.04818 0.380 0.116 0.060 0.336 0.108
#> GSM751367 1 0.793 0.24221 0.540 0.036 0.164 0.112 0.148
#> GSM751368 2 0.927 -0.12195 0.172 0.320 0.120 0.304 0.084
#> GSM751371 4 0.870 -0.11197 0.168 0.044 0.324 0.364 0.100
#> GSM751375 2 0.467 0.54908 0.032 0.804 0.040 0.040 0.084
#> GSM751376 5 0.731 0.65711 0.064 0.080 0.200 0.060 0.596
#> GSM751378 2 0.670 0.50080 0.064 0.656 0.164 0.048 0.068
#> GSM751379 5 0.731 0.65711 0.064 0.080 0.200 0.060 0.596
#> GSM751382 2 0.407 0.55121 0.032 0.840 0.036 0.032 0.060
#> GSM751386 2 0.523 0.53517 0.040 0.772 0.048 0.052 0.088
#> GSM751388 2 0.567 0.53847 0.056 0.748 0.056 0.076 0.064
#> GSM751391 3 0.930 0.15248 0.108 0.124 0.344 0.288 0.136
#> GSM751410 1 0.883 -0.02782 0.372 0.056 0.240 0.252 0.080
#> GSM751414 4 0.860 0.11293 0.348 0.136 0.064 0.372 0.080
#> GSM751361 2 0.880 0.11735 0.128 0.416 0.112 0.272 0.072
#> GSM751365 1 0.885 -0.07226 0.380 0.140 0.124 0.300 0.056
#> GSM751366 4 0.841 0.18176 0.328 0.092 0.184 0.372 0.024
#> GSM751369 4 0.921 0.03859 0.232 0.056 0.276 0.308 0.128
#> GSM751370 1 0.772 0.17101 0.532 0.072 0.048 0.252 0.096
#> GSM751372 1 0.840 0.04881 0.468 0.136 0.064 0.252 0.080
#> GSM751373 4 0.844 0.19258 0.328 0.112 0.156 0.380 0.024
#> GSM751374 5 0.731 0.65711 0.064 0.080 0.200 0.060 0.596
#> GSM751377 2 0.811 0.26448 0.168 0.512 0.056 0.196 0.068
#> GSM751380 3 0.774 0.55962 0.224 0.028 0.504 0.196 0.048
#> GSM751381 2 0.379 0.55624 0.044 0.856 0.028 0.032 0.040
#> GSM751383 2 0.548 0.54095 0.056 0.760 0.052 0.072 0.060
#> GSM751384 2 0.379 0.55814 0.044 0.856 0.032 0.036 0.032
#> GSM751385 2 0.771 0.45518 0.056 0.576 0.140 0.084 0.144
#> GSM751387 2 0.460 0.55568 0.052 0.812 0.040 0.060 0.036
#> GSM751389 3 0.774 0.58633 0.236 0.060 0.500 0.184 0.020
#> GSM751393 5 0.750 0.65504 0.068 0.096 0.192 0.060 0.584
#> GSM751394 2 0.525 0.53604 0.052 0.768 0.032 0.052 0.096
#> GSM751395 5 0.750 0.65504 0.068 0.096 0.192 0.060 0.584
#> GSM751397 2 0.436 0.54914 0.044 0.824 0.024 0.048 0.060
#> GSM751398 2 0.528 0.53456 0.044 0.768 0.040 0.056 0.092
#> GSM751404 4 0.847 0.14405 0.320 0.084 0.220 0.352 0.024
#> GSM751406 3 0.698 0.63158 0.200 0.020 0.608 0.096 0.076
#> GSM751411 1 0.934 -0.05538 0.344 0.184 0.148 0.248 0.076
#> GSM751413 4 0.904 0.15504 0.296 0.144 0.072 0.364 0.124
#> GSM751415 3 0.773 0.58742 0.236 0.064 0.496 0.188 0.016
#> GSM751416 4 0.903 0.14038 0.284 0.252 0.068 0.316 0.080
#> GSM751417 4 0.903 0.14038 0.284 0.252 0.068 0.316 0.080
#> GSM751421 4 0.870 -0.11197 0.168 0.044 0.324 0.364 0.100
#> GSM751422 4 0.870 -0.11197 0.168 0.044 0.324 0.364 0.100
#> GSM751360 4 0.906 0.15723 0.296 0.140 0.076 0.364 0.124
#> GSM751364 4 0.903 0.14038 0.284 0.252 0.068 0.316 0.080
#> GSM751390 2 0.467 0.56374 0.068 0.804 0.052 0.056 0.020
#> GSM751392 2 0.491 0.55204 0.036 0.792 0.056 0.040 0.076
#> GSM751396 2 0.536 0.54176 0.036 0.760 0.052 0.048 0.104
#> GSM751399 3 0.847 0.50484 0.216 0.128 0.448 0.180 0.028
#> GSM751400 3 0.726 0.65433 0.240 0.052 0.564 0.116 0.028
#> GSM751401 3 0.726 0.65433 0.240 0.052 0.564 0.116 0.028
#> GSM751402 3 0.726 0.65433 0.240 0.052 0.564 0.116 0.028
#> GSM751403 3 0.734 0.65141 0.248 0.052 0.552 0.120 0.028
#> GSM751405 3 0.706 0.62992 0.200 0.024 0.604 0.096 0.076
#> GSM751407 3 0.726 0.65433 0.240 0.052 0.564 0.116 0.028
#> GSM751408 3 0.769 0.56743 0.252 0.076 0.488 0.176 0.008
#> GSM751409 3 0.790 0.59806 0.220 0.084 0.500 0.176 0.020
#> GSM751412 3 0.769 0.56743 0.252 0.076 0.488 0.176 0.008
#> GSM751418 4 0.886 0.17592 0.312 0.152 0.156 0.344 0.036
#> GSM751419 4 0.886 0.17592 0.312 0.152 0.156 0.344 0.036
#> GSM751420 3 0.799 0.48932 0.168 0.032 0.496 0.232 0.072
#> GSM751425 2 0.599 0.50352 0.032 0.708 0.056 0.060 0.144
#> GSM751429 3 0.740 0.26100 0.372 0.048 0.460 0.028 0.092
#> GSM751430 5 0.681 0.61134 0.116 0.064 0.024 0.160 0.636
#> GSM751433 2 0.814 0.31271 0.076 0.432 0.064 0.344 0.084
#> GSM751437 3 0.776 0.26907 0.336 0.080 0.464 0.032 0.088
#> GSM751448 3 0.602 0.46290 0.196 0.024 0.668 0.016 0.096
#> GSM751451 2 0.817 0.31536 0.076 0.436 0.068 0.336 0.084
#> GSM751423 2 0.915 0.10570 0.288 0.352 0.112 0.168 0.080
#> GSM751424 2 0.889 0.13997 0.104 0.336 0.040 0.276 0.244
#> GSM751428 1 0.910 -0.04632 0.332 0.320 0.124 0.152 0.072
#> GSM751431 2 0.826 0.31350 0.080 0.432 0.076 0.332 0.080
#> GSM751432 5 0.681 0.61134 0.116 0.064 0.024 0.160 0.636
#> GSM751434 5 0.683 0.61167 0.108 0.068 0.028 0.156 0.640
#> GSM751435 1 0.923 0.00627 0.352 0.284 0.128 0.148 0.088
#> GSM751436 2 0.814 0.31271 0.076 0.432 0.064 0.344 0.084
#> GSM751440 1 0.909 0.01964 0.348 0.280 0.128 0.188 0.056
#> GSM751444 2 0.853 0.42699 0.068 0.492 0.168 0.148 0.124
#> GSM751446 1 0.909 0.01249 0.348 0.288 0.128 0.176 0.060
#> GSM751449 2 0.780 0.46932 0.044 0.560 0.172 0.112 0.112
#> GSM751450 2 0.913 0.10741 0.288 0.356 0.112 0.164 0.080
#> GSM751452 2 0.889 0.13997 0.104 0.336 0.040 0.276 0.244
#> GSM751426 2 0.838 0.32254 0.080 0.432 0.076 0.316 0.096
#> GSM751427 1 0.910 -0.04632 0.332 0.320 0.124 0.152 0.072
#> GSM751438 2 0.795 0.35471 0.064 0.500 0.276 0.064 0.096
#> GSM751439 2 0.921 0.10937 0.156 0.332 0.300 0.140 0.072
#> GSM751441 2 0.598 0.51158 0.044 0.716 0.056 0.056 0.128
#> GSM751442 2 0.900 0.13649 0.152 0.368 0.296 0.112 0.072
#> GSM751443 3 0.611 0.45877 0.196 0.036 0.668 0.016 0.084
#> GSM751445 2 0.780 0.46932 0.044 0.560 0.172 0.112 0.112
#> GSM751447 2 0.598 0.51158 0.044 0.716 0.056 0.056 0.128
#> GSM751453 2 0.592 0.51395 0.044 0.720 0.052 0.056 0.128
#> GSM751454 2 0.592 0.51395 0.044 0.720 0.052 0.056 0.128
#> GSM751455 2 0.900 0.13649 0.152 0.368 0.296 0.112 0.072
#> GSM751456 2 0.900 0.13649 0.152 0.368 0.296 0.112 0.072
#> GSM751457 2 0.611 0.50242 0.032 0.700 0.068 0.056 0.144
#> GSM751458 2 0.611 0.50242 0.032 0.700 0.068 0.056 0.144
cbind(get_classes(res, k = 6), get_membership(res, k = 6))
#> class entropy silhouette p1 p2 p3 p4 p5 p6
#> GSM751298 1 0.624 3.62e-01 0.584 0.044 0.052 0.280 0.016 0.024
#> GSM751304 6 0.553 6.36e-01 0.092 0.040 0.064 0.028 0.044 0.732
#> GSM751305 6 0.553 6.36e-01 0.092 0.040 0.064 0.028 0.044 0.732
#> GSM751307 6 0.684 5.92e-01 0.140 0.056 0.052 0.072 0.052 0.628
#> GSM751310 1 0.650 2.49e-01 0.492 0.036 0.024 0.340 0.000 0.108
#> GSM751314 4 0.528 1.05e-01 0.344 0.016 0.020 0.584 0.000 0.036
#> GSM751316 1 0.653 2.61e-01 0.496 0.036 0.028 0.336 0.000 0.104
#> GSM751318 4 0.555 3.76e-01 0.076 0.088 0.076 0.720 0.028 0.012
#> GSM751342 4 0.421 3.91e-01 0.048 0.032 0.044 0.820 0.020 0.036
#> GSM751346 1 0.306 5.24e-01 0.876 0.020 0.060 0.012 0.012 0.020
#> GSM751347 1 0.306 5.24e-01 0.876 0.020 0.060 0.012 0.012 0.020
#> GSM751348 5 0.415 5.82e-01 0.016 0.052 0.020 0.040 0.820 0.052
#> GSM751349 5 0.415 5.82e-01 0.016 0.052 0.020 0.040 0.820 0.052
#> GSM751352 5 0.764 1.74e-02 0.088 0.148 0.044 0.000 0.380 0.340
#> GSM751353 5 0.764 1.74e-02 0.088 0.148 0.044 0.000 0.380 0.340
#> GSM751354 6 0.551 6.36e-01 0.096 0.048 0.056 0.024 0.044 0.732
#> GSM751355 6 0.551 6.36e-01 0.096 0.048 0.056 0.024 0.044 0.732
#> GSM751358 5 0.686 5.13e-01 0.012 0.152 0.040 0.100 0.600 0.096
#> GSM751359 5 0.686 5.13e-01 0.012 0.152 0.040 0.100 0.600 0.096
#> GSM751294 3 0.919 -2.69e-02 0.096 0.124 0.332 0.064 0.144 0.240
#> GSM751296 1 0.568 4.06e-01 0.636 0.048 0.048 0.248 0.008 0.012
#> GSM751297 1 0.508 4.90e-01 0.764 0.048 0.060 0.068 0.020 0.040
#> GSM751299 6 0.877 2.30e-01 0.096 0.128 0.192 0.012 0.256 0.316
#> GSM751300 1 0.530 4.31e-01 0.668 0.048 0.048 0.224 0.000 0.012
#> GSM751301 4 0.813 -6.46e-02 0.092 0.108 0.028 0.360 0.056 0.356
#> GSM751302 1 0.190 5.28e-01 0.924 0.020 0.048 0.000 0.004 0.004
#> GSM751303 4 0.527 2.90e-01 0.208 0.036 0.028 0.684 0.000 0.044
#> GSM751306 4 0.520 2.90e-01 0.208 0.036 0.028 0.688 0.000 0.040
#> GSM751308 3 0.964 1.17e-01 0.096 0.124 0.268 0.228 0.128 0.156
#> GSM751309 4 0.490 3.35e-01 0.168 0.024 0.040 0.728 0.000 0.040
#> GSM751311 4 0.490 3.35e-01 0.168 0.024 0.040 0.728 0.000 0.040
#> GSM751312 1 0.653 2.61e-01 0.496 0.036 0.028 0.336 0.000 0.104
#> GSM751313 1 0.327 5.18e-01 0.856 0.020 0.052 0.064 0.004 0.004
#> GSM751315 1 0.580 2.28e-01 0.496 0.032 0.012 0.404 0.000 0.056
#> GSM751317 1 0.560 1.32e-01 0.476 0.024 0.024 0.444 0.000 0.032
#> GSM751320 4 0.545 1.33e-01 0.356 0.032 0.032 0.564 0.000 0.016
#> GSM751321 1 0.580 2.23e-01 0.492 0.032 0.012 0.408 0.000 0.056
#> GSM751322 4 0.545 1.33e-01 0.356 0.032 0.032 0.564 0.000 0.016
#> GSM751324 4 0.565 3.44e-01 0.164 0.068 0.068 0.680 0.004 0.016
#> GSM751325 4 0.573 3.31e-01 0.196 0.064 0.060 0.660 0.004 0.016
#> GSM751332 4 0.531 2.34e-01 0.292 0.044 0.028 0.624 0.008 0.004
#> GSM751334 4 0.531 2.34e-01 0.292 0.044 0.028 0.624 0.008 0.004
#> GSM751339 3 0.819 3.03e-01 0.300 0.076 0.344 0.196 0.004 0.080
#> GSM751341 4 0.512 3.62e-01 0.112 0.040 0.036 0.752 0.024 0.036
#> GSM751343 4 0.555 3.76e-01 0.076 0.088 0.076 0.720 0.028 0.012
#> GSM751344 6 0.730 4.97e-01 0.096 0.088 0.036 0.032 0.188 0.560
#> GSM751345 6 0.730 4.97e-01 0.096 0.088 0.036 0.032 0.188 0.560
#> GSM751356 6 0.886 2.16e-01 0.080 0.152 0.224 0.016 0.228 0.300
#> GSM751357 6 0.886 2.16e-01 0.080 0.152 0.224 0.016 0.228 0.300
#> GSM751293 4 0.813 -6.46e-02 0.092 0.108 0.028 0.360 0.056 0.356
#> GSM751295 1 0.190 5.28e-01 0.924 0.020 0.048 0.000 0.004 0.004
#> GSM751319 1 0.580 2.28e-01 0.496 0.032 0.012 0.404 0.000 0.056
#> GSM751323 1 0.536 5.46e-02 0.472 0.028 0.032 0.460 0.000 0.008
#> GSM751326 1 0.513 2.24e-01 0.548 0.032 0.024 0.392 0.000 0.004
#> GSM751327 1 0.505 2.50e-01 0.580 0.032 0.024 0.360 0.000 0.004
#> GSM751328 4 0.525 2.98e-01 0.228 0.036 0.024 0.680 0.016 0.016
#> GSM751329 1 0.402 4.41e-01 0.756 0.024 0.012 0.200 0.004 0.004
#> GSM751330 1 0.386 4.56e-01 0.776 0.024 0.012 0.180 0.004 0.004
#> GSM751331 1 0.188 5.25e-01 0.932 0.004 0.036 0.012 0.008 0.008
#> GSM751333 1 0.341 4.88e-01 0.824 0.012 0.016 0.136 0.008 0.004
#> GSM751335 1 0.384 4.60e-01 0.780 0.020 0.016 0.176 0.004 0.004
#> GSM751336 1 0.188 5.25e-01 0.932 0.004 0.036 0.012 0.008 0.008
#> GSM751337 4 0.752 -1.76e-02 0.276 0.088 0.292 0.332 0.000 0.012
#> GSM751338 3 0.819 3.03e-01 0.300 0.076 0.344 0.196 0.004 0.080
#> GSM751340 3 0.899 2.47e-01 0.168 0.100 0.384 0.088 0.068 0.192
#> GSM751350 1 0.182 5.28e-01 0.928 0.016 0.048 0.000 0.004 0.004
#> GSM751351 1 0.182 5.28e-01 0.928 0.016 0.048 0.000 0.004 0.004
#> GSM751362 1 0.786 2.35e-01 0.496 0.056 0.076 0.236 0.052 0.084
#> GSM751363 1 0.866 8.68e-05 0.336 0.092 0.072 0.336 0.076 0.088
#> GSM751367 1 0.791 2.84e-01 0.512 0.080 0.156 0.084 0.028 0.140
#> GSM751368 4 0.930 1.22e-01 0.128 0.112 0.128 0.308 0.256 0.068
#> GSM751371 3 0.831 3.03e-01 0.092 0.196 0.380 0.260 0.020 0.052
#> GSM751375 5 0.401 5.90e-01 0.024 0.044 0.016 0.028 0.828 0.060
#> GSM751376 6 0.601 5.72e-01 0.032 0.040 0.192 0.044 0.032 0.660
#> GSM751378 5 0.585 4.89e-01 0.040 0.132 0.112 0.016 0.680 0.020
#> GSM751379 6 0.601 5.72e-01 0.032 0.040 0.192 0.044 0.032 0.660
#> GSM751382 5 0.329 5.94e-01 0.024 0.032 0.008 0.028 0.868 0.040
#> GSM751386 5 0.511 5.73e-01 0.040 0.056 0.024 0.052 0.764 0.064
#> GSM751388 5 0.593 5.47e-01 0.052 0.064 0.060 0.064 0.712 0.048
#> GSM751391 3 0.873 2.83e-01 0.060 0.256 0.360 0.188 0.076 0.060
#> GSM751410 1 0.874 -7.33e-02 0.312 0.084 0.284 0.216 0.044 0.060
#> GSM751414 4 0.853 6.15e-02 0.304 0.056 0.100 0.376 0.096 0.068
#> GSM751361 5 0.898 2.64e-02 0.108 0.120 0.108 0.272 0.340 0.052
#> GSM751365 1 0.892 -6.94e-02 0.312 0.072 0.224 0.248 0.104 0.040
#> GSM751366 4 0.837 1.17e-01 0.264 0.068 0.252 0.336 0.056 0.024
#> GSM751369 3 0.908 1.33e-01 0.172 0.152 0.292 0.256 0.028 0.100
#> GSM751370 1 0.786 2.35e-01 0.496 0.056 0.076 0.236 0.052 0.084
#> GSM751372 1 0.850 9.53e-02 0.420 0.068 0.084 0.256 0.100 0.072
#> GSM751373 4 0.849 1.63e-01 0.264 0.072 0.220 0.348 0.072 0.024
#> GSM751374 6 0.601 5.72e-01 0.032 0.040 0.192 0.044 0.032 0.660
#> GSM751377 5 0.812 2.47e-01 0.144 0.080 0.044 0.200 0.476 0.056
#> GSM751380 3 0.653 5.42e-01 0.136 0.072 0.628 0.120 0.012 0.032
#> GSM751381 5 0.293 5.98e-01 0.036 0.020 0.012 0.024 0.888 0.020
#> GSM751383 5 0.570 5.49e-01 0.052 0.064 0.056 0.056 0.728 0.044
#> GSM751384 5 0.284 5.96e-01 0.036 0.016 0.016 0.024 0.892 0.016
#> GSM751385 5 0.750 4.57e-01 0.040 0.136 0.108 0.048 0.564 0.104
#> GSM751387 5 0.450 5.72e-01 0.052 0.028 0.056 0.048 0.800 0.016
#> GSM751389 3 0.572 5.40e-01 0.124 0.036 0.696 0.100 0.032 0.012
#> GSM751393 6 0.629 5.70e-01 0.036 0.036 0.188 0.040 0.056 0.644
#> GSM751394 5 0.497 5.79e-01 0.044 0.048 0.012 0.060 0.768 0.068
#> GSM751395 6 0.629 5.70e-01 0.036 0.036 0.188 0.040 0.056 0.644
#> GSM751397 5 0.379 5.93e-01 0.036 0.028 0.008 0.048 0.840 0.040
#> GSM751398 5 0.517 5.71e-01 0.040 0.060 0.016 0.060 0.756 0.068
#> GSM751404 3 0.831 -8.04e-02 0.252 0.068 0.304 0.304 0.048 0.024
#> GSM751406 3 0.514 5.45e-01 0.100 0.016 0.748 0.048 0.020 0.068
#> GSM751411 1 0.936 -5.35e-02 0.288 0.088 0.192 0.220 0.152 0.060
#> GSM751413 4 0.922 1.18e-01 0.248 0.144 0.088 0.328 0.080 0.112
#> GSM751415 3 0.575 5.40e-01 0.128 0.036 0.692 0.096 0.040 0.008
#> GSM751416 4 0.902 1.26e-01 0.248 0.088 0.068 0.328 0.196 0.072
#> GSM751417 4 0.902 1.26e-01 0.248 0.088 0.068 0.328 0.196 0.072
#> GSM751421 3 0.831 3.03e-01 0.092 0.196 0.380 0.260 0.020 0.052
#> GSM751422 3 0.831 3.03e-01 0.092 0.196 0.380 0.260 0.020 0.052
#> GSM751360 4 0.924 1.24e-01 0.240 0.140 0.096 0.332 0.080 0.112
#> GSM751364 4 0.902 1.26e-01 0.248 0.088 0.068 0.328 0.196 0.072
#> GSM751390 5 0.453 5.66e-01 0.060 0.032 0.072 0.036 0.792 0.008
#> GSM751392 5 0.466 5.86e-01 0.028 0.044 0.044 0.028 0.792 0.064
#> GSM751396 5 0.523 5.78e-01 0.028 0.044 0.044 0.040 0.752 0.092
#> GSM751399 3 0.731 4.81e-01 0.136 0.056 0.576 0.112 0.096 0.024
#> GSM751400 3 0.495 5.76e-01 0.124 0.028 0.756 0.040 0.032 0.020
#> GSM751401 3 0.495 5.76e-01 0.124 0.028 0.756 0.040 0.032 0.020
#> GSM751402 3 0.495 5.76e-01 0.124 0.028 0.756 0.040 0.032 0.020
#> GSM751403 3 0.510 5.76e-01 0.132 0.028 0.744 0.044 0.032 0.020
#> GSM751405 3 0.526 5.44e-01 0.104 0.016 0.740 0.048 0.024 0.068
#> GSM751407 3 0.495 5.76e-01 0.124 0.028 0.756 0.040 0.032 0.020
#> GSM751408 3 0.621 5.23e-01 0.152 0.048 0.652 0.096 0.044 0.008
#> GSM751409 3 0.601 5.51e-01 0.120 0.052 0.680 0.088 0.052 0.008
#> GSM751412 3 0.621 5.23e-01 0.152 0.048 0.652 0.096 0.044 0.008
#> GSM751418 4 0.890 1.65e-01 0.224 0.084 0.236 0.320 0.104 0.032
#> GSM751419 4 0.890 1.65e-01 0.224 0.084 0.236 0.320 0.104 0.032
#> GSM751420 3 0.719 5.09e-01 0.080 0.120 0.584 0.140 0.024 0.052
#> GSM751425 5 0.575 5.13e-01 0.000 0.228 0.028 0.032 0.636 0.076
#> GSM751429 3 0.811 2.16e-01 0.252 0.248 0.360 0.012 0.036 0.092
#> GSM751430 6 0.597 5.25e-01 0.104 0.024 0.024 0.152 0.028 0.668
#> GSM751433 2 0.779 4.75e-01 0.044 0.332 0.016 0.280 0.296 0.032
#> GSM751437 3 0.839 1.92e-01 0.208 0.264 0.356 0.012 0.076 0.084
#> GSM751448 3 0.674 3.71e-01 0.116 0.176 0.580 0.004 0.020 0.104
#> GSM751451 2 0.769 4.76e-01 0.040 0.344 0.016 0.276 0.296 0.028
#> GSM751423 2 0.857 5.38e-01 0.184 0.376 0.064 0.116 0.236 0.024
#> GSM751424 4 0.893 -2.38e-01 0.076 0.128 0.028 0.292 0.260 0.216
#> GSM751428 2 0.855 5.62e-01 0.220 0.364 0.076 0.104 0.220 0.016
#> GSM751431 2 0.763 4.76e-01 0.040 0.340 0.012 0.284 0.296 0.028
#> GSM751432 6 0.597 5.25e-01 0.104 0.024 0.024 0.152 0.028 0.668
#> GSM751434 6 0.598 5.25e-01 0.100 0.036 0.016 0.152 0.028 0.668
#> GSM751435 2 0.886 5.38e-01 0.240 0.336 0.080 0.112 0.200 0.032
#> GSM751436 2 0.779 4.75e-01 0.044 0.332 0.016 0.280 0.296 0.032
#> GSM751440 2 0.841 5.62e-01 0.244 0.368 0.064 0.140 0.176 0.008
#> GSM751444 2 0.811 3.23e-01 0.032 0.364 0.116 0.076 0.356 0.056
#> GSM751446 2 0.839 5.66e-01 0.244 0.372 0.064 0.132 0.180 0.008
#> GSM751449 5 0.736 -1.96e-01 0.012 0.364 0.116 0.040 0.416 0.052
#> GSM751450 2 0.859 5.43e-01 0.184 0.372 0.064 0.120 0.236 0.024
#> GSM751452 4 0.893 -2.38e-01 0.076 0.128 0.028 0.292 0.260 0.216
#> GSM751426 2 0.777 4.68e-01 0.040 0.336 0.012 0.272 0.300 0.040
#> GSM751427 2 0.855 5.62e-01 0.220 0.364 0.076 0.104 0.220 0.016
#> GSM751438 5 0.777 2.35e-02 0.024 0.232 0.264 0.028 0.404 0.048
#> GSM751439 2 0.877 4.59e-01 0.108 0.312 0.260 0.084 0.216 0.020
#> GSM751441 5 0.617 5.18e-01 0.008 0.220 0.048 0.032 0.624 0.068
#> GSM751442 2 0.875 4.44e-01 0.100 0.276 0.272 0.072 0.256 0.024
#> GSM751443 3 0.687 3.65e-01 0.112 0.188 0.572 0.004 0.032 0.092
#> GSM751445 5 0.736 -1.96e-01 0.012 0.364 0.116 0.040 0.416 0.052
#> GSM751447 5 0.617 5.18e-01 0.008 0.220 0.048 0.032 0.624 0.068
#> GSM751453 5 0.617 5.17e-01 0.008 0.220 0.048 0.032 0.624 0.068
#> GSM751454 5 0.617 5.17e-01 0.008 0.220 0.048 0.032 0.624 0.068
#> GSM751455 2 0.875 4.44e-01 0.100 0.276 0.272 0.072 0.256 0.024
#> GSM751456 2 0.875 4.44e-01 0.100 0.276 0.272 0.072 0.256 0.024
#> GSM751457 5 0.597 5.07e-01 0.000 0.232 0.040 0.032 0.620 0.076
#> GSM751458 5 0.597 5.07e-01 0.000 0.232 0.040 0.032 0.620 0.076
Heatmaps for the consensus matrix. It visualizes the probability of two samples to be in a same group.
consensus_heatmap(res, k = 2)
consensus_heatmap(res, k = 3)
consensus_heatmap(res, k = 4)
consensus_heatmap(res, k = 5)
consensus_heatmap(res, k = 6)
Heatmaps for the membership of samples in all partitions to see how consistent they are:
membership_heatmap(res, k = 2)
membership_heatmap(res, k = 3)
membership_heatmap(res, k = 4)
membership_heatmap(res, k = 5)
membership_heatmap(res, k = 6)
As soon as we have had the classes for columns, we can look for signatures which are significantly different between classes which can be candidate marks for certain classes. Following are the heatmaps for signatures.
Signature heatmaps where rows are scaled:
get_signatures(res, k = 2)
get_signatures(res, k = 3)
get_signatures(res, k = 4)
get_signatures(res, k = 5)
get_signatures(res, k = 6)
Signature heatmaps where rows are not scaled:
get_signatures(res, k = 2, scale_rows = FALSE)
get_signatures(res, k = 3, scale_rows = FALSE)
get_signatures(res, k = 4, scale_rows = FALSE)
get_signatures(res, k = 5, scale_rows = FALSE)
get_signatures(res, k = 6, scale_rows = FALSE)
Compare the overlap of signatures from different k:
compare_signatures(res)
get_signature() returns a data frame invisibly. TO get the list of signatures, the function
call should be assigned to a variable explicitly. In following code, if plot argument is set
to FALSE, no heatmap is plotted while only the differential analysis is performed.
# code only for demonstration
tb = get_signature(res, k = ..., plot = FALSE)
An example of the output of tb is:
#> which_row fdr mean_1 mean_2 scaled_mean_1 scaled_mean_2 km
#> 1 38 0.042760348 8.373488 9.131774 -0.5533452 0.5164555 1
#> 2 40 0.018707592 7.106213 8.469186 -0.6173731 0.5762149 1
#> 3 55 0.019134737 10.221463 11.207825 -0.6159697 0.5749050 1
#> 4 59 0.006059896 5.921854 7.869574 -0.6899429 0.6439467 1
#> 5 60 0.018055526 8.928898 10.211722 -0.6204761 0.5791110 1
#> 6 98 0.009384629 15.714769 14.887706 0.6635654 -0.6193277 2
...
The columns in tb are:
which_row: row indices corresponding to the input matrix.fdr: FDR for the differential test. mean_x: The mean value in group x.scaled_mean_x: The mean value in group x after rows are scaled.km: Row groups if k-means clustering is applied to rows.UMAP plot which shows how samples are separated.
dimension_reduction(res, k = 2, method = "UMAP")
dimension_reduction(res, k = 3, method = "UMAP")
dimension_reduction(res, k = 4, method = "UMAP")
dimension_reduction(res, k = 5, method = "UMAP")
dimension_reduction(res, k = 6, method = "UMAP")
Following heatmap shows how subgroups are split when increasing k:
collect_classes(res)
Test correlation between subgroups and known annotations. If the known annotation is numeric, one-way ANOVA test is applied, and if the known annotation is discrete, chi-squared contingency table test is applied.
test_to_known_factors(res)
#> n tissue(p) disease.state(p) agent(p) k
#> SD:hclust 108 3.48e-09 0.00982 0.012140 2
#> SD:hclust 52 5.11e-12 0.94945 0.247269 3
#> SD:hclust 35 3.07e-01 0.27418 0.068071 4
#> SD:hclust 53 7.56e-03 0.00268 0.001330 5
#> SD:hclust 68 1.07e-10 0.00255 0.000309 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 4537 rows and 166 columns.
#> Top rows (454, 908, 1361, 1814, 2268) are extracted by 'SD' method.
#> Subgroups are detected by 'kmeans' method.
#> Performed in total 1250 partitions by row resampling.
#> Best k for subgroups seems to be 3.
#>
#> Following methods can be applied to this 'ConsensusPartition' object:
#> [1] "cola_report" "collect_classes" "collect_plots"
#> [4] "collect_stats" "colnames" "compare_signatures"
#> [7] "consensus_heatmap" "dimension_reduction" "functional_enrichment"
#> [10] "get_anno_col" "get_anno" "get_classes"
#> [13] "get_consensus" "get_matrix" "get_membership"
#> [16] "get_param" "get_signatures" "get_stats"
#> [19] "is_best_k" "is_stable_k" "membership_heatmap"
#> [22] "ncol" "nrow" "plot_ecdf"
#> [25] "rownames" "select_partition_number" "show"
#> [28] "suggest_best_k" "test_to_known_factors"
collect_plots() function collects all the plots made from res for all k (number of partitions)
into one single page to provide an easy and fast comparison between different k.
collect_plots(res)
The plots are:
k and the heatmap of
predicted classes for each k.k.k.k.All the plots in panels can be made by individual functions and they are plotted later in this section.
select_partition_number() produces several plots showing different
statistics for choosing “optimized” k. There are following statistics:
k;k, the area increased is defined as \(A_k - A_{k-1}\).The detailed explanations of these statistics can be found in the cola vignette.
Generally speaking, lower PAC score, higher mean silhouette score or higher
concordance corresponds to better partition. Rand index and Jaccard index
measure how similar the current partition is compared to partition with k-1.
If they are too similar, we won't accept k is better than k-1.
select_partition_number(res)
The numeric values for all these statistics can be obtained by get_stats().
get_stats(res)
#> k 1-PAC mean_silhouette concordance area_increased Rand Jaccard
#> 2 2 0.623 0.921 0.932 0.4399 0.576 0.576
#> 3 3 0.511 0.677 0.811 0.4825 0.756 0.576
#> 4 4 0.573 0.610 0.762 0.1310 0.895 0.700
#> 5 5 0.614 0.587 0.704 0.0686 0.886 0.611
#> 6 6 0.669 0.558 0.707 0.0431 0.920 0.651
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
#> GSM751298 1 0.0672 0.968 0.992 0.008
#> GSM751304 2 0.3584 0.927 0.068 0.932
#> GSM751305 2 0.3879 0.928 0.076 0.924
#> GSM751307 2 0.4562 0.921 0.096 0.904
#> GSM751310 1 0.1184 0.967 0.984 0.016
#> GSM751314 1 0.1184 0.967 0.984 0.016
#> GSM751316 1 0.1843 0.960 0.972 0.028
#> GSM751318 1 0.0672 0.968 0.992 0.008
#> GSM751342 1 0.1414 0.966 0.980 0.020
#> GSM751346 1 0.1633 0.958 0.976 0.024
#> GSM751347 1 0.7299 0.733 0.796 0.204
#> GSM751348 2 0.4298 0.927 0.088 0.912
#> GSM751349 2 0.2043 0.928 0.032 0.968
#> GSM751352 2 0.8144 0.734 0.252 0.748
#> GSM751353 2 0.2778 0.929 0.048 0.952
#> GSM751354 2 0.3584 0.925 0.068 0.932
#> GSM751355 2 0.1414 0.927 0.020 0.980
#> GSM751358 2 0.3114 0.932 0.056 0.944
#> GSM751359 2 0.2043 0.928 0.032 0.968
#> GSM751294 2 0.2236 0.928 0.036 0.964
#> GSM751296 1 0.1184 0.962 0.984 0.016
#> GSM751297 1 0.4298 0.915 0.912 0.088
#> GSM751299 2 0.8207 0.711 0.256 0.744
#> GSM751300 1 0.1184 0.962 0.984 0.016
#> GSM751301 1 0.4161 0.899 0.916 0.084
#> GSM751302 1 0.1633 0.958 0.976 0.024
#> GSM751303 1 0.1184 0.967 0.984 0.016
#> GSM751306 1 0.1184 0.967 0.984 0.016
#> GSM751308 1 0.7299 0.745 0.796 0.204
#> GSM751309 1 0.1184 0.967 0.984 0.016
#> GSM751311 1 0.0938 0.967 0.988 0.012
#> GSM751312 1 0.1184 0.967 0.984 0.016
#> GSM751313 1 0.1414 0.960 0.980 0.020
#> GSM751315 1 0.0938 0.967 0.988 0.012
#> GSM751317 1 0.1184 0.967 0.984 0.016
#> GSM751320 1 0.0672 0.968 0.992 0.008
#> GSM751321 1 0.1184 0.967 0.984 0.016
#> GSM751322 1 0.0938 0.967 0.988 0.012
#> GSM751324 1 0.0672 0.968 0.992 0.008
#> GSM751325 1 0.0938 0.967 0.988 0.012
#> GSM751332 1 0.0938 0.967 0.988 0.012
#> GSM751334 1 0.0938 0.967 0.988 0.012
#> GSM751339 1 0.1633 0.958 0.976 0.024
#> GSM751341 1 0.0938 0.967 0.988 0.012
#> GSM751343 1 0.0672 0.968 0.992 0.008
#> GSM751344 2 0.4939 0.899 0.108 0.892
#> GSM751345 2 0.4939 0.899 0.108 0.892
#> GSM751356 2 0.7950 0.740 0.240 0.760
#> GSM751357 2 0.7950 0.740 0.240 0.760
#> GSM751293 1 0.4022 0.903 0.920 0.080
#> GSM751295 1 0.1633 0.958 0.976 0.024
#> GSM751319 1 0.0938 0.967 0.988 0.012
#> GSM751323 1 0.0376 0.967 0.996 0.004
#> GSM751326 1 0.0938 0.965 0.988 0.012
#> GSM751327 1 0.0672 0.968 0.992 0.008
#> GSM751328 1 0.0938 0.967 0.988 0.012
#> GSM751329 1 0.0938 0.967 0.988 0.012
#> GSM751330 1 0.0376 0.967 0.996 0.004
#> GSM751331 1 0.1843 0.959 0.972 0.028
#> GSM751333 1 0.1184 0.962 0.984 0.016
#> GSM751335 1 0.0376 0.967 0.996 0.004
#> GSM751336 1 0.1633 0.958 0.976 0.024
#> GSM751337 1 0.1414 0.960 0.980 0.020
#> GSM751338 1 0.1633 0.958 0.976 0.024
#> GSM751340 1 0.8713 0.564 0.708 0.292
#> GSM751350 1 0.1633 0.958 0.976 0.024
#> GSM751351 1 0.1633 0.958 0.976 0.024
#> GSM751362 2 0.5408 0.898 0.124 0.876
#> GSM751363 2 0.3733 0.928 0.072 0.928
#> GSM751367 2 0.5946 0.896 0.144 0.856
#> GSM751368 2 0.2603 0.931 0.044 0.956
#> GSM751371 2 0.5842 0.903 0.140 0.860
#> GSM751375 2 0.2043 0.928 0.032 0.968
#> GSM751376 2 0.2603 0.930 0.044 0.956
#> GSM751378 2 0.0938 0.926 0.012 0.988
#> GSM751379 2 0.2948 0.930 0.052 0.948
#> GSM751382 2 0.2043 0.928 0.032 0.968
#> GSM751386 2 0.1843 0.928 0.028 0.972
#> GSM751388 2 0.2236 0.929 0.036 0.964
#> GSM751391 2 0.2423 0.931 0.040 0.960
#> GSM751410 2 0.5842 0.899 0.140 0.860
#> GSM751414 2 0.5737 0.898 0.136 0.864
#> GSM751361 2 0.2236 0.929 0.036 0.964
#> GSM751365 2 0.5519 0.905 0.128 0.872
#> GSM751366 2 0.5842 0.897 0.140 0.860
#> GSM751369 2 0.5629 0.899 0.132 0.868
#> GSM751370 2 0.5737 0.898 0.136 0.864
#> GSM751372 2 0.5408 0.906 0.124 0.876
#> GSM751373 2 0.5737 0.902 0.136 0.864
#> GSM751374 2 0.2948 0.930 0.052 0.948
#> GSM751377 2 0.2236 0.929 0.036 0.964
#> GSM751380 2 0.5294 0.899 0.120 0.880
#> GSM751381 2 0.1843 0.928 0.028 0.972
#> GSM751383 2 0.2603 0.930 0.044 0.956
#> GSM751384 2 0.1633 0.928 0.024 0.976
#> GSM751385 2 0.0672 0.926 0.008 0.992
#> GSM751387 2 0.2043 0.928 0.032 0.968
#> GSM751389 2 0.3879 0.922 0.076 0.924
#> GSM751393 2 0.0938 0.928 0.012 0.988
#> GSM751394 2 0.1843 0.928 0.028 0.972
#> GSM751395 2 0.1184 0.927 0.016 0.984
#> GSM751397 2 0.1843 0.928 0.028 0.972
#> GSM751398 2 0.1843 0.928 0.028 0.972
#> GSM751404 2 0.5519 0.898 0.128 0.872
#> GSM751406 2 0.5408 0.901 0.124 0.876
#> GSM751411 2 0.5294 0.911 0.120 0.880
#> GSM751413 2 0.2603 0.930 0.044 0.956
#> GSM751415 2 0.5294 0.899 0.120 0.880
#> GSM751416 2 0.2778 0.930 0.048 0.952
#> GSM751417 2 0.2778 0.930 0.048 0.952
#> GSM751421 2 0.5737 0.900 0.136 0.864
#> GSM751422 2 0.5737 0.900 0.136 0.864
#> GSM751360 2 0.5519 0.907 0.128 0.872
#> GSM751364 2 0.4939 0.917 0.108 0.892
#> GSM751390 2 0.2236 0.930 0.036 0.964
#> GSM751392 2 0.1843 0.928 0.028 0.972
#> GSM751396 2 0.2236 0.929 0.036 0.964
#> GSM751399 2 0.4690 0.911 0.100 0.900
#> GSM751400 2 0.5178 0.908 0.116 0.884
#> GSM751401 2 0.5629 0.897 0.132 0.868
#> GSM751402 2 0.5737 0.897 0.136 0.864
#> GSM751403 2 0.5294 0.906 0.120 0.880
#> GSM751405 2 0.5519 0.898 0.128 0.872
#> GSM751407 2 0.5408 0.903 0.124 0.876
#> GSM751408 2 0.5059 0.908 0.112 0.888
#> GSM751409 2 0.3879 0.921 0.076 0.924
#> GSM751412 2 0.5059 0.908 0.112 0.888
#> GSM751418 2 0.5629 0.904 0.132 0.868
#> GSM751419 2 0.5629 0.904 0.132 0.868
#> GSM751420 2 0.3879 0.923 0.076 0.924
#> GSM751425 2 0.2236 0.929 0.036 0.964
#> GSM751429 2 0.5294 0.910 0.120 0.880
#> GSM751430 2 0.3114 0.931 0.056 0.944
#> GSM751433 2 0.4161 0.920 0.084 0.916
#> GSM751437 2 0.4562 0.919 0.096 0.904
#> GSM751448 2 0.5629 0.902 0.132 0.868
#> GSM751451 2 0.4161 0.920 0.084 0.916
#> GSM751423 2 0.2423 0.928 0.040 0.960
#> GSM751424 2 0.4161 0.920 0.084 0.916
#> GSM751428 2 0.3879 0.920 0.076 0.924
#> GSM751431 2 0.4161 0.920 0.084 0.916
#> GSM751432 2 0.3879 0.923 0.076 0.924
#> GSM751434 2 0.4161 0.920 0.084 0.916
#> GSM751435 2 0.4022 0.920 0.080 0.920
#> GSM751436 2 0.4161 0.920 0.084 0.916
#> GSM751440 2 0.4161 0.920 0.084 0.916
#> GSM751444 2 0.3733 0.920 0.072 0.928
#> GSM751446 2 0.3431 0.923 0.064 0.936
#> GSM751449 2 0.1843 0.927 0.028 0.972
#> GSM751450 2 0.4161 0.920 0.084 0.916
#> GSM751452 2 0.4161 0.920 0.084 0.916
#> GSM751426 2 0.4161 0.920 0.084 0.916
#> GSM751427 2 0.3733 0.921 0.072 0.928
#> GSM751438 2 0.3274 0.923 0.060 0.940
#> GSM751439 2 0.5629 0.906 0.132 0.868
#> GSM751441 2 0.2423 0.928 0.040 0.960
#> GSM751442 2 0.3879 0.919 0.076 0.924
#> GSM751443 2 0.4939 0.918 0.108 0.892
#> GSM751445 2 0.2043 0.927 0.032 0.968
#> GSM751447 2 0.2603 0.928 0.044 0.956
#> GSM751453 2 0.3879 0.921 0.076 0.924
#> GSM751454 2 0.3879 0.921 0.076 0.924
#> GSM751455 2 0.3879 0.919 0.076 0.924
#> GSM751456 2 0.3879 0.919 0.076 0.924
#> GSM751457 2 0.1843 0.927 0.028 0.972
#> GSM751458 2 0.1843 0.927 0.028 0.972
cbind(get_classes(res, k = 3), get_membership(res, k = 3))
#> class entropy silhouette p1 p2 p3
#> GSM751298 1 0.191 0.9392 0.956 0.028 0.016
#> GSM751304 2 0.781 0.4122 0.056 0.548 0.396
#> GSM751305 2 0.795 0.4248 0.064 0.548 0.388
#> GSM751307 2 0.747 0.5464 0.072 0.656 0.272
#> GSM751310 1 0.232 0.9299 0.944 0.028 0.028
#> GSM751314 1 0.244 0.9301 0.940 0.032 0.028
#> GSM751316 1 0.456 0.8777 0.860 0.064 0.076
#> GSM751318 1 0.256 0.9376 0.936 0.036 0.028
#> GSM751342 1 0.232 0.9319 0.944 0.028 0.028
#> GSM751346 1 0.275 0.9277 0.924 0.064 0.012
#> GSM751347 1 0.425 0.8950 0.872 0.080 0.048
#> GSM751348 2 0.772 0.5857 0.068 0.612 0.320
#> GSM751349 2 0.596 0.5549 0.008 0.692 0.300
#> GSM751352 2 0.822 0.5439 0.152 0.636 0.212
#> GSM751353 2 0.618 0.6038 0.024 0.716 0.260
#> GSM751354 2 0.766 0.4462 0.052 0.572 0.376
#> GSM751355 2 0.679 0.5148 0.028 0.648 0.324
#> GSM751358 2 0.753 0.4380 0.040 0.536 0.424
#> GSM751359 2 0.618 0.4964 0.008 0.660 0.332
#> GSM751294 2 0.728 0.4738 0.036 0.588 0.376
#> GSM751296 1 0.191 0.9391 0.956 0.028 0.016
#> GSM751297 1 0.660 0.7322 0.748 0.084 0.168
#> GSM751299 2 0.828 0.5425 0.160 0.632 0.208
#> GSM751300 1 0.206 0.9359 0.948 0.044 0.008
#> GSM751301 1 0.280 0.9166 0.924 0.060 0.016
#> GSM751302 1 0.275 0.9277 0.924 0.064 0.012
#> GSM751303 1 0.244 0.9301 0.940 0.032 0.028
#> GSM751306 1 0.244 0.9301 0.940 0.032 0.028
#> GSM751308 1 0.885 0.3862 0.568 0.264 0.168
#> GSM751309 1 0.244 0.9301 0.940 0.032 0.028
#> GSM751311 1 0.205 0.9337 0.952 0.020 0.028
#> GSM751312 1 0.295 0.9218 0.920 0.060 0.020
#> GSM751313 1 0.205 0.9375 0.952 0.028 0.020
#> GSM751315 1 0.117 0.9382 0.976 0.008 0.016
#> GSM751317 1 0.219 0.9320 0.948 0.024 0.028
#> GSM751320 1 0.177 0.9400 0.960 0.024 0.016
#> GSM751321 1 0.232 0.9299 0.944 0.028 0.028
#> GSM751322 1 0.164 0.9395 0.964 0.016 0.020
#> GSM751324 1 0.164 0.9395 0.964 0.016 0.020
#> GSM751325 1 0.192 0.9390 0.956 0.024 0.020
#> GSM751332 1 0.192 0.9390 0.956 0.024 0.020
#> GSM751334 1 0.177 0.9398 0.960 0.024 0.016
#> GSM751339 1 0.392 0.9031 0.884 0.036 0.080
#> GSM751341 1 0.164 0.9381 0.964 0.016 0.020
#> GSM751343 1 0.177 0.9398 0.960 0.024 0.016
#> GSM751344 2 0.767 0.5830 0.084 0.648 0.268
#> GSM751345 2 0.767 0.5830 0.084 0.648 0.268
#> GSM751356 2 0.876 0.4929 0.160 0.576 0.264
#> GSM751357 2 0.876 0.4929 0.160 0.576 0.264
#> GSM751293 1 0.280 0.9166 0.924 0.060 0.016
#> GSM751295 1 0.275 0.9277 0.924 0.064 0.012
#> GSM751319 1 0.177 0.9357 0.960 0.016 0.024
#> GSM751323 1 0.177 0.9400 0.960 0.024 0.016
#> GSM751326 1 0.191 0.9397 0.956 0.028 0.016
#> GSM751327 1 0.177 0.9398 0.960 0.024 0.016
#> GSM751328 1 0.148 0.9392 0.968 0.012 0.020
#> GSM751329 1 0.177 0.9392 0.960 0.024 0.016
#> GSM751330 1 0.223 0.9385 0.944 0.044 0.012
#> GSM751331 1 0.249 0.9309 0.932 0.060 0.008
#> GSM751333 1 0.238 0.9377 0.940 0.044 0.016
#> GSM751335 1 0.223 0.9385 0.944 0.044 0.012
#> GSM751336 1 0.265 0.9295 0.928 0.060 0.012
#> GSM751337 1 0.231 0.9381 0.944 0.032 0.024
#> GSM751338 1 0.231 0.9395 0.944 0.032 0.024
#> GSM751340 1 0.930 0.1683 0.456 0.164 0.380
#> GSM751350 1 0.275 0.9277 0.924 0.064 0.012
#> GSM751351 1 0.275 0.9277 0.924 0.064 0.012
#> GSM751362 3 0.215 0.6983 0.016 0.036 0.948
#> GSM751363 3 0.520 0.6405 0.004 0.236 0.760
#> GSM751367 3 0.689 0.5940 0.112 0.152 0.736
#> GSM751368 3 0.619 0.5102 0.004 0.364 0.632
#> GSM751371 3 0.454 0.6082 0.016 0.148 0.836
#> GSM751375 2 0.581 0.4805 0.000 0.664 0.336
#> GSM751376 3 0.623 0.3395 0.012 0.316 0.672
#> GSM751378 3 0.556 0.4267 0.000 0.300 0.700
#> GSM751379 3 0.623 0.3395 0.012 0.316 0.672
#> GSM751382 2 0.593 0.4260 0.000 0.644 0.356
#> GSM751386 3 0.626 0.2893 0.000 0.448 0.552
#> GSM751388 3 0.631 0.2565 0.000 0.488 0.512
#> GSM751391 3 0.483 0.5294 0.004 0.204 0.792
#> GSM751410 3 0.303 0.6726 0.012 0.076 0.912
#> GSM751414 3 0.384 0.7029 0.012 0.116 0.872
#> GSM751361 3 0.573 0.5580 0.000 0.324 0.676
#> GSM751365 3 0.457 0.6933 0.012 0.160 0.828
#> GSM751366 3 0.392 0.7118 0.016 0.112 0.872
#> GSM751369 3 0.407 0.6382 0.016 0.120 0.864
#> GSM751370 3 0.384 0.7029 0.012 0.116 0.872
#> GSM751372 3 0.475 0.6875 0.012 0.172 0.816
#> GSM751373 3 0.497 0.6838 0.012 0.188 0.800
#> GSM751374 3 0.623 0.3395 0.012 0.316 0.672
#> GSM751377 3 0.583 0.5399 0.000 0.340 0.660
#> GSM751380 3 0.290 0.7085 0.016 0.064 0.920
#> GSM751381 3 0.624 0.2929 0.000 0.440 0.560
#> GSM751383 3 0.631 0.2400 0.000 0.496 0.504
#> GSM751384 3 0.590 0.4815 0.000 0.352 0.648
#> GSM751385 3 0.412 0.6613 0.000 0.168 0.832
#> GSM751387 3 0.631 0.2488 0.000 0.488 0.512
#> GSM751389 3 0.240 0.7095 0.004 0.064 0.932
#> GSM751393 3 0.259 0.7018 0.004 0.072 0.924
#> GSM751394 3 0.624 0.2826 0.000 0.440 0.560
#> GSM751395 3 0.587 0.3812 0.004 0.312 0.684
#> GSM751397 3 0.623 0.2936 0.000 0.436 0.564
#> GSM751398 3 0.623 0.3030 0.000 0.436 0.564
#> GSM751404 3 0.377 0.7084 0.016 0.104 0.880
#> GSM751406 3 0.215 0.6914 0.016 0.036 0.948
#> GSM751411 3 0.304 0.7109 0.008 0.084 0.908
#> GSM751413 3 0.566 0.5730 0.004 0.284 0.712
#> GSM751415 3 0.309 0.7081 0.016 0.072 0.912
#> GSM751416 3 0.550 0.5993 0.000 0.292 0.708
#> GSM751417 3 0.550 0.5993 0.000 0.292 0.708
#> GSM751421 3 0.336 0.6685 0.016 0.084 0.900
#> GSM751422 3 0.336 0.6685 0.016 0.084 0.900
#> GSM751360 3 0.200 0.7050 0.012 0.036 0.952
#> GSM751364 3 0.522 0.6684 0.012 0.208 0.780
#> GSM751390 3 0.618 0.4240 0.000 0.416 0.584
#> GSM751392 2 0.631 -0.0734 0.000 0.512 0.488
#> GSM751396 2 0.630 -0.1251 0.000 0.528 0.472
#> GSM751399 3 0.309 0.7153 0.016 0.072 0.912
#> GSM751400 3 0.414 0.7038 0.016 0.124 0.860
#> GSM751401 3 0.385 0.7009 0.016 0.108 0.876
#> GSM751402 3 0.336 0.7061 0.016 0.084 0.900
#> GSM751403 3 0.336 0.7061 0.016 0.084 0.900
#> GSM751405 3 0.238 0.6887 0.016 0.044 0.940
#> GSM751407 3 0.414 0.7038 0.016 0.124 0.860
#> GSM751408 3 0.448 0.7061 0.016 0.144 0.840
#> GSM751409 3 0.203 0.7033 0.016 0.032 0.952
#> GSM751412 3 0.448 0.7061 0.016 0.144 0.840
#> GSM751418 3 0.527 0.6687 0.012 0.212 0.776
#> GSM751419 3 0.527 0.6687 0.012 0.212 0.776
#> GSM751420 3 0.499 0.5979 0.024 0.160 0.816
#> GSM751425 2 0.392 0.7080 0.004 0.856 0.140
#> GSM751429 3 0.651 0.3855 0.028 0.284 0.688
#> GSM751430 2 0.613 0.4990 0.016 0.700 0.284
#> GSM751433 2 0.374 0.7199 0.036 0.892 0.072
#> GSM751437 3 0.647 0.2632 0.016 0.332 0.652
#> GSM751448 3 0.644 0.4038 0.028 0.276 0.696
#> GSM751451 2 0.355 0.7194 0.036 0.900 0.064
#> GSM751423 2 0.390 0.7135 0.008 0.864 0.128
#> GSM751424 2 0.374 0.7199 0.036 0.892 0.072
#> GSM751428 2 0.341 0.7237 0.028 0.904 0.068
#> GSM751431 2 0.374 0.7199 0.036 0.892 0.072
#> GSM751432 2 0.371 0.7193 0.032 0.892 0.076
#> GSM751434 2 0.374 0.7199 0.036 0.892 0.072
#> GSM751435 2 0.308 0.7230 0.024 0.916 0.060
#> GSM751436 2 0.374 0.7199 0.036 0.892 0.072
#> GSM751440 2 0.346 0.7208 0.036 0.904 0.060
#> GSM751444 2 0.420 0.7257 0.024 0.864 0.112
#> GSM751446 2 0.407 0.7251 0.016 0.864 0.120
#> GSM751449 2 0.426 0.7200 0.012 0.848 0.140
#> GSM751450 2 0.353 0.7216 0.032 0.900 0.068
#> GSM751452 2 0.374 0.7199 0.036 0.892 0.072
#> GSM751426 2 0.374 0.7199 0.036 0.892 0.072
#> GSM751427 2 0.305 0.7239 0.020 0.916 0.064
#> GSM751438 2 0.420 0.7228 0.024 0.864 0.112
#> GSM751439 2 0.666 0.5048 0.028 0.668 0.304
#> GSM751441 2 0.414 0.7275 0.020 0.864 0.116
#> GSM751442 2 0.440 0.7225 0.028 0.856 0.116
#> GSM751443 2 0.692 0.2804 0.016 0.536 0.448
#> GSM751445 2 0.447 0.7085 0.004 0.820 0.176
#> GSM751447 2 0.399 0.7278 0.020 0.872 0.108
#> GSM751453 2 0.298 0.7232 0.024 0.920 0.056
#> GSM751454 2 0.298 0.7232 0.024 0.920 0.056
#> GSM751455 2 0.440 0.7225 0.028 0.856 0.116
#> GSM751456 2 0.440 0.7225 0.028 0.856 0.116
#> GSM751457 2 0.599 0.6164 0.008 0.688 0.304
#> GSM751458 2 0.599 0.6164 0.008 0.688 0.304
cbind(get_classes(res, k = 4), get_membership(res, k = 4))
#> class entropy silhouette p1 p2 p3 p4
#> GSM751298 1 0.0376 0.86749 0.992 0.004 0.000 0.004
#> GSM751304 4 0.5132 0.63668 0.000 0.184 0.068 0.748
#> GSM751305 4 0.5250 0.63227 0.000 0.196 0.068 0.736
#> GSM751307 4 0.6598 0.50074 0.036 0.300 0.044 0.620
#> GSM751310 1 0.3544 0.81352 0.852 0.008 0.012 0.128
#> GSM751314 1 0.3432 0.81663 0.860 0.008 0.012 0.120
#> GSM751316 1 0.5453 0.56952 0.620 0.008 0.012 0.360
#> GSM751318 1 0.1256 0.86321 0.964 0.008 0.000 0.028
#> GSM751342 1 0.3272 0.81596 0.860 0.008 0.004 0.128
#> GSM751346 1 0.4803 0.80096 0.732 0.008 0.012 0.248
#> GSM751347 1 0.5155 0.78923 0.716 0.008 0.024 0.252
#> GSM751348 4 0.7684 0.46489 0.064 0.328 0.072 0.536
#> GSM751349 2 0.7049 -0.08477 0.000 0.484 0.124 0.392
#> GSM751352 4 0.5396 0.60487 0.016 0.240 0.028 0.716
#> GSM751353 4 0.5669 0.44736 0.004 0.372 0.024 0.600
#> GSM751354 4 0.4978 0.63417 0.004 0.180 0.052 0.764
#> GSM751355 4 0.5416 0.57935 0.000 0.260 0.048 0.692
#> GSM751358 4 0.7373 0.59128 0.044 0.232 0.112 0.612
#> GSM751359 4 0.6805 0.31808 0.000 0.400 0.100 0.500
#> GSM751294 4 0.5598 0.63122 0.000 0.220 0.076 0.704
#> GSM751296 1 0.2530 0.86349 0.912 0.008 0.008 0.072
#> GSM751297 4 0.6086 -0.21354 0.412 0.008 0.032 0.548
#> GSM751299 4 0.5313 0.60122 0.012 0.244 0.028 0.716
#> GSM751300 1 0.4569 0.81815 0.760 0.008 0.012 0.220
#> GSM751301 1 0.3353 0.84489 0.880 0.060 0.004 0.056
#> GSM751302 1 0.4803 0.80096 0.732 0.008 0.012 0.248
#> GSM751303 1 0.3598 0.80828 0.848 0.008 0.012 0.132
#> GSM751306 1 0.3489 0.81386 0.856 0.008 0.012 0.124
#> GSM751308 4 0.8150 0.08033 0.412 0.120 0.048 0.420
#> GSM751309 1 0.3489 0.81386 0.856 0.008 0.012 0.124
#> GSM751311 1 0.2597 0.84128 0.904 0.008 0.004 0.084
#> GSM751312 1 0.4800 0.75549 0.720 0.008 0.008 0.264
#> GSM751313 1 0.4420 0.82542 0.776 0.008 0.012 0.204
#> GSM751315 1 0.1398 0.85883 0.956 0.000 0.004 0.040
#> GSM751317 1 0.2860 0.83636 0.888 0.004 0.008 0.100
#> GSM751320 1 0.0779 0.86783 0.980 0.004 0.000 0.016
#> GSM751321 1 0.3489 0.81386 0.856 0.008 0.012 0.124
#> GSM751322 1 0.0524 0.86645 0.988 0.004 0.000 0.008
#> GSM751324 1 0.0524 0.86645 0.988 0.004 0.000 0.008
#> GSM751325 1 0.0376 0.86678 0.992 0.004 0.000 0.004
#> GSM751332 1 0.0188 0.86681 0.996 0.004 0.000 0.000
#> GSM751334 1 0.0895 0.86788 0.976 0.004 0.000 0.020
#> GSM751339 1 0.5277 0.78605 0.740 0.008 0.048 0.204
#> GSM751341 1 0.2457 0.84425 0.912 0.008 0.004 0.076
#> GSM751343 1 0.0376 0.86678 0.992 0.004 0.000 0.004
#> GSM751344 4 0.5278 0.56169 0.008 0.284 0.020 0.688
#> GSM751345 4 0.5278 0.56169 0.008 0.284 0.020 0.688
#> GSM751356 4 0.5774 0.62992 0.016 0.216 0.056 0.712
#> GSM751357 4 0.5774 0.62992 0.016 0.216 0.056 0.712
#> GSM751293 1 0.2944 0.85564 0.900 0.044 0.004 0.052
#> GSM751295 1 0.4803 0.80096 0.732 0.008 0.012 0.248
#> GSM751319 1 0.2382 0.84449 0.912 0.004 0.004 0.080
#> GSM751323 1 0.1543 0.86759 0.956 0.008 0.004 0.032
#> GSM751326 1 0.2810 0.85992 0.896 0.008 0.008 0.088
#> GSM751327 1 0.1543 0.86759 0.956 0.008 0.004 0.032
#> GSM751328 1 0.0188 0.86663 0.996 0.000 0.000 0.004
#> GSM751329 1 0.1732 0.86715 0.948 0.008 0.004 0.040
#> GSM751330 1 0.4420 0.82503 0.776 0.008 0.012 0.204
#> GSM751331 1 0.4803 0.80096 0.732 0.008 0.012 0.248
#> GSM751333 1 0.4496 0.82131 0.768 0.008 0.012 0.212
#> GSM751335 1 0.4294 0.82683 0.780 0.008 0.008 0.204
#> GSM751336 1 0.4772 0.80373 0.736 0.008 0.012 0.244
#> GSM751337 1 0.3006 0.85938 0.888 0.008 0.012 0.092
#> GSM751338 1 0.3916 0.84228 0.816 0.008 0.008 0.168
#> GSM751340 4 0.6674 0.46226 0.136 0.012 0.200 0.652
#> GSM751350 1 0.4803 0.80096 0.732 0.008 0.012 0.248
#> GSM751351 1 0.4803 0.80096 0.732 0.008 0.012 0.248
#> GSM751362 3 0.3710 0.58101 0.000 0.004 0.804 0.192
#> GSM751363 3 0.5816 0.55892 0.008 0.068 0.700 0.224
#> GSM751367 3 0.7441 -0.02086 0.064 0.044 0.476 0.416
#> GSM751368 3 0.5736 0.57218 0.004 0.208 0.708 0.080
#> GSM751371 3 0.6538 0.12948 0.012 0.052 0.540 0.396
#> GSM751375 2 0.7387 -0.11217 0.000 0.444 0.164 0.392
#> GSM751376 4 0.6663 0.38727 0.000 0.100 0.344 0.556
#> GSM751378 3 0.7586 0.08968 0.000 0.200 0.436 0.364
#> GSM751379 4 0.6690 0.37084 0.000 0.100 0.352 0.548
#> GSM751382 2 0.7534 -0.07907 0.000 0.448 0.192 0.360
#> GSM751386 3 0.7218 0.37892 0.000 0.316 0.520 0.164
#> GSM751388 3 0.6991 0.38494 0.000 0.324 0.540 0.136
#> GSM751391 3 0.6818 -0.00544 0.008 0.076 0.504 0.412
#> GSM751410 3 0.6024 0.23223 0.012 0.028 0.584 0.376
#> GSM751414 3 0.3089 0.65088 0.008 0.044 0.896 0.052
#> GSM751361 3 0.5079 0.59652 0.004 0.156 0.768 0.072
#> GSM751365 3 0.2221 0.65388 0.008 0.044 0.932 0.016
#> GSM751366 3 0.2549 0.64943 0.004 0.024 0.916 0.056
#> GSM751369 3 0.6300 0.13405 0.008 0.044 0.544 0.404
#> GSM751370 3 0.3170 0.65062 0.008 0.044 0.892 0.056
#> GSM751372 3 0.2632 0.65063 0.008 0.048 0.916 0.028
#> GSM751373 3 0.3544 0.65385 0.008 0.076 0.872 0.044
#> GSM751374 4 0.6690 0.37084 0.000 0.100 0.352 0.548
#> GSM751377 3 0.5226 0.58066 0.000 0.180 0.744 0.076
#> GSM751380 3 0.3266 0.63098 0.000 0.024 0.868 0.108
#> GSM751381 3 0.7218 0.37892 0.000 0.316 0.520 0.164
#> GSM751383 3 0.7020 0.37793 0.000 0.332 0.532 0.136
#> GSM751384 3 0.6563 0.49068 0.000 0.208 0.632 0.160
#> GSM751385 3 0.6091 0.39948 0.000 0.060 0.596 0.344
#> GSM751387 3 0.7006 0.38141 0.000 0.328 0.536 0.136
#> GSM751389 3 0.3495 0.61923 0.000 0.016 0.844 0.140
#> GSM751393 3 0.4327 0.59598 0.000 0.016 0.768 0.216
#> GSM751394 3 0.7268 0.37531 0.000 0.312 0.516 0.172
#> GSM751395 4 0.6648 0.30222 0.000 0.092 0.372 0.536
#> GSM751397 3 0.7374 0.36265 0.000 0.308 0.504 0.188
#> GSM751398 3 0.7149 0.38173 0.000 0.316 0.528 0.156
#> GSM751404 3 0.3308 0.63702 0.000 0.036 0.872 0.092
#> GSM751406 3 0.4608 0.42131 0.000 0.004 0.692 0.304
#> GSM751411 3 0.1610 0.65414 0.000 0.016 0.952 0.032
#> GSM751413 3 0.6371 0.54144 0.004 0.132 0.664 0.200
#> GSM751415 3 0.3080 0.63607 0.000 0.024 0.880 0.096
#> GSM751416 3 0.4963 0.60132 0.004 0.152 0.776 0.068
#> GSM751417 3 0.4963 0.60132 0.004 0.152 0.776 0.068
#> GSM751421 3 0.6131 0.28664 0.008 0.044 0.600 0.348
#> GSM751422 3 0.6131 0.28664 0.008 0.044 0.600 0.348
#> GSM751360 3 0.4235 0.60486 0.004 0.016 0.792 0.188
#> GSM751364 3 0.3915 0.63525 0.008 0.088 0.852 0.052
#> GSM751390 3 0.6488 0.48782 0.000 0.244 0.628 0.128
#> GSM751392 2 0.7666 -0.15577 0.000 0.396 0.392 0.212
#> GSM751396 3 0.7419 0.18304 0.000 0.396 0.436 0.168
#> GSM751399 3 0.2635 0.64646 0.000 0.020 0.904 0.076
#> GSM751400 3 0.3497 0.63519 0.000 0.036 0.860 0.104
#> GSM751401 3 0.3435 0.63541 0.000 0.036 0.864 0.100
#> GSM751402 3 0.3523 0.62990 0.000 0.032 0.856 0.112
#> GSM751403 3 0.3557 0.63375 0.000 0.036 0.856 0.108
#> GSM751405 3 0.4456 0.46847 0.000 0.004 0.716 0.280
#> GSM751407 3 0.3372 0.63733 0.000 0.036 0.868 0.096
#> GSM751408 3 0.3056 0.64662 0.000 0.040 0.888 0.072
#> GSM751409 3 0.3105 0.62876 0.000 0.012 0.868 0.120
#> GSM751412 3 0.2908 0.64812 0.000 0.040 0.896 0.064
#> GSM751418 3 0.2673 0.65292 0.008 0.080 0.904 0.008
#> GSM751419 3 0.2673 0.65292 0.008 0.080 0.904 0.008
#> GSM751420 3 0.6277 0.17742 0.000 0.068 0.572 0.360
#> GSM751425 2 0.1807 0.77785 0.000 0.940 0.008 0.052
#> GSM751429 4 0.7054 0.32364 0.004 0.112 0.372 0.512
#> GSM751430 2 0.7568 0.22467 0.012 0.532 0.284 0.172
#> GSM751433 2 0.2483 0.77617 0.012 0.920 0.012 0.056
#> GSM751437 4 0.7561 0.35419 0.000 0.200 0.348 0.452
#> GSM751448 4 0.6758 0.28009 0.000 0.096 0.400 0.504
#> GSM751451 2 0.1749 0.78345 0.012 0.952 0.012 0.024
#> GSM751423 2 0.1767 0.78293 0.000 0.944 0.012 0.044
#> GSM751424 2 0.2563 0.77418 0.012 0.916 0.012 0.060
#> GSM751428 2 0.1807 0.78966 0.000 0.940 0.008 0.052
#> GSM751431 2 0.1909 0.78345 0.004 0.940 0.008 0.048
#> GSM751432 2 0.2874 0.77135 0.012 0.904 0.020 0.064
#> GSM751434 2 0.2641 0.77569 0.012 0.912 0.012 0.064
#> GSM751435 2 0.1042 0.79144 0.000 0.972 0.008 0.020
#> GSM751436 2 0.2563 0.77418 0.012 0.916 0.012 0.060
#> GSM751440 2 0.0859 0.78901 0.004 0.980 0.008 0.008
#> GSM751444 2 0.2593 0.77727 0.000 0.904 0.016 0.080
#> GSM751446 2 0.3080 0.75889 0.000 0.880 0.024 0.096
#> GSM751449 2 0.3182 0.75566 0.000 0.876 0.028 0.096
#> GSM751450 2 0.1822 0.78504 0.004 0.944 0.008 0.044
#> GSM751452 2 0.2563 0.77418 0.012 0.916 0.012 0.060
#> GSM751426 2 0.2186 0.78034 0.008 0.932 0.012 0.048
#> GSM751427 2 0.1510 0.79044 0.000 0.956 0.016 0.028
#> GSM751438 2 0.3015 0.75951 0.000 0.884 0.024 0.092
#> GSM751439 2 0.5724 0.52044 0.000 0.716 0.140 0.144
#> GSM751441 2 0.2730 0.77109 0.000 0.896 0.016 0.088
#> GSM751442 2 0.2882 0.76363 0.000 0.892 0.024 0.084
#> GSM751443 4 0.7821 0.32456 0.000 0.344 0.260 0.396
#> GSM751445 2 0.3037 0.74830 0.000 0.880 0.020 0.100
#> GSM751447 2 0.2542 0.77124 0.000 0.904 0.012 0.084
#> GSM751453 2 0.1256 0.79100 0.000 0.964 0.008 0.028
#> GSM751454 2 0.1256 0.79100 0.000 0.964 0.008 0.028
#> GSM751455 2 0.2882 0.76363 0.000 0.892 0.024 0.084
#> GSM751456 2 0.2882 0.76363 0.000 0.892 0.024 0.084
#> GSM751457 2 0.5799 0.41834 0.000 0.668 0.068 0.264
#> GSM751458 2 0.5799 0.41834 0.000 0.668 0.068 0.264
cbind(get_classes(res, k = 5), get_membership(res, k = 5))
#> class entropy silhouette p1 p2 p3 p4 p5
#> GSM751298 1 0.2054 0.73975 0.916 0.008 0.000 0.072 0.004
#> GSM751304 4 0.5452 0.70873 0.000 0.068 0.136 0.724 0.072
#> GSM751305 4 0.5504 0.70189 0.000 0.072 0.120 0.724 0.084
#> GSM751307 4 0.6930 0.68098 0.008 0.108 0.124 0.616 0.144
#> GSM751310 1 0.5257 0.54297 0.616 0.004 0.004 0.332 0.044
#> GSM751314 1 0.5197 0.58144 0.652 0.008 0.004 0.292 0.044
#> GSM751316 4 0.5636 0.08417 0.308 0.000 0.028 0.616 0.048
#> GSM751318 1 0.3247 0.71233 0.840 0.008 0.000 0.136 0.016
#> GSM751342 1 0.5078 0.58083 0.656 0.008 0.004 0.296 0.036
#> GSM751346 1 0.5406 0.65130 0.676 0.000 0.016 0.228 0.080
#> GSM751347 1 0.5458 0.64414 0.668 0.000 0.016 0.236 0.080
#> GSM751348 4 0.9153 0.53591 0.072 0.180 0.144 0.392 0.212
#> GSM751349 5 0.7986 0.07312 0.000 0.228 0.148 0.176 0.448
#> GSM751352 4 0.6865 0.71448 0.004 0.160 0.124 0.612 0.100
#> GSM751353 4 0.7655 0.61888 0.000 0.188 0.120 0.500 0.192
#> GSM751354 4 0.6454 0.70738 0.000 0.096 0.132 0.644 0.128
#> GSM751355 4 0.7152 0.65609 0.000 0.116 0.124 0.564 0.196
#> GSM751358 4 0.7281 0.64057 0.060 0.068 0.152 0.616 0.104
#> GSM751359 4 0.7547 0.43681 0.000 0.096 0.128 0.444 0.332
#> GSM751294 4 0.6605 0.70720 0.000 0.124 0.176 0.620 0.080
#> GSM751296 1 0.2853 0.73454 0.876 0.000 0.000 0.072 0.052
#> GSM751297 4 0.7720 -0.06209 0.364 0.004 0.132 0.408 0.092
#> GSM751299 4 0.6813 0.71384 0.004 0.164 0.120 0.616 0.096
#> GSM751300 1 0.4911 0.67950 0.720 0.000 0.008 0.196 0.076
#> GSM751301 1 0.3558 0.69912 0.840 0.036 0.000 0.108 0.016
#> GSM751302 1 0.5432 0.64795 0.672 0.000 0.016 0.232 0.080
#> GSM751303 1 0.5366 0.48497 0.584 0.004 0.004 0.364 0.044
#> GSM751306 1 0.5226 0.55041 0.624 0.004 0.004 0.324 0.044
#> GSM751308 4 0.7296 0.33844 0.364 0.080 0.076 0.468 0.012
#> GSM751309 1 0.5187 0.57087 0.644 0.008 0.004 0.304 0.040
#> GSM751311 1 0.4821 0.61021 0.680 0.008 0.000 0.276 0.036
#> GSM751312 4 0.5485 -0.23309 0.384 0.000 0.012 0.560 0.044
#> GSM751313 1 0.4985 0.67977 0.720 0.000 0.012 0.192 0.076
#> GSM751315 1 0.4210 0.66937 0.756 0.004 0.000 0.204 0.036
#> GSM751317 1 0.5070 0.58561 0.648 0.004 0.004 0.304 0.040
#> GSM751320 1 0.0955 0.74746 0.968 0.000 0.000 0.028 0.004
#> GSM751321 1 0.5119 0.57542 0.648 0.004 0.004 0.300 0.044
#> GSM751322 1 0.2414 0.73528 0.900 0.008 0.000 0.080 0.012
#> GSM751324 1 0.2474 0.73413 0.896 0.008 0.000 0.084 0.012
#> GSM751325 1 0.1717 0.74329 0.936 0.008 0.000 0.052 0.004
#> GSM751332 1 0.1331 0.74550 0.952 0.008 0.000 0.040 0.000
#> GSM751334 1 0.0324 0.74803 0.992 0.000 0.000 0.004 0.004
#> GSM751339 1 0.5757 0.62865 0.688 0.000 0.080 0.176 0.056
#> GSM751341 1 0.4211 0.66863 0.764 0.008 0.004 0.200 0.024
#> GSM751343 1 0.1717 0.74329 0.936 0.008 0.000 0.052 0.004
#> GSM751344 4 0.6722 0.70901 0.000 0.160 0.108 0.616 0.116
#> GSM751345 4 0.6722 0.70901 0.000 0.160 0.108 0.616 0.116
#> GSM751356 4 0.5728 0.71777 0.008 0.116 0.108 0.716 0.052
#> GSM751357 4 0.5728 0.71777 0.008 0.116 0.108 0.716 0.052
#> GSM751293 1 0.3507 0.70240 0.844 0.036 0.000 0.104 0.016
#> GSM751295 1 0.5432 0.64795 0.672 0.000 0.016 0.232 0.080
#> GSM751319 1 0.4752 0.61815 0.684 0.004 0.000 0.272 0.040
#> GSM751323 1 0.0451 0.74804 0.988 0.000 0.000 0.004 0.008
#> GSM751326 1 0.2903 0.73261 0.872 0.000 0.000 0.080 0.048
#> GSM751327 1 0.0579 0.74782 0.984 0.000 0.000 0.008 0.008
#> GSM751328 1 0.2589 0.73259 0.888 0.008 0.000 0.092 0.012
#> GSM751329 1 0.1549 0.74449 0.944 0.000 0.000 0.040 0.016
#> GSM751330 1 0.4702 0.68543 0.732 0.000 0.004 0.192 0.072
#> GSM751331 1 0.5432 0.64795 0.672 0.000 0.016 0.232 0.080
#> GSM751333 1 0.4887 0.67894 0.720 0.000 0.008 0.200 0.072
#> GSM751335 1 0.4702 0.68543 0.732 0.000 0.004 0.192 0.072
#> GSM751336 1 0.5406 0.65039 0.676 0.000 0.016 0.228 0.080
#> GSM751337 1 0.3197 0.73147 0.864 0.000 0.008 0.076 0.052
#> GSM751338 1 0.4356 0.70967 0.776 0.000 0.012 0.156 0.056
#> GSM751340 4 0.6191 0.45617 0.052 0.008 0.352 0.556 0.032
#> GSM751350 1 0.5432 0.64795 0.672 0.000 0.016 0.232 0.080
#> GSM751351 1 0.5432 0.64795 0.672 0.000 0.016 0.232 0.080
#> GSM751362 3 0.4162 0.55618 0.000 0.000 0.768 0.056 0.176
#> GSM751363 5 0.6331 0.26188 0.000 0.008 0.356 0.132 0.504
#> GSM751367 3 0.5314 0.49346 0.012 0.012 0.708 0.200 0.068
#> GSM751368 5 0.5743 0.33995 0.000 0.068 0.392 0.008 0.532
#> GSM751371 3 0.4423 0.51485 0.004 0.020 0.768 0.180 0.028
#> GSM751375 5 0.7449 0.28851 0.000 0.192 0.168 0.112 0.528
#> GSM751376 3 0.6532 0.14755 0.000 0.076 0.560 0.304 0.060
#> GSM751378 5 0.7257 0.25144 0.000 0.100 0.380 0.084 0.436
#> GSM751379 3 0.6537 0.15500 0.000 0.072 0.560 0.304 0.064
#> GSM751382 5 0.7265 0.36483 0.000 0.204 0.180 0.080 0.536
#> GSM751386 5 0.4403 0.67803 0.000 0.112 0.092 0.012 0.784
#> GSM751388 5 0.4377 0.66822 0.000 0.112 0.108 0.004 0.776
#> GSM751391 3 0.4347 0.48525 0.000 0.028 0.756 0.200 0.016
#> GSM751410 3 0.4705 0.52449 0.008 0.008 0.756 0.168 0.060
#> GSM751414 3 0.4818 -0.01620 0.000 0.000 0.520 0.020 0.460
#> GSM751361 5 0.5205 0.50754 0.000 0.040 0.280 0.020 0.660
#> GSM751365 3 0.4627 0.11915 0.000 0.000 0.544 0.012 0.444
#> GSM751366 3 0.3491 0.53581 0.000 0.000 0.768 0.004 0.228
#> GSM751369 3 0.3667 0.54315 0.000 0.012 0.812 0.156 0.020
#> GSM751370 3 0.4979 -0.05609 0.000 0.000 0.492 0.028 0.480
#> GSM751372 5 0.4738 0.02226 0.000 0.000 0.464 0.016 0.520
#> GSM751373 3 0.4127 0.41480 0.000 0.000 0.680 0.008 0.312
#> GSM751374 3 0.6537 0.15500 0.000 0.072 0.560 0.304 0.064
#> GSM751377 5 0.4536 0.57383 0.000 0.048 0.240 0.000 0.712
#> GSM751380 3 0.2773 0.57410 0.000 0.000 0.836 0.000 0.164
#> GSM751381 5 0.4503 0.67720 0.000 0.112 0.092 0.016 0.780
#> GSM751383 5 0.4519 0.66503 0.000 0.112 0.120 0.004 0.764
#> GSM751384 5 0.4523 0.65198 0.000 0.064 0.160 0.012 0.764
#> GSM751385 5 0.6266 0.39938 0.000 0.024 0.360 0.088 0.528
#> GSM751387 5 0.4240 0.67580 0.000 0.112 0.088 0.008 0.792
#> GSM751389 3 0.3343 0.57160 0.000 0.000 0.812 0.016 0.172
#> GSM751393 3 0.5987 0.39489 0.000 0.000 0.556 0.140 0.304
#> GSM751394 5 0.4507 0.67565 0.000 0.112 0.100 0.012 0.776
#> GSM751395 3 0.6694 0.12323 0.000 0.032 0.528 0.308 0.132
#> GSM751397 5 0.4655 0.67140 0.000 0.112 0.112 0.012 0.764
#> GSM751398 5 0.4118 0.67777 0.000 0.112 0.088 0.004 0.796
#> GSM751404 3 0.3074 0.56257 0.000 0.000 0.804 0.000 0.196
#> GSM751406 3 0.2012 0.57263 0.000 0.000 0.920 0.060 0.020
#> GSM751411 3 0.4446 0.05959 0.000 0.000 0.520 0.004 0.476
#> GSM751413 5 0.6685 0.39786 0.000 0.036 0.296 0.128 0.540
#> GSM751415 3 0.3109 0.56248 0.000 0.000 0.800 0.000 0.200
#> GSM751416 5 0.5183 0.46227 0.000 0.036 0.308 0.016 0.640
#> GSM751417 5 0.5183 0.46227 0.000 0.036 0.308 0.016 0.640
#> GSM751421 3 0.3876 0.53837 0.000 0.012 0.796 0.168 0.024
#> GSM751422 3 0.3876 0.53837 0.000 0.012 0.796 0.168 0.024
#> GSM751360 3 0.5678 0.37676 0.000 0.000 0.612 0.128 0.260
#> GSM751364 5 0.4931 0.31527 0.000 0.012 0.372 0.016 0.600
#> GSM751390 5 0.4552 0.64235 0.000 0.068 0.168 0.008 0.756
#> GSM751392 5 0.5665 0.62482 0.000 0.144 0.140 0.028 0.688
#> GSM751396 5 0.4935 0.62995 0.000 0.160 0.112 0.004 0.724
#> GSM751399 3 0.3366 0.53387 0.000 0.000 0.768 0.000 0.232
#> GSM751400 3 0.3143 0.56010 0.000 0.000 0.796 0.000 0.204
#> GSM751401 3 0.3143 0.56010 0.000 0.000 0.796 0.000 0.204
#> GSM751402 3 0.2891 0.57043 0.000 0.000 0.824 0.000 0.176
#> GSM751403 3 0.3109 0.56242 0.000 0.000 0.800 0.000 0.200
#> GSM751405 3 0.3359 0.57087 0.000 0.000 0.844 0.072 0.084
#> GSM751407 3 0.3143 0.56010 0.000 0.000 0.796 0.000 0.204
#> GSM751408 3 0.3461 0.54045 0.000 0.000 0.772 0.004 0.224
#> GSM751409 3 0.2806 0.57442 0.000 0.000 0.844 0.004 0.152
#> GSM751412 3 0.3461 0.54045 0.000 0.000 0.772 0.004 0.224
#> GSM751418 3 0.4510 0.15409 0.000 0.000 0.560 0.008 0.432
#> GSM751419 3 0.4510 0.15409 0.000 0.000 0.560 0.008 0.432
#> GSM751420 3 0.3477 0.55272 0.000 0.036 0.852 0.088 0.024
#> GSM751425 2 0.2409 0.88115 0.000 0.908 0.012 0.020 0.060
#> GSM751429 3 0.6410 0.34030 0.004 0.096 0.628 0.216 0.056
#> GSM751430 5 0.7839 0.21075 0.000 0.336 0.104 0.160 0.400
#> GSM751433 2 0.3413 0.85181 0.000 0.832 0.000 0.044 0.124
#> GSM751437 3 0.6562 0.27927 0.000 0.196 0.604 0.152 0.048
#> GSM751448 3 0.5908 0.37392 0.000 0.080 0.660 0.212 0.048
#> GSM751451 2 0.2795 0.87175 0.000 0.872 0.000 0.028 0.100
#> GSM751423 2 0.2444 0.88338 0.000 0.904 0.016 0.012 0.068
#> GSM751424 2 0.3460 0.84958 0.000 0.828 0.000 0.044 0.128
#> GSM751428 2 0.2264 0.88354 0.000 0.912 0.004 0.024 0.060
#> GSM751431 2 0.3090 0.86411 0.000 0.856 0.000 0.040 0.104
#> GSM751432 2 0.4098 0.82390 0.000 0.796 0.012 0.048 0.144
#> GSM751434 2 0.3507 0.84963 0.000 0.828 0.000 0.052 0.120
#> GSM751435 2 0.1282 0.88980 0.000 0.952 0.000 0.004 0.044
#> GSM751436 2 0.3460 0.84958 0.000 0.828 0.000 0.044 0.128
#> GSM751440 2 0.2006 0.88479 0.000 0.916 0.000 0.012 0.072
#> GSM751444 2 0.1525 0.88429 0.000 0.948 0.004 0.012 0.036
#> GSM751446 2 0.1471 0.87608 0.000 0.952 0.024 0.020 0.004
#> GSM751449 2 0.1372 0.87593 0.000 0.956 0.024 0.016 0.004
#> GSM751450 2 0.2983 0.86895 0.000 0.864 0.000 0.040 0.096
#> GSM751452 2 0.3460 0.84958 0.000 0.828 0.000 0.044 0.128
#> GSM751426 2 0.3141 0.86216 0.000 0.852 0.000 0.040 0.108
#> GSM751427 2 0.1369 0.88759 0.000 0.956 0.008 0.008 0.028
#> GSM751438 2 0.1885 0.86971 0.000 0.936 0.032 0.020 0.012
#> GSM751439 2 0.3262 0.78371 0.000 0.856 0.104 0.020 0.020
#> GSM751441 2 0.2002 0.87120 0.000 0.932 0.020 0.028 0.020
#> GSM751442 2 0.1799 0.87198 0.000 0.940 0.028 0.020 0.012
#> GSM751443 3 0.6628 0.00402 0.000 0.400 0.452 0.128 0.020
#> GSM751445 2 0.1117 0.87859 0.000 0.964 0.020 0.016 0.000
#> GSM751447 2 0.1804 0.87302 0.000 0.940 0.024 0.024 0.012
#> GSM751453 2 0.1605 0.88864 0.000 0.944 0.004 0.012 0.040
#> GSM751454 2 0.1605 0.88864 0.000 0.944 0.004 0.012 0.040
#> GSM751455 2 0.1799 0.87198 0.000 0.940 0.028 0.020 0.012
#> GSM751456 2 0.1799 0.87198 0.000 0.940 0.028 0.020 0.012
#> GSM751457 2 0.5539 0.56495 0.000 0.700 0.148 0.124 0.028
#> GSM751458 2 0.5539 0.56495 0.000 0.700 0.148 0.124 0.028
cbind(get_classes(res, k = 6), get_membership(res, k = 6))
#> class entropy silhouette p1 p2 p3 p4 p5 p6
#> GSM751298 4 0.4022 0.563748 0.360 0.000 0.004 0.628 0.000 0.008
#> GSM751304 6 0.4204 0.719049 0.048 0.032 0.008 0.072 0.028 0.812
#> GSM751305 6 0.4601 0.700834 0.040 0.032 0.008 0.116 0.028 0.776
#> GSM751307 6 0.5549 0.679678 0.040 0.060 0.012 0.088 0.076 0.724
#> GSM751310 4 0.4985 0.714851 0.184 0.004 0.012 0.708 0.016 0.076
#> GSM751314 4 0.4788 0.724162 0.196 0.004 0.008 0.712 0.012 0.068
#> GSM751316 4 0.6390 0.284169 0.152 0.004 0.012 0.484 0.016 0.332
#> GSM751318 4 0.3998 0.603561 0.316 0.004 0.004 0.668 0.000 0.008
#> GSM751342 4 0.3595 0.706784 0.180 0.004 0.000 0.780 0.000 0.036
#> GSM751346 1 0.1116 0.717963 0.960 0.000 0.008 0.004 0.000 0.028
#> GSM751347 1 0.1313 0.711339 0.952 0.000 0.016 0.004 0.000 0.028
#> GSM751348 6 0.7187 0.419660 0.008 0.040 0.020 0.192 0.308 0.432
#> GSM751349 5 0.6124 0.254226 0.000 0.076 0.028 0.044 0.588 0.264
#> GSM751352 6 0.5355 0.722785 0.120 0.052 0.000 0.032 0.080 0.716
#> GSM751353 6 0.5490 0.700408 0.076 0.080 0.000 0.016 0.132 0.696
#> GSM751354 6 0.4675 0.721858 0.088 0.044 0.008 0.028 0.052 0.780
#> GSM751355 6 0.5011 0.713967 0.076 0.056 0.012 0.024 0.072 0.760
#> GSM751358 6 0.5717 0.605797 0.000 0.016 0.032 0.264 0.076 0.612
#> GSM751359 6 0.6400 0.493307 0.000 0.028 0.028 0.112 0.308 0.524
#> GSM751294 6 0.5652 0.727220 0.064 0.048 0.024 0.052 0.088 0.724
#> GSM751296 1 0.3560 0.530502 0.732 0.000 0.004 0.256 0.000 0.008
#> GSM751297 1 0.4615 0.353281 0.688 0.000 0.024 0.020 0.012 0.256
#> GSM751299 6 0.5420 0.722927 0.120 0.060 0.000 0.032 0.076 0.712
#> GSM751300 1 0.1148 0.721541 0.960 0.000 0.004 0.020 0.000 0.016
#> GSM751301 1 0.5986 0.001218 0.472 0.028 0.004 0.408 0.004 0.084
#> GSM751302 1 0.1116 0.717963 0.960 0.000 0.008 0.004 0.000 0.028
#> GSM751303 4 0.4992 0.672548 0.136 0.004 0.012 0.720 0.016 0.112
#> GSM751306 4 0.4873 0.712875 0.176 0.004 0.012 0.720 0.016 0.072
#> GSM751308 6 0.6845 0.381517 0.256 0.032 0.024 0.152 0.012 0.524
#> GSM751309 4 0.4751 0.721117 0.184 0.004 0.012 0.720 0.008 0.072
#> GSM751311 4 0.4705 0.724630 0.192 0.004 0.012 0.720 0.008 0.064
#> GSM751312 4 0.6535 0.353756 0.192 0.004 0.012 0.480 0.016 0.296
#> GSM751313 1 0.1218 0.717775 0.956 0.000 0.004 0.028 0.000 0.012
#> GSM751315 4 0.5107 0.706595 0.260 0.004 0.008 0.656 0.016 0.056
#> GSM751317 4 0.5028 0.720664 0.212 0.004 0.012 0.692 0.016 0.064
#> GSM751320 4 0.3989 0.337427 0.468 0.000 0.004 0.528 0.000 0.000
#> GSM751321 4 0.4993 0.720543 0.192 0.004 0.012 0.704 0.016 0.072
#> GSM751322 4 0.3862 0.541685 0.388 0.000 0.004 0.608 0.000 0.000
#> GSM751324 4 0.3807 0.573235 0.368 0.000 0.004 0.628 0.000 0.000
#> GSM751325 4 0.3950 0.446080 0.432 0.000 0.004 0.564 0.000 0.000
#> GSM751332 4 0.3950 0.439807 0.432 0.000 0.004 0.564 0.000 0.000
#> GSM751334 1 0.3997 -0.247087 0.508 0.000 0.004 0.488 0.000 0.000
#> GSM751339 1 0.4589 0.570576 0.732 0.000 0.052 0.172 0.000 0.044
#> GSM751341 4 0.3807 0.697151 0.228 0.000 0.004 0.740 0.000 0.028
#> GSM751343 4 0.3944 0.456311 0.428 0.000 0.004 0.568 0.000 0.000
#> GSM751344 6 0.5464 0.723485 0.100 0.068 0.000 0.032 0.088 0.712
#> GSM751345 6 0.5464 0.723485 0.100 0.068 0.000 0.032 0.088 0.712
#> GSM751356 6 0.6542 0.704749 0.084 0.048 0.020 0.132 0.072 0.644
#> GSM751357 6 0.6542 0.704749 0.084 0.048 0.020 0.132 0.072 0.644
#> GSM751293 1 0.5821 -0.006344 0.476 0.028 0.004 0.412 0.000 0.080
#> GSM751295 1 0.1116 0.717963 0.960 0.000 0.008 0.004 0.000 0.028
#> GSM751319 4 0.5080 0.719346 0.220 0.004 0.012 0.684 0.016 0.064
#> GSM751323 1 0.3890 0.146657 0.596 0.000 0.004 0.400 0.000 0.000
#> GSM751326 1 0.3163 0.558027 0.764 0.000 0.004 0.232 0.000 0.000
#> GSM751327 1 0.3852 0.204878 0.612 0.000 0.004 0.384 0.000 0.000
#> GSM751328 4 0.3728 0.603513 0.344 0.000 0.004 0.652 0.000 0.000
#> GSM751329 1 0.3795 0.279715 0.632 0.000 0.004 0.364 0.000 0.000
#> GSM751330 1 0.0713 0.718947 0.972 0.000 0.000 0.028 0.000 0.000
#> GSM751331 1 0.0777 0.719986 0.972 0.000 0.004 0.000 0.000 0.024
#> GSM751333 1 0.0603 0.720157 0.980 0.000 0.004 0.016 0.000 0.000
#> GSM751335 1 0.0713 0.718947 0.972 0.000 0.000 0.028 0.000 0.000
#> GSM751336 1 0.0692 0.720517 0.976 0.000 0.004 0.000 0.000 0.020
#> GSM751337 1 0.3298 0.549538 0.756 0.000 0.008 0.236 0.000 0.000
#> GSM751338 1 0.3231 0.606604 0.800 0.000 0.008 0.180 0.000 0.012
#> GSM751340 6 0.6172 0.560370 0.144 0.000 0.172 0.068 0.008 0.608
#> GSM751350 1 0.1003 0.719410 0.964 0.000 0.004 0.004 0.000 0.028
#> GSM751351 1 0.1003 0.719410 0.964 0.000 0.004 0.004 0.000 0.028
#> GSM751362 3 0.5857 0.504625 0.012 0.000 0.628 0.052 0.216 0.092
#> GSM751363 5 0.6213 0.430934 0.000 0.004 0.216 0.068 0.584 0.128
#> GSM751367 3 0.7295 0.356907 0.068 0.004 0.484 0.080 0.072 0.292
#> GSM751368 5 0.6454 0.321940 0.000 0.048 0.372 0.048 0.484 0.048
#> GSM751371 3 0.6116 0.402503 0.000 0.000 0.548 0.096 0.068 0.288
#> GSM751375 5 0.5956 0.388451 0.000 0.076 0.052 0.032 0.640 0.200
#> GSM751376 6 0.6686 0.152392 0.004 0.060 0.332 0.064 0.036 0.504
#> GSM751378 5 0.6574 0.314364 0.000 0.032 0.208 0.028 0.548 0.184
#> GSM751379 6 0.6686 0.152392 0.004 0.060 0.332 0.064 0.036 0.504
#> GSM751382 5 0.5779 0.434014 0.000 0.076 0.052 0.028 0.660 0.184
#> GSM751386 5 0.2383 0.676695 0.000 0.052 0.020 0.000 0.900 0.028
#> GSM751388 5 0.2506 0.668217 0.000 0.052 0.068 0.000 0.880 0.000
#> GSM751391 3 0.5740 0.410832 0.000 0.000 0.572 0.080 0.048 0.300
#> GSM751410 3 0.6376 0.422936 0.012 0.000 0.548 0.088 0.072 0.280
#> GSM751414 5 0.5578 0.215410 0.000 0.004 0.412 0.048 0.500 0.036
#> GSM751361 5 0.4722 0.553045 0.000 0.004 0.216 0.048 0.704 0.028
#> GSM751365 3 0.5054 0.059517 0.000 0.004 0.544 0.036 0.400 0.016
#> GSM751366 3 0.3719 0.547992 0.012 0.004 0.784 0.012 0.180 0.008
#> GSM751369 3 0.5813 0.429338 0.000 0.004 0.584 0.080 0.048 0.284
#> GSM751370 5 0.5730 0.280832 0.000 0.004 0.368 0.052 0.528 0.048
#> GSM751372 5 0.5397 0.284620 0.000 0.004 0.376 0.048 0.544 0.028
#> GSM751373 3 0.4662 0.388521 0.000 0.004 0.668 0.032 0.276 0.020
#> GSM751374 6 0.6686 0.152392 0.004 0.060 0.332 0.064 0.036 0.504
#> GSM751377 5 0.4609 0.584086 0.000 0.016 0.196 0.036 0.728 0.024
#> GSM751380 3 0.2174 0.606649 0.008 0.000 0.896 0.000 0.088 0.008
#> GSM751381 5 0.2461 0.675636 0.000 0.048 0.020 0.004 0.900 0.028
#> GSM751383 5 0.2724 0.664403 0.000 0.052 0.084 0.000 0.864 0.000
#> GSM751384 5 0.2818 0.675312 0.000 0.036 0.044 0.008 0.884 0.028
#> GSM751385 5 0.5384 0.494169 0.000 0.008 0.132 0.024 0.668 0.168
#> GSM751387 5 0.2681 0.674809 0.000 0.048 0.044 0.008 0.888 0.012
#> GSM751389 3 0.4123 0.578736 0.000 0.004 0.788 0.032 0.116 0.060
#> GSM751393 3 0.7066 0.291808 0.000 0.008 0.396 0.052 0.252 0.292
#> GSM751394 5 0.2459 0.673835 0.000 0.052 0.020 0.000 0.896 0.032
#> GSM751395 6 0.6585 0.102268 0.000 0.016 0.312 0.064 0.100 0.508
#> GSM751397 5 0.2693 0.671279 0.000 0.048 0.024 0.004 0.888 0.036
#> GSM751398 5 0.2316 0.678860 0.000 0.044 0.024 0.004 0.908 0.020
#> GSM751404 3 0.2653 0.591208 0.012 0.000 0.844 0.000 0.144 0.000
#> GSM751406 3 0.4219 0.586965 0.012 0.000 0.776 0.024 0.044 0.144
#> GSM751411 5 0.4700 0.062779 0.000 0.000 0.472 0.028 0.492 0.008
#> GSM751413 5 0.6908 0.376862 0.000 0.012 0.176 0.100 0.528 0.184
#> GSM751415 3 0.2794 0.593680 0.012 0.000 0.840 0.004 0.144 0.000
#> GSM751416 5 0.4750 0.536671 0.000 0.004 0.232 0.048 0.692 0.024
#> GSM751417 5 0.4750 0.536671 0.000 0.004 0.232 0.048 0.692 0.024
#> GSM751421 3 0.5908 0.450819 0.000 0.000 0.580 0.088 0.064 0.268
#> GSM751422 3 0.5908 0.450819 0.000 0.000 0.580 0.088 0.064 0.268
#> GSM751360 3 0.7112 0.333813 0.000 0.000 0.448 0.124 0.244 0.184
#> GSM751364 5 0.5181 0.436080 0.000 0.004 0.304 0.048 0.616 0.028
#> GSM751390 5 0.3190 0.661935 0.000 0.044 0.100 0.008 0.844 0.004
#> GSM751392 5 0.4485 0.606673 0.000 0.068 0.064 0.020 0.784 0.064
#> GSM751396 5 0.5506 0.587367 0.004 0.112 0.132 0.024 0.696 0.032
#> GSM751399 3 0.2913 0.560465 0.000 0.004 0.812 0.000 0.180 0.004
#> GSM751400 3 0.2872 0.586867 0.012 0.004 0.832 0.000 0.152 0.000
#> GSM751401 3 0.2692 0.591207 0.012 0.000 0.840 0.000 0.148 0.000
#> GSM751402 3 0.2455 0.601589 0.012 0.000 0.872 0.004 0.112 0.000
#> GSM751403 3 0.2653 0.593309 0.012 0.000 0.844 0.000 0.144 0.000
#> GSM751405 3 0.4549 0.587683 0.012 0.000 0.748 0.016 0.076 0.148
#> GSM751407 3 0.2768 0.585788 0.012 0.000 0.832 0.000 0.156 0.000
#> GSM751408 3 0.3018 0.572265 0.012 0.004 0.816 0.000 0.168 0.000
#> GSM751409 3 0.2418 0.604942 0.000 0.000 0.884 0.008 0.092 0.016
#> GSM751412 3 0.3053 0.568512 0.012 0.004 0.812 0.000 0.172 0.000
#> GSM751418 3 0.5137 0.036171 0.000 0.004 0.536 0.036 0.404 0.020
#> GSM751419 3 0.5137 0.036171 0.000 0.004 0.536 0.036 0.404 0.020
#> GSM751420 3 0.4424 0.527332 0.004 0.000 0.732 0.032 0.032 0.200
#> GSM751425 2 0.3714 0.809745 0.000 0.832 0.032 0.028 0.080 0.028
#> GSM751429 3 0.7853 0.135885 0.052 0.112 0.404 0.044 0.044 0.344
#> GSM751430 2 0.8593 -0.000358 0.008 0.292 0.112 0.080 0.276 0.232
#> GSM751433 2 0.4592 0.794788 0.004 0.768 0.004 0.072 0.096 0.056
#> GSM751437 3 0.7443 0.138781 0.008 0.200 0.420 0.040 0.036 0.296
#> GSM751448 3 0.6941 0.265489 0.028 0.080 0.500 0.032 0.036 0.324
#> GSM751451 2 0.4158 0.814822 0.004 0.800 0.004 0.068 0.080 0.044
#> GSM751423 2 0.3388 0.827848 0.004 0.852 0.012 0.024 0.076 0.032
#> GSM751424 2 0.4592 0.794788 0.004 0.768 0.004 0.072 0.096 0.056
#> GSM751428 2 0.3415 0.826998 0.004 0.856 0.012 0.044 0.040 0.044
#> GSM751431 2 0.4123 0.808353 0.004 0.804 0.004 0.064 0.072 0.052
#> GSM751432 2 0.5495 0.760957 0.004 0.720 0.044 0.072 0.100 0.060
#> GSM751434 2 0.4649 0.792470 0.004 0.764 0.004 0.072 0.096 0.060
#> GSM751435 2 0.2627 0.833362 0.004 0.892 0.004 0.032 0.056 0.012
#> GSM751436 2 0.4592 0.794788 0.004 0.768 0.004 0.072 0.096 0.056
#> GSM751440 2 0.2812 0.830045 0.004 0.876 0.000 0.032 0.072 0.016
#> GSM751444 2 0.2875 0.828583 0.004 0.884 0.008 0.048 0.024 0.032
#> GSM751446 2 0.2439 0.809653 0.000 0.904 0.040 0.008 0.020 0.028
#> GSM751449 2 0.2444 0.808322 0.000 0.904 0.036 0.008 0.020 0.032
#> GSM751450 2 0.4012 0.811102 0.004 0.812 0.004 0.064 0.064 0.052
#> GSM751452 2 0.4592 0.794788 0.004 0.768 0.004 0.072 0.096 0.056
#> GSM751426 2 0.4178 0.806726 0.004 0.800 0.004 0.068 0.072 0.052
#> GSM751427 2 0.2358 0.829187 0.000 0.908 0.012 0.020 0.044 0.016
#> GSM751438 2 0.3387 0.795697 0.004 0.860 0.048 0.028 0.024 0.036
#> GSM751439 2 0.3484 0.773084 0.012 0.848 0.080 0.012 0.016 0.032
#> GSM751441 2 0.3402 0.798059 0.004 0.860 0.044 0.032 0.028 0.032
#> GSM751442 2 0.3083 0.805095 0.004 0.876 0.048 0.024 0.024 0.024
#> GSM751443 3 0.7243 0.038363 0.024 0.352 0.356 0.016 0.016 0.236
#> GSM751445 2 0.2327 0.807919 0.000 0.908 0.028 0.008 0.012 0.044
#> GSM751447 2 0.3175 0.805244 0.004 0.872 0.040 0.020 0.032 0.032
#> GSM751453 2 0.2775 0.831573 0.000 0.888 0.020 0.024 0.048 0.020
#> GSM751454 2 0.2775 0.831573 0.000 0.888 0.020 0.024 0.048 0.020
#> GSM751455 2 0.3000 0.805402 0.004 0.880 0.048 0.020 0.024 0.024
#> GSM751456 2 0.3000 0.805402 0.004 0.880 0.048 0.020 0.024 0.024
#> GSM751457 2 0.6672 0.405960 0.004 0.564 0.116 0.056 0.028 0.232
#> GSM751458 2 0.6672 0.405960 0.004 0.564 0.116 0.056 0.028 0.232
Heatmaps for the consensus matrix. It visualizes the probability of two samples to be in a same group.
consensus_heatmap(res, k = 2)
consensus_heatmap(res, k = 3)
consensus_heatmap(res, k = 4)
consensus_heatmap(res, k = 5)
consensus_heatmap(res, k = 6)
Heatmaps for the membership of samples in all partitions to see how consistent they are:
membership_heatmap(res, k = 2)
membership_heatmap(res, k = 3)
membership_heatmap(res, k = 4)
membership_heatmap(res, k = 5)
membership_heatmap(res, k = 6)
As soon as we have had the classes for columns, we can look for signatures which are significantly different between classes which can be candidate marks for certain classes. Following are the heatmaps for signatures.
Signature heatmaps where rows are scaled:
get_signatures(res, k = 2)
get_signatures(res, k = 3)
get_signatures(res, k = 4)
get_signatures(res, k = 5)
get_signatures(res, k = 6)
Signature heatmaps where rows are not scaled:
get_signatures(res, k = 2, scale_rows = FALSE)
get_signatures(res, k = 3, scale_rows = FALSE)
get_signatures(res, k = 4, scale_rows = FALSE)
get_signatures(res, k = 5, scale_rows = FALSE)
get_signatures(res, k = 6, scale_rows = FALSE)
Compare the overlap of signatures from different k:
compare_signatures(res)
get_signature() returns a data frame invisibly. TO get the list of signatures, the function
call should be assigned to a variable explicitly. In following code, if plot argument is set
to FALSE, no heatmap is plotted while only the differential analysis is performed.
# code only for demonstration
tb = get_signature(res, k = ..., plot = FALSE)
An example of the output of tb is:
#> which_row fdr mean_1 mean_2 scaled_mean_1 scaled_mean_2 km
#> 1 38 0.042760348 8.373488 9.131774 -0.5533452 0.5164555 1
#> 2 40 0.018707592 7.106213 8.469186 -0.6173731 0.5762149 1
#> 3 55 0.019134737 10.221463 11.207825 -0.6159697 0.5749050 1
#> 4 59 0.006059896 5.921854 7.869574 -0.6899429 0.6439467 1
#> 5 60 0.018055526 8.928898 10.211722 -0.6204761 0.5791110 1
#> 6 98 0.009384629 15.714769 14.887706 0.6635654 -0.6193277 2
...
The columns in tb are:
which_row: row indices corresponding to the input matrix.fdr: FDR for the differential test. mean_x: The mean value in group x.scaled_mean_x: The mean value in group x after rows are scaled.km: Row groups if k-means clustering is applied to rows.UMAP plot which shows how samples are separated.
dimension_reduction(res, k = 2, method = "UMAP")
dimension_reduction(res, k = 3, method = "UMAP")
dimension_reduction(res, k = 4, method = "UMAP")
dimension_reduction(res, k = 5, method = "UMAP")
dimension_reduction(res, k = 6, method = "UMAP")
Following heatmap shows how subgroups are split when increasing k:
collect_classes(res)
Test correlation between subgroups and known annotations. If the known annotation is numeric, one-way ANOVA test is applied, and if the known annotation is discrete, chi-squared contingency table test is applied.
test_to_known_factors(res)
#> n tissue(p) disease.state(p) agent(p) k
#> SD:kmeans 166 1.10e-23 0.131028 0.219963 2
#> SD:kmeans 132 4.69e-46 0.775590 0.963588 3
#> SD:kmeans 122 7.85e-50 0.004120 0.013521 4
#> SD:kmeans 127 2.44e-50 0.000712 0.001546 5
#> SD:kmeans 113 5.92e-43 0.003398 0.000241 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 4537 rows and 166 columns.
#> Top rows (454, 908, 1361, 1814, 2268) 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 0.598 0.868 0.931 0.4846 0.516 0.516
#> 3 3 0.720 0.833 0.920 0.3734 0.707 0.486
#> 4 4 0.737 0.707 0.809 0.1252 0.851 0.596
#> 5 5 0.704 0.631 0.779 0.0656 0.884 0.600
#> 6 6 0.720 0.619 0.779 0.0435 0.915 0.629
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
#> GSM751298 1 0.0000 0.9175 1.000 0.000
#> GSM751304 1 0.8327 0.7114 0.736 0.264
#> GSM751305 1 0.8555 0.6907 0.720 0.280
#> GSM751307 1 0.6623 0.7950 0.828 0.172
#> GSM751310 1 0.0000 0.9175 1.000 0.000
#> GSM751314 1 0.0000 0.9175 1.000 0.000
#> GSM751316 1 0.0000 0.9175 1.000 0.000
#> GSM751318 1 0.0000 0.9175 1.000 0.000
#> GSM751342 1 0.0000 0.9175 1.000 0.000
#> GSM751346 1 0.0000 0.9175 1.000 0.000
#> GSM751347 1 0.0376 0.9149 0.996 0.004
#> GSM751348 1 0.7299 0.7708 0.796 0.204
#> GSM751349 2 0.1843 0.9167 0.028 0.972
#> GSM751352 1 0.7815 0.7420 0.768 0.232
#> GSM751353 2 0.7056 0.7264 0.192 0.808
#> GSM751354 1 0.9323 0.5802 0.652 0.348
#> GSM751355 2 0.6148 0.7851 0.152 0.848
#> GSM751358 1 1.0000 0.1906 0.500 0.500
#> GSM751359 2 0.0000 0.9279 0.000 1.000
#> GSM751294 1 0.8443 0.7019 0.728 0.272
#> GSM751296 1 0.0000 0.9175 1.000 0.000
#> GSM751297 1 0.0000 0.9175 1.000 0.000
#> GSM751299 1 0.7815 0.7420 0.768 0.232
#> GSM751300 1 0.0000 0.9175 1.000 0.000
#> GSM751301 1 0.4690 0.8506 0.900 0.100
#> GSM751302 1 0.0000 0.9175 1.000 0.000
#> GSM751303 1 0.0000 0.9175 1.000 0.000
#> GSM751306 1 0.0000 0.9175 1.000 0.000
#> GSM751308 1 0.0672 0.9130 0.992 0.008
#> GSM751309 1 0.0000 0.9175 1.000 0.000
#> GSM751311 1 0.0000 0.9175 1.000 0.000
#> GSM751312 1 0.0000 0.9175 1.000 0.000
#> GSM751313 1 0.0000 0.9175 1.000 0.000
#> GSM751315 1 0.0000 0.9175 1.000 0.000
#> GSM751317 1 0.0000 0.9175 1.000 0.000
#> GSM751320 1 0.0000 0.9175 1.000 0.000
#> GSM751321 1 0.0000 0.9175 1.000 0.000
#> GSM751322 1 0.0000 0.9175 1.000 0.000
#> GSM751324 1 0.0000 0.9175 1.000 0.000
#> GSM751325 1 0.0000 0.9175 1.000 0.000
#> GSM751332 1 0.0000 0.9175 1.000 0.000
#> GSM751334 1 0.0000 0.9175 1.000 0.000
#> GSM751339 1 0.0000 0.9175 1.000 0.000
#> GSM751341 1 0.0000 0.9175 1.000 0.000
#> GSM751343 1 0.0000 0.9175 1.000 0.000
#> GSM751344 1 0.8144 0.7206 0.748 0.252
#> GSM751345 1 0.8081 0.7251 0.752 0.248
#> GSM751356 1 0.7883 0.7381 0.764 0.236
#> GSM751357 1 0.7883 0.7381 0.764 0.236
#> GSM751293 1 0.4562 0.8532 0.904 0.096
#> GSM751295 1 0.0000 0.9175 1.000 0.000
#> GSM751319 1 0.0000 0.9175 1.000 0.000
#> GSM751323 1 0.0000 0.9175 1.000 0.000
#> GSM751326 1 0.0000 0.9175 1.000 0.000
#> GSM751327 1 0.0000 0.9175 1.000 0.000
#> GSM751328 1 0.0000 0.9175 1.000 0.000
#> GSM751329 1 0.0000 0.9175 1.000 0.000
#> GSM751330 1 0.0000 0.9175 1.000 0.000
#> GSM751331 1 0.0000 0.9175 1.000 0.000
#> GSM751333 1 0.0000 0.9175 1.000 0.000
#> GSM751335 1 0.0000 0.9175 1.000 0.000
#> GSM751336 1 0.0000 0.9175 1.000 0.000
#> GSM751337 1 0.0000 0.9175 1.000 0.000
#> GSM751338 1 0.0000 0.9175 1.000 0.000
#> GSM751340 1 0.0000 0.9175 1.000 0.000
#> GSM751350 1 0.0000 0.9175 1.000 0.000
#> GSM751351 1 0.0000 0.9175 1.000 0.000
#> GSM751362 2 0.8081 0.7442 0.248 0.752
#> GSM751363 2 0.1184 0.9259 0.016 0.984
#> GSM751367 1 0.8955 0.4991 0.688 0.312
#> GSM751368 2 0.0000 0.9279 0.000 1.000
#> GSM751371 1 0.9795 0.2169 0.584 0.416
#> GSM751375 2 0.0000 0.9279 0.000 1.000
#> GSM751376 2 0.0938 0.9265 0.012 0.988
#> GSM751378 2 0.0000 0.9279 0.000 1.000
#> GSM751379 2 0.0938 0.9265 0.012 0.988
#> GSM751382 2 0.0000 0.9279 0.000 1.000
#> GSM751386 2 0.0000 0.9279 0.000 1.000
#> GSM751388 2 0.0000 0.9279 0.000 1.000
#> GSM751391 2 0.1414 0.9255 0.020 0.980
#> GSM751410 1 0.6973 0.7273 0.812 0.188
#> GSM751414 2 0.7602 0.7804 0.220 0.780
#> GSM751361 2 0.0000 0.9279 0.000 1.000
#> GSM751365 2 0.5059 0.8813 0.112 0.888
#> GSM751366 2 0.7883 0.7600 0.236 0.764
#> GSM751369 2 0.7745 0.7731 0.228 0.772
#> GSM751370 2 0.7883 0.7594 0.236 0.764
#> GSM751372 2 0.5059 0.8813 0.112 0.888
#> GSM751373 2 0.7602 0.7804 0.220 0.780
#> GSM751374 2 0.0938 0.9265 0.012 0.988
#> GSM751377 2 0.0000 0.9279 0.000 1.000
#> GSM751380 2 0.7453 0.7912 0.212 0.788
#> GSM751381 2 0.0000 0.9279 0.000 1.000
#> GSM751383 2 0.0000 0.9279 0.000 1.000
#> GSM751384 2 0.0000 0.9279 0.000 1.000
#> GSM751385 2 0.0000 0.9279 0.000 1.000
#> GSM751387 2 0.0000 0.9279 0.000 1.000
#> GSM751389 2 0.3274 0.9089 0.060 0.940
#> GSM751393 2 0.0000 0.9279 0.000 1.000
#> GSM751394 2 0.0000 0.9279 0.000 1.000
#> GSM751395 2 0.0000 0.9279 0.000 1.000
#> GSM751397 2 0.0000 0.9279 0.000 1.000
#> GSM751398 2 0.0000 0.9279 0.000 1.000
#> GSM751404 2 0.6887 0.8222 0.184 0.816
#> GSM751406 2 0.6712 0.8297 0.176 0.824
#> GSM751411 2 0.4690 0.8877 0.100 0.900
#> GSM751413 2 0.0000 0.9279 0.000 1.000
#> GSM751415 2 0.7056 0.8142 0.192 0.808
#> GSM751416 2 0.0000 0.9279 0.000 1.000
#> GSM751417 2 0.0000 0.9279 0.000 1.000
#> GSM751421 2 0.7219 0.8049 0.200 0.800
#> GSM751422 2 0.7219 0.8049 0.200 0.800
#> GSM751360 2 0.6343 0.8463 0.160 0.840
#> GSM751364 2 0.3114 0.9117 0.056 0.944
#> GSM751390 2 0.0000 0.9279 0.000 1.000
#> GSM751392 2 0.0000 0.9279 0.000 1.000
#> GSM751396 2 0.0000 0.9279 0.000 1.000
#> GSM751399 2 0.4161 0.8969 0.084 0.916
#> GSM751400 2 0.3431 0.9073 0.064 0.936
#> GSM751401 2 0.6887 0.8222 0.184 0.816
#> GSM751402 2 0.6973 0.8181 0.188 0.812
#> GSM751403 2 0.4690 0.8877 0.100 0.900
#> GSM751405 2 0.6712 0.8297 0.176 0.824
#> GSM751407 2 0.6148 0.8509 0.152 0.848
#> GSM751408 2 0.4690 0.8877 0.100 0.900
#> GSM751409 2 0.3114 0.9106 0.056 0.944
#> GSM751412 2 0.5842 0.8607 0.140 0.860
#> GSM751418 2 0.5059 0.8813 0.112 0.888
#> GSM751419 2 0.5059 0.8813 0.112 0.888
#> GSM751420 2 0.4022 0.9007 0.080 0.920
#> GSM751425 2 0.0000 0.9279 0.000 1.000
#> GSM751429 1 0.9977 -0.0488 0.528 0.472
#> GSM751430 2 0.0376 0.9278 0.004 0.996
#> GSM751433 2 0.1414 0.9235 0.020 0.980
#> GSM751437 2 0.6623 0.8335 0.172 0.828
#> GSM751448 2 0.9522 0.5173 0.372 0.628
#> GSM751451 2 0.0938 0.9263 0.012 0.988
#> GSM751423 2 0.0000 0.9279 0.000 1.000
#> GSM751424 2 0.0672 0.9273 0.008 0.992
#> GSM751428 2 0.0938 0.9263 0.012 0.988
#> GSM751431 2 0.1184 0.9251 0.016 0.984
#> GSM751432 2 0.0376 0.9277 0.004 0.996
#> GSM751434 2 0.1414 0.9235 0.020 0.980
#> GSM751435 2 0.2236 0.9136 0.036 0.964
#> GSM751436 2 0.1184 0.9251 0.016 0.984
#> GSM751440 2 0.1184 0.9251 0.016 0.984
#> GSM751444 2 0.1184 0.9251 0.016 0.984
#> GSM751446 2 0.1184 0.9251 0.016 0.984
#> GSM751449 2 0.0000 0.9279 0.000 1.000
#> GSM751450 2 0.0672 0.9273 0.008 0.992
#> GSM751452 2 0.0672 0.9273 0.008 0.992
#> GSM751426 2 0.1184 0.9251 0.016 0.984
#> GSM751427 2 0.0672 0.9273 0.008 0.992
#> GSM751438 2 0.0672 0.9273 0.008 0.992
#> GSM751439 2 0.6531 0.8431 0.168 0.832
#> GSM751441 2 0.0000 0.9279 0.000 1.000
#> GSM751442 2 0.1184 0.9251 0.016 0.984
#> GSM751443 2 0.6531 0.8423 0.168 0.832
#> GSM751445 2 0.0000 0.9279 0.000 1.000
#> GSM751447 2 0.0000 0.9279 0.000 1.000
#> GSM751453 2 0.0672 0.9273 0.008 0.992
#> GSM751454 2 0.0672 0.9273 0.008 0.992
#> GSM751455 2 0.1184 0.9251 0.016 0.984
#> GSM751456 2 0.1184 0.9251 0.016 0.984
#> GSM751457 2 0.0000 0.9279 0.000 1.000
#> GSM751458 2 0.0000 0.9279 0.000 1.000
cbind(get_classes(res, k = 3), get_membership(res, k = 3))
#> class entropy silhouette p1 p2 p3
#> GSM751298 1 0.0000 0.998 1.000 0.000 0.000
#> GSM751304 2 0.5466 0.799 0.160 0.800 0.040
#> GSM751305 2 0.5355 0.801 0.160 0.804 0.036
#> GSM751307 2 0.6654 0.276 0.456 0.536 0.008
#> GSM751310 1 0.0000 0.998 1.000 0.000 0.000
#> GSM751314 1 0.0000 0.998 1.000 0.000 0.000
#> GSM751316 1 0.0000 0.998 1.000 0.000 0.000
#> GSM751318 1 0.0000 0.998 1.000 0.000 0.000
#> GSM751342 1 0.0000 0.998 1.000 0.000 0.000
#> GSM751346 1 0.0000 0.998 1.000 0.000 0.000
#> GSM751347 1 0.0424 0.990 0.992 0.000 0.008
#> GSM751348 2 0.5024 0.764 0.220 0.776 0.004
#> GSM751349 2 0.4002 0.759 0.000 0.840 0.160
#> GSM751352 2 0.4861 0.788 0.192 0.800 0.008
#> GSM751353 2 0.4453 0.815 0.152 0.836 0.012
#> GSM751354 2 0.5178 0.802 0.164 0.808 0.028
#> GSM751355 2 0.5331 0.806 0.076 0.824 0.100
#> GSM751358 2 0.2492 0.869 0.016 0.936 0.048
#> GSM751359 2 0.4399 0.721 0.000 0.812 0.188
#> GSM751294 2 0.4196 0.839 0.112 0.864 0.024
#> GSM751296 1 0.0000 0.998 1.000 0.000 0.000
#> GSM751297 1 0.0661 0.987 0.988 0.008 0.004
#> GSM751299 2 0.4755 0.794 0.184 0.808 0.008
#> GSM751300 1 0.0000 0.998 1.000 0.000 0.000
#> GSM751301 1 0.0000 0.998 1.000 0.000 0.000
#> GSM751302 1 0.0000 0.998 1.000 0.000 0.000
#> GSM751303 1 0.0000 0.998 1.000 0.000 0.000
#> GSM751306 1 0.0000 0.998 1.000 0.000 0.000
#> GSM751308 1 0.1832 0.952 0.956 0.036 0.008
#> GSM751309 1 0.0000 0.998 1.000 0.000 0.000
#> GSM751311 1 0.0000 0.998 1.000 0.000 0.000
#> GSM751312 1 0.0000 0.998 1.000 0.000 0.000
#> GSM751313 1 0.0000 0.998 1.000 0.000 0.000
#> GSM751315 1 0.0000 0.998 1.000 0.000 0.000
#> GSM751317 1 0.0000 0.998 1.000 0.000 0.000
#> GSM751320 1 0.0000 0.998 1.000 0.000 0.000
#> GSM751321 1 0.0000 0.998 1.000 0.000 0.000
#> GSM751322 1 0.0000 0.998 1.000 0.000 0.000
#> GSM751324 1 0.0000 0.998 1.000 0.000 0.000
#> GSM751325 1 0.0000 0.998 1.000 0.000 0.000
#> GSM751332 1 0.0000 0.998 1.000 0.000 0.000
#> GSM751334 1 0.0000 0.998 1.000 0.000 0.000
#> GSM751339 1 0.0424 0.990 0.992 0.000 0.008
#> GSM751341 1 0.0000 0.998 1.000 0.000 0.000
#> GSM751343 1 0.0000 0.998 1.000 0.000 0.000
#> GSM751344 2 0.4233 0.812 0.160 0.836 0.004
#> GSM751345 2 0.4233 0.812 0.160 0.836 0.004
#> GSM751356 2 0.5072 0.783 0.196 0.792 0.012
#> GSM751357 2 0.5072 0.783 0.196 0.792 0.012
#> GSM751293 1 0.0000 0.998 1.000 0.000 0.000
#> GSM751295 1 0.0000 0.998 1.000 0.000 0.000
#> GSM751319 1 0.0000 0.998 1.000 0.000 0.000
#> GSM751323 1 0.0000 0.998 1.000 0.000 0.000
#> GSM751326 1 0.0000 0.998 1.000 0.000 0.000
#> GSM751327 1 0.0000 0.998 1.000 0.000 0.000
#> GSM751328 1 0.0000 0.998 1.000 0.000 0.000
#> GSM751329 1 0.0000 0.998 1.000 0.000 0.000
#> GSM751330 1 0.0000 0.998 1.000 0.000 0.000
#> GSM751331 1 0.0000 0.998 1.000 0.000 0.000
#> GSM751333 1 0.0000 0.998 1.000 0.000 0.000
#> GSM751335 1 0.0000 0.998 1.000 0.000 0.000
#> GSM751336 1 0.0000 0.998 1.000 0.000 0.000
#> GSM751337 1 0.0000 0.998 1.000 0.000 0.000
#> GSM751338 1 0.0000 0.998 1.000 0.000 0.000
#> GSM751340 1 0.1643 0.954 0.956 0.000 0.044
#> GSM751350 1 0.0000 0.998 1.000 0.000 0.000
#> GSM751351 1 0.0000 0.998 1.000 0.000 0.000
#> GSM751362 3 0.0000 0.848 0.000 0.000 1.000
#> GSM751363 3 0.1529 0.839 0.000 0.040 0.960
#> GSM751367 3 0.5706 0.506 0.320 0.000 0.680
#> GSM751368 3 0.4178 0.755 0.000 0.172 0.828
#> GSM751371 3 0.1636 0.838 0.016 0.020 0.964
#> GSM751375 2 0.4605 0.699 0.000 0.796 0.204
#> GSM751376 3 0.5859 0.433 0.000 0.344 0.656
#> GSM751378 3 0.5591 0.581 0.000 0.304 0.696
#> GSM751379 3 0.5760 0.469 0.000 0.328 0.672
#> GSM751382 2 0.5016 0.638 0.000 0.760 0.240
#> GSM751386 3 0.6045 0.473 0.000 0.380 0.620
#> GSM751388 3 0.6062 0.471 0.000 0.384 0.616
#> GSM751391 3 0.3752 0.753 0.000 0.144 0.856
#> GSM751410 3 0.3116 0.777 0.108 0.000 0.892
#> GSM751414 3 0.0475 0.848 0.004 0.004 0.992
#> GSM751361 3 0.3192 0.800 0.000 0.112 0.888
#> GSM751365 3 0.0237 0.849 0.000 0.004 0.996
#> GSM751366 3 0.0237 0.849 0.000 0.004 0.996
#> GSM751369 3 0.0000 0.848 0.000 0.000 1.000
#> GSM751370 3 0.0424 0.846 0.008 0.000 0.992
#> GSM751372 3 0.0592 0.847 0.000 0.012 0.988
#> GSM751373 3 0.0592 0.848 0.000 0.012 0.988
#> GSM751374 3 0.5760 0.469 0.000 0.328 0.672
#> GSM751377 3 0.3482 0.789 0.000 0.128 0.872
#> GSM751380 3 0.0237 0.849 0.000 0.004 0.996
#> GSM751381 3 0.6062 0.465 0.000 0.384 0.616
#> GSM751383 3 0.6062 0.471 0.000 0.384 0.616
#> GSM751384 3 0.3816 0.768 0.000 0.148 0.852
#> GSM751385 3 0.0747 0.847 0.000 0.016 0.984
#> GSM751387 3 0.6095 0.454 0.000 0.392 0.608
#> GSM751389 3 0.0000 0.848 0.000 0.000 1.000
#> GSM751393 3 0.0237 0.848 0.000 0.004 0.996
#> GSM751394 3 0.6062 0.465 0.000 0.384 0.616
#> GSM751395 3 0.3038 0.795 0.000 0.104 0.896
#> GSM751397 3 0.6045 0.473 0.000 0.380 0.620
#> GSM751398 3 0.6045 0.473 0.000 0.380 0.620
#> GSM751404 3 0.0237 0.849 0.000 0.004 0.996
#> GSM751406 3 0.0000 0.848 0.000 0.000 1.000
#> GSM751411 3 0.0000 0.848 0.000 0.000 1.000
#> GSM751413 3 0.3551 0.786 0.000 0.132 0.868
#> GSM751415 3 0.0237 0.849 0.000 0.004 0.996
#> GSM751416 3 0.2356 0.824 0.000 0.072 0.928
#> GSM751417 3 0.2356 0.824 0.000 0.072 0.928
#> GSM751421 3 0.0000 0.848 0.000 0.000 1.000
#> GSM751422 3 0.0000 0.848 0.000 0.000 1.000
#> GSM751360 3 0.0237 0.848 0.000 0.004 0.996
#> GSM751364 3 0.0747 0.846 0.000 0.016 0.984
#> GSM751390 3 0.4555 0.719 0.000 0.200 0.800
#> GSM751392 3 0.6225 0.355 0.000 0.432 0.568
#> GSM751396 3 0.6204 0.381 0.000 0.424 0.576
#> GSM751399 3 0.0000 0.848 0.000 0.000 1.000
#> GSM751400 3 0.0237 0.849 0.000 0.004 0.996
#> GSM751401 3 0.0237 0.849 0.000 0.004 0.996
#> GSM751402 3 0.0237 0.849 0.000 0.004 0.996
#> GSM751403 3 0.0237 0.849 0.000 0.004 0.996
#> GSM751405 3 0.0000 0.848 0.000 0.000 1.000
#> GSM751407 3 0.0237 0.849 0.000 0.004 0.996
#> GSM751408 3 0.0237 0.849 0.000 0.004 0.996
#> GSM751409 3 0.0000 0.848 0.000 0.000 1.000
#> GSM751412 3 0.0237 0.849 0.000 0.004 0.996
#> GSM751418 3 0.0592 0.848 0.000 0.012 0.988
#> GSM751419 3 0.0592 0.848 0.000 0.012 0.988
#> GSM751420 3 0.1529 0.833 0.000 0.040 0.960
#> GSM751425 2 0.0237 0.888 0.000 0.996 0.004
#> GSM751429 3 0.9281 0.195 0.172 0.340 0.488
#> GSM751430 2 0.4654 0.689 0.000 0.792 0.208
#> GSM751433 2 0.0000 0.890 0.000 1.000 0.000
#> GSM751437 2 0.6204 0.192 0.000 0.576 0.424
#> GSM751448 3 0.7377 0.130 0.032 0.452 0.516
#> GSM751451 2 0.0000 0.890 0.000 1.000 0.000
#> GSM751423 2 0.0000 0.890 0.000 1.000 0.000
#> GSM751424 2 0.0000 0.890 0.000 1.000 0.000
#> GSM751428 2 0.0000 0.890 0.000 1.000 0.000
#> GSM751431 2 0.0000 0.890 0.000 1.000 0.000
#> GSM751432 2 0.0237 0.888 0.000 0.996 0.004
#> GSM751434 2 0.0000 0.890 0.000 1.000 0.000
#> GSM751435 2 0.0000 0.890 0.000 1.000 0.000
#> GSM751436 2 0.0000 0.890 0.000 1.000 0.000
#> GSM751440 2 0.0237 0.889 0.000 0.996 0.004
#> GSM751444 2 0.0000 0.890 0.000 1.000 0.000
#> GSM751446 2 0.0237 0.889 0.000 0.996 0.004
#> GSM751449 2 0.0237 0.889 0.000 0.996 0.004
#> GSM751450 2 0.0000 0.890 0.000 1.000 0.000
#> GSM751452 2 0.0000 0.890 0.000 1.000 0.000
#> GSM751426 2 0.0000 0.890 0.000 1.000 0.000
#> GSM751427 2 0.0237 0.889 0.000 0.996 0.004
#> GSM751438 2 0.0237 0.889 0.000 0.996 0.004
#> GSM751439 2 0.3551 0.776 0.000 0.868 0.132
#> GSM751441 2 0.0000 0.890 0.000 1.000 0.000
#> GSM751442 2 0.0237 0.889 0.000 0.996 0.004
#> GSM751443 2 0.5926 0.367 0.000 0.644 0.356
#> GSM751445 2 0.0000 0.890 0.000 1.000 0.000
#> GSM751447 2 0.0000 0.890 0.000 1.000 0.000
#> GSM751453 2 0.0000 0.890 0.000 1.000 0.000
#> GSM751454 2 0.0000 0.890 0.000 1.000 0.000
#> GSM751455 2 0.0237 0.889 0.000 0.996 0.004
#> GSM751456 2 0.0237 0.889 0.000 0.996 0.004
#> GSM751457 2 0.0892 0.883 0.000 0.980 0.020
#> GSM751458 2 0.0892 0.883 0.000 0.980 0.020
cbind(get_classes(res, k = 4), get_membership(res, k = 4))
#> class entropy silhouette p1 p2 p3 p4
#> GSM751298 1 0.0000 0.9612 1.000 0.000 0.000 0.000
#> GSM751304 4 0.6089 0.6317 0.000 0.080 0.280 0.640
#> GSM751305 4 0.6136 0.6297 0.000 0.080 0.288 0.632
#> GSM751307 4 0.8991 0.5229 0.116 0.144 0.288 0.452
#> GSM751310 1 0.1109 0.9518 0.968 0.000 0.004 0.028
#> GSM751314 1 0.1004 0.9541 0.972 0.000 0.004 0.024
#> GSM751316 1 0.4018 0.7233 0.772 0.000 0.004 0.224
#> GSM751318 1 0.0188 0.9610 0.996 0.000 0.000 0.004
#> GSM751342 1 0.0817 0.9555 0.976 0.000 0.000 0.024
#> GSM751346 1 0.1022 0.9545 0.968 0.000 0.000 0.032
#> GSM751347 1 0.1398 0.9490 0.956 0.004 0.000 0.040
#> GSM751348 4 0.8342 0.5828 0.088 0.108 0.292 0.512
#> GSM751349 3 0.7894 -0.4135 0.000 0.292 0.364 0.344
#> GSM751352 4 0.7066 0.6304 0.020 0.112 0.264 0.604
#> GSM751353 4 0.7425 0.5672 0.000 0.212 0.280 0.508
#> GSM751354 4 0.6307 0.6260 0.000 0.092 0.288 0.620
#> GSM751355 4 0.7142 0.5645 0.000 0.152 0.324 0.524
#> GSM751358 4 0.6906 0.6285 0.036 0.068 0.280 0.616
#> GSM751359 4 0.6857 0.5078 0.000 0.104 0.404 0.492
#> GSM751294 4 0.5873 0.6375 0.000 0.076 0.256 0.668
#> GSM751296 1 0.0000 0.9612 1.000 0.000 0.000 0.000
#> GSM751297 1 0.4382 0.6016 0.704 0.000 0.000 0.296
#> GSM751299 4 0.6854 0.6240 0.004 0.136 0.260 0.600
#> GSM751300 1 0.0817 0.9577 0.976 0.000 0.000 0.024
#> GSM751301 1 0.0336 0.9592 0.992 0.008 0.000 0.000
#> GSM751302 1 0.1118 0.9527 0.964 0.000 0.000 0.036
#> GSM751303 1 0.1004 0.9541 0.972 0.000 0.004 0.024
#> GSM751306 1 0.1109 0.9518 0.968 0.000 0.004 0.028
#> GSM751308 1 0.6058 0.3470 0.604 0.024 0.020 0.352
#> GSM751309 1 0.1004 0.9541 0.972 0.000 0.004 0.024
#> GSM751311 1 0.0376 0.9605 0.992 0.000 0.004 0.004
#> GSM751312 1 0.1902 0.9380 0.932 0.000 0.004 0.064
#> GSM751313 1 0.0817 0.9573 0.976 0.000 0.000 0.024
#> GSM751315 1 0.0376 0.9605 0.992 0.000 0.004 0.004
#> GSM751317 1 0.0524 0.9600 0.988 0.000 0.004 0.008
#> GSM751320 1 0.0000 0.9612 1.000 0.000 0.000 0.000
#> GSM751321 1 0.1004 0.9541 0.972 0.000 0.004 0.024
#> GSM751322 1 0.0188 0.9610 0.996 0.000 0.000 0.004
#> GSM751324 1 0.0188 0.9610 0.996 0.000 0.000 0.004
#> GSM751325 1 0.0188 0.9610 0.996 0.000 0.000 0.004
#> GSM751332 1 0.0000 0.9612 1.000 0.000 0.000 0.000
#> GSM751334 1 0.0000 0.9612 1.000 0.000 0.000 0.000
#> GSM751339 1 0.2973 0.8392 0.856 0.000 0.000 0.144
#> GSM751341 1 0.0469 0.9598 0.988 0.000 0.000 0.012
#> GSM751343 1 0.0188 0.9610 0.996 0.000 0.000 0.004
#> GSM751344 4 0.7201 0.5889 0.000 0.188 0.268 0.544
#> GSM751345 4 0.7201 0.5889 0.000 0.188 0.268 0.544
#> GSM751356 4 0.6313 0.6368 0.004 0.092 0.260 0.644
#> GSM751357 4 0.6313 0.6368 0.004 0.092 0.260 0.644
#> GSM751293 1 0.0188 0.9606 0.996 0.004 0.000 0.000
#> GSM751295 1 0.1118 0.9527 0.964 0.000 0.000 0.036
#> GSM751319 1 0.0376 0.9605 0.992 0.000 0.004 0.004
#> GSM751323 1 0.0000 0.9612 1.000 0.000 0.000 0.000
#> GSM751326 1 0.0000 0.9612 1.000 0.000 0.000 0.000
#> GSM751327 1 0.0000 0.9612 1.000 0.000 0.000 0.000
#> GSM751328 1 0.0000 0.9612 1.000 0.000 0.000 0.000
#> GSM751329 1 0.0000 0.9612 1.000 0.000 0.000 0.000
#> GSM751330 1 0.0817 0.9574 0.976 0.000 0.000 0.024
#> GSM751331 1 0.1118 0.9527 0.964 0.000 0.000 0.036
#> GSM751333 1 0.0921 0.9559 0.972 0.000 0.000 0.028
#> GSM751335 1 0.0817 0.9574 0.976 0.000 0.000 0.024
#> GSM751336 1 0.1118 0.9527 0.964 0.000 0.000 0.036
#> GSM751337 1 0.0000 0.9612 1.000 0.000 0.000 0.000
#> GSM751338 1 0.0921 0.9577 0.972 0.000 0.000 0.028
#> GSM751340 4 0.4608 0.4474 0.304 0.000 0.004 0.692
#> GSM751350 1 0.1118 0.9527 0.964 0.000 0.000 0.036
#> GSM751351 1 0.1118 0.9527 0.964 0.000 0.000 0.036
#> GSM751362 3 0.5000 0.5325 0.000 0.000 0.504 0.496
#> GSM751363 3 0.4123 0.5747 0.000 0.008 0.772 0.220
#> GSM751367 4 0.5873 0.3603 0.232 0.004 0.076 0.688
#> GSM751368 3 0.5369 0.6234 0.000 0.112 0.744 0.144
#> GSM751371 4 0.2847 0.4954 0.016 0.004 0.084 0.896
#> GSM751375 3 0.7599 -0.4147 0.000 0.200 0.424 0.376
#> GSM751376 4 0.1936 0.5806 0.000 0.028 0.032 0.940
#> GSM751378 4 0.6214 0.3910 0.000 0.052 0.468 0.480
#> GSM751379 4 0.1936 0.5806 0.000 0.028 0.032 0.940
#> GSM751382 3 0.7731 -0.3515 0.000 0.248 0.436 0.316
#> GSM751386 3 0.2342 0.5262 0.000 0.080 0.912 0.008
#> GSM751388 3 0.2011 0.5319 0.000 0.080 0.920 0.000
#> GSM751391 4 0.1867 0.5132 0.000 0.000 0.072 0.928
#> GSM751410 4 0.4203 0.4460 0.068 0.000 0.108 0.824
#> GSM751414 3 0.4331 0.6630 0.000 0.000 0.712 0.288
#> GSM751361 3 0.3048 0.6254 0.000 0.016 0.876 0.108
#> GSM751365 3 0.4331 0.6627 0.000 0.000 0.712 0.288
#> GSM751366 3 0.4776 0.6348 0.000 0.000 0.624 0.376
#> GSM751369 4 0.2530 0.4699 0.000 0.004 0.100 0.896
#> GSM751370 3 0.4356 0.6624 0.000 0.000 0.708 0.292
#> GSM751372 3 0.4250 0.6634 0.000 0.000 0.724 0.276
#> GSM751373 3 0.4564 0.6520 0.000 0.000 0.672 0.328
#> GSM751374 4 0.1936 0.5806 0.000 0.028 0.032 0.940
#> GSM751377 3 0.3734 0.6203 0.000 0.044 0.848 0.108
#> GSM751380 3 0.4967 0.5840 0.000 0.000 0.548 0.452
#> GSM751381 3 0.2473 0.5239 0.000 0.080 0.908 0.012
#> GSM751383 3 0.2011 0.5319 0.000 0.080 0.920 0.000
#> GSM751384 3 0.2214 0.5525 0.000 0.044 0.928 0.028
#> GSM751385 3 0.4584 0.0399 0.000 0.004 0.696 0.300
#> GSM751387 3 0.2342 0.5262 0.000 0.080 0.912 0.008
#> GSM751389 3 0.4996 0.5472 0.000 0.000 0.516 0.484
#> GSM751393 3 0.4916 0.5722 0.000 0.000 0.576 0.424
#> GSM751394 3 0.2473 0.5239 0.000 0.080 0.908 0.012
#> GSM751395 4 0.4482 0.5944 0.000 0.008 0.264 0.728
#> GSM751397 3 0.2915 0.5089 0.000 0.080 0.892 0.028
#> GSM751398 3 0.2342 0.5262 0.000 0.080 0.912 0.008
#> GSM751404 3 0.4877 0.6200 0.000 0.000 0.592 0.408
#> GSM751406 4 0.3528 0.3182 0.000 0.000 0.192 0.808
#> GSM751411 3 0.4356 0.6627 0.000 0.000 0.708 0.292
#> GSM751413 3 0.4004 0.5906 0.000 0.024 0.812 0.164
#> GSM751415 3 0.4961 0.5879 0.000 0.000 0.552 0.448
#> GSM751416 3 0.3249 0.6420 0.000 0.008 0.852 0.140
#> GSM751417 3 0.3249 0.6420 0.000 0.008 0.852 0.140
#> GSM751421 4 0.3208 0.4013 0.000 0.004 0.148 0.848
#> GSM751422 4 0.3157 0.4065 0.000 0.004 0.144 0.852
#> GSM751360 3 0.5161 0.5102 0.000 0.004 0.520 0.476
#> GSM751364 3 0.4122 0.6624 0.000 0.004 0.760 0.236
#> GSM751390 3 0.2002 0.5620 0.000 0.044 0.936 0.020
#> GSM751392 3 0.4881 0.3401 0.000 0.196 0.756 0.048
#> GSM751396 3 0.4283 0.3486 0.000 0.256 0.740 0.004
#> GSM751399 3 0.4830 0.6290 0.000 0.000 0.608 0.392
#> GSM751400 3 0.4925 0.6053 0.000 0.000 0.572 0.428
#> GSM751401 3 0.4941 0.5987 0.000 0.000 0.564 0.436
#> GSM751402 3 0.4967 0.5840 0.000 0.000 0.548 0.452
#> GSM751403 3 0.4955 0.5916 0.000 0.000 0.556 0.444
#> GSM751405 4 0.4543 -0.1213 0.000 0.000 0.324 0.676
#> GSM751407 3 0.4877 0.6200 0.000 0.000 0.592 0.408
#> GSM751408 3 0.4843 0.6271 0.000 0.000 0.604 0.396
#> GSM751409 3 0.4967 0.5840 0.000 0.000 0.548 0.452
#> GSM751412 3 0.4843 0.6271 0.000 0.000 0.604 0.396
#> GSM751418 3 0.4331 0.6627 0.000 0.000 0.712 0.288
#> GSM751419 3 0.4331 0.6627 0.000 0.000 0.712 0.288
#> GSM751420 4 0.2593 0.4725 0.000 0.004 0.104 0.892
#> GSM751425 2 0.0376 0.9330 0.000 0.992 0.004 0.004
#> GSM751429 4 0.4100 0.5827 0.032 0.080 0.036 0.852
#> GSM751430 2 0.6055 0.2176 0.000 0.520 0.436 0.044
#> GSM751433 2 0.1004 0.9259 0.000 0.972 0.024 0.004
#> GSM751437 4 0.4361 0.5430 0.000 0.208 0.020 0.772
#> GSM751448 4 0.2057 0.5612 0.008 0.032 0.020 0.940
#> GSM751451 2 0.0469 0.9319 0.000 0.988 0.012 0.000
#> GSM751423 2 0.0336 0.9324 0.000 0.992 0.008 0.000
#> GSM751424 2 0.1004 0.9259 0.000 0.972 0.024 0.004
#> GSM751428 2 0.0524 0.9323 0.000 0.988 0.008 0.004
#> GSM751431 2 0.0779 0.9295 0.000 0.980 0.016 0.004
#> GSM751432 2 0.1004 0.9259 0.000 0.972 0.024 0.004
#> GSM751434 2 0.1004 0.9259 0.000 0.972 0.024 0.004
#> GSM751435 2 0.0000 0.9335 0.000 1.000 0.000 0.000
#> GSM751436 2 0.1004 0.9259 0.000 0.972 0.024 0.004
#> GSM751440 2 0.0188 0.9330 0.000 0.996 0.004 0.000
#> GSM751444 2 0.0921 0.9275 0.000 0.972 0.000 0.028
#> GSM751446 2 0.1211 0.9239 0.000 0.960 0.000 0.040
#> GSM751449 2 0.1211 0.9239 0.000 0.960 0.000 0.040
#> GSM751450 2 0.0469 0.9316 0.000 0.988 0.012 0.000
#> GSM751452 2 0.1004 0.9259 0.000 0.972 0.024 0.004
#> GSM751426 2 0.1004 0.9259 0.000 0.972 0.024 0.004
#> GSM751427 2 0.0336 0.9327 0.000 0.992 0.000 0.008
#> GSM751438 2 0.1211 0.9239 0.000 0.960 0.000 0.040
#> GSM751439 2 0.2662 0.8707 0.000 0.900 0.016 0.084
#> GSM751441 2 0.1545 0.9218 0.000 0.952 0.008 0.040
#> GSM751442 2 0.1211 0.9239 0.000 0.960 0.000 0.040
#> GSM751443 4 0.5483 0.0717 0.000 0.448 0.016 0.536
#> GSM751445 2 0.1211 0.9239 0.000 0.960 0.000 0.040
#> GSM751447 2 0.1211 0.9239 0.000 0.960 0.000 0.040
#> GSM751453 2 0.0000 0.9335 0.000 1.000 0.000 0.000
#> GSM751454 2 0.0000 0.9335 0.000 1.000 0.000 0.000
#> GSM751455 2 0.1211 0.9239 0.000 0.960 0.000 0.040
#> GSM751456 2 0.1211 0.9239 0.000 0.960 0.000 0.040
#> GSM751457 2 0.4193 0.6197 0.000 0.732 0.000 0.268
#> GSM751458 2 0.4193 0.6197 0.000 0.732 0.000 0.268
cbind(get_classes(res, k = 5), get_membership(res, k = 5))
#> class entropy silhouette p1 p2 p3 p4 p5
#> GSM751298 1 0.2719 0.7191 0.884 0.000 0.000 0.068 0.048
#> GSM751304 4 0.3613 0.7577 0.000 0.012 0.016 0.812 0.160
#> GSM751305 4 0.3573 0.7555 0.000 0.012 0.016 0.816 0.156
#> GSM751307 4 0.5107 0.7326 0.040 0.028 0.000 0.696 0.236
#> GSM751310 1 0.4645 0.5912 0.688 0.000 0.000 0.268 0.044
#> GSM751314 1 0.4468 0.6107 0.716 0.000 0.000 0.240 0.044
#> GSM751316 4 0.4883 0.1100 0.300 0.000 0.000 0.652 0.048
#> GSM751318 1 0.2830 0.7094 0.876 0.000 0.000 0.080 0.044
#> GSM751342 1 0.4573 0.5950 0.700 0.000 0.000 0.256 0.044
#> GSM751346 1 0.4478 0.5055 0.628 0.000 0.004 0.360 0.008
#> GSM751347 1 0.5087 0.4694 0.600 0.000 0.020 0.364 0.016
#> GSM751348 4 0.7273 0.4675 0.260 0.016 0.004 0.396 0.324
#> GSM751349 5 0.4339 0.4165 0.000 0.084 0.004 0.136 0.776
#> GSM751352 4 0.4876 0.7169 0.096 0.020 0.000 0.752 0.132
#> GSM751353 4 0.5300 0.6656 0.000 0.068 0.000 0.604 0.328
#> GSM751354 4 0.4063 0.7540 0.004 0.016 0.008 0.768 0.204
#> GSM751355 4 0.4752 0.6863 0.000 0.036 0.000 0.648 0.316
#> GSM751358 4 0.6647 0.5221 0.172 0.008 0.024 0.588 0.208
#> GSM751359 5 0.5012 -0.0289 0.000 0.016 0.012 0.404 0.568
#> GSM751294 4 0.4573 0.7462 0.000 0.020 0.024 0.728 0.228
#> GSM751296 1 0.1430 0.7203 0.944 0.000 0.000 0.052 0.004
#> GSM751297 4 0.6398 0.0108 0.384 0.000 0.024 0.496 0.096
#> GSM751299 4 0.4745 0.7476 0.060 0.032 0.000 0.764 0.144
#> GSM751300 1 0.4003 0.5870 0.704 0.000 0.000 0.288 0.008
#> GSM751301 1 0.1704 0.7153 0.928 0.004 0.000 0.068 0.000
#> GSM751302 1 0.4341 0.5046 0.628 0.000 0.000 0.364 0.008
#> GSM751303 1 0.4817 0.5363 0.656 0.000 0.000 0.300 0.044
#> GSM751306 1 0.4597 0.5908 0.696 0.000 0.000 0.260 0.044
#> GSM751308 1 0.5598 0.0274 0.548 0.008 0.016 0.400 0.028
#> GSM751309 1 0.4597 0.5908 0.696 0.000 0.000 0.260 0.044
#> GSM751311 1 0.4441 0.6164 0.720 0.000 0.000 0.236 0.044
#> GSM751312 4 0.4843 0.0658 0.292 0.000 0.000 0.660 0.048
#> GSM751313 1 0.3957 0.5918 0.712 0.000 0.000 0.280 0.008
#> GSM751315 1 0.4031 0.6717 0.772 0.000 0.000 0.184 0.044
#> GSM751317 1 0.4441 0.6170 0.720 0.000 0.000 0.236 0.044
#> GSM751320 1 0.0566 0.7286 0.984 0.000 0.000 0.012 0.004
#> GSM751321 1 0.4547 0.5991 0.704 0.000 0.000 0.252 0.044
#> GSM751322 1 0.2230 0.7191 0.912 0.000 0.000 0.044 0.044
#> GSM751324 1 0.2514 0.7147 0.896 0.000 0.000 0.060 0.044
#> GSM751325 1 0.1195 0.7273 0.960 0.000 0.000 0.028 0.012
#> GSM751332 1 0.0865 0.7285 0.972 0.000 0.000 0.004 0.024
#> GSM751334 1 0.0000 0.7276 1.000 0.000 0.000 0.000 0.000
#> GSM751339 1 0.4212 0.6236 0.736 0.000 0.024 0.236 0.004
#> GSM751341 1 0.3995 0.6568 0.776 0.000 0.000 0.180 0.044
#> GSM751343 1 0.1082 0.7278 0.964 0.000 0.000 0.028 0.008
#> GSM751344 4 0.4506 0.7471 0.004 0.036 0.000 0.716 0.244
#> GSM751345 4 0.4506 0.7471 0.004 0.036 0.000 0.716 0.244
#> GSM751356 4 0.3367 0.7558 0.000 0.016 0.016 0.840 0.128
#> GSM751357 4 0.3367 0.7558 0.000 0.016 0.016 0.840 0.128
#> GSM751293 1 0.1410 0.7176 0.940 0.000 0.000 0.060 0.000
#> GSM751295 1 0.4341 0.5046 0.628 0.000 0.000 0.364 0.008
#> GSM751319 1 0.4441 0.6324 0.720 0.000 0.000 0.236 0.044
#> GSM751323 1 0.0162 0.7276 0.996 0.000 0.000 0.004 0.000
#> GSM751326 1 0.1282 0.7215 0.952 0.000 0.000 0.044 0.004
#> GSM751327 1 0.0162 0.7276 0.996 0.000 0.000 0.004 0.000
#> GSM751328 1 0.2830 0.7078 0.876 0.000 0.000 0.080 0.044
#> GSM751329 1 0.0771 0.7257 0.976 0.000 0.000 0.020 0.004
#> GSM751330 1 0.4165 0.5572 0.672 0.000 0.000 0.320 0.008
#> GSM751331 1 0.4341 0.5046 0.628 0.000 0.000 0.364 0.008
#> GSM751333 1 0.4218 0.5444 0.660 0.000 0.000 0.332 0.008
#> GSM751335 1 0.4127 0.5654 0.680 0.000 0.000 0.312 0.008
#> GSM751336 1 0.4341 0.5046 0.628 0.000 0.000 0.364 0.008
#> GSM751337 1 0.1502 0.7194 0.940 0.000 0.000 0.056 0.004
#> GSM751338 1 0.3430 0.6493 0.776 0.000 0.000 0.220 0.004
#> GSM751340 4 0.5177 0.6587 0.112 0.000 0.080 0.748 0.060
#> GSM751350 1 0.4341 0.5046 0.628 0.000 0.000 0.364 0.008
#> GSM751351 1 0.4341 0.5046 0.628 0.000 0.000 0.364 0.008
#> GSM751362 3 0.3093 0.6218 0.000 0.000 0.824 0.008 0.168
#> GSM751363 5 0.4101 0.6921 0.000 0.000 0.184 0.048 0.768
#> GSM751367 3 0.7039 0.4654 0.060 0.000 0.552 0.200 0.188
#> GSM751368 5 0.5325 0.5042 0.000 0.028 0.460 0.012 0.500
#> GSM751371 3 0.6253 0.5409 0.020 0.000 0.608 0.184 0.188
#> GSM751375 5 0.2707 0.5467 0.000 0.024 0.008 0.080 0.888
#> GSM751376 3 0.6726 0.2857 0.000 0.012 0.464 0.348 0.176
#> GSM751378 5 0.5066 0.3881 0.000 0.004 0.260 0.064 0.672
#> GSM751379 3 0.6735 0.3000 0.000 0.012 0.468 0.340 0.180
#> GSM751382 5 0.2853 0.5499 0.000 0.040 0.004 0.076 0.880
#> GSM751386 5 0.3611 0.7490 0.000 0.004 0.208 0.008 0.780
#> GSM751388 5 0.3550 0.7433 0.000 0.004 0.236 0.000 0.760
#> GSM751391 3 0.5668 0.5478 0.000 0.000 0.632 0.196 0.172
#> GSM751410 3 0.7161 0.4852 0.080 0.000 0.540 0.140 0.240
#> GSM751414 5 0.4434 0.4616 0.000 0.000 0.460 0.004 0.536
#> GSM751361 5 0.4199 0.7179 0.000 0.004 0.296 0.008 0.692
#> GSM751365 3 0.4118 -0.0125 0.000 0.000 0.660 0.004 0.336
#> GSM751366 3 0.1197 0.6237 0.000 0.000 0.952 0.000 0.048
#> GSM751369 3 0.5307 0.5910 0.000 0.000 0.676 0.168 0.156
#> GSM751370 5 0.4632 0.4985 0.000 0.000 0.448 0.012 0.540
#> GSM751372 5 0.4552 0.5003 0.000 0.000 0.468 0.008 0.524
#> GSM751373 3 0.3160 0.4153 0.000 0.000 0.808 0.004 0.188
#> GSM751374 3 0.6718 0.2942 0.000 0.012 0.468 0.344 0.176
#> GSM751377 5 0.4037 0.7237 0.000 0.004 0.288 0.004 0.704
#> GSM751380 3 0.0162 0.6506 0.000 0.000 0.996 0.000 0.004
#> GSM751381 5 0.3544 0.7491 0.000 0.004 0.200 0.008 0.788
#> GSM751383 5 0.3579 0.7427 0.000 0.004 0.240 0.000 0.756
#> GSM751384 5 0.3519 0.7488 0.000 0.000 0.216 0.008 0.776
#> GSM751385 5 0.3608 0.6432 0.000 0.000 0.112 0.064 0.824
#> GSM751387 5 0.3675 0.7475 0.000 0.004 0.216 0.008 0.772
#> GSM751389 3 0.0324 0.6515 0.000 0.000 0.992 0.004 0.004
#> GSM751393 3 0.5701 0.1873 0.000 0.000 0.604 0.124 0.272
#> GSM751394 5 0.3289 0.7461 0.000 0.004 0.172 0.008 0.816
#> GSM751395 5 0.7053 -0.2836 0.000 0.008 0.336 0.308 0.348
#> GSM751397 5 0.3129 0.7399 0.000 0.004 0.156 0.008 0.832
#> GSM751398 5 0.3489 0.7491 0.000 0.004 0.208 0.004 0.784
#> GSM751404 3 0.0703 0.6434 0.000 0.000 0.976 0.000 0.024
#> GSM751406 3 0.3710 0.6410 0.000 0.000 0.808 0.048 0.144
#> GSM751411 3 0.4451 -0.4393 0.000 0.000 0.504 0.004 0.492
#> GSM751413 5 0.4360 0.6984 0.000 0.000 0.184 0.064 0.752
#> GSM751415 3 0.0510 0.6474 0.000 0.000 0.984 0.000 0.016
#> GSM751416 5 0.4353 0.6941 0.000 0.004 0.328 0.008 0.660
#> GSM751417 5 0.4353 0.6941 0.000 0.004 0.328 0.008 0.660
#> GSM751421 3 0.5059 0.6160 0.000 0.000 0.700 0.124 0.176
#> GSM751422 3 0.5102 0.6136 0.000 0.000 0.696 0.128 0.176
#> GSM751360 5 0.5872 0.2313 0.000 0.000 0.408 0.100 0.492
#> GSM751364 5 0.4419 0.6771 0.000 0.004 0.344 0.008 0.644
#> GSM751390 5 0.3790 0.7370 0.000 0.000 0.272 0.004 0.724
#> GSM751392 5 0.3380 0.7251 0.000 0.028 0.124 0.008 0.840
#> GSM751396 5 0.4799 0.7160 0.000 0.060 0.228 0.004 0.708
#> GSM751399 3 0.1043 0.6320 0.000 0.000 0.960 0.000 0.040
#> GSM751400 3 0.0609 0.6458 0.000 0.000 0.980 0.000 0.020
#> GSM751401 3 0.0609 0.6458 0.000 0.000 0.980 0.000 0.020
#> GSM751402 3 0.0162 0.6506 0.000 0.000 0.996 0.000 0.004
#> GSM751403 3 0.0609 0.6458 0.000 0.000 0.980 0.000 0.020
#> GSM751405 3 0.3848 0.6347 0.000 0.000 0.788 0.040 0.172
#> GSM751407 3 0.0703 0.6434 0.000 0.000 0.976 0.000 0.024
#> GSM751408 3 0.1043 0.6315 0.000 0.000 0.960 0.000 0.040
#> GSM751409 3 0.1121 0.6528 0.000 0.000 0.956 0.000 0.044
#> GSM751412 3 0.1121 0.6278 0.000 0.000 0.956 0.000 0.044
#> GSM751418 3 0.3814 0.1958 0.000 0.000 0.720 0.004 0.276
#> GSM751419 3 0.3814 0.1958 0.000 0.000 0.720 0.004 0.276
#> GSM751420 3 0.4612 0.6299 0.000 0.004 0.752 0.092 0.152
#> GSM751425 2 0.1124 0.9379 0.000 0.960 0.000 0.004 0.036
#> GSM751429 3 0.7903 0.3093 0.016 0.072 0.456 0.288 0.168
#> GSM751430 2 0.8199 -0.2127 0.000 0.360 0.180 0.144 0.316
#> GSM751433 2 0.1648 0.9255 0.000 0.940 0.000 0.020 0.040
#> GSM751437 3 0.7770 0.3573 0.000 0.236 0.476 0.128 0.160
#> GSM751448 3 0.6396 0.4945 0.000 0.024 0.592 0.220 0.164
#> GSM751451 2 0.0609 0.9420 0.000 0.980 0.000 0.000 0.020
#> GSM751423 2 0.0404 0.9435 0.000 0.988 0.000 0.000 0.012
#> GSM751424 2 0.1648 0.9255 0.000 0.940 0.000 0.020 0.040
#> GSM751428 2 0.0579 0.9429 0.000 0.984 0.000 0.008 0.008
#> GSM751431 2 0.0771 0.9411 0.000 0.976 0.000 0.004 0.020
#> GSM751432 2 0.1808 0.9232 0.000 0.936 0.004 0.020 0.040
#> GSM751434 2 0.1648 0.9255 0.000 0.940 0.000 0.020 0.040
#> GSM751435 2 0.0290 0.9432 0.000 0.992 0.000 0.000 0.008
#> GSM751436 2 0.1648 0.9255 0.000 0.940 0.000 0.020 0.040
#> GSM751440 2 0.0404 0.9435 0.000 0.988 0.000 0.000 0.012
#> GSM751444 2 0.0162 0.9430 0.000 0.996 0.000 0.004 0.000
#> GSM751446 2 0.0671 0.9401 0.000 0.980 0.000 0.016 0.004
#> GSM751449 2 0.0671 0.9401 0.000 0.980 0.000 0.016 0.004
#> GSM751450 2 0.0566 0.9429 0.000 0.984 0.000 0.004 0.012
#> GSM751452 2 0.1648 0.9255 0.000 0.940 0.000 0.020 0.040
#> GSM751426 2 0.0865 0.9395 0.000 0.972 0.000 0.004 0.024
#> GSM751427 2 0.0324 0.9428 0.000 0.992 0.000 0.004 0.004
#> GSM751438 2 0.0671 0.9401 0.000 0.980 0.000 0.016 0.004
#> GSM751439 2 0.1597 0.9206 0.000 0.948 0.024 0.020 0.008
#> GSM751441 2 0.0912 0.9384 0.000 0.972 0.000 0.016 0.012
#> GSM751442 2 0.0671 0.9401 0.000 0.980 0.000 0.016 0.004
#> GSM751443 3 0.6844 0.1236 0.000 0.420 0.428 0.112 0.040
#> GSM751445 2 0.0671 0.9401 0.000 0.980 0.000 0.016 0.004
#> GSM751447 2 0.0671 0.9401 0.000 0.980 0.000 0.016 0.004
#> GSM751453 2 0.0404 0.9436 0.000 0.988 0.000 0.000 0.012
#> GSM751454 2 0.0404 0.9436 0.000 0.988 0.000 0.000 0.012
#> GSM751455 2 0.0671 0.9401 0.000 0.980 0.000 0.016 0.004
#> GSM751456 2 0.0671 0.9401 0.000 0.980 0.000 0.016 0.004
#> GSM751457 2 0.3682 0.7887 0.000 0.828 0.012 0.120 0.040
#> GSM751458 2 0.3682 0.7887 0.000 0.828 0.012 0.120 0.040
cbind(get_classes(res, k = 6), get_membership(res, k = 6))
#> class entropy silhouette p1 p2 p3 p4 p5 p6
#> GSM751298 4 0.3595 0.62914 0.288 0.000 0.000 0.704 0.000 0.008
#> GSM751304 6 0.4130 0.68707 0.040 0.008 0.000 0.152 0.024 0.776
#> GSM751305 6 0.4277 0.67722 0.036 0.012 0.004 0.168 0.016 0.764
#> GSM751307 6 0.6064 0.64113 0.088 0.044 0.000 0.148 0.064 0.656
#> GSM751310 4 0.2006 0.75887 0.080 0.000 0.000 0.904 0.000 0.016
#> GSM751314 4 0.1411 0.76655 0.060 0.000 0.000 0.936 0.000 0.004
#> GSM751316 4 0.4671 0.46466 0.156 0.000 0.000 0.688 0.000 0.156
#> GSM751318 4 0.2871 0.71526 0.192 0.000 0.000 0.804 0.004 0.000
#> GSM751342 4 0.0937 0.76237 0.040 0.000 0.000 0.960 0.000 0.000
#> GSM751346 1 0.0692 0.76926 0.976 0.000 0.000 0.004 0.000 0.020
#> GSM751347 1 0.0891 0.75736 0.968 0.000 0.000 0.000 0.008 0.024
#> GSM751348 6 0.6750 0.45454 0.004 0.032 0.004 0.280 0.232 0.448
#> GSM751349 5 0.5187 0.26908 0.000 0.064 0.004 0.016 0.608 0.308
#> GSM751352 6 0.5394 0.66815 0.176 0.016 0.000 0.056 0.064 0.688
#> GSM751353 6 0.5265 0.63782 0.056 0.040 0.000 0.024 0.184 0.696
#> GSM751354 6 0.4646 0.67980 0.164 0.008 0.000 0.048 0.040 0.740
#> GSM751355 6 0.4658 0.65846 0.116 0.004 0.000 0.020 0.124 0.736
#> GSM751358 6 0.5108 0.44966 0.000 0.008 0.004 0.400 0.052 0.536
#> GSM751359 6 0.6399 0.31978 0.000 0.024 0.012 0.140 0.384 0.440
#> GSM751294 6 0.5114 0.68729 0.056 0.044 0.000 0.072 0.084 0.744
#> GSM751296 1 0.3271 0.60638 0.760 0.000 0.000 0.232 0.000 0.008
#> GSM751297 1 0.3867 0.41323 0.744 0.000 0.000 0.036 0.004 0.216
#> GSM751299 6 0.5522 0.68633 0.148 0.032 0.000 0.068 0.056 0.696
#> GSM751300 1 0.0717 0.77084 0.976 0.000 0.000 0.016 0.000 0.008
#> GSM751301 1 0.5160 -0.08563 0.468 0.004 0.000 0.464 0.004 0.060
#> GSM751302 1 0.0692 0.76926 0.976 0.000 0.000 0.004 0.000 0.020
#> GSM751303 4 0.1418 0.74214 0.024 0.000 0.000 0.944 0.000 0.032
#> GSM751306 4 0.1461 0.75823 0.044 0.000 0.000 0.940 0.000 0.016
#> GSM751308 6 0.6333 0.09843 0.304 0.004 0.000 0.256 0.008 0.428
#> GSM751309 4 0.1152 0.76270 0.044 0.000 0.000 0.952 0.000 0.004
#> GSM751311 4 0.1349 0.76652 0.056 0.000 0.000 0.940 0.000 0.004
#> GSM751312 4 0.5123 0.34430 0.244 0.000 0.000 0.616 0.000 0.140
#> GSM751313 1 0.1082 0.76190 0.956 0.000 0.000 0.040 0.004 0.000
#> GSM751315 4 0.2841 0.74099 0.164 0.000 0.000 0.824 0.000 0.012
#> GSM751317 4 0.1951 0.76482 0.060 0.000 0.000 0.916 0.004 0.020
#> GSM751320 4 0.3982 0.21216 0.460 0.000 0.000 0.536 0.004 0.000
#> GSM751321 4 0.1779 0.76510 0.064 0.000 0.000 0.920 0.000 0.016
#> GSM751322 4 0.3265 0.67193 0.248 0.000 0.000 0.748 0.004 0.000
#> GSM751324 4 0.3109 0.69541 0.224 0.000 0.000 0.772 0.004 0.000
#> GSM751325 4 0.3742 0.51888 0.348 0.000 0.000 0.648 0.004 0.000
#> GSM751332 4 0.3830 0.45481 0.376 0.000 0.000 0.620 0.004 0.000
#> GSM751334 1 0.3999 -0.10923 0.500 0.000 0.000 0.496 0.004 0.000
#> GSM751339 1 0.4571 0.61284 0.724 0.000 0.016 0.188 0.004 0.068
#> GSM751341 4 0.2278 0.75433 0.128 0.000 0.000 0.868 0.000 0.004
#> GSM751343 4 0.3769 0.50185 0.356 0.000 0.000 0.640 0.004 0.000
#> GSM751344 6 0.4612 0.68831 0.072 0.004 0.000 0.064 0.100 0.760
#> GSM751345 6 0.4612 0.68831 0.072 0.004 0.000 0.064 0.100 0.760
#> GSM751356 6 0.5771 0.67234 0.068 0.024 0.000 0.184 0.064 0.660
#> GSM751357 6 0.5771 0.67234 0.068 0.024 0.000 0.184 0.064 0.660
#> GSM751293 4 0.5077 0.02909 0.464 0.000 0.000 0.468 0.004 0.064
#> GSM751295 1 0.0692 0.76926 0.976 0.000 0.000 0.004 0.000 0.020
#> GSM751319 4 0.2358 0.75831 0.108 0.000 0.000 0.876 0.000 0.016
#> GSM751323 1 0.3950 0.14962 0.564 0.000 0.000 0.432 0.004 0.000
#> GSM751326 1 0.3136 0.61156 0.768 0.000 0.000 0.228 0.004 0.000
#> GSM751327 1 0.3944 0.16521 0.568 0.000 0.000 0.428 0.004 0.000
#> GSM751328 4 0.2883 0.70960 0.212 0.000 0.000 0.788 0.000 0.000
#> GSM751329 1 0.3795 0.34677 0.632 0.000 0.000 0.364 0.004 0.000
#> GSM751330 1 0.0458 0.77045 0.984 0.000 0.000 0.016 0.000 0.000
#> GSM751331 1 0.0692 0.76926 0.976 0.000 0.000 0.004 0.000 0.020
#> GSM751333 1 0.0935 0.76582 0.964 0.000 0.000 0.032 0.004 0.000
#> GSM751335 1 0.0458 0.77045 0.984 0.000 0.000 0.016 0.000 0.000
#> GSM751336 1 0.0508 0.76980 0.984 0.000 0.000 0.004 0.000 0.012
#> GSM751337 1 0.2964 0.64361 0.792 0.000 0.000 0.204 0.004 0.000
#> GSM751338 1 0.3263 0.66708 0.800 0.000 0.000 0.176 0.004 0.020
#> GSM751340 6 0.6446 0.52922 0.268 0.000 0.076 0.116 0.004 0.536
#> GSM751350 1 0.0692 0.76926 0.976 0.000 0.000 0.004 0.000 0.020
#> GSM751351 1 0.0692 0.76926 0.976 0.000 0.000 0.004 0.000 0.020
#> GSM751362 3 0.4307 0.56441 0.000 0.000 0.704 0.000 0.224 0.072
#> GSM751363 5 0.4982 0.66850 0.000 0.000 0.124 0.044 0.712 0.120
#> GSM751367 3 0.8420 0.05759 0.260 0.012 0.328 0.112 0.052 0.236
#> GSM751368 5 0.6291 0.26317 0.004 0.052 0.404 0.008 0.460 0.072
#> GSM751371 3 0.6302 0.32455 0.000 0.000 0.496 0.156 0.040 0.308
#> GSM751375 5 0.4025 0.57176 0.000 0.016 0.032 0.004 0.760 0.188
#> GSM751376 6 0.4928 0.27495 0.012 0.012 0.300 0.016 0.016 0.644
#> GSM751378 5 0.5204 0.49879 0.000 0.016 0.204 0.000 0.652 0.128
#> GSM751379 6 0.5041 0.25605 0.012 0.012 0.308 0.016 0.020 0.632
#> GSM751382 5 0.3646 0.63730 0.000 0.036 0.032 0.000 0.812 0.120
#> GSM751386 5 0.0725 0.75087 0.000 0.000 0.012 0.000 0.976 0.012
#> GSM751388 5 0.1267 0.75347 0.000 0.000 0.060 0.000 0.940 0.000
#> GSM751391 3 0.5273 0.32060 0.000 0.000 0.536 0.052 0.024 0.388
#> GSM751410 3 0.7170 0.28238 0.004 0.000 0.444 0.216 0.100 0.236
#> GSM751414 5 0.5033 0.41916 0.004 0.000 0.364 0.008 0.572 0.052
#> GSM751361 5 0.2691 0.74449 0.000 0.000 0.088 0.008 0.872 0.032
#> GSM751365 3 0.4138 0.19525 0.000 0.000 0.616 0.004 0.368 0.012
#> GSM751366 3 0.1858 0.69875 0.000 0.000 0.912 0.000 0.076 0.012
#> GSM751369 3 0.5014 0.47919 0.000 0.000 0.620 0.036 0.036 0.308
#> GSM751370 5 0.4732 0.50094 0.000 0.000 0.312 0.008 0.628 0.052
#> GSM751372 5 0.4399 0.47003 0.000 0.000 0.352 0.004 0.616 0.028
#> GSM751373 3 0.3319 0.59048 0.004 0.000 0.800 0.004 0.176 0.016
#> GSM751374 6 0.4962 0.26093 0.012 0.012 0.308 0.016 0.016 0.636
#> GSM751377 5 0.2622 0.73922 0.000 0.000 0.104 0.004 0.868 0.024
#> GSM751380 3 0.0891 0.71560 0.000 0.000 0.968 0.000 0.024 0.008
#> GSM751381 5 0.0717 0.74863 0.000 0.000 0.008 0.000 0.976 0.016
#> GSM751383 5 0.1958 0.74372 0.000 0.000 0.100 0.000 0.896 0.004
#> GSM751384 5 0.1168 0.75292 0.000 0.000 0.028 0.000 0.956 0.016
#> GSM751385 5 0.3726 0.65883 0.000 0.000 0.080 0.004 0.792 0.124
#> GSM751387 5 0.1297 0.75061 0.000 0.000 0.040 0.000 0.948 0.012
#> GSM751389 3 0.2287 0.71436 0.000 0.000 0.904 0.012 0.048 0.036
#> GSM751393 3 0.6416 0.09747 0.000 0.000 0.348 0.012 0.320 0.320
#> GSM751394 5 0.0725 0.74909 0.000 0.000 0.012 0.000 0.976 0.012
#> GSM751395 6 0.5266 0.40404 0.000 0.004 0.204 0.016 0.120 0.656
#> GSM751397 5 0.0891 0.74415 0.000 0.000 0.008 0.000 0.968 0.024
#> GSM751398 5 0.0458 0.75401 0.000 0.000 0.016 0.000 0.984 0.000
#> GSM751404 3 0.1267 0.71338 0.000 0.000 0.940 0.000 0.060 0.000
#> GSM751406 3 0.2976 0.65800 0.000 0.000 0.844 0.012 0.020 0.124
#> GSM751411 5 0.4118 0.39831 0.000 0.000 0.396 0.004 0.592 0.008
#> GSM751413 5 0.5676 0.60690 0.000 0.008 0.084 0.052 0.640 0.216
#> GSM751415 3 0.1267 0.71338 0.000 0.000 0.940 0.000 0.060 0.000
#> GSM751416 5 0.3385 0.69704 0.000 0.000 0.172 0.004 0.796 0.028
#> GSM751417 5 0.3385 0.69704 0.000 0.000 0.172 0.004 0.796 0.028
#> GSM751421 3 0.5103 0.52757 0.000 0.000 0.640 0.040 0.048 0.272
#> GSM751422 3 0.5103 0.52757 0.000 0.000 0.640 0.040 0.048 0.272
#> GSM751360 5 0.6850 0.22106 0.000 0.000 0.280 0.064 0.436 0.220
#> GSM751364 5 0.3753 0.65574 0.000 0.000 0.220 0.004 0.748 0.028
#> GSM751390 5 0.2446 0.73435 0.000 0.000 0.124 0.000 0.864 0.012
#> GSM751392 5 0.2081 0.72129 0.000 0.012 0.036 0.000 0.916 0.036
#> GSM751396 5 0.5372 0.61724 0.004 0.084 0.148 0.008 0.700 0.056
#> GSM751399 3 0.1556 0.70635 0.000 0.000 0.920 0.000 0.080 0.000
#> GSM751400 3 0.1267 0.71338 0.000 0.000 0.940 0.000 0.060 0.000
#> GSM751401 3 0.1267 0.71338 0.000 0.000 0.940 0.000 0.060 0.000
#> GSM751402 3 0.1082 0.71571 0.000 0.000 0.956 0.000 0.040 0.004
#> GSM751403 3 0.1204 0.71406 0.000 0.000 0.944 0.000 0.056 0.000
#> GSM751405 3 0.3715 0.65576 0.000 0.000 0.800 0.008 0.084 0.108
#> GSM751407 3 0.1267 0.71338 0.000 0.000 0.940 0.000 0.060 0.000
#> GSM751408 3 0.1444 0.70712 0.000 0.000 0.928 0.000 0.072 0.000
#> GSM751409 3 0.0914 0.70969 0.000 0.000 0.968 0.000 0.016 0.016
#> GSM751412 3 0.1444 0.70712 0.000 0.000 0.928 0.000 0.072 0.000
#> GSM751418 3 0.3935 0.38946 0.000 0.000 0.688 0.004 0.292 0.016
#> GSM751419 3 0.3935 0.38946 0.000 0.000 0.688 0.004 0.292 0.016
#> GSM751420 3 0.3290 0.60117 0.000 0.000 0.776 0.016 0.000 0.208
#> GSM751425 2 0.1642 0.86899 0.000 0.936 0.000 0.004 0.028 0.032
#> GSM751429 6 0.8025 0.18050 0.256 0.116 0.232 0.016 0.016 0.364
#> GSM751430 6 0.8312 0.11846 0.008 0.284 0.144 0.036 0.216 0.312
#> GSM751433 2 0.3537 0.81997 0.004 0.824 0.000 0.020 0.040 0.112
#> GSM751437 3 0.7105 0.00293 0.008 0.288 0.352 0.020 0.016 0.316
#> GSM751448 3 0.5794 0.26651 0.024 0.032 0.520 0.020 0.012 0.392
#> GSM751451 2 0.2276 0.86160 0.004 0.908 0.000 0.016 0.020 0.052
#> GSM751423 2 0.1003 0.87447 0.000 0.964 0.000 0.004 0.004 0.028
#> GSM751424 2 0.3537 0.81997 0.004 0.824 0.000 0.020 0.040 0.112
#> GSM751428 2 0.1970 0.85849 0.000 0.900 0.000 0.008 0.000 0.092
#> GSM751431 2 0.2645 0.85032 0.004 0.880 0.000 0.012 0.020 0.084
#> GSM751432 2 0.4793 0.76325 0.004 0.760 0.064 0.020 0.040 0.112
#> GSM751434 2 0.3537 0.81997 0.004 0.824 0.000 0.020 0.040 0.112
#> GSM751435 2 0.0603 0.87645 0.004 0.980 0.000 0.000 0.000 0.016
#> GSM751436 2 0.3537 0.81997 0.004 0.824 0.000 0.020 0.040 0.112
#> GSM751440 2 0.0982 0.87448 0.004 0.968 0.000 0.004 0.004 0.020
#> GSM751444 2 0.1987 0.87279 0.004 0.908 0.000 0.004 0.004 0.080
#> GSM751446 2 0.1830 0.86907 0.004 0.928 0.004 0.004 0.008 0.052
#> GSM751449 2 0.1830 0.86907 0.004 0.928 0.004 0.004 0.008 0.052
#> GSM751450 2 0.2365 0.85507 0.004 0.892 0.000 0.012 0.008 0.084
#> GSM751452 2 0.3537 0.81997 0.004 0.824 0.000 0.020 0.040 0.112
#> GSM751426 2 0.2881 0.84457 0.004 0.868 0.000 0.012 0.032 0.084
#> GSM751427 2 0.1007 0.87506 0.004 0.968 0.000 0.004 0.008 0.016
#> GSM751438 2 0.1894 0.86727 0.004 0.924 0.004 0.004 0.008 0.056
#> GSM751439 2 0.2563 0.85311 0.008 0.896 0.028 0.004 0.008 0.056
#> GSM751441 2 0.1995 0.86683 0.004 0.920 0.004 0.004 0.012 0.056
#> GSM751442 2 0.1830 0.86907 0.004 0.928 0.004 0.004 0.008 0.052
#> GSM751443 2 0.6861 0.15866 0.020 0.464 0.244 0.016 0.008 0.248
#> GSM751445 2 0.1956 0.86608 0.004 0.920 0.004 0.004 0.008 0.060
#> GSM751447 2 0.1830 0.86907 0.004 0.928 0.004 0.004 0.008 0.052
#> GSM751453 2 0.0837 0.87730 0.004 0.972 0.000 0.000 0.004 0.020
#> GSM751454 2 0.0837 0.87730 0.004 0.972 0.000 0.000 0.004 0.020
#> GSM751455 2 0.1830 0.86907 0.004 0.928 0.004 0.004 0.008 0.052
#> GSM751456 2 0.1830 0.86907 0.004 0.928 0.004 0.004 0.008 0.052
#> GSM751457 2 0.4489 0.61571 0.008 0.696 0.012 0.024 0.004 0.256
#> GSM751458 2 0.4489 0.61571 0.008 0.696 0.012 0.024 0.004 0.256
Heatmaps for the consensus matrix. It visualizes the probability of two samples to be in a same group.
consensus_heatmap(res, k = 2)
consensus_heatmap(res, k = 3)
consensus_heatmap(res, k = 4)
consensus_heatmap(res, k = 5)
consensus_heatmap(res, k = 6)
Heatmaps for the membership of samples in all partitions to see how consistent they are:
membership_heatmap(res, k = 2)
membership_heatmap(res, k = 3)
membership_heatmap(res, k = 4)
membership_heatmap(res, k = 5)
membership_heatmap(res, k = 6)
As soon as we have had the classes for columns, we can look for signatures which are significantly different between classes which can be candidate marks for certain classes. Following are the heatmaps for signatures.
Signature heatmaps where rows are scaled:
get_signatures(res, k = 2)
get_signatures(res, k = 3)
get_signatures(res, k = 4)
get_signatures(res, k = 5)
get_signatures(res, k = 6)
Signature heatmaps where rows are not scaled:
get_signatures(res, k = 2, scale_rows = FALSE)
get_signatures(res, k = 3, scale_rows = FALSE)
get_signatures(res, k = 4, scale_rows = FALSE)
get_signatures(res, k = 5, scale_rows = FALSE)
get_signatures(res, k = 6, scale_rows = FALSE)
Compare the overlap of signatures from different k:
compare_signatures(res)
get_signature() returns a data frame invisibly. TO get the list of signatures, the function
call should be assigned to a variable explicitly. In following code, if plot argument is set
to FALSE, no heatmap is plotted while only the differential analysis is performed.
# code only for demonstration
tb = get_signature(res, k = ..., plot = FALSE)
An example of the output of tb is:
#> which_row fdr mean_1 mean_2 scaled_mean_1 scaled_mean_2 km
#> 1 38 0.042760348 8.373488 9.131774 -0.5533452 0.5164555 1
#> 2 40 0.018707592 7.106213 8.469186 -0.6173731 0.5762149 1
#> 3 55 0.019134737 10.221463 11.207825 -0.6159697 0.5749050 1
#> 4 59 0.006059896 5.921854 7.869574 -0.6899429 0.6439467 1
#> 5 60 0.018055526 8.928898 10.211722 -0.6204761 0.5791110 1
#> 6 98 0.009384629 15.714769 14.887706 0.6635654 -0.6193277 2
...
The columns in tb are:
which_row: row indices corresponding to the input matrix.fdr: FDR for the differential test. mean_x: The mean value in group x.scaled_mean_x: The mean value in group x after rows are scaled.km: Row groups if k-means clustering is applied to rows.UMAP plot which shows how samples are separated.
dimension_reduction(res, k = 2, method = "UMAP")
dimension_reduction(res, k = 3, method = "UMAP")
dimension_reduction(res, k = 4, method = "UMAP")
dimension_reduction(res, k = 5, method = "UMAP")
dimension_reduction(res, k = 6, method = "UMAP")
Following heatmap shows how subgroups are split when increasing k:
collect_classes(res)
Test correlation between subgroups and known annotations. If the known annotation is numeric, one-way ANOVA test is applied, and if the known annotation is discrete, chi-squared contingency table test is applied.
test_to_known_factors(res)
#> n tissue(p) disease.state(p) agent(p) k
#> SD:skmeans 162 1.43e-31 9.66e-01 8.17e-01 2
#> SD:skmeans 148 7.19e-45 1.22e-01 3.74e-01 3
#> SD:skmeans 146 1.66e-52 4.30e-07 2.42e-06 4
#> SD:skmeans 137 1.39e-54 4.37e-03 5.97e-03 5
#> SD:skmeans 126 2.06e-48 9.64e-03 6.13e-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", "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 4537 rows and 166 columns.
#> Top rows (454, 908, 1361, 1814, 2268) 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 0.256 0.784 0.854 0.4927 0.500 0.500
#> 3 3 0.552 0.726 0.862 0.3377 0.735 0.518
#> 4 4 0.514 0.476 0.695 0.1245 0.808 0.506
#> 5 5 0.584 0.445 0.713 0.0739 0.871 0.557
#> 6 6 0.655 0.438 0.651 0.0407 0.925 0.669
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
#> GSM751298 1 0.0000 0.8689 1.000 0.000
#> GSM751304 2 0.7745 0.8198 0.228 0.772
#> GSM751305 2 0.6531 0.8422 0.168 0.832
#> GSM751307 2 0.7883 0.8180 0.236 0.764
#> GSM751310 1 0.5059 0.8486 0.888 0.112
#> GSM751314 1 0.6623 0.8217 0.828 0.172
#> GSM751316 1 0.3584 0.8546 0.932 0.068
#> GSM751318 1 0.4431 0.8540 0.908 0.092
#> GSM751342 1 0.6148 0.8348 0.848 0.152
#> GSM751346 1 0.0938 0.8647 0.988 0.012
#> GSM751347 1 0.0000 0.8689 1.000 0.000
#> GSM751348 2 0.7376 0.8254 0.208 0.792
#> GSM751349 2 0.6438 0.8464 0.164 0.836
#> GSM751352 2 0.8909 0.7551 0.308 0.692
#> GSM751353 2 0.8267 0.7938 0.260 0.740
#> GSM751354 2 0.7602 0.8206 0.220 0.780
#> GSM751355 2 0.7299 0.8293 0.204 0.796
#> GSM751358 2 0.8081 0.6681 0.248 0.752
#> GSM751359 2 0.3274 0.8471 0.060 0.940
#> GSM751294 2 0.7219 0.8282 0.200 0.800
#> GSM751296 1 0.0000 0.8689 1.000 0.000
#> GSM751297 1 0.4562 0.8404 0.904 0.096
#> GSM751299 2 0.9129 0.7253 0.328 0.672
#> GSM751300 1 0.0000 0.8689 1.000 0.000
#> GSM751301 1 0.4690 0.7994 0.900 0.100
#> GSM751302 1 0.0000 0.8689 1.000 0.000
#> GSM751303 1 0.5059 0.8489 0.888 0.112
#> GSM751306 1 0.6048 0.8353 0.852 0.148
#> GSM751308 1 0.0376 0.8671 0.996 0.004
#> GSM751309 1 0.5629 0.8405 0.868 0.132
#> GSM751311 1 0.1633 0.8684 0.976 0.024
#> GSM751312 1 0.0000 0.8689 1.000 0.000
#> GSM751313 1 0.0376 0.8689 0.996 0.004
#> GSM751315 1 0.0000 0.8689 1.000 0.000
#> GSM751317 1 0.0376 0.8689 0.996 0.004
#> GSM751320 1 0.0000 0.8689 1.000 0.000
#> GSM751321 1 0.0672 0.8691 0.992 0.008
#> GSM751322 1 0.1843 0.8678 0.972 0.028
#> GSM751324 1 0.4161 0.8540 0.916 0.084
#> GSM751325 1 0.0938 0.8694 0.988 0.012
#> GSM751332 1 0.4939 0.8486 0.892 0.108
#> GSM751334 1 0.2948 0.8630 0.948 0.052
#> GSM751339 1 0.0672 0.8678 0.992 0.008
#> GSM751341 1 0.0376 0.8684 0.996 0.004
#> GSM751343 1 0.0000 0.8689 1.000 0.000
#> GSM751344 2 0.8443 0.7870 0.272 0.728
#> GSM751345 2 0.8661 0.7716 0.288 0.712
#> GSM751356 2 0.8327 0.7885 0.264 0.736
#> GSM751357 2 0.8267 0.7929 0.260 0.740
#> GSM751293 1 0.0000 0.8689 1.000 0.000
#> GSM751295 1 0.0000 0.8689 1.000 0.000
#> GSM751319 1 0.0000 0.8689 1.000 0.000
#> GSM751323 1 0.0000 0.8689 1.000 0.000
#> GSM751326 1 0.0000 0.8689 1.000 0.000
#> GSM751327 1 0.0000 0.8689 1.000 0.000
#> GSM751328 1 0.2778 0.8640 0.952 0.048
#> GSM751329 1 0.0000 0.8689 1.000 0.000
#> GSM751330 1 0.0000 0.8689 1.000 0.000
#> GSM751331 1 0.0000 0.8689 1.000 0.000
#> GSM751333 1 0.0000 0.8689 1.000 0.000
#> GSM751335 1 0.0000 0.8689 1.000 0.000
#> GSM751336 1 0.0000 0.8689 1.000 0.000
#> GSM751337 1 0.0376 0.8687 0.996 0.004
#> GSM751338 1 0.0000 0.8689 1.000 0.000
#> GSM751340 1 0.0672 0.8681 0.992 0.008
#> GSM751350 1 0.0000 0.8689 1.000 0.000
#> GSM751351 1 0.0000 0.8689 1.000 0.000
#> GSM751362 1 0.8207 0.7752 0.744 0.256
#> GSM751363 1 0.8267 0.7688 0.740 0.260
#> GSM751367 1 0.8661 0.6880 0.712 0.288
#> GSM751368 2 0.1633 0.8324 0.024 0.976
#> GSM751371 1 0.6247 0.8345 0.844 0.156
#> GSM751375 2 0.6623 0.8339 0.172 0.828
#> GSM751376 2 0.6801 0.8381 0.180 0.820
#> GSM751378 2 0.3274 0.8494 0.060 0.940
#> GSM751379 2 0.4690 0.8521 0.100 0.900
#> GSM751382 2 0.6247 0.8437 0.156 0.844
#> GSM751386 2 0.0938 0.8291 0.012 0.988
#> GSM751388 2 0.1184 0.8300 0.016 0.984
#> GSM751391 2 0.9129 0.4389 0.328 0.672
#> GSM751410 1 0.5178 0.8412 0.884 0.116
#> GSM751414 1 0.9209 0.6962 0.664 0.336
#> GSM751361 2 0.5059 0.7789 0.112 0.888
#> GSM751365 1 0.9710 0.5888 0.600 0.400
#> GSM751366 1 0.8713 0.7426 0.708 0.292
#> GSM751369 1 0.7674 0.7947 0.776 0.224
#> GSM751370 1 0.8661 0.7459 0.712 0.288
#> GSM751372 2 0.9954 -0.1757 0.460 0.540
#> GSM751373 1 0.9393 0.6630 0.644 0.356
#> GSM751374 2 0.5737 0.8556 0.136 0.864
#> GSM751377 2 0.2043 0.8321 0.032 0.968
#> GSM751380 1 0.8386 0.7652 0.732 0.268
#> GSM751381 2 0.2236 0.8423 0.036 0.964
#> GSM751383 2 0.2043 0.8381 0.032 0.968
#> GSM751384 2 0.2043 0.8315 0.032 0.968
#> GSM751385 2 0.6343 0.8430 0.160 0.840
#> GSM751387 2 0.1184 0.8331 0.016 0.984
#> GSM751389 2 0.2603 0.8289 0.044 0.956
#> GSM751393 2 0.2043 0.8311 0.032 0.968
#> GSM751394 2 0.3584 0.8472 0.068 0.932
#> GSM751395 2 0.4562 0.8502 0.096 0.904
#> GSM751397 2 0.3584 0.8489 0.068 0.932
#> GSM751398 2 0.2236 0.8339 0.036 0.964
#> GSM751404 1 0.9170 0.7119 0.668 0.332
#> GSM751406 1 0.7815 0.7833 0.768 0.232
#> GSM751411 1 0.9323 0.6819 0.652 0.348
#> GSM751413 2 0.7139 0.8333 0.196 0.804
#> GSM751415 1 0.8955 0.7279 0.688 0.312
#> GSM751416 2 0.2423 0.8311 0.040 0.960
#> GSM751417 2 0.1843 0.8317 0.028 0.972
#> GSM751421 2 0.9833 0.0329 0.424 0.576
#> GSM751422 1 0.8909 0.7143 0.692 0.308
#> GSM751360 1 0.7602 0.7939 0.780 0.220
#> GSM751364 2 0.9977 -0.2346 0.472 0.528
#> GSM751390 2 0.9710 0.1653 0.400 0.600
#> GSM751392 2 0.2603 0.8468 0.044 0.956
#> GSM751396 2 0.0376 0.8270 0.004 0.996
#> GSM751399 1 0.9896 0.5099 0.560 0.440
#> GSM751400 2 0.4939 0.8356 0.108 0.892
#> GSM751401 1 0.8608 0.7523 0.716 0.284
#> GSM751402 1 0.8555 0.7536 0.720 0.280
#> GSM751403 1 0.9491 0.6442 0.632 0.368
#> GSM751405 1 0.8016 0.7763 0.756 0.244
#> GSM751407 1 0.9000 0.6974 0.684 0.316
#> GSM751408 2 0.2778 0.8397 0.048 0.952
#> GSM751409 2 0.1633 0.8308 0.024 0.976
#> GSM751412 2 0.8443 0.5086 0.272 0.728
#> GSM751418 2 0.9933 -0.1504 0.452 0.548
#> GSM751419 2 0.9427 0.2575 0.360 0.640
#> GSM751420 2 0.1843 0.8407 0.028 0.972
#> GSM751425 2 0.6148 0.8435 0.152 0.848
#> GSM751429 1 0.8661 0.5984 0.712 0.288
#> GSM751430 2 0.7602 0.8241 0.220 0.780
#> GSM751433 2 0.3733 0.8398 0.072 0.928
#> GSM751437 2 0.6247 0.8436 0.156 0.844
#> GSM751448 1 0.6887 0.8073 0.816 0.184
#> GSM751451 2 0.3274 0.8397 0.060 0.940
#> GSM751423 2 0.2778 0.8484 0.048 0.952
#> GSM751424 2 0.3733 0.8513 0.072 0.928
#> GSM751428 2 0.6623 0.8403 0.172 0.828
#> GSM751431 2 0.4431 0.8534 0.092 0.908
#> GSM751432 2 0.5294 0.8353 0.120 0.880
#> GSM751434 2 0.7139 0.8340 0.196 0.804
#> GSM751435 2 0.6438 0.8431 0.164 0.836
#> GSM751436 2 0.4022 0.8357 0.080 0.920
#> GSM751440 2 0.2948 0.8468 0.052 0.948
#> GSM751444 2 0.7602 0.8136 0.220 0.780
#> GSM751446 2 0.5059 0.8541 0.112 0.888
#> GSM751449 2 0.4562 0.8529 0.096 0.904
#> GSM751450 2 0.4022 0.8528 0.080 0.920
#> GSM751452 2 0.5294 0.8474 0.120 0.880
#> GSM751426 2 0.5842 0.8475 0.140 0.860
#> GSM751427 2 0.2603 0.8473 0.044 0.956
#> GSM751438 2 0.4431 0.8532 0.092 0.908
#> GSM751439 2 0.9552 0.4914 0.376 0.624
#> GSM751441 2 0.7219 0.8267 0.200 0.800
#> GSM751442 2 0.8443 0.7680 0.272 0.728
#> GSM751443 1 0.8499 0.5916 0.724 0.276
#> GSM751445 2 0.6048 0.8406 0.148 0.852
#> GSM751447 2 0.7139 0.8281 0.196 0.804
#> GSM751453 2 0.7528 0.8142 0.216 0.784
#> GSM751454 2 0.7219 0.8233 0.200 0.800
#> GSM751455 2 0.6048 0.8468 0.148 0.852
#> GSM751456 2 0.6712 0.8387 0.176 0.824
#> GSM751457 2 0.6438 0.8361 0.164 0.836
#> GSM751458 2 0.6712 0.8319 0.176 0.824
cbind(get_classes(res, k = 3), get_membership(res, k = 3))
#> class entropy silhouette p1 p2 p3
#> GSM751298 1 0.0237 0.9329 0.996 0.004 0.000
#> GSM751304 2 0.9049 0.5140 0.232 0.556 0.212
#> GSM751305 2 0.9456 0.3651 0.200 0.480 0.320
#> GSM751307 2 0.9400 0.3073 0.180 0.464 0.356
#> GSM751310 1 0.3879 0.7954 0.848 0.000 0.152
#> GSM751314 1 0.2711 0.8753 0.912 0.000 0.088
#> GSM751316 1 0.2165 0.8940 0.936 0.000 0.064
#> GSM751318 1 0.2448 0.8814 0.924 0.076 0.000
#> GSM751342 1 0.4179 0.8528 0.876 0.072 0.052
#> GSM751346 1 0.0592 0.9289 0.988 0.012 0.000
#> GSM751347 1 0.0237 0.9333 0.996 0.000 0.004
#> GSM751348 2 0.5585 0.7459 0.092 0.812 0.096
#> GSM751349 2 0.6031 0.7351 0.096 0.788 0.116
#> GSM751352 2 0.6253 0.6762 0.232 0.732 0.036
#> GSM751353 2 0.6911 0.6937 0.180 0.728 0.092
#> GSM751354 2 0.7661 0.6595 0.144 0.684 0.172
#> GSM751355 2 0.9015 0.3717 0.144 0.508 0.348
#> GSM751358 2 0.8568 0.5605 0.200 0.608 0.192
#> GSM751359 2 0.7787 0.4629 0.064 0.588 0.348
#> GSM751294 2 0.4658 0.7562 0.068 0.856 0.076
#> GSM751296 1 0.0000 0.9342 1.000 0.000 0.000
#> GSM751297 1 0.7633 0.5888 0.684 0.184 0.132
#> GSM751299 2 0.5138 0.6694 0.252 0.748 0.000
#> GSM751300 1 0.0000 0.9342 1.000 0.000 0.000
#> GSM751301 1 0.3539 0.8329 0.888 0.100 0.012
#> GSM751302 1 0.0000 0.9342 1.000 0.000 0.000
#> GSM751303 1 0.1411 0.9190 0.964 0.000 0.036
#> GSM751306 1 0.1964 0.9050 0.944 0.000 0.056
#> GSM751308 1 0.1031 0.9237 0.976 0.024 0.000
#> GSM751309 1 0.1411 0.9180 0.964 0.000 0.036
#> GSM751311 1 0.0237 0.9334 0.996 0.000 0.004
#> GSM751312 1 0.0747 0.9287 0.984 0.000 0.016
#> GSM751313 1 0.0000 0.9342 1.000 0.000 0.000
#> GSM751315 1 0.0000 0.9342 1.000 0.000 0.000
#> GSM751317 1 0.0000 0.9342 1.000 0.000 0.000
#> GSM751320 1 0.0000 0.9342 1.000 0.000 0.000
#> GSM751321 1 0.0000 0.9342 1.000 0.000 0.000
#> GSM751322 1 0.0237 0.9334 0.996 0.000 0.004
#> GSM751324 1 0.0747 0.9284 0.984 0.000 0.016
#> GSM751325 1 0.0000 0.9342 1.000 0.000 0.000
#> GSM751332 1 0.1163 0.9221 0.972 0.000 0.028
#> GSM751334 1 0.0424 0.9321 0.992 0.000 0.008
#> GSM751339 1 0.0983 0.9273 0.980 0.004 0.016
#> GSM751341 1 0.1525 0.9167 0.964 0.032 0.004
#> GSM751343 1 0.0424 0.9315 0.992 0.008 0.000
#> GSM751344 2 0.6380 0.7154 0.164 0.760 0.076
#> GSM751345 2 0.6208 0.7189 0.164 0.768 0.068
#> GSM751356 2 0.5722 0.7371 0.132 0.800 0.068
#> GSM751357 2 0.6393 0.7198 0.148 0.764 0.088
#> GSM751293 1 0.0000 0.9342 1.000 0.000 0.000
#> GSM751295 1 0.0000 0.9342 1.000 0.000 0.000
#> GSM751319 1 0.0000 0.9342 1.000 0.000 0.000
#> GSM751323 1 0.0000 0.9342 1.000 0.000 0.000
#> GSM751326 1 0.0000 0.9342 1.000 0.000 0.000
#> GSM751327 1 0.0000 0.9342 1.000 0.000 0.000
#> GSM751328 1 0.0747 0.9284 0.984 0.000 0.016
#> GSM751329 1 0.0000 0.9342 1.000 0.000 0.000
#> GSM751330 1 0.0000 0.9342 1.000 0.000 0.000
#> GSM751331 1 0.0000 0.9342 1.000 0.000 0.000
#> GSM751333 1 0.0000 0.9342 1.000 0.000 0.000
#> GSM751335 1 0.0000 0.9342 1.000 0.000 0.000
#> GSM751336 1 0.0000 0.9342 1.000 0.000 0.000
#> GSM751337 1 0.0237 0.9330 0.996 0.004 0.000
#> GSM751338 1 0.0000 0.9342 1.000 0.000 0.000
#> GSM751340 1 0.2590 0.8881 0.924 0.004 0.072
#> GSM751350 1 0.0000 0.9342 1.000 0.000 0.000
#> GSM751351 1 0.0000 0.9342 1.000 0.000 0.000
#> GSM751362 3 0.5016 0.6659 0.240 0.000 0.760
#> GSM751363 3 0.5016 0.6643 0.240 0.000 0.760
#> GSM751367 1 0.8932 -0.0922 0.456 0.124 0.420
#> GSM751368 3 0.4121 0.7409 0.000 0.168 0.832
#> GSM751371 1 0.2939 0.8824 0.916 0.012 0.072
#> GSM751375 2 0.4371 0.7495 0.032 0.860 0.108
#> GSM751376 2 0.7728 0.5930 0.084 0.640 0.276
#> GSM751378 2 0.6161 0.6104 0.020 0.708 0.272
#> GSM751379 3 0.7107 0.3930 0.036 0.340 0.624
#> GSM751382 2 0.5744 0.7349 0.072 0.800 0.128
#> GSM751386 3 0.4002 0.7448 0.000 0.160 0.840
#> GSM751388 3 0.4002 0.7450 0.000 0.160 0.840
#> GSM751391 2 0.9908 0.1591 0.268 0.372 0.360
#> GSM751410 1 0.5842 0.7314 0.768 0.036 0.196
#> GSM751414 3 0.3213 0.7927 0.092 0.008 0.900
#> GSM751361 3 0.4848 0.7660 0.036 0.128 0.836
#> GSM751365 3 0.0237 0.8180 0.004 0.000 0.996
#> GSM751366 3 0.1643 0.8060 0.044 0.000 0.956
#> GSM751369 1 0.6848 0.2495 0.568 0.016 0.416
#> GSM751370 3 0.2711 0.7963 0.088 0.000 0.912
#> GSM751372 3 0.0000 0.8171 0.000 0.000 1.000
#> GSM751373 3 0.1163 0.8191 0.028 0.000 0.972
#> GSM751374 3 0.7188 0.5041 0.056 0.280 0.664
#> GSM751377 3 0.3941 0.7483 0.000 0.156 0.844
#> GSM751380 3 0.2682 0.7881 0.076 0.004 0.920
#> GSM751381 3 0.5061 0.6928 0.008 0.208 0.784
#> GSM751383 3 0.4062 0.7451 0.000 0.164 0.836
#> GSM751384 3 0.0000 0.8171 0.000 0.000 1.000
#> GSM751385 3 0.7853 0.0245 0.060 0.384 0.556
#> GSM751387 2 0.6045 0.4468 0.000 0.620 0.380
#> GSM751389 3 0.1399 0.8115 0.004 0.028 0.968
#> GSM751393 3 0.1163 0.8160 0.000 0.028 0.972
#> GSM751394 3 0.6955 -0.1416 0.016 0.492 0.492
#> GSM751395 3 0.5202 0.7479 0.044 0.136 0.820
#> GSM751397 3 0.6487 0.5561 0.032 0.268 0.700
#> GSM751398 3 0.4504 0.7049 0.000 0.196 0.804
#> GSM751404 3 0.0000 0.8171 0.000 0.000 1.000
#> GSM751406 3 0.8519 0.1612 0.396 0.096 0.508
#> GSM751411 3 0.0000 0.8171 0.000 0.000 1.000
#> GSM751413 2 0.9259 0.1879 0.156 0.440 0.404
#> GSM751415 3 0.1529 0.8078 0.040 0.000 0.960
#> GSM751416 3 0.3879 0.7517 0.000 0.152 0.848
#> GSM751417 3 0.3941 0.7483 0.000 0.156 0.844
#> GSM751421 3 0.5136 0.7387 0.132 0.044 0.824
#> GSM751422 1 0.7248 0.1487 0.536 0.028 0.436
#> GSM751360 1 0.5465 0.5792 0.712 0.000 0.288
#> GSM751364 3 0.3263 0.8080 0.048 0.040 0.912
#> GSM751390 3 0.2031 0.8147 0.032 0.016 0.952
#> GSM751392 2 0.5503 0.6892 0.020 0.772 0.208
#> GSM751396 2 0.6309 0.1037 0.000 0.504 0.496
#> GSM751399 3 0.0000 0.8171 0.000 0.000 1.000
#> GSM751400 3 0.2383 0.8061 0.044 0.016 0.940
#> GSM751401 3 0.2590 0.7870 0.004 0.072 0.924
#> GSM751402 3 0.1919 0.8112 0.024 0.020 0.956
#> GSM751403 3 0.0661 0.8181 0.008 0.004 0.988
#> GSM751405 3 0.6498 0.2825 0.396 0.008 0.596
#> GSM751407 3 0.1643 0.8090 0.044 0.000 0.956
#> GSM751408 3 0.0747 0.8179 0.016 0.000 0.984
#> GSM751409 3 0.1289 0.8086 0.000 0.032 0.968
#> GSM751412 3 0.0000 0.8171 0.000 0.000 1.000
#> GSM751418 3 0.0237 0.8174 0.000 0.004 0.996
#> GSM751419 3 0.0237 0.8174 0.000 0.004 0.996
#> GSM751420 2 0.6460 0.3215 0.004 0.556 0.440
#> GSM751425 2 0.0000 0.7712 0.000 1.000 0.000
#> GSM751429 3 0.8280 0.0873 0.080 0.404 0.516
#> GSM751430 2 0.9041 0.2922 0.140 0.488 0.372
#> GSM751433 2 0.0592 0.7702 0.012 0.988 0.000
#> GSM751437 2 0.4897 0.6531 0.016 0.812 0.172
#> GSM751448 2 0.9687 0.2536 0.296 0.456 0.248
#> GSM751451 2 0.0000 0.7712 0.000 1.000 0.000
#> GSM751423 2 0.1964 0.7628 0.000 0.944 0.056
#> GSM751424 2 0.4128 0.7281 0.012 0.856 0.132
#> GSM751428 2 0.5659 0.7000 0.052 0.796 0.152
#> GSM751431 2 0.0000 0.7712 0.000 1.000 0.000
#> GSM751432 2 0.7979 0.1802 0.060 0.500 0.440
#> GSM751434 2 0.7453 0.5233 0.064 0.644 0.292
#> GSM751435 2 0.0661 0.7720 0.008 0.988 0.004
#> GSM751436 2 0.2749 0.7596 0.012 0.924 0.064
#> GSM751440 2 0.1877 0.7632 0.012 0.956 0.032
#> GSM751444 2 0.0000 0.7712 0.000 1.000 0.000
#> GSM751446 2 0.0000 0.7712 0.000 1.000 0.000
#> GSM751449 2 0.0000 0.7712 0.000 1.000 0.000
#> GSM751450 2 0.1267 0.7692 0.024 0.972 0.004
#> GSM751452 2 0.6337 0.5975 0.028 0.708 0.264
#> GSM751426 2 0.1015 0.7708 0.012 0.980 0.008
#> GSM751427 2 0.0000 0.7712 0.000 1.000 0.000
#> GSM751438 2 0.0000 0.7712 0.000 1.000 0.000
#> GSM751439 2 0.7525 0.5274 0.108 0.684 0.208
#> GSM751441 2 0.0000 0.7712 0.000 1.000 0.000
#> GSM751442 2 0.0000 0.7712 0.000 1.000 0.000
#> GSM751443 2 0.8624 0.4296 0.240 0.596 0.164
#> GSM751445 2 0.0000 0.7712 0.000 1.000 0.000
#> GSM751447 2 0.0000 0.7712 0.000 1.000 0.000
#> GSM751453 2 0.0000 0.7712 0.000 1.000 0.000
#> GSM751454 2 0.0000 0.7712 0.000 1.000 0.000
#> GSM751455 2 0.0000 0.7712 0.000 1.000 0.000
#> GSM751456 2 0.0000 0.7712 0.000 1.000 0.000
#> GSM751457 2 0.0000 0.7712 0.000 1.000 0.000
#> GSM751458 2 0.0000 0.7712 0.000 1.000 0.000
cbind(get_classes(res, k = 4), get_membership(res, k = 4))
#> class entropy silhouette p1 p2 p3 p4
#> GSM751298 1 0.4454 0.33426 0.692 0.000 0.000 0.308
#> GSM751304 1 0.7712 0.06244 0.436 0.140 0.016 0.408
#> GSM751305 1 0.7814 0.16407 0.548 0.160 0.032 0.260
#> GSM751307 4 0.7892 -0.10363 0.388 0.116 0.036 0.460
#> GSM751310 1 0.1936 0.56286 0.940 0.000 0.028 0.032
#> GSM751314 1 0.0188 0.58732 0.996 0.000 0.000 0.004
#> GSM751316 1 0.2868 0.53151 0.864 0.000 0.000 0.136
#> GSM751318 1 0.3219 0.51807 0.836 0.000 0.000 0.164
#> GSM751342 1 0.0657 0.58573 0.984 0.004 0.000 0.012
#> GSM751346 4 0.5696 0.33631 0.364 0.016 0.012 0.608
#> GSM751347 4 0.4905 0.35039 0.364 0.000 0.004 0.632
#> GSM751348 2 0.7881 0.34888 0.176 0.500 0.020 0.304
#> GSM751349 2 0.6652 0.57647 0.032 0.580 0.040 0.348
#> GSM751352 4 0.5497 0.01250 0.008 0.412 0.008 0.572
#> GSM751353 4 0.5683 -0.17585 0.008 0.452 0.012 0.528
#> GSM751354 4 0.7837 0.13404 0.220 0.248 0.016 0.516
#> GSM751355 4 0.7880 0.01526 0.076 0.260 0.096 0.568
#> GSM751358 1 0.7894 0.18986 0.536 0.188 0.028 0.248
#> GSM751359 1 0.8796 0.07291 0.456 0.144 0.092 0.308
#> GSM751294 2 0.5736 0.62757 0.040 0.712 0.024 0.224
#> GSM751296 4 0.4866 0.31426 0.404 0.000 0.000 0.596
#> GSM751297 4 0.8335 0.18619 0.208 0.212 0.056 0.524
#> GSM751299 4 0.5273 -0.06140 0.008 0.456 0.000 0.536
#> GSM751300 4 0.4746 0.35147 0.368 0.000 0.000 0.632
#> GSM751301 4 0.6055 0.09735 0.436 0.044 0.000 0.520
#> GSM751302 4 0.4746 0.35147 0.368 0.000 0.000 0.632
#> GSM751303 1 0.0817 0.58171 0.976 0.000 0.000 0.024
#> GSM751306 1 0.0707 0.58334 0.980 0.000 0.000 0.020
#> GSM751308 1 0.5822 0.27958 0.648 0.032 0.012 0.308
#> GSM751309 1 0.0000 0.58723 1.000 0.000 0.000 0.000
#> GSM751311 1 0.0000 0.58723 1.000 0.000 0.000 0.000
#> GSM751312 1 0.3569 0.46401 0.804 0.000 0.000 0.196
#> GSM751313 4 0.4888 0.28819 0.412 0.000 0.000 0.588
#> GSM751315 1 0.4679 0.30734 0.648 0.000 0.000 0.352
#> GSM751317 1 0.0921 0.58661 0.972 0.000 0.000 0.028
#> GSM751320 1 0.4948 -0.01204 0.560 0.000 0.000 0.440
#> GSM751321 1 0.1118 0.57989 0.964 0.000 0.000 0.036
#> GSM751322 1 0.4008 0.43531 0.756 0.000 0.000 0.244
#> GSM751324 1 0.2011 0.56588 0.920 0.000 0.000 0.080
#> GSM751325 1 0.3801 0.46764 0.780 0.000 0.000 0.220
#> GSM751332 1 0.6258 0.25506 0.600 0.000 0.076 0.324
#> GSM751334 1 0.6235 0.01966 0.524 0.000 0.056 0.420
#> GSM751339 4 0.6774 0.13362 0.444 0.004 0.080 0.472
#> GSM751341 1 0.0469 0.58657 0.988 0.000 0.000 0.012
#> GSM751343 1 0.5560 0.25858 0.644 0.028 0.004 0.324
#> GSM751344 4 0.5270 0.01650 0.008 0.320 0.012 0.660
#> GSM751345 4 0.5522 -0.00355 0.012 0.324 0.016 0.648
#> GSM751356 4 0.7964 -0.00745 0.352 0.252 0.004 0.392
#> GSM751357 4 0.7860 -0.02815 0.372 0.196 0.008 0.424
#> GSM751293 4 0.5167 0.13581 0.488 0.004 0.000 0.508
#> GSM751295 4 0.4730 0.34958 0.364 0.000 0.000 0.636
#> GSM751319 1 0.4543 0.36900 0.676 0.000 0.000 0.324
#> GSM751323 1 0.4967 -0.05130 0.548 0.000 0.000 0.452
#> GSM751326 4 0.5000 0.11510 0.496 0.000 0.000 0.504
#> GSM751327 4 0.4999 0.15374 0.492 0.000 0.000 0.508
#> GSM751328 1 0.3311 0.51431 0.828 0.000 0.000 0.172
#> GSM751329 4 0.4955 0.23786 0.444 0.000 0.000 0.556
#> GSM751330 4 0.4746 0.35147 0.368 0.000 0.000 0.632
#> GSM751331 4 0.4746 0.35147 0.368 0.000 0.000 0.632
#> GSM751333 4 0.4790 0.33744 0.380 0.000 0.000 0.620
#> GSM751335 4 0.4746 0.35147 0.368 0.000 0.000 0.632
#> GSM751336 4 0.4746 0.35147 0.368 0.000 0.000 0.632
#> GSM751337 4 0.4992 0.19485 0.476 0.000 0.000 0.524
#> GSM751338 4 0.4967 0.23761 0.452 0.000 0.000 0.548
#> GSM751340 1 0.6498 0.02056 0.488 0.000 0.072 0.440
#> GSM751350 4 0.4746 0.35147 0.368 0.000 0.000 0.632
#> GSM751351 4 0.4746 0.35147 0.368 0.000 0.000 0.632
#> GSM751362 3 0.5434 0.63668 0.188 0.000 0.728 0.084
#> GSM751363 3 0.7369 0.43222 0.356 0.004 0.492 0.148
#> GSM751367 1 0.8323 0.21658 0.512 0.072 0.128 0.288
#> GSM751368 3 0.4212 0.66933 0.000 0.216 0.772 0.012
#> GSM751371 1 0.5133 0.48713 0.748 0.020 0.024 0.208
#> GSM751375 2 0.5433 0.69321 0.004 0.688 0.036 0.272
#> GSM751376 2 0.9519 0.15343 0.240 0.388 0.132 0.240
#> GSM751378 2 0.5599 0.57196 0.000 0.672 0.276 0.052
#> GSM751379 3 0.9668 0.23386 0.164 0.228 0.376 0.232
#> GSM751382 2 0.5984 0.62794 0.008 0.660 0.056 0.276
#> GSM751386 3 0.5222 0.72050 0.000 0.112 0.756 0.132
#> GSM751388 3 0.5217 0.72168 0.000 0.108 0.756 0.136
#> GSM751391 3 0.9556 -0.04219 0.208 0.264 0.384 0.144
#> GSM751410 1 0.5469 0.42969 0.764 0.044 0.152 0.040
#> GSM751414 3 0.4956 0.73674 0.056 0.000 0.756 0.188
#> GSM751361 3 0.5612 0.72337 0.008 0.100 0.740 0.152
#> GSM751365 3 0.0000 0.76321 0.000 0.000 1.000 0.000
#> GSM751366 3 0.0336 0.76252 0.008 0.000 0.992 0.000
#> GSM751369 3 0.6491 0.10706 0.432 0.000 0.496 0.072
#> GSM751370 3 0.4719 0.74291 0.048 0.000 0.772 0.180
#> GSM751372 3 0.4150 0.75317 0.056 0.000 0.824 0.120
#> GSM751373 3 0.0895 0.76564 0.004 0.000 0.976 0.020
#> GSM751374 3 0.9571 0.13496 0.196 0.140 0.336 0.328
#> GSM751377 3 0.5167 0.72209 0.000 0.108 0.760 0.132
#> GSM751380 3 0.0779 0.76015 0.016 0.004 0.980 0.000
#> GSM751381 3 0.6116 0.69677 0.004 0.136 0.692 0.168
#> GSM751383 3 0.5277 0.71837 0.000 0.116 0.752 0.132
#> GSM751384 3 0.2921 0.75606 0.000 0.000 0.860 0.140
#> GSM751385 4 0.6574 -0.21331 0.000 0.088 0.364 0.548
#> GSM751387 3 0.7716 0.10983 0.000 0.380 0.396 0.224
#> GSM751389 3 0.0336 0.76243 0.000 0.000 0.992 0.008
#> GSM751393 3 0.3895 0.75216 0.000 0.036 0.832 0.132
#> GSM751394 3 0.7937 0.42060 0.016 0.180 0.456 0.348
#> GSM751395 3 0.8179 0.56292 0.088 0.088 0.512 0.312
#> GSM751397 3 0.7265 0.64508 0.028 0.136 0.612 0.224
#> GSM751398 3 0.6424 0.66040 0.004 0.120 0.652 0.224
#> GSM751404 3 0.0000 0.76321 0.000 0.000 1.000 0.000
#> GSM751406 3 0.8894 0.11342 0.132 0.128 0.480 0.260
#> GSM751411 3 0.0336 0.76323 0.000 0.000 0.992 0.008
#> GSM751413 4 0.9245 -0.22581 0.180 0.124 0.264 0.432
#> GSM751415 3 0.0336 0.76252 0.008 0.000 0.992 0.000
#> GSM751416 3 0.5160 0.72454 0.000 0.104 0.760 0.136
#> GSM751417 3 0.5217 0.72200 0.000 0.108 0.756 0.136
#> GSM751421 3 0.5744 0.67780 0.128 0.036 0.756 0.080
#> GSM751422 3 0.8329 0.16874 0.352 0.052 0.456 0.140
#> GSM751360 1 0.6482 0.33059 0.640 0.000 0.208 0.152
#> GSM751364 3 0.4727 0.73733 0.028 0.008 0.772 0.192
#> GSM751390 3 0.4733 0.74440 0.004 0.044 0.780 0.172
#> GSM751392 2 0.7175 0.54534 0.008 0.524 0.116 0.352
#> GSM751396 3 0.7434 0.41320 0.000 0.232 0.512 0.256
#> GSM751399 3 0.0000 0.76321 0.000 0.000 1.000 0.000
#> GSM751400 3 0.1022 0.76250 0.000 0.000 0.968 0.032
#> GSM751401 3 0.0592 0.75914 0.000 0.016 0.984 0.000
#> GSM751402 3 0.0524 0.76232 0.000 0.004 0.988 0.008
#> GSM751403 3 0.0524 0.76398 0.000 0.004 0.988 0.008
#> GSM751405 3 0.7027 0.35741 0.180 0.008 0.608 0.204
#> GSM751407 3 0.0592 0.76127 0.000 0.000 0.984 0.016
#> GSM751408 3 0.0188 0.76344 0.000 0.000 0.996 0.004
#> GSM751409 3 0.0376 0.76213 0.000 0.004 0.992 0.004
#> GSM751412 3 0.0000 0.76321 0.000 0.000 1.000 0.000
#> GSM751418 3 0.0592 0.76562 0.000 0.000 0.984 0.016
#> GSM751419 3 0.0000 0.76321 0.000 0.000 1.000 0.000
#> GSM751420 2 0.5700 0.34433 0.000 0.560 0.412 0.028
#> GSM751425 2 0.1474 0.78116 0.000 0.948 0.000 0.052
#> GSM751429 2 0.8027 0.33348 0.028 0.500 0.176 0.296
#> GSM751430 4 0.8269 -0.14404 0.020 0.276 0.264 0.440
#> GSM751433 2 0.3577 0.75284 0.012 0.832 0.000 0.156
#> GSM751437 2 0.4671 0.63314 0.000 0.752 0.220 0.028
#> GSM751448 2 0.5940 0.57020 0.000 0.672 0.240 0.088
#> GSM751451 2 0.2216 0.77870 0.000 0.908 0.000 0.092
#> GSM751423 2 0.4418 0.74546 0.008 0.784 0.016 0.192
#> GSM751424 2 0.6444 0.67621 0.040 0.684 0.064 0.212
#> GSM751428 2 0.6725 0.61804 0.004 0.620 0.136 0.240
#> GSM751431 2 0.3266 0.75140 0.000 0.832 0.000 0.168
#> GSM751432 3 0.7770 0.30993 0.008 0.280 0.492 0.220
#> GSM751434 2 0.8855 0.27219 0.056 0.420 0.264 0.260
#> GSM751435 2 0.3306 0.76278 0.000 0.840 0.004 0.156
#> GSM751436 2 0.5062 0.72267 0.032 0.760 0.016 0.192
#> GSM751440 2 0.2401 0.73777 0.004 0.904 0.000 0.092
#> GSM751444 2 0.0707 0.78011 0.000 0.980 0.000 0.020
#> GSM751446 2 0.0000 0.77654 0.000 1.000 0.000 0.000
#> GSM751449 2 0.0000 0.77654 0.000 1.000 0.000 0.000
#> GSM751450 2 0.4098 0.72138 0.012 0.784 0.000 0.204
#> GSM751452 2 0.8371 0.44655 0.052 0.512 0.212 0.224
#> GSM751426 2 0.3810 0.74014 0.008 0.804 0.000 0.188
#> GSM751427 2 0.0000 0.77654 0.000 1.000 0.000 0.000
#> GSM751438 2 0.0000 0.77654 0.000 1.000 0.000 0.000
#> GSM751439 2 0.4399 0.62684 0.000 0.760 0.224 0.016
#> GSM751441 2 0.1474 0.78116 0.000 0.948 0.000 0.052
#> GSM751442 2 0.0000 0.77654 0.000 1.000 0.000 0.000
#> GSM751443 2 0.5363 0.59796 0.000 0.720 0.216 0.064
#> GSM751445 2 0.1474 0.78185 0.000 0.948 0.000 0.052
#> GSM751447 2 0.1474 0.78116 0.000 0.948 0.000 0.052
#> GSM751453 2 0.2921 0.76291 0.000 0.860 0.000 0.140
#> GSM751454 2 0.2081 0.77867 0.000 0.916 0.000 0.084
#> GSM751455 2 0.0000 0.77654 0.000 1.000 0.000 0.000
#> GSM751456 2 0.0000 0.77654 0.000 1.000 0.000 0.000
#> GSM751457 2 0.1474 0.78116 0.000 0.948 0.000 0.052
#> GSM751458 2 0.1474 0.78116 0.000 0.948 0.000 0.052
cbind(get_classes(res, k = 5), get_membership(res, k = 5))
#> class entropy silhouette p1 p2 p3 p4 p5
#> GSM751298 1 0.4978 0.07114 0.496 0.000 0.000 0.476 0.028
#> GSM751304 4 0.5485 0.40400 0.284 0.020 0.000 0.640 0.056
#> GSM751305 4 0.4201 0.52582 0.004 0.064 0.004 0.792 0.136
#> GSM751307 4 0.6790 0.40301 0.232 0.016 0.008 0.548 0.196
#> GSM751310 4 0.1662 0.65614 0.056 0.000 0.004 0.936 0.004
#> GSM751314 4 0.1478 0.65744 0.064 0.000 0.000 0.936 0.000
#> GSM751316 4 0.3366 0.55334 0.232 0.000 0.000 0.768 0.000
#> GSM751318 4 0.4794 0.30329 0.344 0.000 0.000 0.624 0.032
#> GSM751342 4 0.1478 0.65744 0.064 0.000 0.000 0.936 0.000
#> GSM751346 1 0.0912 0.63666 0.972 0.016 0.012 0.000 0.000
#> GSM751347 1 0.0324 0.64495 0.992 0.004 0.004 0.000 0.000
#> GSM751348 5 0.7509 0.13240 0.076 0.372 0.000 0.144 0.408
#> GSM751349 5 0.5368 0.33794 0.092 0.248 0.004 0.000 0.656
#> GSM751352 1 0.6311 0.34016 0.616 0.204 0.000 0.032 0.148
#> GSM751353 1 0.7434 -0.07857 0.364 0.264 0.000 0.032 0.340
#> GSM751354 1 0.7565 0.00594 0.424 0.052 0.000 0.284 0.240
#> GSM751355 5 0.7216 0.06134 0.392 0.128 0.004 0.048 0.428
#> GSM751358 4 0.3649 0.57755 0.000 0.040 0.000 0.808 0.152
#> GSM751359 4 0.4779 0.32276 0.000 0.032 0.000 0.628 0.340
#> GSM751294 2 0.6327 0.30685 0.080 0.596 0.000 0.052 0.272
#> GSM751296 1 0.1597 0.64052 0.940 0.012 0.000 0.048 0.000
#> GSM751297 1 0.7012 0.30975 0.600 0.204 0.024 0.052 0.120
#> GSM751299 1 0.6712 0.25089 0.552 0.256 0.000 0.032 0.160
#> GSM751300 1 0.0162 0.64775 0.996 0.000 0.000 0.004 0.000
#> GSM751301 1 0.5372 0.42188 0.620 0.016 0.000 0.320 0.044
#> GSM751302 1 0.0000 0.64790 1.000 0.000 0.000 0.000 0.000
#> GSM751303 4 0.1478 0.65744 0.064 0.000 0.000 0.936 0.000
#> GSM751306 4 0.1478 0.65744 0.064 0.000 0.000 0.936 0.000
#> GSM751308 4 0.6832 -0.06026 0.424 0.048 0.020 0.456 0.052
#> GSM751309 4 0.1478 0.65744 0.064 0.000 0.000 0.936 0.000
#> GSM751311 4 0.1478 0.65744 0.064 0.000 0.000 0.936 0.000
#> GSM751312 4 0.3949 0.44838 0.332 0.000 0.000 0.668 0.000
#> GSM751313 1 0.1638 0.63453 0.932 0.000 0.000 0.064 0.004
#> GSM751315 1 0.4238 0.28886 0.628 0.000 0.000 0.368 0.004
#> GSM751317 4 0.2516 0.61330 0.140 0.000 0.000 0.860 0.000
#> GSM751320 1 0.4779 0.39438 0.628 0.000 0.000 0.340 0.032
#> GSM751321 4 0.2127 0.64683 0.108 0.000 0.000 0.892 0.000
#> GSM751322 4 0.5046 -0.04281 0.468 0.000 0.000 0.500 0.032
#> GSM751324 4 0.4329 0.45803 0.252 0.000 0.000 0.716 0.032
#> GSM751325 4 0.4989 0.12871 0.416 0.000 0.000 0.552 0.032
#> GSM751332 1 0.6021 0.24310 0.548 0.000 0.056 0.364 0.032
#> GSM751334 1 0.5363 0.41706 0.644 0.000 0.032 0.292 0.032
#> GSM751339 1 0.5509 0.49576 0.680 0.000 0.092 0.208 0.020
#> GSM751341 4 0.1478 0.65744 0.064 0.000 0.000 0.936 0.000
#> GSM751343 1 0.5722 0.23857 0.540 0.024 0.004 0.400 0.032
#> GSM751344 1 0.7188 0.08372 0.472 0.132 0.000 0.060 0.336
#> GSM751345 1 0.7444 0.05964 0.448 0.156 0.000 0.068 0.328
#> GSM751356 4 0.6487 0.28674 0.348 0.080 0.000 0.528 0.044
#> GSM751357 4 0.6386 0.32815 0.320 0.040 0.000 0.556 0.084
#> GSM751293 1 0.3863 0.53768 0.740 0.000 0.000 0.248 0.012
#> GSM751295 1 0.0000 0.64790 1.000 0.000 0.000 0.000 0.000
#> GSM751319 1 0.4118 0.31394 0.660 0.000 0.000 0.336 0.004
#> GSM751323 1 0.4697 0.42507 0.648 0.000 0.000 0.320 0.032
#> GSM751326 1 0.4083 0.52551 0.744 0.000 0.000 0.228 0.028
#> GSM751327 1 0.4073 0.54521 0.752 0.000 0.000 0.216 0.032
#> GSM751328 4 0.4836 0.27895 0.356 0.000 0.000 0.612 0.032
#> GSM751329 1 0.3577 0.58437 0.808 0.000 0.000 0.160 0.032
#> GSM751330 1 0.0000 0.64790 1.000 0.000 0.000 0.000 0.000
#> GSM751331 1 0.0000 0.64790 1.000 0.000 0.000 0.000 0.000
#> GSM751333 1 0.1216 0.64426 0.960 0.000 0.000 0.020 0.020
#> GSM751335 1 0.0000 0.64790 1.000 0.000 0.000 0.000 0.000
#> GSM751336 1 0.0000 0.64790 1.000 0.000 0.000 0.000 0.000
#> GSM751337 1 0.3929 0.55418 0.764 0.000 0.000 0.208 0.028
#> GSM751338 1 0.2971 0.59897 0.836 0.000 0.000 0.156 0.008
#> GSM751340 1 0.5775 0.20034 0.596 0.000 0.048 0.324 0.032
#> GSM751350 1 0.0000 0.64790 1.000 0.000 0.000 0.000 0.000
#> GSM751351 1 0.0000 0.64790 1.000 0.000 0.000 0.000 0.000
#> GSM751362 3 0.6073 0.48374 0.080 0.000 0.676 0.104 0.140
#> GSM751363 3 0.6390 0.15915 0.000 0.000 0.436 0.396 0.168
#> GSM751367 4 0.6650 0.48544 0.112 0.004 0.052 0.596 0.236
#> GSM751368 3 0.5244 0.41450 0.004 0.160 0.728 0.024 0.084
#> GSM751371 4 0.7017 0.24315 0.304 0.020 0.008 0.496 0.172
#> GSM751375 5 0.3489 0.33292 0.000 0.208 0.004 0.004 0.784
#> GSM751376 2 0.9522 -0.02473 0.176 0.344 0.104 0.160 0.216
#> GSM751378 5 0.6772 0.15197 0.000 0.332 0.280 0.000 0.388
#> GSM751379 3 0.9626 -0.11067 0.172 0.112 0.300 0.156 0.260
#> GSM751382 5 0.3809 0.42513 0.000 0.256 0.008 0.000 0.736
#> GSM751386 5 0.4375 0.16338 0.000 0.004 0.420 0.000 0.576
#> GSM751388 5 0.4262 0.11467 0.000 0.000 0.440 0.000 0.560
#> GSM751391 3 0.9053 -0.07081 0.060 0.180 0.356 0.120 0.284
#> GSM751410 4 0.6753 0.50600 0.036 0.044 0.144 0.644 0.132
#> GSM751414 3 0.4425 0.33939 0.008 0.000 0.600 0.000 0.392
#> GSM751361 5 0.4450 -0.07834 0.000 0.004 0.488 0.000 0.508
#> GSM751365 3 0.0290 0.66188 0.000 0.000 0.992 0.000 0.008
#> GSM751366 3 0.1197 0.64634 0.000 0.000 0.952 0.000 0.048
#> GSM751369 3 0.7422 0.23859 0.136 0.000 0.508 0.256 0.100
#> GSM751370 3 0.4597 0.46862 0.024 0.000 0.704 0.012 0.260
#> GSM751372 3 0.3612 0.45880 0.000 0.000 0.732 0.000 0.268
#> GSM751373 3 0.0865 0.65581 0.024 0.000 0.972 0.000 0.004
#> GSM751374 3 0.9483 -0.09947 0.188 0.080 0.320 0.172 0.240
#> GSM751377 3 0.3752 0.43479 0.000 0.000 0.708 0.000 0.292
#> GSM751380 3 0.0290 0.66159 0.000 0.000 0.992 0.000 0.008
#> GSM751381 5 0.4310 0.20265 0.000 0.004 0.392 0.000 0.604
#> GSM751383 3 0.4304 -0.00854 0.000 0.000 0.516 0.000 0.484
#> GSM751384 5 0.4101 0.20086 0.000 0.000 0.372 0.000 0.628
#> GSM751385 5 0.3892 0.48284 0.100 0.004 0.064 0.008 0.824
#> GSM751387 5 0.4577 0.47891 0.000 0.084 0.176 0.000 0.740
#> GSM751389 3 0.0000 0.66263 0.000 0.000 1.000 0.000 0.000
#> GSM751393 3 0.4074 0.34951 0.000 0.000 0.636 0.000 0.364
#> GSM751394 5 0.2230 0.49566 0.000 0.000 0.116 0.000 0.884
#> GSM751395 5 0.4066 0.43362 0.000 0.004 0.196 0.032 0.768
#> GSM751397 5 0.3661 0.34469 0.000 0.000 0.276 0.000 0.724
#> GSM751398 5 0.3837 0.33905 0.000 0.000 0.308 0.000 0.692
#> GSM751404 3 0.0794 0.65411 0.000 0.000 0.972 0.000 0.028
#> GSM751406 3 0.8470 0.03400 0.240 0.160 0.408 0.012 0.180
#> GSM751411 3 0.2929 0.54265 0.000 0.000 0.820 0.000 0.180
#> GSM751413 5 0.6578 0.33587 0.048 0.000 0.180 0.168 0.604
#> GSM751415 3 0.0000 0.66263 0.000 0.000 1.000 0.000 0.000
#> GSM751416 3 0.3796 0.43106 0.000 0.000 0.700 0.000 0.300
#> GSM751417 3 0.3816 0.42728 0.000 0.000 0.696 0.000 0.304
#> GSM751421 3 0.6301 0.43744 0.016 0.028 0.648 0.116 0.192
#> GSM751422 3 0.8799 0.15580 0.136 0.040 0.412 0.200 0.212
#> GSM751360 4 0.7391 0.42537 0.160 0.000 0.156 0.544 0.140
#> GSM751364 3 0.3990 0.42259 0.000 0.000 0.688 0.004 0.308
#> GSM751390 5 0.5731 0.22173 0.036 0.032 0.372 0.000 0.560
#> GSM751392 5 0.1547 0.50955 0.004 0.032 0.016 0.000 0.948
#> GSM751396 5 0.4996 0.42705 0.000 0.052 0.228 0.016 0.704
#> GSM751399 3 0.0162 0.66247 0.000 0.000 0.996 0.000 0.004
#> GSM751400 3 0.0404 0.66022 0.000 0.000 0.988 0.000 0.012
#> GSM751401 3 0.0000 0.66263 0.000 0.000 1.000 0.000 0.000
#> GSM751402 3 0.1270 0.64136 0.000 0.000 0.948 0.000 0.052
#> GSM751403 3 0.0162 0.66216 0.000 0.000 0.996 0.000 0.004
#> GSM751405 3 0.6614 0.35658 0.136 0.012 0.616 0.036 0.200
#> GSM751407 3 0.0000 0.66263 0.000 0.000 1.000 0.000 0.000
#> GSM751408 3 0.0000 0.66263 0.000 0.000 1.000 0.000 0.000
#> GSM751409 3 0.1792 0.62927 0.000 0.000 0.916 0.000 0.084
#> GSM751412 3 0.0000 0.66263 0.000 0.000 1.000 0.000 0.000
#> GSM751418 3 0.1341 0.64365 0.000 0.000 0.944 0.000 0.056
#> GSM751419 3 0.0000 0.66263 0.000 0.000 1.000 0.000 0.000
#> GSM751420 2 0.6198 0.15914 0.004 0.492 0.380 0.000 0.124
#> GSM751425 2 0.2377 0.72970 0.000 0.872 0.000 0.000 0.128
#> GSM751429 2 0.6884 0.35774 0.220 0.592 0.064 0.008 0.116
#> GSM751430 5 0.9257 0.19792 0.208 0.160 0.196 0.068 0.368
#> GSM751433 2 0.5149 0.62863 0.036 0.704 0.000 0.040 0.220
#> GSM751437 2 0.3536 0.59338 0.000 0.812 0.156 0.000 0.032
#> GSM751448 2 0.5423 0.40953 0.000 0.652 0.224 0.000 0.124
#> GSM751451 2 0.3550 0.70364 0.000 0.796 0.000 0.020 0.184
#> GSM751423 5 0.4989 -0.21971 0.000 0.416 0.000 0.032 0.552
#> GSM751424 2 0.6090 0.42918 0.004 0.540 0.040 0.040 0.376
#> GSM751428 2 0.7834 0.40641 0.112 0.488 0.076 0.032 0.292
#> GSM751431 2 0.4562 0.61042 0.000 0.676 0.000 0.032 0.292
#> GSM751432 3 0.7746 -0.17568 0.028 0.160 0.408 0.036 0.368
#> GSM751434 5 0.9131 -0.06190 0.084 0.312 0.208 0.084 0.312
#> GSM751435 2 0.4486 0.66439 0.020 0.732 0.000 0.020 0.228
#> GSM751436 2 0.6228 0.54910 0.040 0.600 0.012 0.052 0.296
#> GSM751440 2 0.1668 0.70226 0.032 0.940 0.000 0.000 0.028
#> GSM751444 2 0.0865 0.73578 0.000 0.972 0.000 0.004 0.024
#> GSM751446 2 0.0000 0.73291 0.000 1.000 0.000 0.000 0.000
#> GSM751449 2 0.0000 0.73291 0.000 1.000 0.000 0.000 0.000
#> GSM751450 2 0.5430 0.61322 0.084 0.704 0.000 0.032 0.180
#> GSM751452 5 0.8408 -0.11247 0.040 0.352 0.168 0.072 0.368
#> GSM751426 2 0.5506 0.58240 0.040 0.636 0.000 0.032 0.292
#> GSM751427 2 0.0000 0.73291 0.000 1.000 0.000 0.000 0.000
#> GSM751438 2 0.0000 0.73291 0.000 1.000 0.000 0.000 0.000
#> GSM751439 2 0.2732 0.61014 0.000 0.840 0.160 0.000 0.000
#> GSM751441 2 0.2329 0.73029 0.000 0.876 0.000 0.000 0.124
#> GSM751442 2 0.0000 0.73291 0.000 1.000 0.000 0.000 0.000
#> GSM751443 2 0.3006 0.60973 0.004 0.836 0.156 0.000 0.004
#> GSM751445 2 0.2389 0.73391 0.000 0.880 0.000 0.004 0.116
#> GSM751447 2 0.2329 0.73029 0.000 0.876 0.000 0.000 0.124
#> GSM751453 2 0.3942 0.66737 0.000 0.748 0.000 0.020 0.232
#> GSM751454 2 0.3203 0.71181 0.000 0.820 0.000 0.012 0.168
#> GSM751455 2 0.0000 0.73291 0.000 1.000 0.000 0.000 0.000
#> GSM751456 2 0.0000 0.73291 0.000 1.000 0.000 0.000 0.000
#> GSM751457 2 0.2280 0.73157 0.000 0.880 0.000 0.000 0.120
#> GSM751458 2 0.2280 0.73157 0.000 0.880 0.000 0.000 0.120
cbind(get_classes(res, k = 6), get_membership(res, k = 6))
#> class entropy silhouette p1 p2 p3 p4 p5 p6
#> GSM751298 1 0.4642 0.4017 0.592 0.000 0.000 0.356 0.000 0.052
#> GSM751304 4 0.5439 0.4838 0.164 0.004 0.000 0.648 0.020 0.164
#> GSM751305 4 0.3101 0.5719 0.000 0.000 0.000 0.756 0.000 0.244
#> GSM751307 4 0.6237 0.3273 0.064 0.000 0.000 0.504 0.100 0.332
#> GSM751310 4 0.1320 0.6697 0.036 0.000 0.000 0.948 0.000 0.016
#> GSM751314 4 0.0937 0.6671 0.040 0.000 0.000 0.960 0.000 0.000
#> GSM751316 4 0.3139 0.6170 0.152 0.000 0.000 0.816 0.000 0.032
#> GSM751318 1 0.4076 0.2842 0.564 0.004 0.000 0.428 0.000 0.004
#> GSM751342 4 0.0937 0.6671 0.040 0.000 0.000 0.960 0.000 0.000
#> GSM751346 1 0.4220 0.2143 0.520 0.008 0.004 0.000 0.000 0.468
#> GSM751347 1 0.3854 0.2345 0.536 0.000 0.000 0.000 0.000 0.464
#> GSM751348 5 0.7590 0.1695 0.048 0.344 0.000 0.164 0.376 0.068
#> GSM751349 5 0.4337 0.4913 0.044 0.172 0.000 0.000 0.748 0.036
#> GSM751352 6 0.6722 0.1330 0.340 0.064 0.000 0.040 0.068 0.488
#> GSM751353 5 0.8015 -0.2323 0.156 0.184 0.000 0.032 0.344 0.284
#> GSM751354 6 0.6862 0.1779 0.272 0.000 0.000 0.128 0.124 0.476
#> GSM751355 6 0.7331 0.3328 0.232 0.052 0.000 0.028 0.276 0.412
#> GSM751358 4 0.2702 0.6562 0.000 0.004 0.000 0.868 0.036 0.092
#> GSM751359 4 0.4662 0.5331 0.000 0.000 0.000 0.688 0.172 0.140
#> GSM751294 2 0.6869 0.2263 0.036 0.524 0.000 0.040 0.204 0.196
#> GSM751296 1 0.4955 0.2971 0.520 0.004 0.000 0.056 0.000 0.420
#> GSM751297 6 0.6702 0.1294 0.324 0.104 0.004 0.008 0.072 0.488
#> GSM751299 6 0.6830 0.1819 0.300 0.116 0.000 0.040 0.044 0.500
#> GSM751300 1 0.3857 0.2307 0.532 0.000 0.000 0.000 0.000 0.468
#> GSM751301 1 0.6071 0.4415 0.488 0.000 0.000 0.296 0.012 0.204
#> GSM751302 1 0.3810 0.2381 0.572 0.000 0.000 0.000 0.000 0.428
#> GSM751303 4 0.0937 0.6671 0.040 0.000 0.000 0.960 0.000 0.000
#> GSM751306 4 0.0937 0.6671 0.040 0.000 0.000 0.960 0.000 0.000
#> GSM751308 1 0.6093 0.3355 0.548 0.020 0.004 0.316 0.020 0.092
#> GSM751309 4 0.0937 0.6671 0.040 0.000 0.000 0.960 0.000 0.000
#> GSM751311 4 0.0937 0.6671 0.040 0.000 0.000 0.960 0.000 0.000
#> GSM751312 4 0.3619 0.5542 0.232 0.000 0.000 0.744 0.000 0.024
#> GSM751313 1 0.4183 0.3721 0.668 0.000 0.000 0.036 0.000 0.296
#> GSM751315 1 0.4555 0.2055 0.540 0.000 0.000 0.424 0.000 0.036
#> GSM751317 4 0.2632 0.5088 0.164 0.000 0.000 0.832 0.000 0.004
#> GSM751320 1 0.4066 0.4659 0.692 0.000 0.000 0.272 0.000 0.036
#> GSM751321 4 0.1814 0.6541 0.100 0.000 0.000 0.900 0.000 0.000
#> GSM751322 1 0.4371 0.3729 0.580 0.000 0.000 0.392 0.000 0.028
#> GSM751324 1 0.3862 0.1987 0.524 0.000 0.000 0.476 0.000 0.000
#> GSM751325 1 0.3706 0.3642 0.620 0.000 0.000 0.380 0.000 0.000
#> GSM751332 1 0.4367 0.4662 0.696 0.000 0.008 0.248 0.000 0.048
#> GSM751334 1 0.3650 0.4934 0.756 0.000 0.004 0.216 0.000 0.024
#> GSM751339 1 0.6519 0.4704 0.500 0.000 0.040 0.200 0.004 0.256
#> GSM751341 4 0.0937 0.6671 0.040 0.000 0.000 0.960 0.000 0.000
#> GSM751343 1 0.4229 0.4477 0.668 0.000 0.000 0.292 0.000 0.040
#> GSM751344 6 0.7189 0.3329 0.208 0.040 0.000 0.064 0.184 0.504
#> GSM751345 6 0.7351 0.3365 0.212 0.044 0.000 0.068 0.192 0.484
#> GSM751356 4 0.7078 0.1643 0.196 0.028 0.000 0.460 0.044 0.272
#> GSM751357 4 0.6868 0.2502 0.188 0.012 0.000 0.500 0.064 0.236
#> GSM751293 1 0.5722 0.4824 0.516 0.000 0.000 0.268 0.000 0.216
#> GSM751295 1 0.3857 0.2307 0.532 0.000 0.000 0.000 0.000 0.468
#> GSM751319 1 0.3975 0.0974 0.544 0.000 0.000 0.452 0.000 0.004
#> GSM751323 1 0.3221 0.4755 0.736 0.000 0.000 0.264 0.000 0.000
#> GSM751326 1 0.3829 0.5144 0.760 0.000 0.000 0.180 0.000 0.060
#> GSM751327 1 0.2823 0.5062 0.796 0.000 0.000 0.204 0.000 0.000
#> GSM751328 1 0.3857 0.2306 0.532 0.000 0.000 0.468 0.000 0.000
#> GSM751329 1 0.2219 0.5249 0.864 0.000 0.000 0.136 0.000 0.000
#> GSM751330 1 0.3578 0.2995 0.660 0.000 0.000 0.000 0.000 0.340
#> GSM751331 1 0.3810 0.2381 0.572 0.000 0.000 0.000 0.000 0.428
#> GSM751333 1 0.2112 0.4689 0.896 0.000 0.000 0.016 0.000 0.088
#> GSM751335 1 0.3371 0.3352 0.708 0.000 0.000 0.000 0.000 0.292
#> GSM751336 1 0.3804 0.2425 0.576 0.000 0.000 0.000 0.000 0.424
#> GSM751337 1 0.4368 0.5242 0.708 0.000 0.000 0.204 0.000 0.088
#> GSM751338 1 0.5428 0.4892 0.572 0.000 0.000 0.176 0.000 0.252
#> GSM751340 1 0.7535 0.0612 0.336 0.000 0.072 0.292 0.020 0.280
#> GSM751350 1 0.3810 0.2381 0.572 0.000 0.000 0.000 0.000 0.428
#> GSM751351 1 0.3810 0.2381 0.572 0.000 0.000 0.000 0.000 0.428
#> GSM751362 3 0.5734 0.5547 0.080 0.000 0.688 0.084 0.116 0.032
#> GSM751363 4 0.6128 -0.0968 0.000 0.000 0.368 0.416 0.208 0.008
#> GSM751367 4 0.7712 0.3586 0.196 0.004 0.036 0.424 0.084 0.256
#> GSM751368 3 0.5270 0.4230 0.000 0.072 0.676 0.000 0.064 0.188
#> GSM751371 1 0.6851 0.1985 0.464 0.004 0.008 0.336 0.100 0.088
#> GSM751375 5 0.3423 0.4464 0.000 0.088 0.000 0.000 0.812 0.100
#> GSM751376 2 0.9103 -0.0861 0.064 0.348 0.068 0.152 0.156 0.212
#> GSM751378 5 0.6243 0.2301 0.000 0.196 0.320 0.000 0.464 0.020
#> GSM751379 6 0.9214 0.1741 0.116 0.064 0.272 0.080 0.184 0.284
#> GSM751382 5 0.3203 0.5473 0.000 0.160 0.004 0.000 0.812 0.024
#> GSM751386 5 0.3468 0.5139 0.000 0.000 0.284 0.000 0.712 0.004
#> GSM751388 5 0.3351 0.5034 0.000 0.000 0.288 0.000 0.712 0.000
#> GSM751391 3 0.9006 0.0732 0.068 0.100 0.380 0.088 0.168 0.196
#> GSM751410 4 0.7149 0.4654 0.044 0.032 0.184 0.576 0.104 0.060
#> GSM751414 3 0.5114 0.2163 0.000 0.000 0.488 0.004 0.440 0.068
#> GSM751361 5 0.4584 0.1847 0.000 0.000 0.404 0.000 0.556 0.040
#> GSM751365 3 0.0363 0.7187 0.000 0.000 0.988 0.000 0.012 0.000
#> GSM751366 3 0.1075 0.7055 0.000 0.000 0.952 0.000 0.048 0.000
#> GSM751369 3 0.7734 0.2606 0.176 0.000 0.476 0.176 0.076 0.096
#> GSM751370 3 0.4495 0.4305 0.024 0.000 0.656 0.008 0.304 0.008
#> GSM751372 3 0.3636 0.4185 0.000 0.000 0.676 0.004 0.320 0.000
#> GSM751373 3 0.1398 0.7017 0.052 0.000 0.940 0.000 0.008 0.000
#> GSM751374 6 0.8271 0.2507 0.104 0.012 0.276 0.076 0.140 0.392
#> GSM751377 3 0.3592 0.3894 0.000 0.000 0.656 0.000 0.344 0.000
#> GSM751380 3 0.0508 0.7188 0.000 0.000 0.984 0.000 0.012 0.004
#> GSM751381 5 0.3411 0.5593 0.000 0.004 0.232 0.000 0.756 0.008
#> GSM751383 5 0.3634 0.4196 0.000 0.000 0.356 0.000 0.644 0.000
#> GSM751384 5 0.3151 0.5337 0.000 0.000 0.252 0.000 0.748 0.000
#> GSM751385 5 0.3552 0.5477 0.004 0.004 0.060 0.000 0.812 0.120
#> GSM751387 5 0.3716 0.6194 0.000 0.076 0.128 0.000 0.792 0.004
#> GSM751389 3 0.0146 0.7193 0.000 0.000 0.996 0.000 0.004 0.000
#> GSM751393 3 0.3899 0.2823 0.000 0.000 0.592 0.000 0.404 0.004
#> GSM751394 5 0.2122 0.6097 0.000 0.000 0.076 0.000 0.900 0.024
#> GSM751395 5 0.4143 0.5911 0.000 0.000 0.120 0.004 0.756 0.120
#> GSM751397 5 0.3101 0.6023 0.000 0.000 0.148 0.000 0.820 0.032
#> GSM751398 5 0.2941 0.5753 0.000 0.000 0.220 0.000 0.780 0.000
#> GSM751404 3 0.0603 0.7149 0.000 0.000 0.980 0.000 0.016 0.004
#> GSM751406 3 0.7875 0.0609 0.088 0.088 0.436 0.004 0.112 0.272
#> GSM751411 3 0.2996 0.5331 0.000 0.000 0.772 0.000 0.228 0.000
#> GSM751413 5 0.7122 0.0285 0.008 0.000 0.080 0.172 0.404 0.336
#> GSM751415 3 0.0000 0.7197 0.000 0.000 1.000 0.000 0.000 0.000
#> GSM751416 3 0.3634 0.3773 0.000 0.000 0.644 0.000 0.356 0.000
#> GSM751417 3 0.3672 0.3585 0.000 0.000 0.632 0.000 0.368 0.000
#> GSM751421 3 0.7209 0.4372 0.088 0.012 0.580 0.104 0.136 0.080
#> GSM751422 3 0.9323 0.0564 0.224 0.056 0.288 0.160 0.188 0.084
#> GSM751360 4 0.7875 0.3039 0.144 0.000 0.136 0.480 0.112 0.128
#> GSM751364 3 0.3647 0.3734 0.000 0.000 0.640 0.000 0.360 0.000
#> GSM751390 5 0.4490 0.5556 0.016 0.028 0.252 0.000 0.696 0.008
#> GSM751392 5 0.1845 0.5596 0.000 0.004 0.008 0.000 0.916 0.072
#> GSM751396 5 0.6001 0.2754 0.000 0.024 0.176 0.000 0.544 0.256
#> GSM751399 3 0.0260 0.7192 0.000 0.000 0.992 0.000 0.008 0.000
#> GSM751400 3 0.0363 0.7174 0.000 0.000 0.988 0.000 0.012 0.000
#> GSM751401 3 0.0000 0.7197 0.000 0.000 1.000 0.000 0.000 0.000
#> GSM751402 3 0.1794 0.6892 0.000 0.000 0.924 0.000 0.040 0.036
#> GSM751403 3 0.0000 0.7197 0.000 0.000 1.000 0.000 0.000 0.000
#> GSM751405 3 0.6013 0.4736 0.060 0.000 0.648 0.024 0.124 0.144
#> GSM751407 3 0.0000 0.7197 0.000 0.000 1.000 0.000 0.000 0.000
#> GSM751408 3 0.0000 0.7197 0.000 0.000 1.000 0.000 0.000 0.000
#> GSM751409 3 0.2685 0.6574 0.000 0.000 0.868 0.000 0.072 0.060
#> GSM751412 3 0.0000 0.7197 0.000 0.000 1.000 0.000 0.000 0.000
#> GSM751418 3 0.1444 0.6898 0.000 0.000 0.928 0.000 0.072 0.000
#> GSM751419 3 0.0146 0.7193 0.000 0.000 0.996 0.000 0.004 0.000
#> GSM751420 2 0.6530 0.0802 0.000 0.420 0.396 0.000 0.096 0.088
#> GSM751425 2 0.1657 0.7163 0.000 0.928 0.000 0.000 0.056 0.016
#> GSM751429 2 0.5655 0.3869 0.048 0.668 0.008 0.012 0.072 0.192
#> GSM751430 6 0.7271 0.2255 0.028 0.072 0.140 0.016 0.220 0.524
#> GSM751433 2 0.5817 0.3376 0.004 0.484 0.000 0.004 0.144 0.364
#> GSM751437 2 0.2501 0.6601 0.000 0.888 0.072 0.000 0.028 0.012
#> GSM751448 2 0.4859 0.4868 0.000 0.692 0.204 0.000 0.080 0.024
#> GSM751451 2 0.5238 0.4690 0.000 0.592 0.000 0.000 0.140 0.268
#> GSM751423 5 0.6005 -0.1300 0.000 0.236 0.000 0.000 0.384 0.380
#> GSM751424 2 0.6346 0.2325 0.000 0.396 0.020 0.000 0.204 0.380
#> GSM751428 6 0.7336 -0.1900 0.040 0.344 0.048 0.000 0.176 0.392
#> GSM751431 2 0.5767 0.3105 0.000 0.448 0.000 0.000 0.176 0.376
#> GSM751432 6 0.7307 0.0788 0.016 0.072 0.320 0.000 0.200 0.392
#> GSM751434 6 0.8031 0.1410 0.016 0.176 0.144 0.036 0.180 0.448
#> GSM751435 2 0.4664 0.6033 0.016 0.724 0.004 0.000 0.088 0.168
#> GSM751436 2 0.6138 0.2879 0.004 0.432 0.008 0.000 0.180 0.376
#> GSM751440 2 0.1204 0.7062 0.016 0.960 0.004 0.000 0.016 0.004
#> GSM751444 2 0.1719 0.7091 0.000 0.924 0.000 0.000 0.016 0.060
#> GSM751446 2 0.0000 0.7192 0.000 1.000 0.000 0.000 0.000 0.000
#> GSM751449 2 0.0146 0.7194 0.000 0.996 0.000 0.000 0.000 0.004
#> GSM751450 2 0.5737 0.3373 0.008 0.488 0.000 0.000 0.136 0.368
#> GSM751452 6 0.7869 0.0351 0.012 0.216 0.128 0.012 0.240 0.392
#> GSM751426 2 0.5767 0.3105 0.000 0.448 0.000 0.000 0.176 0.376
#> GSM751427 2 0.0146 0.7194 0.000 0.996 0.000 0.000 0.000 0.004
#> GSM751438 2 0.0000 0.7192 0.000 1.000 0.000 0.000 0.000 0.000
#> GSM751439 2 0.1444 0.6787 0.000 0.928 0.072 0.000 0.000 0.000
#> GSM751441 2 0.1594 0.7168 0.000 0.932 0.000 0.000 0.052 0.016
#> GSM751442 2 0.0000 0.7192 0.000 1.000 0.000 0.000 0.000 0.000
#> GSM751443 2 0.1732 0.6762 0.000 0.920 0.072 0.000 0.004 0.004
#> GSM751445 2 0.2258 0.7101 0.000 0.896 0.000 0.000 0.060 0.044
#> GSM751447 2 0.1594 0.7168 0.000 0.932 0.000 0.000 0.052 0.016
#> GSM751453 2 0.4131 0.6155 0.000 0.744 0.000 0.000 0.100 0.156
#> GSM751454 2 0.3367 0.6672 0.000 0.816 0.000 0.000 0.080 0.104
#> GSM751455 2 0.0000 0.7192 0.000 1.000 0.000 0.000 0.000 0.000
#> GSM751456 2 0.0000 0.7192 0.000 1.000 0.000 0.000 0.000 0.000
#> GSM751457 2 0.1594 0.7168 0.000 0.932 0.000 0.000 0.052 0.016
#> GSM751458 2 0.1594 0.7168 0.000 0.932 0.000 0.000 0.052 0.016
Heatmaps for the consensus matrix. It visualizes the probability of two samples to be in a same group.
consensus_heatmap(res, k = 2)
consensus_heatmap(res, k = 3)
consensus_heatmap(res, k = 4)
consensus_heatmap(res, k = 5)
consensus_heatmap(res, k = 6)
Heatmaps for the membership of samples in all partitions to see how consistent they are:
membership_heatmap(res, k = 2)
membership_heatmap(res, k = 3)
membership_heatmap(res, k = 4)
membership_heatmap(res, k = 5)
membership_heatmap(res, k = 6)
As soon as we have had the classes for columns, we can look for signatures which are significantly different between classes which can be candidate marks for certain classes. Following are the heatmaps for signatures.
Signature heatmaps where rows are scaled:
get_signatures(res, k = 2)
get_signatures(res, k = 3)
get_signatures(res, k = 4)
get_signatures(res, k = 5)
get_signatures(res, k = 6)
Signature heatmaps where rows are not scaled:
get_signatures(res, k = 2, scale_rows = FALSE)
get_signatures(res, k = 3, scale_rows = FALSE)
get_signatures(res, k = 4, scale_rows = FALSE)
get_signatures(res, k = 5, scale_rows = FALSE)
get_signatures(res, k = 6, scale_rows = FALSE)
Compare the overlap of signatures from different k:
compare_signatures(res)
get_signature() returns a data frame invisibly. TO get the list of signatures, the function
call should be assigned to a variable explicitly. In following code, if plot argument is set
to FALSE, no heatmap is plotted while only the differential analysis is performed.
# code only for demonstration
tb = get_signature(res, k = ..., plot = FALSE)
An example of the output of tb is:
#> which_row fdr mean_1 mean_2 scaled_mean_1 scaled_mean_2 km
#> 1 38 0.042760348 8.373488 9.131774 -0.5533452 0.5164555 1
#> 2 40 0.018707592 7.106213 8.469186 -0.6173731 0.5762149 1
#> 3 55 0.019134737 10.221463 11.207825 -0.6159697 0.5749050 1
#> 4 59 0.006059896 5.921854 7.869574 -0.6899429 0.6439467 1
#> 5 60 0.018055526 8.928898 10.211722 -0.6204761 0.5791110 1
#> 6 98 0.009384629 15.714769 14.887706 0.6635654 -0.6193277 2
...
The columns in tb are:
which_row: row indices corresponding to the input matrix.fdr: FDR for the differential test. mean_x: The mean value in group x.scaled_mean_x: The mean value in group x after rows are scaled.km: Row groups if k-means clustering is applied to rows.UMAP plot which shows how samples are separated.
dimension_reduction(res, k = 2, method = "UMAP")
dimension_reduction(res, k = 3, method = "UMAP")
dimension_reduction(res, k = 4, method = "UMAP")
dimension_reduction(res, k = 5, method = "UMAP")
dimension_reduction(res, k = 6, method = "UMAP")
Following heatmap shows how subgroups are split when increasing k:
collect_classes(res)
Test correlation between subgroups and known annotations. If the known annotation is numeric, one-way ANOVA test is applied, and if the known annotation is discrete, chi-squared contingency table test is applied.
test_to_known_factors(res)
#> n tissue(p) disease.state(p) agent(p) k
#> SD:pam 158 1.05e-09 0.27317 0.310616 2
#> SD:pam 144 4.40e-39 0.14088 0.329931 3
#> SD:pam 91 3.17e-31 0.14727 0.047637 4
#> SD:pam 81 1.03e-29 0.00256 0.000954 5
#> SD:pam 73 1.34e-27 0.01191 0.000133 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 4537 rows and 166 columns.
#> Top rows (454, 908, 1361, 1814, 2268) 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 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 0.725 0.890 0.942 0.4319 0.586 0.586
#> 3 3 0.640 0.789 0.893 0.5173 0.743 0.565
#> 4 4 0.599 0.523 0.787 0.0940 0.946 0.845
#> 5 5 0.633 0.554 0.747 0.0679 0.903 0.709
#> 6 6 0.655 0.502 0.711 0.0550 0.913 0.673
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
#> GSM751298 1 0.0000 0.9678 1.000 0.000
#> GSM751304 2 0.7056 0.7820 0.192 0.808
#> GSM751305 2 0.7056 0.7820 0.192 0.808
#> GSM751307 2 0.9248 0.6038 0.340 0.660
#> GSM751310 1 0.0000 0.9678 1.000 0.000
#> GSM751314 1 0.0000 0.9678 1.000 0.000
#> GSM751316 1 0.0938 0.9576 0.988 0.012
#> GSM751318 1 0.0000 0.9678 1.000 0.000
#> GSM751342 1 0.0938 0.9562 0.988 0.012
#> GSM751346 1 0.0000 0.9678 1.000 0.000
#> GSM751347 2 0.9963 0.2874 0.464 0.536
#> GSM751348 2 0.8608 0.6977 0.284 0.716
#> GSM751349 2 0.3733 0.9117 0.072 0.928
#> GSM751352 2 0.9608 0.5068 0.384 0.616
#> GSM751353 2 0.6887 0.7997 0.184 0.816
#> GSM751354 2 0.7139 0.7798 0.196 0.804
#> GSM751355 2 0.6048 0.8303 0.148 0.852
#> GSM751358 2 0.4690 0.8870 0.100 0.900
#> GSM751359 2 0.0000 0.9267 0.000 1.000
#> GSM751294 2 0.7674 0.7661 0.224 0.776
#> GSM751296 1 0.0000 0.9678 1.000 0.000
#> GSM751297 1 0.9922 0.0212 0.552 0.448
#> GSM751299 2 0.9358 0.5715 0.352 0.648
#> GSM751300 1 0.0000 0.9678 1.000 0.000
#> GSM751301 1 0.7528 0.6759 0.784 0.216
#> GSM751302 1 0.0000 0.9678 1.000 0.000
#> GSM751303 1 0.0000 0.9678 1.000 0.000
#> GSM751306 1 0.0000 0.9678 1.000 0.000
#> GSM751308 1 0.9896 0.0514 0.560 0.440
#> GSM751309 1 0.0000 0.9678 1.000 0.000
#> GSM751311 1 0.0000 0.9678 1.000 0.000
#> GSM751312 1 0.0000 0.9678 1.000 0.000
#> GSM751313 1 0.0000 0.9678 1.000 0.000
#> GSM751315 1 0.0000 0.9678 1.000 0.000
#> GSM751317 1 0.0000 0.9678 1.000 0.000
#> GSM751320 1 0.0000 0.9678 1.000 0.000
#> GSM751321 1 0.0000 0.9678 1.000 0.000
#> GSM751322 1 0.0000 0.9678 1.000 0.000
#> GSM751324 1 0.0000 0.9678 1.000 0.000
#> GSM751325 1 0.0000 0.9678 1.000 0.000
#> GSM751332 1 0.0000 0.9678 1.000 0.000
#> GSM751334 1 0.0000 0.9678 1.000 0.000
#> GSM751339 1 0.0000 0.9678 1.000 0.000
#> GSM751341 1 0.0000 0.9678 1.000 0.000
#> GSM751343 1 0.0000 0.9678 1.000 0.000
#> GSM751344 2 0.8386 0.7190 0.268 0.732
#> GSM751345 2 0.8327 0.7239 0.264 0.736
#> GSM751356 2 0.8909 0.6551 0.308 0.692
#> GSM751357 2 0.8813 0.6687 0.300 0.700
#> GSM751293 1 0.6887 0.7317 0.816 0.184
#> GSM751295 1 0.0000 0.9678 1.000 0.000
#> GSM751319 1 0.0000 0.9678 1.000 0.000
#> GSM751323 1 0.0000 0.9678 1.000 0.000
#> GSM751326 1 0.0000 0.9678 1.000 0.000
#> GSM751327 1 0.0000 0.9678 1.000 0.000
#> GSM751328 1 0.0000 0.9678 1.000 0.000
#> GSM751329 1 0.0000 0.9678 1.000 0.000
#> GSM751330 1 0.0000 0.9678 1.000 0.000
#> GSM751331 1 0.0000 0.9678 1.000 0.000
#> GSM751333 1 0.0000 0.9678 1.000 0.000
#> GSM751335 1 0.0000 0.9678 1.000 0.000
#> GSM751336 1 0.0000 0.9678 1.000 0.000
#> GSM751337 1 0.0000 0.9678 1.000 0.000
#> GSM751338 1 0.0000 0.9678 1.000 0.000
#> GSM751340 2 0.9970 0.2688 0.468 0.532
#> GSM751350 1 0.0000 0.9678 1.000 0.000
#> GSM751351 1 0.0000 0.9678 1.000 0.000
#> GSM751362 2 0.0376 0.9261 0.004 0.996
#> GSM751363 2 0.0376 0.9261 0.004 0.996
#> GSM751367 2 0.2603 0.9112 0.044 0.956
#> GSM751368 2 0.0000 0.9267 0.000 1.000
#> GSM751371 2 0.0938 0.9257 0.012 0.988
#> GSM751375 2 0.0000 0.9267 0.000 1.000
#> GSM751376 2 0.0376 0.9261 0.004 0.996
#> GSM751378 2 0.0000 0.9267 0.000 1.000
#> GSM751379 2 0.0376 0.9261 0.004 0.996
#> GSM751382 2 0.0938 0.9252 0.012 0.988
#> GSM751386 2 0.0000 0.9267 0.000 1.000
#> GSM751388 2 0.0000 0.9267 0.000 1.000
#> GSM751391 2 0.0000 0.9267 0.000 1.000
#> GSM751410 2 0.0938 0.9253 0.012 0.988
#> GSM751414 2 0.0000 0.9267 0.000 1.000
#> GSM751361 2 0.0000 0.9267 0.000 1.000
#> GSM751365 2 0.0000 0.9267 0.000 1.000
#> GSM751366 2 0.0000 0.9267 0.000 1.000
#> GSM751369 2 0.0000 0.9267 0.000 1.000
#> GSM751370 2 0.0376 0.9261 0.004 0.996
#> GSM751372 2 0.0000 0.9267 0.000 1.000
#> GSM751373 2 0.0000 0.9267 0.000 1.000
#> GSM751374 2 0.0376 0.9261 0.004 0.996
#> GSM751377 2 0.0000 0.9267 0.000 1.000
#> GSM751380 2 0.0000 0.9267 0.000 1.000
#> GSM751381 2 0.0000 0.9267 0.000 1.000
#> GSM751383 2 0.0000 0.9267 0.000 1.000
#> GSM751384 2 0.0000 0.9267 0.000 1.000
#> GSM751385 2 0.0000 0.9267 0.000 1.000
#> GSM751387 2 0.0000 0.9267 0.000 1.000
#> GSM751389 2 0.0000 0.9267 0.000 1.000
#> GSM751393 2 0.0000 0.9267 0.000 1.000
#> GSM751394 2 0.0000 0.9267 0.000 1.000
#> GSM751395 2 0.0000 0.9267 0.000 1.000
#> GSM751397 2 0.0000 0.9267 0.000 1.000
#> GSM751398 2 0.0000 0.9267 0.000 1.000
#> GSM751404 2 0.0000 0.9267 0.000 1.000
#> GSM751406 2 0.0376 0.9261 0.004 0.996
#> GSM751411 2 0.0000 0.9267 0.000 1.000
#> GSM751413 2 0.0000 0.9267 0.000 1.000
#> GSM751415 2 0.0000 0.9267 0.000 1.000
#> GSM751416 2 0.0000 0.9267 0.000 1.000
#> GSM751417 2 0.0000 0.9267 0.000 1.000
#> GSM751421 2 0.0000 0.9267 0.000 1.000
#> GSM751422 2 0.0000 0.9267 0.000 1.000
#> GSM751360 2 0.0000 0.9267 0.000 1.000
#> GSM751364 2 0.0000 0.9267 0.000 1.000
#> GSM751390 2 0.0000 0.9267 0.000 1.000
#> GSM751392 2 0.0000 0.9267 0.000 1.000
#> GSM751396 2 0.0672 0.9259 0.008 0.992
#> GSM751399 2 0.0000 0.9267 0.000 1.000
#> GSM751400 2 0.0000 0.9267 0.000 1.000
#> GSM751401 2 0.0000 0.9267 0.000 1.000
#> GSM751402 2 0.0000 0.9267 0.000 1.000
#> GSM751403 2 0.0000 0.9267 0.000 1.000
#> GSM751405 2 0.0376 0.9261 0.004 0.996
#> GSM751407 2 0.0000 0.9267 0.000 1.000
#> GSM751408 2 0.0000 0.9267 0.000 1.000
#> GSM751409 2 0.0000 0.9267 0.000 1.000
#> GSM751412 2 0.0000 0.9267 0.000 1.000
#> GSM751418 2 0.0000 0.9267 0.000 1.000
#> GSM751419 2 0.0000 0.9267 0.000 1.000
#> GSM751420 2 0.0000 0.9267 0.000 1.000
#> GSM751425 2 0.4161 0.9045 0.084 0.916
#> GSM751429 2 0.6531 0.8082 0.168 0.832
#> GSM751430 2 0.4562 0.8982 0.096 0.904
#> GSM751433 2 0.6343 0.8480 0.160 0.840
#> GSM751437 2 0.0938 0.9251 0.012 0.988
#> GSM751448 2 0.4690 0.8761 0.100 0.900
#> GSM751451 2 0.5294 0.8830 0.120 0.880
#> GSM751423 2 0.3733 0.9095 0.072 0.928
#> GSM751424 2 0.5294 0.8830 0.120 0.880
#> GSM751428 2 0.4431 0.9008 0.092 0.908
#> GSM751431 2 0.5294 0.8830 0.120 0.880
#> GSM751432 2 0.4815 0.8939 0.104 0.896
#> GSM751434 2 0.5519 0.8769 0.128 0.872
#> GSM751435 2 0.4690 0.8961 0.100 0.900
#> GSM751436 2 0.5408 0.8800 0.124 0.876
#> GSM751440 2 0.5294 0.8830 0.120 0.880
#> GSM751444 2 0.4431 0.9005 0.092 0.908
#> GSM751446 2 0.4161 0.9045 0.084 0.916
#> GSM751449 2 0.4161 0.9045 0.084 0.916
#> GSM751450 2 0.5059 0.8885 0.112 0.888
#> GSM751452 2 0.5294 0.8830 0.120 0.880
#> GSM751426 2 0.5294 0.8830 0.120 0.880
#> GSM751427 2 0.4161 0.9045 0.084 0.916
#> GSM751438 2 0.4161 0.9045 0.084 0.916
#> GSM751439 2 0.4161 0.9045 0.084 0.916
#> GSM751441 2 0.3274 0.9136 0.060 0.940
#> GSM751442 2 0.4298 0.9026 0.088 0.912
#> GSM751443 2 0.3114 0.9148 0.056 0.944
#> GSM751445 2 0.4161 0.9045 0.084 0.916
#> GSM751447 2 0.4161 0.9045 0.084 0.916
#> GSM751453 2 0.4298 0.9026 0.088 0.912
#> GSM751454 2 0.4298 0.9026 0.088 0.912
#> GSM751455 2 0.4161 0.9045 0.084 0.916
#> GSM751456 2 0.4161 0.9045 0.084 0.916
#> GSM751457 2 0.4022 0.9063 0.080 0.920
#> GSM751458 2 0.3879 0.9079 0.076 0.924
cbind(get_classes(res, k = 3), get_membership(res, k = 3))
#> class entropy silhouette p1 p2 p3
#> GSM751298 1 0.0000 0.9806 1.000 0.000 0.000
#> GSM751304 2 0.9234 0.3136 0.160 0.476 0.364
#> GSM751305 2 0.9329 0.1693 0.164 0.436 0.400
#> GSM751307 2 0.7725 0.6805 0.160 0.680 0.160
#> GSM751310 1 0.0000 0.9806 1.000 0.000 0.000
#> GSM751314 1 0.0000 0.9806 1.000 0.000 0.000
#> GSM751316 1 0.2066 0.9094 0.940 0.000 0.060
#> GSM751318 1 0.0000 0.9806 1.000 0.000 0.000
#> GSM751342 1 0.1031 0.9593 0.976 0.024 0.000
#> GSM751346 1 0.0000 0.9806 1.000 0.000 0.000
#> GSM751347 2 0.9767 0.3920 0.320 0.432 0.248
#> GSM751348 2 0.6372 0.7440 0.152 0.764 0.084
#> GSM751349 2 0.4702 0.6968 0.000 0.788 0.212
#> GSM751352 2 0.7482 0.6871 0.204 0.688 0.108
#> GSM751353 2 0.7615 0.6855 0.148 0.688 0.164
#> GSM751354 2 0.8494 0.5867 0.156 0.608 0.236
#> GSM751355 2 0.8158 0.3699 0.080 0.556 0.364
#> GSM751358 3 0.7091 0.4789 0.040 0.320 0.640
#> GSM751359 3 0.4974 0.7006 0.000 0.236 0.764
#> GSM751294 2 0.8229 0.6075 0.124 0.620 0.256
#> GSM751296 1 0.0000 0.9806 1.000 0.000 0.000
#> GSM751297 2 0.9895 0.3495 0.332 0.396 0.272
#> GSM751299 2 0.7361 0.7008 0.172 0.704 0.124
#> GSM751300 1 0.0000 0.9806 1.000 0.000 0.000
#> GSM751301 1 0.4861 0.7354 0.808 0.180 0.012
#> GSM751302 1 0.0000 0.9806 1.000 0.000 0.000
#> GSM751303 1 0.0000 0.9806 1.000 0.000 0.000
#> GSM751306 1 0.0000 0.9806 1.000 0.000 0.000
#> GSM751308 1 0.7920 0.1810 0.572 0.360 0.068
#> GSM751309 1 0.0000 0.9806 1.000 0.000 0.000
#> GSM751311 1 0.0000 0.9806 1.000 0.000 0.000
#> GSM751312 1 0.0000 0.9806 1.000 0.000 0.000
#> GSM751313 1 0.0000 0.9806 1.000 0.000 0.000
#> GSM751315 1 0.0000 0.9806 1.000 0.000 0.000
#> GSM751317 1 0.0000 0.9806 1.000 0.000 0.000
#> GSM751320 1 0.0000 0.9806 1.000 0.000 0.000
#> GSM751321 1 0.0000 0.9806 1.000 0.000 0.000
#> GSM751322 1 0.0000 0.9806 1.000 0.000 0.000
#> GSM751324 1 0.0000 0.9806 1.000 0.000 0.000
#> GSM751325 1 0.0000 0.9806 1.000 0.000 0.000
#> GSM751332 1 0.0000 0.9806 1.000 0.000 0.000
#> GSM751334 1 0.0000 0.9806 1.000 0.000 0.000
#> GSM751339 1 0.0237 0.9765 0.996 0.000 0.004
#> GSM751341 1 0.0000 0.9806 1.000 0.000 0.000
#> GSM751343 1 0.0000 0.9806 1.000 0.000 0.000
#> GSM751344 2 0.7126 0.7139 0.164 0.720 0.116
#> GSM751345 2 0.7180 0.7107 0.168 0.716 0.116
#> GSM751356 2 0.8125 0.6590 0.172 0.648 0.180
#> GSM751357 2 0.8029 0.6645 0.172 0.656 0.172
#> GSM751293 1 0.2796 0.8785 0.908 0.092 0.000
#> GSM751295 1 0.0000 0.9806 1.000 0.000 0.000
#> GSM751319 1 0.0000 0.9806 1.000 0.000 0.000
#> GSM751323 1 0.0000 0.9806 1.000 0.000 0.000
#> GSM751326 1 0.0000 0.9806 1.000 0.000 0.000
#> GSM751327 1 0.0000 0.9806 1.000 0.000 0.000
#> GSM751328 1 0.0000 0.9806 1.000 0.000 0.000
#> GSM751329 1 0.0000 0.9806 1.000 0.000 0.000
#> GSM751330 1 0.0000 0.9806 1.000 0.000 0.000
#> GSM751331 1 0.0000 0.9806 1.000 0.000 0.000
#> GSM751333 1 0.0000 0.9806 1.000 0.000 0.000
#> GSM751335 1 0.0000 0.9806 1.000 0.000 0.000
#> GSM751336 1 0.0000 0.9806 1.000 0.000 0.000
#> GSM751337 1 0.0000 0.9806 1.000 0.000 0.000
#> GSM751338 1 0.0000 0.9806 1.000 0.000 0.000
#> GSM751340 3 0.9756 0.0275 0.316 0.248 0.436
#> GSM751350 1 0.0000 0.9806 1.000 0.000 0.000
#> GSM751351 1 0.0000 0.9806 1.000 0.000 0.000
#> GSM751362 3 0.0000 0.8353 0.000 0.000 1.000
#> GSM751363 3 0.0592 0.8376 0.000 0.012 0.988
#> GSM751367 3 0.6548 0.2942 0.012 0.372 0.616
#> GSM751368 3 0.4235 0.7813 0.000 0.176 0.824
#> GSM751371 3 0.3267 0.7773 0.000 0.116 0.884
#> GSM751375 2 0.5497 0.5786 0.000 0.708 0.292
#> GSM751376 3 0.6267 0.1014 0.000 0.452 0.548
#> GSM751378 3 0.4235 0.7650 0.000 0.176 0.824
#> GSM751379 3 0.6095 0.2842 0.000 0.392 0.608
#> GSM751382 2 0.5216 0.6334 0.000 0.740 0.260
#> GSM751386 3 0.4654 0.7324 0.000 0.208 0.792
#> GSM751388 3 0.4887 0.7336 0.000 0.228 0.772
#> GSM751391 3 0.3686 0.7666 0.000 0.140 0.860
#> GSM751410 3 0.2200 0.8181 0.004 0.056 0.940
#> GSM751414 3 0.0000 0.8353 0.000 0.000 1.000
#> GSM751361 3 0.2165 0.8357 0.000 0.064 0.936
#> GSM751365 3 0.1411 0.8398 0.000 0.036 0.964
#> GSM751366 3 0.1411 0.8398 0.000 0.036 0.964
#> GSM751369 3 0.2711 0.7989 0.000 0.088 0.912
#> GSM751370 3 0.0000 0.8353 0.000 0.000 1.000
#> GSM751372 3 0.1289 0.8398 0.000 0.032 0.968
#> GSM751373 3 0.1411 0.8398 0.000 0.036 0.964
#> GSM751374 3 0.6244 0.1353 0.000 0.440 0.560
#> GSM751377 3 0.3116 0.8130 0.000 0.108 0.892
#> GSM751380 3 0.1411 0.8398 0.000 0.036 0.964
#> GSM751381 3 0.4605 0.7365 0.000 0.204 0.796
#> GSM751383 3 0.4887 0.7336 0.000 0.228 0.772
#> GSM751384 3 0.1031 0.8378 0.000 0.024 0.976
#> GSM751385 3 0.3941 0.7778 0.000 0.156 0.844
#> GSM751387 3 0.5058 0.7163 0.000 0.244 0.756
#> GSM751389 3 0.1163 0.8398 0.000 0.028 0.972
#> GSM751393 3 0.1753 0.8335 0.000 0.048 0.952
#> GSM751394 3 0.4504 0.7413 0.000 0.196 0.804
#> GSM751395 3 0.4399 0.7563 0.000 0.188 0.812
#> GSM751397 3 0.4002 0.7738 0.000 0.160 0.840
#> GSM751398 3 0.4346 0.7530 0.000 0.184 0.816
#> GSM751404 3 0.1411 0.8398 0.000 0.036 0.964
#> GSM751406 3 0.0000 0.8353 0.000 0.000 1.000
#> GSM751411 3 0.0000 0.8353 0.000 0.000 1.000
#> GSM751413 3 0.4002 0.7803 0.000 0.160 0.840
#> GSM751415 3 0.1411 0.8398 0.000 0.036 0.964
#> GSM751416 3 0.1163 0.8393 0.000 0.028 0.972
#> GSM751417 3 0.1163 0.8393 0.000 0.028 0.972
#> GSM751421 3 0.0000 0.8353 0.000 0.000 1.000
#> GSM751422 3 0.0000 0.8353 0.000 0.000 1.000
#> GSM751360 3 0.0424 0.8377 0.000 0.008 0.992
#> GSM751364 3 0.1860 0.8379 0.000 0.052 0.948
#> GSM751390 3 0.3116 0.8210 0.000 0.108 0.892
#> GSM751392 3 0.5397 0.6571 0.000 0.280 0.720
#> GSM751396 3 0.6026 0.5100 0.000 0.376 0.624
#> GSM751399 3 0.0424 0.8373 0.000 0.008 0.992
#> GSM751400 3 0.1411 0.8398 0.000 0.036 0.964
#> GSM751401 3 0.1411 0.8398 0.000 0.036 0.964
#> GSM751402 3 0.1411 0.8398 0.000 0.036 0.964
#> GSM751403 3 0.1411 0.8398 0.000 0.036 0.964
#> GSM751405 3 0.0000 0.8353 0.000 0.000 1.000
#> GSM751407 3 0.1411 0.8398 0.000 0.036 0.964
#> GSM751408 3 0.1411 0.8398 0.000 0.036 0.964
#> GSM751409 3 0.0237 0.8363 0.000 0.004 0.996
#> GSM751412 3 0.1411 0.8398 0.000 0.036 0.964
#> GSM751418 3 0.1411 0.8398 0.000 0.036 0.964
#> GSM751419 3 0.1411 0.8398 0.000 0.036 0.964
#> GSM751420 3 0.6026 0.3583 0.000 0.376 0.624
#> GSM751425 2 0.0592 0.8358 0.000 0.988 0.012
#> GSM751429 3 0.8577 -0.1641 0.096 0.436 0.468
#> GSM751430 2 0.4887 0.6466 0.000 0.772 0.228
#> GSM751433 2 0.0000 0.8374 0.000 1.000 0.000
#> GSM751437 3 0.5254 0.5801 0.000 0.264 0.736
#> GSM751448 3 0.7492 0.2956 0.052 0.340 0.608
#> GSM751451 2 0.2878 0.7670 0.000 0.904 0.096
#> GSM751423 2 0.2066 0.8092 0.000 0.940 0.060
#> GSM751424 2 0.0000 0.8374 0.000 1.000 0.000
#> GSM751428 2 0.0237 0.8372 0.000 0.996 0.004
#> GSM751431 2 0.0000 0.8374 0.000 1.000 0.000
#> GSM751432 2 0.0424 0.8361 0.000 0.992 0.008
#> GSM751434 2 0.0000 0.8374 0.000 1.000 0.000
#> GSM751435 2 0.0000 0.8374 0.000 1.000 0.000
#> GSM751436 2 0.0000 0.8374 0.000 1.000 0.000
#> GSM751440 2 0.0237 0.8364 0.000 0.996 0.004
#> GSM751444 2 0.0000 0.8374 0.000 1.000 0.000
#> GSM751446 2 0.0000 0.8374 0.000 1.000 0.000
#> GSM751449 2 0.0424 0.8364 0.000 0.992 0.008
#> GSM751450 2 0.0000 0.8374 0.000 1.000 0.000
#> GSM751452 2 0.0000 0.8374 0.000 1.000 0.000
#> GSM751426 2 0.0000 0.8374 0.000 1.000 0.000
#> GSM751427 2 0.0000 0.8374 0.000 1.000 0.000
#> GSM751438 2 0.0000 0.8374 0.000 1.000 0.000
#> GSM751439 2 0.2261 0.7968 0.000 0.932 0.068
#> GSM751441 2 0.1411 0.8251 0.000 0.964 0.036
#> GSM751442 2 0.0237 0.8363 0.000 0.996 0.004
#> GSM751443 2 0.6193 0.5863 0.016 0.692 0.292
#> GSM751445 2 0.0424 0.8364 0.000 0.992 0.008
#> GSM751447 2 0.0237 0.8366 0.000 0.996 0.004
#> GSM751453 2 0.0000 0.8374 0.000 1.000 0.000
#> GSM751454 2 0.0000 0.8374 0.000 1.000 0.000
#> GSM751455 2 0.0000 0.8374 0.000 1.000 0.000
#> GSM751456 2 0.0000 0.8374 0.000 1.000 0.000
#> GSM751457 2 0.0592 0.8358 0.000 0.988 0.012
#> GSM751458 2 0.0592 0.8358 0.000 0.988 0.012
cbind(get_classes(res, k = 4), get_membership(res, k = 4))
#> class entropy silhouette p1 p2 p3 p4
#> GSM751298 1 0.2868 0.8486 0.864 0.000 0.000 0.136
#> GSM751304 2 0.7495 -0.3134 0.000 0.428 0.180 0.392
#> GSM751305 2 0.8113 -0.3800 0.012 0.436 0.260 0.292
#> GSM751307 2 0.6459 0.3621 0.012 0.656 0.096 0.236
#> GSM751310 1 0.0188 0.8667 0.996 0.000 0.000 0.004
#> GSM751314 1 0.0188 0.8650 0.996 0.000 0.000 0.004
#> GSM751316 1 0.3166 0.8382 0.888 0.012 0.020 0.080
#> GSM751318 1 0.0000 0.8667 1.000 0.000 0.000 0.000
#> GSM751342 1 0.2111 0.8452 0.932 0.044 0.000 0.024
#> GSM751346 1 0.5119 0.6823 0.556 0.004 0.000 0.440
#> GSM751347 2 0.8554 -0.0775 0.280 0.388 0.028 0.304
#> GSM751348 2 0.4818 0.5208 0.000 0.748 0.036 0.216
#> GSM751349 2 0.5052 0.5046 0.000 0.720 0.036 0.244
#> GSM751352 2 0.6515 0.3740 0.172 0.664 0.008 0.156
#> GSM751353 2 0.5682 0.3491 0.000 0.612 0.036 0.352
#> GSM751354 2 0.6592 0.0489 0.000 0.524 0.084 0.392
#> GSM751355 2 0.6969 -0.2159 0.000 0.448 0.112 0.440
#> GSM751358 3 0.7707 -0.3445 0.000 0.272 0.452 0.276
#> GSM751359 4 0.7537 0.2208 0.000 0.196 0.348 0.456
#> GSM751294 2 0.6919 0.0448 0.000 0.516 0.116 0.368
#> GSM751296 1 0.4509 0.7807 0.708 0.004 0.000 0.288
#> GSM751297 4 0.7476 0.1699 0.120 0.272 0.032 0.576
#> GSM751299 2 0.5127 0.4178 0.008 0.668 0.008 0.316
#> GSM751300 1 0.4889 0.7419 0.636 0.004 0.000 0.360
#> GSM751301 1 0.6948 0.5662 0.588 0.204 0.000 0.208
#> GSM751302 1 0.5126 0.6792 0.552 0.004 0.000 0.444
#> GSM751303 1 0.0000 0.8667 1.000 0.000 0.000 0.000
#> GSM751306 1 0.0000 0.8667 1.000 0.000 0.000 0.000
#> GSM751308 1 0.8570 0.0829 0.424 0.376 0.080 0.120
#> GSM751309 1 0.0000 0.8667 1.000 0.000 0.000 0.000
#> GSM751311 1 0.0000 0.8667 1.000 0.000 0.000 0.000
#> GSM751312 1 0.2593 0.8545 0.892 0.004 0.000 0.104
#> GSM751313 1 0.2973 0.8464 0.856 0.000 0.000 0.144
#> GSM751315 1 0.0000 0.8667 1.000 0.000 0.000 0.000
#> GSM751317 1 0.0000 0.8667 1.000 0.000 0.000 0.000
#> GSM751320 1 0.0000 0.8667 1.000 0.000 0.000 0.000
#> GSM751321 1 0.0000 0.8667 1.000 0.000 0.000 0.000
#> GSM751322 1 0.0000 0.8667 1.000 0.000 0.000 0.000
#> GSM751324 1 0.0000 0.8667 1.000 0.000 0.000 0.000
#> GSM751325 1 0.0000 0.8667 1.000 0.000 0.000 0.000
#> GSM751332 1 0.0000 0.8667 1.000 0.000 0.000 0.000
#> GSM751334 1 0.0000 0.8667 1.000 0.000 0.000 0.000
#> GSM751339 1 0.3486 0.8323 0.812 0.000 0.000 0.188
#> GSM751341 1 0.2408 0.8568 0.896 0.000 0.000 0.104
#> GSM751343 1 0.0000 0.8667 1.000 0.000 0.000 0.000
#> GSM751344 2 0.4661 0.4834 0.000 0.728 0.016 0.256
#> GSM751345 2 0.4661 0.4834 0.000 0.728 0.016 0.256
#> GSM751356 2 0.6215 0.2929 0.000 0.600 0.072 0.328
#> GSM751357 2 0.5754 0.3623 0.000 0.636 0.048 0.316
#> GSM751293 1 0.6761 0.6209 0.608 0.168 0.000 0.224
#> GSM751295 1 0.5126 0.6792 0.552 0.004 0.000 0.444
#> GSM751319 1 0.0000 0.8667 1.000 0.000 0.000 0.000
#> GSM751323 1 0.0336 0.8666 0.992 0.000 0.000 0.008
#> GSM751326 1 0.1716 0.8614 0.936 0.000 0.000 0.064
#> GSM751327 1 0.0000 0.8667 1.000 0.000 0.000 0.000
#> GSM751328 1 0.0000 0.8667 1.000 0.000 0.000 0.000
#> GSM751329 1 0.0469 0.8666 0.988 0.000 0.000 0.012
#> GSM751330 1 0.3266 0.8389 0.832 0.000 0.000 0.168
#> GSM751331 1 0.5119 0.6830 0.556 0.004 0.000 0.440
#> GSM751333 1 0.2973 0.8470 0.856 0.000 0.000 0.144
#> GSM751335 1 0.3688 0.8231 0.792 0.000 0.000 0.208
#> GSM751336 1 0.4898 0.7035 0.584 0.000 0.000 0.416
#> GSM751337 1 0.2530 0.8543 0.888 0.000 0.000 0.112
#> GSM751338 1 0.3266 0.8396 0.832 0.000 0.000 0.168
#> GSM751340 1 0.9708 -0.2357 0.308 0.136 0.276 0.280
#> GSM751350 1 0.5126 0.6792 0.552 0.004 0.000 0.444
#> GSM751351 1 0.5126 0.6792 0.552 0.004 0.000 0.444
#> GSM751362 3 0.3528 0.5351 0.000 0.000 0.808 0.192
#> GSM751363 3 0.4011 0.5292 0.000 0.008 0.784 0.208
#> GSM751367 3 0.8522 -0.4006 0.036 0.224 0.428 0.312
#> GSM751368 3 0.6362 0.3435 0.000 0.176 0.656 0.168
#> GSM751371 3 0.6120 0.2649 0.000 0.076 0.628 0.296
#> GSM751375 2 0.6383 0.3211 0.000 0.612 0.096 0.292
#> GSM751376 2 0.7729 -0.4443 0.000 0.400 0.228 0.372
#> GSM751378 3 0.7249 0.0269 0.000 0.156 0.496 0.348
#> GSM751379 2 0.7842 -0.5072 0.000 0.376 0.264 0.360
#> GSM751382 2 0.6084 0.4033 0.000 0.660 0.096 0.244
#> GSM751386 3 0.7345 0.1493 0.000 0.184 0.508 0.308
#> GSM751388 3 0.6946 0.2725 0.000 0.168 0.580 0.252
#> GSM751391 3 0.6835 0.0746 0.000 0.136 0.576 0.288
#> GSM751410 3 0.5169 0.4042 0.000 0.032 0.696 0.272
#> GSM751414 3 0.3444 0.5442 0.000 0.000 0.816 0.184
#> GSM751361 3 0.1890 0.6440 0.000 0.008 0.936 0.056
#> GSM751365 3 0.0000 0.6599 0.000 0.000 1.000 0.000
#> GSM751366 3 0.0000 0.6599 0.000 0.000 1.000 0.000
#> GSM751369 3 0.5705 0.3560 0.000 0.064 0.676 0.260
#> GSM751370 3 0.3074 0.5748 0.000 0.000 0.848 0.152
#> GSM751372 3 0.0000 0.6599 0.000 0.000 1.000 0.000
#> GSM751373 3 0.0188 0.6598 0.000 0.000 0.996 0.004
#> GSM751374 2 0.7692 -0.4243 0.000 0.412 0.220 0.368
#> GSM751377 3 0.6522 0.3465 0.000 0.144 0.632 0.224
#> GSM751380 3 0.0000 0.6599 0.000 0.000 1.000 0.000
#> GSM751381 3 0.7438 0.1056 0.000 0.188 0.484 0.328
#> GSM751383 3 0.7005 0.2591 0.000 0.172 0.572 0.256
#> GSM751384 3 0.4706 0.5495 0.000 0.028 0.748 0.224
#> GSM751385 3 0.7541 -0.1527 0.000 0.188 0.424 0.388
#> GSM751387 3 0.7220 0.2007 0.000 0.196 0.544 0.260
#> GSM751389 3 0.0336 0.6593 0.000 0.000 0.992 0.008
#> GSM751393 3 0.5857 0.4443 0.000 0.108 0.696 0.196
#> GSM751394 3 0.7421 0.0390 0.000 0.172 0.456 0.372
#> GSM751395 4 0.7792 0.3864 0.000 0.256 0.332 0.412
#> GSM751397 3 0.7362 0.0559 0.000 0.164 0.464 0.372
#> GSM751398 3 0.7079 0.2469 0.000 0.168 0.556 0.276
#> GSM751404 3 0.0000 0.6599 0.000 0.000 1.000 0.000
#> GSM751406 3 0.4155 0.4815 0.000 0.004 0.756 0.240
#> GSM751411 3 0.1792 0.6344 0.000 0.000 0.932 0.068
#> GSM751413 3 0.6862 0.2176 0.000 0.176 0.596 0.228
#> GSM751415 3 0.0000 0.6599 0.000 0.000 1.000 0.000
#> GSM751416 3 0.0657 0.6570 0.000 0.012 0.984 0.004
#> GSM751417 3 0.0937 0.6552 0.000 0.012 0.976 0.012
#> GSM751421 3 0.3837 0.5197 0.000 0.000 0.776 0.224
#> GSM751422 3 0.4360 0.4859 0.000 0.008 0.744 0.248
#> GSM751360 3 0.2593 0.6261 0.000 0.004 0.892 0.104
#> GSM751364 3 0.0000 0.6599 0.000 0.000 1.000 0.000
#> GSM751390 3 0.4753 0.5384 0.000 0.084 0.788 0.128
#> GSM751392 3 0.7817 -0.1848 0.000 0.296 0.416 0.288
#> GSM751396 3 0.7678 -0.1498 0.000 0.332 0.440 0.228
#> GSM751399 3 0.0188 0.6595 0.000 0.000 0.996 0.004
#> GSM751400 3 0.0817 0.6557 0.000 0.000 0.976 0.024
#> GSM751401 3 0.0000 0.6599 0.000 0.000 1.000 0.000
#> GSM751402 3 0.0000 0.6599 0.000 0.000 1.000 0.000
#> GSM751403 3 0.0188 0.6584 0.000 0.000 0.996 0.004
#> GSM751405 3 0.4072 0.4643 0.000 0.000 0.748 0.252
#> GSM751407 3 0.0000 0.6599 0.000 0.000 1.000 0.000
#> GSM751408 3 0.0000 0.6599 0.000 0.000 1.000 0.000
#> GSM751409 3 0.0469 0.6584 0.000 0.000 0.988 0.012
#> GSM751412 3 0.0000 0.6599 0.000 0.000 1.000 0.000
#> GSM751418 3 0.0000 0.6599 0.000 0.000 1.000 0.000
#> GSM751419 3 0.0000 0.6599 0.000 0.000 1.000 0.000
#> GSM751420 3 0.7733 -0.4781 0.000 0.356 0.412 0.232
#> GSM751425 2 0.1978 0.6972 0.000 0.928 0.004 0.068
#> GSM751429 4 0.7729 0.3534 0.000 0.372 0.228 0.400
#> GSM751430 2 0.5573 0.3256 0.000 0.676 0.272 0.052
#> GSM751433 2 0.1398 0.6928 0.000 0.956 0.004 0.040
#> GSM751437 3 0.7704 -0.4244 0.000 0.232 0.432 0.336
#> GSM751448 4 0.7832 0.4405 0.000 0.260 0.360 0.380
#> GSM751451 2 0.2385 0.6692 0.000 0.920 0.052 0.028
#> GSM751423 2 0.2699 0.6901 0.000 0.904 0.028 0.068
#> GSM751424 2 0.1398 0.6928 0.000 0.956 0.004 0.040
#> GSM751428 2 0.0336 0.7023 0.000 0.992 0.008 0.000
#> GSM751431 2 0.1211 0.6930 0.000 0.960 0.000 0.040
#> GSM751432 2 0.2965 0.6581 0.000 0.892 0.072 0.036
#> GSM751434 2 0.1398 0.6928 0.000 0.956 0.004 0.040
#> GSM751435 2 0.0000 0.7005 0.000 1.000 0.000 0.000
#> GSM751436 2 0.1398 0.6928 0.000 0.956 0.004 0.040
#> GSM751440 2 0.0817 0.7003 0.000 0.976 0.000 0.024
#> GSM751444 2 0.0000 0.7005 0.000 1.000 0.000 0.000
#> GSM751446 2 0.1022 0.7017 0.000 0.968 0.000 0.032
#> GSM751449 2 0.1940 0.6922 0.000 0.924 0.000 0.076
#> GSM751450 2 0.0817 0.6981 0.000 0.976 0.000 0.024
#> GSM751452 2 0.1398 0.6928 0.000 0.956 0.004 0.040
#> GSM751426 2 0.1211 0.6930 0.000 0.960 0.000 0.040
#> GSM751427 2 0.1389 0.6994 0.000 0.952 0.000 0.048
#> GSM751438 2 0.1716 0.6962 0.000 0.936 0.000 0.064
#> GSM751439 2 0.2996 0.6662 0.000 0.892 0.044 0.064
#> GSM751441 2 0.2266 0.6882 0.000 0.912 0.004 0.084
#> GSM751442 2 0.0000 0.7005 0.000 1.000 0.000 0.000
#> GSM751443 2 0.6848 0.1822 0.000 0.592 0.160 0.248
#> GSM751445 2 0.2011 0.6904 0.000 0.920 0.000 0.080
#> GSM751447 2 0.1302 0.7001 0.000 0.956 0.000 0.044
#> GSM751453 2 0.0188 0.7014 0.000 0.996 0.000 0.004
#> GSM751454 2 0.0188 0.7014 0.000 0.996 0.000 0.004
#> GSM751455 2 0.0817 0.7025 0.000 0.976 0.000 0.024
#> GSM751456 2 0.0817 0.7025 0.000 0.976 0.000 0.024
#> GSM751457 2 0.2675 0.6827 0.000 0.892 0.008 0.100
#> GSM751458 2 0.2675 0.6827 0.000 0.892 0.008 0.100
cbind(get_classes(res, k = 5), get_membership(res, k = 5))
#> class entropy silhouette p1 p2 p3 p4 p5
#> GSM751298 4 0.4003 0.5153 0.288 0.000 0.000 0.704 0.008
#> GSM751304 2 0.8067 0.4846 0.204 0.444 0.120 0.004 0.228
#> GSM751305 2 0.8631 -0.0472 0.180 0.300 0.280 0.004 0.236
#> GSM751307 2 0.8047 0.5182 0.188 0.468 0.104 0.012 0.228
#> GSM751310 4 0.1478 0.7721 0.064 0.000 0.000 0.936 0.000
#> GSM751314 4 0.1732 0.7420 0.080 0.000 0.000 0.920 0.000
#> GSM751316 4 0.4634 0.6132 0.188 0.004 0.052 0.748 0.008
#> GSM751318 4 0.1764 0.7699 0.064 0.000 0.000 0.928 0.008
#> GSM751342 4 0.4004 0.6397 0.164 0.032 0.000 0.792 0.012
#> GSM751346 1 0.3452 0.6567 0.756 0.000 0.000 0.244 0.000
#> GSM751347 1 0.7474 -0.0537 0.404 0.400 0.012 0.136 0.048
#> GSM751348 2 0.5809 0.6817 0.180 0.672 0.020 0.004 0.124
#> GSM751349 2 0.5444 0.6391 0.056 0.648 0.020 0.000 0.276
#> GSM751352 2 0.6579 0.5850 0.188 0.612 0.000 0.060 0.140
#> GSM751353 2 0.5966 0.6241 0.196 0.620 0.000 0.008 0.176
#> GSM751354 2 0.6601 0.6062 0.224 0.580 0.024 0.004 0.168
#> GSM751355 2 0.6718 0.6077 0.184 0.568 0.036 0.000 0.212
#> GSM751358 3 0.7721 -0.0332 0.112 0.176 0.504 0.004 0.204
#> GSM751359 5 0.5969 0.6198 0.032 0.072 0.288 0.000 0.608
#> GSM751294 2 0.7102 0.5854 0.212 0.540 0.044 0.004 0.200
#> GSM751296 1 0.4235 0.5329 0.656 0.000 0.000 0.336 0.008
#> GSM751297 1 0.6513 0.0356 0.584 0.256 0.004 0.028 0.128
#> GSM751299 2 0.6083 0.6137 0.204 0.632 0.000 0.024 0.140
#> GSM751300 1 0.3835 0.6360 0.732 0.000 0.000 0.260 0.008
#> GSM751301 4 0.7005 -0.3673 0.388 0.208 0.000 0.388 0.016
#> GSM751302 1 0.3452 0.6567 0.756 0.000 0.000 0.244 0.000
#> GSM751303 4 0.1197 0.7777 0.048 0.000 0.000 0.952 0.000
#> GSM751306 4 0.1270 0.7682 0.052 0.000 0.000 0.948 0.000
#> GSM751308 1 0.8718 0.4118 0.368 0.256 0.060 0.256 0.060
#> GSM751309 4 0.0963 0.7782 0.036 0.000 0.000 0.964 0.000
#> GSM751311 4 0.0162 0.7891 0.004 0.000 0.000 0.996 0.000
#> GSM751312 4 0.3870 0.5774 0.260 0.000 0.004 0.732 0.004
#> GSM751313 4 0.4101 0.3228 0.372 0.000 0.000 0.628 0.000
#> GSM751315 4 0.0404 0.7901 0.012 0.000 0.000 0.988 0.000
#> GSM751317 4 0.0703 0.7830 0.024 0.000 0.000 0.976 0.000
#> GSM751320 4 0.0609 0.7889 0.020 0.000 0.000 0.980 0.000
#> GSM751321 4 0.1043 0.7765 0.040 0.000 0.000 0.960 0.000
#> GSM751322 4 0.0609 0.7889 0.020 0.000 0.000 0.980 0.000
#> GSM751324 4 0.0404 0.7895 0.012 0.000 0.000 0.988 0.000
#> GSM751325 4 0.0609 0.7889 0.020 0.000 0.000 0.980 0.000
#> GSM751332 4 0.1121 0.7736 0.044 0.000 0.000 0.956 0.000
#> GSM751334 4 0.0609 0.7889 0.020 0.000 0.000 0.980 0.000
#> GSM751339 4 0.4304 0.0176 0.484 0.000 0.000 0.516 0.000
#> GSM751341 4 0.4046 0.5130 0.296 0.000 0.000 0.696 0.008
#> GSM751343 4 0.1082 0.7860 0.028 0.000 0.000 0.964 0.008
#> GSM751344 2 0.5544 0.6365 0.192 0.660 0.000 0.004 0.144
#> GSM751345 2 0.5544 0.6365 0.192 0.660 0.000 0.004 0.144
#> GSM751356 2 0.7218 0.5878 0.200 0.552 0.040 0.016 0.192
#> GSM751357 2 0.7035 0.5965 0.200 0.560 0.028 0.016 0.196
#> GSM751293 1 0.6603 0.4253 0.480 0.156 0.000 0.352 0.012
#> GSM751295 1 0.3452 0.6567 0.756 0.000 0.000 0.244 0.000
#> GSM751319 4 0.0290 0.7896 0.008 0.000 0.000 0.992 0.000
#> GSM751323 4 0.0703 0.7880 0.024 0.000 0.000 0.976 0.000
#> GSM751326 4 0.2929 0.6663 0.180 0.000 0.000 0.820 0.000
#> GSM751327 4 0.0703 0.7880 0.024 0.000 0.000 0.976 0.000
#> GSM751328 4 0.0404 0.7893 0.012 0.000 0.000 0.988 0.000
#> GSM751329 4 0.1732 0.7561 0.080 0.000 0.000 0.920 0.000
#> GSM751330 4 0.4242 0.1027 0.428 0.000 0.000 0.572 0.000
#> GSM751331 1 0.3452 0.6567 0.756 0.000 0.000 0.244 0.000
#> GSM751333 4 0.4273 0.0880 0.448 0.000 0.000 0.552 0.000
#> GSM751335 1 0.4294 0.2199 0.532 0.000 0.000 0.468 0.000
#> GSM751336 1 0.3661 0.6262 0.724 0.000 0.000 0.276 0.000
#> GSM751337 4 0.4015 0.3818 0.348 0.000 0.000 0.652 0.000
#> GSM751338 4 0.4278 0.0872 0.452 0.000 0.000 0.548 0.000
#> GSM751340 1 0.9173 0.1959 0.400 0.132 0.228 0.140 0.100
#> GSM751350 1 0.3452 0.6567 0.756 0.000 0.000 0.244 0.000
#> GSM751351 1 0.3452 0.6567 0.756 0.000 0.000 0.244 0.000
#> GSM751362 3 0.3039 0.6150 0.000 0.000 0.808 0.000 0.192
#> GSM751363 3 0.3143 0.6126 0.000 0.000 0.796 0.000 0.204
#> GSM751367 3 0.8742 -0.0424 0.096 0.164 0.436 0.068 0.236
#> GSM751368 3 0.4565 -0.2376 0.000 0.028 0.664 0.000 0.308
#> GSM751371 3 0.5574 0.4375 0.032 0.068 0.672 0.000 0.228
#> GSM751375 2 0.5398 0.6098 0.024 0.644 0.044 0.000 0.288
#> GSM751376 2 0.6911 0.5196 0.076 0.512 0.084 0.000 0.328
#> GSM751378 3 0.6467 -0.6579 0.008 0.140 0.428 0.000 0.424
#> GSM751379 2 0.7290 0.4540 0.076 0.476 0.124 0.000 0.324
#> GSM751382 2 0.5020 0.5997 0.008 0.640 0.036 0.000 0.316
#> GSM751386 5 0.4811 0.7410 0.000 0.020 0.452 0.000 0.528
#> GSM751388 3 0.4830 -0.7067 0.000 0.020 0.492 0.000 0.488
#> GSM751391 3 0.5932 0.3712 0.032 0.100 0.648 0.000 0.220
#> GSM751410 3 0.4618 0.5518 0.048 0.016 0.748 0.000 0.188
#> GSM751414 3 0.2690 0.6419 0.000 0.000 0.844 0.000 0.156
#> GSM751361 3 0.1124 0.6820 0.000 0.004 0.960 0.000 0.036
#> GSM751365 3 0.0162 0.7008 0.000 0.000 0.996 0.000 0.004
#> GSM751366 3 0.0880 0.6998 0.000 0.000 0.968 0.000 0.032
#> GSM751369 3 0.4935 0.5169 0.028 0.040 0.720 0.000 0.212
#> GSM751370 3 0.3039 0.6150 0.000 0.000 0.808 0.000 0.192
#> GSM751372 3 0.0162 0.7008 0.000 0.000 0.996 0.000 0.004
#> GSM751373 3 0.0290 0.6991 0.000 0.000 0.992 0.000 0.008
#> GSM751374 2 0.7109 0.4876 0.076 0.496 0.104 0.000 0.324
#> GSM751377 3 0.4473 -0.4975 0.000 0.008 0.580 0.000 0.412
#> GSM751380 3 0.0404 0.7033 0.000 0.000 0.988 0.000 0.012
#> GSM751381 5 0.5059 0.7615 0.000 0.036 0.416 0.000 0.548
#> GSM751383 3 0.4907 -0.7112 0.000 0.024 0.488 0.000 0.488
#> GSM751384 3 0.3455 0.5054 0.000 0.008 0.784 0.000 0.208
#> GSM751385 5 0.5699 0.6371 0.004 0.068 0.452 0.000 0.476
#> GSM751387 5 0.5048 0.6928 0.000 0.032 0.476 0.000 0.492
#> GSM751389 3 0.0510 0.7016 0.000 0.000 0.984 0.000 0.016
#> GSM751393 3 0.4298 -0.1215 0.000 0.008 0.640 0.000 0.352
#> GSM751394 5 0.4915 0.7532 0.004 0.020 0.420 0.000 0.556
#> GSM751395 5 0.6992 0.4025 0.028 0.176 0.324 0.000 0.472
#> GSM751397 5 0.5225 0.7423 0.020 0.016 0.424 0.000 0.540
#> GSM751398 5 0.4811 0.7404 0.000 0.020 0.452 0.000 0.528
#> GSM751404 3 0.0290 0.6991 0.000 0.000 0.992 0.000 0.008
#> GSM751406 3 0.3360 0.6278 0.012 0.004 0.816 0.000 0.168
#> GSM751411 3 0.1410 0.6869 0.000 0.000 0.940 0.000 0.060
#> GSM751413 3 0.5586 -0.2027 0.004 0.064 0.536 0.000 0.396
#> GSM751415 3 0.0000 0.7010 0.000 0.000 1.000 0.000 0.000
#> GSM751416 3 0.1121 0.6883 0.000 0.000 0.956 0.000 0.044
#> GSM751417 3 0.1282 0.6812 0.000 0.004 0.952 0.000 0.044
#> GSM751421 3 0.3527 0.6055 0.016 0.000 0.792 0.000 0.192
#> GSM751422 3 0.3690 0.5949 0.020 0.000 0.780 0.000 0.200
#> GSM751360 3 0.3039 0.6394 0.012 0.000 0.836 0.000 0.152
#> GSM751364 3 0.0290 0.6998 0.000 0.000 0.992 0.000 0.008
#> GSM751390 3 0.4024 0.2149 0.000 0.028 0.752 0.000 0.220
#> GSM751392 5 0.6137 0.7112 0.000 0.132 0.392 0.000 0.476
#> GSM751396 5 0.6513 0.6078 0.000 0.192 0.384 0.000 0.424
#> GSM751399 3 0.0794 0.6998 0.000 0.000 0.972 0.000 0.028
#> GSM751400 3 0.1116 0.6868 0.004 0.004 0.964 0.000 0.028
#> GSM751401 3 0.0451 0.6994 0.004 0.000 0.988 0.000 0.008
#> GSM751402 3 0.0579 0.6995 0.008 0.000 0.984 0.000 0.008
#> GSM751403 3 0.0290 0.6991 0.000 0.000 0.992 0.000 0.008
#> GSM751405 3 0.3462 0.6032 0.012 0.000 0.792 0.000 0.196
#> GSM751407 3 0.0451 0.6994 0.004 0.000 0.988 0.000 0.008
#> GSM751408 3 0.0404 0.6988 0.000 0.000 0.988 0.000 0.012
#> GSM751409 3 0.0880 0.6981 0.000 0.000 0.968 0.000 0.032
#> GSM751412 3 0.0404 0.6988 0.000 0.000 0.988 0.000 0.012
#> GSM751418 3 0.0404 0.6988 0.000 0.000 0.988 0.000 0.012
#> GSM751419 3 0.0404 0.6988 0.000 0.000 0.988 0.000 0.012
#> GSM751420 2 0.7432 0.3629 0.052 0.460 0.216 0.000 0.272
#> GSM751425 2 0.1502 0.7199 0.004 0.940 0.000 0.000 0.056
#> GSM751429 2 0.7556 0.5521 0.240 0.496 0.072 0.004 0.188
#> GSM751430 2 0.6979 0.3502 0.020 0.476 0.224 0.000 0.280
#> GSM751433 2 0.4359 0.6271 0.020 0.704 0.004 0.000 0.272
#> GSM751437 2 0.8029 0.1884 0.088 0.360 0.276 0.000 0.276
#> GSM751448 2 0.8707 0.2178 0.244 0.292 0.240 0.004 0.220
#> GSM751451 2 0.4986 0.5298 0.004 0.608 0.032 0.000 0.356
#> GSM751423 2 0.3914 0.6758 0.012 0.780 0.016 0.000 0.192
#> GSM751424 2 0.4359 0.6270 0.020 0.704 0.004 0.000 0.272
#> GSM751428 2 0.0771 0.7241 0.004 0.976 0.000 0.000 0.020
#> GSM751431 2 0.3992 0.6335 0.012 0.720 0.000 0.000 0.268
#> GSM751432 2 0.5142 0.6224 0.020 0.692 0.052 0.000 0.236
#> GSM751434 2 0.4208 0.6406 0.020 0.728 0.004 0.000 0.248
#> GSM751435 2 0.0955 0.7223 0.004 0.968 0.000 0.000 0.028
#> GSM751436 2 0.4157 0.6316 0.020 0.716 0.000 0.000 0.264
#> GSM751440 2 0.3461 0.6670 0.004 0.772 0.000 0.000 0.224
#> GSM751444 2 0.0703 0.7220 0.000 0.976 0.000 0.000 0.024
#> GSM751446 2 0.0798 0.7189 0.008 0.976 0.000 0.000 0.016
#> GSM751449 2 0.0992 0.7192 0.008 0.968 0.000 0.000 0.024
#> GSM751450 2 0.3336 0.6636 0.000 0.772 0.000 0.000 0.228
#> GSM751452 2 0.4157 0.6316 0.020 0.716 0.000 0.000 0.264
#> GSM751426 2 0.4132 0.6328 0.020 0.720 0.000 0.000 0.260
#> GSM751427 2 0.1124 0.7247 0.004 0.960 0.000 0.000 0.036
#> GSM751438 2 0.0798 0.7226 0.008 0.976 0.000 0.000 0.016
#> GSM751439 2 0.1731 0.7247 0.008 0.940 0.012 0.000 0.040
#> GSM751441 2 0.1638 0.7230 0.004 0.932 0.000 0.000 0.064
#> GSM751442 2 0.0898 0.7197 0.008 0.972 0.000 0.000 0.020
#> GSM751443 2 0.5764 0.6555 0.120 0.668 0.024 0.000 0.188
#> GSM751445 2 0.0992 0.7192 0.008 0.968 0.000 0.000 0.024
#> GSM751447 2 0.0794 0.7202 0.000 0.972 0.000 0.000 0.028
#> GSM751453 2 0.1638 0.7185 0.004 0.932 0.000 0.000 0.064
#> GSM751454 2 0.1571 0.7192 0.004 0.936 0.000 0.000 0.060
#> GSM751455 2 0.1168 0.7190 0.008 0.960 0.000 0.000 0.032
#> GSM751456 2 0.1168 0.7190 0.008 0.960 0.000 0.000 0.032
#> GSM751457 2 0.3061 0.7001 0.020 0.844 0.000 0.000 0.136
#> GSM751458 2 0.3061 0.7001 0.020 0.844 0.000 0.000 0.136
cbind(get_classes(res, k = 6), get_membership(res, k = 6))
#> class entropy silhouette p1 p2 p3 p4 p5 p6
#> GSM751298 4 0.4150 0.40276 0.392 0.000 0.000 0.592 0.000 0.016
#> GSM751304 6 0.7190 -0.07717 0.000 0.304 0.124 0.020 0.100 0.452
#> GSM751305 6 0.7700 0.06638 0.000 0.136 0.168 0.024 0.268 0.404
#> GSM751307 6 0.7095 0.12820 0.004 0.252 0.088 0.016 0.140 0.500
#> GSM751310 4 0.0547 0.76063 0.020 0.000 0.000 0.980 0.000 0.000
#> GSM751314 4 0.0405 0.75779 0.004 0.000 0.000 0.988 0.000 0.008
#> GSM751316 4 0.3480 0.60984 0.140 0.000 0.044 0.808 0.000 0.008
#> GSM751318 4 0.2706 0.80228 0.124 0.000 0.000 0.852 0.000 0.024
#> GSM751342 4 0.4385 0.65354 0.052 0.032 0.000 0.776 0.016 0.124
#> GSM751346 1 0.1265 0.67804 0.948 0.000 0.000 0.044 0.008 0.000
#> GSM751347 1 0.7537 0.12313 0.404 0.224 0.016 0.084 0.004 0.268
#> GSM751348 2 0.5783 0.15878 0.004 0.476 0.020 0.016 0.052 0.432
#> GSM751349 2 0.6077 -0.03149 0.000 0.400 0.000 0.000 0.300 0.300
#> GSM751352 2 0.4959 0.40752 0.024 0.628 0.000 0.048 0.000 0.300
#> GSM751353 2 0.4541 0.40752 0.004 0.604 0.000 0.016 0.012 0.364
#> GSM751354 2 0.5069 0.36583 0.000 0.572 0.012 0.020 0.024 0.372
#> GSM751355 2 0.5737 0.34770 0.000 0.556 0.044 0.004 0.064 0.332
#> GSM751358 3 0.7436 -0.02432 0.004 0.120 0.424 0.004 0.232 0.216
#> GSM751359 5 0.3730 0.62080 0.000 0.032 0.128 0.000 0.804 0.036
#> GSM751294 2 0.5027 0.32890 0.004 0.516 0.028 0.012 0.004 0.436
#> GSM751296 1 0.2135 0.64829 0.872 0.000 0.000 0.128 0.000 0.000
#> GSM751297 1 0.6579 0.11459 0.436 0.100 0.012 0.040 0.008 0.404
#> GSM751299 2 0.4628 0.40954 0.004 0.632 0.000 0.052 0.000 0.312
#> GSM751300 1 0.1075 0.68052 0.952 0.000 0.000 0.048 0.000 0.000
#> GSM751301 1 0.7023 0.34276 0.504 0.156 0.000 0.244 0.024 0.072
#> GSM751302 1 0.1049 0.68221 0.960 0.000 0.000 0.032 0.008 0.000
#> GSM751303 4 0.0363 0.76578 0.012 0.000 0.000 0.988 0.000 0.000
#> GSM751306 4 0.0291 0.75772 0.004 0.000 0.000 0.992 0.000 0.004
#> GSM751308 1 0.6967 0.41905 0.552 0.204 0.048 0.076 0.000 0.120
#> GSM751309 4 0.0000 0.76330 0.000 0.000 0.000 1.000 0.000 0.000
#> GSM751311 4 0.2703 0.80303 0.172 0.000 0.000 0.824 0.000 0.004
#> GSM751312 4 0.3394 0.51284 0.236 0.000 0.012 0.752 0.000 0.000
#> GSM751313 1 0.4091 0.18791 0.520 0.000 0.000 0.472 0.000 0.008
#> GSM751315 4 0.2340 0.79040 0.148 0.000 0.000 0.852 0.000 0.000
#> GSM751317 4 0.0458 0.76636 0.016 0.000 0.000 0.984 0.000 0.000
#> GSM751320 4 0.3276 0.77170 0.228 0.000 0.000 0.764 0.004 0.004
#> GSM751321 4 0.0363 0.76423 0.012 0.000 0.000 0.988 0.000 0.000
#> GSM751322 4 0.2738 0.80163 0.176 0.000 0.000 0.820 0.000 0.004
#> GSM751324 4 0.2558 0.80562 0.156 0.000 0.000 0.840 0.000 0.004
#> GSM751325 4 0.2738 0.80163 0.176 0.000 0.000 0.820 0.000 0.004
#> GSM751332 4 0.2662 0.80165 0.120 0.000 0.000 0.856 0.000 0.024
#> GSM751334 4 0.2703 0.80303 0.172 0.000 0.000 0.824 0.000 0.004
#> GSM751339 1 0.4275 0.44189 0.644 0.000 0.008 0.328 0.000 0.020
#> GSM751341 4 0.4057 0.25180 0.436 0.000 0.000 0.556 0.000 0.008
#> GSM751343 4 0.3089 0.79405 0.188 0.000 0.000 0.800 0.004 0.008
#> GSM751344 2 0.5059 0.41341 0.004 0.596 0.000 0.036 0.024 0.340
#> GSM751345 2 0.5145 0.40647 0.004 0.584 0.000 0.040 0.024 0.348
#> GSM751356 2 0.5792 0.34595 0.004 0.532 0.036 0.052 0.008 0.368
#> GSM751357 2 0.5697 0.34098 0.004 0.524 0.028 0.052 0.008 0.384
#> GSM751293 1 0.6151 0.40549 0.584 0.132 0.000 0.232 0.012 0.040
#> GSM751295 1 0.1265 0.68052 0.948 0.000 0.000 0.044 0.008 0.000
#> GSM751319 4 0.2597 0.80118 0.176 0.000 0.000 0.824 0.000 0.000
#> GSM751323 4 0.3536 0.74639 0.252 0.000 0.000 0.736 0.004 0.008
#> GSM751326 4 0.4120 0.21530 0.468 0.000 0.000 0.524 0.004 0.004
#> GSM751327 4 0.3243 0.78495 0.208 0.000 0.000 0.780 0.004 0.008
#> GSM751328 4 0.2738 0.80163 0.176 0.000 0.000 0.820 0.000 0.004
#> GSM751329 4 0.3411 0.76058 0.232 0.000 0.000 0.756 0.004 0.008
#> GSM751330 1 0.3835 0.36391 0.656 0.000 0.000 0.336 0.004 0.004
#> GSM751331 1 0.0972 0.68198 0.964 0.000 0.000 0.028 0.008 0.000
#> GSM751333 1 0.3703 0.42601 0.688 0.000 0.000 0.304 0.004 0.004
#> GSM751335 1 0.3565 0.43359 0.692 0.000 0.000 0.304 0.004 0.000
#> GSM751336 1 0.1265 0.68049 0.948 0.000 0.000 0.044 0.008 0.000
#> GSM751337 1 0.3996 0.22193 0.604 0.000 0.000 0.388 0.004 0.004
#> GSM751338 1 0.3850 0.34545 0.652 0.000 0.000 0.340 0.004 0.004
#> GSM751340 6 0.8310 -0.16793 0.288 0.052 0.176 0.148 0.004 0.332
#> GSM751350 1 0.0972 0.68198 0.964 0.000 0.000 0.028 0.008 0.000
#> GSM751351 1 0.0972 0.68198 0.964 0.000 0.000 0.028 0.008 0.000
#> GSM751362 3 0.3512 0.68838 0.000 0.000 0.772 0.000 0.196 0.032
#> GSM751363 3 0.3394 0.68425 0.000 0.000 0.752 0.000 0.236 0.012
#> GSM751367 3 0.8054 0.27718 0.096 0.064 0.484 0.032 0.200 0.124
#> GSM751368 3 0.4122 -0.43645 0.000 0.004 0.520 0.000 0.472 0.004
#> GSM751371 3 0.4988 0.59346 0.000 0.028 0.672 0.000 0.228 0.072
#> GSM751375 2 0.5631 0.09417 0.000 0.452 0.004 0.000 0.416 0.128
#> GSM751376 2 0.6881 0.15538 0.000 0.424 0.068 0.000 0.204 0.304
#> GSM751378 5 0.5866 0.59538 0.000 0.184 0.292 0.000 0.516 0.008
#> GSM751379 2 0.7061 0.13478 0.000 0.416 0.088 0.000 0.212 0.284
#> GSM751382 2 0.5884 0.07903 0.000 0.456 0.008 0.000 0.380 0.156
#> GSM751386 5 0.3383 0.78301 0.000 0.000 0.268 0.000 0.728 0.004
#> GSM751388 5 0.3565 0.76275 0.000 0.000 0.304 0.000 0.692 0.004
#> GSM751391 3 0.5830 0.46711 0.000 0.072 0.604 0.000 0.240 0.084
#> GSM751410 3 0.4373 0.65284 0.000 0.012 0.736 0.000 0.172 0.080
#> GSM751414 3 0.2730 0.72947 0.000 0.000 0.836 0.000 0.152 0.012
#> GSM751361 3 0.2191 0.68897 0.000 0.000 0.876 0.000 0.120 0.004
#> GSM751365 3 0.0935 0.75637 0.000 0.000 0.964 0.000 0.032 0.004
#> GSM751366 3 0.1320 0.77060 0.000 0.000 0.948 0.000 0.036 0.016
#> GSM751369 3 0.4550 0.62795 0.000 0.016 0.704 0.000 0.220 0.060
#> GSM751370 3 0.3201 0.69144 0.000 0.000 0.780 0.000 0.208 0.012
#> GSM751372 3 0.0935 0.75637 0.000 0.000 0.964 0.000 0.032 0.004
#> GSM751373 3 0.1010 0.75627 0.000 0.000 0.960 0.000 0.036 0.004
#> GSM751374 2 0.6880 0.15718 0.000 0.432 0.068 0.000 0.212 0.288
#> GSM751377 5 0.3996 0.48411 0.000 0.000 0.484 0.000 0.512 0.004
#> GSM751380 3 0.1003 0.77027 0.000 0.000 0.964 0.000 0.020 0.016
#> GSM751381 5 0.3411 0.78181 0.000 0.008 0.232 0.000 0.756 0.004
#> GSM751383 5 0.3619 0.75953 0.000 0.000 0.316 0.000 0.680 0.004
#> GSM751384 3 0.3820 0.36462 0.000 0.004 0.660 0.000 0.332 0.004
#> GSM751385 5 0.5383 0.55375 0.000 0.092 0.376 0.000 0.524 0.008
#> GSM751387 5 0.4041 0.76614 0.000 0.016 0.292 0.000 0.684 0.008
#> GSM751389 3 0.1151 0.76551 0.000 0.000 0.956 0.000 0.012 0.032
#> GSM751393 3 0.4181 -0.00835 0.000 0.012 0.600 0.000 0.384 0.004
#> GSM751394 5 0.3163 0.77991 0.000 0.000 0.232 0.000 0.764 0.004
#> GSM751395 5 0.6398 0.33682 0.000 0.196 0.264 0.000 0.500 0.040
#> GSM751397 5 0.3298 0.77196 0.000 0.000 0.236 0.000 0.756 0.008
#> GSM751398 5 0.3405 0.78210 0.000 0.000 0.272 0.000 0.724 0.004
#> GSM751404 3 0.0891 0.76476 0.000 0.000 0.968 0.000 0.008 0.024
#> GSM751406 3 0.4808 0.60632 0.000 0.004 0.684 0.000 0.156 0.156
#> GSM751411 3 0.1398 0.76352 0.000 0.000 0.940 0.000 0.052 0.008
#> GSM751413 5 0.5190 0.28326 0.000 0.028 0.396 0.000 0.536 0.040
#> GSM751415 3 0.0790 0.76399 0.000 0.000 0.968 0.000 0.000 0.032
#> GSM751416 3 0.1644 0.73452 0.000 0.000 0.920 0.000 0.076 0.004
#> GSM751417 3 0.2100 0.69815 0.000 0.000 0.884 0.000 0.112 0.004
#> GSM751421 3 0.3510 0.67942 0.000 0.008 0.772 0.000 0.204 0.016
#> GSM751422 3 0.3708 0.66894 0.000 0.008 0.752 0.000 0.220 0.020
#> GSM751360 3 0.2848 0.72142 0.000 0.000 0.816 0.000 0.176 0.008
#> GSM751364 3 0.1082 0.75393 0.000 0.000 0.956 0.000 0.040 0.004
#> GSM751390 3 0.3606 0.32036 0.000 0.004 0.708 0.000 0.284 0.004
#> GSM751392 5 0.4695 0.74698 0.000 0.044 0.232 0.000 0.692 0.032
#> GSM751396 5 0.5060 0.69710 0.000 0.060 0.256 0.000 0.652 0.032
#> GSM751399 3 0.0622 0.76698 0.000 0.000 0.980 0.000 0.008 0.012
#> GSM751400 3 0.1148 0.76609 0.000 0.004 0.960 0.000 0.020 0.016
#> GSM751401 3 0.1493 0.75399 0.004 0.000 0.936 0.000 0.004 0.056
#> GSM751402 3 0.2494 0.70048 0.000 0.000 0.864 0.000 0.016 0.120
#> GSM751403 3 0.1951 0.74088 0.000 0.000 0.908 0.000 0.016 0.076
#> GSM751405 3 0.4893 0.60649 0.000 0.004 0.668 0.000 0.200 0.128
#> GSM751407 3 0.1080 0.76380 0.004 0.000 0.960 0.000 0.004 0.032
#> GSM751408 3 0.0622 0.76564 0.000 0.000 0.980 0.000 0.008 0.012
#> GSM751409 3 0.0909 0.76888 0.000 0.000 0.968 0.000 0.020 0.012
#> GSM751412 3 0.1003 0.76475 0.000 0.000 0.964 0.000 0.016 0.020
#> GSM751418 3 0.1082 0.75600 0.000 0.000 0.956 0.000 0.040 0.004
#> GSM751419 3 0.1082 0.75600 0.000 0.000 0.956 0.000 0.040 0.004
#> GSM751420 2 0.7313 0.06465 0.000 0.380 0.188 0.000 0.132 0.300
#> GSM751425 2 0.3520 0.44227 0.008 0.816 0.000 0.000 0.076 0.100
#> GSM751429 6 0.6474 -0.20321 0.040 0.372 0.052 0.004 0.044 0.488
#> GSM751430 6 0.7541 0.19982 0.004 0.172 0.204 0.000 0.224 0.396
#> GSM751433 6 0.6412 0.36311 0.016 0.368 0.004 0.000 0.208 0.404
#> GSM751437 6 0.7604 -0.06151 0.000 0.316 0.188 0.004 0.164 0.328
#> GSM751448 6 0.7745 0.00169 0.104 0.216 0.124 0.000 0.084 0.472
#> GSM751451 2 0.6836 -0.37441 0.016 0.344 0.016 0.000 0.292 0.332
#> GSM751423 2 0.5855 0.00216 0.008 0.556 0.004 0.000 0.212 0.220
#> GSM751424 6 0.6278 0.37283 0.016 0.356 0.000 0.000 0.208 0.420
#> GSM751428 2 0.2604 0.50683 0.008 0.880 0.000 0.000 0.036 0.076
#> GSM751431 6 0.6120 0.35548 0.008 0.384 0.000 0.000 0.204 0.404
#> GSM751432 6 0.6739 0.33762 0.016 0.380 0.024 0.000 0.192 0.388
#> GSM751434 2 0.6373 -0.38823 0.016 0.396 0.004 0.000 0.196 0.388
#> GSM751435 2 0.1769 0.51995 0.004 0.924 0.000 0.000 0.012 0.060
#> GSM751436 6 0.6265 0.37217 0.016 0.360 0.000 0.000 0.204 0.420
#> GSM751440 2 0.5997 -0.23625 0.008 0.484 0.000 0.000 0.200 0.308
#> GSM751444 2 0.1297 0.53112 0.000 0.948 0.000 0.000 0.012 0.040
#> GSM751446 2 0.0405 0.54828 0.008 0.988 0.000 0.000 0.004 0.000
#> GSM751449 2 0.0976 0.54881 0.008 0.968 0.000 0.000 0.016 0.008
#> GSM751450 2 0.5940 -0.19749 0.008 0.504 0.000 0.000 0.200 0.288
#> GSM751452 6 0.6265 0.37217 0.016 0.360 0.000 0.000 0.204 0.420
#> GSM751426 6 0.6193 0.36995 0.012 0.364 0.000 0.000 0.204 0.420
#> GSM751427 2 0.0993 0.54928 0.000 0.964 0.000 0.000 0.024 0.012
#> GSM751438 2 0.0779 0.54913 0.008 0.976 0.000 0.000 0.008 0.008
#> GSM751439 2 0.2611 0.50114 0.008 0.864 0.012 0.000 0.000 0.116
#> GSM751441 2 0.1320 0.55110 0.000 0.948 0.000 0.000 0.036 0.016
#> GSM751442 2 0.0551 0.54717 0.004 0.984 0.000 0.000 0.004 0.008
#> GSM751443 2 0.5031 0.31822 0.012 0.540 0.024 0.008 0.004 0.412
#> GSM751445 2 0.1350 0.54827 0.008 0.952 0.000 0.000 0.020 0.020
#> GSM751447 2 0.1341 0.54416 0.000 0.948 0.000 0.000 0.024 0.028
#> GSM751453 2 0.2760 0.47031 0.004 0.868 0.000 0.000 0.052 0.076
#> GSM751454 2 0.2696 0.47417 0.004 0.872 0.000 0.000 0.048 0.076
#> GSM751455 2 0.0551 0.54641 0.004 0.984 0.000 0.000 0.004 0.008
#> GSM751456 2 0.0551 0.54641 0.004 0.984 0.000 0.000 0.004 0.008
#> GSM751457 2 0.1838 0.54692 0.012 0.928 0.000 0.000 0.020 0.040
#> GSM751458 2 0.1838 0.54692 0.012 0.928 0.000 0.000 0.020 0.040
Heatmaps for the consensus matrix. It visualizes the probability of two samples to be in a same group.
consensus_heatmap(res, k = 2)
consensus_heatmap(res, k = 3)
consensus_heatmap(res, k = 4)
consensus_heatmap(res, k = 5)
consensus_heatmap(res, k = 6)
Heatmaps for the membership of samples in all partitions to see how consistent they are:
membership_heatmap(res, k = 2)
membership_heatmap(res, k = 3)
membership_heatmap(res, k = 4)
membership_heatmap(res, k = 5)
membership_heatmap(res, k = 6)
As soon as we have had the classes for columns, we can look for signatures which are significantly different between classes which can be candidate marks for certain classes. Following are the heatmaps for signatures.
Signature heatmaps where rows are scaled:
get_signatures(res, k = 2)
get_signatures(res, k = 3)
get_signatures(res, k = 4)
get_signatures(res, k = 5)
get_signatures(res, k = 6)
Signature heatmaps where rows are not scaled:
get_signatures(res, k = 2, scale_rows = FALSE)
get_signatures(res, k = 3, scale_rows = FALSE)
get_signatures(res, k = 4, scale_rows = FALSE)
get_signatures(res, k = 5, scale_rows = FALSE)
get_signatures(res, k = 6, scale_rows = FALSE)
Compare the overlap of signatures from different k:
compare_signatures(res)
get_signature() returns a data frame invisibly. TO get the list of signatures, the function
call should be assigned to a variable explicitly. In following code, if plot argument is set
to FALSE, no heatmap is plotted while only the differential analysis is performed.
# code only for demonstration
tb = get_signature(res, k = ..., plot = FALSE)
An example of the output of tb is:
#> which_row fdr mean_1 mean_2 scaled_mean_1 scaled_mean_2 km
#> 1 38 0.042760348 8.373488 9.131774 -0.5533452 0.5164555 1
#> 2 40 0.018707592 7.106213 8.469186 -0.6173731 0.5762149 1
#> 3 55 0.019134737 10.221463 11.207825 -0.6159697 0.5749050 1
#> 4 59 0.006059896 5.921854 7.869574 -0.6899429 0.6439467 1
#> 5 60 0.018055526 8.928898 10.211722 -0.6204761 0.5791110 1
#> 6 98 0.009384629 15.714769 14.887706 0.6635654 -0.6193277 2
...
The columns in tb are:
which_row: row indices corresponding to the input matrix.fdr: FDR for the differential test. mean_x: The mean value in group x.scaled_mean_x: The mean value in group x after rows are scaled.km: Row groups if k-means clustering is applied to rows.UMAP plot which shows how samples are separated.
dimension_reduction(res, k = 2, method = "UMAP")
dimension_reduction(res, k = 3, method = "UMAP")
dimension_reduction(res, k = 4, method = "UMAP")
dimension_reduction(res, k = 5, method = "UMAP")
dimension_reduction(res, k = 6, method = "UMAP")
Following heatmap shows how subgroups are split when increasing k:
collect_classes(res)
Test correlation between subgroups and known annotations. If the known annotation is numeric, one-way ANOVA test is applied, and if the known annotation is discrete, chi-squared contingency table test is applied.
test_to_known_factors(res)
#> n tissue(p) disease.state(p) agent(p) k
#> SD:mclust 162 1.20e-22 0.119 0.1947 2
#> SD:mclust 151 3.79e-46 0.468 0.7377 3
#> SD:mclust 111 1.68e-44 0.719 0.9163 4
#> SD:mclust 132 1.78e-35 0.353 0.3560 5
#> SD:mclust 99 1.50e-37 0.204 0.0427 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 4537 rows and 166 columns.
#> Top rows (454, 908, 1361, 1814, 2268) 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 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 0.807 0.902 0.958 0.4613 0.550 0.550
#> 3 3 0.573 0.665 0.847 0.4422 0.732 0.534
#> 4 4 0.586 0.568 0.783 0.1150 0.801 0.497
#> 5 5 0.659 0.613 0.792 0.0691 0.875 0.579
#> 6 6 0.680 0.585 0.736 0.0482 0.887 0.539
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
#> GSM751298 1 0.0000 0.9623 1.000 0.000
#> GSM751304 2 0.9358 0.4929 0.352 0.648
#> GSM751305 2 0.9393 0.4843 0.356 0.644
#> GSM751307 1 0.6973 0.7495 0.812 0.188
#> GSM751310 1 0.0000 0.9623 1.000 0.000
#> GSM751314 1 0.0000 0.9623 1.000 0.000
#> GSM751316 1 0.0000 0.9623 1.000 0.000
#> GSM751318 1 0.0000 0.9623 1.000 0.000
#> GSM751342 1 0.0000 0.9623 1.000 0.000
#> GSM751346 1 0.0000 0.9623 1.000 0.000
#> GSM751347 1 0.4161 0.8807 0.916 0.084
#> GSM751348 2 0.4298 0.8887 0.088 0.912
#> GSM751349 2 0.0000 0.9503 0.000 1.000
#> GSM751352 2 0.9552 0.4370 0.376 0.624
#> GSM751353 2 0.6247 0.8120 0.156 0.844
#> GSM751354 2 0.7219 0.7557 0.200 0.800
#> GSM751355 2 0.2948 0.9148 0.052 0.948
#> GSM751358 2 0.5408 0.8481 0.124 0.876
#> GSM751359 2 0.0000 0.9503 0.000 1.000
#> GSM751294 2 0.0672 0.9460 0.008 0.992
#> GSM751296 1 0.0000 0.9623 1.000 0.000
#> GSM751297 1 0.0672 0.9558 0.992 0.008
#> GSM751299 2 0.8267 0.6684 0.260 0.740
#> GSM751300 1 0.0000 0.9623 1.000 0.000
#> GSM751301 1 0.0000 0.9623 1.000 0.000
#> GSM751302 1 0.0000 0.9623 1.000 0.000
#> GSM751303 1 0.0000 0.9623 1.000 0.000
#> GSM751306 1 0.0000 0.9623 1.000 0.000
#> GSM751308 1 0.0376 0.9590 0.996 0.004
#> GSM751309 1 0.0000 0.9623 1.000 0.000
#> GSM751311 1 0.0000 0.9623 1.000 0.000
#> GSM751312 1 0.0000 0.9623 1.000 0.000
#> GSM751313 1 0.0000 0.9623 1.000 0.000
#> GSM751315 1 0.0000 0.9623 1.000 0.000
#> GSM751317 1 0.0000 0.9623 1.000 0.000
#> GSM751320 1 0.0000 0.9623 1.000 0.000
#> GSM751321 1 0.0000 0.9623 1.000 0.000
#> GSM751322 1 0.0000 0.9623 1.000 0.000
#> GSM751324 1 0.0000 0.9623 1.000 0.000
#> GSM751325 1 0.0000 0.9623 1.000 0.000
#> GSM751332 1 0.0000 0.9623 1.000 0.000
#> GSM751334 1 0.0000 0.9623 1.000 0.000
#> GSM751339 1 0.0000 0.9623 1.000 0.000
#> GSM751341 1 0.0000 0.9623 1.000 0.000
#> GSM751343 1 0.0000 0.9623 1.000 0.000
#> GSM751344 2 0.5059 0.8603 0.112 0.888
#> GSM751345 2 0.6343 0.8072 0.160 0.840
#> GSM751356 2 0.9087 0.5524 0.324 0.676
#> GSM751357 2 0.9087 0.5524 0.324 0.676
#> GSM751293 1 0.0000 0.9623 1.000 0.000
#> GSM751295 1 0.0000 0.9623 1.000 0.000
#> GSM751319 1 0.0000 0.9623 1.000 0.000
#> GSM751323 1 0.0000 0.9623 1.000 0.000
#> GSM751326 1 0.0000 0.9623 1.000 0.000
#> GSM751327 1 0.0000 0.9623 1.000 0.000
#> GSM751328 1 0.0000 0.9623 1.000 0.000
#> GSM751329 1 0.0000 0.9623 1.000 0.000
#> GSM751330 1 0.0000 0.9623 1.000 0.000
#> GSM751331 1 0.0000 0.9623 1.000 0.000
#> GSM751333 1 0.0000 0.9623 1.000 0.000
#> GSM751335 1 0.0000 0.9623 1.000 0.000
#> GSM751336 1 0.0000 0.9623 1.000 0.000
#> GSM751337 1 0.0000 0.9623 1.000 0.000
#> GSM751338 1 0.0000 0.9623 1.000 0.000
#> GSM751340 1 0.0000 0.9623 1.000 0.000
#> GSM751350 1 0.0000 0.9623 1.000 0.000
#> GSM751351 1 0.0000 0.9623 1.000 0.000
#> GSM751362 2 0.8661 0.6029 0.288 0.712
#> GSM751363 2 0.1184 0.9412 0.016 0.984
#> GSM751367 1 0.7376 0.7270 0.792 0.208
#> GSM751368 2 0.0000 0.9503 0.000 1.000
#> GSM751371 1 0.9881 0.2287 0.564 0.436
#> GSM751375 2 0.0000 0.9503 0.000 1.000
#> GSM751376 2 0.0000 0.9503 0.000 1.000
#> GSM751378 2 0.0000 0.9503 0.000 1.000
#> GSM751379 2 0.0000 0.9503 0.000 1.000
#> GSM751382 2 0.0000 0.9503 0.000 1.000
#> GSM751386 2 0.0000 0.9503 0.000 1.000
#> GSM751388 2 0.0000 0.9503 0.000 1.000
#> GSM751391 2 0.0000 0.9503 0.000 1.000
#> GSM751410 1 0.7219 0.7380 0.800 0.200
#> GSM751414 2 0.7602 0.7210 0.220 0.780
#> GSM751361 2 0.0000 0.9503 0.000 1.000
#> GSM751365 2 0.0000 0.9503 0.000 1.000
#> GSM751366 1 0.9209 0.4952 0.664 0.336
#> GSM751369 2 0.3584 0.9014 0.068 0.932
#> GSM751370 1 0.9983 0.0961 0.524 0.476
#> GSM751372 2 0.0000 0.9503 0.000 1.000
#> GSM751373 2 0.9993 0.0404 0.484 0.516
#> GSM751374 2 0.0000 0.9503 0.000 1.000
#> GSM751377 2 0.0000 0.9503 0.000 1.000
#> GSM751380 2 0.5946 0.8240 0.144 0.856
#> GSM751381 2 0.0000 0.9503 0.000 1.000
#> GSM751383 2 0.0000 0.9503 0.000 1.000
#> GSM751384 2 0.0000 0.9503 0.000 1.000
#> GSM751385 2 0.0000 0.9503 0.000 1.000
#> GSM751387 2 0.0000 0.9503 0.000 1.000
#> GSM751389 2 0.0000 0.9503 0.000 1.000
#> GSM751393 2 0.0000 0.9503 0.000 1.000
#> GSM751394 2 0.0000 0.9503 0.000 1.000
#> GSM751395 2 0.0000 0.9503 0.000 1.000
#> GSM751397 2 0.0000 0.9503 0.000 1.000
#> GSM751398 2 0.0000 0.9503 0.000 1.000
#> GSM751404 2 0.0376 0.9482 0.004 0.996
#> GSM751406 2 0.0000 0.9503 0.000 1.000
#> GSM751411 2 0.0000 0.9503 0.000 1.000
#> GSM751413 2 0.0000 0.9503 0.000 1.000
#> GSM751415 2 0.5408 0.8459 0.124 0.876
#> GSM751416 2 0.0000 0.9503 0.000 1.000
#> GSM751417 2 0.0000 0.9503 0.000 1.000
#> GSM751421 2 0.1414 0.9382 0.020 0.980
#> GSM751422 2 0.0376 0.9482 0.004 0.996
#> GSM751360 2 0.0000 0.9503 0.000 1.000
#> GSM751364 2 0.0000 0.9503 0.000 1.000
#> GSM751390 2 0.0000 0.9503 0.000 1.000
#> GSM751392 2 0.0000 0.9503 0.000 1.000
#> GSM751396 2 0.0000 0.9503 0.000 1.000
#> GSM751399 2 0.0000 0.9503 0.000 1.000
#> GSM751400 2 0.0000 0.9503 0.000 1.000
#> GSM751401 2 0.2236 0.9265 0.036 0.964
#> GSM751402 2 0.1414 0.9381 0.020 0.980
#> GSM751403 2 0.0000 0.9503 0.000 1.000
#> GSM751405 2 0.0000 0.9503 0.000 1.000
#> GSM751407 2 0.0000 0.9503 0.000 1.000
#> GSM751408 2 0.0000 0.9503 0.000 1.000
#> GSM751409 2 0.0000 0.9503 0.000 1.000
#> GSM751412 2 0.0000 0.9503 0.000 1.000
#> GSM751418 2 0.0000 0.9503 0.000 1.000
#> GSM751419 2 0.0000 0.9503 0.000 1.000
#> GSM751420 2 0.0000 0.9503 0.000 1.000
#> GSM751425 2 0.0000 0.9503 0.000 1.000
#> GSM751429 2 0.6247 0.8090 0.156 0.844
#> GSM751430 2 0.0376 0.9483 0.004 0.996
#> GSM751433 2 0.7139 0.7662 0.196 0.804
#> GSM751437 2 0.0000 0.9503 0.000 1.000
#> GSM751448 2 0.7219 0.7531 0.200 0.800
#> GSM751451 2 0.0000 0.9503 0.000 1.000
#> GSM751423 2 0.0000 0.9503 0.000 1.000
#> GSM751424 2 0.0000 0.9503 0.000 1.000
#> GSM751428 2 0.0000 0.9503 0.000 1.000
#> GSM751431 2 0.0000 0.9503 0.000 1.000
#> GSM751432 2 0.0000 0.9503 0.000 1.000
#> GSM751434 2 0.4431 0.8824 0.092 0.908
#> GSM751435 2 0.3879 0.8948 0.076 0.924
#> GSM751436 2 0.0376 0.9483 0.004 0.996
#> GSM751440 2 0.1184 0.9410 0.016 0.984
#> GSM751444 2 0.0000 0.9503 0.000 1.000
#> GSM751446 2 0.0000 0.9503 0.000 1.000
#> GSM751449 2 0.0000 0.9503 0.000 1.000
#> GSM751450 2 0.0000 0.9503 0.000 1.000
#> GSM751452 2 0.0000 0.9503 0.000 1.000
#> GSM751426 2 0.0000 0.9503 0.000 1.000
#> GSM751427 2 0.0000 0.9503 0.000 1.000
#> GSM751438 2 0.0000 0.9503 0.000 1.000
#> GSM751439 2 0.0938 0.9436 0.012 0.988
#> GSM751441 2 0.0000 0.9503 0.000 1.000
#> GSM751442 2 0.0938 0.9437 0.012 0.988
#> GSM751443 2 0.0000 0.9503 0.000 1.000
#> GSM751445 2 0.0000 0.9503 0.000 1.000
#> GSM751447 2 0.0000 0.9503 0.000 1.000
#> GSM751453 2 0.0000 0.9503 0.000 1.000
#> GSM751454 2 0.0000 0.9503 0.000 1.000
#> GSM751455 2 0.0000 0.9503 0.000 1.000
#> GSM751456 2 0.0000 0.9503 0.000 1.000
#> GSM751457 2 0.0000 0.9503 0.000 1.000
#> GSM751458 2 0.0000 0.9503 0.000 1.000
cbind(get_classes(res, k = 3), get_membership(res, k = 3))
#> class entropy silhouette p1 p2 p3
#> GSM751298 1 0.0000 0.94940 1.000 0.000 0.000
#> GSM751304 2 0.7213 0.58220 0.212 0.700 0.088
#> GSM751305 2 0.6986 0.55885 0.256 0.688 0.056
#> GSM751307 2 0.6489 0.20173 0.456 0.540 0.004
#> GSM751310 1 0.0475 0.94829 0.992 0.004 0.004
#> GSM751314 1 0.0475 0.94829 0.992 0.004 0.004
#> GSM751316 1 0.0475 0.94829 0.992 0.004 0.004
#> GSM751318 1 0.0000 0.94940 1.000 0.000 0.000
#> GSM751342 1 0.0661 0.94643 0.988 0.008 0.004
#> GSM751346 1 0.6307 0.55582 0.660 0.012 0.328
#> GSM751347 1 0.6735 0.33907 0.564 0.012 0.424
#> GSM751348 2 0.3554 0.73166 0.036 0.900 0.064
#> GSM751349 2 0.0892 0.75723 0.000 0.980 0.020
#> GSM751352 2 0.6012 0.68091 0.088 0.788 0.124
#> GSM751353 2 0.2550 0.74400 0.012 0.932 0.056
#> GSM751354 2 0.7462 0.39134 0.048 0.600 0.352
#> GSM751355 2 0.2448 0.74129 0.000 0.924 0.076
#> GSM751358 2 0.6956 0.48547 0.300 0.660 0.040
#> GSM751359 2 0.2356 0.73546 0.000 0.928 0.072
#> GSM751294 2 0.6204 0.26123 0.000 0.576 0.424
#> GSM751296 1 0.1170 0.94066 0.976 0.008 0.016
#> GSM751297 3 0.8902 0.00251 0.396 0.124 0.480
#> GSM751299 2 0.4411 0.69609 0.016 0.844 0.140
#> GSM751300 1 0.1482 0.93609 0.968 0.012 0.020
#> GSM751301 1 0.2955 0.88110 0.912 0.080 0.008
#> GSM751302 1 0.3618 0.86493 0.884 0.012 0.104
#> GSM751303 1 0.0475 0.94829 0.992 0.004 0.004
#> GSM751306 1 0.0475 0.94829 0.992 0.004 0.004
#> GSM751308 1 0.6451 0.60419 0.684 0.024 0.292
#> GSM751309 1 0.0475 0.94829 0.992 0.004 0.004
#> GSM751311 1 0.0475 0.94829 0.992 0.004 0.004
#> GSM751312 1 0.0475 0.94829 0.992 0.004 0.004
#> GSM751313 1 0.0000 0.94940 1.000 0.000 0.000
#> GSM751315 1 0.0000 0.94940 1.000 0.000 0.000
#> GSM751317 1 0.0475 0.94829 0.992 0.004 0.004
#> GSM751320 1 0.0000 0.94940 1.000 0.000 0.000
#> GSM751321 1 0.0475 0.94829 0.992 0.004 0.004
#> GSM751322 1 0.0000 0.94940 1.000 0.000 0.000
#> GSM751324 1 0.0000 0.94940 1.000 0.000 0.000
#> GSM751325 1 0.0000 0.94940 1.000 0.000 0.000
#> GSM751332 1 0.0000 0.94940 1.000 0.000 0.000
#> GSM751334 1 0.0000 0.94940 1.000 0.000 0.000
#> GSM751339 1 0.0747 0.94345 0.984 0.000 0.016
#> GSM751341 1 0.0475 0.94829 0.992 0.004 0.004
#> GSM751343 1 0.0000 0.94940 1.000 0.000 0.000
#> GSM751344 2 0.2066 0.74273 0.000 0.940 0.060
#> GSM751345 2 0.2165 0.74155 0.000 0.936 0.064
#> GSM751356 2 0.7592 0.57945 0.112 0.680 0.208
#> GSM751357 2 0.6594 0.65596 0.116 0.756 0.128
#> GSM751293 1 0.1170 0.94083 0.976 0.016 0.008
#> GSM751295 1 0.4326 0.82064 0.844 0.012 0.144
#> GSM751319 1 0.0237 0.94866 0.996 0.000 0.004
#> GSM751323 1 0.0000 0.94940 1.000 0.000 0.000
#> GSM751326 1 0.0000 0.94940 1.000 0.000 0.000
#> GSM751327 1 0.0000 0.94940 1.000 0.000 0.000
#> GSM751328 1 0.0000 0.94940 1.000 0.000 0.000
#> GSM751329 1 0.0000 0.94940 1.000 0.000 0.000
#> GSM751330 1 0.0475 0.94742 0.992 0.004 0.004
#> GSM751331 1 0.1482 0.93609 0.968 0.012 0.020
#> GSM751333 1 0.0237 0.94861 0.996 0.004 0.000
#> GSM751335 1 0.0661 0.94590 0.988 0.004 0.008
#> GSM751336 1 0.1620 0.93367 0.964 0.012 0.024
#> GSM751337 1 0.0000 0.94940 1.000 0.000 0.000
#> GSM751338 1 0.0475 0.94742 0.992 0.004 0.004
#> GSM751340 1 0.7074 0.20201 0.500 0.020 0.480
#> GSM751350 1 0.3031 0.89245 0.912 0.012 0.076
#> GSM751351 1 0.1999 0.92517 0.952 0.012 0.036
#> GSM751362 3 0.1182 0.72364 0.012 0.012 0.976
#> GSM751363 3 0.6664 0.19996 0.008 0.464 0.528
#> GSM751367 3 0.6421 0.23374 0.424 0.004 0.572
#> GSM751368 2 0.6295 -0.03204 0.000 0.528 0.472
#> GSM751371 3 0.4390 0.66299 0.148 0.012 0.840
#> GSM751375 2 0.0747 0.75755 0.000 0.984 0.016
#> GSM751376 3 0.5678 0.39023 0.000 0.316 0.684
#> GSM751378 3 0.6302 -0.00253 0.000 0.480 0.520
#> GSM751379 3 0.1529 0.70263 0.000 0.040 0.960
#> GSM751382 2 0.1031 0.75670 0.000 0.976 0.024
#> GSM751386 2 0.5497 0.46997 0.000 0.708 0.292
#> GSM751388 2 0.6079 0.25257 0.000 0.612 0.388
#> GSM751391 3 0.3038 0.68507 0.000 0.104 0.896
#> GSM751410 3 0.3851 0.67042 0.136 0.004 0.860
#> GSM751414 3 0.6752 0.63598 0.152 0.104 0.744
#> GSM751361 3 0.6299 0.18493 0.000 0.476 0.524
#> GSM751365 3 0.4062 0.67629 0.000 0.164 0.836
#> GSM751366 3 0.3148 0.72061 0.036 0.048 0.916
#> GSM751369 3 0.0892 0.71949 0.000 0.020 0.980
#> GSM751370 3 0.6181 0.64933 0.156 0.072 0.772
#> GSM751372 3 0.5254 0.58218 0.000 0.264 0.736
#> GSM751373 3 0.7849 0.55044 0.248 0.104 0.648
#> GSM751374 3 0.4178 0.59371 0.000 0.172 0.828
#> GSM751377 3 0.6305 0.14957 0.000 0.484 0.516
#> GSM751380 3 0.1643 0.72503 0.000 0.044 0.956
#> GSM751381 2 0.4974 0.56544 0.000 0.764 0.236
#> GSM751383 2 0.6111 0.22999 0.000 0.604 0.396
#> GSM751384 3 0.6008 0.42448 0.000 0.372 0.628
#> GSM751385 3 0.6252 0.27690 0.000 0.444 0.556
#> GSM751387 2 0.5098 0.54742 0.000 0.752 0.248
#> GSM751389 3 0.0592 0.72202 0.000 0.012 0.988
#> GSM751393 3 0.3941 0.68324 0.000 0.156 0.844
#> GSM751394 2 0.5785 0.39521 0.000 0.668 0.332
#> GSM751395 2 0.6291 0.10901 0.000 0.532 0.468
#> GSM751397 2 0.6180 0.17766 0.000 0.584 0.416
#> GSM751398 2 0.6095 0.24951 0.000 0.608 0.392
#> GSM751404 3 0.1964 0.72412 0.000 0.056 0.944
#> GSM751406 3 0.0747 0.71744 0.000 0.016 0.984
#> GSM751411 3 0.3116 0.70888 0.000 0.108 0.892
#> GSM751413 2 0.6295 -0.02061 0.000 0.528 0.472
#> GSM751415 3 0.1031 0.72465 0.000 0.024 0.976
#> GSM751416 3 0.6286 0.21161 0.000 0.464 0.536
#> GSM751417 3 0.6291 0.19984 0.000 0.468 0.532
#> GSM751421 3 0.0892 0.72217 0.000 0.020 0.980
#> GSM751422 3 0.1031 0.72294 0.000 0.024 0.976
#> GSM751360 3 0.7983 0.55097 0.124 0.228 0.648
#> GSM751364 3 0.6154 0.35253 0.000 0.408 0.592
#> GSM751390 3 0.6126 0.37397 0.000 0.400 0.600
#> GSM751392 2 0.4605 0.60789 0.000 0.796 0.204
#> GSM751396 2 0.5058 0.55339 0.000 0.756 0.244
#> GSM751399 3 0.2711 0.71875 0.000 0.088 0.912
#> GSM751400 3 0.2400 0.72325 0.004 0.064 0.932
#> GSM751401 3 0.0661 0.72191 0.004 0.008 0.988
#> GSM751402 3 0.0592 0.71934 0.000 0.012 0.988
#> GSM751403 3 0.0592 0.72202 0.000 0.012 0.988
#> GSM751405 3 0.0592 0.71725 0.000 0.012 0.988
#> GSM751407 3 0.2165 0.72320 0.000 0.064 0.936
#> GSM751408 3 0.2711 0.71837 0.000 0.088 0.912
#> GSM751409 3 0.2537 0.72081 0.000 0.080 0.920
#> GSM751412 3 0.2537 0.72053 0.000 0.080 0.920
#> GSM751418 3 0.6229 0.48025 0.008 0.340 0.652
#> GSM751419 3 0.5733 0.50828 0.000 0.324 0.676
#> GSM751420 3 0.1411 0.70962 0.000 0.036 0.964
#> GSM751425 2 0.0892 0.75789 0.000 0.980 0.020
#> GSM751429 3 0.5988 0.27518 0.000 0.368 0.632
#> GSM751430 2 0.5024 0.58502 0.004 0.776 0.220
#> GSM751433 2 0.2486 0.74137 0.060 0.932 0.008
#> GSM751437 3 0.5706 0.38840 0.000 0.320 0.680
#> GSM751448 3 0.4887 0.52384 0.000 0.228 0.772
#> GSM751451 2 0.1031 0.75670 0.000 0.976 0.024
#> GSM751423 2 0.0892 0.75743 0.000 0.980 0.020
#> GSM751424 2 0.1031 0.75670 0.000 0.976 0.024
#> GSM751428 2 0.1031 0.75795 0.000 0.976 0.024
#> GSM751431 2 0.0892 0.75743 0.000 0.980 0.020
#> GSM751432 2 0.2959 0.71350 0.000 0.900 0.100
#> GSM751434 2 0.2313 0.75004 0.032 0.944 0.024
#> GSM751435 2 0.0983 0.75782 0.004 0.980 0.016
#> GSM751436 2 0.1163 0.75545 0.000 0.972 0.028
#> GSM751440 2 0.0892 0.75743 0.000 0.980 0.020
#> GSM751444 2 0.1964 0.74824 0.000 0.944 0.056
#> GSM751446 2 0.4974 0.61703 0.000 0.764 0.236
#> GSM751449 2 0.4178 0.68829 0.000 0.828 0.172
#> GSM751450 2 0.0892 0.75743 0.000 0.980 0.020
#> GSM751452 2 0.1163 0.75545 0.000 0.972 0.028
#> GSM751426 2 0.1031 0.75670 0.000 0.976 0.024
#> GSM751427 2 0.1753 0.75628 0.000 0.952 0.048
#> GSM751438 2 0.5178 0.58521 0.000 0.744 0.256
#> GSM751439 3 0.6244 0.09466 0.000 0.440 0.560
#> GSM751441 2 0.1964 0.74751 0.000 0.944 0.056
#> GSM751442 2 0.4733 0.65007 0.004 0.800 0.196
#> GSM751443 3 0.6095 0.21905 0.000 0.392 0.608
#> GSM751445 2 0.2537 0.74558 0.000 0.920 0.080
#> GSM751447 2 0.2356 0.74319 0.000 0.928 0.072
#> GSM751453 2 0.0592 0.75800 0.000 0.988 0.012
#> GSM751454 2 0.0747 0.75790 0.000 0.984 0.016
#> GSM751455 2 0.5291 0.56757 0.000 0.732 0.268
#> GSM751456 2 0.5706 0.48567 0.000 0.680 0.320
#> GSM751457 2 0.6008 0.39018 0.000 0.628 0.372
#> GSM751458 2 0.5948 0.41261 0.000 0.640 0.360
cbind(get_classes(res, k = 4), get_membership(res, k = 4))
#> class entropy silhouette p1 p2 p3 p4
#> GSM751298 1 0.4431 0.6052 0.696 0.000 0.000 0.304
#> GSM751304 2 0.7585 0.4917 0.256 0.540 0.012 0.192
#> GSM751305 2 0.6746 0.4043 0.404 0.520 0.012 0.064
#> GSM751307 2 0.6103 0.2748 0.476 0.488 0.012 0.024
#> GSM751310 1 0.0592 0.7156 0.984 0.000 0.000 0.016
#> GSM751314 1 0.0336 0.7157 0.992 0.000 0.000 0.008
#> GSM751316 1 0.0844 0.6984 0.980 0.004 0.004 0.012
#> GSM751318 1 0.3528 0.7072 0.808 0.000 0.000 0.192
#> GSM751342 1 0.0779 0.6977 0.980 0.004 0.000 0.016
#> GSM751346 4 0.2216 0.3946 0.092 0.000 0.000 0.908
#> GSM751347 4 0.3306 0.3607 0.156 0.000 0.004 0.840
#> GSM751348 2 0.3370 0.8092 0.080 0.872 0.000 0.048
#> GSM751349 2 0.2676 0.8268 0.044 0.916 0.012 0.028
#> GSM751352 4 0.5773 -0.0440 0.016 0.440 0.008 0.536
#> GSM751353 2 0.2960 0.8190 0.020 0.892 0.004 0.084
#> GSM751354 4 0.6144 0.3727 0.180 0.108 0.012 0.700
#> GSM751355 2 0.7241 0.5627 0.136 0.596 0.020 0.248
#> GSM751358 1 0.5020 0.3849 0.760 0.184 0.004 0.052
#> GSM751359 2 0.5970 0.6794 0.204 0.712 0.056 0.028
#> GSM751294 4 0.7269 -0.0528 0.032 0.408 0.068 0.492
#> GSM751296 4 0.4941 -0.0626 0.436 0.000 0.000 0.564
#> GSM751297 4 0.4717 0.4236 0.084 0.112 0.004 0.800
#> GSM751299 2 0.6210 0.2448 0.036 0.516 0.008 0.440
#> GSM751300 4 0.4888 -0.0064 0.412 0.000 0.000 0.588
#> GSM751301 4 0.7884 0.0130 0.284 0.356 0.000 0.360
#> GSM751302 4 0.3726 0.3175 0.212 0.000 0.000 0.788
#> GSM751303 1 0.0967 0.6945 0.976 0.004 0.004 0.016
#> GSM751306 1 0.0844 0.6984 0.980 0.004 0.004 0.012
#> GSM751308 4 0.5352 0.2162 0.296 0.020 0.008 0.676
#> GSM751309 1 0.0188 0.7093 0.996 0.000 0.000 0.004
#> GSM751311 1 0.0000 0.7118 1.000 0.000 0.000 0.000
#> GSM751312 1 0.0844 0.7011 0.980 0.004 0.004 0.012
#> GSM751313 4 0.4972 -0.1154 0.456 0.000 0.000 0.544
#> GSM751315 1 0.2868 0.7194 0.864 0.000 0.000 0.136
#> GSM751317 1 0.1022 0.7200 0.968 0.000 0.000 0.032
#> GSM751320 1 0.3837 0.6887 0.776 0.000 0.000 0.224
#> GSM751321 1 0.0469 0.7162 0.988 0.000 0.000 0.012
#> GSM751322 1 0.3569 0.7053 0.804 0.000 0.000 0.196
#> GSM751324 1 0.3486 0.7089 0.812 0.000 0.000 0.188
#> GSM751325 1 0.3610 0.7033 0.800 0.000 0.000 0.200
#> GSM751332 1 0.3610 0.7033 0.800 0.000 0.000 0.200
#> GSM751334 1 0.4008 0.6721 0.756 0.000 0.000 0.244
#> GSM751339 4 0.4981 -0.1474 0.464 0.000 0.000 0.536
#> GSM751341 1 0.0707 0.7157 0.980 0.000 0.000 0.020
#> GSM751343 1 0.3649 0.7007 0.796 0.000 0.000 0.204
#> GSM751344 2 0.2830 0.8214 0.032 0.904 0.004 0.060
#> GSM751345 2 0.2731 0.8230 0.028 0.908 0.004 0.060
#> GSM751356 2 0.7226 0.5840 0.192 0.604 0.016 0.188
#> GSM751357 2 0.6744 0.6224 0.188 0.640 0.008 0.164
#> GSM751293 1 0.6930 0.3514 0.524 0.120 0.000 0.356
#> GSM751295 4 0.2921 0.3737 0.140 0.000 0.000 0.860
#> GSM751319 1 0.1792 0.7226 0.932 0.000 0.000 0.068
#> GSM751323 1 0.4643 0.5409 0.656 0.000 0.000 0.344
#> GSM751326 1 0.4985 0.2852 0.532 0.000 0.000 0.468
#> GSM751327 1 0.4134 0.6498 0.740 0.000 0.000 0.260
#> GSM751328 1 0.3444 0.7109 0.816 0.000 0.000 0.184
#> GSM751329 1 0.4877 0.4281 0.592 0.000 0.000 0.408
#> GSM751330 4 0.4985 -0.1487 0.468 0.000 0.000 0.532
#> GSM751331 4 0.4933 -0.0523 0.432 0.000 0.000 0.568
#> GSM751333 4 0.4989 -0.1599 0.472 0.000 0.000 0.528
#> GSM751335 4 0.4996 -0.1966 0.484 0.000 0.000 0.516
#> GSM751336 4 0.4907 -0.0241 0.420 0.000 0.000 0.580
#> GSM751337 4 0.4981 -0.1347 0.464 0.000 0.000 0.536
#> GSM751338 1 0.4989 0.2516 0.528 0.000 0.000 0.472
#> GSM751340 4 0.4622 0.3945 0.096 0.008 0.084 0.812
#> GSM751350 4 0.3907 0.2971 0.232 0.000 0.000 0.768
#> GSM751351 4 0.4522 0.1722 0.320 0.000 0.000 0.680
#> GSM751362 3 0.2665 0.7761 0.008 0.004 0.900 0.088
#> GSM751363 3 0.5246 0.6459 0.216 0.048 0.732 0.004
#> GSM751367 1 0.7851 -0.0981 0.424 0.004 0.224 0.348
#> GSM751368 3 0.3128 0.7600 0.004 0.128 0.864 0.004
#> GSM751371 1 0.7417 0.1034 0.508 0.000 0.284 0.208
#> GSM751375 2 0.2521 0.8273 0.032 0.924 0.016 0.028
#> GSM751376 4 0.8493 0.2013 0.060 0.204 0.232 0.504
#> GSM751378 2 0.7529 0.1634 0.000 0.472 0.324 0.204
#> GSM751379 4 0.7118 -0.1838 0.068 0.024 0.420 0.488
#> GSM751382 2 0.2329 0.8316 0.020 0.932 0.024 0.024
#> GSM751386 3 0.5090 0.5289 0.012 0.312 0.672 0.004
#> GSM751388 3 0.4632 0.6378 0.012 0.244 0.740 0.004
#> GSM751391 3 0.7696 0.3685 0.020 0.140 0.500 0.340
#> GSM751410 3 0.7862 0.0809 0.332 0.000 0.388 0.280
#> GSM751414 3 0.0859 0.8018 0.008 0.008 0.980 0.004
#> GSM751361 3 0.2699 0.7832 0.028 0.068 0.904 0.000
#> GSM751365 3 0.0524 0.8021 0.004 0.008 0.988 0.000
#> GSM751366 3 0.0657 0.7996 0.004 0.000 0.984 0.012
#> GSM751369 3 0.5483 0.4941 0.012 0.008 0.612 0.368
#> GSM751370 3 0.0712 0.8019 0.004 0.008 0.984 0.004
#> GSM751372 3 0.0804 0.8017 0.008 0.012 0.980 0.000
#> GSM751373 3 0.1377 0.8005 0.020 0.008 0.964 0.008
#> GSM751374 4 0.8059 -0.0224 0.064 0.096 0.348 0.492
#> GSM751377 3 0.2480 0.7803 0.008 0.088 0.904 0.000
#> GSM751380 3 0.2197 0.7805 0.000 0.004 0.916 0.080
#> GSM751381 3 0.6241 0.1765 0.032 0.436 0.520 0.012
#> GSM751383 3 0.4370 0.6800 0.008 0.212 0.772 0.008
#> GSM751384 3 0.1543 0.7996 0.008 0.032 0.956 0.004
#> GSM751385 3 0.2730 0.7880 0.000 0.088 0.896 0.016
#> GSM751387 3 0.5553 0.1824 0.004 0.452 0.532 0.012
#> GSM751389 3 0.4769 0.5833 0.000 0.008 0.684 0.308
#> GSM751393 3 0.0804 0.8020 0.000 0.008 0.980 0.012
#> GSM751394 3 0.5968 0.4685 0.036 0.320 0.632 0.012
#> GSM751395 3 0.9139 0.0702 0.084 0.340 0.372 0.204
#> GSM751397 3 0.4970 0.6757 0.028 0.204 0.756 0.012
#> GSM751398 3 0.4946 0.6364 0.016 0.236 0.736 0.012
#> GSM751404 3 0.1661 0.7911 0.000 0.004 0.944 0.052
#> GSM751406 3 0.5099 0.4887 0.000 0.008 0.612 0.380
#> GSM751411 3 0.0804 0.8013 0.000 0.008 0.980 0.012
#> GSM751413 3 0.4105 0.7337 0.032 0.156 0.812 0.000
#> GSM751415 3 0.2714 0.7650 0.000 0.004 0.884 0.112
#> GSM751416 3 0.2342 0.7839 0.008 0.080 0.912 0.000
#> GSM751417 3 0.2342 0.7839 0.008 0.080 0.912 0.000
#> GSM751421 3 0.3681 0.7206 0.000 0.008 0.816 0.176
#> GSM751422 3 0.3591 0.7270 0.000 0.008 0.824 0.168
#> GSM751360 3 0.2271 0.7772 0.076 0.000 0.916 0.008
#> GSM751364 3 0.1854 0.7944 0.012 0.048 0.940 0.000
#> GSM751390 3 0.2234 0.7953 0.004 0.064 0.924 0.008
#> GSM751392 2 0.5093 0.5688 0.008 0.704 0.272 0.016
#> GSM751396 2 0.5172 0.5434 0.008 0.692 0.284 0.016
#> GSM751399 3 0.0895 0.8001 0.000 0.004 0.976 0.020
#> GSM751400 3 0.1109 0.7999 0.000 0.004 0.968 0.028
#> GSM751401 3 0.3355 0.7354 0.000 0.004 0.836 0.160
#> GSM751402 3 0.4990 0.5295 0.000 0.008 0.640 0.352
#> GSM751403 3 0.3032 0.7576 0.000 0.008 0.868 0.124
#> GSM751405 3 0.4936 0.5459 0.000 0.008 0.652 0.340
#> GSM751407 3 0.1211 0.7959 0.000 0.000 0.960 0.040
#> GSM751408 3 0.0895 0.8001 0.000 0.004 0.976 0.020
#> GSM751409 3 0.1557 0.7909 0.000 0.000 0.944 0.056
#> GSM751412 3 0.0895 0.8010 0.000 0.004 0.976 0.020
#> GSM751418 3 0.1042 0.8010 0.008 0.020 0.972 0.000
#> GSM751419 3 0.0592 0.8020 0.000 0.016 0.984 0.000
#> GSM751420 3 0.5399 0.3351 0.000 0.012 0.520 0.468
#> GSM751425 2 0.0927 0.8381 0.000 0.976 0.008 0.016
#> GSM751429 4 0.6730 0.3100 0.040 0.240 0.068 0.652
#> GSM751430 2 0.5072 0.5943 0.012 0.720 0.252 0.016
#> GSM751433 2 0.3723 0.7885 0.048 0.872 0.024 0.056
#> GSM751437 4 0.7503 0.2012 0.000 0.276 0.228 0.496
#> GSM751448 4 0.6788 0.3137 0.000 0.204 0.188 0.608
#> GSM751451 2 0.1953 0.8302 0.044 0.940 0.012 0.004
#> GSM751423 2 0.0524 0.8372 0.000 0.988 0.008 0.004
#> GSM751424 2 0.1471 0.8334 0.004 0.960 0.024 0.012
#> GSM751428 2 0.0895 0.8369 0.000 0.976 0.020 0.004
#> GSM751431 2 0.0592 0.8364 0.000 0.984 0.016 0.000
#> GSM751432 2 0.3403 0.7742 0.004 0.864 0.112 0.020
#> GSM751434 2 0.2639 0.8233 0.024 0.920 0.024 0.032
#> GSM751435 2 0.1174 0.8368 0.000 0.968 0.012 0.020
#> GSM751436 2 0.1593 0.8333 0.004 0.956 0.024 0.016
#> GSM751440 2 0.1059 0.8370 0.000 0.972 0.012 0.016
#> GSM751444 2 0.1109 0.8323 0.000 0.968 0.004 0.028
#> GSM751446 2 0.2255 0.8172 0.000 0.920 0.012 0.068
#> GSM751449 2 0.2060 0.8212 0.000 0.932 0.016 0.052
#> GSM751450 2 0.0592 0.8364 0.000 0.984 0.016 0.000
#> GSM751452 2 0.1739 0.8325 0.008 0.952 0.024 0.016
#> GSM751426 2 0.1004 0.8348 0.000 0.972 0.024 0.004
#> GSM751427 2 0.1297 0.8360 0.000 0.964 0.020 0.016
#> GSM751438 2 0.3372 0.7792 0.000 0.868 0.036 0.096
#> GSM751439 4 0.6500 0.1170 0.000 0.376 0.080 0.544
#> GSM751441 2 0.1022 0.8331 0.000 0.968 0.000 0.032
#> GSM751442 2 0.2101 0.8214 0.000 0.928 0.012 0.060
#> GSM751443 4 0.6362 0.2714 0.000 0.288 0.096 0.616
#> GSM751445 2 0.1545 0.8293 0.000 0.952 0.008 0.040
#> GSM751447 2 0.1305 0.8312 0.000 0.960 0.004 0.036
#> GSM751453 2 0.0804 0.8372 0.000 0.980 0.012 0.008
#> GSM751454 2 0.0804 0.8372 0.000 0.980 0.012 0.008
#> GSM751455 2 0.2335 0.8170 0.000 0.920 0.020 0.060
#> GSM751456 2 0.2623 0.8092 0.000 0.908 0.028 0.064
#> GSM751457 2 0.5712 0.5014 0.000 0.644 0.048 0.308
#> GSM751458 2 0.5646 0.5228 0.000 0.656 0.048 0.296
cbind(get_classes(res, k = 5), get_membership(res, k = 5))
#> class entropy silhouette p1 p2 p3 p4 p5
#> GSM751298 1 0.4086 0.5059 0.704 0.000 0.000 0.284 0.012
#> GSM751304 2 0.7701 0.1824 0.032 0.352 0.008 0.320 0.288
#> GSM751305 4 0.6736 0.0198 0.028 0.308 0.008 0.540 0.116
#> GSM751307 2 0.7429 0.3274 0.092 0.436 0.020 0.392 0.060
#> GSM751310 4 0.1502 0.7688 0.056 0.000 0.000 0.940 0.004
#> GSM751314 4 0.1430 0.7694 0.052 0.000 0.000 0.944 0.004
#> GSM751316 4 0.0865 0.7625 0.024 0.000 0.000 0.972 0.004
#> GSM751318 4 0.4070 0.6347 0.256 0.004 0.000 0.728 0.012
#> GSM751342 4 0.1041 0.7682 0.032 0.000 0.000 0.964 0.004
#> GSM751346 1 0.1571 0.7596 0.936 0.004 0.000 0.000 0.060
#> GSM751347 1 0.1043 0.7750 0.960 0.000 0.000 0.000 0.040
#> GSM751348 2 0.6661 0.3237 0.000 0.444 0.000 0.272 0.284
#> GSM751349 2 0.4805 0.6757 0.000 0.728 0.044 0.020 0.208
#> GSM751352 2 0.7129 0.3267 0.312 0.428 0.000 0.020 0.240
#> GSM751353 2 0.5506 0.6338 0.056 0.660 0.004 0.020 0.260
#> GSM751354 5 0.7873 0.1362 0.280 0.200 0.000 0.096 0.424
#> GSM751355 2 0.7682 0.3960 0.056 0.464 0.044 0.088 0.348
#> GSM751358 4 0.1830 0.7142 0.000 0.028 0.000 0.932 0.040
#> GSM751359 2 0.6157 0.5230 0.000 0.576 0.036 0.316 0.072
#> GSM751294 5 0.3846 0.4987 0.004 0.200 0.000 0.020 0.776
#> GSM751296 1 0.0880 0.7876 0.968 0.000 0.000 0.032 0.000
#> GSM751297 1 0.4807 0.3710 0.632 0.020 0.000 0.008 0.340
#> GSM751299 2 0.6821 0.3700 0.168 0.476 0.000 0.020 0.336
#> GSM751300 1 0.0992 0.7871 0.968 0.000 0.000 0.024 0.008
#> GSM751301 1 0.5419 0.1531 0.548 0.404 0.000 0.032 0.016
#> GSM751302 1 0.0963 0.7772 0.964 0.000 0.000 0.000 0.036
#> GSM751303 4 0.0865 0.7625 0.024 0.000 0.000 0.972 0.004
#> GSM751306 4 0.1041 0.7664 0.032 0.000 0.000 0.964 0.004
#> GSM751308 4 0.7534 0.2379 0.272 0.048 0.000 0.424 0.256
#> GSM751309 4 0.1124 0.7679 0.036 0.000 0.000 0.960 0.004
#> GSM751311 4 0.1282 0.7698 0.044 0.000 0.000 0.952 0.004
#> GSM751312 4 0.2660 0.6844 0.128 0.000 0.000 0.864 0.008
#> GSM751313 1 0.0963 0.7873 0.964 0.000 0.000 0.036 0.000
#> GSM751315 1 0.4151 0.4151 0.652 0.000 0.000 0.344 0.004
#> GSM751317 4 0.1357 0.7700 0.048 0.000 0.000 0.948 0.004
#> GSM751320 1 0.4473 0.2050 0.580 0.000 0.000 0.412 0.008
#> GSM751321 4 0.1357 0.7700 0.048 0.000 0.000 0.948 0.004
#> GSM751322 4 0.4086 0.6055 0.284 0.000 0.000 0.704 0.012
#> GSM751324 4 0.4016 0.6206 0.272 0.000 0.000 0.716 0.012
#> GSM751325 4 0.4109 0.5998 0.288 0.000 0.000 0.700 0.012
#> GSM751332 4 0.4288 0.5403 0.324 0.000 0.000 0.664 0.012
#> GSM751334 1 0.4527 0.2604 0.596 0.000 0.000 0.392 0.012
#> GSM751339 4 0.6641 0.1762 0.368 0.000 0.000 0.408 0.224
#> GSM751341 4 0.2304 0.7530 0.100 0.000 0.000 0.892 0.008
#> GSM751343 4 0.4109 0.5998 0.288 0.000 0.000 0.700 0.012
#> GSM751344 2 0.5379 0.6088 0.028 0.640 0.000 0.036 0.296
#> GSM751345 2 0.5486 0.6007 0.028 0.628 0.000 0.040 0.304
#> GSM751356 5 0.6639 -0.1033 0.008 0.340 0.000 0.180 0.472
#> GSM751357 2 0.6761 0.2804 0.008 0.412 0.000 0.192 0.388
#> GSM751293 1 0.6354 0.3030 0.528 0.316 0.000 0.148 0.008
#> GSM751295 1 0.1197 0.7707 0.952 0.000 0.000 0.000 0.048
#> GSM751319 4 0.2439 0.7487 0.120 0.000 0.000 0.876 0.004
#> GSM751323 1 0.3093 0.6809 0.824 0.000 0.000 0.168 0.008
#> GSM751326 1 0.1522 0.7817 0.944 0.000 0.000 0.044 0.012
#> GSM751327 1 0.4574 0.1729 0.576 0.000 0.000 0.412 0.012
#> GSM751328 4 0.4040 0.6164 0.276 0.000 0.000 0.712 0.012
#> GSM751329 1 0.1444 0.7835 0.948 0.000 0.000 0.040 0.012
#> GSM751330 1 0.0963 0.7873 0.964 0.000 0.000 0.036 0.000
#> GSM751331 1 0.0162 0.7786 0.996 0.000 0.000 0.004 0.000
#> GSM751333 1 0.0963 0.7873 0.964 0.000 0.000 0.036 0.000
#> GSM751335 1 0.0963 0.7873 0.964 0.000 0.000 0.036 0.000
#> GSM751336 1 0.0880 0.7876 0.968 0.000 0.000 0.032 0.000
#> GSM751337 1 0.1331 0.7845 0.952 0.000 0.000 0.040 0.008
#> GSM751338 1 0.3395 0.5871 0.764 0.000 0.000 0.236 0.000
#> GSM751340 5 0.6130 0.4282 0.236 0.000 0.040 0.096 0.628
#> GSM751350 1 0.0880 0.7790 0.968 0.000 0.000 0.000 0.032
#> GSM751351 1 0.0794 0.7805 0.972 0.000 0.000 0.000 0.028
#> GSM751362 3 0.3796 0.4998 0.000 0.000 0.700 0.000 0.300
#> GSM751363 3 0.4270 0.6569 0.000 0.040 0.764 0.188 0.008
#> GSM751367 1 0.7786 0.0153 0.400 0.000 0.072 0.224 0.304
#> GSM751368 3 0.2130 0.8014 0.000 0.080 0.908 0.000 0.012
#> GSM751371 4 0.6087 0.1931 0.000 0.004 0.124 0.540 0.332
#> GSM751375 2 0.4752 0.6679 0.000 0.724 0.036 0.020 0.220
#> GSM751376 5 0.1772 0.6553 0.000 0.020 0.032 0.008 0.940
#> GSM751378 5 0.6398 0.2501 0.004 0.336 0.100 0.020 0.540
#> GSM751379 5 0.2116 0.6679 0.000 0.004 0.076 0.008 0.912
#> GSM751382 2 0.5147 0.6642 0.000 0.716 0.068 0.024 0.192
#> GSM751386 3 0.4037 0.7107 0.000 0.152 0.796 0.012 0.040
#> GSM751388 3 0.3584 0.7482 0.000 0.112 0.836 0.012 0.040
#> GSM751391 5 0.5521 0.5784 0.000 0.008 0.136 0.184 0.672
#> GSM751410 5 0.6204 0.3039 0.004 0.000 0.124 0.384 0.488
#> GSM751414 3 0.1197 0.8098 0.000 0.000 0.952 0.000 0.048
#> GSM751361 3 0.1569 0.8106 0.000 0.044 0.944 0.004 0.008
#> GSM751365 3 0.0510 0.8167 0.000 0.000 0.984 0.000 0.016
#> GSM751366 3 0.1270 0.8069 0.000 0.000 0.948 0.000 0.052
#> GSM751369 5 0.4338 0.5258 0.000 0.000 0.280 0.024 0.696
#> GSM751370 3 0.0865 0.8171 0.000 0.000 0.972 0.004 0.024
#> GSM751372 3 0.0451 0.8176 0.000 0.000 0.988 0.004 0.008
#> GSM751373 3 0.0880 0.8142 0.000 0.000 0.968 0.000 0.032
#> GSM751374 5 0.2282 0.6612 0.012 0.008 0.048 0.012 0.920
#> GSM751377 3 0.1717 0.8076 0.000 0.052 0.936 0.004 0.008
#> GSM751380 3 0.4268 0.1154 0.000 0.000 0.556 0.000 0.444
#> GSM751381 3 0.5246 0.5931 0.000 0.216 0.696 0.020 0.068
#> GSM751383 3 0.3086 0.7673 0.000 0.092 0.864 0.004 0.040
#> GSM751384 3 0.1617 0.8132 0.000 0.020 0.948 0.012 0.020
#> GSM751385 3 0.3354 0.7336 0.000 0.024 0.832 0.004 0.140
#> GSM751387 3 0.4834 0.6104 0.000 0.224 0.716 0.016 0.044
#> GSM751389 5 0.4150 0.3769 0.000 0.000 0.388 0.000 0.612
#> GSM751393 3 0.1965 0.7887 0.000 0.000 0.904 0.000 0.096
#> GSM751394 3 0.4696 0.6818 0.000 0.144 0.760 0.016 0.080
#> GSM751395 5 0.5904 0.5226 0.028 0.128 0.048 0.080 0.716
#> GSM751397 3 0.4536 0.7105 0.000 0.092 0.784 0.024 0.100
#> GSM751398 3 0.3533 0.7513 0.000 0.108 0.840 0.012 0.040
#> GSM751404 3 0.2605 0.7296 0.000 0.000 0.852 0.000 0.148
#> GSM751406 5 0.4268 0.4484 0.008 0.000 0.344 0.000 0.648
#> GSM751411 3 0.0880 0.8127 0.000 0.000 0.968 0.000 0.032
#> GSM751413 3 0.4539 0.7499 0.028 0.076 0.812 0.048 0.036
#> GSM751415 3 0.4219 0.1977 0.000 0.000 0.584 0.000 0.416
#> GSM751416 3 0.1205 0.8138 0.000 0.040 0.956 0.004 0.000
#> GSM751417 3 0.1205 0.8138 0.000 0.040 0.956 0.004 0.000
#> GSM751421 5 0.4494 0.3869 0.000 0.000 0.380 0.012 0.608
#> GSM751422 5 0.4551 0.4097 0.000 0.000 0.368 0.016 0.616
#> GSM751360 3 0.4679 0.5958 0.000 0.000 0.716 0.216 0.068
#> GSM751364 3 0.0671 0.8173 0.000 0.016 0.980 0.004 0.000
#> GSM751390 3 0.1828 0.8081 0.000 0.028 0.936 0.004 0.032
#> GSM751392 2 0.6064 0.2699 0.000 0.516 0.384 0.012 0.088
#> GSM751396 2 0.5966 0.2268 0.020 0.520 0.404 0.004 0.052
#> GSM751399 3 0.1341 0.8055 0.000 0.000 0.944 0.000 0.056
#> GSM751400 3 0.1671 0.7938 0.000 0.000 0.924 0.000 0.076
#> GSM751401 3 0.3999 0.4035 0.000 0.000 0.656 0.000 0.344
#> GSM751402 5 0.4367 0.3065 0.004 0.000 0.416 0.000 0.580
#> GSM751403 3 0.3837 0.4824 0.000 0.000 0.692 0.000 0.308
#> GSM751405 5 0.4321 0.3614 0.004 0.000 0.396 0.000 0.600
#> GSM751407 3 0.1410 0.8036 0.000 0.000 0.940 0.000 0.060
#> GSM751408 3 0.1197 0.8085 0.000 0.000 0.952 0.000 0.048
#> GSM751409 3 0.3913 0.4551 0.000 0.000 0.676 0.000 0.324
#> GSM751412 3 0.1197 0.8085 0.000 0.000 0.952 0.000 0.048
#> GSM751418 3 0.0566 0.8184 0.000 0.004 0.984 0.000 0.012
#> GSM751419 3 0.0566 0.8184 0.000 0.004 0.984 0.000 0.012
#> GSM751420 5 0.3353 0.6066 0.008 0.000 0.196 0.000 0.796
#> GSM751425 2 0.2127 0.7416 0.000 0.892 0.000 0.000 0.108
#> GSM751429 5 0.3850 0.6226 0.088 0.080 0.004 0.004 0.824
#> GSM751430 2 0.6068 0.5570 0.028 0.664 0.220 0.032 0.056
#> GSM751433 2 0.4072 0.7146 0.028 0.832 0.032 0.088 0.020
#> GSM751437 5 0.2722 0.6233 0.008 0.120 0.004 0.000 0.868
#> GSM751448 5 0.2635 0.6524 0.012 0.064 0.020 0.004 0.900
#> GSM751451 2 0.4156 0.5139 0.000 0.700 0.004 0.288 0.008
#> GSM751423 2 0.0727 0.7532 0.000 0.980 0.004 0.004 0.012
#> GSM751424 2 0.3505 0.7326 0.028 0.868 0.044 0.016 0.044
#> GSM751428 2 0.2380 0.7482 0.028 0.920 0.028 0.012 0.012
#> GSM751431 2 0.1074 0.7514 0.000 0.968 0.016 0.012 0.004
#> GSM751432 2 0.3921 0.7211 0.028 0.844 0.064 0.016 0.048
#> GSM751434 2 0.4087 0.7251 0.028 0.840 0.048 0.036 0.048
#> GSM751435 2 0.0794 0.7511 0.000 0.972 0.000 0.000 0.028
#> GSM751436 2 0.3573 0.7323 0.028 0.864 0.040 0.016 0.052
#> GSM751440 2 0.1331 0.7526 0.000 0.952 0.008 0.000 0.040
#> GSM751444 2 0.1638 0.7475 0.000 0.932 0.000 0.004 0.064
#> GSM751446 2 0.1965 0.7328 0.000 0.904 0.000 0.000 0.096
#> GSM751449 2 0.1851 0.7345 0.000 0.912 0.000 0.000 0.088
#> GSM751450 2 0.0968 0.7525 0.000 0.972 0.012 0.012 0.004
#> GSM751452 2 0.3577 0.7317 0.028 0.864 0.044 0.016 0.048
#> GSM751426 2 0.2081 0.7465 0.012 0.932 0.032 0.012 0.012
#> GSM751427 2 0.1502 0.7460 0.000 0.940 0.004 0.000 0.056
#> GSM751438 2 0.3143 0.6636 0.000 0.796 0.000 0.000 0.204
#> GSM751439 5 0.4505 0.3717 0.012 0.384 0.000 0.000 0.604
#> GSM751441 2 0.2732 0.7112 0.000 0.840 0.000 0.000 0.160
#> GSM751442 2 0.1908 0.7339 0.000 0.908 0.000 0.000 0.092
#> GSM751443 5 0.3586 0.5822 0.020 0.188 0.000 0.000 0.792
#> GSM751445 2 0.1965 0.7357 0.000 0.904 0.000 0.000 0.096
#> GSM751447 2 0.2516 0.7203 0.000 0.860 0.000 0.000 0.140
#> GSM751453 2 0.0566 0.7531 0.000 0.984 0.004 0.000 0.012
#> GSM751454 2 0.0771 0.7527 0.000 0.976 0.004 0.000 0.020
#> GSM751455 2 0.1732 0.7370 0.000 0.920 0.000 0.000 0.080
#> GSM751456 2 0.1732 0.7370 0.000 0.920 0.000 0.000 0.080
#> GSM751457 5 0.4135 0.3394 0.004 0.340 0.000 0.000 0.656
#> GSM751458 5 0.4225 0.2819 0.004 0.364 0.000 0.000 0.632
cbind(get_classes(res, k = 6), get_membership(res, k = 6))
#> class entropy silhouette p1 p2 p3 p4 p5 p6
#> GSM751298 1 0.4343 0.3463 0.592 0.000 0.020 0.384 0.000 0.004
#> GSM751304 6 0.3876 0.5648 0.000 0.020 0.028 0.156 0.008 0.788
#> GSM751305 6 0.4144 0.5257 0.000 0.016 0.024 0.196 0.012 0.752
#> GSM751307 6 0.4358 0.5499 0.020 0.032 0.004 0.176 0.012 0.756
#> GSM751310 4 0.2695 0.6948 0.004 0.000 0.008 0.844 0.000 0.144
#> GSM751314 4 0.1194 0.7166 0.004 0.000 0.008 0.956 0.000 0.032
#> GSM751316 4 0.2920 0.6730 0.000 0.000 0.008 0.820 0.004 0.168
#> GSM751318 4 0.3019 0.6957 0.124 0.008 0.020 0.844 0.000 0.004
#> GSM751342 4 0.0767 0.7159 0.004 0.000 0.008 0.976 0.000 0.012
#> GSM751346 1 0.0291 0.9009 0.992 0.000 0.004 0.000 0.000 0.004
#> GSM751347 1 0.0146 0.9029 0.996 0.000 0.004 0.000 0.000 0.000
#> GSM751348 6 0.6156 0.4355 0.000 0.328 0.040 0.112 0.004 0.516
#> GSM751349 2 0.6551 -0.2443 0.000 0.396 0.036 0.000 0.196 0.372
#> GSM751352 6 0.4777 0.5816 0.240 0.080 0.004 0.000 0.004 0.672
#> GSM751353 6 0.4524 0.6045 0.028 0.164 0.032 0.000 0.024 0.752
#> GSM751354 6 0.3742 0.6413 0.052 0.016 0.040 0.060 0.000 0.832
#> GSM751355 6 0.4179 0.6474 0.040 0.032 0.028 0.060 0.020 0.820
#> GSM751358 4 0.3799 0.5406 0.000 0.000 0.020 0.704 0.000 0.276
#> GSM751359 6 0.7341 0.4340 0.000 0.132 0.012 0.200 0.192 0.464
#> GSM751294 6 0.5381 0.4600 0.000 0.152 0.280 0.000 0.000 0.568
#> GSM751296 1 0.0547 0.8977 0.980 0.000 0.000 0.020 0.000 0.000
#> GSM751297 1 0.4051 0.6225 0.756 0.004 0.076 0.000 0.000 0.164
#> GSM751299 6 0.5856 0.5575 0.128 0.204 0.056 0.000 0.000 0.612
#> GSM751300 1 0.0000 0.9052 1.000 0.000 0.000 0.000 0.000 0.000
#> GSM751301 6 0.7095 0.1381 0.328 0.076 0.008 0.176 0.000 0.412
#> GSM751302 1 0.0000 0.9052 1.000 0.000 0.000 0.000 0.000 0.000
#> GSM751303 4 0.2513 0.6918 0.000 0.000 0.008 0.852 0.000 0.140
#> GSM751306 4 0.2615 0.6965 0.004 0.000 0.008 0.852 0.000 0.136
#> GSM751308 4 0.7351 0.0512 0.156 0.012 0.108 0.388 0.000 0.336
#> GSM751309 4 0.2261 0.7074 0.004 0.000 0.008 0.884 0.000 0.104
#> GSM751311 4 0.2261 0.7070 0.004 0.000 0.008 0.884 0.000 0.104
#> GSM751312 4 0.5385 0.5536 0.136 0.000 0.016 0.644 0.004 0.200
#> GSM751313 1 0.0146 0.9038 0.996 0.000 0.000 0.004 0.000 0.000
#> GSM751315 1 0.3960 0.6070 0.736 0.000 0.008 0.224 0.000 0.032
#> GSM751317 4 0.2695 0.6941 0.004 0.000 0.008 0.844 0.000 0.144
#> GSM751320 4 0.4338 -0.0251 0.488 0.000 0.020 0.492 0.000 0.000
#> GSM751321 4 0.2726 0.6959 0.008 0.000 0.008 0.848 0.000 0.136
#> GSM751322 4 0.2932 0.6883 0.140 0.000 0.020 0.836 0.000 0.004
#> GSM751324 4 0.2851 0.6933 0.132 0.000 0.020 0.844 0.000 0.004
#> GSM751325 4 0.3010 0.6826 0.148 0.000 0.020 0.828 0.000 0.004
#> GSM751332 4 0.3296 0.6552 0.180 0.000 0.020 0.796 0.000 0.004
#> GSM751334 4 0.4463 0.0457 0.468 0.000 0.020 0.508 0.000 0.004
#> GSM751339 3 0.6322 -0.1403 0.292 0.000 0.360 0.340 0.000 0.008
#> GSM751341 4 0.0551 0.7160 0.004 0.000 0.004 0.984 0.000 0.008
#> GSM751343 4 0.3010 0.6826 0.148 0.000 0.020 0.828 0.000 0.004
#> GSM751344 6 0.3248 0.6161 0.000 0.116 0.052 0.000 0.004 0.828
#> GSM751345 6 0.3389 0.6181 0.000 0.116 0.052 0.004 0.004 0.824
#> GSM751356 6 0.4718 0.6011 0.000 0.172 0.088 0.024 0.000 0.716
#> GSM751357 6 0.4493 0.5972 0.000 0.192 0.044 0.036 0.000 0.728
#> GSM751293 4 0.6933 0.0573 0.316 0.040 0.004 0.344 0.000 0.296
#> GSM751295 1 0.0291 0.9009 0.992 0.000 0.004 0.000 0.000 0.004
#> GSM751319 4 0.3845 0.6999 0.084 0.000 0.008 0.788 0.000 0.120
#> GSM751323 1 0.3337 0.6387 0.736 0.000 0.004 0.260 0.000 0.000
#> GSM751326 1 0.2311 0.8346 0.880 0.000 0.016 0.104 0.000 0.000
#> GSM751327 4 0.4076 0.1722 0.452 0.000 0.008 0.540 0.000 0.000
#> GSM751328 4 0.2750 0.6937 0.136 0.000 0.020 0.844 0.000 0.000
#> GSM751329 1 0.2070 0.8406 0.892 0.000 0.008 0.100 0.000 0.000
#> GSM751330 1 0.0000 0.9052 1.000 0.000 0.000 0.000 0.000 0.000
#> GSM751331 1 0.0000 0.9052 1.000 0.000 0.000 0.000 0.000 0.000
#> GSM751333 1 0.0000 0.9052 1.000 0.000 0.000 0.000 0.000 0.000
#> GSM751335 1 0.0000 0.9052 1.000 0.000 0.000 0.000 0.000 0.000
#> GSM751336 1 0.0000 0.9052 1.000 0.000 0.000 0.000 0.000 0.000
#> GSM751337 1 0.2214 0.8423 0.888 0.000 0.016 0.096 0.000 0.000
#> GSM751338 1 0.2378 0.7657 0.848 0.000 0.000 0.152 0.000 0.000
#> GSM751340 3 0.5734 0.3980 0.208 0.000 0.596 0.024 0.000 0.172
#> GSM751350 1 0.0000 0.9052 1.000 0.000 0.000 0.000 0.000 0.000
#> GSM751351 1 0.0000 0.9052 1.000 0.000 0.000 0.000 0.000 0.000
#> GSM751362 3 0.3782 0.2940 0.000 0.000 0.588 0.000 0.412 0.000
#> GSM751363 5 0.4681 0.5988 0.000 0.000 0.036 0.128 0.736 0.100
#> GSM751367 3 0.6747 0.3530 0.292 0.000 0.512 0.112 0.028 0.056
#> GSM751368 5 0.2606 0.7257 0.000 0.044 0.048 0.000 0.888 0.020
#> GSM751371 4 0.5165 0.2430 0.000 0.000 0.380 0.552 0.036 0.032
#> GSM751375 6 0.5882 0.4453 0.000 0.272 0.036 0.000 0.124 0.568
#> GSM751376 3 0.4016 0.3767 0.000 0.020 0.684 0.004 0.000 0.292
#> GSM751378 6 0.7552 0.3702 0.000 0.236 0.232 0.000 0.176 0.356
#> GSM751379 3 0.3710 0.4807 0.000 0.004 0.740 0.008 0.008 0.240
#> GSM751382 2 0.6775 -0.2617 0.000 0.328 0.036 0.000 0.312 0.324
#> GSM751386 5 0.2560 0.6984 0.000 0.036 0.000 0.000 0.872 0.092
#> GSM751388 5 0.2058 0.7142 0.000 0.036 0.000 0.000 0.908 0.056
#> GSM751391 3 0.4817 0.5579 0.000 0.000 0.720 0.084 0.040 0.156
#> GSM751410 3 0.4559 0.5650 0.000 0.000 0.724 0.192 0.040 0.044
#> GSM751414 5 0.2697 0.6861 0.000 0.000 0.188 0.000 0.812 0.000
#> GSM751361 5 0.0405 0.7347 0.000 0.008 0.004 0.000 0.988 0.000
#> GSM751365 5 0.2092 0.7173 0.000 0.000 0.124 0.000 0.876 0.000
#> GSM751366 5 0.3288 0.5955 0.000 0.000 0.276 0.000 0.724 0.000
#> GSM751369 3 0.2994 0.6774 0.000 0.000 0.856 0.008 0.076 0.060
#> GSM751370 5 0.2092 0.7188 0.000 0.000 0.124 0.000 0.876 0.000
#> GSM751372 5 0.1765 0.7242 0.000 0.000 0.096 0.000 0.904 0.000
#> GSM751373 5 0.3043 0.6746 0.000 0.004 0.196 0.000 0.796 0.004
#> GSM751374 3 0.3903 0.3866 0.000 0.012 0.680 0.004 0.000 0.304
#> GSM751377 5 0.0508 0.7354 0.000 0.004 0.012 0.000 0.984 0.000
#> GSM751380 3 0.2941 0.6080 0.000 0.000 0.780 0.000 0.220 0.000
#> GSM751381 5 0.4201 0.5636 0.000 0.068 0.004 0.000 0.732 0.196
#> GSM751383 5 0.1408 0.7246 0.000 0.036 0.000 0.000 0.944 0.020
#> GSM751384 5 0.2647 0.7187 0.000 0.016 0.020 0.000 0.876 0.088
#> GSM751385 5 0.5453 0.1646 0.000 0.016 0.076 0.000 0.484 0.424
#> GSM751387 5 0.3971 0.5807 0.000 0.068 0.000 0.000 0.748 0.184
#> GSM751389 3 0.3459 0.6164 0.000 0.000 0.768 0.004 0.212 0.016
#> GSM751393 5 0.5290 0.4303 0.000 0.000 0.244 0.004 0.608 0.144
#> GSM751394 5 0.3727 0.6057 0.000 0.040 0.004 0.000 0.768 0.188
#> GSM751395 6 0.4339 0.5761 0.000 0.024 0.188 0.020 0.020 0.748
#> GSM751397 5 0.3525 0.6261 0.000 0.032 0.004 0.000 0.784 0.180
#> GSM751398 5 0.2106 0.7149 0.000 0.032 0.000 0.000 0.904 0.064
#> GSM751404 5 0.3857 0.1471 0.000 0.000 0.468 0.000 0.532 0.000
#> GSM751406 3 0.2100 0.6787 0.000 0.000 0.884 0.000 0.112 0.004
#> GSM751411 5 0.2178 0.7144 0.000 0.000 0.132 0.000 0.868 0.000
#> GSM751413 5 0.5044 0.3813 0.000 0.012 0.052 0.004 0.596 0.336
#> GSM751415 3 0.3547 0.4417 0.000 0.000 0.668 0.000 0.332 0.000
#> GSM751416 5 0.0790 0.7361 0.000 0.000 0.032 0.000 0.968 0.000
#> GSM751417 5 0.0713 0.7362 0.000 0.000 0.028 0.000 0.972 0.000
#> GSM751421 3 0.2961 0.6744 0.000 0.000 0.840 0.008 0.132 0.020
#> GSM751422 3 0.3219 0.6757 0.000 0.000 0.828 0.012 0.132 0.028
#> GSM751360 5 0.6512 0.1276 0.000 0.000 0.212 0.324 0.432 0.032
#> GSM751364 5 0.1075 0.7348 0.000 0.000 0.048 0.000 0.952 0.000
#> GSM751390 5 0.2364 0.7134 0.000 0.032 0.004 0.000 0.892 0.072
#> GSM751392 5 0.5881 0.1496 0.000 0.232 0.008 0.000 0.528 0.232
#> GSM751396 5 0.5823 0.3226 0.000 0.244 0.020 0.000 0.568 0.168
#> GSM751399 5 0.3221 0.6117 0.000 0.000 0.264 0.000 0.736 0.000
#> GSM751400 5 0.3850 0.4582 0.000 0.004 0.340 0.000 0.652 0.004
#> GSM751401 3 0.3756 0.3164 0.000 0.000 0.600 0.000 0.400 0.000
#> GSM751402 3 0.2527 0.6583 0.000 0.000 0.832 0.000 0.168 0.000
#> GSM751403 3 0.3804 0.2416 0.000 0.000 0.576 0.000 0.424 0.000
#> GSM751405 3 0.2520 0.6684 0.000 0.000 0.844 0.000 0.152 0.004
#> GSM751407 5 0.3721 0.5249 0.000 0.004 0.308 0.000 0.684 0.004
#> GSM751408 5 0.3426 0.5880 0.000 0.004 0.276 0.000 0.720 0.000
#> GSM751409 3 0.3101 0.5802 0.000 0.000 0.756 0.000 0.244 0.000
#> GSM751412 5 0.3136 0.6410 0.000 0.004 0.228 0.000 0.768 0.000
#> GSM751418 5 0.2442 0.7076 0.000 0.004 0.144 0.000 0.852 0.000
#> GSM751419 5 0.2558 0.6999 0.000 0.004 0.156 0.000 0.840 0.000
#> GSM751420 3 0.2138 0.6681 0.000 0.004 0.908 0.000 0.052 0.036
#> GSM751425 2 0.2479 0.7076 0.000 0.892 0.028 0.000 0.016 0.064
#> GSM751429 3 0.5793 0.4044 0.164 0.100 0.648 0.004 0.000 0.084
#> GSM751430 6 0.6419 0.0879 0.000 0.312 0.016 0.000 0.272 0.400
#> GSM751433 2 0.5941 0.4967 0.000 0.608 0.016 0.104 0.036 0.236
#> GSM751437 3 0.3834 0.4490 0.000 0.232 0.732 0.000 0.000 0.036
#> GSM751448 3 0.2527 0.6080 0.004 0.064 0.884 0.000 0.000 0.048
#> GSM751451 2 0.3441 0.5844 0.000 0.768 0.004 0.216 0.008 0.004
#> GSM751423 2 0.1176 0.7312 0.000 0.956 0.000 0.000 0.024 0.020
#> GSM751424 2 0.4725 0.5249 0.000 0.648 0.000 0.000 0.088 0.264
#> GSM751428 2 0.3705 0.6093 0.000 0.740 0.004 0.000 0.020 0.236
#> GSM751431 2 0.2968 0.6851 0.000 0.840 0.004 0.000 0.028 0.128
#> GSM751432 2 0.5657 0.3887 0.000 0.552 0.012 0.000 0.136 0.300
#> GSM751434 2 0.5141 0.4785 0.000 0.608 0.004 0.008 0.076 0.304
#> GSM751435 2 0.0767 0.7367 0.000 0.976 0.004 0.000 0.008 0.012
#> GSM751436 2 0.5358 0.5053 0.000 0.624 0.008 0.016 0.084 0.268
#> GSM751440 2 0.1465 0.7326 0.000 0.948 0.004 0.024 0.004 0.020
#> GSM751444 2 0.2030 0.7323 0.000 0.908 0.028 0.000 0.000 0.064
#> GSM751446 2 0.1500 0.7311 0.000 0.936 0.052 0.000 0.000 0.012
#> GSM751449 2 0.1528 0.7298 0.000 0.936 0.048 0.000 0.000 0.016
#> GSM751450 2 0.2892 0.6867 0.000 0.840 0.000 0.004 0.020 0.136
#> GSM751452 2 0.4963 0.4824 0.000 0.612 0.000 0.000 0.100 0.288
#> GSM751426 2 0.3618 0.6373 0.000 0.768 0.000 0.000 0.040 0.192
#> GSM751427 2 0.0820 0.7347 0.000 0.972 0.012 0.000 0.000 0.016
#> GSM751438 2 0.2672 0.6925 0.000 0.868 0.080 0.000 0.000 0.052
#> GSM751439 2 0.3922 0.4506 0.000 0.664 0.320 0.000 0.000 0.016
#> GSM751441 2 0.2563 0.6940 0.000 0.876 0.052 0.000 0.000 0.072
#> GSM751442 2 0.1320 0.7321 0.000 0.948 0.036 0.000 0.000 0.016
#> GSM751443 3 0.4492 0.2866 0.004 0.340 0.620 0.000 0.000 0.036
#> GSM751445 2 0.1713 0.7295 0.000 0.928 0.044 0.000 0.000 0.028
#> GSM751447 2 0.2129 0.7143 0.000 0.904 0.056 0.000 0.000 0.040
#> GSM751453 2 0.1408 0.7286 0.000 0.944 0.000 0.000 0.020 0.036
#> GSM751454 2 0.1003 0.7330 0.000 0.964 0.000 0.000 0.016 0.020
#> GSM751455 2 0.1528 0.7299 0.000 0.936 0.048 0.000 0.000 0.016
#> GSM751456 2 0.1391 0.7313 0.000 0.944 0.040 0.000 0.000 0.016
#> GSM751457 2 0.5048 0.3881 0.000 0.612 0.272 0.000 0.000 0.116
#> GSM751458 2 0.4913 0.4280 0.000 0.636 0.252 0.000 0.000 0.112
Heatmaps for the consensus matrix. It visualizes the probability of two samples to be in a same group.
consensus_heatmap(res, k = 2)
consensus_heatmap(res, k = 3)
consensus_heatmap(res, k = 4)
consensus_heatmap(res, k = 5)
consensus_heatmap(res, k = 6)
Heatmaps for the membership of samples in all partitions to see how consistent they are:
membership_heatmap(res, k = 2)
membership_heatmap(res, k = 3)
membership_heatmap(res, k = 4)
membership_heatmap(res, k = 5)
membership_heatmap(res, k = 6)
As soon as we have had the classes for columns, we can look for signatures which are significantly different between classes which can be candidate marks for certain classes. Following are the heatmaps for signatures.
Signature heatmaps where rows are scaled:
get_signatures(res, k = 2)
get_signatures(res, k = 3)
get_signatures(res, k = 4)
get_signatures(res, k = 5)
get_signatures(res, k = 6)
Signature heatmaps where rows are not scaled:
get_signatures(res, k = 2, scale_rows = FALSE)
get_signatures(res, k = 3, scale_rows = FALSE)
get_signatures(res, k = 4, scale_rows = FALSE)
get_signatures(res, k = 5, scale_rows = FALSE)
get_signatures(res, k = 6, scale_rows = FALSE)
Compare the overlap of signatures from different k:
compare_signatures(res)
get_signature() returns a data frame invisibly. TO get the list of signatures, the function
call should be assigned to a variable explicitly. In following code, if plot argument is set
to FALSE, no heatmap is plotted while only the differential analysis is performed.
# code only for demonstration
tb = get_signature(res, k = ..., plot = FALSE)
An example of the output of tb is:
#> which_row fdr mean_1 mean_2 scaled_mean_1 scaled_mean_2 km
#> 1 38 0.042760348 8.373488 9.131774 -0.5533452 0.5164555 1
#> 2 40 0.018707592 7.106213 8.469186 -0.6173731 0.5762149 1
#> 3 55 0.019134737 10.221463 11.207825 -0.6159697 0.5749050 1
#> 4 59 0.006059896 5.921854 7.869574 -0.6899429 0.6439467 1
#> 5 60 0.018055526 8.928898 10.211722 -0.6204761 0.5791110 1
#> 6 98 0.009384629 15.714769 14.887706 0.6635654 -0.6193277 2
...
The columns in tb are:
which_row: row indices corresponding to the input matrix.fdr: FDR for the differential test. mean_x: The mean value in group x.scaled_mean_x: The mean value in group x after rows are scaled.km: Row groups if k-means clustering is applied to rows.UMAP plot which shows how samples are separated.
dimension_reduction(res, k = 2, method = "UMAP")
dimension_reduction(res, k = 3, method = "UMAP")
dimension_reduction(res, k = 4, method = "UMAP")
dimension_reduction(res, k = 5, method = "UMAP")
dimension_reduction(res, k = 6, method = "UMAP")
Following heatmap shows how subgroups are split when increasing k:
collect_classes(res)
Test correlation between subgroups and known annotations. If the known annotation is numeric, one-way ANOVA test is applied, and if the known annotation is discrete, chi-squared contingency table test is applied.
test_to_known_factors(res)
#> n tissue(p) disease.state(p) agent(p) k
#> SD:NMF 159 3.05e-23 0.7401 0.85578 2
#> SD:NMF 130 1.33e-34 0.2005 0.44938 3
#> SD:NMF 114 4.55e-34 0.3791 0.25153 4
#> SD:NMF 124 1.55e-37 0.0630 0.00196 5
#> SD:NMF 122 3.01e-44 0.0171 0.00109 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 4537 rows and 166 columns.
#> Top rows (454, 908, 1361, 1814, 2268) 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 0.0563 0.707 0.792 0.3165 0.845 0.845
#> 3 3 0.1053 0.553 0.693 0.6366 0.648 0.584
#> 4 4 0.1627 0.513 0.655 0.1790 0.906 0.833
#> 5 5 0.1893 0.149 0.553 0.0885 0.939 0.888
#> 6 6 0.2656 0.303 0.554 0.0769 0.802 0.598
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
#> GSM751298 2 0.615 0.775 0.152 0.848
#> GSM751304 1 0.767 0.830 0.776 0.224
#> GSM751305 1 0.767 0.830 0.776 0.224
#> GSM751307 1 0.866 0.861 0.712 0.288
#> GSM751310 2 0.552 0.742 0.128 0.872
#> GSM751314 2 0.469 0.746 0.100 0.900
#> GSM751316 2 0.574 0.736 0.136 0.864
#> GSM751318 2 0.494 0.761 0.108 0.892
#> GSM751342 2 0.552 0.754 0.128 0.872
#> GSM751346 2 0.563 0.749 0.132 0.868
#> GSM751347 2 0.563 0.748 0.132 0.868
#> GSM751348 2 0.855 0.666 0.280 0.720
#> GSM751349 2 0.855 0.666 0.280 0.720
#> GSM751352 1 0.881 0.819 0.700 0.300
#> GSM751353 1 0.881 0.819 0.700 0.300
#> GSM751354 1 0.760 0.829 0.780 0.220
#> GSM751355 1 0.760 0.829 0.780 0.220
#> GSM751358 2 0.891 0.647 0.308 0.692
#> GSM751359 2 0.891 0.647 0.308 0.692
#> GSM751294 2 0.866 0.667 0.288 0.712
#> GSM751296 2 0.625 0.775 0.156 0.844
#> GSM751297 2 0.584 0.748 0.140 0.860
#> GSM751299 2 0.917 0.579 0.332 0.668
#> GSM751300 2 0.584 0.754 0.140 0.860
#> GSM751301 1 0.895 0.865 0.688 0.312
#> GSM751302 2 0.552 0.752 0.128 0.872
#> GSM751303 2 0.494 0.738 0.108 0.892
#> GSM751306 2 0.494 0.738 0.108 0.892
#> GSM751308 2 0.680 0.748 0.180 0.820
#> GSM751309 2 0.482 0.739 0.104 0.896
#> GSM751311 2 0.482 0.739 0.104 0.896
#> GSM751312 2 0.574 0.736 0.136 0.864
#> GSM751313 2 0.482 0.757 0.104 0.896
#> GSM751315 2 0.552 0.742 0.128 0.872
#> GSM751317 2 0.552 0.745 0.128 0.872
#> GSM751320 2 0.416 0.767 0.084 0.916
#> GSM751321 2 0.584 0.733 0.140 0.860
#> GSM751322 2 0.402 0.767 0.080 0.920
#> GSM751324 2 0.430 0.769 0.088 0.912
#> GSM751325 2 0.416 0.769 0.084 0.916
#> GSM751332 2 0.430 0.766 0.088 0.912
#> GSM751334 2 0.430 0.766 0.088 0.912
#> GSM751339 2 0.506 0.769 0.112 0.888
#> GSM751341 2 0.552 0.754 0.128 0.872
#> GSM751343 2 0.482 0.762 0.104 0.896
#> GSM751344 1 0.891 0.867 0.692 0.308
#> GSM751345 1 0.891 0.867 0.692 0.308
#> GSM751356 2 0.917 0.587 0.332 0.668
#> GSM751357 2 0.917 0.587 0.332 0.668
#> GSM751293 1 0.895 0.865 0.688 0.312
#> GSM751295 2 0.552 0.752 0.128 0.872
#> GSM751319 2 0.563 0.739 0.132 0.868
#> GSM751323 2 0.402 0.768 0.080 0.920
#> GSM751326 2 0.430 0.768 0.088 0.912
#> GSM751327 2 0.456 0.769 0.096 0.904
#> GSM751328 2 0.469 0.764 0.100 0.900
#> GSM751329 2 0.584 0.770 0.140 0.860
#> GSM751330 2 0.529 0.752 0.120 0.880
#> GSM751331 2 0.541 0.749 0.124 0.876
#> GSM751333 2 0.541 0.749 0.124 0.876
#> GSM751335 2 0.529 0.752 0.120 0.880
#> GSM751336 2 0.541 0.749 0.124 0.876
#> GSM751337 2 0.506 0.769 0.112 0.888
#> GSM751338 2 0.506 0.769 0.112 0.888
#> GSM751340 2 0.861 0.672 0.284 0.716
#> GSM751350 2 0.552 0.752 0.128 0.872
#> GSM751351 2 0.552 0.752 0.128 0.872
#> GSM751362 2 0.541 0.759 0.124 0.876
#> GSM751363 2 0.706 0.728 0.192 0.808
#> GSM751367 2 0.662 0.727 0.172 0.828
#> GSM751368 2 0.563 0.769 0.132 0.868
#> GSM751371 2 0.584 0.753 0.140 0.860
#> GSM751375 2 0.855 0.665 0.280 0.720
#> GSM751376 2 0.978 0.110 0.412 0.588
#> GSM751378 2 0.850 0.686 0.276 0.724
#> GSM751379 2 0.978 0.110 0.412 0.588
#> GSM751382 2 0.866 0.658 0.288 0.712
#> GSM751386 2 0.839 0.688 0.268 0.732
#> GSM751388 2 0.839 0.687 0.268 0.732
#> GSM751391 2 0.662 0.760 0.172 0.828
#> GSM751410 2 0.595 0.732 0.144 0.856
#> GSM751414 2 0.518 0.771 0.116 0.884
#> GSM751361 2 0.625 0.770 0.156 0.844
#> GSM751365 2 0.518 0.770 0.116 0.884
#> GSM751366 2 0.529 0.768 0.120 0.880
#> GSM751369 2 0.574 0.757 0.136 0.864
#> GSM751370 2 0.541 0.759 0.124 0.876
#> GSM751372 2 0.494 0.769 0.108 0.892
#> GSM751373 2 0.469 0.769 0.100 0.900
#> GSM751374 2 0.978 0.110 0.412 0.588
#> GSM751377 2 0.644 0.760 0.164 0.836
#> GSM751380 2 0.529 0.759 0.120 0.880
#> GSM751381 2 0.855 0.667 0.280 0.720
#> GSM751383 2 0.788 0.725 0.236 0.764
#> GSM751384 2 0.844 0.669 0.272 0.728
#> GSM751385 2 0.871 0.700 0.292 0.708
#> GSM751387 2 0.861 0.658 0.284 0.716
#> GSM751389 2 0.574 0.759 0.136 0.864
#> GSM751393 2 0.978 0.112 0.412 0.588
#> GSM751394 2 0.855 0.661 0.280 0.720
#> GSM751395 2 0.978 0.112 0.412 0.588
#> GSM751397 2 0.855 0.661 0.280 0.720
#> GSM751398 2 0.821 0.703 0.256 0.744
#> GSM751404 2 0.518 0.763 0.116 0.884
#> GSM751406 2 0.714 0.721 0.196 0.804
#> GSM751411 2 0.671 0.776 0.176 0.824
#> GSM751413 2 0.595 0.748 0.144 0.856
#> GSM751415 2 0.584 0.753 0.140 0.860
#> GSM751416 2 0.625 0.765 0.156 0.844
#> GSM751417 2 0.625 0.765 0.156 0.844
#> GSM751421 2 0.584 0.753 0.140 0.860
#> GSM751422 2 0.584 0.753 0.140 0.860
#> GSM751360 2 0.541 0.760 0.124 0.876
#> GSM751364 2 0.625 0.767 0.156 0.844
#> GSM751390 2 0.844 0.669 0.272 0.728
#> GSM751392 2 0.861 0.661 0.284 0.716
#> GSM751396 2 0.861 0.663 0.284 0.716
#> GSM751399 2 0.625 0.760 0.156 0.844
#> GSM751400 2 0.722 0.721 0.200 0.800
#> GSM751401 2 0.722 0.721 0.200 0.800
#> GSM751402 2 0.722 0.721 0.200 0.800
#> GSM751403 2 0.680 0.740 0.180 0.820
#> GSM751405 2 0.714 0.721 0.196 0.804
#> GSM751407 2 0.722 0.721 0.200 0.800
#> GSM751408 2 0.584 0.757 0.140 0.860
#> GSM751409 2 0.680 0.761 0.180 0.820
#> GSM751412 2 0.584 0.757 0.140 0.860
#> GSM751418 2 0.469 0.772 0.100 0.900
#> GSM751419 2 0.469 0.772 0.100 0.900
#> GSM751420 2 0.767 0.716 0.224 0.776
#> GSM751425 2 0.904 0.620 0.320 0.680
#> GSM751429 2 0.745 0.696 0.212 0.788
#> GSM751430 1 0.981 0.675 0.580 0.420
#> GSM751433 2 0.866 0.647 0.288 0.712
#> GSM751437 2 0.827 0.663 0.260 0.740
#> GSM751448 2 0.775 0.676 0.228 0.772
#> GSM751451 2 0.866 0.647 0.288 0.712
#> GSM751423 2 0.839 0.708 0.268 0.732
#> GSM751424 2 0.925 0.506 0.340 0.660
#> GSM751428 2 0.844 0.703 0.272 0.728
#> GSM751431 2 0.866 0.647 0.288 0.712
#> GSM751432 1 0.981 0.675 0.580 0.420
#> GSM751434 1 0.981 0.675 0.580 0.420
#> GSM751435 2 0.745 0.748 0.212 0.788
#> GSM751436 2 0.866 0.647 0.288 0.712
#> GSM751440 2 0.753 0.746 0.216 0.784
#> GSM751444 2 0.895 0.643 0.312 0.688
#> GSM751446 2 0.760 0.745 0.220 0.780
#> GSM751449 2 0.917 0.630 0.332 0.668
#> GSM751450 2 0.844 0.703 0.272 0.728
#> GSM751452 2 0.925 0.506 0.340 0.660
#> GSM751426 2 0.871 0.646 0.292 0.708
#> GSM751427 2 0.844 0.703 0.272 0.728
#> GSM751438 2 0.895 0.646 0.312 0.688
#> GSM751439 2 0.788 0.740 0.236 0.764
#> GSM751441 2 0.900 0.629 0.316 0.684
#> GSM751442 2 0.814 0.732 0.252 0.748
#> GSM751443 2 0.775 0.683 0.228 0.772
#> GSM751445 2 0.917 0.630 0.332 0.668
#> GSM751447 2 0.900 0.629 0.316 0.684
#> GSM751453 2 0.900 0.629 0.316 0.684
#> GSM751454 2 0.900 0.629 0.316 0.684
#> GSM751455 2 0.814 0.732 0.252 0.748
#> GSM751456 2 0.814 0.732 0.252 0.748
#> GSM751457 2 0.909 0.628 0.324 0.676
#> GSM751458 2 0.909 0.628 0.324 0.676
cbind(get_classes(res, k = 3), get_membership(res, k = 3))
#> class entropy silhouette p1 p2 p3
#> GSM751298 3 0.668 0.4760 0.024 0.324 0.652
#> GSM751304 1 0.298 0.8322 0.920 0.024 0.056
#> GSM751305 1 0.298 0.8322 0.920 0.024 0.056
#> GSM751307 1 0.499 0.8536 0.836 0.112 0.052
#> GSM751310 3 0.611 0.5997 0.048 0.192 0.760
#> GSM751314 3 0.644 0.5974 0.048 0.220 0.732
#> GSM751316 3 0.626 0.5915 0.052 0.196 0.752
#> GSM751318 3 0.658 0.3632 0.012 0.380 0.608
#> GSM751342 3 0.685 0.4070 0.020 0.380 0.600
#> GSM751346 3 0.441 0.6076 0.016 0.140 0.844
#> GSM751347 3 0.420 0.6071 0.012 0.136 0.852
#> GSM751348 2 0.573 0.7425 0.024 0.760 0.216
#> GSM751349 2 0.573 0.7425 0.024 0.760 0.216
#> GSM751352 1 0.687 0.7918 0.724 0.196 0.080
#> GSM751353 1 0.687 0.7918 0.724 0.196 0.080
#> GSM751354 1 0.301 0.8315 0.920 0.028 0.052
#> GSM751355 1 0.301 0.8315 0.920 0.028 0.052
#> GSM751358 2 0.668 0.6380 0.048 0.708 0.244
#> GSM751359 2 0.668 0.6380 0.048 0.708 0.244
#> GSM751294 3 0.898 -0.3534 0.128 0.432 0.440
#> GSM751296 3 0.596 0.5399 0.016 0.264 0.720
#> GSM751297 3 0.454 0.6090 0.016 0.148 0.836
#> GSM751299 2 0.951 0.3589 0.188 0.428 0.384
#> GSM751300 3 0.487 0.6085 0.024 0.152 0.824
#> GSM751301 1 0.559 0.8582 0.808 0.124 0.068
#> GSM751302 3 0.426 0.6088 0.012 0.140 0.848
#> GSM751303 3 0.632 0.5952 0.040 0.228 0.732
#> GSM751306 3 0.632 0.5952 0.040 0.228 0.732
#> GSM751308 3 0.796 0.1720 0.064 0.392 0.544
#> GSM751309 3 0.644 0.5919 0.040 0.240 0.720
#> GSM751311 3 0.644 0.5919 0.040 0.240 0.720
#> GSM751312 3 0.626 0.5915 0.052 0.196 0.752
#> GSM751313 3 0.312 0.6378 0.000 0.108 0.892
#> GSM751315 3 0.611 0.5967 0.048 0.192 0.760
#> GSM751317 3 0.630 0.5970 0.048 0.208 0.744
#> GSM751320 3 0.586 0.6112 0.024 0.228 0.748
#> GSM751321 3 0.621 0.5912 0.048 0.200 0.752
#> GSM751322 3 0.594 0.6099 0.028 0.224 0.748
#> GSM751324 3 0.650 0.5169 0.020 0.316 0.664
#> GSM751325 3 0.617 0.5231 0.012 0.308 0.680
#> GSM751332 3 0.628 0.4412 0.012 0.324 0.664
#> GSM751334 3 0.628 0.4412 0.012 0.324 0.664
#> GSM751339 3 0.525 0.6116 0.020 0.188 0.792
#> GSM751341 3 0.681 0.4251 0.020 0.372 0.608
#> GSM751343 3 0.642 0.3819 0.008 0.376 0.616
#> GSM751344 1 0.550 0.8589 0.812 0.124 0.064
#> GSM751345 1 0.550 0.8589 0.812 0.124 0.064
#> GSM751356 2 0.943 0.3504 0.176 0.424 0.400
#> GSM751357 2 0.943 0.3504 0.176 0.424 0.400
#> GSM751293 1 0.559 0.8582 0.808 0.124 0.068
#> GSM751295 3 0.426 0.6088 0.012 0.140 0.848
#> GSM751319 3 0.621 0.5946 0.052 0.192 0.756
#> GSM751323 3 0.618 0.5897 0.024 0.260 0.716
#> GSM751326 3 0.617 0.4595 0.012 0.308 0.680
#> GSM751327 3 0.631 0.4623 0.012 0.328 0.660
#> GSM751328 3 0.652 0.4377 0.016 0.340 0.644
#> GSM751329 3 0.546 0.6095 0.020 0.204 0.776
#> GSM751330 3 0.406 0.6150 0.012 0.128 0.860
#> GSM751331 3 0.392 0.6129 0.012 0.120 0.868
#> GSM751333 3 0.392 0.6145 0.012 0.120 0.868
#> GSM751335 3 0.406 0.6150 0.012 0.128 0.860
#> GSM751336 3 0.392 0.6129 0.012 0.120 0.868
#> GSM751337 3 0.525 0.6116 0.020 0.188 0.792
#> GSM751338 3 0.525 0.6116 0.020 0.188 0.792
#> GSM751340 3 0.903 -0.3407 0.132 0.428 0.440
#> GSM751350 3 0.426 0.6088 0.012 0.140 0.848
#> GSM751351 3 0.426 0.6088 0.012 0.140 0.848
#> GSM751362 3 0.455 0.6370 0.024 0.132 0.844
#> GSM751363 3 0.780 0.5651 0.112 0.228 0.660
#> GSM751367 3 0.547 0.6014 0.040 0.160 0.800
#> GSM751368 3 0.733 0.3683 0.040 0.364 0.596
#> GSM751371 3 0.653 0.5926 0.036 0.260 0.704
#> GSM751375 2 0.560 0.7425 0.020 0.764 0.216
#> GSM751376 3 0.915 0.1332 0.384 0.148 0.468
#> GSM751378 2 0.593 0.7112 0.008 0.696 0.296
#> GSM751379 3 0.915 0.1332 0.384 0.148 0.468
#> GSM751382 2 0.555 0.7417 0.020 0.768 0.212
#> GSM751386 2 0.632 0.7185 0.024 0.700 0.276
#> GSM751388 2 0.603 0.7238 0.016 0.712 0.272
#> GSM751391 3 0.764 0.4700 0.056 0.352 0.592
#> GSM751410 3 0.445 0.6407 0.032 0.112 0.856
#> GSM751414 3 0.607 0.5834 0.028 0.236 0.736
#> GSM751361 3 0.729 0.3800 0.040 0.356 0.604
#> GSM751365 3 0.558 0.6178 0.036 0.176 0.788
#> GSM751366 3 0.619 0.5956 0.040 0.216 0.744
#> GSM751369 3 0.639 0.6287 0.048 0.216 0.736
#> GSM751370 3 0.455 0.6370 0.024 0.132 0.844
#> GSM751372 3 0.530 0.6295 0.036 0.156 0.808
#> GSM751373 3 0.599 0.6042 0.036 0.208 0.756
#> GSM751374 3 0.915 0.1332 0.384 0.148 0.468
#> GSM751377 3 0.715 0.0652 0.024 0.444 0.532
#> GSM751380 3 0.606 0.6162 0.048 0.188 0.764
#> GSM751381 2 0.558 0.7418 0.012 0.748 0.240
#> GSM751383 2 0.647 0.5270 0.008 0.604 0.388
#> GSM751384 2 0.554 0.7421 0.008 0.740 0.252
#> GSM751385 2 0.718 0.5276 0.032 0.592 0.376
#> GSM751387 2 0.577 0.7444 0.020 0.748 0.232
#> GSM751389 3 0.585 0.6059 0.040 0.188 0.772
#> GSM751393 3 0.923 0.1195 0.384 0.156 0.460
#> GSM751394 2 0.564 0.7406 0.016 0.752 0.232
#> GSM751395 3 0.923 0.1195 0.384 0.156 0.460
#> GSM751397 2 0.582 0.7444 0.020 0.744 0.236
#> GSM751398 2 0.634 0.6815 0.016 0.672 0.312
#> GSM751404 3 0.629 0.5869 0.044 0.216 0.740
#> GSM751406 3 0.579 0.5956 0.060 0.148 0.792
#> GSM751411 3 0.682 0.3518 0.024 0.348 0.628
#> GSM751413 3 0.706 0.6105 0.076 0.220 0.704
#> GSM751415 3 0.580 0.6016 0.040 0.184 0.776
#> GSM751416 3 0.708 0.3462 0.032 0.356 0.612
#> GSM751417 3 0.708 0.3462 0.032 0.356 0.612
#> GSM751421 3 0.653 0.5926 0.036 0.260 0.704
#> GSM751422 3 0.653 0.5926 0.036 0.260 0.704
#> GSM751360 3 0.652 0.6208 0.048 0.228 0.724
#> GSM751364 3 0.704 0.3592 0.032 0.348 0.620
#> GSM751390 2 0.554 0.7421 0.008 0.740 0.252
#> GSM751392 2 0.560 0.7430 0.020 0.764 0.216
#> GSM751396 2 0.564 0.7451 0.020 0.760 0.220
#> GSM751399 3 0.676 0.5320 0.048 0.252 0.700
#> GSM751400 3 0.585 0.5925 0.060 0.152 0.788
#> GSM751401 3 0.579 0.5950 0.060 0.148 0.792
#> GSM751402 3 0.585 0.5925 0.060 0.152 0.788
#> GSM751403 3 0.572 0.6070 0.052 0.156 0.792
#> GSM751405 3 0.579 0.5956 0.060 0.148 0.792
#> GSM751407 3 0.579 0.5950 0.060 0.148 0.792
#> GSM751408 3 0.658 0.5789 0.052 0.224 0.724
#> GSM751409 3 0.723 0.4763 0.048 0.312 0.640
#> GSM751412 3 0.658 0.5789 0.052 0.224 0.724
#> GSM751418 3 0.600 0.6025 0.040 0.200 0.760
#> GSM751419 3 0.600 0.6025 0.040 0.200 0.760
#> GSM751420 3 0.659 0.5817 0.076 0.180 0.744
#> GSM751425 2 0.554 0.6992 0.024 0.776 0.200
#> GSM751429 3 0.650 0.5148 0.056 0.208 0.736
#> GSM751430 1 0.830 0.6241 0.632 0.172 0.196
#> GSM751433 2 0.766 0.6761 0.064 0.612 0.324
#> GSM751437 3 0.699 0.4544 0.056 0.256 0.688
#> GSM751448 3 0.638 0.5396 0.076 0.164 0.760
#> GSM751451 2 0.764 0.6797 0.064 0.616 0.320
#> GSM751423 2 0.781 0.4563 0.052 0.516 0.432
#> GSM751424 2 0.959 0.5021 0.244 0.476 0.280
#> GSM751428 2 0.788 0.4659 0.056 0.516 0.428
#> GSM751431 2 0.764 0.6772 0.064 0.616 0.320
#> GSM751432 1 0.830 0.6241 0.632 0.172 0.196
#> GSM751434 1 0.830 0.6241 0.632 0.172 0.196
#> GSM751435 3 0.708 0.1271 0.028 0.380 0.592
#> GSM751436 2 0.766 0.6761 0.064 0.612 0.324
#> GSM751440 3 0.725 0.1303 0.036 0.368 0.596
#> GSM751444 2 0.795 0.6838 0.084 0.608 0.308
#> GSM751446 3 0.742 0.1045 0.040 0.388 0.572
#> GSM751449 2 0.786 0.6973 0.088 0.628 0.284
#> GSM751450 2 0.790 0.4537 0.056 0.508 0.436
#> GSM751452 2 0.959 0.5021 0.244 0.476 0.280
#> GSM751426 2 0.783 0.6820 0.076 0.612 0.312
#> GSM751427 2 0.788 0.4659 0.056 0.516 0.428
#> GSM751438 2 0.653 0.6921 0.036 0.704 0.260
#> GSM751439 3 0.762 0.1077 0.048 0.392 0.560
#> GSM751441 2 0.580 0.7074 0.028 0.760 0.212
#> GSM751442 3 0.782 0.0685 0.056 0.400 0.544
#> GSM751443 3 0.621 0.5553 0.068 0.164 0.768
#> GSM751445 2 0.786 0.6973 0.088 0.628 0.284
#> GSM751447 2 0.580 0.7074 0.028 0.760 0.212
#> GSM751453 2 0.580 0.7074 0.028 0.760 0.212
#> GSM751454 2 0.580 0.7074 0.028 0.760 0.212
#> GSM751455 3 0.782 0.0685 0.056 0.400 0.544
#> GSM751456 3 0.782 0.0685 0.056 0.400 0.544
#> GSM751457 2 0.592 0.6937 0.032 0.756 0.212
#> GSM751458 2 0.592 0.6937 0.032 0.756 0.212
cbind(get_classes(res, k = 4), get_membership(res, k = 4))
#> class entropy silhouette p1 p2 p3 p4
#> GSM751298 3 0.665 0.4938 NA 0.172 0.624 0.000
#> GSM751304 4 0.196 0.8209 NA 0.008 0.020 0.944
#> GSM751305 4 0.196 0.8209 NA 0.008 0.020 0.944
#> GSM751307 4 0.339 0.8373 NA 0.068 0.028 0.884
#> GSM751310 3 0.561 0.5733 NA 0.020 0.664 0.016
#> GSM751314 3 0.573 0.5714 NA 0.020 0.656 0.020
#> GSM751316 3 0.574 0.5575 NA 0.016 0.640 0.020
#> GSM751318 3 0.691 0.4666 NA 0.188 0.592 0.000
#> GSM751342 3 0.722 0.4490 NA 0.176 0.532 0.000
#> GSM751346 3 0.359 0.5923 NA 0.040 0.856 0.000
#> GSM751347 3 0.359 0.5917 NA 0.040 0.856 0.000
#> GSM751348 2 0.553 0.6848 NA 0.756 0.156 0.024
#> GSM751349 2 0.553 0.6848 NA 0.756 0.156 0.024
#> GSM751352 4 0.595 0.7490 NA 0.192 0.056 0.720
#> GSM751353 4 0.595 0.7490 NA 0.192 0.056 0.720
#> GSM751354 4 0.217 0.8221 NA 0.008 0.024 0.936
#> GSM751355 4 0.217 0.8221 NA 0.008 0.024 0.936
#> GSM751358 2 0.680 0.3540 NA 0.540 0.064 0.016
#> GSM751359 2 0.680 0.3540 NA 0.540 0.064 0.016
#> GSM751294 3 0.891 0.0244 NA 0.280 0.460 0.096
#> GSM751296 3 0.581 0.5513 NA 0.140 0.708 0.000
#> GSM751297 3 0.385 0.5939 NA 0.044 0.840 0.000
#> GSM751299 3 0.957 -0.0883 NA 0.280 0.380 0.164
#> GSM751300 3 0.415 0.5963 NA 0.056 0.824 0.000
#> GSM751301 4 0.419 0.8461 NA 0.088 0.048 0.844
#> GSM751302 3 0.349 0.5940 NA 0.044 0.864 0.000
#> GSM751303 3 0.561 0.5631 NA 0.016 0.648 0.016
#> GSM751306 3 0.561 0.5631 NA 0.016 0.648 0.016
#> GSM751308 3 0.822 0.3816 NA 0.208 0.540 0.056
#> GSM751309 3 0.599 0.5613 NA 0.032 0.632 0.016
#> GSM751311 3 0.599 0.5613 NA 0.032 0.632 0.016
#> GSM751312 3 0.574 0.5575 NA 0.016 0.640 0.020
#> GSM751313 3 0.390 0.6263 NA 0.036 0.832 0.000
#> GSM751315 3 0.573 0.5699 NA 0.020 0.656 0.020
#> GSM751317 3 0.578 0.5693 NA 0.020 0.648 0.020
#> GSM751320 3 0.547 0.6018 NA 0.044 0.712 0.008
#> GSM751321 3 0.565 0.5571 NA 0.016 0.640 0.016
#> GSM751322 3 0.542 0.6004 NA 0.040 0.712 0.008
#> GSM751324 3 0.665 0.5460 NA 0.132 0.628 0.004
#> GSM751325 3 0.653 0.5540 NA 0.132 0.644 0.004
#> GSM751332 3 0.620 0.5195 NA 0.160 0.672 0.000
#> GSM751334 3 0.620 0.5195 NA 0.160 0.672 0.000
#> GSM751339 3 0.541 0.6135 NA 0.076 0.756 0.012
#> GSM751341 3 0.721 0.4659 NA 0.172 0.532 0.000
#> GSM751343 3 0.687 0.4816 NA 0.180 0.596 0.000
#> GSM751344 4 0.413 0.8467 NA 0.084 0.048 0.848
#> GSM751345 4 0.413 0.8467 NA 0.084 0.048 0.848
#> GSM751356 3 0.954 -0.0588 NA 0.272 0.388 0.152
#> GSM751357 3 0.954 -0.0588 NA 0.272 0.388 0.152
#> GSM751293 4 0.419 0.8461 NA 0.088 0.048 0.844
#> GSM751295 3 0.349 0.5940 NA 0.044 0.864 0.000
#> GSM751319 3 0.580 0.5633 NA 0.020 0.644 0.020
#> GSM751323 3 0.578 0.5932 NA 0.072 0.696 0.004
#> GSM751326 3 0.604 0.5287 NA 0.156 0.688 0.000
#> GSM751327 3 0.620 0.5329 NA 0.168 0.672 0.000
#> GSM751328 3 0.647 0.5111 NA 0.168 0.644 0.000
#> GSM751329 3 0.510 0.5978 NA 0.100 0.764 0.000
#> GSM751330 3 0.335 0.6001 NA 0.044 0.872 0.000
#> GSM751331 3 0.327 0.5967 NA 0.040 0.876 0.000
#> GSM751333 3 0.322 0.5981 NA 0.044 0.880 0.000
#> GSM751335 3 0.335 0.6001 NA 0.044 0.872 0.000
#> GSM751336 3 0.327 0.5967 NA 0.040 0.876 0.000
#> GSM751337 3 0.541 0.6135 NA 0.076 0.756 0.012
#> GSM751338 3 0.541 0.6135 NA 0.076 0.756 0.012
#> GSM751340 3 0.886 0.0590 NA 0.268 0.472 0.096
#> GSM751350 3 0.349 0.5940 NA 0.044 0.864 0.000
#> GSM751351 3 0.349 0.5940 NA 0.044 0.864 0.000
#> GSM751362 3 0.456 0.6190 NA 0.032 0.800 0.012
#> GSM751363 3 0.739 0.5629 NA 0.052 0.616 0.104
#> GSM751367 3 0.540 0.5895 NA 0.032 0.700 0.008
#> GSM751368 3 0.739 0.4677 NA 0.184 0.592 0.020
#> GSM751371 3 0.669 0.5619 NA 0.096 0.604 0.008
#> GSM751375 2 0.434 0.6919 NA 0.816 0.144 0.020
#> GSM751376 3 0.844 0.1213 NA 0.036 0.412 0.360
#> GSM751378 2 0.585 0.6606 NA 0.680 0.236 0.000
#> GSM751379 3 0.844 0.1213 NA 0.036 0.412 0.360
#> GSM751382 2 0.413 0.6904 NA 0.828 0.136 0.020
#> GSM751386 2 0.577 0.6626 NA 0.692 0.236 0.004
#> GSM751388 2 0.550 0.6712 NA 0.708 0.224 0.000
#> GSM751391 3 0.772 0.4751 NA 0.160 0.540 0.024
#> GSM751410 3 0.479 0.6260 NA 0.020 0.752 0.008
#> GSM751414 3 0.647 0.5823 NA 0.100 0.668 0.016
#> GSM751361 3 0.749 0.4652 NA 0.188 0.588 0.024
#> GSM751365 3 0.539 0.6095 NA 0.076 0.764 0.016
#> GSM751366 3 0.593 0.5982 NA 0.108 0.732 0.020
#> GSM751369 3 0.613 0.6119 NA 0.056 0.676 0.020
#> GSM751370 3 0.446 0.6198 NA 0.028 0.804 0.012
#> GSM751372 3 0.503 0.6193 NA 0.056 0.784 0.016
#> GSM751373 3 0.575 0.6043 NA 0.096 0.740 0.016
#> GSM751374 3 0.844 0.1213 NA 0.036 0.412 0.360
#> GSM751377 3 0.767 0.2637 NA 0.308 0.508 0.012
#> GSM751380 3 0.558 0.6020 NA 0.056 0.740 0.020
#> GSM751381 2 0.467 0.7069 NA 0.780 0.168 0.000
#> GSM751383 2 0.672 0.4579 NA 0.560 0.332 0.000
#> GSM751384 2 0.463 0.7082 NA 0.780 0.172 0.000
#> GSM751385 2 0.774 0.4318 NA 0.484 0.332 0.012
#> GSM751387 2 0.496 0.7100 NA 0.776 0.168 0.012
#> GSM751389 3 0.585 0.5856 NA 0.084 0.732 0.020
#> GSM751393 3 0.857 0.1143 NA 0.044 0.404 0.360
#> GSM751394 2 0.478 0.7054 NA 0.784 0.164 0.008
#> GSM751395 3 0.857 0.1143 NA 0.044 0.404 0.360
#> GSM751397 2 0.442 0.7086 NA 0.796 0.160 0.000
#> GSM751398 2 0.611 0.6168 NA 0.652 0.256 0.000
#> GSM751404 3 0.617 0.5875 NA 0.104 0.720 0.028
#> GSM751406 3 0.598 0.5625 NA 0.064 0.712 0.024
#> GSM751411 3 0.741 0.4167 NA 0.236 0.556 0.008
#> GSM751413 3 0.687 0.5980 NA 0.048 0.628 0.056
#> GSM751415 3 0.587 0.5812 NA 0.080 0.728 0.020
#> GSM751416 3 0.758 0.4365 NA 0.212 0.568 0.020
#> GSM751417 3 0.758 0.4365 NA 0.212 0.568 0.020
#> GSM751421 3 0.669 0.5619 NA 0.096 0.604 0.008
#> GSM751422 3 0.669 0.5619 NA 0.096 0.604 0.008
#> GSM751360 3 0.635 0.6072 NA 0.052 0.648 0.024
#> GSM751364 3 0.758 0.4435 NA 0.208 0.568 0.020
#> GSM751390 2 0.463 0.7082 NA 0.780 0.172 0.000
#> GSM751392 2 0.418 0.6901 NA 0.824 0.140 0.020
#> GSM751396 2 0.411 0.6962 NA 0.824 0.144 0.020
#> GSM751399 3 0.686 0.5446 NA 0.136 0.660 0.028
#> GSM751400 3 0.602 0.5596 NA 0.064 0.708 0.024
#> GSM751401 3 0.595 0.5621 NA 0.060 0.712 0.024
#> GSM751402 3 0.602 0.5596 NA 0.064 0.708 0.024
#> GSM751403 3 0.573 0.5820 NA 0.060 0.740 0.028
#> GSM751405 3 0.598 0.5625 NA 0.064 0.712 0.024
#> GSM751407 3 0.595 0.5621 NA 0.060 0.712 0.024
#> GSM751408 3 0.648 0.5713 NA 0.108 0.692 0.028
#> GSM751409 3 0.734 0.4820 NA 0.176 0.612 0.028
#> GSM751412 3 0.648 0.5713 NA 0.108 0.692 0.028
#> GSM751418 3 0.573 0.6038 NA 0.088 0.744 0.020
#> GSM751419 3 0.573 0.6038 NA 0.088 0.744 0.020
#> GSM751420 3 0.644 0.5608 NA 0.068 0.660 0.024
#> GSM751425 2 0.632 0.6580 NA 0.696 0.152 0.016
#> GSM751429 3 0.629 0.5009 NA 0.060 0.584 0.004
#> GSM751430 4 0.695 0.6264 NA 0.104 0.192 0.660
#> GSM751433 2 0.852 0.3352 NA 0.416 0.364 0.048
#> GSM751437 3 0.705 0.4318 NA 0.124 0.544 0.004
#> GSM751448 3 0.646 0.5281 NA 0.056 0.624 0.020
#> GSM751451 2 0.851 0.3512 NA 0.424 0.356 0.048
#> GSM751423 3 0.819 -0.0828 NA 0.364 0.424 0.024
#> GSM751424 3 0.982 -0.2656 NA 0.284 0.304 0.248
#> GSM751428 3 0.821 -0.0951 NA 0.364 0.420 0.024
#> GSM751431 2 0.854 0.3356 NA 0.416 0.360 0.048
#> GSM751432 4 0.695 0.6264 NA 0.104 0.192 0.660
#> GSM751434 4 0.695 0.6264 NA 0.104 0.192 0.660
#> GSM751435 3 0.726 0.3312 NA 0.272 0.588 0.024
#> GSM751436 2 0.852 0.3352 NA 0.416 0.364 0.048
#> GSM751440 3 0.690 0.3428 NA 0.264 0.608 0.012
#> GSM751444 2 0.861 0.3723 NA 0.432 0.340 0.056
#> GSM751446 3 0.720 0.3256 NA 0.276 0.576 0.012
#> GSM751449 2 0.824 0.4776 NA 0.500 0.308 0.056
#> GSM751450 3 0.817 -0.0896 NA 0.364 0.428 0.024
#> GSM751452 3 0.982 -0.2656 NA 0.284 0.304 0.248
#> GSM751426 2 0.861 0.3590 NA 0.424 0.344 0.052
#> GSM751427 3 0.821 -0.0951 NA 0.364 0.420 0.024
#> GSM751438 2 0.673 0.6277 NA 0.648 0.196 0.012
#> GSM751439 3 0.734 0.3219 NA 0.276 0.568 0.016
#> GSM751441 2 0.629 0.6612 NA 0.692 0.164 0.012
#> GSM751442 3 0.721 0.2973 NA 0.296 0.564 0.012
#> GSM751443 3 0.641 0.5518 NA 0.064 0.648 0.020
#> GSM751445 2 0.824 0.4776 NA 0.500 0.308 0.056
#> GSM751447 2 0.629 0.6612 NA 0.692 0.164 0.012
#> GSM751453 2 0.624 0.6630 NA 0.696 0.164 0.012
#> GSM751454 2 0.624 0.6630 NA 0.696 0.164 0.012
#> GSM751455 3 0.721 0.2973 NA 0.296 0.564 0.012
#> GSM751456 3 0.721 0.2973 NA 0.296 0.564 0.012
#> GSM751457 2 0.638 0.6504 NA 0.684 0.164 0.012
#> GSM751458 2 0.638 0.6504 NA 0.684 0.164 0.012
cbind(get_classes(res, k = 5), get_membership(res, k = 5))
#> class entropy silhouette p1 p2 p3 p4 p5
#> GSM751298 3 0.658 0.021892 0.032 0.000 0.576 0.236 0.156
#> GSM751304 2 0.205 0.742366 0.048 0.924 0.004 0.024 0.000
#> GSM751305 2 0.205 0.742366 0.048 0.924 0.004 0.024 0.000
#> GSM751307 2 0.266 0.766695 0.028 0.904 0.008 0.012 0.048
#> GSM751310 3 0.535 -0.355090 0.036 0.000 0.520 0.436 0.008
#> GSM751314 3 0.505 -0.411183 0.024 0.000 0.500 0.472 0.004
#> GSM751316 3 0.526 -0.367781 0.036 0.000 0.492 0.468 0.004
#> GSM751318 3 0.685 -0.117270 0.024 0.000 0.476 0.340 0.160
#> GSM751342 4 0.701 0.168298 0.032 0.000 0.400 0.416 0.152
#> GSM751346 3 0.210 0.223547 0.028 0.000 0.928 0.020 0.024
#> GSM751347 3 0.210 0.224928 0.028 0.000 0.928 0.020 0.024
#> GSM751348 5 0.536 0.444975 0.048 0.040 0.128 0.032 0.752
#> GSM751349 5 0.536 0.444975 0.048 0.040 0.128 0.032 0.752
#> GSM751352 2 0.581 0.634769 0.056 0.704 0.032 0.032 0.176
#> GSM751353 2 0.581 0.634769 0.056 0.704 0.032 0.032 0.176
#> GSM751354 2 0.236 0.741443 0.052 0.912 0.012 0.024 0.000
#> GSM751355 2 0.236 0.741443 0.052 0.912 0.012 0.024 0.000
#> GSM751358 1 0.565 1.000000 0.616 0.004 0.008 0.072 0.300
#> GSM751359 1 0.565 1.000000 0.616 0.004 0.008 0.072 0.300
#> GSM751294 3 0.893 -0.002201 0.080 0.068 0.372 0.240 0.240
#> GSM751296 3 0.533 0.168770 0.024 0.000 0.716 0.144 0.116
#> GSM751297 3 0.245 0.217597 0.028 0.000 0.912 0.032 0.028
#> GSM751299 3 0.952 -0.108341 0.080 0.152 0.284 0.248 0.236
#> GSM751300 3 0.298 0.214954 0.024 0.000 0.884 0.056 0.036
#> GSM751301 2 0.296 0.779269 0.024 0.884 0.016 0.004 0.072
#> GSM751302 3 0.189 0.225858 0.024 0.000 0.936 0.012 0.028
#> GSM751303 3 0.491 -0.426291 0.024 0.000 0.492 0.484 0.000
#> GSM751306 3 0.491 -0.426291 0.024 0.000 0.492 0.484 0.000
#> GSM751308 3 0.816 -0.042749 0.036 0.056 0.424 0.308 0.176
#> GSM751309 4 0.523 0.364026 0.028 0.000 0.476 0.488 0.008
#> GSM751311 4 0.523 0.364026 0.028 0.000 0.476 0.488 0.008
#> GSM751312 3 0.526 -0.367781 0.036 0.000 0.492 0.468 0.004
#> GSM751313 3 0.351 0.147437 0.016 0.000 0.832 0.132 0.020
#> GSM751315 3 0.536 -0.362683 0.036 0.000 0.508 0.448 0.008
#> GSM751317 3 0.536 -0.367311 0.036 0.000 0.500 0.456 0.008
#> GSM751320 3 0.523 -0.283319 0.016 0.000 0.576 0.384 0.024
#> GSM751321 3 0.532 -0.368060 0.040 0.000 0.492 0.464 0.004
#> GSM751322 3 0.517 -0.304032 0.016 0.000 0.568 0.396 0.020
#> GSM751324 3 0.639 -0.239996 0.020 0.000 0.496 0.380 0.104
#> GSM751325 3 0.640 -0.217928 0.020 0.000 0.508 0.364 0.108
#> GSM751332 3 0.639 -0.066049 0.020 0.000 0.560 0.288 0.132
#> GSM751334 3 0.639 -0.066049 0.020 0.000 0.560 0.288 0.132
#> GSM751339 3 0.511 0.074181 0.028 0.000 0.688 0.248 0.036
#> GSM751341 3 0.689 -0.266681 0.028 0.000 0.428 0.400 0.144
#> GSM751343 3 0.680 -0.118484 0.024 0.000 0.484 0.340 0.152
#> GSM751344 2 0.290 0.780186 0.024 0.888 0.016 0.004 0.068
#> GSM751345 2 0.290 0.780186 0.024 0.888 0.016 0.004 0.068
#> GSM751356 3 0.944 -0.080054 0.080 0.132 0.292 0.260 0.236
#> GSM751357 3 0.944 -0.080054 0.080 0.132 0.292 0.260 0.236
#> GSM751293 2 0.296 0.779269 0.024 0.884 0.016 0.004 0.072
#> GSM751295 3 0.189 0.225858 0.024 0.000 0.936 0.012 0.028
#> GSM751319 3 0.536 -0.367562 0.036 0.000 0.496 0.460 0.008
#> GSM751323 3 0.568 -0.283870 0.016 0.000 0.556 0.376 0.052
#> GSM751326 3 0.630 -0.052825 0.020 0.000 0.576 0.276 0.128
#> GSM751327 3 0.625 -0.072008 0.012 0.000 0.564 0.288 0.136
#> GSM751328 3 0.654 -0.093383 0.020 0.000 0.532 0.308 0.140
#> GSM751329 3 0.394 0.180649 0.028 0.000 0.828 0.064 0.080
#> GSM751330 3 0.161 0.218874 0.016 0.000 0.948 0.012 0.024
#> GSM751331 3 0.160 0.222408 0.020 0.000 0.948 0.008 0.024
#> GSM751333 3 0.150 0.220454 0.016 0.000 0.952 0.008 0.024
#> GSM751335 3 0.161 0.218874 0.016 0.000 0.948 0.012 0.024
#> GSM751336 3 0.160 0.222408 0.020 0.000 0.948 0.008 0.024
#> GSM751337 3 0.511 0.074181 0.028 0.000 0.688 0.248 0.036
#> GSM751338 3 0.511 0.074181 0.028 0.000 0.688 0.248 0.036
#> GSM751340 3 0.886 0.029539 0.076 0.068 0.388 0.240 0.228
#> GSM751350 3 0.189 0.225858 0.024 0.000 0.936 0.012 0.028
#> GSM751351 3 0.189 0.225858 0.024 0.000 0.936 0.012 0.028
#> GSM751362 3 0.412 0.122794 0.028 0.008 0.796 0.156 0.012
#> GSM751363 3 0.761 -0.268917 0.064 0.092 0.476 0.336 0.032
#> GSM751367 3 0.532 -0.096719 0.060 0.000 0.676 0.244 0.020
#> GSM751368 3 0.749 -0.122321 0.048 0.012 0.448 0.348 0.144
#> GSM751371 4 0.645 0.515356 0.060 0.004 0.428 0.468 0.040
#> GSM751375 5 0.409 0.460413 0.024 0.020 0.116 0.020 0.820
#> GSM751376 3 0.847 -0.012150 0.068 0.320 0.348 0.232 0.032
#> GSM751378 5 0.619 0.461962 0.060 0.004 0.184 0.092 0.660
#> GSM751379 3 0.847 -0.012150 0.068 0.320 0.348 0.232 0.032
#> GSM751382 5 0.385 0.462007 0.020 0.020 0.120 0.012 0.828
#> GSM751386 5 0.569 0.511315 0.036 0.004 0.204 0.072 0.684
#> GSM751388 5 0.546 0.508572 0.040 0.004 0.196 0.056 0.704
#> GSM751391 4 0.759 0.357396 0.072 0.016 0.348 0.456 0.108
#> GSM751410 3 0.486 -0.147651 0.028 0.000 0.668 0.292 0.012
#> GSM751414 3 0.647 -0.145027 0.048 0.004 0.544 0.340 0.064
#> GSM751361 3 0.749 -0.109880 0.048 0.012 0.460 0.332 0.148
#> GSM751365 3 0.521 0.078833 0.024 0.008 0.704 0.224 0.040
#> GSM751366 3 0.587 0.063554 0.032 0.004 0.632 0.272 0.060
#> GSM751369 3 0.605 -0.381647 0.044 0.012 0.524 0.400 0.020
#> GSM751370 3 0.412 0.128321 0.028 0.008 0.796 0.156 0.012
#> GSM751372 3 0.485 0.081767 0.024 0.008 0.740 0.196 0.032
#> GSM751373 3 0.575 0.060661 0.032 0.004 0.648 0.260 0.056
#> GSM751374 3 0.847 -0.012150 0.068 0.320 0.348 0.232 0.032
#> GSM751377 3 0.776 0.000975 0.048 0.008 0.424 0.268 0.252
#> GSM751380 3 0.549 0.086629 0.044 0.004 0.652 0.276 0.024
#> GSM751381 5 0.359 0.487766 0.024 0.000 0.140 0.012 0.824
#> GSM751383 5 0.694 0.436751 0.044 0.004 0.272 0.136 0.544
#> GSM751384 5 0.396 0.482476 0.028 0.000 0.140 0.024 0.808
#> GSM751385 5 0.829 0.365530 0.088 0.016 0.276 0.220 0.400
#> GSM751387 5 0.407 0.498938 0.016 0.012 0.148 0.020 0.804
#> GSM751389 3 0.572 0.101857 0.040 0.004 0.648 0.264 0.044
#> GSM751393 3 0.849 -0.010697 0.068 0.320 0.340 0.240 0.032
#> GSM751394 5 0.414 0.493463 0.016 0.008 0.140 0.032 0.804
#> GSM751395 3 0.849 -0.010697 0.068 0.320 0.340 0.240 0.032
#> GSM751397 5 0.369 0.483834 0.028 0.000 0.132 0.016 0.824
#> GSM751398 5 0.618 0.488070 0.040 0.004 0.228 0.092 0.636
#> GSM751404 3 0.608 0.089405 0.044 0.004 0.620 0.272 0.060
#> GSM751406 3 0.598 0.092707 0.072 0.004 0.648 0.236 0.040
#> GSM751411 3 0.749 -0.036516 0.060 0.004 0.480 0.280 0.176
#> GSM751413 3 0.680 -0.352202 0.048 0.040 0.472 0.412 0.028
#> GSM751415 3 0.570 0.094186 0.040 0.004 0.644 0.272 0.040
#> GSM751416 3 0.754 -0.030670 0.048 0.012 0.472 0.300 0.168
#> GSM751417 3 0.754 -0.030670 0.048 0.012 0.472 0.300 0.168
#> GSM751421 4 0.645 0.515356 0.060 0.004 0.428 0.468 0.040
#> GSM751422 4 0.645 0.515356 0.060 0.004 0.428 0.468 0.040
#> GSM751360 3 0.644 -0.367939 0.048 0.016 0.488 0.416 0.032
#> GSM751364 3 0.750 -0.037060 0.048 0.012 0.476 0.304 0.160
#> GSM751390 5 0.396 0.482476 0.028 0.000 0.140 0.024 0.808
#> GSM751392 5 0.395 0.458838 0.020 0.020 0.112 0.020 0.828
#> GSM751396 5 0.408 0.471983 0.020 0.016 0.116 0.028 0.820
#> GSM751399 3 0.689 0.082522 0.056 0.008 0.556 0.284 0.096
#> GSM751400 3 0.601 0.093702 0.076 0.004 0.648 0.232 0.040
#> GSM751401 3 0.598 0.095963 0.076 0.004 0.652 0.228 0.040
#> GSM751402 3 0.603 0.092042 0.076 0.004 0.644 0.236 0.040
#> GSM751403 3 0.573 0.110403 0.064 0.004 0.676 0.216 0.040
#> GSM751405 3 0.598 0.092707 0.072 0.004 0.648 0.236 0.040
#> GSM751407 3 0.598 0.095963 0.076 0.004 0.652 0.228 0.040
#> GSM751408 3 0.633 0.096280 0.044 0.008 0.596 0.288 0.064
#> GSM751409 3 0.707 0.036297 0.052 0.008 0.536 0.284 0.120
#> GSM751412 3 0.633 0.096280 0.044 0.008 0.596 0.288 0.064
#> GSM751418 3 0.573 0.046823 0.028 0.008 0.644 0.272 0.048
#> GSM751419 3 0.573 0.046823 0.028 0.008 0.644 0.272 0.048
#> GSM751420 3 0.621 -0.047698 0.060 0.004 0.592 0.300 0.044
#> GSM751425 5 0.744 0.250403 0.196 0.008 0.084 0.168 0.544
#> GSM751429 3 0.620 -0.121026 0.092 0.004 0.580 0.304 0.020
#> GSM751430 2 0.611 0.555794 0.004 0.672 0.168 0.060 0.096
#> GSM751433 5 0.806 0.253274 0.032 0.032 0.316 0.248 0.372
#> GSM751437 3 0.730 -0.127663 0.128 0.004 0.528 0.260 0.080
#> GSM751448 3 0.589 -0.026130 0.084 0.004 0.620 0.276 0.016
#> GSM751451 5 0.807 0.270618 0.032 0.032 0.308 0.252 0.376
#> GSM751423 3 0.786 -0.099595 0.048 0.012 0.392 0.220 0.328
#> GSM751424 3 0.921 -0.212637 0.032 0.240 0.252 0.224 0.252
#> GSM751428 3 0.787 -0.110430 0.048 0.012 0.388 0.224 0.328
#> GSM751431 5 0.807 0.255594 0.032 0.032 0.312 0.252 0.372
#> GSM751432 2 0.611 0.555794 0.004 0.672 0.168 0.060 0.096
#> GSM751434 2 0.611 0.555794 0.004 0.672 0.168 0.060 0.096
#> GSM751435 3 0.675 0.168168 0.016 0.016 0.564 0.148 0.256
#> GSM751436 5 0.806 0.253274 0.032 0.032 0.316 0.248 0.372
#> GSM751440 3 0.636 0.173576 0.016 0.004 0.588 0.140 0.252
#> GSM751444 5 0.826 0.299476 0.040 0.040 0.308 0.236 0.376
#> GSM751446 3 0.680 0.161408 0.032 0.004 0.560 0.160 0.244
#> GSM751449 5 0.835 0.404291 0.064 0.040 0.284 0.192 0.420
#> GSM751450 3 0.784 -0.105420 0.048 0.012 0.396 0.216 0.328
#> GSM751452 3 0.921 -0.203206 0.032 0.240 0.256 0.224 0.248
#> GSM751426 5 0.816 0.277763 0.032 0.040 0.304 0.244 0.380
#> GSM751427 3 0.787 -0.110430 0.048 0.012 0.388 0.224 0.328
#> GSM751438 5 0.769 0.271469 0.196 0.000 0.124 0.184 0.496
#> GSM751439 3 0.666 0.166947 0.028 0.000 0.556 0.168 0.248
#> GSM751441 5 0.739 0.275606 0.192 0.004 0.092 0.168 0.544
#> GSM751442 3 0.651 0.152188 0.016 0.000 0.544 0.160 0.280
#> GSM751443 3 0.578 0.041453 0.072 0.000 0.652 0.240 0.036
#> GSM751445 5 0.835 0.404291 0.064 0.040 0.284 0.192 0.420
#> GSM751447 5 0.739 0.275606 0.192 0.004 0.092 0.168 0.544
#> GSM751453 5 0.736 0.280708 0.188 0.004 0.092 0.168 0.548
#> GSM751454 5 0.736 0.280708 0.188 0.004 0.092 0.168 0.548
#> GSM751455 3 0.651 0.152188 0.016 0.000 0.544 0.160 0.280
#> GSM751456 3 0.651 0.152188 0.016 0.000 0.544 0.160 0.280
#> GSM751457 5 0.748 0.226422 0.204 0.004 0.084 0.184 0.524
#> GSM751458 5 0.748 0.226422 0.204 0.004 0.084 0.184 0.524
cbind(get_classes(res, k = 6), get_membership(res, k = 6))
#> class entropy silhouette p1 p2 p3 p4 p5 p6
#> GSM751298 3 0.6492 0.0468 0.016 0.088 0.556 0.256 0.084 0.000
#> GSM751304 6 0.3001 0.7033 0.096 0.008 0.000 0.020 0.016 0.860
#> GSM751305 6 0.3001 0.7033 0.096 0.008 0.000 0.020 0.016 0.860
#> GSM751307 6 0.2195 0.7462 0.008 0.020 0.000 0.008 0.052 0.912
#> GSM751310 4 0.4741 0.5349 0.012 0.004 0.356 0.600 0.028 0.000
#> GSM751314 4 0.3909 0.5605 0.004 0.004 0.320 0.668 0.004 0.000
#> GSM751316 4 0.4548 0.5418 0.012 0.004 0.320 0.640 0.024 0.000
#> GSM751318 4 0.7336 0.2589 0.028 0.112 0.352 0.404 0.104 0.000
#> GSM751342 4 0.6735 0.3853 0.020 0.100 0.268 0.528 0.084 0.000
#> GSM751346 3 0.1140 0.3473 0.012 0.008 0.964 0.008 0.008 0.000
#> GSM751347 3 0.0912 0.3479 0.012 0.004 0.972 0.004 0.008 0.000
#> GSM751348 5 0.6940 0.4340 0.016 0.260 0.112 0.032 0.536 0.044
#> GSM751349 5 0.6940 0.4340 0.016 0.260 0.112 0.032 0.536 0.044
#> GSM751352 6 0.6244 0.6020 0.048 0.084 0.028 0.024 0.164 0.652
#> GSM751353 6 0.6244 0.6020 0.048 0.084 0.028 0.024 0.164 0.652
#> GSM751354 6 0.3239 0.6986 0.104 0.008 0.004 0.020 0.016 0.848
#> GSM751355 6 0.3239 0.6986 0.104 0.008 0.004 0.020 0.016 0.848
#> GSM751358 1 0.5358 1.0000 0.656 0.200 0.004 0.024 0.116 0.000
#> GSM751359 1 0.5358 1.0000 0.656 0.200 0.004 0.024 0.116 0.000
#> GSM751294 3 0.9052 0.0709 0.068 0.164 0.348 0.148 0.216 0.056
#> GSM751296 3 0.5092 0.2372 0.008 0.064 0.716 0.148 0.064 0.000
#> GSM751297 3 0.1713 0.3439 0.012 0.012 0.940 0.024 0.012 0.000
#> GSM751299 3 0.9635 -0.0346 0.068 0.160 0.256 0.168 0.208 0.140
#> GSM751300 3 0.2257 0.3377 0.008 0.020 0.912 0.044 0.016 0.000
#> GSM751301 6 0.2392 0.7567 0.004 0.032 0.004 0.000 0.064 0.896
#> GSM751302 3 0.0912 0.3455 0.008 0.004 0.972 0.004 0.012 0.000
#> GSM751303 4 0.3861 0.5557 0.008 0.004 0.316 0.672 0.000 0.000
#> GSM751306 4 0.3861 0.5557 0.008 0.004 0.316 0.672 0.000 0.000
#> GSM751308 4 0.8509 0.0972 0.028 0.140 0.312 0.344 0.116 0.060
#> GSM751309 4 0.4423 0.5554 0.008 0.024 0.312 0.652 0.004 0.000
#> GSM751311 4 0.4423 0.5554 0.008 0.024 0.312 0.652 0.004 0.000
#> GSM751312 4 0.4548 0.5418 0.012 0.004 0.320 0.640 0.024 0.000
#> GSM751313 3 0.3906 0.2049 0.024 0.008 0.780 0.168 0.020 0.000
#> GSM751315 4 0.4691 0.5461 0.012 0.004 0.340 0.616 0.028 0.000
#> GSM751317 4 0.4767 0.5521 0.016 0.008 0.328 0.624 0.024 0.000
#> GSM751320 4 0.5166 0.5004 0.016 0.020 0.420 0.524 0.020 0.000
#> GSM751321 4 0.4633 0.5421 0.016 0.004 0.320 0.636 0.024 0.000
#> GSM751322 4 0.5143 0.5135 0.016 0.020 0.404 0.540 0.020 0.000
#> GSM751324 4 0.6671 0.4090 0.024 0.088 0.360 0.468 0.060 0.000
#> GSM751325 4 0.6735 0.3870 0.024 0.088 0.376 0.448 0.064 0.000
#> GSM751332 3 0.6736 -0.2213 0.016 0.088 0.460 0.356 0.080 0.000
#> GSM751334 3 0.6736 -0.2213 0.016 0.088 0.460 0.356 0.080 0.000
#> GSM751339 3 0.5904 0.1319 0.032 0.056 0.620 0.244 0.048 0.000
#> GSM751341 4 0.6705 0.3539 0.016 0.092 0.320 0.492 0.080 0.000
#> GSM751343 4 0.7252 0.2657 0.028 0.100 0.360 0.408 0.104 0.000
#> GSM751344 6 0.2316 0.7576 0.004 0.028 0.004 0.000 0.064 0.900
#> GSM751345 6 0.2316 0.7576 0.004 0.028 0.004 0.000 0.064 0.900
#> GSM751356 3 0.9590 -0.0141 0.068 0.156 0.264 0.180 0.208 0.124
#> GSM751357 3 0.9590 -0.0141 0.068 0.156 0.264 0.180 0.208 0.124
#> GSM751293 6 0.2392 0.7567 0.004 0.032 0.004 0.000 0.064 0.896
#> GSM751295 3 0.0912 0.3455 0.008 0.004 0.972 0.004 0.012 0.000
#> GSM751319 4 0.4635 0.5441 0.012 0.004 0.324 0.632 0.028 0.000
#> GSM751323 4 0.5780 0.4582 0.016 0.052 0.420 0.484 0.028 0.000
#> GSM751326 3 0.6679 -0.2013 0.016 0.084 0.476 0.344 0.080 0.000
#> GSM751327 3 0.6669 -0.2388 0.012 0.080 0.456 0.364 0.088 0.000
#> GSM751328 3 0.6871 -0.2596 0.016 0.088 0.424 0.380 0.092 0.000
#> GSM751329 3 0.3768 0.2840 0.008 0.044 0.824 0.080 0.044 0.000
#> GSM751330 3 0.1377 0.3366 0.004 0.004 0.952 0.016 0.024 0.000
#> GSM751331 3 0.0912 0.3421 0.004 0.004 0.972 0.008 0.012 0.000
#> GSM751333 3 0.0964 0.3397 0.000 0.004 0.968 0.012 0.016 0.000
#> GSM751335 3 0.1377 0.3366 0.004 0.004 0.952 0.016 0.024 0.000
#> GSM751336 3 0.0912 0.3421 0.004 0.004 0.972 0.008 0.012 0.000
#> GSM751337 3 0.5904 0.1319 0.032 0.056 0.620 0.244 0.048 0.000
#> GSM751338 3 0.5904 0.1319 0.032 0.056 0.620 0.244 0.048 0.000
#> GSM751340 3 0.8993 0.0947 0.068 0.156 0.364 0.148 0.208 0.056
#> GSM751350 3 0.0912 0.3455 0.008 0.004 0.972 0.004 0.012 0.000
#> GSM751351 3 0.0912 0.3455 0.008 0.004 0.972 0.004 0.012 0.000
#> GSM751362 3 0.4210 0.1649 0.004 0.008 0.732 0.220 0.032 0.004
#> GSM751363 4 0.7293 0.4283 0.024 0.028 0.332 0.460 0.060 0.096
#> GSM751367 3 0.6137 0.0838 0.048 0.044 0.616 0.224 0.068 0.000
#> GSM751368 4 0.7309 0.3308 0.024 0.100 0.316 0.432 0.128 0.000
#> GSM751371 4 0.7683 0.2995 0.060 0.100 0.252 0.452 0.136 0.000
#> GSM751375 5 0.5619 0.4379 0.004 0.300 0.056 0.024 0.600 0.016
#> GSM751376 3 0.9048 0.0447 0.108 0.048 0.308 0.164 0.092 0.280
#> GSM751378 5 0.6766 0.2178 0.028 0.340 0.112 0.048 0.472 0.000
#> GSM751379 3 0.9048 0.0447 0.108 0.048 0.308 0.164 0.092 0.280
#> GSM751382 5 0.5588 0.4573 0.004 0.292 0.068 0.016 0.604 0.016
#> GSM751386 5 0.7382 0.4422 0.012 0.248 0.172 0.072 0.476 0.020
#> GSM751388 5 0.7189 0.4545 0.016 0.256 0.164 0.056 0.492 0.016
#> GSM751391 4 0.8345 0.2150 0.072 0.160 0.172 0.412 0.176 0.008
#> GSM751410 3 0.5878 -0.0881 0.024 0.032 0.520 0.376 0.048 0.000
#> GSM751414 4 0.6568 0.3551 0.020 0.064 0.392 0.448 0.076 0.000
#> GSM751361 4 0.7282 0.3347 0.024 0.096 0.320 0.432 0.128 0.000
#> GSM751365 3 0.5466 0.0974 0.008 0.020 0.592 0.308 0.072 0.000
#> GSM751366 3 0.6158 0.1047 0.012 0.056 0.536 0.324 0.072 0.000
#> GSM751369 4 0.6703 0.3339 0.052 0.044 0.356 0.484 0.060 0.004
#> GSM751370 3 0.4166 0.1695 0.004 0.008 0.732 0.224 0.028 0.004
#> GSM751372 3 0.5266 0.0428 0.008 0.024 0.632 0.284 0.048 0.004
#> GSM751373 3 0.6076 0.0866 0.012 0.056 0.552 0.312 0.068 0.000
#> GSM751374 3 0.9048 0.0447 0.108 0.048 0.308 0.164 0.092 0.280
#> GSM751377 3 0.8016 -0.1786 0.028 0.120 0.332 0.328 0.184 0.008
#> GSM751380 3 0.5976 0.2663 0.036 0.032 0.600 0.264 0.068 0.000
#> GSM751381 5 0.5744 0.4934 0.008 0.264 0.092 0.020 0.608 0.008
#> GSM751383 5 0.8092 0.3118 0.024 0.188 0.220 0.160 0.396 0.012
#> GSM751384 5 0.5560 0.4644 0.016 0.264 0.088 0.016 0.616 0.000
#> GSM751385 2 0.8254 -0.0417 0.056 0.320 0.196 0.100 0.320 0.008
#> GSM751387 5 0.6231 0.4909 0.008 0.284 0.112 0.032 0.556 0.008
#> GSM751389 3 0.6208 0.2978 0.032 0.040 0.588 0.252 0.088 0.000
#> GSM751393 3 0.9113 0.0233 0.108 0.048 0.296 0.168 0.100 0.280
#> GSM751394 5 0.6225 0.4909 0.004 0.264 0.088 0.048 0.580 0.016
#> GSM751395 3 0.9113 0.0233 0.108 0.048 0.296 0.168 0.100 0.280
#> GSM751397 5 0.5677 0.4876 0.008 0.272 0.092 0.020 0.604 0.004
#> GSM751398 5 0.7706 0.3993 0.016 0.224 0.200 0.092 0.448 0.020
#> GSM751404 3 0.6249 0.1650 0.020 0.060 0.540 0.316 0.064 0.000
#> GSM751406 3 0.6790 0.2978 0.064 0.056 0.572 0.204 0.104 0.000
#> GSM751411 3 0.7693 0.0637 0.028 0.156 0.408 0.276 0.132 0.000
#> GSM751413 4 0.7312 0.3889 0.056 0.048 0.320 0.480 0.064 0.032
#> GSM751415 3 0.6202 0.2924 0.032 0.040 0.584 0.260 0.084 0.000
#> GSM751416 4 0.7602 0.2455 0.028 0.080 0.364 0.380 0.136 0.012
#> GSM751417 4 0.7602 0.2455 0.028 0.080 0.364 0.380 0.136 0.012
#> GSM751421 4 0.7683 0.2995 0.060 0.100 0.252 0.452 0.136 0.000
#> GSM751422 4 0.7683 0.2995 0.060 0.100 0.252 0.452 0.136 0.000
#> GSM751360 4 0.6918 0.3800 0.052 0.052 0.324 0.492 0.076 0.004
#> GSM751364 3 0.7499 -0.2800 0.028 0.080 0.376 0.376 0.132 0.008
#> GSM751390 5 0.5560 0.4644 0.016 0.264 0.088 0.016 0.616 0.000
#> GSM751392 5 0.5588 0.4467 0.004 0.292 0.056 0.024 0.608 0.016
#> GSM751396 5 0.5705 0.4584 0.000 0.288 0.060 0.032 0.600 0.020
#> GSM751399 3 0.7010 0.2153 0.040 0.068 0.500 0.284 0.108 0.000
#> GSM751400 3 0.6710 0.3019 0.060 0.052 0.576 0.208 0.104 0.000
#> GSM751401 3 0.6693 0.3004 0.060 0.048 0.576 0.208 0.108 0.000
#> GSM751402 3 0.6775 0.2993 0.064 0.052 0.572 0.204 0.108 0.000
#> GSM751403 3 0.6242 0.3019 0.048 0.032 0.604 0.220 0.096 0.000
#> GSM751405 3 0.6737 0.3000 0.064 0.052 0.576 0.204 0.104 0.000
#> GSM751407 3 0.6693 0.3004 0.060 0.048 0.576 0.208 0.108 0.000
#> GSM751408 3 0.6556 0.2623 0.032 0.060 0.544 0.280 0.084 0.000
#> GSM751409 3 0.7650 0.2436 0.052 0.116 0.460 0.240 0.132 0.000
#> GSM751412 3 0.6556 0.2623 0.032 0.060 0.544 0.280 0.084 0.000
#> GSM751418 3 0.6083 0.0513 0.020 0.036 0.532 0.340 0.072 0.000
#> GSM751419 3 0.6083 0.0513 0.020 0.036 0.532 0.340 0.072 0.000
#> GSM751420 3 0.7404 0.2030 0.072 0.060 0.480 0.256 0.132 0.000
#> GSM751425 2 0.2536 0.6533 0.000 0.888 0.064 0.040 0.004 0.004
#> GSM751429 3 0.6858 0.0992 0.072 0.068 0.548 0.244 0.068 0.000
#> GSM751430 6 0.5748 0.5648 0.000 0.028 0.160 0.084 0.056 0.672
#> GSM751433 5 0.8180 0.2238 0.020 0.168 0.272 0.216 0.316 0.008
#> GSM751437 3 0.7230 0.1141 0.060 0.208 0.516 0.156 0.060 0.000
#> GSM751448 3 0.6790 0.2061 0.076 0.068 0.576 0.204 0.076 0.000
#> GSM751451 5 0.8200 0.2209 0.020 0.176 0.264 0.216 0.316 0.008
#> GSM751423 3 0.8236 -0.1046 0.036 0.208 0.352 0.172 0.228 0.004
#> GSM751424 3 0.9169 -0.1656 0.016 0.124 0.232 0.220 0.180 0.228
#> GSM751428 3 0.8246 -0.1093 0.036 0.208 0.348 0.172 0.232 0.004
#> GSM751431 5 0.8185 0.2230 0.020 0.168 0.268 0.220 0.316 0.008
#> GSM751432 6 0.5748 0.5648 0.000 0.028 0.160 0.084 0.056 0.672
#> GSM751434 6 0.5748 0.5648 0.000 0.028 0.160 0.084 0.056 0.672
#> GSM751435 3 0.7470 0.2289 0.024 0.112 0.520 0.136 0.188 0.020
#> GSM751436 5 0.8180 0.2238 0.020 0.168 0.272 0.216 0.316 0.008
#> GSM751440 3 0.7055 0.2203 0.024 0.124 0.532 0.128 0.192 0.000
#> GSM751444 5 0.8478 0.1679 0.032 0.208 0.276 0.168 0.300 0.016
#> GSM751446 3 0.7329 0.2269 0.040 0.120 0.516 0.148 0.176 0.000
#> GSM751449 2 0.8289 -0.1717 0.032 0.308 0.264 0.108 0.272 0.016
#> GSM751450 3 0.8234 -0.1065 0.036 0.204 0.352 0.172 0.232 0.004
#> GSM751452 3 0.9164 -0.1607 0.016 0.124 0.232 0.224 0.176 0.228
#> GSM751426 5 0.8365 0.2205 0.024 0.168 0.268 0.208 0.316 0.016
#> GSM751427 3 0.8246 -0.1093 0.036 0.208 0.348 0.172 0.232 0.004
#> GSM751438 2 0.3588 0.6103 0.008 0.824 0.100 0.056 0.012 0.000
#> GSM751439 3 0.7317 0.2478 0.040 0.112 0.516 0.156 0.176 0.000
#> GSM751441 2 0.2619 0.6685 0.000 0.880 0.072 0.040 0.008 0.000
#> GSM751442 3 0.7260 0.2186 0.020 0.184 0.500 0.136 0.160 0.000
#> GSM751443 3 0.6592 0.2669 0.080 0.072 0.612 0.160 0.076 0.000
#> GSM751445 2 0.8289 -0.1717 0.032 0.308 0.264 0.108 0.272 0.016
#> GSM751447 2 0.2619 0.6685 0.000 0.880 0.072 0.040 0.008 0.000
#> GSM751453 2 0.2719 0.6686 0.000 0.876 0.072 0.040 0.012 0.000
#> GSM751454 2 0.2719 0.6686 0.000 0.876 0.072 0.040 0.012 0.000
#> GSM751455 3 0.7260 0.2186 0.020 0.184 0.500 0.136 0.160 0.000
#> GSM751456 3 0.7260 0.2186 0.020 0.184 0.500 0.136 0.160 0.000
#> GSM751457 2 0.2190 0.6353 0.000 0.900 0.060 0.040 0.000 0.000
#> GSM751458 2 0.2190 0.6353 0.000 0.900 0.060 0.040 0.000 0.000
Heatmaps for the consensus matrix. It visualizes the probability of two samples to be in a same group.
consensus_heatmap(res, k = 2)
consensus_heatmap(res, k = 3)
consensus_heatmap(res, k = 4)
consensus_heatmap(res, k = 5)
consensus_heatmap(res, k = 6)
Heatmaps for the membership of samples in all partitions to see how consistent they are:
membership_heatmap(res, k = 2)
membership_heatmap(res, k = 3)
membership_heatmap(res, k = 4)
membership_heatmap(res, k = 5)
membership_heatmap(res, k = 6)
As soon as we have had the classes for columns, we can look for signatures which are significantly different between classes which can be candidate marks for certain classes. Following are the heatmaps for signatures.
Signature heatmaps where rows are scaled:
get_signatures(res, k = 2)
get_signatures(res, k = 3)
get_signatures(res, k = 4)
get_signatures(res, k = 5)
get_signatures(res, k = 6)
Signature heatmaps where rows are not scaled:
get_signatures(res, k = 2, scale_rows = FALSE)
get_signatures(res, k = 3, scale_rows = FALSE)
get_signatures(res, k = 4, scale_rows = FALSE)
get_signatures(res, k = 5, scale_rows = FALSE)
get_signatures(res, k = 6, scale_rows = FALSE)
Compare the overlap of signatures from different k:
compare_signatures(res)
get_signature() returns a data frame invisibly. TO get the list of signatures, the function
call should be assigned to a variable explicitly. In following code, if plot argument is set
to FALSE, no heatmap is plotted while only the differential analysis is performed.
# code only for demonstration
tb = get_signature(res, k = ..., plot = FALSE)
An example of the output of tb is:
#> which_row fdr mean_1 mean_2 scaled_mean_1 scaled_mean_2 km
#> 1 38 0.042760348 8.373488 9.131774 -0.5533452 0.5164555 1
#> 2 40 0.018707592 7.106213 8.469186 -0.6173731 0.5762149 1
#> 3 55 0.019134737 10.221463 11.207825 -0.6159697 0.5749050 1
#> 4 59 0.006059896 5.921854 7.869574 -0.6899429 0.6439467 1
#> 5 60 0.018055526 8.928898 10.211722 -0.6204761 0.5791110 1
#> 6 98 0.009384629 15.714769 14.887706 0.6635654 -0.6193277 2
...
The columns in tb are:
which_row: row indices corresponding to the input matrix.fdr: FDR for the differential test. mean_x: The mean value in group x.scaled_mean_x: The mean value in group x after rows are scaled.km: Row groups if k-means clustering is applied to rows.UMAP plot which shows how samples are separated.
dimension_reduction(res, k = 2, method = "UMAP")
dimension_reduction(res, k = 3, method = "UMAP")
dimension_reduction(res, k = 4, method = "UMAP")
dimension_reduction(res, k = 5, method = "UMAP")
dimension_reduction(res, k = 6, method = "UMAP")
Following heatmap shows how subgroups are split when increasing k:
collect_classes(res)
Test correlation between subgroups and known annotations. If the known annotation is numeric, one-way ANOVA test is applied, and if the known annotation is discrete, chi-squared contingency table test is applied.
test_to_known_factors(res)
#> n tissue(p) disease.state(p) agent(p) k
#> CV:hclust 161 5.09e-03 0.00731 6.68e-03 2
#> CV:hclust 124 3.71e-09 0.00722 2.60e-02 3
#> CV:hclust 115 1.20e-06 0.00362 7.82e-03 4
#> CV:hclust 21 1.38e-03 0.30372 6.44e-01 5
#> CV:hclust 38 7.35e-06 0.02470 2.53e-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", "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 4537 rows and 166 columns.
#> Top rows (454, 908, 1361, 1814, 2268) 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 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 0.183 0.682 0.803 0.4469 0.554 0.554
#> 3 3 0.324 0.670 0.782 0.4125 0.753 0.565
#> 4 4 0.567 0.668 0.771 0.1374 0.931 0.799
#> 5 5 0.652 0.660 0.771 0.0773 0.919 0.728
#> 6 6 0.715 0.605 0.735 0.0417 0.945 0.765
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
#> GSM751298 1 0.388 0.8700 0.924 0.076
#> GSM751304 2 0.987 0.3630 0.432 0.568
#> GSM751305 2 0.981 0.4196 0.420 0.580
#> GSM751307 2 0.978 0.4398 0.412 0.588
#> GSM751310 1 0.163 0.8510 0.976 0.024
#> GSM751314 1 0.163 0.8510 0.976 0.024
#> GSM751316 1 0.163 0.8510 0.976 0.024
#> GSM751318 1 0.388 0.8700 0.924 0.076
#> GSM751342 1 0.184 0.8499 0.972 0.028
#> GSM751346 1 0.469 0.8659 0.900 0.100
#> GSM751347 1 0.958 0.1295 0.620 0.380
#> GSM751348 1 1.000 -0.0898 0.504 0.496
#> GSM751349 2 0.671 0.7174 0.176 0.824
#> GSM751352 2 0.987 0.3131 0.432 0.568
#> GSM751353 2 0.738 0.6906 0.208 0.792
#> GSM751354 2 0.917 0.5609 0.332 0.668
#> GSM751355 2 0.738 0.6890 0.208 0.792
#> GSM751358 1 0.949 0.2233 0.632 0.368
#> GSM751359 2 0.775 0.6927 0.228 0.772
#> GSM751294 2 0.904 0.5466 0.320 0.680
#> GSM751296 1 0.456 0.8677 0.904 0.096
#> GSM751297 1 0.541 0.8473 0.876 0.124
#> GSM751299 1 0.998 0.0239 0.528 0.472
#> GSM751300 1 0.456 0.8677 0.904 0.096
#> GSM751301 1 0.895 0.4702 0.688 0.312
#> GSM751302 1 0.469 0.8659 0.900 0.100
#> GSM751303 1 0.184 0.8499 0.972 0.028
#> GSM751306 1 0.184 0.8499 0.972 0.028
#> GSM751308 1 0.605 0.8128 0.852 0.148
#> GSM751309 1 0.184 0.8499 0.972 0.028
#> GSM751311 1 0.163 0.8462 0.976 0.024
#> GSM751312 1 0.163 0.8462 0.976 0.024
#> GSM751313 1 0.443 0.8683 0.908 0.092
#> GSM751315 1 0.163 0.8536 0.976 0.024
#> GSM751317 1 0.163 0.8510 0.976 0.024
#> GSM751320 1 0.416 0.8676 0.916 0.084
#> GSM751321 1 0.184 0.8499 0.972 0.028
#> GSM751322 1 0.358 0.8696 0.932 0.068
#> GSM751324 1 0.358 0.8696 0.932 0.068
#> GSM751325 1 0.388 0.8700 0.924 0.076
#> GSM751332 1 0.416 0.8676 0.916 0.084
#> GSM751334 1 0.416 0.8676 0.916 0.084
#> GSM751339 1 0.518 0.8525 0.884 0.116
#> GSM751341 1 0.184 0.8499 0.972 0.028
#> GSM751343 1 0.416 0.8676 0.916 0.084
#> GSM751344 2 0.969 0.4067 0.396 0.604
#> GSM751345 2 0.969 0.4067 0.396 0.604
#> GSM751356 1 0.983 0.1358 0.576 0.424
#> GSM751357 1 0.983 0.1358 0.576 0.424
#> GSM751293 1 0.891 0.4713 0.692 0.308
#> GSM751295 1 0.469 0.8659 0.900 0.100
#> GSM751319 1 0.163 0.8462 0.976 0.024
#> GSM751323 1 0.416 0.8676 0.916 0.084
#> GSM751326 1 0.416 0.8692 0.916 0.084
#> GSM751327 1 0.358 0.8700 0.932 0.068
#> GSM751328 1 0.163 0.8510 0.976 0.024
#> GSM751329 1 0.416 0.8676 0.916 0.084
#> GSM751330 1 0.402 0.8688 0.920 0.080
#> GSM751331 1 0.388 0.8642 0.924 0.076
#> GSM751333 1 0.443 0.8683 0.908 0.092
#> GSM751335 1 0.402 0.8688 0.920 0.080
#> GSM751336 1 0.469 0.8659 0.900 0.100
#> GSM751337 1 0.456 0.8672 0.904 0.096
#> GSM751338 1 0.469 0.8658 0.900 0.100
#> GSM751340 1 0.529 0.8501 0.880 0.120
#> GSM751350 1 0.469 0.8659 0.900 0.100
#> GSM751351 1 0.469 0.8659 0.900 0.100
#> GSM751362 2 0.939 0.5515 0.356 0.644
#> GSM751363 2 0.653 0.7266 0.168 0.832
#> GSM751367 2 0.990 0.5036 0.440 0.560
#> GSM751368 2 0.494 0.7344 0.108 0.892
#> GSM751371 2 0.963 0.5448 0.388 0.612
#> GSM751375 2 0.443 0.7320 0.092 0.908
#> GSM751376 2 0.833 0.6864 0.264 0.736
#> GSM751378 2 0.311 0.7269 0.056 0.944
#> GSM751379 2 0.833 0.6864 0.264 0.736
#> GSM751382 2 0.443 0.7313 0.092 0.908
#> GSM751386 2 0.469 0.7328 0.100 0.900
#> GSM751388 2 0.469 0.7328 0.100 0.900
#> GSM751391 2 0.775 0.6856 0.228 0.772
#> GSM751410 2 0.955 0.5433 0.376 0.624
#> GSM751414 2 0.949 0.5758 0.368 0.632
#> GSM751361 2 0.605 0.7327 0.148 0.852
#> GSM751365 2 0.921 0.6037 0.336 0.664
#> GSM751366 2 0.949 0.5499 0.368 0.632
#> GSM751369 2 0.969 0.5229 0.396 0.604
#> GSM751370 2 0.955 0.5650 0.376 0.624
#> GSM751372 2 0.913 0.6155 0.328 0.672
#> GSM751373 2 0.952 0.5706 0.372 0.628
#> GSM751374 2 0.833 0.6864 0.264 0.736
#> GSM751377 2 0.563 0.7330 0.132 0.868
#> GSM751380 2 0.939 0.5515 0.356 0.644
#> GSM751381 2 0.469 0.7328 0.100 0.900
#> GSM751383 2 0.469 0.7328 0.100 0.900
#> GSM751384 2 0.506 0.7343 0.112 0.888
#> GSM751385 2 0.327 0.7291 0.060 0.940
#> GSM751387 2 0.469 0.7328 0.100 0.900
#> GSM751389 2 0.866 0.6279 0.288 0.712
#> GSM751393 2 0.482 0.7283 0.104 0.896
#> GSM751394 2 0.469 0.7328 0.100 0.900
#> GSM751395 2 0.402 0.7320 0.080 0.920
#> GSM751397 2 0.469 0.7328 0.100 0.900
#> GSM751398 2 0.482 0.7332 0.104 0.896
#> GSM751404 2 0.939 0.5515 0.356 0.644
#> GSM751406 2 0.936 0.5524 0.352 0.648
#> GSM751411 2 0.913 0.6089 0.328 0.672
#> GSM751413 2 0.529 0.7345 0.120 0.880
#> GSM751415 2 0.939 0.5515 0.356 0.644
#> GSM751416 2 0.595 0.7318 0.144 0.856
#> GSM751417 2 0.595 0.7318 0.144 0.856
#> GSM751421 2 0.963 0.5448 0.388 0.612
#> GSM751422 2 0.963 0.5448 0.388 0.612
#> GSM751360 2 0.949 0.5644 0.368 0.632
#> GSM751364 2 0.671 0.7227 0.176 0.824
#> GSM751390 2 0.482 0.7334 0.104 0.896
#> GSM751392 2 0.469 0.7328 0.100 0.900
#> GSM751396 2 0.469 0.7328 0.100 0.900
#> GSM751399 2 0.900 0.6040 0.316 0.684
#> GSM751400 2 0.891 0.6101 0.308 0.692
#> GSM751401 2 0.936 0.5524 0.352 0.648
#> GSM751402 2 0.936 0.5524 0.352 0.648
#> GSM751403 2 0.900 0.6005 0.316 0.684
#> GSM751405 2 0.936 0.5524 0.352 0.648
#> GSM751407 2 0.921 0.5752 0.336 0.664
#> GSM751408 2 0.900 0.6040 0.316 0.684
#> GSM751409 2 0.839 0.6437 0.268 0.732
#> GSM751412 2 0.904 0.5994 0.320 0.680
#> GSM751418 2 0.929 0.6056 0.344 0.656
#> GSM751419 2 0.921 0.6072 0.336 0.664
#> GSM751420 2 0.936 0.5715 0.352 0.648
#> GSM751425 2 0.552 0.7158 0.128 0.872
#> GSM751429 2 0.990 0.4736 0.440 0.560
#> GSM751430 2 0.767 0.7004 0.224 0.776
#> GSM751433 2 0.730 0.6842 0.204 0.796
#> GSM751437 2 0.876 0.6105 0.296 0.704
#> GSM751448 2 0.991 0.4610 0.444 0.556
#> GSM751451 2 0.680 0.6996 0.180 0.820
#> GSM751423 2 0.625 0.7129 0.156 0.844
#> GSM751424 2 0.697 0.6922 0.188 0.812
#> GSM751428 2 0.644 0.7054 0.164 0.836
#> GSM751431 2 0.706 0.6933 0.192 0.808
#> GSM751432 2 0.714 0.6923 0.196 0.804
#> GSM751434 2 0.706 0.6858 0.192 0.808
#> GSM751435 2 0.689 0.6917 0.184 0.816
#> GSM751436 2 0.706 0.6858 0.192 0.808
#> GSM751440 2 0.689 0.6967 0.184 0.816
#> GSM751444 2 0.625 0.6996 0.156 0.844
#> GSM751446 2 0.605 0.7045 0.148 0.852
#> GSM751449 2 0.552 0.7110 0.128 0.872
#> GSM751450 2 0.689 0.6967 0.184 0.816
#> GSM751452 2 0.697 0.6826 0.188 0.812
#> GSM751426 2 0.689 0.6967 0.184 0.816
#> GSM751427 2 0.605 0.7097 0.148 0.852
#> GSM751438 2 0.552 0.7110 0.128 0.872
#> GSM751439 2 0.936 0.5493 0.352 0.648
#> GSM751441 2 0.204 0.7166 0.032 0.968
#> GSM751442 2 0.605 0.7045 0.148 0.852
#> GSM751443 2 0.925 0.5620 0.340 0.660
#> GSM751445 2 0.518 0.7100 0.116 0.884
#> GSM751447 2 0.552 0.7095 0.128 0.872
#> GSM751453 2 0.615 0.7068 0.152 0.848
#> GSM751454 2 0.615 0.7068 0.152 0.848
#> GSM751455 2 0.605 0.7045 0.148 0.852
#> GSM751456 2 0.605 0.7045 0.148 0.852
#> GSM751457 2 0.506 0.7136 0.112 0.888
#> GSM751458 2 0.506 0.7136 0.112 0.888
cbind(get_classes(res, k = 3), get_membership(res, k = 3))
#> class entropy silhouette p1 p2 p3
#> GSM751298 1 0.3983 0.8932 0.884 0.048 0.068
#> GSM751304 2 0.8720 0.5369 0.252 0.584 0.164
#> GSM751305 2 0.8673 0.5299 0.252 0.588 0.160
#> GSM751307 2 0.7906 0.5884 0.220 0.656 0.124
#> GSM751310 1 0.1950 0.8456 0.952 0.040 0.008
#> GSM751314 1 0.1950 0.8465 0.952 0.040 0.008
#> GSM751316 1 0.2280 0.8420 0.940 0.052 0.008
#> GSM751318 1 0.3780 0.8928 0.892 0.044 0.064
#> GSM751342 1 0.2063 0.8445 0.948 0.044 0.008
#> GSM751346 1 0.4982 0.8882 0.840 0.064 0.096
#> GSM751347 1 0.7651 0.6748 0.672 0.108 0.220
#> GSM751348 2 0.9268 0.4311 0.348 0.484 0.168
#> GSM751349 2 0.6803 0.5271 0.040 0.680 0.280
#> GSM751352 2 0.8556 0.5511 0.232 0.604 0.164
#> GSM751353 2 0.6438 0.6043 0.064 0.748 0.188
#> GSM751354 2 0.8525 0.5707 0.188 0.612 0.200
#> GSM751355 2 0.6541 0.5999 0.056 0.732 0.212
#> GSM751358 1 0.9193 -0.1526 0.480 0.364 0.156
#> GSM751359 2 0.8311 0.4459 0.132 0.616 0.252
#> GSM751294 2 0.9156 0.5287 0.204 0.540 0.256
#> GSM751296 1 0.4423 0.8934 0.864 0.048 0.088
#> GSM751297 1 0.5696 0.8583 0.800 0.064 0.136
#> GSM751299 2 0.8670 0.5426 0.240 0.592 0.168
#> GSM751300 1 0.4982 0.8882 0.840 0.064 0.096
#> GSM751301 1 0.8457 0.2204 0.512 0.396 0.092
#> GSM751302 1 0.4982 0.8882 0.840 0.064 0.096
#> GSM751303 1 0.2173 0.8420 0.944 0.048 0.008
#> GSM751306 1 0.2063 0.8445 0.948 0.044 0.008
#> GSM751308 1 0.6693 0.8067 0.748 0.104 0.148
#> GSM751309 1 0.2063 0.8445 0.948 0.044 0.008
#> GSM751311 1 0.2063 0.8445 0.948 0.044 0.008
#> GSM751312 1 0.2280 0.8420 0.940 0.052 0.008
#> GSM751313 1 0.4725 0.8912 0.852 0.060 0.088
#> GSM751315 1 0.0829 0.8608 0.984 0.004 0.012
#> GSM751317 1 0.2116 0.8484 0.948 0.040 0.012
#> GSM751320 1 0.4058 0.8938 0.880 0.044 0.076
#> GSM751321 1 0.2063 0.8445 0.948 0.044 0.008
#> GSM751322 1 0.2793 0.8827 0.928 0.028 0.044
#> GSM751324 1 0.2793 0.8827 0.928 0.028 0.044
#> GSM751325 1 0.3875 0.8935 0.888 0.044 0.068
#> GSM751332 1 0.4253 0.8924 0.872 0.048 0.080
#> GSM751334 1 0.4253 0.8924 0.872 0.048 0.080
#> GSM751339 1 0.4725 0.8922 0.852 0.060 0.088
#> GSM751341 1 0.2269 0.8580 0.944 0.040 0.016
#> GSM751343 1 0.4165 0.8935 0.876 0.048 0.076
#> GSM751344 2 0.8058 0.5876 0.212 0.648 0.140
#> GSM751345 2 0.8058 0.5876 0.212 0.648 0.140
#> GSM751356 2 0.9119 0.3558 0.368 0.484 0.148
#> GSM751357 2 0.9119 0.3558 0.368 0.484 0.148
#> GSM751293 1 0.7987 0.5168 0.616 0.292 0.092
#> GSM751295 1 0.4982 0.8882 0.840 0.064 0.096
#> GSM751319 1 0.2063 0.8445 0.948 0.044 0.008
#> GSM751323 1 0.4058 0.8938 0.880 0.044 0.076
#> GSM751326 1 0.4443 0.8923 0.864 0.052 0.084
#> GSM751327 1 0.3683 0.8918 0.896 0.044 0.060
#> GSM751328 1 0.1751 0.8636 0.960 0.028 0.012
#> GSM751329 1 0.4165 0.8935 0.876 0.048 0.076
#> GSM751330 1 0.4725 0.8912 0.852 0.060 0.088
#> GSM751331 1 0.4902 0.8898 0.844 0.064 0.092
#> GSM751333 1 0.4725 0.8912 0.852 0.060 0.088
#> GSM751335 1 0.4725 0.8912 0.852 0.060 0.088
#> GSM751336 1 0.4725 0.8912 0.852 0.060 0.088
#> GSM751337 1 0.4628 0.8914 0.856 0.056 0.088
#> GSM751338 1 0.4725 0.8922 0.852 0.060 0.088
#> GSM751340 1 0.6424 0.8030 0.752 0.068 0.180
#> GSM751350 1 0.5060 0.8870 0.836 0.064 0.100
#> GSM751351 1 0.5060 0.8870 0.836 0.064 0.100
#> GSM751362 3 0.2939 0.7434 0.072 0.012 0.916
#> GSM751363 3 0.6762 0.5306 0.036 0.288 0.676
#> GSM751367 3 0.5285 0.6760 0.148 0.040 0.812
#> GSM751368 3 0.6229 0.4730 0.008 0.340 0.652
#> GSM751371 3 0.3502 0.7374 0.084 0.020 0.896
#> GSM751375 2 0.6500 -0.0216 0.004 0.532 0.464
#> GSM751376 3 0.6562 0.4607 0.036 0.264 0.700
#> GSM751378 3 0.5678 0.5111 0.000 0.316 0.684
#> GSM751379 3 0.6526 0.4672 0.036 0.260 0.704
#> GSM751382 2 0.6516 -0.0816 0.004 0.516 0.480
#> GSM751386 3 0.6489 0.2562 0.004 0.456 0.540
#> GSM751388 3 0.6489 0.2562 0.004 0.456 0.540
#> GSM751391 3 0.3670 0.7152 0.020 0.092 0.888
#> GSM751410 3 0.3587 0.7374 0.088 0.020 0.892
#> GSM751414 3 0.4475 0.7365 0.072 0.064 0.864
#> GSM751361 3 0.6129 0.5614 0.016 0.284 0.700
#> GSM751365 3 0.3530 0.7469 0.068 0.032 0.900
#> GSM751366 3 0.2680 0.7471 0.068 0.008 0.924
#> GSM751369 3 0.4121 0.7289 0.084 0.040 0.876
#> GSM751370 3 0.4458 0.7376 0.080 0.056 0.864
#> GSM751372 3 0.4379 0.7380 0.072 0.060 0.868
#> GSM751373 3 0.3967 0.7430 0.072 0.044 0.884
#> GSM751374 3 0.6562 0.4607 0.036 0.264 0.700
#> GSM751377 3 0.6051 0.5510 0.012 0.292 0.696
#> GSM751380 3 0.2998 0.7470 0.068 0.016 0.916
#> GSM751381 3 0.6489 0.2562 0.004 0.456 0.540
#> GSM751383 3 0.6476 0.2762 0.004 0.448 0.548
#> GSM751384 3 0.5968 0.4612 0.000 0.364 0.636
#> GSM751385 3 0.3686 0.6749 0.000 0.140 0.860
#> GSM751387 3 0.6489 0.2562 0.004 0.456 0.540
#> GSM751389 3 0.2318 0.7373 0.028 0.028 0.944
#> GSM751393 3 0.2845 0.7153 0.012 0.068 0.920
#> GSM751394 3 0.6489 0.2562 0.004 0.456 0.540
#> GSM751395 3 0.4575 0.6342 0.012 0.160 0.828
#> GSM751397 3 0.6476 0.2762 0.004 0.448 0.548
#> GSM751398 3 0.6608 0.3109 0.008 0.432 0.560
#> GSM751404 3 0.2998 0.7470 0.068 0.016 0.916
#> GSM751406 3 0.2998 0.7448 0.068 0.016 0.916
#> GSM751411 3 0.3472 0.7456 0.056 0.040 0.904
#> GSM751413 3 0.6677 0.4732 0.024 0.324 0.652
#> GSM751415 3 0.2998 0.7470 0.068 0.016 0.916
#> GSM751416 3 0.5986 0.5579 0.012 0.284 0.704
#> GSM751417 3 0.5986 0.5579 0.012 0.284 0.704
#> GSM751421 3 0.3502 0.7374 0.084 0.020 0.896
#> GSM751422 3 0.3502 0.7374 0.084 0.020 0.896
#> GSM751360 3 0.2496 0.7467 0.068 0.004 0.928
#> GSM751364 3 0.5678 0.6633 0.032 0.192 0.776
#> GSM751390 3 0.5948 0.4672 0.000 0.360 0.640
#> GSM751392 3 0.6518 0.1700 0.004 0.484 0.512
#> GSM751396 3 0.6520 0.1566 0.004 0.488 0.508
#> GSM751399 3 0.2680 0.7471 0.068 0.008 0.924
#> GSM751400 3 0.2998 0.7448 0.068 0.016 0.916
#> GSM751401 3 0.2998 0.7470 0.068 0.016 0.916
#> GSM751402 3 0.2998 0.7448 0.068 0.016 0.916
#> GSM751403 3 0.2998 0.7470 0.068 0.016 0.916
#> GSM751405 3 0.2998 0.7448 0.068 0.016 0.916
#> GSM751407 3 0.2998 0.7470 0.068 0.016 0.916
#> GSM751408 3 0.2845 0.7474 0.068 0.012 0.920
#> GSM751409 3 0.2743 0.7478 0.052 0.020 0.928
#> GSM751412 3 0.2998 0.7473 0.068 0.016 0.916
#> GSM751418 3 0.4836 0.7322 0.072 0.080 0.848
#> GSM751419 3 0.4836 0.7322 0.072 0.080 0.848
#> GSM751420 3 0.3983 0.7285 0.068 0.048 0.884
#> GSM751425 2 0.5159 0.7290 0.040 0.820 0.140
#> GSM751429 3 0.7058 0.5382 0.100 0.180 0.720
#> GSM751430 2 0.7367 0.5451 0.060 0.648 0.292
#> GSM751433 2 0.4868 0.7508 0.056 0.844 0.100
#> GSM751437 3 0.7624 0.1923 0.052 0.368 0.580
#> GSM751448 3 0.7227 0.5120 0.096 0.200 0.704
#> GSM751451 2 0.5408 0.7415 0.052 0.812 0.136
#> GSM751423 2 0.5473 0.7392 0.052 0.808 0.140
#> GSM751424 2 0.4742 0.7506 0.048 0.848 0.104
#> GSM751428 2 0.5020 0.7517 0.056 0.836 0.108
#> GSM751431 2 0.4818 0.7516 0.048 0.844 0.108
#> GSM751432 2 0.5473 0.7417 0.052 0.808 0.140
#> GSM751434 2 0.5094 0.7439 0.056 0.832 0.112
#> GSM751435 2 0.5138 0.7484 0.052 0.828 0.120
#> GSM751436 2 0.4845 0.7510 0.052 0.844 0.104
#> GSM751440 2 0.5473 0.7392 0.052 0.808 0.140
#> GSM751444 2 0.5473 0.7487 0.052 0.808 0.140
#> GSM751446 2 0.6098 0.7344 0.056 0.768 0.176
#> GSM751449 2 0.6054 0.7327 0.052 0.768 0.180
#> GSM751450 2 0.4920 0.7513 0.052 0.840 0.108
#> GSM751452 2 0.4845 0.7510 0.052 0.844 0.104
#> GSM751426 2 0.5020 0.7512 0.056 0.836 0.108
#> GSM751427 2 0.5307 0.7395 0.048 0.816 0.136
#> GSM751438 2 0.6203 0.7298 0.056 0.760 0.184
#> GSM751439 2 0.7932 0.3908 0.064 0.552 0.384
#> GSM751441 2 0.5551 0.6696 0.016 0.760 0.224
#> GSM751442 2 0.6245 0.7316 0.060 0.760 0.180
#> GSM751443 3 0.7995 -0.1362 0.060 0.460 0.480
#> GSM751445 2 0.5371 0.7462 0.048 0.812 0.140
#> GSM751447 2 0.5875 0.7404 0.056 0.784 0.160
#> GSM751453 2 0.5020 0.7513 0.056 0.836 0.108
#> GSM751454 2 0.5020 0.7513 0.056 0.836 0.108
#> GSM751455 2 0.6245 0.7316 0.060 0.760 0.180
#> GSM751456 2 0.6245 0.7316 0.060 0.760 0.180
#> GSM751457 2 0.7023 0.5166 0.032 0.624 0.344
#> GSM751458 2 0.7023 0.5166 0.032 0.624 0.344
cbind(get_classes(res, k = 4), get_membership(res, k = 4))
#> class entropy silhouette p1 p2 p3 p4
#> GSM751298 1 0.2722 0.8583 0.904 0.032 0.064 0.000
#> GSM751304 4 0.6449 0.6448 0.084 0.148 0.056 0.712
#> GSM751305 4 0.6538 0.6398 0.084 0.156 0.056 0.704
#> GSM751307 4 0.7130 0.6485 0.084 0.240 0.048 0.628
#> GSM751310 1 0.2976 0.7661 0.872 0.000 0.008 0.120
#> GSM751314 1 0.3375 0.7643 0.864 0.008 0.012 0.116
#> GSM751316 1 0.3823 0.7323 0.824 0.008 0.008 0.160
#> GSM751318 1 0.3337 0.8563 0.888 0.032 0.060 0.020
#> GSM751342 1 0.3703 0.7494 0.840 0.008 0.012 0.140
#> GSM751346 1 0.4918 0.8342 0.812 0.040 0.064 0.084
#> GSM751347 1 0.6629 0.7103 0.700 0.052 0.140 0.108
#> GSM751348 4 0.9086 0.4705 0.304 0.236 0.072 0.388
#> GSM751349 4 0.7978 0.1777 0.036 0.368 0.128 0.468
#> GSM751352 4 0.6743 0.6624 0.092 0.196 0.040 0.672
#> GSM751353 4 0.6041 0.5853 0.032 0.276 0.028 0.664
#> GSM751354 4 0.6895 0.6374 0.056 0.192 0.084 0.668
#> GSM751355 4 0.6637 0.5818 0.028 0.264 0.068 0.640
#> GSM751358 4 0.8213 0.3782 0.364 0.076 0.092 0.468
#> GSM751359 4 0.8201 0.4009 0.112 0.244 0.092 0.552
#> GSM751294 4 0.8506 0.5805 0.132 0.200 0.124 0.544
#> GSM751296 1 0.3813 0.8578 0.868 0.036 0.064 0.032
#> GSM751297 1 0.6004 0.7750 0.744 0.044 0.096 0.116
#> GSM751299 4 0.6822 0.6551 0.088 0.212 0.040 0.660
#> GSM751300 1 0.4918 0.8341 0.812 0.040 0.064 0.084
#> GSM751301 4 0.7606 0.3842 0.372 0.144 0.012 0.472
#> GSM751302 1 0.5228 0.8202 0.792 0.040 0.064 0.104
#> GSM751303 1 0.3805 0.7393 0.832 0.008 0.012 0.148
#> GSM751306 1 0.3805 0.7393 0.832 0.008 0.012 0.148
#> GSM751308 1 0.7155 0.5675 0.640 0.056 0.088 0.216
#> GSM751309 1 0.3805 0.7393 0.832 0.008 0.012 0.148
#> GSM751311 1 0.3805 0.7393 0.832 0.008 0.012 0.148
#> GSM751312 1 0.3823 0.7323 0.824 0.008 0.008 0.160
#> GSM751313 1 0.3997 0.8539 0.860 0.040 0.064 0.036
#> GSM751315 1 0.2101 0.8101 0.928 0.000 0.012 0.060
#> GSM751317 1 0.3093 0.7928 0.884 0.004 0.020 0.092
#> GSM751320 1 0.2907 0.8589 0.900 0.032 0.064 0.004
#> GSM751321 1 0.3677 0.7383 0.836 0.008 0.008 0.148
#> GSM751322 1 0.2221 0.8496 0.932 0.016 0.044 0.008
#> GSM751324 1 0.2335 0.8487 0.928 0.020 0.044 0.008
#> GSM751325 1 0.3052 0.8580 0.896 0.032 0.064 0.008
#> GSM751332 1 0.3069 0.8588 0.896 0.036 0.060 0.008
#> GSM751334 1 0.3069 0.8588 0.896 0.036 0.060 0.008
#> GSM751339 1 0.3886 0.8544 0.860 0.040 0.080 0.020
#> GSM751341 1 0.2781 0.7981 0.904 0.008 0.016 0.072
#> GSM751343 1 0.2924 0.8588 0.900 0.036 0.060 0.004
#> GSM751344 4 0.6712 0.6346 0.076 0.256 0.028 0.640
#> GSM751345 4 0.6712 0.6346 0.076 0.256 0.028 0.640
#> GSM751356 4 0.6972 0.6398 0.184 0.124 0.036 0.656
#> GSM751357 4 0.6972 0.6398 0.184 0.124 0.036 0.656
#> GSM751293 4 0.7357 0.2718 0.412 0.112 0.012 0.464
#> GSM751295 1 0.5228 0.8202 0.792 0.040 0.064 0.104
#> GSM751319 1 0.3677 0.7383 0.836 0.008 0.008 0.148
#> GSM751323 1 0.2907 0.8589 0.900 0.032 0.064 0.004
#> GSM751326 1 0.3705 0.8569 0.872 0.040 0.064 0.024
#> GSM751327 1 0.2623 0.8584 0.908 0.028 0.064 0.000
#> GSM751328 1 0.2039 0.8151 0.940 0.008 0.016 0.036
#> GSM751329 1 0.2990 0.8591 0.900 0.036 0.056 0.008
#> GSM751330 1 0.4569 0.8439 0.832 0.040 0.060 0.068
#> GSM751331 1 0.5034 0.8282 0.804 0.040 0.060 0.096
#> GSM751333 1 0.4496 0.8455 0.836 0.040 0.060 0.064
#> GSM751335 1 0.4569 0.8439 0.832 0.040 0.060 0.068
#> GSM751336 1 0.4715 0.8403 0.824 0.040 0.064 0.072
#> GSM751337 1 0.3881 0.8553 0.864 0.040 0.068 0.028
#> GSM751338 1 0.3599 0.8574 0.876 0.040 0.064 0.020
#> GSM751340 1 0.5984 0.7502 0.732 0.040 0.164 0.064
#> GSM751350 1 0.5286 0.8173 0.788 0.040 0.064 0.108
#> GSM751351 1 0.5286 0.8173 0.788 0.040 0.064 0.108
#> GSM751362 3 0.1377 0.7076 0.020 0.008 0.964 0.008
#> GSM751363 3 0.6892 0.5447 0.012 0.104 0.596 0.288
#> GSM751367 3 0.4324 0.6497 0.056 0.024 0.840 0.080
#> GSM751368 3 0.7166 0.5366 0.008 0.244 0.584 0.164
#> GSM751371 3 0.3444 0.6908 0.024 0.032 0.884 0.060
#> GSM751375 4 0.8080 -0.2738 0.004 0.332 0.324 0.340
#> GSM751376 3 0.6649 0.3931 0.004 0.120 0.620 0.256
#> GSM751378 3 0.7105 0.5067 0.004 0.152 0.568 0.276
#> GSM751379 3 0.6649 0.3931 0.004 0.120 0.620 0.256
#> GSM751382 3 0.8061 0.2779 0.004 0.336 0.360 0.300
#> GSM751386 3 0.8015 0.3355 0.004 0.308 0.396 0.292
#> GSM751388 3 0.8006 0.3356 0.004 0.308 0.400 0.288
#> GSM751391 3 0.3709 0.6795 0.004 0.040 0.856 0.100
#> GSM751410 3 0.2261 0.6999 0.036 0.008 0.932 0.024
#> GSM751414 3 0.4147 0.6898 0.008 0.064 0.840 0.088
#> GSM751361 3 0.7027 0.5613 0.008 0.204 0.608 0.180
#> GSM751365 3 0.3232 0.7062 0.012 0.028 0.888 0.072
#> GSM751366 3 0.1617 0.7132 0.012 0.008 0.956 0.024
#> GSM751369 3 0.3391 0.6840 0.020 0.028 0.884 0.068
#> GSM751370 3 0.3591 0.7031 0.016 0.032 0.872 0.080
#> GSM751372 3 0.3374 0.7044 0.012 0.028 0.880 0.080
#> GSM751373 3 0.2636 0.7131 0.012 0.020 0.916 0.052
#> GSM751374 3 0.6649 0.3931 0.004 0.120 0.620 0.256
#> GSM751377 3 0.7163 0.5305 0.004 0.232 0.576 0.188
#> GSM751380 3 0.1271 0.7095 0.012 0.012 0.968 0.008
#> GSM751381 3 0.8006 0.3356 0.004 0.308 0.400 0.288
#> GSM751383 3 0.8006 0.3356 0.004 0.308 0.400 0.288
#> GSM751384 3 0.7469 0.4767 0.004 0.196 0.524 0.276
#> GSM751385 3 0.5677 0.6159 0.000 0.064 0.680 0.256
#> GSM751387 3 0.8006 0.3356 0.004 0.308 0.400 0.288
#> GSM751389 3 0.2057 0.7045 0.008 0.020 0.940 0.032
#> GSM751393 3 0.3551 0.6853 0.004 0.028 0.860 0.108
#> GSM751394 3 0.8006 0.3356 0.004 0.308 0.400 0.288
#> GSM751395 3 0.5714 0.5181 0.004 0.056 0.684 0.256
#> GSM751397 3 0.7998 0.3411 0.004 0.304 0.404 0.288
#> GSM751398 3 0.8007 0.3411 0.004 0.304 0.400 0.292
#> GSM751404 3 0.0937 0.7104 0.012 0.012 0.976 0.000
#> GSM751406 3 0.1749 0.7060 0.012 0.012 0.952 0.024
#> GSM751411 3 0.3709 0.6917 0.004 0.040 0.856 0.100
#> GSM751413 3 0.7675 0.4127 0.012 0.168 0.500 0.320
#> GSM751415 3 0.0937 0.7104 0.012 0.012 0.976 0.000
#> GSM751416 3 0.7092 0.5545 0.008 0.208 0.600 0.184
#> GSM751417 3 0.7092 0.5545 0.008 0.208 0.600 0.184
#> GSM751421 3 0.3444 0.6927 0.024 0.032 0.884 0.060
#> GSM751422 3 0.3444 0.6927 0.024 0.032 0.884 0.060
#> GSM751360 3 0.3030 0.6983 0.020 0.020 0.900 0.060
#> GSM751364 3 0.6214 0.6135 0.004 0.152 0.684 0.160
#> GSM751390 3 0.7429 0.4805 0.004 0.188 0.528 0.280
#> GSM751392 3 0.8043 0.3151 0.004 0.316 0.380 0.300
#> GSM751396 3 0.8048 0.3027 0.004 0.320 0.376 0.300
#> GSM751399 3 0.1509 0.7140 0.008 0.012 0.960 0.020
#> GSM751400 3 0.1271 0.7092 0.012 0.012 0.968 0.008
#> GSM751401 3 0.1124 0.7096 0.012 0.012 0.972 0.004
#> GSM751402 3 0.1124 0.7096 0.012 0.012 0.972 0.004
#> GSM751403 3 0.1124 0.7101 0.012 0.012 0.972 0.004
#> GSM751405 3 0.1124 0.7096 0.012 0.012 0.972 0.004
#> GSM751407 3 0.1124 0.7096 0.012 0.012 0.972 0.004
#> GSM751408 3 0.1271 0.7138 0.008 0.012 0.968 0.012
#> GSM751409 3 0.1394 0.7113 0.008 0.016 0.964 0.012
#> GSM751412 3 0.1721 0.7135 0.008 0.012 0.952 0.028
#> GSM751418 3 0.4067 0.6994 0.012 0.060 0.848 0.080
#> GSM751419 3 0.4067 0.6994 0.012 0.060 0.848 0.080
#> GSM751420 3 0.3159 0.6824 0.012 0.028 0.892 0.068
#> GSM751425 2 0.2686 0.8248 0.012 0.916 0.040 0.032
#> GSM751429 3 0.6367 0.4803 0.032 0.200 0.692 0.076
#> GSM751430 2 0.8061 -0.2183 0.028 0.416 0.152 0.404
#> GSM751433 2 0.4523 0.7721 0.020 0.816 0.036 0.128
#> GSM751437 3 0.6427 -0.0989 0.008 0.440 0.504 0.048
#> GSM751448 3 0.6145 0.4880 0.024 0.196 0.704 0.076
#> GSM751451 2 0.2797 0.8373 0.016 0.912 0.044 0.028
#> GSM751423 2 0.3026 0.8432 0.012 0.900 0.056 0.032
#> GSM751424 2 0.4242 0.7919 0.020 0.836 0.036 0.108
#> GSM751428 2 0.3255 0.8397 0.016 0.892 0.044 0.048
#> GSM751431 2 0.3508 0.8254 0.020 0.880 0.036 0.064
#> GSM751432 2 0.5261 0.7314 0.024 0.772 0.052 0.152
#> GSM751434 2 0.4865 0.7533 0.020 0.792 0.040 0.148
#> GSM751435 2 0.3039 0.8467 0.012 0.900 0.052 0.036
#> GSM751436 2 0.4523 0.7721 0.020 0.816 0.036 0.128
#> GSM751440 2 0.3007 0.8443 0.012 0.900 0.060 0.028
#> GSM751444 2 0.3626 0.8388 0.012 0.872 0.060 0.056
#> GSM751446 2 0.3656 0.8353 0.012 0.868 0.080 0.040
#> GSM751449 2 0.3656 0.8353 0.012 0.868 0.080 0.040
#> GSM751450 2 0.3522 0.8303 0.020 0.880 0.040 0.060
#> GSM751452 2 0.4523 0.7768 0.020 0.816 0.036 0.128
#> GSM751426 2 0.3240 0.8310 0.016 0.892 0.036 0.056
#> GSM751427 2 0.3105 0.8432 0.012 0.896 0.060 0.032
#> GSM751438 2 0.3895 0.8269 0.012 0.856 0.084 0.048
#> GSM751439 2 0.5429 0.6502 0.012 0.728 0.216 0.044
#> GSM751441 2 0.3820 0.8168 0.000 0.848 0.088 0.064
#> GSM751442 2 0.3811 0.8296 0.012 0.860 0.084 0.044
#> GSM751443 2 0.6578 0.3237 0.008 0.524 0.408 0.060
#> GSM751445 2 0.3290 0.8396 0.012 0.888 0.060 0.040
#> GSM751447 2 0.3614 0.8349 0.012 0.872 0.068 0.048
#> GSM751453 2 0.2775 0.8432 0.012 0.912 0.044 0.032
#> GSM751454 2 0.2775 0.8432 0.012 0.912 0.044 0.032
#> GSM751455 2 0.3724 0.8308 0.012 0.864 0.084 0.040
#> GSM751456 2 0.3724 0.8308 0.012 0.864 0.084 0.040
#> GSM751457 2 0.5610 0.6757 0.008 0.732 0.180 0.080
#> GSM751458 2 0.5610 0.6757 0.008 0.732 0.180 0.080
cbind(get_classes(res, k = 5), get_membership(res, k = 5))
#> class entropy silhouette p1 p2 p3 p4 p5
#> GSM751298 1 0.2234 0.7765 0.920 0.036 0.000 0.012 0.032
#> GSM751304 4 0.5365 0.7730 0.064 0.064 0.032 0.764 0.076
#> GSM751305 4 0.5161 0.7595 0.048 0.064 0.032 0.776 0.080
#> GSM751307 4 0.6568 0.7808 0.068 0.132 0.020 0.660 0.120
#> GSM751310 1 0.4078 0.6917 0.796 0.004 0.000 0.128 0.072
#> GSM751314 1 0.4550 0.6662 0.760 0.004 0.000 0.136 0.100
#> GSM751316 1 0.5033 0.6401 0.712 0.004 0.000 0.176 0.108
#> GSM751318 1 0.2416 0.7740 0.916 0.032 0.004 0.016 0.032
#> GSM751342 1 0.4634 0.6582 0.752 0.004 0.000 0.144 0.100
#> GSM751346 1 0.5125 0.7273 0.752 0.048 0.020 0.152 0.028
#> GSM751347 1 0.5828 0.6980 0.712 0.048 0.044 0.160 0.036
#> GSM751348 1 0.8433 -0.4031 0.372 0.088 0.024 0.316 0.200
#> GSM751349 5 0.6523 0.3809 0.020 0.104 0.036 0.208 0.632
#> GSM751352 4 0.5726 0.7915 0.080 0.116 0.012 0.724 0.068
#> GSM751353 4 0.6249 0.7611 0.048 0.128 0.008 0.664 0.152
#> GSM751354 4 0.6134 0.7857 0.060 0.108 0.036 0.708 0.088
#> GSM751355 4 0.6501 0.7519 0.032 0.128 0.032 0.656 0.152
#> GSM751358 4 0.7409 0.2009 0.356 0.016 0.028 0.436 0.164
#> GSM751359 5 0.6958 -0.2376 0.056 0.056 0.020 0.384 0.484
#> GSM751294 4 0.7967 0.6731 0.180 0.100 0.076 0.552 0.092
#> GSM751296 1 0.2934 0.7803 0.892 0.036 0.008 0.048 0.016
#> GSM751297 1 0.5593 0.7031 0.720 0.048 0.024 0.168 0.040
#> GSM751299 4 0.5802 0.7875 0.072 0.124 0.016 0.720 0.068
#> GSM751300 1 0.5032 0.7292 0.756 0.048 0.016 0.152 0.028
#> GSM751301 4 0.6454 0.6120 0.308 0.088 0.000 0.560 0.044
#> GSM751302 1 0.5215 0.7170 0.740 0.052 0.016 0.164 0.028
#> GSM751303 1 0.4850 0.6440 0.732 0.004 0.000 0.156 0.108
#> GSM751306 1 0.4812 0.6473 0.736 0.004 0.000 0.152 0.108
#> GSM751308 1 0.6686 0.2907 0.568 0.060 0.048 0.304 0.020
#> GSM751309 1 0.4812 0.6473 0.736 0.004 0.000 0.152 0.108
#> GSM751311 1 0.4812 0.6473 0.736 0.004 0.000 0.152 0.108
#> GSM751312 1 0.5068 0.6358 0.708 0.004 0.000 0.180 0.108
#> GSM751313 1 0.4491 0.7534 0.804 0.040 0.020 0.108 0.028
#> GSM751315 1 0.2152 0.7550 0.920 0.004 0.000 0.044 0.032
#> GSM751317 1 0.3270 0.7247 0.852 0.004 0.000 0.100 0.044
#> GSM751320 1 0.1356 0.7824 0.956 0.028 0.012 0.000 0.004
#> GSM751321 1 0.4812 0.6473 0.736 0.004 0.000 0.152 0.108
#> GSM751322 1 0.2157 0.7728 0.928 0.024 0.004 0.016 0.028
#> GSM751324 1 0.2243 0.7717 0.924 0.024 0.004 0.016 0.032
#> GSM751325 1 0.1988 0.7795 0.936 0.028 0.008 0.012 0.016
#> GSM751332 1 0.1281 0.7825 0.956 0.032 0.012 0.000 0.000
#> GSM751334 1 0.1569 0.7824 0.948 0.032 0.012 0.008 0.000
#> GSM751339 1 0.3520 0.7747 0.864 0.040 0.024 0.060 0.012
#> GSM751341 1 0.4277 0.6851 0.784 0.004 0.000 0.112 0.100
#> GSM751343 1 0.1569 0.7816 0.948 0.032 0.008 0.000 0.012
#> GSM751344 4 0.6164 0.7874 0.072 0.132 0.012 0.688 0.096
#> GSM751345 4 0.6164 0.7874 0.072 0.132 0.012 0.688 0.096
#> GSM751356 4 0.6344 0.7114 0.108 0.052 0.036 0.688 0.116
#> GSM751357 4 0.6344 0.7114 0.108 0.052 0.036 0.688 0.116
#> GSM751293 4 0.6266 0.5755 0.328 0.072 0.000 0.560 0.040
#> GSM751295 1 0.5215 0.7170 0.740 0.052 0.016 0.164 0.028
#> GSM751319 1 0.4812 0.6473 0.736 0.004 0.000 0.152 0.108
#> GSM751323 1 0.1483 0.7830 0.952 0.028 0.012 0.008 0.000
#> GSM751326 1 0.3320 0.7756 0.872 0.036 0.012 0.064 0.016
#> GSM751327 1 0.1369 0.7830 0.956 0.028 0.008 0.008 0.000
#> GSM751328 1 0.3485 0.7231 0.848 0.004 0.004 0.060 0.084
#> GSM751329 1 0.2756 0.7806 0.900 0.036 0.012 0.044 0.008
#> GSM751330 1 0.4974 0.7350 0.764 0.044 0.020 0.144 0.028
#> GSM751331 1 0.5171 0.7211 0.744 0.044 0.020 0.164 0.028
#> GSM751333 1 0.4817 0.7401 0.776 0.040 0.020 0.136 0.028
#> GSM751335 1 0.4974 0.7350 0.764 0.044 0.020 0.144 0.028
#> GSM751336 1 0.4974 0.7350 0.764 0.044 0.020 0.144 0.028
#> GSM751337 1 0.3494 0.7727 0.864 0.040 0.020 0.064 0.012
#> GSM751338 1 0.3494 0.7749 0.864 0.040 0.020 0.064 0.012
#> GSM751340 1 0.6191 0.6170 0.676 0.040 0.168 0.096 0.020
#> GSM751350 1 0.5252 0.7136 0.736 0.052 0.016 0.168 0.028
#> GSM751351 1 0.5252 0.7136 0.736 0.052 0.016 0.168 0.028
#> GSM751362 3 0.2462 0.7258 0.020 0.004 0.912 0.016 0.048
#> GSM751363 3 0.7226 -0.0907 0.004 0.024 0.420 0.196 0.356
#> GSM751367 3 0.4348 0.6656 0.052 0.012 0.820 0.056 0.060
#> GSM751368 3 0.5982 -0.2425 0.000 0.068 0.484 0.016 0.432
#> GSM751371 3 0.3035 0.7055 0.020 0.008 0.888 0.044 0.040
#> GSM751375 5 0.5282 0.7649 0.000 0.084 0.172 0.028 0.716
#> GSM751376 3 0.6740 0.4018 0.000 0.064 0.556 0.284 0.096
#> GSM751378 5 0.5156 0.6459 0.000 0.040 0.332 0.008 0.620
#> GSM751379 3 0.6793 0.3981 0.000 0.068 0.552 0.284 0.096
#> GSM751382 5 0.4724 0.8026 0.000 0.080 0.168 0.008 0.744
#> GSM751386 5 0.4489 0.8217 0.000 0.068 0.192 0.000 0.740
#> GSM751388 5 0.4489 0.8217 0.000 0.068 0.192 0.000 0.740
#> GSM751391 3 0.2938 0.6986 0.000 0.008 0.880 0.064 0.048
#> GSM751410 3 0.2647 0.7153 0.028 0.008 0.908 0.024 0.032
#> GSM751414 3 0.4251 0.3784 0.000 0.000 0.672 0.012 0.316
#> GSM751361 3 0.5547 -0.2908 0.000 0.048 0.484 0.008 0.460
#> GSM751365 3 0.3783 0.5586 0.000 0.004 0.768 0.012 0.216
#> GSM751366 3 0.1991 0.7083 0.000 0.004 0.916 0.004 0.076
#> GSM751369 3 0.3680 0.6863 0.016 0.012 0.852 0.052 0.068
#> GSM751370 3 0.4533 0.4532 0.012 0.004 0.688 0.008 0.288
#> GSM751372 3 0.4240 0.4479 0.000 0.004 0.700 0.012 0.284
#> GSM751373 3 0.2237 0.7034 0.000 0.008 0.904 0.004 0.084
#> GSM751374 3 0.6793 0.3981 0.000 0.068 0.552 0.284 0.096
#> GSM751377 5 0.5626 0.4074 0.000 0.048 0.432 0.012 0.508
#> GSM751380 3 0.0451 0.7272 0.000 0.004 0.988 0.000 0.008
#> GSM751381 5 0.4489 0.8217 0.000 0.068 0.192 0.000 0.740
#> GSM751383 5 0.4489 0.8217 0.000 0.068 0.192 0.000 0.740
#> GSM751384 5 0.4498 0.7319 0.000 0.032 0.280 0.000 0.688
#> GSM751385 3 0.5786 0.2793 0.000 0.008 0.584 0.088 0.320
#> GSM751387 5 0.4489 0.8217 0.000 0.068 0.192 0.000 0.740
#> GSM751389 3 0.2916 0.7003 0.000 0.012 0.884 0.056 0.048
#> GSM751393 3 0.5213 0.6065 0.000 0.016 0.716 0.160 0.108
#> GSM751394 5 0.4489 0.8217 0.000 0.068 0.192 0.000 0.740
#> GSM751395 3 0.6419 0.4446 0.000 0.032 0.576 0.276 0.116
#> GSM751397 5 0.4462 0.8188 0.000 0.064 0.196 0.000 0.740
#> GSM751398 5 0.4489 0.8217 0.000 0.068 0.192 0.000 0.740
#> GSM751404 3 0.1430 0.7205 0.000 0.004 0.944 0.000 0.052
#> GSM751406 3 0.1593 0.7209 0.008 0.008 0.952 0.016 0.016
#> GSM751411 3 0.3992 0.4783 0.000 0.000 0.720 0.012 0.268
#> GSM751413 3 0.7660 -0.0665 0.000 0.052 0.380 0.252 0.316
#> GSM751415 3 0.1282 0.7230 0.000 0.004 0.952 0.000 0.044
#> GSM751416 5 0.5636 0.3752 0.000 0.048 0.444 0.012 0.496
#> GSM751417 5 0.5636 0.3752 0.000 0.048 0.444 0.012 0.496
#> GSM751421 3 0.3035 0.7055 0.020 0.008 0.888 0.044 0.040
#> GSM751422 3 0.3035 0.7055 0.020 0.008 0.888 0.044 0.040
#> GSM751360 3 0.3014 0.7100 0.016 0.008 0.888 0.044 0.044
#> GSM751364 3 0.5214 -0.0890 0.000 0.024 0.540 0.012 0.424
#> GSM751390 5 0.4498 0.7319 0.000 0.032 0.280 0.000 0.688
#> GSM751392 5 0.4761 0.8004 0.000 0.080 0.172 0.008 0.740
#> GSM751396 5 0.4567 0.8014 0.000 0.080 0.164 0.004 0.752
#> GSM751399 3 0.1864 0.7129 0.000 0.004 0.924 0.004 0.068
#> GSM751400 3 0.1569 0.7253 0.008 0.004 0.944 0.000 0.044
#> GSM751401 3 0.1569 0.7250 0.008 0.004 0.944 0.000 0.044
#> GSM751402 3 0.1016 0.7260 0.008 0.004 0.972 0.004 0.012
#> GSM751403 3 0.1365 0.7253 0.004 0.004 0.952 0.000 0.040
#> GSM751405 3 0.1329 0.7266 0.008 0.004 0.956 0.000 0.032
#> GSM751407 3 0.1717 0.7232 0.008 0.004 0.936 0.000 0.052
#> GSM751408 3 0.1704 0.7138 0.000 0.004 0.928 0.000 0.068
#> GSM751409 3 0.1041 0.7279 0.000 0.000 0.964 0.004 0.032
#> GSM751412 3 0.1768 0.7119 0.000 0.004 0.924 0.000 0.072
#> GSM751418 3 0.4111 0.4619 0.000 0.004 0.708 0.008 0.280
#> GSM751419 3 0.4111 0.4619 0.000 0.004 0.708 0.008 0.280
#> GSM751420 3 0.3012 0.7008 0.008 0.016 0.888 0.040 0.048
#> GSM751425 2 0.3016 0.8380 0.008 0.876 0.008 0.020 0.088
#> GSM751429 3 0.6749 0.4759 0.028 0.188 0.636 0.064 0.084
#> GSM751430 4 0.7960 0.5145 0.008 0.220 0.144 0.484 0.144
#> GSM751433 2 0.4834 0.7461 0.012 0.764 0.008 0.112 0.104
#> GSM751437 2 0.6386 0.1394 0.008 0.464 0.440 0.032 0.056
#> GSM751448 3 0.6511 0.5120 0.024 0.156 0.664 0.068 0.088
#> GSM751451 2 0.3658 0.8313 0.008 0.840 0.012 0.032 0.108
#> GSM751423 2 0.3187 0.8442 0.012 0.872 0.016 0.016 0.084
#> GSM751424 2 0.4176 0.7921 0.012 0.812 0.008 0.064 0.104
#> GSM751428 2 0.3405 0.8299 0.012 0.864 0.012 0.036 0.076
#> GSM751431 2 0.3621 0.8176 0.012 0.848 0.008 0.044 0.088
#> GSM751432 2 0.5349 0.7064 0.016 0.732 0.016 0.140 0.096
#> GSM751434 2 0.5045 0.7148 0.008 0.744 0.012 0.140 0.096
#> GSM751435 2 0.2299 0.8493 0.012 0.916 0.012 0.004 0.056
#> GSM751436 2 0.4834 0.7461 0.012 0.764 0.008 0.112 0.104
#> GSM751440 2 0.2888 0.8475 0.012 0.888 0.020 0.008 0.072
#> GSM751444 2 0.2268 0.8419 0.012 0.924 0.012 0.036 0.016
#> GSM751446 2 0.2547 0.8415 0.012 0.912 0.028 0.012 0.036
#> GSM751449 2 0.2380 0.8441 0.012 0.920 0.028 0.012 0.028
#> GSM751450 2 0.3542 0.8240 0.012 0.856 0.012 0.040 0.080
#> GSM751452 2 0.4692 0.7628 0.012 0.780 0.012 0.096 0.100
#> GSM751426 2 0.3587 0.8172 0.012 0.844 0.004 0.040 0.100
#> GSM751427 2 0.2713 0.8484 0.008 0.896 0.020 0.008 0.068
#> GSM751438 2 0.2636 0.8342 0.008 0.908 0.028 0.020 0.036
#> GSM751439 2 0.3496 0.8059 0.012 0.860 0.072 0.012 0.044
#> GSM751441 2 0.3191 0.8247 0.004 0.876 0.024 0.032 0.064
#> GSM751442 2 0.2636 0.8359 0.008 0.908 0.028 0.020 0.036
#> GSM751443 2 0.6420 0.3267 0.012 0.520 0.376 0.024 0.068
#> GSM751445 2 0.2199 0.8467 0.012 0.928 0.020 0.028 0.012
#> GSM751447 2 0.2715 0.8343 0.008 0.904 0.020 0.028 0.040
#> GSM751453 2 0.2353 0.8468 0.008 0.916 0.004 0.028 0.044
#> GSM751454 2 0.2353 0.8468 0.008 0.916 0.004 0.028 0.044
#> GSM751455 2 0.2636 0.8359 0.008 0.908 0.028 0.020 0.036
#> GSM751456 2 0.2636 0.8359 0.008 0.908 0.028 0.020 0.036
#> GSM751457 2 0.5153 0.7013 0.008 0.764 0.092 0.068 0.068
#> GSM751458 2 0.5153 0.7013 0.008 0.764 0.092 0.068 0.068
cbind(get_classes(res, k = 6), get_membership(res, k = 6))
#> class entropy silhouette p1 p2 p3 p4 p5 p6
#> GSM751298 1 0.4428 0.1922 0.688 0.008 0.016 0.272 0.008 0.008
#> GSM751304 6 0.3275 0.8308 0.012 0.016 0.004 0.092 0.024 0.852
#> GSM751305 6 0.3262 0.8300 0.008 0.020 0.004 0.092 0.024 0.852
#> GSM751307 6 0.3492 0.8273 0.020 0.028 0.000 0.052 0.052 0.848
#> GSM751310 1 0.3838 -0.6541 0.552 0.000 0.000 0.448 0.000 0.000
#> GSM751314 4 0.3996 0.8219 0.484 0.000 0.000 0.512 0.004 0.000
#> GSM751316 4 0.4089 0.8323 0.468 0.000 0.000 0.524 0.000 0.008
#> GSM751318 1 0.4221 0.1592 0.684 0.004 0.020 0.284 0.008 0.000
#> GSM751342 4 0.3979 0.8642 0.456 0.000 0.000 0.540 0.004 0.000
#> GSM751346 1 0.3855 0.6349 0.812 0.032 0.044 0.008 0.000 0.104
#> GSM751347 1 0.4046 0.6268 0.804 0.032 0.056 0.012 0.000 0.096
#> GSM751348 5 0.8054 -0.2626 0.288 0.024 0.000 0.168 0.296 0.224
#> GSM751349 5 0.4891 0.5261 0.012 0.028 0.024 0.044 0.748 0.144
#> GSM751352 6 0.3140 0.8349 0.044 0.020 0.000 0.020 0.048 0.868
#> GSM751353 6 0.3147 0.8246 0.008 0.028 0.000 0.020 0.088 0.856
#> GSM751354 6 0.2979 0.8369 0.036 0.016 0.008 0.028 0.028 0.884
#> GSM751355 6 0.3156 0.8272 0.016 0.032 0.004 0.032 0.044 0.872
#> GSM751358 4 0.6395 0.4028 0.220 0.000 0.008 0.544 0.040 0.188
#> GSM751359 5 0.6864 0.0824 0.016 0.016 0.012 0.328 0.436 0.192
#> GSM751294 6 0.6576 0.6217 0.204 0.036 0.040 0.048 0.056 0.616
#> GSM751296 1 0.3232 0.5828 0.860 0.016 0.024 0.080 0.008 0.012
#> GSM751297 1 0.4192 0.6129 0.788 0.032 0.048 0.012 0.000 0.120
#> GSM751299 6 0.3398 0.8273 0.064 0.024 0.000 0.020 0.040 0.852
#> GSM751300 1 0.3855 0.6349 0.812 0.032 0.044 0.008 0.000 0.104
#> GSM751301 6 0.4526 0.7287 0.152 0.008 0.000 0.056 0.032 0.752
#> GSM751302 1 0.3900 0.6330 0.808 0.032 0.044 0.008 0.000 0.108
#> GSM751303 4 0.3828 0.8791 0.440 0.000 0.000 0.560 0.000 0.000
#> GSM751306 4 0.3838 0.8852 0.448 0.000 0.000 0.552 0.000 0.000
#> GSM751308 1 0.6567 0.2909 0.532 0.016 0.048 0.088 0.012 0.304
#> GSM751309 4 0.3838 0.8852 0.448 0.000 0.000 0.552 0.000 0.000
#> GSM751311 4 0.3838 0.8852 0.448 0.000 0.000 0.552 0.000 0.000
#> GSM751312 4 0.4175 0.8244 0.464 0.000 0.000 0.524 0.000 0.012
#> GSM751313 1 0.2583 0.6461 0.888 0.016 0.044 0.000 0.000 0.052
#> GSM751315 1 0.3894 -0.1087 0.664 0.000 0.008 0.324 0.004 0.000
#> GSM751317 1 0.4323 -0.3175 0.600 0.000 0.020 0.376 0.004 0.000
#> GSM751320 1 0.3734 0.4399 0.776 0.004 0.028 0.184 0.008 0.000
#> GSM751321 4 0.3838 0.8852 0.448 0.000 0.000 0.552 0.000 0.000
#> GSM751322 1 0.4043 0.1333 0.696 0.000 0.020 0.276 0.008 0.000
#> GSM751324 1 0.4001 0.1625 0.704 0.000 0.020 0.268 0.008 0.000
#> GSM751325 1 0.4129 0.3064 0.720 0.004 0.028 0.240 0.008 0.000
#> GSM751332 1 0.4009 0.4338 0.756 0.008 0.032 0.196 0.008 0.000
#> GSM751334 1 0.3851 0.4679 0.776 0.008 0.032 0.176 0.008 0.000
#> GSM751339 1 0.3405 0.6365 0.852 0.012 0.048 0.044 0.000 0.044
#> GSM751341 4 0.4258 0.7856 0.488 0.004 0.000 0.500 0.004 0.004
#> GSM751343 1 0.3973 0.3835 0.744 0.004 0.028 0.216 0.008 0.000
#> GSM751344 6 0.2842 0.8417 0.020 0.032 0.000 0.016 0.048 0.884
#> GSM751345 6 0.2842 0.8417 0.020 0.032 0.000 0.016 0.048 0.884
#> GSM751356 6 0.5062 0.7259 0.048 0.008 0.004 0.220 0.032 0.688
#> GSM751357 6 0.5062 0.7259 0.048 0.008 0.004 0.220 0.032 0.688
#> GSM751293 6 0.4727 0.7048 0.156 0.008 0.000 0.068 0.032 0.736
#> GSM751295 1 0.3900 0.6330 0.808 0.032 0.044 0.008 0.000 0.108
#> GSM751319 4 0.3838 0.8852 0.448 0.000 0.000 0.552 0.000 0.000
#> GSM751323 1 0.3669 0.4539 0.784 0.004 0.028 0.176 0.008 0.000
#> GSM751326 1 0.2230 0.6147 0.916 0.008 0.036 0.028 0.008 0.004
#> GSM751327 1 0.3530 0.4776 0.800 0.004 0.028 0.160 0.008 0.000
#> GSM751328 1 0.4062 -0.6643 0.552 0.000 0.000 0.440 0.008 0.000
#> GSM751329 1 0.2731 0.5794 0.880 0.008 0.032 0.072 0.008 0.000
#> GSM751330 1 0.3024 0.6472 0.856 0.016 0.040 0.000 0.000 0.088
#> GSM751331 1 0.3417 0.6389 0.828 0.020 0.044 0.000 0.000 0.108
#> GSM751333 1 0.3024 0.6472 0.856 0.016 0.040 0.000 0.000 0.088
#> GSM751335 1 0.2955 0.6473 0.860 0.016 0.036 0.000 0.000 0.088
#> GSM751336 1 0.3142 0.6456 0.848 0.016 0.044 0.000 0.000 0.092
#> GSM751337 1 0.2921 0.6382 0.880 0.012 0.044 0.032 0.000 0.032
#> GSM751338 1 0.3271 0.6345 0.860 0.012 0.040 0.048 0.000 0.040
#> GSM751340 1 0.4994 0.5270 0.716 0.012 0.164 0.032 0.000 0.076
#> GSM751350 1 0.3945 0.6299 0.804 0.032 0.044 0.008 0.000 0.112
#> GSM751351 1 0.3945 0.6299 0.804 0.032 0.044 0.008 0.000 0.112
#> GSM751362 3 0.2649 0.7378 0.020 0.000 0.892 0.048 0.032 0.008
#> GSM751363 5 0.7011 0.0772 0.000 0.004 0.368 0.076 0.380 0.172
#> GSM751367 3 0.4644 0.7082 0.052 0.008 0.780 0.088 0.020 0.052
#> GSM751368 3 0.5916 -0.0223 0.000 0.008 0.488 0.064 0.400 0.040
#> GSM751371 3 0.4229 0.7128 0.020 0.004 0.792 0.120 0.024 0.040
#> GSM751375 5 0.3566 0.7096 0.000 0.036 0.088 0.016 0.836 0.024
#> GSM751376 3 0.7351 0.4401 0.016 0.048 0.496 0.188 0.032 0.220
#> GSM751378 5 0.4182 0.6281 0.000 0.024 0.228 0.012 0.728 0.008
#> GSM751379 3 0.7351 0.4401 0.016 0.048 0.496 0.188 0.032 0.220
#> GSM751382 5 0.3204 0.7297 0.000 0.036 0.080 0.016 0.856 0.012
#> GSM751386 5 0.2604 0.7486 0.000 0.028 0.096 0.004 0.872 0.000
#> GSM751388 5 0.2604 0.7486 0.000 0.028 0.096 0.004 0.872 0.000
#> GSM751391 3 0.4133 0.7069 0.004 0.004 0.788 0.120 0.020 0.064
#> GSM751410 3 0.2943 0.7441 0.024 0.004 0.876 0.068 0.020 0.008
#> GSM751414 3 0.4749 0.3134 0.000 0.000 0.612 0.048 0.332 0.008
#> GSM751361 5 0.5159 0.1845 0.000 0.004 0.448 0.052 0.488 0.008
#> GSM751365 3 0.4117 0.5816 0.008 0.000 0.756 0.044 0.184 0.008
#> GSM751366 3 0.2145 0.7327 0.008 0.000 0.912 0.020 0.056 0.004
#> GSM751369 3 0.3932 0.7150 0.016 0.004 0.808 0.120 0.024 0.028
#> GSM751370 3 0.5153 0.3803 0.016 0.000 0.620 0.048 0.304 0.012
#> GSM751372 3 0.5064 0.3574 0.008 0.000 0.616 0.052 0.312 0.012
#> GSM751373 3 0.2847 0.7176 0.004 0.000 0.872 0.036 0.076 0.012
#> GSM751374 3 0.7351 0.4401 0.016 0.048 0.496 0.188 0.032 0.220
#> GSM751377 5 0.5093 0.3570 0.004 0.004 0.380 0.044 0.560 0.008
#> GSM751380 3 0.0551 0.7526 0.004 0.000 0.984 0.000 0.008 0.004
#> GSM751381 5 0.2462 0.7485 0.000 0.028 0.096 0.000 0.876 0.000
#> GSM751383 5 0.2604 0.7486 0.000 0.028 0.096 0.004 0.872 0.000
#> GSM751384 5 0.2618 0.7403 0.000 0.024 0.116 0.000 0.860 0.000
#> GSM751385 3 0.6243 0.1772 0.004 0.004 0.496 0.068 0.364 0.064
#> GSM751387 5 0.2554 0.7482 0.000 0.028 0.092 0.000 0.876 0.004
#> GSM751389 3 0.4851 0.6686 0.008 0.016 0.740 0.160 0.036 0.040
#> GSM751393 3 0.6577 0.5564 0.008 0.016 0.584 0.196 0.060 0.136
#> GSM751394 5 0.2504 0.7474 0.000 0.028 0.088 0.000 0.880 0.004
#> GSM751395 3 0.7061 0.4397 0.004 0.020 0.484 0.212 0.048 0.232
#> GSM751397 5 0.2462 0.7485 0.000 0.028 0.096 0.000 0.876 0.000
#> GSM751398 5 0.2829 0.7445 0.000 0.024 0.096 0.016 0.864 0.000
#> GSM751404 3 0.0972 0.7493 0.008 0.000 0.964 0.000 0.028 0.000
#> GSM751406 3 0.1691 0.7468 0.012 0.000 0.940 0.028 0.008 0.012
#> GSM751411 3 0.4117 0.4795 0.000 0.000 0.704 0.036 0.256 0.004
#> GSM751413 5 0.8101 0.0340 0.004 0.020 0.284 0.164 0.304 0.224
#> GSM751415 3 0.1049 0.7482 0.008 0.000 0.960 0.000 0.032 0.000
#> GSM751416 5 0.5079 0.2853 0.000 0.004 0.416 0.048 0.524 0.008
#> GSM751417 5 0.5079 0.2853 0.000 0.004 0.416 0.048 0.524 0.008
#> GSM751421 3 0.4229 0.7128 0.020 0.004 0.792 0.120 0.024 0.040
#> GSM751422 3 0.4229 0.7128 0.020 0.004 0.792 0.120 0.024 0.040
#> GSM751360 3 0.4429 0.7125 0.016 0.004 0.768 0.148 0.028 0.036
#> GSM751364 5 0.4984 0.1362 0.000 0.000 0.468 0.048 0.476 0.008
#> GSM751390 5 0.2527 0.7445 0.000 0.024 0.108 0.000 0.868 0.000
#> GSM751392 5 0.2818 0.7403 0.000 0.028 0.084 0.008 0.872 0.008
#> GSM751396 5 0.3219 0.7201 0.000 0.036 0.076 0.008 0.856 0.024
#> GSM751399 3 0.1578 0.7407 0.004 0.000 0.936 0.012 0.048 0.000
#> GSM751400 3 0.1088 0.7503 0.016 0.000 0.960 0.000 0.024 0.000
#> GSM751401 3 0.1088 0.7503 0.016 0.000 0.960 0.000 0.024 0.000
#> GSM751402 3 0.0717 0.7508 0.016 0.000 0.976 0.000 0.008 0.000
#> GSM751403 3 0.1074 0.7494 0.012 0.000 0.960 0.000 0.028 0.000
#> GSM751405 3 0.0914 0.7509 0.016 0.000 0.968 0.000 0.016 0.000
#> GSM751407 3 0.1088 0.7503 0.016 0.000 0.960 0.000 0.024 0.000
#> GSM751408 3 0.1152 0.7445 0.004 0.000 0.952 0.000 0.044 0.000
#> GSM751409 3 0.0547 0.7511 0.000 0.000 0.980 0.000 0.020 0.000
#> GSM751412 3 0.1285 0.7414 0.004 0.000 0.944 0.000 0.052 0.000
#> GSM751418 3 0.5064 0.3564 0.008 0.000 0.616 0.052 0.312 0.012
#> GSM751419 3 0.5064 0.3564 0.008 0.000 0.616 0.052 0.312 0.012
#> GSM751420 3 0.3223 0.7268 0.020 0.008 0.864 0.064 0.008 0.036
#> GSM751425 2 0.3788 0.7760 0.008 0.828 0.012 0.060 0.076 0.016
#> GSM751429 3 0.6823 0.5287 0.072 0.160 0.608 0.100 0.020 0.040
#> GSM751430 6 0.7695 0.4085 0.008 0.180 0.096 0.116 0.088 0.512
#> GSM751433 2 0.5853 0.7005 0.016 0.676 0.008 0.076 0.084 0.140
#> GSM751437 2 0.6863 0.2826 0.016 0.468 0.356 0.100 0.032 0.028
#> GSM751448 3 0.6508 0.5931 0.052 0.096 0.648 0.132 0.032 0.040
#> GSM751451 2 0.4331 0.7937 0.008 0.792 0.004 0.060 0.084 0.052
#> GSM751423 2 0.3971 0.8018 0.020 0.824 0.004 0.056 0.056 0.040
#> GSM751424 2 0.5361 0.7392 0.016 0.724 0.008 0.076 0.076 0.100
#> GSM751428 2 0.4566 0.7815 0.020 0.784 0.008 0.068 0.036 0.084
#> GSM751431 2 0.4916 0.7658 0.016 0.760 0.008 0.064 0.072 0.080
#> GSM751432 2 0.6327 0.6140 0.016 0.612 0.008 0.080 0.080 0.204
#> GSM751434 2 0.6306 0.6106 0.016 0.612 0.008 0.080 0.076 0.208
#> GSM751435 2 0.3733 0.8043 0.024 0.840 0.004 0.052 0.044 0.036
#> GSM751436 2 0.5853 0.7005 0.016 0.676 0.008 0.076 0.084 0.140
#> GSM751440 2 0.3641 0.8035 0.020 0.844 0.004 0.044 0.056 0.032
#> GSM751444 2 0.3521 0.7965 0.016 0.848 0.004 0.044 0.024 0.064
#> GSM751446 2 0.2616 0.8016 0.024 0.900 0.004 0.036 0.024 0.012
#> GSM751449 2 0.1736 0.8062 0.004 0.940 0.004 0.012 0.024 0.016
#> GSM751450 2 0.4766 0.7761 0.020 0.772 0.008 0.072 0.048 0.080
#> GSM751452 2 0.5729 0.7136 0.020 0.692 0.008 0.076 0.076 0.128
#> GSM751426 2 0.4806 0.7685 0.016 0.768 0.008 0.060 0.068 0.080
#> GSM751427 2 0.3196 0.8056 0.020 0.868 0.004 0.044 0.048 0.016
#> GSM751438 2 0.3437 0.7763 0.008 0.856 0.016 0.060 0.036 0.024
#> GSM751439 2 0.3018 0.7984 0.024 0.884 0.020 0.036 0.020 0.016
#> GSM751441 2 0.3788 0.7708 0.008 0.836 0.020 0.060 0.052 0.024
#> GSM751442 2 0.3469 0.7803 0.020 0.856 0.012 0.060 0.032 0.020
#> GSM751443 2 0.6145 0.3754 0.020 0.552 0.328 0.056 0.020 0.024
#> GSM751445 2 0.1736 0.8079 0.004 0.940 0.004 0.012 0.016 0.024
#> GSM751447 2 0.3415 0.7776 0.008 0.856 0.012 0.060 0.040 0.024
#> GSM751453 2 0.3617 0.7914 0.012 0.848 0.012 0.052 0.040 0.036
#> GSM751454 2 0.3617 0.7914 0.012 0.848 0.012 0.052 0.040 0.036
#> GSM751455 2 0.3551 0.7802 0.024 0.852 0.012 0.060 0.032 0.020
#> GSM751456 2 0.3551 0.7802 0.024 0.852 0.012 0.060 0.032 0.020
#> GSM751457 2 0.5552 0.6639 0.008 0.704 0.060 0.148 0.040 0.040
#> GSM751458 2 0.5552 0.6639 0.008 0.704 0.060 0.148 0.040 0.040
Heatmaps for the consensus matrix. It visualizes the probability of two samples to be in a same group.
consensus_heatmap(res, k = 2)
consensus_heatmap(res, k = 3)
consensus_heatmap(res, k = 4)
consensus_heatmap(res, k = 5)
consensus_heatmap(res, k = 6)
Heatmaps for the membership of samples in all partitions to see how consistent they are:
membership_heatmap(res, k = 2)
membership_heatmap(res, k = 3)
membership_heatmap(res, k = 4)
membership_heatmap(res, k = 5)
membership_heatmap(res, k = 6)
As soon as we have had the classes for columns, we can look for signatures which are significantly different between classes which can be candidate marks for certain classes. Following are the heatmaps for signatures.
Signature heatmaps where rows are scaled:
get_signatures(res, k = 2)
get_signatures(res, k = 3)
get_signatures(res, k = 4)
get_signatures(res, k = 5)
get_signatures(res, k = 6)
Signature heatmaps where rows are not scaled:
get_signatures(res, k = 2, scale_rows = FALSE)
get_signatures(res, k = 3, scale_rows = FALSE)
get_signatures(res, k = 4, scale_rows = FALSE)
get_signatures(res, k = 5, scale_rows = FALSE)
get_signatures(res, k = 6, scale_rows = FALSE)
Compare the overlap of signatures from different k:
compare_signatures(res)
get_signature() returns a data frame invisibly. TO get the list of signatures, the function
call should be assigned to a variable explicitly. In following code, if plot argument is set
to FALSE, no heatmap is plotted while only the differential analysis is performed.
# code only for demonstration
tb = get_signature(res, k = ..., plot = FALSE)
An example of the output of tb is:
#> which_row fdr mean_1 mean_2 scaled_mean_1 scaled_mean_2 km
#> 1 38 0.042760348 8.373488 9.131774 -0.5533452 0.5164555 1
#> 2 40 0.018707592 7.106213 8.469186 -0.6173731 0.5762149 1
#> 3 55 0.019134737 10.221463 11.207825 -0.6159697 0.5749050 1
#> 4 59 0.006059896 5.921854 7.869574 -0.6899429 0.6439467 1
#> 5 60 0.018055526 8.928898 10.211722 -0.6204761 0.5791110 1
#> 6 98 0.009384629 15.714769 14.887706 0.6635654 -0.6193277 2
...
The columns in tb are:
which_row: row indices corresponding to the input matrix.fdr: FDR for the differential test. mean_x: The mean value in group x.scaled_mean_x: The mean value in group x after rows are scaled.km: Row groups if k-means clustering is applied to rows.UMAP plot which shows how samples are separated.
dimension_reduction(res, k = 2, method = "UMAP")
dimension_reduction(res, k = 3, method = "UMAP")
dimension_reduction(res, k = 4, method = "UMAP")
dimension_reduction(res, k = 5, method = "UMAP")
dimension_reduction(res, k = 6, method = "UMAP")
Following heatmap shows how subgroups are split when increasing k:
collect_classes(res)
Test correlation between subgroups and known annotations. If the known annotation is numeric, one-way ANOVA test is applied, and if the known annotation is discrete, chi-squared contingency table test is applied.
test_to_known_factors(res)
#> n tissue(p) disease.state(p) agent(p) k
#> CV:kmeans 150 6.28e-28 0.27762 0.42918 2
#> CV:kmeans 138 1.70e-43 0.40550 0.76265 3
#> CV:kmeans 137 3.02e-56 0.00799 0.01889 4
#> CV:kmeans 139 1.24e-52 0.01679 0.04654 5
#> CV:kmeans 125 2.58e-44 0.03188 0.00789 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 4537 rows and 166 columns.
#> Top rows (454, 908, 1361, 1814, 2268) 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 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 0.538 0.886 0.933 0.4887 0.521 0.521
#> 3 3 0.789 0.845 0.928 0.3686 0.730 0.519
#> 4 4 0.679 0.698 0.836 0.1163 0.858 0.608
#> 5 5 0.725 0.656 0.807 0.0685 0.916 0.692
#> 6 6 0.745 0.667 0.806 0.0416 0.915 0.632
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
#> GSM751298 1 0.0000 0.949 1.000 0.000
#> GSM751304 1 0.6343 0.837 0.840 0.160
#> GSM751305 1 0.6623 0.825 0.828 0.172
#> GSM751307 1 0.6438 0.833 0.836 0.164
#> GSM751310 1 0.0000 0.949 1.000 0.000
#> GSM751314 1 0.0000 0.949 1.000 0.000
#> GSM751316 1 0.0000 0.949 1.000 0.000
#> GSM751318 1 0.0000 0.949 1.000 0.000
#> GSM751342 1 0.0000 0.949 1.000 0.000
#> GSM751346 1 0.0000 0.949 1.000 0.000
#> GSM751347 1 0.3879 0.888 0.924 0.076
#> GSM751348 1 0.6048 0.848 0.852 0.148
#> GSM751349 2 0.6531 0.792 0.168 0.832
#> GSM751352 1 0.6148 0.845 0.848 0.152
#> GSM751353 2 0.6973 0.766 0.188 0.812
#> GSM751354 1 0.8327 0.703 0.736 0.264
#> GSM751355 2 0.6531 0.791 0.168 0.832
#> GSM751358 1 0.5629 0.860 0.868 0.132
#> GSM751359 2 0.5294 0.844 0.120 0.880
#> GSM751294 1 0.6247 0.842 0.844 0.156
#> GSM751296 1 0.0000 0.949 1.000 0.000
#> GSM751297 1 0.0000 0.949 1.000 0.000
#> GSM751299 1 0.6148 0.845 0.848 0.152
#> GSM751300 1 0.0000 0.949 1.000 0.000
#> GSM751301 1 0.5294 0.869 0.880 0.120
#> GSM751302 1 0.0000 0.949 1.000 0.000
#> GSM751303 1 0.0000 0.949 1.000 0.000
#> GSM751306 1 0.0000 0.949 1.000 0.000
#> GSM751308 1 0.0000 0.949 1.000 0.000
#> GSM751309 1 0.0000 0.949 1.000 0.000
#> GSM751311 1 0.0000 0.949 1.000 0.000
#> GSM751312 1 0.0000 0.949 1.000 0.000
#> GSM751313 1 0.0000 0.949 1.000 0.000
#> GSM751315 1 0.0000 0.949 1.000 0.000
#> GSM751317 1 0.0000 0.949 1.000 0.000
#> GSM751320 1 0.0000 0.949 1.000 0.000
#> GSM751321 1 0.0000 0.949 1.000 0.000
#> GSM751322 1 0.0000 0.949 1.000 0.000
#> GSM751324 1 0.0000 0.949 1.000 0.000
#> GSM751325 1 0.0000 0.949 1.000 0.000
#> GSM751332 1 0.0000 0.949 1.000 0.000
#> GSM751334 1 0.0000 0.949 1.000 0.000
#> GSM751339 1 0.0000 0.949 1.000 0.000
#> GSM751341 1 0.0000 0.949 1.000 0.000
#> GSM751343 1 0.0000 0.949 1.000 0.000
#> GSM751344 1 0.6531 0.829 0.832 0.168
#> GSM751345 1 0.6531 0.829 0.832 0.168
#> GSM751356 1 0.6148 0.845 0.848 0.152
#> GSM751357 1 0.6148 0.845 0.848 0.152
#> GSM751293 1 0.5294 0.869 0.880 0.120
#> GSM751295 1 0.0000 0.949 1.000 0.000
#> GSM751319 1 0.0000 0.949 1.000 0.000
#> GSM751323 1 0.0000 0.949 1.000 0.000
#> GSM751326 1 0.0000 0.949 1.000 0.000
#> GSM751327 1 0.0000 0.949 1.000 0.000
#> GSM751328 1 0.0000 0.949 1.000 0.000
#> GSM751329 1 0.0000 0.949 1.000 0.000
#> GSM751330 1 0.0000 0.949 1.000 0.000
#> GSM751331 1 0.0000 0.949 1.000 0.000
#> GSM751333 1 0.0000 0.949 1.000 0.000
#> GSM751335 1 0.0000 0.949 1.000 0.000
#> GSM751336 1 0.0000 0.949 1.000 0.000
#> GSM751337 1 0.0000 0.949 1.000 0.000
#> GSM751338 1 0.0000 0.949 1.000 0.000
#> GSM751340 1 0.0000 0.949 1.000 0.000
#> GSM751350 1 0.0000 0.949 1.000 0.000
#> GSM751351 1 0.0000 0.949 1.000 0.000
#> GSM751362 2 0.8813 0.703 0.300 0.700
#> GSM751363 2 0.6343 0.799 0.160 0.840
#> GSM751367 1 0.8207 0.612 0.744 0.256
#> GSM751368 2 0.0000 0.911 0.000 1.000
#> GSM751371 2 0.9850 0.410 0.428 0.572
#> GSM751375 2 0.0000 0.911 0.000 1.000
#> GSM751376 2 0.0672 0.911 0.008 0.992
#> GSM751378 2 0.0000 0.911 0.000 1.000
#> GSM751379 2 0.0672 0.911 0.008 0.992
#> GSM751382 2 0.0000 0.911 0.000 1.000
#> GSM751386 2 0.0000 0.911 0.000 1.000
#> GSM751388 2 0.0000 0.911 0.000 1.000
#> GSM751391 2 0.6048 0.857 0.148 0.852
#> GSM751410 1 0.6623 0.762 0.828 0.172
#> GSM751414 2 0.6247 0.853 0.156 0.844
#> GSM751361 2 0.1184 0.911 0.016 0.984
#> GSM751365 2 0.5294 0.876 0.120 0.880
#> GSM751366 2 0.6438 0.847 0.164 0.836
#> GSM751369 2 0.8608 0.716 0.284 0.716
#> GSM751370 2 0.7299 0.820 0.204 0.796
#> GSM751372 2 0.5059 0.881 0.112 0.888
#> GSM751373 2 0.6247 0.853 0.156 0.844
#> GSM751374 2 0.0672 0.911 0.008 0.992
#> GSM751377 2 0.0376 0.911 0.004 0.996
#> GSM751380 2 0.6438 0.847 0.164 0.836
#> GSM751381 2 0.0000 0.911 0.000 1.000
#> GSM751383 2 0.0000 0.911 0.000 1.000
#> GSM751384 2 0.0000 0.911 0.000 1.000
#> GSM751385 2 0.0000 0.911 0.000 1.000
#> GSM751387 2 0.0000 0.911 0.000 1.000
#> GSM751389 2 0.3431 0.900 0.064 0.936
#> GSM751393 2 0.0000 0.911 0.000 1.000
#> GSM751394 2 0.0000 0.911 0.000 1.000
#> GSM751395 2 0.0000 0.911 0.000 1.000
#> GSM751397 2 0.0000 0.911 0.000 1.000
#> GSM751398 2 0.0000 0.911 0.000 1.000
#> GSM751404 2 0.6343 0.850 0.160 0.840
#> GSM751406 2 0.6343 0.850 0.160 0.840
#> GSM751411 2 0.5294 0.876 0.120 0.880
#> GSM751413 2 0.0672 0.911 0.008 0.992
#> GSM751415 2 0.6343 0.850 0.160 0.840
#> GSM751416 2 0.1184 0.911 0.016 0.984
#> GSM751417 2 0.1184 0.911 0.016 0.984
#> GSM751421 2 0.7950 0.775 0.240 0.760
#> GSM751422 2 0.8016 0.770 0.244 0.756
#> GSM751360 2 0.8016 0.770 0.244 0.756
#> GSM751364 2 0.1414 0.910 0.020 0.980
#> GSM751390 2 0.0000 0.911 0.000 1.000
#> GSM751392 2 0.0000 0.911 0.000 1.000
#> GSM751396 2 0.0000 0.911 0.000 1.000
#> GSM751399 2 0.4690 0.886 0.100 0.900
#> GSM751400 2 0.4298 0.893 0.088 0.912
#> GSM751401 2 0.6343 0.850 0.160 0.840
#> GSM751402 2 0.6343 0.850 0.160 0.840
#> GSM751403 2 0.4939 0.882 0.108 0.892
#> GSM751405 2 0.6148 0.856 0.152 0.848
#> GSM751407 2 0.5737 0.867 0.136 0.864
#> GSM751408 2 0.4815 0.884 0.104 0.896
#> GSM751409 2 0.3274 0.901 0.060 0.940
#> GSM751412 2 0.5408 0.874 0.124 0.876
#> GSM751418 2 0.5294 0.876 0.120 0.880
#> GSM751419 2 0.5294 0.876 0.120 0.880
#> GSM751420 2 0.5408 0.876 0.124 0.876
#> GSM751425 2 0.0000 0.911 0.000 1.000
#> GSM751429 2 0.8813 0.689 0.300 0.700
#> GSM751430 2 0.4562 0.864 0.096 0.904
#> GSM751433 2 0.9087 0.510 0.324 0.676
#> GSM751437 2 0.5946 0.862 0.144 0.856
#> GSM751448 2 0.8909 0.677 0.308 0.692
#> GSM751451 2 0.1633 0.906 0.024 0.976
#> GSM751423 2 0.0000 0.911 0.000 1.000
#> GSM751424 2 0.2423 0.900 0.040 0.960
#> GSM751428 2 0.0376 0.911 0.004 0.996
#> GSM751431 2 0.2603 0.898 0.044 0.956
#> GSM751432 2 0.4431 0.867 0.092 0.908
#> GSM751434 2 0.4690 0.861 0.100 0.900
#> GSM751435 2 0.3584 0.884 0.068 0.932
#> GSM751436 2 0.5408 0.839 0.124 0.876
#> GSM751440 2 0.2423 0.900 0.040 0.960
#> GSM751444 2 0.2423 0.900 0.040 0.960
#> GSM751446 2 0.0938 0.909 0.012 0.988
#> GSM751449 2 0.0376 0.911 0.004 0.996
#> GSM751450 2 0.1843 0.905 0.028 0.972
#> GSM751452 2 0.3584 0.884 0.068 0.932
#> GSM751426 2 0.2603 0.898 0.044 0.956
#> GSM751427 2 0.0000 0.911 0.000 1.000
#> GSM751438 2 0.0000 0.911 0.000 1.000
#> GSM751439 2 0.6343 0.858 0.160 0.840
#> GSM751441 2 0.0000 0.911 0.000 1.000
#> GSM751442 2 0.1184 0.908 0.016 0.984
#> GSM751443 2 0.5519 0.873 0.128 0.872
#> GSM751445 2 0.0376 0.911 0.004 0.996
#> GSM751447 2 0.0000 0.911 0.000 1.000
#> GSM751453 2 0.0376 0.911 0.004 0.996
#> GSM751454 2 0.0376 0.911 0.004 0.996
#> GSM751455 2 0.0376 0.911 0.004 0.996
#> GSM751456 2 0.0376 0.911 0.004 0.996
#> GSM751457 2 0.0000 0.911 0.000 1.000
#> GSM751458 2 0.0000 0.911 0.000 1.000
cbind(get_classes(res, k = 3), get_membership(res, k = 3))
#> class entropy silhouette p1 p2 p3
#> GSM751298 1 0.0000 0.978 1.000 0.000 0.000
#> GSM751304 2 0.1919 0.901 0.024 0.956 0.020
#> GSM751305 2 0.1781 0.903 0.020 0.960 0.020
#> GSM751307 2 0.2301 0.880 0.060 0.936 0.004
#> GSM751310 1 0.0000 0.978 1.000 0.000 0.000
#> GSM751314 1 0.0000 0.978 1.000 0.000 0.000
#> GSM751316 1 0.0000 0.978 1.000 0.000 0.000
#> GSM751318 1 0.0000 0.978 1.000 0.000 0.000
#> GSM751342 1 0.0000 0.978 1.000 0.000 0.000
#> GSM751346 1 0.0000 0.978 1.000 0.000 0.000
#> GSM751347 1 0.1411 0.941 0.964 0.000 0.036
#> GSM751348 1 0.5517 0.607 0.728 0.268 0.004
#> GSM751349 2 0.1453 0.902 0.008 0.968 0.024
#> GSM751352 2 0.3375 0.841 0.100 0.892 0.008
#> GSM751353 2 0.0237 0.916 0.000 0.996 0.004
#> GSM751354 2 0.1774 0.904 0.016 0.960 0.024
#> GSM751355 2 0.0237 0.916 0.000 0.996 0.004
#> GSM751358 1 0.6313 0.505 0.676 0.308 0.016
#> GSM751359 2 0.3532 0.811 0.008 0.884 0.108
#> GSM751294 2 0.5992 0.628 0.268 0.716 0.016
#> GSM751296 1 0.0000 0.978 1.000 0.000 0.000
#> GSM751297 1 0.0237 0.974 0.996 0.000 0.004
#> GSM751299 2 0.4531 0.772 0.168 0.824 0.008
#> GSM751300 1 0.0000 0.978 1.000 0.000 0.000
#> GSM751301 1 0.5016 0.678 0.760 0.240 0.000
#> GSM751302 1 0.0000 0.978 1.000 0.000 0.000
#> GSM751303 1 0.0000 0.978 1.000 0.000 0.000
#> GSM751306 1 0.0000 0.978 1.000 0.000 0.000
#> GSM751308 1 0.0237 0.974 0.996 0.000 0.004
#> GSM751309 1 0.0000 0.978 1.000 0.000 0.000
#> GSM751311 1 0.0000 0.978 1.000 0.000 0.000
#> GSM751312 1 0.0000 0.978 1.000 0.000 0.000
#> GSM751313 1 0.0000 0.978 1.000 0.000 0.000
#> GSM751315 1 0.0000 0.978 1.000 0.000 0.000
#> GSM751317 1 0.0000 0.978 1.000 0.000 0.000
#> GSM751320 1 0.0000 0.978 1.000 0.000 0.000
#> GSM751321 1 0.0000 0.978 1.000 0.000 0.000
#> GSM751322 1 0.0000 0.978 1.000 0.000 0.000
#> GSM751324 1 0.0000 0.978 1.000 0.000 0.000
#> GSM751325 1 0.0000 0.978 1.000 0.000 0.000
#> GSM751332 1 0.0000 0.978 1.000 0.000 0.000
#> GSM751334 1 0.0000 0.978 1.000 0.000 0.000
#> GSM751339 1 0.0000 0.978 1.000 0.000 0.000
#> GSM751341 1 0.0000 0.978 1.000 0.000 0.000
#> GSM751343 1 0.0000 0.978 1.000 0.000 0.000
#> GSM751344 2 0.0983 0.910 0.016 0.980 0.004
#> GSM751345 2 0.0983 0.910 0.016 0.980 0.004
#> GSM751356 2 0.6540 0.337 0.408 0.584 0.008
#> GSM751357 2 0.6540 0.337 0.408 0.584 0.008
#> GSM751293 1 0.4235 0.777 0.824 0.176 0.000
#> GSM751295 1 0.0000 0.978 1.000 0.000 0.000
#> GSM751319 1 0.0000 0.978 1.000 0.000 0.000
#> GSM751323 1 0.0000 0.978 1.000 0.000 0.000
#> GSM751326 1 0.0000 0.978 1.000 0.000 0.000
#> GSM751327 1 0.0000 0.978 1.000 0.000 0.000
#> GSM751328 1 0.0000 0.978 1.000 0.000 0.000
#> GSM751329 1 0.0000 0.978 1.000 0.000 0.000
#> GSM751330 1 0.0000 0.978 1.000 0.000 0.000
#> GSM751331 1 0.0000 0.978 1.000 0.000 0.000
#> GSM751333 1 0.0000 0.978 1.000 0.000 0.000
#> GSM751335 1 0.0000 0.978 1.000 0.000 0.000
#> GSM751336 1 0.0000 0.978 1.000 0.000 0.000
#> GSM751337 1 0.0000 0.978 1.000 0.000 0.000
#> GSM751338 1 0.0000 0.978 1.000 0.000 0.000
#> GSM751340 1 0.0592 0.967 0.988 0.000 0.012
#> GSM751350 1 0.0000 0.978 1.000 0.000 0.000
#> GSM751351 1 0.0000 0.978 1.000 0.000 0.000
#> GSM751362 3 0.1163 0.859 0.028 0.000 0.972
#> GSM751363 3 0.2625 0.845 0.000 0.084 0.916
#> GSM751367 3 0.6566 0.433 0.348 0.016 0.636
#> GSM751368 3 0.4842 0.735 0.000 0.224 0.776
#> GSM751371 3 0.1129 0.863 0.020 0.004 0.976
#> GSM751375 3 0.6302 0.276 0.000 0.480 0.520
#> GSM751376 3 0.6225 0.198 0.000 0.432 0.568
#> GSM751378 3 0.3116 0.825 0.000 0.108 0.892
#> GSM751379 3 0.6204 0.224 0.000 0.424 0.576
#> GSM751382 3 0.6154 0.462 0.000 0.408 0.592
#> GSM751386 3 0.5560 0.653 0.000 0.300 0.700
#> GSM751388 3 0.5560 0.653 0.000 0.300 0.700
#> GSM751391 3 0.2261 0.841 0.000 0.068 0.932
#> GSM751410 3 0.3412 0.785 0.124 0.000 0.876
#> GSM751414 3 0.0237 0.871 0.000 0.004 0.996
#> GSM751361 3 0.2711 0.842 0.000 0.088 0.912
#> GSM751365 3 0.0000 0.870 0.000 0.000 1.000
#> GSM751366 3 0.0237 0.871 0.000 0.004 0.996
#> GSM751369 3 0.0475 0.870 0.004 0.004 0.992
#> GSM751370 3 0.0475 0.870 0.004 0.004 0.992
#> GSM751372 3 0.0237 0.871 0.000 0.004 0.996
#> GSM751373 3 0.0424 0.871 0.000 0.008 0.992
#> GSM751374 3 0.6225 0.198 0.000 0.432 0.568
#> GSM751377 3 0.3412 0.820 0.000 0.124 0.876
#> GSM751380 3 0.0237 0.871 0.000 0.004 0.996
#> GSM751381 3 0.5560 0.653 0.000 0.300 0.700
#> GSM751383 3 0.5560 0.653 0.000 0.300 0.700
#> GSM751384 3 0.2165 0.853 0.000 0.064 0.936
#> GSM751385 3 0.0892 0.868 0.000 0.020 0.980
#> GSM751387 3 0.5560 0.653 0.000 0.300 0.700
#> GSM751389 3 0.0237 0.871 0.000 0.004 0.996
#> GSM751393 3 0.0000 0.870 0.000 0.000 1.000
#> GSM751394 3 0.5560 0.653 0.000 0.300 0.700
#> GSM751395 3 0.3879 0.761 0.000 0.152 0.848
#> GSM751397 3 0.5560 0.653 0.000 0.300 0.700
#> GSM751398 3 0.5560 0.653 0.000 0.300 0.700
#> GSM751404 3 0.0237 0.871 0.000 0.004 0.996
#> GSM751406 3 0.0237 0.871 0.000 0.004 0.996
#> GSM751411 3 0.0000 0.870 0.000 0.000 1.000
#> GSM751413 3 0.3551 0.816 0.000 0.132 0.868
#> GSM751415 3 0.0237 0.871 0.000 0.004 0.996
#> GSM751416 3 0.2796 0.840 0.000 0.092 0.908
#> GSM751417 3 0.2796 0.840 0.000 0.092 0.908
#> GSM751421 3 0.0237 0.871 0.000 0.004 0.996
#> GSM751422 3 0.0237 0.871 0.000 0.004 0.996
#> GSM751360 3 0.0000 0.870 0.000 0.000 1.000
#> GSM751364 3 0.1411 0.863 0.000 0.036 0.964
#> GSM751390 3 0.2066 0.855 0.000 0.060 0.940
#> GSM751392 3 0.5678 0.630 0.000 0.316 0.684
#> GSM751396 3 0.5785 0.605 0.000 0.332 0.668
#> GSM751399 3 0.0000 0.870 0.000 0.000 1.000
#> GSM751400 3 0.0237 0.871 0.000 0.004 0.996
#> GSM751401 3 0.0237 0.871 0.000 0.004 0.996
#> GSM751402 3 0.0237 0.871 0.000 0.004 0.996
#> GSM751403 3 0.0237 0.871 0.000 0.004 0.996
#> GSM751405 3 0.0237 0.871 0.000 0.004 0.996
#> GSM751407 3 0.0237 0.871 0.000 0.004 0.996
#> GSM751408 3 0.0237 0.871 0.000 0.004 0.996
#> GSM751409 3 0.0237 0.871 0.000 0.004 0.996
#> GSM751412 3 0.0237 0.871 0.000 0.004 0.996
#> GSM751418 3 0.0592 0.870 0.000 0.012 0.988
#> GSM751419 3 0.0592 0.870 0.000 0.012 0.988
#> GSM751420 3 0.0237 0.871 0.000 0.004 0.996
#> GSM751425 2 0.0000 0.919 0.000 1.000 0.000
#> GSM751429 2 0.9020 0.253 0.140 0.496 0.364
#> GSM751430 2 0.1163 0.901 0.000 0.972 0.028
#> GSM751433 2 0.0000 0.919 0.000 1.000 0.000
#> GSM751437 2 0.6225 0.256 0.000 0.568 0.432
#> GSM751448 2 0.8076 0.234 0.068 0.524 0.408
#> GSM751451 2 0.0000 0.919 0.000 1.000 0.000
#> GSM751423 2 0.0000 0.919 0.000 1.000 0.000
#> GSM751424 2 0.0000 0.919 0.000 1.000 0.000
#> GSM751428 2 0.0000 0.919 0.000 1.000 0.000
#> GSM751431 2 0.0000 0.919 0.000 1.000 0.000
#> GSM751432 2 0.0000 0.919 0.000 1.000 0.000
#> GSM751434 2 0.0000 0.919 0.000 1.000 0.000
#> GSM751435 2 0.0000 0.919 0.000 1.000 0.000
#> GSM751436 2 0.0000 0.919 0.000 1.000 0.000
#> GSM751440 2 0.0000 0.919 0.000 1.000 0.000
#> GSM751444 2 0.0000 0.919 0.000 1.000 0.000
#> GSM751446 2 0.0000 0.919 0.000 1.000 0.000
#> GSM751449 2 0.0000 0.919 0.000 1.000 0.000
#> GSM751450 2 0.0000 0.919 0.000 1.000 0.000
#> GSM751452 2 0.0000 0.919 0.000 1.000 0.000
#> GSM751426 2 0.0000 0.919 0.000 1.000 0.000
#> GSM751427 2 0.0000 0.919 0.000 1.000 0.000
#> GSM751438 2 0.0000 0.919 0.000 1.000 0.000
#> GSM751439 2 0.3752 0.784 0.000 0.856 0.144
#> GSM751441 2 0.0000 0.919 0.000 1.000 0.000
#> GSM751442 2 0.0000 0.919 0.000 1.000 0.000
#> GSM751443 2 0.5465 0.570 0.000 0.712 0.288
#> GSM751445 2 0.0000 0.919 0.000 1.000 0.000
#> GSM751447 2 0.0000 0.919 0.000 1.000 0.000
#> GSM751453 2 0.0000 0.919 0.000 1.000 0.000
#> GSM751454 2 0.0000 0.919 0.000 1.000 0.000
#> GSM751455 2 0.0000 0.919 0.000 1.000 0.000
#> GSM751456 2 0.0000 0.919 0.000 1.000 0.000
#> GSM751457 2 0.0892 0.908 0.000 0.980 0.020
#> GSM751458 2 0.0892 0.908 0.000 0.980 0.020
cbind(get_classes(res, k = 4), get_membership(res, k = 4))
#> class entropy silhouette p1 p2 p3 p4
#> GSM751298 1 0.0336 0.9145 0.992 0.000 0.000 0.008
#> GSM751304 4 0.5532 0.4992 0.004 0.232 0.056 0.708
#> GSM751305 4 0.5247 0.4994 0.000 0.228 0.052 0.720
#> GSM751307 4 0.4776 0.4628 0.016 0.272 0.000 0.712
#> GSM751310 1 0.2530 0.8786 0.888 0.000 0.000 0.112
#> GSM751314 1 0.3266 0.8464 0.832 0.000 0.000 0.168
#> GSM751316 1 0.3444 0.8363 0.816 0.000 0.000 0.184
#> GSM751318 1 0.0336 0.9145 0.992 0.000 0.000 0.008
#> GSM751342 1 0.3486 0.8330 0.812 0.000 0.000 0.188
#> GSM751346 1 0.1302 0.9088 0.956 0.000 0.000 0.044
#> GSM751347 1 0.1902 0.8979 0.932 0.004 0.000 0.064
#> GSM751348 4 0.5968 0.4262 0.236 0.092 0.000 0.672
#> GSM751349 4 0.3577 0.5810 0.000 0.156 0.012 0.832
#> GSM751352 4 0.6050 0.4916 0.032 0.240 0.040 0.688
#> GSM751353 4 0.4813 0.4793 0.012 0.268 0.004 0.716
#> GSM751354 4 0.5659 0.4907 0.008 0.240 0.052 0.700
#> GSM751355 4 0.4482 0.4848 0.008 0.264 0.000 0.728
#> GSM751358 4 0.6961 0.4822 0.184 0.064 0.084 0.668
#> GSM751359 4 0.2775 0.5791 0.000 0.084 0.020 0.896
#> GSM751294 4 0.8493 0.4588 0.192 0.172 0.096 0.540
#> GSM751296 1 0.0469 0.9151 0.988 0.000 0.000 0.012
#> GSM751297 1 0.3161 0.8746 0.896 0.020 0.028 0.056
#> GSM751299 4 0.6585 0.4672 0.068 0.256 0.028 0.648
#> GSM751300 1 0.1302 0.9088 0.956 0.000 0.000 0.044
#> GSM751301 1 0.6316 0.5336 0.612 0.088 0.000 0.300
#> GSM751302 1 0.1302 0.9088 0.956 0.000 0.000 0.044
#> GSM751303 1 0.3444 0.8363 0.816 0.000 0.000 0.184
#> GSM751306 1 0.3444 0.8363 0.816 0.000 0.000 0.184
#> GSM751308 1 0.5202 0.7606 0.788 0.032 0.060 0.120
#> GSM751309 1 0.3444 0.8363 0.816 0.000 0.000 0.184
#> GSM751311 1 0.3569 0.8257 0.804 0.000 0.000 0.196
#> GSM751312 1 0.3486 0.8330 0.812 0.000 0.000 0.188
#> GSM751313 1 0.0336 0.9154 0.992 0.000 0.000 0.008
#> GSM751315 1 0.0921 0.9117 0.972 0.000 0.000 0.028
#> GSM751317 1 0.3123 0.8540 0.844 0.000 0.000 0.156
#> GSM751320 1 0.0000 0.9155 1.000 0.000 0.000 0.000
#> GSM751321 1 0.3444 0.8363 0.816 0.000 0.000 0.184
#> GSM751322 1 0.0336 0.9145 0.992 0.000 0.000 0.008
#> GSM751324 1 0.0336 0.9145 0.992 0.000 0.000 0.008
#> GSM751325 1 0.0000 0.9155 1.000 0.000 0.000 0.000
#> GSM751332 1 0.0000 0.9155 1.000 0.000 0.000 0.000
#> GSM751334 1 0.0000 0.9155 1.000 0.000 0.000 0.000
#> GSM751339 1 0.0804 0.9139 0.980 0.000 0.012 0.008
#> GSM751341 1 0.3400 0.8389 0.820 0.000 0.000 0.180
#> GSM751343 1 0.0000 0.9155 1.000 0.000 0.000 0.000
#> GSM751344 4 0.4770 0.4556 0.012 0.288 0.000 0.700
#> GSM751345 4 0.4770 0.4556 0.012 0.288 0.000 0.700
#> GSM751356 4 0.6528 0.5170 0.076 0.160 0.060 0.704
#> GSM751357 4 0.6528 0.5170 0.076 0.160 0.060 0.704
#> GSM751293 1 0.5108 0.6508 0.672 0.020 0.000 0.308
#> GSM751295 1 0.1302 0.9088 0.956 0.000 0.000 0.044
#> GSM751319 1 0.3444 0.8363 0.816 0.000 0.000 0.184
#> GSM751323 1 0.0000 0.9155 1.000 0.000 0.000 0.000
#> GSM751326 1 0.0000 0.9155 1.000 0.000 0.000 0.000
#> GSM751327 1 0.0000 0.9155 1.000 0.000 0.000 0.000
#> GSM751328 1 0.1118 0.9096 0.964 0.000 0.000 0.036
#> GSM751329 1 0.0000 0.9155 1.000 0.000 0.000 0.000
#> GSM751330 1 0.0921 0.9128 0.972 0.000 0.000 0.028
#> GSM751331 1 0.1211 0.9099 0.960 0.000 0.000 0.040
#> GSM751333 1 0.0921 0.9128 0.972 0.000 0.000 0.028
#> GSM751335 1 0.0817 0.9136 0.976 0.000 0.000 0.024
#> GSM751336 1 0.1211 0.9099 0.960 0.000 0.000 0.040
#> GSM751337 1 0.0336 0.9154 0.992 0.000 0.000 0.008
#> GSM751338 1 0.0336 0.9154 0.992 0.000 0.000 0.008
#> GSM751340 1 0.3818 0.8227 0.852 0.004 0.096 0.048
#> GSM751350 1 0.1302 0.9088 0.956 0.000 0.000 0.044
#> GSM751351 1 0.1302 0.9088 0.956 0.000 0.000 0.044
#> GSM751362 3 0.1256 0.7576 0.028 0.000 0.964 0.008
#> GSM751363 4 0.4222 0.4090 0.000 0.000 0.272 0.728
#> GSM751367 3 0.5347 0.5269 0.216 0.012 0.732 0.040
#> GSM751368 3 0.6222 0.1814 0.000 0.056 0.532 0.412
#> GSM751371 3 0.2882 0.7248 0.016 0.016 0.904 0.064
#> GSM751375 4 0.5620 0.5011 0.000 0.084 0.208 0.708
#> GSM751376 3 0.6186 0.2900 0.000 0.064 0.584 0.352
#> GSM751378 4 0.5564 0.2820 0.000 0.020 0.436 0.544
#> GSM751379 3 0.6171 0.2971 0.000 0.064 0.588 0.348
#> GSM751382 4 0.6403 0.4618 0.000 0.112 0.260 0.628
#> GSM751386 4 0.5403 0.4035 0.000 0.024 0.348 0.628
#> GSM751388 4 0.5403 0.4035 0.000 0.024 0.348 0.628
#> GSM751391 3 0.4379 0.6188 0.000 0.036 0.792 0.172
#> GSM751410 3 0.3067 0.6874 0.104 0.008 0.880 0.008
#> GSM751414 3 0.4072 0.5937 0.000 0.000 0.748 0.252
#> GSM751361 3 0.5229 0.2170 0.000 0.008 0.564 0.428
#> GSM751365 3 0.3486 0.6681 0.000 0.000 0.812 0.188
#> GSM751366 3 0.1637 0.7497 0.000 0.000 0.940 0.060
#> GSM751369 3 0.2872 0.7168 0.012 0.008 0.896 0.084
#> GSM751370 3 0.4284 0.6282 0.012 0.000 0.764 0.224
#> GSM751372 3 0.3801 0.6345 0.000 0.000 0.780 0.220
#> GSM751373 3 0.2530 0.7217 0.000 0.000 0.888 0.112
#> GSM751374 3 0.6186 0.2900 0.000 0.064 0.584 0.352
#> GSM751377 3 0.5399 0.0797 0.000 0.012 0.520 0.468
#> GSM751380 3 0.0000 0.7667 0.000 0.000 1.000 0.000
#> GSM751381 4 0.5403 0.4035 0.000 0.024 0.348 0.628
#> GSM751383 4 0.5403 0.4035 0.000 0.024 0.348 0.628
#> GSM751384 4 0.5453 0.3302 0.000 0.020 0.388 0.592
#> GSM751385 4 0.4776 0.3403 0.000 0.000 0.376 0.624
#> GSM751387 4 0.5403 0.4035 0.000 0.024 0.348 0.628
#> GSM751389 3 0.1398 0.7547 0.000 0.004 0.956 0.040
#> GSM751393 3 0.3479 0.6837 0.000 0.012 0.840 0.148
#> GSM751394 4 0.5386 0.4076 0.000 0.024 0.344 0.632
#> GSM751395 4 0.5861 -0.0173 0.000 0.032 0.476 0.492
#> GSM751397 4 0.5403 0.4035 0.000 0.024 0.348 0.628
#> GSM751398 4 0.5403 0.4035 0.000 0.024 0.348 0.628
#> GSM751404 3 0.0188 0.7670 0.000 0.000 0.996 0.004
#> GSM751406 3 0.0817 0.7604 0.000 0.000 0.976 0.024
#> GSM751411 3 0.3649 0.6508 0.000 0.000 0.796 0.204
#> GSM751413 4 0.4121 0.4961 0.000 0.020 0.184 0.796
#> GSM751415 3 0.0000 0.7667 0.000 0.000 1.000 0.000
#> GSM751416 3 0.5220 0.2325 0.000 0.008 0.568 0.424
#> GSM751417 3 0.5220 0.2325 0.000 0.008 0.568 0.424
#> GSM751421 3 0.2234 0.7362 0.008 0.004 0.924 0.064
#> GSM751422 3 0.2234 0.7362 0.008 0.004 0.924 0.064
#> GSM751360 3 0.1940 0.7514 0.000 0.000 0.924 0.076
#> GSM751364 3 0.4905 0.3876 0.000 0.004 0.632 0.364
#> GSM751390 4 0.5440 0.3389 0.000 0.020 0.384 0.596
#> GSM751392 4 0.5994 0.4430 0.000 0.068 0.296 0.636
#> GSM751396 4 0.6158 0.4566 0.000 0.088 0.272 0.640
#> GSM751399 3 0.0921 0.7630 0.000 0.000 0.972 0.028
#> GSM751400 3 0.0336 0.7667 0.000 0.000 0.992 0.008
#> GSM751401 3 0.0188 0.7670 0.000 0.000 0.996 0.004
#> GSM751402 3 0.0336 0.7651 0.000 0.000 0.992 0.008
#> GSM751403 3 0.0000 0.7667 0.000 0.000 1.000 0.000
#> GSM751405 3 0.0188 0.7660 0.000 0.000 0.996 0.004
#> GSM751407 3 0.0336 0.7667 0.000 0.000 0.992 0.008
#> GSM751408 3 0.0707 0.7645 0.000 0.000 0.980 0.020
#> GSM751409 3 0.0188 0.7670 0.000 0.000 0.996 0.004
#> GSM751412 3 0.1557 0.7515 0.000 0.000 0.944 0.056
#> GSM751418 3 0.3649 0.6505 0.000 0.000 0.796 0.204
#> GSM751419 3 0.3649 0.6505 0.000 0.000 0.796 0.204
#> GSM751420 3 0.3307 0.6911 0.000 0.028 0.868 0.104
#> GSM751425 2 0.1389 0.8994 0.000 0.952 0.000 0.048
#> GSM751429 2 0.7137 0.1018 0.036 0.464 0.448 0.052
#> GSM751430 4 0.5159 0.3479 0.000 0.364 0.012 0.624
#> GSM751433 2 0.2281 0.8742 0.000 0.904 0.000 0.096
#> GSM751437 2 0.5947 0.3573 0.000 0.572 0.384 0.044
#> GSM751448 3 0.6587 0.3156 0.008 0.316 0.596 0.080
#> GSM751451 2 0.1474 0.8975 0.000 0.948 0.000 0.052
#> GSM751423 2 0.1211 0.9011 0.000 0.960 0.000 0.040
#> GSM751424 2 0.2149 0.8795 0.000 0.912 0.000 0.088
#> GSM751428 2 0.1474 0.8987 0.000 0.948 0.000 0.052
#> GSM751431 2 0.1557 0.8975 0.000 0.944 0.000 0.056
#> GSM751432 2 0.2345 0.8726 0.000 0.900 0.000 0.100
#> GSM751434 2 0.2345 0.8726 0.000 0.900 0.000 0.100
#> GSM751435 2 0.0817 0.9034 0.000 0.976 0.000 0.024
#> GSM751436 2 0.2281 0.8742 0.000 0.904 0.000 0.096
#> GSM751440 2 0.1022 0.9023 0.000 0.968 0.000 0.032
#> GSM751444 2 0.0817 0.9017 0.000 0.976 0.000 0.024
#> GSM751446 2 0.0592 0.8969 0.000 0.984 0.000 0.016
#> GSM751449 2 0.0592 0.8969 0.000 0.984 0.000 0.016
#> GSM751450 2 0.1557 0.8975 0.000 0.944 0.000 0.056
#> GSM751452 2 0.2216 0.8773 0.000 0.908 0.000 0.092
#> GSM751426 2 0.1637 0.8952 0.000 0.940 0.000 0.060
#> GSM751427 2 0.0707 0.9037 0.000 0.980 0.000 0.020
#> GSM751438 2 0.0895 0.8952 0.000 0.976 0.004 0.020
#> GSM751439 2 0.1706 0.8766 0.000 0.948 0.036 0.016
#> GSM751441 2 0.1389 0.8837 0.000 0.952 0.000 0.048
#> GSM751442 2 0.0707 0.8965 0.000 0.980 0.000 0.020
#> GSM751443 2 0.5773 0.4584 0.000 0.620 0.336 0.044
#> GSM751445 2 0.0469 0.8994 0.000 0.988 0.000 0.012
#> GSM751447 2 0.0592 0.8977 0.000 0.984 0.000 0.016
#> GSM751453 2 0.0921 0.9036 0.000 0.972 0.000 0.028
#> GSM751454 2 0.0921 0.9036 0.000 0.972 0.000 0.028
#> GSM751455 2 0.0707 0.8965 0.000 0.980 0.000 0.020
#> GSM751456 2 0.0707 0.8965 0.000 0.980 0.000 0.020
#> GSM751457 2 0.2500 0.8517 0.000 0.916 0.040 0.044
#> GSM751458 2 0.2500 0.8517 0.000 0.916 0.040 0.044
cbind(get_classes(res, k = 5), get_membership(res, k = 5))
#> class entropy silhouette p1 p2 p3 p4 p5
#> GSM751298 1 0.2629 0.652 0.860 0.000 0.000 0.136 0.004
#> GSM751304 4 0.4106 0.668 0.020 0.024 0.008 0.804 0.144
#> GSM751305 4 0.4276 0.665 0.024 0.036 0.004 0.796 0.140
#> GSM751307 4 0.4465 0.683 0.000 0.056 0.000 0.732 0.212
#> GSM751310 1 0.4201 0.424 0.592 0.000 0.000 0.408 0.000
#> GSM751314 1 0.4161 0.435 0.608 0.000 0.000 0.392 0.000
#> GSM751316 1 0.4294 0.359 0.532 0.000 0.000 0.468 0.000
#> GSM751318 1 0.2179 0.655 0.888 0.000 0.000 0.112 0.000
#> GSM751342 1 0.4227 0.399 0.580 0.000 0.000 0.420 0.000
#> GSM751346 1 0.3992 0.577 0.712 0.004 0.000 0.280 0.004
#> GSM751347 1 0.4533 0.554 0.688 0.012 0.004 0.288 0.008
#> GSM751348 4 0.7670 0.417 0.288 0.044 0.004 0.404 0.260
#> GSM751349 5 0.3616 0.568 0.000 0.052 0.004 0.116 0.828
#> GSM751352 4 0.5265 0.671 0.036 0.028 0.004 0.684 0.248
#> GSM751353 4 0.6084 0.535 0.000 0.112 0.004 0.508 0.376
#> GSM751354 4 0.4218 0.678 0.004 0.028 0.016 0.784 0.168
#> GSM751355 4 0.5644 0.590 0.000 0.100 0.000 0.584 0.316
#> GSM751358 4 0.6077 0.271 0.284 0.028 0.020 0.620 0.048
#> GSM751359 4 0.5092 0.032 0.000 0.016 0.012 0.508 0.464
#> GSM751294 4 0.7488 0.524 0.192 0.060 0.032 0.564 0.152
#> GSM751296 1 0.1704 0.682 0.928 0.000 0.000 0.068 0.004
#> GSM751297 1 0.4790 0.536 0.672 0.008 0.016 0.296 0.008
#> GSM751299 4 0.5620 0.667 0.040 0.048 0.004 0.672 0.236
#> GSM751300 1 0.3992 0.577 0.712 0.004 0.000 0.280 0.004
#> GSM751301 4 0.6532 0.365 0.356 0.020 0.000 0.500 0.124
#> GSM751302 1 0.4037 0.569 0.704 0.004 0.000 0.288 0.004
#> GSM751303 1 0.4249 0.382 0.568 0.000 0.000 0.432 0.000
#> GSM751306 1 0.4242 0.389 0.572 0.000 0.000 0.428 0.000
#> GSM751308 1 0.4942 0.409 0.668 0.020 0.016 0.292 0.004
#> GSM751309 1 0.4235 0.394 0.576 0.000 0.000 0.424 0.000
#> GSM751311 1 0.4235 0.394 0.576 0.000 0.000 0.424 0.000
#> GSM751312 4 0.4306 -0.363 0.492 0.000 0.000 0.508 0.000
#> GSM751313 1 0.3010 0.646 0.824 0.000 0.000 0.172 0.004
#> GSM751315 1 0.3336 0.588 0.772 0.000 0.000 0.228 0.000
#> GSM751317 1 0.4210 0.416 0.588 0.000 0.000 0.412 0.000
#> GSM751320 1 0.0162 0.684 0.996 0.000 0.000 0.004 0.000
#> GSM751321 1 0.4235 0.394 0.576 0.000 0.000 0.424 0.000
#> GSM751322 1 0.1478 0.672 0.936 0.000 0.000 0.064 0.000
#> GSM751324 1 0.1965 0.661 0.904 0.000 0.000 0.096 0.000
#> GSM751325 1 0.0963 0.679 0.964 0.000 0.000 0.036 0.000
#> GSM751332 1 0.0162 0.684 0.996 0.000 0.000 0.004 0.000
#> GSM751334 1 0.0000 0.684 1.000 0.000 0.000 0.000 0.000
#> GSM751339 1 0.2389 0.670 0.880 0.000 0.004 0.116 0.000
#> GSM751341 1 0.4225 0.464 0.632 0.000 0.000 0.364 0.004
#> GSM751343 1 0.0609 0.682 0.980 0.000 0.000 0.020 0.000
#> GSM751344 4 0.5189 0.660 0.004 0.056 0.004 0.660 0.276
#> GSM751345 4 0.5189 0.660 0.004 0.056 0.004 0.660 0.276
#> GSM751356 4 0.3939 0.579 0.048 0.032 0.016 0.844 0.060
#> GSM751357 4 0.3939 0.579 0.048 0.032 0.016 0.844 0.060
#> GSM751293 4 0.6455 0.364 0.372 0.008 0.000 0.476 0.144
#> GSM751295 1 0.4037 0.569 0.704 0.004 0.000 0.288 0.004
#> GSM751319 1 0.4242 0.394 0.572 0.000 0.000 0.428 0.000
#> GSM751323 1 0.0000 0.684 1.000 0.000 0.000 0.000 0.000
#> GSM751326 1 0.1502 0.680 0.940 0.000 0.000 0.056 0.004
#> GSM751327 1 0.0000 0.684 1.000 0.000 0.000 0.000 0.000
#> GSM751328 1 0.3480 0.568 0.752 0.000 0.000 0.248 0.000
#> GSM751329 1 0.1124 0.682 0.960 0.000 0.000 0.036 0.004
#> GSM751330 1 0.3662 0.601 0.744 0.000 0.000 0.252 0.004
#> GSM751331 1 0.3838 0.579 0.716 0.000 0.000 0.280 0.004
#> GSM751333 1 0.3662 0.601 0.744 0.000 0.000 0.252 0.004
#> GSM751335 1 0.3662 0.601 0.744 0.000 0.000 0.252 0.004
#> GSM751336 1 0.3838 0.579 0.716 0.000 0.000 0.280 0.004
#> GSM751337 1 0.2124 0.673 0.900 0.000 0.000 0.096 0.004
#> GSM751338 1 0.2230 0.671 0.884 0.000 0.000 0.116 0.000
#> GSM751340 1 0.4944 0.548 0.700 0.000 0.092 0.208 0.000
#> GSM751350 1 0.3884 0.573 0.708 0.000 0.000 0.288 0.004
#> GSM751351 1 0.3884 0.573 0.708 0.000 0.000 0.288 0.004
#> GSM751362 3 0.1173 0.814 0.012 0.000 0.964 0.004 0.020
#> GSM751363 5 0.3904 0.640 0.000 0.000 0.052 0.156 0.792
#> GSM751367 3 0.3244 0.747 0.068 0.004 0.864 0.060 0.004
#> GSM751368 5 0.4486 0.746 0.000 0.012 0.220 0.032 0.736
#> GSM751371 3 0.1844 0.801 0.012 0.000 0.936 0.040 0.012
#> GSM751375 5 0.3019 0.762 0.000 0.016 0.056 0.048 0.880
#> GSM751376 3 0.5981 0.479 0.000 0.012 0.624 0.212 0.152
#> GSM751378 5 0.3437 0.749 0.000 0.004 0.176 0.012 0.808
#> GSM751379 3 0.5981 0.479 0.000 0.012 0.624 0.212 0.152
#> GSM751382 5 0.2139 0.801 0.000 0.012 0.056 0.012 0.920
#> GSM751386 5 0.1282 0.803 0.000 0.000 0.044 0.004 0.952
#> GSM751388 5 0.1571 0.815 0.000 0.000 0.060 0.004 0.936
#> GSM751391 3 0.3980 0.708 0.004 0.004 0.804 0.048 0.140
#> GSM751410 3 0.1870 0.797 0.040 0.004 0.936 0.016 0.004
#> GSM751414 5 0.4161 0.487 0.000 0.000 0.392 0.000 0.608
#> GSM751361 5 0.3521 0.741 0.000 0.000 0.232 0.004 0.764
#> GSM751365 3 0.4610 0.164 0.000 0.000 0.596 0.016 0.388
#> GSM751366 3 0.1671 0.780 0.000 0.000 0.924 0.000 0.076
#> GSM751369 3 0.0955 0.810 0.004 0.000 0.968 0.028 0.000
#> GSM751370 5 0.4877 0.281 0.016 0.000 0.456 0.004 0.524
#> GSM751372 5 0.4437 0.295 0.000 0.000 0.464 0.004 0.532
#> GSM751373 3 0.3177 0.613 0.000 0.000 0.792 0.000 0.208
#> GSM751374 3 0.5954 0.485 0.000 0.012 0.628 0.208 0.152
#> GSM751377 5 0.3300 0.765 0.000 0.000 0.204 0.004 0.792
#> GSM751380 3 0.0404 0.816 0.000 0.000 0.988 0.000 0.012
#> GSM751381 5 0.1571 0.815 0.000 0.000 0.060 0.004 0.936
#> GSM751383 5 0.1571 0.815 0.000 0.000 0.060 0.004 0.936
#> GSM751384 5 0.1908 0.812 0.000 0.000 0.092 0.000 0.908
#> GSM751385 5 0.4495 0.662 0.000 0.000 0.244 0.044 0.712
#> GSM751387 5 0.1571 0.815 0.000 0.000 0.060 0.004 0.936
#> GSM751389 3 0.0566 0.814 0.000 0.000 0.984 0.004 0.012
#> GSM751393 3 0.5398 0.526 0.000 0.000 0.648 0.112 0.240
#> GSM751394 5 0.1571 0.815 0.000 0.000 0.060 0.004 0.936
#> GSM751395 3 0.6433 0.274 0.000 0.004 0.508 0.176 0.312
#> GSM751397 5 0.1571 0.815 0.000 0.000 0.060 0.004 0.936
#> GSM751398 5 0.1697 0.815 0.000 0.000 0.060 0.008 0.932
#> GSM751404 3 0.0510 0.815 0.000 0.000 0.984 0.000 0.016
#> GSM751406 3 0.0000 0.815 0.000 0.000 1.000 0.000 0.000
#> GSM751411 3 0.4291 -0.121 0.000 0.000 0.536 0.000 0.464
#> GSM751413 5 0.4982 0.478 0.000 0.000 0.088 0.220 0.692
#> GSM751415 3 0.0510 0.815 0.000 0.000 0.984 0.000 0.016
#> GSM751416 5 0.3550 0.737 0.000 0.000 0.236 0.004 0.760
#> GSM751417 5 0.3550 0.737 0.000 0.000 0.236 0.004 0.760
#> GSM751421 3 0.1412 0.807 0.004 0.000 0.952 0.036 0.008
#> GSM751422 3 0.1412 0.807 0.004 0.000 0.952 0.036 0.008
#> GSM751360 3 0.2740 0.775 0.004 0.000 0.888 0.044 0.064
#> GSM751364 5 0.3814 0.688 0.000 0.000 0.276 0.004 0.720
#> GSM751390 5 0.1704 0.815 0.000 0.000 0.068 0.004 0.928
#> GSM751392 5 0.1704 0.813 0.000 0.000 0.068 0.004 0.928
#> GSM751396 5 0.2378 0.801 0.000 0.016 0.064 0.012 0.908
#> GSM751399 3 0.1121 0.804 0.000 0.000 0.956 0.000 0.044
#> GSM751400 3 0.0510 0.815 0.000 0.000 0.984 0.000 0.016
#> GSM751401 3 0.0510 0.815 0.000 0.000 0.984 0.000 0.016
#> GSM751402 3 0.0404 0.816 0.000 0.000 0.988 0.000 0.012
#> GSM751403 3 0.0510 0.815 0.000 0.000 0.984 0.000 0.016
#> GSM751405 3 0.0404 0.816 0.000 0.000 0.988 0.000 0.012
#> GSM751407 3 0.0510 0.815 0.000 0.000 0.984 0.000 0.016
#> GSM751408 3 0.0963 0.808 0.000 0.000 0.964 0.000 0.036
#> GSM751409 3 0.0000 0.815 0.000 0.000 1.000 0.000 0.000
#> GSM751412 3 0.1478 0.790 0.000 0.000 0.936 0.000 0.064
#> GSM751418 3 0.4304 -0.178 0.000 0.000 0.516 0.000 0.484
#> GSM751419 3 0.4304 -0.178 0.000 0.000 0.516 0.000 0.484
#> GSM751420 3 0.0451 0.813 0.000 0.000 0.988 0.008 0.004
#> GSM751425 2 0.0566 0.914 0.000 0.984 0.000 0.004 0.012
#> GSM751429 3 0.5775 0.470 0.016 0.284 0.624 0.072 0.004
#> GSM751430 4 0.7044 0.372 0.000 0.304 0.008 0.364 0.324
#> GSM751433 2 0.2685 0.871 0.000 0.880 0.000 0.092 0.028
#> GSM751437 2 0.4692 0.121 0.000 0.528 0.460 0.008 0.004
#> GSM751448 3 0.4459 0.631 0.012 0.188 0.760 0.036 0.004
#> GSM751451 2 0.1364 0.911 0.000 0.952 0.000 0.036 0.012
#> GSM751423 2 0.0404 0.917 0.000 0.988 0.000 0.012 0.000
#> GSM751424 2 0.2482 0.880 0.000 0.892 0.000 0.084 0.024
#> GSM751428 2 0.1478 0.904 0.000 0.936 0.000 0.064 0.000
#> GSM751431 2 0.1894 0.897 0.000 0.920 0.000 0.072 0.008
#> GSM751432 2 0.3112 0.849 0.000 0.856 0.000 0.100 0.044
#> GSM751434 2 0.3012 0.853 0.000 0.860 0.000 0.104 0.036
#> GSM751435 2 0.0404 0.917 0.000 0.988 0.000 0.012 0.000
#> GSM751436 2 0.2685 0.871 0.000 0.880 0.000 0.092 0.028
#> GSM751440 2 0.0404 0.917 0.000 0.988 0.000 0.012 0.000
#> GSM751444 2 0.1043 0.912 0.000 0.960 0.000 0.040 0.000
#> GSM751446 2 0.0404 0.914 0.000 0.988 0.000 0.012 0.000
#> GSM751449 2 0.0404 0.914 0.000 0.988 0.000 0.012 0.000
#> GSM751450 2 0.1768 0.899 0.000 0.924 0.000 0.072 0.004
#> GSM751452 2 0.2685 0.871 0.000 0.880 0.000 0.092 0.028
#> GSM751426 2 0.1764 0.901 0.000 0.928 0.000 0.064 0.008
#> GSM751427 2 0.0000 0.916 0.000 1.000 0.000 0.000 0.000
#> GSM751438 2 0.0404 0.914 0.000 0.988 0.000 0.012 0.000
#> GSM751439 2 0.0807 0.909 0.000 0.976 0.012 0.012 0.000
#> GSM751441 2 0.1492 0.891 0.000 0.948 0.004 0.008 0.040
#> GSM751442 2 0.0404 0.914 0.000 0.988 0.000 0.012 0.000
#> GSM751443 2 0.4730 0.252 0.000 0.568 0.416 0.012 0.004
#> GSM751445 2 0.0510 0.917 0.000 0.984 0.000 0.016 0.000
#> GSM751447 2 0.0290 0.915 0.000 0.992 0.000 0.008 0.000
#> GSM751453 2 0.0703 0.917 0.000 0.976 0.000 0.024 0.000
#> GSM751454 2 0.0703 0.917 0.000 0.976 0.000 0.024 0.000
#> GSM751455 2 0.0404 0.914 0.000 0.988 0.000 0.012 0.000
#> GSM751456 2 0.0404 0.914 0.000 0.988 0.000 0.012 0.000
#> GSM751457 2 0.1753 0.885 0.000 0.936 0.032 0.032 0.000
#> GSM751458 2 0.1753 0.885 0.000 0.936 0.032 0.032 0.000
cbind(get_classes(res, k = 6), get_membership(res, k = 6))
#> class entropy silhouette p1 p2 p3 p4 p5 p6
#> GSM751298 4 0.3023 0.6572 0.212 0.000 0.000 0.784 0.000 0.004
#> GSM751304 6 0.3677 0.7085 0.064 0.000 0.000 0.120 0.012 0.804
#> GSM751305 6 0.3663 0.7032 0.048 0.000 0.004 0.128 0.012 0.808
#> GSM751307 6 0.3935 0.7125 0.100 0.008 0.000 0.052 0.032 0.808
#> GSM751310 4 0.0937 0.8005 0.040 0.000 0.000 0.960 0.000 0.000
#> GSM751314 4 0.0458 0.8069 0.016 0.000 0.000 0.984 0.000 0.000
#> GSM751316 4 0.1594 0.7681 0.052 0.000 0.000 0.932 0.000 0.016
#> GSM751318 4 0.3101 0.6116 0.244 0.000 0.000 0.756 0.000 0.000
#> GSM751342 4 0.0713 0.8041 0.028 0.000 0.000 0.972 0.000 0.000
#> GSM751346 1 0.2509 0.7838 0.876 0.000 0.000 0.088 0.000 0.036
#> GSM751347 1 0.2563 0.7808 0.880 0.000 0.000 0.076 0.004 0.040
#> GSM751348 4 0.6915 0.2312 0.076 0.008 0.000 0.488 0.248 0.180
#> GSM751349 5 0.2908 0.7019 0.004 0.020 0.000 0.004 0.848 0.124
#> GSM751352 6 0.4723 0.6974 0.184 0.000 0.000 0.036 0.064 0.716
#> GSM751353 6 0.4112 0.7032 0.088 0.008 0.000 0.012 0.108 0.784
#> GSM751354 6 0.4212 0.7181 0.144 0.004 0.000 0.052 0.028 0.772
#> GSM751355 6 0.3972 0.7130 0.116 0.000 0.000 0.020 0.076 0.788
#> GSM751358 4 0.3770 0.5938 0.032 0.000 0.004 0.800 0.024 0.140
#> GSM751359 5 0.6399 0.1384 0.016 0.008 0.000 0.344 0.444 0.188
#> GSM751294 6 0.7596 0.3599 0.340 0.080 0.012 0.032 0.128 0.408
#> GSM751296 1 0.3795 0.5558 0.632 0.000 0.000 0.364 0.000 0.004
#> GSM751297 1 0.3140 0.7532 0.848 0.004 0.000 0.068 0.004 0.076
#> GSM751299 6 0.5259 0.6867 0.200 0.012 0.000 0.052 0.052 0.684
#> GSM751300 1 0.2404 0.7835 0.884 0.000 0.000 0.080 0.000 0.036
#> GSM751301 6 0.5076 0.6107 0.212 0.000 0.000 0.128 0.008 0.652
#> GSM751302 1 0.2488 0.7796 0.880 0.000 0.000 0.076 0.000 0.044
#> GSM751303 4 0.0000 0.8063 0.000 0.000 0.000 1.000 0.000 0.000
#> GSM751306 4 0.0000 0.8063 0.000 0.000 0.000 1.000 0.000 0.000
#> GSM751308 1 0.6006 0.3651 0.524 0.004 0.008 0.248 0.000 0.216
#> GSM751309 4 0.0000 0.8063 0.000 0.000 0.000 1.000 0.000 0.000
#> GSM751311 4 0.0000 0.8063 0.000 0.000 0.000 1.000 0.000 0.000
#> GSM751312 4 0.1895 0.7498 0.072 0.000 0.000 0.912 0.000 0.016
#> GSM751313 1 0.2704 0.7674 0.844 0.000 0.000 0.140 0.000 0.016
#> GSM751315 4 0.2416 0.7192 0.156 0.000 0.000 0.844 0.000 0.000
#> GSM751317 4 0.0713 0.8057 0.028 0.000 0.000 0.972 0.000 0.000
#> GSM751320 1 0.3864 0.2976 0.520 0.000 0.000 0.480 0.000 0.000
#> GSM751321 4 0.0000 0.8063 0.000 0.000 0.000 1.000 0.000 0.000
#> GSM751322 4 0.3309 0.5157 0.280 0.000 0.000 0.720 0.000 0.000
#> GSM751324 4 0.3101 0.5971 0.244 0.000 0.000 0.756 0.000 0.000
#> GSM751325 4 0.3747 0.1540 0.396 0.000 0.000 0.604 0.000 0.000
#> GSM751332 1 0.3862 0.3064 0.524 0.000 0.000 0.476 0.000 0.000
#> GSM751334 1 0.3810 0.4370 0.572 0.000 0.000 0.428 0.000 0.000
#> GSM751339 1 0.3648 0.6971 0.740 0.000 0.004 0.240 0.000 0.016
#> GSM751341 4 0.1349 0.7941 0.056 0.000 0.000 0.940 0.000 0.004
#> GSM751343 4 0.3838 -0.0606 0.448 0.000 0.000 0.552 0.000 0.000
#> GSM751344 6 0.4055 0.7193 0.100 0.000 0.000 0.040 0.068 0.792
#> GSM751345 6 0.4055 0.7193 0.100 0.000 0.000 0.040 0.068 0.792
#> GSM751356 6 0.6532 0.4142 0.156 0.012 0.000 0.356 0.028 0.448
#> GSM751357 6 0.6532 0.4142 0.156 0.012 0.000 0.356 0.028 0.448
#> GSM751293 6 0.5633 0.4995 0.200 0.000 0.000 0.216 0.008 0.576
#> GSM751295 1 0.2488 0.7796 0.880 0.000 0.000 0.076 0.000 0.044
#> GSM751319 4 0.0146 0.8058 0.004 0.000 0.000 0.996 0.000 0.000
#> GSM751323 1 0.3851 0.3579 0.540 0.000 0.000 0.460 0.000 0.000
#> GSM751326 1 0.2969 0.7169 0.776 0.000 0.000 0.224 0.000 0.000
#> GSM751327 1 0.3817 0.4263 0.568 0.000 0.000 0.432 0.000 0.000
#> GSM751328 4 0.2135 0.7516 0.128 0.000 0.000 0.872 0.000 0.000
#> GSM751329 1 0.3446 0.6359 0.692 0.000 0.000 0.308 0.000 0.000
#> GSM751330 1 0.2404 0.7833 0.884 0.000 0.000 0.080 0.000 0.036
#> GSM751331 1 0.2420 0.7807 0.884 0.000 0.000 0.076 0.000 0.040
#> GSM751333 1 0.2199 0.7818 0.892 0.000 0.000 0.088 0.000 0.020
#> GSM751335 1 0.2404 0.7833 0.884 0.000 0.000 0.080 0.000 0.036
#> GSM751336 1 0.2404 0.7833 0.884 0.000 0.000 0.080 0.000 0.036
#> GSM751337 1 0.3050 0.7129 0.764 0.000 0.000 0.236 0.000 0.000
#> GSM751338 1 0.3265 0.7007 0.748 0.000 0.000 0.248 0.000 0.004
#> GSM751340 1 0.5081 0.6590 0.692 0.000 0.056 0.184 0.000 0.068
#> GSM751350 1 0.2488 0.7796 0.880 0.000 0.000 0.076 0.000 0.044
#> GSM751351 1 0.2488 0.7796 0.880 0.000 0.000 0.076 0.000 0.044
#> GSM751362 3 0.2259 0.7995 0.020 0.000 0.908 0.000 0.040 0.032
#> GSM751363 5 0.6099 0.1942 0.016 0.000 0.048 0.056 0.476 0.404
#> GSM751367 3 0.5577 0.5782 0.192 0.000 0.652 0.036 0.008 0.112
#> GSM751368 5 0.5322 0.5658 0.012 0.004 0.256 0.000 0.624 0.104
#> GSM751371 3 0.4600 0.7104 0.044 0.000 0.764 0.068 0.012 0.112
#> GSM751375 5 0.1785 0.7805 0.000 0.008 0.016 0.000 0.928 0.048
#> GSM751376 6 0.4919 0.4343 0.028 0.032 0.300 0.004 0.000 0.636
#> GSM751378 5 0.2488 0.7318 0.004 0.000 0.124 0.000 0.864 0.008
#> GSM751379 6 0.4834 0.4420 0.028 0.028 0.296 0.004 0.000 0.644
#> GSM751382 5 0.0972 0.7986 0.000 0.008 0.000 0.000 0.964 0.028
#> GSM751386 5 0.0146 0.8118 0.000 0.000 0.000 0.000 0.996 0.004
#> GSM751388 5 0.0000 0.8128 0.000 0.000 0.000 0.000 1.000 0.000
#> GSM751391 3 0.5437 0.4690 0.040 0.000 0.628 0.020 0.036 0.276
#> GSM751410 3 0.4077 0.7398 0.040 0.000 0.804 0.092 0.012 0.052
#> GSM751414 5 0.4700 0.0777 0.008 0.000 0.472 0.000 0.492 0.028
#> GSM751361 5 0.4154 0.6636 0.012 0.000 0.208 0.004 0.740 0.036
#> GSM751365 3 0.4678 0.5099 0.008 0.000 0.672 0.020 0.272 0.028
#> GSM751366 3 0.1461 0.8050 0.000 0.000 0.940 0.000 0.044 0.016
#> GSM751369 3 0.3336 0.7525 0.036 0.000 0.832 0.012 0.004 0.116
#> GSM751370 3 0.4867 0.1984 0.016 0.000 0.548 0.000 0.404 0.032
#> GSM751372 3 0.4761 -0.0171 0.008 0.000 0.492 0.000 0.468 0.032
#> GSM751373 3 0.3306 0.7192 0.008 0.000 0.820 0.000 0.136 0.036
#> GSM751374 6 0.4834 0.4420 0.028 0.028 0.296 0.004 0.000 0.644
#> GSM751377 5 0.3201 0.7357 0.008 0.000 0.148 0.000 0.820 0.024
#> GSM751380 3 0.0405 0.8134 0.004 0.000 0.988 0.000 0.000 0.008
#> GSM751381 5 0.0000 0.8128 0.000 0.000 0.000 0.000 1.000 0.000
#> GSM751383 5 0.0000 0.8128 0.000 0.000 0.000 0.000 1.000 0.000
#> GSM751384 5 0.0146 0.8125 0.000 0.000 0.004 0.000 0.996 0.000
#> GSM751385 5 0.5557 0.4616 0.012 0.000 0.188 0.000 0.600 0.200
#> GSM751387 5 0.0000 0.8128 0.000 0.000 0.000 0.000 1.000 0.000
#> GSM751389 3 0.2182 0.7954 0.020 0.000 0.904 0.000 0.008 0.068
#> GSM751393 6 0.6280 0.0434 0.024 0.004 0.408 0.004 0.128 0.432
#> GSM751394 5 0.0000 0.8128 0.000 0.000 0.000 0.000 1.000 0.000
#> GSM751395 6 0.5029 0.4941 0.024 0.008 0.252 0.000 0.052 0.664
#> GSM751397 5 0.0000 0.8128 0.000 0.000 0.000 0.000 1.000 0.000
#> GSM751398 5 0.0291 0.8115 0.004 0.000 0.000 0.000 0.992 0.004
#> GSM751404 3 0.0260 0.8153 0.000 0.000 0.992 0.000 0.008 0.000
#> GSM751406 3 0.1340 0.8022 0.008 0.000 0.948 0.000 0.004 0.040
#> GSM751411 3 0.4187 0.3694 0.004 0.000 0.624 0.000 0.356 0.016
#> GSM751413 6 0.4881 0.3458 0.024 0.000 0.020 0.016 0.292 0.648
#> GSM751415 3 0.0458 0.8153 0.000 0.000 0.984 0.000 0.016 0.000
#> GSM751416 5 0.3806 0.6709 0.008 0.000 0.212 0.000 0.752 0.028
#> GSM751417 5 0.3806 0.6709 0.008 0.000 0.212 0.000 0.752 0.028
#> GSM751421 3 0.3687 0.7492 0.032 0.000 0.820 0.024 0.012 0.112
#> GSM751422 3 0.3687 0.7492 0.032 0.000 0.820 0.024 0.012 0.112
#> GSM751360 3 0.5088 0.7108 0.040 0.000 0.732 0.048 0.044 0.136
#> GSM751364 5 0.4271 0.5496 0.008 0.000 0.292 0.000 0.672 0.028
#> GSM751390 5 0.0146 0.8125 0.000 0.000 0.004 0.000 0.996 0.000
#> GSM751392 5 0.0870 0.8039 0.000 0.004 0.012 0.000 0.972 0.012
#> GSM751396 5 0.1554 0.7891 0.004 0.008 0.004 0.000 0.940 0.044
#> GSM751399 3 0.1049 0.8116 0.000 0.000 0.960 0.000 0.032 0.008
#> GSM751400 3 0.0508 0.8157 0.000 0.000 0.984 0.000 0.012 0.004
#> GSM751401 3 0.0458 0.8153 0.000 0.000 0.984 0.000 0.016 0.000
#> GSM751402 3 0.0692 0.8131 0.000 0.000 0.976 0.000 0.004 0.020
#> GSM751403 3 0.0508 0.8157 0.000 0.000 0.984 0.000 0.012 0.004
#> GSM751405 3 0.0508 0.8157 0.000 0.000 0.984 0.000 0.012 0.004
#> GSM751407 3 0.0363 0.8154 0.000 0.000 0.988 0.000 0.012 0.000
#> GSM751408 3 0.0632 0.8146 0.000 0.000 0.976 0.000 0.024 0.000
#> GSM751409 3 0.0748 0.8110 0.004 0.000 0.976 0.000 0.004 0.016
#> GSM751412 3 0.0865 0.8122 0.000 0.000 0.964 0.000 0.036 0.000
#> GSM751418 3 0.4503 0.3619 0.008 0.000 0.612 0.000 0.352 0.028
#> GSM751419 3 0.4490 0.3712 0.008 0.000 0.616 0.000 0.348 0.028
#> GSM751420 3 0.2686 0.7731 0.024 0.008 0.880 0.000 0.008 0.080
#> GSM751425 2 0.1036 0.8416 0.004 0.964 0.000 0.000 0.008 0.024
#> GSM751429 2 0.7312 0.0784 0.160 0.408 0.308 0.008 0.000 0.116
#> GSM751430 6 0.4418 0.6067 0.036 0.100 0.000 0.024 0.056 0.784
#> GSM751433 2 0.4672 0.6558 0.024 0.656 0.000 0.004 0.024 0.292
#> GSM751437 2 0.4810 0.5163 0.020 0.664 0.260 0.000 0.000 0.056
#> GSM751448 3 0.5192 0.4862 0.032 0.252 0.644 0.000 0.000 0.072
#> GSM751451 2 0.3010 0.8221 0.028 0.864 0.000 0.008 0.016 0.084
#> GSM751423 2 0.2224 0.8316 0.020 0.904 0.000 0.000 0.012 0.064
#> GSM751424 2 0.4397 0.6931 0.024 0.688 0.000 0.000 0.024 0.264
#> GSM751428 2 0.3017 0.7943 0.020 0.816 0.000 0.000 0.000 0.164
#> GSM751431 2 0.3611 0.7791 0.020 0.788 0.000 0.000 0.020 0.172
#> GSM751432 2 0.4801 0.3290 0.024 0.488 0.000 0.000 0.016 0.472
#> GSM751434 2 0.4795 0.3709 0.024 0.504 0.000 0.000 0.016 0.456
#> GSM751435 2 0.1391 0.8395 0.016 0.944 0.000 0.000 0.000 0.040
#> GSM751436 2 0.4660 0.6410 0.024 0.644 0.000 0.000 0.028 0.304
#> GSM751440 2 0.1838 0.8366 0.020 0.928 0.000 0.000 0.012 0.040
#> GSM751444 2 0.1951 0.8330 0.016 0.908 0.000 0.000 0.000 0.076
#> GSM751446 2 0.0000 0.8406 0.000 1.000 0.000 0.000 0.000 0.000
#> GSM751449 2 0.0146 0.8399 0.000 0.996 0.000 0.000 0.000 0.004
#> GSM751450 2 0.3268 0.7903 0.020 0.808 0.000 0.000 0.008 0.164
#> GSM751452 2 0.4605 0.6409 0.024 0.644 0.000 0.000 0.024 0.308
#> GSM751426 2 0.3395 0.7942 0.020 0.812 0.000 0.000 0.020 0.148
#> GSM751427 2 0.1232 0.8407 0.016 0.956 0.000 0.000 0.004 0.024
#> GSM751438 2 0.0603 0.8367 0.004 0.980 0.000 0.000 0.000 0.016
#> GSM751439 2 0.0405 0.8392 0.000 0.988 0.008 0.000 0.000 0.004
#> GSM751441 2 0.1232 0.8299 0.004 0.956 0.000 0.000 0.024 0.016
#> GSM751442 2 0.0405 0.8388 0.004 0.988 0.000 0.000 0.000 0.008
#> GSM751443 2 0.4428 0.5690 0.016 0.708 0.228 0.000 0.000 0.048
#> GSM751445 2 0.0363 0.8417 0.000 0.988 0.000 0.000 0.000 0.012
#> GSM751447 2 0.0508 0.8379 0.004 0.984 0.000 0.000 0.000 0.012
#> GSM751453 2 0.0972 0.8422 0.008 0.964 0.000 0.000 0.000 0.028
#> GSM751454 2 0.0972 0.8422 0.008 0.964 0.000 0.000 0.000 0.028
#> GSM751455 2 0.0405 0.8388 0.004 0.988 0.000 0.000 0.000 0.008
#> GSM751456 2 0.0405 0.8388 0.004 0.988 0.000 0.000 0.000 0.008
#> GSM751457 2 0.2159 0.7977 0.012 0.904 0.012 0.000 0.000 0.072
#> GSM751458 2 0.2159 0.7977 0.012 0.904 0.012 0.000 0.000 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 tissue(p) disease.state(p) agent(p) k
#> CV:skmeans 165 2.25e-31 0.78253 0.755242 2
#> CV:skmeans 155 1.30e-51 0.37855 0.666966 3
#> CV:skmeans 121 1.90e-48 0.04763 0.163885 4
#> CV:skmeans 131 1.36e-49 0.00561 0.005956 5
#> CV:skmeans 133 5.18e-49 0.00139 0.000205 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 4537 rows and 166 columns.
#> Top rows (454, 908, 1361, 1814, 2268) 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 0.301 0.652 0.839 0.4856 0.511 0.511
#> 3 3 0.526 0.638 0.829 0.3135 0.791 0.614
#> 4 4 0.551 0.642 0.779 0.1308 0.810 0.532
#> 5 5 0.559 0.552 0.725 0.0738 0.937 0.775
#> 6 6 0.697 0.643 0.788 0.0564 0.878 0.539
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
#> GSM751298 1 0.0672 0.8470 0.992 0.008
#> GSM751304 2 0.9358 0.4770 0.352 0.648
#> GSM751305 2 0.9087 0.5167 0.324 0.676
#> GSM751307 2 0.6887 0.7071 0.184 0.816
#> GSM751310 1 0.0938 0.8435 0.988 0.012
#> GSM751314 1 0.0376 0.8482 0.996 0.004
#> GSM751316 1 0.0000 0.8499 1.000 0.000
#> GSM751318 1 0.0672 0.8473 0.992 0.008
#> GSM751342 1 0.0376 0.8476 0.996 0.004
#> GSM751346 1 0.2423 0.8256 0.960 0.040
#> GSM751347 1 0.0938 0.8449 0.988 0.012
#> GSM751348 1 0.8443 0.5358 0.728 0.272
#> GSM751349 2 0.8081 0.6115 0.248 0.752
#> GSM751352 2 0.8081 0.6521 0.248 0.752
#> GSM751353 2 0.6712 0.7000 0.176 0.824
#> GSM751354 2 0.5519 0.7439 0.128 0.872
#> GSM751355 2 0.4939 0.7467 0.108 0.892
#> GSM751358 1 0.8661 0.4977 0.712 0.288
#> GSM751359 2 0.3274 0.7591 0.060 0.940
#> GSM751294 2 0.6531 0.7305 0.168 0.832
#> GSM751296 1 0.0000 0.8499 1.000 0.000
#> GSM751297 1 0.9129 0.3936 0.672 0.328
#> GSM751299 1 0.8763 0.4885 0.704 0.296
#> GSM751300 1 0.0376 0.8482 0.996 0.004
#> GSM751301 1 0.1843 0.8305 0.972 0.028
#> GSM751302 1 0.0000 0.8499 1.000 0.000
#> GSM751303 1 0.0672 0.8474 0.992 0.008
#> GSM751306 1 0.1184 0.8424 0.984 0.016
#> GSM751308 1 0.0938 0.8445 0.988 0.012
#> GSM751309 1 0.0000 0.8499 1.000 0.000
#> GSM751311 1 0.0000 0.8499 1.000 0.000
#> GSM751312 1 0.0376 0.8486 0.996 0.004
#> GSM751313 1 0.0000 0.8499 1.000 0.000
#> GSM751315 1 0.0000 0.8499 1.000 0.000
#> GSM751317 1 0.0000 0.8499 1.000 0.000
#> GSM751320 1 0.0000 0.8499 1.000 0.000
#> GSM751321 1 0.0672 0.8465 0.992 0.008
#> GSM751322 1 0.0376 0.8483 0.996 0.004
#> GSM751324 1 0.0672 0.8474 0.992 0.008
#> GSM751325 1 0.0000 0.8499 1.000 0.000
#> GSM751332 1 0.0000 0.8499 1.000 0.000
#> GSM751334 1 0.0000 0.8499 1.000 0.000
#> GSM751339 1 0.1184 0.8390 0.984 0.016
#> GSM751341 1 0.2948 0.8162 0.948 0.052
#> GSM751343 1 0.0000 0.8499 1.000 0.000
#> GSM751344 2 0.9323 0.4589 0.348 0.652
#> GSM751345 2 0.9427 0.4312 0.360 0.640
#> GSM751356 1 0.9460 0.2644 0.636 0.364
#> GSM751357 1 0.9977 -0.0419 0.528 0.472
#> GSM751293 1 0.0000 0.8499 1.000 0.000
#> GSM751295 1 0.0000 0.8499 1.000 0.000
#> GSM751319 1 0.0376 0.8483 0.996 0.004
#> GSM751323 1 0.0000 0.8499 1.000 0.000
#> GSM751326 1 0.0000 0.8499 1.000 0.000
#> GSM751327 1 0.0000 0.8499 1.000 0.000
#> GSM751328 1 0.0000 0.8499 1.000 0.000
#> GSM751329 1 0.0000 0.8499 1.000 0.000
#> GSM751330 1 0.0000 0.8499 1.000 0.000
#> GSM751331 1 0.0000 0.8499 1.000 0.000
#> GSM751333 1 0.0000 0.8499 1.000 0.000
#> GSM751335 1 0.0000 0.8499 1.000 0.000
#> GSM751336 1 0.0000 0.8499 1.000 0.000
#> GSM751337 1 0.0376 0.8484 0.996 0.004
#> GSM751338 1 0.0000 0.8499 1.000 0.000
#> GSM751340 1 0.7745 0.6013 0.772 0.228
#> GSM751350 1 0.0000 0.8499 1.000 0.000
#> GSM751351 1 0.0000 0.8499 1.000 0.000
#> GSM751362 1 0.9977 -0.1269 0.528 0.472
#> GSM751363 1 0.8608 0.5041 0.716 0.284
#> GSM751367 1 0.9983 -0.1772 0.524 0.476
#> GSM751368 2 0.4161 0.7513 0.084 0.916
#> GSM751371 1 0.6801 0.6742 0.820 0.180
#> GSM751375 2 0.5294 0.7401 0.120 0.880
#> GSM751376 2 0.9983 0.2961 0.476 0.524
#> GSM751378 2 0.1184 0.7572 0.016 0.984
#> GSM751379 2 0.5059 0.7491 0.112 0.888
#> GSM751382 2 0.2603 0.7594 0.044 0.956
#> GSM751386 2 0.0672 0.7540 0.008 0.992
#> GSM751388 2 0.0938 0.7545 0.012 0.988
#> GSM751391 2 1.0000 0.2150 0.500 0.500
#> GSM751410 1 0.8327 0.5503 0.736 0.264
#> GSM751414 2 0.9286 0.5291 0.344 0.656
#> GSM751361 2 0.9635 0.4661 0.388 0.612
#> GSM751365 2 0.9286 0.5323 0.344 0.656
#> GSM751366 1 0.9661 0.2614 0.608 0.392
#> GSM751369 2 0.9996 0.2287 0.488 0.512
#> GSM751370 2 0.9996 0.2338 0.488 0.512
#> GSM751372 2 0.9170 0.5513 0.332 0.668
#> GSM751373 2 0.9710 0.4554 0.400 0.600
#> GSM751374 2 0.4022 0.7624 0.080 0.920
#> GSM751377 2 0.1414 0.7556 0.020 0.980
#> GSM751380 2 0.9580 0.4676 0.380 0.620
#> GSM751381 2 0.0672 0.7540 0.008 0.992
#> GSM751383 2 0.0376 0.7526 0.004 0.996
#> GSM751384 2 0.9209 0.5502 0.336 0.664
#> GSM751385 2 0.0000 0.7511 0.000 1.000
#> GSM751387 2 0.0376 0.7525 0.004 0.996
#> GSM751389 2 0.6887 0.7046 0.184 0.816
#> GSM751393 2 0.6438 0.7139 0.164 0.836
#> GSM751394 2 0.1843 0.7568 0.028 0.972
#> GSM751395 2 0.9209 0.5696 0.336 0.664
#> GSM751397 2 0.0376 0.7526 0.004 0.996
#> GSM751398 2 0.2043 0.7579 0.032 0.968
#> GSM751404 2 0.9129 0.5522 0.328 0.672
#> GSM751406 2 0.9933 0.3294 0.452 0.548
#> GSM751411 2 0.9000 0.5615 0.316 0.684
#> GSM751413 2 0.5059 0.7448 0.112 0.888
#> GSM751415 2 0.9580 0.4676 0.380 0.620
#> GSM751416 2 0.0672 0.7543 0.008 0.992
#> GSM751417 2 0.0000 0.7511 0.000 1.000
#> GSM751421 1 0.9866 0.0234 0.568 0.432
#> GSM751422 1 0.6531 0.6945 0.832 0.168
#> GSM751360 1 0.9815 0.0678 0.580 0.420
#> GSM751364 2 0.9044 0.5626 0.320 0.680
#> GSM751390 2 0.9129 0.5550 0.328 0.672
#> GSM751392 2 0.3584 0.7584 0.068 0.932
#> GSM751396 2 0.1414 0.7556 0.020 0.980
#> GSM751399 2 0.9000 0.5615 0.316 0.684
#> GSM751400 2 0.5842 0.7361 0.140 0.860
#> GSM751401 2 0.9358 0.5211 0.352 0.648
#> GSM751402 2 0.9286 0.5411 0.344 0.656
#> GSM751403 2 0.9087 0.5560 0.324 0.676
#> GSM751405 2 0.9922 0.3395 0.448 0.552
#> GSM751407 2 0.9170 0.5510 0.332 0.668
#> GSM751408 2 0.3114 0.7581 0.056 0.944
#> GSM751409 2 0.6438 0.7098 0.164 0.836
#> GSM751412 2 0.9044 0.5588 0.320 0.680
#> GSM751418 2 0.8955 0.5684 0.312 0.688
#> GSM751419 2 0.9000 0.5615 0.316 0.684
#> GSM751420 2 0.2948 0.7624 0.052 0.948
#> GSM751425 2 0.6712 0.6986 0.176 0.824
#> GSM751429 2 0.9996 0.2889 0.488 0.512
#> GSM751430 2 0.3431 0.7605 0.064 0.936
#> GSM751433 2 0.9963 0.1584 0.464 0.536
#> GSM751437 2 0.9608 0.4856 0.384 0.616
#> GSM751448 2 0.9970 0.3010 0.468 0.532
#> GSM751451 1 0.9850 0.2241 0.572 0.428
#> GSM751423 2 0.4690 0.7559 0.100 0.900
#> GSM751424 2 0.2948 0.7603 0.052 0.948
#> GSM751428 2 0.5946 0.7452 0.144 0.856
#> GSM751431 1 0.9850 0.1921 0.572 0.428
#> GSM751432 2 0.3274 0.7624 0.060 0.940
#> GSM751434 2 0.3584 0.7630 0.068 0.932
#> GSM751435 2 0.4939 0.7557 0.108 0.892
#> GSM751436 2 0.4815 0.7528 0.104 0.896
#> GSM751440 1 0.9933 0.0997 0.548 0.452
#> GSM751444 2 0.5294 0.7510 0.120 0.880
#> GSM751446 2 0.8608 0.5719 0.284 0.716
#> GSM751449 2 0.2236 0.7594 0.036 0.964
#> GSM751450 2 0.3733 0.7620 0.072 0.928
#> GSM751452 2 0.4815 0.7470 0.104 0.896
#> GSM751426 2 0.6973 0.6910 0.188 0.812
#> GSM751427 2 0.2778 0.7625 0.048 0.952
#> GSM751438 2 0.5519 0.7349 0.128 0.872
#> GSM751439 1 0.9635 0.2243 0.612 0.388
#> GSM751441 2 0.3879 0.7518 0.076 0.924
#> GSM751442 1 0.9922 0.1648 0.552 0.448
#> GSM751443 2 0.9988 0.2768 0.480 0.520
#> GSM751445 2 0.2236 0.7603 0.036 0.964
#> GSM751447 2 0.2778 0.7622 0.048 0.952
#> GSM751453 2 0.3274 0.7597 0.060 0.940
#> GSM751454 2 0.2423 0.7585 0.040 0.960
#> GSM751455 2 0.5629 0.7408 0.132 0.868
#> GSM751456 2 0.5629 0.7411 0.132 0.868
#> GSM751457 2 0.3431 0.7614 0.064 0.936
#> GSM751458 2 0.2423 0.7611 0.040 0.960
cbind(get_classes(res, k = 3), get_membership(res, k = 3))
#> class entropy silhouette p1 p2 p3
#> GSM751298 1 0.0592 0.8965 0.988 0.000 0.012
#> GSM751304 3 0.9981 0.1068 0.316 0.320 0.364
#> GSM751305 3 0.9916 0.1634 0.288 0.316 0.396
#> GSM751307 3 0.9061 0.3337 0.148 0.348 0.504
#> GSM751310 1 0.1529 0.8766 0.960 0.000 0.040
#> GSM751314 1 0.1289 0.8898 0.968 0.032 0.000
#> GSM751316 1 0.1411 0.8884 0.964 0.036 0.000
#> GSM751318 1 0.0592 0.8966 0.988 0.000 0.012
#> GSM751342 1 0.1647 0.8871 0.960 0.036 0.004
#> GSM751346 1 0.1163 0.8864 0.972 0.000 0.028
#> GSM751347 1 0.0747 0.8948 0.984 0.000 0.016
#> GSM751348 1 0.9967 -0.2266 0.372 0.324 0.304
#> GSM751349 2 0.8795 0.3912 0.168 0.576 0.256
#> GSM751352 3 0.9641 0.2390 0.224 0.324 0.452
#> GSM751353 3 0.9342 0.2139 0.168 0.380 0.452
#> GSM751354 3 0.8559 0.4369 0.124 0.304 0.572
#> GSM751355 3 0.8487 0.3645 0.100 0.364 0.536
#> GSM751358 1 0.6295 0.6447 0.728 0.036 0.236
#> GSM751359 3 0.6881 0.5294 0.032 0.320 0.648
#> GSM751294 3 0.5625 0.6326 0.076 0.116 0.808
#> GSM751296 1 0.0237 0.8989 0.996 0.000 0.004
#> GSM751297 1 0.6721 0.3247 0.604 0.016 0.380
#> GSM751299 1 0.7267 0.4469 0.668 0.268 0.064
#> GSM751300 1 0.0000 0.9003 1.000 0.000 0.000
#> GSM751301 1 0.1289 0.8773 0.968 0.032 0.000
#> GSM751302 1 0.0000 0.9003 1.000 0.000 0.000
#> GSM751303 1 0.1411 0.8884 0.964 0.036 0.000
#> GSM751306 1 0.1647 0.8878 0.960 0.036 0.004
#> GSM751308 1 0.0592 0.8959 0.988 0.000 0.012
#> GSM751309 1 0.1411 0.8884 0.964 0.036 0.000
#> GSM751311 1 0.1411 0.8884 0.964 0.036 0.000
#> GSM751312 1 0.2152 0.8835 0.948 0.036 0.016
#> GSM751313 1 0.0000 0.9003 1.000 0.000 0.000
#> GSM751315 1 0.0000 0.9003 1.000 0.000 0.000
#> GSM751317 1 0.0000 0.9003 1.000 0.000 0.000
#> GSM751320 1 0.0000 0.9003 1.000 0.000 0.000
#> GSM751321 1 0.1411 0.8884 0.964 0.036 0.000
#> GSM751322 1 0.0424 0.8980 0.992 0.000 0.008
#> GSM751324 1 0.0848 0.8970 0.984 0.008 0.008
#> GSM751325 1 0.0000 0.9003 1.000 0.000 0.000
#> GSM751332 1 0.0000 0.9003 1.000 0.000 0.000
#> GSM751334 1 0.0000 0.9003 1.000 0.000 0.000
#> GSM751339 1 0.0000 0.9003 1.000 0.000 0.000
#> GSM751341 1 0.2926 0.8640 0.924 0.036 0.040
#> GSM751343 1 0.0000 0.9003 1.000 0.000 0.000
#> GSM751344 2 0.9858 -0.0407 0.256 0.396 0.348
#> GSM751345 2 0.9910 -0.0412 0.272 0.384 0.344
#> GSM751356 1 0.6890 0.3526 0.632 0.028 0.340
#> GSM751357 1 0.9206 0.1398 0.524 0.188 0.288
#> GSM751293 1 0.0000 0.9003 1.000 0.000 0.000
#> GSM751295 1 0.0000 0.9003 1.000 0.000 0.000
#> GSM751319 1 0.1411 0.8884 0.964 0.036 0.000
#> GSM751323 1 0.0000 0.9003 1.000 0.000 0.000
#> GSM751326 1 0.0000 0.9003 1.000 0.000 0.000
#> GSM751327 1 0.0000 0.9003 1.000 0.000 0.000
#> GSM751328 1 0.1163 0.8911 0.972 0.028 0.000
#> GSM751329 1 0.0000 0.9003 1.000 0.000 0.000
#> GSM751330 1 0.0000 0.9003 1.000 0.000 0.000
#> GSM751331 1 0.0000 0.9003 1.000 0.000 0.000
#> GSM751333 1 0.0000 0.9003 1.000 0.000 0.000
#> GSM751335 1 0.0000 0.9003 1.000 0.000 0.000
#> GSM751336 1 0.0000 0.9003 1.000 0.000 0.000
#> GSM751337 1 0.0000 0.9003 1.000 0.000 0.000
#> GSM751338 1 0.0000 0.9003 1.000 0.000 0.000
#> GSM751340 1 0.5016 0.6353 0.760 0.000 0.240
#> GSM751350 1 0.0000 0.9003 1.000 0.000 0.000
#> GSM751351 1 0.0000 0.9003 1.000 0.000 0.000
#> GSM751362 3 0.4887 0.5754 0.228 0.000 0.772
#> GSM751363 1 0.5948 0.4196 0.640 0.000 0.360
#> GSM751367 3 0.5360 0.5820 0.220 0.012 0.768
#> GSM751368 3 0.7391 0.5012 0.056 0.308 0.636
#> GSM751371 1 0.4291 0.7324 0.820 0.000 0.180
#> GSM751375 2 0.8228 0.1726 0.084 0.552 0.364
#> GSM751376 3 0.5455 0.5905 0.204 0.020 0.776
#> GSM751378 3 0.5884 0.3662 0.012 0.272 0.716
#> GSM751379 3 0.2682 0.6844 0.004 0.076 0.920
#> GSM751382 2 0.6143 0.4697 0.012 0.684 0.304
#> GSM751386 3 0.5785 0.5371 0.004 0.300 0.696
#> GSM751388 3 0.5024 0.6100 0.004 0.220 0.776
#> GSM751391 3 0.4974 0.5717 0.236 0.000 0.764
#> GSM751410 1 0.6308 0.0866 0.508 0.000 0.492
#> GSM751414 3 0.2356 0.6803 0.072 0.000 0.928
#> GSM751361 3 0.5926 0.4359 0.356 0.000 0.644
#> GSM751365 3 0.0892 0.6922 0.020 0.000 0.980
#> GSM751366 3 0.5678 0.3939 0.316 0.000 0.684
#> GSM751369 3 0.6260 0.2319 0.448 0.000 0.552
#> GSM751370 3 0.5138 0.5386 0.252 0.000 0.748
#> GSM751372 3 0.0592 0.6939 0.012 0.000 0.988
#> GSM751373 3 0.2537 0.6818 0.080 0.000 0.920
#> GSM751374 3 0.2902 0.6855 0.016 0.064 0.920
#> GSM751377 3 0.5216 0.5781 0.000 0.260 0.740
#> GSM751380 3 0.1643 0.6838 0.044 0.000 0.956
#> GSM751381 3 0.6282 0.5117 0.012 0.324 0.664
#> GSM751383 3 0.3816 0.6536 0.000 0.148 0.852
#> GSM751384 3 0.3752 0.6273 0.020 0.096 0.884
#> GSM751385 3 0.2400 0.6835 0.004 0.064 0.932
#> GSM751387 3 0.5244 0.6013 0.004 0.240 0.756
#> GSM751389 3 0.1163 0.6895 0.028 0.000 0.972
#> GSM751393 3 0.0424 0.6932 0.008 0.000 0.992
#> GSM751394 3 0.6359 0.4637 0.008 0.364 0.628
#> GSM751395 3 0.3340 0.6591 0.120 0.000 0.880
#> GSM751397 3 0.2173 0.6917 0.008 0.048 0.944
#> GSM751398 3 0.5831 0.5543 0.008 0.284 0.708
#> GSM751404 3 0.0237 0.6919 0.004 0.000 0.996
#> GSM751406 3 0.4121 0.6166 0.168 0.000 0.832
#> GSM751411 3 0.0000 0.6910 0.000 0.000 1.000
#> GSM751413 3 0.7905 0.4485 0.072 0.340 0.588
#> GSM751415 3 0.1643 0.6838 0.044 0.000 0.956
#> GSM751416 3 0.5178 0.5822 0.000 0.256 0.744
#> GSM751417 3 0.5431 0.5550 0.000 0.284 0.716
#> GSM751421 3 0.5431 0.5146 0.284 0.000 0.716
#> GSM751422 1 0.4504 0.7147 0.804 0.000 0.196
#> GSM751360 1 0.6225 0.1699 0.568 0.000 0.432
#> GSM751364 3 0.0747 0.6952 0.016 0.000 0.984
#> GSM751390 3 0.0747 0.6936 0.016 0.000 0.984
#> GSM751392 3 0.7624 0.3813 0.048 0.392 0.560
#> GSM751396 3 0.5988 0.4634 0.000 0.368 0.632
#> GSM751399 3 0.0000 0.6910 0.000 0.000 1.000
#> GSM751400 3 0.0747 0.6936 0.016 0.000 0.984
#> GSM751401 3 0.1491 0.6884 0.016 0.016 0.968
#> GSM751402 3 0.0237 0.6919 0.004 0.000 0.996
#> GSM751403 3 0.0237 0.6919 0.004 0.000 0.996
#> GSM751405 3 0.3551 0.6434 0.132 0.000 0.868
#> GSM751407 3 0.0237 0.6919 0.004 0.000 0.996
#> GSM751408 3 0.0237 0.6919 0.004 0.000 0.996
#> GSM751409 3 0.0661 0.6920 0.008 0.004 0.988
#> GSM751412 3 0.0000 0.6910 0.000 0.000 1.000
#> GSM751418 3 0.0237 0.6921 0.004 0.000 0.996
#> GSM751419 3 0.0000 0.6910 0.000 0.000 1.000
#> GSM751420 3 0.3918 0.6270 0.004 0.140 0.856
#> GSM751425 2 0.1525 0.7660 0.032 0.964 0.004
#> GSM751429 3 0.8342 -0.2191 0.080 0.456 0.464
#> GSM751430 3 0.6529 0.4571 0.012 0.368 0.620
#> GSM751433 2 0.7283 0.5661 0.260 0.672 0.068
#> GSM751437 2 0.7842 0.3864 0.072 0.600 0.328
#> GSM751448 2 0.8260 0.2246 0.076 0.492 0.432
#> GSM751451 2 0.3213 0.7544 0.060 0.912 0.028
#> GSM751423 2 0.6908 0.4276 0.036 0.656 0.308
#> GSM751424 3 0.6498 0.4235 0.008 0.396 0.596
#> GSM751428 3 0.7757 0.3645 0.052 0.408 0.540
#> GSM751431 2 0.2496 0.7571 0.068 0.928 0.004
#> GSM751432 3 0.6379 0.4638 0.008 0.368 0.624
#> GSM751434 3 0.6330 0.4350 0.004 0.396 0.600
#> GSM751435 2 0.5558 0.6831 0.048 0.800 0.152
#> GSM751436 3 0.7901 0.3665 0.060 0.400 0.540
#> GSM751440 2 0.6496 0.6050 0.056 0.736 0.208
#> GSM751444 2 0.5298 0.6776 0.032 0.804 0.164
#> GSM751446 2 0.2599 0.7631 0.052 0.932 0.016
#> GSM751449 2 0.2486 0.7536 0.008 0.932 0.060
#> GSM751450 2 0.6082 0.5222 0.012 0.692 0.296
#> GSM751452 3 0.7366 0.3897 0.036 0.400 0.564
#> GSM751426 2 0.5875 0.6917 0.136 0.792 0.072
#> GSM751427 2 0.4723 0.6884 0.016 0.824 0.160
#> GSM751438 2 0.1585 0.7608 0.008 0.964 0.028
#> GSM751439 2 0.7997 0.3535 0.072 0.568 0.360
#> GSM751441 2 0.3083 0.7559 0.024 0.916 0.060
#> GSM751442 2 0.1525 0.7657 0.032 0.964 0.004
#> GSM751443 3 0.8387 -0.1514 0.084 0.428 0.488
#> GSM751445 2 0.1620 0.7672 0.024 0.964 0.012
#> GSM751447 2 0.1585 0.7677 0.028 0.964 0.008
#> GSM751453 2 0.1620 0.7674 0.024 0.964 0.012
#> GSM751454 2 0.1620 0.7674 0.024 0.964 0.012
#> GSM751455 2 0.1585 0.7677 0.028 0.964 0.008
#> GSM751456 2 0.1585 0.7677 0.028 0.964 0.008
#> GSM751457 2 0.1585 0.7677 0.028 0.964 0.008
#> GSM751458 2 0.1585 0.7677 0.028 0.964 0.008
cbind(get_classes(res, k = 4), get_membership(res, k = 4))
#> class entropy silhouette p1 p2 p3 p4
#> GSM751298 1 0.0707 0.8845 0.980 0.000 0.020 0.000
#> GSM751304 3 0.9747 -0.1609 0.232 0.280 0.332 0.156
#> GSM751305 1 0.9765 -0.2395 0.340 0.280 0.180 0.200
#> GSM751307 4 0.9650 0.0653 0.188 0.292 0.164 0.356
#> GSM751310 1 0.1388 0.8755 0.960 0.000 0.028 0.012
#> GSM751314 1 0.3444 0.8060 0.816 0.000 0.000 0.184
#> GSM751316 1 0.3444 0.8144 0.816 0.000 0.000 0.184
#> GSM751318 1 0.1004 0.8819 0.972 0.000 0.024 0.004
#> GSM751342 1 0.3528 0.8006 0.808 0.000 0.000 0.192
#> GSM751346 1 0.1284 0.8852 0.964 0.000 0.012 0.024
#> GSM751347 1 0.1151 0.8824 0.968 0.000 0.024 0.008
#> GSM751348 4 0.6740 0.5154 0.208 0.136 0.012 0.644
#> GSM751349 4 0.6482 0.5852 0.168 0.064 0.064 0.704
#> GSM751352 4 0.8770 0.4462 0.232 0.112 0.152 0.504
#> GSM751353 4 0.5924 0.5655 0.172 0.040 0.056 0.732
#> GSM751354 4 0.9476 0.3378 0.156 0.200 0.228 0.416
#> GSM751355 4 0.9654 0.0769 0.184 0.292 0.168 0.356
#> GSM751358 4 0.6650 -0.1659 0.432 0.000 0.084 0.484
#> GSM751359 4 0.3764 0.5649 0.000 0.012 0.172 0.816
#> GSM751294 4 0.8573 0.3911 0.064 0.152 0.336 0.448
#> GSM751296 1 0.0779 0.8882 0.980 0.000 0.004 0.016
#> GSM751297 1 0.6485 0.5299 0.644 0.056 0.272 0.028
#> GSM751299 1 0.6717 0.4402 0.632 0.196 0.004 0.168
#> GSM751300 1 0.0336 0.8879 0.992 0.000 0.000 0.008
#> GSM751301 1 0.1629 0.8705 0.952 0.024 0.000 0.024
#> GSM751302 1 0.0817 0.8861 0.976 0.000 0.000 0.024
#> GSM751303 1 0.3528 0.8006 0.808 0.000 0.000 0.192
#> GSM751306 1 0.3528 0.8006 0.808 0.000 0.000 0.192
#> GSM751308 1 0.1118 0.8743 0.964 0.000 0.036 0.000
#> GSM751309 1 0.3528 0.8006 0.808 0.000 0.000 0.192
#> GSM751311 1 0.3528 0.8006 0.808 0.000 0.000 0.192
#> GSM751312 1 0.3945 0.8000 0.780 0.000 0.004 0.216
#> GSM751313 1 0.0707 0.8871 0.980 0.000 0.000 0.020
#> GSM751315 1 0.0336 0.8879 0.992 0.000 0.000 0.008
#> GSM751317 1 0.1302 0.8778 0.956 0.000 0.000 0.044
#> GSM751320 1 0.0000 0.8874 1.000 0.000 0.000 0.000
#> GSM751321 1 0.3569 0.8011 0.804 0.000 0.000 0.196
#> GSM751322 1 0.0469 0.8863 0.988 0.000 0.012 0.000
#> GSM751324 1 0.0779 0.8847 0.980 0.000 0.016 0.004
#> GSM751325 1 0.0188 0.8877 0.996 0.000 0.004 0.000
#> GSM751332 1 0.0188 0.8878 0.996 0.000 0.000 0.004
#> GSM751334 1 0.0188 0.8878 0.996 0.000 0.000 0.004
#> GSM751339 1 0.0895 0.8867 0.976 0.000 0.004 0.020
#> GSM751341 1 0.3649 0.8011 0.796 0.000 0.000 0.204
#> GSM751343 1 0.0000 0.8874 1.000 0.000 0.000 0.000
#> GSM751344 4 0.7940 0.1918 0.180 0.288 0.024 0.508
#> GSM751345 4 0.8740 0.1474 0.180 0.300 0.068 0.452
#> GSM751356 4 0.6529 0.4647 0.320 0.004 0.084 0.592
#> GSM751357 4 0.6505 0.4435 0.312 0.012 0.068 0.608
#> GSM751293 1 0.0707 0.8873 0.980 0.000 0.000 0.020
#> GSM751295 1 0.0817 0.8861 0.976 0.000 0.000 0.024
#> GSM751319 1 0.3266 0.8218 0.832 0.000 0.000 0.168
#> GSM751323 1 0.0000 0.8874 1.000 0.000 0.000 0.000
#> GSM751326 1 0.0336 0.8879 0.992 0.000 0.000 0.008
#> GSM751327 1 0.0188 0.8879 0.996 0.000 0.000 0.004
#> GSM751328 1 0.1867 0.8656 0.928 0.000 0.000 0.072
#> GSM751329 1 0.0336 0.8879 0.992 0.000 0.000 0.008
#> GSM751330 1 0.0817 0.8861 0.976 0.000 0.000 0.024
#> GSM751331 1 0.0817 0.8861 0.976 0.000 0.000 0.024
#> GSM751333 1 0.0592 0.8876 0.984 0.000 0.000 0.016
#> GSM751335 1 0.0707 0.8872 0.980 0.000 0.000 0.020
#> GSM751336 1 0.0817 0.8861 0.976 0.000 0.000 0.024
#> GSM751337 1 0.0779 0.8870 0.980 0.000 0.004 0.016
#> GSM751338 1 0.0469 0.8879 0.988 0.000 0.000 0.012
#> GSM751340 1 0.4019 0.7146 0.792 0.000 0.196 0.012
#> GSM751350 1 0.0817 0.8861 0.976 0.000 0.000 0.024
#> GSM751351 1 0.0817 0.8861 0.976 0.000 0.000 0.024
#> GSM751362 3 0.3810 0.6302 0.188 0.000 0.804 0.008
#> GSM751363 1 0.7348 0.0970 0.528 0.000 0.240 0.232
#> GSM751367 3 0.5657 0.4314 0.312 0.000 0.644 0.044
#> GSM751368 4 0.8022 0.4465 0.004 0.280 0.332 0.384
#> GSM751371 1 0.3486 0.7295 0.812 0.000 0.188 0.000
#> GSM751375 4 0.7100 0.4958 0.128 0.160 0.052 0.660
#> GSM751376 3 0.4806 0.6762 0.124 0.052 0.804 0.020
#> GSM751378 3 0.4850 0.6727 0.016 0.124 0.800 0.060
#> GSM751379 3 0.3575 0.6918 0.012 0.092 0.868 0.028
#> GSM751382 4 0.5580 0.6431 0.016 0.064 0.180 0.740
#> GSM751386 4 0.4991 0.6361 0.004 0.008 0.316 0.672
#> GSM751388 4 0.4741 0.6266 0.004 0.000 0.328 0.668
#> GSM751391 3 0.3636 0.6642 0.172 0.000 0.820 0.008
#> GSM751410 3 0.4356 0.5137 0.292 0.000 0.708 0.000
#> GSM751414 4 0.4605 0.6222 0.000 0.000 0.336 0.664
#> GSM751361 4 0.4957 0.6306 0.012 0.000 0.320 0.668
#> GSM751365 3 0.0469 0.7754 0.000 0.000 0.988 0.012
#> GSM751366 3 0.2101 0.7428 0.060 0.000 0.928 0.012
#> GSM751369 1 0.5212 0.2723 0.572 0.000 0.420 0.008
#> GSM751370 3 0.6876 0.1617 0.144 0.000 0.576 0.280
#> GSM751372 3 0.5168 -0.4115 0.004 0.000 0.504 0.492
#> GSM751373 3 0.1388 0.7710 0.028 0.000 0.960 0.012
#> GSM751374 3 0.2742 0.7515 0.024 0.032 0.916 0.028
#> GSM751377 4 0.4857 0.6300 0.000 0.008 0.324 0.668
#> GSM751380 3 0.0469 0.7754 0.000 0.000 0.988 0.012
#> GSM751381 4 0.5205 0.6401 0.012 0.008 0.308 0.672
#> GSM751383 4 0.4857 0.6337 0.000 0.008 0.324 0.668
#> GSM751384 4 0.5206 0.6357 0.024 0.000 0.308 0.668
#> GSM751385 3 0.4088 0.5187 0.004 0.000 0.764 0.232
#> GSM751387 4 0.4746 0.6481 0.008 0.004 0.276 0.712
#> GSM751389 3 0.0469 0.7754 0.000 0.000 0.988 0.012
#> GSM751393 4 0.5080 0.5403 0.004 0.000 0.420 0.576
#> GSM751394 4 0.4631 0.6502 0.004 0.008 0.260 0.728
#> GSM751395 4 0.6362 0.6063 0.096 0.000 0.288 0.616
#> GSM751397 4 0.4857 0.6299 0.008 0.000 0.324 0.668
#> GSM751398 4 0.5106 0.6387 0.008 0.008 0.312 0.672
#> GSM751404 3 0.0336 0.7761 0.000 0.000 0.992 0.008
#> GSM751406 3 0.2918 0.7110 0.116 0.000 0.876 0.008
#> GSM751411 3 0.0469 0.7754 0.000 0.000 0.988 0.012
#> GSM751413 4 0.5612 0.6124 0.028 0.008 0.308 0.656
#> GSM751415 3 0.0469 0.7754 0.000 0.000 0.988 0.012
#> GSM751416 4 0.4800 0.6227 0.000 0.004 0.340 0.656
#> GSM751417 4 0.4936 0.6269 0.000 0.008 0.340 0.652
#> GSM751421 3 0.4194 0.5923 0.228 0.000 0.764 0.008
#> GSM751422 1 0.3123 0.7795 0.844 0.000 0.156 0.000
#> GSM751360 1 0.4483 0.5883 0.712 0.000 0.284 0.004
#> GSM751364 4 0.4746 0.6004 0.000 0.000 0.368 0.632
#> GSM751390 4 0.5130 0.6391 0.020 0.000 0.312 0.668
#> GSM751392 4 0.5321 0.6460 0.064 0.016 0.156 0.764
#> GSM751396 4 0.4049 0.6448 0.000 0.008 0.212 0.780
#> GSM751399 3 0.0336 0.7761 0.000 0.000 0.992 0.008
#> GSM751400 3 0.0927 0.7746 0.016 0.000 0.976 0.008
#> GSM751401 3 0.0336 0.7748 0.000 0.000 0.992 0.008
#> GSM751402 3 0.0804 0.7749 0.012 0.000 0.980 0.008
#> GSM751403 3 0.0336 0.7748 0.000 0.000 0.992 0.008
#> GSM751405 3 0.2611 0.7287 0.096 0.000 0.896 0.008
#> GSM751407 3 0.0672 0.7755 0.008 0.000 0.984 0.008
#> GSM751408 3 0.0336 0.7748 0.000 0.000 0.992 0.008
#> GSM751409 3 0.0000 0.7763 0.000 0.000 1.000 0.000
#> GSM751412 3 0.0469 0.7754 0.000 0.000 0.988 0.012
#> GSM751418 3 0.1022 0.7641 0.000 0.000 0.968 0.032
#> GSM751419 3 0.0592 0.7734 0.000 0.000 0.984 0.016
#> GSM751420 3 0.3196 0.7226 0.012 0.104 0.876 0.008
#> GSM751425 2 0.1557 0.7626 0.000 0.944 0.000 0.056
#> GSM751429 2 0.7256 0.0477 0.092 0.448 0.444 0.016
#> GSM751430 4 0.8293 0.1762 0.012 0.324 0.316 0.348
#> GSM751433 2 0.7661 0.5092 0.240 0.592 0.060 0.108
#> GSM751437 2 0.4720 0.3927 0.004 0.672 0.324 0.000
#> GSM751448 3 0.5110 0.4069 0.016 0.328 0.656 0.000
#> GSM751451 2 0.3823 0.7368 0.028 0.852 0.012 0.108
#> GSM751423 2 0.7885 0.3593 0.036 0.484 0.360 0.120
#> GSM751424 4 0.8243 0.1435 0.012 0.356 0.272 0.360
#> GSM751428 2 0.8387 0.3775 0.076 0.492 0.312 0.120
#> GSM751431 2 0.3551 0.7386 0.028 0.860 0.004 0.108
#> GSM751432 3 0.8258 -0.0551 0.024 0.324 0.440 0.212
#> GSM751434 2 0.7932 0.2739 0.028 0.464 0.368 0.140
#> GSM751435 2 0.5086 0.6680 0.048 0.784 0.144 0.024
#> GSM751436 2 0.9284 0.1251 0.100 0.404 0.264 0.232
#> GSM751440 2 0.5232 0.6331 0.028 0.788 0.080 0.104
#> GSM751444 2 0.5603 0.6514 0.032 0.756 0.152 0.060
#> GSM751446 2 0.1004 0.7538 0.024 0.972 0.004 0.000
#> GSM751449 2 0.0921 0.7543 0.000 0.972 0.028 0.000
#> GSM751450 2 0.6413 0.4560 0.008 0.596 0.332 0.064
#> GSM751452 4 0.8717 0.1301 0.040 0.356 0.244 0.360
#> GSM751426 2 0.6750 0.6161 0.148 0.688 0.048 0.116
#> GSM751427 2 0.3845 0.6873 0.012 0.840 0.132 0.016
#> GSM751438 2 0.0000 0.7552 0.000 1.000 0.000 0.000
#> GSM751439 2 0.4973 0.3587 0.008 0.644 0.348 0.000
#> GSM751441 2 0.3150 0.7474 0.004 0.888 0.036 0.072
#> GSM751442 2 0.0000 0.7552 0.000 1.000 0.000 0.000
#> GSM751443 3 0.6016 0.1562 0.044 0.412 0.544 0.000
#> GSM751445 2 0.1557 0.7626 0.000 0.944 0.000 0.056
#> GSM751447 2 0.1557 0.7626 0.000 0.944 0.000 0.056
#> GSM751453 2 0.1557 0.7626 0.000 0.944 0.000 0.056
#> GSM751454 2 0.1557 0.7626 0.000 0.944 0.000 0.056
#> GSM751455 2 0.0000 0.7552 0.000 1.000 0.000 0.000
#> GSM751456 2 0.0000 0.7552 0.000 1.000 0.000 0.000
#> GSM751457 2 0.1474 0.7627 0.000 0.948 0.000 0.052
#> GSM751458 2 0.1474 0.7627 0.000 0.948 0.000 0.052
cbind(get_classes(res, k = 5), get_membership(res, k = 5))
#> class entropy silhouette p1 p2 p3 p4 p5
#> GSM751298 1 0.3985 0.7636 0.772 0.000 0.028 0.196 0.004
#> GSM751304 2 0.7588 0.2630 0.208 0.564 0.116 0.048 0.064
#> GSM751305 2 0.6913 0.2745 0.120 0.612 0.076 0.180 0.012
#> GSM751307 2 0.8021 0.1696 0.344 0.440 0.096 0.060 0.060
#> GSM751310 1 0.5283 0.7685 0.696 0.032 0.004 0.228 0.040
#> GSM751314 1 0.4383 0.6543 0.572 0.000 0.000 0.424 0.004
#> GSM751316 1 0.4506 0.6496 0.676 0.000 0.000 0.296 0.028
#> GSM751318 1 0.3690 0.7629 0.780 0.000 0.020 0.200 0.000
#> GSM751342 1 0.4443 0.6273 0.524 0.000 0.000 0.472 0.004
#> GSM751346 1 0.3052 0.7504 0.876 0.000 0.016 0.036 0.072
#> GSM751347 1 0.2818 0.7413 0.892 0.000 0.020 0.052 0.036
#> GSM751348 5 0.4393 0.6491 0.080 0.012 0.004 0.112 0.792
#> GSM751349 5 0.3748 0.7294 0.048 0.072 0.024 0.008 0.848
#> GSM751352 5 0.7867 0.2629 0.336 0.024 0.160 0.052 0.428
#> GSM751353 5 0.4867 0.6810 0.116 0.052 0.036 0.016 0.780
#> GSM751354 5 0.8520 0.2190 0.296 0.048 0.212 0.060 0.384
#> GSM751355 2 0.8334 0.1967 0.288 0.452 0.112 0.052 0.096
#> GSM751358 4 0.7452 -0.2408 0.236 0.000 0.044 0.432 0.288
#> GSM751359 5 0.6879 0.5392 0.004 0.092 0.068 0.280 0.556
#> GSM751294 5 0.7317 0.1851 0.028 0.004 0.232 0.284 0.452
#> GSM751296 1 0.2681 0.7714 0.892 0.000 0.004 0.052 0.052
#> GSM751297 1 0.7032 0.4346 0.576 0.004 0.216 0.124 0.080
#> GSM751299 1 0.7298 0.3926 0.564 0.152 0.004 0.108 0.172
#> GSM751300 1 0.2378 0.7444 0.904 0.000 0.000 0.048 0.048
#> GSM751301 1 0.4873 0.7679 0.728 0.012 0.004 0.204 0.052
#> GSM751302 1 0.3043 0.7326 0.864 0.000 0.000 0.056 0.080
#> GSM751303 1 0.4555 0.6260 0.520 0.000 0.000 0.472 0.008
#> GSM751306 1 0.4443 0.6273 0.524 0.000 0.000 0.472 0.004
#> GSM751308 1 0.4141 0.7655 0.768 0.000 0.020 0.196 0.016
#> GSM751309 1 0.4443 0.6273 0.524 0.000 0.000 0.472 0.004
#> GSM751311 1 0.4443 0.6273 0.524 0.000 0.000 0.472 0.004
#> GSM751312 1 0.4874 0.6118 0.632 0.000 0.000 0.328 0.040
#> GSM751313 1 0.2520 0.7472 0.896 0.000 0.000 0.048 0.056
#> GSM751315 1 0.0451 0.7687 0.988 0.000 0.000 0.004 0.008
#> GSM751317 1 0.3779 0.7606 0.752 0.000 0.000 0.236 0.012
#> GSM751320 1 0.3387 0.7660 0.796 0.000 0.004 0.196 0.004
#> GSM751321 1 0.3990 0.6453 0.688 0.000 0.000 0.308 0.004
#> GSM751322 1 0.3231 0.7659 0.800 0.000 0.004 0.196 0.000
#> GSM751324 1 0.3496 0.7651 0.788 0.000 0.012 0.200 0.000
#> GSM751325 1 0.3231 0.7659 0.800 0.000 0.004 0.196 0.000
#> GSM751332 1 0.2141 0.7657 0.916 0.000 0.004 0.064 0.016
#> GSM751334 1 0.1862 0.7659 0.932 0.000 0.004 0.048 0.016
#> GSM751339 1 0.4545 0.7724 0.748 0.000 0.008 0.188 0.056
#> GSM751341 1 0.4446 0.6270 0.520 0.000 0.000 0.476 0.004
#> GSM751343 1 0.3231 0.7659 0.800 0.000 0.004 0.196 0.000
#> GSM751344 5 0.6001 0.4689 0.072 0.268 0.020 0.012 0.628
#> GSM751345 5 0.7068 0.3555 0.100 0.300 0.048 0.016 0.536
#> GSM751356 5 0.6324 0.4991 0.228 0.008 0.036 0.100 0.628
#> GSM751357 5 0.7380 0.4078 0.256 0.040 0.032 0.132 0.540
#> GSM751293 1 0.4356 0.7694 0.748 0.000 0.004 0.204 0.044
#> GSM751295 1 0.3102 0.7322 0.860 0.000 0.000 0.056 0.084
#> GSM751319 1 0.3246 0.7163 0.808 0.000 0.000 0.184 0.008
#> GSM751323 1 0.3074 0.7667 0.804 0.000 0.000 0.196 0.000
#> GSM751326 1 0.0693 0.7653 0.980 0.000 0.000 0.008 0.012
#> GSM751327 1 0.2763 0.7773 0.848 0.000 0.000 0.148 0.004
#> GSM751328 1 0.3870 0.7565 0.732 0.000 0.004 0.260 0.004
#> GSM751329 1 0.1648 0.7570 0.940 0.000 0.000 0.040 0.020
#> GSM751330 1 0.2729 0.7382 0.884 0.000 0.000 0.056 0.060
#> GSM751331 1 0.3043 0.7326 0.864 0.000 0.000 0.056 0.080
#> GSM751333 1 0.2067 0.7487 0.920 0.000 0.000 0.048 0.032
#> GSM751335 1 0.2230 0.7474 0.912 0.000 0.000 0.044 0.044
#> GSM751336 1 0.3102 0.7322 0.860 0.000 0.000 0.056 0.084
#> GSM751337 1 0.4545 0.7690 0.740 0.000 0.008 0.204 0.048
#> GSM751338 1 0.4149 0.7743 0.768 0.000 0.004 0.188 0.040
#> GSM751340 1 0.5697 0.6567 0.660 0.000 0.208 0.116 0.016
#> GSM751350 1 0.3102 0.7322 0.860 0.000 0.000 0.056 0.084
#> GSM751351 1 0.3043 0.7326 0.864 0.000 0.000 0.056 0.080
#> GSM751362 3 0.3489 0.6600 0.208 0.004 0.784 0.000 0.004
#> GSM751363 1 0.6709 0.1362 0.500 0.000 0.156 0.020 0.324
#> GSM751367 3 0.6458 0.0189 0.452 0.024 0.452 0.052 0.020
#> GSM751368 5 0.6938 0.3563 0.008 0.340 0.172 0.012 0.468
#> GSM751371 1 0.5960 0.6276 0.608 0.000 0.212 0.176 0.004
#> GSM751375 5 0.3129 0.6778 0.000 0.156 0.008 0.004 0.832
#> GSM751376 3 0.4163 0.7355 0.076 0.008 0.824 0.028 0.064
#> GSM751378 3 0.3888 0.7494 0.004 0.016 0.828 0.048 0.104
#> GSM751379 3 0.3146 0.7793 0.004 0.056 0.876 0.012 0.052
#> GSM751382 5 0.2860 0.7531 0.004 0.044 0.048 0.012 0.892
#> GSM751386 5 0.2179 0.7717 0.000 0.000 0.112 0.000 0.888
#> GSM751388 5 0.2127 0.7722 0.000 0.000 0.108 0.000 0.892
#> GSM751391 3 0.3275 0.7633 0.092 0.008 0.864 0.024 0.012
#> GSM751410 3 0.4140 0.6355 0.200 0.000 0.764 0.028 0.008
#> GSM751414 5 0.3690 0.7207 0.000 0.000 0.224 0.012 0.764
#> GSM751361 5 0.2377 0.7706 0.000 0.000 0.128 0.000 0.872
#> GSM751365 3 0.0968 0.8397 0.004 0.000 0.972 0.012 0.012
#> GSM751366 3 0.1764 0.8240 0.036 0.000 0.940 0.012 0.012
#> GSM751369 3 0.4976 0.1683 0.408 0.004 0.568 0.012 0.008
#> GSM751370 3 0.6943 0.2613 0.216 0.000 0.532 0.036 0.216
#> GSM751372 5 0.4887 0.3714 0.008 0.000 0.444 0.012 0.536
#> GSM751373 3 0.1507 0.8353 0.024 0.000 0.952 0.012 0.012
#> GSM751374 3 0.2115 0.8146 0.004 0.032 0.928 0.008 0.028
#> GSM751377 5 0.2230 0.7718 0.000 0.000 0.116 0.000 0.884
#> GSM751380 3 0.0807 0.8400 0.000 0.000 0.976 0.012 0.012
#> GSM751381 5 0.2127 0.7722 0.000 0.000 0.108 0.000 0.892
#> GSM751383 5 0.2280 0.7724 0.000 0.000 0.120 0.000 0.880
#> GSM751384 5 0.2233 0.7717 0.004 0.000 0.104 0.000 0.892
#> GSM751385 3 0.4305 0.6002 0.000 0.036 0.744 0.004 0.216
#> GSM751387 5 0.2676 0.7652 0.000 0.036 0.080 0.000 0.884
#> GSM751389 3 0.0807 0.8400 0.000 0.000 0.976 0.012 0.012
#> GSM751393 5 0.3509 0.7510 0.004 0.004 0.192 0.004 0.796
#> GSM751394 5 0.2654 0.7677 0.000 0.032 0.084 0.000 0.884
#> GSM751395 5 0.3928 0.7379 0.036 0.004 0.156 0.004 0.800
#> GSM751397 5 0.2179 0.7717 0.000 0.000 0.112 0.000 0.888
#> GSM751398 5 0.2179 0.7717 0.000 0.000 0.112 0.000 0.888
#> GSM751404 3 0.0693 0.8403 0.000 0.000 0.980 0.008 0.012
#> GSM751406 3 0.1202 0.8271 0.032 0.004 0.960 0.000 0.004
#> GSM751411 3 0.0807 0.8400 0.000 0.000 0.976 0.012 0.012
#> GSM751413 5 0.5484 0.6458 0.016 0.056 0.272 0.004 0.652
#> GSM751415 3 0.0807 0.8400 0.000 0.000 0.976 0.012 0.012
#> GSM751416 5 0.2865 0.7699 0.000 0.004 0.132 0.008 0.856
#> GSM751417 5 0.2848 0.7679 0.000 0.004 0.156 0.000 0.840
#> GSM751421 3 0.3333 0.6581 0.208 0.004 0.788 0.000 0.000
#> GSM751422 1 0.4928 0.5919 0.660 0.000 0.284 0.056 0.000
#> GSM751360 1 0.6520 0.5124 0.524 0.000 0.300 0.164 0.012
#> GSM751364 5 0.4063 0.6663 0.000 0.000 0.280 0.012 0.708
#> GSM751390 5 0.2563 0.7747 0.008 0.000 0.120 0.000 0.872
#> GSM751392 5 0.2795 0.7586 0.000 0.056 0.064 0.000 0.880
#> GSM751396 5 0.5309 0.4458 0.000 0.364 0.060 0.000 0.576
#> GSM751399 3 0.0404 0.8407 0.000 0.000 0.988 0.000 0.012
#> GSM751400 3 0.0324 0.8391 0.004 0.004 0.992 0.000 0.000
#> GSM751401 3 0.0324 0.8392 0.000 0.004 0.992 0.000 0.004
#> GSM751402 3 0.0486 0.8385 0.004 0.004 0.988 0.000 0.004
#> GSM751403 3 0.0324 0.8392 0.000 0.004 0.992 0.000 0.004
#> GSM751405 3 0.1356 0.8262 0.028 0.004 0.956 0.000 0.012
#> GSM751407 3 0.0486 0.8394 0.004 0.004 0.988 0.000 0.004
#> GSM751408 3 0.0324 0.8392 0.000 0.004 0.992 0.000 0.004
#> GSM751409 3 0.0451 0.8408 0.000 0.000 0.988 0.004 0.008
#> GSM751412 3 0.0807 0.8400 0.000 0.000 0.976 0.012 0.012
#> GSM751418 3 0.1195 0.8343 0.000 0.000 0.960 0.012 0.028
#> GSM751419 3 0.0807 0.8400 0.000 0.000 0.976 0.012 0.012
#> GSM751420 3 0.2071 0.8023 0.004 0.004 0.928 0.036 0.028
#> GSM751425 2 0.4249 -0.0758 0.000 0.568 0.000 0.432 0.000
#> GSM751429 4 0.8734 0.2432 0.196 0.124 0.168 0.452 0.060
#> GSM751430 2 0.5126 0.3406 0.028 0.668 0.276 0.000 0.028
#> GSM751433 2 0.5780 0.2743 0.188 0.680 0.048 0.084 0.000
#> GSM751437 4 0.7013 0.3769 0.000 0.324 0.192 0.460 0.024
#> GSM751448 3 0.5625 0.4504 0.004 0.192 0.688 0.092 0.024
#> GSM751451 2 0.1412 0.2936 0.036 0.952 0.004 0.008 0.000
#> GSM751423 2 0.4869 0.3465 0.024 0.696 0.260 0.008 0.012
#> GSM751424 2 0.5092 0.3511 0.004 0.700 0.236 0.020 0.040
#> GSM751428 2 0.5750 0.3408 0.080 0.652 0.244 0.020 0.004
#> GSM751431 2 0.1202 0.2956 0.032 0.960 0.004 0.004 0.000
#> GSM751432 2 0.4991 0.3361 0.028 0.668 0.288 0.004 0.012
#> GSM751434 2 0.4393 0.3430 0.012 0.696 0.284 0.004 0.004
#> GSM751435 4 0.7576 0.1502 0.040 0.356 0.148 0.436 0.020
#> GSM751436 2 0.5762 0.3540 0.068 0.676 0.216 0.032 0.008
#> GSM751440 4 0.7242 0.2869 0.040 0.348 0.036 0.496 0.080
#> GSM751444 2 0.6016 0.2556 0.020 0.684 0.152 0.120 0.024
#> GSM751446 2 0.5605 -0.1679 0.012 0.488 0.004 0.460 0.036
#> GSM751449 2 0.5498 -0.1805 0.000 0.496 0.024 0.456 0.024
#> GSM751450 2 0.4963 0.2923 0.016 0.724 0.216 0.024 0.020
#> GSM751452 2 0.5441 0.3549 0.036 0.700 0.192 0.000 0.072
#> GSM751426 2 0.4286 0.3357 0.112 0.804 0.060 0.004 0.020
#> GSM751427 4 0.7156 0.1914 0.004 0.372 0.116 0.456 0.052
#> GSM751438 2 0.4897 -0.1421 0.000 0.516 0.000 0.460 0.024
#> GSM751439 4 0.7129 0.3820 0.000 0.300 0.212 0.460 0.028
#> GSM751441 2 0.5864 -0.1432 0.000 0.524 0.032 0.404 0.040
#> GSM751442 2 0.4897 -0.1421 0.000 0.516 0.000 0.460 0.024
#> GSM751443 3 0.7398 -0.3353 0.028 0.116 0.420 0.404 0.032
#> GSM751445 2 0.4210 -0.0706 0.000 0.588 0.000 0.412 0.000
#> GSM751447 2 0.4249 -0.0758 0.000 0.568 0.000 0.432 0.000
#> GSM751453 2 0.4242 -0.0738 0.000 0.572 0.000 0.428 0.000
#> GSM751454 2 0.4242 -0.0738 0.000 0.572 0.000 0.428 0.000
#> GSM751455 2 0.4897 -0.1421 0.000 0.516 0.000 0.460 0.024
#> GSM751456 2 0.4897 -0.1421 0.000 0.516 0.000 0.460 0.024
#> GSM751457 2 0.4403 -0.0860 0.000 0.560 0.000 0.436 0.004
#> GSM751458 2 0.4397 -0.0806 0.000 0.564 0.000 0.432 0.004
cbind(get_classes(res, k = 6), get_membership(res, k = 6))
#> class entropy silhouette p1 p2 p3 p4 p5 p6
#> GSM751298 4 0.3189 0.64683 0.236 0.000 0.004 0.760 0.000 0.000
#> GSM751304 1 0.5960 -0.01417 0.500 0.000 0.056 0.052 0.008 0.384
#> GSM751305 6 0.5411 0.63447 0.064 0.000 0.040 0.200 0.020 0.676
#> GSM751307 6 0.4929 0.32119 0.404 0.000 0.036 0.016 0.000 0.544
#> GSM751310 4 0.4310 0.32409 0.440 0.000 0.000 0.540 0.000 0.020
#> GSM751314 4 0.2585 0.61127 0.048 0.000 0.000 0.880 0.004 0.068
#> GSM751316 1 0.5593 0.32196 0.524 0.000 0.000 0.332 0.004 0.140
#> GSM751318 4 0.3104 0.65670 0.204 0.000 0.004 0.788 0.000 0.004
#> GSM751342 4 0.3053 0.56386 0.012 0.000 0.000 0.812 0.004 0.172
#> GSM751346 1 0.1674 0.62013 0.924 0.004 0.004 0.068 0.000 0.000
#> GSM751347 1 0.2491 0.60915 0.868 0.000 0.020 0.112 0.000 0.000
#> GSM751348 5 0.5015 0.66898 0.120 0.092 0.004 0.060 0.724 0.000
#> GSM751349 5 0.1551 0.80822 0.004 0.008 0.004 0.016 0.948 0.020
#> GSM751352 1 0.3575 0.56217 0.824 0.000 0.092 0.000 0.056 0.028
#> GSM751353 5 0.3982 0.69182 0.168 0.000 0.008 0.020 0.776 0.028
#> GSM751354 1 0.3629 0.56015 0.820 0.000 0.112 0.004 0.032 0.032
#> GSM751355 1 0.4875 0.33470 0.656 0.000 0.060 0.004 0.012 0.268
#> GSM751358 4 0.6172 0.32012 0.024 0.000 0.016 0.576 0.208 0.176
#> GSM751359 5 0.6176 0.40988 0.012 0.004 0.004 0.200 0.524 0.256
#> GSM751294 5 0.9301 0.00141 0.172 0.204 0.140 0.212 0.248 0.024
#> GSM751296 1 0.3923 -0.02350 0.580 0.004 0.000 0.416 0.000 0.000
#> GSM751297 1 0.3001 0.58983 0.860 0.008 0.096 0.020 0.000 0.016
#> GSM751299 1 0.4974 0.51922 0.752 0.068 0.000 0.040 0.092 0.048
#> GSM751300 1 0.2260 0.60171 0.860 0.000 0.000 0.140 0.000 0.000
#> GSM751301 4 0.3684 0.54443 0.372 0.000 0.000 0.628 0.000 0.000
#> GSM751302 1 0.0363 0.63431 0.988 0.000 0.000 0.012 0.000 0.000
#> GSM751303 4 0.3053 0.56386 0.012 0.000 0.000 0.812 0.004 0.172
#> GSM751306 4 0.3053 0.56386 0.012 0.000 0.000 0.812 0.004 0.172
#> GSM751308 4 0.3605 0.65040 0.224 0.000 0.008 0.756 0.004 0.008
#> GSM751309 4 0.3053 0.56386 0.012 0.000 0.000 0.812 0.004 0.172
#> GSM751311 4 0.3053 0.56386 0.012 0.000 0.000 0.812 0.004 0.172
#> GSM751312 1 0.5437 0.38035 0.592 0.000 0.000 0.232 0.004 0.172
#> GSM751313 1 0.2191 0.60712 0.876 0.000 0.000 0.120 0.000 0.004
#> GSM751315 1 0.3717 0.27607 0.616 0.000 0.000 0.384 0.000 0.000
#> GSM751317 4 0.3141 0.66013 0.200 0.000 0.000 0.788 0.000 0.012
#> GSM751320 4 0.2994 0.65560 0.208 0.000 0.000 0.788 0.000 0.004
#> GSM751321 4 0.5553 0.21154 0.256 0.000 0.000 0.568 0.004 0.172
#> GSM751322 4 0.2912 0.65276 0.216 0.000 0.000 0.784 0.000 0.000
#> GSM751324 4 0.3074 0.65825 0.200 0.000 0.004 0.792 0.000 0.004
#> GSM751325 4 0.2994 0.65560 0.208 0.000 0.000 0.788 0.000 0.004
#> GSM751332 1 0.3866 -0.02288 0.516 0.000 0.000 0.484 0.000 0.000
#> GSM751334 1 0.3868 -0.06096 0.504 0.000 0.000 0.496 0.000 0.000
#> GSM751339 1 0.4070 0.01396 0.568 0.000 0.004 0.424 0.000 0.004
#> GSM751341 4 0.3144 0.56137 0.016 0.000 0.000 0.808 0.004 0.172
#> GSM751343 4 0.2994 0.65560 0.208 0.000 0.000 0.788 0.000 0.004
#> GSM751344 5 0.5399 0.55466 0.240 0.004 0.008 0.004 0.628 0.116
#> GSM751345 5 0.5934 0.48221 0.240 0.000 0.016 0.008 0.572 0.164
#> GSM751356 1 0.6365 0.13318 0.484 0.000 0.016 0.112 0.356 0.032
#> GSM751357 1 0.6851 0.08968 0.436 0.000 0.016 0.152 0.348 0.048
#> GSM751293 4 0.3804 0.58425 0.336 0.000 0.000 0.656 0.000 0.008
#> GSM751295 1 0.0363 0.63431 0.988 0.000 0.000 0.012 0.000 0.000
#> GSM751319 1 0.5602 0.13976 0.500 0.000 0.000 0.364 0.004 0.132
#> GSM751323 4 0.2941 0.65111 0.220 0.000 0.000 0.780 0.000 0.000
#> GSM751326 1 0.3607 0.35280 0.652 0.000 0.000 0.348 0.000 0.000
#> GSM751327 4 0.3717 0.40786 0.384 0.000 0.000 0.616 0.000 0.000
#> GSM751328 4 0.3645 0.64277 0.236 0.000 0.000 0.740 0.000 0.024
#> GSM751329 1 0.3737 0.25248 0.608 0.000 0.000 0.392 0.000 0.000
#> GSM751330 1 0.1141 0.63201 0.948 0.000 0.000 0.052 0.000 0.000
#> GSM751331 1 0.0363 0.63431 0.988 0.000 0.000 0.012 0.000 0.000
#> GSM751333 1 0.2491 0.58226 0.836 0.000 0.000 0.164 0.000 0.000
#> GSM751335 1 0.2491 0.58351 0.836 0.000 0.000 0.164 0.000 0.000
#> GSM751336 1 0.0363 0.63431 0.988 0.000 0.000 0.012 0.000 0.000
#> GSM751337 4 0.3864 0.56330 0.344 0.000 0.004 0.648 0.000 0.004
#> GSM751338 1 0.3986 -0.07532 0.532 0.000 0.000 0.464 0.000 0.004
#> GSM751340 4 0.6178 0.00865 0.388 0.000 0.180 0.416 0.000 0.016
#> GSM751350 1 0.0603 0.63406 0.980 0.000 0.000 0.016 0.000 0.004
#> GSM751351 1 0.0692 0.63364 0.976 0.000 0.000 0.020 0.000 0.004
#> GSM751362 3 0.4122 0.71411 0.080 0.000 0.780 0.120 0.004 0.016
#> GSM751363 5 0.7539 0.13284 0.204 0.000 0.108 0.244 0.424 0.020
#> GSM751367 1 0.6012 0.24682 0.492 0.000 0.348 0.136 0.000 0.024
#> GSM751368 5 0.5669 0.24407 0.004 0.004 0.104 0.008 0.544 0.336
#> GSM751371 4 0.5288 0.47598 0.156 0.000 0.252 0.592 0.000 0.000
#> GSM751375 5 0.1787 0.78432 0.008 0.004 0.000 0.000 0.920 0.068
#> GSM751376 3 0.4014 0.76702 0.128 0.036 0.800 0.012 0.008 0.016
#> GSM751378 3 0.2006 0.86890 0.008 0.016 0.924 0.004 0.044 0.004
#> GSM751379 3 0.3587 0.81532 0.048 0.012 0.848 0.008 0.036 0.048
#> GSM751382 5 0.0665 0.81536 0.008 0.004 0.000 0.000 0.980 0.008
#> GSM751386 5 0.0363 0.82008 0.000 0.000 0.012 0.000 0.988 0.000
#> GSM751388 5 0.0363 0.82008 0.000 0.000 0.012 0.000 0.988 0.000
#> GSM751391 3 0.2366 0.84926 0.056 0.000 0.900 0.024 0.000 0.020
#> GSM751410 3 0.3150 0.76242 0.104 0.000 0.832 0.064 0.000 0.000
#> GSM751414 5 0.2958 0.72921 0.000 0.000 0.160 0.008 0.824 0.008
#> GSM751361 5 0.0858 0.81881 0.000 0.000 0.028 0.004 0.968 0.000
#> GSM751365 3 0.0779 0.88875 0.000 0.000 0.976 0.008 0.008 0.008
#> GSM751366 3 0.1026 0.88780 0.004 0.000 0.968 0.012 0.008 0.008
#> GSM751369 3 0.4533 0.53685 0.044 0.000 0.684 0.256 0.000 0.016
#> GSM751370 3 0.6316 0.30577 0.260 0.000 0.512 0.020 0.200 0.008
#> GSM751372 5 0.4512 0.41897 0.008 0.000 0.380 0.012 0.592 0.008
#> GSM751373 3 0.1323 0.88475 0.020 0.000 0.956 0.008 0.008 0.008
#> GSM751374 3 0.2639 0.83636 0.084 0.000 0.876 0.008 0.000 0.032
#> GSM751377 5 0.0458 0.82037 0.000 0.000 0.016 0.000 0.984 0.000
#> GSM751380 3 0.0779 0.88875 0.000 0.000 0.976 0.008 0.008 0.008
#> GSM751381 5 0.0363 0.82008 0.000 0.000 0.012 0.000 0.988 0.000
#> GSM751383 5 0.0547 0.81965 0.000 0.000 0.020 0.000 0.980 0.000
#> GSM751384 5 0.0363 0.82008 0.000 0.000 0.012 0.000 0.988 0.000
#> GSM751385 3 0.3566 0.62614 0.000 0.000 0.744 0.000 0.236 0.020
#> GSM751387 5 0.0622 0.81796 0.000 0.000 0.012 0.000 0.980 0.008
#> GSM751389 3 0.0779 0.88875 0.000 0.000 0.976 0.008 0.008 0.008
#> GSM751393 5 0.1923 0.80018 0.004 0.000 0.064 0.000 0.916 0.016
#> GSM751394 5 0.0622 0.81837 0.000 0.000 0.012 0.000 0.980 0.008
#> GSM751395 5 0.3840 0.73425 0.120 0.000 0.076 0.000 0.792 0.012
#> GSM751397 5 0.0363 0.82008 0.000 0.000 0.012 0.000 0.988 0.000
#> GSM751398 5 0.0363 0.82008 0.000 0.000 0.012 0.000 0.988 0.000
#> GSM751404 3 0.0436 0.89107 0.000 0.000 0.988 0.004 0.004 0.004
#> GSM751406 3 0.1109 0.88631 0.004 0.000 0.964 0.012 0.004 0.016
#> GSM751411 3 0.0665 0.89081 0.000 0.000 0.980 0.008 0.004 0.008
#> GSM751413 5 0.4604 0.60704 0.016 0.000 0.220 0.000 0.700 0.064
#> GSM751415 3 0.0665 0.88918 0.000 0.000 0.980 0.008 0.004 0.008
#> GSM751416 5 0.1296 0.81474 0.000 0.000 0.032 0.004 0.952 0.012
#> GSM751417 5 0.1225 0.81587 0.000 0.000 0.036 0.000 0.952 0.012
#> GSM751421 3 0.3964 0.73259 0.120 0.000 0.792 0.068 0.004 0.016
#> GSM751422 4 0.6316 0.28503 0.188 0.000 0.340 0.452 0.012 0.008
#> GSM751360 4 0.5509 0.43098 0.104 0.000 0.296 0.584 0.008 0.008
#> GSM751364 5 0.3678 0.64977 0.000 0.000 0.228 0.016 0.748 0.008
#> GSM751390 5 0.0858 0.82054 0.004 0.000 0.028 0.000 0.968 0.000
#> GSM751392 5 0.0603 0.81483 0.000 0.000 0.004 0.000 0.980 0.016
#> GSM751396 6 0.3995 0.14865 0.000 0.000 0.004 0.000 0.480 0.516
#> GSM751399 3 0.0665 0.89174 0.000 0.000 0.980 0.004 0.008 0.008
#> GSM751400 3 0.0862 0.88805 0.004 0.000 0.972 0.008 0.000 0.016
#> GSM751401 3 0.0603 0.88880 0.000 0.000 0.980 0.004 0.000 0.016
#> GSM751402 3 0.0862 0.88805 0.004 0.000 0.972 0.008 0.000 0.016
#> GSM751403 3 0.0603 0.88880 0.000 0.000 0.980 0.004 0.000 0.016
#> GSM751405 3 0.0964 0.88715 0.004 0.000 0.968 0.012 0.000 0.016
#> GSM751407 3 0.0717 0.88867 0.000 0.000 0.976 0.008 0.000 0.016
#> GSM751408 3 0.0458 0.88916 0.000 0.000 0.984 0.000 0.000 0.016
#> GSM751409 3 0.0436 0.89163 0.000 0.000 0.988 0.004 0.004 0.004
#> GSM751412 3 0.0436 0.89112 0.000 0.000 0.988 0.004 0.004 0.004
#> GSM751418 3 0.1230 0.88080 0.000 0.000 0.956 0.008 0.028 0.008
#> GSM751419 3 0.0779 0.88875 0.000 0.000 0.976 0.008 0.008 0.008
#> GSM751420 3 0.1235 0.88490 0.008 0.008 0.960 0.008 0.000 0.016
#> GSM751425 2 0.1863 0.87531 0.000 0.896 0.000 0.000 0.000 0.104
#> GSM751429 2 0.4750 0.61286 0.180 0.688 0.128 0.004 0.000 0.000
#> GSM751430 6 0.3841 0.75985 0.004 0.008 0.224 0.004 0.012 0.748
#> GSM751433 6 0.4421 0.70005 0.052 0.040 0.004 0.144 0.000 0.760
#> GSM751437 2 0.0363 0.88045 0.000 0.988 0.012 0.000 0.000 0.000
#> GSM751448 3 0.3659 0.62941 0.004 0.268 0.720 0.004 0.000 0.004
#> GSM751451 6 0.3844 0.66572 0.008 0.180 0.004 0.036 0.000 0.772
#> GSM751423 6 0.3874 0.77335 0.028 0.012 0.208 0.000 0.000 0.752
#> GSM751424 6 0.3691 0.78544 0.004 0.032 0.132 0.000 0.024 0.808
#> GSM751428 6 0.3951 0.78500 0.056 0.004 0.168 0.004 0.000 0.768
#> GSM751431 6 0.3786 0.66516 0.008 0.220 0.000 0.024 0.000 0.748
#> GSM751432 6 0.3519 0.75276 0.000 0.008 0.232 0.008 0.000 0.752
#> GSM751434 6 0.3679 0.77483 0.004 0.016 0.208 0.008 0.000 0.764
#> GSM751435 2 0.4675 0.70577 0.044 0.744 0.140 0.004 0.000 0.068
#> GSM751436 6 0.4299 0.78574 0.028 0.004 0.124 0.072 0.000 0.772
#> GSM751440 2 0.1774 0.86677 0.004 0.936 0.004 0.024 0.004 0.028
#> GSM751444 6 0.5884 0.59832 0.028 0.272 0.140 0.000 0.000 0.560
#> GSM751446 2 0.0922 0.87468 0.024 0.968 0.004 0.000 0.000 0.004
#> GSM751449 2 0.1176 0.87445 0.000 0.956 0.024 0.000 0.000 0.020
#> GSM751450 6 0.4593 0.74970 0.008 0.152 0.124 0.000 0.000 0.716
#> GSM751452 6 0.4036 0.78572 0.020 0.032 0.108 0.004 0.028 0.808
#> GSM751426 6 0.5215 0.75428 0.056 0.072 0.040 0.052 0.024 0.756
#> GSM751427 2 0.3399 0.78930 0.004 0.836 0.100 0.000 0.040 0.020
#> GSM751438 2 0.1007 0.88190 0.000 0.956 0.000 0.000 0.000 0.044
#> GSM751439 2 0.0935 0.87264 0.004 0.964 0.032 0.000 0.000 0.000
#> GSM751441 2 0.3259 0.85060 0.004 0.844 0.020 0.000 0.032 0.100
#> GSM751442 2 0.0000 0.88154 0.000 1.000 0.000 0.000 0.000 0.000
#> GSM751443 2 0.4136 0.55229 0.032 0.692 0.272 0.004 0.000 0.000
#> GSM751445 2 0.2219 0.85358 0.000 0.864 0.000 0.000 0.000 0.136
#> GSM751447 2 0.1814 0.87618 0.000 0.900 0.000 0.000 0.000 0.100
#> GSM751453 2 0.2003 0.87043 0.000 0.884 0.000 0.000 0.000 0.116
#> GSM751454 2 0.2003 0.87043 0.000 0.884 0.000 0.000 0.000 0.116
#> GSM751455 2 0.0000 0.88154 0.000 1.000 0.000 0.000 0.000 0.000
#> GSM751456 2 0.0000 0.88154 0.000 1.000 0.000 0.000 0.000 0.000
#> GSM751457 2 0.1765 0.87735 0.000 0.904 0.000 0.000 0.000 0.096
#> GSM751458 2 0.1814 0.87618 0.000 0.900 0.000 0.000 0.000 0.100
Heatmaps for the consensus matrix. It visualizes the probability of two samples to be in a same group.
consensus_heatmap(res, k = 2)
consensus_heatmap(res, k = 3)
consensus_heatmap(res, k = 4)
consensus_heatmap(res, k = 5)
consensus_heatmap(res, k = 6)
Heatmaps for the membership of samples in all partitions to see how consistent they are:
membership_heatmap(res, k = 2)
membership_heatmap(res, k = 3)
membership_heatmap(res, k = 4)
membership_heatmap(res, k = 5)
membership_heatmap(res, k = 6)
As soon as we have had the classes for columns, we can look for signatures which are significantly different between classes which can be candidate marks for certain classes. Following are the heatmaps for signatures.
Signature heatmaps where rows are scaled:
get_signatures(res, k = 2)
get_signatures(res, k = 3)
get_signatures(res, k = 4)
get_signatures(res, k = 5)
get_signatures(res, k = 6)
Signature heatmaps where rows are not scaled:
get_signatures(res, k = 2, scale_rows = FALSE)
get_signatures(res, k = 3, scale_rows = FALSE)
get_signatures(res, k = 4, scale_rows = FALSE)
get_signatures(res, k = 5, scale_rows = FALSE)
get_signatures(res, k = 6, scale_rows = FALSE)
Compare the overlap of signatures from different k:
compare_signatures(res)
get_signature() returns a data frame invisibly. TO get the list of signatures, the function
call should be assigned to a variable explicitly. In following code, if plot argument is set
to FALSE, no heatmap is plotted while only the differential analysis is performed.
# code only for demonstration
tb = get_signature(res, k = ..., plot = FALSE)
An example of the output of tb is:
#> which_row fdr mean_1 mean_2 scaled_mean_1 scaled_mean_2 km
#> 1 38 0.042760348 8.373488 9.131774 -0.5533452 0.5164555 1
#> 2 40 0.018707592 7.106213 8.469186 -0.6173731 0.5762149 1
#> 3 55 0.019134737 10.221463 11.207825 -0.6159697 0.5749050 1
#> 4 59 0.006059896 5.921854 7.869574 -0.6899429 0.6439467 1
#> 5 60 0.018055526 8.928898 10.211722 -0.6204761 0.5791110 1
#> 6 98 0.009384629 15.714769 14.887706 0.6635654 -0.6193277 2
...
The columns in tb are:
which_row: row indices corresponding to the input matrix.fdr: FDR for the differential test. mean_x: The mean value in group x.scaled_mean_x: The mean value in group x after rows are scaled.km: Row groups if k-means clustering is applied to rows.UMAP plot which shows how samples are separated.
dimension_reduction(res, k = 2, method = "UMAP")
dimension_reduction(res, k = 3, method = "UMAP")
dimension_reduction(res, k = 4, method = "UMAP")
dimension_reduction(res, k = 5, method = "UMAP")
dimension_reduction(res, k = 6, method = "UMAP")
Following heatmap shows how subgroups are split when increasing k:
collect_classes(res)
Test correlation between subgroups and known annotations. If the known annotation is numeric, one-way ANOVA test is applied, and if the known annotation is discrete, chi-squared contingency table test is applied.
test_to_known_factors(res)
#> n tissue(p) disease.state(p) agent(p) k
#> CV:pam 133 1.94e-19 1.000 0.95160 2
#> CV:pam 125 7.45e-49 0.760 0.29176 3
#> CV:pam 132 9.92e-48 0.428 0.09062 4
#> CV:pam 109 5.37e-19 0.202 0.09600 5
#> CV:pam 133 8.10e-45 0.826 0.00284 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 4537 rows and 166 columns.
#> Top rows (454, 908, 1361, 1814, 2268) 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 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 0.506 0.819 0.867 0.4252 0.608 0.608
#> 3 3 0.462 0.801 0.864 0.5025 0.722 0.544
#> 4 4 0.508 0.630 0.756 0.1043 0.941 0.827
#> 5 5 0.640 0.680 0.795 0.0704 0.915 0.726
#> 6 6 0.696 0.628 0.794 0.0794 0.895 0.591
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
#> GSM751298 1 0.2948 0.969 0.948 0.052
#> GSM751304 2 0.9460 0.715 0.364 0.636
#> GSM751305 2 0.9460 0.715 0.364 0.636
#> GSM751307 2 0.9460 0.715 0.364 0.636
#> GSM751310 1 0.0000 0.955 1.000 0.000
#> GSM751314 1 0.0000 0.955 1.000 0.000
#> GSM751316 1 0.0000 0.955 1.000 0.000
#> GSM751318 1 0.2603 0.970 0.956 0.044
#> GSM751342 1 0.0376 0.954 0.996 0.004
#> GSM751346 1 0.2948 0.968 0.948 0.052
#> GSM751347 2 0.6343 0.790 0.160 0.840
#> GSM751348 2 0.9460 0.713 0.364 0.636
#> GSM751349 2 0.6973 0.787 0.188 0.812
#> GSM751352 2 0.9323 0.730 0.348 0.652
#> GSM751353 2 0.7453 0.780 0.212 0.788
#> GSM751354 2 0.9323 0.731 0.348 0.652
#> GSM751355 2 0.6973 0.785 0.188 0.812
#> GSM751358 2 0.9686 0.671 0.396 0.604
#> GSM751359 2 0.7528 0.782 0.216 0.784
#> GSM751294 2 0.9087 0.739 0.324 0.676
#> GSM751296 1 0.3274 0.965 0.940 0.060
#> GSM751297 2 0.9460 0.664 0.364 0.636
#> GSM751299 2 0.9323 0.730 0.348 0.652
#> GSM751300 1 0.3274 0.965 0.940 0.060
#> GSM751301 2 0.9661 0.671 0.392 0.608
#> GSM751302 1 0.2423 0.967 0.960 0.040
#> GSM751303 1 0.0000 0.955 1.000 0.000
#> GSM751306 1 0.0000 0.955 1.000 0.000
#> GSM751308 2 0.9635 0.665 0.388 0.612
#> GSM751309 1 0.0000 0.955 1.000 0.000
#> GSM751311 1 0.0000 0.955 1.000 0.000
#> GSM751312 1 0.0000 0.955 1.000 0.000
#> GSM751313 1 0.3274 0.962 0.940 0.060
#> GSM751315 1 0.0376 0.957 0.996 0.004
#> GSM751317 1 0.0000 0.955 1.000 0.000
#> GSM751320 1 0.2948 0.969 0.948 0.052
#> GSM751321 1 0.0000 0.955 1.000 0.000
#> GSM751322 1 0.2236 0.969 0.964 0.036
#> GSM751324 1 0.2236 0.969 0.964 0.036
#> GSM751325 1 0.2948 0.969 0.948 0.052
#> GSM751332 1 0.2948 0.969 0.948 0.052
#> GSM751334 1 0.2948 0.969 0.948 0.052
#> GSM751339 1 0.2948 0.969 0.948 0.052
#> GSM751341 1 0.0000 0.955 1.000 0.000
#> GSM751343 1 0.2948 0.969 0.948 0.052
#> GSM751344 2 0.9286 0.733 0.344 0.656
#> GSM751345 2 0.9286 0.733 0.344 0.656
#> GSM751356 2 0.9522 0.705 0.372 0.628
#> GSM751357 2 0.9522 0.705 0.372 0.628
#> GSM751293 2 0.9993 0.477 0.484 0.516
#> GSM751295 1 0.2236 0.966 0.964 0.036
#> GSM751319 1 0.0000 0.955 1.000 0.000
#> GSM751323 1 0.2948 0.969 0.948 0.052
#> GSM751326 1 0.2948 0.969 0.948 0.052
#> GSM751327 1 0.2236 0.969 0.964 0.036
#> GSM751328 1 0.0000 0.955 1.000 0.000
#> GSM751329 1 0.2948 0.969 0.948 0.052
#> GSM751330 1 0.3114 0.966 0.944 0.056
#> GSM751331 1 0.3584 0.959 0.932 0.068
#> GSM751333 1 0.3274 0.963 0.940 0.060
#> GSM751335 1 0.2948 0.969 0.948 0.052
#> GSM751336 1 0.3114 0.966 0.944 0.056
#> GSM751337 1 0.2948 0.969 0.948 0.052
#> GSM751338 1 0.2948 0.969 0.948 0.052
#> GSM751340 2 0.9661 0.614 0.392 0.608
#> GSM751350 1 0.3584 0.958 0.932 0.068
#> GSM751351 1 0.3431 0.962 0.936 0.064
#> GSM751362 2 0.0000 0.808 0.000 1.000
#> GSM751363 2 0.4022 0.804 0.080 0.920
#> GSM751367 2 0.4690 0.802 0.100 0.900
#> GSM751368 2 0.0376 0.809 0.004 0.996
#> GSM751371 2 0.0000 0.808 0.000 1.000
#> GSM751375 2 0.1414 0.809 0.020 0.980
#> GSM751376 2 0.5408 0.798 0.124 0.876
#> GSM751378 2 0.0376 0.809 0.004 0.996
#> GSM751379 2 0.4690 0.802 0.100 0.900
#> GSM751382 2 0.0938 0.809 0.012 0.988
#> GSM751386 2 0.0376 0.809 0.004 0.996
#> GSM751388 2 0.0376 0.809 0.004 0.996
#> GSM751391 2 0.1184 0.809 0.016 0.984
#> GSM751410 2 0.0376 0.809 0.004 0.996
#> GSM751414 2 0.0000 0.808 0.000 1.000
#> GSM751361 2 0.0000 0.808 0.000 1.000
#> GSM751365 2 0.0000 0.808 0.000 1.000
#> GSM751366 2 0.0000 0.808 0.000 1.000
#> GSM751369 2 0.0000 0.808 0.000 1.000
#> GSM751370 2 0.0000 0.808 0.000 1.000
#> GSM751372 2 0.0000 0.808 0.000 1.000
#> GSM751373 2 0.0000 0.808 0.000 1.000
#> GSM751374 2 0.5408 0.798 0.124 0.876
#> GSM751377 2 0.0000 0.808 0.000 1.000
#> GSM751380 2 0.0000 0.808 0.000 1.000
#> GSM751381 2 0.0376 0.809 0.004 0.996
#> GSM751383 2 0.0376 0.809 0.004 0.996
#> GSM751384 2 0.0000 0.808 0.000 1.000
#> GSM751385 2 0.0376 0.809 0.004 0.996
#> GSM751387 2 0.0376 0.809 0.004 0.996
#> GSM751389 2 0.0000 0.808 0.000 1.000
#> GSM751393 2 0.0376 0.809 0.004 0.996
#> GSM751394 2 0.0376 0.809 0.004 0.996
#> GSM751395 2 0.1633 0.809 0.024 0.976
#> GSM751397 2 0.0376 0.809 0.004 0.996
#> GSM751398 2 0.0376 0.809 0.004 0.996
#> GSM751404 2 0.0000 0.808 0.000 1.000
#> GSM751406 2 0.0000 0.808 0.000 1.000
#> GSM751411 2 0.0000 0.808 0.000 1.000
#> GSM751413 2 0.3584 0.806 0.068 0.932
#> GSM751415 2 0.0000 0.808 0.000 1.000
#> GSM751416 2 0.0000 0.808 0.000 1.000
#> GSM751417 2 0.0000 0.808 0.000 1.000
#> GSM751421 2 0.0000 0.808 0.000 1.000
#> GSM751422 2 0.0000 0.808 0.000 1.000
#> GSM751360 2 0.0000 0.808 0.000 1.000
#> GSM751364 2 0.0000 0.808 0.000 1.000
#> GSM751390 2 0.0376 0.809 0.004 0.996
#> GSM751392 2 0.0376 0.809 0.004 0.996
#> GSM751396 2 0.0376 0.809 0.004 0.996
#> GSM751399 2 0.0000 0.808 0.000 1.000
#> GSM751400 2 0.0000 0.808 0.000 1.000
#> GSM751401 2 0.0000 0.808 0.000 1.000
#> GSM751402 2 0.0000 0.808 0.000 1.000
#> GSM751403 2 0.0000 0.808 0.000 1.000
#> GSM751405 2 0.0000 0.808 0.000 1.000
#> GSM751407 2 0.0000 0.808 0.000 1.000
#> GSM751408 2 0.0000 0.808 0.000 1.000
#> GSM751409 2 0.0000 0.808 0.000 1.000
#> GSM751412 2 0.0000 0.808 0.000 1.000
#> GSM751418 2 0.0000 0.808 0.000 1.000
#> GSM751419 2 0.0000 0.808 0.000 1.000
#> GSM751420 2 0.3879 0.805 0.076 0.924
#> GSM751425 2 0.9323 0.731 0.348 0.652
#> GSM751429 2 0.9087 0.745 0.324 0.676
#> GSM751430 2 0.6712 0.786 0.176 0.824
#> GSM751433 2 0.9491 0.710 0.368 0.632
#> GSM751437 2 0.9129 0.743 0.328 0.672
#> GSM751448 2 0.8955 0.749 0.312 0.688
#> GSM751451 2 0.9248 0.736 0.340 0.660
#> GSM751423 2 0.8909 0.752 0.308 0.692
#> GSM751424 2 0.9323 0.731 0.348 0.652
#> GSM751428 2 0.9358 0.728 0.352 0.648
#> GSM751431 2 0.9323 0.731 0.348 0.652
#> GSM751432 2 0.8909 0.751 0.308 0.692
#> GSM751434 2 0.9358 0.728 0.352 0.648
#> GSM751435 2 0.9358 0.728 0.352 0.648
#> GSM751436 2 0.9393 0.724 0.356 0.644
#> GSM751440 2 0.9358 0.728 0.352 0.648
#> GSM751444 2 0.9323 0.731 0.348 0.652
#> GSM751446 2 0.9323 0.731 0.348 0.652
#> GSM751449 2 0.9358 0.728 0.352 0.648
#> GSM751450 2 0.9323 0.731 0.348 0.652
#> GSM751452 2 0.9323 0.731 0.348 0.652
#> GSM751426 2 0.9358 0.728 0.352 0.648
#> GSM751427 2 0.9209 0.739 0.336 0.664
#> GSM751438 2 0.9358 0.728 0.352 0.648
#> GSM751439 2 0.9323 0.731 0.348 0.652
#> GSM751441 2 0.8499 0.764 0.276 0.724
#> GSM751442 2 0.9323 0.731 0.348 0.652
#> GSM751443 2 0.9358 0.728 0.352 0.648
#> GSM751445 2 0.9358 0.728 0.352 0.648
#> GSM751447 2 0.9358 0.728 0.352 0.648
#> GSM751453 2 0.9358 0.728 0.352 0.648
#> GSM751454 2 0.9358 0.728 0.352 0.648
#> GSM751455 2 0.9323 0.731 0.348 0.652
#> GSM751456 2 0.9323 0.731 0.348 0.652
#> GSM751457 2 0.9358 0.728 0.352 0.648
#> GSM751458 2 0.9358 0.728 0.352 0.648
cbind(get_classes(res, k = 3), get_membership(res, k = 3))
#> class entropy silhouette p1 p2 p3
#> GSM751298 1 0.4280 0.8681 0.856 0.124 0.020
#> GSM751304 2 0.2031 0.8532 0.032 0.952 0.016
#> GSM751305 2 0.2414 0.8545 0.020 0.940 0.040
#> GSM751307 2 0.1919 0.8538 0.024 0.956 0.020
#> GSM751310 1 0.4504 0.8235 0.804 0.196 0.000
#> GSM751314 1 0.4452 0.8262 0.808 0.192 0.000
#> GSM751316 1 0.4555 0.8204 0.800 0.200 0.000
#> GSM751318 1 0.2959 0.8708 0.900 0.100 0.000
#> GSM751342 1 0.4750 0.8047 0.784 0.216 0.000
#> GSM751346 1 0.4489 0.8464 0.856 0.108 0.036
#> GSM751347 2 0.7279 0.5649 0.056 0.652 0.292
#> GSM751348 2 0.2384 0.8562 0.008 0.936 0.056
#> GSM751349 2 0.5291 0.6399 0.000 0.732 0.268
#> GSM751352 2 0.2031 0.8590 0.016 0.952 0.032
#> GSM751353 2 0.2096 0.8559 0.004 0.944 0.052
#> GSM751354 2 0.2116 0.8615 0.012 0.948 0.040
#> GSM751355 2 0.2945 0.8363 0.004 0.908 0.088
#> GSM751358 2 0.7801 0.4968 0.076 0.616 0.308
#> GSM751359 3 0.6683 0.0857 0.008 0.496 0.496
#> GSM751294 2 0.2955 0.8473 0.008 0.912 0.080
#> GSM751296 1 0.3973 0.8638 0.880 0.088 0.032
#> GSM751297 2 0.7764 0.4062 0.328 0.604 0.068
#> GSM751299 2 0.2443 0.8581 0.028 0.940 0.032
#> GSM751300 1 0.4335 0.8472 0.864 0.100 0.036
#> GSM751301 2 0.4799 0.7685 0.132 0.836 0.032
#> GSM751302 1 0.4489 0.8464 0.856 0.108 0.036
#> GSM751303 1 0.4555 0.8204 0.800 0.200 0.000
#> GSM751306 1 0.4555 0.8204 0.800 0.200 0.000
#> GSM751308 2 0.7124 0.5205 0.272 0.672 0.056
#> GSM751309 1 0.4555 0.8204 0.800 0.200 0.000
#> GSM751311 1 0.4654 0.8141 0.792 0.208 0.000
#> GSM751312 1 0.4605 0.8181 0.796 0.204 0.000
#> GSM751313 1 0.2569 0.8801 0.936 0.032 0.032
#> GSM751315 1 0.2356 0.8767 0.928 0.072 0.000
#> GSM751317 1 0.4504 0.8235 0.804 0.196 0.000
#> GSM751320 1 0.0475 0.8756 0.992 0.004 0.004
#> GSM751321 1 0.4555 0.8204 0.800 0.200 0.000
#> GSM751322 1 0.0424 0.8761 0.992 0.008 0.000
#> GSM751324 1 0.0592 0.8771 0.988 0.012 0.000
#> GSM751325 1 0.0424 0.8761 0.992 0.008 0.000
#> GSM751332 1 0.0661 0.8764 0.988 0.004 0.008
#> GSM751334 1 0.0424 0.8744 0.992 0.000 0.008
#> GSM751339 1 0.2187 0.8770 0.948 0.028 0.024
#> GSM751341 1 0.5551 0.8149 0.768 0.212 0.020
#> GSM751343 1 0.1315 0.8766 0.972 0.008 0.020
#> GSM751344 2 0.2187 0.8564 0.028 0.948 0.024
#> GSM751345 2 0.2187 0.8564 0.028 0.948 0.024
#> GSM751356 2 0.2681 0.8522 0.040 0.932 0.028
#> GSM751357 2 0.2550 0.8524 0.040 0.936 0.024
#> GSM751293 2 0.5461 0.6436 0.216 0.768 0.016
#> GSM751295 1 0.4563 0.8424 0.852 0.112 0.036
#> GSM751319 1 0.4555 0.8204 0.800 0.200 0.000
#> GSM751323 1 0.0475 0.8756 0.992 0.004 0.004
#> GSM751326 1 0.1585 0.8756 0.964 0.008 0.028
#> GSM751327 1 0.0237 0.8748 0.996 0.004 0.000
#> GSM751328 1 0.4062 0.8438 0.836 0.164 0.000
#> GSM751329 1 0.0475 0.8756 0.992 0.004 0.004
#> GSM751330 1 0.1585 0.8756 0.964 0.008 0.028
#> GSM751331 1 0.5659 0.8173 0.796 0.152 0.052
#> GSM751333 1 0.1711 0.8755 0.960 0.008 0.032
#> GSM751335 1 0.1585 0.8756 0.964 0.008 0.028
#> GSM751336 1 0.3406 0.8663 0.904 0.068 0.028
#> GSM751337 1 0.2056 0.8772 0.952 0.024 0.024
#> GSM751338 1 0.1919 0.8771 0.956 0.020 0.024
#> GSM751340 1 0.8350 0.3069 0.532 0.380 0.088
#> GSM751350 1 0.5047 0.8311 0.824 0.140 0.036
#> GSM751351 1 0.4915 0.8346 0.832 0.132 0.036
#> GSM751362 3 0.3267 0.8698 0.000 0.116 0.884
#> GSM751363 3 0.5706 0.6421 0.000 0.320 0.680
#> GSM751367 2 0.7546 0.3206 0.044 0.560 0.396
#> GSM751368 3 0.4346 0.8369 0.000 0.184 0.816
#> GSM751371 3 0.3619 0.8631 0.000 0.136 0.864
#> GSM751375 2 0.6305 -0.1819 0.000 0.516 0.484
#> GSM751376 2 0.5216 0.6377 0.000 0.740 0.260
#> GSM751378 3 0.4931 0.8264 0.000 0.232 0.768
#> GSM751379 2 0.5431 0.5925 0.000 0.716 0.284
#> GSM751382 3 0.5178 0.7737 0.000 0.256 0.744
#> GSM751386 3 0.4062 0.8370 0.000 0.164 0.836
#> GSM751388 3 0.4062 0.8370 0.000 0.164 0.836
#> GSM751391 3 0.5988 0.5259 0.000 0.368 0.632
#> GSM751410 3 0.3267 0.8708 0.000 0.116 0.884
#> GSM751414 3 0.1289 0.8619 0.000 0.032 0.968
#> GSM751361 3 0.3192 0.8626 0.000 0.112 0.888
#> GSM751365 3 0.1411 0.8623 0.000 0.036 0.964
#> GSM751366 3 0.2959 0.8718 0.000 0.100 0.900
#> GSM751369 3 0.5070 0.7642 0.004 0.224 0.772
#> GSM751370 3 0.1529 0.8655 0.000 0.040 0.960
#> GSM751372 3 0.1411 0.8638 0.000 0.036 0.964
#> GSM751373 3 0.1643 0.8659 0.000 0.044 0.956
#> GSM751374 2 0.5058 0.6716 0.000 0.756 0.244
#> GSM751377 3 0.3816 0.8448 0.000 0.148 0.852
#> GSM751380 3 0.3267 0.8698 0.000 0.116 0.884
#> GSM751381 3 0.4062 0.8370 0.000 0.164 0.836
#> GSM751383 3 0.4062 0.8370 0.000 0.164 0.836
#> GSM751384 3 0.3482 0.8652 0.000 0.128 0.872
#> GSM751385 3 0.5098 0.8106 0.000 0.248 0.752
#> GSM751387 3 0.4062 0.8370 0.000 0.164 0.836
#> GSM751389 3 0.4605 0.8257 0.000 0.204 0.796
#> GSM751393 3 0.4931 0.8249 0.000 0.232 0.768
#> GSM751394 3 0.4062 0.8370 0.000 0.164 0.836
#> GSM751395 2 0.6280 -0.0457 0.000 0.540 0.460
#> GSM751397 3 0.4062 0.8370 0.000 0.164 0.836
#> GSM751398 3 0.4062 0.8370 0.000 0.164 0.836
#> GSM751404 3 0.3412 0.8677 0.000 0.124 0.876
#> GSM751406 3 0.3412 0.8677 0.000 0.124 0.876
#> GSM751411 3 0.1860 0.8687 0.000 0.052 0.948
#> GSM751413 3 0.6126 0.4894 0.000 0.400 0.600
#> GSM751415 3 0.3412 0.8677 0.000 0.124 0.876
#> GSM751416 3 0.3551 0.8531 0.000 0.132 0.868
#> GSM751417 3 0.3482 0.8515 0.000 0.128 0.872
#> GSM751421 3 0.3340 0.8690 0.000 0.120 0.880
#> GSM751422 3 0.3038 0.8723 0.000 0.104 0.896
#> GSM751360 3 0.1964 0.8691 0.000 0.056 0.944
#> GSM751364 3 0.2066 0.8633 0.000 0.060 0.940
#> GSM751390 3 0.3192 0.8669 0.000 0.112 0.888
#> GSM751392 3 0.4062 0.8370 0.000 0.164 0.836
#> GSM751396 3 0.4346 0.8312 0.000 0.184 0.816
#> GSM751399 3 0.3116 0.8721 0.000 0.108 0.892
#> GSM751400 3 0.3752 0.8599 0.000 0.144 0.856
#> GSM751401 3 0.3412 0.8677 0.000 0.124 0.876
#> GSM751402 3 0.3412 0.8677 0.000 0.124 0.876
#> GSM751403 3 0.3412 0.8677 0.000 0.124 0.876
#> GSM751405 3 0.3412 0.8677 0.000 0.124 0.876
#> GSM751407 3 0.3412 0.8677 0.000 0.124 0.876
#> GSM751408 3 0.3340 0.8691 0.000 0.120 0.880
#> GSM751409 3 0.3941 0.8621 0.000 0.156 0.844
#> GSM751412 3 0.3192 0.8714 0.000 0.112 0.888
#> GSM751418 3 0.1411 0.8614 0.000 0.036 0.964
#> GSM751419 3 0.1289 0.8619 0.000 0.032 0.968
#> GSM751420 2 0.5785 0.5088 0.000 0.668 0.332
#> GSM751425 2 0.2356 0.8542 0.000 0.928 0.072
#> GSM751429 2 0.6168 0.7684 0.096 0.780 0.124
#> GSM751430 2 0.3686 0.7885 0.000 0.860 0.140
#> GSM751433 2 0.2682 0.8343 0.004 0.920 0.076
#> GSM751437 2 0.5733 0.5419 0.000 0.676 0.324
#> GSM751448 2 0.7273 0.7053 0.156 0.712 0.132
#> GSM751451 2 0.4842 0.6910 0.000 0.776 0.224
#> GSM751423 2 0.4605 0.7420 0.000 0.796 0.204
#> GSM751424 2 0.2066 0.8403 0.000 0.940 0.060
#> GSM751428 2 0.1411 0.8598 0.000 0.964 0.036
#> GSM751431 2 0.2165 0.8399 0.000 0.936 0.064
#> GSM751432 2 0.1163 0.8561 0.000 0.972 0.028
#> GSM751434 2 0.0747 0.8538 0.000 0.984 0.016
#> GSM751435 2 0.1989 0.8612 0.004 0.948 0.048
#> GSM751436 2 0.2261 0.8367 0.000 0.932 0.068
#> GSM751440 2 0.4062 0.8017 0.000 0.836 0.164
#> GSM751444 2 0.1525 0.8592 0.004 0.964 0.032
#> GSM751446 2 0.1765 0.8592 0.004 0.956 0.040
#> GSM751449 2 0.1411 0.8587 0.000 0.964 0.036
#> GSM751450 2 0.1163 0.8541 0.000 0.972 0.028
#> GSM751452 2 0.1989 0.8435 0.004 0.948 0.048
#> GSM751426 2 0.2066 0.8403 0.000 0.940 0.060
#> GSM751427 2 0.3038 0.8390 0.000 0.896 0.104
#> GSM751438 2 0.1753 0.8570 0.000 0.952 0.048
#> GSM751439 2 0.3587 0.8344 0.020 0.892 0.088
#> GSM751441 2 0.1989 0.8593 0.004 0.948 0.048
#> GSM751442 2 0.1643 0.8580 0.000 0.956 0.044
#> GSM751443 2 0.3359 0.8376 0.016 0.900 0.084
#> GSM751445 2 0.1411 0.8587 0.000 0.964 0.036
#> GSM751447 2 0.1411 0.8587 0.000 0.964 0.036
#> GSM751453 2 0.1289 0.8590 0.000 0.968 0.032
#> GSM751454 2 0.1289 0.8590 0.000 0.968 0.032
#> GSM751455 2 0.1643 0.8580 0.000 0.956 0.044
#> GSM751456 2 0.1643 0.8580 0.000 0.956 0.044
#> GSM751457 2 0.1753 0.8570 0.000 0.952 0.048
#> GSM751458 2 0.1753 0.8570 0.000 0.952 0.048
cbind(get_classes(res, k = 4), get_membership(res, k = 4))
#> class entropy silhouette p1 p2 p3 p4
#> GSM751298 1 0.4931 0.8021 0.792 0.028 0.036 0.144
#> GSM751304 2 0.5085 0.5864 0.008 0.616 0.000 0.376
#> GSM751305 2 0.5050 0.5518 0.000 0.588 0.004 0.408
#> GSM751307 2 0.5159 0.5937 0.012 0.624 0.000 0.364
#> GSM751310 1 0.4630 0.7545 0.732 0.016 0.000 0.252
#> GSM751314 1 0.4567 0.7576 0.740 0.016 0.000 0.244
#> GSM751316 1 0.4748 0.7466 0.716 0.016 0.000 0.268
#> GSM751318 1 0.2593 0.8084 0.904 0.016 0.000 0.080
#> GSM751342 1 0.5141 0.7355 0.700 0.032 0.000 0.268
#> GSM751346 1 0.6960 0.6955 0.664 0.096 0.052 0.188
#> GSM751347 2 0.6641 0.3961 0.020 0.596 0.324 0.060
#> GSM751348 2 0.5924 0.6924 0.020 0.692 0.048 0.240
#> GSM751349 2 0.6373 0.4657 0.004 0.576 0.064 0.356
#> GSM751352 2 0.5007 0.7056 0.012 0.752 0.028 0.208
#> GSM751353 2 0.4425 0.6925 0.004 0.800 0.036 0.160
#> GSM751354 2 0.5040 0.7148 0.008 0.764 0.048 0.180
#> GSM751355 2 0.4595 0.6749 0.000 0.780 0.044 0.176
#> GSM751358 2 0.8346 0.1965 0.016 0.380 0.304 0.300
#> GSM751359 4 0.7034 0.1637 0.004 0.364 0.112 0.520
#> GSM751294 2 0.3997 0.7005 0.012 0.840 0.120 0.028
#> GSM751296 1 0.5245 0.7785 0.776 0.032 0.044 0.148
#> GSM751297 2 0.8786 0.1933 0.336 0.440 0.108 0.116
#> GSM751299 2 0.5200 0.7096 0.012 0.748 0.040 0.200
#> GSM751300 1 0.6828 0.7010 0.672 0.092 0.048 0.188
#> GSM751301 2 0.5867 0.6297 0.060 0.668 0.004 0.268
#> GSM751302 1 0.6960 0.6955 0.664 0.096 0.052 0.188
#> GSM751303 1 0.4748 0.7466 0.716 0.016 0.000 0.268
#> GSM751306 1 0.4748 0.7466 0.716 0.016 0.000 0.268
#> GSM751308 2 0.8731 0.3010 0.300 0.472 0.108 0.120
#> GSM751309 1 0.4748 0.7466 0.716 0.016 0.000 0.268
#> GSM751311 1 0.4882 0.7414 0.708 0.020 0.000 0.272
#> GSM751312 1 0.5402 0.7539 0.652 0.016 0.008 0.324
#> GSM751313 1 0.4181 0.7942 0.820 0.000 0.052 0.128
#> GSM751315 1 0.3401 0.7945 0.840 0.008 0.000 0.152
#> GSM751317 1 0.4630 0.7545 0.732 0.016 0.000 0.252
#> GSM751320 1 0.0000 0.8150 1.000 0.000 0.000 0.000
#> GSM751321 1 0.4720 0.7487 0.720 0.016 0.000 0.264
#> GSM751322 1 0.1576 0.8120 0.948 0.004 0.000 0.048
#> GSM751324 1 0.1661 0.8115 0.944 0.004 0.000 0.052
#> GSM751325 1 0.1109 0.8144 0.968 0.004 0.000 0.028
#> GSM751332 1 0.0000 0.8150 1.000 0.000 0.000 0.000
#> GSM751334 1 0.0000 0.8150 1.000 0.000 0.000 0.000
#> GSM751339 1 0.4219 0.7924 0.820 0.004 0.040 0.136
#> GSM751341 1 0.6635 0.7456 0.564 0.028 0.040 0.368
#> GSM751343 1 0.1004 0.8161 0.972 0.004 0.000 0.024
#> GSM751344 2 0.4606 0.6729 0.012 0.724 0.000 0.264
#> GSM751345 2 0.4635 0.6705 0.012 0.720 0.000 0.268
#> GSM751356 2 0.6346 0.6177 0.012 0.600 0.052 0.336
#> GSM751357 2 0.6060 0.6184 0.012 0.612 0.036 0.340
#> GSM751293 2 0.7344 0.5569 0.120 0.576 0.024 0.280
#> GSM751295 1 0.7015 0.6910 0.660 0.100 0.052 0.188
#> GSM751319 1 0.4748 0.7466 0.716 0.016 0.000 0.268
#> GSM751323 1 0.0000 0.8150 1.000 0.000 0.000 0.000
#> GSM751326 1 0.2799 0.8074 0.884 0.000 0.008 0.108
#> GSM751327 1 0.1118 0.8136 0.964 0.000 0.000 0.036
#> GSM751328 1 0.4175 0.7722 0.776 0.012 0.000 0.212
#> GSM751329 1 0.0188 0.8151 0.996 0.000 0.000 0.004
#> GSM751330 1 0.3231 0.8058 0.868 0.004 0.012 0.116
#> GSM751331 1 0.7403 0.6818 0.620 0.104 0.056 0.220
#> GSM751333 1 0.3813 0.8023 0.828 0.000 0.024 0.148
#> GSM751335 1 0.3216 0.8045 0.864 0.004 0.008 0.124
#> GSM751336 1 0.5686 0.7595 0.748 0.048 0.040 0.164
#> GSM751337 1 0.4219 0.7924 0.820 0.004 0.040 0.136
#> GSM751338 1 0.4167 0.7935 0.824 0.004 0.040 0.132
#> GSM751340 1 0.8819 0.3484 0.492 0.252 0.128 0.128
#> GSM751350 1 0.7173 0.6840 0.644 0.104 0.052 0.200
#> GSM751351 1 0.7086 0.6899 0.652 0.100 0.052 0.196
#> GSM751362 3 0.1520 0.7493 0.000 0.020 0.956 0.024
#> GSM751363 3 0.7595 -0.3567 0.000 0.372 0.428 0.200
#> GSM751367 3 0.7594 -0.1785 0.032 0.436 0.440 0.092
#> GSM751368 4 0.7830 0.7241 0.000 0.272 0.324 0.404
#> GSM751371 3 0.1576 0.7353 0.000 0.048 0.948 0.004
#> GSM751375 2 0.7489 -0.1461 0.000 0.492 0.212 0.296
#> GSM751376 2 0.5636 0.5612 0.004 0.724 0.184 0.088
#> GSM751378 3 0.7453 -0.5179 0.000 0.192 0.484 0.324
#> GSM751379 2 0.5609 0.5358 0.000 0.712 0.200 0.088
#> GSM751382 4 0.7726 0.7580 0.000 0.260 0.296 0.444
#> GSM751386 4 0.7169 0.8870 0.000 0.152 0.332 0.516
#> GSM751388 4 0.7181 0.8886 0.000 0.152 0.336 0.512
#> GSM751391 3 0.6957 -0.1677 0.000 0.416 0.472 0.112
#> GSM751410 3 0.0927 0.7524 0.000 0.016 0.976 0.008
#> GSM751414 3 0.1042 0.7456 0.000 0.008 0.972 0.020
#> GSM751361 3 0.6110 0.1894 0.000 0.100 0.660 0.240
#> GSM751365 3 0.2542 0.6986 0.000 0.012 0.904 0.084
#> GSM751366 3 0.0779 0.7514 0.000 0.016 0.980 0.004
#> GSM751369 3 0.3695 0.5815 0.000 0.156 0.828 0.016
#> GSM751370 3 0.0927 0.7451 0.000 0.008 0.976 0.016
#> GSM751372 3 0.2021 0.7238 0.000 0.012 0.932 0.056
#> GSM751373 3 0.0927 0.7451 0.000 0.008 0.976 0.016
#> GSM751374 2 0.5532 0.5928 0.004 0.736 0.168 0.092
#> GSM751377 4 0.7021 0.7437 0.000 0.120 0.400 0.480
#> GSM751380 3 0.0592 0.7525 0.000 0.016 0.984 0.000
#> GSM751381 4 0.7181 0.8886 0.000 0.152 0.336 0.512
#> GSM751383 4 0.7181 0.8886 0.000 0.152 0.336 0.512
#> GSM751384 3 0.6194 0.1194 0.000 0.096 0.644 0.260
#> GSM751385 3 0.7866 -0.6149 0.000 0.280 0.384 0.336
#> GSM751387 4 0.7181 0.8886 0.000 0.152 0.336 0.512
#> GSM751389 3 0.4898 0.4954 0.000 0.156 0.772 0.072
#> GSM751393 3 0.7387 -0.3515 0.000 0.224 0.520 0.256
#> GSM751394 4 0.7181 0.8886 0.000 0.152 0.336 0.512
#> GSM751395 2 0.7325 0.2333 0.000 0.532 0.232 0.236
#> GSM751397 4 0.7193 0.8833 0.000 0.152 0.340 0.508
#> GSM751398 4 0.7193 0.8840 0.000 0.152 0.340 0.508
#> GSM751404 3 0.0817 0.7541 0.000 0.024 0.976 0.000
#> GSM751406 3 0.0921 0.7540 0.000 0.028 0.972 0.000
#> GSM751411 3 0.2032 0.7360 0.000 0.028 0.936 0.036
#> GSM751413 2 0.7359 0.0869 0.000 0.508 0.188 0.304
#> GSM751415 3 0.0817 0.7541 0.000 0.024 0.976 0.000
#> GSM751416 3 0.6536 -0.1539 0.000 0.096 0.580 0.324
#> GSM751417 3 0.6536 -0.1511 0.000 0.096 0.580 0.324
#> GSM751421 3 0.0895 0.7519 0.000 0.020 0.976 0.004
#> GSM751422 3 0.0707 0.7533 0.000 0.020 0.980 0.000
#> GSM751360 3 0.0804 0.7506 0.000 0.012 0.980 0.008
#> GSM751364 3 0.4227 0.5797 0.000 0.060 0.820 0.120
#> GSM751390 3 0.6326 0.0731 0.000 0.104 0.632 0.264
#> GSM751392 4 0.7181 0.8858 0.000 0.152 0.336 0.512
#> GSM751396 4 0.7393 0.8618 0.000 0.180 0.332 0.488
#> GSM751399 3 0.1706 0.7439 0.000 0.036 0.948 0.016
#> GSM751400 3 0.2999 0.6409 0.000 0.132 0.864 0.004
#> GSM751401 3 0.0817 0.7541 0.000 0.024 0.976 0.000
#> GSM751402 3 0.0817 0.7541 0.000 0.024 0.976 0.000
#> GSM751403 3 0.1302 0.7457 0.000 0.044 0.956 0.000
#> GSM751405 3 0.0921 0.7540 0.000 0.028 0.972 0.000
#> GSM751407 3 0.0817 0.7541 0.000 0.024 0.976 0.000
#> GSM751408 3 0.1109 0.7529 0.000 0.028 0.968 0.004
#> GSM751409 3 0.4419 0.5786 0.000 0.084 0.812 0.104
#> GSM751412 3 0.0895 0.7538 0.000 0.020 0.976 0.004
#> GSM751418 3 0.1042 0.7412 0.000 0.008 0.972 0.020
#> GSM751419 3 0.1042 0.7385 0.000 0.008 0.972 0.020
#> GSM751420 2 0.6197 0.3248 0.000 0.604 0.324 0.072
#> GSM751425 2 0.3324 0.6860 0.000 0.852 0.012 0.136
#> GSM751429 2 0.6617 0.5555 0.120 0.676 0.180 0.024
#> GSM751430 2 0.5908 0.5705 0.004 0.636 0.048 0.312
#> GSM751433 2 0.4228 0.6756 0.008 0.760 0.000 0.232
#> GSM751437 2 0.5387 0.2880 0.000 0.584 0.400 0.016
#> GSM751448 2 0.6970 0.5130 0.144 0.644 0.188 0.024
#> GSM751451 2 0.5072 0.6821 0.000 0.740 0.052 0.208
#> GSM751423 2 0.5055 0.6895 0.004 0.768 0.068 0.160
#> GSM751424 2 0.4194 0.6738 0.008 0.764 0.000 0.228
#> GSM751428 2 0.1786 0.7227 0.008 0.948 0.008 0.036
#> GSM751431 2 0.3982 0.6748 0.004 0.776 0.000 0.220
#> GSM751432 2 0.4548 0.6716 0.008 0.752 0.008 0.232
#> GSM751434 2 0.4295 0.6708 0.008 0.752 0.000 0.240
#> GSM751435 2 0.2153 0.7259 0.008 0.936 0.020 0.036
#> GSM751436 2 0.4295 0.6708 0.008 0.752 0.000 0.240
#> GSM751440 2 0.4538 0.7142 0.004 0.808 0.064 0.124
#> GSM751444 2 0.1575 0.7176 0.004 0.956 0.012 0.028
#> GSM751446 2 0.2179 0.7103 0.000 0.924 0.064 0.012
#> GSM751449 2 0.2335 0.7117 0.000 0.920 0.060 0.020
#> GSM751450 2 0.3494 0.6928 0.004 0.824 0.000 0.172
#> GSM751452 2 0.4228 0.6732 0.008 0.760 0.000 0.232
#> GSM751426 2 0.3831 0.6830 0.004 0.792 0.000 0.204
#> GSM751427 2 0.3648 0.7199 0.004 0.864 0.076 0.056
#> GSM751438 2 0.2271 0.7065 0.000 0.916 0.076 0.008
#> GSM751439 2 0.3577 0.6505 0.000 0.832 0.156 0.012
#> GSM751441 2 0.3641 0.7134 0.008 0.868 0.052 0.072
#> GSM751442 2 0.2522 0.7094 0.000 0.908 0.076 0.016
#> GSM751443 2 0.4258 0.6504 0.020 0.812 0.156 0.012
#> GSM751445 2 0.2408 0.7120 0.000 0.920 0.044 0.036
#> GSM751447 2 0.1833 0.7135 0.000 0.944 0.024 0.032
#> GSM751453 2 0.1151 0.7116 0.000 0.968 0.008 0.024
#> GSM751454 2 0.1452 0.7115 0.000 0.956 0.008 0.036
#> GSM751455 2 0.2271 0.7065 0.000 0.916 0.076 0.008
#> GSM751456 2 0.2342 0.7046 0.000 0.912 0.080 0.008
#> GSM751457 2 0.2300 0.7096 0.000 0.920 0.064 0.016
#> GSM751458 2 0.2300 0.7096 0.000 0.920 0.064 0.016
cbind(get_classes(res, k = 5), get_membership(res, k = 5))
#> class entropy silhouette p1 p2 p3 p4 p5
#> GSM751298 1 0.4523 0.6156 0.712 0.028 0.000 0.252 0.008
#> GSM751304 2 0.4546 0.7216 0.012 0.756 0.000 0.176 0.056
#> GSM751305 2 0.5451 0.6922 0.016 0.708 0.012 0.184 0.080
#> GSM751307 2 0.4675 0.7269 0.020 0.764 0.000 0.144 0.072
#> GSM751310 4 0.1074 0.7387 0.012 0.016 0.000 0.968 0.004
#> GSM751314 4 0.1074 0.7397 0.016 0.012 0.000 0.968 0.004
#> GSM751316 4 0.0693 0.7365 0.008 0.012 0.000 0.980 0.000
#> GSM751318 4 0.4405 0.6604 0.260 0.020 0.000 0.712 0.008
#> GSM751342 4 0.1331 0.7097 0.000 0.040 0.000 0.952 0.008
#> GSM751346 1 0.2536 0.7377 0.900 0.044 0.000 0.052 0.004
#> GSM751347 2 0.6664 0.5613 0.132 0.564 0.272 0.008 0.024
#> GSM751348 2 0.5981 0.7683 0.064 0.724 0.052 0.100 0.060
#> GSM751349 2 0.5815 0.6806 0.004 0.660 0.044 0.056 0.236
#> GSM751352 2 0.5104 0.7693 0.056 0.768 0.012 0.104 0.060
#> GSM751353 2 0.4997 0.7726 0.016 0.776 0.036 0.080 0.092
#> GSM751354 2 0.5808 0.7768 0.056 0.732 0.040 0.108 0.064
#> GSM751355 2 0.5306 0.7606 0.020 0.752 0.036 0.068 0.124
#> GSM751358 2 0.8246 0.4074 0.044 0.428 0.272 0.208 0.048
#> GSM751359 5 0.7587 -0.0348 0.000 0.376 0.092 0.132 0.400
#> GSM751294 2 0.6201 0.7741 0.084 0.712 0.064 0.072 0.068
#> GSM751296 1 0.2653 0.7287 0.880 0.024 0.000 0.096 0.000
#> GSM751297 1 0.7074 -0.0935 0.468 0.388 0.052 0.076 0.016
#> GSM751299 2 0.4989 0.7712 0.056 0.776 0.012 0.100 0.056
#> GSM751300 1 0.2308 0.7372 0.912 0.036 0.000 0.048 0.004
#> GSM751301 2 0.5966 0.7109 0.144 0.688 0.004 0.108 0.056
#> GSM751302 1 0.2464 0.7363 0.904 0.044 0.000 0.048 0.004
#> GSM751303 4 0.0404 0.7359 0.000 0.012 0.000 0.988 0.000
#> GSM751306 4 0.0404 0.7359 0.000 0.012 0.000 0.988 0.000
#> GSM751308 1 0.7069 0.2047 0.520 0.316 0.032 0.112 0.020
#> GSM751309 4 0.0404 0.7359 0.000 0.012 0.000 0.988 0.000
#> GSM751311 4 0.0609 0.7325 0.000 0.020 0.000 0.980 0.000
#> GSM751312 4 0.3081 0.5852 0.156 0.012 0.000 0.832 0.000
#> GSM751313 1 0.3849 0.6347 0.752 0.016 0.000 0.232 0.000
#> GSM751315 4 0.3840 0.6896 0.208 0.012 0.000 0.772 0.008
#> GSM751317 4 0.0960 0.7381 0.008 0.016 0.000 0.972 0.004
#> GSM751320 4 0.4389 0.5618 0.368 0.004 0.000 0.624 0.004
#> GSM751321 4 0.0404 0.7359 0.000 0.012 0.000 0.988 0.000
#> GSM751322 4 0.4260 0.6306 0.308 0.004 0.000 0.680 0.008
#> GSM751324 4 0.4318 0.6403 0.296 0.008 0.000 0.688 0.008
#> GSM751325 4 0.4253 0.6077 0.332 0.004 0.000 0.660 0.004
#> GSM751332 4 0.4238 0.5655 0.368 0.000 0.000 0.628 0.004
#> GSM751334 4 0.4251 0.5594 0.372 0.000 0.000 0.624 0.004
#> GSM751339 1 0.3280 0.6914 0.812 0.012 0.000 0.176 0.000
#> GSM751341 1 0.5088 0.2997 0.528 0.036 0.000 0.436 0.000
#> GSM751343 4 0.4586 0.3016 0.468 0.004 0.000 0.524 0.004
#> GSM751344 2 0.4065 0.7487 0.016 0.808 0.000 0.120 0.056
#> GSM751345 2 0.4112 0.7469 0.016 0.804 0.000 0.124 0.056
#> GSM751356 2 0.5982 0.7293 0.060 0.684 0.016 0.188 0.052
#> GSM751357 2 0.5820 0.7309 0.060 0.692 0.012 0.188 0.048
#> GSM751293 2 0.6641 0.6230 0.236 0.588 0.000 0.120 0.056
#> GSM751295 1 0.2464 0.7363 0.904 0.044 0.000 0.048 0.004
#> GSM751319 4 0.0404 0.7359 0.000 0.012 0.000 0.988 0.000
#> GSM751323 4 0.4251 0.5594 0.372 0.000 0.000 0.624 0.004
#> GSM751326 1 0.4045 0.3372 0.644 0.000 0.000 0.356 0.000
#> GSM751327 4 0.4317 0.6194 0.320 0.004 0.000 0.668 0.008
#> GSM751328 4 0.2289 0.7314 0.080 0.012 0.000 0.904 0.004
#> GSM751329 4 0.4288 0.5363 0.384 0.000 0.000 0.612 0.004
#> GSM751330 1 0.3861 0.5244 0.712 0.004 0.000 0.284 0.000
#> GSM751331 1 0.3363 0.7102 0.860 0.056 0.004 0.072 0.008
#> GSM751333 1 0.3905 0.6247 0.752 0.012 0.004 0.232 0.000
#> GSM751335 1 0.3814 0.5321 0.720 0.004 0.000 0.276 0.000
#> GSM751336 1 0.1740 0.7284 0.932 0.012 0.000 0.056 0.000
#> GSM751337 1 0.3318 0.6882 0.808 0.012 0.000 0.180 0.000
#> GSM751338 1 0.3355 0.6850 0.804 0.012 0.000 0.184 0.000
#> GSM751340 1 0.5353 0.5857 0.728 0.160 0.056 0.052 0.004
#> GSM751350 1 0.2387 0.7375 0.908 0.040 0.000 0.048 0.004
#> GSM751351 1 0.2387 0.7375 0.908 0.040 0.000 0.048 0.004
#> GSM751362 3 0.1205 0.8779 0.004 0.000 0.956 0.000 0.040
#> GSM751363 3 0.7645 -0.2734 0.008 0.320 0.352 0.028 0.292
#> GSM751367 2 0.7559 0.2593 0.200 0.388 0.364 0.004 0.044
#> GSM751368 5 0.6015 0.5377 0.004 0.248 0.156 0.000 0.592
#> GSM751371 3 0.1618 0.8547 0.008 0.040 0.944 0.000 0.008
#> GSM751375 2 0.5716 0.3403 0.004 0.552 0.080 0.000 0.364
#> GSM751376 2 0.6499 0.7103 0.080 0.656 0.048 0.032 0.184
#> GSM751378 5 0.5824 0.6283 0.016 0.104 0.248 0.000 0.632
#> GSM751379 2 0.6563 0.7094 0.080 0.652 0.052 0.032 0.184
#> GSM751382 5 0.5568 0.4429 0.000 0.308 0.096 0.000 0.596
#> GSM751386 5 0.2036 0.7636 0.000 0.024 0.056 0.000 0.920
#> GSM751388 5 0.2036 0.7636 0.000 0.024 0.056 0.000 0.920
#> GSM751391 2 0.8068 0.2439 0.068 0.404 0.284 0.012 0.232
#> GSM751410 3 0.1186 0.8837 0.008 0.008 0.964 0.000 0.020
#> GSM751414 3 0.0771 0.8849 0.004 0.000 0.976 0.000 0.020
#> GSM751361 3 0.4348 0.4215 0.000 0.016 0.668 0.000 0.316
#> GSM751365 3 0.2771 0.7845 0.000 0.000 0.860 0.012 0.128
#> GSM751366 3 0.0324 0.8852 0.004 0.000 0.992 0.000 0.004
#> GSM751369 3 0.3627 0.7053 0.032 0.120 0.832 0.000 0.016
#> GSM751370 3 0.0671 0.8865 0.004 0.000 0.980 0.000 0.016
#> GSM751372 3 0.1270 0.8663 0.000 0.000 0.948 0.000 0.052
#> GSM751373 3 0.0162 0.8843 0.004 0.000 0.996 0.000 0.000
#> GSM751374 2 0.6475 0.7184 0.080 0.660 0.044 0.036 0.180
#> GSM751377 5 0.3710 0.6862 0.000 0.024 0.192 0.000 0.784
#> GSM751380 3 0.0486 0.8832 0.004 0.004 0.988 0.000 0.004
#> GSM751381 5 0.2036 0.7636 0.000 0.024 0.056 0.000 0.920
#> GSM751383 5 0.2236 0.7620 0.000 0.024 0.068 0.000 0.908
#> GSM751384 5 0.4559 0.1915 0.000 0.008 0.480 0.000 0.512
#> GSM751385 5 0.6857 0.3932 0.040 0.288 0.144 0.000 0.528
#> GSM751387 5 0.2036 0.7636 0.000 0.024 0.056 0.000 0.920
#> GSM751389 3 0.5640 0.5521 0.044 0.088 0.708 0.004 0.156
#> GSM751393 5 0.7328 0.4520 0.044 0.172 0.308 0.004 0.472
#> GSM751394 5 0.2124 0.7641 0.000 0.028 0.056 0.000 0.916
#> GSM751395 2 0.6653 0.5798 0.056 0.580 0.068 0.012 0.284
#> GSM751397 5 0.2036 0.7636 0.000 0.024 0.056 0.000 0.920
#> GSM751398 5 0.2236 0.7614 0.000 0.024 0.068 0.000 0.908
#> GSM751404 3 0.0000 0.8847 0.000 0.000 1.000 0.000 0.000
#> GSM751406 3 0.1041 0.8687 0.032 0.000 0.964 0.000 0.004
#> GSM751411 3 0.1851 0.8376 0.000 0.000 0.912 0.000 0.088
#> GSM751413 2 0.5895 0.4580 0.004 0.576 0.072 0.012 0.336
#> GSM751415 3 0.0510 0.8856 0.000 0.000 0.984 0.000 0.016
#> GSM751416 5 0.4817 0.3761 0.000 0.024 0.404 0.000 0.572
#> GSM751417 5 0.4663 0.4321 0.000 0.020 0.376 0.000 0.604
#> GSM751421 3 0.0867 0.8820 0.008 0.008 0.976 0.000 0.008
#> GSM751422 3 0.0740 0.8829 0.004 0.008 0.980 0.000 0.008
#> GSM751360 3 0.0486 0.8832 0.004 0.004 0.988 0.000 0.004
#> GSM751364 3 0.2304 0.8146 0.000 0.008 0.892 0.000 0.100
#> GSM751390 3 0.4656 -0.1613 0.000 0.012 0.508 0.000 0.480
#> GSM751392 5 0.2388 0.7630 0.000 0.028 0.072 0.000 0.900
#> GSM751396 5 0.4111 0.7260 0.000 0.120 0.092 0.000 0.788
#> GSM751399 3 0.0510 0.8857 0.000 0.000 0.984 0.000 0.016
#> GSM751400 3 0.2931 0.8065 0.040 0.044 0.888 0.000 0.028
#> GSM751401 3 0.0000 0.8847 0.000 0.000 1.000 0.000 0.000
#> GSM751402 3 0.0865 0.8755 0.024 0.000 0.972 0.000 0.004
#> GSM751403 3 0.0162 0.8851 0.000 0.000 0.996 0.000 0.004
#> GSM751405 3 0.0955 0.8724 0.028 0.000 0.968 0.000 0.004
#> GSM751407 3 0.0000 0.8847 0.000 0.000 1.000 0.000 0.000
#> GSM751408 3 0.0290 0.8857 0.000 0.000 0.992 0.000 0.008
#> GSM751409 3 0.3266 0.6758 0.000 0.004 0.796 0.000 0.200
#> GSM751412 3 0.0404 0.8861 0.000 0.000 0.988 0.000 0.012
#> GSM751418 3 0.0609 0.8835 0.000 0.000 0.980 0.000 0.020
#> GSM751419 3 0.0510 0.8845 0.000 0.000 0.984 0.000 0.016
#> GSM751420 2 0.6908 0.5465 0.064 0.568 0.252 0.004 0.112
#> GSM751425 2 0.3511 0.7687 0.020 0.864 0.052 0.012 0.052
#> GSM751429 2 0.6783 0.6128 0.240 0.584 0.132 0.024 0.020
#> GSM751430 2 0.4761 0.7200 0.020 0.752 0.004 0.048 0.176
#> GSM751433 2 0.3957 0.7569 0.024 0.832 0.004 0.068 0.072
#> GSM751437 2 0.5915 0.3594 0.056 0.544 0.380 0.008 0.012
#> GSM751448 2 0.6718 0.5272 0.292 0.536 0.148 0.008 0.016
#> GSM751451 2 0.4076 0.7407 0.004 0.812 0.100 0.008 0.076
#> GSM751423 2 0.3758 0.7732 0.028 0.840 0.060 0.000 0.072
#> GSM751424 2 0.3204 0.7631 0.020 0.872 0.004 0.028 0.076
#> GSM751428 2 0.1700 0.7821 0.020 0.948 0.008 0.012 0.012
#> GSM751431 2 0.2635 0.7644 0.020 0.900 0.004 0.012 0.064
#> GSM751432 2 0.4321 0.7528 0.020 0.804 0.004 0.072 0.100
#> GSM751434 2 0.4037 0.7503 0.024 0.820 0.000 0.084 0.072
#> GSM751435 2 0.2690 0.7889 0.028 0.908 0.016 0.024 0.024
#> GSM751436 2 0.3988 0.7560 0.020 0.828 0.004 0.072 0.076
#> GSM751440 2 0.4531 0.7767 0.056 0.804 0.084 0.008 0.048
#> GSM751444 2 0.2364 0.7816 0.036 0.916 0.036 0.004 0.008
#> GSM751446 2 0.3585 0.7715 0.076 0.856 0.040 0.012 0.016
#> GSM751449 2 0.3466 0.7719 0.076 0.856 0.040 0.000 0.028
#> GSM751450 2 0.2095 0.7747 0.008 0.920 0.012 0.000 0.060
#> GSM751452 2 0.4107 0.7557 0.020 0.820 0.004 0.076 0.080
#> GSM751426 2 0.2797 0.7688 0.016 0.896 0.008 0.020 0.060
#> GSM751427 2 0.3739 0.7812 0.068 0.848 0.044 0.004 0.036
#> GSM751438 2 0.3890 0.7694 0.080 0.840 0.040 0.008 0.032
#> GSM751439 2 0.4799 0.7333 0.116 0.768 0.092 0.004 0.020
#> GSM751441 2 0.4438 0.7821 0.060 0.816 0.044 0.016 0.064
#> GSM751442 2 0.3542 0.7724 0.072 0.860 0.036 0.012 0.020
#> GSM751443 2 0.4653 0.7583 0.092 0.792 0.080 0.012 0.024
#> GSM751445 2 0.3289 0.7755 0.072 0.868 0.040 0.004 0.016
#> GSM751447 2 0.3151 0.7750 0.060 0.880 0.036 0.012 0.012
#> GSM751453 2 0.2283 0.7756 0.028 0.924 0.024 0.016 0.008
#> GSM751454 2 0.2555 0.7781 0.028 0.912 0.032 0.020 0.008
#> GSM751455 2 0.3858 0.7684 0.076 0.844 0.040 0.012 0.028
#> GSM751456 2 0.3858 0.7684 0.076 0.844 0.040 0.012 0.028
#> GSM751457 2 0.3858 0.7684 0.076 0.844 0.040 0.012 0.028
#> GSM751458 2 0.3917 0.7676 0.080 0.840 0.040 0.012 0.028
cbind(get_classes(res, k = 6), get_membership(res, k = 6))
#> class entropy silhouette p1 p2 p3 p4 p5 p6
#> GSM751298 1 0.3426 0.6522 0.764 0.004 0.000 0.220 0.000 0.012
#> GSM751304 6 0.2660 0.6571 0.000 0.048 0.000 0.084 0.000 0.868
#> GSM751305 6 0.2757 0.6345 0.000 0.016 0.000 0.104 0.016 0.864
#> GSM751307 6 0.1442 0.6686 0.000 0.012 0.000 0.040 0.004 0.944
#> GSM751310 4 0.1152 0.7570 0.044 0.000 0.000 0.952 0.000 0.004
#> GSM751314 4 0.1349 0.7576 0.056 0.000 0.000 0.940 0.000 0.004
#> GSM751316 4 0.0547 0.7500 0.020 0.000 0.000 0.980 0.000 0.000
#> GSM751318 4 0.3990 0.6462 0.304 0.004 0.000 0.676 0.000 0.016
#> GSM751342 4 0.1471 0.7172 0.004 0.000 0.000 0.932 0.000 0.064
#> GSM751346 1 0.2094 0.7830 0.908 0.068 0.000 0.008 0.000 0.016
#> GSM751347 2 0.7261 0.3375 0.224 0.448 0.192 0.000 0.004 0.132
#> GSM751348 6 0.3766 0.6547 0.008 0.156 0.012 0.004 0.024 0.796
#> GSM751349 6 0.5355 0.5425 0.000 0.136 0.028 0.004 0.164 0.668
#> GSM751352 6 0.3521 0.5548 0.008 0.212 0.000 0.008 0.004 0.768
#> GSM751353 6 0.3809 0.5780 0.000 0.240 0.000 0.004 0.024 0.732
#> GSM751354 6 0.4151 0.1659 0.004 0.412 0.000 0.008 0.000 0.576
#> GSM751355 6 0.4154 0.4416 0.000 0.324 0.000 0.004 0.020 0.652
#> GSM751358 6 0.8466 0.1680 0.008 0.088 0.224 0.240 0.092 0.348
#> GSM751359 5 0.6753 0.4255 0.000 0.072 0.044 0.092 0.560 0.232
#> GSM751294 2 0.4227 0.4467 0.004 0.640 0.004 0.004 0.008 0.340
#> GSM751296 1 0.1542 0.7870 0.936 0.004 0.000 0.052 0.000 0.008
#> GSM751297 1 0.5138 0.5402 0.668 0.196 0.008 0.008 0.000 0.120
#> GSM751299 6 0.3702 0.5485 0.012 0.224 0.000 0.008 0.004 0.752
#> GSM751300 1 0.1542 0.7858 0.936 0.052 0.000 0.008 0.000 0.004
#> GSM751301 6 0.3153 0.6231 0.128 0.032 0.000 0.008 0.000 0.832
#> GSM751302 1 0.2036 0.7847 0.912 0.064 0.000 0.008 0.000 0.016
#> GSM751303 4 0.0363 0.7515 0.012 0.000 0.000 0.988 0.000 0.000
#> GSM751306 4 0.0363 0.7515 0.012 0.000 0.000 0.988 0.000 0.000
#> GSM751308 1 0.4523 0.6433 0.740 0.112 0.004 0.012 0.000 0.132
#> GSM751309 4 0.0363 0.7515 0.012 0.000 0.000 0.988 0.000 0.000
#> GSM751311 4 0.0547 0.7385 0.000 0.000 0.000 0.980 0.000 0.020
#> GSM751312 4 0.2135 0.6697 0.128 0.000 0.000 0.872 0.000 0.000
#> GSM751313 1 0.2595 0.7276 0.836 0.000 0.004 0.160 0.000 0.000
#> GSM751315 4 0.3454 0.6990 0.224 0.004 0.000 0.760 0.000 0.012
#> GSM751317 4 0.1194 0.7569 0.032 0.004 0.000 0.956 0.000 0.008
#> GSM751320 4 0.3872 0.5519 0.392 0.004 0.000 0.604 0.000 0.000
#> GSM751321 4 0.0458 0.7529 0.016 0.000 0.000 0.984 0.000 0.000
#> GSM751322 4 0.3894 0.6352 0.324 0.004 0.000 0.664 0.000 0.008
#> GSM751324 4 0.3861 0.6414 0.316 0.004 0.000 0.672 0.000 0.008
#> GSM751325 4 0.3892 0.6106 0.352 0.004 0.000 0.640 0.000 0.004
#> GSM751332 4 0.3727 0.5610 0.388 0.000 0.000 0.612 0.000 0.000
#> GSM751334 4 0.3737 0.5568 0.392 0.000 0.000 0.608 0.000 0.000
#> GSM751339 1 0.1714 0.7746 0.908 0.000 0.000 0.092 0.000 0.000
#> GSM751341 1 0.4467 0.4917 0.632 0.000 0.000 0.320 0.000 0.048
#> GSM751343 1 0.4225 -0.2004 0.508 0.004 0.000 0.480 0.000 0.008
#> GSM751344 6 0.1889 0.6788 0.004 0.056 0.000 0.020 0.000 0.920
#> GSM751345 6 0.1951 0.6791 0.004 0.060 0.000 0.020 0.000 0.916
#> GSM751356 6 0.4969 0.5030 0.012 0.224 0.000 0.100 0.000 0.664
#> GSM751357 6 0.4691 0.5493 0.008 0.196 0.000 0.100 0.000 0.696
#> GSM751293 6 0.3635 0.5685 0.180 0.032 0.000 0.008 0.000 0.780
#> GSM751295 1 0.2036 0.7847 0.912 0.064 0.000 0.008 0.000 0.016
#> GSM751319 4 0.0363 0.7515 0.012 0.000 0.000 0.988 0.000 0.000
#> GSM751323 4 0.3756 0.5427 0.400 0.000 0.000 0.600 0.000 0.000
#> GSM751326 1 0.3244 0.5644 0.732 0.000 0.000 0.268 0.000 0.000
#> GSM751327 4 0.3983 0.6084 0.348 0.004 0.000 0.640 0.000 0.008
#> GSM751328 4 0.2308 0.7467 0.108 0.004 0.000 0.880 0.000 0.008
#> GSM751329 4 0.3765 0.5409 0.404 0.000 0.000 0.596 0.000 0.000
#> GSM751330 1 0.2912 0.6430 0.784 0.000 0.000 0.216 0.000 0.000
#> GSM751331 1 0.2036 0.7802 0.912 0.064 0.000 0.008 0.000 0.016
#> GSM751333 1 0.2243 0.7690 0.880 0.004 0.004 0.112 0.000 0.000
#> GSM751335 1 0.3266 0.5267 0.728 0.000 0.000 0.272 0.000 0.000
#> GSM751336 1 0.0603 0.7849 0.980 0.004 0.000 0.016 0.000 0.000
#> GSM751337 1 0.1957 0.7650 0.888 0.000 0.000 0.112 0.000 0.000
#> GSM751338 1 0.2178 0.7513 0.868 0.000 0.000 0.132 0.000 0.000
#> GSM751340 1 0.3919 0.7497 0.824 0.052 0.024 0.048 0.000 0.052
#> GSM751350 1 0.1584 0.7831 0.928 0.064 0.000 0.000 0.000 0.008
#> GSM751351 1 0.1471 0.7831 0.932 0.064 0.000 0.000 0.000 0.004
#> GSM751362 3 0.1490 0.8911 0.016 0.024 0.948 0.000 0.008 0.004
#> GSM751363 5 0.6762 0.4137 0.000 0.076 0.168 0.004 0.500 0.252
#> GSM751367 3 0.7395 0.0467 0.284 0.180 0.408 0.000 0.008 0.120
#> GSM751368 5 0.3356 0.7299 0.000 0.024 0.064 0.000 0.840 0.072
#> GSM751371 3 0.1003 0.8824 0.000 0.020 0.964 0.000 0.000 0.016
#> GSM751375 5 0.5976 -0.1210 0.000 0.112 0.028 0.000 0.444 0.416
#> GSM751376 2 0.4823 0.5330 0.000 0.672 0.004 0.004 0.088 0.232
#> GSM751378 5 0.4733 0.6337 0.008 0.040 0.232 0.000 0.696 0.024
#> GSM751379 2 0.5218 0.5270 0.000 0.652 0.012 0.004 0.116 0.216
#> GSM751382 5 0.3697 0.6919 0.000 0.044 0.040 0.000 0.816 0.100
#> GSM751386 5 0.0547 0.7587 0.000 0.000 0.020 0.000 0.980 0.000
#> GSM751388 5 0.0146 0.7530 0.000 0.000 0.004 0.000 0.996 0.000
#> GSM751391 3 0.7652 -0.1664 0.012 0.180 0.380 0.000 0.276 0.152
#> GSM751410 3 0.1452 0.8768 0.032 0.008 0.948 0.000 0.004 0.008
#> GSM751414 3 0.1003 0.8861 0.000 0.016 0.964 0.000 0.020 0.000
#> GSM751361 5 0.4465 0.1588 0.000 0.020 0.472 0.000 0.504 0.004
#> GSM751365 3 0.2800 0.8398 0.008 0.020 0.880 0.000 0.068 0.024
#> GSM751366 3 0.0000 0.8904 0.000 0.000 1.000 0.000 0.000 0.000
#> GSM751369 3 0.2734 0.8297 0.020 0.088 0.872 0.000 0.000 0.020
#> GSM751370 3 0.0291 0.8920 0.000 0.000 0.992 0.000 0.004 0.004
#> GSM751372 3 0.1901 0.8792 0.000 0.028 0.924 0.000 0.040 0.008
#> GSM751373 3 0.0260 0.8911 0.000 0.000 0.992 0.000 0.008 0.000
#> GSM751374 2 0.4823 0.5360 0.000 0.672 0.004 0.004 0.088 0.232
#> GSM751377 5 0.2814 0.7077 0.000 0.008 0.172 0.000 0.820 0.000
#> GSM751380 3 0.0260 0.8933 0.000 0.008 0.992 0.000 0.000 0.000
#> GSM751381 5 0.0146 0.7530 0.000 0.000 0.004 0.000 0.996 0.000
#> GSM751383 5 0.0790 0.7597 0.000 0.000 0.032 0.000 0.968 0.000
#> GSM751384 5 0.4283 0.4186 0.000 0.024 0.384 0.000 0.592 0.000
#> GSM751385 5 0.5116 0.6253 0.004 0.120 0.064 0.000 0.716 0.096
#> GSM751387 5 0.0458 0.7574 0.000 0.000 0.016 0.000 0.984 0.000
#> GSM751389 3 0.4505 0.7157 0.004 0.128 0.760 0.000 0.064 0.044
#> GSM751393 5 0.6812 0.3943 0.008 0.148 0.304 0.000 0.472 0.068
#> GSM751394 5 0.0146 0.7530 0.000 0.000 0.004 0.000 0.996 0.000
#> GSM751395 2 0.6349 0.0801 0.004 0.368 0.004 0.000 0.292 0.332
#> GSM751397 5 0.0146 0.7530 0.000 0.000 0.004 0.000 0.996 0.000
#> GSM751398 5 0.0547 0.7564 0.000 0.000 0.020 0.000 0.980 0.000
#> GSM751404 3 0.0547 0.8944 0.000 0.020 0.980 0.000 0.000 0.000
#> GSM751406 3 0.1219 0.8889 0.000 0.048 0.948 0.000 0.004 0.000
#> GSM751411 3 0.2294 0.8590 0.000 0.036 0.892 0.000 0.072 0.000
#> GSM751413 5 0.5655 0.2889 0.000 0.092 0.028 0.000 0.552 0.328
#> GSM751415 3 0.0951 0.8953 0.000 0.020 0.968 0.000 0.008 0.004
#> GSM751416 5 0.3859 0.5880 0.000 0.020 0.288 0.000 0.692 0.000
#> GSM751417 5 0.3840 0.5940 0.000 0.020 0.284 0.000 0.696 0.000
#> GSM751421 3 0.0291 0.8927 0.000 0.004 0.992 0.000 0.004 0.000
#> GSM751422 3 0.0291 0.8914 0.000 0.004 0.992 0.000 0.000 0.004
#> GSM751360 3 0.0603 0.8903 0.000 0.004 0.980 0.000 0.016 0.000
#> GSM751364 3 0.4078 0.3606 0.000 0.020 0.640 0.000 0.340 0.000
#> GSM751390 5 0.4124 0.5218 0.000 0.024 0.332 0.000 0.644 0.000
#> GSM751392 5 0.0632 0.7590 0.000 0.000 0.024 0.000 0.976 0.000
#> GSM751396 5 0.1442 0.7577 0.000 0.012 0.040 0.000 0.944 0.004
#> GSM751399 3 0.1151 0.8938 0.000 0.032 0.956 0.000 0.012 0.000
#> GSM751400 3 0.2257 0.8604 0.008 0.068 0.904 0.000 0.008 0.012
#> GSM751401 3 0.0858 0.8939 0.000 0.028 0.968 0.000 0.004 0.000
#> GSM751402 3 0.0935 0.8933 0.000 0.032 0.964 0.000 0.004 0.000
#> GSM751403 3 0.0935 0.8939 0.000 0.032 0.964 0.000 0.004 0.000
#> GSM751405 3 0.1152 0.8907 0.000 0.044 0.952 0.000 0.004 0.000
#> GSM751407 3 0.0858 0.8942 0.000 0.028 0.968 0.000 0.004 0.000
#> GSM751408 3 0.0972 0.8947 0.000 0.028 0.964 0.000 0.008 0.000
#> GSM751409 3 0.3313 0.7663 0.004 0.036 0.812 0.000 0.148 0.000
#> GSM751412 3 0.1245 0.8931 0.000 0.032 0.952 0.000 0.016 0.000
#> GSM751418 3 0.2060 0.8331 0.000 0.016 0.900 0.000 0.084 0.000
#> GSM751419 3 0.1682 0.8638 0.000 0.020 0.928 0.000 0.052 0.000
#> GSM751420 2 0.5490 0.5021 0.004 0.652 0.212 0.000 0.048 0.084
#> GSM751425 2 0.5661 -0.1460 0.004 0.464 0.020 0.000 0.076 0.436
#> GSM751429 2 0.5353 0.5552 0.136 0.684 0.068 0.000 0.000 0.112
#> GSM751430 6 0.1938 0.6748 0.000 0.040 0.000 0.004 0.036 0.920
#> GSM751433 6 0.1728 0.6858 0.008 0.064 0.000 0.004 0.000 0.924
#> GSM751437 2 0.4752 0.3820 0.004 0.620 0.324 0.000 0.004 0.048
#> GSM751448 2 0.5900 0.4658 0.220 0.608 0.080 0.000 0.000 0.092
#> GSM751451 6 0.6367 0.3614 0.004 0.284 0.032 0.000 0.176 0.504
#> GSM751423 6 0.6424 0.1334 0.004 0.384 0.036 0.000 0.144 0.432
#> GSM751424 6 0.2520 0.6514 0.004 0.152 0.000 0.000 0.000 0.844
#> GSM751428 6 0.4058 0.4039 0.008 0.372 0.000 0.000 0.004 0.616
#> GSM751431 6 0.2871 0.6259 0.004 0.192 0.000 0.000 0.000 0.804
#> GSM751432 6 0.1732 0.6828 0.000 0.072 0.000 0.004 0.004 0.920
#> GSM751434 6 0.1155 0.6805 0.004 0.036 0.000 0.004 0.000 0.956
#> GSM751435 6 0.4102 0.4320 0.012 0.356 0.000 0.000 0.004 0.628
#> GSM751436 6 0.1219 0.6823 0.000 0.048 0.000 0.004 0.000 0.948
#> GSM751440 6 0.6236 0.2290 0.012 0.388 0.040 0.000 0.088 0.472
#> GSM751444 2 0.4107 0.0533 0.004 0.540 0.000 0.000 0.004 0.452
#> GSM751446 2 0.2340 0.6658 0.000 0.852 0.000 0.000 0.000 0.148
#> GSM751449 2 0.2135 0.6755 0.000 0.872 0.000 0.000 0.000 0.128
#> GSM751450 6 0.3684 0.5247 0.004 0.300 0.000 0.000 0.004 0.692
#> GSM751452 6 0.1471 0.6829 0.000 0.064 0.000 0.004 0.000 0.932
#> GSM751426 6 0.3052 0.5996 0.004 0.216 0.000 0.000 0.000 0.780
#> GSM751427 2 0.4741 0.4502 0.004 0.640 0.024 0.000 0.024 0.308
#> GSM751438 2 0.2048 0.6765 0.000 0.880 0.000 0.000 0.000 0.120
#> GSM751439 2 0.2982 0.6610 0.032 0.856 0.016 0.000 0.000 0.096
#> GSM751441 2 0.4490 0.4702 0.008 0.664 0.004 0.004 0.024 0.296
#> GSM751442 2 0.2527 0.6519 0.000 0.832 0.000 0.000 0.000 0.168
#> GSM751443 2 0.2402 0.6701 0.000 0.868 0.012 0.000 0.000 0.120
#> GSM751445 2 0.2912 0.5894 0.000 0.784 0.000 0.000 0.000 0.216
#> GSM751447 2 0.3371 0.4688 0.000 0.708 0.000 0.000 0.000 0.292
#> GSM751453 6 0.3997 0.1875 0.004 0.488 0.000 0.000 0.000 0.508
#> GSM751454 6 0.3998 0.1760 0.004 0.492 0.000 0.000 0.000 0.504
#> GSM751455 2 0.1863 0.6763 0.000 0.896 0.000 0.000 0.000 0.104
#> GSM751456 2 0.1863 0.6763 0.000 0.896 0.000 0.000 0.000 0.104
#> GSM751457 2 0.1863 0.6769 0.000 0.896 0.000 0.000 0.000 0.104
#> GSM751458 2 0.1863 0.6769 0.000 0.896 0.000 0.000 0.000 0.104
Heatmaps for the consensus matrix. It visualizes the probability of two samples to be in a same group.
consensus_heatmap(res, k = 2)
consensus_heatmap(res, k = 3)
consensus_heatmap(res, k = 4)
consensus_heatmap(res, k = 5)
consensus_heatmap(res, k = 6)
Heatmaps for the membership of samples in all partitions to see how consistent they are:
membership_heatmap(res, k = 2)
membership_heatmap(res, k = 3)
membership_heatmap(res, k = 4)
membership_heatmap(res, k = 5)
membership_heatmap(res, k = 6)
As soon as we have had the classes for columns, we can look for signatures which are significantly different between classes which can be candidate marks for certain classes. Following are the heatmaps for signatures.
Signature heatmaps where rows are scaled:
get_signatures(res, k = 2)
get_signatures(res, k = 3)
get_signatures(res, k = 4)
get_signatures(res, k = 5)
get_signatures(res, k = 6)
Signature heatmaps where rows are not scaled:
get_signatures(res, k = 2, scale_rows = FALSE)
get_signatures(res, k = 3, scale_rows = FALSE)
get_signatures(res, k = 4, scale_rows = FALSE)
get_signatures(res, k = 5, scale_rows = FALSE)
get_signatures(res, k = 6, scale_rows = FALSE)
Compare the overlap of signatures from different k:
compare_signatures(res)
get_signature() returns a data frame invisibly. TO get the list of signatures, the function
call should be assigned to a variable explicitly. In following code, if plot argument is set
to FALSE, no heatmap is plotted while only the differential analysis is performed.
# code only for demonstration
tb = get_signature(res, k = ..., plot = FALSE)
An example of the output of tb is:
#> which_row fdr mean_1 mean_2 scaled_mean_1 scaled_mean_2 km
#> 1 38 0.042760348 8.373488 9.131774 -0.5533452 0.5164555 1
#> 2 40 0.018707592 7.106213 8.469186 -0.6173731 0.5762149 1
#> 3 55 0.019134737 10.221463 11.207825 -0.6159697 0.5749050 1
#> 4 59 0.006059896 5.921854 7.869574 -0.6899429 0.6439467 1
#> 5 60 0.018055526 8.928898 10.211722 -0.6204761 0.5791110 1
#> 6 98 0.009384629 15.714769 14.887706 0.6635654 -0.6193277 2
...
The columns in tb are:
which_row: row indices corresponding to the input matrix.fdr: FDR for the differential test. mean_x: The mean value in group x.scaled_mean_x: The mean value in group x after rows are scaled.km: Row groups if k-means clustering is applied to rows.UMAP plot which shows how samples are separated.
dimension_reduction(res, k = 2, method = "UMAP")
dimension_reduction(res, k = 3, method = "UMAP")
dimension_reduction(res, k = 4, method = "UMAP")
dimension_reduction(res, k = 5, method = "UMAP")
dimension_reduction(res, k = 6, method = "UMAP")
Following heatmap shows how subgroups are split when increasing k:
collect_classes(res)
Test correlation between subgroups and known annotations. If the known annotation is numeric, one-way ANOVA test is applied, and if the known annotation is discrete, chi-squared contingency table test is applied.
test_to_known_factors(res)
#> n tissue(p) disease.state(p) agent(p) k
#> CV:mclust 165 2.86e-20 0.162 0.25061 2
#> CV:mclust 158 9.32e-45 0.118 0.34258 3
#> CV:mclust 142 3.37e-40 0.180 0.29863 4
#> CV:mclust 145 1.17e-36 0.193 0.05507 5
#> CV:mclust 134 3.90e-36 0.192 0.00365 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 4537 rows and 166 columns.
#> Top rows (454, 908, 1361, 1814, 2268) 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 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 0.715 0.877 0.942 0.4599 0.550 0.550
#> 3 3 0.644 0.757 0.892 0.4482 0.711 0.506
#> 4 4 0.631 0.579 0.737 0.1228 0.864 0.633
#> 5 5 0.625 0.454 0.650 0.0626 0.802 0.408
#> 6 6 0.769 0.706 0.833 0.0455 0.911 0.606
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
#> GSM751298 1 0.0000 0.9395 1.000 0.000
#> GSM751304 2 0.9286 0.4978 0.344 0.656
#> GSM751305 2 0.8813 0.5941 0.300 0.700
#> GSM751307 1 1.0000 0.0210 0.504 0.496
#> GSM751310 1 0.0000 0.9395 1.000 0.000
#> GSM751314 1 0.0000 0.9395 1.000 0.000
#> GSM751316 1 0.0000 0.9395 1.000 0.000
#> GSM751318 1 0.0000 0.9395 1.000 0.000
#> GSM751342 1 0.0000 0.9395 1.000 0.000
#> GSM751346 1 0.5629 0.8419 0.868 0.132
#> GSM751347 2 0.9944 0.1565 0.456 0.544
#> GSM751348 2 0.7950 0.6960 0.240 0.760
#> GSM751349 2 0.0000 0.9379 0.000 1.000
#> GSM751352 2 0.4690 0.8730 0.100 0.900
#> GSM751353 2 0.1633 0.9297 0.024 0.976
#> GSM751354 2 0.5842 0.8320 0.140 0.860
#> GSM751355 2 0.1184 0.9336 0.016 0.984
#> GSM751358 1 0.6148 0.7960 0.848 0.152
#> GSM751359 2 0.6623 0.8066 0.172 0.828
#> GSM751294 2 0.2043 0.9258 0.032 0.968
#> GSM751296 1 0.0376 0.9372 0.996 0.004
#> GSM751297 1 0.6247 0.8151 0.844 0.156
#> GSM751299 2 0.4690 0.8740 0.100 0.900
#> GSM751300 1 0.0672 0.9360 0.992 0.008
#> GSM751301 1 0.6801 0.7872 0.820 0.180
#> GSM751302 1 0.4690 0.8722 0.900 0.100
#> GSM751303 1 0.0000 0.9395 1.000 0.000
#> GSM751306 1 0.0000 0.9395 1.000 0.000
#> GSM751308 1 0.1843 0.9236 0.972 0.028
#> GSM751309 1 0.0000 0.9395 1.000 0.000
#> GSM751311 1 0.0000 0.9395 1.000 0.000
#> GSM751312 1 0.0000 0.9395 1.000 0.000
#> GSM751313 1 0.0000 0.9395 1.000 0.000
#> GSM751315 1 0.0000 0.9395 1.000 0.000
#> GSM751317 1 0.0000 0.9395 1.000 0.000
#> GSM751320 1 0.0000 0.9395 1.000 0.000
#> GSM751321 1 0.0000 0.9395 1.000 0.000
#> GSM751322 1 0.0000 0.9395 1.000 0.000
#> GSM751324 1 0.0000 0.9395 1.000 0.000
#> GSM751325 1 0.0000 0.9395 1.000 0.000
#> GSM751332 1 0.0000 0.9395 1.000 0.000
#> GSM751334 1 0.0000 0.9395 1.000 0.000
#> GSM751339 1 0.0000 0.9395 1.000 0.000
#> GSM751341 1 0.0000 0.9395 1.000 0.000
#> GSM751343 1 0.0000 0.9395 1.000 0.000
#> GSM751344 2 0.3584 0.9001 0.068 0.932
#> GSM751345 2 0.3879 0.8940 0.076 0.924
#> GSM751356 1 0.9833 0.2645 0.576 0.424
#> GSM751357 1 0.9815 0.2840 0.580 0.420
#> GSM751293 1 0.2603 0.9159 0.956 0.044
#> GSM751295 1 0.3431 0.9023 0.936 0.064
#> GSM751319 1 0.0000 0.9395 1.000 0.000
#> GSM751323 1 0.0000 0.9395 1.000 0.000
#> GSM751326 1 0.0000 0.9395 1.000 0.000
#> GSM751327 1 0.0000 0.9395 1.000 0.000
#> GSM751328 1 0.0000 0.9395 1.000 0.000
#> GSM751329 1 0.0000 0.9395 1.000 0.000
#> GSM751330 1 0.0000 0.9395 1.000 0.000
#> GSM751331 1 0.1414 0.9275 0.980 0.020
#> GSM751333 1 0.0000 0.9395 1.000 0.000
#> GSM751335 1 0.0000 0.9395 1.000 0.000
#> GSM751336 1 0.0000 0.9395 1.000 0.000
#> GSM751337 1 0.0000 0.9395 1.000 0.000
#> GSM751338 1 0.0000 0.9395 1.000 0.000
#> GSM751340 1 0.0000 0.9395 1.000 0.000
#> GSM751350 1 0.1414 0.9275 0.980 0.020
#> GSM751351 1 0.1414 0.9275 0.980 0.020
#> GSM751362 2 0.9795 0.3656 0.416 0.584
#> GSM751363 2 0.5294 0.8701 0.120 0.880
#> GSM751367 1 0.8144 0.6558 0.748 0.252
#> GSM751368 2 0.1184 0.9362 0.016 0.984
#> GSM751371 1 0.9998 -0.0108 0.508 0.492
#> GSM751375 2 0.0000 0.9379 0.000 1.000
#> GSM751376 2 0.0672 0.9376 0.008 0.992
#> GSM751378 2 0.0000 0.9379 0.000 1.000
#> GSM751379 2 0.0000 0.9379 0.000 1.000
#> GSM751382 2 0.0000 0.9379 0.000 1.000
#> GSM751386 2 0.0000 0.9379 0.000 1.000
#> GSM751388 2 0.0000 0.9379 0.000 1.000
#> GSM751391 2 0.0376 0.9376 0.004 0.996
#> GSM751410 1 0.5737 0.8211 0.864 0.136
#> GSM751414 2 0.6343 0.8210 0.160 0.840
#> GSM751361 2 0.1633 0.9342 0.024 0.976
#> GSM751365 2 0.4939 0.8792 0.108 0.892
#> GSM751366 2 0.9522 0.4418 0.372 0.628
#> GSM751369 2 0.9358 0.4853 0.352 0.648
#> GSM751370 2 0.7528 0.7497 0.216 0.784
#> GSM751372 2 0.2778 0.9245 0.048 0.952
#> GSM751373 2 0.6343 0.8210 0.160 0.840
#> GSM751374 2 0.0000 0.9379 0.000 1.000
#> GSM751377 2 0.0938 0.9369 0.012 0.988
#> GSM751380 2 0.7815 0.7239 0.232 0.768
#> GSM751381 2 0.0000 0.9379 0.000 1.000
#> GSM751383 2 0.0000 0.9379 0.000 1.000
#> GSM751384 2 0.1414 0.9353 0.020 0.980
#> GSM751385 2 0.0000 0.9379 0.000 1.000
#> GSM751387 2 0.0000 0.9379 0.000 1.000
#> GSM751389 2 0.1633 0.9342 0.024 0.976
#> GSM751393 2 0.1633 0.9342 0.024 0.976
#> GSM751394 2 0.0000 0.9379 0.000 1.000
#> GSM751395 2 0.0672 0.9379 0.008 0.992
#> GSM751397 2 0.0938 0.9369 0.012 0.988
#> GSM751398 2 0.0672 0.9374 0.008 0.992
#> GSM751404 2 0.2043 0.9312 0.032 0.968
#> GSM751406 2 0.1843 0.9329 0.028 0.972
#> GSM751411 2 0.1633 0.9342 0.024 0.976
#> GSM751413 2 0.1633 0.9352 0.024 0.976
#> GSM751415 2 0.6531 0.8120 0.168 0.832
#> GSM751416 2 0.1633 0.9342 0.024 0.976
#> GSM751417 2 0.1633 0.9342 0.024 0.976
#> GSM751421 2 0.6623 0.8077 0.172 0.828
#> GSM751422 2 0.7219 0.7719 0.200 0.800
#> GSM751360 2 0.2423 0.9277 0.040 0.960
#> GSM751364 2 0.1633 0.9342 0.024 0.976
#> GSM751390 2 0.0672 0.9374 0.008 0.992
#> GSM751392 2 0.0000 0.9379 0.000 1.000
#> GSM751396 2 0.0000 0.9379 0.000 1.000
#> GSM751399 2 0.1633 0.9342 0.024 0.976
#> GSM751400 2 0.1633 0.9342 0.024 0.976
#> GSM751401 2 0.2236 0.9293 0.036 0.964
#> GSM751402 2 0.2043 0.9312 0.032 0.968
#> GSM751403 2 0.1633 0.9342 0.024 0.976
#> GSM751405 2 0.1843 0.9329 0.028 0.972
#> GSM751407 2 0.1633 0.9342 0.024 0.976
#> GSM751408 2 0.1633 0.9342 0.024 0.976
#> GSM751409 2 0.1633 0.9342 0.024 0.976
#> GSM751412 2 0.1633 0.9342 0.024 0.976
#> GSM751418 2 0.1633 0.9342 0.024 0.976
#> GSM751419 2 0.1633 0.9342 0.024 0.976
#> GSM751420 2 0.0938 0.9371 0.012 0.988
#> GSM751425 2 0.0000 0.9379 0.000 1.000
#> GSM751429 2 0.7376 0.7480 0.208 0.792
#> GSM751430 2 0.2603 0.9184 0.044 0.956
#> GSM751433 2 0.5629 0.8415 0.132 0.868
#> GSM751437 2 0.0000 0.9379 0.000 1.000
#> GSM751448 2 0.9000 0.5628 0.316 0.684
#> GSM751451 2 0.0000 0.9379 0.000 1.000
#> GSM751423 2 0.0000 0.9379 0.000 1.000
#> GSM751424 2 0.0000 0.9379 0.000 1.000
#> GSM751428 2 0.0000 0.9379 0.000 1.000
#> GSM751431 2 0.0000 0.9379 0.000 1.000
#> GSM751432 2 0.0672 0.9363 0.008 0.992
#> GSM751434 2 0.3274 0.9072 0.060 0.940
#> GSM751435 2 0.0672 0.9363 0.008 0.992
#> GSM751436 2 0.2603 0.9186 0.044 0.956
#> GSM751440 2 0.0000 0.9379 0.000 1.000
#> GSM751444 2 0.0000 0.9379 0.000 1.000
#> GSM751446 2 0.0000 0.9379 0.000 1.000
#> GSM751449 2 0.0000 0.9379 0.000 1.000
#> GSM751450 2 0.0000 0.9379 0.000 1.000
#> GSM751452 2 0.0938 0.9351 0.012 0.988
#> GSM751426 2 0.0000 0.9379 0.000 1.000
#> GSM751427 2 0.0000 0.9379 0.000 1.000
#> GSM751438 2 0.0000 0.9379 0.000 1.000
#> GSM751439 2 0.3733 0.8965 0.072 0.928
#> GSM751441 2 0.0000 0.9379 0.000 1.000
#> GSM751442 2 0.0000 0.9379 0.000 1.000
#> GSM751443 2 0.0000 0.9379 0.000 1.000
#> GSM751445 2 0.0000 0.9379 0.000 1.000
#> GSM751447 2 0.0000 0.9379 0.000 1.000
#> GSM751453 2 0.0000 0.9379 0.000 1.000
#> GSM751454 2 0.0000 0.9379 0.000 1.000
#> GSM751455 2 0.0000 0.9379 0.000 1.000
#> GSM751456 2 0.0000 0.9379 0.000 1.000
#> GSM751457 2 0.0000 0.9379 0.000 1.000
#> GSM751458 2 0.0000 0.9379 0.000 1.000
cbind(get_classes(res, k = 3), get_membership(res, k = 3))
#> class entropy silhouette p1 p2 p3
#> GSM751298 1 0.0000 0.944 1.000 0.000 0.000
#> GSM751304 2 0.3272 0.786 0.104 0.892 0.004
#> GSM751305 2 0.4465 0.725 0.176 0.820 0.004
#> GSM751307 2 0.2796 0.799 0.092 0.908 0.000
#> GSM751310 1 0.0237 0.944 0.996 0.000 0.004
#> GSM751314 1 0.0237 0.944 0.996 0.000 0.004
#> GSM751316 1 0.0237 0.944 0.996 0.000 0.004
#> GSM751318 1 0.0237 0.944 0.996 0.000 0.004
#> GSM751342 1 0.0237 0.944 0.996 0.000 0.004
#> GSM751346 1 0.7825 0.636 0.672 0.172 0.156
#> GSM751347 1 0.7337 0.251 0.540 0.032 0.428
#> GSM751348 2 0.1529 0.833 0.040 0.960 0.000
#> GSM751349 2 0.0424 0.847 0.000 0.992 0.008
#> GSM751352 2 0.0237 0.846 0.004 0.996 0.000
#> GSM751353 2 0.0000 0.847 0.000 1.000 0.000
#> GSM751354 2 0.4842 0.641 0.000 0.776 0.224
#> GSM751355 2 0.0000 0.847 0.000 1.000 0.000
#> GSM751358 1 0.1765 0.913 0.956 0.040 0.004
#> GSM751359 2 0.6447 0.669 0.196 0.744 0.060
#> GSM751294 2 0.5845 0.503 0.004 0.688 0.308
#> GSM751296 1 0.0000 0.944 1.000 0.000 0.000
#> GSM751297 1 0.9601 0.267 0.464 0.224 0.312
#> GSM751299 2 0.0829 0.844 0.004 0.984 0.012
#> GSM751300 1 0.1267 0.927 0.972 0.024 0.004
#> GSM751301 2 0.0892 0.841 0.020 0.980 0.000
#> GSM751302 1 0.5728 0.728 0.772 0.196 0.032
#> GSM751303 1 0.0237 0.944 0.996 0.000 0.004
#> GSM751306 1 0.0237 0.944 0.996 0.000 0.004
#> GSM751308 1 0.8028 0.614 0.656 0.168 0.176
#> GSM751309 1 0.0237 0.944 0.996 0.000 0.004
#> GSM751311 1 0.0237 0.944 0.996 0.000 0.004
#> GSM751312 1 0.0237 0.944 0.996 0.000 0.004
#> GSM751313 1 0.0000 0.944 1.000 0.000 0.000
#> GSM751315 1 0.0237 0.944 0.996 0.000 0.004
#> GSM751317 1 0.0237 0.944 0.996 0.000 0.004
#> GSM751320 1 0.0000 0.944 1.000 0.000 0.000
#> GSM751321 1 0.0237 0.944 0.996 0.000 0.004
#> GSM751322 1 0.0237 0.944 0.996 0.000 0.004
#> GSM751324 1 0.0237 0.944 0.996 0.000 0.004
#> GSM751325 1 0.0237 0.944 0.996 0.000 0.004
#> GSM751332 1 0.0000 0.944 1.000 0.000 0.000
#> GSM751334 1 0.0000 0.944 1.000 0.000 0.000
#> GSM751339 1 0.0000 0.944 1.000 0.000 0.000
#> GSM751341 1 0.0237 0.944 0.996 0.000 0.004
#> GSM751343 1 0.0000 0.944 1.000 0.000 0.000
#> GSM751344 2 0.0000 0.847 0.000 1.000 0.000
#> GSM751345 2 0.0237 0.846 0.004 0.996 0.000
#> GSM751356 2 0.6141 0.662 0.232 0.736 0.032
#> GSM751357 2 0.5335 0.672 0.232 0.760 0.008
#> GSM751293 2 0.4452 0.697 0.192 0.808 0.000
#> GSM751295 1 0.7633 0.637 0.680 0.200 0.120
#> GSM751319 1 0.0237 0.944 0.996 0.000 0.004
#> GSM751323 1 0.0000 0.944 1.000 0.000 0.000
#> GSM751326 1 0.0000 0.944 1.000 0.000 0.000
#> GSM751327 1 0.0000 0.944 1.000 0.000 0.000
#> GSM751328 1 0.0237 0.944 0.996 0.000 0.004
#> GSM751329 1 0.0000 0.944 1.000 0.000 0.000
#> GSM751330 1 0.0000 0.944 1.000 0.000 0.000
#> GSM751331 1 0.1031 0.930 0.976 0.024 0.000
#> GSM751333 1 0.0000 0.944 1.000 0.000 0.000
#> GSM751335 1 0.0000 0.944 1.000 0.000 0.000
#> GSM751336 1 0.0000 0.944 1.000 0.000 0.000
#> GSM751337 1 0.0000 0.944 1.000 0.000 0.000
#> GSM751338 1 0.0000 0.944 1.000 0.000 0.000
#> GSM751340 1 0.4842 0.716 0.776 0.000 0.224
#> GSM751350 1 0.2959 0.864 0.900 0.100 0.000
#> GSM751351 1 0.1860 0.908 0.948 0.052 0.000
#> GSM751362 3 0.0237 0.826 0.004 0.000 0.996
#> GSM751363 3 0.6696 0.492 0.020 0.348 0.632
#> GSM751367 3 0.6104 0.400 0.348 0.004 0.648
#> GSM751368 3 0.6307 0.125 0.000 0.488 0.512
#> GSM751371 3 0.1315 0.823 0.020 0.008 0.972
#> GSM751375 2 0.3752 0.739 0.000 0.856 0.144
#> GSM751376 3 0.5733 0.461 0.000 0.324 0.676
#> GSM751378 3 0.2959 0.791 0.000 0.100 0.900
#> GSM751379 3 0.4702 0.655 0.000 0.212 0.788
#> GSM751382 2 0.3752 0.740 0.000 0.856 0.144
#> GSM751386 2 0.5835 0.420 0.000 0.660 0.340
#> GSM751388 2 0.6111 0.274 0.000 0.604 0.396
#> GSM751391 3 0.1289 0.817 0.000 0.032 0.968
#> GSM751410 3 0.0424 0.824 0.008 0.000 0.992
#> GSM751414 3 0.2651 0.802 0.060 0.012 0.928
#> GSM751361 3 0.5650 0.563 0.000 0.312 0.688
#> GSM751365 3 0.0983 0.824 0.004 0.016 0.980
#> GSM751366 3 0.0000 0.827 0.000 0.000 1.000
#> GSM751369 3 0.0661 0.826 0.004 0.008 0.988
#> GSM751370 3 0.1529 0.812 0.040 0.000 0.960
#> GSM751372 3 0.1989 0.812 0.004 0.048 0.948
#> GSM751373 3 0.3644 0.759 0.124 0.004 0.872
#> GSM751374 3 0.6215 0.204 0.000 0.428 0.572
#> GSM751377 3 0.5905 0.491 0.000 0.352 0.648
#> GSM751380 3 0.0237 0.828 0.000 0.004 0.996
#> GSM751381 2 0.5968 0.361 0.000 0.636 0.364
#> GSM751383 2 0.6140 0.247 0.000 0.596 0.404
#> GSM751384 3 0.5216 0.638 0.000 0.260 0.740
#> GSM751385 3 0.5254 0.634 0.000 0.264 0.736
#> GSM751387 2 0.6026 0.331 0.000 0.624 0.376
#> GSM751389 3 0.0424 0.827 0.000 0.008 0.992
#> GSM751393 3 0.0592 0.827 0.000 0.012 0.988
#> GSM751394 2 0.6168 0.224 0.000 0.588 0.412
#> GSM751395 3 0.4399 0.730 0.000 0.188 0.812
#> GSM751397 3 0.6154 0.369 0.000 0.408 0.592
#> GSM751398 3 0.6295 0.185 0.000 0.472 0.528
#> GSM751404 3 0.0237 0.828 0.000 0.004 0.996
#> GSM751406 3 0.0424 0.827 0.000 0.008 0.992
#> GSM751411 3 0.0237 0.828 0.000 0.004 0.996
#> GSM751413 3 0.6305 0.149 0.000 0.484 0.516
#> GSM751415 3 0.0237 0.828 0.000 0.004 0.996
#> GSM751416 3 0.5621 0.569 0.000 0.308 0.692
#> GSM751417 3 0.5706 0.549 0.000 0.320 0.680
#> GSM751421 3 0.0237 0.828 0.000 0.004 0.996
#> GSM751422 3 0.0237 0.828 0.000 0.004 0.996
#> GSM751360 3 0.0592 0.824 0.012 0.000 0.988
#> GSM751364 3 0.5254 0.632 0.000 0.264 0.736
#> GSM751390 3 0.5363 0.620 0.000 0.276 0.724
#> GSM751392 2 0.5650 0.481 0.000 0.688 0.312
#> GSM751396 2 0.5363 0.549 0.000 0.724 0.276
#> GSM751399 3 0.0237 0.828 0.000 0.004 0.996
#> GSM751400 3 0.0237 0.828 0.000 0.004 0.996
#> GSM751401 3 0.0237 0.828 0.000 0.004 0.996
#> GSM751402 3 0.0237 0.828 0.000 0.004 0.996
#> GSM751403 3 0.0237 0.828 0.000 0.004 0.996
#> GSM751405 3 0.0237 0.828 0.000 0.004 0.996
#> GSM751407 3 0.0237 0.828 0.000 0.004 0.996
#> GSM751408 3 0.0237 0.828 0.000 0.004 0.996
#> GSM751409 3 0.0237 0.828 0.000 0.004 0.996
#> GSM751412 3 0.0237 0.828 0.000 0.004 0.996
#> GSM751418 3 0.4453 0.743 0.012 0.152 0.836
#> GSM751419 3 0.3551 0.763 0.000 0.132 0.868
#> GSM751420 3 0.0747 0.825 0.000 0.016 0.984
#> GSM751425 2 0.0424 0.848 0.000 0.992 0.008
#> GSM751429 3 0.5536 0.608 0.012 0.236 0.752
#> GSM751430 2 0.0475 0.847 0.004 0.992 0.004
#> GSM751433 2 0.0424 0.847 0.000 0.992 0.008
#> GSM751437 3 0.4750 0.642 0.000 0.216 0.784
#> GSM751448 3 0.4033 0.731 0.008 0.136 0.856
#> GSM751451 2 0.0592 0.847 0.000 0.988 0.012
#> GSM751423 2 0.0592 0.847 0.000 0.988 0.012
#> GSM751424 2 0.0237 0.848 0.000 0.996 0.004
#> GSM751428 2 0.0237 0.848 0.000 0.996 0.004
#> GSM751431 2 0.0237 0.848 0.000 0.996 0.004
#> GSM751432 2 0.0237 0.848 0.000 0.996 0.004
#> GSM751434 2 0.0237 0.848 0.000 0.996 0.004
#> GSM751435 2 0.0237 0.848 0.000 0.996 0.004
#> GSM751436 2 0.0424 0.847 0.000 0.992 0.008
#> GSM751440 2 0.0424 0.848 0.000 0.992 0.008
#> GSM751444 2 0.0237 0.848 0.000 0.996 0.004
#> GSM751446 2 0.2356 0.810 0.000 0.928 0.072
#> GSM751449 2 0.2711 0.797 0.000 0.912 0.088
#> GSM751450 2 0.0424 0.848 0.000 0.992 0.008
#> GSM751452 2 0.0237 0.848 0.000 0.996 0.004
#> GSM751426 2 0.0237 0.848 0.000 0.996 0.004
#> GSM751427 2 0.0424 0.848 0.000 0.992 0.008
#> GSM751438 2 0.4887 0.639 0.000 0.772 0.228
#> GSM751439 2 0.6280 0.133 0.000 0.540 0.460
#> GSM751441 2 0.0424 0.848 0.000 0.992 0.008
#> GSM751442 2 0.2261 0.813 0.000 0.932 0.068
#> GSM751443 3 0.6260 0.149 0.000 0.448 0.552
#> GSM751445 2 0.0424 0.847 0.000 0.992 0.008
#> GSM751447 2 0.0237 0.848 0.000 0.996 0.004
#> GSM751453 2 0.0237 0.848 0.000 0.996 0.004
#> GSM751454 2 0.0237 0.848 0.000 0.996 0.004
#> GSM751455 2 0.3412 0.764 0.000 0.876 0.124
#> GSM751456 2 0.4178 0.712 0.000 0.828 0.172
#> GSM751457 2 0.5706 0.485 0.000 0.680 0.320
#> GSM751458 2 0.5810 0.453 0.000 0.664 0.336
cbind(get_classes(res, k = 4), get_membership(res, k = 4))
#> class entropy silhouette p1 p2 p3 p4
#> GSM751298 1 0.0707 0.8980 0.980 0.000 0.000 0.020
#> GSM751304 2 0.4936 0.6459 0.000 0.624 0.004 0.372
#> GSM751305 2 0.5511 0.6315 0.012 0.604 0.008 0.376
#> GSM751307 2 0.4854 0.6761 0.004 0.676 0.004 0.316
#> GSM751310 1 0.1940 0.8937 0.924 0.000 0.000 0.076
#> GSM751314 1 0.1867 0.8949 0.928 0.000 0.000 0.072
#> GSM751316 1 0.1940 0.8937 0.924 0.000 0.000 0.076
#> GSM751318 1 0.0469 0.9009 0.988 0.000 0.000 0.012
#> GSM751342 1 0.1940 0.8937 0.924 0.000 0.000 0.076
#> GSM751346 4 0.7230 0.5222 0.272 0.168 0.004 0.556
#> GSM751347 4 0.8206 0.3080 0.372 0.028 0.176 0.424
#> GSM751348 2 0.6515 0.6283 0.128 0.624 0.000 0.248
#> GSM751349 2 0.6479 0.5836 0.000 0.636 0.140 0.224
#> GSM751352 2 0.4746 0.6605 0.000 0.632 0.000 0.368
#> GSM751353 2 0.4608 0.6829 0.000 0.692 0.004 0.304
#> GSM751354 4 0.5064 -0.2655 0.004 0.360 0.004 0.632
#> GSM751355 2 0.4632 0.6809 0.000 0.688 0.004 0.308
#> GSM751358 1 0.2673 0.8828 0.904 0.008 0.008 0.080
#> GSM751359 3 0.9047 -0.0662 0.064 0.320 0.368 0.248
#> GSM751294 4 0.5374 0.2382 0.028 0.252 0.012 0.708
#> GSM751296 1 0.3743 0.7751 0.824 0.016 0.000 0.160
#> GSM751297 4 0.6039 0.5775 0.148 0.136 0.008 0.708
#> GSM751299 2 0.4961 0.6048 0.000 0.552 0.000 0.448
#> GSM751300 1 0.4630 0.6547 0.732 0.016 0.000 0.252
#> GSM751301 2 0.5807 0.6516 0.052 0.636 0.000 0.312
#> GSM751302 4 0.7171 0.2383 0.400 0.136 0.000 0.464
#> GSM751303 1 0.2125 0.8917 0.920 0.000 0.004 0.076
#> GSM751306 1 0.2125 0.8917 0.920 0.000 0.004 0.076
#> GSM751308 4 0.6689 0.2812 0.412 0.076 0.004 0.508
#> GSM751309 1 0.2125 0.8917 0.920 0.000 0.004 0.076
#> GSM751311 1 0.1940 0.8937 0.924 0.000 0.000 0.076
#> GSM751312 1 0.1940 0.8937 0.924 0.000 0.000 0.076
#> GSM751313 1 0.1716 0.8766 0.936 0.000 0.000 0.064
#> GSM751315 1 0.1792 0.8957 0.932 0.000 0.000 0.068
#> GSM751317 1 0.1940 0.8937 0.924 0.000 0.000 0.076
#> GSM751320 1 0.0336 0.8997 0.992 0.000 0.000 0.008
#> GSM751321 1 0.1940 0.8937 0.924 0.000 0.000 0.076
#> GSM751322 1 0.1389 0.8992 0.952 0.000 0.000 0.048
#> GSM751324 1 0.0921 0.9007 0.972 0.000 0.000 0.028
#> GSM751325 1 0.0000 0.9002 1.000 0.000 0.000 0.000
#> GSM751332 1 0.0469 0.8989 0.988 0.000 0.000 0.012
#> GSM751334 1 0.0469 0.8989 0.988 0.000 0.000 0.012
#> GSM751339 1 0.1637 0.8778 0.940 0.000 0.000 0.060
#> GSM751341 1 0.1867 0.8949 0.928 0.000 0.000 0.072
#> GSM751343 1 0.0336 0.8995 0.992 0.000 0.000 0.008
#> GSM751344 2 0.4608 0.6825 0.000 0.692 0.004 0.304
#> GSM751345 2 0.4608 0.6825 0.000 0.692 0.004 0.304
#> GSM751356 2 0.6773 0.5343 0.104 0.532 0.000 0.364
#> GSM751357 2 0.6682 0.5710 0.112 0.576 0.000 0.312
#> GSM751293 2 0.6121 0.6470 0.072 0.620 0.000 0.308
#> GSM751295 4 0.6971 0.5137 0.276 0.156 0.000 0.568
#> GSM751319 1 0.1940 0.8937 0.924 0.000 0.000 0.076
#> GSM751323 1 0.0469 0.8989 0.988 0.000 0.000 0.012
#> GSM751326 1 0.0592 0.8982 0.984 0.000 0.000 0.016
#> GSM751327 1 0.0336 0.8995 0.992 0.000 0.000 0.008
#> GSM751328 1 0.1474 0.8987 0.948 0.000 0.000 0.052
#> GSM751329 1 0.0469 0.8989 0.988 0.000 0.000 0.012
#> GSM751330 1 0.2469 0.8470 0.892 0.000 0.000 0.108
#> GSM751331 1 0.4331 0.6378 0.712 0.000 0.000 0.288
#> GSM751333 1 0.1474 0.8856 0.948 0.000 0.000 0.052
#> GSM751335 1 0.1637 0.8813 0.940 0.000 0.000 0.060
#> GSM751336 1 0.2921 0.8163 0.860 0.000 0.000 0.140
#> GSM751337 1 0.2408 0.8453 0.896 0.000 0.000 0.104
#> GSM751338 1 0.0707 0.8973 0.980 0.000 0.000 0.020
#> GSM751340 1 0.5713 0.2700 0.604 0.000 0.036 0.360
#> GSM751350 1 0.5311 0.5042 0.648 0.024 0.000 0.328
#> GSM751351 1 0.4844 0.5816 0.688 0.012 0.000 0.300
#> GSM751362 3 0.5193 0.4159 0.020 0.000 0.656 0.324
#> GSM751363 3 0.5140 0.4884 0.016 0.032 0.752 0.200
#> GSM751367 4 0.7363 0.2035 0.168 0.000 0.356 0.476
#> GSM751368 3 0.3910 0.5355 0.000 0.156 0.820 0.024
#> GSM751371 3 0.6762 0.2227 0.104 0.000 0.536 0.360
#> GSM751375 2 0.5833 0.6322 0.000 0.692 0.096 0.212
#> GSM751376 4 0.5050 0.3958 0.000 0.028 0.268 0.704
#> GSM751378 3 0.5911 0.4564 0.000 0.112 0.692 0.196
#> GSM751379 4 0.5110 0.2912 0.000 0.016 0.328 0.656
#> GSM751382 3 0.7587 -0.0740 0.000 0.392 0.412 0.196
#> GSM751386 3 0.7269 0.2665 0.000 0.264 0.536 0.200
#> GSM751388 3 0.7028 0.3431 0.000 0.228 0.576 0.196
#> GSM751391 3 0.5611 0.2780 0.000 0.024 0.564 0.412
#> GSM751410 3 0.5837 0.2744 0.036 0.000 0.564 0.400
#> GSM751414 3 0.0657 0.6128 0.000 0.012 0.984 0.004
#> GSM751361 3 0.1209 0.6089 0.000 0.032 0.964 0.004
#> GSM751365 3 0.1004 0.6125 0.000 0.004 0.972 0.024
#> GSM751366 3 0.2281 0.5945 0.000 0.000 0.904 0.096
#> GSM751369 3 0.4955 0.2392 0.000 0.000 0.556 0.444
#> GSM751370 3 0.0712 0.6125 0.004 0.008 0.984 0.004
#> GSM751372 3 0.0469 0.6126 0.000 0.012 0.988 0.000
#> GSM751373 3 0.1890 0.6060 0.008 0.000 0.936 0.056
#> GSM751374 4 0.4956 0.4266 0.000 0.036 0.232 0.732
#> GSM751377 3 0.1635 0.6046 0.000 0.044 0.948 0.008
#> GSM751380 3 0.4817 0.3493 0.000 0.000 0.612 0.388
#> GSM751381 3 0.7318 0.2365 0.000 0.280 0.524 0.196
#> GSM751383 3 0.6969 0.3566 0.000 0.224 0.584 0.192
#> GSM751384 3 0.3745 0.5609 0.000 0.088 0.852 0.060
#> GSM751385 3 0.2871 0.6059 0.000 0.032 0.896 0.072
#> GSM751387 3 0.7231 0.2742 0.000 0.268 0.540 0.192
#> GSM751389 3 0.4925 0.2745 0.000 0.000 0.572 0.428
#> GSM751393 3 0.3444 0.5653 0.000 0.000 0.816 0.184
#> GSM751394 3 0.7098 0.3215 0.000 0.244 0.564 0.192
#> GSM751395 4 0.6616 0.1176 0.000 0.108 0.308 0.584
#> GSM751397 3 0.5849 0.4655 0.000 0.164 0.704 0.132
#> GSM751398 3 0.6690 0.3972 0.000 0.188 0.620 0.192
#> GSM751404 3 0.4679 0.4002 0.000 0.000 0.648 0.352
#> GSM751406 3 0.4955 0.2381 0.000 0.000 0.556 0.444
#> GSM751411 3 0.0469 0.6125 0.000 0.000 0.988 0.012
#> GSM751413 3 0.6420 0.3718 0.004 0.268 0.632 0.096
#> GSM751415 3 0.4761 0.3731 0.000 0.000 0.628 0.372
#> GSM751416 3 0.1305 0.6080 0.000 0.036 0.960 0.004
#> GSM751417 3 0.1305 0.6080 0.000 0.036 0.960 0.004
#> GSM751421 3 0.4817 0.3496 0.000 0.000 0.612 0.388
#> GSM751422 3 0.4661 0.4062 0.000 0.000 0.652 0.348
#> GSM751360 3 0.2888 0.5821 0.004 0.000 0.872 0.124
#> GSM751364 3 0.1109 0.6096 0.000 0.028 0.968 0.004
#> GSM751390 3 0.5151 0.5056 0.000 0.100 0.760 0.140
#> GSM751392 3 0.7369 0.1643 0.000 0.324 0.496 0.180
#> GSM751396 2 0.7488 0.1344 0.000 0.436 0.384 0.180
#> GSM751399 3 0.1302 0.6086 0.000 0.000 0.956 0.044
#> GSM751400 3 0.4697 0.3954 0.000 0.000 0.644 0.356
#> GSM751401 3 0.4817 0.3489 0.000 0.000 0.612 0.388
#> GSM751402 3 0.4933 0.2661 0.000 0.000 0.568 0.432
#> GSM751403 3 0.4543 0.4327 0.000 0.000 0.676 0.324
#> GSM751405 3 0.4888 0.3068 0.000 0.000 0.588 0.412
#> GSM751407 3 0.4431 0.4526 0.000 0.000 0.696 0.304
#> GSM751408 3 0.2530 0.5879 0.000 0.000 0.888 0.112
#> GSM751409 3 0.4431 0.4526 0.000 0.000 0.696 0.304
#> GSM751412 3 0.1867 0.6026 0.000 0.000 0.928 0.072
#> GSM751418 3 0.1059 0.6136 0.000 0.016 0.972 0.012
#> GSM751419 3 0.1059 0.6136 0.000 0.016 0.972 0.012
#> GSM751420 4 0.4898 0.1159 0.000 0.000 0.416 0.584
#> GSM751425 2 0.1109 0.7105 0.000 0.968 0.004 0.028
#> GSM751429 4 0.7092 0.5762 0.036 0.244 0.096 0.624
#> GSM751430 2 0.4608 0.6826 0.000 0.692 0.004 0.304
#> GSM751433 2 0.2654 0.7245 0.000 0.888 0.004 0.108
#> GSM751437 4 0.6567 0.5425 0.000 0.308 0.104 0.588
#> GSM751448 4 0.6999 0.5373 0.008 0.236 0.152 0.604
#> GSM751451 2 0.1284 0.7128 0.000 0.964 0.024 0.012
#> GSM751423 2 0.0672 0.7161 0.000 0.984 0.008 0.008
#> GSM751424 2 0.2466 0.7249 0.000 0.900 0.004 0.096
#> GSM751428 2 0.1576 0.7176 0.000 0.948 0.004 0.048
#> GSM751431 2 0.0592 0.7213 0.000 0.984 0.000 0.016
#> GSM751432 2 0.4220 0.7011 0.000 0.748 0.004 0.248
#> GSM751434 2 0.3982 0.7124 0.000 0.776 0.004 0.220
#> GSM751435 2 0.1389 0.7035 0.000 0.952 0.000 0.048
#> GSM751436 2 0.3908 0.7087 0.000 0.784 0.004 0.212
#> GSM751440 2 0.2399 0.6969 0.000 0.920 0.032 0.048
#> GSM751444 2 0.1867 0.6933 0.000 0.928 0.000 0.072
#> GSM751446 2 0.3837 0.5276 0.000 0.776 0.000 0.224
#> GSM751449 2 0.3074 0.6197 0.000 0.848 0.000 0.152
#> GSM751450 2 0.0469 0.7173 0.000 0.988 0.000 0.012
#> GSM751452 2 0.4053 0.7044 0.000 0.768 0.004 0.228
#> GSM751426 2 0.0657 0.7202 0.000 0.984 0.004 0.012
#> GSM751427 2 0.2796 0.6775 0.000 0.892 0.016 0.092
#> GSM751438 2 0.4761 0.2839 0.000 0.664 0.004 0.332
#> GSM751439 4 0.6129 0.4623 0.024 0.372 0.020 0.584
#> GSM751441 2 0.2542 0.6803 0.000 0.904 0.012 0.084
#> GSM751442 2 0.3688 0.5492 0.000 0.792 0.000 0.208
#> GSM751443 4 0.5773 0.4884 0.004 0.352 0.032 0.612
#> GSM751445 2 0.2149 0.6872 0.000 0.912 0.000 0.088
#> GSM751447 2 0.2081 0.6820 0.000 0.916 0.000 0.084
#> GSM751453 2 0.0921 0.7110 0.000 0.972 0.000 0.028
#> GSM751454 2 0.1118 0.7082 0.000 0.964 0.000 0.036
#> GSM751455 2 0.4164 0.4583 0.000 0.736 0.000 0.264
#> GSM751456 2 0.4277 0.4264 0.000 0.720 0.000 0.280
#> GSM751457 2 0.5678 -0.1749 0.000 0.524 0.024 0.452
#> GSM751458 2 0.5682 -0.1865 0.000 0.520 0.024 0.456
cbind(get_classes(res, k = 5), get_membership(res, k = 5))
#> class entropy silhouette p1 p2 p3 p4 p5
#> GSM751298 1 0.3366 0.62564 0.784 0.004 0.000 0.212 0.000
#> GSM751304 4 0.6757 0.02040 0.000 0.240 0.008 0.480 0.272
#> GSM751305 4 0.6141 0.08414 0.000 0.196 0.008 0.596 0.200
#> GSM751307 4 0.6774 -0.04320 0.000 0.288 0.000 0.392 0.320
#> GSM751310 4 0.4150 0.02721 0.388 0.000 0.000 0.612 0.000
#> GSM751314 4 0.4171 0.00919 0.396 0.000 0.000 0.604 0.000
#> GSM751316 4 0.4288 0.02908 0.384 0.000 0.004 0.612 0.000
#> GSM751318 1 0.4192 0.41594 0.596 0.000 0.000 0.404 0.000
#> GSM751342 4 0.4150 0.02721 0.388 0.000 0.000 0.612 0.000
#> GSM751346 1 0.5295 0.52797 0.732 0.144 0.064 0.060 0.000
#> GSM751347 1 0.4891 0.57288 0.780 0.032 0.040 0.028 0.120
#> GSM751348 2 0.8510 0.04383 0.152 0.352 0.008 0.296 0.192
#> GSM751349 5 0.3884 0.33719 0.000 0.288 0.000 0.004 0.708
#> GSM751352 4 0.7885 -0.04194 0.060 0.280 0.004 0.384 0.272
#> GSM751353 4 0.6792 -0.05637 0.000 0.296 0.000 0.380 0.324
#> GSM751354 4 0.8666 0.00451 0.136 0.196 0.024 0.392 0.252
#> GSM751355 4 0.7053 -0.05001 0.004 0.292 0.004 0.384 0.316
#> GSM751358 4 0.5058 0.02463 0.336 0.008 0.020 0.628 0.008
#> GSM751359 5 0.6371 0.38971 0.004 0.160 0.008 0.260 0.568
#> GSM751294 2 0.9583 0.20001 0.176 0.316 0.252 0.140 0.116
#> GSM751296 1 0.1787 0.67863 0.940 0.032 0.012 0.016 0.000
#> GSM751297 1 0.7183 0.38330 0.580 0.120 0.192 0.100 0.008
#> GSM751299 2 0.8411 0.08751 0.112 0.344 0.008 0.296 0.240
#> GSM751300 1 0.2989 0.64417 0.880 0.036 0.016 0.068 0.000
#> GSM751301 4 0.8121 -0.00741 0.108 0.252 0.000 0.376 0.264
#> GSM751302 1 0.4213 0.60101 0.808 0.048 0.036 0.108 0.000
#> GSM751303 4 0.4138 0.03213 0.384 0.000 0.000 0.616 0.000
#> GSM751306 4 0.4138 0.03213 0.384 0.000 0.000 0.616 0.000
#> GSM751308 1 0.8199 0.40988 0.448 0.112 0.168 0.256 0.016
#> GSM751309 4 0.4150 0.02721 0.388 0.000 0.000 0.612 0.000
#> GSM751311 4 0.4138 0.03213 0.384 0.000 0.000 0.616 0.000
#> GSM751312 4 0.4288 0.01309 0.384 0.000 0.004 0.612 0.000
#> GSM751313 1 0.0727 0.68327 0.980 0.004 0.004 0.012 0.000
#> GSM751315 1 0.4249 0.27997 0.568 0.000 0.000 0.432 0.000
#> GSM751317 4 0.4161 0.01814 0.392 0.000 0.000 0.608 0.000
#> GSM751320 1 0.3796 0.55579 0.700 0.000 0.000 0.300 0.000
#> GSM751321 4 0.4150 0.02721 0.388 0.000 0.000 0.612 0.000
#> GSM751322 1 0.4307 0.21615 0.500 0.000 0.000 0.500 0.000
#> GSM751324 1 0.4256 0.35784 0.564 0.000 0.000 0.436 0.000
#> GSM751325 1 0.4030 0.49465 0.648 0.000 0.000 0.352 0.000
#> GSM751332 1 0.3730 0.56643 0.712 0.000 0.000 0.288 0.000
#> GSM751334 1 0.3395 0.60448 0.764 0.000 0.000 0.236 0.000
#> GSM751339 1 0.3727 0.61708 0.768 0.000 0.016 0.216 0.000
#> GSM751341 4 0.4331 -0.00536 0.400 0.000 0.004 0.596 0.000
#> GSM751343 1 0.3876 0.53896 0.684 0.000 0.000 0.316 0.000
#> GSM751344 4 0.6788 -0.05476 0.000 0.296 0.000 0.384 0.320
#> GSM751345 4 0.6788 -0.05476 0.000 0.296 0.000 0.384 0.320
#> GSM751356 4 0.7602 0.07783 0.044 0.240 0.040 0.532 0.144
#> GSM751357 4 0.7131 0.01342 0.028 0.288 0.012 0.512 0.160
#> GSM751293 4 0.8274 0.04333 0.164 0.228 0.000 0.392 0.216
#> GSM751295 1 0.4717 0.58205 0.780 0.048 0.072 0.100 0.000
#> GSM751319 4 0.4150 0.02721 0.388 0.000 0.000 0.612 0.000
#> GSM751323 1 0.3752 0.56288 0.708 0.000 0.000 0.292 0.000
#> GSM751326 1 0.0880 0.67978 0.968 0.000 0.000 0.032 0.000
#> GSM751327 1 0.3837 0.54760 0.692 0.000 0.000 0.308 0.000
#> GSM751328 4 0.4273 -0.12479 0.448 0.000 0.000 0.552 0.000
#> GSM751329 1 0.1478 0.67375 0.936 0.000 0.000 0.064 0.000
#> GSM751330 1 0.0992 0.68165 0.968 0.008 0.000 0.024 0.000
#> GSM751331 1 0.4221 0.51875 0.756 0.020 0.008 0.212 0.004
#> GSM751333 1 0.0880 0.68282 0.968 0.000 0.000 0.032 0.000
#> GSM751335 1 0.0880 0.68260 0.968 0.000 0.000 0.032 0.000
#> GSM751336 1 0.1799 0.66997 0.940 0.020 0.012 0.028 0.000
#> GSM751337 1 0.0981 0.68334 0.972 0.012 0.008 0.008 0.000
#> GSM751338 1 0.2561 0.65222 0.856 0.000 0.000 0.144 0.000
#> GSM751340 1 0.5044 0.33275 0.556 0.000 0.408 0.036 0.000
#> GSM751350 1 0.4082 0.59362 0.804 0.032 0.028 0.136 0.000
#> GSM751351 1 0.3959 0.59345 0.808 0.028 0.024 0.140 0.000
#> GSM751362 3 0.1934 0.74755 0.004 0.000 0.928 0.016 0.052
#> GSM751363 5 0.6172 0.47043 0.000 0.000 0.176 0.280 0.544
#> GSM751367 3 0.4331 0.52746 0.292 0.008 0.692 0.004 0.004
#> GSM751368 5 0.4877 0.53362 0.000 0.024 0.312 0.012 0.652
#> GSM751371 3 0.3607 0.65309 0.028 0.008 0.820 0.144 0.000
#> GSM751375 5 0.6211 -0.00479 0.000 0.324 0.008 0.128 0.540
#> GSM751376 3 0.5083 0.60277 0.012 0.044 0.768 0.072 0.104
#> GSM751378 5 0.3950 0.64730 0.000 0.068 0.136 0.000 0.796
#> GSM751379 3 0.3758 0.66967 0.004 0.028 0.844 0.044 0.080
#> GSM751382 5 0.2753 0.62362 0.000 0.136 0.008 0.000 0.856
#> GSM751386 5 0.2260 0.67829 0.000 0.064 0.028 0.000 0.908
#> GSM751388 5 0.2260 0.67829 0.000 0.064 0.028 0.000 0.908
#> GSM751391 3 0.2370 0.72862 0.000 0.000 0.904 0.056 0.040
#> GSM751410 3 0.1686 0.74571 0.028 0.000 0.944 0.020 0.008
#> GSM751414 5 0.4256 0.36101 0.000 0.000 0.436 0.000 0.564
#> GSM751361 5 0.4251 0.48127 0.000 0.004 0.372 0.000 0.624
#> GSM751365 3 0.5457 -0.19594 0.000 0.000 0.480 0.060 0.460
#> GSM751366 3 0.3480 0.52686 0.000 0.000 0.752 0.000 0.248
#> GSM751369 3 0.1278 0.74461 0.004 0.000 0.960 0.020 0.016
#> GSM751370 5 0.4304 0.24631 0.000 0.000 0.484 0.000 0.516
#> GSM751372 5 0.5137 0.34650 0.000 0.000 0.424 0.040 0.536
#> GSM751373 3 0.4114 0.21724 0.000 0.000 0.624 0.000 0.376
#> GSM751374 3 0.5595 0.53397 0.004 0.040 0.712 0.096 0.148
#> GSM751377 5 0.4283 0.51354 0.000 0.008 0.348 0.000 0.644
#> GSM751380 3 0.0794 0.75262 0.000 0.000 0.972 0.000 0.028
#> GSM751381 5 0.2110 0.67532 0.000 0.072 0.016 0.000 0.912
#> GSM751383 5 0.2378 0.67859 0.000 0.048 0.048 0.000 0.904
#> GSM751384 5 0.4355 0.61181 0.000 0.044 0.224 0.000 0.732
#> GSM751385 3 0.6565 0.17169 0.000 0.028 0.536 0.124 0.312
#> GSM751387 5 0.2270 0.67410 0.000 0.076 0.020 0.000 0.904
#> GSM751389 3 0.0566 0.75102 0.000 0.004 0.984 0.000 0.012
#> GSM751393 3 0.3039 0.69623 0.000 0.000 0.836 0.012 0.152
#> GSM751394 5 0.2236 0.67648 0.000 0.068 0.024 0.000 0.908
#> GSM751395 3 0.6876 0.15752 0.000 0.008 0.448 0.272 0.272
#> GSM751397 5 0.3115 0.67063 0.000 0.036 0.112 0.000 0.852
#> GSM751398 5 0.2491 0.67739 0.000 0.036 0.068 0.000 0.896
#> GSM751404 3 0.1043 0.75032 0.000 0.000 0.960 0.000 0.040
#> GSM751406 3 0.0324 0.75087 0.004 0.000 0.992 0.004 0.000
#> GSM751411 3 0.4307 -0.22209 0.000 0.000 0.504 0.000 0.496
#> GSM751413 5 0.8308 0.16221 0.000 0.132 0.240 0.308 0.320
#> GSM751415 3 0.0794 0.75262 0.000 0.000 0.972 0.000 0.028
#> GSM751416 5 0.4151 0.51743 0.000 0.004 0.344 0.000 0.652
#> GSM751417 5 0.4182 0.50870 0.000 0.004 0.352 0.000 0.644
#> GSM751421 3 0.0451 0.75350 0.000 0.000 0.988 0.008 0.004
#> GSM751422 3 0.1493 0.75094 0.000 0.000 0.948 0.028 0.024
#> GSM751360 3 0.4164 0.63096 0.000 0.000 0.784 0.120 0.096
#> GSM751364 5 0.4264 0.47544 0.000 0.004 0.376 0.000 0.620
#> GSM751390 5 0.3649 0.65592 0.000 0.040 0.152 0.000 0.808
#> GSM751392 5 0.2900 0.66767 0.000 0.108 0.028 0.000 0.864
#> GSM751396 5 0.3236 0.60973 0.000 0.152 0.020 0.000 0.828
#> GSM751399 3 0.4030 0.28983 0.000 0.000 0.648 0.000 0.352
#> GSM751400 3 0.1270 0.74598 0.000 0.000 0.948 0.000 0.052
#> GSM751401 3 0.0794 0.75279 0.000 0.000 0.972 0.000 0.028
#> GSM751402 3 0.0324 0.75169 0.004 0.000 0.992 0.000 0.004
#> GSM751403 3 0.0963 0.75127 0.000 0.000 0.964 0.000 0.036
#> GSM751405 3 0.0162 0.75216 0.000 0.000 0.996 0.000 0.004
#> GSM751407 3 0.2074 0.70940 0.000 0.000 0.896 0.000 0.104
#> GSM751408 3 0.3424 0.53849 0.000 0.000 0.760 0.000 0.240
#> GSM751409 3 0.1478 0.73951 0.000 0.000 0.936 0.000 0.064
#> GSM751412 3 0.3774 0.42939 0.000 0.000 0.704 0.000 0.296
#> GSM751418 5 0.4307 0.20173 0.000 0.000 0.496 0.000 0.504
#> GSM751419 5 0.4306 0.21438 0.000 0.000 0.492 0.000 0.508
#> GSM751420 3 0.1721 0.73111 0.028 0.020 0.944 0.004 0.004
#> GSM751425 2 0.1430 0.73773 0.000 0.944 0.000 0.004 0.052
#> GSM751429 3 0.6535 0.17102 0.168 0.328 0.496 0.008 0.000
#> GSM751430 4 0.6939 -0.06670 0.000 0.296 0.004 0.364 0.336
#> GSM751433 2 0.5973 0.46527 0.000 0.580 0.000 0.256 0.164
#> GSM751437 2 0.5364 0.11044 0.036 0.496 0.460 0.008 0.000
#> GSM751448 3 0.5217 0.37339 0.056 0.288 0.648 0.008 0.000
#> GSM751451 2 0.4219 0.63751 0.000 0.780 0.000 0.104 0.116
#> GSM751423 2 0.1197 0.73811 0.000 0.952 0.000 0.000 0.048
#> GSM751424 2 0.5862 0.48904 0.000 0.604 0.000 0.220 0.176
#> GSM751428 2 0.4069 0.65727 0.000 0.788 0.000 0.136 0.076
#> GSM751431 2 0.3390 0.69038 0.000 0.840 0.000 0.100 0.060
#> GSM751432 2 0.6758 0.21036 0.000 0.404 0.000 0.292 0.304
#> GSM751434 2 0.6634 0.28887 0.000 0.452 0.000 0.288 0.260
#> GSM751435 2 0.0671 0.74236 0.000 0.980 0.000 0.004 0.016
#> GSM751436 2 0.6586 0.30989 0.000 0.464 0.000 0.244 0.292
#> GSM751440 2 0.0963 0.74073 0.000 0.964 0.000 0.000 0.036
#> GSM751444 2 0.1082 0.74033 0.000 0.964 0.000 0.028 0.008
#> GSM751446 2 0.0324 0.73986 0.000 0.992 0.004 0.004 0.000
#> GSM751449 2 0.0613 0.74010 0.000 0.984 0.008 0.004 0.004
#> GSM751450 2 0.2850 0.70615 0.000 0.872 0.000 0.092 0.036
#> GSM751452 2 0.6661 0.27276 0.000 0.440 0.000 0.256 0.304
#> GSM751426 2 0.3303 0.69647 0.000 0.848 0.000 0.076 0.076
#> GSM751427 2 0.1205 0.73956 0.000 0.956 0.004 0.000 0.040
#> GSM751438 2 0.2193 0.69411 0.000 0.900 0.092 0.008 0.000
#> GSM751439 2 0.4743 0.51872 0.048 0.700 0.248 0.004 0.000
#> GSM751441 2 0.0324 0.74139 0.000 0.992 0.000 0.004 0.004
#> GSM751442 2 0.0579 0.73861 0.000 0.984 0.008 0.008 0.000
#> GSM751443 2 0.5523 0.30248 0.064 0.564 0.368 0.004 0.000
#> GSM751445 2 0.0671 0.74218 0.000 0.980 0.000 0.016 0.004
#> GSM751447 2 0.0324 0.74139 0.000 0.992 0.000 0.004 0.004
#> GSM751453 2 0.1493 0.73731 0.000 0.948 0.000 0.024 0.028
#> GSM751454 2 0.1300 0.73906 0.000 0.956 0.000 0.016 0.028
#> GSM751455 2 0.0833 0.73597 0.004 0.976 0.016 0.004 0.000
#> GSM751456 2 0.1116 0.73135 0.004 0.964 0.028 0.004 0.000
#> GSM751457 2 0.3597 0.62387 0.000 0.800 0.180 0.008 0.012
#> GSM751458 2 0.3597 0.62531 0.000 0.800 0.180 0.008 0.012
cbind(get_classes(res, k = 6), get_membership(res, k = 6))
#> class entropy silhouette p1 p2 p3 p4 p5 p6
#> GSM751298 4 0.4314 0.1273 0.484 0.000 0.000 0.500 0.004 0.012
#> GSM751304 6 0.1894 0.8146 0.016 0.000 0.012 0.040 0.004 0.928
#> GSM751305 6 0.2187 0.8093 0.012 0.000 0.012 0.064 0.004 0.908
#> GSM751307 6 0.1635 0.8184 0.016 0.004 0.004 0.008 0.024 0.944
#> GSM751310 4 0.0665 0.8019 0.008 0.000 0.004 0.980 0.000 0.008
#> GSM751314 4 0.0363 0.8024 0.012 0.000 0.000 0.988 0.000 0.000
#> GSM751316 4 0.0508 0.7966 0.000 0.000 0.004 0.984 0.000 0.012
#> GSM751318 4 0.3287 0.6821 0.220 0.000 0.000 0.768 0.000 0.012
#> GSM751342 4 0.0520 0.8017 0.008 0.000 0.000 0.984 0.000 0.008
#> GSM751346 1 0.2143 0.8323 0.924 0.016 0.020 0.020 0.004 0.016
#> GSM751347 1 0.2512 0.8214 0.896 0.008 0.004 0.028 0.060 0.004
#> GSM751348 2 0.8920 -0.0382 0.168 0.300 0.004 0.192 0.156 0.180
#> GSM751349 5 0.3316 0.6874 0.020 0.056 0.000 0.000 0.840 0.084
#> GSM751352 6 0.2485 0.8012 0.084 0.008 0.000 0.000 0.024 0.884
#> GSM751353 6 0.1924 0.8121 0.028 0.004 0.000 0.000 0.048 0.920
#> GSM751354 6 0.1647 0.8168 0.032 0.004 0.016 0.000 0.008 0.940
#> GSM751355 6 0.1456 0.8190 0.020 0.008 0.004 0.004 0.012 0.952
#> GSM751358 4 0.1858 0.7536 0.016 0.000 0.004 0.932 0.024 0.024
#> GSM751359 5 0.5035 0.5760 0.016 0.004 0.004 0.256 0.660 0.060
#> GSM751294 2 0.8455 0.0325 0.244 0.344 0.132 0.000 0.096 0.184
#> GSM751296 1 0.3588 0.8213 0.828 0.028 0.012 0.112 0.004 0.016
#> GSM751297 1 0.3406 0.7461 0.848 0.032 0.064 0.000 0.008 0.048
#> GSM751299 6 0.5294 0.6439 0.144 0.156 0.000 0.000 0.032 0.668
#> GSM751300 1 0.1434 0.8558 0.940 0.000 0.000 0.048 0.000 0.012
#> GSM751301 6 0.1802 0.8047 0.072 0.000 0.000 0.000 0.012 0.916
#> GSM751302 1 0.2156 0.8395 0.920 0.008 0.008 0.032 0.004 0.028
#> GSM751303 4 0.0405 0.7990 0.000 0.000 0.004 0.988 0.000 0.008
#> GSM751306 4 0.0405 0.8018 0.004 0.000 0.000 0.988 0.000 0.008
#> GSM751308 1 0.7717 -0.1015 0.372 0.032 0.124 0.364 0.012 0.096
#> GSM751309 4 0.0260 0.8005 0.000 0.000 0.000 0.992 0.000 0.008
#> GSM751311 4 0.0508 0.8005 0.004 0.000 0.000 0.984 0.000 0.012
#> GSM751312 4 0.1053 0.7909 0.020 0.000 0.004 0.964 0.000 0.012
#> GSM751313 1 0.1714 0.8540 0.908 0.000 0.000 0.092 0.000 0.000
#> GSM751315 4 0.3841 0.3030 0.380 0.000 0.000 0.616 0.000 0.004
#> GSM751317 4 0.0405 0.8025 0.008 0.000 0.000 0.988 0.000 0.004
#> GSM751320 4 0.3923 0.4720 0.372 0.000 0.000 0.620 0.000 0.008
#> GSM751321 4 0.0405 0.8018 0.004 0.000 0.000 0.988 0.000 0.008
#> GSM751322 4 0.2593 0.7422 0.148 0.000 0.000 0.844 0.000 0.008
#> GSM751324 4 0.2882 0.7188 0.180 0.000 0.000 0.812 0.000 0.008
#> GSM751325 4 0.3653 0.5862 0.300 0.000 0.000 0.692 0.000 0.008
#> GSM751332 4 0.3911 0.4771 0.368 0.000 0.000 0.624 0.000 0.008
#> GSM751334 1 0.3847 0.4260 0.644 0.000 0.000 0.348 0.000 0.008
#> GSM751339 1 0.5081 0.2086 0.544 0.000 0.072 0.380 0.000 0.004
#> GSM751341 4 0.0993 0.8001 0.024 0.000 0.000 0.964 0.000 0.012
#> GSM751343 4 0.3992 0.4860 0.364 0.000 0.000 0.624 0.000 0.012
#> GSM751344 6 0.1232 0.8178 0.016 0.004 0.000 0.000 0.024 0.956
#> GSM751345 6 0.1232 0.8178 0.016 0.004 0.000 0.000 0.024 0.956
#> GSM751356 6 0.7257 0.4921 0.036 0.140 0.028 0.244 0.036 0.516
#> GSM751357 6 0.6710 0.5717 0.040 0.172 0.008 0.164 0.036 0.580
#> GSM751293 6 0.3801 0.7349 0.136 0.004 0.000 0.036 0.024 0.800
#> GSM751295 1 0.2006 0.8272 0.928 0.008 0.032 0.012 0.004 0.016
#> GSM751319 4 0.0520 0.8016 0.008 0.000 0.000 0.984 0.000 0.008
#> GSM751323 4 0.4025 0.3611 0.416 0.000 0.000 0.576 0.000 0.008
#> GSM751326 1 0.2100 0.8413 0.884 0.000 0.000 0.112 0.000 0.004
#> GSM751327 4 0.3934 0.4613 0.376 0.000 0.000 0.616 0.000 0.008
#> GSM751328 4 0.1643 0.7849 0.068 0.000 0.000 0.924 0.000 0.008
#> GSM751329 1 0.2346 0.8289 0.868 0.000 0.000 0.124 0.000 0.008
#> GSM751330 1 0.1663 0.8553 0.912 0.000 0.000 0.088 0.000 0.000
#> GSM751331 1 0.2255 0.8256 0.892 0.000 0.000 0.028 0.000 0.080
#> GSM751333 1 0.1806 0.8555 0.908 0.000 0.000 0.088 0.000 0.004
#> GSM751335 1 0.1714 0.8541 0.908 0.000 0.000 0.092 0.000 0.000
#> GSM751336 1 0.1644 0.8568 0.920 0.000 0.000 0.076 0.000 0.004
#> GSM751337 1 0.1858 0.8536 0.904 0.000 0.000 0.092 0.000 0.004
#> GSM751338 1 0.2805 0.7617 0.812 0.000 0.000 0.184 0.000 0.004
#> GSM751340 3 0.4893 0.1220 0.400 0.000 0.536 0.064 0.000 0.000
#> GSM751350 1 0.1408 0.8507 0.944 0.000 0.000 0.036 0.000 0.020
#> GSM751351 1 0.1528 0.8551 0.936 0.000 0.000 0.048 0.000 0.016
#> GSM751362 3 0.2400 0.8099 0.024 0.000 0.896 0.016 0.064 0.000
#> GSM751363 5 0.6875 0.3955 0.024 0.000 0.076 0.108 0.500 0.292
#> GSM751367 3 0.3907 0.6362 0.268 0.000 0.704 0.000 0.000 0.028
#> GSM751368 5 0.4518 0.6900 0.024 0.004 0.236 0.000 0.704 0.032
#> GSM751371 3 0.2846 0.7850 0.020 0.000 0.864 0.100 0.004 0.012
#> GSM751375 5 0.5299 0.2655 0.024 0.036 0.016 0.000 0.596 0.328
#> GSM751376 3 0.3909 0.6667 0.024 0.012 0.756 0.004 0.000 0.204
#> GSM751378 5 0.3369 0.7460 0.016 0.024 0.084 0.000 0.848 0.028
#> GSM751379 3 0.3317 0.7241 0.016 0.012 0.804 0.000 0.000 0.168
#> GSM751382 5 0.2088 0.7609 0.016 0.024 0.004 0.000 0.920 0.036
#> GSM751386 5 0.1167 0.7850 0.012 0.000 0.008 0.000 0.960 0.020
#> GSM751388 5 0.1148 0.7900 0.004 0.000 0.016 0.000 0.960 0.020
#> GSM751391 3 0.2001 0.8156 0.020 0.000 0.920 0.016 0.000 0.044
#> GSM751410 3 0.1370 0.8256 0.036 0.000 0.948 0.012 0.000 0.004
#> GSM751414 5 0.3879 0.6410 0.020 0.000 0.292 0.000 0.688 0.000
#> GSM751361 5 0.3253 0.7381 0.020 0.000 0.192 0.000 0.788 0.000
#> GSM751365 5 0.5419 0.5128 0.020 0.000 0.324 0.084 0.572 0.000
#> GSM751366 3 0.3514 0.6226 0.020 0.000 0.752 0.000 0.228 0.000
#> GSM751369 3 0.1282 0.8223 0.024 0.004 0.956 0.004 0.000 0.012
#> GSM751370 5 0.3998 0.5768 0.016 0.000 0.340 0.000 0.644 0.000
#> GSM751372 5 0.4096 0.6654 0.020 0.000 0.268 0.012 0.700 0.000
#> GSM751373 3 0.4237 0.1776 0.020 0.000 0.584 0.000 0.396 0.000
#> GSM751374 3 0.4381 0.5733 0.020 0.020 0.692 0.000 0.004 0.264
#> GSM751377 5 0.2945 0.7597 0.020 0.000 0.156 0.000 0.824 0.000
#> GSM751380 3 0.1480 0.8215 0.020 0.000 0.940 0.000 0.040 0.000
#> GSM751381 5 0.1377 0.7784 0.016 0.004 0.004 0.000 0.952 0.024
#> GSM751383 5 0.1053 0.7885 0.004 0.000 0.012 0.000 0.964 0.020
#> GSM751384 5 0.1053 0.7928 0.012 0.004 0.020 0.000 0.964 0.000
#> GSM751385 3 0.6063 0.0751 0.032 0.000 0.444 0.000 0.116 0.408
#> GSM751387 5 0.1647 0.7765 0.016 0.004 0.008 0.000 0.940 0.032
#> GSM751389 3 0.1262 0.8288 0.016 0.000 0.956 0.000 0.020 0.008
#> GSM751393 3 0.3878 0.7628 0.016 0.000 0.800 0.004 0.112 0.068
#> GSM751394 5 0.1167 0.7850 0.012 0.000 0.008 0.000 0.960 0.020
#> GSM751395 6 0.4299 0.6730 0.004 0.008 0.200 0.020 0.024 0.744
#> GSM751397 5 0.0767 0.7906 0.012 0.000 0.008 0.000 0.976 0.004
#> GSM751398 5 0.1275 0.7906 0.012 0.000 0.016 0.000 0.956 0.016
#> GSM751404 3 0.1528 0.8178 0.016 0.000 0.936 0.000 0.048 0.000
#> GSM751406 3 0.0972 0.8240 0.028 0.000 0.964 0.000 0.000 0.008
#> GSM751411 5 0.4039 0.5549 0.016 0.000 0.352 0.000 0.632 0.000
#> GSM751413 6 0.4390 0.6700 0.008 0.000 0.160 0.024 0.052 0.756
#> GSM751415 3 0.1461 0.8223 0.016 0.000 0.940 0.000 0.044 0.000
#> GSM751416 5 0.2945 0.7594 0.020 0.000 0.156 0.000 0.824 0.000
#> GSM751417 5 0.2945 0.7593 0.020 0.000 0.156 0.000 0.824 0.000
#> GSM751421 3 0.1180 0.8246 0.024 0.000 0.960 0.004 0.004 0.008
#> GSM751422 3 0.1312 0.8254 0.020 0.000 0.956 0.012 0.004 0.008
#> GSM751360 3 0.3118 0.7948 0.020 0.000 0.860 0.084 0.024 0.012
#> GSM751364 5 0.3253 0.7386 0.020 0.000 0.192 0.000 0.788 0.000
#> GSM751390 5 0.1078 0.7915 0.012 0.000 0.016 0.000 0.964 0.008
#> GSM751392 5 0.1672 0.7818 0.016 0.004 0.012 0.000 0.940 0.028
#> GSM751396 5 0.2189 0.7636 0.016 0.020 0.008 0.000 0.916 0.040
#> GSM751399 3 0.3541 0.6148 0.020 0.000 0.748 0.000 0.232 0.000
#> GSM751400 3 0.1082 0.8255 0.004 0.000 0.956 0.000 0.040 0.000
#> GSM751401 3 0.1082 0.8260 0.004 0.000 0.956 0.000 0.040 0.000
#> GSM751402 3 0.1180 0.8272 0.024 0.004 0.960 0.000 0.008 0.004
#> GSM751403 3 0.1408 0.8258 0.020 0.000 0.944 0.000 0.036 0.000
#> GSM751405 3 0.1074 0.8274 0.012 0.000 0.960 0.000 0.028 0.000
#> GSM751407 3 0.1625 0.8137 0.012 0.000 0.928 0.000 0.060 0.000
#> GSM751408 3 0.2402 0.7671 0.012 0.000 0.868 0.000 0.120 0.000
#> GSM751409 3 0.0937 0.8257 0.000 0.000 0.960 0.000 0.040 0.000
#> GSM751412 3 0.3629 0.5657 0.016 0.000 0.724 0.000 0.260 0.000
#> GSM751418 5 0.4167 0.5149 0.020 0.000 0.368 0.000 0.612 0.000
#> GSM751419 5 0.4167 0.5149 0.020 0.000 0.368 0.000 0.612 0.000
#> GSM751420 3 0.1483 0.8200 0.036 0.012 0.944 0.000 0.000 0.008
#> GSM751425 2 0.1741 0.8402 0.012 0.936 0.008 0.000 0.036 0.008
#> GSM751429 3 0.5486 0.5238 0.244 0.156 0.592 0.000 0.000 0.008
#> GSM751430 6 0.2377 0.8092 0.008 0.032 0.004 0.008 0.040 0.908
#> GSM751433 6 0.5500 0.4341 0.004 0.336 0.004 0.044 0.036 0.576
#> GSM751437 2 0.4254 0.2999 0.020 0.576 0.404 0.000 0.000 0.000
#> GSM751448 3 0.3728 0.6764 0.044 0.180 0.772 0.000 0.000 0.004
#> GSM751451 2 0.3803 0.7044 0.004 0.788 0.000 0.156 0.040 0.012
#> GSM751423 2 0.1237 0.8417 0.004 0.956 0.000 0.000 0.020 0.020
#> GSM751424 6 0.4884 0.4514 0.004 0.340 0.004 0.004 0.044 0.604
#> GSM751428 2 0.4122 0.4649 0.004 0.660 0.000 0.000 0.020 0.316
#> GSM751431 2 0.3705 0.6318 0.004 0.748 0.000 0.000 0.024 0.224
#> GSM751432 6 0.3600 0.7613 0.004 0.124 0.004 0.008 0.044 0.816
#> GSM751434 6 0.3667 0.7526 0.008 0.140 0.004 0.008 0.032 0.808
#> GSM751435 2 0.0862 0.8465 0.004 0.972 0.000 0.000 0.008 0.016
#> GSM751436 6 0.4398 0.6770 0.004 0.208 0.004 0.004 0.056 0.724
#> GSM751440 2 0.0665 0.8479 0.004 0.980 0.000 0.000 0.008 0.008
#> GSM751444 2 0.1226 0.8370 0.004 0.952 0.000 0.000 0.004 0.040
#> GSM751446 2 0.0146 0.8497 0.004 0.996 0.000 0.000 0.000 0.000
#> GSM751449 2 0.0146 0.8495 0.000 0.996 0.000 0.000 0.004 0.000
#> GSM751450 2 0.3154 0.6971 0.004 0.800 0.000 0.000 0.012 0.184
#> GSM751452 6 0.4390 0.6943 0.004 0.192 0.004 0.008 0.056 0.736
#> GSM751426 2 0.3781 0.6500 0.004 0.756 0.000 0.000 0.036 0.204
#> GSM751427 2 0.0806 0.8469 0.000 0.972 0.000 0.000 0.020 0.008
#> GSM751438 2 0.0964 0.8457 0.016 0.968 0.012 0.000 0.004 0.000
#> GSM751439 2 0.0993 0.8428 0.012 0.964 0.024 0.000 0.000 0.000
#> GSM751441 2 0.0964 0.8457 0.016 0.968 0.012 0.000 0.004 0.000
#> GSM751442 2 0.0405 0.8495 0.008 0.988 0.004 0.000 0.000 0.000
#> GSM751443 2 0.3261 0.6705 0.016 0.780 0.204 0.000 0.000 0.000
#> GSM751445 2 0.0405 0.8487 0.000 0.988 0.000 0.000 0.004 0.008
#> GSM751447 2 0.0964 0.8457 0.016 0.968 0.012 0.000 0.004 0.000
#> GSM751453 2 0.1282 0.8445 0.004 0.956 0.004 0.000 0.012 0.024
#> GSM751454 2 0.1007 0.8484 0.004 0.968 0.004 0.000 0.008 0.016
#> GSM751455 2 0.0363 0.8494 0.012 0.988 0.000 0.000 0.000 0.000
#> GSM751456 2 0.0363 0.8495 0.012 0.988 0.000 0.000 0.000 0.000
#> GSM751457 2 0.1608 0.8336 0.016 0.940 0.036 0.000 0.004 0.004
#> GSM751458 2 0.1534 0.8360 0.016 0.944 0.032 0.000 0.004 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)
#> Error in mat[ceiling(1:nr/h_ratio), ceiling(1:nc/w_ratio), drop = FALSE]: subscript out of bounds
get_signatures(res, k = 6, scale_rows = FALSE)
Compare the overlap of signatures from different k:
compare_signatures(res)
get_signature() returns a data frame invisibly. TO get the list of signatures, the function
call should be assigned to a variable explicitly. In following code, if plot argument is set
to FALSE, no heatmap is plotted while only the differential analysis is performed.
# code only for demonstration
tb = get_signature(res, k = ..., plot = FALSE)
An example of the output of tb is:
#> which_row fdr mean_1 mean_2 scaled_mean_1 scaled_mean_2 km
#> 1 38 0.042760348 8.373488 9.131774 -0.5533452 0.5164555 1
#> 2 40 0.018707592 7.106213 8.469186 -0.6173731 0.5762149 1
#> 3 55 0.019134737 10.221463 11.207825 -0.6159697 0.5749050 1
#> 4 59 0.006059896 5.921854 7.869574 -0.6899429 0.6439467 1
#> 5 60 0.018055526 8.928898 10.211722 -0.6204761 0.5791110 1
#> 6 98 0.009384629 15.714769 14.887706 0.6635654 -0.6193277 2
...
The columns in tb are:
which_row: row indices corresponding to the input matrix.fdr: FDR for the differential test. mean_x: The mean value in group x.scaled_mean_x: The mean value in group x after rows are scaled.km: Row groups if k-means clustering is applied to rows.UMAP plot which shows how samples are separated.
dimension_reduction(res, k = 2, method = "UMAP")
dimension_reduction(res, k = 3, method = "UMAP")
dimension_reduction(res, k = 4, method = "UMAP")
dimension_reduction(res, k = 5, method = "UMAP")
dimension_reduction(res, k = 6, method = "UMAP")
Following heatmap shows how subgroups are split when increasing k:
collect_classes(res)
Test correlation between subgroups and known annotations. If the known annotation is numeric, one-way ANOVA test is applied, and if the known annotation is discrete, chi-squared contingency table test is applied.
test_to_known_factors(res)
#> n tissue(p) disease.state(p) agent(p) k
#> CV:NMF 157 1.94e-23 0.56581 0.735064 2
#> CV:NMF 144 2.23e-37 0.19944 0.482350 3
#> CV:NMF 113 4.21e-31 0.00903 0.051045 4
#> CV:NMF 97 3.59e-39 0.20309 0.117011 5
#> CV:NMF 144 3.69e-44 0.10057 0.000498 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 4537 rows and 166 columns.
#> Top rows (454, 908, 1361, 1814, 2268) are extracted by 'MAD' method.
#> Subgroups are detected by 'hclust' method.
#> Performed in total 1250 partitions by row resampling.
#> Best k for subgroups seems to be 3.
#>
#> Following methods can be applied to this 'ConsensusPartition' object:
#> [1] "cola_report" "collect_classes" "collect_plots"
#> [4] "collect_stats" "colnames" "compare_signatures"
#> [7] "consensus_heatmap" "dimension_reduction" "functional_enrichment"
#> [10] "get_anno_col" "get_anno" "get_classes"
#> [13] "get_consensus" "get_matrix" "get_membership"
#> [16] "get_param" "get_signatures" "get_stats"
#> [19] "is_best_k" "is_stable_k" "membership_heatmap"
#> [22] "ncol" "nrow" "plot_ecdf"
#> [25] "rownames" "select_partition_number" "show"
#> [28] "suggest_best_k" "test_to_known_factors"
collect_plots() function collects all the plots made from res for all k (number of partitions)
into one single page to provide an easy and fast comparison between different k.
collect_plots(res)
The plots are:
k and the heatmap of
predicted classes for each k.k.k.k.All the plots in panels can be made by individual functions and they are plotted later in this section.
select_partition_number() produces several plots showing different
statistics for choosing “optimized” k. There are following statistics:
k;k, the area increased is defined as \(A_k - A_{k-1}\).The detailed explanations of these statistics can be found in the cola vignette.
Generally speaking, lower PAC score, higher mean silhouette score or higher
concordance corresponds to better partition. Rand index and Jaccard index
measure how similar the current partition is compared to partition with k-1.
If they are too similar, we won't accept k is better than k-1.
select_partition_number(res)
The numeric values for all these statistics can be obtained by get_stats().
get_stats(res)
#> k 1-PAC mean_silhouette concordance area_increased Rand Jaccard
#> 2 2 0.0469 0.689 0.754 0.3634 0.796 0.796
#> 3 3 0.0521 0.379 0.634 0.5726 0.663 0.580
#> 4 4 0.1703 0.429 0.629 0.1504 0.814 0.637
#> 5 5 0.2769 0.412 0.599 0.0905 0.916 0.781
#> 6 6 0.3499 0.360 0.580 0.0634 0.914 0.746
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
#> GSM751298 1 0.697 0.832 0.812 0.188
#> GSM751304 2 0.738 0.756 0.208 0.792
#> GSM751305 2 0.738 0.756 0.208 0.792
#> GSM751307 2 0.833 0.710 0.264 0.736
#> GSM751310 2 0.866 0.653 0.288 0.712
#> GSM751314 2 0.844 0.666 0.272 0.728
#> GSM751316 2 0.881 0.656 0.300 0.700
#> GSM751318 2 0.469 0.755 0.100 0.900
#> GSM751342 2 0.456 0.755 0.096 0.904
#> GSM751346 1 0.615 0.831 0.848 0.152
#> GSM751347 1 0.615 0.831 0.848 0.152
#> GSM751348 2 0.469 0.747 0.100 0.900
#> GSM751349 2 0.430 0.750 0.088 0.912
#> GSM751352 2 0.584 0.737 0.140 0.860
#> GSM751353 2 0.552 0.744 0.128 0.872
#> GSM751354 2 0.855 0.681 0.280 0.720
#> GSM751355 2 0.855 0.681 0.280 0.720
#> GSM751358 2 0.662 0.761 0.172 0.828
#> GSM751359 2 0.662 0.761 0.172 0.828
#> GSM751294 2 0.680 0.751 0.180 0.820
#> GSM751296 1 0.871 0.734 0.708 0.292
#> GSM751297 1 0.653 0.835 0.832 0.168
#> GSM751299 2 0.634 0.730 0.160 0.840
#> GSM751300 1 0.697 0.832 0.812 0.188
#> GSM751301 2 0.662 0.711 0.172 0.828
#> GSM751302 1 0.625 0.832 0.844 0.156
#> GSM751303 2 0.844 0.678 0.272 0.728
#> GSM751306 2 0.839 0.668 0.268 0.732
#> GSM751308 2 0.730 0.748 0.204 0.796
#> GSM751309 2 0.760 0.715 0.220 0.780
#> GSM751311 2 0.760 0.715 0.220 0.780
#> GSM751312 2 0.881 0.656 0.300 0.700
#> GSM751313 1 0.876 0.777 0.704 0.296
#> GSM751315 2 0.921 0.571 0.336 0.664
#> GSM751317 2 0.886 0.615 0.304 0.696
#> GSM751320 2 0.963 0.404 0.388 0.612
#> GSM751321 2 0.886 0.619 0.304 0.696
#> GSM751322 2 0.891 0.562 0.308 0.692
#> GSM751324 2 0.745 0.695 0.212 0.788
#> GSM751325 2 0.821 0.616 0.256 0.744
#> GSM751332 2 0.904 0.600 0.320 0.680
#> GSM751334 2 0.904 0.600 0.320 0.680
#> GSM751339 2 0.985 0.453 0.428 0.572
#> GSM751341 1 0.949 0.555 0.632 0.368
#> GSM751343 2 0.634 0.737 0.160 0.840
#> GSM751344 2 0.615 0.723 0.152 0.848
#> GSM751345 2 0.615 0.723 0.152 0.848
#> GSM751356 2 0.634 0.740 0.160 0.840
#> GSM751357 2 0.634 0.740 0.160 0.840
#> GSM751293 2 0.662 0.711 0.172 0.828
#> GSM751295 1 0.625 0.832 0.844 0.156
#> GSM751319 2 0.929 0.555 0.344 0.656
#> GSM751323 2 0.961 0.390 0.384 0.616
#> GSM751326 2 0.999 -0.075 0.480 0.520
#> GSM751327 1 1.000 0.220 0.504 0.496
#> GSM751328 2 0.904 0.600 0.320 0.680
#> GSM751329 1 0.939 0.696 0.644 0.356
#> GSM751330 1 0.939 0.696 0.644 0.356
#> GSM751331 1 0.814 0.812 0.748 0.252
#> GSM751333 1 0.895 0.759 0.688 0.312
#> GSM751335 1 0.881 0.775 0.700 0.300
#> GSM751336 1 0.814 0.812 0.748 0.252
#> GSM751337 2 0.980 0.328 0.416 0.584
#> GSM751338 2 0.990 0.414 0.440 0.560
#> GSM751340 2 0.985 0.453 0.428 0.572
#> GSM751350 1 0.625 0.832 0.844 0.156
#> GSM751351 1 0.625 0.832 0.844 0.156
#> GSM751362 2 0.987 0.515 0.432 0.568
#> GSM751363 2 0.855 0.708 0.280 0.720
#> GSM751367 2 0.985 0.497 0.428 0.572
#> GSM751368 2 0.738 0.748 0.208 0.792
#> GSM751371 2 0.781 0.745 0.232 0.768
#> GSM751375 2 0.402 0.756 0.080 0.920
#> GSM751376 2 0.795 0.725 0.240 0.760
#> GSM751378 2 0.662 0.765 0.172 0.828
#> GSM751379 2 0.795 0.725 0.240 0.760
#> GSM751382 2 0.402 0.756 0.080 0.920
#> GSM751386 2 0.358 0.756 0.068 0.932
#> GSM751388 2 0.373 0.755 0.072 0.928
#> GSM751391 2 0.781 0.752 0.232 0.768
#> GSM751410 2 0.855 0.728 0.280 0.720
#> GSM751414 2 0.939 0.626 0.356 0.644
#> GSM751361 2 0.605 0.750 0.148 0.852
#> GSM751365 2 0.808 0.739 0.248 0.752
#> GSM751366 2 0.939 0.627 0.356 0.644
#> GSM751369 2 0.814 0.732 0.252 0.748
#> GSM751370 2 0.992 0.489 0.448 0.552
#> GSM751372 2 0.980 0.557 0.416 0.584
#> GSM751373 2 0.939 0.626 0.356 0.644
#> GSM751374 2 0.795 0.725 0.240 0.760
#> GSM751377 2 0.706 0.755 0.192 0.808
#> GSM751380 2 0.904 0.699 0.320 0.680
#> GSM751381 2 0.388 0.755 0.076 0.924
#> GSM751383 2 0.416 0.758 0.084 0.916
#> GSM751384 2 0.494 0.765 0.108 0.892
#> GSM751385 2 0.615 0.769 0.152 0.848
#> GSM751387 2 0.416 0.754 0.084 0.916
#> GSM751389 2 0.833 0.730 0.264 0.736
#> GSM751393 2 0.795 0.725 0.240 0.760
#> GSM751394 2 0.343 0.756 0.064 0.936
#> GSM751395 2 0.795 0.725 0.240 0.760
#> GSM751397 2 0.388 0.757 0.076 0.924
#> GSM751398 2 0.343 0.757 0.064 0.936
#> GSM751404 2 0.981 0.546 0.420 0.580
#> GSM751406 2 0.987 0.539 0.432 0.568
#> GSM751411 2 0.775 0.746 0.228 0.772
#> GSM751413 2 0.753 0.745 0.216 0.784
#> GSM751415 2 0.833 0.730 0.264 0.736
#> GSM751416 2 0.844 0.712 0.272 0.728
#> GSM751417 2 0.844 0.712 0.272 0.728
#> GSM751421 2 0.775 0.741 0.228 0.772
#> GSM751422 2 0.775 0.741 0.228 0.772
#> GSM751360 2 0.781 0.739 0.232 0.768
#> GSM751364 2 0.844 0.712 0.272 0.728
#> GSM751390 2 0.506 0.761 0.112 0.888
#> GSM751392 2 0.416 0.756 0.084 0.916
#> GSM751396 2 0.388 0.755 0.076 0.924
#> GSM751399 2 0.932 0.644 0.348 0.652
#> GSM751400 2 0.992 0.514 0.448 0.552
#> GSM751401 2 0.991 0.521 0.444 0.556
#> GSM751402 2 0.992 0.514 0.448 0.552
#> GSM751403 2 0.991 0.522 0.444 0.556
#> GSM751405 2 0.987 0.538 0.432 0.568
#> GSM751407 2 0.992 0.514 0.448 0.552
#> GSM751408 2 0.978 0.559 0.412 0.588
#> GSM751409 2 0.753 0.752 0.216 0.784
#> GSM751412 2 0.971 0.573 0.400 0.600
#> GSM751418 2 0.795 0.735 0.240 0.760
#> GSM751419 2 0.795 0.735 0.240 0.760
#> GSM751420 2 0.983 0.560 0.424 0.576
#> GSM751425 2 0.494 0.753 0.108 0.892
#> GSM751429 2 0.985 0.488 0.428 0.572
#> GSM751430 2 0.469 0.760 0.100 0.900
#> GSM751433 2 0.388 0.739 0.076 0.924
#> GSM751437 2 0.866 0.740 0.288 0.712
#> GSM751448 2 0.998 0.433 0.476 0.524
#> GSM751451 2 0.373 0.740 0.072 0.928
#> GSM751423 2 0.814 0.759 0.252 0.748
#> GSM751424 2 0.469 0.758 0.100 0.900
#> GSM751428 2 0.584 0.757 0.140 0.860
#> GSM751431 2 0.416 0.742 0.084 0.916
#> GSM751432 2 0.469 0.760 0.100 0.900
#> GSM751434 2 0.469 0.760 0.100 0.900
#> GSM751435 2 0.574 0.758 0.136 0.864
#> GSM751436 2 0.388 0.739 0.076 0.924
#> GSM751440 2 0.574 0.761 0.136 0.864
#> GSM751444 2 0.402 0.750 0.080 0.920
#> GSM751446 2 0.482 0.752 0.104 0.896
#> GSM751449 2 0.482 0.749 0.104 0.896
#> GSM751450 2 0.456 0.756 0.096 0.904
#> GSM751452 2 0.469 0.758 0.100 0.900
#> GSM751426 2 0.443 0.753 0.092 0.908
#> GSM751427 2 0.584 0.757 0.140 0.860
#> GSM751438 2 0.584 0.762 0.140 0.860
#> GSM751439 2 0.469 0.748 0.100 0.900
#> GSM751441 2 0.506 0.750 0.112 0.888
#> GSM751442 2 0.469 0.748 0.100 0.900
#> GSM751443 2 0.995 0.456 0.460 0.540
#> GSM751445 2 0.482 0.749 0.104 0.896
#> GSM751447 2 0.506 0.750 0.112 0.888
#> GSM751453 2 0.469 0.751 0.100 0.900
#> GSM751454 2 0.469 0.751 0.100 0.900
#> GSM751455 2 0.469 0.748 0.100 0.900
#> GSM751456 2 0.469 0.748 0.100 0.900
#> GSM751457 2 0.469 0.752 0.100 0.900
#> GSM751458 2 0.469 0.752 0.100 0.900
cbind(get_classes(res, k = 3), get_membership(res, k = 3))
#> class entropy silhouette p1 p2 p3
#> GSM751298 1 0.423 0.683195 0.872 0.084 0.044
#> GSM751304 2 0.814 0.317143 0.112 0.620 0.268
#> GSM751305 2 0.814 0.317143 0.112 0.620 0.268
#> GSM751307 2 0.962 -0.022657 0.236 0.468 0.296
#> GSM751310 2 0.981 -0.102214 0.256 0.424 0.320
#> GSM751314 2 0.979 -0.125034 0.236 0.384 0.380
#> GSM751316 2 0.971 -0.101042 0.224 0.424 0.352
#> GSM751318 2 0.817 0.158444 0.072 0.512 0.416
#> GSM751342 2 0.811 0.194532 0.072 0.536 0.392
#> GSM751346 1 0.341 0.684596 0.904 0.068 0.028
#> GSM751347 1 0.341 0.684596 0.904 0.068 0.028
#> GSM751348 2 0.489 0.578604 0.060 0.844 0.096
#> GSM751349 2 0.397 0.587827 0.044 0.884 0.072
#> GSM751352 2 0.517 0.560799 0.092 0.832 0.076
#> GSM751353 2 0.466 0.574482 0.076 0.856 0.068
#> GSM751354 2 0.822 0.348282 0.184 0.640 0.176
#> GSM751355 2 0.822 0.348282 0.184 0.640 0.176
#> GSM751358 2 0.594 0.503352 0.028 0.748 0.224
#> GSM751359 2 0.594 0.503352 0.028 0.748 0.224
#> GSM751294 2 0.674 0.511425 0.100 0.744 0.156
#> GSM751296 1 0.677 0.622121 0.744 0.144 0.112
#> GSM751297 1 0.415 0.680266 0.876 0.080 0.044
#> GSM751299 2 0.589 0.539713 0.104 0.796 0.100
#> GSM751300 1 0.423 0.683195 0.872 0.084 0.044
#> GSM751301 2 0.862 0.240356 0.132 0.572 0.296
#> GSM751302 1 0.328 0.685852 0.908 0.068 0.024
#> GSM751303 3 0.967 0.100494 0.212 0.392 0.396
#> GSM751306 2 0.978 -0.119562 0.232 0.388 0.380
#> GSM751308 2 0.874 0.235973 0.124 0.536 0.340
#> GSM751309 2 0.948 0.059224 0.200 0.472 0.328
#> GSM751311 2 0.948 0.059224 0.200 0.472 0.328
#> GSM751312 2 0.971 -0.101042 0.224 0.424 0.352
#> GSM751313 1 0.701 0.648234 0.720 0.092 0.188
#> GSM751315 2 0.998 -0.167050 0.324 0.364 0.312
#> GSM751317 2 0.989 -0.123914 0.272 0.396 0.332
#> GSM751320 1 0.986 0.115125 0.392 0.256 0.352
#> GSM751321 2 0.987 -0.103819 0.268 0.408 0.324
#> GSM751322 2 0.997 -0.128251 0.304 0.368 0.328
#> GSM751324 2 0.962 -0.068569 0.204 0.408 0.388
#> GSM751325 2 0.982 -0.101074 0.244 0.392 0.364
#> GSM751332 3 0.990 -0.001232 0.316 0.284 0.400
#> GSM751334 3 0.990 -0.001232 0.316 0.284 0.400
#> GSM751339 3 0.903 0.240413 0.308 0.160 0.532
#> GSM751341 1 0.792 0.529412 0.664 0.184 0.152
#> GSM751343 2 0.904 0.068269 0.136 0.472 0.392
#> GSM751344 2 0.548 0.550934 0.108 0.816 0.076
#> GSM751345 2 0.548 0.550934 0.108 0.816 0.076
#> GSM751356 2 0.625 0.540361 0.104 0.776 0.120
#> GSM751357 2 0.625 0.540361 0.104 0.776 0.120
#> GSM751293 2 0.862 0.240356 0.132 0.572 0.296
#> GSM751295 1 0.328 0.685852 0.908 0.068 0.024
#> GSM751319 2 0.996 -0.160435 0.328 0.372 0.300
#> GSM751323 1 0.986 0.133543 0.396 0.256 0.348
#> GSM751326 1 0.946 0.365466 0.484 0.204 0.312
#> GSM751327 1 0.934 0.375005 0.512 0.208 0.280
#> GSM751328 3 0.989 -0.002214 0.316 0.280 0.404
#> GSM751329 1 0.784 0.597643 0.668 0.140 0.192
#> GSM751330 1 0.784 0.597643 0.668 0.140 0.192
#> GSM751331 1 0.608 0.671923 0.784 0.088 0.128
#> GSM751333 1 0.713 0.647608 0.716 0.104 0.180
#> GSM751335 1 0.683 0.656849 0.736 0.096 0.168
#> GSM751336 1 0.608 0.671923 0.784 0.088 0.128
#> GSM751337 1 0.971 0.181262 0.408 0.220 0.372
#> GSM751338 3 0.904 0.219434 0.320 0.156 0.524
#> GSM751340 3 0.907 0.243407 0.308 0.164 0.528
#> GSM751350 1 0.341 0.686902 0.904 0.068 0.028
#> GSM751351 1 0.341 0.686902 0.904 0.068 0.028
#> GSM751362 3 0.891 0.496228 0.220 0.208 0.572
#> GSM751363 2 0.887 -0.024105 0.124 0.496 0.380
#> GSM751367 1 0.999 -0.393896 0.360 0.320 0.320
#> GSM751368 2 0.779 0.254798 0.064 0.588 0.348
#> GSM751371 2 0.748 0.000796 0.036 0.508 0.456
#> GSM751375 2 0.468 0.577545 0.040 0.848 0.112
#> GSM751376 2 0.767 0.301704 0.072 0.628 0.300
#> GSM751378 2 0.706 0.383818 0.048 0.664 0.288
#> GSM751379 2 0.767 0.301704 0.072 0.628 0.300
#> GSM751382 2 0.468 0.577545 0.040 0.848 0.112
#> GSM751386 2 0.480 0.571341 0.032 0.836 0.132
#> GSM751388 2 0.473 0.572332 0.032 0.840 0.128
#> GSM751391 2 0.767 0.194566 0.052 0.568 0.380
#> GSM751410 3 0.847 0.293500 0.092 0.404 0.504
#> GSM751414 3 0.954 0.364939 0.208 0.328 0.464
#> GSM751361 2 0.661 0.371098 0.016 0.628 0.356
#> GSM751365 2 0.805 0.186764 0.076 0.568 0.356
#> GSM751366 3 0.951 0.317372 0.200 0.336 0.464
#> GSM751369 3 0.774 0.162332 0.048 0.448 0.504
#> GSM751370 3 0.938 0.491804 0.232 0.256 0.512
#> GSM751372 3 0.960 0.418359 0.216 0.328 0.456
#> GSM751373 3 0.950 0.310383 0.196 0.344 0.460
#> GSM751374 2 0.767 0.301704 0.072 0.628 0.300
#> GSM751377 2 0.742 0.348748 0.060 0.640 0.300
#> GSM751380 3 0.858 0.310314 0.100 0.396 0.504
#> GSM751381 2 0.454 0.575944 0.028 0.848 0.124
#> GSM751383 2 0.580 0.561646 0.044 0.780 0.176
#> GSM751384 2 0.512 0.567781 0.028 0.812 0.160
#> GSM751385 2 0.611 0.493920 0.028 0.732 0.240
#> GSM751387 2 0.533 0.571660 0.044 0.812 0.144
#> GSM751389 3 0.807 0.134841 0.064 0.464 0.472
#> GSM751393 2 0.756 0.320302 0.072 0.644 0.284
#> GSM751394 2 0.473 0.573408 0.032 0.840 0.128
#> GSM751395 2 0.759 0.317932 0.072 0.640 0.288
#> GSM751397 2 0.506 0.566043 0.032 0.820 0.148
#> GSM751398 2 0.499 0.568776 0.032 0.824 0.144
#> GSM751404 3 0.891 0.521551 0.176 0.260 0.564
#> GSM751406 3 0.781 0.555175 0.144 0.184 0.672
#> GSM751411 2 0.806 0.039827 0.068 0.532 0.400
#> GSM751413 2 0.786 0.091442 0.056 0.528 0.416
#> GSM751415 3 0.807 0.134841 0.064 0.464 0.472
#> GSM751416 2 0.851 0.036024 0.096 0.512 0.392
#> GSM751417 2 0.851 0.036024 0.096 0.512 0.392
#> GSM751421 3 0.730 0.067938 0.028 0.484 0.488
#> GSM751422 3 0.730 0.067938 0.028 0.484 0.488
#> GSM751360 2 0.716 0.052565 0.024 0.524 0.452
#> GSM751364 2 0.851 0.036024 0.096 0.512 0.392
#> GSM751390 2 0.585 0.562695 0.048 0.780 0.172
#> GSM751392 2 0.468 0.577971 0.040 0.848 0.112
#> GSM751396 2 0.493 0.581630 0.032 0.828 0.140
#> GSM751399 3 0.796 0.499831 0.092 0.288 0.620
#> GSM751400 3 0.802 0.561675 0.160 0.184 0.656
#> GSM751401 3 0.797 0.561295 0.160 0.180 0.660
#> GSM751402 3 0.788 0.559180 0.160 0.172 0.668
#> GSM751403 3 0.787 0.559314 0.156 0.176 0.668
#> GSM751405 3 0.771 0.553447 0.144 0.176 0.680
#> GSM751407 3 0.802 0.561675 0.160 0.184 0.656
#> GSM751408 3 0.829 0.541019 0.140 0.236 0.624
#> GSM751409 2 0.774 0.009004 0.048 0.504 0.448
#> GSM751412 3 0.837 0.526187 0.132 0.260 0.608
#> GSM751418 2 0.830 0.081511 0.080 0.508 0.412
#> GSM751419 2 0.830 0.081511 0.080 0.508 0.412
#> GSM751420 3 0.865 0.510234 0.136 0.292 0.572
#> GSM751425 2 0.427 0.584650 0.052 0.872 0.076
#> GSM751429 3 0.983 0.340213 0.368 0.244 0.388
#> GSM751430 2 0.536 0.579566 0.064 0.820 0.116
#> GSM751433 2 0.459 0.554689 0.032 0.848 0.120
#> GSM751437 3 0.868 0.234323 0.104 0.420 0.476
#> GSM751448 3 0.875 0.437469 0.276 0.152 0.572
#> GSM751451 2 0.480 0.552397 0.032 0.836 0.132
#> GSM751423 2 0.788 0.311021 0.072 0.592 0.336
#> GSM751424 2 0.529 0.581821 0.064 0.824 0.112
#> GSM751428 2 0.613 0.560010 0.084 0.780 0.136
#> GSM751431 2 0.478 0.554801 0.036 0.840 0.124
#> GSM751432 2 0.536 0.579566 0.064 0.820 0.116
#> GSM751434 2 0.536 0.579566 0.064 0.820 0.116
#> GSM751435 2 0.600 0.574407 0.084 0.788 0.128
#> GSM751436 2 0.459 0.554689 0.032 0.848 0.120
#> GSM751440 2 0.649 0.557398 0.084 0.756 0.160
#> GSM751444 2 0.452 0.577690 0.032 0.852 0.116
#> GSM751446 2 0.552 0.566332 0.068 0.812 0.120
#> GSM751449 2 0.459 0.572636 0.048 0.856 0.096
#> GSM751450 2 0.514 0.577013 0.044 0.824 0.132
#> GSM751452 2 0.529 0.581821 0.064 0.824 0.112
#> GSM751426 2 0.453 0.579705 0.040 0.856 0.104
#> GSM751427 2 0.613 0.560010 0.084 0.780 0.136
#> GSM751438 2 0.624 0.547282 0.072 0.768 0.160
#> GSM751439 2 0.530 0.568463 0.068 0.824 0.108
#> GSM751441 2 0.487 0.581072 0.056 0.844 0.100
#> GSM751442 2 0.523 0.569374 0.068 0.828 0.104
#> GSM751443 3 0.895 0.455856 0.272 0.172 0.556
#> GSM751445 2 0.459 0.572636 0.048 0.856 0.096
#> GSM751447 2 0.487 0.581072 0.056 0.844 0.100
#> GSM751453 2 0.492 0.578998 0.052 0.840 0.108
#> GSM751454 2 0.492 0.578998 0.052 0.840 0.108
#> GSM751455 2 0.523 0.569374 0.068 0.828 0.104
#> GSM751456 2 0.523 0.569374 0.068 0.828 0.104
#> GSM751457 2 0.448 0.575407 0.044 0.860 0.096
#> GSM751458 2 0.448 0.575407 0.044 0.860 0.096
cbind(get_classes(res, k = 4), get_membership(res, k = 4))
#> class entropy silhouette p1 p2 p3 p4
#> GSM751298 4 0.427 0.70963 0.040 0.056 0.056 0.848
#> GSM751304 2 0.814 0.32840 0.192 0.572 0.156 0.080
#> GSM751305 2 0.814 0.32840 0.192 0.572 0.156 0.080
#> GSM751307 2 0.948 -0.10385 0.228 0.412 0.148 0.212
#> GSM751310 1 0.916 0.44005 0.380 0.336 0.092 0.192
#> GSM751314 1 0.912 0.50653 0.432 0.284 0.104 0.180
#> GSM751316 1 0.926 0.41524 0.360 0.352 0.108 0.180
#> GSM751318 1 0.738 0.23763 0.476 0.396 0.116 0.012
#> GSM751342 1 0.728 0.19449 0.464 0.420 0.104 0.012
#> GSM751346 4 0.292 0.72375 0.004 0.036 0.060 0.900
#> GSM751347 4 0.292 0.72375 0.004 0.036 0.060 0.900
#> GSM751348 2 0.519 0.61248 0.104 0.792 0.072 0.032
#> GSM751349 2 0.436 0.62723 0.084 0.836 0.060 0.020
#> GSM751352 2 0.514 0.61047 0.060 0.800 0.092 0.048
#> GSM751353 2 0.460 0.62219 0.052 0.828 0.084 0.036
#> GSM751354 2 0.780 0.44368 0.056 0.592 0.196 0.156
#> GSM751355 2 0.780 0.44368 0.056 0.592 0.196 0.156
#> GSM751358 2 0.619 0.57209 0.112 0.688 0.192 0.008
#> GSM751359 2 0.619 0.57209 0.112 0.688 0.192 0.008
#> GSM751294 2 0.632 0.56672 0.072 0.704 0.184 0.040
#> GSM751296 4 0.658 0.61600 0.132 0.096 0.064 0.708
#> GSM751297 4 0.399 0.71237 0.020 0.048 0.076 0.856
#> GSM751299 2 0.588 0.59508 0.060 0.756 0.112 0.072
#> GSM751300 4 0.427 0.70963 0.040 0.056 0.056 0.848
#> GSM751301 2 0.763 -0.10180 0.408 0.472 0.056 0.064
#> GSM751302 4 0.256 0.72372 0.000 0.032 0.056 0.912
#> GSM751303 1 0.919 0.48535 0.416 0.300 0.112 0.172
#> GSM751306 1 0.915 0.50262 0.428 0.288 0.108 0.176
#> GSM751308 2 0.857 0.17820 0.272 0.476 0.196 0.056
#> GSM751309 1 0.893 0.43267 0.392 0.372 0.104 0.132
#> GSM751311 1 0.893 0.43267 0.392 0.372 0.104 0.132
#> GSM751312 1 0.926 0.41524 0.360 0.352 0.108 0.180
#> GSM751313 4 0.618 0.56580 0.272 0.028 0.040 0.660
#> GSM751315 1 0.914 0.48838 0.392 0.280 0.076 0.252
#> GSM751317 1 0.914 0.49063 0.392 0.312 0.084 0.212
#> GSM751320 1 0.829 0.32347 0.516 0.160 0.056 0.268
#> GSM751321 1 0.915 0.48762 0.384 0.320 0.084 0.212
#> GSM751322 1 0.869 0.48604 0.460 0.292 0.064 0.184
#> GSM751324 1 0.795 0.43547 0.532 0.308 0.076 0.084
#> GSM751325 1 0.825 0.44268 0.508 0.304 0.068 0.120
#> GSM751332 1 0.835 0.38959 0.520 0.192 0.056 0.232
#> GSM751334 1 0.835 0.38959 0.520 0.192 0.056 0.232
#> GSM751339 3 0.897 0.03592 0.352 0.072 0.380 0.196
#> GSM751341 4 0.750 0.51004 0.168 0.132 0.068 0.632
#> GSM751343 1 0.771 0.35027 0.508 0.356 0.092 0.044
#> GSM751344 2 0.567 0.60585 0.064 0.772 0.088 0.076
#> GSM751345 2 0.567 0.60585 0.064 0.772 0.088 0.076
#> GSM751356 2 0.602 0.58990 0.068 0.744 0.128 0.060
#> GSM751357 2 0.602 0.58990 0.068 0.744 0.128 0.060
#> GSM751293 2 0.763 -0.10180 0.408 0.472 0.056 0.064
#> GSM751295 4 0.275 0.72374 0.004 0.032 0.056 0.908
#> GSM751319 1 0.910 0.48120 0.392 0.284 0.072 0.252
#> GSM751323 1 0.844 0.30352 0.504 0.164 0.064 0.268
#> GSM751326 1 0.812 0.02952 0.432 0.132 0.040 0.396
#> GSM751327 1 0.838 0.08000 0.440 0.144 0.052 0.364
#> GSM751328 1 0.841 0.39076 0.516 0.192 0.060 0.232
#> GSM751329 4 0.688 0.41920 0.336 0.072 0.020 0.572
#> GSM751330 4 0.688 0.41920 0.336 0.072 0.020 0.572
#> GSM751331 4 0.514 0.63883 0.188 0.028 0.024 0.760
#> GSM751333 4 0.625 0.53853 0.312 0.028 0.032 0.628
#> GSM751335 4 0.591 0.55424 0.300 0.024 0.024 0.652
#> GSM751336 4 0.514 0.63883 0.188 0.028 0.024 0.760
#> GSM751337 1 0.851 0.22824 0.500 0.132 0.084 0.284
#> GSM751338 3 0.901 0.02704 0.352 0.072 0.372 0.204
#> GSM751340 3 0.902 0.03490 0.352 0.076 0.376 0.196
#> GSM751350 4 0.248 0.72473 0.000 0.032 0.052 0.916
#> GSM751351 4 0.248 0.72473 0.000 0.032 0.052 0.916
#> GSM751362 3 0.865 0.30781 0.300 0.116 0.480 0.104
#> GSM751363 2 0.906 -0.08317 0.292 0.420 0.204 0.084
#> GSM751367 4 0.986 -0.24678 0.244 0.256 0.180 0.320
#> GSM751368 2 0.808 0.27421 0.248 0.544 0.156 0.052
#> GSM751371 2 0.821 0.07629 0.284 0.404 0.300 0.012
#> GSM751375 2 0.454 0.62458 0.044 0.828 0.096 0.032
#> GSM751376 2 0.650 0.32084 0.028 0.564 0.376 0.032
#> GSM751378 2 0.676 0.44148 0.092 0.604 0.292 0.012
#> GSM751379 2 0.650 0.32084 0.028 0.564 0.376 0.032
#> GSM751382 2 0.454 0.62458 0.044 0.828 0.096 0.032
#> GSM751386 2 0.468 0.61422 0.060 0.816 0.104 0.020
#> GSM751388 2 0.462 0.61636 0.060 0.820 0.100 0.020
#> GSM751391 2 0.815 0.26119 0.220 0.480 0.276 0.024
#> GSM751410 3 0.881 0.12770 0.320 0.304 0.336 0.040
#> GSM751414 1 0.913 0.13305 0.436 0.252 0.216 0.096
#> GSM751361 2 0.726 0.39387 0.248 0.560 0.188 0.004
#> GSM751365 2 0.809 0.25994 0.164 0.504 0.296 0.036
#> GSM751366 1 0.946 0.15398 0.380 0.288 0.208 0.124
#> GSM751369 2 0.833 -0.10242 0.236 0.376 0.368 0.020
#> GSM751370 3 0.913 0.24290 0.328 0.160 0.404 0.108
#> GSM751372 3 0.940 0.18768 0.304 0.240 0.356 0.100
#> GSM751373 1 0.943 0.16224 0.388 0.284 0.204 0.124
#> GSM751374 2 0.650 0.32084 0.028 0.564 0.376 0.032
#> GSM751377 2 0.787 0.37236 0.196 0.576 0.180 0.048
#> GSM751380 3 0.899 0.11588 0.224 0.348 0.364 0.064
#> GSM751381 2 0.435 0.62078 0.056 0.836 0.088 0.020
#> GSM751383 2 0.583 0.59270 0.108 0.748 0.116 0.028
#> GSM751384 2 0.501 0.61977 0.052 0.788 0.140 0.020
#> GSM751385 2 0.577 0.56284 0.068 0.692 0.236 0.004
#> GSM751387 2 0.521 0.61173 0.072 0.788 0.112 0.028
#> GSM751389 3 0.831 0.09080 0.180 0.388 0.400 0.032
#> GSM751393 2 0.645 0.35377 0.028 0.580 0.360 0.032
#> GSM751394 2 0.464 0.61648 0.064 0.816 0.104 0.016
#> GSM751395 2 0.646 0.34823 0.028 0.576 0.364 0.032
#> GSM751397 2 0.481 0.61146 0.064 0.804 0.116 0.016
#> GSM751398 2 0.495 0.61044 0.072 0.800 0.108 0.020
#> GSM751404 3 0.724 0.49935 0.140 0.184 0.636 0.040
#> GSM751406 3 0.278 0.57613 0.008 0.072 0.904 0.016
#> GSM751411 2 0.814 0.06429 0.168 0.440 0.364 0.028
#> GSM751413 2 0.863 0.11159 0.280 0.448 0.224 0.048
#> GSM751415 3 0.831 0.09080 0.180 0.388 0.400 0.032
#> GSM751416 2 0.866 0.03119 0.296 0.436 0.220 0.048
#> GSM751417 2 0.866 0.03119 0.296 0.436 0.220 0.048
#> GSM751421 2 0.821 0.00554 0.280 0.400 0.308 0.012
#> GSM751422 2 0.821 0.00554 0.280 0.400 0.308 0.012
#> GSM751360 2 0.828 0.13597 0.280 0.436 0.264 0.020
#> GSM751364 2 0.866 0.03119 0.296 0.436 0.220 0.048
#> GSM751390 2 0.569 0.60775 0.076 0.756 0.136 0.032
#> GSM751392 2 0.454 0.62450 0.044 0.828 0.096 0.032
#> GSM751396 2 0.510 0.62233 0.100 0.792 0.088 0.020
#> GSM751399 3 0.542 0.54543 0.064 0.188 0.740 0.008
#> GSM751400 3 0.456 0.58622 0.056 0.088 0.828 0.028
#> GSM751401 3 0.426 0.58443 0.048 0.080 0.844 0.028
#> GSM751402 3 0.402 0.58432 0.040 0.076 0.856 0.028
#> GSM751403 3 0.381 0.58491 0.032 0.080 0.864 0.024
#> GSM751405 3 0.233 0.56277 0.004 0.056 0.924 0.016
#> GSM751407 3 0.456 0.58622 0.056 0.088 0.828 0.028
#> GSM751408 3 0.595 0.56070 0.084 0.164 0.728 0.024
#> GSM751409 3 0.758 -0.01128 0.136 0.420 0.432 0.012
#> GSM751412 3 0.595 0.55132 0.084 0.184 0.716 0.016
#> GSM751418 2 0.871 0.06934 0.292 0.456 0.188 0.064
#> GSM751419 2 0.871 0.06934 0.292 0.456 0.188 0.064
#> GSM751420 3 0.477 0.56641 0.016 0.192 0.772 0.020
#> GSM751425 2 0.443 0.62966 0.060 0.840 0.052 0.048
#> GSM751429 4 0.968 -0.15973 0.196 0.160 0.316 0.328
#> GSM751430 2 0.490 0.59736 0.104 0.808 0.032 0.056
#> GSM751433 2 0.391 0.57060 0.180 0.808 0.004 0.008
#> GSM751437 3 0.903 0.13573 0.248 0.304 0.384 0.064
#> GSM751448 3 0.610 0.45549 0.064 0.048 0.728 0.160
#> GSM751451 2 0.433 0.56552 0.184 0.792 0.016 0.008
#> GSM751423 2 0.829 0.33408 0.252 0.500 0.208 0.040
#> GSM751424 2 0.496 0.59588 0.108 0.804 0.032 0.056
#> GSM751428 2 0.602 0.58701 0.112 0.748 0.064 0.076
#> GSM751431 2 0.418 0.57051 0.180 0.800 0.008 0.012
#> GSM751432 2 0.490 0.59736 0.104 0.808 0.032 0.056
#> GSM751434 2 0.490 0.59736 0.104 0.808 0.032 0.056
#> GSM751435 2 0.601 0.60060 0.128 0.744 0.052 0.076
#> GSM751436 2 0.391 0.57060 0.180 0.808 0.004 0.008
#> GSM751440 2 0.617 0.57321 0.164 0.720 0.036 0.080
#> GSM751444 2 0.449 0.61181 0.124 0.820 0.028 0.028
#> GSM751446 2 0.532 0.58807 0.136 0.776 0.028 0.060
#> GSM751449 2 0.506 0.61666 0.072 0.804 0.084 0.040
#> GSM751450 2 0.517 0.58772 0.164 0.772 0.028 0.036
#> GSM751452 2 0.496 0.59588 0.108 0.804 0.032 0.056
#> GSM751426 2 0.452 0.60511 0.136 0.812 0.016 0.036
#> GSM751427 2 0.602 0.58701 0.112 0.748 0.064 0.076
#> GSM751438 2 0.647 0.59232 0.084 0.704 0.164 0.048
#> GSM751439 2 0.523 0.59559 0.128 0.784 0.032 0.056
#> GSM751441 2 0.501 0.61940 0.080 0.808 0.068 0.044
#> GSM751442 2 0.523 0.59527 0.128 0.784 0.032 0.056
#> GSM751443 3 0.656 0.47477 0.068 0.072 0.704 0.156
#> GSM751445 2 0.506 0.61666 0.072 0.804 0.084 0.040
#> GSM751447 2 0.501 0.61940 0.080 0.808 0.068 0.044
#> GSM751453 2 0.503 0.61318 0.096 0.804 0.060 0.040
#> GSM751454 2 0.503 0.61318 0.096 0.804 0.060 0.040
#> GSM751455 2 0.523 0.59527 0.128 0.784 0.032 0.056
#> GSM751456 2 0.523 0.59527 0.128 0.784 0.032 0.056
#> GSM751457 2 0.497 0.62037 0.060 0.808 0.092 0.040
#> GSM751458 2 0.497 0.62037 0.060 0.808 0.092 0.040
cbind(get_classes(res, k = 5), get_membership(res, k = 5))
#> class entropy silhouette p1 p2 p3 p4 p5
#> GSM751298 1 0.2732 0.6842 0.904 0.024 0.008 0.032 0.032
#> GSM751304 2 0.7286 0.1885 0.028 0.544 0.080 0.280 0.068
#> GSM751305 2 0.7286 0.1885 0.028 0.544 0.080 0.280 0.068
#> GSM751307 2 0.9164 -0.3453 0.176 0.332 0.076 0.304 0.112
#> GSM751310 4 0.7820 0.4791 0.088 0.252 0.028 0.512 0.120
#> GSM751314 4 0.8469 0.2917 0.096 0.204 0.028 0.416 0.256
#> GSM751316 4 0.7898 0.4821 0.084 0.276 0.036 0.496 0.108
#> GSM751318 5 0.5717 0.4363 0.000 0.256 0.040 0.056 0.648
#> GSM751342 5 0.5785 0.4096 0.000 0.280 0.040 0.052 0.628
#> GSM751346 1 0.1130 0.7025 0.968 0.012 0.012 0.004 0.004
#> GSM751347 1 0.1130 0.7025 0.968 0.012 0.012 0.004 0.004
#> GSM751348 2 0.5278 0.5863 0.012 0.716 0.048 0.024 0.200
#> GSM751349 2 0.4451 0.6080 0.012 0.780 0.032 0.016 0.160
#> GSM751352 2 0.5242 0.5963 0.032 0.756 0.072 0.020 0.120
#> GSM751353 2 0.4683 0.6095 0.028 0.796 0.060 0.020 0.096
#> GSM751354 2 0.7602 0.4154 0.144 0.576 0.156 0.084 0.040
#> GSM751355 2 0.7602 0.4154 0.144 0.576 0.156 0.084 0.040
#> GSM751358 2 0.6631 0.5070 0.004 0.620 0.136 0.060 0.180
#> GSM751359 2 0.6631 0.5070 0.004 0.620 0.136 0.060 0.180
#> GSM751294 2 0.6452 0.5388 0.020 0.648 0.156 0.032 0.144
#> GSM751296 1 0.4912 0.5758 0.748 0.052 0.008 0.020 0.172
#> GSM751297 1 0.2405 0.6864 0.920 0.020 0.024 0.024 0.012
#> GSM751299 2 0.5848 0.5795 0.048 0.720 0.092 0.024 0.116
#> GSM751300 1 0.2732 0.6842 0.904 0.024 0.008 0.032 0.032
#> GSM751301 5 0.5942 0.3550 0.032 0.344 0.012 0.032 0.580
#> GSM751302 1 0.0740 0.7017 0.980 0.008 0.008 0.000 0.004
#> GSM751303 4 0.8412 0.3485 0.088 0.228 0.028 0.424 0.232
#> GSM751306 4 0.8479 0.3115 0.096 0.212 0.028 0.416 0.248
#> GSM751308 2 0.7481 0.0803 0.020 0.408 0.172 0.024 0.376
#> GSM751309 5 0.8482 -0.1677 0.064 0.256 0.032 0.320 0.328
#> GSM751311 5 0.8482 -0.1677 0.064 0.256 0.032 0.320 0.328
#> GSM751312 4 0.7898 0.4821 0.084 0.276 0.036 0.496 0.108
#> GSM751313 1 0.6490 0.4679 0.516 0.008 0.008 0.344 0.124
#> GSM751315 4 0.8211 0.3847 0.140 0.192 0.024 0.488 0.156
#> GSM751317 4 0.8281 0.4141 0.116 0.224 0.028 0.472 0.160
#> GSM751320 5 0.7302 0.4820 0.192 0.064 0.008 0.188 0.548
#> GSM751321 4 0.8244 0.4240 0.116 0.228 0.028 0.476 0.152
#> GSM751322 5 0.7680 0.5159 0.140 0.168 0.012 0.140 0.540
#> GSM751324 5 0.6074 0.5538 0.060 0.176 0.004 0.088 0.672
#> GSM751325 5 0.6247 0.5643 0.072 0.176 0.004 0.088 0.660
#> GSM751332 5 0.6890 0.5525 0.164 0.096 0.000 0.144 0.596
#> GSM751334 5 0.6890 0.5525 0.164 0.096 0.000 0.144 0.596
#> GSM751339 3 0.8528 0.0635 0.092 0.024 0.356 0.308 0.220
#> GSM751341 1 0.5925 0.4776 0.664 0.084 0.012 0.024 0.216
#> GSM751343 5 0.5200 0.5121 0.016 0.216 0.020 0.036 0.712
#> GSM751344 2 0.5527 0.5919 0.052 0.740 0.064 0.020 0.124
#> GSM751345 2 0.5527 0.5919 0.052 0.740 0.064 0.020 0.124
#> GSM751356 2 0.6237 0.5667 0.040 0.688 0.108 0.032 0.132
#> GSM751357 2 0.6237 0.5667 0.040 0.688 0.108 0.032 0.132
#> GSM751293 5 0.5942 0.3550 0.032 0.344 0.012 0.032 0.580
#> GSM751295 1 0.0902 0.7018 0.976 0.008 0.008 0.004 0.004
#> GSM751319 4 0.8199 0.3965 0.140 0.200 0.024 0.488 0.148
#> GSM751323 5 0.7184 0.5053 0.196 0.076 0.008 0.148 0.572
#> GSM751326 5 0.7564 0.2533 0.288 0.060 0.000 0.212 0.440
#> GSM751327 5 0.7839 0.3378 0.244 0.068 0.008 0.228 0.452
#> GSM751328 5 0.6855 0.5526 0.164 0.096 0.000 0.140 0.600
#> GSM751329 1 0.7411 0.2481 0.424 0.028 0.004 0.292 0.252
#> GSM751330 1 0.7411 0.2481 0.424 0.028 0.004 0.292 0.252
#> GSM751331 1 0.5342 0.5856 0.676 0.004 0.004 0.228 0.088
#> GSM751333 1 0.6880 0.4060 0.460 0.008 0.004 0.324 0.204
#> GSM751335 1 0.6664 0.4337 0.488 0.004 0.004 0.316 0.188
#> GSM751336 1 0.5342 0.5856 0.676 0.004 0.004 0.228 0.088
#> GSM751337 5 0.7563 0.4335 0.196 0.048 0.036 0.172 0.548
#> GSM751338 3 0.8597 0.0560 0.100 0.024 0.352 0.300 0.224
#> GSM751340 3 0.8589 0.0601 0.092 0.028 0.356 0.304 0.220
#> GSM751350 1 0.1473 0.7029 0.956 0.008 0.008 0.020 0.008
#> GSM751351 1 0.1473 0.7029 0.956 0.008 0.008 0.020 0.008
#> GSM751362 4 0.6679 0.0177 0.016 0.052 0.344 0.536 0.052
#> GSM751363 4 0.7693 0.4418 0.024 0.316 0.100 0.480 0.080
#> GSM751367 4 0.9273 0.2883 0.300 0.196 0.108 0.312 0.084
#> GSM751368 2 0.7413 0.0169 0.020 0.480 0.064 0.344 0.092
#> GSM751371 2 0.8514 -0.1720 0.000 0.312 0.228 0.192 0.268
#> GSM751375 2 0.5073 0.6021 0.028 0.780 0.048 0.060 0.084
#> GSM751376 2 0.6835 0.3251 0.024 0.528 0.344 0.044 0.060
#> GSM751378 2 0.7545 0.3715 0.016 0.528 0.240 0.072 0.144
#> GSM751379 2 0.6835 0.3251 0.024 0.528 0.344 0.044 0.060
#> GSM751382 2 0.5073 0.6021 0.028 0.780 0.048 0.060 0.084
#> GSM751386 2 0.5472 0.5823 0.024 0.752 0.056 0.092 0.076
#> GSM751388 2 0.5309 0.5905 0.024 0.764 0.056 0.080 0.076
#> GSM751391 2 0.8340 0.0424 0.004 0.404 0.200 0.160 0.232
#> GSM751410 4 0.8792 0.1359 0.008 0.248 0.224 0.296 0.224
#> GSM751414 4 0.7306 0.4428 0.032 0.156 0.080 0.600 0.132
#> GSM751361 2 0.7804 0.2294 0.004 0.484 0.104 0.220 0.188
#> GSM751365 2 0.8616 0.0370 0.024 0.408 0.216 0.220 0.132
#> GSM751366 4 0.7875 0.4482 0.036 0.224 0.112 0.528 0.100
#> GSM751369 3 0.8621 -0.1010 0.008 0.296 0.328 0.188 0.180
#> GSM751370 4 0.7161 0.1521 0.020 0.092 0.280 0.548 0.060
#> GSM751372 4 0.7553 0.2507 0.020 0.164 0.248 0.516 0.052
#> GSM751373 4 0.7815 0.4487 0.036 0.228 0.108 0.532 0.096
#> GSM751374 2 0.6835 0.3251 0.024 0.528 0.344 0.044 0.060
#> GSM751377 2 0.7320 0.1073 0.028 0.496 0.080 0.340 0.056
#> GSM751380 4 0.8650 0.2161 0.016 0.256 0.264 0.340 0.124
#> GSM751381 2 0.4975 0.5961 0.024 0.784 0.040 0.076 0.076
#> GSM751383 2 0.6358 0.5698 0.032 0.692 0.096 0.088 0.092
#> GSM751384 2 0.5767 0.5913 0.020 0.728 0.096 0.060 0.096
#> GSM751385 2 0.6670 0.5145 0.012 0.628 0.188 0.060 0.112
#> GSM751387 2 0.5852 0.5887 0.028 0.728 0.088 0.068 0.088
#> GSM751389 3 0.8467 -0.0053 0.008 0.312 0.348 0.188 0.144
#> GSM751393 2 0.6683 0.3574 0.024 0.544 0.336 0.036 0.060
#> GSM751394 2 0.5270 0.5927 0.020 0.764 0.060 0.092 0.064
#> GSM751395 2 0.6695 0.3519 0.024 0.540 0.340 0.036 0.060
#> GSM751397 2 0.5617 0.5790 0.020 0.740 0.064 0.096 0.080
#> GSM751398 2 0.5686 0.5753 0.024 0.736 0.060 0.104 0.076
#> GSM751404 3 0.6655 0.4128 0.008 0.152 0.604 0.200 0.036
#> GSM751406 3 0.1918 0.5832 0.004 0.048 0.932 0.012 0.004
#> GSM751411 2 0.8785 -0.1280 0.020 0.328 0.268 0.248 0.136
#> GSM751413 2 0.8668 -0.2367 0.016 0.352 0.180 0.292 0.160
#> GSM751415 3 0.8467 -0.0053 0.008 0.312 0.348 0.188 0.144
#> GSM751416 4 0.7624 0.3421 0.012 0.340 0.124 0.452 0.072
#> GSM751417 4 0.7624 0.3421 0.012 0.340 0.124 0.452 0.072
#> GSM751421 2 0.8767 -0.2116 0.008 0.312 0.232 0.216 0.232
#> GSM751422 2 0.8767 -0.2116 0.008 0.312 0.232 0.216 0.232
#> GSM751360 2 0.8693 -0.1735 0.008 0.336 0.196 0.248 0.212
#> GSM751364 4 0.7624 0.3421 0.012 0.340 0.124 0.452 0.072
#> GSM751390 2 0.6302 0.5841 0.032 0.692 0.112 0.060 0.104
#> GSM751392 2 0.5009 0.6039 0.028 0.784 0.048 0.056 0.084
#> GSM751396 2 0.5326 0.6080 0.020 0.760 0.056 0.072 0.092
#> GSM751399 3 0.5604 0.5094 0.008 0.152 0.712 0.096 0.032
#> GSM751400 3 0.3200 0.5961 0.012 0.068 0.876 0.032 0.012
#> GSM751401 3 0.3064 0.5941 0.016 0.052 0.888 0.020 0.024
#> GSM751402 3 0.2674 0.5941 0.012 0.052 0.904 0.016 0.016
#> GSM751403 3 0.2744 0.5945 0.012 0.056 0.900 0.016 0.016
#> GSM751405 3 0.2074 0.5677 0.004 0.032 0.928 0.032 0.004
#> GSM751407 3 0.3200 0.5961 0.012 0.068 0.876 0.032 0.012
#> GSM751408 3 0.5161 0.5512 0.008 0.140 0.748 0.072 0.032
#> GSM751409 3 0.8128 0.0783 0.016 0.336 0.404 0.100 0.144
#> GSM751412 3 0.5374 0.5364 0.008 0.152 0.732 0.068 0.040
#> GSM751418 2 0.8052 -0.2050 0.024 0.384 0.128 0.380 0.084
#> GSM751419 2 0.8052 -0.2050 0.024 0.384 0.128 0.380 0.084
#> GSM751420 3 0.4009 0.5526 0.004 0.168 0.792 0.028 0.008
#> GSM751425 2 0.4044 0.6135 0.032 0.840 0.024 0.040 0.064
#> GSM751429 1 0.9521 -0.1327 0.296 0.116 0.212 0.268 0.108
#> GSM751430 2 0.5555 0.5738 0.060 0.744 0.020 0.096 0.080
#> GSM751433 2 0.4754 0.5648 0.004 0.732 0.016 0.036 0.212
#> GSM751437 3 0.9287 -0.0560 0.040 0.216 0.276 0.228 0.240
#> GSM751448 3 0.6297 0.4583 0.148 0.024 0.672 0.120 0.036
#> GSM751451 2 0.5036 0.5596 0.004 0.716 0.024 0.040 0.216
#> GSM751423 2 0.8479 0.1588 0.024 0.428 0.136 0.160 0.252
#> GSM751424 2 0.5560 0.5731 0.060 0.744 0.020 0.088 0.088
#> GSM751428 2 0.5970 0.5614 0.052 0.724 0.048 0.084 0.092
#> GSM751431 2 0.4889 0.5664 0.004 0.728 0.020 0.040 0.208
#> GSM751432 2 0.5555 0.5738 0.060 0.744 0.020 0.096 0.080
#> GSM751434 2 0.5555 0.5738 0.060 0.744 0.020 0.096 0.080
#> GSM751435 2 0.6042 0.5769 0.060 0.708 0.028 0.076 0.128
#> GSM751436 2 0.4754 0.5648 0.004 0.732 0.016 0.036 0.212
#> GSM751440 2 0.6133 0.5493 0.060 0.684 0.016 0.076 0.164
#> GSM751444 2 0.4444 0.6013 0.004 0.796 0.044 0.036 0.120
#> GSM751446 2 0.5041 0.5733 0.028 0.776 0.032 0.060 0.104
#> GSM751449 2 0.4559 0.5972 0.016 0.808 0.076 0.048 0.052
#> GSM751450 2 0.5265 0.5746 0.008 0.720 0.012 0.092 0.168
#> GSM751452 2 0.5560 0.5731 0.060 0.744 0.020 0.088 0.088
#> GSM751426 2 0.4703 0.5957 0.008 0.776 0.020 0.064 0.132
#> GSM751427 2 0.5970 0.5614 0.052 0.724 0.048 0.084 0.092
#> GSM751438 2 0.5804 0.5697 0.020 0.716 0.144 0.060 0.060
#> GSM751439 2 0.4885 0.5815 0.028 0.788 0.036 0.052 0.096
#> GSM751441 2 0.4383 0.6002 0.016 0.820 0.056 0.052 0.056
#> GSM751442 2 0.4885 0.5809 0.028 0.788 0.036 0.052 0.096
#> GSM751443 3 0.6725 0.4593 0.144 0.048 0.652 0.116 0.040
#> GSM751445 2 0.4559 0.5972 0.016 0.808 0.076 0.048 0.052
#> GSM751447 2 0.4383 0.6002 0.016 0.820 0.056 0.052 0.056
#> GSM751453 2 0.4422 0.5931 0.016 0.816 0.040 0.072 0.056
#> GSM751454 2 0.4422 0.5931 0.016 0.816 0.040 0.072 0.056
#> GSM751455 2 0.4885 0.5809 0.028 0.788 0.036 0.052 0.096
#> GSM751456 2 0.4885 0.5809 0.028 0.788 0.036 0.052 0.096
#> GSM751457 2 0.4345 0.6004 0.016 0.820 0.076 0.040 0.048
#> GSM751458 2 0.4345 0.6004 0.016 0.820 0.076 0.040 0.048
cbind(get_classes(res, k = 6), get_membership(res, k = 6))
#> class entropy silhouette p1 p2 p3 p4 p5 p6
#> GSM751298 1 0.2341 0.66188 0.908 0.008 0.000 0.044 0.016 0.024
#> GSM751304 2 0.6510 0.19458 0.004 0.520 0.048 0.068 0.328 0.032
#> GSM751305 2 0.6510 0.19458 0.004 0.520 0.048 0.068 0.328 0.032
#> GSM751307 5 0.8286 -0.03410 0.132 0.300 0.024 0.052 0.380 0.112
#> GSM751310 5 0.5941 0.28612 0.036 0.184 0.008 0.084 0.656 0.032
#> GSM751314 5 0.6540 0.27300 0.044 0.144 0.004 0.236 0.556 0.016
#> GSM751316 5 0.5548 0.26285 0.024 0.224 0.012 0.064 0.660 0.016
#> GSM751318 4 0.4735 0.45344 0.000 0.152 0.020 0.744 0.052 0.032
#> GSM751342 4 0.4876 0.42751 0.000 0.176 0.020 0.724 0.048 0.032
#> GSM751346 1 0.0551 0.68224 0.984 0.000 0.004 0.000 0.008 0.004
#> GSM751347 1 0.0551 0.68224 0.984 0.000 0.004 0.000 0.008 0.004
#> GSM751348 2 0.5602 0.50068 0.000 0.644 0.020 0.220 0.024 0.092
#> GSM751349 2 0.4861 0.55344 0.000 0.716 0.016 0.184 0.020 0.064
#> GSM751352 2 0.5342 0.54850 0.012 0.704 0.024 0.160 0.016 0.084
#> GSM751353 2 0.5004 0.56971 0.012 0.732 0.020 0.156 0.020 0.060
#> GSM751354 2 0.7288 0.38146 0.120 0.592 0.084 0.040 0.060 0.104
#> GSM751355 2 0.7288 0.38146 0.120 0.592 0.084 0.040 0.060 0.104
#> GSM751358 2 0.7040 0.28720 0.000 0.568 0.112 0.144 0.056 0.120
#> GSM751359 2 0.7040 0.28720 0.000 0.568 0.112 0.144 0.056 0.120
#> GSM751294 2 0.6352 0.45055 0.008 0.632 0.108 0.148 0.020 0.084
#> GSM751296 1 0.4340 0.55281 0.752 0.032 0.000 0.180 0.016 0.020
#> GSM751297 1 0.2144 0.66424 0.924 0.008 0.012 0.016 0.012 0.028
#> GSM751299 2 0.5464 0.52975 0.028 0.720 0.036 0.120 0.016 0.080
#> GSM751300 1 0.2341 0.66188 0.908 0.008 0.000 0.044 0.016 0.024
#> GSM751301 4 0.5251 0.36527 0.024 0.260 0.008 0.656 0.016 0.036
#> GSM751302 1 0.0717 0.68267 0.976 0.000 0.000 0.000 0.008 0.016
#> GSM751303 5 0.6437 0.29618 0.028 0.176 0.008 0.216 0.560 0.012
#> GSM751306 5 0.6503 0.28985 0.040 0.152 0.004 0.228 0.560 0.016
#> GSM751308 4 0.7248 -0.08482 0.008 0.384 0.128 0.388 0.016 0.076
#> GSM751309 5 0.6569 0.16396 0.020 0.180 0.008 0.352 0.436 0.004
#> GSM751311 5 0.6569 0.16396 0.020 0.180 0.008 0.352 0.436 0.004
#> GSM751312 5 0.5548 0.26285 0.024 0.224 0.012 0.064 0.660 0.016
#> GSM751313 1 0.7108 0.36217 0.372 0.000 0.000 0.092 0.340 0.196
#> GSM751315 5 0.6013 0.30532 0.064 0.140 0.004 0.108 0.660 0.024
#> GSM751317 5 0.5801 0.30774 0.048 0.156 0.004 0.120 0.660 0.012
#> GSM751320 4 0.6377 0.50263 0.124 0.024 0.000 0.568 0.244 0.040
#> GSM751321 5 0.5890 0.30746 0.052 0.164 0.004 0.108 0.656 0.016
#> GSM751322 4 0.6637 0.52798 0.088 0.096 0.000 0.580 0.204 0.032
#> GSM751324 4 0.4745 0.57444 0.044 0.100 0.000 0.744 0.108 0.004
#> GSM751325 4 0.5053 0.58799 0.048 0.100 0.000 0.728 0.112 0.012
#> GSM751332 4 0.5735 0.56507 0.128 0.036 0.000 0.652 0.168 0.016
#> GSM751334 4 0.5735 0.56507 0.128 0.036 0.000 0.652 0.168 0.016
#> GSM751339 5 0.8043 -0.01061 0.028 0.012 0.304 0.140 0.368 0.148
#> GSM751341 1 0.5376 0.45823 0.668 0.060 0.004 0.224 0.024 0.020
#> GSM751343 4 0.3978 0.53817 0.012 0.112 0.008 0.808 0.044 0.016
#> GSM751344 2 0.5070 0.54692 0.028 0.744 0.020 0.120 0.016 0.072
#> GSM751345 2 0.5070 0.54692 0.028 0.744 0.020 0.120 0.016 0.072
#> GSM751356 2 0.5880 0.49619 0.020 0.684 0.064 0.136 0.016 0.080
#> GSM751357 2 0.5880 0.49619 0.020 0.684 0.064 0.136 0.016 0.080
#> GSM751293 4 0.5251 0.36527 0.024 0.260 0.008 0.656 0.016 0.036
#> GSM751295 1 0.0820 0.68284 0.972 0.000 0.000 0.000 0.012 0.016
#> GSM751319 5 0.5981 0.30665 0.072 0.148 0.004 0.096 0.660 0.020
#> GSM751323 4 0.6499 0.52817 0.136 0.032 0.004 0.600 0.180 0.048
#> GSM751326 4 0.7197 0.32129 0.204 0.012 0.000 0.480 0.196 0.108
#> GSM751327 4 0.7586 0.39161 0.140 0.028 0.004 0.468 0.224 0.136
#> GSM751328 4 0.5649 0.56634 0.128 0.036 0.000 0.656 0.168 0.012
#> GSM751329 1 0.7901 0.12887 0.296 0.012 0.000 0.232 0.284 0.176
#> GSM751330 1 0.7901 0.12887 0.296 0.012 0.000 0.232 0.284 0.176
#> GSM751331 1 0.5918 0.53040 0.580 0.000 0.000 0.048 0.256 0.116
#> GSM751333 1 0.7532 0.28747 0.316 0.000 0.000 0.168 0.316 0.200
#> GSM751335 1 0.7422 0.32645 0.352 0.000 0.000 0.148 0.308 0.192
#> GSM751336 1 0.5918 0.53040 0.580 0.000 0.000 0.048 0.256 0.116
#> GSM751337 4 0.6955 0.47279 0.124 0.016 0.032 0.564 0.208 0.056
#> GSM751338 5 0.8078 -0.00619 0.032 0.012 0.304 0.144 0.368 0.140
#> GSM751340 5 0.8022 -0.01275 0.028 0.012 0.304 0.140 0.372 0.144
#> GSM751350 1 0.1644 0.68218 0.932 0.000 0.000 0.000 0.028 0.040
#> GSM751351 1 0.1644 0.68218 0.932 0.000 0.000 0.000 0.028 0.040
#> GSM751362 5 0.6817 0.00703 0.000 0.032 0.228 0.008 0.372 0.360
#> GSM751363 5 0.7302 0.08747 0.000 0.228 0.052 0.060 0.492 0.168
#> GSM751367 5 0.8713 -0.04469 0.256 0.152 0.048 0.036 0.348 0.160
#> GSM751368 2 0.7544 -0.06601 0.000 0.384 0.040 0.080 0.344 0.152
#> GSM751371 2 0.8950 -0.73234 0.000 0.228 0.168 0.184 0.208 0.212
#> GSM751375 2 0.4840 0.56594 0.012 0.768 0.016 0.080 0.072 0.052
#> GSM751376 2 0.7240 0.28599 0.024 0.504 0.272 0.052 0.028 0.120
#> GSM751378 2 0.7787 0.08477 0.004 0.484 0.204 0.088 0.096 0.124
#> GSM751379 2 0.7240 0.28599 0.024 0.504 0.272 0.052 0.028 0.120
#> GSM751382 2 0.4840 0.56594 0.012 0.768 0.016 0.080 0.072 0.052
#> GSM751386 2 0.5480 0.54551 0.008 0.716 0.024 0.076 0.116 0.060
#> GSM751388 2 0.5579 0.55024 0.008 0.716 0.036 0.076 0.100 0.064
#> GSM751391 2 0.8676 -0.51361 0.000 0.336 0.152 0.144 0.176 0.192
#> GSM751410 6 0.8500 0.56390 0.000 0.180 0.136 0.108 0.224 0.352
#> GSM751414 5 0.6279 0.08614 0.000 0.096 0.020 0.060 0.588 0.236
#> GSM751361 2 0.8201 -0.02456 0.000 0.400 0.076 0.136 0.204 0.184
#> GSM751365 2 0.8513 -0.25682 0.008 0.328 0.204 0.072 0.268 0.120
#> GSM751366 5 0.7315 0.13374 0.004 0.140 0.092 0.056 0.540 0.168
#> GSM751369 3 0.8802 -0.60967 0.000 0.228 0.252 0.116 0.176 0.228
#> GSM751370 5 0.6917 0.04853 0.000 0.044 0.180 0.016 0.436 0.324
#> GSM751372 5 0.7306 0.04067 0.000 0.116 0.160 0.008 0.412 0.304
#> GSM751373 5 0.7305 0.13650 0.004 0.144 0.088 0.056 0.540 0.168
#> GSM751374 2 0.7240 0.28599 0.024 0.504 0.272 0.052 0.028 0.120
#> GSM751377 2 0.7453 0.01980 0.008 0.412 0.040 0.044 0.328 0.168
#> GSM751380 5 0.8545 -0.29335 0.004 0.176 0.216 0.084 0.356 0.164
#> GSM751381 2 0.5171 0.55895 0.008 0.736 0.016 0.080 0.108 0.052
#> GSM751383 2 0.6383 0.53616 0.012 0.660 0.072 0.088 0.100 0.068
#> GSM751384 2 0.6207 0.52752 0.008 0.672 0.068 0.088 0.088 0.076
#> GSM751385 2 0.7149 0.36903 0.004 0.568 0.164 0.096 0.084 0.084
#> GSM751387 2 0.5976 0.55508 0.012 0.692 0.072 0.088 0.088 0.048
#> GSM751389 3 0.8517 -0.29277 0.004 0.244 0.316 0.072 0.232 0.132
#> GSM751393 2 0.7097 0.31432 0.024 0.524 0.260 0.052 0.024 0.116
#> GSM751394 2 0.5524 0.55373 0.008 0.712 0.024 0.064 0.120 0.072
#> GSM751395 2 0.7078 0.31256 0.024 0.524 0.264 0.052 0.024 0.112
#> GSM751397 2 0.5802 0.53571 0.008 0.692 0.028 0.076 0.120 0.076
#> GSM751398 2 0.5718 0.53025 0.008 0.696 0.024 0.076 0.124 0.072
#> GSM751404 3 0.6160 0.37560 0.000 0.100 0.624 0.020 0.184 0.072
#> GSM751406 3 0.1633 0.58615 0.000 0.024 0.932 0.000 0.000 0.044
#> GSM751411 5 0.8750 -0.31379 0.008 0.264 0.216 0.076 0.272 0.164
#> GSM751413 5 0.8405 -0.30794 0.000 0.288 0.096 0.100 0.300 0.216
#> GSM751415 3 0.8517 -0.29277 0.004 0.244 0.316 0.072 0.232 0.132
#> GSM751416 5 0.7513 0.11742 0.000 0.232 0.064 0.052 0.456 0.196
#> GSM751417 5 0.7513 0.11742 0.000 0.232 0.064 0.052 0.456 0.196
#> GSM751421 6 0.8858 0.68826 0.000 0.228 0.152 0.148 0.224 0.248
#> GSM751422 6 0.8858 0.68826 0.000 0.228 0.152 0.148 0.224 0.248
#> GSM751360 5 0.8640 -0.52364 0.000 0.244 0.108 0.128 0.260 0.260
#> GSM751364 5 0.7509 0.11384 0.000 0.236 0.064 0.052 0.456 0.192
#> GSM751390 2 0.6323 0.54194 0.012 0.664 0.092 0.096 0.080 0.056
#> GSM751392 2 0.4779 0.56910 0.012 0.772 0.016 0.080 0.072 0.048
#> GSM751396 2 0.5366 0.57909 0.008 0.724 0.020 0.088 0.104 0.056
#> GSM751399 3 0.5613 0.48398 0.000 0.108 0.692 0.024 0.064 0.112
#> GSM751400 3 0.2151 0.60980 0.004 0.040 0.920 0.008 0.016 0.012
#> GSM751401 3 0.1916 0.60800 0.008 0.028 0.932 0.020 0.008 0.004
#> GSM751402 3 0.1476 0.60855 0.004 0.028 0.948 0.012 0.008 0.000
#> GSM751403 3 0.1698 0.60723 0.004 0.032 0.940 0.008 0.004 0.012
#> GSM751405 3 0.2262 0.56213 0.000 0.016 0.896 0.000 0.008 0.080
#> GSM751407 3 0.2151 0.60980 0.004 0.040 0.920 0.008 0.016 0.012
#> GSM751408 3 0.4334 0.54632 0.004 0.100 0.784 0.020 0.080 0.012
#> GSM751409 3 0.8181 -0.20205 0.004 0.292 0.380 0.088 0.132 0.104
#> GSM751412 3 0.4703 0.52206 0.004 0.116 0.760 0.028 0.076 0.016
#> GSM751418 5 0.8195 0.06734 0.004 0.280 0.116 0.072 0.380 0.148
#> GSM751419 5 0.8195 0.06734 0.004 0.280 0.116 0.072 0.380 0.148
#> GSM751420 3 0.3804 0.52977 0.000 0.152 0.792 0.004 0.020 0.032
#> GSM751425 2 0.4766 0.57608 0.008 0.764 0.008 0.068 0.060 0.092
#> GSM751429 5 0.9376 -0.12885 0.252 0.096 0.144 0.056 0.260 0.192
#> GSM751430 2 0.6106 0.55220 0.028 0.668 0.020 0.116 0.124 0.044
#> GSM751433 2 0.5775 0.53594 0.000 0.644 0.020 0.212 0.068 0.056
#> GSM751437 6 0.9260 0.47949 0.020 0.168 0.220 0.144 0.208 0.240
#> GSM751448 3 0.6488 0.38311 0.148 0.016 0.588 0.012 0.040 0.196
#> GSM751451 2 0.5929 0.53023 0.000 0.632 0.024 0.216 0.064 0.064
#> GSM751423 2 0.8704 -0.36924 0.008 0.360 0.108 0.156 0.188 0.180
#> GSM751424 2 0.6039 0.55720 0.028 0.668 0.016 0.128 0.120 0.040
#> GSM751428 2 0.6536 0.51085 0.028 0.648 0.040 0.068 0.124 0.092
#> GSM751431 2 0.5774 0.54202 0.000 0.648 0.020 0.204 0.072 0.056
#> GSM751432 2 0.6106 0.55220 0.028 0.668 0.020 0.116 0.124 0.044
#> GSM751434 2 0.6106 0.55220 0.028 0.668 0.020 0.116 0.124 0.044
#> GSM751435 2 0.6781 0.52885 0.040 0.624 0.032 0.116 0.128 0.060
#> GSM751436 2 0.5775 0.53594 0.000 0.644 0.020 0.212 0.068 0.056
#> GSM751440 2 0.6865 0.48987 0.040 0.604 0.020 0.140 0.132 0.064
#> GSM751444 2 0.5254 0.56182 0.000 0.716 0.028 0.140 0.044 0.072
#> GSM751446 2 0.5891 0.51986 0.012 0.688 0.024 0.108 0.092 0.076
#> GSM751449 2 0.5052 0.56771 0.004 0.756 0.052 0.068 0.048 0.072
#> GSM751450 2 0.6169 0.53349 0.008 0.628 0.012 0.164 0.136 0.052
#> GSM751452 2 0.6039 0.55720 0.028 0.668 0.016 0.128 0.120 0.040
#> GSM751426 2 0.5853 0.56732 0.008 0.676 0.024 0.152 0.084 0.056
#> GSM751427 2 0.6536 0.51085 0.028 0.648 0.040 0.068 0.124 0.092
#> GSM751438 2 0.6109 0.53021 0.008 0.672 0.112 0.064 0.044 0.100
#> GSM751439 2 0.5655 0.53413 0.012 0.712 0.032 0.100 0.080 0.064
#> GSM751441 2 0.5015 0.57870 0.004 0.756 0.036 0.084 0.056 0.064
#> GSM751442 2 0.5655 0.53424 0.012 0.712 0.032 0.100 0.080 0.064
#> GSM751443 3 0.6876 0.37642 0.144 0.040 0.576 0.016 0.040 0.184
#> GSM751445 2 0.5052 0.56771 0.004 0.756 0.052 0.068 0.048 0.072
#> GSM751447 2 0.5015 0.57870 0.004 0.756 0.036 0.084 0.056 0.064
#> GSM751453 2 0.5323 0.56209 0.004 0.732 0.036 0.064 0.096 0.068
#> GSM751454 2 0.5323 0.56209 0.004 0.732 0.036 0.064 0.096 0.068
#> GSM751455 2 0.5655 0.53424 0.012 0.712 0.032 0.100 0.080 0.064
#> GSM751456 2 0.5655 0.53424 0.012 0.712 0.032 0.100 0.080 0.064
#> GSM751457 2 0.4827 0.57292 0.004 0.772 0.052 0.064 0.044 0.064
#> GSM751458 2 0.4827 0.57292 0.004 0.772 0.052 0.064 0.044 0.064
Heatmaps for the consensus matrix. It visualizes the probability of two samples to be in a same group.
consensus_heatmap(res, k = 2)
consensus_heatmap(res, k = 3)
consensus_heatmap(res, k = 4)
consensus_heatmap(res, k = 5)
consensus_heatmap(res, k = 6)
Heatmaps for the membership of samples in all partitions to see how consistent they are:
membership_heatmap(res, k = 2)
membership_heatmap(res, k = 3)
membership_heatmap(res, k = 4)
membership_heatmap(res, k = 5)
membership_heatmap(res, k = 6)
As soon as we have had the classes for columns, we can look for signatures which are significantly different between classes which can be candidate marks for certain classes. Following are the heatmaps for signatures.
Signature heatmaps where rows are scaled:
get_signatures(res, k = 2)
get_signatures(res, k = 3)
get_signatures(res, k = 4)
get_signatures(res, k = 5)
get_signatures(res, k = 6)
Signature heatmaps where rows are not scaled:
get_signatures(res, k = 2, scale_rows = FALSE)
get_signatures(res, k = 3, scale_rows = FALSE)
get_signatures(res, k = 4, scale_rows = FALSE)
get_signatures(res, k = 5, scale_rows = FALSE)
get_signatures(res, k = 6, scale_rows = FALSE)
Compare the overlap of signatures from different k:
compare_signatures(res)
get_signature() returns a data frame invisibly. TO get the list of signatures, the function
call should be assigned to a variable explicitly. In following code, if plot argument is set
to FALSE, no heatmap is plotted while only the differential analysis is performed.
# code only for demonstration
tb = get_signature(res, k = ..., plot = FALSE)
An example of the output of tb is:
#> which_row fdr mean_1 mean_2 scaled_mean_1 scaled_mean_2 km
#> 1 38 0.042760348 8.373488 9.131774 -0.5533452 0.5164555 1
#> 2 40 0.018707592 7.106213 8.469186 -0.6173731 0.5762149 1
#> 3 55 0.019134737 10.221463 11.207825 -0.6159697 0.5749050 1
#> 4 59 0.006059896 5.921854 7.869574 -0.6899429 0.6439467 1
#> 5 60 0.018055526 8.928898 10.211722 -0.6204761 0.5791110 1
#> 6 98 0.009384629 15.714769 14.887706 0.6635654 -0.6193277 2
...
The columns in tb are:
which_row: row indices corresponding to the input matrix.fdr: FDR for the differential test. mean_x: The mean value in group x.scaled_mean_x: The mean value in group x after rows are scaled.km: Row groups if k-means clustering is applied to rows.UMAP plot which shows how samples are separated.
dimension_reduction(res, k = 2, method = "UMAP")
dimension_reduction(res, k = 3, method = "UMAP")
dimension_reduction(res, k = 4, method = "UMAP")
dimension_reduction(res, k = 5, method = "UMAP")
dimension_reduction(res, k = 6, method = "UMAP")
Following heatmap shows how subgroups are split when increasing k:
collect_classes(res)
Test correlation between subgroups and known annotations. If the known annotation is numeric, one-way ANOVA test is applied, and if the known annotation is discrete, chi-squared contingency table test is applied.
test_to_known_factors(res)
#> n tissue(p) disease.state(p) agent(p) k
#> MAD:hclust 153 8.76e-08 0.573 0.10539 2
#> MAD:hclust 86 3.22e-14 0.162 0.02139 3
#> MAD:hclust 87 7.59e-13 0.224 0.01078 4
#> MAD:hclust 89 1.56e-13 0.127 0.00335 5
#> MAD:hclust 85 5.53e-15 0.210 0.01231 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 4537 rows and 166 columns.
#> Top rows (454, 908, 1361, 1814, 2268) 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 0.964 0.940 0.963 0.4117 0.581 0.581
#> 3 3 0.427 0.623 0.758 0.5500 0.752 0.573
#> 4 4 0.479 0.561 0.671 0.1364 0.858 0.612
#> 5 5 0.577 0.515 0.658 0.0797 0.863 0.551
#> 6 6 0.644 0.556 0.709 0.0477 0.905 0.606
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
#> GSM751298 1 0.1184 0.932 0.984 0.016
#> GSM751304 2 0.1184 0.978 0.016 0.984
#> GSM751305 2 0.1184 0.977 0.016 0.984
#> GSM751307 2 0.2236 0.970 0.036 0.964
#> GSM751310 1 0.8016 0.729 0.756 0.244
#> GSM751314 1 0.2423 0.923 0.960 0.040
#> GSM751316 1 0.9970 0.218 0.532 0.468
#> GSM751318 1 0.8555 0.668 0.720 0.280
#> GSM751342 1 0.9963 0.231 0.536 0.464
#> GSM751346 1 0.1184 0.930 0.984 0.016
#> GSM751347 1 0.4431 0.887 0.908 0.092
#> GSM751348 2 0.1414 0.976 0.020 0.980
#> GSM751349 2 0.0672 0.978 0.008 0.992
#> GSM751352 2 0.2423 0.970 0.040 0.960
#> GSM751353 2 0.0938 0.979 0.012 0.988
#> GSM751354 2 0.0938 0.977 0.012 0.988
#> GSM751355 2 0.0672 0.978 0.008 0.992
#> GSM751358 2 0.0376 0.979 0.004 0.996
#> GSM751359 2 0.0672 0.978 0.008 0.992
#> GSM751294 2 0.0938 0.977 0.012 0.988
#> GSM751296 1 0.1184 0.930 0.984 0.016
#> GSM751297 1 0.4431 0.894 0.908 0.092
#> GSM751299 2 0.2423 0.967 0.040 0.960
#> GSM751300 1 0.1184 0.930 0.984 0.016
#> GSM751301 1 0.0938 0.932 0.988 0.012
#> GSM751302 1 0.1184 0.930 0.984 0.016
#> GSM751303 1 0.8267 0.705 0.740 0.260
#> GSM751306 1 0.7056 0.797 0.808 0.192
#> GSM751308 2 0.9661 0.331 0.392 0.608
#> GSM751309 1 0.6438 0.828 0.836 0.164
#> GSM751311 1 0.0938 0.932 0.988 0.012
#> GSM751312 1 0.4022 0.900 0.920 0.080
#> GSM751313 1 0.0376 0.932 0.996 0.004
#> GSM751315 1 0.0938 0.932 0.988 0.012
#> GSM751317 1 0.5737 0.856 0.864 0.136
#> GSM751320 1 0.0376 0.933 0.996 0.004
#> GSM751321 1 0.0938 0.932 0.988 0.012
#> GSM751322 1 0.0938 0.932 0.988 0.012
#> GSM751324 1 0.0938 0.932 0.988 0.012
#> GSM751325 1 0.0938 0.932 0.988 0.012
#> GSM751332 1 0.0938 0.932 0.988 0.012
#> GSM751334 1 0.0938 0.932 0.988 0.012
#> GSM751339 1 0.4815 0.879 0.896 0.104
#> GSM751341 1 0.2778 0.919 0.952 0.048
#> GSM751343 1 0.0376 0.933 0.996 0.004
#> GSM751344 2 0.2236 0.972 0.036 0.964
#> GSM751345 2 0.2236 0.972 0.036 0.964
#> GSM751356 2 0.1184 0.978 0.016 0.984
#> GSM751357 2 0.1184 0.978 0.016 0.984
#> GSM751293 1 0.0938 0.932 0.988 0.012
#> GSM751295 1 0.1184 0.930 0.984 0.016
#> GSM751319 1 0.0938 0.932 0.988 0.012
#> GSM751323 1 0.0376 0.933 0.996 0.004
#> GSM751326 1 0.0000 0.933 1.000 0.000
#> GSM751327 1 0.0376 0.933 0.996 0.004
#> GSM751328 1 0.0938 0.932 0.988 0.012
#> GSM751329 1 0.0938 0.932 0.988 0.012
#> GSM751330 1 0.0376 0.933 0.996 0.004
#> GSM751331 1 0.0000 0.933 1.000 0.000
#> GSM751333 1 0.0000 0.933 1.000 0.000
#> GSM751335 1 0.0376 0.933 0.996 0.004
#> GSM751336 1 0.0672 0.931 0.992 0.008
#> GSM751337 1 0.0672 0.931 0.992 0.008
#> GSM751338 1 0.0376 0.932 0.996 0.004
#> GSM751340 1 0.9000 0.597 0.684 0.316
#> GSM751350 1 0.1184 0.930 0.984 0.016
#> GSM751351 1 0.1184 0.930 0.984 0.016
#> GSM751362 2 0.1184 0.978 0.016 0.984
#> GSM751363 2 0.1184 0.977 0.016 0.984
#> GSM751367 2 0.3274 0.947 0.060 0.940
#> GSM751368 2 0.1184 0.977 0.016 0.984
#> GSM751371 2 0.1184 0.977 0.016 0.984
#> GSM751375 2 0.0672 0.978 0.008 0.992
#> GSM751376 2 0.0938 0.977 0.012 0.988
#> GSM751378 2 0.0376 0.978 0.004 0.996
#> GSM751379 2 0.0938 0.977 0.012 0.988
#> GSM751382 2 0.0672 0.978 0.008 0.992
#> GSM751386 2 0.0376 0.979 0.004 0.996
#> GSM751388 2 0.0672 0.978 0.008 0.992
#> GSM751391 2 0.0938 0.978 0.012 0.988
#> GSM751410 2 0.0938 0.978 0.012 0.988
#> GSM751414 2 0.1184 0.977 0.016 0.984
#> GSM751361 2 0.1184 0.977 0.016 0.984
#> GSM751365 2 0.0938 0.978 0.012 0.988
#> GSM751366 2 0.0938 0.978 0.012 0.988
#> GSM751369 2 0.0938 0.978 0.012 0.988
#> GSM751370 2 0.0938 0.978 0.012 0.988
#> GSM751372 2 0.0938 0.978 0.012 0.988
#> GSM751373 2 0.2423 0.968 0.040 0.960
#> GSM751374 2 0.0938 0.977 0.012 0.988
#> GSM751377 2 0.0672 0.978 0.008 0.992
#> GSM751380 2 0.0672 0.978 0.008 0.992
#> GSM751381 2 0.0672 0.978 0.008 0.992
#> GSM751383 2 0.2043 0.971 0.032 0.968
#> GSM751384 2 0.0000 0.979 0.000 1.000
#> GSM751385 2 0.0000 0.979 0.000 1.000
#> GSM751387 2 0.0376 0.979 0.004 0.996
#> GSM751389 2 0.0376 0.978 0.004 0.996
#> GSM751393 2 0.0376 0.978 0.004 0.996
#> GSM751394 2 0.0672 0.978 0.008 0.992
#> GSM751395 2 0.0376 0.978 0.004 0.996
#> GSM751397 2 0.0672 0.978 0.008 0.992
#> GSM751398 2 0.0672 0.978 0.008 0.992
#> GSM751404 2 0.0938 0.978 0.012 0.988
#> GSM751406 2 0.0938 0.977 0.012 0.988
#> GSM751411 2 0.0376 0.979 0.004 0.996
#> GSM751413 2 0.1184 0.977 0.016 0.984
#> GSM751415 2 0.0938 0.978 0.012 0.988
#> GSM751416 2 0.1184 0.977 0.016 0.984
#> GSM751417 2 0.1184 0.977 0.016 0.984
#> GSM751421 2 0.1184 0.977 0.016 0.984
#> GSM751422 2 0.1184 0.977 0.016 0.984
#> GSM751360 2 0.1184 0.977 0.016 0.984
#> GSM751364 2 0.1184 0.977 0.016 0.984
#> GSM751390 2 0.0376 0.979 0.004 0.996
#> GSM751392 2 0.0672 0.978 0.008 0.992
#> GSM751396 2 0.1184 0.978 0.016 0.984
#> GSM751399 2 0.0376 0.978 0.004 0.996
#> GSM751400 2 0.2236 0.968 0.036 0.964
#> GSM751401 2 0.2043 0.970 0.032 0.968
#> GSM751402 2 0.2236 0.968 0.036 0.964
#> GSM751403 2 0.1184 0.977 0.016 0.984
#> GSM751405 2 0.0938 0.977 0.012 0.988
#> GSM751407 2 0.2043 0.970 0.032 0.968
#> GSM751408 2 0.1633 0.974 0.024 0.976
#> GSM751409 2 0.0376 0.978 0.004 0.996
#> GSM751412 2 0.0672 0.979 0.008 0.992
#> GSM751418 2 0.2423 0.968 0.040 0.960
#> GSM751419 2 0.2423 0.968 0.040 0.960
#> GSM751420 2 0.0938 0.977 0.012 0.988
#> GSM751425 2 0.0672 0.978 0.008 0.992
#> GSM751429 2 0.1843 0.973 0.028 0.972
#> GSM751430 2 0.0672 0.978 0.008 0.992
#> GSM751433 2 0.2236 0.970 0.036 0.964
#> GSM751437 2 0.0938 0.977 0.012 0.988
#> GSM751448 2 0.0938 0.977 0.012 0.988
#> GSM751451 2 0.2423 0.968 0.040 0.960
#> GSM751423 2 0.0938 0.979 0.012 0.988
#> GSM751424 2 0.2236 0.970 0.036 0.964
#> GSM751428 2 0.2043 0.972 0.032 0.968
#> GSM751431 2 0.1843 0.973 0.028 0.972
#> GSM751432 2 0.2043 0.972 0.032 0.968
#> GSM751434 2 0.2948 0.959 0.052 0.948
#> GSM751435 2 0.3114 0.958 0.056 0.944
#> GSM751436 2 0.2948 0.959 0.052 0.948
#> GSM751440 2 0.2778 0.962 0.048 0.952
#> GSM751444 2 0.2423 0.970 0.040 0.960
#> GSM751446 2 0.2043 0.971 0.032 0.968
#> GSM751449 2 0.0938 0.977 0.012 0.988
#> GSM751450 2 0.1843 0.973 0.028 0.972
#> GSM751452 2 0.2236 0.970 0.036 0.964
#> GSM751426 2 0.2948 0.959 0.052 0.948
#> GSM751427 2 0.1184 0.977 0.016 0.984
#> GSM751438 2 0.0938 0.977 0.012 0.988
#> GSM751439 2 0.2778 0.963 0.048 0.952
#> GSM751441 2 0.0938 0.977 0.012 0.988
#> GSM751442 2 0.3114 0.957 0.056 0.944
#> GSM751443 2 0.0938 0.977 0.012 0.988
#> GSM751445 2 0.0938 0.977 0.012 0.988
#> GSM751447 2 0.0938 0.978 0.012 0.988
#> GSM751453 2 0.3114 0.959 0.056 0.944
#> GSM751454 2 0.3114 0.959 0.056 0.944
#> GSM751455 2 0.3114 0.957 0.056 0.944
#> GSM751456 2 0.3114 0.957 0.056 0.944
#> GSM751457 2 0.0938 0.977 0.012 0.988
#> GSM751458 2 0.0938 0.977 0.012 0.988
cbind(get_classes(res, k = 3), get_membership(res, k = 3))
#> class entropy silhouette p1 p2 p3
#> GSM751298 1 0.2050 0.8924 0.952 0.020 0.028
#> GSM751304 2 0.6228 0.3213 0.012 0.672 0.316
#> GSM751305 2 0.5775 0.4491 0.012 0.728 0.260
#> GSM751307 2 0.4059 0.6388 0.012 0.860 0.128
#> GSM751310 1 0.6025 0.7195 0.740 0.232 0.028
#> GSM751314 1 0.2280 0.8809 0.940 0.052 0.008
#> GSM751316 1 0.8425 0.3774 0.552 0.348 0.100
#> GSM751318 1 0.7810 0.5745 0.640 0.268 0.092
#> GSM751342 1 0.7184 0.2393 0.504 0.472 0.024
#> GSM751346 1 0.2939 0.8842 0.916 0.012 0.072
#> GSM751347 1 0.3973 0.8740 0.880 0.032 0.088
#> GSM751348 2 0.4531 0.5872 0.008 0.824 0.168
#> GSM751349 2 0.3116 0.6435 0.000 0.892 0.108
#> GSM751352 2 0.4062 0.5972 0.000 0.836 0.164
#> GSM751353 2 0.3412 0.6380 0.000 0.876 0.124
#> GSM751354 2 0.5591 0.4216 0.000 0.696 0.304
#> GSM751355 2 0.5178 0.4754 0.000 0.744 0.256
#> GSM751358 2 0.5325 0.4957 0.004 0.748 0.248
#> GSM751359 2 0.4291 0.5818 0.000 0.820 0.180
#> GSM751294 2 0.5138 0.4895 0.000 0.748 0.252
#> GSM751296 1 0.2173 0.8905 0.944 0.008 0.048
#> GSM751297 1 0.6425 0.7952 0.764 0.140 0.096
#> GSM751299 2 0.4399 0.5789 0.000 0.812 0.188
#> GSM751300 1 0.2939 0.8842 0.916 0.012 0.072
#> GSM751301 1 0.4291 0.8140 0.840 0.152 0.008
#> GSM751302 1 0.2939 0.8842 0.916 0.012 0.072
#> GSM751303 1 0.6490 0.6792 0.708 0.256 0.036
#> GSM751306 1 0.5220 0.7614 0.780 0.208 0.012
#> GSM751308 2 0.8688 0.3561 0.208 0.596 0.196
#> GSM751309 1 0.4912 0.7767 0.796 0.196 0.008
#> GSM751311 1 0.1525 0.8904 0.964 0.032 0.004
#> GSM751312 1 0.6208 0.7604 0.752 0.200 0.048
#> GSM751313 1 0.1643 0.8920 0.956 0.000 0.044
#> GSM751315 1 0.0237 0.8957 0.996 0.004 0.000
#> GSM751317 1 0.5020 0.7792 0.796 0.192 0.012
#> GSM751320 1 0.0000 0.8957 1.000 0.000 0.000
#> GSM751321 1 0.0237 0.8957 0.996 0.004 0.000
#> GSM751322 1 0.0424 0.8954 0.992 0.008 0.000
#> GSM751324 1 0.0829 0.8946 0.984 0.012 0.004
#> GSM751325 1 0.0592 0.8949 0.988 0.012 0.000
#> GSM751332 1 0.0592 0.8949 0.988 0.012 0.000
#> GSM751334 1 0.0424 0.8954 0.992 0.008 0.000
#> GSM751339 1 0.7085 0.6927 0.716 0.188 0.096
#> GSM751341 1 0.2947 0.8829 0.920 0.060 0.020
#> GSM751343 1 0.0592 0.8949 0.988 0.012 0.000
#> GSM751344 2 0.3619 0.6109 0.000 0.864 0.136
#> GSM751345 2 0.3619 0.6109 0.000 0.864 0.136
#> GSM751356 2 0.5325 0.4883 0.004 0.748 0.248
#> GSM751357 2 0.5325 0.4883 0.004 0.748 0.248
#> GSM751293 1 0.4473 0.8013 0.828 0.164 0.008
#> GSM751295 1 0.2939 0.8842 0.916 0.012 0.072
#> GSM751319 1 0.0592 0.8953 0.988 0.012 0.000
#> GSM751323 1 0.0000 0.8957 1.000 0.000 0.000
#> GSM751326 1 0.0747 0.8952 0.984 0.000 0.016
#> GSM751327 1 0.0000 0.8957 1.000 0.000 0.000
#> GSM751328 1 0.0592 0.8949 0.988 0.012 0.000
#> GSM751329 1 0.0661 0.8959 0.988 0.008 0.004
#> GSM751330 1 0.2096 0.8903 0.944 0.004 0.052
#> GSM751331 1 0.2550 0.8883 0.932 0.012 0.056
#> GSM751333 1 0.1643 0.8920 0.956 0.000 0.044
#> GSM751335 1 0.2096 0.8903 0.944 0.004 0.052
#> GSM751336 1 0.2550 0.8883 0.932 0.012 0.056
#> GSM751337 1 0.0237 0.8957 0.996 0.000 0.004
#> GSM751338 1 0.0237 0.8957 0.996 0.000 0.004
#> GSM751340 1 0.9446 0.2684 0.500 0.272 0.228
#> GSM751350 1 0.2939 0.8842 0.916 0.012 0.072
#> GSM751351 1 0.2939 0.8842 0.916 0.012 0.072
#> GSM751362 3 0.5285 0.6829 0.004 0.244 0.752
#> GSM751363 3 0.6696 0.6658 0.020 0.348 0.632
#> GSM751367 3 0.8976 0.5424 0.152 0.316 0.532
#> GSM751368 3 0.6260 0.1352 0.000 0.448 0.552
#> GSM751371 3 0.7263 0.5851 0.036 0.372 0.592
#> GSM751375 2 0.3412 0.6413 0.000 0.876 0.124
#> GSM751376 2 0.6309 -0.2551 0.000 0.504 0.496
#> GSM751378 3 0.6274 0.4034 0.000 0.456 0.544
#> GSM751379 3 0.6267 0.3749 0.000 0.452 0.548
#> GSM751382 2 0.3551 0.6374 0.000 0.868 0.132
#> GSM751386 2 0.6204 -0.0380 0.000 0.576 0.424
#> GSM751388 3 0.6260 0.0265 0.000 0.448 0.552
#> GSM751391 2 0.6632 0.0867 0.012 0.596 0.392
#> GSM751410 3 0.6387 0.6564 0.020 0.300 0.680
#> GSM751414 3 0.6016 0.7115 0.020 0.256 0.724
#> GSM751361 3 0.6735 0.5208 0.012 0.424 0.564
#> GSM751365 3 0.4261 0.6571 0.012 0.140 0.848
#> GSM751366 3 0.4418 0.7029 0.020 0.132 0.848
#> GSM751369 3 0.5815 0.6473 0.004 0.304 0.692
#> GSM751370 3 0.5977 0.7099 0.020 0.252 0.728
#> GSM751372 3 0.5578 0.7071 0.012 0.240 0.748
#> GSM751373 3 0.5036 0.6192 0.020 0.172 0.808
#> GSM751374 3 0.6274 0.3652 0.000 0.456 0.544
#> GSM751377 3 0.5835 0.6205 0.000 0.340 0.660
#> GSM751380 3 0.4840 0.7177 0.016 0.168 0.816
#> GSM751381 2 0.6192 -0.0218 0.000 0.580 0.420
#> GSM751383 3 0.6180 0.1304 0.000 0.416 0.584
#> GSM751384 3 0.5678 0.6852 0.000 0.316 0.684
#> GSM751385 3 0.5835 0.6568 0.000 0.340 0.660
#> GSM751387 3 0.6260 0.0258 0.000 0.448 0.552
#> GSM751389 3 0.4654 0.7078 0.000 0.208 0.792
#> GSM751393 3 0.5327 0.6866 0.000 0.272 0.728
#> GSM751394 2 0.6215 -0.0536 0.000 0.572 0.428
#> GSM751395 2 0.6305 -0.2509 0.000 0.516 0.484
#> GSM751397 2 0.6286 -0.2647 0.000 0.536 0.464
#> GSM751398 2 0.6225 -0.0679 0.000 0.568 0.432
#> GSM751404 3 0.2448 0.6795 0.000 0.076 0.924
#> GSM751406 3 0.5016 0.6895 0.000 0.240 0.760
#> GSM751411 3 0.5016 0.7188 0.000 0.240 0.760
#> GSM751413 3 0.6745 0.5625 0.012 0.428 0.560
#> GSM751415 3 0.4452 0.7114 0.000 0.192 0.808
#> GSM751416 3 0.5992 0.6909 0.016 0.268 0.716
#> GSM751417 3 0.5992 0.6909 0.016 0.268 0.716
#> GSM751421 3 0.6161 0.6879 0.020 0.272 0.708
#> GSM751422 3 0.6229 0.6840 0.020 0.280 0.700
#> GSM751360 3 0.6627 0.6682 0.020 0.336 0.644
#> GSM751364 3 0.5803 0.6889 0.016 0.248 0.736
#> GSM751390 3 0.5650 0.4238 0.000 0.312 0.688
#> GSM751392 2 0.6154 0.0364 0.000 0.592 0.408
#> GSM751396 2 0.6280 0.2660 0.000 0.540 0.460
#> GSM751399 3 0.4235 0.7189 0.000 0.176 0.824
#> GSM751400 3 0.2711 0.6748 0.000 0.088 0.912
#> GSM751401 3 0.2448 0.6795 0.000 0.076 0.924
#> GSM751402 3 0.2625 0.6797 0.000 0.084 0.916
#> GSM751403 3 0.2959 0.6850 0.000 0.100 0.900
#> GSM751405 3 0.5058 0.6886 0.000 0.244 0.756
#> GSM751407 3 0.2448 0.6795 0.000 0.076 0.924
#> GSM751408 3 0.2959 0.6722 0.000 0.100 0.900
#> GSM751409 3 0.4452 0.7181 0.000 0.192 0.808
#> GSM751412 3 0.3038 0.6703 0.000 0.104 0.896
#> GSM751418 3 0.4953 0.6176 0.016 0.176 0.808
#> GSM751419 3 0.4953 0.6176 0.016 0.176 0.808
#> GSM751420 3 0.4399 0.6870 0.000 0.188 0.812
#> GSM751425 2 0.2066 0.6584 0.000 0.940 0.060
#> GSM751429 3 0.6307 0.3007 0.000 0.488 0.512
#> GSM751430 2 0.5216 0.6463 0.000 0.740 0.260
#> GSM751433 2 0.4605 0.6501 0.000 0.796 0.204
#> GSM751437 3 0.6154 0.4694 0.000 0.408 0.592
#> GSM751448 3 0.6111 0.4929 0.000 0.396 0.604
#> GSM751451 2 0.4733 0.6426 0.004 0.800 0.196
#> GSM751423 2 0.2261 0.6598 0.000 0.932 0.068
#> GSM751424 2 0.4702 0.6513 0.000 0.788 0.212
#> GSM751428 2 0.4974 0.6495 0.000 0.764 0.236
#> GSM751431 2 0.4605 0.6501 0.000 0.796 0.204
#> GSM751432 2 0.4842 0.6505 0.000 0.776 0.224
#> GSM751434 2 0.4702 0.6513 0.000 0.788 0.212
#> GSM751435 2 0.4931 0.6492 0.000 0.768 0.232
#> GSM751436 2 0.4702 0.6513 0.000 0.788 0.212
#> GSM751440 2 0.4887 0.6445 0.000 0.772 0.228
#> GSM751444 2 0.4750 0.6560 0.000 0.784 0.216
#> GSM751446 2 0.3816 0.6669 0.000 0.852 0.148
#> GSM751449 2 0.3340 0.6629 0.000 0.880 0.120
#> GSM751450 2 0.4654 0.6539 0.000 0.792 0.208
#> GSM751452 2 0.4702 0.6513 0.000 0.788 0.212
#> GSM751426 2 0.4702 0.6513 0.000 0.788 0.212
#> GSM751427 2 0.4842 0.6570 0.000 0.776 0.224
#> GSM751438 2 0.3551 0.6647 0.000 0.868 0.132
#> GSM751439 2 0.5560 0.6197 0.000 0.700 0.300
#> GSM751441 2 0.4974 0.6617 0.000 0.764 0.236
#> GSM751442 2 0.5058 0.6486 0.000 0.756 0.244
#> GSM751443 2 0.5882 0.3140 0.000 0.652 0.348
#> GSM751445 2 0.2959 0.6524 0.000 0.900 0.100
#> GSM751447 2 0.4605 0.6610 0.000 0.796 0.204
#> GSM751453 2 0.4750 0.6535 0.000 0.784 0.216
#> GSM751454 2 0.4750 0.6535 0.000 0.784 0.216
#> GSM751455 2 0.5138 0.6503 0.000 0.748 0.252
#> GSM751456 2 0.5138 0.6503 0.000 0.748 0.252
#> GSM751457 2 0.4291 0.6058 0.000 0.820 0.180
#> GSM751458 2 0.4291 0.6058 0.000 0.820 0.180
cbind(get_classes(res, k = 4), get_membership(res, k = 4))
#> class entropy silhouette p1 p2 p3 p4
#> GSM751298 1 0.3335 0.79741 0.860 0.120 0.000 0.020
#> GSM751304 4 0.3707 0.57176 0.004 0.032 0.112 0.852
#> GSM751305 4 0.4253 0.56172 0.004 0.044 0.132 0.820
#> GSM751307 4 0.6567 0.46479 0.016 0.136 0.176 0.672
#> GSM751310 1 0.6542 0.58521 0.668 0.020 0.100 0.212
#> GSM751314 1 0.4080 0.75120 0.848 0.016 0.088 0.048
#> GSM751316 4 0.7398 0.18374 0.336 0.020 0.112 0.532
#> GSM751318 1 0.6700 0.53798 0.640 0.068 0.032 0.260
#> GSM751342 1 0.6460 0.40024 0.580 0.048 0.016 0.356
#> GSM751346 1 0.5658 0.72712 0.632 0.328 0.000 0.040
#> GSM751347 1 0.6381 0.71252 0.604 0.328 0.012 0.056
#> GSM751348 4 0.3846 0.53736 0.024 0.088 0.028 0.860
#> GSM751349 4 0.5998 0.40692 0.000 0.200 0.116 0.684
#> GSM751352 4 0.3108 0.50458 0.000 0.112 0.016 0.872
#> GSM751353 4 0.4916 0.42734 0.000 0.184 0.056 0.760
#> GSM751354 4 0.4462 0.54093 0.000 0.132 0.064 0.804
#> GSM751355 4 0.5280 0.51136 0.000 0.124 0.124 0.752
#> GSM751358 4 0.3508 0.56400 0.004 0.064 0.060 0.872
#> GSM751359 4 0.5010 0.52119 0.000 0.120 0.108 0.772
#> GSM751294 4 0.2936 0.56023 0.004 0.056 0.040 0.900
#> GSM751296 1 0.4361 0.77751 0.772 0.208 0.000 0.020
#> GSM751297 1 0.7866 0.60615 0.488 0.328 0.020 0.164
#> GSM751299 4 0.4290 0.44561 0.000 0.212 0.016 0.772
#> GSM751300 1 0.5658 0.72712 0.632 0.328 0.000 0.040
#> GSM751301 1 0.4332 0.72526 0.800 0.040 0.000 0.160
#> GSM751302 1 0.5658 0.72712 0.632 0.328 0.000 0.040
#> GSM751303 1 0.6864 0.48406 0.600 0.016 0.092 0.292
#> GSM751306 1 0.6429 0.59816 0.676 0.020 0.092 0.212
#> GSM751308 4 0.6380 0.31429 0.300 0.064 0.012 0.624
#> GSM751309 1 0.5515 0.66179 0.740 0.016 0.056 0.188
#> GSM751311 1 0.3215 0.77459 0.888 0.016 0.020 0.076
#> GSM751312 1 0.8919 0.47001 0.460 0.152 0.104 0.284
#> GSM751313 1 0.4663 0.75884 0.716 0.272 0.000 0.012
#> GSM751315 1 0.2231 0.80907 0.932 0.044 0.012 0.012
#> GSM751317 1 0.6396 0.58854 0.668 0.016 0.088 0.228
#> GSM751320 1 0.0564 0.80602 0.988 0.004 0.004 0.004
#> GSM751321 1 0.2465 0.80809 0.924 0.044 0.020 0.012
#> GSM751322 1 0.0992 0.80259 0.976 0.008 0.004 0.012
#> GSM751324 1 0.1394 0.80089 0.964 0.008 0.012 0.016
#> GSM751325 1 0.0859 0.80314 0.980 0.008 0.004 0.008
#> GSM751332 1 0.0992 0.80346 0.976 0.008 0.012 0.004
#> GSM751334 1 0.0712 0.80391 0.984 0.008 0.004 0.004
#> GSM751339 1 0.7032 0.50289 0.576 0.048 0.048 0.328
#> GSM751341 1 0.2207 0.80344 0.932 0.024 0.004 0.040
#> GSM751343 1 0.1339 0.80102 0.964 0.008 0.004 0.024
#> GSM751344 4 0.3495 0.49335 0.000 0.140 0.016 0.844
#> GSM751345 4 0.3495 0.49335 0.000 0.140 0.016 0.844
#> GSM751356 4 0.3001 0.55436 0.004 0.064 0.036 0.896
#> GSM751357 4 0.3001 0.55436 0.004 0.064 0.036 0.896
#> GSM751293 1 0.4332 0.72526 0.800 0.040 0.000 0.160
#> GSM751295 1 0.5658 0.72712 0.632 0.328 0.000 0.040
#> GSM751319 1 0.2529 0.80978 0.920 0.048 0.008 0.024
#> GSM751323 1 0.0817 0.80765 0.976 0.024 0.000 0.000
#> GSM751326 1 0.1940 0.80650 0.924 0.076 0.000 0.000
#> GSM751327 1 0.0895 0.80759 0.976 0.020 0.000 0.004
#> GSM751328 1 0.0712 0.80391 0.984 0.008 0.004 0.004
#> GSM751329 1 0.0469 0.80545 0.988 0.012 0.000 0.000
#> GSM751330 1 0.5108 0.74349 0.672 0.308 0.000 0.020
#> GSM751331 1 0.5639 0.72888 0.636 0.324 0.000 0.040
#> GSM751333 1 0.4284 0.77273 0.764 0.224 0.000 0.012
#> GSM751335 1 0.5108 0.74349 0.672 0.308 0.000 0.020
#> GSM751336 1 0.5432 0.73542 0.652 0.316 0.000 0.032
#> GSM751337 1 0.1716 0.80734 0.936 0.064 0.000 0.000
#> GSM751338 1 0.2179 0.80879 0.924 0.064 0.000 0.012
#> GSM751340 4 0.8339 0.14405 0.288 0.048 0.172 0.492
#> GSM751350 1 0.5658 0.72712 0.632 0.328 0.000 0.040
#> GSM751351 1 0.5658 0.72712 0.632 0.328 0.000 0.040
#> GSM751362 3 0.4964 0.56655 0.000 0.032 0.724 0.244
#> GSM751363 3 0.5321 0.48166 0.000 0.032 0.672 0.296
#> GSM751367 3 0.7516 0.36973 0.096 0.048 0.580 0.276
#> GSM751368 3 0.6673 0.28609 0.000 0.140 0.608 0.252
#> GSM751371 4 0.7073 0.11664 0.108 0.008 0.348 0.536
#> GSM751375 4 0.6240 0.37564 0.000 0.200 0.136 0.664
#> GSM751376 4 0.5489 0.38178 0.000 0.060 0.240 0.700
#> GSM751378 4 0.5658 0.21932 0.000 0.040 0.328 0.632
#> GSM751379 4 0.5861 0.27437 0.000 0.060 0.296 0.644
#> GSM751382 4 0.6429 0.38383 0.000 0.192 0.160 0.648
#> GSM751386 4 0.6970 -0.06091 0.000 0.112 0.444 0.444
#> GSM751388 3 0.7133 0.15586 0.000 0.148 0.520 0.332
#> GSM751391 4 0.4872 0.50231 0.004 0.032 0.212 0.752
#> GSM751410 3 0.5353 0.31529 0.000 0.012 0.556 0.432
#> GSM751414 3 0.3390 0.62889 0.000 0.016 0.852 0.132
#> GSM751361 3 0.5681 0.29903 0.000 0.028 0.568 0.404
#> GSM751365 3 0.2032 0.63195 0.000 0.036 0.936 0.028
#> GSM751366 3 0.1820 0.64645 0.000 0.020 0.944 0.036
#> GSM751369 3 0.5774 0.23675 0.000 0.028 0.508 0.464
#> GSM751370 3 0.3224 0.63129 0.000 0.016 0.864 0.120
#> GSM751372 3 0.2949 0.63977 0.000 0.024 0.888 0.088
#> GSM751373 3 0.2565 0.62413 0.000 0.056 0.912 0.032
#> GSM751374 4 0.5861 0.27437 0.000 0.060 0.296 0.644
#> GSM751377 3 0.5759 0.50879 0.000 0.080 0.688 0.232
#> GSM751380 3 0.3501 0.63267 0.000 0.020 0.848 0.132
#> GSM751381 4 0.7003 -0.00521 0.000 0.116 0.424 0.460
#> GSM751383 3 0.7300 0.19190 0.000 0.180 0.516 0.304
#> GSM751384 3 0.5367 0.50494 0.000 0.032 0.664 0.304
#> GSM751385 3 0.5771 0.28665 0.000 0.028 0.512 0.460
#> GSM751387 3 0.7385 0.11417 0.000 0.176 0.484 0.340
#> GSM751389 3 0.5256 0.56172 0.000 0.040 0.700 0.260
#> GSM751393 3 0.5861 0.30408 0.000 0.032 0.492 0.476
#> GSM751394 3 0.6969 0.04389 0.000 0.112 0.452 0.436
#> GSM751395 4 0.4877 0.43954 0.000 0.044 0.204 0.752
#> GSM751397 4 0.6844 -0.07932 0.000 0.100 0.444 0.456
#> GSM751398 3 0.6969 0.03886 0.000 0.112 0.448 0.440
#> GSM751404 3 0.4419 0.61985 0.000 0.084 0.812 0.104
#> GSM751406 3 0.5574 0.53889 0.000 0.048 0.668 0.284
#> GSM751411 3 0.3196 0.64202 0.000 0.008 0.856 0.136
#> GSM751413 3 0.6189 0.28666 0.000 0.060 0.568 0.372
#> GSM751415 3 0.4008 0.62951 0.000 0.032 0.820 0.148
#> GSM751416 3 0.3694 0.62863 0.000 0.032 0.844 0.124
#> GSM751417 3 0.3694 0.62863 0.000 0.032 0.844 0.124
#> GSM751421 3 0.4372 0.54171 0.000 0.004 0.728 0.268
#> GSM751422 3 0.4584 0.51001 0.000 0.004 0.696 0.300
#> GSM751360 3 0.5313 0.40502 0.000 0.016 0.608 0.376
#> GSM751364 3 0.3149 0.63813 0.000 0.032 0.880 0.088
#> GSM751390 3 0.6874 0.29445 0.000 0.136 0.568 0.296
#> GSM751392 4 0.7042 0.10412 0.000 0.124 0.388 0.488
#> GSM751396 3 0.7731 0.01967 0.000 0.248 0.436 0.316
#> GSM751399 3 0.4511 0.62334 0.000 0.040 0.784 0.176
#> GSM751400 3 0.4784 0.60967 0.000 0.100 0.788 0.112
#> GSM751401 3 0.4786 0.60976 0.000 0.104 0.788 0.108
#> GSM751402 3 0.4718 0.61133 0.000 0.092 0.792 0.116
#> GSM751403 3 0.4700 0.61299 0.000 0.084 0.792 0.124
#> GSM751405 3 0.5442 0.53977 0.000 0.040 0.672 0.288
#> GSM751407 3 0.4728 0.61154 0.000 0.104 0.792 0.104
#> GSM751408 3 0.4168 0.62337 0.000 0.080 0.828 0.092
#> GSM751409 3 0.4590 0.61619 0.000 0.036 0.772 0.192
#> GSM751412 3 0.4235 0.62254 0.000 0.084 0.824 0.092
#> GSM751418 3 0.2623 0.62262 0.000 0.064 0.908 0.028
#> GSM751419 3 0.2623 0.62262 0.000 0.064 0.908 0.028
#> GSM751420 3 0.5861 0.49380 0.000 0.060 0.644 0.296
#> GSM751425 4 0.5784 -0.26477 0.000 0.412 0.032 0.556
#> GSM751429 4 0.7458 0.25111 0.012 0.136 0.340 0.512
#> GSM751430 4 0.7613 -0.52958 0.004 0.404 0.172 0.420
#> GSM751433 2 0.6751 0.85877 0.004 0.588 0.108 0.300
#> GSM751437 4 0.6495 0.11587 0.000 0.084 0.356 0.560
#> GSM751448 4 0.6822 -0.07567 0.000 0.100 0.412 0.488
#> GSM751451 2 0.7034 0.81544 0.008 0.548 0.108 0.336
#> GSM751423 2 0.5861 0.47374 0.000 0.492 0.032 0.476
#> GSM751424 2 0.6799 0.86023 0.004 0.584 0.112 0.300
#> GSM751428 2 0.6167 0.87595 0.000 0.648 0.096 0.256
#> GSM751431 2 0.6669 0.87131 0.004 0.604 0.108 0.284
#> GSM751432 2 0.6799 0.86023 0.004 0.584 0.112 0.300
#> GSM751434 2 0.6780 0.86118 0.004 0.588 0.112 0.296
#> GSM751435 2 0.6221 0.87633 0.000 0.644 0.100 0.256
#> GSM751436 2 0.6731 0.86135 0.004 0.592 0.108 0.296
#> GSM751440 2 0.6370 0.87519 0.004 0.644 0.100 0.252
#> GSM751444 2 0.6323 0.87324 0.000 0.628 0.100 0.272
#> GSM751446 2 0.6310 0.73311 0.000 0.576 0.072 0.352
#> GSM751449 2 0.6188 0.63906 0.000 0.548 0.056 0.396
#> GSM751450 2 0.6476 0.87750 0.004 0.632 0.104 0.260
#> GSM751452 2 0.6799 0.86023 0.004 0.584 0.112 0.300
#> GSM751426 2 0.6552 0.87513 0.004 0.624 0.108 0.264
#> GSM751427 2 0.6182 0.86883 0.000 0.636 0.088 0.276
#> GSM751438 2 0.6223 0.68043 0.000 0.556 0.060 0.384
#> GSM751439 2 0.6552 0.78722 0.000 0.628 0.144 0.228
#> GSM751441 2 0.6430 0.86026 0.000 0.596 0.092 0.312
#> GSM751442 2 0.6323 0.86283 0.000 0.628 0.100 0.272
#> GSM751443 4 0.7456 0.25135 0.000 0.316 0.196 0.488
#> GSM751445 2 0.5696 0.47790 0.000 0.496 0.024 0.480
#> GSM751447 2 0.6415 0.87784 0.000 0.612 0.100 0.288
#> GSM751453 2 0.6426 0.87921 0.000 0.620 0.108 0.272
#> GSM751454 2 0.6426 0.87921 0.000 0.620 0.108 0.272
#> GSM751455 2 0.6323 0.86283 0.000 0.628 0.100 0.272
#> GSM751456 2 0.6323 0.86283 0.000 0.628 0.100 0.272
#> GSM751457 4 0.5678 0.16135 0.000 0.316 0.044 0.640
#> GSM751458 4 0.5678 0.16135 0.000 0.316 0.044 0.640
cbind(get_classes(res, k = 5), get_membership(res, k = 5))
#> class entropy silhouette p1 p2 p3 p4 p5
#> GSM751298 4 0.2798 0.58751 0.140 0.008 0.000 0.852 0.000
#> GSM751304 5 0.4601 0.51704 0.084 0.080 0.032 0.008 0.796
#> GSM751305 5 0.4470 0.51605 0.096 0.084 0.016 0.008 0.796
#> GSM751307 5 0.7591 0.45029 0.200 0.196 0.052 0.024 0.528
#> GSM751310 4 0.5937 0.56862 0.128 0.012 0.008 0.652 0.200
#> GSM751314 4 0.3680 0.70790 0.088 0.020 0.000 0.840 0.052
#> GSM751316 5 0.6664 0.27796 0.132 0.028 0.008 0.256 0.576
#> GSM751318 4 0.5299 0.62682 0.052 0.060 0.000 0.724 0.164
#> GSM751342 4 0.5338 0.60683 0.056 0.040 0.000 0.704 0.200
#> GSM751346 1 0.4438 0.94232 0.608 0.004 0.000 0.384 0.004
#> GSM751347 1 0.4790 0.89554 0.632 0.004 0.008 0.344 0.012
#> GSM751348 5 0.5227 0.50164 0.032 0.136 0.012 0.072 0.748
#> GSM751349 5 0.6311 0.46472 0.096 0.224 0.056 0.000 0.624
#> GSM751352 5 0.4715 0.48144 0.048 0.168 0.016 0.008 0.760
#> GSM751353 5 0.4943 0.47899 0.076 0.200 0.008 0.000 0.716
#> GSM751354 5 0.5875 0.50948 0.128 0.148 0.044 0.000 0.680
#> GSM751355 5 0.6269 0.50446 0.136 0.148 0.064 0.000 0.652
#> GSM751358 5 0.4697 0.51659 0.028 0.124 0.036 0.024 0.788
#> GSM751359 5 0.5041 0.52516 0.080 0.152 0.028 0.000 0.740
#> GSM751294 5 0.4966 0.50892 0.040 0.124 0.048 0.016 0.772
#> GSM751296 4 0.3949 0.01062 0.300 0.000 0.000 0.696 0.004
#> GSM751297 1 0.5312 0.78602 0.644 0.004 0.004 0.288 0.060
#> GSM751299 5 0.5152 0.46779 0.104 0.164 0.004 0.008 0.720
#> GSM751300 1 0.4438 0.94232 0.608 0.004 0.000 0.384 0.004
#> GSM751301 4 0.3898 0.67111 0.032 0.028 0.000 0.820 0.120
#> GSM751302 1 0.4438 0.94232 0.608 0.004 0.000 0.384 0.004
#> GSM751303 4 0.5950 0.57396 0.112 0.020 0.004 0.648 0.216
#> GSM751306 4 0.5576 0.61509 0.112 0.020 0.004 0.696 0.168
#> GSM751308 5 0.6910 0.00869 0.040 0.072 0.020 0.372 0.496
#> GSM751309 4 0.4857 0.65689 0.088 0.020 0.000 0.752 0.140
#> GSM751311 4 0.2949 0.73310 0.048 0.016 0.000 0.884 0.052
#> GSM751312 5 0.7213 -0.09626 0.324 0.008 0.008 0.264 0.396
#> GSM751313 1 0.4557 0.81615 0.516 0.000 0.000 0.476 0.008
#> GSM751315 4 0.2871 0.70802 0.088 0.000 0.000 0.872 0.040
#> GSM751317 4 0.5657 0.58348 0.116 0.012 0.000 0.656 0.216
#> GSM751320 4 0.1041 0.72000 0.032 0.000 0.000 0.964 0.004
#> GSM751321 4 0.2813 0.71130 0.084 0.000 0.000 0.876 0.040
#> GSM751322 4 0.0613 0.74371 0.004 0.008 0.000 0.984 0.004
#> GSM751324 4 0.1686 0.74521 0.028 0.020 0.000 0.944 0.008
#> GSM751325 4 0.0854 0.73953 0.008 0.012 0.000 0.976 0.004
#> GSM751332 4 0.1485 0.73670 0.032 0.020 0.000 0.948 0.000
#> GSM751334 4 0.1153 0.72835 0.024 0.008 0.000 0.964 0.004
#> GSM751339 4 0.7030 0.35494 0.128 0.000 0.052 0.492 0.328
#> GSM751341 4 0.1960 0.73912 0.048 0.020 0.000 0.928 0.004
#> GSM751343 4 0.0968 0.74543 0.004 0.012 0.000 0.972 0.012
#> GSM751344 5 0.4557 0.48051 0.056 0.172 0.004 0.008 0.760
#> GSM751345 5 0.4557 0.48051 0.056 0.172 0.004 0.008 0.760
#> GSM751356 5 0.5078 0.50690 0.044 0.124 0.040 0.024 0.768
#> GSM751357 5 0.5078 0.50690 0.044 0.124 0.040 0.024 0.768
#> GSM751293 4 0.3946 0.67092 0.032 0.028 0.000 0.816 0.124
#> GSM751295 1 0.4438 0.94232 0.608 0.004 0.000 0.384 0.004
#> GSM751319 4 0.3215 0.69899 0.092 0.000 0.000 0.852 0.056
#> GSM751323 4 0.1557 0.70132 0.052 0.000 0.000 0.940 0.008
#> GSM751326 4 0.2612 0.59181 0.124 0.000 0.000 0.868 0.008
#> GSM751327 4 0.1628 0.69755 0.056 0.000 0.000 0.936 0.008
#> GSM751328 4 0.1012 0.73185 0.020 0.012 0.000 0.968 0.000
#> GSM751329 4 0.1443 0.71194 0.044 0.004 0.000 0.948 0.004
#> GSM751330 1 0.4446 0.92816 0.592 0.000 0.000 0.400 0.008
#> GSM751331 1 0.4438 0.94044 0.608 0.004 0.000 0.384 0.004
#> GSM751333 1 0.4561 0.79042 0.504 0.000 0.000 0.488 0.008
#> GSM751335 1 0.4446 0.92816 0.592 0.000 0.000 0.400 0.008
#> GSM751336 1 0.4564 0.93709 0.600 0.004 0.000 0.388 0.008
#> GSM751337 4 0.2304 0.64204 0.100 0.000 0.000 0.892 0.008
#> GSM751338 4 0.2570 0.68928 0.084 0.000 0.000 0.888 0.028
#> GSM751340 5 0.7769 0.17096 0.156 0.012 0.088 0.248 0.496
#> GSM751350 1 0.4438 0.94232 0.608 0.004 0.000 0.384 0.004
#> GSM751351 1 0.4438 0.94232 0.608 0.004 0.000 0.384 0.004
#> GSM751362 3 0.5694 0.41170 0.136 0.004 0.636 0.000 0.224
#> GSM751363 5 0.7467 -0.19242 0.296 0.032 0.312 0.000 0.360
#> GSM751367 3 0.8585 0.15350 0.232 0.040 0.344 0.068 0.316
#> GSM751368 3 0.8251 0.23751 0.216 0.144 0.380 0.000 0.260
#> GSM751371 5 0.7399 0.33583 0.132 0.024 0.152 0.104 0.588
#> GSM751375 5 0.6813 0.44336 0.108 0.240 0.076 0.000 0.576
#> GSM751376 5 0.6441 0.39470 0.064 0.080 0.260 0.000 0.596
#> GSM751378 5 0.5616 0.33219 0.024 0.040 0.360 0.000 0.576
#> GSM751379 5 0.6645 0.35317 0.072 0.076 0.292 0.000 0.560
#> GSM751382 5 0.7132 0.43544 0.108 0.240 0.104 0.000 0.548
#> GSM751386 5 0.7996 0.09508 0.188 0.116 0.284 0.000 0.412
#> GSM751388 5 0.8140 -0.01224 0.176 0.136 0.324 0.000 0.364
#> GSM751391 5 0.6228 0.47256 0.092 0.064 0.136 0.020 0.688
#> GSM751410 5 0.6833 -0.00401 0.160 0.020 0.376 0.000 0.444
#> GSM751414 3 0.6701 0.48716 0.260 0.020 0.532 0.000 0.188
#> GSM751361 5 0.7489 -0.12639 0.252 0.040 0.308 0.000 0.400
#> GSM751365 3 0.6442 0.54362 0.196 0.052 0.620 0.000 0.132
#> GSM751366 3 0.3559 0.60170 0.096 0.004 0.836 0.000 0.064
#> GSM751369 5 0.6650 0.05013 0.120 0.024 0.420 0.000 0.436
#> GSM751370 3 0.6765 0.49046 0.264 0.028 0.536 0.000 0.172
#> GSM751372 3 0.6551 0.50732 0.260 0.024 0.560 0.000 0.156
#> GSM751373 3 0.6414 0.55778 0.184 0.056 0.628 0.000 0.132
#> GSM751374 5 0.6645 0.35317 0.072 0.076 0.292 0.000 0.560
#> GSM751377 3 0.7730 0.24072 0.240 0.064 0.404 0.000 0.292
#> GSM751380 3 0.3421 0.58002 0.080 0.000 0.840 0.000 0.080
#> GSM751381 5 0.7945 0.12323 0.176 0.120 0.276 0.000 0.428
#> GSM751383 3 0.8298 0.09311 0.176 0.168 0.348 0.000 0.308
#> GSM751384 3 0.7467 0.11849 0.188 0.052 0.404 0.000 0.356
#> GSM751385 5 0.6991 0.17886 0.168 0.040 0.276 0.000 0.516
#> GSM751387 5 0.8312 -0.02008 0.172 0.176 0.304 0.000 0.348
#> GSM751389 3 0.2920 0.51016 0.016 0.000 0.852 0.000 0.132
#> GSM751393 5 0.6175 0.21120 0.100 0.012 0.376 0.000 0.512
#> GSM751394 5 0.7978 0.06428 0.196 0.108 0.288 0.000 0.408
#> GSM751395 5 0.5395 0.45839 0.040 0.052 0.216 0.000 0.692
#> GSM751397 5 0.7790 0.11968 0.188 0.096 0.272 0.000 0.444
#> GSM751398 5 0.8001 0.08075 0.200 0.112 0.276 0.000 0.412
#> GSM751404 3 0.1934 0.60060 0.008 0.040 0.932 0.000 0.020
#> GSM751406 3 0.3890 0.45547 0.036 0.004 0.792 0.000 0.168
#> GSM751411 3 0.5693 0.54840 0.196 0.016 0.664 0.000 0.124
#> GSM751413 5 0.7688 -0.04617 0.288 0.060 0.244 0.000 0.408
#> GSM751415 3 0.1753 0.59939 0.032 0.000 0.936 0.000 0.032
#> GSM751416 3 0.7123 0.45150 0.264 0.040 0.500 0.000 0.196
#> GSM751417 3 0.7123 0.45150 0.264 0.040 0.500 0.000 0.196
#> GSM751421 3 0.6848 0.25754 0.196 0.012 0.436 0.000 0.356
#> GSM751422 3 0.6854 0.18496 0.192 0.012 0.408 0.000 0.388
#> GSM751360 5 0.7568 -0.16628 0.264 0.028 0.300 0.008 0.400
#> GSM751364 3 0.6905 0.48132 0.264 0.036 0.528 0.000 0.172
#> GSM751390 3 0.7813 0.21123 0.140 0.128 0.444 0.000 0.288
#> GSM751392 5 0.7725 0.23609 0.172 0.132 0.204 0.000 0.492
#> GSM751396 2 0.8392 -0.25097 0.148 0.320 0.248 0.000 0.284
#> GSM751399 3 0.1082 0.59958 0.008 0.000 0.964 0.000 0.028
#> GSM751400 3 0.2032 0.59904 0.004 0.052 0.924 0.000 0.020
#> GSM751401 3 0.2142 0.59581 0.004 0.048 0.920 0.000 0.028
#> GSM751402 3 0.2283 0.59099 0.008 0.036 0.916 0.000 0.040
#> GSM751403 3 0.2661 0.58021 0.008 0.044 0.896 0.000 0.052
#> GSM751405 3 0.4426 0.42088 0.052 0.004 0.748 0.000 0.196
#> GSM751407 3 0.1960 0.59848 0.004 0.048 0.928 0.000 0.020
#> GSM751408 3 0.1960 0.60001 0.004 0.048 0.928 0.000 0.020
#> GSM751409 3 0.1408 0.59759 0.008 0.000 0.948 0.000 0.044
#> GSM751412 3 0.2011 0.60126 0.008 0.044 0.928 0.000 0.020
#> GSM751418 3 0.6302 0.56104 0.156 0.064 0.648 0.000 0.132
#> GSM751419 3 0.6302 0.56104 0.156 0.064 0.648 0.000 0.132
#> GSM751420 3 0.4640 0.39899 0.032 0.024 0.740 0.000 0.204
#> GSM751425 2 0.5014 0.23729 0.020 0.560 0.008 0.000 0.412
#> GSM751429 5 0.8321 0.28027 0.136 0.132 0.288 0.020 0.424
#> GSM751430 2 0.6902 0.23687 0.120 0.564 0.040 0.012 0.264
#> GSM751433 2 0.3098 0.76447 0.028 0.884 0.008 0.024 0.056
#> GSM751437 5 0.6703 0.20057 0.052 0.080 0.408 0.000 0.460
#> GSM751448 3 0.6813 0.00897 0.072 0.076 0.508 0.000 0.344
#> GSM751451 2 0.2816 0.77176 0.024 0.896 0.004 0.024 0.052
#> GSM751423 2 0.4216 0.56484 0.008 0.720 0.012 0.000 0.260
#> GSM751424 2 0.2822 0.76783 0.024 0.896 0.008 0.016 0.056
#> GSM751428 2 0.1243 0.79229 0.008 0.960 0.004 0.000 0.028
#> GSM751431 2 0.2243 0.78088 0.024 0.924 0.004 0.016 0.032
#> GSM751432 2 0.2918 0.76593 0.028 0.892 0.012 0.012 0.056
#> GSM751434 2 0.2909 0.76579 0.028 0.892 0.008 0.016 0.056
#> GSM751435 2 0.0807 0.79090 0.000 0.976 0.012 0.000 0.012
#> GSM751436 2 0.2919 0.76684 0.024 0.892 0.008 0.020 0.056
#> GSM751440 2 0.1362 0.78896 0.012 0.960 0.016 0.008 0.004
#> GSM751444 2 0.1978 0.78713 0.032 0.932 0.012 0.000 0.024
#> GSM751446 2 0.3331 0.75930 0.032 0.864 0.032 0.000 0.072
#> GSM751449 2 0.4082 0.70622 0.028 0.804 0.032 0.000 0.136
#> GSM751450 2 0.1975 0.78337 0.024 0.936 0.004 0.016 0.020
#> GSM751452 2 0.2822 0.76783 0.024 0.896 0.008 0.016 0.056
#> GSM751426 2 0.1871 0.78196 0.020 0.940 0.004 0.012 0.024
#> GSM751427 2 0.2087 0.78401 0.020 0.928 0.020 0.000 0.032
#> GSM751438 2 0.3809 0.73370 0.036 0.832 0.032 0.000 0.100
#> GSM751439 2 0.3372 0.75649 0.032 0.864 0.044 0.000 0.060
#> GSM751441 2 0.2266 0.78100 0.016 0.912 0.008 0.000 0.064
#> GSM751442 2 0.2249 0.77967 0.020 0.920 0.020 0.000 0.040
#> GSM751443 2 0.7778 -0.09594 0.056 0.336 0.308 0.000 0.300
#> GSM751445 2 0.4818 0.56691 0.028 0.700 0.020 0.000 0.252
#> GSM751447 2 0.1701 0.78600 0.016 0.936 0.000 0.000 0.048
#> GSM751453 2 0.1179 0.79079 0.016 0.964 0.004 0.000 0.016
#> GSM751454 2 0.1179 0.79079 0.016 0.964 0.004 0.000 0.016
#> GSM751455 2 0.2249 0.77967 0.020 0.920 0.020 0.000 0.040
#> GSM751456 2 0.2249 0.77967 0.020 0.920 0.020 0.000 0.040
#> GSM751457 2 0.5977 0.06202 0.036 0.464 0.040 0.000 0.460
#> GSM751458 2 0.5977 0.06202 0.036 0.464 0.040 0.000 0.460
cbind(get_classes(res, k = 6), get_membership(res, k = 6))
#> class entropy silhouette p1 p2 p3 p4 p5 p6
#> GSM751298 4 0.3761 0.610261 0.236 0.004 0.000 0.740 0.016 0.004
#> GSM751304 6 0.3880 0.548015 0.016 0.008 0.008 0.044 0.112 0.812
#> GSM751305 6 0.4145 0.538248 0.020 0.004 0.012 0.048 0.124 0.792
#> GSM751307 5 0.7056 -0.081541 0.044 0.072 0.020 0.044 0.472 0.348
#> GSM751310 4 0.5589 0.560831 0.016 0.000 0.008 0.624 0.216 0.136
#> GSM751314 4 0.3469 0.730666 0.020 0.000 0.004 0.828 0.112 0.036
#> GSM751316 6 0.6447 0.335326 0.028 0.000 0.012 0.232 0.204 0.524
#> GSM751318 4 0.2893 0.744474 0.032 0.008 0.000 0.868 0.008 0.084
#> GSM751342 4 0.3469 0.735998 0.028 0.008 0.000 0.832 0.024 0.108
#> GSM751346 1 0.3262 0.936055 0.820 0.004 0.000 0.148 0.020 0.008
#> GSM751347 1 0.3293 0.924238 0.828 0.004 0.000 0.132 0.020 0.016
#> GSM751348 6 0.3894 0.565577 0.016 0.028 0.004 0.020 0.124 0.808
#> GSM751349 6 0.5961 0.252479 0.040 0.052 0.024 0.000 0.336 0.548
#> GSM751352 6 0.2439 0.587462 0.016 0.028 0.000 0.004 0.052 0.900
#> GSM751353 6 0.4804 0.467910 0.036 0.036 0.008 0.000 0.220 0.700
#> GSM751354 6 0.4857 0.526095 0.068 0.012 0.020 0.000 0.188 0.712
#> GSM751355 6 0.5543 0.343083 0.052 0.016 0.024 0.000 0.332 0.576
#> GSM751358 6 0.2387 0.589115 0.016 0.012 0.008 0.016 0.036 0.912
#> GSM751359 6 0.5050 0.400709 0.032 0.036 0.008 0.000 0.276 0.648
#> GSM751294 6 0.2064 0.589370 0.012 0.016 0.008 0.012 0.024 0.928
#> GSM751296 4 0.4493 0.055476 0.436 0.004 0.000 0.540 0.016 0.004
#> GSM751297 1 0.4290 0.843664 0.792 0.004 0.012 0.104 0.036 0.052
#> GSM751299 6 0.2688 0.583302 0.048 0.024 0.000 0.000 0.044 0.884
#> GSM751300 1 0.3262 0.936055 0.820 0.004 0.000 0.148 0.020 0.008
#> GSM751301 4 0.4094 0.675714 0.040 0.008 0.004 0.768 0.008 0.172
#> GSM751302 1 0.2845 0.939527 0.836 0.000 0.000 0.148 0.008 0.008
#> GSM751303 4 0.5446 0.588124 0.020 0.000 0.004 0.644 0.140 0.192
#> GSM751306 4 0.4569 0.670853 0.016 0.000 0.004 0.740 0.132 0.108
#> GSM751308 6 0.4900 0.157483 0.012 0.012 0.008 0.368 0.012 0.588
#> GSM751309 4 0.3332 0.737157 0.020 0.000 0.000 0.840 0.068 0.072
#> GSM751311 4 0.1092 0.773940 0.000 0.000 0.000 0.960 0.020 0.020
#> GSM751312 6 0.7456 0.201060 0.148 0.000 0.008 0.228 0.188 0.428
#> GSM751313 1 0.4250 0.824629 0.720 0.000 0.004 0.224 0.048 0.004
#> GSM751315 4 0.4222 0.715858 0.088 0.000 0.004 0.784 0.092 0.032
#> GSM751317 4 0.5240 0.612687 0.016 0.000 0.004 0.664 0.132 0.184
#> GSM751320 4 0.1983 0.773395 0.072 0.000 0.000 0.908 0.020 0.000
#> GSM751321 4 0.4220 0.712514 0.084 0.000 0.004 0.784 0.096 0.032
#> GSM751322 4 0.1007 0.776967 0.044 0.000 0.000 0.956 0.000 0.000
#> GSM751324 4 0.0858 0.778548 0.028 0.000 0.000 0.968 0.004 0.000
#> GSM751325 4 0.1364 0.775311 0.048 0.000 0.004 0.944 0.004 0.000
#> GSM751332 4 0.2179 0.768535 0.064 0.000 0.008 0.908 0.016 0.004
#> GSM751334 4 0.2806 0.758273 0.084 0.000 0.012 0.872 0.028 0.004
#> GSM751339 4 0.6864 0.254488 0.068 0.000 0.040 0.440 0.072 0.380
#> GSM751341 4 0.2365 0.768709 0.084 0.004 0.000 0.892 0.012 0.008
#> GSM751343 4 0.1082 0.777175 0.040 0.000 0.000 0.956 0.004 0.000
#> GSM751344 6 0.2677 0.576307 0.016 0.024 0.000 0.000 0.084 0.876
#> GSM751345 6 0.2677 0.576307 0.016 0.024 0.000 0.000 0.084 0.876
#> GSM751356 6 0.2074 0.586406 0.012 0.016 0.008 0.016 0.020 0.928
#> GSM751357 6 0.2074 0.586406 0.012 0.016 0.008 0.016 0.020 0.928
#> GSM751293 4 0.4127 0.674524 0.040 0.008 0.004 0.764 0.008 0.176
#> GSM751295 1 0.2944 0.939109 0.832 0.000 0.000 0.148 0.012 0.008
#> GSM751319 4 0.4242 0.715075 0.092 0.000 0.004 0.784 0.084 0.036
#> GSM751323 4 0.3234 0.737025 0.120 0.000 0.012 0.836 0.028 0.004
#> GSM751326 4 0.3925 0.653229 0.196 0.000 0.012 0.760 0.028 0.004
#> GSM751327 4 0.3190 0.740853 0.116 0.000 0.012 0.840 0.028 0.004
#> GSM751328 4 0.2119 0.769022 0.060 0.000 0.008 0.912 0.016 0.004
#> GSM751329 4 0.2858 0.752877 0.096 0.000 0.008 0.864 0.028 0.004
#> GSM751330 1 0.3380 0.926896 0.812 0.000 0.008 0.152 0.024 0.004
#> GSM751331 1 0.2692 0.936819 0.840 0.000 0.000 0.148 0.012 0.000
#> GSM751333 1 0.4384 0.773168 0.688 0.000 0.012 0.268 0.028 0.004
#> GSM751335 1 0.3380 0.926896 0.812 0.000 0.008 0.152 0.024 0.004
#> GSM751336 1 0.3048 0.931871 0.824 0.000 0.000 0.152 0.020 0.004
#> GSM751337 4 0.3349 0.706383 0.164 0.000 0.008 0.804 0.024 0.000
#> GSM751338 4 0.4572 0.715390 0.124 0.000 0.004 0.756 0.044 0.072
#> GSM751340 6 0.7180 0.375736 0.052 0.000 0.056 0.168 0.212 0.512
#> GSM751350 1 0.2624 0.940632 0.844 0.000 0.000 0.148 0.004 0.004
#> GSM751351 1 0.2624 0.940632 0.844 0.000 0.000 0.148 0.004 0.004
#> GSM751362 3 0.5874 0.387983 0.040 0.000 0.576 0.000 0.264 0.120
#> GSM751363 5 0.4708 0.478769 0.016 0.004 0.152 0.016 0.744 0.068
#> GSM751367 5 0.7316 0.107971 0.052 0.000 0.264 0.052 0.468 0.164
#> GSM751368 5 0.6132 0.420778 0.000 0.084 0.288 0.008 0.560 0.060
#> GSM751371 6 0.7671 0.320396 0.036 0.004 0.132 0.144 0.216 0.468
#> GSM751375 6 0.6364 0.025663 0.044 0.060 0.032 0.000 0.408 0.456
#> GSM751376 6 0.6227 0.472723 0.048 0.016 0.228 0.000 0.120 0.588
#> GSM751378 6 0.6826 0.211767 0.040 0.012 0.324 0.000 0.188 0.436
#> GSM751379 6 0.6396 0.433979 0.048 0.016 0.256 0.000 0.124 0.556
#> GSM751382 6 0.6536 -0.000312 0.048 0.052 0.048 0.000 0.404 0.448
#> GSM751386 5 0.6350 0.507250 0.036 0.024 0.128 0.000 0.568 0.244
#> GSM751388 5 0.6581 0.547473 0.036 0.040 0.168 0.000 0.572 0.184
#> GSM751391 6 0.6000 0.488057 0.028 0.008 0.116 0.052 0.128 0.668
#> GSM751410 3 0.7441 -0.001838 0.048 0.000 0.324 0.028 0.308 0.292
#> GSM751414 5 0.5152 0.202090 0.020 0.000 0.372 0.016 0.568 0.024
#> GSM751361 5 0.5868 0.534669 0.020 0.012 0.152 0.016 0.648 0.152
#> GSM751365 3 0.4697 -0.007657 0.008 0.028 0.500 0.000 0.464 0.000
#> GSM751366 3 0.3329 0.536293 0.004 0.008 0.768 0.000 0.220 0.000
#> GSM751369 3 0.7067 -0.006197 0.044 0.000 0.400 0.016 0.216 0.324
#> GSM751370 5 0.4502 0.266913 0.016 0.000 0.368 0.000 0.600 0.016
#> GSM751372 5 0.4595 0.247437 0.016 0.008 0.380 0.000 0.588 0.008
#> GSM751373 3 0.5314 0.129323 0.008 0.052 0.516 0.012 0.412 0.000
#> GSM751374 6 0.6396 0.433979 0.048 0.016 0.256 0.000 0.124 0.556
#> GSM751377 5 0.5131 0.516747 0.020 0.016 0.232 0.000 0.672 0.060
#> GSM751380 3 0.2865 0.629072 0.004 0.004 0.848 0.000 0.128 0.016
#> GSM751381 5 0.6481 0.486523 0.040 0.024 0.128 0.000 0.548 0.260
#> GSM751383 5 0.7409 0.513722 0.036 0.100 0.232 0.000 0.480 0.152
#> GSM751384 5 0.6555 0.529944 0.040 0.012 0.208 0.000 0.528 0.212
#> GSM751385 5 0.6393 0.396779 0.036 0.008 0.144 0.000 0.504 0.308
#> GSM751387 5 0.7318 0.510741 0.036 0.100 0.164 0.000 0.504 0.196
#> GSM751389 3 0.2689 0.649049 0.012 0.004 0.884 0.000 0.040 0.060
#> GSM751393 6 0.6698 0.310141 0.036 0.004 0.276 0.000 0.240 0.444
#> GSM751394 5 0.6127 0.521133 0.036 0.020 0.120 0.000 0.596 0.228
#> GSM751395 6 0.5672 0.508855 0.028 0.004 0.180 0.000 0.160 0.628
#> GSM751397 5 0.6414 0.496634 0.040 0.024 0.124 0.000 0.560 0.252
#> GSM751398 5 0.6199 0.525773 0.032 0.028 0.124 0.000 0.596 0.220
#> GSM751404 3 0.2164 0.666843 0.000 0.056 0.908 0.000 0.028 0.008
#> GSM751406 3 0.3419 0.601220 0.008 0.000 0.820 0.000 0.056 0.116
#> GSM751411 3 0.4593 0.092273 0.020 0.000 0.556 0.000 0.412 0.012
#> GSM751413 5 0.4333 0.506619 0.016 0.004 0.104 0.016 0.784 0.076
#> GSM751415 3 0.2178 0.667471 0.012 0.008 0.912 0.000 0.056 0.012
#> GSM751416 5 0.4365 0.338163 0.012 0.008 0.332 0.000 0.640 0.008
#> GSM751417 5 0.4365 0.338163 0.012 0.008 0.332 0.000 0.640 0.008
#> GSM751421 5 0.7000 -0.037414 0.036 0.000 0.372 0.028 0.396 0.168
#> GSM751422 5 0.7062 -0.001959 0.036 0.000 0.352 0.028 0.400 0.184
#> GSM751360 5 0.6065 0.362310 0.024 0.004 0.168 0.032 0.632 0.140
#> GSM751364 5 0.4329 0.304844 0.012 0.008 0.352 0.000 0.624 0.004
#> GSM751390 5 0.7687 0.445562 0.040 0.100 0.304 0.000 0.400 0.156
#> GSM751392 5 0.6540 0.359493 0.044 0.028 0.096 0.000 0.508 0.324
#> GSM751396 5 0.7999 0.345992 0.040 0.284 0.124 0.008 0.396 0.148
#> GSM751399 3 0.1536 0.670006 0.000 0.004 0.940 0.000 0.040 0.016
#> GSM751400 3 0.2462 0.665532 0.000 0.064 0.892 0.000 0.012 0.032
#> GSM751401 3 0.1942 0.667228 0.000 0.064 0.916 0.000 0.012 0.008
#> GSM751402 3 0.1767 0.677426 0.000 0.036 0.932 0.000 0.012 0.020
#> GSM751403 3 0.1980 0.670608 0.000 0.036 0.920 0.000 0.008 0.036
#> GSM751405 3 0.3743 0.578166 0.008 0.000 0.792 0.000 0.064 0.136
#> GSM751407 3 0.2123 0.664484 0.000 0.064 0.908 0.000 0.020 0.008
#> GSM751408 3 0.2228 0.665022 0.004 0.056 0.908 0.000 0.024 0.008
#> GSM751409 3 0.2228 0.672538 0.004 0.008 0.908 0.000 0.056 0.024
#> GSM751412 3 0.2271 0.663007 0.004 0.056 0.904 0.000 0.032 0.004
#> GSM751418 3 0.4929 0.199168 0.008 0.052 0.564 0.000 0.376 0.000
#> GSM751419 3 0.4929 0.199168 0.008 0.052 0.564 0.000 0.376 0.000
#> GSM751420 3 0.3728 0.604064 0.004 0.024 0.812 0.000 0.044 0.116
#> GSM751425 2 0.5923 0.072310 0.016 0.464 0.000 0.000 0.136 0.384
#> GSM751429 6 0.8802 0.256564 0.096 0.108 0.252 0.016 0.228 0.300
#> GSM751430 2 0.7357 0.064605 0.036 0.428 0.020 0.020 0.304 0.192
#> GSM751433 2 0.3912 0.776251 0.012 0.824 0.008 0.028 0.076 0.052
#> GSM751437 6 0.7464 0.203599 0.044 0.080 0.356 0.000 0.128 0.392
#> GSM751448 3 0.7393 0.124124 0.072 0.080 0.484 0.000 0.100 0.264
#> GSM751451 2 0.3557 0.787164 0.008 0.848 0.008 0.040 0.048 0.048
#> GSM751423 2 0.5187 0.514037 0.020 0.648 0.000 0.004 0.080 0.248
#> GSM751424 2 0.3933 0.775144 0.012 0.824 0.012 0.024 0.076 0.052
#> GSM751428 2 0.1514 0.811969 0.004 0.944 0.012 0.000 0.036 0.004
#> GSM751431 2 0.3152 0.796329 0.008 0.868 0.004 0.028 0.056 0.036
#> GSM751432 2 0.3852 0.774944 0.012 0.828 0.012 0.020 0.076 0.052
#> GSM751434 2 0.3880 0.775989 0.012 0.828 0.012 0.024 0.072 0.052
#> GSM751435 2 0.0993 0.811302 0.000 0.964 0.012 0.000 0.024 0.000
#> GSM751436 2 0.3912 0.776251 0.012 0.824 0.008 0.028 0.076 0.052
#> GSM751440 2 0.1198 0.811720 0.004 0.960 0.004 0.012 0.020 0.000
#> GSM751444 2 0.1558 0.805223 0.012 0.948 0.004 0.004 0.020 0.012
#> GSM751446 2 0.3949 0.753358 0.040 0.820 0.032 0.000 0.032 0.076
#> GSM751449 2 0.4790 0.703829 0.040 0.764 0.044 0.000 0.056 0.096
#> GSM751450 2 0.2638 0.802336 0.008 0.892 0.000 0.028 0.052 0.020
#> GSM751452 2 0.3933 0.775144 0.012 0.824 0.012 0.024 0.076 0.052
#> GSM751426 2 0.2781 0.800963 0.008 0.888 0.004 0.028 0.052 0.020
#> GSM751427 2 0.2138 0.803511 0.028 0.920 0.012 0.000 0.028 0.012
#> GSM751438 2 0.4571 0.719220 0.040 0.780 0.040 0.000 0.052 0.088
#> GSM751439 2 0.3890 0.760544 0.040 0.828 0.044 0.000 0.040 0.048
#> GSM751441 2 0.3046 0.787108 0.036 0.868 0.004 0.000 0.036 0.056
#> GSM751442 2 0.2658 0.792322 0.032 0.896 0.008 0.004 0.020 0.040
#> GSM751443 2 0.7923 -0.066990 0.044 0.332 0.312 0.000 0.092 0.220
#> GSM751445 2 0.5602 0.554353 0.044 0.660 0.024 0.000 0.064 0.208
#> GSM751447 2 0.2640 0.793803 0.032 0.892 0.004 0.000 0.032 0.040
#> GSM751453 2 0.1325 0.811746 0.004 0.956 0.008 0.004 0.024 0.004
#> GSM751454 2 0.1325 0.811746 0.004 0.956 0.008 0.004 0.024 0.004
#> GSM751455 2 0.2820 0.790356 0.032 0.888 0.008 0.004 0.028 0.040
#> GSM751456 2 0.2820 0.790356 0.032 0.888 0.008 0.004 0.028 0.040
#> GSM751457 6 0.7437 0.225286 0.052 0.332 0.072 0.000 0.124 0.420
#> GSM751458 6 0.7437 0.225286 0.052 0.332 0.072 0.000 0.124 0.420
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)
#> Error in mat[ceiling(1:nr/h_ratio), ceiling(1:nc/w_ratio), drop = FALSE]: subscript out of bounds
get_signatures(res, k = 5, scale_rows = FALSE)
get_signatures(res, k = 6, scale_rows = FALSE)
Compare the overlap of signatures from different k:
compare_signatures(res)
get_signature() returns a data frame invisibly. TO get the list of signatures, the function
call should be assigned to a variable explicitly. In following code, if plot argument is set
to FALSE, no heatmap is plotted while only the differential analysis is performed.
# code only for demonstration
tb = get_signature(res, k = ..., plot = FALSE)
An example of the output of tb is:
#> which_row fdr mean_1 mean_2 scaled_mean_1 scaled_mean_2 km
#> 1 38 0.042760348 8.373488 9.131774 -0.5533452 0.5164555 1
#> 2 40 0.018707592 7.106213 8.469186 -0.6173731 0.5762149 1
#> 3 55 0.019134737 10.221463 11.207825 -0.6159697 0.5749050 1
#> 4 59 0.006059896 5.921854 7.869574 -0.6899429 0.6439467 1
#> 5 60 0.018055526 8.928898 10.211722 -0.6204761 0.5791110 1
#> 6 98 0.009384629 15.714769 14.887706 0.6635654 -0.6193277 2
...
The columns in tb are:
which_row: row indices corresponding to the input matrix.fdr: FDR for the differential test. mean_x: The mean value in group x.scaled_mean_x: The mean value in group x after rows are scaled.km: Row groups if k-means clustering is applied to rows.UMAP plot which shows how samples are separated.
dimension_reduction(res, k = 2, method = "UMAP")
dimension_reduction(res, k = 3, method = "UMAP")
dimension_reduction(res, k = 4, method = "UMAP")
dimension_reduction(res, k = 5, method = "UMAP")
dimension_reduction(res, k = 6, method = "UMAP")
Following heatmap shows how subgroups are split when increasing k:
collect_classes(res)
Test correlation between subgroups and known annotations. If the known annotation is numeric, one-way ANOVA test is applied, and if the known annotation is discrete, chi-squared contingency table test is applied.
test_to_known_factors(res)
#> n tissue(p) disease.state(p) agent(p) k
#> MAD:kmeans 163 6.55e-23 5.45e-02 9.40e-02 2
#> MAD:kmeans 132 8.90e-44 1.31e-01 3.79e-01 3
#> MAD:kmeans 114 2.46e-45 2.29e-07 5.39e-06 4
#> MAD:kmeans 102 9.17e-40 1.49e-05 8.16e-05 5
#> MAD:kmeans 112 2.24e-41 1.34e-02 6.18e-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", "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 4537 rows and 166 columns.
#> Top rows (454, 908, 1361, 1814, 2268) are extracted by 'MAD' method.
#> Subgroups are detected by 'skmeans' method.
#> Performed in total 1250 partitions by row resampling.
#> Best k for subgroups seems to be 2.
#>
#> Following methods can be applied to this 'ConsensusPartition' object:
#> [1] "cola_report" "collect_classes" "collect_plots"
#> [4] "collect_stats" "colnames" "compare_signatures"
#> [7] "consensus_heatmap" "dimension_reduction" "functional_enrichment"
#> [10] "get_anno_col" "get_anno" "get_classes"
#> [13] "get_consensus" "get_matrix" "get_membership"
#> [16] "get_param" "get_signatures" "get_stats"
#> [19] "is_best_k" "is_stable_k" "membership_heatmap"
#> [22] "ncol" "nrow" "plot_ecdf"
#> [25] "rownames" "select_partition_number" "show"
#> [28] "suggest_best_k" "test_to_known_factors"
collect_plots() function collects all the plots made from res for all k (number of partitions)
into one single page to provide an easy and fast comparison between different k.
collect_plots(res)
The plots are:
k and the heatmap of
predicted classes for each k.k.k.k.All the plots in panels can be made by individual functions and they are plotted later in this section.
select_partition_number() produces several plots showing different
statistics for choosing “optimized” k. There are following statistics:
k;k, the area increased is defined as \(A_k - A_{k-1}\).The detailed explanations of these statistics can be found in the cola vignette.
Generally speaking, lower PAC score, higher mean silhouette score or higher
concordance corresponds to better partition. Rand index and Jaccard index
measure how similar the current partition is compared to partition with k-1.
If they are too similar, we won't accept k is better than k-1.
select_partition_number(res)
The numeric values for all these statistics can be obtained by get_stats().
get_stats(res)
#> k 1-PAC mean_silhouette concordance area_increased Rand Jaccard
#> 2 2 0.542 0.814 0.913 0.4752 0.550 0.550
#> 3 3 0.652 0.787 0.884 0.4024 0.734 0.537
#> 4 4 0.727 0.693 0.821 0.1210 0.851 0.593
#> 5 5 0.650 0.481 0.709 0.0650 0.875 0.578
#> 6 6 0.685 0.531 0.732 0.0456 0.879 0.518
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
#> GSM751298 1 0.0000 0.9371 1.000 0.000
#> GSM751304 2 0.2778 0.8631 0.048 0.952
#> GSM751305 2 0.1843 0.8728 0.028 0.972
#> GSM751307 1 0.7745 0.7034 0.772 0.228
#> GSM751310 1 0.3431 0.8889 0.936 0.064
#> GSM751314 1 0.0000 0.9371 1.000 0.000
#> GSM751316 1 0.7219 0.7362 0.800 0.200
#> GSM751318 1 0.0672 0.9330 0.992 0.008
#> GSM751342 1 0.5519 0.8245 0.872 0.128
#> GSM751346 1 0.0000 0.9371 1.000 0.000
#> GSM751347 1 0.1184 0.9272 0.984 0.016
#> GSM751348 2 0.9977 0.0349 0.472 0.528
#> GSM751349 2 0.0000 0.8811 0.000 1.000
#> GSM751352 1 0.9087 0.4704 0.676 0.324
#> GSM751353 2 0.0000 0.8811 0.000 1.000
#> GSM751354 2 0.0672 0.8796 0.008 0.992
#> GSM751355 2 0.0000 0.8811 0.000 1.000
#> GSM751358 2 0.1843 0.8730 0.028 0.972
#> GSM751359 2 0.0000 0.8811 0.000 1.000
#> GSM751294 2 0.8016 0.6398 0.244 0.756
#> GSM751296 1 0.0000 0.9371 1.000 0.000
#> GSM751297 1 0.2948 0.8994 0.948 0.052
#> GSM751299 1 0.9815 0.2806 0.580 0.420
#> GSM751300 1 0.0000 0.9371 1.000 0.000
#> GSM751301 1 0.0000 0.9371 1.000 0.000
#> GSM751302 1 0.0000 0.9371 1.000 0.000
#> GSM751303 1 0.3879 0.8777 0.924 0.076
#> GSM751306 1 0.1843 0.9189 0.972 0.028
#> GSM751308 1 0.0672 0.9331 0.992 0.008
#> GSM751309 1 0.0672 0.9331 0.992 0.008
#> GSM751311 1 0.0000 0.9371 1.000 0.000
#> GSM751312 1 0.0938 0.9303 0.988 0.012
#> GSM751313 1 0.0000 0.9371 1.000 0.000
#> GSM751315 1 0.0000 0.9371 1.000 0.000
#> GSM751317 1 0.0672 0.9330 0.992 0.008
#> GSM751320 1 0.0000 0.9371 1.000 0.000
#> GSM751321 1 0.0000 0.9371 1.000 0.000
#> GSM751322 1 0.0000 0.9371 1.000 0.000
#> GSM751324 1 0.0000 0.9371 1.000 0.000
#> GSM751325 1 0.0000 0.9371 1.000 0.000
#> GSM751332 1 0.0000 0.9371 1.000 0.000
#> GSM751334 1 0.0000 0.9371 1.000 0.000
#> GSM751339 1 0.2043 0.9159 0.968 0.032
#> GSM751341 1 0.0000 0.9371 1.000 0.000
#> GSM751343 1 0.0000 0.9371 1.000 0.000
#> GSM751344 2 0.9754 0.2559 0.408 0.592
#> GSM751345 2 0.9775 0.2434 0.412 0.588
#> GSM751356 2 0.9866 0.1741 0.432 0.568
#> GSM751357 2 0.9866 0.1741 0.432 0.568
#> GSM751293 1 0.0000 0.9371 1.000 0.000
#> GSM751295 1 0.0000 0.9371 1.000 0.000
#> GSM751319 1 0.0000 0.9371 1.000 0.000
#> GSM751323 1 0.0000 0.9371 1.000 0.000
#> GSM751326 1 0.0000 0.9371 1.000 0.000
#> GSM751327 1 0.0000 0.9371 1.000 0.000
#> GSM751328 1 0.0000 0.9371 1.000 0.000
#> GSM751329 1 0.0000 0.9371 1.000 0.000
#> GSM751330 1 0.0000 0.9371 1.000 0.000
#> GSM751331 1 0.0000 0.9371 1.000 0.000
#> GSM751333 1 0.0000 0.9371 1.000 0.000
#> GSM751335 1 0.0000 0.9371 1.000 0.000
#> GSM751336 1 0.0000 0.9371 1.000 0.000
#> GSM751337 1 0.0000 0.9371 1.000 0.000
#> GSM751338 1 0.0000 0.9371 1.000 0.000
#> GSM751340 1 0.6531 0.7761 0.832 0.168
#> GSM751350 1 0.0000 0.9371 1.000 0.000
#> GSM751351 1 0.0000 0.9371 1.000 0.000
#> GSM751362 2 0.7056 0.7318 0.192 0.808
#> GSM751363 2 0.4431 0.8355 0.092 0.908
#> GSM751367 1 0.9552 0.4336 0.624 0.376
#> GSM751368 2 0.0000 0.8811 0.000 1.000
#> GSM751371 2 0.9922 0.1582 0.448 0.552
#> GSM751375 2 0.0000 0.8811 0.000 1.000
#> GSM751376 2 0.0000 0.8811 0.000 1.000
#> GSM751378 2 0.0000 0.8811 0.000 1.000
#> GSM751379 2 0.0000 0.8811 0.000 1.000
#> GSM751382 2 0.0000 0.8811 0.000 1.000
#> GSM751386 2 0.0000 0.8811 0.000 1.000
#> GSM751388 2 0.0000 0.8811 0.000 1.000
#> GSM751391 2 0.1414 0.8767 0.020 0.980
#> GSM751410 2 0.8267 0.6332 0.260 0.740
#> GSM751414 2 0.9460 0.4085 0.364 0.636
#> GSM751361 2 0.0000 0.8811 0.000 1.000
#> GSM751365 2 0.0672 0.8801 0.008 0.992
#> GSM751366 2 0.9988 0.1830 0.480 0.520
#> GSM751369 2 0.4298 0.8378 0.088 0.912
#> GSM751370 2 0.9323 0.4505 0.348 0.652
#> GSM751372 2 0.2948 0.8623 0.052 0.948
#> GSM751373 1 0.9754 0.1202 0.592 0.408
#> GSM751374 2 0.0000 0.8811 0.000 1.000
#> GSM751377 2 0.0000 0.8811 0.000 1.000
#> GSM751380 2 0.9954 0.2595 0.460 0.540
#> GSM751381 2 0.0000 0.8811 0.000 1.000
#> GSM751383 2 0.6247 0.8171 0.156 0.844
#> GSM751384 2 0.0000 0.8811 0.000 1.000
#> GSM751385 2 0.0000 0.8811 0.000 1.000
#> GSM751387 2 0.0000 0.8811 0.000 1.000
#> GSM751389 2 0.0000 0.8811 0.000 1.000
#> GSM751393 2 0.0000 0.8811 0.000 1.000
#> GSM751394 2 0.0000 0.8811 0.000 1.000
#> GSM751395 2 0.0000 0.8811 0.000 1.000
#> GSM751397 2 0.0000 0.8811 0.000 1.000
#> GSM751398 2 0.0000 0.8811 0.000 1.000
#> GSM751404 2 0.6623 0.8085 0.172 0.828
#> GSM751406 2 0.0000 0.8811 0.000 1.000
#> GSM751411 2 0.0000 0.8811 0.000 1.000
#> GSM751413 2 0.0672 0.8797 0.008 0.992
#> GSM751415 2 0.0938 0.8791 0.012 0.988
#> GSM751416 2 0.0000 0.8811 0.000 1.000
#> GSM751417 2 0.0000 0.8811 0.000 1.000
#> GSM751421 2 0.5519 0.8038 0.128 0.872
#> GSM751422 2 0.4298 0.8377 0.088 0.912
#> GSM751360 2 0.4161 0.8406 0.084 0.916
#> GSM751364 2 0.0672 0.8801 0.008 0.992
#> GSM751390 2 0.1843 0.8764 0.028 0.972
#> GSM751392 2 0.0000 0.8811 0.000 1.000
#> GSM751396 2 0.4939 0.8455 0.108 0.892
#> GSM751399 2 0.0000 0.8811 0.000 1.000
#> GSM751400 2 0.7219 0.7828 0.200 0.800
#> GSM751401 2 0.7376 0.7766 0.208 0.792
#> GSM751402 2 0.7815 0.7533 0.232 0.768
#> GSM751403 2 0.2778 0.8706 0.048 0.952
#> GSM751405 2 0.0000 0.8811 0.000 1.000
#> GSM751407 2 0.7376 0.7766 0.208 0.792
#> GSM751408 2 0.7139 0.7874 0.196 0.804
#> GSM751409 2 0.0000 0.8811 0.000 1.000
#> GSM751412 2 0.4815 0.8493 0.104 0.896
#> GSM751418 2 0.7376 0.7775 0.208 0.792
#> GSM751419 2 0.7376 0.7775 0.208 0.792
#> GSM751420 2 0.0000 0.8811 0.000 1.000
#> GSM751425 2 0.0000 0.8811 0.000 1.000
#> GSM751429 1 0.9977 0.1492 0.528 0.472
#> GSM751430 2 0.4022 0.8598 0.080 0.920
#> GSM751433 2 0.7602 0.7669 0.220 0.780
#> GSM751437 2 0.2043 0.8724 0.032 0.968
#> GSM751448 2 0.6623 0.7649 0.172 0.828
#> GSM751451 2 0.5737 0.8357 0.136 0.864
#> GSM751423 2 0.0000 0.8811 0.000 1.000
#> GSM751424 2 0.5294 0.8414 0.120 0.880
#> GSM751428 2 0.6048 0.8244 0.148 0.852
#> GSM751431 2 0.1414 0.8779 0.020 0.980
#> GSM751432 2 0.6712 0.8040 0.176 0.824
#> GSM751434 2 0.7376 0.7766 0.208 0.792
#> GSM751435 2 0.7528 0.7682 0.216 0.784
#> GSM751436 2 0.7376 0.7766 0.208 0.792
#> GSM751440 2 0.7528 0.7682 0.216 0.784
#> GSM751444 2 0.5737 0.8330 0.136 0.864
#> GSM751446 2 0.0000 0.8811 0.000 1.000
#> GSM751449 2 0.0000 0.8811 0.000 1.000
#> GSM751450 2 0.4939 0.8479 0.108 0.892
#> GSM751452 2 0.6148 0.8221 0.152 0.848
#> GSM751426 2 0.7376 0.7766 0.208 0.792
#> GSM751427 2 0.0000 0.8811 0.000 1.000
#> GSM751438 2 0.0000 0.8811 0.000 1.000
#> GSM751439 2 0.6973 0.7939 0.188 0.812
#> GSM751441 2 0.0000 0.8811 0.000 1.000
#> GSM751442 2 0.7453 0.7723 0.212 0.788
#> GSM751443 2 0.0376 0.8808 0.004 0.996
#> GSM751445 2 0.0000 0.8811 0.000 1.000
#> GSM751447 2 0.1414 0.8782 0.020 0.980
#> GSM751453 2 0.6712 0.8036 0.176 0.824
#> GSM751454 2 0.6712 0.8036 0.176 0.824
#> GSM751455 2 0.7299 0.7795 0.204 0.796
#> GSM751456 2 0.7299 0.7795 0.204 0.796
#> GSM751457 2 0.0000 0.8811 0.000 1.000
#> GSM751458 2 0.0000 0.8811 0.000 1.000
cbind(get_classes(res, k = 3), get_membership(res, k = 3))
#> class entropy silhouette p1 p2 p3
#> GSM751298 1 0.0000 0.9868 1.000 0.000 0.000
#> GSM751304 2 0.6204 0.4649 0.000 0.576 0.424
#> GSM751305 2 0.5678 0.6763 0.000 0.684 0.316
#> GSM751307 2 0.9517 0.4157 0.320 0.472 0.208
#> GSM751310 1 0.0000 0.9868 1.000 0.000 0.000
#> GSM751314 1 0.0000 0.9868 1.000 0.000 0.000
#> GSM751316 1 0.4834 0.7182 0.792 0.004 0.204
#> GSM751318 1 0.0747 0.9726 0.984 0.016 0.000
#> GSM751342 1 0.2173 0.9309 0.944 0.008 0.048
#> GSM751346 1 0.0000 0.9868 1.000 0.000 0.000
#> GSM751347 1 0.0000 0.9868 1.000 0.000 0.000
#> GSM751348 2 0.7984 0.6744 0.132 0.652 0.216
#> GSM751349 2 0.4702 0.7690 0.000 0.788 0.212
#> GSM751352 2 0.6141 0.6657 0.232 0.736 0.032
#> GSM751353 2 0.4750 0.7672 0.000 0.784 0.216
#> GSM751354 2 0.5560 0.6958 0.000 0.700 0.300
#> GSM751355 2 0.5760 0.6522 0.000 0.672 0.328
#> GSM751358 2 0.5465 0.7136 0.000 0.712 0.288
#> GSM751359 2 0.5529 0.7005 0.000 0.704 0.296
#> GSM751294 2 0.5497 0.7096 0.000 0.708 0.292
#> GSM751296 1 0.0000 0.9868 1.000 0.000 0.000
#> GSM751297 1 0.0000 0.9868 1.000 0.000 0.000
#> GSM751299 2 0.6337 0.6754 0.220 0.736 0.044
#> GSM751300 1 0.0000 0.9868 1.000 0.000 0.000
#> GSM751301 1 0.0000 0.9868 1.000 0.000 0.000
#> GSM751302 1 0.0000 0.9868 1.000 0.000 0.000
#> GSM751303 1 0.0592 0.9758 0.988 0.000 0.012
#> GSM751306 1 0.0000 0.9868 1.000 0.000 0.000
#> GSM751308 1 0.3293 0.8801 0.900 0.088 0.012
#> GSM751309 1 0.0000 0.9868 1.000 0.000 0.000
#> GSM751311 1 0.0000 0.9868 1.000 0.000 0.000
#> GSM751312 1 0.0000 0.9868 1.000 0.000 0.000
#> GSM751313 1 0.0000 0.9868 1.000 0.000 0.000
#> GSM751315 1 0.0000 0.9868 1.000 0.000 0.000
#> GSM751317 1 0.0000 0.9868 1.000 0.000 0.000
#> GSM751320 1 0.0000 0.9868 1.000 0.000 0.000
#> GSM751321 1 0.0000 0.9868 1.000 0.000 0.000
#> GSM751322 1 0.0000 0.9868 1.000 0.000 0.000
#> GSM751324 1 0.0000 0.9868 1.000 0.000 0.000
#> GSM751325 1 0.0000 0.9868 1.000 0.000 0.000
#> GSM751332 1 0.0000 0.9868 1.000 0.000 0.000
#> GSM751334 1 0.0000 0.9868 1.000 0.000 0.000
#> GSM751339 1 0.0424 0.9800 0.992 0.000 0.008
#> GSM751341 1 0.0000 0.9868 1.000 0.000 0.000
#> GSM751343 1 0.0000 0.9868 1.000 0.000 0.000
#> GSM751344 2 0.4931 0.7688 0.004 0.784 0.212
#> GSM751345 2 0.4931 0.7688 0.004 0.784 0.212
#> GSM751356 2 0.6685 0.7305 0.048 0.708 0.244
#> GSM751357 2 0.6685 0.7305 0.048 0.708 0.244
#> GSM751293 1 0.0000 0.9868 1.000 0.000 0.000
#> GSM751295 1 0.0000 0.9868 1.000 0.000 0.000
#> GSM751319 1 0.0000 0.9868 1.000 0.000 0.000
#> GSM751323 1 0.0000 0.9868 1.000 0.000 0.000
#> GSM751326 1 0.0000 0.9868 1.000 0.000 0.000
#> GSM751327 1 0.0000 0.9868 1.000 0.000 0.000
#> GSM751328 1 0.0000 0.9868 1.000 0.000 0.000
#> GSM751329 1 0.0000 0.9868 1.000 0.000 0.000
#> GSM751330 1 0.0000 0.9868 1.000 0.000 0.000
#> GSM751331 1 0.0000 0.9868 1.000 0.000 0.000
#> GSM751333 1 0.0000 0.9868 1.000 0.000 0.000
#> GSM751335 1 0.0000 0.9868 1.000 0.000 0.000
#> GSM751336 1 0.0000 0.9868 1.000 0.000 0.000
#> GSM751337 1 0.0000 0.9868 1.000 0.000 0.000
#> GSM751338 1 0.0000 0.9868 1.000 0.000 0.000
#> GSM751340 1 0.4291 0.7683 0.820 0.000 0.180
#> GSM751350 1 0.0000 0.9868 1.000 0.000 0.000
#> GSM751351 1 0.0000 0.9868 1.000 0.000 0.000
#> GSM751362 3 0.0237 0.7884 0.000 0.004 0.996
#> GSM751363 3 0.0892 0.7897 0.000 0.020 0.980
#> GSM751367 3 0.7152 0.1167 0.444 0.024 0.532
#> GSM751368 3 0.6126 0.5608 0.000 0.400 0.600
#> GSM751371 3 0.3875 0.7452 0.068 0.044 0.888
#> GSM751375 2 0.4796 0.7680 0.000 0.780 0.220
#> GSM751376 3 0.5905 0.2578 0.000 0.352 0.648
#> GSM751378 3 0.3482 0.7346 0.000 0.128 0.872
#> GSM751379 3 0.5760 0.3287 0.000 0.328 0.672
#> GSM751382 2 0.5138 0.7472 0.000 0.748 0.252
#> GSM751386 3 0.4796 0.6324 0.000 0.220 0.780
#> GSM751388 3 0.6140 0.5393 0.000 0.404 0.596
#> GSM751391 3 0.5882 0.3052 0.000 0.348 0.652
#> GSM751410 3 0.0424 0.7885 0.000 0.008 0.992
#> GSM751414 3 0.0237 0.7895 0.004 0.000 0.996
#> GSM751361 3 0.3116 0.7605 0.000 0.108 0.892
#> GSM751365 3 0.4654 0.7292 0.000 0.208 0.792
#> GSM751366 3 0.4654 0.7274 0.000 0.208 0.792
#> GSM751369 3 0.0892 0.7875 0.000 0.020 0.980
#> GSM751370 3 0.0475 0.7907 0.004 0.004 0.992
#> GSM751372 3 0.1529 0.7932 0.000 0.040 0.960
#> GSM751373 3 0.5109 0.7219 0.008 0.212 0.780
#> GSM751374 3 0.5785 0.3170 0.000 0.332 0.668
#> GSM751377 3 0.1860 0.7870 0.000 0.052 0.948
#> GSM751380 3 0.4324 0.7662 0.028 0.112 0.860
#> GSM751381 3 0.4702 0.6440 0.000 0.212 0.788
#> GSM751383 3 0.6111 0.5678 0.000 0.396 0.604
#> GSM751384 3 0.1529 0.7862 0.000 0.040 0.960
#> GSM751385 3 0.0892 0.7880 0.000 0.020 0.980
#> GSM751387 3 0.6244 0.4845 0.000 0.440 0.560
#> GSM751389 3 0.1163 0.7923 0.000 0.028 0.972
#> GSM751393 3 0.0747 0.7882 0.000 0.016 0.984
#> GSM751394 3 0.4555 0.6596 0.000 0.200 0.800
#> GSM751395 3 0.4346 0.6780 0.000 0.184 0.816
#> GSM751397 3 0.4346 0.6794 0.000 0.184 0.816
#> GSM751398 3 0.4555 0.6598 0.000 0.200 0.800
#> GSM751404 3 0.4702 0.7245 0.000 0.212 0.788
#> GSM751406 3 0.0237 0.7884 0.000 0.004 0.996
#> GSM751411 3 0.0000 0.7892 0.000 0.000 1.000
#> GSM751413 3 0.2261 0.7739 0.000 0.068 0.932
#> GSM751415 3 0.1529 0.7916 0.000 0.040 0.960
#> GSM751416 3 0.1031 0.7910 0.000 0.024 0.976
#> GSM751417 3 0.1031 0.7910 0.000 0.024 0.976
#> GSM751421 3 0.0237 0.7884 0.000 0.004 0.996
#> GSM751422 3 0.0237 0.7884 0.000 0.004 0.996
#> GSM751360 3 0.0892 0.7894 0.000 0.020 0.980
#> GSM751364 3 0.3340 0.7781 0.000 0.120 0.880
#> GSM751390 3 0.5785 0.6423 0.000 0.332 0.668
#> GSM751392 3 0.5497 0.5257 0.000 0.292 0.708
#> GSM751396 2 0.5988 0.0578 0.000 0.632 0.368
#> GSM751399 3 0.0592 0.7918 0.000 0.012 0.988
#> GSM751400 3 0.4702 0.7245 0.000 0.212 0.788
#> GSM751401 3 0.4702 0.7245 0.000 0.212 0.788
#> GSM751402 3 0.4750 0.7253 0.000 0.216 0.784
#> GSM751403 3 0.4702 0.7280 0.000 0.212 0.788
#> GSM751405 3 0.0237 0.7884 0.000 0.004 0.996
#> GSM751407 3 0.4702 0.7245 0.000 0.212 0.788
#> GSM751408 3 0.4702 0.7245 0.000 0.212 0.788
#> GSM751409 3 0.0892 0.7921 0.000 0.020 0.980
#> GSM751412 3 0.4702 0.7245 0.000 0.212 0.788
#> GSM751418 3 0.4796 0.7217 0.000 0.220 0.780
#> GSM751419 3 0.4796 0.7217 0.000 0.220 0.780
#> GSM751420 3 0.4504 0.7371 0.000 0.196 0.804
#> GSM751425 2 0.4702 0.7690 0.000 0.788 0.212
#> GSM751429 3 0.9431 0.1576 0.280 0.220 0.500
#> GSM751430 2 0.0424 0.8081 0.000 0.992 0.008
#> GSM751433 2 0.0237 0.8075 0.000 0.996 0.004
#> GSM751437 3 0.4654 0.6046 0.000 0.208 0.792
#> GSM751448 3 0.5656 0.4365 0.004 0.284 0.712
#> GSM751451 2 0.0237 0.8075 0.000 0.996 0.004
#> GSM751423 2 0.4702 0.7690 0.000 0.788 0.212
#> GSM751424 2 0.0237 0.8075 0.000 0.996 0.004
#> GSM751428 2 0.0237 0.8075 0.000 0.996 0.004
#> GSM751431 2 0.0237 0.8075 0.000 0.996 0.004
#> GSM751432 2 0.0237 0.8075 0.000 0.996 0.004
#> GSM751434 2 0.0237 0.8075 0.000 0.996 0.004
#> GSM751435 2 0.0592 0.8041 0.000 0.988 0.012
#> GSM751436 2 0.0237 0.8075 0.000 0.996 0.004
#> GSM751440 2 0.0747 0.8021 0.000 0.984 0.016
#> GSM751444 2 0.0424 0.8059 0.000 0.992 0.008
#> GSM751446 2 0.2356 0.8061 0.000 0.928 0.072
#> GSM751449 2 0.4452 0.7792 0.000 0.808 0.192
#> GSM751450 2 0.0237 0.8075 0.000 0.996 0.004
#> GSM751452 2 0.0237 0.8075 0.000 0.996 0.004
#> GSM751426 2 0.0237 0.8075 0.000 0.996 0.004
#> GSM751427 2 0.0592 0.8032 0.000 0.988 0.012
#> GSM751438 2 0.3192 0.8003 0.000 0.888 0.112
#> GSM751439 2 0.1964 0.7720 0.000 0.944 0.056
#> GSM751441 2 0.0237 0.8084 0.000 0.996 0.004
#> GSM751442 2 0.0592 0.8032 0.000 0.988 0.012
#> GSM751443 2 0.5926 0.6199 0.000 0.644 0.356
#> GSM751445 2 0.4702 0.7690 0.000 0.788 0.212
#> GSM751447 2 0.0000 0.8076 0.000 1.000 0.000
#> GSM751453 2 0.0237 0.8075 0.000 0.996 0.004
#> GSM751454 2 0.0237 0.8075 0.000 0.996 0.004
#> GSM751455 2 0.0592 0.8032 0.000 0.988 0.012
#> GSM751456 2 0.0592 0.8032 0.000 0.988 0.012
#> GSM751457 2 0.4887 0.7627 0.000 0.772 0.228
#> GSM751458 2 0.4887 0.7627 0.000 0.772 0.228
cbind(get_classes(res, k = 4), get_membership(res, k = 4))
#> class entropy silhouette p1 p2 p3 p4
#> GSM751298 1 0.0188 0.9624 0.996 0.000 0.000 0.004
#> GSM751304 4 0.1452 0.6852 0.000 0.008 0.036 0.956
#> GSM751305 4 0.1297 0.6880 0.000 0.016 0.020 0.964
#> GSM751307 4 0.7640 0.4079 0.264 0.180 0.016 0.540
#> GSM751310 1 0.0672 0.9574 0.984 0.000 0.008 0.008
#> GSM751314 1 0.0188 0.9619 0.996 0.000 0.004 0.000
#> GSM751316 1 0.5047 0.5043 0.668 0.000 0.016 0.316
#> GSM751318 1 0.1209 0.9427 0.964 0.032 0.000 0.004
#> GSM751342 1 0.3625 0.7796 0.828 0.012 0.000 0.160
#> GSM751346 1 0.1022 0.9536 0.968 0.000 0.000 0.032
#> GSM751347 1 0.1209 0.9517 0.964 0.000 0.004 0.032
#> GSM751348 4 0.2831 0.6854 0.040 0.044 0.008 0.908
#> GSM751349 4 0.4677 0.6259 0.000 0.176 0.048 0.776
#> GSM751352 4 0.2909 0.6795 0.036 0.052 0.008 0.904
#> GSM751353 4 0.2647 0.6698 0.000 0.120 0.000 0.880
#> GSM751354 4 0.1284 0.6866 0.000 0.012 0.024 0.964
#> GSM751355 4 0.2596 0.6728 0.000 0.024 0.068 0.908
#> GSM751358 4 0.2317 0.6850 0.004 0.036 0.032 0.928
#> GSM751359 4 0.2586 0.6817 0.000 0.040 0.048 0.912
#> GSM751294 4 0.1406 0.6831 0.000 0.016 0.024 0.960
#> GSM751296 1 0.0336 0.9614 0.992 0.000 0.000 0.008
#> GSM751297 1 0.2076 0.9299 0.932 0.004 0.008 0.056
#> GSM751299 4 0.2586 0.6749 0.048 0.040 0.000 0.912
#> GSM751300 1 0.1022 0.9536 0.968 0.000 0.000 0.032
#> GSM751301 1 0.1022 0.9478 0.968 0.000 0.000 0.032
#> GSM751302 1 0.1022 0.9536 0.968 0.000 0.000 0.032
#> GSM751303 1 0.1938 0.9199 0.936 0.000 0.012 0.052
#> GSM751306 1 0.0336 0.9605 0.992 0.000 0.008 0.000
#> GSM751308 4 0.5815 -0.0115 0.476 0.012 0.012 0.500
#> GSM751309 1 0.0188 0.9620 0.996 0.000 0.000 0.004
#> GSM751311 1 0.0000 0.9629 1.000 0.000 0.000 0.000
#> GSM751312 1 0.1584 0.9444 0.952 0.000 0.012 0.036
#> GSM751313 1 0.0188 0.9627 0.996 0.000 0.000 0.004
#> GSM751315 1 0.0000 0.9629 1.000 0.000 0.000 0.000
#> GSM751317 1 0.0188 0.9619 0.996 0.000 0.004 0.000
#> GSM751320 1 0.0000 0.9629 1.000 0.000 0.000 0.000
#> GSM751321 1 0.0000 0.9629 1.000 0.000 0.000 0.000
#> GSM751322 1 0.0000 0.9629 1.000 0.000 0.000 0.000
#> GSM751324 1 0.0000 0.9629 1.000 0.000 0.000 0.000
#> GSM751325 1 0.0000 0.9629 1.000 0.000 0.000 0.000
#> GSM751332 1 0.0000 0.9629 1.000 0.000 0.000 0.000
#> GSM751334 1 0.0000 0.9629 1.000 0.000 0.000 0.000
#> GSM751339 1 0.4088 0.7889 0.820 0.000 0.040 0.140
#> GSM751341 1 0.0336 0.9614 0.992 0.000 0.000 0.008
#> GSM751343 1 0.0000 0.9629 1.000 0.000 0.000 0.000
#> GSM751344 4 0.1489 0.6893 0.000 0.044 0.004 0.952
#> GSM751345 4 0.1302 0.6892 0.000 0.044 0.000 0.956
#> GSM751356 4 0.1406 0.6831 0.000 0.016 0.024 0.960
#> GSM751357 4 0.1406 0.6831 0.000 0.016 0.024 0.960
#> GSM751293 1 0.1302 0.9373 0.956 0.000 0.000 0.044
#> GSM751295 1 0.1022 0.9536 0.968 0.000 0.000 0.032
#> GSM751319 1 0.0000 0.9629 1.000 0.000 0.000 0.000
#> GSM751323 1 0.0000 0.9629 1.000 0.000 0.000 0.000
#> GSM751326 1 0.0000 0.9629 1.000 0.000 0.000 0.000
#> GSM751327 1 0.0000 0.9629 1.000 0.000 0.000 0.000
#> GSM751328 1 0.0000 0.9629 1.000 0.000 0.000 0.000
#> GSM751329 1 0.0000 0.9629 1.000 0.000 0.000 0.000
#> GSM751330 1 0.0188 0.9627 0.996 0.000 0.000 0.004
#> GSM751331 1 0.0921 0.9550 0.972 0.000 0.000 0.028
#> GSM751333 1 0.0188 0.9627 0.996 0.000 0.000 0.004
#> GSM751335 1 0.0000 0.9629 1.000 0.000 0.000 0.000
#> GSM751336 1 0.0921 0.9550 0.972 0.000 0.000 0.028
#> GSM751337 1 0.0000 0.9629 1.000 0.000 0.000 0.000
#> GSM751338 1 0.0188 0.9627 0.996 0.000 0.000 0.004
#> GSM751340 1 0.6150 0.3393 0.580 0.000 0.060 0.360
#> GSM751350 1 0.1022 0.9536 0.968 0.000 0.000 0.032
#> GSM751351 1 0.1022 0.9536 0.968 0.000 0.000 0.032
#> GSM751362 3 0.3942 0.5876 0.000 0.000 0.764 0.236
#> GSM751363 3 0.4605 0.4075 0.000 0.000 0.664 0.336
#> GSM751367 3 0.8375 0.1309 0.332 0.028 0.424 0.216
#> GSM751368 3 0.6572 0.3957 0.000 0.272 0.608 0.120
#> GSM751371 4 0.5974 0.3338 0.036 0.008 0.348 0.608
#> GSM751375 4 0.4758 0.6260 0.000 0.156 0.064 0.780
#> GSM751376 4 0.3208 0.6157 0.000 0.004 0.148 0.848
#> GSM751378 4 0.3311 0.6315 0.000 0.000 0.172 0.828
#> GSM751379 4 0.4877 0.3331 0.000 0.008 0.328 0.664
#> GSM751382 4 0.5272 0.6094 0.000 0.172 0.084 0.744
#> GSM751386 4 0.4950 0.3402 0.000 0.004 0.376 0.620
#> GSM751388 4 0.5590 0.1269 0.000 0.020 0.456 0.524
#> GSM751391 4 0.4611 0.6113 0.008 0.032 0.172 0.788
#> GSM751410 4 0.5147 0.0808 0.000 0.004 0.460 0.536
#> GSM751414 3 0.1022 0.7263 0.000 0.000 0.968 0.032
#> GSM751361 3 0.4998 -0.0440 0.000 0.000 0.512 0.488
#> GSM751365 3 0.1820 0.7242 0.000 0.020 0.944 0.036
#> GSM751366 3 0.0000 0.7306 0.000 0.000 1.000 0.000
#> GSM751369 3 0.4992 0.1282 0.000 0.000 0.524 0.476
#> GSM751370 3 0.1211 0.7266 0.000 0.000 0.960 0.040
#> GSM751372 3 0.1211 0.7252 0.000 0.000 0.960 0.040
#> GSM751373 3 0.2019 0.7248 0.004 0.024 0.940 0.032
#> GSM751374 4 0.4836 0.3515 0.000 0.008 0.320 0.672
#> GSM751377 3 0.3908 0.5794 0.000 0.004 0.784 0.212
#> GSM751380 3 0.1557 0.7252 0.000 0.000 0.944 0.056
#> GSM751381 4 0.5070 0.3455 0.000 0.008 0.372 0.620
#> GSM751383 3 0.6919 0.1769 0.000 0.116 0.516 0.368
#> GSM751384 3 0.4989 0.0027 0.000 0.000 0.528 0.472
#> GSM751385 4 0.4193 0.5222 0.000 0.000 0.268 0.732
#> GSM751387 4 0.6491 0.1028 0.000 0.072 0.432 0.496
#> GSM751389 3 0.3726 0.6131 0.000 0.000 0.788 0.212
#> GSM751393 4 0.4585 0.4236 0.000 0.000 0.332 0.668
#> GSM751394 4 0.5231 0.3265 0.000 0.012 0.384 0.604
#> GSM751395 4 0.2011 0.6726 0.000 0.000 0.080 0.920
#> GSM751397 4 0.4679 0.3863 0.000 0.000 0.352 0.648
#> GSM751398 4 0.4991 0.3148 0.000 0.004 0.388 0.608
#> GSM751404 3 0.2021 0.7309 0.000 0.024 0.936 0.040
#> GSM751406 3 0.4585 0.4552 0.000 0.000 0.668 0.332
#> GSM751411 3 0.1118 0.7290 0.000 0.000 0.964 0.036
#> GSM751413 3 0.5236 0.1339 0.000 0.008 0.560 0.432
#> GSM751415 3 0.1792 0.7211 0.000 0.000 0.932 0.068
#> GSM751416 3 0.2081 0.7073 0.000 0.000 0.916 0.084
#> GSM751417 3 0.2081 0.7073 0.000 0.000 0.916 0.084
#> GSM751421 3 0.4072 0.5525 0.000 0.000 0.748 0.252
#> GSM751422 3 0.4585 0.4232 0.000 0.000 0.668 0.332
#> GSM751360 3 0.4855 0.3356 0.000 0.000 0.600 0.400
#> GSM751364 3 0.1867 0.7136 0.000 0.000 0.928 0.072
#> GSM751390 3 0.6607 0.1207 0.000 0.084 0.516 0.400
#> GSM751392 4 0.5207 0.4651 0.000 0.028 0.292 0.680
#> GSM751396 2 0.7606 0.1008 0.000 0.476 0.248 0.276
#> GSM751399 3 0.1389 0.7300 0.000 0.000 0.952 0.048
#> GSM751400 3 0.3245 0.7164 0.000 0.056 0.880 0.064
#> GSM751401 3 0.2816 0.7237 0.000 0.036 0.900 0.064
#> GSM751402 3 0.2730 0.7149 0.000 0.016 0.896 0.088
#> GSM751403 3 0.3047 0.6985 0.000 0.012 0.872 0.116
#> GSM751405 3 0.4522 0.4778 0.000 0.000 0.680 0.320
#> GSM751407 3 0.2589 0.7260 0.000 0.044 0.912 0.044
#> GSM751408 3 0.1733 0.7318 0.000 0.024 0.948 0.028
#> GSM751409 3 0.1557 0.7284 0.000 0.000 0.944 0.056
#> GSM751412 3 0.1520 0.7318 0.000 0.024 0.956 0.020
#> GSM751418 3 0.1833 0.7249 0.000 0.024 0.944 0.032
#> GSM751419 3 0.1833 0.7249 0.000 0.024 0.944 0.032
#> GSM751420 3 0.5599 0.4072 0.000 0.032 0.616 0.352
#> GSM751425 2 0.4992 0.0452 0.000 0.524 0.000 0.476
#> GSM751429 4 0.9052 0.3565 0.140 0.192 0.184 0.484
#> GSM751430 2 0.4776 0.5669 0.000 0.712 0.016 0.272
#> GSM751433 2 0.0707 0.8947 0.000 0.980 0.000 0.020
#> GSM751437 4 0.5062 0.4265 0.000 0.024 0.284 0.692
#> GSM751448 3 0.5295 0.1230 0.000 0.008 0.504 0.488
#> GSM751451 2 0.0469 0.8989 0.000 0.988 0.000 0.012
#> GSM751423 2 0.4304 0.5471 0.000 0.716 0.000 0.284
#> GSM751424 2 0.0707 0.8947 0.000 0.980 0.000 0.020
#> GSM751428 2 0.0188 0.8995 0.000 0.996 0.000 0.004
#> GSM751431 2 0.0336 0.8984 0.000 0.992 0.000 0.008
#> GSM751432 2 0.0707 0.8947 0.000 0.980 0.000 0.020
#> GSM751434 2 0.0707 0.8947 0.000 0.980 0.000 0.020
#> GSM751435 2 0.0000 0.8998 0.000 1.000 0.000 0.000
#> GSM751436 2 0.0707 0.8947 0.000 0.980 0.000 0.020
#> GSM751440 2 0.0000 0.8998 0.000 1.000 0.000 0.000
#> GSM751444 2 0.0469 0.8991 0.000 0.988 0.000 0.012
#> GSM751446 2 0.1109 0.8930 0.000 0.968 0.004 0.028
#> GSM751449 2 0.2376 0.8536 0.000 0.916 0.016 0.068
#> GSM751450 2 0.0000 0.8998 0.000 1.000 0.000 0.000
#> GSM751452 2 0.0707 0.8947 0.000 0.980 0.000 0.020
#> GSM751426 2 0.0000 0.8998 0.000 1.000 0.000 0.000
#> GSM751427 2 0.0592 0.8986 0.000 0.984 0.000 0.016
#> GSM751438 2 0.1510 0.8859 0.000 0.956 0.016 0.028
#> GSM751439 2 0.1042 0.8953 0.000 0.972 0.008 0.020
#> GSM751441 2 0.0707 0.8975 0.000 0.980 0.000 0.020
#> GSM751442 2 0.0707 0.8975 0.000 0.980 0.000 0.020
#> GSM751443 2 0.6523 0.3150 0.000 0.564 0.088 0.348
#> GSM751445 2 0.4454 0.5249 0.000 0.692 0.000 0.308
#> GSM751447 2 0.0592 0.8984 0.000 0.984 0.000 0.016
#> GSM751453 2 0.0000 0.8998 0.000 1.000 0.000 0.000
#> GSM751454 2 0.0000 0.8998 0.000 1.000 0.000 0.000
#> GSM751455 2 0.0707 0.8975 0.000 0.980 0.000 0.020
#> GSM751456 2 0.0707 0.8975 0.000 0.980 0.000 0.020
#> GSM751457 4 0.5244 0.2725 0.000 0.388 0.012 0.600
#> GSM751458 4 0.5244 0.2725 0.000 0.388 0.012 0.600
cbind(get_classes(res, k = 5), get_membership(res, k = 5))
#> class entropy silhouette p1 p2 p3 p4 p5
#> GSM751298 1 0.3003 0.7450 0.812 0.000 0.000 0.188 0.000
#> GSM751304 4 0.5820 0.2779 0.004 0.004 0.068 0.504 0.420
#> GSM751305 4 0.5775 0.2422 0.004 0.012 0.048 0.500 0.436
#> GSM751307 5 0.7505 -0.0369 0.104 0.112 0.000 0.340 0.444
#> GSM751310 1 0.3835 0.6479 0.744 0.000 0.000 0.244 0.012
#> GSM751314 1 0.2074 0.7260 0.896 0.000 0.000 0.104 0.000
#> GSM751316 4 0.6054 0.2185 0.284 0.000 0.004 0.572 0.140
#> GSM751318 1 0.3247 0.6741 0.840 0.008 0.000 0.136 0.016
#> GSM751342 1 0.3798 0.6348 0.808 0.000 0.000 0.128 0.064
#> GSM751346 1 0.4359 0.6452 0.584 0.000 0.004 0.412 0.000
#> GSM751347 1 0.4689 0.6240 0.560 0.000 0.016 0.424 0.000
#> GSM751348 5 0.6629 -0.2344 0.140 0.004 0.012 0.352 0.492
#> GSM751349 5 0.4559 0.2711 0.000 0.088 0.004 0.152 0.756
#> GSM751352 4 0.5205 0.2903 0.012 0.008 0.020 0.612 0.348
#> GSM751353 5 0.5769 -0.0196 0.000 0.072 0.020 0.296 0.612
#> GSM751354 5 0.5180 -0.1833 0.000 0.012 0.020 0.480 0.488
#> GSM751355 5 0.4791 0.0627 0.000 0.008 0.016 0.360 0.616
#> GSM751358 5 0.6413 -0.2772 0.036 0.000 0.076 0.400 0.488
#> GSM751359 5 0.4698 0.1140 0.000 0.008 0.040 0.244 0.708
#> GSM751294 5 0.6033 -0.2984 0.004 0.000 0.100 0.428 0.468
#> GSM751296 1 0.3661 0.7213 0.724 0.000 0.000 0.276 0.000
#> GSM751297 1 0.5384 0.5719 0.512 0.000 0.032 0.444 0.012
#> GSM751299 4 0.4762 0.2926 0.020 0.004 0.008 0.672 0.296
#> GSM751300 1 0.4219 0.6464 0.584 0.000 0.000 0.416 0.000
#> GSM751301 1 0.2748 0.7283 0.880 0.008 0.000 0.096 0.016
#> GSM751302 1 0.4219 0.6464 0.584 0.000 0.000 0.416 0.000
#> GSM751303 1 0.3662 0.5629 0.744 0.000 0.000 0.252 0.004
#> GSM751306 1 0.3048 0.6662 0.820 0.000 0.000 0.176 0.004
#> GSM751308 1 0.6863 -0.2733 0.440 0.000 0.024 0.384 0.152
#> GSM751309 1 0.2179 0.7133 0.888 0.000 0.000 0.112 0.000
#> GSM751311 1 0.1544 0.7380 0.932 0.000 0.000 0.068 0.000
#> GSM751312 4 0.4375 -0.5052 0.420 0.000 0.000 0.576 0.004
#> GSM751313 1 0.3949 0.6930 0.668 0.000 0.000 0.332 0.000
#> GSM751315 1 0.3274 0.7548 0.780 0.000 0.000 0.220 0.000
#> GSM751317 1 0.3336 0.6576 0.772 0.000 0.000 0.228 0.000
#> GSM751320 1 0.1608 0.7670 0.928 0.000 0.000 0.072 0.000
#> GSM751321 1 0.3452 0.7453 0.756 0.000 0.000 0.244 0.000
#> GSM751322 1 0.0794 0.7518 0.972 0.000 0.000 0.028 0.000
#> GSM751324 1 0.1043 0.7487 0.960 0.000 0.000 0.040 0.000
#> GSM751325 1 0.0794 0.7518 0.972 0.000 0.000 0.028 0.000
#> GSM751332 1 0.0404 0.7585 0.988 0.000 0.000 0.012 0.000
#> GSM751334 1 0.0404 0.7585 0.988 0.000 0.000 0.012 0.000
#> GSM751339 1 0.5719 0.4601 0.588 0.000 0.072 0.328 0.012
#> GSM751341 1 0.0963 0.7619 0.964 0.000 0.000 0.036 0.000
#> GSM751343 1 0.1043 0.7485 0.960 0.000 0.000 0.040 0.000
#> GSM751344 5 0.4769 -0.1669 0.000 0.012 0.004 0.440 0.544
#> GSM751345 5 0.4887 -0.1799 0.000 0.012 0.008 0.444 0.536
#> GSM751356 4 0.6037 0.2654 0.016 0.000 0.072 0.464 0.448
#> GSM751357 4 0.6038 0.2601 0.016 0.000 0.072 0.460 0.452
#> GSM751293 1 0.2452 0.7243 0.896 0.004 0.000 0.084 0.016
#> GSM751295 1 0.4219 0.6464 0.584 0.000 0.000 0.416 0.000
#> GSM751319 1 0.3586 0.7420 0.736 0.000 0.000 0.264 0.000
#> GSM751323 1 0.1478 0.7677 0.936 0.000 0.000 0.064 0.000
#> GSM751326 1 0.2424 0.7640 0.868 0.000 0.000 0.132 0.000
#> GSM751327 1 0.1478 0.7672 0.936 0.000 0.000 0.064 0.000
#> GSM751328 1 0.0510 0.7589 0.984 0.000 0.000 0.016 0.000
#> GSM751329 1 0.0794 0.7628 0.972 0.000 0.000 0.028 0.000
#> GSM751330 1 0.4126 0.6689 0.620 0.000 0.000 0.380 0.000
#> GSM751331 1 0.4219 0.6464 0.584 0.000 0.000 0.416 0.000
#> GSM751333 1 0.3816 0.7072 0.696 0.000 0.000 0.304 0.000
#> GSM751335 1 0.4126 0.6687 0.620 0.000 0.000 0.380 0.000
#> GSM751336 1 0.4219 0.6464 0.584 0.000 0.000 0.416 0.000
#> GSM751337 1 0.1965 0.7669 0.904 0.000 0.000 0.096 0.000
#> GSM751338 1 0.2648 0.7642 0.848 0.000 0.000 0.152 0.000
#> GSM751340 4 0.6808 0.2622 0.268 0.000 0.104 0.560 0.068
#> GSM751350 1 0.4219 0.6464 0.584 0.000 0.000 0.416 0.000
#> GSM751351 1 0.4219 0.6464 0.584 0.000 0.000 0.416 0.000
#> GSM751362 3 0.4933 0.5138 0.000 0.000 0.704 0.096 0.200
#> GSM751363 5 0.5727 0.3554 0.008 0.004 0.172 0.152 0.664
#> GSM751367 4 0.8817 0.1487 0.184 0.016 0.248 0.340 0.212
#> GSM751368 5 0.6990 0.1201 0.000 0.100 0.352 0.064 0.484
#> GSM751371 4 0.8319 0.2937 0.164 0.000 0.248 0.376 0.212
#> GSM751375 5 0.3745 0.3623 0.000 0.068 0.008 0.096 0.828
#> GSM751376 4 0.6796 0.2433 0.000 0.000 0.316 0.380 0.304
#> GSM751378 5 0.5930 -0.0436 0.000 0.000 0.372 0.112 0.516
#> GSM751379 3 0.6746 -0.2485 0.000 0.000 0.380 0.360 0.260
#> GSM751382 5 0.4607 0.3479 0.000 0.112 0.016 0.100 0.772
#> GSM751386 5 0.2516 0.5153 0.000 0.000 0.140 0.000 0.860
#> GSM751388 5 0.3509 0.4769 0.000 0.008 0.196 0.004 0.792
#> GSM751391 4 0.7625 0.2962 0.032 0.008 0.252 0.392 0.316
#> GSM751410 3 0.6587 0.1955 0.008 0.000 0.520 0.240 0.232
#> GSM751414 3 0.5798 0.3334 0.000 0.000 0.556 0.108 0.336
#> GSM751361 5 0.5211 0.4172 0.000 0.000 0.212 0.112 0.676
#> GSM751365 3 0.5083 0.4210 0.000 0.000 0.652 0.068 0.280
#> GSM751366 3 0.3116 0.6004 0.000 0.000 0.860 0.064 0.076
#> GSM751369 3 0.6335 0.0963 0.000 0.000 0.520 0.276 0.204
#> GSM751370 3 0.5934 0.2128 0.000 0.000 0.496 0.108 0.396
#> GSM751372 3 0.5779 0.2177 0.000 0.000 0.508 0.092 0.400
#> GSM751373 3 0.5506 0.4221 0.000 0.008 0.644 0.088 0.260
#> GSM751374 3 0.6752 -0.2450 0.000 0.000 0.384 0.352 0.264
#> GSM751377 5 0.5246 0.1913 0.000 0.000 0.344 0.060 0.596
#> GSM751380 3 0.2026 0.6325 0.016 0.000 0.928 0.044 0.012
#> GSM751381 5 0.2583 0.5140 0.000 0.000 0.132 0.004 0.864
#> GSM751383 5 0.5030 0.3820 0.000 0.060 0.264 0.004 0.672
#> GSM751384 5 0.3612 0.4267 0.000 0.000 0.268 0.000 0.732
#> GSM751385 5 0.3427 0.4437 0.000 0.000 0.108 0.056 0.836
#> GSM751387 5 0.4510 0.4784 0.000 0.056 0.184 0.008 0.752
#> GSM751389 3 0.2012 0.6108 0.000 0.000 0.920 0.020 0.060
#> GSM751393 5 0.6626 -0.0358 0.000 0.000 0.352 0.224 0.424
#> GSM751394 5 0.2894 0.5149 0.000 0.008 0.124 0.008 0.860
#> GSM751395 5 0.6301 -0.1515 0.000 0.000 0.180 0.308 0.512
#> GSM751397 5 0.2179 0.5087 0.000 0.000 0.112 0.000 0.888
#> GSM751398 5 0.2674 0.5154 0.000 0.000 0.140 0.004 0.856
#> GSM751404 3 0.1357 0.6351 0.000 0.004 0.948 0.000 0.048
#> GSM751406 3 0.3365 0.5493 0.000 0.000 0.836 0.044 0.120
#> GSM751411 3 0.4967 0.4515 0.000 0.000 0.660 0.060 0.280
#> GSM751413 5 0.5523 0.3923 0.000 0.016 0.144 0.152 0.688
#> GSM751415 3 0.0451 0.6400 0.000 0.000 0.988 0.008 0.004
#> GSM751416 5 0.5896 -0.1262 0.000 0.000 0.448 0.100 0.452
#> GSM751417 5 0.5896 -0.1262 0.000 0.000 0.448 0.100 0.452
#> GSM751421 3 0.5628 0.4819 0.000 0.000 0.632 0.148 0.220
#> GSM751422 3 0.6118 0.3740 0.000 0.000 0.548 0.164 0.288
#> GSM751360 5 0.6625 0.2248 0.012 0.000 0.232 0.228 0.528
#> GSM751364 3 0.5857 0.1056 0.000 0.000 0.460 0.096 0.444
#> GSM751390 5 0.5464 0.3051 0.000 0.064 0.348 0.004 0.584
#> GSM751392 5 0.2403 0.4893 0.000 0.012 0.072 0.012 0.904
#> GSM751396 5 0.6041 0.3032 0.000 0.344 0.104 0.008 0.544
#> GSM751399 3 0.1638 0.6322 0.000 0.000 0.932 0.004 0.064
#> GSM751400 3 0.2027 0.6351 0.000 0.024 0.928 0.008 0.040
#> GSM751401 3 0.1106 0.6388 0.000 0.012 0.964 0.000 0.024
#> GSM751402 3 0.0566 0.6392 0.000 0.004 0.984 0.000 0.012
#> GSM751403 3 0.1117 0.6348 0.000 0.000 0.964 0.016 0.020
#> GSM751405 3 0.3868 0.5228 0.000 0.000 0.800 0.060 0.140
#> GSM751407 3 0.1522 0.6348 0.000 0.012 0.944 0.000 0.044
#> GSM751408 3 0.1430 0.6342 0.000 0.004 0.944 0.000 0.052
#> GSM751409 3 0.0880 0.6395 0.000 0.000 0.968 0.000 0.032
#> GSM751412 3 0.1430 0.6342 0.000 0.004 0.944 0.000 0.052
#> GSM751418 3 0.5295 0.3825 0.000 0.004 0.628 0.064 0.304
#> GSM751419 3 0.5276 0.3888 0.000 0.004 0.632 0.064 0.300
#> GSM751420 3 0.3420 0.5485 0.000 0.004 0.836 0.036 0.124
#> GSM751425 2 0.6203 0.1824 0.000 0.504 0.004 0.128 0.364
#> GSM751429 4 0.8456 0.1545 0.036 0.072 0.320 0.376 0.196
#> GSM751430 2 0.4921 0.3699 0.000 0.604 0.000 0.036 0.360
#> GSM751433 2 0.1492 0.8591 0.004 0.948 0.000 0.008 0.040
#> GSM751437 3 0.7166 0.0216 0.000 0.048 0.500 0.176 0.276
#> GSM751448 3 0.6335 0.2422 0.000 0.024 0.604 0.192 0.180
#> GSM751451 2 0.1405 0.8658 0.008 0.956 0.000 0.020 0.016
#> GSM751423 2 0.4708 0.5892 0.000 0.712 0.000 0.068 0.220
#> GSM751424 2 0.1331 0.8605 0.000 0.952 0.000 0.008 0.040
#> GSM751428 2 0.0324 0.8715 0.000 0.992 0.000 0.004 0.004
#> GSM751431 2 0.0771 0.8687 0.000 0.976 0.000 0.004 0.020
#> GSM751432 2 0.1331 0.8605 0.000 0.952 0.000 0.008 0.040
#> GSM751434 2 0.1492 0.8591 0.004 0.948 0.000 0.008 0.040
#> GSM751435 2 0.0162 0.8716 0.000 0.996 0.000 0.004 0.000
#> GSM751436 2 0.1492 0.8591 0.004 0.948 0.000 0.008 0.040
#> GSM751440 2 0.0162 0.8715 0.000 0.996 0.000 0.004 0.000
#> GSM751444 2 0.0865 0.8699 0.000 0.972 0.000 0.024 0.004
#> GSM751446 2 0.1412 0.8643 0.000 0.952 0.008 0.036 0.004
#> GSM751449 2 0.2409 0.8373 0.000 0.908 0.008 0.056 0.028
#> GSM751450 2 0.0451 0.8710 0.000 0.988 0.000 0.004 0.008
#> GSM751452 2 0.1331 0.8605 0.000 0.952 0.000 0.008 0.040
#> GSM751426 2 0.0671 0.8696 0.000 0.980 0.000 0.004 0.016
#> GSM751427 2 0.0771 0.8701 0.000 0.976 0.000 0.020 0.004
#> GSM751438 2 0.2027 0.8520 0.000 0.928 0.008 0.040 0.024
#> GSM751439 2 0.1822 0.8576 0.000 0.936 0.024 0.036 0.004
#> GSM751441 2 0.1168 0.8672 0.000 0.960 0.000 0.032 0.008
#> GSM751442 2 0.1041 0.8681 0.000 0.964 0.000 0.032 0.004
#> GSM751443 3 0.8155 -0.0886 0.000 0.332 0.356 0.168 0.144
#> GSM751445 2 0.5503 0.5401 0.000 0.672 0.008 0.128 0.192
#> GSM751447 2 0.0955 0.8691 0.000 0.968 0.000 0.028 0.004
#> GSM751453 2 0.0324 0.8716 0.000 0.992 0.000 0.004 0.004
#> GSM751454 2 0.0324 0.8716 0.000 0.992 0.000 0.004 0.004
#> GSM751455 2 0.1041 0.8681 0.000 0.964 0.000 0.032 0.004
#> GSM751456 2 0.1041 0.8681 0.000 0.964 0.000 0.032 0.004
#> GSM751457 2 0.7806 -0.2218 0.000 0.348 0.060 0.308 0.284
#> GSM751458 2 0.7806 -0.2218 0.000 0.348 0.060 0.308 0.284
cbind(get_classes(res, k = 6), get_membership(res, k = 6))
#> class entropy silhouette p1 p2 p3 p4 p5 p6
#> GSM751298 4 0.3737 0.26224 0.392 0.000 0.000 0.608 0.000 0.000
#> GSM751304 6 0.3716 0.59488 0.048 0.000 0.024 0.016 0.084 0.828
#> GSM751305 6 0.3949 0.58874 0.044 0.004 0.008 0.032 0.100 0.812
#> GSM751307 5 0.8345 -0.12812 0.208 0.116 0.000 0.080 0.336 0.260
#> GSM751310 4 0.4557 0.63452 0.120 0.000 0.000 0.752 0.080 0.048
#> GSM751314 4 0.1977 0.72933 0.032 0.000 0.000 0.920 0.040 0.008
#> GSM751316 1 0.7299 0.06039 0.316 0.000 0.000 0.276 0.096 0.312
#> GSM751318 4 0.2377 0.70597 0.024 0.008 0.000 0.892 0.000 0.076
#> GSM751342 4 0.2637 0.69485 0.024 0.000 0.000 0.876 0.012 0.088
#> GSM751346 1 0.2805 0.77477 0.812 0.000 0.000 0.184 0.000 0.004
#> GSM751347 1 0.2944 0.75422 0.832 0.000 0.008 0.148 0.000 0.012
#> GSM751348 6 0.4365 0.54462 0.020 0.000 0.008 0.120 0.084 0.768
#> GSM751349 6 0.5470 0.34131 0.036 0.048 0.012 0.004 0.264 0.636
#> GSM751352 6 0.3504 0.58581 0.172 0.000 0.008 0.008 0.016 0.796
#> GSM751353 6 0.3650 0.56931 0.056 0.020 0.000 0.000 0.112 0.812
#> GSM751354 6 0.5900 0.51662 0.280 0.012 0.020 0.000 0.116 0.572
#> GSM751355 6 0.5933 0.45662 0.224 0.008 0.008 0.000 0.204 0.556
#> GSM751358 6 0.2469 0.60739 0.020 0.000 0.028 0.012 0.036 0.904
#> GSM751359 6 0.3635 0.50489 0.016 0.008 0.004 0.004 0.184 0.784
#> GSM751294 6 0.2489 0.61184 0.032 0.008 0.040 0.008 0.008 0.904
#> GSM751296 1 0.3838 0.26087 0.552 0.000 0.000 0.448 0.000 0.000
#> GSM751297 1 0.3315 0.72413 0.836 0.000 0.016 0.116 0.008 0.024
#> GSM751299 6 0.4367 0.29285 0.408 0.004 0.004 0.000 0.012 0.572
#> GSM751300 1 0.2730 0.77348 0.808 0.000 0.000 0.192 0.000 0.000
#> GSM751301 4 0.3633 0.69906 0.120 0.000 0.000 0.800 0.004 0.076
#> GSM751302 1 0.2697 0.77522 0.812 0.000 0.000 0.188 0.000 0.000
#> GSM751303 4 0.3671 0.65957 0.036 0.000 0.000 0.820 0.056 0.088
#> GSM751306 4 0.2847 0.70521 0.036 0.000 0.000 0.876 0.048 0.040
#> GSM751308 4 0.5491 0.11228 0.044 0.004 0.024 0.480 0.004 0.444
#> GSM751309 4 0.2046 0.72580 0.032 0.000 0.000 0.916 0.008 0.044
#> GSM751311 4 0.0922 0.74518 0.004 0.000 0.000 0.968 0.004 0.024
#> GSM751312 1 0.5416 0.52600 0.656 0.000 0.000 0.204 0.056 0.084
#> GSM751313 1 0.3555 0.66680 0.712 0.000 0.000 0.280 0.000 0.008
#> GSM751315 4 0.4288 0.41406 0.308 0.000 0.000 0.660 0.020 0.012
#> GSM751317 4 0.3848 0.67396 0.084 0.000 0.000 0.808 0.036 0.072
#> GSM751320 4 0.1863 0.73433 0.104 0.000 0.000 0.896 0.000 0.000
#> GSM751321 4 0.4364 0.40897 0.308 0.000 0.000 0.656 0.024 0.012
#> GSM751322 4 0.0632 0.74773 0.024 0.000 0.000 0.976 0.000 0.000
#> GSM751324 4 0.0458 0.74758 0.016 0.000 0.000 0.984 0.000 0.000
#> GSM751325 4 0.0937 0.74697 0.040 0.000 0.000 0.960 0.000 0.000
#> GSM751332 4 0.1714 0.73494 0.092 0.000 0.000 0.908 0.000 0.000
#> GSM751334 4 0.1814 0.73233 0.100 0.000 0.000 0.900 0.000 0.000
#> GSM751339 4 0.6775 0.27138 0.248 0.000 0.040 0.492 0.016 0.204
#> GSM751341 4 0.2234 0.72328 0.124 0.000 0.000 0.872 0.000 0.004
#> GSM751343 4 0.0891 0.74931 0.024 0.000 0.000 0.968 0.000 0.008
#> GSM751344 6 0.3411 0.58469 0.084 0.008 0.004 0.000 0.072 0.832
#> GSM751345 6 0.3356 0.58630 0.084 0.008 0.004 0.000 0.068 0.836
#> GSM751356 6 0.2582 0.61004 0.060 0.000 0.028 0.012 0.008 0.892
#> GSM751357 6 0.2582 0.61004 0.060 0.000 0.028 0.012 0.008 0.892
#> GSM751293 4 0.3424 0.70027 0.092 0.000 0.000 0.812 0.000 0.096
#> GSM751295 1 0.2697 0.77522 0.812 0.000 0.000 0.188 0.000 0.000
#> GSM751319 4 0.4389 -0.02569 0.444 0.000 0.000 0.536 0.008 0.012
#> GSM751323 4 0.2762 0.67112 0.196 0.000 0.000 0.804 0.000 0.000
#> GSM751326 4 0.3647 0.39132 0.360 0.000 0.000 0.640 0.000 0.000
#> GSM751327 4 0.2597 0.68899 0.176 0.000 0.000 0.824 0.000 0.000
#> GSM751328 4 0.1714 0.73456 0.092 0.000 0.000 0.908 0.000 0.000
#> GSM751329 4 0.2416 0.70381 0.156 0.000 0.000 0.844 0.000 0.000
#> GSM751330 1 0.2823 0.76494 0.796 0.000 0.000 0.204 0.000 0.000
#> GSM751331 1 0.2697 0.77470 0.812 0.000 0.000 0.188 0.000 0.000
#> GSM751333 1 0.3636 0.59515 0.676 0.000 0.000 0.320 0.000 0.004
#> GSM751335 1 0.2854 0.76121 0.792 0.000 0.000 0.208 0.000 0.000
#> GSM751336 1 0.2697 0.77470 0.812 0.000 0.000 0.188 0.000 0.000
#> GSM751337 4 0.3351 0.54813 0.288 0.000 0.000 0.712 0.000 0.000
#> GSM751338 4 0.4071 0.45438 0.304 0.000 0.000 0.672 0.004 0.020
#> GSM751340 6 0.7765 -0.07998 0.296 0.000 0.044 0.264 0.064 0.332
#> GSM751350 1 0.2664 0.77532 0.816 0.000 0.000 0.184 0.000 0.000
#> GSM751351 1 0.2664 0.77532 0.816 0.000 0.000 0.184 0.000 0.000
#> GSM751362 3 0.5977 0.41449 0.024 0.000 0.508 0.000 0.332 0.136
#> GSM751363 5 0.3023 0.54191 0.012 0.000 0.072 0.016 0.868 0.032
#> GSM751367 1 0.8367 0.07484 0.368 0.020 0.136 0.072 0.304 0.100
#> GSM751368 5 0.6584 0.36597 0.040 0.092 0.256 0.004 0.564 0.044
#> GSM751371 6 0.7774 0.26833 0.032 0.000 0.132 0.288 0.156 0.392
#> GSM751375 6 0.6193 0.09725 0.060 0.052 0.020 0.000 0.352 0.516
#> GSM751376 6 0.5995 0.38676 0.052 0.004 0.256 0.000 0.104 0.584
#> GSM751378 6 0.5873 0.33256 0.024 0.000 0.296 0.000 0.136 0.544
#> GSM751379 6 0.6324 0.32032 0.056 0.004 0.280 0.000 0.124 0.536
#> GSM751382 6 0.6741 0.02664 0.052 0.076 0.044 0.000 0.352 0.476
#> GSM751386 5 0.5212 0.49975 0.032 0.000 0.060 0.000 0.620 0.288
#> GSM751388 5 0.5600 0.52641 0.036 0.004 0.092 0.000 0.620 0.248
#> GSM751391 6 0.6028 0.49741 0.028 0.000 0.172 0.060 0.096 0.644
#> GSM751410 3 0.7184 0.12894 0.028 0.004 0.364 0.020 0.288 0.296
#> GSM751414 5 0.4015 0.28765 0.008 0.000 0.328 0.008 0.656 0.000
#> GSM751361 5 0.4672 0.54953 0.024 0.000 0.040 0.012 0.716 0.208
#> GSM751365 5 0.3995 0.04047 0.004 0.000 0.480 0.000 0.516 0.000
#> GSM751366 3 0.3052 0.56031 0.004 0.000 0.780 0.000 0.216 0.000
#> GSM751369 3 0.6391 0.04889 0.020 0.000 0.408 0.004 0.184 0.384
#> GSM751370 5 0.3383 0.40714 0.004 0.000 0.268 0.000 0.728 0.000
#> GSM751372 5 0.3351 0.38623 0.000 0.000 0.288 0.000 0.712 0.000
#> GSM751373 3 0.4393 0.09816 0.012 0.000 0.532 0.000 0.448 0.008
#> GSM751374 6 0.6290 0.32640 0.056 0.004 0.280 0.000 0.120 0.540
#> GSM751377 5 0.3820 0.56551 0.016 0.004 0.148 0.000 0.792 0.040
#> GSM751380 3 0.2442 0.64897 0.004 0.000 0.852 0.000 0.144 0.000
#> GSM751381 5 0.5371 0.46007 0.032 0.000 0.064 0.000 0.588 0.316
#> GSM751383 5 0.6364 0.55235 0.040 0.012 0.232 0.000 0.556 0.160
#> GSM751384 5 0.5853 0.50402 0.032 0.000 0.128 0.000 0.568 0.272
#> GSM751385 6 0.6150 -0.19435 0.032 0.000 0.128 0.000 0.420 0.420
#> GSM751387 5 0.6088 0.49358 0.040 0.008 0.112 0.000 0.564 0.276
#> GSM751389 3 0.2213 0.68980 0.012 0.000 0.908 0.000 0.032 0.048
#> GSM751393 6 0.6185 0.26214 0.020 0.000 0.312 0.000 0.188 0.480
#> GSM751394 5 0.4880 0.53271 0.032 0.004 0.044 0.000 0.680 0.240
#> GSM751395 6 0.4605 0.55958 0.024 0.000 0.164 0.000 0.084 0.728
#> GSM751397 5 0.5229 0.49158 0.032 0.000 0.060 0.000 0.616 0.292
#> GSM751398 5 0.5056 0.51972 0.036 0.004 0.044 0.000 0.656 0.260
#> GSM751404 3 0.0547 0.69657 0.000 0.000 0.980 0.000 0.020 0.000
#> GSM751406 3 0.3220 0.64845 0.016 0.000 0.844 0.000 0.052 0.088
#> GSM751411 3 0.4222 -0.00737 0.004 0.000 0.516 0.000 0.472 0.008
#> GSM751413 5 0.3172 0.55557 0.020 0.020 0.028 0.008 0.872 0.052
#> GSM751415 3 0.1007 0.69458 0.000 0.000 0.956 0.000 0.044 0.000
#> GSM751416 5 0.2969 0.47036 0.000 0.000 0.224 0.000 0.776 0.000
#> GSM751417 5 0.2969 0.47036 0.000 0.000 0.224 0.000 0.776 0.000
#> GSM751421 3 0.6412 0.25475 0.020 0.000 0.420 0.012 0.396 0.152
#> GSM751422 5 0.6622 -0.18360 0.024 0.000 0.344 0.012 0.432 0.188
#> GSM751360 5 0.5395 0.41077 0.020 0.000 0.088 0.048 0.700 0.144
#> GSM751364 5 0.3101 0.45453 0.000 0.000 0.244 0.000 0.756 0.000
#> GSM751390 5 0.7149 0.38189 0.036 0.024 0.340 0.000 0.372 0.228
#> GSM751392 5 0.5706 0.37068 0.044 0.008 0.048 0.000 0.540 0.360
#> GSM751396 5 0.8089 0.24736 0.080 0.300 0.104 0.000 0.368 0.148
#> GSM751399 3 0.2149 0.67736 0.004 0.000 0.900 0.000 0.080 0.016
#> GSM751400 3 0.0964 0.69673 0.000 0.004 0.968 0.000 0.012 0.016
#> GSM751401 3 0.0146 0.69702 0.000 0.000 0.996 0.000 0.004 0.000
#> GSM751402 3 0.0508 0.69791 0.000 0.000 0.984 0.000 0.004 0.012
#> GSM751403 3 0.1149 0.69633 0.008 0.000 0.960 0.000 0.008 0.024
#> GSM751405 3 0.4052 0.61668 0.024 0.000 0.784 0.000 0.076 0.116
#> GSM751407 3 0.0363 0.69646 0.000 0.000 0.988 0.000 0.012 0.000
#> GSM751408 3 0.1075 0.68443 0.000 0.000 0.952 0.000 0.048 0.000
#> GSM751409 3 0.1010 0.69410 0.000 0.000 0.960 0.000 0.036 0.004
#> GSM751412 3 0.1333 0.67943 0.000 0.000 0.944 0.000 0.048 0.008
#> GSM751418 3 0.3867 -0.01478 0.000 0.000 0.512 0.000 0.488 0.000
#> GSM751419 3 0.3867 -0.01478 0.000 0.000 0.512 0.000 0.488 0.000
#> GSM751420 3 0.2457 0.66989 0.008 0.004 0.896 0.000 0.036 0.056
#> GSM751425 2 0.5463 -0.07123 0.016 0.464 0.000 0.000 0.076 0.444
#> GSM751429 1 0.8478 -0.05114 0.424 0.124 0.132 0.012 0.160 0.148
#> GSM751430 2 0.6689 0.41977 0.080 0.544 0.012 0.000 0.220 0.144
#> GSM751433 2 0.3176 0.80835 0.056 0.860 0.004 0.000 0.048 0.032
#> GSM751437 3 0.7545 -0.10415 0.056 0.096 0.384 0.004 0.084 0.376
#> GSM751448 3 0.7159 0.25381 0.084 0.052 0.516 0.000 0.104 0.244
#> GSM751451 2 0.2968 0.81688 0.032 0.880 0.004 0.008 0.036 0.040
#> GSM751423 2 0.5099 0.53679 0.036 0.672 0.000 0.000 0.076 0.216
#> GSM751424 2 0.3176 0.80835 0.056 0.860 0.004 0.000 0.048 0.032
#> GSM751428 2 0.1478 0.83249 0.032 0.944 0.000 0.000 0.004 0.020
#> GSM751431 2 0.2602 0.81852 0.052 0.888 0.000 0.000 0.040 0.020
#> GSM751432 2 0.3176 0.80835 0.056 0.860 0.004 0.000 0.048 0.032
#> GSM751434 2 0.3176 0.80835 0.056 0.860 0.004 0.000 0.048 0.032
#> GSM751435 2 0.0779 0.83218 0.008 0.976 0.008 0.000 0.008 0.000
#> GSM751436 2 0.3176 0.80835 0.056 0.860 0.004 0.000 0.048 0.032
#> GSM751440 2 0.0291 0.83244 0.004 0.992 0.004 0.000 0.000 0.000
#> GSM751444 2 0.2170 0.82856 0.044 0.916 0.008 0.000 0.016 0.016
#> GSM751446 2 0.2795 0.81118 0.044 0.884 0.008 0.000 0.044 0.020
#> GSM751449 2 0.3692 0.77231 0.048 0.828 0.004 0.000 0.056 0.064
#> GSM751450 2 0.2058 0.82607 0.048 0.916 0.000 0.000 0.024 0.012
#> GSM751452 2 0.3176 0.80835 0.056 0.860 0.004 0.000 0.048 0.032
#> GSM751426 2 0.2444 0.82099 0.052 0.896 0.000 0.000 0.036 0.016
#> GSM751427 2 0.2351 0.82108 0.040 0.908 0.008 0.000 0.028 0.016
#> GSM751438 2 0.3434 0.78988 0.048 0.848 0.008 0.000 0.044 0.052
#> GSM751439 2 0.3070 0.80656 0.044 0.872 0.016 0.000 0.044 0.024
#> GSM751441 2 0.2750 0.81328 0.040 0.888 0.008 0.000 0.028 0.036
#> GSM751442 2 0.2439 0.81907 0.040 0.904 0.008 0.000 0.028 0.020
#> GSM751443 2 0.8035 -0.00952 0.080 0.352 0.308 0.000 0.076 0.184
#> GSM751445 2 0.5491 0.41214 0.052 0.596 0.000 0.000 0.056 0.296
#> GSM751447 2 0.2258 0.82163 0.040 0.912 0.008 0.000 0.028 0.012
#> GSM751453 2 0.1237 0.83243 0.020 0.956 0.000 0.000 0.020 0.004
#> GSM751454 2 0.1237 0.83243 0.020 0.956 0.000 0.000 0.020 0.004
#> GSM751455 2 0.2439 0.81907 0.040 0.904 0.008 0.000 0.028 0.020
#> GSM751456 2 0.2439 0.81907 0.040 0.904 0.008 0.000 0.028 0.020
#> GSM751457 6 0.6569 0.18698 0.064 0.356 0.016 0.000 0.088 0.476
#> GSM751458 6 0.6569 0.18698 0.064 0.356 0.016 0.000 0.088 0.476
Heatmaps for the consensus matrix. It visualizes the probability of two samples to be in a same group.
consensus_heatmap(res, k = 2)
consensus_heatmap(res, k = 3)
consensus_heatmap(res, k = 4)
consensus_heatmap(res, k = 5)
consensus_heatmap(res, k = 6)
Heatmaps for the membership of samples in all partitions to see how consistent they are:
membership_heatmap(res, k = 2)
membership_heatmap(res, k = 3)
membership_heatmap(res, k = 4)
membership_heatmap(res, k = 5)
membership_heatmap(res, k = 6)
As soon as we have had the classes for columns, we can look for signatures which are significantly different between classes which can be candidate marks for certain classes. Following are the heatmaps for signatures.
Signature heatmaps where rows are scaled:
get_signatures(res, k = 2)
get_signatures(res, k = 3)
get_signatures(res, k = 4)
get_signatures(res, k = 5)
get_signatures(res, k = 6)
Signature heatmaps where rows are not scaled:
get_signatures(res, k = 2, scale_rows = FALSE)
get_signatures(res, k = 3, scale_rows = FALSE)
get_signatures(res, k = 4, scale_rows = FALSE)
get_signatures(res, k = 5, scale_rows = FALSE)
get_signatures(res, k = 6, scale_rows = FALSE)
Compare the overlap of signatures from different k:
compare_signatures(res)
get_signature() returns a data frame invisibly. TO get the list of signatures, the function
call should be assigned to a variable explicitly. In following code, if plot argument is set
to FALSE, no heatmap is plotted while only the differential analysis is performed.
# code only for demonstration
tb = get_signature(res, k = ..., plot = FALSE)
An example of the output of tb is:
#> which_row fdr mean_1 mean_2 scaled_mean_1 scaled_mean_2 km
#> 1 38 0.042760348 8.373488 9.131774 -0.5533452 0.5164555 1
#> 2 40 0.018707592 7.106213 8.469186 -0.6173731 0.5762149 1
#> 3 55 0.019134737 10.221463 11.207825 -0.6159697 0.5749050 1
#> 4 59 0.006059896 5.921854 7.869574 -0.6899429 0.6439467 1
#> 5 60 0.018055526 8.928898 10.211722 -0.6204761 0.5791110 1
#> 6 98 0.009384629 15.714769 14.887706 0.6635654 -0.6193277 2
...
The columns in tb are:
which_row: row indices corresponding to the input matrix.fdr: FDR for the differential test. mean_x: The mean value in group x.scaled_mean_x: The mean value in group x after rows are scaled.km: Row groups if k-means clustering is applied to rows.UMAP plot which shows how samples are separated.
dimension_reduction(res, k = 2, method = "UMAP")
dimension_reduction(res, k = 3, method = "UMAP")
dimension_reduction(res, k = 4, method = "UMAP")
dimension_reduction(res, k = 5, method = "UMAP")
dimension_reduction(res, k = 6, method = "UMAP")
Following heatmap shows how subgroups are split when increasing k:
collect_classes(res)
Test correlation between subgroups and known annotations. If the known annotation is numeric, one-way ANOVA test is applied, and if the known annotation is discrete, chi-squared contingency table test is applied.
test_to_known_factors(res)
#> n tissue(p) disease.state(p) agent(p) k
#> MAD:skmeans 151 4.34e-26 3.44e-01 5.07e-01 2
#> MAD:skmeans 155 9.83e-47 1.81e-01 4.45e-01 3
#> MAD:skmeans 128 1.64e-46 5.61e-07 4.24e-06 4
#> MAD:skmeans 96 9.56e-39 5.25e-01 2.53e-01 5
#> MAD:skmeans 106 7.24e-39 6.32e-04 6.80e-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", "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 4537 rows and 166 columns.
#> Top rows (454, 908, 1361, 1814, 2268) 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 0.385 0.717 0.857 0.4680 0.529 0.529
#> 3 3 0.474 0.703 0.821 0.3421 0.773 0.593
#> 4 4 0.521 0.683 0.808 0.1402 0.874 0.677
#> 5 5 0.582 0.533 0.742 0.0887 0.895 0.659
#> 6 6 0.649 0.554 0.738 0.0494 0.927 0.688
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
#> GSM751298 1 0.3274 0.7859 0.940 0.060
#> GSM751304 2 0.8813 0.5987 0.300 0.700
#> GSM751305 2 0.9491 0.4782 0.368 0.632
#> GSM751307 1 0.5842 0.7547 0.860 0.140
#> GSM751310 1 0.1633 0.7839 0.976 0.024
#> GSM751314 1 0.0376 0.7887 0.996 0.004
#> GSM751316 1 0.7139 0.6879 0.804 0.196
#> GSM751318 1 0.0672 0.7881 0.992 0.008
#> GSM751342 1 0.1633 0.7839 0.976 0.024
#> GSM751346 1 0.7815 0.6951 0.768 0.232
#> GSM751347 1 0.9993 0.3528 0.516 0.484
#> GSM751348 2 0.9988 0.0961 0.480 0.520
#> GSM751349 2 0.0000 0.8556 0.000 1.000
#> GSM751352 2 0.0672 0.8559 0.008 0.992
#> GSM751353 2 0.0000 0.8556 0.000 1.000
#> GSM751354 2 0.8443 0.6366 0.272 0.728
#> GSM751355 2 0.5629 0.7904 0.132 0.868
#> GSM751358 2 0.9909 0.2967 0.444 0.556
#> GSM751359 2 0.7745 0.6947 0.228 0.772
#> GSM751294 2 0.8016 0.6744 0.244 0.756
#> GSM751296 1 0.1184 0.7906 0.984 0.016
#> GSM751297 1 0.9850 0.1999 0.572 0.428
#> GSM751299 2 0.0672 0.8557 0.008 0.992
#> GSM751300 1 0.6623 0.7449 0.828 0.172
#> GSM751301 1 0.7674 0.7049 0.776 0.224
#> GSM751302 1 0.9850 0.4433 0.572 0.428
#> GSM751303 1 0.3733 0.7738 0.928 0.072
#> GSM751306 1 0.1633 0.7839 0.976 0.024
#> GSM751308 2 0.9635 0.4682 0.388 0.612
#> GSM751309 1 0.1184 0.7858 0.984 0.016
#> GSM751311 1 0.0000 0.7886 1.000 0.000
#> GSM751312 1 0.9427 0.3835 0.640 0.360
#> GSM751313 1 0.0000 0.7886 1.000 0.000
#> GSM751315 1 0.0376 0.7887 0.996 0.004
#> GSM751317 1 0.1633 0.7839 0.976 0.024
#> GSM751320 1 0.0000 0.7886 1.000 0.000
#> GSM751321 1 0.0672 0.7880 0.992 0.008
#> GSM751322 1 0.0000 0.7886 1.000 0.000
#> GSM751324 1 0.0000 0.7886 1.000 0.000
#> GSM751325 1 0.0000 0.7886 1.000 0.000
#> GSM751332 1 0.0938 0.7906 0.988 0.012
#> GSM751334 1 0.1414 0.7901 0.980 0.020
#> GSM751339 1 0.3879 0.7755 0.924 0.076
#> GSM751341 1 0.0376 0.7887 0.996 0.004
#> GSM751343 1 0.0000 0.7886 1.000 0.000
#> GSM751344 2 0.3879 0.8280 0.076 0.924
#> GSM751345 2 0.3584 0.8335 0.068 0.932
#> GSM751356 2 0.7528 0.7101 0.216 0.784
#> GSM751357 2 0.8016 0.6764 0.244 0.756
#> GSM751293 1 0.6438 0.7447 0.836 0.164
#> GSM751295 1 0.8386 0.6581 0.732 0.268
#> GSM751319 1 0.4431 0.7756 0.908 0.092
#> GSM751323 1 0.5629 0.7555 0.868 0.132
#> GSM751326 1 0.8499 0.6576 0.724 0.276
#> GSM751327 1 0.5737 0.7607 0.864 0.136
#> GSM751328 1 0.2236 0.7886 0.964 0.036
#> GSM751329 1 0.8386 0.6609 0.732 0.268
#> GSM751330 1 0.8608 0.6489 0.716 0.284
#> GSM751331 1 0.9909 0.4119 0.556 0.444
#> GSM751333 1 0.8081 0.6821 0.752 0.248
#> GSM751335 1 0.8909 0.6199 0.692 0.308
#> GSM751336 1 0.9909 0.4119 0.556 0.444
#> GSM751337 1 0.0672 0.7904 0.992 0.008
#> GSM751338 1 0.0000 0.7886 1.000 0.000
#> GSM751340 1 0.9248 0.4730 0.660 0.340
#> GSM751350 1 0.9209 0.5886 0.664 0.336
#> GSM751351 1 0.9000 0.6112 0.684 0.316
#> GSM751362 2 0.9710 0.4090 0.400 0.600
#> GSM751363 1 0.6247 0.7261 0.844 0.156
#> GSM751367 1 0.9686 0.3481 0.604 0.396
#> GSM751368 2 0.0672 0.8560 0.008 0.992
#> GSM751371 2 0.9977 0.2116 0.472 0.528
#> GSM751375 2 0.0000 0.8556 0.000 1.000
#> GSM751376 2 0.8144 0.6672 0.252 0.748
#> GSM751378 2 0.6801 0.7461 0.180 0.820
#> GSM751379 2 0.8763 0.6136 0.296 0.704
#> GSM751382 2 0.3274 0.8383 0.060 0.940
#> GSM751386 2 0.0000 0.8556 0.000 1.000
#> GSM751388 2 0.0376 0.8559 0.004 0.996
#> GSM751391 2 0.9087 0.5624 0.324 0.676
#> GSM751410 1 0.7815 0.6362 0.768 0.232
#> GSM751414 1 0.2948 0.7824 0.948 0.052
#> GSM751361 2 0.3114 0.8338 0.056 0.944
#> GSM751365 2 0.9996 0.0128 0.488 0.512
#> GSM751366 1 0.6438 0.7126 0.836 0.164
#> GSM751369 2 0.4298 0.8263 0.088 0.912
#> GSM751370 1 0.9522 0.3938 0.628 0.372
#> GSM751372 2 0.7453 0.7192 0.212 0.788
#> GSM751373 1 0.9988 0.3324 0.520 0.480
#> GSM751374 2 0.8144 0.6643 0.252 0.748
#> GSM751377 2 0.2236 0.8490 0.036 0.964
#> GSM751380 1 0.9775 0.1961 0.588 0.412
#> GSM751381 2 0.6531 0.7568 0.168 0.832
#> GSM751383 2 0.1184 0.8549 0.016 0.984
#> GSM751384 2 0.6247 0.7687 0.156 0.844
#> GSM751385 2 0.0000 0.8556 0.000 1.000
#> GSM751387 2 0.0000 0.8556 0.000 1.000
#> GSM751389 2 0.7602 0.7081 0.220 0.780
#> GSM751393 2 0.1633 0.8530 0.024 0.976
#> GSM751394 2 0.0376 0.8559 0.004 0.996
#> GSM751395 2 0.1633 0.8528 0.024 0.976
#> GSM751397 2 0.0376 0.8560 0.004 0.996
#> GSM751398 2 0.0000 0.8556 0.000 1.000
#> GSM751404 2 0.6438 0.7861 0.164 0.836
#> GSM751406 2 0.5842 0.7860 0.140 0.860
#> GSM751411 1 0.7056 0.6935 0.808 0.192
#> GSM751413 2 0.8499 0.6149 0.276 0.724
#> GSM751415 1 0.9661 0.2878 0.608 0.392
#> GSM751416 2 0.0000 0.8556 0.000 1.000
#> GSM751417 2 0.0000 0.8556 0.000 1.000
#> GSM751421 2 0.6343 0.7713 0.160 0.840
#> GSM751422 2 0.3733 0.8336 0.072 0.928
#> GSM751360 2 0.9944 0.2613 0.456 0.544
#> GSM751364 2 0.2043 0.8506 0.032 0.968
#> GSM751390 2 0.2043 0.8502 0.032 0.968
#> GSM751392 2 0.0000 0.8556 0.000 1.000
#> GSM751396 2 0.1184 0.8549 0.016 0.984
#> GSM751399 2 0.0376 0.8560 0.004 0.996
#> GSM751400 2 0.1633 0.8533 0.024 0.976
#> GSM751401 2 0.2948 0.8411 0.052 0.948
#> GSM751402 2 0.2948 0.8448 0.052 0.948
#> GSM751403 2 0.1414 0.8544 0.020 0.980
#> GSM751405 2 0.8955 0.5767 0.312 0.688
#> GSM751407 2 0.2043 0.8542 0.032 0.968
#> GSM751408 2 0.1414 0.8544 0.020 0.980
#> GSM751409 2 0.5946 0.7785 0.144 0.856
#> GSM751412 2 0.8555 0.5737 0.280 0.720
#> GSM751418 1 0.9909 0.4278 0.556 0.444
#> GSM751419 2 0.8016 0.5504 0.244 0.756
#> GSM751420 2 0.1843 0.8560 0.028 0.972
#> GSM751425 2 0.0000 0.8556 0.000 1.000
#> GSM751429 1 0.9393 0.4448 0.644 0.356
#> GSM751430 2 0.0000 0.8556 0.000 1.000
#> GSM751433 2 0.4022 0.8128 0.080 0.920
#> GSM751437 2 0.9896 0.3065 0.440 0.560
#> GSM751448 2 0.9833 0.3905 0.424 0.576
#> GSM751451 2 0.2603 0.8467 0.044 0.956
#> GSM751423 2 0.2948 0.8416 0.052 0.948
#> GSM751424 2 0.0376 0.8560 0.004 0.996
#> GSM751428 2 0.1414 0.8544 0.020 0.980
#> GSM751431 2 0.0000 0.8556 0.000 1.000
#> GSM751432 2 0.0376 0.8560 0.004 0.996
#> GSM751434 2 0.1633 0.8533 0.024 0.976
#> GSM751435 2 0.1633 0.8533 0.024 0.976
#> GSM751436 2 0.1633 0.8533 0.024 0.976
#> GSM751440 2 0.1633 0.8533 0.024 0.976
#> GSM751444 2 0.1633 0.8533 0.024 0.976
#> GSM751446 2 0.1633 0.8533 0.024 0.976
#> GSM751449 2 0.1633 0.8533 0.024 0.976
#> GSM751450 2 0.9922 -0.0103 0.448 0.552
#> GSM751452 2 0.0938 0.8556 0.012 0.988
#> GSM751426 2 0.1633 0.8533 0.024 0.976
#> GSM751427 2 0.1414 0.8544 0.020 0.980
#> GSM751438 2 0.1633 0.8533 0.024 0.976
#> GSM751439 2 0.1633 0.8533 0.024 0.976
#> GSM751441 2 0.1633 0.8533 0.024 0.976
#> GSM751442 2 0.1633 0.8533 0.024 0.976
#> GSM751443 2 0.1633 0.8533 0.024 0.976
#> GSM751445 2 0.0000 0.8556 0.000 1.000
#> GSM751447 2 0.1633 0.8533 0.024 0.976
#> GSM751453 2 0.1633 0.8533 0.024 0.976
#> GSM751454 2 0.1633 0.8533 0.024 0.976
#> GSM751455 2 0.1633 0.8533 0.024 0.976
#> GSM751456 2 0.1633 0.8533 0.024 0.976
#> GSM751457 2 0.0672 0.8557 0.008 0.992
#> GSM751458 2 0.0672 0.8557 0.008 0.992
cbind(get_classes(res, k = 3), get_membership(res, k = 3))
#> class entropy silhouette p1 p2 p3
#> GSM751298 1 0.6142 0.7874 0.748 0.040 0.212
#> GSM751304 2 0.6696 0.5444 0.020 0.632 0.348
#> GSM751305 2 0.7209 0.4975 0.036 0.604 0.360
#> GSM751307 1 0.8442 0.6024 0.548 0.100 0.352
#> GSM751310 1 0.6102 0.7368 0.672 0.008 0.320
#> GSM751314 1 0.5327 0.7696 0.728 0.000 0.272
#> GSM751316 1 0.9587 0.4122 0.440 0.204 0.356
#> GSM751318 1 0.6771 0.7562 0.684 0.040 0.276
#> GSM751342 1 0.5810 0.7263 0.664 0.000 0.336
#> GSM751346 1 0.1832 0.7704 0.956 0.008 0.036
#> GSM751347 1 0.5988 0.6584 0.776 0.168 0.056
#> GSM751348 3 0.8085 0.4069 0.084 0.332 0.584
#> GSM751349 2 0.3482 0.7993 0.000 0.872 0.128
#> GSM751352 2 0.1585 0.8215 0.028 0.964 0.008
#> GSM751353 2 0.3038 0.8098 0.000 0.896 0.104
#> GSM751354 2 0.6169 0.5496 0.004 0.636 0.360
#> GSM751355 2 0.4887 0.7263 0.000 0.772 0.228
#> GSM751358 3 0.6565 0.4788 0.048 0.232 0.720
#> GSM751359 2 0.5327 0.6749 0.000 0.728 0.272
#> GSM751294 2 0.5810 0.5944 0.000 0.664 0.336
#> GSM751296 1 0.2066 0.7879 0.940 0.000 0.060
#> GSM751297 3 0.2527 0.6851 0.044 0.020 0.936
#> GSM751299 2 0.2165 0.8215 0.000 0.936 0.064
#> GSM751300 1 0.0892 0.7749 0.980 0.020 0.000
#> GSM751301 1 0.6107 0.6916 0.764 0.184 0.052
#> GSM751302 1 0.2711 0.7421 0.912 0.088 0.000
#> GSM751303 1 0.7622 0.6762 0.608 0.060 0.332
#> GSM751306 1 0.6075 0.7398 0.676 0.008 0.316
#> GSM751308 2 0.7830 0.5070 0.136 0.668 0.196
#> GSM751309 1 0.5785 0.7295 0.668 0.000 0.332
#> GSM751311 1 0.5216 0.7752 0.740 0.000 0.260
#> GSM751312 2 0.9947 -0.0573 0.288 0.376 0.336
#> GSM751313 1 0.1289 0.7879 0.968 0.000 0.032
#> GSM751315 1 0.5216 0.7752 0.740 0.000 0.260
#> GSM751317 1 0.6369 0.7369 0.668 0.016 0.316
#> GSM751320 1 0.5016 0.7826 0.760 0.000 0.240
#> GSM751321 1 0.5216 0.7752 0.740 0.000 0.260
#> GSM751322 1 0.5016 0.7824 0.760 0.000 0.240
#> GSM751324 1 0.5216 0.7752 0.740 0.000 0.260
#> GSM751325 1 0.5058 0.7810 0.756 0.000 0.244
#> GSM751332 1 0.3038 0.7957 0.896 0.000 0.104
#> GSM751334 1 0.2400 0.7897 0.932 0.004 0.064
#> GSM751339 1 0.8341 0.3215 0.468 0.080 0.452
#> GSM751341 1 0.5706 0.7386 0.680 0.000 0.320
#> GSM751343 1 0.5058 0.7810 0.756 0.000 0.244
#> GSM751344 2 0.4235 0.7683 0.000 0.824 0.176
#> GSM751345 2 0.4062 0.7786 0.000 0.836 0.164
#> GSM751356 2 0.5591 0.6354 0.000 0.696 0.304
#> GSM751357 2 0.5650 0.6232 0.000 0.688 0.312
#> GSM751293 1 0.5237 0.7454 0.824 0.120 0.056
#> GSM751295 1 0.2772 0.7474 0.916 0.080 0.004
#> GSM751319 1 0.2749 0.7903 0.924 0.012 0.064
#> GSM751323 1 0.2116 0.7833 0.948 0.012 0.040
#> GSM751326 1 0.1411 0.7689 0.964 0.036 0.000
#> GSM751327 1 0.1015 0.7764 0.980 0.012 0.008
#> GSM751328 1 0.2448 0.7921 0.924 0.000 0.076
#> GSM751329 1 0.2297 0.7806 0.944 0.020 0.036
#> GSM751330 1 0.1529 0.7670 0.960 0.040 0.000
#> GSM751331 1 0.2878 0.7369 0.904 0.096 0.000
#> GSM751333 1 0.0747 0.7730 0.984 0.016 0.000
#> GSM751335 1 0.0892 0.7716 0.980 0.020 0.000
#> GSM751336 1 0.2878 0.7369 0.904 0.096 0.000
#> GSM751337 1 0.3619 0.7943 0.864 0.000 0.136
#> GSM751338 1 0.3686 0.7939 0.860 0.000 0.140
#> GSM751340 1 0.9818 0.2978 0.408 0.248 0.344
#> GSM751350 1 0.1529 0.7670 0.960 0.040 0.000
#> GSM751351 1 0.0892 0.7716 0.980 0.020 0.000
#> GSM751362 3 0.1129 0.6921 0.004 0.020 0.976
#> GSM751363 1 0.9193 0.4834 0.480 0.156 0.364
#> GSM751367 2 0.9997 -0.1601 0.324 0.344 0.332
#> GSM751368 2 0.0661 0.8224 0.008 0.988 0.004
#> GSM751371 2 0.8457 0.3931 0.100 0.544 0.356
#> GSM751375 2 0.3412 0.8010 0.000 0.876 0.124
#> GSM751376 3 0.3192 0.7544 0.000 0.112 0.888
#> GSM751378 3 0.4235 0.7516 0.000 0.176 0.824
#> GSM751379 3 0.2590 0.7292 0.004 0.072 0.924
#> GSM751382 2 0.3686 0.7961 0.000 0.860 0.140
#> GSM751386 2 0.3551 0.7997 0.000 0.868 0.132
#> GSM751388 2 0.2878 0.8126 0.000 0.904 0.096
#> GSM751391 2 0.7099 0.4504 0.028 0.588 0.384
#> GSM751410 3 0.6488 0.4162 0.160 0.084 0.756
#> GSM751414 1 0.7065 0.6794 0.616 0.032 0.352
#> GSM751361 2 0.3141 0.8182 0.020 0.912 0.068
#> GSM751365 3 0.4195 0.7559 0.012 0.136 0.852
#> GSM751366 3 0.2569 0.6649 0.032 0.032 0.936
#> GSM751369 3 0.5138 0.7297 0.000 0.252 0.748
#> GSM751370 3 0.9996 -0.1805 0.320 0.336 0.344
#> GSM751372 2 0.5737 0.6245 0.012 0.732 0.256
#> GSM751373 1 0.6786 0.3159 0.540 0.448 0.012
#> GSM751374 3 0.2625 0.7388 0.000 0.084 0.916
#> GSM751377 3 0.5431 0.7005 0.000 0.284 0.716
#> GSM751380 3 0.4335 0.6648 0.036 0.100 0.864
#> GSM751381 2 0.5008 0.7485 0.016 0.804 0.180
#> GSM751383 2 0.0237 0.8238 0.000 0.996 0.004
#> GSM751384 2 0.6451 0.3904 0.008 0.608 0.384
#> GSM751385 2 0.6302 -0.0703 0.000 0.520 0.480
#> GSM751387 2 0.0892 0.8242 0.000 0.980 0.020
#> GSM751389 3 0.4002 0.7561 0.000 0.160 0.840
#> GSM751393 3 0.5138 0.7139 0.000 0.252 0.748
#> GSM751394 2 0.3192 0.8064 0.000 0.888 0.112
#> GSM751395 3 0.5058 0.7196 0.000 0.244 0.756
#> GSM751397 2 0.3412 0.8022 0.000 0.876 0.124
#> GSM751398 2 0.2959 0.8130 0.000 0.900 0.100
#> GSM751404 3 0.5988 0.7171 0.008 0.304 0.688
#> GSM751406 3 0.4121 0.7566 0.000 0.168 0.832
#> GSM751411 3 0.0983 0.6707 0.016 0.004 0.980
#> GSM751413 2 0.7398 0.6385 0.120 0.700 0.180
#> GSM751415 3 0.1267 0.6612 0.024 0.004 0.972
#> GSM751416 2 0.0592 0.8253 0.000 0.988 0.012
#> GSM751417 2 0.0237 0.8237 0.000 0.996 0.004
#> GSM751421 2 0.5138 0.6884 0.000 0.748 0.252
#> GSM751422 2 0.4514 0.7827 0.012 0.832 0.156
#> GSM751360 2 0.8102 0.4193 0.076 0.556 0.368
#> GSM751364 2 0.1765 0.8253 0.004 0.956 0.040
#> GSM751390 2 0.2703 0.8021 0.016 0.928 0.056
#> GSM751392 2 0.2711 0.8152 0.000 0.912 0.088
#> GSM751396 2 0.0000 0.8229 0.000 1.000 0.000
#> GSM751399 3 0.5529 0.6985 0.000 0.296 0.704
#> GSM751400 2 0.0592 0.8184 0.000 0.988 0.012
#> GSM751401 3 0.6111 0.6357 0.000 0.396 0.604
#> GSM751402 3 0.6026 0.6555 0.000 0.376 0.624
#> GSM751403 3 0.5988 0.6566 0.000 0.368 0.632
#> GSM751405 3 0.1999 0.7076 0.012 0.036 0.952
#> GSM751407 3 0.6026 0.6571 0.000 0.376 0.624
#> GSM751408 3 0.6180 0.6109 0.000 0.416 0.584
#> GSM751409 3 0.4504 0.7456 0.000 0.196 0.804
#> GSM751412 3 0.6200 0.7110 0.012 0.312 0.676
#> GSM751418 3 0.7328 0.6688 0.044 0.344 0.612
#> GSM751419 3 0.6111 0.6357 0.000 0.396 0.604
#> GSM751420 3 0.6282 0.6516 0.004 0.384 0.612
#> GSM751425 2 0.3412 0.8010 0.000 0.876 0.124
#> GSM751429 3 0.1647 0.7093 0.004 0.036 0.960
#> GSM751430 2 0.0237 0.8237 0.000 0.996 0.004
#> GSM751433 2 0.1964 0.7872 0.056 0.944 0.000
#> GSM751437 3 0.0237 0.6823 0.000 0.004 0.996
#> GSM751448 3 0.1647 0.6840 0.036 0.004 0.960
#> GSM751451 2 0.0592 0.8200 0.012 0.988 0.000
#> GSM751423 2 0.3879 0.7866 0.000 0.848 0.152
#> GSM751424 2 0.0237 0.8237 0.000 0.996 0.004
#> GSM751428 2 0.0000 0.8229 0.000 1.000 0.000
#> GSM751431 2 0.0000 0.8229 0.000 1.000 0.000
#> GSM751432 2 0.0000 0.8229 0.000 1.000 0.000
#> GSM751434 2 0.0000 0.8229 0.000 1.000 0.000
#> GSM751435 2 0.0000 0.8229 0.000 1.000 0.000
#> GSM751436 2 0.0000 0.8229 0.000 1.000 0.000
#> GSM751440 2 0.0424 0.8243 0.000 0.992 0.008
#> GSM751444 2 0.0000 0.8229 0.000 1.000 0.000
#> GSM751446 2 0.0592 0.8253 0.000 0.988 0.012
#> GSM751449 2 0.1031 0.8235 0.000 0.976 0.024
#> GSM751450 2 0.8389 0.1456 0.372 0.536 0.092
#> GSM751452 2 0.0000 0.8229 0.000 1.000 0.000
#> GSM751426 2 0.0000 0.8229 0.000 1.000 0.000
#> GSM751427 2 0.0000 0.8229 0.000 1.000 0.000
#> GSM751438 2 0.1643 0.8214 0.000 0.956 0.044
#> GSM751439 2 0.0892 0.8229 0.000 0.980 0.020
#> GSM751441 2 0.0000 0.8229 0.000 1.000 0.000
#> GSM751442 2 0.0000 0.8229 0.000 1.000 0.000
#> GSM751443 2 0.2448 0.8172 0.000 0.924 0.076
#> GSM751445 2 0.2959 0.8119 0.000 0.900 0.100
#> GSM751447 2 0.0000 0.8229 0.000 1.000 0.000
#> GSM751453 2 0.0000 0.8229 0.000 1.000 0.000
#> GSM751454 2 0.0000 0.8229 0.000 1.000 0.000
#> GSM751455 2 0.0000 0.8229 0.000 1.000 0.000
#> GSM751456 2 0.0000 0.8229 0.000 1.000 0.000
#> GSM751457 2 0.3340 0.8023 0.000 0.880 0.120
#> GSM751458 2 0.3340 0.8023 0.000 0.880 0.120
cbind(get_classes(res, k = 4), get_membership(res, k = 4))
#> class entropy silhouette p1 p2 p3 p4
#> GSM751298 1 0.6439 0.00647 0.488 0.048 0.008 0.456
#> GSM751304 2 0.7169 0.37496 0.000 0.508 0.148 0.344
#> GSM751305 4 0.5266 0.58949 0.000 0.140 0.108 0.752
#> GSM751307 4 0.7544 0.41873 0.276 0.104 0.044 0.576
#> GSM751310 4 0.2530 0.70682 0.100 0.000 0.004 0.896
#> GSM751314 4 0.2469 0.70433 0.108 0.000 0.000 0.892
#> GSM751316 4 0.5805 0.63975 0.160 0.048 0.048 0.744
#> GSM751318 4 0.3933 0.65477 0.196 0.004 0.004 0.796
#> GSM751342 4 0.3249 0.69771 0.140 0.000 0.008 0.852
#> GSM751346 1 0.0336 0.78738 0.992 0.000 0.008 0.000
#> GSM751347 1 0.2271 0.73910 0.928 0.052 0.012 0.008
#> GSM751348 3 0.7888 -0.01622 0.004 0.228 0.400 0.368
#> GSM751349 2 0.4867 0.77099 0.000 0.736 0.232 0.032
#> GSM751352 2 0.1724 0.83181 0.000 0.948 0.020 0.032
#> GSM751353 2 0.3249 0.81757 0.000 0.852 0.140 0.008
#> GSM751354 2 0.6656 0.65796 0.000 0.608 0.256 0.136
#> GSM751355 2 0.6549 0.69524 0.000 0.612 0.268 0.120
#> GSM751358 4 0.5035 0.59437 0.000 0.052 0.204 0.744
#> GSM751359 2 0.5890 0.71614 0.000 0.660 0.268 0.072
#> GSM751294 2 0.6594 0.65965 0.000 0.624 0.228 0.148
#> GSM751296 1 0.4406 0.52709 0.700 0.000 0.000 0.300
#> GSM751297 3 0.7778 0.28839 0.216 0.008 0.488 0.288
#> GSM751299 2 0.3791 0.81307 0.016 0.844 0.128 0.012
#> GSM751300 1 0.0188 0.79096 0.996 0.000 0.000 0.004
#> GSM751301 4 0.7001 0.29346 0.352 0.112 0.004 0.532
#> GSM751302 1 0.0000 0.79150 1.000 0.000 0.000 0.000
#> GSM751303 4 0.2401 0.70660 0.092 0.004 0.000 0.904
#> GSM751306 4 0.2408 0.70595 0.104 0.000 0.000 0.896
#> GSM751308 4 0.6094 0.23928 0.032 0.416 0.008 0.544
#> GSM751309 4 0.2345 0.70671 0.100 0.000 0.000 0.900
#> GSM751311 4 0.3024 0.68832 0.148 0.000 0.000 0.852
#> GSM751312 4 0.3174 0.69245 0.048 0.052 0.008 0.892
#> GSM751313 1 0.2868 0.70079 0.864 0.000 0.000 0.136
#> GSM751315 4 0.2814 0.69625 0.132 0.000 0.000 0.868
#> GSM751317 4 0.2345 0.70671 0.100 0.000 0.000 0.900
#> GSM751320 4 0.4331 0.55744 0.288 0.000 0.000 0.712
#> GSM751321 4 0.2647 0.70086 0.120 0.000 0.000 0.880
#> GSM751322 4 0.3975 0.61017 0.240 0.000 0.000 0.760
#> GSM751324 4 0.2647 0.70088 0.120 0.000 0.000 0.880
#> GSM751325 4 0.4382 0.54320 0.296 0.000 0.000 0.704
#> GSM751332 1 0.4857 0.55953 0.700 0.000 0.016 0.284
#> GSM751334 1 0.4018 0.63772 0.772 0.004 0.000 0.224
#> GSM751339 4 0.5658 0.48789 0.280 0.012 0.032 0.676
#> GSM751341 4 0.2593 0.70719 0.104 0.000 0.004 0.892
#> GSM751343 4 0.4008 0.60751 0.244 0.000 0.000 0.756
#> GSM751344 2 0.6327 0.73110 0.000 0.648 0.228 0.124
#> GSM751345 2 0.5136 0.76767 0.000 0.728 0.224 0.048
#> GSM751356 2 0.6626 0.66088 0.000 0.624 0.216 0.160
#> GSM751357 2 0.6678 0.65764 0.000 0.620 0.208 0.172
#> GSM751293 4 0.6440 0.33646 0.356 0.080 0.000 0.564
#> GSM751295 1 0.0336 0.78867 0.992 0.000 0.000 0.008
#> GSM751319 4 0.5132 0.15998 0.448 0.004 0.000 0.548
#> GSM751323 1 0.4961 0.10742 0.552 0.000 0.000 0.448
#> GSM751326 1 0.0188 0.79081 0.996 0.000 0.000 0.004
#> GSM751327 1 0.3907 0.59092 0.768 0.000 0.000 0.232
#> GSM751328 1 0.4134 0.60203 0.740 0.000 0.000 0.260
#> GSM751329 1 0.3908 0.65066 0.784 0.004 0.000 0.212
#> GSM751330 1 0.0000 0.79150 1.000 0.000 0.000 0.000
#> GSM751331 1 0.0000 0.79150 1.000 0.000 0.000 0.000
#> GSM751333 1 0.0000 0.79150 1.000 0.000 0.000 0.000
#> GSM751335 1 0.0000 0.79150 1.000 0.000 0.000 0.000
#> GSM751336 1 0.0000 0.79150 1.000 0.000 0.000 0.000
#> GSM751337 1 0.3444 0.65408 0.816 0.000 0.000 0.184
#> GSM751338 1 0.4382 0.47786 0.704 0.000 0.000 0.296
#> GSM751340 1 0.8365 -0.10131 0.416 0.156 0.044 0.384
#> GSM751350 1 0.0000 0.79150 1.000 0.000 0.000 0.000
#> GSM751351 1 0.0000 0.79150 1.000 0.000 0.000 0.000
#> GSM751362 3 0.3402 0.74281 0.000 0.004 0.832 0.164
#> GSM751363 4 0.4397 0.59140 0.020 0.012 0.168 0.800
#> GSM751367 4 0.8810 0.14867 0.328 0.224 0.052 0.396
#> GSM751368 2 0.1743 0.82288 0.000 0.940 0.056 0.004
#> GSM751371 4 0.2124 0.66845 0.000 0.028 0.040 0.932
#> GSM751375 2 0.5558 0.76733 0.000 0.712 0.208 0.080
#> GSM751376 3 0.2522 0.78028 0.000 0.016 0.908 0.076
#> GSM751378 3 0.1798 0.78326 0.000 0.040 0.944 0.016
#> GSM751379 3 0.3080 0.77819 0.000 0.024 0.880 0.096
#> GSM751382 2 0.5633 0.77179 0.000 0.716 0.184 0.100
#> GSM751386 2 0.6138 0.72794 0.000 0.648 0.260 0.092
#> GSM751388 2 0.4718 0.79707 0.000 0.792 0.116 0.092
#> GSM751391 4 0.7620 0.21446 0.000 0.316 0.224 0.460
#> GSM751410 4 0.6524 0.37103 0.016 0.056 0.336 0.592
#> GSM751414 4 0.6281 0.41660 0.236 0.008 0.092 0.664
#> GSM751361 2 0.5833 0.69893 0.000 0.692 0.096 0.212
#> GSM751365 3 0.3758 0.76616 0.000 0.048 0.848 0.104
#> GSM751366 3 0.4609 0.68040 0.000 0.024 0.752 0.224
#> GSM751369 3 0.3354 0.78673 0.000 0.084 0.872 0.044
#> GSM751370 4 0.9275 0.05196 0.320 0.140 0.144 0.396
#> GSM751372 2 0.6205 0.64735 0.000 0.668 0.136 0.196
#> GSM751373 2 0.6770 -0.12313 0.464 0.468 0.044 0.024
#> GSM751374 3 0.2882 0.77938 0.000 0.024 0.892 0.084
#> GSM751377 3 0.4419 0.74520 0.000 0.104 0.812 0.084
#> GSM751380 3 0.4692 0.68990 0.000 0.032 0.756 0.212
#> GSM751381 2 0.6198 0.73591 0.000 0.672 0.152 0.176
#> GSM751383 2 0.2542 0.81128 0.000 0.904 0.012 0.084
#> GSM751384 2 0.6979 0.46821 0.000 0.504 0.376 0.120
#> GSM751385 3 0.6336 0.21245 0.000 0.304 0.608 0.088
#> GSM751387 2 0.3453 0.81087 0.000 0.868 0.052 0.080
#> GSM751389 3 0.1398 0.78904 0.000 0.004 0.956 0.040
#> GSM751393 3 0.1767 0.78288 0.000 0.044 0.944 0.012
#> GSM751394 2 0.5220 0.78521 0.000 0.752 0.156 0.092
#> GSM751395 3 0.1767 0.78288 0.000 0.044 0.944 0.012
#> GSM751397 2 0.5705 0.76263 0.000 0.704 0.204 0.092
#> GSM751398 2 0.5309 0.78341 0.000 0.744 0.164 0.092
#> GSM751404 3 0.4465 0.76385 0.000 0.144 0.800 0.056
#> GSM751406 3 0.1888 0.78545 0.000 0.044 0.940 0.016
#> GSM751411 3 0.3400 0.73921 0.000 0.000 0.820 0.180
#> GSM751413 2 0.7307 0.71028 0.040 0.628 0.192 0.140
#> GSM751415 3 0.3583 0.71935 0.000 0.004 0.816 0.180
#> GSM751416 2 0.3745 0.79417 0.000 0.852 0.060 0.088
#> GSM751417 2 0.3286 0.79972 0.000 0.876 0.044 0.080
#> GSM751421 2 0.6282 0.70530 0.000 0.664 0.176 0.160
#> GSM751422 2 0.4800 0.77584 0.000 0.760 0.196 0.044
#> GSM751360 4 0.2944 0.65258 0.004 0.044 0.052 0.900
#> GSM751364 2 0.4300 0.79730 0.000 0.820 0.088 0.092
#> GSM751390 2 0.4541 0.79429 0.004 0.812 0.100 0.084
#> GSM751392 2 0.4931 0.79226 0.000 0.776 0.132 0.092
#> GSM751396 2 0.2342 0.81296 0.000 0.912 0.008 0.080
#> GSM751399 3 0.1807 0.79566 0.000 0.052 0.940 0.008
#> GSM751400 2 0.0592 0.82619 0.000 0.984 0.016 0.000
#> GSM751401 3 0.4193 0.71354 0.000 0.268 0.732 0.000
#> GSM751402 3 0.4088 0.74074 0.000 0.232 0.764 0.004
#> GSM751403 3 0.3400 0.76469 0.000 0.180 0.820 0.000
#> GSM751405 3 0.3196 0.76036 0.000 0.008 0.856 0.136
#> GSM751407 3 0.4122 0.73299 0.000 0.236 0.760 0.004
#> GSM751408 3 0.4454 0.68705 0.000 0.308 0.692 0.000
#> GSM751409 3 0.1297 0.79167 0.000 0.020 0.964 0.016
#> GSM751412 3 0.4188 0.76471 0.000 0.148 0.812 0.040
#> GSM751418 3 0.5744 0.71038 0.004 0.224 0.700 0.072
#> GSM751419 3 0.4193 0.71440 0.000 0.268 0.732 0.000
#> GSM751420 3 0.4831 0.72071 0.000 0.280 0.704 0.016
#> GSM751425 2 0.4019 0.79476 0.000 0.792 0.196 0.012
#> GSM751429 3 0.3217 0.75012 0.000 0.012 0.860 0.128
#> GSM751430 2 0.0336 0.83070 0.000 0.992 0.008 0.000
#> GSM751433 2 0.1411 0.81945 0.020 0.960 0.000 0.020
#> GSM751437 3 0.2408 0.75979 0.000 0.000 0.896 0.104
#> GSM751448 3 0.3172 0.77042 0.012 0.004 0.872 0.112
#> GSM751451 2 0.0817 0.82595 0.000 0.976 0.000 0.024
#> GSM751423 2 0.4139 0.80340 0.000 0.800 0.176 0.024
#> GSM751424 2 0.0188 0.82979 0.000 0.996 0.004 0.000
#> GSM751428 2 0.0000 0.82894 0.000 1.000 0.000 0.000
#> GSM751431 2 0.0000 0.82894 0.000 1.000 0.000 0.000
#> GSM751432 2 0.0000 0.82894 0.000 1.000 0.000 0.000
#> GSM751434 2 0.0000 0.82894 0.000 1.000 0.000 0.000
#> GSM751435 2 0.0000 0.82894 0.000 1.000 0.000 0.000
#> GSM751436 2 0.0000 0.82894 0.000 1.000 0.000 0.000
#> GSM751440 2 0.0895 0.83147 0.000 0.976 0.020 0.004
#> GSM751444 2 0.0188 0.82838 0.000 0.996 0.000 0.004
#> GSM751446 2 0.1109 0.83310 0.000 0.968 0.028 0.004
#> GSM751449 2 0.2466 0.82170 0.000 0.900 0.096 0.004
#> GSM751450 2 0.5925 0.69006 0.156 0.736 0.032 0.076
#> GSM751452 2 0.0000 0.82894 0.000 1.000 0.000 0.000
#> GSM751426 2 0.0000 0.82894 0.000 1.000 0.000 0.000
#> GSM751427 2 0.0000 0.82894 0.000 1.000 0.000 0.000
#> GSM751438 2 0.2773 0.81454 0.000 0.880 0.116 0.004
#> GSM751439 2 0.1661 0.82666 0.000 0.944 0.052 0.004
#> GSM751441 2 0.0000 0.82894 0.000 1.000 0.000 0.000
#> GSM751442 2 0.0188 0.82838 0.000 0.996 0.000 0.004
#> GSM751443 2 0.3808 0.79404 0.000 0.812 0.176 0.012
#> GSM751445 2 0.3545 0.80078 0.000 0.828 0.164 0.008
#> GSM751447 2 0.0000 0.82894 0.000 1.000 0.000 0.000
#> GSM751453 2 0.0000 0.82894 0.000 1.000 0.000 0.000
#> GSM751454 2 0.0000 0.82894 0.000 1.000 0.000 0.000
#> GSM751455 2 0.0188 0.82838 0.000 0.996 0.000 0.004
#> GSM751456 2 0.0188 0.82838 0.000 0.996 0.000 0.004
#> GSM751457 2 0.3933 0.78288 0.000 0.792 0.200 0.008
#> GSM751458 2 0.3852 0.78705 0.000 0.800 0.192 0.008
cbind(get_classes(res, k = 5), get_membership(res, k = 5))
#> class entropy silhouette p1 p2 p3 p4 p5
#> GSM751298 4 0.5972 0.1169 0.416 0.056 0.000 0.504 0.024
#> GSM751304 2 0.7349 0.0616 0.000 0.356 0.024 0.296 0.324
#> GSM751305 4 0.4848 0.5758 0.000 0.092 0.008 0.736 0.164
#> GSM751307 4 0.7854 0.1922 0.248 0.084 0.000 0.420 0.248
#> GSM751310 4 0.1430 0.7179 0.052 0.000 0.000 0.944 0.004
#> GSM751314 4 0.1270 0.7180 0.052 0.000 0.000 0.948 0.000
#> GSM751316 4 0.5499 0.5867 0.136 0.036 0.004 0.720 0.104
#> GSM751318 4 0.2660 0.6881 0.128 0.000 0.000 0.864 0.008
#> GSM751342 4 0.2130 0.7124 0.080 0.000 0.000 0.908 0.012
#> GSM751346 1 0.2589 0.7091 0.888 0.000 0.008 0.012 0.092
#> GSM751347 1 0.1728 0.7376 0.940 0.036 0.004 0.000 0.020
#> GSM751348 4 0.8203 0.1191 0.004 0.148 0.160 0.408 0.280
#> GSM751349 2 0.4538 -0.0544 0.000 0.540 0.008 0.000 0.452
#> GSM751352 2 0.3697 0.5901 0.000 0.820 0.000 0.080 0.100
#> GSM751353 2 0.3359 0.5791 0.000 0.816 0.020 0.000 0.164
#> GSM751354 2 0.6011 0.0223 0.000 0.488 0.020 0.064 0.428
#> GSM751355 5 0.4822 0.5495 0.000 0.288 0.048 0.000 0.664
#> GSM751358 4 0.5031 0.5146 0.000 0.012 0.036 0.656 0.296
#> GSM751359 2 0.5403 0.2129 0.000 0.556 0.052 0.004 0.388
#> GSM751294 2 0.6929 0.2204 0.000 0.428 0.032 0.140 0.400
#> GSM751296 1 0.5091 0.2913 0.584 0.000 0.000 0.372 0.044
#> GSM751297 3 0.8524 0.3091 0.164 0.004 0.348 0.228 0.256
#> GSM751299 2 0.6317 0.4741 0.032 0.636 0.048 0.040 0.244
#> GSM751300 1 0.0486 0.7611 0.988 0.000 0.004 0.004 0.004
#> GSM751301 4 0.5257 0.4773 0.284 0.060 0.000 0.648 0.008
#> GSM751302 1 0.0162 0.7610 0.996 0.000 0.004 0.000 0.000
#> GSM751303 4 0.1043 0.7153 0.040 0.000 0.000 0.960 0.000
#> GSM751306 4 0.1270 0.7180 0.052 0.000 0.000 0.948 0.000
#> GSM751308 4 0.6364 0.1959 0.008 0.356 0.000 0.500 0.136
#> GSM751309 4 0.1270 0.7180 0.052 0.000 0.000 0.948 0.000
#> GSM751311 4 0.1732 0.7119 0.080 0.000 0.000 0.920 0.000
#> GSM751312 4 0.2273 0.6972 0.032 0.024 0.000 0.920 0.024
#> GSM751313 1 0.2674 0.6798 0.856 0.000 0.004 0.140 0.000
#> GSM751315 4 0.1478 0.7165 0.064 0.000 0.000 0.936 0.000
#> GSM751317 4 0.1270 0.7180 0.052 0.000 0.000 0.948 0.000
#> GSM751320 4 0.3461 0.6133 0.224 0.000 0.000 0.772 0.004
#> GSM751321 4 0.1410 0.7174 0.060 0.000 0.000 0.940 0.000
#> GSM751322 4 0.2930 0.6638 0.164 0.000 0.000 0.832 0.004
#> GSM751324 4 0.1341 0.7177 0.056 0.000 0.000 0.944 0.000
#> GSM751325 4 0.3676 0.6005 0.232 0.004 0.000 0.760 0.004
#> GSM751332 1 0.5228 0.4124 0.620 0.004 0.020 0.336 0.020
#> GSM751334 1 0.4081 0.4909 0.696 0.004 0.000 0.296 0.004
#> GSM751339 4 0.7150 0.1471 0.264 0.016 0.012 0.492 0.216
#> GSM751341 4 0.1502 0.7183 0.056 0.000 0.000 0.940 0.004
#> GSM751343 4 0.3010 0.6587 0.172 0.000 0.000 0.824 0.004
#> GSM751344 5 0.4691 0.5030 0.000 0.276 0.000 0.044 0.680
#> GSM751345 2 0.5252 0.3785 0.000 0.580 0.000 0.056 0.364
#> GSM751356 2 0.6799 0.2480 0.000 0.472 0.024 0.148 0.356
#> GSM751357 2 0.6596 0.2339 0.000 0.472 0.012 0.152 0.364
#> GSM751293 4 0.4797 0.5065 0.280 0.040 0.000 0.676 0.004
#> GSM751295 1 0.0451 0.7590 0.988 0.000 0.004 0.008 0.000
#> GSM751319 4 0.4286 0.4239 0.340 0.004 0.000 0.652 0.004
#> GSM751323 4 0.4420 0.2020 0.448 0.000 0.000 0.548 0.004
#> GSM751326 1 0.0671 0.7570 0.980 0.004 0.000 0.016 0.000
#> GSM751327 1 0.3928 0.4543 0.700 0.000 0.000 0.296 0.004
#> GSM751328 1 0.4253 0.4388 0.660 0.004 0.000 0.332 0.004
#> GSM751329 1 0.4059 0.4970 0.700 0.004 0.000 0.292 0.004
#> GSM751330 1 0.0162 0.7608 0.996 0.000 0.000 0.000 0.004
#> GSM751331 1 0.0162 0.7610 0.996 0.000 0.004 0.000 0.000
#> GSM751333 1 0.0162 0.7607 0.996 0.000 0.000 0.004 0.000
#> GSM751335 1 0.0162 0.7608 0.996 0.000 0.000 0.000 0.004
#> GSM751336 1 0.0162 0.7610 0.996 0.000 0.004 0.000 0.000
#> GSM751337 1 0.2813 0.6631 0.832 0.000 0.000 0.168 0.000
#> GSM751338 1 0.5170 0.4775 0.660 0.000 0.004 0.268 0.068
#> GSM751340 1 0.8388 0.0512 0.344 0.104 0.012 0.328 0.212
#> GSM751350 1 0.0162 0.7610 0.996 0.000 0.004 0.000 0.000
#> GSM751351 1 0.0162 0.7610 0.996 0.000 0.004 0.000 0.000
#> GSM751362 3 0.4599 0.7291 0.000 0.000 0.744 0.100 0.156
#> GSM751363 5 0.4874 0.1791 0.000 0.000 0.032 0.368 0.600
#> GSM751367 1 0.8541 0.0264 0.332 0.144 0.008 0.304 0.212
#> GSM751368 2 0.3934 0.4701 0.000 0.748 0.236 0.004 0.012
#> GSM751371 4 0.2681 0.6688 0.000 0.012 0.004 0.876 0.108
#> GSM751375 5 0.4219 0.5066 0.000 0.416 0.000 0.000 0.584
#> GSM751376 3 0.4015 0.7085 0.000 0.004 0.724 0.008 0.264
#> GSM751378 3 0.4512 0.6916 0.000 0.020 0.676 0.004 0.300
#> GSM751379 3 0.4234 0.7128 0.000 0.004 0.724 0.020 0.252
#> GSM751382 5 0.4310 0.5868 0.000 0.392 0.000 0.004 0.604
#> GSM751386 5 0.5461 0.6289 0.000 0.284 0.096 0.000 0.620
#> GSM751388 5 0.5125 0.5625 0.000 0.416 0.040 0.000 0.544
#> GSM751391 4 0.7681 0.1915 0.000 0.264 0.108 0.472 0.156
#> GSM751410 4 0.7042 0.2893 0.008 0.028 0.140 0.480 0.344
#> GSM751414 5 0.7355 0.3037 0.096 0.004 0.148 0.204 0.548
#> GSM751361 2 0.5516 0.2843 0.000 0.644 0.000 0.136 0.220
#> GSM751365 3 0.1924 0.7481 0.000 0.008 0.924 0.004 0.064
#> GSM751366 3 0.2438 0.7423 0.000 0.000 0.900 0.060 0.040
#> GSM751369 3 0.4486 0.7086 0.000 0.012 0.712 0.020 0.256
#> GSM751370 5 0.8798 -0.0229 0.284 0.012 0.192 0.208 0.304
#> GSM751372 2 0.6464 0.2178 0.000 0.560 0.304 0.096 0.040
#> GSM751373 1 0.7166 0.2268 0.424 0.292 0.268 0.008 0.008
#> GSM751374 3 0.4015 0.7085 0.000 0.004 0.724 0.008 0.264
#> GSM751377 3 0.4552 -0.0492 0.000 0.008 0.524 0.000 0.468
#> GSM751380 3 0.1740 0.7467 0.000 0.012 0.932 0.056 0.000
#> GSM751381 5 0.5640 0.6121 0.000 0.336 0.012 0.064 0.588
#> GSM751383 2 0.4666 -0.3066 0.000 0.572 0.016 0.000 0.412
#> GSM751384 5 0.5217 0.5822 0.000 0.168 0.088 0.024 0.720
#> GSM751385 5 0.5489 0.5430 0.000 0.216 0.136 0.000 0.648
#> GSM751387 2 0.4278 -0.3572 0.000 0.548 0.000 0.000 0.452
#> GSM751389 3 0.1410 0.7621 0.000 0.000 0.940 0.000 0.060
#> GSM751393 3 0.3884 0.7073 0.000 0.004 0.708 0.000 0.288
#> GSM751394 5 0.4201 0.5769 0.000 0.408 0.000 0.000 0.592
#> GSM751395 3 0.3861 0.7071 0.000 0.004 0.712 0.000 0.284
#> GSM751397 5 0.4114 0.5921 0.000 0.376 0.000 0.000 0.624
#> GSM751398 5 0.4219 0.5710 0.000 0.416 0.000 0.000 0.584
#> GSM751404 3 0.1717 0.7457 0.000 0.008 0.936 0.004 0.052
#> GSM751406 3 0.4260 0.6935 0.000 0.008 0.680 0.004 0.308
#> GSM751411 5 0.5414 0.0922 0.000 0.000 0.412 0.060 0.528
#> GSM751413 5 0.5892 0.5758 0.028 0.292 0.052 0.008 0.620
#> GSM751415 3 0.2685 0.7396 0.000 0.000 0.880 0.092 0.028
#> GSM751416 5 0.6710 0.5034 0.000 0.340 0.252 0.000 0.408
#> GSM751417 5 0.6571 0.4893 0.000 0.392 0.204 0.000 0.404
#> GSM751421 2 0.6365 0.2369 0.000 0.564 0.056 0.064 0.316
#> GSM751422 2 0.5392 0.4666 0.000 0.668 0.056 0.024 0.252
#> GSM751360 4 0.4925 0.4083 0.000 0.020 0.012 0.624 0.344
#> GSM751364 5 0.6752 0.4809 0.000 0.352 0.264 0.000 0.384
#> GSM751390 2 0.5123 -0.3991 0.004 0.492 0.028 0.000 0.476
#> GSM751392 5 0.4262 0.5391 0.000 0.440 0.000 0.000 0.560
#> GSM751396 2 0.4192 -0.2557 0.000 0.596 0.000 0.000 0.404
#> GSM751399 3 0.1410 0.7500 0.000 0.000 0.940 0.000 0.060
#> GSM751400 2 0.1357 0.6538 0.000 0.948 0.048 0.000 0.004
#> GSM751401 3 0.1410 0.7382 0.000 0.060 0.940 0.000 0.000
#> GSM751402 3 0.2588 0.7346 0.000 0.060 0.892 0.000 0.048
#> GSM751403 3 0.2376 0.7562 0.000 0.044 0.904 0.000 0.052
#> GSM751405 3 0.4850 0.7119 0.000 0.000 0.700 0.076 0.224
#> GSM751407 3 0.1668 0.7448 0.000 0.032 0.940 0.000 0.028
#> GSM751408 3 0.2124 0.7194 0.000 0.096 0.900 0.000 0.004
#> GSM751409 3 0.2561 0.7533 0.000 0.000 0.856 0.000 0.144
#> GSM751412 3 0.1638 0.7436 0.000 0.004 0.932 0.000 0.064
#> GSM751418 3 0.2369 0.7350 0.000 0.056 0.908 0.032 0.004
#> GSM751419 3 0.1410 0.7382 0.000 0.060 0.940 0.000 0.000
#> GSM751420 3 0.5040 0.5630 0.000 0.284 0.664 0.012 0.040
#> GSM751425 2 0.3366 0.5483 0.000 0.784 0.004 0.000 0.212
#> GSM751429 3 0.5986 0.5661 0.000 0.008 0.508 0.088 0.396
#> GSM751430 2 0.0290 0.6634 0.000 0.992 0.000 0.000 0.008
#> GSM751433 2 0.1372 0.6560 0.016 0.956 0.000 0.024 0.004
#> GSM751437 3 0.5534 0.5635 0.000 0.000 0.508 0.068 0.424
#> GSM751448 3 0.5196 0.6256 0.000 0.004 0.576 0.040 0.380
#> GSM751451 2 0.0963 0.6563 0.000 0.964 0.000 0.036 0.000
#> GSM751423 2 0.3439 0.5616 0.000 0.800 0.004 0.008 0.188
#> GSM751424 2 0.0162 0.6634 0.000 0.996 0.000 0.000 0.004
#> GSM751428 2 0.0000 0.6640 0.000 1.000 0.000 0.000 0.000
#> GSM751431 2 0.0000 0.6640 0.000 1.000 0.000 0.000 0.000
#> GSM751432 2 0.0162 0.6633 0.000 0.996 0.004 0.000 0.000
#> GSM751434 2 0.0000 0.6640 0.000 1.000 0.000 0.000 0.000
#> GSM751435 2 0.0000 0.6640 0.000 1.000 0.000 0.000 0.000
#> GSM751436 2 0.0162 0.6626 0.000 0.996 0.000 0.000 0.004
#> GSM751440 2 0.3039 0.6129 0.000 0.836 0.000 0.012 0.152
#> GSM751444 2 0.2771 0.6151 0.000 0.860 0.000 0.012 0.128
#> GSM751446 2 0.3203 0.6079 0.000 0.820 0.000 0.012 0.168
#> GSM751449 2 0.4815 0.5776 0.000 0.724 0.056 0.012 0.208
#> GSM751450 2 0.4974 0.5343 0.120 0.760 0.000 0.060 0.060
#> GSM751452 2 0.0000 0.6640 0.000 1.000 0.000 0.000 0.000
#> GSM751426 2 0.0000 0.6640 0.000 1.000 0.000 0.000 0.000
#> GSM751427 2 0.1571 0.6533 0.000 0.936 0.000 0.004 0.060
#> GSM751438 2 0.5017 0.5579 0.000 0.696 0.056 0.012 0.236
#> GSM751439 2 0.4007 0.5953 0.000 0.776 0.020 0.012 0.192
#> GSM751441 2 0.0000 0.6640 0.000 1.000 0.000 0.000 0.000
#> GSM751442 2 0.2909 0.6083 0.000 0.848 0.000 0.012 0.140
#> GSM751443 2 0.5699 0.4849 0.000 0.612 0.072 0.016 0.300
#> GSM751445 2 0.4199 0.5557 0.000 0.764 0.056 0.000 0.180
#> GSM751447 2 0.0000 0.6640 0.000 1.000 0.000 0.000 0.000
#> GSM751453 2 0.0000 0.6640 0.000 1.000 0.000 0.000 0.000
#> GSM751454 2 0.0000 0.6640 0.000 1.000 0.000 0.000 0.000
#> GSM751455 2 0.2909 0.6083 0.000 0.848 0.000 0.012 0.140
#> GSM751456 2 0.2909 0.6083 0.000 0.848 0.000 0.012 0.140
#> GSM751457 2 0.4639 0.5057 0.000 0.708 0.056 0.000 0.236
#> GSM751458 2 0.4465 0.5256 0.000 0.732 0.056 0.000 0.212
cbind(get_classes(res, k = 6), get_membership(res, k = 6))
#> class entropy silhouette p1 p2 p3 p4 p5 p6
#> GSM751298 4 0.6476 0.11895 0.328 0.072 0.000 0.516 0.032 0.052
#> GSM751304 6 0.6009 0.48511 0.000 0.108 0.004 0.212 0.068 0.608
#> GSM751305 4 0.4356 0.54713 0.000 0.032 0.000 0.764 0.092 0.112
#> GSM751307 4 0.7491 0.02628 0.212 0.128 0.000 0.360 0.296 0.004
#> GSM751310 4 0.0000 0.76705 0.000 0.000 0.000 1.000 0.000 0.000
#> GSM751314 4 0.0000 0.76705 0.000 0.000 0.000 1.000 0.000 0.000
#> GSM751316 4 0.6106 0.44823 0.108 0.020 0.004 0.648 0.072 0.148
#> GSM751318 4 0.1320 0.75191 0.036 0.000 0.000 0.948 0.000 0.016
#> GSM751342 4 0.0665 0.76538 0.008 0.000 0.000 0.980 0.004 0.008
#> GSM751346 1 0.3599 0.62521 0.820 0.000 0.000 0.020 0.076 0.084
#> GSM751347 1 0.2358 0.72108 0.908 0.016 0.000 0.020 0.044 0.012
#> GSM751348 4 0.8498 -0.08861 0.004 0.140 0.144 0.384 0.212 0.116
#> GSM751349 5 0.4808 0.21106 0.000 0.472 0.000 0.000 0.476 0.052
#> GSM751352 2 0.5100 0.26111 0.000 0.596 0.000 0.036 0.036 0.332
#> GSM751353 2 0.3533 0.62298 0.000 0.816 0.012 0.000 0.112 0.060
#> GSM751354 2 0.6700 0.11811 0.000 0.480 0.012 0.044 0.300 0.164
#> GSM751355 5 0.4950 0.67874 0.000 0.236 0.016 0.000 0.664 0.084
#> GSM751358 6 0.5732 0.26942 0.000 0.004 0.024 0.348 0.088 0.536
#> GSM751359 2 0.6062 0.19968 0.000 0.512 0.020 0.000 0.292 0.176
#> GSM751294 6 0.5089 0.51689 0.000 0.100 0.008 0.060 0.108 0.724
#> GSM751296 1 0.5720 0.16758 0.468 0.000 0.000 0.428 0.044 0.060
#> GSM751297 6 0.8659 0.15776 0.128 0.004 0.196 0.112 0.224 0.336
#> GSM751299 6 0.4386 0.36111 0.012 0.292 0.012 0.000 0.012 0.672
#> GSM751300 1 0.1408 0.75054 0.944 0.000 0.000 0.020 0.000 0.036
#> GSM751301 4 0.4383 0.59377 0.172 0.024 0.000 0.748 0.004 0.052
#> GSM751302 1 0.0909 0.74902 0.968 0.000 0.000 0.020 0.000 0.012
#> GSM751303 4 0.0260 0.76260 0.000 0.000 0.000 0.992 0.000 0.008
#> GSM751306 4 0.0000 0.76705 0.000 0.000 0.000 1.000 0.000 0.000
#> GSM751308 6 0.6128 0.32359 0.012 0.180 0.000 0.316 0.004 0.488
#> GSM751309 4 0.0000 0.76705 0.000 0.000 0.000 1.000 0.000 0.000
#> GSM751311 4 0.0622 0.76424 0.012 0.000 0.000 0.980 0.000 0.008
#> GSM751312 4 0.1490 0.74713 0.024 0.008 0.000 0.948 0.004 0.016
#> GSM751313 1 0.2378 0.69428 0.848 0.000 0.000 0.152 0.000 0.000
#> GSM751315 4 0.0000 0.76705 0.000 0.000 0.000 1.000 0.000 0.000
#> GSM751317 4 0.0000 0.76705 0.000 0.000 0.000 1.000 0.000 0.000
#> GSM751320 4 0.3027 0.66724 0.148 0.000 0.000 0.824 0.000 0.028
#> GSM751321 4 0.0000 0.76705 0.000 0.000 0.000 1.000 0.000 0.000
#> GSM751322 4 0.2325 0.72422 0.060 0.000 0.000 0.892 0.000 0.048
#> GSM751324 4 0.0260 0.76561 0.008 0.000 0.000 0.992 0.000 0.000
#> GSM751325 4 0.3473 0.65350 0.144 0.004 0.000 0.804 0.000 0.048
#> GSM751332 1 0.5658 0.35837 0.532 0.004 0.024 0.380 0.012 0.048
#> GSM751334 1 0.4551 0.44068 0.608 0.000 0.000 0.344 0.000 0.048
#> GSM751339 6 0.5851 0.30526 0.208 0.008 0.000 0.252 0.000 0.532
#> GSM751341 4 0.0000 0.76705 0.000 0.000 0.000 1.000 0.000 0.000
#> GSM751343 4 0.2499 0.71838 0.072 0.000 0.000 0.880 0.000 0.048
#> GSM751344 5 0.5478 0.03588 0.000 0.124 0.000 0.000 0.452 0.424
#> GSM751345 6 0.6046 0.27349 0.000 0.312 0.004 0.000 0.232 0.452
#> GSM751356 6 0.5941 0.49707 0.000 0.192 0.004 0.076 0.104 0.624
#> GSM751357 6 0.6461 0.46438 0.000 0.208 0.004 0.072 0.160 0.556
#> GSM751293 4 0.3835 0.61425 0.164 0.004 0.000 0.772 0.000 0.060
#> GSM751295 1 0.1074 0.74665 0.960 0.000 0.000 0.028 0.000 0.012
#> GSM751319 4 0.3941 0.56176 0.208 0.004 0.000 0.744 0.000 0.044
#> GSM751323 4 0.4436 0.38512 0.312 0.000 0.000 0.640 0.000 0.048
#> GSM751326 1 0.1719 0.74883 0.932 0.004 0.000 0.032 0.000 0.032
#> GSM751327 1 0.4620 0.34576 0.584 0.000 0.000 0.368 0.000 0.048
#> GSM751328 1 0.4640 0.38600 0.576 0.000 0.000 0.376 0.000 0.048
#> GSM751329 1 0.4551 0.44068 0.608 0.000 0.000 0.344 0.000 0.048
#> GSM751330 1 0.1616 0.74761 0.932 0.000 0.000 0.020 0.000 0.048
#> GSM751331 1 0.0909 0.74902 0.968 0.000 0.000 0.020 0.000 0.012
#> GSM751333 1 0.0993 0.75111 0.964 0.000 0.000 0.024 0.000 0.012
#> GSM751335 1 0.1616 0.74761 0.932 0.000 0.000 0.020 0.000 0.048
#> GSM751336 1 0.0909 0.74902 0.968 0.000 0.000 0.020 0.000 0.012
#> GSM751337 1 0.3236 0.67911 0.796 0.000 0.000 0.180 0.000 0.024
#> GSM751338 1 0.5352 0.39132 0.592 0.000 0.000 0.204 0.000 0.204
#> GSM751340 6 0.5815 0.37001 0.168 0.012 0.000 0.248 0.004 0.568
#> GSM751350 1 0.0909 0.74902 0.968 0.000 0.000 0.020 0.000 0.012
#> GSM751351 1 0.0909 0.74902 0.968 0.000 0.000 0.020 0.000 0.012
#> GSM751362 3 0.4971 0.68103 0.000 0.000 0.688 0.072 0.036 0.204
#> GSM751363 5 0.3990 0.48302 0.000 0.004 0.012 0.240 0.728 0.016
#> GSM751367 1 0.8224 0.05314 0.320 0.156 0.000 0.268 0.212 0.044
#> GSM751368 2 0.3690 0.47281 0.000 0.700 0.288 0.000 0.012 0.000
#> GSM751371 4 0.2043 0.71348 0.000 0.012 0.000 0.912 0.064 0.012
#> GSM751375 5 0.3565 0.66226 0.000 0.304 0.000 0.000 0.692 0.004
#> GSM751376 3 0.4473 0.67130 0.000 0.000 0.676 0.000 0.072 0.252
#> GSM751378 3 0.4861 0.61882 0.000 0.008 0.660 0.000 0.244 0.088
#> GSM751379 3 0.4444 0.67086 0.000 0.000 0.676 0.000 0.068 0.256
#> GSM751382 5 0.2996 0.73275 0.000 0.228 0.000 0.000 0.772 0.000
#> GSM751386 5 0.3587 0.73381 0.000 0.188 0.040 0.000 0.772 0.000
#> GSM751388 5 0.3394 0.73391 0.000 0.236 0.012 0.000 0.752 0.000
#> GSM751391 4 0.7490 0.09699 0.000 0.220 0.080 0.500 0.096 0.104
#> GSM751410 4 0.7632 -0.21943 0.020 0.000 0.092 0.340 0.316 0.232
#> GSM751414 5 0.4990 0.44495 0.056 0.000 0.084 0.148 0.712 0.000
#> GSM751361 2 0.5599 0.21048 0.000 0.568 0.000 0.136 0.284 0.012
#> GSM751365 3 0.2404 0.74740 0.000 0.000 0.872 0.016 0.112 0.000
#> GSM751366 3 0.2016 0.75803 0.000 0.000 0.920 0.016 0.040 0.024
#> GSM751369 3 0.4830 0.66796 0.000 0.004 0.668 0.008 0.072 0.248
#> GSM751370 5 0.7651 0.13012 0.276 0.012 0.196 0.140 0.376 0.000
#> GSM751372 2 0.5480 0.30391 0.000 0.560 0.344 0.056 0.040 0.000
#> GSM751373 1 0.7196 0.13775 0.376 0.256 0.316 0.024 0.012 0.016
#> GSM751374 3 0.4444 0.67086 0.000 0.000 0.676 0.000 0.068 0.256
#> GSM751377 5 0.3899 0.45162 0.000 0.008 0.364 0.000 0.628 0.000
#> GSM751380 3 0.0692 0.76990 0.000 0.004 0.976 0.020 0.000 0.000
#> GSM751381 5 0.3359 0.73343 0.000 0.196 0.012 0.008 0.784 0.000
#> GSM751383 5 0.4428 0.60659 0.000 0.388 0.032 0.000 0.580 0.000
#> GSM751384 5 0.2152 0.61158 0.000 0.036 0.040 0.000 0.912 0.012
#> GSM751385 5 0.5818 0.59977 0.000 0.192 0.092 0.000 0.628 0.088
#> GSM751387 5 0.3728 0.66516 0.000 0.344 0.000 0.000 0.652 0.004
#> GSM751389 3 0.2230 0.77164 0.000 0.000 0.892 0.000 0.024 0.084
#> GSM751393 3 0.4675 0.68267 0.000 0.000 0.672 0.000 0.104 0.224
#> GSM751394 5 0.2996 0.73033 0.000 0.228 0.000 0.000 0.772 0.000
#> GSM751395 3 0.4596 0.67788 0.000 0.000 0.672 0.000 0.088 0.240
#> GSM751397 5 0.3052 0.73132 0.000 0.216 0.000 0.000 0.780 0.004
#> GSM751398 5 0.3215 0.73136 0.000 0.240 0.000 0.000 0.756 0.004
#> GSM751404 3 0.0837 0.77159 0.004 0.000 0.972 0.004 0.020 0.000
#> GSM751406 3 0.5063 0.60261 0.000 0.000 0.604 0.000 0.112 0.284
#> GSM751411 5 0.4072 0.51635 0.000 0.000 0.260 0.032 0.704 0.004
#> GSM751413 5 0.5778 0.66064 0.024 0.204 0.016 0.000 0.628 0.128
#> GSM751415 3 0.2344 0.75198 0.000 0.000 0.892 0.076 0.028 0.004
#> GSM751416 5 0.5461 0.65293 0.000 0.200 0.228 0.000 0.572 0.000
#> GSM751417 5 0.5504 0.65678 0.000 0.252 0.188 0.000 0.560 0.000
#> GSM751421 2 0.6725 0.22127 0.000 0.528 0.020 0.052 0.240 0.160
#> GSM751422 2 0.5935 0.46857 0.000 0.620 0.020 0.024 0.164 0.172
#> GSM751360 4 0.4507 0.17592 0.000 0.008 0.004 0.544 0.432 0.012
#> GSM751364 5 0.5956 0.56129 0.000 0.256 0.292 0.000 0.452 0.000
#> GSM751390 5 0.4601 0.63730 0.000 0.308 0.028 0.000 0.644 0.020
#> GSM751392 5 0.3126 0.72744 0.000 0.248 0.000 0.000 0.752 0.000
#> GSM751396 5 0.3854 0.50879 0.000 0.464 0.000 0.000 0.536 0.000
#> GSM751399 3 0.1049 0.77206 0.000 0.000 0.960 0.000 0.032 0.008
#> GSM751400 2 0.1668 0.68791 0.000 0.928 0.060 0.000 0.008 0.004
#> GSM751401 3 0.0717 0.76731 0.000 0.016 0.976 0.000 0.000 0.008
#> GSM751402 3 0.3241 0.68428 0.000 0.016 0.836 0.000 0.036 0.112
#> GSM751403 3 0.3048 0.72846 0.000 0.012 0.844 0.000 0.028 0.116
#> GSM751405 3 0.5426 0.66259 0.000 0.000 0.676 0.072 0.104 0.148
#> GSM751407 3 0.1237 0.77180 0.000 0.004 0.956 0.000 0.020 0.020
#> GSM751408 3 0.1707 0.74580 0.000 0.056 0.928 0.000 0.012 0.004
#> GSM751409 3 0.3270 0.75012 0.000 0.000 0.820 0.000 0.060 0.120
#> GSM751412 3 0.1462 0.76983 0.000 0.000 0.936 0.000 0.056 0.008
#> GSM751418 3 0.1624 0.75645 0.000 0.008 0.936 0.044 0.012 0.000
#> GSM751419 3 0.0893 0.76712 0.000 0.016 0.972 0.004 0.004 0.004
#> GSM751420 3 0.5303 0.53900 0.000 0.244 0.652 0.008 0.036 0.060
#> GSM751425 2 0.3588 0.57184 0.000 0.776 0.000 0.000 0.180 0.044
#> GSM751429 6 0.7105 0.00158 0.024 0.000 0.292 0.032 0.252 0.400
#> GSM751430 2 0.0146 0.70392 0.000 0.996 0.000 0.000 0.000 0.004
#> GSM751433 2 0.1396 0.69510 0.012 0.952 0.000 0.024 0.008 0.004
#> GSM751437 6 0.6913 0.06965 0.020 0.000 0.268 0.020 0.304 0.388
#> GSM751448 6 0.6594 -0.04802 0.020 0.004 0.308 0.004 0.224 0.440
#> GSM751451 2 0.1204 0.68488 0.000 0.944 0.000 0.056 0.000 0.000
#> GSM751423 2 0.3364 0.56524 0.000 0.780 0.000 0.000 0.196 0.024
#> GSM751424 2 0.0146 0.70392 0.000 0.996 0.000 0.000 0.000 0.004
#> GSM751428 2 0.0000 0.70364 0.000 1.000 0.000 0.000 0.000 0.000
#> GSM751431 2 0.0000 0.70364 0.000 1.000 0.000 0.000 0.000 0.000
#> GSM751432 2 0.0146 0.70392 0.000 0.996 0.000 0.000 0.000 0.004
#> GSM751434 2 0.0146 0.70338 0.000 0.996 0.004 0.000 0.000 0.000
#> GSM751435 2 0.0547 0.70465 0.000 0.980 0.000 0.000 0.000 0.020
#> GSM751436 2 0.0260 0.70129 0.000 0.992 0.000 0.000 0.008 0.000
#> GSM751440 2 0.5614 0.44825 0.020 0.608 0.000 0.000 0.196 0.176
#> GSM751444 2 0.5479 0.44467 0.016 0.620 0.000 0.000 0.168 0.196
#> GSM751446 2 0.5862 0.40836 0.020 0.568 0.000 0.000 0.204 0.208
#> GSM751449 2 0.6645 0.22295 0.020 0.420 0.016 0.000 0.188 0.356
#> GSM751450 2 0.4433 0.62685 0.068 0.792 0.000 0.048 0.056 0.036
#> GSM751452 2 0.0146 0.70392 0.000 0.996 0.000 0.000 0.000 0.004
#> GSM751426 2 0.0000 0.70364 0.000 1.000 0.000 0.000 0.000 0.000
#> GSM751427 2 0.3047 0.65706 0.008 0.852 0.000 0.000 0.060 0.080
#> GSM751438 2 0.6675 0.17748 0.020 0.392 0.016 0.000 0.192 0.380
#> GSM751439 2 0.6349 0.31707 0.020 0.492 0.008 0.000 0.184 0.296
#> GSM751441 2 0.0547 0.70465 0.000 0.980 0.000 0.000 0.000 0.020
#> GSM751442 2 0.5639 0.42706 0.020 0.604 0.000 0.000 0.176 0.200
#> GSM751443 6 0.6697 -0.12916 0.020 0.328 0.016 0.000 0.208 0.428
#> GSM751445 2 0.4253 0.55821 0.000 0.732 0.020 0.000 0.040 0.208
#> GSM751447 2 0.0547 0.70465 0.000 0.980 0.000 0.000 0.000 0.020
#> GSM751453 2 0.0547 0.70465 0.000 0.980 0.000 0.000 0.000 0.020
#> GSM751454 2 0.0547 0.70465 0.000 0.980 0.000 0.000 0.000 0.020
#> GSM751455 2 0.5639 0.42706 0.020 0.604 0.000 0.000 0.176 0.200
#> GSM751456 2 0.5639 0.42706 0.020 0.604 0.000 0.000 0.176 0.200
#> GSM751457 2 0.4807 0.50894 0.000 0.680 0.024 0.000 0.060 0.236
#> GSM751458 2 0.4557 0.53692 0.000 0.712 0.028 0.000 0.048 0.212
Heatmaps for the consensus matrix. It visualizes the probability of two samples to be in a same group.
consensus_heatmap(res, k = 2)
consensus_heatmap(res, k = 3)
consensus_heatmap(res, k = 4)
consensus_heatmap(res, k = 5)
consensus_heatmap(res, k = 6)
Heatmaps for the membership of samples in all partitions to see how consistent they are:
membership_heatmap(res, k = 2)
membership_heatmap(res, k = 3)
membership_heatmap(res, k = 4)
membership_heatmap(res, k = 5)
membership_heatmap(res, k = 6)
As soon as we have had the classes for columns, we can look for signatures which are significantly different between classes which can be candidate marks for certain classes. Following are the heatmaps for signatures.
Signature heatmaps where rows are scaled:
get_signatures(res, k = 2)
get_signatures(res, k = 3)
get_signatures(res, k = 4)
get_signatures(res, k = 5)
get_signatures(res, k = 6)
Signature heatmaps where rows are not scaled:
get_signatures(res, k = 2, scale_rows = FALSE)
get_signatures(res, k = 3, scale_rows = FALSE)
get_signatures(res, k = 4, scale_rows = FALSE)
get_signatures(res, k = 5, scale_rows = FALSE)
get_signatures(res, k = 6, scale_rows = FALSE)
Compare the overlap of signatures from different k:
compare_signatures(res)
get_signature() returns a data frame invisibly. TO get the list of signatures, the function
call should be assigned to a variable explicitly. In following code, if plot argument is set
to FALSE, no heatmap is plotted while only the differential analysis is performed.
# code only for demonstration
tb = get_signature(res, k = ..., plot = FALSE)
An example of the output of tb is:
#> which_row fdr mean_1 mean_2 scaled_mean_1 scaled_mean_2 km
#> 1 38 0.042760348 8.373488 9.131774 -0.5533452 0.5164555 1
#> 2 40 0.018707592 7.106213 8.469186 -0.6173731 0.5762149 1
#> 3 55 0.019134737 10.221463 11.207825 -0.6159697 0.5749050 1
#> 4 59 0.006059896 5.921854 7.869574 -0.6899429 0.6439467 1
#> 5 60 0.018055526 8.928898 10.211722 -0.6204761 0.5791110 1
#> 6 98 0.009384629 15.714769 14.887706 0.6635654 -0.6193277 2
...
The columns in tb are:
which_row: row indices corresponding to the input matrix.fdr: FDR for the differential test. mean_x: The mean value in group x.scaled_mean_x: The mean value in group x after rows are scaled.km: Row groups if k-means clustering is applied to rows.UMAP plot which shows how samples are separated.
dimension_reduction(res, k = 2, method = "UMAP")
dimension_reduction(res, k = 3, method = "UMAP")
dimension_reduction(res, k = 4, method = "UMAP")
dimension_reduction(res, k = 5, method = "UMAP")
dimension_reduction(res, k = 6, method = "UMAP")
Following heatmap shows how subgroups are split when increasing k:
collect_classes(res)
Test correlation between subgroups and known annotations. If the known annotation is numeric, one-way ANOVA test is applied, and if the known annotation is discrete, chi-squared contingency table test is applied.
test_to_known_factors(res)
#> n tissue(p) disease.state(p) agent(p) k
#> MAD:pam 141 2.60e-17 1.000 0.96370 2
#> MAD:pam 148 6.73e-26 0.897 0.90556 3
#> MAD:pam 145 4.13e-24 0.165 0.00479 4
#> MAD:pam 118 4.21e-36 0.399 0.00282 5
#> MAD:pam 112 1.30e-37 0.868 0.04072 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 4537 rows and 166 columns.
#> Top rows (454, 908, 1361, 1814, 2268) are extracted by 'MAD' method.
#> Subgroups are detected by 'mclust' method.
#> Performed in total 1250 partitions by row resampling.
#> Best k for subgroups seems to be 2.
#>
#> Following methods can be applied to this 'ConsensusPartition' object:
#> [1] "cola_report" "collect_classes" "collect_plots"
#> [4] "collect_stats" "colnames" "compare_signatures"
#> [7] "consensus_heatmap" "dimension_reduction" "functional_enrichment"
#> [10] "get_anno_col" "get_anno" "get_classes"
#> [13] "get_consensus" "get_matrix" "get_membership"
#> [16] "get_param" "get_signatures" "get_stats"
#> [19] "is_best_k" "is_stable_k" "membership_heatmap"
#> [22] "ncol" "nrow" "plot_ecdf"
#> [25] "rownames" "select_partition_number" "show"
#> [28] "suggest_best_k" "test_to_known_factors"
collect_plots() function collects all the plots made from res for all k (number of partitions)
into one single page to provide an easy and fast comparison between different k.
collect_plots(res)
The plots are:
k and the heatmap of
predicted classes for each k.k.k.k.All the plots in panels can be made by individual functions and they are plotted later in this section.
select_partition_number() produces several plots showing different
statistics for choosing “optimized” k. There are following statistics:
k;k, the area increased is defined as \(A_k - A_{k-1}\).The detailed explanations of these statistics can be found in the cola vignette.
Generally speaking, lower PAC score, higher mean silhouette score or higher
concordance corresponds to better partition. Rand index and Jaccard index
measure how similar the current partition is compared to partition with k-1.
If they are too similar, we won't accept k is better than k-1.
select_partition_number(res)
The numeric values for all these statistics can be obtained by get_stats().
get_stats(res)
#> k 1-PAC mean_silhouette concordance area_increased Rand Jaccard
#> 2 2 0.908 0.942 0.973 0.4021 0.592 0.592
#> 3 3 0.443 0.686 0.768 0.5112 0.736 0.557
#> 4 4 0.459 0.627 0.791 0.1223 0.896 0.721
#> 5 5 0.506 0.535 0.731 0.0944 0.887 0.655
#> 6 6 0.516 0.472 0.668 0.0523 0.850 0.489
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
#> GSM751298 1 0.1843 0.9277 0.972 0.028
#> GSM751304 2 0.0000 0.9834 0.000 1.000
#> GSM751305 2 0.0000 0.9834 0.000 1.000
#> GSM751307 2 0.0376 0.9818 0.004 0.996
#> GSM751310 1 0.7219 0.7840 0.800 0.200
#> GSM751314 1 0.1414 0.9317 0.980 0.020
#> GSM751316 2 0.9993 -0.0548 0.484 0.516
#> GSM751318 1 0.2236 0.9242 0.964 0.036
#> GSM751342 2 0.9087 0.4889 0.324 0.676
#> GSM751346 1 0.0000 0.9402 1.000 0.000
#> GSM751347 1 0.7528 0.7605 0.784 0.216
#> GSM751348 2 0.0000 0.9834 0.000 1.000
#> GSM751349 2 0.0000 0.9834 0.000 1.000
#> GSM751352 2 0.2043 0.9601 0.032 0.968
#> GSM751353 2 0.0000 0.9834 0.000 1.000
#> GSM751354 2 0.0376 0.9816 0.004 0.996
#> GSM751355 2 0.0000 0.9834 0.000 1.000
#> GSM751358 2 0.0672 0.9791 0.008 0.992
#> GSM751359 2 0.0000 0.9834 0.000 1.000
#> GSM751294 2 0.0000 0.9834 0.000 1.000
#> GSM751296 1 0.0000 0.9402 1.000 0.000
#> GSM751297 1 0.5946 0.8461 0.856 0.144
#> GSM751299 2 0.6343 0.8028 0.160 0.840
#> GSM751300 1 0.0000 0.9402 1.000 0.000
#> GSM751301 1 0.9209 0.5485 0.664 0.336
#> GSM751302 1 0.0000 0.9402 1.000 0.000
#> GSM751303 1 0.8081 0.7163 0.752 0.248
#> GSM751306 1 0.5059 0.8742 0.888 0.112
#> GSM751308 2 0.6343 0.8025 0.160 0.840
#> GSM751309 1 0.4298 0.8922 0.912 0.088
#> GSM751311 1 0.0000 0.9402 1.000 0.000
#> GSM751312 1 0.6148 0.8378 0.848 0.152
#> GSM751313 1 0.0000 0.9402 1.000 0.000
#> GSM751315 1 0.0000 0.9402 1.000 0.000
#> GSM751317 1 0.4690 0.8835 0.900 0.100
#> GSM751320 1 0.0000 0.9402 1.000 0.000
#> GSM751321 1 0.0000 0.9402 1.000 0.000
#> GSM751322 1 0.0000 0.9402 1.000 0.000
#> GSM751324 1 0.0000 0.9402 1.000 0.000
#> GSM751325 1 0.0000 0.9402 1.000 0.000
#> GSM751332 1 0.0000 0.9402 1.000 0.000
#> GSM751334 1 0.0000 0.9402 1.000 0.000
#> GSM751339 1 0.7528 0.7621 0.784 0.216
#> GSM751341 1 0.4562 0.8862 0.904 0.096
#> GSM751343 1 0.0000 0.9402 1.000 0.000
#> GSM751344 2 0.0000 0.9834 0.000 1.000
#> GSM751345 2 0.0376 0.9817 0.004 0.996
#> GSM751356 2 0.1184 0.9724 0.016 0.984
#> GSM751357 2 0.0672 0.9790 0.008 0.992
#> GSM751293 1 0.8327 0.6778 0.736 0.264
#> GSM751295 1 0.0000 0.9402 1.000 0.000
#> GSM751319 1 0.0000 0.9402 1.000 0.000
#> GSM751323 1 0.0000 0.9402 1.000 0.000
#> GSM751326 1 0.0000 0.9402 1.000 0.000
#> GSM751327 1 0.0000 0.9402 1.000 0.000
#> GSM751328 1 0.0000 0.9402 1.000 0.000
#> GSM751329 1 0.0000 0.9402 1.000 0.000
#> GSM751330 1 0.0000 0.9402 1.000 0.000
#> GSM751331 1 0.0000 0.9402 1.000 0.000
#> GSM751333 1 0.0000 0.9402 1.000 0.000
#> GSM751335 1 0.0000 0.9402 1.000 0.000
#> GSM751336 1 0.0000 0.9402 1.000 0.000
#> GSM751337 1 0.0000 0.9402 1.000 0.000
#> GSM751338 1 0.0000 0.9402 1.000 0.000
#> GSM751340 1 0.9881 0.3003 0.564 0.436
#> GSM751350 1 0.0000 0.9402 1.000 0.000
#> GSM751351 1 0.0000 0.9402 1.000 0.000
#> GSM751362 2 0.0000 0.9834 0.000 1.000
#> GSM751363 2 0.0000 0.9834 0.000 1.000
#> GSM751367 2 0.7219 0.7290 0.200 0.800
#> GSM751368 2 0.0376 0.9831 0.004 0.996
#> GSM751371 2 0.3274 0.9304 0.060 0.940
#> GSM751375 2 0.0000 0.9834 0.000 1.000
#> GSM751376 2 0.0000 0.9834 0.000 1.000
#> GSM751378 2 0.0000 0.9834 0.000 1.000
#> GSM751379 2 0.0000 0.9834 0.000 1.000
#> GSM751382 2 0.0000 0.9834 0.000 1.000
#> GSM751386 2 0.0000 0.9834 0.000 1.000
#> GSM751388 2 0.0376 0.9831 0.004 0.996
#> GSM751391 2 0.1843 0.9637 0.028 0.972
#> GSM751410 2 0.0000 0.9834 0.000 1.000
#> GSM751414 2 0.0376 0.9831 0.004 0.996
#> GSM751361 2 0.1414 0.9713 0.020 0.980
#> GSM751365 2 0.0376 0.9831 0.004 0.996
#> GSM751366 2 0.0376 0.9831 0.004 0.996
#> GSM751369 2 0.0000 0.9834 0.000 1.000
#> GSM751370 2 0.0000 0.9834 0.000 1.000
#> GSM751372 2 0.0000 0.9834 0.000 1.000
#> GSM751373 2 0.2236 0.9559 0.036 0.964
#> GSM751374 2 0.0000 0.9834 0.000 1.000
#> GSM751377 2 0.0000 0.9834 0.000 1.000
#> GSM751380 2 0.1414 0.9708 0.020 0.980
#> GSM751381 2 0.0000 0.9834 0.000 1.000
#> GSM751383 2 0.0376 0.9831 0.004 0.996
#> GSM751384 2 0.0000 0.9834 0.000 1.000
#> GSM751385 2 0.0000 0.9834 0.000 1.000
#> GSM751387 2 0.0376 0.9831 0.004 0.996
#> GSM751389 2 0.0000 0.9834 0.000 1.000
#> GSM751393 2 0.0000 0.9834 0.000 1.000
#> GSM751394 2 0.0000 0.9834 0.000 1.000
#> GSM751395 2 0.0000 0.9834 0.000 1.000
#> GSM751397 2 0.0000 0.9834 0.000 1.000
#> GSM751398 2 0.0000 0.9834 0.000 1.000
#> GSM751404 2 0.0376 0.9831 0.004 0.996
#> GSM751406 2 0.0000 0.9834 0.000 1.000
#> GSM751411 2 0.0000 0.9834 0.000 1.000
#> GSM751413 2 0.0000 0.9834 0.000 1.000
#> GSM751415 2 0.0376 0.9831 0.004 0.996
#> GSM751416 2 0.0000 0.9834 0.000 1.000
#> GSM751417 2 0.0000 0.9834 0.000 1.000
#> GSM751421 2 0.0000 0.9834 0.000 1.000
#> GSM751422 2 0.0000 0.9834 0.000 1.000
#> GSM751360 2 0.1184 0.9724 0.016 0.984
#> GSM751364 2 0.0376 0.9831 0.004 0.996
#> GSM751390 2 0.0376 0.9831 0.004 0.996
#> GSM751392 2 0.0000 0.9834 0.000 1.000
#> GSM751396 2 0.0376 0.9831 0.004 0.996
#> GSM751399 2 0.0000 0.9834 0.000 1.000
#> GSM751400 2 0.0376 0.9831 0.004 0.996
#> GSM751401 2 0.0672 0.9808 0.008 0.992
#> GSM751402 2 0.0672 0.9809 0.008 0.992
#> GSM751403 2 0.0376 0.9831 0.004 0.996
#> GSM751405 2 0.0000 0.9834 0.000 1.000
#> GSM751407 2 0.0376 0.9831 0.004 0.996
#> GSM751408 2 0.0376 0.9831 0.004 0.996
#> GSM751409 2 0.0000 0.9834 0.000 1.000
#> GSM751412 2 0.0376 0.9831 0.004 0.996
#> GSM751418 2 0.0376 0.9831 0.004 0.996
#> GSM751419 2 0.0376 0.9831 0.004 0.996
#> GSM751420 2 0.0000 0.9834 0.000 1.000
#> GSM751425 2 0.0000 0.9834 0.000 1.000
#> GSM751429 2 0.0376 0.9818 0.004 0.996
#> GSM751430 2 0.0376 0.9831 0.004 0.996
#> GSM751433 2 0.1633 0.9673 0.024 0.976
#> GSM751437 2 0.0000 0.9834 0.000 1.000
#> GSM751448 2 0.0376 0.9831 0.004 0.996
#> GSM751451 2 0.2603 0.9481 0.044 0.956
#> GSM751423 2 0.0000 0.9834 0.000 1.000
#> GSM751424 2 0.0376 0.9831 0.004 0.996
#> GSM751428 2 0.0376 0.9831 0.004 0.996
#> GSM751431 2 0.0672 0.9807 0.008 0.992
#> GSM751432 2 0.0376 0.9831 0.004 0.996
#> GSM751434 2 0.0376 0.9831 0.004 0.996
#> GSM751435 2 0.0376 0.9831 0.004 0.996
#> GSM751436 2 0.0376 0.9831 0.004 0.996
#> GSM751440 2 0.0376 0.9831 0.004 0.996
#> GSM751444 2 0.0376 0.9831 0.004 0.996
#> GSM751446 2 0.0000 0.9834 0.000 1.000
#> GSM751449 2 0.0000 0.9834 0.000 1.000
#> GSM751450 2 0.0376 0.9831 0.004 0.996
#> GSM751452 2 0.0376 0.9831 0.004 0.996
#> GSM751426 2 0.0376 0.9831 0.004 0.996
#> GSM751427 2 0.0000 0.9834 0.000 1.000
#> GSM751438 2 0.0000 0.9834 0.000 1.000
#> GSM751439 2 0.0376 0.9831 0.004 0.996
#> GSM751441 2 0.0000 0.9834 0.000 1.000
#> GSM751442 2 0.0376 0.9831 0.004 0.996
#> GSM751443 2 0.0672 0.9808 0.008 0.992
#> GSM751445 2 0.0000 0.9834 0.000 1.000
#> GSM751447 2 0.0376 0.9831 0.004 0.996
#> GSM751453 2 0.0376 0.9831 0.004 0.996
#> GSM751454 2 0.0376 0.9831 0.004 0.996
#> GSM751455 2 0.0376 0.9831 0.004 0.996
#> GSM751456 2 0.0376 0.9831 0.004 0.996
#> GSM751457 2 0.0000 0.9834 0.000 1.000
#> GSM751458 2 0.0000 0.9834 0.000 1.000
cbind(get_classes(res, k = 3), get_membership(res, k = 3))
#> class entropy silhouette p1 p2 p3
#> GSM751298 1 0.2866 0.9064 0.916 0.076 0.008
#> GSM751304 3 0.3816 0.6997 0.000 0.148 0.852
#> GSM751305 3 0.5098 0.5307 0.000 0.248 0.752
#> GSM751307 2 0.6398 0.7353 0.008 0.620 0.372
#> GSM751310 1 0.7403 0.6996 0.688 0.096 0.216
#> GSM751314 1 0.3293 0.9002 0.900 0.088 0.012
#> GSM751316 3 0.7396 -0.0606 0.480 0.032 0.488
#> GSM751318 1 0.5165 0.8703 0.832 0.096 0.072
#> GSM751342 1 0.9918 0.0294 0.384 0.276 0.340
#> GSM751346 1 0.1643 0.9092 0.956 0.044 0.000
#> GSM751347 1 0.7672 0.7440 0.684 0.160 0.156
#> GSM751348 3 0.6252 -0.2761 0.000 0.444 0.556
#> GSM751349 2 0.5706 0.7582 0.000 0.680 0.320
#> GSM751352 2 0.6905 0.5802 0.016 0.544 0.440
#> GSM751353 2 0.6045 0.7195 0.000 0.620 0.380
#> GSM751354 3 0.6680 -0.4922 0.008 0.484 0.508
#> GSM751355 2 0.6509 0.6077 0.004 0.524 0.472
#> GSM751358 3 0.4399 0.6373 0.000 0.188 0.812
#> GSM751359 2 0.6295 0.5225 0.000 0.528 0.472
#> GSM751294 3 0.4931 0.5974 0.000 0.232 0.768
#> GSM751296 1 0.1529 0.9112 0.960 0.040 0.000
#> GSM751297 1 0.5657 0.8652 0.808 0.104 0.088
#> GSM751299 2 0.8771 0.4772 0.132 0.544 0.324
#> GSM751300 1 0.1643 0.9092 0.956 0.044 0.000
#> GSM751301 1 0.6956 0.6422 0.660 0.300 0.040
#> GSM751302 1 0.1643 0.9092 0.956 0.044 0.000
#> GSM751303 1 0.7444 0.7033 0.684 0.096 0.220
#> GSM751306 1 0.5663 0.8464 0.808 0.096 0.096
#> GSM751308 3 0.8647 0.4332 0.192 0.208 0.600
#> GSM751309 1 0.4790 0.8775 0.848 0.096 0.056
#> GSM751311 1 0.2590 0.9057 0.924 0.072 0.004
#> GSM751312 1 0.5554 0.8399 0.812 0.076 0.112
#> GSM751313 1 0.0747 0.9121 0.984 0.016 0.000
#> GSM751315 1 0.2165 0.9071 0.936 0.064 0.000
#> GSM751317 1 0.5075 0.8692 0.836 0.096 0.068
#> GSM751320 1 0.0592 0.9125 0.988 0.012 0.000
#> GSM751321 1 0.2749 0.9061 0.924 0.064 0.012
#> GSM751322 1 0.1289 0.9116 0.968 0.032 0.000
#> GSM751324 1 0.2165 0.9071 0.936 0.064 0.000
#> GSM751325 1 0.0892 0.9122 0.980 0.020 0.000
#> GSM751332 1 0.2261 0.9069 0.932 0.068 0.000
#> GSM751334 1 0.0892 0.9122 0.980 0.020 0.000
#> GSM751339 1 0.4677 0.8256 0.840 0.028 0.132
#> GSM751341 1 0.4423 0.8856 0.864 0.088 0.048
#> GSM751343 1 0.1411 0.9112 0.964 0.036 0.000
#> GSM751344 2 0.5882 0.7547 0.000 0.652 0.348
#> GSM751345 2 0.5905 0.7537 0.000 0.648 0.352
#> GSM751356 3 0.4796 0.6173 0.000 0.220 0.780
#> GSM751357 3 0.5397 0.4946 0.000 0.280 0.720
#> GSM751293 1 0.6414 0.7259 0.716 0.248 0.036
#> GSM751295 1 0.1643 0.9092 0.956 0.044 0.000
#> GSM751319 1 0.2066 0.9076 0.940 0.060 0.000
#> GSM751323 1 0.0592 0.9125 0.988 0.012 0.000
#> GSM751326 1 0.0592 0.9125 0.988 0.012 0.000
#> GSM751327 1 0.0237 0.9127 0.996 0.004 0.000
#> GSM751328 1 0.2165 0.9075 0.936 0.064 0.000
#> GSM751329 1 0.0592 0.9123 0.988 0.012 0.000
#> GSM751330 1 0.1289 0.9113 0.968 0.032 0.000
#> GSM751331 1 0.1643 0.9092 0.956 0.044 0.000
#> GSM751333 1 0.0592 0.9125 0.988 0.012 0.000
#> GSM751335 1 0.1289 0.9113 0.968 0.032 0.000
#> GSM751336 1 0.1643 0.9092 0.956 0.044 0.000
#> GSM751337 1 0.0747 0.9121 0.984 0.016 0.000
#> GSM751338 1 0.0592 0.9125 0.988 0.012 0.000
#> GSM751340 1 0.6896 0.3810 0.588 0.020 0.392
#> GSM751350 1 0.1643 0.9092 0.956 0.044 0.000
#> GSM751351 1 0.1643 0.9092 0.956 0.044 0.000
#> GSM751362 3 0.2537 0.7261 0.000 0.080 0.920
#> GSM751363 3 0.2165 0.7174 0.000 0.064 0.936
#> GSM751367 3 0.6977 0.4904 0.212 0.076 0.712
#> GSM751368 2 0.6305 0.5426 0.000 0.516 0.484
#> GSM751371 3 0.2152 0.7024 0.036 0.016 0.948
#> GSM751375 2 0.5650 0.7447 0.000 0.688 0.312
#> GSM751376 3 0.5291 0.5531 0.000 0.268 0.732
#> GSM751378 3 0.5497 0.5263 0.000 0.292 0.708
#> GSM751379 3 0.4291 0.6595 0.000 0.180 0.820
#> GSM751382 2 0.5810 0.7575 0.000 0.664 0.336
#> GSM751386 2 0.6204 0.6195 0.000 0.576 0.424
#> GSM751388 2 0.5431 0.7064 0.000 0.716 0.284
#> GSM751391 3 0.1289 0.7264 0.000 0.032 0.968
#> GSM751410 3 0.1289 0.7290 0.000 0.032 0.968
#> GSM751414 3 0.0475 0.7144 0.004 0.004 0.992
#> GSM751361 3 0.1399 0.7243 0.004 0.028 0.968
#> GSM751365 3 0.3482 0.6663 0.000 0.128 0.872
#> GSM751366 3 0.1453 0.7152 0.008 0.024 0.968
#> GSM751369 3 0.1860 0.7301 0.000 0.052 0.948
#> GSM751370 3 0.0424 0.7176 0.000 0.008 0.992
#> GSM751372 3 0.1031 0.7249 0.000 0.024 0.976
#> GSM751373 3 0.7058 0.5180 0.100 0.180 0.720
#> GSM751374 3 0.5058 0.5404 0.000 0.244 0.756
#> GSM751377 2 0.6235 0.5920 0.000 0.564 0.436
#> GSM751380 3 0.1399 0.7145 0.004 0.028 0.968
#> GSM751381 2 0.6267 0.5150 0.000 0.548 0.452
#> GSM751383 2 0.5754 0.6776 0.004 0.700 0.296
#> GSM751384 3 0.5706 0.4784 0.000 0.320 0.680
#> GSM751385 3 0.5926 0.3727 0.000 0.356 0.644
#> GSM751387 2 0.5517 0.7010 0.004 0.728 0.268
#> GSM751389 3 0.3267 0.7185 0.000 0.116 0.884
#> GSM751393 3 0.5988 0.3247 0.000 0.368 0.632
#> GSM751394 2 0.6095 0.6719 0.000 0.608 0.392
#> GSM751395 3 0.6126 0.1724 0.000 0.400 0.600
#> GSM751397 3 0.6274 -0.1297 0.000 0.456 0.544
#> GSM751398 2 0.6126 0.6442 0.000 0.600 0.400
#> GSM751404 3 0.4605 0.6762 0.000 0.204 0.796
#> GSM751406 3 0.2959 0.7222 0.000 0.100 0.900
#> GSM751411 3 0.1753 0.7304 0.000 0.048 0.952
#> GSM751413 3 0.6225 -0.3089 0.000 0.432 0.568
#> GSM751415 3 0.0592 0.7201 0.000 0.012 0.988
#> GSM751416 3 0.1289 0.7239 0.000 0.032 0.968
#> GSM751417 3 0.1529 0.7229 0.000 0.040 0.960
#> GSM751421 3 0.0592 0.7201 0.000 0.012 0.988
#> GSM751422 3 0.1031 0.7240 0.000 0.024 0.976
#> GSM751360 3 0.0892 0.7232 0.000 0.020 0.980
#> GSM751364 3 0.1753 0.7227 0.000 0.048 0.952
#> GSM751390 3 0.6280 0.1739 0.000 0.460 0.540
#> GSM751392 2 0.5988 0.6962 0.000 0.632 0.368
#> GSM751396 2 0.4629 0.7443 0.004 0.808 0.188
#> GSM751399 3 0.3192 0.7200 0.000 0.112 0.888
#> GSM751400 3 0.6081 0.5108 0.004 0.344 0.652
#> GSM751401 3 0.6247 0.6282 0.044 0.212 0.744
#> GSM751402 3 0.6109 0.6705 0.080 0.140 0.780
#> GSM751403 3 0.4002 0.7114 0.000 0.160 0.840
#> GSM751405 3 0.2959 0.7217 0.000 0.100 0.900
#> GSM751407 3 0.5461 0.6281 0.008 0.244 0.748
#> GSM751408 3 0.5325 0.6329 0.004 0.248 0.748
#> GSM751409 3 0.3482 0.7147 0.000 0.128 0.872
#> GSM751412 3 0.4974 0.6458 0.000 0.236 0.764
#> GSM751418 3 0.4682 0.5941 0.004 0.192 0.804
#> GSM751419 3 0.4409 0.6120 0.004 0.172 0.824
#> GSM751420 3 0.4121 0.6819 0.000 0.168 0.832
#> GSM751425 2 0.5810 0.7476 0.000 0.664 0.336
#> GSM751429 3 0.6105 0.5275 0.024 0.252 0.724
#> GSM751430 2 0.4351 0.7376 0.004 0.828 0.168
#> GSM751433 2 0.6542 0.7283 0.060 0.736 0.204
#> GSM751437 3 0.2959 0.7228 0.000 0.100 0.900
#> GSM751448 3 0.4868 0.7117 0.056 0.100 0.844
#> GSM751451 2 0.8132 0.6215 0.096 0.600 0.304
#> GSM751423 2 0.6111 0.7200 0.000 0.604 0.396
#> GSM751424 2 0.4629 0.7396 0.004 0.808 0.188
#> GSM751428 2 0.4883 0.7575 0.004 0.788 0.208
#> GSM751431 2 0.5986 0.7688 0.012 0.704 0.284
#> GSM751432 2 0.4351 0.7344 0.004 0.828 0.168
#> GSM751434 2 0.4521 0.7364 0.004 0.816 0.180
#> GSM751435 2 0.4755 0.7429 0.008 0.808 0.184
#> GSM751436 2 0.4575 0.7362 0.004 0.812 0.184
#> GSM751440 2 0.5461 0.7522 0.016 0.768 0.216
#> GSM751444 2 0.5650 0.7636 0.000 0.688 0.312
#> GSM751446 2 0.5905 0.7505 0.000 0.648 0.352
#> GSM751449 2 0.5968 0.7199 0.000 0.636 0.364
#> GSM751450 2 0.5365 0.7655 0.004 0.744 0.252
#> GSM751452 2 0.4575 0.7362 0.004 0.812 0.184
#> GSM751426 2 0.4575 0.7362 0.004 0.812 0.184
#> GSM751427 2 0.5905 0.7474 0.000 0.648 0.352
#> GSM751438 2 0.6079 0.7124 0.000 0.612 0.388
#> GSM751439 3 0.6483 0.0401 0.008 0.392 0.600
#> GSM751441 2 0.5810 0.7580 0.000 0.664 0.336
#> GSM751442 2 0.4931 0.7508 0.004 0.784 0.212
#> GSM751443 3 0.4963 0.6360 0.008 0.200 0.792
#> GSM751445 2 0.5905 0.7172 0.000 0.648 0.352
#> GSM751447 2 0.4452 0.7545 0.000 0.808 0.192
#> GSM751453 2 0.4465 0.7360 0.004 0.820 0.176
#> GSM751454 2 0.4351 0.7344 0.004 0.828 0.168
#> GSM751455 2 0.4978 0.7536 0.004 0.780 0.216
#> GSM751456 2 0.4931 0.7502 0.004 0.784 0.212
#> GSM751457 2 0.6140 0.6465 0.000 0.596 0.404
#> GSM751458 2 0.6180 0.6160 0.000 0.584 0.416
cbind(get_classes(res, k = 4), get_membership(res, k = 4))
#> class entropy silhouette p1 p2 p3 p4
#> GSM751298 1 0.5735 -0.3468 0.576 0.032 0.000 0.392
#> GSM751304 3 0.4015 0.6969 0.000 0.116 0.832 0.052
#> GSM751305 3 0.6219 0.4459 0.000 0.264 0.640 0.096
#> GSM751307 2 0.4381 0.7442 0.008 0.780 0.200 0.012
#> GSM751310 1 0.5265 0.3857 0.684 0.024 0.288 0.004
#> GSM751314 1 0.0712 0.7753 0.984 0.004 0.008 0.004
#> GSM751316 3 0.5918 0.2561 0.396 0.032 0.568 0.004
#> GSM751318 1 0.2473 0.7118 0.908 0.012 0.080 0.000
#> GSM751342 3 0.7571 0.2733 0.336 0.180 0.480 0.004
#> GSM751346 4 0.4406 0.8491 0.300 0.000 0.000 0.700
#> GSM751347 4 0.6534 0.7849 0.284 0.060 0.024 0.632
#> GSM751348 2 0.5842 0.3369 0.000 0.520 0.448 0.032
#> GSM751349 2 0.4636 0.7484 0.000 0.772 0.188 0.040
#> GSM751352 2 0.4408 0.7286 0.004 0.756 0.232 0.008
#> GSM751353 2 0.5132 0.7410 0.000 0.748 0.184 0.068
#> GSM751354 2 0.5710 0.7145 0.004 0.700 0.228 0.068
#> GSM751355 2 0.5842 0.7118 0.000 0.688 0.220 0.092
#> GSM751358 3 0.4724 0.6795 0.000 0.112 0.792 0.096
#> GSM751359 2 0.6963 0.3140 0.000 0.464 0.424 0.112
#> GSM751294 3 0.5392 0.5658 0.000 0.204 0.724 0.072
#> GSM751296 4 0.4730 0.7918 0.364 0.000 0.000 0.636
#> GSM751297 4 0.6789 0.7243 0.280 0.020 0.084 0.616
#> GSM751299 2 0.4822 0.7324 0.024 0.756 0.212 0.008
#> GSM751300 4 0.4134 0.8668 0.260 0.000 0.000 0.740
#> GSM751301 1 0.6099 0.0791 0.500 0.464 0.012 0.024
#> GSM751302 4 0.3726 0.8659 0.212 0.000 0.000 0.788
#> GSM751303 1 0.5110 0.2992 0.620 0.004 0.372 0.004
#> GSM751306 1 0.3072 0.6496 0.868 0.004 0.124 0.004
#> GSM751308 3 0.6439 0.5851 0.108 0.188 0.684 0.020
#> GSM751309 1 0.2651 0.6894 0.896 0.004 0.096 0.004
#> GSM751311 1 0.0000 0.7805 1.000 0.000 0.000 0.000
#> GSM751312 1 0.6333 0.2767 0.604 0.040 0.336 0.020
#> GSM751313 1 0.1637 0.7508 0.940 0.000 0.000 0.060
#> GSM751315 1 0.0336 0.7814 0.992 0.000 0.000 0.008
#> GSM751317 1 0.2586 0.6950 0.900 0.004 0.092 0.004
#> GSM751320 1 0.0469 0.7805 0.988 0.000 0.000 0.012
#> GSM751321 1 0.0336 0.7814 0.992 0.000 0.000 0.008
#> GSM751322 1 0.0336 0.7811 0.992 0.000 0.000 0.008
#> GSM751324 1 0.0188 0.7811 0.996 0.000 0.000 0.004
#> GSM751325 1 0.0336 0.7811 0.992 0.000 0.000 0.008
#> GSM751332 1 0.0000 0.7805 1.000 0.000 0.000 0.000
#> GSM751334 1 0.0336 0.7811 0.992 0.000 0.000 0.008
#> GSM751339 1 0.4356 0.6122 0.804 0.000 0.148 0.048
#> GSM751341 1 0.5682 0.5306 0.748 0.016 0.116 0.120
#> GSM751343 1 0.0469 0.7805 0.988 0.000 0.000 0.012
#> GSM751344 2 0.3925 0.7480 0.000 0.808 0.176 0.016
#> GSM751345 2 0.3969 0.7475 0.000 0.804 0.180 0.016
#> GSM751356 3 0.5292 0.5635 0.000 0.216 0.724 0.060
#> GSM751357 3 0.6013 0.4049 0.000 0.288 0.640 0.072
#> GSM751293 1 0.6387 0.0897 0.532 0.412 0.008 0.048
#> GSM751295 4 0.3726 0.8659 0.212 0.000 0.000 0.788
#> GSM751319 1 0.0469 0.7804 0.988 0.000 0.000 0.012
#> GSM751323 1 0.0592 0.7797 0.984 0.000 0.000 0.016
#> GSM751326 1 0.1302 0.7626 0.956 0.000 0.000 0.044
#> GSM751327 1 0.0592 0.7797 0.984 0.000 0.000 0.016
#> GSM751328 1 0.0188 0.7808 0.996 0.000 0.000 0.004
#> GSM751329 1 0.1557 0.7417 0.944 0.000 0.000 0.056
#> GSM751330 4 0.4972 0.6584 0.456 0.000 0.000 0.544
#> GSM751331 4 0.3726 0.8659 0.212 0.000 0.000 0.788
#> GSM751333 1 0.1389 0.7597 0.952 0.000 0.000 0.048
#> GSM751335 4 0.4977 0.6497 0.460 0.000 0.000 0.540
#> GSM751336 4 0.4250 0.8626 0.276 0.000 0.000 0.724
#> GSM751337 1 0.1474 0.7569 0.948 0.000 0.000 0.052
#> GSM751338 1 0.1389 0.7597 0.952 0.000 0.000 0.048
#> GSM751340 3 0.6096 0.2266 0.376 0.004 0.576 0.044
#> GSM751350 4 0.3726 0.8659 0.212 0.000 0.000 0.788
#> GSM751351 4 0.3726 0.8659 0.212 0.000 0.000 0.788
#> GSM751362 3 0.1174 0.7361 0.000 0.020 0.968 0.012
#> GSM751363 3 0.3948 0.7235 0.000 0.064 0.840 0.096
#> GSM751367 3 0.7659 0.3775 0.200 0.240 0.544 0.016
#> GSM751368 3 0.6278 0.1220 0.000 0.408 0.532 0.060
#> GSM751371 3 0.2522 0.7318 0.016 0.000 0.908 0.076
#> GSM751375 2 0.5212 0.7399 0.000 0.740 0.192 0.068
#> GSM751376 3 0.6249 0.2642 0.000 0.336 0.592 0.072
#> GSM751378 3 0.5361 0.6049 0.000 0.148 0.744 0.108
#> GSM751379 3 0.6170 0.2886 0.000 0.332 0.600 0.068
#> GSM751382 2 0.4669 0.7553 0.000 0.780 0.168 0.052
#> GSM751386 2 0.6587 0.6168 0.000 0.596 0.292 0.112
#> GSM751388 2 0.5710 0.5992 0.000 0.708 0.192 0.100
#> GSM751391 3 0.2342 0.7389 0.000 0.008 0.912 0.080
#> GSM751410 3 0.1722 0.7403 0.000 0.008 0.944 0.048
#> GSM751414 3 0.1978 0.7364 0.000 0.004 0.928 0.068
#> GSM751361 3 0.2960 0.7351 0.004 0.020 0.892 0.084
#> GSM751365 3 0.5395 0.6562 0.000 0.184 0.732 0.084
#> GSM751366 3 0.2441 0.7376 0.004 0.020 0.920 0.056
#> GSM751369 3 0.1520 0.7406 0.000 0.020 0.956 0.024
#> GSM751370 3 0.1978 0.7367 0.000 0.004 0.928 0.068
#> GSM751372 3 0.2919 0.7389 0.000 0.044 0.896 0.060
#> GSM751373 3 0.6324 0.6321 0.068 0.160 0.716 0.056
#> GSM751374 3 0.6599 -0.1366 0.000 0.432 0.488 0.080
#> GSM751377 2 0.6587 0.5235 0.000 0.576 0.324 0.100
#> GSM751380 3 0.1970 0.7377 0.000 0.008 0.932 0.060
#> GSM751381 2 0.6980 0.3785 0.000 0.484 0.400 0.116
#> GSM751383 2 0.5690 0.5683 0.000 0.708 0.196 0.096
#> GSM751384 3 0.5781 0.4782 0.000 0.252 0.676 0.072
#> GSM751385 3 0.6495 0.3411 0.000 0.284 0.608 0.108
#> GSM751387 2 0.4487 0.7031 0.000 0.808 0.092 0.100
#> GSM751389 3 0.2227 0.7305 0.000 0.036 0.928 0.036
#> GSM751393 3 0.6876 0.0724 0.000 0.352 0.532 0.116
#> GSM751394 2 0.6806 0.5083 0.000 0.544 0.344 0.112
#> GSM751395 3 0.6995 -0.0771 0.000 0.384 0.496 0.120
#> GSM751397 3 0.6974 -0.0835 0.000 0.396 0.488 0.116
#> GSM751398 2 0.6809 0.5162 0.000 0.552 0.332 0.116
#> GSM751404 3 0.3324 0.7032 0.000 0.136 0.852 0.012
#> GSM751406 3 0.1929 0.7320 0.000 0.036 0.940 0.024
#> GSM751411 3 0.1820 0.7432 0.000 0.020 0.944 0.036
#> GSM751413 3 0.6489 0.1107 0.000 0.372 0.548 0.080
#> GSM751415 3 0.1209 0.7392 0.000 0.004 0.964 0.032
#> GSM751416 3 0.2984 0.7355 0.000 0.028 0.888 0.084
#> GSM751417 3 0.3439 0.7327 0.000 0.048 0.868 0.084
#> GSM751421 3 0.2053 0.7361 0.000 0.004 0.924 0.072
#> GSM751422 3 0.2271 0.7365 0.000 0.008 0.916 0.076
#> GSM751360 3 0.2473 0.7359 0.000 0.012 0.908 0.080
#> GSM751364 3 0.4297 0.7175 0.000 0.096 0.820 0.084
#> GSM751390 2 0.6412 0.3420 0.000 0.592 0.320 0.088
#> GSM751392 2 0.6104 0.6877 0.000 0.664 0.232 0.104
#> GSM751396 2 0.1388 0.7397 0.000 0.960 0.028 0.012
#> GSM751399 3 0.1837 0.7331 0.000 0.028 0.944 0.028
#> GSM751400 2 0.6253 0.2146 0.000 0.564 0.372 0.064
#> GSM751401 3 0.4554 0.6642 0.028 0.164 0.796 0.012
#> GSM751402 3 0.3607 0.7184 0.032 0.096 0.864 0.008
#> GSM751403 3 0.3015 0.7246 0.000 0.092 0.884 0.024
#> GSM751405 3 0.1837 0.7331 0.000 0.028 0.944 0.028
#> GSM751407 3 0.4453 0.6211 0.000 0.244 0.744 0.012
#> GSM751408 3 0.4776 0.6244 0.000 0.244 0.732 0.024
#> GSM751409 3 0.2751 0.7295 0.000 0.056 0.904 0.040
#> GSM751412 3 0.4079 0.6656 0.000 0.180 0.800 0.020
#> GSM751418 3 0.6015 0.5710 0.000 0.268 0.652 0.080
#> GSM751419 3 0.5723 0.6122 0.000 0.220 0.696 0.084
#> GSM751420 3 0.5690 0.4765 0.000 0.268 0.672 0.060
#> GSM751425 2 0.5292 0.7353 0.000 0.728 0.208 0.064
#> GSM751429 2 0.6383 0.4490 0.004 0.556 0.380 0.060
#> GSM751430 2 0.0336 0.7376 0.000 0.992 0.008 0.000
#> GSM751433 2 0.2751 0.7288 0.040 0.904 0.056 0.000
#> GSM751437 3 0.1798 0.7327 0.000 0.040 0.944 0.016
#> GSM751448 3 0.3708 0.6713 0.000 0.148 0.832 0.020
#> GSM751451 2 0.6276 0.2339 0.048 0.576 0.368 0.008
#> GSM751423 2 0.6071 0.6154 0.000 0.612 0.324 0.064
#> GSM751424 2 0.0188 0.7354 0.000 0.996 0.004 0.000
#> GSM751428 2 0.0895 0.7433 0.000 0.976 0.020 0.004
#> GSM751431 2 0.2587 0.7525 0.012 0.908 0.076 0.004
#> GSM751432 2 0.0188 0.7354 0.000 0.996 0.004 0.000
#> GSM751434 2 0.0188 0.7354 0.000 0.996 0.004 0.000
#> GSM751435 2 0.0336 0.7376 0.000 0.992 0.008 0.000
#> GSM751436 2 0.0524 0.7346 0.004 0.988 0.008 0.000
#> GSM751440 2 0.1256 0.7399 0.008 0.964 0.028 0.000
#> GSM751444 2 0.3172 0.7546 0.000 0.840 0.160 0.000
#> GSM751446 2 0.4049 0.7403 0.000 0.780 0.212 0.008
#> GSM751449 2 0.5179 0.7297 0.000 0.728 0.220 0.052
#> GSM751450 2 0.1716 0.7526 0.000 0.936 0.064 0.000
#> GSM751452 2 0.0188 0.7354 0.000 0.996 0.004 0.000
#> GSM751426 2 0.0188 0.7354 0.000 0.996 0.004 0.000
#> GSM751427 2 0.4839 0.7434 0.000 0.756 0.200 0.044
#> GSM751438 2 0.5022 0.7328 0.000 0.736 0.220 0.044
#> GSM751439 2 0.5760 0.2808 0.000 0.524 0.448 0.028
#> GSM751441 2 0.4633 0.7551 0.000 0.780 0.172 0.048
#> GSM751442 2 0.0592 0.7405 0.000 0.984 0.016 0.000
#> GSM751443 3 0.6435 0.0486 0.000 0.396 0.532 0.072
#> GSM751445 2 0.5533 0.7230 0.000 0.708 0.220 0.072
#> GSM751447 2 0.1151 0.7443 0.000 0.968 0.024 0.008
#> GSM751453 2 0.0188 0.7354 0.000 0.996 0.004 0.000
#> GSM751454 2 0.0188 0.7354 0.000 0.996 0.004 0.000
#> GSM751455 2 0.0927 0.7423 0.000 0.976 0.016 0.008
#> GSM751456 2 0.0779 0.7416 0.000 0.980 0.016 0.004
#> GSM751457 2 0.5810 0.6921 0.000 0.672 0.256 0.072
#> GSM751458 2 0.6111 0.6794 0.000 0.652 0.256 0.092
cbind(get_classes(res, k = 5), get_membership(res, k = 5))
#> class entropy silhouette p1 p2 p3 p4 p5
#> GSM751298 1 0.5749 0.52844 0.580 0.052 0.004 0.348 0.016
#> GSM751304 3 0.4668 0.21067 0.000 0.044 0.684 0.000 0.272
#> GSM751305 3 0.5864 -0.23278 0.000 0.128 0.572 0.000 0.300
#> GSM751307 2 0.5792 0.44874 0.004 0.632 0.184 0.000 0.180
#> GSM751310 4 0.5544 0.63249 0.000 0.004 0.192 0.660 0.144
#> GSM751314 4 0.3525 0.78864 0.000 0.004 0.024 0.816 0.156
#> GSM751316 3 0.5179 0.32301 0.000 0.004 0.600 0.352 0.044
#> GSM751318 4 0.5867 0.66681 0.000 0.024 0.124 0.656 0.196
#> GSM751342 3 0.7664 0.25982 0.000 0.072 0.424 0.192 0.312
#> GSM751346 1 0.1768 0.88268 0.924 0.000 0.000 0.072 0.004
#> GSM751347 1 0.4145 0.82390 0.824 0.088 0.016 0.056 0.016
#> GSM751348 3 0.6678 -0.49537 0.000 0.256 0.432 0.000 0.312
#> GSM751349 2 0.5668 0.50888 0.000 0.632 0.172 0.000 0.196
#> GSM751352 2 0.5159 0.59693 0.004 0.708 0.184 0.004 0.100
#> GSM751353 2 0.5610 0.54513 0.000 0.640 0.180 0.000 0.180
#> GSM751354 2 0.5581 0.52071 0.000 0.636 0.224 0.000 0.140
#> GSM751355 2 0.6156 0.39365 0.000 0.560 0.224 0.000 0.216
#> GSM751358 3 0.4589 0.24589 0.000 0.048 0.704 0.000 0.248
#> GSM751359 5 0.6458 0.65497 0.000 0.224 0.280 0.000 0.496
#> GSM751294 5 0.5236 0.42029 0.000 0.048 0.408 0.000 0.544
#> GSM751296 1 0.3300 0.79921 0.792 0.000 0.000 0.204 0.004
#> GSM751297 1 0.4242 0.81752 0.828 0.044 0.056 0.056 0.016
#> GSM751299 2 0.5835 0.58247 0.016 0.680 0.188 0.016 0.100
#> GSM751300 1 0.1043 0.88864 0.960 0.000 0.000 0.040 0.000
#> GSM751301 2 0.6969 0.27725 0.112 0.560 0.012 0.268 0.048
#> GSM751302 1 0.0609 0.88750 0.980 0.000 0.000 0.020 0.000
#> GSM751303 4 0.6328 0.51824 0.000 0.004 0.252 0.548 0.196
#> GSM751306 4 0.4565 0.75024 0.000 0.008 0.064 0.752 0.176
#> GSM751308 3 0.7004 0.28930 0.008 0.092 0.496 0.052 0.352
#> GSM751309 4 0.4184 0.76394 0.000 0.004 0.048 0.772 0.176
#> GSM751311 4 0.1124 0.84972 0.000 0.004 0.000 0.960 0.036
#> GSM751312 4 0.5884 0.40508 0.000 0.016 0.320 0.584 0.080
#> GSM751313 4 0.1043 0.84597 0.040 0.000 0.000 0.960 0.000
#> GSM751315 4 0.0898 0.85370 0.008 0.000 0.000 0.972 0.020
#> GSM751317 4 0.4252 0.76113 0.000 0.004 0.052 0.768 0.176
#> GSM751320 4 0.0510 0.85353 0.016 0.000 0.000 0.984 0.000
#> GSM751321 4 0.1041 0.85279 0.000 0.000 0.004 0.964 0.032
#> GSM751322 4 0.0162 0.85417 0.004 0.000 0.000 0.996 0.000
#> GSM751324 4 0.0510 0.85502 0.000 0.000 0.000 0.984 0.016
#> GSM751325 4 0.0162 0.85417 0.004 0.000 0.000 0.996 0.000
#> GSM751332 4 0.0963 0.85167 0.000 0.000 0.000 0.964 0.036
#> GSM751334 4 0.0162 0.85417 0.004 0.000 0.000 0.996 0.000
#> GSM751339 4 0.5719 0.67235 0.012 0.004 0.124 0.668 0.192
#> GSM751341 4 0.7776 0.31390 0.268 0.036 0.108 0.512 0.076
#> GSM751343 4 0.0510 0.85301 0.016 0.000 0.000 0.984 0.000
#> GSM751344 2 0.5245 0.59437 0.012 0.704 0.180 0.000 0.104
#> GSM751345 2 0.5279 0.59525 0.016 0.704 0.184 0.000 0.096
#> GSM751356 3 0.5670 -0.21522 0.004 0.068 0.512 0.000 0.416
#> GSM751357 3 0.6232 -0.40954 0.004 0.124 0.464 0.000 0.408
#> GSM751293 2 0.7159 0.17100 0.120 0.496 0.008 0.328 0.048
#> GSM751295 1 0.0609 0.88750 0.980 0.000 0.000 0.020 0.000
#> GSM751319 4 0.1403 0.85039 0.024 0.000 0.000 0.952 0.024
#> GSM751323 4 0.0609 0.85256 0.020 0.000 0.000 0.980 0.000
#> GSM751326 4 0.0703 0.85170 0.024 0.000 0.000 0.976 0.000
#> GSM751327 4 0.0510 0.85301 0.016 0.000 0.000 0.984 0.000
#> GSM751328 4 0.0703 0.85228 0.000 0.000 0.000 0.976 0.024
#> GSM751329 4 0.3305 0.59352 0.224 0.000 0.000 0.776 0.000
#> GSM751330 1 0.3210 0.77901 0.788 0.000 0.000 0.212 0.000
#> GSM751331 1 0.0609 0.88750 0.980 0.000 0.000 0.020 0.000
#> GSM751333 4 0.0880 0.84990 0.032 0.000 0.000 0.968 0.000
#> GSM751335 1 0.3452 0.74440 0.756 0.000 0.000 0.244 0.000
#> GSM751336 1 0.1478 0.88536 0.936 0.000 0.000 0.064 0.000
#> GSM751337 4 0.0880 0.84990 0.032 0.000 0.000 0.968 0.000
#> GSM751338 4 0.0794 0.85052 0.028 0.000 0.000 0.972 0.000
#> GSM751340 3 0.6071 0.24653 0.008 0.004 0.548 0.348 0.092
#> GSM751350 1 0.0609 0.88750 0.980 0.000 0.000 0.020 0.000
#> GSM751351 1 0.0609 0.88750 0.980 0.000 0.000 0.020 0.000
#> GSM751362 3 0.2763 0.59352 0.000 0.004 0.848 0.000 0.148
#> GSM751363 3 0.2077 0.58033 0.000 0.040 0.920 0.000 0.040
#> GSM751367 3 0.7914 0.00917 0.052 0.184 0.540 0.072 0.152
#> GSM751368 3 0.6688 -0.30704 0.000 0.220 0.460 0.004 0.316
#> GSM751371 3 0.3467 0.58134 0.000 0.004 0.832 0.036 0.128
#> GSM751375 2 0.5597 0.52417 0.000 0.640 0.160 0.000 0.200
#> GSM751376 5 0.5448 0.56255 0.000 0.076 0.340 0.000 0.584
#> GSM751378 5 0.5185 0.51936 0.000 0.048 0.384 0.000 0.568
#> GSM751379 5 0.5449 0.48369 0.000 0.068 0.376 0.000 0.556
#> GSM751382 2 0.5399 0.54671 0.000 0.664 0.148 0.000 0.188
#> GSM751386 5 0.6454 0.53402 0.000 0.304 0.208 0.000 0.488
#> GSM751388 2 0.5895 -0.29655 0.000 0.456 0.100 0.000 0.444
#> GSM751391 3 0.2513 0.61521 0.000 0.000 0.876 0.008 0.116
#> GSM751410 3 0.0963 0.60561 0.000 0.000 0.964 0.000 0.036
#> GSM751414 3 0.0798 0.62092 0.000 0.008 0.976 0.000 0.016
#> GSM751361 3 0.2679 0.61810 0.008 0.016 0.896 0.008 0.072
#> GSM751365 3 0.3769 0.55978 0.004 0.172 0.796 0.000 0.028
#> GSM751366 3 0.2673 0.62047 0.000 0.028 0.892 0.008 0.072
#> GSM751369 3 0.1197 0.60974 0.000 0.000 0.952 0.000 0.048
#> GSM751370 3 0.0807 0.62097 0.000 0.012 0.976 0.000 0.012
#> GSM751372 3 0.1668 0.62113 0.000 0.028 0.940 0.000 0.032
#> GSM751373 3 0.4504 0.55188 0.000 0.156 0.772 0.024 0.048
#> GSM751374 5 0.6284 0.61550 0.000 0.172 0.320 0.000 0.508
#> GSM751377 5 0.6374 0.47337 0.000 0.360 0.172 0.000 0.468
#> GSM751380 3 0.2577 0.61741 0.000 0.016 0.892 0.008 0.084
#> GSM751381 5 0.6417 0.61336 0.000 0.264 0.228 0.000 0.508
#> GSM751383 2 0.5790 -0.21608 0.000 0.500 0.092 0.000 0.408
#> GSM751384 5 0.5820 0.54090 0.000 0.100 0.376 0.000 0.524
#> GSM751385 5 0.5756 0.64959 0.000 0.112 0.312 0.000 0.576
#> GSM751387 2 0.5423 0.01155 0.000 0.548 0.064 0.000 0.388
#> GSM751389 3 0.4415 0.21588 0.000 0.008 0.604 0.000 0.388
#> GSM751393 5 0.5738 0.67691 0.000 0.132 0.264 0.000 0.604
#> GSM751394 5 0.6444 0.52667 0.000 0.316 0.200 0.000 0.484
#> GSM751395 5 0.5993 0.69228 0.000 0.164 0.260 0.000 0.576
#> GSM751397 5 0.6166 0.69134 0.000 0.180 0.272 0.000 0.548
#> GSM751398 5 0.6410 0.53312 0.000 0.320 0.192 0.000 0.488
#> GSM751404 3 0.5516 0.49948 0.000 0.136 0.644 0.000 0.220
#> GSM751406 3 0.3876 0.47463 0.000 0.000 0.684 0.000 0.316
#> GSM751411 3 0.2136 0.59670 0.000 0.008 0.904 0.000 0.088
#> GSM751413 3 0.6387 -0.36496 0.000 0.196 0.500 0.000 0.304
#> GSM751415 3 0.2177 0.62150 0.000 0.008 0.908 0.004 0.080
#> GSM751416 3 0.1200 0.61912 0.008 0.012 0.964 0.000 0.016
#> GSM751417 3 0.1756 0.61345 0.008 0.016 0.940 0.000 0.036
#> GSM751421 3 0.0324 0.61559 0.000 0.004 0.992 0.000 0.004
#> GSM751422 3 0.0566 0.61355 0.000 0.004 0.984 0.000 0.012
#> GSM751360 3 0.1779 0.62043 0.004 0.008 0.940 0.008 0.040
#> GSM751364 3 0.3096 0.60270 0.008 0.108 0.860 0.000 0.024
#> GSM751390 5 0.6107 0.44193 0.000 0.372 0.132 0.000 0.496
#> GSM751392 2 0.6274 -0.29402 0.000 0.428 0.148 0.000 0.424
#> GSM751396 2 0.2848 0.55513 0.000 0.840 0.004 0.000 0.156
#> GSM751399 3 0.3586 0.48451 0.000 0.000 0.736 0.000 0.264
#> GSM751400 5 0.6206 0.48919 0.000 0.304 0.168 0.000 0.528
#> GSM751401 3 0.5632 0.53586 0.000 0.140 0.668 0.012 0.180
#> GSM751402 3 0.5510 0.52032 0.000 0.100 0.640 0.004 0.256
#> GSM751403 3 0.5443 0.47560 0.000 0.084 0.604 0.000 0.312
#> GSM751405 3 0.3928 0.49699 0.000 0.004 0.700 0.000 0.296
#> GSM751407 3 0.6416 0.26717 0.000 0.180 0.464 0.000 0.356
#> GSM751408 3 0.6456 0.21335 0.000 0.184 0.448 0.000 0.368
#> GSM751409 3 0.4674 0.09639 0.000 0.016 0.568 0.000 0.416
#> GSM751412 3 0.5798 0.46243 0.000 0.156 0.608 0.000 0.236
#> GSM751418 3 0.3779 0.53877 0.000 0.200 0.776 0.000 0.024
#> GSM751419 3 0.3807 0.55041 0.004 0.176 0.792 0.000 0.028
#> GSM751420 5 0.4980 0.46450 0.000 0.036 0.380 0.000 0.584
#> GSM751425 2 0.5849 0.47575 0.000 0.608 0.196 0.000 0.196
#> GSM751429 2 0.6913 -0.20348 0.004 0.388 0.320 0.000 0.288
#> GSM751430 2 0.0865 0.64592 0.000 0.972 0.004 0.000 0.024
#> GSM751433 2 0.2171 0.63481 0.000 0.924 0.028 0.032 0.016
#> GSM751437 3 0.3857 0.44842 0.000 0.000 0.688 0.000 0.312
#> GSM751448 3 0.5039 0.19746 0.000 0.032 0.512 0.000 0.456
#> GSM751451 3 0.7629 -0.00661 0.000 0.272 0.384 0.048 0.296
#> GSM751423 5 0.6807 0.48034 0.000 0.336 0.300 0.000 0.364
#> GSM751424 2 0.0404 0.64328 0.000 0.988 0.000 0.000 0.012
#> GSM751428 2 0.2299 0.66004 0.004 0.912 0.032 0.000 0.052
#> GSM751431 2 0.2476 0.65506 0.000 0.904 0.064 0.012 0.020
#> GSM751432 2 0.0703 0.64350 0.000 0.976 0.000 0.000 0.024
#> GSM751434 2 0.0510 0.64271 0.000 0.984 0.000 0.000 0.016
#> GSM751435 2 0.1173 0.65415 0.004 0.964 0.012 0.000 0.020
#> GSM751436 2 0.0566 0.64319 0.000 0.984 0.000 0.004 0.012
#> GSM751440 2 0.2308 0.65167 0.000 0.912 0.048 0.004 0.036
#> GSM751444 2 0.4105 0.64531 0.008 0.804 0.128 0.004 0.056
#> GSM751446 2 0.5605 0.55338 0.012 0.656 0.228 0.000 0.104
#> GSM751449 2 0.5964 0.50239 0.004 0.608 0.208 0.000 0.180
#> GSM751450 2 0.1717 0.66197 0.000 0.936 0.052 0.004 0.008
#> GSM751452 2 0.0510 0.64188 0.000 0.984 0.000 0.000 0.016
#> GSM751426 2 0.0510 0.64188 0.000 0.984 0.000 0.000 0.016
#> GSM751427 2 0.5411 0.57021 0.000 0.664 0.160 0.000 0.176
#> GSM751438 2 0.5592 0.52208 0.000 0.636 0.220 0.000 0.144
#> GSM751439 2 0.6226 0.26163 0.004 0.524 0.332 0.000 0.140
#> GSM751441 2 0.4901 0.60745 0.000 0.716 0.116 0.000 0.168
#> GSM751442 2 0.2438 0.65747 0.008 0.908 0.044 0.000 0.040
#> GSM751443 5 0.6717 0.30662 0.000 0.264 0.320 0.000 0.416
#> GSM751445 2 0.6132 0.47210 0.004 0.584 0.200 0.000 0.212
#> GSM751447 2 0.2450 0.65878 0.000 0.896 0.028 0.000 0.076
#> GSM751453 2 0.0510 0.64271 0.000 0.984 0.000 0.000 0.016
#> GSM751454 2 0.0404 0.64419 0.000 0.988 0.000 0.000 0.012
#> GSM751455 2 0.2766 0.65652 0.012 0.892 0.040 0.000 0.056
#> GSM751456 2 0.2846 0.65552 0.012 0.888 0.048 0.000 0.052
#> GSM751457 2 0.6369 0.40098 0.004 0.544 0.216 0.000 0.236
#> GSM751458 2 0.6595 0.25052 0.004 0.488 0.212 0.000 0.296
cbind(get_classes(res, k = 6), get_membership(res, k = 6))
#> class entropy silhouette p1 p2 p3 p4 p5 p6
#> GSM751298 1 0.5208 0.4394 0.540 0.040 0.016 0.396 0.000 0.008
#> GSM751304 5 0.6019 0.0539 0.000 0.000 0.244 0.000 0.400 0.356
#> GSM751305 6 0.5660 -0.2313 0.000 0.012 0.108 0.000 0.412 0.468
#> GSM751307 2 0.4591 0.2789 0.004 0.640 0.008 0.004 0.024 0.320
#> GSM751310 4 0.5685 0.6049 0.004 0.016 0.072 0.616 0.268 0.024
#> GSM751314 4 0.4146 0.7383 0.004 0.012 0.060 0.764 0.160 0.000
#> GSM751316 5 0.7434 0.2798 0.008 0.008 0.100 0.308 0.412 0.164
#> GSM751318 4 0.5650 0.5659 0.000 0.028 0.080 0.564 0.324 0.004
#> GSM751342 5 0.6617 0.2850 0.000 0.080 0.100 0.188 0.592 0.040
#> GSM751346 1 0.1714 0.8242 0.908 0.000 0.000 0.092 0.000 0.000
#> GSM751347 1 0.5752 0.6875 0.688 0.008 0.112 0.056 0.020 0.116
#> GSM751348 6 0.6890 0.1333 0.000 0.196 0.080 0.000 0.272 0.452
#> GSM751349 6 0.4542 0.2646 0.000 0.412 0.028 0.000 0.004 0.556
#> GSM751352 6 0.5142 0.1450 0.004 0.328 0.020 0.004 0.040 0.604
#> GSM751353 6 0.2636 0.4469 0.000 0.120 0.016 0.000 0.004 0.860
#> GSM751354 6 0.3993 0.4242 0.000 0.148 0.040 0.000 0.032 0.780
#> GSM751355 6 0.2829 0.4859 0.000 0.096 0.024 0.000 0.016 0.864
#> GSM751358 5 0.5876 0.2401 0.000 0.004 0.152 0.004 0.472 0.368
#> GSM751359 6 0.5870 0.3105 0.000 0.100 0.244 0.000 0.060 0.596
#> GSM751294 6 0.5536 -0.0785 0.000 0.004 0.380 0.000 0.120 0.496
#> GSM751296 1 0.3101 0.7212 0.756 0.000 0.000 0.244 0.000 0.000
#> GSM751297 1 0.4906 0.7525 0.744 0.004 0.136 0.052 0.016 0.048
#> GSM751299 6 0.6027 0.1238 0.008 0.244 0.120 0.004 0.032 0.592
#> GSM751300 1 0.0632 0.8314 0.976 0.000 0.000 0.024 0.000 0.000
#> GSM751301 2 0.7261 0.2528 0.128 0.480 0.028 0.276 0.004 0.084
#> GSM751302 1 0.0146 0.8285 0.996 0.000 0.000 0.004 0.000 0.000
#> GSM751303 4 0.5704 0.4782 0.004 0.020 0.084 0.500 0.392 0.000
#> GSM751306 4 0.4782 0.7006 0.004 0.016 0.080 0.704 0.196 0.000
#> GSM751308 5 0.7550 0.2598 0.020 0.080 0.160 0.052 0.532 0.156
#> GSM751309 4 0.4694 0.7035 0.004 0.012 0.080 0.708 0.196 0.000
#> GSM751311 4 0.1074 0.8338 0.000 0.012 0.028 0.960 0.000 0.000
#> GSM751312 4 0.7409 0.2242 0.008 0.016 0.184 0.452 0.260 0.080
#> GSM751313 4 0.1010 0.8260 0.036 0.000 0.000 0.960 0.004 0.000
#> GSM751315 4 0.0653 0.8376 0.004 0.004 0.012 0.980 0.000 0.000
#> GSM751317 4 0.4782 0.7008 0.004 0.016 0.080 0.704 0.196 0.000
#> GSM751320 4 0.0405 0.8350 0.008 0.000 0.000 0.988 0.004 0.000
#> GSM751321 4 0.1053 0.8358 0.000 0.004 0.012 0.964 0.020 0.000
#> GSM751322 4 0.0260 0.8370 0.000 0.000 0.008 0.992 0.000 0.000
#> GSM751324 4 0.0820 0.8369 0.000 0.000 0.016 0.972 0.012 0.000
#> GSM751325 4 0.0260 0.8370 0.000 0.000 0.008 0.992 0.000 0.000
#> GSM751332 4 0.1053 0.8357 0.000 0.004 0.020 0.964 0.012 0.000
#> GSM751334 4 0.0405 0.8367 0.004 0.000 0.008 0.988 0.000 0.000
#> GSM751339 4 0.5810 0.6079 0.024 0.008 0.136 0.604 0.228 0.000
#> GSM751341 4 0.7966 0.1115 0.300 0.052 0.072 0.440 0.084 0.052
#> GSM751343 4 0.0405 0.8372 0.004 0.000 0.008 0.988 0.000 0.000
#> GSM751344 6 0.4096 0.2686 0.000 0.268 0.020 0.000 0.012 0.700
#> GSM751345 6 0.4233 0.2645 0.004 0.268 0.020 0.000 0.012 0.696
#> GSM751356 6 0.6296 -0.1499 0.004 0.008 0.304 0.000 0.244 0.440
#> GSM751357 6 0.6124 0.0861 0.004 0.020 0.248 0.000 0.192 0.536
#> GSM751293 2 0.7484 0.1433 0.144 0.428 0.028 0.316 0.008 0.076
#> GSM751295 1 0.0260 0.8296 0.992 0.000 0.000 0.008 0.000 0.000
#> GSM751319 4 0.0665 0.8374 0.008 0.004 0.008 0.980 0.000 0.000
#> GSM751323 4 0.0405 0.8350 0.008 0.000 0.000 0.988 0.004 0.000
#> GSM751326 4 0.0935 0.8280 0.032 0.000 0.000 0.964 0.004 0.000
#> GSM751327 4 0.0508 0.8343 0.012 0.000 0.000 0.984 0.004 0.000
#> GSM751328 4 0.0603 0.8365 0.000 0.004 0.016 0.980 0.000 0.000
#> GSM751329 4 0.1296 0.8186 0.044 0.004 0.004 0.948 0.000 0.000
#> GSM751330 1 0.3592 0.5471 0.656 0.000 0.000 0.344 0.000 0.000
#> GSM751331 1 0.0146 0.8285 0.996 0.000 0.000 0.004 0.000 0.000
#> GSM751333 4 0.1010 0.8255 0.036 0.000 0.000 0.960 0.004 0.000
#> GSM751335 1 0.3737 0.4566 0.608 0.000 0.000 0.392 0.000 0.000
#> GSM751336 1 0.1663 0.8260 0.912 0.000 0.000 0.088 0.000 0.000
#> GSM751337 4 0.0935 0.8268 0.032 0.000 0.000 0.964 0.004 0.000
#> GSM751338 4 0.0935 0.8282 0.032 0.000 0.000 0.964 0.004 0.000
#> GSM751340 5 0.6968 0.2781 0.016 0.008 0.200 0.244 0.492 0.040
#> GSM751350 1 0.0146 0.8285 0.996 0.000 0.000 0.004 0.000 0.000
#> GSM751351 1 0.0146 0.8285 0.996 0.000 0.000 0.004 0.000 0.000
#> GSM751362 5 0.5468 0.1581 0.000 0.000 0.380 0.000 0.492 0.128
#> GSM751363 5 0.3876 0.6056 0.000 0.000 0.024 0.000 0.700 0.276
#> GSM751367 5 0.7883 0.2450 0.032 0.096 0.076 0.048 0.376 0.372
#> GSM751368 5 0.5945 0.3839 0.000 0.104 0.036 0.000 0.512 0.348
#> GSM751371 5 0.3098 0.5671 0.000 0.012 0.032 0.028 0.868 0.060
#> GSM751375 6 0.4456 0.3891 0.000 0.276 0.044 0.000 0.008 0.672
#> GSM751376 6 0.4948 0.1732 0.000 0.004 0.316 0.000 0.076 0.604
#> GSM751378 6 0.5366 -0.0443 0.000 0.004 0.380 0.000 0.100 0.516
#> GSM751379 6 0.5603 -0.0991 0.000 0.004 0.384 0.000 0.128 0.484
#> GSM751382 6 0.4976 0.2917 0.000 0.388 0.036 0.000 0.020 0.556
#> GSM751386 6 0.5785 0.3675 0.000 0.140 0.224 0.000 0.036 0.600
#> GSM751388 6 0.6438 0.2876 0.000 0.304 0.204 0.000 0.032 0.460
#> GSM751391 5 0.3370 0.6365 0.000 0.000 0.044 0.004 0.812 0.140
#> GSM751410 5 0.4418 0.6197 0.000 0.000 0.100 0.000 0.708 0.192
#> GSM751414 5 0.3748 0.6441 0.000 0.004 0.064 0.000 0.784 0.148
#> GSM751361 5 0.2757 0.6486 0.000 0.008 0.004 0.004 0.848 0.136
#> GSM751365 5 0.4411 0.5879 0.000 0.124 0.008 0.000 0.736 0.132
#> GSM751366 5 0.3858 0.5933 0.000 0.024 0.108 0.000 0.800 0.068
#> GSM751369 5 0.4707 0.5773 0.000 0.000 0.112 0.000 0.672 0.216
#> GSM751370 5 0.4243 0.6346 0.000 0.004 0.104 0.000 0.744 0.148
#> GSM751372 5 0.4500 0.6087 0.000 0.008 0.068 0.000 0.700 0.224
#> GSM751373 5 0.5664 0.5389 0.000 0.140 0.068 0.032 0.688 0.072
#> GSM751374 6 0.4946 0.2551 0.000 0.008 0.260 0.000 0.088 0.644
#> GSM751377 6 0.6476 0.3345 0.000 0.200 0.216 0.000 0.060 0.524
#> GSM751380 5 0.3315 0.6027 0.000 0.008 0.092 0.000 0.832 0.068
#> GSM751381 6 0.5916 0.3236 0.000 0.120 0.248 0.000 0.048 0.584
#> GSM751383 2 0.6674 -0.2438 0.000 0.376 0.236 0.000 0.036 0.352
#> GSM751384 6 0.5091 0.0812 0.000 0.004 0.364 0.000 0.076 0.556
#> GSM751385 6 0.5095 0.1331 0.000 0.008 0.344 0.000 0.072 0.576
#> GSM751387 6 0.6161 0.2668 0.000 0.320 0.168 0.000 0.024 0.488
#> GSM751389 3 0.5828 0.5381 0.000 0.004 0.512 0.000 0.200 0.284
#> GSM751393 6 0.4973 0.1557 0.000 0.016 0.368 0.000 0.044 0.572
#> GSM751394 6 0.6050 0.3577 0.000 0.184 0.204 0.000 0.040 0.572
#> GSM751395 6 0.4624 0.1983 0.000 0.012 0.340 0.000 0.032 0.616
#> GSM751397 6 0.5623 0.2552 0.000 0.064 0.304 0.000 0.052 0.580
#> GSM751398 6 0.6085 0.3406 0.000 0.164 0.224 0.000 0.044 0.568
#> GSM751404 3 0.6674 0.6124 0.000 0.136 0.500 0.000 0.268 0.096
#> GSM751406 3 0.4316 0.6223 0.000 0.000 0.728 0.000 0.144 0.128
#> GSM751411 5 0.5045 0.5442 0.000 0.004 0.116 0.000 0.636 0.244
#> GSM751413 5 0.5976 0.2757 0.000 0.092 0.040 0.000 0.464 0.404
#> GSM751415 5 0.4125 0.5941 0.000 0.004 0.140 0.000 0.756 0.100
#> GSM751416 5 0.3323 0.6431 0.000 0.008 0.008 0.000 0.780 0.204
#> GSM751417 5 0.3357 0.6358 0.000 0.008 0.004 0.000 0.764 0.224
#> GSM751421 5 0.3945 0.6367 0.000 0.004 0.048 0.000 0.748 0.200
#> GSM751422 5 0.3798 0.6350 0.000 0.004 0.032 0.000 0.748 0.216
#> GSM751360 5 0.2562 0.6418 0.000 0.004 0.004 0.004 0.860 0.128
#> GSM751364 5 0.4317 0.6173 0.000 0.088 0.016 0.000 0.752 0.144
#> GSM751390 6 0.6857 0.0734 0.000 0.224 0.324 0.000 0.056 0.396
#> GSM751392 6 0.5920 0.3915 0.000 0.212 0.176 0.000 0.032 0.580
#> GSM751396 2 0.3313 0.6040 0.000 0.812 0.036 0.000 0.004 0.148
#> GSM751399 3 0.5628 0.5725 0.000 0.000 0.540 0.000 0.240 0.220
#> GSM751400 3 0.7000 0.1851 0.000 0.176 0.388 0.000 0.088 0.348
#> GSM751401 3 0.6335 0.3398 0.000 0.132 0.432 0.008 0.400 0.028
#> GSM751402 3 0.5570 0.5969 0.000 0.104 0.596 0.000 0.272 0.028
#> GSM751403 3 0.5325 0.6335 0.000 0.092 0.680 0.000 0.164 0.064
#> GSM751405 3 0.4563 0.6094 0.000 0.004 0.708 0.000 0.176 0.112
#> GSM751407 3 0.6779 0.6389 0.000 0.172 0.520 0.000 0.180 0.128
#> GSM751408 3 0.6927 0.6306 0.000 0.160 0.500 0.000 0.184 0.156
#> GSM751409 3 0.6018 0.4473 0.000 0.004 0.444 0.000 0.212 0.340
#> GSM751412 3 0.6979 0.5850 0.000 0.156 0.452 0.000 0.280 0.112
#> GSM751418 5 0.4389 0.5313 0.000 0.168 0.012 0.000 0.736 0.084
#> GSM751419 5 0.4225 0.5380 0.000 0.160 0.008 0.000 0.748 0.084
#> GSM751420 6 0.5817 -0.1431 0.000 0.012 0.384 0.000 0.132 0.472
#> GSM751425 6 0.4452 0.4279 0.000 0.288 0.040 0.000 0.008 0.664
#> GSM751429 6 0.5845 0.3574 0.004 0.080 0.156 0.000 0.116 0.644
#> GSM751430 2 0.2213 0.6866 0.000 0.888 0.008 0.000 0.004 0.100
#> GSM751433 2 0.2645 0.6745 0.000 0.896 0.024 0.016 0.028 0.036
#> GSM751437 3 0.4896 0.5986 0.000 0.000 0.652 0.000 0.216 0.132
#> GSM751448 3 0.4917 0.5451 0.004 0.000 0.668 0.000 0.140 0.188
#> GSM751451 5 0.6832 0.2706 0.000 0.300 0.056 0.024 0.492 0.128
#> GSM751423 6 0.6124 0.3336 0.000 0.300 0.088 0.000 0.072 0.540
#> GSM751424 2 0.1340 0.6874 0.000 0.948 0.008 0.000 0.004 0.040
#> GSM751428 2 0.4467 0.2467 0.000 0.496 0.004 0.000 0.020 0.480
#> GSM751431 2 0.3528 0.6091 0.000 0.820 0.012 0.012 0.028 0.128
#> GSM751432 2 0.3161 0.6344 0.000 0.776 0.008 0.000 0.000 0.216
#> GSM751434 2 0.3163 0.6244 0.000 0.764 0.004 0.000 0.000 0.232
#> GSM751435 2 0.3890 0.4476 0.000 0.596 0.000 0.000 0.004 0.400
#> GSM751436 2 0.1268 0.6873 0.000 0.952 0.008 0.000 0.004 0.036
#> GSM751440 2 0.3409 0.6385 0.000 0.840 0.016 0.008 0.048 0.088
#> GSM751444 6 0.5071 -0.0391 0.000 0.376 0.012 0.000 0.056 0.556
#> GSM751446 6 0.4438 0.3443 0.000 0.208 0.020 0.000 0.052 0.720
#> GSM751449 6 0.2122 0.4856 0.000 0.076 0.000 0.000 0.024 0.900
#> GSM751450 2 0.2723 0.6588 0.000 0.856 0.004 0.000 0.020 0.120
#> GSM751452 2 0.1340 0.6882 0.000 0.948 0.008 0.000 0.004 0.040
#> GSM751426 2 0.1477 0.6900 0.000 0.940 0.008 0.000 0.004 0.048
#> GSM751427 6 0.3352 0.4312 0.000 0.148 0.008 0.000 0.032 0.812
#> GSM751438 6 0.3187 0.4565 0.000 0.112 0.008 0.000 0.044 0.836
#> GSM751439 6 0.5299 0.3735 0.000 0.120 0.036 0.000 0.176 0.668
#> GSM751441 6 0.3525 0.3813 0.000 0.180 0.004 0.000 0.032 0.784
#> GSM751442 6 0.4262 -0.2700 0.000 0.476 0.000 0.000 0.016 0.508
#> GSM751443 6 0.6093 0.1146 0.004 0.032 0.312 0.000 0.124 0.528
#> GSM751445 6 0.1957 0.4882 0.000 0.072 0.008 0.000 0.008 0.912
#> GSM751447 6 0.4546 -0.1989 0.000 0.444 0.008 0.000 0.020 0.528
#> GSM751453 2 0.3847 0.5161 0.000 0.644 0.008 0.000 0.000 0.348
#> GSM751454 2 0.3833 0.5205 0.000 0.648 0.008 0.000 0.000 0.344
#> GSM751455 6 0.4268 -0.1490 0.000 0.428 0.012 0.000 0.004 0.556
#> GSM751456 6 0.4457 -0.1486 0.000 0.432 0.008 0.000 0.016 0.544
#> GSM751457 6 0.2351 0.5043 0.000 0.052 0.036 0.000 0.012 0.900
#> GSM751458 6 0.2358 0.4994 0.000 0.040 0.048 0.000 0.012 0.900
Heatmaps for the consensus matrix. It visualizes the probability of two samples to be in a same group.
consensus_heatmap(res, k = 2)
consensus_heatmap(res, k = 3)
consensus_heatmap(res, k = 4)
consensus_heatmap(res, k = 5)
consensus_heatmap(res, k = 6)
Heatmaps for the membership of samples in all partitions to see how consistent they are:
membership_heatmap(res, k = 2)
membership_heatmap(res, k = 3)
membership_heatmap(res, k = 4)
membership_heatmap(res, k = 5)
membership_heatmap(res, k = 6)
As soon as we have had the classes for columns, we can look for signatures which are significantly different between classes which can be candidate marks for certain classes. Following are the heatmaps for signatures.
Signature heatmaps where rows are scaled:
get_signatures(res, k = 2)
get_signatures(res, k = 3)
get_signatures(res, k = 4)
get_signatures(res, k = 5)
get_signatures(res, k = 6)
Signature heatmaps where rows are not scaled:
get_signatures(res, k = 2, scale_rows = FALSE)
get_signatures(res, k = 3, scale_rows = FALSE)
get_signatures(res, k = 4, scale_rows = FALSE)
get_signatures(res, k = 5, scale_rows = FALSE)
get_signatures(res, k = 6, scale_rows = FALSE)
Compare the overlap of signatures from different k:
compare_signatures(res)
get_signature() returns a data frame invisibly. TO get the list of signatures, the function
call should be assigned to a variable explicitly. In following code, if plot argument is set
to FALSE, no heatmap is plotted while only the differential analysis is performed.
# code only for demonstration
tb = get_signature(res, k = ..., plot = FALSE)
An example of the output of tb is:
#> which_row fdr mean_1 mean_2 scaled_mean_1 scaled_mean_2 km
#> 1 38 0.042760348 8.373488 9.131774 -0.5533452 0.5164555 1
#> 2 40 0.018707592 7.106213 8.469186 -0.6173731 0.5762149 1
#> 3 55 0.019134737 10.221463 11.207825 -0.6159697 0.5749050 1
#> 4 59 0.006059896 5.921854 7.869574 -0.6899429 0.6439467 1
#> 5 60 0.018055526 8.928898 10.211722 -0.6204761 0.5791110 1
#> 6 98 0.009384629 15.714769 14.887706 0.6635654 -0.6193277 2
...
The columns in tb are:
which_row: row indices corresponding to the input matrix.fdr: FDR for the differential test. mean_x: The mean value in group x.scaled_mean_x: The mean value in group x after rows are scaled.km: Row groups if k-means clustering is applied to rows.UMAP plot which shows how samples are separated.
dimension_reduction(res, k = 2, method = "UMAP")
dimension_reduction(res, k = 3, method = "UMAP")
dimension_reduction(res, k = 4, method = "UMAP")
dimension_reduction(res, k = 5, method = "UMAP")
dimension_reduction(res, k = 6, method = "UMAP")
Following heatmap shows how subgroups are split when increasing k:
collect_classes(res)
Test correlation between subgroups and known annotations. If the known annotation is numeric, one-way ANOVA test is applied, and if the known annotation is discrete, chi-squared contingency table test is applied.
test_to_known_factors(res)
#> n tissue(p) disease.state(p) agent(p) k
#> MAD:mclust 163 2.98e-22 0.066 0.117 2
#> MAD:mclust 149 2.78e-32 0.106 0.331 3
#> MAD:mclust 134 9.74e-28 0.217 0.298 4
#> MAD:mclust 116 2.56e-33 0.610 0.185 5
#> MAD:mclust 89 1.50e-28 0.936 0.378 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 4537 rows and 166 columns.
#> Top rows (454, 908, 1361, 1814, 2268) are extracted by 'MAD' method.
#> Subgroups are detected by 'NMF' method.
#> Performed in total 1250 partitions by row resampling.
#> Best k for subgroups seems to be 2.
#>
#> Following methods can be applied to this 'ConsensusPartition' object:
#> [1] "cola_report" "collect_classes" "collect_plots"
#> [4] "collect_stats" "colnames" "compare_signatures"
#> [7] "consensus_heatmap" "dimension_reduction" "functional_enrichment"
#> [10] "get_anno_col" "get_anno" "get_classes"
#> [13] "get_consensus" "get_matrix" "get_membership"
#> [16] "get_param" "get_signatures" "get_stats"
#> [19] "is_best_k" "is_stable_k" "membership_heatmap"
#> [22] "ncol" "nrow" "plot_ecdf"
#> [25] "rownames" "select_partition_number" "show"
#> [28] "suggest_best_k" "test_to_known_factors"
collect_plots() function collects all the plots made from res for all k (number of partitions)
into one single page to provide an easy and fast comparison between different k.
collect_plots(res)
The plots are:
k and the heatmap of
predicted classes for each k.k.k.k.All the plots in panels can be made by individual functions and they are plotted later in this section.
select_partition_number() produces several plots showing different
statistics for choosing “optimized” k. There are following statistics:
k;k, the area increased is defined as \(A_k - A_{k-1}\).The detailed explanations of these statistics can be found in the cola vignette.
Generally speaking, lower PAC score, higher mean silhouette score or higher
concordance corresponds to better partition. Rand index and Jaccard index
measure how similar the current partition is compared to partition with k-1.
If they are too similar, we won't accept k is better than k-1.
select_partition_number(res)
The numeric values for all these statistics can be obtained by get_stats().
get_stats(res)
#> k 1-PAC mean_silhouette concordance area_increased Rand Jaccard
#> 2 2 0.862 0.904 0.956 0.4653 0.543 0.543
#> 3 3 0.534 0.683 0.837 0.4237 0.738 0.539
#> 4 4 0.523 0.442 0.715 0.1189 0.774 0.452
#> 5 5 0.681 0.718 0.825 0.0704 0.853 0.524
#> 6 6 0.711 0.650 0.805 0.0441 0.946 0.750
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
#> GSM751298 1 0.0000 0.956 1.000 0.000
#> GSM751304 2 0.2423 0.938 0.040 0.960
#> GSM751305 2 0.1414 0.948 0.020 0.980
#> GSM751307 1 0.1414 0.946 0.980 0.020
#> GSM751310 1 0.0000 0.956 1.000 0.000
#> GSM751314 1 0.0000 0.956 1.000 0.000
#> GSM751316 1 0.0000 0.956 1.000 0.000
#> GSM751318 1 0.1843 0.940 0.972 0.028
#> GSM751342 1 0.1414 0.945 0.980 0.020
#> GSM751346 1 0.0000 0.956 1.000 0.000
#> GSM751347 1 0.4298 0.881 0.912 0.088
#> GSM751348 2 0.9954 0.161 0.460 0.540
#> GSM751349 2 0.0000 0.953 0.000 1.000
#> GSM751352 2 0.9754 0.365 0.408 0.592
#> GSM751353 2 0.2603 0.935 0.044 0.956
#> GSM751354 2 0.4022 0.908 0.080 0.920
#> GSM751355 2 0.1414 0.947 0.020 0.980
#> GSM751358 2 0.0000 0.953 0.000 1.000
#> GSM751359 2 0.0000 0.953 0.000 1.000
#> GSM751294 2 0.0672 0.951 0.008 0.992
#> GSM751296 1 0.0000 0.956 1.000 0.000
#> GSM751297 1 0.1184 0.946 0.984 0.016
#> GSM751299 2 0.7139 0.781 0.196 0.804
#> GSM751300 1 0.0000 0.956 1.000 0.000
#> GSM751301 1 0.0672 0.953 0.992 0.008
#> GSM751302 1 0.0000 0.956 1.000 0.000
#> GSM751303 1 0.0376 0.955 0.996 0.004
#> GSM751306 1 0.0000 0.956 1.000 0.000
#> GSM751308 1 0.6247 0.804 0.844 0.156
#> GSM751309 1 0.0000 0.956 1.000 0.000
#> GSM751311 1 0.0376 0.955 0.996 0.004
#> GSM751312 1 0.0000 0.956 1.000 0.000
#> GSM751313 1 0.0000 0.956 1.000 0.000
#> GSM751315 1 0.0000 0.956 1.000 0.000
#> GSM751317 1 0.0376 0.955 0.996 0.004
#> GSM751320 1 0.0000 0.956 1.000 0.000
#> GSM751321 1 0.0000 0.956 1.000 0.000
#> GSM751322 1 0.0000 0.956 1.000 0.000
#> GSM751324 1 0.0672 0.953 0.992 0.008
#> GSM751325 1 0.0376 0.955 0.996 0.004
#> GSM751332 1 0.1184 0.948 0.984 0.016
#> GSM751334 1 0.0672 0.953 0.992 0.008
#> GSM751339 1 0.0376 0.954 0.996 0.004
#> GSM751341 1 0.0000 0.956 1.000 0.000
#> GSM751343 1 0.0376 0.955 0.996 0.004
#> GSM751344 2 0.1843 0.945 0.028 0.972
#> GSM751345 2 0.4431 0.899 0.092 0.908
#> GSM751356 2 0.2043 0.943 0.032 0.968
#> GSM751357 2 0.1184 0.949 0.016 0.984
#> GSM751293 1 0.0672 0.953 0.992 0.008
#> GSM751295 1 0.0000 0.956 1.000 0.000
#> GSM751319 1 0.0000 0.956 1.000 0.000
#> GSM751323 1 0.0000 0.956 1.000 0.000
#> GSM751326 1 0.0000 0.956 1.000 0.000
#> GSM751327 1 0.0000 0.956 1.000 0.000
#> GSM751328 1 0.0938 0.951 0.988 0.012
#> GSM751329 1 0.0672 0.953 0.992 0.008
#> GSM751330 1 0.0000 0.956 1.000 0.000
#> GSM751331 1 0.0000 0.956 1.000 0.000
#> GSM751333 1 0.0000 0.956 1.000 0.000
#> GSM751335 1 0.0000 0.956 1.000 0.000
#> GSM751336 1 0.0000 0.956 1.000 0.000
#> GSM751337 1 0.0000 0.956 1.000 0.000
#> GSM751338 1 0.0000 0.956 1.000 0.000
#> GSM751340 1 0.4298 0.884 0.912 0.088
#> GSM751350 1 0.0000 0.956 1.000 0.000
#> GSM751351 1 0.0000 0.956 1.000 0.000
#> GSM751362 2 0.2423 0.938 0.040 0.960
#> GSM751363 2 0.9248 0.487 0.340 0.660
#> GSM751367 1 0.0376 0.954 0.996 0.004
#> GSM751368 2 0.0376 0.952 0.004 0.996
#> GSM751371 1 0.5946 0.832 0.856 0.144
#> GSM751375 2 0.0000 0.953 0.000 1.000
#> GSM751376 2 0.2043 0.942 0.032 0.968
#> GSM751378 2 0.0000 0.953 0.000 1.000
#> GSM751379 2 0.2043 0.942 0.032 0.968
#> GSM751382 2 0.0672 0.951 0.008 0.992
#> GSM751386 2 0.0000 0.953 0.000 1.000
#> GSM751388 2 0.0000 0.953 0.000 1.000
#> GSM751391 2 0.3584 0.915 0.068 0.932
#> GSM751410 1 0.9954 0.107 0.540 0.460
#> GSM751414 1 0.6148 0.818 0.848 0.152
#> GSM751361 2 0.0000 0.953 0.000 1.000
#> GSM751365 2 0.0000 0.953 0.000 1.000
#> GSM751366 2 0.9661 0.343 0.392 0.608
#> GSM751369 2 0.1633 0.946 0.024 0.976
#> GSM751370 2 0.5294 0.869 0.120 0.880
#> GSM751372 2 0.0000 0.953 0.000 1.000
#> GSM751373 1 0.9580 0.423 0.620 0.380
#> GSM751374 2 0.2423 0.938 0.040 0.960
#> GSM751377 2 0.0000 0.953 0.000 1.000
#> GSM751380 2 0.9815 0.303 0.420 0.580
#> GSM751381 2 0.0000 0.953 0.000 1.000
#> GSM751383 2 0.0000 0.953 0.000 1.000
#> GSM751384 2 0.0000 0.953 0.000 1.000
#> GSM751385 2 0.0000 0.953 0.000 1.000
#> GSM751387 2 0.0000 0.953 0.000 1.000
#> GSM751389 2 0.0672 0.951 0.008 0.992
#> GSM751393 2 0.0000 0.953 0.000 1.000
#> GSM751394 2 0.0000 0.953 0.000 1.000
#> GSM751395 2 0.0376 0.952 0.004 0.996
#> GSM751397 2 0.0000 0.953 0.000 1.000
#> GSM751398 2 0.0000 0.953 0.000 1.000
#> GSM751404 2 0.0000 0.953 0.000 1.000
#> GSM751406 2 0.1414 0.947 0.020 0.980
#> GSM751411 2 0.0000 0.953 0.000 1.000
#> GSM751413 2 0.0672 0.951 0.008 0.992
#> GSM751415 2 0.0376 0.952 0.004 0.996
#> GSM751416 2 0.0000 0.953 0.000 1.000
#> GSM751417 2 0.0000 0.953 0.000 1.000
#> GSM751421 2 0.3114 0.924 0.056 0.944
#> GSM751422 2 0.0000 0.953 0.000 1.000
#> GSM751360 2 0.3114 0.922 0.056 0.944
#> GSM751364 2 0.0000 0.953 0.000 1.000
#> GSM751390 2 0.0000 0.953 0.000 1.000
#> GSM751392 2 0.0000 0.953 0.000 1.000
#> GSM751396 2 0.0000 0.953 0.000 1.000
#> GSM751399 2 0.0672 0.951 0.008 0.992
#> GSM751400 2 0.0000 0.953 0.000 1.000
#> GSM751401 2 0.1184 0.949 0.016 0.984
#> GSM751402 2 0.1843 0.944 0.028 0.972
#> GSM751403 2 0.0000 0.953 0.000 1.000
#> GSM751405 2 0.1633 0.946 0.024 0.976
#> GSM751407 2 0.0000 0.953 0.000 1.000
#> GSM751408 2 0.0000 0.953 0.000 1.000
#> GSM751409 2 0.0000 0.953 0.000 1.000
#> GSM751412 2 0.0000 0.953 0.000 1.000
#> GSM751418 2 0.0000 0.953 0.000 1.000
#> GSM751419 2 0.0000 0.953 0.000 1.000
#> GSM751420 2 0.0672 0.951 0.008 0.992
#> GSM751425 2 0.0000 0.953 0.000 1.000
#> GSM751429 1 0.9635 0.334 0.612 0.388
#> GSM751430 2 0.4022 0.904 0.080 0.920
#> GSM751433 1 0.9491 0.441 0.632 0.368
#> GSM751437 2 0.4161 0.906 0.084 0.916
#> GSM751448 2 0.4022 0.909 0.080 0.920
#> GSM751451 2 0.9522 0.401 0.372 0.628
#> GSM751423 2 0.0000 0.953 0.000 1.000
#> GSM751424 2 0.0376 0.952 0.004 0.996
#> GSM751428 2 0.2043 0.943 0.032 0.968
#> GSM751431 2 0.0000 0.953 0.000 1.000
#> GSM751432 2 0.0672 0.951 0.008 0.992
#> GSM751434 2 0.6623 0.804 0.172 0.828
#> GSM751435 2 0.3274 0.922 0.060 0.940
#> GSM751436 2 0.6438 0.811 0.164 0.836
#> GSM751440 2 0.6801 0.792 0.180 0.820
#> GSM751444 2 0.0000 0.953 0.000 1.000
#> GSM751446 2 0.0672 0.951 0.008 0.992
#> GSM751449 2 0.0000 0.953 0.000 1.000
#> GSM751450 2 0.4022 0.904 0.080 0.920
#> GSM751452 2 0.1843 0.942 0.028 0.972
#> GSM751426 2 0.5294 0.864 0.120 0.880
#> GSM751427 2 0.0000 0.953 0.000 1.000
#> GSM751438 2 0.0376 0.952 0.004 0.996
#> GSM751439 2 0.2778 0.933 0.048 0.952
#> GSM751441 2 0.0000 0.953 0.000 1.000
#> GSM751442 2 0.4431 0.894 0.092 0.908
#> GSM751443 2 0.3114 0.927 0.056 0.944
#> GSM751445 2 0.0000 0.953 0.000 1.000
#> GSM751447 2 0.0000 0.953 0.000 1.000
#> GSM751453 2 0.0376 0.952 0.004 0.996
#> GSM751454 2 0.0000 0.953 0.000 1.000
#> GSM751455 2 0.0376 0.952 0.004 0.996
#> GSM751456 2 0.0938 0.950 0.012 0.988
#> GSM751457 2 0.0938 0.950 0.012 0.988
#> GSM751458 2 0.0376 0.952 0.004 0.996
cbind(get_classes(res, k = 3), get_membership(res, k = 3))
#> class entropy silhouette p1 p2 p3
#> GSM751298 1 0.0983 0.89440 0.980 0.004 0.016
#> GSM751304 3 0.2152 0.76248 0.016 0.036 0.948
#> GSM751305 2 0.7181 0.28393 0.028 0.564 0.408
#> GSM751307 1 0.6298 0.41847 0.608 0.388 0.004
#> GSM751310 1 0.2152 0.89266 0.948 0.036 0.016
#> GSM751314 1 0.2793 0.88861 0.928 0.044 0.028
#> GSM751316 1 0.3482 0.84487 0.872 0.000 0.128
#> GSM751318 1 0.3692 0.87614 0.896 0.056 0.048
#> GSM751342 1 0.3134 0.88470 0.916 0.052 0.032
#> GSM751346 1 0.6169 0.48113 0.636 0.004 0.360
#> GSM751347 1 0.6516 0.14359 0.516 0.004 0.480
#> GSM751348 2 0.9579 0.04017 0.368 0.432 0.200
#> GSM751349 2 0.1753 0.79234 0.000 0.952 0.048
#> GSM751352 2 0.9937 -0.02167 0.328 0.384 0.288
#> GSM751353 2 0.3983 0.75648 0.048 0.884 0.068
#> GSM751354 3 0.5588 0.69614 0.068 0.124 0.808
#> GSM751355 3 0.6282 0.39713 0.004 0.384 0.612
#> GSM751358 3 0.6057 0.47392 0.004 0.340 0.656
#> GSM751359 2 0.3619 0.75660 0.000 0.864 0.136
#> GSM751294 3 0.1860 0.76125 0.000 0.052 0.948
#> GSM751296 1 0.1399 0.89123 0.968 0.004 0.028
#> GSM751297 3 0.6247 0.27568 0.376 0.004 0.620
#> GSM751299 3 0.9074 0.31019 0.156 0.328 0.516
#> GSM751300 1 0.2200 0.88131 0.940 0.004 0.056
#> GSM751301 1 0.5244 0.70451 0.756 0.240 0.004
#> GSM751302 1 0.3349 0.84850 0.888 0.004 0.108
#> GSM751303 1 0.3155 0.88516 0.916 0.044 0.040
#> GSM751306 1 0.2689 0.89043 0.932 0.036 0.032
#> GSM751308 1 0.7464 0.35889 0.560 0.040 0.400
#> GSM751309 1 0.3042 0.88690 0.920 0.040 0.040
#> GSM751311 1 0.2663 0.88951 0.932 0.044 0.024
#> GSM751312 1 0.1753 0.88809 0.952 0.000 0.048
#> GSM751313 1 0.1411 0.89279 0.964 0.000 0.036
#> GSM751315 1 0.0424 0.89583 0.992 0.000 0.008
#> GSM751317 1 0.2443 0.89254 0.940 0.028 0.032
#> GSM751320 1 0.0592 0.89559 0.988 0.000 0.012
#> GSM751321 1 0.0424 0.89583 0.992 0.000 0.008
#> GSM751322 1 0.2152 0.89233 0.948 0.036 0.016
#> GSM751324 1 0.3039 0.88647 0.920 0.044 0.036
#> GSM751325 1 0.2383 0.89091 0.940 0.044 0.016
#> GSM751332 1 0.2527 0.88985 0.936 0.044 0.020
#> GSM751334 1 0.2414 0.89105 0.940 0.040 0.020
#> GSM751339 1 0.6148 0.53884 0.640 0.004 0.356
#> GSM751341 1 0.1129 0.89311 0.976 0.004 0.020
#> GSM751343 1 0.2793 0.88861 0.928 0.044 0.028
#> GSM751344 2 0.5060 0.70786 0.028 0.816 0.156
#> GSM751345 2 0.7256 0.56817 0.124 0.712 0.164
#> GSM751356 3 0.3722 0.74161 0.024 0.088 0.888
#> GSM751357 3 0.5723 0.62124 0.016 0.240 0.744
#> GSM751293 1 0.5443 0.67730 0.736 0.260 0.004
#> GSM751295 1 0.4233 0.79977 0.836 0.004 0.160
#> GSM751319 1 0.0237 0.89549 0.996 0.000 0.004
#> GSM751323 1 0.0424 0.89507 0.992 0.000 0.008
#> GSM751326 1 0.0592 0.89443 0.988 0.000 0.012
#> GSM751327 1 0.1905 0.89414 0.956 0.028 0.016
#> GSM751328 1 0.2229 0.89071 0.944 0.044 0.012
#> GSM751329 1 0.1950 0.89264 0.952 0.040 0.008
#> GSM751330 1 0.0983 0.89363 0.980 0.004 0.016
#> GSM751331 1 0.2301 0.87954 0.936 0.004 0.060
#> GSM751333 1 0.0747 0.89424 0.984 0.000 0.016
#> GSM751335 1 0.0829 0.89400 0.984 0.004 0.012
#> GSM751336 1 0.2400 0.87747 0.932 0.004 0.064
#> GSM751337 1 0.1163 0.89486 0.972 0.000 0.028
#> GSM751338 1 0.2261 0.88628 0.932 0.000 0.068
#> GSM751340 3 0.6309 -0.19710 0.500 0.000 0.500
#> GSM751350 1 0.3112 0.85883 0.900 0.004 0.096
#> GSM751351 1 0.2496 0.87566 0.928 0.004 0.068
#> GSM751362 3 0.1015 0.75652 0.008 0.012 0.980
#> GSM751363 3 0.9577 -0.00331 0.196 0.400 0.404
#> GSM751367 1 0.4047 0.81770 0.848 0.004 0.148
#> GSM751368 2 0.1878 0.79485 0.004 0.952 0.044
#> GSM751371 1 0.6761 0.65596 0.700 0.048 0.252
#> GSM751375 2 0.1753 0.79234 0.000 0.952 0.048
#> GSM751376 3 0.1647 0.75991 0.004 0.036 0.960
#> GSM751378 3 0.4291 0.70759 0.000 0.180 0.820
#> GSM751379 3 0.1399 0.75984 0.004 0.028 0.968
#> GSM751382 2 0.1289 0.79328 0.000 0.968 0.032
#> GSM751386 2 0.4399 0.70045 0.000 0.812 0.188
#> GSM751388 2 0.1529 0.79314 0.000 0.960 0.040
#> GSM751391 3 0.6431 0.67344 0.084 0.156 0.760
#> GSM751410 3 0.2031 0.73941 0.032 0.016 0.952
#> GSM751414 3 0.7839 0.27740 0.380 0.060 0.560
#> GSM751361 2 0.6081 0.44998 0.004 0.652 0.344
#> GSM751365 2 0.6008 0.39040 0.000 0.628 0.372
#> GSM751366 3 0.5731 0.70372 0.088 0.108 0.804
#> GSM751369 3 0.1267 0.75871 0.004 0.024 0.972
#> GSM751370 3 0.6148 0.61114 0.028 0.244 0.728
#> GSM751372 3 0.6468 0.18320 0.004 0.444 0.552
#> GSM751373 2 0.7782 0.49310 0.248 0.652 0.100
#> GSM751374 3 0.1877 0.75993 0.012 0.032 0.956
#> GSM751377 2 0.4062 0.72655 0.000 0.836 0.164
#> GSM751380 3 0.4887 0.71381 0.096 0.060 0.844
#> GSM751381 2 0.4796 0.66051 0.000 0.780 0.220
#> GSM751383 2 0.3038 0.77045 0.000 0.896 0.104
#> GSM751384 2 0.6235 0.22344 0.000 0.564 0.436
#> GSM751385 3 0.6244 0.21057 0.000 0.440 0.560
#> GSM751387 2 0.1643 0.79283 0.000 0.956 0.044
#> GSM751389 3 0.2165 0.75831 0.000 0.064 0.936
#> GSM751393 3 0.5291 0.60799 0.000 0.268 0.732
#> GSM751394 2 0.2066 0.79126 0.000 0.940 0.060
#> GSM751395 3 0.5431 0.57103 0.000 0.284 0.716
#> GSM751397 2 0.5760 0.49878 0.000 0.672 0.328
#> GSM751398 2 0.2711 0.78119 0.000 0.912 0.088
#> GSM751404 3 0.4178 0.71392 0.000 0.172 0.828
#> GSM751406 3 0.1163 0.75913 0.000 0.028 0.972
#> GSM751411 3 0.6111 0.34535 0.000 0.396 0.604
#> GSM751413 2 0.3459 0.78094 0.012 0.892 0.096
#> GSM751415 3 0.1878 0.76133 0.004 0.044 0.952
#> GSM751416 2 0.6111 0.37191 0.000 0.604 0.396
#> GSM751417 2 0.5859 0.47450 0.000 0.656 0.344
#> GSM751421 3 0.4280 0.73425 0.020 0.124 0.856
#> GSM751422 3 0.4047 0.72697 0.004 0.148 0.848
#> GSM751360 2 0.8206 0.03602 0.072 0.480 0.448
#> GSM751364 2 0.6264 0.37918 0.004 0.616 0.380
#> GSM751390 2 0.5988 0.39828 0.000 0.632 0.368
#> GSM751392 2 0.1753 0.79234 0.000 0.952 0.048
#> GSM751396 2 0.1129 0.79153 0.004 0.976 0.020
#> GSM751399 3 0.3116 0.74936 0.000 0.108 0.892
#> GSM751400 3 0.6286 0.11631 0.000 0.464 0.536
#> GSM751401 3 0.2448 0.76006 0.000 0.076 0.924
#> GSM751402 3 0.0747 0.75819 0.000 0.016 0.984
#> GSM751403 3 0.2066 0.75973 0.000 0.060 0.940
#> GSM751405 3 0.1163 0.75913 0.000 0.028 0.972
#> GSM751407 3 0.4654 0.68154 0.000 0.208 0.792
#> GSM751408 3 0.6062 0.40432 0.000 0.384 0.616
#> GSM751409 3 0.5138 0.63871 0.000 0.252 0.748
#> GSM751412 3 0.5591 0.57115 0.000 0.304 0.696
#> GSM751418 2 0.5785 0.52899 0.004 0.696 0.300
#> GSM751419 2 0.5982 0.47975 0.004 0.668 0.328
#> GSM751420 3 0.3116 0.74818 0.000 0.108 0.892
#> GSM751425 2 0.1753 0.79234 0.000 0.952 0.048
#> GSM751429 3 0.5202 0.60622 0.220 0.008 0.772
#> GSM751430 2 0.1315 0.78532 0.020 0.972 0.008
#> GSM751433 2 0.2383 0.75500 0.044 0.940 0.016
#> GSM751437 3 0.1015 0.75552 0.012 0.008 0.980
#> GSM751448 3 0.1643 0.74048 0.044 0.000 0.956
#> GSM751451 2 0.2806 0.75112 0.040 0.928 0.032
#> GSM751423 2 0.1753 0.79448 0.000 0.952 0.048
#> GSM751424 2 0.0592 0.78243 0.012 0.988 0.000
#> GSM751428 2 0.2269 0.79314 0.016 0.944 0.040
#> GSM751431 2 0.0829 0.78359 0.012 0.984 0.004
#> GSM751432 2 0.1031 0.79306 0.000 0.976 0.024
#> GSM751434 2 0.1031 0.77959 0.024 0.976 0.000
#> GSM751435 2 0.1620 0.79005 0.024 0.964 0.012
#> GSM751436 2 0.1399 0.77377 0.028 0.968 0.004
#> GSM751440 2 0.1585 0.77486 0.028 0.964 0.008
#> GSM751444 2 0.2066 0.79357 0.000 0.940 0.060
#> GSM751446 2 0.5178 0.62222 0.000 0.744 0.256
#> GSM751449 2 0.5650 0.50573 0.000 0.688 0.312
#> GSM751450 2 0.1289 0.77364 0.032 0.968 0.000
#> GSM751452 2 0.0592 0.78243 0.012 0.988 0.000
#> GSM751426 2 0.0892 0.77953 0.020 0.980 0.000
#> GSM751427 2 0.2625 0.78526 0.000 0.916 0.084
#> GSM751438 2 0.6308 -0.01800 0.000 0.508 0.492
#> GSM751439 3 0.5036 0.66937 0.020 0.172 0.808
#> GSM751441 2 0.2165 0.79105 0.000 0.936 0.064
#> GSM751442 2 0.4563 0.70971 0.036 0.852 0.112
#> GSM751443 3 0.2116 0.74566 0.040 0.012 0.948
#> GSM751445 2 0.4555 0.68671 0.000 0.800 0.200
#> GSM751447 2 0.1643 0.79283 0.000 0.956 0.044
#> GSM751453 2 0.1031 0.79306 0.000 0.976 0.024
#> GSM751454 2 0.1163 0.79314 0.000 0.972 0.028
#> GSM751455 2 0.4293 0.71205 0.004 0.832 0.164
#> GSM751456 2 0.4110 0.71605 0.004 0.844 0.152
#> GSM751457 3 0.5859 0.46167 0.000 0.344 0.656
#> GSM751458 3 0.5465 0.57317 0.000 0.288 0.712
cbind(get_classes(res, k = 4), get_membership(res, k = 4))
#> class entropy silhouette p1 p2 p3 p4
#> GSM751298 4 0.4981 -0.026454 0.464 0.000 0.000 0.536
#> GSM751304 3 0.6159 0.374347 0.112 0.004 0.680 0.204
#> GSM751305 3 0.7298 0.421554 0.292 0.128 0.564 0.016
#> GSM751307 1 0.8007 0.084403 0.380 0.268 0.004 0.348
#> GSM751310 1 0.1824 0.662636 0.936 0.000 0.004 0.060
#> GSM751314 1 0.0188 0.675324 0.996 0.000 0.000 0.004
#> GSM751316 1 0.4706 0.582472 0.788 0.000 0.072 0.140
#> GSM751318 1 0.0564 0.671690 0.988 0.004 0.004 0.004
#> GSM751342 1 0.0524 0.671625 0.988 0.008 0.000 0.004
#> GSM751346 4 0.1661 0.462388 0.052 0.000 0.004 0.944
#> GSM751347 4 0.1978 0.456705 0.068 0.000 0.004 0.928
#> GSM751348 1 0.7516 0.237817 0.560 0.280 0.024 0.136
#> GSM751349 2 0.0000 0.818674 0.000 1.000 0.000 0.000
#> GSM751352 4 0.6284 0.369823 0.012 0.228 0.088 0.672
#> GSM751353 2 0.3498 0.724373 0.000 0.832 0.008 0.160
#> GSM751354 4 0.3351 0.460731 0.000 0.008 0.148 0.844
#> GSM751355 4 0.6646 0.205765 0.000 0.156 0.224 0.620
#> GSM751358 1 0.9690 -0.035968 0.364 0.176 0.268 0.192
#> GSM751359 2 0.4855 0.073847 0.000 0.600 0.400 0.000
#> GSM751294 3 0.6370 -0.033356 0.032 0.016 0.476 0.476
#> GSM751296 4 0.4916 0.073748 0.424 0.000 0.000 0.576
#> GSM751297 4 0.0657 0.469882 0.004 0.000 0.012 0.984
#> GSM751299 4 0.4102 0.460985 0.004 0.056 0.104 0.836
#> GSM751300 4 0.4907 0.082104 0.420 0.000 0.000 0.580
#> GSM751301 1 0.7811 0.130305 0.412 0.268 0.000 0.320
#> GSM751302 4 0.4222 0.314349 0.272 0.000 0.000 0.728
#> GSM751303 1 0.0524 0.672385 0.988 0.000 0.008 0.004
#> GSM751306 1 0.0376 0.675379 0.992 0.000 0.004 0.004
#> GSM751308 1 0.7469 0.048350 0.504 0.052 0.060 0.384
#> GSM751309 1 0.0524 0.672385 0.988 0.000 0.008 0.004
#> GSM751311 1 0.0000 0.674767 1.000 0.000 0.000 0.000
#> GSM751312 1 0.5161 0.123093 0.520 0.000 0.004 0.476
#> GSM751313 1 0.5000 0.060079 0.500 0.000 0.000 0.500
#> GSM751315 1 0.4304 0.487995 0.716 0.000 0.000 0.284
#> GSM751317 1 0.0524 0.674166 0.988 0.000 0.004 0.008
#> GSM751320 1 0.3024 0.616566 0.852 0.000 0.000 0.148
#> GSM751321 1 0.4477 0.449710 0.688 0.000 0.000 0.312
#> GSM751322 1 0.0469 0.675205 0.988 0.000 0.000 0.012
#> GSM751324 1 0.0000 0.674767 1.000 0.000 0.000 0.000
#> GSM751325 1 0.0336 0.675590 0.992 0.000 0.000 0.008
#> GSM751332 1 0.1398 0.668245 0.956 0.004 0.000 0.040
#> GSM751334 1 0.0336 0.675238 0.992 0.000 0.000 0.008
#> GSM751339 1 0.5664 0.420706 0.720 0.000 0.156 0.124
#> GSM751341 1 0.5396 0.116934 0.524 0.000 0.012 0.464
#> GSM751343 1 0.0188 0.673896 0.996 0.000 0.000 0.004
#> GSM751344 2 0.4544 0.687293 0.000 0.788 0.048 0.164
#> GSM751345 2 0.5325 0.626591 0.000 0.728 0.068 0.204
#> GSM751356 4 0.7566 0.085769 0.100 0.028 0.388 0.484
#> GSM751357 4 0.8341 0.075541 0.092 0.088 0.352 0.468
#> GSM751293 1 0.7694 0.192328 0.448 0.308 0.000 0.244
#> GSM751295 4 0.3486 0.390161 0.188 0.000 0.000 0.812
#> GSM751319 1 0.4916 0.248374 0.576 0.000 0.000 0.424
#> GSM751323 1 0.3528 0.581927 0.808 0.000 0.000 0.192
#> GSM751326 1 0.4730 0.353474 0.636 0.000 0.000 0.364
#> GSM751327 1 0.0707 0.674669 0.980 0.000 0.000 0.020
#> GSM751328 1 0.2281 0.644547 0.904 0.000 0.000 0.096
#> GSM751329 1 0.4585 0.403943 0.668 0.000 0.000 0.332
#> GSM751330 4 0.4989 -0.048535 0.472 0.000 0.000 0.528
#> GSM751331 4 0.4941 0.046089 0.436 0.000 0.000 0.564
#> GSM751333 1 0.5165 0.095147 0.512 0.000 0.004 0.484
#> GSM751335 4 0.4992 -0.060303 0.476 0.000 0.000 0.524
#> GSM751336 4 0.4925 0.065354 0.428 0.000 0.000 0.572
#> GSM751337 1 0.4164 0.507488 0.736 0.000 0.000 0.264
#> GSM751338 1 0.2282 0.646148 0.924 0.000 0.052 0.024
#> GSM751340 1 0.7540 0.056441 0.480 0.000 0.304 0.216
#> GSM751350 4 0.4103 0.330471 0.256 0.000 0.000 0.744
#> GSM751351 4 0.4500 0.254811 0.316 0.000 0.000 0.684
#> GSM751362 3 0.2408 0.494704 0.000 0.000 0.896 0.104
#> GSM751363 3 0.6537 0.501274 0.200 0.164 0.636 0.000
#> GSM751367 4 0.7393 -0.032944 0.400 0.000 0.164 0.436
#> GSM751368 2 0.5320 0.000393 0.012 0.572 0.416 0.000
#> GSM751371 1 0.2924 0.604107 0.884 0.000 0.100 0.016
#> GSM751375 2 0.0188 0.817289 0.000 0.996 0.004 0.000
#> GSM751376 3 0.5158 0.008940 0.000 0.004 0.524 0.472
#> GSM751378 3 0.7401 0.369862 0.004 0.164 0.512 0.320
#> GSM751379 3 0.4989 0.015206 0.000 0.000 0.528 0.472
#> GSM751382 2 0.0188 0.817289 0.000 0.996 0.004 0.000
#> GSM751386 3 0.4948 0.369055 0.000 0.440 0.560 0.000
#> GSM751388 2 0.4955 -0.101741 0.000 0.556 0.444 0.000
#> GSM751391 1 0.8087 0.191177 0.536 0.064 0.280 0.120
#> GSM751410 3 0.5962 0.333152 0.080 0.000 0.660 0.260
#> GSM751414 3 0.4615 0.480382 0.240 0.008 0.744 0.008
#> GSM751361 3 0.7413 0.419242 0.252 0.232 0.516 0.000
#> GSM751365 3 0.5465 0.424224 0.020 0.392 0.588 0.000
#> GSM751366 3 0.2197 0.565480 0.048 0.024 0.928 0.000
#> GSM751369 3 0.5349 0.246250 0.024 0.000 0.640 0.336
#> GSM751370 3 0.4126 0.586977 0.040 0.088 0.848 0.024
#> GSM751372 3 0.4661 0.543464 0.016 0.256 0.728 0.000
#> GSM751373 3 0.7250 0.371124 0.160 0.336 0.504 0.000
#> GSM751374 3 0.4989 0.015206 0.000 0.000 0.528 0.472
#> GSM751377 3 0.4916 0.387729 0.000 0.424 0.576 0.000
#> GSM751380 3 0.3271 0.536530 0.132 0.000 0.856 0.012
#> GSM751381 3 0.4941 0.374234 0.000 0.436 0.564 0.000
#> GSM751383 3 0.4967 0.345272 0.000 0.452 0.548 0.000
#> GSM751384 3 0.4804 0.441707 0.000 0.384 0.616 0.000
#> GSM751385 3 0.4406 0.520506 0.000 0.300 0.700 0.000
#> GSM751387 2 0.4585 0.253038 0.000 0.668 0.332 0.000
#> GSM751389 3 0.3219 0.445714 0.000 0.000 0.836 0.164
#> GSM751393 3 0.4327 0.564033 0.000 0.216 0.768 0.016
#> GSM751394 3 0.5000 0.235924 0.000 0.496 0.504 0.000
#> GSM751395 3 0.6440 0.542595 0.000 0.208 0.644 0.148
#> GSM751397 3 0.4888 0.407308 0.000 0.412 0.588 0.000
#> GSM751398 3 0.5163 0.282162 0.000 0.480 0.516 0.004
#> GSM751404 3 0.3547 0.582123 0.000 0.144 0.840 0.016
#> GSM751406 3 0.4961 0.063144 0.000 0.000 0.552 0.448
#> GSM751411 3 0.4072 0.548954 0.000 0.252 0.748 0.000
#> GSM751413 3 0.5838 0.323879 0.032 0.444 0.524 0.000
#> GSM751415 3 0.3176 0.536298 0.084 0.000 0.880 0.036
#> GSM751416 3 0.4522 0.491152 0.000 0.320 0.680 0.000
#> GSM751417 3 0.4776 0.445997 0.000 0.376 0.624 0.000
#> GSM751421 3 0.2799 0.539996 0.108 0.000 0.884 0.008
#> GSM751422 3 0.3249 0.535291 0.140 0.000 0.852 0.008
#> GSM751360 3 0.5643 0.236810 0.440 0.016 0.540 0.004
#> GSM751364 3 0.4872 0.464180 0.004 0.356 0.640 0.000
#> GSM751390 3 0.4948 0.372281 0.000 0.440 0.560 0.000
#> GSM751392 2 0.4830 0.070632 0.000 0.608 0.392 0.000
#> GSM751396 2 0.2125 0.759572 0.004 0.920 0.076 0.000
#> GSM751399 3 0.1356 0.566257 0.000 0.032 0.960 0.008
#> GSM751400 3 0.5007 0.467150 0.000 0.356 0.636 0.008
#> GSM751401 3 0.2739 0.543468 0.000 0.036 0.904 0.060
#> GSM751402 3 0.4605 0.243095 0.000 0.000 0.664 0.336
#> GSM751403 3 0.5062 0.313982 0.000 0.020 0.680 0.300
#> GSM751405 3 0.4790 0.184111 0.000 0.000 0.620 0.380
#> GSM751407 3 0.4158 0.554965 0.000 0.224 0.768 0.008
#> GSM751408 3 0.4535 0.527216 0.000 0.292 0.704 0.004
#> GSM751409 3 0.3157 0.585179 0.000 0.144 0.852 0.004
#> GSM751412 3 0.4222 0.538910 0.000 0.272 0.728 0.000
#> GSM751418 3 0.5070 0.401562 0.004 0.416 0.580 0.000
#> GSM751419 3 0.5039 0.417299 0.004 0.404 0.592 0.000
#> GSM751420 3 0.6659 0.091605 0.000 0.084 0.468 0.448
#> GSM751425 2 0.0000 0.818674 0.000 1.000 0.000 0.000
#> GSM751429 4 0.3289 0.461450 0.004 0.004 0.140 0.852
#> GSM751430 2 0.1847 0.786331 0.004 0.940 0.052 0.004
#> GSM751433 2 0.3208 0.735339 0.148 0.848 0.004 0.000
#> GSM751437 3 0.5147 0.035688 0.004 0.000 0.536 0.460
#> GSM751448 4 0.5167 0.016915 0.004 0.000 0.488 0.508
#> GSM751451 2 0.4843 0.333437 0.396 0.604 0.000 0.000
#> GSM751423 2 0.0657 0.820018 0.004 0.984 0.012 0.000
#> GSM751424 2 0.0895 0.820405 0.020 0.976 0.004 0.000
#> GSM751428 2 0.1209 0.816683 0.000 0.964 0.004 0.032
#> GSM751431 2 0.0817 0.820243 0.024 0.976 0.000 0.000
#> GSM751432 2 0.0376 0.818463 0.004 0.992 0.004 0.000
#> GSM751434 2 0.1004 0.820059 0.024 0.972 0.004 0.000
#> GSM751435 2 0.0921 0.818560 0.000 0.972 0.000 0.028
#> GSM751436 2 0.1576 0.811945 0.048 0.948 0.004 0.000
#> GSM751440 2 0.2714 0.768111 0.112 0.884 0.000 0.004
#> GSM751444 2 0.2731 0.772812 0.004 0.896 0.092 0.008
#> GSM751446 2 0.4290 0.633721 0.000 0.772 0.212 0.016
#> GSM751449 2 0.4595 0.653065 0.000 0.776 0.184 0.040
#> GSM751450 2 0.2081 0.790383 0.084 0.916 0.000 0.000
#> GSM751452 2 0.0657 0.820356 0.012 0.984 0.004 0.000
#> GSM751426 2 0.1211 0.815268 0.040 0.960 0.000 0.000
#> GSM751427 2 0.0927 0.819514 0.000 0.976 0.016 0.008
#> GSM751438 2 0.6712 0.294387 0.000 0.552 0.344 0.104
#> GSM751439 4 0.6642 0.074189 0.000 0.084 0.424 0.492
#> GSM751441 2 0.0927 0.819131 0.000 0.976 0.016 0.008
#> GSM751442 2 0.3501 0.786855 0.044 0.884 0.040 0.032
#> GSM751443 4 0.5406 0.030611 0.000 0.012 0.480 0.508
#> GSM751445 2 0.3051 0.769331 0.000 0.884 0.088 0.028
#> GSM751447 2 0.0336 0.819440 0.000 0.992 0.000 0.008
#> GSM751453 2 0.0000 0.818674 0.000 1.000 0.000 0.000
#> GSM751454 2 0.0188 0.819578 0.004 0.996 0.000 0.000
#> GSM751455 2 0.2140 0.803574 0.008 0.932 0.052 0.008
#> GSM751456 2 0.2271 0.803238 0.012 0.928 0.052 0.008
#> GSM751457 3 0.7768 -0.025337 0.000 0.240 0.400 0.360
#> GSM751458 3 0.7697 -0.014375 0.000 0.220 0.404 0.376
cbind(get_classes(res, k = 5), get_membership(res, k = 5))
#> class entropy silhouette p1 p2 p3 p4 p5
#> GSM751298 1 0.1644 0.8248 0.940 0.004 0.008 0.048 0.000
#> GSM751304 5 0.7060 0.2096 0.032 0.028 0.084 0.368 0.488
#> GSM751305 4 0.7554 0.3852 0.020 0.088 0.204 0.552 0.136
#> GSM751307 1 0.4850 0.7385 0.772 0.080 0.052 0.096 0.000
#> GSM751310 4 0.4835 0.2959 0.384 0.004 0.020 0.592 0.000
#> GSM751314 4 0.1924 0.7781 0.064 0.008 0.004 0.924 0.000
#> GSM751316 4 0.6536 0.3019 0.372 0.028 0.012 0.516 0.072
#> GSM751318 4 0.0912 0.7793 0.012 0.016 0.000 0.972 0.000
#> GSM751342 4 0.1012 0.7789 0.012 0.020 0.000 0.968 0.000
#> GSM751346 1 0.3242 0.7339 0.816 0.000 0.000 0.012 0.172
#> GSM751347 1 0.1717 0.8106 0.936 0.000 0.004 0.008 0.052
#> GSM751348 4 0.5216 0.5943 0.024 0.180 0.000 0.716 0.080
#> GSM751349 2 0.2017 0.8622 0.000 0.912 0.080 0.008 0.000
#> GSM751352 5 0.7510 0.2938 0.256 0.284 0.000 0.044 0.416
#> GSM751353 2 0.4189 0.7581 0.152 0.796 0.012 0.012 0.028
#> GSM751354 1 0.5435 0.0940 0.512 0.000 0.060 0.000 0.428
#> GSM751355 3 0.6047 0.3770 0.292 0.016 0.588 0.000 0.104
#> GSM751358 4 0.5724 0.5178 0.020 0.088 0.004 0.664 0.224
#> GSM751359 2 0.6317 0.0546 0.012 0.464 0.448 0.044 0.032
#> GSM751294 5 0.4025 0.7178 0.020 0.048 0.020 0.076 0.836
#> GSM751296 1 0.1281 0.8286 0.956 0.000 0.000 0.032 0.012
#> GSM751297 1 0.2625 0.7788 0.876 0.000 0.016 0.000 0.108
#> GSM751299 5 0.6838 0.3388 0.328 0.104 0.004 0.044 0.520
#> GSM751300 1 0.0609 0.8271 0.980 0.000 0.000 0.020 0.000
#> GSM751301 1 0.7044 0.0309 0.360 0.332 0.000 0.300 0.008
#> GSM751302 1 0.1469 0.8203 0.948 0.000 0.000 0.016 0.036
#> GSM751303 4 0.1365 0.7822 0.040 0.004 0.004 0.952 0.000
#> GSM751306 4 0.1443 0.7815 0.044 0.004 0.004 0.948 0.000
#> GSM751308 4 0.5544 0.4657 0.028 0.048 0.000 0.636 0.288
#> GSM751309 4 0.1205 0.7822 0.040 0.000 0.004 0.956 0.000
#> GSM751311 4 0.1626 0.7814 0.044 0.016 0.000 0.940 0.000
#> GSM751312 1 0.1526 0.8263 0.948 0.004 0.004 0.040 0.004
#> GSM751313 1 0.2761 0.7983 0.872 0.000 0.024 0.104 0.000
#> GSM751315 1 0.3816 0.5434 0.696 0.000 0.000 0.304 0.000
#> GSM751317 4 0.2767 0.7733 0.040 0.024 0.004 0.900 0.032
#> GSM751320 4 0.3730 0.5698 0.288 0.000 0.000 0.712 0.000
#> GSM751321 1 0.3388 0.7213 0.792 0.000 0.008 0.200 0.000
#> GSM751322 4 0.1774 0.7803 0.052 0.016 0.000 0.932 0.000
#> GSM751324 4 0.1626 0.7814 0.044 0.016 0.000 0.940 0.000
#> GSM751325 4 0.1701 0.7812 0.048 0.016 0.000 0.936 0.000
#> GSM751332 4 0.3777 0.6799 0.192 0.020 0.004 0.784 0.000
#> GSM751334 4 0.1956 0.7733 0.076 0.008 0.000 0.916 0.000
#> GSM751339 4 0.4245 0.6662 0.016 0.028 0.000 0.768 0.188
#> GSM751341 1 0.6756 0.3980 0.532 0.012 0.008 0.272 0.176
#> GSM751343 4 0.1626 0.7814 0.044 0.016 0.000 0.940 0.000
#> GSM751344 2 0.6588 0.6039 0.144 0.660 0.036 0.044 0.116
#> GSM751345 2 0.7092 0.4694 0.148 0.588 0.024 0.044 0.196
#> GSM751356 5 0.4524 0.7009 0.028 0.056 0.016 0.096 0.804
#> GSM751357 5 0.5610 0.6621 0.032 0.096 0.024 0.116 0.732
#> GSM751293 4 0.6873 0.2508 0.216 0.316 0.000 0.456 0.012
#> GSM751295 1 0.1710 0.8186 0.940 0.000 0.004 0.016 0.040
#> GSM751319 1 0.1965 0.8063 0.904 0.000 0.000 0.096 0.000
#> GSM751323 4 0.3366 0.6652 0.232 0.000 0.000 0.768 0.000
#> GSM751326 1 0.3766 0.6348 0.728 0.004 0.000 0.268 0.000
#> GSM751327 4 0.2130 0.7770 0.080 0.012 0.000 0.908 0.000
#> GSM751328 4 0.3852 0.6460 0.220 0.020 0.000 0.760 0.000
#> GSM751329 1 0.3427 0.7262 0.796 0.012 0.000 0.192 0.000
#> GSM751330 1 0.1043 0.8251 0.960 0.000 0.000 0.040 0.000
#> GSM751331 1 0.0510 0.8270 0.984 0.000 0.000 0.016 0.000
#> GSM751333 1 0.3982 0.7297 0.792 0.020 0.000 0.168 0.020
#> GSM751335 1 0.1043 0.8251 0.960 0.000 0.000 0.040 0.000
#> GSM751336 1 0.0880 0.8266 0.968 0.000 0.000 0.032 0.000
#> GSM751337 4 0.4537 0.3354 0.396 0.012 0.000 0.592 0.000
#> GSM751338 4 0.3566 0.7620 0.056 0.028 0.000 0.852 0.064
#> GSM751340 4 0.5498 0.1157 0.020 0.028 0.000 0.484 0.468
#> GSM751350 1 0.0898 0.8220 0.972 0.000 0.000 0.008 0.020
#> GSM751351 1 0.0451 0.8252 0.988 0.000 0.000 0.008 0.004
#> GSM751362 3 0.4294 0.0478 0.000 0.000 0.532 0.000 0.468
#> GSM751363 3 0.1808 0.8373 0.000 0.004 0.936 0.040 0.020
#> GSM751367 1 0.5099 0.6622 0.716 0.000 0.204 0.044 0.036
#> GSM751368 3 0.3093 0.8305 0.000 0.168 0.824 0.008 0.000
#> GSM751371 4 0.1988 0.7636 0.008 0.016 0.000 0.928 0.048
#> GSM751375 2 0.3642 0.8119 0.020 0.820 0.144 0.016 0.000
#> GSM751376 5 0.1708 0.7796 0.016 0.004 0.032 0.004 0.944
#> GSM751378 5 0.5145 0.7228 0.004 0.068 0.128 0.048 0.752
#> GSM751379 5 0.1648 0.7821 0.020 0.000 0.040 0.000 0.940
#> GSM751382 2 0.3003 0.8447 0.020 0.872 0.092 0.016 0.000
#> GSM751386 3 0.1671 0.8644 0.000 0.076 0.924 0.000 0.000
#> GSM751388 3 0.2230 0.8539 0.000 0.116 0.884 0.000 0.000
#> GSM751391 4 0.3759 0.6808 0.004 0.036 0.004 0.816 0.140
#> GSM751410 5 0.5951 0.2979 0.000 0.000 0.116 0.364 0.520
#> GSM751414 3 0.1830 0.8268 0.000 0.000 0.932 0.040 0.028
#> GSM751361 3 0.5515 0.6578 0.000 0.056 0.680 0.224 0.040
#> GSM751365 3 0.1831 0.8670 0.000 0.076 0.920 0.004 0.000
#> GSM751366 3 0.1877 0.8161 0.000 0.000 0.924 0.012 0.064
#> GSM751369 5 0.2589 0.7733 0.000 0.008 0.048 0.044 0.900
#> GSM751370 3 0.1195 0.8350 0.000 0.000 0.960 0.012 0.028
#> GSM751372 3 0.0898 0.8602 0.000 0.020 0.972 0.000 0.008
#> GSM751373 3 0.2504 0.8629 0.000 0.064 0.896 0.040 0.000
#> GSM751374 5 0.1893 0.7821 0.024 0.000 0.048 0.000 0.928
#> GSM751377 3 0.1608 0.8656 0.000 0.072 0.928 0.000 0.000
#> GSM751380 3 0.4312 0.7202 0.000 0.000 0.772 0.104 0.124
#> GSM751381 3 0.2574 0.8513 0.000 0.112 0.876 0.012 0.000
#> GSM751383 3 0.2561 0.8438 0.000 0.144 0.856 0.000 0.000
#> GSM751384 3 0.1544 0.8662 0.000 0.068 0.932 0.000 0.000
#> GSM751385 3 0.2396 0.8664 0.004 0.068 0.904 0.000 0.024
#> GSM751387 3 0.4395 0.6799 0.012 0.272 0.704 0.012 0.000
#> GSM751389 5 0.4161 0.3751 0.000 0.000 0.392 0.000 0.608
#> GSM751393 3 0.3323 0.8443 0.012 0.044 0.864 0.004 0.076
#> GSM751394 3 0.1792 0.8630 0.000 0.084 0.916 0.000 0.000
#> GSM751395 5 0.6631 0.2539 0.024 0.040 0.384 0.044 0.508
#> GSM751397 3 0.1732 0.8637 0.000 0.080 0.920 0.000 0.000
#> GSM751398 3 0.1732 0.8637 0.000 0.080 0.920 0.000 0.000
#> GSM751404 3 0.2863 0.8392 0.000 0.060 0.876 0.000 0.064
#> GSM751406 5 0.1830 0.7810 0.008 0.000 0.068 0.000 0.924
#> GSM751411 3 0.0609 0.8440 0.000 0.000 0.980 0.000 0.020
#> GSM751413 3 0.1798 0.8671 0.000 0.064 0.928 0.004 0.004
#> GSM751415 3 0.5516 0.4368 0.000 0.000 0.608 0.096 0.296
#> GSM751416 3 0.1412 0.8646 0.000 0.036 0.952 0.008 0.004
#> GSM751417 3 0.1270 0.8662 0.000 0.052 0.948 0.000 0.000
#> GSM751421 3 0.4177 0.7116 0.000 0.004 0.776 0.052 0.168
#> GSM751422 3 0.4859 0.6690 0.000 0.004 0.732 0.112 0.152
#> GSM751360 4 0.5378 0.3450 0.000 0.024 0.352 0.596 0.028
#> GSM751364 3 0.0963 0.8649 0.000 0.036 0.964 0.000 0.000
#> GSM751390 3 0.3196 0.8112 0.000 0.192 0.804 0.000 0.004
#> GSM751392 3 0.3611 0.7743 0.004 0.208 0.780 0.008 0.000
#> GSM751396 2 0.4029 0.5154 0.004 0.680 0.316 0.000 0.000
#> GSM751399 3 0.2561 0.7831 0.000 0.000 0.856 0.000 0.144
#> GSM751400 3 0.3048 0.8230 0.000 0.176 0.820 0.000 0.004
#> GSM751401 3 0.4464 0.5646 0.000 0.028 0.684 0.000 0.288
#> GSM751402 5 0.3266 0.7193 0.004 0.000 0.200 0.000 0.796
#> GSM751403 5 0.3013 0.7511 0.000 0.008 0.160 0.000 0.832
#> GSM751405 5 0.2074 0.7770 0.000 0.000 0.104 0.000 0.896
#> GSM751407 3 0.3098 0.8359 0.000 0.148 0.836 0.000 0.016
#> GSM751408 3 0.1894 0.8661 0.000 0.072 0.920 0.000 0.008
#> GSM751409 3 0.2079 0.8333 0.000 0.020 0.916 0.000 0.064
#> GSM751412 3 0.1872 0.8630 0.000 0.052 0.928 0.000 0.020
#> GSM751418 3 0.1608 0.8678 0.000 0.072 0.928 0.000 0.000
#> GSM751419 3 0.1792 0.8661 0.000 0.084 0.916 0.000 0.000
#> GSM751420 5 0.3359 0.7746 0.016 0.064 0.060 0.000 0.860
#> GSM751425 2 0.2278 0.8571 0.000 0.908 0.060 0.000 0.032
#> GSM751429 1 0.4757 0.6200 0.716 0.000 0.080 0.000 0.204
#> GSM751430 2 0.5037 0.5659 0.056 0.664 0.276 0.004 0.000
#> GSM751433 2 0.1952 0.8345 0.000 0.912 0.004 0.084 0.000
#> GSM751437 5 0.2189 0.7783 0.012 0.000 0.084 0.000 0.904
#> GSM751448 5 0.1877 0.7799 0.012 0.000 0.064 0.000 0.924
#> GSM751451 2 0.3424 0.6700 0.000 0.760 0.000 0.240 0.000
#> GSM751423 2 0.3320 0.8371 0.000 0.856 0.096 0.016 0.032
#> GSM751424 2 0.1124 0.8717 0.000 0.960 0.036 0.004 0.000
#> GSM751428 2 0.1549 0.8708 0.016 0.944 0.040 0.000 0.000
#> GSM751431 2 0.1106 0.8715 0.000 0.964 0.024 0.012 0.000
#> GSM751432 2 0.1768 0.8600 0.004 0.924 0.072 0.000 0.000
#> GSM751434 2 0.2238 0.8591 0.020 0.912 0.064 0.004 0.000
#> GSM751435 2 0.1168 0.8726 0.008 0.960 0.032 0.000 0.000
#> GSM751436 2 0.1195 0.8712 0.000 0.960 0.028 0.012 0.000
#> GSM751440 2 0.1717 0.8547 0.000 0.936 0.008 0.052 0.004
#> GSM751444 2 0.3018 0.8220 0.000 0.876 0.024 0.020 0.080
#> GSM751446 2 0.4149 0.7417 0.004 0.792 0.080 0.000 0.124
#> GSM751449 2 0.3595 0.8000 0.004 0.828 0.048 0.000 0.120
#> GSM751450 2 0.1522 0.8587 0.000 0.944 0.012 0.044 0.000
#> GSM751452 2 0.1124 0.8717 0.000 0.960 0.036 0.004 0.000
#> GSM751426 2 0.1195 0.8712 0.000 0.960 0.028 0.012 0.000
#> GSM751427 2 0.2152 0.8674 0.004 0.920 0.044 0.000 0.032
#> GSM751438 2 0.4443 0.6401 0.008 0.724 0.028 0.000 0.240
#> GSM751439 5 0.3745 0.7591 0.012 0.088 0.068 0.000 0.832
#> GSM751441 2 0.1988 0.8714 0.008 0.928 0.048 0.000 0.016
#> GSM751442 2 0.1777 0.8625 0.012 0.944 0.004 0.020 0.020
#> GSM751443 5 0.1970 0.7806 0.012 0.004 0.060 0.000 0.924
#> GSM751445 2 0.3130 0.8301 0.000 0.856 0.048 0.000 0.096
#> GSM751447 2 0.1484 0.8713 0.000 0.944 0.048 0.000 0.008
#> GSM751453 2 0.1043 0.8704 0.000 0.960 0.040 0.000 0.000
#> GSM751454 2 0.1043 0.8704 0.000 0.960 0.040 0.000 0.000
#> GSM751455 2 0.1554 0.8720 0.004 0.952 0.024 0.008 0.012
#> GSM751456 2 0.1554 0.8708 0.004 0.952 0.024 0.008 0.012
#> GSM751457 5 0.4408 0.6285 0.008 0.224 0.032 0.000 0.736
#> GSM751458 5 0.3463 0.7428 0.008 0.124 0.032 0.000 0.836
cbind(get_classes(res, k = 6), get_membership(res, k = 6))
#> class entropy silhouette p1 p2 p3 p4 p5 p6
#> GSM751298 1 0.1988 0.82077 0.912 0.000 0.004 0.072 0.004 0.008
#> GSM751304 6 0.3181 0.65239 0.000 0.004 0.068 0.052 0.020 0.856
#> GSM751305 6 0.4534 0.53422 0.000 0.008 0.020 0.204 0.044 0.724
#> GSM751307 1 0.5882 0.67672 0.700 0.064 0.012 0.092 0.052 0.080
#> GSM751310 4 0.4960 0.42443 0.312 0.000 0.000 0.620 0.028 0.040
#> GSM751314 4 0.1837 0.79088 0.044 0.000 0.004 0.928 0.004 0.020
#> GSM751316 4 0.6472 0.35663 0.280 0.000 0.008 0.440 0.012 0.260
#> GSM751318 4 0.0993 0.79465 0.000 0.012 0.000 0.964 0.000 0.024
#> GSM751342 4 0.0820 0.79584 0.000 0.012 0.000 0.972 0.000 0.016
#> GSM751346 1 0.1088 0.83370 0.960 0.000 0.024 0.000 0.000 0.016
#> GSM751347 1 0.0520 0.83816 0.984 0.000 0.008 0.000 0.000 0.008
#> GSM751348 6 0.5674 0.45987 0.000 0.116 0.008 0.348 0.004 0.524
#> GSM751349 2 0.4813 0.44049 0.000 0.648 0.000 0.000 0.104 0.248
#> GSM751352 6 0.4195 0.64674 0.172 0.024 0.040 0.004 0.000 0.760
#> GSM751353 6 0.4962 0.54912 0.092 0.276 0.004 0.000 0.000 0.628
#> GSM751354 1 0.5126 0.08738 0.544 0.000 0.052 0.000 0.016 0.388
#> GSM751355 5 0.6261 0.15116 0.292 0.000 0.016 0.000 0.460 0.232
#> GSM751358 6 0.3720 0.60064 0.000 0.012 0.020 0.208 0.000 0.760
#> GSM751359 6 0.4769 0.53565 0.000 0.068 0.000 0.008 0.272 0.652
#> GSM751294 6 0.2760 0.65821 0.000 0.016 0.100 0.012 0.004 0.868
#> GSM751296 1 0.1053 0.83754 0.964 0.000 0.004 0.020 0.000 0.012
#> GSM751297 1 0.1321 0.83023 0.952 0.000 0.024 0.000 0.004 0.020
#> GSM751299 6 0.4041 0.64221 0.172 0.020 0.044 0.000 0.000 0.764
#> GSM751300 1 0.0146 0.83855 0.996 0.000 0.000 0.000 0.000 0.004
#> GSM751301 6 0.6584 0.45314 0.244 0.064 0.000 0.188 0.000 0.504
#> GSM751302 1 0.0146 0.83796 0.996 0.000 0.000 0.000 0.004 0.000
#> GSM751303 4 0.1285 0.79185 0.000 0.000 0.000 0.944 0.004 0.052
#> GSM751306 4 0.1080 0.79692 0.004 0.000 0.000 0.960 0.004 0.032
#> GSM751308 6 0.3819 0.63088 0.000 0.004 0.052 0.176 0.000 0.768
#> GSM751309 4 0.0713 0.79591 0.000 0.000 0.000 0.972 0.000 0.028
#> GSM751311 4 0.1078 0.79737 0.008 0.012 0.000 0.964 0.000 0.016
#> GSM751312 1 0.1801 0.82427 0.924 0.000 0.000 0.016 0.004 0.056
#> GSM751313 1 0.2252 0.81732 0.900 0.000 0.012 0.072 0.000 0.016
#> GSM751315 1 0.4079 0.33951 0.608 0.000 0.000 0.380 0.004 0.008
#> GSM751317 4 0.2879 0.72736 0.004 0.000 0.000 0.816 0.004 0.176
#> GSM751320 4 0.3298 0.62763 0.236 0.000 0.000 0.756 0.000 0.008
#> GSM751321 1 0.3680 0.66792 0.744 0.000 0.000 0.232 0.004 0.020
#> GSM751322 4 0.0713 0.79781 0.028 0.000 0.000 0.972 0.000 0.000
#> GSM751324 4 0.0260 0.79716 0.008 0.000 0.000 0.992 0.000 0.000
#> GSM751325 4 0.0891 0.79828 0.024 0.008 0.000 0.968 0.000 0.000
#> GSM751332 4 0.2165 0.76008 0.108 0.000 0.000 0.884 0.000 0.008
#> GSM751334 4 0.1141 0.79139 0.052 0.000 0.000 0.948 0.000 0.000
#> GSM751339 4 0.4393 0.52070 0.000 0.000 0.044 0.640 0.000 0.316
#> GSM751341 1 0.4702 0.35340 0.572 0.000 0.016 0.388 0.000 0.024
#> GSM751343 4 0.0820 0.79554 0.000 0.012 0.000 0.972 0.000 0.016
#> GSM751344 6 0.4316 0.66561 0.072 0.124 0.012 0.004 0.012 0.776
#> GSM751345 6 0.3350 0.68287 0.068 0.076 0.012 0.004 0.000 0.840
#> GSM751356 6 0.2685 0.66706 0.000 0.016 0.080 0.020 0.004 0.880
#> GSM751357 6 0.2730 0.67289 0.004 0.028 0.068 0.012 0.004 0.884
#> GSM751293 6 0.6767 0.48234 0.140 0.092 0.004 0.260 0.000 0.504
#> GSM751295 1 0.0405 0.83659 0.988 0.000 0.008 0.000 0.004 0.000
#> GSM751319 1 0.1686 0.82390 0.924 0.000 0.000 0.064 0.000 0.012
#> GSM751323 4 0.3287 0.67896 0.220 0.000 0.000 0.768 0.000 0.012
#> GSM751326 1 0.3861 0.50319 0.640 0.000 0.000 0.352 0.000 0.008
#> GSM751327 4 0.2407 0.79165 0.056 0.004 0.000 0.892 0.000 0.048
#> GSM751328 4 0.2695 0.73123 0.144 0.008 0.000 0.844 0.000 0.004
#> GSM751329 1 0.3782 0.68943 0.752 0.016 0.000 0.216 0.000 0.016
#> GSM751330 1 0.0508 0.83834 0.984 0.000 0.000 0.004 0.000 0.012
#> GSM751331 1 0.0603 0.83771 0.980 0.000 0.004 0.000 0.000 0.016
#> GSM751333 1 0.3068 0.77740 0.840 0.000 0.000 0.072 0.000 0.088
#> GSM751335 1 0.0508 0.83834 0.984 0.000 0.000 0.004 0.000 0.012
#> GSM751336 1 0.0363 0.83788 0.988 0.000 0.000 0.000 0.000 0.012
#> GSM751337 4 0.3976 0.30799 0.380 0.000 0.004 0.612 0.000 0.004
#> GSM751338 4 0.3736 0.63796 0.008 0.000 0.008 0.716 0.000 0.268
#> GSM751340 4 0.6054 0.12741 0.004 0.000 0.180 0.412 0.004 0.400
#> GSM751350 1 0.0603 0.83687 0.980 0.000 0.004 0.000 0.000 0.016
#> GSM751351 1 0.0603 0.83687 0.980 0.000 0.004 0.000 0.000 0.016
#> GSM751362 3 0.3014 0.63518 0.000 0.000 0.804 0.000 0.184 0.012
#> GSM751363 5 0.2165 0.79133 0.004 0.000 0.008 0.024 0.912 0.052
#> GSM751367 1 0.6066 0.60780 0.652 0.000 0.128 0.064 0.124 0.032
#> GSM751368 5 0.3264 0.74812 0.000 0.136 0.004 0.000 0.820 0.040
#> GSM751371 4 0.2700 0.73844 0.000 0.000 0.004 0.836 0.004 0.156
#> GSM751375 6 0.5879 0.24961 0.000 0.376 0.008 0.000 0.156 0.460
#> GSM751376 3 0.3742 0.42284 0.004 0.000 0.648 0.000 0.000 0.348
#> GSM751378 3 0.6460 -0.04645 0.000 0.032 0.412 0.000 0.188 0.368
#> GSM751379 3 0.3052 0.59957 0.004 0.000 0.780 0.000 0.000 0.216
#> GSM751382 2 0.5602 -0.10683 0.004 0.476 0.004 0.000 0.108 0.408
#> GSM751386 5 0.2263 0.77307 0.000 0.016 0.000 0.000 0.884 0.100
#> GSM751388 5 0.2201 0.78828 0.000 0.048 0.000 0.000 0.900 0.052
#> GSM751391 4 0.3915 0.61114 0.000 0.000 0.020 0.704 0.004 0.272
#> GSM751410 3 0.3676 0.63970 0.000 0.000 0.808 0.088 0.092 0.012
#> GSM751414 5 0.3250 0.77109 0.012 0.000 0.052 0.048 0.860 0.028
#> GSM751361 5 0.5956 0.20119 0.000 0.004 0.000 0.316 0.472 0.208
#> GSM751365 5 0.0976 0.79909 0.000 0.008 0.008 0.016 0.968 0.000
#> GSM751366 5 0.3352 0.73414 0.000 0.000 0.144 0.024 0.816 0.016
#> GSM751369 3 0.4644 0.50528 0.000 0.000 0.660 0.068 0.004 0.268
#> GSM751370 5 0.1605 0.79627 0.000 0.000 0.012 0.016 0.940 0.032
#> GSM751372 5 0.1586 0.79935 0.000 0.004 0.004 0.012 0.940 0.040
#> GSM751373 5 0.2289 0.79703 0.000 0.024 0.008 0.036 0.912 0.020
#> GSM751374 3 0.3337 0.57110 0.004 0.000 0.736 0.000 0.000 0.260
#> GSM751377 5 0.0862 0.79990 0.000 0.008 0.004 0.000 0.972 0.016
#> GSM751380 5 0.5184 0.52708 0.000 0.000 0.256 0.088 0.636 0.020
#> GSM751381 5 0.3534 0.60610 0.000 0.016 0.000 0.000 0.740 0.244
#> GSM751383 5 0.2488 0.78790 0.000 0.076 0.000 0.000 0.880 0.044
#> GSM751384 5 0.1668 0.79429 0.000 0.008 0.004 0.000 0.928 0.060
#> GSM751385 5 0.4092 0.39156 0.000 0.020 0.000 0.000 0.636 0.344
#> GSM751387 5 0.5728 0.03967 0.000 0.168 0.000 0.000 0.452 0.380
#> GSM751389 3 0.4991 -0.01238 0.000 0.000 0.476 0.000 0.456 0.068
#> GSM751393 6 0.5014 0.23956 0.000 0.008 0.056 0.000 0.392 0.544
#> GSM751394 5 0.1720 0.79576 0.000 0.040 0.000 0.000 0.928 0.032
#> GSM751395 6 0.4208 0.59406 0.000 0.028 0.140 0.000 0.064 0.768
#> GSM751397 5 0.1802 0.78786 0.000 0.012 0.000 0.000 0.916 0.072
#> GSM751398 5 0.2641 0.78102 0.000 0.048 0.004 0.000 0.876 0.072
#> GSM751404 5 0.3796 0.69648 0.000 0.032 0.188 0.000 0.768 0.012
#> GSM751406 3 0.1901 0.67329 0.004 0.000 0.912 0.000 0.008 0.076
#> GSM751411 5 0.1377 0.79775 0.000 0.004 0.024 0.004 0.952 0.016
#> GSM751413 5 0.3151 0.77500 0.000 0.052 0.004 0.016 0.856 0.072
#> GSM751415 3 0.5029 0.01119 0.000 0.000 0.492 0.052 0.448 0.008
#> GSM751416 5 0.0972 0.79913 0.000 0.008 0.000 0.000 0.964 0.028
#> GSM751417 5 0.0891 0.79863 0.000 0.008 0.000 0.000 0.968 0.024
#> GSM751421 5 0.5302 0.38594 0.000 0.000 0.340 0.048 0.576 0.036
#> GSM751422 5 0.5902 0.49231 0.000 0.000 0.184 0.156 0.608 0.052
#> GSM751360 4 0.4932 0.52430 0.000 0.000 0.000 0.644 0.228 0.128
#> GSM751364 5 0.1218 0.79900 0.000 0.004 0.000 0.012 0.956 0.028
#> GSM751390 5 0.4424 0.71193 0.000 0.156 0.016 0.000 0.740 0.088
#> GSM751392 5 0.5335 0.37454 0.000 0.140 0.000 0.000 0.568 0.292
#> GSM751396 2 0.5121 -0.00238 0.000 0.492 0.008 0.000 0.440 0.060
#> GSM751399 5 0.2618 0.75860 0.000 0.000 0.116 0.000 0.860 0.024
#> GSM751400 5 0.4457 0.69069 0.000 0.168 0.028 0.000 0.740 0.064
#> GSM751401 5 0.4803 0.12706 0.000 0.020 0.464 0.000 0.496 0.020
#> GSM751402 3 0.2346 0.66255 0.000 0.000 0.868 0.000 0.124 0.008
#> GSM751403 3 0.3992 0.63991 0.000 0.000 0.760 0.000 0.136 0.104
#> GSM751405 3 0.2003 0.68277 0.000 0.000 0.912 0.000 0.044 0.044
#> GSM751407 5 0.4029 0.73166 0.000 0.124 0.068 0.000 0.784 0.024
#> GSM751408 5 0.2475 0.78808 0.000 0.060 0.036 0.000 0.892 0.012
#> GSM751409 5 0.3287 0.67425 0.000 0.000 0.220 0.000 0.768 0.012
#> GSM751412 5 0.2476 0.78633 0.000 0.032 0.072 0.000 0.888 0.008
#> GSM751418 5 0.1490 0.79971 0.000 0.024 0.008 0.016 0.948 0.004
#> GSM751419 5 0.1268 0.79901 0.000 0.036 0.008 0.004 0.952 0.000
#> GSM751420 3 0.3253 0.67592 0.004 0.040 0.856 0.000 0.044 0.056
#> GSM751425 2 0.2781 0.80506 0.000 0.868 0.008 0.000 0.040 0.084
#> GSM751429 1 0.5191 0.18771 0.496 0.000 0.448 0.020 0.016 0.020
#> GSM751430 2 0.5732 0.46713 0.020 0.604 0.008 0.000 0.240 0.128
#> GSM751433 2 0.2334 0.82592 0.000 0.904 0.004 0.040 0.008 0.044
#> GSM751437 3 0.1204 0.67620 0.004 0.016 0.960 0.000 0.016 0.004
#> GSM751448 3 0.1082 0.67484 0.004 0.000 0.956 0.000 0.000 0.040
#> GSM751451 2 0.2520 0.75755 0.000 0.844 0.000 0.152 0.000 0.004
#> GSM751423 2 0.3594 0.78451 0.000 0.832 0.016 0.012 0.064 0.076
#> GSM751424 2 0.2206 0.82137 0.000 0.904 0.008 0.000 0.024 0.064
#> GSM751428 2 0.2208 0.83342 0.012 0.912 0.008 0.000 0.016 0.052
#> GSM751431 2 0.0748 0.84254 0.000 0.976 0.004 0.004 0.000 0.016
#> GSM751432 2 0.2753 0.80232 0.000 0.872 0.008 0.000 0.048 0.072
#> GSM751434 2 0.2905 0.80531 0.004 0.872 0.008 0.004 0.040 0.072
#> GSM751435 2 0.1116 0.84632 0.008 0.960 0.028 0.000 0.000 0.004
#> GSM751436 2 0.2232 0.82449 0.000 0.908 0.008 0.008 0.016 0.060
#> GSM751440 2 0.1370 0.84519 0.000 0.948 0.036 0.012 0.000 0.004
#> GSM751444 2 0.2257 0.81000 0.000 0.876 0.116 0.000 0.000 0.008
#> GSM751446 2 0.3340 0.72539 0.000 0.784 0.196 0.000 0.016 0.004
#> GSM751449 2 0.3348 0.76934 0.000 0.812 0.152 0.000 0.020 0.016
#> GSM751450 2 0.1251 0.84584 0.000 0.956 0.012 0.024 0.000 0.008
#> GSM751452 2 0.2123 0.82302 0.000 0.908 0.008 0.000 0.020 0.064
#> GSM751426 2 0.0748 0.84195 0.000 0.976 0.004 0.004 0.000 0.016
#> GSM751427 2 0.2110 0.83305 0.000 0.900 0.084 0.000 0.012 0.004
#> GSM751438 2 0.3534 0.65749 0.000 0.740 0.244 0.000 0.000 0.016
#> GSM751439 3 0.3448 0.47441 0.000 0.280 0.716 0.000 0.000 0.004
#> GSM751441 2 0.2208 0.84137 0.008 0.912 0.052 0.000 0.012 0.016
#> GSM751442 2 0.1555 0.84049 0.004 0.932 0.060 0.000 0.000 0.004
#> GSM751443 3 0.1320 0.66836 0.000 0.036 0.948 0.000 0.000 0.016
#> GSM751445 2 0.3171 0.81736 0.000 0.856 0.060 0.000 0.040 0.044
#> GSM751447 2 0.1555 0.84384 0.000 0.940 0.040 0.000 0.008 0.012
#> GSM751453 2 0.0260 0.84424 0.000 0.992 0.000 0.000 0.000 0.008
#> GSM751454 2 0.0146 0.84479 0.000 0.996 0.000 0.000 0.000 0.004
#> GSM751455 2 0.1471 0.83991 0.000 0.932 0.064 0.000 0.000 0.004
#> GSM751456 2 0.1387 0.83934 0.000 0.932 0.068 0.000 0.000 0.000
#> GSM751457 3 0.5361 0.01077 0.000 0.444 0.448 0.000 0.000 0.108
#> GSM751458 3 0.5479 0.17800 0.000 0.388 0.484 0.000 0.000 0.128
Heatmaps for the consensus matrix. It visualizes the probability of two samples to be in a same group.
consensus_heatmap(res, k = 2)
consensus_heatmap(res, k = 3)
consensus_heatmap(res, k = 4)
consensus_heatmap(res, k = 5)
consensus_heatmap(res, k = 6)
Heatmaps for the membership of samples in all partitions to see how consistent they are:
membership_heatmap(res, k = 2)
membership_heatmap(res, k = 3)
membership_heatmap(res, k = 4)
membership_heatmap(res, k = 5)
membership_heatmap(res, k = 6)
As soon as we have had the classes for columns, we can look for signatures which are significantly different between classes which can be candidate marks for certain classes. Following are the heatmaps for signatures.
Signature heatmaps where rows are scaled:
get_signatures(res, k = 2)
get_signatures(res, k = 3)
get_signatures(res, k = 4)
get_signatures(res, k = 5)
get_signatures(res, k = 6)
Signature heatmaps where rows are not scaled:
get_signatures(res, k = 2, scale_rows = FALSE)
get_signatures(res, k = 3, scale_rows = FALSE)
get_signatures(res, k = 4, scale_rows = FALSE)
get_signatures(res, k = 5, scale_rows = FALSE)
get_signatures(res, k = 6, scale_rows = FALSE)
Compare the overlap of signatures from different k:
compare_signatures(res)
get_signature() returns a data frame invisibly. TO get the list of signatures, the function
call should be assigned to a variable explicitly. In following code, if plot argument is set
to FALSE, no heatmap is plotted while only the differential analysis is performed.
# code only for demonstration
tb = get_signature(res, k = ..., plot = FALSE)
An example of the output of tb is:
#> which_row fdr mean_1 mean_2 scaled_mean_1 scaled_mean_2 km
#> 1 38 0.042760348 8.373488 9.131774 -0.5533452 0.5164555 1
#> 2 40 0.018707592 7.106213 8.469186 -0.6173731 0.5762149 1
#> 3 55 0.019134737 10.221463 11.207825 -0.6159697 0.5749050 1
#> 4 59 0.006059896 5.921854 7.869574 -0.6899429 0.6439467 1
#> 5 60 0.018055526 8.928898 10.211722 -0.6204761 0.5791110 1
#> 6 98 0.009384629 15.714769 14.887706 0.6635654 -0.6193277 2
...
The columns in tb are:
which_row: row indices corresponding to the input matrix.fdr: FDR for the differential test. mean_x: The mean value in group x.scaled_mean_x: The mean value in group x after rows are scaled.km: Row groups if k-means clustering is applied to rows.UMAP plot which shows how samples are separated.
dimension_reduction(res, k = 2, method = "UMAP")
dimension_reduction(res, k = 3, method = "UMAP")
dimension_reduction(res, k = 4, method = "UMAP")
dimension_reduction(res, k = 5, method = "UMAP")
dimension_reduction(res, k = 6, method = "UMAP")
Following heatmap shows how subgroups are split when increasing k:
collect_classes(res)
Test correlation between subgroups and known annotations. If the known annotation is numeric, one-way ANOVA test is applied, and if the known annotation is discrete, chi-squared contingency table test is applied.
test_to_known_factors(res)
#> n tissue(p) disease.state(p) agent(p) k
#> MAD:NMF 156 2.47e-21 1.000 0.9812 2
#> MAD:NMF 134 4.04e-24 0.439 0.7087 3
#> MAD:NMF 76 4.36e-23 0.202 0.4334 4
#> MAD:NMF 144 3.24e-38 0.505 0.2700 5
#> MAD:NMF 134 2.16e-43 0.123 0.0433 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 4537 rows and 166 columns.
#> Top rows (454, 908, 1361, 1814, 2268) are extracted by 'ATC' method.
#> Subgroups are detected by 'hclust' method.
#> Performed in total 1250 partitions by row resampling.
#> Best k for subgroups seems to be 2.
#>
#> Following methods can be applied to this 'ConsensusPartition' object:
#> [1] "cola_report" "collect_classes" "collect_plots"
#> [4] "collect_stats" "colnames" "compare_signatures"
#> [7] "consensus_heatmap" "dimension_reduction" "functional_enrichment"
#> [10] "get_anno_col" "get_anno" "get_classes"
#> [13] "get_consensus" "get_matrix" "get_membership"
#> [16] "get_param" "get_signatures" "get_stats"
#> [19] "is_best_k" "is_stable_k" "membership_heatmap"
#> [22] "ncol" "nrow" "plot_ecdf"
#> [25] "rownames" "select_partition_number" "show"
#> [28] "suggest_best_k" "test_to_known_factors"
collect_plots() function collects all the plots made from res for all k (number of partitions)
into one single page to provide an easy and fast comparison between different k.
collect_plots(res)
The plots are:
k and the heatmap of
predicted classes for each k.k.k.k.All the plots in panels can be made by individual functions and they are plotted later in this section.
select_partition_number() produces several plots showing different
statistics for choosing “optimized” k. There are following statistics:
k;k, the area increased is defined as \(A_k - A_{k-1}\).The detailed explanations of these statistics can be found in the cola vignette.
Generally speaking, lower PAC score, higher mean silhouette score or higher
concordance corresponds to better partition. Rand index and Jaccard index
measure how similar the current partition is compared to partition with k-1.
If they are too similar, we won't accept k is better than k-1.
select_partition_number(res)
The numeric values for all these statistics can be obtained by get_stats().
get_stats(res)
#> k 1-PAC mean_silhouette concordance area_increased Rand Jaccard
#> 2 2 0.155 0.666 0.813 0.4599 0.500 0.500
#> 3 3 0.227 0.512 0.734 0.2806 0.880 0.763
#> 4 4 0.290 0.513 0.704 0.1510 0.907 0.773
#> 5 5 0.396 0.465 0.661 0.1006 0.922 0.765
#> 6 6 0.493 0.482 0.687 0.0503 0.957 0.837
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
#> GSM751298 1 0.574 0.7504 0.864 0.136
#> GSM751304 2 0.563 0.8022 0.132 0.868
#> GSM751305 2 0.563 0.8022 0.132 0.868
#> GSM751307 2 0.456 0.8233 0.096 0.904
#> GSM751310 1 0.388 0.7540 0.924 0.076
#> GSM751314 1 0.373 0.7536 0.928 0.072
#> GSM751316 1 0.388 0.7540 0.924 0.076
#> GSM751318 1 0.595 0.7340 0.856 0.144
#> GSM751342 1 0.781 0.7017 0.768 0.232
#> GSM751346 1 0.563 0.7481 0.868 0.132
#> GSM751347 1 0.574 0.7476 0.864 0.136
#> GSM751348 2 0.634 0.7916 0.160 0.840
#> GSM751349 2 0.204 0.8375 0.032 0.968
#> GSM751352 2 0.327 0.8361 0.060 0.940
#> GSM751353 2 0.295 0.8333 0.052 0.948
#> GSM751354 2 0.402 0.8152 0.080 0.920
#> GSM751355 2 0.402 0.8152 0.080 0.920
#> GSM751358 2 0.529 0.8221 0.120 0.880
#> GSM751359 2 0.327 0.8384 0.060 0.940
#> GSM751294 2 0.955 0.3605 0.376 0.624
#> GSM751296 1 0.574 0.7519 0.864 0.136
#> GSM751297 1 0.563 0.7481 0.868 0.132
#> GSM751299 2 0.662 0.7631 0.172 0.828
#> GSM751300 1 0.541 0.7510 0.876 0.124
#> GSM751301 2 0.402 0.8365 0.080 0.920
#> GSM751302 1 0.552 0.7488 0.872 0.128
#> GSM751303 1 0.373 0.7536 0.928 0.072
#> GSM751306 1 0.373 0.7536 0.928 0.072
#> GSM751308 2 0.992 0.0425 0.448 0.552
#> GSM751309 1 0.416 0.7527 0.916 0.084
#> GSM751311 1 0.416 0.7527 0.916 0.084
#> GSM751312 1 0.388 0.7540 0.924 0.076
#> GSM751313 1 0.163 0.7356 0.976 0.024
#> GSM751315 1 0.388 0.7540 0.924 0.076
#> GSM751317 1 0.388 0.7540 0.924 0.076
#> GSM751320 1 0.278 0.7466 0.952 0.048
#> GSM751321 1 0.388 0.7540 0.924 0.076
#> GSM751322 1 0.278 0.7466 0.952 0.048
#> GSM751324 1 0.278 0.7466 0.952 0.048
#> GSM751325 1 0.278 0.7466 0.952 0.048
#> GSM751332 1 0.327 0.7484 0.940 0.060
#> GSM751334 1 0.327 0.7484 0.940 0.060
#> GSM751339 1 0.343 0.7488 0.936 0.064
#> GSM751341 1 0.574 0.7534 0.864 0.136
#> GSM751343 1 0.456 0.7420 0.904 0.096
#> GSM751344 2 0.278 0.8308 0.048 0.952
#> GSM751345 2 0.278 0.8308 0.048 0.952
#> GSM751356 2 0.952 0.3723 0.372 0.628
#> GSM751357 2 0.952 0.3723 0.372 0.628
#> GSM751293 2 0.402 0.8365 0.080 0.920
#> GSM751295 1 0.552 0.7488 0.872 0.128
#> GSM751319 1 0.388 0.7540 0.924 0.076
#> GSM751323 1 0.278 0.7466 0.952 0.048
#> GSM751326 1 0.184 0.7378 0.972 0.028
#> GSM751327 1 0.184 0.7378 0.972 0.028
#> GSM751328 1 0.327 0.7484 0.940 0.060
#> GSM751329 1 0.278 0.7495 0.952 0.048
#> GSM751330 1 0.343 0.7543 0.936 0.064
#> GSM751331 1 0.402 0.7533 0.920 0.080
#> GSM751333 1 0.184 0.7378 0.972 0.028
#> GSM751335 1 0.343 0.7543 0.936 0.064
#> GSM751336 1 0.278 0.7473 0.952 0.048
#> GSM751337 1 0.204 0.7431 0.968 0.032
#> GSM751338 1 0.343 0.7488 0.936 0.064
#> GSM751340 1 0.343 0.7488 0.936 0.064
#> GSM751350 1 0.430 0.7535 0.912 0.088
#> GSM751351 1 0.430 0.7535 0.912 0.088
#> GSM751362 1 0.921 0.5809 0.664 0.336
#> GSM751363 1 0.999 0.1871 0.520 0.480
#> GSM751367 1 0.584 0.7473 0.860 0.140
#> GSM751368 1 0.999 0.1825 0.516 0.484
#> GSM751371 1 0.839 0.6796 0.732 0.268
#> GSM751375 2 0.224 0.8401 0.036 0.964
#> GSM751376 2 0.494 0.8220 0.108 0.892
#> GSM751378 2 0.494 0.8250 0.108 0.892
#> GSM751379 2 0.494 0.8220 0.108 0.892
#> GSM751382 2 0.224 0.8401 0.036 0.964
#> GSM751386 2 0.260 0.8424 0.044 0.956
#> GSM751388 2 0.242 0.8412 0.040 0.960
#> GSM751391 1 0.895 0.6359 0.688 0.312
#> GSM751410 1 0.904 0.6215 0.680 0.320
#> GSM751414 1 0.722 0.7260 0.800 0.200
#> GSM751361 1 0.996 0.2703 0.536 0.464
#> GSM751365 1 0.932 0.5798 0.652 0.348
#> GSM751366 1 0.839 0.6753 0.732 0.268
#> GSM751369 1 0.929 0.6060 0.656 0.344
#> GSM751370 1 0.821 0.6808 0.744 0.256
#> GSM751372 1 0.891 0.6300 0.692 0.308
#> GSM751373 1 0.821 0.6867 0.744 0.256
#> GSM751374 2 0.494 0.8220 0.108 0.892
#> GSM751377 2 0.855 0.6396 0.280 0.720
#> GSM751380 1 0.943 0.5597 0.640 0.360
#> GSM751381 2 0.242 0.8412 0.040 0.960
#> GSM751383 2 0.327 0.8444 0.060 0.940
#> GSM751384 2 0.295 0.8427 0.052 0.948
#> GSM751385 2 0.469 0.8396 0.100 0.900
#> GSM751387 2 0.224 0.8401 0.036 0.964
#> GSM751389 1 0.999 0.2759 0.520 0.480
#> GSM751393 2 0.494 0.8220 0.108 0.892
#> GSM751394 2 0.224 0.8401 0.036 0.964
#> GSM751395 2 0.494 0.8220 0.108 0.892
#> GSM751397 2 0.242 0.8412 0.040 0.960
#> GSM751398 2 0.278 0.8424 0.048 0.952
#> GSM751404 1 0.993 0.3466 0.548 0.452
#> GSM751406 1 1.000 0.2313 0.508 0.492
#> GSM751411 2 0.946 0.3731 0.364 0.636
#> GSM751413 1 1.000 0.1268 0.504 0.496
#> GSM751415 1 0.999 0.2759 0.520 0.480
#> GSM751416 1 0.992 0.3224 0.552 0.448
#> GSM751417 1 0.992 0.3224 0.552 0.448
#> GSM751421 1 0.839 0.6796 0.732 0.268
#> GSM751422 1 0.839 0.6796 0.732 0.268
#> GSM751360 1 0.855 0.6729 0.720 0.280
#> GSM751364 1 0.985 0.3992 0.572 0.428
#> GSM751390 2 0.295 0.8427 0.052 0.948
#> GSM751392 2 0.224 0.8401 0.036 0.964
#> GSM751396 2 0.224 0.8401 0.036 0.964
#> GSM751399 1 1.000 0.2313 0.508 0.492
#> GSM751400 1 1.000 0.2313 0.508 0.492
#> GSM751401 1 1.000 0.2313 0.508 0.492
#> GSM751402 1 1.000 0.2313 0.508 0.492
#> GSM751403 1 1.000 0.2313 0.508 0.492
#> GSM751405 1 1.000 0.2313 0.508 0.492
#> GSM751407 1 1.000 0.2043 0.500 0.500
#> GSM751408 1 1.000 0.2229 0.504 0.496
#> GSM751409 2 0.963 0.2708 0.388 0.612
#> GSM751412 1 1.000 0.2237 0.504 0.496
#> GSM751418 1 0.895 0.6185 0.688 0.312
#> GSM751419 1 0.895 0.6185 0.688 0.312
#> GSM751420 1 0.999 0.2561 0.516 0.484
#> GSM751425 2 0.224 0.8395 0.036 0.964
#> GSM751429 1 0.584 0.7473 0.860 0.140
#> GSM751430 2 0.541 0.8221 0.124 0.876
#> GSM751433 2 0.895 0.5715 0.312 0.688
#> GSM751437 2 0.991 0.0198 0.444 0.556
#> GSM751448 1 0.998 0.2953 0.528 0.472
#> GSM751451 2 0.921 0.5026 0.336 0.664
#> GSM751423 2 0.653 0.7848 0.168 0.832
#> GSM751424 2 0.886 0.5898 0.304 0.696
#> GSM751428 2 0.529 0.8262 0.120 0.880
#> GSM751431 2 0.895 0.5715 0.312 0.688
#> GSM751432 2 0.541 0.8221 0.124 0.876
#> GSM751434 2 0.541 0.8221 0.124 0.876
#> GSM751435 2 0.775 0.7159 0.228 0.772
#> GSM751436 2 0.895 0.5715 0.312 0.688
#> GSM751440 2 0.775 0.7159 0.228 0.772
#> GSM751444 2 0.260 0.8399 0.044 0.956
#> GSM751446 2 0.745 0.7356 0.212 0.788
#> GSM751449 2 0.278 0.8421 0.048 0.952
#> GSM751450 2 0.671 0.7788 0.176 0.824
#> GSM751452 2 0.886 0.5898 0.304 0.696
#> GSM751426 2 0.886 0.5898 0.304 0.696
#> GSM751427 2 0.529 0.8262 0.120 0.880
#> GSM751438 2 0.278 0.8413 0.048 0.952
#> GSM751439 2 0.775 0.7147 0.228 0.772
#> GSM751441 2 0.260 0.8399 0.044 0.956
#> GSM751442 2 0.745 0.7356 0.212 0.788
#> GSM751443 1 0.998 0.2953 0.528 0.472
#> GSM751445 2 0.242 0.8406 0.040 0.960
#> GSM751447 2 0.260 0.8399 0.044 0.956
#> GSM751453 2 0.260 0.8399 0.044 0.956
#> GSM751454 2 0.260 0.8399 0.044 0.956
#> GSM751455 2 0.745 0.7356 0.212 0.788
#> GSM751456 2 0.745 0.7356 0.212 0.788
#> GSM751457 2 0.260 0.8421 0.044 0.956
#> GSM751458 2 0.260 0.8421 0.044 0.956
cbind(get_classes(res, k = 3), get_membership(res, k = 3))
#> class entropy silhouette p1 p2 p3
#> GSM751298 1 0.453 0.6919 0.856 0.040 0.104
#> GSM751304 3 0.779 -0.2150 0.052 0.420 0.528
#> GSM751305 3 0.779 -0.2150 0.052 0.420 0.528
#> GSM751307 2 0.695 0.2858 0.016 0.500 0.484
#> GSM751310 1 0.421 0.7217 0.872 0.088 0.040
#> GSM751314 1 0.432 0.7215 0.868 0.088 0.044
#> GSM751316 1 0.421 0.7217 0.872 0.088 0.040
#> GSM751318 1 0.621 0.6669 0.768 0.164 0.068
#> GSM751342 1 0.709 0.5889 0.688 0.248 0.064
#> GSM751346 1 0.445 0.6747 0.856 0.032 0.112
#> GSM751347 1 0.456 0.6735 0.852 0.036 0.112
#> GSM751348 2 0.479 0.6561 0.112 0.844 0.044
#> GSM751349 2 0.127 0.6900 0.004 0.972 0.024
#> GSM751352 2 0.614 0.5285 0.012 0.684 0.304
#> GSM751353 2 0.593 0.5256 0.008 0.696 0.296
#> GSM751354 3 0.655 -0.1497 0.008 0.412 0.580
#> GSM751355 3 0.655 -0.1497 0.008 0.412 0.580
#> GSM751358 2 0.447 0.6551 0.060 0.864 0.076
#> GSM751359 2 0.240 0.6835 0.004 0.932 0.064
#> GSM751294 2 0.930 0.1774 0.300 0.508 0.192
#> GSM751296 1 0.497 0.7044 0.840 0.060 0.100
#> GSM751297 1 0.445 0.6747 0.856 0.032 0.112
#> GSM751299 2 0.760 0.5390 0.124 0.684 0.192
#> GSM751300 1 0.417 0.6845 0.868 0.028 0.104
#> GSM751301 2 0.703 0.4229 0.024 0.580 0.396
#> GSM751302 1 0.432 0.6765 0.860 0.028 0.112
#> GSM751303 1 0.432 0.7215 0.868 0.088 0.044
#> GSM751306 1 0.432 0.7215 0.868 0.088 0.044
#> GSM751308 2 0.939 0.0276 0.368 0.456 0.176
#> GSM751309 1 0.466 0.7187 0.852 0.100 0.048
#> GSM751311 1 0.466 0.7187 0.852 0.100 0.048
#> GSM751312 1 0.421 0.7217 0.872 0.088 0.040
#> GSM751313 1 0.103 0.6993 0.976 0.000 0.024
#> GSM751315 1 0.409 0.7218 0.876 0.088 0.036
#> GSM751317 1 0.421 0.7217 0.872 0.088 0.040
#> GSM751320 1 0.331 0.7220 0.908 0.064 0.028
#> GSM751321 1 0.421 0.7217 0.872 0.088 0.040
#> GSM751322 1 0.331 0.7220 0.908 0.064 0.028
#> GSM751324 1 0.331 0.7220 0.908 0.064 0.028
#> GSM751325 1 0.331 0.7220 0.908 0.064 0.028
#> GSM751332 1 0.333 0.7256 0.904 0.076 0.020
#> GSM751334 1 0.333 0.7256 0.904 0.076 0.020
#> GSM751339 1 0.386 0.6933 0.888 0.040 0.072
#> GSM751341 1 0.523 0.7079 0.828 0.068 0.104
#> GSM751343 1 0.543 0.6977 0.816 0.120 0.064
#> GSM751344 2 0.615 0.4165 0.000 0.592 0.408
#> GSM751345 2 0.615 0.4165 0.000 0.592 0.408
#> GSM751356 2 0.928 0.1836 0.296 0.512 0.192
#> GSM751357 2 0.928 0.1836 0.296 0.512 0.192
#> GSM751293 2 0.703 0.4229 0.024 0.580 0.396
#> GSM751295 1 0.432 0.6765 0.860 0.028 0.112
#> GSM751319 1 0.421 0.7217 0.872 0.088 0.040
#> GSM751323 1 0.331 0.7220 0.908 0.064 0.028
#> GSM751326 1 0.145 0.7041 0.968 0.008 0.024
#> GSM751327 1 0.145 0.7041 0.968 0.008 0.024
#> GSM751328 1 0.333 0.7256 0.904 0.076 0.020
#> GSM751329 1 0.188 0.7179 0.956 0.032 0.012
#> GSM751330 1 0.268 0.7190 0.932 0.040 0.028
#> GSM751331 1 0.318 0.7026 0.912 0.024 0.064
#> GSM751333 1 0.127 0.7022 0.972 0.004 0.024
#> GSM751335 1 0.268 0.7190 0.932 0.040 0.028
#> GSM751336 1 0.223 0.7030 0.944 0.012 0.044
#> GSM751337 1 0.257 0.7141 0.936 0.032 0.032
#> GSM751338 1 0.386 0.6933 0.888 0.040 0.072
#> GSM751340 1 0.386 0.6933 0.888 0.040 0.072
#> GSM751350 1 0.346 0.6994 0.900 0.024 0.076
#> GSM751351 1 0.346 0.6994 0.900 0.024 0.076
#> GSM751362 1 0.842 0.2563 0.584 0.116 0.300
#> GSM751363 1 0.940 0.1002 0.432 0.396 0.172
#> GSM751367 1 0.507 0.6746 0.832 0.052 0.116
#> GSM751368 1 0.874 0.1260 0.452 0.440 0.108
#> GSM751371 1 0.738 0.5908 0.684 0.228 0.088
#> GSM751375 2 0.176 0.6879 0.004 0.956 0.040
#> GSM751376 3 0.713 0.1546 0.028 0.392 0.580
#> GSM751378 2 0.446 0.6486 0.056 0.864 0.080
#> GSM751379 3 0.713 0.1546 0.028 0.392 0.580
#> GSM751382 2 0.176 0.6879 0.004 0.956 0.040
#> GSM751386 2 0.176 0.6884 0.004 0.956 0.040
#> GSM751388 2 0.153 0.6878 0.004 0.964 0.032
#> GSM751391 1 0.808 0.5306 0.632 0.252 0.116
#> GSM751410 1 0.868 0.4125 0.596 0.212 0.192
#> GSM751414 1 0.631 0.6758 0.768 0.148 0.084
#> GSM751361 1 0.814 0.2249 0.480 0.452 0.068
#> GSM751365 1 0.856 0.4602 0.600 0.244 0.156
#> GSM751366 1 0.765 0.5743 0.684 0.140 0.176
#> GSM751369 1 0.891 0.4277 0.572 0.200 0.228
#> GSM751370 1 0.750 0.5434 0.696 0.140 0.164
#> GSM751372 1 0.830 0.4937 0.632 0.196 0.172
#> GSM751373 1 0.677 0.6274 0.720 0.216 0.064
#> GSM751374 3 0.713 0.1546 0.028 0.392 0.580
#> GSM751377 2 0.676 0.5348 0.224 0.716 0.060
#> GSM751380 1 0.899 0.2893 0.560 0.192 0.248
#> GSM751381 2 0.153 0.6878 0.004 0.964 0.032
#> GSM751383 2 0.219 0.6934 0.024 0.948 0.028
#> GSM751384 2 0.218 0.6859 0.020 0.948 0.032
#> GSM751385 2 0.440 0.6838 0.044 0.864 0.092
#> GSM751387 2 0.165 0.6878 0.004 0.960 0.036
#> GSM751389 1 0.982 -0.1763 0.420 0.260 0.320
#> GSM751393 3 0.713 0.1546 0.028 0.392 0.580
#> GSM751394 2 0.165 0.6878 0.004 0.960 0.036
#> GSM751395 3 0.713 0.1546 0.028 0.392 0.580
#> GSM751397 2 0.165 0.6879 0.004 0.960 0.036
#> GSM751398 2 0.183 0.6887 0.008 0.956 0.036
#> GSM751404 1 0.944 -0.1350 0.468 0.188 0.344
#> GSM751406 3 0.909 0.4137 0.400 0.140 0.460
#> GSM751411 2 0.867 0.0952 0.324 0.552 0.124
#> GSM751413 1 0.943 0.0449 0.416 0.408 0.176
#> GSM751415 1 0.983 -0.1741 0.420 0.264 0.316
#> GSM751416 1 0.806 0.2792 0.496 0.440 0.064
#> GSM751417 1 0.806 0.2792 0.496 0.440 0.064
#> GSM751421 1 0.749 0.5925 0.680 0.224 0.096
#> GSM751422 1 0.749 0.5925 0.680 0.224 0.096
#> GSM751360 1 0.770 0.5786 0.664 0.232 0.104
#> GSM751364 1 0.855 0.3425 0.516 0.384 0.100
#> GSM751390 2 0.218 0.6859 0.020 0.948 0.032
#> GSM751392 2 0.176 0.6879 0.004 0.956 0.040
#> GSM751396 2 0.165 0.6878 0.004 0.960 0.036
#> GSM751399 3 0.909 0.4137 0.400 0.140 0.460
#> GSM751400 3 0.909 0.4137 0.400 0.140 0.460
#> GSM751401 3 0.914 0.4063 0.404 0.144 0.452
#> GSM751402 3 0.910 0.4063 0.404 0.140 0.456
#> GSM751403 3 0.909 0.4137 0.400 0.140 0.460
#> GSM751405 3 0.909 0.4137 0.400 0.140 0.460
#> GSM751407 3 0.940 0.3683 0.404 0.172 0.424
#> GSM751408 3 0.937 0.3453 0.408 0.168 0.424
#> GSM751409 2 0.969 -0.1908 0.292 0.456 0.252
#> GSM751412 1 0.955 -0.3585 0.412 0.192 0.396
#> GSM751418 1 0.748 0.5337 0.648 0.284 0.068
#> GSM751419 1 0.748 0.5337 0.648 0.284 0.068
#> GSM751420 3 0.910 0.3965 0.408 0.140 0.452
#> GSM751425 2 0.268 0.6860 0.008 0.924 0.068
#> GSM751429 1 0.496 0.6740 0.836 0.048 0.116
#> GSM751430 2 0.767 0.3035 0.044 0.500 0.456
#> GSM751433 2 0.686 0.5075 0.252 0.696 0.052
#> GSM751437 2 0.997 -0.3577 0.340 0.360 0.300
#> GSM751448 3 0.878 0.3479 0.420 0.112 0.468
#> GSM751451 2 0.703 0.4541 0.284 0.668 0.048
#> GSM751423 2 0.485 0.6595 0.128 0.836 0.036
#> GSM751424 2 0.678 0.5188 0.244 0.704 0.052
#> GSM751428 2 0.509 0.6820 0.088 0.836 0.076
#> GSM751431 2 0.686 0.5075 0.252 0.696 0.052
#> GSM751432 2 0.767 0.3035 0.044 0.500 0.456
#> GSM751434 2 0.767 0.3035 0.044 0.500 0.456
#> GSM751435 2 0.616 0.6018 0.188 0.760 0.052
#> GSM751436 2 0.686 0.5075 0.252 0.696 0.052
#> GSM751440 2 0.616 0.6018 0.188 0.760 0.052
#> GSM751444 2 0.407 0.6652 0.016 0.864 0.120
#> GSM751446 2 0.632 0.6062 0.172 0.760 0.068
#> GSM751449 2 0.435 0.6608 0.020 0.852 0.128
#> GSM751450 2 0.503 0.6549 0.132 0.828 0.040
#> GSM751452 2 0.678 0.5188 0.244 0.704 0.052
#> GSM751426 2 0.678 0.5188 0.244 0.704 0.052
#> GSM751427 2 0.509 0.6820 0.088 0.836 0.076
#> GSM751438 2 0.421 0.6643 0.020 0.860 0.120
#> GSM751439 2 0.754 0.5273 0.172 0.692 0.136
#> GSM751441 2 0.400 0.6673 0.016 0.868 0.116
#> GSM751442 2 0.632 0.6062 0.172 0.760 0.068
#> GSM751443 3 0.878 0.3479 0.420 0.112 0.468
#> GSM751445 2 0.406 0.6628 0.012 0.860 0.128
#> GSM751447 2 0.385 0.6711 0.016 0.876 0.108
#> GSM751453 2 0.385 0.6711 0.016 0.876 0.108
#> GSM751454 2 0.385 0.6711 0.016 0.876 0.108
#> GSM751455 2 0.632 0.6062 0.172 0.760 0.068
#> GSM751456 2 0.632 0.6062 0.172 0.760 0.068
#> GSM751457 2 0.441 0.6536 0.016 0.844 0.140
#> GSM751458 2 0.441 0.6536 0.016 0.844 0.140
cbind(get_classes(res, k = 4), get_membership(res, k = 4))
#> class entropy silhouette p1 p2 p3 p4
#> GSM751298 1 0.699 0.549767 0.632 0.020 0.212 0.136
#> GSM751304 4 0.552 0.732916 0.036 0.180 0.036 0.748
#> GSM751305 4 0.552 0.732916 0.036 0.180 0.036 0.748
#> GSM751307 4 0.559 0.777550 0.016 0.280 0.024 0.680
#> GSM751310 1 0.250 0.646814 0.924 0.032 0.012 0.032
#> GSM751314 1 0.283 0.644837 0.912 0.032 0.020 0.036
#> GSM751316 1 0.250 0.646814 0.924 0.032 0.012 0.032
#> GSM751318 1 0.610 0.554582 0.744 0.072 0.108 0.076
#> GSM751342 1 0.702 0.508648 0.672 0.160 0.100 0.068
#> GSM751346 1 0.704 0.510226 0.596 0.008 0.248 0.148
#> GSM751347 1 0.717 0.507706 0.592 0.012 0.244 0.152
#> GSM751348 2 0.495 0.597917 0.100 0.808 0.044 0.048
#> GSM751349 2 0.175 0.634377 0.012 0.952 0.024 0.012
#> GSM751352 2 0.628 -0.268309 0.000 0.556 0.064 0.380
#> GSM751353 2 0.625 -0.237810 0.000 0.564 0.064 0.372
#> GSM751354 4 0.693 0.686094 0.004 0.196 0.192 0.608
#> GSM751355 4 0.693 0.686094 0.004 0.196 0.192 0.608
#> GSM751358 2 0.571 0.557317 0.064 0.768 0.100 0.068
#> GSM751359 2 0.438 0.609607 0.028 0.836 0.092 0.044
#> GSM751294 2 0.949 0.074975 0.200 0.388 0.276 0.136
#> GSM751296 1 0.658 0.594252 0.676 0.020 0.176 0.128
#> GSM751297 1 0.704 0.510226 0.596 0.008 0.248 0.148
#> GSM751299 2 0.866 0.017522 0.076 0.500 0.208 0.216
#> GSM751300 1 0.683 0.534549 0.624 0.008 0.224 0.144
#> GSM751301 4 0.637 0.602627 0.024 0.444 0.024 0.508
#> GSM751302 1 0.701 0.515097 0.600 0.008 0.244 0.148
#> GSM751303 1 0.271 0.645602 0.916 0.032 0.016 0.036
#> GSM751306 1 0.271 0.645602 0.916 0.032 0.016 0.036
#> GSM751308 2 0.955 -0.032776 0.268 0.344 0.272 0.116
#> GSM751309 1 0.312 0.640087 0.900 0.032 0.044 0.024
#> GSM751311 1 0.312 0.640087 0.900 0.032 0.044 0.024
#> GSM751312 1 0.250 0.646814 0.924 0.032 0.012 0.032
#> GSM751313 1 0.604 0.574498 0.684 0.000 0.188 0.128
#> GSM751315 1 0.262 0.646652 0.920 0.032 0.016 0.032
#> GSM751317 1 0.262 0.645896 0.920 0.032 0.016 0.032
#> GSM751320 1 0.290 0.644173 0.904 0.008 0.056 0.032
#> GSM751321 1 0.262 0.645896 0.920 0.032 0.016 0.032
#> GSM751322 1 0.290 0.644173 0.904 0.008 0.056 0.032
#> GSM751324 1 0.281 0.644176 0.908 0.008 0.052 0.032
#> GSM751325 1 0.281 0.644176 0.908 0.008 0.052 0.032
#> GSM751332 1 0.338 0.647649 0.884 0.016 0.068 0.032
#> GSM751334 1 0.338 0.647649 0.884 0.016 0.068 0.032
#> GSM751339 1 0.625 0.516272 0.644 0.000 0.252 0.104
#> GSM751341 1 0.672 0.596370 0.668 0.024 0.176 0.132
#> GSM751343 1 0.489 0.598272 0.812 0.044 0.096 0.048
#> GSM751344 4 0.556 0.646885 0.000 0.432 0.020 0.548
#> GSM751345 4 0.556 0.646885 0.000 0.432 0.020 0.548
#> GSM751356 2 0.948 0.077754 0.200 0.392 0.272 0.136
#> GSM751357 2 0.948 0.077754 0.200 0.392 0.272 0.136
#> GSM751293 4 0.637 0.602627 0.024 0.444 0.024 0.508
#> GSM751295 1 0.701 0.515097 0.600 0.008 0.244 0.148
#> GSM751319 1 0.262 0.645896 0.920 0.032 0.016 0.032
#> GSM751323 1 0.291 0.644911 0.904 0.008 0.052 0.036
#> GSM751326 1 0.562 0.600500 0.724 0.000 0.152 0.124
#> GSM751327 1 0.562 0.600500 0.724 0.000 0.152 0.124
#> GSM751328 1 0.338 0.647649 0.884 0.016 0.068 0.032
#> GSM751329 1 0.445 0.637693 0.816 0.008 0.124 0.052
#> GSM751330 1 0.562 0.620146 0.748 0.012 0.124 0.116
#> GSM751331 1 0.676 0.557285 0.644 0.012 0.200 0.144
#> GSM751333 1 0.576 0.591763 0.712 0.000 0.160 0.128
#> GSM751335 1 0.567 0.618779 0.744 0.012 0.124 0.120
#> GSM751336 1 0.623 0.570765 0.680 0.004 0.184 0.132
#> GSM751337 1 0.599 0.599971 0.700 0.004 0.180 0.116
#> GSM751338 1 0.625 0.516272 0.644 0.000 0.252 0.104
#> GSM751340 1 0.625 0.516272 0.644 0.000 0.252 0.104
#> GSM751350 1 0.688 0.550174 0.632 0.012 0.204 0.152
#> GSM751351 1 0.688 0.550174 0.632 0.012 0.204 0.152
#> GSM751362 3 0.703 0.227443 0.356 0.032 0.552 0.060
#> GSM751363 1 0.864 0.182503 0.456 0.280 0.052 0.212
#> GSM751367 1 0.741 0.506652 0.584 0.028 0.260 0.128
#> GSM751368 1 0.810 0.127748 0.468 0.372 0.060 0.100
#> GSM751371 1 0.712 0.521866 0.656 0.152 0.144 0.048
#> GSM751375 2 0.138 0.633224 0.008 0.964 0.020 0.008
#> GSM751376 3 0.792 -0.045775 0.024 0.192 0.520 0.264
#> GSM751378 2 0.483 0.567026 0.036 0.780 0.172 0.012
#> GSM751379 3 0.792 -0.045775 0.024 0.192 0.520 0.264
#> GSM751382 2 0.138 0.633224 0.008 0.964 0.020 0.008
#> GSM751386 2 0.172 0.634700 0.008 0.952 0.028 0.012
#> GSM751388 2 0.144 0.635194 0.008 0.960 0.028 0.004
#> GSM751391 1 0.760 0.462942 0.604 0.180 0.172 0.044
#> GSM751410 1 0.846 0.096033 0.436 0.132 0.368 0.064
#> GSM751414 1 0.711 0.565024 0.652 0.080 0.200 0.068
#> GSM751361 1 0.771 0.203915 0.488 0.384 0.068 0.060
#> GSM751365 1 0.856 0.253226 0.464 0.148 0.320 0.068
#> GSM751366 1 0.730 0.361011 0.548 0.056 0.344 0.052
#> GSM751369 1 0.793 0.294185 0.528 0.112 0.308 0.052
#> GSM751370 1 0.805 0.223413 0.456 0.068 0.392 0.084
#> GSM751372 1 0.834 0.275604 0.480 0.120 0.332 0.068
#> GSM751373 1 0.749 0.550956 0.632 0.144 0.160 0.064
#> GSM751374 3 0.792 -0.045775 0.024 0.192 0.520 0.264
#> GSM751377 2 0.625 0.480425 0.228 0.684 0.060 0.028
#> GSM751380 3 0.754 0.224493 0.368 0.088 0.508 0.036
#> GSM751381 2 0.144 0.635194 0.008 0.960 0.028 0.004
#> GSM751383 2 0.225 0.641742 0.020 0.932 0.040 0.008
#> GSM751384 2 0.233 0.636653 0.016 0.924 0.056 0.004
#> GSM751385 2 0.540 0.555015 0.040 0.780 0.064 0.116
#> GSM751387 2 0.123 0.633869 0.008 0.968 0.020 0.004
#> GSM751389 3 0.689 0.545832 0.240 0.128 0.620 0.012
#> GSM751393 3 0.792 -0.045775 0.024 0.192 0.520 0.264
#> GSM751394 2 0.134 0.633487 0.008 0.964 0.024 0.004
#> GSM751395 3 0.792 -0.045775 0.024 0.192 0.520 0.264
#> GSM751397 2 0.154 0.635638 0.008 0.956 0.032 0.004
#> GSM751398 2 0.172 0.634678 0.008 0.952 0.028 0.012
#> GSM751404 3 0.593 0.554558 0.264 0.076 0.660 0.000
#> GSM751406 3 0.348 0.697543 0.148 0.012 0.840 0.000
#> GSM751411 2 0.804 -0.000578 0.200 0.448 0.336 0.016
#> GSM751413 1 0.874 0.145492 0.440 0.288 0.056 0.216
#> GSM751415 3 0.698 0.537856 0.240 0.136 0.612 0.012
#> GSM751416 1 0.752 0.255395 0.508 0.376 0.060 0.056
#> GSM751417 1 0.752 0.255395 0.508 0.376 0.060 0.056
#> GSM751421 1 0.723 0.525498 0.652 0.144 0.148 0.056
#> GSM751422 1 0.723 0.525498 0.652 0.144 0.148 0.056
#> GSM751360 1 0.733 0.510820 0.636 0.156 0.160 0.048
#> GSM751364 1 0.811 0.343789 0.504 0.328 0.100 0.068
#> GSM751390 2 0.233 0.636653 0.016 0.924 0.056 0.004
#> GSM751392 2 0.138 0.633224 0.008 0.964 0.020 0.008
#> GSM751396 2 0.134 0.633487 0.008 0.964 0.024 0.004
#> GSM751399 3 0.348 0.697543 0.148 0.012 0.840 0.000
#> GSM751400 3 0.380 0.697474 0.148 0.012 0.832 0.008
#> GSM751401 3 0.365 0.696727 0.152 0.016 0.832 0.000
#> GSM751402 3 0.353 0.695783 0.152 0.012 0.836 0.000
#> GSM751403 3 0.348 0.697543 0.148 0.012 0.840 0.000
#> GSM751405 3 0.348 0.697543 0.148 0.012 0.840 0.000
#> GSM751407 3 0.462 0.681502 0.164 0.052 0.784 0.000
#> GSM751408 3 0.483 0.673444 0.176 0.056 0.768 0.000
#> GSM751409 3 0.772 0.370378 0.172 0.324 0.492 0.012
#> GSM751412 3 0.540 0.659351 0.184 0.084 0.732 0.000
#> GSM751418 1 0.776 0.480761 0.588 0.224 0.132 0.056
#> GSM751419 1 0.776 0.480761 0.588 0.224 0.132 0.056
#> GSM751420 3 0.390 0.694173 0.156 0.012 0.824 0.008
#> GSM751425 2 0.322 0.618302 0.012 0.892 0.052 0.044
#> GSM751429 1 0.735 0.505767 0.584 0.024 0.264 0.128
#> GSM751430 4 0.649 0.775701 0.044 0.280 0.036 0.640
#> GSM751433 2 0.584 0.444095 0.300 0.648 0.004 0.048
#> GSM751437 3 0.773 0.476464 0.196 0.240 0.544 0.020
#> GSM751448 3 0.363 0.659491 0.156 0.004 0.832 0.008
#> GSM751451 2 0.627 0.409189 0.328 0.612 0.016 0.044
#> GSM751423 2 0.521 0.599278 0.140 0.780 0.028 0.052
#> GSM751424 2 0.575 0.451990 0.296 0.656 0.004 0.044
#> GSM751428 2 0.487 0.621515 0.076 0.816 0.044 0.064
#> GSM751431 2 0.584 0.444095 0.300 0.648 0.004 0.048
#> GSM751432 4 0.649 0.775701 0.044 0.280 0.036 0.640
#> GSM751434 4 0.649 0.775701 0.044 0.280 0.036 0.640
#> GSM751435 2 0.631 0.574463 0.156 0.716 0.084 0.044
#> GSM751436 2 0.584 0.444095 0.300 0.648 0.004 0.048
#> GSM751440 2 0.639 0.573044 0.156 0.712 0.084 0.048
#> GSM751444 2 0.500 0.571827 0.012 0.788 0.128 0.072
#> GSM751446 2 0.643 0.576233 0.144 0.712 0.096 0.048
#> GSM751449 2 0.510 0.561725 0.012 0.780 0.136 0.072
#> GSM751450 2 0.534 0.594994 0.144 0.772 0.028 0.056
#> GSM751452 2 0.575 0.451990 0.296 0.656 0.004 0.044
#> GSM751426 2 0.575 0.451990 0.296 0.656 0.004 0.044
#> GSM751427 2 0.487 0.621515 0.076 0.816 0.044 0.064
#> GSM751438 2 0.512 0.571294 0.016 0.784 0.128 0.072
#> GSM751439 2 0.725 0.513930 0.144 0.644 0.164 0.048
#> GSM751441 2 0.495 0.574088 0.012 0.792 0.124 0.072
#> GSM751442 2 0.643 0.576233 0.144 0.712 0.096 0.048
#> GSM751443 3 0.363 0.659491 0.156 0.004 0.832 0.008
#> GSM751445 2 0.494 0.562234 0.008 0.788 0.128 0.076
#> GSM751447 2 0.484 0.580094 0.012 0.800 0.116 0.072
#> GSM751453 2 0.484 0.580094 0.012 0.800 0.116 0.072
#> GSM751454 2 0.484 0.580094 0.012 0.800 0.116 0.072
#> GSM751455 2 0.643 0.576233 0.144 0.712 0.096 0.048
#> GSM751456 2 0.643 0.576233 0.144 0.712 0.096 0.048
#> GSM751457 2 0.522 0.553262 0.012 0.772 0.140 0.076
#> GSM751458 2 0.522 0.553262 0.012 0.772 0.140 0.076
cbind(get_classes(res, k = 5), get_membership(res, k = 5))
#> class entropy silhouette p1 p2 p3 p4 p5
#> GSM751298 1 0.6477 0.8206 0.524 0.008 0.176 0.292 0.000
#> GSM751304 5 0.3826 0.7203 0.032 0.080 0.000 0.052 0.836
#> GSM751305 5 0.3826 0.7203 0.032 0.080 0.000 0.052 0.836
#> GSM751307 5 0.3845 0.7876 0.008 0.160 0.004 0.024 0.804
#> GSM751310 4 0.1554 0.5281 0.024 0.008 0.004 0.952 0.012
#> GSM751314 4 0.1375 0.5303 0.016 0.008 0.008 0.960 0.008
#> GSM751316 4 0.1554 0.5281 0.024 0.008 0.004 0.952 0.012
#> GSM751318 4 0.5488 0.5035 0.108 0.044 0.044 0.752 0.052
#> GSM751342 4 0.6300 0.4937 0.100 0.120 0.040 0.692 0.048
#> GSM751346 1 0.6076 0.8432 0.572 0.000 0.196 0.232 0.000
#> GSM751347 1 0.6175 0.8383 0.576 0.004 0.192 0.228 0.000
#> GSM751348 2 0.5412 0.5921 0.112 0.740 0.012 0.100 0.036
#> GSM751349 2 0.1809 0.6590 0.060 0.928 0.000 0.000 0.012
#> GSM751352 2 0.6311 -0.1521 0.080 0.500 0.020 0.004 0.396
#> GSM751353 2 0.5928 -0.0953 0.084 0.520 0.008 0.000 0.388
#> GSM751354 5 0.5981 0.6583 0.060 0.104 0.144 0.004 0.688
#> GSM751355 5 0.5981 0.6583 0.060 0.104 0.144 0.004 0.688
#> GSM751358 2 0.6349 0.5226 0.160 0.680 0.060 0.040 0.060
#> GSM751359 2 0.4929 0.5892 0.152 0.756 0.052 0.004 0.036
#> GSM751294 2 0.9285 0.0494 0.200 0.344 0.260 0.096 0.100
#> GSM751296 1 0.6372 0.5591 0.456 0.008 0.128 0.408 0.000
#> GSM751297 1 0.6076 0.8432 0.572 0.000 0.196 0.232 0.000
#> GSM751299 2 0.8598 -0.0551 0.148 0.408 0.200 0.020 0.224
#> GSM751300 1 0.6130 0.8445 0.556 0.000 0.180 0.264 0.000
#> GSM751301 5 0.6863 0.6204 0.120 0.328 0.004 0.036 0.512
#> GSM751302 1 0.6049 0.8444 0.576 0.000 0.192 0.232 0.000
#> GSM751303 4 0.1347 0.5293 0.020 0.008 0.004 0.960 0.008
#> GSM751306 4 0.1347 0.5293 0.020 0.008 0.004 0.960 0.008
#> GSM751308 2 0.9526 -0.0235 0.168 0.308 0.264 0.168 0.092
#> GSM751309 4 0.1794 0.5343 0.024 0.008 0.012 0.944 0.012
#> GSM751311 4 0.1794 0.5343 0.024 0.008 0.012 0.944 0.012
#> GSM751312 4 0.1554 0.5281 0.024 0.008 0.004 0.952 0.012
#> GSM751313 1 0.7392 0.6850 0.412 0.000 0.172 0.364 0.052
#> GSM751315 4 0.1587 0.5303 0.020 0.008 0.008 0.952 0.012
#> GSM751317 4 0.1460 0.5293 0.020 0.008 0.004 0.956 0.012
#> GSM751320 4 0.3781 0.4699 0.092 0.000 0.036 0.836 0.036
#> GSM751321 4 0.1587 0.5298 0.020 0.008 0.008 0.952 0.012
#> GSM751322 4 0.3781 0.4699 0.092 0.000 0.036 0.836 0.036
#> GSM751324 4 0.3702 0.4736 0.092 0.000 0.032 0.840 0.036
#> GSM751325 4 0.3702 0.4736 0.092 0.000 0.032 0.840 0.036
#> GSM751332 4 0.5123 0.3740 0.180 0.004 0.048 0.732 0.036
#> GSM751334 4 0.5123 0.3740 0.180 0.004 0.048 0.732 0.036
#> GSM751339 4 0.7605 -0.0521 0.240 0.000 0.248 0.448 0.064
#> GSM751341 1 0.6442 0.4975 0.444 0.012 0.124 0.420 0.000
#> GSM751343 4 0.4960 0.5011 0.120 0.024 0.040 0.776 0.040
#> GSM751344 5 0.6055 0.6565 0.100 0.316 0.004 0.008 0.572
#> GSM751345 5 0.6055 0.6565 0.100 0.316 0.004 0.008 0.572
#> GSM751356 2 0.9278 0.0529 0.200 0.348 0.256 0.096 0.100
#> GSM751357 2 0.9278 0.0529 0.200 0.348 0.256 0.096 0.100
#> GSM751293 5 0.6863 0.6204 0.120 0.328 0.004 0.036 0.512
#> GSM751295 1 0.6049 0.8444 0.576 0.000 0.192 0.232 0.000
#> GSM751319 4 0.1460 0.5293 0.020 0.008 0.004 0.956 0.012
#> GSM751323 4 0.3756 0.4725 0.096 0.000 0.032 0.836 0.036
#> GSM751326 4 0.7128 -0.5812 0.384 0.000 0.136 0.432 0.048
#> GSM751327 4 0.7125 -0.5741 0.380 0.000 0.136 0.436 0.048
#> GSM751328 4 0.5123 0.3740 0.180 0.004 0.048 0.732 0.036
#> GSM751329 4 0.6598 -0.3684 0.336 0.000 0.112 0.520 0.032
#> GSM751330 4 0.6781 -0.5809 0.412 0.000 0.112 0.440 0.036
#> GSM751331 1 0.6943 0.8225 0.512 0.000 0.164 0.288 0.036
#> GSM751333 1 0.7237 0.6487 0.420 0.000 0.144 0.384 0.052
#> GSM751335 4 0.6783 -0.5888 0.416 0.000 0.112 0.436 0.036
#> GSM751336 1 0.7040 0.7872 0.480 0.000 0.164 0.320 0.036
#> GSM751337 4 0.7158 -0.3424 0.328 0.000 0.152 0.472 0.048
#> GSM751338 4 0.7605 -0.0521 0.240 0.000 0.248 0.448 0.064
#> GSM751340 4 0.7605 -0.0521 0.240 0.000 0.248 0.448 0.064
#> GSM751350 1 0.6818 0.8317 0.520 0.000 0.168 0.284 0.028
#> GSM751351 1 0.6818 0.8317 0.520 0.000 0.168 0.284 0.028
#> GSM751362 3 0.6767 0.2776 0.212 0.012 0.596 0.144 0.036
#> GSM751363 4 0.7567 0.2191 0.048 0.184 0.012 0.480 0.276
#> GSM751367 1 0.6899 0.8090 0.516 0.012 0.220 0.244 0.008
#> GSM751368 4 0.7595 0.2219 0.076 0.320 0.012 0.472 0.120
#> GSM751371 4 0.7108 0.4604 0.104 0.120 0.104 0.632 0.040
#> GSM751375 2 0.1492 0.6599 0.040 0.948 0.004 0.000 0.008
#> GSM751376 3 0.8024 0.0856 0.168 0.104 0.440 0.008 0.280
#> GSM751378 2 0.5075 0.5673 0.092 0.740 0.148 0.012 0.008
#> GSM751379 3 0.8024 0.0856 0.168 0.104 0.440 0.008 0.280
#> GSM751382 2 0.1492 0.6599 0.040 0.948 0.004 0.000 0.008
#> GSM751386 2 0.2043 0.6595 0.048 0.928 0.008 0.004 0.012
#> GSM751388 2 0.1569 0.6593 0.044 0.944 0.008 0.000 0.004
#> GSM751391 4 0.7676 0.4214 0.120 0.152 0.128 0.568 0.032
#> GSM751410 3 0.8516 0.0540 0.160 0.096 0.384 0.324 0.036
#> GSM751414 4 0.7637 0.1559 0.208 0.052 0.184 0.528 0.028
#> GSM751361 4 0.7103 0.2472 0.072 0.352 0.020 0.500 0.056
#> GSM751365 4 0.8881 0.1049 0.176 0.124 0.292 0.364 0.044
#> GSM751366 4 0.7683 -0.0736 0.208 0.032 0.344 0.400 0.016
#> GSM751369 4 0.8238 0.2742 0.164 0.056 0.276 0.452 0.052
#> GSM751370 3 0.8290 -0.1228 0.224 0.048 0.420 0.264 0.044
#> GSM751372 4 0.8803 0.0532 0.184 0.104 0.328 0.340 0.044
#> GSM751373 4 0.7971 0.2585 0.184 0.116 0.148 0.524 0.028
#> GSM751374 3 0.8024 0.0856 0.168 0.104 0.440 0.008 0.280
#> GSM751377 2 0.6324 0.4949 0.076 0.648 0.016 0.212 0.048
#> GSM751380 3 0.7157 0.3646 0.128 0.040 0.560 0.248 0.024
#> GSM751381 2 0.1569 0.6593 0.044 0.944 0.008 0.000 0.004
#> GSM751383 2 0.2467 0.6628 0.052 0.912 0.012 0.012 0.012
#> GSM751384 2 0.2637 0.6535 0.060 0.900 0.028 0.008 0.004
#> GSM751385 2 0.5737 0.5423 0.076 0.720 0.044 0.020 0.140
#> GSM751387 2 0.1443 0.6597 0.044 0.948 0.004 0.000 0.004
#> GSM751389 3 0.6256 0.5653 0.104 0.108 0.680 0.100 0.008
#> GSM751393 3 0.8024 0.0856 0.168 0.104 0.440 0.008 0.280
#> GSM751394 2 0.1443 0.6599 0.044 0.948 0.004 0.000 0.004
#> GSM751395 3 0.8024 0.0856 0.168 0.104 0.440 0.008 0.280
#> GSM751397 2 0.1644 0.6600 0.048 0.940 0.008 0.000 0.004
#> GSM751398 2 0.1913 0.6594 0.044 0.932 0.008 0.000 0.016
#> GSM751404 3 0.4968 0.5936 0.068 0.052 0.760 0.120 0.000
#> GSM751406 3 0.0865 0.6845 0.000 0.000 0.972 0.024 0.004
#> GSM751411 2 0.8122 -0.0480 0.144 0.388 0.348 0.108 0.012
#> GSM751413 4 0.7797 0.1844 0.056 0.192 0.016 0.464 0.272
#> GSM751415 3 0.6406 0.5608 0.104 0.112 0.672 0.100 0.012
#> GSM751416 4 0.7168 0.2941 0.084 0.344 0.020 0.500 0.052
#> GSM751417 4 0.7168 0.2941 0.084 0.344 0.020 0.500 0.052
#> GSM751421 4 0.7195 0.4549 0.120 0.112 0.104 0.624 0.040
#> GSM751422 4 0.7195 0.4549 0.120 0.112 0.104 0.624 0.040
#> GSM751360 4 0.7485 0.4433 0.128 0.116 0.120 0.596 0.040
#> GSM751364 4 0.7887 0.3452 0.136 0.300 0.052 0.472 0.040
#> GSM751390 2 0.2637 0.6535 0.060 0.900 0.028 0.008 0.004
#> GSM751392 2 0.1492 0.6599 0.040 0.948 0.004 0.000 0.008
#> GSM751396 2 0.1443 0.6599 0.044 0.948 0.004 0.000 0.004
#> GSM751399 3 0.0703 0.6850 0.000 0.000 0.976 0.024 0.000
#> GSM751400 3 0.1153 0.6856 0.004 0.000 0.964 0.024 0.008
#> GSM751401 3 0.1026 0.6851 0.004 0.004 0.968 0.024 0.000
#> GSM751402 3 0.0865 0.6841 0.004 0.000 0.972 0.024 0.000
#> GSM751403 3 0.0703 0.6850 0.000 0.000 0.976 0.024 0.000
#> GSM751405 3 0.0865 0.6845 0.000 0.000 0.972 0.024 0.004
#> GSM751407 3 0.2696 0.6752 0.028 0.032 0.900 0.040 0.000
#> GSM751408 3 0.3018 0.6708 0.036 0.036 0.884 0.044 0.000
#> GSM751409 3 0.7277 0.3896 0.140 0.292 0.508 0.052 0.008
#> GSM751412 3 0.3742 0.6587 0.044 0.064 0.844 0.048 0.000
#> GSM751418 4 0.8061 0.3699 0.140 0.188 0.096 0.528 0.048
#> GSM751419 4 0.8061 0.3699 0.140 0.188 0.096 0.528 0.048
#> GSM751420 3 0.1393 0.6839 0.012 0.000 0.956 0.024 0.008
#> GSM751425 2 0.3089 0.6517 0.068 0.880 0.012 0.008 0.032
#> GSM751429 1 0.6809 0.8092 0.516 0.012 0.224 0.244 0.004
#> GSM751430 5 0.4715 0.7881 0.016 0.168 0.008 0.048 0.760
#> GSM751433 2 0.5014 0.4568 0.008 0.628 0.000 0.332 0.032
#> GSM751437 3 0.7314 0.4996 0.132 0.216 0.556 0.088 0.008
#> GSM751448 3 0.2930 0.6458 0.076 0.000 0.880 0.032 0.012
#> GSM751451 2 0.5313 0.4272 0.024 0.596 0.000 0.356 0.024
#> GSM751423 2 0.4569 0.6148 0.032 0.772 0.004 0.160 0.032
#> GSM751424 2 0.4922 0.4648 0.008 0.636 0.000 0.328 0.028
#> GSM751428 2 0.4624 0.6481 0.080 0.804 0.020 0.060 0.036
#> GSM751431 2 0.5014 0.4568 0.008 0.628 0.000 0.332 0.032
#> GSM751432 5 0.4715 0.7881 0.016 0.168 0.008 0.048 0.760
#> GSM751434 5 0.4715 0.7881 0.016 0.168 0.008 0.048 0.760
#> GSM751435 2 0.5792 0.6042 0.104 0.720 0.052 0.108 0.016
#> GSM751436 2 0.5014 0.4568 0.008 0.628 0.000 0.332 0.032
#> GSM751440 2 0.5884 0.6031 0.104 0.716 0.052 0.108 0.020
#> GSM751444 2 0.4954 0.6062 0.116 0.768 0.060 0.004 0.052
#> GSM751446 2 0.6249 0.5995 0.100 0.700 0.064 0.100 0.036
#> GSM751449 2 0.5099 0.5989 0.108 0.760 0.076 0.004 0.052
#> GSM751450 2 0.4565 0.6112 0.032 0.768 0.004 0.168 0.028
#> GSM751452 2 0.4922 0.4648 0.008 0.636 0.000 0.328 0.028
#> GSM751426 2 0.4922 0.4648 0.008 0.636 0.000 0.328 0.028
#> GSM751427 2 0.4624 0.6481 0.080 0.804 0.020 0.060 0.036
#> GSM751438 2 0.5016 0.6045 0.116 0.764 0.064 0.004 0.052
#> GSM751439 2 0.7028 0.5476 0.100 0.636 0.128 0.100 0.036
#> GSM751441 2 0.4889 0.6081 0.116 0.772 0.056 0.004 0.052
#> GSM751442 2 0.6249 0.5995 0.100 0.700 0.064 0.100 0.036
#> GSM751443 3 0.2930 0.6458 0.076 0.000 0.880 0.032 0.012
#> GSM751445 2 0.4998 0.6016 0.104 0.768 0.068 0.004 0.056
#> GSM751447 2 0.4755 0.6136 0.116 0.780 0.048 0.004 0.052
#> GSM751453 2 0.4755 0.6136 0.116 0.780 0.048 0.004 0.052
#> GSM751454 2 0.4755 0.6136 0.116 0.780 0.048 0.004 0.052
#> GSM751455 2 0.6249 0.5995 0.100 0.700 0.064 0.100 0.036
#> GSM751456 2 0.6249 0.5995 0.100 0.700 0.064 0.100 0.036
#> GSM751457 2 0.5227 0.5926 0.104 0.752 0.084 0.004 0.056
#> GSM751458 2 0.5227 0.5926 0.104 0.752 0.084 0.004 0.056
cbind(get_classes(res, k = 6), get_membership(res, k = 6))
#> class entropy silhouette p1 p2 p3 p4 p5 p6
#> GSM751298 1 0.3327 0.77529 0.836 0.008 0.040 0.108 0.008 0.000
#> GSM751304 6 0.3023 0.67065 0.000 0.028 0.000 0.056 0.052 0.864
#> GSM751305 6 0.3023 0.67065 0.000 0.028 0.000 0.056 0.052 0.864
#> GSM751307 6 0.2622 0.72283 0.008 0.088 0.000 0.016 0.008 0.880
#> GSM751310 4 0.2574 0.59165 0.080 0.008 0.000 0.884 0.024 0.004
#> GSM751314 4 0.2382 0.59291 0.072 0.008 0.000 0.896 0.020 0.004
#> GSM751316 4 0.2574 0.59165 0.080 0.008 0.000 0.884 0.024 0.004
#> GSM751318 4 0.4611 0.55796 0.016 0.036 0.016 0.764 0.144 0.024
#> GSM751342 4 0.5381 0.51720 0.020 0.112 0.016 0.712 0.120 0.020
#> GSM751346 1 0.2583 0.78001 0.884 0.000 0.056 0.052 0.008 0.000
#> GSM751347 1 0.2775 0.77823 0.880 0.008 0.052 0.052 0.008 0.000
#> GSM751348 2 0.5580 0.44495 0.016 0.700 0.012 0.100 0.128 0.044
#> GSM751349 2 0.2195 0.60314 0.012 0.916 0.004 0.004 0.044 0.020
#> GSM751352 2 0.6212 -0.15866 0.004 0.428 0.004 0.008 0.168 0.388
#> GSM751353 2 0.5979 -0.04381 0.008 0.464 0.004 0.000 0.152 0.372
#> GSM751354 6 0.4930 0.60574 0.016 0.052 0.104 0.000 0.084 0.744
#> GSM751355 6 0.4930 0.60574 0.016 0.052 0.104 0.000 0.084 0.744
#> GSM751358 2 0.6559 0.05837 0.048 0.564 0.040 0.032 0.284 0.032
#> GSM751359 2 0.5667 0.30493 0.048 0.640 0.032 0.008 0.248 0.024
#> GSM751294 5 0.8375 0.94271 0.040 0.292 0.248 0.068 0.316 0.036
#> GSM751296 1 0.4706 0.58095 0.664 0.008 0.032 0.280 0.016 0.000
#> GSM751297 1 0.2583 0.78001 0.884 0.000 0.056 0.052 0.008 0.000
#> GSM751299 2 0.8493 -0.58566 0.028 0.296 0.192 0.016 0.252 0.216
#> GSM751300 1 0.2617 0.78625 0.876 0.000 0.040 0.080 0.004 0.000
#> GSM751301 6 0.6718 0.51408 0.016 0.244 0.004 0.020 0.236 0.480
#> GSM751302 1 0.2520 0.78120 0.888 0.000 0.052 0.052 0.008 0.000
#> GSM751303 4 0.2599 0.59217 0.076 0.008 0.000 0.884 0.028 0.004
#> GSM751306 4 0.2599 0.59217 0.076 0.008 0.000 0.884 0.028 0.004
#> GSM751308 5 0.8855 0.84192 0.048 0.264 0.244 0.136 0.272 0.036
#> GSM751309 4 0.2037 0.59546 0.036 0.008 0.004 0.924 0.024 0.004
#> GSM751311 4 0.2037 0.59546 0.036 0.008 0.004 0.924 0.024 0.004
#> GSM751312 4 0.2574 0.59165 0.080 0.008 0.000 0.884 0.024 0.004
#> GSM751313 1 0.5586 0.71386 0.640 0.000 0.040 0.160 0.160 0.000
#> GSM751315 4 0.2350 0.59317 0.076 0.008 0.000 0.896 0.016 0.004
#> GSM751317 4 0.2520 0.59235 0.076 0.008 0.000 0.888 0.024 0.004
#> GSM751320 4 0.4032 0.51541 0.120 0.000 0.004 0.784 0.080 0.012
#> GSM751321 4 0.2350 0.59282 0.076 0.008 0.000 0.896 0.016 0.004
#> GSM751322 4 0.4032 0.51541 0.120 0.000 0.004 0.784 0.080 0.012
#> GSM751324 4 0.3990 0.51909 0.116 0.000 0.004 0.788 0.080 0.012
#> GSM751325 4 0.3990 0.51909 0.116 0.000 0.004 0.788 0.080 0.012
#> GSM751332 4 0.4909 0.36397 0.248 0.000 0.004 0.668 0.064 0.016
#> GSM751334 4 0.4909 0.36397 0.248 0.000 0.004 0.668 0.064 0.016
#> GSM751339 4 0.7619 -0.01617 0.216 0.000 0.192 0.328 0.264 0.000
#> GSM751341 1 0.5132 0.52057 0.624 0.012 0.028 0.304 0.032 0.000
#> GSM751343 4 0.4326 0.54983 0.032 0.016 0.012 0.776 0.148 0.016
#> GSM751344 6 0.6155 0.56474 0.016 0.228 0.004 0.004 0.204 0.544
#> GSM751345 6 0.6155 0.56474 0.016 0.228 0.004 0.004 0.204 0.544
#> GSM751356 5 0.8369 0.94516 0.040 0.292 0.244 0.068 0.320 0.036
#> GSM751357 5 0.8369 0.94516 0.040 0.292 0.244 0.068 0.320 0.036
#> GSM751293 6 0.6718 0.51408 0.016 0.244 0.004 0.020 0.236 0.480
#> GSM751295 1 0.2520 0.78120 0.888 0.000 0.052 0.052 0.008 0.000
#> GSM751319 4 0.2520 0.59235 0.076 0.008 0.000 0.888 0.024 0.004
#> GSM751323 4 0.4131 0.51404 0.120 0.000 0.004 0.776 0.088 0.012
#> GSM751326 1 0.5894 0.65156 0.572 0.000 0.032 0.252 0.144 0.000
#> GSM751327 1 0.5924 0.64685 0.568 0.000 0.032 0.252 0.148 0.000
#> GSM751328 4 0.4909 0.36397 0.248 0.000 0.004 0.668 0.064 0.016
#> GSM751329 1 0.5398 0.52684 0.572 0.000 0.012 0.344 0.056 0.016
#> GSM751330 1 0.5130 0.67758 0.640 0.000 0.012 0.260 0.084 0.004
#> GSM751331 1 0.3860 0.78619 0.804 0.000 0.028 0.084 0.084 0.000
#> GSM751333 1 0.5508 0.71086 0.636 0.000 0.028 0.176 0.160 0.000
#> GSM751335 1 0.5154 0.68097 0.640 0.000 0.012 0.256 0.088 0.004
#> GSM751336 1 0.4465 0.77246 0.752 0.000 0.028 0.112 0.108 0.000
#> GSM751337 1 0.6711 0.34889 0.412 0.000 0.068 0.368 0.152 0.000
#> GSM751338 4 0.7619 -0.01617 0.216 0.000 0.192 0.328 0.264 0.000
#> GSM751340 4 0.7619 -0.01617 0.216 0.000 0.192 0.328 0.264 0.000
#> GSM751350 1 0.3597 0.78860 0.824 0.000 0.028 0.080 0.068 0.000
#> GSM751351 1 0.3597 0.78860 0.824 0.000 0.028 0.080 0.068 0.000
#> GSM751362 3 0.6762 0.36475 0.296 0.008 0.528 0.080 0.052 0.036
#> GSM751363 4 0.7213 0.24755 0.056 0.120 0.004 0.448 0.040 0.332
#> GSM751367 1 0.4174 0.75187 0.800 0.012 0.080 0.084 0.012 0.012
#> GSM751368 4 0.7567 0.25298 0.068 0.288 0.008 0.460 0.060 0.116
#> GSM751371 4 0.6507 0.49482 0.064 0.112 0.076 0.656 0.068 0.024
#> GSM751375 2 0.1655 0.59738 0.000 0.936 0.004 0.004 0.044 0.012
#> GSM751376 3 0.7358 0.06295 0.012 0.052 0.384 0.008 0.300 0.244
#> GSM751378 2 0.5518 0.28921 0.024 0.680 0.152 0.012 0.124 0.008
#> GSM751379 3 0.7358 0.06295 0.012 0.052 0.384 0.008 0.300 0.244
#> GSM751382 2 0.1655 0.59738 0.000 0.936 0.004 0.004 0.044 0.012
#> GSM751386 2 0.2946 0.58179 0.004 0.872 0.008 0.008 0.072 0.036
#> GSM751388 2 0.2322 0.58642 0.004 0.904 0.008 0.004 0.064 0.016
#> GSM751391 4 0.7159 0.41905 0.072 0.140 0.104 0.592 0.068 0.024
#> GSM751410 3 0.8313 0.06016 0.160 0.068 0.368 0.308 0.068 0.028
#> GSM751414 4 0.7283 0.26318 0.300 0.048 0.132 0.472 0.032 0.016
#> GSM751361 4 0.6848 0.25817 0.056 0.324 0.016 0.508 0.056 0.040
#> GSM751365 4 0.8651 0.13804 0.240 0.104 0.264 0.312 0.044 0.036
#> GSM751366 4 0.7594 0.06749 0.284 0.028 0.292 0.348 0.032 0.016
#> GSM751369 4 0.8009 0.30825 0.104 0.048 0.240 0.472 0.092 0.044
#> GSM751370 3 0.8072 0.07171 0.320 0.044 0.360 0.196 0.044 0.036
#> GSM751372 4 0.8573 0.11335 0.244 0.096 0.280 0.304 0.040 0.036
#> GSM751373 4 0.7550 0.34319 0.268 0.112 0.096 0.476 0.032 0.016
#> GSM751374 3 0.7358 0.06295 0.012 0.052 0.384 0.008 0.300 0.244
#> GSM751377 2 0.6467 0.35041 0.048 0.616 0.016 0.208 0.048 0.064
#> GSM751380 3 0.7293 0.31126 0.144 0.032 0.516 0.236 0.048 0.024
#> GSM751381 2 0.2322 0.58642 0.004 0.904 0.008 0.004 0.064 0.016
#> GSM751383 2 0.3381 0.57961 0.008 0.852 0.012 0.012 0.076 0.040
#> GSM751384 2 0.2849 0.56006 0.004 0.872 0.028 0.004 0.084 0.008
#> GSM751385 2 0.5982 0.40165 0.012 0.656 0.036 0.024 0.100 0.172
#> GSM751387 2 0.2006 0.59300 0.000 0.916 0.004 0.004 0.060 0.016
#> GSM751389 3 0.6533 0.42353 0.132 0.092 0.636 0.076 0.056 0.008
#> GSM751393 3 0.7358 0.06295 0.012 0.052 0.384 0.008 0.300 0.244
#> GSM751394 2 0.1723 0.59618 0.000 0.932 0.004 0.004 0.048 0.012
#> GSM751395 3 0.7358 0.06295 0.012 0.052 0.384 0.008 0.300 0.244
#> GSM751397 2 0.1956 0.58953 0.004 0.920 0.004 0.004 0.060 0.008
#> GSM751398 2 0.2663 0.58487 0.004 0.888 0.008 0.008 0.068 0.024
#> GSM751404 3 0.4972 0.51983 0.084 0.044 0.752 0.092 0.024 0.004
#> GSM751406 3 0.0935 0.60794 0.032 0.000 0.964 0.000 0.004 0.000
#> GSM751411 2 0.8326 -0.35446 0.124 0.344 0.316 0.076 0.132 0.008
#> GSM751413 4 0.7436 0.21231 0.060 0.124 0.008 0.432 0.044 0.332
#> GSM751415 3 0.6575 0.41616 0.132 0.096 0.632 0.076 0.056 0.008
#> GSM751416 4 0.7102 0.28766 0.076 0.316 0.016 0.492 0.060 0.040
#> GSM751417 4 0.7102 0.28766 0.076 0.316 0.016 0.492 0.060 0.040
#> GSM751421 4 0.6644 0.49968 0.080 0.104 0.076 0.648 0.064 0.028
#> GSM751422 4 0.6644 0.49968 0.080 0.104 0.076 0.648 0.064 0.028
#> GSM751360 4 0.6900 0.48805 0.080 0.108 0.084 0.624 0.080 0.024
#> GSM751364 4 0.7818 0.29775 0.136 0.272 0.048 0.456 0.056 0.032
#> GSM751390 2 0.2849 0.56006 0.004 0.872 0.028 0.004 0.084 0.008
#> GSM751392 2 0.1655 0.59738 0.000 0.936 0.004 0.004 0.044 0.012
#> GSM751396 2 0.1723 0.59618 0.000 0.932 0.004 0.004 0.048 0.012
#> GSM751399 3 0.0790 0.60847 0.032 0.000 0.968 0.000 0.000 0.000
#> GSM751400 3 0.1155 0.60901 0.036 0.000 0.956 0.000 0.004 0.004
#> GSM751401 3 0.1010 0.60882 0.036 0.004 0.960 0.000 0.000 0.000
#> GSM751402 3 0.0865 0.60957 0.036 0.000 0.964 0.000 0.000 0.000
#> GSM751403 3 0.0790 0.60847 0.032 0.000 0.968 0.000 0.000 0.000
#> GSM751405 3 0.0935 0.60794 0.032 0.000 0.964 0.000 0.004 0.000
#> GSM751407 3 0.2775 0.59158 0.048 0.024 0.888 0.020 0.020 0.000
#> GSM751408 3 0.2918 0.58800 0.052 0.020 0.880 0.020 0.028 0.000
#> GSM751409 3 0.7472 0.00671 0.100 0.240 0.492 0.036 0.124 0.008
#> GSM751412 3 0.3646 0.56438 0.056 0.048 0.840 0.024 0.032 0.000
#> GSM751418 4 0.7682 0.43918 0.180 0.184 0.072 0.500 0.032 0.032
#> GSM751419 4 0.7682 0.43918 0.180 0.184 0.072 0.500 0.032 0.032
#> GSM751420 3 0.1296 0.60906 0.044 0.000 0.948 0.000 0.004 0.004
#> GSM751425 2 0.2633 0.59278 0.000 0.864 0.000 0.004 0.112 0.020
#> GSM751429 1 0.4076 0.75383 0.804 0.012 0.080 0.084 0.012 0.008
#> GSM751430 6 0.3481 0.72181 0.004 0.100 0.000 0.040 0.024 0.832
#> GSM751433 2 0.5313 0.35366 0.016 0.608 0.000 0.312 0.028 0.036
#> GSM751437 3 0.7292 0.19472 0.108 0.160 0.560 0.076 0.088 0.008
#> GSM751448 3 0.3060 0.56683 0.088 0.000 0.852 0.004 0.052 0.004
#> GSM751451 2 0.5297 0.31214 0.024 0.584 0.000 0.344 0.028 0.020
#> GSM751423 2 0.4253 0.55286 0.004 0.772 0.004 0.148 0.048 0.024
#> GSM751424 2 0.5233 0.36408 0.016 0.616 0.000 0.308 0.028 0.032
#> GSM751428 2 0.4414 0.58575 0.040 0.796 0.004 0.060 0.072 0.028
#> GSM751431 2 0.5313 0.35366 0.016 0.608 0.000 0.312 0.028 0.036
#> GSM751432 6 0.3481 0.72181 0.004 0.100 0.000 0.040 0.024 0.832
#> GSM751434 6 0.3481 0.72181 0.004 0.100 0.000 0.040 0.024 0.832
#> GSM751435 2 0.5459 0.51526 0.116 0.716 0.020 0.096 0.036 0.016
#> GSM751436 2 0.5313 0.35366 0.016 0.608 0.000 0.312 0.028 0.036
#> GSM751440 2 0.5525 0.51318 0.116 0.712 0.020 0.096 0.040 0.016
#> GSM751444 2 0.4912 0.51406 0.012 0.724 0.028 0.008 0.180 0.048
#> GSM751446 2 0.6070 0.50496 0.104 0.688 0.024 0.088 0.048 0.048
#> GSM751449 2 0.5021 0.50107 0.008 0.716 0.040 0.008 0.180 0.048
#> GSM751450 2 0.4246 0.54677 0.004 0.768 0.004 0.156 0.048 0.020
#> GSM751452 2 0.5233 0.36408 0.016 0.616 0.000 0.308 0.028 0.032
#> GSM751426 2 0.5233 0.36408 0.016 0.616 0.000 0.308 0.028 0.032
#> GSM751427 2 0.4414 0.58575 0.040 0.796 0.004 0.060 0.072 0.028
#> GSM751438 2 0.4983 0.51069 0.012 0.720 0.032 0.008 0.180 0.048
#> GSM751439 2 0.6846 0.42458 0.104 0.632 0.088 0.088 0.052 0.036
#> GSM751441 2 0.4850 0.51778 0.012 0.728 0.028 0.008 0.180 0.044
#> GSM751442 2 0.6070 0.50496 0.104 0.688 0.024 0.088 0.048 0.048
#> GSM751443 3 0.3060 0.56683 0.088 0.000 0.852 0.004 0.052 0.004
#> GSM751445 2 0.4879 0.50695 0.008 0.720 0.036 0.004 0.184 0.048
#> GSM751447 2 0.4759 0.52583 0.012 0.732 0.020 0.008 0.180 0.048
#> GSM751453 2 0.4759 0.52583 0.012 0.732 0.020 0.008 0.180 0.048
#> GSM751454 2 0.4759 0.52583 0.012 0.732 0.020 0.008 0.180 0.048
#> GSM751455 2 0.6070 0.50496 0.104 0.688 0.024 0.088 0.048 0.048
#> GSM751456 2 0.6070 0.50496 0.104 0.688 0.024 0.088 0.048 0.048
#> GSM751457 2 0.5069 0.49078 0.008 0.708 0.048 0.004 0.184 0.048
#> GSM751458 2 0.5069 0.49078 0.008 0.708 0.048 0.004 0.184 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 tissue(p) disease.state(p) agent(p) k
#> ATC:hclust 136 1.97e-10 0.3437 0.514406 2
#> ATC:hclust 112 9.62e-13 0.8475 0.912583 3
#> ATC:hclust 125 3.50e-18 0.0579 0.024978 4
#> ATC:hclust 100 3.38e-15 0.1248 0.011913 5
#> ATC:hclust 106 1.43e-17 0.1098 0.000332 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 4537 rows and 166 columns.
#> Top rows (454, 908, 1361, 1814, 2268) 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 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 0.683 0.915 0.941 0.4298 0.592 0.592
#> 3 3 0.776 0.884 0.925 0.5263 0.731 0.552
#> 4 4 0.615 0.550 0.770 0.1203 0.969 0.909
#> 5 5 0.621 0.516 0.685 0.0671 0.840 0.526
#> 6 6 0.662 0.598 0.737 0.0455 0.926 0.673
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
#> GSM751298 1 0.0376 0.981 0.996 0.004
#> GSM751304 2 0.0672 0.926 0.008 0.992
#> GSM751305 2 0.0672 0.926 0.008 0.992
#> GSM751307 2 0.2236 0.921 0.036 0.964
#> GSM751310 1 0.1184 0.983 0.984 0.016
#> GSM751314 1 0.1184 0.983 0.984 0.016
#> GSM751316 1 0.1184 0.983 0.984 0.016
#> GSM751318 1 0.1184 0.983 0.984 0.016
#> GSM751342 1 0.2236 0.966 0.964 0.036
#> GSM751346 1 0.0672 0.974 0.992 0.008
#> GSM751347 2 0.7528 0.827 0.216 0.784
#> GSM751348 2 0.0938 0.926 0.012 0.988
#> GSM751349 2 0.0672 0.926 0.008 0.992
#> GSM751352 2 0.0938 0.926 0.012 0.988
#> GSM751353 2 0.0376 0.925 0.004 0.996
#> GSM751354 2 0.1184 0.924 0.016 0.984
#> GSM751355 2 0.1184 0.924 0.016 0.984
#> GSM751358 2 0.0376 0.925 0.004 0.996
#> GSM751359 2 0.0672 0.926 0.008 0.992
#> GSM751294 2 0.1184 0.922 0.016 0.984
#> GSM751296 1 0.0000 0.980 1.000 0.000
#> GSM751297 1 0.2423 0.950 0.960 0.040
#> GSM751299 2 0.1633 0.924 0.024 0.976
#> GSM751300 1 0.0000 0.980 1.000 0.000
#> GSM751301 2 0.2603 0.917 0.044 0.956
#> GSM751302 1 0.0000 0.980 1.000 0.000
#> GSM751303 1 0.1184 0.983 0.984 0.016
#> GSM751306 1 0.1184 0.983 0.984 0.016
#> GSM751308 2 0.6973 0.841 0.188 0.812
#> GSM751309 1 0.1184 0.983 0.984 0.016
#> GSM751311 1 0.1184 0.983 0.984 0.016
#> GSM751312 1 0.1184 0.983 0.984 0.016
#> GSM751313 1 0.0000 0.980 1.000 0.000
#> GSM751315 1 0.1184 0.983 0.984 0.016
#> GSM751317 1 0.1184 0.983 0.984 0.016
#> GSM751320 1 0.1184 0.983 0.984 0.016
#> GSM751321 1 0.1184 0.983 0.984 0.016
#> GSM751322 1 0.1184 0.983 0.984 0.016
#> GSM751324 1 0.1184 0.983 0.984 0.016
#> GSM751325 1 0.1184 0.983 0.984 0.016
#> GSM751332 1 0.1184 0.983 0.984 0.016
#> GSM751334 1 0.1184 0.983 0.984 0.016
#> GSM751339 1 0.0672 0.974 0.992 0.008
#> GSM751341 1 0.0000 0.980 1.000 0.000
#> GSM751343 1 0.1184 0.983 0.984 0.016
#> GSM751344 2 0.0672 0.926 0.008 0.992
#> GSM751345 2 0.0672 0.926 0.008 0.992
#> GSM751356 2 0.0672 0.925 0.008 0.992
#> GSM751357 2 0.0672 0.925 0.008 0.992
#> GSM751293 2 0.2603 0.917 0.044 0.956
#> GSM751295 1 0.0000 0.980 1.000 0.000
#> GSM751319 1 0.1184 0.983 0.984 0.016
#> GSM751323 1 0.0938 0.983 0.988 0.012
#> GSM751326 1 0.0000 0.980 1.000 0.000
#> GSM751327 1 0.0938 0.983 0.988 0.012
#> GSM751328 1 0.1184 0.983 0.984 0.016
#> GSM751329 1 0.1184 0.983 0.984 0.016
#> GSM751330 1 0.1184 0.983 0.984 0.016
#> GSM751331 1 0.0376 0.981 0.996 0.004
#> GSM751333 1 0.0000 0.980 1.000 0.000
#> GSM751335 1 0.1184 0.983 0.984 0.016
#> GSM751336 1 0.0000 0.980 1.000 0.000
#> GSM751337 1 0.0672 0.974 0.992 0.008
#> GSM751338 1 0.0376 0.977 0.996 0.004
#> GSM751340 1 0.0672 0.974 0.992 0.008
#> GSM751350 1 0.0000 0.980 1.000 0.000
#> GSM751351 1 0.0000 0.980 1.000 0.000
#> GSM751362 2 0.6973 0.841 0.188 0.812
#> GSM751363 2 0.0672 0.926 0.008 0.992
#> GSM751367 1 0.8813 0.481 0.700 0.300
#> GSM751368 2 0.0672 0.926 0.008 0.992
#> GSM751371 2 0.8713 0.705 0.292 0.708
#> GSM751375 2 0.0672 0.926 0.008 0.992
#> GSM751376 2 0.1184 0.922 0.016 0.984
#> GSM751378 2 0.0938 0.923 0.012 0.988
#> GSM751379 2 0.1843 0.922 0.028 0.972
#> GSM751382 2 0.0672 0.926 0.008 0.992
#> GSM751386 2 0.0672 0.926 0.008 0.992
#> GSM751388 2 0.0672 0.926 0.008 0.992
#> GSM751391 2 0.3584 0.910 0.068 0.932
#> GSM751410 2 0.7056 0.838 0.192 0.808
#> GSM751414 2 0.8499 0.736 0.276 0.724
#> GSM751361 2 0.0672 0.926 0.008 0.992
#> GSM751365 2 0.6247 0.863 0.156 0.844
#> GSM751366 2 0.8955 0.680 0.312 0.688
#> GSM751369 2 0.6973 0.841 0.188 0.812
#> GSM751370 2 0.8386 0.738 0.268 0.732
#> GSM751372 2 0.6712 0.847 0.176 0.824
#> GSM751373 2 0.8608 0.728 0.284 0.716
#> GSM751374 2 0.1843 0.922 0.028 0.972
#> GSM751377 2 0.0672 0.926 0.008 0.992
#> GSM751380 2 0.7299 0.826 0.204 0.796
#> GSM751381 2 0.0672 0.926 0.008 0.992
#> GSM751383 2 0.0672 0.926 0.008 0.992
#> GSM751384 2 0.0000 0.925 0.000 1.000
#> GSM751385 2 0.0376 0.924 0.004 0.996
#> GSM751387 2 0.0672 0.926 0.008 0.992
#> GSM751389 2 0.5294 0.887 0.120 0.880
#> GSM751393 2 0.1184 0.922 0.016 0.984
#> GSM751394 2 0.0672 0.926 0.008 0.992
#> GSM751395 2 0.1184 0.922 0.016 0.984
#> GSM751397 2 0.0672 0.926 0.008 0.992
#> GSM751398 2 0.0672 0.926 0.008 0.992
#> GSM751404 2 0.6973 0.841 0.188 0.812
#> GSM751406 2 0.6973 0.841 0.188 0.812
#> GSM751411 2 0.5519 0.877 0.128 0.872
#> GSM751413 2 0.0672 0.926 0.008 0.992
#> GSM751415 2 0.6973 0.841 0.188 0.812
#> GSM751416 2 0.0672 0.926 0.008 0.992
#> GSM751417 2 0.0672 0.926 0.008 0.992
#> GSM751421 2 0.6973 0.839 0.188 0.812
#> GSM751422 2 0.6801 0.843 0.180 0.820
#> GSM751360 2 0.6712 0.844 0.176 0.824
#> GSM751364 2 0.4690 0.897 0.100 0.900
#> GSM751390 2 0.0000 0.925 0.000 1.000
#> GSM751392 2 0.0672 0.926 0.008 0.992
#> GSM751396 2 0.0672 0.926 0.008 0.992
#> GSM751399 2 0.6048 0.870 0.148 0.852
#> GSM751400 2 0.4022 0.906 0.080 0.920
#> GSM751401 2 0.6973 0.841 0.188 0.812
#> GSM751402 2 0.6973 0.841 0.188 0.812
#> GSM751403 2 0.6438 0.860 0.164 0.836
#> GSM751405 2 0.6973 0.841 0.188 0.812
#> GSM751407 2 0.6973 0.841 0.188 0.812
#> GSM751408 2 0.6048 0.870 0.148 0.852
#> GSM751409 2 0.5059 0.891 0.112 0.888
#> GSM751412 2 0.6801 0.848 0.180 0.820
#> GSM751418 2 0.6973 0.840 0.188 0.812
#> GSM751419 2 0.6801 0.844 0.180 0.820
#> GSM751420 2 0.5408 0.884 0.124 0.876
#> GSM751425 2 0.0672 0.926 0.008 0.992
#> GSM751429 2 0.7528 0.824 0.216 0.784
#> GSM751430 2 0.0672 0.926 0.008 0.992
#> GSM751433 2 0.2236 0.921 0.036 0.964
#> GSM751437 2 0.6973 0.841 0.188 0.812
#> GSM751448 2 0.6973 0.841 0.188 0.812
#> GSM751451 2 0.2236 0.921 0.036 0.964
#> GSM751423 2 0.2236 0.921 0.036 0.964
#> GSM751424 2 0.2236 0.921 0.036 0.964
#> GSM751428 2 0.2236 0.921 0.036 0.964
#> GSM751431 2 0.2236 0.921 0.036 0.964
#> GSM751432 2 0.2236 0.921 0.036 0.964
#> GSM751434 2 0.2236 0.921 0.036 0.964
#> GSM751435 2 0.2236 0.921 0.036 0.964
#> GSM751436 2 0.2236 0.921 0.036 0.964
#> GSM751440 2 0.2236 0.921 0.036 0.964
#> GSM751444 2 0.2778 0.922 0.048 0.952
#> GSM751446 2 0.2778 0.922 0.048 0.952
#> GSM751449 2 0.1184 0.922 0.016 0.984
#> GSM751450 2 0.2236 0.921 0.036 0.964
#> GSM751452 2 0.2236 0.921 0.036 0.964
#> GSM751426 2 0.2236 0.921 0.036 0.964
#> GSM751427 2 0.2236 0.922 0.036 0.964
#> GSM751438 2 0.1184 0.922 0.016 0.984
#> GSM751439 2 0.6247 0.874 0.156 0.844
#> GSM751441 2 0.1184 0.924 0.016 0.984
#> GSM751442 2 0.2423 0.922 0.040 0.960
#> GSM751443 2 0.5519 0.882 0.128 0.872
#> GSM751445 2 0.0938 0.923 0.012 0.988
#> GSM751447 2 0.2236 0.921 0.036 0.964
#> GSM751453 2 0.2236 0.921 0.036 0.964
#> GSM751454 2 0.2236 0.921 0.036 0.964
#> GSM751455 2 0.2423 0.922 0.040 0.960
#> GSM751456 2 0.2423 0.922 0.040 0.960
#> GSM751457 2 0.1184 0.922 0.016 0.984
#> GSM751458 2 0.1184 0.922 0.016 0.984
cbind(get_classes(res, k = 3), get_membership(res, k = 3))
#> class entropy silhouette p1 p2 p3
#> GSM751298 1 0.0983 0.978 0.980 0.004 0.016
#> GSM751304 2 0.3941 0.827 0.000 0.844 0.156
#> GSM751305 2 0.3941 0.827 0.000 0.844 0.156
#> GSM751307 2 0.1031 0.925 0.000 0.976 0.024
#> GSM751310 1 0.0829 0.979 0.984 0.004 0.012
#> GSM751314 1 0.0424 0.981 0.992 0.000 0.008
#> GSM751316 1 0.0829 0.979 0.984 0.004 0.012
#> GSM751318 1 0.1182 0.975 0.976 0.012 0.012
#> GSM751342 1 0.2339 0.942 0.940 0.048 0.012
#> GSM751346 1 0.1267 0.977 0.972 0.004 0.024
#> GSM751347 3 0.6306 0.729 0.052 0.200 0.748
#> GSM751348 2 0.1031 0.927 0.000 0.976 0.024
#> GSM751349 2 0.1031 0.926 0.000 0.976 0.024
#> GSM751352 2 0.1753 0.919 0.000 0.952 0.048
#> GSM751353 2 0.1163 0.925 0.000 0.972 0.028
#> GSM751354 2 0.3941 0.836 0.000 0.844 0.156
#> GSM751355 2 0.1411 0.925 0.000 0.964 0.036
#> GSM751358 2 0.6664 0.132 0.008 0.528 0.464
#> GSM751359 2 0.2066 0.920 0.000 0.940 0.060
#> GSM751294 3 0.3192 0.870 0.000 0.112 0.888
#> GSM751296 1 0.1267 0.977 0.972 0.004 0.024
#> GSM751297 3 0.5873 0.517 0.312 0.004 0.684
#> GSM751299 2 0.1860 0.917 0.000 0.948 0.052
#> GSM751300 1 0.1267 0.977 0.972 0.004 0.024
#> GSM751301 2 0.1337 0.920 0.012 0.972 0.016
#> GSM751302 1 0.1267 0.977 0.972 0.004 0.024
#> GSM751303 1 0.1182 0.975 0.976 0.012 0.012
#> GSM751306 1 0.0829 0.979 0.984 0.004 0.012
#> GSM751308 3 0.3998 0.865 0.060 0.056 0.884
#> GSM751309 1 0.1015 0.977 0.980 0.008 0.012
#> GSM751311 1 0.1015 0.977 0.980 0.008 0.012
#> GSM751312 1 0.0829 0.979 0.984 0.004 0.012
#> GSM751313 1 0.1129 0.978 0.976 0.004 0.020
#> GSM751315 1 0.0424 0.981 0.992 0.000 0.008
#> GSM751317 1 0.1015 0.977 0.980 0.008 0.012
#> GSM751320 1 0.0424 0.981 0.992 0.000 0.008
#> GSM751321 1 0.0424 0.981 0.992 0.000 0.008
#> GSM751322 1 0.0424 0.981 0.992 0.000 0.008
#> GSM751324 1 0.0424 0.981 0.992 0.000 0.008
#> GSM751325 1 0.0424 0.981 0.992 0.000 0.008
#> GSM751332 1 0.0237 0.981 0.996 0.000 0.004
#> GSM751334 1 0.0237 0.981 0.996 0.000 0.004
#> GSM751339 1 0.1031 0.979 0.976 0.000 0.024
#> GSM751341 1 0.0983 0.978 0.980 0.004 0.016
#> GSM751343 1 0.0424 0.981 0.992 0.000 0.008
#> GSM751344 2 0.1163 0.924 0.000 0.972 0.028
#> GSM751345 2 0.1163 0.924 0.000 0.972 0.028
#> GSM751356 2 0.4452 0.794 0.000 0.808 0.192
#> GSM751357 2 0.4452 0.794 0.000 0.808 0.192
#> GSM751293 2 0.1337 0.920 0.012 0.972 0.016
#> GSM751295 1 0.1267 0.977 0.972 0.004 0.024
#> GSM751319 1 0.0424 0.981 0.992 0.000 0.008
#> GSM751323 1 0.0237 0.981 0.996 0.000 0.004
#> GSM751326 1 0.1129 0.978 0.976 0.004 0.020
#> GSM751327 1 0.0237 0.981 0.996 0.000 0.004
#> GSM751328 1 0.0237 0.981 0.996 0.000 0.004
#> GSM751329 1 0.0237 0.981 0.996 0.000 0.004
#> GSM751330 1 0.1129 0.978 0.976 0.004 0.020
#> GSM751331 1 0.1267 0.977 0.972 0.004 0.024
#> GSM751333 1 0.1129 0.978 0.976 0.004 0.020
#> GSM751335 1 0.1129 0.978 0.976 0.004 0.020
#> GSM751336 1 0.1129 0.978 0.976 0.004 0.020
#> GSM751337 1 0.1129 0.978 0.976 0.004 0.020
#> GSM751338 1 0.0747 0.981 0.984 0.000 0.016
#> GSM751340 1 0.4887 0.716 0.772 0.000 0.228
#> GSM751350 1 0.1267 0.977 0.972 0.004 0.024
#> GSM751351 1 0.1267 0.977 0.972 0.004 0.024
#> GSM751362 3 0.1529 0.903 0.000 0.040 0.960
#> GSM751363 2 0.3030 0.891 0.004 0.904 0.092
#> GSM751367 3 0.7286 0.113 0.464 0.028 0.508
#> GSM751368 2 0.2096 0.913 0.004 0.944 0.052
#> GSM751371 3 0.6526 0.644 0.260 0.036 0.704
#> GSM751375 2 0.0892 0.926 0.000 0.980 0.020
#> GSM751376 3 0.2878 0.876 0.000 0.096 0.904
#> GSM751378 3 0.5465 0.627 0.000 0.288 0.712
#> GSM751379 3 0.2878 0.876 0.000 0.096 0.904
#> GSM751382 2 0.1031 0.926 0.000 0.976 0.024
#> GSM751386 2 0.2625 0.904 0.000 0.916 0.084
#> GSM751388 2 0.2625 0.904 0.000 0.916 0.084
#> GSM751391 3 0.5692 0.690 0.008 0.268 0.724
#> GSM751410 3 0.1832 0.900 0.008 0.036 0.956
#> GSM751414 3 0.4887 0.852 0.096 0.060 0.844
#> GSM751361 2 0.6057 0.496 0.004 0.656 0.340
#> GSM751365 3 0.2860 0.890 0.004 0.084 0.912
#> GSM751366 3 0.2269 0.897 0.016 0.040 0.944
#> GSM751369 3 0.1411 0.900 0.000 0.036 0.964
#> GSM751370 3 0.3375 0.889 0.044 0.048 0.908
#> GSM751372 3 0.1753 0.901 0.000 0.048 0.952
#> GSM751373 3 0.7500 0.734 0.164 0.140 0.696
#> GSM751374 3 0.2878 0.876 0.000 0.096 0.904
#> GSM751377 2 0.2537 0.903 0.000 0.920 0.080
#> GSM751380 3 0.2063 0.899 0.008 0.044 0.948
#> GSM751381 2 0.2625 0.904 0.000 0.916 0.084
#> GSM751383 2 0.2625 0.904 0.000 0.916 0.084
#> GSM751384 3 0.6095 0.401 0.000 0.392 0.608
#> GSM751385 2 0.5621 0.627 0.000 0.692 0.308
#> GSM751387 2 0.2625 0.904 0.000 0.916 0.084
#> GSM751389 3 0.1411 0.902 0.000 0.036 0.964
#> GSM751393 3 0.1411 0.902 0.000 0.036 0.964
#> GSM751394 2 0.2625 0.904 0.000 0.916 0.084
#> GSM751395 3 0.2066 0.897 0.000 0.060 0.940
#> GSM751397 2 0.2711 0.901 0.000 0.912 0.088
#> GSM751398 2 0.2625 0.904 0.000 0.916 0.084
#> GSM751404 3 0.1643 0.903 0.000 0.044 0.956
#> GSM751406 3 0.1643 0.903 0.000 0.044 0.956
#> GSM751411 3 0.2165 0.898 0.000 0.064 0.936
#> GSM751413 2 0.1878 0.920 0.004 0.952 0.044
#> GSM751415 3 0.1529 0.903 0.000 0.040 0.960
#> GSM751416 2 0.5902 0.553 0.004 0.680 0.316
#> GSM751417 2 0.5902 0.553 0.004 0.680 0.316
#> GSM751421 3 0.2527 0.896 0.020 0.044 0.936
#> GSM751422 3 0.2527 0.896 0.020 0.044 0.936
#> GSM751360 3 0.2998 0.888 0.016 0.068 0.916
#> GSM751364 3 0.5443 0.709 0.004 0.260 0.736
#> GSM751390 3 0.6008 0.453 0.000 0.372 0.628
#> GSM751392 2 0.2625 0.904 0.000 0.916 0.084
#> GSM751396 2 0.0592 0.927 0.000 0.988 0.012
#> GSM751399 3 0.1643 0.903 0.000 0.044 0.956
#> GSM751400 3 0.1643 0.903 0.000 0.044 0.956
#> GSM751401 3 0.1643 0.903 0.000 0.044 0.956
#> GSM751402 3 0.1529 0.903 0.000 0.040 0.960
#> GSM751403 3 0.1643 0.903 0.000 0.044 0.956
#> GSM751405 3 0.1643 0.903 0.000 0.044 0.956
#> GSM751407 3 0.1643 0.903 0.000 0.044 0.956
#> GSM751408 3 0.1643 0.903 0.000 0.044 0.956
#> GSM751409 3 0.1643 0.903 0.000 0.044 0.956
#> GSM751412 3 0.1643 0.903 0.000 0.044 0.956
#> GSM751418 3 0.5070 0.762 0.004 0.224 0.772
#> GSM751419 3 0.5024 0.766 0.004 0.220 0.776
#> GSM751420 3 0.1529 0.903 0.000 0.040 0.960
#> GSM751425 2 0.0892 0.926 0.000 0.980 0.020
#> GSM751429 3 0.1585 0.893 0.008 0.028 0.964
#> GSM751430 2 0.0892 0.926 0.000 0.980 0.020
#> GSM751433 2 0.0475 0.923 0.004 0.992 0.004
#> GSM751437 3 0.1643 0.903 0.000 0.044 0.956
#> GSM751448 3 0.1031 0.896 0.000 0.024 0.976
#> GSM751451 2 0.1170 0.918 0.008 0.976 0.016
#> GSM751423 2 0.0661 0.926 0.004 0.988 0.008
#> GSM751424 2 0.0475 0.926 0.004 0.992 0.004
#> GSM751428 2 0.0424 0.925 0.000 0.992 0.008
#> GSM751431 2 0.0475 0.923 0.004 0.992 0.004
#> GSM751432 2 0.0424 0.926 0.000 0.992 0.008
#> GSM751434 2 0.0424 0.925 0.000 0.992 0.008
#> GSM751435 2 0.0747 0.926 0.000 0.984 0.016
#> GSM751436 2 0.0475 0.926 0.004 0.992 0.004
#> GSM751440 2 0.0661 0.926 0.004 0.988 0.008
#> GSM751444 2 0.0592 0.926 0.000 0.988 0.012
#> GSM751446 2 0.0747 0.926 0.000 0.984 0.016
#> GSM751449 2 0.3116 0.867 0.000 0.892 0.108
#> GSM751450 2 0.0475 0.926 0.004 0.992 0.004
#> GSM751452 2 0.0475 0.926 0.004 0.992 0.004
#> GSM751426 2 0.0475 0.926 0.004 0.992 0.004
#> GSM751427 2 0.1411 0.922 0.000 0.964 0.036
#> GSM751438 2 0.5431 0.588 0.000 0.716 0.284
#> GSM751439 3 0.3412 0.865 0.000 0.124 0.876
#> GSM751441 2 0.0892 0.926 0.000 0.980 0.020
#> GSM751442 2 0.2066 0.909 0.000 0.940 0.060
#> GSM751443 3 0.2878 0.878 0.000 0.096 0.904
#> GSM751445 2 0.1163 0.925 0.000 0.972 0.028
#> GSM751447 2 0.0592 0.926 0.000 0.988 0.012
#> GSM751453 2 0.0592 0.926 0.000 0.988 0.012
#> GSM751454 2 0.0592 0.926 0.000 0.988 0.012
#> GSM751455 2 0.2066 0.909 0.000 0.940 0.060
#> GSM751456 2 0.2066 0.909 0.000 0.940 0.060
#> GSM751457 3 0.4062 0.829 0.000 0.164 0.836
#> GSM751458 3 0.4062 0.829 0.000 0.164 0.836
cbind(get_classes(res, k = 4), get_membership(res, k = 4))
#> class entropy silhouette p1 p2 p3 p4
#> GSM751298 1 0.4086 0.830 0.776 0.000 0.008 0.216
#> GSM751304 4 0.7062 0.160 0.016 0.452 0.076 0.456
#> GSM751305 2 0.6956 -0.267 0.016 0.460 0.068 0.456
#> GSM751307 2 0.4516 0.471 0.000 0.736 0.012 0.252
#> GSM751310 1 0.2081 0.860 0.916 0.000 0.000 0.084
#> GSM751314 1 0.2081 0.860 0.916 0.000 0.000 0.084
#> GSM751316 1 0.2530 0.845 0.888 0.000 0.000 0.112
#> GSM751318 1 0.2814 0.831 0.868 0.000 0.000 0.132
#> GSM751342 1 0.3552 0.811 0.848 0.024 0.000 0.128
#> GSM751346 1 0.4422 0.811 0.736 0.000 0.008 0.256
#> GSM751347 3 0.8289 0.310 0.136 0.056 0.484 0.324
#> GSM751348 2 0.4500 0.422 0.000 0.684 0.000 0.316
#> GSM751349 2 0.3975 0.453 0.000 0.760 0.000 0.240
#> GSM751352 2 0.5038 0.310 0.000 0.652 0.012 0.336
#> GSM751353 2 0.4277 0.428 0.000 0.720 0.000 0.280
#> GSM751354 2 0.6840 0.120 0.000 0.520 0.108 0.372
#> GSM751355 2 0.4663 0.473 0.000 0.716 0.012 0.272
#> GSM751358 4 0.8375 0.484 0.064 0.216 0.192 0.528
#> GSM751359 2 0.5837 0.121 0.000 0.564 0.036 0.400
#> GSM751294 3 0.6698 0.301 0.000 0.104 0.556 0.340
#> GSM751296 1 0.4328 0.818 0.748 0.000 0.008 0.244
#> GSM751297 3 0.7614 0.268 0.232 0.000 0.468 0.300
#> GSM751299 2 0.5498 0.252 0.000 0.576 0.020 0.404
#> GSM751300 1 0.4422 0.811 0.736 0.000 0.008 0.256
#> GSM751301 2 0.4584 0.422 0.000 0.696 0.004 0.300
#> GSM751302 1 0.4422 0.811 0.736 0.000 0.008 0.256
#> GSM751303 1 0.2589 0.841 0.884 0.000 0.000 0.116
#> GSM751306 1 0.2216 0.856 0.908 0.000 0.000 0.092
#> GSM751308 3 0.7820 0.376 0.128 0.040 0.540 0.292
#> GSM751309 1 0.2149 0.858 0.912 0.000 0.000 0.088
#> GSM751311 1 0.2149 0.858 0.912 0.000 0.000 0.088
#> GSM751312 1 0.2281 0.854 0.904 0.000 0.000 0.096
#> GSM751313 1 0.3486 0.848 0.812 0.000 0.000 0.188
#> GSM751315 1 0.1389 0.872 0.952 0.000 0.000 0.048
#> GSM751317 1 0.2408 0.849 0.896 0.000 0.000 0.104
#> GSM751320 1 0.0000 0.878 1.000 0.000 0.000 0.000
#> GSM751321 1 0.1792 0.866 0.932 0.000 0.000 0.068
#> GSM751322 1 0.1302 0.872 0.956 0.000 0.000 0.044
#> GSM751324 1 0.1302 0.872 0.956 0.000 0.000 0.044
#> GSM751325 1 0.1302 0.872 0.956 0.000 0.000 0.044
#> GSM751332 1 0.0817 0.879 0.976 0.000 0.000 0.024
#> GSM751334 1 0.0592 0.878 0.984 0.000 0.000 0.016
#> GSM751339 1 0.2706 0.871 0.900 0.000 0.020 0.080
#> GSM751341 1 0.3498 0.852 0.832 0.000 0.008 0.160
#> GSM751343 1 0.0592 0.876 0.984 0.000 0.000 0.016
#> GSM751344 2 0.4477 0.392 0.000 0.688 0.000 0.312
#> GSM751345 2 0.4477 0.392 0.000 0.688 0.000 0.312
#> GSM751356 4 0.7242 0.277 0.016 0.416 0.092 0.476
#> GSM751357 4 0.7197 0.265 0.016 0.420 0.088 0.476
#> GSM751293 2 0.4509 0.430 0.000 0.708 0.004 0.288
#> GSM751295 1 0.4422 0.811 0.736 0.000 0.008 0.256
#> GSM751319 1 0.1792 0.866 0.932 0.000 0.000 0.068
#> GSM751323 1 0.0000 0.878 1.000 0.000 0.000 0.000
#> GSM751326 1 0.3486 0.848 0.812 0.000 0.000 0.188
#> GSM751327 1 0.0469 0.879 0.988 0.000 0.000 0.012
#> GSM751328 1 0.0921 0.879 0.972 0.000 0.000 0.028
#> GSM751329 1 0.1557 0.875 0.944 0.000 0.000 0.056
#> GSM751330 1 0.3649 0.842 0.796 0.000 0.000 0.204
#> GSM751331 1 0.3764 0.837 0.784 0.000 0.000 0.216
#> GSM751333 1 0.3486 0.848 0.812 0.000 0.000 0.188
#> GSM751335 1 0.3649 0.842 0.796 0.000 0.000 0.204
#> GSM751336 1 0.3649 0.842 0.796 0.000 0.000 0.204
#> GSM751337 1 0.3400 0.850 0.820 0.000 0.000 0.180
#> GSM751338 1 0.1557 0.878 0.944 0.000 0.000 0.056
#> GSM751340 1 0.6509 0.555 0.632 0.000 0.228 0.140
#> GSM751350 1 0.4422 0.811 0.736 0.000 0.008 0.256
#> GSM751351 1 0.4422 0.811 0.736 0.000 0.008 0.256
#> GSM751362 3 0.0376 0.702 0.000 0.004 0.992 0.004
#> GSM751363 2 0.7010 -0.216 0.004 0.452 0.100 0.444
#> GSM751367 3 0.7726 0.194 0.296 0.000 0.444 0.260
#> GSM751368 2 0.6135 0.247 0.000 0.608 0.068 0.324
#> GSM751371 3 0.8069 0.206 0.320 0.016 0.452 0.212
#> GSM751375 2 0.4372 0.421 0.000 0.728 0.004 0.268
#> GSM751376 3 0.5328 0.524 0.000 0.048 0.704 0.248
#> GSM751378 3 0.7276 -0.117 0.000 0.224 0.540 0.236
#> GSM751379 3 0.5328 0.524 0.000 0.048 0.704 0.248
#> GSM751382 2 0.4567 0.410 0.000 0.716 0.008 0.276
#> GSM751386 2 0.5979 0.298 0.000 0.652 0.076 0.272
#> GSM751388 2 0.5979 0.298 0.000 0.652 0.076 0.272
#> GSM751391 3 0.7163 0.275 0.016 0.104 0.556 0.324
#> GSM751410 3 0.2843 0.670 0.020 0.000 0.892 0.088
#> GSM751414 3 0.5893 0.505 0.048 0.020 0.696 0.236
#> GSM751361 4 0.8013 0.504 0.004 0.324 0.280 0.392
#> GSM751365 3 0.5052 0.507 0.000 0.036 0.720 0.244
#> GSM751366 3 0.2198 0.683 0.008 0.000 0.920 0.072
#> GSM751369 3 0.1675 0.698 0.004 0.004 0.948 0.044
#> GSM751370 3 0.5060 0.547 0.028 0.008 0.736 0.228
#> GSM751372 3 0.3402 0.632 0.000 0.004 0.832 0.164
#> GSM751373 3 0.7437 0.362 0.064 0.092 0.616 0.228
#> GSM751374 3 0.5328 0.524 0.000 0.048 0.704 0.248
#> GSM751377 2 0.6194 0.273 0.000 0.628 0.084 0.288
#> GSM751380 3 0.0779 0.700 0.004 0.000 0.980 0.016
#> GSM751381 2 0.5979 0.298 0.000 0.652 0.076 0.272
#> GSM751383 2 0.5979 0.298 0.000 0.652 0.076 0.272
#> GSM751384 3 0.7811 -0.422 0.000 0.308 0.416 0.276
#> GSM751385 2 0.7515 -0.251 0.000 0.448 0.188 0.364
#> GSM751387 2 0.5979 0.298 0.000 0.652 0.076 0.272
#> GSM751389 3 0.0657 0.702 0.000 0.004 0.984 0.012
#> GSM751393 3 0.3257 0.641 0.000 0.004 0.844 0.152
#> GSM751394 2 0.5785 0.320 0.000 0.664 0.064 0.272
#> GSM751395 3 0.5968 0.425 0.000 0.084 0.664 0.252
#> GSM751397 2 0.6065 0.279 0.000 0.644 0.080 0.276
#> GSM751398 2 0.6052 0.279 0.000 0.640 0.076 0.284
#> GSM751404 3 0.0188 0.702 0.000 0.004 0.996 0.000
#> GSM751406 3 0.0524 0.702 0.000 0.004 0.988 0.008
#> GSM751411 3 0.4574 0.544 0.000 0.024 0.756 0.220
#> GSM751413 2 0.5936 0.144 0.000 0.576 0.044 0.380
#> GSM751415 3 0.0188 0.702 0.000 0.004 0.996 0.000
#> GSM751416 4 0.8078 0.495 0.004 0.332 0.320 0.344
#> GSM751417 4 0.8077 0.494 0.004 0.336 0.316 0.344
#> GSM751421 3 0.3554 0.649 0.020 0.000 0.844 0.136
#> GSM751422 3 0.3554 0.649 0.020 0.000 0.844 0.136
#> GSM751360 3 0.5750 0.504 0.028 0.024 0.688 0.260
#> GSM751364 3 0.6911 0.187 0.004 0.120 0.572 0.304
#> GSM751390 3 0.7793 -0.405 0.000 0.300 0.424 0.276
#> GSM751392 2 0.5979 0.298 0.000 0.652 0.076 0.272
#> GSM751396 2 0.4690 0.407 0.000 0.712 0.012 0.276
#> GSM751399 3 0.0188 0.702 0.000 0.004 0.996 0.000
#> GSM751400 3 0.0376 0.702 0.000 0.004 0.992 0.004
#> GSM751401 3 0.0188 0.702 0.000 0.004 0.996 0.000
#> GSM751402 3 0.0188 0.702 0.000 0.004 0.996 0.000
#> GSM751403 3 0.0524 0.702 0.000 0.004 0.988 0.008
#> GSM751405 3 0.0524 0.702 0.000 0.004 0.988 0.008
#> GSM751407 3 0.0188 0.702 0.000 0.004 0.996 0.000
#> GSM751408 3 0.0779 0.699 0.000 0.004 0.980 0.016
#> GSM751409 3 0.0188 0.702 0.000 0.004 0.996 0.000
#> GSM751412 3 0.1004 0.696 0.000 0.004 0.972 0.024
#> GSM751418 3 0.6420 0.364 0.004 0.108 0.644 0.244
#> GSM751419 3 0.6420 0.364 0.004 0.108 0.644 0.244
#> GSM751420 3 0.1211 0.694 0.000 0.000 0.960 0.040
#> GSM751425 2 0.2530 0.553 0.000 0.896 0.004 0.100
#> GSM751429 3 0.4610 0.574 0.020 0.000 0.744 0.236
#> GSM751430 2 0.4434 0.494 0.000 0.756 0.016 0.228
#> GSM751433 2 0.2142 0.577 0.000 0.928 0.016 0.056
#> GSM751437 3 0.1109 0.696 0.000 0.004 0.968 0.028
#> GSM751448 3 0.3105 0.648 0.000 0.004 0.856 0.140
#> GSM751451 2 0.3881 0.475 0.000 0.812 0.016 0.172
#> GSM751423 2 0.2593 0.567 0.000 0.904 0.016 0.080
#> GSM751424 2 0.2222 0.577 0.000 0.924 0.016 0.060
#> GSM751428 2 0.2796 0.574 0.000 0.892 0.016 0.092
#> GSM751431 2 0.1975 0.579 0.000 0.936 0.016 0.048
#> GSM751432 2 0.2796 0.568 0.000 0.892 0.016 0.092
#> GSM751434 2 0.2796 0.568 0.000 0.892 0.016 0.092
#> GSM751435 2 0.3280 0.549 0.000 0.860 0.016 0.124
#> GSM751436 2 0.2222 0.577 0.000 0.924 0.016 0.060
#> GSM751440 2 0.2928 0.569 0.000 0.880 0.012 0.108
#> GSM751444 2 0.3925 0.525 0.000 0.808 0.016 0.176
#> GSM751446 2 0.3881 0.517 0.000 0.812 0.016 0.172
#> GSM751449 2 0.4880 0.464 0.000 0.760 0.052 0.188
#> GSM751450 2 0.2060 0.578 0.000 0.932 0.016 0.052
#> GSM751452 2 0.2222 0.577 0.000 0.924 0.016 0.060
#> GSM751426 2 0.2060 0.578 0.000 0.932 0.016 0.052
#> GSM751427 2 0.3790 0.532 0.000 0.820 0.016 0.164
#> GSM751438 2 0.5889 0.360 0.000 0.696 0.116 0.188
#> GSM751439 3 0.7042 0.306 0.000 0.240 0.572 0.188
#> GSM751441 2 0.3991 0.518 0.000 0.808 0.020 0.172
#> GSM751442 2 0.4466 0.495 0.000 0.784 0.036 0.180
#> GSM751443 3 0.4669 0.583 0.000 0.036 0.764 0.200
#> GSM751445 2 0.3881 0.518 0.000 0.812 0.016 0.172
#> GSM751447 2 0.3390 0.542 0.000 0.852 0.016 0.132
#> GSM751453 2 0.2662 0.570 0.000 0.900 0.016 0.084
#> GSM751454 2 0.2522 0.570 0.000 0.908 0.016 0.076
#> GSM751455 2 0.4466 0.495 0.000 0.784 0.036 0.180
#> GSM751456 2 0.4466 0.495 0.000 0.784 0.036 0.180
#> GSM751457 3 0.7576 0.142 0.000 0.256 0.484 0.260
#> GSM751458 3 0.7576 0.142 0.000 0.256 0.484 0.260
cbind(get_classes(res, k = 5), get_membership(res, k = 5))
#> class entropy silhouette p1 p2 p3 p4 p5
#> GSM751298 1 0.1285 0.7335 0.956 0.000 0.004 0.036 0.004
#> GSM751304 5 0.7408 0.0670 0.000 0.164 0.056 0.384 0.396
#> GSM751305 5 0.7386 0.0689 0.000 0.160 0.056 0.388 0.396
#> GSM751307 2 0.6807 0.2345 0.012 0.428 0.000 0.184 0.376
#> GSM751310 4 0.4402 0.8171 0.352 0.000 0.000 0.636 0.012
#> GSM751314 4 0.4354 0.8180 0.368 0.000 0.000 0.624 0.008
#> GSM751316 4 0.4503 0.7833 0.312 0.000 0.000 0.664 0.024
#> GSM751318 4 0.4109 0.7650 0.288 0.000 0.000 0.700 0.012
#> GSM751342 4 0.4695 0.7649 0.296 0.008 0.000 0.672 0.024
#> GSM751346 1 0.0867 0.7486 0.976 0.008 0.008 0.000 0.008
#> GSM751347 1 0.5708 0.4603 0.684 0.044 0.220 0.020 0.032
#> GSM751348 5 0.6723 0.2143 0.000 0.356 0.020 0.148 0.476
#> GSM751349 5 0.4196 0.4311 0.000 0.356 0.000 0.004 0.640
#> GSM751352 5 0.7554 -0.0481 0.012 0.304 0.024 0.248 0.412
#> GSM751353 5 0.6189 0.0134 0.000 0.384 0.000 0.140 0.476
#> GSM751354 2 0.9194 0.1019 0.080 0.324 0.100 0.200 0.296
#> GSM751355 2 0.6728 0.1029 0.012 0.428 0.004 0.144 0.412
#> GSM751358 5 0.7372 0.1961 0.000 0.072 0.132 0.360 0.436
#> GSM751359 5 0.4843 0.4880 0.000 0.216 0.016 0.048 0.720
#> GSM751294 3 0.8189 0.1381 0.000 0.128 0.368 0.208 0.296
#> GSM751296 1 0.0486 0.7481 0.988 0.000 0.004 0.004 0.004
#> GSM751297 1 0.4916 0.4861 0.716 0.032 0.228 0.016 0.008
#> GSM751299 2 0.8136 0.0950 0.044 0.380 0.028 0.236 0.312
#> GSM751300 1 0.0867 0.7486 0.976 0.008 0.008 0.000 0.008
#> GSM751301 2 0.6972 0.2235 0.012 0.416 0.000 0.228 0.344
#> GSM751302 1 0.0867 0.7486 0.976 0.008 0.008 0.000 0.008
#> GSM751303 4 0.4232 0.7925 0.312 0.000 0.000 0.676 0.012
#> GSM751306 4 0.4371 0.8146 0.344 0.000 0.000 0.644 0.012
#> GSM751308 3 0.8466 0.3174 0.040 0.072 0.380 0.324 0.184
#> GSM751309 4 0.4182 0.8184 0.352 0.000 0.000 0.644 0.004
#> GSM751311 4 0.4252 0.8141 0.340 0.000 0.000 0.652 0.008
#> GSM751312 4 0.4555 0.8109 0.344 0.000 0.000 0.636 0.020
#> GSM751313 1 0.2519 0.6618 0.884 0.000 0.000 0.100 0.016
#> GSM751315 4 0.4436 0.8094 0.396 0.000 0.000 0.596 0.008
#> GSM751317 4 0.4251 0.7968 0.316 0.000 0.000 0.672 0.012
#> GSM751320 4 0.4420 0.7557 0.448 0.000 0.000 0.548 0.004
#> GSM751321 4 0.4380 0.8166 0.376 0.000 0.000 0.616 0.008
#> GSM751322 4 0.4192 0.8043 0.404 0.000 0.000 0.596 0.000
#> GSM751324 4 0.4192 0.8043 0.404 0.000 0.000 0.596 0.000
#> GSM751325 4 0.4192 0.8043 0.404 0.000 0.000 0.596 0.000
#> GSM751332 4 0.4655 0.7093 0.476 0.000 0.000 0.512 0.012
#> GSM751334 4 0.4655 0.7093 0.476 0.000 0.000 0.512 0.012
#> GSM751339 4 0.6527 0.5170 0.416 0.000 0.056 0.468 0.060
#> GSM751341 1 0.2877 0.5711 0.848 0.000 0.004 0.144 0.004
#> GSM751343 4 0.4397 0.7745 0.432 0.000 0.000 0.564 0.004
#> GSM751344 2 0.6929 0.1933 0.012 0.424 0.000 0.216 0.348
#> GSM751345 2 0.6929 0.1933 0.012 0.424 0.000 0.216 0.348
#> GSM751356 5 0.7896 0.1646 0.000 0.188 0.104 0.284 0.424
#> GSM751357 5 0.7896 0.1646 0.000 0.188 0.104 0.284 0.424
#> GSM751293 2 0.6946 0.2277 0.012 0.428 0.000 0.224 0.336
#> GSM751295 1 0.0867 0.7486 0.976 0.008 0.008 0.000 0.008
#> GSM751319 4 0.4341 0.8188 0.364 0.000 0.000 0.628 0.008
#> GSM751323 4 0.4637 0.7442 0.452 0.000 0.000 0.536 0.012
#> GSM751326 1 0.2270 0.6967 0.904 0.000 0.000 0.076 0.020
#> GSM751327 4 0.4827 0.7011 0.476 0.000 0.000 0.504 0.020
#> GSM751328 4 0.4542 0.7444 0.456 0.000 0.000 0.536 0.008
#> GSM751329 1 0.4590 -0.5048 0.568 0.000 0.000 0.420 0.012
#> GSM751330 1 0.1877 0.7109 0.924 0.000 0.000 0.064 0.012
#> GSM751331 1 0.1267 0.7419 0.960 0.004 0.000 0.024 0.012
#> GSM751333 1 0.2208 0.6989 0.908 0.000 0.000 0.072 0.020
#> GSM751335 1 0.1877 0.7109 0.924 0.000 0.000 0.064 0.012
#> GSM751336 1 0.1399 0.7353 0.952 0.000 0.000 0.028 0.020
#> GSM751337 1 0.2625 0.6525 0.876 0.000 0.000 0.108 0.016
#> GSM751338 1 0.5044 -0.6529 0.504 0.000 0.000 0.464 0.032
#> GSM751340 4 0.7901 0.2747 0.292 0.000 0.200 0.412 0.096
#> GSM751350 1 0.0867 0.7486 0.976 0.008 0.008 0.000 0.008
#> GSM751351 1 0.0867 0.7486 0.976 0.008 0.008 0.000 0.008
#> GSM751362 3 0.0579 0.7507 0.000 0.000 0.984 0.008 0.008
#> GSM751363 5 0.6753 0.2754 0.000 0.176 0.040 0.216 0.568
#> GSM751367 1 0.6557 0.2253 0.564 0.012 0.316 0.056 0.052
#> GSM751368 5 0.5932 0.3072 0.000 0.320 0.016 0.084 0.580
#> GSM751371 4 0.7499 0.0173 0.072 0.008 0.312 0.480 0.128
#> GSM751375 5 0.4200 0.4878 0.000 0.320 0.004 0.004 0.672
#> GSM751376 3 0.7869 0.4758 0.056 0.108 0.560 0.168 0.108
#> GSM751378 3 0.6015 0.0492 0.000 0.088 0.484 0.008 0.420
#> GSM751379 3 0.7869 0.4758 0.056 0.108 0.560 0.168 0.108
#> GSM751382 5 0.4251 0.5043 0.000 0.316 0.012 0.000 0.672
#> GSM751386 5 0.4526 0.5235 0.000 0.300 0.028 0.000 0.672
#> GSM751388 5 0.4526 0.5235 0.000 0.300 0.028 0.000 0.672
#> GSM751391 3 0.7200 0.4264 0.000 0.032 0.464 0.276 0.228
#> GSM751410 3 0.4063 0.6993 0.000 0.004 0.800 0.112 0.084
#> GSM751414 3 0.5963 0.5419 0.008 0.008 0.604 0.092 0.288
#> GSM751361 5 0.6771 0.3041 0.000 0.076 0.240 0.104 0.580
#> GSM751365 3 0.5427 0.5601 0.000 0.008 0.636 0.072 0.284
#> GSM751366 3 0.3604 0.7119 0.004 0.004 0.836 0.048 0.108
#> GSM751369 3 0.2504 0.7426 0.000 0.000 0.896 0.040 0.064
#> GSM751370 3 0.5553 0.5569 0.004 0.004 0.624 0.076 0.292
#> GSM751372 3 0.4525 0.6454 0.000 0.000 0.724 0.056 0.220
#> GSM751373 3 0.6846 0.4860 0.020 0.032 0.560 0.100 0.288
#> GSM751374 3 0.7869 0.4758 0.056 0.108 0.560 0.168 0.108
#> GSM751377 5 0.5044 0.5254 0.000 0.272 0.044 0.012 0.672
#> GSM751380 3 0.1630 0.7452 0.000 0.004 0.944 0.016 0.036
#> GSM751381 5 0.4526 0.5235 0.000 0.300 0.028 0.000 0.672
#> GSM751383 5 0.4526 0.5235 0.000 0.300 0.028 0.000 0.672
#> GSM751384 5 0.5940 0.4015 0.000 0.140 0.292 0.000 0.568
#> GSM751385 5 0.6467 0.4587 0.000 0.168 0.112 0.084 0.636
#> GSM751387 5 0.4526 0.5235 0.000 0.300 0.028 0.000 0.672
#> GSM751389 3 0.1300 0.7412 0.000 0.000 0.956 0.028 0.016
#> GSM751393 3 0.5244 0.6138 0.004 0.024 0.728 0.160 0.084
#> GSM751394 5 0.4380 0.5158 0.000 0.304 0.020 0.000 0.676
#> GSM751395 3 0.7159 0.4258 0.004 0.060 0.552 0.184 0.200
#> GSM751397 5 0.4691 0.5293 0.000 0.276 0.044 0.000 0.680
#> GSM751398 5 0.4622 0.5296 0.000 0.276 0.040 0.000 0.684
#> GSM751404 3 0.0324 0.7500 0.000 0.004 0.992 0.000 0.004
#> GSM751406 3 0.0162 0.7496 0.000 0.000 0.996 0.004 0.000
#> GSM751411 3 0.4886 0.5648 0.000 0.008 0.668 0.036 0.288
#> GSM751413 5 0.6487 0.1196 0.000 0.256 0.004 0.220 0.520
#> GSM751415 3 0.0740 0.7504 0.000 0.004 0.980 0.008 0.008
#> GSM751416 5 0.6915 0.2277 0.000 0.088 0.300 0.080 0.532
#> GSM751417 5 0.6915 0.2277 0.000 0.088 0.300 0.080 0.532
#> GSM751421 3 0.4732 0.6790 0.000 0.004 0.744 0.144 0.108
#> GSM751422 3 0.4732 0.6790 0.000 0.004 0.744 0.144 0.108
#> GSM751360 3 0.5726 0.6080 0.000 0.004 0.640 0.188 0.168
#> GSM751364 3 0.6451 0.2543 0.000 0.040 0.464 0.072 0.424
#> GSM751390 5 0.5901 0.3836 0.000 0.132 0.300 0.000 0.568
#> GSM751392 5 0.4526 0.5235 0.000 0.300 0.028 0.000 0.672
#> GSM751396 5 0.4270 0.5003 0.000 0.320 0.012 0.000 0.668
#> GSM751399 3 0.0451 0.7503 0.000 0.000 0.988 0.004 0.008
#> GSM751400 3 0.0000 0.7496 0.000 0.000 1.000 0.000 0.000
#> GSM751401 3 0.0324 0.7500 0.000 0.004 0.992 0.000 0.004
#> GSM751402 3 0.0000 0.7496 0.000 0.000 1.000 0.000 0.000
#> GSM751403 3 0.0162 0.7496 0.000 0.000 0.996 0.004 0.000
#> GSM751405 3 0.0162 0.7496 0.000 0.000 0.996 0.004 0.000
#> GSM751407 3 0.0162 0.7499 0.000 0.000 0.996 0.000 0.004
#> GSM751408 3 0.0609 0.7492 0.000 0.000 0.980 0.000 0.020
#> GSM751409 3 0.0566 0.7499 0.000 0.004 0.984 0.000 0.012
#> GSM751412 3 0.1704 0.7311 0.000 0.004 0.928 0.000 0.068
#> GSM751418 3 0.6177 0.4834 0.000 0.036 0.580 0.076 0.308
#> GSM751419 3 0.6177 0.4834 0.000 0.036 0.580 0.076 0.308
#> GSM751420 3 0.1538 0.7368 0.036 0.000 0.948 0.008 0.008
#> GSM751425 2 0.4101 0.2619 0.000 0.628 0.000 0.000 0.372
#> GSM751429 3 0.6324 0.3071 0.368 0.076 0.528 0.020 0.008
#> GSM751430 2 0.6356 0.2611 0.000 0.468 0.000 0.168 0.364
#> GSM751433 2 0.4793 0.4946 0.000 0.684 0.000 0.056 0.260
#> GSM751437 3 0.2253 0.7333 0.020 0.036 0.924 0.012 0.008
#> GSM751448 3 0.4893 0.6567 0.072 0.068 0.788 0.056 0.016
#> GSM751451 2 0.5600 0.3465 0.000 0.588 0.000 0.096 0.316
#> GSM751423 2 0.4380 0.4273 0.000 0.676 0.000 0.020 0.304
#> GSM751424 2 0.4793 0.4946 0.000 0.684 0.000 0.056 0.260
#> GSM751428 2 0.4765 0.5160 0.000 0.704 0.000 0.068 0.228
#> GSM751431 2 0.4666 0.5032 0.000 0.704 0.000 0.056 0.240
#> GSM751432 2 0.5112 0.4909 0.000 0.664 0.000 0.080 0.256
#> GSM751434 2 0.5112 0.4909 0.000 0.664 0.000 0.080 0.256
#> GSM751435 2 0.2464 0.5508 0.016 0.888 0.000 0.000 0.096
#> GSM751436 2 0.4793 0.4946 0.000 0.684 0.000 0.056 0.260
#> GSM751440 2 0.4096 0.4623 0.004 0.724 0.000 0.012 0.260
#> GSM751444 2 0.1211 0.5551 0.000 0.960 0.000 0.024 0.016
#> GSM751446 2 0.2087 0.5369 0.020 0.928 0.000 0.032 0.020
#> GSM751449 2 0.3195 0.5111 0.028 0.884 0.016 0.040 0.032
#> GSM751450 2 0.4693 0.5053 0.000 0.700 0.000 0.056 0.244
#> GSM751452 2 0.4769 0.4983 0.000 0.688 0.000 0.056 0.256
#> GSM751426 2 0.4719 0.5019 0.000 0.696 0.000 0.056 0.248
#> GSM751427 2 0.2513 0.5290 0.008 0.900 0.004 0.012 0.076
#> GSM751438 2 0.4065 0.4707 0.032 0.840 0.060 0.040 0.028
#> GSM751439 2 0.6663 0.1887 0.064 0.576 0.296 0.040 0.024
#> GSM751441 2 0.2082 0.5366 0.016 0.928 0.000 0.032 0.024
#> GSM751442 2 0.2429 0.5315 0.028 0.916 0.004 0.032 0.020
#> GSM751443 3 0.6540 0.4708 0.072 0.288 0.584 0.044 0.012
#> GSM751445 2 0.1753 0.5456 0.000 0.936 0.000 0.032 0.032
#> GSM751447 2 0.1281 0.5555 0.000 0.956 0.000 0.012 0.032
#> GSM751453 2 0.1952 0.5567 0.000 0.912 0.000 0.004 0.084
#> GSM751454 2 0.1952 0.5565 0.000 0.912 0.000 0.004 0.084
#> GSM751455 2 0.2522 0.5292 0.028 0.912 0.004 0.032 0.024
#> GSM751456 2 0.2522 0.5292 0.028 0.912 0.004 0.032 0.024
#> GSM751457 2 0.8049 -0.0527 0.036 0.424 0.352 0.096 0.092
#> GSM751458 2 0.8049 -0.0527 0.036 0.424 0.352 0.096 0.092
cbind(get_classes(res, k = 6), get_membership(res, k = 6))
#> class entropy silhouette p1 p2 p3 p4 p5 p6
#> GSM751298 1 0.3634 0.78853 0.696 0.000 0.008 0.296 0.000 0.000
#> GSM751304 6 0.2638 0.59255 0.008 0.028 0.000 0.020 0.052 0.892
#> GSM751305 6 0.2831 0.59217 0.016 0.028 0.000 0.020 0.052 0.884
#> GSM751307 6 0.6571 0.39644 0.056 0.156 0.000 0.004 0.284 0.500
#> GSM751310 4 0.1409 0.85175 0.008 0.012 0.000 0.948 0.000 0.032
#> GSM751314 4 0.1409 0.85231 0.008 0.012 0.000 0.948 0.000 0.032
#> GSM751316 4 0.2222 0.82443 0.008 0.012 0.000 0.896 0.000 0.084
#> GSM751318 4 0.2758 0.77373 0.036 0.012 0.000 0.872 0.000 0.080
#> GSM751342 4 0.2472 0.80914 0.016 0.024 0.000 0.900 0.008 0.052
#> GSM751346 1 0.3507 0.82854 0.764 0.008 0.012 0.216 0.000 0.000
#> GSM751347 1 0.3974 0.69097 0.784 0.008 0.140 0.060 0.008 0.000
#> GSM751348 5 0.5572 0.14160 0.024 0.060 0.004 0.012 0.604 0.296
#> GSM751349 5 0.1340 0.68716 0.008 0.040 0.000 0.000 0.948 0.004
#> GSM751352 6 0.4603 0.58053 0.020 0.068 0.000 0.000 0.200 0.712
#> GSM751353 5 0.5218 0.00438 0.012 0.072 0.000 0.000 0.560 0.356
#> GSM751354 6 0.7559 0.51413 0.112 0.140 0.068 0.000 0.176 0.504
#> GSM751355 5 0.6538 -0.16951 0.072 0.124 0.000 0.000 0.464 0.340
#> GSM751358 6 0.6899 0.46572 0.068 0.048 0.028 0.072 0.184 0.600
#> GSM751359 5 0.3060 0.58818 0.020 0.012 0.000 0.000 0.836 0.132
#> GSM751294 6 0.7237 0.44858 0.052 0.092 0.168 0.008 0.124 0.556
#> GSM751296 1 0.3420 0.82573 0.748 0.000 0.012 0.240 0.000 0.000
#> GSM751297 1 0.3922 0.69312 0.784 0.008 0.140 0.064 0.000 0.004
#> GSM751299 6 0.5811 0.56369 0.048 0.148 0.000 0.000 0.188 0.616
#> GSM751300 1 0.3507 0.82854 0.764 0.008 0.012 0.216 0.000 0.000
#> GSM751301 6 0.5644 0.53419 0.020 0.140 0.000 0.004 0.224 0.612
#> GSM751302 1 0.3507 0.82854 0.764 0.008 0.012 0.216 0.000 0.000
#> GSM751303 4 0.1921 0.83661 0.012 0.012 0.000 0.920 0.000 0.056
#> GSM751306 4 0.1296 0.85085 0.004 0.012 0.000 0.952 0.000 0.032
#> GSM751308 6 0.7328 0.33955 0.060 0.064 0.196 0.128 0.012 0.540
#> GSM751309 4 0.1151 0.85189 0.000 0.012 0.000 0.956 0.000 0.032
#> GSM751311 4 0.1225 0.85133 0.000 0.012 0.000 0.952 0.000 0.036
#> GSM751312 4 0.1888 0.83864 0.004 0.012 0.000 0.916 0.000 0.068
#> GSM751313 1 0.4652 0.76226 0.628 0.032 0.000 0.324 0.000 0.016
#> GSM751315 4 0.1434 0.85159 0.012 0.012 0.000 0.948 0.000 0.028
#> GSM751317 4 0.1769 0.83929 0.004 0.012 0.000 0.924 0.000 0.060
#> GSM751320 4 0.0922 0.84226 0.024 0.004 0.000 0.968 0.000 0.004
#> GSM751321 4 0.1332 0.85199 0.008 0.012 0.000 0.952 0.000 0.028
#> GSM751322 4 0.0692 0.84650 0.020 0.000 0.000 0.976 0.000 0.004
#> GSM751324 4 0.0547 0.84580 0.020 0.000 0.000 0.980 0.000 0.000
#> GSM751325 4 0.0547 0.84580 0.020 0.000 0.000 0.980 0.000 0.000
#> GSM751332 4 0.2095 0.79448 0.076 0.016 0.000 0.904 0.000 0.004
#> GSM751334 4 0.2377 0.78560 0.076 0.024 0.000 0.892 0.000 0.008
#> GSM751339 4 0.6416 0.45246 0.148 0.040 0.040 0.600 0.000 0.172
#> GSM751341 1 0.4083 0.49450 0.532 0.000 0.008 0.460 0.000 0.000
#> GSM751343 4 0.0837 0.84412 0.020 0.004 0.000 0.972 0.000 0.004
#> GSM751344 6 0.5422 0.54183 0.020 0.120 0.000 0.000 0.240 0.620
#> GSM751345 6 0.5422 0.54183 0.020 0.120 0.000 0.000 0.240 0.620
#> GSM751356 6 0.6153 0.51766 0.040 0.076 0.012 0.036 0.196 0.640
#> GSM751357 6 0.6153 0.51766 0.040 0.076 0.012 0.036 0.196 0.640
#> GSM751293 6 0.5666 0.53314 0.020 0.140 0.000 0.004 0.228 0.608
#> GSM751295 1 0.3507 0.82854 0.764 0.008 0.012 0.216 0.000 0.000
#> GSM751319 4 0.1218 0.85250 0.004 0.012 0.000 0.956 0.000 0.028
#> GSM751323 4 0.1666 0.82558 0.036 0.020 0.000 0.936 0.000 0.008
#> GSM751326 1 0.4638 0.76927 0.632 0.032 0.000 0.320 0.000 0.016
#> GSM751327 4 0.2724 0.77415 0.076 0.032 0.000 0.876 0.000 0.016
#> GSM751328 4 0.1152 0.83147 0.044 0.004 0.000 0.952 0.000 0.000
#> GSM751329 4 0.3652 0.54090 0.212 0.020 0.000 0.760 0.000 0.008
#> GSM751330 1 0.4122 0.79971 0.680 0.020 0.000 0.292 0.000 0.008
#> GSM751331 1 0.3783 0.82044 0.728 0.008 0.004 0.252 0.000 0.008
#> GSM751333 1 0.4652 0.76308 0.628 0.032 0.000 0.324 0.000 0.016
#> GSM751335 1 0.4216 0.79824 0.676 0.020 0.000 0.292 0.000 0.012
#> GSM751336 1 0.4362 0.81243 0.692 0.028 0.004 0.264 0.000 0.012
#> GSM751337 1 0.4828 0.67196 0.568 0.032 0.000 0.384 0.000 0.016
#> GSM751338 4 0.4426 0.63059 0.156 0.032 0.000 0.748 0.000 0.064
#> GSM751340 4 0.7468 0.32686 0.116 0.044 0.120 0.504 0.004 0.212
#> GSM751350 1 0.3507 0.82854 0.764 0.008 0.012 0.216 0.000 0.000
#> GSM751351 1 0.3507 0.82854 0.764 0.008 0.012 0.216 0.000 0.000
#> GSM751362 3 0.1887 0.71857 0.024 0.020 0.932 0.000 0.008 0.016
#> GSM751363 6 0.7103 0.08629 0.076 0.056 0.036 0.016 0.380 0.436
#> GSM751367 1 0.6042 0.50137 0.624 0.028 0.216 0.096 0.004 0.032
#> GSM751368 5 0.6743 0.35066 0.068 0.092 0.044 0.008 0.592 0.196
#> GSM751371 4 0.7617 0.13236 0.076 0.020 0.192 0.420 0.012 0.280
#> GSM751375 5 0.0713 0.70029 0.000 0.028 0.000 0.000 0.972 0.000
#> GSM751376 3 0.7569 0.19779 0.128 0.184 0.432 0.000 0.020 0.236
#> GSM751378 5 0.4326 0.39725 0.004 0.016 0.304 0.000 0.664 0.012
#> GSM751379 3 0.7569 0.19779 0.128 0.184 0.432 0.000 0.020 0.236
#> GSM751382 5 0.0713 0.70029 0.000 0.028 0.000 0.000 0.972 0.000
#> GSM751386 5 0.0717 0.70860 0.000 0.016 0.008 0.000 0.976 0.000
#> GSM751388 5 0.0717 0.70860 0.000 0.016 0.008 0.000 0.976 0.000
#> GSM751391 6 0.6905 0.04051 0.072 0.036 0.308 0.048 0.020 0.516
#> GSM751410 3 0.5244 0.64068 0.064 0.024 0.728 0.024 0.020 0.140
#> GSM751414 3 0.7177 0.52500 0.068 0.032 0.560 0.024 0.184 0.132
#> GSM751361 5 0.7465 0.24995 0.080 0.028 0.168 0.016 0.504 0.204
#> GSM751365 3 0.6579 0.52925 0.064 0.028 0.592 0.008 0.212 0.096
#> GSM751366 3 0.3921 0.68709 0.048 0.024 0.828 0.008 0.024 0.068
#> GSM751369 3 0.4920 0.65889 0.080 0.052 0.740 0.000 0.012 0.116
#> GSM751370 3 0.6879 0.51876 0.068 0.032 0.572 0.012 0.208 0.108
#> GSM751372 3 0.5990 0.60762 0.060 0.020 0.664 0.008 0.140 0.108
#> GSM751373 3 0.7489 0.47477 0.072 0.036 0.524 0.028 0.208 0.132
#> GSM751374 3 0.7569 0.19779 0.128 0.184 0.432 0.000 0.020 0.236
#> GSM751377 5 0.2827 0.64685 0.040 0.012 0.020 0.000 0.884 0.044
#> GSM751380 3 0.3075 0.70326 0.040 0.012 0.872 0.004 0.016 0.056
#> GSM751381 5 0.0717 0.70860 0.000 0.016 0.008 0.000 0.976 0.000
#> GSM751383 5 0.0820 0.70778 0.000 0.016 0.012 0.000 0.972 0.000
#> GSM751384 5 0.3261 0.54503 0.004 0.004 0.192 0.000 0.792 0.008
#> GSM751385 5 0.4445 0.36272 0.008 0.008 0.036 0.000 0.696 0.252
#> GSM751387 5 0.0717 0.70860 0.000 0.016 0.008 0.000 0.976 0.000
#> GSM751389 3 0.3220 0.67195 0.064 0.048 0.856 0.000 0.004 0.028
#> GSM751393 3 0.6989 0.34932 0.104 0.112 0.540 0.000 0.032 0.212
#> GSM751394 5 0.0717 0.70860 0.000 0.016 0.008 0.000 0.976 0.000
#> GSM751395 3 0.7610 -0.02105 0.108 0.124 0.372 0.000 0.040 0.356
#> GSM751397 5 0.1053 0.70159 0.004 0.012 0.020 0.000 0.964 0.000
#> GSM751398 5 0.0725 0.70663 0.000 0.012 0.012 0.000 0.976 0.000
#> GSM751404 3 0.0146 0.72623 0.000 0.000 0.996 0.000 0.004 0.000
#> GSM751406 3 0.1294 0.71915 0.008 0.024 0.956 0.000 0.004 0.008
#> GSM751411 3 0.5302 0.58966 0.040 0.020 0.684 0.000 0.200 0.056
#> GSM751413 6 0.6641 0.30590 0.072 0.080 0.012 0.008 0.316 0.512
#> GSM751415 3 0.0665 0.72600 0.008 0.000 0.980 0.000 0.004 0.008
#> GSM751416 5 0.7403 0.19005 0.064 0.036 0.272 0.012 0.480 0.136
#> GSM751417 5 0.7403 0.19005 0.064 0.036 0.272 0.012 0.480 0.136
#> GSM751421 3 0.6271 0.58367 0.088 0.028 0.632 0.028 0.028 0.196
#> GSM751422 3 0.6271 0.58367 0.088 0.028 0.632 0.028 0.028 0.196
#> GSM751360 3 0.7251 0.46861 0.100 0.028 0.516 0.040 0.048 0.268
#> GSM751364 3 0.7324 0.25453 0.064 0.032 0.440 0.012 0.340 0.112
#> GSM751390 5 0.3402 0.54331 0.004 0.008 0.196 0.000 0.784 0.008
#> GSM751392 5 0.0717 0.70860 0.000 0.016 0.008 0.000 0.976 0.000
#> GSM751396 5 0.1080 0.69766 0.004 0.032 0.000 0.000 0.960 0.004
#> GSM751399 3 0.0665 0.72633 0.000 0.008 0.980 0.000 0.008 0.004
#> GSM751400 3 0.0912 0.72321 0.008 0.012 0.972 0.000 0.004 0.004
#> GSM751401 3 0.0146 0.72623 0.000 0.000 0.996 0.000 0.004 0.000
#> GSM751402 3 0.0798 0.72485 0.004 0.012 0.976 0.000 0.004 0.004
#> GSM751403 3 0.1180 0.72045 0.008 0.024 0.960 0.000 0.004 0.004
#> GSM751405 3 0.1294 0.71915 0.008 0.024 0.956 0.000 0.004 0.008
#> GSM751407 3 0.0146 0.72623 0.000 0.000 0.996 0.000 0.004 0.000
#> GSM751408 3 0.0260 0.72642 0.000 0.000 0.992 0.000 0.008 0.000
#> GSM751409 3 0.0551 0.72615 0.008 0.000 0.984 0.000 0.004 0.004
#> GSM751412 3 0.1116 0.72264 0.008 0.000 0.960 0.000 0.028 0.004
#> GSM751418 3 0.7001 0.47423 0.064 0.036 0.548 0.012 0.236 0.104
#> GSM751419 3 0.7001 0.47423 0.064 0.036 0.548 0.012 0.236 0.104
#> GSM751420 3 0.1899 0.70971 0.028 0.032 0.928 0.000 0.004 0.008
#> GSM751425 5 0.3971 -0.35190 0.000 0.448 0.000 0.000 0.548 0.004
#> GSM751429 1 0.5186 0.20785 0.560 0.064 0.364 0.008 0.000 0.004
#> GSM751430 6 0.6554 0.28906 0.048 0.172 0.000 0.000 0.332 0.448
#> GSM751433 2 0.6163 0.61614 0.036 0.512 0.000 0.000 0.308 0.144
#> GSM751437 3 0.2315 0.70731 0.032 0.040 0.908 0.000 0.004 0.016
#> GSM751448 3 0.5189 0.54567 0.108 0.152 0.696 0.000 0.004 0.040
#> GSM751451 2 0.6662 0.51004 0.040 0.476 0.000 0.020 0.332 0.132
#> GSM751423 2 0.5418 0.56673 0.032 0.520 0.000 0.000 0.396 0.052
#> GSM751424 2 0.6163 0.61614 0.036 0.512 0.000 0.000 0.308 0.144
#> GSM751428 2 0.6258 0.61240 0.044 0.524 0.000 0.000 0.276 0.156
#> GSM751431 2 0.6013 0.62701 0.032 0.528 0.000 0.000 0.308 0.132
#> GSM751432 2 0.6507 0.53905 0.044 0.484 0.000 0.000 0.268 0.204
#> GSM751434 2 0.6535 0.52483 0.044 0.480 0.000 0.000 0.260 0.216
#> GSM751435 2 0.4273 0.69625 0.012 0.704 0.000 0.000 0.248 0.036
#> GSM751436 2 0.6163 0.61614 0.036 0.512 0.000 0.000 0.308 0.144
#> GSM751440 2 0.5208 0.62821 0.032 0.584 0.004 0.000 0.344 0.036
#> GSM751444 2 0.2957 0.68796 0.008 0.836 0.000 0.000 0.140 0.016
#> GSM751446 2 0.2968 0.68223 0.016 0.816 0.000 0.000 0.168 0.000
#> GSM751449 2 0.3184 0.65281 0.032 0.832 0.004 0.000 0.128 0.004
#> GSM751450 2 0.6074 0.62542 0.036 0.524 0.000 0.000 0.308 0.132
#> GSM751452 2 0.6163 0.61614 0.036 0.512 0.000 0.000 0.308 0.144
#> GSM751426 2 0.6074 0.62542 0.036 0.524 0.000 0.000 0.308 0.132
#> GSM751427 2 0.3605 0.69555 0.008 0.756 0.004 0.000 0.224 0.008
#> GSM751438 2 0.3397 0.63706 0.032 0.832 0.020 0.000 0.112 0.004
#> GSM751439 2 0.4453 0.46348 0.036 0.752 0.164 0.000 0.040 0.008
#> GSM751441 2 0.3239 0.67854 0.024 0.808 0.000 0.000 0.164 0.004
#> GSM751442 2 0.3421 0.67469 0.028 0.804 0.004 0.000 0.160 0.004
#> GSM751443 3 0.5758 0.30853 0.076 0.392 0.500 0.000 0.004 0.028
#> GSM751445 2 0.2975 0.66286 0.016 0.840 0.000 0.000 0.132 0.012
#> GSM751447 2 0.3340 0.69639 0.004 0.784 0.000 0.000 0.196 0.016
#> GSM751453 2 0.4184 0.69904 0.008 0.720 0.000 0.000 0.228 0.044
#> GSM751454 2 0.4012 0.69975 0.008 0.728 0.000 0.000 0.232 0.032
#> GSM751455 2 0.3421 0.67469 0.028 0.804 0.004 0.000 0.160 0.004
#> GSM751456 2 0.3421 0.67469 0.028 0.804 0.004 0.000 0.160 0.004
#> GSM751457 2 0.7044 0.03028 0.112 0.516 0.236 0.000 0.024 0.112
#> GSM751458 2 0.7044 0.03028 0.112 0.516 0.236 0.000 0.024 0.112
Heatmaps for the consensus matrix. It visualizes the probability of two samples to be in a same group.
consensus_heatmap(res, k = 2)
consensus_heatmap(res, k = 3)
consensus_heatmap(res, k = 4)
consensus_heatmap(res, k = 5)
consensus_heatmap(res, k = 6)
Heatmaps for the membership of samples in all partitions to see how consistent they are:
membership_heatmap(res, k = 2)
membership_heatmap(res, k = 3)
membership_heatmap(res, k = 4)
membership_heatmap(res, k = 5)
membership_heatmap(res, k = 6)
As soon as we have had the classes for columns, we can look for signatures which are significantly different between classes which can be candidate marks for certain classes. Following are the heatmaps for signatures.
Signature heatmaps where rows are scaled:
get_signatures(res, k = 2)
get_signatures(res, k = 3)
get_signatures(res, k = 4)
get_signatures(res, k = 5)
get_signatures(res, k = 6)
Signature heatmaps where rows are not scaled:
get_signatures(res, k = 2, scale_rows = FALSE)
get_signatures(res, k = 3, scale_rows = FALSE)
get_signatures(res, k = 4, scale_rows = FALSE)
get_signatures(res, k = 5, scale_rows = FALSE)
get_signatures(res, k = 6, scale_rows = FALSE)
Compare the overlap of signatures from different k:
compare_signatures(res)
get_signature() returns a data frame invisibly. TO get the list of signatures, the function
call should be assigned to a variable explicitly. In following code, if plot argument is set
to FALSE, no heatmap is plotted while only the differential analysis is performed.
# code only for demonstration
tb = get_signature(res, k = ..., plot = FALSE)
An example of the output of tb is:
#> which_row fdr mean_1 mean_2 scaled_mean_1 scaled_mean_2 km
#> 1 38 0.042760348 8.373488 9.131774 -0.5533452 0.5164555 1
#> 2 40 0.018707592 7.106213 8.469186 -0.6173731 0.5762149 1
#> 3 55 0.019134737 10.221463 11.207825 -0.6159697 0.5749050 1
#> 4 59 0.006059896 5.921854 7.869574 -0.6899429 0.6439467 1
#> 5 60 0.018055526 8.928898 10.211722 -0.6204761 0.5791110 1
#> 6 98 0.009384629 15.714769 14.887706 0.6635654 -0.6193277 2
...
The columns in tb are:
which_row: row indices corresponding to the input matrix.fdr: FDR for the differential test. mean_x: The mean value in group x.scaled_mean_x: The mean value in group x after rows are scaled.km: Row groups if k-means clustering is applied to rows.UMAP plot which shows how samples are separated.
dimension_reduction(res, k = 2, method = "UMAP")
dimension_reduction(res, k = 3, method = "UMAP")
dimension_reduction(res, k = 4, method = "UMAP")
dimension_reduction(res, k = 5, method = "UMAP")
dimension_reduction(res, k = 6, method = "UMAP")
Following heatmap shows how subgroups are split when increasing k:
collect_classes(res)
Test correlation between subgroups and known annotations. If the known annotation is numeric, one-way ANOVA test is applied, and if the known annotation is discrete, chi-squared contingency table test is applied.
test_to_known_factors(res)
#> n tissue(p) disease.state(p) agent(p) k
#> ATC:kmeans 165 5.52e-21 0.139 0.2205 2
#> ATC:kmeans 161 1.05e-25 0.185 0.1813 3
#> ATC:kmeans 104 9.64e-37 0.578 0.7308 4
#> ATC:kmeans 102 1.14e-36 0.323 0.0472 5
#> ATC:kmeans 129 9.20e-44 0.212 0.1239 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 4537 rows and 166 columns.
#> Top rows (454, 908, 1361, 1814, 2268) are extracted by 'ATC' method.
#> Subgroups are detected by 'skmeans' method.
#> Performed in total 1250 partitions by row resampling.
#> Best k for subgroups seems to be 2.
#>
#> Following methods can be applied to this 'ConsensusPartition' object:
#> [1] "cola_report" "collect_classes" "collect_plots"
#> [4] "collect_stats" "colnames" "compare_signatures"
#> [7] "consensus_heatmap" "dimension_reduction" "functional_enrichment"
#> [10] "get_anno_col" "get_anno" "get_classes"
#> [13] "get_consensus" "get_matrix" "get_membership"
#> [16] "get_param" "get_signatures" "get_stats"
#> [19] "is_best_k" "is_stable_k" "membership_heatmap"
#> [22] "ncol" "nrow" "plot_ecdf"
#> [25] "rownames" "select_partition_number" "show"
#> [28] "suggest_best_k" "test_to_known_factors"
collect_plots() function collects all the plots made from res for all k (number of partitions)
into one single page to provide an easy and fast comparison between different k.
collect_plots(res)
The plots are:
k and the heatmap of
predicted classes for each k.k.k.k.All the plots in panels can be made by individual functions and they are plotted later in this section.
select_partition_number() produces several plots showing different
statistics for choosing “optimized” k. There are following statistics:
k;k, the area increased is defined as \(A_k - A_{k-1}\).The detailed explanations of these statistics can be found in the cola vignette.
Generally speaking, lower PAC score, higher mean silhouette score or higher
concordance corresponds to better partition. Rand index and Jaccard index
measure how similar the current partition is compared to partition with k-1.
If they are too similar, we won't accept k is better than k-1.
select_partition_number(res)
The numeric values for all these statistics can be obtained by get_stats().
get_stats(res)
#> k 1-PAC mean_silhouette concordance area_increased Rand Jaccard
#> 2 2 0.950 0.940 0.975 0.5021 0.498 0.498
#> 3 3 0.858 0.886 0.950 0.3257 0.751 0.540
#> 4 4 0.686 0.646 0.811 0.1238 0.859 0.612
#> 5 5 0.666 0.528 0.721 0.0629 0.937 0.760
#> 6 6 0.744 0.618 0.801 0.0469 0.884 0.534
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
#> GSM751298 1 0.0000 0.974 1.000 0.000
#> GSM751304 2 0.0376 0.971 0.004 0.996
#> GSM751305 2 0.0376 0.971 0.004 0.996
#> GSM751307 2 0.0000 0.974 0.000 1.000
#> GSM751310 1 0.0000 0.974 1.000 0.000
#> GSM751314 1 0.0000 0.974 1.000 0.000
#> GSM751316 1 0.0000 0.974 1.000 0.000
#> GSM751318 1 0.0000 0.974 1.000 0.000
#> GSM751342 1 0.1184 0.962 0.984 0.016
#> GSM751346 1 0.0000 0.974 1.000 0.000
#> GSM751347 1 0.0376 0.971 0.996 0.004
#> GSM751348 2 0.0000 0.974 0.000 1.000
#> GSM751349 2 0.0000 0.974 0.000 1.000
#> GSM751352 2 0.0000 0.974 0.000 1.000
#> GSM751353 2 0.0000 0.974 0.000 1.000
#> GSM751354 2 0.0000 0.974 0.000 1.000
#> GSM751355 2 0.0000 0.974 0.000 1.000
#> GSM751358 2 0.0000 0.974 0.000 1.000
#> GSM751359 2 0.0000 0.974 0.000 1.000
#> GSM751294 2 0.0000 0.974 0.000 1.000
#> GSM751296 1 0.0000 0.974 1.000 0.000
#> GSM751297 1 0.0000 0.974 1.000 0.000
#> GSM751299 2 0.0000 0.974 0.000 1.000
#> GSM751300 1 0.0000 0.974 1.000 0.000
#> GSM751301 2 0.0376 0.971 0.004 0.996
#> GSM751302 1 0.0000 0.974 1.000 0.000
#> GSM751303 1 0.0000 0.974 1.000 0.000
#> GSM751306 1 0.0000 0.974 1.000 0.000
#> GSM751308 1 0.0000 0.974 1.000 0.000
#> GSM751309 1 0.0000 0.974 1.000 0.000
#> GSM751311 1 0.0000 0.974 1.000 0.000
#> GSM751312 1 0.0000 0.974 1.000 0.000
#> GSM751313 1 0.0000 0.974 1.000 0.000
#> GSM751315 1 0.0000 0.974 1.000 0.000
#> GSM751317 1 0.0000 0.974 1.000 0.000
#> GSM751320 1 0.0000 0.974 1.000 0.000
#> GSM751321 1 0.0000 0.974 1.000 0.000
#> GSM751322 1 0.0000 0.974 1.000 0.000
#> GSM751324 1 0.0000 0.974 1.000 0.000
#> GSM751325 1 0.0000 0.974 1.000 0.000
#> GSM751332 1 0.0000 0.974 1.000 0.000
#> GSM751334 1 0.0000 0.974 1.000 0.000
#> GSM751339 1 0.0000 0.974 1.000 0.000
#> GSM751341 1 0.0000 0.974 1.000 0.000
#> GSM751343 1 0.0000 0.974 1.000 0.000
#> GSM751344 2 0.0000 0.974 0.000 1.000
#> GSM751345 2 0.0000 0.974 0.000 1.000
#> GSM751356 2 0.0000 0.974 0.000 1.000
#> GSM751357 2 0.0000 0.974 0.000 1.000
#> GSM751293 2 0.0376 0.971 0.004 0.996
#> GSM751295 1 0.0000 0.974 1.000 0.000
#> GSM751319 1 0.0000 0.974 1.000 0.000
#> GSM751323 1 0.0000 0.974 1.000 0.000
#> GSM751326 1 0.0000 0.974 1.000 0.000
#> GSM751327 1 0.0000 0.974 1.000 0.000
#> GSM751328 1 0.0000 0.974 1.000 0.000
#> GSM751329 1 0.0000 0.974 1.000 0.000
#> GSM751330 1 0.0000 0.974 1.000 0.000
#> GSM751331 1 0.0000 0.974 1.000 0.000
#> GSM751333 1 0.0000 0.974 1.000 0.000
#> GSM751335 1 0.0000 0.974 1.000 0.000
#> GSM751336 1 0.0000 0.974 1.000 0.000
#> GSM751337 1 0.0000 0.974 1.000 0.000
#> GSM751338 1 0.0000 0.974 1.000 0.000
#> GSM751340 1 0.0000 0.974 1.000 0.000
#> GSM751350 1 0.0000 0.974 1.000 0.000
#> GSM751351 1 0.0000 0.974 1.000 0.000
#> GSM751362 1 0.0000 0.974 1.000 0.000
#> GSM751363 2 0.1633 0.954 0.024 0.976
#> GSM751367 1 0.0000 0.974 1.000 0.000
#> GSM751368 2 0.0000 0.974 0.000 1.000
#> GSM751371 1 0.0000 0.974 1.000 0.000
#> GSM751375 2 0.0000 0.974 0.000 1.000
#> GSM751376 2 0.0000 0.974 0.000 1.000
#> GSM751378 2 0.0000 0.974 0.000 1.000
#> GSM751379 2 0.0000 0.974 0.000 1.000
#> GSM751382 2 0.0000 0.974 0.000 1.000
#> GSM751386 2 0.0000 0.974 0.000 1.000
#> GSM751388 2 0.0000 0.974 0.000 1.000
#> GSM751391 2 0.9427 0.449 0.360 0.640
#> GSM751410 1 0.0000 0.974 1.000 0.000
#> GSM751414 1 0.0000 0.974 1.000 0.000
#> GSM751361 2 0.0376 0.971 0.004 0.996
#> GSM751365 1 0.6973 0.769 0.812 0.188
#> GSM751366 1 0.0000 0.974 1.000 0.000
#> GSM751369 1 0.0000 0.974 1.000 0.000
#> GSM751370 1 0.0000 0.974 1.000 0.000
#> GSM751372 1 0.4022 0.902 0.920 0.080
#> GSM751373 1 0.0000 0.974 1.000 0.000
#> GSM751374 2 0.0000 0.974 0.000 1.000
#> GSM751377 2 0.0000 0.974 0.000 1.000
#> GSM751380 1 0.0000 0.974 1.000 0.000
#> GSM751381 2 0.0000 0.974 0.000 1.000
#> GSM751383 2 0.0000 0.974 0.000 1.000
#> GSM751384 2 0.0000 0.974 0.000 1.000
#> GSM751385 2 0.0000 0.974 0.000 1.000
#> GSM751387 2 0.0000 0.974 0.000 1.000
#> GSM751389 2 0.6247 0.809 0.156 0.844
#> GSM751393 2 0.0000 0.974 0.000 1.000
#> GSM751394 2 0.0000 0.974 0.000 1.000
#> GSM751395 2 0.0000 0.974 0.000 1.000
#> GSM751397 2 0.0000 0.974 0.000 1.000
#> GSM751398 2 0.0000 0.974 0.000 1.000
#> GSM751404 1 0.0376 0.971 0.996 0.004
#> GSM751406 1 0.2236 0.946 0.964 0.036
#> GSM751411 1 0.9209 0.508 0.664 0.336
#> GSM751413 2 0.0376 0.971 0.004 0.996
#> GSM751415 1 0.0000 0.974 1.000 0.000
#> GSM751416 2 0.1184 0.961 0.016 0.984
#> GSM751417 2 0.0376 0.971 0.004 0.996
#> GSM751421 1 0.0000 0.974 1.000 0.000
#> GSM751422 1 0.0000 0.974 1.000 0.000
#> GSM751360 1 0.0672 0.968 0.992 0.008
#> GSM751364 1 0.9963 0.150 0.536 0.464
#> GSM751390 2 0.0000 0.974 0.000 1.000
#> GSM751392 2 0.0000 0.974 0.000 1.000
#> GSM751396 2 0.0000 0.974 0.000 1.000
#> GSM751399 2 0.9896 0.213 0.440 0.560
#> GSM751400 2 0.5059 0.863 0.112 0.888
#> GSM751401 1 0.0376 0.971 0.996 0.004
#> GSM751402 1 0.0376 0.971 0.996 0.004
#> GSM751403 1 0.8555 0.616 0.720 0.280
#> GSM751405 1 0.2236 0.946 0.964 0.036
#> GSM751407 1 0.2603 0.939 0.956 0.044
#> GSM751408 1 0.9580 0.395 0.620 0.380
#> GSM751409 2 0.5629 0.840 0.132 0.868
#> GSM751412 1 0.3431 0.920 0.936 0.064
#> GSM751418 1 0.1184 0.962 0.984 0.016
#> GSM751419 1 0.1633 0.956 0.976 0.024
#> GSM751420 2 0.8016 0.682 0.244 0.756
#> GSM751425 2 0.0000 0.974 0.000 1.000
#> GSM751429 1 0.0376 0.971 0.996 0.004
#> GSM751430 2 0.0000 0.974 0.000 1.000
#> GSM751433 2 0.0000 0.974 0.000 1.000
#> GSM751437 1 0.2423 0.943 0.960 0.040
#> GSM751448 1 0.0376 0.971 0.996 0.004
#> GSM751451 2 0.0376 0.971 0.004 0.996
#> GSM751423 2 0.0000 0.974 0.000 1.000
#> GSM751424 2 0.0000 0.974 0.000 1.000
#> GSM751428 2 0.0000 0.974 0.000 1.000
#> GSM751431 2 0.0000 0.974 0.000 1.000
#> GSM751432 2 0.0000 0.974 0.000 1.000
#> GSM751434 2 0.0000 0.974 0.000 1.000
#> GSM751435 2 0.0000 0.974 0.000 1.000
#> GSM751436 2 0.0000 0.974 0.000 1.000
#> GSM751440 2 0.0000 0.974 0.000 1.000
#> GSM751444 2 0.0000 0.974 0.000 1.000
#> GSM751446 2 0.0000 0.974 0.000 1.000
#> GSM751449 2 0.0000 0.974 0.000 1.000
#> GSM751450 2 0.0000 0.974 0.000 1.000
#> GSM751452 2 0.0000 0.974 0.000 1.000
#> GSM751426 2 0.0000 0.974 0.000 1.000
#> GSM751427 2 0.0000 0.974 0.000 1.000
#> GSM751438 2 0.0000 0.974 0.000 1.000
#> GSM751439 2 0.9170 0.512 0.332 0.668
#> GSM751441 2 0.0000 0.974 0.000 1.000
#> GSM751442 2 0.0000 0.974 0.000 1.000
#> GSM751443 2 0.9000 0.547 0.316 0.684
#> GSM751445 2 0.0000 0.974 0.000 1.000
#> GSM751447 2 0.0000 0.974 0.000 1.000
#> GSM751453 2 0.0000 0.974 0.000 1.000
#> GSM751454 2 0.0000 0.974 0.000 1.000
#> GSM751455 2 0.0000 0.974 0.000 1.000
#> GSM751456 2 0.0000 0.974 0.000 1.000
#> GSM751457 2 0.0000 0.974 0.000 1.000
#> GSM751458 2 0.0000 0.974 0.000 1.000
cbind(get_classes(res, k = 3), get_membership(res, k = 3))
#> class entropy silhouette p1 p2 p3
#> GSM751298 1 0.0000 0.9533 1.000 0.000 0.000
#> GSM751304 2 0.3412 0.8543 0.000 0.876 0.124
#> GSM751305 2 0.3116 0.8709 0.000 0.892 0.108
#> GSM751307 2 0.0000 0.9523 0.000 1.000 0.000
#> GSM751310 1 0.0000 0.9533 1.000 0.000 0.000
#> GSM751314 1 0.0000 0.9533 1.000 0.000 0.000
#> GSM751316 1 0.0000 0.9533 1.000 0.000 0.000
#> GSM751318 1 0.0000 0.9533 1.000 0.000 0.000
#> GSM751342 1 0.0237 0.9496 0.996 0.004 0.000
#> GSM751346 1 0.0000 0.9533 1.000 0.000 0.000
#> GSM751347 1 0.5831 0.6067 0.708 0.008 0.284
#> GSM751348 2 0.0000 0.9523 0.000 1.000 0.000
#> GSM751349 2 0.0000 0.9523 0.000 1.000 0.000
#> GSM751352 2 0.0747 0.9451 0.000 0.984 0.016
#> GSM751353 2 0.0000 0.9523 0.000 1.000 0.000
#> GSM751354 2 0.2796 0.8866 0.000 0.908 0.092
#> GSM751355 2 0.0000 0.9523 0.000 1.000 0.000
#> GSM751358 3 0.6432 0.2586 0.004 0.428 0.568
#> GSM751359 2 0.1289 0.9390 0.000 0.968 0.032
#> GSM751294 3 0.1964 0.9050 0.000 0.056 0.944
#> GSM751296 1 0.0000 0.9533 1.000 0.000 0.000
#> GSM751297 1 0.5621 0.5698 0.692 0.000 0.308
#> GSM751299 2 0.1031 0.9410 0.000 0.976 0.024
#> GSM751300 1 0.0000 0.9533 1.000 0.000 0.000
#> GSM751301 2 0.0237 0.9505 0.004 0.996 0.000
#> GSM751302 1 0.0000 0.9533 1.000 0.000 0.000
#> GSM751303 1 0.0000 0.9533 1.000 0.000 0.000
#> GSM751306 1 0.0000 0.9533 1.000 0.000 0.000
#> GSM751308 1 0.6286 0.1628 0.536 0.000 0.464
#> GSM751309 1 0.0000 0.9533 1.000 0.000 0.000
#> GSM751311 1 0.0000 0.9533 1.000 0.000 0.000
#> GSM751312 1 0.0000 0.9533 1.000 0.000 0.000
#> GSM751313 1 0.0000 0.9533 1.000 0.000 0.000
#> GSM751315 1 0.0000 0.9533 1.000 0.000 0.000
#> GSM751317 1 0.0000 0.9533 1.000 0.000 0.000
#> GSM751320 1 0.0000 0.9533 1.000 0.000 0.000
#> GSM751321 1 0.0000 0.9533 1.000 0.000 0.000
#> GSM751322 1 0.0000 0.9533 1.000 0.000 0.000
#> GSM751324 1 0.0000 0.9533 1.000 0.000 0.000
#> GSM751325 1 0.0000 0.9533 1.000 0.000 0.000
#> GSM751332 1 0.0000 0.9533 1.000 0.000 0.000
#> GSM751334 1 0.0000 0.9533 1.000 0.000 0.000
#> GSM751339 1 0.0237 0.9501 0.996 0.000 0.004
#> GSM751341 1 0.0000 0.9533 1.000 0.000 0.000
#> GSM751343 1 0.0000 0.9533 1.000 0.000 0.000
#> GSM751344 2 0.0000 0.9523 0.000 1.000 0.000
#> GSM751345 2 0.0000 0.9523 0.000 1.000 0.000
#> GSM751356 2 0.4121 0.8000 0.000 0.832 0.168
#> GSM751357 2 0.4062 0.8054 0.000 0.836 0.164
#> GSM751293 2 0.0237 0.9505 0.004 0.996 0.000
#> GSM751295 1 0.0000 0.9533 1.000 0.000 0.000
#> GSM751319 1 0.0000 0.9533 1.000 0.000 0.000
#> GSM751323 1 0.0000 0.9533 1.000 0.000 0.000
#> GSM751326 1 0.0000 0.9533 1.000 0.000 0.000
#> GSM751327 1 0.0000 0.9533 1.000 0.000 0.000
#> GSM751328 1 0.0000 0.9533 1.000 0.000 0.000
#> GSM751329 1 0.0000 0.9533 1.000 0.000 0.000
#> GSM751330 1 0.0000 0.9533 1.000 0.000 0.000
#> GSM751331 1 0.0000 0.9533 1.000 0.000 0.000
#> GSM751333 1 0.0000 0.9533 1.000 0.000 0.000
#> GSM751335 1 0.0000 0.9533 1.000 0.000 0.000
#> GSM751336 1 0.0000 0.9533 1.000 0.000 0.000
#> GSM751337 1 0.0000 0.9533 1.000 0.000 0.000
#> GSM751338 1 0.0000 0.9533 1.000 0.000 0.000
#> GSM751340 1 0.1964 0.9064 0.944 0.000 0.056
#> GSM751350 1 0.0000 0.9533 1.000 0.000 0.000
#> GSM751351 1 0.0000 0.9533 1.000 0.000 0.000
#> GSM751362 3 0.0000 0.9294 0.000 0.000 1.000
#> GSM751363 2 0.3116 0.8771 0.000 0.892 0.108
#> GSM751367 1 0.1529 0.9197 0.960 0.000 0.040
#> GSM751368 2 0.1163 0.9410 0.000 0.972 0.028
#> GSM751371 1 0.5363 0.6123 0.724 0.000 0.276
#> GSM751375 2 0.0000 0.9523 0.000 1.000 0.000
#> GSM751376 3 0.1289 0.9164 0.000 0.032 0.968
#> GSM751378 3 0.2165 0.8988 0.000 0.064 0.936
#> GSM751379 3 0.1289 0.9164 0.000 0.032 0.968
#> GSM751382 2 0.0000 0.9523 0.000 1.000 0.000
#> GSM751386 2 0.1411 0.9369 0.000 0.964 0.036
#> GSM751388 2 0.1411 0.9369 0.000 0.964 0.036
#> GSM751391 3 0.3116 0.8725 0.000 0.108 0.892
#> GSM751410 3 0.0000 0.9294 0.000 0.000 1.000
#> GSM751414 1 0.6308 0.0359 0.508 0.000 0.492
#> GSM751361 3 0.6309 -0.0121 0.000 0.496 0.504
#> GSM751365 3 0.0000 0.9294 0.000 0.000 1.000
#> GSM751366 3 0.1031 0.9186 0.024 0.000 0.976
#> GSM751369 3 0.0000 0.9294 0.000 0.000 1.000
#> GSM751370 3 0.4555 0.7403 0.200 0.000 0.800
#> GSM751372 3 0.0000 0.9294 0.000 0.000 1.000
#> GSM751373 1 0.5835 0.4763 0.660 0.000 0.340
#> GSM751374 3 0.1289 0.9164 0.000 0.032 0.968
#> GSM751377 2 0.1643 0.9321 0.000 0.956 0.044
#> GSM751380 3 0.0000 0.9294 0.000 0.000 1.000
#> GSM751381 2 0.1411 0.9369 0.000 0.964 0.036
#> GSM751383 2 0.1411 0.9369 0.000 0.964 0.036
#> GSM751384 3 0.3412 0.8471 0.000 0.124 0.876
#> GSM751385 2 0.5785 0.5299 0.000 0.668 0.332
#> GSM751387 2 0.1411 0.9369 0.000 0.964 0.036
#> GSM751389 3 0.0000 0.9294 0.000 0.000 1.000
#> GSM751393 3 0.0000 0.9294 0.000 0.000 1.000
#> GSM751394 2 0.1411 0.9369 0.000 0.964 0.036
#> GSM751395 3 0.0237 0.9284 0.000 0.004 0.996
#> GSM751397 2 0.2165 0.9179 0.000 0.936 0.064
#> GSM751398 2 0.1643 0.9322 0.000 0.956 0.044
#> GSM751404 3 0.0000 0.9294 0.000 0.000 1.000
#> GSM751406 3 0.0000 0.9294 0.000 0.000 1.000
#> GSM751411 3 0.0000 0.9294 0.000 0.000 1.000
#> GSM751413 2 0.1163 0.9418 0.000 0.972 0.028
#> GSM751415 3 0.0000 0.9294 0.000 0.000 1.000
#> GSM751416 2 0.6302 0.0739 0.000 0.520 0.480
#> GSM751417 2 0.6302 0.0739 0.000 0.520 0.480
#> GSM751421 3 0.1643 0.9067 0.044 0.000 0.956
#> GSM751422 3 0.1643 0.9067 0.044 0.000 0.956
#> GSM751360 3 0.2796 0.8674 0.092 0.000 0.908
#> GSM751364 3 0.3295 0.8735 0.008 0.096 0.896
#> GSM751390 3 0.2959 0.8709 0.000 0.100 0.900
#> GSM751392 2 0.1411 0.9369 0.000 0.964 0.036
#> GSM751396 2 0.0424 0.9497 0.000 0.992 0.008
#> GSM751399 3 0.0000 0.9294 0.000 0.000 1.000
#> GSM751400 3 0.0000 0.9294 0.000 0.000 1.000
#> GSM751401 3 0.0000 0.9294 0.000 0.000 1.000
#> GSM751402 3 0.0000 0.9294 0.000 0.000 1.000
#> GSM751403 3 0.0000 0.9294 0.000 0.000 1.000
#> GSM751405 3 0.0000 0.9294 0.000 0.000 1.000
#> GSM751407 3 0.0000 0.9294 0.000 0.000 1.000
#> GSM751408 3 0.0000 0.9294 0.000 0.000 1.000
#> GSM751409 3 0.0000 0.9294 0.000 0.000 1.000
#> GSM751412 3 0.0000 0.9294 0.000 0.000 1.000
#> GSM751418 3 0.4708 0.8244 0.120 0.036 0.844
#> GSM751419 3 0.3572 0.8807 0.060 0.040 0.900
#> GSM751420 3 0.0000 0.9294 0.000 0.000 1.000
#> GSM751425 2 0.0000 0.9523 0.000 1.000 0.000
#> GSM751429 3 0.5098 0.6440 0.248 0.000 0.752
#> GSM751430 2 0.0000 0.9523 0.000 1.000 0.000
#> GSM751433 2 0.0000 0.9523 0.000 1.000 0.000
#> GSM751437 3 0.0000 0.9294 0.000 0.000 1.000
#> GSM751448 3 0.0592 0.9240 0.012 0.000 0.988
#> GSM751451 2 0.0000 0.9523 0.000 1.000 0.000
#> GSM751423 2 0.0000 0.9523 0.000 1.000 0.000
#> GSM751424 2 0.0000 0.9523 0.000 1.000 0.000
#> GSM751428 2 0.0000 0.9523 0.000 1.000 0.000
#> GSM751431 2 0.0000 0.9523 0.000 1.000 0.000
#> GSM751432 2 0.0000 0.9523 0.000 1.000 0.000
#> GSM751434 2 0.0000 0.9523 0.000 1.000 0.000
#> GSM751435 2 0.0000 0.9523 0.000 1.000 0.000
#> GSM751436 2 0.0000 0.9523 0.000 1.000 0.000
#> GSM751440 2 0.0000 0.9523 0.000 1.000 0.000
#> GSM751444 2 0.0000 0.9523 0.000 1.000 0.000
#> GSM751446 2 0.0000 0.9523 0.000 1.000 0.000
#> GSM751449 2 0.1529 0.9295 0.000 0.960 0.040
#> GSM751450 2 0.0000 0.9523 0.000 1.000 0.000
#> GSM751452 2 0.0000 0.9523 0.000 1.000 0.000
#> GSM751426 2 0.0000 0.9523 0.000 1.000 0.000
#> GSM751427 2 0.0000 0.9523 0.000 1.000 0.000
#> GSM751438 2 0.4750 0.7118 0.000 0.784 0.216
#> GSM751439 3 0.4178 0.7990 0.000 0.172 0.828
#> GSM751441 2 0.0000 0.9523 0.000 1.000 0.000
#> GSM751442 2 0.0237 0.9509 0.000 0.996 0.004
#> GSM751443 3 0.1411 0.9140 0.000 0.036 0.964
#> GSM751445 2 0.0000 0.9523 0.000 1.000 0.000
#> GSM751447 2 0.0000 0.9523 0.000 1.000 0.000
#> GSM751453 2 0.0000 0.9523 0.000 1.000 0.000
#> GSM751454 2 0.0000 0.9523 0.000 1.000 0.000
#> GSM751455 2 0.0237 0.9509 0.000 0.996 0.004
#> GSM751456 2 0.0237 0.9509 0.000 0.996 0.004
#> GSM751457 3 0.4750 0.7381 0.000 0.216 0.784
#> GSM751458 3 0.4702 0.7439 0.000 0.212 0.788
cbind(get_classes(res, k = 4), get_membership(res, k = 4))
#> class entropy silhouette p1 p2 p3 p4
#> GSM751298 1 0.0469 0.95081 0.988 0.012 0.000 0.000
#> GSM751304 4 0.5850 0.45082 0.000 0.116 0.184 0.700
#> GSM751305 4 0.5731 0.46065 0.000 0.116 0.172 0.712
#> GSM751307 4 0.4933 0.10387 0.000 0.432 0.000 0.568
#> GSM751310 1 0.0707 0.95246 0.980 0.000 0.000 0.020
#> GSM751314 1 0.0707 0.95246 0.980 0.000 0.000 0.020
#> GSM751316 1 0.0817 0.95054 0.976 0.000 0.000 0.024
#> GSM751318 1 0.1022 0.94573 0.968 0.000 0.000 0.032
#> GSM751342 1 0.0707 0.95246 0.980 0.000 0.000 0.020
#> GSM751346 1 0.0592 0.94922 0.984 0.016 0.000 0.000
#> GSM751347 1 0.7691 0.24035 0.520 0.168 0.296 0.016
#> GSM751348 2 0.5406 -0.13793 0.012 0.508 0.000 0.480
#> GSM751349 4 0.4356 0.45638 0.000 0.292 0.000 0.708
#> GSM751352 2 0.6214 -0.08742 0.000 0.480 0.052 0.468
#> GSM751353 4 0.4830 0.26472 0.000 0.392 0.000 0.608
#> GSM751354 4 0.7581 0.16114 0.000 0.360 0.200 0.440
#> GSM751355 4 0.5004 0.29125 0.000 0.392 0.004 0.604
#> GSM751358 4 0.7112 0.35732 0.012 0.160 0.224 0.604
#> GSM751359 4 0.3015 0.65381 0.000 0.092 0.024 0.884
#> GSM751294 3 0.7752 0.15594 0.000 0.264 0.436 0.300
#> GSM751296 1 0.0592 0.94922 0.984 0.016 0.000 0.000
#> GSM751297 1 0.5947 0.43715 0.628 0.060 0.312 0.000
#> GSM751299 2 0.5720 0.19547 0.000 0.652 0.052 0.296
#> GSM751300 1 0.0592 0.94922 0.984 0.016 0.000 0.000
#> GSM751301 4 0.5155 0.00667 0.004 0.468 0.000 0.528
#> GSM751302 1 0.0592 0.94922 0.984 0.016 0.000 0.000
#> GSM751303 1 0.1022 0.94573 0.968 0.000 0.000 0.032
#> GSM751306 1 0.0707 0.95246 0.980 0.000 0.000 0.020
#> GSM751308 3 0.8676 0.23295 0.332 0.220 0.404 0.044
#> GSM751309 1 0.0707 0.95246 0.980 0.000 0.000 0.020
#> GSM751311 1 0.0707 0.95246 0.980 0.000 0.000 0.020
#> GSM751312 1 0.0592 0.95369 0.984 0.000 0.000 0.016
#> GSM751313 1 0.0000 0.95449 1.000 0.000 0.000 0.000
#> GSM751315 1 0.0592 0.95369 0.984 0.000 0.000 0.016
#> GSM751317 1 0.0817 0.95054 0.976 0.000 0.000 0.024
#> GSM751320 1 0.0188 0.95456 0.996 0.000 0.000 0.004
#> GSM751321 1 0.0592 0.95369 0.984 0.000 0.000 0.016
#> GSM751322 1 0.0592 0.95369 0.984 0.000 0.000 0.016
#> GSM751324 1 0.0592 0.95369 0.984 0.000 0.000 0.016
#> GSM751325 1 0.0592 0.95369 0.984 0.000 0.000 0.016
#> GSM751332 1 0.0000 0.95449 1.000 0.000 0.000 0.000
#> GSM751334 1 0.0000 0.95449 1.000 0.000 0.000 0.000
#> GSM751339 1 0.2124 0.89565 0.924 0.000 0.068 0.008
#> GSM751341 1 0.0469 0.95101 0.988 0.012 0.000 0.000
#> GSM751343 1 0.0336 0.95445 0.992 0.000 0.000 0.008
#> GSM751344 4 0.4941 0.11880 0.000 0.436 0.000 0.564
#> GSM751345 4 0.4941 0.11880 0.000 0.436 0.000 0.564
#> GSM751356 4 0.7550 0.23602 0.000 0.372 0.192 0.436
#> GSM751357 4 0.7550 0.23602 0.000 0.372 0.192 0.436
#> GSM751293 4 0.5163 -0.01217 0.004 0.480 0.000 0.516
#> GSM751295 1 0.0592 0.94922 0.984 0.016 0.000 0.000
#> GSM751319 1 0.0592 0.95369 0.984 0.000 0.000 0.016
#> GSM751323 1 0.0188 0.95456 0.996 0.000 0.000 0.004
#> GSM751326 1 0.0000 0.95449 1.000 0.000 0.000 0.000
#> GSM751327 1 0.0188 0.95456 0.996 0.000 0.000 0.004
#> GSM751328 1 0.0000 0.95449 1.000 0.000 0.000 0.000
#> GSM751329 1 0.0000 0.95449 1.000 0.000 0.000 0.000
#> GSM751330 1 0.0000 0.95449 1.000 0.000 0.000 0.000
#> GSM751331 1 0.0000 0.95449 1.000 0.000 0.000 0.000
#> GSM751333 1 0.0000 0.95449 1.000 0.000 0.000 0.000
#> GSM751335 1 0.0000 0.95449 1.000 0.000 0.000 0.000
#> GSM751336 1 0.0000 0.95449 1.000 0.000 0.000 0.000
#> GSM751337 1 0.0000 0.95449 1.000 0.000 0.000 0.000
#> GSM751338 1 0.0336 0.95445 0.992 0.000 0.000 0.008
#> GSM751340 1 0.3852 0.74563 0.800 0.000 0.192 0.008
#> GSM751350 1 0.0592 0.94922 0.984 0.016 0.000 0.000
#> GSM751351 1 0.0592 0.94922 0.984 0.016 0.000 0.000
#> GSM751362 3 0.0000 0.77190 0.000 0.000 1.000 0.000
#> GSM751363 4 0.0804 0.63496 0.000 0.008 0.012 0.980
#> GSM751367 1 0.2928 0.84620 0.880 0.012 0.108 0.000
#> GSM751368 4 0.1867 0.63961 0.000 0.072 0.000 0.928
#> GSM751371 1 0.6746 0.32174 0.572 0.012 0.340 0.076
#> GSM751375 4 0.2868 0.64196 0.000 0.136 0.000 0.864
#> GSM751376 3 0.5756 0.58408 0.000 0.224 0.692 0.084
#> GSM751378 4 0.7221 0.06958 0.000 0.140 0.424 0.436
#> GSM751379 3 0.5756 0.58408 0.000 0.224 0.692 0.084
#> GSM751382 4 0.2704 0.65005 0.000 0.124 0.000 0.876
#> GSM751386 4 0.2737 0.66364 0.000 0.104 0.008 0.888
#> GSM751388 4 0.2737 0.66364 0.000 0.104 0.008 0.888
#> GSM751391 3 0.5742 0.59559 0.004 0.068 0.696 0.232
#> GSM751410 3 0.1661 0.76044 0.000 0.004 0.944 0.052
#> GSM751414 3 0.7212 0.42114 0.160 0.000 0.516 0.324
#> GSM751361 4 0.4011 0.46322 0.000 0.008 0.208 0.784
#> GSM751365 3 0.4843 0.47409 0.000 0.000 0.604 0.396
#> GSM751366 3 0.4011 0.66643 0.008 0.000 0.784 0.208
#> GSM751369 3 0.0804 0.76781 0.000 0.008 0.980 0.012
#> GSM751370 3 0.6309 0.49480 0.076 0.000 0.588 0.336
#> GSM751372 3 0.4356 0.59887 0.000 0.000 0.708 0.292
#> GSM751373 3 0.7782 0.32078 0.296 0.000 0.428 0.276
#> GSM751374 3 0.5756 0.58408 0.000 0.224 0.692 0.084
#> GSM751377 4 0.2737 0.66364 0.000 0.104 0.008 0.888
#> GSM751380 3 0.0000 0.77190 0.000 0.000 1.000 0.000
#> GSM751381 4 0.2737 0.66364 0.000 0.104 0.008 0.888
#> GSM751383 4 0.2737 0.66364 0.000 0.104 0.008 0.888
#> GSM751384 4 0.6091 0.27393 0.000 0.060 0.344 0.596
#> GSM751385 4 0.3761 0.64769 0.000 0.080 0.068 0.852
#> GSM751387 4 0.2737 0.66364 0.000 0.104 0.008 0.888
#> GSM751389 3 0.0336 0.77061 0.000 0.008 0.992 0.000
#> GSM751393 3 0.3505 0.71106 0.000 0.048 0.864 0.088
#> GSM751394 4 0.2593 0.66196 0.000 0.104 0.004 0.892
#> GSM751395 3 0.6764 0.26692 0.000 0.112 0.556 0.332
#> GSM751397 4 0.2737 0.66364 0.000 0.104 0.008 0.888
#> GSM751398 4 0.2675 0.66360 0.000 0.100 0.008 0.892
#> GSM751404 3 0.0336 0.77141 0.000 0.000 0.992 0.008
#> GSM751406 3 0.0000 0.77190 0.000 0.000 1.000 0.000
#> GSM751411 3 0.4790 0.48981 0.000 0.000 0.620 0.380
#> GSM751413 4 0.2011 0.62631 0.000 0.080 0.000 0.920
#> GSM751415 3 0.0000 0.77190 0.000 0.000 1.000 0.000
#> GSM751416 4 0.4770 0.32314 0.000 0.012 0.288 0.700
#> GSM751417 4 0.4770 0.32314 0.000 0.012 0.288 0.700
#> GSM751421 3 0.2441 0.75326 0.012 0.004 0.916 0.068
#> GSM751422 3 0.2310 0.75445 0.008 0.004 0.920 0.068
#> GSM751360 3 0.4053 0.65502 0.004 0.000 0.768 0.228
#> GSM751364 3 0.4967 0.38007 0.000 0.000 0.548 0.452
#> GSM751390 4 0.6041 0.30758 0.000 0.060 0.332 0.608
#> GSM751392 4 0.2737 0.66364 0.000 0.104 0.008 0.888
#> GSM751396 4 0.2589 0.65161 0.000 0.116 0.000 0.884
#> GSM751399 3 0.0336 0.77141 0.000 0.000 0.992 0.008
#> GSM751400 3 0.0188 0.77177 0.000 0.000 0.996 0.004
#> GSM751401 3 0.0000 0.77190 0.000 0.000 1.000 0.000
#> GSM751402 3 0.0000 0.77190 0.000 0.000 1.000 0.000
#> GSM751403 3 0.0000 0.77190 0.000 0.000 1.000 0.000
#> GSM751405 3 0.0000 0.77190 0.000 0.000 1.000 0.000
#> GSM751407 3 0.0336 0.77141 0.000 0.000 0.992 0.008
#> GSM751408 3 0.2081 0.74182 0.000 0.000 0.916 0.084
#> GSM751409 3 0.0000 0.77190 0.000 0.000 1.000 0.000
#> GSM751412 3 0.3311 0.68214 0.000 0.000 0.828 0.172
#> GSM751418 3 0.4877 0.45959 0.000 0.000 0.592 0.408
#> GSM751419 3 0.4866 0.46591 0.000 0.000 0.596 0.404
#> GSM751420 3 0.1637 0.75315 0.000 0.060 0.940 0.000
#> GSM751425 2 0.4500 0.57442 0.000 0.684 0.000 0.316
#> GSM751429 3 0.7196 0.48049 0.212 0.236 0.552 0.000
#> GSM751430 4 0.4961 0.05787 0.000 0.448 0.000 0.552
#> GSM751433 2 0.4382 0.60957 0.000 0.704 0.000 0.296
#> GSM751437 3 0.2589 0.72576 0.000 0.116 0.884 0.000
#> GSM751448 3 0.3356 0.68676 0.000 0.176 0.824 0.000
#> GSM751451 2 0.4761 0.54551 0.000 0.628 0.000 0.372
#> GSM751423 2 0.4382 0.60855 0.000 0.704 0.000 0.296
#> GSM751424 2 0.4382 0.60957 0.000 0.704 0.000 0.296
#> GSM751428 2 0.4277 0.62342 0.000 0.720 0.000 0.280
#> GSM751431 2 0.4304 0.62032 0.000 0.716 0.000 0.284
#> GSM751432 2 0.4356 0.61395 0.000 0.708 0.000 0.292
#> GSM751434 2 0.4382 0.61356 0.000 0.704 0.000 0.296
#> GSM751435 2 0.2345 0.68507 0.000 0.900 0.000 0.100
#> GSM751436 2 0.4382 0.60957 0.000 0.704 0.000 0.296
#> GSM751440 2 0.3610 0.66424 0.000 0.800 0.000 0.200
#> GSM751444 2 0.0921 0.68242 0.000 0.972 0.000 0.028
#> GSM751446 2 0.0000 0.67542 0.000 1.000 0.000 0.000
#> GSM751449 2 0.0336 0.66988 0.000 0.992 0.008 0.000
#> GSM751450 2 0.4304 0.62058 0.000 0.716 0.000 0.284
#> GSM751452 2 0.4382 0.60957 0.000 0.704 0.000 0.296
#> GSM751426 2 0.4356 0.61395 0.000 0.708 0.000 0.292
#> GSM751427 2 0.0921 0.68112 0.000 0.972 0.000 0.028
#> GSM751438 2 0.1867 0.61396 0.000 0.928 0.072 0.000
#> GSM751439 2 0.3942 0.44486 0.000 0.764 0.236 0.000
#> GSM751441 2 0.0000 0.67542 0.000 1.000 0.000 0.000
#> GSM751442 2 0.0000 0.67542 0.000 1.000 0.000 0.000
#> GSM751443 3 0.4730 0.47918 0.000 0.364 0.636 0.000
#> GSM751445 2 0.0336 0.67589 0.000 0.992 0.000 0.008
#> GSM751447 2 0.1211 0.68411 0.000 0.960 0.000 0.040
#> GSM751453 2 0.3172 0.67701 0.000 0.840 0.000 0.160
#> GSM751454 2 0.3074 0.67845 0.000 0.848 0.000 0.152
#> GSM751455 2 0.0000 0.67542 0.000 1.000 0.000 0.000
#> GSM751456 2 0.0000 0.67542 0.000 1.000 0.000 0.000
#> GSM751457 2 0.5784 -0.01282 0.000 0.556 0.412 0.032
#> GSM751458 2 0.5792 -0.02521 0.000 0.552 0.416 0.032
cbind(get_classes(res, k = 5), get_membership(res, k = 5))
#> class entropy silhouette p1 p2 p3 p4 p5
#> GSM751298 1 0.4219 0.6363 0.584 0.000 0.000 0.416 0.000
#> GSM751304 4 0.7648 0.2221 0.156 0.028 0.052 0.516 0.248
#> GSM751305 4 0.7521 0.2178 0.160 0.024 0.044 0.516 0.256
#> GSM751307 4 0.6748 0.1410 0.000 0.284 0.000 0.408 0.308
#> GSM751310 1 0.0609 0.7299 0.980 0.000 0.000 0.020 0.000
#> GSM751314 1 0.0609 0.7301 0.980 0.000 0.000 0.020 0.000
#> GSM751316 1 0.1544 0.7035 0.932 0.000 0.000 0.068 0.000
#> GSM751318 1 0.1908 0.6822 0.908 0.000 0.000 0.092 0.000
#> GSM751342 1 0.1502 0.7089 0.940 0.004 0.000 0.056 0.000
#> GSM751346 1 0.4287 0.6102 0.540 0.000 0.000 0.460 0.000
#> GSM751347 4 0.8557 -0.0894 0.196 0.140 0.164 0.460 0.040
#> GSM751348 5 0.7547 0.1110 0.080 0.256 0.000 0.184 0.480
#> GSM751349 5 0.3010 0.5457 0.000 0.172 0.000 0.004 0.824
#> GSM751352 4 0.6972 0.1723 0.000 0.224 0.012 0.404 0.360
#> GSM751353 5 0.6342 -0.0223 0.000 0.208 0.000 0.272 0.520
#> GSM751354 4 0.7741 0.1904 0.000 0.128 0.120 0.428 0.324
#> GSM751355 5 0.6438 -0.0460 0.000 0.220 0.000 0.280 0.500
#> GSM751358 4 0.8747 0.0510 0.288 0.028 0.100 0.296 0.288
#> GSM751359 5 0.2532 0.6424 0.000 0.012 0.008 0.088 0.892
#> GSM751294 3 0.8677 -0.0579 0.012 0.156 0.348 0.232 0.252
#> GSM751296 1 0.4273 0.6201 0.552 0.000 0.000 0.448 0.000
#> GSM751297 4 0.7111 -0.2359 0.276 0.024 0.240 0.460 0.000
#> GSM751299 2 0.7207 -0.2478 0.000 0.360 0.016 0.328 0.296
#> GSM751300 1 0.4283 0.6140 0.544 0.000 0.000 0.456 0.000
#> GSM751301 4 0.7130 0.1458 0.016 0.284 0.000 0.412 0.288
#> GSM751302 1 0.4287 0.6102 0.540 0.000 0.000 0.460 0.000
#> GSM751303 1 0.1544 0.7035 0.932 0.000 0.000 0.068 0.000
#> GSM751306 1 0.1043 0.7211 0.960 0.000 0.000 0.040 0.000
#> GSM751308 1 0.8348 -0.1534 0.388 0.140 0.248 0.220 0.004
#> GSM751309 1 0.1043 0.7211 0.960 0.000 0.000 0.040 0.000
#> GSM751311 1 0.1121 0.7191 0.956 0.000 0.000 0.044 0.000
#> GSM751312 1 0.0963 0.7231 0.964 0.000 0.000 0.036 0.000
#> GSM751313 1 0.4182 0.6474 0.600 0.000 0.000 0.400 0.000
#> GSM751315 1 0.0162 0.7348 0.996 0.000 0.000 0.004 0.000
#> GSM751317 1 0.1544 0.7034 0.932 0.000 0.000 0.068 0.000
#> GSM751320 1 0.1043 0.7397 0.960 0.000 0.000 0.040 0.000
#> GSM751321 1 0.0404 0.7326 0.988 0.000 0.000 0.012 0.000
#> GSM751322 1 0.0000 0.7357 1.000 0.000 0.000 0.000 0.000
#> GSM751324 1 0.0000 0.7357 1.000 0.000 0.000 0.000 0.000
#> GSM751325 1 0.0162 0.7363 0.996 0.000 0.000 0.004 0.000
#> GSM751332 1 0.2424 0.7298 0.868 0.000 0.000 0.132 0.000
#> GSM751334 1 0.2424 0.7298 0.868 0.000 0.000 0.132 0.000
#> GSM751339 1 0.3112 0.6987 0.856 0.000 0.044 0.100 0.000
#> GSM751341 1 0.4088 0.6573 0.632 0.000 0.000 0.368 0.000
#> GSM751343 1 0.0609 0.7380 0.980 0.000 0.000 0.020 0.000
#> GSM751344 4 0.6625 0.2223 0.000 0.220 0.000 0.412 0.368
#> GSM751345 4 0.6625 0.2223 0.000 0.220 0.000 0.412 0.368
#> GSM751356 5 0.9272 -0.0734 0.112 0.148 0.108 0.280 0.352
#> GSM751357 5 0.9204 -0.0649 0.104 0.152 0.104 0.280 0.360
#> GSM751293 4 0.7383 0.1823 0.032 0.268 0.000 0.408 0.292
#> GSM751295 1 0.4287 0.6102 0.540 0.000 0.000 0.460 0.000
#> GSM751319 1 0.0880 0.7251 0.968 0.000 0.000 0.032 0.000
#> GSM751323 1 0.1121 0.7398 0.956 0.000 0.000 0.044 0.000
#> GSM751326 1 0.4249 0.6306 0.568 0.000 0.000 0.432 0.000
#> GSM751327 1 0.1544 0.7392 0.932 0.000 0.000 0.068 0.000
#> GSM751328 1 0.2690 0.7243 0.844 0.000 0.000 0.156 0.000
#> GSM751329 1 0.3661 0.6891 0.724 0.000 0.000 0.276 0.000
#> GSM751330 1 0.4262 0.6258 0.560 0.000 0.000 0.440 0.000
#> GSM751331 1 0.4283 0.6140 0.544 0.000 0.000 0.456 0.000
#> GSM751333 1 0.4227 0.6375 0.580 0.000 0.000 0.420 0.000
#> GSM751335 1 0.4262 0.6258 0.560 0.000 0.000 0.440 0.000
#> GSM751336 1 0.4273 0.6205 0.552 0.000 0.000 0.448 0.000
#> GSM751337 1 0.4192 0.6458 0.596 0.000 0.000 0.404 0.000
#> GSM751338 1 0.1410 0.7396 0.940 0.000 0.000 0.060 0.000
#> GSM751340 1 0.4386 0.5824 0.764 0.000 0.140 0.096 0.000
#> GSM751350 1 0.4283 0.6140 0.544 0.000 0.000 0.456 0.000
#> GSM751351 1 0.4283 0.6140 0.544 0.000 0.000 0.456 0.000
#> GSM751362 3 0.0000 0.7367 0.000 0.000 1.000 0.000 0.000
#> GSM751363 5 0.5686 0.4074 0.052 0.008 0.012 0.324 0.604
#> GSM751367 4 0.6241 -0.4757 0.412 0.008 0.112 0.468 0.000
#> GSM751368 5 0.4798 0.5219 0.004 0.052 0.004 0.224 0.716
#> GSM751371 1 0.5693 0.3123 0.644 0.000 0.188 0.164 0.004
#> GSM751375 5 0.1195 0.6934 0.000 0.028 0.000 0.012 0.960
#> GSM751376 3 0.5938 0.4634 0.000 0.128 0.648 0.200 0.024
#> GSM751378 5 0.5083 0.3117 0.000 0.036 0.364 0.004 0.596
#> GSM751379 3 0.5938 0.4634 0.000 0.128 0.648 0.200 0.024
#> GSM751382 5 0.0794 0.7021 0.000 0.028 0.000 0.000 0.972
#> GSM751386 5 0.0451 0.7093 0.000 0.008 0.004 0.000 0.988
#> GSM751388 5 0.0451 0.7093 0.000 0.008 0.004 0.000 0.988
#> GSM751391 4 0.7676 -0.0132 0.332 0.012 0.296 0.336 0.024
#> GSM751410 3 0.3636 0.6644 0.080 0.000 0.832 0.084 0.004
#> GSM751414 3 0.7924 0.2037 0.192 0.000 0.404 0.100 0.304
#> GSM751361 5 0.4758 0.5912 0.040 0.000 0.068 0.120 0.772
#> GSM751365 3 0.6021 0.1598 0.008 0.000 0.476 0.088 0.428
#> GSM751366 3 0.3735 0.6744 0.016 0.000 0.836 0.076 0.072
#> GSM751369 3 0.0865 0.7293 0.000 0.000 0.972 0.024 0.004
#> GSM751370 3 0.7142 0.1701 0.076 0.000 0.440 0.096 0.388
#> GSM751372 3 0.5576 0.4158 0.004 0.000 0.604 0.084 0.308
#> GSM751373 3 0.8348 0.1230 0.268 0.000 0.324 0.136 0.272
#> GSM751374 3 0.5938 0.4634 0.000 0.128 0.648 0.200 0.024
#> GSM751377 5 0.1153 0.7023 0.000 0.008 0.004 0.024 0.964
#> GSM751380 3 0.0609 0.7332 0.000 0.000 0.980 0.020 0.000
#> GSM751381 5 0.0451 0.7093 0.000 0.008 0.004 0.000 0.988
#> GSM751383 5 0.0451 0.7093 0.000 0.008 0.004 0.000 0.988
#> GSM751384 5 0.3047 0.6100 0.000 0.004 0.160 0.004 0.832
#> GSM751385 5 0.3292 0.6088 0.000 0.004 0.032 0.120 0.844
#> GSM751387 5 0.0451 0.7093 0.000 0.008 0.004 0.000 0.988
#> GSM751389 3 0.0324 0.7340 0.000 0.000 0.992 0.004 0.004
#> GSM751393 3 0.4682 0.5775 0.000 0.036 0.760 0.164 0.040
#> GSM751394 5 0.0451 0.7093 0.000 0.008 0.004 0.000 0.988
#> GSM751395 3 0.7176 0.2529 0.000 0.072 0.540 0.220 0.168
#> GSM751397 5 0.0451 0.7093 0.000 0.008 0.004 0.000 0.988
#> GSM751398 5 0.0613 0.7086 0.000 0.008 0.004 0.004 0.984
#> GSM751404 3 0.0000 0.7367 0.000 0.000 1.000 0.000 0.000
#> GSM751406 3 0.0000 0.7367 0.000 0.000 1.000 0.000 0.000
#> GSM751411 3 0.5320 0.2153 0.000 0.000 0.524 0.052 0.424
#> GSM751413 5 0.5882 0.1654 0.028 0.044 0.000 0.424 0.504
#> GSM751415 3 0.0162 0.7365 0.000 0.000 0.996 0.004 0.000
#> GSM751416 5 0.5384 0.5204 0.012 0.004 0.184 0.100 0.700
#> GSM751417 5 0.5384 0.5204 0.012 0.004 0.184 0.100 0.700
#> GSM751421 3 0.4788 0.5939 0.136 0.000 0.740 0.120 0.004
#> GSM751422 3 0.4877 0.5886 0.136 0.000 0.732 0.128 0.004
#> GSM751360 3 0.7171 0.3602 0.256 0.000 0.520 0.164 0.060
#> GSM751364 5 0.5916 0.2113 0.012 0.000 0.328 0.088 0.572
#> GSM751390 5 0.2732 0.6126 0.000 0.000 0.160 0.000 0.840
#> GSM751392 5 0.0451 0.7093 0.000 0.008 0.004 0.000 0.988
#> GSM751396 5 0.0794 0.7029 0.000 0.028 0.000 0.000 0.972
#> GSM751399 3 0.0162 0.7364 0.000 0.000 0.996 0.000 0.004
#> GSM751400 3 0.0000 0.7367 0.000 0.000 1.000 0.000 0.000
#> GSM751401 3 0.0000 0.7367 0.000 0.000 1.000 0.000 0.000
#> GSM751402 3 0.0000 0.7367 0.000 0.000 1.000 0.000 0.000
#> GSM751403 3 0.0000 0.7367 0.000 0.000 1.000 0.000 0.000
#> GSM751405 3 0.0000 0.7367 0.000 0.000 1.000 0.000 0.000
#> GSM751407 3 0.0000 0.7367 0.000 0.000 1.000 0.000 0.000
#> GSM751408 3 0.0510 0.7335 0.000 0.000 0.984 0.000 0.016
#> GSM751409 3 0.0162 0.7365 0.000 0.000 0.996 0.004 0.000
#> GSM751412 3 0.1894 0.7075 0.000 0.000 0.920 0.008 0.072
#> GSM751418 3 0.6666 0.1121 0.040 0.000 0.436 0.092 0.432
#> GSM751419 3 0.6666 0.1121 0.040 0.000 0.436 0.092 0.432
#> GSM751420 3 0.0912 0.7267 0.000 0.012 0.972 0.016 0.000
#> GSM751425 2 0.4166 0.5104 0.000 0.648 0.000 0.004 0.348
#> GSM751429 4 0.6964 -0.0876 0.028 0.156 0.392 0.424 0.000
#> GSM751430 2 0.6817 -0.0614 0.000 0.348 0.000 0.344 0.308
#> GSM751433 2 0.5372 0.6281 0.000 0.668 0.000 0.180 0.152
#> GSM751437 3 0.2130 0.6908 0.000 0.080 0.908 0.012 0.000
#> GSM751448 3 0.2595 0.6784 0.000 0.080 0.888 0.032 0.000
#> GSM751451 2 0.6864 0.5269 0.104 0.600 0.000 0.128 0.168
#> GSM751423 2 0.4701 0.6471 0.000 0.720 0.000 0.076 0.204
#> GSM751424 2 0.5372 0.6281 0.000 0.668 0.000 0.180 0.152
#> GSM751428 2 0.5050 0.6497 0.000 0.700 0.000 0.180 0.120
#> GSM751431 2 0.5120 0.6481 0.000 0.696 0.000 0.164 0.140
#> GSM751432 2 0.5460 0.6162 0.000 0.656 0.000 0.196 0.148
#> GSM751434 2 0.5460 0.6162 0.000 0.656 0.000 0.196 0.148
#> GSM751435 2 0.2221 0.7098 0.000 0.912 0.000 0.036 0.052
#> GSM751436 2 0.5372 0.6281 0.000 0.668 0.000 0.180 0.152
#> GSM751440 2 0.2921 0.6965 0.000 0.856 0.000 0.020 0.124
#> GSM751444 2 0.0955 0.7060 0.000 0.968 0.000 0.028 0.004
#> GSM751446 2 0.0162 0.6996 0.000 0.996 0.000 0.004 0.000
#> GSM751449 2 0.0162 0.6996 0.000 0.996 0.000 0.004 0.000
#> GSM751450 2 0.5074 0.6508 0.000 0.700 0.000 0.168 0.132
#> GSM751452 2 0.5372 0.6281 0.000 0.668 0.000 0.180 0.152
#> GSM751426 2 0.5046 0.6522 0.000 0.704 0.000 0.156 0.140
#> GSM751427 2 0.0671 0.7005 0.000 0.980 0.000 0.004 0.016
#> GSM751438 2 0.1430 0.6589 0.000 0.944 0.052 0.004 0.000
#> GSM751439 2 0.3013 0.5321 0.000 0.832 0.160 0.008 0.000
#> GSM751441 2 0.0162 0.6996 0.000 0.996 0.000 0.004 0.000
#> GSM751442 2 0.0162 0.6996 0.000 0.996 0.000 0.004 0.000
#> GSM751443 3 0.5002 0.3718 0.000 0.364 0.596 0.040 0.000
#> GSM751445 2 0.0324 0.6975 0.000 0.992 0.000 0.004 0.004
#> GSM751447 2 0.0451 0.7036 0.000 0.988 0.000 0.008 0.004
#> GSM751453 2 0.2989 0.7050 0.000 0.868 0.000 0.060 0.072
#> GSM751454 2 0.2661 0.7082 0.000 0.888 0.000 0.056 0.056
#> GSM751455 2 0.0162 0.6996 0.000 0.996 0.000 0.004 0.000
#> GSM751456 2 0.0162 0.6996 0.000 0.996 0.000 0.004 0.000
#> GSM751457 2 0.6380 0.1155 0.000 0.520 0.336 0.132 0.012
#> GSM751458 2 0.6380 0.1155 0.000 0.520 0.336 0.132 0.012
cbind(get_classes(res, k = 6), get_membership(res, k = 6))
#> class entropy silhouette p1 p2 p3 p4 p5 p6
#> GSM751298 1 0.2260 0.89474 0.860 0.000 0.000 0.140 0.000 0.000
#> GSM751304 6 0.2066 0.55122 0.012 0.000 0.004 0.040 0.024 0.920
#> GSM751305 6 0.2201 0.54985 0.012 0.000 0.004 0.048 0.024 0.912
#> GSM751307 6 0.4133 0.55782 0.060 0.052 0.000 0.000 0.100 0.788
#> GSM751310 4 0.0632 0.87538 0.024 0.000 0.000 0.976 0.000 0.000
#> GSM751314 4 0.0632 0.87538 0.024 0.000 0.000 0.976 0.000 0.000
#> GSM751316 4 0.0458 0.87024 0.016 0.000 0.000 0.984 0.000 0.000
#> GSM751318 4 0.0622 0.85415 0.012 0.000 0.000 0.980 0.000 0.008
#> GSM751342 4 0.0508 0.86862 0.012 0.000 0.000 0.984 0.000 0.004
#> GSM751346 1 0.1387 0.93240 0.932 0.000 0.000 0.068 0.000 0.000
#> GSM751347 1 0.2077 0.85981 0.916 0.032 0.044 0.004 0.004 0.000
#> GSM751348 5 0.6890 0.17572 0.008 0.172 0.000 0.088 0.508 0.224
#> GSM751349 5 0.2633 0.68990 0.000 0.104 0.000 0.000 0.864 0.032
#> GSM751352 6 0.5222 0.50927 0.044 0.080 0.000 0.004 0.188 0.684
#> GSM751353 6 0.4605 0.38028 0.004 0.040 0.000 0.000 0.356 0.600
#> GSM751354 6 0.5754 0.52678 0.096 0.076 0.020 0.000 0.132 0.676
#> GSM751355 6 0.5151 0.46024 0.016 0.060 0.004 0.000 0.312 0.608
#> GSM751358 4 0.6927 0.00964 0.020 0.004 0.016 0.404 0.248 0.308
#> GSM751359 5 0.3206 0.63531 0.004 0.008 0.000 0.008 0.808 0.172
#> GSM751294 6 0.8341 0.17580 0.016 0.204 0.236 0.020 0.196 0.328
#> GSM751296 1 0.1556 0.93047 0.920 0.000 0.000 0.080 0.000 0.000
#> GSM751297 1 0.2000 0.88766 0.920 0.004 0.044 0.028 0.000 0.004
#> GSM751299 6 0.6615 0.24661 0.048 0.332 0.000 0.000 0.184 0.436
#> GSM751300 1 0.1387 0.93240 0.932 0.000 0.000 0.068 0.000 0.000
#> GSM751301 6 0.3479 0.56477 0.032 0.048 0.000 0.016 0.056 0.848
#> GSM751302 1 0.1387 0.93240 0.932 0.000 0.000 0.068 0.000 0.000
#> GSM751303 4 0.0458 0.87360 0.016 0.000 0.000 0.984 0.000 0.000
#> GSM751306 4 0.0632 0.87538 0.024 0.000 0.000 0.976 0.000 0.000
#> GSM751308 4 0.6833 0.34278 0.024 0.076 0.120 0.528 0.000 0.252
#> GSM751309 4 0.0547 0.87476 0.020 0.000 0.000 0.980 0.000 0.000
#> GSM751311 4 0.0547 0.87476 0.020 0.000 0.000 0.980 0.000 0.000
#> GSM751312 4 0.0937 0.87207 0.040 0.000 0.000 0.960 0.000 0.000
#> GSM751313 1 0.2823 0.82352 0.796 0.000 0.000 0.204 0.000 0.000
#> GSM751315 4 0.0713 0.87484 0.028 0.000 0.000 0.972 0.000 0.000
#> GSM751317 4 0.0458 0.87383 0.016 0.000 0.000 0.984 0.000 0.000
#> GSM751320 4 0.1387 0.85683 0.068 0.000 0.000 0.932 0.000 0.000
#> GSM751321 4 0.0713 0.87484 0.028 0.000 0.000 0.972 0.000 0.000
#> GSM751322 4 0.0632 0.87538 0.024 0.000 0.000 0.976 0.000 0.000
#> GSM751324 4 0.0632 0.87538 0.024 0.000 0.000 0.976 0.000 0.000
#> GSM751325 4 0.0632 0.87538 0.024 0.000 0.000 0.976 0.000 0.000
#> GSM751332 4 0.2762 0.72764 0.196 0.000 0.000 0.804 0.000 0.000
#> GSM751334 4 0.2697 0.74066 0.188 0.000 0.000 0.812 0.000 0.000
#> GSM751339 4 0.2637 0.81501 0.096 0.000 0.008 0.872 0.000 0.024
#> GSM751341 1 0.3244 0.72964 0.732 0.000 0.000 0.268 0.000 0.000
#> GSM751343 4 0.1007 0.86892 0.044 0.000 0.000 0.956 0.000 0.000
#> GSM751344 6 0.3667 0.57388 0.028 0.032 0.000 0.000 0.136 0.804
#> GSM751345 6 0.3667 0.57388 0.028 0.032 0.000 0.000 0.136 0.804
#> GSM751356 6 0.8048 0.21450 0.016 0.208 0.024 0.108 0.264 0.380
#> GSM751357 6 0.7998 0.21623 0.016 0.208 0.024 0.100 0.268 0.384
#> GSM751293 6 0.3801 0.56981 0.036 0.044 0.000 0.020 0.072 0.828
#> GSM751295 1 0.1387 0.93240 0.932 0.000 0.000 0.068 0.000 0.000
#> GSM751319 4 0.0713 0.87484 0.028 0.000 0.000 0.972 0.000 0.000
#> GSM751323 4 0.1610 0.84625 0.084 0.000 0.000 0.916 0.000 0.000
#> GSM751326 1 0.2003 0.91249 0.884 0.000 0.000 0.116 0.000 0.000
#> GSM751327 4 0.1910 0.82907 0.108 0.000 0.000 0.892 0.000 0.000
#> GSM751328 4 0.2631 0.74762 0.180 0.000 0.000 0.820 0.000 0.000
#> GSM751329 4 0.3817 0.17730 0.432 0.000 0.000 0.568 0.000 0.000
#> GSM751330 1 0.1663 0.92784 0.912 0.000 0.000 0.088 0.000 0.000
#> GSM751331 1 0.1387 0.93240 0.932 0.000 0.000 0.068 0.000 0.000
#> GSM751333 1 0.2378 0.88313 0.848 0.000 0.000 0.152 0.000 0.000
#> GSM751335 1 0.1765 0.92419 0.904 0.000 0.000 0.096 0.000 0.000
#> GSM751336 1 0.1501 0.93155 0.924 0.000 0.000 0.076 0.000 0.000
#> GSM751337 1 0.2854 0.82095 0.792 0.000 0.000 0.208 0.000 0.000
#> GSM751338 4 0.2146 0.82318 0.116 0.000 0.000 0.880 0.000 0.004
#> GSM751340 4 0.3657 0.76833 0.072 0.000 0.060 0.824 0.000 0.044
#> GSM751350 1 0.1387 0.93240 0.932 0.000 0.000 0.068 0.000 0.000
#> GSM751351 1 0.1387 0.93240 0.932 0.000 0.000 0.068 0.000 0.000
#> GSM751362 3 0.0291 0.78306 0.000 0.000 0.992 0.000 0.004 0.004
#> GSM751363 6 0.4900 0.29543 0.024 0.000 0.008 0.032 0.288 0.648
#> GSM751367 1 0.1716 0.90569 0.932 0.000 0.028 0.036 0.000 0.004
#> GSM751368 5 0.4758 0.17956 0.020 0.012 0.004 0.000 0.528 0.436
#> GSM751371 4 0.2450 0.80026 0.032 0.000 0.016 0.900 0.004 0.048
#> GSM751375 5 0.1410 0.76680 0.004 0.008 0.000 0.000 0.944 0.044
#> GSM751376 3 0.6097 0.24334 0.024 0.152 0.488 0.000 0.000 0.336
#> GSM751378 5 0.4141 0.49427 0.000 0.008 0.296 0.000 0.676 0.020
#> GSM751379 3 0.6105 0.23523 0.024 0.152 0.484 0.000 0.000 0.340
#> GSM751382 5 0.0717 0.78672 0.000 0.008 0.000 0.000 0.976 0.016
#> GSM751386 5 0.0603 0.78867 0.000 0.004 0.000 0.000 0.980 0.016
#> GSM751388 5 0.0603 0.78867 0.000 0.004 0.000 0.000 0.980 0.016
#> GSM751391 4 0.6898 0.02210 0.032 0.004 0.256 0.380 0.004 0.324
#> GSM751410 3 0.4201 0.70391 0.028 0.000 0.792 0.108 0.016 0.056
#> GSM751414 3 0.7715 0.11651 0.040 0.000 0.380 0.180 0.312 0.088
#> GSM751361 5 0.4114 0.68467 0.036 0.000 0.044 0.016 0.800 0.104
#> GSM751365 3 0.5995 0.07360 0.028 0.000 0.464 0.008 0.412 0.088
#> GSM751366 3 0.3021 0.73346 0.028 0.000 0.872 0.008 0.048 0.044
#> GSM751369 3 0.1584 0.76166 0.000 0.000 0.928 0.008 0.000 0.064
#> GSM751370 3 0.6873 0.02203 0.032 0.000 0.412 0.064 0.404 0.088
#> GSM751372 3 0.5663 0.38271 0.032 0.000 0.584 0.004 0.296 0.084
#> GSM751373 3 0.8265 0.05670 0.084 0.000 0.312 0.228 0.288 0.088
#> GSM751374 3 0.6105 0.23523 0.024 0.152 0.484 0.000 0.000 0.340
#> GSM751377 5 0.1340 0.77776 0.008 0.004 0.000 0.000 0.948 0.040
#> GSM751380 3 0.0653 0.78073 0.004 0.000 0.980 0.000 0.004 0.012
#> GSM751381 5 0.0603 0.78867 0.000 0.004 0.000 0.000 0.980 0.016
#> GSM751383 5 0.0603 0.78867 0.000 0.004 0.000 0.000 0.980 0.016
#> GSM751384 5 0.0865 0.77344 0.000 0.000 0.036 0.000 0.964 0.000
#> GSM751385 5 0.4177 0.45873 0.000 0.004 0.032 0.000 0.684 0.280
#> GSM751387 5 0.0603 0.78867 0.000 0.004 0.000 0.000 0.980 0.016
#> GSM751389 3 0.0547 0.77879 0.000 0.000 0.980 0.000 0.000 0.020
#> GSM751393 3 0.5189 0.43669 0.004 0.056 0.620 0.000 0.024 0.296
#> GSM751394 5 0.0603 0.78867 0.000 0.004 0.000 0.000 0.980 0.016
#> GSM751395 6 0.6202 -0.09837 0.004 0.080 0.424 0.000 0.056 0.436
#> GSM751397 5 0.0603 0.78867 0.000 0.004 0.000 0.000 0.980 0.016
#> GSM751398 5 0.0603 0.78867 0.000 0.004 0.000 0.000 0.980 0.016
#> GSM751404 3 0.0260 0.78245 0.000 0.000 0.992 0.000 0.008 0.000
#> GSM751406 3 0.0363 0.78133 0.000 0.000 0.988 0.000 0.000 0.012
#> GSM751411 3 0.5323 0.31874 0.020 0.000 0.576 0.004 0.340 0.060
#> GSM751413 6 0.3342 0.52728 0.028 0.000 0.004 0.008 0.140 0.820
#> GSM751415 3 0.0291 0.78252 0.000 0.000 0.992 0.000 0.004 0.004
#> GSM751416 5 0.4775 0.64508 0.036 0.000 0.100 0.012 0.748 0.104
#> GSM751417 5 0.4730 0.64846 0.036 0.000 0.096 0.012 0.752 0.104
#> GSM751421 3 0.4770 0.67789 0.036 0.000 0.748 0.112 0.012 0.092
#> GSM751422 3 0.4816 0.67610 0.036 0.000 0.744 0.112 0.012 0.096
#> GSM751360 3 0.6595 0.21526 0.036 0.000 0.436 0.388 0.020 0.120
#> GSM751364 5 0.5493 0.46069 0.032 0.000 0.240 0.004 0.632 0.092
#> GSM751390 5 0.1010 0.77604 0.000 0.004 0.036 0.000 0.960 0.000
#> GSM751392 5 0.0603 0.78867 0.000 0.004 0.000 0.000 0.980 0.016
#> GSM751396 5 0.1410 0.76997 0.004 0.008 0.000 0.000 0.944 0.044
#> GSM751399 3 0.0291 0.78314 0.000 0.000 0.992 0.000 0.004 0.004
#> GSM751400 3 0.0363 0.78133 0.000 0.000 0.988 0.000 0.000 0.012
#> GSM751401 3 0.0146 0.78276 0.000 0.000 0.996 0.000 0.004 0.000
#> GSM751402 3 0.0000 0.78250 0.000 0.000 1.000 0.000 0.000 0.000
#> GSM751403 3 0.0363 0.78133 0.000 0.000 0.988 0.000 0.000 0.012
#> GSM751405 3 0.0363 0.78133 0.000 0.000 0.988 0.000 0.000 0.012
#> GSM751407 3 0.0146 0.78276 0.000 0.000 0.996 0.000 0.004 0.000
#> GSM751408 3 0.0363 0.78187 0.000 0.000 0.988 0.000 0.012 0.000
#> GSM751409 3 0.0146 0.78276 0.000 0.000 0.996 0.000 0.004 0.000
#> GSM751412 3 0.1082 0.76978 0.000 0.000 0.956 0.000 0.040 0.004
#> GSM751418 5 0.6287 0.02786 0.032 0.000 0.404 0.020 0.456 0.088
#> GSM751419 5 0.6287 0.02786 0.032 0.000 0.404 0.020 0.456 0.088
#> GSM751420 3 0.1149 0.77157 0.008 0.008 0.960 0.000 0.000 0.024
#> GSM751425 2 0.4481 0.28052 0.004 0.556 0.000 0.000 0.416 0.024
#> GSM751429 1 0.3685 0.73951 0.796 0.120 0.080 0.000 0.000 0.004
#> GSM751430 6 0.3822 0.55516 0.020 0.068 0.000 0.000 0.112 0.800
#> GSM751433 6 0.5487 0.14230 0.016 0.416 0.000 0.000 0.080 0.488
#> GSM751437 3 0.2491 0.71500 0.000 0.112 0.868 0.000 0.000 0.020
#> GSM751448 3 0.3054 0.70734 0.028 0.088 0.856 0.000 0.000 0.028
#> GSM751451 2 0.7672 0.17730 0.036 0.448 0.000 0.188 0.120 0.208
#> GSM751423 2 0.5848 0.29361 0.016 0.560 0.000 0.000 0.200 0.224
#> GSM751424 6 0.5484 0.15196 0.016 0.412 0.000 0.000 0.080 0.492
#> GSM751428 6 0.4970 0.12966 0.016 0.436 0.000 0.000 0.036 0.512
#> GSM751431 6 0.5464 0.04605 0.016 0.452 0.000 0.000 0.076 0.456
#> GSM751432 6 0.5153 0.23395 0.016 0.376 0.000 0.000 0.056 0.552
#> GSM751434 6 0.5193 0.25647 0.020 0.360 0.000 0.000 0.056 0.564
#> GSM751435 2 0.2306 0.69213 0.004 0.888 0.000 0.000 0.016 0.092
#> GSM751436 6 0.5484 0.15196 0.016 0.412 0.000 0.000 0.080 0.492
#> GSM751440 2 0.4053 0.60337 0.012 0.772 0.000 0.000 0.136 0.080
#> GSM751444 2 0.1434 0.72339 0.012 0.940 0.000 0.000 0.000 0.048
#> GSM751446 2 0.0146 0.73956 0.000 0.996 0.000 0.000 0.000 0.004
#> GSM751449 2 0.0291 0.73802 0.004 0.992 0.000 0.000 0.000 0.004
#> GSM751450 2 0.5464 -0.09677 0.016 0.460 0.000 0.000 0.076 0.448
#> GSM751452 6 0.5442 0.15566 0.016 0.412 0.000 0.000 0.076 0.496
#> GSM751426 2 0.5464 -0.09677 0.016 0.460 0.000 0.000 0.076 0.448
#> GSM751427 2 0.1074 0.73222 0.000 0.960 0.000 0.000 0.028 0.012
#> GSM751438 2 0.0551 0.73396 0.004 0.984 0.008 0.000 0.000 0.004
#> GSM751439 2 0.1410 0.70379 0.008 0.944 0.044 0.000 0.000 0.004
#> GSM751441 2 0.0291 0.73974 0.004 0.992 0.000 0.000 0.000 0.004
#> GSM751442 2 0.0146 0.73951 0.004 0.996 0.000 0.000 0.000 0.000
#> GSM751443 2 0.4805 0.20190 0.024 0.584 0.368 0.000 0.000 0.024
#> GSM751445 2 0.0291 0.73834 0.004 0.992 0.000 0.000 0.000 0.004
#> GSM751447 2 0.0858 0.73374 0.000 0.968 0.000 0.000 0.004 0.028
#> GSM751453 2 0.3043 0.64799 0.008 0.836 0.000 0.000 0.024 0.132
#> GSM751454 2 0.2871 0.66366 0.008 0.852 0.000 0.000 0.024 0.116
#> GSM751455 2 0.0146 0.73951 0.004 0.996 0.000 0.000 0.000 0.000
#> GSM751456 2 0.0146 0.73951 0.004 0.996 0.000 0.000 0.000 0.000
#> GSM751457 2 0.4507 0.45655 0.008 0.724 0.112 0.000 0.000 0.156
#> GSM751458 2 0.4507 0.45655 0.008 0.724 0.112 0.000 0.000 0.156
Heatmaps for the consensus matrix. It visualizes the probability of two samples to be in a same group.
consensus_heatmap(res, k = 2)
consensus_heatmap(res, k = 3)
consensus_heatmap(res, k = 4)
consensus_heatmap(res, k = 5)
consensus_heatmap(res, k = 6)
Heatmaps for the membership of samples in all partitions to see how consistent they are:
membership_heatmap(res, k = 2)
membership_heatmap(res, k = 3)
membership_heatmap(res, k = 4)
membership_heatmap(res, k = 5)
membership_heatmap(res, k = 6)
As soon as we have had the classes for columns, we can look for signatures which are significantly different between classes which can be candidate marks for certain classes. Following are the heatmaps for signatures.
Signature heatmaps where rows are scaled:
get_signatures(res, k = 2)
get_signatures(res, k = 3)
get_signatures(res, k = 4)
get_signatures(res, k = 5)
get_signatures(res, k = 6)
Signature heatmaps where rows are not scaled:
get_signatures(res, k = 2, scale_rows = FALSE)
get_signatures(res, k = 3, scale_rows = FALSE)
get_signatures(res, k = 4, scale_rows = FALSE)
get_signatures(res, k = 5, scale_rows = FALSE)
get_signatures(res, k = 6, scale_rows = FALSE)
Compare the overlap of signatures from different k:
compare_signatures(res)
get_signature() returns a data frame invisibly. TO get the list of signatures, the function
call should be assigned to a variable explicitly. In following code, if plot argument is set
to FALSE, no heatmap is plotted while only the differential analysis is performed.
# code only for demonstration
tb = get_signature(res, k = ..., plot = FALSE)
An example of the output of tb is:
#> which_row fdr mean_1 mean_2 scaled_mean_1 scaled_mean_2 km
#> 1 38 0.042760348 8.373488 9.131774 -0.5533452 0.5164555 1
#> 2 40 0.018707592 7.106213 8.469186 -0.6173731 0.5762149 1
#> 3 55 0.019134737 10.221463 11.207825 -0.6159697 0.5749050 1
#> 4 59 0.006059896 5.921854 7.869574 -0.6899429 0.6439467 1
#> 5 60 0.018055526 8.928898 10.211722 -0.6204761 0.5791110 1
#> 6 98 0.009384629 15.714769 14.887706 0.6635654 -0.6193277 2
...
The columns in tb are:
which_row: row indices corresponding to the input matrix.fdr: FDR for the differential test. mean_x: The mean value in group x.scaled_mean_x: The mean value in group x after rows are scaled.km: Row groups if k-means clustering is applied to rows.UMAP plot which shows how samples are separated.
dimension_reduction(res, k = 2, method = "UMAP")
dimension_reduction(res, k = 3, method = "UMAP")
dimension_reduction(res, k = 4, method = "UMAP")
dimension_reduction(res, k = 5, method = "UMAP")
dimension_reduction(res, k = 6, method = "UMAP")
Following heatmap shows how subgroups are split when increasing k:
collect_classes(res)
Test correlation between subgroups and known annotations. If the known annotation is numeric, one-way ANOVA test is applied, and if the known annotation is discrete, chi-squared contingency table test is applied.
test_to_known_factors(res)
#> n tissue(p) disease.state(p) agent(p) k
#> ATC:skmeans 162 6.17e-09 0.3143 0.41321 2
#> ATC:skmeans 159 1.25e-26 0.2280 0.18057 3
#> ATC:skmeans 123 2.10e-45 0.1234 0.20861 4
#> ATC:skmeans 121 1.12e-44 0.2274 0.24289 5
#> ATC:skmeans 120 9.36e-35 0.0312 0.00352 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 4537 rows and 166 columns.
#> Top rows (454, 908, 1361, 1814, 2268) 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 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 0.537 0.675 0.873 0.4730 0.497 0.497
#> 3 3 0.731 0.817 0.917 0.3931 0.724 0.501
#> 4 4 0.616 0.576 0.767 0.1084 0.908 0.739
#> 5 5 0.629 0.626 0.779 0.0733 0.889 0.639
#> 6 6 0.664 0.442 0.684 0.0512 0.896 0.583
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
#> GSM751298 1 0.0000 0.86328 1.000 0.000
#> GSM751304 2 0.9491 0.45980 0.368 0.632
#> GSM751305 2 0.9775 0.37724 0.412 0.588
#> GSM751307 2 0.9170 0.52506 0.332 0.668
#> GSM751310 1 0.0672 0.86025 0.992 0.008
#> GSM751314 1 0.0000 0.86328 1.000 0.000
#> GSM751316 1 0.0000 0.86328 1.000 0.000
#> GSM751318 1 0.0000 0.86328 1.000 0.000
#> GSM751342 1 0.0000 0.86328 1.000 0.000
#> GSM751346 1 0.0000 0.86328 1.000 0.000
#> GSM751347 1 0.9993 -0.11422 0.516 0.484
#> GSM751348 2 0.2778 0.78386 0.048 0.952
#> GSM751349 2 0.0000 0.80884 0.000 1.000
#> GSM751352 2 0.0000 0.80884 0.000 1.000
#> GSM751353 2 0.0000 0.80884 0.000 1.000
#> GSM751354 2 0.8661 0.58039 0.288 0.712
#> GSM751355 2 0.0000 0.80884 0.000 1.000
#> GSM751358 1 0.9754 0.20196 0.592 0.408
#> GSM751359 2 0.3114 0.79061 0.056 0.944
#> GSM751294 2 0.1633 0.80340 0.024 0.976
#> GSM751296 1 0.0000 0.86328 1.000 0.000
#> GSM751297 1 0.2043 0.84879 0.968 0.032
#> GSM751299 2 0.0000 0.80884 0.000 1.000
#> GSM751300 1 0.0672 0.85911 0.992 0.008
#> GSM751301 2 0.3114 0.77688 0.056 0.944
#> GSM751302 1 0.0672 0.85911 0.992 0.008
#> GSM751303 1 0.0000 0.86328 1.000 0.000
#> GSM751306 1 0.0000 0.86328 1.000 0.000
#> GSM751308 1 0.6531 0.68458 0.832 0.168
#> GSM751309 1 0.0000 0.86328 1.000 0.000
#> GSM751311 1 0.0000 0.86328 1.000 0.000
#> GSM751312 1 0.0000 0.86328 1.000 0.000
#> GSM751313 1 0.0000 0.86328 1.000 0.000
#> GSM751315 1 0.0000 0.86328 1.000 0.000
#> GSM751317 1 0.0000 0.86328 1.000 0.000
#> GSM751320 1 0.0000 0.86328 1.000 0.000
#> GSM751321 1 0.0000 0.86328 1.000 0.000
#> GSM751322 1 0.0000 0.86328 1.000 0.000
#> GSM751324 1 0.0000 0.86328 1.000 0.000
#> GSM751325 1 0.0000 0.86328 1.000 0.000
#> GSM751332 1 0.0000 0.86328 1.000 0.000
#> GSM751334 1 0.0000 0.86328 1.000 0.000
#> GSM751339 1 0.0000 0.86328 1.000 0.000
#> GSM751341 1 0.0000 0.86328 1.000 0.000
#> GSM751343 1 0.0000 0.86328 1.000 0.000
#> GSM751344 2 0.0000 0.80884 0.000 1.000
#> GSM751345 2 0.0000 0.80884 0.000 1.000
#> GSM751356 2 0.0000 0.80884 0.000 1.000
#> GSM751357 2 0.0000 0.80884 0.000 1.000
#> GSM751293 2 0.3431 0.77228 0.064 0.936
#> GSM751295 1 0.0376 0.86134 0.996 0.004
#> GSM751319 1 0.0000 0.86328 1.000 0.000
#> GSM751323 1 0.0000 0.86328 1.000 0.000
#> GSM751326 1 0.0000 0.86328 1.000 0.000
#> GSM751327 1 0.0000 0.86328 1.000 0.000
#> GSM751328 1 0.0000 0.86328 1.000 0.000
#> GSM751329 1 0.0000 0.86328 1.000 0.000
#> GSM751330 1 0.0000 0.86328 1.000 0.000
#> GSM751331 1 0.4298 0.80219 0.912 0.088
#> GSM751333 1 0.0000 0.86328 1.000 0.000
#> GSM751335 1 0.0938 0.85770 0.988 0.012
#> GSM751336 1 0.0000 0.86328 1.000 0.000
#> GSM751337 1 0.0000 0.86328 1.000 0.000
#> GSM751338 1 0.0000 0.86328 1.000 0.000
#> GSM751340 1 0.0000 0.86328 1.000 0.000
#> GSM751350 1 0.5842 0.72615 0.860 0.140
#> GSM751351 1 0.3274 0.81915 0.940 0.060
#> GSM751362 1 0.2423 0.84091 0.960 0.040
#> GSM751363 1 0.9833 0.12814 0.576 0.424
#> GSM751367 1 0.9710 0.20712 0.600 0.400
#> GSM751368 2 0.9944 0.28337 0.456 0.544
#> GSM751371 1 0.0000 0.86328 1.000 0.000
#> GSM751375 2 0.0000 0.80884 0.000 1.000
#> GSM751376 2 0.2603 0.79587 0.044 0.956
#> GSM751378 2 0.2236 0.79904 0.036 0.964
#> GSM751379 2 0.8443 0.60375 0.272 0.728
#> GSM751382 2 0.0000 0.80884 0.000 1.000
#> GSM751386 2 0.8861 0.55960 0.304 0.696
#> GSM751388 2 0.9608 0.43473 0.384 0.616
#> GSM751391 2 1.0000 0.13291 0.496 0.504
#> GSM751410 1 0.0000 0.86328 1.000 0.000
#> GSM751414 1 0.2423 0.84285 0.960 0.040
#> GSM751361 1 0.9993 -0.09262 0.516 0.484
#> GSM751365 1 0.6247 0.72460 0.844 0.156
#> GSM751366 1 0.0376 0.86191 0.996 0.004
#> GSM751369 1 0.3114 0.83077 0.944 0.056
#> GSM751370 1 0.1843 0.85025 0.972 0.028
#> GSM751372 1 0.9983 -0.06349 0.524 0.476
#> GSM751373 1 0.6438 0.71531 0.836 0.164
#> GSM751374 2 0.9323 0.49736 0.348 0.652
#> GSM751377 2 0.9944 0.28337 0.456 0.544
#> GSM751380 1 0.0000 0.86328 1.000 0.000
#> GSM751381 2 0.8267 0.61416 0.260 0.740
#> GSM751383 2 0.9933 0.29340 0.452 0.548
#> GSM751384 2 0.9954 0.27271 0.460 0.540
#> GSM751385 2 0.9580 0.44098 0.380 0.620
#> GSM751387 2 0.4690 0.76246 0.100 0.900
#> GSM751389 2 0.9954 0.27271 0.460 0.540
#> GSM751393 2 0.9954 0.27271 0.460 0.540
#> GSM751394 2 0.0000 0.80884 0.000 1.000
#> GSM751395 2 0.9933 0.29307 0.452 0.548
#> GSM751397 2 0.9933 0.29334 0.452 0.548
#> GSM751398 2 0.9944 0.28337 0.456 0.544
#> GSM751404 1 0.1843 0.85025 0.972 0.028
#> GSM751406 1 0.4161 0.81051 0.916 0.084
#> GSM751411 1 0.7602 0.63077 0.780 0.220
#> GSM751413 2 0.9850 0.34729 0.428 0.572
#> GSM751415 1 0.0000 0.86328 1.000 0.000
#> GSM751416 2 0.9944 0.28337 0.456 0.544
#> GSM751417 2 0.9944 0.28337 0.456 0.544
#> GSM751421 1 0.9754 0.19717 0.592 0.408
#> GSM751422 1 0.3431 0.82778 0.936 0.064
#> GSM751360 1 0.0000 0.86328 1.000 0.000
#> GSM751364 1 0.9866 0.09607 0.568 0.432
#> GSM751390 2 0.9993 0.20156 0.484 0.516
#> GSM751392 2 0.0000 0.80884 0.000 1.000
#> GSM751396 2 0.4690 0.76268 0.100 0.900
#> GSM751399 1 0.9944 0.02511 0.544 0.456
#> GSM751400 2 0.9944 0.28337 0.456 0.544
#> GSM751401 1 0.1633 0.85319 0.976 0.024
#> GSM751402 1 0.3114 0.83420 0.944 0.056
#> GSM751403 1 0.9896 0.08469 0.560 0.440
#> GSM751405 1 0.3879 0.81716 0.924 0.076
#> GSM751407 1 0.8861 0.47757 0.696 0.304
#> GSM751408 2 0.9954 0.27271 0.460 0.540
#> GSM751409 2 0.9944 0.28337 0.456 0.544
#> GSM751412 1 0.9983 -0.08294 0.524 0.476
#> GSM751418 1 0.9944 -0.00319 0.544 0.456
#> GSM751419 1 0.9977 -0.06622 0.528 0.472
#> GSM751420 2 0.9922 0.30163 0.448 0.552
#> GSM751425 2 0.0000 0.80884 0.000 1.000
#> GSM751429 1 0.9983 -0.08119 0.524 0.476
#> GSM751430 2 0.2603 0.79576 0.044 0.956
#> GSM751433 2 0.1633 0.80005 0.024 0.976
#> GSM751437 1 0.9044 0.44427 0.680 0.320
#> GSM751448 1 0.3114 0.82917 0.944 0.056
#> GSM751451 2 0.2603 0.79629 0.044 0.956
#> GSM751423 2 0.0000 0.80884 0.000 1.000
#> GSM751424 2 0.0000 0.80884 0.000 1.000
#> GSM751428 2 0.1414 0.80477 0.020 0.980
#> GSM751431 2 0.0000 0.80884 0.000 1.000
#> GSM751432 2 0.0000 0.80884 0.000 1.000
#> GSM751434 2 0.0376 0.80815 0.004 0.996
#> GSM751435 2 0.0000 0.80884 0.000 1.000
#> GSM751436 2 0.0000 0.80884 0.000 1.000
#> GSM751440 2 0.5408 0.74840 0.124 0.876
#> GSM751444 2 0.0000 0.80884 0.000 1.000
#> GSM751446 2 0.0000 0.80884 0.000 1.000
#> GSM751449 2 0.0000 0.80884 0.000 1.000
#> GSM751450 2 0.1843 0.80251 0.028 0.972
#> GSM751452 2 0.0000 0.80884 0.000 1.000
#> GSM751426 2 0.0000 0.80884 0.000 1.000
#> GSM751427 2 0.0000 0.80884 0.000 1.000
#> GSM751438 2 0.0000 0.80884 0.000 1.000
#> GSM751439 2 0.1633 0.79548 0.024 0.976
#> GSM751441 2 0.0000 0.80884 0.000 1.000
#> GSM751442 2 0.0000 0.80884 0.000 1.000
#> GSM751443 2 0.1843 0.79270 0.028 0.972
#> GSM751445 2 0.0000 0.80884 0.000 1.000
#> GSM751447 2 0.0000 0.80884 0.000 1.000
#> GSM751453 2 0.0000 0.80884 0.000 1.000
#> GSM751454 2 0.0000 0.80884 0.000 1.000
#> GSM751455 2 0.0000 0.80884 0.000 1.000
#> GSM751456 2 0.0000 0.80884 0.000 1.000
#> GSM751457 2 0.0000 0.80884 0.000 1.000
#> GSM751458 2 0.0000 0.80884 0.000 1.000
cbind(get_classes(res, k = 3), get_membership(res, k = 3))
#> class entropy silhouette p1 p2 p3
#> GSM751298 1 0.0892 0.9017 0.980 0.000 0.020
#> GSM751304 2 0.5882 0.4524 0.000 0.652 0.348
#> GSM751305 2 0.6299 0.0694 0.000 0.524 0.476
#> GSM751307 2 0.8386 0.5215 0.156 0.620 0.224
#> GSM751310 3 0.6045 0.3715 0.380 0.000 0.620
#> GSM751314 1 0.3038 0.8555 0.896 0.000 0.104
#> GSM751316 1 0.6286 0.1752 0.536 0.000 0.464
#> GSM751318 1 0.0237 0.9044 0.996 0.000 0.004
#> GSM751342 1 0.2356 0.8792 0.928 0.000 0.072
#> GSM751346 1 0.2448 0.8776 0.924 0.000 0.076
#> GSM751347 3 0.6915 0.6974 0.140 0.124 0.736
#> GSM751348 2 0.3784 0.8148 0.132 0.864 0.004
#> GSM751349 2 0.0983 0.9147 0.016 0.980 0.004
#> GSM751352 2 0.0237 0.9212 0.000 0.996 0.004
#> GSM751353 2 0.0237 0.9212 0.000 0.996 0.004
#> GSM751354 2 0.4931 0.6775 0.000 0.768 0.232
#> GSM751355 2 0.0237 0.9212 0.000 0.996 0.004
#> GSM751358 3 0.4887 0.8221 0.060 0.096 0.844
#> GSM751359 2 0.3192 0.8479 0.000 0.888 0.112
#> GSM751294 2 0.1643 0.9024 0.000 0.956 0.044
#> GSM751296 1 0.0000 0.9046 1.000 0.000 0.000
#> GSM751297 3 0.5815 0.5159 0.304 0.004 0.692
#> GSM751299 2 0.0237 0.9212 0.000 0.996 0.004
#> GSM751300 1 0.3116 0.8522 0.892 0.000 0.108
#> GSM751301 2 0.4351 0.7738 0.168 0.828 0.004
#> GSM751302 1 0.5178 0.6887 0.744 0.000 0.256
#> GSM751303 1 0.6204 0.3215 0.576 0.000 0.424
#> GSM751306 1 0.2261 0.8815 0.932 0.000 0.068
#> GSM751308 1 0.2845 0.8766 0.920 0.012 0.068
#> GSM751309 1 0.0237 0.9044 0.996 0.000 0.004
#> GSM751311 1 0.4062 0.7998 0.836 0.000 0.164
#> GSM751312 1 0.6235 0.2691 0.564 0.000 0.436
#> GSM751313 1 0.0000 0.9046 1.000 0.000 0.000
#> GSM751315 1 0.0747 0.9029 0.984 0.000 0.016
#> GSM751317 1 0.1964 0.8879 0.944 0.000 0.056
#> GSM751320 1 0.0000 0.9046 1.000 0.000 0.000
#> GSM751321 1 0.0592 0.9035 0.988 0.000 0.012
#> GSM751322 1 0.0000 0.9046 1.000 0.000 0.000
#> GSM751324 1 0.0237 0.9044 0.996 0.000 0.004
#> GSM751325 1 0.0000 0.9046 1.000 0.000 0.000
#> GSM751332 1 0.0000 0.9046 1.000 0.000 0.000
#> GSM751334 1 0.0000 0.9046 1.000 0.000 0.000
#> GSM751339 1 0.1753 0.8835 0.952 0.000 0.048
#> GSM751341 1 0.5178 0.6831 0.744 0.000 0.256
#> GSM751343 1 0.0000 0.9046 1.000 0.000 0.000
#> GSM751344 2 0.0237 0.9212 0.000 0.996 0.004
#> GSM751345 2 0.0237 0.9212 0.000 0.996 0.004
#> GSM751356 2 0.0000 0.9210 0.000 1.000 0.000
#> GSM751357 2 0.0000 0.9210 0.000 1.000 0.000
#> GSM751293 2 0.4351 0.7736 0.168 0.828 0.004
#> GSM751295 1 0.5058 0.7068 0.756 0.000 0.244
#> GSM751319 1 0.0747 0.9030 0.984 0.000 0.016
#> GSM751323 1 0.0000 0.9046 1.000 0.000 0.000
#> GSM751326 1 0.0000 0.9046 1.000 0.000 0.000
#> GSM751327 1 0.0000 0.9046 1.000 0.000 0.000
#> GSM751328 1 0.0000 0.9046 1.000 0.000 0.000
#> GSM751329 1 0.0000 0.9046 1.000 0.000 0.000
#> GSM751330 1 0.0000 0.9046 1.000 0.000 0.000
#> GSM751331 1 0.2681 0.8766 0.932 0.040 0.028
#> GSM751333 1 0.0000 0.9046 1.000 0.000 0.000
#> GSM751335 1 0.0237 0.9045 0.996 0.000 0.004
#> GSM751336 1 0.0237 0.9045 0.996 0.000 0.004
#> GSM751337 1 0.0000 0.9046 1.000 0.000 0.000
#> GSM751338 1 0.0000 0.9046 1.000 0.000 0.000
#> GSM751340 1 0.3267 0.8500 0.884 0.000 0.116
#> GSM751350 1 0.5236 0.7793 0.804 0.028 0.168
#> GSM751351 1 0.5656 0.6316 0.712 0.004 0.284
#> GSM751362 3 0.0237 0.8932 0.004 0.000 0.996
#> GSM751363 3 0.2173 0.8756 0.048 0.008 0.944
#> GSM751367 3 0.5202 0.7806 0.136 0.044 0.820
#> GSM751368 3 0.1964 0.8764 0.000 0.056 0.944
#> GSM751371 1 0.5254 0.6709 0.736 0.000 0.264
#> GSM751375 2 0.0237 0.9212 0.000 0.996 0.004
#> GSM751376 2 0.2796 0.8697 0.000 0.908 0.092
#> GSM751378 2 0.3038 0.8632 0.000 0.896 0.104
#> GSM751379 3 0.6302 0.0595 0.000 0.480 0.520
#> GSM751382 2 0.0237 0.9212 0.000 0.996 0.004
#> GSM751386 3 0.4555 0.7332 0.000 0.200 0.800
#> GSM751388 3 0.3551 0.8151 0.000 0.132 0.868
#> GSM751391 2 0.8404 -0.0122 0.084 0.464 0.452
#> GSM751410 3 0.5690 0.5429 0.288 0.004 0.708
#> GSM751414 3 0.1860 0.8742 0.052 0.000 0.948
#> GSM751361 3 0.1529 0.8839 0.000 0.040 0.960
#> GSM751365 3 0.0000 0.8940 0.000 0.000 1.000
#> GSM751366 3 0.0424 0.8926 0.008 0.000 0.992
#> GSM751369 3 0.3816 0.7732 0.148 0.000 0.852
#> GSM751370 3 0.1529 0.8801 0.040 0.000 0.960
#> GSM751372 3 0.0000 0.8940 0.000 0.000 1.000
#> GSM751373 3 0.1964 0.8720 0.056 0.000 0.944
#> GSM751374 2 0.6225 0.2430 0.000 0.568 0.432
#> GSM751377 3 0.1964 0.8764 0.000 0.056 0.944
#> GSM751380 3 0.0237 0.8932 0.004 0.000 0.996
#> GSM751381 3 0.5138 0.6493 0.000 0.252 0.748
#> GSM751383 3 0.1643 0.8818 0.000 0.044 0.956
#> GSM751384 3 0.0000 0.8940 0.000 0.000 1.000
#> GSM751385 3 0.6307 0.0192 0.000 0.488 0.512
#> GSM751387 2 0.3340 0.8334 0.000 0.880 0.120
#> GSM751389 3 0.0237 0.8932 0.000 0.004 0.996
#> GSM751393 3 0.0000 0.8940 0.000 0.000 1.000
#> GSM751394 2 0.0237 0.9212 0.000 0.996 0.004
#> GSM751395 3 0.0592 0.8930 0.000 0.012 0.988
#> GSM751397 3 0.1753 0.8802 0.000 0.048 0.952
#> GSM751398 3 0.1964 0.8764 0.000 0.056 0.944
#> GSM751404 3 0.0000 0.8940 0.000 0.000 1.000
#> GSM751406 3 0.2448 0.8488 0.076 0.000 0.924
#> GSM751411 3 0.0000 0.8940 0.000 0.000 1.000
#> GSM751413 2 0.7188 -0.0352 0.024 0.488 0.488
#> GSM751415 3 0.0237 0.8932 0.004 0.000 0.996
#> GSM751416 3 0.1964 0.8764 0.000 0.056 0.944
#> GSM751417 3 0.1964 0.8764 0.000 0.056 0.944
#> GSM751421 3 0.0475 0.8941 0.004 0.004 0.992
#> GSM751422 3 0.0424 0.8926 0.008 0.000 0.992
#> GSM751360 3 0.5178 0.6349 0.256 0.000 0.744
#> GSM751364 3 0.1525 0.8843 0.032 0.004 0.964
#> GSM751390 3 0.0000 0.8940 0.000 0.000 1.000
#> GSM751392 2 0.0592 0.9187 0.000 0.988 0.012
#> GSM751396 2 0.2959 0.8535 0.000 0.900 0.100
#> GSM751399 3 0.0000 0.8940 0.000 0.000 1.000
#> GSM751400 3 0.1031 0.8879 0.000 0.024 0.976
#> GSM751401 3 0.0237 0.8932 0.000 0.004 0.996
#> GSM751402 3 0.0000 0.8940 0.000 0.000 1.000
#> GSM751403 3 0.0237 0.8932 0.000 0.004 0.996
#> GSM751405 3 0.0237 0.8932 0.000 0.004 0.996
#> GSM751407 3 0.0000 0.8940 0.000 0.000 1.000
#> GSM751408 3 0.0000 0.8940 0.000 0.000 1.000
#> GSM751409 3 0.0000 0.8940 0.000 0.000 1.000
#> GSM751412 3 0.0000 0.8940 0.000 0.000 1.000
#> GSM751418 3 0.0237 0.8939 0.004 0.000 0.996
#> GSM751419 3 0.0000 0.8940 0.000 0.000 1.000
#> GSM751420 3 0.6126 0.2929 0.000 0.400 0.600
#> GSM751425 2 0.0237 0.9212 0.000 0.996 0.004
#> GSM751429 3 0.3752 0.8357 0.096 0.020 0.884
#> GSM751430 2 0.1753 0.8981 0.000 0.952 0.048
#> GSM751433 2 0.2280 0.8902 0.052 0.940 0.008
#> GSM751437 3 0.1337 0.8891 0.012 0.016 0.972
#> GSM751448 3 0.6330 0.2444 0.396 0.004 0.600
#> GSM751451 2 0.2165 0.8881 0.000 0.936 0.064
#> GSM751423 2 0.0237 0.9212 0.000 0.996 0.004
#> GSM751424 2 0.0237 0.9212 0.000 0.996 0.004
#> GSM751428 2 0.0892 0.9151 0.000 0.980 0.020
#> GSM751431 2 0.0237 0.9212 0.000 0.996 0.004
#> GSM751432 2 0.0237 0.9212 0.000 0.996 0.004
#> GSM751434 2 0.0424 0.9202 0.000 0.992 0.008
#> GSM751435 2 0.0000 0.9210 0.000 1.000 0.000
#> GSM751436 2 0.0237 0.9212 0.000 0.996 0.004
#> GSM751440 2 0.4731 0.8056 0.032 0.840 0.128
#> GSM751444 2 0.0000 0.9210 0.000 1.000 0.000
#> GSM751446 2 0.0000 0.9210 0.000 1.000 0.000
#> GSM751449 2 0.0000 0.9210 0.000 1.000 0.000
#> GSM751450 2 0.1751 0.9073 0.012 0.960 0.028
#> GSM751452 2 0.0237 0.9212 0.000 0.996 0.004
#> GSM751426 2 0.0237 0.9212 0.000 0.996 0.004
#> GSM751427 2 0.0000 0.9210 0.000 1.000 0.000
#> GSM751438 2 0.0000 0.9210 0.000 1.000 0.000
#> GSM751439 2 0.0747 0.9148 0.000 0.984 0.016
#> GSM751441 2 0.0000 0.9210 0.000 1.000 0.000
#> GSM751442 2 0.0000 0.9210 0.000 1.000 0.000
#> GSM751443 2 0.1753 0.8968 0.000 0.952 0.048
#> GSM751445 2 0.0000 0.9210 0.000 1.000 0.000
#> GSM751447 2 0.0000 0.9210 0.000 1.000 0.000
#> GSM751453 2 0.0000 0.9210 0.000 1.000 0.000
#> GSM751454 2 0.0000 0.9210 0.000 1.000 0.000
#> GSM751455 2 0.0000 0.9210 0.000 1.000 0.000
#> GSM751456 2 0.0000 0.9210 0.000 1.000 0.000
#> GSM751457 2 0.0000 0.9210 0.000 1.000 0.000
#> GSM751458 2 0.0000 0.9210 0.000 1.000 0.000
cbind(get_classes(res, k = 4), get_membership(res, k = 4))
#> class entropy silhouette p1 p2 p3 p4
#> GSM751298 1 0.1042 0.7352 0.972 0.000 0.020 0.008
#> GSM751304 2 0.5057 0.3569 0.000 0.648 0.340 0.012
#> GSM751305 2 0.5273 0.1110 0.000 0.536 0.456 0.008
#> GSM751307 2 0.8289 0.1438 0.064 0.532 0.244 0.160
#> GSM751310 1 0.7762 0.1974 0.428 0.012 0.400 0.160
#> GSM751314 1 0.2654 0.6868 0.888 0.000 0.108 0.004
#> GSM751316 1 0.7037 0.2209 0.464 0.000 0.416 0.120
#> GSM751318 1 0.0000 0.7352 1.000 0.000 0.000 0.000
#> GSM751342 1 0.1978 0.7134 0.928 0.000 0.068 0.004
#> GSM751346 4 0.5366 -0.4095 0.440 0.000 0.012 0.548
#> GSM751347 4 0.7358 0.1242 0.088 0.024 0.400 0.488
#> GSM751348 2 0.5446 0.7373 0.100 0.760 0.012 0.128
#> GSM751349 2 0.3237 0.8290 0.040 0.888 0.008 0.064
#> GSM751352 2 0.2515 0.8417 0.012 0.912 0.004 0.072
#> GSM751353 2 0.0524 0.8396 0.000 0.988 0.004 0.008
#> GSM751354 2 0.6240 0.4769 0.000 0.664 0.200 0.136
#> GSM751355 2 0.1545 0.8318 0.000 0.952 0.008 0.040
#> GSM751358 1 0.8347 -0.0756 0.376 0.016 0.320 0.288
#> GSM751359 2 0.4224 0.7657 0.000 0.824 0.100 0.076
#> GSM751294 4 0.5167 -0.2137 0.000 0.488 0.004 0.508
#> GSM751296 1 0.1940 0.7326 0.924 0.000 0.000 0.076
#> GSM751297 4 0.4395 0.2662 0.016 0.004 0.204 0.776
#> GSM751299 2 0.2266 0.8410 0.000 0.912 0.004 0.084
#> GSM751300 1 0.7008 0.3881 0.448 0.000 0.116 0.436
#> GSM751301 2 0.3072 0.7571 0.124 0.868 0.004 0.004
#> GSM751302 4 0.7686 -0.2436 0.336 0.000 0.228 0.436
#> GSM751303 1 0.4889 0.3732 0.636 0.000 0.360 0.004
#> GSM751306 1 0.2053 0.7129 0.924 0.000 0.072 0.004
#> GSM751308 1 0.3102 0.6565 0.872 0.004 0.008 0.116
#> GSM751309 1 0.0188 0.7340 0.996 0.000 0.000 0.004
#> GSM751311 1 0.3448 0.6288 0.828 0.000 0.168 0.004
#> GSM751312 3 0.7910 -0.3336 0.304 0.000 0.352 0.344
#> GSM751313 1 0.4916 0.5298 0.576 0.000 0.000 0.424
#> GSM751315 1 0.4054 0.6929 0.796 0.000 0.016 0.188
#> GSM751317 1 0.1824 0.7194 0.936 0.000 0.060 0.004
#> GSM751320 1 0.0000 0.7352 1.000 0.000 0.000 0.000
#> GSM751321 1 0.3937 0.6968 0.800 0.000 0.012 0.188
#> GSM751322 1 0.0000 0.7352 1.000 0.000 0.000 0.000
#> GSM751324 1 0.0188 0.7340 0.996 0.000 0.000 0.004
#> GSM751325 1 0.0000 0.7352 1.000 0.000 0.000 0.000
#> GSM751332 1 0.3975 0.6641 0.760 0.000 0.000 0.240
#> GSM751334 1 0.3764 0.6780 0.784 0.000 0.000 0.216
#> GSM751339 1 0.3668 0.6652 0.808 0.000 0.004 0.188
#> GSM751341 1 0.4872 0.5171 0.728 0.000 0.244 0.028
#> GSM751343 1 0.0000 0.7352 1.000 0.000 0.000 0.000
#> GSM751344 2 0.0376 0.8395 0.000 0.992 0.004 0.004
#> GSM751345 2 0.0376 0.8395 0.000 0.992 0.004 0.004
#> GSM751356 2 0.2704 0.8229 0.000 0.876 0.000 0.124
#> GSM751357 2 0.2647 0.8270 0.000 0.880 0.000 0.120
#> GSM751293 2 0.4976 0.4031 0.340 0.652 0.004 0.004
#> GSM751295 4 0.7516 -0.2267 0.328 0.000 0.200 0.472
#> GSM751319 1 0.4661 0.6509 0.728 0.000 0.016 0.256
#> GSM751323 1 0.0000 0.7352 1.000 0.000 0.000 0.000
#> GSM751326 1 0.4916 0.5298 0.576 0.000 0.000 0.424
#> GSM751327 1 0.0188 0.7358 0.996 0.000 0.000 0.004
#> GSM751328 1 0.0592 0.7362 0.984 0.000 0.000 0.016
#> GSM751329 1 0.4103 0.6539 0.744 0.000 0.000 0.256
#> GSM751330 1 0.4916 0.5298 0.576 0.000 0.000 0.424
#> GSM751331 1 0.5882 0.4916 0.536 0.016 0.012 0.436
#> GSM751333 1 0.4916 0.5298 0.576 0.000 0.000 0.424
#> GSM751335 1 0.4916 0.5298 0.576 0.000 0.000 0.424
#> GSM751336 1 0.4933 0.5226 0.568 0.000 0.000 0.432
#> GSM751337 1 0.0000 0.7352 1.000 0.000 0.000 0.000
#> GSM751338 1 0.3219 0.6798 0.836 0.000 0.000 0.164
#> GSM751340 1 0.4880 0.6451 0.760 0.000 0.052 0.188
#> GSM751350 4 0.7596 -0.3132 0.380 0.004 0.172 0.444
#> GSM751351 4 0.7862 -0.2101 0.316 0.004 0.240 0.440
#> GSM751362 3 0.4713 0.5115 0.000 0.000 0.640 0.360
#> GSM751363 3 0.0804 0.7315 0.008 0.012 0.980 0.000
#> GSM751367 3 0.6908 0.3305 0.080 0.044 0.648 0.228
#> GSM751368 3 0.0707 0.7308 0.000 0.020 0.980 0.000
#> GSM751371 1 0.4053 0.5584 0.768 0.000 0.228 0.004
#> GSM751375 2 0.1584 0.8299 0.000 0.952 0.012 0.036
#> GSM751376 4 0.5594 -0.0893 0.000 0.460 0.020 0.520
#> GSM751378 4 0.5971 -0.0372 0.000 0.428 0.040 0.532
#> GSM751379 4 0.7845 0.1193 0.000 0.292 0.304 0.404
#> GSM751382 2 0.2153 0.8343 0.020 0.936 0.008 0.036
#> GSM751386 3 0.4332 0.5771 0.000 0.176 0.792 0.032
#> GSM751388 3 0.3404 0.6615 0.000 0.104 0.864 0.032
#> GSM751391 3 0.8616 -0.1839 0.036 0.364 0.368 0.232
#> GSM751410 3 0.7656 0.1545 0.296 0.004 0.488 0.212
#> GSM751414 3 0.0844 0.7303 0.004 0.004 0.980 0.012
#> GSM751361 3 0.0707 0.7308 0.000 0.020 0.980 0.000
#> GSM751365 3 0.0469 0.7329 0.000 0.000 0.988 0.012
#> GSM751366 3 0.0592 0.7328 0.000 0.000 0.984 0.016
#> GSM751369 3 0.7176 0.3753 0.132 0.004 0.524 0.340
#> GSM751370 3 0.0779 0.7318 0.000 0.004 0.980 0.016
#> GSM751372 3 0.0188 0.7336 0.000 0.000 0.996 0.004
#> GSM751373 3 0.0967 0.7288 0.004 0.004 0.976 0.016
#> GSM751374 4 0.7476 0.1743 0.000 0.412 0.176 0.412
#> GSM751377 3 0.0921 0.7280 0.000 0.028 0.972 0.000
#> GSM751380 3 0.2408 0.7093 0.000 0.000 0.896 0.104
#> GSM751381 3 0.4833 0.4997 0.000 0.228 0.740 0.032
#> GSM751383 3 0.1833 0.7185 0.000 0.024 0.944 0.032
#> GSM751384 3 0.1488 0.7242 0.000 0.012 0.956 0.032
#> GSM751385 3 0.7008 -0.0451 0.000 0.436 0.448 0.116
#> GSM751387 2 0.3948 0.7359 0.000 0.828 0.136 0.036
#> GSM751389 3 0.4855 0.4692 0.000 0.000 0.600 0.400
#> GSM751393 3 0.5193 0.4603 0.000 0.008 0.580 0.412
#> GSM751394 2 0.1833 0.8286 0.000 0.944 0.024 0.032
#> GSM751395 3 0.6292 0.4011 0.000 0.060 0.524 0.416
#> GSM751397 3 0.1833 0.7185 0.000 0.024 0.944 0.032
#> GSM751398 3 0.2892 0.6892 0.000 0.068 0.896 0.036
#> GSM751404 3 0.4406 0.5677 0.000 0.000 0.700 0.300
#> GSM751406 3 0.5568 0.3598 0.012 0.004 0.516 0.468
#> GSM751411 3 0.1557 0.7321 0.000 0.000 0.944 0.056
#> GSM751413 2 0.5165 0.0655 0.000 0.512 0.484 0.004
#> GSM751415 3 0.4855 0.4728 0.000 0.000 0.600 0.400
#> GSM751416 3 0.0707 0.7308 0.000 0.020 0.980 0.000
#> GSM751417 3 0.0707 0.7308 0.000 0.020 0.980 0.000
#> GSM751421 3 0.0657 0.7347 0.000 0.004 0.984 0.012
#> GSM751422 3 0.0524 0.7335 0.004 0.000 0.988 0.008
#> GSM751360 3 0.7711 0.0682 0.400 0.028 0.460 0.112
#> GSM751364 3 0.0336 0.7337 0.000 0.008 0.992 0.000
#> GSM751390 3 0.2329 0.7267 0.000 0.012 0.916 0.072
#> GSM751392 2 0.2722 0.8154 0.000 0.904 0.064 0.032
#> GSM751396 2 0.3497 0.7567 0.000 0.860 0.104 0.036
#> GSM751399 3 0.2973 0.6925 0.000 0.000 0.856 0.144
#> GSM751400 3 0.2813 0.7172 0.000 0.024 0.896 0.080
#> GSM751401 3 0.3266 0.6770 0.000 0.000 0.832 0.168
#> GSM751402 3 0.4643 0.5339 0.000 0.000 0.656 0.344
#> GSM751403 3 0.4888 0.4603 0.000 0.000 0.588 0.412
#> GSM751405 3 0.4888 0.4603 0.000 0.000 0.588 0.412
#> GSM751407 3 0.3074 0.6918 0.000 0.000 0.848 0.152
#> GSM751408 3 0.1716 0.7253 0.000 0.000 0.936 0.064
#> GSM751409 3 0.4866 0.4691 0.000 0.000 0.596 0.404
#> GSM751412 3 0.2149 0.7186 0.000 0.000 0.912 0.088
#> GSM751418 3 0.0188 0.7337 0.000 0.004 0.996 0.000
#> GSM751419 3 0.0376 0.7339 0.000 0.004 0.992 0.004
#> GSM751420 4 0.7426 0.2386 0.000 0.264 0.224 0.512
#> GSM751425 2 0.1978 0.8409 0.000 0.928 0.004 0.068
#> GSM751429 3 0.5460 0.3839 0.016 0.008 0.640 0.336
#> GSM751430 2 0.1489 0.8270 0.000 0.952 0.044 0.004
#> GSM751433 2 0.1229 0.8353 0.020 0.968 0.008 0.004
#> GSM751437 4 0.5590 -0.2979 0.000 0.020 0.456 0.524
#> GSM751448 4 0.5640 0.0823 0.052 0.004 0.256 0.688
#> GSM751451 2 0.2149 0.8018 0.000 0.912 0.088 0.000
#> GSM751423 2 0.0524 0.8412 0.000 0.988 0.008 0.004
#> GSM751424 2 0.0376 0.8395 0.000 0.992 0.004 0.004
#> GSM751428 2 0.1004 0.8374 0.000 0.972 0.024 0.004
#> GSM751431 2 0.0376 0.8410 0.000 0.992 0.004 0.004
#> GSM751432 2 0.0376 0.8395 0.000 0.992 0.004 0.004
#> GSM751434 2 0.0524 0.8397 0.000 0.988 0.008 0.004
#> GSM751435 2 0.2081 0.8362 0.000 0.916 0.000 0.084
#> GSM751436 2 0.0524 0.8391 0.000 0.988 0.008 0.004
#> GSM751440 2 0.5506 0.7028 0.004 0.744 0.136 0.116
#> GSM751444 2 0.1637 0.8414 0.000 0.940 0.000 0.060
#> GSM751446 2 0.2589 0.8236 0.000 0.884 0.000 0.116
#> GSM751449 2 0.2589 0.8236 0.000 0.884 0.000 0.116
#> GSM751450 2 0.1543 0.8327 0.008 0.956 0.032 0.004
#> GSM751452 2 0.0376 0.8395 0.000 0.992 0.004 0.004
#> GSM751426 2 0.0376 0.8395 0.000 0.992 0.004 0.004
#> GSM751427 2 0.2589 0.8236 0.000 0.884 0.000 0.116
#> GSM751438 2 0.2589 0.8236 0.000 0.884 0.000 0.116
#> GSM751439 2 0.3583 0.7748 0.000 0.816 0.004 0.180
#> GSM751441 2 0.2081 0.8362 0.000 0.916 0.000 0.084
#> GSM751442 2 0.2589 0.8236 0.000 0.884 0.000 0.116
#> GSM751443 4 0.5108 0.2356 0.000 0.308 0.020 0.672
#> GSM751445 2 0.2345 0.8309 0.000 0.900 0.000 0.100
#> GSM751447 2 0.2081 0.8362 0.000 0.916 0.000 0.084
#> GSM751453 2 0.2011 0.8373 0.000 0.920 0.000 0.080
#> GSM751454 2 0.2081 0.8362 0.000 0.916 0.000 0.084
#> GSM751455 2 0.2589 0.8236 0.000 0.884 0.000 0.116
#> GSM751456 2 0.2589 0.8236 0.000 0.884 0.000 0.116
#> GSM751457 2 0.4916 0.3466 0.000 0.576 0.000 0.424
#> GSM751458 2 0.4961 0.2828 0.000 0.552 0.000 0.448
cbind(get_classes(res, k = 5), get_membership(res, k = 5))
#> class entropy silhouette p1 p2 p3 p4 p5
#> GSM751298 4 0.2625 0.7441 0.108 0.000 0.016 0.876 0.000
#> GSM751304 2 0.5102 0.4484 0.000 0.620 0.336 0.036 0.008
#> GSM751305 2 0.5100 0.1895 0.000 0.516 0.448 0.036 0.000
#> GSM751307 2 0.6455 0.3525 0.208 0.544 0.240 0.008 0.000
#> GSM751310 4 0.6377 0.1179 0.336 0.000 0.180 0.484 0.000
#> GSM751314 4 0.1908 0.7439 0.000 0.000 0.092 0.908 0.000
#> GSM751316 4 0.6718 0.0910 0.272 0.000 0.308 0.420 0.000
#> GSM751318 4 0.0794 0.7651 0.028 0.000 0.000 0.972 0.000
#> GSM751342 4 0.1197 0.7638 0.000 0.000 0.048 0.952 0.000
#> GSM751346 1 0.3670 0.7711 0.832 0.000 0.008 0.100 0.060
#> GSM751347 1 0.3718 0.7063 0.784 0.000 0.196 0.004 0.016
#> GSM751348 2 0.7214 0.6439 0.144 0.576 0.028 0.044 0.208
#> GSM751349 2 0.5519 0.7304 0.152 0.704 0.020 0.004 0.120
#> GSM751352 2 0.4959 0.7551 0.144 0.736 0.012 0.000 0.108
#> GSM751353 2 0.1278 0.7877 0.020 0.960 0.016 0.000 0.004
#> GSM751354 2 0.6484 0.6015 0.196 0.624 0.108 0.000 0.072
#> GSM751355 2 0.3715 0.7406 0.112 0.832 0.024 0.000 0.032
#> GSM751358 4 0.7385 0.2648 0.052 0.000 0.240 0.476 0.232
#> GSM751359 2 0.6923 0.6153 0.140 0.628 0.104 0.016 0.112
#> GSM751294 5 0.4835 0.3319 0.048 0.244 0.008 0.000 0.700
#> GSM751296 4 0.3861 0.5224 0.284 0.000 0.000 0.712 0.004
#> GSM751297 1 0.4757 0.6646 0.732 0.000 0.120 0.000 0.148
#> GSM751299 2 0.4194 0.7783 0.084 0.800 0.012 0.000 0.104
#> GSM751300 1 0.3301 0.7830 0.848 0.000 0.080 0.072 0.000
#> GSM751301 2 0.2693 0.7689 0.028 0.896 0.016 0.060 0.000
#> GSM751302 1 0.2909 0.7551 0.848 0.000 0.140 0.012 0.000
#> GSM751303 4 0.2852 0.6784 0.000 0.000 0.172 0.828 0.000
#> GSM751306 4 0.1478 0.7586 0.000 0.000 0.064 0.936 0.000
#> GSM751308 4 0.1918 0.7544 0.012 0.004 0.004 0.932 0.048
#> GSM751309 4 0.0000 0.7635 0.000 0.000 0.000 1.000 0.000
#> GSM751311 4 0.2179 0.7293 0.000 0.000 0.112 0.888 0.000
#> GSM751312 1 0.5205 0.6320 0.672 0.000 0.224 0.104 0.000
#> GSM751313 1 0.2966 0.7744 0.816 0.000 0.000 0.184 0.000
#> GSM751315 4 0.4740 -0.2608 0.468 0.000 0.016 0.516 0.000
#> GSM751317 4 0.1270 0.7635 0.000 0.000 0.052 0.948 0.000
#> GSM751320 4 0.0963 0.7631 0.036 0.000 0.000 0.964 0.000
#> GSM751321 4 0.4627 -0.1860 0.444 0.000 0.012 0.544 0.000
#> GSM751322 4 0.0794 0.7651 0.028 0.000 0.000 0.972 0.000
#> GSM751324 4 0.0000 0.7635 0.000 0.000 0.000 1.000 0.000
#> GSM751325 4 0.0794 0.7651 0.028 0.000 0.000 0.972 0.000
#> GSM751332 1 0.4150 0.5504 0.612 0.000 0.000 0.388 0.000
#> GSM751334 1 0.4306 0.3055 0.508 0.000 0.000 0.492 0.000
#> GSM751339 4 0.3197 0.6780 0.140 0.000 0.000 0.836 0.024
#> GSM751341 4 0.3829 0.6475 0.028 0.000 0.196 0.776 0.000
#> GSM751343 4 0.0794 0.7651 0.028 0.000 0.000 0.972 0.000
#> GSM751344 2 0.1549 0.7846 0.040 0.944 0.016 0.000 0.000
#> GSM751345 2 0.0693 0.7868 0.008 0.980 0.012 0.000 0.000
#> GSM751356 2 0.5322 0.7173 0.092 0.688 0.000 0.012 0.208
#> GSM751357 2 0.5827 0.7117 0.112 0.660 0.012 0.008 0.208
#> GSM751293 2 0.5358 0.4602 0.028 0.636 0.004 0.308 0.024
#> GSM751295 1 0.3359 0.7638 0.848 0.000 0.112 0.016 0.024
#> GSM751319 1 0.4482 0.6054 0.636 0.000 0.016 0.348 0.000
#> GSM751323 4 0.0963 0.7631 0.036 0.000 0.000 0.964 0.000
#> GSM751326 1 0.2966 0.7737 0.816 0.000 0.000 0.184 0.000
#> GSM751327 4 0.1478 0.7567 0.064 0.000 0.000 0.936 0.000
#> GSM751328 4 0.2074 0.7313 0.104 0.000 0.000 0.896 0.000
#> GSM751329 1 0.3999 0.6174 0.656 0.000 0.000 0.344 0.000
#> GSM751330 1 0.2891 0.7780 0.824 0.000 0.000 0.176 0.000
#> GSM751331 1 0.2763 0.7823 0.848 0.000 0.004 0.148 0.000
#> GSM751333 1 0.2891 0.7780 0.824 0.000 0.000 0.176 0.000
#> GSM751335 1 0.2891 0.7780 0.824 0.000 0.000 0.176 0.000
#> GSM751336 1 0.2648 0.7805 0.848 0.000 0.000 0.152 0.000
#> GSM751337 4 0.1270 0.7607 0.052 0.000 0.000 0.948 0.000
#> GSM751338 4 0.2929 0.6626 0.180 0.000 0.000 0.820 0.000
#> GSM751340 4 0.4660 0.6492 0.136 0.000 0.060 0.772 0.032
#> GSM751350 1 0.3393 0.7755 0.848 0.000 0.100 0.044 0.008
#> GSM751351 1 0.3022 0.7564 0.848 0.000 0.136 0.012 0.004
#> GSM751362 5 0.4283 0.3426 0.000 0.000 0.456 0.000 0.544
#> GSM751363 3 0.0703 0.7588 0.000 0.024 0.976 0.000 0.000
#> GSM751367 1 0.5179 0.2744 0.520 0.024 0.448 0.004 0.004
#> GSM751368 3 0.0880 0.7576 0.000 0.032 0.968 0.000 0.000
#> GSM751371 4 0.2966 0.6812 0.000 0.000 0.184 0.816 0.000
#> GSM751375 2 0.4339 0.7129 0.140 0.788 0.024 0.000 0.048
#> GSM751376 5 0.2362 0.6500 0.000 0.076 0.024 0.000 0.900
#> GSM751378 5 0.4041 0.5681 0.136 0.044 0.016 0.000 0.804
#> GSM751379 5 0.5605 0.6104 0.000 0.168 0.192 0.000 0.640
#> GSM751382 2 0.4945 0.7121 0.144 0.752 0.036 0.000 0.068
#> GSM751386 3 0.5736 0.5755 0.140 0.116 0.696 0.000 0.048
#> GSM751388 3 0.5235 0.6184 0.140 0.076 0.736 0.000 0.048
#> GSM751391 5 0.7119 0.3015 0.004 0.156 0.316 0.036 0.488
#> GSM751410 3 0.6658 -0.0927 0.004 0.000 0.404 0.192 0.400
#> GSM751414 3 0.1059 0.7577 0.004 0.020 0.968 0.008 0.000
#> GSM751361 3 0.0609 0.7591 0.000 0.020 0.980 0.000 0.000
#> GSM751365 3 0.0963 0.7432 0.000 0.000 0.964 0.000 0.036
#> GSM751366 3 0.1831 0.7268 0.004 0.000 0.920 0.000 0.076
#> GSM751369 5 0.5525 0.5297 0.000 0.000 0.240 0.124 0.636
#> GSM751370 3 0.0693 0.7508 0.012 0.000 0.980 0.000 0.008
#> GSM751372 3 0.0703 0.7466 0.000 0.000 0.976 0.000 0.024
#> GSM751373 3 0.1173 0.7563 0.012 0.020 0.964 0.004 0.000
#> GSM751374 5 0.5339 0.6130 0.000 0.224 0.116 0.000 0.660
#> GSM751377 3 0.2946 0.7144 0.088 0.044 0.868 0.000 0.000
#> GSM751380 3 0.3039 0.6009 0.000 0.000 0.808 0.000 0.192
#> GSM751381 3 0.5906 0.5470 0.140 0.132 0.680 0.000 0.048
#> GSM751383 3 0.4867 0.6448 0.140 0.048 0.760 0.000 0.052
#> GSM751384 3 0.4867 0.6448 0.140 0.048 0.760 0.000 0.052
#> GSM751385 2 0.8359 -0.1100 0.140 0.328 0.264 0.000 0.268
#> GSM751387 2 0.5971 0.6378 0.140 0.676 0.132 0.000 0.052
#> GSM751389 5 0.3796 0.5747 0.000 0.000 0.300 0.000 0.700
#> GSM751393 5 0.4341 0.4211 0.000 0.004 0.404 0.000 0.592
#> GSM751394 2 0.5177 0.6868 0.140 0.740 0.072 0.000 0.048
#> GSM751395 5 0.5714 0.4615 0.000 0.116 0.292 0.000 0.592
#> GSM751397 3 0.4799 0.6449 0.140 0.048 0.764 0.000 0.048
#> GSM751398 3 0.5645 0.5947 0.140 0.108 0.704 0.000 0.048
#> GSM751404 3 0.4306 -0.0475 0.000 0.000 0.508 0.000 0.492
#> GSM751406 5 0.3003 0.6428 0.000 0.000 0.188 0.000 0.812
#> GSM751411 3 0.5118 0.5756 0.068 0.008 0.684 0.000 0.240
#> GSM751413 2 0.4287 0.2149 0.000 0.540 0.460 0.000 0.000
#> GSM751415 5 0.3561 0.5995 0.000 0.000 0.260 0.000 0.740
#> GSM751416 3 0.0609 0.7591 0.000 0.020 0.980 0.000 0.000
#> GSM751417 3 0.0609 0.7591 0.000 0.020 0.980 0.000 0.000
#> GSM751421 3 0.1686 0.7572 0.000 0.020 0.944 0.008 0.028
#> GSM751422 3 0.1356 0.7481 0.000 0.004 0.956 0.012 0.028
#> GSM751360 4 0.6915 0.0680 0.000 0.008 0.376 0.384 0.232
#> GSM751364 3 0.0609 0.7591 0.000 0.020 0.980 0.000 0.000
#> GSM751390 3 0.5449 0.6333 0.140 0.048 0.720 0.000 0.092
#> GSM751392 2 0.5597 0.6722 0.140 0.708 0.104 0.000 0.048
#> GSM751396 2 0.5290 0.6750 0.140 0.732 0.080 0.000 0.048
#> GSM751399 3 0.3796 0.5042 0.000 0.000 0.700 0.000 0.300
#> GSM751400 3 0.4114 0.5692 0.000 0.024 0.732 0.000 0.244
#> GSM751401 3 0.4015 0.4106 0.000 0.000 0.652 0.000 0.348
#> GSM751402 5 0.4227 0.2925 0.000 0.000 0.420 0.000 0.580
#> GSM751403 5 0.3586 0.5947 0.000 0.000 0.264 0.000 0.736
#> GSM751405 5 0.3508 0.6043 0.000 0.000 0.252 0.000 0.748
#> GSM751407 3 0.3949 0.4432 0.000 0.000 0.668 0.000 0.332
#> GSM751408 3 0.2424 0.6923 0.000 0.000 0.868 0.000 0.132
#> GSM751409 5 0.3561 0.6006 0.000 0.000 0.260 0.000 0.740
#> GSM751412 3 0.3661 0.5401 0.000 0.000 0.724 0.000 0.276
#> GSM751418 3 0.1117 0.7587 0.000 0.020 0.964 0.000 0.016
#> GSM751419 3 0.1117 0.7588 0.000 0.020 0.964 0.000 0.016
#> GSM751420 5 0.2325 0.6656 0.000 0.028 0.068 0.000 0.904
#> GSM751425 2 0.2992 0.7851 0.024 0.872 0.012 0.000 0.092
#> GSM751429 3 0.6816 0.1456 0.220 0.012 0.480 0.000 0.288
#> GSM751430 2 0.0880 0.7861 0.000 0.968 0.032 0.000 0.000
#> GSM751433 2 0.0771 0.7867 0.004 0.976 0.020 0.000 0.000
#> GSM751437 5 0.1788 0.6551 0.004 0.008 0.056 0.000 0.932
#> GSM751448 5 0.1638 0.6583 0.004 0.000 0.064 0.000 0.932
#> GSM751451 2 0.2424 0.7431 0.000 0.868 0.132 0.000 0.000
#> GSM751423 2 0.1059 0.7875 0.008 0.968 0.020 0.000 0.004
#> GSM751424 2 0.0404 0.7864 0.000 0.988 0.012 0.000 0.000
#> GSM751428 2 0.0880 0.7863 0.000 0.968 0.032 0.000 0.000
#> GSM751431 2 0.0566 0.7871 0.000 0.984 0.012 0.000 0.004
#> GSM751432 2 0.0404 0.7864 0.000 0.988 0.012 0.000 0.000
#> GSM751434 2 0.0510 0.7869 0.000 0.984 0.016 0.000 0.000
#> GSM751435 2 0.2909 0.7625 0.012 0.848 0.000 0.000 0.140
#> GSM751436 2 0.0609 0.7866 0.000 0.980 0.020 0.000 0.000
#> GSM751440 2 0.5881 0.6467 0.012 0.636 0.144 0.000 0.208
#> GSM751444 2 0.2522 0.7704 0.012 0.880 0.000 0.000 0.108
#> GSM751446 2 0.3563 0.7303 0.012 0.780 0.000 0.000 0.208
#> GSM751449 2 0.3563 0.7303 0.012 0.780 0.000 0.000 0.208
#> GSM751450 2 0.1408 0.7831 0.008 0.948 0.044 0.000 0.000
#> GSM751452 2 0.0404 0.7864 0.000 0.988 0.012 0.000 0.000
#> GSM751426 2 0.0404 0.7864 0.000 0.988 0.012 0.000 0.000
#> GSM751427 2 0.3563 0.7303 0.012 0.780 0.000 0.000 0.208
#> GSM751438 2 0.3563 0.7303 0.012 0.780 0.000 0.000 0.208
#> GSM751439 2 0.4444 0.5713 0.012 0.624 0.000 0.000 0.364
#> GSM751441 2 0.2909 0.7625 0.012 0.848 0.000 0.000 0.140
#> GSM751442 2 0.3563 0.7303 0.012 0.780 0.000 0.000 0.208
#> GSM751443 5 0.3136 0.6253 0.052 0.072 0.008 0.000 0.868
#> GSM751445 2 0.3163 0.7532 0.012 0.824 0.000 0.000 0.164
#> GSM751447 2 0.2909 0.7625 0.012 0.848 0.000 0.000 0.140
#> GSM751453 2 0.2864 0.7642 0.012 0.852 0.000 0.000 0.136
#> GSM751454 2 0.2909 0.7625 0.012 0.848 0.000 0.000 0.140
#> GSM751455 2 0.3563 0.7303 0.012 0.780 0.000 0.000 0.208
#> GSM751456 2 0.3563 0.7303 0.012 0.780 0.000 0.000 0.208
#> GSM751457 5 0.4574 -0.0366 0.012 0.412 0.000 0.000 0.576
#> GSM751458 5 0.4371 0.1986 0.012 0.344 0.000 0.000 0.644
cbind(get_classes(res, k = 6), get_membership(res, k = 6))
#> class entropy silhouette p1 p2 p3 p4 p5 p6
#> GSM751298 4 0.2841 0.7119 0.164 0.012 0.000 0.824 0.000 0.000
#> GSM751304 6 0.5513 0.2731 0.000 0.364 0.012 0.032 0.040 0.552
#> GSM751305 6 0.5709 0.1623 0.000 0.404 0.008 0.032 0.056 0.500
#> GSM751307 6 0.4874 0.4048 0.068 0.208 0.004 0.000 0.024 0.696
#> GSM751310 4 0.5882 0.3291 0.312 0.156 0.004 0.520 0.008 0.000
#> GSM751314 4 0.1843 0.7545 0.000 0.080 0.004 0.912 0.004 0.000
#> GSM751316 4 0.7266 0.2424 0.236 0.260 0.020 0.424 0.060 0.000
#> GSM751318 4 0.0713 0.7598 0.028 0.000 0.000 0.972 0.000 0.000
#> GSM751342 4 0.1493 0.7590 0.000 0.056 0.004 0.936 0.004 0.000
#> GSM751346 1 0.0603 0.8062 0.980 0.004 0.016 0.000 0.000 0.000
#> GSM751347 1 0.2595 0.7506 0.880 0.084 0.016 0.000 0.020 0.000
#> GSM751348 2 0.6693 0.1647 0.008 0.400 0.004 0.016 0.340 0.232
#> GSM751349 6 0.6174 0.2117 0.020 0.164 0.000 0.000 0.404 0.412
#> GSM751352 6 0.7134 0.1494 0.096 0.224 0.000 0.000 0.268 0.412
#> GSM751353 6 0.1863 0.5582 0.000 0.000 0.000 0.000 0.104 0.896
#> GSM751354 6 0.8309 0.1680 0.204 0.080 0.108 0.000 0.280 0.328
#> GSM751355 6 0.3636 0.4417 0.000 0.000 0.004 0.000 0.320 0.676
#> GSM751358 4 0.7286 0.2270 0.000 0.292 0.164 0.396 0.148 0.000
#> GSM751359 5 0.6003 -0.1515 0.000 0.132 0.008 0.012 0.492 0.356
#> GSM751294 2 0.5972 0.3687 0.000 0.560 0.256 0.000 0.152 0.032
#> GSM751296 4 0.3971 0.3523 0.448 0.004 0.000 0.548 0.000 0.000
#> GSM751297 1 0.3616 0.6855 0.792 0.076 0.132 0.000 0.000 0.000
#> GSM751299 6 0.6534 -0.0245 0.080 0.348 0.004 0.000 0.096 0.472
#> GSM751300 1 0.0146 0.8146 0.996 0.004 0.000 0.000 0.000 0.000
#> GSM751301 6 0.3299 0.4674 0.028 0.000 0.000 0.140 0.012 0.820
#> GSM751302 1 0.0146 0.8146 0.996 0.004 0.000 0.000 0.000 0.000
#> GSM751303 4 0.2243 0.7388 0.000 0.112 0.004 0.880 0.004 0.000
#> GSM751306 4 0.1615 0.7584 0.000 0.064 0.004 0.928 0.004 0.000
#> GSM751308 4 0.2770 0.7465 0.004 0.084 0.024 0.876 0.008 0.004
#> GSM751309 4 0.1296 0.7579 0.000 0.044 0.004 0.948 0.004 0.000
#> GSM751311 4 0.1843 0.7545 0.000 0.080 0.004 0.912 0.004 0.000
#> GSM751312 1 0.5404 0.5490 0.640 0.236 0.008 0.096 0.020 0.000
#> GSM751313 1 0.2092 0.7835 0.876 0.000 0.000 0.124 0.000 0.000
#> GSM751315 4 0.5014 -0.0519 0.460 0.048 0.004 0.484 0.004 0.000
#> GSM751317 4 0.1555 0.7596 0.000 0.060 0.004 0.932 0.004 0.000
#> GSM751320 4 0.0790 0.7589 0.032 0.000 0.000 0.968 0.000 0.000
#> GSM751321 4 0.4939 0.0617 0.428 0.044 0.004 0.520 0.004 0.000
#> GSM751322 4 0.0972 0.7609 0.028 0.008 0.000 0.964 0.000 0.000
#> GSM751324 4 0.0146 0.7609 0.004 0.000 0.000 0.996 0.000 0.000
#> GSM751325 4 0.0713 0.7598 0.028 0.000 0.000 0.972 0.000 0.000
#> GSM751332 1 0.3810 0.3394 0.572 0.000 0.000 0.428 0.000 0.000
#> GSM751334 4 0.3860 -0.0864 0.472 0.000 0.000 0.528 0.000 0.000
#> GSM751339 4 0.3312 0.6421 0.180 0.000 0.028 0.792 0.000 0.000
#> GSM751341 4 0.4364 0.6513 0.064 0.192 0.004 0.732 0.008 0.000
#> GSM751343 4 0.0790 0.7589 0.032 0.000 0.000 0.968 0.000 0.000
#> GSM751344 6 0.3419 0.5272 0.008 0.024 0.000 0.000 0.172 0.796
#> GSM751345 6 0.3252 0.5421 0.008 0.048 0.000 0.000 0.112 0.832
#> GSM751356 2 0.5438 0.4108 0.000 0.572 0.000 0.004 0.140 0.284
#> GSM751357 2 0.6172 0.2042 0.000 0.432 0.000 0.008 0.328 0.232
#> GSM751293 6 0.5371 0.1706 0.032 0.032 0.000 0.356 0.012 0.568
#> GSM751295 1 0.0146 0.8141 0.996 0.000 0.004 0.000 0.000 0.000
#> GSM751319 1 0.4722 0.4648 0.628 0.048 0.004 0.316 0.004 0.000
#> GSM751323 4 0.0790 0.7589 0.032 0.000 0.000 0.968 0.000 0.000
#> GSM751326 1 0.2219 0.7746 0.864 0.000 0.000 0.136 0.000 0.000
#> GSM751327 4 0.1556 0.7477 0.080 0.000 0.000 0.920 0.000 0.000
#> GSM751328 4 0.2048 0.7251 0.120 0.000 0.000 0.880 0.000 0.000
#> GSM751329 1 0.3647 0.4819 0.640 0.000 0.000 0.360 0.000 0.000
#> GSM751330 1 0.2048 0.7869 0.880 0.000 0.000 0.120 0.000 0.000
#> GSM751331 1 0.0000 0.8147 1.000 0.000 0.000 0.000 0.000 0.000
#> GSM751333 1 0.2048 0.7869 0.880 0.000 0.000 0.120 0.000 0.000
#> GSM751335 1 0.2048 0.7869 0.880 0.000 0.000 0.120 0.000 0.000
#> GSM751336 1 0.0000 0.8147 1.000 0.000 0.000 0.000 0.000 0.000
#> GSM751337 4 0.1327 0.7530 0.064 0.000 0.000 0.936 0.000 0.000
#> GSM751338 4 0.2996 0.6229 0.228 0.000 0.000 0.772 0.000 0.000
#> GSM751340 4 0.5983 0.5676 0.172 0.132 0.048 0.632 0.016 0.000
#> GSM751350 1 0.0000 0.8147 1.000 0.000 0.000 0.000 0.000 0.000
#> GSM751351 1 0.0146 0.8146 0.996 0.004 0.000 0.000 0.000 0.000
#> GSM751362 3 0.4537 0.4716 0.000 0.072 0.664 0.000 0.264 0.000
#> GSM751363 5 0.6022 0.5004 0.000 0.348 0.100 0.000 0.508 0.044
#> GSM751367 1 0.7382 0.1710 0.464 0.288 0.056 0.008 0.144 0.040
#> GSM751368 5 0.6076 0.4999 0.000 0.348 0.100 0.000 0.504 0.048
#> GSM751371 4 0.3386 0.6768 0.000 0.176 0.016 0.796 0.012 0.000
#> GSM751375 6 0.3862 0.3295 0.000 0.000 0.000 0.000 0.476 0.524
#> GSM751376 3 0.3273 0.4598 0.000 0.212 0.776 0.000 0.004 0.008
#> GSM751378 3 0.5246 0.2564 0.000 0.064 0.496 0.000 0.428 0.012
#> GSM751379 3 0.4024 0.6173 0.012 0.056 0.812 0.000 0.056 0.064
#> GSM751382 5 0.4602 -0.3566 0.004 0.028 0.000 0.000 0.484 0.484
#> GSM751386 5 0.1918 0.4042 0.000 0.008 0.000 0.000 0.904 0.088
#> GSM751388 5 0.1610 0.4050 0.000 0.000 0.000 0.000 0.916 0.084
#> GSM751391 3 0.6654 0.3712 0.000 0.348 0.484 0.032 0.056 0.080
#> GSM751410 2 0.6696 -0.4064 0.000 0.432 0.360 0.116 0.092 0.000
#> GSM751414 5 0.6167 0.5013 0.024 0.348 0.100 0.004 0.512 0.012
#> GSM751361 5 0.5570 0.5099 0.000 0.348 0.100 0.000 0.536 0.016
#> GSM751365 5 0.5556 0.4738 0.000 0.348 0.148 0.000 0.504 0.000
#> GSM751366 5 0.5815 0.4200 0.000 0.328 0.200 0.000 0.472 0.000
#> GSM751369 3 0.3182 0.6305 0.000 0.136 0.828 0.024 0.012 0.000
#> GSM751370 5 0.5884 0.4934 0.020 0.348 0.112 0.004 0.516 0.000
#> GSM751372 5 0.5409 0.4930 0.000 0.348 0.128 0.000 0.524 0.000
#> GSM751373 5 0.6103 0.5007 0.028 0.348 0.100 0.000 0.512 0.012
#> GSM751374 3 0.3241 0.6040 0.012 0.044 0.844 0.000 0.004 0.096
#> GSM751377 5 0.5575 0.4496 0.000 0.192 0.096 0.000 0.648 0.064
#> GSM751380 5 0.6067 0.2406 0.000 0.284 0.312 0.000 0.404 0.000
#> GSM751381 5 0.1610 0.4050 0.000 0.000 0.000 0.000 0.916 0.084
#> GSM751383 5 0.1753 0.4028 0.000 0.000 0.004 0.000 0.912 0.084
#> GSM751384 5 0.1531 0.4042 0.000 0.000 0.004 0.000 0.928 0.068
#> GSM751385 5 0.5552 0.0152 0.000 0.000 0.196 0.000 0.552 0.252
#> GSM751387 5 0.4057 -0.1570 0.000 0.012 0.000 0.000 0.600 0.388
#> GSM751389 3 0.2510 0.6471 0.000 0.028 0.872 0.000 0.100 0.000
#> GSM751393 3 0.4384 0.5254 0.000 0.040 0.692 0.000 0.256 0.012
#> GSM751394 6 0.3868 0.3059 0.000 0.000 0.000 0.000 0.496 0.504
#> GSM751395 3 0.5729 0.4757 0.000 0.040 0.620 0.000 0.184 0.156
#> GSM751397 5 0.1610 0.4050 0.000 0.000 0.000 0.000 0.916 0.084
#> GSM751398 5 0.2454 0.3650 0.000 0.000 0.000 0.000 0.840 0.160
#> GSM751404 3 0.4061 0.4961 0.000 0.044 0.708 0.000 0.248 0.000
#> GSM751406 3 0.0260 0.6644 0.000 0.000 0.992 0.000 0.008 0.000
#> GSM751411 5 0.5759 0.0175 0.000 0.148 0.336 0.000 0.508 0.008
#> GSM751413 6 0.5002 0.2697 0.000 0.292 0.012 0.000 0.072 0.624
#> GSM751415 3 0.1563 0.6649 0.000 0.012 0.932 0.000 0.056 0.000
#> GSM751416 5 0.5478 0.5107 0.000 0.344 0.100 0.000 0.544 0.012
#> GSM751417 5 0.5560 0.5109 0.000 0.344 0.100 0.000 0.540 0.016
#> GSM751421 5 0.6081 0.4761 0.000 0.352 0.144 0.012 0.484 0.008
#> GSM751422 5 0.5861 0.4738 0.000 0.360 0.132 0.016 0.492 0.000
#> GSM751360 4 0.7074 0.0816 0.000 0.320 0.220 0.380 0.080 0.000
#> GSM751364 5 0.5488 0.5102 0.000 0.348 0.100 0.000 0.540 0.012
#> GSM751390 5 0.2846 0.3619 0.000 0.000 0.060 0.000 0.856 0.084
#> GSM751392 5 0.3747 -0.1635 0.000 0.000 0.000 0.000 0.604 0.396
#> GSM751396 6 0.3797 0.3645 0.000 0.000 0.000 0.000 0.420 0.580
#> GSM751399 3 0.5824 0.1352 0.000 0.216 0.484 0.000 0.300 0.000
#> GSM751400 3 0.6333 0.0224 0.000 0.256 0.440 0.000 0.288 0.016
#> GSM751401 3 0.5597 0.2324 0.000 0.180 0.532 0.000 0.288 0.000
#> GSM751402 3 0.3835 0.5584 0.000 0.056 0.756 0.000 0.188 0.000
#> GSM751403 3 0.1349 0.6652 0.000 0.004 0.940 0.000 0.056 0.000
#> GSM751405 3 0.0260 0.6646 0.000 0.000 0.992 0.000 0.008 0.000
#> GSM751407 3 0.5592 0.2523 0.000 0.200 0.544 0.000 0.256 0.000
#> GSM751408 5 0.5992 0.3188 0.000 0.292 0.268 0.000 0.440 0.000
#> GSM751409 3 0.1745 0.6653 0.000 0.020 0.924 0.000 0.056 0.000
#> GSM751412 3 0.5956 0.0509 0.000 0.256 0.452 0.000 0.292 0.000
#> GSM751418 5 0.5728 0.4958 0.000 0.348 0.128 0.000 0.512 0.012
#> GSM751419 5 0.5630 0.4835 0.000 0.348 0.140 0.000 0.508 0.004
#> GSM751420 3 0.2214 0.5969 0.000 0.096 0.888 0.000 0.016 0.000
#> GSM751425 6 0.4002 0.2352 0.000 0.260 0.000 0.000 0.036 0.704
#> GSM751429 2 0.4503 0.1563 0.096 0.760 0.052 0.000 0.092 0.000
#> GSM751430 6 0.0547 0.5772 0.000 0.020 0.000 0.000 0.000 0.980
#> GSM751433 6 0.0363 0.5784 0.000 0.000 0.000 0.000 0.012 0.988
#> GSM751437 2 0.3868 0.1291 0.000 0.508 0.492 0.000 0.000 0.000
#> GSM751448 3 0.1765 0.5772 0.000 0.096 0.904 0.000 0.000 0.000
#> GSM751451 6 0.3049 0.4963 0.000 0.048 0.004 0.000 0.104 0.844
#> GSM751423 6 0.0632 0.5785 0.000 0.000 0.000 0.000 0.024 0.976
#> GSM751424 6 0.0000 0.5764 0.000 0.000 0.000 0.000 0.000 1.000
#> GSM751428 6 0.0622 0.5746 0.000 0.012 0.000 0.000 0.008 0.980
#> GSM751431 6 0.0000 0.5764 0.000 0.000 0.000 0.000 0.000 1.000
#> GSM751432 6 0.0000 0.5764 0.000 0.000 0.000 0.000 0.000 1.000
#> GSM751434 6 0.0146 0.5772 0.000 0.004 0.000 0.000 0.000 0.996
#> GSM751435 6 0.3737 -0.0992 0.000 0.392 0.000 0.000 0.000 0.608
#> GSM751436 6 0.0363 0.5784 0.000 0.000 0.000 0.000 0.012 0.988
#> GSM751440 2 0.4135 0.3701 0.000 0.584 0.004 0.000 0.008 0.404
#> GSM751444 6 0.3351 0.1699 0.000 0.288 0.000 0.000 0.000 0.712
#> GSM751446 2 0.3866 0.4176 0.000 0.516 0.000 0.000 0.000 0.484
#> GSM751449 2 0.3864 0.4211 0.000 0.520 0.000 0.000 0.000 0.480
#> GSM751450 6 0.1088 0.5756 0.000 0.024 0.000 0.000 0.016 0.960
#> GSM751452 6 0.0000 0.5764 0.000 0.000 0.000 0.000 0.000 1.000
#> GSM751426 6 0.0000 0.5764 0.000 0.000 0.000 0.000 0.000 1.000
#> GSM751427 2 0.3866 0.4176 0.000 0.516 0.000 0.000 0.000 0.484
#> GSM751438 2 0.3864 0.4211 0.000 0.520 0.000 0.000 0.000 0.480
#> GSM751439 2 0.5409 0.4759 0.000 0.524 0.128 0.000 0.000 0.348
#> GSM751441 6 0.3747 -0.1106 0.000 0.396 0.000 0.000 0.000 0.604
#> GSM751442 2 0.3866 0.4176 0.000 0.516 0.000 0.000 0.000 0.484
#> GSM751443 2 0.4481 0.2174 0.008 0.520 0.456 0.000 0.000 0.016
#> GSM751445 6 0.3782 -0.1667 0.000 0.412 0.000 0.000 0.000 0.588
#> GSM751447 6 0.3747 -0.1106 0.000 0.396 0.000 0.000 0.000 0.604
#> GSM751453 6 0.3717 -0.0794 0.000 0.384 0.000 0.000 0.000 0.616
#> GSM751454 6 0.3747 -0.1106 0.000 0.396 0.000 0.000 0.000 0.604
#> GSM751455 2 0.3866 0.4176 0.000 0.516 0.000 0.000 0.000 0.484
#> GSM751456 2 0.3866 0.4176 0.000 0.516 0.000 0.000 0.000 0.484
#> GSM751457 2 0.5658 0.4823 0.000 0.520 0.292 0.000 0.000 0.188
#> GSM751458 2 0.5547 0.4514 0.000 0.508 0.344 0.000 0.000 0.148
Heatmaps for the consensus matrix. It visualizes the probability of two samples to be in a same group.
consensus_heatmap(res, k = 2)
consensus_heatmap(res, k = 3)
consensus_heatmap(res, k = 4)
consensus_heatmap(res, k = 5)
consensus_heatmap(res, k = 6)
Heatmaps for the membership of samples in all partitions to see how consistent they are:
membership_heatmap(res, k = 2)
membership_heatmap(res, k = 3)
membership_heatmap(res, k = 4)
membership_heatmap(res, k = 5)
membership_heatmap(res, k = 6)
As soon as we have had the classes for columns, we can look for signatures which are significantly different between classes which can be candidate marks for certain classes. Following are the heatmaps for signatures.
Signature heatmaps where rows are scaled:
get_signatures(res, k = 2)
get_signatures(res, k = 3)
get_signatures(res, k = 4)
get_signatures(res, k = 5)
get_signatures(res, k = 6)
Signature heatmaps where rows are not scaled:
get_signatures(res, k = 2, scale_rows = FALSE)
get_signatures(res, k = 3, scale_rows = FALSE)
get_signatures(res, k = 4, scale_rows = FALSE)
get_signatures(res, k = 5, scale_rows = FALSE)
get_signatures(res, k = 6, scale_rows = FALSE)
Compare the overlap of signatures from different k:
compare_signatures(res)
get_signature() returns a data frame invisibly. TO get the list of signatures, the function
call should be assigned to a variable explicitly. In following code, if plot argument is set
to FALSE, no heatmap is plotted while only the differential analysis is performed.
# code only for demonstration
tb = get_signature(res, k = ..., plot = FALSE)
An example of the output of tb is:
#> which_row fdr mean_1 mean_2 scaled_mean_1 scaled_mean_2 km
#> 1 38 0.042760348 8.373488 9.131774 -0.5533452 0.5164555 1
#> 2 40 0.018707592 7.106213 8.469186 -0.6173731 0.5762149 1
#> 3 55 0.019134737 10.221463 11.207825 -0.6159697 0.5749050 1
#> 4 59 0.006059896 5.921854 7.869574 -0.6899429 0.6439467 1
#> 5 60 0.018055526 8.928898 10.211722 -0.6204761 0.5791110 1
#> 6 98 0.009384629 15.714769 14.887706 0.6635654 -0.6193277 2
...
The columns in tb are:
which_row: row indices corresponding to the input matrix.fdr: FDR for the differential test. mean_x: The mean value in group x.scaled_mean_x: The mean value in group x after rows are scaled.km: Row groups if k-means clustering is applied to rows.UMAP plot which shows how samples are separated.
dimension_reduction(res, k = 2, method = "UMAP")
dimension_reduction(res, k = 3, method = "UMAP")
dimension_reduction(res, k = 4, method = "UMAP")
dimension_reduction(res, k = 5, method = "UMAP")
dimension_reduction(res, k = 6, method = "UMAP")
Following heatmap shows how subgroups are split when increasing k:
collect_classes(res)
Test correlation between subgroups and known annotations. If the known annotation is numeric, one-way ANOVA test is applied, and if the known annotation is discrete, chi-squared contingency table test is applied.
test_to_known_factors(res)
#> n tissue(p) disease.state(p) agent(p) k
#> ATC:pam 127 5.46e-11 0.164 0.249 2
#> ATC:pam 153 1.12e-34 0.242 0.457 3
#> ATC:pam 119 1.59e-31 0.411 0.755 4
#> ATC:pam 139 2.27e-32 0.422 0.202 5
#> ATC:pam 75 9.54e-22 0.904 0.187 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 4537 rows and 166 columns.
#> Top rows (454, 908, 1361, 1814, 2268) are extracted by 'ATC' method.
#> Subgroups are detected by 'mclust' method.
#> Performed in total 1250 partitions by row resampling.
#> Best k for subgroups seems to be 2.
#>
#> Following methods can be applied to this 'ConsensusPartition' object:
#> [1] "cola_report" "collect_classes" "collect_plots"
#> [4] "collect_stats" "colnames" "compare_signatures"
#> [7] "consensus_heatmap" "dimension_reduction" "functional_enrichment"
#> [10] "get_anno_col" "get_anno" "get_classes"
#> [13] "get_consensus" "get_matrix" "get_membership"
#> [16] "get_param" "get_signatures" "get_stats"
#> [19] "is_best_k" "is_stable_k" "membership_heatmap"
#> [22] "ncol" "nrow" "plot_ecdf"
#> [25] "rownames" "select_partition_number" "show"
#> [28] "suggest_best_k" "test_to_known_factors"
collect_plots() function collects all the plots made from res for all k (number of partitions)
into one single page to provide an easy and fast comparison between different k.
collect_plots(res)
The plots are:
k and the heatmap of
predicted classes for each k.k.k.k.All the plots in panels can be made by individual functions and they are plotted later in this section.
select_partition_number() produces several plots showing different
statistics for choosing “optimized” k. There are following statistics:
k;k, the area increased is defined as \(A_k - A_{k-1}\).The detailed explanations of these statistics can be found in the cola vignette.
Generally speaking, lower PAC score, higher mean silhouette score or higher
concordance corresponds to better partition. Rand index and Jaccard index
measure how similar the current partition is compared to partition with k-1.
If they are too similar, we won't accept k is better than k-1.
select_partition_number(res)
The numeric values for all these statistics can be obtained by get_stats().
get_stats(res)
#> k 1-PAC mean_silhouette concordance area_increased Rand Jaccard
#> 2 2 1.000 0.962 0.978 0.4070 0.597 0.597
#> 3 3 0.653 0.746 0.886 0.6114 0.731 0.552
#> 4 4 0.649 0.729 0.854 0.0827 0.905 0.737
#> 5 5 0.720 0.659 0.776 0.0906 0.895 0.661
#> 6 6 0.753 0.722 0.846 0.0607 0.906 0.617
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
#> GSM751298 1 0.1414 0.967 0.980 0.020
#> GSM751304 2 0.0672 0.980 0.008 0.992
#> GSM751305 2 0.0672 0.980 0.008 0.992
#> GSM751307 2 0.1184 0.977 0.016 0.984
#> GSM751310 1 0.1184 0.974 0.984 0.016
#> GSM751314 1 0.1184 0.974 0.984 0.016
#> GSM751316 1 0.1184 0.974 0.984 0.016
#> GSM751318 1 0.1633 0.971 0.976 0.024
#> GSM751342 2 0.9944 0.135 0.456 0.544
#> GSM751346 1 0.0938 0.970 0.988 0.012
#> GSM751347 2 0.6712 0.797 0.176 0.824
#> GSM751348 2 0.0000 0.981 0.000 1.000
#> GSM751349 2 0.0376 0.980 0.004 0.996
#> GSM751352 2 0.1184 0.977 0.016 0.984
#> GSM751353 2 0.1184 0.977 0.016 0.984
#> GSM751354 2 0.1184 0.977 0.016 0.984
#> GSM751355 2 0.1184 0.977 0.016 0.984
#> GSM751358 2 0.0672 0.980 0.008 0.992
#> GSM751359 2 0.0376 0.981 0.004 0.996
#> GSM751294 2 0.0672 0.980 0.008 0.992
#> GSM751296 1 0.0938 0.970 0.988 0.012
#> GSM751297 1 0.6247 0.824 0.844 0.156
#> GSM751299 2 0.1184 0.977 0.016 0.984
#> GSM751300 1 0.0938 0.970 0.988 0.012
#> GSM751301 2 0.1633 0.973 0.024 0.976
#> GSM751302 1 0.0938 0.970 0.988 0.012
#> GSM751303 1 0.1184 0.974 0.984 0.016
#> GSM751306 1 0.1184 0.974 0.984 0.016
#> GSM751308 2 0.0672 0.980 0.008 0.992
#> GSM751309 1 0.1184 0.974 0.984 0.016
#> GSM751311 1 0.1184 0.974 0.984 0.016
#> GSM751312 1 0.1184 0.974 0.984 0.016
#> GSM751313 1 0.0672 0.972 0.992 0.008
#> GSM751315 1 0.1184 0.974 0.984 0.016
#> GSM751317 1 0.1184 0.974 0.984 0.016
#> GSM751320 1 0.1184 0.974 0.984 0.016
#> GSM751321 1 0.1184 0.974 0.984 0.016
#> GSM751322 1 0.1184 0.974 0.984 0.016
#> GSM751324 1 0.1184 0.974 0.984 0.016
#> GSM751325 1 0.1184 0.974 0.984 0.016
#> GSM751332 1 0.0938 0.973 0.988 0.012
#> GSM751334 1 0.1184 0.974 0.984 0.016
#> GSM751339 1 0.2603 0.956 0.956 0.044
#> GSM751341 1 0.1184 0.969 0.984 0.016
#> GSM751343 1 0.1184 0.974 0.984 0.016
#> GSM751344 2 0.1184 0.977 0.016 0.984
#> GSM751345 2 0.1184 0.977 0.016 0.984
#> GSM751356 2 0.0672 0.980 0.008 0.992
#> GSM751357 2 0.0672 0.980 0.008 0.992
#> GSM751293 2 0.1843 0.970 0.028 0.972
#> GSM751295 1 0.0938 0.970 0.988 0.012
#> GSM751319 1 0.1184 0.974 0.984 0.016
#> GSM751323 1 0.1184 0.974 0.984 0.016
#> GSM751326 1 0.0938 0.970 0.988 0.012
#> GSM751327 1 0.1184 0.974 0.984 0.016
#> GSM751328 1 0.0672 0.973 0.992 0.008
#> GSM751329 1 0.0938 0.970 0.988 0.012
#> GSM751330 1 0.0938 0.970 0.988 0.012
#> GSM751331 1 0.0938 0.970 0.988 0.012
#> GSM751333 1 0.0376 0.971 0.996 0.004
#> GSM751335 1 0.0938 0.970 0.988 0.012
#> GSM751336 1 0.0938 0.970 0.988 0.012
#> GSM751337 1 0.0376 0.971 0.996 0.004
#> GSM751338 1 0.1414 0.973 0.980 0.020
#> GSM751340 1 0.8499 0.645 0.724 0.276
#> GSM751350 1 0.0938 0.970 0.988 0.012
#> GSM751351 1 0.0938 0.970 0.988 0.012
#> GSM751362 2 0.0672 0.980 0.008 0.992
#> GSM751363 2 0.0672 0.980 0.008 0.992
#> GSM751367 1 0.8763 0.594 0.704 0.296
#> GSM751368 2 0.0376 0.981 0.004 0.996
#> GSM751371 2 0.8081 0.671 0.248 0.752
#> GSM751375 2 0.0000 0.981 0.000 1.000
#> GSM751376 2 0.1414 0.978 0.020 0.980
#> GSM751378 2 0.0672 0.980 0.008 0.992
#> GSM751379 2 0.1184 0.977 0.016 0.984
#> GSM751382 2 0.0000 0.981 0.000 1.000
#> GSM751386 2 0.0000 0.981 0.000 1.000
#> GSM751388 2 0.0000 0.981 0.000 1.000
#> GSM751391 2 0.0672 0.980 0.008 0.992
#> GSM751410 2 0.0672 0.980 0.008 0.992
#> GSM751414 2 0.3733 0.922 0.072 0.928
#> GSM751361 2 0.0672 0.980 0.008 0.992
#> GSM751365 2 0.0672 0.980 0.008 0.992
#> GSM751366 2 0.6712 0.789 0.176 0.824
#> GSM751369 2 0.0672 0.980 0.008 0.992
#> GSM751370 2 0.0672 0.980 0.008 0.992
#> GSM751372 2 0.0672 0.980 0.008 0.992
#> GSM751373 2 0.2778 0.948 0.048 0.952
#> GSM751374 2 0.1184 0.977 0.016 0.984
#> GSM751377 2 0.0000 0.981 0.000 1.000
#> GSM751380 2 0.0672 0.980 0.008 0.992
#> GSM751381 2 0.0000 0.981 0.000 1.000
#> GSM751383 2 0.0000 0.981 0.000 1.000
#> GSM751384 2 0.0672 0.980 0.008 0.992
#> GSM751385 2 0.0000 0.981 0.000 1.000
#> GSM751387 2 0.0000 0.981 0.000 1.000
#> GSM751389 2 0.0672 0.980 0.008 0.992
#> GSM751393 2 0.0376 0.981 0.004 0.996
#> GSM751394 2 0.0000 0.981 0.000 1.000
#> GSM751395 2 0.0376 0.981 0.004 0.996
#> GSM751397 2 0.0672 0.980 0.008 0.992
#> GSM751398 2 0.0000 0.981 0.000 1.000
#> GSM751404 2 0.0672 0.980 0.008 0.992
#> GSM751406 2 0.0672 0.980 0.008 0.992
#> GSM751411 2 0.0672 0.980 0.008 0.992
#> GSM751413 2 0.0376 0.981 0.004 0.996
#> GSM751415 2 0.0672 0.980 0.008 0.992
#> GSM751416 2 0.0672 0.980 0.008 0.992
#> GSM751417 2 0.0672 0.980 0.008 0.992
#> GSM751421 2 0.0672 0.980 0.008 0.992
#> GSM751422 2 0.0672 0.980 0.008 0.992
#> GSM751360 2 0.0672 0.980 0.008 0.992
#> GSM751364 2 0.0672 0.980 0.008 0.992
#> GSM751390 2 0.0672 0.980 0.008 0.992
#> GSM751392 2 0.0000 0.981 0.000 1.000
#> GSM751396 2 0.0000 0.981 0.000 1.000
#> GSM751399 2 0.0672 0.980 0.008 0.992
#> GSM751400 2 0.0376 0.981 0.004 0.996
#> GSM751401 2 0.0672 0.980 0.008 0.992
#> GSM751402 2 0.0672 0.980 0.008 0.992
#> GSM751403 2 0.0672 0.980 0.008 0.992
#> GSM751405 2 0.0672 0.980 0.008 0.992
#> GSM751407 2 0.0672 0.980 0.008 0.992
#> GSM751408 2 0.0672 0.980 0.008 0.992
#> GSM751409 2 0.0672 0.980 0.008 0.992
#> GSM751412 2 0.0672 0.980 0.008 0.992
#> GSM751418 2 0.0672 0.980 0.008 0.992
#> GSM751419 2 0.0672 0.980 0.008 0.992
#> GSM751420 2 0.1184 0.977 0.016 0.984
#> GSM751425 2 0.0000 0.981 0.000 1.000
#> GSM751429 2 0.2236 0.964 0.036 0.964
#> GSM751430 2 0.1184 0.977 0.016 0.984
#> GSM751433 2 0.0000 0.981 0.000 1.000
#> GSM751437 2 0.0672 0.980 0.008 0.992
#> GSM751448 2 0.1633 0.978 0.024 0.976
#> GSM751451 2 0.0672 0.980 0.008 0.992
#> GSM751423 2 0.0376 0.981 0.004 0.996
#> GSM751424 2 0.0672 0.979 0.008 0.992
#> GSM751428 2 0.1184 0.977 0.016 0.984
#> GSM751431 2 0.0000 0.981 0.000 1.000
#> GSM751432 2 0.1184 0.977 0.016 0.984
#> GSM751434 2 0.1184 0.977 0.016 0.984
#> GSM751435 2 0.1184 0.977 0.016 0.984
#> GSM751436 2 0.0672 0.979 0.008 0.992
#> GSM751440 2 0.0000 0.981 0.000 1.000
#> GSM751444 2 0.1184 0.977 0.016 0.984
#> GSM751446 2 0.1184 0.977 0.016 0.984
#> GSM751449 2 0.1184 0.977 0.016 0.984
#> GSM751450 2 0.1184 0.977 0.016 0.984
#> GSM751452 2 0.1184 0.977 0.016 0.984
#> GSM751426 2 0.1184 0.977 0.016 0.984
#> GSM751427 2 0.1184 0.977 0.016 0.984
#> GSM751438 2 0.1184 0.977 0.016 0.984
#> GSM751439 2 0.1184 0.977 0.016 0.984
#> GSM751441 2 0.1184 0.977 0.016 0.984
#> GSM751442 2 0.1184 0.977 0.016 0.984
#> GSM751443 2 0.1184 0.977 0.016 0.984
#> GSM751445 2 0.1184 0.977 0.016 0.984
#> GSM751447 2 0.1184 0.977 0.016 0.984
#> GSM751453 2 0.1184 0.977 0.016 0.984
#> GSM751454 2 0.1184 0.977 0.016 0.984
#> GSM751455 2 0.1184 0.977 0.016 0.984
#> GSM751456 2 0.1184 0.977 0.016 0.984
#> GSM751457 2 0.1184 0.977 0.016 0.984
#> GSM751458 2 0.1184 0.977 0.016 0.984
cbind(get_classes(res, k = 3), get_membership(res, k = 3))
#> class entropy silhouette p1 p2 p3
#> GSM751298 1 0.0237 0.9645 0.996 0.000 0.004
#> GSM751304 2 0.6280 0.2612 0.000 0.540 0.460
#> GSM751305 2 0.6244 0.3118 0.000 0.560 0.440
#> GSM751307 2 0.0000 0.8303 0.000 1.000 0.000
#> GSM751310 1 0.0000 0.9654 1.000 0.000 0.000
#> GSM751314 1 0.0000 0.9654 1.000 0.000 0.000
#> GSM751316 1 0.1753 0.9247 0.952 0.000 0.048
#> GSM751318 1 0.4233 0.7939 0.836 0.004 0.160
#> GSM751342 3 0.7489 0.0611 0.468 0.036 0.496
#> GSM751346 1 0.0592 0.9621 0.988 0.000 0.012
#> GSM751347 3 0.6925 0.2904 0.016 0.452 0.532
#> GSM751348 2 0.4702 0.7332 0.000 0.788 0.212
#> GSM751349 2 0.2165 0.8182 0.000 0.936 0.064
#> GSM751352 2 0.0000 0.8303 0.000 1.000 0.000
#> GSM751353 2 0.0000 0.8303 0.000 1.000 0.000
#> GSM751354 2 0.0237 0.8294 0.000 0.996 0.004
#> GSM751355 2 0.0000 0.8303 0.000 1.000 0.000
#> GSM751358 3 0.1860 0.7971 0.000 0.052 0.948
#> GSM751359 2 0.5678 0.5751 0.000 0.684 0.316
#> GSM751294 3 0.1289 0.8044 0.000 0.032 0.968
#> GSM751296 1 0.0424 0.9634 0.992 0.000 0.008
#> GSM751297 3 0.8361 0.3544 0.092 0.364 0.544
#> GSM751299 2 0.0237 0.8293 0.000 0.996 0.004
#> GSM751300 1 0.0592 0.9621 0.988 0.000 0.012
#> GSM751301 2 0.0000 0.8303 0.000 1.000 0.000
#> GSM751302 1 0.0592 0.9621 0.988 0.000 0.012
#> GSM751303 1 0.3686 0.8236 0.860 0.000 0.140
#> GSM751306 1 0.0000 0.9654 1.000 0.000 0.000
#> GSM751308 3 0.1170 0.8085 0.008 0.016 0.976
#> GSM751309 1 0.0000 0.9654 1.000 0.000 0.000
#> GSM751311 1 0.0000 0.9654 1.000 0.000 0.000
#> GSM751312 1 0.0237 0.9633 0.996 0.000 0.004
#> GSM751313 1 0.0000 0.9654 1.000 0.000 0.000
#> GSM751315 1 0.0000 0.9654 1.000 0.000 0.000
#> GSM751317 1 0.0237 0.9633 0.996 0.000 0.004
#> GSM751320 1 0.0000 0.9654 1.000 0.000 0.000
#> GSM751321 1 0.0000 0.9654 1.000 0.000 0.000
#> GSM751322 1 0.0000 0.9654 1.000 0.000 0.000
#> GSM751324 1 0.0000 0.9654 1.000 0.000 0.000
#> GSM751325 1 0.0000 0.9654 1.000 0.000 0.000
#> GSM751332 1 0.0000 0.9654 1.000 0.000 0.000
#> GSM751334 1 0.0000 0.9654 1.000 0.000 0.000
#> GSM751339 1 0.4504 0.7444 0.804 0.000 0.196
#> GSM751341 1 0.0592 0.9571 0.988 0.012 0.000
#> GSM751343 1 0.0000 0.9654 1.000 0.000 0.000
#> GSM751344 2 0.0000 0.8303 0.000 1.000 0.000
#> GSM751345 2 0.0000 0.8303 0.000 1.000 0.000
#> GSM751356 3 0.2711 0.7772 0.000 0.088 0.912
#> GSM751357 3 0.5529 0.5003 0.000 0.296 0.704
#> GSM751293 2 0.0000 0.8303 0.000 1.000 0.000
#> GSM751295 1 0.0592 0.9621 0.988 0.000 0.012
#> GSM751319 1 0.0000 0.9654 1.000 0.000 0.000
#> GSM751323 1 0.0000 0.9654 1.000 0.000 0.000
#> GSM751326 1 0.0000 0.9654 1.000 0.000 0.000
#> GSM751327 1 0.0000 0.9654 1.000 0.000 0.000
#> GSM751328 1 0.0000 0.9654 1.000 0.000 0.000
#> GSM751329 1 0.0000 0.9654 1.000 0.000 0.000
#> GSM751330 1 0.0424 0.9634 0.992 0.000 0.008
#> GSM751331 1 0.0592 0.9621 0.988 0.000 0.012
#> GSM751333 1 0.0000 0.9654 1.000 0.000 0.000
#> GSM751335 1 0.0237 0.9645 0.996 0.000 0.004
#> GSM751336 1 0.0592 0.9621 0.988 0.000 0.012
#> GSM751337 1 0.0000 0.9654 1.000 0.000 0.000
#> GSM751338 1 0.0000 0.9654 1.000 0.000 0.000
#> GSM751340 1 0.6111 0.3357 0.604 0.000 0.396
#> GSM751350 1 0.0592 0.9621 0.988 0.000 0.012
#> GSM751351 1 0.0592 0.9621 0.988 0.000 0.012
#> GSM751362 3 0.0592 0.8091 0.000 0.012 0.988
#> GSM751363 2 0.6274 0.2692 0.000 0.544 0.456
#> GSM751367 1 0.8649 0.4642 0.596 0.232 0.172
#> GSM751368 2 0.6180 0.3667 0.000 0.584 0.416
#> GSM751371 3 0.5036 0.6873 0.172 0.020 0.808
#> GSM751375 2 0.2165 0.8184 0.000 0.936 0.064
#> GSM751376 3 0.6267 0.3034 0.000 0.452 0.548
#> GSM751378 3 0.5988 0.3209 0.000 0.368 0.632
#> GSM751379 3 0.6280 0.2868 0.000 0.460 0.540
#> GSM751382 2 0.3038 0.8039 0.000 0.896 0.104
#> GSM751386 2 0.4062 0.7708 0.000 0.836 0.164
#> GSM751388 2 0.4555 0.7393 0.000 0.800 0.200
#> GSM751391 3 0.1529 0.8033 0.000 0.040 0.960
#> GSM751410 3 0.0747 0.8090 0.000 0.016 0.984
#> GSM751414 3 0.3530 0.7717 0.068 0.032 0.900
#> GSM751361 3 0.5291 0.5365 0.000 0.268 0.732
#> GSM751365 3 0.1529 0.8031 0.000 0.040 0.960
#> GSM751366 3 0.1585 0.7987 0.028 0.008 0.964
#> GSM751369 3 0.0592 0.8091 0.000 0.012 0.988
#> GSM751370 3 0.1399 0.8072 0.004 0.028 0.968
#> GSM751372 3 0.1163 0.8071 0.000 0.028 0.972
#> GSM751373 3 0.5842 0.6568 0.196 0.036 0.768
#> GSM751374 3 0.6295 0.2578 0.000 0.472 0.528
#> GSM751377 2 0.4291 0.7587 0.000 0.820 0.180
#> GSM751380 3 0.0592 0.8091 0.000 0.012 0.988
#> GSM751381 2 0.4605 0.7349 0.000 0.796 0.204
#> GSM751383 2 0.4291 0.7586 0.000 0.820 0.180
#> GSM751384 3 0.6154 0.1920 0.000 0.408 0.592
#> GSM751385 2 0.4235 0.7626 0.000 0.824 0.176
#> GSM751387 2 0.4291 0.7588 0.000 0.820 0.180
#> GSM751389 3 0.1289 0.8043 0.000 0.032 0.968
#> GSM751393 3 0.4842 0.6294 0.000 0.224 0.776
#> GSM751394 2 0.4291 0.7587 0.000 0.820 0.180
#> GSM751395 2 0.6154 0.3845 0.000 0.592 0.408
#> GSM751397 2 0.6008 0.4668 0.000 0.628 0.372
#> GSM751398 2 0.5178 0.6697 0.000 0.744 0.256
#> GSM751404 3 0.0592 0.8091 0.000 0.012 0.988
#> GSM751406 3 0.0592 0.8091 0.000 0.012 0.988
#> GSM751411 3 0.1289 0.8061 0.000 0.032 0.968
#> GSM751413 2 0.5968 0.4838 0.000 0.636 0.364
#> GSM751415 3 0.0592 0.8091 0.000 0.012 0.988
#> GSM751416 3 0.6192 0.1412 0.000 0.420 0.580
#> GSM751417 3 0.6308 -0.1308 0.000 0.492 0.508
#> GSM751421 3 0.0892 0.8087 0.000 0.020 0.980
#> GSM751422 3 0.0892 0.8087 0.000 0.020 0.980
#> GSM751360 3 0.1289 0.8061 0.000 0.032 0.968
#> GSM751364 3 0.2448 0.7814 0.000 0.076 0.924
#> GSM751390 3 0.6244 0.0769 0.000 0.440 0.560
#> GSM751392 2 0.4062 0.7708 0.000 0.836 0.164
#> GSM751396 2 0.3482 0.7930 0.000 0.872 0.128
#> GSM751399 3 0.0592 0.8091 0.000 0.012 0.988
#> GSM751400 3 0.2261 0.7857 0.000 0.068 0.932
#> GSM751401 3 0.0592 0.8091 0.000 0.012 0.988
#> GSM751402 3 0.0592 0.8091 0.000 0.012 0.988
#> GSM751403 3 0.0592 0.8091 0.000 0.012 0.988
#> GSM751405 3 0.0592 0.8091 0.000 0.012 0.988
#> GSM751407 3 0.0592 0.8091 0.000 0.012 0.988
#> GSM751408 3 0.0592 0.8091 0.000 0.012 0.988
#> GSM751409 3 0.0592 0.8091 0.000 0.012 0.988
#> GSM751412 3 0.0592 0.8091 0.000 0.012 0.988
#> GSM751418 3 0.3482 0.7359 0.000 0.128 0.872
#> GSM751419 3 0.1643 0.8012 0.000 0.044 0.956
#> GSM751420 3 0.5948 0.4701 0.000 0.360 0.640
#> GSM751425 2 0.3412 0.7948 0.000 0.876 0.124
#> GSM751429 3 0.6252 0.3197 0.000 0.444 0.556
#> GSM751430 2 0.0000 0.8303 0.000 1.000 0.000
#> GSM751433 2 0.3686 0.7883 0.000 0.860 0.140
#> GSM751437 3 0.0592 0.8091 0.000 0.012 0.988
#> GSM751448 3 0.5016 0.6287 0.000 0.240 0.760
#> GSM751451 2 0.6274 0.2692 0.000 0.544 0.456
#> GSM751423 2 0.5621 0.5889 0.000 0.692 0.308
#> GSM751424 2 0.0592 0.8301 0.000 0.988 0.012
#> GSM751428 2 0.0000 0.8303 0.000 1.000 0.000
#> GSM751431 2 0.4399 0.7527 0.000 0.812 0.188
#> GSM751432 2 0.0000 0.8303 0.000 1.000 0.000
#> GSM751434 2 0.0000 0.8303 0.000 1.000 0.000
#> GSM751435 2 0.0000 0.8303 0.000 1.000 0.000
#> GSM751436 2 0.0592 0.8301 0.000 0.988 0.012
#> GSM751440 2 0.3412 0.7968 0.000 0.876 0.124
#> GSM751444 2 0.0000 0.8303 0.000 1.000 0.000
#> GSM751446 2 0.0000 0.8303 0.000 1.000 0.000
#> GSM751449 2 0.1529 0.8077 0.000 0.960 0.040
#> GSM751450 2 0.0592 0.8301 0.000 0.988 0.012
#> GSM751452 2 0.0000 0.8303 0.000 1.000 0.000
#> GSM751426 2 0.0237 0.8305 0.000 0.996 0.004
#> GSM751427 2 0.0237 0.8294 0.000 0.996 0.004
#> GSM751438 2 0.5216 0.4943 0.000 0.740 0.260
#> GSM751439 3 0.6260 0.3117 0.000 0.448 0.552
#> GSM751441 2 0.0000 0.8303 0.000 1.000 0.000
#> GSM751442 2 0.0424 0.8277 0.000 0.992 0.008
#> GSM751443 3 0.6260 0.3117 0.000 0.448 0.552
#> GSM751445 2 0.0000 0.8303 0.000 1.000 0.000
#> GSM751447 2 0.0000 0.8303 0.000 1.000 0.000
#> GSM751453 2 0.0000 0.8303 0.000 1.000 0.000
#> GSM751454 2 0.0000 0.8303 0.000 1.000 0.000
#> GSM751455 2 0.0237 0.8294 0.000 0.996 0.004
#> GSM751456 2 0.0747 0.8236 0.000 0.984 0.016
#> GSM751457 2 0.5905 0.2746 0.000 0.648 0.352
#> GSM751458 2 0.6026 0.2018 0.000 0.624 0.376
cbind(get_classes(res, k = 4), get_membership(res, k = 4))
#> class entropy silhouette p1 p2 p3 p4
#> GSM751298 4 0.3668 0.8012 0.188 0.000 0.004 0.808
#> GSM751304 3 0.6385 0.2009 0.012 0.428 0.520 0.040
#> GSM751305 2 0.7142 0.0120 0.044 0.476 0.436 0.044
#> GSM751307 2 0.1004 0.8451 0.004 0.972 0.000 0.024
#> GSM751310 1 0.0376 0.8773 0.992 0.004 0.004 0.000
#> GSM751314 1 0.0336 0.8757 0.992 0.008 0.000 0.000
#> GSM751316 1 0.1953 0.8368 0.940 0.012 0.044 0.004
#> GSM751318 1 0.3060 0.7779 0.888 0.016 0.088 0.008
#> GSM751342 1 0.6345 0.1186 0.516 0.016 0.436 0.032
#> GSM751346 4 0.3355 0.8196 0.160 0.000 0.004 0.836
#> GSM751347 4 0.7200 0.3466 0.004 0.280 0.160 0.556
#> GSM751348 2 0.4947 0.6808 0.024 0.752 0.212 0.012
#> GSM751349 2 0.1509 0.8390 0.020 0.960 0.008 0.012
#> GSM751352 2 0.2011 0.8349 0.000 0.920 0.000 0.080
#> GSM751353 2 0.1474 0.8448 0.000 0.948 0.000 0.052
#> GSM751354 2 0.2216 0.8320 0.000 0.908 0.000 0.092
#> GSM751355 2 0.2216 0.8353 0.000 0.908 0.000 0.092
#> GSM751358 3 0.3626 0.7981 0.012 0.056 0.872 0.060
#> GSM751359 2 0.6223 0.5214 0.052 0.656 0.272 0.020
#> GSM751294 3 0.0927 0.8200 0.000 0.008 0.976 0.016
#> GSM751296 4 0.3355 0.8196 0.160 0.000 0.004 0.836
#> GSM751297 4 0.2636 0.7056 0.012 0.020 0.052 0.916
#> GSM751299 2 0.2401 0.8281 0.000 0.904 0.004 0.092
#> GSM751300 4 0.3355 0.8196 0.160 0.000 0.004 0.836
#> GSM751301 2 0.1677 0.8445 0.012 0.948 0.000 0.040
#> GSM751302 4 0.3355 0.8196 0.160 0.000 0.004 0.836
#> GSM751303 1 0.1863 0.8411 0.944 0.012 0.040 0.004
#> GSM751306 1 0.0336 0.8757 0.992 0.008 0.000 0.000
#> GSM751308 3 0.0188 0.8208 0.000 0.000 0.996 0.004
#> GSM751309 1 0.0188 0.8775 0.996 0.004 0.000 0.000
#> GSM751311 1 0.0524 0.8749 0.988 0.008 0.004 0.000
#> GSM751312 1 0.1004 0.8680 0.972 0.004 0.024 0.000
#> GSM751313 1 0.3052 0.7560 0.860 0.000 0.004 0.136
#> GSM751315 1 0.0188 0.8792 0.996 0.000 0.000 0.004
#> GSM751317 1 0.0712 0.8720 0.984 0.008 0.004 0.004
#> GSM751320 1 0.0188 0.8792 0.996 0.000 0.000 0.004
#> GSM751321 1 0.0188 0.8792 0.996 0.000 0.000 0.004
#> GSM751322 1 0.0188 0.8792 0.996 0.000 0.000 0.004
#> GSM751324 1 0.0188 0.8792 0.996 0.000 0.000 0.004
#> GSM751325 1 0.0188 0.8792 0.996 0.000 0.000 0.004
#> GSM751332 1 0.0188 0.8792 0.996 0.000 0.000 0.004
#> GSM751334 1 0.0188 0.8792 0.996 0.000 0.000 0.004
#> GSM751339 1 0.3550 0.7845 0.860 0.000 0.096 0.044
#> GSM751341 4 0.4991 0.6193 0.316 0.008 0.004 0.672
#> GSM751343 1 0.0707 0.8711 0.980 0.000 0.000 0.020
#> GSM751344 2 0.1389 0.8431 0.000 0.952 0.000 0.048
#> GSM751345 2 0.1474 0.8424 0.000 0.948 0.000 0.052
#> GSM751356 3 0.2774 0.8143 0.004 0.044 0.908 0.044
#> GSM751357 3 0.4090 0.7683 0.004 0.140 0.824 0.032
#> GSM751293 2 0.1398 0.8442 0.004 0.956 0.000 0.040
#> GSM751295 4 0.3355 0.8196 0.160 0.000 0.004 0.836
#> GSM751319 1 0.0188 0.8792 0.996 0.000 0.000 0.004
#> GSM751323 1 0.1302 0.8553 0.956 0.000 0.000 0.044
#> GSM751326 4 0.4781 0.6230 0.336 0.000 0.004 0.660
#> GSM751327 1 0.1637 0.8395 0.940 0.000 0.000 0.060
#> GSM751328 1 0.0921 0.8683 0.972 0.000 0.000 0.028
#> GSM751329 1 0.4250 0.5144 0.724 0.000 0.000 0.276
#> GSM751330 4 0.4103 0.7399 0.256 0.000 0.000 0.744
#> GSM751331 4 0.3355 0.8196 0.160 0.000 0.004 0.836
#> GSM751333 1 0.4509 0.4889 0.708 0.000 0.004 0.288
#> GSM751335 4 0.4477 0.6667 0.312 0.000 0.000 0.688
#> GSM751336 4 0.3355 0.8196 0.160 0.000 0.004 0.836
#> GSM751337 1 0.4872 0.3040 0.640 0.000 0.004 0.356
#> GSM751338 1 0.1902 0.8346 0.932 0.000 0.004 0.064
#> GSM751340 1 0.4955 0.4354 0.648 0.000 0.344 0.008
#> GSM751350 4 0.3355 0.8196 0.160 0.000 0.004 0.836
#> GSM751351 4 0.3355 0.8196 0.160 0.000 0.004 0.836
#> GSM751362 3 0.0592 0.8209 0.000 0.000 0.984 0.016
#> GSM751363 3 0.7330 0.1232 0.052 0.420 0.480 0.048
#> GSM751367 4 0.6292 0.6481 0.080 0.128 0.064 0.728
#> GSM751368 2 0.6009 0.4957 0.052 0.648 0.292 0.008
#> GSM751371 3 0.4549 0.7445 0.108 0.016 0.820 0.056
#> GSM751375 2 0.1624 0.8368 0.028 0.952 0.000 0.020
#> GSM751376 3 0.6809 0.2748 0.000 0.360 0.532 0.108
#> GSM751378 3 0.4426 0.6964 0.004 0.196 0.780 0.020
#> GSM751379 3 0.6889 0.1754 0.000 0.396 0.496 0.108
#> GSM751382 2 0.1958 0.8350 0.028 0.944 0.020 0.008
#> GSM751386 2 0.3259 0.8194 0.032 0.892 0.056 0.020
#> GSM751388 2 0.4696 0.7556 0.044 0.808 0.128 0.020
#> GSM751391 3 0.2287 0.8121 0.004 0.012 0.924 0.060
#> GSM751410 3 0.0707 0.8194 0.000 0.000 0.980 0.020
#> GSM751414 3 0.1994 0.8126 0.008 0.004 0.936 0.052
#> GSM751361 3 0.4633 0.7711 0.028 0.088 0.824 0.060
#> GSM751365 3 0.2830 0.8081 0.004 0.032 0.904 0.060
#> GSM751366 3 0.0817 0.8147 0.024 0.000 0.976 0.000
#> GSM751369 3 0.0469 0.8210 0.000 0.000 0.988 0.012
#> GSM751370 3 0.1661 0.8135 0.000 0.004 0.944 0.052
#> GSM751372 3 0.1576 0.8148 0.000 0.004 0.948 0.048
#> GSM751373 3 0.4922 0.7385 0.116 0.036 0.804 0.044
#> GSM751374 2 0.6929 -0.0193 0.000 0.452 0.440 0.108
#> GSM751377 2 0.4071 0.7802 0.036 0.840 0.112 0.012
#> GSM751380 3 0.0188 0.8209 0.000 0.000 0.996 0.004
#> GSM751381 2 0.4643 0.7600 0.044 0.812 0.124 0.020
#> GSM751383 2 0.4182 0.7846 0.036 0.840 0.104 0.020
#> GSM751384 3 0.4976 0.6293 0.004 0.260 0.716 0.020
#> GSM751385 2 0.3873 0.7794 0.008 0.832 0.144 0.016
#> GSM751387 2 0.4235 0.7869 0.044 0.840 0.096 0.020
#> GSM751389 3 0.0927 0.8200 0.000 0.008 0.976 0.016
#> GSM751393 3 0.4050 0.7190 0.000 0.168 0.808 0.024
#> GSM751394 2 0.3954 0.7986 0.040 0.856 0.084 0.020
#> GSM751395 3 0.5526 0.2657 0.000 0.416 0.564 0.020
#> GSM751397 2 0.6428 0.4391 0.052 0.620 0.308 0.020
#> GSM751398 2 0.5425 0.6888 0.052 0.752 0.176 0.020
#> GSM751404 3 0.0592 0.8209 0.000 0.000 0.984 0.016
#> GSM751406 3 0.0592 0.8209 0.000 0.000 0.984 0.016
#> GSM751411 3 0.2409 0.8144 0.004 0.040 0.924 0.032
#> GSM751413 2 0.5583 0.5999 0.048 0.704 0.240 0.008
#> GSM751415 3 0.0469 0.8210 0.000 0.000 0.988 0.012
#> GSM751416 3 0.6395 0.5767 0.028 0.248 0.664 0.060
#> GSM751417 3 0.6428 0.4790 0.020 0.308 0.620 0.052
#> GSM751421 3 0.1118 0.8169 0.000 0.000 0.964 0.036
#> GSM751422 3 0.1389 0.8144 0.000 0.000 0.952 0.048
#> GSM751360 3 0.3272 0.8021 0.004 0.052 0.884 0.060
#> GSM751364 3 0.3104 0.8048 0.004 0.044 0.892 0.060
#> GSM751390 3 0.5005 0.6125 0.004 0.264 0.712 0.020
#> GSM751392 2 0.3817 0.8043 0.040 0.864 0.076 0.020
#> GSM751396 2 0.2261 0.8311 0.036 0.932 0.024 0.008
#> GSM751399 3 0.0592 0.8209 0.000 0.000 0.984 0.016
#> GSM751400 3 0.1182 0.8188 0.000 0.016 0.968 0.016
#> GSM751401 3 0.0592 0.8209 0.000 0.000 0.984 0.016
#> GSM751402 3 0.0592 0.8209 0.000 0.000 0.984 0.016
#> GSM751403 3 0.0592 0.8209 0.000 0.000 0.984 0.016
#> GSM751405 3 0.0592 0.8209 0.000 0.000 0.984 0.016
#> GSM751407 3 0.0592 0.8209 0.000 0.000 0.984 0.016
#> GSM751408 3 0.0592 0.8209 0.000 0.000 0.984 0.016
#> GSM751409 3 0.0592 0.8209 0.000 0.000 0.984 0.016
#> GSM751412 3 0.0592 0.8209 0.000 0.000 0.984 0.016
#> GSM751418 3 0.4490 0.7562 0.012 0.112 0.820 0.056
#> GSM751419 3 0.2549 0.8110 0.004 0.024 0.916 0.056
#> GSM751420 3 0.6483 0.3995 0.000 0.312 0.592 0.096
#> GSM751425 2 0.2074 0.8343 0.032 0.940 0.016 0.012
#> GSM751429 4 0.7896 0.0302 0.000 0.296 0.336 0.368
#> GSM751430 2 0.0336 0.8440 0.000 0.992 0.000 0.008
#> GSM751433 2 0.2055 0.8346 0.008 0.936 0.048 0.008
#> GSM751437 3 0.0592 0.8209 0.000 0.000 0.984 0.016
#> GSM751448 3 0.5375 0.6351 0.000 0.116 0.744 0.140
#> GSM751451 3 0.6931 0.0930 0.040 0.440 0.484 0.036
#> GSM751423 2 0.5040 0.6936 0.048 0.764 0.180 0.008
#> GSM751424 2 0.0524 0.8423 0.004 0.988 0.000 0.008
#> GSM751428 2 0.1792 0.8389 0.000 0.932 0.000 0.068
#> GSM751431 2 0.3695 0.7909 0.028 0.856 0.108 0.008
#> GSM751432 2 0.1022 0.8440 0.000 0.968 0.000 0.032
#> GSM751434 2 0.1557 0.8413 0.000 0.944 0.000 0.056
#> GSM751435 2 0.1940 0.8361 0.000 0.924 0.000 0.076
#> GSM751436 2 0.0524 0.8423 0.004 0.988 0.000 0.008
#> GSM751440 2 0.3091 0.8196 0.048 0.896 0.048 0.008
#> GSM751444 2 0.2266 0.8323 0.000 0.912 0.004 0.084
#> GSM751446 2 0.2334 0.8304 0.000 0.908 0.004 0.088
#> GSM751449 2 0.4022 0.7843 0.000 0.836 0.068 0.096
#> GSM751450 2 0.1545 0.8344 0.040 0.952 0.000 0.008
#> GSM751452 2 0.0469 0.8438 0.000 0.988 0.000 0.012
#> GSM751426 2 0.0524 0.8423 0.004 0.988 0.000 0.008
#> GSM751427 2 0.1867 0.8377 0.000 0.928 0.000 0.072
#> GSM751438 2 0.5280 0.6889 0.000 0.748 0.156 0.096
#> GSM751439 3 0.7281 0.1535 0.000 0.380 0.468 0.152
#> GSM751441 2 0.2149 0.8317 0.000 0.912 0.000 0.088
#> GSM751442 2 0.2401 0.8281 0.000 0.904 0.004 0.092
#> GSM751443 3 0.6938 0.1522 0.000 0.400 0.488 0.112
#> GSM751445 2 0.2593 0.8276 0.000 0.892 0.004 0.104
#> GSM751447 2 0.1940 0.8361 0.000 0.924 0.000 0.076
#> GSM751453 2 0.1637 0.8409 0.000 0.940 0.000 0.060
#> GSM751454 2 0.1792 0.8389 0.000 0.932 0.000 0.068
#> GSM751455 2 0.2401 0.8281 0.000 0.904 0.004 0.092
#> GSM751456 2 0.2401 0.8281 0.000 0.904 0.004 0.092
#> GSM751457 2 0.6717 0.3279 0.000 0.560 0.332 0.108
#> GSM751458 2 0.6875 0.2187 0.000 0.520 0.368 0.112
cbind(get_classes(res, k = 5), get_membership(res, k = 5))
#> class entropy silhouette p1 p2 p3 p4 p5
#> GSM751298 1 0.0290 0.8702 0.992 0.000 0.000 0.008 0.000
#> GSM751304 5 0.5668 0.6485 0.000 0.084 0.332 0.004 0.580
#> GSM751305 5 0.5755 0.6254 0.000 0.088 0.312 0.008 0.592
#> GSM751307 2 0.0609 0.8228 0.000 0.980 0.000 0.000 0.020
#> GSM751310 4 0.0000 0.9328 0.000 0.000 0.000 1.000 0.000
#> GSM751314 4 0.0000 0.9328 0.000 0.000 0.000 1.000 0.000
#> GSM751316 4 0.0000 0.9328 0.000 0.000 0.000 1.000 0.000
#> GSM751318 4 0.3102 0.7862 0.000 0.000 0.084 0.860 0.056
#> GSM751342 3 0.7611 -0.3661 0.004 0.032 0.348 0.304 0.312
#> GSM751346 1 0.0162 0.8709 0.996 0.000 0.000 0.004 0.000
#> GSM751347 1 0.6578 0.4315 0.532 0.332 0.044 0.000 0.092
#> GSM751348 2 0.6482 0.0417 0.000 0.468 0.200 0.000 0.332
#> GSM751349 2 0.3395 0.7803 0.000 0.764 0.000 0.000 0.236
#> GSM751352 2 0.0865 0.8161 0.000 0.972 0.004 0.000 0.024
#> GSM751353 2 0.2377 0.8127 0.000 0.872 0.000 0.000 0.128
#> GSM751354 2 0.2011 0.7738 0.000 0.908 0.004 0.000 0.088
#> GSM751355 2 0.0955 0.8101 0.000 0.968 0.004 0.000 0.028
#> GSM751358 5 0.4273 0.7333 0.000 0.000 0.448 0.000 0.552
#> GSM751359 5 0.4602 0.0886 0.000 0.252 0.032 0.008 0.708
#> GSM751294 3 0.1059 0.5719 0.004 0.020 0.968 0.000 0.008
#> GSM751296 1 0.0162 0.8709 0.996 0.000 0.000 0.004 0.000
#> GSM751297 1 0.1471 0.8495 0.952 0.020 0.024 0.000 0.004
#> GSM751299 2 0.2136 0.7703 0.008 0.904 0.000 0.000 0.088
#> GSM751300 1 0.0162 0.8709 0.996 0.000 0.000 0.004 0.000
#> GSM751301 2 0.0162 0.8218 0.000 0.996 0.000 0.000 0.004
#> GSM751302 1 0.0162 0.8709 0.996 0.000 0.000 0.004 0.000
#> GSM751303 4 0.0912 0.9107 0.000 0.000 0.012 0.972 0.016
#> GSM751306 4 0.0000 0.9328 0.000 0.000 0.000 1.000 0.000
#> GSM751308 3 0.4102 -0.1522 0.004 0.004 0.692 0.000 0.300
#> GSM751309 4 0.0000 0.9328 0.000 0.000 0.000 1.000 0.000
#> GSM751311 4 0.0000 0.9328 0.000 0.000 0.000 1.000 0.000
#> GSM751312 4 0.0000 0.9328 0.000 0.000 0.000 1.000 0.000
#> GSM751313 4 0.4242 0.1858 0.428 0.000 0.000 0.572 0.000
#> GSM751315 4 0.0000 0.9328 0.000 0.000 0.000 1.000 0.000
#> GSM751317 4 0.0000 0.9328 0.000 0.000 0.000 1.000 0.000
#> GSM751320 4 0.0404 0.9273 0.012 0.000 0.000 0.988 0.000
#> GSM751321 4 0.0000 0.9328 0.000 0.000 0.000 1.000 0.000
#> GSM751322 4 0.0000 0.9328 0.000 0.000 0.000 1.000 0.000
#> GSM751324 4 0.0000 0.9328 0.000 0.000 0.000 1.000 0.000
#> GSM751325 4 0.0000 0.9328 0.000 0.000 0.000 1.000 0.000
#> GSM751332 4 0.0000 0.9328 0.000 0.000 0.000 1.000 0.000
#> GSM751334 4 0.0000 0.9328 0.000 0.000 0.000 1.000 0.000
#> GSM751339 4 0.3454 0.8001 0.100 0.000 0.064 0.836 0.000
#> GSM751341 1 0.2787 0.7906 0.856 0.004 0.004 0.136 0.000
#> GSM751343 4 0.0162 0.9307 0.004 0.000 0.000 0.996 0.000
#> GSM751344 2 0.0162 0.8219 0.000 0.996 0.000 0.000 0.004
#> GSM751345 2 0.0000 0.8208 0.000 1.000 0.000 0.000 0.000
#> GSM751356 5 0.5396 0.6945 0.000 0.056 0.444 0.000 0.500
#> GSM751357 5 0.5894 0.5786 0.000 0.112 0.356 0.000 0.532
#> GSM751293 2 0.0162 0.8218 0.000 0.996 0.000 0.000 0.004
#> GSM751295 1 0.0162 0.8709 0.996 0.000 0.000 0.004 0.000
#> GSM751319 4 0.0000 0.9328 0.000 0.000 0.000 1.000 0.000
#> GSM751323 4 0.0703 0.9201 0.024 0.000 0.000 0.976 0.000
#> GSM751326 1 0.1544 0.8457 0.932 0.000 0.000 0.068 0.000
#> GSM751327 4 0.0880 0.9145 0.032 0.000 0.000 0.968 0.000
#> GSM751328 4 0.0290 0.9298 0.008 0.000 0.000 0.992 0.000
#> GSM751329 4 0.3210 0.7155 0.212 0.000 0.000 0.788 0.000
#> GSM751330 1 0.2020 0.8268 0.900 0.000 0.000 0.100 0.000
#> GSM751331 1 0.0162 0.8709 0.996 0.000 0.000 0.004 0.000
#> GSM751333 1 0.4045 0.4550 0.644 0.000 0.000 0.356 0.000
#> GSM751335 1 0.2471 0.7970 0.864 0.000 0.000 0.136 0.000
#> GSM751336 1 0.0609 0.8668 0.980 0.000 0.000 0.020 0.000
#> GSM751337 1 0.3424 0.6683 0.760 0.000 0.000 0.240 0.000
#> GSM751338 4 0.2074 0.8511 0.104 0.000 0.000 0.896 0.000
#> GSM751340 4 0.5810 0.2816 0.004 0.000 0.364 0.544 0.088
#> GSM751350 1 0.0162 0.8709 0.996 0.000 0.000 0.004 0.000
#> GSM751351 1 0.0162 0.8709 0.996 0.000 0.000 0.004 0.000
#> GSM751362 3 0.0162 0.5851 0.000 0.000 0.996 0.000 0.004
#> GSM751363 5 0.5691 0.6986 0.000 0.064 0.392 0.008 0.536
#> GSM751367 1 0.4280 0.7518 0.800 0.120 0.032 0.000 0.048
#> GSM751368 2 0.6589 0.3350 0.000 0.516 0.212 0.008 0.264
#> GSM751371 5 0.4632 0.7287 0.000 0.000 0.448 0.012 0.540
#> GSM751375 2 0.3661 0.7625 0.000 0.724 0.000 0.000 0.276
#> GSM751376 3 0.6126 0.4356 0.008 0.300 0.564 0.000 0.128
#> GSM751378 3 0.5607 0.2192 0.004 0.064 0.524 0.000 0.408
#> GSM751379 3 0.6113 0.3769 0.008 0.356 0.528 0.000 0.108
#> GSM751382 2 0.3480 0.7749 0.000 0.752 0.000 0.000 0.248
#> GSM751386 2 0.3999 0.7215 0.000 0.656 0.000 0.000 0.344
#> GSM751388 2 0.4327 0.7039 0.000 0.632 0.000 0.008 0.360
#> GSM751391 5 0.4278 0.7316 0.000 0.000 0.452 0.000 0.548
#> GSM751410 3 0.4135 -0.2746 0.004 0.000 0.656 0.000 0.340
#> GSM751414 5 0.4425 0.7307 0.000 0.000 0.452 0.004 0.544
#> GSM751361 5 0.4415 0.7338 0.000 0.000 0.444 0.004 0.552
#> GSM751365 5 0.4278 0.7316 0.000 0.000 0.452 0.000 0.548
#> GSM751366 3 0.3266 0.2208 0.004 0.000 0.796 0.000 0.200
#> GSM751369 3 0.2011 0.4805 0.004 0.000 0.908 0.000 0.088
#> GSM751370 5 0.4300 0.7023 0.000 0.000 0.476 0.000 0.524
#> GSM751372 3 0.4307 -0.6746 0.000 0.000 0.504 0.000 0.496
#> GSM751373 5 0.5483 0.6828 0.000 0.000 0.424 0.064 0.512
#> GSM751374 3 0.6061 0.3626 0.008 0.368 0.524 0.000 0.100
#> GSM751377 2 0.3983 0.7257 0.000 0.660 0.000 0.000 0.340
#> GSM751380 3 0.2719 0.3624 0.004 0.000 0.852 0.000 0.144
#> GSM751381 2 0.4541 0.6839 0.000 0.608 0.004 0.008 0.380
#> GSM751383 2 0.4060 0.7102 0.000 0.640 0.000 0.000 0.360
#> GSM751384 5 0.5120 0.3858 0.004 0.104 0.192 0.000 0.700
#> GSM751385 2 0.4976 0.5538 0.000 0.504 0.028 0.000 0.468
#> GSM751387 2 0.4283 0.7140 0.000 0.644 0.000 0.008 0.348
#> GSM751389 3 0.0162 0.5870 0.000 0.004 0.996 0.000 0.000
#> GSM751393 3 0.5024 0.3386 0.004 0.040 0.628 0.000 0.328
#> GSM751394 2 0.4135 0.7209 0.000 0.656 0.000 0.004 0.340
#> GSM751395 5 0.6160 -0.0217 0.008 0.116 0.344 0.000 0.532
#> GSM751397 5 0.4834 -0.0878 0.000 0.308 0.028 0.008 0.656
#> GSM751398 2 0.4758 0.6285 0.000 0.560 0.008 0.008 0.424
#> GSM751404 3 0.0000 0.5884 0.000 0.000 1.000 0.000 0.000
#> GSM751406 3 0.0000 0.5884 0.000 0.000 1.000 0.000 0.000
#> GSM751411 3 0.4448 -0.6570 0.004 0.000 0.516 0.000 0.480
#> GSM751413 2 0.6233 0.4813 0.000 0.524 0.124 0.008 0.344
#> GSM751415 3 0.0703 0.5644 0.000 0.000 0.976 0.000 0.024
#> GSM751416 5 0.4562 0.7341 0.000 0.004 0.444 0.004 0.548
#> GSM751417 5 0.4670 0.7340 0.000 0.008 0.440 0.004 0.548
#> GSM751421 5 0.4446 0.7002 0.004 0.000 0.476 0.000 0.520
#> GSM751422 5 0.4294 0.7130 0.000 0.000 0.468 0.000 0.532
#> GSM751360 5 0.4278 0.7316 0.000 0.000 0.452 0.000 0.548
#> GSM751364 5 0.4278 0.7316 0.000 0.000 0.452 0.000 0.548
#> GSM751390 5 0.5198 0.3349 0.000 0.148 0.164 0.000 0.688
#> GSM751392 2 0.4151 0.7183 0.000 0.652 0.000 0.004 0.344
#> GSM751396 2 0.3534 0.7714 0.000 0.744 0.000 0.000 0.256
#> GSM751399 3 0.0000 0.5884 0.000 0.000 1.000 0.000 0.000
#> GSM751400 3 0.1471 0.5743 0.004 0.024 0.952 0.000 0.020
#> GSM751401 3 0.0000 0.5884 0.000 0.000 1.000 0.000 0.000
#> GSM751402 3 0.0000 0.5884 0.000 0.000 1.000 0.000 0.000
#> GSM751403 3 0.0000 0.5884 0.000 0.000 1.000 0.000 0.000
#> GSM751405 3 0.0000 0.5884 0.000 0.000 1.000 0.000 0.000
#> GSM751407 3 0.0000 0.5884 0.000 0.000 1.000 0.000 0.000
#> GSM751408 3 0.0000 0.5884 0.000 0.000 1.000 0.000 0.000
#> GSM751409 3 0.0833 0.5741 0.004 0.004 0.976 0.000 0.016
#> GSM751412 3 0.0000 0.5884 0.000 0.000 1.000 0.000 0.000
#> GSM751418 5 0.4622 0.7335 0.000 0.012 0.440 0.000 0.548
#> GSM751419 5 0.4278 0.7316 0.000 0.000 0.452 0.000 0.548
#> GSM751420 3 0.5919 0.4296 0.004 0.316 0.568 0.000 0.112
#> GSM751425 2 0.3730 0.7560 0.000 0.712 0.000 0.000 0.288
#> GSM751429 1 0.7754 0.2742 0.420 0.316 0.176 0.000 0.088
#> GSM751430 2 0.0794 0.8231 0.000 0.972 0.000 0.000 0.028
#> GSM751433 2 0.4042 0.7749 0.000 0.756 0.032 0.000 0.212
#> GSM751437 3 0.0000 0.5884 0.000 0.000 1.000 0.000 0.000
#> GSM751448 3 0.6007 0.4717 0.072 0.160 0.676 0.000 0.092
#> GSM751451 5 0.5986 0.6813 0.000 0.088 0.396 0.008 0.508
#> GSM751423 2 0.4702 0.7470 0.000 0.700 0.036 0.008 0.256
#> GSM751424 2 0.2852 0.8005 0.000 0.828 0.000 0.000 0.172
#> GSM751428 2 0.0000 0.8208 0.000 1.000 0.000 0.000 0.000
#> GSM751431 2 0.3534 0.7714 0.000 0.744 0.000 0.000 0.256
#> GSM751432 2 0.0162 0.8214 0.000 0.996 0.000 0.000 0.004
#> GSM751434 2 0.0000 0.8208 0.000 1.000 0.000 0.000 0.000
#> GSM751435 2 0.0290 0.8189 0.000 0.992 0.000 0.000 0.008
#> GSM751436 2 0.2424 0.8103 0.000 0.868 0.000 0.000 0.132
#> GSM751440 2 0.3612 0.7909 0.000 0.832 0.064 0.004 0.100
#> GSM751444 2 0.0693 0.8145 0.008 0.980 0.000 0.000 0.012
#> GSM751446 2 0.0898 0.8118 0.008 0.972 0.000 0.000 0.020
#> GSM751449 2 0.4224 0.6398 0.008 0.792 0.120 0.000 0.080
#> GSM751450 2 0.2074 0.8153 0.000 0.896 0.000 0.000 0.104
#> GSM751452 2 0.0290 0.8220 0.000 0.992 0.000 0.000 0.008
#> GSM751426 2 0.0609 0.8232 0.000 0.980 0.000 0.000 0.020
#> GSM751427 2 0.0703 0.8231 0.000 0.976 0.000 0.000 0.024
#> GSM751438 2 0.5385 0.3911 0.008 0.660 0.248 0.000 0.084
#> GSM751439 3 0.6875 0.3294 0.056 0.368 0.480 0.000 0.096
#> GSM751441 2 0.0510 0.8194 0.000 0.984 0.000 0.000 0.016
#> GSM751442 2 0.2136 0.7691 0.008 0.904 0.000 0.000 0.088
#> GSM751443 3 0.6019 0.3652 0.008 0.368 0.528 0.000 0.096
#> GSM751445 2 0.0898 0.8110 0.008 0.972 0.000 0.000 0.020
#> GSM751447 2 0.0162 0.8198 0.000 0.996 0.000 0.000 0.004
#> GSM751453 2 0.0000 0.8208 0.000 1.000 0.000 0.000 0.000
#> GSM751454 2 0.0000 0.8208 0.000 1.000 0.000 0.000 0.000
#> GSM751455 2 0.2017 0.7766 0.008 0.912 0.000 0.000 0.080
#> GSM751456 2 0.2249 0.7644 0.008 0.896 0.000 0.000 0.096
#> GSM751457 3 0.6023 0.3231 0.008 0.392 0.508 0.000 0.092
#> GSM751458 3 0.6271 0.3476 0.008 0.360 0.508 0.000 0.124
cbind(get_classes(res, k = 6), get_membership(res, k = 6))
#> class entropy silhouette p1 p2 p3 p4 p5 p6
#> GSM751298 1 0.0000 0.9302 1.000 0.000 0.000 0.000 0.000 0.000
#> GSM751304 5 0.1865 0.7465 0.000 0.000 0.040 0.000 0.920 0.040
#> GSM751305 5 0.1649 0.7441 0.000 0.000 0.032 0.000 0.932 0.036
#> GSM751307 6 0.2340 0.7114 0.000 0.148 0.000 0.000 0.000 0.852
#> GSM751310 4 0.0000 0.9608 0.000 0.000 0.000 1.000 0.000 0.000
#> GSM751314 4 0.0000 0.9608 0.000 0.000 0.000 1.000 0.000 0.000
#> GSM751316 4 0.0632 0.9427 0.000 0.000 0.000 0.976 0.024 0.000
#> GSM751318 4 0.3078 0.7390 0.000 0.000 0.012 0.796 0.192 0.000
#> GSM751342 5 0.5308 0.1952 0.000 0.000 0.088 0.424 0.484 0.004
#> GSM751346 1 0.0000 0.9302 1.000 0.000 0.000 0.000 0.000 0.000
#> GSM751347 2 0.3657 0.7114 0.168 0.788 0.020 0.000 0.000 0.024
#> GSM751348 5 0.5552 0.2334 0.000 0.032 0.064 0.000 0.516 0.388
#> GSM751349 6 0.2826 0.7271 0.000 0.052 0.000 0.000 0.092 0.856
#> GSM751352 6 0.3838 0.1688 0.000 0.448 0.000 0.000 0.000 0.552
#> GSM751353 6 0.3551 0.7187 0.000 0.192 0.000 0.000 0.036 0.772
#> GSM751354 2 0.2219 0.7986 0.000 0.864 0.000 0.000 0.000 0.136
#> GSM751355 2 0.2912 0.7218 0.000 0.784 0.000 0.000 0.000 0.216
#> GSM751358 5 0.1957 0.7850 0.000 0.000 0.112 0.000 0.888 0.000
#> GSM751359 5 0.4548 0.3252 0.000 0.056 0.000 0.000 0.632 0.312
#> GSM751294 3 0.1176 0.8404 0.000 0.020 0.956 0.000 0.024 0.000
#> GSM751296 1 0.0000 0.9302 1.000 0.000 0.000 0.000 0.000 0.000
#> GSM751297 1 0.0777 0.9153 0.972 0.024 0.004 0.000 0.000 0.000
#> GSM751299 2 0.2378 0.7899 0.000 0.848 0.000 0.000 0.000 0.152
#> GSM751300 1 0.0000 0.9302 1.000 0.000 0.000 0.000 0.000 0.000
#> GSM751301 6 0.2378 0.7093 0.000 0.152 0.000 0.000 0.000 0.848
#> GSM751302 1 0.0000 0.9302 1.000 0.000 0.000 0.000 0.000 0.000
#> GSM751303 4 0.1204 0.9125 0.000 0.000 0.000 0.944 0.056 0.000
#> GSM751306 4 0.0000 0.9608 0.000 0.000 0.000 1.000 0.000 0.000
#> GSM751308 3 0.3869 -0.0716 0.000 0.000 0.500 0.000 0.500 0.000
#> GSM751309 4 0.0000 0.9608 0.000 0.000 0.000 1.000 0.000 0.000
#> GSM751311 4 0.0000 0.9608 0.000 0.000 0.000 1.000 0.000 0.000
#> GSM751312 4 0.0000 0.9608 0.000 0.000 0.000 1.000 0.000 0.000
#> GSM751313 1 0.3817 0.2878 0.568 0.000 0.000 0.432 0.000 0.000
#> GSM751315 4 0.0000 0.9608 0.000 0.000 0.000 1.000 0.000 0.000
#> GSM751317 4 0.0000 0.9608 0.000 0.000 0.000 1.000 0.000 0.000
#> GSM751320 4 0.0146 0.9590 0.004 0.000 0.000 0.996 0.000 0.000
#> GSM751321 4 0.0000 0.9608 0.000 0.000 0.000 1.000 0.000 0.000
#> GSM751322 4 0.0000 0.9608 0.000 0.000 0.000 1.000 0.000 0.000
#> GSM751324 4 0.0000 0.9608 0.000 0.000 0.000 1.000 0.000 0.000
#> GSM751325 4 0.0000 0.9608 0.000 0.000 0.000 1.000 0.000 0.000
#> GSM751332 4 0.0000 0.9608 0.000 0.000 0.000 1.000 0.000 0.000
#> GSM751334 4 0.0000 0.9608 0.000 0.000 0.000 1.000 0.000 0.000
#> GSM751339 4 0.4494 0.6232 0.092 0.000 0.216 0.692 0.000 0.000
#> GSM751341 1 0.0865 0.9173 0.964 0.000 0.000 0.036 0.000 0.000
#> GSM751343 4 0.0000 0.9608 0.000 0.000 0.000 1.000 0.000 0.000
#> GSM751344 6 0.2378 0.7093 0.000 0.152 0.000 0.000 0.000 0.848
#> GSM751345 6 0.2378 0.7093 0.000 0.152 0.000 0.000 0.000 0.848
#> GSM751356 5 0.2887 0.7758 0.000 0.000 0.120 0.000 0.844 0.036
#> GSM751357 5 0.3602 0.7084 0.000 0.000 0.072 0.000 0.792 0.136
#> GSM751293 6 0.2378 0.7093 0.000 0.152 0.000 0.000 0.000 0.848
#> GSM751295 1 0.0000 0.9302 1.000 0.000 0.000 0.000 0.000 0.000
#> GSM751319 4 0.0000 0.9608 0.000 0.000 0.000 1.000 0.000 0.000
#> GSM751323 4 0.0363 0.9543 0.012 0.000 0.000 0.988 0.000 0.000
#> GSM751326 1 0.0713 0.9211 0.972 0.000 0.000 0.028 0.000 0.000
#> GSM751327 4 0.0260 0.9569 0.008 0.000 0.000 0.992 0.000 0.000
#> GSM751328 4 0.0363 0.9548 0.012 0.000 0.000 0.988 0.000 0.000
#> GSM751329 4 0.2340 0.8197 0.148 0.000 0.000 0.852 0.000 0.000
#> GSM751330 1 0.1007 0.9133 0.956 0.000 0.000 0.044 0.000 0.000
#> GSM751331 1 0.0000 0.9302 1.000 0.000 0.000 0.000 0.000 0.000
#> GSM751333 1 0.2697 0.7811 0.812 0.000 0.000 0.188 0.000 0.000
#> GSM751335 1 0.1141 0.9082 0.948 0.000 0.000 0.052 0.000 0.000
#> GSM751336 1 0.0000 0.9302 1.000 0.000 0.000 0.000 0.000 0.000
#> GSM751337 1 0.2048 0.8501 0.880 0.000 0.000 0.120 0.000 0.000
#> GSM751338 4 0.2135 0.8393 0.128 0.000 0.000 0.872 0.000 0.000
#> GSM751340 3 0.5392 0.2764 0.012 0.000 0.528 0.376 0.084 0.000
#> GSM751350 1 0.0000 0.9302 1.000 0.000 0.000 0.000 0.000 0.000
#> GSM751351 1 0.0000 0.9302 1.000 0.000 0.000 0.000 0.000 0.000
#> GSM751362 3 0.0632 0.8486 0.000 0.000 0.976 0.000 0.024 0.000
#> GSM751363 5 0.1908 0.7827 0.000 0.000 0.096 0.000 0.900 0.004
#> GSM751367 1 0.3543 0.7575 0.812 0.124 0.012 0.000 0.052 0.000
#> GSM751368 6 0.4615 0.2733 0.000 0.000 0.040 0.000 0.424 0.536
#> GSM751371 5 0.3088 0.7568 0.000 0.000 0.120 0.048 0.832 0.000
#> GSM751375 6 0.2812 0.7121 0.000 0.048 0.000 0.000 0.096 0.856
#> GSM751376 3 0.3866 -0.0810 0.000 0.484 0.516 0.000 0.000 0.000
#> GSM751378 5 0.6964 0.1660 0.000 0.128 0.288 0.000 0.452 0.132
#> GSM751379 2 0.3240 0.6728 0.000 0.752 0.244 0.000 0.000 0.004
#> GSM751382 6 0.2121 0.7325 0.000 0.012 0.000 0.000 0.096 0.892
#> GSM751386 6 0.4038 0.6557 0.000 0.056 0.000 0.000 0.216 0.728
#> GSM751388 6 0.4167 0.6383 0.000 0.056 0.000 0.000 0.236 0.708
#> GSM751391 5 0.1957 0.7850 0.000 0.000 0.112 0.000 0.888 0.000
#> GSM751410 5 0.3860 0.0911 0.000 0.000 0.472 0.000 0.528 0.000
#> GSM751414 5 0.2784 0.7681 0.000 0.000 0.124 0.028 0.848 0.000
#> GSM751361 5 0.1957 0.7850 0.000 0.000 0.112 0.000 0.888 0.000
#> GSM751365 5 0.1957 0.7850 0.000 0.000 0.112 0.000 0.888 0.000
#> GSM751366 3 0.3428 0.5254 0.000 0.000 0.696 0.000 0.304 0.000
#> GSM751369 3 0.2823 0.6906 0.000 0.000 0.796 0.000 0.204 0.000
#> GSM751370 5 0.2527 0.7475 0.000 0.000 0.168 0.000 0.832 0.000
#> GSM751372 5 0.2416 0.7598 0.000 0.000 0.156 0.000 0.844 0.000
#> GSM751373 5 0.3352 0.7436 0.000 0.000 0.112 0.072 0.816 0.000
#> GSM751374 2 0.2362 0.7736 0.000 0.860 0.136 0.000 0.000 0.004
#> GSM751377 6 0.3608 0.6326 0.000 0.012 0.000 0.000 0.272 0.716
#> GSM751380 3 0.3076 0.6370 0.000 0.000 0.760 0.000 0.240 0.000
#> GSM751381 6 0.4635 0.4929 0.000 0.056 0.000 0.000 0.336 0.608
#> GSM751383 6 0.4427 0.5774 0.000 0.056 0.000 0.000 0.284 0.660
#> GSM751384 5 0.4037 0.6359 0.000 0.056 0.036 0.000 0.788 0.120
#> GSM751385 5 0.4975 -0.0616 0.000 0.068 0.000 0.000 0.504 0.428
#> GSM751387 6 0.4167 0.6387 0.000 0.056 0.000 0.000 0.236 0.708
#> GSM751389 3 0.0260 0.8519 0.000 0.000 0.992 0.000 0.008 0.000
#> GSM751393 3 0.6191 0.4496 0.000 0.156 0.600 0.000 0.128 0.116
#> GSM751394 6 0.3739 0.6764 0.000 0.056 0.000 0.000 0.176 0.768
#> GSM751395 5 0.6160 0.3934 0.000 0.216 0.064 0.000 0.576 0.144
#> GSM751397 5 0.4578 0.3013 0.000 0.056 0.000 0.000 0.624 0.320
#> GSM751398 6 0.4829 0.2942 0.000 0.056 0.000 0.000 0.424 0.520
#> GSM751404 3 0.0260 0.8519 0.000 0.000 0.992 0.000 0.008 0.000
#> GSM751406 3 0.0260 0.8519 0.000 0.000 0.992 0.000 0.008 0.000
#> GSM751411 5 0.2631 0.7398 0.000 0.000 0.180 0.000 0.820 0.000
#> GSM751413 6 0.4155 0.4662 0.000 0.000 0.020 0.000 0.364 0.616
#> GSM751415 3 0.2340 0.7544 0.000 0.000 0.852 0.000 0.148 0.000
#> GSM751416 5 0.1957 0.7850 0.000 0.000 0.112 0.000 0.888 0.000
#> GSM751417 5 0.1957 0.7850 0.000 0.000 0.112 0.000 0.888 0.000
#> GSM751421 5 0.2854 0.7039 0.000 0.000 0.208 0.000 0.792 0.000
#> GSM751422 5 0.2912 0.6916 0.000 0.000 0.216 0.000 0.784 0.000
#> GSM751360 5 0.1957 0.7850 0.000 0.000 0.112 0.000 0.888 0.000
#> GSM751364 5 0.1957 0.7850 0.000 0.000 0.112 0.000 0.888 0.000
#> GSM751390 5 0.4072 0.6049 0.000 0.060 0.020 0.000 0.772 0.148
#> GSM751392 6 0.4065 0.6530 0.000 0.056 0.000 0.000 0.220 0.724
#> GSM751396 6 0.1814 0.7281 0.000 0.000 0.000 0.000 0.100 0.900
#> GSM751399 3 0.0363 0.8516 0.000 0.000 0.988 0.000 0.012 0.000
#> GSM751400 3 0.1003 0.8356 0.000 0.028 0.964 0.000 0.004 0.004
#> GSM751401 3 0.0260 0.8519 0.000 0.000 0.992 0.000 0.008 0.000
#> GSM751402 3 0.0260 0.8519 0.000 0.000 0.992 0.000 0.008 0.000
#> GSM751403 3 0.0260 0.8519 0.000 0.000 0.992 0.000 0.008 0.000
#> GSM751405 3 0.0260 0.8519 0.000 0.000 0.992 0.000 0.008 0.000
#> GSM751407 3 0.0260 0.8519 0.000 0.000 0.992 0.000 0.008 0.000
#> GSM751408 3 0.0363 0.8516 0.000 0.000 0.988 0.000 0.012 0.000
#> GSM751409 3 0.1444 0.8211 0.000 0.000 0.928 0.000 0.072 0.000
#> GSM751412 3 0.0547 0.8499 0.000 0.000 0.980 0.000 0.020 0.000
#> GSM751418 5 0.1957 0.7850 0.000 0.000 0.112 0.000 0.888 0.000
#> GSM751419 5 0.1957 0.7850 0.000 0.000 0.112 0.000 0.888 0.000
#> GSM751420 2 0.4111 0.2122 0.000 0.536 0.456 0.000 0.004 0.004
#> GSM751425 6 0.2842 0.7110 0.000 0.044 0.000 0.000 0.104 0.852
#> GSM751429 2 0.3758 0.6956 0.176 0.772 0.048 0.000 0.000 0.004
#> GSM751430 6 0.2260 0.7151 0.000 0.140 0.000 0.000 0.000 0.860
#> GSM751433 6 0.1615 0.7366 0.000 0.004 0.004 0.000 0.064 0.928
#> GSM751437 3 0.0260 0.8519 0.000 0.000 0.992 0.000 0.008 0.000
#> GSM751448 3 0.2446 0.7016 0.012 0.124 0.864 0.000 0.000 0.000
#> GSM751451 5 0.2311 0.7824 0.000 0.000 0.104 0.000 0.880 0.016
#> GSM751423 6 0.3037 0.6993 0.000 0.000 0.016 0.000 0.176 0.808
#> GSM751424 6 0.1003 0.7397 0.000 0.020 0.000 0.000 0.016 0.964
#> GSM751428 6 0.2378 0.7093 0.000 0.152 0.000 0.000 0.000 0.848
#> GSM751431 6 0.2006 0.7254 0.000 0.004 0.000 0.000 0.104 0.892
#> GSM751432 6 0.2378 0.7093 0.000 0.152 0.000 0.000 0.000 0.848
#> GSM751434 6 0.2378 0.7093 0.000 0.152 0.000 0.000 0.000 0.848
#> GSM751435 6 0.2378 0.7093 0.000 0.152 0.000 0.000 0.000 0.848
#> GSM751436 6 0.0972 0.7393 0.000 0.028 0.000 0.000 0.008 0.964
#> GSM751440 6 0.2747 0.7353 0.000 0.040 0.024 0.000 0.056 0.880
#> GSM751444 6 0.3288 0.5496 0.000 0.276 0.000 0.000 0.000 0.724
#> GSM751446 6 0.3737 0.3137 0.000 0.392 0.000 0.000 0.000 0.608
#> GSM751449 2 0.2383 0.8131 0.000 0.880 0.024 0.000 0.000 0.096
#> GSM751450 6 0.1686 0.7359 0.000 0.064 0.000 0.000 0.012 0.924
#> GSM751452 6 0.2300 0.7131 0.000 0.144 0.000 0.000 0.000 0.856
#> GSM751426 6 0.2191 0.7223 0.000 0.120 0.000 0.000 0.004 0.876
#> GSM751427 6 0.4136 0.2074 0.000 0.428 0.000 0.000 0.012 0.560
#> GSM751438 2 0.2201 0.8146 0.000 0.896 0.028 0.000 0.000 0.076
#> GSM751439 2 0.2501 0.7828 0.016 0.872 0.108 0.000 0.000 0.004
#> GSM751441 2 0.3862 0.1075 0.000 0.524 0.000 0.000 0.000 0.476
#> GSM751442 2 0.2178 0.7996 0.000 0.868 0.000 0.000 0.000 0.132
#> GSM751443 2 0.3109 0.7032 0.000 0.772 0.224 0.000 0.000 0.004
#> GSM751445 2 0.2912 0.6950 0.000 0.784 0.000 0.000 0.000 0.216
#> GSM751447 6 0.2378 0.7093 0.000 0.152 0.000 0.000 0.000 0.848
#> GSM751453 6 0.2378 0.7093 0.000 0.152 0.000 0.000 0.000 0.848
#> GSM751454 6 0.2378 0.7093 0.000 0.152 0.000 0.000 0.000 0.848
#> GSM751455 2 0.2378 0.7893 0.000 0.848 0.000 0.000 0.000 0.152
#> GSM751456 2 0.2260 0.7959 0.000 0.860 0.000 0.000 0.000 0.140
#> GSM751457 2 0.2199 0.7981 0.000 0.892 0.088 0.000 0.000 0.020
#> GSM751458 2 0.2581 0.7772 0.000 0.856 0.128 0.000 0.000 0.016
Heatmaps for the consensus matrix. It visualizes the probability of two samples to be in a same group.
consensus_heatmap(res, k = 2)
consensus_heatmap(res, k = 3)
consensus_heatmap(res, k = 4)
consensus_heatmap(res, k = 5)
consensus_heatmap(res, k = 6)
Heatmaps for the membership of samples in all partitions to see how consistent they are:
membership_heatmap(res, k = 2)
membership_heatmap(res, k = 3)
membership_heatmap(res, k = 4)
membership_heatmap(res, k = 5)
membership_heatmap(res, k = 6)
As soon as we have had the classes for columns, we can look for signatures which are significantly different between classes which can be candidate marks for certain classes. Following are the heatmaps for signatures.
Signature heatmaps where rows are scaled:
get_signatures(res, k = 2)
get_signatures(res, k = 3)
get_signatures(res, k = 4)
get_signatures(res, k = 5)
get_signatures(res, k = 6)
Signature heatmaps where rows are not scaled:
get_signatures(res, k = 2, scale_rows = FALSE)
get_signatures(res, k = 3, scale_rows = FALSE)
get_signatures(res, k = 4, scale_rows = FALSE)
get_signatures(res, k = 5, scale_rows = FALSE)
get_signatures(res, k = 6, scale_rows = FALSE)
Compare the overlap of signatures from different k:
compare_signatures(res)
get_signature() returns a data frame invisibly. TO get the list of signatures, the function
call should be assigned to a variable explicitly. In following code, if plot argument is set
to FALSE, no heatmap is plotted while only the differential analysis is performed.
# code only for demonstration
tb = get_signature(res, k = ..., plot = FALSE)
An example of the output of tb is:
#> which_row fdr mean_1 mean_2 scaled_mean_1 scaled_mean_2 km
#> 1 38 0.042760348 8.373488 9.131774 -0.5533452 0.5164555 1
#> 2 40 0.018707592 7.106213 8.469186 -0.6173731 0.5762149 1
#> 3 55 0.019134737 10.221463 11.207825 -0.6159697 0.5749050 1
#> 4 59 0.006059896 5.921854 7.869574 -0.6899429 0.6439467 1
#> 5 60 0.018055526 8.928898 10.211722 -0.6204761 0.5791110 1
#> 6 98 0.009384629 15.714769 14.887706 0.6635654 -0.6193277 2
...
The columns in tb are:
which_row: row indices corresponding to the input matrix.fdr: FDR for the differential test. mean_x: The mean value in group x.scaled_mean_x: The mean value in group x after rows are scaled.km: Row groups if k-means clustering is applied to rows.UMAP plot which shows how samples are separated.
dimension_reduction(res, k = 2, method = "UMAP")
dimension_reduction(res, k = 3, method = "UMAP")
dimension_reduction(res, k = 4, method = "UMAP")
dimension_reduction(res, k = 5, method = "UMAP")
dimension_reduction(res, k = 6, method = "UMAP")
Following heatmap shows how subgroups are split when increasing k:
collect_classes(res)
Test correlation between subgroups and known annotations. If the known annotation is numeric, one-way ANOVA test is applied, and if the known annotation is discrete, chi-squared contingency table test is applied.
test_to_known_factors(res)
#> n tissue(p) disease.state(p) agent(p) k
#> ATC:mclust 165 4.98e-20 0.139 0.2205 2
#> ATC:mclust 138 1.91e-26 0.214 0.4383 3
#> ATC:mclust 144 1.34e-25 0.578 0.3316 4
#> ATC:mclust 133 1.31e-21 0.310 0.0408 5
#> ATC:mclust 144 2.34e-24 0.562 0.0283 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 4537 rows and 166 columns.
#> Top rows (454, 908, 1361, 1814, 2268) are extracted by 'ATC' method.
#> Subgroups are detected by 'NMF' method.
#> Performed in total 1250 partitions by row resampling.
#> Best k for subgroups seems to be 3.
#>
#> Following methods can be applied to this 'ConsensusPartition' object:
#> [1] "cola_report" "collect_classes" "collect_plots"
#> [4] "collect_stats" "colnames" "compare_signatures"
#> [7] "consensus_heatmap" "dimension_reduction" "functional_enrichment"
#> [10] "get_anno_col" "get_anno" "get_classes"
#> [13] "get_consensus" "get_matrix" "get_membership"
#> [16] "get_param" "get_signatures" "get_stats"
#> [19] "is_best_k" "is_stable_k" "membership_heatmap"
#> [22] "ncol" "nrow" "plot_ecdf"
#> [25] "rownames" "select_partition_number" "show"
#> [28] "suggest_best_k" "test_to_known_factors"
collect_plots() function collects all the plots made from res for all k (number of partitions)
into one single page to provide an easy and fast comparison between different k.
collect_plots(res)
The plots are:
k and the heatmap of
predicted classes for each k.k.k.k.All the plots in panels can be made by individual functions and they are plotted later in this section.
select_partition_number() produces several plots showing different
statistics for choosing “optimized” k. There are following statistics:
k;k, the area increased is defined as \(A_k - A_{k-1}\).The detailed explanations of these statistics can be found in the cola vignette.
Generally speaking, lower PAC score, higher mean silhouette score or higher
concordance corresponds to better partition. Rand index and Jaccard index
measure how similar the current partition is compared to partition with k-1.
If they are too similar, we won't accept k is better than k-1.
select_partition_number(res)
The numeric values for all these statistics can be obtained by get_stats().
get_stats(res)
#> k 1-PAC mean_silhouette concordance area_increased Rand Jaccard
#> 2 2 0.899 0.926 0.968 0.4782 0.523 0.523
#> 3 3 0.905 0.890 0.956 0.3907 0.739 0.533
#> 4 4 0.605 0.559 0.760 0.1190 0.821 0.538
#> 5 5 0.651 0.606 0.759 0.0701 0.813 0.428
#> 6 6 0.785 0.758 0.843 0.0470 0.901 0.579
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
#> GSM751298 1 0.0000 0.963 1.000 0.000
#> GSM751304 2 0.1184 0.958 0.016 0.984
#> GSM751305 2 0.3733 0.914 0.072 0.928
#> GSM751307 2 0.0000 0.968 0.000 1.000
#> GSM751310 1 0.0000 0.963 1.000 0.000
#> GSM751314 1 0.0000 0.963 1.000 0.000
#> GSM751316 1 0.0000 0.963 1.000 0.000
#> GSM751318 1 0.0000 0.963 1.000 0.000
#> GSM751342 1 0.0000 0.963 1.000 0.000
#> GSM751346 1 0.0000 0.963 1.000 0.000
#> GSM751347 2 0.2948 0.930 0.052 0.948
#> GSM751348 2 0.0000 0.968 0.000 1.000
#> GSM751349 2 0.0000 0.968 0.000 1.000
#> GSM751352 2 0.0000 0.968 0.000 1.000
#> GSM751353 2 0.0000 0.968 0.000 1.000
#> GSM751354 2 0.0000 0.968 0.000 1.000
#> GSM751355 2 0.0000 0.968 0.000 1.000
#> GSM751358 2 0.2778 0.935 0.048 0.952
#> GSM751359 2 0.0000 0.968 0.000 1.000
#> GSM751294 2 0.0000 0.968 0.000 1.000
#> GSM751296 1 0.0000 0.963 1.000 0.000
#> GSM751297 1 0.0376 0.959 0.996 0.004
#> GSM751299 2 0.0000 0.968 0.000 1.000
#> GSM751300 1 0.0000 0.963 1.000 0.000
#> GSM751301 2 0.4161 0.902 0.084 0.916
#> GSM751302 1 0.0000 0.963 1.000 0.000
#> GSM751303 1 0.0000 0.963 1.000 0.000
#> GSM751306 1 0.0000 0.963 1.000 0.000
#> GSM751308 1 0.0000 0.963 1.000 0.000
#> GSM751309 1 0.0000 0.963 1.000 0.000
#> GSM751311 1 0.0000 0.963 1.000 0.000
#> GSM751312 1 0.0000 0.963 1.000 0.000
#> GSM751313 1 0.0000 0.963 1.000 0.000
#> GSM751315 1 0.0000 0.963 1.000 0.000
#> GSM751317 1 0.0000 0.963 1.000 0.000
#> GSM751320 1 0.0000 0.963 1.000 0.000
#> GSM751321 1 0.0000 0.963 1.000 0.000
#> GSM751322 1 0.0000 0.963 1.000 0.000
#> GSM751324 1 0.0000 0.963 1.000 0.000
#> GSM751325 1 0.0000 0.963 1.000 0.000
#> GSM751332 1 0.0000 0.963 1.000 0.000
#> GSM751334 1 0.0000 0.963 1.000 0.000
#> GSM751339 1 0.0000 0.963 1.000 0.000
#> GSM751341 1 0.0000 0.963 1.000 0.000
#> GSM751343 1 0.0000 0.963 1.000 0.000
#> GSM751344 2 0.0000 0.968 0.000 1.000
#> GSM751345 2 0.0000 0.968 0.000 1.000
#> GSM751356 2 0.0000 0.968 0.000 1.000
#> GSM751357 2 0.0000 0.968 0.000 1.000
#> GSM751293 2 0.2236 0.944 0.036 0.964
#> GSM751295 1 0.0000 0.963 1.000 0.000
#> GSM751319 1 0.0000 0.963 1.000 0.000
#> GSM751323 1 0.0000 0.963 1.000 0.000
#> GSM751326 1 0.0000 0.963 1.000 0.000
#> GSM751327 1 0.0000 0.963 1.000 0.000
#> GSM751328 1 0.0000 0.963 1.000 0.000
#> GSM751329 1 0.0000 0.963 1.000 0.000
#> GSM751330 1 0.0000 0.963 1.000 0.000
#> GSM751331 1 0.0000 0.963 1.000 0.000
#> GSM751333 1 0.0000 0.963 1.000 0.000
#> GSM751335 1 0.0000 0.963 1.000 0.000
#> GSM751336 1 0.0000 0.963 1.000 0.000
#> GSM751337 1 0.0000 0.963 1.000 0.000
#> GSM751338 1 0.0000 0.963 1.000 0.000
#> GSM751340 1 0.0000 0.963 1.000 0.000
#> GSM751350 1 0.0000 0.963 1.000 0.000
#> GSM751351 1 0.0000 0.963 1.000 0.000
#> GSM751362 2 0.8386 0.646 0.268 0.732
#> GSM751363 2 0.7815 0.709 0.232 0.768
#> GSM751367 1 0.0000 0.963 1.000 0.000
#> GSM751368 2 0.0672 0.964 0.008 0.992
#> GSM751371 1 0.0000 0.963 1.000 0.000
#> GSM751375 2 0.0000 0.968 0.000 1.000
#> GSM751376 2 0.0000 0.968 0.000 1.000
#> GSM751378 2 0.0000 0.968 0.000 1.000
#> GSM751379 2 0.0000 0.968 0.000 1.000
#> GSM751382 2 0.0000 0.968 0.000 1.000
#> GSM751386 2 0.0000 0.968 0.000 1.000
#> GSM751388 2 0.0000 0.968 0.000 1.000
#> GSM751391 1 0.9775 0.298 0.588 0.412
#> GSM751410 1 0.0000 0.963 1.000 0.000
#> GSM751414 1 0.0000 0.963 1.000 0.000
#> GSM751361 2 0.2778 0.935 0.048 0.952
#> GSM751365 2 0.2043 0.947 0.032 0.968
#> GSM751366 1 0.0000 0.963 1.000 0.000
#> GSM751369 1 0.9248 0.487 0.660 0.340
#> GSM751370 1 0.0376 0.959 0.996 0.004
#> GSM751372 2 0.5178 0.868 0.116 0.884
#> GSM751373 1 0.0000 0.963 1.000 0.000
#> GSM751374 2 0.0000 0.968 0.000 1.000
#> GSM751377 2 0.0000 0.968 0.000 1.000
#> GSM751380 1 0.0000 0.963 1.000 0.000
#> GSM751381 2 0.0000 0.968 0.000 1.000
#> GSM751383 2 0.0000 0.968 0.000 1.000
#> GSM751384 2 0.0000 0.968 0.000 1.000
#> GSM751385 2 0.0000 0.968 0.000 1.000
#> GSM751387 2 0.0000 0.968 0.000 1.000
#> GSM751389 2 0.0000 0.968 0.000 1.000
#> GSM751393 2 0.0000 0.968 0.000 1.000
#> GSM751394 2 0.0000 0.968 0.000 1.000
#> GSM751395 2 0.0000 0.968 0.000 1.000
#> GSM751397 2 0.0000 0.968 0.000 1.000
#> GSM751398 2 0.0000 0.968 0.000 1.000
#> GSM751404 2 0.3431 0.919 0.064 0.936
#> GSM751406 2 0.0000 0.968 0.000 1.000
#> GSM751411 2 0.0000 0.968 0.000 1.000
#> GSM751413 2 0.4022 0.906 0.080 0.920
#> GSM751415 1 0.8555 0.622 0.720 0.280
#> GSM751416 2 0.5842 0.840 0.140 0.860
#> GSM751417 2 0.0672 0.963 0.008 0.992
#> GSM751421 1 0.0000 0.963 1.000 0.000
#> GSM751422 1 0.2948 0.916 0.948 0.052
#> GSM751360 1 0.9044 0.529 0.680 0.320
#> GSM751364 2 0.5059 0.872 0.112 0.888
#> GSM751390 2 0.0000 0.968 0.000 1.000
#> GSM751392 2 0.0000 0.968 0.000 1.000
#> GSM751396 2 0.0000 0.968 0.000 1.000
#> GSM751399 2 0.0000 0.968 0.000 1.000
#> GSM751400 2 0.0000 0.968 0.000 1.000
#> GSM751401 2 0.8207 0.658 0.256 0.744
#> GSM751402 2 0.9522 0.398 0.372 0.628
#> GSM751403 2 0.0000 0.968 0.000 1.000
#> GSM751405 2 0.0000 0.968 0.000 1.000
#> GSM751407 2 0.0000 0.968 0.000 1.000
#> GSM751408 2 0.0000 0.968 0.000 1.000
#> GSM751409 2 0.0000 0.968 0.000 1.000
#> GSM751412 2 0.0000 0.968 0.000 1.000
#> GSM751418 1 0.8555 0.609 0.720 0.280
#> GSM751419 2 0.9866 0.253 0.432 0.568
#> GSM751420 2 0.0000 0.968 0.000 1.000
#> GSM751425 2 0.0000 0.968 0.000 1.000
#> GSM751429 1 0.5408 0.843 0.876 0.124
#> GSM751430 2 0.0000 0.968 0.000 1.000
#> GSM751433 2 0.3114 0.928 0.056 0.944
#> GSM751437 2 0.0376 0.966 0.004 0.996
#> GSM751448 1 0.9909 0.223 0.556 0.444
#> GSM751451 2 0.9000 0.553 0.316 0.684
#> GSM751423 2 0.0000 0.968 0.000 1.000
#> GSM751424 2 0.0000 0.968 0.000 1.000
#> GSM751428 2 0.0000 0.968 0.000 1.000
#> GSM751431 2 0.0000 0.968 0.000 1.000
#> GSM751432 2 0.0000 0.968 0.000 1.000
#> GSM751434 2 0.0000 0.968 0.000 1.000
#> GSM751435 2 0.0000 0.968 0.000 1.000
#> GSM751436 2 0.0000 0.968 0.000 1.000
#> GSM751440 2 0.3584 0.917 0.068 0.932
#> GSM751444 2 0.0000 0.968 0.000 1.000
#> GSM751446 2 0.0000 0.968 0.000 1.000
#> GSM751449 2 0.0000 0.968 0.000 1.000
#> GSM751450 2 0.0000 0.968 0.000 1.000
#> GSM751452 2 0.0000 0.968 0.000 1.000
#> GSM751426 2 0.0000 0.968 0.000 1.000
#> GSM751427 2 0.0000 0.968 0.000 1.000
#> GSM751438 2 0.0000 0.968 0.000 1.000
#> GSM751439 2 0.5629 0.843 0.132 0.868
#> GSM751441 2 0.0000 0.968 0.000 1.000
#> GSM751442 2 0.0000 0.968 0.000 1.000
#> GSM751443 2 0.0000 0.968 0.000 1.000
#> GSM751445 2 0.0000 0.968 0.000 1.000
#> GSM751447 2 0.0000 0.968 0.000 1.000
#> GSM751453 2 0.0000 0.968 0.000 1.000
#> GSM751454 2 0.0000 0.968 0.000 1.000
#> GSM751455 2 0.0000 0.968 0.000 1.000
#> GSM751456 2 0.0000 0.968 0.000 1.000
#> GSM751457 2 0.0000 0.968 0.000 1.000
#> GSM751458 2 0.0000 0.968 0.000 1.000
cbind(get_classes(res, k = 3), get_membership(res, k = 3))
#> class entropy silhouette p1 p2 p3
#> GSM751298 1 0.0000 0.9837 1.000 0.000 0.000
#> GSM751304 2 0.1163 0.9292 0.028 0.972 0.000
#> GSM751305 2 0.1860 0.9075 0.052 0.948 0.000
#> GSM751307 2 0.0000 0.9516 0.000 1.000 0.000
#> GSM751310 1 0.0000 0.9837 1.000 0.000 0.000
#> GSM751314 1 0.0000 0.9837 1.000 0.000 0.000
#> GSM751316 1 0.0000 0.9837 1.000 0.000 0.000
#> GSM751318 1 0.0000 0.9837 1.000 0.000 0.000
#> GSM751342 1 0.0000 0.9837 1.000 0.000 0.000
#> GSM751346 3 0.6111 0.3443 0.396 0.000 0.604
#> GSM751347 3 0.0475 0.9208 0.004 0.004 0.992
#> GSM751348 2 0.0000 0.9516 0.000 1.000 0.000
#> GSM751349 2 0.0000 0.9516 0.000 1.000 0.000
#> GSM751352 2 0.0000 0.9516 0.000 1.000 0.000
#> GSM751353 2 0.0000 0.9516 0.000 1.000 0.000
#> GSM751354 3 0.6008 0.3943 0.000 0.372 0.628
#> GSM751355 2 0.0000 0.9516 0.000 1.000 0.000
#> GSM751358 2 0.8730 0.0398 0.108 0.472 0.420
#> GSM751359 2 0.0000 0.9516 0.000 1.000 0.000
#> GSM751294 3 0.0000 0.9247 0.000 0.000 1.000
#> GSM751296 1 0.0000 0.9837 1.000 0.000 0.000
#> GSM751297 3 0.0000 0.9247 0.000 0.000 1.000
#> GSM751299 2 0.0237 0.9489 0.000 0.996 0.004
#> GSM751300 1 0.0000 0.9837 1.000 0.000 0.000
#> GSM751301 2 0.0000 0.9516 0.000 1.000 0.000
#> GSM751302 1 0.0000 0.9837 1.000 0.000 0.000
#> GSM751303 1 0.0000 0.9837 1.000 0.000 0.000
#> GSM751306 1 0.0000 0.9837 1.000 0.000 0.000
#> GSM751308 3 0.0747 0.9151 0.016 0.000 0.984
#> GSM751309 1 0.0000 0.9837 1.000 0.000 0.000
#> GSM751311 1 0.0000 0.9837 1.000 0.000 0.000
#> GSM751312 1 0.0000 0.9837 1.000 0.000 0.000
#> GSM751313 1 0.0000 0.9837 1.000 0.000 0.000
#> GSM751315 1 0.0000 0.9837 1.000 0.000 0.000
#> GSM751317 1 0.0000 0.9837 1.000 0.000 0.000
#> GSM751320 1 0.0000 0.9837 1.000 0.000 0.000
#> GSM751321 1 0.0000 0.9837 1.000 0.000 0.000
#> GSM751322 1 0.0000 0.9837 1.000 0.000 0.000
#> GSM751324 1 0.0000 0.9837 1.000 0.000 0.000
#> GSM751325 1 0.0000 0.9837 1.000 0.000 0.000
#> GSM751332 1 0.0000 0.9837 1.000 0.000 0.000
#> GSM751334 1 0.0000 0.9837 1.000 0.000 0.000
#> GSM751339 1 0.0237 0.9801 0.996 0.000 0.004
#> GSM751341 1 0.0000 0.9837 1.000 0.000 0.000
#> GSM751343 1 0.0000 0.9837 1.000 0.000 0.000
#> GSM751344 2 0.0000 0.9516 0.000 1.000 0.000
#> GSM751345 2 0.0000 0.9516 0.000 1.000 0.000
#> GSM751356 2 0.6062 0.3719 0.000 0.616 0.384
#> GSM751357 2 0.3619 0.8170 0.000 0.864 0.136
#> GSM751293 2 0.0000 0.9516 0.000 1.000 0.000
#> GSM751295 1 0.0592 0.9728 0.988 0.000 0.012
#> GSM751319 1 0.0000 0.9837 1.000 0.000 0.000
#> GSM751323 1 0.0000 0.9837 1.000 0.000 0.000
#> GSM751326 1 0.0000 0.9837 1.000 0.000 0.000
#> GSM751327 1 0.0000 0.9837 1.000 0.000 0.000
#> GSM751328 1 0.0000 0.9837 1.000 0.000 0.000
#> GSM751329 1 0.0000 0.9837 1.000 0.000 0.000
#> GSM751330 1 0.0000 0.9837 1.000 0.000 0.000
#> GSM751331 1 0.0000 0.9837 1.000 0.000 0.000
#> GSM751333 1 0.0000 0.9837 1.000 0.000 0.000
#> GSM751335 1 0.0000 0.9837 1.000 0.000 0.000
#> GSM751336 1 0.0000 0.9837 1.000 0.000 0.000
#> GSM751337 1 0.0000 0.9837 1.000 0.000 0.000
#> GSM751338 1 0.0000 0.9837 1.000 0.000 0.000
#> GSM751340 1 0.4452 0.7481 0.808 0.000 0.192
#> GSM751350 1 0.0000 0.9837 1.000 0.000 0.000
#> GSM751351 1 0.0000 0.9837 1.000 0.000 0.000
#> GSM751362 3 0.0000 0.9247 0.000 0.000 1.000
#> GSM751363 2 0.4121 0.7792 0.168 0.832 0.000
#> GSM751367 1 0.0424 0.9765 0.992 0.000 0.008
#> GSM751368 2 0.0000 0.9516 0.000 1.000 0.000
#> GSM751371 1 0.0000 0.9837 1.000 0.000 0.000
#> GSM751375 2 0.0000 0.9516 0.000 1.000 0.000
#> GSM751376 3 0.0000 0.9247 0.000 0.000 1.000
#> GSM751378 3 0.3267 0.8240 0.000 0.116 0.884
#> GSM751379 3 0.0000 0.9247 0.000 0.000 1.000
#> GSM751382 2 0.0000 0.9516 0.000 1.000 0.000
#> GSM751386 2 0.0000 0.9516 0.000 1.000 0.000
#> GSM751388 2 0.0000 0.9516 0.000 1.000 0.000
#> GSM751391 3 0.9118 0.4762 0.220 0.232 0.548
#> GSM751410 3 0.0000 0.9247 0.000 0.000 1.000
#> GSM751414 1 0.0000 0.9837 1.000 0.000 0.000
#> GSM751361 2 0.4629 0.7450 0.004 0.808 0.188
#> GSM751365 3 0.1964 0.8851 0.056 0.000 0.944
#> GSM751366 3 0.0237 0.9226 0.004 0.000 0.996
#> GSM751369 3 0.0000 0.9247 0.000 0.000 1.000
#> GSM751370 1 0.6308 -0.0606 0.508 0.000 0.492
#> GSM751372 3 0.0237 0.9226 0.004 0.000 0.996
#> GSM751373 1 0.0000 0.9837 1.000 0.000 0.000
#> GSM751374 3 0.0000 0.9247 0.000 0.000 1.000
#> GSM751377 2 0.0000 0.9516 0.000 1.000 0.000
#> GSM751380 3 0.0000 0.9247 0.000 0.000 1.000
#> GSM751381 2 0.0000 0.9516 0.000 1.000 0.000
#> GSM751383 2 0.0000 0.9516 0.000 1.000 0.000
#> GSM751384 2 0.6291 0.1171 0.000 0.532 0.468
#> GSM751385 2 0.6026 0.3913 0.000 0.624 0.376
#> GSM751387 2 0.0000 0.9516 0.000 1.000 0.000
#> GSM751389 3 0.0000 0.9247 0.000 0.000 1.000
#> GSM751393 3 0.0000 0.9247 0.000 0.000 1.000
#> GSM751394 2 0.0000 0.9516 0.000 1.000 0.000
#> GSM751395 3 0.0237 0.9224 0.000 0.004 0.996
#> GSM751397 2 0.0000 0.9516 0.000 1.000 0.000
#> GSM751398 2 0.0000 0.9516 0.000 1.000 0.000
#> GSM751404 3 0.0000 0.9247 0.000 0.000 1.000
#> GSM751406 3 0.0000 0.9247 0.000 0.000 1.000
#> GSM751411 3 0.0000 0.9247 0.000 0.000 1.000
#> GSM751413 2 0.0000 0.9516 0.000 1.000 0.000
#> GSM751415 3 0.0000 0.9247 0.000 0.000 1.000
#> GSM751416 2 0.1647 0.9211 0.036 0.960 0.004
#> GSM751417 2 0.0592 0.9431 0.000 0.988 0.012
#> GSM751421 3 0.3340 0.8251 0.120 0.000 0.880
#> GSM751422 3 0.2537 0.8645 0.080 0.000 0.920
#> GSM751360 3 0.6154 0.3428 0.408 0.000 0.592
#> GSM751364 3 0.9152 0.0587 0.144 0.424 0.432
#> GSM751390 3 0.6168 0.2810 0.000 0.412 0.588
#> GSM751392 2 0.0000 0.9516 0.000 1.000 0.000
#> GSM751396 2 0.0000 0.9516 0.000 1.000 0.000
#> GSM751399 3 0.0000 0.9247 0.000 0.000 1.000
#> GSM751400 3 0.0000 0.9247 0.000 0.000 1.000
#> GSM751401 3 0.0000 0.9247 0.000 0.000 1.000
#> GSM751402 3 0.0000 0.9247 0.000 0.000 1.000
#> GSM751403 3 0.0000 0.9247 0.000 0.000 1.000
#> GSM751405 3 0.0000 0.9247 0.000 0.000 1.000
#> GSM751407 3 0.0000 0.9247 0.000 0.000 1.000
#> GSM751408 3 0.0000 0.9247 0.000 0.000 1.000
#> GSM751409 3 0.0000 0.9247 0.000 0.000 1.000
#> GSM751412 3 0.0000 0.9247 0.000 0.000 1.000
#> GSM751418 1 0.1711 0.9458 0.960 0.008 0.032
#> GSM751419 3 0.7164 0.1839 0.452 0.024 0.524
#> GSM751420 3 0.0000 0.9247 0.000 0.000 1.000
#> GSM751425 2 0.0000 0.9516 0.000 1.000 0.000
#> GSM751429 3 0.0592 0.9172 0.012 0.000 0.988
#> GSM751430 2 0.0000 0.9516 0.000 1.000 0.000
#> GSM751433 2 0.0000 0.9516 0.000 1.000 0.000
#> GSM751437 3 0.0000 0.9247 0.000 0.000 1.000
#> GSM751448 3 0.0000 0.9247 0.000 0.000 1.000
#> GSM751451 2 0.0237 0.9488 0.004 0.996 0.000
#> GSM751423 2 0.0000 0.9516 0.000 1.000 0.000
#> GSM751424 2 0.0000 0.9516 0.000 1.000 0.000
#> GSM751428 2 0.0000 0.9516 0.000 1.000 0.000
#> GSM751431 2 0.0000 0.9516 0.000 1.000 0.000
#> GSM751432 2 0.0000 0.9516 0.000 1.000 0.000
#> GSM751434 2 0.0000 0.9516 0.000 1.000 0.000
#> GSM751435 2 0.0000 0.9516 0.000 1.000 0.000
#> GSM751436 2 0.0000 0.9516 0.000 1.000 0.000
#> GSM751440 2 0.0000 0.9516 0.000 1.000 0.000
#> GSM751444 2 0.0000 0.9516 0.000 1.000 0.000
#> GSM751446 2 0.0000 0.9516 0.000 1.000 0.000
#> GSM751449 2 0.6192 0.2634 0.000 0.580 0.420
#> GSM751450 2 0.0000 0.9516 0.000 1.000 0.000
#> GSM751452 2 0.0000 0.9516 0.000 1.000 0.000
#> GSM751426 2 0.0000 0.9516 0.000 1.000 0.000
#> GSM751427 2 0.0000 0.9516 0.000 1.000 0.000
#> GSM751438 3 0.3752 0.7893 0.000 0.144 0.856
#> GSM751439 3 0.0000 0.9247 0.000 0.000 1.000
#> GSM751441 2 0.0000 0.9516 0.000 1.000 0.000
#> GSM751442 2 0.1031 0.9337 0.000 0.976 0.024
#> GSM751443 3 0.0000 0.9247 0.000 0.000 1.000
#> GSM751445 2 0.0000 0.9516 0.000 1.000 0.000
#> GSM751447 2 0.0000 0.9516 0.000 1.000 0.000
#> GSM751453 2 0.0000 0.9516 0.000 1.000 0.000
#> GSM751454 2 0.0000 0.9516 0.000 1.000 0.000
#> GSM751455 2 0.1411 0.9236 0.000 0.964 0.036
#> GSM751456 2 0.2711 0.8733 0.000 0.912 0.088
#> GSM751457 3 0.0000 0.9247 0.000 0.000 1.000
#> GSM751458 3 0.0000 0.9247 0.000 0.000 1.000
cbind(get_classes(res, k = 4), get_membership(res, k = 4))
#> class entropy silhouette p1 p2 p3 p4
#> GSM751298 4 0.4948 0.06717 0.440 0.000 0.000 0.560
#> GSM751304 2 0.7225 0.49591 0.208 0.628 0.128 0.036
#> GSM751305 2 0.7608 0.37506 0.312 0.544 0.108 0.036
#> GSM751307 2 0.1389 0.84309 0.000 0.952 0.000 0.048
#> GSM751310 1 0.0592 0.80266 0.984 0.000 0.000 0.016
#> GSM751314 1 0.0188 0.80416 0.996 0.000 0.000 0.004
#> GSM751316 1 0.0000 0.80354 1.000 0.000 0.000 0.000
#> GSM751318 1 0.0000 0.80354 1.000 0.000 0.000 0.000
#> GSM751342 1 0.0000 0.80354 1.000 0.000 0.000 0.000
#> GSM751346 4 0.2214 0.55066 0.044 0.000 0.028 0.928
#> GSM751347 4 0.1716 0.52748 0.000 0.000 0.064 0.936
#> GSM751348 2 0.2522 0.83920 0.016 0.920 0.012 0.052
#> GSM751349 2 0.1406 0.84272 0.000 0.960 0.024 0.016
#> GSM751352 2 0.1389 0.84537 0.000 0.952 0.000 0.048
#> GSM751353 2 0.1022 0.84598 0.000 0.968 0.000 0.032
#> GSM751354 4 0.5565 0.32625 0.000 0.232 0.068 0.700
#> GSM751355 2 0.1389 0.84401 0.000 0.952 0.000 0.048
#> GSM751358 3 0.6548 0.40901 0.336 0.064 0.588 0.012
#> GSM751359 3 0.5774 -0.15422 0.004 0.480 0.496 0.020
#> GSM751294 3 0.4920 0.39497 0.004 0.000 0.628 0.368
#> GSM751296 4 0.4277 0.41120 0.280 0.000 0.000 0.720
#> GSM751297 4 0.2469 0.50952 0.000 0.000 0.108 0.892
#> GSM751299 2 0.4843 0.51074 0.000 0.604 0.000 0.396
#> GSM751300 4 0.4585 0.33276 0.332 0.000 0.000 0.668
#> GSM751301 2 0.1474 0.84186 0.000 0.948 0.000 0.052
#> GSM751302 4 0.3801 0.46980 0.220 0.000 0.000 0.780
#> GSM751303 1 0.0000 0.80354 1.000 0.000 0.000 0.000
#> GSM751306 1 0.0000 0.80354 1.000 0.000 0.000 0.000
#> GSM751308 4 0.7660 0.00446 0.276 0.000 0.260 0.464
#> GSM751309 1 0.0000 0.80354 1.000 0.000 0.000 0.000
#> GSM751311 1 0.0000 0.80354 1.000 0.000 0.000 0.000
#> GSM751312 1 0.1389 0.79184 0.952 0.000 0.000 0.048
#> GSM751313 1 0.4967 0.24215 0.548 0.000 0.000 0.452
#> GSM751315 1 0.1389 0.79285 0.952 0.000 0.000 0.048
#> GSM751317 1 0.0000 0.80354 1.000 0.000 0.000 0.000
#> GSM751320 1 0.2589 0.75554 0.884 0.000 0.000 0.116
#> GSM751321 1 0.2814 0.74016 0.868 0.000 0.000 0.132
#> GSM751322 1 0.0188 0.80416 0.996 0.000 0.000 0.004
#> GSM751324 1 0.0188 0.80416 0.996 0.000 0.000 0.004
#> GSM751325 1 0.0336 0.80400 0.992 0.000 0.000 0.008
#> GSM751332 1 0.3801 0.65702 0.780 0.000 0.000 0.220
#> GSM751334 1 0.3610 0.67921 0.800 0.000 0.000 0.200
#> GSM751339 1 0.0817 0.79150 0.976 0.000 0.000 0.024
#> GSM751341 4 0.4643 0.31222 0.344 0.000 0.000 0.656
#> GSM751343 1 0.0188 0.80416 0.996 0.000 0.000 0.004
#> GSM751344 2 0.1118 0.84479 0.000 0.964 0.000 0.036
#> GSM751345 2 0.1118 0.84479 0.000 0.964 0.000 0.036
#> GSM751356 3 0.9714 0.33225 0.204 0.248 0.368 0.180
#> GSM751357 2 0.7527 0.52359 0.072 0.624 0.196 0.108
#> GSM751293 2 0.1389 0.84550 0.000 0.952 0.000 0.048
#> GSM751295 4 0.2760 0.53494 0.128 0.000 0.000 0.872
#> GSM751319 1 0.0469 0.80351 0.988 0.000 0.000 0.012
#> GSM751323 1 0.2760 0.74493 0.872 0.000 0.000 0.128
#> GSM751326 1 0.5000 0.08916 0.500 0.000 0.000 0.500
#> GSM751327 1 0.2281 0.76613 0.904 0.000 0.000 0.096
#> GSM751328 1 0.3801 0.65618 0.780 0.000 0.000 0.220
#> GSM751329 1 0.4250 0.58401 0.724 0.000 0.000 0.276
#> GSM751330 1 0.4941 0.28495 0.564 0.000 0.000 0.436
#> GSM751331 4 0.4948 0.05609 0.440 0.000 0.000 0.560
#> GSM751333 1 0.4948 0.27492 0.560 0.000 0.000 0.440
#> GSM751335 1 0.4830 0.38461 0.608 0.000 0.000 0.392
#> GSM751336 4 0.4961 0.04303 0.448 0.000 0.000 0.552
#> GSM751337 4 0.4955 0.05685 0.444 0.000 0.000 0.556
#> GSM751338 1 0.0188 0.80416 0.996 0.000 0.000 0.004
#> GSM751340 1 0.2670 0.72421 0.904 0.000 0.024 0.072
#> GSM751350 4 0.4193 0.42002 0.268 0.000 0.000 0.732
#> GSM751351 4 0.4624 0.31179 0.340 0.000 0.000 0.660
#> GSM751362 3 0.4406 0.46226 0.000 0.000 0.700 0.300
#> GSM751363 1 0.7677 0.12020 0.524 0.116 0.328 0.032
#> GSM751367 4 0.4855 0.28952 0.352 0.000 0.004 0.644
#> GSM751368 2 0.3606 0.76991 0.000 0.840 0.140 0.020
#> GSM751371 1 0.0336 0.79903 0.992 0.000 0.008 0.000
#> GSM751375 2 0.1042 0.84387 0.000 0.972 0.020 0.008
#> GSM751376 3 0.4916 0.27442 0.000 0.000 0.576 0.424
#> GSM751378 3 0.2546 0.59871 0.000 0.092 0.900 0.008
#> GSM751379 4 0.4981 -0.02102 0.000 0.000 0.464 0.536
#> GSM751382 2 0.2300 0.82677 0.000 0.920 0.064 0.016
#> GSM751386 2 0.4950 0.45300 0.000 0.620 0.376 0.004
#> GSM751388 2 0.4720 0.54849 0.000 0.672 0.324 0.004
#> GSM751391 1 0.6929 0.43673 0.676 0.128 0.144 0.052
#> GSM751410 3 0.5994 0.49822 0.156 0.000 0.692 0.152
#> GSM751414 1 0.4353 0.54683 0.756 0.000 0.232 0.012
#> GSM751361 3 0.6547 0.46193 0.296 0.084 0.612 0.008
#> GSM751365 3 0.3498 0.58301 0.160 0.008 0.832 0.000
#> GSM751366 3 0.2623 0.60543 0.064 0.000 0.908 0.028
#> GSM751369 3 0.4605 0.42554 0.000 0.000 0.664 0.336
#> GSM751370 3 0.4718 0.53427 0.216 0.004 0.756 0.024
#> GSM751372 3 0.0992 0.62237 0.008 0.004 0.976 0.012
#> GSM751373 1 0.3795 0.74148 0.856 0.004 0.060 0.080
#> GSM751374 4 0.4907 0.11097 0.000 0.000 0.420 0.580
#> GSM751377 2 0.5229 0.33803 0.000 0.564 0.428 0.008
#> GSM751380 3 0.5458 0.48779 0.076 0.000 0.720 0.204
#> GSM751381 2 0.5204 0.45718 0.000 0.612 0.376 0.012
#> GSM751383 2 0.5060 0.37985 0.000 0.584 0.412 0.004
#> GSM751384 3 0.4086 0.53189 0.000 0.216 0.776 0.008
#> GSM751385 3 0.5492 0.32747 0.000 0.328 0.640 0.032
#> GSM751387 2 0.4999 0.54364 0.000 0.660 0.328 0.012
#> GSM751389 3 0.4605 0.41972 0.000 0.000 0.664 0.336
#> GSM751393 3 0.1489 0.62219 0.000 0.004 0.952 0.044
#> GSM751394 2 0.4391 0.64681 0.000 0.740 0.252 0.008
#> GSM751395 3 0.4137 0.57501 0.000 0.012 0.780 0.208
#> GSM751397 3 0.5388 -0.04538 0.000 0.456 0.532 0.012
#> GSM751398 3 0.5511 -0.15203 0.000 0.484 0.500 0.016
#> GSM751404 3 0.3837 0.53775 0.000 0.000 0.776 0.224
#> GSM751406 3 0.4624 0.41120 0.000 0.000 0.660 0.340
#> GSM751411 3 0.0336 0.62046 0.000 0.008 0.992 0.000
#> GSM751413 2 0.1452 0.84485 0.000 0.956 0.008 0.036
#> GSM751415 3 0.2589 0.59924 0.000 0.000 0.884 0.116
#> GSM751416 3 0.7038 0.46017 0.248 0.148 0.596 0.008
#> GSM751417 3 0.6809 0.44480 0.152 0.228 0.616 0.004
#> GSM751421 3 0.5742 0.42598 0.300 0.000 0.648 0.052
#> GSM751422 3 0.4464 0.56648 0.208 0.000 0.768 0.024
#> GSM751360 3 0.5214 0.45496 0.336 0.004 0.648 0.012
#> GSM751364 3 0.5431 0.53091 0.224 0.064 0.712 0.000
#> GSM751390 3 0.3810 0.55095 0.000 0.188 0.804 0.008
#> GSM751392 2 0.4770 0.60042 0.000 0.700 0.288 0.012
#> GSM751396 2 0.1151 0.84336 0.000 0.968 0.024 0.008
#> GSM751399 3 0.0707 0.62125 0.000 0.000 0.980 0.020
#> GSM751400 3 0.3688 0.54840 0.000 0.000 0.792 0.208
#> GSM751401 3 0.4543 0.43540 0.000 0.000 0.676 0.324
#> GSM751402 3 0.4843 0.30528 0.000 0.000 0.604 0.396
#> GSM751403 3 0.3837 0.53839 0.000 0.000 0.776 0.224
#> GSM751405 3 0.4477 0.44991 0.000 0.000 0.688 0.312
#> GSM751407 3 0.2814 0.59255 0.000 0.000 0.868 0.132
#> GSM751408 3 0.0592 0.62143 0.000 0.000 0.984 0.016
#> GSM751409 3 0.1022 0.62027 0.000 0.000 0.968 0.032
#> GSM751412 3 0.0336 0.62136 0.000 0.000 0.992 0.008
#> GSM751418 3 0.6928 0.41121 0.268 0.024 0.616 0.092
#> GSM751419 3 0.4225 0.56759 0.184 0.024 0.792 0.000
#> GSM751420 4 0.4989 0.00753 0.000 0.000 0.472 0.528
#> GSM751425 2 0.1411 0.84325 0.000 0.960 0.020 0.020
#> GSM751429 4 0.2760 0.49302 0.000 0.000 0.128 0.872
#> GSM751430 2 0.1118 0.84479 0.000 0.964 0.000 0.036
#> GSM751433 2 0.0927 0.84665 0.000 0.976 0.008 0.016
#> GSM751437 3 0.4961 0.18454 0.000 0.000 0.552 0.448
#> GSM751448 4 0.4866 0.16795 0.000 0.000 0.404 0.596
#> GSM751451 1 0.6749 -0.10139 0.468 0.464 0.048 0.020
#> GSM751423 2 0.1411 0.84325 0.000 0.960 0.020 0.020
#> GSM751424 2 0.0921 0.84574 0.000 0.972 0.000 0.028
#> GSM751428 2 0.1211 0.84614 0.000 0.960 0.000 0.040
#> GSM751431 2 0.1042 0.84511 0.000 0.972 0.008 0.020
#> GSM751432 2 0.0921 0.84574 0.000 0.972 0.000 0.028
#> GSM751434 2 0.0921 0.84574 0.000 0.972 0.000 0.028
#> GSM751435 2 0.2760 0.80413 0.000 0.872 0.000 0.128
#> GSM751436 2 0.1151 0.84627 0.000 0.968 0.008 0.024
#> GSM751440 2 0.1820 0.84208 0.000 0.944 0.020 0.036
#> GSM751444 2 0.2011 0.83188 0.000 0.920 0.000 0.080
#> GSM751446 2 0.2216 0.82294 0.000 0.908 0.000 0.092
#> GSM751449 2 0.6745 0.19479 0.000 0.480 0.092 0.428
#> GSM751450 2 0.1042 0.84511 0.000 0.972 0.008 0.020
#> GSM751452 2 0.0921 0.84574 0.000 0.972 0.000 0.028
#> GSM751426 2 0.0779 0.84699 0.000 0.980 0.004 0.016
#> GSM751427 2 0.2843 0.82676 0.000 0.892 0.020 0.088
#> GSM751438 4 0.6506 0.27119 0.000 0.132 0.240 0.628
#> GSM751439 4 0.4420 0.37514 0.000 0.012 0.240 0.748
#> GSM751441 2 0.2011 0.82828 0.000 0.920 0.000 0.080
#> GSM751442 2 0.5112 0.46559 0.000 0.608 0.008 0.384
#> GSM751443 4 0.4585 0.27565 0.000 0.000 0.332 0.668
#> GSM751445 2 0.2011 0.83188 0.000 0.920 0.000 0.080
#> GSM751447 2 0.1474 0.83902 0.000 0.948 0.000 0.052
#> GSM751453 2 0.1211 0.84456 0.000 0.960 0.000 0.040
#> GSM751454 2 0.1118 0.84299 0.000 0.964 0.000 0.036
#> GSM751455 2 0.4328 0.68528 0.000 0.748 0.008 0.244
#> GSM751456 2 0.5016 0.46087 0.000 0.600 0.004 0.396
#> GSM751457 4 0.5838 -0.04326 0.000 0.032 0.444 0.524
#> GSM751458 3 0.5696 0.13447 0.000 0.024 0.496 0.480
cbind(get_classes(res, k = 5), get_membership(res, k = 5))
#> class entropy silhouette p1 p2 p3 p4 p5
#> GSM751298 1 0.2471 0.86789 0.864 0.000 0.000 0.136 0.000
#> GSM751304 2 0.5863 0.22130 0.012 0.588 0.048 0.336 0.016
#> GSM751305 4 0.5895 0.19197 0.012 0.448 0.036 0.488 0.016
#> GSM751307 2 0.1538 0.70362 0.036 0.948 0.008 0.000 0.008
#> GSM751310 4 0.3053 0.64728 0.164 0.000 0.000 0.828 0.008
#> GSM751314 4 0.1124 0.76612 0.036 0.000 0.000 0.960 0.004
#> GSM751316 4 0.0451 0.77893 0.004 0.000 0.000 0.988 0.008
#> GSM751318 4 0.0000 0.77909 0.000 0.000 0.000 1.000 0.000
#> GSM751342 4 0.0290 0.77786 0.000 0.000 0.008 0.992 0.000
#> GSM751346 1 0.2411 0.79958 0.884 0.000 0.108 0.008 0.000
#> GSM751347 1 0.2074 0.79652 0.896 0.000 0.104 0.000 0.000
#> GSM751348 2 0.9429 0.43596 0.096 0.308 0.264 0.220 0.112
#> GSM751349 2 0.5957 0.70128 0.084 0.684 0.084 0.000 0.148
#> GSM751352 2 0.2284 0.69742 0.020 0.920 0.044 0.004 0.012
#> GSM751353 2 0.1854 0.71703 0.008 0.936 0.020 0.000 0.036
#> GSM751354 2 0.5790 -0.07070 0.048 0.508 0.424 0.000 0.020
#> GSM751355 2 0.1074 0.71383 0.004 0.968 0.016 0.000 0.012
#> GSM751358 4 0.4360 0.67148 0.028 0.000 0.052 0.792 0.128
#> GSM751359 5 0.6650 0.22605 0.024 0.336 0.088 0.016 0.536
#> GSM751294 3 0.3182 0.70566 0.028 0.004 0.864 0.008 0.096
#> GSM751296 1 0.2304 0.86987 0.892 0.000 0.008 0.100 0.000
#> GSM751297 1 0.3884 0.54549 0.708 0.000 0.288 0.000 0.004
#> GSM751299 2 0.6184 0.49071 0.088 0.576 0.312 0.004 0.020
#> GSM751300 1 0.2074 0.87016 0.896 0.000 0.000 0.104 0.000
#> GSM751301 2 0.1898 0.70234 0.016 0.940 0.024 0.008 0.012
#> GSM751302 1 0.2585 0.85448 0.896 0.004 0.036 0.064 0.000
#> GSM751303 4 0.0324 0.77907 0.004 0.000 0.000 0.992 0.004
#> GSM751306 4 0.0451 0.77868 0.008 0.000 0.000 0.988 0.004
#> GSM751308 4 0.5730 0.24937 0.032 0.000 0.404 0.532 0.032
#> GSM751309 4 0.0324 0.77907 0.004 0.000 0.000 0.992 0.004
#> GSM751311 4 0.0162 0.77892 0.004 0.000 0.000 0.996 0.000
#> GSM751312 4 0.3430 0.57186 0.220 0.000 0.000 0.776 0.004
#> GSM751313 1 0.2813 0.85773 0.832 0.000 0.000 0.168 0.000
#> GSM751315 4 0.4249 -0.01319 0.432 0.000 0.000 0.568 0.000
#> GSM751317 4 0.0451 0.77893 0.004 0.000 0.000 0.988 0.008
#> GSM751320 4 0.4297 -0.17677 0.472 0.000 0.000 0.528 0.000
#> GSM751321 4 0.3730 0.44050 0.288 0.000 0.000 0.712 0.000
#> GSM751322 4 0.0404 0.77771 0.012 0.000 0.000 0.988 0.000
#> GSM751324 4 0.0404 0.77771 0.012 0.000 0.000 0.988 0.000
#> GSM751325 4 0.0404 0.77771 0.012 0.000 0.000 0.988 0.000
#> GSM751332 1 0.3612 0.75712 0.732 0.000 0.000 0.268 0.000
#> GSM751334 1 0.3983 0.64632 0.660 0.000 0.000 0.340 0.000
#> GSM751339 4 0.1442 0.76956 0.012 0.000 0.032 0.952 0.004
#> GSM751341 1 0.4700 0.77981 0.728 0.000 0.088 0.184 0.000
#> GSM751343 4 0.0290 0.77846 0.008 0.000 0.000 0.992 0.000
#> GSM751344 2 0.1667 0.70264 0.012 0.948 0.024 0.004 0.012
#> GSM751345 2 0.1667 0.70264 0.012 0.948 0.024 0.004 0.012
#> GSM751356 4 0.7559 0.26077 0.076 0.044 0.352 0.472 0.056
#> GSM751357 3 0.8551 -0.13005 0.072 0.140 0.364 0.360 0.064
#> GSM751293 2 0.1988 0.70377 0.016 0.936 0.028 0.008 0.012
#> GSM751295 1 0.2520 0.84265 0.896 0.000 0.056 0.048 0.000
#> GSM751319 4 0.0898 0.77554 0.020 0.000 0.000 0.972 0.008
#> GSM751323 4 0.3508 0.51083 0.252 0.000 0.000 0.748 0.000
#> GSM751326 1 0.2605 0.86450 0.852 0.000 0.000 0.148 0.000
#> GSM751327 4 0.2074 0.71316 0.104 0.000 0.000 0.896 0.000
#> GSM751328 1 0.4171 0.53509 0.604 0.000 0.000 0.396 0.000
#> GSM751329 1 0.3242 0.81717 0.784 0.000 0.000 0.216 0.000
#> GSM751330 1 0.2852 0.85282 0.828 0.000 0.000 0.172 0.000
#> GSM751331 1 0.3176 0.84863 0.856 0.064 0.000 0.080 0.000
#> GSM751333 1 0.2773 0.85768 0.836 0.000 0.000 0.164 0.000
#> GSM751335 1 0.2891 0.84995 0.824 0.000 0.000 0.176 0.000
#> GSM751336 1 0.2280 0.87011 0.880 0.000 0.000 0.120 0.000
#> GSM751337 1 0.2516 0.86895 0.860 0.000 0.000 0.140 0.000
#> GSM751338 4 0.0510 0.77782 0.016 0.000 0.000 0.984 0.000
#> GSM751340 4 0.2796 0.72966 0.008 0.000 0.116 0.868 0.008
#> GSM751350 1 0.2351 0.86569 0.896 0.000 0.016 0.088 0.000
#> GSM751351 1 0.2408 0.87007 0.892 0.008 0.004 0.096 0.000
#> GSM751362 3 0.4323 0.64873 0.012 0.000 0.656 0.000 0.332
#> GSM751363 5 0.6328 0.41339 0.016 0.404 0.004 0.088 0.488
#> GSM751367 1 0.3110 0.85141 0.876 0.044 0.020 0.060 0.000
#> GSM751368 2 0.4738 0.00182 0.004 0.564 0.000 0.012 0.420
#> GSM751371 4 0.0324 0.77868 0.000 0.000 0.004 0.992 0.004
#> GSM751375 2 0.5268 0.70021 0.044 0.728 0.072 0.000 0.156
#> GSM751376 3 0.3963 0.72720 0.028 0.004 0.788 0.004 0.176
#> GSM751378 5 0.3739 0.59250 0.020 0.024 0.136 0.000 0.820
#> GSM751379 3 0.4933 0.71722 0.048 0.056 0.756 0.000 0.140
#> GSM751382 2 0.6712 0.18632 0.052 0.436 0.080 0.000 0.432
#> GSM751386 5 0.4552 0.58292 0.004 0.240 0.040 0.000 0.716
#> GSM751388 5 0.5079 0.54971 0.012 0.236 0.060 0.000 0.692
#> GSM751391 4 0.3187 0.73209 0.012 0.016 0.084 0.872 0.016
#> GSM751410 4 0.6792 -0.17719 0.004 0.000 0.364 0.404 0.228
#> GSM751414 5 0.5045 0.43937 0.056 0.000 0.000 0.308 0.636
#> GSM751361 5 0.4805 0.56640 0.004 0.032 0.008 0.260 0.696
#> GSM751365 5 0.3213 0.61488 0.000 0.004 0.064 0.072 0.860
#> GSM751366 5 0.3612 0.51017 0.004 0.000 0.184 0.016 0.796
#> GSM751369 3 0.4231 0.71629 0.016 0.000 0.740 0.012 0.232
#> GSM751370 5 0.4143 0.60225 0.048 0.000 0.060 0.072 0.820
#> GSM751372 5 0.2674 0.56442 0.000 0.000 0.140 0.004 0.856
#> GSM751373 5 0.6889 0.17591 0.192 0.016 0.000 0.340 0.452
#> GSM751374 3 0.5084 0.71382 0.052 0.064 0.748 0.000 0.136
#> GSM751377 5 0.4217 0.60981 0.012 0.244 0.012 0.000 0.732
#> GSM751380 3 0.4897 0.60295 0.004 0.000 0.616 0.028 0.352
#> GSM751381 5 0.5155 0.54145 0.016 0.216 0.068 0.000 0.700
#> GSM751383 5 0.4544 0.60081 0.012 0.208 0.040 0.000 0.740
#> GSM751384 5 0.2676 0.66459 0.000 0.080 0.036 0.000 0.884
#> GSM751385 5 0.4906 0.60859 0.008 0.292 0.036 0.000 0.664
#> GSM751387 5 0.5156 0.54380 0.020 0.220 0.060 0.000 0.700
#> GSM751389 3 0.4026 0.71411 0.020 0.000 0.736 0.000 0.244
#> GSM751393 5 0.4560 -0.29247 0.000 0.008 0.484 0.000 0.508
#> GSM751394 5 0.5274 0.49970 0.020 0.268 0.048 0.000 0.664
#> GSM751395 3 0.6659 0.57028 0.012 0.204 0.560 0.008 0.216
#> GSM751397 5 0.4078 0.62397 0.004 0.180 0.040 0.000 0.776
#> GSM751398 5 0.3550 0.63637 0.000 0.236 0.004 0.000 0.760
#> GSM751404 5 0.4150 0.04719 0.000 0.000 0.388 0.000 0.612
#> GSM751406 3 0.4276 0.71424 0.032 0.000 0.724 0.000 0.244
#> GSM751411 5 0.2377 0.57637 0.000 0.000 0.128 0.000 0.872
#> GSM751413 2 0.2053 0.69394 0.012 0.932 0.024 0.004 0.028
#> GSM751415 3 0.4302 0.35421 0.000 0.000 0.520 0.000 0.480
#> GSM751416 5 0.4873 0.66617 0.004 0.140 0.012 0.092 0.752
#> GSM751417 5 0.4759 0.66872 0.004 0.156 0.012 0.072 0.756
#> GSM751421 4 0.6087 0.27956 0.000 0.000 0.160 0.552 0.288
#> GSM751422 4 0.6127 0.26535 0.000 0.000 0.152 0.532 0.316
#> GSM751360 4 0.4219 0.54647 0.004 0.000 0.016 0.716 0.264
#> GSM751364 5 0.3706 0.66162 0.000 0.064 0.020 0.076 0.840
#> GSM751390 5 0.2236 0.66609 0.000 0.068 0.024 0.000 0.908
#> GSM751392 5 0.5459 0.49967 0.028 0.240 0.060 0.000 0.672
#> GSM751396 2 0.5782 0.41329 0.032 0.580 0.044 0.000 0.344
#> GSM751399 5 0.3003 0.51486 0.000 0.000 0.188 0.000 0.812
#> GSM751400 5 0.4118 0.19781 0.004 0.000 0.336 0.000 0.660
#> GSM751401 3 0.4610 0.55834 0.016 0.000 0.596 0.000 0.388
#> GSM751402 3 0.4536 0.71483 0.048 0.000 0.712 0.000 0.240
#> GSM751403 3 0.3895 0.65697 0.000 0.000 0.680 0.000 0.320
#> GSM751405 3 0.4181 0.70082 0.020 0.000 0.712 0.000 0.268
#> GSM751407 5 0.3424 0.43587 0.000 0.000 0.240 0.000 0.760
#> GSM751408 5 0.2648 0.55600 0.000 0.000 0.152 0.000 0.848
#> GSM751409 5 0.3274 0.46844 0.000 0.000 0.220 0.000 0.780
#> GSM751412 5 0.2561 0.56348 0.000 0.000 0.144 0.000 0.856
#> GSM751418 5 0.4960 0.63047 0.108 0.028 0.020 0.068 0.776
#> GSM751419 5 0.3302 0.64049 0.000 0.020 0.044 0.072 0.864
#> GSM751420 3 0.4714 0.72092 0.084 0.000 0.724 0.000 0.192
#> GSM751425 2 0.6051 0.70922 0.084 0.680 0.108 0.000 0.128
#> GSM751429 1 0.4045 0.42955 0.644 0.000 0.356 0.000 0.000
#> GSM751430 2 0.0854 0.71254 0.004 0.976 0.008 0.000 0.012
#> GSM751433 2 0.2627 0.72347 0.020 0.908 0.008 0.024 0.040
#> GSM751437 3 0.4017 0.72646 0.064 0.000 0.788 0.000 0.148
#> GSM751448 3 0.4558 0.72250 0.088 0.000 0.744 0.000 0.168
#> GSM751451 4 0.6059 0.57845 0.080 0.048 0.068 0.720 0.084
#> GSM751423 2 0.5918 0.70978 0.088 0.692 0.096 0.000 0.124
#> GSM751424 2 0.0609 0.72048 0.000 0.980 0.000 0.000 0.020
#> GSM751428 2 0.0981 0.72342 0.012 0.972 0.008 0.000 0.008
#> GSM751431 2 0.5568 0.71740 0.072 0.720 0.096 0.000 0.112
#> GSM751432 2 0.0290 0.71891 0.000 0.992 0.000 0.000 0.008
#> GSM751434 2 0.0162 0.71829 0.000 0.996 0.000 0.000 0.004
#> GSM751435 2 0.6952 0.68832 0.096 0.576 0.216 0.000 0.112
#> GSM751436 2 0.1116 0.72196 0.004 0.964 0.004 0.000 0.028
#> GSM751440 2 0.7018 0.69578 0.092 0.588 0.192 0.004 0.124
#> GSM751444 2 0.6364 0.69036 0.088 0.628 0.212 0.000 0.072
#> GSM751446 2 0.7083 0.67393 0.092 0.552 0.240 0.000 0.116
#> GSM751449 3 0.7445 -0.42552 0.092 0.352 0.440 0.000 0.116
#> GSM751450 2 0.4772 0.73255 0.072 0.780 0.068 0.000 0.080
#> GSM751452 2 0.0771 0.72110 0.000 0.976 0.004 0.000 0.020
#> GSM751426 2 0.4956 0.72360 0.068 0.764 0.060 0.000 0.108
#> GSM751427 2 0.7160 0.67665 0.096 0.548 0.232 0.000 0.124
#> GSM751438 3 0.5930 0.27857 0.092 0.100 0.692 0.000 0.116
#> GSM751439 3 0.4037 0.58168 0.152 0.012 0.796 0.000 0.040
#> GSM751441 2 0.7043 0.67220 0.092 0.556 0.240 0.000 0.112
#> GSM751442 2 0.7325 0.65831 0.092 0.528 0.260 0.004 0.116
#> GSM751443 3 0.2574 0.66633 0.112 0.000 0.876 0.000 0.012
#> GSM751445 2 0.6475 0.67085 0.088 0.600 0.248 0.000 0.064
#> GSM751447 2 0.6978 0.68233 0.092 0.568 0.228 0.000 0.112
#> GSM751453 2 0.6267 0.71231 0.088 0.660 0.140 0.000 0.112
#> GSM751454 2 0.6825 0.69604 0.088 0.592 0.204 0.000 0.116
#> GSM751455 2 0.7186 0.65218 0.088 0.524 0.272 0.000 0.116
#> GSM751456 2 0.7217 0.64513 0.088 0.516 0.280 0.000 0.116
#> GSM751457 3 0.2483 0.60582 0.048 0.028 0.908 0.000 0.016
#> GSM751458 3 0.2395 0.63158 0.048 0.024 0.912 0.000 0.016
cbind(get_classes(res, k = 6), get_membership(res, k = 6))
#> class entropy silhouette p1 p2 p3 p4 p5 p6
#> GSM751298 1 0.0436 0.917 0.988 0.004 0.000 0.004 0.000 0.004
#> GSM751304 6 0.2053 0.759 0.000 0.000 0.004 0.108 0.000 0.888
#> GSM751305 6 0.1958 0.764 0.000 0.000 0.004 0.100 0.000 0.896
#> GSM751307 6 0.2231 0.807 0.028 0.048 0.000 0.000 0.016 0.908
#> GSM751310 4 0.2886 0.770 0.144 0.000 0.000 0.836 0.016 0.004
#> GSM751314 4 0.1096 0.859 0.008 0.004 0.000 0.964 0.020 0.004
#> GSM751316 4 0.0603 0.856 0.000 0.000 0.000 0.980 0.004 0.016
#> GSM751318 4 0.0951 0.858 0.000 0.004 0.000 0.968 0.020 0.008
#> GSM751342 4 0.1218 0.857 0.000 0.004 0.000 0.956 0.028 0.012
#> GSM751346 1 0.0547 0.913 0.980 0.000 0.020 0.000 0.000 0.000
#> GSM751347 1 0.0000 0.920 1.000 0.000 0.000 0.000 0.000 0.000
#> GSM751348 2 0.3972 0.732 0.000 0.792 0.000 0.104 0.024 0.080
#> GSM751349 2 0.3053 0.757 0.000 0.812 0.000 0.000 0.168 0.020
#> GSM751352 6 0.0982 0.797 0.004 0.020 0.004 0.000 0.004 0.968
#> GSM751353 6 0.2398 0.794 0.000 0.104 0.000 0.000 0.020 0.876
#> GSM751354 6 0.1269 0.783 0.020 0.012 0.012 0.000 0.000 0.956
#> GSM751355 6 0.1151 0.805 0.000 0.032 0.000 0.000 0.012 0.956
#> GSM751358 4 0.1225 0.844 0.000 0.000 0.012 0.952 0.000 0.036
#> GSM751359 5 0.4472 0.708 0.000 0.124 0.008 0.004 0.740 0.124
#> GSM751294 3 0.3801 0.759 0.000 0.040 0.788 0.020 0.000 0.152
#> GSM751296 1 0.0551 0.917 0.984 0.004 0.008 0.000 0.000 0.004
#> GSM751297 1 0.2877 0.764 0.820 0.000 0.168 0.000 0.000 0.012
#> GSM751299 6 0.4451 0.532 0.000 0.248 0.072 0.000 0.000 0.680
#> GSM751300 1 0.0000 0.920 1.000 0.000 0.000 0.000 0.000 0.000
#> GSM751301 6 0.1863 0.809 0.004 0.060 0.000 0.000 0.016 0.920
#> GSM751302 1 0.0000 0.920 1.000 0.000 0.000 0.000 0.000 0.000
#> GSM751303 4 0.0363 0.859 0.000 0.000 0.000 0.988 0.012 0.000
#> GSM751306 4 0.0547 0.859 0.000 0.000 0.000 0.980 0.020 0.000
#> GSM751308 4 0.5311 0.214 0.000 0.032 0.396 0.528 0.000 0.044
#> GSM751309 4 0.0603 0.859 0.000 0.004 0.000 0.980 0.016 0.000
#> GSM751311 4 0.1116 0.858 0.000 0.004 0.000 0.960 0.028 0.008
#> GSM751312 4 0.3121 0.742 0.180 0.000 0.000 0.804 0.004 0.012
#> GSM751313 1 0.0146 0.919 0.996 0.000 0.000 0.004 0.000 0.000
#> GSM751315 1 0.4161 0.177 0.540 0.000 0.000 0.448 0.012 0.000
#> GSM751317 4 0.0291 0.858 0.000 0.000 0.000 0.992 0.004 0.004
#> GSM751320 1 0.4396 0.481 0.636 0.004 0.000 0.332 0.024 0.004
#> GSM751321 4 0.3938 0.494 0.324 0.000 0.000 0.660 0.016 0.000
#> GSM751322 4 0.1116 0.857 0.000 0.004 0.000 0.960 0.028 0.008
#> GSM751324 4 0.1116 0.857 0.000 0.004 0.000 0.960 0.028 0.008
#> GSM751325 4 0.1218 0.857 0.000 0.004 0.000 0.956 0.028 0.012
#> GSM751332 1 0.2214 0.883 0.912 0.004 0.000 0.044 0.028 0.012
#> GSM751334 1 0.2508 0.869 0.892 0.004 0.000 0.068 0.024 0.012
#> GSM751339 4 0.0622 0.855 0.000 0.000 0.012 0.980 0.000 0.008
#> GSM751341 1 0.3228 0.821 0.840 0.004 0.020 0.120 0.008 0.008
#> GSM751343 4 0.0767 0.859 0.000 0.004 0.000 0.976 0.012 0.008
#> GSM751344 6 0.1398 0.808 0.000 0.052 0.000 0.000 0.008 0.940
#> GSM751345 6 0.1152 0.807 0.000 0.044 0.000 0.000 0.004 0.952
#> GSM751356 4 0.6772 0.387 0.000 0.128 0.132 0.508 0.000 0.232
#> GSM751357 4 0.7368 0.194 0.000 0.180 0.128 0.396 0.004 0.292
#> GSM751293 6 0.1707 0.810 0.004 0.056 0.000 0.000 0.012 0.928
#> GSM751295 1 0.0000 0.920 1.000 0.000 0.000 0.000 0.000 0.000
#> GSM751319 4 0.0665 0.859 0.008 0.000 0.000 0.980 0.008 0.004
#> GSM751323 4 0.3926 0.646 0.232 0.004 0.000 0.736 0.020 0.008
#> GSM751326 1 0.0405 0.917 0.988 0.004 0.000 0.000 0.000 0.008
#> GSM751327 4 0.2631 0.786 0.124 0.004 0.000 0.860 0.004 0.008
#> GSM751328 1 0.3894 0.726 0.764 0.004 0.000 0.192 0.028 0.012
#> GSM751329 1 0.1375 0.904 0.952 0.004 0.000 0.008 0.028 0.008
#> GSM751330 1 0.0000 0.920 1.000 0.000 0.000 0.000 0.000 0.000
#> GSM751331 1 0.0000 0.920 1.000 0.000 0.000 0.000 0.000 0.000
#> GSM751333 1 0.0146 0.919 0.996 0.000 0.000 0.004 0.000 0.000
#> GSM751335 1 0.0000 0.920 1.000 0.000 0.000 0.000 0.000 0.000
#> GSM751336 1 0.0000 0.920 1.000 0.000 0.000 0.000 0.000 0.000
#> GSM751337 1 0.2383 0.880 0.904 0.004 0.060 0.012 0.008 0.012
#> GSM751338 4 0.0260 0.857 0.000 0.000 0.000 0.992 0.000 0.008
#> GSM751340 4 0.3287 0.672 0.000 0.000 0.220 0.768 0.000 0.012
#> GSM751350 1 0.0000 0.920 1.000 0.000 0.000 0.000 0.000 0.000
#> GSM751351 1 0.0000 0.920 1.000 0.000 0.000 0.000 0.000 0.000
#> GSM751362 3 0.1814 0.814 0.000 0.000 0.900 0.000 0.100 0.000
#> GSM751363 6 0.3794 0.646 0.000 0.000 0.000 0.028 0.248 0.724
#> GSM751367 1 0.0000 0.920 1.000 0.000 0.000 0.000 0.000 0.000
#> GSM751368 5 0.4844 0.435 0.000 0.064 0.000 0.008 0.628 0.300
#> GSM751371 4 0.0260 0.857 0.000 0.000 0.000 0.992 0.000 0.008
#> GSM751375 6 0.5865 0.226 0.000 0.360 0.000 0.000 0.200 0.440
#> GSM751376 3 0.3098 0.767 0.000 0.024 0.812 0.000 0.000 0.164
#> GSM751378 5 0.4393 0.710 0.000 0.112 0.172 0.000 0.716 0.000
#> GSM751379 3 0.3236 0.755 0.000 0.024 0.796 0.000 0.000 0.180
#> GSM751382 5 0.4331 0.090 0.000 0.464 0.000 0.000 0.516 0.020
#> GSM751386 5 0.1549 0.839 0.000 0.044 0.000 0.000 0.936 0.020
#> GSM751388 5 0.2163 0.819 0.000 0.092 0.000 0.000 0.892 0.016
#> GSM751391 4 0.1088 0.849 0.000 0.000 0.016 0.960 0.000 0.024
#> GSM751410 3 0.4129 0.126 0.000 0.000 0.564 0.424 0.012 0.000
#> GSM751414 5 0.2941 0.806 0.024 0.000 0.048 0.060 0.868 0.000
#> GSM751361 5 0.2006 0.812 0.000 0.004 0.000 0.104 0.892 0.000
#> GSM751365 5 0.1563 0.827 0.000 0.000 0.056 0.012 0.932 0.000
#> GSM751366 5 0.3454 0.703 0.004 0.000 0.224 0.012 0.760 0.000
#> GSM751369 3 0.1807 0.824 0.000 0.000 0.920 0.020 0.000 0.060
#> GSM751370 5 0.2485 0.812 0.056 0.000 0.040 0.012 0.892 0.000
#> GSM751372 5 0.2494 0.794 0.000 0.000 0.120 0.016 0.864 0.000
#> GSM751373 5 0.4509 0.662 0.148 0.000 0.004 0.116 0.728 0.004
#> GSM751374 3 0.3236 0.756 0.000 0.024 0.796 0.000 0.000 0.180
#> GSM751377 5 0.1297 0.841 0.000 0.040 0.000 0.000 0.948 0.012
#> GSM751380 3 0.1411 0.832 0.000 0.000 0.936 0.004 0.060 0.000
#> GSM751381 5 0.2214 0.817 0.000 0.096 0.000 0.000 0.888 0.016
#> GSM751383 5 0.1528 0.838 0.000 0.048 0.000 0.000 0.936 0.016
#> GSM751384 5 0.0964 0.842 0.000 0.016 0.012 0.000 0.968 0.004
#> GSM751385 6 0.5019 0.269 0.000 0.012 0.052 0.000 0.376 0.560
#> GSM751387 5 0.2163 0.819 0.000 0.092 0.000 0.000 0.892 0.016
#> GSM751389 3 0.1500 0.830 0.000 0.000 0.936 0.000 0.012 0.052
#> GSM751393 3 0.4910 0.681 0.000 0.000 0.656 0.000 0.152 0.192
#> GSM751394 5 0.2350 0.811 0.000 0.100 0.000 0.000 0.880 0.020
#> GSM751395 6 0.3468 0.463 0.000 0.008 0.264 0.000 0.000 0.728
#> GSM751397 5 0.0993 0.842 0.000 0.024 0.000 0.000 0.964 0.012
#> GSM751398 5 0.1088 0.842 0.000 0.024 0.000 0.000 0.960 0.016
#> GSM751404 3 0.3198 0.606 0.000 0.000 0.740 0.000 0.260 0.000
#> GSM751406 3 0.0547 0.834 0.000 0.000 0.980 0.000 0.020 0.000
#> GSM751411 5 0.1501 0.824 0.000 0.000 0.076 0.000 0.924 0.000
#> GSM751413 6 0.1779 0.809 0.000 0.064 0.000 0.000 0.016 0.920
#> GSM751415 3 0.1610 0.821 0.000 0.000 0.916 0.000 0.084 0.000
#> GSM751416 5 0.0779 0.843 0.000 0.008 0.000 0.008 0.976 0.008
#> GSM751417 5 0.0964 0.843 0.000 0.016 0.000 0.004 0.968 0.012
#> GSM751421 4 0.3993 0.538 0.000 0.000 0.300 0.676 0.024 0.000
#> GSM751422 4 0.4003 0.604 0.000 0.000 0.248 0.716 0.032 0.004
#> GSM751360 4 0.1251 0.847 0.000 0.000 0.012 0.956 0.024 0.008
#> GSM751364 5 0.0363 0.840 0.000 0.000 0.012 0.000 0.988 0.000
#> GSM751390 5 0.1232 0.841 0.000 0.016 0.024 0.000 0.956 0.004
#> GSM751392 5 0.2404 0.806 0.000 0.112 0.000 0.000 0.872 0.016
#> GSM751396 5 0.3221 0.725 0.000 0.188 0.000 0.000 0.792 0.020
#> GSM751399 5 0.3330 0.605 0.000 0.000 0.284 0.000 0.716 0.000
#> GSM751400 3 0.3592 0.454 0.000 0.000 0.656 0.000 0.344 0.000
#> GSM751401 3 0.1556 0.823 0.000 0.000 0.920 0.000 0.080 0.000
#> GSM751402 3 0.0713 0.835 0.000 0.000 0.972 0.000 0.028 0.000
#> GSM751403 3 0.1387 0.829 0.000 0.000 0.932 0.000 0.068 0.000
#> GSM751405 3 0.0937 0.835 0.000 0.000 0.960 0.000 0.040 0.000
#> GSM751407 5 0.3851 0.172 0.000 0.000 0.460 0.000 0.540 0.000
#> GSM751408 5 0.2454 0.767 0.000 0.000 0.160 0.000 0.840 0.000
#> GSM751409 5 0.3843 0.216 0.000 0.000 0.452 0.000 0.548 0.000
#> GSM751412 5 0.2135 0.796 0.000 0.000 0.128 0.000 0.872 0.000
#> GSM751418 5 0.1515 0.833 0.020 0.000 0.028 0.008 0.944 0.000
#> GSM751419 5 0.1616 0.829 0.000 0.000 0.048 0.020 0.932 0.000
#> GSM751420 3 0.0260 0.833 0.000 0.000 0.992 0.000 0.008 0.000
#> GSM751425 2 0.1867 0.863 0.000 0.916 0.000 0.000 0.064 0.020
#> GSM751429 1 0.4375 0.617 0.700 0.032 0.248 0.000 0.000 0.020
#> GSM751430 6 0.1779 0.809 0.000 0.064 0.000 0.000 0.016 0.920
#> GSM751433 6 0.4697 0.486 0.000 0.368 0.000 0.004 0.044 0.584
#> GSM751437 3 0.0790 0.828 0.000 0.032 0.968 0.000 0.000 0.000
#> GSM751448 3 0.0692 0.828 0.000 0.020 0.976 0.000 0.000 0.004
#> GSM751451 4 0.4273 0.460 0.000 0.324 0.000 0.648 0.016 0.012
#> GSM751423 2 0.1807 0.867 0.000 0.920 0.000 0.000 0.060 0.020
#> GSM751424 6 0.3841 0.688 0.000 0.256 0.000 0.000 0.028 0.716
#> GSM751428 6 0.3898 0.640 0.000 0.296 0.000 0.000 0.020 0.684
#> GSM751431 2 0.3534 0.730 0.000 0.796 0.000 0.008 0.036 0.160
#> GSM751432 6 0.3315 0.741 0.000 0.200 0.000 0.000 0.020 0.780
#> GSM751434 6 0.3202 0.757 0.000 0.176 0.000 0.000 0.024 0.800
#> GSM751435 2 0.0520 0.896 0.000 0.984 0.000 0.000 0.008 0.008
#> GSM751436 6 0.4201 0.625 0.000 0.300 0.000 0.000 0.036 0.664
#> GSM751440 2 0.1168 0.890 0.000 0.956 0.000 0.000 0.028 0.016
#> GSM751444 2 0.0806 0.891 0.000 0.972 0.008 0.000 0.000 0.020
#> GSM751446 2 0.0146 0.897 0.000 0.996 0.000 0.000 0.000 0.004
#> GSM751449 2 0.1320 0.877 0.000 0.948 0.036 0.000 0.000 0.016
#> GSM751450 2 0.2831 0.792 0.000 0.840 0.000 0.000 0.024 0.136
#> GSM751452 6 0.3719 0.696 0.000 0.248 0.000 0.000 0.024 0.728
#> GSM751426 2 0.3730 0.710 0.000 0.772 0.000 0.000 0.060 0.168
#> GSM751427 2 0.0405 0.897 0.000 0.988 0.000 0.000 0.008 0.004
#> GSM751438 2 0.2432 0.817 0.000 0.876 0.100 0.000 0.000 0.024
#> GSM751439 2 0.3652 0.497 0.000 0.672 0.324 0.000 0.000 0.004
#> GSM751441 2 0.0520 0.896 0.000 0.984 0.008 0.000 0.000 0.008
#> GSM751442 2 0.0508 0.895 0.000 0.984 0.012 0.000 0.000 0.004
#> GSM751443 3 0.2632 0.737 0.000 0.164 0.832 0.000 0.000 0.004
#> GSM751445 2 0.1524 0.872 0.000 0.932 0.008 0.000 0.000 0.060
#> GSM751447 2 0.0260 0.897 0.000 0.992 0.000 0.000 0.000 0.008
#> GSM751453 2 0.1334 0.882 0.000 0.948 0.000 0.000 0.020 0.032
#> GSM751454 2 0.0891 0.892 0.000 0.968 0.000 0.000 0.008 0.024
#> GSM751455 2 0.0363 0.895 0.000 0.988 0.012 0.000 0.000 0.000
#> GSM751456 2 0.0547 0.894 0.000 0.980 0.020 0.000 0.000 0.000
#> GSM751457 3 0.5042 0.428 0.000 0.332 0.576 0.000 0.000 0.092
#> GSM751458 3 0.4728 0.579 0.000 0.256 0.652 0.000 0.000 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 tissue(p) disease.state(p) agent(p) k
#> ATC:NMF 161 1.71e-12 0.388 0.5556 2
#> ATC:NMF 153 5.97e-19 0.251 0.2672 3
#> ATC:NMF 102 2.52e-19 0.077 0.1778 4
#> ATC:NMF 134 1.00e-29 0.336 0.2388 5
#> ATC:NMF 147 7.25e-33 0.208 0.0554 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