Date: 2021-07-22 18:28:48 CEST, cola version: 1.9.4
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First the variable is renamed to res_rh.
res_rh = rh
The partition hierarchy and all available functions which can be applied to res_rh object.
res_rh
#> A 'HierarchicalPartition' object with 4 combinations of top-value methods and partitioning methods.
#> On a matrix with 375746 rows and 312 columns.
#> Performed in total 81200 partitions.
#> There are 37 groups under the following parameters:
#> - min_samples: 6
#> - mean_silhouette_cutoff: 0.9
#> - min_n_signatures: 1000 (signatures are selected based on:)
#> - fdr_cutoff: 0.05
#> - group_diff: 0.25
#>
#> Hierarchy of the partition:
#> 0, 312 cols
#> |-- 01, 154 cols, 23697 signatures
#> | |-- 011, 58 cols, 17838 signatures
#> | | |-- 0111, 32 cols, 2087 signatures
#> | | | |-- 01111, 11 cols (b)
#> | | | |-- 01112, 12 cols, 68 signatures (c)
#> | | | `-- 01113, 9 cols (b)
#> | | |-- 0112, 10 cols (b)
#> | | `-- 0113, 16 cols, 4079 signatures
#> | | |-- 01131, 7 cols (b)
#> | | |-- 01132, 7 cols (b)
#> | | `-- 01133, 2 cols (b)
#> | |-- 012, 31 cols, 15278 signatures
#> | | |-- 0121, 15 cols, 4774 signatures
#> | | | |-- 01211, 7 cols (b)
#> | | | `-- 01212, 8 cols (b)
#> | | |-- 0122, 10 cols (b)
#> | | `-- 0123, 6 cols (b)
#> | `-- 013, 65 cols, 17125 signatures
#> | |-- 0131, 39 cols, 1061 signatures
#> | | |-- 01311, 14 cols, 202 signatures (c)
#> | | |-- 01312, 17 cols, 197 signatures (c)
#> | | `-- 01313, 8 cols (b)
#> | |-- 0132, 9 cols (b)
#> | |-- 0133, 7 cols (b)
#> | `-- 0134, 10 cols (b)
#> |-- 02, 117 cols, 12995 signatures
#> | |-- 021, 53 cols, 1228 signatures
#> | | |-- 0211, 37 cols, 1463 signatures
#> | | | |-- 02111, 26 cols, 8634 signatures
#> | | | | |-- 021111, 14 cols, 164 signatures (c)
#> | | | | |-- 021112, 3 cols (b)
#> | | | | |-- 021113, 4 cols (b)
#> | | | | `-- 021114, 5 cols (b)
#> | | | `-- 02112, 11 cols (b)
#> | | `-- 0212, 16 cols, 218 signatures (c)
#> | |-- 022, 36 cols, 3801 signatures
#> | | |-- 0221, 4 cols (b)
#> | | `-- 0222, 32 cols, 1658 signatures
#> | | |-- 02221, 16 cols, 2263 signatures
#> | | | |-- 022211, 2 cols (b)
#> | | | |-- 022212, 12 cols, 6 signatures (c)
#> | | | `-- 022213, 2 cols (b)
#> | | `-- 02222, 16 cols, 211 signatures (c)
#> | `-- 023, 28 cols, 1579 signatures
#> | |-- 0231, 9 cols (b)
#> | |-- 0232, 13 cols, 687 signatures (c)
#> | `-- 0233, 6 cols (b)
#> `-- 03, 41 cols, 5174 signatures
#> |-- 031, 25 cols, 10323 signatures
#> | |-- 0311, 14 cols, 7545 signatures
#> | | |-- 03111, 2 cols (b)
#> | | `-- 03112, 12 cols, 1032 signatures
#> | | |-- 031121, 2 cols (b)
#> | | `-- 031122, 10 cols (b)
#> | |-- 0312, 5 cols (b)
#> | `-- 0313, 6 cols (b)
#> `-- 032, 16 cols, 896 signatures (c)
#> Stop reason:
#> b) Subgroup had too few columns.
#> c) There were too few signatures.
#>
#> Following methods can be applied to this 'HierarchicalPartition' object:
#> [1] "all_leaves" "all_nodes" "cola_report" "collect_classes"
#> [5] "colnames" "compare_signatures" "dimension_reduction" "functional_enrichment"
#> [9] "get_anno_col" "get_anno" "get_children_nodes" "get_classes"
#> [13] "get_matrix" "get_signatures" "is_leaf_node" "max_depth"
#> [17] "merge_node" "ncol" "node_info" "node_level"
#> [21] "nrow" "rownames" "show" "split_node"
#> [25] "suggest_best_k" "test_to_known_factors" "top_rows_heatmap" "top_rows_overlap"
#>
#> You can get result for a single node by e.g. object["01"]
The call of hierarchical_partition() was:
#> hierarchical_partition(data = mat, top_n = 1000, top_value_method = c("SD", "ATC"),
#> partition_method = c("kmeans", "skmeans"), subset = 500, group_diff = 0.25, min_n_signatures = 1000,
#> filter_fun = function(mat) {
#> s = rowSds(mat)
#> order(-s)[1:30000]
#> }, max_k = 8, scale_rows = FALSE, cores = 4)
Dimension of the input matrix:
mat = get_matrix(res_rh)
dim(mat)
#> [1] 375746 312
All the methods that were tried:
res_rh@param$combination_method
#> [[1]]
#> [1] "SD" "kmeans"
#>
#> [[2]]
#> [1] "ATC" "kmeans"
#>
#> [[3]]
#> [1] "SD" "skmeans"
#>
#> [[4]]
#> [1] "ATC" "skmeans"
The density distribution for each sample is visualized as 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, ylab = "value", cluster_columns = TRUE, show_column_names = FALSE,
mc.cores = 1)
Some values about the hierarchy:
all_nodes(res_rh)
#> [1] "0" "01" "011" "0111" "01111" "01112" "01113" "0112" "0113" "01131"
#> [11] "01132" "01133" "012" "0121" "01211" "01212" "0122" "0123" "013" "0131"
#> [21] "01311" "01312" "01313" "0132" "0133" "0134" "02" "021" "0211" "02111"
#> [31] "021111" "021112" "021113" "021114" "02112" "0212" "022" "0221" "0222" "02221"
#> [41] "022211" "022212" "022213" "02222" "023" "0231" "0232" "0233" "03" "031"
#> [51] "0311" "03111" "03112" "031121" "031122" "0312" "0313" "032"
all_leaves(res_rh)
#> [1] "01111" "01112" "01113" "0112" "01131" "01132" "01133" "01211" "01212" "0122"
#> [11] "0123" "01311" "01312" "01313" "0132" "0133" "0134" "021111" "021112" "021113"
#> [21] "021114" "02112" "0212" "0221" "022211" "022212" "022213" "02222" "0231" "0232"
#> [31] "0233" "03111" "031121" "031122" "0312" "0313" "032"
node_info(res_rh)
#> id best_method depth best_k n_columns n_signatures p_signatures is_leaf
#> 1 0 SD:kmeans 1 3 312 30030 0.079921 FALSE
#> 2 01 ATC:kmeans 2 3 154 23697 0.063067 FALSE
#> 3 011 ATC:kmeans 3 3 58 17838 0.047474 FALSE
#> 4 0111 ATC:skmeans 4 3 32 2087 0.005554 FALSE
#> 5 01111 not applied 5 NA 11 NA NA TRUE
#> 6 01112 ATC:skmeans 5 3 12 68 0.000181 TRUE
#> 7 01113 not applied 5 NA 9 NA NA TRUE
#> 8 0112 not applied 4 NA 10 NA NA TRUE
#> 9 0113 ATC:skmeans 4 3 16 4079 0.010856 FALSE
#> 10 01131 not applied 5 NA 7 NA NA TRUE
#> 11 01132 not applied 5 NA 7 NA NA TRUE
#> 12 01133 not applied 5 NA 2 NA NA TRUE
#> 13 012 ATC:skmeans 3 3 31 15278 0.040660 FALSE
#> 14 0121 ATC:kmeans 4 2 15 4774 0.012705 FALSE
#> 15 01211 not applied 5 NA 7 NA NA TRUE
#> 16 01212 not applied 5 NA 8 NA NA TRUE
#> 17 0122 not applied 4 NA 10 NA NA TRUE
#> 18 0123 not applied 4 NA 6 NA NA TRUE
#> 19 013 ATC:skmeans 3 4 65 17125 0.045576 FALSE
#> 20 0131 ATC:skmeans 4 3 39 1061 0.002824 FALSE
#> 21 01311 ATC:kmeans 5 2 14 202 0.000538 TRUE
#> 22 01312 ATC:kmeans 5 2 17 197 0.000524 TRUE
#> 23 01313 not applied 5 NA 8 NA NA TRUE
#> 24 0132 not applied 4 NA 9 NA NA TRUE
#> 25 0133 not applied 4 NA 7 NA NA TRUE
#> 26 0134 not applied 4 NA 10 NA NA TRUE
#> 27 02 ATC:kmeans 2 3 117 12995 0.034585 FALSE
#> 28 021 SD:kmeans 3 2 53 1228 0.003268 FALSE
#> 29 0211 ATC:kmeans 4 2 37 1463 0.003894 FALSE
#> 30 02111 ATC:kmeans 5 4 26 8634 0.022978 FALSE
#> 31 021111 ATC:kmeans 6 2 14 164 0.000436 TRUE
#> 32 021112 not applied 6 NA 3 NA NA TRUE
#> 33 021113 not applied 6 NA 4 NA NA TRUE
#> 34 021114 not applied 6 NA 5 NA NA TRUE
#> 35 02112 not applied 5 NA 11 NA NA TRUE
#> 36 0212 ATC:kmeans 4 2 16 218 0.000580 TRUE
#> 37 022 ATC:skmeans 3 2 36 3801 0.010116 FALSE
#> 38 0221 not applied 4 NA 4 NA NA TRUE
#> 39 0222 ATC:kmeans 4 2 32 1658 0.004413 FALSE
#> 40 02221 ATC:skmeans 5 3 16 2263 0.006023 FALSE
#> 41 022211 not applied 6 NA 2 NA NA TRUE
#> 42 022212 ATC:skmeans 6 3 12 6 0.000016 TRUE
#> 43 022213 not applied 6 NA 2 NA NA TRUE
#> 44 02222 ATC:skmeans 5 2 16 211 0.000562 TRUE
#> 45 023 ATC:skmeans 3 3 28 1579 0.004202 FALSE
#> 46 0231 not applied 4 NA 9 NA NA TRUE
#> 47 0232 ATC:skmeans 4 2 13 687 0.001828 TRUE
#> 48 0233 not applied 4 NA 6 NA NA TRUE
#> 49 03 ATC:kmeans 2 2 41 5174 0.013770 FALSE
#> 50 031 ATC:kmeans 3 3 25 10323 0.027473 FALSE
#> 51 0311 ATC:skmeans 4 2 14 7545 0.020080 FALSE
#> 52 03111 not applied 5 NA 2 NA NA TRUE
#> 53 03112 ATC:skmeans 5 2 12 1032 0.002747 FALSE
#> 54 031121 not applied 6 NA 2 NA NA TRUE
#> 55 031122 not applied 6 NA 10 NA NA TRUE
#> 56 0312 not applied 4 NA 5 NA NA TRUE
#> 57 0313 not applied 4 NA 6 NA NA TRUE
#> 58 032 ATC:kmeans 3 2 16 896 0.002385 TRUE
In the output from node_info(), there are the following columns:
id: The node id.best_method: The best method selected.depth: Depth of the node in the hierarchy.best_k: Best number of groups of the partition on that node.n_columns: Number of columns in the submatrix.n_signatures: Number of signatures with the best_k.p_signatures: Proportion of hte signatures in total number of rows in the matrix.is_leaf: Whether the node is a leaf.Labels of nodes are encoded in a special way. The number of digits correspond to the depth of the node in the hierarchy and the value of the digits correspond to the index of the subgroup in the current node, E.g. a label of “012” means the node is the second subgroup of the partition which is the first subgroup of the root node.
Following table shows the best k (number of partitions) for each node in the
partition hierarchy. Clicking on the node name in the table goes to the
corresponding section for the partitioning on that node.
The cola vignette explains the definition of the metrics used for determining the best number of partitions.
suggest_best_k(res_rh)
| Node | Best method | Is leaf | Best k | 1-PAC | Mean silhouette | Concordance | #samples | |
|---|---|---|---|---|---|---|---|---|
| Node0 | SD:kmeans | 3 | 1.00 | 0.98 | 0.99 | 312 | ** | |
| Node01 | ATC:kmeans | 3 | 1.00 | 0.99 | 1.00 | 154 | ** | |
| Node011 | ATC:kmeans | 3 | 1.00 | 1.00 | 1.00 | 58 | ** | |
| Node0111 | ATC:skmeans | 3 | 1.00 | 1.00 | 1.00 | 32 | ** | |
| Node01111-leaf | not applied | ✓ (b) | 11 | |||||
| Node01112-leaf | ATC:skmeans | ✓ (c) | 7 | 0.94 | 0.50 | 0.84 | 12 | * |
| Node01113-leaf | not applied | ✓ (b) | 9 | |||||
| Node0112-leaf | not applied | ✓ (b) | 10 | |||||
| Node0113 | ATC:skmeans | 4 | 1.00 | 1.00 | 1.00 | 16 | ** | |
| Node01131-leaf | not applied | ✓ (b) | 7 | |||||
| Node01132-leaf | not applied | ✓ (b) | 7 | |||||
| Node01133-leaf | not applied | ✓ (b) | 2 | |||||
| Node012 | ATC:skmeans | 3 | 1.00 | 0.99 | 0.99 | 31 | ** | |
| Node0121 | ATC:kmeans | 5 | 0.95 | 0.83 | 0.97 | 15 | ** | |
| Node01211-leaf | not applied | ✓ (b) | 7 | |||||
| Node01212-leaf | not applied | ✓ (b) | 8 | |||||
| Node0122-leaf | not applied | ✓ (b) | 10 | |||||
| Node0123-leaf | not applied | ✓ (b) | 6 | |||||
| Node013 | ATC:skmeans | 4 | 1.00 | 0.99 | 1.00 | 65 | ** | |
| Node0131 | ATC:skmeans | 3 | 1.00 | 0.99 | 0.99 | 39 | ** | |
| Node01311-leaf | ATC:kmeans | ✓ (c) | 2 | 1.00 | 1.00 | 1.00 | 14 | ** |
| Node01312-leaf | ATC:kmeans | ✓ (c) | 2 | 1.00 | 1.00 | 1.00 | 17 | ** |
| Node01313-leaf | not applied | ✓ (b) | 8 | |||||
| Node0132-leaf | not applied | ✓ (b) | 9 | |||||
| Node0133-leaf | not applied | ✓ (b) | 7 | |||||
| Node0134-leaf | not applied | ✓ (b) | 10 | |||||
| Node02 | ATC:kmeans | 3 | 1.00 | 0.97 | 0.98 | 117 | ** | |
| Node021 | SD:kmeans | 2 | 1.00 | 0.97 | 0.97 | 53 | ** | |
| Node0211 | ATC:kmeans | 2 | 1.00 | 1.00 | 1.00 | 37 | ** | |
| Node02111 | ATC:kmeans | 4 | 1.00 | 0.95 | 0.97 | 26 | ** | |
| Node021111-leaf | ATC:kmeans | ✓ (c) | 3 | 1.00 | 0.92 | 0.99 | 14 | ** |
| Node021112-leaf | not applied | ✓ (b) | 3 | |||||
| Node021113-leaf | not applied | ✓ (b) | 4 | |||||
| Node021114-leaf | not applied | ✓ (b) | 5 | |||||
| Node02112-leaf | not applied | ✓ (b) | 11 | |||||
| Node0212-leaf | ATC:kmeans | ✓ (c) | 2 | 1.00 | 1.00 | 1.00 | 16 | ** |
| Node022 | ATC:skmeans | 2 | 1.00 | 0.97 | 0.98 | 36 | ** | |
| Node0221-leaf | not applied | ✓ (b) | 4 | |||||
| Node0222 | ATC:kmeans | 3 | 1.00 | 0.93 | 0.97 | 32 | ** | |
| Node02221 | ATC:skmeans | 2 | 1.00 | 0.99 | 0.99 | 16 | ** | |
| Node022211-leaf | not applied | ✓ (b) | 2 | |||||
| Node022212-leaf | ATC:skmeans | ✓ (c) | 8 | 0.94 | 0.46 | 0.97 | 12 | * |
| Node022213-leaf | not applied | ✓ (b) | 2 | |||||
| Node02222-leaf | ATC:skmeans | ✓ (c) | 3 | 1.00 | 0.99 | 1.00 | 16 | ** |
| Node023 | ATC:skmeans | 3 | 1.00 | 1.00 | 1.00 | 28 | ** | |
| Node0231-leaf | not applied | ✓ (b) | 9 | |||||
| Node0232-leaf | ATC:skmeans | ✓ (c) | 3 | 1.00 | 0.92 | 1.00 | 13 | ** |
| Node0233-leaf | not applied | ✓ (b) | 6 | |||||
| Node03 | ATC:kmeans | 2 | 1.00 | 1.00 | 1.00 | 41 | ** | |
| Node031 | ATC:kmeans | 3 | 1.00 | 0.95 | 0.98 | 25 | ** | |
| Node0311 | ATC:skmeans | 2 | 1.00 | 1.00 | 1.00 | 14 | ** | |
| Node03111-leaf | not applied | ✓ (b) | 2 | |||||
| Node03112 | ATC:skmeans | 7 | 0.92 | 0.59 | 0.94 | 12 | * | |
| Node031121-leaf | not applied | ✓ (b) | 2 | |||||
| Node031122-leaf | not applied | ✓ (b) | 10 | |||||
| Node0312-leaf | not applied | ✓ (b) | 5 | |||||
| Node0313-leaf | not applied | ✓ (b) | 6 | |||||
| Node032-leaf | ATC:kmeans | ✓ (c) | 2 | 1.00 | 1.00 | 1.00 | 16 | ** |
Stop reason: b) Subgroup had too few columns. c) There were too few signatures.
**: 1-PAC > 0.95, *: 1-PAC > 0.9
The nodes of the hierarchy can be merged by setting the merge_node parameters. Here we
control the hierarchy with the min_n_signatures parameter. The value of min_n_signatures is
from node_info().
collect_classes(res_rh, merge_node = merge_node_param(min_n_signatures = 1032))
collect_classes(res_rh, merge_node = merge_node_param(min_n_signatures = 1061))
collect_classes(res_rh, merge_node = merge_node_param(min_n_signatures = 1228))
collect_classes(res_rh, merge_node = merge_node_param(min_n_signatures = 1463))
#> Error in lt[[hierarchy[i, 1]]]$AddChildNode({: attempt to apply non-function
collect_classes(res_rh, merge_node = merge_node_param(min_n_signatures = 1579))
collect_classes(res_rh, merge_node = merge_node_param(min_n_signatures = 1658))
collect_classes(res_rh, merge_node = merge_node_param(min_n_signatures = 2087))
collect_classes(res_rh, merge_node = merge_node_param(min_n_signatures = 2263))
collect_classes(res_rh, merge_node = merge_node_param(min_n_signatures = 3801))
collect_classes(res_rh, merge_node = merge_node_param(min_n_signatures = 4079))
collect_classes(res_rh, merge_node = merge_node_param(min_n_signatures = 4774))
collect_classes(res_rh, merge_node = merge_node_param(min_n_signatures = 5174))
collect_classes(res_rh, merge_node = merge_node_param(min_n_signatures = 7545))
#> Error in lt[[hierarchy[i, 1]]]$AddChildNode({: attempt to apply non-function
collect_classes(res_rh, merge_node = merge_node_param(min_n_signatures = 8634))
collect_classes(res_rh, merge_node = merge_node_param(min_n_signatures = 10323))
collect_classes(res_rh, merge_node = merge_node_param(min_n_signatures = 12995))
collect_classes(res_rh, merge_node = merge_node_param(min_n_signatures = 15278))
collect_classes(res_rh, merge_node = merge_node_param(min_n_signatures = 17125))
collect_classes(res_rh, merge_node = merge_node_param(min_n_signatures = 17838))
collect_classes(res_rh, merge_node = merge_node_param(min_n_signatures = 23697))
collect_classes(res_rh, merge_node = merge_node_param(min_n_signatures = 30030))
Following shows the table of the partitions (You need to click the show/hide code output link to see it).
get_classes(res_rh, merge_node = merge_node_param(min_n_signatures = 1032))
#> TCGA.EK.A3GK.01 TCGA.GH.A9DA.01 TCGA.VS.A94Y.01 TCGA.MY.A5BF.11 TCGA.VS.A94Z.01 TCGA.EA.A4BA.01
#> "0132" "0231" "0132" "0112" "01313" "0133"
#> TCGA.ZJ.A8QQ.01 TCGA.FU.A3EO.11 TCGA.DG.A2KJ.01 TCGA.VS.A954.01 TCGA.MA.AA42.01 TCGA.C5.A8YQ.01
#> "0231" "0112" "01113" "0212" "021113" "021112"
#> TCGA.DS.A7WF.01 TCGA.EK.A2R7.01 TCGA.EK.A3GJ.01 TCGA.C5.A902.01 TCGA.MA.AA3W.01 TCGA.C5.A905.01
#> "0312" "01312" "0233" "0232" "021111" "01211"
#> TCGA.EK.A2RN.01 TCGA.FU.A57G.01 TCGA.C5.A8YR.01 TCGA.EK.A2R9.01 TCGA.FU.A3EO.01 TCGA.IR.A3LC.01
#> "01311" "0112" "0133" "02112" "031122" "0212"
#> TCGA.VS.A8QA.01 TCGA.C5.A3HD.01 TCGA.MY.A5BE.01 TCGA.EA.A50E.01 TCGA.VS.A8QH.01 TCGA.ZJ.A8QR.01
#> "0313" "0233" "01112" "0212" "01113" "01212"
#> TCGA.C5.A907.01 TCGA.IR.A3LK.01 TCGA.C5.A8ZZ.01 TCGA.VS.A8EK.01 TCGA.C5.A7UC.01 TCGA.C5.A8XJ.01
#> "01113" "022212" "0123" "0212" "01111" "01312"
#> TCGA.IR.A3LH.01 TCGA.EK.A3GM.01 TCGA.VS.A8Q8.01 TCGA.EK.A2RO.01 TCGA.MY.A5BD.01 TCGA.2W.A8YY.01
#> "0231" "01131" "01311" "02112" "0312" "0122"
#> TCGA.C5.A2LZ.01 TCGA.C5.A901.01 TCGA.VS.A953.01 TCGA.MU.A51Y.01 TCGA.EK.A2RK.01 TCGA.UC.A7PD.01
#> "02222" "0212" "0212" "01112" "01312" "01111"
#> TCGA.EA.A3HS.01 TCGA.VS.A8QM.01 TCGA.EA.A3HU.01 TCGA.VS.A94X.01 TCGA.C5.A7CO.01 TCGA.C5.A3HF.01
#> "02112" "01112" "01112" "01111" "021113" "01113"
#> TCGA.IR.A3LL.01 TCGA.MY.A913.01 TCGA.VS.A952.01 TCGA.IR.A3LI.01 TCGA.VS.A94W.01 TCGA.MY.A5BF.01
#> "0232" "01111" "0313" "0313" "021111" "0232"
#> TCGA.EK.A2RC.01 TCGA.VS.A8EL.01 TCGA.EA.A97N.01 TCGA.EA.A3HQ.01 TCGA.EK.A2RD.01 TCGA.C5.A8YT.01
#> "02222" "0231" "01212" "02222" "01312" "0112"
#> TCGA.FU.A3HZ.01 TCGA.VS.A8EJ.01 TCGA.C5.A3HL.01 TCGA.UC.A7PF.01 TCGA.C5.A8XK.01 TCGA.EX.A8YF.01
#> "0122" "0112" "01312" "0232" "0132" "01113"
#> TCGA.HM.A4S6.01 TCGA.VS.A8Q9.01 TCGA.MA.AA41.01 TCGA.EK.A3GN.01 TCGA.MA.AA3Y.01 TCGA.MA.AA3Z.01
#> "01313" "0231" "021114" "0212" "01111" "01312"
#> TCGA.EK.A2RE.01 TCGA.C5.A1BQ.01 TCGA.ZJ.A8QO.01 TCGA.JW.A852.01 TCGA.DS.A7WH.01 TCGA.JW.AAVH.01
#> "01311" "01313" "021113" "0212" "032" "022213"
#> TCGA.EA.A556.01 TCGA.EA.A44S.01 TCGA.4J.AA1J.01 TCGA.IR.A3L7.01 TCGA.C5.A7X3.01 TCGA.HG.A2PA.01
#> "0133" "01212" "01212" "02222" "0132" "01112"
#> TCGA.C5.A8XH.01 TCGA.C5.A7XC.01 TCGA.VS.A8EI.01 TCGA.VS.A8QC.01 TCGA.C5.A7UH.01 TCGA.WL.A834.01
#> "0233" "01311" "0231" "02222" "01211" "02222"
#> TCGA.C5.A8XI.01 TCGA.DS.A7WI.01 TCGA.VS.A8QF.01 TCGA.EA.A3HR.01 TCGA.DG.A2KL.01 TCGA.EK.A2RL.01
#> "0232" "0233" "02222" "01313" "01311" "031122"
#> TCGA.EK.A2PG.01 TCGA.BI.A0VR.01 TCGA.DS.A0VL.01 TCGA.VS.A8EC.01 TCGA.EA.A3QE.01 TCGA.DS.A0VM.01
#> "022212" "01312" "01311" "0221" "021111" "021114"
#> TCGA.FU.A3HY.01 TCGA.Q1.A5R1.01 TCGA.DR.A0ZM.01 TCGA.Q1.A6DW.01 TCGA.DS.A0VK.01 TCGA.DS.A3LQ.01
#> "022212" "031122" "0134" "0212" "01312" "0221"
#> TCGA.EA.A3QD.01 TCGA.JW.A5VJ.01 TCGA.LP.A5U3.01 TCGA.EA.A6QX.01 TCGA.EK.A2RA.01 TCGA.FU.A5XV.01
#> "0232" "0134" "02222" "02222" "022212" "01212"
#> TCGA.Q1.A5R2.01 TCGA.HM.A3JJ.01 TCGA.C5.A2LS.01 TCGA.C5.A7X8.01 TCGA.EK.A2RJ.01 TCGA.EA.A3HT.01
#> "022212" "01312" "0313" "032" "0133" "01311"
#> TCGA.LP.A7HU.01 TCGA.MU.A8JM.01 TCGA.EK.A2IP.01 TCGA.JW.A5VL.01 TCGA.FU.A3TX.01 TCGA.DG.A2KK.01
#> "0312" "021111" "02222" "022211" "01133" "0313"
#> TCGA.EK.A2PI.01 TCGA.Q1.A73S.01 TCGA.EK.A2IR.01 TCGA.HM.A6W2.01 TCGA.VS.A8EH.01 TCGA.JW.A5VH.01
#> "01312" "0122" "02112" "0122" "01132" "0122"
#> TCGA.C5.A2LV.01 TCGA.VS.A8EB.01 TCGA.RA.A741.01 TCGA.VS.A8EG.01 TCGA.DG.A2KH.01 TCGA.C5.A7UE.01
#> "0212" "01132" "01112" "02222" "01131" "021111"
#> TCGA.C5.A2LT.01 TCGA.EA.A5ZD.01 TCGA.Q1.A73R.01 TCGA.JW.A5VK.01 TCGA.EK.A2RM.01 TCGA.C5.A7UI.01
#> "01111" "0134" "0312" "0221" "01131" "01313"
#> TCGA.EK.A2PL.01 TCGA.EK.A2PM.01 TCGA.EK.A2GZ.01 TCGA.HM.A3JK.01 TCGA.C5.A2M1.01 TCGA.HM.A6W2.06
#> "01311" "0123" "01112" "01112" "031122" "0122"
#> TCGA.C5.A7X5.01 TCGA.IR.A3LA.01 TCGA.EK.A2PK.01 TCGA.EA.A5ZF.01 TCGA.XS.A8TJ.01 TCGA.BI.A0VS.01
#> "0233" "0122" "0133" "0132" "021111" "0132"
#> TCGA.DS.A0VN.01 TCGA.JX.A5QV.01 TCGA.EK.A2R8.01 TCGA.EA.A1QS.01 TCGA.C5.A3HE.01 TCGA.IR.A3LF.01
#> "021114" "01311" "0132" "01112" "032" "031122"
#> TCGA.DR.A0ZL.01 TCGA.FU.A3WB.01 TCGA.JX.A3PZ.01 TCGA.EA.A5O9.01 TCGA.HM.A3JJ.11 TCGA.DS.A5RQ.01
#> "021111" "02112" "0133" "02112" "0112" "01311"
#> TCGA.EK.A2H0.01 TCGA.EX.A1H6.01 TCGA.EA.A5ZE.01 TCGA.C5.A2LY.01 TCGA.FU.A3TQ.01 TCGA.EK.A2RB.01
#> "0231" "032" "02112" "01132" "02222" "022212"
#> TCGA.JW.A5VI.01 TCGA.EK.A2H1.01 TCGA.JX.A3Q8.01 TCGA.FU.A3YQ.01 TCGA.EX.A69L.01 TCGA.C5.A7CH.01
#> "021114" "0112" "0313" "021111" "01311" "021114"
#> TCGA.FU.A2QG.01 TCGA.C5.A2M2.01 TCGA.JW.A5VG.01 TCGA.PN.A8MA.01 TCGA.DG.A2KM.01 TCGA.C5.A2LX.01
#> "01212" "031122" "01132" "0122" "0112" "02222"
#> TCGA.EX.A3L1.01 TCGA.LP.A5U2.01 TCGA.FU.A3NI.01 TCGA.Q1.A5R3.01 TCGA.FU.A770.01 TCGA.C5.A7CM.01
#> "01111" "0212" "0232" "01312" "032" "01131"
#> TCGA.JX.A3Q0.01 TCGA.EA.A5FO.01 TCGA.VS.A9V3.01 TCGA.C5.A7CL.01 TCGA.VS.A959.01 TCGA.LP.A4AX.01
#> "01211" "0312" "0212" "01311" "01113" "01111"
#> TCGA.C5.A1MN.01 TCGA.ZJ.AAXN.01 TCGA.MA.AA3X.01 TCGA.UC.A7PG.01 TCGA.Q1.A6DV.01 TCGA.DS.A1OD.01
#> "022212" "0132" "01211" "01311" "032" "01312"
#> TCGA.C5.A1M7.01 TCGA.BI.A20A.01 TCGA.VS.A9UO.01 TCGA.EA.A1QT.01 TCGA.EX.A69M.01 TCGA.VS.A9UH.01
#> "0134" "021113" "032" "022213" "0232" "01111"
#> TCGA.VS.A9U7.01 TCGA.ZJ.AAXD.01 TCGA.VS.A9UB.01 TCGA.EA.A410.01 TCGA.ZJ.AB0I.01 TCGA.VS.A9UD.01
#> "02222" "01312" "01111" "0122" "01212" "0232"
#> TCGA.VS.A9U6.01 TCGA.ZX.AA5X.01 TCGA.C5.A0TN.01 TCGA.C5.A7CJ.01 TCGA.C5.A1MJ.01 TCGA.EA.A78R.01
#> "01132" "021111" "01132" "021111" "032" "0232"
#> TCGA.VS.A9UY.01 TCGA.VS.A9U5.01 TCGA.DS.A1OC.01 TCGA.ZJ.AAXB.01 TCGA.EX.A449.01 TCGA.C5.A1BL.01
#> "022211" "0212" "0233" "0123" "031122" "022212"
#> TCGA.VS.A9UQ.01 TCGA.DS.A1OB.01 TCGA.HG.A9SC.01 TCGA.ZJ.AAXT.01 TCGA.IR.A3LB.01 TCGA.C5.A1ML.01
#> "031122" "0123" "0123" "0134" "032" "01133"
#> TCGA.VS.A9UV.01 TCGA.LP.A4AU.01 TCGA.Q1.A6DT.01 TCGA.C5.A1M8.01 TCGA.C5.A1ME.01 TCGA.ZJ.AAXU.01
#> "0212" "01113" "021112" "0212" "032" "01312"
#> TCGA.VS.A957.01 TCGA.VS.A9V5.01 TCGA.MU.A5YI.01 TCGA.ZJ.AAX4.01 TCGA.C5.A1MK.01 TCGA.JW.A69B.01
#> "02222" "03111" "02112" "02112" "01313" "031121"
#> TCGA.VS.A958.01 TCGA.ZJ.AAXJ.01 TCGA.R2.A69V.01 TCGA.EA.A411.01 TCGA.VS.A9UP.01 TCGA.C5.A1MI.01
#> "0134" "0232" "01113" "0123" "01113" "01131"
#> TCGA.DS.A1O9.01 TCGA.VS.A9UZ.01 TCGA.EA.A43B.01 TCGA.ZJ.AAX8.01 TCGA.ZJ.AAXI.01 TCGA.VS.A9UT.01
#> "021111" "031122" "0231" "01112" "022212" "0112"
#> TCGA.DS.A1OA.01 TCGA.C5.A1MQ.01 TCGA.VS.A9V0.01 TCGA.VS.A9UC.01 TCGA.ZJ.AAXA.01 TCGA.Q1.A73P.01
#> "02222" "0231" "0133" "021112" "01211" "031122"
#> TCGA.VS.A9V2.01 TCGA.VS.A9UU.01 TCGA.LP.A4AV.01 TCGA.VS.A9UR.01 TCGA.VS.A9V1.01 TCGA.C5.A7CG.01
#> "021111" "0232" "01313" "032" "032" "0212"
#> TCGA.UC.A7PI.01 TCGA.EX.A1H5.01 TCGA.ZJ.AAXF.01 TCGA.VS.A9UL.01 TCGA.EA.A3Y4.01 TCGA.C5.A7CK.01
#> "032" "02112" "01112" "032" "0132" "0232"
#> TCGA.UC.A7PG.06 TCGA.VS.A9UJ.01 TCGA.Q1.A73O.01 TCGA.VS.A950.01 TCGA.EA.A439.01 TCGA.VS.A9UM.01
#> "01211" "0122" "0134" "022212" "01131" "01211"
#> TCGA.C5.A1MP.01 TCGA.VS.A9UI.01 TCGA.ZJ.AB0H.01 TCGA.Q1.A73Q.01 TCGA.C5.A1MH.01 TCGA.VS.A9V4.01
#> "01313" "022212" "01312" "0221" "021111" "0112"
#> TCGA.FU.A40J.01 TCGA.VS.A9UA.01 TCGA.LP.A4AW.01 TCGA.MA.AA43.01 TCGA.C5.A1BN.01 TCGA.VS.AA62.01
#> "03111" "01311" "01312" "032" "01212" "01111"
#> TCGA.C5.A1BM.01 TCGA.C5.A1M6.01 TCGA.C5.A1BE.01 TCGA.FU.A23K.01 TCGA.C5.A1BJ.01 TCGA.FU.A23L.01
#> "0134" "01131" "01312" "032" "01112" "0134"
#> TCGA.C5.A1M5.01 TCGA.C5.A1MF.01 TCGA.C5.A1BF.01 TCGA.C5.A1BK.01 TCGA.C5.A1BI.01 TCGA.C5.A1M9.01
#> "022212" "02112" "01132" "021111" "0134" "031121"
get_classes(res_rh, merge_node = merge_node_param(min_n_signatures = 1061))
#> TCGA.EK.A3GK.01 TCGA.GH.A9DA.01 TCGA.VS.A94Y.01 TCGA.MY.A5BF.11 TCGA.VS.A94Z.01 TCGA.EA.A4BA.01
#> "0132" "0231" "0132" "0112" "01313" "0133"
#> TCGA.ZJ.A8QQ.01 TCGA.FU.A3EO.11 TCGA.DG.A2KJ.01 TCGA.VS.A954.01 TCGA.MA.AA42.01 TCGA.C5.A8YQ.01
#> "0231" "0112" "01113" "0212" "021113" "021112"
#> TCGA.DS.A7WF.01 TCGA.EK.A2R7.01 TCGA.EK.A3GJ.01 TCGA.C5.A902.01 TCGA.MA.AA3W.01 TCGA.C5.A905.01
#> "0312" "01312" "0233" "0232" "021111" "01211"
#> TCGA.EK.A2RN.01 TCGA.FU.A57G.01 TCGA.C5.A8YR.01 TCGA.EK.A2R9.01 TCGA.FU.A3EO.01 TCGA.IR.A3LC.01
#> "01311" "0112" "0133" "02112" "03112" "0212"
#> TCGA.VS.A8QA.01 TCGA.C5.A3HD.01 TCGA.MY.A5BE.01 TCGA.EA.A50E.01 TCGA.VS.A8QH.01 TCGA.ZJ.A8QR.01
#> "0313" "0233" "01112" "0212" "01113" "01212"
#> TCGA.C5.A907.01 TCGA.IR.A3LK.01 TCGA.C5.A8ZZ.01 TCGA.VS.A8EK.01 TCGA.C5.A7UC.01 TCGA.C5.A8XJ.01
#> "01113" "022212" "0123" "0212" "01111" "01312"
#> TCGA.IR.A3LH.01 TCGA.EK.A3GM.01 TCGA.VS.A8Q8.01 TCGA.EK.A2RO.01 TCGA.MY.A5BD.01 TCGA.2W.A8YY.01
#> "0231" "01131" "01311" "02112" "0312" "0122"
#> TCGA.C5.A2LZ.01 TCGA.C5.A901.01 TCGA.VS.A953.01 TCGA.MU.A51Y.01 TCGA.EK.A2RK.01 TCGA.UC.A7PD.01
#> "02222" "0212" "0212" "01112" "01312" "01111"
#> TCGA.EA.A3HS.01 TCGA.VS.A8QM.01 TCGA.EA.A3HU.01 TCGA.VS.A94X.01 TCGA.C5.A7CO.01 TCGA.C5.A3HF.01
#> "02112" "01112" "01112" "01111" "021113" "01113"
#> TCGA.IR.A3LL.01 TCGA.MY.A913.01 TCGA.VS.A952.01 TCGA.IR.A3LI.01 TCGA.VS.A94W.01 TCGA.MY.A5BF.01
#> "0232" "01111" "0313" "0313" "021111" "0232"
#> TCGA.EK.A2RC.01 TCGA.VS.A8EL.01 TCGA.EA.A97N.01 TCGA.EA.A3HQ.01 TCGA.EK.A2RD.01 TCGA.C5.A8YT.01
#> "02222" "0231" "01212" "02222" "01312" "0112"
#> TCGA.FU.A3HZ.01 TCGA.VS.A8EJ.01 TCGA.C5.A3HL.01 TCGA.UC.A7PF.01 TCGA.C5.A8XK.01 TCGA.EX.A8YF.01
#> "0122" "0112" "01312" "0232" "0132" "01113"
#> TCGA.HM.A4S6.01 TCGA.VS.A8Q9.01 TCGA.MA.AA41.01 TCGA.EK.A3GN.01 TCGA.MA.AA3Y.01 TCGA.MA.AA3Z.01
#> "01313" "0231" "021114" "0212" "01111" "01312"
#> TCGA.EK.A2RE.01 TCGA.C5.A1BQ.01 TCGA.ZJ.A8QO.01 TCGA.JW.A852.01 TCGA.DS.A7WH.01 TCGA.JW.AAVH.01
#> "01311" "01313" "021113" "0212" "032" "022213"
#> TCGA.EA.A556.01 TCGA.EA.A44S.01 TCGA.4J.AA1J.01 TCGA.IR.A3L7.01 TCGA.C5.A7X3.01 TCGA.HG.A2PA.01
#> "0133" "01212" "01212" "02222" "0132" "01112"
#> TCGA.C5.A8XH.01 TCGA.C5.A7XC.01 TCGA.VS.A8EI.01 TCGA.VS.A8QC.01 TCGA.C5.A7UH.01 TCGA.WL.A834.01
#> "0233" "01311" "0231" "02222" "01211" "02222"
#> TCGA.C5.A8XI.01 TCGA.DS.A7WI.01 TCGA.VS.A8QF.01 TCGA.EA.A3HR.01 TCGA.DG.A2KL.01 TCGA.EK.A2RL.01
#> "0232" "0233" "02222" "01313" "01311" "03112"
#> TCGA.EK.A2PG.01 TCGA.BI.A0VR.01 TCGA.DS.A0VL.01 TCGA.VS.A8EC.01 TCGA.EA.A3QE.01 TCGA.DS.A0VM.01
#> "022212" "01312" "01311" "0221" "021111" "021114"
#> TCGA.FU.A3HY.01 TCGA.Q1.A5R1.01 TCGA.DR.A0ZM.01 TCGA.Q1.A6DW.01 TCGA.DS.A0VK.01 TCGA.DS.A3LQ.01
#> "022212" "03112" "0134" "0212" "01312" "0221"
#> TCGA.EA.A3QD.01 TCGA.JW.A5VJ.01 TCGA.LP.A5U3.01 TCGA.EA.A6QX.01 TCGA.EK.A2RA.01 TCGA.FU.A5XV.01
#> "0232" "0134" "02222" "02222" "022212" "01212"
#> TCGA.Q1.A5R2.01 TCGA.HM.A3JJ.01 TCGA.C5.A2LS.01 TCGA.C5.A7X8.01 TCGA.EK.A2RJ.01 TCGA.EA.A3HT.01
#> "022212" "01312" "0313" "032" "0133" "01311"
#> TCGA.LP.A7HU.01 TCGA.MU.A8JM.01 TCGA.EK.A2IP.01 TCGA.JW.A5VL.01 TCGA.FU.A3TX.01 TCGA.DG.A2KK.01
#> "0312" "021111" "02222" "022211" "01133" "0313"
#> TCGA.EK.A2PI.01 TCGA.Q1.A73S.01 TCGA.EK.A2IR.01 TCGA.HM.A6W2.01 TCGA.VS.A8EH.01 TCGA.JW.A5VH.01
#> "01312" "0122" "02112" "0122" "01132" "0122"
#> TCGA.C5.A2LV.01 TCGA.VS.A8EB.01 TCGA.RA.A741.01 TCGA.VS.A8EG.01 TCGA.DG.A2KH.01 TCGA.C5.A7UE.01
#> "0212" "01132" "01112" "02222" "01131" "021111"
#> TCGA.C5.A2LT.01 TCGA.EA.A5ZD.01 TCGA.Q1.A73R.01 TCGA.JW.A5VK.01 TCGA.EK.A2RM.01 TCGA.C5.A7UI.01
#> "01111" "0134" "0312" "0221" "01131" "01313"
#> TCGA.EK.A2PL.01 TCGA.EK.A2PM.01 TCGA.EK.A2GZ.01 TCGA.HM.A3JK.01 TCGA.C5.A2M1.01 TCGA.HM.A6W2.06
#> "01311" "0123" "01112" "01112" "03112" "0122"
#> TCGA.C5.A7X5.01 TCGA.IR.A3LA.01 TCGA.EK.A2PK.01 TCGA.EA.A5ZF.01 TCGA.XS.A8TJ.01 TCGA.BI.A0VS.01
#> "0233" "0122" "0133" "0132" "021111" "0132"
#> TCGA.DS.A0VN.01 TCGA.JX.A5QV.01 TCGA.EK.A2R8.01 TCGA.EA.A1QS.01 TCGA.C5.A3HE.01 TCGA.IR.A3LF.01
#> "021114" "01311" "0132" "01112" "032" "03112"
#> TCGA.DR.A0ZL.01 TCGA.FU.A3WB.01 TCGA.JX.A3PZ.01 TCGA.EA.A5O9.01 TCGA.HM.A3JJ.11 TCGA.DS.A5RQ.01
#> "021111" "02112" "0133" "02112" "0112" "01311"
#> TCGA.EK.A2H0.01 TCGA.EX.A1H6.01 TCGA.EA.A5ZE.01 TCGA.C5.A2LY.01 TCGA.FU.A3TQ.01 TCGA.EK.A2RB.01
#> "0231" "032" "02112" "01132" "02222" "022212"
#> TCGA.JW.A5VI.01 TCGA.EK.A2H1.01 TCGA.JX.A3Q8.01 TCGA.FU.A3YQ.01 TCGA.EX.A69L.01 TCGA.C5.A7CH.01
#> "021114" "0112" "0313" "021111" "01311" "021114"
#> TCGA.FU.A2QG.01 TCGA.C5.A2M2.01 TCGA.JW.A5VG.01 TCGA.PN.A8MA.01 TCGA.DG.A2KM.01 TCGA.C5.A2LX.01
#> "01212" "03112" "01132" "0122" "0112" "02222"
#> TCGA.EX.A3L1.01 TCGA.LP.A5U2.01 TCGA.FU.A3NI.01 TCGA.Q1.A5R3.01 TCGA.FU.A770.01 TCGA.C5.A7CM.01
#> "01111" "0212" "0232" "01312" "032" "01131"
#> TCGA.JX.A3Q0.01 TCGA.EA.A5FO.01 TCGA.VS.A9V3.01 TCGA.C5.A7CL.01 TCGA.VS.A959.01 TCGA.LP.A4AX.01
#> "01211" "0312" "0212" "01311" "01113" "01111"
#> TCGA.C5.A1MN.01 TCGA.ZJ.AAXN.01 TCGA.MA.AA3X.01 TCGA.UC.A7PG.01 TCGA.Q1.A6DV.01 TCGA.DS.A1OD.01
#> "022212" "0132" "01211" "01311" "032" "01312"
#> TCGA.C5.A1M7.01 TCGA.BI.A20A.01 TCGA.VS.A9UO.01 TCGA.EA.A1QT.01 TCGA.EX.A69M.01 TCGA.VS.A9UH.01
#> "0134" "021113" "032" "022213" "0232" "01111"
#> TCGA.VS.A9U7.01 TCGA.ZJ.AAXD.01 TCGA.VS.A9UB.01 TCGA.EA.A410.01 TCGA.ZJ.AB0I.01 TCGA.VS.A9UD.01
#> "02222" "01312" "01111" "0122" "01212" "0232"
#> TCGA.VS.A9U6.01 TCGA.ZX.AA5X.01 TCGA.C5.A0TN.01 TCGA.C5.A7CJ.01 TCGA.C5.A1MJ.01 TCGA.EA.A78R.01
#> "01132" "021111" "01132" "021111" "032" "0232"
#> TCGA.VS.A9UY.01 TCGA.VS.A9U5.01 TCGA.DS.A1OC.01 TCGA.ZJ.AAXB.01 TCGA.EX.A449.01 TCGA.C5.A1BL.01
#> "022211" "0212" "0233" "0123" "03112" "022212"
#> TCGA.VS.A9UQ.01 TCGA.DS.A1OB.01 TCGA.HG.A9SC.01 TCGA.ZJ.AAXT.01 TCGA.IR.A3LB.01 TCGA.C5.A1ML.01
#> "03112" "0123" "0123" "0134" "032" "01133"
#> TCGA.VS.A9UV.01 TCGA.LP.A4AU.01 TCGA.Q1.A6DT.01 TCGA.C5.A1M8.01 TCGA.C5.A1ME.01 TCGA.ZJ.AAXU.01
#> "0212" "01113" "021112" "0212" "032" "01312"
#> TCGA.VS.A957.01 TCGA.VS.A9V5.01 TCGA.MU.A5YI.01 TCGA.ZJ.AAX4.01 TCGA.C5.A1MK.01 TCGA.JW.A69B.01
#> "02222" "03111" "02112" "02112" "01313" "03112"
#> TCGA.VS.A958.01 TCGA.ZJ.AAXJ.01 TCGA.R2.A69V.01 TCGA.EA.A411.01 TCGA.VS.A9UP.01 TCGA.C5.A1MI.01
#> "0134" "0232" "01113" "0123" "01113" "01131"
#> TCGA.DS.A1O9.01 TCGA.VS.A9UZ.01 TCGA.EA.A43B.01 TCGA.ZJ.AAX8.01 TCGA.ZJ.AAXI.01 TCGA.VS.A9UT.01
#> "021111" "03112" "0231" "01112" "022212" "0112"
#> TCGA.DS.A1OA.01 TCGA.C5.A1MQ.01 TCGA.VS.A9V0.01 TCGA.VS.A9UC.01 TCGA.ZJ.AAXA.01 TCGA.Q1.A73P.01
#> "02222" "0231" "0133" "021112" "01211" "03112"
#> TCGA.VS.A9V2.01 TCGA.VS.A9UU.01 TCGA.LP.A4AV.01 TCGA.VS.A9UR.01 TCGA.VS.A9V1.01 TCGA.C5.A7CG.01
#> "021111" "0232" "01313" "032" "032" "0212"
#> TCGA.UC.A7PI.01 TCGA.EX.A1H5.01 TCGA.ZJ.AAXF.01 TCGA.VS.A9UL.01 TCGA.EA.A3Y4.01 TCGA.C5.A7CK.01
#> "032" "02112" "01112" "032" "0132" "0232"
#> TCGA.UC.A7PG.06 TCGA.VS.A9UJ.01 TCGA.Q1.A73O.01 TCGA.VS.A950.01 TCGA.EA.A439.01 TCGA.VS.A9UM.01
#> "01211" "0122" "0134" "022212" "01131" "01211"
#> TCGA.C5.A1MP.01 TCGA.VS.A9UI.01 TCGA.ZJ.AB0H.01 TCGA.Q1.A73Q.01 TCGA.C5.A1MH.01 TCGA.VS.A9V4.01
#> "01313" "022212" "01312" "0221" "021111" "0112"
#> TCGA.FU.A40J.01 TCGA.VS.A9UA.01 TCGA.LP.A4AW.01 TCGA.MA.AA43.01 TCGA.C5.A1BN.01 TCGA.VS.AA62.01
#> "03111" "01311" "01312" "032" "01212" "01111"
#> TCGA.C5.A1BM.01 TCGA.C5.A1M6.01 TCGA.C5.A1BE.01 TCGA.FU.A23K.01 TCGA.C5.A1BJ.01 TCGA.FU.A23L.01
#> "0134" "01131" "01312" "032" "01112" "0134"
#> TCGA.C5.A1M5.01 TCGA.C5.A1MF.01 TCGA.C5.A1BF.01 TCGA.C5.A1BK.01 TCGA.C5.A1BI.01 TCGA.C5.A1M9.01
#> "022212" "02112" "01132" "021111" "0134" "03112"
get_classes(res_rh, merge_node = merge_node_param(min_n_signatures = 1228))
#> TCGA.EK.A3GK.01 TCGA.GH.A9DA.01 TCGA.VS.A94Y.01 TCGA.MY.A5BF.11 TCGA.VS.A94Z.01 TCGA.EA.A4BA.01
#> "0132" "0231" "0132" "0112" "0131" "0133"
#> TCGA.ZJ.A8QQ.01 TCGA.FU.A3EO.11 TCGA.DG.A2KJ.01 TCGA.VS.A954.01 TCGA.MA.AA42.01 TCGA.C5.A8YQ.01
#> "0231" "0112" "01113" "0212" "021113" "021112"
#> TCGA.DS.A7WF.01 TCGA.EK.A2R7.01 TCGA.EK.A3GJ.01 TCGA.C5.A902.01 TCGA.MA.AA3W.01 TCGA.C5.A905.01
#> "0312" "0131" "0233" "0232" "021111" "01211"
#> TCGA.EK.A2RN.01 TCGA.FU.A57G.01 TCGA.C5.A8YR.01 TCGA.EK.A2R9.01 TCGA.FU.A3EO.01 TCGA.IR.A3LC.01
#> "0131" "0112" "0133" "02112" "03112" "0212"
#> TCGA.VS.A8QA.01 TCGA.C5.A3HD.01 TCGA.MY.A5BE.01 TCGA.EA.A50E.01 TCGA.VS.A8QH.01 TCGA.ZJ.A8QR.01
#> "0313" "0233" "01112" "0212" "01113" "01212"
#> TCGA.C5.A907.01 TCGA.IR.A3LK.01 TCGA.C5.A8ZZ.01 TCGA.VS.A8EK.01 TCGA.C5.A7UC.01 TCGA.C5.A8XJ.01
#> "01113" "022212" "0123" "0212" "01111" "0131"
#> TCGA.IR.A3LH.01 TCGA.EK.A3GM.01 TCGA.VS.A8Q8.01 TCGA.EK.A2RO.01 TCGA.MY.A5BD.01 TCGA.2W.A8YY.01
#> "0231" "01131" "0131" "02112" "0312" "0122"
#> TCGA.C5.A2LZ.01 TCGA.C5.A901.01 TCGA.VS.A953.01 TCGA.MU.A51Y.01 TCGA.EK.A2RK.01 TCGA.UC.A7PD.01
#> "02222" "0212" "0212" "01112" "0131" "01111"
#> TCGA.EA.A3HS.01 TCGA.VS.A8QM.01 TCGA.EA.A3HU.01 TCGA.VS.A94X.01 TCGA.C5.A7CO.01 TCGA.C5.A3HF.01
#> "02112" "01112" "01112" "01111" "021113" "01113"
#> TCGA.IR.A3LL.01 TCGA.MY.A913.01 TCGA.VS.A952.01 TCGA.IR.A3LI.01 TCGA.VS.A94W.01 TCGA.MY.A5BF.01
#> "0232" "01111" "0313" "0313" "021111" "0232"
#> TCGA.EK.A2RC.01 TCGA.VS.A8EL.01 TCGA.EA.A97N.01 TCGA.EA.A3HQ.01 TCGA.EK.A2RD.01 TCGA.C5.A8YT.01
#> "02222" "0231" "01212" "02222" "0131" "0112"
#> TCGA.FU.A3HZ.01 TCGA.VS.A8EJ.01 TCGA.C5.A3HL.01 TCGA.UC.A7PF.01 TCGA.C5.A8XK.01 TCGA.EX.A8YF.01
#> "0122" "0112" "0131" "0232" "0132" "01113"
#> TCGA.HM.A4S6.01 TCGA.VS.A8Q9.01 TCGA.MA.AA41.01 TCGA.EK.A3GN.01 TCGA.MA.AA3Y.01 TCGA.MA.AA3Z.01
#> "0131" "0231" "021114" "0212" "01111" "0131"
#> TCGA.EK.A2RE.01 TCGA.C5.A1BQ.01 TCGA.ZJ.A8QO.01 TCGA.JW.A852.01 TCGA.DS.A7WH.01 TCGA.JW.AAVH.01
#> "0131" "0131" "021113" "0212" "032" "022213"
#> TCGA.EA.A556.01 TCGA.EA.A44S.01 TCGA.4J.AA1J.01 TCGA.IR.A3L7.01 TCGA.C5.A7X3.01 TCGA.HG.A2PA.01
#> "0133" "01212" "01212" "02222" "0132" "01112"
#> TCGA.C5.A8XH.01 TCGA.C5.A7XC.01 TCGA.VS.A8EI.01 TCGA.VS.A8QC.01 TCGA.C5.A7UH.01 TCGA.WL.A834.01
#> "0233" "0131" "0231" "02222" "01211" "02222"
#> TCGA.C5.A8XI.01 TCGA.DS.A7WI.01 TCGA.VS.A8QF.01 TCGA.EA.A3HR.01 TCGA.DG.A2KL.01 TCGA.EK.A2RL.01
#> "0232" "0233" "02222" "0131" "0131" "03112"
#> TCGA.EK.A2PG.01 TCGA.BI.A0VR.01 TCGA.DS.A0VL.01 TCGA.VS.A8EC.01 TCGA.EA.A3QE.01 TCGA.DS.A0VM.01
#> "022212" "0131" "0131" "0221" "021111" "021114"
#> TCGA.FU.A3HY.01 TCGA.Q1.A5R1.01 TCGA.DR.A0ZM.01 TCGA.Q1.A6DW.01 TCGA.DS.A0VK.01 TCGA.DS.A3LQ.01
#> "022212" "03112" "0134" "0212" "0131" "0221"
#> TCGA.EA.A3QD.01 TCGA.JW.A5VJ.01 TCGA.LP.A5U3.01 TCGA.EA.A6QX.01 TCGA.EK.A2RA.01 TCGA.FU.A5XV.01
#> "0232" "0134" "02222" "02222" "022212" "01212"
#> TCGA.Q1.A5R2.01 TCGA.HM.A3JJ.01 TCGA.C5.A2LS.01 TCGA.C5.A7X8.01 TCGA.EK.A2RJ.01 TCGA.EA.A3HT.01
#> "022212" "0131" "0313" "032" "0133" "0131"
#> TCGA.LP.A7HU.01 TCGA.MU.A8JM.01 TCGA.EK.A2IP.01 TCGA.JW.A5VL.01 TCGA.FU.A3TX.01 TCGA.DG.A2KK.01
#> "0312" "021111" "02222" "022211" "01133" "0313"
#> TCGA.EK.A2PI.01 TCGA.Q1.A73S.01 TCGA.EK.A2IR.01 TCGA.HM.A6W2.01 TCGA.VS.A8EH.01 TCGA.JW.A5VH.01
#> "0131" "0122" "02112" "0122" "01132" "0122"
#> TCGA.C5.A2LV.01 TCGA.VS.A8EB.01 TCGA.RA.A741.01 TCGA.VS.A8EG.01 TCGA.DG.A2KH.01 TCGA.C5.A7UE.01
#> "0212" "01132" "01112" "02222" "01131" "021111"
#> TCGA.C5.A2LT.01 TCGA.EA.A5ZD.01 TCGA.Q1.A73R.01 TCGA.JW.A5VK.01 TCGA.EK.A2RM.01 TCGA.C5.A7UI.01
#> "01111" "0134" "0312" "0221" "01131" "0131"
#> TCGA.EK.A2PL.01 TCGA.EK.A2PM.01 TCGA.EK.A2GZ.01 TCGA.HM.A3JK.01 TCGA.C5.A2M1.01 TCGA.HM.A6W2.06
#> "0131" "0123" "01112" "01112" "03112" "0122"
#> TCGA.C5.A7X5.01 TCGA.IR.A3LA.01 TCGA.EK.A2PK.01 TCGA.EA.A5ZF.01 TCGA.XS.A8TJ.01 TCGA.BI.A0VS.01
#> "0233" "0122" "0133" "0132" "021111" "0132"
#> TCGA.DS.A0VN.01 TCGA.JX.A5QV.01 TCGA.EK.A2R8.01 TCGA.EA.A1QS.01 TCGA.C5.A3HE.01 TCGA.IR.A3LF.01
#> "021114" "0131" "0132" "01112" "032" "03112"
#> TCGA.DR.A0ZL.01 TCGA.FU.A3WB.01 TCGA.JX.A3PZ.01 TCGA.EA.A5O9.01 TCGA.HM.A3JJ.11 TCGA.DS.A5RQ.01
#> "021111" "02112" "0133" "02112" "0112" "0131"
#> TCGA.EK.A2H0.01 TCGA.EX.A1H6.01 TCGA.EA.A5ZE.01 TCGA.C5.A2LY.01 TCGA.FU.A3TQ.01 TCGA.EK.A2RB.01
#> "0231" "032" "02112" "01132" "02222" "022212"
#> TCGA.JW.A5VI.01 TCGA.EK.A2H1.01 TCGA.JX.A3Q8.01 TCGA.FU.A3YQ.01 TCGA.EX.A69L.01 TCGA.C5.A7CH.01
#> "021114" "0112" "0313" "021111" "0131" "021114"
#> TCGA.FU.A2QG.01 TCGA.C5.A2M2.01 TCGA.JW.A5VG.01 TCGA.PN.A8MA.01 TCGA.DG.A2KM.01 TCGA.C5.A2LX.01
#> "01212" "03112" "01132" "0122" "0112" "02222"
#> TCGA.EX.A3L1.01 TCGA.LP.A5U2.01 TCGA.FU.A3NI.01 TCGA.Q1.A5R3.01 TCGA.FU.A770.01 TCGA.C5.A7CM.01
#> "01111" "0212" "0232" "0131" "032" "01131"
#> TCGA.JX.A3Q0.01 TCGA.EA.A5FO.01 TCGA.VS.A9V3.01 TCGA.C5.A7CL.01 TCGA.VS.A959.01 TCGA.LP.A4AX.01
#> "01211" "0312" "0212" "0131" "01113" "01111"
#> TCGA.C5.A1MN.01 TCGA.ZJ.AAXN.01 TCGA.MA.AA3X.01 TCGA.UC.A7PG.01 TCGA.Q1.A6DV.01 TCGA.DS.A1OD.01
#> "022212" "0132" "01211" "0131" "032" "0131"
#> TCGA.C5.A1M7.01 TCGA.BI.A20A.01 TCGA.VS.A9UO.01 TCGA.EA.A1QT.01 TCGA.EX.A69M.01 TCGA.VS.A9UH.01
#> "0134" "021113" "032" "022213" "0232" "01111"
#> TCGA.VS.A9U7.01 TCGA.ZJ.AAXD.01 TCGA.VS.A9UB.01 TCGA.EA.A410.01 TCGA.ZJ.AB0I.01 TCGA.VS.A9UD.01
#> "02222" "0131" "01111" "0122" "01212" "0232"
#> TCGA.VS.A9U6.01 TCGA.ZX.AA5X.01 TCGA.C5.A0TN.01 TCGA.C5.A7CJ.01 TCGA.C5.A1MJ.01 TCGA.EA.A78R.01
#> "01132" "021111" "01132" "021111" "032" "0232"
#> TCGA.VS.A9UY.01 TCGA.VS.A9U5.01 TCGA.DS.A1OC.01 TCGA.ZJ.AAXB.01 TCGA.EX.A449.01 TCGA.C5.A1BL.01
#> "022211" "0212" "0233" "0123" "03112" "022212"
#> TCGA.VS.A9UQ.01 TCGA.DS.A1OB.01 TCGA.HG.A9SC.01 TCGA.ZJ.AAXT.01 TCGA.IR.A3LB.01 TCGA.C5.A1ML.01
#> "03112" "0123" "0123" "0134" "032" "01133"
#> TCGA.VS.A9UV.01 TCGA.LP.A4AU.01 TCGA.Q1.A6DT.01 TCGA.C5.A1M8.01 TCGA.C5.A1ME.01 TCGA.ZJ.AAXU.01
#> "0212" "01113" "021112" "0212" "032" "0131"
#> TCGA.VS.A957.01 TCGA.VS.A9V5.01 TCGA.MU.A5YI.01 TCGA.ZJ.AAX4.01 TCGA.C5.A1MK.01 TCGA.JW.A69B.01
#> "02222" "03111" "02112" "02112" "0131" "03112"
#> TCGA.VS.A958.01 TCGA.ZJ.AAXJ.01 TCGA.R2.A69V.01 TCGA.EA.A411.01 TCGA.VS.A9UP.01 TCGA.C5.A1MI.01
#> "0134" "0232" "01113" "0123" "01113" "01131"
#> TCGA.DS.A1O9.01 TCGA.VS.A9UZ.01 TCGA.EA.A43B.01 TCGA.ZJ.AAX8.01 TCGA.ZJ.AAXI.01 TCGA.VS.A9UT.01
#> "021111" "03112" "0231" "01112" "022212" "0112"
#> TCGA.DS.A1OA.01 TCGA.C5.A1MQ.01 TCGA.VS.A9V0.01 TCGA.VS.A9UC.01 TCGA.ZJ.AAXA.01 TCGA.Q1.A73P.01
#> "02222" "0231" "0133" "021112" "01211" "03112"
#> TCGA.VS.A9V2.01 TCGA.VS.A9UU.01 TCGA.LP.A4AV.01 TCGA.VS.A9UR.01 TCGA.VS.A9V1.01 TCGA.C5.A7CG.01
#> "021111" "0232" "0131" "032" "032" "0212"
#> TCGA.UC.A7PI.01 TCGA.EX.A1H5.01 TCGA.ZJ.AAXF.01 TCGA.VS.A9UL.01 TCGA.EA.A3Y4.01 TCGA.C5.A7CK.01
#> "032" "02112" "01112" "032" "0132" "0232"
#> TCGA.UC.A7PG.06 TCGA.VS.A9UJ.01 TCGA.Q1.A73O.01 TCGA.VS.A950.01 TCGA.EA.A439.01 TCGA.VS.A9UM.01
#> "01211" "0122" "0134" "022212" "01131" "01211"
#> TCGA.C5.A1MP.01 TCGA.VS.A9UI.01 TCGA.ZJ.AB0H.01 TCGA.Q1.A73Q.01 TCGA.C5.A1MH.01 TCGA.VS.A9V4.01
#> "0131" "022212" "0131" "0221" "021111" "0112"
#> TCGA.FU.A40J.01 TCGA.VS.A9UA.01 TCGA.LP.A4AW.01 TCGA.MA.AA43.01 TCGA.C5.A1BN.01 TCGA.VS.AA62.01
#> "03111" "0131" "0131" "032" "01212" "01111"
#> TCGA.C5.A1BM.01 TCGA.C5.A1M6.01 TCGA.C5.A1BE.01 TCGA.FU.A23K.01 TCGA.C5.A1BJ.01 TCGA.FU.A23L.01
#> "0134" "01131" "0131" "032" "01112" "0134"
#> TCGA.C5.A1M5.01 TCGA.C5.A1MF.01 TCGA.C5.A1BF.01 TCGA.C5.A1BK.01 TCGA.C5.A1BI.01 TCGA.C5.A1M9.01
#> "022212" "02112" "01132" "021111" "0134" "03112"
get_classes(res_rh, merge_node = merge_node_param(min_n_signatures = 1463))
#> TCGA.EK.A3GK.01 TCGA.GH.A9DA.01 TCGA.VS.A94Y.01 TCGA.MY.A5BF.11 TCGA.VS.A94Z.01 TCGA.EA.A4BA.01
#> "0132" "0231" "0132" "0112" "0131" "0133"
#> TCGA.ZJ.A8QQ.01 TCGA.FU.A3EO.11 TCGA.DG.A2KJ.01 TCGA.VS.A954.01 TCGA.MA.AA42.01 TCGA.C5.A8YQ.01
#> "0231" "0112" "01113" "021" "021113" "021112"
#> TCGA.DS.A7WF.01 TCGA.EK.A2R7.01 TCGA.EK.A3GJ.01 TCGA.C5.A902.01 TCGA.MA.AA3W.01 TCGA.C5.A905.01
#> "0312" "0131" "0233" "0232" "021111" "01211"
#> TCGA.EK.A2RN.01 TCGA.FU.A57G.01 TCGA.C5.A8YR.01 TCGA.EK.A2R9.01 TCGA.FU.A3EO.01 TCGA.IR.A3LC.01
#> "0131" "0112" "0133" "021" "03112" "021"
#> TCGA.VS.A8QA.01 TCGA.C5.A3HD.01 TCGA.MY.A5BE.01 TCGA.EA.A50E.01 TCGA.VS.A8QH.01 TCGA.ZJ.A8QR.01
#> "0313" "0233" "01112" "021" "01113" "01212"
#> TCGA.C5.A907.01 TCGA.IR.A3LK.01 TCGA.C5.A8ZZ.01 TCGA.VS.A8EK.01 TCGA.C5.A7UC.01 TCGA.C5.A8XJ.01
#> "01113" "022212" "0123" "021" "01111" "0131"
#> TCGA.IR.A3LH.01 TCGA.EK.A3GM.01 TCGA.VS.A8Q8.01 TCGA.EK.A2RO.01 TCGA.MY.A5BD.01 TCGA.2W.A8YY.01
#> "0231" "01131" "0131" "021" "0312" "0122"
#> TCGA.C5.A2LZ.01 TCGA.C5.A901.01 TCGA.VS.A953.01 TCGA.MU.A51Y.01 TCGA.EK.A2RK.01 TCGA.UC.A7PD.01
#> "02222" "021" "021" "01112" "0131" "01111"
#> TCGA.EA.A3HS.01 TCGA.VS.A8QM.01 TCGA.EA.A3HU.01 TCGA.VS.A94X.01 TCGA.C5.A7CO.01 TCGA.C5.A3HF.01
#> "021" "01112" "01112" "01111" "021113" "01113"
#> TCGA.IR.A3LL.01 TCGA.MY.A913.01 TCGA.VS.A952.01 TCGA.IR.A3LI.01 TCGA.VS.A94W.01 TCGA.MY.A5BF.01
#> "0232" "01111" "0313" "0313" "021111" "0232"
#> TCGA.EK.A2RC.01 TCGA.VS.A8EL.01 TCGA.EA.A97N.01 TCGA.EA.A3HQ.01 TCGA.EK.A2RD.01 TCGA.C5.A8YT.01
#> "02222" "0231" "01212" "02222" "0131" "0112"
#> TCGA.FU.A3HZ.01 TCGA.VS.A8EJ.01 TCGA.C5.A3HL.01 TCGA.UC.A7PF.01 TCGA.C5.A8XK.01 TCGA.EX.A8YF.01
#> "0122" "0112" "0131" "0232" "0132" "01113"
#> TCGA.HM.A4S6.01 TCGA.VS.A8Q9.01 TCGA.MA.AA41.01 TCGA.EK.A3GN.01 TCGA.MA.AA3Y.01 TCGA.MA.AA3Z.01
#> "0131" "0231" "021114" "021" "01111" "0131"
#> TCGA.EK.A2RE.01 TCGA.C5.A1BQ.01 TCGA.ZJ.A8QO.01 TCGA.JW.A852.01 TCGA.DS.A7WH.01 TCGA.JW.AAVH.01
#> "0131" "0131" "021113" "021" "032" "022213"
#> TCGA.EA.A556.01 TCGA.EA.A44S.01 TCGA.4J.AA1J.01 TCGA.IR.A3L7.01 TCGA.C5.A7X3.01 TCGA.HG.A2PA.01
#> "0133" "01212" "01212" "02222" "0132" "01112"
#> TCGA.C5.A8XH.01 TCGA.C5.A7XC.01 TCGA.VS.A8EI.01 TCGA.VS.A8QC.01 TCGA.C5.A7UH.01 TCGA.WL.A834.01
#> "0233" "0131" "0231" "02222" "01211" "02222"
#> TCGA.C5.A8XI.01 TCGA.DS.A7WI.01 TCGA.VS.A8QF.01 TCGA.EA.A3HR.01 TCGA.DG.A2KL.01 TCGA.EK.A2RL.01
#> "0232" "0233" "02222" "0131" "0131" "03112"
#> TCGA.EK.A2PG.01 TCGA.BI.A0VR.01 TCGA.DS.A0VL.01 TCGA.VS.A8EC.01 TCGA.EA.A3QE.01 TCGA.DS.A0VM.01
#> "022212" "0131" "0131" "0221" "021111" "021114"
#> TCGA.FU.A3HY.01 TCGA.Q1.A5R1.01 TCGA.DR.A0ZM.01 TCGA.Q1.A6DW.01 TCGA.DS.A0VK.01 TCGA.DS.A3LQ.01
#> "022212" "03112" "0134" "021" "0131" "0221"
#> TCGA.EA.A3QD.01 TCGA.JW.A5VJ.01 TCGA.LP.A5U3.01 TCGA.EA.A6QX.01 TCGA.EK.A2RA.01 TCGA.FU.A5XV.01
#> "0232" "0134" "02222" "02222" "022212" "01212"
#> TCGA.Q1.A5R2.01 TCGA.HM.A3JJ.01 TCGA.C5.A2LS.01 TCGA.C5.A7X8.01 TCGA.EK.A2RJ.01 TCGA.EA.A3HT.01
#> "022212" "0131" "0313" "032" "0133" "0131"
#> TCGA.LP.A7HU.01 TCGA.MU.A8JM.01 TCGA.EK.A2IP.01 TCGA.JW.A5VL.01 TCGA.FU.A3TX.01 TCGA.DG.A2KK.01
#> "0312" "021111" "02222" "022211" "01133" "0313"
#> TCGA.EK.A2PI.01 TCGA.Q1.A73S.01 TCGA.EK.A2IR.01 TCGA.HM.A6W2.01 TCGA.VS.A8EH.01 TCGA.JW.A5VH.01
#> "0131" "0122" "021" "0122" "01132" "0122"
#> TCGA.C5.A2LV.01 TCGA.VS.A8EB.01 TCGA.RA.A741.01 TCGA.VS.A8EG.01 TCGA.DG.A2KH.01 TCGA.C5.A7UE.01
#> "021" "01132" "01112" "02222" "01131" "021111"
#> TCGA.C5.A2LT.01 TCGA.EA.A5ZD.01 TCGA.Q1.A73R.01 TCGA.JW.A5VK.01 TCGA.EK.A2RM.01 TCGA.C5.A7UI.01
#> "01111" "0134" "0312" "0221" "01131" "0131"
#> TCGA.EK.A2PL.01 TCGA.EK.A2PM.01 TCGA.EK.A2GZ.01 TCGA.HM.A3JK.01 TCGA.C5.A2M1.01 TCGA.HM.A6W2.06
#> "0131" "0123" "01112" "01112" "03112" "0122"
#> TCGA.C5.A7X5.01 TCGA.IR.A3LA.01 TCGA.EK.A2PK.01 TCGA.EA.A5ZF.01 TCGA.XS.A8TJ.01 TCGA.BI.A0VS.01
#> "0233" "0122" "0133" "0132" "021111" "0132"
#> TCGA.DS.A0VN.01 TCGA.JX.A5QV.01 TCGA.EK.A2R8.01 TCGA.EA.A1QS.01 TCGA.C5.A3HE.01 TCGA.IR.A3LF.01
#> "021114" "0131" "0132" "01112" "032" "03112"
#> TCGA.DR.A0ZL.01 TCGA.FU.A3WB.01 TCGA.JX.A3PZ.01 TCGA.EA.A5O9.01 TCGA.HM.A3JJ.11 TCGA.DS.A5RQ.01
#> "021111" "021" "0133" "021" "0112" "0131"
#> TCGA.EK.A2H0.01 TCGA.EX.A1H6.01 TCGA.EA.A5ZE.01 TCGA.C5.A2LY.01 TCGA.FU.A3TQ.01 TCGA.EK.A2RB.01
#> "0231" "032" "021" "01132" "02222" "022212"
#> TCGA.JW.A5VI.01 TCGA.EK.A2H1.01 TCGA.JX.A3Q8.01 TCGA.FU.A3YQ.01 TCGA.EX.A69L.01 TCGA.C5.A7CH.01
#> "021114" "0112" "0313" "021111" "0131" "021114"
#> TCGA.FU.A2QG.01 TCGA.C5.A2M2.01 TCGA.JW.A5VG.01 TCGA.PN.A8MA.01 TCGA.DG.A2KM.01 TCGA.C5.A2LX.01
#> "01212" "03112" "01132" "0122" "0112" "02222"
#> TCGA.EX.A3L1.01 TCGA.LP.A5U2.01 TCGA.FU.A3NI.01 TCGA.Q1.A5R3.01 TCGA.FU.A770.01 TCGA.C5.A7CM.01
#> "01111" "021" "0232" "0131" "032" "01131"
#> TCGA.JX.A3Q0.01 TCGA.EA.A5FO.01 TCGA.VS.A9V3.01 TCGA.C5.A7CL.01 TCGA.VS.A959.01 TCGA.LP.A4AX.01
#> "01211" "0312" "021" "0131" "01113" "01111"
#> TCGA.C5.A1MN.01 TCGA.ZJ.AAXN.01 TCGA.MA.AA3X.01 TCGA.UC.A7PG.01 TCGA.Q1.A6DV.01 TCGA.DS.A1OD.01
#> "022212" "0132" "01211" "0131" "032" "0131"
#> TCGA.C5.A1M7.01 TCGA.BI.A20A.01 TCGA.VS.A9UO.01 TCGA.EA.A1QT.01 TCGA.EX.A69M.01 TCGA.VS.A9UH.01
#> "0134" "021113" "032" "022213" "0232" "01111"
#> TCGA.VS.A9U7.01 TCGA.ZJ.AAXD.01 TCGA.VS.A9UB.01 TCGA.EA.A410.01 TCGA.ZJ.AB0I.01 TCGA.VS.A9UD.01
#> "02222" "0131" "01111" "0122" "01212" "0232"
#> TCGA.VS.A9U6.01 TCGA.ZX.AA5X.01 TCGA.C5.A0TN.01 TCGA.C5.A7CJ.01 TCGA.C5.A1MJ.01 TCGA.EA.A78R.01
#> "01132" "021111" "01132" "021111" "032" "0232"
#> TCGA.VS.A9UY.01 TCGA.VS.A9U5.01 TCGA.DS.A1OC.01 TCGA.ZJ.AAXB.01 TCGA.EX.A449.01 TCGA.C5.A1BL.01
#> "022211" "021" "0233" "0123" "03112" "022212"
#> TCGA.VS.A9UQ.01 TCGA.DS.A1OB.01 TCGA.HG.A9SC.01 TCGA.ZJ.AAXT.01 TCGA.IR.A3LB.01 TCGA.C5.A1ML.01
#> "03112" "0123" "0123" "0134" "032" "01133"
#> TCGA.VS.A9UV.01 TCGA.LP.A4AU.01 TCGA.Q1.A6DT.01 TCGA.C5.A1M8.01 TCGA.C5.A1ME.01 TCGA.ZJ.AAXU.01
#> "021" "01113" "021112" "021" "032" "0131"
#> TCGA.VS.A957.01 TCGA.VS.A9V5.01 TCGA.MU.A5YI.01 TCGA.ZJ.AAX4.01 TCGA.C5.A1MK.01 TCGA.JW.A69B.01
#> "02222" "03111" "021" "021" "0131" "03112"
#> TCGA.VS.A958.01 TCGA.ZJ.AAXJ.01 TCGA.R2.A69V.01 TCGA.EA.A411.01 TCGA.VS.A9UP.01 TCGA.C5.A1MI.01
#> "0134" "0232" "01113" "0123" "01113" "01131"
#> TCGA.DS.A1O9.01 TCGA.VS.A9UZ.01 TCGA.EA.A43B.01 TCGA.ZJ.AAX8.01 TCGA.ZJ.AAXI.01 TCGA.VS.A9UT.01
#> "021111" "03112" "0231" "01112" "022212" "0112"
#> TCGA.DS.A1OA.01 TCGA.C5.A1MQ.01 TCGA.VS.A9V0.01 TCGA.VS.A9UC.01 TCGA.ZJ.AAXA.01 TCGA.Q1.A73P.01
#> "02222" "0231" "0133" "021112" "01211" "03112"
#> TCGA.VS.A9V2.01 TCGA.VS.A9UU.01 TCGA.LP.A4AV.01 TCGA.VS.A9UR.01 TCGA.VS.A9V1.01 TCGA.C5.A7CG.01
#> "021111" "0232" "0131" "032" "032" "021"
#> TCGA.UC.A7PI.01 TCGA.EX.A1H5.01 TCGA.ZJ.AAXF.01 TCGA.VS.A9UL.01 TCGA.EA.A3Y4.01 TCGA.C5.A7CK.01
#> "032" "021" "01112" "032" "0132" "0232"
#> TCGA.UC.A7PG.06 TCGA.VS.A9UJ.01 TCGA.Q1.A73O.01 TCGA.VS.A950.01 TCGA.EA.A439.01 TCGA.VS.A9UM.01
#> "01211" "0122" "0134" "022212" "01131" "01211"
#> TCGA.C5.A1MP.01 TCGA.VS.A9UI.01 TCGA.ZJ.AB0H.01 TCGA.Q1.A73Q.01 TCGA.C5.A1MH.01 TCGA.VS.A9V4.01
#> "0131" "022212" "0131" "0221" "021111" "0112"
#> TCGA.FU.A40J.01 TCGA.VS.A9UA.01 TCGA.LP.A4AW.01 TCGA.MA.AA43.01 TCGA.C5.A1BN.01 TCGA.VS.AA62.01
#> "03111" "0131" "0131" "032" "01212" "01111"
#> TCGA.C5.A1BM.01 TCGA.C5.A1M6.01 TCGA.C5.A1BE.01 TCGA.FU.A23K.01 TCGA.C5.A1BJ.01 TCGA.FU.A23L.01
#> "0134" "01131" "0131" "032" "01112" "0134"
#> TCGA.C5.A1M5.01 TCGA.C5.A1MF.01 TCGA.C5.A1BF.01 TCGA.C5.A1BK.01 TCGA.C5.A1BI.01 TCGA.C5.A1M9.01
#> "022212" "021" "01132" "021111" "0134" "03112"
get_classes(res_rh, merge_node = merge_node_param(min_n_signatures = 1579))
#> TCGA.EK.A3GK.01 TCGA.GH.A9DA.01 TCGA.VS.A94Y.01 TCGA.MY.A5BF.11 TCGA.VS.A94Z.01 TCGA.EA.A4BA.01
#> "0132" "0231" "0132" "0112" "0131" "0133"
#> TCGA.ZJ.A8QQ.01 TCGA.FU.A3EO.11 TCGA.DG.A2KJ.01 TCGA.VS.A954.01 TCGA.MA.AA42.01 TCGA.C5.A8YQ.01
#> "0231" "0112" "01113" "021" "021" "021"
#> TCGA.DS.A7WF.01 TCGA.EK.A2R7.01 TCGA.EK.A3GJ.01 TCGA.C5.A902.01 TCGA.MA.AA3W.01 TCGA.C5.A905.01
#> "0312" "0131" "0233" "0232" "021" "01211"
#> TCGA.EK.A2RN.01 TCGA.FU.A57G.01 TCGA.C5.A8YR.01 TCGA.EK.A2R9.01 TCGA.FU.A3EO.01 TCGA.IR.A3LC.01
#> "0131" "0112" "0133" "021" "03112" "021"
#> TCGA.VS.A8QA.01 TCGA.C5.A3HD.01 TCGA.MY.A5BE.01 TCGA.EA.A50E.01 TCGA.VS.A8QH.01 TCGA.ZJ.A8QR.01
#> "0313" "0233" "01112" "021" "01113" "01212"
#> TCGA.C5.A907.01 TCGA.IR.A3LK.01 TCGA.C5.A8ZZ.01 TCGA.VS.A8EK.01 TCGA.C5.A7UC.01 TCGA.C5.A8XJ.01
#> "01113" "022212" "0123" "021" "01111" "0131"
#> TCGA.IR.A3LH.01 TCGA.EK.A3GM.01 TCGA.VS.A8Q8.01 TCGA.EK.A2RO.01 TCGA.MY.A5BD.01 TCGA.2W.A8YY.01
#> "0231" "01131" "0131" "021" "0312" "0122"
#> TCGA.C5.A2LZ.01 TCGA.C5.A901.01 TCGA.VS.A953.01 TCGA.MU.A51Y.01 TCGA.EK.A2RK.01 TCGA.UC.A7PD.01
#> "02222" "021" "021" "01112" "0131" "01111"
#> TCGA.EA.A3HS.01 TCGA.VS.A8QM.01 TCGA.EA.A3HU.01 TCGA.VS.A94X.01 TCGA.C5.A7CO.01 TCGA.C5.A3HF.01
#> "021" "01112" "01112" "01111" "021" "01113"
#> TCGA.IR.A3LL.01 TCGA.MY.A913.01 TCGA.VS.A952.01 TCGA.IR.A3LI.01 TCGA.VS.A94W.01 TCGA.MY.A5BF.01
#> "0232" "01111" "0313" "0313" "021" "0232"
#> TCGA.EK.A2RC.01 TCGA.VS.A8EL.01 TCGA.EA.A97N.01 TCGA.EA.A3HQ.01 TCGA.EK.A2RD.01 TCGA.C5.A8YT.01
#> "02222" "0231" "01212" "02222" "0131" "0112"
#> TCGA.FU.A3HZ.01 TCGA.VS.A8EJ.01 TCGA.C5.A3HL.01 TCGA.UC.A7PF.01 TCGA.C5.A8XK.01 TCGA.EX.A8YF.01
#> "0122" "0112" "0131" "0232" "0132" "01113"
#> TCGA.HM.A4S6.01 TCGA.VS.A8Q9.01 TCGA.MA.AA41.01 TCGA.EK.A3GN.01 TCGA.MA.AA3Y.01 TCGA.MA.AA3Z.01
#> "0131" "0231" "021" "021" "01111" "0131"
#> TCGA.EK.A2RE.01 TCGA.C5.A1BQ.01 TCGA.ZJ.A8QO.01 TCGA.JW.A852.01 TCGA.DS.A7WH.01 TCGA.JW.AAVH.01
#> "0131" "0131" "021" "021" "032" "022213"
#> TCGA.EA.A556.01 TCGA.EA.A44S.01 TCGA.4J.AA1J.01 TCGA.IR.A3L7.01 TCGA.C5.A7X3.01 TCGA.HG.A2PA.01
#> "0133" "01212" "01212" "02222" "0132" "01112"
#> TCGA.C5.A8XH.01 TCGA.C5.A7XC.01 TCGA.VS.A8EI.01 TCGA.VS.A8QC.01 TCGA.C5.A7UH.01 TCGA.WL.A834.01
#> "0233" "0131" "0231" "02222" "01211" "02222"
#> TCGA.C5.A8XI.01 TCGA.DS.A7WI.01 TCGA.VS.A8QF.01 TCGA.EA.A3HR.01 TCGA.DG.A2KL.01 TCGA.EK.A2RL.01
#> "0232" "0233" "02222" "0131" "0131" "03112"
#> TCGA.EK.A2PG.01 TCGA.BI.A0VR.01 TCGA.DS.A0VL.01 TCGA.VS.A8EC.01 TCGA.EA.A3QE.01 TCGA.DS.A0VM.01
#> "022212" "0131" "0131" "0221" "021" "021"
#> TCGA.FU.A3HY.01 TCGA.Q1.A5R1.01 TCGA.DR.A0ZM.01 TCGA.Q1.A6DW.01 TCGA.DS.A0VK.01 TCGA.DS.A3LQ.01
#> "022212" "03112" "0134" "021" "0131" "0221"
#> TCGA.EA.A3QD.01 TCGA.JW.A5VJ.01 TCGA.LP.A5U3.01 TCGA.EA.A6QX.01 TCGA.EK.A2RA.01 TCGA.FU.A5XV.01
#> "0232" "0134" "02222" "02222" "022212" "01212"
#> TCGA.Q1.A5R2.01 TCGA.HM.A3JJ.01 TCGA.C5.A2LS.01 TCGA.C5.A7X8.01 TCGA.EK.A2RJ.01 TCGA.EA.A3HT.01
#> "022212" "0131" "0313" "032" "0133" "0131"
#> TCGA.LP.A7HU.01 TCGA.MU.A8JM.01 TCGA.EK.A2IP.01 TCGA.JW.A5VL.01 TCGA.FU.A3TX.01 TCGA.DG.A2KK.01
#> "0312" "021" "02222" "022211" "01133" "0313"
#> TCGA.EK.A2PI.01 TCGA.Q1.A73S.01 TCGA.EK.A2IR.01 TCGA.HM.A6W2.01 TCGA.VS.A8EH.01 TCGA.JW.A5VH.01
#> "0131" "0122" "021" "0122" "01132" "0122"
#> TCGA.C5.A2LV.01 TCGA.VS.A8EB.01 TCGA.RA.A741.01 TCGA.VS.A8EG.01 TCGA.DG.A2KH.01 TCGA.C5.A7UE.01
#> "021" "01132" "01112" "02222" "01131" "021"
#> TCGA.C5.A2LT.01 TCGA.EA.A5ZD.01 TCGA.Q1.A73R.01 TCGA.JW.A5VK.01 TCGA.EK.A2RM.01 TCGA.C5.A7UI.01
#> "01111" "0134" "0312" "0221" "01131" "0131"
#> TCGA.EK.A2PL.01 TCGA.EK.A2PM.01 TCGA.EK.A2GZ.01 TCGA.HM.A3JK.01 TCGA.C5.A2M1.01 TCGA.HM.A6W2.06
#> "0131" "0123" "01112" "01112" "03112" "0122"
#> TCGA.C5.A7X5.01 TCGA.IR.A3LA.01 TCGA.EK.A2PK.01 TCGA.EA.A5ZF.01 TCGA.XS.A8TJ.01 TCGA.BI.A0VS.01
#> "0233" "0122" "0133" "0132" "021" "0132"
#> TCGA.DS.A0VN.01 TCGA.JX.A5QV.01 TCGA.EK.A2R8.01 TCGA.EA.A1QS.01 TCGA.C5.A3HE.01 TCGA.IR.A3LF.01
#> "021" "0131" "0132" "01112" "032" "03112"
#> TCGA.DR.A0ZL.01 TCGA.FU.A3WB.01 TCGA.JX.A3PZ.01 TCGA.EA.A5O9.01 TCGA.HM.A3JJ.11 TCGA.DS.A5RQ.01
#> "021" "021" "0133" "021" "0112" "0131"
#> TCGA.EK.A2H0.01 TCGA.EX.A1H6.01 TCGA.EA.A5ZE.01 TCGA.C5.A2LY.01 TCGA.FU.A3TQ.01 TCGA.EK.A2RB.01
#> "0231" "032" "021" "01132" "02222" "022212"
#> TCGA.JW.A5VI.01 TCGA.EK.A2H1.01 TCGA.JX.A3Q8.01 TCGA.FU.A3YQ.01 TCGA.EX.A69L.01 TCGA.C5.A7CH.01
#> "021" "0112" "0313" "021" "0131" "021"
#> TCGA.FU.A2QG.01 TCGA.C5.A2M2.01 TCGA.JW.A5VG.01 TCGA.PN.A8MA.01 TCGA.DG.A2KM.01 TCGA.C5.A2LX.01
#> "01212" "03112" "01132" "0122" "0112" "02222"
#> TCGA.EX.A3L1.01 TCGA.LP.A5U2.01 TCGA.FU.A3NI.01 TCGA.Q1.A5R3.01 TCGA.FU.A770.01 TCGA.C5.A7CM.01
#> "01111" "021" "0232" "0131" "032" "01131"
#> TCGA.JX.A3Q0.01 TCGA.EA.A5FO.01 TCGA.VS.A9V3.01 TCGA.C5.A7CL.01 TCGA.VS.A959.01 TCGA.LP.A4AX.01
#> "01211" "0312" "021" "0131" "01113" "01111"
#> TCGA.C5.A1MN.01 TCGA.ZJ.AAXN.01 TCGA.MA.AA3X.01 TCGA.UC.A7PG.01 TCGA.Q1.A6DV.01 TCGA.DS.A1OD.01
#> "022212" "0132" "01211" "0131" "032" "0131"
#> TCGA.C5.A1M7.01 TCGA.BI.A20A.01 TCGA.VS.A9UO.01 TCGA.EA.A1QT.01 TCGA.EX.A69M.01 TCGA.VS.A9UH.01
#> "0134" "021" "032" "022213" "0232" "01111"
#> TCGA.VS.A9U7.01 TCGA.ZJ.AAXD.01 TCGA.VS.A9UB.01 TCGA.EA.A410.01 TCGA.ZJ.AB0I.01 TCGA.VS.A9UD.01
#> "02222" "0131" "01111" "0122" "01212" "0232"
#> TCGA.VS.A9U6.01 TCGA.ZX.AA5X.01 TCGA.C5.A0TN.01 TCGA.C5.A7CJ.01 TCGA.C5.A1MJ.01 TCGA.EA.A78R.01
#> "01132" "021" "01132" "021" "032" "0232"
#> TCGA.VS.A9UY.01 TCGA.VS.A9U5.01 TCGA.DS.A1OC.01 TCGA.ZJ.AAXB.01 TCGA.EX.A449.01 TCGA.C5.A1BL.01
#> "022211" "021" "0233" "0123" "03112" "022212"
#> TCGA.VS.A9UQ.01 TCGA.DS.A1OB.01 TCGA.HG.A9SC.01 TCGA.ZJ.AAXT.01 TCGA.IR.A3LB.01 TCGA.C5.A1ML.01
#> "03112" "0123" "0123" "0134" "032" "01133"
#> TCGA.VS.A9UV.01 TCGA.LP.A4AU.01 TCGA.Q1.A6DT.01 TCGA.C5.A1M8.01 TCGA.C5.A1ME.01 TCGA.ZJ.AAXU.01
#> "021" "01113" "021" "021" "032" "0131"
#> TCGA.VS.A957.01 TCGA.VS.A9V5.01 TCGA.MU.A5YI.01 TCGA.ZJ.AAX4.01 TCGA.C5.A1MK.01 TCGA.JW.A69B.01
#> "02222" "03111" "021" "021" "0131" "03112"
#> TCGA.VS.A958.01 TCGA.ZJ.AAXJ.01 TCGA.R2.A69V.01 TCGA.EA.A411.01 TCGA.VS.A9UP.01 TCGA.C5.A1MI.01
#> "0134" "0232" "01113" "0123" "01113" "01131"
#> TCGA.DS.A1O9.01 TCGA.VS.A9UZ.01 TCGA.EA.A43B.01 TCGA.ZJ.AAX8.01 TCGA.ZJ.AAXI.01 TCGA.VS.A9UT.01
#> "021" "03112" "0231" "01112" "022212" "0112"
#> TCGA.DS.A1OA.01 TCGA.C5.A1MQ.01 TCGA.VS.A9V0.01 TCGA.VS.A9UC.01 TCGA.ZJ.AAXA.01 TCGA.Q1.A73P.01
#> "02222" "0231" "0133" "021" "01211" "03112"
#> TCGA.VS.A9V2.01 TCGA.VS.A9UU.01 TCGA.LP.A4AV.01 TCGA.VS.A9UR.01 TCGA.VS.A9V1.01 TCGA.C5.A7CG.01
#> "021" "0232" "0131" "032" "032" "021"
#> TCGA.UC.A7PI.01 TCGA.EX.A1H5.01 TCGA.ZJ.AAXF.01 TCGA.VS.A9UL.01 TCGA.EA.A3Y4.01 TCGA.C5.A7CK.01
#> "032" "021" "01112" "032" "0132" "0232"
#> TCGA.UC.A7PG.06 TCGA.VS.A9UJ.01 TCGA.Q1.A73O.01 TCGA.VS.A950.01 TCGA.EA.A439.01 TCGA.VS.A9UM.01
#> "01211" "0122" "0134" "022212" "01131" "01211"
#> TCGA.C5.A1MP.01 TCGA.VS.A9UI.01 TCGA.ZJ.AB0H.01 TCGA.Q1.A73Q.01 TCGA.C5.A1MH.01 TCGA.VS.A9V4.01
#> "0131" "022212" "0131" "0221" "021" "0112"
#> TCGA.FU.A40J.01 TCGA.VS.A9UA.01 TCGA.LP.A4AW.01 TCGA.MA.AA43.01 TCGA.C5.A1BN.01 TCGA.VS.AA62.01
#> "03111" "0131" "0131" "032" "01212" "01111"
#> TCGA.C5.A1BM.01 TCGA.C5.A1M6.01 TCGA.C5.A1BE.01 TCGA.FU.A23K.01 TCGA.C5.A1BJ.01 TCGA.FU.A23L.01
#> "0134" "01131" "0131" "032" "01112" "0134"
#> TCGA.C5.A1M5.01 TCGA.C5.A1MF.01 TCGA.C5.A1BF.01 TCGA.C5.A1BK.01 TCGA.C5.A1BI.01 TCGA.C5.A1M9.01
#> "022212" "021" "01132" "021" "0134" "03112"
get_classes(res_rh, merge_node = merge_node_param(min_n_signatures = 1658))
#> TCGA.EK.A3GK.01 TCGA.GH.A9DA.01 TCGA.VS.A94Y.01 TCGA.MY.A5BF.11 TCGA.VS.A94Z.01 TCGA.EA.A4BA.01
#> "0132" "023" "0132" "0112" "0131" "0133"
#> TCGA.ZJ.A8QQ.01 TCGA.FU.A3EO.11 TCGA.DG.A2KJ.01 TCGA.VS.A954.01 TCGA.MA.AA42.01 TCGA.C5.A8YQ.01
#> "023" "0112" "01113" "021" "021" "021"
#> TCGA.DS.A7WF.01 TCGA.EK.A2R7.01 TCGA.EK.A3GJ.01 TCGA.C5.A902.01 TCGA.MA.AA3W.01 TCGA.C5.A905.01
#> "0312" "0131" "023" "023" "021" "01211"
#> TCGA.EK.A2RN.01 TCGA.FU.A57G.01 TCGA.C5.A8YR.01 TCGA.EK.A2R9.01 TCGA.FU.A3EO.01 TCGA.IR.A3LC.01
#> "0131" "0112" "0133" "021" "03112" "021"
#> TCGA.VS.A8QA.01 TCGA.C5.A3HD.01 TCGA.MY.A5BE.01 TCGA.EA.A50E.01 TCGA.VS.A8QH.01 TCGA.ZJ.A8QR.01
#> "0313" "023" "01112" "021" "01113" "01212"
#> TCGA.C5.A907.01 TCGA.IR.A3LK.01 TCGA.C5.A8ZZ.01 TCGA.VS.A8EK.01 TCGA.C5.A7UC.01 TCGA.C5.A8XJ.01
#> "01113" "022212" "0123" "021" "01111" "0131"
#> TCGA.IR.A3LH.01 TCGA.EK.A3GM.01 TCGA.VS.A8Q8.01 TCGA.EK.A2RO.01 TCGA.MY.A5BD.01 TCGA.2W.A8YY.01
#> "023" "01131" "0131" "021" "0312" "0122"
#> TCGA.C5.A2LZ.01 TCGA.C5.A901.01 TCGA.VS.A953.01 TCGA.MU.A51Y.01 TCGA.EK.A2RK.01 TCGA.UC.A7PD.01
#> "02222" "021" "021" "01112" "0131" "01111"
#> TCGA.EA.A3HS.01 TCGA.VS.A8QM.01 TCGA.EA.A3HU.01 TCGA.VS.A94X.01 TCGA.C5.A7CO.01 TCGA.C5.A3HF.01
#> "021" "01112" "01112" "01111" "021" "01113"
#> TCGA.IR.A3LL.01 TCGA.MY.A913.01 TCGA.VS.A952.01 TCGA.IR.A3LI.01 TCGA.VS.A94W.01 TCGA.MY.A5BF.01
#> "023" "01111" "0313" "0313" "021" "023"
#> TCGA.EK.A2RC.01 TCGA.VS.A8EL.01 TCGA.EA.A97N.01 TCGA.EA.A3HQ.01 TCGA.EK.A2RD.01 TCGA.C5.A8YT.01
#> "02222" "023" "01212" "02222" "0131" "0112"
#> TCGA.FU.A3HZ.01 TCGA.VS.A8EJ.01 TCGA.C5.A3HL.01 TCGA.UC.A7PF.01 TCGA.C5.A8XK.01 TCGA.EX.A8YF.01
#> "0122" "0112" "0131" "023" "0132" "01113"
#> TCGA.HM.A4S6.01 TCGA.VS.A8Q9.01 TCGA.MA.AA41.01 TCGA.EK.A3GN.01 TCGA.MA.AA3Y.01 TCGA.MA.AA3Z.01
#> "0131" "023" "021" "021" "01111" "0131"
#> TCGA.EK.A2RE.01 TCGA.C5.A1BQ.01 TCGA.ZJ.A8QO.01 TCGA.JW.A852.01 TCGA.DS.A7WH.01 TCGA.JW.AAVH.01
#> "0131" "0131" "021" "021" "032" "022213"
#> TCGA.EA.A556.01 TCGA.EA.A44S.01 TCGA.4J.AA1J.01 TCGA.IR.A3L7.01 TCGA.C5.A7X3.01 TCGA.HG.A2PA.01
#> "0133" "01212" "01212" "02222" "0132" "01112"
#> TCGA.C5.A8XH.01 TCGA.C5.A7XC.01 TCGA.VS.A8EI.01 TCGA.VS.A8QC.01 TCGA.C5.A7UH.01 TCGA.WL.A834.01
#> "023" "0131" "023" "02222" "01211" "02222"
#> TCGA.C5.A8XI.01 TCGA.DS.A7WI.01 TCGA.VS.A8QF.01 TCGA.EA.A3HR.01 TCGA.DG.A2KL.01 TCGA.EK.A2RL.01
#> "023" "023" "02222" "0131" "0131" "03112"
#> TCGA.EK.A2PG.01 TCGA.BI.A0VR.01 TCGA.DS.A0VL.01 TCGA.VS.A8EC.01 TCGA.EA.A3QE.01 TCGA.DS.A0VM.01
#> "022212" "0131" "0131" "0221" "021" "021"
#> TCGA.FU.A3HY.01 TCGA.Q1.A5R1.01 TCGA.DR.A0ZM.01 TCGA.Q1.A6DW.01 TCGA.DS.A0VK.01 TCGA.DS.A3LQ.01
#> "022212" "03112" "0134" "021" "0131" "0221"
#> TCGA.EA.A3QD.01 TCGA.JW.A5VJ.01 TCGA.LP.A5U3.01 TCGA.EA.A6QX.01 TCGA.EK.A2RA.01 TCGA.FU.A5XV.01
#> "023" "0134" "02222" "02222" "022212" "01212"
#> TCGA.Q1.A5R2.01 TCGA.HM.A3JJ.01 TCGA.C5.A2LS.01 TCGA.C5.A7X8.01 TCGA.EK.A2RJ.01 TCGA.EA.A3HT.01
#> "022212" "0131" "0313" "032" "0133" "0131"
#> TCGA.LP.A7HU.01 TCGA.MU.A8JM.01 TCGA.EK.A2IP.01 TCGA.JW.A5VL.01 TCGA.FU.A3TX.01 TCGA.DG.A2KK.01
#> "0312" "021" "02222" "022211" "01133" "0313"
#> TCGA.EK.A2PI.01 TCGA.Q1.A73S.01 TCGA.EK.A2IR.01 TCGA.HM.A6W2.01 TCGA.VS.A8EH.01 TCGA.JW.A5VH.01
#> "0131" "0122" "021" "0122" "01132" "0122"
#> TCGA.C5.A2LV.01 TCGA.VS.A8EB.01 TCGA.RA.A741.01 TCGA.VS.A8EG.01 TCGA.DG.A2KH.01 TCGA.C5.A7UE.01
#> "021" "01132" "01112" "02222" "01131" "021"
#> TCGA.C5.A2LT.01 TCGA.EA.A5ZD.01 TCGA.Q1.A73R.01 TCGA.JW.A5VK.01 TCGA.EK.A2RM.01 TCGA.C5.A7UI.01
#> "01111" "0134" "0312" "0221" "01131" "0131"
#> TCGA.EK.A2PL.01 TCGA.EK.A2PM.01 TCGA.EK.A2GZ.01 TCGA.HM.A3JK.01 TCGA.C5.A2M1.01 TCGA.HM.A6W2.06
#> "0131" "0123" "01112" "01112" "03112" "0122"
#> TCGA.C5.A7X5.01 TCGA.IR.A3LA.01 TCGA.EK.A2PK.01 TCGA.EA.A5ZF.01 TCGA.XS.A8TJ.01 TCGA.BI.A0VS.01
#> "023" "0122" "0133" "0132" "021" "0132"
#> TCGA.DS.A0VN.01 TCGA.JX.A5QV.01 TCGA.EK.A2R8.01 TCGA.EA.A1QS.01 TCGA.C5.A3HE.01 TCGA.IR.A3LF.01
#> "021" "0131" "0132" "01112" "032" "03112"
#> TCGA.DR.A0ZL.01 TCGA.FU.A3WB.01 TCGA.JX.A3PZ.01 TCGA.EA.A5O9.01 TCGA.HM.A3JJ.11 TCGA.DS.A5RQ.01
#> "021" "021" "0133" "021" "0112" "0131"
#> TCGA.EK.A2H0.01 TCGA.EX.A1H6.01 TCGA.EA.A5ZE.01 TCGA.C5.A2LY.01 TCGA.FU.A3TQ.01 TCGA.EK.A2RB.01
#> "023" "032" "021" "01132" "02222" "022212"
#> TCGA.JW.A5VI.01 TCGA.EK.A2H1.01 TCGA.JX.A3Q8.01 TCGA.FU.A3YQ.01 TCGA.EX.A69L.01 TCGA.C5.A7CH.01
#> "021" "0112" "0313" "021" "0131" "021"
#> TCGA.FU.A2QG.01 TCGA.C5.A2M2.01 TCGA.JW.A5VG.01 TCGA.PN.A8MA.01 TCGA.DG.A2KM.01 TCGA.C5.A2LX.01
#> "01212" "03112" "01132" "0122" "0112" "02222"
#> TCGA.EX.A3L1.01 TCGA.LP.A5U2.01 TCGA.FU.A3NI.01 TCGA.Q1.A5R3.01 TCGA.FU.A770.01 TCGA.C5.A7CM.01
#> "01111" "021" "023" "0131" "032" "01131"
#> TCGA.JX.A3Q0.01 TCGA.EA.A5FO.01 TCGA.VS.A9V3.01 TCGA.C5.A7CL.01 TCGA.VS.A959.01 TCGA.LP.A4AX.01
#> "01211" "0312" "021" "0131" "01113" "01111"
#> TCGA.C5.A1MN.01 TCGA.ZJ.AAXN.01 TCGA.MA.AA3X.01 TCGA.UC.A7PG.01 TCGA.Q1.A6DV.01 TCGA.DS.A1OD.01
#> "022212" "0132" "01211" "0131" "032" "0131"
#> TCGA.C5.A1M7.01 TCGA.BI.A20A.01 TCGA.VS.A9UO.01 TCGA.EA.A1QT.01 TCGA.EX.A69M.01 TCGA.VS.A9UH.01
#> "0134" "021" "032" "022213" "023" "01111"
#> TCGA.VS.A9U7.01 TCGA.ZJ.AAXD.01 TCGA.VS.A9UB.01 TCGA.EA.A410.01 TCGA.ZJ.AB0I.01 TCGA.VS.A9UD.01
#> "02222" "0131" "01111" "0122" "01212" "023"
#> TCGA.VS.A9U6.01 TCGA.ZX.AA5X.01 TCGA.C5.A0TN.01 TCGA.C5.A7CJ.01 TCGA.C5.A1MJ.01 TCGA.EA.A78R.01
#> "01132" "021" "01132" "021" "032" "023"
#> TCGA.VS.A9UY.01 TCGA.VS.A9U5.01 TCGA.DS.A1OC.01 TCGA.ZJ.AAXB.01 TCGA.EX.A449.01 TCGA.C5.A1BL.01
#> "022211" "021" "023" "0123" "03112" "022212"
#> TCGA.VS.A9UQ.01 TCGA.DS.A1OB.01 TCGA.HG.A9SC.01 TCGA.ZJ.AAXT.01 TCGA.IR.A3LB.01 TCGA.C5.A1ML.01
#> "03112" "0123" "0123" "0134" "032" "01133"
#> TCGA.VS.A9UV.01 TCGA.LP.A4AU.01 TCGA.Q1.A6DT.01 TCGA.C5.A1M8.01 TCGA.C5.A1ME.01 TCGA.ZJ.AAXU.01
#> "021" "01113" "021" "021" "032" "0131"
#> TCGA.VS.A957.01 TCGA.VS.A9V5.01 TCGA.MU.A5YI.01 TCGA.ZJ.AAX4.01 TCGA.C5.A1MK.01 TCGA.JW.A69B.01
#> "02222" "03111" "021" "021" "0131" "03112"
#> TCGA.VS.A958.01 TCGA.ZJ.AAXJ.01 TCGA.R2.A69V.01 TCGA.EA.A411.01 TCGA.VS.A9UP.01 TCGA.C5.A1MI.01
#> "0134" "023" "01113" "0123" "01113" "01131"
#> TCGA.DS.A1O9.01 TCGA.VS.A9UZ.01 TCGA.EA.A43B.01 TCGA.ZJ.AAX8.01 TCGA.ZJ.AAXI.01 TCGA.VS.A9UT.01
#> "021" "03112" "023" "01112" "022212" "0112"
#> TCGA.DS.A1OA.01 TCGA.C5.A1MQ.01 TCGA.VS.A9V0.01 TCGA.VS.A9UC.01 TCGA.ZJ.AAXA.01 TCGA.Q1.A73P.01
#> "02222" "023" "0133" "021" "01211" "03112"
#> TCGA.VS.A9V2.01 TCGA.VS.A9UU.01 TCGA.LP.A4AV.01 TCGA.VS.A9UR.01 TCGA.VS.A9V1.01 TCGA.C5.A7CG.01
#> "021" "023" "0131" "032" "032" "021"
#> TCGA.UC.A7PI.01 TCGA.EX.A1H5.01 TCGA.ZJ.AAXF.01 TCGA.VS.A9UL.01 TCGA.EA.A3Y4.01 TCGA.C5.A7CK.01
#> "032" "021" "01112" "032" "0132" "023"
#> TCGA.UC.A7PG.06 TCGA.VS.A9UJ.01 TCGA.Q1.A73O.01 TCGA.VS.A950.01 TCGA.EA.A439.01 TCGA.VS.A9UM.01
#> "01211" "0122" "0134" "022212" "01131" "01211"
#> TCGA.C5.A1MP.01 TCGA.VS.A9UI.01 TCGA.ZJ.AB0H.01 TCGA.Q1.A73Q.01 TCGA.C5.A1MH.01 TCGA.VS.A9V4.01
#> "0131" "022212" "0131" "0221" "021" "0112"
#> TCGA.FU.A40J.01 TCGA.VS.A9UA.01 TCGA.LP.A4AW.01 TCGA.MA.AA43.01 TCGA.C5.A1BN.01 TCGA.VS.AA62.01
#> "03111" "0131" "0131" "032" "01212" "01111"
#> TCGA.C5.A1BM.01 TCGA.C5.A1M6.01 TCGA.C5.A1BE.01 TCGA.FU.A23K.01 TCGA.C5.A1BJ.01 TCGA.FU.A23L.01
#> "0134" "01131" "0131" "032" "01112" "0134"
#> TCGA.C5.A1M5.01 TCGA.C5.A1MF.01 TCGA.C5.A1BF.01 TCGA.C5.A1BK.01 TCGA.C5.A1BI.01 TCGA.C5.A1M9.01
#> "022212" "021" "01132" "021" "0134" "03112"
get_classes(res_rh, merge_node = merge_node_param(min_n_signatures = 2087))
#> TCGA.EK.A3GK.01 TCGA.GH.A9DA.01 TCGA.VS.A94Y.01 TCGA.MY.A5BF.11 TCGA.VS.A94Z.01 TCGA.EA.A4BA.01
#> "0132" "023" "0132" "0112" "0131" "0133"
#> TCGA.ZJ.A8QQ.01 TCGA.FU.A3EO.11 TCGA.DG.A2KJ.01 TCGA.VS.A954.01 TCGA.MA.AA42.01 TCGA.C5.A8YQ.01
#> "023" "0112" "01113" "021" "021" "021"
#> TCGA.DS.A7WF.01 TCGA.EK.A2R7.01 TCGA.EK.A3GJ.01 TCGA.C5.A902.01 TCGA.MA.AA3W.01 TCGA.C5.A905.01
#> "0312" "0131" "023" "023" "021" "01211"
#> TCGA.EK.A2RN.01 TCGA.FU.A57G.01 TCGA.C5.A8YR.01 TCGA.EK.A2R9.01 TCGA.FU.A3EO.01 TCGA.IR.A3LC.01
#> "0131" "0112" "0133" "021" "03112" "021"
#> TCGA.VS.A8QA.01 TCGA.C5.A3HD.01 TCGA.MY.A5BE.01 TCGA.EA.A50E.01 TCGA.VS.A8QH.01 TCGA.ZJ.A8QR.01
#> "0313" "023" "01112" "021" "01113" "01212"
#> TCGA.C5.A907.01 TCGA.IR.A3LK.01 TCGA.C5.A8ZZ.01 TCGA.VS.A8EK.01 TCGA.C5.A7UC.01 TCGA.C5.A8XJ.01
#> "01113" "0222" "0123" "021" "01111" "0131"
#> TCGA.IR.A3LH.01 TCGA.EK.A3GM.01 TCGA.VS.A8Q8.01 TCGA.EK.A2RO.01 TCGA.MY.A5BD.01 TCGA.2W.A8YY.01
#> "023" "01131" "0131" "021" "0312" "0122"
#> TCGA.C5.A2LZ.01 TCGA.C5.A901.01 TCGA.VS.A953.01 TCGA.MU.A51Y.01 TCGA.EK.A2RK.01 TCGA.UC.A7PD.01
#> "0222" "021" "021" "01112" "0131" "01111"
#> TCGA.EA.A3HS.01 TCGA.VS.A8QM.01 TCGA.EA.A3HU.01 TCGA.VS.A94X.01 TCGA.C5.A7CO.01 TCGA.C5.A3HF.01
#> "021" "01112" "01112" "01111" "021" "01113"
#> TCGA.IR.A3LL.01 TCGA.MY.A913.01 TCGA.VS.A952.01 TCGA.IR.A3LI.01 TCGA.VS.A94W.01 TCGA.MY.A5BF.01
#> "023" "01111" "0313" "0313" "021" "023"
#> TCGA.EK.A2RC.01 TCGA.VS.A8EL.01 TCGA.EA.A97N.01 TCGA.EA.A3HQ.01 TCGA.EK.A2RD.01 TCGA.C5.A8YT.01
#> "0222" "023" "01212" "0222" "0131" "0112"
#> TCGA.FU.A3HZ.01 TCGA.VS.A8EJ.01 TCGA.C5.A3HL.01 TCGA.UC.A7PF.01 TCGA.C5.A8XK.01 TCGA.EX.A8YF.01
#> "0122" "0112" "0131" "023" "0132" "01113"
#> TCGA.HM.A4S6.01 TCGA.VS.A8Q9.01 TCGA.MA.AA41.01 TCGA.EK.A3GN.01 TCGA.MA.AA3Y.01 TCGA.MA.AA3Z.01
#> "0131" "023" "021" "021" "01111" "0131"
#> TCGA.EK.A2RE.01 TCGA.C5.A1BQ.01 TCGA.ZJ.A8QO.01 TCGA.JW.A852.01 TCGA.DS.A7WH.01 TCGA.JW.AAVH.01
#> "0131" "0131" "021" "021" "032" "0222"
#> TCGA.EA.A556.01 TCGA.EA.A44S.01 TCGA.4J.AA1J.01 TCGA.IR.A3L7.01 TCGA.C5.A7X3.01 TCGA.HG.A2PA.01
#> "0133" "01212" "01212" "0222" "0132" "01112"
#> TCGA.C5.A8XH.01 TCGA.C5.A7XC.01 TCGA.VS.A8EI.01 TCGA.VS.A8QC.01 TCGA.C5.A7UH.01 TCGA.WL.A834.01
#> "023" "0131" "023" "0222" "01211" "0222"
#> TCGA.C5.A8XI.01 TCGA.DS.A7WI.01 TCGA.VS.A8QF.01 TCGA.EA.A3HR.01 TCGA.DG.A2KL.01 TCGA.EK.A2RL.01
#> "023" "023" "0222" "0131" "0131" "03112"
#> TCGA.EK.A2PG.01 TCGA.BI.A0VR.01 TCGA.DS.A0VL.01 TCGA.VS.A8EC.01 TCGA.EA.A3QE.01 TCGA.DS.A0VM.01
#> "0222" "0131" "0131" "0221" "021" "021"
#> TCGA.FU.A3HY.01 TCGA.Q1.A5R1.01 TCGA.DR.A0ZM.01 TCGA.Q1.A6DW.01 TCGA.DS.A0VK.01 TCGA.DS.A3LQ.01
#> "0222" "03112" "0134" "021" "0131" "0221"
#> TCGA.EA.A3QD.01 TCGA.JW.A5VJ.01 TCGA.LP.A5U3.01 TCGA.EA.A6QX.01 TCGA.EK.A2RA.01 TCGA.FU.A5XV.01
#> "023" "0134" "0222" "0222" "0222" "01212"
#> TCGA.Q1.A5R2.01 TCGA.HM.A3JJ.01 TCGA.C5.A2LS.01 TCGA.C5.A7X8.01 TCGA.EK.A2RJ.01 TCGA.EA.A3HT.01
#> "0222" "0131" "0313" "032" "0133" "0131"
#> TCGA.LP.A7HU.01 TCGA.MU.A8JM.01 TCGA.EK.A2IP.01 TCGA.JW.A5VL.01 TCGA.FU.A3TX.01 TCGA.DG.A2KK.01
#> "0312" "021" "0222" "0222" "01133" "0313"
#> TCGA.EK.A2PI.01 TCGA.Q1.A73S.01 TCGA.EK.A2IR.01 TCGA.HM.A6W2.01 TCGA.VS.A8EH.01 TCGA.JW.A5VH.01
#> "0131" "0122" "021" "0122" "01132" "0122"
#> TCGA.C5.A2LV.01 TCGA.VS.A8EB.01 TCGA.RA.A741.01 TCGA.VS.A8EG.01 TCGA.DG.A2KH.01 TCGA.C5.A7UE.01
#> "021" "01132" "01112" "0222" "01131" "021"
#> TCGA.C5.A2LT.01 TCGA.EA.A5ZD.01 TCGA.Q1.A73R.01 TCGA.JW.A5VK.01 TCGA.EK.A2RM.01 TCGA.C5.A7UI.01
#> "01111" "0134" "0312" "0221" "01131" "0131"
#> TCGA.EK.A2PL.01 TCGA.EK.A2PM.01 TCGA.EK.A2GZ.01 TCGA.HM.A3JK.01 TCGA.C5.A2M1.01 TCGA.HM.A6W2.06
#> "0131" "0123" "01112" "01112" "03112" "0122"
#> TCGA.C5.A7X5.01 TCGA.IR.A3LA.01 TCGA.EK.A2PK.01 TCGA.EA.A5ZF.01 TCGA.XS.A8TJ.01 TCGA.BI.A0VS.01
#> "023" "0122" "0133" "0132" "021" "0132"
#> TCGA.DS.A0VN.01 TCGA.JX.A5QV.01 TCGA.EK.A2R8.01 TCGA.EA.A1QS.01 TCGA.C5.A3HE.01 TCGA.IR.A3LF.01
#> "021" "0131" "0132" "01112" "032" "03112"
#> TCGA.DR.A0ZL.01 TCGA.FU.A3WB.01 TCGA.JX.A3PZ.01 TCGA.EA.A5O9.01 TCGA.HM.A3JJ.11 TCGA.DS.A5RQ.01
#> "021" "021" "0133" "021" "0112" "0131"
#> TCGA.EK.A2H0.01 TCGA.EX.A1H6.01 TCGA.EA.A5ZE.01 TCGA.C5.A2LY.01 TCGA.FU.A3TQ.01 TCGA.EK.A2RB.01
#> "023" "032" "021" "01132" "0222" "0222"
#> TCGA.JW.A5VI.01 TCGA.EK.A2H1.01 TCGA.JX.A3Q8.01 TCGA.FU.A3YQ.01 TCGA.EX.A69L.01 TCGA.C5.A7CH.01
#> "021" "0112" "0313" "021" "0131" "021"
#> TCGA.FU.A2QG.01 TCGA.C5.A2M2.01 TCGA.JW.A5VG.01 TCGA.PN.A8MA.01 TCGA.DG.A2KM.01 TCGA.C5.A2LX.01
#> "01212" "03112" "01132" "0122" "0112" "0222"
#> TCGA.EX.A3L1.01 TCGA.LP.A5U2.01 TCGA.FU.A3NI.01 TCGA.Q1.A5R3.01 TCGA.FU.A770.01 TCGA.C5.A7CM.01
#> "01111" "021" "023" "0131" "032" "01131"
#> TCGA.JX.A3Q0.01 TCGA.EA.A5FO.01 TCGA.VS.A9V3.01 TCGA.C5.A7CL.01 TCGA.VS.A959.01 TCGA.LP.A4AX.01
#> "01211" "0312" "021" "0131" "01113" "01111"
#> TCGA.C5.A1MN.01 TCGA.ZJ.AAXN.01 TCGA.MA.AA3X.01 TCGA.UC.A7PG.01 TCGA.Q1.A6DV.01 TCGA.DS.A1OD.01
#> "0222" "0132" "01211" "0131" "032" "0131"
#> TCGA.C5.A1M7.01 TCGA.BI.A20A.01 TCGA.VS.A9UO.01 TCGA.EA.A1QT.01 TCGA.EX.A69M.01 TCGA.VS.A9UH.01
#> "0134" "021" "032" "0222" "023" "01111"
#> TCGA.VS.A9U7.01 TCGA.ZJ.AAXD.01 TCGA.VS.A9UB.01 TCGA.EA.A410.01 TCGA.ZJ.AB0I.01 TCGA.VS.A9UD.01
#> "0222" "0131" "01111" "0122" "01212" "023"
#> TCGA.VS.A9U6.01 TCGA.ZX.AA5X.01 TCGA.C5.A0TN.01 TCGA.C5.A7CJ.01 TCGA.C5.A1MJ.01 TCGA.EA.A78R.01
#> "01132" "021" "01132" "021" "032" "023"
#> TCGA.VS.A9UY.01 TCGA.VS.A9U5.01 TCGA.DS.A1OC.01 TCGA.ZJ.AAXB.01 TCGA.EX.A449.01 TCGA.C5.A1BL.01
#> "0222" "021" "023" "0123" "03112" "0222"
#> TCGA.VS.A9UQ.01 TCGA.DS.A1OB.01 TCGA.HG.A9SC.01 TCGA.ZJ.AAXT.01 TCGA.IR.A3LB.01 TCGA.C5.A1ML.01
#> "03112" "0123" "0123" "0134" "032" "01133"
#> TCGA.VS.A9UV.01 TCGA.LP.A4AU.01 TCGA.Q1.A6DT.01 TCGA.C5.A1M8.01 TCGA.C5.A1ME.01 TCGA.ZJ.AAXU.01
#> "021" "01113" "021" "021" "032" "0131"
#> TCGA.VS.A957.01 TCGA.VS.A9V5.01 TCGA.MU.A5YI.01 TCGA.ZJ.AAX4.01 TCGA.C5.A1MK.01 TCGA.JW.A69B.01
#> "0222" "03111" "021" "021" "0131" "03112"
#> TCGA.VS.A958.01 TCGA.ZJ.AAXJ.01 TCGA.R2.A69V.01 TCGA.EA.A411.01 TCGA.VS.A9UP.01 TCGA.C5.A1MI.01
#> "0134" "023" "01113" "0123" "01113" "01131"
#> TCGA.DS.A1O9.01 TCGA.VS.A9UZ.01 TCGA.EA.A43B.01 TCGA.ZJ.AAX8.01 TCGA.ZJ.AAXI.01 TCGA.VS.A9UT.01
#> "021" "03112" "023" "01112" "0222" "0112"
#> TCGA.DS.A1OA.01 TCGA.C5.A1MQ.01 TCGA.VS.A9V0.01 TCGA.VS.A9UC.01 TCGA.ZJ.AAXA.01 TCGA.Q1.A73P.01
#> "0222" "023" "0133" "021" "01211" "03112"
#> TCGA.VS.A9V2.01 TCGA.VS.A9UU.01 TCGA.LP.A4AV.01 TCGA.VS.A9UR.01 TCGA.VS.A9V1.01 TCGA.C5.A7CG.01
#> "021" "023" "0131" "032" "032" "021"
#> TCGA.UC.A7PI.01 TCGA.EX.A1H5.01 TCGA.ZJ.AAXF.01 TCGA.VS.A9UL.01 TCGA.EA.A3Y4.01 TCGA.C5.A7CK.01
#> "032" "021" "01112" "032" "0132" "023"
#> TCGA.UC.A7PG.06 TCGA.VS.A9UJ.01 TCGA.Q1.A73O.01 TCGA.VS.A950.01 TCGA.EA.A439.01 TCGA.VS.A9UM.01
#> "01211" "0122" "0134" "0222" "01131" "01211"
#> TCGA.C5.A1MP.01 TCGA.VS.A9UI.01 TCGA.ZJ.AB0H.01 TCGA.Q1.A73Q.01 TCGA.C5.A1MH.01 TCGA.VS.A9V4.01
#> "0131" "0222" "0131" "0221" "021" "0112"
#> TCGA.FU.A40J.01 TCGA.VS.A9UA.01 TCGA.LP.A4AW.01 TCGA.MA.AA43.01 TCGA.C5.A1BN.01 TCGA.VS.AA62.01
#> "03111" "0131" "0131" "032" "01212" "01111"
#> TCGA.C5.A1BM.01 TCGA.C5.A1M6.01 TCGA.C5.A1BE.01 TCGA.FU.A23K.01 TCGA.C5.A1BJ.01 TCGA.FU.A23L.01
#> "0134" "01131" "0131" "032" "01112" "0134"
#> TCGA.C5.A1M5.01 TCGA.C5.A1MF.01 TCGA.C5.A1BF.01 TCGA.C5.A1BK.01 TCGA.C5.A1BI.01 TCGA.C5.A1M9.01
#> "0222" "021" "01132" "021" "0134" "03112"
get_classes(res_rh, merge_node = merge_node_param(min_n_signatures = 2263))
#> TCGA.EK.A3GK.01 TCGA.GH.A9DA.01 TCGA.VS.A94Y.01 TCGA.MY.A5BF.11 TCGA.VS.A94Z.01 TCGA.EA.A4BA.01
#> "0132" "023" "0132" "0112" "0131" "0133"
#> TCGA.ZJ.A8QQ.01 TCGA.FU.A3EO.11 TCGA.DG.A2KJ.01 TCGA.VS.A954.01 TCGA.MA.AA42.01 TCGA.C5.A8YQ.01
#> "023" "0112" "0111" "021" "021" "021"
#> TCGA.DS.A7WF.01 TCGA.EK.A2R7.01 TCGA.EK.A3GJ.01 TCGA.C5.A902.01 TCGA.MA.AA3W.01 TCGA.C5.A905.01
#> "0312" "0131" "023" "023" "021" "01211"
#> TCGA.EK.A2RN.01 TCGA.FU.A57G.01 TCGA.C5.A8YR.01 TCGA.EK.A2R9.01 TCGA.FU.A3EO.01 TCGA.IR.A3LC.01
#> "0131" "0112" "0133" "021" "03112" "021"
#> TCGA.VS.A8QA.01 TCGA.C5.A3HD.01 TCGA.MY.A5BE.01 TCGA.EA.A50E.01 TCGA.VS.A8QH.01 TCGA.ZJ.A8QR.01
#> "0313" "023" "0111" "021" "0111" "01212"
#> TCGA.C5.A907.01 TCGA.IR.A3LK.01 TCGA.C5.A8ZZ.01 TCGA.VS.A8EK.01 TCGA.C5.A7UC.01 TCGA.C5.A8XJ.01
#> "0111" "0222" "0123" "021" "0111" "0131"
#> TCGA.IR.A3LH.01 TCGA.EK.A3GM.01 TCGA.VS.A8Q8.01 TCGA.EK.A2RO.01 TCGA.MY.A5BD.01 TCGA.2W.A8YY.01
#> "023" "01131" "0131" "021" "0312" "0122"
#> TCGA.C5.A2LZ.01 TCGA.C5.A901.01 TCGA.VS.A953.01 TCGA.MU.A51Y.01 TCGA.EK.A2RK.01 TCGA.UC.A7PD.01
#> "0222" "021" "021" "0111" "0131" "0111"
#> TCGA.EA.A3HS.01 TCGA.VS.A8QM.01 TCGA.EA.A3HU.01 TCGA.VS.A94X.01 TCGA.C5.A7CO.01 TCGA.C5.A3HF.01
#> "021" "0111" "0111" "0111" "021" "0111"
#> TCGA.IR.A3LL.01 TCGA.MY.A913.01 TCGA.VS.A952.01 TCGA.IR.A3LI.01 TCGA.VS.A94W.01 TCGA.MY.A5BF.01
#> "023" "0111" "0313" "0313" "021" "023"
#> TCGA.EK.A2RC.01 TCGA.VS.A8EL.01 TCGA.EA.A97N.01 TCGA.EA.A3HQ.01 TCGA.EK.A2RD.01 TCGA.C5.A8YT.01
#> "0222" "023" "01212" "0222" "0131" "0112"
#> TCGA.FU.A3HZ.01 TCGA.VS.A8EJ.01 TCGA.C5.A3HL.01 TCGA.UC.A7PF.01 TCGA.C5.A8XK.01 TCGA.EX.A8YF.01
#> "0122" "0112" "0131" "023" "0132" "0111"
#> TCGA.HM.A4S6.01 TCGA.VS.A8Q9.01 TCGA.MA.AA41.01 TCGA.EK.A3GN.01 TCGA.MA.AA3Y.01 TCGA.MA.AA3Z.01
#> "0131" "023" "021" "021" "0111" "0131"
#> TCGA.EK.A2RE.01 TCGA.C5.A1BQ.01 TCGA.ZJ.A8QO.01 TCGA.JW.A852.01 TCGA.DS.A7WH.01 TCGA.JW.AAVH.01
#> "0131" "0131" "021" "021" "032" "0222"
#> TCGA.EA.A556.01 TCGA.EA.A44S.01 TCGA.4J.AA1J.01 TCGA.IR.A3L7.01 TCGA.C5.A7X3.01 TCGA.HG.A2PA.01
#> "0133" "01212" "01212" "0222" "0132" "0111"
#> TCGA.C5.A8XH.01 TCGA.C5.A7XC.01 TCGA.VS.A8EI.01 TCGA.VS.A8QC.01 TCGA.C5.A7UH.01 TCGA.WL.A834.01
#> "023" "0131" "023" "0222" "01211" "0222"
#> TCGA.C5.A8XI.01 TCGA.DS.A7WI.01 TCGA.VS.A8QF.01 TCGA.EA.A3HR.01 TCGA.DG.A2KL.01 TCGA.EK.A2RL.01
#> "023" "023" "0222" "0131" "0131" "03112"
#> TCGA.EK.A2PG.01 TCGA.BI.A0VR.01 TCGA.DS.A0VL.01 TCGA.VS.A8EC.01 TCGA.EA.A3QE.01 TCGA.DS.A0VM.01
#> "0222" "0131" "0131" "0221" "021" "021"
#> TCGA.FU.A3HY.01 TCGA.Q1.A5R1.01 TCGA.DR.A0ZM.01 TCGA.Q1.A6DW.01 TCGA.DS.A0VK.01 TCGA.DS.A3LQ.01
#> "0222" "03112" "0134" "021" "0131" "0221"
#> TCGA.EA.A3QD.01 TCGA.JW.A5VJ.01 TCGA.LP.A5U3.01 TCGA.EA.A6QX.01 TCGA.EK.A2RA.01 TCGA.FU.A5XV.01
#> "023" "0134" "0222" "0222" "0222" "01212"
#> TCGA.Q1.A5R2.01 TCGA.HM.A3JJ.01 TCGA.C5.A2LS.01 TCGA.C5.A7X8.01 TCGA.EK.A2RJ.01 TCGA.EA.A3HT.01
#> "0222" "0131" "0313" "032" "0133" "0131"
#> TCGA.LP.A7HU.01 TCGA.MU.A8JM.01 TCGA.EK.A2IP.01 TCGA.JW.A5VL.01 TCGA.FU.A3TX.01 TCGA.DG.A2KK.01
#> "0312" "021" "0222" "0222" "01133" "0313"
#> TCGA.EK.A2PI.01 TCGA.Q1.A73S.01 TCGA.EK.A2IR.01 TCGA.HM.A6W2.01 TCGA.VS.A8EH.01 TCGA.JW.A5VH.01
#> "0131" "0122" "021" "0122" "01132" "0122"
#> TCGA.C5.A2LV.01 TCGA.VS.A8EB.01 TCGA.RA.A741.01 TCGA.VS.A8EG.01 TCGA.DG.A2KH.01 TCGA.C5.A7UE.01
#> "021" "01132" "0111" "0222" "01131" "021"
#> TCGA.C5.A2LT.01 TCGA.EA.A5ZD.01 TCGA.Q1.A73R.01 TCGA.JW.A5VK.01 TCGA.EK.A2RM.01 TCGA.C5.A7UI.01
#> "0111" "0134" "0312" "0221" "01131" "0131"
#> TCGA.EK.A2PL.01 TCGA.EK.A2PM.01 TCGA.EK.A2GZ.01 TCGA.HM.A3JK.01 TCGA.C5.A2M1.01 TCGA.HM.A6W2.06
#> "0131" "0123" "0111" "0111" "03112" "0122"
#> TCGA.C5.A7X5.01 TCGA.IR.A3LA.01 TCGA.EK.A2PK.01 TCGA.EA.A5ZF.01 TCGA.XS.A8TJ.01 TCGA.BI.A0VS.01
#> "023" "0122" "0133" "0132" "021" "0132"
#> TCGA.DS.A0VN.01 TCGA.JX.A5QV.01 TCGA.EK.A2R8.01 TCGA.EA.A1QS.01 TCGA.C5.A3HE.01 TCGA.IR.A3LF.01
#> "021" "0131" "0132" "0111" "032" "03112"
#> TCGA.DR.A0ZL.01 TCGA.FU.A3WB.01 TCGA.JX.A3PZ.01 TCGA.EA.A5O9.01 TCGA.HM.A3JJ.11 TCGA.DS.A5RQ.01
#> "021" "021" "0133" "021" "0112" "0131"
#> TCGA.EK.A2H0.01 TCGA.EX.A1H6.01 TCGA.EA.A5ZE.01 TCGA.C5.A2LY.01 TCGA.FU.A3TQ.01 TCGA.EK.A2RB.01
#> "023" "032" "021" "01132" "0222" "0222"
#> TCGA.JW.A5VI.01 TCGA.EK.A2H1.01 TCGA.JX.A3Q8.01 TCGA.FU.A3YQ.01 TCGA.EX.A69L.01 TCGA.C5.A7CH.01
#> "021" "0112" "0313" "021" "0131" "021"
#> TCGA.FU.A2QG.01 TCGA.C5.A2M2.01 TCGA.JW.A5VG.01 TCGA.PN.A8MA.01 TCGA.DG.A2KM.01 TCGA.C5.A2LX.01
#> "01212" "03112" "01132" "0122" "0112" "0222"
#> TCGA.EX.A3L1.01 TCGA.LP.A5U2.01 TCGA.FU.A3NI.01 TCGA.Q1.A5R3.01 TCGA.FU.A770.01 TCGA.C5.A7CM.01
#> "0111" "021" "023" "0131" "032" "01131"
#> TCGA.JX.A3Q0.01 TCGA.EA.A5FO.01 TCGA.VS.A9V3.01 TCGA.C5.A7CL.01 TCGA.VS.A959.01 TCGA.LP.A4AX.01
#> "01211" "0312" "021" "0131" "0111" "0111"
#> TCGA.C5.A1MN.01 TCGA.ZJ.AAXN.01 TCGA.MA.AA3X.01 TCGA.UC.A7PG.01 TCGA.Q1.A6DV.01 TCGA.DS.A1OD.01
#> "0222" "0132" "01211" "0131" "032" "0131"
#> TCGA.C5.A1M7.01 TCGA.BI.A20A.01 TCGA.VS.A9UO.01 TCGA.EA.A1QT.01 TCGA.EX.A69M.01 TCGA.VS.A9UH.01
#> "0134" "021" "032" "0222" "023" "0111"
#> TCGA.VS.A9U7.01 TCGA.ZJ.AAXD.01 TCGA.VS.A9UB.01 TCGA.EA.A410.01 TCGA.ZJ.AB0I.01 TCGA.VS.A9UD.01
#> "0222" "0131" "0111" "0122" "01212" "023"
#> TCGA.VS.A9U6.01 TCGA.ZX.AA5X.01 TCGA.C5.A0TN.01 TCGA.C5.A7CJ.01 TCGA.C5.A1MJ.01 TCGA.EA.A78R.01
#> "01132" "021" "01132" "021" "032" "023"
#> TCGA.VS.A9UY.01 TCGA.VS.A9U5.01 TCGA.DS.A1OC.01 TCGA.ZJ.AAXB.01 TCGA.EX.A449.01 TCGA.C5.A1BL.01
#> "0222" "021" "023" "0123" "03112" "0222"
#> TCGA.VS.A9UQ.01 TCGA.DS.A1OB.01 TCGA.HG.A9SC.01 TCGA.ZJ.AAXT.01 TCGA.IR.A3LB.01 TCGA.C5.A1ML.01
#> "03112" "0123" "0123" "0134" "032" "01133"
#> TCGA.VS.A9UV.01 TCGA.LP.A4AU.01 TCGA.Q1.A6DT.01 TCGA.C5.A1M8.01 TCGA.C5.A1ME.01 TCGA.ZJ.AAXU.01
#> "021" "0111" "021" "021" "032" "0131"
#> TCGA.VS.A957.01 TCGA.VS.A9V5.01 TCGA.MU.A5YI.01 TCGA.ZJ.AAX4.01 TCGA.C5.A1MK.01 TCGA.JW.A69B.01
#> "0222" "03111" "021" "021" "0131" "03112"
#> TCGA.VS.A958.01 TCGA.ZJ.AAXJ.01 TCGA.R2.A69V.01 TCGA.EA.A411.01 TCGA.VS.A9UP.01 TCGA.C5.A1MI.01
#> "0134" "023" "0111" "0123" "0111" "01131"
#> TCGA.DS.A1O9.01 TCGA.VS.A9UZ.01 TCGA.EA.A43B.01 TCGA.ZJ.AAX8.01 TCGA.ZJ.AAXI.01 TCGA.VS.A9UT.01
#> "021" "03112" "023" "0111" "0222" "0112"
#> TCGA.DS.A1OA.01 TCGA.C5.A1MQ.01 TCGA.VS.A9V0.01 TCGA.VS.A9UC.01 TCGA.ZJ.AAXA.01 TCGA.Q1.A73P.01
#> "0222" "023" "0133" "021" "01211" "03112"
#> TCGA.VS.A9V2.01 TCGA.VS.A9UU.01 TCGA.LP.A4AV.01 TCGA.VS.A9UR.01 TCGA.VS.A9V1.01 TCGA.C5.A7CG.01
#> "021" "023" "0131" "032" "032" "021"
#> TCGA.UC.A7PI.01 TCGA.EX.A1H5.01 TCGA.ZJ.AAXF.01 TCGA.VS.A9UL.01 TCGA.EA.A3Y4.01 TCGA.C5.A7CK.01
#> "032" "021" "0111" "032" "0132" "023"
#> TCGA.UC.A7PG.06 TCGA.VS.A9UJ.01 TCGA.Q1.A73O.01 TCGA.VS.A950.01 TCGA.EA.A439.01 TCGA.VS.A9UM.01
#> "01211" "0122" "0134" "0222" "01131" "01211"
#> TCGA.C5.A1MP.01 TCGA.VS.A9UI.01 TCGA.ZJ.AB0H.01 TCGA.Q1.A73Q.01 TCGA.C5.A1MH.01 TCGA.VS.A9V4.01
#> "0131" "0222" "0131" "0221" "021" "0112"
#> TCGA.FU.A40J.01 TCGA.VS.A9UA.01 TCGA.LP.A4AW.01 TCGA.MA.AA43.01 TCGA.C5.A1BN.01 TCGA.VS.AA62.01
#> "03111" "0131" "0131" "032" "01212" "0111"
#> TCGA.C5.A1BM.01 TCGA.C5.A1M6.01 TCGA.C5.A1BE.01 TCGA.FU.A23K.01 TCGA.C5.A1BJ.01 TCGA.FU.A23L.01
#> "0134" "01131" "0131" "032" "0111" "0134"
#> TCGA.C5.A1M5.01 TCGA.C5.A1MF.01 TCGA.C5.A1BF.01 TCGA.C5.A1BK.01 TCGA.C5.A1BI.01 TCGA.C5.A1M9.01
#> "0222" "021" "01132" "021" "0134" "03112"
get_classes(res_rh, merge_node = merge_node_param(min_n_signatures = 3801))
#> TCGA.EK.A3GK.01 TCGA.GH.A9DA.01 TCGA.VS.A94Y.01 TCGA.MY.A5BF.11 TCGA.VS.A94Z.01 TCGA.EA.A4BA.01
#> "0132" "023" "0132" "0112" "0131" "0133"
#> TCGA.ZJ.A8QQ.01 TCGA.FU.A3EO.11 TCGA.DG.A2KJ.01 TCGA.VS.A954.01 TCGA.MA.AA42.01 TCGA.C5.A8YQ.01
#> "023" "0112" "0111" "021" "021" "021"
#> TCGA.DS.A7WF.01 TCGA.EK.A2R7.01 TCGA.EK.A3GJ.01 TCGA.C5.A902.01 TCGA.MA.AA3W.01 TCGA.C5.A905.01
#> "0312" "0131" "023" "023" "021" "01211"
#> TCGA.EK.A2RN.01 TCGA.FU.A57G.01 TCGA.C5.A8YR.01 TCGA.EK.A2R9.01 TCGA.FU.A3EO.01 TCGA.IR.A3LC.01
#> "0131" "0112" "0133" "021" "03112" "021"
#> TCGA.VS.A8QA.01 TCGA.C5.A3HD.01 TCGA.MY.A5BE.01 TCGA.EA.A50E.01 TCGA.VS.A8QH.01 TCGA.ZJ.A8QR.01
#> "0313" "023" "0111" "021" "0111" "01212"
#> TCGA.C5.A907.01 TCGA.IR.A3LK.01 TCGA.C5.A8ZZ.01 TCGA.VS.A8EK.01 TCGA.C5.A7UC.01 TCGA.C5.A8XJ.01
#> "0111" "0222" "0123" "021" "0111" "0131"
#> TCGA.IR.A3LH.01 TCGA.EK.A3GM.01 TCGA.VS.A8Q8.01 TCGA.EK.A2RO.01 TCGA.MY.A5BD.01 TCGA.2W.A8YY.01
#> "023" "01131" "0131" "021" "0312" "0122"
#> TCGA.C5.A2LZ.01 TCGA.C5.A901.01 TCGA.VS.A953.01 TCGA.MU.A51Y.01 TCGA.EK.A2RK.01 TCGA.UC.A7PD.01
#> "0222" "021" "021" "0111" "0131" "0111"
#> TCGA.EA.A3HS.01 TCGA.VS.A8QM.01 TCGA.EA.A3HU.01 TCGA.VS.A94X.01 TCGA.C5.A7CO.01 TCGA.C5.A3HF.01
#> "021" "0111" "0111" "0111" "021" "0111"
#> TCGA.IR.A3LL.01 TCGA.MY.A913.01 TCGA.VS.A952.01 TCGA.IR.A3LI.01 TCGA.VS.A94W.01 TCGA.MY.A5BF.01
#> "023" "0111" "0313" "0313" "021" "023"
#> TCGA.EK.A2RC.01 TCGA.VS.A8EL.01 TCGA.EA.A97N.01 TCGA.EA.A3HQ.01 TCGA.EK.A2RD.01 TCGA.C5.A8YT.01
#> "0222" "023" "01212" "0222" "0131" "0112"
#> TCGA.FU.A3HZ.01 TCGA.VS.A8EJ.01 TCGA.C5.A3HL.01 TCGA.UC.A7PF.01 TCGA.C5.A8XK.01 TCGA.EX.A8YF.01
#> "0122" "0112" "0131" "023" "0132" "0111"
#> TCGA.HM.A4S6.01 TCGA.VS.A8Q9.01 TCGA.MA.AA41.01 TCGA.EK.A3GN.01 TCGA.MA.AA3Y.01 TCGA.MA.AA3Z.01
#> "0131" "023" "021" "021" "0111" "0131"
#> TCGA.EK.A2RE.01 TCGA.C5.A1BQ.01 TCGA.ZJ.A8QO.01 TCGA.JW.A852.01 TCGA.DS.A7WH.01 TCGA.JW.AAVH.01
#> "0131" "0131" "021" "021" "032" "0222"
#> TCGA.EA.A556.01 TCGA.EA.A44S.01 TCGA.4J.AA1J.01 TCGA.IR.A3L7.01 TCGA.C5.A7X3.01 TCGA.HG.A2PA.01
#> "0133" "01212" "01212" "0222" "0132" "0111"
#> TCGA.C5.A8XH.01 TCGA.C5.A7XC.01 TCGA.VS.A8EI.01 TCGA.VS.A8QC.01 TCGA.C5.A7UH.01 TCGA.WL.A834.01
#> "023" "0131" "023" "0222" "01211" "0222"
#> TCGA.C5.A8XI.01 TCGA.DS.A7WI.01 TCGA.VS.A8QF.01 TCGA.EA.A3HR.01 TCGA.DG.A2KL.01 TCGA.EK.A2RL.01
#> "023" "023" "0222" "0131" "0131" "03112"
#> TCGA.EK.A2PG.01 TCGA.BI.A0VR.01 TCGA.DS.A0VL.01 TCGA.VS.A8EC.01 TCGA.EA.A3QE.01 TCGA.DS.A0VM.01
#> "0222" "0131" "0131" "0221" "021" "021"
#> TCGA.FU.A3HY.01 TCGA.Q1.A5R1.01 TCGA.DR.A0ZM.01 TCGA.Q1.A6DW.01 TCGA.DS.A0VK.01 TCGA.DS.A3LQ.01
#> "0222" "03112" "0134" "021" "0131" "0221"
#> TCGA.EA.A3QD.01 TCGA.JW.A5VJ.01 TCGA.LP.A5U3.01 TCGA.EA.A6QX.01 TCGA.EK.A2RA.01 TCGA.FU.A5XV.01
#> "023" "0134" "0222" "0222" "0222" "01212"
#> TCGA.Q1.A5R2.01 TCGA.HM.A3JJ.01 TCGA.C5.A2LS.01 TCGA.C5.A7X8.01 TCGA.EK.A2RJ.01 TCGA.EA.A3HT.01
#> "0222" "0131" "0313" "032" "0133" "0131"
#> TCGA.LP.A7HU.01 TCGA.MU.A8JM.01 TCGA.EK.A2IP.01 TCGA.JW.A5VL.01 TCGA.FU.A3TX.01 TCGA.DG.A2KK.01
#> "0312" "021" "0222" "0222" "01133" "0313"
#> TCGA.EK.A2PI.01 TCGA.Q1.A73S.01 TCGA.EK.A2IR.01 TCGA.HM.A6W2.01 TCGA.VS.A8EH.01 TCGA.JW.A5VH.01
#> "0131" "0122" "021" "0122" "01132" "0122"
#> TCGA.C5.A2LV.01 TCGA.VS.A8EB.01 TCGA.RA.A741.01 TCGA.VS.A8EG.01 TCGA.DG.A2KH.01 TCGA.C5.A7UE.01
#> "021" "01132" "0111" "0222" "01131" "021"
#> TCGA.C5.A2LT.01 TCGA.EA.A5ZD.01 TCGA.Q1.A73R.01 TCGA.JW.A5VK.01 TCGA.EK.A2RM.01 TCGA.C5.A7UI.01
#> "0111" "0134" "0312" "0221" "01131" "0131"
#> TCGA.EK.A2PL.01 TCGA.EK.A2PM.01 TCGA.EK.A2GZ.01 TCGA.HM.A3JK.01 TCGA.C5.A2M1.01 TCGA.HM.A6W2.06
#> "0131" "0123" "0111" "0111" "03112" "0122"
#> TCGA.C5.A7X5.01 TCGA.IR.A3LA.01 TCGA.EK.A2PK.01 TCGA.EA.A5ZF.01 TCGA.XS.A8TJ.01 TCGA.BI.A0VS.01
#> "023" "0122" "0133" "0132" "021" "0132"
#> TCGA.DS.A0VN.01 TCGA.JX.A5QV.01 TCGA.EK.A2R8.01 TCGA.EA.A1QS.01 TCGA.C5.A3HE.01 TCGA.IR.A3LF.01
#> "021" "0131" "0132" "0111" "032" "03112"
#> TCGA.DR.A0ZL.01 TCGA.FU.A3WB.01 TCGA.JX.A3PZ.01 TCGA.EA.A5O9.01 TCGA.HM.A3JJ.11 TCGA.DS.A5RQ.01
#> "021" "021" "0133" "021" "0112" "0131"
#> TCGA.EK.A2H0.01 TCGA.EX.A1H6.01 TCGA.EA.A5ZE.01 TCGA.C5.A2LY.01 TCGA.FU.A3TQ.01 TCGA.EK.A2RB.01
#> "023" "032" "021" "01132" "0222" "0222"
#> TCGA.JW.A5VI.01 TCGA.EK.A2H1.01 TCGA.JX.A3Q8.01 TCGA.FU.A3YQ.01 TCGA.EX.A69L.01 TCGA.C5.A7CH.01
#> "021" "0112" "0313" "021" "0131" "021"
#> TCGA.FU.A2QG.01 TCGA.C5.A2M2.01 TCGA.JW.A5VG.01 TCGA.PN.A8MA.01 TCGA.DG.A2KM.01 TCGA.C5.A2LX.01
#> "01212" "03112" "01132" "0122" "0112" "0222"
#> TCGA.EX.A3L1.01 TCGA.LP.A5U2.01 TCGA.FU.A3NI.01 TCGA.Q1.A5R3.01 TCGA.FU.A770.01 TCGA.C5.A7CM.01
#> "0111" "021" "023" "0131" "032" "01131"
#> TCGA.JX.A3Q0.01 TCGA.EA.A5FO.01 TCGA.VS.A9V3.01 TCGA.C5.A7CL.01 TCGA.VS.A959.01 TCGA.LP.A4AX.01
#> "01211" "0312" "021" "0131" "0111" "0111"
#> TCGA.C5.A1MN.01 TCGA.ZJ.AAXN.01 TCGA.MA.AA3X.01 TCGA.UC.A7PG.01 TCGA.Q1.A6DV.01 TCGA.DS.A1OD.01
#> "0222" "0132" "01211" "0131" "032" "0131"
#> TCGA.C5.A1M7.01 TCGA.BI.A20A.01 TCGA.VS.A9UO.01 TCGA.EA.A1QT.01 TCGA.EX.A69M.01 TCGA.VS.A9UH.01
#> "0134" "021" "032" "0222" "023" "0111"
#> TCGA.VS.A9U7.01 TCGA.ZJ.AAXD.01 TCGA.VS.A9UB.01 TCGA.EA.A410.01 TCGA.ZJ.AB0I.01 TCGA.VS.A9UD.01
#> "0222" "0131" "0111" "0122" "01212" "023"
#> TCGA.VS.A9U6.01 TCGA.ZX.AA5X.01 TCGA.C5.A0TN.01 TCGA.C5.A7CJ.01 TCGA.C5.A1MJ.01 TCGA.EA.A78R.01
#> "01132" "021" "01132" "021" "032" "023"
#> TCGA.VS.A9UY.01 TCGA.VS.A9U5.01 TCGA.DS.A1OC.01 TCGA.ZJ.AAXB.01 TCGA.EX.A449.01 TCGA.C5.A1BL.01
#> "0222" "021" "023" "0123" "03112" "0222"
#> TCGA.VS.A9UQ.01 TCGA.DS.A1OB.01 TCGA.HG.A9SC.01 TCGA.ZJ.AAXT.01 TCGA.IR.A3LB.01 TCGA.C5.A1ML.01
#> "03112" "0123" "0123" "0134" "032" "01133"
#> TCGA.VS.A9UV.01 TCGA.LP.A4AU.01 TCGA.Q1.A6DT.01 TCGA.C5.A1M8.01 TCGA.C5.A1ME.01 TCGA.ZJ.AAXU.01
#> "021" "0111" "021" "021" "032" "0131"
#> TCGA.VS.A957.01 TCGA.VS.A9V5.01 TCGA.MU.A5YI.01 TCGA.ZJ.AAX4.01 TCGA.C5.A1MK.01 TCGA.JW.A69B.01
#> "0222" "03111" "021" "021" "0131" "03112"
#> TCGA.VS.A958.01 TCGA.ZJ.AAXJ.01 TCGA.R2.A69V.01 TCGA.EA.A411.01 TCGA.VS.A9UP.01 TCGA.C5.A1MI.01
#> "0134" "023" "0111" "0123" "0111" "01131"
#> TCGA.DS.A1O9.01 TCGA.VS.A9UZ.01 TCGA.EA.A43B.01 TCGA.ZJ.AAX8.01 TCGA.ZJ.AAXI.01 TCGA.VS.A9UT.01
#> "021" "03112" "023" "0111" "0222" "0112"
#> TCGA.DS.A1OA.01 TCGA.C5.A1MQ.01 TCGA.VS.A9V0.01 TCGA.VS.A9UC.01 TCGA.ZJ.AAXA.01 TCGA.Q1.A73P.01
#> "0222" "023" "0133" "021" "01211" "03112"
#> TCGA.VS.A9V2.01 TCGA.VS.A9UU.01 TCGA.LP.A4AV.01 TCGA.VS.A9UR.01 TCGA.VS.A9V1.01 TCGA.C5.A7CG.01
#> "021" "023" "0131" "032" "032" "021"
#> TCGA.UC.A7PI.01 TCGA.EX.A1H5.01 TCGA.ZJ.AAXF.01 TCGA.VS.A9UL.01 TCGA.EA.A3Y4.01 TCGA.C5.A7CK.01
#> "032" "021" "0111" "032" "0132" "023"
#> TCGA.UC.A7PG.06 TCGA.VS.A9UJ.01 TCGA.Q1.A73O.01 TCGA.VS.A950.01 TCGA.EA.A439.01 TCGA.VS.A9UM.01
#> "01211" "0122" "0134" "0222" "01131" "01211"
#> TCGA.C5.A1MP.01 TCGA.VS.A9UI.01 TCGA.ZJ.AB0H.01 TCGA.Q1.A73Q.01 TCGA.C5.A1MH.01 TCGA.VS.A9V4.01
#> "0131" "0222" "0131" "0221" "021" "0112"
#> TCGA.FU.A40J.01 TCGA.VS.A9UA.01 TCGA.LP.A4AW.01 TCGA.MA.AA43.01 TCGA.C5.A1BN.01 TCGA.VS.AA62.01
#> "03111" "0131" "0131" "032" "01212" "0111"
#> TCGA.C5.A1BM.01 TCGA.C5.A1M6.01 TCGA.C5.A1BE.01 TCGA.FU.A23K.01 TCGA.C5.A1BJ.01 TCGA.FU.A23L.01
#> "0134" "01131" "0131" "032" "0111" "0134"
#> TCGA.C5.A1M5.01 TCGA.C5.A1MF.01 TCGA.C5.A1BF.01 TCGA.C5.A1BK.01 TCGA.C5.A1BI.01 TCGA.C5.A1M9.01
#> "0222" "021" "01132" "021" "0134" "03112"
get_classes(res_rh, merge_node = merge_node_param(min_n_signatures = 4079))
#> TCGA.EK.A3GK.01 TCGA.GH.A9DA.01 TCGA.VS.A94Y.01 TCGA.MY.A5BF.11 TCGA.VS.A94Z.01 TCGA.EA.A4BA.01
#> "0132" "023" "0132" "0112" "0131" "0133"
#> TCGA.ZJ.A8QQ.01 TCGA.FU.A3EO.11 TCGA.DG.A2KJ.01 TCGA.VS.A954.01 TCGA.MA.AA42.01 TCGA.C5.A8YQ.01
#> "023" "0112" "0111" "021" "021" "021"
#> TCGA.DS.A7WF.01 TCGA.EK.A2R7.01 TCGA.EK.A3GJ.01 TCGA.C5.A902.01 TCGA.MA.AA3W.01 TCGA.C5.A905.01
#> "0312" "0131" "023" "023" "021" "01211"
#> TCGA.EK.A2RN.01 TCGA.FU.A57G.01 TCGA.C5.A8YR.01 TCGA.EK.A2R9.01 TCGA.FU.A3EO.01 TCGA.IR.A3LC.01
#> "0131" "0112" "0133" "021" "03112" "021"
#> TCGA.VS.A8QA.01 TCGA.C5.A3HD.01 TCGA.MY.A5BE.01 TCGA.EA.A50E.01 TCGA.VS.A8QH.01 TCGA.ZJ.A8QR.01
#> "0313" "023" "0111" "021" "0111" "01212"
#> TCGA.C5.A907.01 TCGA.IR.A3LK.01 TCGA.C5.A8ZZ.01 TCGA.VS.A8EK.01 TCGA.C5.A7UC.01 TCGA.C5.A8XJ.01
#> "0111" "022" "0123" "021" "0111" "0131"
#> TCGA.IR.A3LH.01 TCGA.EK.A3GM.01 TCGA.VS.A8Q8.01 TCGA.EK.A2RO.01 TCGA.MY.A5BD.01 TCGA.2W.A8YY.01
#> "023" "01131" "0131" "021" "0312" "0122"
#> TCGA.C5.A2LZ.01 TCGA.C5.A901.01 TCGA.VS.A953.01 TCGA.MU.A51Y.01 TCGA.EK.A2RK.01 TCGA.UC.A7PD.01
#> "022" "021" "021" "0111" "0131" "0111"
#> TCGA.EA.A3HS.01 TCGA.VS.A8QM.01 TCGA.EA.A3HU.01 TCGA.VS.A94X.01 TCGA.C5.A7CO.01 TCGA.C5.A3HF.01
#> "021" "0111" "0111" "0111" "021" "0111"
#> TCGA.IR.A3LL.01 TCGA.MY.A913.01 TCGA.VS.A952.01 TCGA.IR.A3LI.01 TCGA.VS.A94W.01 TCGA.MY.A5BF.01
#> "023" "0111" "0313" "0313" "021" "023"
#> TCGA.EK.A2RC.01 TCGA.VS.A8EL.01 TCGA.EA.A97N.01 TCGA.EA.A3HQ.01 TCGA.EK.A2RD.01 TCGA.C5.A8YT.01
#> "022" "023" "01212" "022" "0131" "0112"
#> TCGA.FU.A3HZ.01 TCGA.VS.A8EJ.01 TCGA.C5.A3HL.01 TCGA.UC.A7PF.01 TCGA.C5.A8XK.01 TCGA.EX.A8YF.01
#> "0122" "0112" "0131" "023" "0132" "0111"
#> TCGA.HM.A4S6.01 TCGA.VS.A8Q9.01 TCGA.MA.AA41.01 TCGA.EK.A3GN.01 TCGA.MA.AA3Y.01 TCGA.MA.AA3Z.01
#> "0131" "023" "021" "021" "0111" "0131"
#> TCGA.EK.A2RE.01 TCGA.C5.A1BQ.01 TCGA.ZJ.A8QO.01 TCGA.JW.A852.01 TCGA.DS.A7WH.01 TCGA.JW.AAVH.01
#> "0131" "0131" "021" "021" "032" "022"
#> TCGA.EA.A556.01 TCGA.EA.A44S.01 TCGA.4J.AA1J.01 TCGA.IR.A3L7.01 TCGA.C5.A7X3.01 TCGA.HG.A2PA.01
#> "0133" "01212" "01212" "022" "0132" "0111"
#> TCGA.C5.A8XH.01 TCGA.C5.A7XC.01 TCGA.VS.A8EI.01 TCGA.VS.A8QC.01 TCGA.C5.A7UH.01 TCGA.WL.A834.01
#> "023" "0131" "023" "022" "01211" "022"
#> TCGA.C5.A8XI.01 TCGA.DS.A7WI.01 TCGA.VS.A8QF.01 TCGA.EA.A3HR.01 TCGA.DG.A2KL.01 TCGA.EK.A2RL.01
#> "023" "023" "022" "0131" "0131" "03112"
#> TCGA.EK.A2PG.01 TCGA.BI.A0VR.01 TCGA.DS.A0VL.01 TCGA.VS.A8EC.01 TCGA.EA.A3QE.01 TCGA.DS.A0VM.01
#> "022" "0131" "0131" "022" "021" "021"
#> TCGA.FU.A3HY.01 TCGA.Q1.A5R1.01 TCGA.DR.A0ZM.01 TCGA.Q1.A6DW.01 TCGA.DS.A0VK.01 TCGA.DS.A3LQ.01
#> "022" "03112" "0134" "021" "0131" "022"
#> TCGA.EA.A3QD.01 TCGA.JW.A5VJ.01 TCGA.LP.A5U3.01 TCGA.EA.A6QX.01 TCGA.EK.A2RA.01 TCGA.FU.A5XV.01
#> "023" "0134" "022" "022" "022" "01212"
#> TCGA.Q1.A5R2.01 TCGA.HM.A3JJ.01 TCGA.C5.A2LS.01 TCGA.C5.A7X8.01 TCGA.EK.A2RJ.01 TCGA.EA.A3HT.01
#> "022" "0131" "0313" "032" "0133" "0131"
#> TCGA.LP.A7HU.01 TCGA.MU.A8JM.01 TCGA.EK.A2IP.01 TCGA.JW.A5VL.01 TCGA.FU.A3TX.01 TCGA.DG.A2KK.01
#> "0312" "021" "022" "022" "01133" "0313"
#> TCGA.EK.A2PI.01 TCGA.Q1.A73S.01 TCGA.EK.A2IR.01 TCGA.HM.A6W2.01 TCGA.VS.A8EH.01 TCGA.JW.A5VH.01
#> "0131" "0122" "021" "0122" "01132" "0122"
#> TCGA.C5.A2LV.01 TCGA.VS.A8EB.01 TCGA.RA.A741.01 TCGA.VS.A8EG.01 TCGA.DG.A2KH.01 TCGA.C5.A7UE.01
#> "021" "01132" "0111" "022" "01131" "021"
#> TCGA.C5.A2LT.01 TCGA.EA.A5ZD.01 TCGA.Q1.A73R.01 TCGA.JW.A5VK.01 TCGA.EK.A2RM.01 TCGA.C5.A7UI.01
#> "0111" "0134" "0312" "022" "01131" "0131"
#> TCGA.EK.A2PL.01 TCGA.EK.A2PM.01 TCGA.EK.A2GZ.01 TCGA.HM.A3JK.01 TCGA.C5.A2M1.01 TCGA.HM.A6W2.06
#> "0131" "0123" "0111" "0111" "03112" "0122"
#> TCGA.C5.A7X5.01 TCGA.IR.A3LA.01 TCGA.EK.A2PK.01 TCGA.EA.A5ZF.01 TCGA.XS.A8TJ.01 TCGA.BI.A0VS.01
#> "023" "0122" "0133" "0132" "021" "0132"
#> TCGA.DS.A0VN.01 TCGA.JX.A5QV.01 TCGA.EK.A2R8.01 TCGA.EA.A1QS.01 TCGA.C5.A3HE.01 TCGA.IR.A3LF.01
#> "021" "0131" "0132" "0111" "032" "03112"
#> TCGA.DR.A0ZL.01 TCGA.FU.A3WB.01 TCGA.JX.A3PZ.01 TCGA.EA.A5O9.01 TCGA.HM.A3JJ.11 TCGA.DS.A5RQ.01
#> "021" "021" "0133" "021" "0112" "0131"
#> TCGA.EK.A2H0.01 TCGA.EX.A1H6.01 TCGA.EA.A5ZE.01 TCGA.C5.A2LY.01 TCGA.FU.A3TQ.01 TCGA.EK.A2RB.01
#> "023" "032" "021" "01132" "022" "022"
#> TCGA.JW.A5VI.01 TCGA.EK.A2H1.01 TCGA.JX.A3Q8.01 TCGA.FU.A3YQ.01 TCGA.EX.A69L.01 TCGA.C5.A7CH.01
#> "021" "0112" "0313" "021" "0131" "021"
#> TCGA.FU.A2QG.01 TCGA.C5.A2M2.01 TCGA.JW.A5VG.01 TCGA.PN.A8MA.01 TCGA.DG.A2KM.01 TCGA.C5.A2LX.01
#> "01212" "03112" "01132" "0122" "0112" "022"
#> TCGA.EX.A3L1.01 TCGA.LP.A5U2.01 TCGA.FU.A3NI.01 TCGA.Q1.A5R3.01 TCGA.FU.A770.01 TCGA.C5.A7CM.01
#> "0111" "021" "023" "0131" "032" "01131"
#> TCGA.JX.A3Q0.01 TCGA.EA.A5FO.01 TCGA.VS.A9V3.01 TCGA.C5.A7CL.01 TCGA.VS.A959.01 TCGA.LP.A4AX.01
#> "01211" "0312" "021" "0131" "0111" "0111"
#> TCGA.C5.A1MN.01 TCGA.ZJ.AAXN.01 TCGA.MA.AA3X.01 TCGA.UC.A7PG.01 TCGA.Q1.A6DV.01 TCGA.DS.A1OD.01
#> "022" "0132" "01211" "0131" "032" "0131"
#> TCGA.C5.A1M7.01 TCGA.BI.A20A.01 TCGA.VS.A9UO.01 TCGA.EA.A1QT.01 TCGA.EX.A69M.01 TCGA.VS.A9UH.01
#> "0134" "021" "032" "022" "023" "0111"
#> TCGA.VS.A9U7.01 TCGA.ZJ.AAXD.01 TCGA.VS.A9UB.01 TCGA.EA.A410.01 TCGA.ZJ.AB0I.01 TCGA.VS.A9UD.01
#> "022" "0131" "0111" "0122" "01212" "023"
#> TCGA.VS.A9U6.01 TCGA.ZX.AA5X.01 TCGA.C5.A0TN.01 TCGA.C5.A7CJ.01 TCGA.C5.A1MJ.01 TCGA.EA.A78R.01
#> "01132" "021" "01132" "021" "032" "023"
#> TCGA.VS.A9UY.01 TCGA.VS.A9U5.01 TCGA.DS.A1OC.01 TCGA.ZJ.AAXB.01 TCGA.EX.A449.01 TCGA.C5.A1BL.01
#> "022" "021" "023" "0123" "03112" "022"
#> TCGA.VS.A9UQ.01 TCGA.DS.A1OB.01 TCGA.HG.A9SC.01 TCGA.ZJ.AAXT.01 TCGA.IR.A3LB.01 TCGA.C5.A1ML.01
#> "03112" "0123" "0123" "0134" "032" "01133"
#> TCGA.VS.A9UV.01 TCGA.LP.A4AU.01 TCGA.Q1.A6DT.01 TCGA.C5.A1M8.01 TCGA.C5.A1ME.01 TCGA.ZJ.AAXU.01
#> "021" "0111" "021" "021" "032" "0131"
#> TCGA.VS.A957.01 TCGA.VS.A9V5.01 TCGA.MU.A5YI.01 TCGA.ZJ.AAX4.01 TCGA.C5.A1MK.01 TCGA.JW.A69B.01
#> "022" "03111" "021" "021" "0131" "03112"
#> TCGA.VS.A958.01 TCGA.ZJ.AAXJ.01 TCGA.R2.A69V.01 TCGA.EA.A411.01 TCGA.VS.A9UP.01 TCGA.C5.A1MI.01
#> "0134" "023" "0111" "0123" "0111" "01131"
#> TCGA.DS.A1O9.01 TCGA.VS.A9UZ.01 TCGA.EA.A43B.01 TCGA.ZJ.AAX8.01 TCGA.ZJ.AAXI.01 TCGA.VS.A9UT.01
#> "021" "03112" "023" "0111" "022" "0112"
#> TCGA.DS.A1OA.01 TCGA.C5.A1MQ.01 TCGA.VS.A9V0.01 TCGA.VS.A9UC.01 TCGA.ZJ.AAXA.01 TCGA.Q1.A73P.01
#> "022" "023" "0133" "021" "01211" "03112"
#> TCGA.VS.A9V2.01 TCGA.VS.A9UU.01 TCGA.LP.A4AV.01 TCGA.VS.A9UR.01 TCGA.VS.A9V1.01 TCGA.C5.A7CG.01
#> "021" "023" "0131" "032" "032" "021"
#> TCGA.UC.A7PI.01 TCGA.EX.A1H5.01 TCGA.ZJ.AAXF.01 TCGA.VS.A9UL.01 TCGA.EA.A3Y4.01 TCGA.C5.A7CK.01
#> "032" "021" "0111" "032" "0132" "023"
#> TCGA.UC.A7PG.06 TCGA.VS.A9UJ.01 TCGA.Q1.A73O.01 TCGA.VS.A950.01 TCGA.EA.A439.01 TCGA.VS.A9UM.01
#> "01211" "0122" "0134" "022" "01131" "01211"
#> TCGA.C5.A1MP.01 TCGA.VS.A9UI.01 TCGA.ZJ.AB0H.01 TCGA.Q1.A73Q.01 TCGA.C5.A1MH.01 TCGA.VS.A9V4.01
#> "0131" "022" "0131" "022" "021" "0112"
#> TCGA.FU.A40J.01 TCGA.VS.A9UA.01 TCGA.LP.A4AW.01 TCGA.MA.AA43.01 TCGA.C5.A1BN.01 TCGA.VS.AA62.01
#> "03111" "0131" "0131" "032" "01212" "0111"
#> TCGA.C5.A1BM.01 TCGA.C5.A1M6.01 TCGA.C5.A1BE.01 TCGA.FU.A23K.01 TCGA.C5.A1BJ.01 TCGA.FU.A23L.01
#> "0134" "01131" "0131" "032" "0111" "0134"
#> TCGA.C5.A1M5.01 TCGA.C5.A1MF.01 TCGA.C5.A1BF.01 TCGA.C5.A1BK.01 TCGA.C5.A1BI.01 TCGA.C5.A1M9.01
#> "022" "021" "01132" "021" "0134" "03112"
get_classes(res_rh, merge_node = merge_node_param(min_n_signatures = 4774))
#> TCGA.EK.A3GK.01 TCGA.GH.A9DA.01 TCGA.VS.A94Y.01 TCGA.MY.A5BF.11 TCGA.VS.A94Z.01 TCGA.EA.A4BA.01
#> "0132" "023" "0132" "0112" "0131" "0133"
#> TCGA.ZJ.A8QQ.01 TCGA.FU.A3EO.11 TCGA.DG.A2KJ.01 TCGA.VS.A954.01 TCGA.MA.AA42.01 TCGA.C5.A8YQ.01
#> "023" "0112" "0111" "021" "021" "021"
#> TCGA.DS.A7WF.01 TCGA.EK.A2R7.01 TCGA.EK.A3GJ.01 TCGA.C5.A902.01 TCGA.MA.AA3W.01 TCGA.C5.A905.01
#> "0312" "0131" "023" "023" "021" "01211"
#> TCGA.EK.A2RN.01 TCGA.FU.A57G.01 TCGA.C5.A8YR.01 TCGA.EK.A2R9.01 TCGA.FU.A3EO.01 TCGA.IR.A3LC.01
#> "0131" "0112" "0133" "021" "03112" "021"
#> TCGA.VS.A8QA.01 TCGA.C5.A3HD.01 TCGA.MY.A5BE.01 TCGA.EA.A50E.01 TCGA.VS.A8QH.01 TCGA.ZJ.A8QR.01
#> "0313" "023" "0111" "021" "0111" "01212"
#> TCGA.C5.A907.01 TCGA.IR.A3LK.01 TCGA.C5.A8ZZ.01 TCGA.VS.A8EK.01 TCGA.C5.A7UC.01 TCGA.C5.A8XJ.01
#> "0111" "022" "0123" "021" "0111" "0131"
#> TCGA.IR.A3LH.01 TCGA.EK.A3GM.01 TCGA.VS.A8Q8.01 TCGA.EK.A2RO.01 TCGA.MY.A5BD.01 TCGA.2W.A8YY.01
#> "023" "0113" "0131" "021" "0312" "0122"
#> TCGA.C5.A2LZ.01 TCGA.C5.A901.01 TCGA.VS.A953.01 TCGA.MU.A51Y.01 TCGA.EK.A2RK.01 TCGA.UC.A7PD.01
#> "022" "021" "021" "0111" "0131" "0111"
#> TCGA.EA.A3HS.01 TCGA.VS.A8QM.01 TCGA.EA.A3HU.01 TCGA.VS.A94X.01 TCGA.C5.A7CO.01 TCGA.C5.A3HF.01
#> "021" "0111" "0111" "0111" "021" "0111"
#> TCGA.IR.A3LL.01 TCGA.MY.A913.01 TCGA.VS.A952.01 TCGA.IR.A3LI.01 TCGA.VS.A94W.01 TCGA.MY.A5BF.01
#> "023" "0111" "0313" "0313" "021" "023"
#> TCGA.EK.A2RC.01 TCGA.VS.A8EL.01 TCGA.EA.A97N.01 TCGA.EA.A3HQ.01 TCGA.EK.A2RD.01 TCGA.C5.A8YT.01
#> "022" "023" "01212" "022" "0131" "0112"
#> TCGA.FU.A3HZ.01 TCGA.VS.A8EJ.01 TCGA.C5.A3HL.01 TCGA.UC.A7PF.01 TCGA.C5.A8XK.01 TCGA.EX.A8YF.01
#> "0122" "0112" "0131" "023" "0132" "0111"
#> TCGA.HM.A4S6.01 TCGA.VS.A8Q9.01 TCGA.MA.AA41.01 TCGA.EK.A3GN.01 TCGA.MA.AA3Y.01 TCGA.MA.AA3Z.01
#> "0131" "023" "021" "021" "0111" "0131"
#> TCGA.EK.A2RE.01 TCGA.C5.A1BQ.01 TCGA.ZJ.A8QO.01 TCGA.JW.A852.01 TCGA.DS.A7WH.01 TCGA.JW.AAVH.01
#> "0131" "0131" "021" "021" "032" "022"
#> TCGA.EA.A556.01 TCGA.EA.A44S.01 TCGA.4J.AA1J.01 TCGA.IR.A3L7.01 TCGA.C5.A7X3.01 TCGA.HG.A2PA.01
#> "0133" "01212" "01212" "022" "0132" "0111"
#> TCGA.C5.A8XH.01 TCGA.C5.A7XC.01 TCGA.VS.A8EI.01 TCGA.VS.A8QC.01 TCGA.C5.A7UH.01 TCGA.WL.A834.01
#> "023" "0131" "023" "022" "01211" "022"
#> TCGA.C5.A8XI.01 TCGA.DS.A7WI.01 TCGA.VS.A8QF.01 TCGA.EA.A3HR.01 TCGA.DG.A2KL.01 TCGA.EK.A2RL.01
#> "023" "023" "022" "0131" "0131" "03112"
#> TCGA.EK.A2PG.01 TCGA.BI.A0VR.01 TCGA.DS.A0VL.01 TCGA.VS.A8EC.01 TCGA.EA.A3QE.01 TCGA.DS.A0VM.01
#> "022" "0131" "0131" "022" "021" "021"
#> TCGA.FU.A3HY.01 TCGA.Q1.A5R1.01 TCGA.DR.A0ZM.01 TCGA.Q1.A6DW.01 TCGA.DS.A0VK.01 TCGA.DS.A3LQ.01
#> "022" "03112" "0134" "021" "0131" "022"
#> TCGA.EA.A3QD.01 TCGA.JW.A5VJ.01 TCGA.LP.A5U3.01 TCGA.EA.A6QX.01 TCGA.EK.A2RA.01 TCGA.FU.A5XV.01
#> "023" "0134" "022" "022" "022" "01212"
#> TCGA.Q1.A5R2.01 TCGA.HM.A3JJ.01 TCGA.C5.A2LS.01 TCGA.C5.A7X8.01 TCGA.EK.A2RJ.01 TCGA.EA.A3HT.01
#> "022" "0131" "0313" "032" "0133" "0131"
#> TCGA.LP.A7HU.01 TCGA.MU.A8JM.01 TCGA.EK.A2IP.01 TCGA.JW.A5VL.01 TCGA.FU.A3TX.01 TCGA.DG.A2KK.01
#> "0312" "021" "022" "022" "0113" "0313"
#> TCGA.EK.A2PI.01 TCGA.Q1.A73S.01 TCGA.EK.A2IR.01 TCGA.HM.A6W2.01 TCGA.VS.A8EH.01 TCGA.JW.A5VH.01
#> "0131" "0122" "021" "0122" "0113" "0122"
#> TCGA.C5.A2LV.01 TCGA.VS.A8EB.01 TCGA.RA.A741.01 TCGA.VS.A8EG.01 TCGA.DG.A2KH.01 TCGA.C5.A7UE.01
#> "021" "0113" "0111" "022" "0113" "021"
#> TCGA.C5.A2LT.01 TCGA.EA.A5ZD.01 TCGA.Q1.A73R.01 TCGA.JW.A5VK.01 TCGA.EK.A2RM.01 TCGA.C5.A7UI.01
#> "0111" "0134" "0312" "022" "0113" "0131"
#> TCGA.EK.A2PL.01 TCGA.EK.A2PM.01 TCGA.EK.A2GZ.01 TCGA.HM.A3JK.01 TCGA.C5.A2M1.01 TCGA.HM.A6W2.06
#> "0131" "0123" "0111" "0111" "03112" "0122"
#> TCGA.C5.A7X5.01 TCGA.IR.A3LA.01 TCGA.EK.A2PK.01 TCGA.EA.A5ZF.01 TCGA.XS.A8TJ.01 TCGA.BI.A0VS.01
#> "023" "0122" "0133" "0132" "021" "0132"
#> TCGA.DS.A0VN.01 TCGA.JX.A5QV.01 TCGA.EK.A2R8.01 TCGA.EA.A1QS.01 TCGA.C5.A3HE.01 TCGA.IR.A3LF.01
#> "021" "0131" "0132" "0111" "032" "03112"
#> TCGA.DR.A0ZL.01 TCGA.FU.A3WB.01 TCGA.JX.A3PZ.01 TCGA.EA.A5O9.01 TCGA.HM.A3JJ.11 TCGA.DS.A5RQ.01
#> "021" "021" "0133" "021" "0112" "0131"
#> TCGA.EK.A2H0.01 TCGA.EX.A1H6.01 TCGA.EA.A5ZE.01 TCGA.C5.A2LY.01 TCGA.FU.A3TQ.01 TCGA.EK.A2RB.01
#> "023" "032" "021" "0113" "022" "022"
#> TCGA.JW.A5VI.01 TCGA.EK.A2H1.01 TCGA.JX.A3Q8.01 TCGA.FU.A3YQ.01 TCGA.EX.A69L.01 TCGA.C5.A7CH.01
#> "021" "0112" "0313" "021" "0131" "021"
#> TCGA.FU.A2QG.01 TCGA.C5.A2M2.01 TCGA.JW.A5VG.01 TCGA.PN.A8MA.01 TCGA.DG.A2KM.01 TCGA.C5.A2LX.01
#> "01212" "03112" "0113" "0122" "0112" "022"
#> TCGA.EX.A3L1.01 TCGA.LP.A5U2.01 TCGA.FU.A3NI.01 TCGA.Q1.A5R3.01 TCGA.FU.A770.01 TCGA.C5.A7CM.01
#> "0111" "021" "023" "0131" "032" "0113"
#> TCGA.JX.A3Q0.01 TCGA.EA.A5FO.01 TCGA.VS.A9V3.01 TCGA.C5.A7CL.01 TCGA.VS.A959.01 TCGA.LP.A4AX.01
#> "01211" "0312" "021" "0131" "0111" "0111"
#> TCGA.C5.A1MN.01 TCGA.ZJ.AAXN.01 TCGA.MA.AA3X.01 TCGA.UC.A7PG.01 TCGA.Q1.A6DV.01 TCGA.DS.A1OD.01
#> "022" "0132" "01211" "0131" "032" "0131"
#> TCGA.C5.A1M7.01 TCGA.BI.A20A.01 TCGA.VS.A9UO.01 TCGA.EA.A1QT.01 TCGA.EX.A69M.01 TCGA.VS.A9UH.01
#> "0134" "021" "032" "022" "023" "0111"
#> TCGA.VS.A9U7.01 TCGA.ZJ.AAXD.01 TCGA.VS.A9UB.01 TCGA.EA.A410.01 TCGA.ZJ.AB0I.01 TCGA.VS.A9UD.01
#> "022" "0131" "0111" "0122" "01212" "023"
#> TCGA.VS.A9U6.01 TCGA.ZX.AA5X.01 TCGA.C5.A0TN.01 TCGA.C5.A7CJ.01 TCGA.C5.A1MJ.01 TCGA.EA.A78R.01
#> "0113" "021" "0113" "021" "032" "023"
#> TCGA.VS.A9UY.01 TCGA.VS.A9U5.01 TCGA.DS.A1OC.01 TCGA.ZJ.AAXB.01 TCGA.EX.A449.01 TCGA.C5.A1BL.01
#> "022" "021" "023" "0123" "03112" "022"
#> TCGA.VS.A9UQ.01 TCGA.DS.A1OB.01 TCGA.HG.A9SC.01 TCGA.ZJ.AAXT.01 TCGA.IR.A3LB.01 TCGA.C5.A1ML.01
#> "03112" "0123" "0123" "0134" "032" "0113"
#> TCGA.VS.A9UV.01 TCGA.LP.A4AU.01 TCGA.Q1.A6DT.01 TCGA.C5.A1M8.01 TCGA.C5.A1ME.01 TCGA.ZJ.AAXU.01
#> "021" "0111" "021" "021" "032" "0131"
#> TCGA.VS.A957.01 TCGA.VS.A9V5.01 TCGA.MU.A5YI.01 TCGA.ZJ.AAX4.01 TCGA.C5.A1MK.01 TCGA.JW.A69B.01
#> "022" "03111" "021" "021" "0131" "03112"
#> TCGA.VS.A958.01 TCGA.ZJ.AAXJ.01 TCGA.R2.A69V.01 TCGA.EA.A411.01 TCGA.VS.A9UP.01 TCGA.C5.A1MI.01
#> "0134" "023" "0111" "0123" "0111" "0113"
#> TCGA.DS.A1O9.01 TCGA.VS.A9UZ.01 TCGA.EA.A43B.01 TCGA.ZJ.AAX8.01 TCGA.ZJ.AAXI.01 TCGA.VS.A9UT.01
#> "021" "03112" "023" "0111" "022" "0112"
#> TCGA.DS.A1OA.01 TCGA.C5.A1MQ.01 TCGA.VS.A9V0.01 TCGA.VS.A9UC.01 TCGA.ZJ.AAXA.01 TCGA.Q1.A73P.01
#> "022" "023" "0133" "021" "01211" "03112"
#> TCGA.VS.A9V2.01 TCGA.VS.A9UU.01 TCGA.LP.A4AV.01 TCGA.VS.A9UR.01 TCGA.VS.A9V1.01 TCGA.C5.A7CG.01
#> "021" "023" "0131" "032" "032" "021"
#> TCGA.UC.A7PI.01 TCGA.EX.A1H5.01 TCGA.ZJ.AAXF.01 TCGA.VS.A9UL.01 TCGA.EA.A3Y4.01 TCGA.C5.A7CK.01
#> "032" "021" "0111" "032" "0132" "023"
#> TCGA.UC.A7PG.06 TCGA.VS.A9UJ.01 TCGA.Q1.A73O.01 TCGA.VS.A950.01 TCGA.EA.A439.01 TCGA.VS.A9UM.01
#> "01211" "0122" "0134" "022" "0113" "01211"
#> TCGA.C5.A1MP.01 TCGA.VS.A9UI.01 TCGA.ZJ.AB0H.01 TCGA.Q1.A73Q.01 TCGA.C5.A1MH.01 TCGA.VS.A9V4.01
#> "0131" "022" "0131" "022" "021" "0112"
#> TCGA.FU.A40J.01 TCGA.VS.A9UA.01 TCGA.LP.A4AW.01 TCGA.MA.AA43.01 TCGA.C5.A1BN.01 TCGA.VS.AA62.01
#> "03111" "0131" "0131" "032" "01212" "0111"
#> TCGA.C5.A1BM.01 TCGA.C5.A1M6.01 TCGA.C5.A1BE.01 TCGA.FU.A23K.01 TCGA.C5.A1BJ.01 TCGA.FU.A23L.01
#> "0134" "0113" "0131" "032" "0111" "0134"
#> TCGA.C5.A1M5.01 TCGA.C5.A1MF.01 TCGA.C5.A1BF.01 TCGA.C5.A1BK.01 TCGA.C5.A1BI.01 TCGA.C5.A1M9.01
#> "022" "021" "0113" "021" "0134" "03112"
get_classes(res_rh, merge_node = merge_node_param(min_n_signatures = 5174))
#> TCGA.EK.A3GK.01 TCGA.GH.A9DA.01 TCGA.VS.A94Y.01 TCGA.MY.A5BF.11 TCGA.VS.A94Z.01 TCGA.EA.A4BA.01
#> "0132" "023" "0132" "0112" "0131" "0133"
#> TCGA.ZJ.A8QQ.01 TCGA.FU.A3EO.11 TCGA.DG.A2KJ.01 TCGA.VS.A954.01 TCGA.MA.AA42.01 TCGA.C5.A8YQ.01
#> "023" "0112" "0111" "021" "021" "021"
#> TCGA.DS.A7WF.01 TCGA.EK.A2R7.01 TCGA.EK.A3GJ.01 TCGA.C5.A902.01 TCGA.MA.AA3W.01 TCGA.C5.A905.01
#> "0312" "0131" "023" "023" "021" "0121"
#> TCGA.EK.A2RN.01 TCGA.FU.A57G.01 TCGA.C5.A8YR.01 TCGA.EK.A2R9.01 TCGA.FU.A3EO.01 TCGA.IR.A3LC.01
#> "0131" "0112" "0133" "021" "03112" "021"
#> TCGA.VS.A8QA.01 TCGA.C5.A3HD.01 TCGA.MY.A5BE.01 TCGA.EA.A50E.01 TCGA.VS.A8QH.01 TCGA.ZJ.A8QR.01
#> "0313" "023" "0111" "021" "0111" "0121"
#> TCGA.C5.A907.01 TCGA.IR.A3LK.01 TCGA.C5.A8ZZ.01 TCGA.VS.A8EK.01 TCGA.C5.A7UC.01 TCGA.C5.A8XJ.01
#> "0111" "022" "0123" "021" "0111" "0131"
#> TCGA.IR.A3LH.01 TCGA.EK.A3GM.01 TCGA.VS.A8Q8.01 TCGA.EK.A2RO.01 TCGA.MY.A5BD.01 TCGA.2W.A8YY.01
#> "023" "0113" "0131" "021" "0312" "0122"
#> TCGA.C5.A2LZ.01 TCGA.C5.A901.01 TCGA.VS.A953.01 TCGA.MU.A51Y.01 TCGA.EK.A2RK.01 TCGA.UC.A7PD.01
#> "022" "021" "021" "0111" "0131" "0111"
#> TCGA.EA.A3HS.01 TCGA.VS.A8QM.01 TCGA.EA.A3HU.01 TCGA.VS.A94X.01 TCGA.C5.A7CO.01 TCGA.C5.A3HF.01
#> "021" "0111" "0111" "0111" "021" "0111"
#> TCGA.IR.A3LL.01 TCGA.MY.A913.01 TCGA.VS.A952.01 TCGA.IR.A3LI.01 TCGA.VS.A94W.01 TCGA.MY.A5BF.01
#> "023" "0111" "0313" "0313" "021" "023"
#> TCGA.EK.A2RC.01 TCGA.VS.A8EL.01 TCGA.EA.A97N.01 TCGA.EA.A3HQ.01 TCGA.EK.A2RD.01 TCGA.C5.A8YT.01
#> "022" "023" "0121" "022" "0131" "0112"
#> TCGA.FU.A3HZ.01 TCGA.VS.A8EJ.01 TCGA.C5.A3HL.01 TCGA.UC.A7PF.01 TCGA.C5.A8XK.01 TCGA.EX.A8YF.01
#> "0122" "0112" "0131" "023" "0132" "0111"
#> TCGA.HM.A4S6.01 TCGA.VS.A8Q9.01 TCGA.MA.AA41.01 TCGA.EK.A3GN.01 TCGA.MA.AA3Y.01 TCGA.MA.AA3Z.01
#> "0131" "023" "021" "021" "0111" "0131"
#> TCGA.EK.A2RE.01 TCGA.C5.A1BQ.01 TCGA.ZJ.A8QO.01 TCGA.JW.A852.01 TCGA.DS.A7WH.01 TCGA.JW.AAVH.01
#> "0131" "0131" "021" "021" "032" "022"
#> TCGA.EA.A556.01 TCGA.EA.A44S.01 TCGA.4J.AA1J.01 TCGA.IR.A3L7.01 TCGA.C5.A7X3.01 TCGA.HG.A2PA.01
#> "0133" "0121" "0121" "022" "0132" "0111"
#> TCGA.C5.A8XH.01 TCGA.C5.A7XC.01 TCGA.VS.A8EI.01 TCGA.VS.A8QC.01 TCGA.C5.A7UH.01 TCGA.WL.A834.01
#> "023" "0131" "023" "022" "0121" "022"
#> TCGA.C5.A8XI.01 TCGA.DS.A7WI.01 TCGA.VS.A8QF.01 TCGA.EA.A3HR.01 TCGA.DG.A2KL.01 TCGA.EK.A2RL.01
#> "023" "023" "022" "0131" "0131" "03112"
#> TCGA.EK.A2PG.01 TCGA.BI.A0VR.01 TCGA.DS.A0VL.01 TCGA.VS.A8EC.01 TCGA.EA.A3QE.01 TCGA.DS.A0VM.01
#> "022" "0131" "0131" "022" "021" "021"
#> TCGA.FU.A3HY.01 TCGA.Q1.A5R1.01 TCGA.DR.A0ZM.01 TCGA.Q1.A6DW.01 TCGA.DS.A0VK.01 TCGA.DS.A3LQ.01
#> "022" "03112" "0134" "021" "0131" "022"
#> TCGA.EA.A3QD.01 TCGA.JW.A5VJ.01 TCGA.LP.A5U3.01 TCGA.EA.A6QX.01 TCGA.EK.A2RA.01 TCGA.FU.A5XV.01
#> "023" "0134" "022" "022" "022" "0121"
#> TCGA.Q1.A5R2.01 TCGA.HM.A3JJ.01 TCGA.C5.A2LS.01 TCGA.C5.A7X8.01 TCGA.EK.A2RJ.01 TCGA.EA.A3HT.01
#> "022" "0131" "0313" "032" "0133" "0131"
#> TCGA.LP.A7HU.01 TCGA.MU.A8JM.01 TCGA.EK.A2IP.01 TCGA.JW.A5VL.01 TCGA.FU.A3TX.01 TCGA.DG.A2KK.01
#> "0312" "021" "022" "022" "0113" "0313"
#> TCGA.EK.A2PI.01 TCGA.Q1.A73S.01 TCGA.EK.A2IR.01 TCGA.HM.A6W2.01 TCGA.VS.A8EH.01 TCGA.JW.A5VH.01
#> "0131" "0122" "021" "0122" "0113" "0122"
#> TCGA.C5.A2LV.01 TCGA.VS.A8EB.01 TCGA.RA.A741.01 TCGA.VS.A8EG.01 TCGA.DG.A2KH.01 TCGA.C5.A7UE.01
#> "021" "0113" "0111" "022" "0113" "021"
#> TCGA.C5.A2LT.01 TCGA.EA.A5ZD.01 TCGA.Q1.A73R.01 TCGA.JW.A5VK.01 TCGA.EK.A2RM.01 TCGA.C5.A7UI.01
#> "0111" "0134" "0312" "022" "0113" "0131"
#> TCGA.EK.A2PL.01 TCGA.EK.A2PM.01 TCGA.EK.A2GZ.01 TCGA.HM.A3JK.01 TCGA.C5.A2M1.01 TCGA.HM.A6W2.06
#> "0131" "0123" "0111" "0111" "03112" "0122"
#> TCGA.C5.A7X5.01 TCGA.IR.A3LA.01 TCGA.EK.A2PK.01 TCGA.EA.A5ZF.01 TCGA.XS.A8TJ.01 TCGA.BI.A0VS.01
#> "023" "0122" "0133" "0132" "021" "0132"
#> TCGA.DS.A0VN.01 TCGA.JX.A5QV.01 TCGA.EK.A2R8.01 TCGA.EA.A1QS.01 TCGA.C5.A3HE.01 TCGA.IR.A3LF.01
#> "021" "0131" "0132" "0111" "032" "03112"
#> TCGA.DR.A0ZL.01 TCGA.FU.A3WB.01 TCGA.JX.A3PZ.01 TCGA.EA.A5O9.01 TCGA.HM.A3JJ.11 TCGA.DS.A5RQ.01
#> "021" "021" "0133" "021" "0112" "0131"
#> TCGA.EK.A2H0.01 TCGA.EX.A1H6.01 TCGA.EA.A5ZE.01 TCGA.C5.A2LY.01 TCGA.FU.A3TQ.01 TCGA.EK.A2RB.01
#> "023" "032" "021" "0113" "022" "022"
#> TCGA.JW.A5VI.01 TCGA.EK.A2H1.01 TCGA.JX.A3Q8.01 TCGA.FU.A3YQ.01 TCGA.EX.A69L.01 TCGA.C5.A7CH.01
#> "021" "0112" "0313" "021" "0131" "021"
#> TCGA.FU.A2QG.01 TCGA.C5.A2M2.01 TCGA.JW.A5VG.01 TCGA.PN.A8MA.01 TCGA.DG.A2KM.01 TCGA.C5.A2LX.01
#> "0121" "03112" "0113" "0122" "0112" "022"
#> TCGA.EX.A3L1.01 TCGA.LP.A5U2.01 TCGA.FU.A3NI.01 TCGA.Q1.A5R3.01 TCGA.FU.A770.01 TCGA.C5.A7CM.01
#> "0111" "021" "023" "0131" "032" "0113"
#> TCGA.JX.A3Q0.01 TCGA.EA.A5FO.01 TCGA.VS.A9V3.01 TCGA.C5.A7CL.01 TCGA.VS.A959.01 TCGA.LP.A4AX.01
#> "0121" "0312" "021" "0131" "0111" "0111"
#> TCGA.C5.A1MN.01 TCGA.ZJ.AAXN.01 TCGA.MA.AA3X.01 TCGA.UC.A7PG.01 TCGA.Q1.A6DV.01 TCGA.DS.A1OD.01
#> "022" "0132" "0121" "0131" "032" "0131"
#> TCGA.C5.A1M7.01 TCGA.BI.A20A.01 TCGA.VS.A9UO.01 TCGA.EA.A1QT.01 TCGA.EX.A69M.01 TCGA.VS.A9UH.01
#> "0134" "021" "032" "022" "023" "0111"
#> TCGA.VS.A9U7.01 TCGA.ZJ.AAXD.01 TCGA.VS.A9UB.01 TCGA.EA.A410.01 TCGA.ZJ.AB0I.01 TCGA.VS.A9UD.01
#> "022" "0131" "0111" "0122" "0121" "023"
#> TCGA.VS.A9U6.01 TCGA.ZX.AA5X.01 TCGA.C5.A0TN.01 TCGA.C5.A7CJ.01 TCGA.C5.A1MJ.01 TCGA.EA.A78R.01
#> "0113" "021" "0113" "021" "032" "023"
#> TCGA.VS.A9UY.01 TCGA.VS.A9U5.01 TCGA.DS.A1OC.01 TCGA.ZJ.AAXB.01 TCGA.EX.A449.01 TCGA.C5.A1BL.01
#> "022" "021" "023" "0123" "03112" "022"
#> TCGA.VS.A9UQ.01 TCGA.DS.A1OB.01 TCGA.HG.A9SC.01 TCGA.ZJ.AAXT.01 TCGA.IR.A3LB.01 TCGA.C5.A1ML.01
#> "03112" "0123" "0123" "0134" "032" "0113"
#> TCGA.VS.A9UV.01 TCGA.LP.A4AU.01 TCGA.Q1.A6DT.01 TCGA.C5.A1M8.01 TCGA.C5.A1ME.01 TCGA.ZJ.AAXU.01
#> "021" "0111" "021" "021" "032" "0131"
#> TCGA.VS.A957.01 TCGA.VS.A9V5.01 TCGA.MU.A5YI.01 TCGA.ZJ.AAX4.01 TCGA.C5.A1MK.01 TCGA.JW.A69B.01
#> "022" "03111" "021" "021" "0131" "03112"
#> TCGA.VS.A958.01 TCGA.ZJ.AAXJ.01 TCGA.R2.A69V.01 TCGA.EA.A411.01 TCGA.VS.A9UP.01 TCGA.C5.A1MI.01
#> "0134" "023" "0111" "0123" "0111" "0113"
#> TCGA.DS.A1O9.01 TCGA.VS.A9UZ.01 TCGA.EA.A43B.01 TCGA.ZJ.AAX8.01 TCGA.ZJ.AAXI.01 TCGA.VS.A9UT.01
#> "021" "03112" "023" "0111" "022" "0112"
#> TCGA.DS.A1OA.01 TCGA.C5.A1MQ.01 TCGA.VS.A9V0.01 TCGA.VS.A9UC.01 TCGA.ZJ.AAXA.01 TCGA.Q1.A73P.01
#> "022" "023" "0133" "021" "0121" "03112"
#> TCGA.VS.A9V2.01 TCGA.VS.A9UU.01 TCGA.LP.A4AV.01 TCGA.VS.A9UR.01 TCGA.VS.A9V1.01 TCGA.C5.A7CG.01
#> "021" "023" "0131" "032" "032" "021"
#> TCGA.UC.A7PI.01 TCGA.EX.A1H5.01 TCGA.ZJ.AAXF.01 TCGA.VS.A9UL.01 TCGA.EA.A3Y4.01 TCGA.C5.A7CK.01
#> "032" "021" "0111" "032" "0132" "023"
#> TCGA.UC.A7PG.06 TCGA.VS.A9UJ.01 TCGA.Q1.A73O.01 TCGA.VS.A950.01 TCGA.EA.A439.01 TCGA.VS.A9UM.01
#> "0121" "0122" "0134" "022" "0113" "0121"
#> TCGA.C5.A1MP.01 TCGA.VS.A9UI.01 TCGA.ZJ.AB0H.01 TCGA.Q1.A73Q.01 TCGA.C5.A1MH.01 TCGA.VS.A9V4.01
#> "0131" "022" "0131" "022" "021" "0112"
#> TCGA.FU.A40J.01 TCGA.VS.A9UA.01 TCGA.LP.A4AW.01 TCGA.MA.AA43.01 TCGA.C5.A1BN.01 TCGA.VS.AA62.01
#> "03111" "0131" "0131" "032" "0121" "0111"
#> TCGA.C5.A1BM.01 TCGA.C5.A1M6.01 TCGA.C5.A1BE.01 TCGA.FU.A23K.01 TCGA.C5.A1BJ.01 TCGA.FU.A23L.01
#> "0134" "0113" "0131" "032" "0111" "0134"
#> TCGA.C5.A1M5.01 TCGA.C5.A1MF.01 TCGA.C5.A1BF.01 TCGA.C5.A1BK.01 TCGA.C5.A1BI.01 TCGA.C5.A1M9.01
#> "022" "021" "0113" "021" "0134" "03112"
get_classes(res_rh, merge_node = merge_node_param(min_n_signatures = 7545))
#> TCGA.EK.A3GK.01 TCGA.GH.A9DA.01 TCGA.VS.A94Y.01 TCGA.MY.A5BF.11 TCGA.VS.A94Z.01 TCGA.EA.A4BA.01
#> "0132" "023" "0132" "0112" "0131" "0133"
#> TCGA.ZJ.A8QQ.01 TCGA.FU.A3EO.11 TCGA.DG.A2KJ.01 TCGA.VS.A954.01 TCGA.MA.AA42.01 TCGA.C5.A8YQ.01
#> "023" "0112" "0111" "021" "021" "021"
#> TCGA.DS.A7WF.01 TCGA.EK.A2R7.01 TCGA.EK.A3GJ.01 TCGA.C5.A902.01 TCGA.MA.AA3W.01 TCGA.C5.A905.01
#> "03" "0131" "023" "023" "021" "0121"
#> TCGA.EK.A2RN.01 TCGA.FU.A57G.01 TCGA.C5.A8YR.01 TCGA.EK.A2R9.01 TCGA.FU.A3EO.01 TCGA.IR.A3LC.01
#> "0131" "0112" "0133" "021" "03112" "021"
#> TCGA.VS.A8QA.01 TCGA.C5.A3HD.01 TCGA.MY.A5BE.01 TCGA.EA.A50E.01 TCGA.VS.A8QH.01 TCGA.ZJ.A8QR.01
#> "03" "023" "0111" "021" "0111" "0121"
#> TCGA.C5.A907.01 TCGA.IR.A3LK.01 TCGA.C5.A8ZZ.01 TCGA.VS.A8EK.01 TCGA.C5.A7UC.01 TCGA.C5.A8XJ.01
#> "0111" "022" "0123" "021" "0111" "0131"
#> TCGA.IR.A3LH.01 TCGA.EK.A3GM.01 TCGA.VS.A8Q8.01 TCGA.EK.A2RO.01 TCGA.MY.A5BD.01 TCGA.2W.A8YY.01
#> "023" "0113" "0131" "021" "03" "0122"
#> TCGA.C5.A2LZ.01 TCGA.C5.A901.01 TCGA.VS.A953.01 TCGA.MU.A51Y.01 TCGA.EK.A2RK.01 TCGA.UC.A7PD.01
#> "022" "021" "021" "0111" "0131" "0111"
#> TCGA.EA.A3HS.01 TCGA.VS.A8QM.01 TCGA.EA.A3HU.01 TCGA.VS.A94X.01 TCGA.C5.A7CO.01 TCGA.C5.A3HF.01
#> "021" "0111" "0111" "0111" "021" "0111"
#> TCGA.IR.A3LL.01 TCGA.MY.A913.01 TCGA.VS.A952.01 TCGA.IR.A3LI.01 TCGA.VS.A94W.01 TCGA.MY.A5BF.01
#> "023" "0111" "03" "03" "021" "023"
#> TCGA.EK.A2RC.01 TCGA.VS.A8EL.01 TCGA.EA.A97N.01 TCGA.EA.A3HQ.01 TCGA.EK.A2RD.01 TCGA.C5.A8YT.01
#> "022" "023" "0121" "022" "0131" "0112"
#> TCGA.FU.A3HZ.01 TCGA.VS.A8EJ.01 TCGA.C5.A3HL.01 TCGA.UC.A7PF.01 TCGA.C5.A8XK.01 TCGA.EX.A8YF.01
#> "0122" "0112" "0131" "023" "0132" "0111"
#> TCGA.HM.A4S6.01 TCGA.VS.A8Q9.01 TCGA.MA.AA41.01 TCGA.EK.A3GN.01 TCGA.MA.AA3Y.01 TCGA.MA.AA3Z.01
#> "0131" "023" "021" "021" "0111" "0131"
#> TCGA.EK.A2RE.01 TCGA.C5.A1BQ.01 TCGA.ZJ.A8QO.01 TCGA.JW.A852.01 TCGA.DS.A7WH.01 TCGA.JW.AAVH.01
#> "0131" "0131" "021" "021" "03" "022"
#> TCGA.EA.A556.01 TCGA.EA.A44S.01 TCGA.4J.AA1J.01 TCGA.IR.A3L7.01 TCGA.C5.A7X3.01 TCGA.HG.A2PA.01
#> "0133" "0121" "0121" "022" "0132" "0111"
#> TCGA.C5.A8XH.01 TCGA.C5.A7XC.01 TCGA.VS.A8EI.01 TCGA.VS.A8QC.01 TCGA.C5.A7UH.01 TCGA.WL.A834.01
#> "023" "0131" "023" "022" "0121" "022"
#> TCGA.C5.A8XI.01 TCGA.DS.A7WI.01 TCGA.VS.A8QF.01 TCGA.EA.A3HR.01 TCGA.DG.A2KL.01 TCGA.EK.A2RL.01
#> "023" "023" "022" "0131" "0131" "03112"
#> TCGA.EK.A2PG.01 TCGA.BI.A0VR.01 TCGA.DS.A0VL.01 TCGA.VS.A8EC.01 TCGA.EA.A3QE.01 TCGA.DS.A0VM.01
#> "022" "0131" "0131" "022" "021" "021"
#> TCGA.FU.A3HY.01 TCGA.Q1.A5R1.01 TCGA.DR.A0ZM.01 TCGA.Q1.A6DW.01 TCGA.DS.A0VK.01 TCGA.DS.A3LQ.01
#> "022" "03112" "0134" "021" "0131" "022"
#> TCGA.EA.A3QD.01 TCGA.JW.A5VJ.01 TCGA.LP.A5U3.01 TCGA.EA.A6QX.01 TCGA.EK.A2RA.01 TCGA.FU.A5XV.01
#> "023" "0134" "022" "022" "022" "0121"
#> TCGA.Q1.A5R2.01 TCGA.HM.A3JJ.01 TCGA.C5.A2LS.01 TCGA.C5.A7X8.01 TCGA.EK.A2RJ.01 TCGA.EA.A3HT.01
#> "022" "0131" "03" "03" "0133" "0131"
#> TCGA.LP.A7HU.01 TCGA.MU.A8JM.01 TCGA.EK.A2IP.01 TCGA.JW.A5VL.01 TCGA.FU.A3TX.01 TCGA.DG.A2KK.01
#> "03" "021" "022" "022" "0113" "03"
#> TCGA.EK.A2PI.01 TCGA.Q1.A73S.01 TCGA.EK.A2IR.01 TCGA.HM.A6W2.01 TCGA.VS.A8EH.01 TCGA.JW.A5VH.01
#> "0131" "0122" "021" "0122" "0113" "0122"
#> TCGA.C5.A2LV.01 TCGA.VS.A8EB.01 TCGA.RA.A741.01 TCGA.VS.A8EG.01 TCGA.DG.A2KH.01 TCGA.C5.A7UE.01
#> "021" "0113" "0111" "022" "0113" "021"
#> TCGA.C5.A2LT.01 TCGA.EA.A5ZD.01 TCGA.Q1.A73R.01 TCGA.JW.A5VK.01 TCGA.EK.A2RM.01 TCGA.C5.A7UI.01
#> "0111" "0134" "03" "022" "0113" "0131"
#> TCGA.EK.A2PL.01 TCGA.EK.A2PM.01 TCGA.EK.A2GZ.01 TCGA.HM.A3JK.01 TCGA.C5.A2M1.01 TCGA.HM.A6W2.06
#> "0131" "0123" "0111" "0111" "03112" "0122"
#> TCGA.C5.A7X5.01 TCGA.IR.A3LA.01 TCGA.EK.A2PK.01 TCGA.EA.A5ZF.01 TCGA.XS.A8TJ.01 TCGA.BI.A0VS.01
#> "023" "0122" "0133" "0132" "021" "0132"
#> TCGA.DS.A0VN.01 TCGA.JX.A5QV.01 TCGA.EK.A2R8.01 TCGA.EA.A1QS.01 TCGA.C5.A3HE.01 TCGA.IR.A3LF.01
#> "021" "0131" "0132" "0111" "03" "03112"
#> TCGA.DR.A0ZL.01 TCGA.FU.A3WB.01 TCGA.JX.A3PZ.01 TCGA.EA.A5O9.01 TCGA.HM.A3JJ.11 TCGA.DS.A5RQ.01
#> "021" "021" "0133" "021" "0112" "0131"
#> TCGA.EK.A2H0.01 TCGA.EX.A1H6.01 TCGA.EA.A5ZE.01 TCGA.C5.A2LY.01 TCGA.FU.A3TQ.01 TCGA.EK.A2RB.01
#> "023" "03" "021" "0113" "022" "022"
#> TCGA.JW.A5VI.01 TCGA.EK.A2H1.01 TCGA.JX.A3Q8.01 TCGA.FU.A3YQ.01 TCGA.EX.A69L.01 TCGA.C5.A7CH.01
#> "021" "0112" "03" "021" "0131" "021"
#> TCGA.FU.A2QG.01 TCGA.C5.A2M2.01 TCGA.JW.A5VG.01 TCGA.PN.A8MA.01 TCGA.DG.A2KM.01 TCGA.C5.A2LX.01
#> "0121" "03112" "0113" "0122" "0112" "022"
#> TCGA.EX.A3L1.01 TCGA.LP.A5U2.01 TCGA.FU.A3NI.01 TCGA.Q1.A5R3.01 TCGA.FU.A770.01 TCGA.C5.A7CM.01
#> "0111" "021" "023" "0131" "03" "0113"
#> TCGA.JX.A3Q0.01 TCGA.EA.A5FO.01 TCGA.VS.A9V3.01 TCGA.C5.A7CL.01 TCGA.VS.A959.01 TCGA.LP.A4AX.01
#> "0121" "03" "021" "0131" "0111" "0111"
#> TCGA.C5.A1MN.01 TCGA.ZJ.AAXN.01 TCGA.MA.AA3X.01 TCGA.UC.A7PG.01 TCGA.Q1.A6DV.01 TCGA.DS.A1OD.01
#> "022" "0132" "0121" "0131" "03" "0131"
#> TCGA.C5.A1M7.01 TCGA.BI.A20A.01 TCGA.VS.A9UO.01 TCGA.EA.A1QT.01 TCGA.EX.A69M.01 TCGA.VS.A9UH.01
#> "0134" "021" "03" "022" "023" "0111"
#> TCGA.VS.A9U7.01 TCGA.ZJ.AAXD.01 TCGA.VS.A9UB.01 TCGA.EA.A410.01 TCGA.ZJ.AB0I.01 TCGA.VS.A9UD.01
#> "022" "0131" "0111" "0122" "0121" "023"
#> TCGA.VS.A9U6.01 TCGA.ZX.AA5X.01 TCGA.C5.A0TN.01 TCGA.C5.A7CJ.01 TCGA.C5.A1MJ.01 TCGA.EA.A78R.01
#> "0113" "021" "0113" "021" "03" "023"
#> TCGA.VS.A9UY.01 TCGA.VS.A9U5.01 TCGA.DS.A1OC.01 TCGA.ZJ.AAXB.01 TCGA.EX.A449.01 TCGA.C5.A1BL.01
#> "022" "021" "023" "0123" "03112" "022"
#> TCGA.VS.A9UQ.01 TCGA.DS.A1OB.01 TCGA.HG.A9SC.01 TCGA.ZJ.AAXT.01 TCGA.IR.A3LB.01 TCGA.C5.A1ML.01
#> "03112" "0123" "0123" "0134" "03" "0113"
#> TCGA.VS.A9UV.01 TCGA.LP.A4AU.01 TCGA.Q1.A6DT.01 TCGA.C5.A1M8.01 TCGA.C5.A1ME.01 TCGA.ZJ.AAXU.01
#> "021" "0111" "021" "021" "03" "0131"
#> TCGA.VS.A957.01 TCGA.VS.A9V5.01 TCGA.MU.A5YI.01 TCGA.ZJ.AAX4.01 TCGA.C5.A1MK.01 TCGA.JW.A69B.01
#> "022" "03111" "021" "021" "0131" "03112"
#> TCGA.VS.A958.01 TCGA.ZJ.AAXJ.01 TCGA.R2.A69V.01 TCGA.EA.A411.01 TCGA.VS.A9UP.01 TCGA.C5.A1MI.01
#> "0134" "023" "0111" "0123" "0111" "0113"
#> TCGA.DS.A1O9.01 TCGA.VS.A9UZ.01 TCGA.EA.A43B.01 TCGA.ZJ.AAX8.01 TCGA.ZJ.AAXI.01 TCGA.VS.A9UT.01
#> "021" "03112" "023" "0111" "022" "0112"
#> TCGA.DS.A1OA.01 TCGA.C5.A1MQ.01 TCGA.VS.A9V0.01 TCGA.VS.A9UC.01 TCGA.ZJ.AAXA.01 TCGA.Q1.A73P.01
#> "022" "023" "0133" "021" "0121" "03112"
#> TCGA.VS.A9V2.01 TCGA.VS.A9UU.01 TCGA.LP.A4AV.01 TCGA.VS.A9UR.01 TCGA.VS.A9V1.01 TCGA.C5.A7CG.01
#> "021" "023" "0131" "03" "03" "021"
#> TCGA.UC.A7PI.01 TCGA.EX.A1H5.01 TCGA.ZJ.AAXF.01 TCGA.VS.A9UL.01 TCGA.EA.A3Y4.01 TCGA.C5.A7CK.01
#> "03" "021" "0111" "03" "0132" "023"
#> TCGA.UC.A7PG.06 TCGA.VS.A9UJ.01 TCGA.Q1.A73O.01 TCGA.VS.A950.01 TCGA.EA.A439.01 TCGA.VS.A9UM.01
#> "0121" "0122" "0134" "022" "0113" "0121"
#> TCGA.C5.A1MP.01 TCGA.VS.A9UI.01 TCGA.ZJ.AB0H.01 TCGA.Q1.A73Q.01 TCGA.C5.A1MH.01 TCGA.VS.A9V4.01
#> "0131" "022" "0131" "022" "021" "0112"
#> TCGA.FU.A40J.01 TCGA.VS.A9UA.01 TCGA.LP.A4AW.01 TCGA.MA.AA43.01 TCGA.C5.A1BN.01 TCGA.VS.AA62.01
#> "03111" "0131" "0131" "03" "0121" "0111"
#> TCGA.C5.A1BM.01 TCGA.C5.A1M6.01 TCGA.C5.A1BE.01 TCGA.FU.A23K.01 TCGA.C5.A1BJ.01 TCGA.FU.A23L.01
#> "0134" "0113" "0131" "03" "0111" "0134"
#> TCGA.C5.A1M5.01 TCGA.C5.A1MF.01 TCGA.C5.A1BF.01 TCGA.C5.A1BK.01 TCGA.C5.A1BI.01 TCGA.C5.A1M9.01
#> "022" "021" "0113" "021" "0134" "03112"
get_classes(res_rh, merge_node = merge_node_param(min_n_signatures = 8634))
#> TCGA.EK.A3GK.01 TCGA.GH.A9DA.01 TCGA.VS.A94Y.01 TCGA.MY.A5BF.11 TCGA.VS.A94Z.01 TCGA.EA.A4BA.01
#> "0132" "023" "0132" "0112" "0131" "0133"
#> TCGA.ZJ.A8QQ.01 TCGA.FU.A3EO.11 TCGA.DG.A2KJ.01 TCGA.VS.A954.01 TCGA.MA.AA42.01 TCGA.C5.A8YQ.01
#> "023" "0112" "0111" "021" "021" "021"
#> TCGA.DS.A7WF.01 TCGA.EK.A2R7.01 TCGA.EK.A3GJ.01 TCGA.C5.A902.01 TCGA.MA.AA3W.01 TCGA.C5.A905.01
#> "03" "0131" "023" "023" "021" "0121"
#> TCGA.EK.A2RN.01 TCGA.FU.A57G.01 TCGA.C5.A8YR.01 TCGA.EK.A2R9.01 TCGA.FU.A3EO.01 TCGA.IR.A3LC.01
#> "0131" "0112" "0133" "021" "03" "021"
#> TCGA.VS.A8QA.01 TCGA.C5.A3HD.01 TCGA.MY.A5BE.01 TCGA.EA.A50E.01 TCGA.VS.A8QH.01 TCGA.ZJ.A8QR.01
#> "03" "023" "0111" "021" "0111" "0121"
#> TCGA.C5.A907.01 TCGA.IR.A3LK.01 TCGA.C5.A8ZZ.01 TCGA.VS.A8EK.01 TCGA.C5.A7UC.01 TCGA.C5.A8XJ.01
#> "0111" "022" "0123" "021" "0111" "0131"
#> TCGA.IR.A3LH.01 TCGA.EK.A3GM.01 TCGA.VS.A8Q8.01 TCGA.EK.A2RO.01 TCGA.MY.A5BD.01 TCGA.2W.A8YY.01
#> "023" "0113" "0131" "021" "03" "0122"
#> TCGA.C5.A2LZ.01 TCGA.C5.A901.01 TCGA.VS.A953.01 TCGA.MU.A51Y.01 TCGA.EK.A2RK.01 TCGA.UC.A7PD.01
#> "022" "021" "021" "0111" "0131" "0111"
#> TCGA.EA.A3HS.01 TCGA.VS.A8QM.01 TCGA.EA.A3HU.01 TCGA.VS.A94X.01 TCGA.C5.A7CO.01 TCGA.C5.A3HF.01
#> "021" "0111" "0111" "0111" "021" "0111"
#> TCGA.IR.A3LL.01 TCGA.MY.A913.01 TCGA.VS.A952.01 TCGA.IR.A3LI.01 TCGA.VS.A94W.01 TCGA.MY.A5BF.01
#> "023" "0111" "03" "03" "021" "023"
#> TCGA.EK.A2RC.01 TCGA.VS.A8EL.01 TCGA.EA.A97N.01 TCGA.EA.A3HQ.01 TCGA.EK.A2RD.01 TCGA.C5.A8YT.01
#> "022" "023" "0121" "022" "0131" "0112"
#> TCGA.FU.A3HZ.01 TCGA.VS.A8EJ.01 TCGA.C5.A3HL.01 TCGA.UC.A7PF.01 TCGA.C5.A8XK.01 TCGA.EX.A8YF.01
#> "0122" "0112" "0131" "023" "0132" "0111"
#> TCGA.HM.A4S6.01 TCGA.VS.A8Q9.01 TCGA.MA.AA41.01 TCGA.EK.A3GN.01 TCGA.MA.AA3Y.01 TCGA.MA.AA3Z.01
#> "0131" "023" "021" "021" "0111" "0131"
#> TCGA.EK.A2RE.01 TCGA.C5.A1BQ.01 TCGA.ZJ.A8QO.01 TCGA.JW.A852.01 TCGA.DS.A7WH.01 TCGA.JW.AAVH.01
#> "0131" "0131" "021" "021" "03" "022"
#> TCGA.EA.A556.01 TCGA.EA.A44S.01 TCGA.4J.AA1J.01 TCGA.IR.A3L7.01 TCGA.C5.A7X3.01 TCGA.HG.A2PA.01
#> "0133" "0121" "0121" "022" "0132" "0111"
#> TCGA.C5.A8XH.01 TCGA.C5.A7XC.01 TCGA.VS.A8EI.01 TCGA.VS.A8QC.01 TCGA.C5.A7UH.01 TCGA.WL.A834.01
#> "023" "0131" "023" "022" "0121" "022"
#> TCGA.C5.A8XI.01 TCGA.DS.A7WI.01 TCGA.VS.A8QF.01 TCGA.EA.A3HR.01 TCGA.DG.A2KL.01 TCGA.EK.A2RL.01
#> "023" "023" "022" "0131" "0131" "03"
#> TCGA.EK.A2PG.01 TCGA.BI.A0VR.01 TCGA.DS.A0VL.01 TCGA.VS.A8EC.01 TCGA.EA.A3QE.01 TCGA.DS.A0VM.01
#> "022" "0131" "0131" "022" "021" "021"
#> TCGA.FU.A3HY.01 TCGA.Q1.A5R1.01 TCGA.DR.A0ZM.01 TCGA.Q1.A6DW.01 TCGA.DS.A0VK.01 TCGA.DS.A3LQ.01
#> "022" "03" "0134" "021" "0131" "022"
#> TCGA.EA.A3QD.01 TCGA.JW.A5VJ.01 TCGA.LP.A5U3.01 TCGA.EA.A6QX.01 TCGA.EK.A2RA.01 TCGA.FU.A5XV.01
#> "023" "0134" "022" "022" "022" "0121"
#> TCGA.Q1.A5R2.01 TCGA.HM.A3JJ.01 TCGA.C5.A2LS.01 TCGA.C5.A7X8.01 TCGA.EK.A2RJ.01 TCGA.EA.A3HT.01
#> "022" "0131" "03" "03" "0133" "0131"
#> TCGA.LP.A7HU.01 TCGA.MU.A8JM.01 TCGA.EK.A2IP.01 TCGA.JW.A5VL.01 TCGA.FU.A3TX.01 TCGA.DG.A2KK.01
#> "03" "021" "022" "022" "0113" "03"
#> TCGA.EK.A2PI.01 TCGA.Q1.A73S.01 TCGA.EK.A2IR.01 TCGA.HM.A6W2.01 TCGA.VS.A8EH.01 TCGA.JW.A5VH.01
#> "0131" "0122" "021" "0122" "0113" "0122"
#> TCGA.C5.A2LV.01 TCGA.VS.A8EB.01 TCGA.RA.A741.01 TCGA.VS.A8EG.01 TCGA.DG.A2KH.01 TCGA.C5.A7UE.01
#> "021" "0113" "0111" "022" "0113" "021"
#> TCGA.C5.A2LT.01 TCGA.EA.A5ZD.01 TCGA.Q1.A73R.01 TCGA.JW.A5VK.01 TCGA.EK.A2RM.01 TCGA.C5.A7UI.01
#> "0111" "0134" "03" "022" "0113" "0131"
#> TCGA.EK.A2PL.01 TCGA.EK.A2PM.01 TCGA.EK.A2GZ.01 TCGA.HM.A3JK.01 TCGA.C5.A2M1.01 TCGA.HM.A6W2.06
#> "0131" "0123" "0111" "0111" "03" "0122"
#> TCGA.C5.A7X5.01 TCGA.IR.A3LA.01 TCGA.EK.A2PK.01 TCGA.EA.A5ZF.01 TCGA.XS.A8TJ.01 TCGA.BI.A0VS.01
#> "023" "0122" "0133" "0132" "021" "0132"
#> TCGA.DS.A0VN.01 TCGA.JX.A5QV.01 TCGA.EK.A2R8.01 TCGA.EA.A1QS.01 TCGA.C5.A3HE.01 TCGA.IR.A3LF.01
#> "021" "0131" "0132" "0111" "03" "03"
#> TCGA.DR.A0ZL.01 TCGA.FU.A3WB.01 TCGA.JX.A3PZ.01 TCGA.EA.A5O9.01 TCGA.HM.A3JJ.11 TCGA.DS.A5RQ.01
#> "021" "021" "0133" "021" "0112" "0131"
#> TCGA.EK.A2H0.01 TCGA.EX.A1H6.01 TCGA.EA.A5ZE.01 TCGA.C5.A2LY.01 TCGA.FU.A3TQ.01 TCGA.EK.A2RB.01
#> "023" "03" "021" "0113" "022" "022"
#> TCGA.JW.A5VI.01 TCGA.EK.A2H1.01 TCGA.JX.A3Q8.01 TCGA.FU.A3YQ.01 TCGA.EX.A69L.01 TCGA.C5.A7CH.01
#> "021" "0112" "03" "021" "0131" "021"
#> TCGA.FU.A2QG.01 TCGA.C5.A2M2.01 TCGA.JW.A5VG.01 TCGA.PN.A8MA.01 TCGA.DG.A2KM.01 TCGA.C5.A2LX.01
#> "0121" "03" "0113" "0122" "0112" "022"
#> TCGA.EX.A3L1.01 TCGA.LP.A5U2.01 TCGA.FU.A3NI.01 TCGA.Q1.A5R3.01 TCGA.FU.A770.01 TCGA.C5.A7CM.01
#> "0111" "021" "023" "0131" "03" "0113"
#> TCGA.JX.A3Q0.01 TCGA.EA.A5FO.01 TCGA.VS.A9V3.01 TCGA.C5.A7CL.01 TCGA.VS.A959.01 TCGA.LP.A4AX.01
#> "0121" "03" "021" "0131" "0111" "0111"
#> TCGA.C5.A1MN.01 TCGA.ZJ.AAXN.01 TCGA.MA.AA3X.01 TCGA.UC.A7PG.01 TCGA.Q1.A6DV.01 TCGA.DS.A1OD.01
#> "022" "0132" "0121" "0131" "03" "0131"
#> TCGA.C5.A1M7.01 TCGA.BI.A20A.01 TCGA.VS.A9UO.01 TCGA.EA.A1QT.01 TCGA.EX.A69M.01 TCGA.VS.A9UH.01
#> "0134" "021" "03" "022" "023" "0111"
#> TCGA.VS.A9U7.01 TCGA.ZJ.AAXD.01 TCGA.VS.A9UB.01 TCGA.EA.A410.01 TCGA.ZJ.AB0I.01 TCGA.VS.A9UD.01
#> "022" "0131" "0111" "0122" "0121" "023"
#> TCGA.VS.A9U6.01 TCGA.ZX.AA5X.01 TCGA.C5.A0TN.01 TCGA.C5.A7CJ.01 TCGA.C5.A1MJ.01 TCGA.EA.A78R.01
#> "0113" "021" "0113" "021" "03" "023"
#> TCGA.VS.A9UY.01 TCGA.VS.A9U5.01 TCGA.DS.A1OC.01 TCGA.ZJ.AAXB.01 TCGA.EX.A449.01 TCGA.C5.A1BL.01
#> "022" "021" "023" "0123" "03" "022"
#> TCGA.VS.A9UQ.01 TCGA.DS.A1OB.01 TCGA.HG.A9SC.01 TCGA.ZJ.AAXT.01 TCGA.IR.A3LB.01 TCGA.C5.A1ML.01
#> "03" "0123" "0123" "0134" "03" "0113"
#> TCGA.VS.A9UV.01 TCGA.LP.A4AU.01 TCGA.Q1.A6DT.01 TCGA.C5.A1M8.01 TCGA.C5.A1ME.01 TCGA.ZJ.AAXU.01
#> "021" "0111" "021" "021" "03" "0131"
#> TCGA.VS.A957.01 TCGA.VS.A9V5.01 TCGA.MU.A5YI.01 TCGA.ZJ.AAX4.01 TCGA.C5.A1MK.01 TCGA.JW.A69B.01
#> "022" "03" "021" "021" "0131" "03"
#> TCGA.VS.A958.01 TCGA.ZJ.AAXJ.01 TCGA.R2.A69V.01 TCGA.EA.A411.01 TCGA.VS.A9UP.01 TCGA.C5.A1MI.01
#> "0134" "023" "0111" "0123" "0111" "0113"
#> TCGA.DS.A1O9.01 TCGA.VS.A9UZ.01 TCGA.EA.A43B.01 TCGA.ZJ.AAX8.01 TCGA.ZJ.AAXI.01 TCGA.VS.A9UT.01
#> "021" "03" "023" "0111" "022" "0112"
#> TCGA.DS.A1OA.01 TCGA.C5.A1MQ.01 TCGA.VS.A9V0.01 TCGA.VS.A9UC.01 TCGA.ZJ.AAXA.01 TCGA.Q1.A73P.01
#> "022" "023" "0133" "021" "0121" "03"
#> TCGA.VS.A9V2.01 TCGA.VS.A9UU.01 TCGA.LP.A4AV.01 TCGA.VS.A9UR.01 TCGA.VS.A9V1.01 TCGA.C5.A7CG.01
#> "021" "023" "0131" "03" "03" "021"
#> TCGA.UC.A7PI.01 TCGA.EX.A1H5.01 TCGA.ZJ.AAXF.01 TCGA.VS.A9UL.01 TCGA.EA.A3Y4.01 TCGA.C5.A7CK.01
#> "03" "021" "0111" "03" "0132" "023"
#> TCGA.UC.A7PG.06 TCGA.VS.A9UJ.01 TCGA.Q1.A73O.01 TCGA.VS.A950.01 TCGA.EA.A439.01 TCGA.VS.A9UM.01
#> "0121" "0122" "0134" "022" "0113" "0121"
#> TCGA.C5.A1MP.01 TCGA.VS.A9UI.01 TCGA.ZJ.AB0H.01 TCGA.Q1.A73Q.01 TCGA.C5.A1MH.01 TCGA.VS.A9V4.01
#> "0131" "022" "0131" "022" "021" "0112"
#> TCGA.FU.A40J.01 TCGA.VS.A9UA.01 TCGA.LP.A4AW.01 TCGA.MA.AA43.01 TCGA.C5.A1BN.01 TCGA.VS.AA62.01
#> "03" "0131" "0131" "03" "0121" "0111"
#> TCGA.C5.A1BM.01 TCGA.C5.A1M6.01 TCGA.C5.A1BE.01 TCGA.FU.A23K.01 TCGA.C5.A1BJ.01 TCGA.FU.A23L.01
#> "0134" "0113" "0131" "03" "0111" "0134"
#> TCGA.C5.A1M5.01 TCGA.C5.A1MF.01 TCGA.C5.A1BF.01 TCGA.C5.A1BK.01 TCGA.C5.A1BI.01 TCGA.C5.A1M9.01
#> "022" "021" "0113" "021" "0134" "03"
get_classes(res_rh, merge_node = merge_node_param(min_n_signatures = 10323))
#> TCGA.EK.A3GK.01 TCGA.GH.A9DA.01 TCGA.VS.A94Y.01 TCGA.MY.A5BF.11 TCGA.VS.A94Z.01 TCGA.EA.A4BA.01
#> "0132" "023" "0132" "0112" "0131" "0133"
#> TCGA.ZJ.A8QQ.01 TCGA.FU.A3EO.11 TCGA.DG.A2KJ.01 TCGA.VS.A954.01 TCGA.MA.AA42.01 TCGA.C5.A8YQ.01
#> "023" "0112" "0111" "021" "021" "021"
#> TCGA.DS.A7WF.01 TCGA.EK.A2R7.01 TCGA.EK.A3GJ.01 TCGA.C5.A902.01 TCGA.MA.AA3W.01 TCGA.C5.A905.01
#> "03" "0131" "023" "023" "021" "0121"
#> TCGA.EK.A2RN.01 TCGA.FU.A57G.01 TCGA.C5.A8YR.01 TCGA.EK.A2R9.01 TCGA.FU.A3EO.01 TCGA.IR.A3LC.01
#> "0131" "0112" "0133" "021" "03" "021"
#> TCGA.VS.A8QA.01 TCGA.C5.A3HD.01 TCGA.MY.A5BE.01 TCGA.EA.A50E.01 TCGA.VS.A8QH.01 TCGA.ZJ.A8QR.01
#> "03" "023" "0111" "021" "0111" "0121"
#> TCGA.C5.A907.01 TCGA.IR.A3LK.01 TCGA.C5.A8ZZ.01 TCGA.VS.A8EK.01 TCGA.C5.A7UC.01 TCGA.C5.A8XJ.01
#> "0111" "022" "0123" "021" "0111" "0131"
#> TCGA.IR.A3LH.01 TCGA.EK.A3GM.01 TCGA.VS.A8Q8.01 TCGA.EK.A2RO.01 TCGA.MY.A5BD.01 TCGA.2W.A8YY.01
#> "023" "0113" "0131" "021" "03" "0122"
#> TCGA.C5.A2LZ.01 TCGA.C5.A901.01 TCGA.VS.A953.01 TCGA.MU.A51Y.01 TCGA.EK.A2RK.01 TCGA.UC.A7PD.01
#> "022" "021" "021" "0111" "0131" "0111"
#> TCGA.EA.A3HS.01 TCGA.VS.A8QM.01 TCGA.EA.A3HU.01 TCGA.VS.A94X.01 TCGA.C5.A7CO.01 TCGA.C5.A3HF.01
#> "021" "0111" "0111" "0111" "021" "0111"
#> TCGA.IR.A3LL.01 TCGA.MY.A913.01 TCGA.VS.A952.01 TCGA.IR.A3LI.01 TCGA.VS.A94W.01 TCGA.MY.A5BF.01
#> "023" "0111" "03" "03" "021" "023"
#> TCGA.EK.A2RC.01 TCGA.VS.A8EL.01 TCGA.EA.A97N.01 TCGA.EA.A3HQ.01 TCGA.EK.A2RD.01 TCGA.C5.A8YT.01
#> "022" "023" "0121" "022" "0131" "0112"
#> TCGA.FU.A3HZ.01 TCGA.VS.A8EJ.01 TCGA.C5.A3HL.01 TCGA.UC.A7PF.01 TCGA.C5.A8XK.01 TCGA.EX.A8YF.01
#> "0122" "0112" "0131" "023" "0132" "0111"
#> TCGA.HM.A4S6.01 TCGA.VS.A8Q9.01 TCGA.MA.AA41.01 TCGA.EK.A3GN.01 TCGA.MA.AA3Y.01 TCGA.MA.AA3Z.01
#> "0131" "023" "021" "021" "0111" "0131"
#> TCGA.EK.A2RE.01 TCGA.C5.A1BQ.01 TCGA.ZJ.A8QO.01 TCGA.JW.A852.01 TCGA.DS.A7WH.01 TCGA.JW.AAVH.01
#> "0131" "0131" "021" "021" "03" "022"
#> TCGA.EA.A556.01 TCGA.EA.A44S.01 TCGA.4J.AA1J.01 TCGA.IR.A3L7.01 TCGA.C5.A7X3.01 TCGA.HG.A2PA.01
#> "0133" "0121" "0121" "022" "0132" "0111"
#> TCGA.C5.A8XH.01 TCGA.C5.A7XC.01 TCGA.VS.A8EI.01 TCGA.VS.A8QC.01 TCGA.C5.A7UH.01 TCGA.WL.A834.01
#> "023" "0131" "023" "022" "0121" "022"
#> TCGA.C5.A8XI.01 TCGA.DS.A7WI.01 TCGA.VS.A8QF.01 TCGA.EA.A3HR.01 TCGA.DG.A2KL.01 TCGA.EK.A2RL.01
#> "023" "023" "022" "0131" "0131" "03"
#> TCGA.EK.A2PG.01 TCGA.BI.A0VR.01 TCGA.DS.A0VL.01 TCGA.VS.A8EC.01 TCGA.EA.A3QE.01 TCGA.DS.A0VM.01
#> "022" "0131" "0131" "022" "021" "021"
#> TCGA.FU.A3HY.01 TCGA.Q1.A5R1.01 TCGA.DR.A0ZM.01 TCGA.Q1.A6DW.01 TCGA.DS.A0VK.01 TCGA.DS.A3LQ.01
#> "022" "03" "0134" "021" "0131" "022"
#> TCGA.EA.A3QD.01 TCGA.JW.A5VJ.01 TCGA.LP.A5U3.01 TCGA.EA.A6QX.01 TCGA.EK.A2RA.01 TCGA.FU.A5XV.01
#> "023" "0134" "022" "022" "022" "0121"
#> TCGA.Q1.A5R2.01 TCGA.HM.A3JJ.01 TCGA.C5.A2LS.01 TCGA.C5.A7X8.01 TCGA.EK.A2RJ.01 TCGA.EA.A3HT.01
#> "022" "0131" "03" "03" "0133" "0131"
#> TCGA.LP.A7HU.01 TCGA.MU.A8JM.01 TCGA.EK.A2IP.01 TCGA.JW.A5VL.01 TCGA.FU.A3TX.01 TCGA.DG.A2KK.01
#> "03" "021" "022" "022" "0113" "03"
#> TCGA.EK.A2PI.01 TCGA.Q1.A73S.01 TCGA.EK.A2IR.01 TCGA.HM.A6W2.01 TCGA.VS.A8EH.01 TCGA.JW.A5VH.01
#> "0131" "0122" "021" "0122" "0113" "0122"
#> TCGA.C5.A2LV.01 TCGA.VS.A8EB.01 TCGA.RA.A741.01 TCGA.VS.A8EG.01 TCGA.DG.A2KH.01 TCGA.C5.A7UE.01
#> "021" "0113" "0111" "022" "0113" "021"
#> TCGA.C5.A2LT.01 TCGA.EA.A5ZD.01 TCGA.Q1.A73R.01 TCGA.JW.A5VK.01 TCGA.EK.A2RM.01 TCGA.C5.A7UI.01
#> "0111" "0134" "03" "022" "0113" "0131"
#> TCGA.EK.A2PL.01 TCGA.EK.A2PM.01 TCGA.EK.A2GZ.01 TCGA.HM.A3JK.01 TCGA.C5.A2M1.01 TCGA.HM.A6W2.06
#> "0131" "0123" "0111" "0111" "03" "0122"
#> TCGA.C5.A7X5.01 TCGA.IR.A3LA.01 TCGA.EK.A2PK.01 TCGA.EA.A5ZF.01 TCGA.XS.A8TJ.01 TCGA.BI.A0VS.01
#> "023" "0122" "0133" "0132" "021" "0132"
#> TCGA.DS.A0VN.01 TCGA.JX.A5QV.01 TCGA.EK.A2R8.01 TCGA.EA.A1QS.01 TCGA.C5.A3HE.01 TCGA.IR.A3LF.01
#> "021" "0131" "0132" "0111" "03" "03"
#> TCGA.DR.A0ZL.01 TCGA.FU.A3WB.01 TCGA.JX.A3PZ.01 TCGA.EA.A5O9.01 TCGA.HM.A3JJ.11 TCGA.DS.A5RQ.01
#> "021" "021" "0133" "021" "0112" "0131"
#> TCGA.EK.A2H0.01 TCGA.EX.A1H6.01 TCGA.EA.A5ZE.01 TCGA.C5.A2LY.01 TCGA.FU.A3TQ.01 TCGA.EK.A2RB.01
#> "023" "03" "021" "0113" "022" "022"
#> TCGA.JW.A5VI.01 TCGA.EK.A2H1.01 TCGA.JX.A3Q8.01 TCGA.FU.A3YQ.01 TCGA.EX.A69L.01 TCGA.C5.A7CH.01
#> "021" "0112" "03" "021" "0131" "021"
#> TCGA.FU.A2QG.01 TCGA.C5.A2M2.01 TCGA.JW.A5VG.01 TCGA.PN.A8MA.01 TCGA.DG.A2KM.01 TCGA.C5.A2LX.01
#> "0121" "03" "0113" "0122" "0112" "022"
#> TCGA.EX.A3L1.01 TCGA.LP.A5U2.01 TCGA.FU.A3NI.01 TCGA.Q1.A5R3.01 TCGA.FU.A770.01 TCGA.C5.A7CM.01
#> "0111" "021" "023" "0131" "03" "0113"
#> TCGA.JX.A3Q0.01 TCGA.EA.A5FO.01 TCGA.VS.A9V3.01 TCGA.C5.A7CL.01 TCGA.VS.A959.01 TCGA.LP.A4AX.01
#> "0121" "03" "021" "0131" "0111" "0111"
#> TCGA.C5.A1MN.01 TCGA.ZJ.AAXN.01 TCGA.MA.AA3X.01 TCGA.UC.A7PG.01 TCGA.Q1.A6DV.01 TCGA.DS.A1OD.01
#> "022" "0132" "0121" "0131" "03" "0131"
#> TCGA.C5.A1M7.01 TCGA.BI.A20A.01 TCGA.VS.A9UO.01 TCGA.EA.A1QT.01 TCGA.EX.A69M.01 TCGA.VS.A9UH.01
#> "0134" "021" "03" "022" "023" "0111"
#> TCGA.VS.A9U7.01 TCGA.ZJ.AAXD.01 TCGA.VS.A9UB.01 TCGA.EA.A410.01 TCGA.ZJ.AB0I.01 TCGA.VS.A9UD.01
#> "022" "0131" "0111" "0122" "0121" "023"
#> TCGA.VS.A9U6.01 TCGA.ZX.AA5X.01 TCGA.C5.A0TN.01 TCGA.C5.A7CJ.01 TCGA.C5.A1MJ.01 TCGA.EA.A78R.01
#> "0113" "021" "0113" "021" "03" "023"
#> TCGA.VS.A9UY.01 TCGA.VS.A9U5.01 TCGA.DS.A1OC.01 TCGA.ZJ.AAXB.01 TCGA.EX.A449.01 TCGA.C5.A1BL.01
#> "022" "021" "023" "0123" "03" "022"
#> TCGA.VS.A9UQ.01 TCGA.DS.A1OB.01 TCGA.HG.A9SC.01 TCGA.ZJ.AAXT.01 TCGA.IR.A3LB.01 TCGA.C5.A1ML.01
#> "03" "0123" "0123" "0134" "03" "0113"
#> TCGA.VS.A9UV.01 TCGA.LP.A4AU.01 TCGA.Q1.A6DT.01 TCGA.C5.A1M8.01 TCGA.C5.A1ME.01 TCGA.ZJ.AAXU.01
#> "021" "0111" "021" "021" "03" "0131"
#> TCGA.VS.A957.01 TCGA.VS.A9V5.01 TCGA.MU.A5YI.01 TCGA.ZJ.AAX4.01 TCGA.C5.A1MK.01 TCGA.JW.A69B.01
#> "022" "03" "021" "021" "0131" "03"
#> TCGA.VS.A958.01 TCGA.ZJ.AAXJ.01 TCGA.R2.A69V.01 TCGA.EA.A411.01 TCGA.VS.A9UP.01 TCGA.C5.A1MI.01
#> "0134" "023" "0111" "0123" "0111" "0113"
#> TCGA.DS.A1O9.01 TCGA.VS.A9UZ.01 TCGA.EA.A43B.01 TCGA.ZJ.AAX8.01 TCGA.ZJ.AAXI.01 TCGA.VS.A9UT.01
#> "021" "03" "023" "0111" "022" "0112"
#> TCGA.DS.A1OA.01 TCGA.C5.A1MQ.01 TCGA.VS.A9V0.01 TCGA.VS.A9UC.01 TCGA.ZJ.AAXA.01 TCGA.Q1.A73P.01
#> "022" "023" "0133" "021" "0121" "03"
#> TCGA.VS.A9V2.01 TCGA.VS.A9UU.01 TCGA.LP.A4AV.01 TCGA.VS.A9UR.01 TCGA.VS.A9V1.01 TCGA.C5.A7CG.01
#> "021" "023" "0131" "03" "03" "021"
#> TCGA.UC.A7PI.01 TCGA.EX.A1H5.01 TCGA.ZJ.AAXF.01 TCGA.VS.A9UL.01 TCGA.EA.A3Y4.01 TCGA.C5.A7CK.01
#> "03" "021" "0111" "03" "0132" "023"
#> TCGA.UC.A7PG.06 TCGA.VS.A9UJ.01 TCGA.Q1.A73O.01 TCGA.VS.A950.01 TCGA.EA.A439.01 TCGA.VS.A9UM.01
#> "0121" "0122" "0134" "022" "0113" "0121"
#> TCGA.C5.A1MP.01 TCGA.VS.A9UI.01 TCGA.ZJ.AB0H.01 TCGA.Q1.A73Q.01 TCGA.C5.A1MH.01 TCGA.VS.A9V4.01
#> "0131" "022" "0131" "022" "021" "0112"
#> TCGA.FU.A40J.01 TCGA.VS.A9UA.01 TCGA.LP.A4AW.01 TCGA.MA.AA43.01 TCGA.C5.A1BN.01 TCGA.VS.AA62.01
#> "03" "0131" "0131" "03" "0121" "0111"
#> TCGA.C5.A1BM.01 TCGA.C5.A1M6.01 TCGA.C5.A1BE.01 TCGA.FU.A23K.01 TCGA.C5.A1BJ.01 TCGA.FU.A23L.01
#> "0134" "0113" "0131" "03" "0111" "0134"
#> TCGA.C5.A1M5.01 TCGA.C5.A1MF.01 TCGA.C5.A1BF.01 TCGA.C5.A1BK.01 TCGA.C5.A1BI.01 TCGA.C5.A1M9.01
#> "022" "021" "0113" "021" "0134" "03"
get_classes(res_rh, merge_node = merge_node_param(min_n_signatures = 12995))
#> TCGA.EK.A3GK.01 TCGA.GH.A9DA.01 TCGA.VS.A94Y.01 TCGA.MY.A5BF.11 TCGA.VS.A94Z.01 TCGA.EA.A4BA.01
#> "0132" "023" "0132" "0112" "0131" "0133"
#> TCGA.ZJ.A8QQ.01 TCGA.FU.A3EO.11 TCGA.DG.A2KJ.01 TCGA.VS.A954.01 TCGA.MA.AA42.01 TCGA.C5.A8YQ.01
#> "023" "0112" "0111" "021" "021" "021"
#> TCGA.DS.A7WF.01 TCGA.EK.A2R7.01 TCGA.EK.A3GJ.01 TCGA.C5.A902.01 TCGA.MA.AA3W.01 TCGA.C5.A905.01
#> "03" "0131" "023" "023" "021" "0121"
#> TCGA.EK.A2RN.01 TCGA.FU.A57G.01 TCGA.C5.A8YR.01 TCGA.EK.A2R9.01 TCGA.FU.A3EO.01 TCGA.IR.A3LC.01
#> "0131" "0112" "0133" "021" "03" "021"
#> TCGA.VS.A8QA.01 TCGA.C5.A3HD.01 TCGA.MY.A5BE.01 TCGA.EA.A50E.01 TCGA.VS.A8QH.01 TCGA.ZJ.A8QR.01
#> "03" "023" "0111" "021" "0111" "0121"
#> TCGA.C5.A907.01 TCGA.IR.A3LK.01 TCGA.C5.A8ZZ.01 TCGA.VS.A8EK.01 TCGA.C5.A7UC.01 TCGA.C5.A8XJ.01
#> "0111" "022" "0123" "021" "0111" "0131"
#> TCGA.IR.A3LH.01 TCGA.EK.A3GM.01 TCGA.VS.A8Q8.01 TCGA.EK.A2RO.01 TCGA.MY.A5BD.01 TCGA.2W.A8YY.01
#> "023" "0113" "0131" "021" "03" "0122"
#> TCGA.C5.A2LZ.01 TCGA.C5.A901.01 TCGA.VS.A953.01 TCGA.MU.A51Y.01 TCGA.EK.A2RK.01 TCGA.UC.A7PD.01
#> "022" "021" "021" "0111" "0131" "0111"
#> TCGA.EA.A3HS.01 TCGA.VS.A8QM.01 TCGA.EA.A3HU.01 TCGA.VS.A94X.01 TCGA.C5.A7CO.01 TCGA.C5.A3HF.01
#> "021" "0111" "0111" "0111" "021" "0111"
#> TCGA.IR.A3LL.01 TCGA.MY.A913.01 TCGA.VS.A952.01 TCGA.IR.A3LI.01 TCGA.VS.A94W.01 TCGA.MY.A5BF.01
#> "023" "0111" "03" "03" "021" "023"
#> TCGA.EK.A2RC.01 TCGA.VS.A8EL.01 TCGA.EA.A97N.01 TCGA.EA.A3HQ.01 TCGA.EK.A2RD.01 TCGA.C5.A8YT.01
#> "022" "023" "0121" "022" "0131" "0112"
#> TCGA.FU.A3HZ.01 TCGA.VS.A8EJ.01 TCGA.C5.A3HL.01 TCGA.UC.A7PF.01 TCGA.C5.A8XK.01 TCGA.EX.A8YF.01
#> "0122" "0112" "0131" "023" "0132" "0111"
#> TCGA.HM.A4S6.01 TCGA.VS.A8Q9.01 TCGA.MA.AA41.01 TCGA.EK.A3GN.01 TCGA.MA.AA3Y.01 TCGA.MA.AA3Z.01
#> "0131" "023" "021" "021" "0111" "0131"
#> TCGA.EK.A2RE.01 TCGA.C5.A1BQ.01 TCGA.ZJ.A8QO.01 TCGA.JW.A852.01 TCGA.DS.A7WH.01 TCGA.JW.AAVH.01
#> "0131" "0131" "021" "021" "03" "022"
#> TCGA.EA.A556.01 TCGA.EA.A44S.01 TCGA.4J.AA1J.01 TCGA.IR.A3L7.01 TCGA.C5.A7X3.01 TCGA.HG.A2PA.01
#> "0133" "0121" "0121" "022" "0132" "0111"
#> TCGA.C5.A8XH.01 TCGA.C5.A7XC.01 TCGA.VS.A8EI.01 TCGA.VS.A8QC.01 TCGA.C5.A7UH.01 TCGA.WL.A834.01
#> "023" "0131" "023" "022" "0121" "022"
#> TCGA.C5.A8XI.01 TCGA.DS.A7WI.01 TCGA.VS.A8QF.01 TCGA.EA.A3HR.01 TCGA.DG.A2KL.01 TCGA.EK.A2RL.01
#> "023" "023" "022" "0131" "0131" "03"
#> TCGA.EK.A2PG.01 TCGA.BI.A0VR.01 TCGA.DS.A0VL.01 TCGA.VS.A8EC.01 TCGA.EA.A3QE.01 TCGA.DS.A0VM.01
#> "022" "0131" "0131" "022" "021" "021"
#> TCGA.FU.A3HY.01 TCGA.Q1.A5R1.01 TCGA.DR.A0ZM.01 TCGA.Q1.A6DW.01 TCGA.DS.A0VK.01 TCGA.DS.A3LQ.01
#> "022" "03" "0134" "021" "0131" "022"
#> TCGA.EA.A3QD.01 TCGA.JW.A5VJ.01 TCGA.LP.A5U3.01 TCGA.EA.A6QX.01 TCGA.EK.A2RA.01 TCGA.FU.A5XV.01
#> "023" "0134" "022" "022" "022" "0121"
#> TCGA.Q1.A5R2.01 TCGA.HM.A3JJ.01 TCGA.C5.A2LS.01 TCGA.C5.A7X8.01 TCGA.EK.A2RJ.01 TCGA.EA.A3HT.01
#> "022" "0131" "03" "03" "0133" "0131"
#> TCGA.LP.A7HU.01 TCGA.MU.A8JM.01 TCGA.EK.A2IP.01 TCGA.JW.A5VL.01 TCGA.FU.A3TX.01 TCGA.DG.A2KK.01
#> "03" "021" "022" "022" "0113" "03"
#> TCGA.EK.A2PI.01 TCGA.Q1.A73S.01 TCGA.EK.A2IR.01 TCGA.HM.A6W2.01 TCGA.VS.A8EH.01 TCGA.JW.A5VH.01
#> "0131" "0122" "021" "0122" "0113" "0122"
#> TCGA.C5.A2LV.01 TCGA.VS.A8EB.01 TCGA.RA.A741.01 TCGA.VS.A8EG.01 TCGA.DG.A2KH.01 TCGA.C5.A7UE.01
#> "021" "0113" "0111" "022" "0113" "021"
#> TCGA.C5.A2LT.01 TCGA.EA.A5ZD.01 TCGA.Q1.A73R.01 TCGA.JW.A5VK.01 TCGA.EK.A2RM.01 TCGA.C5.A7UI.01
#> "0111" "0134" "03" "022" "0113" "0131"
#> TCGA.EK.A2PL.01 TCGA.EK.A2PM.01 TCGA.EK.A2GZ.01 TCGA.HM.A3JK.01 TCGA.C5.A2M1.01 TCGA.HM.A6W2.06
#> "0131" "0123" "0111" "0111" "03" "0122"
#> TCGA.C5.A7X5.01 TCGA.IR.A3LA.01 TCGA.EK.A2PK.01 TCGA.EA.A5ZF.01 TCGA.XS.A8TJ.01 TCGA.BI.A0VS.01
#> "023" "0122" "0133" "0132" "021" "0132"
#> TCGA.DS.A0VN.01 TCGA.JX.A5QV.01 TCGA.EK.A2R8.01 TCGA.EA.A1QS.01 TCGA.C5.A3HE.01 TCGA.IR.A3LF.01
#> "021" "0131" "0132" "0111" "03" "03"
#> TCGA.DR.A0ZL.01 TCGA.FU.A3WB.01 TCGA.JX.A3PZ.01 TCGA.EA.A5O9.01 TCGA.HM.A3JJ.11 TCGA.DS.A5RQ.01
#> "021" "021" "0133" "021" "0112" "0131"
#> TCGA.EK.A2H0.01 TCGA.EX.A1H6.01 TCGA.EA.A5ZE.01 TCGA.C5.A2LY.01 TCGA.FU.A3TQ.01 TCGA.EK.A2RB.01
#> "023" "03" "021" "0113" "022" "022"
#> TCGA.JW.A5VI.01 TCGA.EK.A2H1.01 TCGA.JX.A3Q8.01 TCGA.FU.A3YQ.01 TCGA.EX.A69L.01 TCGA.C5.A7CH.01
#> "021" "0112" "03" "021" "0131" "021"
#> TCGA.FU.A2QG.01 TCGA.C5.A2M2.01 TCGA.JW.A5VG.01 TCGA.PN.A8MA.01 TCGA.DG.A2KM.01 TCGA.C5.A2LX.01
#> "0121" "03" "0113" "0122" "0112" "022"
#> TCGA.EX.A3L1.01 TCGA.LP.A5U2.01 TCGA.FU.A3NI.01 TCGA.Q1.A5R3.01 TCGA.FU.A770.01 TCGA.C5.A7CM.01
#> "0111" "021" "023" "0131" "03" "0113"
#> TCGA.JX.A3Q0.01 TCGA.EA.A5FO.01 TCGA.VS.A9V3.01 TCGA.C5.A7CL.01 TCGA.VS.A959.01 TCGA.LP.A4AX.01
#> "0121" "03" "021" "0131" "0111" "0111"
#> TCGA.C5.A1MN.01 TCGA.ZJ.AAXN.01 TCGA.MA.AA3X.01 TCGA.UC.A7PG.01 TCGA.Q1.A6DV.01 TCGA.DS.A1OD.01
#> "022" "0132" "0121" "0131" "03" "0131"
#> TCGA.C5.A1M7.01 TCGA.BI.A20A.01 TCGA.VS.A9UO.01 TCGA.EA.A1QT.01 TCGA.EX.A69M.01 TCGA.VS.A9UH.01
#> "0134" "021" "03" "022" "023" "0111"
#> TCGA.VS.A9U7.01 TCGA.ZJ.AAXD.01 TCGA.VS.A9UB.01 TCGA.EA.A410.01 TCGA.ZJ.AB0I.01 TCGA.VS.A9UD.01
#> "022" "0131" "0111" "0122" "0121" "023"
#> TCGA.VS.A9U6.01 TCGA.ZX.AA5X.01 TCGA.C5.A0TN.01 TCGA.C5.A7CJ.01 TCGA.C5.A1MJ.01 TCGA.EA.A78R.01
#> "0113" "021" "0113" "021" "03" "023"
#> TCGA.VS.A9UY.01 TCGA.VS.A9U5.01 TCGA.DS.A1OC.01 TCGA.ZJ.AAXB.01 TCGA.EX.A449.01 TCGA.C5.A1BL.01
#> "022" "021" "023" "0123" "03" "022"
#> TCGA.VS.A9UQ.01 TCGA.DS.A1OB.01 TCGA.HG.A9SC.01 TCGA.ZJ.AAXT.01 TCGA.IR.A3LB.01 TCGA.C5.A1ML.01
#> "03" "0123" "0123" "0134" "03" "0113"
#> TCGA.VS.A9UV.01 TCGA.LP.A4AU.01 TCGA.Q1.A6DT.01 TCGA.C5.A1M8.01 TCGA.C5.A1ME.01 TCGA.ZJ.AAXU.01
#> "021" "0111" "021" "021" "03" "0131"
#> TCGA.VS.A957.01 TCGA.VS.A9V5.01 TCGA.MU.A5YI.01 TCGA.ZJ.AAX4.01 TCGA.C5.A1MK.01 TCGA.JW.A69B.01
#> "022" "03" "021" "021" "0131" "03"
#> TCGA.VS.A958.01 TCGA.ZJ.AAXJ.01 TCGA.R2.A69V.01 TCGA.EA.A411.01 TCGA.VS.A9UP.01 TCGA.C5.A1MI.01
#> "0134" "023" "0111" "0123" "0111" "0113"
#> TCGA.DS.A1O9.01 TCGA.VS.A9UZ.01 TCGA.EA.A43B.01 TCGA.ZJ.AAX8.01 TCGA.ZJ.AAXI.01 TCGA.VS.A9UT.01
#> "021" "03" "023" "0111" "022" "0112"
#> TCGA.DS.A1OA.01 TCGA.C5.A1MQ.01 TCGA.VS.A9V0.01 TCGA.VS.A9UC.01 TCGA.ZJ.AAXA.01 TCGA.Q1.A73P.01
#> "022" "023" "0133" "021" "0121" "03"
#> TCGA.VS.A9V2.01 TCGA.VS.A9UU.01 TCGA.LP.A4AV.01 TCGA.VS.A9UR.01 TCGA.VS.A9V1.01 TCGA.C5.A7CG.01
#> "021" "023" "0131" "03" "03" "021"
#> TCGA.UC.A7PI.01 TCGA.EX.A1H5.01 TCGA.ZJ.AAXF.01 TCGA.VS.A9UL.01 TCGA.EA.A3Y4.01 TCGA.C5.A7CK.01
#> "03" "021" "0111" "03" "0132" "023"
#> TCGA.UC.A7PG.06 TCGA.VS.A9UJ.01 TCGA.Q1.A73O.01 TCGA.VS.A950.01 TCGA.EA.A439.01 TCGA.VS.A9UM.01
#> "0121" "0122" "0134" "022" "0113" "0121"
#> TCGA.C5.A1MP.01 TCGA.VS.A9UI.01 TCGA.ZJ.AB0H.01 TCGA.Q1.A73Q.01 TCGA.C5.A1MH.01 TCGA.VS.A9V4.01
#> "0131" "022" "0131" "022" "021" "0112"
#> TCGA.FU.A40J.01 TCGA.VS.A9UA.01 TCGA.LP.A4AW.01 TCGA.MA.AA43.01 TCGA.C5.A1BN.01 TCGA.VS.AA62.01
#> "03" "0131" "0131" "03" "0121" "0111"
#> TCGA.C5.A1BM.01 TCGA.C5.A1M6.01 TCGA.C5.A1BE.01 TCGA.FU.A23K.01 TCGA.C5.A1BJ.01 TCGA.FU.A23L.01
#> "0134" "0113" "0131" "03" "0111" "0134"
#> TCGA.C5.A1M5.01 TCGA.C5.A1MF.01 TCGA.C5.A1BF.01 TCGA.C5.A1BK.01 TCGA.C5.A1BI.01 TCGA.C5.A1M9.01
#> "022" "021" "0113" "021" "0134" "03"
get_classes(res_rh, merge_node = merge_node_param(min_n_signatures = 15278))
#> TCGA.EK.A3GK.01 TCGA.GH.A9DA.01 TCGA.VS.A94Y.01 TCGA.MY.A5BF.11 TCGA.VS.A94Z.01 TCGA.EA.A4BA.01
#> "0132" "02" "0132" "0112" "0131" "0133"
#> TCGA.ZJ.A8QQ.01 TCGA.FU.A3EO.11 TCGA.DG.A2KJ.01 TCGA.VS.A954.01 TCGA.MA.AA42.01 TCGA.C5.A8YQ.01
#> "02" "0112" "0111" "02" "02" "02"
#> TCGA.DS.A7WF.01 TCGA.EK.A2R7.01 TCGA.EK.A3GJ.01 TCGA.C5.A902.01 TCGA.MA.AA3W.01 TCGA.C5.A905.01
#> "03" "0131" "02" "02" "02" "0121"
#> TCGA.EK.A2RN.01 TCGA.FU.A57G.01 TCGA.C5.A8YR.01 TCGA.EK.A2R9.01 TCGA.FU.A3EO.01 TCGA.IR.A3LC.01
#> "0131" "0112" "0133" "02" "03" "02"
#> TCGA.VS.A8QA.01 TCGA.C5.A3HD.01 TCGA.MY.A5BE.01 TCGA.EA.A50E.01 TCGA.VS.A8QH.01 TCGA.ZJ.A8QR.01
#> "03" "02" "0111" "02" "0111" "0121"
#> TCGA.C5.A907.01 TCGA.IR.A3LK.01 TCGA.C5.A8ZZ.01 TCGA.VS.A8EK.01 TCGA.C5.A7UC.01 TCGA.C5.A8XJ.01
#> "0111" "02" "0123" "02" "0111" "0131"
#> TCGA.IR.A3LH.01 TCGA.EK.A3GM.01 TCGA.VS.A8Q8.01 TCGA.EK.A2RO.01 TCGA.MY.A5BD.01 TCGA.2W.A8YY.01
#> "02" "0113" "0131" "02" "03" "0122"
#> TCGA.C5.A2LZ.01 TCGA.C5.A901.01 TCGA.VS.A953.01 TCGA.MU.A51Y.01 TCGA.EK.A2RK.01 TCGA.UC.A7PD.01
#> "02" "02" "02" "0111" "0131" "0111"
#> TCGA.EA.A3HS.01 TCGA.VS.A8QM.01 TCGA.EA.A3HU.01 TCGA.VS.A94X.01 TCGA.C5.A7CO.01 TCGA.C5.A3HF.01
#> "02" "0111" "0111" "0111" "02" "0111"
#> TCGA.IR.A3LL.01 TCGA.MY.A913.01 TCGA.VS.A952.01 TCGA.IR.A3LI.01 TCGA.VS.A94W.01 TCGA.MY.A5BF.01
#> "02" "0111" "03" "03" "02" "02"
#> TCGA.EK.A2RC.01 TCGA.VS.A8EL.01 TCGA.EA.A97N.01 TCGA.EA.A3HQ.01 TCGA.EK.A2RD.01 TCGA.C5.A8YT.01
#> "02" "02" "0121" "02" "0131" "0112"
#> TCGA.FU.A3HZ.01 TCGA.VS.A8EJ.01 TCGA.C5.A3HL.01 TCGA.UC.A7PF.01 TCGA.C5.A8XK.01 TCGA.EX.A8YF.01
#> "0122" "0112" "0131" "02" "0132" "0111"
#> TCGA.HM.A4S6.01 TCGA.VS.A8Q9.01 TCGA.MA.AA41.01 TCGA.EK.A3GN.01 TCGA.MA.AA3Y.01 TCGA.MA.AA3Z.01
#> "0131" "02" "02" "02" "0111" "0131"
#> TCGA.EK.A2RE.01 TCGA.C5.A1BQ.01 TCGA.ZJ.A8QO.01 TCGA.JW.A852.01 TCGA.DS.A7WH.01 TCGA.JW.AAVH.01
#> "0131" "0131" "02" "02" "03" "02"
#> TCGA.EA.A556.01 TCGA.EA.A44S.01 TCGA.4J.AA1J.01 TCGA.IR.A3L7.01 TCGA.C5.A7X3.01 TCGA.HG.A2PA.01
#> "0133" "0121" "0121" "02" "0132" "0111"
#> TCGA.C5.A8XH.01 TCGA.C5.A7XC.01 TCGA.VS.A8EI.01 TCGA.VS.A8QC.01 TCGA.C5.A7UH.01 TCGA.WL.A834.01
#> "02" "0131" "02" "02" "0121" "02"
#> TCGA.C5.A8XI.01 TCGA.DS.A7WI.01 TCGA.VS.A8QF.01 TCGA.EA.A3HR.01 TCGA.DG.A2KL.01 TCGA.EK.A2RL.01
#> "02" "02" "02" "0131" "0131" "03"
#> TCGA.EK.A2PG.01 TCGA.BI.A0VR.01 TCGA.DS.A0VL.01 TCGA.VS.A8EC.01 TCGA.EA.A3QE.01 TCGA.DS.A0VM.01
#> "02" "0131" "0131" "02" "02" "02"
#> TCGA.FU.A3HY.01 TCGA.Q1.A5R1.01 TCGA.DR.A0ZM.01 TCGA.Q1.A6DW.01 TCGA.DS.A0VK.01 TCGA.DS.A3LQ.01
#> "02" "03" "0134" "02" "0131" "02"
#> TCGA.EA.A3QD.01 TCGA.JW.A5VJ.01 TCGA.LP.A5U3.01 TCGA.EA.A6QX.01 TCGA.EK.A2RA.01 TCGA.FU.A5XV.01
#> "02" "0134" "02" "02" "02" "0121"
#> TCGA.Q1.A5R2.01 TCGA.HM.A3JJ.01 TCGA.C5.A2LS.01 TCGA.C5.A7X8.01 TCGA.EK.A2RJ.01 TCGA.EA.A3HT.01
#> "02" "0131" "03" "03" "0133" "0131"
#> TCGA.LP.A7HU.01 TCGA.MU.A8JM.01 TCGA.EK.A2IP.01 TCGA.JW.A5VL.01 TCGA.FU.A3TX.01 TCGA.DG.A2KK.01
#> "03" "02" "02" "02" "0113" "03"
#> TCGA.EK.A2PI.01 TCGA.Q1.A73S.01 TCGA.EK.A2IR.01 TCGA.HM.A6W2.01 TCGA.VS.A8EH.01 TCGA.JW.A5VH.01
#> "0131" "0122" "02" "0122" "0113" "0122"
#> TCGA.C5.A2LV.01 TCGA.VS.A8EB.01 TCGA.RA.A741.01 TCGA.VS.A8EG.01 TCGA.DG.A2KH.01 TCGA.C5.A7UE.01
#> "02" "0113" "0111" "02" "0113" "02"
#> TCGA.C5.A2LT.01 TCGA.EA.A5ZD.01 TCGA.Q1.A73R.01 TCGA.JW.A5VK.01 TCGA.EK.A2RM.01 TCGA.C5.A7UI.01
#> "0111" "0134" "03" "02" "0113" "0131"
#> TCGA.EK.A2PL.01 TCGA.EK.A2PM.01 TCGA.EK.A2GZ.01 TCGA.HM.A3JK.01 TCGA.C5.A2M1.01 TCGA.HM.A6W2.06
#> "0131" "0123" "0111" "0111" "03" "0122"
#> TCGA.C5.A7X5.01 TCGA.IR.A3LA.01 TCGA.EK.A2PK.01 TCGA.EA.A5ZF.01 TCGA.XS.A8TJ.01 TCGA.BI.A0VS.01
#> "02" "0122" "0133" "0132" "02" "0132"
#> TCGA.DS.A0VN.01 TCGA.JX.A5QV.01 TCGA.EK.A2R8.01 TCGA.EA.A1QS.01 TCGA.C5.A3HE.01 TCGA.IR.A3LF.01
#> "02" "0131" "0132" "0111" "03" "03"
#> TCGA.DR.A0ZL.01 TCGA.FU.A3WB.01 TCGA.JX.A3PZ.01 TCGA.EA.A5O9.01 TCGA.HM.A3JJ.11 TCGA.DS.A5RQ.01
#> "02" "02" "0133" "02" "0112" "0131"
#> TCGA.EK.A2H0.01 TCGA.EX.A1H6.01 TCGA.EA.A5ZE.01 TCGA.C5.A2LY.01 TCGA.FU.A3TQ.01 TCGA.EK.A2RB.01
#> "02" "03" "02" "0113" "02" "02"
#> TCGA.JW.A5VI.01 TCGA.EK.A2H1.01 TCGA.JX.A3Q8.01 TCGA.FU.A3YQ.01 TCGA.EX.A69L.01 TCGA.C5.A7CH.01
#> "02" "0112" "03" "02" "0131" "02"
#> TCGA.FU.A2QG.01 TCGA.C5.A2M2.01 TCGA.JW.A5VG.01 TCGA.PN.A8MA.01 TCGA.DG.A2KM.01 TCGA.C5.A2LX.01
#> "0121" "03" "0113" "0122" "0112" "02"
#> TCGA.EX.A3L1.01 TCGA.LP.A5U2.01 TCGA.FU.A3NI.01 TCGA.Q1.A5R3.01 TCGA.FU.A770.01 TCGA.C5.A7CM.01
#> "0111" "02" "02" "0131" "03" "0113"
#> TCGA.JX.A3Q0.01 TCGA.EA.A5FO.01 TCGA.VS.A9V3.01 TCGA.C5.A7CL.01 TCGA.VS.A959.01 TCGA.LP.A4AX.01
#> "0121" "03" "02" "0131" "0111" "0111"
#> TCGA.C5.A1MN.01 TCGA.ZJ.AAXN.01 TCGA.MA.AA3X.01 TCGA.UC.A7PG.01 TCGA.Q1.A6DV.01 TCGA.DS.A1OD.01
#> "02" "0132" "0121" "0131" "03" "0131"
#> TCGA.C5.A1M7.01 TCGA.BI.A20A.01 TCGA.VS.A9UO.01 TCGA.EA.A1QT.01 TCGA.EX.A69M.01 TCGA.VS.A9UH.01
#> "0134" "02" "03" "02" "02" "0111"
#> TCGA.VS.A9U7.01 TCGA.ZJ.AAXD.01 TCGA.VS.A9UB.01 TCGA.EA.A410.01 TCGA.ZJ.AB0I.01 TCGA.VS.A9UD.01
#> "02" "0131" "0111" "0122" "0121" "02"
#> TCGA.VS.A9U6.01 TCGA.ZX.AA5X.01 TCGA.C5.A0TN.01 TCGA.C5.A7CJ.01 TCGA.C5.A1MJ.01 TCGA.EA.A78R.01
#> "0113" "02" "0113" "02" "03" "02"
#> TCGA.VS.A9UY.01 TCGA.VS.A9U5.01 TCGA.DS.A1OC.01 TCGA.ZJ.AAXB.01 TCGA.EX.A449.01 TCGA.C5.A1BL.01
#> "02" "02" "02" "0123" "03" "02"
#> TCGA.VS.A9UQ.01 TCGA.DS.A1OB.01 TCGA.HG.A9SC.01 TCGA.ZJ.AAXT.01 TCGA.IR.A3LB.01 TCGA.C5.A1ML.01
#> "03" "0123" "0123" "0134" "03" "0113"
#> TCGA.VS.A9UV.01 TCGA.LP.A4AU.01 TCGA.Q1.A6DT.01 TCGA.C5.A1M8.01 TCGA.C5.A1ME.01 TCGA.ZJ.AAXU.01
#> "02" "0111" "02" "02" "03" "0131"
#> TCGA.VS.A957.01 TCGA.VS.A9V5.01 TCGA.MU.A5YI.01 TCGA.ZJ.AAX4.01 TCGA.C5.A1MK.01 TCGA.JW.A69B.01
#> "02" "03" "02" "02" "0131" "03"
#> TCGA.VS.A958.01 TCGA.ZJ.AAXJ.01 TCGA.R2.A69V.01 TCGA.EA.A411.01 TCGA.VS.A9UP.01 TCGA.C5.A1MI.01
#> "0134" "02" "0111" "0123" "0111" "0113"
#> TCGA.DS.A1O9.01 TCGA.VS.A9UZ.01 TCGA.EA.A43B.01 TCGA.ZJ.AAX8.01 TCGA.ZJ.AAXI.01 TCGA.VS.A9UT.01
#> "02" "03" "02" "0111" "02" "0112"
#> TCGA.DS.A1OA.01 TCGA.C5.A1MQ.01 TCGA.VS.A9V0.01 TCGA.VS.A9UC.01 TCGA.ZJ.AAXA.01 TCGA.Q1.A73P.01
#> "02" "02" "0133" "02" "0121" "03"
#> TCGA.VS.A9V2.01 TCGA.VS.A9UU.01 TCGA.LP.A4AV.01 TCGA.VS.A9UR.01 TCGA.VS.A9V1.01 TCGA.C5.A7CG.01
#> "02" "02" "0131" "03" "03" "02"
#> TCGA.UC.A7PI.01 TCGA.EX.A1H5.01 TCGA.ZJ.AAXF.01 TCGA.VS.A9UL.01 TCGA.EA.A3Y4.01 TCGA.C5.A7CK.01
#> "03" "02" "0111" "03" "0132" "02"
#> TCGA.UC.A7PG.06 TCGA.VS.A9UJ.01 TCGA.Q1.A73O.01 TCGA.VS.A950.01 TCGA.EA.A439.01 TCGA.VS.A9UM.01
#> "0121" "0122" "0134" "02" "0113" "0121"
#> TCGA.C5.A1MP.01 TCGA.VS.A9UI.01 TCGA.ZJ.AB0H.01 TCGA.Q1.A73Q.01 TCGA.C5.A1MH.01 TCGA.VS.A9V4.01
#> "0131" "02" "0131" "02" "02" "0112"
#> TCGA.FU.A40J.01 TCGA.VS.A9UA.01 TCGA.LP.A4AW.01 TCGA.MA.AA43.01 TCGA.C5.A1BN.01 TCGA.VS.AA62.01
#> "03" "0131" "0131" "03" "0121" "0111"
#> TCGA.C5.A1BM.01 TCGA.C5.A1M6.01 TCGA.C5.A1BE.01 TCGA.FU.A23K.01 TCGA.C5.A1BJ.01 TCGA.FU.A23L.01
#> "0134" "0113" "0131" "03" "0111" "0134"
#> TCGA.C5.A1M5.01 TCGA.C5.A1MF.01 TCGA.C5.A1BF.01 TCGA.C5.A1BK.01 TCGA.C5.A1BI.01 TCGA.C5.A1M9.01
#> "02" "02" "0113" "02" "0134" "03"
get_classes(res_rh, merge_node = merge_node_param(min_n_signatures = 17125))
#> TCGA.EK.A3GK.01 TCGA.GH.A9DA.01 TCGA.VS.A94Y.01 TCGA.MY.A5BF.11 TCGA.VS.A94Z.01 TCGA.EA.A4BA.01
#> "0132" "02" "0132" "0112" "0131" "0133"
#> TCGA.ZJ.A8QQ.01 TCGA.FU.A3EO.11 TCGA.DG.A2KJ.01 TCGA.VS.A954.01 TCGA.MA.AA42.01 TCGA.C5.A8YQ.01
#> "02" "0112" "0111" "02" "02" "02"
#> TCGA.DS.A7WF.01 TCGA.EK.A2R7.01 TCGA.EK.A3GJ.01 TCGA.C5.A902.01 TCGA.MA.AA3W.01 TCGA.C5.A905.01
#> "03" "0131" "02" "02" "02" "012"
#> TCGA.EK.A2RN.01 TCGA.FU.A57G.01 TCGA.C5.A8YR.01 TCGA.EK.A2R9.01 TCGA.FU.A3EO.01 TCGA.IR.A3LC.01
#> "0131" "0112" "0133" "02" "03" "02"
#> TCGA.VS.A8QA.01 TCGA.C5.A3HD.01 TCGA.MY.A5BE.01 TCGA.EA.A50E.01 TCGA.VS.A8QH.01 TCGA.ZJ.A8QR.01
#> "03" "02" "0111" "02" "0111" "012"
#> TCGA.C5.A907.01 TCGA.IR.A3LK.01 TCGA.C5.A8ZZ.01 TCGA.VS.A8EK.01 TCGA.C5.A7UC.01 TCGA.C5.A8XJ.01
#> "0111" "02" "012" "02" "0111" "0131"
#> TCGA.IR.A3LH.01 TCGA.EK.A3GM.01 TCGA.VS.A8Q8.01 TCGA.EK.A2RO.01 TCGA.MY.A5BD.01 TCGA.2W.A8YY.01
#> "02" "0113" "0131" "02" "03" "012"
#> TCGA.C5.A2LZ.01 TCGA.C5.A901.01 TCGA.VS.A953.01 TCGA.MU.A51Y.01 TCGA.EK.A2RK.01 TCGA.UC.A7PD.01
#> "02" "02" "02" "0111" "0131" "0111"
#> TCGA.EA.A3HS.01 TCGA.VS.A8QM.01 TCGA.EA.A3HU.01 TCGA.VS.A94X.01 TCGA.C5.A7CO.01 TCGA.C5.A3HF.01
#> "02" "0111" "0111" "0111" "02" "0111"
#> TCGA.IR.A3LL.01 TCGA.MY.A913.01 TCGA.VS.A952.01 TCGA.IR.A3LI.01 TCGA.VS.A94W.01 TCGA.MY.A5BF.01
#> "02" "0111" "03" "03" "02" "02"
#> TCGA.EK.A2RC.01 TCGA.VS.A8EL.01 TCGA.EA.A97N.01 TCGA.EA.A3HQ.01 TCGA.EK.A2RD.01 TCGA.C5.A8YT.01
#> "02" "02" "012" "02" "0131" "0112"
#> TCGA.FU.A3HZ.01 TCGA.VS.A8EJ.01 TCGA.C5.A3HL.01 TCGA.UC.A7PF.01 TCGA.C5.A8XK.01 TCGA.EX.A8YF.01
#> "012" "0112" "0131" "02" "0132" "0111"
#> TCGA.HM.A4S6.01 TCGA.VS.A8Q9.01 TCGA.MA.AA41.01 TCGA.EK.A3GN.01 TCGA.MA.AA3Y.01 TCGA.MA.AA3Z.01
#> "0131" "02" "02" "02" "0111" "0131"
#> TCGA.EK.A2RE.01 TCGA.C5.A1BQ.01 TCGA.ZJ.A8QO.01 TCGA.JW.A852.01 TCGA.DS.A7WH.01 TCGA.JW.AAVH.01
#> "0131" "0131" "02" "02" "03" "02"
#> TCGA.EA.A556.01 TCGA.EA.A44S.01 TCGA.4J.AA1J.01 TCGA.IR.A3L7.01 TCGA.C5.A7X3.01 TCGA.HG.A2PA.01
#> "0133" "012" "012" "02" "0132" "0111"
#> TCGA.C5.A8XH.01 TCGA.C5.A7XC.01 TCGA.VS.A8EI.01 TCGA.VS.A8QC.01 TCGA.C5.A7UH.01 TCGA.WL.A834.01
#> "02" "0131" "02" "02" "012" "02"
#> TCGA.C5.A8XI.01 TCGA.DS.A7WI.01 TCGA.VS.A8QF.01 TCGA.EA.A3HR.01 TCGA.DG.A2KL.01 TCGA.EK.A2RL.01
#> "02" "02" "02" "0131" "0131" "03"
#> TCGA.EK.A2PG.01 TCGA.BI.A0VR.01 TCGA.DS.A0VL.01 TCGA.VS.A8EC.01 TCGA.EA.A3QE.01 TCGA.DS.A0VM.01
#> "02" "0131" "0131" "02" "02" "02"
#> TCGA.FU.A3HY.01 TCGA.Q1.A5R1.01 TCGA.DR.A0ZM.01 TCGA.Q1.A6DW.01 TCGA.DS.A0VK.01 TCGA.DS.A3LQ.01
#> "02" "03" "0134" "02" "0131" "02"
#> TCGA.EA.A3QD.01 TCGA.JW.A5VJ.01 TCGA.LP.A5U3.01 TCGA.EA.A6QX.01 TCGA.EK.A2RA.01 TCGA.FU.A5XV.01
#> "02" "0134" "02" "02" "02" "012"
#> TCGA.Q1.A5R2.01 TCGA.HM.A3JJ.01 TCGA.C5.A2LS.01 TCGA.C5.A7X8.01 TCGA.EK.A2RJ.01 TCGA.EA.A3HT.01
#> "02" "0131" "03" "03" "0133" "0131"
#> TCGA.LP.A7HU.01 TCGA.MU.A8JM.01 TCGA.EK.A2IP.01 TCGA.JW.A5VL.01 TCGA.FU.A3TX.01 TCGA.DG.A2KK.01
#> "03" "02" "02" "02" "0113" "03"
#> TCGA.EK.A2PI.01 TCGA.Q1.A73S.01 TCGA.EK.A2IR.01 TCGA.HM.A6W2.01 TCGA.VS.A8EH.01 TCGA.JW.A5VH.01
#> "0131" "012" "02" "012" "0113" "012"
#> TCGA.C5.A2LV.01 TCGA.VS.A8EB.01 TCGA.RA.A741.01 TCGA.VS.A8EG.01 TCGA.DG.A2KH.01 TCGA.C5.A7UE.01
#> "02" "0113" "0111" "02" "0113" "02"
#> TCGA.C5.A2LT.01 TCGA.EA.A5ZD.01 TCGA.Q1.A73R.01 TCGA.JW.A5VK.01 TCGA.EK.A2RM.01 TCGA.C5.A7UI.01
#> "0111" "0134" "03" "02" "0113" "0131"
#> TCGA.EK.A2PL.01 TCGA.EK.A2PM.01 TCGA.EK.A2GZ.01 TCGA.HM.A3JK.01 TCGA.C5.A2M1.01 TCGA.HM.A6W2.06
#> "0131" "012" "0111" "0111" "03" "012"
#> TCGA.C5.A7X5.01 TCGA.IR.A3LA.01 TCGA.EK.A2PK.01 TCGA.EA.A5ZF.01 TCGA.XS.A8TJ.01 TCGA.BI.A0VS.01
#> "02" "012" "0133" "0132" "02" "0132"
#> TCGA.DS.A0VN.01 TCGA.JX.A5QV.01 TCGA.EK.A2R8.01 TCGA.EA.A1QS.01 TCGA.C5.A3HE.01 TCGA.IR.A3LF.01
#> "02" "0131" "0132" "0111" "03" "03"
#> TCGA.DR.A0ZL.01 TCGA.FU.A3WB.01 TCGA.JX.A3PZ.01 TCGA.EA.A5O9.01 TCGA.HM.A3JJ.11 TCGA.DS.A5RQ.01
#> "02" "02" "0133" "02" "0112" "0131"
#> TCGA.EK.A2H0.01 TCGA.EX.A1H6.01 TCGA.EA.A5ZE.01 TCGA.C5.A2LY.01 TCGA.FU.A3TQ.01 TCGA.EK.A2RB.01
#> "02" "03" "02" "0113" "02" "02"
#> TCGA.JW.A5VI.01 TCGA.EK.A2H1.01 TCGA.JX.A3Q8.01 TCGA.FU.A3YQ.01 TCGA.EX.A69L.01 TCGA.C5.A7CH.01
#> "02" "0112" "03" "02" "0131" "02"
#> TCGA.FU.A2QG.01 TCGA.C5.A2M2.01 TCGA.JW.A5VG.01 TCGA.PN.A8MA.01 TCGA.DG.A2KM.01 TCGA.C5.A2LX.01
#> "012" "03" "0113" "012" "0112" "02"
#> TCGA.EX.A3L1.01 TCGA.LP.A5U2.01 TCGA.FU.A3NI.01 TCGA.Q1.A5R3.01 TCGA.FU.A770.01 TCGA.C5.A7CM.01
#> "0111" "02" "02" "0131" "03" "0113"
#> TCGA.JX.A3Q0.01 TCGA.EA.A5FO.01 TCGA.VS.A9V3.01 TCGA.C5.A7CL.01 TCGA.VS.A959.01 TCGA.LP.A4AX.01
#> "012" "03" "02" "0131" "0111" "0111"
#> TCGA.C5.A1MN.01 TCGA.ZJ.AAXN.01 TCGA.MA.AA3X.01 TCGA.UC.A7PG.01 TCGA.Q1.A6DV.01 TCGA.DS.A1OD.01
#> "02" "0132" "012" "0131" "03" "0131"
#> TCGA.C5.A1M7.01 TCGA.BI.A20A.01 TCGA.VS.A9UO.01 TCGA.EA.A1QT.01 TCGA.EX.A69M.01 TCGA.VS.A9UH.01
#> "0134" "02" "03" "02" "02" "0111"
#> TCGA.VS.A9U7.01 TCGA.ZJ.AAXD.01 TCGA.VS.A9UB.01 TCGA.EA.A410.01 TCGA.ZJ.AB0I.01 TCGA.VS.A9UD.01
#> "02" "0131" "0111" "012" "012" "02"
#> TCGA.VS.A9U6.01 TCGA.ZX.AA5X.01 TCGA.C5.A0TN.01 TCGA.C5.A7CJ.01 TCGA.C5.A1MJ.01 TCGA.EA.A78R.01
#> "0113" "02" "0113" "02" "03" "02"
#> TCGA.VS.A9UY.01 TCGA.VS.A9U5.01 TCGA.DS.A1OC.01 TCGA.ZJ.AAXB.01 TCGA.EX.A449.01 TCGA.C5.A1BL.01
#> "02" "02" "02" "012" "03" "02"
#> TCGA.VS.A9UQ.01 TCGA.DS.A1OB.01 TCGA.HG.A9SC.01 TCGA.ZJ.AAXT.01 TCGA.IR.A3LB.01 TCGA.C5.A1ML.01
#> "03" "012" "012" "0134" "03" "0113"
#> TCGA.VS.A9UV.01 TCGA.LP.A4AU.01 TCGA.Q1.A6DT.01 TCGA.C5.A1M8.01 TCGA.C5.A1ME.01 TCGA.ZJ.AAXU.01
#> "02" "0111" "02" "02" "03" "0131"
#> TCGA.VS.A957.01 TCGA.VS.A9V5.01 TCGA.MU.A5YI.01 TCGA.ZJ.AAX4.01 TCGA.C5.A1MK.01 TCGA.JW.A69B.01
#> "02" "03" "02" "02" "0131" "03"
#> TCGA.VS.A958.01 TCGA.ZJ.AAXJ.01 TCGA.R2.A69V.01 TCGA.EA.A411.01 TCGA.VS.A9UP.01 TCGA.C5.A1MI.01
#> "0134" "02" "0111" "012" "0111" "0113"
#> TCGA.DS.A1O9.01 TCGA.VS.A9UZ.01 TCGA.EA.A43B.01 TCGA.ZJ.AAX8.01 TCGA.ZJ.AAXI.01 TCGA.VS.A9UT.01
#> "02" "03" "02" "0111" "02" "0112"
#> TCGA.DS.A1OA.01 TCGA.C5.A1MQ.01 TCGA.VS.A9V0.01 TCGA.VS.A9UC.01 TCGA.ZJ.AAXA.01 TCGA.Q1.A73P.01
#> "02" "02" "0133" "02" "012" "03"
#> TCGA.VS.A9V2.01 TCGA.VS.A9UU.01 TCGA.LP.A4AV.01 TCGA.VS.A9UR.01 TCGA.VS.A9V1.01 TCGA.C5.A7CG.01
#> "02" "02" "0131" "03" "03" "02"
#> TCGA.UC.A7PI.01 TCGA.EX.A1H5.01 TCGA.ZJ.AAXF.01 TCGA.VS.A9UL.01 TCGA.EA.A3Y4.01 TCGA.C5.A7CK.01
#> "03" "02" "0111" "03" "0132" "02"
#> TCGA.UC.A7PG.06 TCGA.VS.A9UJ.01 TCGA.Q1.A73O.01 TCGA.VS.A950.01 TCGA.EA.A439.01 TCGA.VS.A9UM.01
#> "012" "012" "0134" "02" "0113" "012"
#> TCGA.C5.A1MP.01 TCGA.VS.A9UI.01 TCGA.ZJ.AB0H.01 TCGA.Q1.A73Q.01 TCGA.C5.A1MH.01 TCGA.VS.A9V4.01
#> "0131" "02" "0131" "02" "02" "0112"
#> TCGA.FU.A40J.01 TCGA.VS.A9UA.01 TCGA.LP.A4AW.01 TCGA.MA.AA43.01 TCGA.C5.A1BN.01 TCGA.VS.AA62.01
#> "03" "0131" "0131" "03" "012" "0111"
#> TCGA.C5.A1BM.01 TCGA.C5.A1M6.01 TCGA.C5.A1BE.01 TCGA.FU.A23K.01 TCGA.C5.A1BJ.01 TCGA.FU.A23L.01
#> "0134" "0113" "0131" "03" "0111" "0134"
#> TCGA.C5.A1M5.01 TCGA.C5.A1MF.01 TCGA.C5.A1BF.01 TCGA.C5.A1BK.01 TCGA.C5.A1BI.01 TCGA.C5.A1M9.01
#> "02" "02" "0113" "02" "0134" "03"
get_classes(res_rh, merge_node = merge_node_param(min_n_signatures = 17838))
#> TCGA.EK.A3GK.01 TCGA.GH.A9DA.01 TCGA.VS.A94Y.01 TCGA.MY.A5BF.11 TCGA.VS.A94Z.01 TCGA.EA.A4BA.01
#> "013" "02" "013" "0112" "013" "013"
#> TCGA.ZJ.A8QQ.01 TCGA.FU.A3EO.11 TCGA.DG.A2KJ.01 TCGA.VS.A954.01 TCGA.MA.AA42.01 TCGA.C5.A8YQ.01
#> "02" "0112" "0111" "02" "02" "02"
#> TCGA.DS.A7WF.01 TCGA.EK.A2R7.01 TCGA.EK.A3GJ.01 TCGA.C5.A902.01 TCGA.MA.AA3W.01 TCGA.C5.A905.01
#> "03" "013" "02" "02" "02" "012"
#> TCGA.EK.A2RN.01 TCGA.FU.A57G.01 TCGA.C5.A8YR.01 TCGA.EK.A2R9.01 TCGA.FU.A3EO.01 TCGA.IR.A3LC.01
#> "013" "0112" "013" "02" "03" "02"
#> TCGA.VS.A8QA.01 TCGA.C5.A3HD.01 TCGA.MY.A5BE.01 TCGA.EA.A50E.01 TCGA.VS.A8QH.01 TCGA.ZJ.A8QR.01
#> "03" "02" "0111" "02" "0111" "012"
#> TCGA.C5.A907.01 TCGA.IR.A3LK.01 TCGA.C5.A8ZZ.01 TCGA.VS.A8EK.01 TCGA.C5.A7UC.01 TCGA.C5.A8XJ.01
#> "0111" "02" "012" "02" "0111" "013"
#> TCGA.IR.A3LH.01 TCGA.EK.A3GM.01 TCGA.VS.A8Q8.01 TCGA.EK.A2RO.01 TCGA.MY.A5BD.01 TCGA.2W.A8YY.01
#> "02" "0113" "013" "02" "03" "012"
#> TCGA.C5.A2LZ.01 TCGA.C5.A901.01 TCGA.VS.A953.01 TCGA.MU.A51Y.01 TCGA.EK.A2RK.01 TCGA.UC.A7PD.01
#> "02" "02" "02" "0111" "013" "0111"
#> TCGA.EA.A3HS.01 TCGA.VS.A8QM.01 TCGA.EA.A3HU.01 TCGA.VS.A94X.01 TCGA.C5.A7CO.01 TCGA.C5.A3HF.01
#> "02" "0111" "0111" "0111" "02" "0111"
#> TCGA.IR.A3LL.01 TCGA.MY.A913.01 TCGA.VS.A952.01 TCGA.IR.A3LI.01 TCGA.VS.A94W.01 TCGA.MY.A5BF.01
#> "02" "0111" "03" "03" "02" "02"
#> TCGA.EK.A2RC.01 TCGA.VS.A8EL.01 TCGA.EA.A97N.01 TCGA.EA.A3HQ.01 TCGA.EK.A2RD.01 TCGA.C5.A8YT.01
#> "02" "02" "012" "02" "013" "0112"
#> TCGA.FU.A3HZ.01 TCGA.VS.A8EJ.01 TCGA.C5.A3HL.01 TCGA.UC.A7PF.01 TCGA.C5.A8XK.01 TCGA.EX.A8YF.01
#> "012" "0112" "013" "02" "013" "0111"
#> TCGA.HM.A4S6.01 TCGA.VS.A8Q9.01 TCGA.MA.AA41.01 TCGA.EK.A3GN.01 TCGA.MA.AA3Y.01 TCGA.MA.AA3Z.01
#> "013" "02" "02" "02" "0111" "013"
#> TCGA.EK.A2RE.01 TCGA.C5.A1BQ.01 TCGA.ZJ.A8QO.01 TCGA.JW.A852.01 TCGA.DS.A7WH.01 TCGA.JW.AAVH.01
#> "013" "013" "02" "02" "03" "02"
#> TCGA.EA.A556.01 TCGA.EA.A44S.01 TCGA.4J.AA1J.01 TCGA.IR.A3L7.01 TCGA.C5.A7X3.01 TCGA.HG.A2PA.01
#> "013" "012" "012" "02" "013" "0111"
#> TCGA.C5.A8XH.01 TCGA.C5.A7XC.01 TCGA.VS.A8EI.01 TCGA.VS.A8QC.01 TCGA.C5.A7UH.01 TCGA.WL.A834.01
#> "02" "013" "02" "02" "012" "02"
#> TCGA.C5.A8XI.01 TCGA.DS.A7WI.01 TCGA.VS.A8QF.01 TCGA.EA.A3HR.01 TCGA.DG.A2KL.01 TCGA.EK.A2RL.01
#> "02" "02" "02" "013" "013" "03"
#> TCGA.EK.A2PG.01 TCGA.BI.A0VR.01 TCGA.DS.A0VL.01 TCGA.VS.A8EC.01 TCGA.EA.A3QE.01 TCGA.DS.A0VM.01
#> "02" "013" "013" "02" "02" "02"
#> TCGA.FU.A3HY.01 TCGA.Q1.A5R1.01 TCGA.DR.A0ZM.01 TCGA.Q1.A6DW.01 TCGA.DS.A0VK.01 TCGA.DS.A3LQ.01
#> "02" "03" "013" "02" "013" "02"
#> TCGA.EA.A3QD.01 TCGA.JW.A5VJ.01 TCGA.LP.A5U3.01 TCGA.EA.A6QX.01 TCGA.EK.A2RA.01 TCGA.FU.A5XV.01
#> "02" "013" "02" "02" "02" "012"
#> TCGA.Q1.A5R2.01 TCGA.HM.A3JJ.01 TCGA.C5.A2LS.01 TCGA.C5.A7X8.01 TCGA.EK.A2RJ.01 TCGA.EA.A3HT.01
#> "02" "013" "03" "03" "013" "013"
#> TCGA.LP.A7HU.01 TCGA.MU.A8JM.01 TCGA.EK.A2IP.01 TCGA.JW.A5VL.01 TCGA.FU.A3TX.01 TCGA.DG.A2KK.01
#> "03" "02" "02" "02" "0113" "03"
#> TCGA.EK.A2PI.01 TCGA.Q1.A73S.01 TCGA.EK.A2IR.01 TCGA.HM.A6W2.01 TCGA.VS.A8EH.01 TCGA.JW.A5VH.01
#> "013" "012" "02" "012" "0113" "012"
#> TCGA.C5.A2LV.01 TCGA.VS.A8EB.01 TCGA.RA.A741.01 TCGA.VS.A8EG.01 TCGA.DG.A2KH.01 TCGA.C5.A7UE.01
#> "02" "0113" "0111" "02" "0113" "02"
#> TCGA.C5.A2LT.01 TCGA.EA.A5ZD.01 TCGA.Q1.A73R.01 TCGA.JW.A5VK.01 TCGA.EK.A2RM.01 TCGA.C5.A7UI.01
#> "0111" "013" "03" "02" "0113" "013"
#> TCGA.EK.A2PL.01 TCGA.EK.A2PM.01 TCGA.EK.A2GZ.01 TCGA.HM.A3JK.01 TCGA.C5.A2M1.01 TCGA.HM.A6W2.06
#> "013" "012" "0111" "0111" "03" "012"
#> TCGA.C5.A7X5.01 TCGA.IR.A3LA.01 TCGA.EK.A2PK.01 TCGA.EA.A5ZF.01 TCGA.XS.A8TJ.01 TCGA.BI.A0VS.01
#> "02" "012" "013" "013" "02" "013"
#> TCGA.DS.A0VN.01 TCGA.JX.A5QV.01 TCGA.EK.A2R8.01 TCGA.EA.A1QS.01 TCGA.C5.A3HE.01 TCGA.IR.A3LF.01
#> "02" "013" "013" "0111" "03" "03"
#> TCGA.DR.A0ZL.01 TCGA.FU.A3WB.01 TCGA.JX.A3PZ.01 TCGA.EA.A5O9.01 TCGA.HM.A3JJ.11 TCGA.DS.A5RQ.01
#> "02" "02" "013" "02" "0112" "013"
#> TCGA.EK.A2H0.01 TCGA.EX.A1H6.01 TCGA.EA.A5ZE.01 TCGA.C5.A2LY.01 TCGA.FU.A3TQ.01 TCGA.EK.A2RB.01
#> "02" "03" "02" "0113" "02" "02"
#> TCGA.JW.A5VI.01 TCGA.EK.A2H1.01 TCGA.JX.A3Q8.01 TCGA.FU.A3YQ.01 TCGA.EX.A69L.01 TCGA.C5.A7CH.01
#> "02" "0112" "03" "02" "013" "02"
#> TCGA.FU.A2QG.01 TCGA.C5.A2M2.01 TCGA.JW.A5VG.01 TCGA.PN.A8MA.01 TCGA.DG.A2KM.01 TCGA.C5.A2LX.01
#> "012" "03" "0113" "012" "0112" "02"
#> TCGA.EX.A3L1.01 TCGA.LP.A5U2.01 TCGA.FU.A3NI.01 TCGA.Q1.A5R3.01 TCGA.FU.A770.01 TCGA.C5.A7CM.01
#> "0111" "02" "02" "013" "03" "0113"
#> TCGA.JX.A3Q0.01 TCGA.EA.A5FO.01 TCGA.VS.A9V3.01 TCGA.C5.A7CL.01 TCGA.VS.A959.01 TCGA.LP.A4AX.01
#> "012" "03" "02" "013" "0111" "0111"
#> TCGA.C5.A1MN.01 TCGA.ZJ.AAXN.01 TCGA.MA.AA3X.01 TCGA.UC.A7PG.01 TCGA.Q1.A6DV.01 TCGA.DS.A1OD.01
#> "02" "013" "012" "013" "03" "013"
#> TCGA.C5.A1M7.01 TCGA.BI.A20A.01 TCGA.VS.A9UO.01 TCGA.EA.A1QT.01 TCGA.EX.A69M.01 TCGA.VS.A9UH.01
#> "013" "02" "03" "02" "02" "0111"
#> TCGA.VS.A9U7.01 TCGA.ZJ.AAXD.01 TCGA.VS.A9UB.01 TCGA.EA.A410.01 TCGA.ZJ.AB0I.01 TCGA.VS.A9UD.01
#> "02" "013" "0111" "012" "012" "02"
#> TCGA.VS.A9U6.01 TCGA.ZX.AA5X.01 TCGA.C5.A0TN.01 TCGA.C5.A7CJ.01 TCGA.C5.A1MJ.01 TCGA.EA.A78R.01
#> "0113" "02" "0113" "02" "03" "02"
#> TCGA.VS.A9UY.01 TCGA.VS.A9U5.01 TCGA.DS.A1OC.01 TCGA.ZJ.AAXB.01 TCGA.EX.A449.01 TCGA.C5.A1BL.01
#> "02" "02" "02" "012" "03" "02"
#> TCGA.VS.A9UQ.01 TCGA.DS.A1OB.01 TCGA.HG.A9SC.01 TCGA.ZJ.AAXT.01 TCGA.IR.A3LB.01 TCGA.C5.A1ML.01
#> "03" "012" "012" "013" "03" "0113"
#> TCGA.VS.A9UV.01 TCGA.LP.A4AU.01 TCGA.Q1.A6DT.01 TCGA.C5.A1M8.01 TCGA.C5.A1ME.01 TCGA.ZJ.AAXU.01
#> "02" "0111" "02" "02" "03" "013"
#> TCGA.VS.A957.01 TCGA.VS.A9V5.01 TCGA.MU.A5YI.01 TCGA.ZJ.AAX4.01 TCGA.C5.A1MK.01 TCGA.JW.A69B.01
#> "02" "03" "02" "02" "013" "03"
#> TCGA.VS.A958.01 TCGA.ZJ.AAXJ.01 TCGA.R2.A69V.01 TCGA.EA.A411.01 TCGA.VS.A9UP.01 TCGA.C5.A1MI.01
#> "013" "02" "0111" "012" "0111" "0113"
#> TCGA.DS.A1O9.01 TCGA.VS.A9UZ.01 TCGA.EA.A43B.01 TCGA.ZJ.AAX8.01 TCGA.ZJ.AAXI.01 TCGA.VS.A9UT.01
#> "02" "03" "02" "0111" "02" "0112"
#> TCGA.DS.A1OA.01 TCGA.C5.A1MQ.01 TCGA.VS.A9V0.01 TCGA.VS.A9UC.01 TCGA.ZJ.AAXA.01 TCGA.Q1.A73P.01
#> "02" "02" "013" "02" "012" "03"
#> TCGA.VS.A9V2.01 TCGA.VS.A9UU.01 TCGA.LP.A4AV.01 TCGA.VS.A9UR.01 TCGA.VS.A9V1.01 TCGA.C5.A7CG.01
#> "02" "02" "013" "03" "03" "02"
#> TCGA.UC.A7PI.01 TCGA.EX.A1H5.01 TCGA.ZJ.AAXF.01 TCGA.VS.A9UL.01 TCGA.EA.A3Y4.01 TCGA.C5.A7CK.01
#> "03" "02" "0111" "03" "013" "02"
#> TCGA.UC.A7PG.06 TCGA.VS.A9UJ.01 TCGA.Q1.A73O.01 TCGA.VS.A950.01 TCGA.EA.A439.01 TCGA.VS.A9UM.01
#> "012" "012" "013" "02" "0113" "012"
#> TCGA.C5.A1MP.01 TCGA.VS.A9UI.01 TCGA.ZJ.AB0H.01 TCGA.Q1.A73Q.01 TCGA.C5.A1MH.01 TCGA.VS.A9V4.01
#> "013" "02" "013" "02" "02" "0112"
#> TCGA.FU.A40J.01 TCGA.VS.A9UA.01 TCGA.LP.A4AW.01 TCGA.MA.AA43.01 TCGA.C5.A1BN.01 TCGA.VS.AA62.01
#> "03" "013" "013" "03" "012" "0111"
#> TCGA.C5.A1BM.01 TCGA.C5.A1M6.01 TCGA.C5.A1BE.01 TCGA.FU.A23K.01 TCGA.C5.A1BJ.01 TCGA.FU.A23L.01
#> "013" "0113" "013" "03" "0111" "013"
#> TCGA.C5.A1M5.01 TCGA.C5.A1MF.01 TCGA.C5.A1BF.01 TCGA.C5.A1BK.01 TCGA.C5.A1BI.01 TCGA.C5.A1M9.01
#> "02" "02" "0113" "02" "013" "03"
get_classes(res_rh, merge_node = merge_node_param(min_n_signatures = 23697))
#> TCGA.EK.A3GK.01 TCGA.GH.A9DA.01 TCGA.VS.A94Y.01 TCGA.MY.A5BF.11 TCGA.VS.A94Z.01 TCGA.EA.A4BA.01
#> "013" "02" "013" "011" "013" "013"
#> TCGA.ZJ.A8QQ.01 TCGA.FU.A3EO.11 TCGA.DG.A2KJ.01 TCGA.VS.A954.01 TCGA.MA.AA42.01 TCGA.C5.A8YQ.01
#> "02" "011" "011" "02" "02" "02"
#> TCGA.DS.A7WF.01 TCGA.EK.A2R7.01 TCGA.EK.A3GJ.01 TCGA.C5.A902.01 TCGA.MA.AA3W.01 TCGA.C5.A905.01
#> "03" "013" "02" "02" "02" "012"
#> TCGA.EK.A2RN.01 TCGA.FU.A57G.01 TCGA.C5.A8YR.01 TCGA.EK.A2R9.01 TCGA.FU.A3EO.01 TCGA.IR.A3LC.01
#> "013" "011" "013" "02" "03" "02"
#> TCGA.VS.A8QA.01 TCGA.C5.A3HD.01 TCGA.MY.A5BE.01 TCGA.EA.A50E.01 TCGA.VS.A8QH.01 TCGA.ZJ.A8QR.01
#> "03" "02" "011" "02" "011" "012"
#> TCGA.C5.A907.01 TCGA.IR.A3LK.01 TCGA.C5.A8ZZ.01 TCGA.VS.A8EK.01 TCGA.C5.A7UC.01 TCGA.C5.A8XJ.01
#> "011" "02" "012" "02" "011" "013"
#> TCGA.IR.A3LH.01 TCGA.EK.A3GM.01 TCGA.VS.A8Q8.01 TCGA.EK.A2RO.01 TCGA.MY.A5BD.01 TCGA.2W.A8YY.01
#> "02" "011" "013" "02" "03" "012"
#> TCGA.C5.A2LZ.01 TCGA.C5.A901.01 TCGA.VS.A953.01 TCGA.MU.A51Y.01 TCGA.EK.A2RK.01 TCGA.UC.A7PD.01
#> "02" "02" "02" "011" "013" "011"
#> TCGA.EA.A3HS.01 TCGA.VS.A8QM.01 TCGA.EA.A3HU.01 TCGA.VS.A94X.01 TCGA.C5.A7CO.01 TCGA.C5.A3HF.01
#> "02" "011" "011" "011" "02" "011"
#> TCGA.IR.A3LL.01 TCGA.MY.A913.01 TCGA.VS.A952.01 TCGA.IR.A3LI.01 TCGA.VS.A94W.01 TCGA.MY.A5BF.01
#> "02" "011" "03" "03" "02" "02"
#> TCGA.EK.A2RC.01 TCGA.VS.A8EL.01 TCGA.EA.A97N.01 TCGA.EA.A3HQ.01 TCGA.EK.A2RD.01 TCGA.C5.A8YT.01
#> "02" "02" "012" "02" "013" "011"
#> TCGA.FU.A3HZ.01 TCGA.VS.A8EJ.01 TCGA.C5.A3HL.01 TCGA.UC.A7PF.01 TCGA.C5.A8XK.01 TCGA.EX.A8YF.01
#> "012" "011" "013" "02" "013" "011"
#> TCGA.HM.A4S6.01 TCGA.VS.A8Q9.01 TCGA.MA.AA41.01 TCGA.EK.A3GN.01 TCGA.MA.AA3Y.01 TCGA.MA.AA3Z.01
#> "013" "02" "02" "02" "011" "013"
#> TCGA.EK.A2RE.01 TCGA.C5.A1BQ.01 TCGA.ZJ.A8QO.01 TCGA.JW.A852.01 TCGA.DS.A7WH.01 TCGA.JW.AAVH.01
#> "013" "013" "02" "02" "03" "02"
#> TCGA.EA.A556.01 TCGA.EA.A44S.01 TCGA.4J.AA1J.01 TCGA.IR.A3L7.01 TCGA.C5.A7X3.01 TCGA.HG.A2PA.01
#> "013" "012" "012" "02" "013" "011"
#> TCGA.C5.A8XH.01 TCGA.C5.A7XC.01 TCGA.VS.A8EI.01 TCGA.VS.A8QC.01 TCGA.C5.A7UH.01 TCGA.WL.A834.01
#> "02" "013" "02" "02" "012" "02"
#> TCGA.C5.A8XI.01 TCGA.DS.A7WI.01 TCGA.VS.A8QF.01 TCGA.EA.A3HR.01 TCGA.DG.A2KL.01 TCGA.EK.A2RL.01
#> "02" "02" "02" "013" "013" "03"
#> TCGA.EK.A2PG.01 TCGA.BI.A0VR.01 TCGA.DS.A0VL.01 TCGA.VS.A8EC.01 TCGA.EA.A3QE.01 TCGA.DS.A0VM.01
#> "02" "013" "013" "02" "02" "02"
#> TCGA.FU.A3HY.01 TCGA.Q1.A5R1.01 TCGA.DR.A0ZM.01 TCGA.Q1.A6DW.01 TCGA.DS.A0VK.01 TCGA.DS.A3LQ.01
#> "02" "03" "013" "02" "013" "02"
#> TCGA.EA.A3QD.01 TCGA.JW.A5VJ.01 TCGA.LP.A5U3.01 TCGA.EA.A6QX.01 TCGA.EK.A2RA.01 TCGA.FU.A5XV.01
#> "02" "013" "02" "02" "02" "012"
#> TCGA.Q1.A5R2.01 TCGA.HM.A3JJ.01 TCGA.C5.A2LS.01 TCGA.C5.A7X8.01 TCGA.EK.A2RJ.01 TCGA.EA.A3HT.01
#> "02" "013" "03" "03" "013" "013"
#> TCGA.LP.A7HU.01 TCGA.MU.A8JM.01 TCGA.EK.A2IP.01 TCGA.JW.A5VL.01 TCGA.FU.A3TX.01 TCGA.DG.A2KK.01
#> "03" "02" "02" "02" "011" "03"
#> TCGA.EK.A2PI.01 TCGA.Q1.A73S.01 TCGA.EK.A2IR.01 TCGA.HM.A6W2.01 TCGA.VS.A8EH.01 TCGA.JW.A5VH.01
#> "013" "012" "02" "012" "011" "012"
#> TCGA.C5.A2LV.01 TCGA.VS.A8EB.01 TCGA.RA.A741.01 TCGA.VS.A8EG.01 TCGA.DG.A2KH.01 TCGA.C5.A7UE.01
#> "02" "011" "011" "02" "011" "02"
#> TCGA.C5.A2LT.01 TCGA.EA.A5ZD.01 TCGA.Q1.A73R.01 TCGA.JW.A5VK.01 TCGA.EK.A2RM.01 TCGA.C5.A7UI.01
#> "011" "013" "03" "02" "011" "013"
#> TCGA.EK.A2PL.01 TCGA.EK.A2PM.01 TCGA.EK.A2GZ.01 TCGA.HM.A3JK.01 TCGA.C5.A2M1.01 TCGA.HM.A6W2.06
#> "013" "012" "011" "011" "03" "012"
#> TCGA.C5.A7X5.01 TCGA.IR.A3LA.01 TCGA.EK.A2PK.01 TCGA.EA.A5ZF.01 TCGA.XS.A8TJ.01 TCGA.BI.A0VS.01
#> "02" "012" "013" "013" "02" "013"
#> TCGA.DS.A0VN.01 TCGA.JX.A5QV.01 TCGA.EK.A2R8.01 TCGA.EA.A1QS.01 TCGA.C5.A3HE.01 TCGA.IR.A3LF.01
#> "02" "013" "013" "011" "03" "03"
#> TCGA.DR.A0ZL.01 TCGA.FU.A3WB.01 TCGA.JX.A3PZ.01 TCGA.EA.A5O9.01 TCGA.HM.A3JJ.11 TCGA.DS.A5RQ.01
#> "02" "02" "013" "02" "011" "013"
#> TCGA.EK.A2H0.01 TCGA.EX.A1H6.01 TCGA.EA.A5ZE.01 TCGA.C5.A2LY.01 TCGA.FU.A3TQ.01 TCGA.EK.A2RB.01
#> "02" "03" "02" "011" "02" "02"
#> TCGA.JW.A5VI.01 TCGA.EK.A2H1.01 TCGA.JX.A3Q8.01 TCGA.FU.A3YQ.01 TCGA.EX.A69L.01 TCGA.C5.A7CH.01
#> "02" "011" "03" "02" "013" "02"
#> TCGA.FU.A2QG.01 TCGA.C5.A2M2.01 TCGA.JW.A5VG.01 TCGA.PN.A8MA.01 TCGA.DG.A2KM.01 TCGA.C5.A2LX.01
#> "012" "03" "011" "012" "011" "02"
#> TCGA.EX.A3L1.01 TCGA.LP.A5U2.01 TCGA.FU.A3NI.01 TCGA.Q1.A5R3.01 TCGA.FU.A770.01 TCGA.C5.A7CM.01
#> "011" "02" "02" "013" "03" "011"
#> TCGA.JX.A3Q0.01 TCGA.EA.A5FO.01 TCGA.VS.A9V3.01 TCGA.C5.A7CL.01 TCGA.VS.A959.01 TCGA.LP.A4AX.01
#> "012" "03" "02" "013" "011" "011"
#> TCGA.C5.A1MN.01 TCGA.ZJ.AAXN.01 TCGA.MA.AA3X.01 TCGA.UC.A7PG.01 TCGA.Q1.A6DV.01 TCGA.DS.A1OD.01
#> "02" "013" "012" "013" "03" "013"
#> TCGA.C5.A1M7.01 TCGA.BI.A20A.01 TCGA.VS.A9UO.01 TCGA.EA.A1QT.01 TCGA.EX.A69M.01 TCGA.VS.A9UH.01
#> "013" "02" "03" "02" "02" "011"
#> TCGA.VS.A9U7.01 TCGA.ZJ.AAXD.01 TCGA.VS.A9UB.01 TCGA.EA.A410.01 TCGA.ZJ.AB0I.01 TCGA.VS.A9UD.01
#> "02" "013" "011" "012" "012" "02"
#> TCGA.VS.A9U6.01 TCGA.ZX.AA5X.01 TCGA.C5.A0TN.01 TCGA.C5.A7CJ.01 TCGA.C5.A1MJ.01 TCGA.EA.A78R.01
#> "011" "02" "011" "02" "03" "02"
#> TCGA.VS.A9UY.01 TCGA.VS.A9U5.01 TCGA.DS.A1OC.01 TCGA.ZJ.AAXB.01 TCGA.EX.A449.01 TCGA.C5.A1BL.01
#> "02" "02" "02" "012" "03" "02"
#> TCGA.VS.A9UQ.01 TCGA.DS.A1OB.01 TCGA.HG.A9SC.01 TCGA.ZJ.AAXT.01 TCGA.IR.A3LB.01 TCGA.C5.A1ML.01
#> "03" "012" "012" "013" "03" "011"
#> TCGA.VS.A9UV.01 TCGA.LP.A4AU.01 TCGA.Q1.A6DT.01 TCGA.C5.A1M8.01 TCGA.C5.A1ME.01 TCGA.ZJ.AAXU.01
#> "02" "011" "02" "02" "03" "013"
#> TCGA.VS.A957.01 TCGA.VS.A9V5.01 TCGA.MU.A5YI.01 TCGA.ZJ.AAX4.01 TCGA.C5.A1MK.01 TCGA.JW.A69B.01
#> "02" "03" "02" "02" "013" "03"
#> TCGA.VS.A958.01 TCGA.ZJ.AAXJ.01 TCGA.R2.A69V.01 TCGA.EA.A411.01 TCGA.VS.A9UP.01 TCGA.C5.A1MI.01
#> "013" "02" "011" "012" "011" "011"
#> TCGA.DS.A1O9.01 TCGA.VS.A9UZ.01 TCGA.EA.A43B.01 TCGA.ZJ.AAX8.01 TCGA.ZJ.AAXI.01 TCGA.VS.A9UT.01
#> "02" "03" "02" "011" "02" "011"
#> TCGA.DS.A1OA.01 TCGA.C5.A1MQ.01 TCGA.VS.A9V0.01 TCGA.VS.A9UC.01 TCGA.ZJ.AAXA.01 TCGA.Q1.A73P.01
#> "02" "02" "013" "02" "012" "03"
#> TCGA.VS.A9V2.01 TCGA.VS.A9UU.01 TCGA.LP.A4AV.01 TCGA.VS.A9UR.01 TCGA.VS.A9V1.01 TCGA.C5.A7CG.01
#> "02" "02" "013" "03" "03" "02"
#> TCGA.UC.A7PI.01 TCGA.EX.A1H5.01 TCGA.ZJ.AAXF.01 TCGA.VS.A9UL.01 TCGA.EA.A3Y4.01 TCGA.C5.A7CK.01
#> "03" "02" "011" "03" "013" "02"
#> TCGA.UC.A7PG.06 TCGA.VS.A9UJ.01 TCGA.Q1.A73O.01 TCGA.VS.A950.01 TCGA.EA.A439.01 TCGA.VS.A9UM.01
#> "012" "012" "013" "02" "011" "012"
#> TCGA.C5.A1MP.01 TCGA.VS.A9UI.01 TCGA.ZJ.AB0H.01 TCGA.Q1.A73Q.01 TCGA.C5.A1MH.01 TCGA.VS.A9V4.01
#> "013" "02" "013" "02" "02" "011"
#> TCGA.FU.A40J.01 TCGA.VS.A9UA.01 TCGA.LP.A4AW.01 TCGA.MA.AA43.01 TCGA.C5.A1BN.01 TCGA.VS.AA62.01
#> "03" "013" "013" "03" "012" "011"
#> TCGA.C5.A1BM.01 TCGA.C5.A1M6.01 TCGA.C5.A1BE.01 TCGA.FU.A23K.01 TCGA.C5.A1BJ.01 TCGA.FU.A23L.01
#> "013" "011" "013" "03" "011" "013"
#> TCGA.C5.A1M5.01 TCGA.C5.A1MF.01 TCGA.C5.A1BF.01 TCGA.C5.A1BK.01 TCGA.C5.A1BI.01 TCGA.C5.A1M9.01
#> "02" "02" "011" "02" "013" "03"
get_classes(res_rh, merge_node = merge_node_param(min_n_signatures = 30030))
#> TCGA.EK.A3GK.01 TCGA.GH.A9DA.01 TCGA.VS.A94Y.01 TCGA.MY.A5BF.11 TCGA.VS.A94Z.01 TCGA.EA.A4BA.01
#> "01" "02" "01" "01" "01" "01"
#> TCGA.ZJ.A8QQ.01 TCGA.FU.A3EO.11 TCGA.DG.A2KJ.01 TCGA.VS.A954.01 TCGA.MA.AA42.01 TCGA.C5.A8YQ.01
#> "02" "01" "01" "02" "02" "02"
#> TCGA.DS.A7WF.01 TCGA.EK.A2R7.01 TCGA.EK.A3GJ.01 TCGA.C5.A902.01 TCGA.MA.AA3W.01 TCGA.C5.A905.01
#> "03" "01" "02" "02" "02" "01"
#> TCGA.EK.A2RN.01 TCGA.FU.A57G.01 TCGA.C5.A8YR.01 TCGA.EK.A2R9.01 TCGA.FU.A3EO.01 TCGA.IR.A3LC.01
#> "01" "01" "01" "02" "03" "02"
#> TCGA.VS.A8QA.01 TCGA.C5.A3HD.01 TCGA.MY.A5BE.01 TCGA.EA.A50E.01 TCGA.VS.A8QH.01 TCGA.ZJ.A8QR.01
#> "03" "02" "01" "02" "01" "01"
#> TCGA.C5.A907.01 TCGA.IR.A3LK.01 TCGA.C5.A8ZZ.01 TCGA.VS.A8EK.01 TCGA.C5.A7UC.01 TCGA.C5.A8XJ.01
#> "01" "02" "01" "02" "01" "01"
#> TCGA.IR.A3LH.01 TCGA.EK.A3GM.01 TCGA.VS.A8Q8.01 TCGA.EK.A2RO.01 TCGA.MY.A5BD.01 TCGA.2W.A8YY.01
#> "02" "01" "01" "02" "03" "01"
#> TCGA.C5.A2LZ.01 TCGA.C5.A901.01 TCGA.VS.A953.01 TCGA.MU.A51Y.01 TCGA.EK.A2RK.01 TCGA.UC.A7PD.01
#> "02" "02" "02" "01" "01" "01"
#> TCGA.EA.A3HS.01 TCGA.VS.A8QM.01 TCGA.EA.A3HU.01 TCGA.VS.A94X.01 TCGA.C5.A7CO.01 TCGA.C5.A3HF.01
#> "02" "01" "01" "01" "02" "01"
#> TCGA.IR.A3LL.01 TCGA.MY.A913.01 TCGA.VS.A952.01 TCGA.IR.A3LI.01 TCGA.VS.A94W.01 TCGA.MY.A5BF.01
#> "02" "01" "03" "03" "02" "02"
#> TCGA.EK.A2RC.01 TCGA.VS.A8EL.01 TCGA.EA.A97N.01 TCGA.EA.A3HQ.01 TCGA.EK.A2RD.01 TCGA.C5.A8YT.01
#> "02" "02" "01" "02" "01" "01"
#> TCGA.FU.A3HZ.01 TCGA.VS.A8EJ.01 TCGA.C5.A3HL.01 TCGA.UC.A7PF.01 TCGA.C5.A8XK.01 TCGA.EX.A8YF.01
#> "01" "01" "01" "02" "01" "01"
#> TCGA.HM.A4S6.01 TCGA.VS.A8Q9.01 TCGA.MA.AA41.01 TCGA.EK.A3GN.01 TCGA.MA.AA3Y.01 TCGA.MA.AA3Z.01
#> "01" "02" "02" "02" "01" "01"
#> TCGA.EK.A2RE.01 TCGA.C5.A1BQ.01 TCGA.ZJ.A8QO.01 TCGA.JW.A852.01 TCGA.DS.A7WH.01 TCGA.JW.AAVH.01
#> "01" "01" "02" "02" "03" "02"
#> TCGA.EA.A556.01 TCGA.EA.A44S.01 TCGA.4J.AA1J.01 TCGA.IR.A3L7.01 TCGA.C5.A7X3.01 TCGA.HG.A2PA.01
#> "01" "01" "01" "02" "01" "01"
#> TCGA.C5.A8XH.01 TCGA.C5.A7XC.01 TCGA.VS.A8EI.01 TCGA.VS.A8QC.01 TCGA.C5.A7UH.01 TCGA.WL.A834.01
#> "02" "01" "02" "02" "01" "02"
#> TCGA.C5.A8XI.01 TCGA.DS.A7WI.01 TCGA.VS.A8QF.01 TCGA.EA.A3HR.01 TCGA.DG.A2KL.01 TCGA.EK.A2RL.01
#> "02" "02" "02" "01" "01" "03"
#> TCGA.EK.A2PG.01 TCGA.BI.A0VR.01 TCGA.DS.A0VL.01 TCGA.VS.A8EC.01 TCGA.EA.A3QE.01 TCGA.DS.A0VM.01
#> "02" "01" "01" "02" "02" "02"
#> TCGA.FU.A3HY.01 TCGA.Q1.A5R1.01 TCGA.DR.A0ZM.01 TCGA.Q1.A6DW.01 TCGA.DS.A0VK.01 TCGA.DS.A3LQ.01
#> "02" "03" "01" "02" "01" "02"
#> TCGA.EA.A3QD.01 TCGA.JW.A5VJ.01 TCGA.LP.A5U3.01 TCGA.EA.A6QX.01 TCGA.EK.A2RA.01 TCGA.FU.A5XV.01
#> "02" "01" "02" "02" "02" "01"
#> TCGA.Q1.A5R2.01 TCGA.HM.A3JJ.01 TCGA.C5.A2LS.01 TCGA.C5.A7X8.01 TCGA.EK.A2RJ.01 TCGA.EA.A3HT.01
#> "02" "01" "03" "03" "01" "01"
#> TCGA.LP.A7HU.01 TCGA.MU.A8JM.01 TCGA.EK.A2IP.01 TCGA.JW.A5VL.01 TCGA.FU.A3TX.01 TCGA.DG.A2KK.01
#> "03" "02" "02" "02" "01" "03"
#> TCGA.EK.A2PI.01 TCGA.Q1.A73S.01 TCGA.EK.A2IR.01 TCGA.HM.A6W2.01 TCGA.VS.A8EH.01 TCGA.JW.A5VH.01
#> "01" "01" "02" "01" "01" "01"
#> TCGA.C5.A2LV.01 TCGA.VS.A8EB.01 TCGA.RA.A741.01 TCGA.VS.A8EG.01 TCGA.DG.A2KH.01 TCGA.C5.A7UE.01
#> "02" "01" "01" "02" "01" "02"
#> TCGA.C5.A2LT.01 TCGA.EA.A5ZD.01 TCGA.Q1.A73R.01 TCGA.JW.A5VK.01 TCGA.EK.A2RM.01 TCGA.C5.A7UI.01
#> "01" "01" "03" "02" "01" "01"
#> TCGA.EK.A2PL.01 TCGA.EK.A2PM.01 TCGA.EK.A2GZ.01 TCGA.HM.A3JK.01 TCGA.C5.A2M1.01 TCGA.HM.A6W2.06
#> "01" "01" "01" "01" "03" "01"
#> TCGA.C5.A7X5.01 TCGA.IR.A3LA.01 TCGA.EK.A2PK.01 TCGA.EA.A5ZF.01 TCGA.XS.A8TJ.01 TCGA.BI.A0VS.01
#> "02" "01" "01" "01" "02" "01"
#> TCGA.DS.A0VN.01 TCGA.JX.A5QV.01 TCGA.EK.A2R8.01 TCGA.EA.A1QS.01 TCGA.C5.A3HE.01 TCGA.IR.A3LF.01
#> "02" "01" "01" "01" "03" "03"
#> TCGA.DR.A0ZL.01 TCGA.FU.A3WB.01 TCGA.JX.A3PZ.01 TCGA.EA.A5O9.01 TCGA.HM.A3JJ.11 TCGA.DS.A5RQ.01
#> "02" "02" "01" "02" "01" "01"
#> TCGA.EK.A2H0.01 TCGA.EX.A1H6.01 TCGA.EA.A5ZE.01 TCGA.C5.A2LY.01 TCGA.FU.A3TQ.01 TCGA.EK.A2RB.01
#> "02" "03" "02" "01" "02" "02"
#> TCGA.JW.A5VI.01 TCGA.EK.A2H1.01 TCGA.JX.A3Q8.01 TCGA.FU.A3YQ.01 TCGA.EX.A69L.01 TCGA.C5.A7CH.01
#> "02" "01" "03" "02" "01" "02"
#> TCGA.FU.A2QG.01 TCGA.C5.A2M2.01 TCGA.JW.A5VG.01 TCGA.PN.A8MA.01 TCGA.DG.A2KM.01 TCGA.C5.A2LX.01
#> "01" "03" "01" "01" "01" "02"
#> TCGA.EX.A3L1.01 TCGA.LP.A5U2.01 TCGA.FU.A3NI.01 TCGA.Q1.A5R3.01 TCGA.FU.A770.01 TCGA.C5.A7CM.01
#> "01" "02" "02" "01" "03" "01"
#> TCGA.JX.A3Q0.01 TCGA.EA.A5FO.01 TCGA.VS.A9V3.01 TCGA.C5.A7CL.01 TCGA.VS.A959.01 TCGA.LP.A4AX.01
#> "01" "03" "02" "01" "01" "01"
#> TCGA.C5.A1MN.01 TCGA.ZJ.AAXN.01 TCGA.MA.AA3X.01 TCGA.UC.A7PG.01 TCGA.Q1.A6DV.01 TCGA.DS.A1OD.01
#> "02" "01" "01" "01" "03" "01"
#> TCGA.C5.A1M7.01 TCGA.BI.A20A.01 TCGA.VS.A9UO.01 TCGA.EA.A1QT.01 TCGA.EX.A69M.01 TCGA.VS.A9UH.01
#> "01" "02" "03" "02" "02" "01"
#> TCGA.VS.A9U7.01 TCGA.ZJ.AAXD.01 TCGA.VS.A9UB.01 TCGA.EA.A410.01 TCGA.ZJ.AB0I.01 TCGA.VS.A9UD.01
#> "02" "01" "01" "01" "01" "02"
#> TCGA.VS.A9U6.01 TCGA.ZX.AA5X.01 TCGA.C5.A0TN.01 TCGA.C5.A7CJ.01 TCGA.C5.A1MJ.01 TCGA.EA.A78R.01
#> "01" "02" "01" "02" "03" "02"
#> TCGA.VS.A9UY.01 TCGA.VS.A9U5.01 TCGA.DS.A1OC.01 TCGA.ZJ.AAXB.01 TCGA.EX.A449.01 TCGA.C5.A1BL.01
#> "02" "02" "02" "01" "03" "02"
#> TCGA.VS.A9UQ.01 TCGA.DS.A1OB.01 TCGA.HG.A9SC.01 TCGA.ZJ.AAXT.01 TCGA.IR.A3LB.01 TCGA.C5.A1ML.01
#> "03" "01" "01" "01" "03" "01"
#> TCGA.VS.A9UV.01 TCGA.LP.A4AU.01 TCGA.Q1.A6DT.01 TCGA.C5.A1M8.01 TCGA.C5.A1ME.01 TCGA.ZJ.AAXU.01
#> "02" "01" "02" "02" "03" "01"
#> TCGA.VS.A957.01 TCGA.VS.A9V5.01 TCGA.MU.A5YI.01 TCGA.ZJ.AAX4.01 TCGA.C5.A1MK.01 TCGA.JW.A69B.01
#> "02" "03" "02" "02" "01" "03"
#> TCGA.VS.A958.01 TCGA.ZJ.AAXJ.01 TCGA.R2.A69V.01 TCGA.EA.A411.01 TCGA.VS.A9UP.01 TCGA.C5.A1MI.01
#> "01" "02" "01" "01" "01" "01"
#> TCGA.DS.A1O9.01 TCGA.VS.A9UZ.01 TCGA.EA.A43B.01 TCGA.ZJ.AAX8.01 TCGA.ZJ.AAXI.01 TCGA.VS.A9UT.01
#> "02" "03" "02" "01" "02" "01"
#> TCGA.DS.A1OA.01 TCGA.C5.A1MQ.01 TCGA.VS.A9V0.01 TCGA.VS.A9UC.01 TCGA.ZJ.AAXA.01 TCGA.Q1.A73P.01
#> "02" "02" "01" "02" "01" "03"
#> TCGA.VS.A9V2.01 TCGA.VS.A9UU.01 TCGA.LP.A4AV.01 TCGA.VS.A9UR.01 TCGA.VS.A9V1.01 TCGA.C5.A7CG.01
#> "02" "02" "01" "03" "03" "02"
#> TCGA.UC.A7PI.01 TCGA.EX.A1H5.01 TCGA.ZJ.AAXF.01 TCGA.VS.A9UL.01 TCGA.EA.A3Y4.01 TCGA.C5.A7CK.01
#> "03" "02" "01" "03" "01" "02"
#> TCGA.UC.A7PG.06 TCGA.VS.A9UJ.01 TCGA.Q1.A73O.01 TCGA.VS.A950.01 TCGA.EA.A439.01 TCGA.VS.A9UM.01
#> "01" "01" "01" "02" "01" "01"
#> TCGA.C5.A1MP.01 TCGA.VS.A9UI.01 TCGA.ZJ.AB0H.01 TCGA.Q1.A73Q.01 TCGA.C5.A1MH.01 TCGA.VS.A9V4.01
#> "01" "02" "01" "02" "02" "01"
#> TCGA.FU.A40J.01 TCGA.VS.A9UA.01 TCGA.LP.A4AW.01 TCGA.MA.AA43.01 TCGA.C5.A1BN.01 TCGA.VS.AA62.01
#> "03" "01" "01" "03" "01" "01"
#> TCGA.C5.A1BM.01 TCGA.C5.A1M6.01 TCGA.C5.A1BE.01 TCGA.FU.A23K.01 TCGA.C5.A1BJ.01 TCGA.FU.A23L.01
#> "01" "01" "01" "03" "01" "01"
#> TCGA.C5.A1M5.01 TCGA.C5.A1MF.01 TCGA.C5.A1BF.01 TCGA.C5.A1BK.01 TCGA.C5.A1BI.01 TCGA.C5.A1M9.01
#> "02" "02" "01" "02" "01" "03"
Heatmaps of the top rows:
top_rows_heatmap(res_rh)
#> Error in h(simpleError(msg, call)) :
#> error in evaluating the argument 'object' in selecting a method for function 'draw': no applicable method for 'height' applied to an object of class "list"
Top rows on each node:
top_rows_overlap(res_rh, method = "upset")
UMAP plot which shows how samples are separated.
par(mfrow = c(1, 2))
dimension_reduction(res_rh, merge_node = merge_node_param(min_n_signatures = 1032),
method = "UMAP", top_value_method = "SD", top_n = 40000, scale_rows = FALSE)
dimension_reduction(res_rh, merge_node = merge_node_param(min_n_signatures = 1032),
method = "UMAP", top_value_method = "ATC", top_n = 40000, scale_rows = TRUE)
par(mfrow = c(1, 2))
dimension_reduction(res_rh, merge_node = merge_node_param(min_n_signatures = 1061),
method = "UMAP", top_value_method = "SD", top_n = 40000, scale_rows = FALSE)
dimension_reduction(res_rh, merge_node = merge_node_param(min_n_signatures = 1061),
method = "UMAP", top_value_method = "ATC", top_n = 40000, scale_rows = TRUE)
par(mfrow = c(1, 2))
dimension_reduction(res_rh, merge_node = merge_node_param(min_n_signatures = 1228),
method = "UMAP", top_value_method = "SD", top_n = 40000, scale_rows = FALSE)
dimension_reduction(res_rh, merge_node = merge_node_param(min_n_signatures = 1228),
method = "UMAP", top_value_method = "ATC", top_n = 40000, scale_rows = TRUE)
par(mfrow = c(1, 2))
dimension_reduction(res_rh, merge_node = merge_node_param(min_n_signatures = 1463),
method = "UMAP", top_value_method = "SD", top_n = 40000, scale_rows = FALSE)
dimension_reduction(res_rh, merge_node = merge_node_param(min_n_signatures = 1463),
method = "UMAP", top_value_method = "ATC", top_n = 40000, scale_rows = TRUE)
par(mfrow = c(1, 2))
dimension_reduction(res_rh, merge_node = merge_node_param(min_n_signatures = 1579),
method = "UMAP", top_value_method = "SD", top_n = 40000, scale_rows = FALSE)
dimension_reduction(res_rh, merge_node = merge_node_param(min_n_signatures = 1579),
method = "UMAP", top_value_method = "ATC", top_n = 40000, scale_rows = TRUE)
par(mfrow = c(1, 2))
dimension_reduction(res_rh, merge_node = merge_node_param(min_n_signatures = 1658),
method = "UMAP", top_value_method = "SD", top_n = 40000, scale_rows = FALSE)
dimension_reduction(res_rh, merge_node = merge_node_param(min_n_signatures = 1658),
method = "UMAP", top_value_method = "ATC", top_n = 40000, scale_rows = TRUE)
par(mfrow = c(1, 2))
dimension_reduction(res_rh, merge_node = merge_node_param(min_n_signatures = 2087),
method = "UMAP", top_value_method = "SD", top_n = 40000, scale_rows = FALSE)
dimension_reduction(res_rh, merge_node = merge_node_param(min_n_signatures = 2087),
method = "UMAP", top_value_method = "ATC", top_n = 40000, scale_rows = TRUE)
par(mfrow = c(1, 2))
dimension_reduction(res_rh, merge_node = merge_node_param(min_n_signatures = 2263),
method = "UMAP", top_value_method = "SD", top_n = 40000, scale_rows = FALSE)
dimension_reduction(res_rh, merge_node = merge_node_param(min_n_signatures = 2263),
method = "UMAP", top_value_method = "ATC", top_n = 40000, scale_rows = TRUE)
par(mfrow = c(1, 2))
dimension_reduction(res_rh, merge_node = merge_node_param(min_n_signatures = 3801),
method = "UMAP", top_value_method = "SD", top_n = 40000, scale_rows = FALSE)
dimension_reduction(res_rh, merge_node = merge_node_param(min_n_signatures = 3801),
method = "UMAP", top_value_method = "ATC", top_n = 40000, scale_rows = TRUE)
par(mfrow = c(1, 2))
dimension_reduction(res_rh, merge_node = merge_node_param(min_n_signatures = 4079),
method = "UMAP", top_value_method = "SD", top_n = 40000, scale_rows = FALSE)
dimension_reduction(res_rh, merge_node = merge_node_param(min_n_signatures = 4079),
method = "UMAP", top_value_method = "ATC", top_n = 40000, scale_rows = TRUE)
par(mfrow = c(1, 2))
dimension_reduction(res_rh, merge_node = merge_node_param(min_n_signatures = 4774),
method = "UMAP", top_value_method = "SD", top_n = 40000, scale_rows = FALSE)
dimension_reduction(res_rh, merge_node = merge_node_param(min_n_signatures = 4774),
method = "UMAP", top_value_method = "ATC", top_n = 40000, scale_rows = TRUE)
par(mfrow = c(1, 2))
dimension_reduction(res_rh, merge_node = merge_node_param(min_n_signatures = 5174),
method = "UMAP", top_value_method = "SD", top_n = 40000, scale_rows = FALSE)
dimension_reduction(res_rh, merge_node = merge_node_param(min_n_signatures = 5174),
method = "UMAP", top_value_method = "ATC", top_n = 40000, scale_rows = TRUE)
par(mfrow = c(1, 2))
dimension_reduction(res_rh, merge_node = merge_node_param(min_n_signatures = 7545),
method = "UMAP", top_value_method = "SD", top_n = 40000, scale_rows = FALSE)
dimension_reduction(res_rh, merge_node = merge_node_param(min_n_signatures = 7545),
method = "UMAP", top_value_method = "ATC", top_n = 40000, scale_rows = TRUE)
par(mfrow = c(1, 2))
dimension_reduction(res_rh, merge_node = merge_node_param(min_n_signatures = 8634),
method = "UMAP", top_value_method = "SD", top_n = 40000, scale_rows = FALSE)
dimension_reduction(res_rh, merge_node = merge_node_param(min_n_signatures = 8634),
method = "UMAP", top_value_method = "ATC", top_n = 40000, scale_rows = TRUE)
par(mfrow = c(1, 2))
dimension_reduction(res_rh, merge_node = merge_node_param(min_n_signatures = 10323),
method = "UMAP", top_value_method = "SD", top_n = 40000, scale_rows = FALSE)
dimension_reduction(res_rh, merge_node = merge_node_param(min_n_signatures = 10323),
method = "UMAP", top_value_method = "ATC", top_n = 40000, scale_rows = TRUE)
par(mfrow = c(1, 2))
dimension_reduction(res_rh, merge_node = merge_node_param(min_n_signatures = 12995),
method = "UMAP", top_value_method = "SD", top_n = 40000, scale_rows = FALSE)
dimension_reduction(res_rh, merge_node = merge_node_param(min_n_signatures = 12995),
method = "UMAP", top_value_method = "ATC", top_n = 40000, scale_rows = TRUE)
par(mfrow = c(1, 2))
dimension_reduction(res_rh, merge_node = merge_node_param(min_n_signatures = 15278),
method = "UMAP", top_value_method = "SD", top_n = 40000, scale_rows = FALSE)
dimension_reduction(res_rh, merge_node = merge_node_param(min_n_signatures = 15278),
method = "UMAP", top_value_method = "ATC", top_n = 40000, scale_rows = TRUE)
par(mfrow = c(1, 2))
dimension_reduction(res_rh, merge_node = merge_node_param(min_n_signatures = 17125),
method = "UMAP", top_value_method = "SD", top_n = 40000, scale_rows = FALSE)
dimension_reduction(res_rh, merge_node = merge_node_param(min_n_signatures = 17125),
method = "UMAP", top_value_method = "ATC", top_n = 40000, scale_rows = TRUE)
par(mfrow = c(1, 2))
dimension_reduction(res_rh, merge_node = merge_node_param(min_n_signatures = 17838),
method = "UMAP", top_value_method = "SD", top_n = 40000, scale_rows = FALSE)
dimension_reduction(res_rh, merge_node = merge_node_param(min_n_signatures = 17838),
method = "UMAP", top_value_method = "ATC", top_n = 40000, scale_rows = TRUE)
par(mfrow = c(1, 2))
dimension_reduction(res_rh, merge_node = merge_node_param(min_n_signatures = 23697),
method = "UMAP", top_value_method = "SD", top_n = 40000, scale_rows = FALSE)
dimension_reduction(res_rh, merge_node = merge_node_param(min_n_signatures = 23697),
method = "UMAP", top_value_method = "ATC", top_n = 40000, scale_rows = TRUE)
par(mfrow = c(1, 2))
dimension_reduction(res_rh, merge_node = merge_node_param(min_n_signatures = 30030),
method = "UMAP", top_value_method = "SD", top_n = 40000, scale_rows = FALSE)
dimension_reduction(res_rh, merge_node = merge_node_param(min_n_signatures = 30030),
method = "UMAP", top_value_method = "ATC", top_n = 40000, scale_rows = TRUE)
Signatures on the heatmap are the union of all signatures found on every node on the hierarchy. The number of k-means on rows are automatically selected by the function.
get_signatures(res_rh, merge_node = merge_node_param(min_n_signatures = 1032))
get_signatures(res_rh, merge_node = merge_node_param(min_n_signatures = 1061))
get_signatures(res_rh, merge_node = merge_node_param(min_n_signatures = 1228))
get_signatures(res_rh, merge_node = merge_node_param(min_n_signatures = 1463))
#> Error in lt[[hierarchy[i, 1]]]$AddChildNode({: attempt to apply non-function
get_signatures(res_rh, merge_node = merge_node_param(min_n_signatures = 1579))
get_signatures(res_rh, merge_node = merge_node_param(min_n_signatures = 1658))
get_signatures(res_rh, merge_node = merge_node_param(min_n_signatures = 2087))
get_signatures(res_rh, merge_node = merge_node_param(min_n_signatures = 2263))
get_signatures(res_rh, merge_node = merge_node_param(min_n_signatures = 3801))
get_signatures(res_rh, merge_node = merge_node_param(min_n_signatures = 4079))
get_signatures(res_rh, merge_node = merge_node_param(min_n_signatures = 4774))
get_signatures(res_rh, merge_node = merge_node_param(min_n_signatures = 5174))
get_signatures(res_rh, merge_node = merge_node_param(min_n_signatures = 7545))
#> Error in lt[[hierarchy[i, 1]]]$AddChildNode({: attempt to apply non-function
get_signatures(res_rh, merge_node = merge_node_param(min_n_signatures = 8634))
get_signatures(res_rh, merge_node = merge_node_param(min_n_signatures = 10323))
get_signatures(res_rh, merge_node = merge_node_param(min_n_signatures = 12995))
get_signatures(res_rh, merge_node = merge_node_param(min_n_signatures = 15278))
get_signatures(res_rh, merge_node = merge_node_param(min_n_signatures = 17125))
get_signatures(res_rh, merge_node = merge_node_param(min_n_signatures = 17838))
get_signatures(res_rh, merge_node = merge_node_param(min_n_signatures = 23697))
get_signatures(res_rh, merge_node = merge_node_param(min_n_signatures = 30030))
Compare signatures from different nodes:
compare_signatures(res_rh, verbose = FALSE)
If there are too many signatures, top_signatures = ... can be set to only show the
signatures with the highest FDRs. Note it only works on every node and the final signatures
are the union of all signatures of all nodes.
# code only for demonstration
# e.g. to show the top 500 most significant rows on each node.
tb = get_signature(res_rh, top_signatures = 500)
Child nodes: Node01 , Node02 , Node03 .
The object with results only for a single top-value method and a single partitioning method can be extracted as:
res = res_rh["0"]
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, 7, 8.
#> On a matrix with 30000 rows and 312 columns.
#> Top rows (1000) are extracted by 'SD' method.
#> Subgroups are detected by 'kmeans' method.
#> Performed in total 350 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_partitions"
#> [7] "compare_signatures" "consensus_heatmap" "dimension_reduction"
#> [10] "functional_enrichment" "get_anno_col" "get_anno"
#> [13] "get_classes" "get_consensus" "get_matrix"
#> [16] "get_membership" "get_param" "get_signatures"
#> [19] "get_stats" "is_best_k" "is_stable_k"
#> [22] "membership_heatmap" "ncol" "nrow"
#> [25] "plot_ecdf" "predict_classes" "rownames"
#> [28] "select_partition_number" "show" "suggest_best_k"
#> [31] "test_to_known_factors" "top_rows_heatmap"
collect_plots() function collects all the plots made from res for all k (number of subgroups)
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, higher 1-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 0.984 0.994 0.4872 0.515 0.515
#> 3 3 1.000 0.982 0.993 0.2322 0.778 0.609
#> 4 4 0.696 0.745 0.874 0.2016 0.773 0.495
#> 5 5 0.690 0.649 0.824 0.0798 0.881 0.607
#> 6 6 0.692 0.610 0.785 0.0528 0.891 0.573
#> 7 7 0.740 0.530 0.736 0.0321 0.903 0.555
#> 8 8 0.791 0.716 0.819 0.0209 0.915 0.544
suggest_best_k() suggests the best \(k\) based on these statistics. The rules are as follows:
suggest_best_k(res)
#> [1] 3
#> attr(,"optional")
#> [1] 2
There is also optional best \(k\) = 2 that is worth to check.
Following is 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 subgroup
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
#> TCGA.EK.A3GK.01 1 0.000 0.991 1.00 0.00
#> TCGA.GH.A9DA.01 1 0.000 0.991 1.00 0.00
#> TCGA.VS.A94Y.01 1 0.000 0.991 1.00 0.00
#> TCGA.MY.A5BF.11 1 0.000 0.991 1.00 0.00
#> TCGA.VS.A94Z.01 1 0.000 0.991 1.00 0.00
#> TCGA.EA.A4BA.01 1 0.000 0.991 1.00 0.00
#> TCGA.ZJ.A8QQ.01 2 0.000 0.997 0.00 1.00
#> TCGA.FU.A3EO.11 1 0.000 0.991 1.00 0.00
#> TCGA.DG.A2KJ.01 1 0.000 0.991 1.00 0.00
#> TCGA.VS.A954.01 2 0.000 0.997 0.00 1.00
#> TCGA.MA.AA42.01 2 0.000 0.997 0.00 1.00
#> TCGA.C5.A8YQ.01 1 0.000 0.991 1.00 0.00
#> TCGA.DS.A7WF.01 2 0.000 0.997 0.00 1.00
#> TCGA.EK.A2R7.01 1 0.000 0.991 1.00 0.00
#> TCGA.EK.A3GJ.01 2 0.000 0.997 0.00 1.00
#> TCGA.C5.A902.01 2 0.000 0.997 0.00 1.00
#> TCGA.MA.AA3W.01 2 0.855 0.607 0.28 0.72
#> TCGA.C5.A905.01 1 0.000 0.991 1.00 0.00
#> TCGA.EK.A2RN.01 1 0.000 0.991 1.00 0.00
#> TCGA.FU.A57G.01 1 0.000 0.991 1.00 0.00
#> TCGA.C5.A8YR.01 1 0.000 0.991 1.00 0.00
#> TCGA.EK.A2R9.01 2 0.000 0.997 0.00 1.00
#> TCGA.FU.A3EO.01 2 0.000 0.997 0.00 1.00
#> TCGA.IR.A3LC.01 2 0.000 0.997 0.00 1.00
#> TCGA.VS.A8QA.01 2 0.000 0.997 0.00 1.00
#> TCGA.C5.A3HD.01 2 0.000 0.997 0.00 1.00
#> TCGA.MY.A5BE.01 1 0.000 0.991 1.00 0.00
#> TCGA.EA.A50E.01 2 0.000 0.997 0.00 1.00
#> TCGA.VS.A8QH.01 1 0.000 0.991 1.00 0.00
#> TCGA.ZJ.A8QR.01 1 0.000 0.991 1.00 0.00
#> TCGA.C5.A907.01 1 0.000 0.991 1.00 0.00
#> TCGA.IR.A3LK.01 1 0.000 0.991 1.00 0.00
#> TCGA.C5.A8ZZ.01 1 0.000 0.991 1.00 0.00
#> TCGA.VS.A8EK.01 2 0.000 0.997 0.00 1.00
#> TCGA.C5.A7UC.01 1 0.000 0.991 1.00 0.00
#> TCGA.C5.A8XJ.01 1 0.000 0.991 1.00 0.00
#> TCGA.IR.A3LH.01 2 0.000 0.997 0.00 1.00
#> TCGA.EK.A3GM.01 1 0.000 0.991 1.00 0.00
#> TCGA.VS.A8Q8.01 1 0.000 0.991 1.00 0.00
#> TCGA.EK.A2RO.01 2 0.000 0.997 0.00 1.00
#> TCGA.MY.A5BD.01 2 0.000 0.997 0.00 1.00
#> TCGA.2W.A8YY.01 1 0.000 0.991 1.00 0.00
#> TCGA.C5.A2LZ.01 2 0.000 0.997 0.00 1.00
#> TCGA.C5.A901.01 2 0.000 0.997 0.00 1.00
#> TCGA.VS.A953.01 2 0.000 0.997 0.00 1.00
#> TCGA.MU.A51Y.01 1 0.000 0.991 1.00 0.00
#> TCGA.EK.A2RK.01 1 0.000 0.991 1.00 0.00
#> TCGA.UC.A7PD.01 1 0.000 0.991 1.00 0.00
#> TCGA.EA.A3HS.01 1 0.000 0.991 1.00 0.00
#> TCGA.VS.A8QM.01 1 0.000 0.991 1.00 0.00
#> TCGA.EA.A3HU.01 1 0.000 0.991 1.00 0.00
#> TCGA.VS.A94X.01 1 0.000 0.991 1.00 0.00
#> TCGA.C5.A7CO.01 2 0.000 0.997 0.00 1.00
#> TCGA.C5.A3HF.01 1 0.000 0.991 1.00 0.00
#> TCGA.IR.A3LL.01 1 0.141 0.972 0.98 0.02
#> TCGA.MY.A913.01 1 0.000 0.991 1.00 0.00
#> TCGA.VS.A952.01 2 0.000 0.997 0.00 1.00
#> TCGA.IR.A3LI.01 2 0.000 0.997 0.00 1.00
#> TCGA.VS.A94W.01 1 0.000 0.991 1.00 0.00
#> TCGA.MY.A5BF.01 2 0.000 0.997 0.00 1.00
#> TCGA.EK.A2RC.01 1 0.000 0.991 1.00 0.00
#> TCGA.VS.A8EL.01 2 0.000 0.997 0.00 1.00
#> TCGA.EA.A97N.01 1 0.000 0.991 1.00 0.00
#> TCGA.EA.A3HQ.01 2 0.000 0.997 0.00 1.00
#> TCGA.EK.A2RD.01 1 0.000 0.991 1.00 0.00
#> TCGA.C5.A8YT.01 1 0.000 0.991 1.00 0.00
#> TCGA.FU.A3HZ.01 1 0.000 0.991 1.00 0.00
#> TCGA.VS.A8EJ.01 1 0.000 0.991 1.00 0.00
#> TCGA.C5.A3HL.01 1 0.000 0.991 1.00 0.00
#> TCGA.UC.A7PF.01 1 0.000 0.991 1.00 0.00
#> TCGA.C5.A8XK.01 1 0.000 0.991 1.00 0.00
#> TCGA.EX.A8YF.01 1 0.000 0.991 1.00 0.00
#> TCGA.HM.A4S6.01 1 0.000 0.991 1.00 0.00
#> TCGA.VS.A8Q9.01 2 0.000 0.997 0.00 1.00
#> TCGA.MA.AA41.01 2 0.000 0.997 0.00 1.00
#> TCGA.EK.A3GN.01 2 0.000 0.997 0.00 1.00
#> TCGA.MA.AA3Y.01 1 0.000 0.991 1.00 0.00
#> TCGA.MA.AA3Z.01 1 0.000 0.991 1.00 0.00
#> TCGA.EK.A2RE.01 1 0.000 0.991 1.00 0.00
#> TCGA.C5.A1BQ.01 1 0.000 0.991 1.00 0.00
#> TCGA.ZJ.A8QO.01 2 0.000 0.997 0.00 1.00
#> TCGA.JW.A852.01 2 0.000 0.997 0.00 1.00
#> TCGA.DS.A7WH.01 2 0.000 0.997 0.00 1.00
#> TCGA.JW.AAVH.01 2 0.000 0.997 0.00 1.00
#> TCGA.EA.A556.01 1 0.000 0.991 1.00 0.00
#> TCGA.EA.A44S.01 1 0.000 0.991 1.00 0.00
#> TCGA.4J.AA1J.01 1 0.000 0.991 1.00 0.00
#> TCGA.IR.A3L7.01 2 0.000 0.997 0.00 1.00
#> TCGA.C5.A7X3.01 1 0.000 0.991 1.00 0.00
#> TCGA.HG.A2PA.01 1 0.000 0.991 1.00 0.00
#> TCGA.C5.A8XH.01 2 0.000 0.997 0.00 1.00
#> TCGA.C5.A7XC.01 1 0.000 0.991 1.00 0.00
#> TCGA.VS.A8EI.01 1 0.827 0.651 0.74 0.26
#> TCGA.VS.A8QC.01 2 0.000 0.997 0.00 1.00
#> TCGA.C5.A7UH.01 1 0.000 0.991 1.00 0.00
#> TCGA.WL.A834.01 2 0.000 0.997 0.00 1.00
#> TCGA.C5.A8XI.01 2 0.000 0.997 0.00 1.00
#> TCGA.DS.A7WI.01 1 0.000 0.991 1.00 0.00
#> TCGA.VS.A8QF.01 2 0.000 0.997 0.00 1.00
#> TCGA.EA.A3HR.01 1 0.000 0.991 1.00 0.00
#> TCGA.DG.A2KL.01 1 0.000 0.991 1.00 0.00
#> TCGA.EK.A2RL.01 2 0.000 0.997 0.00 1.00
#> TCGA.EK.A2PG.01 2 0.000 0.997 0.00 1.00
#> TCGA.BI.A0VR.01 1 0.000 0.991 1.00 0.00
#> TCGA.DS.A0VL.01 1 0.000 0.991 1.00 0.00
#> TCGA.VS.A8EC.01 2 0.000 0.997 0.00 1.00
#> TCGA.EA.A3QE.01 2 0.000 0.997 0.00 1.00
#> TCGA.DS.A0VM.01 2 0.000 0.997 0.00 1.00
#> TCGA.FU.A3HY.01 1 0.141 0.972 0.98 0.02
#> TCGA.Q1.A5R1.01 2 0.000 0.997 0.00 1.00
#> TCGA.DR.A0ZM.01 1 0.000 0.991 1.00 0.00
#> TCGA.Q1.A6DW.01 2 0.000 0.997 0.00 1.00
#> TCGA.DS.A0VK.01 1 0.000 0.991 1.00 0.00
#> TCGA.DS.A3LQ.01 1 0.881 0.575 0.70 0.30
#> TCGA.EA.A3QD.01 2 0.000 0.997 0.00 1.00
#> TCGA.JW.A5VJ.01 1 0.000 0.991 1.00 0.00
#> TCGA.LP.A5U3.01 2 0.000 0.997 0.00 1.00
#> TCGA.EA.A6QX.01 2 0.000 0.997 0.00 1.00
#> TCGA.EK.A2RA.01 2 0.000 0.997 0.00 1.00
#> TCGA.FU.A5XV.01 1 0.000 0.991 1.00 0.00
#> TCGA.Q1.A5R2.01 2 0.000 0.997 0.00 1.00
#> TCGA.HM.A3JJ.01 1 0.000 0.991 1.00 0.00
#> TCGA.C5.A2LS.01 2 0.000 0.997 0.00 1.00
#> TCGA.C5.A7X8.01 2 0.000 0.997 0.00 1.00
#> TCGA.EK.A2RJ.01 1 0.000 0.991 1.00 0.00
#> TCGA.EA.A3HT.01 1 0.000 0.991 1.00 0.00
#> TCGA.LP.A7HU.01 2 0.000 0.997 0.00 1.00
#> TCGA.MU.A8JM.01 1 0.000 0.991 1.00 0.00
#> TCGA.EK.A2IP.01 1 0.000 0.991 1.00 0.00
#> TCGA.JW.A5VL.01 2 0.000 0.997 0.00 1.00
#> TCGA.FU.A3TX.01 1 0.000 0.991 1.00 0.00
#> TCGA.DG.A2KK.01 2 0.000 0.997 0.00 1.00
#> TCGA.EK.A2PI.01 1 0.000 0.991 1.00 0.00
#> TCGA.Q1.A73S.01 1 0.000 0.991 1.00 0.00
#> TCGA.EK.A2IR.01 1 0.000 0.991 1.00 0.00
#> TCGA.HM.A6W2.01 1 0.000 0.991 1.00 0.00
#> TCGA.VS.A8EH.01 1 0.000 0.991 1.00 0.00
#> TCGA.JW.A5VH.01 1 0.000 0.991 1.00 0.00
#> TCGA.C5.A2LV.01 2 0.000 0.997 0.00 1.00
#> TCGA.VS.A8EB.01 1 0.000 0.991 1.00 0.00
#> TCGA.RA.A741.01 1 0.000 0.991 1.00 0.00
#> TCGA.VS.A8EG.01 2 0.000 0.997 0.00 1.00
#> TCGA.DG.A2KH.01 1 0.000 0.991 1.00 0.00
#> TCGA.C5.A7UE.01 2 0.141 0.977 0.02 0.98
#> TCGA.C5.A2LT.01 1 0.000 0.991 1.00 0.00
#> TCGA.EA.A5ZD.01 1 0.000 0.991 1.00 0.00
#> TCGA.Q1.A73R.01 2 0.000 0.997 0.00 1.00
#> TCGA.JW.A5VK.01 2 0.000 0.997 0.00 1.00
#> TCGA.EK.A2RM.01 1 0.000 0.991 1.00 0.00
#> TCGA.C5.A7UI.01 1 0.000 0.991 1.00 0.00
#> TCGA.EK.A2PL.01 1 0.000 0.991 1.00 0.00
#> TCGA.EK.A2PM.01 1 0.000 0.991 1.00 0.00
#> TCGA.EK.A2GZ.01 1 0.000 0.991 1.00 0.00
#> TCGA.HM.A3JK.01 1 0.000 0.991 1.00 0.00
#> TCGA.C5.A2M1.01 2 0.000 0.997 0.00 1.00
#> TCGA.HM.A6W2.06 1 0.000 0.991 1.00 0.00
#> TCGA.C5.A7X5.01 2 0.000 0.997 0.00 1.00
#> TCGA.IR.A3LA.01 1 0.000 0.991 1.00 0.00
#> TCGA.EK.A2PK.01 1 0.000 0.991 1.00 0.00
#> TCGA.EA.A5ZF.01 1 0.000 0.991 1.00 0.00
#> TCGA.XS.A8TJ.01 1 0.000 0.991 1.00 0.00
#> TCGA.BI.A0VS.01 1 0.000 0.991 1.00 0.00
#> TCGA.DS.A0VN.01 1 0.000 0.991 1.00 0.00
#> TCGA.JX.A5QV.01 1 0.000 0.991 1.00 0.00
#> TCGA.EK.A2R8.01 1 0.000 0.991 1.00 0.00
#> TCGA.EA.A1QS.01 1 0.000 0.991 1.00 0.00
#> TCGA.C5.A3HE.01 2 0.000 0.997 0.00 1.00
#> TCGA.IR.A3LF.01 2 0.000 0.997 0.00 1.00
#> TCGA.DR.A0ZL.01 1 0.000 0.991 1.00 0.00
#> TCGA.FU.A3WB.01 2 0.000 0.997 0.00 1.00
#> TCGA.JX.A3PZ.01 1 0.000 0.991 1.00 0.00
#> TCGA.EA.A5O9.01 2 0.000 0.997 0.00 1.00
#> TCGA.HM.A3JJ.11 1 0.000 0.991 1.00 0.00
#> TCGA.DS.A5RQ.01 1 0.000 0.991 1.00 0.00
#> TCGA.EK.A2H0.01 2 0.000 0.997 0.00 1.00
#> TCGA.EX.A1H6.01 2 0.000 0.997 0.00 1.00
#> TCGA.EA.A5ZE.01 2 0.000 0.997 0.00 1.00
#> TCGA.C5.A2LY.01 1 0.000 0.991 1.00 0.00
#> TCGA.FU.A3TQ.01 1 0.000 0.991 1.00 0.00
#> TCGA.EK.A2RB.01 2 0.000 0.997 0.00 1.00
#> TCGA.JW.A5VI.01 1 0.000 0.991 1.00 0.00
#> TCGA.EK.A2H1.01 1 0.000 0.991 1.00 0.00
#> TCGA.JX.A3Q8.01 2 0.000 0.997 0.00 1.00
#> TCGA.FU.A3YQ.01 1 0.000 0.991 1.00 0.00
#> TCGA.EX.A69L.01 1 0.000 0.991 1.00 0.00
#> TCGA.C5.A7CH.01 2 0.000 0.997 0.00 1.00
#> TCGA.FU.A2QG.01 1 0.000 0.991 1.00 0.00
#> TCGA.C5.A2M2.01 2 0.000 0.997 0.00 1.00
#> TCGA.JW.A5VG.01 1 0.000 0.991 1.00 0.00
#> TCGA.PN.A8MA.01 1 0.000 0.991 1.00 0.00
#> TCGA.DG.A2KM.01 1 0.000 0.991 1.00 0.00
#> TCGA.C5.A2LX.01 2 0.000 0.997 0.00 1.00
#> TCGA.EX.A3L1.01 1 0.000 0.991 1.00 0.00
#> TCGA.LP.A5U2.01 2 0.000 0.997 0.00 1.00
#> TCGA.FU.A3NI.01 2 0.000 0.997 0.00 1.00
#> TCGA.Q1.A5R3.01 1 0.000 0.991 1.00 0.00
#> TCGA.FU.A770.01 2 0.000 0.997 0.00 1.00
#> TCGA.C5.A7CM.01 1 0.000 0.991 1.00 0.00
#> TCGA.JX.A3Q0.01 1 0.000 0.991 1.00 0.00
#> TCGA.EA.A5FO.01 2 0.000 0.997 0.00 1.00
#> TCGA.VS.A9V3.01 2 0.000 0.997 0.00 1.00
#> TCGA.C5.A7CL.01 1 0.000 0.991 1.00 0.00
#> TCGA.VS.A959.01 1 0.000 0.991 1.00 0.00
#> TCGA.LP.A4AX.01 1 0.000 0.991 1.00 0.00
#> TCGA.C5.A1MN.01 2 0.000 0.997 0.00 1.00
#> TCGA.ZJ.AAXN.01 1 0.000 0.991 1.00 0.00
#> TCGA.MA.AA3X.01 1 0.000 0.991 1.00 0.00
#> TCGA.UC.A7PG.01 1 0.000 0.991 1.00 0.00
#> TCGA.Q1.A6DV.01 2 0.000 0.997 0.00 1.00
#> TCGA.DS.A1OD.01 1 0.000 0.991 1.00 0.00
#> TCGA.C5.A1M7.01 1 0.000 0.991 1.00 0.00
#> TCGA.BI.A20A.01 2 0.000 0.997 0.00 1.00
#> TCGA.VS.A9UO.01 2 0.000 0.997 0.00 1.00
#> TCGA.EA.A1QT.01 2 0.000 0.997 0.00 1.00
#> TCGA.EX.A69M.01 2 0.000 0.997 0.00 1.00
#> TCGA.VS.A9UH.01 1 0.000 0.991 1.00 0.00
#> TCGA.VS.A9U7.01 2 0.000 0.997 0.00 1.00
#> TCGA.ZJ.AAXD.01 1 0.000 0.991 1.00 0.00
#> TCGA.VS.A9UB.01 1 0.000 0.991 1.00 0.00
#> TCGA.EA.A410.01 1 0.000 0.991 1.00 0.00
#> TCGA.ZJ.AB0I.01 1 0.000 0.991 1.00 0.00
#> TCGA.VS.A9UD.01 2 0.000 0.997 0.00 1.00
#> TCGA.VS.A9U6.01 1 0.000 0.991 1.00 0.00
#> TCGA.ZX.AA5X.01 2 0.000 0.997 0.00 1.00
#> TCGA.C5.A0TN.01 1 0.000 0.991 1.00 0.00
#> TCGA.C5.A7CJ.01 1 0.000 0.991 1.00 0.00
#> TCGA.C5.A1MJ.01 2 0.000 0.997 0.00 1.00
#> TCGA.EA.A78R.01 2 0.000 0.997 0.00 1.00
#> TCGA.VS.A9UY.01 2 0.000 0.997 0.00 1.00
#> TCGA.VS.A9U5.01 2 0.000 0.997 0.00 1.00
#> TCGA.DS.A1OC.01 1 0.000 0.991 1.00 0.00
#> TCGA.ZJ.AAXB.01 1 0.000 0.991 1.00 0.00
#> TCGA.EX.A449.01 2 0.000 0.997 0.00 1.00
#> TCGA.C5.A1BL.01 2 0.000 0.997 0.00 1.00
#> TCGA.VS.A9UQ.01 2 0.000 0.997 0.00 1.00
#> TCGA.DS.A1OB.01 1 0.000 0.991 1.00 0.00
#> TCGA.HG.A9SC.01 1 0.000 0.991 1.00 0.00
#> TCGA.ZJ.AAXT.01 1 0.000 0.991 1.00 0.00
#> TCGA.IR.A3LB.01 2 0.000 0.997 0.00 1.00
#> TCGA.C5.A1ML.01 1 0.000 0.991 1.00 0.00
#> TCGA.VS.A9UV.01 2 0.000 0.997 0.00 1.00
#> TCGA.LP.A4AU.01 1 0.000 0.991 1.00 0.00
#> TCGA.Q1.A6DT.01 2 0.000 0.997 0.00 1.00
#> TCGA.C5.A1M8.01 2 0.000 0.997 0.00 1.00
#> TCGA.C5.A1ME.01 2 0.000 0.997 0.00 1.00
#> TCGA.ZJ.AAXU.01 1 0.000 0.991 1.00 0.00
#> TCGA.VS.A957.01 2 0.000 0.997 0.00 1.00
#> TCGA.VS.A9V5.01 2 0.000 0.997 0.00 1.00
#> TCGA.MU.A5YI.01 2 0.000 0.997 0.00 1.00
#> TCGA.ZJ.AAX4.01 2 0.000 0.997 0.00 1.00
#> TCGA.C5.A1MK.01 1 0.000 0.991 1.00 0.00
#> TCGA.JW.A69B.01 2 0.000 0.997 0.00 1.00
#> TCGA.VS.A958.01 1 0.000 0.991 1.00 0.00
#> TCGA.ZJ.AAXJ.01 2 0.000 0.997 0.00 1.00
#> TCGA.R2.A69V.01 1 0.000 0.991 1.00 0.00
#> TCGA.EA.A411.01 1 0.000 0.991 1.00 0.00
#> TCGA.VS.A9UP.01 1 0.000 0.991 1.00 0.00
#> TCGA.C5.A1MI.01 1 0.000 0.991 1.00 0.00
#> TCGA.DS.A1O9.01 2 0.000 0.997 0.00 1.00
#> TCGA.VS.A9UZ.01 2 0.000 0.997 0.00 1.00
#> TCGA.EA.A43B.01 2 0.000 0.997 0.00 1.00
#> TCGA.ZJ.AAX8.01 1 0.000 0.991 1.00 0.00
#> TCGA.ZJ.AAXI.01 2 0.000 0.997 0.00 1.00
#> TCGA.VS.A9UT.01 1 0.000 0.991 1.00 0.00
#> TCGA.DS.A1OA.01 1 0.000 0.991 1.00 0.00
#> TCGA.C5.A1MQ.01 2 0.000 0.997 0.00 1.00
#> TCGA.VS.A9V0.01 1 0.000 0.991 1.00 0.00
#> TCGA.VS.A9UC.01 1 0.000 0.991 1.00 0.00
#> TCGA.ZJ.AAXA.01 1 0.000 0.991 1.00 0.00
#> TCGA.Q1.A73P.01 2 0.000 0.997 0.00 1.00
#> TCGA.VS.A9V2.01 2 0.000 0.997 0.00 1.00
#> TCGA.VS.A9UU.01 2 0.000 0.997 0.00 1.00
#> TCGA.LP.A4AV.01 1 0.000 0.991 1.00 0.00
#> TCGA.VS.A9UR.01 2 0.000 0.997 0.00 1.00
#> TCGA.VS.A9V1.01 1 0.958 0.393 0.62 0.38
#> TCGA.C5.A7CG.01 2 0.000 0.997 0.00 1.00
#> TCGA.UC.A7PI.01 2 0.000 0.997 0.00 1.00
#> TCGA.EX.A1H5.01 1 0.995 0.154 0.54 0.46
#> TCGA.ZJ.AAXF.01 1 0.000 0.991 1.00 0.00
#> TCGA.VS.A9UL.01 2 0.000 0.997 0.00 1.00
#> TCGA.EA.A3Y4.01 1 0.000 0.991 1.00 0.00
#> TCGA.C5.A7CK.01 2 0.000 0.997 0.00 1.00
#> TCGA.UC.A7PG.06 1 0.000 0.991 1.00 0.00
#> TCGA.VS.A9UJ.01 1 0.000 0.991 1.00 0.00
#> TCGA.Q1.A73O.01 1 0.000 0.991 1.00 0.00
#> TCGA.VS.A950.01 2 0.469 0.887 0.10 0.90
#> TCGA.EA.A439.01 1 0.000 0.991 1.00 0.00
#> TCGA.VS.A9UM.01 1 0.000 0.991 1.00 0.00
#> TCGA.C5.A1MP.01 1 0.000 0.991 1.00 0.00
#> TCGA.VS.A9UI.01 1 0.141 0.972 0.98 0.02
#> TCGA.ZJ.AB0H.01 1 0.000 0.991 1.00 0.00
#> TCGA.Q1.A73Q.01 1 0.000 0.991 1.00 0.00
#> TCGA.C5.A1MH.01 1 0.000 0.991 1.00 0.00
#> TCGA.VS.A9V4.01 1 0.000 0.991 1.00 0.00
#> TCGA.FU.A40J.01 2 0.000 0.997 0.00 1.00
#> TCGA.VS.A9UA.01 1 0.000 0.991 1.00 0.00
#> TCGA.LP.A4AW.01 1 0.000 0.991 1.00 0.00
#> TCGA.MA.AA43.01 2 0.000 0.997 0.00 1.00
#> TCGA.C5.A1BN.01 1 0.000 0.991 1.00 0.00
#> TCGA.VS.AA62.01 1 0.000 0.991 1.00 0.00
#> TCGA.C5.A1BM.01 1 0.000 0.991 1.00 0.00
#> TCGA.C5.A1M6.01 1 0.469 0.885 0.90 0.10
#> TCGA.C5.A1BE.01 1 0.000 0.991 1.00 0.00
#> TCGA.FU.A23K.01 2 0.000 0.997 0.00 1.00
#> TCGA.C5.A1BJ.01 1 0.000 0.991 1.00 0.00
#> TCGA.FU.A23L.01 1 0.000 0.991 1.00 0.00
#> TCGA.C5.A1M5.01 2 0.000 0.997 0.00 1.00
#> TCGA.C5.A1MF.01 2 0.000 0.997 0.00 1.00
#> TCGA.C5.A1BF.01 1 0.000 0.991 1.00 0.00
#> TCGA.C5.A1BK.01 2 0.000 0.997 0.00 1.00
#> TCGA.C5.A1BI.01 1 0.000 0.991 1.00 0.00
#> TCGA.C5.A1M9.01 2 0.000 0.997 0.00 1.00
cbind(get_classes(res, k = 3), get_membership(res, k = 3))
#> class entropy silhouette p1 p2 p3
#> TCGA.EK.A3GK.01 1 0.0000 0.9972 1.00 0.00 0.00
#> TCGA.GH.A9DA.01 2 0.0000 0.9807 0.00 1.00 0.00
#> TCGA.VS.A94Y.01 1 0.0000 0.9972 1.00 0.00 0.00
#> TCGA.MY.A5BF.11 1 0.0000 0.9972 1.00 0.00 0.00
#> TCGA.VS.A94Z.01 1 0.0000 0.9972 1.00 0.00 0.00
#> TCGA.EA.A4BA.01 1 0.0000 0.9972 1.00 0.00 0.00
#> TCGA.ZJ.A8QQ.01 2 0.0000 0.9807 0.00 1.00 0.00
#> TCGA.FU.A3EO.11 1 0.0000 0.9972 1.00 0.00 0.00
#> TCGA.DG.A2KJ.01 1 0.0000 0.9972 1.00 0.00 0.00
#> TCGA.VS.A954.01 2 0.0000 0.9807 0.00 1.00 0.00
#> TCGA.MA.AA42.01 2 0.0000 0.9807 0.00 1.00 0.00
#> TCGA.C5.A8YQ.01 2 0.0000 0.9807 0.00 1.00 0.00
#> TCGA.DS.A7WF.01 3 0.0000 1.0000 0.00 0.00 1.00
#> TCGA.EK.A2R7.01 1 0.0000 0.9972 1.00 0.00 0.00
#> TCGA.EK.A3GJ.01 2 0.0000 0.9807 0.00 1.00 0.00
#> TCGA.C5.A902.01 2 0.0000 0.9807 0.00 1.00 0.00
#> TCGA.MA.AA3W.01 2 0.0000 0.9807 0.00 1.00 0.00
#> TCGA.C5.A905.01 1 0.0000 0.9972 1.00 0.00 0.00
#> TCGA.EK.A2RN.01 1 0.0000 0.9972 1.00 0.00 0.00
#> TCGA.FU.A57G.01 1 0.0000 0.9972 1.00 0.00 0.00
#> TCGA.C5.A8YR.01 1 0.0000 0.9972 1.00 0.00 0.00
#> TCGA.EK.A2R9.01 2 0.0000 0.9807 0.00 1.00 0.00
#> TCGA.FU.A3EO.01 3 0.0000 1.0000 0.00 0.00 1.00
#> TCGA.IR.A3LC.01 2 0.4002 0.8041 0.00 0.84 0.16
#> TCGA.VS.A8QA.01 3 0.0000 1.0000 0.00 0.00 1.00
#> TCGA.C5.A3HD.01 2 0.0000 0.9807 0.00 1.00 0.00
#> TCGA.MY.A5BE.01 1 0.0000 0.9972 1.00 0.00 0.00
#> TCGA.EA.A50E.01 2 0.0000 0.9807 0.00 1.00 0.00
#> TCGA.VS.A8QH.01 1 0.0000 0.9972 1.00 0.00 0.00
#> TCGA.ZJ.A8QR.01 1 0.2066 0.9279 0.94 0.06 0.00
#> TCGA.C5.A907.01 1 0.0000 0.9972 1.00 0.00 0.00
#> TCGA.IR.A3LK.01 2 0.0000 0.9807 0.00 1.00 0.00
#> TCGA.C5.A8ZZ.01 1 0.0000 0.9972 1.00 0.00 0.00
#> TCGA.VS.A8EK.01 2 0.0000 0.9807 0.00 1.00 0.00
#> TCGA.C5.A7UC.01 1 0.0000 0.9972 1.00 0.00 0.00
#> TCGA.C5.A8XJ.01 1 0.0000 0.9972 1.00 0.00 0.00
#> TCGA.IR.A3LH.01 2 0.0000 0.9807 0.00 1.00 0.00
#> TCGA.EK.A3GM.01 1 0.0000 0.9972 1.00 0.00 0.00
#> TCGA.VS.A8Q8.01 1 0.0000 0.9972 1.00 0.00 0.00
#> TCGA.EK.A2RO.01 2 0.0000 0.9807 0.00 1.00 0.00
#> TCGA.MY.A5BD.01 3 0.0000 1.0000 0.00 0.00 1.00
#> TCGA.2W.A8YY.01 1 0.0000 0.9972 1.00 0.00 0.00
#> TCGA.C5.A2LZ.01 2 0.0000 0.9807 0.00 1.00 0.00
#> TCGA.C5.A901.01 2 0.0000 0.9807 0.00 1.00 0.00
#> TCGA.VS.A953.01 2 0.0000 0.9807 0.00 1.00 0.00
#> TCGA.MU.A51Y.01 1 0.0000 0.9972 1.00 0.00 0.00
#> TCGA.EK.A2RK.01 1 0.0000 0.9972 1.00 0.00 0.00
#> TCGA.UC.A7PD.01 1 0.0000 0.9972 1.00 0.00 0.00
#> TCGA.EA.A3HS.01 2 0.0000 0.9807 0.00 1.00 0.00
#> TCGA.VS.A8QM.01 1 0.0000 0.9972 1.00 0.00 0.00
#> TCGA.EA.A3HU.01 1 0.0000 0.9972 1.00 0.00 0.00
#> TCGA.VS.A94X.01 1 0.0000 0.9972 1.00 0.00 0.00
#> TCGA.C5.A7CO.01 2 0.0000 0.9807 0.00 1.00 0.00
#> TCGA.C5.A3HF.01 1 0.0000 0.9972 1.00 0.00 0.00
#> TCGA.IR.A3LL.01 2 0.0000 0.9807 0.00 1.00 0.00
#> TCGA.MY.A913.01 1 0.0000 0.9972 1.00 0.00 0.00
#> TCGA.VS.A952.01 3 0.0000 1.0000 0.00 0.00 1.00
#> TCGA.IR.A3LI.01 3 0.0000 1.0000 0.00 0.00 1.00
#> TCGA.VS.A94W.01 2 0.0000 0.9807 0.00 1.00 0.00
#> TCGA.MY.A5BF.01 2 0.0000 0.9807 0.00 1.00 0.00
#> TCGA.EK.A2RC.01 2 0.0000 0.9807 0.00 1.00 0.00
#> TCGA.VS.A8EL.01 2 0.0000 0.9807 0.00 1.00 0.00
#> TCGA.EA.A97N.01 1 0.0000 0.9972 1.00 0.00 0.00
#> TCGA.EA.A3HQ.01 2 0.0000 0.9807 0.00 1.00 0.00
#> TCGA.EK.A2RD.01 1 0.0000 0.9972 1.00 0.00 0.00
#> TCGA.C5.A8YT.01 1 0.0000 0.9972 1.00 0.00 0.00
#> TCGA.FU.A3HZ.01 1 0.0000 0.9972 1.00 0.00 0.00
#> TCGA.VS.A8EJ.01 1 0.0000 0.9972 1.00 0.00 0.00
#> TCGA.C5.A3HL.01 1 0.0000 0.9972 1.00 0.00 0.00
#> TCGA.UC.A7PF.01 2 0.0000 0.9807 0.00 1.00 0.00
#> TCGA.C5.A8XK.01 1 0.0000 0.9972 1.00 0.00 0.00
#> TCGA.EX.A8YF.01 1 0.0000 0.9972 1.00 0.00 0.00
#> TCGA.HM.A4S6.01 1 0.0000 0.9972 1.00 0.00 0.00
#> TCGA.VS.A8Q9.01 2 0.0000 0.9807 0.00 1.00 0.00
#> TCGA.MA.AA41.01 2 0.0000 0.9807 0.00 1.00 0.00
#> TCGA.EK.A3GN.01 2 0.0000 0.9807 0.00 1.00 0.00
#> TCGA.MA.AA3Y.01 1 0.0000 0.9972 1.00 0.00 0.00
#> TCGA.MA.AA3Z.01 1 0.0000 0.9972 1.00 0.00 0.00
#> TCGA.EK.A2RE.01 1 0.0000 0.9972 1.00 0.00 0.00
#> TCGA.C5.A1BQ.01 1 0.0000 0.9972 1.00 0.00 0.00
#> TCGA.ZJ.A8QO.01 2 0.0000 0.9807 0.00 1.00 0.00
#> TCGA.JW.A852.01 2 0.0000 0.9807 0.00 1.00 0.00
#> TCGA.DS.A7WH.01 3 0.0000 1.0000 0.00 0.00 1.00
#> TCGA.JW.AAVH.01 2 0.0000 0.9807 0.00 1.00 0.00
#> TCGA.EA.A556.01 1 0.0000 0.9972 1.00 0.00 0.00
#> TCGA.EA.A44S.01 1 0.0000 0.9972 1.00 0.00 0.00
#> TCGA.4J.AA1J.01 1 0.0000 0.9972 1.00 0.00 0.00
#> TCGA.IR.A3L7.01 2 0.0000 0.9807 0.00 1.00 0.00
#> TCGA.C5.A7X3.01 1 0.0000 0.9972 1.00 0.00 0.00
#> TCGA.HG.A2PA.01 1 0.0000 0.9972 1.00 0.00 0.00
#> TCGA.C5.A8XH.01 2 0.0000 0.9807 0.00 1.00 0.00
#> TCGA.C5.A7XC.01 1 0.0000 0.9972 1.00 0.00 0.00
#> TCGA.VS.A8EI.01 2 0.0000 0.9807 0.00 1.00 0.00
#> TCGA.VS.A8QC.01 2 0.0000 0.9807 0.00 1.00 0.00
#> TCGA.C5.A7UH.01 1 0.0000 0.9972 1.00 0.00 0.00
#> TCGA.WL.A834.01 2 0.0000 0.9807 0.00 1.00 0.00
#> TCGA.C5.A8XI.01 2 0.0000 0.9807 0.00 1.00 0.00
#> TCGA.DS.A7WI.01 2 0.0000 0.9807 0.00 1.00 0.00
#> TCGA.VS.A8QF.01 2 0.0000 0.9807 0.00 1.00 0.00
#> TCGA.EA.A3HR.01 1 0.0000 0.9972 1.00 0.00 0.00
#> TCGA.DG.A2KL.01 1 0.0000 0.9972 1.00 0.00 0.00
#> TCGA.EK.A2RL.01 3 0.0000 1.0000 0.00 0.00 1.00
#> TCGA.EK.A2PG.01 2 0.0000 0.9807 0.00 1.00 0.00
#> TCGA.BI.A0VR.01 1 0.0000 0.9972 1.00 0.00 0.00
#> TCGA.DS.A0VL.01 1 0.0000 0.9972 1.00 0.00 0.00
#> TCGA.VS.A8EC.01 2 0.0000 0.9807 0.00 1.00 0.00
#> TCGA.EA.A3QE.01 2 0.0000 0.9807 0.00 1.00 0.00
#> TCGA.DS.A0VM.01 2 0.0000 0.9807 0.00 1.00 0.00
#> TCGA.FU.A3HY.01 2 0.0000 0.9807 0.00 1.00 0.00
#> TCGA.Q1.A5R1.01 3 0.0000 1.0000 0.00 0.00 1.00
#> TCGA.DR.A0ZM.01 1 0.0000 0.9972 1.00 0.00 0.00
#> TCGA.Q1.A6DW.01 2 0.0000 0.9807 0.00 1.00 0.00
#> TCGA.DS.A0VK.01 1 0.2066 0.9281 0.94 0.06 0.00
#> TCGA.DS.A3LQ.01 2 0.0000 0.9807 0.00 1.00 0.00
#> TCGA.EA.A3QD.01 2 0.0000 0.9807 0.00 1.00 0.00
#> TCGA.JW.A5VJ.01 1 0.0000 0.9972 1.00 0.00 0.00
#> TCGA.LP.A5U3.01 2 0.0000 0.9807 0.00 1.00 0.00
#> TCGA.EA.A6QX.01 2 0.0000 0.9807 0.00 1.00 0.00
#> TCGA.EK.A2RA.01 2 0.0000 0.9807 0.00 1.00 0.00
#> TCGA.FU.A5XV.01 1 0.0892 0.9749 0.98 0.02 0.00
#> TCGA.Q1.A5R2.01 2 0.0000 0.9807 0.00 1.00 0.00
#> TCGA.HM.A3JJ.01 1 0.0000 0.9972 1.00 0.00 0.00
#> TCGA.C5.A2LS.01 3 0.0000 1.0000 0.00 0.00 1.00
#> TCGA.C5.A7X8.01 3 0.0000 1.0000 0.00 0.00 1.00
#> TCGA.EK.A2RJ.01 1 0.0000 0.9972 1.00 0.00 0.00
#> TCGA.EA.A3HT.01 1 0.0000 0.9972 1.00 0.00 0.00
#> TCGA.LP.A7HU.01 3 0.0000 1.0000 0.00 0.00 1.00
#> TCGA.MU.A8JM.01 2 0.0000 0.9807 0.00 1.00 0.00
#> TCGA.EK.A2IP.01 2 0.2959 0.8571 0.10 0.90 0.00
#> TCGA.JW.A5VL.01 2 0.0000 0.9807 0.00 1.00 0.00
#> TCGA.FU.A3TX.01 1 0.0000 0.9972 1.00 0.00 0.00
#> TCGA.DG.A2KK.01 3 0.0000 1.0000 0.00 0.00 1.00
#> TCGA.EK.A2PI.01 1 0.0000 0.9972 1.00 0.00 0.00
#> TCGA.Q1.A73S.01 1 0.0000 0.9972 1.00 0.00 0.00
#> TCGA.EK.A2IR.01 2 0.6309 0.0107 0.50 0.50 0.00
#> TCGA.HM.A6W2.01 1 0.0000 0.9972 1.00 0.00 0.00
#> TCGA.VS.A8EH.01 1 0.0000 0.9972 1.00 0.00 0.00
#> TCGA.JW.A5VH.01 1 0.0000 0.9972 1.00 0.00 0.00
#> TCGA.C5.A2LV.01 2 0.0000 0.9807 0.00 1.00 0.00
#> TCGA.VS.A8EB.01 1 0.2959 0.8760 0.90 0.10 0.00
#> TCGA.RA.A741.01 1 0.0000 0.9972 1.00 0.00 0.00
#> TCGA.VS.A8EG.01 2 0.0000 0.9807 0.00 1.00 0.00
#> TCGA.DG.A2KH.01 1 0.0000 0.9972 1.00 0.00 0.00
#> TCGA.C5.A7UE.01 2 0.0000 0.9807 0.00 1.00 0.00
#> TCGA.C5.A2LT.01 1 0.0000 0.9972 1.00 0.00 0.00
#> TCGA.EA.A5ZD.01 1 0.0000 0.9972 1.00 0.00 0.00
#> TCGA.Q1.A73R.01 3 0.0000 1.0000 0.00 0.00 1.00
#> TCGA.JW.A5VK.01 2 0.0000 0.9807 0.00 1.00 0.00
#> TCGA.EK.A2RM.01 1 0.0000 0.9972 1.00 0.00 0.00
#> TCGA.C5.A7UI.01 1 0.2537 0.9019 0.92 0.08 0.00
#> TCGA.EK.A2PL.01 1 0.0000 0.9972 1.00 0.00 0.00
#> TCGA.EK.A2PM.01 1 0.0000 0.9972 1.00 0.00 0.00
#> TCGA.EK.A2GZ.01 1 0.0000 0.9972 1.00 0.00 0.00
#> TCGA.HM.A3JK.01 1 0.0000 0.9972 1.00 0.00 0.00
#> TCGA.C5.A2M1.01 3 0.0000 1.0000 0.00 0.00 1.00
#> TCGA.HM.A6W2.06 1 0.0000 0.9972 1.00 0.00 0.00
#> TCGA.C5.A7X5.01 2 0.0000 0.9807 0.00 1.00 0.00
#> TCGA.IR.A3LA.01 1 0.0000 0.9972 1.00 0.00 0.00
#> TCGA.EK.A2PK.01 1 0.0000 0.9972 1.00 0.00 0.00
#> TCGA.EA.A5ZF.01 1 0.0000 0.9972 1.00 0.00 0.00
#> TCGA.XS.A8TJ.01 2 0.5216 0.6150 0.26 0.74 0.00
#> TCGA.BI.A0VS.01 1 0.0000 0.9972 1.00 0.00 0.00
#> TCGA.DS.A0VN.01 2 0.2066 0.9103 0.06 0.94 0.00
#> TCGA.JX.A5QV.01 1 0.0000 0.9972 1.00 0.00 0.00
#> TCGA.EK.A2R8.01 1 0.0000 0.9972 1.00 0.00 0.00
#> TCGA.EA.A1QS.01 1 0.0000 0.9972 1.00 0.00 0.00
#> TCGA.C5.A3HE.01 3 0.0000 1.0000 0.00 0.00 1.00
#> TCGA.IR.A3LF.01 3 0.0000 1.0000 0.00 0.00 1.00
#> TCGA.DR.A0ZL.01 2 0.3340 0.8292 0.12 0.88 0.00
#> TCGA.FU.A3WB.01 2 0.0000 0.9807 0.00 1.00 0.00
#> TCGA.JX.A3PZ.01 1 0.0000 0.9972 1.00 0.00 0.00
#> TCGA.EA.A5O9.01 2 0.0000 0.9807 0.00 1.00 0.00
#> TCGA.HM.A3JJ.11 1 0.0000 0.9972 1.00 0.00 0.00
#> TCGA.DS.A5RQ.01 1 0.0000 0.9972 1.00 0.00 0.00
#> TCGA.EK.A2H0.01 2 0.0000 0.9807 0.00 1.00 0.00
#> TCGA.EX.A1H6.01 3 0.0000 1.0000 0.00 0.00 1.00
#> TCGA.EA.A5ZE.01 2 0.0000 0.9807 0.00 1.00 0.00
#> TCGA.C5.A2LY.01 1 0.0000 0.9972 1.00 0.00 0.00
#> TCGA.FU.A3TQ.01 2 0.0000 0.9807 0.00 1.00 0.00
#> TCGA.EK.A2RB.01 2 0.0000 0.9807 0.00 1.00 0.00
#> TCGA.JW.A5VI.01 2 0.2537 0.8842 0.08 0.92 0.00
#> TCGA.EK.A2H1.01 1 0.0000 0.9972 1.00 0.00 0.00
#> TCGA.JX.A3Q8.01 3 0.0000 1.0000 0.00 0.00 1.00
#> TCGA.FU.A3YQ.01 2 0.0000 0.9807 0.00 1.00 0.00
#> TCGA.EX.A69L.01 1 0.0000 0.9972 1.00 0.00 0.00
#> TCGA.C5.A7CH.01 2 0.0000 0.9807 0.00 1.00 0.00
#> TCGA.FU.A2QG.01 1 0.0000 0.9972 1.00 0.00 0.00
#> TCGA.C5.A2M2.01 3 0.0000 1.0000 0.00 0.00 1.00
#> TCGA.JW.A5VG.01 1 0.0000 0.9972 1.00 0.00 0.00
#> TCGA.PN.A8MA.01 1 0.0000 0.9972 1.00 0.00 0.00
#> TCGA.DG.A2KM.01 1 0.0000 0.9972 1.00 0.00 0.00
#> TCGA.C5.A2LX.01 2 0.0000 0.9807 0.00 1.00 0.00
#> TCGA.EX.A3L1.01 1 0.0000 0.9972 1.00 0.00 0.00
#> TCGA.LP.A5U2.01 2 0.0000 0.9807 0.00 1.00 0.00
#> TCGA.FU.A3NI.01 2 0.0000 0.9807 0.00 1.00 0.00
#> TCGA.Q1.A5R3.01 1 0.0000 0.9972 1.00 0.00 0.00
#> TCGA.FU.A770.01 3 0.0000 1.0000 0.00 0.00 1.00
#> TCGA.C5.A7CM.01 1 0.0000 0.9972 1.00 0.00 0.00
#> TCGA.JX.A3Q0.01 1 0.0000 0.9972 1.00 0.00 0.00
#> TCGA.EA.A5FO.01 3 0.0000 1.0000 0.00 0.00 1.00
#> TCGA.VS.A9V3.01 2 0.0000 0.9807 0.00 1.00 0.00
#> TCGA.C5.A7CL.01 1 0.0000 0.9972 1.00 0.00 0.00
#> TCGA.VS.A959.01 1 0.0000 0.9972 1.00 0.00 0.00
#> TCGA.LP.A4AX.01 1 0.0000 0.9972 1.00 0.00 0.00
#> TCGA.C5.A1MN.01 2 0.0000 0.9807 0.00 1.00 0.00
#> TCGA.ZJ.AAXN.01 1 0.0000 0.9972 1.00 0.00 0.00
#> TCGA.MA.AA3X.01 1 0.0000 0.9972 1.00 0.00 0.00
#> TCGA.UC.A7PG.01 1 0.0000 0.9972 1.00 0.00 0.00
#> TCGA.Q1.A6DV.01 3 0.0000 1.0000 0.00 0.00 1.00
#> TCGA.DS.A1OD.01 1 0.0000 0.9972 1.00 0.00 0.00
#> TCGA.C5.A1M7.01 1 0.0000 0.9972 1.00 0.00 0.00
#> TCGA.BI.A20A.01 2 0.0000 0.9807 0.00 1.00 0.00
#> TCGA.VS.A9UO.01 3 0.0000 1.0000 0.00 0.00 1.00
#> TCGA.EA.A1QT.01 2 0.0000 0.9807 0.00 1.00 0.00
#> TCGA.EX.A69M.01 2 0.0000 0.9807 0.00 1.00 0.00
#> TCGA.VS.A9UH.01 1 0.0000 0.9972 1.00 0.00 0.00
#> TCGA.VS.A9U7.01 2 0.0000 0.9807 0.00 1.00 0.00
#> TCGA.ZJ.AAXD.01 1 0.0000 0.9972 1.00 0.00 0.00
#> TCGA.VS.A9UB.01 1 0.0000 0.9972 1.00 0.00 0.00
#> TCGA.EA.A410.01 1 0.0000 0.9972 1.00 0.00 0.00
#> TCGA.ZJ.AB0I.01 1 0.0000 0.9972 1.00 0.00 0.00
#> TCGA.VS.A9UD.01 2 0.0000 0.9807 0.00 1.00 0.00
#> TCGA.VS.A9U6.01 1 0.0000 0.9972 1.00 0.00 0.00
#> TCGA.ZX.AA5X.01 2 0.0000 0.9807 0.00 1.00 0.00
#> TCGA.C5.A0TN.01 1 0.0000 0.9972 1.00 0.00 0.00
#> TCGA.C5.A7CJ.01 2 0.0000 0.9807 0.00 1.00 0.00
#> TCGA.C5.A1MJ.01 3 0.0000 1.0000 0.00 0.00 1.00
#> TCGA.EA.A78R.01 2 0.0000 0.9807 0.00 1.00 0.00
#> TCGA.VS.A9UY.01 2 0.0000 0.9807 0.00 1.00 0.00
#> TCGA.VS.A9U5.01 2 0.1529 0.9434 0.00 0.96 0.04
#> TCGA.DS.A1OC.01 2 0.1529 0.9344 0.04 0.96 0.00
#> TCGA.ZJ.AAXB.01 1 0.0000 0.9972 1.00 0.00 0.00
#> TCGA.EX.A449.01 3 0.0000 1.0000 0.00 0.00 1.00
#> TCGA.C5.A1BL.01 2 0.0000 0.9807 0.00 1.00 0.00
#> TCGA.VS.A9UQ.01 3 0.0000 1.0000 0.00 0.00 1.00
#> TCGA.DS.A1OB.01 1 0.0000 0.9972 1.00 0.00 0.00
#> TCGA.HG.A9SC.01 1 0.0000 0.9972 1.00 0.00 0.00
#> TCGA.ZJ.AAXT.01 1 0.0000 0.9972 1.00 0.00 0.00
#> TCGA.IR.A3LB.01 3 0.0000 1.0000 0.00 0.00 1.00
#> TCGA.C5.A1ML.01 1 0.0000 0.9972 1.00 0.00 0.00
#> TCGA.VS.A9UV.01 2 0.3340 0.8556 0.00 0.88 0.12
#> TCGA.LP.A4AU.01 1 0.0000 0.9972 1.00 0.00 0.00
#> TCGA.Q1.A6DT.01 2 0.0000 0.9807 0.00 1.00 0.00
#> TCGA.C5.A1M8.01 2 0.0000 0.9807 0.00 1.00 0.00
#> TCGA.C5.A1ME.01 3 0.0000 1.0000 0.00 0.00 1.00
#> TCGA.ZJ.AAXU.01 1 0.0000 0.9972 1.00 0.00 0.00
#> TCGA.VS.A957.01 2 0.0000 0.9807 0.00 1.00 0.00
#> TCGA.VS.A9V5.01 3 0.0000 1.0000 0.00 0.00 1.00
#> TCGA.MU.A5YI.01 2 0.0000 0.9807 0.00 1.00 0.00
#> TCGA.ZJ.AAX4.01 2 0.0000 0.9807 0.00 1.00 0.00
#> TCGA.C5.A1MK.01 1 0.0000 0.9972 1.00 0.00 0.00
#> TCGA.JW.A69B.01 3 0.0000 1.0000 0.00 0.00 1.00
#> TCGA.VS.A958.01 1 0.0000 0.9972 1.00 0.00 0.00
#> TCGA.ZJ.AAXJ.01 2 0.0000 0.9807 0.00 1.00 0.00
#> TCGA.R2.A69V.01 1 0.0000 0.9972 1.00 0.00 0.00
#> TCGA.EA.A411.01 1 0.0000 0.9972 1.00 0.00 0.00
#> TCGA.VS.A9UP.01 1 0.0000 0.9972 1.00 0.00 0.00
#> TCGA.C5.A1MI.01 1 0.0000 0.9972 1.00 0.00 0.00
#> TCGA.DS.A1O9.01 2 0.0000 0.9807 0.00 1.00 0.00
#> TCGA.VS.A9UZ.01 3 0.0000 1.0000 0.00 0.00 1.00
#> TCGA.EA.A43B.01 2 0.0000 0.9807 0.00 1.00 0.00
#> TCGA.ZJ.AAX8.01 1 0.0000 0.9972 1.00 0.00 0.00
#> TCGA.ZJ.AAXI.01 2 0.0000 0.9807 0.00 1.00 0.00
#> TCGA.VS.A9UT.01 1 0.0000 0.9972 1.00 0.00 0.00
#> TCGA.DS.A1OA.01 2 0.0000 0.9807 0.00 1.00 0.00
#> TCGA.C5.A1MQ.01 2 0.0000 0.9807 0.00 1.00 0.00
#> TCGA.VS.A9V0.01 1 0.0000 0.9972 1.00 0.00 0.00
#> TCGA.VS.A9UC.01 2 0.0000 0.9807 0.00 1.00 0.00
#> TCGA.ZJ.AAXA.01 1 0.0000 0.9972 1.00 0.00 0.00
#> TCGA.Q1.A73P.01 3 0.0000 1.0000 0.00 0.00 1.00
#> TCGA.VS.A9V2.01 2 0.0000 0.9807 0.00 1.00 0.00
#> TCGA.VS.A9UU.01 2 0.0000 0.9807 0.00 1.00 0.00
#> TCGA.LP.A4AV.01 1 0.0000 0.9972 1.00 0.00 0.00
#> TCGA.VS.A9UR.01 3 0.0000 1.0000 0.00 0.00 1.00
#> TCGA.VS.A9V1.01 3 0.0000 1.0000 0.00 0.00 1.00
#> TCGA.C5.A7CG.01 2 0.0000 0.9807 0.00 1.00 0.00
#> TCGA.UC.A7PI.01 3 0.0000 1.0000 0.00 0.00 1.00
#> TCGA.EX.A1H5.01 2 0.0000 0.9807 0.00 1.00 0.00
#> TCGA.ZJ.AAXF.01 1 0.0000 0.9972 1.00 0.00 0.00
#> TCGA.VS.A9UL.01 3 0.0000 1.0000 0.00 0.00 1.00
#> TCGA.EA.A3Y4.01 1 0.0000 0.9972 1.00 0.00 0.00
#> TCGA.C5.A7CK.01 2 0.0000 0.9807 0.00 1.00 0.00
#> TCGA.UC.A7PG.06 1 0.0000 0.9972 1.00 0.00 0.00
#> TCGA.VS.A9UJ.01 1 0.0000 0.9972 1.00 0.00 0.00
#> TCGA.Q1.A73O.01 1 0.0000 0.9972 1.00 0.00 0.00
#> TCGA.VS.A950.01 2 0.0000 0.9807 0.00 1.00 0.00
#> TCGA.EA.A439.01 1 0.0000 0.9972 1.00 0.00 0.00
#> TCGA.VS.A9UM.01 1 0.0000 0.9972 1.00 0.00 0.00
#> TCGA.C5.A1MP.01 1 0.0000 0.9972 1.00 0.00 0.00
#> TCGA.VS.A9UI.01 2 0.0000 0.9807 0.00 1.00 0.00
#> TCGA.ZJ.AB0H.01 1 0.0000 0.9972 1.00 0.00 0.00
#> TCGA.Q1.A73Q.01 2 0.0000 0.9807 0.00 1.00 0.00
#> TCGA.C5.A1MH.01 2 0.5560 0.5498 0.30 0.70 0.00
#> TCGA.VS.A9V4.01 1 0.0000 0.9972 1.00 0.00 0.00
#> TCGA.FU.A40J.01 3 0.0000 1.0000 0.00 0.00 1.00
#> TCGA.VS.A9UA.01 1 0.0000 0.9972 1.00 0.00 0.00
#> TCGA.LP.A4AW.01 1 0.0000 0.9972 1.00 0.00 0.00
#> TCGA.MA.AA43.01 3 0.0000 1.0000 0.00 0.00 1.00
#> TCGA.C5.A1BN.01 1 0.0000 0.9972 1.00 0.00 0.00
#> TCGA.VS.AA62.01 1 0.0000 0.9972 1.00 0.00 0.00
#> TCGA.C5.A1BM.01 1 0.0000 0.9972 1.00 0.00 0.00
#> TCGA.C5.A1M6.01 1 0.1529 0.9517 0.96 0.04 0.00
#> TCGA.C5.A1BE.01 1 0.0000 0.9972 1.00 0.00 0.00
#> TCGA.FU.A23K.01 3 0.0000 1.0000 0.00 0.00 1.00
#> TCGA.C5.A1BJ.01 1 0.0000 0.9972 1.00 0.00 0.00
#> TCGA.FU.A23L.01 1 0.0000 0.9972 1.00 0.00 0.00
#> TCGA.C5.A1M5.01 2 0.0000 0.9807 0.00 1.00 0.00
#> TCGA.C5.A1MF.01 2 0.0000 0.9807 0.00 1.00 0.00
#> TCGA.C5.A1BF.01 1 0.0000 0.9972 1.00 0.00 0.00
#> TCGA.C5.A1BK.01 2 0.0000 0.9807 0.00 1.00 0.00
#> TCGA.C5.A1BI.01 1 0.0000 0.9972 1.00 0.00 0.00
#> TCGA.C5.A1M9.01 3 0.0000 1.0000 0.00 0.00 1.00
cbind(get_classes(res, k = 4), get_membership(res, k = 4))
#> class entropy silhouette p1 p2 p3 p4
#> TCGA.EK.A3GK.01 4 0.6554 0.08736 0.40 0.00 0.08 0.52
#> TCGA.GH.A9DA.01 1 0.4994 -0.06256 0.52 0.48 0.00 0.00
#> TCGA.VS.A94Y.01 1 0.0000 0.78741 1.00 0.00 0.00 0.00
#> TCGA.MY.A5BF.11 4 0.2011 0.86720 0.08 0.00 0.00 0.92
#> TCGA.VS.A94Z.01 1 0.0000 0.78741 1.00 0.00 0.00 0.00
#> TCGA.EA.A4BA.01 4 0.2011 0.86720 0.08 0.00 0.00 0.92
#> TCGA.ZJ.A8QQ.01 2 0.0000 0.90587 0.00 1.00 0.00 0.00
#> TCGA.FU.A3EO.11 4 0.2011 0.86720 0.08 0.00 0.00 0.92
#> TCGA.DG.A2KJ.01 4 0.2706 0.74627 0.02 0.00 0.08 0.90
#> TCGA.VS.A954.01 2 0.0000 0.90587 0.00 1.00 0.00 0.00
#> TCGA.MA.AA42.01 2 0.2011 0.89992 0.08 0.92 0.00 0.00
#> TCGA.C5.A8YQ.01 1 0.3975 0.58413 0.76 0.24 0.00 0.00
#> TCGA.DS.A7WF.01 3 0.2011 0.94367 0.00 0.08 0.92 0.00
#> TCGA.EK.A2R7.01 1 0.4907 0.13056 0.58 0.00 0.00 0.42
#> TCGA.EK.A3GJ.01 2 0.2011 0.89992 0.08 0.92 0.00 0.00
#> TCGA.C5.A902.01 2 0.0000 0.90587 0.00 1.00 0.00 0.00
#> TCGA.MA.AA3W.01 1 0.4977 0.00649 0.54 0.46 0.00 0.00
#> TCGA.C5.A905.01 1 0.2647 0.71735 0.88 0.00 0.00 0.12
#> TCGA.EK.A2RN.01 1 0.0000 0.78741 1.00 0.00 0.00 0.00
#> TCGA.FU.A57G.01 4 0.2011 0.86720 0.08 0.00 0.00 0.92
#> TCGA.C5.A8YR.01 4 0.2647 0.85510 0.12 0.00 0.00 0.88
#> TCGA.EK.A2R9.01 2 0.4994 0.20006 0.48 0.52 0.00 0.00
#> TCGA.FU.A3EO.01 3 0.2011 0.94367 0.00 0.08 0.92 0.00
#> TCGA.IR.A3LC.01 2 0.1211 0.87168 0.00 0.96 0.04 0.00
#> TCGA.VS.A8QA.01 3 0.2011 0.94367 0.00 0.08 0.92 0.00
#> TCGA.C5.A3HD.01 2 0.2921 0.86857 0.14 0.86 0.00 0.00
#> TCGA.MY.A5BE.01 1 0.6336 0.08036 0.48 0.00 0.06 0.46
#> TCGA.EA.A50E.01 2 0.0000 0.90587 0.00 1.00 0.00 0.00
#> TCGA.VS.A8QH.01 4 0.2706 0.74627 0.02 0.00 0.08 0.90
#> TCGA.ZJ.A8QR.01 1 0.0707 0.78269 0.98 0.02 0.00 0.00
#> TCGA.C5.A907.01 4 0.2011 0.75590 0.00 0.00 0.08 0.92
#> TCGA.IR.A3LK.01 1 0.2011 0.75791 0.92 0.08 0.00 0.00
#> TCGA.C5.A8ZZ.01 1 0.1637 0.75738 0.94 0.00 0.00 0.06
#> TCGA.VS.A8EK.01 2 0.0000 0.90587 0.00 1.00 0.00 0.00
#> TCGA.C5.A7UC.01 4 0.4948 0.33974 0.44 0.00 0.00 0.56
#> TCGA.C5.A8XJ.01 1 0.2345 0.73164 0.90 0.00 0.00 0.10
#> TCGA.IR.A3LH.01 2 0.3247 0.88165 0.06 0.88 0.06 0.00
#> TCGA.EK.A3GM.01 4 0.2706 0.74627 0.02 0.00 0.08 0.90
#> TCGA.VS.A8Q8.01 1 0.4522 0.41005 0.68 0.00 0.00 0.32
#> TCGA.EK.A2RO.01 2 0.3801 0.78254 0.22 0.78 0.00 0.00
#> TCGA.MY.A5BD.01 3 0.2011 0.94367 0.00 0.08 0.92 0.00
#> TCGA.2W.A8YY.01 4 0.2706 0.74627 0.02 0.00 0.08 0.90
#> TCGA.C5.A2LZ.01 2 0.2921 0.86877 0.14 0.86 0.00 0.00
#> TCGA.C5.A901.01 2 0.0000 0.90587 0.00 1.00 0.00 0.00
#> TCGA.VS.A953.01 2 0.0000 0.90587 0.00 1.00 0.00 0.00
#> TCGA.MU.A51Y.01 1 0.0000 0.78741 1.00 0.00 0.00 0.00
#> TCGA.EK.A2RK.01 1 0.4907 0.12025 0.58 0.00 0.00 0.42
#> TCGA.UC.A7PD.01 4 0.2647 0.85510 0.12 0.00 0.00 0.88
#> TCGA.EA.A3HS.01 1 0.2011 0.75791 0.92 0.08 0.00 0.00
#> TCGA.VS.A8QM.01 4 0.3172 0.82560 0.16 0.00 0.00 0.84
#> TCGA.EA.A3HU.01 1 0.0000 0.78741 1.00 0.00 0.00 0.00
#> TCGA.VS.A94X.01 4 0.2011 0.86720 0.08 0.00 0.00 0.92
#> TCGA.C5.A7CO.01 2 0.2647 0.88216 0.12 0.88 0.00 0.00
#> TCGA.C5.A3HF.01 4 0.2706 0.74627 0.02 0.00 0.08 0.90
#> TCGA.IR.A3LL.01 1 0.4948 0.08464 0.56 0.44 0.00 0.00
#> TCGA.MY.A913.01 4 0.0000 0.81454 0.00 0.00 0.00 1.00
#> TCGA.VS.A952.01 3 0.2011 0.94367 0.00 0.08 0.92 0.00
#> TCGA.IR.A3LI.01 3 0.2011 0.94367 0.00 0.08 0.92 0.00
#> TCGA.VS.A94W.01 1 0.3610 0.64332 0.80 0.20 0.00 0.00
#> TCGA.MY.A5BF.01 2 0.0000 0.90587 0.00 1.00 0.00 0.00
#> TCGA.EK.A2RC.01 1 0.2011 0.75791 0.92 0.08 0.00 0.00
#> TCGA.VS.A8EL.01 2 0.0707 0.90680 0.02 0.98 0.00 0.00
#> TCGA.EA.A97N.01 1 0.3172 0.68017 0.84 0.00 0.00 0.16
#> TCGA.EA.A3HQ.01 2 0.0000 0.90587 0.00 1.00 0.00 0.00
#> TCGA.EK.A2RD.01 1 0.0000 0.78741 1.00 0.00 0.00 0.00
#> TCGA.C5.A8YT.01 4 0.2011 0.86720 0.08 0.00 0.00 0.92
#> TCGA.FU.A3HZ.01 4 0.2011 0.86720 0.08 0.00 0.00 0.92
#> TCGA.VS.A8EJ.01 4 0.2011 0.86720 0.08 0.00 0.00 0.92
#> TCGA.C5.A3HL.01 4 0.2647 0.85510 0.12 0.00 0.00 0.88
#> TCGA.UC.A7PF.01 1 0.4855 0.23175 0.60 0.40 0.00 0.00
#> TCGA.C5.A8XK.01 1 0.6262 0.24846 0.54 0.00 0.06 0.40
#> TCGA.EX.A8YF.01 4 0.0000 0.81454 0.00 0.00 0.00 1.00
#> TCGA.HM.A4S6.01 1 0.0000 0.78741 1.00 0.00 0.00 0.00
#> TCGA.VS.A8Q9.01 2 0.3172 0.85099 0.16 0.84 0.00 0.00
#> TCGA.MA.AA41.01 2 0.2011 0.89992 0.08 0.92 0.00 0.00
#> TCGA.EK.A3GN.01 2 0.0000 0.90587 0.00 1.00 0.00 0.00
#> TCGA.MA.AA3Y.01 4 0.3172 0.82560 0.16 0.00 0.00 0.84
#> TCGA.MA.AA3Z.01 1 0.0000 0.78741 1.00 0.00 0.00 0.00
#> TCGA.EK.A2RE.01 1 0.5000 -0.17415 0.50 0.00 0.00 0.50
#> TCGA.C5.A1BQ.01 1 0.0000 0.78741 1.00 0.00 0.00 0.00
#> TCGA.ZJ.A8QO.01 2 0.2921 0.86857 0.14 0.86 0.00 0.00
#> TCGA.JW.A852.01 2 0.0000 0.90587 0.00 1.00 0.00 0.00
#> TCGA.DS.A7WH.01 3 0.0000 0.91574 0.00 0.00 1.00 0.00
#> TCGA.JW.AAVH.01 1 0.4790 0.27948 0.62 0.38 0.00 0.00
#> TCGA.EA.A556.01 4 0.2011 0.86720 0.08 0.00 0.00 0.92
#> TCGA.EA.A44S.01 1 0.2011 0.74422 0.92 0.00 0.00 0.08
#> TCGA.4J.AA1J.01 1 0.2647 0.71735 0.88 0.00 0.00 0.12
#> TCGA.IR.A3L7.01 2 0.0000 0.90587 0.00 1.00 0.00 0.00
#> TCGA.C5.A7X3.01 4 0.2011 0.86720 0.08 0.00 0.00 0.92
#> TCGA.HG.A2PA.01 1 0.0707 0.78079 0.98 0.00 0.00 0.02
#> TCGA.C5.A8XH.01 2 0.2921 0.86857 0.14 0.86 0.00 0.00
#> TCGA.C5.A7XC.01 1 0.3172 0.68017 0.84 0.00 0.00 0.16
#> TCGA.VS.A8EI.01 2 0.4977 0.25830 0.46 0.54 0.00 0.00
#> TCGA.VS.A8QC.01 2 0.0000 0.90587 0.00 1.00 0.00 0.00
#> TCGA.C5.A7UH.01 1 0.3172 0.68017 0.84 0.00 0.00 0.16
#> TCGA.WL.A834.01 2 0.0000 0.90587 0.00 1.00 0.00 0.00
#> TCGA.C5.A8XI.01 2 0.0000 0.90587 0.00 1.00 0.00 0.00
#> TCGA.DS.A7WI.01 1 0.4624 0.38560 0.66 0.34 0.00 0.00
#> TCGA.VS.A8QF.01 2 0.0000 0.90587 0.00 1.00 0.00 0.00
#> TCGA.EA.A3HR.01 1 0.3975 0.56900 0.76 0.00 0.00 0.24
#> TCGA.DG.A2KL.01 1 0.0000 0.78741 1.00 0.00 0.00 0.00
#> TCGA.EK.A2RL.01 3 0.2011 0.94367 0.00 0.08 0.92 0.00
#> TCGA.EK.A2PG.01 2 0.0000 0.90587 0.00 1.00 0.00 0.00
#> TCGA.BI.A0VR.01 1 0.0000 0.78741 1.00 0.00 0.00 0.00
#> TCGA.DS.A0VL.01 1 0.0000 0.78741 1.00 0.00 0.00 0.00
#> TCGA.VS.A8EC.01 2 0.0000 0.90587 0.00 1.00 0.00 0.00
#> TCGA.EA.A3QE.01 2 0.3172 0.85099 0.16 0.84 0.00 0.00
#> TCGA.DS.A0VM.01 2 0.2011 0.89992 0.08 0.92 0.00 0.00
#> TCGA.FU.A3HY.01 1 0.2647 0.73192 0.88 0.12 0.00 0.00
#> TCGA.Q1.A5R1.01 3 0.2011 0.94367 0.00 0.08 0.92 0.00
#> TCGA.DR.A0ZM.01 4 0.4948 0.33386 0.44 0.00 0.00 0.56
#> TCGA.Q1.A6DW.01 2 0.0000 0.90587 0.00 1.00 0.00 0.00
#> TCGA.DS.A0VK.01 1 0.0000 0.78741 1.00 0.00 0.00 0.00
#> TCGA.DS.A3LQ.01 1 0.4907 0.15366 0.58 0.42 0.00 0.00
#> TCGA.EA.A3QD.01 2 0.0000 0.90587 0.00 1.00 0.00 0.00
#> TCGA.JW.A5VJ.01 4 0.4713 0.51994 0.36 0.00 0.00 0.64
#> TCGA.LP.A5U3.01 2 0.0000 0.90587 0.00 1.00 0.00 0.00
#> TCGA.EA.A6QX.01 2 0.2647 0.88151 0.12 0.88 0.00 0.00
#> TCGA.EK.A2RA.01 2 0.0000 0.90587 0.00 1.00 0.00 0.00
#> TCGA.FU.A5XV.01 1 0.0000 0.78741 1.00 0.00 0.00 0.00
#> TCGA.Q1.A5R2.01 2 0.2011 0.89992 0.08 0.92 0.00 0.00
#> TCGA.HM.A3JJ.01 1 0.0000 0.78741 1.00 0.00 0.00 0.00
#> TCGA.C5.A2LS.01 3 0.1637 0.93851 0.00 0.06 0.94 0.00
#> TCGA.C5.A7X8.01 3 0.2011 0.88244 0.00 0.00 0.92 0.08
#> TCGA.EK.A2RJ.01 4 0.2011 0.86720 0.08 0.00 0.00 0.92
#> TCGA.EA.A3HT.01 1 0.3172 0.68017 0.84 0.00 0.00 0.16
#> TCGA.LP.A7HU.01 3 0.2011 0.94367 0.00 0.08 0.92 0.00
#> TCGA.MU.A8JM.01 1 0.2345 0.74691 0.90 0.10 0.00 0.00
#> TCGA.EK.A2IP.01 1 0.1637 0.76804 0.94 0.06 0.00 0.00
#> TCGA.JW.A5VL.01 2 0.2345 0.89257 0.10 0.90 0.00 0.00
#> TCGA.FU.A3TX.01 1 0.4277 0.49864 0.72 0.00 0.00 0.28
#> TCGA.DG.A2KK.01 3 0.2011 0.94367 0.00 0.08 0.92 0.00
#> TCGA.EK.A2PI.01 1 0.0000 0.78741 1.00 0.00 0.00 0.00
#> TCGA.Q1.A73S.01 4 0.2011 0.86720 0.08 0.00 0.00 0.92
#> TCGA.EK.A2IR.01 1 0.3610 0.64561 0.80 0.20 0.00 0.00
#> TCGA.HM.A6W2.01 4 0.2011 0.86720 0.08 0.00 0.00 0.92
#> TCGA.VS.A8EH.01 1 0.5957 0.23233 0.54 0.00 0.04 0.42
#> TCGA.JW.A5VH.01 4 0.2011 0.86720 0.08 0.00 0.00 0.92
#> TCGA.C5.A2LV.01 2 0.0000 0.90587 0.00 1.00 0.00 0.00
#> TCGA.VS.A8EB.01 1 0.1211 0.77617 0.96 0.04 0.00 0.00
#> TCGA.RA.A741.01 1 0.4624 0.36650 0.66 0.00 0.00 0.34
#> TCGA.VS.A8EG.01 2 0.2647 0.88216 0.12 0.88 0.00 0.00
#> TCGA.DG.A2KH.01 4 0.2011 0.75590 0.00 0.00 0.08 0.92
#> TCGA.C5.A7UE.01 2 0.3801 0.78254 0.22 0.78 0.00 0.00
#> TCGA.C5.A2LT.01 4 0.3610 0.79466 0.20 0.00 0.00 0.80
#> TCGA.EA.A5ZD.01 1 0.5000 -0.17415 0.50 0.00 0.00 0.50
#> TCGA.Q1.A73R.01 3 0.2011 0.94367 0.00 0.08 0.92 0.00
#> TCGA.JW.A5VK.01 2 0.2011 0.89992 0.08 0.92 0.00 0.00
#> TCGA.EK.A2RM.01 4 0.2011 0.75590 0.00 0.00 0.08 0.92
#> TCGA.C5.A7UI.01 1 0.0707 0.78269 0.98 0.02 0.00 0.00
#> TCGA.EK.A2PL.01 1 0.1211 0.76854 0.96 0.00 0.00 0.04
#> TCGA.EK.A2PM.01 4 0.3172 0.82552 0.16 0.00 0.00 0.84
#> TCGA.EK.A2GZ.01 1 0.1637 0.76081 0.94 0.00 0.00 0.06
#> TCGA.HM.A3JK.01 1 0.0000 0.78741 1.00 0.00 0.00 0.00
#> TCGA.C5.A2M1.01 3 0.2011 0.94367 0.00 0.08 0.92 0.00
#> TCGA.HM.A6W2.06 4 0.2011 0.86720 0.08 0.00 0.00 0.92
#> TCGA.C5.A7X5.01 2 0.0000 0.90587 0.00 1.00 0.00 0.00
#> TCGA.IR.A3LA.01 4 0.2011 0.86720 0.08 0.00 0.00 0.92
#> TCGA.EK.A2PK.01 4 0.0000 0.81454 0.00 0.00 0.00 1.00
#> TCGA.EA.A5ZF.01 4 0.2011 0.86720 0.08 0.00 0.00 0.92
#> TCGA.XS.A8TJ.01 1 0.1211 0.77617 0.96 0.04 0.00 0.00
#> TCGA.BI.A0VS.01 1 0.3610 0.63324 0.80 0.00 0.00 0.20
#> TCGA.DS.A0VN.01 1 0.1637 0.76793 0.94 0.06 0.00 0.00
#> TCGA.JX.A5QV.01 1 0.3975 0.57330 0.76 0.00 0.00 0.24
#> TCGA.EK.A2R8.01 4 0.2011 0.86720 0.08 0.00 0.00 0.92
#> TCGA.EA.A1QS.01 4 0.2647 0.85510 0.12 0.00 0.00 0.88
#> TCGA.C5.A3HE.01 3 0.4790 0.45809 0.00 0.00 0.62 0.38
#> TCGA.IR.A3LF.01 3 0.2011 0.94367 0.00 0.08 0.92 0.00
#> TCGA.DR.A0ZL.01 1 0.2011 0.75791 0.92 0.08 0.00 0.00
#> TCGA.FU.A3WB.01 2 0.2921 0.86857 0.14 0.86 0.00 0.00
#> TCGA.JX.A3PZ.01 4 0.2921 0.84135 0.14 0.00 0.00 0.86
#> TCGA.EA.A5O9.01 2 0.2011 0.89992 0.08 0.92 0.00 0.00
#> TCGA.HM.A3JJ.11 4 0.2011 0.86720 0.08 0.00 0.00 0.92
#> TCGA.DS.A5RQ.01 1 0.0000 0.78741 1.00 0.00 0.00 0.00
#> TCGA.EK.A2H0.01 2 0.0000 0.90587 0.00 1.00 0.00 0.00
#> TCGA.EX.A1H6.01 3 0.0000 0.91574 0.00 0.00 1.00 0.00
#> TCGA.EA.A5ZE.01 2 0.2011 0.89992 0.08 0.92 0.00 0.00
#> TCGA.C5.A2LY.01 1 0.0000 0.78741 1.00 0.00 0.00 0.00
#> TCGA.FU.A3TQ.01 1 0.2011 0.75791 0.92 0.08 0.00 0.00
#> TCGA.EK.A2RB.01 2 0.2011 0.89992 0.08 0.92 0.00 0.00
#> TCGA.JW.A5VI.01 1 0.2011 0.75791 0.92 0.08 0.00 0.00
#> TCGA.EK.A2H1.01 4 0.2011 0.86720 0.08 0.00 0.00 0.92
#> TCGA.JX.A3Q8.01 3 0.2011 0.94367 0.00 0.08 0.92 0.00
#> TCGA.FU.A3YQ.01 1 0.4522 0.43116 0.68 0.32 0.00 0.00
#> TCGA.EX.A69L.01 1 0.0000 0.78741 1.00 0.00 0.00 0.00
#> TCGA.C5.A7CH.01 2 0.1211 0.90597 0.04 0.96 0.00 0.00
#> TCGA.FU.A2QG.01 1 0.3172 0.68017 0.84 0.00 0.00 0.16
#> TCGA.C5.A2M2.01 3 0.2011 0.94367 0.00 0.08 0.92 0.00
#> TCGA.JW.A5VG.01 4 0.2647 0.85510 0.12 0.00 0.00 0.88
#> TCGA.PN.A8MA.01 4 0.3975 0.72566 0.24 0.00 0.00 0.76
#> TCGA.DG.A2KM.01 4 0.2647 0.85510 0.12 0.00 0.00 0.88
#> TCGA.C5.A2LX.01 2 0.0000 0.90587 0.00 1.00 0.00 0.00
#> TCGA.EX.A3L1.01 4 0.2011 0.86720 0.08 0.00 0.00 0.92
#> TCGA.LP.A5U2.01 2 0.0000 0.90587 0.00 1.00 0.00 0.00
#> TCGA.FU.A3NI.01 2 0.0707 0.90680 0.02 0.98 0.00 0.00
#> TCGA.Q1.A5R3.01 1 0.2921 0.69999 0.86 0.00 0.00 0.14
#> TCGA.FU.A770.01 3 0.2011 0.88244 0.00 0.00 0.92 0.08
#> TCGA.C5.A7CM.01 4 0.2706 0.74627 0.02 0.00 0.08 0.90
#> TCGA.JX.A3Q0.01 1 0.3172 0.68017 0.84 0.00 0.00 0.16
#> TCGA.EA.A5FO.01 3 0.2011 0.94367 0.00 0.08 0.92 0.00
#> TCGA.VS.A9V3.01 2 0.0000 0.90587 0.00 1.00 0.00 0.00
#> TCGA.C5.A7CL.01 1 0.0000 0.78741 1.00 0.00 0.00 0.00
#> TCGA.VS.A959.01 4 0.6605 -0.01456 0.44 0.00 0.08 0.48
#> TCGA.LP.A4AX.01 1 0.6336 0.08036 0.48 0.00 0.06 0.46
#> TCGA.C5.A1MN.01 2 0.1211 0.90597 0.04 0.96 0.00 0.00
#> TCGA.ZJ.AAXN.01 4 0.2647 0.85510 0.12 0.00 0.00 0.88
#> TCGA.MA.AA3X.01 1 0.3610 0.62915 0.80 0.00 0.00 0.20
#> TCGA.UC.A7PG.01 1 0.0000 0.78741 1.00 0.00 0.00 0.00
#> TCGA.Q1.A6DV.01 3 0.2011 0.88244 0.00 0.00 0.92 0.08
#> TCGA.DS.A1OD.01 1 0.0000 0.78741 1.00 0.00 0.00 0.00
#> TCGA.C5.A1M7.01 1 0.3172 0.68017 0.84 0.00 0.00 0.16
#> TCGA.BI.A20A.01 2 0.3172 0.85099 0.16 0.84 0.00 0.00
#> TCGA.VS.A9UO.01 3 0.0000 0.91574 0.00 0.00 1.00 0.00
#> TCGA.EA.A1QT.01 2 0.2345 0.89257 0.10 0.90 0.00 0.00
#> TCGA.EX.A69M.01 2 0.0000 0.90587 0.00 1.00 0.00 0.00
#> TCGA.VS.A9UH.01 1 0.5570 0.20434 0.54 0.00 0.02 0.44
#> TCGA.VS.A9U7.01 2 0.0000 0.90587 0.00 1.00 0.00 0.00
#> TCGA.ZJ.AAXD.01 1 0.0707 0.77908 0.98 0.00 0.00 0.02
#> TCGA.VS.A9UB.01 4 0.3247 0.77663 0.06 0.00 0.06 0.88
#> TCGA.EA.A410.01 4 0.2011 0.86720 0.08 0.00 0.00 0.92
#> TCGA.ZJ.AB0I.01 1 0.5000 -0.17415 0.50 0.00 0.00 0.50
#> TCGA.VS.A9UD.01 2 0.3611 0.87218 0.08 0.86 0.06 0.00
#> TCGA.VS.A9U6.01 1 0.0000 0.78741 1.00 0.00 0.00 0.00
#> TCGA.ZX.AA5X.01 1 0.5000 -0.14677 0.50 0.50 0.00 0.00
#> TCGA.C5.A0TN.01 4 0.2647 0.85510 0.12 0.00 0.00 0.88
#> TCGA.C5.A7CJ.01 1 0.2011 0.75791 0.92 0.08 0.00 0.00
#> TCGA.C5.A1MJ.01 3 0.2011 0.88244 0.00 0.00 0.92 0.08
#> TCGA.EA.A78R.01 2 0.3611 0.87218 0.08 0.86 0.06 0.00
#> TCGA.VS.A9UY.01 2 0.0000 0.90587 0.00 1.00 0.00 0.00
#> TCGA.VS.A9U5.01 2 0.0000 0.90587 0.00 1.00 0.00 0.00
#> TCGA.DS.A1OC.01 1 0.3801 0.61540 0.78 0.22 0.00 0.00
#> TCGA.ZJ.AAXB.01 4 0.2921 0.83316 0.14 0.00 0.00 0.86
#> TCGA.EX.A449.01 3 0.2011 0.94367 0.00 0.08 0.92 0.00
#> TCGA.C5.A1BL.01 2 0.2011 0.89992 0.08 0.92 0.00 0.00
#> TCGA.VS.A9UQ.01 3 0.1637 0.93851 0.00 0.06 0.94 0.00
#> TCGA.DS.A1OB.01 1 0.3172 0.68017 0.84 0.00 0.00 0.16
#> TCGA.HG.A9SC.01 1 0.4994 -0.10800 0.52 0.00 0.00 0.48
#> TCGA.ZJ.AAXT.01 4 0.3172 0.82560 0.16 0.00 0.00 0.84
#> TCGA.IR.A3LB.01 3 0.0000 0.91574 0.00 0.00 1.00 0.00
#> TCGA.C5.A1ML.01 4 0.2345 0.86218 0.10 0.00 0.00 0.90
#> TCGA.VS.A9UV.01 2 0.1637 0.85109 0.00 0.94 0.06 0.00
#> TCGA.LP.A4AU.01 4 0.2011 0.86720 0.08 0.00 0.00 0.92
#> TCGA.Q1.A6DT.01 2 0.2011 0.89992 0.08 0.92 0.00 0.00
#> TCGA.C5.A1M8.01 2 0.0000 0.90587 0.00 1.00 0.00 0.00
#> TCGA.C5.A1ME.01 3 0.0000 0.91574 0.00 0.00 1.00 0.00
#> TCGA.ZJ.AAXU.01 1 0.0000 0.78741 1.00 0.00 0.00 0.00
#> TCGA.VS.A957.01 2 0.4277 0.69464 0.28 0.72 0.00 0.00
#> TCGA.VS.A9V5.01 3 0.2011 0.94367 0.00 0.08 0.92 0.00
#> TCGA.MU.A5YI.01 2 0.4277 0.69128 0.28 0.72 0.00 0.00
#> TCGA.ZJ.AAX4.01 2 0.2011 0.89992 0.08 0.92 0.00 0.00
#> TCGA.C5.A1MK.01 1 0.3172 0.68017 0.84 0.00 0.00 0.16
#> TCGA.JW.A69B.01 3 0.2011 0.94367 0.00 0.08 0.92 0.00
#> TCGA.VS.A958.01 4 0.4994 0.22246 0.48 0.00 0.00 0.52
#> TCGA.ZJ.AAXJ.01 2 0.0000 0.90587 0.00 1.00 0.00 0.00
#> TCGA.R2.A69V.01 4 0.2647 0.85510 0.12 0.00 0.00 0.88
#> TCGA.EA.A411.01 1 0.3172 0.68017 0.84 0.00 0.00 0.16
#> TCGA.VS.A9UP.01 4 0.2011 0.86720 0.08 0.00 0.00 0.92
#> TCGA.C5.A1MI.01 4 0.0707 0.80149 0.00 0.00 0.02 0.98
#> TCGA.DS.A1O9.01 2 0.3801 0.78313 0.22 0.78 0.00 0.00
#> TCGA.VS.A9UZ.01 3 0.2011 0.94367 0.00 0.08 0.92 0.00
#> TCGA.EA.A43B.01 2 0.5841 0.78812 0.10 0.76 0.06 0.08
#> TCGA.ZJ.AAX8.01 4 0.3172 0.82560 0.16 0.00 0.00 0.84
#> TCGA.ZJ.AAXI.01 2 0.0000 0.90587 0.00 1.00 0.00 0.00
#> TCGA.VS.A9UT.01 4 0.2011 0.86720 0.08 0.00 0.00 0.92
#> TCGA.DS.A1OA.01 1 0.2345 0.74677 0.90 0.10 0.00 0.00
#> TCGA.C5.A1MQ.01 2 0.4292 0.78817 0.00 0.82 0.10 0.08
#> TCGA.VS.A9V0.01 4 0.2011 0.86720 0.08 0.00 0.00 0.92
#> TCGA.VS.A9UC.01 1 0.2011 0.75791 0.92 0.08 0.00 0.00
#> TCGA.ZJ.AAXA.01 1 0.4994 -0.10800 0.52 0.00 0.00 0.48
#> TCGA.Q1.A73P.01 3 0.2011 0.94367 0.00 0.08 0.92 0.00
#> TCGA.VS.A9V2.01 2 0.2921 0.86857 0.14 0.86 0.00 0.00
#> TCGA.VS.A9UU.01 2 0.0707 0.90680 0.02 0.98 0.00 0.00
#> TCGA.LP.A4AV.01 1 0.2921 0.69988 0.86 0.00 0.00 0.14
#> TCGA.VS.A9UR.01 3 0.0707 0.92452 0.00 0.02 0.98 0.00
#> TCGA.VS.A9V1.01 3 0.4907 0.37645 0.00 0.00 0.58 0.42
#> TCGA.C5.A7CG.01 2 0.0000 0.90587 0.00 1.00 0.00 0.00
#> TCGA.UC.A7PI.01 3 0.2011 0.94367 0.00 0.08 0.92 0.00
#> TCGA.EX.A1H5.01 1 0.4977 0.00767 0.54 0.46 0.00 0.00
#> TCGA.ZJ.AAXF.01 1 0.2345 0.73338 0.90 0.00 0.00 0.10
#> TCGA.VS.A9UL.01 3 0.2011 0.88244 0.00 0.00 0.92 0.08
#> TCGA.EA.A3Y4.01 4 0.4855 0.43480 0.40 0.00 0.00 0.60
#> TCGA.C5.A7CK.01 2 0.0000 0.90587 0.00 1.00 0.00 0.00
#> TCGA.UC.A7PG.06 1 0.0000 0.78741 1.00 0.00 0.00 0.00
#> TCGA.VS.A9UJ.01 4 0.2011 0.86720 0.08 0.00 0.00 0.92
#> TCGA.Q1.A73O.01 4 0.4977 0.28311 0.46 0.00 0.00 0.54
#> TCGA.VS.A950.01 2 0.4855 0.43551 0.40 0.60 0.00 0.00
#> TCGA.EA.A439.01 4 0.4292 0.67710 0.10 0.00 0.08 0.82
#> TCGA.VS.A9UM.01 1 0.0000 0.78741 1.00 0.00 0.00 0.00
#> TCGA.C5.A1MP.01 1 0.3172 0.68017 0.84 0.00 0.00 0.16
#> TCGA.VS.A9UI.01 1 0.3172 0.68917 0.84 0.16 0.00 0.00
#> TCGA.ZJ.AB0H.01 1 0.0000 0.78741 1.00 0.00 0.00 0.00
#> TCGA.Q1.A73Q.01 1 0.3610 0.64015 0.80 0.20 0.00 0.00
#> TCGA.C5.A1MH.01 1 0.1637 0.76793 0.94 0.06 0.00 0.00
#> TCGA.VS.A9V4.01 4 0.2011 0.86720 0.08 0.00 0.00 0.92
#> TCGA.FU.A40J.01 3 0.2011 0.94367 0.00 0.08 0.92 0.00
#> TCGA.VS.A9UA.01 1 0.0000 0.78741 1.00 0.00 0.00 0.00
#> TCGA.LP.A4AW.01 1 0.0000 0.78741 1.00 0.00 0.00 0.00
#> TCGA.MA.AA43.01 3 0.2011 0.88244 0.00 0.00 0.92 0.08
#> TCGA.C5.A1BN.01 1 0.4948 0.04432 0.56 0.00 0.00 0.44
#> TCGA.VS.AA62.01 4 0.2647 0.85510 0.12 0.00 0.00 0.88
#> TCGA.C5.A1BM.01 4 0.4994 0.22246 0.48 0.00 0.00 0.52
#> TCGA.C5.A1M6.01 4 0.6586 0.03207 0.42 0.00 0.08 0.50
#> TCGA.C5.A1BE.01 1 0.0000 0.78741 1.00 0.00 0.00 0.00
#> TCGA.FU.A23K.01 3 0.2011 0.88244 0.00 0.00 0.92 0.08
#> TCGA.C5.A1BJ.01 1 0.0000 0.78741 1.00 0.00 0.00 0.00
#> TCGA.FU.A23L.01 4 0.2345 0.86218 0.10 0.00 0.00 0.90
#> TCGA.C5.A1M5.01 2 0.1637 0.90374 0.06 0.94 0.00 0.00
#> TCGA.C5.A1MF.01 2 0.4277 0.69464 0.28 0.72 0.00 0.00
#> TCGA.C5.A1BF.01 4 0.2647 0.85510 0.12 0.00 0.00 0.88
#> TCGA.C5.A1BK.01 2 0.2345 0.89242 0.10 0.90 0.00 0.00
#> TCGA.C5.A1BI.01 4 0.5000 0.15539 0.50 0.00 0.00 0.50
#> TCGA.C5.A1M9.01 3 0.2011 0.94367 0.00 0.08 0.92 0.00
cbind(get_classes(res, k = 5), get_membership(res, k = 5))
#> class entropy silhouette p1 p2 p3 p4 p5
#> TCGA.EK.A3GK.01 5 0.1732 0.537595 0.00 0.00 0.00 0.08 0.92
#> TCGA.GH.A9DA.01 5 0.5579 0.424345 0.30 0.10 0.00 0.00 0.60
#> TCGA.VS.A94Y.01 1 0.3424 0.565953 0.76 0.00 0.00 0.00 0.24
#> TCGA.MY.A5BF.11 4 0.0609 0.775500 0.00 0.00 0.00 0.98 0.02
#> TCGA.VS.A94Z.01 1 0.0609 0.791019 0.98 0.00 0.00 0.00 0.02
#> TCGA.EA.A4BA.01 4 0.1410 0.766294 0.00 0.00 0.00 0.94 0.06
#> TCGA.ZJ.A8QQ.01 2 0.2280 0.818933 0.00 0.88 0.00 0.00 0.12
#> TCGA.FU.A3EO.11 4 0.0609 0.775500 0.00 0.00 0.00 0.98 0.02
#> TCGA.DG.A2KJ.01 5 0.3796 0.330765 0.00 0.00 0.00 0.30 0.70
#> TCGA.VS.A954.01 2 0.1043 0.850812 0.00 0.96 0.00 0.00 0.04
#> TCGA.MA.AA42.01 2 0.2929 0.772838 0.00 0.82 0.00 0.00 0.18
#> TCGA.C5.A8YQ.01 5 0.5607 0.352599 0.38 0.08 0.00 0.00 0.54
#> TCGA.DS.A7WF.01 3 0.0000 0.941552 0.00 0.00 1.00 0.00 0.00
#> TCGA.EK.A2R7.01 1 0.4540 0.340967 0.64 0.00 0.00 0.34 0.02
#> TCGA.EK.A3GJ.01 2 0.2280 0.818933 0.00 0.88 0.00 0.00 0.12
#> TCGA.C5.A902.01 2 0.1043 0.850812 0.00 0.96 0.00 0.00 0.04
#> TCGA.MA.AA3W.01 1 0.5854 0.270180 0.60 0.16 0.00 0.00 0.24
#> TCGA.C5.A905.01 1 0.1043 0.798739 0.96 0.00 0.00 0.04 0.00
#> TCGA.EK.A2RN.01 1 0.0609 0.800815 0.98 0.00 0.00 0.02 0.00
#> TCGA.FU.A57G.01 4 0.1410 0.766294 0.00 0.00 0.00 0.94 0.06
#> TCGA.C5.A8YR.01 4 0.3109 0.715497 0.00 0.00 0.00 0.80 0.20
#> TCGA.EK.A2R9.01 1 0.5558 0.228586 0.56 0.36 0.00 0.00 0.08
#> TCGA.FU.A3EO.01 3 0.0000 0.941552 0.00 0.00 1.00 0.00 0.00
#> TCGA.IR.A3LC.01 2 0.1648 0.847689 0.00 0.94 0.02 0.00 0.04
#> TCGA.VS.A8QA.01 3 0.0000 0.941552 0.00 0.00 1.00 0.00 0.00
#> TCGA.C5.A3HD.01 2 0.4227 0.448134 0.00 0.58 0.00 0.00 0.42
#> TCGA.MY.A5BE.01 5 0.3034 0.571021 0.06 0.02 0.00 0.04 0.88
#> TCGA.EA.A50E.01 2 0.1043 0.850812 0.00 0.96 0.00 0.00 0.04
#> TCGA.VS.A8QH.01 5 0.3796 0.330765 0.00 0.00 0.00 0.30 0.70
#> TCGA.ZJ.A8QR.01 1 0.0609 0.794757 0.98 0.00 0.00 0.00 0.02
#> TCGA.C5.A907.01 5 0.4060 0.198076 0.00 0.00 0.00 0.36 0.64
#> TCGA.IR.A3LK.01 1 0.1648 0.775468 0.94 0.02 0.00 0.00 0.04
#> TCGA.C5.A8ZZ.01 1 0.1043 0.799814 0.96 0.00 0.00 0.04 0.00
#> TCGA.VS.A8EK.01 2 0.1043 0.850812 0.00 0.96 0.00 0.00 0.04
#> TCGA.C5.A7UC.01 4 0.5048 0.458608 0.38 0.00 0.00 0.58 0.04
#> TCGA.C5.A8XJ.01 1 0.0609 0.800815 0.98 0.00 0.00 0.02 0.00
#> TCGA.IR.A3LH.01 5 0.4307 -0.308065 0.00 0.50 0.00 0.00 0.50
#> TCGA.EK.A3GM.01 5 0.3796 0.330765 0.00 0.00 0.00 0.30 0.70
#> TCGA.VS.A8Q8.01 4 0.4726 0.438278 0.40 0.00 0.00 0.58 0.02
#> TCGA.EK.A2RO.01 2 0.5131 0.370388 0.04 0.54 0.00 0.00 0.42
#> TCGA.MY.A5BD.01 3 0.0000 0.941552 0.00 0.00 1.00 0.00 0.00
#> TCGA.2W.A8YY.01 5 0.3895 0.311060 0.00 0.00 0.00 0.32 0.68
#> TCGA.C5.A2LZ.01 2 0.3690 0.673234 0.20 0.78 0.00 0.00 0.02
#> TCGA.C5.A901.01 2 0.0609 0.841977 0.02 0.98 0.00 0.00 0.00
#> TCGA.VS.A953.01 2 0.1043 0.850812 0.00 0.96 0.00 0.00 0.04
#> TCGA.MU.A51Y.01 1 0.5068 0.427747 0.64 0.00 0.00 0.06 0.30
#> TCGA.EK.A2RK.01 4 0.4613 0.503635 0.36 0.00 0.00 0.62 0.02
#> TCGA.UC.A7PD.01 4 0.3731 0.724617 0.04 0.00 0.00 0.80 0.16
#> TCGA.EA.A3HS.01 1 0.1043 0.786028 0.96 0.00 0.00 0.00 0.04
#> TCGA.VS.A8QM.01 4 0.4437 0.705629 0.10 0.00 0.00 0.76 0.14
#> TCGA.EA.A3HU.01 1 0.3641 0.721379 0.82 0.00 0.00 0.06 0.12
#> TCGA.VS.A94X.01 4 0.1043 0.771526 0.00 0.00 0.00 0.96 0.04
#> TCGA.C5.A7CO.01 2 0.3796 0.641263 0.00 0.70 0.00 0.00 0.30
#> TCGA.C5.A3HF.01 5 0.3796 0.330765 0.00 0.00 0.00 0.30 0.70
#> TCGA.IR.A3LL.01 5 0.6296 0.310305 0.36 0.16 0.00 0.00 0.48
#> TCGA.MY.A913.01 4 0.3109 0.715497 0.00 0.00 0.00 0.80 0.20
#> TCGA.VS.A952.01 3 0.0000 0.941552 0.00 0.00 1.00 0.00 0.00
#> TCGA.IR.A3LI.01 3 0.0000 0.941552 0.00 0.00 1.00 0.00 0.00
#> TCGA.VS.A94W.01 5 0.4767 0.276548 0.42 0.02 0.00 0.00 0.56
#> TCGA.MY.A5BF.01 2 0.1732 0.839901 0.00 0.92 0.00 0.00 0.08
#> TCGA.EK.A2RC.01 1 0.1648 0.775468 0.94 0.02 0.00 0.00 0.04
#> TCGA.VS.A8EL.01 2 0.2929 0.772838 0.00 0.82 0.00 0.00 0.18
#> TCGA.EA.A97N.01 1 0.1410 0.794139 0.94 0.00 0.00 0.06 0.00
#> TCGA.EA.A3HQ.01 2 0.0609 0.841977 0.02 0.98 0.00 0.00 0.00
#> TCGA.EK.A2RD.01 1 0.1043 0.799814 0.96 0.00 0.00 0.04 0.00
#> TCGA.C5.A8YT.01 4 0.0609 0.775500 0.00 0.00 0.00 0.98 0.02
#> TCGA.FU.A3HZ.01 4 0.1410 0.766294 0.00 0.00 0.00 0.94 0.06
#> TCGA.VS.A8EJ.01 4 0.1410 0.766294 0.00 0.00 0.00 0.94 0.06
#> TCGA.C5.A3HL.01 4 0.2077 0.768746 0.04 0.00 0.00 0.92 0.04
#> TCGA.UC.A7PF.01 5 0.5838 0.363080 0.36 0.06 0.00 0.02 0.56
#> TCGA.C5.A8XK.01 5 0.3110 0.570908 0.08 0.00 0.00 0.06 0.86
#> TCGA.EX.A8YF.01 4 0.3109 0.709051 0.00 0.00 0.00 0.80 0.20
#> TCGA.HM.A4S6.01 1 0.1043 0.799814 0.96 0.00 0.00 0.04 0.00
#> TCGA.VS.A8Q9.01 2 0.4262 0.406802 0.00 0.56 0.00 0.00 0.44
#> TCGA.MA.AA41.01 2 0.1648 0.829048 0.04 0.94 0.00 0.00 0.02
#> TCGA.EK.A3GN.01 2 0.0609 0.841977 0.02 0.98 0.00 0.00 0.00
#> TCGA.MA.AA3Y.01 4 0.4373 0.705163 0.08 0.00 0.00 0.76 0.16
#> TCGA.MA.AA3Z.01 1 0.0000 0.797382 1.00 0.00 0.00 0.00 0.00
#> TCGA.EK.A2RE.01 4 0.4126 0.486301 0.38 0.00 0.00 0.62 0.00
#> TCGA.C5.A1BQ.01 1 0.0609 0.791019 0.98 0.00 0.00 0.00 0.02
#> TCGA.ZJ.A8QO.01 2 0.4527 0.675821 0.04 0.70 0.00 0.00 0.26
#> TCGA.JW.A852.01 2 0.1043 0.850812 0.00 0.96 0.00 0.00 0.04
#> TCGA.DS.A7WH.01 3 0.2732 0.829233 0.00 0.00 0.84 0.00 0.16
#> TCGA.JW.AAVH.01 1 0.3999 0.517977 0.74 0.24 0.00 0.00 0.02
#> TCGA.EA.A556.01 4 0.1410 0.766294 0.00 0.00 0.00 0.94 0.06
#> TCGA.EA.A44S.01 1 0.2331 0.773393 0.90 0.00 0.00 0.08 0.02
#> TCGA.4J.AA1J.01 1 0.1043 0.798739 0.96 0.00 0.00 0.04 0.00
#> TCGA.IR.A3L7.01 2 0.0609 0.841977 0.02 0.98 0.00 0.00 0.00
#> TCGA.C5.A7X3.01 4 0.2020 0.763801 0.00 0.00 0.00 0.90 0.10
#> TCGA.HG.A2PA.01 5 0.5534 0.357836 0.36 0.02 0.00 0.04 0.58
#> TCGA.C5.A8XH.01 2 0.4227 0.448134 0.00 0.58 0.00 0.00 0.42
#> TCGA.C5.A7XC.01 1 0.2616 0.758149 0.88 0.00 0.00 0.10 0.02
#> TCGA.VS.A8EI.01 5 0.6327 0.392277 0.28 0.20 0.00 0.00 0.52
#> TCGA.VS.A8QC.01 2 0.0609 0.841977 0.02 0.98 0.00 0.00 0.00
#> TCGA.C5.A7UH.01 1 0.1410 0.794139 0.94 0.00 0.00 0.06 0.00
#> TCGA.WL.A834.01 2 0.1216 0.837291 0.02 0.96 0.00 0.00 0.02
#> TCGA.C5.A8XI.01 2 0.1043 0.850812 0.00 0.96 0.00 0.00 0.04
#> TCGA.DS.A7WI.01 5 0.5297 0.364700 0.36 0.06 0.00 0.00 0.58
#> TCGA.VS.A8QF.01 2 0.0609 0.841977 0.02 0.98 0.00 0.00 0.00
#> TCGA.EA.A3HR.01 1 0.4360 0.449142 0.68 0.00 0.00 0.30 0.02
#> TCGA.DG.A2KL.01 1 0.2077 0.792358 0.92 0.00 0.00 0.04 0.04
#> TCGA.EK.A2RL.01 3 0.0000 0.941552 0.00 0.00 1.00 0.00 0.00
#> TCGA.EK.A2PG.01 2 0.0609 0.841977 0.02 0.98 0.00 0.00 0.00
#> TCGA.BI.A0VR.01 1 0.2438 0.783338 0.90 0.00 0.00 0.04 0.06
#> TCGA.DS.A0VL.01 1 0.1648 0.798545 0.94 0.00 0.00 0.04 0.02
#> TCGA.VS.A8EC.01 2 0.1043 0.850812 0.00 0.96 0.00 0.00 0.04
#> TCGA.EA.A3QE.01 2 0.4726 0.477535 0.02 0.58 0.00 0.00 0.40
#> TCGA.DS.A0VM.01 2 0.1648 0.829048 0.04 0.94 0.00 0.00 0.02
#> TCGA.FU.A3HY.01 1 0.2077 0.761012 0.92 0.04 0.00 0.00 0.04
#> TCGA.Q1.A5R1.01 3 0.0000 0.941552 0.00 0.00 1.00 0.00 0.00
#> TCGA.DR.A0ZM.01 4 0.3796 0.595214 0.30 0.00 0.00 0.70 0.00
#> TCGA.Q1.A6DW.01 2 0.1043 0.850812 0.00 0.96 0.00 0.00 0.04
#> TCGA.DS.A0VK.01 1 0.0609 0.791019 0.98 0.00 0.00 0.00 0.02
#> TCGA.DS.A3LQ.01 1 0.5854 0.260897 0.60 0.16 0.00 0.00 0.24
#> TCGA.EA.A3QD.01 2 0.1043 0.850812 0.00 0.96 0.00 0.00 0.04
#> TCGA.JW.A5VJ.01 4 0.3852 0.678641 0.22 0.00 0.00 0.76 0.02
#> TCGA.LP.A5U3.01 2 0.1216 0.837291 0.02 0.96 0.00 0.00 0.02
#> TCGA.EA.A6QX.01 2 0.4540 0.454185 0.34 0.64 0.00 0.00 0.02
#> TCGA.EK.A2RA.01 2 0.0609 0.841977 0.02 0.98 0.00 0.00 0.00
#> TCGA.FU.A5XV.01 1 0.0609 0.794757 0.98 0.00 0.00 0.00 0.02
#> TCGA.Q1.A5R2.01 2 0.1216 0.837291 0.02 0.96 0.00 0.00 0.02
#> TCGA.HM.A3JJ.01 1 0.0609 0.791019 0.98 0.00 0.00 0.00 0.02
#> TCGA.C5.A2LS.01 3 0.0000 0.941552 0.00 0.00 1.00 0.00 0.00
#> TCGA.C5.A7X8.01 5 0.4287 -0.230762 0.00 0.00 0.46 0.00 0.54
#> TCGA.EK.A2RJ.01 4 0.0609 0.775500 0.00 0.00 0.00 0.98 0.02
#> TCGA.EA.A3HT.01 1 0.1732 0.781731 0.92 0.00 0.00 0.08 0.00
#> TCGA.LP.A7HU.01 3 0.0000 0.941552 0.00 0.00 1.00 0.00 0.00
#> TCGA.MU.A8JM.01 1 0.4990 0.266483 0.60 0.04 0.00 0.00 0.36
#> TCGA.EK.A2IP.01 1 0.0609 0.791019 0.98 0.00 0.00 0.00 0.02
#> TCGA.JW.A5VL.01 2 0.4132 0.585962 0.26 0.72 0.00 0.00 0.02
#> TCGA.FU.A3TX.01 5 0.5828 0.279867 0.38 0.00 0.00 0.10 0.52
#> TCGA.DG.A2KK.01 3 0.0000 0.941552 0.00 0.00 1.00 0.00 0.00
#> TCGA.EK.A2PI.01 5 0.5425 0.218419 0.42 0.00 0.00 0.06 0.52
#> TCGA.Q1.A73S.01 4 0.1410 0.766294 0.00 0.00 0.00 0.94 0.06
#> TCGA.EK.A2IR.01 5 0.5588 0.335643 0.38 0.04 0.00 0.02 0.56
#> TCGA.HM.A6W2.01 4 0.1410 0.766294 0.00 0.00 0.00 0.94 0.06
#> TCGA.VS.A8EH.01 5 0.4671 0.525090 0.20 0.02 0.00 0.04 0.74
#> TCGA.JW.A5VH.01 4 0.1410 0.766294 0.00 0.00 0.00 0.94 0.06
#> TCGA.C5.A2LV.01 2 0.1732 0.839901 0.00 0.92 0.00 0.00 0.08
#> TCGA.VS.A8EB.01 1 0.4798 0.001684 0.54 0.02 0.00 0.00 0.44
#> TCGA.RA.A741.01 4 0.6047 0.316235 0.40 0.00 0.00 0.48 0.12
#> TCGA.VS.A8EG.01 2 0.2077 0.827867 0.04 0.92 0.00 0.00 0.04
#> TCGA.DG.A2KH.01 5 0.3796 0.330765 0.00 0.00 0.00 0.30 0.70
#> TCGA.C5.A7UE.01 5 0.6344 -0.054237 0.16 0.40 0.00 0.00 0.44
#> TCGA.C5.A2LT.01 4 0.5927 0.272551 0.12 0.00 0.00 0.54 0.34
#> TCGA.EA.A5ZD.01 4 0.4726 0.438278 0.40 0.00 0.00 0.58 0.02
#> TCGA.Q1.A73R.01 3 0.0000 0.941552 0.00 0.00 1.00 0.00 0.00
#> TCGA.JW.A5VK.01 2 0.1648 0.829048 0.04 0.94 0.00 0.00 0.02
#> TCGA.EK.A2RM.01 5 0.4126 0.171904 0.00 0.00 0.00 0.38 0.62
#> TCGA.C5.A7UI.01 1 0.1043 0.786028 0.96 0.00 0.00 0.00 0.04
#> TCGA.EK.A2PL.01 1 0.1410 0.794139 0.94 0.00 0.00 0.06 0.00
#> TCGA.EK.A2PM.01 4 0.1043 0.775623 0.04 0.00 0.00 0.96 0.00
#> TCGA.EK.A2GZ.01 5 0.5425 0.218419 0.42 0.00 0.00 0.06 0.52
#> TCGA.HM.A3JK.01 5 0.5457 0.106848 0.46 0.00 0.00 0.06 0.48
#> TCGA.C5.A2M1.01 3 0.0000 0.941552 0.00 0.00 1.00 0.00 0.00
#> TCGA.HM.A6W2.06 4 0.1410 0.766294 0.00 0.00 0.00 0.94 0.06
#> TCGA.C5.A7X5.01 2 0.1732 0.839901 0.00 0.92 0.00 0.00 0.08
#> TCGA.IR.A3LA.01 4 0.1410 0.766294 0.00 0.00 0.00 0.94 0.06
#> TCGA.EK.A2PK.01 4 0.3109 0.709051 0.00 0.00 0.00 0.80 0.20
#> TCGA.EA.A5ZF.01 4 0.1410 0.766294 0.00 0.00 0.00 0.94 0.06
#> TCGA.XS.A8TJ.01 1 0.1043 0.786028 0.96 0.00 0.00 0.00 0.04
#> TCGA.BI.A0VS.01 1 0.4767 0.132068 0.56 0.00 0.00 0.42 0.02
#> TCGA.DS.A0VN.01 1 0.4675 0.198582 0.60 0.02 0.00 0.00 0.38
#> TCGA.JX.A5QV.01 1 0.6019 0.064096 0.50 0.00 0.00 0.38 0.12
#> TCGA.EK.A2R8.01 4 0.0609 0.775500 0.00 0.00 0.00 0.98 0.02
#> TCGA.EA.A1QS.01 4 0.2012 0.770878 0.02 0.00 0.00 0.92 0.06
#> TCGA.C5.A3HE.01 5 0.3868 0.425144 0.00 0.00 0.14 0.06 0.80
#> TCGA.IR.A3LF.01 3 0.0000 0.941552 0.00 0.00 1.00 0.00 0.00
#> TCGA.DR.A0ZL.01 1 0.1043 0.786028 0.96 0.00 0.00 0.00 0.04
#> TCGA.FU.A3WB.01 2 0.4767 0.412853 0.02 0.56 0.00 0.00 0.42
#> TCGA.JX.A3PZ.01 4 0.2754 0.761807 0.04 0.00 0.00 0.88 0.08
#> TCGA.EA.A5O9.01 2 0.1732 0.839901 0.00 0.92 0.00 0.00 0.08
#> TCGA.HM.A3JJ.11 4 0.0609 0.775500 0.00 0.00 0.00 0.98 0.02
#> TCGA.DS.A5RQ.01 1 0.1043 0.799814 0.96 0.00 0.00 0.04 0.00
#> TCGA.EK.A2H0.01 2 0.2280 0.818933 0.00 0.88 0.00 0.00 0.12
#> TCGA.EX.A1H6.01 3 0.3274 0.776570 0.00 0.00 0.78 0.00 0.22
#> TCGA.EA.A5ZE.01 2 0.1043 0.850812 0.00 0.96 0.00 0.00 0.04
#> TCGA.C5.A2LY.01 1 0.5447 0.000527 0.50 0.00 0.00 0.06 0.44
#> TCGA.FU.A3TQ.01 1 0.3424 0.568122 0.76 0.00 0.00 0.00 0.24
#> TCGA.EK.A2RB.01 2 0.1648 0.829048 0.04 0.94 0.00 0.00 0.02
#> TCGA.JW.A5VI.01 1 0.4829 -0.136959 0.50 0.02 0.00 0.00 0.48
#> TCGA.EK.A2H1.01 4 0.0000 0.777188 0.00 0.00 0.00 1.00 0.00
#> TCGA.JX.A3Q8.01 3 0.0000 0.941552 0.00 0.00 1.00 0.00 0.00
#> TCGA.FU.A3YQ.01 5 0.4767 0.269253 0.42 0.02 0.00 0.00 0.56
#> TCGA.EX.A69L.01 1 0.2438 0.782010 0.90 0.00 0.00 0.04 0.06
#> TCGA.C5.A7CH.01 2 0.1043 0.850812 0.00 0.96 0.00 0.00 0.04
#> TCGA.FU.A2QG.01 1 0.1410 0.794139 0.94 0.00 0.00 0.06 0.00
#> TCGA.C5.A2M2.01 3 0.0000 0.941552 0.00 0.00 1.00 0.00 0.00
#> TCGA.JW.A5VG.01 4 0.3513 0.720060 0.02 0.00 0.00 0.80 0.18
#> TCGA.PN.A8MA.01 4 0.5297 0.448146 0.36 0.00 0.00 0.58 0.06
#> TCGA.DG.A2KM.01 4 0.3731 0.724617 0.04 0.00 0.00 0.80 0.16
#> TCGA.C5.A2LX.01 2 0.1043 0.850812 0.00 0.96 0.00 0.00 0.04
#> TCGA.EX.A3L1.01 4 0.2929 0.721926 0.00 0.00 0.00 0.82 0.18
#> TCGA.LP.A5U2.01 2 0.0000 0.846000 0.00 1.00 0.00 0.00 0.00
#> TCGA.FU.A3NI.01 2 0.1732 0.839901 0.00 0.92 0.00 0.00 0.08
#> TCGA.Q1.A5R3.01 1 0.1410 0.794139 0.94 0.00 0.00 0.06 0.00
#> TCGA.FU.A770.01 5 0.4302 -0.284683 0.00 0.00 0.48 0.00 0.52
#> TCGA.C5.A7CM.01 5 0.3796 0.330765 0.00 0.00 0.00 0.30 0.70
#> TCGA.JX.A3Q0.01 1 0.1410 0.794139 0.94 0.00 0.00 0.06 0.00
#> TCGA.EA.A5FO.01 3 0.0000 0.941552 0.00 0.00 1.00 0.00 0.00
#> TCGA.VS.A9V3.01 2 0.0609 0.841977 0.02 0.98 0.00 0.00 0.00
#> TCGA.C5.A7CL.01 5 0.5663 0.250142 0.42 0.02 0.00 0.04 0.52
#> TCGA.VS.A959.01 5 0.1732 0.547277 0.00 0.00 0.00 0.08 0.92
#> TCGA.LP.A4AX.01 5 0.2675 0.562538 0.04 0.02 0.00 0.04 0.90
#> TCGA.C5.A1MN.01 2 0.1043 0.850812 0.00 0.96 0.00 0.00 0.04
#> TCGA.ZJ.AAXN.01 4 0.2012 0.770878 0.02 0.00 0.00 0.92 0.06
#> TCGA.MA.AA3X.01 1 0.3424 0.571573 0.76 0.00 0.00 0.24 0.00
#> TCGA.UC.A7PG.01 1 0.1043 0.799814 0.96 0.00 0.00 0.04 0.00
#> TCGA.Q1.A6DV.01 5 0.4060 0.016303 0.00 0.00 0.36 0.00 0.64
#> TCGA.DS.A1OD.01 1 0.1216 0.799158 0.96 0.00 0.00 0.02 0.02
#> TCGA.C5.A1M7.01 1 0.3641 0.711389 0.82 0.00 0.00 0.12 0.06
#> TCGA.BI.A20A.01 2 0.4767 0.412853 0.02 0.56 0.00 0.00 0.42
#> TCGA.VS.A9UO.01 3 0.3561 0.734421 0.00 0.00 0.74 0.00 0.26
#> TCGA.EA.A1QT.01 2 0.2873 0.764527 0.12 0.86 0.00 0.00 0.02
#> TCGA.EX.A69M.01 2 0.2280 0.818933 0.00 0.88 0.00 0.00 0.12
#> TCGA.VS.A9UH.01 5 0.5136 0.461784 0.26 0.00 0.00 0.08 0.66
#> TCGA.VS.A9U7.01 2 0.1216 0.837291 0.02 0.96 0.00 0.00 0.02
#> TCGA.ZJ.AAXD.01 1 0.1410 0.792832 0.94 0.00 0.00 0.06 0.00
#> TCGA.VS.A9UB.01 5 0.4252 0.357734 0.02 0.00 0.00 0.28 0.70
#> TCGA.EA.A410.01 4 0.1410 0.766294 0.00 0.00 0.00 0.94 0.06
#> TCGA.ZJ.AB0I.01 4 0.4060 0.521304 0.36 0.00 0.00 0.64 0.00
#> TCGA.VS.A9UD.01 2 0.4227 0.448134 0.00 0.58 0.00 0.00 0.42
#> TCGA.VS.A9U6.01 1 0.1648 0.795202 0.94 0.00 0.00 0.02 0.04
#> TCGA.ZX.AA5X.01 5 0.6296 0.318702 0.36 0.16 0.00 0.00 0.48
#> TCGA.C5.A0TN.01 4 0.3731 0.724617 0.04 0.00 0.00 0.80 0.16
#> TCGA.C5.A7CJ.01 1 0.3109 0.616584 0.80 0.00 0.00 0.00 0.20
#> TCGA.C5.A1MJ.01 3 0.3895 0.662895 0.00 0.00 0.68 0.00 0.32
#> TCGA.EA.A78R.01 2 0.4227 0.448134 0.00 0.58 0.00 0.00 0.42
#> TCGA.VS.A9UY.01 2 0.1648 0.829048 0.04 0.94 0.00 0.00 0.02
#> TCGA.VS.A9U5.01 2 0.1648 0.847689 0.00 0.94 0.02 0.00 0.04
#> TCGA.DS.A1OC.01 5 0.5095 0.333952 0.40 0.04 0.00 0.00 0.56
#> TCGA.ZJ.AAXB.01 4 0.3731 0.705951 0.16 0.00 0.00 0.80 0.04
#> TCGA.EX.A449.01 3 0.0000 0.941552 0.00 0.00 1.00 0.00 0.00
#> TCGA.C5.A1BL.01 2 0.2012 0.814416 0.06 0.92 0.00 0.00 0.02
#> TCGA.VS.A9UQ.01 3 0.0000 0.941552 0.00 0.00 1.00 0.00 0.00
#> TCGA.DS.A1OB.01 1 0.1410 0.794139 0.94 0.00 0.00 0.06 0.00
#> TCGA.HG.A9SC.01 4 0.4227 0.404991 0.42 0.00 0.00 0.58 0.00
#> TCGA.ZJ.AAXT.01 4 0.3868 0.728906 0.06 0.00 0.00 0.80 0.14
#> TCGA.IR.A3LB.01 3 0.1410 0.904264 0.00 0.00 0.94 0.00 0.06
#> TCGA.C5.A1ML.01 4 0.1216 0.775379 0.02 0.00 0.00 0.96 0.02
#> TCGA.VS.A9UV.01 2 0.1648 0.847689 0.00 0.94 0.02 0.00 0.04
#> TCGA.LP.A4AU.01 4 0.2929 0.718553 0.00 0.00 0.00 0.82 0.18
#> TCGA.Q1.A6DT.01 2 0.2438 0.830415 0.04 0.90 0.00 0.00 0.06
#> TCGA.C5.A1M8.01 2 0.0609 0.841977 0.02 0.98 0.00 0.00 0.00
#> TCGA.C5.A1ME.01 3 0.3274 0.776570 0.00 0.00 0.78 0.00 0.22
#> TCGA.ZJ.AAXU.01 1 0.1216 0.799158 0.96 0.00 0.00 0.02 0.02
#> TCGA.VS.A957.01 2 0.5263 0.513759 0.24 0.66 0.00 0.00 0.10
#> TCGA.VS.A9V5.01 3 0.0000 0.941552 0.00 0.00 1.00 0.00 0.00
#> TCGA.MU.A5YI.01 2 0.5425 0.322128 0.06 0.52 0.00 0.00 0.42
#> TCGA.ZJ.AAX4.01 2 0.2020 0.830467 0.00 0.90 0.00 0.00 0.10
#> TCGA.C5.A1MK.01 1 0.1410 0.794139 0.94 0.00 0.00 0.06 0.00
#> TCGA.JW.A69B.01 3 0.0000 0.941552 0.00 0.00 1.00 0.00 0.00
#> TCGA.VS.A958.01 4 0.4726 0.438278 0.40 0.00 0.00 0.58 0.02
#> TCGA.ZJ.AAXJ.01 2 0.1043 0.850812 0.00 0.96 0.00 0.00 0.04
#> TCGA.R2.A69V.01 4 0.3731 0.724617 0.04 0.00 0.00 0.80 0.16
#> TCGA.EA.A411.01 1 0.1410 0.794139 0.94 0.00 0.00 0.06 0.00
#> TCGA.VS.A9UP.01 4 0.1732 0.762395 0.00 0.00 0.00 0.92 0.08
#> TCGA.C5.A1MI.01 4 0.4126 0.439000 0.00 0.00 0.00 0.62 0.38
#> TCGA.DS.A1O9.01 2 0.5689 0.273589 0.08 0.48 0.00 0.00 0.44
#> TCGA.VS.A9UZ.01 3 0.0000 0.941552 0.00 0.00 1.00 0.00 0.00
#> TCGA.EA.A43B.01 5 0.2280 0.522615 0.00 0.12 0.00 0.00 0.88
#> TCGA.ZJ.AAX8.01 4 0.4075 0.717969 0.06 0.00 0.00 0.78 0.16
#> TCGA.ZJ.AAXI.01 2 0.1648 0.829048 0.04 0.94 0.00 0.00 0.02
#> TCGA.VS.A9UT.01 4 0.1043 0.771526 0.00 0.00 0.00 0.96 0.04
#> TCGA.DS.A1OA.01 1 0.2077 0.761012 0.92 0.04 0.00 0.00 0.04
#> TCGA.C5.A1MQ.01 5 0.2732 0.475384 0.00 0.16 0.00 0.00 0.84
#> TCGA.VS.A9V0.01 4 0.1410 0.766294 0.00 0.00 0.00 0.94 0.06
#> TCGA.VS.A9UC.01 1 0.4287 -0.009806 0.54 0.00 0.00 0.00 0.46
#> TCGA.ZJ.AAXA.01 4 0.4227 0.404991 0.42 0.00 0.00 0.58 0.00
#> TCGA.Q1.A73P.01 3 0.0000 0.941552 0.00 0.00 1.00 0.00 0.00
#> TCGA.VS.A9V2.01 2 0.4060 0.552150 0.00 0.64 0.00 0.00 0.36
#> TCGA.VS.A9UU.01 2 0.2929 0.772838 0.00 0.82 0.00 0.00 0.18
#> TCGA.LP.A4AV.01 1 0.1043 0.798739 0.96 0.00 0.00 0.04 0.00
#> TCGA.VS.A9UR.01 3 0.0000 0.941552 0.00 0.00 1.00 0.00 0.00
#> TCGA.VS.A9V1.01 5 0.4876 0.292020 0.00 0.00 0.22 0.08 0.70
#> TCGA.C5.A7CG.01 2 0.1043 0.850812 0.00 0.96 0.00 0.00 0.04
#> TCGA.UC.A7PI.01 3 0.0000 0.941552 0.00 0.00 1.00 0.00 0.00
#> TCGA.EX.A1H5.01 5 0.6184 0.294834 0.38 0.14 0.00 0.00 0.48
#> TCGA.ZJ.AAXF.01 1 0.6146 0.371365 0.56 0.00 0.00 0.24 0.20
#> TCGA.VS.A9UL.01 3 0.3895 0.662895 0.00 0.00 0.68 0.00 0.32
#> TCGA.EA.A3Y4.01 4 0.4227 0.416101 0.42 0.00 0.00 0.58 0.00
#> TCGA.C5.A7CK.01 2 0.1043 0.850812 0.00 0.96 0.00 0.00 0.04
#> TCGA.UC.A7PG.06 1 0.1043 0.799814 0.96 0.00 0.00 0.04 0.00
#> TCGA.VS.A9UJ.01 4 0.1410 0.766294 0.00 0.00 0.00 0.94 0.06
#> TCGA.Q1.A73O.01 4 0.4540 0.536735 0.34 0.00 0.00 0.64 0.02
#> TCGA.VS.A950.01 1 0.5447 0.096843 0.50 0.44 0.00 0.00 0.06
#> TCGA.EA.A439.01 5 0.1732 0.537595 0.00 0.00 0.00 0.08 0.92
#> TCGA.VS.A9UM.01 1 0.0609 0.791019 0.98 0.00 0.00 0.00 0.02
#> TCGA.C5.A1MP.01 1 0.2929 0.685365 0.82 0.00 0.00 0.18 0.00
#> TCGA.VS.A9UI.01 1 0.3291 0.675507 0.84 0.12 0.00 0.00 0.04
#> TCGA.ZJ.AB0H.01 1 0.1216 0.799158 0.96 0.00 0.00 0.02 0.02
#> TCGA.Q1.A73Q.01 1 0.3037 0.698982 0.86 0.10 0.00 0.00 0.04
#> TCGA.C5.A1MH.01 1 0.2020 0.743332 0.90 0.00 0.00 0.00 0.10
#> TCGA.VS.A9V4.01 4 0.1410 0.766294 0.00 0.00 0.00 0.94 0.06
#> TCGA.FU.A40J.01 3 0.0000 0.941552 0.00 0.00 1.00 0.00 0.00
#> TCGA.VS.A9UA.01 5 0.5447 0.165219 0.44 0.00 0.00 0.06 0.50
#> TCGA.LP.A4AW.01 1 0.0609 0.791019 0.98 0.00 0.00 0.00 0.02
#> TCGA.MA.AA43.01 5 0.3684 0.243276 0.00 0.00 0.28 0.00 0.72
#> TCGA.C5.A1BN.01 1 0.4307 -0.213208 0.50 0.00 0.00 0.50 0.00
#> TCGA.VS.AA62.01 4 0.3521 0.735288 0.04 0.00 0.00 0.82 0.14
#> TCGA.C5.A1BM.01 4 0.4540 0.536735 0.34 0.00 0.00 0.64 0.02
#> TCGA.C5.A1M6.01 5 0.1732 0.537595 0.00 0.00 0.00 0.08 0.92
#> TCGA.C5.A1BE.01 1 0.2616 0.752614 0.88 0.00 0.00 0.02 0.10
#> TCGA.FU.A23K.01 3 0.4262 0.445685 0.00 0.00 0.56 0.00 0.44
#> TCGA.C5.A1BJ.01 1 0.1410 0.794139 0.94 0.00 0.00 0.06 0.00
#> TCGA.FU.A23L.01 4 0.1216 0.775379 0.02 0.00 0.00 0.96 0.02
#> TCGA.C5.A1M5.01 2 0.1216 0.837291 0.02 0.96 0.00 0.00 0.02
#> TCGA.C5.A1MF.01 5 0.5646 0.049474 0.08 0.40 0.00 0.00 0.52
#> TCGA.C5.A1BF.01 4 0.3037 0.755350 0.04 0.00 0.00 0.86 0.10
#> TCGA.C5.A1BK.01 2 0.3106 0.808201 0.02 0.84 0.00 0.00 0.14
#> TCGA.C5.A1BI.01 4 0.4726 0.438278 0.40 0.00 0.00 0.58 0.02
#> TCGA.C5.A1M9.01 3 0.0000 0.941552 0.00 0.00 1.00 0.00 0.00
cbind(get_classes(res, k = 6), get_membership(res, k = 6))
#> class entropy silhouette p1 p2 p3 p4 p5 p6
#> TCGA.EK.A3GK.01 6 0.4172 0.6128 0.00 0.00 0.00 0.04 0.28 0.68
#> TCGA.GH.A9DA.01 5 0.0547 0.7264 0.02 0.00 0.00 0.00 0.98 0.00
#> TCGA.VS.A94Y.01 5 0.4380 0.4995 0.22 0.00 0.00 0.00 0.70 0.08
#> TCGA.MY.A5BF.11 4 0.0547 0.6921 0.00 0.00 0.00 0.98 0.00 0.02
#> TCGA.VS.A94Z.01 1 0.4393 0.6488 0.72 0.00 0.00 0.00 0.14 0.14
#> TCGA.EA.A4BA.01 4 0.2260 0.6327 0.00 0.00 0.00 0.86 0.00 0.14
#> TCGA.ZJ.A8QQ.01 2 0.3409 0.4998 0.00 0.70 0.00 0.00 0.30 0.00
#> TCGA.FU.A3EO.11 4 0.0547 0.6921 0.00 0.00 0.00 0.98 0.00 0.02
#> TCGA.DG.A2KJ.01 6 0.4608 0.6937 0.00 0.00 0.00 0.22 0.10 0.68
#> TCGA.VS.A954.01 2 0.0937 0.7519 0.00 0.96 0.00 0.00 0.04 0.00
#> TCGA.MA.AA42.01 2 0.3797 0.2390 0.00 0.58 0.00 0.00 0.42 0.00
#> TCGA.C5.A8YQ.01 5 0.0547 0.7264 0.02 0.00 0.00 0.00 0.98 0.00
#> TCGA.DS.A7WF.01 3 0.0000 0.8796 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.EK.A2R7.01 1 0.1480 0.7091 0.94 0.00 0.00 0.04 0.00 0.02
#> TCGA.EK.A3GJ.01 2 0.3578 0.4269 0.00 0.66 0.00 0.00 0.34 0.00
#> TCGA.C5.A902.01 2 0.0937 0.7519 0.00 0.96 0.00 0.00 0.04 0.00
#> TCGA.MA.AA3W.01 5 0.6273 0.3652 0.18 0.06 0.00 0.00 0.56 0.20
#> TCGA.C5.A905.01 1 0.2190 0.7369 0.90 0.00 0.00 0.00 0.04 0.06
#> TCGA.EK.A2RN.01 1 0.0937 0.7438 0.96 0.00 0.00 0.00 0.04 0.00
#> TCGA.FU.A57G.01 4 0.2260 0.6327 0.00 0.00 0.00 0.86 0.00 0.14
#> TCGA.C5.A8YR.01 4 0.5362 0.5944 0.06 0.00 0.00 0.68 0.12 0.14
#> TCGA.EK.A2R9.01 2 0.7475 0.2665 0.20 0.36 0.00 0.00 0.16 0.28
#> TCGA.FU.A3EO.01 3 0.0000 0.8796 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.IR.A3LC.01 2 0.0937 0.7519 0.00 0.96 0.00 0.00 0.04 0.00
#> TCGA.VS.A8QA.01 3 0.0000 0.8796 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.C5.A3HD.01 5 0.3819 0.5717 0.00 0.28 0.00 0.00 0.70 0.02
#> TCGA.MY.A5BE.01 5 0.2941 0.5735 0.00 0.00 0.00 0.00 0.78 0.22
#> TCGA.EA.A50E.01 2 0.0937 0.7519 0.00 0.96 0.00 0.00 0.04 0.00
#> TCGA.VS.A8QH.01 6 0.4608 0.6937 0.00 0.00 0.00 0.22 0.10 0.68
#> TCGA.ZJ.A8QR.01 1 0.4165 0.6582 0.74 0.00 0.00 0.00 0.16 0.10
#> TCGA.C5.A907.01 6 0.4711 0.6008 0.00 0.00 0.00 0.28 0.08 0.64
#> TCGA.IR.A3LK.01 1 0.5774 0.5132 0.56 0.02 0.00 0.00 0.14 0.28
#> TCGA.C5.A8ZZ.01 1 0.0547 0.7425 0.98 0.00 0.00 0.00 0.02 0.00
#> TCGA.VS.A8EK.01 2 0.0937 0.7519 0.00 0.96 0.00 0.00 0.04 0.00
#> TCGA.C5.A7UC.01 1 0.5106 -0.1063 0.50 0.00 0.00 0.44 0.02 0.04
#> TCGA.C5.A8XJ.01 1 0.1865 0.7410 0.92 0.00 0.00 0.00 0.04 0.04
#> TCGA.IR.A3LH.01 5 0.3156 0.6586 0.00 0.18 0.00 0.00 0.80 0.02
#> TCGA.EK.A3GM.01 6 0.4608 0.6937 0.00 0.00 0.00 0.22 0.10 0.68
#> TCGA.VS.A8Q8.01 1 0.4078 0.3026 0.64 0.00 0.00 0.34 0.02 0.00
#> TCGA.EK.A2RO.01 5 0.2956 0.6912 0.00 0.12 0.00 0.00 0.84 0.04
#> TCGA.MY.A5BD.01 3 0.0000 0.8796 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.2W.A8YY.01 6 0.3647 0.4870 0.00 0.00 0.00 0.36 0.00 0.64
#> TCGA.C5.A2LZ.01 2 0.6365 0.4973 0.06 0.52 0.00 0.00 0.14 0.28
#> TCGA.C5.A901.01 2 0.1814 0.7411 0.00 0.90 0.00 0.00 0.00 0.10
#> TCGA.VS.A953.01 2 0.0937 0.7519 0.00 0.96 0.00 0.00 0.04 0.00
#> TCGA.MU.A51Y.01 5 0.4646 0.1348 0.46 0.00 0.00 0.00 0.50 0.04
#> TCGA.EK.A2RK.01 1 0.3409 0.4145 0.70 0.00 0.00 0.30 0.00 0.00
#> TCGA.UC.A7PD.01 4 0.5835 0.6054 0.12 0.00 0.00 0.64 0.10 0.14
#> TCGA.EA.A3HS.01 1 0.4566 0.6346 0.70 0.00 0.00 0.00 0.14 0.16
#> TCGA.VS.A8QM.01 4 0.6376 0.5478 0.22 0.00 0.00 0.56 0.10 0.12
#> TCGA.EA.A3HU.01 1 0.3706 0.3201 0.62 0.00 0.00 0.00 0.38 0.00
#> TCGA.VS.A94X.01 4 0.0000 0.6891 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.C5.A7CO.01 5 0.3409 0.5245 0.00 0.30 0.00 0.00 0.70 0.00
#> TCGA.C5.A3HF.01 6 0.4608 0.6937 0.00 0.00 0.00 0.22 0.10 0.68
#> TCGA.IR.A3LL.01 5 0.0547 0.7264 0.02 0.00 0.00 0.00 0.98 0.00
#> TCGA.MY.A913.01 4 0.4838 0.5776 0.02 0.00 0.00 0.70 0.10 0.18
#> TCGA.VS.A952.01 3 0.0000 0.8796 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.IR.A3LI.01 3 0.0000 0.8796 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.VS.A94W.01 5 0.1865 0.7202 0.04 0.00 0.00 0.00 0.92 0.04
#> TCGA.MY.A5BF.01 2 0.3076 0.5864 0.00 0.76 0.00 0.00 0.24 0.00
#> TCGA.EK.A2RC.01 1 0.5774 0.5132 0.56 0.02 0.00 0.00 0.14 0.28
#> TCGA.VS.A8EL.01 2 0.3756 0.2911 0.00 0.60 0.00 0.00 0.40 0.00
#> TCGA.EA.A97N.01 1 0.0000 0.7373 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.EA.A3HQ.01 2 0.1267 0.7460 0.00 0.94 0.00 0.00 0.00 0.06
#> TCGA.EK.A2RD.01 1 0.0547 0.7425 0.98 0.00 0.00 0.00 0.02 0.00
#> TCGA.C5.A8YT.01 4 0.0547 0.6921 0.00 0.00 0.00 0.98 0.00 0.02
#> TCGA.FU.A3HZ.01 4 0.2260 0.6327 0.00 0.00 0.00 0.86 0.00 0.14
#> TCGA.VS.A8EJ.01 4 0.2048 0.6458 0.00 0.00 0.00 0.88 0.00 0.12
#> TCGA.C5.A3HL.01 4 0.3819 0.5925 0.28 0.00 0.00 0.70 0.02 0.00
#> TCGA.UC.A7PF.01 5 0.1807 0.7162 0.02 0.00 0.00 0.00 0.92 0.06
#> TCGA.C5.A8XK.01 5 0.3706 0.2538 0.00 0.00 0.00 0.00 0.62 0.38
#> TCGA.EX.A8YF.01 4 0.4462 0.5295 0.00 0.00 0.00 0.66 0.06 0.28
#> TCGA.HM.A4S6.01 1 0.0547 0.7425 0.98 0.00 0.00 0.00 0.02 0.00
#> TCGA.VS.A8Q9.01 5 0.2454 0.6746 0.00 0.16 0.00 0.00 0.84 0.00
#> TCGA.MA.AA41.01 2 0.5029 0.5954 0.00 0.62 0.00 0.00 0.12 0.26
#> TCGA.EK.A3GN.01 2 0.2474 0.7514 0.00 0.88 0.00 0.00 0.04 0.08
#> TCGA.MA.AA3Y.01 4 0.6307 0.5702 0.18 0.00 0.00 0.58 0.10 0.14
#> TCGA.MA.AA3Z.01 1 0.3270 0.7084 0.82 0.00 0.00 0.00 0.06 0.12
#> TCGA.EK.A2RE.01 1 0.3706 0.2476 0.62 0.00 0.00 0.38 0.00 0.00
#> TCGA.C5.A1BQ.01 1 0.4393 0.6488 0.72 0.00 0.00 0.00 0.14 0.14
#> TCGA.ZJ.A8QO.01 5 0.2581 0.6761 0.00 0.12 0.00 0.00 0.86 0.02
#> TCGA.JW.A852.01 2 0.0937 0.7519 0.00 0.96 0.00 0.00 0.04 0.00
#> TCGA.DS.A7WH.01 3 0.3578 0.5833 0.00 0.00 0.66 0.00 0.00 0.34
#> TCGA.JW.AAVH.01 1 0.7437 0.1327 0.36 0.22 0.00 0.00 0.14 0.28
#> TCGA.EA.A556.01 4 0.2048 0.6458 0.00 0.00 0.00 0.88 0.00 0.12
#> TCGA.EA.A44S.01 1 0.0000 0.7373 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.4J.AA1J.01 1 0.1865 0.7410 0.92 0.00 0.00 0.00 0.04 0.04
#> TCGA.IR.A3L7.01 2 0.2048 0.7366 0.00 0.88 0.00 0.00 0.00 0.12
#> TCGA.C5.A7X3.01 4 0.4468 0.6479 0.06 0.00 0.00 0.76 0.06 0.12
#> TCGA.HG.A2PA.01 5 0.3045 0.6839 0.10 0.00 0.00 0.00 0.84 0.06
#> TCGA.C5.A8XH.01 5 0.3711 0.5982 0.00 0.26 0.00 0.00 0.72 0.02
#> TCGA.C5.A7XC.01 1 0.1807 0.6953 0.92 0.00 0.00 0.06 0.02 0.00
#> TCGA.VS.A8EI.01 5 0.0547 0.7264 0.02 0.00 0.00 0.00 0.98 0.00
#> TCGA.VS.A8QC.01 2 0.1814 0.7411 0.00 0.90 0.00 0.00 0.00 0.10
#> TCGA.C5.A7UH.01 1 0.0547 0.7425 0.98 0.00 0.00 0.00 0.02 0.00
#> TCGA.WL.A834.01 2 0.2260 0.7307 0.00 0.86 0.00 0.00 0.00 0.14
#> TCGA.C5.A8XI.01 2 0.0937 0.7519 0.00 0.96 0.00 0.00 0.04 0.00
#> TCGA.DS.A7WI.01 5 0.1480 0.7209 0.02 0.00 0.00 0.00 0.94 0.04
#> TCGA.VS.A8QF.01 2 0.1814 0.7411 0.00 0.90 0.00 0.00 0.00 0.10
#> TCGA.EA.A3HR.01 1 0.2454 0.6240 0.84 0.00 0.00 0.16 0.00 0.00
#> TCGA.DG.A2KL.01 1 0.1267 0.7388 0.94 0.00 0.00 0.00 0.06 0.00
#> TCGA.EK.A2RL.01 3 0.0000 0.8796 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.EK.A2PG.01 2 0.1814 0.7411 0.00 0.90 0.00 0.00 0.00 0.10
#> TCGA.BI.A0VR.01 1 0.2454 0.6684 0.84 0.00 0.00 0.00 0.16 0.00
#> TCGA.DS.A0VL.01 1 0.3163 0.7105 0.82 0.00 0.00 0.00 0.04 0.14
#> TCGA.VS.A8EC.01 2 0.0937 0.7519 0.00 0.96 0.00 0.00 0.04 0.00
#> TCGA.EA.A3QE.01 5 0.2048 0.6910 0.00 0.12 0.00 0.00 0.88 0.00
#> TCGA.DS.A0VM.01 2 0.5120 0.5787 0.00 0.60 0.00 0.00 0.12 0.28
#> TCGA.FU.A3HY.01 1 0.6101 0.5005 0.54 0.04 0.00 0.00 0.14 0.28
#> TCGA.Q1.A5R1.01 3 0.0000 0.8796 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.DR.A0ZM.01 4 0.3864 0.1759 0.48 0.00 0.00 0.52 0.00 0.00
#> TCGA.Q1.A6DW.01 2 0.0937 0.7519 0.00 0.96 0.00 0.00 0.04 0.00
#> TCGA.DS.A0VK.01 1 0.4566 0.6346 0.70 0.00 0.00 0.00 0.14 0.16
#> TCGA.DS.A3LQ.01 5 0.4495 0.5479 0.06 0.02 0.00 0.00 0.72 0.20
#> TCGA.EA.A3QD.01 2 0.0937 0.7519 0.00 0.96 0.00 0.00 0.04 0.00
#> TCGA.JW.A5VJ.01 4 0.3864 0.1842 0.48 0.00 0.00 0.52 0.00 0.00
#> TCGA.LP.A5U3.01 2 0.4380 0.6541 0.00 0.70 0.00 0.00 0.08 0.22
#> TCGA.EA.A6QX.01 2 0.7078 0.4054 0.14 0.44 0.00 0.00 0.14 0.28
#> TCGA.EK.A2RA.01 2 0.2790 0.7250 0.00 0.84 0.00 0.00 0.02 0.14
#> TCGA.FU.A5XV.01 1 0.3787 0.6881 0.78 0.00 0.00 0.00 0.10 0.12
#> TCGA.Q1.A5R2.01 2 0.3163 0.7194 0.00 0.82 0.00 0.00 0.04 0.14
#> TCGA.HM.A3JJ.01 1 0.4393 0.6488 0.72 0.00 0.00 0.00 0.14 0.14
#> TCGA.C5.A2LS.01 3 0.0000 0.8796 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.C5.A7X8.01 3 0.4632 0.3182 0.00 0.00 0.52 0.00 0.04 0.44
#> TCGA.EK.A2RJ.01 4 0.0547 0.6921 0.00 0.00 0.00 0.98 0.00 0.02
#> TCGA.EA.A3HT.01 1 0.0000 0.7373 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.LP.A7HU.01 3 0.0000 0.8796 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.MU.A8JM.01 5 0.2094 0.7030 0.08 0.00 0.00 0.00 0.90 0.02
#> TCGA.EK.A2IP.01 1 0.4863 0.6051 0.66 0.00 0.00 0.00 0.14 0.20
#> TCGA.JW.A5VL.01 2 0.6939 0.4289 0.12 0.46 0.00 0.00 0.14 0.28
#> TCGA.FU.A3TX.01 5 0.3787 0.6329 0.12 0.00 0.00 0.00 0.78 0.10
#> TCGA.DG.A2KK.01 3 0.0000 0.8796 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.EK.A2PI.01 5 0.3045 0.6839 0.10 0.00 0.00 0.00 0.84 0.06
#> TCGA.Q1.A73S.01 4 0.1814 0.6565 0.00 0.00 0.00 0.90 0.00 0.10
#> TCGA.EK.A2IR.01 5 0.2190 0.7130 0.04 0.00 0.00 0.00 0.90 0.06
#> TCGA.HM.A6W2.01 4 0.2260 0.6327 0.00 0.00 0.00 0.86 0.00 0.14
#> TCGA.VS.A8EH.01 5 0.2728 0.6882 0.04 0.00 0.00 0.00 0.86 0.10
#> TCGA.JW.A5VH.01 4 0.2260 0.6327 0.00 0.00 0.00 0.86 0.00 0.14
#> TCGA.C5.A2LV.01 2 0.3076 0.5850 0.00 0.76 0.00 0.00 0.24 0.00
#> TCGA.VS.A8EB.01 5 0.1814 0.6917 0.10 0.00 0.00 0.00 0.90 0.00
#> TCGA.RA.A741.01 1 0.5514 0.0294 0.52 0.00 0.00 0.38 0.08 0.02
#> TCGA.VS.A8EG.01 2 0.5173 0.5955 0.00 0.62 0.00 0.00 0.20 0.18
#> TCGA.DG.A2KH.01 6 0.4608 0.6937 0.00 0.00 0.00 0.22 0.10 0.68
#> TCGA.C5.A7UE.01 5 0.2629 0.7058 0.02 0.08 0.00 0.00 0.88 0.02
#> TCGA.C5.A2LT.01 4 0.6777 0.3083 0.10 0.00 0.00 0.48 0.28 0.14
#> TCGA.EA.A5ZD.01 1 0.4199 0.2003 0.60 0.00 0.00 0.38 0.02 0.00
#> TCGA.Q1.A73R.01 3 0.0000 0.8796 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.JW.A5VK.01 2 0.4727 0.6284 0.00 0.66 0.00 0.00 0.10 0.24
#> TCGA.EK.A2RM.01 6 0.3647 0.4833 0.00 0.00 0.00 0.36 0.00 0.64
#> TCGA.C5.A7UI.01 1 0.4566 0.6346 0.70 0.00 0.00 0.00 0.14 0.16
#> TCGA.EK.A2PL.01 1 0.1092 0.7385 0.96 0.00 0.00 0.00 0.02 0.02
#> TCGA.EK.A2PM.01 4 0.3499 0.5253 0.32 0.00 0.00 0.68 0.00 0.00
#> TCGA.EK.A2GZ.01 5 0.3321 0.6697 0.10 0.00 0.00 0.00 0.82 0.08
#> TCGA.HM.A3JK.01 5 0.3679 0.6110 0.20 0.00 0.00 0.00 0.76 0.04
#> TCGA.C5.A2M1.01 3 0.0000 0.8796 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.HM.A6W2.06 4 0.2260 0.6327 0.00 0.00 0.00 0.86 0.00 0.14
#> TCGA.C5.A7X5.01 2 0.3076 0.5864 0.00 0.76 0.00 0.00 0.24 0.00
#> TCGA.IR.A3LA.01 4 0.2260 0.6327 0.00 0.00 0.00 0.86 0.00 0.14
#> TCGA.EK.A2PK.01 4 0.4962 0.5352 0.02 0.00 0.00 0.64 0.06 0.28
#> TCGA.EA.A5ZF.01 4 0.2260 0.6327 0.00 0.00 0.00 0.86 0.00 0.14
#> TCGA.XS.A8TJ.01 1 0.5027 0.5750 0.64 0.00 0.00 0.00 0.20 0.16
#> TCGA.BI.A0VS.01 1 0.3315 0.5459 0.78 0.00 0.00 0.20 0.02 0.00
#> TCGA.DS.A0VN.01 5 0.1267 0.7162 0.06 0.00 0.00 0.00 0.94 0.00
#> TCGA.JX.A5QV.01 1 0.5189 0.2039 0.58 0.00 0.00 0.34 0.06 0.02
#> TCGA.EK.A2R8.01 4 0.1092 0.6935 0.02 0.00 0.00 0.96 0.00 0.02
#> TCGA.EA.A1QS.01 4 0.4995 0.6535 0.12 0.00 0.00 0.72 0.08 0.08
#> TCGA.C5.A3HE.01 6 0.4887 0.6427 0.00 0.00 0.08 0.02 0.22 0.68
#> TCGA.IR.A3LF.01 3 0.0000 0.8796 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.DR.A0ZL.01 1 0.5027 0.5750 0.64 0.00 0.00 0.00 0.20 0.16
#> TCGA.FU.A3WB.01 5 0.3711 0.5982 0.00 0.26 0.00 0.00 0.72 0.02
#> TCGA.JX.A3PZ.01 4 0.5397 0.6232 0.20 0.00 0.00 0.66 0.08 0.06
#> TCGA.EA.A5O9.01 2 0.3647 0.3869 0.00 0.64 0.00 0.00 0.36 0.00
#> TCGA.HM.A3JJ.11 4 0.0547 0.6921 0.00 0.00 0.00 0.98 0.00 0.02
#> TCGA.DS.A5RQ.01 1 0.0547 0.7425 0.98 0.00 0.00 0.00 0.02 0.00
#> TCGA.EK.A2H0.01 2 0.3409 0.4998 0.00 0.70 0.00 0.00 0.30 0.00
#> TCGA.EX.A1H6.01 3 0.3578 0.5833 0.00 0.00 0.66 0.00 0.00 0.34
#> TCGA.EA.A5ZE.01 2 0.1480 0.7525 0.00 0.94 0.00 0.00 0.04 0.02
#> TCGA.C5.A2LY.01 5 0.5120 0.4061 0.28 0.00 0.00 0.00 0.60 0.12
#> TCGA.FU.A3TQ.01 5 0.3821 0.5615 0.22 0.00 0.00 0.00 0.74 0.04
#> TCGA.EK.A2RB.01 2 0.4613 0.6294 0.00 0.66 0.00 0.00 0.08 0.26
#> TCGA.JW.A5VI.01 5 0.0937 0.7211 0.04 0.00 0.00 0.00 0.96 0.00
#> TCGA.EK.A2H1.01 4 0.1865 0.6941 0.04 0.00 0.00 0.92 0.00 0.04
#> TCGA.JX.A3Q8.01 3 0.0000 0.8796 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.FU.A3YQ.01 5 0.0547 0.7264 0.02 0.00 0.00 0.00 0.98 0.00
#> TCGA.EX.A69L.01 1 0.1556 0.7318 0.92 0.00 0.00 0.00 0.08 0.00
#> TCGA.C5.A7CH.01 2 0.0937 0.7519 0.00 0.96 0.00 0.00 0.04 0.00
#> TCGA.FU.A2QG.01 1 0.0000 0.7373 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.C5.A2M2.01 3 0.0000 0.8796 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.JW.A5VG.01 4 0.5835 0.6054 0.12 0.00 0.00 0.64 0.10 0.14
#> TCGA.PN.A8MA.01 4 0.5364 0.3346 0.30 0.00 0.00 0.56 0.00 0.14
#> TCGA.DG.A2KM.01 4 0.5835 0.6054 0.12 0.00 0.00 0.64 0.10 0.14
#> TCGA.C5.A2LX.01 2 0.0937 0.7519 0.00 0.96 0.00 0.00 0.04 0.00
#> TCGA.EX.A3L1.01 4 0.4664 0.6332 0.06 0.00 0.00 0.74 0.06 0.14
#> TCGA.LP.A5U2.01 2 0.0547 0.7500 0.00 0.98 0.00 0.00 0.00 0.02
#> TCGA.FU.A3NI.01 2 0.2941 0.6086 0.00 0.78 0.00 0.00 0.22 0.00
#> TCGA.Q1.A5R3.01 1 0.0000 0.7373 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.FU.A770.01 3 0.4632 0.3182 0.00 0.00 0.52 0.00 0.04 0.44
#> TCGA.C5.A7CM.01 6 0.4608 0.6937 0.00 0.00 0.00 0.22 0.10 0.68
#> TCGA.JX.A3Q0.01 1 0.0547 0.7425 0.98 0.00 0.00 0.00 0.02 0.00
#> TCGA.EA.A5FO.01 3 0.0000 0.8796 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.VS.A9V3.01 2 0.2048 0.7366 0.00 0.88 0.00 0.00 0.00 0.12
#> TCGA.C5.A7CL.01 5 0.3045 0.6839 0.10 0.00 0.00 0.00 0.84 0.06
#> TCGA.VS.A959.01 6 0.3851 0.2284 0.00 0.00 0.00 0.00 0.46 0.54
#> TCGA.LP.A4AX.01 5 0.3198 0.5170 0.00 0.00 0.00 0.00 0.74 0.26
#> TCGA.C5.A1MN.01 2 0.0937 0.7519 0.00 0.96 0.00 0.00 0.04 0.00
#> TCGA.ZJ.AAXN.01 4 0.5256 0.6347 0.18 0.00 0.00 0.68 0.08 0.06
#> TCGA.MA.AA3X.01 1 0.0547 0.7280 0.98 0.00 0.00 0.02 0.00 0.00
#> TCGA.UC.A7PG.01 1 0.0937 0.7438 0.96 0.00 0.00 0.00 0.04 0.00
#> TCGA.Q1.A6DV.01 6 0.4420 0.2191 0.00 0.00 0.34 0.00 0.04 0.62
#> TCGA.DS.A1OD.01 1 0.2190 0.7399 0.90 0.00 0.00 0.00 0.06 0.04
#> TCGA.C5.A1M7.01 1 0.2794 0.6697 0.86 0.00 0.00 0.08 0.06 0.00
#> TCGA.BI.A20A.01 5 0.3460 0.6317 0.00 0.22 0.00 0.00 0.76 0.02
#> TCGA.VS.A9UO.01 3 0.3647 0.5549 0.00 0.00 0.64 0.00 0.00 0.36
#> TCGA.EA.A1QT.01 2 0.5774 0.5368 0.02 0.56 0.00 0.00 0.14 0.28
#> TCGA.EX.A69M.01 2 0.3409 0.4998 0.00 0.70 0.00 0.00 0.30 0.00
#> TCGA.VS.A9UH.01 5 0.3821 0.5524 0.04 0.00 0.00 0.00 0.74 0.22
#> TCGA.VS.A9U7.01 2 0.2454 0.7256 0.00 0.84 0.00 0.00 0.00 0.16
#> TCGA.ZJ.AAXD.01 1 0.0547 0.7307 0.98 0.00 0.00 0.00 0.02 0.00
#> TCGA.VS.A9UB.01 5 0.6449 -0.1892 0.02 0.00 0.00 0.28 0.42 0.28
#> TCGA.EA.A410.01 4 0.2260 0.6327 0.00 0.00 0.00 0.86 0.00 0.14
#> TCGA.ZJ.AB0I.01 1 0.3706 0.2476 0.62 0.00 0.00 0.38 0.00 0.00
#> TCGA.VS.A9UD.01 5 0.3711 0.5982 0.00 0.26 0.00 0.00 0.72 0.02
#> TCGA.VS.A9U6.01 1 0.3544 0.6998 0.80 0.00 0.00 0.00 0.08 0.12
#> TCGA.ZX.AA5X.01 5 0.2190 0.6957 0.04 0.00 0.00 0.00 0.90 0.06
#> TCGA.C5.A0TN.01 4 0.5615 0.6226 0.12 0.00 0.00 0.66 0.08 0.14
#> TCGA.C5.A7CJ.01 5 0.5037 0.1474 0.38 0.00 0.00 0.00 0.54 0.08
#> TCGA.C5.A1MJ.01 3 0.3797 0.4537 0.00 0.00 0.58 0.00 0.00 0.42
#> TCGA.EA.A78R.01 5 0.3592 0.6169 0.00 0.24 0.00 0.00 0.74 0.02
#> TCGA.VS.A9UY.01 2 0.4380 0.6541 0.00 0.70 0.00 0.00 0.08 0.22
#> TCGA.VS.A9U5.01 2 0.0937 0.7519 0.00 0.96 0.00 0.00 0.04 0.00
#> TCGA.DS.A1OC.01 5 0.1807 0.7162 0.02 0.00 0.00 0.00 0.92 0.06
#> TCGA.ZJ.AAXB.01 4 0.4244 0.6009 0.20 0.00 0.00 0.72 0.00 0.08
#> TCGA.EX.A449.01 3 0.0000 0.8796 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.C5.A1BL.01 2 0.5289 0.5583 0.00 0.58 0.00 0.00 0.14 0.28
#> TCGA.VS.A9UQ.01 3 0.0000 0.8796 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.DS.A1OB.01 1 0.0000 0.7373 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.HG.A9SC.01 1 0.2631 0.5969 0.82 0.00 0.00 0.18 0.00 0.00
#> TCGA.ZJ.AAXT.01 4 0.6180 0.5448 0.26 0.00 0.00 0.56 0.08 0.10
#> TCGA.IR.A3LB.01 3 0.3309 0.6520 0.00 0.00 0.72 0.00 0.00 0.28
#> TCGA.C5.A1ML.01 4 0.3688 0.6614 0.14 0.00 0.00 0.80 0.02 0.04
#> TCGA.VS.A9UV.01 2 0.0937 0.7519 0.00 0.96 0.00 0.00 0.04 0.00
#> TCGA.LP.A4AU.01 4 0.4361 0.6352 0.04 0.00 0.00 0.76 0.06 0.14
#> TCGA.Q1.A6DT.01 2 0.5419 0.6128 0.00 0.58 0.00 0.00 0.22 0.20
#> TCGA.C5.A1M8.01 2 0.1814 0.7411 0.00 0.90 0.00 0.00 0.00 0.10
#> TCGA.C5.A1ME.01 3 0.3499 0.6076 0.00 0.00 0.68 0.00 0.00 0.32
#> TCGA.ZJ.AAXU.01 1 0.3045 0.7172 0.84 0.00 0.00 0.00 0.06 0.10
#> TCGA.VS.A957.01 2 0.6636 0.4077 0.04 0.44 0.00 0.00 0.24 0.28
#> TCGA.VS.A9V5.01 3 0.0000 0.8796 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.MU.A5YI.01 5 0.3315 0.6503 0.00 0.20 0.00 0.00 0.78 0.02
#> TCGA.ZJ.AAX4.01 2 0.3647 0.3863 0.00 0.64 0.00 0.00 0.36 0.00
#> TCGA.C5.A1MK.01 1 0.0000 0.7373 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.JW.A69B.01 3 0.0000 0.8796 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.VS.A958.01 1 0.4282 0.0746 0.56 0.00 0.00 0.42 0.02 0.00
#> TCGA.ZJ.AAXJ.01 2 0.2631 0.6510 0.00 0.82 0.00 0.00 0.18 0.00
#> TCGA.R2.A69V.01 4 0.5835 0.6054 0.12 0.00 0.00 0.64 0.10 0.14
#> TCGA.EA.A411.01 1 0.0000 0.7373 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.VS.A9UP.01 4 0.2260 0.6327 0.00 0.00 0.00 0.86 0.00 0.14
#> TCGA.C5.A1MI.01 4 0.3756 0.3298 0.00 0.00 0.00 0.60 0.00 0.40
#> TCGA.DS.A1O9.01 5 0.2345 0.7116 0.02 0.06 0.00 0.00 0.90 0.02
#> TCGA.VS.A9UZ.01 3 0.0000 0.8796 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.EA.A43B.01 5 0.2260 0.6508 0.00 0.00 0.00 0.00 0.86 0.14
#> TCGA.ZJ.AAX8.01 4 0.6430 0.5521 0.20 0.00 0.00 0.56 0.10 0.14
#> TCGA.ZJ.AAXI.01 2 0.4727 0.6284 0.00 0.66 0.00 0.00 0.10 0.24
#> TCGA.VS.A9UT.01 4 0.0547 0.6838 0.00 0.00 0.00 0.98 0.00 0.02
#> TCGA.DS.A1OA.01 1 0.6101 0.5005 0.54 0.04 0.00 0.00 0.14 0.28
#> TCGA.C5.A1MQ.01 5 0.5452 -0.0277 0.00 0.12 0.00 0.00 0.44 0.44
#> TCGA.VS.A9V0.01 4 0.2048 0.6458 0.00 0.00 0.00 0.88 0.00 0.12
#> TCGA.VS.A9UC.01 5 0.2794 0.6709 0.08 0.00 0.00 0.00 0.86 0.06
#> TCGA.ZJ.AAXA.01 1 0.2631 0.5969 0.82 0.00 0.00 0.18 0.00 0.00
#> TCGA.Q1.A73P.01 3 0.0000 0.8796 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.VS.A9V2.01 5 0.2941 0.6374 0.00 0.22 0.00 0.00 0.78 0.00
#> TCGA.VS.A9UU.01 2 0.3851 0.1098 0.00 0.54 0.00 0.00 0.46 0.00
#> TCGA.LP.A4AV.01 1 0.1865 0.7410 0.92 0.00 0.00 0.00 0.04 0.04
#> TCGA.VS.A9UR.01 3 0.0000 0.8796 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.VS.A9V1.01 6 0.5190 0.6956 0.00 0.00 0.04 0.18 0.10 0.68
#> TCGA.C5.A7CG.01 2 0.0937 0.7519 0.00 0.96 0.00 0.00 0.04 0.00
#> TCGA.UC.A7PI.01 3 0.0000 0.8796 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.EX.A1H5.01 5 0.2403 0.7203 0.04 0.02 0.00 0.00 0.90 0.04
#> TCGA.ZJ.AAXF.01 1 0.7143 0.0299 0.40 0.00 0.00 0.20 0.30 0.10
#> TCGA.VS.A9UL.01 3 0.3828 0.4145 0.00 0.00 0.56 0.00 0.00 0.44
#> TCGA.EA.A3Y4.01 1 0.4764 0.0268 0.54 0.00 0.00 0.42 0.02 0.02
#> TCGA.C5.A7CK.01 2 0.0937 0.7519 0.00 0.96 0.00 0.00 0.04 0.00
#> TCGA.UC.A7PG.06 1 0.0937 0.7438 0.96 0.00 0.00 0.00 0.04 0.00
#> TCGA.VS.A9UJ.01 4 0.2260 0.6327 0.00 0.00 0.00 0.86 0.00 0.14
#> TCGA.Q1.A73O.01 1 0.4801 -0.1222 0.50 0.00 0.00 0.46 0.02 0.02
#> TCGA.VS.A950.01 2 0.7195 0.3803 0.16 0.42 0.00 0.00 0.14 0.28
#> TCGA.EA.A439.01 6 0.3578 0.5239 0.00 0.00 0.00 0.00 0.34 0.66
#> TCGA.VS.A9UM.01 1 0.3475 0.6989 0.80 0.00 0.00 0.00 0.06 0.14
#> TCGA.C5.A1MP.01 1 0.1267 0.7063 0.94 0.00 0.00 0.06 0.00 0.00
#> TCGA.VS.A9UI.01 1 0.6777 0.4091 0.48 0.10 0.00 0.00 0.14 0.28
#> TCGA.ZJ.AB0H.01 1 0.2190 0.7399 0.90 0.00 0.00 0.00 0.06 0.04
#> TCGA.Q1.A73Q.01 1 0.5919 0.4891 0.54 0.02 0.00 0.00 0.16 0.28
#> TCGA.C5.A1MH.01 1 0.5354 0.4960 0.58 0.00 0.00 0.00 0.26 0.16
#> TCGA.VS.A9V4.01 4 0.2260 0.6463 0.00 0.00 0.00 0.86 0.00 0.14
#> TCGA.FU.A40J.01 3 0.0000 0.8796 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.VS.A9UA.01 5 0.4887 0.5371 0.16 0.00 0.00 0.02 0.70 0.12
#> TCGA.LP.A4AW.01 1 0.4393 0.6488 0.72 0.00 0.00 0.00 0.14 0.14
#> TCGA.MA.AA43.01 6 0.5628 0.4370 0.00 0.00 0.22 0.00 0.24 0.54
#> TCGA.C5.A1BN.01 1 0.2454 0.6207 0.84 0.00 0.00 0.16 0.00 0.00
#> TCGA.VS.AA62.01 4 0.5615 0.6226 0.12 0.00 0.00 0.66 0.08 0.14
#> TCGA.C5.A1BM.01 1 0.3828 0.0634 0.56 0.00 0.00 0.44 0.00 0.00
#> TCGA.C5.A1M6.01 6 0.3647 0.4927 0.00 0.00 0.00 0.00 0.36 0.64
#> TCGA.C5.A1BE.01 1 0.4420 0.4354 0.62 0.00 0.00 0.00 0.34 0.04
#> TCGA.FU.A23K.01 3 0.4310 0.3696 0.00 0.00 0.54 0.00 0.02 0.44
#> TCGA.C5.A1BJ.01 1 0.0547 0.7425 0.98 0.00 0.00 0.00 0.02 0.00
#> TCGA.FU.A23L.01 4 0.2631 0.6537 0.18 0.00 0.00 0.82 0.00 0.00
#> TCGA.C5.A1M5.01 2 0.2981 0.7184 0.00 0.82 0.00 0.00 0.02 0.16
#> TCGA.C5.A1MF.01 6 0.6215 -0.1865 0.02 0.30 0.00 0.00 0.20 0.48
#> TCGA.C5.A1BF.01 4 0.5778 0.6177 0.16 0.00 0.00 0.64 0.08 0.12
#> TCGA.C5.A1BK.01 2 0.5029 0.5861 0.00 0.62 0.00 0.00 0.26 0.12
#> TCGA.C5.A1BI.01 1 0.4144 0.2549 0.62 0.00 0.00 0.36 0.02 0.00
#> TCGA.C5.A1M9.01 3 0.0000 0.8796 0.00 0.00 1.00 0.00 0.00 0.00
cbind(get_classes(res, k = 7), get_membership(res, k = 7))
#> class entropy silhouette p1 p2 p3 p4 p5 p6 p7
#> TCGA.EK.A3GK.01 6 0.2278 0.72318 0.00 0.00 0.00 0.04 0.08 0.88 0.00
#> TCGA.GH.A9DA.01 5 0.1363 0.77751 0.02 0.00 0.00 0.04 0.94 0.00 0.00
#> TCGA.VS.A94Y.01 5 0.3815 0.46327 0.02 0.00 0.00 0.00 0.62 0.00 0.36
#> TCGA.MY.A5BF.11 4 0.4353 0.57680 0.24 0.00 0.00 0.66 0.00 0.10 0.00
#> TCGA.VS.A94Z.01 7 0.3139 0.12565 0.30 0.00 0.00 0.00 0.00 0.00 0.70
#> TCGA.EA.A4BA.01 4 0.5375 0.49794 0.34 0.00 0.00 0.46 0.00 0.20 0.00
#> TCGA.ZJ.A8QQ.01 2 0.3909 0.27920 0.02 0.58 0.00 0.00 0.40 0.00 0.00
#> TCGA.FU.A3EO.11 4 0.4353 0.57680 0.24 0.00 0.00 0.66 0.00 0.10 0.00
#> TCGA.DG.A2KJ.01 6 0.2376 0.71361 0.00 0.00 0.00 0.12 0.02 0.86 0.00
#> TCGA.VS.A954.01 2 0.0504 0.77492 0.00 0.98 0.00 0.00 0.02 0.00 0.00
#> TCGA.MA.AA42.01 5 0.3985 0.06971 0.02 0.46 0.00 0.00 0.52 0.00 0.00
#> TCGA.C5.A8YQ.01 5 0.0504 0.78026 0.00 0.00 0.00 0.02 0.98 0.00 0.00
#> TCGA.DS.A7WF.01 3 0.0000 0.99807 0.00 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.EK.A2R7.01 1 0.4993 0.61167 0.62 0.00 0.00 0.12 0.00 0.02 0.24
#> TCGA.EK.A3GJ.01 2 0.3985 0.10007 0.02 0.52 0.00 0.00 0.46 0.00 0.00
#> TCGA.C5.A902.01 2 0.0504 0.77492 0.00 0.98 0.00 0.00 0.02 0.00 0.00
#> TCGA.MA.AA3W.01 7 0.4070 0.21877 0.02 0.02 0.00 0.00 0.30 0.00 0.66
#> TCGA.C5.A905.01 1 0.3562 0.37266 0.50 0.00 0.00 0.00 0.00 0.00 0.50
#> TCGA.EK.A2RN.01 1 0.3968 0.50672 0.54 0.00 0.00 0.00 0.00 0.02 0.44
#> TCGA.FU.A57G.01 4 0.5375 0.49794 0.34 0.00 0.00 0.46 0.00 0.20 0.00
#> TCGA.C5.A8YR.01 4 0.3114 0.56216 0.04 0.00 0.00 0.84 0.04 0.08 0.00
#> TCGA.EK.A2R9.01 7 0.3722 0.33711 0.00 0.18 0.00 0.00 0.04 0.02 0.76
#> TCGA.FU.A3EO.01 3 0.0000 0.99807 0.00 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.IR.A3LC.01 2 0.0504 0.77492 0.00 0.98 0.00 0.00 0.02 0.00 0.00
#> TCGA.VS.A8QA.01 3 0.0000 0.99807 0.00 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.C5.A3HD.01 5 0.1886 0.72608 0.00 0.12 0.00 0.00 0.88 0.00 0.00
#> TCGA.MY.A5BE.01 5 0.1928 0.75596 0.00 0.00 0.00 0.08 0.90 0.02 0.00
#> TCGA.EA.A50E.01 2 0.0504 0.77492 0.00 0.98 0.00 0.00 0.02 0.00 0.00
#> TCGA.VS.A8QH.01 6 0.2376 0.71361 0.00 0.00 0.00 0.12 0.02 0.86 0.00
#> TCGA.ZJ.A8QR.01 7 0.5152 0.08112 0.24 0.00 0.00 0.00 0.14 0.02 0.60
#> TCGA.C5.A907.01 6 0.3517 0.50516 0.00 0.00 0.00 0.28 0.02 0.70 0.00
#> TCGA.IR.A3LK.01 7 0.0504 0.46899 0.02 0.00 0.00 0.00 0.00 0.00 0.98
#> TCGA.C5.A8ZZ.01 1 0.4461 0.54881 0.62 0.00 0.00 0.00 0.02 0.04 0.32
#> TCGA.VS.A8EK.01 2 0.0504 0.77492 0.00 0.98 0.00 0.00 0.02 0.00 0.00
#> TCGA.C5.A7UC.01 4 0.3968 -0.23368 0.44 0.00 0.00 0.54 0.00 0.00 0.02
#> TCGA.C5.A8XJ.01 7 0.3562 -0.41130 0.50 0.00 0.00 0.00 0.00 0.00 0.50
#> TCGA.IR.A3LH.01 5 0.1363 0.76964 0.02 0.04 0.00 0.00 0.94 0.00 0.00
#> TCGA.EK.A3GM.01 6 0.2376 0.71361 0.00 0.00 0.00 0.12 0.02 0.86 0.00
#> TCGA.VS.A8Q8.01 1 0.4328 0.53128 0.60 0.00 0.00 0.34 0.00 0.00 0.06
#> TCGA.EK.A2RO.01 5 0.1860 0.77605 0.00 0.04 0.00 0.00 0.92 0.02 0.02
#> TCGA.MY.A5BD.01 3 0.0000 0.99807 0.00 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.2W.A8YY.01 6 0.2016 0.65450 0.04 0.00 0.00 0.06 0.00 0.90 0.00
#> TCGA.C5.A2LZ.01 7 0.3943 -0.13413 0.00 0.42 0.00 0.00 0.00 0.02 0.56
#> TCGA.C5.A901.01 2 0.1928 0.74209 0.00 0.90 0.00 0.00 0.00 0.02 0.08
#> TCGA.VS.A953.01 2 0.0504 0.77492 0.00 0.98 0.00 0.00 0.02 0.00 0.00
#> TCGA.MU.A51Y.01 5 0.6436 0.32829 0.14 0.00 0.00 0.26 0.50 0.02 0.08
#> TCGA.EK.A2RK.01 1 0.4629 0.59958 0.64 0.00 0.00 0.20 0.00 0.00 0.16
#> TCGA.UC.A7PD.01 4 0.2769 0.56871 0.02 0.00 0.00 0.86 0.04 0.08 0.00
#> TCGA.EA.A3HS.01 7 0.2081 0.39055 0.14 0.00 0.00 0.00 0.00 0.00 0.86
#> TCGA.VS.A8QM.01 4 0.3991 0.39262 0.22 0.00 0.00 0.72 0.04 0.02 0.00
#> TCGA.EA.A3HU.01 5 0.6884 0.09150 0.24 0.00 0.00 0.26 0.40 0.02 0.08
#> TCGA.VS.A94X.01 4 0.4248 0.58167 0.26 0.00 0.00 0.66 0.00 0.08 0.00
#> TCGA.C5.A7CO.01 5 0.1886 0.72608 0.00 0.12 0.00 0.00 0.88 0.00 0.00
#> TCGA.C5.A3HF.01 6 0.2376 0.71361 0.00 0.00 0.00 0.12 0.02 0.86 0.00
#> TCGA.IR.A3LL.01 5 0.0504 0.78026 0.00 0.00 0.00 0.02 0.98 0.00 0.00
#> TCGA.MY.A913.01 4 0.2278 0.57250 0.00 0.00 0.00 0.88 0.04 0.08 0.00
#> TCGA.VS.A952.01 3 0.0000 0.99807 0.00 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.IR.A3LI.01 3 0.0000 0.99807 0.00 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.VS.A94W.01 5 0.2159 0.76759 0.00 0.00 0.00 0.02 0.90 0.02 0.06
#> TCGA.MY.A5BF.01 2 0.3221 0.46798 0.00 0.68 0.00 0.00 0.32 0.00 0.00
#> TCGA.EK.A2RC.01 7 0.0504 0.46899 0.02 0.00 0.00 0.00 0.00 0.00 0.98
#> TCGA.VS.A8EL.01 5 0.3994 0.00984 0.02 0.48 0.00 0.00 0.50 0.00 0.00
#> TCGA.EA.A97N.01 1 0.3413 0.57797 0.62 0.00 0.00 0.00 0.00 0.00 0.38
#> TCGA.EA.A3HQ.01 2 0.1006 0.76139 0.00 0.96 0.00 0.00 0.00 0.02 0.02
#> TCGA.EK.A2RD.01 1 0.3943 0.53404 0.56 0.00 0.00 0.00 0.00 0.02 0.42
#> TCGA.C5.A8YT.01 4 0.4353 0.57680 0.24 0.00 0.00 0.66 0.00 0.10 0.00
#> TCGA.FU.A3HZ.01 4 0.5375 0.49794 0.34 0.00 0.00 0.46 0.00 0.20 0.00
#> TCGA.VS.A8EJ.01 4 0.5375 0.49794 0.34 0.00 0.00 0.46 0.00 0.20 0.00
#> TCGA.C5.A3HL.01 4 0.4305 0.39289 0.28 0.00 0.00 0.66 0.02 0.04 0.00
#> TCGA.UC.A7PF.01 5 0.0504 0.78026 0.00 0.00 0.00 0.02 0.98 0.00 0.00
#> TCGA.C5.A8XK.01 5 0.5602 0.48937 0.02 0.00 0.00 0.24 0.58 0.14 0.02
#> TCGA.EX.A8YF.01 4 0.2572 0.55525 0.00 0.00 0.00 0.80 0.00 0.20 0.00
#> TCGA.HM.A4S6.01 1 0.3968 0.50672 0.54 0.00 0.00 0.00 0.00 0.02 0.44
#> TCGA.VS.A8Q9.01 5 0.1006 0.77600 0.02 0.02 0.00 0.00 0.96 0.00 0.00
#> TCGA.MA.AA41.01 7 0.3985 -0.26327 0.00 0.46 0.00 0.00 0.00 0.02 0.52
#> TCGA.EK.A3GN.01 2 0.2163 0.74889 0.00 0.88 0.00 0.00 0.02 0.00 0.10
#> TCGA.MA.AA3Y.01 4 0.3149 0.55942 0.04 0.00 0.00 0.84 0.06 0.06 0.00
#> TCGA.MA.AA3Z.01 7 0.3496 -0.19840 0.42 0.00 0.00 0.00 0.00 0.00 0.58
#> TCGA.EK.A2RE.01 1 0.4742 0.59703 0.62 0.00 0.00 0.22 0.00 0.00 0.16
#> TCGA.C5.A1BQ.01 7 0.3358 -0.04505 0.36 0.00 0.00 0.00 0.00 0.00 0.64
#> TCGA.ZJ.A8QO.01 5 0.1860 0.76944 0.02 0.02 0.00 0.00 0.92 0.00 0.04
#> TCGA.JW.A852.01 2 0.0504 0.77492 0.00 0.98 0.00 0.00 0.02 0.00 0.00
#> TCGA.DS.A7WH.01 6 0.3358 0.58703 0.00 0.00 0.36 0.00 0.00 0.64 0.00
#> TCGA.JW.AAVH.01 7 0.1928 0.47503 0.00 0.08 0.00 0.00 0.00 0.02 0.90
#> TCGA.EA.A556.01 4 0.5375 0.49794 0.34 0.00 0.00 0.46 0.00 0.20 0.00
#> TCGA.EA.A44S.01 1 0.5447 0.61482 0.60 0.00 0.00 0.12 0.02 0.02 0.24
#> TCGA.4J.AA1J.01 1 0.3558 0.42464 0.52 0.00 0.00 0.00 0.00 0.00 0.48
#> TCGA.IR.A3L7.01 2 0.3052 0.67180 0.00 0.78 0.00 0.00 0.00 0.02 0.20
#> TCGA.C5.A7X3.01 4 0.1928 0.57865 0.00 0.00 0.00 0.90 0.02 0.08 0.00
#> TCGA.HG.A2PA.01 5 0.1166 0.77307 0.00 0.00 0.00 0.06 0.94 0.00 0.00
#> TCGA.C5.A8XH.01 5 0.2376 0.72061 0.02 0.12 0.00 0.00 0.86 0.00 0.00
#> TCGA.C5.A7XC.01 1 0.4873 0.61189 0.60 0.00 0.00 0.18 0.00 0.00 0.22
#> TCGA.VS.A8EI.01 5 0.1006 0.77966 0.02 0.00 0.00 0.02 0.96 0.00 0.00
#> TCGA.VS.A8QC.01 2 0.2376 0.72425 0.00 0.86 0.00 0.00 0.00 0.02 0.12
#> TCGA.C5.A7UH.01 1 0.3413 0.57797 0.62 0.00 0.00 0.00 0.00 0.00 0.38
#> TCGA.WL.A834.01 2 0.3606 0.57964 0.00 0.68 0.00 0.00 0.00 0.02 0.30
#> TCGA.C5.A8XI.01 2 0.0504 0.77492 0.00 0.98 0.00 0.00 0.02 0.00 0.00
#> TCGA.DS.A7WI.01 5 0.1006 0.77966 0.02 0.00 0.00 0.02 0.96 0.00 0.00
#> TCGA.VS.A8QF.01 2 0.2376 0.72425 0.00 0.86 0.00 0.00 0.00 0.02 0.12
#> TCGA.EA.A3HR.01 1 0.4873 0.60102 0.60 0.00 0.00 0.22 0.00 0.00 0.18
#> TCGA.DG.A2KL.01 1 0.5659 0.47900 0.50 0.00 0.00 0.02 0.10 0.02 0.36
#> TCGA.EK.A2RL.01 3 0.0000 0.99807 0.00 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.EK.A2PG.01 2 0.2163 0.73426 0.00 0.88 0.00 0.00 0.00 0.02 0.10
#> TCGA.BI.A0VR.01 1 0.5888 0.28860 0.40 0.00 0.00 0.00 0.22 0.02 0.36
#> TCGA.DS.A0VL.01 7 0.3994 -0.40069 0.48 0.00 0.00 0.00 0.00 0.02 0.50
#> TCGA.VS.A8EC.01 2 0.0504 0.77492 0.00 0.98 0.00 0.00 0.02 0.00 0.00
#> TCGA.EA.A3QE.01 5 0.1363 0.76964 0.02 0.04 0.00 0.00 0.94 0.00 0.00
#> TCGA.DS.A0VM.01 7 0.3968 -0.21078 0.00 0.44 0.00 0.00 0.00 0.02 0.54
#> TCGA.FU.A3HY.01 7 0.0504 0.48091 0.00 0.02 0.00 0.00 0.00 0.00 0.98
#> TCGA.Q1.A5R1.01 3 0.0000 0.99807 0.00 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.DR.A0ZM.01 1 0.4003 0.43271 0.64 0.00 0.00 0.32 0.00 0.00 0.04
#> TCGA.Q1.A6DW.01 2 0.0504 0.77492 0.00 0.98 0.00 0.00 0.02 0.00 0.00
#> TCGA.DS.A0VK.01 7 0.2422 0.34947 0.18 0.00 0.00 0.00 0.00 0.00 0.82
#> TCGA.DS.A3LQ.01 5 0.3546 0.34654 0.00 0.00 0.00 0.00 0.54 0.00 0.46
#> TCGA.EA.A3QD.01 2 0.0504 0.77492 0.00 0.98 0.00 0.00 0.02 0.00 0.00
#> TCGA.JW.A5VJ.01 1 0.3985 0.26318 0.52 0.00 0.00 0.46 0.00 0.00 0.02
#> TCGA.LP.A5U3.01 2 0.3815 0.50854 0.00 0.62 0.00 0.00 0.00 0.02 0.36
#> TCGA.EA.A6QX.01 7 0.3685 0.11498 0.00 0.32 0.00 0.00 0.00 0.02 0.66
#> TCGA.EK.A2RA.01 2 0.3517 0.59905 0.00 0.70 0.00 0.00 0.00 0.02 0.28
#> TCGA.FU.A5XV.01 7 0.3358 -0.04091 0.36 0.00 0.00 0.00 0.00 0.00 0.64
#> TCGA.Q1.A5R2.01 2 0.3755 0.53436 0.00 0.64 0.00 0.00 0.00 0.02 0.34
#> TCGA.HM.A3JJ.01 7 0.3139 0.12426 0.30 0.00 0.00 0.00 0.00 0.00 0.70
#> TCGA.C5.A2LS.01 3 0.0000 0.99807 0.00 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.C5.A7X8.01 6 0.3927 0.64402 0.00 0.00 0.30 0.00 0.04 0.66 0.00
#> TCGA.EK.A2RJ.01 4 0.4353 0.57680 0.24 0.00 0.00 0.66 0.00 0.10 0.00
#> TCGA.EA.A3HT.01 1 0.3815 0.59158 0.62 0.00 0.00 0.02 0.00 0.00 0.36
#> TCGA.LP.A7HU.01 3 0.0000 0.99807 0.00 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.MU.A8JM.01 5 0.2864 0.74710 0.00 0.00 0.00 0.02 0.84 0.02 0.12
#> TCGA.EK.A2IP.01 7 0.2259 0.37282 0.16 0.00 0.00 0.00 0.00 0.00 0.84
#> TCGA.JW.A5VL.01 7 0.3755 0.06342 0.00 0.34 0.00 0.00 0.00 0.02 0.64
#> TCGA.FU.A3TX.01 5 0.4797 0.54116 0.06 0.00 0.00 0.26 0.64 0.04 0.00
#> TCGA.DG.A2KK.01 3 0.0000 0.99807 0.00 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.EK.A2PI.01 5 0.2213 0.76584 0.04 0.00 0.00 0.02 0.90 0.04 0.00
#> TCGA.Q1.A73S.01 4 0.5474 0.47431 0.36 0.00 0.00 0.42 0.00 0.22 0.00
#> TCGA.EK.A2IR.01 5 0.2213 0.76584 0.04 0.00 0.00 0.02 0.90 0.04 0.00
#> TCGA.HM.A6W2.01 4 0.5375 0.49794 0.34 0.00 0.00 0.46 0.00 0.20 0.00
#> TCGA.VS.A8EH.01 5 0.2213 0.76584 0.04 0.00 0.00 0.02 0.90 0.04 0.00
#> TCGA.JW.A5VH.01 4 0.5375 0.49794 0.34 0.00 0.00 0.46 0.00 0.20 0.00
#> TCGA.C5.A2LV.01 2 0.3047 0.53391 0.00 0.72 0.00 0.00 0.28 0.00 0.00
#> TCGA.VS.A8EB.01 5 0.3257 0.75183 0.04 0.00 0.00 0.02 0.84 0.02 0.08
#> TCGA.RA.A741.01 4 0.4244 -0.10827 0.42 0.00 0.00 0.54 0.04 0.00 0.00
#> TCGA.VS.A8EG.01 2 0.5381 0.38657 0.00 0.50 0.00 0.00 0.12 0.02 0.36
#> TCGA.DG.A2KH.01 6 0.2376 0.71361 0.00 0.00 0.00 0.12 0.02 0.86 0.00
#> TCGA.C5.A7UE.01 5 0.1006 0.77523 0.00 0.02 0.00 0.00 0.96 0.00 0.02
#> TCGA.C5.A2LT.01 4 0.5023 0.29875 0.04 0.00 0.00 0.62 0.26 0.08 0.00
#> TCGA.EA.A5ZD.01 1 0.3985 0.35198 0.52 0.00 0.00 0.46 0.00 0.00 0.02
#> TCGA.Q1.A73R.01 3 0.0000 0.99807 0.00 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.JW.A5VK.01 2 0.3943 0.42147 0.00 0.56 0.00 0.00 0.00 0.02 0.42
#> TCGA.EK.A2RM.01 6 0.5233 -0.09306 0.28 0.00 0.00 0.20 0.00 0.52 0.00
#> TCGA.C5.A7UI.01 7 0.2422 0.34702 0.18 0.00 0.00 0.00 0.00 0.00 0.82
#> TCGA.EK.A2PL.01 7 0.3558 -0.37730 0.48 0.00 0.00 0.00 0.00 0.00 0.52
#> TCGA.EK.A2PM.01 4 0.3525 0.37338 0.44 0.00 0.00 0.56 0.00 0.00 0.00
#> TCGA.EK.A2GZ.01 5 0.4110 0.70707 0.06 0.00 0.00 0.10 0.78 0.04 0.02
#> TCGA.HM.A3JK.01 5 0.4933 0.58433 0.06 0.00 0.00 0.20 0.68 0.02 0.04
#> TCGA.C5.A2M1.01 3 0.0000 0.99807 0.00 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.HM.A6W2.06 4 0.5375 0.49794 0.34 0.00 0.00 0.46 0.00 0.20 0.00
#> TCGA.C5.A7X5.01 2 0.3221 0.46798 0.00 0.68 0.00 0.00 0.32 0.00 0.00
#> TCGA.IR.A3LA.01 4 0.5375 0.49794 0.34 0.00 0.00 0.46 0.00 0.20 0.00
#> TCGA.EK.A2PK.01 4 0.2745 0.57039 0.00 0.00 0.00 0.82 0.02 0.16 0.00
#> TCGA.EA.A5ZF.01 4 0.5485 0.46624 0.38 0.00 0.00 0.40 0.00 0.22 0.00
#> TCGA.XS.A8TJ.01 7 0.3058 0.39295 0.10 0.00 0.00 0.00 0.08 0.00 0.82
#> TCGA.BI.A0VS.01 1 0.5286 0.58937 0.64 0.00 0.00 0.16 0.02 0.02 0.16
#> TCGA.DS.A0VN.01 5 0.1505 0.77740 0.00 0.00 0.00 0.02 0.94 0.02 0.02
#> TCGA.JX.A5QV.01 1 0.5569 0.38739 0.52 0.00 0.00 0.36 0.06 0.02 0.04
#> TCGA.EK.A2R8.01 4 0.4121 0.58372 0.20 0.00 0.00 0.70 0.00 0.10 0.00
#> TCGA.EA.A1QS.01 4 0.1006 0.59801 0.02 0.00 0.00 0.96 0.02 0.00 0.00
#> TCGA.C5.A3HE.01 6 0.3404 0.74500 0.00 0.00 0.06 0.04 0.08 0.82 0.00
#> TCGA.IR.A3LF.01 3 0.0000 0.99807 0.00 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.DR.A0ZL.01 7 0.2803 0.42595 0.06 0.00 0.00 0.00 0.10 0.00 0.84
#> TCGA.FU.A3WB.01 5 0.1886 0.72608 0.00 0.12 0.00 0.00 0.88 0.00 0.00
#> TCGA.JX.A3PZ.01 4 0.2163 0.56160 0.10 0.00 0.00 0.88 0.02 0.00 0.00
#> TCGA.EA.A5O9.01 5 0.3562 -0.04589 0.00 0.50 0.00 0.00 0.50 0.00 0.00
#> TCGA.HM.A3JJ.11 4 0.4353 0.57680 0.24 0.00 0.00 0.66 0.00 0.10 0.00
#> TCGA.DS.A5RQ.01 1 0.3909 0.55363 0.58 0.00 0.00 0.00 0.00 0.02 0.40
#> TCGA.EK.A2H0.01 2 0.3909 0.27920 0.02 0.58 0.00 0.00 0.40 0.00 0.00
#> TCGA.EX.A1H6.01 6 0.3358 0.58703 0.00 0.00 0.36 0.00 0.00 0.64 0.00
#> TCGA.EA.A5ZE.01 2 0.1006 0.77161 0.00 0.96 0.00 0.00 0.02 0.00 0.02
#> TCGA.C5.A2LY.01 5 0.5760 0.38128 0.14 0.00 0.00 0.28 0.54 0.02 0.02
#> TCGA.FU.A3TQ.01 5 0.3307 0.65059 0.00 0.00 0.00 0.00 0.74 0.02 0.24
#> TCGA.EK.A2RB.01 2 0.3968 0.38882 0.00 0.54 0.00 0.00 0.00 0.02 0.44
#> TCGA.JW.A5VI.01 5 0.1006 0.78058 0.00 0.00 0.00 0.02 0.96 0.00 0.02
#> TCGA.EK.A2H1.01 4 0.0504 0.60006 0.00 0.00 0.00 0.98 0.00 0.02 0.00
#> TCGA.JX.A3Q8.01 3 0.0000 0.99807 0.00 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.FU.A3YQ.01 5 0.1505 0.78104 0.02 0.00 0.00 0.02 0.94 0.00 0.02
#> TCGA.EX.A69L.01 1 0.6163 0.53411 0.48 0.00 0.00 0.14 0.04 0.02 0.32
#> TCGA.C5.A7CH.01 2 0.0504 0.77492 0.00 0.98 0.00 0.00 0.02 0.00 0.00
#> TCGA.FU.A2QG.01 1 0.3413 0.57797 0.62 0.00 0.00 0.00 0.00 0.00 0.38
#> TCGA.C5.A2M2.01 3 0.0000 0.99807 0.00 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.JW.A5VG.01 4 0.2769 0.56871 0.02 0.00 0.00 0.86 0.04 0.08 0.00
#> TCGA.PN.A8MA.01 1 0.5052 -0.27505 0.62 0.00 0.00 0.14 0.00 0.22 0.02
#> TCGA.DG.A2KM.01 4 0.2769 0.56871 0.02 0.00 0.00 0.86 0.04 0.08 0.00
#> TCGA.C5.A2LX.01 2 0.0504 0.77492 0.00 0.98 0.00 0.00 0.02 0.00 0.00
#> TCGA.EX.A3L1.01 4 0.1928 0.57865 0.00 0.00 0.00 0.90 0.02 0.08 0.00
#> TCGA.LP.A5U2.01 2 0.0504 0.76668 0.00 0.98 0.00 0.00 0.00 0.02 0.00
#> TCGA.FU.A3NI.01 2 0.3221 0.46798 0.00 0.68 0.00 0.00 0.32 0.00 0.00
#> TCGA.Q1.A5R3.01 1 0.3459 0.56135 0.60 0.00 0.00 0.00 0.00 0.00 0.40
#> TCGA.FU.A770.01 6 0.3927 0.64402 0.00 0.00 0.30 0.00 0.04 0.66 0.00
#> TCGA.C5.A7CM.01 6 0.2376 0.71361 0.00 0.00 0.00 0.12 0.02 0.86 0.00
#> TCGA.JX.A3Q0.01 1 0.3496 0.53589 0.58 0.00 0.00 0.00 0.00 0.00 0.42
#> TCGA.EA.A5FO.01 3 0.0000 0.99807 0.00 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.VS.A9V3.01 2 0.2569 0.71278 0.00 0.84 0.00 0.00 0.00 0.02 0.14
#> TCGA.C5.A7CL.01 5 0.2421 0.75700 0.00 0.00 0.00 0.08 0.88 0.02 0.02
#> TCGA.VS.A959.01 6 0.4547 0.36125 0.00 0.00 0.00 0.08 0.34 0.58 0.00
#> TCGA.LP.A4AX.01 5 0.3289 0.71641 0.02 0.00 0.00 0.10 0.82 0.06 0.00
#> TCGA.C5.A1MN.01 2 0.0504 0.77492 0.00 0.98 0.00 0.00 0.02 0.00 0.00
#> TCGA.ZJ.AAXN.01 4 0.1006 0.59801 0.02 0.00 0.00 0.96 0.02 0.00 0.00
#> TCGA.MA.AA3X.01 1 0.3413 0.57797 0.62 0.00 0.00 0.00 0.00 0.00 0.38
#> TCGA.UC.A7PG.01 1 0.3943 0.53404 0.56 0.00 0.00 0.00 0.00 0.02 0.42
#> TCGA.Q1.A6DV.01 6 0.2906 0.71924 0.00 0.00 0.18 0.00 0.02 0.80 0.00
#> TCGA.DS.A1OD.01 7 0.3985 -0.35758 0.46 0.00 0.00 0.00 0.00 0.02 0.52
#> TCGA.C5.A1M7.01 1 0.4514 0.38020 0.48 0.00 0.00 0.46 0.00 0.00 0.06
#> TCGA.BI.A20A.01 5 0.0863 0.77177 0.00 0.04 0.00 0.00 0.96 0.00 0.00
#> TCGA.VS.A9UO.01 6 0.3294 0.61185 0.00 0.00 0.34 0.00 0.00 0.66 0.00
#> TCGA.EA.A1QT.01 7 0.3968 -0.18922 0.00 0.44 0.00 0.00 0.00 0.02 0.54
#> TCGA.EX.A69M.01 2 0.3943 0.22481 0.02 0.56 0.00 0.00 0.42 0.00 0.00
#> TCGA.VS.A9UH.01 5 0.4938 0.44159 0.02 0.00 0.00 0.32 0.58 0.08 0.00
#> TCGA.VS.A9U7.01 2 0.3815 0.50854 0.00 0.62 0.00 0.00 0.00 0.02 0.36
#> TCGA.ZJ.AAXD.01 1 0.4615 0.61413 0.60 0.00 0.00 0.10 0.00 0.00 0.30
#> TCGA.VS.A9UB.01 4 0.4992 0.25609 0.02 0.00 0.00 0.60 0.28 0.10 0.00
#> TCGA.EA.A410.01 4 0.5332 0.49422 0.38 0.00 0.00 0.44 0.00 0.18 0.00
#> TCGA.ZJ.AB0I.01 1 0.4742 0.59703 0.62 0.00 0.00 0.22 0.00 0.00 0.16
#> TCGA.VS.A9UD.01 5 0.1886 0.72608 0.00 0.12 0.00 0.00 0.88 0.00 0.00
#> TCGA.VS.A9U6.01 7 0.3815 -0.07386 0.36 0.00 0.00 0.00 0.00 0.02 0.62
#> TCGA.ZX.AA5X.01 5 0.2906 0.71515 0.02 0.00 0.00 0.00 0.80 0.00 0.18
#> TCGA.C5.A0TN.01 4 0.2769 0.56871 0.02 0.00 0.00 0.86 0.04 0.08 0.00
#> TCGA.C5.A7CJ.01 5 0.3968 0.26096 0.00 0.00 0.00 0.00 0.54 0.02 0.44
#> TCGA.C5.A1MJ.01 6 0.3294 0.61185 0.00 0.00 0.34 0.00 0.00 0.66 0.00
#> TCGA.EA.A78R.01 5 0.1363 0.76964 0.02 0.04 0.00 0.00 0.94 0.00 0.00
#> TCGA.VS.A9UY.01 2 0.3909 0.45237 0.00 0.58 0.00 0.00 0.00 0.02 0.40
#> TCGA.VS.A9U5.01 2 0.0504 0.77492 0.00 0.98 0.00 0.00 0.02 0.00 0.00
#> TCGA.DS.A1OC.01 5 0.0504 0.78026 0.00 0.00 0.00 0.02 0.98 0.00 0.00
#> TCGA.ZJ.AAXB.01 1 0.4500 -0.17158 0.68 0.00 0.00 0.22 0.00 0.08 0.02
#> TCGA.EX.A449.01 3 0.0000 0.99807 0.00 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.C5.A1BL.01 7 0.3968 -0.21078 0.00 0.44 0.00 0.00 0.00 0.02 0.54
#> TCGA.VS.A9UQ.01 3 0.0000 0.99807 0.00 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.DS.A1OB.01 1 0.3413 0.57797 0.62 0.00 0.00 0.00 0.00 0.00 0.38
#> TCGA.HG.A9SC.01 1 0.4070 0.60160 0.62 0.00 0.00 0.04 0.00 0.00 0.34
#> TCGA.ZJ.AAXT.01 4 0.4193 0.44001 0.20 0.00 0.00 0.72 0.04 0.04 0.00
#> TCGA.IR.A3LB.01 6 0.3358 0.58703 0.00 0.00 0.36 0.00 0.00 0.64 0.00
#> TCGA.C5.A1ML.01 4 0.5086 0.51996 0.36 0.00 0.00 0.50 0.00 0.14 0.00
#> TCGA.VS.A9UV.01 2 0.0504 0.77492 0.00 0.98 0.00 0.00 0.02 0.00 0.00
#> TCGA.LP.A4AU.01 4 0.2163 0.57895 0.00 0.00 0.00 0.88 0.02 0.10 0.00
#> TCGA.Q1.A6DT.01 7 0.5888 -0.32583 0.02 0.36 0.00 0.00 0.22 0.00 0.40
#> TCGA.C5.A1M8.01 2 0.2376 0.72529 0.00 0.86 0.00 0.00 0.00 0.02 0.12
#> TCGA.C5.A1ME.01 6 0.3358 0.58703 0.00 0.00 0.36 0.00 0.00 0.64 0.00
#> TCGA.ZJ.AAXU.01 7 0.3867 -0.13275 0.38 0.00 0.00 0.00 0.00 0.02 0.60
#> TCGA.VS.A957.01 7 0.4577 -0.00988 0.00 0.36 0.00 0.00 0.02 0.04 0.58
#> TCGA.VS.A9V5.01 3 0.0000 0.99807 0.00 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.MU.A5YI.01 5 0.0863 0.77177 0.00 0.04 0.00 0.00 0.96 0.00 0.00
#> TCGA.ZJ.AAX4.01 2 0.3459 0.29802 0.00 0.60 0.00 0.00 0.40 0.00 0.00
#> TCGA.C5.A1MK.01 1 0.3525 0.50707 0.56 0.00 0.00 0.00 0.00 0.00 0.44
#> TCGA.JW.A69B.01 3 0.0000 0.99807 0.00 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.VS.A958.01 1 0.3985 0.35198 0.52 0.00 0.00 0.46 0.00 0.00 0.02
#> TCGA.ZJ.AAXJ.01 2 0.2708 0.61671 0.00 0.78 0.00 0.00 0.22 0.00 0.00
#> TCGA.R2.A69V.01 4 0.2769 0.56871 0.02 0.00 0.00 0.86 0.04 0.08 0.00
#> TCGA.EA.A411.01 1 0.3413 0.57797 0.62 0.00 0.00 0.00 0.00 0.00 0.38
#> TCGA.VS.A9UP.01 4 0.5485 0.46624 0.38 0.00 0.00 0.40 0.00 0.22 0.00
#> TCGA.C5.A1MI.01 1 0.5631 -0.59267 0.36 0.00 0.00 0.34 0.00 0.30 0.00
#> TCGA.DS.A1O9.01 5 0.1006 0.77741 0.02 0.00 0.00 0.00 0.96 0.00 0.02
#> TCGA.VS.A9UZ.01 3 0.0000 0.99807 0.00 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.EA.A43B.01 5 0.1006 0.77966 0.02 0.00 0.00 0.02 0.96 0.00 0.00
#> TCGA.ZJ.AAX8.01 4 0.3149 0.56438 0.06 0.00 0.00 0.84 0.04 0.06 0.00
#> TCGA.ZJ.AAXI.01 2 0.3943 0.42147 0.00 0.56 0.00 0.00 0.00 0.02 0.42
#> TCGA.VS.A9UT.01 4 0.4353 0.57680 0.24 0.00 0.00 0.66 0.00 0.10 0.00
#> TCGA.DS.A1OA.01 7 0.0504 0.48091 0.00 0.02 0.00 0.00 0.00 0.00 0.98
#> TCGA.C5.A1MQ.01 6 0.3815 0.44655 0.02 0.00 0.00 0.00 0.36 0.62 0.00
#> TCGA.VS.A9V0.01 4 0.5375 0.49794 0.34 0.00 0.00 0.46 0.00 0.20 0.00
#> TCGA.VS.A9UC.01 5 0.3307 0.66435 0.02 0.00 0.00 0.00 0.74 0.00 0.24
#> TCGA.ZJ.AAXA.01 1 0.4538 0.61959 0.62 0.00 0.00 0.10 0.00 0.00 0.28
#> TCGA.Q1.A73P.01 3 0.0000 0.99807 0.00 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.VS.A9V2.01 5 0.1363 0.76964 0.02 0.04 0.00 0.00 0.94 0.00 0.00
#> TCGA.VS.A9UU.01 5 0.3985 0.08339 0.02 0.46 0.00 0.00 0.52 0.00 0.00
#> TCGA.LP.A4AV.01 1 0.3558 0.42464 0.52 0.00 0.00 0.00 0.00 0.00 0.48
#> TCGA.VS.A9UR.01 3 0.0863 0.94738 0.00 0.00 0.96 0.00 0.00 0.04 0.00
#> TCGA.VS.A9V1.01 6 0.2654 0.72561 0.00 0.00 0.02 0.10 0.02 0.86 0.00
#> TCGA.C5.A7CG.01 2 0.0504 0.77492 0.00 0.98 0.00 0.00 0.02 0.00 0.00
#> TCGA.UC.A7PI.01 3 0.0000 0.99807 0.00 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.EX.A1H5.01 5 0.2376 0.74559 0.00 0.00 0.00 0.00 0.86 0.02 0.12
#> TCGA.ZJ.AAXF.01 4 0.5723 0.04481 0.30 0.00 0.00 0.48 0.20 0.02 0.00
#> TCGA.VS.A9UL.01 6 0.3294 0.61185 0.00 0.00 0.34 0.00 0.00 0.66 0.00
#> TCGA.EA.A3Y4.01 4 0.3994 -0.30087 0.48 0.00 0.00 0.50 0.00 0.00 0.02
#> TCGA.C5.A7CK.01 2 0.0504 0.77492 0.00 0.98 0.00 0.00 0.02 0.00 0.00
#> TCGA.UC.A7PG.06 1 0.3459 0.56135 0.60 0.00 0.00 0.00 0.00 0.00 0.40
#> TCGA.VS.A9UJ.01 4 0.5375 0.49794 0.34 0.00 0.00 0.46 0.00 0.20 0.00
#> TCGA.Q1.A73O.01 1 0.3985 0.35198 0.52 0.00 0.00 0.46 0.00 0.00 0.02
#> TCGA.VS.A950.01 7 0.2906 0.37591 0.00 0.18 0.00 0.00 0.02 0.00 0.80
#> TCGA.EA.A439.01 6 0.3000 0.70786 0.04 0.00 0.00 0.02 0.10 0.84 0.00
#> TCGA.VS.A9UM.01 7 0.3459 -0.14027 0.40 0.00 0.00 0.00 0.00 0.00 0.60
#> TCGA.C5.A1MP.01 1 0.4698 0.61849 0.62 0.00 0.00 0.14 0.00 0.00 0.24
#> TCGA.VS.A9UI.01 7 0.0504 0.48091 0.00 0.02 0.00 0.00 0.00 0.00 0.98
#> TCGA.ZJ.AB0H.01 7 0.3968 -0.30737 0.44 0.00 0.00 0.00 0.00 0.02 0.54
#> TCGA.Q1.A73Q.01 7 0.0504 0.47769 0.00 0.00 0.00 0.00 0.02 0.00 0.98
#> TCGA.C5.A1MH.01 7 0.2708 0.38390 0.00 0.00 0.00 0.00 0.22 0.00 0.78
#> TCGA.VS.A9V4.01 4 0.5007 0.53188 0.28 0.00 0.00 0.56 0.00 0.16 0.00
#> TCGA.FU.A40J.01 3 0.0000 0.99807 0.00 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.VS.A9UA.01 5 0.4778 0.41181 0.06 0.00 0.00 0.34 0.58 0.02 0.00
#> TCGA.LP.A4AW.01 7 0.2832 0.25427 0.24 0.00 0.00 0.00 0.00 0.00 0.76
#> TCGA.MA.AA43.01 6 0.3867 0.70754 0.00 0.00 0.14 0.00 0.12 0.74 0.00
#> TCGA.C5.A1BN.01 1 0.4538 0.61959 0.62 0.00 0.00 0.10 0.00 0.00 0.28
#> TCGA.VS.AA62.01 4 0.2278 0.57250 0.00 0.00 0.00 0.88 0.04 0.08 0.00
#> TCGA.C5.A1BM.01 1 0.3968 0.36314 0.54 0.00 0.00 0.44 0.00 0.00 0.02
#> TCGA.C5.A1M6.01 6 0.2163 0.72233 0.00 0.00 0.00 0.02 0.10 0.88 0.00
#> TCGA.C5.A1BE.01 7 0.5669 0.07028 0.20 0.00 0.00 0.00 0.28 0.02 0.50
#> TCGA.FU.A23K.01 6 0.3685 0.62717 0.00 0.00 0.32 0.00 0.02 0.66 0.00
#> TCGA.C5.A1BJ.01 1 0.3546 0.49014 0.54 0.00 0.00 0.00 0.00 0.00 0.46
#> TCGA.FU.A23L.01 4 0.4597 0.54525 0.36 0.00 0.00 0.56 0.00 0.08 0.00
#> TCGA.C5.A1M5.01 2 0.3755 0.53436 0.00 0.64 0.00 0.00 0.00 0.02 0.34
#> TCGA.C5.A1MF.01 7 0.5240 0.16734 0.00 0.14 0.00 0.00 0.02 0.26 0.58
#> TCGA.C5.A1BF.01 4 0.2857 0.57370 0.04 0.00 0.00 0.86 0.04 0.06 0.00
#> TCGA.C5.A1BK.01 5 0.5931 -0.05504 0.02 0.34 0.00 0.00 0.40 0.00 0.24
#> TCGA.C5.A1BI.01 1 0.4266 0.38996 0.52 0.00 0.00 0.44 0.00 0.00 0.04
#> TCGA.C5.A1M9.01 3 0.0000 0.99807 0.00 0.00 1.00 0.00 0.00 0.00 0.00
cbind(get_classes(res, k = 8), get_membership(res, k = 8))
#> class entropy silhouette p1 p2 p3 p4 p5 p6 p7 p8
#> TCGA.EK.A3GK.01 6 0.2132 0.8417 0.00 0.00 0.00 0.08 0.00 0.88 0.00 0.04
#> TCGA.GH.A9DA.01 5 0.1275 0.8097 0.00 0.00 0.00 0.04 0.94 0.00 0.02 0.00
#> TCGA.VS.A94Y.01 5 0.4046 0.6814 0.02 0.00 0.00 0.06 0.74 0.02 0.16 0.00
#> TCGA.MY.A5BF.11 8 0.2938 0.6305 0.00 0.00 0.00 0.30 0.00 0.00 0.00 0.70
#> TCGA.VS.A94Z.01 1 0.4837 0.5012 0.58 0.00 0.00 0.02 0.06 0.02 0.32 0.00
#> TCGA.EA.A4BA.01 8 0.0941 0.8140 0.00 0.00 0.00 0.02 0.00 0.02 0.00 0.96
#> TCGA.ZJ.A8QQ.01 2 0.2406 0.7444 0.00 0.80 0.00 0.00 0.20 0.00 0.00 0.00
#> TCGA.FU.A3EO.11 8 0.2938 0.6305 0.00 0.00 0.00 0.30 0.00 0.00 0.00 0.70
#> TCGA.DG.A2KJ.01 6 0.2132 0.8436 0.00 0.00 0.00 0.04 0.00 0.88 0.00 0.08
#> TCGA.VS.A954.01 2 0.1275 0.8118 0.00 0.94 0.00 0.02 0.00 0.04 0.00 0.00
#> TCGA.MA.AA42.01 2 0.3193 0.4944 0.00 0.62 0.00 0.00 0.38 0.00 0.00 0.00
#> TCGA.C5.A8YQ.01 5 0.2348 0.8087 0.00 0.00 0.00 0.06 0.88 0.02 0.04 0.00
#> TCGA.DS.A7WF.01 3 0.0000 0.9901 0.00 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.EK.A2R7.01 1 0.0941 0.7717 0.96 0.00 0.00 0.02 0.00 0.00 0.02 0.00
#> TCGA.EK.A3GJ.01 2 0.3977 0.6620 0.00 0.70 0.00 0.02 0.24 0.02 0.02 0.00
#> TCGA.C5.A902.01 2 0.0000 0.8281 0.00 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.MA.AA3W.01 7 0.5530 0.0472 0.04 0.00 0.00 0.06 0.40 0.04 0.46 0.00
#> TCGA.C5.A905.01 1 0.1557 0.7801 0.92 0.00 0.00 0.00 0.00 0.02 0.06 0.00
#> TCGA.EK.A2RN.01 1 0.1557 0.7736 0.92 0.00 0.00 0.06 0.00 0.02 0.00 0.00
#> TCGA.FU.A57G.01 8 0.0808 0.8144 0.00 0.00 0.00 0.04 0.00 0.00 0.00 0.96
#> TCGA.C5.A8YR.01 4 0.2114 0.7506 0.00 0.00 0.00 0.84 0.00 0.00 0.00 0.16
#> TCGA.EK.A2R9.01 7 0.4401 0.7260 0.04 0.02 0.00 0.04 0.06 0.08 0.76 0.00
#> TCGA.FU.A3EO.01 3 0.0000 0.9901 0.00 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.IR.A3LC.01 2 0.0000 0.8281 0.00 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.VS.A8QA.01 3 0.0000 0.9901 0.00 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.C5.A3HD.01 5 0.4046 0.7035 0.00 0.16 0.00 0.06 0.74 0.02 0.02 0.00
#> TCGA.MY.A5BE.01 5 0.2267 0.8005 0.00 0.00 0.00 0.18 0.82 0.00 0.00 0.00
#> TCGA.EA.A50E.01 2 0.0000 0.8281 0.00 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.VS.A8QH.01 6 0.2348 0.8472 0.00 0.00 0.00 0.04 0.02 0.88 0.00 0.06
#> TCGA.ZJ.A8QR.01 1 0.5589 0.5156 0.56 0.00 0.00 0.04 0.18 0.02 0.20 0.00
#> TCGA.C5.A907.01 6 0.4433 0.3954 0.00 0.00 0.00 0.34 0.00 0.56 0.00 0.10
#> TCGA.IR.A3LK.01 7 0.3891 0.5997 0.14 0.00 0.00 0.02 0.06 0.02 0.76 0.00
#> TCGA.C5.A8ZZ.01 1 0.1741 0.7648 0.92 0.00 0.00 0.02 0.00 0.00 0.04 0.02
#> TCGA.VS.A8EK.01 2 0.0000 0.8281 0.00 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.C5.A7UC.01 4 0.2852 0.6399 0.28 0.00 0.00 0.72 0.00 0.00 0.00 0.00
#> TCGA.C5.A8XJ.01 1 0.1557 0.7801 0.92 0.00 0.00 0.00 0.00 0.02 0.06 0.00
#> TCGA.IR.A3LH.01 5 0.1557 0.8027 0.00 0.06 0.00 0.00 0.92 0.00 0.02 0.00
#> TCGA.EK.A3GM.01 6 0.2132 0.8436 0.00 0.00 0.00 0.04 0.00 0.88 0.00 0.08
#> TCGA.VS.A8Q8.01 1 0.2267 0.6218 0.82 0.00 0.00 0.18 0.00 0.00 0.00 0.00
#> TCGA.EK.A2RO.01 5 0.5163 0.7362 0.02 0.02 0.00 0.10 0.70 0.10 0.04 0.02
#> TCGA.MY.A5BD.01 3 0.0000 0.9901 0.00 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.2W.A8YY.01 6 0.2856 0.7552 0.00 0.00 0.00 0.02 0.00 0.78 0.00 0.20
#> TCGA.C5.A2LZ.01 7 0.2265 0.7700 0.02 0.08 0.00 0.00 0.02 0.00 0.88 0.00
#> TCGA.C5.A901.01 2 0.2267 0.6617 0.00 0.82 0.00 0.00 0.00 0.00 0.18 0.00
#> TCGA.VS.A953.01 2 0.0000 0.8281 0.00 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.MU.A51Y.01 5 0.5583 0.5279 0.24 0.00 0.00 0.20 0.52 0.02 0.00 0.02
#> TCGA.EK.A2RK.01 1 0.1275 0.7586 0.94 0.00 0.00 0.04 0.00 0.00 0.02 0.00
#> TCGA.UC.A7PD.01 4 0.2404 0.7716 0.02 0.00 0.00 0.84 0.00 0.00 0.00 0.14
#> TCGA.EA.A3HS.01 1 0.4994 0.3562 0.50 0.00 0.00 0.02 0.06 0.02 0.40 0.00
#> TCGA.VS.A8QM.01 4 0.3263 0.7321 0.12 0.00 0.00 0.78 0.00 0.00 0.00 0.10
#> TCGA.EA.A3HU.01 5 0.5738 0.3492 0.34 0.00 0.00 0.18 0.44 0.02 0.00 0.02
#> TCGA.VS.A94X.01 8 0.3746 0.5960 0.00 0.00 0.00 0.32 0.00 0.00 0.04 0.64
#> TCGA.C5.A7CO.01 5 0.3720 0.7479 0.00 0.12 0.00 0.06 0.78 0.02 0.02 0.00
#> TCGA.C5.A3HF.01 6 0.2132 0.8436 0.00 0.00 0.00 0.04 0.00 0.88 0.00 0.08
#> TCGA.IR.A3LL.01 5 0.2025 0.8156 0.00 0.00 0.00 0.10 0.88 0.00 0.02 0.00
#> TCGA.MY.A913.01 4 0.2569 0.7660 0.02 0.00 0.00 0.82 0.00 0.00 0.00 0.16
#> TCGA.VS.A952.01 3 0.0000 0.9901 0.00 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.IR.A3LI.01 3 0.0000 0.9901 0.00 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.VS.A94W.01 5 0.3903 0.7865 0.02 0.00 0.00 0.12 0.78 0.02 0.04 0.02
#> TCGA.MY.A5BF.01 2 0.3763 0.7565 0.00 0.78 0.00 0.02 0.10 0.08 0.02 0.00
#> TCGA.EK.A2RC.01 7 0.3530 0.6604 0.10 0.00 0.00 0.02 0.06 0.02 0.80 0.00
#> TCGA.VS.A8EL.01 2 0.3015 0.6076 0.00 0.68 0.00 0.00 0.32 0.00 0.00 0.00
#> TCGA.EA.A97N.01 1 0.0000 0.7803 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.EA.A3HQ.01 2 0.1341 0.7753 0.00 0.92 0.00 0.00 0.00 0.00 0.08 0.00
#> TCGA.EK.A2RD.01 1 0.1741 0.7740 0.92 0.00 0.00 0.04 0.00 0.02 0.00 0.02
#> TCGA.C5.A8YT.01 8 0.2938 0.6305 0.00 0.00 0.00 0.30 0.00 0.00 0.00 0.70
#> TCGA.FU.A3HZ.01 8 0.0941 0.8140 0.00 0.00 0.00 0.02 0.00 0.02 0.00 0.96
#> TCGA.VS.A8EJ.01 8 0.1091 0.8132 0.00 0.00 0.00 0.06 0.00 0.00 0.00 0.94
#> TCGA.C5.A3HL.01 4 0.5238 0.5218 0.24 0.00 0.00 0.56 0.00 0.00 0.04 0.16
#> TCGA.UC.A7PF.01 5 0.2859 0.8032 0.00 0.00 0.00 0.14 0.82 0.02 0.02 0.00
#> TCGA.C5.A8XK.01 5 0.4487 0.6306 0.02 0.00 0.00 0.28 0.62 0.08 0.00 0.00
#> TCGA.EX.A8YF.01 4 0.2981 0.6912 0.00 0.00 0.00 0.76 0.00 0.02 0.00 0.22
#> TCGA.HM.A4S6.01 1 0.1557 0.7736 0.92 0.00 0.00 0.06 0.00 0.02 0.00 0.00
#> TCGA.VS.A8Q9.01 5 0.1275 0.8050 0.00 0.04 0.00 0.00 0.94 0.00 0.02 0.00
#> TCGA.MA.AA41.01 7 0.2224 0.7644 0.00 0.12 0.00 0.00 0.02 0.00 0.86 0.00
#> TCGA.EK.A3GN.01 2 0.3374 0.4037 0.00 0.68 0.00 0.00 0.02 0.00 0.30 0.00
#> TCGA.MA.AA3Y.01 4 0.2484 0.7636 0.02 0.00 0.00 0.86 0.02 0.00 0.00 0.10
#> TCGA.MA.AA3Z.01 1 0.3303 0.7028 0.76 0.00 0.00 0.02 0.00 0.02 0.20 0.00
#> TCGA.EK.A2RE.01 1 0.1563 0.7198 0.90 0.00 0.00 0.10 0.00 0.00 0.00 0.00
#> TCGA.C5.A1BQ.01 1 0.4917 0.5690 0.62 0.00 0.00 0.04 0.06 0.02 0.26 0.00
#> TCGA.ZJ.A8QO.01 5 0.0941 0.8059 0.00 0.02 0.00 0.00 0.96 0.00 0.02 0.00
#> TCGA.JW.A852.01 2 0.0000 0.8281 0.00 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.DS.A7WH.01 6 0.3169 0.8067 0.00 0.00 0.18 0.00 0.02 0.78 0.00 0.02
#> TCGA.JW.AAVH.01 7 0.1557 0.7500 0.06 0.00 0.00 0.00 0.02 0.00 0.92 0.00
#> TCGA.EA.A556.01 8 0.1091 0.8132 0.00 0.00 0.00 0.06 0.00 0.00 0.00 0.94
#> TCGA.EA.A44S.01 1 0.0941 0.7790 0.96 0.00 0.00 0.02 0.00 0.00 0.00 0.02
#> TCGA.4J.AA1J.01 1 0.1557 0.7801 0.92 0.00 0.00 0.00 0.00 0.02 0.06 0.00
#> TCGA.IR.A3L7.01 7 0.3237 0.4944 0.00 0.40 0.00 0.00 0.00 0.00 0.60 0.00
#> TCGA.C5.A7X3.01 4 0.2569 0.7660 0.02 0.00 0.00 0.82 0.00 0.00 0.00 0.16
#> TCGA.HG.A2PA.01 5 0.2719 0.7958 0.00 0.00 0.00 0.18 0.80 0.00 0.00 0.02
#> TCGA.C5.A8XH.01 5 0.3627 0.7248 0.00 0.14 0.00 0.04 0.78 0.02 0.02 0.00
#> TCGA.C5.A7XC.01 1 0.0471 0.7808 0.98 0.00 0.00 0.02 0.00 0.00 0.00 0.00
#> TCGA.VS.A8EI.01 5 0.1275 0.8097 0.00 0.00 0.00 0.04 0.94 0.00 0.02 0.00
#> TCGA.VS.A8QC.01 2 0.2406 0.6333 0.00 0.80 0.00 0.00 0.00 0.00 0.20 0.00
#> TCGA.C5.A7UH.01 1 0.0471 0.7816 0.98 0.00 0.00 0.00 0.00 0.00 0.02 0.00
#> TCGA.WL.A834.01 7 0.3237 0.4944 0.00 0.40 0.00 0.00 0.00 0.00 0.60 0.00
#> TCGA.C5.A8XI.01 2 0.1557 0.8019 0.00 0.92 0.00 0.02 0.00 0.06 0.00 0.00
#> TCGA.DS.A7WI.01 5 0.1091 0.8145 0.00 0.00 0.00 0.06 0.94 0.00 0.00 0.00
#> TCGA.VS.A8QF.01 2 0.2406 0.6333 0.00 0.80 0.00 0.00 0.00 0.00 0.20 0.00
#> TCGA.EA.A3HR.01 1 0.1947 0.6809 0.86 0.00 0.00 0.14 0.00 0.00 0.00 0.00
#> TCGA.DG.A2KL.01 1 0.2265 0.7602 0.88 0.00 0.00 0.08 0.00 0.02 0.00 0.02
#> TCGA.EK.A2RL.01 3 0.0000 0.9901 0.00 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.EK.A2PG.01 2 0.2406 0.6323 0.00 0.80 0.00 0.00 0.00 0.00 0.20 0.00
#> TCGA.BI.A0VR.01 1 0.3951 0.6792 0.76 0.00 0.00 0.08 0.12 0.02 0.00 0.02
#> TCGA.DS.A0VL.01 1 0.4030 0.7208 0.78 0.00 0.00 0.10 0.04 0.02 0.04 0.02
#> TCGA.VS.A8EC.01 2 0.0000 0.8281 0.00 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.EA.A3QE.01 5 0.0941 0.8059 0.00 0.02 0.00 0.00 0.96 0.00 0.02 0.00
#> TCGA.DS.A0VM.01 7 0.2132 0.7671 0.00 0.08 0.00 0.00 0.04 0.00 0.88 0.00
#> TCGA.FU.A3HY.01 7 0.2624 0.7235 0.06 0.00 0.00 0.00 0.06 0.02 0.86 0.00
#> TCGA.Q1.A5R1.01 3 0.0471 0.9844 0.00 0.00 0.98 0.00 0.00 0.00 0.00 0.02
#> TCGA.DR.A0ZM.01 1 0.3374 0.3560 0.68 0.00 0.00 0.30 0.00 0.00 0.00 0.02
#> TCGA.Q1.A6DW.01 2 0.2020 0.7885 0.00 0.90 0.00 0.02 0.00 0.06 0.02 0.00
#> TCGA.DS.A0VK.01 1 0.4933 0.4335 0.54 0.00 0.00 0.02 0.06 0.02 0.36 0.00
#> TCGA.DS.A3LQ.01 5 0.3714 0.3102 0.00 0.00 0.00 0.02 0.54 0.00 0.44 0.00
#> TCGA.EA.A3QD.01 2 0.0000 0.8281 0.00 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.JW.A5VJ.01 1 0.3971 -0.1096 0.54 0.00 0.00 0.42 0.00 0.00 0.00 0.04
#> TCGA.LP.A5U3.01 7 0.4704 0.6081 0.00 0.28 0.00 0.02 0.02 0.06 0.62 0.00
#> TCGA.EA.A6QX.01 7 0.1741 0.7649 0.02 0.04 0.00 0.00 0.02 0.00 0.92 0.00
#> TCGA.EK.A2RA.01 7 0.3237 0.5021 0.00 0.40 0.00 0.00 0.00 0.00 0.60 0.00
#> TCGA.FU.A5XV.01 1 0.4530 0.6113 0.66 0.00 0.00 0.02 0.06 0.02 0.24 0.00
#> TCGA.Q1.A5R2.01 7 0.3015 0.6198 0.00 0.32 0.00 0.00 0.00 0.00 0.68 0.00
#> TCGA.HM.A3JJ.01 1 0.5122 0.4802 0.56 0.00 0.00 0.04 0.06 0.02 0.32 0.00
#> TCGA.C5.A2LS.01 3 0.0471 0.9844 0.00 0.00 0.98 0.00 0.00 0.00 0.00 0.02
#> TCGA.C5.A7X8.01 6 0.2224 0.8513 0.00 0.00 0.12 0.00 0.02 0.86 0.00 0.00
#> TCGA.EK.A2RJ.01 8 0.3142 0.5143 0.00 0.00 0.00 0.36 0.00 0.00 0.00 0.64
#> TCGA.EA.A3HT.01 1 0.0000 0.7803 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.LP.A7HU.01 3 0.0000 0.9901 0.00 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.MU.A8JM.01 5 0.2864 0.7941 0.00 0.00 0.00 0.08 0.84 0.02 0.06 0.00
#> TCGA.EK.A2IP.01 1 0.4994 0.3510 0.50 0.00 0.00 0.02 0.06 0.02 0.40 0.00
#> TCGA.JW.A5VL.01 7 0.1557 0.7679 0.00 0.06 0.00 0.00 0.02 0.00 0.92 0.00
#> TCGA.FU.A3TX.01 5 0.4622 0.7121 0.02 0.00 0.00 0.26 0.64 0.00 0.06 0.02
#> TCGA.DG.A2KK.01 3 0.0000 0.9901 0.00 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.EK.A2PI.01 5 0.4046 0.7855 0.00 0.00 0.00 0.16 0.74 0.02 0.06 0.02
#> TCGA.Q1.A73S.01 8 0.1091 0.8132 0.00 0.00 0.00 0.06 0.00 0.00 0.00 0.94
#> TCGA.EK.A2IR.01 5 0.4046 0.7855 0.00 0.00 0.00 0.16 0.74 0.02 0.06 0.02
#> TCGA.HM.A6W2.01 8 0.0941 0.8140 0.00 0.00 0.00 0.02 0.00 0.02 0.00 0.96
#> TCGA.VS.A8EH.01 5 0.4046 0.7855 0.00 0.00 0.00 0.16 0.74 0.02 0.06 0.02
#> TCGA.JW.A5VH.01 8 0.0941 0.8140 0.00 0.00 0.00 0.02 0.00 0.02 0.00 0.96
#> TCGA.C5.A2LV.01 2 0.2025 0.7911 0.00 0.88 0.00 0.00 0.10 0.02 0.00 0.00
#> TCGA.VS.A8EB.01 5 0.2132 0.7855 0.00 0.00 0.00 0.04 0.88 0.00 0.08 0.00
#> TCGA.RA.A741.01 4 0.2650 0.6586 0.24 0.00 0.00 0.76 0.00 0.00 0.00 0.00
#> TCGA.VS.A8EG.01 7 0.6219 0.5769 0.02 0.24 0.00 0.06 0.06 0.08 0.54 0.00
#> TCGA.DG.A2KH.01 6 0.2132 0.8436 0.00 0.00 0.00 0.04 0.00 0.88 0.00 0.08
#> TCGA.C5.A7UE.01 5 0.2807 0.8035 0.00 0.02 0.00 0.06 0.86 0.02 0.04 0.00
#> TCGA.C5.A2LT.01 4 0.2569 0.6725 0.02 0.00 0.00 0.82 0.16 0.00 0.00 0.00
#> TCGA.EA.A5ZD.01 4 0.3333 0.2164 0.50 0.00 0.00 0.50 0.00 0.00 0.00 0.00
#> TCGA.Q1.A73R.01 3 0.0000 0.9901 0.00 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.JW.A5VK.01 7 0.2856 0.7307 0.00 0.20 0.00 0.00 0.02 0.00 0.78 0.00
#> TCGA.EK.A2RM.01 8 0.4241 0.4754 0.00 0.00 0.00 0.04 0.00 0.26 0.04 0.66
#> TCGA.C5.A7UI.01 1 0.5321 0.4572 0.54 0.00 0.00 0.04 0.08 0.02 0.32 0.00
#> TCGA.EK.A2PL.01 1 0.2204 0.7805 0.90 0.00 0.00 0.02 0.02 0.02 0.04 0.00
#> TCGA.EK.A2PM.01 1 0.5259 -0.3165 0.38 0.00 0.00 0.32 0.00 0.00 0.00 0.30
#> TCGA.EK.A2GZ.01 5 0.4313 0.7654 0.02 0.00 0.00 0.20 0.70 0.00 0.06 0.02
#> TCGA.HM.A3JK.01 5 0.4174 0.7442 0.04 0.00 0.00 0.22 0.70 0.02 0.00 0.02
#> TCGA.C5.A2M1.01 3 0.0471 0.9844 0.00 0.00 0.98 0.00 0.00 0.00 0.00 0.02
#> TCGA.HM.A6W2.06 8 0.0941 0.8140 0.00 0.00 0.00 0.02 0.00 0.02 0.00 0.96
#> TCGA.C5.A7X5.01 2 0.2265 0.7922 0.00 0.88 0.00 0.00 0.08 0.02 0.02 0.00
#> TCGA.IR.A3LA.01 8 0.0941 0.8140 0.00 0.00 0.00 0.02 0.00 0.02 0.00 0.96
#> TCGA.EK.A2PK.01 4 0.2981 0.6912 0.00 0.00 0.00 0.76 0.00 0.02 0.00 0.22
#> TCGA.EA.A5ZF.01 8 0.2071 0.7967 0.00 0.00 0.00 0.04 0.00 0.02 0.04 0.90
#> TCGA.XS.A8TJ.01 1 0.6113 0.2391 0.40 0.00 0.00 0.04 0.22 0.02 0.32 0.00
#> TCGA.BI.A0VS.01 1 0.2348 0.7455 0.88 0.00 0.00 0.06 0.00 0.00 0.04 0.02
#> TCGA.DS.A0VN.01 5 0.1275 0.8097 0.00 0.00 0.00 0.04 0.94 0.00 0.02 0.00
#> TCGA.JX.A5QV.01 1 0.4162 0.4724 0.66 0.00 0.00 0.28 0.00 0.02 0.02 0.02
#> TCGA.EK.A2R8.01 8 0.3299 0.2883 0.00 0.00 0.00 0.44 0.00 0.00 0.00 0.56
#> TCGA.EA.A1QS.01 4 0.2569 0.7660 0.02 0.00 0.00 0.82 0.00 0.00 0.00 0.16
#> TCGA.C5.A3HE.01 6 0.2532 0.8551 0.00 0.00 0.02 0.04 0.02 0.88 0.00 0.04
#> TCGA.IR.A3LF.01 3 0.0000 0.9901 0.00 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.DR.A0ZL.01 1 0.6447 0.1478 0.38 0.00 0.00 0.06 0.18 0.04 0.34 0.00
#> TCGA.FU.A3WB.01 5 0.5181 0.6572 0.00 0.14 0.00 0.10 0.66 0.06 0.04 0.00
#> TCGA.JX.A3PZ.01 4 0.2818 0.7665 0.06 0.00 0.00 0.82 0.00 0.00 0.00 0.12
#> TCGA.EA.A5O9.01 2 0.4491 0.3053 0.00 0.54 0.00 0.02 0.40 0.02 0.02 0.00
#> TCGA.HM.A3JJ.11 8 0.2938 0.6305 0.00 0.00 0.00 0.30 0.00 0.00 0.00 0.70
#> TCGA.DS.A5RQ.01 1 0.0471 0.7811 0.98 0.00 0.00 0.00 0.00 0.00 0.00 0.02
#> TCGA.EK.A2H0.01 2 0.2406 0.7444 0.00 0.80 0.00 0.00 0.20 0.00 0.00 0.00
#> TCGA.EX.A1H6.01 6 0.3169 0.8067 0.00 0.00 0.18 0.00 0.02 0.78 0.00 0.02
#> TCGA.EA.A5ZE.01 2 0.0471 0.8180 0.00 0.98 0.00 0.00 0.00 0.00 0.02 0.00
#> TCGA.C5.A2LY.01 5 0.5252 0.5923 0.12 0.00 0.00 0.28 0.56 0.02 0.00 0.02
#> TCGA.FU.A3TQ.01 5 0.5208 0.6754 0.04 0.00 0.00 0.10 0.66 0.02 0.16 0.02
#> TCGA.EK.A2RB.01 7 0.2404 0.7590 0.00 0.14 0.00 0.00 0.02 0.00 0.84 0.00
#> TCGA.JW.A5VI.01 5 0.1091 0.8137 0.00 0.00 0.00 0.06 0.94 0.00 0.00 0.00
#> TCGA.EK.A2H1.01 4 0.2406 0.7252 0.00 0.00 0.00 0.80 0.00 0.00 0.00 0.20
#> TCGA.JX.A3Q8.01 3 0.0000 0.9901 0.00 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.FU.A3YQ.01 5 0.1275 0.8097 0.00 0.00 0.00 0.04 0.94 0.00 0.02 0.00
#> TCGA.EX.A69L.01 1 0.3135 0.7244 0.82 0.00 0.00 0.12 0.02 0.02 0.00 0.02
#> TCGA.C5.A7CH.01 2 0.1091 0.8120 0.00 0.94 0.00 0.00 0.00 0.06 0.00 0.00
#> TCGA.FU.A2QG.01 1 0.0000 0.7803 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.C5.A2M2.01 3 0.0000 0.9901 0.00 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.JW.A5VG.01 4 0.2404 0.7716 0.02 0.00 0.00 0.84 0.00 0.00 0.00 0.14
#> TCGA.PN.A8MA.01 8 0.3770 0.6950 0.12 0.00 0.00 0.04 0.00 0.02 0.04 0.78
#> TCGA.DG.A2KM.01 4 0.2404 0.7716 0.02 0.00 0.00 0.84 0.00 0.00 0.00 0.14
#> TCGA.C5.A2LX.01 2 0.0000 0.8281 0.00 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.EX.A3L1.01 4 0.2569 0.7660 0.02 0.00 0.00 0.82 0.00 0.00 0.00 0.16
#> TCGA.LP.A5U2.01 2 0.3319 0.7245 0.00 0.82 0.00 0.02 0.02 0.06 0.08 0.00
#> TCGA.FU.A3NI.01 2 0.2404 0.7704 0.00 0.84 0.00 0.00 0.14 0.02 0.00 0.00
#> TCGA.Q1.A5R3.01 1 0.0941 0.7828 0.96 0.00 0.00 0.00 0.00 0.02 0.02 0.00
#> TCGA.FU.A770.01 6 0.2859 0.8385 0.00 0.00 0.14 0.00 0.02 0.82 0.00 0.02
#> TCGA.C5.A7CM.01 6 0.2132 0.8436 0.00 0.00 0.00 0.04 0.00 0.88 0.00 0.08
#> TCGA.JX.A3Q0.01 1 0.0471 0.7816 0.98 0.00 0.00 0.00 0.00 0.00 0.02 0.00
#> TCGA.EA.A5FO.01 3 0.0000 0.9901 0.00 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.VS.A9V3.01 7 0.3299 0.4059 0.00 0.44 0.00 0.00 0.00 0.00 0.56 0.00
#> TCGA.C5.A7CL.01 5 0.3616 0.7862 0.02 0.00 0.00 0.18 0.76 0.02 0.00 0.02
#> TCGA.VS.A959.01 6 0.3922 0.4367 0.00 0.00 0.00 0.06 0.30 0.64 0.00 0.00
#> TCGA.LP.A4AX.01 5 0.2267 0.7795 0.00 0.00 0.00 0.18 0.82 0.00 0.00 0.00
#> TCGA.C5.A1MN.01 2 0.0000 0.8281 0.00 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.ZJ.AAXN.01 4 0.2569 0.7660 0.02 0.00 0.00 0.82 0.00 0.00 0.00 0.16
#> TCGA.MA.AA3X.01 1 0.0471 0.7816 0.98 0.00 0.00 0.00 0.00 0.00 0.02 0.00
#> TCGA.UC.A7PG.01 1 0.0808 0.7817 0.96 0.00 0.00 0.04 0.00 0.00 0.00 0.00
#> TCGA.Q1.A6DV.01 6 0.2591 0.8594 0.00 0.00 0.08 0.00 0.02 0.86 0.00 0.04
#> TCGA.DS.A1OD.01 1 0.3535 0.7556 0.82 0.00 0.00 0.06 0.02 0.02 0.06 0.02
#> TCGA.C5.A1M7.01 4 0.3193 0.3663 0.38 0.00 0.00 0.62 0.00 0.00 0.00 0.00
#> TCGA.BI.A20A.01 5 0.3319 0.7790 0.00 0.08 0.00 0.06 0.82 0.02 0.02 0.00
#> TCGA.VS.A9UO.01 6 0.2859 0.8385 0.00 0.00 0.14 0.00 0.02 0.82 0.00 0.02
#> TCGA.EA.A1QT.01 7 0.1341 0.7706 0.00 0.08 0.00 0.00 0.00 0.00 0.92 0.00
#> TCGA.EX.A69M.01 2 0.2267 0.7585 0.00 0.82 0.00 0.00 0.18 0.00 0.00 0.00
#> TCGA.VS.A9UH.01 4 0.3329 -0.1274 0.00 0.00 0.00 0.52 0.48 0.00 0.00 0.00
#> TCGA.VS.A9U7.01 7 0.4775 0.5803 0.00 0.30 0.00 0.02 0.02 0.06 0.60 0.00
#> TCGA.ZJ.AAXD.01 1 0.0941 0.7785 0.96 0.00 0.00 0.02 0.00 0.00 0.00 0.02
#> TCGA.VS.A9UB.01 4 0.2404 0.6660 0.00 0.00 0.00 0.84 0.14 0.02 0.00 0.00
#> TCGA.EA.A410.01 8 0.1275 0.8017 0.04 0.00 0.00 0.02 0.00 0.00 0.00 0.94
#> TCGA.ZJ.AB0I.01 1 0.2114 0.6495 0.84 0.00 0.00 0.16 0.00 0.00 0.00 0.00
#> TCGA.VS.A9UD.01 5 0.3785 0.7004 0.00 0.16 0.00 0.04 0.76 0.02 0.02 0.00
#> TCGA.VS.A9U6.01 1 0.4034 0.7175 0.76 0.00 0.00 0.06 0.02 0.04 0.12 0.00
#> TCGA.ZX.AA5X.01 5 0.3627 0.7011 0.02 0.00 0.00 0.04 0.78 0.02 0.14 0.00
#> TCGA.C5.A0TN.01 4 0.2404 0.7716 0.02 0.00 0.00 0.84 0.00 0.00 0.00 0.14
#> TCGA.C5.A7CJ.01 5 0.4202 0.6900 0.04 0.00 0.00 0.06 0.74 0.02 0.14 0.00
#> TCGA.C5.A1MJ.01 6 0.2859 0.8385 0.00 0.00 0.14 0.00 0.02 0.82 0.00 0.02
#> TCGA.EA.A78R.01 5 0.1804 0.7899 0.00 0.08 0.00 0.02 0.90 0.00 0.00 0.00
#> TCGA.VS.A9UY.01 7 0.2981 0.7163 0.00 0.22 0.00 0.00 0.02 0.00 0.76 0.00
#> TCGA.VS.A9U5.01 2 0.0000 0.8281 0.00 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.DS.A1OC.01 5 0.2484 0.8101 0.00 0.00 0.00 0.10 0.86 0.02 0.02 0.00
#> TCGA.ZJ.AAXB.01 8 0.2719 0.6670 0.18 0.00 0.00 0.02 0.00 0.00 0.00 0.80
#> TCGA.EX.A449.01 3 0.0000 0.9901 0.00 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.C5.A1BL.01 7 0.2025 0.7684 0.00 0.10 0.00 0.00 0.02 0.00 0.88 0.00
#> TCGA.VS.A9UQ.01 3 0.0471 0.9844 0.00 0.00 0.98 0.00 0.00 0.00 0.00 0.02
#> TCGA.DS.A1OB.01 1 0.0471 0.7816 0.98 0.00 0.00 0.00 0.00 0.00 0.02 0.00
#> TCGA.HG.A9SC.01 1 0.0471 0.7761 0.98 0.00 0.00 0.02 0.00 0.00 0.00 0.00
#> TCGA.ZJ.AAXT.01 4 0.4061 0.6938 0.14 0.00 0.00 0.72 0.00 0.00 0.02 0.12
#> TCGA.IR.A3LB.01 6 0.3426 0.7597 0.00 0.00 0.22 0.00 0.02 0.74 0.00 0.02
#> TCGA.C5.A1ML.01 8 0.3002 0.7609 0.02 0.00 0.00 0.12 0.00 0.00 0.04 0.82
#> TCGA.VS.A9UV.01 2 0.0000 0.8281 0.00 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.LP.A4AU.01 4 0.2406 0.7252 0.00 0.00 0.00 0.80 0.00 0.00 0.00 0.20
#> TCGA.Q1.A6DT.01 7 0.4190 0.6754 0.00 0.14 0.00 0.00 0.20 0.00 0.66 0.00
#> TCGA.C5.A1M8.01 2 0.4995 0.3045 0.00 0.60 0.00 0.04 0.02 0.06 0.28 0.00
#> TCGA.C5.A1ME.01 6 0.3169 0.8067 0.00 0.00 0.18 0.00 0.02 0.78 0.00 0.02
#> TCGA.ZJ.AAXU.01 1 0.3785 0.7120 0.76 0.00 0.00 0.04 0.02 0.02 0.16 0.00
#> TCGA.VS.A957.01 7 0.4921 0.7128 0.02 0.06 0.00 0.06 0.06 0.08 0.72 0.00
#> TCGA.VS.A9V5.01 3 0.0471 0.9844 0.00 0.00 0.98 0.00 0.00 0.00 0.00 0.02
#> TCGA.MU.A5YI.01 5 0.3319 0.7790 0.00 0.08 0.00 0.06 0.82 0.02 0.02 0.00
#> TCGA.ZJ.AAX4.01 2 0.3748 0.6997 0.00 0.74 0.00 0.02 0.20 0.02 0.02 0.00
#> TCGA.C5.A1MK.01 1 0.1741 0.7824 0.92 0.00 0.00 0.02 0.00 0.02 0.04 0.00
#> TCGA.JW.A69B.01 3 0.0000 0.9901 0.00 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.VS.A958.01 4 0.3083 0.5756 0.34 0.00 0.00 0.66 0.00 0.00 0.00 0.00
#> TCGA.ZJ.AAXJ.01 2 0.1804 0.7999 0.00 0.90 0.00 0.00 0.08 0.02 0.00 0.00
#> TCGA.R2.A69V.01 4 0.2484 0.7636 0.02 0.00 0.00 0.86 0.02 0.00 0.00 0.10
#> TCGA.EA.A411.01 1 0.0941 0.7828 0.96 0.00 0.00 0.00 0.00 0.02 0.02 0.00
#> TCGA.VS.A9UP.01 8 0.2071 0.7967 0.00 0.00 0.00 0.04 0.00 0.02 0.04 0.90
#> TCGA.C5.A1MI.01 8 0.3397 0.7257 0.00 0.00 0.00 0.06 0.00 0.10 0.04 0.80
#> TCGA.DS.A1O9.01 5 0.1408 0.8075 0.00 0.02 0.00 0.02 0.94 0.00 0.02 0.00
#> TCGA.VS.A9UZ.01 3 0.0000 0.9901 0.00 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.EA.A43B.01 5 0.1804 0.8107 0.00 0.02 0.00 0.08 0.90 0.00 0.00 0.00
#> TCGA.ZJ.AAX8.01 4 0.2591 0.7627 0.04 0.00 0.00 0.86 0.02 0.00 0.00 0.08
#> TCGA.ZJ.AAXI.01 7 0.3170 0.7151 0.00 0.20 0.00 0.00 0.00 0.04 0.76 0.00
#> TCGA.VS.A9UT.01 8 0.2852 0.6567 0.00 0.00 0.00 0.28 0.00 0.00 0.00 0.72
#> TCGA.DS.A1OA.01 7 0.2165 0.7350 0.06 0.00 0.00 0.00 0.06 0.00 0.88 0.00
#> TCGA.C5.A1MQ.01 6 0.2756 0.7011 0.00 0.00 0.00 0.00 0.26 0.74 0.00 0.00
#> TCGA.VS.A9V0.01 8 0.1091 0.8132 0.00 0.00 0.00 0.06 0.00 0.00 0.00 0.94
#> TCGA.VS.A9UC.01 5 0.3154 0.7146 0.00 0.00 0.00 0.06 0.78 0.00 0.16 0.00
#> TCGA.ZJ.AAXA.01 1 0.0471 0.7761 0.98 0.00 0.00 0.02 0.00 0.00 0.00 0.00
#> TCGA.Q1.A73P.01 3 0.0471 0.9844 0.00 0.00 0.98 0.00 0.00 0.00 0.00 0.02
#> TCGA.VS.A9V2.01 5 0.1091 0.8019 0.00 0.06 0.00 0.00 0.94 0.00 0.00 0.00
#> TCGA.VS.A9UU.01 2 0.3015 0.6076 0.00 0.68 0.00 0.00 0.32 0.00 0.00 0.00
#> TCGA.LP.A4AV.01 1 0.1557 0.7801 0.92 0.00 0.00 0.00 0.00 0.02 0.06 0.00
#> TCGA.VS.A9UR.01 3 0.1741 0.9260 0.00 0.00 0.92 0.00 0.02 0.04 0.00 0.02
#> TCGA.VS.A9V1.01 6 0.2348 0.8536 0.00 0.00 0.02 0.04 0.00 0.88 0.00 0.06
#> TCGA.C5.A7CG.01 2 0.0000 0.8281 0.00 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.UC.A7PI.01 3 0.0941 0.9694 0.00 0.00 0.96 0.00 0.02 0.00 0.00 0.02
#> TCGA.EX.A1H5.01 5 0.5200 0.7197 0.02 0.00 0.00 0.10 0.68 0.08 0.10 0.02
#> TCGA.ZJ.AAXF.01 4 0.3675 0.6434 0.14 0.00 0.00 0.76 0.08 0.00 0.00 0.02
#> TCGA.VS.A9UL.01 6 0.2404 0.8433 0.00 0.00 0.14 0.00 0.02 0.84 0.00 0.00
#> TCGA.EA.A3Y4.01 4 0.3374 0.6040 0.30 0.00 0.00 0.68 0.00 0.02 0.00 0.00
#> TCGA.C5.A7CK.01 2 0.0000 0.8281 0.00 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.UC.A7PG.06 1 0.0471 0.7836 0.98 0.00 0.00 0.02 0.00 0.00 0.00 0.00
#> TCGA.VS.A9UJ.01 8 0.0941 0.8140 0.00 0.00 0.00 0.02 0.00 0.02 0.00 0.96
#> TCGA.Q1.A73O.01 4 0.3291 0.6361 0.28 0.00 0.00 0.70 0.00 0.00 0.00 0.02
#> TCGA.VS.A950.01 7 0.2025 0.7460 0.00 0.02 0.00 0.00 0.10 0.00 0.88 0.00
#> TCGA.EA.A439.01 6 0.3402 0.8228 0.00 0.00 0.00 0.06 0.02 0.82 0.04 0.06
#> TCGA.VS.A9UM.01 1 0.3537 0.6659 0.72 0.00 0.00 0.02 0.00 0.02 0.24 0.00
#> TCGA.C5.A1MP.01 1 0.0471 0.7761 0.98 0.00 0.00 0.02 0.00 0.00 0.00 0.00
#> TCGA.VS.A9UI.01 7 0.2165 0.7350 0.06 0.00 0.00 0.00 0.06 0.00 0.88 0.00
#> TCGA.ZJ.AB0H.01 1 0.3847 0.7368 0.78 0.00 0.00 0.06 0.04 0.02 0.10 0.00
#> TCGA.Q1.A73Q.01 7 0.3319 0.6982 0.08 0.00 0.00 0.02 0.06 0.02 0.82 0.00
#> TCGA.C5.A1MH.01 5 0.6033 0.2274 0.14 0.00 0.00 0.04 0.46 0.04 0.32 0.00
#> TCGA.VS.A9V4.01 8 0.2650 0.6981 0.00 0.00 0.00 0.24 0.00 0.00 0.00 0.76
#> TCGA.FU.A40J.01 3 0.0471 0.9844 0.00 0.00 0.98 0.00 0.00 0.00 0.00 0.02
#> TCGA.VS.A9UA.01 5 0.5213 0.5492 0.10 0.00 0.00 0.32 0.54 0.02 0.00 0.02
#> TCGA.LP.A4AW.01 1 0.5122 0.4802 0.56 0.00 0.00 0.04 0.06 0.02 0.32 0.00
#> TCGA.MA.AA43.01 6 0.2350 0.8556 0.00 0.00 0.10 0.00 0.04 0.86 0.00 0.00
#> TCGA.C5.A1BN.01 1 0.0471 0.7761 0.98 0.00 0.00 0.02 0.00 0.00 0.00 0.00
#> TCGA.VS.AA62.01 4 0.2569 0.7660 0.02 0.00 0.00 0.82 0.00 0.00 0.00 0.16
#> TCGA.C5.A1BM.01 1 0.3318 -0.1237 0.54 0.00 0.00 0.46 0.00 0.00 0.00 0.00
#> TCGA.C5.A1M6.01 6 0.2132 0.8340 0.00 0.00 0.00 0.00 0.08 0.88 0.00 0.04
#> TCGA.C5.A1BE.01 1 0.5966 0.0875 0.46 0.00 0.00 0.10 0.36 0.02 0.04 0.02
#> TCGA.FU.A23K.01 6 0.2859 0.8385 0.00 0.00 0.14 0.00 0.02 0.82 0.00 0.02
#> TCGA.C5.A1BJ.01 1 0.2482 0.7728 0.88 0.00 0.00 0.06 0.02 0.02 0.02 0.00
#> TCGA.FU.A23L.01 8 0.4570 0.5921 0.06 0.00 0.00 0.28 0.00 0.00 0.04 0.62
#> TCGA.C5.A1M5.01 7 0.5064 0.5741 0.00 0.30 0.00 0.04 0.02 0.06 0.58 0.00
#> TCGA.C5.A1MF.01 7 0.4794 0.6890 0.02 0.02 0.00 0.04 0.06 0.16 0.70 0.00
#> TCGA.C5.A1BF.01 4 0.2114 0.7506 0.00 0.00 0.00 0.84 0.00 0.00 0.00 0.16
#> TCGA.C5.A1BK.01 5 0.5243 0.3153 0.00 0.14 0.00 0.02 0.58 0.02 0.24 0.00
#> TCGA.C5.A1BI.01 1 0.3333 -0.2510 0.50 0.00 0.00 0.50 0.00 0.00 0.00 0.00
#> TCGA.C5.A1M9.01 3 0.0471 0.9844 0.00 0.00 0.98 0.00 0.00 0.00 0.00 0.02
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)
consensus_heatmap(res, k = 7)
consensus_heatmap(res, k = 8)
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)
membership_heatmap(res, k = 7)
membership_heatmap(res, k = 8)
As soon as the classes for columns are determined, the signatures that are significantly different between subgroups can be looked for. Following are the heatmaps for signatures.
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)
get_signatures(res, k = 7)
get_signatures(res, k = 8)
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 (which is done by automatically selecting number of clusters).If there are too many signatures, top_signatures = ... can be set to only show the
signatures with the highest FDRs:
# code only for demonstration
# e.g. to show the top 500 most significant rows
tb = get_signature(res, k = ..., top_signatures = 500)
If the signatures are defined as these which are uniquely high in current group, diff_method argument
can be set to "uniquely_high_in_one_group":
# code only for demonstration
tb = get_signature(res, k = ..., diff_method = "uniquely_high_in_one_group")
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")
dimension_reduction(res, k = 7, method = "UMAP")
dimension_reduction(res, k = 8, method = "UMAP")
Following heatmap shows how subgroups are split when increasing k:
collect_classes(res)
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.
Parent node: Node0. Child nodes: Node011 , Node012 , Node013 , Node021 , Node022 , Node023 , Node031 , Node032-leaf .
The object with results only for a single top-value method and a single partitioning method can be extracted as:
res = res_rh["01"]
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, 7, 8.
#> On a matrix with 30000 rows and 154 columns.
#> Top rows (1000) are extracted by 'ATC' method.
#> Subgroups are detected by 'kmeans' method.
#> Performed in total 350 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_partitions"
#> [7] "compare_signatures" "consensus_heatmap" "dimension_reduction"
#> [10] "functional_enrichment" "get_anno_col" "get_anno"
#> [13] "get_classes" "get_consensus" "get_matrix"
#> [16] "get_membership" "get_param" "get_signatures"
#> [19] "get_stats" "is_best_k" "is_stable_k"
#> [22] "membership_heatmap" "ncol" "nrow"
#> [25] "plot_ecdf" "predict_classes" "rownames"
#> [28] "select_partition_number" "show" "suggest_best_k"
#> [31] "test_to_known_factors" "top_rows_heatmap"
collect_plots() function collects all the plots made from res for all k (number of subgroups)
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, higher 1-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 0.993 0.996 0.4766 0.524 0.524
#> 3 3 1.000 0.995 0.998 0.3501 0.656 0.438
#> 4 4 0.865 0.852 0.920 0.1308 0.906 0.742
#> 5 5 0.802 0.826 0.871 0.0622 0.882 0.617
#> 6 6 0.786 0.656 0.827 0.0430 0.982 0.922
#> 7 7 0.795 0.718 0.804 0.0266 0.928 0.684
#> 8 8 0.741 0.523 0.711 0.0148 0.967 0.824
suggest_best_k() suggests the best \(k\) based on these statistics. The rules are as follows:
suggest_best_k(res)
#> [1] 3
#> attr(,"optional")
#> [1] 2
There is also optional best \(k\) = 2 that is worth to check.
Following is 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 subgroup
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
#> TCGA.EK.A3GK.01 1 0.242 0.961 0.96 0.04
#> TCGA.VS.A94Y.01 1 0.000 0.996 1.00 0.00
#> TCGA.MY.A5BF.11 1 0.000 0.996 1.00 0.00
#> TCGA.VS.A94Z.01 1 0.000 0.996 1.00 0.00
#> TCGA.EA.A4BA.01 1 0.000 0.996 1.00 0.00
#> TCGA.FU.A3EO.11 1 0.000 0.996 1.00 0.00
#> TCGA.DG.A2KJ.01 1 0.000 0.996 1.00 0.00
#> TCGA.EK.A2R7.01 2 0.141 0.981 0.02 0.98
#> TCGA.C5.A905.01 2 0.000 0.997 0.00 1.00
#> TCGA.EK.A2RN.01 2 0.000 0.997 0.00 1.00
#> TCGA.FU.A57G.01 1 0.000 0.996 1.00 0.00
#> TCGA.C5.A8YR.01 2 0.000 0.997 0.00 1.00
#> TCGA.MY.A5BE.01 1 0.000 0.996 1.00 0.00
#> TCGA.VS.A8QH.01 1 0.000 0.996 1.00 0.00
#> TCGA.ZJ.A8QR.01 2 0.000 0.997 0.00 1.00
#> TCGA.C5.A907.01 1 0.000 0.996 1.00 0.00
#> TCGA.C5.A8ZZ.01 2 0.000 0.997 0.00 1.00
#> TCGA.C5.A7UC.01 1 0.000 0.996 1.00 0.00
#> TCGA.C5.A8XJ.01 1 0.000 0.996 1.00 0.00
#> TCGA.EK.A3GM.01 1 0.000 0.996 1.00 0.00
#> TCGA.VS.A8Q8.01 2 0.000 0.997 0.00 1.00
#> TCGA.2W.A8YY.01 2 0.000 0.997 0.00 1.00
#> TCGA.MU.A51Y.01 1 0.000 0.996 1.00 0.00
#> TCGA.EK.A2RK.01 2 0.000 0.997 0.00 1.00
#> TCGA.UC.A7PD.01 1 0.000 0.996 1.00 0.00
#> TCGA.VS.A8QM.01 1 0.000 0.996 1.00 0.00
#> TCGA.EA.A3HU.01 1 0.000 0.996 1.00 0.00
#> TCGA.VS.A94X.01 1 0.000 0.996 1.00 0.00
#> TCGA.C5.A3HF.01 1 0.000 0.996 1.00 0.00
#> TCGA.MY.A913.01 1 0.000 0.996 1.00 0.00
#> TCGA.EA.A97N.01 2 0.000 0.997 0.00 1.00
#> TCGA.EK.A2RD.01 2 0.000 0.997 0.00 1.00
#> TCGA.C5.A8YT.01 1 0.000 0.996 1.00 0.00
#> TCGA.FU.A3HZ.01 2 0.000 0.997 0.00 1.00
#> TCGA.VS.A8EJ.01 1 0.000 0.996 1.00 0.00
#> TCGA.C5.A3HL.01 1 0.000 0.996 1.00 0.00
#> TCGA.C5.A8XK.01 2 0.000 0.997 0.00 1.00
#> TCGA.EX.A8YF.01 1 0.000 0.996 1.00 0.00
#> TCGA.HM.A4S6.01 2 0.000 0.997 0.00 1.00
#> TCGA.MA.AA3Y.01 1 0.000 0.996 1.00 0.00
#> TCGA.MA.AA3Z.01 2 0.000 0.997 0.00 1.00
#> TCGA.EK.A2RE.01 2 0.000 0.997 0.00 1.00
#> TCGA.C5.A1BQ.01 1 0.000 0.996 1.00 0.00
#> TCGA.EA.A556.01 2 0.242 0.961 0.04 0.96
#> TCGA.EA.A44S.01 2 0.000 0.997 0.00 1.00
#> TCGA.4J.AA1J.01 2 0.000 0.997 0.00 1.00
#> TCGA.C5.A7X3.01 1 0.000 0.996 1.00 0.00
#> TCGA.HG.A2PA.01 1 0.000 0.996 1.00 0.00
#> TCGA.C5.A7XC.01 2 0.000 0.997 0.00 1.00
#> TCGA.C5.A7UH.01 2 0.000 0.997 0.00 1.00
#> TCGA.EA.A3HR.01 2 0.000 0.997 0.00 1.00
#> TCGA.DG.A2KL.01 2 0.000 0.997 0.00 1.00
#> TCGA.BI.A0VR.01 1 0.000 0.996 1.00 0.00
#> TCGA.DS.A0VL.01 1 0.327 0.940 0.94 0.06
#> TCGA.DR.A0ZM.01 2 0.000 0.997 0.00 1.00
#> TCGA.DS.A0VK.01 1 0.327 0.940 0.94 0.06
#> TCGA.JW.A5VJ.01 1 0.000 0.996 1.00 0.00
#> TCGA.FU.A5XV.01 2 0.000 0.997 0.00 1.00
#> TCGA.HM.A3JJ.01 1 0.000 0.996 1.00 0.00
#> TCGA.EK.A2RJ.01 2 0.141 0.981 0.02 0.98
#> TCGA.EA.A3HT.01 1 0.000 0.996 1.00 0.00
#> TCGA.FU.A3TX.01 1 0.000 0.996 1.00 0.00
#> TCGA.EK.A2PI.01 1 0.000 0.996 1.00 0.00
#> TCGA.Q1.A73S.01 2 0.000 0.997 0.00 1.00
#> TCGA.HM.A6W2.01 2 0.000 0.997 0.00 1.00
#> TCGA.VS.A8EH.01 1 0.000 0.996 1.00 0.00
#> TCGA.JW.A5VH.01 2 0.000 0.997 0.00 1.00
#> TCGA.VS.A8EB.01 1 0.000 0.996 1.00 0.00
#> TCGA.RA.A741.01 1 0.000 0.996 1.00 0.00
#> TCGA.DG.A2KH.01 1 0.000 0.996 1.00 0.00
#> TCGA.C5.A2LT.01 1 0.000 0.996 1.00 0.00
#> TCGA.EA.A5ZD.01 1 0.000 0.996 1.00 0.00
#> TCGA.EK.A2RM.01 1 0.000 0.996 1.00 0.00
#> TCGA.C5.A7UI.01 2 0.000 0.997 0.00 1.00
#> TCGA.EK.A2PL.01 2 0.000 0.997 0.00 1.00
#> TCGA.EK.A2PM.01 2 0.000 0.997 0.00 1.00
#> TCGA.EK.A2GZ.01 1 0.000 0.996 1.00 0.00
#> TCGA.HM.A3JK.01 1 0.000 0.996 1.00 0.00
#> TCGA.HM.A6W2.06 2 0.000 0.997 0.00 1.00
#> TCGA.IR.A3LA.01 2 0.000 0.997 0.00 1.00
#> TCGA.EK.A2PK.01 1 0.000 0.996 1.00 0.00
#> TCGA.EA.A5ZF.01 2 0.141 0.981 0.02 0.98
#> TCGA.BI.A0VS.01 2 0.000 0.997 0.00 1.00
#> TCGA.JX.A5QV.01 2 0.141 0.981 0.02 0.98
#> TCGA.EK.A2R8.01 1 0.000 0.996 1.00 0.00
#> TCGA.EA.A1QS.01 1 0.000 0.996 1.00 0.00
#> TCGA.JX.A3PZ.01 1 0.000 0.996 1.00 0.00
#> TCGA.HM.A3JJ.11 1 0.000 0.996 1.00 0.00
#> TCGA.DS.A5RQ.01 2 0.000 0.997 0.00 1.00
#> TCGA.C5.A2LY.01 1 0.000 0.996 1.00 0.00
#> TCGA.EK.A2H1.01 1 0.000 0.996 1.00 0.00
#> TCGA.EX.A69L.01 1 0.000 0.996 1.00 0.00
#> TCGA.FU.A2QG.01 2 0.000 0.997 0.00 1.00
#> TCGA.JW.A5VG.01 1 0.000 0.996 1.00 0.00
#> TCGA.PN.A8MA.01 2 0.000 0.997 0.00 1.00
#> TCGA.DG.A2KM.01 1 0.000 0.996 1.00 0.00
#> TCGA.EX.A3L1.01 1 0.000 0.996 1.00 0.00
#> TCGA.Q1.A5R3.01 2 0.000 0.997 0.00 1.00
#> TCGA.C5.A7CM.01 1 0.000 0.996 1.00 0.00
#> TCGA.JX.A3Q0.01 2 0.000 0.997 0.00 1.00
#> TCGA.C5.A7CL.01 1 0.000 0.996 1.00 0.00
#> TCGA.VS.A959.01 1 0.000 0.996 1.00 0.00
#> TCGA.LP.A4AX.01 1 0.000 0.996 1.00 0.00
#> TCGA.ZJ.AAXN.01 1 0.000 0.996 1.00 0.00
#> TCGA.MA.AA3X.01 2 0.000 0.997 0.00 1.00
#> TCGA.UC.A7PG.01 2 0.000 0.997 0.00 1.00
#> TCGA.DS.A1OD.01 1 0.000 0.996 1.00 0.00
#> TCGA.C5.A1M7.01 1 0.000 0.996 1.00 0.00
#> TCGA.VS.A9UH.01 1 0.000 0.996 1.00 0.00
#> TCGA.ZJ.AAXD.01 1 0.000 0.996 1.00 0.00
#> TCGA.VS.A9UB.01 1 0.000 0.996 1.00 0.00
#> TCGA.EA.A410.01 2 0.000 0.997 0.00 1.00
#> TCGA.ZJ.AB0I.01 2 0.000 0.997 0.00 1.00
#> TCGA.VS.A9U6.01 1 0.000 0.996 1.00 0.00
#> TCGA.C5.A0TN.01 1 0.000 0.996 1.00 0.00
#> TCGA.ZJ.AAXB.01 2 0.000 0.997 0.00 1.00
#> TCGA.DS.A1OB.01 2 0.000 0.997 0.00 1.00
#> TCGA.HG.A9SC.01 2 0.000 0.997 0.00 1.00
#> TCGA.ZJ.AAXT.01 1 0.242 0.961 0.96 0.04
#> TCGA.C5.A1ML.01 1 0.000 0.996 1.00 0.00
#> TCGA.LP.A4AU.01 1 0.000 0.996 1.00 0.00
#> TCGA.ZJ.AAXU.01 1 0.000 0.996 1.00 0.00
#> TCGA.C5.A1MK.01 2 0.000 0.997 0.00 1.00
#> TCGA.VS.A958.01 1 0.000 0.996 1.00 0.00
#> TCGA.R2.A69V.01 1 0.000 0.996 1.00 0.00
#> TCGA.EA.A411.01 2 0.000 0.997 0.00 1.00
#> TCGA.VS.A9UP.01 1 0.000 0.996 1.00 0.00
#> TCGA.C5.A1MI.01 1 0.000 0.996 1.00 0.00
#> TCGA.ZJ.AAX8.01 1 0.000 0.996 1.00 0.00
#> TCGA.VS.A9UT.01 1 0.000 0.996 1.00 0.00
#> TCGA.VS.A9V0.01 1 0.000 0.996 1.00 0.00
#> TCGA.ZJ.AAXA.01 2 0.000 0.997 0.00 1.00
#> TCGA.LP.A4AV.01 2 0.000 0.997 0.00 1.00
#> TCGA.ZJ.AAXF.01 1 0.000 0.996 1.00 0.00
#> TCGA.EA.A3Y4.01 2 0.141 0.981 0.02 0.98
#> TCGA.UC.A7PG.06 2 0.000 0.997 0.00 1.00
#> TCGA.VS.A9UJ.01 2 0.000 0.997 0.00 1.00
#> TCGA.Q1.A73O.01 1 0.000 0.996 1.00 0.00
#> TCGA.EA.A439.01 1 0.000 0.996 1.00 0.00
#> TCGA.VS.A9UM.01 2 0.000 0.997 0.00 1.00
#> TCGA.C5.A1MP.01 1 0.242 0.961 0.96 0.04
#> TCGA.ZJ.AB0H.01 1 0.242 0.961 0.96 0.04
#> TCGA.VS.A9V4.01 1 0.000 0.996 1.00 0.00
#> TCGA.VS.A9UA.01 1 0.000 0.996 1.00 0.00
#> TCGA.LP.A4AW.01 1 0.327 0.940 0.94 0.06
#> TCGA.C5.A1BN.01 2 0.000 0.997 0.00 1.00
#> TCGA.VS.AA62.01 1 0.000 0.996 1.00 0.00
#> TCGA.C5.A1BM.01 1 0.242 0.961 0.96 0.04
#> TCGA.C5.A1M6.01 1 0.000 0.996 1.00 0.00
#> TCGA.C5.A1BE.01 2 0.141 0.981 0.02 0.98
#> TCGA.C5.A1BJ.01 1 0.000 0.996 1.00 0.00
#> TCGA.FU.A23L.01 1 0.000 0.996 1.00 0.00
#> TCGA.C5.A1BF.01 1 0.000 0.996 1.00 0.00
#> TCGA.C5.A1BI.01 1 0.000 0.996 1.00 0.00
cbind(get_classes(res, k = 3), get_membership(res, k = 3))
#> class entropy silhouette p1 p2 p3
#> TCGA.EK.A3GK.01 3 0.0000 1.000 0.00 0.00 1.00
#> TCGA.VS.A94Y.01 3 0.0000 1.000 0.00 0.00 1.00
#> TCGA.MY.A5BF.11 1 0.0000 0.995 1.00 0.00 0.00
#> TCGA.VS.A94Z.01 3 0.0000 1.000 0.00 0.00 1.00
#> TCGA.EA.A4BA.01 3 0.0000 1.000 0.00 0.00 1.00
#> TCGA.FU.A3EO.11 1 0.0000 0.995 1.00 0.00 0.00
#> TCGA.DG.A2KJ.01 1 0.0000 0.995 1.00 0.00 0.00
#> TCGA.EK.A2R7.01 3 0.0000 1.000 0.00 0.00 1.00
#> TCGA.C5.A905.01 2 0.0000 0.996 0.00 1.00 0.00
#> TCGA.EK.A2RN.01 3 0.0000 1.000 0.00 0.00 1.00
#> TCGA.FU.A57G.01 1 0.0000 0.995 1.00 0.00 0.00
#> TCGA.C5.A8YR.01 3 0.0000 1.000 0.00 0.00 1.00
#> TCGA.MY.A5BE.01 1 0.0000 0.995 1.00 0.00 0.00
#> TCGA.VS.A8QH.01 1 0.0000 0.995 1.00 0.00 0.00
#> TCGA.ZJ.A8QR.01 2 0.0000 0.996 0.00 1.00 0.00
#> TCGA.C5.A907.01 1 0.0000 0.995 1.00 0.00 0.00
#> TCGA.C5.A8ZZ.01 2 0.0000 0.996 0.00 1.00 0.00
#> TCGA.C5.A7UC.01 1 0.0892 0.974 0.98 0.00 0.02
#> TCGA.C5.A8XJ.01 3 0.0000 1.000 0.00 0.00 1.00
#> TCGA.EK.A3GM.01 1 0.0000 0.995 1.00 0.00 0.00
#> TCGA.VS.A8Q8.01 3 0.0000 1.000 0.00 0.00 1.00
#> TCGA.2W.A8YY.01 2 0.0000 0.996 0.00 1.00 0.00
#> TCGA.MU.A51Y.01 1 0.0000 0.995 1.00 0.00 0.00
#> TCGA.EK.A2RK.01 3 0.0000 1.000 0.00 0.00 1.00
#> TCGA.UC.A7PD.01 1 0.0000 0.995 1.00 0.00 0.00
#> TCGA.VS.A8QM.01 1 0.0000 0.995 1.00 0.00 0.00
#> TCGA.EA.A3HU.01 1 0.0000 0.995 1.00 0.00 0.00
#> TCGA.VS.A94X.01 1 0.2537 0.902 0.92 0.00 0.08
#> TCGA.C5.A3HF.01 1 0.0000 0.995 1.00 0.00 0.00
#> TCGA.MY.A913.01 1 0.0000 0.995 1.00 0.00 0.00
#> TCGA.EA.A97N.01 2 0.3340 0.864 0.00 0.88 0.12
#> TCGA.EK.A2RD.01 3 0.0000 1.000 0.00 0.00 1.00
#> TCGA.C5.A8YT.01 1 0.0000 0.995 1.00 0.00 0.00
#> TCGA.FU.A3HZ.01 2 0.0000 0.996 0.00 1.00 0.00
#> TCGA.VS.A8EJ.01 1 0.0000 0.995 1.00 0.00 0.00
#> TCGA.C5.A3HL.01 3 0.0000 1.000 0.00 0.00 1.00
#> TCGA.C5.A8XK.01 3 0.0000 1.000 0.00 0.00 1.00
#> TCGA.EX.A8YF.01 1 0.0000 0.995 1.00 0.00 0.00
#> TCGA.HM.A4S6.01 3 0.0000 1.000 0.00 0.00 1.00
#> TCGA.MA.AA3Y.01 1 0.0000 0.995 1.00 0.00 0.00
#> TCGA.MA.AA3Z.01 3 0.0000 1.000 0.00 0.00 1.00
#> TCGA.EK.A2RE.01 3 0.0000 1.000 0.00 0.00 1.00
#> TCGA.C5.A1BQ.01 3 0.0000 1.000 0.00 0.00 1.00
#> TCGA.EA.A556.01 3 0.0000 1.000 0.00 0.00 1.00
#> TCGA.EA.A44S.01 2 0.0000 0.996 0.00 1.00 0.00
#> TCGA.4J.AA1J.01 2 0.0000 0.996 0.00 1.00 0.00
#> TCGA.C5.A7X3.01 3 0.0000 1.000 0.00 0.00 1.00
#> TCGA.HG.A2PA.01 1 0.0000 0.995 1.00 0.00 0.00
#> TCGA.C5.A7XC.01 3 0.0000 1.000 0.00 0.00 1.00
#> TCGA.C5.A7UH.01 2 0.0000 0.996 0.00 1.00 0.00
#> TCGA.EA.A3HR.01 3 0.0000 1.000 0.00 0.00 1.00
#> TCGA.DG.A2KL.01 3 0.0000 1.000 0.00 0.00 1.00
#> TCGA.BI.A0VR.01 3 0.0000 1.000 0.00 0.00 1.00
#> TCGA.DS.A0VL.01 3 0.0000 1.000 0.00 0.00 1.00
#> TCGA.DR.A0ZM.01 3 0.0000 1.000 0.00 0.00 1.00
#> TCGA.DS.A0VK.01 3 0.0000 1.000 0.00 0.00 1.00
#> TCGA.JW.A5VJ.01 3 0.0000 1.000 0.00 0.00 1.00
#> TCGA.FU.A5XV.01 2 0.0000 0.996 0.00 1.00 0.00
#> TCGA.HM.A3JJ.01 3 0.0000 1.000 0.00 0.00 1.00
#> TCGA.EK.A2RJ.01 3 0.0000 1.000 0.00 0.00 1.00
#> TCGA.EA.A3HT.01 3 0.0000 1.000 0.00 0.00 1.00
#> TCGA.FU.A3TX.01 1 0.0000 0.995 1.00 0.00 0.00
#> TCGA.EK.A2PI.01 3 0.0000 1.000 0.00 0.00 1.00
#> TCGA.Q1.A73S.01 2 0.0000 0.996 0.00 1.00 0.00
#> TCGA.HM.A6W2.01 2 0.0000 0.996 0.00 1.00 0.00
#> TCGA.VS.A8EH.01 1 0.0000 0.995 1.00 0.00 0.00
#> TCGA.JW.A5VH.01 2 0.0000 0.996 0.00 1.00 0.00
#> TCGA.VS.A8EB.01 1 0.0000 0.995 1.00 0.00 0.00
#> TCGA.RA.A741.01 1 0.0000 0.995 1.00 0.00 0.00
#> TCGA.DG.A2KH.01 1 0.0000 0.995 1.00 0.00 0.00
#> TCGA.C5.A2LT.01 1 0.0000 0.995 1.00 0.00 0.00
#> TCGA.EA.A5ZD.01 3 0.0000 1.000 0.00 0.00 1.00
#> TCGA.EK.A2RM.01 1 0.0000 0.995 1.00 0.00 0.00
#> TCGA.C5.A7UI.01 3 0.0000 1.000 0.00 0.00 1.00
#> TCGA.EK.A2PL.01 3 0.0000 1.000 0.00 0.00 1.00
#> TCGA.EK.A2PM.01 2 0.0000 0.996 0.00 1.00 0.00
#> TCGA.EK.A2GZ.01 1 0.0000 0.995 1.00 0.00 0.00
#> TCGA.HM.A3JK.01 1 0.0000 0.995 1.00 0.00 0.00
#> TCGA.HM.A6W2.06 2 0.0000 0.996 0.00 1.00 0.00
#> TCGA.IR.A3LA.01 2 0.0000 0.996 0.00 1.00 0.00
#> TCGA.EK.A2PK.01 3 0.0000 1.000 0.00 0.00 1.00
#> TCGA.EA.A5ZF.01 3 0.0000 1.000 0.00 0.00 1.00
#> TCGA.BI.A0VS.01 3 0.0000 1.000 0.00 0.00 1.00
#> TCGA.JX.A5QV.01 3 0.0000 1.000 0.00 0.00 1.00
#> TCGA.EK.A2R8.01 3 0.0000 1.000 0.00 0.00 1.00
#> TCGA.EA.A1QS.01 1 0.0000 0.995 1.00 0.00 0.00
#> TCGA.JX.A3PZ.01 3 0.0000 1.000 0.00 0.00 1.00
#> TCGA.HM.A3JJ.11 1 0.0000 0.995 1.00 0.00 0.00
#> TCGA.DS.A5RQ.01 3 0.0000 1.000 0.00 0.00 1.00
#> TCGA.C5.A2LY.01 1 0.0000 0.995 1.00 0.00 0.00
#> TCGA.EK.A2H1.01 1 0.0000 0.995 1.00 0.00 0.00
#> TCGA.EX.A69L.01 3 0.0000 1.000 0.00 0.00 1.00
#> TCGA.FU.A2QG.01 2 0.0000 0.996 0.00 1.00 0.00
#> TCGA.JW.A5VG.01 1 0.0000 0.995 1.00 0.00 0.00
#> TCGA.PN.A8MA.01 2 0.0000 0.996 0.00 1.00 0.00
#> TCGA.DG.A2KM.01 1 0.0000 0.995 1.00 0.00 0.00
#> TCGA.EX.A3L1.01 1 0.0000 0.995 1.00 0.00 0.00
#> TCGA.Q1.A5R3.01 3 0.0000 1.000 0.00 0.00 1.00
#> TCGA.C5.A7CM.01 1 0.0000 0.995 1.00 0.00 0.00
#> TCGA.JX.A3Q0.01 2 0.0000 0.996 0.00 1.00 0.00
#> TCGA.C5.A7CL.01 3 0.0000 1.000 0.00 0.00 1.00
#> TCGA.VS.A959.01 1 0.0000 0.995 1.00 0.00 0.00
#> TCGA.LP.A4AX.01 1 0.0000 0.995 1.00 0.00 0.00
#> TCGA.ZJ.AAXN.01 3 0.0000 1.000 0.00 0.00 1.00
#> TCGA.MA.AA3X.01 2 0.0000 0.996 0.00 1.00 0.00
#> TCGA.UC.A7PG.01 3 0.0000 1.000 0.00 0.00 1.00
#> TCGA.DS.A1OD.01 3 0.0000 1.000 0.00 0.00 1.00
#> TCGA.C5.A1M7.01 3 0.0000 1.000 0.00 0.00 1.00
#> TCGA.VS.A9UH.01 1 0.0000 0.995 1.00 0.00 0.00
#> TCGA.ZJ.AAXD.01 3 0.0000 1.000 0.00 0.00 1.00
#> TCGA.VS.A9UB.01 1 0.0000 0.995 1.00 0.00 0.00
#> TCGA.EA.A410.01 2 0.0000 0.996 0.00 1.00 0.00
#> TCGA.ZJ.AB0I.01 2 0.0000 0.996 0.00 1.00 0.00
#> TCGA.VS.A9U6.01 1 0.0000 0.995 1.00 0.00 0.00
#> TCGA.C5.A0TN.01 1 0.0000 0.995 1.00 0.00 0.00
#> TCGA.ZJ.AAXB.01 2 0.0000 0.996 0.00 1.00 0.00
#> TCGA.DS.A1OB.01 2 0.0000 0.996 0.00 1.00 0.00
#> TCGA.HG.A9SC.01 2 0.0000 0.996 0.00 1.00 0.00
#> TCGA.ZJ.AAXT.01 3 0.0000 1.000 0.00 0.00 1.00
#> TCGA.C5.A1ML.01 1 0.3340 0.850 0.88 0.00 0.12
#> TCGA.LP.A4AU.01 1 0.0000 0.995 1.00 0.00 0.00
#> TCGA.ZJ.AAXU.01 3 0.0000 1.000 0.00 0.00 1.00
#> TCGA.C5.A1MK.01 3 0.0000 1.000 0.00 0.00 1.00
#> TCGA.VS.A958.01 3 0.0000 1.000 0.00 0.00 1.00
#> TCGA.R2.A69V.01 1 0.0000 0.995 1.00 0.00 0.00
#> TCGA.EA.A411.01 2 0.0000 0.996 0.00 1.00 0.00
#> TCGA.VS.A9UP.01 1 0.0000 0.995 1.00 0.00 0.00
#> TCGA.C5.A1MI.01 1 0.0000 0.995 1.00 0.00 0.00
#> TCGA.ZJ.AAX8.01 1 0.0000 0.995 1.00 0.00 0.00
#> TCGA.VS.A9UT.01 1 0.0000 0.995 1.00 0.00 0.00
#> TCGA.VS.A9V0.01 3 0.0000 1.000 0.00 0.00 1.00
#> TCGA.ZJ.AAXA.01 2 0.0000 0.996 0.00 1.00 0.00
#> TCGA.LP.A4AV.01 3 0.0000 1.000 0.00 0.00 1.00
#> TCGA.ZJ.AAXF.01 1 0.0000 0.995 1.00 0.00 0.00
#> TCGA.EA.A3Y4.01 3 0.0000 1.000 0.00 0.00 1.00
#> TCGA.UC.A7PG.06 2 0.0000 0.996 0.00 1.00 0.00
#> TCGA.VS.A9UJ.01 2 0.0000 0.996 0.00 1.00 0.00
#> TCGA.Q1.A73O.01 3 0.0892 0.977 0.02 0.00 0.98
#> TCGA.EA.A439.01 1 0.0000 0.995 1.00 0.00 0.00
#> TCGA.VS.A9UM.01 2 0.0000 0.996 0.00 1.00 0.00
#> TCGA.C5.A1MP.01 3 0.0000 1.000 0.00 0.00 1.00
#> TCGA.ZJ.AB0H.01 3 0.0000 1.000 0.00 0.00 1.00
#> TCGA.VS.A9V4.01 1 0.0000 0.995 1.00 0.00 0.00
#> TCGA.VS.A9UA.01 3 0.0000 1.000 0.00 0.00 1.00
#> TCGA.LP.A4AW.01 3 0.0000 1.000 0.00 0.00 1.00
#> TCGA.C5.A1BN.01 2 0.0000 0.996 0.00 1.00 0.00
#> TCGA.VS.AA62.01 1 0.0000 0.995 1.00 0.00 0.00
#> TCGA.C5.A1BM.01 3 0.0000 1.000 0.00 0.00 1.00
#> TCGA.C5.A1M6.01 1 0.0000 0.995 1.00 0.00 0.00
#> TCGA.C5.A1BE.01 3 0.0000 1.000 0.00 0.00 1.00
#> TCGA.C5.A1BJ.01 1 0.0000 0.995 1.00 0.00 0.00
#> TCGA.FU.A23L.01 3 0.0000 1.000 0.00 0.00 1.00
#> TCGA.C5.A1BF.01 1 0.0000 0.995 1.00 0.00 0.00
#> TCGA.C5.A1BI.01 3 0.0000 1.000 0.00 0.00 1.00
cbind(get_classes(res, k = 4), get_membership(res, k = 4))
#> class entropy silhouette p1 p2 p3 p4
#> TCGA.EK.A3GK.01 4 0.0707 0.9577 0.00 0.00 0.02 0.98
#> TCGA.VS.A94Y.01 4 0.0707 0.9577 0.00 0.00 0.02 0.98
#> TCGA.MY.A5BF.11 1 0.0000 0.9669 1.00 0.00 0.00 0.00
#> TCGA.VS.A94Z.01 3 0.4522 0.6619 0.00 0.00 0.68 0.32
#> TCGA.EA.A4BA.01 4 0.0707 0.9577 0.00 0.00 0.02 0.98
#> TCGA.FU.A3EO.11 1 0.0000 0.9669 1.00 0.00 0.00 0.00
#> TCGA.DG.A2KJ.01 1 0.0000 0.9669 1.00 0.00 0.00 0.00
#> TCGA.EK.A2R7.01 3 0.2345 0.7853 0.00 0.00 0.90 0.10
#> TCGA.C5.A905.01 2 0.0000 0.9434 0.00 1.00 0.00 0.00
#> TCGA.EK.A2RN.01 3 0.0707 0.7946 0.00 0.00 0.98 0.02
#> TCGA.FU.A57G.01 4 0.1211 0.9149 0.04 0.00 0.00 0.96
#> TCGA.C5.A8YR.01 4 0.4855 0.3437 0.00 0.00 0.40 0.60
#> TCGA.MY.A5BE.01 1 0.0000 0.9669 1.00 0.00 0.00 0.00
#> TCGA.VS.A8QH.01 1 0.0000 0.9669 1.00 0.00 0.00 0.00
#> TCGA.ZJ.A8QR.01 2 0.1211 0.9249 0.00 0.96 0.04 0.00
#> TCGA.C5.A907.01 1 0.0000 0.9669 1.00 0.00 0.00 0.00
#> TCGA.C5.A8ZZ.01 2 0.3400 0.8220 0.00 0.82 0.18 0.00
#> TCGA.C5.A7UC.01 1 0.5147 0.6294 0.74 0.00 0.06 0.20
#> TCGA.C5.A8XJ.01 3 0.4790 0.5895 0.00 0.00 0.62 0.38
#> TCGA.EK.A3GM.01 1 0.0000 0.9669 1.00 0.00 0.00 0.00
#> TCGA.VS.A8Q8.01 3 0.0707 0.7946 0.00 0.00 0.98 0.02
#> TCGA.2W.A8YY.01 2 0.0707 0.9422 0.00 0.98 0.00 0.02
#> TCGA.MU.A51Y.01 1 0.0000 0.9669 1.00 0.00 0.00 0.00
#> TCGA.EK.A2RK.01 3 0.0707 0.7946 0.00 0.00 0.98 0.02
#> TCGA.UC.A7PD.01 1 0.0000 0.9669 1.00 0.00 0.00 0.00
#> TCGA.VS.A8QM.01 1 0.5428 0.3157 0.60 0.00 0.02 0.38
#> TCGA.EA.A3HU.01 1 0.0000 0.9669 1.00 0.00 0.00 0.00
#> TCGA.VS.A94X.01 4 0.1411 0.9402 0.02 0.00 0.02 0.96
#> TCGA.C5.A3HF.01 1 0.0000 0.9669 1.00 0.00 0.00 0.00
#> TCGA.MY.A913.01 1 0.0000 0.9669 1.00 0.00 0.00 0.00
#> TCGA.EA.A97N.01 3 0.1211 0.7713 0.00 0.04 0.96 0.00
#> TCGA.EK.A2RD.01 3 0.0707 0.7946 0.00 0.00 0.98 0.02
#> TCGA.C5.A8YT.01 1 0.0000 0.9669 1.00 0.00 0.00 0.00
#> TCGA.FU.A3HZ.01 2 0.0707 0.9422 0.00 0.98 0.00 0.02
#> TCGA.VS.A8EJ.01 1 0.0000 0.9669 1.00 0.00 0.00 0.00
#> TCGA.C5.A3HL.01 3 0.4134 0.7133 0.00 0.00 0.74 0.26
#> TCGA.C5.A8XK.01 3 0.0707 0.7946 0.00 0.00 0.98 0.02
#> TCGA.EX.A8YF.01 1 0.0000 0.9669 1.00 0.00 0.00 0.00
#> TCGA.HM.A4S6.01 3 0.0707 0.7946 0.00 0.00 0.98 0.02
#> TCGA.MA.AA3Y.01 1 0.0000 0.9669 1.00 0.00 0.00 0.00
#> TCGA.MA.AA3Z.01 3 0.0000 0.7938 0.00 0.00 1.00 0.00
#> TCGA.EK.A2RE.01 3 0.0707 0.7946 0.00 0.00 0.98 0.02
#> TCGA.C5.A1BQ.01 3 0.3610 0.7479 0.00 0.00 0.80 0.20
#> TCGA.EA.A556.01 4 0.0707 0.9577 0.00 0.00 0.02 0.98
#> TCGA.EA.A44S.01 2 0.4790 0.5487 0.00 0.62 0.38 0.00
#> TCGA.4J.AA1J.01 2 0.0000 0.9434 0.00 1.00 0.00 0.00
#> TCGA.C5.A7X3.01 4 0.0707 0.9577 0.00 0.00 0.02 0.98
#> TCGA.HG.A2PA.01 1 0.0000 0.9669 1.00 0.00 0.00 0.00
#> TCGA.C5.A7XC.01 3 0.0707 0.7946 0.00 0.00 0.98 0.02
#> TCGA.C5.A7UH.01 2 0.0000 0.9434 0.00 1.00 0.00 0.00
#> TCGA.EA.A3HR.01 3 0.0000 0.7938 0.00 0.00 1.00 0.00
#> TCGA.DG.A2KL.01 3 0.0707 0.7946 0.00 0.00 0.98 0.02
#> TCGA.BI.A0VR.01 3 0.4790 0.5895 0.00 0.00 0.62 0.38
#> TCGA.DS.A0VL.01 3 0.0000 0.7938 0.00 0.00 1.00 0.00
#> TCGA.DR.A0ZM.01 3 0.0707 0.7946 0.00 0.00 0.98 0.02
#> TCGA.DS.A0VK.01 3 0.0707 0.7947 0.00 0.00 0.98 0.02
#> TCGA.JW.A5VJ.01 4 0.2011 0.8992 0.00 0.00 0.08 0.92
#> TCGA.FU.A5XV.01 2 0.2647 0.8706 0.00 0.88 0.12 0.00
#> TCGA.HM.A3JJ.01 3 0.4522 0.6619 0.00 0.00 0.68 0.32
#> TCGA.EK.A2RJ.01 4 0.0707 0.9577 0.00 0.00 0.02 0.98
#> TCGA.EA.A3HT.01 3 0.3610 0.7479 0.00 0.00 0.80 0.20
#> TCGA.FU.A3TX.01 1 0.0000 0.9669 1.00 0.00 0.00 0.00
#> TCGA.EK.A2PI.01 4 0.0707 0.9577 0.00 0.00 0.02 0.98
#> TCGA.Q1.A73S.01 2 0.0707 0.9422 0.00 0.98 0.00 0.02
#> TCGA.HM.A6W2.01 2 0.0707 0.9422 0.00 0.98 0.00 0.02
#> TCGA.VS.A8EH.01 1 0.0000 0.9669 1.00 0.00 0.00 0.00
#> TCGA.JW.A5VH.01 2 0.0707 0.9422 0.00 0.98 0.00 0.02
#> TCGA.VS.A8EB.01 1 0.0000 0.9669 1.00 0.00 0.00 0.00
#> TCGA.RA.A741.01 1 0.1913 0.9085 0.94 0.00 0.02 0.04
#> TCGA.DG.A2KH.01 1 0.0000 0.9669 1.00 0.00 0.00 0.00
#> TCGA.C5.A2LT.01 1 0.0000 0.9669 1.00 0.00 0.00 0.00
#> TCGA.EA.A5ZD.01 3 0.4790 0.5895 0.00 0.00 0.62 0.38
#> TCGA.EK.A2RM.01 1 0.0000 0.9669 1.00 0.00 0.00 0.00
#> TCGA.C5.A7UI.01 3 0.0707 0.7946 0.00 0.00 0.98 0.02
#> TCGA.EK.A2PL.01 3 0.0707 0.7946 0.00 0.00 0.98 0.02
#> TCGA.EK.A2PM.01 2 0.3610 0.8041 0.00 0.80 0.20 0.00
#> TCGA.EK.A2GZ.01 1 0.0000 0.9669 1.00 0.00 0.00 0.00
#> TCGA.HM.A3JK.01 1 0.0000 0.9669 1.00 0.00 0.00 0.00
#> TCGA.HM.A6W2.06 2 0.0707 0.9422 0.00 0.98 0.00 0.02
#> TCGA.IR.A3LA.01 2 0.0707 0.9422 0.00 0.98 0.00 0.02
#> TCGA.EK.A2PK.01 4 0.0707 0.9577 0.00 0.00 0.02 0.98
#> TCGA.EA.A5ZF.01 4 0.0707 0.9577 0.00 0.00 0.02 0.98
#> TCGA.BI.A0VS.01 3 0.4134 0.5170 0.00 0.00 0.74 0.26
#> TCGA.JX.A5QV.01 3 0.1211 0.7952 0.00 0.00 0.96 0.04
#> TCGA.EK.A2R8.01 4 0.1211 0.9414 0.00 0.00 0.04 0.96
#> TCGA.EA.A1QS.01 1 0.0000 0.9669 1.00 0.00 0.00 0.00
#> TCGA.JX.A3PZ.01 4 0.0707 0.9577 0.00 0.00 0.02 0.98
#> TCGA.HM.A3JJ.11 1 0.0000 0.9669 1.00 0.00 0.00 0.00
#> TCGA.DS.A5RQ.01 3 0.0707 0.7946 0.00 0.00 0.98 0.02
#> TCGA.C5.A2LY.01 1 0.0000 0.9669 1.00 0.00 0.00 0.00
#> TCGA.EK.A2H1.01 1 0.0000 0.9669 1.00 0.00 0.00 0.00
#> TCGA.EX.A69L.01 3 0.4790 0.5895 0.00 0.00 0.62 0.38
#> TCGA.FU.A2QG.01 2 0.3801 0.7833 0.00 0.78 0.22 0.00
#> TCGA.JW.A5VG.01 1 0.0000 0.9669 1.00 0.00 0.00 0.00
#> TCGA.PN.A8MA.01 2 0.0707 0.9422 0.00 0.98 0.00 0.02
#> TCGA.DG.A2KM.01 1 0.0000 0.9669 1.00 0.00 0.00 0.00
#> TCGA.EX.A3L1.01 1 0.0000 0.9669 1.00 0.00 0.00 0.00
#> TCGA.Q1.A5R3.01 3 0.0000 0.7938 0.00 0.00 1.00 0.00
#> TCGA.C5.A7CM.01 1 0.0000 0.9669 1.00 0.00 0.00 0.00
#> TCGA.JX.A3Q0.01 2 0.0000 0.9434 0.00 1.00 0.00 0.00
#> TCGA.C5.A7CL.01 3 0.4134 0.7133 0.00 0.00 0.74 0.26
#> TCGA.VS.A959.01 1 0.0000 0.9669 1.00 0.00 0.00 0.00
#> TCGA.LP.A4AX.01 1 0.0000 0.9669 1.00 0.00 0.00 0.00
#> TCGA.ZJ.AAXN.01 4 0.1211 0.9414 0.00 0.00 0.04 0.96
#> TCGA.MA.AA3X.01 2 0.0000 0.9434 0.00 1.00 0.00 0.00
#> TCGA.UC.A7PG.01 3 0.1411 0.7806 0.00 0.02 0.96 0.02
#> TCGA.DS.A1OD.01 3 0.4790 0.5895 0.00 0.00 0.62 0.38
#> TCGA.C5.A1M7.01 3 0.4790 0.5895 0.00 0.00 0.62 0.38
#> TCGA.VS.A9UH.01 1 0.0000 0.9669 1.00 0.00 0.00 0.00
#> TCGA.ZJ.AAXD.01 3 0.3975 0.7261 0.00 0.00 0.76 0.24
#> TCGA.VS.A9UB.01 1 0.0000 0.9669 1.00 0.00 0.00 0.00
#> TCGA.EA.A410.01 2 0.0707 0.9422 0.00 0.98 0.00 0.02
#> TCGA.ZJ.AB0I.01 2 0.0000 0.9434 0.00 1.00 0.00 0.00
#> TCGA.VS.A9U6.01 1 0.0000 0.9669 1.00 0.00 0.00 0.00
#> TCGA.C5.A0TN.01 1 0.0000 0.9669 1.00 0.00 0.00 0.00
#> TCGA.ZJ.AAXB.01 2 0.0707 0.9422 0.00 0.98 0.00 0.02
#> TCGA.DS.A1OB.01 2 0.1637 0.9128 0.00 0.94 0.06 0.00
#> TCGA.HG.A9SC.01 2 0.0000 0.9434 0.00 1.00 0.00 0.00
#> TCGA.ZJ.AAXT.01 3 0.4522 0.6828 0.00 0.00 0.68 0.32
#> TCGA.C5.A1ML.01 1 0.6988 0.0645 0.50 0.00 0.12 0.38
#> TCGA.LP.A4AU.01 1 0.0000 0.9669 1.00 0.00 0.00 0.00
#> TCGA.ZJ.AAXU.01 3 0.4624 0.6400 0.00 0.00 0.66 0.34
#> TCGA.C5.A1MK.01 3 0.0707 0.7946 0.00 0.00 0.98 0.02
#> TCGA.VS.A958.01 3 0.4790 0.5895 0.00 0.00 0.62 0.38
#> TCGA.R2.A69V.01 1 0.0000 0.9669 1.00 0.00 0.00 0.00
#> TCGA.EA.A411.01 2 0.0000 0.9434 0.00 1.00 0.00 0.00
#> TCGA.VS.A9UP.01 1 0.0000 0.9669 1.00 0.00 0.00 0.00
#> TCGA.C5.A1MI.01 1 0.0000 0.9669 1.00 0.00 0.00 0.00
#> TCGA.ZJ.AAX8.01 1 0.0000 0.9669 1.00 0.00 0.00 0.00
#> TCGA.VS.A9UT.01 1 0.0000 0.9669 1.00 0.00 0.00 0.00
#> TCGA.VS.A9V0.01 4 0.0707 0.9577 0.00 0.00 0.02 0.98
#> TCGA.ZJ.AAXA.01 2 0.0000 0.9434 0.00 1.00 0.00 0.00
#> TCGA.LP.A4AV.01 3 0.0707 0.7946 0.00 0.00 0.98 0.02
#> TCGA.ZJ.AAXF.01 1 0.5428 0.3157 0.60 0.00 0.02 0.38
#> TCGA.EA.A3Y4.01 4 0.0707 0.9577 0.00 0.00 0.02 0.98
#> TCGA.UC.A7PG.06 2 0.0000 0.9434 0.00 1.00 0.00 0.00
#> TCGA.VS.A9UJ.01 2 0.0707 0.9422 0.00 0.98 0.00 0.02
#> TCGA.Q1.A73O.01 3 0.7602 0.2010 0.20 0.00 0.42 0.38
#> TCGA.EA.A439.01 1 0.0000 0.9669 1.00 0.00 0.00 0.00
#> TCGA.VS.A9UM.01 2 0.0000 0.9434 0.00 1.00 0.00 0.00
#> TCGA.C5.A1MP.01 3 0.3400 0.7562 0.00 0.00 0.82 0.18
#> TCGA.ZJ.AB0H.01 3 0.3400 0.7562 0.00 0.00 0.82 0.18
#> TCGA.VS.A9V4.01 4 0.1211 0.9149 0.04 0.00 0.00 0.96
#> TCGA.VS.A9UA.01 3 0.4790 0.5895 0.00 0.00 0.62 0.38
#> TCGA.LP.A4AW.01 3 0.3610 0.7479 0.00 0.00 0.80 0.20
#> TCGA.C5.A1BN.01 2 0.3610 0.8041 0.00 0.80 0.20 0.00
#> TCGA.VS.AA62.01 1 0.0000 0.9669 1.00 0.00 0.00 0.00
#> TCGA.C5.A1BM.01 3 0.4522 0.6828 0.00 0.00 0.68 0.32
#> TCGA.C5.A1M6.01 1 0.0000 0.9669 1.00 0.00 0.00 0.00
#> TCGA.C5.A1BE.01 3 0.0000 0.7938 0.00 0.00 1.00 0.00
#> TCGA.C5.A1BJ.01 1 0.0707 0.9481 0.98 0.00 0.02 0.00
#> TCGA.FU.A23L.01 4 0.0707 0.9577 0.00 0.00 0.02 0.98
#> TCGA.C5.A1BF.01 1 0.0000 0.9669 1.00 0.00 0.00 0.00
#> TCGA.C5.A1BI.01 3 0.4790 0.5895 0.00 0.00 0.62 0.38
cbind(get_classes(res, k = 5), get_membership(res, k = 5))
#> class entropy silhouette p1 p2 p3 p4 p5
#> TCGA.EK.A3GK.01 4 0.0000 0.959 0.00 0.00 0.00 1.00 0.00
#> TCGA.VS.A94Y.01 4 0.0000 0.959 0.00 0.00 0.00 1.00 0.00
#> TCGA.MY.A5BF.11 1 0.2929 0.895 0.82 0.00 0.18 0.00 0.00
#> TCGA.VS.A94Z.01 3 0.3983 0.855 0.00 0.00 0.66 0.00 0.34
#> TCGA.EA.A4BA.01 4 0.1410 0.946 0.00 0.00 0.06 0.94 0.00
#> TCGA.FU.A3EO.11 1 0.2929 0.895 0.82 0.00 0.18 0.00 0.00
#> TCGA.DG.A2KJ.01 1 0.2929 0.895 0.82 0.00 0.18 0.00 0.00
#> TCGA.EK.A2R7.01 3 0.4182 0.773 0.00 0.00 0.60 0.00 0.40
#> TCGA.C5.A905.01 2 0.2020 0.934 0.00 0.90 0.10 0.00 0.00
#> TCGA.EK.A2RN.01 5 0.0000 0.782 0.00 0.00 0.00 0.00 1.00
#> TCGA.FU.A57G.01 4 0.1410 0.946 0.00 0.00 0.06 0.94 0.00
#> TCGA.C5.A8YR.01 4 0.3513 0.776 0.00 0.00 0.02 0.80 0.18
#> TCGA.MY.A5BE.01 1 0.2929 0.895 0.82 0.00 0.18 0.00 0.00
#> TCGA.VS.A8QH.01 1 0.0000 0.911 1.00 0.00 0.00 0.00 0.00
#> TCGA.ZJ.A8QR.01 2 0.5659 0.455 0.00 0.58 0.10 0.00 0.32
#> TCGA.C5.A907.01 1 0.0000 0.911 1.00 0.00 0.00 0.00 0.00
#> TCGA.C5.A8ZZ.01 5 0.5263 0.462 0.00 0.24 0.10 0.00 0.66
#> TCGA.C5.A7UC.01 3 0.4456 0.555 0.32 0.00 0.66 0.00 0.02
#> TCGA.C5.A8XJ.01 3 0.3983 0.855 0.00 0.00 0.66 0.00 0.34
#> TCGA.EK.A3GM.01 1 0.2929 0.895 0.82 0.00 0.18 0.00 0.00
#> TCGA.VS.A8Q8.01 5 0.1043 0.779 0.00 0.00 0.04 0.00 0.96
#> TCGA.2W.A8YY.01 2 0.0000 0.934 0.00 1.00 0.00 0.00 0.00
#> TCGA.MU.A51Y.01 1 0.0609 0.911 0.98 0.00 0.02 0.00 0.00
#> TCGA.EK.A2RK.01 5 0.0000 0.782 0.00 0.00 0.00 0.00 1.00
#> TCGA.UC.A7PD.01 1 0.1732 0.909 0.92 0.00 0.08 0.00 0.00
#> TCGA.VS.A8QM.01 3 0.4126 0.475 0.38 0.00 0.62 0.00 0.00
#> TCGA.EA.A3HU.01 1 0.0000 0.911 1.00 0.00 0.00 0.00 0.00
#> TCGA.VS.A94X.01 4 0.0000 0.959 0.00 0.00 0.00 1.00 0.00
#> TCGA.C5.A3HF.01 1 0.2929 0.895 0.82 0.00 0.18 0.00 0.00
#> TCGA.MY.A913.01 1 0.0000 0.911 1.00 0.00 0.00 0.00 0.00
#> TCGA.EA.A97N.01 5 0.2020 0.736 0.00 0.00 0.10 0.00 0.90
#> TCGA.EK.A2RD.01 5 0.1043 0.779 0.00 0.00 0.04 0.00 0.96
#> TCGA.C5.A8YT.01 1 0.2929 0.895 0.82 0.00 0.18 0.00 0.00
#> TCGA.FU.A3HZ.01 2 0.0000 0.934 0.00 1.00 0.00 0.00 0.00
#> TCGA.VS.A8EJ.01 1 0.2929 0.895 0.82 0.00 0.18 0.00 0.00
#> TCGA.C5.A3HL.01 3 0.3983 0.855 0.00 0.00 0.66 0.00 0.34
#> TCGA.C5.A8XK.01 5 0.1043 0.779 0.00 0.00 0.04 0.00 0.96
#> TCGA.EX.A8YF.01 1 0.1732 0.909 0.92 0.00 0.08 0.00 0.00
#> TCGA.HM.A4S6.01 5 0.1043 0.779 0.00 0.00 0.04 0.00 0.96
#> TCGA.MA.AA3Y.01 1 0.0000 0.911 1.00 0.00 0.00 0.00 0.00
#> TCGA.MA.AA3Z.01 5 0.2280 0.666 0.00 0.00 0.12 0.00 0.88
#> TCGA.EK.A2RE.01 5 0.0000 0.782 0.00 0.00 0.00 0.00 1.00
#> TCGA.C5.A1BQ.01 3 0.3983 0.855 0.00 0.00 0.66 0.00 0.34
#> TCGA.EA.A556.01 4 0.1410 0.946 0.00 0.00 0.06 0.94 0.00
#> TCGA.EA.A44S.01 5 0.5263 0.462 0.00 0.24 0.10 0.00 0.66
#> TCGA.4J.AA1J.01 2 0.3037 0.909 0.00 0.86 0.10 0.00 0.04
#> TCGA.C5.A7X3.01 4 0.0000 0.959 0.00 0.00 0.00 1.00 0.00
#> TCGA.HG.A2PA.01 1 0.0000 0.911 1.00 0.00 0.00 0.00 0.00
#> TCGA.C5.A7XC.01 5 0.1043 0.779 0.00 0.00 0.04 0.00 0.96
#> TCGA.C5.A7UH.01 2 0.2020 0.934 0.00 0.90 0.10 0.00 0.00
#> TCGA.EA.A3HR.01 5 0.1410 0.756 0.00 0.00 0.06 0.00 0.94
#> TCGA.DG.A2KL.01 5 0.1043 0.779 0.00 0.00 0.04 0.00 0.96
#> TCGA.BI.A0VR.01 3 0.3983 0.855 0.00 0.00 0.66 0.00 0.34
#> TCGA.DS.A0VL.01 3 0.3983 0.855 0.00 0.00 0.66 0.00 0.34
#> TCGA.DR.A0ZM.01 5 0.0000 0.782 0.00 0.00 0.00 0.00 1.00
#> TCGA.DS.A0VK.01 3 0.3983 0.855 0.00 0.00 0.66 0.00 0.34
#> TCGA.JW.A5VJ.01 3 0.5686 0.480 0.04 0.00 0.62 0.30 0.04
#> TCGA.FU.A5XV.01 5 0.5659 0.300 0.00 0.32 0.10 0.00 0.58
#> TCGA.HM.A3JJ.01 3 0.3983 0.855 0.00 0.00 0.66 0.00 0.34
#> TCGA.EK.A2RJ.01 4 0.0609 0.954 0.00 0.00 0.02 0.98 0.00
#> TCGA.EA.A3HT.01 3 0.3983 0.855 0.00 0.00 0.66 0.00 0.34
#> TCGA.FU.A3TX.01 1 0.2929 0.895 0.82 0.00 0.18 0.00 0.00
#> TCGA.EK.A2PI.01 4 0.0000 0.959 0.00 0.00 0.00 1.00 0.00
#> TCGA.Q1.A73S.01 2 0.0000 0.934 0.00 1.00 0.00 0.00 0.00
#> TCGA.HM.A6W2.01 2 0.0000 0.934 0.00 1.00 0.00 0.00 0.00
#> TCGA.VS.A8EH.01 1 0.0000 0.911 1.00 0.00 0.00 0.00 0.00
#> TCGA.JW.A5VH.01 2 0.0000 0.934 0.00 1.00 0.00 0.00 0.00
#> TCGA.VS.A8EB.01 1 0.2732 0.898 0.84 0.00 0.16 0.00 0.00
#> TCGA.RA.A741.01 1 0.4182 0.174 0.60 0.00 0.40 0.00 0.00
#> TCGA.DG.A2KH.01 1 0.2929 0.895 0.82 0.00 0.18 0.00 0.00
#> TCGA.C5.A2LT.01 1 0.0000 0.911 1.00 0.00 0.00 0.00 0.00
#> TCGA.EA.A5ZD.01 3 0.3983 0.855 0.00 0.00 0.66 0.00 0.34
#> TCGA.EK.A2RM.01 1 0.2929 0.895 0.82 0.00 0.18 0.00 0.00
#> TCGA.C5.A7UI.01 5 0.1043 0.779 0.00 0.00 0.04 0.00 0.96
#> TCGA.EK.A2PL.01 5 0.1043 0.779 0.00 0.00 0.04 0.00 0.96
#> TCGA.EK.A2PM.01 5 0.5263 0.462 0.00 0.24 0.10 0.00 0.66
#> TCGA.EK.A2GZ.01 1 0.0000 0.911 1.00 0.00 0.00 0.00 0.00
#> TCGA.HM.A3JK.01 1 0.2929 0.895 0.82 0.00 0.18 0.00 0.00
#> TCGA.HM.A6W2.06 2 0.0000 0.934 0.00 1.00 0.00 0.00 0.00
#> TCGA.IR.A3LA.01 2 0.0000 0.934 0.00 1.00 0.00 0.00 0.00
#> TCGA.EK.A2PK.01 4 0.0000 0.959 0.00 0.00 0.00 1.00 0.00
#> TCGA.EA.A5ZF.01 4 0.1043 0.952 0.00 0.00 0.04 0.96 0.00
#> TCGA.BI.A0VS.01 5 0.3513 0.632 0.00 0.00 0.02 0.18 0.80
#> TCGA.JX.A5QV.01 5 0.3895 0.054 0.00 0.00 0.32 0.00 0.68
#> TCGA.EK.A2R8.01 3 0.4921 0.393 0.04 0.00 0.62 0.34 0.00
#> TCGA.EA.A1QS.01 1 0.2929 0.895 0.82 0.00 0.18 0.00 0.00
#> TCGA.JX.A3PZ.01 4 0.0000 0.959 0.00 0.00 0.00 1.00 0.00
#> TCGA.HM.A3JJ.11 1 0.2929 0.895 0.82 0.00 0.18 0.00 0.00
#> TCGA.DS.A5RQ.01 5 0.1043 0.779 0.00 0.00 0.04 0.00 0.96
#> TCGA.C5.A2LY.01 1 0.0000 0.911 1.00 0.00 0.00 0.00 0.00
#> TCGA.EK.A2H1.01 1 0.2929 0.895 0.82 0.00 0.18 0.00 0.00
#> TCGA.EX.A69L.01 3 0.3983 0.855 0.00 0.00 0.66 0.00 0.34
#> TCGA.FU.A2QG.01 5 0.5263 0.462 0.00 0.24 0.10 0.00 0.66
#> TCGA.JW.A5VG.01 1 0.0000 0.911 1.00 0.00 0.00 0.00 0.00
#> TCGA.PN.A8MA.01 2 0.0000 0.934 0.00 1.00 0.00 0.00 0.00
#> TCGA.DG.A2KM.01 1 0.0000 0.911 1.00 0.00 0.00 0.00 0.00
#> TCGA.EX.A3L1.01 1 0.2929 0.895 0.82 0.00 0.18 0.00 0.00
#> TCGA.Q1.A5R3.01 5 0.2280 0.666 0.00 0.00 0.12 0.00 0.88
#> TCGA.C5.A7CM.01 1 0.1410 0.910 0.94 0.00 0.06 0.00 0.00
#> TCGA.JX.A3Q0.01 2 0.2020 0.934 0.00 0.90 0.10 0.00 0.00
#> TCGA.C5.A7CL.01 3 0.3983 0.855 0.00 0.00 0.66 0.00 0.34
#> TCGA.VS.A959.01 1 0.0000 0.911 1.00 0.00 0.00 0.00 0.00
#> TCGA.LP.A4AX.01 1 0.2929 0.895 0.82 0.00 0.18 0.00 0.00
#> TCGA.ZJ.AAXN.01 4 0.2797 0.869 0.06 0.00 0.06 0.88 0.00
#> TCGA.MA.AA3X.01 2 0.2020 0.934 0.00 0.90 0.10 0.00 0.00
#> TCGA.UC.A7PG.01 5 0.0000 0.782 0.00 0.00 0.00 0.00 1.00
#> TCGA.DS.A1OD.01 3 0.3983 0.855 0.00 0.00 0.66 0.00 0.34
#> TCGA.C5.A1M7.01 3 0.3983 0.855 0.00 0.00 0.66 0.00 0.34
#> TCGA.VS.A9UH.01 1 0.0000 0.911 1.00 0.00 0.00 0.00 0.00
#> TCGA.ZJ.AAXD.01 3 0.3983 0.855 0.00 0.00 0.66 0.00 0.34
#> TCGA.VS.A9UB.01 1 0.0000 0.911 1.00 0.00 0.00 0.00 0.00
#> TCGA.EA.A410.01 2 0.0000 0.934 0.00 1.00 0.00 0.00 0.00
#> TCGA.ZJ.AB0I.01 2 0.2020 0.934 0.00 0.90 0.10 0.00 0.00
#> TCGA.VS.A9U6.01 1 0.0000 0.911 1.00 0.00 0.00 0.00 0.00
#> TCGA.C5.A0TN.01 1 0.0000 0.911 1.00 0.00 0.00 0.00 0.00
#> TCGA.ZJ.AAXB.01 2 0.0000 0.934 0.00 1.00 0.00 0.00 0.00
#> TCGA.DS.A1OB.01 5 0.5659 0.300 0.00 0.32 0.10 0.00 0.58
#> TCGA.HG.A9SC.01 2 0.2020 0.934 0.00 0.90 0.10 0.00 0.00
#> TCGA.ZJ.AAXT.01 3 0.3983 0.855 0.00 0.00 0.66 0.00 0.34
#> TCGA.C5.A1ML.01 3 0.5136 0.615 0.26 0.00 0.66 0.00 0.08
#> TCGA.LP.A4AU.01 1 0.0000 0.911 1.00 0.00 0.00 0.00 0.00
#> TCGA.ZJ.AAXU.01 3 0.3983 0.855 0.00 0.00 0.66 0.00 0.34
#> TCGA.C5.A1MK.01 5 0.1043 0.779 0.00 0.00 0.04 0.00 0.96
#> TCGA.VS.A958.01 3 0.3983 0.855 0.00 0.00 0.66 0.00 0.34
#> TCGA.R2.A69V.01 1 0.0000 0.911 1.00 0.00 0.00 0.00 0.00
#> TCGA.EA.A411.01 2 0.3037 0.909 0.00 0.86 0.10 0.00 0.04
#> TCGA.VS.A9UP.01 1 0.1410 0.910 0.94 0.00 0.06 0.00 0.00
#> TCGA.C5.A1MI.01 1 0.0000 0.911 1.00 0.00 0.00 0.00 0.00
#> TCGA.ZJ.AAX8.01 1 0.0000 0.911 1.00 0.00 0.00 0.00 0.00
#> TCGA.VS.A9UT.01 1 0.2929 0.895 0.82 0.00 0.18 0.00 0.00
#> TCGA.VS.A9V0.01 4 0.1410 0.946 0.00 0.00 0.06 0.94 0.00
#> TCGA.ZJ.AAXA.01 2 0.2020 0.934 0.00 0.90 0.10 0.00 0.00
#> TCGA.LP.A4AV.01 5 0.2077 0.770 0.00 0.00 0.04 0.04 0.92
#> TCGA.ZJ.AAXF.01 3 0.4613 0.500 0.36 0.00 0.62 0.02 0.00
#> TCGA.EA.A3Y4.01 4 0.0000 0.959 0.00 0.00 0.00 1.00 0.00
#> TCGA.UC.A7PG.06 2 0.2020 0.934 0.00 0.90 0.10 0.00 0.00
#> TCGA.VS.A9UJ.01 2 0.0000 0.934 0.00 1.00 0.00 0.00 0.00
#> TCGA.Q1.A73O.01 3 0.5574 0.623 0.24 0.00 0.66 0.02 0.08
#> TCGA.EA.A439.01 1 0.2929 0.895 0.82 0.00 0.18 0.00 0.00
#> TCGA.VS.A9UM.01 2 0.2020 0.934 0.00 0.90 0.10 0.00 0.00
#> TCGA.C5.A1MP.01 3 0.3983 0.855 0.00 0.00 0.66 0.00 0.34
#> TCGA.ZJ.AB0H.01 3 0.3983 0.855 0.00 0.00 0.66 0.00 0.34
#> TCGA.VS.A9V4.01 4 0.2732 0.810 0.16 0.00 0.00 0.84 0.00
#> TCGA.VS.A9UA.01 3 0.4456 0.839 0.00 0.00 0.66 0.02 0.32
#> TCGA.LP.A4AW.01 3 0.3983 0.855 0.00 0.00 0.66 0.00 0.34
#> TCGA.C5.A1BN.01 5 0.5263 0.462 0.00 0.24 0.10 0.00 0.66
#> TCGA.VS.AA62.01 1 0.0000 0.911 1.00 0.00 0.00 0.00 0.00
#> TCGA.C5.A1BM.01 3 0.3983 0.855 0.00 0.00 0.66 0.00 0.34
#> TCGA.C5.A1M6.01 1 0.0000 0.911 1.00 0.00 0.00 0.00 0.00
#> TCGA.C5.A1BE.01 3 0.4227 0.740 0.00 0.00 0.58 0.00 0.42
#> TCGA.C5.A1BJ.01 3 0.4126 0.475 0.38 0.00 0.62 0.00 0.00
#> TCGA.FU.A23L.01 4 0.0000 0.959 0.00 0.00 0.00 1.00 0.00
#> TCGA.C5.A1BF.01 1 0.2929 0.895 0.82 0.00 0.18 0.00 0.00
#> TCGA.C5.A1BI.01 3 0.3983 0.855 0.00 0.00 0.66 0.00 0.34
cbind(get_classes(res, k = 6), get_membership(res, k = 6))
#> class entropy silhouette p1 p2 p3 p4 p5 p6
#> TCGA.EK.A3GK.01 4 0.2094 0.8557 0.00 0.00 0.00 0.90 0.02 0.08
#> TCGA.VS.A94Y.01 4 0.2474 0.8405 0.00 0.00 0.08 0.88 0.00 0.04
#> TCGA.MY.A5BF.11 1 0.0547 0.5931 0.98 0.00 0.00 0.00 0.00 0.02
#> TCGA.VS.A94Z.01 3 0.0000 0.8400 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.EA.A4BA.01 4 0.3315 0.8313 0.00 0.00 0.00 0.78 0.02 0.20
#> TCGA.FU.A3EO.11 1 0.0547 0.5931 0.98 0.00 0.00 0.00 0.00 0.02
#> TCGA.DG.A2KJ.01 1 0.1267 0.6015 0.94 0.00 0.00 0.00 0.00 0.06
#> TCGA.EK.A2R7.01 3 0.3679 0.6307 0.00 0.00 0.76 0.00 0.20 0.04
#> TCGA.C5.A905.01 2 0.3351 0.8863 0.00 0.80 0.00 0.00 0.04 0.16
#> TCGA.EK.A2RN.01 5 0.2094 0.8115 0.00 0.00 0.08 0.00 0.90 0.02
#> TCGA.FU.A57G.01 4 0.3156 0.8199 0.00 0.00 0.00 0.80 0.02 0.18
#> TCGA.C5.A8YR.01 4 0.4566 0.7256 0.00 0.00 0.00 0.70 0.14 0.16
#> TCGA.MY.A5BE.01 1 0.0000 0.6000 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.VS.A8QH.01 6 0.4651 -0.4503 0.48 0.00 0.04 0.00 0.00 0.48
#> TCGA.ZJ.A8QR.01 5 0.5888 -0.0572 0.00 0.32 0.00 0.00 0.46 0.22
#> TCGA.C5.A907.01 1 0.3706 0.4475 0.62 0.00 0.00 0.00 0.00 0.38
#> TCGA.C5.A8ZZ.01 5 0.3351 0.6801 0.00 0.04 0.00 0.00 0.80 0.16
#> TCGA.C5.A7UC.01 3 0.4199 0.1301 0.02 0.00 0.60 0.00 0.00 0.38
#> TCGA.C5.A8XJ.01 3 0.1480 0.8273 0.00 0.00 0.94 0.00 0.02 0.04
#> TCGA.EK.A3GM.01 1 0.0547 0.5931 0.98 0.00 0.00 0.00 0.00 0.02
#> TCGA.VS.A8Q8.01 5 0.2941 0.7516 0.00 0.00 0.22 0.00 0.78 0.00
#> TCGA.2W.A8YY.01 2 0.0000 0.8803 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.MU.A51Y.01 1 0.3647 0.4699 0.64 0.00 0.00 0.00 0.00 0.36
#> TCGA.EK.A2RK.01 5 0.2094 0.8115 0.00 0.00 0.08 0.00 0.90 0.02
#> TCGA.UC.A7PD.01 1 0.3409 0.5166 0.70 0.00 0.00 0.00 0.00 0.30
#> TCGA.VS.A8QM.01 3 0.4609 -0.1299 0.04 0.00 0.54 0.00 0.00 0.42
#> TCGA.EA.A3HU.01 1 0.3756 0.4115 0.60 0.00 0.00 0.00 0.00 0.40
#> TCGA.VS.A94X.01 4 0.2474 0.8405 0.00 0.00 0.08 0.88 0.00 0.04
#> TCGA.C5.A3HF.01 1 0.0547 0.5931 0.98 0.00 0.00 0.00 0.00 0.02
#> TCGA.MY.A913.01 1 0.3706 0.4475 0.62 0.00 0.00 0.00 0.00 0.38
#> TCGA.EA.A97N.01 5 0.1480 0.7952 0.00 0.00 0.04 0.00 0.94 0.02
#> TCGA.EK.A2RD.01 5 0.2260 0.8183 0.00 0.00 0.14 0.00 0.86 0.00
#> TCGA.C5.A8YT.01 1 0.0547 0.5931 0.98 0.00 0.00 0.00 0.00 0.02
#> TCGA.FU.A3HZ.01 2 0.0000 0.8803 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.VS.A8EJ.01 1 0.1807 0.5494 0.92 0.00 0.00 0.00 0.02 0.06
#> TCGA.C5.A3HL.01 3 0.0547 0.8369 0.00 0.00 0.98 0.00 0.00 0.02
#> TCGA.C5.A8XK.01 5 0.3270 0.8020 0.00 0.00 0.12 0.00 0.82 0.06
#> TCGA.EX.A8YF.01 1 0.3076 0.5492 0.76 0.00 0.00 0.00 0.00 0.24
#> TCGA.HM.A4S6.01 5 0.2260 0.8183 0.00 0.00 0.14 0.00 0.86 0.00
#> TCGA.MA.AA3Y.01 1 0.3756 0.4115 0.60 0.00 0.00 0.00 0.00 0.40
#> TCGA.MA.AA3Z.01 5 0.4576 0.4143 0.00 0.00 0.40 0.00 0.56 0.04
#> TCGA.EK.A2RE.01 5 0.1556 0.8111 0.00 0.00 0.08 0.00 0.92 0.00
#> TCGA.C5.A1BQ.01 3 0.0547 0.8369 0.00 0.00 0.98 0.00 0.00 0.02
#> TCGA.EA.A556.01 4 0.3315 0.8313 0.00 0.00 0.00 0.78 0.02 0.20
#> TCGA.EA.A44S.01 5 0.2190 0.7464 0.00 0.04 0.00 0.00 0.90 0.06
#> TCGA.4J.AA1J.01 2 0.4328 0.8374 0.00 0.72 0.00 0.00 0.10 0.18
#> TCGA.C5.A7X3.01 4 0.2794 0.8408 0.00 0.00 0.08 0.86 0.00 0.06
#> TCGA.HG.A2PA.01 1 0.3706 0.4479 0.62 0.00 0.00 0.00 0.00 0.38
#> TCGA.C5.A7XC.01 5 0.3679 0.7491 0.00 0.00 0.20 0.00 0.76 0.04
#> TCGA.C5.A7UH.01 2 0.3351 0.8863 0.00 0.80 0.00 0.00 0.04 0.16
#> TCGA.EA.A3HR.01 5 0.4420 0.5423 0.00 0.00 0.34 0.00 0.62 0.04
#> TCGA.DG.A2KL.01 5 0.2260 0.8183 0.00 0.00 0.14 0.00 0.86 0.00
#> TCGA.BI.A0VR.01 3 0.0000 0.8400 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.DS.A0VL.01 3 0.3163 0.7151 0.00 0.00 0.82 0.00 0.14 0.04
#> TCGA.DR.A0ZM.01 5 0.2048 0.8182 0.00 0.00 0.12 0.00 0.88 0.00
#> TCGA.DS.A0VK.01 3 0.3163 0.7151 0.00 0.00 0.82 0.00 0.14 0.04
#> TCGA.JW.A5VJ.01 3 0.3544 0.7086 0.00 0.00 0.80 0.12 0.00 0.08
#> TCGA.FU.A5XV.01 5 0.4094 0.6105 0.00 0.08 0.00 0.00 0.74 0.18
#> TCGA.HM.A3JJ.01 3 0.0000 0.8400 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.EK.A2RJ.01 4 0.2350 0.8518 0.00 0.00 0.00 0.88 0.02 0.10
#> TCGA.EA.A3HT.01 3 0.1092 0.8304 0.00 0.00 0.96 0.00 0.02 0.02
#> TCGA.FU.A3TX.01 1 0.0000 0.6000 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.EK.A2PI.01 4 0.2094 0.8460 0.00 0.00 0.08 0.90 0.00 0.02
#> TCGA.Q1.A73S.01 2 0.0547 0.8835 0.00 0.98 0.00 0.00 0.00 0.02
#> TCGA.HM.A6W2.01 2 0.1814 0.8422 0.00 0.90 0.00 0.00 0.00 0.10
#> TCGA.VS.A8EH.01 1 0.3756 0.4115 0.60 0.00 0.00 0.00 0.00 0.40
#> TCGA.JW.A5VH.01 2 0.0000 0.8803 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.VS.A8EB.01 1 0.1267 0.6009 0.94 0.00 0.00 0.00 0.00 0.06
#> TCGA.RA.A741.01 6 0.5575 0.2026 0.14 0.00 0.40 0.00 0.00 0.46
#> TCGA.DG.A2KH.01 1 0.0937 0.5797 0.96 0.00 0.00 0.00 0.00 0.04
#> TCGA.C5.A2LT.01 1 0.3706 0.4475 0.62 0.00 0.00 0.00 0.00 0.38
#> TCGA.EA.A5ZD.01 3 0.0937 0.8242 0.00 0.00 0.96 0.00 0.00 0.04
#> TCGA.EK.A2RM.01 1 0.1556 0.5925 0.92 0.00 0.00 0.00 0.00 0.08
#> TCGA.C5.A7UI.01 5 0.2260 0.8183 0.00 0.00 0.14 0.00 0.86 0.00
#> TCGA.EK.A2PL.01 5 0.2260 0.8183 0.00 0.00 0.14 0.00 0.86 0.00
#> TCGA.EK.A2PM.01 5 0.3163 0.7062 0.00 0.04 0.00 0.00 0.82 0.14
#> TCGA.EK.A2GZ.01 1 0.3706 0.4479 0.62 0.00 0.00 0.00 0.00 0.38
#> TCGA.HM.A3JK.01 1 0.0547 0.6017 0.98 0.00 0.00 0.00 0.00 0.02
#> TCGA.HM.A6W2.06 2 0.0000 0.8803 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.IR.A3LA.01 2 0.0000 0.8803 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.EK.A2PK.01 4 0.2094 0.8557 0.00 0.00 0.00 0.90 0.02 0.08
#> TCGA.EA.A5ZF.01 4 0.3315 0.8313 0.00 0.00 0.00 0.78 0.02 0.20
#> TCGA.BI.A0VS.01 5 0.4566 0.5589 0.00 0.00 0.00 0.14 0.70 0.16
#> TCGA.JX.A5QV.01 3 0.4420 0.3102 0.00 0.00 0.62 0.00 0.34 0.04
#> TCGA.EK.A2R8.01 3 0.3321 0.7153 0.00 0.00 0.82 0.08 0.00 0.10
#> TCGA.EA.A1QS.01 1 0.0000 0.6000 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.JX.A3PZ.01 4 0.0547 0.8558 0.00 0.00 0.00 0.98 0.00 0.02
#> TCGA.HM.A3JJ.11 1 0.0547 0.5931 0.98 0.00 0.00 0.00 0.00 0.02
#> TCGA.DS.A5RQ.01 5 0.2790 0.8124 0.00 0.00 0.14 0.00 0.84 0.02
#> TCGA.C5.A2LY.01 1 0.3706 0.4479 0.62 0.00 0.00 0.00 0.00 0.38
#> TCGA.EK.A2H1.01 1 0.0000 0.6000 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.EX.A69L.01 3 0.0000 0.8400 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.FU.A2QG.01 5 0.3351 0.6801 0.00 0.04 0.00 0.00 0.80 0.16
#> TCGA.JW.A5VG.01 1 0.3706 0.4475 0.62 0.00 0.00 0.00 0.00 0.38
#> TCGA.PN.A8MA.01 2 0.1556 0.8538 0.00 0.92 0.00 0.00 0.00 0.08
#> TCGA.DG.A2KM.01 1 0.3828 0.2852 0.56 0.00 0.00 0.00 0.00 0.44
#> TCGA.EX.A3L1.01 1 0.0000 0.6000 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.Q1.A5R3.01 5 0.4576 0.4143 0.00 0.00 0.40 0.00 0.56 0.04
#> TCGA.C5.A7CM.01 1 0.3499 0.5088 0.68 0.00 0.00 0.00 0.00 0.32
#> TCGA.JX.A3Q0.01 2 0.3351 0.8863 0.00 0.80 0.00 0.00 0.04 0.16
#> TCGA.C5.A7CL.01 3 0.0000 0.8400 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.VS.A959.01 1 0.3828 0.3188 0.56 0.00 0.00 0.00 0.00 0.44
#> TCGA.LP.A4AX.01 1 0.0000 0.6000 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.ZJ.AAXN.01 4 0.4165 0.7276 0.00 0.00 0.16 0.74 0.00 0.10
#> TCGA.MA.AA3X.01 2 0.3351 0.8863 0.00 0.80 0.00 0.00 0.04 0.16
#> TCGA.UC.A7PG.01 5 0.1556 0.8111 0.00 0.00 0.08 0.00 0.92 0.00
#> TCGA.DS.A1OD.01 3 0.0000 0.8400 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.C5.A1M7.01 3 0.0547 0.8339 0.00 0.00 0.98 0.00 0.00 0.02
#> TCGA.VS.A9UH.01 1 0.3706 0.4475 0.62 0.00 0.00 0.00 0.00 0.38
#> TCGA.ZJ.AAXD.01 3 0.0547 0.8369 0.00 0.00 0.98 0.00 0.00 0.02
#> TCGA.VS.A9UB.01 1 0.3828 0.2852 0.56 0.00 0.00 0.00 0.00 0.44
#> TCGA.EA.A410.01 2 0.0000 0.8803 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.ZJ.AB0I.01 2 0.3351 0.8863 0.00 0.80 0.00 0.00 0.04 0.16
#> TCGA.VS.A9U6.01 1 0.3706 0.4479 0.62 0.00 0.00 0.00 0.00 0.38
#> TCGA.C5.A0TN.01 1 0.3828 0.2852 0.56 0.00 0.00 0.00 0.00 0.44
#> TCGA.ZJ.AAXB.01 2 0.0000 0.8803 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.DS.A1OB.01 5 0.4475 0.5692 0.00 0.10 0.00 0.00 0.70 0.20
#> TCGA.HG.A9SC.01 2 0.3523 0.8783 0.00 0.78 0.00 0.00 0.04 0.18
#> TCGA.ZJ.AAXT.01 3 0.0000 0.8400 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.C5.A1ML.01 3 0.3111 0.7276 0.02 0.00 0.84 0.00 0.02 0.12
#> TCGA.LP.A4AU.01 1 0.3647 0.4714 0.64 0.00 0.00 0.00 0.00 0.36
#> TCGA.ZJ.AAXU.01 3 0.0000 0.8400 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.C5.A1MK.01 5 0.2260 0.8183 0.00 0.00 0.14 0.00 0.86 0.00
#> TCGA.VS.A958.01 3 0.0547 0.8319 0.00 0.00 0.98 0.00 0.00 0.02
#> TCGA.R2.A69V.01 1 0.3828 0.2852 0.56 0.00 0.00 0.00 0.00 0.44
#> TCGA.EA.A411.01 2 0.4608 0.8180 0.00 0.68 0.00 0.00 0.10 0.22
#> TCGA.VS.A9UP.01 1 0.3409 0.5085 0.70 0.00 0.00 0.00 0.00 0.30
#> TCGA.C5.A1MI.01 1 0.4282 0.3607 0.56 0.00 0.00 0.00 0.02 0.42
#> TCGA.ZJ.AAX8.01 1 0.3756 0.4115 0.60 0.00 0.00 0.00 0.00 0.40
#> TCGA.VS.A9UT.01 1 0.2454 0.5819 0.84 0.00 0.00 0.00 0.00 0.16
#> TCGA.VS.A9V0.01 4 0.2581 0.8429 0.00 0.00 0.00 0.86 0.02 0.12
#> TCGA.ZJ.AAXA.01 2 0.3351 0.8863 0.00 0.80 0.00 0.00 0.04 0.16
#> TCGA.LP.A4AV.01 5 0.2260 0.8183 0.00 0.00 0.14 0.00 0.86 0.00
#> TCGA.ZJ.AAXF.01 3 0.5058 -0.0873 0.04 0.00 0.54 0.02 0.00 0.40
#> TCGA.EA.A3Y4.01 4 0.2094 0.8557 0.00 0.00 0.00 0.90 0.02 0.08
#> TCGA.UC.A7PG.06 2 0.3351 0.8863 0.00 0.80 0.00 0.00 0.04 0.16
#> TCGA.VS.A9UJ.01 2 0.1814 0.8422 0.00 0.90 0.00 0.00 0.00 0.10
#> TCGA.Q1.A73O.01 3 0.3460 0.5956 0.00 0.00 0.76 0.02 0.00 0.22
#> TCGA.EA.A439.01 1 0.0937 0.5797 0.96 0.00 0.00 0.00 0.00 0.04
#> TCGA.VS.A9UM.01 2 0.3351 0.8863 0.00 0.80 0.00 0.00 0.04 0.16
#> TCGA.C5.A1MP.01 3 0.2094 0.7903 0.00 0.00 0.90 0.00 0.08 0.02
#> TCGA.ZJ.AB0H.01 3 0.2094 0.7903 0.00 0.00 0.90 0.00 0.08 0.02
#> TCGA.VS.A9V4.01 4 0.5083 0.4722 0.00 0.00 0.10 0.58 0.00 0.32
#> TCGA.VS.A9UA.01 3 0.1092 0.8250 0.00 0.00 0.96 0.02 0.00 0.02
#> TCGA.LP.A4AW.01 3 0.2094 0.7903 0.00 0.00 0.90 0.00 0.08 0.02
#> TCGA.C5.A1BN.01 5 0.3351 0.6801 0.00 0.04 0.00 0.00 0.80 0.16
#> TCGA.VS.AA62.01 1 0.3756 0.4115 0.60 0.00 0.00 0.00 0.00 0.40
#> TCGA.C5.A1BM.01 3 0.0000 0.8400 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.C5.A1M6.01 1 0.4310 0.2966 0.54 0.00 0.00 0.00 0.02 0.44
#> TCGA.C5.A1BE.01 3 0.3679 0.6307 0.00 0.00 0.76 0.00 0.20 0.04
#> TCGA.C5.A1BJ.01 3 0.5110 -0.3447 0.08 0.00 0.48 0.00 0.00 0.44
#> TCGA.FU.A23L.01 4 0.2094 0.8460 0.00 0.00 0.08 0.90 0.00 0.02
#> TCGA.C5.A1BF.01 1 0.0000 0.6000 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.C5.A1BI.01 3 0.0937 0.8242 0.00 0.00 0.96 0.00 0.00 0.04
cbind(get_classes(res, k = 7), get_membership(res, k = 7))
#> class entropy silhouette p1 p2 p3 p4 p5 p6 p7
#> TCGA.EK.A3GK.01 4 0.4305 0.7111 0.00 0.00 0.00 0.66 0.04 0.02 0.28
#> TCGA.VS.A94Y.01 4 0.1505 0.7611 0.02 0.00 0.02 0.94 0.00 0.02 0.00
#> TCGA.MY.A5BF.11 6 0.3413 0.9477 0.38 0.00 0.00 0.00 0.00 0.62 0.00
#> TCGA.VS.A94Z.01 3 0.0863 0.8688 0.00 0.00 0.96 0.00 0.04 0.00 0.00
#> TCGA.EA.A4BA.01 4 0.4902 0.6948 0.00 0.00 0.00 0.54 0.00 0.12 0.34
#> TCGA.FU.A3EO.11 6 0.3413 0.9477 0.38 0.00 0.00 0.00 0.00 0.62 0.00
#> TCGA.DG.A2KJ.01 6 0.3909 0.9157 0.40 0.00 0.00 0.00 0.00 0.58 0.02
#> TCGA.EK.A2R7.01 3 0.3745 0.6182 0.00 0.00 0.70 0.00 0.26 0.04 0.00
#> TCGA.C5.A905.01 2 0.0000 0.8827 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.EK.A2RN.01 5 0.0863 0.7903 0.00 0.00 0.04 0.00 0.96 0.00 0.00
#> TCGA.FU.A57G.01 4 0.5007 0.6904 0.00 0.00 0.00 0.56 0.00 0.16 0.28
#> TCGA.C5.A8YR.01 4 0.5132 0.6075 0.00 0.00 0.00 0.46 0.08 0.02 0.44
#> TCGA.MY.A5BE.01 6 0.3413 0.9477 0.38 0.00 0.00 0.00 0.00 0.62 0.00
#> TCGA.VS.A8QH.01 1 0.3404 0.6323 0.82 0.00 0.06 0.00 0.00 0.08 0.04
#> TCGA.ZJ.A8QR.01 2 0.5606 -0.0338 0.00 0.38 0.00 0.00 0.34 0.00 0.28
#> TCGA.C5.A907.01 1 0.1006 0.7297 0.96 0.00 0.00 0.00 0.00 0.02 0.02
#> TCGA.C5.A8ZZ.01 5 0.3908 0.6825 0.00 0.08 0.00 0.00 0.72 0.00 0.20
#> TCGA.C5.A7UC.01 1 0.4386 0.1637 0.54 0.00 0.42 0.00 0.00 0.02 0.02
#> TCGA.C5.A8XJ.01 3 0.0504 0.8620 0.00 0.00 0.98 0.00 0.00 0.00 0.02
#> TCGA.EK.A3GM.01 6 0.3413 0.9477 0.38 0.00 0.00 0.00 0.00 0.62 0.00
#> TCGA.VS.A8Q8.01 5 0.2745 0.7243 0.00 0.00 0.16 0.00 0.82 0.02 0.00
#> TCGA.2W.A8YY.01 2 0.1664 0.8790 0.00 0.92 0.00 0.00 0.00 0.06 0.02
#> TCGA.MU.A51Y.01 1 0.2278 0.6723 0.88 0.00 0.00 0.00 0.00 0.08 0.04
#> TCGA.EK.A2RK.01 5 0.0863 0.7903 0.00 0.00 0.04 0.00 0.96 0.00 0.00
#> TCGA.UC.A7PD.01 1 0.2016 0.6960 0.90 0.00 0.00 0.00 0.00 0.06 0.04
#> TCGA.VS.A8QM.01 3 0.3994 0.0278 0.48 0.00 0.50 0.00 0.00 0.02 0.00
#> TCGA.EA.A3HU.01 1 0.1718 0.7104 0.92 0.00 0.00 0.00 0.00 0.04 0.04
#> TCGA.VS.A94X.01 4 0.1505 0.7611 0.02 0.00 0.02 0.94 0.00 0.02 0.00
#> TCGA.C5.A3HF.01 6 0.3413 0.9477 0.38 0.00 0.00 0.00 0.00 0.62 0.00
#> TCGA.MY.A913.01 1 0.1006 0.7297 0.96 0.00 0.00 0.00 0.00 0.02 0.02
#> TCGA.EA.A97N.01 5 0.3086 0.7471 0.00 0.00 0.04 0.00 0.80 0.00 0.16
#> TCGA.EK.A2RD.01 5 0.1166 0.7909 0.00 0.00 0.06 0.00 0.94 0.00 0.00
#> TCGA.C5.A8YT.01 6 0.3413 0.9477 0.38 0.00 0.00 0.00 0.00 0.62 0.00
#> TCGA.FU.A3HZ.01 2 0.1664 0.8790 0.00 0.92 0.00 0.00 0.00 0.06 0.02
#> TCGA.VS.A8EJ.01 6 0.4070 0.8346 0.34 0.00 0.00 0.00 0.00 0.62 0.04
#> TCGA.C5.A3HL.01 3 0.0504 0.8712 0.00 0.00 0.98 0.00 0.02 0.00 0.00
#> TCGA.C5.A8XK.01 5 0.4675 0.5495 0.00 0.00 0.02 0.04 0.66 0.02 0.26
#> TCGA.EX.A8YF.01 1 0.2572 0.4434 0.80 0.00 0.00 0.00 0.00 0.20 0.00
#> TCGA.HM.A4S6.01 5 0.1166 0.7909 0.00 0.00 0.06 0.00 0.94 0.00 0.00
#> TCGA.MA.AA3Y.01 1 0.0504 0.7318 0.98 0.00 0.00 0.00 0.00 0.02 0.00
#> TCGA.MA.AA3Z.01 5 0.4003 0.4536 0.00 0.00 0.32 0.00 0.64 0.04 0.00
#> TCGA.EK.A2RE.01 5 0.2509 0.7815 0.00 0.00 0.04 0.00 0.88 0.02 0.06
#> TCGA.C5.A1BQ.01 3 0.1363 0.8657 0.00 0.00 0.94 0.00 0.04 0.02 0.00
#> TCGA.EA.A556.01 4 0.4902 0.6948 0.00 0.00 0.00 0.54 0.00 0.12 0.34
#> TCGA.EA.A44S.01 5 0.3667 0.6970 0.00 0.06 0.00 0.00 0.74 0.00 0.20
#> TCGA.4J.AA1J.01 2 0.3052 0.7517 0.00 0.78 0.00 0.00 0.02 0.00 0.20
#> TCGA.C5.A7X3.01 4 0.2654 0.7316 0.02 0.00 0.10 0.86 0.00 0.02 0.00
#> TCGA.HG.A2PA.01 1 0.1363 0.7238 0.94 0.00 0.00 0.00 0.00 0.02 0.04
#> TCGA.C5.A7XC.01 5 0.2163 0.7661 0.00 0.00 0.10 0.00 0.88 0.02 0.00
#> TCGA.C5.A7UH.01 2 0.0000 0.8827 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.EA.A3HR.01 5 0.3745 0.5752 0.00 0.00 0.26 0.00 0.70 0.04 0.00
#> TCGA.DG.A2KL.01 5 0.1664 0.7869 0.00 0.00 0.06 0.00 0.92 0.02 0.00
#> TCGA.BI.A0VR.01 3 0.0000 0.8696 0.00 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.DS.A0VL.01 3 0.3745 0.6182 0.00 0.00 0.70 0.00 0.26 0.04 0.00
#> TCGA.DR.A0ZM.01 5 0.2745 0.6889 0.00 0.00 0.00 0.00 0.82 0.02 0.16
#> TCGA.DS.A0VK.01 3 0.3519 0.6766 0.00 0.00 0.74 0.00 0.22 0.04 0.00
#> TCGA.JW.A5VJ.01 3 0.3307 0.6028 0.00 0.00 0.74 0.24 0.00 0.02 0.00
#> TCGA.FU.A5XV.01 5 0.4309 0.6539 0.00 0.12 0.00 0.00 0.68 0.00 0.20
#> TCGA.HM.A3JJ.01 3 0.0000 0.8696 0.00 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.EK.A2RJ.01 4 0.4622 0.6777 0.00 0.00 0.00 0.56 0.04 0.02 0.38
#> TCGA.EA.A3HT.01 3 0.1166 0.8637 0.00 0.00 0.94 0.00 0.06 0.00 0.00
#> TCGA.FU.A3TX.01 6 0.3867 0.9353 0.38 0.00 0.00 0.00 0.00 0.60 0.02
#> TCGA.EK.A2PI.01 4 0.0863 0.7634 0.00 0.00 0.04 0.96 0.00 0.00 0.00
#> TCGA.Q1.A73S.01 2 0.0504 0.8814 0.00 0.98 0.00 0.00 0.00 0.02 0.00
#> TCGA.HM.A6W2.01 2 0.4121 0.7550 0.00 0.70 0.00 0.00 0.00 0.10 0.20
#> TCGA.VS.A8EH.01 1 0.1363 0.7317 0.94 0.00 0.00 0.00 0.00 0.02 0.04
#> TCGA.JW.A5VH.01 2 0.1664 0.8790 0.00 0.92 0.00 0.00 0.00 0.06 0.02
#> TCGA.VS.A8EB.01 1 0.4266 -0.6219 0.52 0.00 0.00 0.00 0.00 0.44 0.04
#> TCGA.RA.A741.01 1 0.3984 0.4609 0.68 0.00 0.28 0.00 0.00 0.02 0.02
#> TCGA.DG.A2KH.01 6 0.3755 0.8932 0.34 0.00 0.00 0.00 0.00 0.64 0.02
#> TCGA.C5.A2LT.01 1 0.0504 0.7329 0.98 0.00 0.00 0.00 0.00 0.00 0.02
#> TCGA.EA.A5ZD.01 3 0.0504 0.8660 0.00 0.00 0.98 0.00 0.00 0.02 0.00
#> TCGA.EK.A2RM.01 6 0.4514 0.5705 0.46 0.00 0.00 0.00 0.00 0.48 0.06
#> TCGA.C5.A7UI.01 5 0.1166 0.7909 0.00 0.00 0.06 0.00 0.94 0.00 0.00
#> TCGA.EK.A2PL.01 5 0.1664 0.7869 0.00 0.00 0.06 0.00 0.92 0.02 0.00
#> TCGA.EK.A2PM.01 5 0.4264 0.6049 0.00 0.06 0.00 0.00 0.62 0.00 0.32
#> TCGA.EK.A2GZ.01 1 0.2278 0.6723 0.88 0.00 0.00 0.00 0.00 0.08 0.04
#> TCGA.HM.A3JK.01 6 0.4214 0.8896 0.40 0.00 0.00 0.00 0.00 0.56 0.04
#> TCGA.HM.A6W2.06 2 0.1664 0.8790 0.00 0.92 0.00 0.00 0.00 0.06 0.02
#> TCGA.IR.A3LA.01 2 0.1664 0.8790 0.00 0.92 0.00 0.00 0.00 0.06 0.02
#> TCGA.EK.A2PK.01 4 0.2422 0.7558 0.00 0.00 0.00 0.82 0.00 0.00 0.18
#> TCGA.EA.A5ZF.01 4 0.5574 0.6659 0.00 0.00 0.00 0.44 0.04 0.10 0.42
#> TCGA.BI.A0VS.01 5 0.4828 0.4087 0.00 0.00 0.00 0.06 0.56 0.02 0.36
#> TCGA.JX.A5QV.01 3 0.4175 0.3522 0.00 0.00 0.58 0.00 0.38 0.04 0.00
#> TCGA.EK.A2R8.01 3 0.1860 0.8271 0.00 0.00 0.92 0.04 0.00 0.02 0.02
#> TCGA.EA.A1QS.01 6 0.3413 0.9477 0.38 0.00 0.00 0.00 0.00 0.62 0.00
#> TCGA.JX.A3PZ.01 4 0.1006 0.7611 0.02 0.00 0.00 0.96 0.00 0.02 0.00
#> TCGA.HM.A3JJ.11 6 0.3413 0.9477 0.38 0.00 0.00 0.00 0.00 0.62 0.00
#> TCGA.DS.A5RQ.01 5 0.1664 0.7869 0.00 0.00 0.06 0.00 0.92 0.02 0.00
#> TCGA.C5.A2LY.01 1 0.2278 0.6723 0.88 0.00 0.00 0.00 0.00 0.08 0.04
#> TCGA.EK.A2H1.01 6 0.3413 0.9477 0.38 0.00 0.00 0.00 0.00 0.62 0.00
#> TCGA.EX.A69L.01 3 0.0504 0.8660 0.00 0.00 0.98 0.00 0.00 0.02 0.00
#> TCGA.FU.A2QG.01 5 0.3667 0.6970 0.00 0.06 0.00 0.00 0.74 0.00 0.20
#> TCGA.JW.A5VG.01 1 0.1006 0.7297 0.96 0.00 0.00 0.00 0.00 0.02 0.02
#> TCGA.PN.A8MA.01 2 0.3487 0.8199 0.00 0.78 0.00 0.00 0.00 0.10 0.12
#> TCGA.DG.A2KM.01 1 0.0504 0.7321 0.98 0.00 0.00 0.00 0.00 0.02 0.00
#> TCGA.EX.A3L1.01 6 0.3413 0.9477 0.38 0.00 0.00 0.00 0.00 0.62 0.00
#> TCGA.Q1.A5R3.01 5 0.4070 0.4059 0.00 0.00 0.34 0.00 0.62 0.04 0.00
#> TCGA.C5.A7CM.01 1 0.3370 0.5611 0.78 0.00 0.00 0.00 0.00 0.16 0.06
#> TCGA.JX.A3Q0.01 2 0.0000 0.8827 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.C5.A7CL.01 3 0.1664 0.8653 0.00 0.00 0.92 0.00 0.06 0.02 0.00
#> TCGA.VS.A959.01 1 0.2016 0.6896 0.90 0.00 0.00 0.00 0.00 0.06 0.04
#> TCGA.LP.A4AX.01 6 0.3413 0.9477 0.38 0.00 0.00 0.00 0.00 0.62 0.00
#> TCGA.ZJ.AAXN.01 4 0.5102 0.6252 0.10 0.00 0.16 0.68 0.00 0.04 0.02
#> TCGA.MA.AA3X.01 2 0.0000 0.8827 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.UC.A7PG.01 5 0.2016 0.7797 0.00 0.00 0.04 0.00 0.90 0.00 0.06
#> TCGA.DS.A1OD.01 3 0.0000 0.8696 0.00 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.C5.A1M7.01 3 0.0504 0.8660 0.00 0.00 0.98 0.00 0.00 0.02 0.00
#> TCGA.VS.A9UH.01 1 0.1006 0.7297 0.96 0.00 0.00 0.00 0.00 0.02 0.02
#> TCGA.ZJ.AAXD.01 3 0.0000 0.8696 0.00 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.VS.A9UB.01 1 0.1363 0.7197 0.94 0.00 0.00 0.00 0.00 0.04 0.02
#> TCGA.EA.A410.01 2 0.1664 0.8790 0.00 0.92 0.00 0.00 0.00 0.06 0.02
#> TCGA.ZJ.AB0I.01 2 0.0000 0.8827 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.VS.A9U6.01 1 0.2278 0.6723 0.88 0.00 0.00 0.00 0.00 0.08 0.04
#> TCGA.C5.A0TN.01 1 0.1006 0.7297 0.96 0.00 0.00 0.00 0.00 0.02 0.02
#> TCGA.ZJ.AAXB.01 2 0.1664 0.8790 0.00 0.92 0.00 0.00 0.00 0.06 0.02
#> TCGA.DS.A1OB.01 5 0.5007 0.5417 0.00 0.16 0.00 0.00 0.56 0.00 0.28
#> TCGA.HG.A9SC.01 2 0.2422 0.7873 0.00 0.82 0.00 0.00 0.00 0.00 0.18
#> TCGA.ZJ.AAXT.01 3 0.1166 0.8637 0.00 0.00 0.94 0.00 0.06 0.00 0.00
#> TCGA.C5.A1ML.01 3 0.2016 0.7976 0.06 0.00 0.90 0.00 0.00 0.00 0.04
#> TCGA.LP.A4AU.01 1 0.0504 0.7318 0.98 0.00 0.00 0.00 0.00 0.02 0.00
#> TCGA.ZJ.AAXU.01 3 0.0504 0.8712 0.00 0.00 0.98 0.00 0.02 0.00 0.00
#> TCGA.C5.A1MK.01 5 0.1166 0.7909 0.00 0.00 0.06 0.00 0.94 0.00 0.00
#> TCGA.VS.A958.01 3 0.0504 0.8660 0.00 0.00 0.98 0.00 0.00 0.02 0.00
#> TCGA.R2.A69V.01 1 0.0504 0.7321 0.98 0.00 0.00 0.00 0.00 0.02 0.00
#> TCGA.EA.A411.01 2 0.3780 0.7297 0.00 0.72 0.00 0.00 0.02 0.02 0.24
#> TCGA.VS.A9UP.01 1 0.4487 0.0421 0.60 0.00 0.00 0.00 0.00 0.32 0.08
#> TCGA.C5.A1MI.01 1 0.3263 0.6449 0.80 0.00 0.00 0.00 0.00 0.12 0.08
#> TCGA.ZJ.AAX8.01 1 0.0504 0.7318 0.98 0.00 0.00 0.00 0.00 0.02 0.00
#> TCGA.VS.A9UT.01 1 0.3968 -0.6190 0.54 0.00 0.00 0.00 0.00 0.44 0.02
#> TCGA.VS.A9V0.01 4 0.4535 0.7149 0.00 0.00 0.00 0.64 0.00 0.12 0.24
#> TCGA.ZJ.AAXA.01 2 0.0000 0.8827 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.LP.A4AV.01 5 0.3709 0.6736 0.00 0.00 0.02 0.02 0.78 0.02 0.16
#> TCGA.ZJ.AAXF.01 1 0.3994 -0.0398 0.50 0.00 0.48 0.00 0.00 0.02 0.00
#> TCGA.EA.A3Y4.01 4 0.4388 0.7015 0.00 0.00 0.00 0.64 0.04 0.02 0.30
#> TCGA.UC.A7PG.06 2 0.2081 0.8108 0.00 0.86 0.00 0.00 0.00 0.00 0.14
#> TCGA.VS.A9UJ.01 2 0.3985 0.7735 0.00 0.72 0.00 0.00 0.00 0.10 0.18
#> TCGA.Q1.A73O.01 3 0.2569 0.7257 0.14 0.00 0.84 0.00 0.00 0.02 0.00
#> TCGA.EA.A439.01 6 0.4127 0.8739 0.36 0.00 0.00 0.00 0.00 0.60 0.04
#> TCGA.VS.A9UM.01 2 0.0000 0.8827 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.C5.A1MP.01 3 0.1433 0.8536 0.00 0.00 0.92 0.00 0.08 0.00 0.00
#> TCGA.ZJ.AB0H.01 3 0.1671 0.8395 0.00 0.00 0.90 0.00 0.10 0.00 0.00
#> TCGA.VS.A9V4.01 4 0.6500 0.2295 0.38 0.00 0.08 0.42 0.00 0.08 0.04
#> TCGA.VS.A9UA.01 3 0.0504 0.8660 0.00 0.00 0.98 0.00 0.00 0.02 0.00
#> TCGA.LP.A4AW.01 3 0.1166 0.8637 0.00 0.00 0.94 0.00 0.06 0.00 0.00
#> TCGA.C5.A1BN.01 5 0.3908 0.6825 0.00 0.08 0.00 0.00 0.72 0.00 0.20
#> TCGA.VS.AA62.01 1 0.0504 0.7329 0.98 0.00 0.00 0.00 0.00 0.00 0.02
#> TCGA.C5.A1BM.01 3 0.1166 0.8637 0.00 0.00 0.94 0.00 0.06 0.00 0.00
#> TCGA.C5.A1M6.01 1 0.3965 0.6228 0.76 0.00 0.02 0.00 0.00 0.12 0.10
#> TCGA.C5.A1BE.01 3 0.3745 0.6182 0.00 0.00 0.70 0.00 0.26 0.04 0.00
#> TCGA.C5.A1BJ.01 1 0.4356 0.2148 0.56 0.00 0.40 0.00 0.00 0.02 0.02
#> TCGA.FU.A23L.01 4 0.0863 0.7634 0.00 0.00 0.04 0.96 0.00 0.00 0.00
#> TCGA.C5.A1BF.01 6 0.3867 0.9353 0.38 0.00 0.00 0.00 0.00 0.60 0.02
#> TCGA.C5.A1BI.01 3 0.0504 0.8660 0.00 0.00 0.98 0.00 0.00 0.02 0.00
cbind(get_classes(res, k = 8), get_membership(res, k = 8))
#> class entropy silhouette p1 p2 p3 p4 p5 p6 p7 p8
#> TCGA.EK.A3GK.01 4 0.4770 0.20247 0.00 0.00 0.04 0.52 0.02 0.02 0.40 0.00
#> TCGA.VS.A94Y.01 4 0.1091 0.36418 0.00 0.00 0.06 0.94 0.00 0.00 0.00 0.00
#> TCGA.MY.A5BF.11 6 0.3272 0.94811 0.42 0.00 0.00 0.00 0.00 0.58 0.00 0.00
#> TCGA.VS.A94Z.01 3 0.1275 0.75318 0.00 0.00 0.94 0.00 0.04 0.02 0.00 0.00
#> TCGA.EA.A4BA.01 8 0.4224 0.87591 0.00 0.00 0.00 0.46 0.00 0.00 0.06 0.48
#> TCGA.FU.A3EO.11 6 0.3272 0.94811 0.42 0.00 0.00 0.00 0.00 0.58 0.00 0.00
#> TCGA.DG.A2KJ.01 1 0.4619 -0.70241 0.48 0.00 0.00 0.00 0.02 0.44 0.00 0.06
#> TCGA.EK.A2R7.01 3 0.5449 0.37125 0.00 0.00 0.52 0.00 0.34 0.04 0.06 0.04
#> TCGA.C5.A905.01 2 0.2725 0.80521 0.00 0.82 0.00 0.00 0.00 0.04 0.00 0.14
#> TCGA.EK.A2RN.01 5 0.1275 0.57795 0.00 0.00 0.04 0.00 0.94 0.00 0.02 0.00
#> TCGA.FU.A57G.01 8 0.3318 0.75547 0.00 0.00 0.00 0.46 0.00 0.00 0.00 0.54
#> TCGA.C5.A8YR.01 7 0.4717 -0.25784 0.00 0.00 0.00 0.36 0.02 0.08 0.54 0.00
#> TCGA.MY.A5BE.01 6 0.3272 0.94811 0.42 0.00 0.00 0.00 0.00 0.58 0.00 0.00
#> TCGA.VS.A8QH.01 1 0.4627 0.49220 0.70 0.00 0.14 0.02 0.00 0.04 0.00 0.10
#> TCGA.ZJ.A8QR.01 7 0.6086 0.01281 0.00 0.22 0.00 0.00 0.30 0.02 0.42 0.04
#> TCGA.C5.A907.01 1 0.1741 0.65708 0.92 0.00 0.00 0.02 0.00 0.02 0.00 0.04
#> TCGA.C5.A8ZZ.01 5 0.4607 0.13896 0.00 0.04 0.00 0.00 0.54 0.00 0.38 0.04
#> TCGA.C5.A7UC.01 3 0.6285 0.07457 0.36 0.00 0.44 0.02 0.00 0.04 0.08 0.06
#> TCGA.C5.A8XJ.01 3 0.2624 0.72149 0.00 0.00 0.86 0.00 0.00 0.06 0.02 0.06
#> TCGA.EK.A3GM.01 6 0.3272 0.94811 0.42 0.00 0.00 0.00 0.00 0.58 0.00 0.00
#> TCGA.VS.A8Q8.01 5 0.3868 0.50136 0.00 0.00 0.22 0.00 0.72 0.02 0.02 0.02
#> TCGA.2W.A8YY.01 2 0.0000 0.80808 0.00 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.MU.A51Y.01 1 0.3369 0.61582 0.82 0.00 0.00 0.00 0.02 0.04 0.08 0.04
#> TCGA.EK.A2RK.01 5 0.1275 0.58229 0.00 0.00 0.04 0.00 0.94 0.00 0.00 0.02
#> TCGA.UC.A7PD.01 1 0.2407 0.58997 0.86 0.00 0.00 0.00 0.00 0.08 0.00 0.06
#> TCGA.VS.A8QM.01 3 0.4458 0.25917 0.38 0.00 0.56 0.02 0.00 0.02 0.00 0.02
#> TCGA.EA.A3HU.01 1 0.3369 0.61582 0.82 0.00 0.00 0.00 0.02 0.04 0.08 0.04
#> TCGA.VS.A94X.01 4 0.1091 0.36418 0.00 0.00 0.06 0.94 0.00 0.00 0.00 0.00
#> TCGA.C5.A3HF.01 6 0.3272 0.94811 0.42 0.00 0.00 0.00 0.00 0.58 0.00 0.00
#> TCGA.MY.A913.01 1 0.1741 0.65708 0.92 0.00 0.00 0.02 0.00 0.02 0.00 0.04
#> TCGA.EA.A97N.01 5 0.3504 0.40660 0.00 0.00 0.04 0.00 0.70 0.00 0.26 0.00
#> TCGA.EK.A2RD.01 5 0.1341 0.59091 0.00 0.00 0.08 0.00 0.92 0.00 0.00 0.00
#> TCGA.C5.A8YT.01 6 0.3272 0.94811 0.42 0.00 0.00 0.00 0.00 0.58 0.00 0.00
#> TCGA.FU.A3HZ.01 2 0.0000 0.80808 0.00 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.VS.A8EJ.01 1 0.6011 -0.48036 0.40 0.00 0.00 0.00 0.04 0.36 0.02 0.18
#> TCGA.C5.A3HL.01 3 0.2858 0.74294 0.00 0.00 0.86 0.00 0.04 0.04 0.04 0.02
#> TCGA.C5.A8XK.01 5 0.5646 -0.03432 0.00 0.00 0.04 0.06 0.48 0.02 0.38 0.02
#> TCGA.EX.A8YF.01 1 0.2224 0.52939 0.86 0.00 0.00 0.00 0.00 0.12 0.00 0.02
#> TCGA.HM.A4S6.01 5 0.1341 0.59091 0.00 0.00 0.08 0.00 0.92 0.00 0.00 0.00
#> TCGA.MA.AA3Y.01 1 0.1275 0.66511 0.94 0.00 0.00 0.00 0.00 0.00 0.02 0.04
#> TCGA.MA.AA3Z.01 5 0.5123 0.40778 0.00 0.00 0.24 0.00 0.62 0.04 0.06 0.04
#> TCGA.EK.A2RE.01 5 0.2725 0.51197 0.00 0.00 0.04 0.00 0.82 0.00 0.14 0.00
#> TCGA.C5.A1BQ.01 3 0.3402 0.72929 0.00 0.00 0.82 0.00 0.06 0.04 0.06 0.02
#> TCGA.EA.A556.01 8 0.4224 0.87591 0.00 0.00 0.00 0.46 0.00 0.00 0.06 0.48
#> TCGA.EA.A44S.01 5 0.3862 0.21794 0.00 0.04 0.00 0.00 0.60 0.00 0.36 0.00
#> TCGA.4J.AA1J.01 2 0.5026 0.38166 0.00 0.50 0.00 0.00 0.04 0.00 0.38 0.08
#> TCGA.C5.A7X3.01 4 0.2569 0.34600 0.00 0.00 0.16 0.82 0.00 0.00 0.00 0.02
#> TCGA.HG.A2PA.01 1 0.1804 0.65024 0.90 0.00 0.00 0.00 0.00 0.00 0.08 0.02
#> TCGA.C5.A7XC.01 5 0.3748 0.51588 0.00 0.00 0.20 0.00 0.74 0.02 0.02 0.02
#> TCGA.C5.A7UH.01 2 0.2725 0.80521 0.00 0.82 0.00 0.00 0.00 0.04 0.00 0.14
#> TCGA.EA.A3HR.01 5 0.5026 0.43505 0.00 0.00 0.22 0.00 0.64 0.04 0.06 0.04
#> TCGA.DG.A2KL.01 5 0.1804 0.58989 0.00 0.00 0.08 0.00 0.90 0.00 0.00 0.02
#> TCGA.BI.A0VR.01 3 0.0000 0.74700 0.00 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.DS.A0VL.01 3 0.5404 0.41322 0.00 0.00 0.54 0.00 0.32 0.04 0.06 0.04
#> TCGA.DR.A0ZM.01 5 0.4375 0.29011 0.00 0.00 0.04 0.02 0.66 0.02 0.26 0.00
#> TCGA.DS.A0VK.01 3 0.5404 0.41322 0.00 0.00 0.54 0.00 0.32 0.04 0.06 0.04
#> TCGA.JW.A5VJ.01 3 0.3618 0.22632 0.00 0.00 0.60 0.38 0.00 0.00 0.00 0.02
#> TCGA.FU.A5XV.01 5 0.4607 0.13896 0.00 0.04 0.00 0.00 0.54 0.00 0.38 0.04
#> TCGA.HM.A3JJ.01 3 0.0471 0.75061 0.00 0.00 0.98 0.00 0.00 0.00 0.02 0.00
#> TCGA.EK.A2RJ.01 4 0.3943 0.16804 0.00 0.00 0.00 0.56 0.00 0.04 0.40 0.00
#> TCGA.EA.A3HT.01 3 0.4202 0.66854 0.00 0.00 0.74 0.00 0.14 0.04 0.06 0.02
#> TCGA.FU.A3TX.01 6 0.4077 0.88533 0.40 0.00 0.00 0.00 0.00 0.56 0.02 0.02
#> TCGA.EK.A2PI.01 4 0.1341 0.36068 0.00 0.00 0.08 0.92 0.00 0.00 0.00 0.00
#> TCGA.Q1.A73S.01 2 0.1275 0.80890 0.00 0.94 0.00 0.00 0.00 0.02 0.00 0.04
#> TCGA.HM.A6W2.01 2 0.4893 0.56098 0.00 0.64 0.00 0.00 0.00 0.18 0.12 0.06
#> TCGA.VS.A8EH.01 1 0.3771 0.63856 0.80 0.00 0.00 0.02 0.02 0.02 0.08 0.06
#> TCGA.JW.A5VH.01 2 0.0000 0.80808 0.00 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.VS.A8EB.01 1 0.5740 -0.36756 0.50 0.00 0.00 0.00 0.02 0.32 0.08 0.08
#> TCGA.RA.A741.01 1 0.5500 0.21910 0.52 0.00 0.34 0.02 0.00 0.02 0.08 0.02
#> TCGA.DG.A2KH.01 6 0.4556 0.81408 0.38 0.00 0.00 0.00 0.02 0.54 0.00 0.06
#> TCGA.C5.A2LT.01 1 0.1741 0.65708 0.92 0.00 0.00 0.02 0.00 0.02 0.00 0.04
#> TCGA.EA.A5ZD.01 3 0.0471 0.74331 0.00 0.00 0.98 0.00 0.00 0.00 0.00 0.02
#> TCGA.EK.A2RM.01 1 0.5837 -0.29594 0.48 0.00 0.00 0.00 0.04 0.30 0.02 0.16
#> TCGA.C5.A7UI.01 5 0.1341 0.59091 0.00 0.00 0.08 0.00 0.92 0.00 0.00 0.00
#> TCGA.EK.A2PL.01 5 0.1804 0.58989 0.00 0.00 0.08 0.00 0.90 0.00 0.00 0.02
#> TCGA.EK.A2PM.01 5 0.5065 -0.10656 0.00 0.04 0.00 0.00 0.44 0.08 0.44 0.00
#> TCGA.EK.A2GZ.01 1 0.3369 0.61582 0.82 0.00 0.00 0.00 0.02 0.04 0.08 0.04
#> TCGA.HM.A3JK.01 6 0.5048 0.77282 0.40 0.00 0.00 0.00 0.00 0.48 0.08 0.04
#> TCGA.HM.A6W2.06 2 0.0000 0.80808 0.00 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.IR.A3LA.01 2 0.0000 0.80808 0.00 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.EK.A2PK.01 4 0.2856 0.24741 0.00 0.00 0.00 0.78 0.00 0.02 0.20 0.00
#> TCGA.EA.A5ZF.01 4 0.5246 -0.52141 0.00 0.00 0.00 0.38 0.00 0.00 0.28 0.34
#> TCGA.BI.A0VS.01 7 0.5366 0.07378 0.00 0.00 0.02 0.04 0.34 0.08 0.52 0.00
#> TCGA.JX.A5QV.01 3 0.5530 0.23422 0.00 0.00 0.46 0.00 0.40 0.04 0.06 0.04
#> TCGA.EK.A2R8.01 3 0.2204 0.68970 0.02 0.00 0.90 0.04 0.00 0.02 0.00 0.02
#> TCGA.EA.A1QS.01 6 0.3272 0.94811 0.42 0.00 0.00 0.00 0.00 0.58 0.00 0.00
#> TCGA.JX.A3PZ.01 4 0.0000 0.30600 0.00 0.00 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.HM.A3JJ.11 6 0.3272 0.94811 0.42 0.00 0.00 0.00 0.00 0.58 0.00 0.00
#> TCGA.DS.A5RQ.01 5 0.3131 0.56552 0.00 0.00 0.06 0.00 0.84 0.02 0.04 0.04
#> TCGA.C5.A2LY.01 1 0.3637 0.61540 0.80 0.00 0.00 0.00 0.02 0.04 0.08 0.06
#> TCGA.EK.A2H1.01 6 0.3272 0.94811 0.42 0.00 0.00 0.00 0.00 0.58 0.00 0.00
#> TCGA.EX.A69L.01 3 0.0471 0.74331 0.00 0.00 0.98 0.00 0.00 0.00 0.00 0.02
#> TCGA.FU.A2QG.01 5 0.4607 0.13896 0.00 0.04 0.00 0.00 0.54 0.00 0.38 0.04
#> TCGA.JW.A5VG.01 1 0.1741 0.65708 0.92 0.00 0.00 0.02 0.00 0.02 0.00 0.04
#> TCGA.PN.A8MA.01 2 0.4646 0.58277 0.00 0.66 0.00 0.00 0.00 0.18 0.12 0.04
#> TCGA.DG.A2KM.01 1 0.1408 0.66067 0.94 0.00 0.00 0.02 0.00 0.02 0.00 0.02
#> TCGA.EX.A3L1.01 6 0.3272 0.94811 0.42 0.00 0.00 0.00 0.00 0.58 0.00 0.00
#> TCGA.Q1.A5R3.01 5 0.5123 0.40778 0.00 0.00 0.24 0.00 0.62 0.04 0.06 0.04
#> TCGA.C5.A7CM.01 1 0.3397 0.57526 0.80 0.00 0.00 0.00 0.04 0.10 0.00 0.06
#> TCGA.JX.A3Q0.01 2 0.2725 0.80521 0.00 0.82 0.00 0.00 0.00 0.04 0.00 0.14
#> TCGA.C5.A7CL.01 3 0.2265 0.74425 0.00 0.00 0.88 0.00 0.08 0.02 0.00 0.02
#> TCGA.VS.A959.01 1 0.3319 0.63450 0.82 0.00 0.00 0.02 0.02 0.06 0.00 0.08
#> TCGA.LP.A4AX.01 6 0.3272 0.94811 0.42 0.00 0.00 0.00 0.00 0.58 0.00 0.00
#> TCGA.ZJ.AAXN.01 4 0.3873 0.28851 0.06 0.00 0.20 0.72 0.00 0.00 0.00 0.02
#> TCGA.MA.AA3X.01 2 0.2725 0.80521 0.00 0.82 0.00 0.00 0.00 0.04 0.00 0.14
#> TCGA.UC.A7PG.01 5 0.2547 0.52787 0.00 0.00 0.04 0.00 0.84 0.00 0.12 0.00
#> TCGA.DS.A1OD.01 3 0.0471 0.75009 0.00 0.00 0.98 0.00 0.00 0.02 0.00 0.00
#> TCGA.C5.A1M7.01 3 0.0471 0.74331 0.00 0.00 0.98 0.00 0.00 0.00 0.00 0.02
#> TCGA.VS.A9UH.01 1 0.1275 0.64955 0.94 0.00 0.00 0.00 0.00 0.02 0.00 0.04
#> TCGA.ZJ.AAXD.01 3 0.1741 0.74720 0.00 0.00 0.92 0.00 0.02 0.02 0.04 0.00
#> TCGA.VS.A9UB.01 1 0.2020 0.65503 0.90 0.00 0.00 0.02 0.00 0.02 0.00 0.06
#> TCGA.EA.A410.01 2 0.0000 0.80808 0.00 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.ZJ.AB0I.01 2 0.2725 0.80521 0.00 0.82 0.00 0.00 0.00 0.04 0.00 0.14
#> TCGA.VS.A9U6.01 1 0.3369 0.61582 0.82 0.00 0.00 0.00 0.02 0.04 0.08 0.04
#> TCGA.C5.A0TN.01 1 0.2020 0.65503 0.90 0.00 0.00 0.02 0.00 0.02 0.00 0.06
#> TCGA.ZJ.AAXB.01 2 0.0000 0.80808 0.00 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.DS.A1OB.01 5 0.5976 -0.15999 0.00 0.10 0.00 0.00 0.42 0.08 0.38 0.02
#> TCGA.HG.A9SC.01 2 0.4134 0.58574 0.00 0.62 0.00 0.00 0.00 0.00 0.30 0.08
#> TCGA.ZJ.AAXT.01 3 0.2224 0.72531 0.00 0.00 0.86 0.00 0.12 0.02 0.00 0.00
#> TCGA.C5.A1ML.01 3 0.4921 0.59803 0.06 0.00 0.72 0.00 0.02 0.06 0.06 0.08
#> TCGA.LP.A4AU.01 1 0.0941 0.65248 0.96 0.00 0.00 0.00 0.00 0.02 0.00 0.02
#> TCGA.ZJ.AAXU.01 3 0.1607 0.75301 0.00 0.00 0.92 0.00 0.04 0.04 0.00 0.00
#> TCGA.C5.A1MK.01 5 0.3021 0.54958 0.00 0.00 0.16 0.00 0.80 0.02 0.02 0.00
#> TCGA.VS.A958.01 3 0.0471 0.74331 0.00 0.00 0.98 0.00 0.00 0.00 0.00 0.02
#> TCGA.R2.A69V.01 1 0.1408 0.66067 0.94 0.00 0.00 0.02 0.00 0.02 0.00 0.02
#> TCGA.EA.A411.01 2 0.5486 0.36958 0.00 0.50 0.00 0.00 0.04 0.06 0.36 0.04
#> TCGA.VS.A9UP.01 1 0.4528 0.40813 0.68 0.00 0.00 0.00 0.04 0.14 0.00 0.14
#> TCGA.C5.A1MI.01 1 0.4337 0.52620 0.70 0.00 0.00 0.00 0.04 0.10 0.00 0.16
#> TCGA.ZJ.AAX8.01 1 0.0471 0.66596 0.98 0.00 0.00 0.00 0.00 0.00 0.02 0.00
#> TCGA.VS.A9UT.01 1 0.3198 0.04643 0.72 0.00 0.00 0.00 0.00 0.26 0.00 0.02
#> TCGA.VS.A9V0.01 4 0.3318 -0.82327 0.00 0.00 0.00 0.54 0.00 0.00 0.00 0.46
#> TCGA.ZJ.AAXA.01 2 0.2725 0.80521 0.00 0.82 0.00 0.00 0.00 0.04 0.00 0.14
#> TCGA.LP.A4AV.01 5 0.4599 0.23174 0.00 0.00 0.04 0.02 0.60 0.02 0.32 0.00
#> TCGA.ZJ.AAXF.01 3 0.4702 0.26935 0.36 0.00 0.56 0.04 0.00 0.02 0.00 0.02
#> TCGA.EA.A3Y4.01 4 0.5044 0.18859 0.00 0.00 0.04 0.50 0.02 0.04 0.40 0.00
#> TCGA.UC.A7PG.06 2 0.4188 0.74781 0.00 0.72 0.00 0.00 0.00 0.04 0.10 0.14
#> TCGA.VS.A9UJ.01 2 0.4893 0.56098 0.00 0.64 0.00 0.00 0.00 0.18 0.12 0.06
#> TCGA.Q1.A73O.01 3 0.4061 0.51565 0.18 0.00 0.74 0.02 0.00 0.02 0.02 0.02
#> TCGA.EA.A439.01 6 0.5061 0.68582 0.42 0.00 0.00 0.00 0.04 0.46 0.00 0.08
#> TCGA.VS.A9UM.01 2 0.2725 0.80521 0.00 0.82 0.00 0.00 0.00 0.04 0.00 0.14
#> TCGA.C5.A1MP.01 3 0.4202 0.66854 0.00 0.00 0.74 0.00 0.14 0.04 0.06 0.02
#> TCGA.ZJ.AB0H.01 3 0.4511 0.65289 0.00 0.00 0.72 0.00 0.14 0.04 0.06 0.04
#> TCGA.VS.A9V4.01 4 0.6344 0.00548 0.36 0.00 0.14 0.38 0.00 0.02 0.00 0.10
#> TCGA.VS.A9UA.01 3 0.0471 0.74331 0.00 0.00 0.98 0.00 0.00 0.00 0.00 0.02
#> TCGA.LP.A4AW.01 3 0.4202 0.66854 0.00 0.00 0.74 0.00 0.14 0.04 0.06 0.02
#> TCGA.C5.A1BN.01 5 0.4607 0.13896 0.00 0.04 0.00 0.00 0.54 0.00 0.38 0.04
#> TCGA.VS.AA62.01 1 0.1741 0.66224 0.92 0.00 0.00 0.02 0.00 0.02 0.00 0.04
#> TCGA.C5.A1BM.01 3 0.2547 0.72072 0.00 0.00 0.84 0.00 0.12 0.04 0.00 0.00
#> TCGA.C5.A1M6.01 1 0.6063 0.40568 0.54 0.00 0.08 0.00 0.04 0.14 0.00 0.20
#> TCGA.C5.A1BE.01 3 0.5449 0.37125 0.00 0.00 0.52 0.00 0.34 0.04 0.06 0.04
#> TCGA.C5.A1BJ.01 1 0.5581 0.06328 0.46 0.00 0.40 0.02 0.00 0.02 0.08 0.02
#> TCGA.FU.A23L.01 4 0.1341 0.36068 0.00 0.00 0.08 0.92 0.00 0.00 0.00 0.00
#> TCGA.C5.A1BF.01 6 0.3272 0.94811 0.42 0.00 0.00 0.00 0.00 0.58 0.00 0.00
#> TCGA.C5.A1BI.01 3 0.0471 0.74331 0.00 0.00 0.98 0.00 0.00 0.00 0.00 0.02
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)
consensus_heatmap(res, k = 7)
consensus_heatmap(res, k = 8)
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)
membership_heatmap(res, k = 7)
membership_heatmap(res, k = 8)
As soon as the classes for columns are determined, the signatures that are significantly different between subgroups can be looked for. Following are the heatmaps for signatures.
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)
get_signatures(res, k = 7)
get_signatures(res, k = 8)
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 (which is done by automatically selecting number of clusters).If there are too many signatures, top_signatures = ... can be set to only show the
signatures with the highest FDRs:
# code only for demonstration
# e.g. to show the top 500 most significant rows
tb = get_signature(res, k = ..., top_signatures = 500)
If the signatures are defined as these which are uniquely high in current group, diff_method argument
can be set to "uniquely_high_in_one_group":
# code only for demonstration
tb = get_signature(res, k = ..., diff_method = "uniquely_high_in_one_group")
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")
dimension_reduction(res, k = 7, method = "UMAP")
dimension_reduction(res, k = 8, method = "UMAP")
Following heatmap shows how subgroups are split when increasing k:
collect_classes(res)
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.
Parent node: Node01. Child nodes: Node0111 , Node0112-leaf , Node0113 , Node0121 , Node0122-leaf , Node0123-leaf , Node0131 , Node0132-leaf , Node0133-leaf , Node0134-leaf , Node0211 , Node0212-leaf , Node0221-leaf , Node0222 , Node0231-leaf , Node0232-leaf , Node0233-leaf , Node0311 , Node0312-leaf , Node0313-leaf .
The object with results only for a single top-value method and a single partitioning method can be extracted as:
res = res_rh["011"]
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, 7, 8.
#> On a matrix with 30000 rows and 58 columns.
#> Top rows (1000) are extracted by 'ATC' method.
#> Subgroups are detected by 'kmeans' method.
#> Performed in total 350 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_partitions"
#> [7] "compare_signatures" "consensus_heatmap" "dimension_reduction"
#> [10] "functional_enrichment" "get_anno_col" "get_anno"
#> [13] "get_classes" "get_consensus" "get_matrix"
#> [16] "get_membership" "get_param" "get_signatures"
#> [19] "get_stats" "is_best_k" "is_stable_k"
#> [22] "membership_heatmap" "ncol" "nrow"
#> [25] "plot_ecdf" "predict_classes" "rownames"
#> [28] "select_partition_number" "show" "suggest_best_k"
#> [31] "test_to_known_factors" "top_rows_heatmap"
collect_plots() function collects all the plots made from res for all k (number of subgroups)
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, higher 1-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 0.968 0.988 0.4513 0.552 0.552
#> 3 3 1.000 1.000 1.000 0.3306 0.598 0.406
#> 4 4 0.810 0.868 0.927 0.1904 0.789 0.520
#> 5 5 0.865 0.815 0.889 0.0619 0.928 0.754
#> 6 6 0.800 0.812 0.868 0.0336 0.967 0.869
#> 7 7 0.804 0.690 0.849 0.0381 0.964 0.845
#> 8 8 0.774 0.650 0.832 0.0136 0.996 0.978
suggest_best_k() suggests the best \(k\) based on these statistics. The rules are as follows:
suggest_best_k(res)
#> [1] 3
#> attr(,"optional")
#> [1] 2
There is also optional best \(k\) = 2 that is worth to check.
Following is 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 subgroup
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
#> TCGA.MY.A5BF.11 2 0.000 0.987 0.00 1.00
#> TCGA.FU.A3EO.11 2 0.000 0.987 0.00 1.00
#> TCGA.DG.A2KJ.01 1 0.000 0.988 1.00 0.00
#> TCGA.FU.A57G.01 2 0.000 0.987 0.00 1.00
#> TCGA.MY.A5BE.01 1 0.995 0.122 0.54 0.46
#> TCGA.VS.A8QH.01 1 0.000 0.988 1.00 0.00
#> TCGA.C5.A907.01 1 0.000 0.988 1.00 0.00
#> TCGA.C5.A7UC.01 1 0.000 0.988 1.00 0.00
#> TCGA.EK.A3GM.01 1 0.000 0.988 1.00 0.00
#> TCGA.MU.A51Y.01 1 0.000 0.988 1.00 0.00
#> TCGA.UC.A7PD.01 1 0.000 0.988 1.00 0.00
#> TCGA.VS.A8QM.01 2 0.000 0.987 0.00 1.00
#> TCGA.EA.A3HU.01 1 0.000 0.988 1.00 0.00
#> TCGA.VS.A94X.01 1 0.000 0.988 1.00 0.00
#> TCGA.C5.A3HF.01 1 0.000 0.988 1.00 0.00
#> TCGA.MY.A913.01 1 0.000 0.988 1.00 0.00
#> TCGA.C5.A8YT.01 2 0.000 0.987 0.00 1.00
#> TCGA.VS.A8EJ.01 2 0.000 0.987 0.00 1.00
#> TCGA.EX.A8YF.01 1 0.000 0.988 1.00 0.00
#> TCGA.MA.AA3Y.01 1 0.000 0.988 1.00 0.00
#> TCGA.HG.A2PA.01 1 0.000 0.988 1.00 0.00
#> TCGA.FU.A3TX.01 1 0.000 0.988 1.00 0.00
#> TCGA.VS.A8EH.01 1 0.000 0.988 1.00 0.00
#> TCGA.VS.A8EB.01 1 0.000 0.988 1.00 0.00
#> TCGA.RA.A741.01 1 0.000 0.988 1.00 0.00
#> TCGA.DG.A2KH.01 1 0.000 0.988 1.00 0.00
#> TCGA.C5.A2LT.01 1 0.000 0.988 1.00 0.00
#> TCGA.EK.A2RM.01 1 0.000 0.988 1.00 0.00
#> TCGA.EK.A2GZ.01 1 0.000 0.988 1.00 0.00
#> TCGA.HM.A3JK.01 1 0.000 0.988 1.00 0.00
#> TCGA.EA.A1QS.01 2 0.141 0.970 0.02 0.98
#> TCGA.HM.A3JJ.11 2 0.000 0.987 0.00 1.00
#> TCGA.C5.A2LY.01 1 0.000 0.988 1.00 0.00
#> TCGA.EK.A2H1.01 2 0.000 0.987 0.00 1.00
#> TCGA.JW.A5VG.01 1 0.000 0.988 1.00 0.00
#> TCGA.DG.A2KM.01 2 0.000 0.987 0.00 1.00
#> TCGA.EX.A3L1.01 2 0.000 0.987 0.00 1.00
#> TCGA.C5.A7CM.01 1 0.000 0.988 1.00 0.00
#> TCGA.VS.A959.01 1 0.000 0.988 1.00 0.00
#> TCGA.LP.A4AX.01 1 0.000 0.988 1.00 0.00
#> TCGA.VS.A9UH.01 2 0.722 0.746 0.20 0.80
#> TCGA.VS.A9UB.01 1 0.000 0.988 1.00 0.00
#> TCGA.VS.A9U6.01 1 0.000 0.988 1.00 0.00
#> TCGA.C5.A0TN.01 1 0.000 0.988 1.00 0.00
#> TCGA.C5.A1ML.01 1 0.000 0.988 1.00 0.00
#> TCGA.LP.A4AU.01 2 0.000 0.987 0.00 1.00
#> TCGA.R2.A69V.01 2 0.000 0.987 0.00 1.00
#> TCGA.VS.A9UP.01 1 0.000 0.988 1.00 0.00
#> TCGA.C5.A1MI.01 1 0.000 0.988 1.00 0.00
#> TCGA.ZJ.AAX8.01 2 0.000 0.987 0.00 1.00
#> TCGA.VS.A9UT.01 2 0.000 0.987 0.00 1.00
#> TCGA.ZJ.AAXF.01 2 0.000 0.987 0.00 1.00
#> TCGA.EA.A439.01 1 0.000 0.988 1.00 0.00
#> TCGA.VS.A9V4.01 2 0.000 0.987 0.00 1.00
#> TCGA.VS.AA62.01 2 0.000 0.987 0.00 1.00
#> TCGA.C5.A1M6.01 1 0.000 0.988 1.00 0.00
#> TCGA.C5.A1BJ.01 1 0.000 0.988 1.00 0.00
#> TCGA.C5.A1BF.01 1 0.000 0.988 1.00 0.00
cbind(get_classes(res, k = 3), get_membership(res, k = 3))
#> class entropy silhouette p1 p2 p3
#> TCGA.MY.A5BF.11 2 0 1 0 1 0
#> TCGA.FU.A3EO.11 2 0 1 0 1 0
#> TCGA.DG.A2KJ.01 1 0 1 1 0 0
#> TCGA.FU.A57G.01 2 0 1 0 1 0
#> TCGA.MY.A5BE.01 1 0 1 1 0 0
#> TCGA.VS.A8QH.01 1 0 1 1 0 0
#> TCGA.C5.A907.01 1 0 1 1 0 0
#> TCGA.C5.A7UC.01 1 0 1 1 0 0
#> TCGA.EK.A3GM.01 3 0 1 0 0 1
#> TCGA.MU.A51Y.01 1 0 1 1 0 0
#> TCGA.UC.A7PD.01 1 0 1 1 0 0
#> TCGA.VS.A8QM.01 1 0 1 1 0 0
#> TCGA.EA.A3HU.01 1 0 1 1 0 0
#> TCGA.VS.A94X.01 1 0 1 1 0 0
#> TCGA.C5.A3HF.01 1 0 1 1 0 0
#> TCGA.MY.A913.01 1 0 1 1 0 0
#> TCGA.C5.A8YT.01 2 0 1 0 1 0
#> TCGA.VS.A8EJ.01 2 0 1 0 1 0
#> TCGA.EX.A8YF.01 1 0 1 1 0 0
#> TCGA.MA.AA3Y.01 1 0 1 1 0 0
#> TCGA.HG.A2PA.01 1 0 1 1 0 0
#> TCGA.FU.A3TX.01 3 0 1 0 0 1
#> TCGA.VS.A8EH.01 3 0 1 0 0 1
#> TCGA.VS.A8EB.01 3 0 1 0 0 1
#> TCGA.RA.A741.01 1 0 1 1 0 0
#> TCGA.DG.A2KH.01 3 0 1 0 0 1
#> TCGA.C5.A2LT.01 1 0 1 1 0 0
#> TCGA.EK.A2RM.01 3 0 1 0 0 1
#> TCGA.EK.A2GZ.01 1 0 1 1 0 0
#> TCGA.HM.A3JK.01 1 0 1 1 0 0
#> TCGA.EA.A1QS.01 1 0 1 1 0 0
#> TCGA.HM.A3JJ.11 2 0 1 0 1 0
#> TCGA.C5.A2LY.01 3 0 1 0 0 1
#> TCGA.EK.A2H1.01 2 0 1 0 1 0
#> TCGA.JW.A5VG.01 3 0 1 0 0 1
#> TCGA.DG.A2KM.01 2 0 1 0 1 0
#> TCGA.EX.A3L1.01 1 0 1 1 0 0
#> TCGA.C5.A7CM.01 3 0 1 0 0 1
#> TCGA.VS.A959.01 1 0 1 1 0 0
#> TCGA.LP.A4AX.01 1 0 1 1 0 0
#> TCGA.VS.A9UH.01 1 0 1 1 0 0
#> TCGA.VS.A9UB.01 1 0 1 1 0 0
#> TCGA.VS.A9U6.01 3 0 1 0 0 1
#> TCGA.C5.A0TN.01 3 0 1 0 0 1
#> TCGA.C5.A1ML.01 3 0 1 0 0 1
#> TCGA.LP.A4AU.01 1 0 1 1 0 0
#> TCGA.R2.A69V.01 1 0 1 1 0 0
#> TCGA.VS.A9UP.01 1 0 1 1 0 0
#> TCGA.C5.A1MI.01 3 0 1 0 0 1
#> TCGA.ZJ.AAX8.01 1 0 1 1 0 0
#> TCGA.VS.A9UT.01 2 0 1 0 1 0
#> TCGA.ZJ.AAXF.01 1 0 1 1 0 0
#> TCGA.EA.A439.01 3 0 1 0 0 1
#> TCGA.VS.A9V4.01 2 0 1 0 1 0
#> TCGA.VS.AA62.01 1 0 1 1 0 0
#> TCGA.C5.A1M6.01 3 0 1 0 0 1
#> TCGA.C5.A1BJ.01 1 0 1 1 0 0
#> TCGA.C5.A1BF.01 3 0 1 0 0 1
cbind(get_classes(res, k = 4), get_membership(res, k = 4))
#> class entropy silhouette p1 p2 p3 p4
#> TCGA.MY.A5BF.11 2 0.0000 0.99588 0.00 1.00 0.00 0.00
#> TCGA.FU.A3EO.11 2 0.0000 0.99588 0.00 1.00 0.00 0.00
#> TCGA.DG.A2KJ.01 1 0.0000 0.93407 1.00 0.00 0.00 0.00
#> TCGA.FU.A57G.01 2 0.0707 0.98757 0.00 0.98 0.00 0.02
#> TCGA.MY.A5BE.01 4 0.2921 0.90343 0.14 0.00 0.00 0.86
#> TCGA.VS.A8QH.01 1 0.0000 0.93407 1.00 0.00 0.00 0.00
#> TCGA.C5.A907.01 1 0.0000 0.93407 1.00 0.00 0.00 0.00
#> TCGA.C5.A7UC.01 1 0.0000 0.93407 1.00 0.00 0.00 0.00
#> TCGA.EK.A3GM.01 3 0.0000 0.94839 0.00 0.00 1.00 0.00
#> TCGA.MU.A51Y.01 1 0.0000 0.93407 1.00 0.00 0.00 0.00
#> TCGA.UC.A7PD.01 1 0.0000 0.93407 1.00 0.00 0.00 0.00
#> TCGA.VS.A8QM.01 4 0.2921 0.90343 0.14 0.00 0.00 0.86
#> TCGA.EA.A3HU.01 1 0.0000 0.93407 1.00 0.00 0.00 0.00
#> TCGA.VS.A94X.01 1 0.1637 0.88489 0.94 0.00 0.00 0.06
#> TCGA.C5.A3HF.01 4 0.4977 0.44752 0.46 0.00 0.00 0.54
#> TCGA.MY.A913.01 1 0.0000 0.93407 1.00 0.00 0.00 0.00
#> TCGA.C5.A8YT.01 2 0.0000 0.99588 0.00 1.00 0.00 0.00
#> TCGA.VS.A8EJ.01 2 0.0707 0.98757 0.00 0.98 0.00 0.02
#> TCGA.EX.A8YF.01 1 0.0000 0.93407 1.00 0.00 0.00 0.00
#> TCGA.MA.AA3Y.01 1 0.0707 0.91567 0.98 0.00 0.00 0.02
#> TCGA.HG.A2PA.01 1 0.0000 0.93407 1.00 0.00 0.00 0.00
#> TCGA.FU.A3TX.01 3 0.0000 0.94839 0.00 0.00 1.00 0.00
#> TCGA.VS.A8EH.01 3 0.0000 0.94839 0.00 0.00 1.00 0.00
#> TCGA.VS.A8EB.01 3 0.0000 0.94839 0.00 0.00 1.00 0.00
#> TCGA.RA.A741.01 1 0.0000 0.93407 1.00 0.00 0.00 0.00
#> TCGA.DG.A2KH.01 3 0.0000 0.94839 0.00 0.00 1.00 0.00
#> TCGA.C5.A2LT.01 1 0.0000 0.93407 1.00 0.00 0.00 0.00
#> TCGA.EK.A2RM.01 3 0.0000 0.94839 0.00 0.00 1.00 0.00
#> TCGA.EK.A2GZ.01 1 0.0000 0.93407 1.00 0.00 0.00 0.00
#> TCGA.HM.A3JK.01 1 0.0000 0.93407 1.00 0.00 0.00 0.00
#> TCGA.EA.A1QS.01 4 0.2921 0.90343 0.14 0.00 0.00 0.86
#> TCGA.HM.A3JJ.11 2 0.0000 0.99588 0.00 1.00 0.00 0.00
#> TCGA.C5.A2LY.01 1 0.5000 -0.04653 0.50 0.00 0.50 0.00
#> TCGA.EK.A2H1.01 4 0.2921 0.71595 0.00 0.14 0.00 0.86
#> TCGA.JW.A5VG.01 3 0.4994 0.00656 0.48 0.00 0.52 0.00
#> TCGA.DG.A2KM.01 4 0.2921 0.71595 0.00 0.14 0.00 0.86
#> TCGA.EX.A3L1.01 4 0.2921 0.90343 0.14 0.00 0.00 0.86
#> TCGA.C5.A7CM.01 3 0.0000 0.94839 0.00 0.00 1.00 0.00
#> TCGA.VS.A959.01 1 0.0000 0.93407 1.00 0.00 0.00 0.00
#> TCGA.LP.A4AX.01 1 0.1211 0.89347 0.96 0.00 0.00 0.04
#> TCGA.VS.A9UH.01 4 0.2921 0.90343 0.14 0.00 0.00 0.86
#> TCGA.VS.A9UB.01 1 0.0000 0.93407 1.00 0.00 0.00 0.00
#> TCGA.VS.A9U6.01 3 0.0000 0.94839 0.00 0.00 1.00 0.00
#> TCGA.C5.A0TN.01 3 0.0000 0.94839 0.00 0.00 1.00 0.00
#> TCGA.C5.A1ML.01 3 0.1637 0.90243 0.00 0.00 0.94 0.06
#> TCGA.LP.A4AU.01 4 0.2921 0.90343 0.14 0.00 0.00 0.86
#> TCGA.R2.A69V.01 4 0.2921 0.90343 0.14 0.00 0.00 0.86
#> TCGA.VS.A9UP.01 1 0.1637 0.88489 0.94 0.00 0.00 0.06
#> TCGA.C5.A1MI.01 3 0.0000 0.94839 0.00 0.00 1.00 0.00
#> TCGA.ZJ.AAX8.01 4 0.2921 0.90343 0.14 0.00 0.00 0.86
#> TCGA.VS.A9UT.01 2 0.0000 0.99588 0.00 1.00 0.00 0.00
#> TCGA.ZJ.AAXF.01 4 0.2921 0.90343 0.14 0.00 0.00 0.86
#> TCGA.EA.A439.01 3 0.0000 0.94839 0.00 0.00 1.00 0.00
#> TCGA.VS.A9V4.01 2 0.0000 0.99588 0.00 1.00 0.00 0.00
#> TCGA.VS.AA62.01 4 0.2921 0.90343 0.14 0.00 0.00 0.86
#> TCGA.C5.A1M6.01 3 0.0000 0.94839 0.00 0.00 1.00 0.00
#> TCGA.C5.A1BJ.01 4 0.4977 0.44752 0.46 0.00 0.00 0.54
#> TCGA.C5.A1BF.01 1 0.4855 0.28774 0.60 0.00 0.40 0.00
cbind(get_classes(res, k = 5), get_membership(res, k = 5))
#> class entropy silhouette p1 p2 p3 p4 p5
#> TCGA.MY.A5BF.11 2 0.0000 0.954 0.00 1.00 0.00 0.00 0.00
#> TCGA.FU.A3EO.11 2 0.0000 0.954 0.00 1.00 0.00 0.00 0.00
#> TCGA.DG.A2KJ.01 1 0.1410 0.829 0.94 0.00 0.00 0.00 0.06
#> TCGA.FU.A57G.01 2 0.3274 0.853 0.00 0.78 0.00 0.00 0.22
#> TCGA.MY.A5BE.01 4 0.1732 0.937 0.00 0.00 0.00 0.92 0.08
#> TCGA.VS.A8QH.01 1 0.2732 0.779 0.84 0.00 0.00 0.00 0.16
#> TCGA.C5.A907.01 1 0.0000 0.883 1.00 0.00 0.00 0.00 0.00
#> TCGA.C5.A7UC.01 1 0.0000 0.883 1.00 0.00 0.00 0.00 0.00
#> TCGA.EK.A3GM.01 3 0.0000 0.753 0.00 0.00 1.00 0.00 0.00
#> TCGA.MU.A51Y.01 1 0.0000 0.883 1.00 0.00 0.00 0.00 0.00
#> TCGA.UC.A7PD.01 1 0.1732 0.847 0.92 0.00 0.00 0.00 0.08
#> TCGA.VS.A8QM.01 4 0.0000 0.977 0.00 0.00 0.00 1.00 0.00
#> TCGA.EA.A3HU.01 1 0.0000 0.883 1.00 0.00 0.00 0.00 0.00
#> TCGA.VS.A94X.01 1 0.2280 0.810 0.88 0.00 0.00 0.00 0.12
#> TCGA.C5.A3HF.01 1 0.5607 0.304 0.54 0.00 0.00 0.38 0.08
#> TCGA.MY.A913.01 1 0.0000 0.883 1.00 0.00 0.00 0.00 0.00
#> TCGA.C5.A8YT.01 2 0.0000 0.954 0.00 1.00 0.00 0.00 0.00
#> TCGA.VS.A8EJ.01 2 0.3274 0.853 0.00 0.78 0.00 0.00 0.22
#> TCGA.EX.A8YF.01 1 0.1410 0.829 0.94 0.00 0.00 0.00 0.06
#> TCGA.MA.AA3Y.01 1 0.1732 0.847 0.92 0.00 0.00 0.00 0.08
#> TCGA.HG.A2PA.01 1 0.1043 0.870 0.96 0.00 0.00 0.00 0.04
#> TCGA.FU.A3TX.01 3 0.0000 0.753 0.00 0.00 1.00 0.00 0.00
#> TCGA.VS.A8EH.01 3 0.0000 0.753 0.00 0.00 1.00 0.00 0.00
#> TCGA.VS.A8EB.01 3 0.0000 0.753 0.00 0.00 1.00 0.00 0.00
#> TCGA.RA.A741.01 1 0.0609 0.877 0.98 0.00 0.00 0.00 0.02
#> TCGA.DG.A2KH.01 3 0.0000 0.753 0.00 0.00 1.00 0.00 0.00
#> TCGA.C5.A2LT.01 1 0.0000 0.883 1.00 0.00 0.00 0.00 0.00
#> TCGA.EK.A2RM.01 3 0.1043 0.744 0.00 0.00 0.96 0.00 0.04
#> TCGA.EK.A2GZ.01 1 0.0000 0.883 1.00 0.00 0.00 0.00 0.00
#> TCGA.HM.A3JK.01 1 0.0000 0.883 1.00 0.00 0.00 0.00 0.00
#> TCGA.EA.A1QS.01 4 0.1732 0.937 0.00 0.00 0.00 0.92 0.08
#> TCGA.HM.A3JJ.11 2 0.0000 0.954 0.00 1.00 0.00 0.00 0.00
#> TCGA.C5.A2LY.01 5 0.6766 0.868 0.30 0.00 0.30 0.00 0.40
#> TCGA.EK.A2H1.01 4 0.0000 0.977 0.00 0.00 0.00 1.00 0.00
#> TCGA.JW.A5VG.01 5 0.6766 0.868 0.30 0.00 0.30 0.00 0.40
#> TCGA.DG.A2KM.01 4 0.0000 0.977 0.00 0.00 0.00 1.00 0.00
#> TCGA.EX.A3L1.01 4 0.0000 0.977 0.00 0.00 0.00 1.00 0.00
#> TCGA.C5.A7CM.01 3 0.4726 0.376 0.02 0.00 0.58 0.00 0.40
#> TCGA.VS.A959.01 1 0.0000 0.883 1.00 0.00 0.00 0.00 0.00
#> TCGA.LP.A4AX.01 1 0.1732 0.847 0.92 0.00 0.00 0.00 0.08
#> TCGA.VS.A9UH.01 4 0.1732 0.937 0.00 0.00 0.00 0.92 0.08
#> TCGA.VS.A9UB.01 1 0.0000 0.883 1.00 0.00 0.00 0.00 0.00
#> TCGA.VS.A9U6.01 3 0.4726 0.376 0.02 0.00 0.58 0.00 0.40
#> TCGA.C5.A0TN.01 3 0.4182 0.425 0.00 0.00 0.60 0.00 0.40
#> TCGA.C5.A1ML.01 3 0.4307 0.317 0.00 0.00 0.50 0.00 0.50
#> TCGA.LP.A4AU.01 4 0.0000 0.977 0.00 0.00 0.00 1.00 0.00
#> TCGA.R2.A69V.01 4 0.0000 0.977 0.00 0.00 0.00 1.00 0.00
#> TCGA.VS.A9UP.01 1 0.2020 0.813 0.90 0.00 0.00 0.00 0.10
#> TCGA.C5.A1MI.01 3 0.1043 0.744 0.00 0.00 0.96 0.00 0.04
#> TCGA.ZJ.AAX8.01 4 0.0609 0.969 0.00 0.00 0.00 0.98 0.02
#> TCGA.VS.A9UT.01 2 0.0000 0.954 0.00 1.00 0.00 0.00 0.00
#> TCGA.ZJ.AAXF.01 4 0.0000 0.977 0.00 0.00 0.00 1.00 0.00
#> TCGA.EA.A439.01 3 0.4182 0.425 0.00 0.00 0.60 0.00 0.40
#> TCGA.VS.A9V4.01 2 0.0000 0.954 0.00 1.00 0.00 0.00 0.00
#> TCGA.VS.AA62.01 4 0.0000 0.977 0.00 0.00 0.00 1.00 0.00
#> TCGA.C5.A1M6.01 3 0.0000 0.753 0.00 0.00 1.00 0.00 0.00
#> TCGA.C5.A1BJ.01 1 0.5607 0.304 0.54 0.00 0.00 0.38 0.08
#> TCGA.C5.A1BF.01 5 0.6555 0.781 0.40 0.00 0.20 0.00 0.40
cbind(get_classes(res, k = 6), get_membership(res, k = 6))
#> class entropy silhouette p1 p2 p3 p4 p5 p6
#> TCGA.MY.A5BF.11 2 0.0000 0.920 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.FU.A3EO.11 2 0.0000 0.920 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.DG.A2KJ.01 1 0.1807 0.814 0.92 0.00 0.00 0.00 0.02 0.06
#> TCGA.FU.A57G.01 2 0.4121 0.802 0.00 0.72 0.06 0.00 0.22 0.00
#> TCGA.MY.A5BE.01 4 0.3007 0.874 0.02 0.00 0.08 0.86 0.04 0.00
#> TCGA.VS.A8QH.01 1 0.4380 0.689 0.70 0.00 0.22 0.00 0.08 0.00
#> TCGA.C5.A907.01 1 0.0547 0.845 0.98 0.00 0.00 0.00 0.00 0.02
#> TCGA.C5.A7UC.01 1 0.0547 0.845 0.98 0.00 0.00 0.00 0.00 0.02
#> TCGA.EK.A3GM.01 3 0.3578 0.974 0.00 0.00 0.66 0.00 0.00 0.34
#> TCGA.MU.A51Y.01 1 0.0547 0.845 0.98 0.00 0.00 0.00 0.00 0.02
#> TCGA.UC.A7PD.01 1 0.2629 0.801 0.88 0.00 0.08 0.02 0.02 0.00
#> TCGA.VS.A8QM.01 4 0.0000 0.929 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.EA.A3HU.01 1 0.0547 0.845 0.98 0.00 0.00 0.00 0.00 0.02
#> TCGA.VS.A94X.01 1 0.4246 0.491 0.58 0.00 0.02 0.00 0.40 0.00
#> TCGA.C5.A3HF.01 1 0.5750 0.372 0.54 0.00 0.08 0.34 0.04 0.00
#> TCGA.MY.A913.01 1 0.0547 0.845 0.98 0.00 0.00 0.00 0.00 0.02
#> TCGA.C5.A8YT.01 2 0.0000 0.920 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.VS.A8EJ.01 2 0.4121 0.802 0.00 0.72 0.06 0.00 0.22 0.00
#> TCGA.EX.A8YF.01 1 0.1807 0.814 0.92 0.00 0.00 0.00 0.02 0.06
#> TCGA.MA.AA3Y.01 1 0.3007 0.789 0.86 0.00 0.08 0.02 0.04 0.00
#> TCGA.HG.A2PA.01 1 0.1267 0.828 0.94 0.00 0.06 0.00 0.00 0.00
#> TCGA.FU.A3TX.01 3 0.4078 0.971 0.00 0.00 0.64 0.00 0.02 0.34
#> TCGA.VS.A8EH.01 3 0.4078 0.971 0.00 0.00 0.64 0.00 0.02 0.34
#> TCGA.VS.A8EB.01 3 0.4078 0.971 0.00 0.00 0.64 0.00 0.02 0.34
#> TCGA.RA.A741.01 1 0.1267 0.828 0.94 0.00 0.06 0.00 0.00 0.00
#> TCGA.DG.A2KH.01 3 0.3578 0.974 0.00 0.00 0.66 0.00 0.00 0.34
#> TCGA.C5.A2LT.01 1 0.0547 0.845 0.98 0.00 0.00 0.00 0.00 0.02
#> TCGA.EK.A2RM.01 3 0.3706 0.944 0.00 0.00 0.62 0.00 0.00 0.38
#> TCGA.EK.A2GZ.01 1 0.0547 0.845 0.98 0.00 0.00 0.00 0.00 0.02
#> TCGA.HM.A3JK.01 1 0.0547 0.845 0.98 0.00 0.00 0.00 0.00 0.02
#> TCGA.EA.A1QS.01 4 0.3007 0.874 0.02 0.00 0.08 0.86 0.04 0.00
#> TCGA.HM.A3JJ.11 2 0.0000 0.920 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.C5.A2LY.01 6 0.3198 0.687 0.26 0.00 0.00 0.00 0.00 0.74
#> TCGA.EK.A2H1.01 4 0.2956 0.832 0.00 0.00 0.04 0.84 0.12 0.00
#> TCGA.JW.A5VG.01 6 0.3198 0.687 0.26 0.00 0.00 0.00 0.00 0.74
#> TCGA.DG.A2KM.01 4 0.2956 0.832 0.00 0.00 0.04 0.84 0.12 0.00
#> TCGA.EX.A3L1.01 4 0.0000 0.929 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.C5.A7CM.01 6 0.1267 0.701 0.06 0.00 0.00 0.00 0.00 0.94
#> TCGA.VS.A959.01 1 0.0000 0.844 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.LP.A4AX.01 1 0.4626 0.691 0.74 0.00 0.08 0.14 0.04 0.00
#> TCGA.VS.A9UH.01 4 0.3007 0.874 0.02 0.00 0.08 0.86 0.04 0.00
#> TCGA.VS.A9UB.01 1 0.0000 0.844 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.VS.A9U6.01 6 0.0937 0.691 0.04 0.00 0.00 0.00 0.00 0.96
#> TCGA.C5.A0TN.01 6 0.0937 0.620 0.00 0.00 0.04 0.00 0.00 0.96
#> TCGA.C5.A1ML.01 6 0.4503 0.470 0.00 0.00 0.08 0.00 0.24 0.68
#> TCGA.LP.A4AU.01 4 0.0000 0.929 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.R2.A69V.01 4 0.0000 0.929 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.VS.A9UP.01 1 0.3756 0.493 0.60 0.00 0.00 0.00 0.40 0.00
#> TCGA.C5.A1MI.01 3 0.3706 0.944 0.00 0.00 0.62 0.00 0.00 0.38
#> TCGA.ZJ.AAX8.01 4 0.1480 0.911 0.00 0.00 0.02 0.94 0.04 0.00
#> TCGA.VS.A9UT.01 2 0.0000 0.920 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.ZJ.AAXF.01 4 0.0000 0.929 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.EA.A439.01 6 0.1267 0.603 0.00 0.00 0.06 0.00 0.00 0.94
#> TCGA.VS.A9V4.01 2 0.2956 0.835 0.00 0.84 0.04 0.00 0.12 0.00
#> TCGA.VS.AA62.01 4 0.0000 0.929 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.C5.A1M6.01 3 0.3578 0.974 0.00 0.00 0.66 0.00 0.00 0.34
#> TCGA.C5.A1BJ.01 1 0.5750 0.372 0.54 0.00 0.08 0.34 0.04 0.00
#> TCGA.C5.A1BF.01 6 0.3309 0.667 0.28 0.00 0.00 0.00 0.00 0.72
cbind(get_classes(res, k = 7), get_membership(res, k = 7))
#> class entropy silhouette p1 p2 p3 p4 p5 p6 p7
#> TCGA.MY.A5BF.11 2 0.0000 0.903 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.FU.A3EO.11 2 0.0000 0.903 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.DG.A2KJ.01 1 0.1718 0.625 0.92 0.00 0.00 0.00 0.00 0.04 0.04
#> TCGA.FU.A57G.01 2 0.4699 0.736 0.00 0.66 0.00 0.00 0.24 0.06 0.04
#> TCGA.MY.A5BE.01 4 0.3358 0.623 0.00 0.00 0.00 0.64 0.00 0.00 0.36
#> TCGA.VS.A8QH.01 7 0.4622 0.000 0.38 0.00 0.00 0.00 0.04 0.02 0.56
#> TCGA.C5.A907.01 1 0.1363 0.657 0.94 0.00 0.00 0.00 0.02 0.00 0.04
#> TCGA.C5.A7UC.01 1 0.1166 0.658 0.94 0.00 0.00 0.00 0.06 0.00 0.00
#> TCGA.EK.A3GM.01 3 0.0504 0.967 0.00 0.00 0.98 0.00 0.02 0.00 0.00
#> TCGA.MU.A51Y.01 1 0.0000 0.687 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.UC.A7PD.01 1 0.3911 0.254 0.70 0.00 0.00 0.00 0.06 0.00 0.24
#> TCGA.VS.A8QM.01 4 0.0504 0.845 0.00 0.00 0.00 0.98 0.00 0.00 0.02
#> TCGA.EA.A3HU.01 1 0.0000 0.687 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.VS.A94X.01 5 0.3909 0.852 0.40 0.00 0.00 0.00 0.58 0.00 0.02
#> TCGA.C5.A3HF.01 1 0.5232 -0.385 0.46 0.00 0.00 0.16 0.00 0.00 0.38
#> TCGA.MY.A913.01 1 0.1664 0.644 0.92 0.00 0.00 0.00 0.06 0.00 0.02
#> TCGA.C5.A8YT.01 2 0.0000 0.903 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.VS.A8EJ.01 2 0.4821 0.736 0.00 0.66 0.00 0.00 0.22 0.08 0.04
#> TCGA.EX.A8YF.01 1 0.2213 0.607 0.90 0.00 0.00 0.00 0.02 0.04 0.04
#> TCGA.MA.AA3Y.01 1 0.3413 -0.130 0.62 0.00 0.00 0.00 0.00 0.00 0.38
#> TCGA.HG.A2PA.01 1 0.1671 0.617 0.90 0.00 0.00 0.00 0.00 0.00 0.10
#> TCGA.FU.A3TX.01 3 0.0000 0.969 0.00 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.VS.A8EH.01 3 0.0504 0.968 0.00 0.00 0.98 0.00 0.00 0.00 0.02
#> TCGA.VS.A8EB.01 3 0.0000 0.969 0.00 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.RA.A741.01 1 0.2163 0.608 0.88 0.00 0.00 0.00 0.02 0.00 0.10
#> TCGA.DG.A2KH.01 3 0.0504 0.967 0.00 0.00 0.98 0.00 0.02 0.00 0.00
#> TCGA.C5.A2LT.01 1 0.0000 0.687 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.EK.A2RM.01 3 0.1664 0.935 0.00 0.00 0.92 0.00 0.00 0.06 0.02
#> TCGA.EK.A2GZ.01 1 0.0504 0.678 0.98 0.00 0.00 0.00 0.00 0.02 0.00
#> TCGA.HM.A3JK.01 1 0.0504 0.678 0.98 0.00 0.00 0.00 0.00 0.02 0.00
#> TCGA.EA.A1QS.01 4 0.3358 0.623 0.00 0.00 0.00 0.64 0.00 0.00 0.36
#> TCGA.HM.A3JJ.11 2 0.0000 0.903 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.C5.A2LY.01 6 0.3086 0.820 0.16 0.00 0.04 0.00 0.00 0.80 0.00
#> TCGA.EK.A2H1.01 4 0.2654 0.773 0.00 0.00 0.00 0.86 0.02 0.02 0.10
#> TCGA.JW.A5VG.01 6 0.3086 0.820 0.16 0.00 0.04 0.00 0.00 0.80 0.00
#> TCGA.DG.A2KM.01 4 0.2654 0.773 0.00 0.00 0.00 0.86 0.02 0.02 0.10
#> TCGA.EX.A3L1.01 4 0.0000 0.843 0.00 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.C5.A7CM.01 6 0.3058 0.852 0.08 0.00 0.10 0.00 0.00 0.82 0.00
#> TCGA.VS.A959.01 1 0.1166 0.662 0.94 0.00 0.00 0.00 0.00 0.00 0.06
#> TCGA.LP.A4AX.01 1 0.4426 -0.261 0.56 0.00 0.00 0.06 0.00 0.00 0.38
#> TCGA.VS.A9UH.01 4 0.3358 0.623 0.00 0.00 0.00 0.64 0.00 0.00 0.36
#> TCGA.VS.A9UB.01 1 0.1166 0.662 0.94 0.00 0.00 0.00 0.00 0.00 0.06
#> TCGA.VS.A9U6.01 6 0.3058 0.852 0.08 0.00 0.10 0.00 0.00 0.82 0.00
#> TCGA.C5.A0TN.01 6 0.2906 0.792 0.00 0.00 0.18 0.00 0.00 0.80 0.02
#> TCGA.C5.A1ML.01 6 0.5755 0.564 0.00 0.00 0.08 0.00 0.16 0.58 0.18
#> TCGA.LP.A4AU.01 4 0.0000 0.843 0.00 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.R2.A69V.01 4 0.0504 0.845 0.00 0.00 0.00 0.98 0.00 0.00 0.02
#> TCGA.VS.A9UP.01 5 0.4408 0.850 0.44 0.00 0.00 0.00 0.52 0.02 0.02
#> TCGA.C5.A1MI.01 3 0.1664 0.935 0.00 0.00 0.92 0.00 0.00 0.06 0.02
#> TCGA.ZJ.AAX8.01 4 0.2422 0.776 0.00 0.00 0.00 0.82 0.00 0.00 0.18
#> TCGA.VS.A9UT.01 2 0.0000 0.903 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.ZJ.AAXF.01 4 0.0863 0.842 0.00 0.00 0.00 0.96 0.00 0.00 0.04
#> TCGA.EA.A439.01 6 0.2422 0.800 0.00 0.00 0.18 0.00 0.00 0.82 0.00
#> TCGA.VS.A9V4.01 2 0.2654 0.829 0.00 0.86 0.00 0.00 0.02 0.02 0.10
#> TCGA.VS.AA62.01 4 0.0000 0.843 0.00 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.C5.A1M6.01 3 0.0504 0.968 0.00 0.00 0.98 0.00 0.00 0.00 0.02
#> TCGA.C5.A1BJ.01 1 0.5232 -0.385 0.46 0.00 0.00 0.16 0.00 0.00 0.38
#> TCGA.C5.A1BF.01 6 0.3228 0.802 0.16 0.00 0.02 0.00 0.00 0.80 0.02
cbind(get_classes(res, k = 8), get_membership(res, k = 8))
#> class entropy silhouette p1 p2 p3 p4 p5 p6 p7 p8
#> TCGA.MY.A5BF.11 2 0.0000 0.86097 0.00 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.FU.A3EO.11 2 0.0000 0.86097 0.00 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.DG.A2KJ.01 1 0.3078 0.46702 0.82 0.00 0.00 0.00 0.02 0.10 0.06 0.00
#> TCGA.FU.A57G.01 2 0.3618 0.63323 0.00 0.60 0.00 0.00 0.00 0.00 0.38 0.02
#> TCGA.MY.A5BE.01 4 0.3015 0.64166 0.00 0.00 0.00 0.68 0.00 0.00 0.00 0.32
#> TCGA.VS.A8QH.01 7 0.6597 0.00000 0.32 0.00 0.00 0.00 0.08 0.04 0.38 0.18
#> TCGA.C5.A907.01 1 0.1557 0.61752 0.92 0.00 0.00 0.00 0.02 0.00 0.06 0.00
#> TCGA.C5.A7UC.01 1 0.2132 0.61680 0.88 0.00 0.00 0.00 0.04 0.00 0.00 0.08
#> TCGA.EK.A3GM.01 3 0.2224 0.85235 0.00 0.00 0.86 0.00 0.00 0.02 0.12 0.00
#> TCGA.MU.A51Y.01 1 0.0000 0.68793 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.UC.A7PD.01 1 0.3594 0.33122 0.68 0.00 0.00 0.00 0.04 0.00 0.00 0.28
#> TCGA.VS.A8QM.01 4 0.0000 0.80662 0.00 0.00 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.EA.A3HU.01 1 0.0000 0.68793 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.VS.A94X.01 5 0.3083 0.89862 0.34 0.00 0.00 0.00 0.66 0.00 0.00 0.00
#> TCGA.C5.A3HF.01 1 0.5103 -0.11728 0.44 0.00 0.00 0.22 0.00 0.00 0.00 0.34
#> TCGA.MY.A913.01 1 0.1887 0.62185 0.90 0.00 0.00 0.00 0.04 0.00 0.00 0.06
#> TCGA.C5.A8YT.01 2 0.0000 0.86097 0.00 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.VS.A8EJ.01 2 0.3618 0.63323 0.00 0.60 0.00 0.00 0.00 0.00 0.38 0.02
#> TCGA.EX.A8YF.01 1 0.2864 0.50563 0.84 0.00 0.00 0.00 0.02 0.08 0.06 0.00
#> TCGA.MA.AA3Y.01 1 0.4050 0.13937 0.60 0.00 0.00 0.06 0.00 0.00 0.00 0.34
#> TCGA.HG.A2PA.01 1 0.1563 0.62745 0.90 0.00 0.00 0.00 0.00 0.00 0.00 0.10
#> TCGA.FU.A3TX.01 3 0.1607 0.85354 0.00 0.00 0.92 0.00 0.04 0.00 0.04 0.00
#> TCGA.VS.A8EH.01 3 0.2071 0.85372 0.00 0.00 0.90 0.00 0.04 0.02 0.04 0.00
#> TCGA.VS.A8EB.01 3 0.1607 0.85354 0.00 0.00 0.92 0.00 0.04 0.00 0.04 0.00
#> TCGA.RA.A741.01 1 0.2025 0.61825 0.88 0.00 0.00 0.00 0.02 0.00 0.00 0.10
#> TCGA.DG.A2KH.01 3 0.2224 0.85235 0.00 0.00 0.86 0.00 0.00 0.02 0.12 0.00
#> TCGA.C5.A2LT.01 1 0.0000 0.68793 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.EK.A2RM.01 3 0.1765 0.83458 0.00 0.00 0.88 0.00 0.00 0.12 0.00 0.00
#> TCGA.EK.A2GZ.01 1 0.0000 0.68793 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.HM.A3JK.01 1 0.0000 0.68793 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.EA.A1QS.01 4 0.3015 0.64166 0.00 0.00 0.00 0.68 0.00 0.00 0.00 0.32
#> TCGA.HM.A3JJ.11 2 0.0000 0.86097 0.00 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.C5.A2LY.01 6 0.2569 0.72777 0.16 0.00 0.02 0.00 0.00 0.82 0.00 0.00
#> TCGA.EK.A2H1.01 4 0.4138 0.64865 0.00 0.00 0.00 0.72 0.08 0.04 0.00 0.16
#> TCGA.JW.A5VG.01 6 0.2404 0.73661 0.14 0.00 0.02 0.00 0.00 0.84 0.00 0.00
#> TCGA.DG.A2KM.01 4 0.4138 0.64865 0.00 0.00 0.00 0.72 0.08 0.04 0.00 0.16
#> TCGA.EX.A3L1.01 4 0.1275 0.79508 0.00 0.00 0.00 0.94 0.02 0.00 0.00 0.04
#> TCGA.C5.A7CM.01 6 0.2818 0.75701 0.06 0.00 0.12 0.00 0.00 0.82 0.00 0.00
#> TCGA.VS.A959.01 1 0.0000 0.68793 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.LP.A4AX.01 1 0.4723 -0.00558 0.52 0.00 0.00 0.14 0.00 0.00 0.00 0.34
#> TCGA.VS.A9UH.01 4 0.3015 0.64166 0.00 0.00 0.00 0.68 0.00 0.00 0.00 0.32
#> TCGA.VS.A9UB.01 1 0.0471 0.68155 0.98 0.00 0.00 0.00 0.00 0.00 0.00 0.02
#> TCGA.VS.A9U6.01 6 0.2350 0.74996 0.04 0.00 0.10 0.00 0.00 0.86 0.00 0.00
#> TCGA.C5.A0TN.01 6 0.3503 0.56735 0.00 0.00 0.12 0.00 0.08 0.78 0.02 0.00
#> TCGA.C5.A1ML.01 8 0.6175 0.00000 0.00 0.00 0.04 0.00 0.12 0.36 0.06 0.42
#> TCGA.LP.A4AU.01 4 0.1275 0.79508 0.00 0.00 0.00 0.94 0.02 0.00 0.00 0.04
#> TCGA.R2.A69V.01 4 0.0000 0.80662 0.00 0.00 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.VS.A9UP.01 5 0.3193 0.89875 0.38 0.00 0.00 0.00 0.62 0.00 0.00 0.00
#> TCGA.C5.A1MI.01 3 0.3054 0.81171 0.00 0.00 0.80 0.00 0.00 0.12 0.08 0.00
#> TCGA.ZJ.AAX8.01 4 0.1947 0.76634 0.00 0.00 0.00 0.86 0.00 0.00 0.00 0.14
#> TCGA.VS.A9UT.01 2 0.0000 0.86097 0.00 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.ZJ.AAXF.01 4 0.1091 0.79726 0.00 0.00 0.00 0.94 0.00 0.00 0.00 0.06
#> TCGA.EA.A439.01 6 0.2267 0.65159 0.00 0.00 0.18 0.00 0.00 0.82 0.00 0.00
#> TCGA.VS.A9V4.01 2 0.3586 0.72975 0.00 0.78 0.00 0.00 0.06 0.04 0.00 0.12
#> TCGA.VS.AA62.01 4 0.1275 0.79508 0.00 0.00 0.00 0.94 0.02 0.00 0.00 0.04
#> TCGA.C5.A1M6.01 3 0.0808 0.87244 0.00 0.00 0.96 0.00 0.00 0.04 0.00 0.00
#> TCGA.C5.A1BJ.01 1 0.5103 -0.11728 0.44 0.00 0.00 0.22 0.00 0.00 0.00 0.34
#> TCGA.C5.A1BF.01 6 0.2569 0.72777 0.16 0.00 0.02 0.00 0.00 0.82 0.00 0.00
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)
consensus_heatmap(res, k = 7)
consensus_heatmap(res, k = 8)
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)
membership_heatmap(res, k = 7)
membership_heatmap(res, k = 8)
As soon as the classes for columns are determined, the signatures that are significantly different between subgroups can be looked for. Following are the heatmaps for signatures.
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)
get_signatures(res, k = 7)
get_signatures(res, k = 8)
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 (which is done by automatically selecting number of clusters).If there are too many signatures, top_signatures = ... can be set to only show the
signatures with the highest FDRs:
# code only for demonstration
# e.g. to show the top 500 most significant rows
tb = get_signature(res, k = ..., top_signatures = 500)
If the signatures are defined as these which are uniquely high in current group, diff_method argument
can be set to "uniquely_high_in_one_group":
# code only for demonstration
tb = get_signature(res, k = ..., diff_method = "uniquely_high_in_one_group")
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")
dimension_reduction(res, k = 7, method = "UMAP")
dimension_reduction(res, k = 8, method = "UMAP")
Following heatmap shows how subgroups are split when increasing k:
collect_classes(res)
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.
Parent node: Node011. Child nodes: Node01111-leaf , Node01112-leaf , Node01113-leaf , Node01131-leaf , Node01132-leaf , Node01133-leaf , Node01211-leaf , Node01212-leaf , Node01311-leaf , Node01312-leaf , Node01313-leaf , Node02111 , Node02112-leaf , Node02221 , Node02222-leaf , Node03111-leaf , Node03112 .
The object with results only for a single top-value method and a single partitioning method can be extracted as:
res = res_rh["0111"]
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, 7, 8.
#> On a matrix with 30000 rows and 32 columns.
#> Top rows (1000) are extracted by 'ATC' method.
#> Subgroups are detected by 'skmeans' method.
#> Performed in total 350 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_partitions"
#> [7] "compare_signatures" "consensus_heatmap" "dimension_reduction"
#> [10] "functional_enrichment" "get_anno_col" "get_anno"
#> [13] "get_classes" "get_consensus" "get_matrix"
#> [16] "get_membership" "get_param" "get_signatures"
#> [19] "get_stats" "is_best_k" "is_stable_k"
#> [22] "membership_heatmap" "ncol" "nrow"
#> [25] "plot_ecdf" "predict_classes" "rownames"
#> [28] "select_partition_number" "show" "suggest_best_k"
#> [31] "test_to_known_factors" "top_rows_heatmap"
collect_plots() function collects all the plots made from res for all k (number of subgroups)
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, higher 1-PAC score, higher mean silhouette score or higher
concordance corresponds to better partition. Rand index and Jaccard index
measure how similar the current partition is compared to partition with k-1.
If they are too similar, we won't accept k is better than k-1.
select_partition_number(res)
The numeric values for all these statistics can be obtained by get_stats().
get_stats(res)
#> k 1-PAC mean_silhouette concordance area_increased Rand Jaccard
#> 2 2 1.000 1.000 1.000 0.4844 0.516 0.516
#> 3 3 1.000 0.999 0.999 0.4113 0.768 0.564
#> 4 4 0.979 0.904 0.975 0.0340 0.980 0.936
#> 5 5 0.892 0.887 0.932 0.0634 0.923 0.752
#> 6 6 0.770 0.724 0.843 0.0494 1.000 1.000
#> 7 7 0.738 0.655 0.809 0.0371 0.986 0.942
#> 8 8 0.752 0.570 0.780 0.0271 0.903 0.600
suggest_best_k() suggests the best \(k\) based on these statistics. The rules are as follows:
suggest_best_k(res)
#> [1] 3
#> attr(,"optional")
#> [1] 2
There is also optional best \(k\) = 2 that is worth to check.
Following is 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 subgroup
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
#> TCGA.DG.A2KJ.01 2 0 1 0 1
#> TCGA.MY.A5BE.01 2 0 1 0 1
#> TCGA.VS.A8QH.01 2 0 1 0 1
#> TCGA.C5.A907.01 1 0 1 1 0
#> TCGA.C5.A7UC.01 1 0 1 1 0
#> TCGA.MU.A51Y.01 2 0 1 0 1
#> TCGA.UC.A7PD.01 1 0 1 1 0
#> TCGA.VS.A8QM.01 2 0 1 0 1
#> TCGA.EA.A3HU.01 2 0 1 0 1
#> TCGA.VS.A94X.01 1 0 1 1 0
#> TCGA.C5.A3HF.01 2 0 1 0 1
#> TCGA.MY.A913.01 1 0 1 1 0
#> TCGA.EX.A8YF.01 2 0 1 0 1
#> TCGA.MA.AA3Y.01 1 0 1 1 0
#> TCGA.HG.A2PA.01 2 0 1 0 1
#> TCGA.RA.A741.01 2 0 1 0 1
#> TCGA.C5.A2LT.01 1 0 1 1 0
#> TCGA.EK.A2GZ.01 2 0 1 0 1
#> TCGA.HM.A3JK.01 2 0 1 0 1
#> TCGA.EA.A1QS.01 2 0 1 0 1
#> TCGA.EX.A3L1.01 1 0 1 1 0
#> TCGA.VS.A959.01 2 0 1 0 1
#> TCGA.LP.A4AX.01 1 0 1 1 0
#> TCGA.VS.A9UH.01 1 0 1 1 0
#> TCGA.VS.A9UB.01 1 0 1 1 0
#> TCGA.LP.A4AU.01 2 0 1 0 1
#> TCGA.R2.A69V.01 2 0 1 0 1
#> TCGA.VS.A9UP.01 2 0 1 0 1
#> TCGA.ZJ.AAX8.01 2 0 1 0 1
#> TCGA.ZJ.AAXF.01 2 0 1 0 1
#> TCGA.VS.AA62.01 1 0 1 1 0
#> TCGA.C5.A1BJ.01 2 0 1 0 1
cbind(get_classes(res, k = 3), get_membership(res, k = 3))
#> class entropy silhouette p1 p2 p3
#> TCGA.DG.A2KJ.01 3 0.0000 0.997 0 0.00 1.00
#> TCGA.MY.A5BE.01 2 0.0000 1.000 0 1.00 0.00
#> TCGA.VS.A8QH.01 3 0.0000 0.997 0 0.00 1.00
#> TCGA.C5.A907.01 3 0.0000 0.997 0 0.00 1.00
#> TCGA.C5.A7UC.01 1 0.0000 1.000 1 0.00 0.00
#> TCGA.MU.A51Y.01 2 0.0000 1.000 0 1.00 0.00
#> TCGA.UC.A7PD.01 1 0.0000 1.000 1 0.00 0.00
#> TCGA.VS.A8QM.01 2 0.0000 1.000 0 1.00 0.00
#> TCGA.EA.A3HU.01 2 0.0000 1.000 0 1.00 0.00
#> TCGA.VS.A94X.01 1 0.0000 1.000 1 0.00 0.00
#> TCGA.C5.A3HF.01 3 0.0000 0.997 0 0.00 1.00
#> TCGA.MY.A913.01 1 0.0000 1.000 1 0.00 0.00
#> TCGA.EX.A8YF.01 3 0.0000 0.997 0 0.00 1.00
#> TCGA.MA.AA3Y.01 1 0.0000 1.000 1 0.00 0.00
#> TCGA.HG.A2PA.01 2 0.0000 1.000 0 1.00 0.00
#> TCGA.RA.A741.01 2 0.0000 1.000 0 1.00 0.00
#> TCGA.C5.A2LT.01 1 0.0000 1.000 1 0.00 0.00
#> TCGA.EK.A2GZ.01 2 0.0000 1.000 0 1.00 0.00
#> TCGA.HM.A3JK.01 2 0.0000 1.000 0 1.00 0.00
#> TCGA.EA.A1QS.01 2 0.0000 1.000 0 1.00 0.00
#> TCGA.EX.A3L1.01 1 0.0000 1.000 1 0.00 0.00
#> TCGA.VS.A959.01 3 0.0000 0.997 0 0.00 1.00
#> TCGA.LP.A4AX.01 1 0.0000 1.000 1 0.00 0.00
#> TCGA.VS.A9UH.01 1 0.0000 1.000 1 0.00 0.00
#> TCGA.VS.A9UB.01 1 0.0000 1.000 1 0.00 0.00
#> TCGA.LP.A4AU.01 3 0.0000 0.997 0 0.00 1.00
#> TCGA.R2.A69V.01 3 0.0892 0.979 0 0.02 0.98
#> TCGA.VS.A9UP.01 3 0.0000 0.997 0 0.00 1.00
#> TCGA.ZJ.AAX8.01 2 0.0000 1.000 0 1.00 0.00
#> TCGA.ZJ.AAXF.01 2 0.0000 1.000 0 1.00 0.00
#> TCGA.VS.AA62.01 1 0.0000 1.000 1 0.00 0.00
#> TCGA.C5.A1BJ.01 2 0.0000 1.000 0 1.00 0.00
cbind(get_classes(res, k = 4), get_membership(res, k = 4))
#> class entropy silhouette p1 p2 p3 p4
#> TCGA.DG.A2KJ.01 3 0.0000 0.920 0.00 0.00 1.00 0.00
#> TCGA.MY.A5BE.01 2 0.0000 0.998 0.00 1.00 0.00 0.00
#> TCGA.VS.A8QH.01 3 0.0000 0.920 0.00 0.00 1.00 0.00
#> TCGA.C5.A907.01 3 0.0000 0.920 0.00 0.00 1.00 0.00
#> TCGA.C5.A7UC.01 4 0.0707 0.000 0.02 0.00 0.00 0.98
#> TCGA.MU.A51Y.01 2 0.0000 0.998 0.00 1.00 0.00 0.00
#> TCGA.UC.A7PD.01 1 0.3172 0.812 0.84 0.00 0.00 0.16
#> TCGA.VS.A8QM.01 2 0.0000 0.998 0.00 1.00 0.00 0.00
#> TCGA.EA.A3HU.01 2 0.0000 0.998 0.00 1.00 0.00 0.00
#> TCGA.VS.A94X.01 1 0.0707 0.962 0.98 0.00 0.00 0.02
#> TCGA.C5.A3HF.01 3 0.0000 0.920 0.00 0.00 1.00 0.00
#> TCGA.MY.A913.01 1 0.0707 0.962 0.98 0.00 0.00 0.02
#> TCGA.EX.A8YF.01 3 0.0000 0.920 0.00 0.00 1.00 0.00
#> TCGA.MA.AA3Y.01 1 0.0000 0.966 1.00 0.00 0.00 0.00
#> TCGA.HG.A2PA.01 2 0.0000 0.998 0.00 1.00 0.00 0.00
#> TCGA.RA.A741.01 2 0.0000 0.998 0.00 1.00 0.00 0.00
#> TCGA.C5.A2LT.01 1 0.2011 0.923 0.92 0.00 0.00 0.08
#> TCGA.EK.A2GZ.01 2 0.0000 0.998 0.00 1.00 0.00 0.00
#> TCGA.HM.A3JK.01 2 0.0000 0.998 0.00 1.00 0.00 0.00
#> TCGA.EA.A1QS.01 2 0.0707 0.979 0.00 0.98 0.00 0.02
#> TCGA.EX.A3L1.01 1 0.0000 0.966 1.00 0.00 0.00 0.00
#> TCGA.VS.A959.01 3 0.0000 0.920 0.00 0.00 1.00 0.00
#> TCGA.LP.A4AX.01 1 0.0000 0.966 1.00 0.00 0.00 0.00
#> TCGA.VS.A9UH.01 1 0.0000 0.966 1.00 0.00 0.00 0.00
#> TCGA.VS.A9UB.01 1 0.0707 0.962 0.98 0.00 0.00 0.02
#> TCGA.LP.A4AU.01 3 0.0000 0.920 0.00 0.00 1.00 0.00
#> TCGA.R2.A69V.01 3 0.4977 0.151 0.46 0.00 0.54 0.00
#> TCGA.VS.A9UP.01 3 0.0000 0.920 0.00 0.00 1.00 0.00
#> TCGA.ZJ.AAX8.01 2 0.0000 0.998 0.00 1.00 0.00 0.00
#> TCGA.ZJ.AAXF.01 2 0.0000 0.998 0.00 1.00 0.00 0.00
#> TCGA.VS.AA62.01 1 0.0000 0.966 1.00 0.00 0.00 0.00
#> TCGA.C5.A1BJ.01 2 0.0000 0.998 0.00 1.00 0.00 0.00
cbind(get_classes(res, k = 5), get_membership(res, k = 5))
#> class entropy silhouette p1 p2 p3 p4 p5
#> TCGA.DG.A2KJ.01 3 0.0000 0.980 0.00 0.00 1.00 0.00 0.00
#> TCGA.MY.A5BE.01 2 0.1043 0.963 0.00 0.96 0.00 0.00 0.04
#> TCGA.VS.A8QH.01 3 0.0000 0.980 0.00 0.00 1.00 0.00 0.00
#> TCGA.C5.A907.01 3 0.2020 0.901 0.00 0.00 0.90 0.00 0.10
#> TCGA.C5.A7UC.01 4 0.0000 0.000 0.00 0.00 0.00 1.00 0.00
#> TCGA.MU.A51Y.01 2 0.0000 0.966 0.00 1.00 0.00 0.00 0.00
#> TCGA.UC.A7PD.01 1 0.3513 0.667 0.80 0.00 0.00 0.18 0.02
#> TCGA.VS.A8QM.01 2 0.1043 0.963 0.00 0.96 0.00 0.00 0.04
#> TCGA.EA.A3HU.01 2 0.1043 0.963 0.00 0.96 0.00 0.00 0.04
#> TCGA.VS.A94X.01 5 0.3274 0.865 0.22 0.00 0.00 0.00 0.78
#> TCGA.C5.A3HF.01 3 0.0000 0.980 0.00 0.00 1.00 0.00 0.00
#> TCGA.MY.A913.01 5 0.3796 0.920 0.30 0.00 0.00 0.00 0.70
#> TCGA.EX.A8YF.01 3 0.0609 0.970 0.00 0.00 0.98 0.00 0.02
#> TCGA.MA.AA3Y.01 1 0.0000 0.879 1.00 0.00 0.00 0.00 0.00
#> TCGA.HG.A2PA.01 2 0.0000 0.966 0.00 1.00 0.00 0.00 0.00
#> TCGA.RA.A741.01 2 0.0000 0.966 0.00 1.00 0.00 0.00 0.00
#> TCGA.C5.A2LT.01 5 0.4921 0.863 0.34 0.00 0.00 0.04 0.62
#> TCGA.EK.A2GZ.01 2 0.0000 0.966 0.00 1.00 0.00 0.00 0.00
#> TCGA.HM.A3JK.01 2 0.1732 0.914 0.00 0.92 0.00 0.00 0.08
#> TCGA.EA.A1QS.01 2 0.1732 0.914 0.00 0.92 0.00 0.00 0.08
#> TCGA.EX.A3L1.01 1 0.0000 0.879 1.00 0.00 0.00 0.00 0.00
#> TCGA.VS.A959.01 3 0.0609 0.964 0.00 0.00 0.98 0.00 0.02
#> TCGA.LP.A4AX.01 1 0.0000 0.879 1.00 0.00 0.00 0.00 0.00
#> TCGA.VS.A9UH.01 1 0.0000 0.879 1.00 0.00 0.00 0.00 0.00
#> TCGA.VS.A9UB.01 5 0.3796 0.917 0.30 0.00 0.00 0.00 0.70
#> TCGA.LP.A4AU.01 3 0.0000 0.980 0.00 0.00 1.00 0.00 0.00
#> TCGA.R2.A69V.01 1 0.5236 0.535 0.72 0.06 0.18 0.00 0.04
#> TCGA.VS.A9UP.01 3 0.0000 0.980 0.00 0.00 1.00 0.00 0.00
#> TCGA.ZJ.AAX8.01 2 0.1043 0.963 0.00 0.96 0.00 0.00 0.04
#> TCGA.ZJ.AAXF.01 2 0.1043 0.963 0.00 0.96 0.00 0.00 0.04
#> TCGA.VS.AA62.01 1 0.0000 0.879 1.00 0.00 0.00 0.00 0.00
#> TCGA.C5.A1BJ.01 2 0.0000 0.966 0.00 1.00 0.00 0.00 0.00
cbind(get_classes(res, k = 6), get_membership(res, k = 6))
#> class entropy silhouette p1 p2 p3 p4 p5 p6
#> TCGA.DG.A2KJ.01 3 0.0000 0.855 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.MY.A5BE.01 2 0.3309 0.758 0.00 0.72 0.00 0.00 0.28 0.00
#> TCGA.VS.A8QH.01 3 0.0000 0.855 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.C5.A907.01 3 0.4845 0.417 0.00 0.00 0.54 0.00 0.40 0.06
#> TCGA.C5.A7UC.01 4 0.0000 0.000 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.MU.A51Y.01 2 0.0937 0.766 0.00 0.96 0.00 0.00 0.04 0.00
#> TCGA.UC.A7PD.01 1 0.2981 0.662 0.82 0.00 0.00 0.16 0.00 0.02
#> TCGA.VS.A8QM.01 2 0.3198 0.772 0.00 0.74 0.00 0.00 0.26 0.00
#> TCGA.EA.A3HU.01 2 0.2793 0.789 0.00 0.80 0.00 0.00 0.20 0.00
#> TCGA.VS.A94X.01 6 0.2581 0.738 0.12 0.00 0.00 0.00 0.02 0.86
#> TCGA.C5.A3HF.01 3 0.0000 0.855 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.MY.A913.01 6 0.3499 0.849 0.32 0.00 0.00 0.00 0.00 0.68
#> TCGA.EX.A8YF.01 3 0.1807 0.836 0.00 0.00 0.92 0.00 0.06 0.02
#> TCGA.MA.AA3Y.01 1 0.0000 0.824 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.HG.A2PA.01 2 0.0937 0.766 0.00 0.96 0.00 0.00 0.04 0.00
#> TCGA.RA.A741.01 2 0.2454 0.794 0.00 0.84 0.00 0.00 0.16 0.00
#> TCGA.C5.A2LT.01 6 0.3499 0.862 0.32 0.00 0.00 0.00 0.00 0.68
#> TCGA.EK.A2GZ.01 2 0.0000 0.780 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.HM.A3JK.01 2 0.4462 0.494 0.00 0.66 0.00 0.00 0.28 0.06
#> TCGA.EA.A1QS.01 2 0.4462 0.494 0.00 0.66 0.00 0.00 0.28 0.06
#> TCGA.EX.A3L1.01 1 0.0000 0.824 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.VS.A959.01 3 0.3198 0.615 0.00 0.00 0.74 0.00 0.26 0.00
#> TCGA.LP.A4AX.01 1 0.0547 0.827 0.98 0.00 0.00 0.00 0.00 0.02
#> TCGA.VS.A9UH.01 1 0.0547 0.827 0.98 0.00 0.00 0.00 0.00 0.02
#> TCGA.VS.A9UB.01 6 0.3076 0.868 0.24 0.00 0.00 0.00 0.00 0.76
#> TCGA.LP.A4AU.01 3 0.1556 0.837 0.00 0.00 0.92 0.00 0.08 0.00
#> TCGA.R2.A69V.01 1 0.6642 0.214 0.50 0.14 0.04 0.00 0.30 0.02
#> TCGA.VS.A9UP.01 3 0.1556 0.818 0.00 0.00 0.92 0.00 0.08 0.00
#> TCGA.ZJ.AAX8.01 2 0.3076 0.781 0.00 0.76 0.00 0.00 0.24 0.00
#> TCGA.ZJ.AAXF.01 2 0.3198 0.772 0.00 0.74 0.00 0.00 0.26 0.00
#> TCGA.VS.AA62.01 1 0.0547 0.827 0.98 0.00 0.00 0.00 0.00 0.02
#> TCGA.C5.A1BJ.01 2 0.0000 0.780 0.00 1.00 0.00 0.00 0.00 0.00
cbind(get_classes(res, k = 7), get_membership(res, k = 7))
#> class entropy silhouette p1 p2 p3 p4 p5 p6 p7
#> TCGA.DG.A2KJ.01 3 0.0000 0.901 0.00 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.MY.A5BE.01 5 0.3546 0.617 0.00 0.46 0.00 0.00 0.54 0.00 0.00
#> TCGA.VS.A8QH.01 3 0.0504 0.899 0.00 0.00 0.98 0.00 0.00 0.00 0.02
#> TCGA.C5.A907.01 7 0.2081 0.000 0.00 0.00 0.14 0.00 0.00 0.00 0.86
#> TCGA.C5.A7UC.01 4 0.0000 0.000 0.00 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.MU.A51Y.01 5 0.0504 0.665 0.00 0.02 0.00 0.00 0.98 0.00 0.00
#> TCGA.UC.A7PD.01 1 0.4966 0.552 0.68 0.12 0.00 0.16 0.00 0.02 0.02
#> TCGA.VS.A8QM.01 5 0.3546 0.617 0.00 0.46 0.00 0.00 0.54 0.00 0.00
#> TCGA.EA.A3HU.01 5 0.2832 0.686 0.00 0.24 0.00 0.00 0.76 0.00 0.00
#> TCGA.VS.A94X.01 6 0.0863 0.591 0.00 0.04 0.00 0.00 0.00 0.96 0.00
#> TCGA.C5.A3HF.01 3 0.0504 0.898 0.00 0.00 0.98 0.00 0.00 0.00 0.02
#> TCGA.MY.A913.01 6 0.4211 0.778 0.26 0.04 0.00 0.00 0.00 0.68 0.02
#> TCGA.EX.A8YF.01 3 0.1671 0.855 0.00 0.00 0.90 0.00 0.00 0.00 0.10
#> TCGA.MA.AA3Y.01 1 0.1166 0.799 0.94 0.06 0.00 0.00 0.00 0.00 0.00
#> TCGA.HG.A2PA.01 5 0.0504 0.665 0.00 0.02 0.00 0.00 0.98 0.00 0.00
#> TCGA.RA.A741.01 5 0.3745 0.673 0.00 0.26 0.00 0.00 0.70 0.00 0.04
#> TCGA.C5.A2LT.01 6 0.4033 0.774 0.22 0.08 0.00 0.00 0.00 0.70 0.00
#> TCGA.EK.A2GZ.01 5 0.0000 0.672 0.00 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.HM.A3JK.01 5 0.4070 0.313 0.00 0.34 0.00 0.00 0.62 0.00 0.04
#> TCGA.EA.A1QS.01 5 0.4070 0.313 0.00 0.34 0.00 0.00 0.62 0.00 0.04
#> TCGA.EX.A3L1.01 1 0.1166 0.799 0.94 0.06 0.00 0.00 0.00 0.00 0.00
#> TCGA.VS.A959.01 3 0.2745 0.753 0.00 0.16 0.82 0.00 0.00 0.00 0.02
#> TCGA.LP.A4AX.01 1 0.0000 0.808 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.VS.A9UH.01 1 0.0000 0.808 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.VS.A9UB.01 6 0.2708 0.783 0.22 0.00 0.00 0.00 0.00 0.78 0.00
#> TCGA.LP.A4AU.01 3 0.1433 0.868 0.00 0.00 0.92 0.00 0.00 0.00 0.08
#> TCGA.R2.A69V.01 1 0.4244 0.241 0.54 0.42 0.00 0.00 0.04 0.00 0.00
#> TCGA.VS.A9UP.01 3 0.1664 0.870 0.00 0.06 0.92 0.00 0.00 0.00 0.02
#> TCGA.ZJ.AAX8.01 5 0.3459 0.646 0.00 0.40 0.00 0.00 0.60 0.00 0.00
#> TCGA.ZJ.AAXF.01 5 0.3546 0.617 0.00 0.46 0.00 0.00 0.54 0.00 0.00
#> TCGA.VS.AA62.01 1 0.0000 0.808 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.C5.A1BJ.01 5 0.0863 0.681 0.00 0.04 0.00 0.00 0.96 0.00 0.00
cbind(get_classes(res, k = 8), get_membership(res, k = 8))
#> class entropy silhouette p1 p2 p3 p4 p5 p6 p7 p8
#> TCGA.DG.A2KJ.01 3 0.0000 0.8223 0.00 0.00 1.00 0.0 0.00 0.00 0.00 0.00
#> TCGA.MY.A5BE.01 5 0.0471 0.6824 0.02 0.00 0.00 0.0 0.98 0.00 0.00 0.00
#> TCGA.VS.A8QH.01 3 0.1091 0.8097 0.00 0.00 0.94 0.0 0.00 0.00 0.06 0.00
#> TCGA.C5.A907.01 7 0.0808 0.0000 0.00 0.00 0.04 0.0 0.00 0.00 0.96 0.00
#> TCGA.C5.A7UC.01 4 0.0000 0.0000 0.00 0.00 0.00 1.0 0.00 0.00 0.00 0.00
#> TCGA.MU.A51Y.01 2 0.3142 0.6350 0.00 0.64 0.00 0.0 0.36 0.00 0.00 0.00
#> TCGA.UC.A7PD.01 8 0.6234 0.2694 0.26 0.06 0.00 0.1 0.00 0.04 0.02 0.52
#> TCGA.VS.A8QM.01 5 0.0000 0.6912 0.00 0.00 0.00 0.0 1.00 0.00 0.00 0.00
#> TCGA.EA.A3HU.01 5 0.2938 0.2302 0.00 0.30 0.00 0.0 0.70 0.00 0.00 0.00
#> TCGA.VS.A94X.01 6 0.3193 0.2197 0.38 0.00 0.00 0.0 0.00 0.62 0.00 0.00
#> TCGA.C5.A3HF.01 3 0.0000 0.8223 0.00 0.00 1.00 0.0 0.00 0.00 0.00 0.00
#> TCGA.MY.A913.01 6 0.3774 0.6659 0.08 0.00 0.00 0.0 0.00 0.70 0.00 0.22
#> TCGA.EX.A8YF.01 3 0.2534 0.6842 0.00 0.00 0.78 0.0 0.00 0.00 0.22 0.00
#> TCGA.MA.AA3Y.01 8 0.0471 0.8379 0.02 0.00 0.00 0.0 0.00 0.00 0.00 0.98
#> TCGA.HG.A2PA.01 2 0.3142 0.6350 0.00 0.64 0.00 0.0 0.36 0.00 0.00 0.00
#> TCGA.RA.A741.01 5 0.4247 0.0506 0.10 0.28 0.00 0.0 0.62 0.00 0.00 0.00
#> TCGA.C5.A2LT.01 6 0.4621 0.5606 0.08 0.02 0.00 0.0 0.00 0.58 0.00 0.32
#> TCGA.EK.A2GZ.01 2 0.3272 0.5698 0.00 0.58 0.00 0.0 0.42 0.00 0.00 0.00
#> TCGA.HM.A3JK.01 2 0.2547 0.4355 0.12 0.84 0.00 0.0 0.04 0.00 0.00 0.00
#> TCGA.EA.A1QS.01 2 0.2725 0.4169 0.14 0.82 0.00 0.0 0.04 0.00 0.00 0.00
#> TCGA.EX.A3L1.01 8 0.0471 0.8379 0.02 0.00 0.00 0.0 0.00 0.00 0.00 0.98
#> TCGA.VS.A959.01 3 0.4096 0.5605 0.06 0.00 0.68 0.0 0.24 0.00 0.02 0.00
#> TCGA.LP.A4AX.01 8 0.1091 0.8329 0.00 0.00 0.00 0.0 0.00 0.06 0.00 0.94
#> TCGA.VS.A9UH.01 8 0.0808 0.8406 0.00 0.00 0.00 0.0 0.00 0.04 0.00 0.96
#> TCGA.VS.A9UB.01 6 0.2114 0.6667 0.00 0.00 0.00 0.0 0.00 0.84 0.00 0.16
#> TCGA.LP.A4AU.01 3 0.3454 0.7313 0.04 0.00 0.80 0.0 0.02 0.00 0.12 0.02
#> TCGA.R2.A69V.01 5 0.4050 0.2048 0.06 0.00 0.00 0.0 0.60 0.00 0.00 0.34
#> TCGA.VS.A9UP.01 3 0.2348 0.7763 0.04 0.00 0.88 0.0 0.06 0.00 0.02 0.00
#> TCGA.ZJ.AAX8.01 5 0.1091 0.6569 0.00 0.06 0.00 0.0 0.94 0.00 0.00 0.00
#> TCGA.ZJ.AAXF.01 5 0.0000 0.6912 0.00 0.00 0.00 0.0 1.00 0.00 0.00 0.00
#> TCGA.VS.AA62.01 8 0.1091 0.8304 0.00 0.00 0.00 0.0 0.00 0.06 0.00 0.94
#> TCGA.C5.A1BJ.01 2 0.3272 0.5699 0.00 0.58 0.00 0.0 0.42 0.00 0.00 0.00
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)
consensus_heatmap(res, k = 7)
consensus_heatmap(res, k = 8)
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)
membership_heatmap(res, k = 7)
membership_heatmap(res, k = 8)
As soon as the classes for columns are determined, the signatures that are significantly different between subgroups can be looked for. Following are the heatmaps for signatures.
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)
get_signatures(res, k = 7)
get_signatures(res, k = 8)
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 (which is done by automatically selecting number of clusters).If there are too many signatures, top_signatures = ... can be set to only show the
signatures with the highest FDRs:
# code only for demonstration
# e.g. to show the top 500 most significant rows
tb = get_signature(res, k = ..., top_signatures = 500)
If the signatures are defined as these which are uniquely high in current group, diff_method argument
can be set to "uniquely_high_in_one_group":
# code only for demonstration
tb = get_signature(res, k = ..., diff_method = "uniquely_high_in_one_group")
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")
dimension_reduction(res, k = 7, method = "UMAP")
dimension_reduction(res, k = 8, method = "UMAP")
Following heatmap shows how subgroups are split when increasing k:
collect_classes(res)
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.
Parent node: Node011. Child nodes: Node01111-leaf , Node01112-leaf , Node01113-leaf , Node01131-leaf , Node01132-leaf , Node01133-leaf , Node01211-leaf , Node01212-leaf , Node01311-leaf , Node01312-leaf , Node01313-leaf , Node02111 , Node02112-leaf , Node02221 , Node02222-leaf , Node03111-leaf , Node03112 .
The object with results only for a single top-value method and a single partitioning method can be extracted as:
res = res_rh["0113"]
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, 7, 8.
#> On a matrix with 30000 rows and 16 columns.
#> Top rows (1000) are extracted by 'ATC' method.
#> Subgroups are detected by 'skmeans' method.
#> Performed in total 350 partitions by row resampling.
#> Best k for subgroups seems to be 4.
#>
#> Following methods can be applied to this 'ConsensusPartition' object:
#> [1] "cola_report" "collect_classes" "collect_plots"
#> [4] "collect_stats" "colnames" "compare_partitions"
#> [7] "compare_signatures" "consensus_heatmap" "dimension_reduction"
#> [10] "functional_enrichment" "get_anno_col" "get_anno"
#> [13] "get_classes" "get_consensus" "get_matrix"
#> [16] "get_membership" "get_param" "get_signatures"
#> [19] "get_stats" "is_best_k" "is_stable_k"
#> [22] "membership_heatmap" "ncol" "nrow"
#> [25] "plot_ecdf" "predict_classes" "rownames"
#> [28] "select_partition_number" "show" "suggest_best_k"
#> [31] "test_to_known_factors" "top_rows_heatmap"
collect_plots() function collects all the plots made from res for all k (number of subgroups)
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, higher 1-PAC score, higher mean silhouette score or higher
concordance corresponds to better partition. Rand index and Jaccard index
measure how similar the current partition is compared to partition with k-1.
If they are too similar, we won't accept k is better than k-1.
select_partition_number(res)
The numeric values for all these statistics can be obtained by get_stats().
get_stats(res)
#> k 1-PAC mean_silhouette concordance area_increased Rand Jaccard
#> 2 2 1.000 1.000 1.000 0.5255 0.475 0.475
#> 3 3 1.000 1.000 1.000 0.2218 0.883 0.754
#> 4 4 1.000 0.997 0.999 0.1556 0.900 0.721
#> 5 5 0.967 0.894 0.948 0.0242 0.975 0.903
#> 6 6 0.975 0.790 0.978 0.0219 0.992 0.964
#> 7 7 0.992 0.739 0.994 0.0198 0.983 0.926
#> 8 8 0.975 0.585 0.959 0.0163 0.992 0.960
suggest_best_k() suggests the best \(k\) based on these statistics. The rules are as follows:
suggest_best_k(res)
#> [1] 4
#> attr(,"optional")
#> [1] 2 3
There is also optional best \(k\) = 2 3 that is worth to check.
Following is 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 subgroup
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
#> TCGA.EK.A3GM.01 1 0 1 1 0
#> TCGA.FU.A3TX.01 2 0 1 0 1
#> TCGA.VS.A8EH.01 2 0 1 0 1
#> TCGA.VS.A8EB.01 2 0 1 0 1
#> TCGA.DG.A2KH.01 1 0 1 1 0
#> TCGA.EK.A2RM.01 1 0 1 1 0
#> TCGA.C5.A2LY.01 2 0 1 0 1
#> TCGA.JW.A5VG.01 2 0 1 0 1
#> TCGA.C5.A7CM.01 1 0 1 1 0
#> TCGA.VS.A9U6.01 2 0 1 0 1
#> TCGA.C5.A0TN.01 2 0 1 0 1
#> TCGA.C5.A1ML.01 2 0 1 0 1
#> TCGA.C5.A1MI.01 1 0 1 1 0
#> TCGA.EA.A439.01 1 0 1 1 0
#> TCGA.C5.A1M6.01 1 0 1 1 0
#> TCGA.C5.A1BF.01 2 0 1 0 1
cbind(get_classes(res, k = 3), get_membership(res, k = 3))
#> class entropy silhouette p1 p2 p3
#> TCGA.EK.A3GM.01 1 0 1 1 0 0
#> TCGA.FU.A3TX.01 3 0 1 0 0 1
#> TCGA.VS.A8EH.01 2 0 1 0 1 0
#> TCGA.VS.A8EB.01 2 0 1 0 1 0
#> TCGA.DG.A2KH.01 1 0 1 1 0 0
#> TCGA.EK.A2RM.01 1 0 1 1 0 0
#> TCGA.C5.A2LY.01 2 0 1 0 1 0
#> TCGA.JW.A5VG.01 2 0 1 0 1 0
#> TCGA.C5.A7CM.01 1 0 1 1 0 0
#> TCGA.VS.A9U6.01 2 0 1 0 1 0
#> TCGA.C5.A0TN.01 2 0 1 0 1 0
#> TCGA.C5.A1ML.01 3 0 1 0 0 1
#> TCGA.C5.A1MI.01 1 0 1 1 0 0
#> TCGA.EA.A439.01 1 0 1 1 0 0
#> TCGA.C5.A1M6.01 1 0 1 1 0 0
#> TCGA.C5.A1BF.01 2 0 1 0 1 0
cbind(get_classes(res, k = 4), get_membership(res, k = 4))
#> class entropy silhouette p1 p2 p3 p4
#> TCGA.EK.A3GM.01 1 0.0000 1.000 1 0.00 0 0.00
#> TCGA.FU.A3TX.01 3 0.0000 1.000 0 0.00 1 0.00
#> TCGA.VS.A8EH.01 2 0.0707 0.978 0 0.98 0 0.02
#> TCGA.VS.A8EB.01 4 0.0000 1.000 0 0.00 0 1.00
#> TCGA.DG.A2KH.01 1 0.0000 1.000 1 0.00 0 0.00
#> TCGA.EK.A2RM.01 1 0.0000 1.000 1 0.00 0 0.00
#> TCGA.C5.A2LY.01 2 0.0000 0.993 0 1.00 0 0.00
#> TCGA.JW.A5VG.01 4 0.0000 1.000 0 0.00 0 1.00
#> TCGA.C5.A7CM.01 1 0.0000 1.000 1 0.00 0 0.00
#> TCGA.VS.A9U6.01 2 0.0000 0.993 0 1.00 0 0.00
#> TCGA.C5.A0TN.01 4 0.0000 1.000 0 0.00 0 1.00
#> TCGA.C5.A1ML.01 3 0.0000 1.000 0 0.00 1 0.00
#> TCGA.C5.A1MI.01 1 0.0000 1.000 1 0.00 0 0.00
#> TCGA.EA.A439.01 1 0.0000 1.000 1 0.00 0 0.00
#> TCGA.C5.A1M6.01 1 0.0000 1.000 1 0.00 0 0.00
#> TCGA.C5.A1BF.01 2 0.0000 0.993 0 1.00 0 0.00
cbind(get_classes(res, k = 5), get_membership(res, k = 5))
#> class entropy silhouette p1 p2 p3 p4 p5
#> TCGA.EK.A3GM.01 1 0.000 1.000 1 0.00 0.00 0 0.00
#> TCGA.FU.A3TX.01 3 0.000 0.649 0 0.00 1.00 0 0.00
#> TCGA.VS.A8EH.01 5 0.000 0.000 0 0.00 0.00 0 1.00
#> TCGA.VS.A8EB.01 4 0.000 1.000 0 0.00 0.00 1 0.00
#> TCGA.DG.A2KH.01 1 0.000 1.000 1 0.00 0.00 0 0.00
#> TCGA.EK.A2RM.01 1 0.000 1.000 1 0.00 0.00 0 0.00
#> TCGA.C5.A2LY.01 2 0.423 1.000 0 0.58 0.00 0 0.42
#> TCGA.JW.A5VG.01 4 0.000 1.000 0 0.00 0.00 1 0.00
#> TCGA.C5.A7CM.01 1 0.000 1.000 1 0.00 0.00 0 0.00
#> TCGA.VS.A9U6.01 2 0.423 1.000 0 0.58 0.00 0 0.42
#> TCGA.C5.A0TN.01 4 0.000 1.000 0 0.00 0.00 1 0.00
#> TCGA.C5.A1ML.01 3 0.423 0.649 0 0.42 0.58 0 0.00
#> TCGA.C5.A1MI.01 1 0.000 1.000 1 0.00 0.00 0 0.00
#> TCGA.EA.A439.01 1 0.000 1.000 1 0.00 0.00 0 0.00
#> TCGA.C5.A1M6.01 1 0.000 1.000 1 0.00 0.00 0 0.00
#> TCGA.C5.A1BF.01 2 0.423 1.000 0 0.58 0.00 0 0.42
cbind(get_classes(res, k = 6), get_membership(res, k = 6))
#> class entropy silhouette p1 p2 p3 p4 p5 p6
#> TCGA.EK.A3GM.01 1 0.0000 1.000 1 0.00 0.00 0.00 0.00 0.00
#> TCGA.FU.A3TX.01 3 0.0000 0.000 0 0.00 1.00 0.00 0.00 0.00
#> TCGA.VS.A8EH.01 5 0.0000 0.000 0 0.00 0.00 0.00 1.00 0.00
#> TCGA.VS.A8EB.01 4 0.0547 0.983 0 0.00 0.00 0.98 0.00 0.02
#> TCGA.DG.A2KH.01 1 0.0000 1.000 1 0.00 0.00 0.00 0.00 0.00
#> TCGA.EK.A2RM.01 1 0.0000 1.000 1 0.00 0.00 0.00 0.00 0.00
#> TCGA.C5.A2LY.01 2 0.0937 0.912 0 0.96 0.00 0.00 0.04 0.00
#> TCGA.JW.A5VG.01 4 0.0000 0.991 0 0.00 0.00 1.00 0.00 0.00
#> TCGA.C5.A7CM.01 1 0.0000 1.000 1 0.00 0.00 0.00 0.00 0.00
#> TCGA.VS.A9U6.01 2 0.2094 0.892 0 0.90 0.00 0.00 0.08 0.02
#> TCGA.C5.A0TN.01 4 0.0000 0.991 0 0.00 0.00 1.00 0.00 0.00
#> TCGA.C5.A1ML.01 6 0.2048 0.000 0 0.00 0.12 0.00 0.00 0.88
#> TCGA.C5.A1MI.01 1 0.0000 1.000 1 0.00 0.00 0.00 0.00 0.00
#> TCGA.EA.A439.01 1 0.0000 1.000 1 0.00 0.00 0.00 0.00 0.00
#> TCGA.C5.A1M6.01 1 0.0000 1.000 1 0.00 0.00 0.00 0.00 0.00
#> TCGA.C5.A1BF.01 2 0.1556 0.866 0 0.92 0.00 0.00 0.00 0.08
cbind(get_classes(res, k = 7), get_membership(res, k = 7))
#> class entropy silhouette p1 p2 p3 p4 p5 p6 p7
#> TCGA.EK.A3GM.01 1 0.0000 1.000 1 0.00 0 0 0 0 0.00
#> TCGA.FU.A3TX.01 3 0.0000 0.000 0 0.00 1 0 0 0 0.00
#> TCGA.VS.A8EH.01 5 0.0000 0.000 0 0.00 0 0 1 0 0.00
#> TCGA.VS.A8EB.01 4 0.0000 1.000 0 0.00 0 1 0 0 0.00
#> TCGA.DG.A2KH.01 1 0.0000 1.000 1 0.00 0 0 0 0 0.00
#> TCGA.EK.A2RM.01 1 0.0000 1.000 1 0.00 0 0 0 0 0.00
#> TCGA.C5.A2LY.01 2 0.1166 0.910 0 0.94 0 0 0 0 0.06
#> TCGA.JW.A5VG.01 4 0.0000 1.000 0 0.00 0 1 0 0 0.00
#> TCGA.C5.A7CM.01 1 0.0000 1.000 1 0.00 0 0 0 0 0.00
#> TCGA.VS.A9U6.01 2 0.0863 0.911 0 0.96 0 0 0 0 0.04
#> TCGA.C5.A0TN.01 4 0.0000 1.000 0 0.00 0 1 0 0 0.00
#> TCGA.C5.A1ML.01 6 0.0000 0.000 0 0.00 0 0 0 1 0.00
#> TCGA.C5.A1MI.01 1 0.0000 1.000 1 0.00 0 0 0 0 0.00
#> TCGA.EA.A439.01 1 0.0000 1.000 1 0.00 0 0 0 0 0.00
#> TCGA.C5.A1M6.01 1 0.0000 1.000 1 0.00 0 0 0 0 0.00
#> TCGA.C5.A1BF.01 7 0.0000 0.000 0 0.00 0 0 0 0 1.00
cbind(get_classes(res, k = 8), get_membership(res, k = 8))
#> class entropy silhouette p1 p2 p3 p4 p5 p6 p7 p8
#> TCGA.EK.A3GM.01 1 0.0000 0.991 1.00 0.00 0 0.00 0 0 0.00 0.0
#> TCGA.FU.A3TX.01 3 0.0000 0.000 0.00 0.00 1 0.00 0 0 0.00 0.0
#> TCGA.VS.A8EH.01 5 0.0000 0.000 0.00 0.00 0 0.00 1 0 0.00 0.0
#> TCGA.VS.A8EB.01 4 0.2852 0.722 0.00 0.28 0 0.72 0 0 0.00 0.0
#> TCGA.DG.A2KH.01 1 0.0000 0.991 1.00 0.00 0 0.00 0 0 0.00 0.0
#> TCGA.EK.A2RM.01 1 0.0808 0.967 0.96 0.04 0 0.00 0 0 0.00 0.0
#> TCGA.C5.A2LY.01 2 0.3374 0.000 0.00 0.68 0 0.00 0 0 0.02 0.3
#> TCGA.JW.A5VG.01 4 0.0000 0.871 0.00 0.00 0 1.00 0 0 0.00 0.0
#> TCGA.C5.A7CM.01 1 0.0000 0.991 1.00 0.00 0 0.00 0 0 0.00 0.0
#> TCGA.VS.A9U6.01 8 0.0000 0.000 0.00 0.00 0 0.00 0 0 0.00 1.0
#> TCGA.C5.A0TN.01 4 0.0000 0.871 0.00 0.00 0 1.00 0 0 0.00 0.0
#> TCGA.C5.A1ML.01 6 0.0000 0.000 0.00 0.00 0 0.00 0 1 0.00 0.0
#> TCGA.C5.A1MI.01 1 0.0471 0.981 0.98 0.02 0 0.00 0 0 0.00 0.0
#> TCGA.EA.A439.01 1 0.0000 0.991 1.00 0.00 0 0.00 0 0 0.00 0.0
#> TCGA.C5.A1M6.01 1 0.0000 0.991 1.00 0.00 0 0.00 0 0 0.00 0.0
#> TCGA.C5.A1BF.01 7 0.0000 0.000 0.00 0.00 0 0.00 0 0 1.00 0.0
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)
consensus_heatmap(res, k = 7)
consensus_heatmap(res, k = 8)
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)
membership_heatmap(res, k = 7)
membership_heatmap(res, k = 8)
As soon as the classes for columns are determined, the signatures that are significantly different between subgroups can be looked for. Following are the heatmaps for signatures.
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)
get_signatures(res, k = 7)
get_signatures(res, k = 8)
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 (which is done by automatically selecting number of clusters).If there are too many signatures, top_signatures = ... can be set to only show the
signatures with the highest FDRs:
# code only for demonstration
# e.g. to show the top 500 most significant rows
tb = get_signature(res, k = ..., top_signatures = 500)
If the signatures are defined as these which are uniquely high in current group, diff_method argument
can be set to "uniquely_high_in_one_group":
# code only for demonstration
tb = get_signature(res, k = ..., diff_method = "uniquely_high_in_one_group")
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")
dimension_reduction(res, k = 7, method = "UMAP")
dimension_reduction(res, k = 8, method = "UMAP")
Following heatmap shows how subgroups are split when increasing k:
collect_classes(res)
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.
Parent node: Node01. Child nodes: Node0111 , Node0112-leaf , Node0113 , Node0121 , Node0122-leaf , Node0123-leaf , Node0131 , Node0132-leaf , Node0133-leaf , Node0134-leaf , Node0211 , Node0212-leaf , Node0221-leaf , Node0222 , Node0231-leaf , Node0232-leaf , Node0233-leaf , Node0311 , Node0312-leaf , Node0313-leaf .
The object with results only for a single top-value method and a single partitioning method can be extracted as:
res = res_rh["012"]
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, 7, 8.
#> On a matrix with 30000 rows and 31 columns.
#> Top rows (1000) are extracted by 'ATC' method.
#> Subgroups are detected by 'skmeans' method.
#> Performed in total 350 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_partitions"
#> [7] "compare_signatures" "consensus_heatmap" "dimension_reduction"
#> [10] "functional_enrichment" "get_anno_col" "get_anno"
#> [13] "get_classes" "get_consensus" "get_matrix"
#> [16] "get_membership" "get_param" "get_signatures"
#> [19] "get_stats" "is_best_k" "is_stable_k"
#> [22] "membership_heatmap" "ncol" "nrow"
#> [25] "plot_ecdf" "predict_classes" "rownames"
#> [28] "select_partition_number" "show" "suggest_best_k"
#> [31] "test_to_known_factors" "top_rows_heatmap"
collect_plots() function collects all the plots made from res for all k (number of subgroups)
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, higher 1-PAC score, higher mean silhouette score or higher
concordance corresponds to better partition. Rand index and Jaccard index
measure how similar the current partition is compared to partition with k-1.
If they are too similar, we won't accept k is better than k-1.
select_partition_number(res)
The numeric values for all these statistics can be obtained by get_stats().
get_stats(res)
#> k 1-PAC mean_silhouette concordance area_increased Rand Jaccard
#> 2 2 1.000 1.000 1.000 0.5037 0.497 0.497
#> 3 3 1.000 0.987 0.994 0.2746 0.819 0.650
#> 4 4 0.963 0.880 0.958 0.0239 0.989 0.970
#> 5 5 0.828 0.751 0.906 0.1118 0.890 0.695
#> 6 6 0.766 0.712 0.870 0.0458 0.927 0.734
#> 7 7 0.754 0.661 0.839 0.0285 0.981 0.915
#> 8 8 0.793 0.616 0.874 0.0192 0.981 0.914
suggest_best_k() suggests the best \(k\) based on these statistics. The rules are as follows:
suggest_best_k(res)
#> [1] 3
#> attr(,"optional")
#> [1] 2
There is also optional best \(k\) = 2 that is worth to check.
Following is 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 subgroup
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
#> TCGA.C5.A905.01 1 0 1 1 0
#> TCGA.ZJ.A8QR.01 1 0 1 1 0
#> TCGA.C5.A8ZZ.01 1 0 1 1 0
#> TCGA.2W.A8YY.01 2 0 1 0 1
#> TCGA.EA.A97N.01 1 0 1 1 0
#> TCGA.FU.A3HZ.01 2 0 1 0 1
#> TCGA.EA.A44S.01 1 0 1 1 0
#> TCGA.4J.AA1J.01 1 0 1 1 0
#> TCGA.C5.A7UH.01 1 0 1 1 0
#> TCGA.FU.A5XV.01 1 0 1 1 0
#> TCGA.Q1.A73S.01 2 0 1 0 1
#> TCGA.HM.A6W2.01 2 0 1 0 1
#> TCGA.JW.A5VH.01 2 0 1 0 1
#> TCGA.EK.A2PM.01 2 0 1 0 1
#> TCGA.HM.A6W2.06 2 0 1 0 1
#> TCGA.IR.A3LA.01 2 0 1 0 1
#> TCGA.FU.A2QG.01 1 0 1 1 0
#> TCGA.PN.A8MA.01 2 0 1 0 1
#> TCGA.JX.A3Q0.01 1 0 1 1 0
#> TCGA.MA.AA3X.01 1 0 1 1 0
#> TCGA.EA.A410.01 2 0 1 0 1
#> TCGA.ZJ.AB0I.01 1 0 1 1 0
#> TCGA.ZJ.AAXB.01 2 0 1 0 1
#> TCGA.DS.A1OB.01 1 0 1 1 0
#> TCGA.HG.A9SC.01 1 0 1 1 0
#> TCGA.EA.A411.01 2 0 1 0 1
#> TCGA.ZJ.AAXA.01 1 0 1 1 0
#> TCGA.UC.A7PG.06 1 0 1 1 0
#> TCGA.VS.A9UJ.01 2 0 1 0 1
#> TCGA.VS.A9UM.01 1 0 1 1 0
#> TCGA.C5.A1BN.01 1 0 1 1 0
cbind(get_classes(res, k = 3), get_membership(res, k = 3))
#> class entropy silhouette p1 p2 p3
#> TCGA.C5.A905.01 1 0.000 1.000 1.00 0.00 0.00
#> TCGA.ZJ.A8QR.01 1 0.000 1.000 1.00 0.00 0.00
#> TCGA.C5.A8ZZ.01 3 0.000 0.960 0.00 0.00 1.00
#> TCGA.2W.A8YY.01 2 0.000 1.000 0.00 1.00 0.00
#> TCGA.EA.A97N.01 1 0.000 1.000 1.00 0.00 0.00
#> TCGA.FU.A3HZ.01 2 0.000 1.000 0.00 1.00 0.00
#> TCGA.EA.A44S.01 1 0.000 1.000 1.00 0.00 0.00
#> TCGA.4J.AA1J.01 1 0.000 1.000 1.00 0.00 0.00
#> TCGA.C5.A7UH.01 1 0.000 1.000 1.00 0.00 0.00
#> TCGA.FU.A5XV.01 1 0.000 1.000 1.00 0.00 0.00
#> TCGA.Q1.A73S.01 2 0.000 1.000 0.00 1.00 0.00
#> TCGA.HM.A6W2.01 2 0.000 1.000 0.00 1.00 0.00
#> TCGA.JW.A5VH.01 2 0.000 1.000 0.00 1.00 0.00
#> TCGA.EK.A2PM.01 3 0.000 0.960 0.00 0.00 1.00
#> TCGA.HM.A6W2.06 2 0.000 1.000 0.00 1.00 0.00
#> TCGA.IR.A3LA.01 2 0.000 1.000 0.00 1.00 0.00
#> TCGA.FU.A2QG.01 1 0.000 1.000 1.00 0.00 0.00
#> TCGA.PN.A8MA.01 2 0.000 1.000 0.00 1.00 0.00
#> TCGA.JX.A3Q0.01 1 0.000 1.000 1.00 0.00 0.00
#> TCGA.MA.AA3X.01 1 0.000 1.000 1.00 0.00 0.00
#> TCGA.EA.A410.01 2 0.000 1.000 0.00 1.00 0.00
#> TCGA.ZJ.AB0I.01 1 0.000 1.000 1.00 0.00 0.00
#> TCGA.ZJ.AAXB.01 3 0.153 0.934 0.00 0.04 0.96
#> TCGA.DS.A1OB.01 3 0.000 0.960 0.00 0.00 1.00
#> TCGA.HG.A9SC.01 3 0.369 0.835 0.14 0.00 0.86
#> TCGA.EA.A411.01 3 0.000 0.960 0.00 0.00 1.00
#> TCGA.ZJ.AAXA.01 1 0.000 1.000 1.00 0.00 0.00
#> TCGA.UC.A7PG.06 1 0.000 1.000 1.00 0.00 0.00
#> TCGA.VS.A9UJ.01 2 0.000 1.000 0.00 1.00 0.00
#> TCGA.VS.A9UM.01 1 0.000 1.000 1.00 0.00 0.00
#> TCGA.C5.A1BN.01 1 0.000 1.000 1.00 0.00 0.00
cbind(get_classes(res, k = 4), get_membership(res, k = 4))
#> class entropy silhouette p1 p2 p3 p4
#> TCGA.C5.A905.01 1 0.0000 0.996 1.00 0.00 0.00 0.00
#> TCGA.ZJ.A8QR.01 1 0.0000 0.996 1.00 0.00 0.00 0.00
#> TCGA.C5.A8ZZ.01 3 0.3610 0.668 0.00 0.00 0.80 0.20
#> TCGA.2W.A8YY.01 2 0.0000 0.979 0.00 1.00 0.00 0.00
#> TCGA.EA.A97N.01 1 0.0707 0.982 0.98 0.00 0.02 0.00
#> TCGA.FU.A3HZ.01 2 0.0000 0.979 0.00 1.00 0.00 0.00
#> TCGA.EA.A44S.01 1 0.0707 0.982 0.98 0.00 0.02 0.00
#> TCGA.4J.AA1J.01 1 0.0000 0.996 1.00 0.00 0.00 0.00
#> TCGA.C5.A7UH.01 1 0.0000 0.996 1.00 0.00 0.00 0.00
#> TCGA.FU.A5XV.01 1 0.0707 0.982 0.98 0.00 0.02 0.00
#> TCGA.Q1.A73S.01 2 0.0000 0.979 0.00 1.00 0.00 0.00
#> TCGA.HM.A6W2.01 2 0.0000 0.979 0.00 1.00 0.00 0.00
#> TCGA.JW.A5VH.01 2 0.0000 0.979 0.00 1.00 0.00 0.00
#> TCGA.EK.A2PM.01 3 0.3610 0.668 0.00 0.00 0.80 0.20
#> TCGA.HM.A6W2.06 2 0.0000 0.979 0.00 1.00 0.00 0.00
#> TCGA.IR.A3LA.01 2 0.0000 0.979 0.00 1.00 0.00 0.00
#> TCGA.FU.A2QG.01 1 0.0000 0.996 1.00 0.00 0.00 0.00
#> TCGA.PN.A8MA.01 2 0.3400 0.773 0.00 0.82 0.00 0.18
#> TCGA.JX.A3Q0.01 1 0.0000 0.996 1.00 0.00 0.00 0.00
#> TCGA.MA.AA3X.01 1 0.0000 0.996 1.00 0.00 0.00 0.00
#> TCGA.EA.A410.01 2 0.0000 0.979 0.00 1.00 0.00 0.00
#> TCGA.ZJ.AB0I.01 1 0.0000 0.996 1.00 0.00 0.00 0.00
#> TCGA.ZJ.AAXB.01 4 0.3400 0.000 0.00 0.00 0.18 0.82
#> TCGA.DS.A1OB.01 3 0.0000 0.650 0.00 0.00 1.00 0.00
#> TCGA.HG.A9SC.01 3 0.4472 0.383 0.22 0.00 0.76 0.02
#> TCGA.EA.A411.01 3 0.3975 0.426 0.00 0.00 0.76 0.24
#> TCGA.ZJ.AAXA.01 1 0.0000 0.996 1.00 0.00 0.00 0.00
#> TCGA.UC.A7PG.06 1 0.0000 0.996 1.00 0.00 0.00 0.00
#> TCGA.VS.A9UJ.01 2 0.0000 0.979 0.00 1.00 0.00 0.00
#> TCGA.VS.A9UM.01 1 0.0000 0.996 1.00 0.00 0.00 0.00
#> TCGA.C5.A1BN.01 1 0.0000 0.996 1.00 0.00 0.00 0.00
cbind(get_classes(res, k = 5), get_membership(res, k = 5))
#> class entropy silhouette p1 p2 p3 p4 p5
#> TCGA.C5.A905.01 1 0.0000 0.869 1.00 0.00 0.00 0.00 0.00
#> TCGA.ZJ.A8QR.01 1 0.4126 0.386 0.62 0.00 0.00 0.00 0.38
#> TCGA.C5.A8ZZ.01 3 0.2732 0.764 0.00 0.00 0.84 0.00 0.16
#> TCGA.2W.A8YY.01 2 0.0000 0.979 0.00 1.00 0.00 0.00 0.00
#> TCGA.EA.A97N.01 5 0.3983 0.411 0.34 0.00 0.00 0.00 0.66
#> TCGA.FU.A3HZ.01 2 0.0000 0.979 0.00 1.00 0.00 0.00 0.00
#> TCGA.EA.A44S.01 5 0.0609 0.546 0.02 0.00 0.00 0.00 0.98
#> TCGA.4J.AA1J.01 1 0.0000 0.869 1.00 0.00 0.00 0.00 0.00
#> TCGA.C5.A7UH.01 1 0.1043 0.866 0.96 0.00 0.00 0.00 0.04
#> TCGA.FU.A5XV.01 5 0.4262 0.139 0.44 0.00 0.00 0.00 0.56
#> TCGA.Q1.A73S.01 2 0.0000 0.979 0.00 1.00 0.00 0.00 0.00
#> TCGA.HM.A6W2.01 2 0.0000 0.979 0.00 1.00 0.00 0.00 0.00
#> TCGA.JW.A5VH.01 2 0.0000 0.979 0.00 1.00 0.00 0.00 0.00
#> TCGA.EK.A2PM.01 3 0.0000 0.768 0.00 0.00 1.00 0.00 0.00
#> TCGA.HM.A6W2.06 2 0.0000 0.979 0.00 1.00 0.00 0.00 0.00
#> TCGA.IR.A3LA.01 2 0.0000 0.979 0.00 1.00 0.00 0.00 0.00
#> TCGA.FU.A2QG.01 1 0.1410 0.860 0.94 0.00 0.00 0.00 0.06
#> TCGA.PN.A8MA.01 2 0.2929 0.776 0.00 0.82 0.00 0.18 0.00
#> TCGA.JX.A3Q0.01 1 0.0000 0.869 1.00 0.00 0.00 0.00 0.00
#> TCGA.MA.AA3X.01 1 0.1043 0.866 0.96 0.00 0.00 0.00 0.04
#> TCGA.EA.A410.01 2 0.0000 0.979 0.00 1.00 0.00 0.00 0.00
#> TCGA.ZJ.AB0I.01 1 0.2280 0.806 0.88 0.00 0.00 0.00 0.12
#> TCGA.ZJ.AAXB.01 4 0.0000 0.491 0.00 0.00 0.00 1.00 0.00
#> TCGA.DS.A1OB.01 5 0.2732 0.376 0.00 0.00 0.16 0.00 0.84
#> TCGA.HG.A9SC.01 5 0.0609 0.531 0.00 0.00 0.02 0.00 0.98
#> TCGA.EA.A411.01 4 0.5972 0.427 0.00 0.00 0.14 0.56 0.30
#> TCGA.ZJ.AAXA.01 1 0.0000 0.869 1.00 0.00 0.00 0.00 0.00
#> TCGA.UC.A7PG.06 1 0.2280 0.817 0.88 0.00 0.00 0.00 0.12
#> TCGA.VS.A9UJ.01 2 0.0000 0.979 0.00 1.00 0.00 0.00 0.00
#> TCGA.VS.A9UM.01 1 0.0000 0.869 1.00 0.00 0.00 0.00 0.00
#> TCGA.C5.A1BN.01 1 0.4182 0.294 0.60 0.00 0.00 0.00 0.40
cbind(get_classes(res, k = 6), get_membership(res, k = 6))
#> class entropy silhouette p1 p2 p3 p4 p5 p6
#> TCGA.C5.A905.01 1 0.0000 0.9173 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.ZJ.A8QR.01 6 0.6070 0.2360 0.28 0.00 0.00 0.00 0.32 0.40
#> TCGA.C5.A8ZZ.01 3 0.4393 0.6352 0.00 0.00 0.72 0.00 0.14 0.14
#> TCGA.2W.A8YY.01 2 0.0000 0.9772 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.EA.A97N.01 5 0.4360 0.4731 0.26 0.00 0.00 0.00 0.68 0.06
#> TCGA.FU.A3HZ.01 2 0.0000 0.9772 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.EA.A44S.01 5 0.1556 0.5231 0.08 0.00 0.00 0.00 0.92 0.00
#> TCGA.4J.AA1J.01 1 0.0000 0.9173 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.C5.A7UH.01 1 0.2094 0.8673 0.90 0.00 0.00 0.00 0.08 0.02
#> TCGA.FU.A5XV.01 5 0.4462 0.4553 0.28 0.00 0.00 0.00 0.66 0.06
#> TCGA.Q1.A73S.01 2 0.0547 0.9628 0.00 0.98 0.00 0.00 0.00 0.02
#> TCGA.HM.A6W2.01 2 0.0000 0.9772 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.JW.A5VH.01 2 0.0000 0.9772 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.EK.A2PM.01 3 0.0000 0.6578 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.HM.A6W2.06 2 0.0000 0.9772 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.IR.A3LA.01 2 0.0000 0.9772 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.FU.A2QG.01 1 0.1865 0.8800 0.92 0.00 0.00 0.00 0.04 0.04
#> TCGA.PN.A8MA.01 2 0.2981 0.7840 0.00 0.82 0.00 0.16 0.00 0.02
#> TCGA.JX.A3Q0.01 1 0.0000 0.9173 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.MA.AA3X.01 1 0.2190 0.8672 0.90 0.00 0.00 0.00 0.06 0.04
#> TCGA.EA.A410.01 2 0.0000 0.9772 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.ZJ.AB0I.01 6 0.3916 0.4146 0.30 0.00 0.00 0.00 0.02 0.68
#> TCGA.ZJ.AAXB.01 4 0.0000 0.2427 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.DS.A1OB.01 5 0.4328 0.1320 0.00 0.00 0.10 0.00 0.72 0.18
#> TCGA.HG.A9SC.01 5 0.0937 0.4454 0.00 0.00 0.00 0.00 0.96 0.04
#> TCGA.EA.A411.01 4 0.7465 0.0963 0.00 0.00 0.14 0.32 0.32 0.22
#> TCGA.ZJ.AAXA.01 1 0.0000 0.9173 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.UC.A7PG.06 1 0.2728 0.8146 0.86 0.00 0.00 0.00 0.10 0.04
#> TCGA.VS.A9UJ.01 2 0.0000 0.9772 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.VS.A9UM.01 1 0.0000 0.9173 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.C5.A1BN.01 5 0.5235 0.1818 0.38 0.00 0.00 0.00 0.52 0.10
cbind(get_classes(res, k = 7), get_membership(res, k = 7))
#> class entropy silhouette p1 p2 p3 p4 p5 p6 p7
#> TCGA.C5.A905.01 1 0.000 0.8839 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.ZJ.A8QR.01 5 0.640 0.1946 0.18 0.00 0.00 0.00 0.38 0.36 0.08
#> TCGA.C5.A8ZZ.01 3 0.442 0.5409 0.00 0.00 0.50 0.00 0.02 0.02 0.46
#> TCGA.2W.A8YY.01 2 0.000 0.9598 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.EA.A97N.01 5 0.189 0.6316 0.12 0.00 0.00 0.00 0.88 0.00 0.00
#> TCGA.FU.A3HZ.01 2 0.000 0.9598 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.EA.A44S.01 5 0.101 0.5951 0.02 0.00 0.00 0.00 0.96 0.02 0.00
#> TCGA.4J.AA1J.01 1 0.000 0.8839 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.C5.A7UH.01 1 0.301 0.8074 0.82 0.00 0.00 0.00 0.12 0.06 0.00
#> TCGA.FU.A5XV.01 5 0.339 0.6091 0.20 0.00 0.00 0.00 0.76 0.04 0.00
#> TCGA.Q1.A73S.01 2 0.136 0.9140 0.00 0.94 0.00 0.00 0.00 0.02 0.04
#> TCGA.HM.A6W2.01 2 0.000 0.9598 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.JW.A5VH.01 2 0.000 0.9598 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.EK.A2PM.01 3 0.000 0.5414 0.00 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.HM.A6W2.06 2 0.000 0.9598 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.IR.A3LA.01 2 0.000 0.9598 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.FU.A2QG.01 1 0.251 0.8327 0.86 0.00 0.00 0.00 0.10 0.04 0.00
#> TCGA.PN.A8MA.01 2 0.463 0.6123 0.00 0.70 0.00 0.16 0.00 0.04 0.10
#> TCGA.JX.A3Q0.01 1 0.000 0.8839 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.MA.AA3X.01 1 0.291 0.7752 0.80 0.00 0.00 0.00 0.18 0.02 0.00
#> TCGA.EA.A410.01 2 0.000 0.9598 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.ZJ.AB0I.01 6 0.513 -0.0606 0.14 0.00 0.00 0.00 0.00 0.46 0.40
#> TCGA.ZJ.AAXB.01 4 0.000 0.0000 0.00 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.DS.A1OB.01 5 0.487 0.0927 0.00 0.00 0.06 0.00 0.54 0.38 0.02
#> TCGA.HG.A9SC.01 5 0.257 0.5109 0.00 0.00 0.00 0.00 0.84 0.14 0.02
#> TCGA.EA.A411.01 6 0.651 -0.3607 0.00 0.00 0.02 0.36 0.12 0.42 0.08
#> TCGA.ZJ.AAXA.01 1 0.000 0.8839 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.UC.A7PG.06 1 0.352 0.6385 0.70 0.00 0.00 0.00 0.28 0.02 0.00
#> TCGA.VS.A9UJ.01 2 0.000 0.9598 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.VS.A9UM.01 1 0.000 0.8839 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.C5.A1BN.01 5 0.434 0.5259 0.28 0.00 0.00 0.00 0.64 0.08 0.00
cbind(get_classes(res, k = 8), get_membership(res, k = 8))
#> class entropy silhouette p1 p2 p3 p4 p5 p6 p7 p8
#> TCGA.C5.A905.01 1 0.0000 0.8825 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.ZJ.A8QR.01 5 0.6959 0.2308 0.16 0.00 0.08 0.00 0.42 0.22 0.12 0.00
#> TCGA.C5.A8ZZ.01 3 0.2406 0.0000 0.00 0.00 0.80 0.00 0.00 0.00 0.00 0.20
#> TCGA.2W.A8YY.01 2 0.0000 0.9383 0.00 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.EA.A97N.01 5 0.1341 0.6283 0.08 0.00 0.00 0.00 0.92 0.00 0.00 0.00
#> TCGA.FU.A3HZ.01 2 0.0000 0.9383 0.00 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.EA.A44S.01 5 0.1275 0.5180 0.00 0.00 0.00 0.00 0.94 0.02 0.04 0.00
#> TCGA.4J.AA1J.01 1 0.0471 0.8737 0.98 0.00 0.00 0.00 0.00 0.02 0.00 0.00
#> TCGA.C5.A7UH.01 1 0.2267 0.7856 0.82 0.00 0.00 0.00 0.18 0.00 0.00 0.00
#> TCGA.FU.A5XV.01 5 0.2680 0.6370 0.12 0.00 0.00 0.00 0.84 0.02 0.02 0.00
#> TCGA.Q1.A73S.01 2 0.1091 0.8928 0.00 0.94 0.00 0.00 0.00 0.00 0.06 0.00
#> TCGA.HM.A6W2.01 2 0.0000 0.9383 0.00 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.JW.A5VH.01 2 0.0000 0.9383 0.00 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.EK.A2PM.01 8 0.0000 0.0000 0.00 0.00 0.00 0.00 0.00 0.00 0.00 1.00
#> TCGA.HM.A6W2.06 2 0.0000 0.9383 0.00 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.IR.A3LA.01 2 0.0000 0.9383 0.00 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.FU.A2QG.01 1 0.1804 0.8478 0.90 0.00 0.02 0.00 0.08 0.00 0.00 0.00
#> TCGA.PN.A8MA.01 2 0.5499 0.2167 0.00 0.50 0.08 0.10 0.00 0.00 0.32 0.00
#> TCGA.JX.A3Q0.01 1 0.0000 0.8825 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.MA.AA3X.01 1 0.2267 0.7830 0.82 0.00 0.00 0.00 0.18 0.00 0.00 0.00
#> TCGA.EA.A410.01 2 0.0000 0.9383 0.00 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.ZJ.AB0I.01 6 0.0471 0.0000 0.02 0.00 0.00 0.00 0.00 0.98 0.00 0.00
#> TCGA.ZJ.AAXB.01 4 0.0000 0.0000 0.00 0.00 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.DS.A1OB.01 7 0.5162 0.3555 0.00 0.00 0.10 0.00 0.36 0.00 0.50 0.04
#> TCGA.HG.A9SC.01 5 0.3808 -0.0347 0.00 0.00 0.02 0.00 0.66 0.02 0.30 0.00
#> TCGA.EA.A411.01 7 0.5602 0.2328 0.00 0.00 0.16 0.18 0.06 0.00 0.58 0.02
#> TCGA.ZJ.AAXA.01 1 0.0000 0.8825 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.UC.A7PG.06 1 0.3083 0.5140 0.66 0.00 0.00 0.00 0.34 0.00 0.00 0.00
#> TCGA.VS.A9UJ.01 2 0.0000 0.9383 0.00 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.VS.A9UM.01 1 0.0000 0.8825 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.C5.A1BN.01 5 0.4147 0.5640 0.24 0.00 0.00 0.00 0.68 0.04 0.04 0.00
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)
consensus_heatmap(res, k = 7)
consensus_heatmap(res, k = 8)
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)
membership_heatmap(res, k = 7)
membership_heatmap(res, k = 8)
As soon as the classes for columns are determined, the signatures that are significantly different between subgroups can be looked for. Following are the heatmaps for signatures.
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)
get_signatures(res, k = 7)
get_signatures(res, k = 8)
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 (which is done by automatically selecting number of clusters).If there are too many signatures, top_signatures = ... can be set to only show the
signatures with the highest FDRs:
# code only for demonstration
# e.g. to show the top 500 most significant rows
tb = get_signature(res, k = ..., top_signatures = 500)
If the signatures are defined as these which are uniquely high in current group, diff_method argument
can be set to "uniquely_high_in_one_group":
# code only for demonstration
tb = get_signature(res, k = ..., diff_method = "uniquely_high_in_one_group")
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")
dimension_reduction(res, k = 7, method = "UMAP")
dimension_reduction(res, k = 8, method = "UMAP")
Following heatmap shows how subgroups are split when increasing k:
collect_classes(res)
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.
Parent node: Node012. Child nodes: Node01111-leaf , Node01112-leaf , Node01113-leaf , Node01131-leaf , Node01132-leaf , Node01133-leaf , Node01211-leaf , Node01212-leaf , Node01311-leaf , Node01312-leaf , Node01313-leaf , Node02111 , Node02112-leaf , Node02221 , Node02222-leaf , Node03111-leaf , Node03112 .
The object with results only for a single top-value method and a single partitioning method can be extracted as:
res = res_rh["0121"]
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, 7, 8.
#> On a matrix with 30000 rows and 15 columns.
#> Top rows (1000) are extracted by 'ATC' method.
#> Subgroups are detected by 'kmeans' method.
#> Performed in total 350 partitions by row resampling.
#> Best k for subgroups seems to be 5.
#>
#> Following methods can be applied to this 'ConsensusPartition' object:
#> [1] "cola_report" "collect_classes" "collect_plots"
#> [4] "collect_stats" "colnames" "compare_partitions"
#> [7] "compare_signatures" "consensus_heatmap" "dimension_reduction"
#> [10] "functional_enrichment" "get_anno_col" "get_anno"
#> [13] "get_classes" "get_consensus" "get_matrix"
#> [16] "get_membership" "get_param" "get_signatures"
#> [19] "get_stats" "is_best_k" "is_stable_k"
#> [22] "membership_heatmap" "ncol" "nrow"
#> [25] "plot_ecdf" "predict_classes" "rownames"
#> [28] "select_partition_number" "show" "suggest_best_k"
#> [31] "test_to_known_factors" "top_rows_heatmap"
collect_plots() function collects all the plots made from res for all k (number of subgroups)
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, higher 1-PAC score, higher mean silhouette score or higher
concordance corresponds to better partition. Rand index and Jaccard index
measure how similar the current partition is compared to partition with k-1.
If they are too similar, we won't accept k is better than k-1.
select_partition_number(res)
The numeric values for all these statistics can be obtained by get_stats().
get_stats(res)
#> k 1-PAC mean_silhouette concordance area_increased Rand Jaccard
#> 2 2 1.000 1.000 1.000 0.5338 0.467 0.467
#> 3 3 0.790 0.927 0.936 0.2681 0.848 0.673
#> 4 4 0.895 0.934 0.963 0.1128 0.905 0.706
#> 5 5 0.952 0.830 0.973 0.0240 0.952 0.815
#> 6 6 0.905 0.718 0.928 0.0433 1.000 1.000
#> 7 7 0.886 0.615 0.917 0.0431 0.933 0.708
#> 8 8 0.876 0.523 0.821 0.0329 0.962 0.765
suggest_best_k() suggests the best \(k\) based on these statistics. The rules are as follows:
suggest_best_k(res)
#> [1] 5
#> attr(,"optional")
#> [1] 2
There is also optional best \(k\) = 2 that is worth to check.
Following is 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 subgroup
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
#> TCGA.C5.A905.01 1 0 1 1 0
#> TCGA.ZJ.A8QR.01 2 0 1 0 1
#> TCGA.EA.A97N.01 2 0 1 0 1
#> TCGA.EA.A44S.01 2 0 1 0 1
#> TCGA.4J.AA1J.01 2 0 1 0 1
#> TCGA.C5.A7UH.01 1 0 1 1 0
#> TCGA.FU.A5XV.01 2 0 1 0 1
#> TCGA.FU.A2QG.01 2 0 1 0 1
#> TCGA.JX.A3Q0.01 1 0 1 1 0
#> TCGA.MA.AA3X.01 1 0 1 1 0
#> TCGA.ZJ.AB0I.01 2 0 1 0 1
#> TCGA.ZJ.AAXA.01 1 0 1 1 0
#> TCGA.UC.A7PG.06 1 0 1 1 0
#> TCGA.VS.A9UM.01 1 0 1 1 0
#> TCGA.C5.A1BN.01 2 0 1 0 1
cbind(get_classes(res, k = 3), get_membership(res, k = 3))
#> class entropy silhouette p1 p2 p3
#> TCGA.C5.A905.01 1 0.000 0.964 1.00 0.00 0.00
#> TCGA.ZJ.A8QR.01 2 0.502 1.000 0.00 0.76 0.24
#> TCGA.EA.A97N.01 3 0.502 0.703 0.00 0.24 0.76
#> TCGA.EA.A44S.01 3 0.000 0.888 0.00 0.00 1.00
#> TCGA.4J.AA1J.01 3 0.000 0.888 0.00 0.00 1.00
#> TCGA.C5.A7UH.01 1 0.000 0.964 1.00 0.00 0.00
#> TCGA.FU.A5XV.01 2 0.502 1.000 0.00 0.76 0.24
#> TCGA.FU.A2QG.01 3 0.000 0.888 0.00 0.00 1.00
#> TCGA.JX.A3Q0.01 1 0.000 0.964 1.00 0.00 0.00
#> TCGA.MA.AA3X.01 1 0.000 0.964 1.00 0.00 0.00
#> TCGA.ZJ.AB0I.01 2 0.502 1.000 0.00 0.76 0.24
#> TCGA.ZJ.AAXA.01 1 0.000 0.964 1.00 0.00 0.00
#> TCGA.UC.A7PG.06 1 0.502 0.753 0.76 0.24 0.00
#> TCGA.VS.A9UM.01 1 0.000 0.964 1.00 0.00 0.00
#> TCGA.C5.A1BN.01 2 0.502 1.000 0.00 0.76 0.24
cbind(get_classes(res, k = 4), get_membership(res, k = 4))
#> class entropy silhouette p1 p2 p3 p4
#> TCGA.C5.A905.01 1 0.000 1.000 1.00 0 0.00 0.00
#> TCGA.ZJ.A8QR.01 2 0.000 1.000 0.00 1 0.00 0.00
#> TCGA.EA.A97N.01 4 0.361 0.669 0.00 0 0.20 0.80
#> TCGA.EA.A44S.01 3 0.000 0.906 0.00 0 1.00 0.00
#> TCGA.4J.AA1J.01 3 0.000 0.906 0.00 0 1.00 0.00
#> TCGA.C5.A7UH.01 1 0.000 1.000 1.00 0 0.00 0.00
#> TCGA.FU.A5XV.01 2 0.000 1.000 0.00 1 0.00 0.00
#> TCGA.FU.A2QG.01 3 0.340 0.814 0.00 0 0.82 0.18
#> TCGA.JX.A3Q0.01 1 0.000 1.000 1.00 0 0.00 0.00
#> TCGA.MA.AA3X.01 1 0.000 1.000 1.00 0 0.00 0.00
#> TCGA.ZJ.AB0I.01 2 0.000 1.000 0.00 1 0.00 0.00
#> TCGA.ZJ.AAXA.01 1 0.000 1.000 1.00 0 0.00 0.00
#> TCGA.UC.A7PG.06 4 0.340 0.709 0.18 0 0.00 0.82
#> TCGA.VS.A9UM.01 1 0.000 1.000 1.00 0 0.00 0.00
#> TCGA.C5.A1BN.01 2 0.000 1.000 0.00 1 0.00 0.00
cbind(get_classes(res, k = 5), get_membership(res, k = 5))
#> class entropy silhouette p1 p2 p3 p4 p5
#> TCGA.C5.A905.01 1 0.000 1.000 1.00 0 0.00 0.00 0.0
#> TCGA.ZJ.A8QR.01 2 0.000 1.000 0.00 1 0.00 0.00 0.0
#> TCGA.EA.A97N.01 3 0.228 0.742 0.00 0 0.88 0.12 0.0
#> TCGA.EA.A44S.01 3 0.202 0.860 0.00 0 0.90 0.00 0.1
#> TCGA.4J.AA1J.01 3 0.304 0.851 0.00 0 0.86 0.04 0.1
#> TCGA.C5.A7UH.01 1 0.000 1.000 1.00 0 0.00 0.00 0.0
#> TCGA.FU.A5XV.01 2 0.000 1.000 0.00 1 0.00 0.00 0.0
#> TCGA.FU.A2QG.01 5 0.000 0.000 0.00 0 0.00 0.00 1.0
#> TCGA.JX.A3Q0.01 1 0.000 1.000 1.00 0 0.00 0.00 0.0
#> TCGA.MA.AA3X.01 1 0.000 1.000 1.00 0 0.00 0.00 0.0
#> TCGA.ZJ.AB0I.01 2 0.000 1.000 0.00 1 0.00 0.00 0.0
#> TCGA.ZJ.AAXA.01 1 0.000 1.000 1.00 0 0.00 0.00 0.0
#> TCGA.UC.A7PG.06 4 0.104 0.000 0.04 0 0.00 0.96 0.0
#> TCGA.VS.A9UM.01 1 0.000 1.000 1.00 0 0.00 0.00 0.0
#> TCGA.C5.A1BN.01 2 0.000 1.000 0.00 1 0.00 0.00 0.0
cbind(get_classes(res, k = 6), get_membership(res, k = 6))
#> class entropy silhouette p1 p2 p3 p4 p5 p6
#> TCGA.C5.A905.01 1 0.0000 0.910 1.00 0.0 0.00 0.00 0.00 0
#> TCGA.ZJ.A8QR.01 2 0.0000 0.970 0.00 1.0 0.00 0.00 0.00 0
#> TCGA.EA.A97N.01 3 0.4609 0.490 0.00 0.0 0.54 0.42 0.04 0
#> TCGA.EA.A44S.01 3 0.0000 0.760 0.00 0.0 1.00 0.00 0.00 0
#> TCGA.4J.AA1J.01 3 0.0547 0.756 0.00 0.0 0.98 0.02 0.00 0
#> TCGA.C5.A7UH.01 1 0.3851 0.394 0.54 0.0 0.00 0.46 0.00 0
#> TCGA.FU.A5XV.01 2 0.0000 0.970 0.00 1.0 0.00 0.00 0.00 0
#> TCGA.FU.A2QG.01 5 0.0937 0.000 0.00 0.0 0.04 0.00 0.96 0
#> TCGA.JX.A3Q0.01 1 0.0000 0.910 1.00 0.0 0.00 0.00 0.00 0
#> TCGA.MA.AA3X.01 1 0.0000 0.910 1.00 0.0 0.00 0.00 0.00 0
#> TCGA.ZJ.AB0I.01 2 0.1814 0.905 0.00 0.9 0.00 0.10 0.00 0
#> TCGA.ZJ.AAXA.01 1 0.0000 0.910 1.00 0.0 0.00 0.00 0.00 0
#> TCGA.UC.A7PG.06 6 0.0000 0.000 0.00 0.0 0.00 0.00 0.00 1
#> TCGA.VS.A9UM.01 1 0.0000 0.910 1.00 0.0 0.00 0.00 0.00 0
#> TCGA.C5.A1BN.01 2 0.0000 0.970 0.00 1.0 0.00 0.00 0.00 0
cbind(get_classes(res, k = 7), get_membership(res, k = 7))
#> class entropy silhouette p1 p2 p3 p4 p5 p6 p7
#> TCGA.C5.A905.01 1 0.000 0.887 1.00 0.00 0.00 0.00 0.00 0 0.00
#> TCGA.ZJ.A8QR.01 2 0.000 0.982 0.00 1.00 0.00 0.00 0.00 0 0.00
#> TCGA.EA.A97N.01 7 0.000 0.000 0.00 0.00 0.00 0.00 0.00 0 1.00
#> TCGA.EA.A44S.01 3 0.397 0.678 0.00 0.00 0.54 0.00 0.02 0 0.44
#> TCGA.4J.AA1J.01 3 0.566 0.690 0.00 0.00 0.42 0.16 0.02 0 0.40
#> TCGA.C5.A7UH.01 4 0.242 0.000 0.18 0.00 0.00 0.82 0.00 0 0.00
#> TCGA.FU.A5XV.01 2 0.000 0.982 0.00 1.00 0.00 0.00 0.00 0 0.00
#> TCGA.FU.A2QG.01 5 0.000 0.000 0.00 0.00 0.00 0.00 1.00 0 0.00
#> TCGA.JX.A3Q0.01 1 0.341 0.416 0.62 0.00 0.38 0.00 0.00 0 0.00
#> TCGA.MA.AA3X.01 1 0.000 0.887 1.00 0.00 0.00 0.00 0.00 0 0.00
#> TCGA.ZJ.AB0I.01 2 0.136 0.944 0.00 0.94 0.04 0.02 0.00 0 0.00
#> TCGA.ZJ.AAXA.01 1 0.000 0.887 1.00 0.00 0.00 0.00 0.00 0 0.00
#> TCGA.UC.A7PG.06 6 0.000 0.000 0.00 0.00 0.00 0.00 0.00 1 0.00
#> TCGA.VS.A9UM.01 1 0.000 0.887 1.00 0.00 0.00 0.00 0.00 0 0.00
#> TCGA.C5.A1BN.01 2 0.000 0.982 0.00 1.00 0.00 0.00 0.00 0 0.00
cbind(get_classes(res, k = 8), get_membership(res, k = 8))
#> class entropy silhouette p1 p2 p3 p4 p5 p6 p7 p8
#> TCGA.C5.A905.01 1 0.0000 0.876 1.00 0.00 0.00 0.00 0.00 0 0.00 0.00
#> TCGA.ZJ.A8QR.01 2 0.0000 0.944 0.00 1.00 0.00 0.00 0.00 0 0.00 0.00
#> TCGA.EA.A97N.01 7 0.2406 0.000 0.00 0.00 0.20 0.00 0.00 0 0.80 0.00
#> TCGA.EA.A44S.01 3 0.0808 0.506 0.00 0.00 0.96 0.00 0.00 0 0.04 0.00
#> TCGA.4J.AA1J.01 3 0.3142 0.522 0.00 0.00 0.64 0.00 0.36 0 0.00 0.00
#> TCGA.C5.A7UH.01 4 0.1341 0.000 0.08 0.00 0.00 0.92 0.00 0 0.00 0.00
#> TCGA.FU.A5XV.01 2 0.0000 0.944 0.00 1.00 0.00 0.00 0.00 0 0.00 0.00
#> TCGA.FU.A2QG.01 5 0.3142 0.000 0.00 0.00 0.00 0.00 0.64 0 0.00 0.36
#> TCGA.JX.A3Q0.01 8 0.3272 0.000 0.42 0.00 0.00 0.00 0.00 0 0.00 0.58
#> TCGA.MA.AA3X.01 1 0.0000 0.876 1.00 0.00 0.00 0.00 0.00 0 0.00 0.00
#> TCGA.ZJ.AB0I.01 2 0.3185 0.820 0.00 0.82 0.00 0.08 0.00 0 0.04 0.06
#> TCGA.ZJ.AAXA.01 1 0.0000 0.876 1.00 0.00 0.00 0.00 0.00 0 0.00 0.00
#> TCGA.UC.A7PG.06 6 0.0000 0.000 0.00 0.00 0.00 0.00 0.00 1 0.00 0.00
#> TCGA.VS.A9UM.01 1 0.3154 0.539 0.78 0.00 0.00 0.00 0.00 0 0.16 0.06
#> TCGA.C5.A1BN.01 2 0.0000 0.944 0.00 1.00 0.00 0.00 0.00 0 0.00 0.00
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)
consensus_heatmap(res, k = 7)
consensus_heatmap(res, k = 8)
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)
membership_heatmap(res, k = 7)
membership_heatmap(res, k = 8)
As soon as the classes for columns are determined, the signatures that are significantly different between subgroups can be looked for. Following are the heatmaps for signatures.
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)
get_signatures(res, k = 7)
get_signatures(res, k = 8)
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 (which is done by automatically selecting number of clusters).If there are too many signatures, top_signatures = ... can be set to only show the
signatures with the highest FDRs:
# code only for demonstration
# e.g. to show the top 500 most significant rows
tb = get_signature(res, k = ..., top_signatures = 500)
If the signatures are defined as these which are uniquely high in current group, diff_method argument
can be set to "uniquely_high_in_one_group":
# code only for demonstration
tb = get_signature(res, k = ..., diff_method = "uniquely_high_in_one_group")
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")
dimension_reduction(res, k = 7, method = "UMAP")
dimension_reduction(res, k = 8, method = "UMAP")
Following heatmap shows how subgroups are split when increasing k:
collect_classes(res)
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.
Parent node: Node01. Child nodes: Node0111 , Node0112-leaf , Node0113 , Node0121 , Node0122-leaf , Node0123-leaf , Node0131 , Node0132-leaf , Node0133-leaf , Node0134-leaf , Node0211 , Node0212-leaf , Node0221-leaf , Node0222 , Node0231-leaf , Node0232-leaf , Node0233-leaf , Node0311 , Node0312-leaf , Node0313-leaf .
The object with results only for a single top-value method and a single partitioning method can be extracted as:
res = res_rh["013"]
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, 7, 8.
#> On a matrix with 30000 rows and 65 columns.
#> Top rows (1000) are extracted by 'ATC' method.
#> Subgroups are detected by 'skmeans' method.
#> Performed in total 350 partitions by row resampling.
#> Best k for subgroups seems to be 4.
#>
#> Following methods can be applied to this 'ConsensusPartition' object:
#> [1] "cola_report" "collect_classes" "collect_plots"
#> [4] "collect_stats" "colnames" "compare_partitions"
#> [7] "compare_signatures" "consensus_heatmap" "dimension_reduction"
#> [10] "functional_enrichment" "get_anno_col" "get_anno"
#> [13] "get_classes" "get_consensus" "get_matrix"
#> [16] "get_membership" "get_param" "get_signatures"
#> [19] "get_stats" "is_best_k" "is_stable_k"
#> [22] "membership_heatmap" "ncol" "nrow"
#> [25] "plot_ecdf" "predict_classes" "rownames"
#> [28] "select_partition_number" "show" "suggest_best_k"
#> [31] "test_to_known_factors" "top_rows_heatmap"
collect_plots() function collects all the plots made from res for all k (number of subgroups)
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, higher 1-PAC score, higher mean silhouette score or higher
concordance corresponds to better partition. Rand index and Jaccard index
measure how similar the current partition is compared to partition with k-1.
If they are too similar, we won't accept k is better than k-1.
select_partition_number(res)
The numeric values for all these statistics can be obtained by get_stats().
get_stats(res)
#> k 1-PAC mean_silhouette concordance area_increased Rand Jaccard
#> 2 2 0.999 0.960 0.984 0.3637 0.639 0.639
#> 3 3 1.000 0.999 1.000 0.4258 0.781 0.673
#> 4 4 1.000 0.993 0.997 0.1502 0.903 0.804
#> 5 5 0.930 0.892 0.958 0.0487 0.982 0.955
#> 6 6 0.842 0.845 0.918 0.0509 0.969 0.920
#> 7 7 0.715 0.761 0.884 0.0272 0.995 0.987
#> 8 8 0.707 0.576 0.822 0.0427 0.971 0.921
suggest_best_k() suggests the best \(k\) based on these statistics. The rules are as follows:
suggest_best_k(res)
#> [1] 4
#> attr(,"optional")
#> [1] 2 3
There is also optional best \(k\) = 2 3 that is worth to check.
Following is 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 subgroup
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
#> TCGA.EK.A3GK.01 1 0.141 0.967 0.98 0.02
#> TCGA.VS.A94Y.01 2 0.000 0.969 0.00 1.00
#> TCGA.VS.A94Z.01 1 0.000 0.987 1.00 0.00
#> TCGA.EA.A4BA.01 2 0.000 0.969 0.00 1.00
#> TCGA.EK.A2R7.01 1 0.000 0.987 1.00 0.00
#> TCGA.EK.A2RN.01 1 0.000 0.987 1.00 0.00
#> TCGA.C5.A8YR.01 2 0.000 0.969 0.00 1.00
#> TCGA.C5.A8XJ.01 1 0.000 0.987 1.00 0.00
#> TCGA.VS.A8Q8.01 1 0.000 0.987 1.00 0.00
#> TCGA.EK.A2RK.01 1 0.000 0.987 1.00 0.00
#> TCGA.EK.A2RD.01 1 0.000 0.987 1.00 0.00
#> TCGA.C5.A3HL.01 1 0.000 0.987 1.00 0.00
#> TCGA.C5.A8XK.01 2 0.722 0.766 0.20 0.80
#> TCGA.HM.A4S6.01 1 0.000 0.987 1.00 0.00
#> TCGA.MA.AA3Z.01 1 0.000 0.987 1.00 0.00
#> TCGA.EK.A2RE.01 1 0.000 0.987 1.00 0.00
#> TCGA.C5.A1BQ.01 1 0.000 0.987 1.00 0.00
#> TCGA.EA.A556.01 2 0.000 0.969 0.00 1.00
#> TCGA.C5.A7X3.01 2 0.000 0.969 0.00 1.00
#> TCGA.C5.A7XC.01 1 0.000 0.987 1.00 0.00
#> TCGA.EA.A3HR.01 1 0.000 0.987 1.00 0.00
#> TCGA.DG.A2KL.01 1 0.000 0.987 1.00 0.00
#> TCGA.BI.A0VR.01 1 0.000 0.987 1.00 0.00
#> TCGA.DS.A0VL.01 1 0.000 0.987 1.00 0.00
#> TCGA.DR.A0ZM.01 2 0.584 0.848 0.14 0.86
#> TCGA.DS.A0VK.01 1 0.000 0.987 1.00 0.00
#> TCGA.JW.A5VJ.01 1 0.000 0.987 1.00 0.00
#> TCGA.HM.A3JJ.01 1 0.000 0.987 1.00 0.00
#> TCGA.EK.A2RJ.01 2 0.000 0.969 0.00 1.00
#> TCGA.EA.A3HT.01 1 0.000 0.987 1.00 0.00
#> TCGA.EK.A2PI.01 1 0.000 0.987 1.00 0.00
#> TCGA.EA.A5ZD.01 1 0.000 0.987 1.00 0.00
#> TCGA.C5.A7UI.01 1 0.000 0.987 1.00 0.00
#> TCGA.EK.A2PL.01 1 0.000 0.987 1.00 0.00
#> TCGA.EK.A2PK.01 2 0.000 0.969 0.00 1.00
#> TCGA.EA.A5ZF.01 1 0.995 0.101 0.54 0.46
#> TCGA.BI.A0VS.01 2 0.000 0.969 0.00 1.00
#> TCGA.JX.A5QV.01 1 0.000 0.987 1.00 0.00
#> TCGA.EK.A2R8.01 1 0.584 0.825 0.86 0.14
#> TCGA.JX.A3PZ.01 2 0.000 0.969 0.00 1.00
#> TCGA.DS.A5RQ.01 1 0.000 0.987 1.00 0.00
#> TCGA.EX.A69L.01 1 0.000 0.987 1.00 0.00
#> TCGA.Q1.A5R3.01 1 0.000 0.987 1.00 0.00
#> TCGA.C5.A7CL.01 1 0.000 0.987 1.00 0.00
#> TCGA.ZJ.AAXN.01 2 0.000 0.969 0.00 1.00
#> TCGA.UC.A7PG.01 1 0.000 0.987 1.00 0.00
#> TCGA.DS.A1OD.01 1 0.000 0.987 1.00 0.00
#> TCGA.C5.A1M7.01 1 0.000 0.987 1.00 0.00
#> TCGA.ZJ.AAXD.01 1 0.000 0.987 1.00 0.00
#> TCGA.ZJ.AAXT.01 1 0.000 0.987 1.00 0.00
#> TCGA.ZJ.AAXU.01 1 0.000 0.987 1.00 0.00
#> TCGA.C5.A1MK.01 1 0.000 0.987 1.00 0.00
#> TCGA.VS.A958.01 1 0.000 0.987 1.00 0.00
#> TCGA.VS.A9V0.01 2 0.000 0.969 0.00 1.00
#> TCGA.LP.A4AV.01 1 0.000 0.987 1.00 0.00
#> TCGA.EA.A3Y4.01 2 0.000 0.969 0.00 1.00
#> TCGA.Q1.A73O.01 1 0.000 0.987 1.00 0.00
#> TCGA.C5.A1MP.01 1 0.000 0.987 1.00 0.00
#> TCGA.ZJ.AB0H.01 1 0.000 0.987 1.00 0.00
#> TCGA.VS.A9UA.01 1 0.000 0.987 1.00 0.00
#> TCGA.LP.A4AW.01 1 0.000 0.987 1.00 0.00
#> TCGA.C5.A1BM.01 1 0.000 0.987 1.00 0.00
#> TCGA.C5.A1BE.01 1 0.000 0.987 1.00 0.00
#> TCGA.FU.A23L.01 2 0.402 0.909 0.08 0.92
#> TCGA.C5.A1BI.01 1 0.000 0.987 1.00 0.00
cbind(get_classes(res, k = 3), get_membership(res, k = 3))
#> class entropy silhouette p1 p2 p3
#> TCGA.EK.A3GK.01 2 0.0000 0.998 0.00 1.00 0
#> TCGA.VS.A94Y.01 2 0.0000 0.998 0.00 1.00 0
#> TCGA.VS.A94Z.01 1 0.0000 1.000 1.00 0.00 0
#> TCGA.EA.A4BA.01 3 0.0000 1.000 0.00 0.00 1
#> TCGA.EK.A2R7.01 1 0.0000 1.000 1.00 0.00 0
#> TCGA.EK.A2RN.01 1 0.0000 1.000 1.00 0.00 0
#> TCGA.C5.A8YR.01 3 0.0000 1.000 0.00 0.00 1
#> TCGA.C5.A8XJ.01 1 0.0000 1.000 1.00 0.00 0
#> TCGA.VS.A8Q8.01 1 0.0000 1.000 1.00 0.00 0
#> TCGA.EK.A2RK.01 1 0.0000 1.000 1.00 0.00 0
#> TCGA.EK.A2RD.01 1 0.0000 1.000 1.00 0.00 0
#> TCGA.C5.A3HL.01 1 0.0000 1.000 1.00 0.00 0
#> TCGA.C5.A8XK.01 2 0.0000 0.998 0.00 1.00 0
#> TCGA.HM.A4S6.01 1 0.0000 1.000 1.00 0.00 0
#> TCGA.MA.AA3Z.01 1 0.0000 1.000 1.00 0.00 0
#> TCGA.EK.A2RE.01 1 0.0000 1.000 1.00 0.00 0
#> TCGA.C5.A1BQ.01 1 0.0000 1.000 1.00 0.00 0
#> TCGA.EA.A556.01 3 0.0000 1.000 0.00 0.00 1
#> TCGA.C5.A7X3.01 2 0.0000 0.998 0.00 1.00 0
#> TCGA.C5.A7XC.01 1 0.0000 1.000 1.00 0.00 0
#> TCGA.EA.A3HR.01 1 0.0000 1.000 1.00 0.00 0
#> TCGA.DG.A2KL.01 1 0.0000 1.000 1.00 0.00 0
#> TCGA.BI.A0VR.01 1 0.0000 1.000 1.00 0.00 0
#> TCGA.DS.A0VL.01 1 0.0000 1.000 1.00 0.00 0
#> TCGA.DR.A0ZM.01 2 0.0000 0.998 0.00 1.00 0
#> TCGA.DS.A0VK.01 1 0.0000 1.000 1.00 0.00 0
#> TCGA.JW.A5VJ.01 2 0.0000 0.998 0.00 1.00 0
#> TCGA.HM.A3JJ.01 1 0.0000 1.000 1.00 0.00 0
#> TCGA.EK.A2RJ.01 3 0.0000 1.000 0.00 0.00 1
#> TCGA.EA.A3HT.01 1 0.0000 1.000 1.00 0.00 0
#> TCGA.EK.A2PI.01 1 0.0000 1.000 1.00 0.00 0
#> TCGA.EA.A5ZD.01 1 0.0000 1.000 1.00 0.00 0
#> TCGA.C5.A7UI.01 1 0.0000 1.000 1.00 0.00 0
#> TCGA.EK.A2PL.01 1 0.0000 1.000 1.00 0.00 0
#> TCGA.EK.A2PK.01 3 0.0000 1.000 0.00 0.00 1
#> TCGA.EA.A5ZF.01 2 0.0000 0.998 0.00 1.00 0
#> TCGA.BI.A0VS.01 2 0.0000 0.998 0.00 1.00 0
#> TCGA.JX.A5QV.01 1 0.0000 1.000 1.00 0.00 0
#> TCGA.EK.A2R8.01 2 0.0000 0.998 0.00 1.00 0
#> TCGA.JX.A3PZ.01 3 0.0000 1.000 0.00 0.00 1
#> TCGA.DS.A5RQ.01 1 0.0000 1.000 1.00 0.00 0
#> TCGA.EX.A69L.01 1 0.0000 1.000 1.00 0.00 0
#> TCGA.Q1.A5R3.01 1 0.0000 1.000 1.00 0.00 0
#> TCGA.C5.A7CL.01 1 0.0000 1.000 1.00 0.00 0
#> TCGA.ZJ.AAXN.01 2 0.0000 0.998 0.00 1.00 0
#> TCGA.UC.A7PG.01 1 0.0000 1.000 1.00 0.00 0
#> TCGA.DS.A1OD.01 1 0.0000 1.000 1.00 0.00 0
#> TCGA.C5.A1M7.01 2 0.0000 0.998 0.00 1.00 0
#> TCGA.ZJ.AAXD.01 1 0.0000 1.000 1.00 0.00 0
#> TCGA.ZJ.AAXT.01 2 0.0000 0.998 0.00 1.00 0
#> TCGA.ZJ.AAXU.01 1 0.0000 1.000 1.00 0.00 0
#> TCGA.C5.A1MK.01 1 0.0000 1.000 1.00 0.00 0
#> TCGA.VS.A958.01 1 0.0000 1.000 1.00 0.00 0
#> TCGA.VS.A9V0.01 3 0.0000 1.000 0.00 0.00 1
#> TCGA.LP.A4AV.01 1 0.0000 1.000 1.00 0.00 0
#> TCGA.EA.A3Y4.01 2 0.0000 0.998 0.00 1.00 0
#> TCGA.Q1.A73O.01 1 0.0000 1.000 1.00 0.00 0
#> TCGA.C5.A1MP.01 1 0.0000 1.000 1.00 0.00 0
#> TCGA.ZJ.AB0H.01 1 0.0000 1.000 1.00 0.00 0
#> TCGA.VS.A9UA.01 1 0.0000 1.000 1.00 0.00 0
#> TCGA.LP.A4AW.01 1 0.0000 1.000 1.00 0.00 0
#> TCGA.C5.A1BM.01 2 0.0892 0.968 0.02 0.98 0
#> TCGA.C5.A1BE.01 1 0.0000 1.000 1.00 0.00 0
#> TCGA.FU.A23L.01 2 0.0000 0.998 0.00 1.00 0
#> TCGA.C5.A1BI.01 2 0.0000 0.998 0.00 1.00 0
cbind(get_classes(res, k = 4), get_membership(res, k = 4))
#> class entropy silhouette p1 p2 p3 p4
#> TCGA.EK.A3GK.01 2 0.0000 0.994 0.00 1.00 0.00 0.00
#> TCGA.VS.A94Y.01 2 0.0000 0.994 0.00 1.00 0.00 0.00
#> TCGA.VS.A94Z.01 1 0.2011 0.914 0.92 0.00 0.00 0.08
#> TCGA.EA.A4BA.01 3 0.0000 0.997 0.00 0.00 1.00 0.00
#> TCGA.EK.A2R7.01 1 0.0000 0.997 1.00 0.00 0.00 0.00
#> TCGA.EK.A2RN.01 1 0.0000 0.997 1.00 0.00 0.00 0.00
#> TCGA.C5.A8YR.01 3 0.0000 0.997 0.00 0.00 1.00 0.00
#> TCGA.C5.A8XJ.01 1 0.0000 0.997 1.00 0.00 0.00 0.00
#> TCGA.VS.A8Q8.01 1 0.0000 0.997 1.00 0.00 0.00 0.00
#> TCGA.EK.A2RK.01 1 0.0000 0.997 1.00 0.00 0.00 0.00
#> TCGA.EK.A2RD.01 1 0.0000 0.997 1.00 0.00 0.00 0.00
#> TCGA.C5.A3HL.01 1 0.0000 0.997 1.00 0.00 0.00 0.00
#> TCGA.C5.A8XK.01 2 0.0000 0.994 0.00 1.00 0.00 0.00
#> TCGA.HM.A4S6.01 1 0.0000 0.997 1.00 0.00 0.00 0.00
#> TCGA.MA.AA3Z.01 1 0.0000 0.997 1.00 0.00 0.00 0.00
#> TCGA.EK.A2RE.01 1 0.0000 0.997 1.00 0.00 0.00 0.00
#> TCGA.C5.A1BQ.01 1 0.0000 0.997 1.00 0.00 0.00 0.00
#> TCGA.EA.A556.01 3 0.0000 0.997 0.00 0.00 1.00 0.00
#> TCGA.C5.A7X3.01 2 0.0000 0.994 0.00 1.00 0.00 0.00
#> TCGA.C5.A7XC.01 1 0.0000 0.997 1.00 0.00 0.00 0.00
#> TCGA.EA.A3HR.01 1 0.0000 0.997 1.00 0.00 0.00 0.00
#> TCGA.DG.A2KL.01 1 0.0000 0.997 1.00 0.00 0.00 0.00
#> TCGA.BI.A0VR.01 1 0.0000 0.997 1.00 0.00 0.00 0.00
#> TCGA.DS.A0VL.01 1 0.0000 0.997 1.00 0.00 0.00 0.00
#> TCGA.DR.A0ZM.01 4 0.0707 0.978 0.00 0.02 0.00 0.98
#> TCGA.DS.A0VK.01 1 0.0000 0.997 1.00 0.00 0.00 0.00
#> TCGA.JW.A5VJ.01 4 0.0000 0.993 0.00 0.00 0.00 1.00
#> TCGA.HM.A3JJ.01 1 0.0000 0.997 1.00 0.00 0.00 0.00
#> TCGA.EK.A2RJ.01 3 0.0000 0.997 0.00 0.00 1.00 0.00
#> TCGA.EA.A3HT.01 1 0.0000 0.997 1.00 0.00 0.00 0.00
#> TCGA.EK.A2PI.01 1 0.0707 0.978 0.98 0.00 0.00 0.02
#> TCGA.EA.A5ZD.01 4 0.0000 0.993 0.00 0.00 0.00 1.00
#> TCGA.C5.A7UI.01 1 0.0000 0.997 1.00 0.00 0.00 0.00
#> TCGA.EK.A2PL.01 1 0.0000 0.997 1.00 0.00 0.00 0.00
#> TCGA.EK.A2PK.01 3 0.0707 0.980 0.00 0.02 0.98 0.00
#> TCGA.EA.A5ZF.01 2 0.0000 0.994 0.00 1.00 0.00 0.00
#> TCGA.BI.A0VS.01 2 0.0000 0.994 0.00 1.00 0.00 0.00
#> TCGA.JX.A5QV.01 1 0.0000 0.997 1.00 0.00 0.00 0.00
#> TCGA.EK.A2R8.01 2 0.0707 0.978 0.00 0.98 0.00 0.02
#> TCGA.JX.A3PZ.01 3 0.0000 0.997 0.00 0.00 1.00 0.00
#> TCGA.DS.A5RQ.01 1 0.0000 0.997 1.00 0.00 0.00 0.00
#> TCGA.EX.A69L.01 1 0.0000 0.997 1.00 0.00 0.00 0.00
#> TCGA.Q1.A5R3.01 1 0.0000 0.997 1.00 0.00 0.00 0.00
#> TCGA.C5.A7CL.01 1 0.0000 0.997 1.00 0.00 0.00 0.00
#> TCGA.ZJ.AAXN.01 2 0.0707 0.978 0.00 0.98 0.00 0.02
#> TCGA.UC.A7PG.01 1 0.0000 0.997 1.00 0.00 0.00 0.00
#> TCGA.DS.A1OD.01 1 0.0000 0.997 1.00 0.00 0.00 0.00
#> TCGA.C5.A1M7.01 4 0.0000 0.993 0.00 0.00 0.00 1.00
#> TCGA.ZJ.AAXD.01 1 0.0000 0.997 1.00 0.00 0.00 0.00
#> TCGA.ZJ.AAXT.01 4 0.0000 0.993 0.00 0.00 0.00 1.00
#> TCGA.ZJ.AAXU.01 1 0.0000 0.997 1.00 0.00 0.00 0.00
#> TCGA.C5.A1MK.01 1 0.0000 0.997 1.00 0.00 0.00 0.00
#> TCGA.VS.A958.01 4 0.0000 0.993 0.00 0.00 0.00 1.00
#> TCGA.VS.A9V0.01 3 0.0000 0.997 0.00 0.00 1.00 0.00
#> TCGA.LP.A4AV.01 1 0.0000 0.997 1.00 0.00 0.00 0.00
#> TCGA.EA.A3Y4.01 2 0.0000 0.994 0.00 1.00 0.00 0.00
#> TCGA.Q1.A73O.01 4 0.0000 0.993 0.00 0.00 0.00 1.00
#> TCGA.C5.A1MP.01 1 0.0000 0.997 1.00 0.00 0.00 0.00
#> TCGA.ZJ.AB0H.01 1 0.0000 0.997 1.00 0.00 0.00 0.00
#> TCGA.VS.A9UA.01 1 0.0000 0.997 1.00 0.00 0.00 0.00
#> TCGA.LP.A4AW.01 1 0.0000 0.997 1.00 0.00 0.00 0.00
#> TCGA.C5.A1BM.01 4 0.0000 0.993 0.00 0.00 0.00 1.00
#> TCGA.C5.A1BE.01 1 0.0000 0.997 1.00 0.00 0.00 0.00
#> TCGA.FU.A23L.01 4 0.1211 0.960 0.00 0.04 0.00 0.96
#> TCGA.C5.A1BI.01 4 0.0000 0.993 0.00 0.00 0.00 1.00
cbind(get_classes(res, k = 5), get_membership(res, k = 5))
#> class entropy silhouette p1 p2 p3 p4 p5
#> TCGA.EK.A3GK.01 2 0.1043 0.9207 0.00 0.96 0.00 0.04 0.00
#> TCGA.VS.A94Y.01 2 0.0000 0.9242 0.00 1.00 0.00 0.00 0.00
#> TCGA.VS.A94Z.01 1 0.4262 0.0984 0.56 0.00 0.00 0.44 0.00
#> TCGA.EA.A4BA.01 3 0.0000 0.9912 0.00 0.00 1.00 0.00 0.00
#> TCGA.EK.A2R7.01 1 0.0000 0.9692 1.00 0.00 0.00 0.00 0.00
#> TCGA.EK.A2RN.01 1 0.0609 0.9552 0.98 0.00 0.00 0.00 0.02
#> TCGA.C5.A8YR.01 3 0.0000 0.9912 0.00 0.00 1.00 0.00 0.00
#> TCGA.C5.A8XJ.01 1 0.1043 0.9388 0.96 0.00 0.00 0.00 0.04
#> TCGA.VS.A8Q8.01 1 0.1732 0.8842 0.92 0.00 0.00 0.08 0.00
#> TCGA.EK.A2RK.01 1 0.0000 0.9692 1.00 0.00 0.00 0.00 0.00
#> TCGA.EK.A2RD.01 1 0.0000 0.9692 1.00 0.00 0.00 0.00 0.00
#> TCGA.C5.A3HL.01 1 0.0000 0.9692 1.00 0.00 0.00 0.00 0.00
#> TCGA.C5.A8XK.01 2 0.0609 0.9257 0.00 0.98 0.00 0.02 0.00
#> TCGA.HM.A4S6.01 1 0.0000 0.9692 1.00 0.00 0.00 0.00 0.00
#> TCGA.MA.AA3Z.01 1 0.0000 0.9692 1.00 0.00 0.00 0.00 0.00
#> TCGA.EK.A2RE.01 1 0.0000 0.9692 1.00 0.00 0.00 0.00 0.00
#> TCGA.C5.A1BQ.01 1 0.0000 0.9692 1.00 0.00 0.00 0.00 0.00
#> TCGA.EA.A556.01 3 0.0000 0.9912 0.00 0.00 1.00 0.00 0.00
#> TCGA.C5.A7X3.01 2 0.0000 0.9242 0.00 1.00 0.00 0.00 0.00
#> TCGA.C5.A7XC.01 1 0.0000 0.9692 1.00 0.00 0.00 0.00 0.00
#> TCGA.EA.A3HR.01 1 0.0000 0.9692 1.00 0.00 0.00 0.00 0.00
#> TCGA.DG.A2KL.01 1 0.0609 0.9552 0.98 0.00 0.00 0.00 0.02
#> TCGA.BI.A0VR.01 1 0.0000 0.9692 1.00 0.00 0.00 0.00 0.00
#> TCGA.DS.A0VL.01 1 0.0000 0.9692 1.00 0.00 0.00 0.00 0.00
#> TCGA.DR.A0ZM.01 4 0.4433 0.6969 0.00 0.06 0.00 0.74 0.20
#> TCGA.DS.A0VK.01 1 0.0000 0.9692 1.00 0.00 0.00 0.00 0.00
#> TCGA.JW.A5VJ.01 4 0.3895 0.6307 0.00 0.00 0.00 0.68 0.32
#> TCGA.HM.A3JJ.01 1 0.0000 0.9692 1.00 0.00 0.00 0.00 0.00
#> TCGA.EK.A2RJ.01 3 0.0000 0.9912 0.00 0.00 1.00 0.00 0.00
#> TCGA.EA.A3HT.01 1 0.0000 0.9692 1.00 0.00 0.00 0.00 0.00
#> TCGA.EK.A2PI.01 5 0.2516 0.0000 0.14 0.00 0.00 0.00 0.86
#> TCGA.EA.A5ZD.01 4 0.0000 0.8556 0.00 0.00 0.00 1.00 0.00
#> TCGA.C5.A7UI.01 1 0.0000 0.9692 1.00 0.00 0.00 0.00 0.00
#> TCGA.EK.A2PL.01 1 0.1043 0.9388 0.96 0.00 0.00 0.00 0.04
#> TCGA.EK.A2PK.01 3 0.1043 0.9461 0.00 0.04 0.96 0.00 0.00
#> TCGA.EA.A5ZF.01 2 0.1043 0.9207 0.00 0.96 0.00 0.04 0.00
#> TCGA.BI.A0VS.01 2 0.2516 0.8218 0.00 0.86 0.00 0.00 0.14
#> TCGA.JX.A5QV.01 1 0.1216 0.9400 0.96 0.00 0.00 0.02 0.02
#> TCGA.EK.A2R8.01 2 0.2020 0.8761 0.00 0.90 0.00 0.10 0.00
#> TCGA.JX.A3PZ.01 3 0.0000 0.9912 0.00 0.00 1.00 0.00 0.00
#> TCGA.DS.A5RQ.01 1 0.0000 0.9692 1.00 0.00 0.00 0.00 0.00
#> TCGA.EX.A69L.01 1 0.0000 0.9692 1.00 0.00 0.00 0.00 0.00
#> TCGA.Q1.A5R3.01 1 0.0000 0.9692 1.00 0.00 0.00 0.00 0.00
#> TCGA.C5.A7CL.01 1 0.0609 0.9552 0.98 0.00 0.00 0.00 0.02
#> TCGA.ZJ.AAXN.01 2 0.3291 0.7866 0.00 0.84 0.00 0.12 0.04
#> TCGA.UC.A7PG.01 1 0.0000 0.9692 1.00 0.00 0.00 0.00 0.00
#> TCGA.DS.A1OD.01 1 0.0000 0.9692 1.00 0.00 0.00 0.00 0.00
#> TCGA.C5.A1M7.01 4 0.0000 0.8556 0.00 0.00 0.00 1.00 0.00
#> TCGA.ZJ.AAXD.01 1 0.0000 0.9692 1.00 0.00 0.00 0.00 0.00
#> TCGA.ZJ.AAXT.01 4 0.0000 0.8556 0.00 0.00 0.00 1.00 0.00
#> TCGA.ZJ.AAXU.01 1 0.0000 0.9692 1.00 0.00 0.00 0.00 0.00
#> TCGA.C5.A1MK.01 1 0.0000 0.9692 1.00 0.00 0.00 0.00 0.00
#> TCGA.VS.A958.01 4 0.2020 0.6829 0.10 0.00 0.00 0.90 0.00
#> TCGA.VS.A9V0.01 3 0.0000 0.9912 0.00 0.00 1.00 0.00 0.00
#> TCGA.LP.A4AV.01 1 0.3697 0.7557 0.82 0.00 0.00 0.08 0.10
#> TCGA.EA.A3Y4.01 2 0.0000 0.9242 0.00 1.00 0.00 0.00 0.00
#> TCGA.Q1.A73O.01 4 0.0000 0.8556 0.00 0.00 0.00 1.00 0.00
#> TCGA.C5.A1MP.01 1 0.0000 0.9692 1.00 0.00 0.00 0.00 0.00
#> TCGA.ZJ.AB0H.01 1 0.0000 0.9692 1.00 0.00 0.00 0.00 0.00
#> TCGA.VS.A9UA.01 1 0.0000 0.9692 1.00 0.00 0.00 0.00 0.00
#> TCGA.LP.A4AW.01 1 0.1410 0.9067 0.94 0.00 0.00 0.06 0.00
#> TCGA.C5.A1BM.01 4 0.0000 0.8556 0.00 0.00 0.00 1.00 0.00
#> TCGA.C5.A1BE.01 1 0.0000 0.9692 1.00 0.00 0.00 0.00 0.00
#> TCGA.FU.A23L.01 4 0.6146 0.4621 0.00 0.20 0.00 0.56 0.24
#> TCGA.C5.A1BI.01 4 0.0000 0.8556 0.00 0.00 0.00 1.00 0.00
cbind(get_classes(res, k = 6), get_membership(res, k = 6))
#> class entropy silhouette p1 p2 p3 p4 p5 p6
#> TCGA.EK.A3GK.01 2 0.2474 0.772 0.00 0.88 0.00 0.08 0.00 0.04
#> TCGA.VS.A94Y.01 2 0.1556 0.794 0.00 0.92 0.00 0.00 0.00 0.08
#> TCGA.VS.A94Z.01 4 0.3460 0.401 0.22 0.00 0.00 0.76 0.00 0.02
#> TCGA.EA.A4BA.01 3 0.0000 0.976 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.EK.A2R7.01 1 0.0937 0.939 0.96 0.00 0.00 0.00 0.00 0.04
#> TCGA.EK.A2RN.01 1 0.1807 0.908 0.92 0.00 0.00 0.00 0.02 0.06
#> TCGA.C5.A8YR.01 3 0.0000 0.976 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.C5.A8XJ.01 1 0.2190 0.890 0.90 0.00 0.00 0.00 0.06 0.04
#> TCGA.VS.A8Q8.01 1 0.4495 0.683 0.72 0.00 0.00 0.20 0.02 0.06
#> TCGA.EK.A2RK.01 1 0.0000 0.948 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.EK.A2RD.01 1 0.0000 0.948 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.C5.A3HL.01 1 0.0000 0.948 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.C5.A8XK.01 2 0.1092 0.791 0.00 0.96 0.00 0.02 0.00 0.02
#> TCGA.HM.A4S6.01 1 0.1092 0.938 0.96 0.00 0.00 0.02 0.00 0.02
#> TCGA.MA.AA3Z.01 1 0.0000 0.948 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.EK.A2RE.01 1 0.0547 0.943 0.98 0.00 0.00 0.00 0.00 0.02
#> TCGA.C5.A1BQ.01 1 0.0000 0.948 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.EA.A556.01 3 0.0000 0.976 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.C5.A7X3.01 2 0.2048 0.790 0.00 0.88 0.00 0.00 0.00 0.12
#> TCGA.C5.A7XC.01 1 0.2581 0.855 0.86 0.00 0.00 0.12 0.00 0.02
#> TCGA.EA.A3HR.01 1 0.0547 0.942 0.98 0.00 0.00 0.00 0.00 0.02
#> TCGA.DG.A2KL.01 1 0.1092 0.932 0.96 0.00 0.00 0.00 0.02 0.02
#> TCGA.BI.A0VR.01 1 0.0547 0.945 0.98 0.00 0.00 0.00 0.00 0.02
#> TCGA.DS.A0VL.01 1 0.0000 0.948 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.DR.A0ZM.01 6 0.4873 0.685 0.00 0.06 0.00 0.42 0.00 0.52
#> TCGA.DS.A0VK.01 1 0.0000 0.948 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.JW.A5VJ.01 6 0.5544 0.633 0.00 0.02 0.00 0.40 0.08 0.50
#> TCGA.HM.A3JJ.01 1 0.0547 0.945 0.98 0.00 0.00 0.00 0.00 0.02
#> TCGA.EK.A2RJ.01 3 0.0000 0.976 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.EA.A3HT.01 1 0.0000 0.948 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.EK.A2PI.01 5 0.0000 0.000 0.00 0.00 0.00 0.00 1.00 0.00
#> TCGA.EA.A5ZD.01 4 0.0000 0.835 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.C5.A7UI.01 1 0.1092 0.938 0.96 0.00 0.00 0.02 0.00 0.02
#> TCGA.EK.A2PL.01 1 0.2512 0.874 0.88 0.00 0.00 0.00 0.06 0.06
#> TCGA.EK.A2PK.01 3 0.2474 0.844 0.00 0.08 0.88 0.00 0.00 0.04
#> TCGA.EA.A5ZF.01 2 0.2350 0.770 0.00 0.88 0.00 0.10 0.00 0.02
#> TCGA.BI.A0VS.01 2 0.4067 0.605 0.00 0.70 0.00 0.00 0.04 0.26
#> TCGA.JX.A5QV.01 1 0.4967 0.704 0.72 0.00 0.00 0.10 0.12 0.06
#> TCGA.EK.A2R8.01 2 0.3309 0.569 0.00 0.72 0.00 0.28 0.00 0.00
#> TCGA.JX.A3PZ.01 3 0.0000 0.976 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.DS.A5RQ.01 1 0.0000 0.948 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.EX.A69L.01 1 0.0547 0.945 0.98 0.00 0.00 0.00 0.00 0.02
#> TCGA.Q1.A5R3.01 1 0.0000 0.948 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.C5.A7CL.01 1 0.1807 0.922 0.92 0.00 0.00 0.00 0.02 0.06
#> TCGA.ZJ.AAXN.01 2 0.4462 0.582 0.00 0.66 0.00 0.06 0.00 0.28
#> TCGA.UC.A7PG.01 1 0.0000 0.948 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.DS.A1OD.01 1 0.0547 0.945 0.98 0.00 0.00 0.00 0.00 0.02
#> TCGA.C5.A1M7.01 4 0.0000 0.835 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.ZJ.AAXD.01 1 0.0000 0.948 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.ZJ.AAXT.01 4 0.0547 0.818 0.00 0.00 0.00 0.98 0.00 0.02
#> TCGA.ZJ.AAXU.01 1 0.0000 0.948 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.C5.A1MK.01 1 0.1480 0.927 0.94 0.00 0.00 0.04 0.00 0.02
#> TCGA.VS.A958.01 4 0.1480 0.786 0.04 0.00 0.00 0.94 0.00 0.02
#> TCGA.VS.A9V0.01 3 0.0000 0.976 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.LP.A4AV.01 1 0.5955 0.521 0.62 0.00 0.00 0.16 0.14 0.08
#> TCGA.EA.A3Y4.01 2 0.2048 0.790 0.00 0.88 0.00 0.00 0.00 0.12
#> TCGA.Q1.A73O.01 4 0.0937 0.806 0.04 0.00 0.00 0.96 0.00 0.00
#> TCGA.C5.A1MP.01 1 0.0547 0.945 0.98 0.00 0.00 0.00 0.00 0.02
#> TCGA.ZJ.AB0H.01 1 0.0547 0.945 0.98 0.00 0.00 0.00 0.00 0.02
#> TCGA.VS.A9UA.01 1 0.0547 0.945 0.98 0.00 0.00 0.00 0.00 0.02
#> TCGA.LP.A4AW.01 1 0.2094 0.895 0.90 0.00 0.00 0.08 0.00 0.02
#> TCGA.C5.A1BM.01 4 0.0937 0.797 0.00 0.00 0.00 0.96 0.00 0.04
#> TCGA.C5.A1BE.01 1 0.0000 0.948 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.FU.A23L.01 6 0.4608 0.612 0.00 0.10 0.00 0.22 0.00 0.68
#> TCGA.C5.A1BI.01 4 0.0000 0.835 0.00 0.00 0.00 1.00 0.00 0.00
cbind(get_classes(res, k = 7), get_membership(res, k = 7))
#> class entropy silhouette p1 p2 p3 p4 p5 p6 p7
#> TCGA.EK.A3GK.01 2 0.2708 0.646 0.00 0.78 0.00 0.00 0.00 0.22 0.00
#> TCGA.VS.A94Y.01 2 0.3086 0.591 0.00 0.80 0.00 0.00 0.00 0.16 0.04
#> TCGA.VS.A94Z.01 4 0.3388 0.409 0.20 0.00 0.00 0.76 0.00 0.04 0.00
#> TCGA.EA.A4BA.01 3 0.0000 0.933 0.00 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.EK.A2R7.01 1 0.3289 0.844 0.82 0.00 0.00 0.06 0.02 0.10 0.00
#> TCGA.EK.A2RN.01 1 0.2163 0.871 0.88 0.00 0.00 0.00 0.02 0.10 0.00
#> TCGA.C5.A8YR.01 3 0.0000 0.933 0.00 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.C5.A8XJ.01 1 0.1928 0.892 0.90 0.00 0.00 0.00 0.02 0.08 0.00
#> TCGA.VS.A8Q8.01 1 0.4538 0.585 0.62 0.00 0.00 0.28 0.00 0.10 0.00
#> TCGA.EK.A2RK.01 1 0.0000 0.918 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.EK.A2RD.01 1 0.0000 0.918 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.C5.A3HL.01 1 0.0000 0.918 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.C5.A8XK.01 2 0.2081 0.666 0.00 0.86 0.00 0.00 0.00 0.14 0.00
#> TCGA.HM.A4S6.01 1 0.3011 0.836 0.82 0.00 0.00 0.12 0.00 0.06 0.00
#> TCGA.MA.AA3Z.01 1 0.0000 0.918 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.EK.A2RE.01 1 0.0504 0.913 0.98 0.00 0.00 0.00 0.00 0.02 0.00
#> TCGA.C5.A1BQ.01 1 0.0000 0.918 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.EA.A556.01 3 0.0000 0.933 0.00 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.C5.A7X3.01 2 0.0863 0.663 0.00 0.96 0.00 0.00 0.00 0.00 0.04
#> TCGA.C5.A7XC.01 1 0.3770 0.759 0.74 0.00 0.00 0.18 0.00 0.08 0.00
#> TCGA.EA.A3HR.01 1 0.1166 0.908 0.94 0.00 0.00 0.00 0.00 0.06 0.00
#> TCGA.DG.A2KL.01 1 0.2163 0.882 0.88 0.00 0.00 0.00 0.02 0.10 0.00
#> TCGA.BI.A0VR.01 1 0.0000 0.918 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.DS.A0VL.01 1 0.0000 0.918 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.DR.A0ZM.01 4 0.4701 -0.295 0.00 0.04 0.00 0.50 0.00 0.02 0.44
#> TCGA.DS.A0VK.01 1 0.0000 0.918 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.JW.A5VJ.01 7 0.5536 0.439 0.00 0.00 0.00 0.18 0.06 0.16 0.60
#> TCGA.HM.A3JJ.01 1 0.1363 0.908 0.94 0.00 0.00 0.02 0.00 0.04 0.00
#> TCGA.EK.A2RJ.01 3 0.0000 0.933 0.00 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.EA.A3HT.01 1 0.0000 0.918 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.EK.A2PI.01 5 0.0000 0.000 0.00 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.EA.A5ZD.01 4 0.0000 0.819 0.00 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.C5.A7UI.01 1 0.2016 0.890 0.90 0.00 0.00 0.06 0.00 0.04 0.00
#> TCGA.EK.A2PL.01 1 0.2421 0.886 0.88 0.00 0.00 0.02 0.02 0.08 0.00
#> TCGA.EK.A2PK.01 3 0.3687 0.733 0.00 0.12 0.76 0.00 0.00 0.12 0.00
#> TCGA.EA.A5ZF.01 2 0.4708 0.574 0.00 0.64 0.00 0.02 0.00 0.26 0.08
#> TCGA.BI.A0VS.01 2 0.5334 0.381 0.00 0.58 0.00 0.00 0.02 0.20 0.20
#> TCGA.JX.A5QV.01 1 0.4992 0.682 0.66 0.00 0.00 0.16 0.04 0.14 0.00
#> TCGA.EK.A2R8.01 2 0.5086 0.264 0.00 0.50 0.00 0.36 0.00 0.14 0.00
#> TCGA.JX.A3PZ.01 3 0.2259 0.836 0.00 0.00 0.84 0.00 0.00 0.16 0.00
#> TCGA.DS.A5RQ.01 1 0.0000 0.918 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.EX.A69L.01 1 0.0504 0.916 0.98 0.00 0.00 0.00 0.00 0.02 0.00
#> TCGA.Q1.A5R3.01 1 0.0000 0.918 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.C5.A7CL.01 1 0.2016 0.894 0.90 0.00 0.00 0.04 0.00 0.06 0.00
#> TCGA.ZJ.AAXN.01 2 0.5338 0.157 0.00 0.52 0.00 0.08 0.00 0.04 0.36
#> TCGA.UC.A7PG.01 1 0.0000 0.918 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.DS.A1OD.01 1 0.0504 0.916 0.98 0.00 0.00 0.00 0.00 0.02 0.00
#> TCGA.C5.A1M7.01 4 0.0000 0.819 0.00 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.ZJ.AAXD.01 1 0.0000 0.918 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.ZJ.AAXT.01 4 0.1718 0.740 0.00 0.00 0.00 0.92 0.00 0.04 0.04
#> TCGA.ZJ.AAXU.01 1 0.0000 0.918 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.C5.A1MK.01 1 0.2912 0.831 0.82 0.00 0.00 0.14 0.00 0.04 0.00
#> TCGA.VS.A958.01 4 0.0000 0.819 0.00 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.VS.A9V0.01 3 0.0000 0.933 0.00 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.LP.A4AV.01 1 0.6450 0.279 0.46 0.00 0.00 0.26 0.12 0.16 0.00
#> TCGA.EA.A3Y4.01 2 0.1363 0.663 0.00 0.94 0.00 0.00 0.00 0.04 0.02
#> TCGA.Q1.A73O.01 4 0.0000 0.819 0.00 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.C5.A1MP.01 1 0.0000 0.918 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.ZJ.AB0H.01 1 0.0863 0.911 0.96 0.00 0.00 0.00 0.00 0.04 0.00
#> TCGA.VS.A9UA.01 1 0.1363 0.907 0.94 0.00 0.00 0.02 0.00 0.04 0.00
#> TCGA.LP.A4AW.01 1 0.2906 0.798 0.80 0.00 0.00 0.18 0.00 0.02 0.00
#> TCGA.C5.A1BM.01 4 0.1363 0.773 0.00 0.00 0.00 0.94 0.00 0.02 0.04
#> TCGA.C5.A1BE.01 1 0.0000 0.918 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.FU.A23L.01 7 0.4045 0.488 0.00 0.14 0.00 0.14 0.00 0.00 0.72
#> TCGA.C5.A1BI.01 4 0.0000 0.819 0.00 0.00 0.00 1.00 0.00 0.00 0.00
cbind(get_classes(res, k = 8), get_membership(res, k = 8))
#> class entropy silhouette p1 p2 p3 p4 p5 p6 p7 p8
#> TCGA.EK.A3GK.01 2 0.1408 0.3946 0.00 0.94 0.00 0.00 0.00 0.02 0.02 0.02
#> TCGA.VS.A94Y.01 8 0.3083 0.0912 0.00 0.34 0.00 0.00 0.00 0.00 0.00 0.66
#> TCGA.VS.A94Z.01 4 0.1887 0.7708 0.06 0.00 0.00 0.90 0.00 0.04 0.00 0.00
#> TCGA.EA.A4BA.01 3 0.0471 0.8532 0.00 0.00 0.98 0.00 0.00 0.02 0.00 0.00
#> TCGA.EK.A2R7.01 1 0.3227 0.6390 0.78 0.08 0.00 0.00 0.00 0.14 0.00 0.00
#> TCGA.EK.A2RN.01 1 0.2852 0.4799 0.72 0.00 0.00 0.00 0.00 0.28 0.00 0.00
#> TCGA.C5.A8YR.01 3 0.0000 0.8621 0.00 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.C5.A8XJ.01 1 0.2756 0.5451 0.74 0.00 0.00 0.00 0.00 0.26 0.00 0.00
#> TCGA.VS.A8Q8.01 1 0.5116 -0.6198 0.46 0.00 0.00 0.26 0.00 0.28 0.00 0.00
#> TCGA.EK.A2RK.01 1 0.0471 0.7593 0.98 0.00 0.00 0.00 0.00 0.02 0.00 0.00
#> TCGA.EK.A2RD.01 1 0.1091 0.7663 0.94 0.00 0.00 0.00 0.00 0.06 0.00 0.00
#> TCGA.C5.A3HL.01 1 0.0000 0.7745 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.C5.A8XK.01 2 0.2719 0.3323 0.00 0.80 0.00 0.00 0.00 0.02 0.00 0.18
#> TCGA.HM.A4S6.01 1 0.3657 0.5080 0.72 0.00 0.00 0.08 0.00 0.20 0.00 0.00
#> TCGA.MA.AA3Z.01 1 0.0000 0.7745 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.EK.A2RE.01 1 0.2484 0.6322 0.86 0.00 0.00 0.02 0.00 0.10 0.00 0.02
#> TCGA.C5.A1BQ.01 1 0.0000 0.7745 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.EA.A556.01 3 0.0000 0.8621 0.00 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.C5.A7X3.01 2 0.3995 0.1597 0.00 0.60 0.00 0.02 0.00 0.02 0.00 0.36
#> TCGA.C5.A7XC.01 1 0.4069 0.3188 0.68 0.00 0.00 0.18 0.00 0.14 0.00 0.00
#> TCGA.EA.A3HR.01 1 0.2267 0.6768 0.82 0.00 0.00 0.00 0.00 0.18 0.00 0.00
#> TCGA.DG.A2KL.01 1 0.2267 0.6768 0.82 0.00 0.00 0.00 0.00 0.18 0.00 0.00
#> TCGA.BI.A0VR.01 1 0.0000 0.7745 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.DS.A0VL.01 1 0.0000 0.7745 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.DR.A0ZM.01 7 0.5349 0.5160 0.00 0.04 0.00 0.30 0.00 0.06 0.56 0.04
#> TCGA.DS.A0VK.01 1 0.0000 0.7745 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.JW.A5VJ.01 7 0.4988 0.3879 0.00 0.00 0.00 0.08 0.06 0.14 0.68 0.04
#> TCGA.HM.A3JJ.01 1 0.1765 0.7381 0.88 0.00 0.00 0.00 0.00 0.12 0.00 0.00
#> TCGA.EK.A2RJ.01 3 0.0000 0.8621 0.00 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.EA.A3HT.01 1 0.0000 0.7745 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.EK.A2PI.01 5 0.0471 0.0000 0.00 0.00 0.00 0.00 0.98 0.02 0.00 0.00
#> TCGA.EA.A5ZD.01 4 0.0000 0.8797 0.00 0.00 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.C5.A7UI.01 1 0.2719 0.6596 0.80 0.00 0.00 0.02 0.00 0.18 0.00 0.00
#> TCGA.EK.A2PL.01 1 0.2852 0.5043 0.72 0.00 0.00 0.00 0.00 0.28 0.00 0.00
#> TCGA.EK.A2PK.01 3 0.4636 0.3932 0.00 0.04 0.52 0.00 0.00 0.04 0.00 0.40
#> TCGA.EA.A5ZF.01 2 0.3181 0.3716 0.00 0.84 0.00 0.02 0.02 0.02 0.08 0.02
#> TCGA.BI.A0VS.01 8 0.6156 0.2145 0.00 0.26 0.00 0.00 0.02 0.04 0.28 0.40
#> TCGA.JX.A5QV.01 1 0.4622 -0.2199 0.56 0.00 0.00 0.14 0.00 0.30 0.00 0.00
#> TCGA.EK.A2R8.01 2 0.4028 0.2632 0.00 0.66 0.00 0.28 0.00 0.02 0.00 0.04
#> TCGA.JX.A3PZ.01 3 0.3843 0.6576 0.00 0.00 0.70 0.00 0.00 0.04 0.02 0.24
#> TCGA.DS.A5RQ.01 1 0.0000 0.7745 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.EX.A69L.01 1 0.1091 0.7662 0.94 0.00 0.00 0.00 0.00 0.06 0.00 0.00
#> TCGA.Q1.A5R3.01 1 0.0471 0.7744 0.98 0.00 0.00 0.00 0.00 0.02 0.00 0.00
#> TCGA.C5.A7CL.01 1 0.3431 0.5609 0.74 0.00 0.00 0.06 0.00 0.20 0.00 0.00
#> TCGA.ZJ.AAXN.01 2 0.6823 -0.1111 0.00 0.34 0.00 0.02 0.00 0.18 0.18 0.28
#> TCGA.UC.A7PG.01 1 0.0471 0.7744 0.98 0.00 0.00 0.00 0.00 0.02 0.00 0.00
#> TCGA.DS.A1OD.01 1 0.1341 0.7590 0.92 0.00 0.00 0.00 0.00 0.08 0.00 0.00
#> TCGA.C5.A1M7.01 4 0.0000 0.8797 0.00 0.00 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.ZJ.AAXD.01 1 0.0000 0.7745 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.ZJ.AAXT.01 4 0.3262 0.7324 0.00 0.02 0.00 0.82 0.00 0.04 0.10 0.02
#> TCGA.ZJ.AAXU.01 1 0.0000 0.7745 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.C5.A1MK.01 1 0.3856 0.4485 0.70 0.00 0.00 0.10 0.00 0.20 0.00 0.00
#> TCGA.VS.A958.01 4 0.1275 0.8398 0.02 0.00 0.00 0.94 0.00 0.04 0.00 0.00
#> TCGA.VS.A9V0.01 3 0.0000 0.8621 0.00 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.LP.A4AV.01 6 0.5273 0.0000 0.36 0.00 0.00 0.16 0.02 0.46 0.00 0.00
#> TCGA.EA.A3Y4.01 2 0.3618 0.0697 0.00 0.60 0.00 0.00 0.00 0.02 0.00 0.38
#> TCGA.Q1.A73O.01 4 0.0471 0.8733 0.02 0.00 0.00 0.98 0.00 0.00 0.00 0.00
#> TCGA.C5.A1MP.01 1 0.0000 0.7745 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.ZJ.AB0H.01 1 0.1563 0.7501 0.90 0.00 0.00 0.00 0.00 0.10 0.00 0.00
#> TCGA.VS.A9UA.01 1 0.2888 0.6639 0.80 0.00 0.00 0.04 0.00 0.16 0.00 0.00
#> TCGA.LP.A4AW.01 1 0.2856 0.4208 0.78 0.00 0.00 0.20 0.00 0.02 0.00 0.00
#> TCGA.C5.A1BM.01 4 0.2132 0.8107 0.00 0.00 0.00 0.88 0.00 0.04 0.08 0.00
#> TCGA.C5.A1BE.01 1 0.0000 0.7745 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.FU.A23L.01 7 0.5207 0.4663 0.00 0.04 0.00 0.10 0.02 0.04 0.68 0.12
#> TCGA.C5.A1BI.01 4 0.0808 0.8583 0.00 0.00 0.00 0.96 0.00 0.00 0.04 0.00
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)
consensus_heatmap(res, k = 7)
consensus_heatmap(res, k = 8)
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)
membership_heatmap(res, k = 7)
membership_heatmap(res, k = 8)
As soon as the classes for columns are determined, the signatures that are significantly different between subgroups can be looked for. Following are the heatmaps for signatures.
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)
get_signatures(res, k = 7)
get_signatures(res, k = 8)
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 (which is done by automatically selecting number of clusters).If there are too many signatures, top_signatures = ... can be set to only show the
signatures with the highest FDRs:
# code only for demonstration
# e.g. to show the top 500 most significant rows
tb = get_signature(res, k = ..., top_signatures = 500)
If the signatures are defined as these which are uniquely high in current group, diff_method argument
can be set to "uniquely_high_in_one_group":
# code only for demonstration
tb = get_signature(res, k = ..., diff_method = "uniquely_high_in_one_group")
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")
dimension_reduction(res, k = 7, method = "UMAP")
dimension_reduction(res, k = 8, method = "UMAP")
Following heatmap shows how subgroups are split when increasing k:
collect_classes(res)
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.
Parent node: Node013. Child nodes: Node01111-leaf , Node01112-leaf , Node01113-leaf , Node01131-leaf , Node01132-leaf , Node01133-leaf , Node01211-leaf , Node01212-leaf , Node01311-leaf , Node01312-leaf , Node01313-leaf , Node02111 , Node02112-leaf , Node02221 , Node02222-leaf , Node03111-leaf , Node03112 .
The object with results only for a single top-value method and a single partitioning method can be extracted as:
res = res_rh["0131"]
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, 7, 8.
#> On a matrix with 30000 rows and 39 columns.
#> Top rows (1000) are extracted by 'ATC' method.
#> Subgroups are detected by 'skmeans' method.
#> Performed in total 350 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_partitions"
#> [7] "compare_signatures" "consensus_heatmap" "dimension_reduction"
#> [10] "functional_enrichment" "get_anno_col" "get_anno"
#> [13] "get_classes" "get_consensus" "get_matrix"
#> [16] "get_membership" "get_param" "get_signatures"
#> [19] "get_stats" "is_best_k" "is_stable_k"
#> [22] "membership_heatmap" "ncol" "nrow"
#> [25] "plot_ecdf" "predict_classes" "rownames"
#> [28] "select_partition_number" "show" "suggest_best_k"
#> [31] "test_to_known_factors" "top_rows_heatmap"
collect_plots() function collects all the plots made from res for all k (number of subgroups)
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, higher 1-PAC score, higher mean silhouette score or higher
concordance corresponds to better partition. Rand index and Jaccard index
measure how similar the current partition is compared to partition with k-1.
If they are too similar, we won't accept k is better than k-1.
select_partition_number(res)
The numeric values for all these statistics can be obtained by get_stats().
get_stats(res)
#> k 1-PAC mean_silhouette concordance area_increased Rand Jaccard
#> 2 2 1.000 1.000 1.000 0.4863 0.514 0.514
#> 3 3 1.000 0.991 0.992 0.3470 0.787 0.602
#> 4 4 0.883 0.791 0.870 0.0835 0.946 0.843
#> 5 5 0.739 0.691 0.852 0.0861 0.923 0.747
#> 6 6 0.700 0.667 0.834 0.0419 0.957 0.824
#> 7 7 0.716 0.492 0.686 0.0326 0.919 0.653
#> 8 8 0.715 0.499 0.762 0.0282 0.930 0.649
suggest_best_k() suggests the best \(k\) based on these statistics. The rules are as follows:
suggest_best_k(res)
#> [1] 3
#> attr(,"optional")
#> [1] 2
There is also optional best \(k\) = 2 that is worth to check.
Following is 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 subgroup
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
#> TCGA.VS.A94Z.01 2 0 1 0 1
#> TCGA.EK.A2R7.01 2 0 1 0 1
#> TCGA.EK.A2RN.01 1 0 1 1 0
#> TCGA.C5.A8XJ.01 2 0 1 0 1
#> TCGA.VS.A8Q8.01 1 0 1 1 0
#> TCGA.EK.A2RK.01 2 0 1 0 1
#> TCGA.EK.A2RD.01 2 0 1 0 1
#> TCGA.C5.A3HL.01 2 0 1 0 1
#> TCGA.HM.A4S6.01 2 0 1 0 1
#> TCGA.MA.AA3Z.01 2 0 1 0 1
#> TCGA.EK.A2RE.01 1 0 1 1 0
#> TCGA.C5.A1BQ.01 2 0 1 0 1
#> TCGA.C5.A7XC.01 1 0 1 1 0
#> TCGA.EA.A3HR.01 2 0 1 0 1
#> TCGA.DG.A2KL.01 1 0 1 1 0
#> TCGA.BI.A0VR.01 2 0 1 0 1
#> TCGA.DS.A0VL.01 1 0 1 1 0
#> TCGA.DS.A0VK.01 2 0 1 0 1
#> TCGA.HM.A3JJ.01 2 0 1 0 1
#> TCGA.EA.A3HT.01 1 0 1 1 0
#> TCGA.EK.A2PI.01 2 0 1 0 1
#> TCGA.C5.A7UI.01 2 0 1 0 1
#> TCGA.EK.A2PL.01 1 0 1 1 0
#> TCGA.JX.A5QV.01 1 0 1 1 0
#> TCGA.DS.A5RQ.01 1 0 1 1 0
#> TCGA.EX.A69L.01 1 0 1 1 0
#> TCGA.Q1.A5R3.01 2 0 1 0 1
#> TCGA.C5.A7CL.01 1 0 1 1 0
#> TCGA.UC.A7PG.01 1 0 1 1 0
#> TCGA.DS.A1OD.01 2 0 1 0 1
#> TCGA.ZJ.AAXD.01 1 0 1 1 0
#> TCGA.ZJ.AAXU.01 2 0 1 0 1
#> TCGA.C5.A1MK.01 2 0 1 0 1
#> TCGA.LP.A4AV.01 2 0 1 0 1
#> TCGA.C5.A1MP.01 2 0 1 0 1
#> TCGA.ZJ.AB0H.01 2 0 1 0 1
#> TCGA.VS.A9UA.01 1 0 1 1 0
#> TCGA.LP.A4AW.01 2 0 1 0 1
#> TCGA.C5.A1BE.01 2 0 1 0 1
cbind(get_classes(res, k = 3), get_membership(res, k = 3))
#> class entropy silhouette p1 p2 p3
#> TCGA.VS.A94Z.01 3 0.0892 0.997 0.00 0.02 0.98
#> TCGA.EK.A2R7.01 2 0.0000 0.996 0.00 1.00 0.00
#> TCGA.EK.A2RN.01 1 0.0892 0.984 0.98 0.00 0.02
#> TCGA.C5.A8XJ.01 2 0.0000 0.996 0.00 1.00 0.00
#> TCGA.VS.A8Q8.01 1 0.0000 0.992 1.00 0.00 0.00
#> TCGA.EK.A2RK.01 2 0.0000 0.996 0.00 1.00 0.00
#> TCGA.EK.A2RD.01 2 0.0892 0.978 0.00 0.98 0.02
#> TCGA.C5.A3HL.01 2 0.0000 0.996 0.00 1.00 0.00
#> TCGA.HM.A4S6.01 3 0.0000 0.977 0.00 0.00 1.00
#> TCGA.MA.AA3Z.01 2 0.0000 0.996 0.00 1.00 0.00
#> TCGA.EK.A2RE.01 1 0.0000 0.992 1.00 0.00 0.00
#> TCGA.C5.A1BQ.01 3 0.0892 0.997 0.00 0.02 0.98
#> TCGA.C5.A7XC.01 1 0.0892 0.984 0.98 0.00 0.02
#> TCGA.EA.A3HR.01 3 0.0892 0.997 0.00 0.02 0.98
#> TCGA.DG.A2KL.01 1 0.0000 0.992 1.00 0.00 0.00
#> TCGA.BI.A0VR.01 2 0.0000 0.996 0.00 1.00 0.00
#> TCGA.DS.A0VL.01 1 0.0892 0.974 0.98 0.02 0.00
#> TCGA.DS.A0VK.01 2 0.0000 0.996 0.00 1.00 0.00
#> TCGA.HM.A3JJ.01 2 0.0000 0.996 0.00 1.00 0.00
#> TCGA.EA.A3HT.01 1 0.0000 0.992 1.00 0.00 0.00
#> TCGA.EK.A2PI.01 2 0.0892 0.977 0.02 0.98 0.00
#> TCGA.C5.A7UI.01 3 0.0892 0.997 0.00 0.02 0.98
#> TCGA.EK.A2PL.01 1 0.0000 0.992 1.00 0.00 0.00
#> TCGA.JX.A5QV.01 1 0.0000 0.992 1.00 0.00 0.00
#> TCGA.DS.A5RQ.01 1 0.0000 0.992 1.00 0.00 0.00
#> TCGA.EX.A69L.01 1 0.0892 0.984 0.98 0.00 0.02
#> TCGA.Q1.A5R3.01 2 0.0000 0.996 0.00 1.00 0.00
#> TCGA.C5.A7CL.01 1 0.0000 0.992 1.00 0.00 0.00
#> TCGA.UC.A7PG.01 1 0.1529 0.969 0.96 0.00 0.04
#> TCGA.DS.A1OD.01 2 0.0000 0.996 0.00 1.00 0.00
#> TCGA.ZJ.AAXD.01 2 0.0892 0.977 0.02 0.98 0.00
#> TCGA.ZJ.AAXU.01 2 0.0000 0.996 0.00 1.00 0.00
#> TCGA.C5.A1MK.01 3 0.0892 0.997 0.00 0.02 0.98
#> TCGA.LP.A4AV.01 3 0.0892 0.997 0.00 0.02 0.98
#> TCGA.C5.A1MP.01 3 0.0892 0.997 0.00 0.02 0.98
#> TCGA.ZJ.AB0H.01 2 0.0000 0.996 0.00 1.00 0.00
#> TCGA.VS.A9UA.01 1 0.0000 0.992 1.00 0.00 0.00
#> TCGA.LP.A4AW.01 2 0.0000 0.996 0.00 1.00 0.00
#> TCGA.C5.A1BE.01 2 0.0000 0.996 0.00 1.00 0.00
cbind(get_classes(res, k = 4), get_membership(res, k = 4))
#> class entropy silhouette p1 p2 p3 p4
#> TCGA.VS.A94Z.01 3 0.0707 0.9922 0.00 0.02 0.98 0.00
#> TCGA.EK.A2R7.01 2 0.0000 0.9655 0.00 1.00 0.00 0.00
#> TCGA.EK.A2RN.01 4 0.5594 1.0000 0.46 0.00 0.02 0.52
#> TCGA.C5.A8XJ.01 2 0.0000 0.9655 0.00 1.00 0.00 0.00
#> TCGA.VS.A8Q8.01 1 0.4855 0.4625 0.60 0.00 0.00 0.40
#> TCGA.EK.A2RK.01 2 0.0707 0.9562 0.00 0.98 0.02 0.00
#> TCGA.EK.A2RD.01 2 0.1637 0.9252 0.00 0.94 0.06 0.00
#> TCGA.C5.A3HL.01 2 0.0707 0.9562 0.02 0.98 0.00 0.00
#> TCGA.HM.A4S6.01 3 0.0000 0.9764 0.00 0.00 1.00 0.00
#> TCGA.MA.AA3Z.01 2 0.1211 0.9495 0.00 0.96 0.00 0.04
#> TCGA.EK.A2RE.01 1 0.4948 0.4510 0.56 0.00 0.00 0.44
#> TCGA.C5.A1BQ.01 3 0.0707 0.9922 0.00 0.02 0.98 0.00
#> TCGA.C5.A7XC.01 4 0.5594 1.0000 0.46 0.00 0.02 0.52
#> TCGA.EA.A3HR.01 3 0.0707 0.9922 0.00 0.02 0.98 0.00
#> TCGA.DG.A2KL.01 1 0.0707 0.4873 0.98 0.00 0.00 0.02
#> TCGA.BI.A0VR.01 2 0.0707 0.9570 0.02 0.98 0.00 0.00
#> TCGA.DS.A0VL.01 1 0.6201 -0.0326 0.62 0.30 0.00 0.08
#> TCGA.DS.A0VK.01 2 0.0000 0.9655 0.00 1.00 0.00 0.00
#> TCGA.HM.A3JJ.01 2 0.1211 0.9495 0.00 0.96 0.00 0.04
#> TCGA.EA.A3HT.01 1 0.4994 -0.8902 0.52 0.00 0.00 0.48
#> TCGA.EK.A2PI.01 2 0.0707 0.9562 0.02 0.98 0.00 0.00
#> TCGA.C5.A7UI.01 3 0.0707 0.9922 0.00 0.02 0.98 0.00
#> TCGA.EK.A2PL.01 1 0.4994 0.4319 0.52 0.00 0.00 0.48
#> TCGA.JX.A5QV.01 1 0.0000 0.5087 1.00 0.00 0.00 0.00
#> TCGA.DS.A5RQ.01 1 0.0000 0.5087 1.00 0.00 0.00 0.00
#> TCGA.EX.A69L.01 4 0.5594 1.0000 0.46 0.00 0.02 0.52
#> TCGA.Q1.A5R3.01 2 0.3606 0.8460 0.02 0.84 0.00 0.14
#> TCGA.C5.A7CL.01 1 0.0707 0.4873 0.98 0.00 0.00 0.02
#> TCGA.UC.A7PG.01 4 0.5594 1.0000 0.46 0.00 0.02 0.52
#> TCGA.DS.A1OD.01 2 0.0000 0.9655 0.00 1.00 0.00 0.00
#> TCGA.ZJ.AAXD.01 2 0.3172 0.8094 0.16 0.84 0.00 0.00
#> TCGA.ZJ.AAXU.01 2 0.0000 0.9655 0.00 1.00 0.00 0.00
#> TCGA.C5.A1MK.01 3 0.0707 0.9922 0.00 0.02 0.98 0.00
#> TCGA.LP.A4AV.01 3 0.0000 0.9764 0.00 0.00 1.00 0.00
#> TCGA.C5.A1MP.01 3 0.0707 0.9922 0.00 0.02 0.98 0.00
#> TCGA.ZJ.AB0H.01 2 0.0000 0.9655 0.00 1.00 0.00 0.00
#> TCGA.VS.A9UA.01 1 0.0000 0.5087 1.00 0.00 0.00 0.00
#> TCGA.LP.A4AW.01 2 0.0000 0.9655 0.00 1.00 0.00 0.00
#> TCGA.C5.A1BE.01 2 0.0000 0.9655 0.00 1.00 0.00 0.00
cbind(get_classes(res, k = 5), get_membership(res, k = 5))
#> class entropy silhouette p1 p2 p3 p4 p5
#> TCGA.VS.A94Z.01 3 0.0000 0.96824 0.00 0.00 1.00 0.00 0.00
#> TCGA.EK.A2R7.01 2 0.1648 0.82838 0.00 0.94 0.00 0.04 0.02
#> TCGA.EK.A2RN.01 4 0.2280 0.98038 0.12 0.00 0.00 0.88 0.00
#> TCGA.C5.A8XJ.01 2 0.2077 0.82508 0.00 0.92 0.00 0.04 0.04
#> TCGA.VS.A8Q8.01 1 0.4644 0.26598 0.68 0.00 0.00 0.04 0.28
#> TCGA.EK.A2RK.01 2 0.2077 0.82508 0.00 0.92 0.00 0.04 0.04
#> TCGA.EK.A2RD.01 2 0.3731 0.72936 0.00 0.80 0.16 0.00 0.04
#> TCGA.C5.A3HL.01 2 0.3099 0.80794 0.04 0.88 0.00 0.04 0.04
#> TCGA.HM.A4S6.01 3 0.0609 0.96093 0.00 0.00 0.98 0.02 0.00
#> TCGA.MA.AA3Z.01 2 0.5470 0.39514 0.00 0.60 0.02 0.04 0.34
#> TCGA.EK.A2RE.01 5 0.5131 0.00183 0.42 0.00 0.00 0.04 0.54
#> TCGA.C5.A1BQ.01 3 0.1410 0.96277 0.00 0.00 0.94 0.00 0.06
#> TCGA.C5.A7XC.01 4 0.2516 0.98008 0.14 0.00 0.00 0.86 0.00
#> TCGA.EA.A3HR.01 3 0.1410 0.96277 0.00 0.00 0.94 0.00 0.06
#> TCGA.DG.A2KL.01 1 0.1043 0.64478 0.96 0.00 0.00 0.00 0.04
#> TCGA.BI.A0VR.01 2 0.4045 0.77500 0.04 0.84 0.02 0.06 0.04
#> TCGA.DS.A0VL.01 1 0.6894 0.31864 0.58 0.10 0.00 0.10 0.22
#> TCGA.DS.A0VK.01 2 0.2012 0.81637 0.00 0.92 0.00 0.02 0.06
#> TCGA.HM.A3JJ.01 2 0.5534 0.35132 0.00 0.58 0.04 0.02 0.36
#> TCGA.EA.A3HT.01 1 0.4798 -0.11367 0.54 0.00 0.00 0.44 0.02
#> TCGA.EK.A2PI.01 2 0.3099 0.80794 0.04 0.88 0.00 0.04 0.04
#> TCGA.C5.A7UI.01 3 0.0000 0.96824 0.00 0.00 1.00 0.00 0.00
#> TCGA.EK.A2PL.01 5 0.2732 0.36316 0.16 0.00 0.00 0.00 0.84
#> TCGA.JX.A5QV.01 1 0.0609 0.66126 0.98 0.00 0.00 0.02 0.00
#> TCGA.DS.A5RQ.01 1 0.1216 0.65639 0.96 0.00 0.00 0.02 0.02
#> TCGA.EX.A69L.01 4 0.2516 0.98008 0.14 0.00 0.00 0.86 0.00
#> TCGA.Q1.A5R3.01 5 0.5588 -0.05746 0.00 0.38 0.02 0.04 0.56
#> TCGA.C5.A7CL.01 1 0.1410 0.63416 0.94 0.00 0.00 0.00 0.06
#> TCGA.UC.A7PG.01 4 0.2280 0.98038 0.12 0.00 0.00 0.88 0.00
#> TCGA.DS.A1OD.01 2 0.2012 0.82176 0.00 0.92 0.02 0.00 0.06
#> TCGA.ZJ.AAXD.01 1 0.4829 0.04262 0.50 0.48 0.00 0.00 0.02
#> TCGA.ZJ.AAXU.01 2 0.0609 0.83114 0.00 0.98 0.00 0.00 0.02
#> TCGA.C5.A1MK.01 3 0.0609 0.96868 0.00 0.00 0.98 0.00 0.02
#> TCGA.LP.A4AV.01 3 0.0609 0.96093 0.00 0.00 0.98 0.02 0.00
#> TCGA.C5.A1MP.01 3 0.1410 0.96277 0.00 0.00 0.94 0.00 0.06
#> TCGA.ZJ.AB0H.01 2 0.3110 0.79235 0.00 0.86 0.06 0.00 0.08
#> TCGA.VS.A9UA.01 1 0.0000 0.65929 1.00 0.00 0.00 0.00 0.00
#> TCGA.LP.A4AW.01 2 0.2012 0.81957 0.00 0.92 0.02 0.00 0.06
#> TCGA.C5.A1BE.01 2 0.2077 0.82618 0.00 0.92 0.00 0.04 0.04
cbind(get_classes(res, k = 6), get_membership(res, k = 6))
#> class entropy silhouette p1 p2 p3 p4 p5 p6
#> TCGA.VS.A94Z.01 3 0.2629 0.8775 0.00 0.02 0.88 0.00 0.08 0.02
#> TCGA.EK.A2R7.01 2 0.1480 0.7490 0.00 0.94 0.00 0.00 0.02 0.04
#> TCGA.EK.A2RN.01 4 0.1480 0.9368 0.04 0.00 0.00 0.94 0.02 0.00
#> TCGA.C5.A8XJ.01 2 0.2020 0.7371 0.00 0.92 0.02 0.00 0.02 0.04
#> TCGA.VS.A8Q8.01 1 0.3756 0.0232 0.60 0.00 0.00 0.00 0.00 0.40
#> TCGA.EK.A2RK.01 2 0.3103 0.6904 0.00 0.86 0.06 0.00 0.04 0.04
#> TCGA.EK.A2RD.01 2 0.5370 0.6686 0.00 0.70 0.10 0.02 0.14 0.04
#> TCGA.C5.A3HL.01 2 0.0937 0.7458 0.00 0.96 0.00 0.00 0.00 0.04
#> TCGA.HM.A4S6.01 3 0.2020 0.9060 0.00 0.00 0.92 0.04 0.02 0.02
#> TCGA.MA.AA3Z.01 5 0.3198 0.4734 0.00 0.26 0.00 0.00 0.74 0.00
#> TCGA.EK.A2RE.01 6 0.3523 0.0000 0.18 0.00 0.00 0.00 0.04 0.78
#> TCGA.C5.A1BQ.01 3 0.2175 0.9109 0.00 0.02 0.92 0.02 0.02 0.02
#> TCGA.C5.A7XC.01 4 0.1556 0.9435 0.08 0.00 0.00 0.92 0.00 0.00
#> TCGA.EA.A3HR.01 3 0.2880 0.8907 0.00 0.02 0.88 0.02 0.02 0.06
#> TCGA.DG.A2KL.01 1 0.1807 0.6825 0.92 0.00 0.00 0.02 0.00 0.06
#> TCGA.BI.A0VR.01 2 0.5054 0.7192 0.00 0.72 0.02 0.06 0.16 0.04
#> TCGA.DS.A0VL.01 1 0.5577 0.5025 0.66 0.02 0.00 0.14 0.16 0.02
#> TCGA.DS.A0VK.01 2 0.3460 0.7368 0.00 0.76 0.00 0.00 0.22 0.02
#> TCGA.HM.A3JJ.01 5 0.4844 0.2933 0.00 0.32 0.04 0.02 0.62 0.00
#> TCGA.EA.A3HT.01 1 0.3499 0.4766 0.68 0.00 0.00 0.32 0.00 0.00
#> TCGA.EK.A2PI.01 2 0.1480 0.7339 0.02 0.94 0.00 0.00 0.00 0.04
#> TCGA.C5.A7UI.01 3 0.1092 0.9178 0.00 0.00 0.96 0.00 0.02 0.02
#> TCGA.EK.A2PL.01 5 0.5037 -0.2946 0.08 0.00 0.00 0.00 0.54 0.38
#> TCGA.JX.A5QV.01 1 0.0937 0.7152 0.96 0.00 0.00 0.04 0.00 0.00
#> TCGA.DS.A5RQ.01 1 0.0937 0.7086 0.96 0.00 0.00 0.04 0.00 0.00
#> TCGA.EX.A69L.01 4 0.2094 0.9353 0.08 0.00 0.00 0.90 0.00 0.02
#> TCGA.Q1.A5R3.01 5 0.2512 0.4309 0.00 0.06 0.00 0.00 0.88 0.06
#> TCGA.C5.A7CL.01 1 0.2190 0.6757 0.90 0.00 0.00 0.04 0.00 0.06
#> TCGA.UC.A7PG.01 4 0.2345 0.9355 0.06 0.00 0.02 0.90 0.02 0.00
#> TCGA.DS.A1OD.01 2 0.4489 0.7174 0.00 0.72 0.02 0.02 0.22 0.02
#> TCGA.ZJ.AAXD.01 1 0.4675 0.3507 0.66 0.28 0.00 0.00 0.02 0.04
#> TCGA.ZJ.AAXU.01 2 0.4197 0.7398 0.00 0.76 0.02 0.02 0.18 0.02
#> TCGA.C5.A1MK.01 3 0.0547 0.9230 0.00 0.02 0.98 0.00 0.00 0.00
#> TCGA.LP.A4AV.01 3 0.2020 0.9076 0.00 0.00 0.92 0.02 0.02 0.04
#> TCGA.C5.A1MP.01 3 0.1635 0.9133 0.00 0.00 0.94 0.02 0.02 0.02
#> TCGA.ZJ.AB0H.01 2 0.5337 0.5534 0.00 0.60 0.02 0.02 0.32 0.04
#> TCGA.VS.A9UA.01 1 0.0937 0.7152 0.96 0.00 0.00 0.04 0.00 0.00
#> TCGA.LP.A4AW.01 2 0.3976 0.7259 0.00 0.74 0.00 0.02 0.22 0.02
#> TCGA.C5.A1BE.01 2 0.0937 0.7458 0.00 0.96 0.00 0.00 0.00 0.04
cbind(get_classes(res, k = 7), get_membership(res, k = 7))
#> class entropy silhouette p1 p2 p3 p4 p5 p6 p7
#> TCGA.VS.A94Z.01 3 0.1671 0.8068 0.00 0.00 0.90 0.00 0.10 0.00 0.00
#> TCGA.EK.A2R7.01 2 0.1664 0.5335 0.00 0.92 0.00 0.00 0.06 0.00 0.02
#> TCGA.EK.A2RN.01 4 0.0863 0.9568 0.00 0.00 0.00 0.96 0.00 0.00 0.04
#> TCGA.C5.A8XJ.01 2 0.4671 0.4525 0.00 0.68 0.02 0.00 0.14 0.00 0.16
#> TCGA.VS.A8Q8.01 1 0.3558 0.1406 0.52 0.00 0.00 0.00 0.00 0.48 0.00
#> TCGA.EK.A2RK.01 2 0.4873 0.3969 0.00 0.60 0.00 0.00 0.18 0.00 0.22
#> TCGA.EK.A2RD.01 2 0.6550 0.1193 0.04 0.48 0.10 0.00 0.30 0.00 0.08
#> TCGA.C5.A3HL.01 2 0.0000 0.5421 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.HM.A4S6.01 3 0.0504 0.8609 0.00 0.00 0.98 0.02 0.00 0.00 0.00
#> TCGA.MA.AA3Z.01 5 0.3058 0.3448 0.00 0.10 0.00 0.00 0.82 0.00 0.08
#> TCGA.EK.A2RE.01 6 0.0504 0.0000 0.02 0.00 0.00 0.00 0.00 0.98 0.00
#> TCGA.C5.A1BQ.01 3 0.3722 0.7786 0.00 0.00 0.76 0.00 0.04 0.02 0.18
#> TCGA.C5.A7XC.01 4 0.0504 0.9568 0.02 0.00 0.00 0.98 0.00 0.00 0.00
#> TCGA.EA.A3HR.01 3 0.3991 0.7450 0.00 0.00 0.72 0.00 0.04 0.02 0.22
#> TCGA.DG.A2KL.01 1 0.2509 0.7543 0.88 0.00 0.00 0.06 0.00 0.04 0.02
#> TCGA.BI.A0VR.01 2 0.6507 0.0164 0.04 0.50 0.06 0.04 0.32 0.00 0.04
#> TCGA.DS.A0VL.01 1 0.4604 0.5689 0.70 0.00 0.00 0.06 0.18 0.00 0.06
#> TCGA.DS.A0VK.01 2 0.4514 -0.0355 0.00 0.48 0.00 0.00 0.46 0.00 0.06
#> TCGA.HM.A3JJ.01 5 0.4295 0.4574 0.00 0.14 0.06 0.00 0.74 0.00 0.06
#> TCGA.EA.A3HT.01 1 0.3745 0.5839 0.70 0.00 0.00 0.26 0.00 0.00 0.04
#> TCGA.EK.A2PI.01 2 0.0000 0.5421 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.C5.A7UI.01 3 0.0000 0.8638 0.00 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.EK.A2PL.01 7 0.6413 0.0000 0.06 0.00 0.00 0.00 0.30 0.26 0.38
#> TCGA.JX.A5QV.01 1 0.0000 0.7679 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.DS.A5RQ.01 1 0.0863 0.7630 0.96 0.00 0.00 0.00 0.00 0.00 0.04
#> TCGA.EX.A69L.01 4 0.0504 0.9568 0.02 0.00 0.00 0.98 0.00 0.00 0.00
#> TCGA.Q1.A5R3.01 5 0.4146 -0.4954 0.00 0.02 0.00 0.00 0.64 0.02 0.32
#> TCGA.C5.A7CL.01 1 0.2769 0.7473 0.86 0.00 0.00 0.04 0.00 0.08 0.02
#> TCGA.UC.A7PG.01 4 0.0863 0.9568 0.00 0.00 0.00 0.96 0.00 0.00 0.04
#> TCGA.DS.A1OD.01 5 0.5625 0.0658 0.00 0.40 0.06 0.00 0.46 0.00 0.08
#> TCGA.ZJ.AAXD.01 2 0.4844 -0.0848 0.44 0.50 0.00 0.00 0.02 0.02 0.02
#> TCGA.ZJ.AAXU.01 2 0.5212 -0.0987 0.00 0.48 0.04 0.00 0.42 0.00 0.06
#> TCGA.C5.A1MK.01 3 0.0504 0.8662 0.00 0.00 0.98 0.00 0.00 0.00 0.02
#> TCGA.LP.A4AV.01 3 0.3228 0.7428 0.00 0.00 0.80 0.02 0.02 0.00 0.16
#> TCGA.C5.A1MP.01 3 0.1664 0.8594 0.00 0.00 0.92 0.00 0.02 0.00 0.06
#> TCGA.ZJ.AB0H.01 5 0.4649 0.3292 0.00 0.30 0.06 0.00 0.62 0.00 0.02
#> TCGA.VS.A9UA.01 1 0.2213 0.7447 0.90 0.04 0.00 0.00 0.00 0.04 0.02
#> TCGA.LP.A4AW.01 5 0.4954 0.1282 0.00 0.40 0.04 0.00 0.52 0.00 0.04
#> TCGA.C5.A1BE.01 2 0.0000 0.5421 0.00 1.00 0.00 0.00 0.00 0.00 0.00
cbind(get_classes(res, k = 8), get_membership(res, k = 8))
#> class entropy silhouette p1 p2 p3 p4 p5 p6 p7 p8
#> TCGA.VS.A94Z.01 3 0.2025 0.4959 0.00 0.00 0.88 0.00 0.10 0.00 0.00 0.02
#> TCGA.EK.A2R7.01 2 0.1887 0.6199 0.00 0.90 0.00 0.00 0.06 0.00 0.00 0.04
#> TCGA.EK.A2RN.01 4 0.1275 0.8956 0.00 0.00 0.00 0.94 0.00 0.00 0.02 0.04
#> TCGA.C5.A8XJ.01 2 0.4672 0.5232 0.00 0.62 0.00 0.00 0.12 0.00 0.02 0.24
#> TCGA.VS.A8Q8.01 1 0.4399 0.1076 0.50 0.00 0.00 0.00 0.02 0.44 0.00 0.04
#> TCGA.EK.A2RK.01 2 0.5313 0.4817 0.00 0.54 0.02 0.00 0.12 0.00 0.02 0.30
#> TCGA.EK.A2RD.01 5 0.5615 0.5906 0.02 0.30 0.02 0.02 0.56 0.00 0.02 0.06
#> TCGA.C5.A3HL.01 2 0.0000 0.6443 0.00 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.HM.A4S6.01 3 0.2071 0.5112 0.00 0.00 0.90 0.02 0.04 0.00 0.00 0.04
#> TCGA.MA.AA3Z.01 5 0.5371 0.2998 0.00 0.06 0.00 0.00 0.60 0.02 0.22 0.10
#> TCGA.EK.A2RE.01 6 0.0471 0.0000 0.02 0.00 0.00 0.00 0.00 0.98 0.00 0.00
#> TCGA.C5.A1BQ.01 3 0.3991 -0.4372 0.00 0.00 0.62 0.00 0.06 0.00 0.00 0.32
#> TCGA.C5.A7XC.01 4 0.0471 0.9330 0.02 0.00 0.00 0.98 0.00 0.00 0.00 0.00
#> TCGA.EA.A3HR.01 8 0.4224 0.0000 0.00 0.00 0.46 0.00 0.06 0.00 0.00 0.48
#> TCGA.DG.A2KL.01 1 0.3002 0.6789 0.82 0.00 0.00 0.04 0.00 0.12 0.00 0.02
#> TCGA.BI.A0VR.01 5 0.5306 0.6144 0.04 0.32 0.00 0.02 0.56 0.00 0.02 0.04
#> TCGA.DS.A0VL.01 1 0.6336 0.4608 0.58 0.08 0.00 0.06 0.16 0.00 0.06 0.06
#> TCGA.DS.A0VK.01 2 0.5480 -0.1116 0.00 0.42 0.00 0.00 0.42 0.02 0.02 0.12
#> TCGA.HM.A3JJ.01 5 0.5763 0.4484 0.00 0.14 0.04 0.00 0.58 0.02 0.20 0.02
#> TCGA.EA.A3HT.01 1 0.4845 0.5895 0.70 0.04 0.00 0.16 0.04 0.00 0.04 0.02
#> TCGA.EK.A2PI.01 2 0.0000 0.6443 0.00 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.C5.A7UI.01 3 0.1275 0.5159 0.00 0.00 0.94 0.00 0.02 0.00 0.00 0.04
#> TCGA.EK.A2PL.01 7 0.2859 0.5399 0.02 0.00 0.00 0.00 0.00 0.14 0.82 0.02
#> TCGA.JX.A5QV.01 1 0.0941 0.7213 0.96 0.00 0.00 0.00 0.00 0.00 0.02 0.02
#> TCGA.DS.A5RQ.01 1 0.1408 0.7149 0.94 0.02 0.00 0.00 0.00 0.00 0.02 0.02
#> TCGA.EX.A69L.01 4 0.1275 0.9225 0.02 0.00 0.00 0.94 0.04 0.00 0.00 0.00
#> TCGA.Q1.A5R3.01 7 0.2534 0.6098 0.00 0.00 0.00 0.00 0.22 0.00 0.78 0.00
#> TCGA.C5.A7CL.01 1 0.3627 0.6448 0.78 0.00 0.00 0.04 0.02 0.14 0.00 0.02
#> TCGA.UC.A7PG.01 4 0.1741 0.9129 0.04 0.00 0.02 0.92 0.02 0.00 0.00 0.00
#> TCGA.DS.A1OD.01 5 0.3015 0.6678 0.00 0.32 0.00 0.00 0.68 0.00 0.00 0.00
#> TCGA.ZJ.AAXD.01 2 0.5435 0.2526 0.28 0.56 0.00 0.00 0.08 0.00 0.06 0.02
#> TCGA.ZJ.AAXU.01 5 0.3142 0.6662 0.00 0.36 0.00 0.00 0.64 0.00 0.00 0.00
#> TCGA.C5.A1MK.01 3 0.2725 0.3218 0.00 0.00 0.82 0.00 0.04 0.00 0.00 0.14
#> TCGA.LP.A4AV.01 3 0.3514 0.2448 0.00 0.00 0.64 0.02 0.00 0.00 0.00 0.34
#> TCGA.C5.A1MP.01 3 0.4211 0.0835 0.00 0.00 0.70 0.02 0.16 0.00 0.00 0.12
#> TCGA.ZJ.AB0H.01 5 0.3941 0.6910 0.00 0.26 0.00 0.00 0.68 0.02 0.04 0.00
#> TCGA.VS.A9UA.01 1 0.1741 0.7211 0.92 0.00 0.00 0.00 0.00 0.02 0.02 0.04
#> TCGA.LP.A4AW.01 5 0.4276 0.6011 0.00 0.28 0.02 0.00 0.64 0.00 0.00 0.06
#> TCGA.C5.A1BE.01 2 0.0471 0.6369 0.00 0.98 0.00 0.00 0.02 0.00 0.00 0.00
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)
consensus_heatmap(res, k = 7)
consensus_heatmap(res, k = 8)
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)
membership_heatmap(res, k = 7)
membership_heatmap(res, k = 8)
As soon as the classes for columns are determined, the signatures that are significantly different between subgroups can be looked for. Following are the heatmaps for signatures.
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)
get_signatures(res, k = 7)
get_signatures(res, k = 8)
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 (which is done by automatically selecting number of clusters).If there are too many signatures, top_signatures = ... can be set to only show the
signatures with the highest FDRs:
# code only for demonstration
# e.g. to show the top 500 most significant rows
tb = get_signature(res, k = ..., top_signatures = 500)
If the signatures are defined as these which are uniquely high in current group, diff_method argument
can be set to "uniquely_high_in_one_group":
# code only for demonstration
tb = get_signature(res, k = ..., diff_method = "uniquely_high_in_one_group")
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")
dimension_reduction(res, k = 7, method = "UMAP")
dimension_reduction(res, k = 8, method = "UMAP")
Following heatmap shows how subgroups are split when increasing k:
collect_classes(res)
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.
Parent node: Node0. Child nodes: Node011 , Node012 , Node013 , Node021 , Node022 , Node023 , Node031 , Node032-leaf .
The object with results only for a single top-value method and a single partitioning method can be extracted as:
res = res_rh["02"]
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, 7, 8.
#> On a matrix with 30000 rows and 117 columns.
#> Top rows (1000) are extracted by 'ATC' method.
#> Subgroups are detected by 'kmeans' method.
#> Performed in total 350 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_partitions"
#> [7] "compare_signatures" "consensus_heatmap" "dimension_reduction"
#> [10] "functional_enrichment" "get_anno_col" "get_anno"
#> [13] "get_classes" "get_consensus" "get_matrix"
#> [16] "get_membership" "get_param" "get_signatures"
#> [19] "get_stats" "is_best_k" "is_stable_k"
#> [22] "membership_heatmap" "ncol" "nrow"
#> [25] "plot_ecdf" "predict_classes" "rownames"
#> [28] "select_partition_number" "show" "suggest_best_k"
#> [31] "test_to_known_factors" "top_rows_heatmap"
collect_plots() function collects all the plots made from res for all k (number of subgroups)
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, higher 1-PAC score, higher mean silhouette score or higher
concordance corresponds to better partition. Rand index and Jaccard index
measure how similar the current partition is compared to partition with k-1.
If they are too similar, we won't accept k is better than k-1.
select_partition_number(res)
The numeric values for all these statistics can be obtained by get_stats().
get_stats(res)
#> k 1-PAC mean_silhouette concordance area_increased Rand Jaccard
#> 2 2 1.000 0.978 0.991 0.5030 0.497 0.497
#> 3 3 1.000 0.970 0.984 0.2896 0.664 0.433
#> 4 4 0.734 0.815 0.890 0.1424 0.808 0.520
#> 5 5 0.712 0.715 0.839 0.0674 0.865 0.540
#> 6 6 0.735 0.646 0.765 0.0420 0.939 0.713
#> 7 7 0.768 0.627 0.814 0.0277 0.937 0.682
#> 8 8 0.773 0.580 0.751 0.0221 0.961 0.775
suggest_best_k() suggests the best \(k\) based on these statistics. The rules are as follows:
suggest_best_k(res)
#> [1] 3
#> attr(,"optional")
#> [1] 2
There is also optional best \(k\) = 2 that is worth to check.
Following is 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 subgroup
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
#> TCGA.GH.A9DA.01 1 0.000 0.990 1.00 0.00
#> TCGA.ZJ.A8QQ.01 1 0.000 0.990 1.00 0.00
#> TCGA.VS.A954.01 1 0.000 0.990 1.00 0.00
#> TCGA.MA.AA42.01 1 0.000 0.990 1.00 0.00
#> TCGA.C5.A8YQ.01 1 0.000 0.990 1.00 0.00
#> TCGA.EK.A3GJ.01 1 0.000 0.990 1.00 0.00
#> TCGA.C5.A902.01 1 0.000 0.990 1.00 0.00
#> TCGA.MA.AA3W.01 2 0.000 0.992 0.00 1.00
#> TCGA.EK.A2R9.01 1 0.000 0.990 1.00 0.00
#> TCGA.IR.A3LC.01 2 0.000 0.992 0.00 1.00
#> TCGA.C5.A3HD.01 1 0.000 0.990 1.00 0.00
#> TCGA.EA.A50E.01 1 0.000 0.990 1.00 0.00
#> TCGA.IR.A3LK.01 2 0.000 0.992 0.00 1.00
#> TCGA.VS.A8EK.01 2 0.000 0.992 0.00 1.00
#> TCGA.IR.A3LH.01 1 0.000 0.990 1.00 0.00
#> TCGA.EK.A2RO.01 1 0.855 0.612 0.72 0.28
#> TCGA.C5.A2LZ.01 2 0.000 0.992 0.00 1.00
#> TCGA.C5.A901.01 1 0.000 0.990 1.00 0.00
#> TCGA.VS.A953.01 1 0.000 0.990 1.00 0.00
#> TCGA.EA.A3HS.01 2 0.000 0.992 0.00 1.00
#> TCGA.C5.A7CO.01 2 0.000 0.992 0.00 1.00
#> TCGA.IR.A3LL.01 1 0.000 0.990 1.00 0.00
#> TCGA.VS.A94W.01 1 0.000 0.990 1.00 0.00
#> TCGA.MY.A5BF.01 1 0.000 0.990 1.00 0.00
#> TCGA.EK.A2RC.01 2 0.000 0.992 0.00 1.00
#> TCGA.VS.A8EL.01 1 0.000 0.990 1.00 0.00
#> TCGA.EA.A3HQ.01 2 0.000 0.992 0.00 1.00
#> TCGA.UC.A7PF.01 1 0.000 0.990 1.00 0.00
#> TCGA.VS.A8Q9.01 1 0.000 0.990 1.00 0.00
#> TCGA.MA.AA41.01 1 0.000 0.990 1.00 0.00
#> TCGA.EK.A3GN.01 1 0.000 0.990 1.00 0.00
#> TCGA.ZJ.A8QO.01 1 0.000 0.990 1.00 0.00
#> TCGA.JW.A852.01 2 0.000 0.992 0.00 1.00
#> TCGA.JW.AAVH.01 2 0.000 0.992 0.00 1.00
#> TCGA.IR.A3L7.01 2 0.000 0.992 0.00 1.00
#> TCGA.C5.A8XH.01 1 0.000 0.990 1.00 0.00
#> TCGA.VS.A8EI.01 1 0.000 0.990 1.00 0.00
#> TCGA.VS.A8QC.01 2 0.000 0.992 0.00 1.00
#> TCGA.WL.A834.01 2 0.000 0.992 0.00 1.00
#> TCGA.C5.A8XI.01 1 0.000 0.990 1.00 0.00
#> TCGA.DS.A7WI.01 1 0.000 0.990 1.00 0.00
#> TCGA.VS.A8QF.01 2 0.000 0.992 0.00 1.00
#> TCGA.EK.A2PG.01 2 0.000 0.992 0.00 1.00
#> TCGA.VS.A8EC.01 2 0.000 0.992 0.00 1.00
#> TCGA.EA.A3QE.01 1 0.000 0.990 1.00 0.00
#> TCGA.DS.A0VM.01 2 0.000 0.992 0.00 1.00
#> TCGA.FU.A3HY.01 2 0.000 0.992 0.00 1.00
#> TCGA.Q1.A6DW.01 2 0.000 0.992 0.00 1.00
#> TCGA.DS.A3LQ.01 2 0.000 0.992 0.00 1.00
#> TCGA.EA.A3QD.01 1 0.000 0.990 1.00 0.00
#> TCGA.LP.A5U3.01 2 0.000 0.992 0.00 1.00
#> TCGA.EA.A6QX.01 2 0.000 0.992 0.00 1.00
#> TCGA.EK.A2RA.01 2 0.000 0.992 0.00 1.00
#> TCGA.Q1.A5R2.01 2 0.000 0.992 0.00 1.00
#> TCGA.MU.A8JM.01 1 0.000 0.990 1.00 0.00
#> TCGA.EK.A2IP.01 2 0.000 0.992 0.00 1.00
#> TCGA.JW.A5VL.01 2 0.000 0.992 0.00 1.00
#> TCGA.EK.A2IR.01 2 0.000 0.992 0.00 1.00
#> TCGA.C5.A2LV.01 1 0.000 0.990 1.00 0.00
#> TCGA.VS.A8EG.01 2 0.000 0.992 0.00 1.00
#> TCGA.C5.A7UE.01 2 0.000 0.992 0.00 1.00
#> TCGA.JW.A5VK.01 2 0.000 0.992 0.00 1.00
#> TCGA.C5.A7X5.01 1 0.000 0.990 1.00 0.00
#> TCGA.XS.A8TJ.01 2 0.000 0.992 0.00 1.00
#> TCGA.DS.A0VN.01 1 0.000 0.990 1.00 0.00
#> TCGA.DR.A0ZL.01 2 0.000 0.992 0.00 1.00
#> TCGA.FU.A3WB.01 1 0.000 0.990 1.00 0.00
#> TCGA.EA.A5O9.01 2 0.000 0.992 0.00 1.00
#> TCGA.EK.A2H0.01 1 0.000 0.990 1.00 0.00
#> TCGA.EA.A5ZE.01 1 0.000 0.990 1.00 0.00
#> TCGA.FU.A3TQ.01 2 0.000 0.992 0.00 1.00
#> TCGA.EK.A2RB.01 2 0.000 0.992 0.00 1.00
#> TCGA.JW.A5VI.01 1 0.000 0.990 1.00 0.00
#> TCGA.FU.A3YQ.01 1 0.000 0.990 1.00 0.00
#> TCGA.C5.A7CH.01 2 0.971 0.318 0.40 0.60
#> TCGA.C5.A2LX.01 2 0.000 0.992 0.00 1.00
#> TCGA.LP.A5U2.01 1 0.000 0.990 1.00 0.00
#> TCGA.FU.A3NI.01 1 0.000 0.990 1.00 0.00
#> TCGA.VS.A9V3.01 2 0.000 0.992 0.00 1.00
#> TCGA.C5.A1MN.01 2 0.000 0.992 0.00 1.00
#> TCGA.BI.A20A.01 1 0.000 0.990 1.00 0.00
#> TCGA.EA.A1QT.01 2 0.000 0.992 0.00 1.00
#> TCGA.EX.A69M.01 1 0.000 0.990 1.00 0.00
#> TCGA.VS.A9U7.01 2 0.000 0.992 0.00 1.00
#> TCGA.VS.A9UD.01 1 0.000 0.990 1.00 0.00
#> TCGA.ZX.AA5X.01 1 0.000 0.990 1.00 0.00
#> TCGA.C5.A7CJ.01 1 0.904 0.531 0.68 0.32
#> TCGA.EA.A78R.01 1 0.000 0.990 1.00 0.00
#> TCGA.VS.A9UY.01 2 0.000 0.992 0.00 1.00
#> TCGA.VS.A9U5.01 1 0.000 0.990 1.00 0.00
#> TCGA.DS.A1OC.01 1 0.000 0.990 1.00 0.00
#> TCGA.C5.A1BL.01 2 0.000 0.992 0.00 1.00
#> TCGA.VS.A9UV.01 2 0.000 0.992 0.00 1.00
#> TCGA.Q1.A6DT.01 1 0.000 0.990 1.00 0.00
#> TCGA.C5.A1M8.01 2 0.000 0.992 0.00 1.00
#> TCGA.VS.A957.01 2 0.000 0.992 0.00 1.00
#> TCGA.MU.A5YI.01 1 0.000 0.990 1.00 0.00
#> TCGA.ZJ.AAX4.01 1 0.000 0.990 1.00 0.00
#> TCGA.ZJ.AAXJ.01 1 0.000 0.990 1.00 0.00
#> TCGA.DS.A1O9.01 1 0.000 0.990 1.00 0.00
#> TCGA.EA.A43B.01 1 0.000 0.990 1.00 0.00
#> TCGA.ZJ.AAXI.01 2 0.000 0.992 0.00 1.00
#> TCGA.DS.A1OA.01 2 0.000 0.992 0.00 1.00
#> TCGA.C5.A1MQ.01 1 0.000 0.990 1.00 0.00
#> TCGA.VS.A9UC.01 2 0.000 0.992 0.00 1.00
#> TCGA.VS.A9V2.01 1 0.000 0.990 1.00 0.00
#> TCGA.VS.A9UU.01 1 0.000 0.990 1.00 0.00
#> TCGA.C5.A7CG.01 1 0.000 0.990 1.00 0.00
#> TCGA.EX.A1H5.01 2 0.000 0.992 0.00 1.00
#> TCGA.C5.A7CK.01 1 0.000 0.990 1.00 0.00
#> TCGA.VS.A950.01 2 0.000 0.992 0.00 1.00
#> TCGA.VS.A9UI.01 2 0.000 0.992 0.00 1.00
#> TCGA.Q1.A73Q.01 2 0.000 0.992 0.00 1.00
#> TCGA.C5.A1MH.01 1 0.000 0.990 1.00 0.00
#> TCGA.C5.A1M5.01 2 0.000 0.992 0.00 1.00
#> TCGA.C5.A1MF.01 1 0.000 0.990 1.00 0.00
#> TCGA.C5.A1BK.01 1 0.000 0.990 1.00 0.00
cbind(get_classes(res, k = 3), get_membership(res, k = 3))
#> class entropy silhouette p1 p2 p3
#> TCGA.GH.A9DA.01 3 0.0000 1.000 0.00 0.00 1.00
#> TCGA.ZJ.A8QQ.01 3 0.0000 1.000 0.00 0.00 1.00
#> TCGA.VS.A954.01 1 0.0892 0.969 0.98 0.00 0.02
#> TCGA.MA.AA42.01 1 0.0000 0.980 1.00 0.00 0.00
#> TCGA.C5.A8YQ.01 1 0.2066 0.944 0.94 0.00 0.06
#> TCGA.EK.A3GJ.01 3 0.0000 1.000 0.00 0.00 1.00
#> TCGA.C5.A902.01 3 0.0000 1.000 0.00 0.00 1.00
#> TCGA.MA.AA3W.01 1 0.0000 0.980 1.00 0.00 0.00
#> TCGA.EK.A2R9.01 1 0.0000 0.980 1.00 0.00 0.00
#> TCGA.IR.A3LC.01 1 0.0000 0.980 1.00 0.00 0.00
#> TCGA.C5.A3HD.01 3 0.0000 1.000 0.00 0.00 1.00
#> TCGA.EA.A50E.01 1 0.2066 0.944 0.94 0.00 0.06
#> TCGA.IR.A3LK.01 2 0.0000 0.973 0.00 1.00 0.00
#> TCGA.VS.A8EK.01 1 0.0000 0.980 1.00 0.00 0.00
#> TCGA.IR.A3LH.01 3 0.0000 1.000 0.00 0.00 1.00
#> TCGA.EK.A2RO.01 1 0.0000 0.980 1.00 0.00 0.00
#> TCGA.C5.A2LZ.01 2 0.0000 0.973 0.00 1.00 0.00
#> TCGA.C5.A901.01 1 0.0000 0.980 1.00 0.00 0.00
#> TCGA.VS.A953.01 1 0.0000 0.980 1.00 0.00 0.00
#> TCGA.EA.A3HS.01 1 0.0000 0.980 1.00 0.00 0.00
#> TCGA.C5.A7CO.01 1 0.0000 0.980 1.00 0.00 0.00
#> TCGA.IR.A3LL.01 3 0.0000 1.000 0.00 0.00 1.00
#> TCGA.VS.A94W.01 1 0.0000 0.980 1.00 0.00 0.00
#> TCGA.MY.A5BF.01 3 0.0000 1.000 0.00 0.00 1.00
#> TCGA.EK.A2RC.01 2 0.0000 0.973 0.00 1.00 0.00
#> TCGA.VS.A8EL.01 3 0.0000 1.000 0.00 0.00 1.00
#> TCGA.EA.A3HQ.01 2 0.0000 0.973 0.00 1.00 0.00
#> TCGA.UC.A7PF.01 3 0.0000 1.000 0.00 0.00 1.00
#> TCGA.VS.A8Q9.01 3 0.0000 1.000 0.00 0.00 1.00
#> TCGA.MA.AA41.01 1 0.2066 0.944 0.94 0.00 0.06
#> TCGA.EK.A3GN.01 1 0.0000 0.980 1.00 0.00 0.00
#> TCGA.ZJ.A8QO.01 1 0.0000 0.980 1.00 0.00 0.00
#> TCGA.JW.A852.01 1 0.0000 0.980 1.00 0.00 0.00
#> TCGA.JW.AAVH.01 2 0.0000 0.973 0.00 1.00 0.00
#> TCGA.IR.A3L7.01 2 0.0000 0.973 0.00 1.00 0.00
#> TCGA.C5.A8XH.01 3 0.0000 1.000 0.00 0.00 1.00
#> TCGA.VS.A8EI.01 3 0.0000 1.000 0.00 0.00 1.00
#> TCGA.VS.A8QC.01 2 0.0000 0.973 0.00 1.00 0.00
#> TCGA.WL.A834.01 2 0.1529 0.946 0.04 0.96 0.00
#> TCGA.C5.A8XI.01 3 0.0000 1.000 0.00 0.00 1.00
#> TCGA.DS.A7WI.01 3 0.0000 1.000 0.00 0.00 1.00
#> TCGA.VS.A8QF.01 2 0.5016 0.721 0.24 0.76 0.00
#> TCGA.EK.A2PG.01 2 0.0000 0.973 0.00 1.00 0.00
#> TCGA.VS.A8EC.01 2 0.0000 0.973 0.00 1.00 0.00
#> TCGA.EA.A3QE.01 1 0.0000 0.980 1.00 0.00 0.00
#> TCGA.DS.A0VM.01 1 0.0000 0.980 1.00 0.00 0.00
#> TCGA.FU.A3HY.01 2 0.0000 0.973 0.00 1.00 0.00
#> TCGA.Q1.A6DW.01 1 0.0000 0.980 1.00 0.00 0.00
#> TCGA.DS.A3LQ.01 2 0.2066 0.932 0.06 0.94 0.00
#> TCGA.EA.A3QD.01 3 0.0000 1.000 0.00 0.00 1.00
#> TCGA.LP.A5U3.01 2 0.0000 0.973 0.00 1.00 0.00
#> TCGA.EA.A6QX.01 2 0.0000 0.973 0.00 1.00 0.00
#> TCGA.EK.A2RA.01 2 0.0000 0.973 0.00 1.00 0.00
#> TCGA.Q1.A5R2.01 2 0.4002 0.830 0.16 0.84 0.00
#> TCGA.MU.A8JM.01 1 0.2066 0.944 0.94 0.00 0.06
#> TCGA.EK.A2IP.01 2 0.0000 0.973 0.00 1.00 0.00
#> TCGA.JW.A5VL.01 2 0.0000 0.973 0.00 1.00 0.00
#> TCGA.EK.A2IR.01 1 0.0000 0.980 1.00 0.00 0.00
#> TCGA.C5.A2LV.01 1 0.0000 0.980 1.00 0.00 0.00
#> TCGA.VS.A8EG.01 2 0.2066 0.932 0.06 0.94 0.00
#> TCGA.C5.A7UE.01 1 0.0000 0.980 1.00 0.00 0.00
#> TCGA.JW.A5VK.01 2 0.0000 0.973 0.00 1.00 0.00
#> TCGA.C5.A7X5.01 3 0.0000 1.000 0.00 0.00 1.00
#> TCGA.XS.A8TJ.01 1 0.0000 0.980 1.00 0.00 0.00
#> TCGA.DS.A0VN.01 1 0.0000 0.980 1.00 0.00 0.00
#> TCGA.DR.A0ZL.01 1 0.0000 0.980 1.00 0.00 0.00
#> TCGA.FU.A3WB.01 1 0.0000 0.980 1.00 0.00 0.00
#> TCGA.EA.A5O9.01 1 0.0000 0.980 1.00 0.00 0.00
#> TCGA.EK.A2H0.01 3 0.0000 1.000 0.00 0.00 1.00
#> TCGA.EA.A5ZE.01 1 0.2066 0.944 0.94 0.00 0.06
#> TCGA.FU.A3TQ.01 2 0.2066 0.932 0.06 0.94 0.00
#> TCGA.EK.A2RB.01 2 0.0000 0.973 0.00 1.00 0.00
#> TCGA.JW.A5VI.01 1 0.0000 0.980 1.00 0.00 0.00
#> TCGA.FU.A3YQ.01 1 0.2066 0.944 0.94 0.00 0.06
#> TCGA.C5.A7CH.01 1 0.0000 0.980 1.00 0.00 0.00
#> TCGA.C5.A2LX.01 2 0.3340 0.875 0.12 0.88 0.00
#> TCGA.LP.A5U2.01 1 0.0000 0.980 1.00 0.00 0.00
#> TCGA.FU.A3NI.01 3 0.0000 1.000 0.00 0.00 1.00
#> TCGA.VS.A9V3.01 1 0.0000 0.980 1.00 0.00 0.00
#> TCGA.C5.A1MN.01 2 0.3340 0.875 0.12 0.88 0.00
#> TCGA.BI.A20A.01 1 0.2066 0.944 0.94 0.00 0.06
#> TCGA.EA.A1QT.01 2 0.0000 0.973 0.00 1.00 0.00
#> TCGA.EX.A69M.01 3 0.0000 1.000 0.00 0.00 1.00
#> TCGA.VS.A9U7.01 2 0.0000 0.973 0.00 1.00 0.00
#> TCGA.VS.A9UD.01 3 0.0000 1.000 0.00 0.00 1.00
#> TCGA.ZX.AA5X.01 1 0.2066 0.944 0.94 0.00 0.06
#> TCGA.C5.A7CJ.01 1 0.0000 0.980 1.00 0.00 0.00
#> TCGA.EA.A78R.01 3 0.0000 1.000 0.00 0.00 1.00
#> TCGA.VS.A9UY.01 2 0.0000 0.973 0.00 1.00 0.00
#> TCGA.VS.A9U5.01 1 0.0000 0.980 1.00 0.00 0.00
#> TCGA.DS.A1OC.01 3 0.0000 1.000 0.00 0.00 1.00
#> TCGA.C5.A1BL.01 2 0.0000 0.973 0.00 1.00 0.00
#> TCGA.VS.A9UV.01 1 0.0000 0.980 1.00 0.00 0.00
#> TCGA.Q1.A6DT.01 1 0.0000 0.980 1.00 0.00 0.00
#> TCGA.C5.A1M8.01 1 0.5016 0.669 0.76 0.24 0.00
#> TCGA.VS.A957.01 2 0.0000 0.973 0.00 1.00 0.00
#> TCGA.MU.A5YI.01 1 0.2066 0.944 0.94 0.00 0.06
#> TCGA.ZJ.AAX4.01 1 0.0000 0.980 1.00 0.00 0.00
#> TCGA.ZJ.AAXJ.01 3 0.0000 1.000 0.00 0.00 1.00
#> TCGA.DS.A1O9.01 1 0.1529 0.957 0.96 0.00 0.04
#> TCGA.EA.A43B.01 3 0.0000 1.000 0.00 0.00 1.00
#> TCGA.ZJ.AAXI.01 2 0.0000 0.973 0.00 1.00 0.00
#> TCGA.DS.A1OA.01 2 0.0000 0.973 0.00 1.00 0.00
#> TCGA.C5.A1MQ.01 3 0.0000 1.000 0.00 0.00 1.00
#> TCGA.VS.A9UC.01 1 0.0000 0.980 1.00 0.00 0.00
#> TCGA.VS.A9V2.01 1 0.0000 0.980 1.00 0.00 0.00
#> TCGA.VS.A9UU.01 3 0.0000 1.000 0.00 0.00 1.00
#> TCGA.C5.A7CG.01 1 0.0000 0.980 1.00 0.00 0.00
#> TCGA.EX.A1H5.01 1 0.0892 0.965 0.98 0.02 0.00
#> TCGA.C5.A7CK.01 3 0.0000 1.000 0.00 0.00 1.00
#> TCGA.VS.A950.01 2 0.0000 0.973 0.00 1.00 0.00
#> TCGA.VS.A9UI.01 2 0.0000 0.973 0.00 1.00 0.00
#> TCGA.Q1.A73Q.01 2 0.0000 0.973 0.00 1.00 0.00
#> TCGA.C5.A1MH.01 1 0.0000 0.980 1.00 0.00 0.00
#> TCGA.C5.A1M5.01 2 0.0000 0.973 0.00 1.00 0.00
#> TCGA.C5.A1MF.01 1 0.2066 0.944 0.94 0.00 0.06
#> TCGA.C5.A1BK.01 1 0.2066 0.944 0.94 0.00 0.06
cbind(get_classes(res, k = 4), get_membership(res, k = 4))
#> class entropy silhouette p1 p2 p3 p4
#> TCGA.GH.A9DA.01 3 0.000 0.946 0.00 0.00 1.00 0.00
#> TCGA.ZJ.A8QQ.01 3 0.000 0.946 0.00 0.00 1.00 0.00
#> TCGA.VS.A954.01 1 0.265 0.864 0.88 0.00 0.00 0.12
#> TCGA.MA.AA42.01 1 0.121 0.873 0.96 0.00 0.00 0.04
#> TCGA.C5.A8YQ.01 1 0.164 0.878 0.94 0.00 0.00 0.06
#> TCGA.EK.A3GJ.01 3 0.000 0.946 0.00 0.00 1.00 0.00
#> TCGA.C5.A902.01 3 0.000 0.946 0.00 0.00 1.00 0.00
#> TCGA.MA.AA3W.01 4 0.340 0.777 0.18 0.00 0.00 0.82
#> TCGA.EK.A2R9.01 1 0.340 0.830 0.82 0.00 0.00 0.18
#> TCGA.IR.A3LC.01 4 0.479 0.511 0.38 0.00 0.00 0.62
#> TCGA.C5.A3HD.01 3 0.000 0.946 0.00 0.00 1.00 0.00
#> TCGA.EA.A50E.01 1 0.141 0.874 0.96 0.00 0.02 0.02
#> TCGA.IR.A3LK.01 2 0.000 0.928 0.00 1.00 0.00 0.00
#> TCGA.VS.A8EK.01 4 0.340 0.777 0.18 0.00 0.00 0.82
#> TCGA.IR.A3LH.01 3 0.000 0.946 0.00 0.00 1.00 0.00
#> TCGA.EK.A2RO.01 1 0.471 0.662 0.64 0.00 0.00 0.36
#> TCGA.C5.A2LZ.01 2 0.000 0.928 0.00 1.00 0.00 0.00
#> TCGA.C5.A901.01 1 0.265 0.864 0.88 0.00 0.00 0.12
#> TCGA.VS.A953.01 1 0.234 0.848 0.90 0.00 0.00 0.10
#> TCGA.EA.A3HS.01 4 0.121 0.753 0.04 0.00 0.00 0.96
#> TCGA.C5.A7CO.01 4 0.398 0.741 0.24 0.00 0.00 0.76
#> TCGA.IR.A3LL.01 3 0.000 0.946 0.00 0.00 1.00 0.00
#> TCGA.VS.A94W.01 1 0.265 0.834 0.88 0.00 0.00 0.12
#> TCGA.MY.A5BF.01 3 0.000 0.946 0.00 0.00 1.00 0.00
#> TCGA.EK.A2RC.01 4 0.441 0.650 0.00 0.30 0.00 0.70
#> TCGA.VS.A8EL.01 3 0.000 0.946 0.00 0.00 1.00 0.00
#> TCGA.EA.A3HQ.01 4 0.441 0.650 0.00 0.30 0.00 0.70
#> TCGA.UC.A7PF.01 3 0.428 0.652 0.28 0.00 0.72 0.00
#> TCGA.VS.A8Q9.01 3 0.000 0.946 0.00 0.00 1.00 0.00
#> TCGA.MA.AA41.01 1 0.265 0.864 0.88 0.00 0.00 0.12
#> TCGA.EK.A3GN.01 1 0.164 0.869 0.94 0.00 0.00 0.06
#> TCGA.ZJ.A8QO.01 1 0.234 0.848 0.90 0.00 0.00 0.10
#> TCGA.JW.A852.01 4 0.413 0.718 0.26 0.00 0.00 0.74
#> TCGA.JW.AAVH.01 2 0.000 0.928 0.00 1.00 0.00 0.00
#> TCGA.IR.A3L7.01 4 0.441 0.650 0.00 0.30 0.00 0.70
#> TCGA.C5.A8XH.01 3 0.000 0.946 0.00 0.00 1.00 0.00
#> TCGA.VS.A8EI.01 3 0.428 0.652 0.28 0.00 0.72 0.00
#> TCGA.VS.A8QC.01 4 0.428 0.673 0.00 0.28 0.00 0.72
#> TCGA.WL.A834.01 4 0.380 0.729 0.00 0.22 0.00 0.78
#> TCGA.C5.A8XI.01 3 0.000 0.946 0.00 0.00 1.00 0.00
#> TCGA.DS.A7WI.01 3 0.000 0.946 0.00 0.00 1.00 0.00
#> TCGA.VS.A8QF.01 4 0.429 0.786 0.10 0.08 0.00 0.82
#> TCGA.EK.A2PG.01 2 0.000 0.928 0.00 1.00 0.00 0.00
#> TCGA.VS.A8EC.01 2 0.499 -0.194 0.00 0.52 0.00 0.48
#> TCGA.EA.A3QE.01 1 0.121 0.873 0.96 0.00 0.00 0.04
#> TCGA.DS.A0VM.01 4 0.340 0.777 0.18 0.00 0.00 0.82
#> TCGA.FU.A3HY.01 2 0.000 0.928 0.00 1.00 0.00 0.00
#> TCGA.Q1.A6DW.01 4 0.361 0.609 0.20 0.00 0.00 0.80
#> TCGA.DS.A3LQ.01 4 0.380 0.729 0.00 0.22 0.00 0.78
#> TCGA.EA.A3QD.01 3 0.413 0.683 0.26 0.00 0.74 0.00
#> TCGA.LP.A5U3.01 4 0.441 0.650 0.00 0.30 0.00 0.70
#> TCGA.EA.A6QX.01 2 0.000 0.928 0.00 1.00 0.00 0.00
#> TCGA.EK.A2RA.01 2 0.000 0.928 0.00 1.00 0.00 0.00
#> TCGA.Q1.A5R2.01 4 0.429 0.786 0.10 0.08 0.00 0.82
#> TCGA.MU.A8JM.01 1 0.201 0.874 0.92 0.00 0.00 0.08
#> TCGA.EK.A2IP.01 2 0.413 0.572 0.00 0.74 0.00 0.26
#> TCGA.JW.A5VL.01 2 0.000 0.928 0.00 1.00 0.00 0.00
#> TCGA.EK.A2IR.01 4 0.398 0.741 0.24 0.00 0.00 0.76
#> TCGA.C5.A2LV.01 1 0.265 0.834 0.88 0.00 0.00 0.12
#> TCGA.VS.A8EG.01 4 0.201 0.761 0.00 0.08 0.00 0.92
#> TCGA.C5.A7UE.01 4 0.380 0.759 0.22 0.00 0.00 0.78
#> TCGA.JW.A5VK.01 2 0.000 0.928 0.00 1.00 0.00 0.00
#> TCGA.C5.A7X5.01 3 0.000 0.946 0.00 0.00 1.00 0.00
#> TCGA.XS.A8TJ.01 4 0.340 0.777 0.18 0.00 0.00 0.82
#> TCGA.DS.A0VN.01 1 0.265 0.834 0.88 0.00 0.00 0.12
#> TCGA.DR.A0ZL.01 4 0.201 0.770 0.08 0.00 0.00 0.92
#> TCGA.FU.A3WB.01 1 0.340 0.830 0.82 0.00 0.00 0.18
#> TCGA.EA.A5O9.01 4 0.495 0.359 0.44 0.00 0.00 0.56
#> TCGA.EK.A2H0.01 3 0.000 0.946 0.00 0.00 1.00 0.00
#> TCGA.EA.A5ZE.01 1 0.265 0.864 0.88 0.00 0.00 0.12
#> TCGA.FU.A3TQ.01 4 0.380 0.729 0.00 0.22 0.00 0.78
#> TCGA.EK.A2RB.01 2 0.000 0.928 0.00 1.00 0.00 0.00
#> TCGA.JW.A5VI.01 1 0.000 0.881 1.00 0.00 0.00 0.00
#> TCGA.FU.A3YQ.01 1 0.121 0.873 0.96 0.00 0.00 0.04
#> TCGA.C5.A7CH.01 1 0.361 0.730 0.80 0.00 0.00 0.20
#> TCGA.C5.A2LX.01 4 0.429 0.786 0.10 0.08 0.00 0.82
#> TCGA.LP.A5U2.01 1 0.340 0.830 0.82 0.00 0.00 0.18
#> TCGA.FU.A3NI.01 3 0.164 0.905 0.06 0.00 0.94 0.00
#> TCGA.VS.A9V3.01 4 0.121 0.753 0.04 0.00 0.00 0.96
#> TCGA.C5.A1MN.01 4 0.429 0.786 0.10 0.08 0.00 0.82
#> TCGA.BI.A20A.01 1 0.121 0.873 0.96 0.00 0.00 0.04
#> TCGA.EA.A1QT.01 2 0.000 0.928 0.00 1.00 0.00 0.00
#> TCGA.EX.A69M.01 3 0.000 0.946 0.00 0.00 1.00 0.00
#> TCGA.VS.A9U7.01 2 0.471 0.322 0.00 0.64 0.00 0.36
#> TCGA.VS.A9UD.01 3 0.000 0.946 0.00 0.00 1.00 0.00
#> TCGA.ZX.AA5X.01 1 0.265 0.864 0.88 0.00 0.00 0.12
#> TCGA.C5.A7CJ.01 1 0.201 0.852 0.92 0.00 0.00 0.08
#> TCGA.EA.A78R.01 3 0.000 0.946 0.00 0.00 1.00 0.00
#> TCGA.VS.A9UY.01 2 0.000 0.928 0.00 1.00 0.00 0.00
#> TCGA.VS.A9U5.01 1 0.000 0.881 1.00 0.00 0.00 0.00
#> TCGA.DS.A1OC.01 3 0.441 0.615 0.30 0.00 0.70 0.00
#> TCGA.C5.A1BL.01 4 0.441 0.650 0.00 0.30 0.00 0.70
#> TCGA.VS.A9UV.01 4 0.121 0.753 0.04 0.00 0.00 0.96
#> TCGA.Q1.A6DT.01 1 0.121 0.873 0.96 0.00 0.00 0.04
#> TCGA.C5.A1M8.01 4 0.121 0.753 0.04 0.00 0.00 0.96
#> TCGA.VS.A957.01 4 0.398 0.683 0.00 0.24 0.00 0.76
#> TCGA.MU.A5YI.01 1 0.292 0.854 0.86 0.00 0.00 0.14
#> TCGA.ZJ.AAX4.01 1 0.340 0.830 0.82 0.00 0.00 0.18
#> TCGA.ZJ.AAXJ.01 3 0.000 0.946 0.00 0.00 1.00 0.00
#> TCGA.DS.A1O9.01 1 0.000 0.881 1.00 0.00 0.00 0.00
#> TCGA.EA.A43B.01 3 0.000 0.946 0.00 0.00 1.00 0.00
#> TCGA.ZJ.AAXI.01 2 0.000 0.928 0.00 1.00 0.00 0.00
#> TCGA.DS.A1OA.01 2 0.000 0.928 0.00 1.00 0.00 0.00
#> TCGA.C5.A1MQ.01 3 0.000 0.946 0.00 0.00 1.00 0.00
#> TCGA.VS.A9UC.01 4 0.292 0.784 0.14 0.00 0.00 0.86
#> TCGA.VS.A9V2.01 1 0.265 0.834 0.88 0.00 0.00 0.12
#> TCGA.VS.A9UU.01 3 0.164 0.905 0.06 0.00 0.94 0.00
#> TCGA.C5.A7CG.01 1 0.265 0.864 0.88 0.00 0.00 0.12
#> TCGA.EX.A1H5.01 4 0.121 0.753 0.04 0.00 0.00 0.96
#> TCGA.C5.A7CK.01 1 0.413 0.633 0.74 0.00 0.26 0.00
#> TCGA.VS.A950.01 2 0.000 0.928 0.00 1.00 0.00 0.00
#> TCGA.VS.A9UI.01 2 0.000 0.928 0.00 1.00 0.00 0.00
#> TCGA.Q1.A73Q.01 4 0.441 0.650 0.00 0.30 0.00 0.70
#> TCGA.C5.A1MH.01 1 0.164 0.869 0.94 0.00 0.00 0.06
#> TCGA.C5.A1M5.01 2 0.000 0.928 0.00 1.00 0.00 0.00
#> TCGA.C5.A1MF.01 1 0.340 0.830 0.82 0.00 0.00 0.18
#> TCGA.C5.A1BK.01 1 0.121 0.875 0.96 0.00 0.04 0.00
cbind(get_classes(res, k = 5), get_membership(res, k = 5))
#> class entropy silhouette p1 p2 p3 p4 p5
#> TCGA.GH.A9DA.01 3 0.0000 0.887 0.00 0.00 1.00 0.00 0.00
#> TCGA.ZJ.A8QQ.01 3 0.0000 0.887 0.00 0.00 1.00 0.00 0.00
#> TCGA.VS.A954.01 1 0.1732 0.792 0.92 0.00 0.00 0.00 0.08
#> TCGA.MA.AA42.01 5 0.3983 0.474 0.34 0.00 0.00 0.00 0.66
#> TCGA.C5.A8YQ.01 1 0.1410 0.783 0.94 0.00 0.00 0.00 0.06
#> TCGA.EK.A3GJ.01 3 0.0000 0.887 0.00 0.00 1.00 0.00 0.00
#> TCGA.C5.A902.01 3 0.0000 0.887 0.00 0.00 1.00 0.00 0.00
#> TCGA.MA.AA3W.01 5 0.4748 0.468 0.04 0.00 0.00 0.30 0.66
#> TCGA.EK.A2R9.01 1 0.2754 0.772 0.88 0.00 0.00 0.04 0.08
#> TCGA.IR.A3LC.01 5 0.3390 0.657 0.06 0.00 0.00 0.10 0.84
#> TCGA.C5.A3HD.01 3 0.0000 0.887 0.00 0.00 1.00 0.00 0.00
#> TCGA.EA.A50E.01 1 0.3895 0.546 0.68 0.00 0.00 0.00 0.32
#> TCGA.IR.A3LK.01 2 0.1410 0.953 0.00 0.94 0.00 0.06 0.00
#> TCGA.VS.A8EK.01 5 0.3796 0.404 0.00 0.00 0.00 0.30 0.70
#> TCGA.IR.A3LH.01 3 0.0000 0.887 0.00 0.00 1.00 0.00 0.00
#> TCGA.EK.A2RO.01 5 0.5382 0.605 0.26 0.00 0.00 0.10 0.64
#> TCGA.C5.A2LZ.01 2 0.1410 0.953 0.00 0.94 0.00 0.06 0.00
#> TCGA.C5.A901.01 1 0.1732 0.792 0.92 0.00 0.00 0.00 0.08
#> TCGA.VS.A953.01 5 0.3424 0.576 0.24 0.00 0.00 0.00 0.76
#> TCGA.EA.A3HS.01 4 0.3109 0.791 0.00 0.00 0.00 0.80 0.20
#> TCGA.C5.A7CO.01 5 0.2929 0.547 0.00 0.00 0.00 0.18 0.82
#> TCGA.IR.A3LL.01 3 0.2280 0.822 0.12 0.00 0.88 0.00 0.00
#> TCGA.VS.A94W.01 5 0.3109 0.619 0.20 0.00 0.00 0.00 0.80
#> TCGA.MY.A5BF.01 3 0.0000 0.887 0.00 0.00 1.00 0.00 0.00
#> TCGA.EK.A2RC.01 4 0.2331 0.797 0.00 0.08 0.00 0.90 0.02
#> TCGA.VS.A8EL.01 3 0.4437 0.718 0.14 0.00 0.76 0.00 0.10
#> TCGA.EA.A3HQ.01 4 0.1410 0.805 0.00 0.06 0.00 0.94 0.00
#> TCGA.UC.A7PF.01 3 0.5861 0.224 0.40 0.00 0.50 0.00 0.10
#> TCGA.VS.A8Q9.01 3 0.3868 0.758 0.14 0.00 0.80 0.00 0.06
#> TCGA.MA.AA41.01 1 0.0609 0.787 0.98 0.00 0.00 0.00 0.02
#> TCGA.EK.A3GN.01 5 0.3274 0.601 0.22 0.00 0.00 0.00 0.78
#> TCGA.ZJ.A8QO.01 5 0.3561 0.541 0.26 0.00 0.00 0.00 0.74
#> TCGA.JW.A852.01 5 0.2929 0.547 0.00 0.00 0.00 0.18 0.82
#> TCGA.JW.AAVH.01 2 0.0000 0.947 0.00 1.00 0.00 0.00 0.00
#> TCGA.IR.A3L7.01 4 0.2012 0.808 0.00 0.06 0.00 0.92 0.02
#> TCGA.C5.A8XH.01 3 0.0000 0.887 0.00 0.00 1.00 0.00 0.00
#> TCGA.VS.A8EI.01 3 0.5861 0.224 0.40 0.00 0.50 0.00 0.10
#> TCGA.VS.A8QC.01 4 0.2012 0.808 0.00 0.06 0.00 0.92 0.02
#> TCGA.WL.A834.01 4 0.2516 0.803 0.00 0.00 0.00 0.86 0.14
#> TCGA.C5.A8XI.01 3 0.0000 0.887 0.00 0.00 1.00 0.00 0.00
#> TCGA.DS.A7WI.01 3 0.0000 0.887 0.00 0.00 1.00 0.00 0.00
#> TCGA.VS.A8QF.01 4 0.3983 0.611 0.00 0.00 0.00 0.66 0.34
#> TCGA.EK.A2PG.01 2 0.0000 0.947 0.00 1.00 0.00 0.00 0.00
#> TCGA.VS.A8EC.01 2 0.5854 0.515 0.00 0.60 0.00 0.24 0.16
#> TCGA.EA.A3QE.01 5 0.4287 0.114 0.46 0.00 0.00 0.00 0.54
#> TCGA.DS.A0VM.01 5 0.3424 0.512 0.00 0.00 0.00 0.24 0.76
#> TCGA.FU.A3HY.01 2 0.1410 0.953 0.00 0.94 0.00 0.06 0.00
#> TCGA.Q1.A6DW.01 5 0.5733 0.605 0.16 0.00 0.00 0.22 0.62
#> TCGA.DS.A3LQ.01 4 0.3274 0.766 0.00 0.00 0.00 0.78 0.22
#> TCGA.EA.A3QD.01 3 0.5884 0.158 0.42 0.00 0.48 0.00 0.10
#> TCGA.LP.A5U3.01 4 0.1410 0.805 0.00 0.06 0.00 0.94 0.00
#> TCGA.EA.A6QX.01 2 0.1410 0.953 0.00 0.94 0.00 0.06 0.00
#> TCGA.EK.A2RA.01 2 0.1410 0.953 0.00 0.94 0.00 0.06 0.00
#> TCGA.Q1.A5R2.01 4 0.4060 0.594 0.00 0.00 0.00 0.64 0.36
#> TCGA.MU.A8JM.01 1 0.2020 0.771 0.90 0.00 0.00 0.00 0.10
#> TCGA.EK.A2IP.01 4 0.3274 0.630 0.00 0.22 0.00 0.78 0.00
#> TCGA.JW.A5VL.01 2 0.0000 0.947 0.00 1.00 0.00 0.00 0.00
#> TCGA.EK.A2IR.01 5 0.3274 0.531 0.00 0.00 0.00 0.22 0.78
#> TCGA.C5.A2LV.01 5 0.3274 0.601 0.22 0.00 0.00 0.00 0.78
#> TCGA.VS.A8EG.01 4 0.2020 0.808 0.00 0.00 0.00 0.90 0.10
#> TCGA.C5.A7UE.01 5 0.2929 0.547 0.00 0.00 0.00 0.18 0.82
#> TCGA.JW.A5VK.01 2 0.0000 0.947 0.00 1.00 0.00 0.00 0.00
#> TCGA.C5.A7X5.01 3 0.0000 0.887 0.00 0.00 1.00 0.00 0.00
#> TCGA.XS.A8TJ.01 5 0.3983 0.343 0.00 0.00 0.00 0.34 0.66
#> TCGA.DS.A0VN.01 5 0.3274 0.601 0.22 0.00 0.00 0.00 0.78
#> TCGA.DR.A0ZL.01 4 0.4726 0.439 0.02 0.00 0.00 0.58 0.40
#> TCGA.FU.A3WB.01 1 0.2754 0.772 0.88 0.00 0.00 0.04 0.08
#> TCGA.EA.A5O9.01 5 0.3037 0.646 0.04 0.00 0.00 0.10 0.86
#> TCGA.EK.A2H0.01 3 0.0000 0.887 0.00 0.00 1.00 0.00 0.00
#> TCGA.EA.A5ZE.01 1 0.1732 0.792 0.92 0.00 0.00 0.00 0.08
#> TCGA.FU.A3TQ.01 4 0.2280 0.810 0.00 0.00 0.00 0.88 0.12
#> TCGA.EK.A2RB.01 2 0.0609 0.950 0.00 0.98 0.00 0.02 0.00
#> TCGA.JW.A5VI.01 1 0.4060 0.550 0.64 0.00 0.00 0.00 0.36
#> TCGA.FU.A3YQ.01 1 0.3895 0.546 0.68 0.00 0.00 0.00 0.32
#> TCGA.C5.A7CH.01 5 0.4373 0.676 0.16 0.00 0.00 0.08 0.76
#> TCGA.C5.A2LX.01 4 0.4182 0.515 0.00 0.00 0.00 0.60 0.40
#> TCGA.LP.A5U2.01 1 0.2754 0.772 0.88 0.00 0.00 0.04 0.08
#> TCGA.FU.A3NI.01 1 0.3983 0.271 0.66 0.00 0.34 0.00 0.00
#> TCGA.VS.A9V3.01 4 0.2280 0.805 0.00 0.00 0.00 0.88 0.12
#> TCGA.C5.A1MN.01 4 0.4126 0.558 0.00 0.00 0.00 0.62 0.38
#> TCGA.BI.A20A.01 1 0.3983 0.515 0.66 0.00 0.00 0.00 0.34
#> TCGA.EA.A1QT.01 2 0.0000 0.947 0.00 1.00 0.00 0.00 0.00
#> TCGA.EX.A69M.01 3 0.0000 0.887 0.00 0.00 1.00 0.00 0.00
#> TCGA.VS.A9U7.01 4 0.3274 0.630 0.00 0.22 0.00 0.78 0.00
#> TCGA.VS.A9UD.01 3 0.1410 0.860 0.06 0.00 0.94 0.00 0.00
#> TCGA.ZX.AA5X.01 1 0.0609 0.787 0.98 0.00 0.00 0.00 0.02
#> TCGA.C5.A7CJ.01 5 0.5263 0.643 0.24 0.00 0.00 0.10 0.66
#> TCGA.EA.A78R.01 3 0.1732 0.849 0.08 0.00 0.92 0.00 0.00
#> TCGA.VS.A9UY.01 2 0.0000 0.947 0.00 1.00 0.00 0.00 0.00
#> TCGA.VS.A9U5.01 5 0.4182 0.203 0.40 0.00 0.00 0.00 0.60
#> TCGA.DS.A1OC.01 1 0.5263 0.503 0.66 0.00 0.24 0.00 0.10
#> TCGA.C5.A1BL.01 4 0.4170 0.757 0.00 0.14 0.00 0.78 0.08
#> TCGA.VS.A9UV.01 4 0.2280 0.805 0.00 0.00 0.00 0.88 0.12
#> TCGA.Q1.A6DT.01 1 0.3983 0.546 0.66 0.00 0.00 0.00 0.34
#> TCGA.C5.A1M8.01 4 0.2280 0.801 0.00 0.00 0.00 0.88 0.12
#> TCGA.VS.A957.01 4 0.1043 0.805 0.00 0.04 0.00 0.96 0.00
#> TCGA.MU.A5YI.01 1 0.1732 0.792 0.92 0.00 0.00 0.00 0.08
#> TCGA.ZJ.AAX4.01 1 0.2331 0.783 0.90 0.00 0.00 0.02 0.08
#> TCGA.ZJ.AAXJ.01 3 0.0000 0.887 0.00 0.00 1.00 0.00 0.00
#> TCGA.DS.A1O9.01 1 0.2280 0.763 0.88 0.00 0.00 0.00 0.12
#> TCGA.EA.A43B.01 3 0.0000 0.887 0.00 0.00 1.00 0.00 0.00
#> TCGA.ZJ.AAXI.01 2 0.0000 0.947 0.00 1.00 0.00 0.00 0.00
#> TCGA.DS.A1OA.01 2 0.1410 0.953 0.00 0.94 0.00 0.06 0.00
#> TCGA.C5.A1MQ.01 3 0.0000 0.887 0.00 0.00 1.00 0.00 0.00
#> TCGA.VS.A9UC.01 5 0.3983 0.312 0.00 0.00 0.00 0.34 0.66
#> TCGA.VS.A9V2.01 5 0.3109 0.619 0.20 0.00 0.00 0.00 0.80
#> TCGA.VS.A9UU.01 3 0.5487 0.512 0.28 0.00 0.62 0.00 0.10
#> TCGA.C5.A7CG.01 1 0.1732 0.792 0.92 0.00 0.00 0.00 0.08
#> TCGA.EX.A1H5.01 4 0.2020 0.808 0.00 0.00 0.00 0.90 0.10
#> TCGA.C5.A7CK.01 1 0.3971 0.711 0.80 0.00 0.10 0.00 0.10
#> TCGA.VS.A950.01 2 0.1410 0.953 0.00 0.94 0.00 0.06 0.00
#> TCGA.VS.A9UI.01 2 0.1410 0.953 0.00 0.94 0.00 0.06 0.00
#> TCGA.Q1.A73Q.01 4 0.2873 0.780 0.00 0.02 0.00 0.86 0.12
#> TCGA.C5.A1MH.01 5 0.3895 0.477 0.32 0.00 0.00 0.00 0.68
#> TCGA.C5.A1M5.01 2 0.1410 0.953 0.00 0.94 0.00 0.06 0.00
#> TCGA.C5.A1MF.01 1 0.2331 0.783 0.90 0.00 0.00 0.02 0.08
#> TCGA.C5.A1BK.01 1 0.2020 0.771 0.90 0.00 0.00 0.00 0.10
cbind(get_classes(res, k = 6), get_membership(res, k = 6))
#> class entropy silhouette p1 p2 p3 p4 p5 p6
#> TCGA.GH.A9DA.01 3 0.0000 0.8531 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.ZJ.A8QQ.01 3 0.0000 0.8531 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.VS.A954.01 6 0.4646 0.8684 0.46 0.00 0.00 0.00 0.04 0.50
#> TCGA.MA.AA42.01 5 0.3756 0.0217 0.40 0.00 0.00 0.00 0.60 0.00
#> TCGA.C5.A8YQ.01 1 0.3544 0.3767 0.80 0.00 0.00 0.00 0.12 0.08
#> TCGA.EK.A3GJ.01 3 0.0000 0.8531 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.C5.A902.01 3 0.0000 0.8531 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.MA.AA3W.01 5 0.5304 0.5561 0.06 0.00 0.00 0.28 0.62 0.04
#> TCGA.EK.A2R9.01 6 0.4246 0.8637 0.40 0.00 0.00 0.00 0.02 0.58
#> TCGA.IR.A3LC.01 5 0.1556 0.6909 0.00 0.00 0.00 0.08 0.92 0.00
#> TCGA.C5.A3HD.01 3 0.0000 0.8531 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.EA.A50E.01 1 0.3578 0.5792 0.66 0.00 0.00 0.00 0.34 0.00
#> TCGA.IR.A3LK.01 2 0.1865 0.8988 0.00 0.92 0.00 0.04 0.00 0.04
#> TCGA.VS.A8EK.01 5 0.4247 0.5688 0.00 0.00 0.00 0.24 0.70 0.06
#> TCGA.IR.A3LH.01 3 0.0000 0.8531 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.EK.A2RO.01 6 0.6319 0.1707 0.20 0.00 0.00 0.02 0.36 0.42
#> TCGA.C5.A2LZ.01 2 0.0547 0.9271 0.00 0.98 0.00 0.02 0.00 0.00
#> TCGA.C5.A901.01 6 0.4632 0.8788 0.44 0.00 0.00 0.00 0.04 0.52
#> TCGA.VS.A953.01 5 0.2048 0.6194 0.12 0.00 0.00 0.00 0.88 0.00
#> TCGA.EA.A3HS.01 4 0.4179 0.7160 0.02 0.00 0.00 0.76 0.06 0.16
#> TCGA.C5.A7CO.01 5 0.3270 0.6596 0.00 0.00 0.00 0.06 0.82 0.12
#> TCGA.IR.A3LL.01 3 0.3756 0.4001 0.40 0.00 0.60 0.00 0.00 0.00
#> TCGA.VS.A94W.01 5 0.2260 0.6080 0.14 0.00 0.00 0.00 0.86 0.00
#> TCGA.MY.A5BF.01 3 0.0000 0.8531 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.EK.A2RC.01 4 0.2403 0.7919 0.00 0.04 0.00 0.90 0.02 0.04
#> TCGA.VS.A8EL.01 3 0.4609 0.2645 0.42 0.00 0.54 0.00 0.04 0.00
#> TCGA.EA.A3HQ.01 4 0.0000 0.8098 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.UC.A7PF.01 1 0.4758 0.2893 0.58 0.00 0.36 0.00 0.06 0.00
#> TCGA.VS.A8Q9.01 3 0.4282 0.3142 0.42 0.00 0.56 0.00 0.02 0.00
#> TCGA.MA.AA41.01 1 0.3821 -0.2970 0.74 0.00 0.00 0.00 0.04 0.22
#> TCGA.EK.A3GN.01 5 0.2631 0.6174 0.18 0.00 0.00 0.00 0.82 0.00
#> TCGA.ZJ.A8QO.01 5 0.2260 0.6080 0.14 0.00 0.00 0.00 0.86 0.00
#> TCGA.JW.A852.01 5 0.4711 0.5668 0.00 0.00 0.00 0.08 0.64 0.28
#> TCGA.JW.AAVH.01 2 0.1556 0.9179 0.00 0.92 0.00 0.00 0.00 0.08
#> TCGA.IR.A3L7.01 4 0.0547 0.8075 0.00 0.02 0.00 0.98 0.00 0.00
#> TCGA.C5.A8XH.01 3 0.0000 0.8531 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.VS.A8EI.01 1 0.4926 0.5210 0.64 0.00 0.24 0.00 0.12 0.00
#> TCGA.VS.A8QC.01 4 0.2020 0.7970 0.00 0.02 0.00 0.92 0.02 0.04
#> TCGA.WL.A834.01 4 0.0547 0.8068 0.00 0.00 0.00 0.98 0.02 0.00
#> TCGA.C5.A8XI.01 3 0.0000 0.8531 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.DS.A7WI.01 3 0.0000 0.8531 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.VS.A8QF.01 4 0.4758 0.2408 0.00 0.00 0.00 0.58 0.36 0.06
#> TCGA.EK.A2PG.01 2 0.1556 0.9179 0.00 0.92 0.00 0.00 0.00 0.08
#> TCGA.VS.A8EC.01 2 0.6382 0.3707 0.00 0.50 0.00 0.08 0.10 0.32
#> TCGA.EA.A3QE.01 1 0.3706 0.5298 0.62 0.00 0.00 0.00 0.38 0.00
#> TCGA.DS.A0VM.01 5 0.3821 0.6006 0.00 0.00 0.00 0.22 0.74 0.04
#> TCGA.FU.A3HY.01 2 0.1865 0.8988 0.00 0.92 0.00 0.04 0.00 0.04
#> TCGA.Q1.A6DW.01 5 0.6001 0.5333 0.04 0.00 0.00 0.18 0.58 0.20
#> TCGA.DS.A3LQ.01 4 0.5363 0.5759 0.00 0.02 0.00 0.58 0.08 0.32
#> TCGA.EA.A3QD.01 1 0.4534 0.2332 0.58 0.00 0.38 0.00 0.04 0.00
#> TCGA.LP.A5U3.01 4 0.0000 0.8098 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.EA.A6QX.01 2 0.0547 0.9271 0.00 0.98 0.00 0.02 0.00 0.00
#> TCGA.EK.A2RA.01 2 0.0547 0.9271 0.00 0.98 0.00 0.02 0.00 0.00
#> TCGA.Q1.A5R2.01 4 0.5265 0.1244 0.00 0.00 0.00 0.50 0.40 0.10
#> TCGA.MU.A8JM.01 1 0.2981 0.5202 0.82 0.00 0.00 0.00 0.16 0.02
#> TCGA.EK.A2IP.01 4 0.2728 0.7627 0.00 0.10 0.00 0.86 0.00 0.04
#> TCGA.JW.A5VL.01 2 0.1556 0.9179 0.00 0.92 0.00 0.00 0.00 0.08
#> TCGA.EK.A2IR.01 5 0.4798 0.5604 0.00 0.00 0.00 0.08 0.62 0.30
#> TCGA.C5.A2LV.01 5 0.2048 0.6194 0.12 0.00 0.00 0.00 0.88 0.00
#> TCGA.VS.A8EG.01 4 0.1807 0.8024 0.00 0.00 0.00 0.92 0.02 0.06
#> TCGA.C5.A7UE.01 5 0.4711 0.5668 0.00 0.00 0.00 0.08 0.64 0.28
#> TCGA.JW.A5VK.01 2 0.1556 0.9179 0.00 0.92 0.00 0.00 0.00 0.08
#> TCGA.C5.A7X5.01 3 0.0000 0.8531 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.XS.A8TJ.01 5 0.4844 0.5006 0.02 0.00 0.00 0.32 0.62 0.04
#> TCGA.DS.A0VN.01 5 0.2048 0.6194 0.12 0.00 0.00 0.00 0.88 0.00
#> TCGA.DR.A0ZL.01 4 0.6158 0.0122 0.04 0.00 0.00 0.48 0.36 0.12
#> TCGA.FU.A3WB.01 6 0.4246 0.8637 0.40 0.00 0.00 0.00 0.02 0.58
#> TCGA.EA.A5O9.01 5 0.3475 0.6499 0.00 0.00 0.00 0.06 0.80 0.14
#> TCGA.EK.A2H0.01 3 0.0000 0.8531 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.EA.A5ZE.01 6 0.4632 0.8788 0.44 0.00 0.00 0.00 0.04 0.52
#> TCGA.FU.A3TQ.01 4 0.2512 0.7799 0.00 0.00 0.00 0.88 0.06 0.06
#> TCGA.EK.A2RB.01 2 0.0000 0.9261 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.JW.A5VI.01 1 0.5012 0.4754 0.60 0.00 0.00 0.00 0.30 0.10
#> TCGA.FU.A3YQ.01 1 0.3578 0.5792 0.66 0.00 0.00 0.00 0.34 0.00
#> TCGA.C5.A7CH.01 5 0.2403 0.6759 0.04 0.00 0.00 0.04 0.90 0.02
#> TCGA.C5.A2LX.01 5 0.5564 0.1692 0.00 0.02 0.00 0.42 0.48 0.08
#> TCGA.LP.A5U2.01 6 0.4246 0.8637 0.40 0.00 0.00 0.00 0.02 0.58
#> TCGA.FU.A3NI.01 1 0.5841 -0.0647 0.48 0.00 0.30 0.00 0.00 0.22
#> TCGA.VS.A9V3.01 4 0.1807 0.8032 0.00 0.00 0.00 0.92 0.02 0.06
#> TCGA.C5.A1MN.01 5 0.5071 0.2593 0.00 0.00 0.00 0.40 0.52 0.08
#> TCGA.BI.A20A.01 1 0.3647 0.5592 0.64 0.00 0.00 0.00 0.36 0.00
#> TCGA.EA.A1QT.01 2 0.1556 0.9179 0.00 0.92 0.00 0.00 0.00 0.08
#> TCGA.EX.A69M.01 3 0.0000 0.8531 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.VS.A9U7.01 4 0.1556 0.7852 0.00 0.08 0.00 0.92 0.00 0.00
#> TCGA.VS.A9UD.01 3 0.3499 0.5319 0.32 0.00 0.68 0.00 0.00 0.00
#> TCGA.ZX.AA5X.01 1 0.4482 -0.6201 0.60 0.00 0.00 0.00 0.04 0.36
#> TCGA.C5.A7CJ.01 5 0.5157 0.5995 0.14 0.00 0.00 0.06 0.70 0.10
#> TCGA.EA.A78R.01 3 0.3706 0.4375 0.38 0.00 0.62 0.00 0.00 0.00
#> TCGA.VS.A9UY.01 2 0.1556 0.9179 0.00 0.92 0.00 0.00 0.00 0.08
#> TCGA.VS.A9U5.01 5 0.4711 0.3706 0.28 0.00 0.00 0.00 0.64 0.08
#> TCGA.DS.A1OC.01 1 0.3819 0.4145 0.70 0.00 0.28 0.00 0.00 0.02
#> TCGA.C5.A1BL.01 4 0.4541 0.6938 0.00 0.16 0.00 0.74 0.04 0.06
#> TCGA.VS.A9UV.01 4 0.1807 0.8024 0.00 0.00 0.00 0.92 0.02 0.06
#> TCGA.Q1.A6DT.01 1 0.3578 0.5579 0.66 0.00 0.00 0.00 0.34 0.00
#> TCGA.C5.A1M8.01 4 0.3679 0.7222 0.00 0.00 0.00 0.76 0.04 0.20
#> TCGA.VS.A957.01 4 0.1267 0.8025 0.00 0.00 0.00 0.94 0.00 0.06
#> TCGA.MU.A5YI.01 6 0.4632 0.8788 0.44 0.00 0.00 0.00 0.04 0.52
#> TCGA.ZJ.AAX4.01 6 0.4646 0.8626 0.46 0.00 0.00 0.00 0.04 0.50
#> TCGA.ZJ.AAXJ.01 3 0.0000 0.8531 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.DS.A1O9.01 1 0.2793 0.5524 0.80 0.00 0.00 0.00 0.20 0.00
#> TCGA.EA.A43B.01 3 0.0000 0.8531 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.ZJ.AAXI.01 2 0.1556 0.9179 0.00 0.92 0.00 0.00 0.00 0.08
#> TCGA.DS.A1OA.01 2 0.0547 0.9271 0.00 0.98 0.00 0.02 0.00 0.00
#> TCGA.C5.A1MQ.01 3 0.0000 0.8531 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.VS.A9UC.01 5 0.4360 0.5519 0.00 0.00 0.00 0.26 0.68 0.06
#> TCGA.VS.A9V2.01 5 0.2260 0.6080 0.14 0.00 0.00 0.00 0.86 0.00
#> TCGA.VS.A9UU.01 3 0.4651 0.0600 0.48 0.00 0.48 0.00 0.04 0.00
#> TCGA.C5.A7CG.01 6 0.4646 0.8589 0.46 0.00 0.00 0.00 0.04 0.50
#> TCGA.EX.A1H5.01 4 0.1807 0.8024 0.00 0.00 0.00 0.92 0.02 0.06
#> TCGA.C5.A7CK.01 1 0.4004 0.5963 0.76 0.00 0.12 0.00 0.12 0.00
#> TCGA.VS.A950.01 2 0.1865 0.8988 0.00 0.92 0.00 0.04 0.00 0.04
#> TCGA.VS.A9UI.01 2 0.0547 0.9271 0.00 0.98 0.00 0.02 0.00 0.00
#> TCGA.Q1.A73Q.01 4 0.4765 0.6148 0.00 0.02 0.00 0.64 0.04 0.30
#> TCGA.C5.A1MH.01 5 0.4727 0.4757 0.24 0.00 0.00 0.00 0.66 0.10
#> TCGA.C5.A1M5.01 2 0.0547 0.9271 0.00 0.98 0.00 0.02 0.00 0.00
#> TCGA.C5.A1MF.01 6 0.4609 0.8801 0.42 0.00 0.00 0.00 0.04 0.54
#> TCGA.C5.A1BK.01 1 0.2790 0.5623 0.84 0.00 0.00 0.00 0.14 0.02
cbind(get_classes(res, k = 7), get_membership(res, k = 7))
#> class entropy silhouette p1 p2 p3 p4 p5 p6 p7
#> TCGA.GH.A9DA.01 3 0.0000 0.99060 0.00 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.ZJ.A8QQ.01 3 0.0000 0.99060 0.00 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.VS.A954.01 6 0.2572 0.83327 0.08 0.00 0.00 0.00 0.00 0.86 0.06
#> TCGA.MA.AA42.01 1 0.3617 0.49189 0.76 0.00 0.00 0.00 0.16 0.00 0.08
#> TCGA.C5.A8YQ.01 1 0.5073 0.39406 0.54 0.00 0.00 0.00 0.00 0.16 0.30
#> TCGA.EK.A3GJ.01 3 0.0000 0.99060 0.00 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.C5.A902.01 3 0.0863 0.97144 0.00 0.00 0.96 0.00 0.00 0.00 0.04
#> TCGA.MA.AA3W.01 5 0.6280 0.19060 0.04 0.00 0.00 0.16 0.46 0.02 0.32
#> TCGA.EK.A2R9.01 6 0.1006 0.83350 0.02 0.00 0.00 0.02 0.00 0.96 0.00
#> TCGA.IR.A3LC.01 5 0.4850 0.34941 0.12 0.00 0.00 0.00 0.56 0.00 0.32
#> TCGA.C5.A3HD.01 3 0.0000 0.99060 0.00 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.EA.A50E.01 1 0.0504 0.72110 0.98 0.00 0.00 0.00 0.02 0.00 0.00
#> TCGA.IR.A3LK.01 2 0.2016 0.87601 0.00 0.90 0.00 0.04 0.00 0.00 0.06
#> TCGA.VS.A8EK.01 5 0.4778 0.30386 0.00 0.00 0.00 0.06 0.58 0.02 0.34
#> TCGA.IR.A3LH.01 3 0.0000 0.99060 0.00 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.EK.A2RO.01 6 0.4963 0.36037 0.00 0.00 0.00 0.02 0.16 0.64 0.18
#> TCGA.C5.A2LZ.01 2 0.0863 0.90108 0.00 0.96 0.00 0.04 0.00 0.00 0.00
#> TCGA.C5.A901.01 6 0.1928 0.84764 0.08 0.00 0.00 0.00 0.00 0.90 0.02
#> TCGA.VS.A953.01 5 0.5512 0.23412 0.26 0.00 0.00 0.00 0.44 0.00 0.30
#> TCGA.EA.A3HS.01 4 0.5597 0.57585 0.00 0.00 0.00 0.56 0.16 0.04 0.24
#> TCGA.C5.A7CO.01 5 0.4338 0.37098 0.08 0.00 0.00 0.00 0.64 0.00 0.28
#> TCGA.IR.A3LL.01 1 0.3139 0.64685 0.70 0.00 0.30 0.00 0.00 0.00 0.00
#> TCGA.VS.A94W.01 5 0.5338 0.34248 0.20 0.00 0.00 0.00 0.48 0.00 0.32
#> TCGA.MY.A5BF.01 3 0.0863 0.97144 0.00 0.00 0.96 0.00 0.00 0.00 0.04
#> TCGA.EK.A2RC.01 4 0.2572 0.77587 0.00 0.06 0.00 0.86 0.00 0.00 0.08
#> TCGA.VS.A8EL.01 1 0.2945 0.69245 0.74 0.00 0.26 0.00 0.00 0.00 0.00
#> TCGA.EA.A3HQ.01 4 0.0000 0.81652 0.00 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.UC.A7PF.01 1 0.2259 0.74308 0.84 0.00 0.16 0.00 0.00 0.00 0.00
#> TCGA.VS.A8Q9.01 1 0.3139 0.64685 0.70 0.00 0.30 0.00 0.00 0.00 0.00
#> TCGA.MA.AA41.01 1 0.5589 -0.04702 0.40 0.00 0.00 0.00 0.00 0.32 0.28
#> TCGA.EK.A3GN.01 7 0.5324 -0.26943 0.18 0.00 0.00 0.00 0.22 0.02 0.58
#> TCGA.ZJ.A8QO.01 5 0.5452 0.30662 0.24 0.00 0.00 0.00 0.46 0.00 0.30
#> TCGA.JW.A852.01 5 0.0000 0.19470 0.00 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.JW.AAVH.01 2 0.1886 0.88356 0.00 0.88 0.00 0.00 0.00 0.00 0.12
#> TCGA.IR.A3L7.01 4 0.0504 0.81276 0.00 0.00 0.00 0.98 0.00 0.00 0.02
#> TCGA.C5.A8XH.01 3 0.0000 0.99060 0.00 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.VS.A8EI.01 1 0.1886 0.74978 0.88 0.00 0.12 0.00 0.00 0.00 0.00
#> TCGA.VS.A8QC.01 4 0.2376 0.77773 0.00 0.02 0.00 0.86 0.00 0.00 0.12
#> TCGA.WL.A834.01 4 0.1363 0.80377 0.00 0.00 0.00 0.94 0.02 0.00 0.04
#> TCGA.C5.A8XI.01 3 0.0863 0.97144 0.00 0.00 0.96 0.00 0.00 0.00 0.04
#> TCGA.DS.A7WI.01 3 0.0000 0.99060 0.00 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.VS.A8QF.01 7 0.5631 -0.32627 0.00 0.00 0.00 0.30 0.34 0.00 0.36
#> TCGA.EK.A2PG.01 2 0.1886 0.88356 0.00 0.88 0.00 0.00 0.00 0.00 0.12
#> TCGA.VS.A8EC.01 2 0.5948 0.38868 0.02 0.48 0.00 0.04 0.36 0.00 0.10
#> TCGA.EA.A3QE.01 1 0.2016 0.66727 0.90 0.00 0.00 0.00 0.04 0.00 0.06
#> TCGA.DS.A0VM.01 5 0.4547 0.28957 0.00 0.00 0.00 0.08 0.58 0.00 0.34
#> TCGA.FU.A3HY.01 2 0.1718 0.88742 0.00 0.92 0.00 0.04 0.00 0.00 0.04
#> TCGA.Q1.A6DW.01 5 0.5853 0.20904 0.00 0.00 0.00 0.04 0.48 0.16 0.32
#> TCGA.DS.A3LQ.01 4 0.4657 0.52371 0.02 0.00 0.00 0.54 0.40 0.00 0.04
#> TCGA.EA.A3QD.01 1 0.2572 0.72918 0.80 0.00 0.20 0.00 0.00 0.00 0.00
#> TCGA.LP.A5U3.01 4 0.0000 0.81652 0.00 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.EA.A6QX.01 2 0.1363 0.89570 0.00 0.94 0.00 0.04 0.00 0.00 0.02
#> TCGA.EK.A2RA.01 2 0.0504 0.90261 0.00 0.98 0.00 0.02 0.00 0.00 0.00
#> TCGA.Q1.A5R2.01 5 0.5631 -0.24458 0.00 0.00 0.00 0.30 0.36 0.00 0.34
#> TCGA.MU.A8JM.01 1 0.1886 0.69846 0.88 0.00 0.00 0.00 0.00 0.12 0.00
#> TCGA.EK.A2IP.01 4 0.1433 0.79627 0.00 0.08 0.00 0.92 0.00 0.00 0.00
#> TCGA.JW.A5VL.01 2 0.1886 0.88356 0.00 0.88 0.00 0.00 0.00 0.00 0.12
#> TCGA.EK.A2IR.01 5 0.1006 0.15877 0.02 0.00 0.00 0.00 0.96 0.00 0.02
#> TCGA.C5.A2LV.01 5 0.5490 0.26162 0.24 0.00 0.00 0.00 0.44 0.00 0.32
#> TCGA.VS.A8EG.01 4 0.2213 0.80388 0.00 0.00 0.00 0.90 0.02 0.04 0.04
#> TCGA.C5.A7UE.01 5 0.0000 0.19470 0.00 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.JW.A5VK.01 2 0.1886 0.88356 0.00 0.88 0.00 0.00 0.00 0.00 0.12
#> TCGA.C5.A7X5.01 3 0.0000 0.99060 0.00 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.XS.A8TJ.01 5 0.5604 0.18049 0.02 0.00 0.00 0.16 0.48 0.00 0.34
#> TCGA.DS.A0VN.01 5 0.5453 0.27997 0.22 0.00 0.00 0.00 0.44 0.00 0.34
#> TCGA.DR.A0ZL.01 5 0.6898 0.00905 0.02 0.00 0.00 0.22 0.38 0.08 0.30
#> TCGA.FU.A3WB.01 6 0.1006 0.83350 0.02 0.00 0.00 0.02 0.00 0.96 0.00
#> TCGA.EA.A5O9.01 5 0.4127 0.18839 0.00 0.00 0.00 0.00 0.60 0.04 0.36
#> TCGA.EK.A2H0.01 3 0.0000 0.99060 0.00 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.EA.A5ZE.01 6 0.1433 0.85127 0.08 0.00 0.00 0.00 0.00 0.92 0.00
#> TCGA.FU.A3TQ.01 4 0.3927 0.67574 0.00 0.02 0.00 0.76 0.08 0.00 0.14
#> TCGA.EK.A2RB.01 2 0.0504 0.90261 0.00 0.98 0.00 0.02 0.00 0.00 0.00
#> TCGA.JW.A5VI.01 1 0.4016 0.57796 0.76 0.00 0.00 0.00 0.06 0.14 0.04
#> TCGA.FU.A3YQ.01 1 0.0504 0.72110 0.98 0.00 0.00 0.00 0.02 0.00 0.00
#> TCGA.C5.A7CH.01 5 0.5047 0.33583 0.14 0.00 0.00 0.00 0.52 0.00 0.34
#> TCGA.C5.A2LX.01 5 0.5579 -0.16152 0.00 0.00 0.00 0.26 0.38 0.00 0.36
#> TCGA.LP.A5U2.01 6 0.1006 0.83350 0.02 0.00 0.00 0.02 0.00 0.96 0.00
#> TCGA.FU.A3NI.01 6 0.6850 0.21323 0.20 0.00 0.26 0.00 0.00 0.38 0.16
#> TCGA.VS.A9V3.01 4 0.4161 0.75475 0.00 0.00 0.00 0.76 0.08 0.06 0.10
#> TCGA.C5.A1MN.01 5 0.5517 -0.10427 0.00 0.00 0.00 0.24 0.42 0.00 0.34
#> TCGA.BI.A20A.01 1 0.0504 0.72110 0.98 0.00 0.00 0.00 0.02 0.00 0.00
#> TCGA.EA.A1QT.01 2 0.1886 0.88356 0.00 0.88 0.00 0.00 0.00 0.00 0.12
#> TCGA.EX.A69M.01 3 0.0863 0.97144 0.00 0.00 0.96 0.00 0.00 0.00 0.04
#> TCGA.VS.A9U7.01 4 0.0863 0.81008 0.00 0.04 0.00 0.96 0.00 0.00 0.00
#> TCGA.VS.A9UD.01 1 0.3562 0.24461 0.50 0.00 0.50 0.00 0.00 0.00 0.00
#> TCGA.ZX.AA5X.01 6 0.3139 0.57230 0.30 0.00 0.00 0.00 0.00 0.70 0.00
#> TCGA.C5.A7CJ.01 5 0.6435 0.30250 0.10 0.00 0.00 0.02 0.48 0.10 0.30
#> TCGA.EA.A78R.01 1 0.3459 0.48663 0.60 0.00 0.40 0.00 0.00 0.00 0.00
#> TCGA.VS.A9UY.01 2 0.1886 0.88356 0.00 0.88 0.00 0.00 0.00 0.00 0.12
#> TCGA.VS.A9U5.01 5 0.6805 0.17424 0.20 0.00 0.00 0.00 0.40 0.16 0.24
#> TCGA.DS.A1OC.01 1 0.3208 0.74001 0.82 0.00 0.12 0.00 0.00 0.04 0.02
#> TCGA.C5.A1BL.01 4 0.5391 0.58877 0.00 0.18 0.00 0.62 0.06 0.00 0.14
#> TCGA.VS.A9UV.01 4 0.3343 0.77206 0.00 0.00 0.00 0.82 0.10 0.04 0.04
#> TCGA.Q1.A6DT.01 1 0.3867 0.45263 0.60 0.00 0.00 0.00 0.02 0.00 0.38
#> TCGA.C5.A1M8.01 4 0.4840 0.70697 0.00 0.00 0.00 0.68 0.18 0.08 0.06
#> TCGA.VS.A957.01 4 0.1363 0.80943 0.00 0.00 0.00 0.94 0.00 0.04 0.02
#> TCGA.MU.A5YI.01 6 0.1433 0.85127 0.08 0.00 0.00 0.00 0.00 0.92 0.00
#> TCGA.ZJ.AAX4.01 6 0.3244 0.74352 0.04 0.00 0.00 0.00 0.00 0.78 0.18
#> TCGA.ZJ.AAXJ.01 3 0.0000 0.99060 0.00 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.DS.A1O9.01 1 0.1671 0.70779 0.90 0.00 0.00 0.00 0.00 0.10 0.00
#> TCGA.EA.A43B.01 3 0.0000 0.99060 0.00 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.ZJ.AAXI.01 2 0.1886 0.88356 0.00 0.88 0.00 0.00 0.00 0.00 0.12
#> TCGA.DS.A1OA.01 2 0.0863 0.90108 0.00 0.96 0.00 0.04 0.00 0.00 0.00
#> TCGA.C5.A1MQ.01 3 0.0000 0.99060 0.00 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.VS.A9UC.01 5 0.5194 0.24832 0.00 0.00 0.00 0.06 0.50 0.04 0.40
#> TCGA.VS.A9V2.01 5 0.5164 0.35633 0.20 0.00 0.00 0.00 0.54 0.00 0.26
#> TCGA.VS.A9UU.01 1 0.2832 0.71001 0.76 0.00 0.24 0.00 0.00 0.00 0.00
#> TCGA.C5.A7CG.01 6 0.1433 0.85127 0.08 0.00 0.00 0.00 0.00 0.92 0.00
#> TCGA.EX.A1H5.01 4 0.2213 0.80388 0.00 0.00 0.00 0.90 0.02 0.04 0.04
#> TCGA.C5.A7CK.01 1 0.2512 0.74376 0.86 0.00 0.10 0.00 0.00 0.04 0.00
#> TCGA.VS.A950.01 2 0.2278 0.86132 0.00 0.88 0.00 0.04 0.00 0.00 0.08
#> TCGA.VS.A9UI.01 2 0.0863 0.90108 0.00 0.96 0.00 0.04 0.00 0.00 0.00
#> TCGA.Q1.A73Q.01 4 0.4974 0.57330 0.02 0.02 0.00 0.58 0.34 0.00 0.04
#> TCGA.C5.A1MH.01 5 0.6543 0.26437 0.16 0.00 0.00 0.00 0.42 0.12 0.30
#> TCGA.C5.A1M5.01 2 0.0863 0.90108 0.00 0.96 0.00 0.04 0.00 0.00 0.00
#> TCGA.C5.A1MF.01 6 0.1433 0.85127 0.08 0.00 0.00 0.00 0.00 0.92 0.00
#> TCGA.C5.A1BK.01 1 0.1671 0.70779 0.90 0.00 0.00 0.00 0.00 0.10 0.00
cbind(get_classes(res, k = 8), get_membership(res, k = 8))
#> class entropy silhouette p1 p2 p3 p4 p5 p6 p7 p8
#> TCGA.GH.A9DA.01 3 0.0000 0.9618 0.00 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.ZJ.A8QQ.01 3 0.0000 0.9618 0.00 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.VS.A954.01 6 0.2350 0.7796 0.04 0.00 0.00 0.00 0.00 0.86 0.10 0.00
#> TCGA.MA.AA42.01 1 0.6245 -0.3298 0.42 0.00 0.00 0.00 0.18 0.00 0.26 0.14
#> TCGA.C5.A8YQ.01 1 0.5133 -0.0660 0.40 0.00 0.00 0.00 0.00 0.22 0.38 0.00
#> TCGA.EK.A3GJ.01 3 0.0000 0.9618 0.00 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.C5.A902.01 3 0.2165 0.9078 0.00 0.00 0.88 0.00 0.00 0.00 0.06 0.06
#> TCGA.MA.AA3W.01 5 0.2591 0.4361 0.02 0.00 0.00 0.08 0.86 0.04 0.00 0.00
#> TCGA.EK.A2R9.01 6 0.0471 0.8097 0.02 0.00 0.00 0.00 0.00 0.98 0.00 0.00
#> TCGA.IR.A3LC.01 5 0.6095 0.1093 0.08 0.00 0.00 0.00 0.40 0.00 0.28 0.24
#> TCGA.C5.A3HD.01 3 0.0000 0.9618 0.00 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.EA.A50E.01 1 0.1091 0.6816 0.94 0.00 0.00 0.00 0.00 0.00 0.06 0.00
#> TCGA.IR.A3LK.01 2 0.2532 0.7981 0.00 0.88 0.00 0.04 0.02 0.00 0.04 0.02
#> TCGA.VS.A8EK.01 5 0.3320 0.4106 0.00 0.00 0.00 0.04 0.80 0.00 0.04 0.12
#> TCGA.IR.A3LH.01 3 0.1091 0.9212 0.06 0.00 0.94 0.00 0.00 0.00 0.00 0.00
#> TCGA.EK.A2RO.01 6 0.4917 0.3516 0.00 0.00 0.00 0.04 0.26 0.62 0.06 0.02
#> TCGA.C5.A2LZ.01 2 0.0471 0.8616 0.00 0.98 0.00 0.02 0.00 0.00 0.00 0.00
#> TCGA.C5.A901.01 6 0.1607 0.8058 0.04 0.00 0.00 0.00 0.00 0.92 0.04 0.00
#> TCGA.VS.A953.01 7 0.6343 -0.2171 0.12 0.00 0.00 0.00 0.32 0.00 0.34 0.22
#> TCGA.EA.A3HS.01 4 0.6186 0.2674 0.00 0.00 0.00 0.48 0.14 0.02 0.26 0.10
#> TCGA.C5.A7CO.01 5 0.5861 0.2332 0.08 0.00 0.00 0.00 0.48 0.00 0.20 0.24
#> TCGA.IR.A3LL.01 1 0.2569 0.6988 0.82 0.00 0.16 0.00 0.00 0.00 0.02 0.00
#> TCGA.VS.A94W.01 5 0.5861 0.1566 0.12 0.00 0.00 0.00 0.50 0.00 0.24 0.14
#> TCGA.MY.A5BF.01 3 0.2165 0.9078 0.00 0.00 0.88 0.00 0.00 0.00 0.06 0.06
#> TCGA.EK.A2RC.01 4 0.4727 0.4827 0.00 0.22 0.00 0.62 0.14 0.00 0.00 0.02
#> TCGA.VS.A8EL.01 1 0.2114 0.7080 0.84 0.00 0.16 0.00 0.00 0.00 0.00 0.00
#> TCGA.EA.A3HQ.01 4 0.0941 0.7417 0.00 0.02 0.00 0.96 0.02 0.00 0.00 0.00
#> TCGA.UC.A7PF.01 1 0.1765 0.7249 0.88 0.00 0.12 0.00 0.00 0.00 0.00 0.00
#> TCGA.VS.A8Q9.01 1 0.2114 0.7080 0.84 0.00 0.16 0.00 0.00 0.00 0.00 0.00
#> TCGA.MA.AA41.01 7 0.5221 -0.1551 0.36 0.00 0.00 0.00 0.00 0.26 0.38 0.00
#> TCGA.EK.A3GN.01 7 0.5317 0.0732 0.08 0.00 0.00 0.00 0.22 0.00 0.58 0.12
#> TCGA.ZJ.A8QO.01 5 0.5989 0.1211 0.14 0.00 0.00 0.00 0.48 0.00 0.24 0.14
#> TCGA.JW.A852.01 8 0.4174 0.4193 0.00 0.00 0.00 0.02 0.32 0.00 0.04 0.62
#> TCGA.JW.AAVH.01 2 0.3523 0.8234 0.00 0.78 0.00 0.00 0.00 0.02 0.10 0.10
#> TCGA.IR.A3L7.01 4 0.0941 0.7417 0.00 0.02 0.00 0.96 0.02 0.00 0.00 0.00
#> TCGA.C5.A8XH.01 3 0.0000 0.9618 0.00 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.VS.A8EI.01 1 0.1341 0.7267 0.92 0.00 0.08 0.00 0.00 0.00 0.00 0.00
#> TCGA.VS.A8QC.01 4 0.4371 0.5481 0.00 0.14 0.00 0.68 0.16 0.00 0.00 0.02
#> TCGA.WL.A834.01 4 0.0471 0.7394 0.00 0.00 0.00 0.98 0.02 0.00 0.00 0.00
#> TCGA.C5.A8XI.01 3 0.2165 0.9078 0.00 0.00 0.88 0.00 0.00 0.00 0.06 0.06
#> TCGA.DS.A7WI.01 3 0.0000 0.9618 0.00 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.VS.A8QF.01 5 0.3095 0.3072 0.00 0.00 0.00 0.24 0.74 0.00 0.00 0.02
#> TCGA.EK.A2PG.01 2 0.3523 0.8234 0.00 0.78 0.00 0.00 0.00 0.02 0.10 0.10
#> TCGA.VS.A8EC.01 8 0.5823 0.4413 0.00 0.26 0.00 0.06 0.10 0.00 0.04 0.54
#> TCGA.EA.A3QE.01 1 0.4138 0.3773 0.72 0.00 0.00 0.00 0.04 0.00 0.16 0.08
#> TCGA.DS.A0VM.01 5 0.2864 0.4250 0.00 0.00 0.00 0.02 0.84 0.00 0.06 0.08
#> TCGA.FU.A3HY.01 2 0.1741 0.8274 0.00 0.92 0.00 0.04 0.00 0.00 0.02 0.02
#> TCGA.Q1.A6DW.01 5 0.5700 0.2887 0.00 0.00 0.00 0.10 0.62 0.08 0.08 0.12
#> TCGA.DS.A3LQ.01 8 0.5159 0.3851 0.00 0.02 0.00 0.30 0.16 0.00 0.00 0.52
#> TCGA.EA.A3QD.01 1 0.1765 0.7249 0.88 0.00 0.12 0.00 0.00 0.00 0.00 0.00
#> TCGA.LP.A5U3.01 4 0.0941 0.7417 0.00 0.02 0.00 0.96 0.02 0.00 0.00 0.00
#> TCGA.EA.A6QX.01 2 0.0941 0.8538 0.00 0.96 0.00 0.02 0.00 0.00 0.02 0.00
#> TCGA.EK.A2RA.01 2 0.0471 0.8616 0.00 0.98 0.00 0.02 0.00 0.00 0.00 0.00
#> TCGA.Q1.A5R2.01 5 0.3431 0.3127 0.00 0.00 0.00 0.20 0.74 0.00 0.00 0.06
#> TCGA.MU.A8JM.01 1 0.2624 0.6789 0.86 0.00 0.00 0.00 0.02 0.06 0.06 0.00
#> TCGA.EK.A2IP.01 4 0.3303 0.6064 0.00 0.20 0.00 0.76 0.02 0.00 0.00 0.02
#> TCGA.JW.A5VL.01 2 0.3523 0.8234 0.00 0.78 0.00 0.00 0.00 0.02 0.10 0.10
#> TCGA.EK.A2IR.01 8 0.3291 0.4789 0.00 0.00 0.00 0.02 0.28 0.00 0.00 0.70
#> TCGA.C5.A2LV.01 5 0.6237 -0.0232 0.10 0.00 0.00 0.00 0.34 0.00 0.34 0.22
#> TCGA.VS.A8EG.01 4 0.2020 0.7294 0.00 0.00 0.00 0.90 0.00 0.02 0.02 0.06
#> TCGA.C5.A7UE.01 8 0.3808 0.3879 0.00 0.00 0.00 0.00 0.34 0.00 0.04 0.62
#> TCGA.JW.A5VK.01 2 0.3523 0.8234 0.00 0.78 0.00 0.00 0.00 0.02 0.10 0.10
#> TCGA.C5.A7X5.01 3 0.0000 0.9618 0.00 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.XS.A8TJ.01 5 0.1804 0.4378 0.02 0.00 0.00 0.08 0.90 0.00 0.00 0.00
#> TCGA.DS.A0VN.01 5 0.6343 -0.0201 0.12 0.00 0.00 0.00 0.34 0.00 0.32 0.22
#> TCGA.DR.A0ZL.01 5 0.3270 0.4172 0.02 0.00 0.00 0.12 0.80 0.06 0.00 0.00
#> TCGA.FU.A3WB.01 6 0.0471 0.8097 0.02 0.00 0.00 0.00 0.00 0.98 0.00 0.00
#> TCGA.EA.A5O9.01 5 0.6049 0.1691 0.04 0.00 0.00 0.02 0.44 0.00 0.28 0.22
#> TCGA.EK.A2H0.01 3 0.0000 0.9618 0.00 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.EA.A5ZE.01 6 0.1275 0.8067 0.04 0.00 0.00 0.00 0.00 0.94 0.02 0.00
#> TCGA.FU.A3TQ.01 5 0.4803 -0.2278 0.00 0.08 0.00 0.44 0.46 0.00 0.00 0.02
#> TCGA.EK.A2RB.01 2 0.0000 0.8609 0.00 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.JW.A5VI.01 1 0.5098 0.2967 0.66 0.00 0.00 0.00 0.08 0.10 0.14 0.02
#> TCGA.FU.A3YQ.01 1 0.1557 0.6701 0.92 0.00 0.00 0.00 0.02 0.00 0.06 0.00
#> TCGA.C5.A7CH.01 5 0.6009 0.1334 0.08 0.00 0.00 0.00 0.42 0.00 0.30 0.20
#> TCGA.C5.A2LX.01 5 0.3873 0.3230 0.00 0.00 0.00 0.20 0.72 0.00 0.02 0.06
#> TCGA.LP.A5U2.01 6 0.0471 0.8097 0.02 0.00 0.00 0.00 0.00 0.98 0.00 0.00
#> TCGA.FU.A3NI.01 6 0.7035 0.2069 0.24 0.00 0.14 0.00 0.00 0.38 0.18 0.06
#> TCGA.VS.A9V3.01 4 0.3637 0.6863 0.00 0.00 0.00 0.80 0.06 0.02 0.04 0.08
#> TCGA.C5.A1MN.01 5 0.4893 0.3033 0.00 0.00 0.00 0.18 0.64 0.00 0.06 0.12
#> TCGA.BI.A20A.01 1 0.0808 0.6830 0.96 0.00 0.00 0.00 0.00 0.00 0.04 0.00
#> TCGA.EA.A1QT.01 2 0.3523 0.8234 0.00 0.78 0.00 0.00 0.00 0.02 0.10 0.10
#> TCGA.EX.A69M.01 3 0.2165 0.9078 0.00 0.00 0.88 0.00 0.00 0.00 0.06 0.06
#> TCGA.VS.A9U7.01 4 0.1804 0.7162 0.00 0.08 0.00 0.90 0.02 0.00 0.00 0.00
#> TCGA.VS.A9UD.01 1 0.3449 0.5161 0.66 0.00 0.32 0.00 0.00 0.00 0.02 0.00
#> TCGA.ZX.AA5X.01 6 0.4358 0.2229 0.40 0.00 0.00 0.00 0.02 0.54 0.04 0.00
#> TCGA.C5.A7CJ.01 5 0.3903 0.4402 0.06 0.00 0.00 0.00 0.78 0.06 0.08 0.02
#> TCGA.EA.A78R.01 1 0.2981 0.6403 0.76 0.00 0.22 0.00 0.00 0.00 0.02 0.00
#> TCGA.VS.A9UY.01 2 0.3523 0.8234 0.00 0.78 0.00 0.00 0.00 0.02 0.10 0.10
#> TCGA.VS.A9U5.01 5 0.7133 0.0822 0.16 0.00 0.00 0.00 0.42 0.14 0.14 0.14
#> TCGA.DS.A1OC.01 1 0.3314 0.6664 0.80 0.00 0.02 0.00 0.00 0.08 0.10 0.00
#> TCGA.C5.A1BL.01 4 0.6185 0.1194 0.00 0.26 0.00 0.38 0.30 0.00 0.02 0.04
#> TCGA.VS.A9UV.01 4 0.3048 0.7020 0.00 0.00 0.00 0.84 0.04 0.02 0.02 0.08
#> TCGA.Q1.A6DT.01 7 0.4325 0.1804 0.38 0.00 0.00 0.00 0.04 0.00 0.56 0.02
#> TCGA.C5.A1M8.01 4 0.4034 0.6498 0.00 0.00 0.00 0.76 0.06 0.02 0.04 0.12
#> TCGA.VS.A957.01 4 0.2020 0.7294 0.00 0.00 0.00 0.90 0.00 0.02 0.02 0.06
#> TCGA.MU.A5YI.01 6 0.0808 0.8127 0.04 0.00 0.00 0.00 0.00 0.96 0.00 0.00
#> TCGA.ZJ.AAX4.01 6 0.2856 0.7021 0.02 0.00 0.00 0.00 0.00 0.78 0.20 0.00
#> TCGA.ZJ.AAXJ.01 3 0.0000 0.9618 0.00 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.DS.A1O9.01 1 0.2348 0.6810 0.88 0.00 0.00 0.00 0.02 0.04 0.06 0.00
#> TCGA.EA.A43B.01 3 0.1091 0.9212 0.06 0.00 0.94 0.00 0.00 0.00 0.00 0.00
#> TCGA.ZJ.AAXI.01 2 0.3523 0.8234 0.00 0.78 0.00 0.00 0.00 0.02 0.10 0.10
#> TCGA.DS.A1OA.01 2 0.0471 0.8616 0.00 0.98 0.00 0.02 0.00 0.00 0.00 0.00
#> TCGA.C5.A1MQ.01 3 0.0000 0.9618 0.00 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.VS.A9UC.01 5 0.3687 0.3738 0.00 0.00 0.00 0.08 0.78 0.00 0.06 0.08
#> TCGA.VS.A9V2.01 5 0.5902 0.1806 0.12 0.00 0.00 0.00 0.50 0.00 0.22 0.16
#> TCGA.VS.A9UU.01 1 0.1947 0.7176 0.86 0.00 0.14 0.00 0.00 0.00 0.00 0.00
#> TCGA.C5.A7CG.01 6 0.2674 0.7610 0.06 0.00 0.00 0.00 0.04 0.86 0.04 0.00
#> TCGA.EX.A1H5.01 4 0.2482 0.7203 0.00 0.00 0.00 0.88 0.02 0.02 0.02 0.06
#> TCGA.C5.A7CK.01 1 0.2348 0.6982 0.88 0.00 0.02 0.00 0.00 0.06 0.04 0.00
#> TCGA.VS.A950.01 2 0.2858 0.7760 0.00 0.86 0.00 0.04 0.04 0.00 0.04 0.02
#> TCGA.VS.A9UI.01 2 0.0471 0.8616 0.00 0.98 0.00 0.02 0.00 0.00 0.00 0.00
#> TCGA.Q1.A73Q.01 8 0.4751 0.2514 0.00 0.02 0.00 0.38 0.08 0.00 0.00 0.52
#> TCGA.C5.A1MH.01 5 0.4339 0.4113 0.10 0.00 0.00 0.00 0.74 0.06 0.08 0.02
#> TCGA.C5.A1M5.01 2 0.0471 0.8616 0.00 0.98 0.00 0.02 0.00 0.00 0.00 0.00
#> TCGA.C5.A1MF.01 6 0.0808 0.8127 0.04 0.00 0.00 0.00 0.00 0.96 0.00 0.00
#> TCGA.C5.A1BK.01 1 0.2348 0.6810 0.88 0.00 0.00 0.00 0.02 0.04 0.06 0.00
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)
consensus_heatmap(res, k = 7)
consensus_heatmap(res, k = 8)
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)
membership_heatmap(res, k = 7)
membership_heatmap(res, k = 8)
As soon as the classes for columns are determined, the signatures that are significantly different between subgroups can be looked for. Following are the heatmaps for signatures.
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)
get_signatures(res, k = 7)
get_signatures(res, k = 8)
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 (which is done by automatically selecting number of clusters).If there are too many signatures, top_signatures = ... can be set to only show the
signatures with the highest FDRs:
# code only for demonstration
# e.g. to show the top 500 most significant rows
tb = get_signature(res, k = ..., top_signatures = 500)
If the signatures are defined as these which are uniquely high in current group, diff_method argument
can be set to "uniquely_high_in_one_group":
# code only for demonstration
tb = get_signature(res, k = ..., diff_method = "uniquely_high_in_one_group")
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")
dimension_reduction(res, k = 7, method = "UMAP")
dimension_reduction(res, k = 8, method = "UMAP")
Following heatmap shows how subgroups are split when increasing k:
collect_classes(res)
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.
Parent node: Node02. Child nodes: Node0111 , Node0112-leaf , Node0113 , Node0121 , Node0122-leaf , Node0123-leaf , Node0131 , Node0132-leaf , Node0133-leaf , Node0134-leaf , Node0211 , Node0212-leaf , Node0221-leaf , Node0222 , Node0231-leaf , Node0232-leaf , Node0233-leaf , Node0311 , Node0312-leaf , Node0313-leaf .
The object with results only for a single top-value method and a single partitioning method can be extracted as:
res = res_rh["021"]
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, 7, 8.
#> On a matrix with 30000 rows and 53 columns.
#> Top rows (1000) are extracted by 'SD' method.
#> Subgroups are detected by 'kmeans' method.
#> Performed in total 350 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_partitions"
#> [7] "compare_signatures" "consensus_heatmap" "dimension_reduction"
#> [10] "functional_enrichment" "get_anno_col" "get_anno"
#> [13] "get_classes" "get_consensus" "get_matrix"
#> [16] "get_membership" "get_param" "get_signatures"
#> [19] "get_stats" "is_best_k" "is_stable_k"
#> [22] "membership_heatmap" "ncol" "nrow"
#> [25] "plot_ecdf" "predict_classes" "rownames"
#> [28] "select_partition_number" "show" "suggest_best_k"
#> [31] "test_to_known_factors" "top_rows_heatmap"
collect_plots() function collects all the plots made from res for all k (number of subgroups)
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, higher 1-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 0.967 0.974 0.4335 0.570 0.570
#> 3 3 0.713 0.873 0.932 0.4688 0.774 0.609
#> 4 4 0.621 0.545 0.779 0.1259 0.904 0.757
#> 5 5 0.651 0.716 0.822 0.0565 0.847 0.576
#> 6 6 0.642 0.653 0.802 0.0361 0.970 0.882
#> 7 7 0.686 0.639 0.778 0.0305 0.986 0.942
#> 8 8 0.688 0.612 0.759 0.0255 0.953 0.796
suggest_best_k() suggests the best \(k\) based on these statistics. The rules are as follows:
suggest_best_k(res)
#> [1] 2
Following is 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 subgroup
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
#> TCGA.VS.A954.01 2 0.000 0.968 0.00 1.00
#> TCGA.MA.AA42.01 1 0.141 0.972 0.98 0.02
#> TCGA.C5.A8YQ.01 1 0.141 0.973 0.98 0.02
#> TCGA.MA.AA3W.01 1 0.000 0.978 1.00 0.00
#> TCGA.EK.A2R9.01 1 0.000 0.978 1.00 0.00
#> TCGA.IR.A3LC.01 2 0.141 0.976 0.02 0.98
#> TCGA.EA.A50E.01 2 0.141 0.976 0.02 0.98
#> TCGA.VS.A8EK.01 2 0.141 0.976 0.02 0.98
#> TCGA.EK.A2RO.01 1 0.327 0.955 0.94 0.06
#> TCGA.C5.A901.01 2 0.402 0.939 0.08 0.92
#> TCGA.VS.A953.01 2 0.000 0.968 0.00 1.00
#> TCGA.EA.A3HS.01 1 0.000 0.978 1.00 0.00
#> TCGA.C5.A7CO.01 1 0.402 0.944 0.92 0.08
#> TCGA.VS.A94W.01 1 0.141 0.973 0.98 0.02
#> TCGA.MA.AA41.01 1 0.000 0.978 1.00 0.00
#> TCGA.EK.A3GN.01 2 0.141 0.976 0.02 0.98
#> TCGA.ZJ.A8QO.01 1 0.000 0.978 1.00 0.00
#> TCGA.JW.A852.01 2 0.141 0.976 0.02 0.98
#> TCGA.EA.A3QE.01 1 0.141 0.972 0.98 0.02
#> TCGA.DS.A0VM.01 1 0.000 0.978 1.00 0.00
#> TCGA.Q1.A6DW.01 2 0.000 0.968 0.00 1.00
#> TCGA.MU.A8JM.01 1 0.141 0.973 0.98 0.02
#> TCGA.EK.A2IR.01 1 0.402 0.944 0.92 0.08
#> TCGA.C5.A2LV.01 2 0.000 0.968 0.00 1.00
#> TCGA.C5.A7UE.01 1 0.141 0.973 0.98 0.02
#> TCGA.XS.A8TJ.01 1 0.000 0.978 1.00 0.00
#> TCGA.DS.A0VN.01 1 0.141 0.973 0.98 0.02
#> TCGA.DR.A0ZL.01 1 0.000 0.978 1.00 0.00
#> TCGA.FU.A3WB.01 1 0.402 0.944 0.92 0.08
#> TCGA.EA.A5O9.01 1 0.402 0.944 0.92 0.08
#> TCGA.EA.A5ZE.01 1 0.000 0.978 1.00 0.00
#> TCGA.JW.A5VI.01 1 0.141 0.973 0.98 0.02
#> TCGA.FU.A3YQ.01 1 0.000 0.978 1.00 0.00
#> TCGA.C5.A7CH.01 1 0.242 0.959 0.96 0.04
#> TCGA.LP.A5U2.01 2 0.141 0.976 0.02 0.98
#> TCGA.VS.A9V3.01 2 0.402 0.939 0.08 0.92
#> TCGA.BI.A20A.01 1 0.402 0.944 0.92 0.08
#> TCGA.ZX.AA5X.01 1 0.000 0.978 1.00 0.00
#> TCGA.C5.A7CJ.01 1 0.000 0.978 1.00 0.00
#> TCGA.VS.A9U5.01 2 0.141 0.976 0.02 0.98
#> TCGA.VS.A9UV.01 2 0.141 0.976 0.02 0.98
#> TCGA.Q1.A6DT.01 1 0.000 0.978 1.00 0.00
#> TCGA.C5.A1M8.01 2 0.402 0.932 0.08 0.92
#> TCGA.MU.A5YI.01 1 0.402 0.944 0.92 0.08
#> TCGA.ZJ.AAX4.01 1 0.402 0.944 0.92 0.08
#> TCGA.DS.A1O9.01 1 0.000 0.978 1.00 0.00
#> TCGA.VS.A9UC.01 1 0.000 0.978 1.00 0.00
#> TCGA.VS.A9V2.01 1 0.141 0.972 0.98 0.02
#> TCGA.C5.A7CG.01 2 0.529 0.907 0.12 0.88
#> TCGA.EX.A1H5.01 1 0.141 0.973 0.98 0.02
#> TCGA.C5.A1MH.01 1 0.000 0.978 1.00 0.00
#> TCGA.C5.A1MF.01 1 0.000 0.978 1.00 0.00
#> TCGA.C5.A1BK.01 1 0.000 0.978 1.00 0.00
cbind(get_classes(res, k = 3), get_membership(res, k = 3))
#> class entropy silhouette p1 p2 p3
#> TCGA.VS.A954.01 2 0.0892 0.954 0.00 0.98 0.02
#> TCGA.MA.AA42.01 1 0.0892 0.930 0.98 0.00 0.02
#> TCGA.C5.A8YQ.01 3 0.4796 0.784 0.22 0.00 0.78
#> TCGA.MA.AA3W.01 1 0.0000 0.941 1.00 0.00 0.00
#> TCGA.EK.A2R9.01 1 0.6126 0.391 0.60 0.00 0.40
#> TCGA.IR.A3LC.01 2 0.0000 0.962 0.00 1.00 0.00
#> TCGA.EA.A50E.01 2 0.0000 0.962 0.00 1.00 0.00
#> TCGA.VS.A8EK.01 2 0.0000 0.962 0.00 1.00 0.00
#> TCGA.EK.A2RO.01 3 0.0892 0.829 0.02 0.00 0.98
#> TCGA.C5.A901.01 2 0.0892 0.957 0.00 0.98 0.02
#> TCGA.VS.A953.01 2 0.0000 0.962 0.00 1.00 0.00
#> TCGA.EA.A3HS.01 1 0.0000 0.941 1.00 0.00 0.00
#> TCGA.C5.A7CO.01 3 0.2537 0.861 0.08 0.00 0.92
#> TCGA.VS.A94W.01 1 0.4555 0.760 0.80 0.00 0.20
#> TCGA.MA.AA41.01 1 0.0000 0.941 1.00 0.00 0.00
#> TCGA.EK.A3GN.01 2 0.0000 0.962 0.00 1.00 0.00
#> TCGA.ZJ.A8QO.01 1 0.0892 0.930 0.98 0.00 0.02
#> TCGA.JW.A852.01 2 0.0892 0.957 0.00 0.98 0.02
#> TCGA.EA.A3QE.01 1 0.0000 0.941 1.00 0.00 0.00
#> TCGA.DS.A0VM.01 1 0.0892 0.930 0.98 0.00 0.02
#> TCGA.Q1.A6DW.01 3 0.6045 0.244 0.00 0.38 0.62
#> TCGA.MU.A8JM.01 1 0.0000 0.941 1.00 0.00 0.00
#> TCGA.EK.A2IR.01 3 0.3340 0.872 0.12 0.00 0.88
#> TCGA.C5.A2LV.01 2 0.0892 0.952 0.00 0.98 0.02
#> TCGA.C5.A7UE.01 3 0.6244 0.386 0.44 0.00 0.56
#> TCGA.XS.A8TJ.01 1 0.0000 0.941 1.00 0.00 0.00
#> TCGA.DS.A0VN.01 1 0.0000 0.941 1.00 0.00 0.00
#> TCGA.DR.A0ZL.01 1 0.0000 0.941 1.00 0.00 0.00
#> TCGA.FU.A3WB.01 3 0.0892 0.829 0.02 0.00 0.98
#> TCGA.EA.A5O9.01 3 0.3340 0.872 0.12 0.00 0.88
#> TCGA.EA.A5ZE.01 1 0.0892 0.930 0.98 0.00 0.02
#> TCGA.JW.A5VI.01 1 0.0000 0.941 1.00 0.00 0.00
#> TCGA.FU.A3YQ.01 1 0.0000 0.941 1.00 0.00 0.00
#> TCGA.C5.A7CH.01 1 0.7144 0.631 0.70 0.08 0.22
#> TCGA.LP.A5U2.01 2 0.3340 0.888 0.00 0.88 0.12
#> TCGA.VS.A9V3.01 2 0.0892 0.957 0.00 0.98 0.02
#> TCGA.BI.A20A.01 3 0.3340 0.872 0.12 0.00 0.88
#> TCGA.ZX.AA5X.01 1 0.2959 0.856 0.90 0.00 0.10
#> TCGA.C5.A7CJ.01 1 0.0000 0.941 1.00 0.00 0.00
#> TCGA.VS.A9U5.01 2 0.0000 0.962 0.00 1.00 0.00
#> TCGA.VS.A9UV.01 2 0.0000 0.962 0.00 1.00 0.00
#> TCGA.Q1.A6DT.01 1 0.0000 0.941 1.00 0.00 0.00
#> TCGA.C5.A1M8.01 2 0.4291 0.820 0.00 0.82 0.18
#> TCGA.MU.A5YI.01 3 0.3340 0.872 0.12 0.00 0.88
#> TCGA.ZJ.AAX4.01 3 0.3340 0.872 0.12 0.00 0.88
#> TCGA.DS.A1O9.01 1 0.0000 0.941 1.00 0.00 0.00
#> TCGA.VS.A9UC.01 1 0.0000 0.941 1.00 0.00 0.00
#> TCGA.VS.A9V2.01 1 0.0000 0.941 1.00 0.00 0.00
#> TCGA.C5.A7CG.01 2 0.3832 0.848 0.10 0.88 0.02
#> TCGA.EX.A1H5.01 3 0.0892 0.829 0.02 0.00 0.98
#> TCGA.C5.A1MH.01 1 0.0000 0.941 1.00 0.00 0.00
#> TCGA.C5.A1MF.01 1 0.4796 0.736 0.78 0.00 0.22
#> TCGA.C5.A1BK.01 1 0.0892 0.930 0.98 0.00 0.02
cbind(get_classes(res, k = 4), get_membership(res, k = 4))
#> class entropy silhouette p1 p2 p3 p4
#> TCGA.VS.A954.01 2 0.1411 0.797151 0.00 0.96 0.02 0.02
#> TCGA.MA.AA42.01 1 0.3400 0.726417 0.82 0.00 0.00 0.18
#> TCGA.C5.A8YQ.01 4 0.7040 -0.532608 0.12 0.00 0.42 0.46
#> TCGA.MA.AA3W.01 1 0.0707 0.794639 0.98 0.00 0.00 0.02
#> TCGA.EK.A2R9.01 1 0.7602 -0.000277 0.42 0.00 0.38 0.20
#> TCGA.IR.A3LC.01 2 0.0000 0.808787 0.00 1.00 0.00 0.00
#> TCGA.EA.A50E.01 2 0.2345 0.781806 0.00 0.90 0.00 0.10
#> TCGA.VS.A8EK.01 2 0.1637 0.802891 0.00 0.94 0.00 0.06
#> TCGA.EK.A2RO.01 3 0.0707 0.454650 0.02 0.00 0.98 0.00
#> TCGA.C5.A901.01 2 0.5594 0.352235 0.02 0.52 0.00 0.46
#> TCGA.VS.A953.01 2 0.1211 0.792428 0.00 0.96 0.00 0.04
#> TCGA.EA.A3HS.01 1 0.2345 0.765346 0.90 0.00 0.00 0.10
#> TCGA.C5.A7CO.01 3 0.4134 0.540596 0.00 0.00 0.74 0.26
#> TCGA.VS.A94W.01 1 0.5271 0.427252 0.64 0.00 0.34 0.02
#> TCGA.MA.AA41.01 1 0.2647 0.768426 0.88 0.00 0.00 0.12
#> TCGA.EK.A3GN.01 2 0.4277 0.673850 0.00 0.72 0.00 0.28
#> TCGA.ZJ.A8QO.01 1 0.2011 0.785109 0.92 0.00 0.00 0.08
#> TCGA.JW.A852.01 2 0.4642 0.661738 0.02 0.74 0.00 0.24
#> TCGA.EA.A3QE.01 1 0.2647 0.769243 0.88 0.00 0.00 0.12
#> TCGA.DS.A0VM.01 1 0.3172 0.739818 0.84 0.00 0.00 0.16
#> TCGA.Q1.A6DW.01 3 0.5175 0.257955 0.00 0.12 0.76 0.12
#> TCGA.MU.A8JM.01 1 0.2345 0.765346 0.90 0.00 0.00 0.10
#> TCGA.EK.A2IR.01 3 0.4907 0.511259 0.00 0.00 0.58 0.42
#> TCGA.C5.A2LV.01 2 0.2011 0.778285 0.00 0.92 0.00 0.08
#> TCGA.C5.A7UE.01 1 0.6617 0.346139 0.60 0.00 0.28 0.12
#> TCGA.XS.A8TJ.01 1 0.0000 0.796028 1.00 0.00 0.00 0.00
#> TCGA.DS.A0VN.01 1 0.2345 0.765346 0.90 0.00 0.00 0.10
#> TCGA.DR.A0ZL.01 1 0.0707 0.794639 0.98 0.00 0.00 0.02
#> TCGA.FU.A3WB.01 3 0.4277 0.566581 0.00 0.00 0.72 0.28
#> TCGA.EA.A5O9.01 3 0.4948 0.499952 0.00 0.00 0.56 0.44
#> TCGA.EA.A5ZE.01 1 0.1637 0.790102 0.94 0.00 0.00 0.06
#> TCGA.JW.A5VI.01 1 0.1211 0.790484 0.96 0.00 0.00 0.04
#> TCGA.FU.A3YQ.01 1 0.0707 0.796022 0.98 0.00 0.00 0.02
#> TCGA.C5.A7CH.01 4 0.7344 0.045264 0.16 0.00 0.38 0.46
#> TCGA.LP.A5U2.01 3 0.7888 -0.200489 0.00 0.32 0.38 0.30
#> TCGA.VS.A9V3.01 2 0.6005 0.297665 0.04 0.50 0.00 0.46
#> TCGA.BI.A20A.01 3 0.4522 0.566131 0.00 0.00 0.68 0.32
#> TCGA.ZX.AA5X.01 1 0.7346 0.205703 0.52 0.00 0.28 0.20
#> TCGA.C5.A7CJ.01 1 0.1211 0.789751 0.96 0.00 0.00 0.04
#> TCGA.VS.A9U5.01 2 0.0000 0.808787 0.00 1.00 0.00 0.00
#> TCGA.VS.A9UV.01 2 0.0000 0.808787 0.00 1.00 0.00 0.00
#> TCGA.Q1.A6DT.01 1 0.4948 0.330833 0.56 0.00 0.00 0.44
#> TCGA.C5.A1M8.01 3 0.8437 -0.218737 0.04 0.18 0.42 0.36
#> TCGA.MU.A5YI.01 3 0.4522 0.566131 0.00 0.00 0.68 0.32
#> TCGA.ZJ.AAX4.01 3 0.4624 0.560451 0.00 0.00 0.66 0.34
#> TCGA.DS.A1O9.01 1 0.1211 0.793864 0.96 0.00 0.00 0.04
#> TCGA.VS.A9UC.01 1 0.0707 0.796022 0.98 0.00 0.00 0.02
#> TCGA.VS.A9V2.01 1 0.2921 0.755958 0.86 0.00 0.00 0.14
#> TCGA.C5.A7CG.01 4 0.6831 -0.392516 0.10 0.42 0.00 0.48
#> TCGA.EX.A1H5.01 3 0.1637 0.418779 0.06 0.00 0.94 0.00
#> TCGA.C5.A1MH.01 1 0.0000 0.796028 1.00 0.00 0.00 0.00
#> TCGA.C5.A1MF.01 1 0.7414 0.140828 0.48 0.00 0.34 0.18
#> TCGA.C5.A1BK.01 1 0.4134 0.636008 0.74 0.00 0.00 0.26
cbind(get_classes(res, k = 5), get_membership(res, k = 5))
#> class entropy silhouette p1 p2 p3 p4 p5
#> TCGA.VS.A954.01 2 0.3868 0.711 0.00 0.80 0.00 0.06 0.14
#> TCGA.MA.AA42.01 1 0.4890 0.749 0.76 0.02 0.04 0.16 0.02
#> TCGA.C5.A8YQ.01 3 0.6379 0.714 0.08 0.00 0.64 0.18 0.10
#> TCGA.MA.AA3W.01 1 0.1732 0.872 0.92 0.00 0.00 0.00 0.08
#> TCGA.EK.A2R9.01 5 0.4268 0.630 0.20 0.00 0.02 0.02 0.76
#> TCGA.IR.A3LC.01 2 0.1410 0.844 0.00 0.94 0.00 0.00 0.06
#> TCGA.EA.A50E.01 2 0.0609 0.845 0.00 0.98 0.00 0.02 0.00
#> TCGA.VS.A8EK.01 2 0.0609 0.845 0.00 0.98 0.00 0.02 0.00
#> TCGA.EK.A2RO.01 5 0.4126 0.437 0.00 0.00 0.38 0.00 0.62
#> TCGA.C5.A901.01 4 0.3895 0.591 0.00 0.32 0.00 0.68 0.00
#> TCGA.VS.A953.01 2 0.2012 0.813 0.00 0.92 0.00 0.06 0.02
#> TCGA.EA.A3HS.01 1 0.2438 0.875 0.90 0.00 0.00 0.06 0.04
#> TCGA.C5.A7CO.01 3 0.7170 0.336 0.04 0.00 0.42 0.16 0.38
#> TCGA.VS.A94W.01 5 0.4360 0.576 0.30 0.00 0.02 0.00 0.68
#> TCGA.MA.AA41.01 1 0.2012 0.872 0.92 0.00 0.00 0.06 0.02
#> TCGA.EK.A3GN.01 4 0.4262 0.386 0.00 0.44 0.00 0.56 0.00
#> TCGA.ZJ.A8QO.01 1 0.3521 0.799 0.82 0.00 0.04 0.14 0.00
#> TCGA.JW.A852.01 2 0.5305 0.224 0.00 0.64 0.02 0.30 0.04
#> TCGA.EA.A3QE.01 1 0.2249 0.875 0.92 0.02 0.00 0.04 0.02
#> TCGA.DS.A0VM.01 1 0.4254 0.720 0.74 0.00 0.00 0.22 0.04
#> TCGA.Q1.A6DW.01 5 0.4398 0.531 0.00 0.00 0.24 0.04 0.72
#> TCGA.MU.A8JM.01 1 0.2012 0.872 0.92 0.00 0.00 0.06 0.02
#> TCGA.EK.A2IR.01 3 0.5129 0.770 0.02 0.00 0.72 0.18 0.08
#> TCGA.C5.A2LV.01 2 0.2331 0.798 0.00 0.90 0.00 0.08 0.02
#> TCGA.C5.A7UE.01 1 0.3700 0.809 0.84 0.00 0.08 0.06 0.02
#> TCGA.XS.A8TJ.01 1 0.1043 0.886 0.96 0.00 0.00 0.00 0.04
#> TCGA.DS.A0VN.01 1 0.2012 0.872 0.92 0.00 0.00 0.06 0.02
#> TCGA.DR.A0ZL.01 1 0.1732 0.872 0.92 0.00 0.00 0.00 0.08
#> TCGA.FU.A3WB.01 3 0.0609 0.794 0.00 0.00 0.98 0.00 0.02
#> TCGA.EA.A5O9.01 3 0.4449 0.789 0.02 0.00 0.78 0.14 0.06
#> TCGA.EA.A5ZE.01 1 0.2331 0.873 0.90 0.00 0.00 0.02 0.08
#> TCGA.JW.A5VI.01 1 0.1648 0.888 0.94 0.00 0.00 0.02 0.04
#> TCGA.FU.A3YQ.01 1 0.0609 0.888 0.98 0.00 0.00 0.02 0.00
#> TCGA.C5.A7CH.01 4 0.6980 0.085 0.04 0.02 0.08 0.50 0.36
#> TCGA.LP.A5U2.01 5 0.4216 0.508 0.00 0.10 0.00 0.12 0.78
#> TCGA.VS.A9V3.01 4 0.5305 0.616 0.02 0.30 0.00 0.64 0.04
#> TCGA.BI.A20A.01 3 0.0609 0.811 0.02 0.00 0.98 0.00 0.00
#> TCGA.ZX.AA5X.01 5 0.4767 0.360 0.42 0.00 0.00 0.02 0.56
#> TCGA.C5.A7CJ.01 1 0.1216 0.889 0.96 0.00 0.00 0.02 0.02
#> TCGA.VS.A9U5.01 2 0.0609 0.851 0.00 0.98 0.00 0.00 0.02
#> TCGA.VS.A9UV.01 2 0.1410 0.844 0.00 0.94 0.00 0.00 0.06
#> TCGA.Q1.A6DT.01 4 0.5958 0.424 0.24 0.04 0.00 0.64 0.08
#> TCGA.C5.A1M8.01 5 0.4527 0.528 0.02 0.08 0.00 0.12 0.78
#> TCGA.MU.A5YI.01 3 0.0609 0.811 0.02 0.00 0.98 0.00 0.00
#> TCGA.ZJ.AAX4.01 3 0.0609 0.811 0.02 0.00 0.98 0.00 0.00
#> TCGA.DS.A1O9.01 1 0.2873 0.838 0.86 0.00 0.00 0.12 0.02
#> TCGA.VS.A9UC.01 1 0.1648 0.884 0.94 0.00 0.00 0.02 0.04
#> TCGA.VS.A9V2.01 1 0.2249 0.875 0.92 0.02 0.00 0.04 0.02
#> TCGA.C5.A7CG.01 4 0.6142 0.618 0.04 0.28 0.02 0.62 0.04
#> TCGA.EX.A1H5.01 5 0.4921 0.510 0.04 0.00 0.34 0.00 0.62
#> TCGA.C5.A1MH.01 1 0.1043 0.886 0.96 0.00 0.00 0.00 0.04
#> TCGA.C5.A1MF.01 5 0.4268 0.630 0.20 0.00 0.02 0.02 0.76
#> TCGA.C5.A1BK.01 1 0.3697 0.833 0.82 0.00 0.00 0.08 0.10
cbind(get_classes(res, k = 6), get_membership(res, k = 6))
#> class entropy silhouette p1 p2 p3 p4 p5 p6
#> TCGA.VS.A954.01 2 0.4664 0.6423 0.00 0.74 0.00 0.06 0.06 0.14
#> TCGA.MA.AA42.01 1 0.4088 0.7544 0.78 0.00 0.00 0.10 0.02 0.10
#> TCGA.C5.A8YQ.01 6 0.3706 -0.0166 0.00 0.00 0.38 0.00 0.00 0.62
#> TCGA.MA.AA3W.01 1 0.1480 0.8277 0.94 0.00 0.00 0.02 0.04 0.00
#> TCGA.EK.A2R9.01 5 0.2581 0.6435 0.12 0.00 0.00 0.02 0.86 0.00
#> TCGA.IR.A3LC.01 2 0.0000 0.8273 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.EA.A50E.01 2 0.1480 0.8078 0.00 0.94 0.00 0.04 0.00 0.02
#> TCGA.VS.A8EK.01 2 0.1480 0.8177 0.00 0.94 0.00 0.02 0.00 0.04
#> TCGA.EK.A2RO.01 5 0.3592 0.5762 0.00 0.00 0.24 0.00 0.74 0.02
#> TCGA.C5.A901.01 4 0.2631 0.6841 0.00 0.18 0.00 0.82 0.00 0.00
#> TCGA.VS.A953.01 2 0.3851 0.7517 0.00 0.82 0.02 0.08 0.06 0.02
#> TCGA.EA.A3HS.01 1 0.3309 0.7092 0.72 0.00 0.00 0.00 0.00 0.28
#> TCGA.C5.A7CO.01 6 0.6103 0.2175 0.00 0.00 0.30 0.00 0.32 0.38
#> TCGA.VS.A94W.01 5 0.4222 0.5236 0.26 0.00 0.02 0.02 0.70 0.00
#> TCGA.MA.AA41.01 1 0.3499 0.6836 0.68 0.00 0.00 0.00 0.00 0.32
#> TCGA.EK.A3GN.01 4 0.4552 0.5253 0.00 0.30 0.00 0.64 0.00 0.06
#> TCGA.ZJ.A8QO.01 1 0.3321 0.7781 0.82 0.00 0.00 0.08 0.00 0.10
#> TCGA.JW.A852.01 2 0.5363 0.2389 0.00 0.58 0.00 0.32 0.02 0.08
#> TCGA.EA.A3QE.01 1 0.1807 0.8348 0.92 0.00 0.00 0.00 0.02 0.06
#> TCGA.DS.A0VM.01 1 0.4222 0.6215 0.70 0.00 0.00 0.26 0.02 0.02
#> TCGA.Q1.A6DW.01 5 0.5106 0.5844 0.00 0.04 0.20 0.00 0.68 0.08
#> TCGA.MU.A8JM.01 1 0.2793 0.7748 0.80 0.00 0.00 0.00 0.00 0.20
#> TCGA.EK.A2IR.01 3 0.3756 0.0630 0.00 0.00 0.60 0.00 0.00 0.40
#> TCGA.C5.A2LV.01 2 0.4770 0.7182 0.00 0.76 0.02 0.10 0.06 0.06
#> TCGA.C5.A7UE.01 1 0.3460 0.7469 0.76 0.00 0.02 0.00 0.00 0.22
#> TCGA.XS.A8TJ.01 1 0.0547 0.8356 0.98 0.00 0.00 0.00 0.02 0.00
#> TCGA.DS.A0VN.01 1 0.3076 0.7483 0.76 0.00 0.00 0.00 0.00 0.24
#> TCGA.DR.A0ZL.01 1 0.1480 0.8277 0.94 0.00 0.00 0.02 0.04 0.00
#> TCGA.FU.A3WB.01 3 0.0547 0.7370 0.02 0.00 0.98 0.00 0.00 0.00
#> TCGA.EA.A5O9.01 3 0.3578 0.2515 0.00 0.00 0.66 0.00 0.00 0.34
#> TCGA.EA.A5ZE.01 1 0.3631 0.7939 0.82 0.00 0.00 0.10 0.04 0.04
#> TCGA.JW.A5VI.01 1 0.2048 0.8130 0.88 0.00 0.00 0.00 0.00 0.12
#> TCGA.FU.A3YQ.01 1 0.0547 0.8354 0.98 0.00 0.00 0.00 0.00 0.02
#> TCGA.C5.A7CH.01 4 0.5402 0.2519 0.04 0.00 0.02 0.58 0.34 0.02
#> TCGA.LP.A5U2.01 5 0.5709 0.4752 0.00 0.06 0.00 0.14 0.64 0.16
#> TCGA.VS.A9V3.01 4 0.2981 0.6969 0.02 0.16 0.00 0.82 0.00 0.00
#> TCGA.BI.A20A.01 3 0.0547 0.7370 0.02 0.00 0.98 0.00 0.00 0.00
#> TCGA.ZX.AA5X.01 1 0.4700 0.3233 0.60 0.00 0.00 0.06 0.34 0.00
#> TCGA.C5.A7CJ.01 1 0.0937 0.8362 0.96 0.00 0.00 0.00 0.00 0.04
#> TCGA.VS.A9U5.01 2 0.0547 0.8257 0.00 0.98 0.00 0.00 0.00 0.02
#> TCGA.VS.A9UV.01 2 0.0000 0.8273 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.Q1.A6DT.01 4 0.4678 0.5507 0.16 0.00 0.00 0.72 0.02 0.10
#> TCGA.C5.A1M8.01 5 0.5709 0.4752 0.00 0.06 0.00 0.14 0.64 0.16
#> TCGA.MU.A5YI.01 3 0.0547 0.7370 0.02 0.00 0.98 0.00 0.00 0.00
#> TCGA.ZJ.AAX4.01 3 0.1092 0.7244 0.02 0.00 0.96 0.00 0.00 0.02
#> TCGA.DS.A1O9.01 1 0.1865 0.8299 0.92 0.00 0.00 0.04 0.00 0.04
#> TCGA.VS.A9UC.01 1 0.1807 0.8256 0.92 0.00 0.00 0.06 0.02 0.00
#> TCGA.VS.A9V2.01 1 0.2725 0.8276 0.88 0.00 0.00 0.04 0.02 0.06
#> TCGA.C5.A7CG.01 4 0.5615 0.6315 0.12 0.14 0.00 0.66 0.00 0.08
#> TCGA.EX.A1H5.01 5 0.4460 0.5919 0.04 0.00 0.24 0.02 0.70 0.00
#> TCGA.C5.A1MH.01 1 0.0547 0.8356 0.98 0.00 0.00 0.00 0.02 0.00
#> TCGA.C5.A1MF.01 5 0.3483 0.6315 0.12 0.00 0.00 0.02 0.82 0.04
#> TCGA.C5.A1BK.01 1 0.3795 0.7716 0.80 0.00 0.00 0.12 0.06 0.02
cbind(get_classes(res, k = 7), get_membership(res, k = 7))
#> class entropy silhouette p1 p2 p3 p4 p5 p6 p7
#> TCGA.VS.A954.01 2 0.3994 0.1708 0.00 0.50 0.00 0.02 0.00 0.00 0.48
#> TCGA.MA.AA42.01 1 0.6858 0.4596 0.50 0.00 0.04 0.14 0.00 0.18 0.14
#> TCGA.C5.A8YQ.01 6 0.4070 0.6134 0.02 0.00 0.30 0.02 0.00 0.66 0.00
#> TCGA.MA.AA3W.01 1 0.1664 0.8151 0.92 0.00 0.00 0.02 0.06 0.00 0.00
#> TCGA.EK.A2R9.01 5 0.0504 0.6222 0.02 0.00 0.00 0.00 0.98 0.00 0.00
#> TCGA.IR.A3LC.01 2 0.0000 0.7268 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.EA.A50E.01 2 0.1860 0.6926 0.00 0.92 0.00 0.02 0.00 0.04 0.02
#> TCGA.VS.A8EK.01 2 0.2512 0.6859 0.00 0.86 0.00 0.10 0.00 0.04 0.00
#> TCGA.EK.A2RO.01 5 0.3526 0.6054 0.00 0.00 0.18 0.00 0.76 0.00 0.06
#> TCGA.C5.A901.01 4 0.2572 0.6293 0.00 0.20 0.00 0.80 0.00 0.00 0.00
#> TCGA.VS.A953.01 2 0.4536 0.6302 0.00 0.72 0.00 0.06 0.00 0.08 0.14
#> TCGA.EA.A3HS.01 1 0.3922 0.7695 0.80 0.00 0.00 0.06 0.02 0.06 0.06
#> TCGA.C5.A7CO.01 6 0.6494 0.4766 0.00 0.00 0.20 0.02 0.06 0.48 0.24
#> TCGA.VS.A94W.01 5 0.2259 0.5224 0.16 0.00 0.00 0.00 0.84 0.00 0.00
#> TCGA.MA.AA41.01 1 0.3691 0.7661 0.80 0.00 0.00 0.06 0.00 0.06 0.08
#> TCGA.EK.A3GN.01 4 0.3841 0.4454 0.00 0.28 0.00 0.68 0.00 0.04 0.00
#> TCGA.ZJ.A8QO.01 1 0.6600 0.5036 0.54 0.00 0.04 0.14 0.00 0.16 0.12
#> TCGA.JW.A852.01 2 0.6583 -0.0722 0.00 0.46 0.00 0.20 0.00 0.18 0.16
#> TCGA.EA.A3QE.01 1 0.2509 0.8084 0.88 0.00 0.02 0.00 0.00 0.06 0.04
#> TCGA.DS.A0VM.01 1 0.5536 0.6835 0.66 0.00 0.00 0.14 0.06 0.10 0.04
#> TCGA.Q1.A6DW.01 5 0.6405 0.0715 0.00 0.00 0.14 0.04 0.48 0.04 0.30
#> TCGA.MU.A8JM.01 1 0.2769 0.7878 0.86 0.00 0.00 0.04 0.00 0.02 0.08
#> TCGA.EK.A2IR.01 6 0.3459 0.5538 0.00 0.00 0.40 0.00 0.00 0.60 0.00
#> TCGA.C5.A2LV.01 2 0.5373 0.5826 0.00 0.64 0.00 0.10 0.00 0.12 0.14
#> TCGA.C5.A7UE.01 1 0.3257 0.7849 0.84 0.00 0.04 0.02 0.00 0.02 0.08
#> TCGA.XS.A8TJ.01 1 0.1166 0.8172 0.94 0.00 0.00 0.00 0.06 0.00 0.00
#> TCGA.DS.A0VN.01 1 0.2769 0.7878 0.86 0.00 0.00 0.04 0.00 0.02 0.08
#> TCGA.DR.A0ZL.01 1 0.1664 0.8151 0.92 0.00 0.00 0.02 0.06 0.00 0.00
#> TCGA.FU.A3WB.01 3 0.1166 0.7666 0.00 0.00 0.94 0.00 0.06 0.00 0.00
#> TCGA.EA.A5O9.01 3 0.4269 -0.2497 0.02 0.00 0.60 0.02 0.00 0.36 0.00
#> TCGA.EA.A5ZE.01 1 0.5661 0.7183 0.66 0.00 0.00 0.08 0.06 0.12 0.08
#> TCGA.JW.A5VI.01 1 0.2355 0.8101 0.90 0.00 0.02 0.04 0.00 0.02 0.02
#> TCGA.FU.A3YQ.01 1 0.1505 0.8161 0.94 0.00 0.02 0.00 0.00 0.02 0.02
#> TCGA.C5.A7CH.01 4 0.5027 0.2970 0.04 0.00 0.00 0.58 0.32 0.06 0.00
#> TCGA.LP.A5U2.01 7 0.3606 0.9527 0.00 0.02 0.00 0.00 0.30 0.00 0.68
#> TCGA.VS.A9V3.01 4 0.4378 0.6056 0.00 0.20 0.00 0.70 0.00 0.02 0.08
#> TCGA.BI.A20A.01 3 0.0504 0.8043 0.00 0.00 0.98 0.00 0.02 0.00 0.00
#> TCGA.ZX.AA5X.01 1 0.3606 0.6082 0.68 0.00 0.00 0.02 0.30 0.00 0.00
#> TCGA.C5.A7CJ.01 1 0.1860 0.8160 0.92 0.00 0.00 0.02 0.04 0.00 0.02
#> TCGA.VS.A9U5.01 2 0.0000 0.7268 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.VS.A9UV.01 2 0.0000 0.7268 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.Q1.A6DT.01 4 0.3940 0.5458 0.08 0.00 0.00 0.78 0.08 0.06 0.00
#> TCGA.C5.A1M8.01 7 0.3221 0.9520 0.00 0.00 0.00 0.00 0.32 0.00 0.68
#> TCGA.MU.A5YI.01 3 0.0504 0.8043 0.00 0.00 0.98 0.00 0.02 0.00 0.00
#> TCGA.ZJ.AAX4.01 3 0.0000 0.7919 0.00 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.DS.A1O9.01 1 0.5946 0.7101 0.66 0.00 0.04 0.08 0.06 0.12 0.04
#> TCGA.VS.A9UC.01 1 0.3346 0.8011 0.84 0.00 0.00 0.04 0.06 0.04 0.02
#> TCGA.VS.A9V2.01 1 0.2769 0.8040 0.86 0.00 0.02 0.00 0.00 0.08 0.04
#> TCGA.C5.A7CG.01 4 0.7361 0.4723 0.02 0.20 0.02 0.48 0.02 0.16 0.10
#> TCGA.EX.A1H5.01 5 0.3052 0.6215 0.00 0.00 0.20 0.00 0.78 0.00 0.02
#> TCGA.C5.A1MH.01 1 0.1166 0.8172 0.94 0.00 0.00 0.00 0.06 0.00 0.00
#> TCGA.C5.A1MF.01 5 0.1505 0.5971 0.02 0.00 0.00 0.02 0.94 0.00 0.02
#> TCGA.C5.A1BK.01 1 0.4171 0.7839 0.78 0.00 0.00 0.06 0.06 0.08 0.02
cbind(get_classes(res, k = 8), get_membership(res, k = 8))
#> class entropy silhouette p1 p2 p3 p4 p5 p6 p7 p8
#> TCGA.VS.A954.01 2 0.3737 0.2330 0.00 0.50 0.00 0.00 0.00 0.00 0.48 0.02
#> TCGA.MA.AA42.01 8 0.4955 0.4128 0.34 0.00 0.04 0.08 0.00 0.00 0.00 0.54
#> TCGA.C5.A8YQ.01 6 0.2265 0.6495 0.00 0.00 0.08 0.02 0.00 0.88 0.00 0.02
#> TCGA.MA.AA3W.01 1 0.2020 0.7318 0.90 0.00 0.00 0.00 0.06 0.00 0.02 0.02
#> TCGA.EK.A2R9.01 5 0.2807 0.3753 0.04 0.00 0.02 0.00 0.86 0.00 0.02 0.06
#> TCGA.IR.A3LC.01 2 0.0471 0.7734 0.00 0.98 0.00 0.00 0.00 0.00 0.02 0.00
#> TCGA.EA.A50E.01 2 0.2348 0.7199 0.00 0.88 0.00 0.04 0.00 0.00 0.02 0.06
#> TCGA.VS.A8EK.01 2 0.3185 0.7130 0.00 0.82 0.00 0.06 0.00 0.00 0.08 0.04
#> TCGA.EK.A2RO.01 5 0.3942 0.5113 0.00 0.00 0.34 0.02 0.62 0.00 0.02 0.00
#> TCGA.C5.A901.01 4 0.1887 0.7018 0.00 0.06 0.00 0.90 0.00 0.00 0.00 0.04
#> TCGA.VS.A953.01 2 0.5780 0.6136 0.00 0.62 0.00 0.02 0.04 0.06 0.12 0.14
#> TCGA.EA.A3HS.01 1 0.5504 0.5757 0.62 0.00 0.00 0.00 0.04 0.14 0.06 0.14
#> TCGA.C5.A7CO.01 6 0.6569 0.5009 0.04 0.02 0.10 0.00 0.06 0.58 0.14 0.06
#> TCGA.VS.A94W.01 5 0.4417 0.2725 0.36 0.00 0.02 0.00 0.58 0.00 0.02 0.02
#> TCGA.MA.AA41.01 1 0.5887 0.5627 0.56 0.00 0.00 0.00 0.04 0.16 0.06 0.18
#> TCGA.EK.A3GN.01 4 0.3337 0.6553 0.00 0.16 0.00 0.78 0.00 0.00 0.02 0.04
#> TCGA.ZJ.A8QO.01 8 0.4860 0.3336 0.40 0.00 0.04 0.06 0.00 0.00 0.00 0.50
#> TCGA.JW.A852.01 8 0.4841 0.1876 0.00 0.34 0.00 0.16 0.00 0.00 0.00 0.50
#> TCGA.EA.A3QE.01 1 0.3135 0.7061 0.82 0.02 0.00 0.00 0.00 0.02 0.02 0.12
#> TCGA.DS.A0VM.01 1 0.5003 0.3805 0.62 0.00 0.00 0.12 0.02 0.00 0.02 0.22
#> TCGA.Q1.A6DW.01 5 0.5575 0.3275 0.00 0.00 0.32 0.04 0.46 0.00 0.18 0.00
#> TCGA.MU.A8JM.01 1 0.4262 0.6754 0.74 0.00 0.00 0.00 0.02 0.08 0.04 0.12
#> TCGA.EK.A2IR.01 6 0.2534 0.6677 0.00 0.00 0.22 0.00 0.00 0.78 0.00 0.00
#> TCGA.C5.A2LV.01 2 0.6452 0.5739 0.00 0.56 0.00 0.06 0.04 0.06 0.14 0.14
#> TCGA.C5.A7UE.01 1 0.4704 0.6592 0.72 0.00 0.02 0.00 0.02 0.08 0.04 0.12
#> TCGA.XS.A8TJ.01 1 0.0941 0.7453 0.96 0.00 0.00 0.00 0.00 0.00 0.02 0.02
#> TCGA.DS.A0VN.01 1 0.4262 0.6754 0.74 0.00 0.00 0.00 0.02 0.08 0.04 0.12
#> TCGA.DR.A0ZL.01 1 0.2020 0.7318 0.90 0.00 0.00 0.00 0.06 0.00 0.02 0.02
#> TCGA.FU.A3WB.01 3 0.0941 0.8660 0.00 0.00 0.96 0.02 0.02 0.00 0.00 0.00
#> TCGA.EA.A5O9.01 6 0.3299 0.3718 0.00 0.00 0.44 0.00 0.00 0.56 0.00 0.00
#> TCGA.EA.A5ZE.01 1 0.5158 0.5520 0.64 0.02 0.00 0.00 0.02 0.02 0.10 0.20
#> TCGA.JW.A5VI.01 1 0.2265 0.7447 0.88 0.00 0.00 0.00 0.00 0.02 0.02 0.08
#> TCGA.FU.A3YQ.01 1 0.2484 0.7335 0.86 0.00 0.00 0.00 0.02 0.02 0.00 0.10
#> TCGA.C5.A7CH.01 4 0.3991 0.5225 0.06 0.00 0.00 0.70 0.22 0.02 0.00 0.00
#> TCGA.LP.A5U2.01 7 0.2534 0.9345 0.00 0.00 0.00 0.00 0.22 0.00 0.78 0.00
#> TCGA.VS.A9V3.01 4 0.3744 0.5463 0.00 0.06 0.00 0.74 0.02 0.00 0.00 0.18
#> TCGA.BI.A20A.01 3 0.0808 0.9368 0.00 0.00 0.96 0.00 0.00 0.04 0.00 0.00
#> TCGA.ZX.AA5X.01 1 0.4057 0.6085 0.72 0.00 0.00 0.04 0.20 0.00 0.02 0.02
#> TCGA.C5.A7CJ.01 1 0.2348 0.7472 0.88 0.00 0.00 0.00 0.04 0.00 0.02 0.06
#> TCGA.VS.A9U5.01 2 0.0471 0.7734 0.00 0.98 0.00 0.00 0.00 0.00 0.02 0.00
#> TCGA.VS.A9UV.01 2 0.0471 0.7734 0.00 0.98 0.00 0.00 0.00 0.00 0.02 0.00
#> TCGA.Q1.A6DT.01 4 0.1804 0.6842 0.08 0.00 0.00 0.90 0.00 0.02 0.00 0.00
#> TCGA.C5.A1M8.01 7 0.3551 0.9344 0.00 0.00 0.00 0.00 0.22 0.00 0.72 0.06
#> TCGA.MU.A5YI.01 3 0.0808 0.9368 0.00 0.00 0.96 0.00 0.00 0.04 0.00 0.00
#> TCGA.ZJ.AAX4.01 3 0.1341 0.9005 0.00 0.00 0.92 0.00 0.00 0.08 0.00 0.00
#> TCGA.DS.A1O9.01 1 0.3748 0.6321 0.74 0.00 0.00 0.02 0.00 0.02 0.02 0.20
#> TCGA.VS.A9UC.01 1 0.3048 0.7158 0.84 0.00 0.00 0.02 0.02 0.00 0.04 0.08
#> TCGA.VS.A9V2.01 1 0.4075 0.6603 0.76 0.02 0.00 0.04 0.00 0.02 0.02 0.14
#> TCGA.C5.A7CG.01 8 0.4680 -0.0679 0.00 0.12 0.00 0.40 0.00 0.00 0.00 0.48
#> TCGA.EX.A1H5.01 5 0.4367 0.5169 0.02 0.00 0.34 0.02 0.60 0.00 0.02 0.00
#> TCGA.C5.A1MH.01 1 0.0941 0.7453 0.96 0.00 0.00 0.00 0.00 0.00 0.02 0.02
#> TCGA.C5.A1MF.01 5 0.3454 0.3172 0.06 0.00 0.00 0.00 0.80 0.00 0.06 0.08
#> TCGA.C5.A1BK.01 1 0.4294 0.6714 0.76 0.00 0.00 0.04 0.06 0.02 0.02 0.10
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)
consensus_heatmap(res, k = 7)
consensus_heatmap(res, k = 8)
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)
membership_heatmap(res, k = 7)
membership_heatmap(res, k = 8)
As soon as the classes for columns are determined, the signatures that are significantly different between subgroups can be looked for. Following are the heatmaps for signatures.
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)
get_signatures(res, k = 7)
get_signatures(res, k = 8)
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 (which is done by automatically selecting number of clusters).If there are too many signatures, top_signatures = ... can be set to only show the
signatures with the highest FDRs:
# code only for demonstration
# e.g. to show the top 500 most significant rows
tb = get_signature(res, k = ..., top_signatures = 500)
If the signatures are defined as these which are uniquely high in current group, diff_method argument
can be set to "uniquely_high_in_one_group":
# code only for demonstration
tb = get_signature(res, k = ..., diff_method = "uniquely_high_in_one_group")
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")
dimension_reduction(res, k = 7, method = "UMAP")
dimension_reduction(res, k = 8, method = "UMAP")
Following heatmap shows how subgroups are split when increasing k:
collect_classes(res)
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.
Parent node: Node021. Child nodes: Node01111-leaf , Node01112-leaf , Node01113-leaf , Node01131-leaf , Node01132-leaf , Node01133-leaf , Node01211-leaf , Node01212-leaf , Node01311-leaf , Node01312-leaf , Node01313-leaf , Node02111 , Node02112-leaf , Node02221 , Node02222-leaf , Node03111-leaf , Node03112 .
The object with results only for a single top-value method and a single partitioning method can be extracted as:
res = res_rh["0211"]
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, 7, 8.
#> On a matrix with 30000 rows and 37 columns.
#> Top rows (1000) are extracted by 'ATC' method.
#> Subgroups are detected by 'kmeans' method.
#> Performed in total 350 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_partitions"
#> [7] "compare_signatures" "consensus_heatmap" "dimension_reduction"
#> [10] "functional_enrichment" "get_anno_col" "get_anno"
#> [13] "get_classes" "get_consensus" "get_matrix"
#> [16] "get_membership" "get_param" "get_signatures"
#> [19] "get_stats" "is_best_k" "is_stable_k"
#> [22] "membership_heatmap" "ncol" "nrow"
#> [25] "plot_ecdf" "predict_classes" "rownames"
#> [28] "select_partition_number" "show" "suggest_best_k"
#> [31] "test_to_known_factors" "top_rows_heatmap"
collect_plots() function collects all the plots made from res for all k (number of subgroups)
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, higher 1-PAC score, higher mean silhouette score or higher
concordance corresponds to better partition. Rand index and Jaccard index
measure how similar the current partition is compared to partition with k-1.
If they are too similar, we won't accept k is better than k-1.
select_partition_number(res)
The numeric values for all these statistics can be obtained by get_stats().
get_stats(res)
#> k 1-PAC mean_silhouette concordance area_increased Rand Jaccard
#> 2 2 1.000 1.000 1.000 0.4300 0.571 0.571
#> 3 3 0.677 0.862 0.936 0.4556 0.694 0.505
#> 4 4 0.730 0.411 0.749 0.1789 0.824 0.597
#> 5 5 0.813 0.913 0.927 0.0713 0.794 0.448
#> 6 6 0.864 0.791 0.869 0.0294 1.000 1.000
#> 7 7 0.862 0.659 0.800 0.0232 0.968 0.847
#> 8 8 0.845 0.703 0.800 0.0180 0.917 0.586
suggest_best_k() suggests the best \(k\) based on these statistics. The rules are as follows:
suggest_best_k(res)
#> [1] 2
Following is 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 subgroup
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
#> TCGA.MA.AA42.01 1 0 1 1 0
#> TCGA.C5.A8YQ.01 1 0 1 1 0
#> TCGA.MA.AA3W.01 1 0 1 1 0
#> TCGA.EK.A2R9.01 2 0 1 0 1
#> TCGA.EK.A2RO.01 2 0 1 0 1
#> TCGA.EA.A3HS.01 2 0 1 0 1
#> TCGA.C5.A7CO.01 1 0 1 1 0
#> TCGA.VS.A94W.01 1 0 1 1 0
#> TCGA.MA.AA41.01 1 0 1 1 0
#> TCGA.ZJ.A8QO.01 1 0 1 1 0
#> TCGA.EA.A3QE.01 1 0 1 1 0
#> TCGA.DS.A0VM.01 1 0 1 1 0
#> TCGA.MU.A8JM.01 1 0 1 1 0
#> TCGA.EK.A2IR.01 2 0 1 0 1
#> TCGA.C5.A7UE.01 1 0 1 1 0
#> TCGA.XS.A8TJ.01 1 0 1 1 0
#> TCGA.DS.A0VN.01 1 0 1 1 0
#> TCGA.DR.A0ZL.01 1 0 1 1 0
#> TCGA.FU.A3WB.01 2 0 1 0 1
#> TCGA.EA.A5O9.01 2 0 1 0 1
#> TCGA.EA.A5ZE.01 2 0 1 0 1
#> TCGA.JW.A5VI.01 1 0 1 1 0
#> TCGA.FU.A3YQ.01 1 0 1 1 0
#> TCGA.C5.A7CH.01 1 0 1 1 0
#> TCGA.BI.A20A.01 1 0 1 1 0
#> TCGA.ZX.AA5X.01 1 0 1 1 0
#> TCGA.C5.A7CJ.01 1 0 1 1 0
#> TCGA.Q1.A6DT.01 1 0 1 1 0
#> TCGA.MU.A5YI.01 2 0 1 0 1
#> TCGA.ZJ.AAX4.01 2 0 1 0 1
#> TCGA.DS.A1O9.01 1 0 1 1 0
#> TCGA.VS.A9UC.01 1 0 1 1 0
#> TCGA.VS.A9V2.01 1 0 1 1 0
#> TCGA.EX.A1H5.01 2 0 1 0 1
#> TCGA.C5.A1MH.01 1 0 1 1 0
#> TCGA.C5.A1MF.01 2 0 1 0 1
#> TCGA.C5.A1BK.01 1 0 1 1 0
cbind(get_classes(res, k = 3), get_membership(res, k = 3))
#> class entropy silhouette p1 p2 p3
#> TCGA.MA.AA42.01 1 0.0000 0.949 1.00 0.00 0.00
#> TCGA.C5.A8YQ.01 3 0.0000 0.802 0.00 0.00 1.00
#> TCGA.MA.AA3W.01 1 0.0000 0.949 1.00 0.00 0.00
#> TCGA.EK.A2R9.01 2 0.0000 1.000 0.00 1.00 0.00
#> TCGA.EK.A2RO.01 2 0.0000 1.000 0.00 1.00 0.00
#> TCGA.EA.A3HS.01 3 0.0000 0.802 0.00 0.00 1.00
#> TCGA.C5.A7CO.01 3 0.0000 0.802 0.00 0.00 1.00
#> TCGA.VS.A94W.01 1 0.0000 0.949 1.00 0.00 0.00
#> TCGA.MA.AA41.01 3 0.0892 0.804 0.02 0.00 0.98
#> TCGA.ZJ.A8QO.01 1 0.5216 0.641 0.74 0.00 0.26
#> TCGA.EA.A3QE.01 1 0.0000 0.949 1.00 0.00 0.00
#> TCGA.DS.A0VM.01 3 0.5706 0.607 0.32 0.00 0.68
#> TCGA.MU.A8JM.01 1 0.4002 0.805 0.84 0.00 0.16
#> TCGA.EK.A2IR.01 3 0.4002 0.665 0.00 0.16 0.84
#> TCGA.C5.A7UE.01 3 0.5706 0.607 0.32 0.00 0.68
#> TCGA.XS.A8TJ.01 1 0.0000 0.949 1.00 0.00 0.00
#> TCGA.DS.A0VN.01 1 0.0000 0.949 1.00 0.00 0.00
#> TCGA.DR.A0ZL.01 1 0.0000 0.949 1.00 0.00 0.00
#> TCGA.FU.A3WB.01 2 0.0000 1.000 0.00 1.00 0.00
#> TCGA.EA.A5O9.01 3 0.0000 0.802 0.00 0.00 1.00
#> TCGA.EA.A5ZE.01 2 0.0000 1.000 0.00 1.00 0.00
#> TCGA.JW.A5VI.01 1 0.4002 0.805 0.84 0.00 0.16
#> TCGA.FU.A3YQ.01 1 0.0000 0.949 1.00 0.00 0.00
#> TCGA.C5.A7CH.01 3 0.0892 0.804 0.02 0.00 0.98
#> TCGA.BI.A20A.01 3 0.5706 0.607 0.32 0.00 0.68
#> TCGA.ZX.AA5X.01 1 0.0000 0.949 1.00 0.00 0.00
#> TCGA.C5.A7CJ.01 1 0.0000 0.949 1.00 0.00 0.00
#> TCGA.Q1.A6DT.01 1 0.4002 0.805 0.84 0.00 0.16
#> TCGA.MU.A5YI.01 2 0.0000 1.000 0.00 1.00 0.00
#> TCGA.ZJ.AAX4.01 3 0.4002 0.665 0.00 0.16 0.84
#> TCGA.DS.A1O9.01 1 0.0000 0.949 1.00 0.00 0.00
#> TCGA.VS.A9UC.01 3 0.5706 0.607 0.32 0.00 0.68
#> TCGA.VS.A9V2.01 1 0.0000 0.949 1.00 0.00 0.00
#> TCGA.EX.A1H5.01 2 0.0000 1.000 0.00 1.00 0.00
#> TCGA.C5.A1MH.01 1 0.0000 0.949 1.00 0.00 0.00
#> TCGA.C5.A1MF.01 2 0.0000 1.000 0.00 1.00 0.00
#> TCGA.C5.A1BK.01 1 0.0000 0.949 1.00 0.00 0.00
cbind(get_classes(res, k = 4), get_membership(res, k = 4))
#> class entropy silhouette p1 p2 p3 p4
#> TCGA.MA.AA42.01 4 0.500 0.4959 0.50 0 0.00 0.50
#> TCGA.C5.A8YQ.01 3 0.491 0.4304 0.00 0 0.58 0.42
#> TCGA.MA.AA3W.01 1 0.479 0.5241 0.62 0 0.00 0.38
#> TCGA.EK.A2R9.01 2 0.000 1.0000 0.00 1 0.00 0.00
#> TCGA.EK.A2RO.01 2 0.000 1.0000 0.00 1 0.00 0.00
#> TCGA.EA.A3HS.01 3 0.000 0.6816 0.00 0 1.00 0.00
#> TCGA.C5.A7CO.01 3 0.164 0.6840 0.00 0 0.94 0.06
#> TCGA.VS.A94W.01 1 0.479 0.5241 0.62 0 0.00 0.38
#> TCGA.MA.AA41.01 3 0.630 0.1396 0.42 0 0.52 0.06
#> TCGA.ZJ.A8QO.01 1 0.704 -0.5829 0.46 0 0.12 0.42
#> TCGA.EA.A3QE.01 1 0.498 0.4681 0.54 0 0.00 0.46
#> TCGA.DS.A0VM.01 1 0.704 -0.3811 0.46 0 0.42 0.12
#> TCGA.MU.A8JM.01 1 0.361 -0.1259 0.80 0 0.20 0.00
#> TCGA.EK.A2IR.01 3 0.340 0.6575 0.00 0 0.82 0.18
#> TCGA.C5.A7UE.01 1 0.491 -0.2855 0.58 0 0.42 0.00
#> TCGA.XS.A8TJ.01 1 0.479 0.5241 0.62 0 0.00 0.38
#> TCGA.DS.A0VN.01 4 0.361 0.0669 0.20 0 0.00 0.80
#> TCGA.DR.A0ZL.01 1 0.479 0.5241 0.62 0 0.00 0.38
#> TCGA.FU.A3WB.01 2 0.000 1.0000 0.00 1 0.00 0.00
#> TCGA.EA.A5O9.01 3 0.340 0.6575 0.00 0 0.82 0.18
#> TCGA.EA.A5ZE.01 2 0.000 1.0000 0.00 1 0.00 0.00
#> TCGA.JW.A5VI.01 1 0.361 -0.1259 0.80 0 0.20 0.00
#> TCGA.FU.A3YQ.01 1 0.498 0.4681 0.54 0 0.00 0.46
#> TCGA.C5.A7CH.01 3 0.704 0.0290 0.42 0 0.46 0.12
#> TCGA.BI.A20A.01 1 0.704 -0.5829 0.46 0 0.12 0.42
#> TCGA.ZX.AA5X.01 1 0.479 0.5241 0.62 0 0.00 0.38
#> TCGA.C5.A7CJ.01 1 0.479 0.5241 0.62 0 0.00 0.38
#> TCGA.Q1.A6DT.01 1 0.599 -0.6406 0.52 0 0.04 0.44
#> TCGA.MU.A5YI.01 2 0.000 1.0000 0.00 1 0.00 0.00
#> TCGA.ZJ.AAX4.01 3 0.000 0.6816 0.00 0 1.00 0.00
#> TCGA.DS.A1O9.01 1 0.479 0.5241 0.62 0 0.00 0.38
#> TCGA.VS.A9UC.01 4 0.704 0.3283 0.42 0 0.12 0.46
#> TCGA.VS.A9V2.01 1 0.499 0.4470 0.52 0 0.00 0.48
#> TCGA.EX.A1H5.01 2 0.000 1.0000 0.00 1 0.00 0.00
#> TCGA.C5.A1MH.01 1 0.491 0.4980 0.58 0 0.00 0.42
#> TCGA.C5.A1MF.01 2 0.000 1.0000 0.00 1 0.00 0.00
#> TCGA.C5.A1BK.01 1 0.479 0.5241 0.62 0 0.00 0.38
cbind(get_classes(res, k = 5), get_membership(res, k = 5))
#> class entropy silhouette p1 p2 p3 p4 p5
#> TCGA.MA.AA42.01 4 0.2797 0.866 0.06 0.00 0.00 0.88 0.06
#> TCGA.C5.A8YQ.01 3 0.1648 0.922 0.00 0.00 0.94 0.02 0.04
#> TCGA.MA.AA3W.01 1 0.0000 0.960 1.00 0.00 0.00 0.00 0.00
#> TCGA.EK.A2R9.01 2 0.2020 0.935 0.00 0.90 0.00 0.10 0.00
#> TCGA.EK.A2RO.01 2 0.0000 0.971 0.00 1.00 0.00 0.00 0.00
#> TCGA.EA.A3HS.01 5 0.2732 0.800 0.00 0.00 0.16 0.00 0.84
#> TCGA.C5.A7CO.01 3 0.2020 0.919 0.00 0.00 0.90 0.00 0.10
#> TCGA.VS.A94W.01 1 0.0000 0.960 1.00 0.00 0.00 0.00 0.00
#> TCGA.MA.AA41.01 5 0.0000 0.874 0.00 0.00 0.00 0.00 1.00
#> TCGA.ZJ.A8QO.01 4 0.3922 0.899 0.04 0.00 0.00 0.78 0.18
#> TCGA.EA.A3QE.01 1 0.2020 0.917 0.90 0.00 0.00 0.10 0.00
#> TCGA.DS.A0VM.01 5 0.0609 0.877 0.02 0.00 0.00 0.00 0.98
#> TCGA.MU.A8JM.01 5 0.2020 0.877 0.10 0.00 0.00 0.00 0.90
#> TCGA.EK.A2IR.01 3 0.1216 0.941 0.00 0.00 0.96 0.02 0.02
#> TCGA.C5.A7UE.01 5 0.2020 0.877 0.10 0.00 0.00 0.00 0.90
#> TCGA.XS.A8TJ.01 1 0.0000 0.960 1.00 0.00 0.00 0.00 0.00
#> TCGA.DS.A0VN.01 4 0.2280 0.798 0.12 0.00 0.00 0.88 0.00
#> TCGA.DR.A0ZL.01 1 0.0000 0.960 1.00 0.00 0.00 0.00 0.00
#> TCGA.FU.A3WB.01 2 0.2020 0.935 0.00 0.90 0.00 0.10 0.00
#> TCGA.EA.A5O9.01 3 0.0609 0.942 0.00 0.00 0.98 0.00 0.02
#> TCGA.EA.A5ZE.01 2 0.0000 0.971 0.00 1.00 0.00 0.00 0.00
#> TCGA.JW.A5VI.01 5 0.2020 0.877 0.10 0.00 0.00 0.00 0.90
#> TCGA.FU.A3YQ.01 1 0.2020 0.917 0.90 0.00 0.00 0.10 0.00
#> TCGA.C5.A7CH.01 5 0.0000 0.874 0.00 0.00 0.00 0.00 1.00
#> TCGA.BI.A20A.01 4 0.4094 0.890 0.02 0.00 0.02 0.78 0.18
#> TCGA.ZX.AA5X.01 1 0.0000 0.960 1.00 0.00 0.00 0.00 0.00
#> TCGA.C5.A7CJ.01 1 0.0000 0.960 1.00 0.00 0.00 0.00 0.00
#> TCGA.Q1.A6DT.01 4 0.4449 0.900 0.06 0.00 0.02 0.78 0.14
#> TCGA.MU.A5YI.01 2 0.0000 0.971 0.00 1.00 0.00 0.00 0.00
#> TCGA.ZJ.AAX4.01 5 0.3561 0.684 0.00 0.00 0.26 0.00 0.74
#> TCGA.DS.A1O9.01 1 0.0000 0.960 1.00 0.00 0.00 0.00 0.00
#> TCGA.VS.A9UC.01 4 0.4312 0.887 0.02 0.00 0.04 0.78 0.16
#> TCGA.VS.A9V2.01 1 0.2020 0.917 0.90 0.00 0.00 0.10 0.00
#> TCGA.EX.A1H5.01 2 0.0000 0.971 0.00 1.00 0.00 0.00 0.00
#> TCGA.C5.A1MH.01 1 0.2020 0.917 0.90 0.00 0.00 0.10 0.00
#> TCGA.C5.A1MF.01 2 0.0609 0.967 0.00 0.98 0.00 0.02 0.00
#> TCGA.C5.A1BK.01 1 0.0000 0.960 1.00 0.00 0.00 0.00 0.00
cbind(get_classes(res, k = 6), get_membership(res, k = 6))
#> class entropy silhouette p1 p2 p3 p4 p5 p6
#> TCGA.MA.AA42.01 4 0.3198 0.643 0.00 0.00 0.26 0.74 0.00 0.00
#> TCGA.C5.A8YQ.01 6 0.4393 0.598 0.00 0.00 0.14 0.14 0.00 0.72
#> TCGA.MA.AA3W.01 1 0.0000 0.928 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.EK.A2R9.01 2 0.1267 0.955 0.00 0.94 0.06 0.00 0.00 0.00
#> TCGA.EK.A2RO.01 2 0.0000 0.982 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.EA.A3HS.01 5 0.4711 0.623 0.00 0.00 0.28 0.00 0.64 0.08
#> TCGA.C5.A7CO.01 6 0.5736 0.292 0.00 0.00 0.34 0.00 0.18 0.48
#> TCGA.VS.A94W.01 1 0.0547 0.924 0.98 0.00 0.02 0.00 0.00 0.00
#> TCGA.MA.AA41.01 5 0.2790 0.765 0.00 0.00 0.14 0.00 0.84 0.02
#> TCGA.ZJ.A8QO.01 4 0.6397 0.523 0.02 0.00 0.28 0.44 0.26 0.00
#> TCGA.EA.A3QE.01 1 0.3787 0.797 0.78 0.00 0.10 0.12 0.00 0.00
#> TCGA.DS.A0VM.01 5 0.0547 0.802 0.00 0.00 0.02 0.00 0.98 0.00
#> TCGA.MU.A8JM.01 5 0.1267 0.814 0.06 0.00 0.00 0.00 0.94 0.00
#> TCGA.EK.A2IR.01 6 0.2048 0.689 0.00 0.00 0.12 0.00 0.00 0.88
#> TCGA.C5.A7UE.01 5 0.1267 0.814 0.06 0.00 0.00 0.00 0.94 0.00
#> TCGA.XS.A8TJ.01 1 0.0000 0.928 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.DS.A0VN.01 4 0.1814 0.644 0.00 0.00 0.10 0.90 0.00 0.00
#> TCGA.DR.A0ZL.01 1 0.0000 0.928 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.FU.A3WB.01 2 0.1267 0.955 0.00 0.94 0.06 0.00 0.00 0.00
#> TCGA.EA.A5O9.01 6 0.0000 0.707 0.00 0.00 0.00 0.00 0.00 1.00
#> TCGA.EA.A5ZE.01 2 0.0000 0.982 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.JW.A5VI.01 5 0.1267 0.814 0.06 0.00 0.00 0.00 0.94 0.00
#> TCGA.FU.A3YQ.01 1 0.3787 0.797 0.78 0.00 0.10 0.12 0.00 0.00
#> TCGA.C5.A7CH.01 5 0.0937 0.808 0.00 0.00 0.04 0.00 0.96 0.00
#> TCGA.BI.A20A.01 4 0.6397 0.523 0.02 0.00 0.28 0.44 0.26 0.00
#> TCGA.ZX.AA5X.01 1 0.0000 0.928 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.C5.A7CJ.01 1 0.0547 0.924 0.98 0.00 0.02 0.00 0.00 0.00
#> TCGA.Q1.A6DT.01 4 0.0547 0.655 0.00 0.00 0.00 0.98 0.02 0.00
#> TCGA.MU.A5YI.01 2 0.0000 0.982 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.ZJ.AAX4.01 5 0.5867 0.401 0.00 0.00 0.28 0.00 0.48 0.24
#> TCGA.DS.A1O9.01 1 0.0547 0.924 0.98 0.00 0.02 0.00 0.00 0.00
#> TCGA.VS.A9UC.01 4 0.2350 0.639 0.00 0.00 0.10 0.88 0.02 0.00
#> TCGA.VS.A9V2.01 1 0.4004 0.791 0.76 0.00 0.12 0.12 0.00 0.00
#> TCGA.EX.A1H5.01 2 0.0000 0.982 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.C5.A1MH.01 1 0.1092 0.912 0.96 0.00 0.02 0.02 0.00 0.00
#> TCGA.C5.A1MF.01 2 0.0000 0.982 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.C5.A1BK.01 1 0.0000 0.928 1.00 0.00 0.00 0.00 0.00 0.00
cbind(get_classes(res, k = 7), get_membership(res, k = 7))
#> class entropy silhouette p1 p2 p3 p4 p5 p6 p7
#> TCGA.MA.AA42.01 7 0.3047 -0.1565 0.00 0.00 0.00 0.28 0.00 0.00 0.72
#> TCGA.C5.A8YQ.01 6 0.3685 0.4431 0.00 0.00 0.02 0.32 0.00 0.66 0.00
#> TCGA.MA.AA3W.01 1 0.0000 0.8732 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.EK.A2R9.01 2 0.1860 0.9427 0.00 0.92 0.02 0.00 0.02 0.00 0.04
#> TCGA.EK.A2RO.01 2 0.0000 0.9706 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.EA.A3HS.01 3 0.3139 0.8872 0.00 0.00 0.70 0.00 0.30 0.00 0.00
#> TCGA.C5.A7CO.01 7 0.7594 -0.0153 0.00 0.00 0.30 0.12 0.16 0.08 0.34
#> TCGA.VS.A94W.01 1 0.0000 0.8732 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.MA.AA41.01 5 0.2572 0.6557 0.00 0.00 0.20 0.00 0.80 0.00 0.00
#> TCGA.ZJ.A8QO.01 4 0.6613 -0.2190 0.00 0.00 0.10 0.36 0.20 0.00 0.34
#> TCGA.EA.A3QE.01 1 0.3496 0.5187 0.58 0.00 0.00 0.00 0.00 0.00 0.42
#> TCGA.DS.A0VM.01 5 0.0504 0.8769 0.00 0.00 0.00 0.02 0.98 0.00 0.00
#> TCGA.MU.A8JM.01 5 0.1006 0.8930 0.02 0.00 0.02 0.00 0.96 0.00 0.00
#> TCGA.EK.A2IR.01 6 0.4640 0.4993 0.00 0.00 0.18 0.00 0.00 0.64 0.18
#> TCGA.C5.A7UE.01 5 0.1006 0.8930 0.02 0.00 0.02 0.00 0.96 0.00 0.00
#> TCGA.XS.A8TJ.01 1 0.0000 0.8732 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.DS.A0VN.01 4 0.3496 0.0304 0.00 0.00 0.00 0.58 0.00 0.00 0.42
#> TCGA.DR.A0ZL.01 1 0.0000 0.8732 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.FU.A3WB.01 2 0.1860 0.9427 0.00 0.92 0.02 0.00 0.02 0.00 0.04
#> TCGA.EA.A5O9.01 6 0.3047 0.4950 0.00 0.00 0.28 0.00 0.00 0.72 0.00
#> TCGA.EA.A5ZE.01 2 0.0504 0.9621 0.00 0.98 0.00 0.00 0.00 0.00 0.02
#> TCGA.JW.A5VI.01 5 0.0504 0.8885 0.02 0.00 0.00 0.00 0.98 0.00 0.00
#> TCGA.FU.A3YQ.01 1 0.3496 0.5187 0.58 0.00 0.00 0.00 0.00 0.00 0.42
#> TCGA.C5.A7CH.01 5 0.1928 0.8322 0.00 0.00 0.08 0.02 0.90 0.00 0.00
#> TCGA.BI.A20A.01 4 0.6613 -0.2190 0.00 0.00 0.10 0.36 0.20 0.00 0.34
#> TCGA.ZX.AA5X.01 1 0.0000 0.8732 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.C5.A7CJ.01 1 0.0000 0.8732 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.Q1.A6DT.01 4 0.1671 0.2858 0.00 0.00 0.00 0.90 0.00 0.00 0.10
#> TCGA.MU.A5YI.01 2 0.0000 0.9706 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.ZJ.AAX4.01 3 0.2832 0.8913 0.00 0.00 0.76 0.00 0.24 0.00 0.00
#> TCGA.DS.A1O9.01 1 0.0000 0.8732 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.VS.A9UC.01 4 0.0000 0.2835 0.00 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.VS.A9V2.01 1 0.3496 0.5187 0.58 0.00 0.00 0.00 0.00 0.00 0.42
#> TCGA.EX.A1H5.01 2 0.0000 0.9706 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.C5.A1MH.01 1 0.0504 0.8617 0.98 0.00 0.00 0.00 0.00 0.00 0.02
#> TCGA.C5.A1MF.01 2 0.0504 0.9676 0.00 0.98 0.00 0.00 0.00 0.00 0.02
#> TCGA.C5.A1BK.01 1 0.0000 0.8732 1.00 0.00 0.00 0.00 0.00 0.00 0.00
cbind(get_classes(res, k = 8), get_membership(res, k = 8))
#> class entropy silhouette p1 p2 p3 p4 p5 p6 p7 p8
#> TCGA.MA.AA42.01 3 0.4141 0.0443 0.00 0.00 0.56 0.06 0.00 0.00 0.38 0.00
#> TCGA.C5.A8YQ.01 6 0.4040 0.0344 0.00 0.00 0.02 0.38 0.00 0.58 0.02 0.00
#> TCGA.MA.AA3W.01 1 0.0000 0.9964 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.EK.A2R9.01 2 0.3048 0.8784 0.00 0.84 0.04 0.02 0.00 0.00 0.02 0.08
#> TCGA.EK.A2RO.01 2 0.0000 0.9355 0.00 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.EA.A3HS.01 3 0.7027 -0.5532 0.00 0.00 0.32 0.12 0.18 0.32 0.06 0.00
#> TCGA.C5.A7CO.01 7 0.3589 0.7769 0.00 0.00 0.00 0.00 0.10 0.16 0.74 0.00
#> TCGA.VS.A94W.01 1 0.0000 0.9964 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.MA.AA41.01 5 0.3402 0.7958 0.00 0.00 0.06 0.02 0.82 0.04 0.06 0.00
#> TCGA.ZJ.A8QO.01 7 0.1947 0.8891 0.00 0.00 0.00 0.00 0.14 0.00 0.86 0.00
#> TCGA.EA.A3QE.01 3 0.3237 0.4667 0.40 0.00 0.60 0.00 0.00 0.00 0.00 0.00
#> TCGA.DS.A0VM.01 5 0.0941 0.9054 0.00 0.00 0.00 0.00 0.96 0.00 0.02 0.02
#> TCGA.MU.A8JM.01 5 0.1874 0.9098 0.02 0.00 0.02 0.02 0.92 0.02 0.00 0.00
#> TCGA.EK.A2IR.01 8 0.1563 0.0000 0.00 0.00 0.00 0.00 0.00 0.10 0.00 0.90
#> TCGA.C5.A7UE.01 5 0.1874 0.9092 0.00 0.00 0.02 0.02 0.92 0.02 0.02 0.00
#> TCGA.XS.A8TJ.01 1 0.0000 0.9964 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.DS.A0VN.01 3 0.4199 -0.0697 0.00 0.00 0.60 0.32 0.00 0.00 0.08 0.00
#> TCGA.DR.A0ZL.01 1 0.0000 0.9964 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.FU.A3WB.01 2 0.3048 0.8784 0.00 0.84 0.04 0.02 0.00 0.00 0.02 0.08
#> TCGA.EA.A5O9.01 6 0.1091 0.1656 0.00 0.00 0.00 0.00 0.00 0.94 0.00 0.06
#> TCGA.EA.A5ZE.01 2 0.0941 0.9186 0.00 0.96 0.02 0.00 0.00 0.00 0.02 0.00
#> TCGA.JW.A5VI.01 5 0.0471 0.9109 0.02 0.00 0.00 0.00 0.98 0.00 0.00 0.00
#> TCGA.FU.A3YQ.01 3 0.3237 0.4667 0.40 0.00 0.60 0.00 0.00 0.00 0.00 0.00
#> TCGA.C5.A7CH.01 5 0.0941 0.9058 0.00 0.00 0.02 0.00 0.96 0.00 0.00 0.02
#> TCGA.BI.A20A.01 7 0.1947 0.8891 0.00 0.00 0.00 0.00 0.14 0.00 0.86 0.00
#> TCGA.ZX.AA5X.01 1 0.0000 0.9964 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.C5.A7CJ.01 1 0.0000 0.9964 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.Q1.A6DT.01 4 0.3263 0.8255 0.00 0.00 0.10 0.78 0.00 0.00 0.12 0.00
#> TCGA.MU.A5YI.01 2 0.0000 0.9355 0.00 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.ZJ.AAX4.01 6 0.7323 0.0808 0.00 0.00 0.30 0.12 0.16 0.34 0.06 0.02
#> TCGA.DS.A1O9.01 1 0.0000 0.9964 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.VS.A9UC.01 4 0.2534 0.8225 0.00 0.00 0.00 0.78 0.00 0.00 0.22 0.00
#> TCGA.VS.A9V2.01 3 0.3237 0.4667 0.40 0.00 0.60 0.00 0.00 0.00 0.00 0.00
#> TCGA.EX.A1H5.01 2 0.0471 0.9344 0.00 0.98 0.00 0.00 0.00 0.00 0.02 0.00
#> TCGA.C5.A1MH.01 1 0.0471 0.9707 0.98 0.00 0.02 0.00 0.00 0.00 0.00 0.00
#> TCGA.C5.A1MF.01 2 0.0941 0.9314 0.00 0.96 0.00 0.00 0.00 0.00 0.02 0.02
#> TCGA.C5.A1BK.01 1 0.0000 0.9964 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
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)
consensus_heatmap(res, k = 7)
consensus_heatmap(res, k = 8)
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)
membership_heatmap(res, k = 7)
membership_heatmap(res, k = 8)
As soon as the classes for columns are determined, the signatures that are significantly different between subgroups can be looked for. Following are the heatmaps for signatures.
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)
get_signatures(res, k = 7)
get_signatures(res, k = 8)
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 (which is done by automatically selecting number of clusters).If there are too many signatures, top_signatures = ... can be set to only show the
signatures with the highest FDRs:
# code only for demonstration
# e.g. to show the top 500 most significant rows
tb = get_signature(res, k = ..., top_signatures = 500)
If the signatures are defined as these which are uniquely high in current group, diff_method argument
can be set to "uniquely_high_in_one_group":
# code only for demonstration
tb = get_signature(res, k = ..., diff_method = "uniquely_high_in_one_group")
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")
dimension_reduction(res, k = 7, method = "UMAP")
dimension_reduction(res, k = 8, method = "UMAP")
Following heatmap shows how subgroups are split when increasing k:
collect_classes(res)
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.
Parent node: Node0211. Child nodes: Node021111-leaf , Node021112-leaf , Node021113-leaf , Node021114-leaf , Node022211-leaf , Node022212-leaf , Node022213-leaf , Node031121-leaf , Node031122-leaf .
The object with results only for a single top-value method and a single partitioning method can be extracted as:
res = res_rh["02111"]
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, 7, 8.
#> On a matrix with 30000 rows and 26 columns.
#> Top rows (1000) are extracted by 'ATC' method.
#> Subgroups are detected by 'kmeans' method.
#> Performed in total 350 partitions by row resampling.
#> Best k for subgroups seems to be 4.
#>
#> Following methods can be applied to this 'ConsensusPartition' object:
#> [1] "cola_report" "collect_classes" "collect_plots"
#> [4] "collect_stats" "colnames" "compare_partitions"
#> [7] "compare_signatures" "consensus_heatmap" "dimension_reduction"
#> [10] "functional_enrichment" "get_anno_col" "get_anno"
#> [13] "get_classes" "get_consensus" "get_matrix"
#> [16] "get_membership" "get_param" "get_signatures"
#> [19] "get_stats" "is_best_k" "is_stable_k"
#> [22] "membership_heatmap" "ncol" "nrow"
#> [25] "plot_ecdf" "predict_classes" "rownames"
#> [28] "select_partition_number" "show" "suggest_best_k"
#> [31] "test_to_known_factors" "top_rows_heatmap"
collect_plots() function collects all the plots made from res for all k (number of subgroups)
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, higher 1-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 0.995 0.996 0.4053 0.591 0.591
#> 3 3 0.720 0.861 0.923 0.4407 0.785 0.643
#> 4 4 1.000 0.951 0.968 0.1479 0.895 0.752
#> 5 5 0.779 0.804 0.860 0.1258 0.862 0.612
#> 6 6 0.787 0.702 0.829 0.0393 0.954 0.830
#> 7 7 0.866 0.818 0.878 0.0486 0.895 0.595
#> 8 8 0.833 0.816 0.903 0.0259 0.991 0.940
suggest_best_k() suggests the best \(k\) based on these statistics. The rules are as follows:
suggest_best_k(res)
#> [1] 4
#> attr(,"optional")
#> [1] 2
There is also optional best \(k\) = 2 that is worth to check.
Following is 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 subgroup
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
#> TCGA.MA.AA42.01 1 0.000 1.000 1.00 0.00
#> TCGA.C5.A8YQ.01 2 0.000 0.984 0.00 1.00
#> TCGA.MA.AA3W.01 1 0.000 1.000 1.00 0.00
#> TCGA.C5.A7CO.01 2 0.242 0.970 0.04 0.96
#> TCGA.VS.A94W.01 1 0.000 1.000 1.00 0.00
#> TCGA.MA.AA41.01 2 0.141 0.986 0.02 0.98
#> TCGA.ZJ.A8QO.01 1 0.000 1.000 1.00 0.00
#> TCGA.EA.A3QE.01 1 0.000 1.000 1.00 0.00
#> TCGA.DS.A0VM.01 1 0.000 1.000 1.00 0.00
#> TCGA.MU.A8JM.01 1 0.000 1.000 1.00 0.00
#> TCGA.C5.A7UE.01 1 0.000 1.000 1.00 0.00
#> TCGA.XS.A8TJ.01 1 0.000 1.000 1.00 0.00
#> TCGA.DS.A0VN.01 2 0.141 0.986 0.02 0.98
#> TCGA.DR.A0ZL.01 1 0.000 1.000 1.00 0.00
#> TCGA.JW.A5VI.01 1 0.000 1.000 1.00 0.00
#> TCGA.FU.A3YQ.01 1 0.000 1.000 1.00 0.00
#> TCGA.C5.A7CH.01 2 0.141 0.986 0.02 0.98
#> TCGA.BI.A20A.01 1 0.000 1.000 1.00 0.00
#> TCGA.ZX.AA5X.01 1 0.000 1.000 1.00 0.00
#> TCGA.C5.A7CJ.01 1 0.000 1.000 1.00 0.00
#> TCGA.Q1.A6DT.01 2 0.000 0.984 0.00 1.00
#> TCGA.DS.A1O9.01 1 0.000 1.000 1.00 0.00
#> TCGA.VS.A9UC.01 2 0.000 0.984 0.00 1.00
#> TCGA.VS.A9V2.01 1 0.000 1.000 1.00 0.00
#> TCGA.C5.A1MH.01 1 0.000 1.000 1.00 0.00
#> TCGA.C5.A1BK.01 1 0.000 1.000 1.00 0.00
cbind(get_classes(res, k = 3), get_membership(res, k = 3))
#> class entropy silhouette p1 p2 p3
#> TCGA.MA.AA42.01 3 0.369 0.860 0.14 0.00 0.86
#> TCGA.C5.A8YQ.01 2 0.000 0.677 0.00 1.00 0.00
#> TCGA.MA.AA3W.01 1 0.000 0.988 1.00 0.00 0.00
#> TCGA.C5.A7CO.01 3 0.000 0.772 0.00 0.00 1.00
#> TCGA.VS.A94W.01 1 0.000 0.988 1.00 0.00 0.00
#> TCGA.MA.AA41.01 2 0.630 0.528 0.00 0.52 0.48
#> TCGA.ZJ.A8QO.01 3 0.369 0.860 0.14 0.00 0.86
#> TCGA.EA.A3QE.01 1 0.000 0.988 1.00 0.00 0.00
#> TCGA.DS.A0VM.01 3 0.000 0.772 0.00 0.00 1.00
#> TCGA.MU.A8JM.01 1 0.000 0.988 1.00 0.00 0.00
#> TCGA.C5.A7UE.01 1 0.000 0.988 1.00 0.00 0.00
#> TCGA.XS.A8TJ.01 1 0.000 0.988 1.00 0.00 0.00
#> TCGA.DS.A0VN.01 2 0.630 0.528 0.00 0.52 0.48
#> TCGA.DR.A0ZL.01 1 0.000 0.988 1.00 0.00 0.00
#> TCGA.JW.A5VI.01 1 0.369 0.817 0.86 0.00 0.14
#> TCGA.FU.A3YQ.01 1 0.000 0.988 1.00 0.00 0.00
#> TCGA.C5.A7CH.01 2 0.630 0.528 0.00 0.52 0.48
#> TCGA.BI.A20A.01 3 0.369 0.860 0.14 0.00 0.86
#> TCGA.ZX.AA5X.01 1 0.000 0.988 1.00 0.00 0.00
#> TCGA.C5.A7CJ.01 1 0.000 0.988 1.00 0.00 0.00
#> TCGA.Q1.A6DT.01 2 0.000 0.677 0.00 1.00 0.00
#> TCGA.DS.A1O9.01 1 0.000 0.988 1.00 0.00 0.00
#> TCGA.VS.A9UC.01 2 0.000 0.677 0.00 1.00 0.00
#> TCGA.VS.A9V2.01 1 0.000 0.988 1.00 0.00 0.00
#> TCGA.C5.A1MH.01 1 0.000 0.988 1.00 0.00 0.00
#> TCGA.C5.A1BK.01 1 0.000 0.988 1.00 0.00 0.00
cbind(get_classes(res, k = 4), get_membership(res, k = 4))
#> class entropy silhouette p1 p2 p3 p4
#> TCGA.MA.AA42.01 3 0.000 1.000 0.00 0.00 1.00 0.00
#> TCGA.C5.A8YQ.01 2 0.164 1.000 0.00 0.94 0.00 0.06
#> TCGA.MA.AA3W.01 1 0.164 0.937 0.94 0.06 0.00 0.00
#> TCGA.C5.A7CO.01 3 0.000 1.000 0.00 0.00 1.00 0.00
#> TCGA.VS.A94W.01 1 0.000 0.962 1.00 0.00 0.00 0.00
#> TCGA.MA.AA41.01 4 0.000 0.943 0.00 0.00 0.00 1.00
#> TCGA.ZJ.A8QO.01 3 0.000 1.000 0.00 0.00 1.00 0.00
#> TCGA.EA.A3QE.01 1 0.000 0.962 1.00 0.00 0.00 0.00
#> TCGA.DS.A0VM.01 4 0.234 0.914 0.06 0.00 0.02 0.92
#> TCGA.MU.A8JM.01 1 0.000 0.962 1.00 0.00 0.00 0.00
#> TCGA.C5.A7UE.01 1 0.000 0.962 1.00 0.00 0.00 0.00
#> TCGA.XS.A8TJ.01 1 0.000 0.962 1.00 0.00 0.00 0.00
#> TCGA.DS.A0VN.01 4 0.000 0.943 0.00 0.00 0.00 1.00
#> TCGA.DR.A0ZL.01 1 0.164 0.937 0.94 0.06 0.00 0.00
#> TCGA.JW.A5VI.01 4 0.201 0.902 0.08 0.00 0.00 0.92
#> TCGA.FU.A3YQ.01 1 0.000 0.962 1.00 0.00 0.00 0.00
#> TCGA.C5.A7CH.01 4 0.000 0.943 0.00 0.00 0.00 1.00
#> TCGA.BI.A20A.01 3 0.000 1.000 0.00 0.00 1.00 0.00
#> TCGA.ZX.AA5X.01 1 0.164 0.937 0.94 0.06 0.00 0.00
#> TCGA.C5.A7CJ.01 1 0.000 0.962 1.00 0.00 0.00 0.00
#> TCGA.Q1.A6DT.01 2 0.164 1.000 0.00 0.94 0.00 0.06
#> TCGA.DS.A1O9.01 1 0.398 0.664 0.76 0.00 0.00 0.24
#> TCGA.VS.A9UC.01 2 0.164 1.000 0.00 0.94 0.00 0.06
#> TCGA.VS.A9V2.01 1 0.000 0.962 1.00 0.00 0.00 0.00
#> TCGA.C5.A1MH.01 1 0.000 0.962 1.00 0.00 0.00 0.00
#> TCGA.C5.A1BK.01 1 0.164 0.937 0.94 0.06 0.00 0.00
cbind(get_classes(res, k = 5), get_membership(res, k = 5))
#> class entropy silhouette p1 p2 p3 p4 p5
#> TCGA.MA.AA42.01 3 0.0000 0.995 0.00 0.00 1.00 0.00 0.00
#> TCGA.C5.A8YQ.01 2 0.0000 0.979 0.00 1.00 0.00 0.00 0.00
#> TCGA.MA.AA3W.01 1 0.4060 0.651 0.64 0.00 0.00 0.00 0.36
#> TCGA.C5.A7CO.01 3 0.0609 0.985 0.00 0.00 0.98 0.00 0.02
#> TCGA.VS.A94W.01 1 0.0000 0.777 1.00 0.00 0.00 0.00 0.00
#> TCGA.MA.AA41.01 4 0.1043 0.963 0.00 0.00 0.00 0.96 0.04
#> TCGA.ZJ.A8QO.01 3 0.0000 0.995 0.00 0.00 1.00 0.00 0.00
#> TCGA.EA.A3QE.01 1 0.0000 0.777 1.00 0.00 0.00 0.00 0.00
#> TCGA.DS.A0VM.01 5 0.5979 0.429 0.12 0.00 0.00 0.36 0.52
#> TCGA.MU.A8JM.01 5 0.4302 0.699 0.48 0.00 0.00 0.00 0.52
#> TCGA.C5.A7UE.01 5 0.4302 0.699 0.48 0.00 0.00 0.00 0.52
#> TCGA.XS.A8TJ.01 1 0.0000 0.777 1.00 0.00 0.00 0.00 0.00
#> TCGA.DS.A0VN.01 4 0.0000 0.981 0.00 0.00 0.00 1.00 0.00
#> TCGA.DR.A0ZL.01 1 0.4060 0.651 0.64 0.00 0.00 0.00 0.36
#> TCGA.JW.A5VI.01 5 0.6200 0.511 0.16 0.00 0.00 0.32 0.52
#> TCGA.FU.A3YQ.01 1 0.0000 0.777 1.00 0.00 0.00 0.00 0.00
#> TCGA.C5.A7CH.01 4 0.0000 0.981 0.00 0.00 0.00 1.00 0.00
#> TCGA.BI.A20A.01 3 0.0000 0.995 0.00 0.00 1.00 0.00 0.00
#> TCGA.ZX.AA5X.01 1 0.4060 0.651 0.64 0.00 0.00 0.00 0.36
#> TCGA.C5.A7CJ.01 1 0.0000 0.777 1.00 0.00 0.00 0.00 0.00
#> TCGA.Q1.A6DT.01 2 0.0000 0.979 0.00 1.00 0.00 0.00 0.00
#> TCGA.DS.A1O9.01 5 0.4818 0.713 0.46 0.00 0.00 0.02 0.52
#> TCGA.VS.A9UC.01 2 0.1410 0.957 0.00 0.94 0.00 0.00 0.06
#> TCGA.VS.A9V2.01 1 0.0000 0.777 1.00 0.00 0.00 0.00 0.00
#> TCGA.C5.A1MH.01 1 0.0000 0.777 1.00 0.00 0.00 0.00 0.00
#> TCGA.C5.A1BK.01 1 0.4060 0.651 0.64 0.00 0.00 0.00 0.36
cbind(get_classes(res, k = 6), get_membership(res, k = 6))
#> class entropy silhouette p1 p2 p3 p4 p5 p6
#> TCGA.MA.AA42.01 6 0.0000 0.956 0.00 0.00 0.00 0.00 0.00 1.00
#> TCGA.C5.A8YQ.01 2 0.0547 0.916 0.00 0.98 0.00 0.00 0.02 0.00
#> TCGA.MA.AA3W.01 1 0.3851 0.555 0.54 0.00 0.00 0.00 0.46 0.00
#> TCGA.C5.A7CO.01 6 0.2956 0.861 0.00 0.00 0.12 0.00 0.04 0.84
#> TCGA.VS.A94W.01 1 0.0000 0.717 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.MA.AA41.01 4 0.3756 0.658 0.00 0.00 0.40 0.60 0.00 0.00
#> TCGA.ZJ.A8QO.01 6 0.0000 0.956 0.00 0.00 0.00 0.00 0.00 1.00
#> TCGA.EA.A3QE.01 1 0.0000 0.717 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.DS.A0VM.01 5 0.6561 0.646 0.04 0.00 0.28 0.22 0.46 0.00
#> TCGA.MU.A8JM.01 5 0.6023 0.716 0.32 0.00 0.26 0.00 0.42 0.00
#> TCGA.C5.A7UE.01 1 0.5447 -0.584 0.46 0.00 0.12 0.00 0.42 0.00
#> TCGA.XS.A8TJ.01 1 0.0000 0.717 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.DS.A0VN.01 4 0.0547 0.829 0.00 0.02 0.00 0.98 0.00 0.00
#> TCGA.DR.A0ZL.01 1 0.3851 0.555 0.54 0.00 0.00 0.00 0.46 0.00
#> TCGA.JW.A5VI.01 5 0.6939 0.750 0.12 0.00 0.28 0.14 0.46 0.00
#> TCGA.FU.A3YQ.01 1 0.0000 0.717 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.C5.A7CH.01 4 0.0000 0.829 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.BI.A20A.01 6 0.0000 0.956 0.00 0.00 0.00 0.00 0.00 1.00
#> TCGA.ZX.AA5X.01 1 0.3851 0.555 0.54 0.00 0.00 0.00 0.46 0.00
#> TCGA.C5.A7CJ.01 1 0.0000 0.717 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.Q1.A6DT.01 2 0.0000 0.919 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.DS.A1O9.01 5 0.6561 0.773 0.28 0.00 0.22 0.04 0.46 0.00
#> TCGA.VS.A9UC.01 2 0.2981 0.848 0.00 0.82 0.16 0.00 0.02 0.00
#> TCGA.VS.A9V2.01 1 0.0547 0.700 0.98 0.00 0.00 0.00 0.02 0.00
#> TCGA.C5.A1MH.01 1 0.0000 0.717 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.C5.A1BK.01 1 0.3851 0.555 0.54 0.00 0.00 0.00 0.46 0.00
cbind(get_classes(res, k = 7), get_membership(res, k = 7))
#> class entropy silhouette p1 p2 p3 p4 p5 p6 p7
#> TCGA.MA.AA42.01 6 0.0000 0.920 0.00 0.00 0.00 0.00 0.00 1.00 0.00
#> TCGA.C5.A8YQ.01 2 0.0504 0.917 0.02 0.98 0.00 0.00 0.00 0.00 0.00
#> TCGA.MA.AA3W.01 7 0.0000 1.000 0.00 0.00 0.00 0.00 0.00 0.00 1.00
#> TCGA.C5.A7CO.01 6 0.4092 0.735 0.08 0.00 0.02 0.16 0.00 0.74 0.00
#> TCGA.VS.A94W.01 1 0.3358 0.874 0.64 0.00 0.00 0.00 0.00 0.00 0.36
#> TCGA.MA.AA41.01 3 0.0504 0.000 0.00 0.00 0.98 0.00 0.02 0.00 0.00
#> TCGA.ZJ.A8QO.01 6 0.0000 0.920 0.00 0.00 0.00 0.00 0.00 1.00 0.00
#> TCGA.EA.A3QE.01 1 0.3358 0.874 0.64 0.00 0.00 0.00 0.00 0.00 0.36
#> TCGA.DS.A0VM.01 5 0.3086 0.709 0.16 0.00 0.00 0.04 0.80 0.00 0.00
#> TCGA.MU.A8JM.01 5 0.2512 0.823 0.10 0.00 0.00 0.04 0.86 0.00 0.00
#> TCGA.C5.A7UE.01 1 0.4283 -0.238 0.48 0.00 0.00 0.04 0.48 0.00 0.00
#> TCGA.XS.A8TJ.01 1 0.3358 0.874 0.64 0.00 0.00 0.00 0.00 0.00 0.36
#> TCGA.DS.A0VN.01 4 0.3221 1.000 0.00 0.00 0.32 0.68 0.00 0.00 0.00
#> TCGA.DR.A0ZL.01 7 0.0000 1.000 0.00 0.00 0.00 0.00 0.00 0.00 1.00
#> TCGA.JW.A5VI.01 5 0.0000 0.833 0.00 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.FU.A3YQ.01 1 0.3358 0.874 0.64 0.00 0.00 0.00 0.00 0.00 0.36
#> TCGA.C5.A7CH.01 4 0.3221 1.000 0.00 0.00 0.32 0.68 0.00 0.00 0.00
#> TCGA.BI.A20A.01 6 0.0000 0.920 0.00 0.00 0.00 0.00 0.00 1.00 0.00
#> TCGA.ZX.AA5X.01 7 0.0000 1.000 0.00 0.00 0.00 0.00 0.00 0.00 1.00
#> TCGA.C5.A7CJ.01 1 0.3358 0.874 0.64 0.00 0.00 0.00 0.00 0.00 0.36
#> TCGA.Q1.A6DT.01 2 0.0000 0.921 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.DS.A1O9.01 5 0.1433 0.845 0.08 0.00 0.00 0.00 0.92 0.00 0.00
#> TCGA.VS.A9UC.01 2 0.2829 0.850 0.08 0.84 0.00 0.08 0.00 0.00 0.00
#> TCGA.VS.A9V2.01 1 0.3358 0.874 0.64 0.00 0.00 0.00 0.00 0.00 0.36
#> TCGA.C5.A1MH.01 1 0.3358 0.874 0.64 0.00 0.00 0.00 0.00 0.00 0.36
#> TCGA.C5.A1BK.01 7 0.0000 1.000 0.00 0.00 0.00 0.00 0.00 0.00 1.00
cbind(get_classes(res, k = 8), get_membership(res, k = 8))
#> class entropy silhouette p1 p2 p3 p4 p5 p6 p7 p8
#> TCGA.MA.AA42.01 6 0.0000 0.970 0.00 0.00 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.C5.A8YQ.01 2 0.0808 0.891 0.00 0.96 0.00 0.00 0.00 0.00 0.00 0.04
#> TCGA.MA.AA3W.01 7 0.2267 1.000 0.18 0.00 0.00 0.00 0.00 0.00 0.82 0.00
#> TCGA.C5.A7CO.01 8 0.3272 0.000 0.00 0.00 0.00 0.00 0.00 0.42 0.00 0.58
#> TCGA.VS.A94W.01 1 0.0000 0.932 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.MA.AA41.01 3 0.1804 0.000 0.00 0.00 0.90 0.08 0.02 0.00 0.00 0.00
#> TCGA.ZJ.A8QO.01 6 0.0941 0.938 0.00 0.00 0.02 0.02 0.00 0.96 0.00 0.00
#> TCGA.EA.A3QE.01 1 0.0000 0.932 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.DS.A0VM.01 5 0.4326 0.542 0.00 0.00 0.04 0.00 0.64 0.00 0.04 0.28
#> TCGA.MU.A8JM.01 5 0.3080 0.745 0.06 0.00 0.02 0.00 0.84 0.00 0.02 0.06
#> TCGA.C5.A7UE.01 1 0.4775 0.329 0.60 0.00 0.02 0.00 0.30 0.00 0.02 0.06
#> TCGA.XS.A8TJ.01 1 0.0000 0.932 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.DS.A0VN.01 4 0.0471 1.000 0.00 0.00 0.00 0.98 0.02 0.00 0.00 0.00
#> TCGA.DR.A0ZL.01 7 0.2267 1.000 0.18 0.00 0.00 0.00 0.00 0.00 0.82 0.00
#> TCGA.JW.A5VI.01 5 0.0000 0.786 0.00 0.00 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.FU.A3YQ.01 1 0.0000 0.932 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.C5.A7CH.01 4 0.0471 1.000 0.00 0.00 0.00 0.98 0.02 0.00 0.00 0.00
#> TCGA.BI.A20A.01 6 0.0000 0.970 0.00 0.00 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.ZX.AA5X.01 7 0.2267 1.000 0.18 0.00 0.00 0.00 0.00 0.00 0.82 0.00
#> TCGA.C5.A7CJ.01 1 0.0000 0.932 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.Q1.A6DT.01 2 0.0000 0.900 0.00 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.DS.A1O9.01 5 0.1091 0.793 0.06 0.00 0.00 0.00 0.94 0.00 0.00 0.00
#> TCGA.VS.A9UC.01 2 0.3002 0.820 0.00 0.82 0.02 0.00 0.00 0.00 0.12 0.04
#> TCGA.VS.A9V2.01 1 0.0000 0.932 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.C5.A1MH.01 1 0.0000 0.932 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.C5.A1BK.01 7 0.2267 1.000 0.18 0.00 0.00 0.00 0.00 0.00 0.82 0.00
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)
consensus_heatmap(res, k = 7)
consensus_heatmap(res, k = 8)
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)
membership_heatmap(res, k = 7)
membership_heatmap(res, k = 8)
As soon as the classes for columns are determined, the signatures that are significantly different between subgroups can be looked for. Following are the heatmaps for signatures.
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)
get_signatures(res, k = 7)
get_signatures(res, k = 8)
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 (which is done by automatically selecting number of clusters).If there are too many signatures, top_signatures = ... can be set to only show the
signatures with the highest FDRs:
# code only for demonstration
# e.g. to show the top 500 most significant rows
tb = get_signature(res, k = ..., top_signatures = 500)
If the signatures are defined as these which are uniquely high in current group, diff_method argument
can be set to "uniquely_high_in_one_group":
# code only for demonstration
tb = get_signature(res, k = ..., diff_method = "uniquely_high_in_one_group")
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")
dimension_reduction(res, k = 7, method = "UMAP")
dimension_reduction(res, k = 8, method = "UMAP")
Following heatmap shows how subgroups are split when increasing k:
collect_classes(res)
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.
Parent node: Node02. Child nodes: Node0111 , Node0112-leaf , Node0113 , Node0121 , Node0122-leaf , Node0123-leaf , Node0131 , Node0132-leaf , Node0133-leaf , Node0134-leaf , Node0211 , Node0212-leaf , Node0221-leaf , Node0222 , Node0231-leaf , Node0232-leaf , Node0233-leaf , Node0311 , Node0312-leaf , Node0313-leaf .
The object with results only for a single top-value method and a single partitioning method can be extracted as:
res = res_rh["022"]
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, 7, 8.
#> On a matrix with 30000 rows and 36 columns.
#> Top rows (1000) are extracted by 'ATC' method.
#> Subgroups are detected by 'skmeans' method.
#> Performed in total 350 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_partitions"
#> [7] "compare_signatures" "consensus_heatmap" "dimension_reduction"
#> [10] "functional_enrichment" "get_anno_col" "get_anno"
#> [13] "get_classes" "get_consensus" "get_matrix"
#> [16] "get_membership" "get_param" "get_signatures"
#> [19] "get_stats" "is_best_k" "is_stable_k"
#> [22] "membership_heatmap" "ncol" "nrow"
#> [25] "plot_ecdf" "predict_classes" "rownames"
#> [28] "select_partition_number" "show" "suggest_best_k"
#> [31] "test_to_known_factors" "top_rows_heatmap"
collect_plots() function collects all the plots made from res for all k (number of subgroups)
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, higher 1-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 0.971 0.982 0.2243 0.797 0.797
#> 3 3 0.788 0.883 0.939 1.6051 0.608 0.508
#> 4 4 0.822 0.868 0.943 0.1437 0.919 0.802
#> 5 5 0.651 0.731 0.872 0.0490 0.979 0.938
#> 6 6 0.629 0.698 0.839 0.0389 0.997 0.990
#> 7 7 0.663 0.657 0.823 0.0408 0.970 0.905
#> 8 8 0.647 0.533 0.777 0.0363 0.983 0.940
suggest_best_k() suggests the best \(k\) based on these statistics. The rules are as follows:
suggest_best_k(res)
#> [1] 2
Following is 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 subgroup
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
#> TCGA.IR.A3LK.01 2 0.000 0.979 0.00 1.00
#> TCGA.C5.A2LZ.01 2 0.000 0.979 0.00 1.00
#> TCGA.EK.A2RC.01 2 0.000 0.979 0.00 1.00
#> TCGA.EA.A3HQ.01 2 0.000 0.979 0.00 1.00
#> TCGA.JW.AAVH.01 2 0.000 0.979 0.00 1.00
#> TCGA.IR.A3L7.01 2 0.000 0.979 0.00 1.00
#> TCGA.VS.A8QC.01 2 0.000 0.979 0.00 1.00
#> TCGA.WL.A834.01 2 0.000 0.979 0.00 1.00
#> TCGA.VS.A8QF.01 2 0.000 0.979 0.00 1.00
#> TCGA.EK.A2PG.01 2 0.000 0.979 0.00 1.00
#> TCGA.VS.A8EC.01 1 0.000 1.000 1.00 0.00
#> TCGA.FU.A3HY.01 2 0.000 0.979 0.00 1.00
#> TCGA.DS.A3LQ.01 1 0.000 1.000 1.00 0.00
#> TCGA.LP.A5U3.01 2 0.000 0.979 0.00 1.00
#> TCGA.EA.A6QX.01 2 0.000 0.979 0.00 1.00
#> TCGA.EK.A2RA.01 2 0.402 0.933 0.08 0.92
#> TCGA.Q1.A5R2.01 2 0.402 0.933 0.08 0.92
#> TCGA.EK.A2IP.01 2 0.000 0.979 0.00 1.00
#> TCGA.JW.A5VL.01 2 0.000 0.979 0.00 1.00
#> TCGA.VS.A8EG.01 2 0.000 0.979 0.00 1.00
#> TCGA.JW.A5VK.01 1 0.000 1.000 1.00 0.00
#> TCGA.FU.A3TQ.01 2 0.000 0.979 0.00 1.00
#> TCGA.EK.A2RB.01 2 0.402 0.933 0.08 0.92
#> TCGA.C5.A2LX.01 2 0.141 0.969 0.02 0.98
#> TCGA.C5.A1MN.01 2 0.402 0.933 0.08 0.92
#> TCGA.EA.A1QT.01 2 0.000 0.979 0.00 1.00
#> TCGA.VS.A9U7.01 2 0.000 0.979 0.00 1.00
#> TCGA.VS.A9UY.01 2 0.000 0.979 0.00 1.00
#> TCGA.C5.A1BL.01 2 0.402 0.933 0.08 0.92
#> TCGA.VS.A957.01 2 0.000 0.979 0.00 1.00
#> TCGA.ZJ.AAXI.01 2 0.000 0.979 0.00 1.00
#> TCGA.DS.A1OA.01 2 0.000 0.979 0.00 1.00
#> TCGA.VS.A950.01 2 0.469 0.916 0.10 0.90
#> TCGA.VS.A9UI.01 2 0.327 0.947 0.06 0.94
#> TCGA.Q1.A73Q.01 1 0.000 1.000 1.00 0.00
#> TCGA.C5.A1M5.01 2 0.327 0.947 0.06 0.94
cbind(get_classes(res, k = 3), get_membership(res, k = 3))
#> class entropy silhouette p1 p2 p3
#> TCGA.IR.A3LK.01 2 0.540 0.625 0 0.72 0.28
#> TCGA.C5.A2LZ.01 2 0.000 0.940 0 1.00 0.00
#> TCGA.EK.A2RC.01 2 0.000 0.940 0 1.00 0.00
#> TCGA.EA.A3HQ.01 2 0.000 0.940 0 1.00 0.00
#> TCGA.JW.AAVH.01 3 0.207 0.900 0 0.06 0.94
#> TCGA.IR.A3L7.01 2 0.000 0.940 0 1.00 0.00
#> TCGA.VS.A8QC.01 2 0.000 0.940 0 1.00 0.00
#> TCGA.WL.A834.01 2 0.000 0.940 0 1.00 0.00
#> TCGA.VS.A8QF.01 2 0.000 0.940 0 1.00 0.00
#> TCGA.EK.A2PG.01 2 0.595 0.398 0 0.64 0.36
#> TCGA.VS.A8EC.01 1 0.000 1.000 1 0.00 0.00
#> TCGA.FU.A3HY.01 2 0.583 0.469 0 0.66 0.34
#> TCGA.DS.A3LQ.01 1 0.000 1.000 1 0.00 0.00
#> TCGA.LP.A5U3.01 2 0.000 0.940 0 1.00 0.00
#> TCGA.EA.A6QX.01 2 0.000 0.940 0 1.00 0.00
#> TCGA.EK.A2RA.01 3 0.153 0.908 0 0.04 0.96
#> TCGA.Q1.A5R2.01 3 0.334 0.874 0 0.12 0.88
#> TCGA.EK.A2IP.01 2 0.000 0.940 0 1.00 0.00
#> TCGA.JW.A5VL.01 3 0.207 0.873 0 0.06 0.94
#> TCGA.VS.A8EG.01 2 0.000 0.940 0 1.00 0.00
#> TCGA.JW.A5VK.01 1 0.000 1.000 1 0.00 0.00
#> TCGA.FU.A3TQ.01 2 0.000 0.940 0 1.00 0.00
#> TCGA.EK.A2RB.01 3 0.207 0.908 0 0.06 0.94
#> TCGA.C5.A2LX.01 3 0.556 0.664 0 0.30 0.70
#> TCGA.C5.A1MN.01 3 0.153 0.908 0 0.04 0.96
#> TCGA.EA.A1QT.01 3 0.153 0.902 0 0.04 0.96
#> TCGA.VS.A9U7.01 2 0.000 0.940 0 1.00 0.00
#> TCGA.VS.A9UY.01 3 0.254 0.860 0 0.08 0.92
#> TCGA.C5.A1BL.01 3 0.207 0.907 0 0.06 0.94
#> TCGA.VS.A957.01 2 0.000 0.940 0 1.00 0.00
#> TCGA.ZJ.AAXI.01 2 0.000 0.940 0 1.00 0.00
#> TCGA.DS.A1OA.01 2 0.000 0.940 0 1.00 0.00
#> TCGA.VS.A950.01 3 0.153 0.908 0 0.04 0.96
#> TCGA.VS.A9UI.01 3 0.153 0.908 0 0.04 0.96
#> TCGA.Q1.A73Q.01 1 0.000 1.000 1 0.00 0.00
#> TCGA.C5.A1M5.01 3 0.522 0.728 0 0.26 0.74
cbind(get_classes(res, k = 4), get_membership(res, k = 4))
#> class entropy silhouette p1 p2 p3 p4
#> TCGA.IR.A3LK.01 4 0.2921 0.682 0 0.14 0.00 0.86
#> TCGA.C5.A2LZ.01 2 0.0707 0.938 0 0.98 0.02 0.00
#> TCGA.EK.A2RC.01 2 0.1211 0.926 0 0.96 0.04 0.00
#> TCGA.EA.A3HQ.01 2 0.0000 0.947 0 1.00 0.00 0.00
#> TCGA.JW.AAVH.01 4 0.7121 0.394 0 0.16 0.30 0.54
#> TCGA.IR.A3L7.01 2 0.0000 0.947 0 1.00 0.00 0.00
#> TCGA.VS.A8QC.01 2 0.0000 0.947 0 1.00 0.00 0.00
#> TCGA.WL.A834.01 2 0.0000 0.947 0 1.00 0.00 0.00
#> TCGA.VS.A8QF.01 2 0.2921 0.810 0 0.86 0.00 0.14
#> TCGA.EK.A2PG.01 2 0.6656 0.389 0 0.62 0.16 0.22
#> TCGA.VS.A8EC.01 1 0.0000 1.000 1 0.00 0.00 0.00
#> TCGA.FU.A3HY.01 2 0.2921 0.812 0 0.86 0.14 0.00
#> TCGA.DS.A3LQ.01 1 0.0000 1.000 1 0.00 0.00 0.00
#> TCGA.LP.A5U3.01 2 0.0000 0.947 0 1.00 0.00 0.00
#> TCGA.EA.A6QX.01 2 0.0707 0.936 0 0.98 0.00 0.02
#> TCGA.EK.A2RA.01 3 0.1211 0.904 0 0.00 0.96 0.04
#> TCGA.Q1.A5R2.01 3 0.0000 0.914 0 0.00 1.00 0.00
#> TCGA.EK.A2IP.01 2 0.0000 0.947 0 1.00 0.00 0.00
#> TCGA.JW.A5VL.01 4 0.0707 0.750 0 0.00 0.02 0.98
#> TCGA.VS.A8EG.01 2 0.0000 0.947 0 1.00 0.00 0.00
#> TCGA.JW.A5VK.01 1 0.0000 1.000 1 0.00 0.00 0.00
#> TCGA.FU.A3TQ.01 2 0.1211 0.926 0 0.96 0.04 0.00
#> TCGA.EK.A2RB.01 3 0.0000 0.914 0 0.00 1.00 0.00
#> TCGA.C5.A2LX.01 3 0.2345 0.810 0 0.10 0.90 0.00
#> TCGA.C5.A1MN.01 3 0.0707 0.911 0 0.00 0.98 0.02
#> TCGA.EA.A1QT.01 3 0.5392 0.492 0 0.04 0.68 0.28
#> TCGA.VS.A9U7.01 2 0.0000 0.947 0 1.00 0.00 0.00
#> TCGA.VS.A9UY.01 4 0.0707 0.750 0 0.00 0.02 0.98
#> TCGA.C5.A1BL.01 3 0.0000 0.914 0 0.00 1.00 0.00
#> TCGA.VS.A957.01 2 0.0000 0.947 0 1.00 0.00 0.00
#> TCGA.ZJ.AAXI.01 2 0.0000 0.947 0 1.00 0.00 0.00
#> TCGA.DS.A1OA.01 2 0.0707 0.938 0 0.98 0.02 0.00
#> TCGA.VS.A950.01 3 0.0707 0.911 0 0.00 0.98 0.02
#> TCGA.VS.A9UI.01 3 0.2011 0.881 0 0.00 0.92 0.08
#> TCGA.Q1.A73Q.01 1 0.0000 1.000 1 0.00 0.00 0.00
#> TCGA.C5.A1M5.01 3 0.1211 0.887 0 0.04 0.96 0.00
cbind(get_classes(res, k = 5), get_membership(res, k = 5))
#> class entropy silhouette p1 p2 p3 p4 p5
#> TCGA.IR.A3LK.01 4 0.6064 0.237 0 0.12 0.00 0.46 0.42
#> TCGA.C5.A2LZ.01 2 0.2754 0.841 0 0.88 0.04 0.00 0.08
#> TCGA.EK.A2RC.01 2 0.2012 0.857 0 0.92 0.02 0.00 0.06
#> TCGA.EA.A3HQ.01 2 0.0000 0.878 0 1.00 0.00 0.00 0.00
#> TCGA.JW.AAVH.01 5 0.7820 0.265 0 0.12 0.14 0.32 0.42
#> TCGA.IR.A3L7.01 2 0.0000 0.878 0 1.00 0.00 0.00 0.00
#> TCGA.VS.A8QC.01 2 0.3455 0.827 0 0.86 0.04 0.06 0.04
#> TCGA.WL.A834.01 2 0.0000 0.878 0 1.00 0.00 0.00 0.00
#> TCGA.VS.A8QF.01 2 0.3291 0.807 0 0.84 0.00 0.12 0.04
#> TCGA.EK.A2PG.01 2 0.8132 -0.122 0 0.42 0.18 0.24 0.16
#> TCGA.VS.A8EC.01 1 0.0000 1.000 1 0.00 0.00 0.00 0.00
#> TCGA.FU.A3HY.01 2 0.6693 0.487 0 0.62 0.14 0.14 0.10
#> TCGA.DS.A3LQ.01 1 0.0000 1.000 1 0.00 0.00 0.00 0.00
#> TCGA.LP.A5U3.01 2 0.0000 0.878 0 1.00 0.00 0.00 0.00
#> TCGA.EA.A6QX.01 2 0.3421 0.797 0 0.84 0.00 0.08 0.08
#> TCGA.EK.A2RA.01 3 0.1216 0.791 0 0.00 0.96 0.02 0.02
#> TCGA.Q1.A5R2.01 3 0.0000 0.802 0 0.00 1.00 0.00 0.00
#> TCGA.EK.A2IP.01 2 0.2438 0.854 0 0.90 0.00 0.04 0.06
#> TCGA.JW.A5VL.01 4 0.0000 0.657 0 0.00 0.00 1.00 0.00
#> TCGA.VS.A8EG.01 2 0.0000 0.878 0 1.00 0.00 0.00 0.00
#> TCGA.JW.A5VK.01 1 0.0000 1.000 1 0.00 0.00 0.00 0.00
#> TCGA.FU.A3TQ.01 2 0.2438 0.847 0 0.90 0.04 0.00 0.06
#> TCGA.EK.A2RB.01 3 0.2020 0.733 0 0.00 0.90 0.00 0.10
#> TCGA.C5.A2LX.01 3 0.5820 0.211 0 0.24 0.64 0.02 0.10
#> TCGA.C5.A1MN.01 3 0.0609 0.799 0 0.00 0.98 0.02 0.00
#> TCGA.EA.A1QT.01 5 0.7010 0.393 0 0.02 0.34 0.20 0.44
#> TCGA.VS.A9U7.01 2 0.0000 0.878 0 1.00 0.00 0.00 0.00
#> TCGA.VS.A9UY.01 4 0.0000 0.657 0 0.00 0.00 1.00 0.00
#> TCGA.C5.A1BL.01 3 0.0000 0.802 0 0.00 1.00 0.00 0.00
#> TCGA.VS.A957.01 2 0.0000 0.878 0 1.00 0.00 0.00 0.00
#> TCGA.ZJ.AAXI.01 2 0.1216 0.873 0 0.96 0.00 0.02 0.02
#> TCGA.DS.A1OA.01 2 0.2516 0.830 0 0.86 0.00 0.00 0.14
#> TCGA.VS.A950.01 3 0.0609 0.797 0 0.00 0.98 0.02 0.00
#> TCGA.VS.A9UI.01 3 0.4890 0.502 0 0.00 0.72 0.14 0.14
#> TCGA.Q1.A73Q.01 1 0.0000 1.000 1 0.00 0.00 0.00 0.00
#> TCGA.C5.A1M5.01 3 0.3868 0.619 0 0.06 0.80 0.00 0.14
cbind(get_classes(res, k = 6), get_membership(res, k = 6))
#> class entropy silhouette p1 p2 p3 p4 p5 p6
#> TCGA.IR.A3LK.01 6 0.3475 0.000 0.00 0.06 0.00 0.14 0.00 0.80
#> TCGA.C5.A2LZ.01 2 0.3258 0.801 0.00 0.84 0.04 0.00 0.10 0.02
#> TCGA.EK.A2RC.01 2 0.1635 0.833 0.00 0.94 0.02 0.00 0.02 0.02
#> TCGA.EA.A3HQ.01 2 0.0547 0.846 0.00 0.98 0.00 0.00 0.02 0.00
#> TCGA.JW.AAVH.01 5 0.7737 0.233 0.00 0.04 0.20 0.34 0.34 0.08
#> TCGA.IR.A3L7.01 2 0.0547 0.846 0.00 0.98 0.00 0.00 0.02 0.00
#> TCGA.VS.A8QC.01 2 0.2345 0.833 0.00 0.90 0.02 0.02 0.06 0.00
#> TCGA.WL.A834.01 2 0.0937 0.843 0.00 0.96 0.00 0.00 0.04 0.00
#> TCGA.VS.A8QF.01 2 0.3600 0.791 0.00 0.82 0.00 0.08 0.08 0.02
#> TCGA.EK.A2PG.01 2 0.8649 -0.345 0.00 0.30 0.14 0.12 0.18 0.26
#> TCGA.VS.A8EC.01 1 0.2190 0.916 0.90 0.00 0.00 0.00 0.06 0.04
#> TCGA.FU.A3HY.01 2 0.7123 0.271 0.00 0.50 0.24 0.02 0.12 0.12
#> TCGA.DS.A3LQ.01 1 0.0000 0.952 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.LP.A5U3.01 2 0.0547 0.846 0.00 0.98 0.00 0.00 0.02 0.00
#> TCGA.EA.A6QX.01 2 0.4756 0.723 0.00 0.74 0.00 0.06 0.10 0.10
#> TCGA.EK.A2RA.01 3 0.2629 0.725 0.00 0.00 0.88 0.02 0.08 0.02
#> TCGA.Q1.A5R2.01 3 0.1267 0.746 0.00 0.00 0.94 0.00 0.06 0.00
#> TCGA.EK.A2IP.01 2 0.3697 0.783 0.00 0.82 0.00 0.04 0.08 0.06
#> TCGA.JW.A5VL.01 4 0.0937 0.890 0.00 0.00 0.00 0.96 0.00 0.04
#> TCGA.VS.A8EG.01 2 0.0937 0.844 0.00 0.96 0.00 0.00 0.04 0.00
#> TCGA.JW.A5VK.01 1 0.1092 0.949 0.96 0.00 0.00 0.00 0.02 0.02
#> TCGA.FU.A3TQ.01 2 0.3045 0.798 0.00 0.86 0.06 0.00 0.06 0.02
#> TCGA.EK.A2RB.01 3 0.3045 0.678 0.00 0.00 0.84 0.00 0.10 0.06
#> TCGA.C5.A2LX.01 3 0.4864 0.297 0.00 0.26 0.66 0.00 0.06 0.02
#> TCGA.C5.A1MN.01 3 0.2956 0.703 0.00 0.00 0.84 0.00 0.12 0.04
#> TCGA.EA.A1QT.01 5 0.6141 0.372 0.00 0.00 0.38 0.16 0.44 0.02
#> TCGA.VS.A9U7.01 2 0.0547 0.846 0.00 0.98 0.00 0.00 0.02 0.00
#> TCGA.VS.A9UY.01 4 0.1480 0.890 0.00 0.00 0.00 0.94 0.04 0.02
#> TCGA.C5.A1BL.01 3 0.0547 0.751 0.00 0.00 0.98 0.00 0.02 0.00
#> TCGA.VS.A957.01 2 0.0547 0.842 0.00 0.98 0.00 0.00 0.02 0.00
#> TCGA.ZJ.AAXI.01 2 0.2190 0.828 0.00 0.90 0.00 0.04 0.06 0.00
#> TCGA.DS.A1OA.01 2 0.2956 0.805 0.00 0.84 0.00 0.00 0.12 0.04
#> TCGA.VS.A950.01 3 0.2190 0.738 0.00 0.00 0.90 0.00 0.06 0.04
#> TCGA.VS.A9UI.01 3 0.3324 0.680 0.00 0.02 0.84 0.08 0.06 0.00
#> TCGA.Q1.A73Q.01 1 0.0547 0.944 0.98 0.00 0.02 0.00 0.00 0.00
#> TCGA.C5.A1M5.01 3 0.3045 0.640 0.00 0.10 0.84 0.00 0.06 0.00
cbind(get_classes(res, k = 7), get_membership(res, k = 7))
#> class entropy silhouette p1 p2 p3 p4 p5 p6 p7
#> TCGA.IR.A3LK.01 7 0.1718 0.000 0.00 0.04 0.00 0.04 0.00 0.00 0.92
#> TCGA.C5.A2LZ.01 2 0.2259 0.761 0.00 0.84 0.16 0.00 0.00 0.00 0.00
#> TCGA.EK.A2RC.01 2 0.3086 0.734 0.00 0.80 0.16 0.00 0.00 0.00 0.04
#> TCGA.EA.A3HQ.01 2 0.0000 0.829 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.JW.AAVH.01 5 0.6580 0.234 0.00 0.00 0.10 0.10 0.56 0.16 0.08
#> TCGA.IR.A3L7.01 2 0.0504 0.826 0.00 0.98 0.00 0.00 0.00 0.02 0.00
#> TCGA.VS.A8QC.01 2 0.2803 0.773 0.00 0.84 0.06 0.00 0.00 0.10 0.00
#> TCGA.WL.A834.01 2 0.0000 0.829 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.VS.A8QF.01 2 0.3541 0.743 0.00 0.80 0.02 0.08 0.00 0.00 0.10
#> TCGA.EK.A2PG.01 5 0.8732 -0.061 0.00 0.24 0.10 0.06 0.24 0.16 0.20
#> TCGA.VS.A8EC.01 1 0.2421 0.878 0.88 0.00 0.00 0.00 0.02 0.08 0.02
#> TCGA.FU.A3HY.01 2 0.8346 -0.226 0.00 0.30 0.20 0.14 0.02 0.22 0.12
#> TCGA.DS.A3LQ.01 1 0.0000 0.942 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.LP.A5U3.01 2 0.0000 0.829 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.EA.A6QX.01 2 0.5630 0.480 0.00 0.62 0.00 0.02 0.06 0.10 0.20
#> TCGA.EK.A2RA.01 3 0.2912 0.724 0.00 0.00 0.82 0.04 0.00 0.14 0.00
#> TCGA.Q1.A5R2.01 3 0.0000 0.744 0.00 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.EK.A2IP.01 2 0.3292 0.760 0.00 0.84 0.00 0.02 0.02 0.06 0.06
#> TCGA.JW.A5VL.01 4 0.0863 0.852 0.00 0.00 0.00 0.96 0.04 0.00 0.00
#> TCGA.VS.A8EG.01 2 0.0000 0.829 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.JW.A5VK.01 1 0.0000 0.942 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.FU.A3TQ.01 2 0.3530 0.690 0.00 0.76 0.20 0.00 0.02 0.02 0.00
#> TCGA.EK.A2RB.01 3 0.4070 0.545 0.00 0.00 0.62 0.04 0.00 0.34 0.00
#> TCGA.C5.A2LX.01 3 0.5703 0.413 0.02 0.18 0.64 0.00 0.02 0.10 0.04
#> TCGA.C5.A1MN.01 3 0.4675 0.623 0.02 0.00 0.66 0.02 0.04 0.26 0.00
#> TCGA.EA.A1QT.01 5 0.4643 0.249 0.00 0.00 0.12 0.06 0.74 0.04 0.04
#> TCGA.VS.A9U7.01 2 0.0000 0.829 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.VS.A9UY.01 4 0.2509 0.851 0.00 0.00 0.00 0.88 0.04 0.06 0.02
#> TCGA.C5.A1BL.01 3 0.0000 0.744 0.00 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.VS.A957.01 2 0.0504 0.826 0.00 0.98 0.02 0.00 0.00 0.00 0.00
#> TCGA.ZJ.AAXI.01 2 0.2003 0.816 0.00 0.92 0.02 0.02 0.00 0.02 0.02
#> TCGA.DS.A1OA.01 2 0.4472 0.721 0.00 0.76 0.04 0.00 0.04 0.08 0.08
#> TCGA.VS.A950.01 3 0.2745 0.721 0.00 0.00 0.82 0.00 0.02 0.16 0.00
#> TCGA.VS.A9UI.01 3 0.4565 0.659 0.00 0.00 0.72 0.02 0.08 0.16 0.02
#> TCGA.Q1.A73Q.01 1 0.1505 0.914 0.94 0.00 0.02 0.00 0.02 0.02 0.00
#> TCGA.C5.A1M5.01 3 0.4110 0.644 0.02 0.06 0.78 0.00 0.00 0.10 0.04
cbind(get_classes(res, k = 8), get_membership(res, k = 8))
#> class entropy silhouette p1 p2 p3 p4 p5 p6 p7 p8
#> TCGA.IR.A3LK.01 7 0.1563 0.0817 0.00 0.00 0.00 0.10 0.00 0.00 0.90 0.00
#> TCGA.C5.A2LZ.01 6 0.4097 0.6518 0.00 0.02 0.08 0.00 0.00 0.70 0.00 0.20
#> TCGA.EK.A2RC.01 6 0.3337 0.7093 0.00 0.00 0.04 0.00 0.02 0.78 0.00 0.16
#> TCGA.EA.A3HQ.01 6 0.0000 0.7816 0.00 0.00 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.JW.AAVH.01 5 0.7597 0.1369 0.00 0.28 0.06 0.10 0.36 0.00 0.12 0.08
#> TCGA.IR.A3L7.01 6 0.0000 0.7816 0.00 0.00 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.VS.A8QC.01 6 0.5307 0.6083 0.00 0.08 0.10 0.08 0.00 0.68 0.02 0.04
#> TCGA.WL.A834.01 6 0.0000 0.7816 0.00 0.00 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.VS.A8QF.01 6 0.3928 0.6451 0.00 0.02 0.00 0.18 0.02 0.74 0.04 0.00
#> TCGA.EK.A2PG.01 7 0.8928 0.0817 0.00 0.06 0.10 0.14 0.14 0.14 0.28 0.14
#> TCGA.VS.A8EC.01 1 0.2547 0.8385 0.84 0.12 0.00 0.00 0.00 0.00 0.04 0.00
#> TCGA.FU.A3HY.01 6 0.8008 -0.1853 0.00 0.22 0.16 0.14 0.00 0.32 0.10 0.06
#> TCGA.DS.A3LQ.01 1 0.0000 0.8951 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.LP.A5U3.01 6 0.0000 0.7816 0.00 0.00 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.EA.A6QX.01 6 0.6083 0.0721 0.00 0.38 0.00 0.08 0.00 0.42 0.08 0.04
#> TCGA.EK.A2RA.01 3 0.3843 0.3441 0.00 0.00 0.70 0.02 0.04 0.00 0.00 0.24
#> TCGA.Q1.A5R2.01 3 0.2856 0.3238 0.00 0.00 0.78 0.00 0.02 0.00 0.00 0.20
#> TCGA.EK.A2IP.01 6 0.4077 0.6927 0.00 0.10 0.00 0.08 0.02 0.76 0.04 0.00
#> TCGA.JW.A5VL.01 4 0.1741 0.7042 0.00 0.02 0.00 0.92 0.02 0.00 0.04 0.00
#> TCGA.VS.A8EG.01 6 0.0471 0.7785 0.00 0.00 0.00 0.00 0.00 0.98 0.00 0.02
#> TCGA.JW.A5VK.01 1 0.1607 0.8886 0.92 0.04 0.00 0.00 0.00 0.00 0.00 0.04
#> TCGA.FU.A3TQ.01 6 0.3337 0.6975 0.00 0.02 0.04 0.00 0.00 0.78 0.00 0.16
#> TCGA.EK.A2RB.01 8 0.4702 0.0000 0.00 0.02 0.36 0.04 0.02 0.00 0.00 0.56
#> TCGA.C5.A2LX.01 3 0.4022 0.3668 0.00 0.00 0.74 0.00 0.04 0.12 0.00 0.10
#> TCGA.C5.A1MN.01 3 0.3970 0.2966 0.00 0.10 0.68 0.00 0.00 0.00 0.00 0.22
#> TCGA.EA.A1QT.01 5 0.1887 0.2214 0.00 0.00 0.06 0.00 0.90 0.00 0.04 0.00
#> TCGA.VS.A9U7.01 6 0.0000 0.7816 0.00 0.00 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.VS.A9UY.01 4 0.3771 0.7003 0.00 0.08 0.02 0.80 0.06 0.00 0.02 0.02
#> TCGA.C5.A1BL.01 3 0.2888 0.4275 0.00 0.04 0.80 0.00 0.00 0.00 0.00 0.16
#> TCGA.VS.A957.01 6 0.1091 0.7696 0.00 0.00 0.00 0.00 0.00 0.94 0.00 0.06
#> TCGA.ZJ.AAXI.01 6 0.3002 0.7279 0.00 0.12 0.00 0.04 0.00 0.82 0.00 0.02
#> TCGA.DS.A1OA.01 6 0.5004 0.6571 0.00 0.08 0.02 0.00 0.02 0.70 0.08 0.10
#> TCGA.VS.A950.01 3 0.2404 0.4687 0.00 0.02 0.84 0.00 0.00 0.00 0.00 0.14
#> TCGA.VS.A9UI.01 3 0.5641 0.3560 0.00 0.06 0.66 0.04 0.06 0.00 0.08 0.10
#> TCGA.Q1.A73Q.01 1 0.2020 0.8473 0.90 0.02 0.06 0.00 0.00 0.00 0.00 0.02
#> TCGA.C5.A1M5.01 3 0.3454 0.4847 0.00 0.02 0.80 0.00 0.02 0.04 0.00 0.12
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)
consensus_heatmap(res, k = 7)
consensus_heatmap(res, k = 8)
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)
membership_heatmap(res, k = 7)
membership_heatmap(res, k = 8)
As soon as the classes for columns are determined, the signatures that are significantly different between subgroups can be looked for. Following are the heatmaps for signatures.
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)
get_signatures(res, k = 7)
get_signatures(res, k = 8)
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 (which is done by automatically selecting number of clusters).If there are too many signatures, top_signatures = ... can be set to only show the
signatures with the highest FDRs:
# code only for demonstration
# e.g. to show the top 500 most significant rows
tb = get_signature(res, k = ..., top_signatures = 500)
If the signatures are defined as these which are uniquely high in current group, diff_method argument
can be set to "uniquely_high_in_one_group":
# code only for demonstration
tb = get_signature(res, k = ..., diff_method = "uniquely_high_in_one_group")
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")
dimension_reduction(res, k = 7, method = "UMAP")
dimension_reduction(res, k = 8, method = "UMAP")
Following heatmap shows how subgroups are split when increasing k:
collect_classes(res)
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.
Parent node: Node022. Child nodes: Node01111-leaf , Node01112-leaf , Node01113-leaf , Node01131-leaf , Node01132-leaf , Node01133-leaf , Node01211-leaf , Node01212-leaf , Node01311-leaf , Node01312-leaf , Node01313-leaf , Node02111 , Node02112-leaf , Node02221 , Node02222-leaf , Node03111-leaf , Node03112 .
The object with results only for a single top-value method and a single partitioning method can be extracted as:
res = res_rh["0222"]
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, 7, 8.
#> On a matrix with 30000 rows and 32 columns.
#> Top rows (1000) are extracted by 'ATC' method.
#> Subgroups are detected by 'kmeans' method.
#> Performed in total 350 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_partitions"
#> [7] "compare_signatures" "consensus_heatmap" "dimension_reduction"
#> [10] "functional_enrichment" "get_anno_col" "get_anno"
#> [13] "get_classes" "get_consensus" "get_matrix"
#> [16] "get_membership" "get_param" "get_signatures"
#> [19] "get_stats" "is_best_k" "is_stable_k"
#> [22] "membership_heatmap" "ncol" "nrow"
#> [25] "plot_ecdf" "predict_classes" "rownames"
#> [28] "select_partition_number" "show" "suggest_best_k"
#> [31] "test_to_known_factors" "top_rows_heatmap"
collect_plots() function collects all the plots made from res for all k (number of subgroups)
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, higher 1-PAC score, higher mean silhouette score or higher
concordance corresponds to better partition. Rand index and Jaccard index
measure how similar the current partition is compared to partition with k-1.
If they are too similar, we won't accept k is better than k-1.
select_partition_number(res)
The numeric values for all these statistics can be obtained by get_stats().
get_stats(res)
#> k 1-PAC mean_silhouette concordance area_increased Rand Jaccard
#> 2 2 1.000 0.974 0.987 0.5148 0.484 0.484
#> 3 3 1.000 0.926 0.973 0.2781 0.643 0.398
#> 4 4 0.834 0.825 0.885 0.1384 0.861 0.619
#> 5 5 0.789 0.859 0.827 0.0524 0.919 0.683
#> 6 6 0.811 0.844 0.873 0.0458 1.000 1.000
#> 7 7 0.772 0.703 0.834 0.0219 0.992 0.956
#> 8 8 0.809 0.740 0.821 0.0188 0.952 0.733
suggest_best_k() suggests the best \(k\) based on these statistics. The rules are as follows:
suggest_best_k(res)
#> [1] 3
#> attr(,"optional")
#> [1] 2
There is also optional best \(k\) = 2 that is worth to check.
Following is 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 subgroup
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
#> TCGA.IR.A3LK.01 1 0.000 0.980 1.00 0.00
#> TCGA.C5.A2LZ.01 2 0.141 0.977 0.02 0.98
#> TCGA.EK.A2RC.01 2 0.000 0.992 0.00 1.00
#> TCGA.EA.A3HQ.01 2 0.000 0.992 0.00 1.00
#> TCGA.JW.AAVH.01 1 0.000 0.980 1.00 0.00
#> TCGA.IR.A3L7.01 2 0.000 0.992 0.00 1.00
#> TCGA.VS.A8QC.01 2 0.000 0.992 0.00 1.00
#> TCGA.WL.A834.01 2 0.000 0.992 0.00 1.00
#> TCGA.VS.A8QF.01 2 0.141 0.977 0.02 0.98
#> TCGA.EK.A2PG.01 1 0.000 0.980 1.00 0.00
#> TCGA.FU.A3HY.01 1 0.000 0.980 1.00 0.00
#> TCGA.LP.A5U3.01 2 0.000 0.992 0.00 1.00
#> TCGA.EA.A6QX.01 2 0.402 0.915 0.08 0.92
#> TCGA.EK.A2RA.01 1 0.000 0.980 1.00 0.00
#> TCGA.Q1.A5R2.01 1 0.327 0.935 0.94 0.06
#> TCGA.EK.A2IP.01 2 0.000 0.992 0.00 1.00
#> TCGA.JW.A5VL.01 1 0.000 0.980 1.00 0.00
#> TCGA.VS.A8EG.01 2 0.000 0.992 0.00 1.00
#> TCGA.FU.A3TQ.01 2 0.000 0.992 0.00 1.00
#> TCGA.EK.A2RB.01 1 0.000 0.980 1.00 0.00
#> TCGA.C5.A2LX.01 2 0.000 0.992 0.00 1.00
#> TCGA.C5.A1MN.01 1 0.000 0.980 1.00 0.00
#> TCGA.EA.A1QT.01 1 0.000 0.980 1.00 0.00
#> TCGA.VS.A9U7.01 2 0.000 0.992 0.00 1.00
#> TCGA.VS.A9UY.01 1 0.000 0.980 1.00 0.00
#> TCGA.C5.A1BL.01 1 0.000 0.980 1.00 0.00
#> TCGA.VS.A957.01 2 0.000 0.992 0.00 1.00
#> TCGA.ZJ.AAXI.01 1 0.680 0.792 0.82 0.18
#> TCGA.DS.A1OA.01 2 0.000 0.992 0.00 1.00
#> TCGA.VS.A950.01 1 0.000 0.980 1.00 0.00
#> TCGA.VS.A9UI.01 1 0.000 0.980 1.00 0.00
#> TCGA.C5.A1M5.01 1 0.327 0.935 0.94 0.06
cbind(get_classes(res, k = 3), get_membership(res, k = 3))
#> class entropy silhouette p1 p2 p3
#> TCGA.IR.A3LK.01 1 0.000 0.949 1.00 0.00 0.0
#> TCGA.C5.A2LZ.01 2 0.000 0.963 0.00 1.00 0.0
#> TCGA.EK.A2RC.01 2 0.000 0.963 0.00 1.00 0.0
#> TCGA.EA.A3HQ.01 3 0.000 1.000 0.00 0.00 1.0
#> TCGA.JW.AAVH.01 1 0.000 0.949 1.00 0.00 0.0
#> TCGA.IR.A3L7.01 3 0.000 1.000 0.00 0.00 1.0
#> TCGA.VS.A8QC.01 2 0.000 0.963 0.00 1.00 0.0
#> TCGA.WL.A834.01 3 0.000 1.000 0.00 0.00 1.0
#> TCGA.VS.A8QF.01 2 0.000 0.963 0.00 1.00 0.0
#> TCGA.EK.A2PG.01 2 0.153 0.930 0.04 0.96 0.0
#> TCGA.FU.A3HY.01 2 0.207 0.911 0.06 0.94 0.0
#> TCGA.LP.A5U3.01 3 0.000 1.000 0.00 0.00 1.0
#> TCGA.EA.A6QX.01 2 0.000 0.963 0.00 1.00 0.0
#> TCGA.EK.A2RA.01 1 0.000 0.949 1.00 0.00 0.0
#> TCGA.Q1.A5R2.01 2 0.000 0.963 0.00 1.00 0.0
#> TCGA.EK.A2IP.01 2 0.000 0.963 0.00 1.00 0.0
#> TCGA.JW.A5VL.01 1 0.000 0.949 1.00 0.00 0.0
#> TCGA.VS.A8EG.01 3 0.000 1.000 0.00 0.00 1.0
#> TCGA.FU.A3TQ.01 2 0.613 0.320 0.00 0.60 0.4
#> TCGA.EK.A2RB.01 1 0.000 0.949 1.00 0.00 0.0
#> TCGA.C5.A2LX.01 2 0.000 0.963 0.00 1.00 0.0
#> TCGA.C5.A1MN.01 2 0.000 0.963 0.00 1.00 0.0
#> TCGA.EA.A1QT.01 1 0.000 0.949 1.00 0.00 0.0
#> TCGA.VS.A9U7.01 3 0.000 1.000 0.00 0.00 1.0
#> TCGA.VS.A9UY.01 1 0.000 0.949 1.00 0.00 0.0
#> TCGA.C5.A1BL.01 1 0.604 0.380 0.62 0.38 0.0
#> TCGA.VS.A957.01 3 0.000 1.000 0.00 0.00 1.0
#> TCGA.ZJ.AAXI.01 2 0.000 0.963 0.00 1.00 0.0
#> TCGA.DS.A1OA.01 2 0.000 0.963 0.00 1.00 0.0
#> TCGA.VS.A950.01 1 0.000 0.949 1.00 0.00 0.0
#> TCGA.VS.A9UI.01 1 0.000 0.949 1.00 0.00 0.0
#> TCGA.C5.A1M5.01 2 0.000 0.963 0.00 1.00 0.0
cbind(get_classes(res, k = 4), get_membership(res, k = 4))
#> class entropy silhouette p1 p2 p3 p4
#> TCGA.IR.A3LK.01 1 0.4790 0.571 0.62 0.00 0.00 0.38
#> TCGA.C5.A2LZ.01 2 0.2345 0.495 0.00 0.90 0.00 0.10
#> TCGA.EK.A2RC.01 4 0.4977 0.953 0.00 0.46 0.00 0.54
#> TCGA.EA.A3HQ.01 3 0.0000 0.989 0.00 0.00 1.00 0.00
#> TCGA.JW.AAVH.01 1 0.0000 0.954 1.00 0.00 0.00 0.00
#> TCGA.IR.A3L7.01 3 0.1211 0.973 0.00 0.00 0.96 0.04
#> TCGA.VS.A8QC.01 2 0.2647 0.450 0.00 0.88 0.00 0.12
#> TCGA.WL.A834.01 3 0.1211 0.973 0.00 0.00 0.96 0.04
#> TCGA.VS.A8QF.01 2 0.0707 0.631 0.00 0.98 0.00 0.02
#> TCGA.EK.A2PG.01 2 0.4790 0.614 0.00 0.62 0.00 0.38
#> TCGA.FU.A3HY.01 2 0.4713 0.627 0.00 0.64 0.00 0.36
#> TCGA.LP.A5U3.01 3 0.0000 0.989 0.00 0.00 1.00 0.00
#> TCGA.EA.A6QX.01 2 0.1211 0.639 0.00 0.96 0.00 0.04
#> TCGA.EK.A2RA.01 1 0.0000 0.954 1.00 0.00 0.00 0.00
#> TCGA.Q1.A5R2.01 2 0.1211 0.672 0.00 0.96 0.00 0.04
#> TCGA.EK.A2IP.01 4 0.4977 0.953 0.00 0.46 0.00 0.54
#> TCGA.JW.A5VL.01 1 0.0000 0.954 1.00 0.00 0.00 0.00
#> TCGA.VS.A8EG.01 3 0.0000 0.989 0.00 0.00 1.00 0.00
#> TCGA.FU.A3TQ.01 4 0.6150 0.823 0.00 0.36 0.06 0.58
#> TCGA.EK.A2RB.01 1 0.0707 0.941 0.98 0.00 0.00 0.02
#> TCGA.C5.A2LX.01 4 0.4977 0.953 0.00 0.46 0.00 0.54
#> TCGA.C5.A1MN.01 2 0.4713 0.627 0.00 0.64 0.00 0.36
#> TCGA.EA.A1QT.01 1 0.0000 0.954 1.00 0.00 0.00 0.00
#> TCGA.VS.A9U7.01 3 0.0000 0.989 0.00 0.00 1.00 0.00
#> TCGA.VS.A9UY.01 1 0.0000 0.954 1.00 0.00 0.00 0.00
#> TCGA.C5.A1BL.01 2 0.5355 0.613 0.02 0.62 0.00 0.36
#> TCGA.VS.A957.01 3 0.0000 0.989 0.00 0.00 1.00 0.00
#> TCGA.ZJ.AAXI.01 2 0.0000 0.649 0.00 1.00 0.00 0.00
#> TCGA.DS.A1OA.01 4 0.4977 0.953 0.00 0.46 0.00 0.54
#> TCGA.VS.A950.01 1 0.0000 0.954 1.00 0.00 0.00 0.00
#> TCGA.VS.A9UI.01 1 0.0000 0.954 1.00 0.00 0.00 0.00
#> TCGA.C5.A1M5.01 2 0.1637 0.676 0.00 0.94 0.00 0.06
cbind(get_classes(res, k = 5), get_membership(res, k = 5))
#> class entropy silhouette p1 p2 p3 p4 p5
#> TCGA.IR.A3LK.01 5 0.5444 0.491 0.18 0.00 0.00 0.16 0.66
#> TCGA.C5.A2LZ.01 2 0.2280 0.697 0.00 0.88 0.00 0.12 0.00
#> TCGA.EK.A2RC.01 4 0.4227 0.961 0.00 0.42 0.00 0.58 0.00
#> TCGA.EA.A3HQ.01 3 0.0000 0.938 0.00 0.00 1.00 0.00 0.00
#> TCGA.JW.AAVH.01 1 0.0609 0.971 0.98 0.00 0.00 0.02 0.00
#> TCGA.IR.A3L7.01 3 0.4170 0.836 0.00 0.00 0.78 0.08 0.14
#> TCGA.VS.A8QC.01 2 0.2020 0.720 0.00 0.90 0.00 0.10 0.00
#> TCGA.WL.A834.01 3 0.4170 0.836 0.00 0.00 0.78 0.08 0.14
#> TCGA.VS.A8QF.01 2 0.1216 0.822 0.00 0.96 0.00 0.02 0.02
#> TCGA.EK.A2PG.01 5 0.5210 0.682 0.00 0.20 0.00 0.12 0.68
#> TCGA.FU.A3HY.01 5 0.3983 0.742 0.00 0.34 0.00 0.00 0.66
#> TCGA.LP.A5U3.01 3 0.0000 0.938 0.00 0.00 1.00 0.00 0.00
#> TCGA.EA.A6QX.01 2 0.2873 0.745 0.00 0.86 0.00 0.12 0.02
#> TCGA.EK.A2RA.01 1 0.0000 0.970 1.00 0.00 0.00 0.00 0.00
#> TCGA.Q1.A5R2.01 2 0.2280 0.775 0.00 0.88 0.00 0.00 0.12
#> TCGA.EK.A2IP.01 4 0.4227 0.961 0.00 0.42 0.00 0.58 0.00
#> TCGA.JW.A5VL.01 1 0.0609 0.971 0.98 0.00 0.00 0.02 0.00
#> TCGA.VS.A8EG.01 3 0.0000 0.938 0.00 0.00 1.00 0.00 0.00
#> TCGA.FU.A3TQ.01 4 0.3983 0.852 0.00 0.34 0.00 0.66 0.00
#> TCGA.EK.A2RB.01 1 0.2873 0.840 0.86 0.00 0.00 0.02 0.12
#> TCGA.C5.A2LX.01 4 0.4227 0.961 0.00 0.42 0.00 0.58 0.00
#> TCGA.C5.A1MN.01 5 0.4540 0.738 0.00 0.34 0.00 0.02 0.64
#> TCGA.EA.A1QT.01 1 0.0609 0.971 0.98 0.00 0.00 0.02 0.00
#> TCGA.VS.A9U7.01 3 0.0000 0.938 0.00 0.00 1.00 0.00 0.00
#> TCGA.VS.A9UY.01 1 0.0609 0.971 0.98 0.00 0.00 0.02 0.00
#> TCGA.C5.A1BL.01 5 0.4540 0.737 0.02 0.34 0.00 0.00 0.64
#> TCGA.VS.A957.01 3 0.0000 0.938 0.00 0.00 1.00 0.00 0.00
#> TCGA.ZJ.AAXI.01 2 0.0609 0.833 0.00 0.98 0.00 0.00 0.02
#> TCGA.DS.A1OA.01 4 0.4227 0.961 0.00 0.42 0.00 0.58 0.00
#> TCGA.VS.A950.01 1 0.0000 0.970 1.00 0.00 0.00 0.00 0.00
#> TCGA.VS.A9UI.01 1 0.0000 0.970 1.00 0.00 0.00 0.00 0.00
#> TCGA.C5.A1M5.01 2 0.1732 0.816 0.00 0.92 0.00 0.00 0.08
cbind(get_classes(res, k = 6), get_membership(res, k = 6))
#> class entropy silhouette p1 p2 p3 p4 p5 p6
#> TCGA.IR.A3LK.01 5 0.2512 0.581 0.06 0.00 0.06 0.00 0.88 0.00
#> TCGA.C5.A2LZ.01 2 0.1814 0.847 0.00 0.90 0.00 0.10 0.00 0.00
#> TCGA.EK.A2RC.01 4 0.1814 0.954 0.00 0.10 0.00 0.90 0.00 0.00
#> TCGA.EA.A3HQ.01 6 0.0000 0.908 0.00 0.00 0.00 0.00 0.00 1.00
#> TCGA.JW.AAVH.01 1 0.0000 0.925 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.IR.A3L7.01 6 0.4094 0.805 0.00 0.00 0.18 0.08 0.00 0.74
#> TCGA.VS.A8QC.01 2 0.2581 0.834 0.00 0.86 0.02 0.12 0.00 0.00
#> TCGA.WL.A834.01 6 0.4094 0.805 0.00 0.00 0.18 0.08 0.00 0.74
#> TCGA.VS.A8QF.01 2 0.1807 0.864 0.00 0.92 0.00 0.06 0.02 0.00
#> TCGA.EK.A2PG.01 5 0.2048 0.664 0.00 0.12 0.00 0.00 0.88 0.00
#> TCGA.FU.A3HY.01 5 0.5801 0.728 0.00 0.26 0.24 0.00 0.50 0.00
#> TCGA.LP.A5U3.01 6 0.0000 0.908 0.00 0.00 0.00 0.00 0.00 1.00
#> TCGA.EA.A6QX.01 2 0.4574 0.663 0.00 0.68 0.26 0.04 0.02 0.00
#> TCGA.EK.A2RA.01 1 0.1556 0.918 0.92 0.00 0.08 0.00 0.00 0.00
#> TCGA.Q1.A5R2.01 2 0.0937 0.836 0.00 0.96 0.00 0.00 0.04 0.00
#> TCGA.EK.A2IP.01 4 0.2350 0.951 0.00 0.10 0.02 0.88 0.00 0.00
#> TCGA.JW.A5VL.01 1 0.0000 0.925 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.VS.A8EG.01 6 0.0000 0.908 0.00 0.00 0.00 0.00 0.00 1.00
#> TCGA.FU.A3TQ.01 4 0.0547 0.886 0.00 0.02 0.00 0.98 0.00 0.00
#> TCGA.EK.A2RB.01 1 0.4002 0.627 0.66 0.00 0.32 0.00 0.02 0.00
#> TCGA.C5.A2LX.01 4 0.2260 0.938 0.00 0.14 0.00 0.86 0.00 0.00
#> TCGA.C5.A1MN.01 5 0.6023 0.703 0.00 0.26 0.32 0.00 0.42 0.00
#> TCGA.EA.A1QT.01 1 0.0000 0.925 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.VS.A9U7.01 6 0.2728 0.852 0.00 0.00 0.10 0.00 0.04 0.86
#> TCGA.VS.A9UY.01 1 0.0000 0.925 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.C5.A1BL.01 5 0.5867 0.730 0.00 0.24 0.28 0.00 0.48 0.00
#> TCGA.VS.A957.01 6 0.0000 0.908 0.00 0.00 0.00 0.00 0.00 1.00
#> TCGA.ZJ.AAXI.01 2 0.1092 0.864 0.00 0.96 0.02 0.02 0.00 0.00
#> TCGA.DS.A1OA.01 4 0.2048 0.952 0.00 0.12 0.00 0.88 0.00 0.00
#> TCGA.VS.A950.01 1 0.1556 0.918 0.92 0.00 0.08 0.00 0.00 0.00
#> TCGA.VS.A9UI.01 1 0.1556 0.918 0.92 0.00 0.08 0.00 0.00 0.00
#> TCGA.C5.A1M5.01 2 0.0937 0.836 0.00 0.96 0.00 0.00 0.04 0.00
cbind(get_classes(res, k = 7), get_membership(res, k = 7))
#> class entropy silhouette p1 p2 p3 p4 p5 p6 p7
#> TCGA.IR.A3LK.01 3 0.375 0.000 0.02 0.00 0.64 0.00 0.34 0.00 0.00
#> TCGA.C5.A2LZ.01 2 0.275 0.826 0.00 0.82 0.00 0.16 0.02 0.00 0.00
#> TCGA.EK.A2RC.01 4 0.117 0.894 0.00 0.06 0.00 0.94 0.00 0.00 0.00
#> TCGA.EA.A3HQ.01 6 0.000 0.807 0.00 0.00 0.00 0.00 0.00 1.00 0.00
#> TCGA.JW.AAVH.01 1 0.000 0.870 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.IR.A3L7.01 6 0.356 0.552 0.00 0.00 0.00 0.00 0.00 0.50 0.50
#> TCGA.VS.A8QC.01 2 0.242 0.813 0.00 0.82 0.00 0.18 0.00 0.00 0.00
#> TCGA.WL.A834.01 6 0.356 0.552 0.00 0.00 0.00 0.00 0.00 0.50 0.50
#> TCGA.VS.A8QF.01 2 0.470 0.800 0.00 0.70 0.00 0.16 0.08 0.00 0.06
#> TCGA.EK.A2PG.01 5 0.441 -0.504 0.00 0.02 0.44 0.00 0.52 0.00 0.02
#> TCGA.FU.A3HY.01 5 0.117 0.658 0.00 0.06 0.00 0.00 0.94 0.00 0.00
#> TCGA.LP.A5U3.01 6 0.000 0.807 0.00 0.00 0.00 0.00 0.00 1.00 0.00
#> TCGA.EA.A6QX.01 2 0.388 0.582 0.00 0.78 0.04 0.02 0.02 0.00 0.14
#> TCGA.EK.A2RA.01 1 0.251 0.856 0.86 0.00 0.04 0.00 0.00 0.00 0.10
#> TCGA.Q1.A5R2.01 2 0.377 0.782 0.00 0.74 0.00 0.08 0.18 0.00 0.00
#> TCGA.EK.A2IP.01 4 0.277 0.854 0.00 0.04 0.08 0.86 0.00 0.00 0.02
#> TCGA.JW.A5VL.01 1 0.000 0.870 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.VS.A8EG.01 6 0.000 0.807 0.00 0.00 0.00 0.00 0.00 1.00 0.00
#> TCGA.FU.A3TQ.01 4 0.291 0.719 0.00 0.02 0.00 0.80 0.00 0.00 0.18
#> TCGA.EK.A2RB.01 1 0.634 0.358 0.46 0.00 0.04 0.02 0.30 0.00 0.18
#> TCGA.C5.A2LX.01 4 0.228 0.864 0.00 0.08 0.00 0.88 0.00 0.00 0.04
#> TCGA.C5.A1MN.01 5 0.256 0.625 0.00 0.04 0.04 0.00 0.88 0.00 0.04
#> TCGA.EA.A1QT.01 1 0.000 0.870 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.VS.A9U7.01 6 0.385 0.703 0.00 0.00 0.16 0.02 0.00 0.76 0.06
#> TCGA.VS.A9UY.01 1 0.000 0.870 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.C5.A1BL.01 5 0.251 0.634 0.00 0.06 0.02 0.00 0.88 0.00 0.04
#> TCGA.VS.A957.01 6 0.000 0.807 0.00 0.00 0.00 0.00 0.00 1.00 0.00
#> TCGA.ZJ.AAXI.01 2 0.272 0.838 0.00 0.84 0.00 0.12 0.04 0.00 0.00
#> TCGA.DS.A1OA.01 4 0.117 0.894 0.00 0.06 0.00 0.94 0.00 0.00 0.00
#> TCGA.VS.A950.01 1 0.251 0.856 0.86 0.00 0.04 0.00 0.00 0.00 0.10
#> TCGA.VS.A9UI.01 1 0.251 0.856 0.86 0.00 0.04 0.00 0.00 0.00 0.10
#> TCGA.C5.A1M5.01 2 0.470 0.771 0.00 0.70 0.00 0.08 0.16 0.00 0.06
cbind(get_classes(res, k = 8), get_membership(res, k = 8))
#> class entropy silhouette p1 p2 p3 p4 p5 p6 p7 p8
#> TCGA.IR.A3LK.01 3 0.3404 0.6609 0.04 0.00 0.72 0.00 0.00 0.00 0.00 0.24
#> TCGA.C5.A2LZ.01 2 0.0941 0.8193 0.00 0.96 0.00 0.02 0.00 0.00 0.00 0.02
#> TCGA.EK.A2RC.01 4 0.1341 0.8427 0.00 0.08 0.00 0.92 0.00 0.00 0.00 0.00
#> TCGA.EA.A3HQ.01 6 0.0000 0.8489 0.00 0.00 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.JW.AAVH.01 1 0.0471 0.8862 0.98 0.00 0.00 0.00 0.00 0.00 0.02 0.00
#> TCGA.IR.A3L7.01 7 0.3193 1.0000 0.00 0.00 0.00 0.00 0.00 0.38 0.62 0.00
#> TCGA.VS.A8QC.01 2 0.0941 0.8144 0.00 0.96 0.02 0.02 0.00 0.00 0.00 0.00
#> TCGA.WL.A834.01 7 0.3193 1.0000 0.00 0.00 0.00 0.00 0.00 0.38 0.62 0.00
#> TCGA.VS.A8QF.01 2 0.3337 0.7175 0.00 0.78 0.00 0.02 0.16 0.00 0.00 0.04
#> TCGA.EK.A2PG.01 3 0.4955 0.6158 0.00 0.08 0.54 0.00 0.04 0.00 0.00 0.34
#> TCGA.FU.A3HY.01 8 0.2114 0.5207 0.00 0.16 0.00 0.00 0.00 0.00 0.00 0.84
#> TCGA.LP.A5U3.01 6 0.0000 0.8489 0.00 0.00 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.EA.A6QX.01 2 0.5666 0.4854 0.00 0.60 0.16 0.02 0.04 0.00 0.16 0.02
#> TCGA.EK.A2RA.01 1 0.3270 0.8561 0.80 0.00 0.00 0.00 0.12 0.00 0.06 0.02
#> TCGA.Q1.A5R2.01 2 0.0808 0.8093 0.00 0.96 0.00 0.00 0.00 0.00 0.00 0.04
#> TCGA.EK.A2IP.01 4 0.5673 0.6771 0.00 0.06 0.06 0.66 0.10 0.00 0.06 0.06
#> TCGA.JW.A5VL.01 1 0.0000 0.8914 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.VS.A8EG.01 6 0.0000 0.8489 0.00 0.00 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.FU.A3TQ.01 4 0.3073 0.7697 0.00 0.00 0.00 0.80 0.10 0.00 0.10 0.00
#> TCGA.EK.A2RB.01 8 0.5658 0.0353 0.32 0.00 0.00 0.04 0.20 0.00 0.00 0.44
#> TCGA.C5.A2LX.01 4 0.3970 0.7736 0.00 0.08 0.00 0.72 0.18 0.00 0.02 0.00
#> TCGA.C5.A1MN.01 8 0.4069 0.4448 0.00 0.18 0.00 0.00 0.14 0.00 0.00 0.68
#> TCGA.EA.A1QT.01 1 0.0471 0.8862 0.98 0.00 0.00 0.00 0.00 0.00 0.02 0.00
#> TCGA.VS.A9U7.01 6 0.5040 0.2973 0.00 0.00 0.06 0.00 0.24 0.60 0.10 0.00
#> TCGA.VS.A9UY.01 1 0.0000 0.8914 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.C5.A1BL.01 8 0.2404 0.5219 0.00 0.14 0.00 0.00 0.02 0.00 0.00 0.84
#> TCGA.VS.A957.01 6 0.0471 0.8371 0.00 0.00 0.00 0.00 0.00 0.98 0.00 0.02
#> TCGA.ZJ.AAXI.01 2 0.0471 0.8190 0.00 0.98 0.02 0.00 0.00 0.00 0.00 0.00
#> TCGA.DS.A1OA.01 4 0.1341 0.8427 0.00 0.08 0.00 0.92 0.00 0.00 0.00 0.00
#> TCGA.VS.A950.01 1 0.3270 0.8561 0.80 0.00 0.00 0.00 0.12 0.00 0.06 0.02
#> TCGA.VS.A9UI.01 1 0.3270 0.8561 0.80 0.00 0.00 0.00 0.12 0.00 0.06 0.02
#> TCGA.C5.A1M5.01 2 0.3589 0.6901 0.00 0.74 0.00 0.00 0.16 0.00 0.00 0.10
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)
consensus_heatmap(res, k = 7)
consensus_heatmap(res, k = 8)
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)
membership_heatmap(res, k = 7)
membership_heatmap(res, k = 8)
As soon as the classes for columns are determined, the signatures that are significantly different between subgroups can be looked for. Following are the heatmaps for signatures.
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)
get_signatures(res, k = 7)
get_signatures(res, k = 8)
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 (which is done by automatically selecting number of clusters).If there are too many signatures, top_signatures = ... can be set to only show the
signatures with the highest FDRs:
# code only for demonstration
# e.g. to show the top 500 most significant rows
tb = get_signature(res, k = ..., top_signatures = 500)
If the signatures are defined as these which are uniquely high in current group, diff_method argument
can be set to "uniquely_high_in_one_group":
# code only for demonstration
tb = get_signature(res, k = ..., diff_method = "uniquely_high_in_one_group")
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")
dimension_reduction(res, k = 7, method = "UMAP")
dimension_reduction(res, k = 8, method = "UMAP")
Following heatmap shows how subgroups are split when increasing k:
collect_classes(res)
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.
Parent node: Node0222. Child nodes: Node021111-leaf , Node021112-leaf , Node021113-leaf , Node021114-leaf , Node022211-leaf , Node022212-leaf , Node022213-leaf , Node031121-leaf , Node031122-leaf .
The object with results only for a single top-value method and a single partitioning method can be extracted as:
res = res_rh["02221"]
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, 7, 8.
#> On a matrix with 30000 rows and 16 columns.
#> Top rows (1000) are extracted by 'ATC' method.
#> Subgroups are detected by 'skmeans' method.
#> Performed in total 350 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_partitions"
#> [7] "compare_signatures" "consensus_heatmap" "dimension_reduction"
#> [10] "functional_enrichment" "get_anno_col" "get_anno"
#> [13] "get_classes" "get_consensus" "get_matrix"
#> [16] "get_membership" "get_param" "get_signatures"
#> [19] "get_stats" "is_best_k" "is_stable_k"
#> [22] "membership_heatmap" "ncol" "nrow"
#> [25] "plot_ecdf" "predict_classes" "rownames"
#> [28] "select_partition_number" "show" "suggest_best_k"
#> [31] "test_to_known_factors" "top_rows_heatmap"
collect_plots() function collects all the plots made from res for all k (number of subgroups)
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, higher 1-PAC score, higher mean silhouette score or higher
concordance corresponds to better partition. Rand index and Jaccard index
measure how similar the current partition is compared to partition with k-1.
If they are too similar, we won't accept k is better than k-1.
select_partition_number(res)
The numeric values for all these statistics can be obtained by get_stats().
get_stats(res)
#> k 1-PAC mean_silhouette concordance area_increased Rand Jaccard
#> 2 2 1.000 0.991 0.993 0.2376 0.767 0.767
#> 3 3 0.892 0.982 0.991 0.8699 0.800 0.739
#> 4 4 0.867 0.874 0.968 0.2462 0.908 0.838
#> 5 5 0.717 0.687 0.902 0.1450 0.917 0.825
#> 6 6 0.683 0.589 0.881 0.1169 0.925 0.809
#> 7 7 0.692 0.548 0.901 0.0428 0.992 0.974
#> 8 8 0.767 0.482 0.920 0.0725 0.933 0.784
suggest_best_k() suggests the best \(k\) based on these statistics. The rules are as follows:
suggest_best_k(res)
#> [1] 2
Following is 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 subgroup
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
#> TCGA.IR.A3LK.01 2 0.000 0.994 0.00 1.00
#> TCGA.JW.AAVH.01 2 0.141 0.980 0.02 0.98
#> TCGA.EK.A2PG.01 2 0.000 0.994 0.00 1.00
#> TCGA.FU.A3HY.01 2 0.000 0.994 0.00 1.00
#> TCGA.EK.A2RA.01 2 0.000 0.994 0.00 1.00
#> TCGA.Q1.A5R2.01 2 0.000 0.994 0.00 1.00
#> TCGA.JW.A5VL.01 1 0.141 1.000 0.98 0.02
#> TCGA.EK.A2RB.01 2 0.000 0.994 0.00 1.00
#> TCGA.C5.A1MN.01 2 0.000 0.994 0.00 1.00
#> TCGA.EA.A1QT.01 2 0.141 0.980 0.02 0.98
#> TCGA.VS.A9UY.01 1 0.141 1.000 0.98 0.02
#> TCGA.C5.A1BL.01 2 0.000 0.994 0.00 1.00
#> TCGA.ZJ.AAXI.01 2 0.141 0.979 0.02 0.98
#> TCGA.VS.A950.01 2 0.000 0.994 0.00 1.00
#> TCGA.VS.A9UI.01 2 0.141 0.979 0.02 0.98
#> TCGA.C5.A1M5.01 2 0.000 0.994 0.00 1.00
cbind(get_classes(res, k = 3), get_membership(res, k = 3))
#> class entropy silhouette p1 p2 p3
#> TCGA.IR.A3LK.01 2 0.0000 0.987 0.00 1.00 0
#> TCGA.JW.AAVH.01 3 0.0000 1.000 0.00 0.00 1
#> TCGA.EK.A2PG.01 2 0.0000 0.987 0.00 1.00 0
#> TCGA.FU.A3HY.01 2 0.0000 0.987 0.00 1.00 0
#> TCGA.EK.A2RA.01 2 0.0000 0.987 0.00 1.00 0
#> TCGA.Q1.A5R2.01 2 0.0000 0.987 0.00 1.00 0
#> TCGA.JW.A5VL.01 1 0.0000 1.000 1.00 0.00 0
#> TCGA.EK.A2RB.01 2 0.0000 0.987 0.00 1.00 0
#> TCGA.C5.A1MN.01 2 0.0000 0.987 0.00 1.00 0
#> TCGA.EA.A1QT.01 3 0.0000 1.000 0.00 0.00 1
#> TCGA.VS.A9UY.01 1 0.0000 1.000 1.00 0.00 0
#> TCGA.C5.A1BL.01 2 0.0000 0.987 0.00 1.00 0
#> TCGA.ZJ.AAXI.01 2 0.0892 0.971 0.02 0.98 0
#> TCGA.VS.A950.01 2 0.0000 0.987 0.00 1.00 0
#> TCGA.VS.A9UI.01 2 0.3340 0.865 0.12 0.88 0
#> TCGA.C5.A1M5.01 2 0.0000 0.987 0.00 1.00 0
cbind(get_classes(res, k = 4), get_membership(res, k = 4))
#> class entropy silhouette p1 p2 p3 p4
#> TCGA.IR.A3LK.01 2 0.2011 0.899 0.00 0.92 0 0.08
#> TCGA.JW.AAVH.01 3 0.0000 1.000 0.00 0.00 1 0.00
#> TCGA.EK.A2PG.01 2 0.0707 0.941 0.00 0.98 0 0.02
#> TCGA.FU.A3HY.01 2 0.0000 0.952 0.00 1.00 0 0.00
#> TCGA.EK.A2RA.01 2 0.1637 0.914 0.00 0.94 0 0.06
#> TCGA.Q1.A5R2.01 2 0.0000 0.952 0.00 1.00 0 0.00
#> TCGA.JW.A5VL.01 1 0.0000 0.984 1.00 0.00 0 0.00
#> TCGA.EK.A2RB.01 2 0.0000 0.952 0.00 1.00 0 0.00
#> TCGA.C5.A1MN.01 2 0.0000 0.952 0.00 1.00 0 0.00
#> TCGA.EA.A1QT.01 3 0.0000 1.000 0.00 0.00 1 0.00
#> TCGA.VS.A9UY.01 1 0.0707 0.984 0.98 0.00 0 0.02
#> TCGA.C5.A1BL.01 2 0.0000 0.952 0.00 1.00 0 0.00
#> TCGA.ZJ.AAXI.01 4 0.1211 0.000 0.00 0.04 0 0.96
#> TCGA.VS.A950.01 2 0.0000 0.952 0.00 1.00 0 0.00
#> TCGA.VS.A9UI.01 2 0.5902 0.596 0.16 0.70 0 0.14
#> TCGA.C5.A1M5.01 2 0.0000 0.952 0.00 1.00 0 0.00
cbind(get_classes(res, k = 5), get_membership(res, k = 5))
#> class entropy silhouette p1 p2 p3 p4 p5
#> TCGA.IR.A3LK.01 2 0.5258 0.386 0.00 0.68 0 0.18 0.14
#> TCGA.JW.AAVH.01 3 0.0000 1.000 0.00 0.00 1 0.00 0.00
#> TCGA.EK.A2PG.01 2 0.1732 0.824 0.00 0.92 0 0.00 0.08
#> TCGA.FU.A3HY.01 2 0.0000 0.877 0.00 1.00 0 0.00 0.00
#> TCGA.EK.A2RA.01 2 0.3561 0.551 0.00 0.74 0 0.00 0.26
#> TCGA.Q1.A5R2.01 2 0.0000 0.877 0.00 1.00 0 0.00 0.00
#> TCGA.JW.A5VL.01 1 0.0000 0.573 1.00 0.00 0 0.00 0.00
#> TCGA.EK.A2RB.01 2 0.0000 0.877 0.00 1.00 0 0.00 0.00
#> TCGA.C5.A1MN.01 2 0.0000 0.877 0.00 1.00 0 0.00 0.00
#> TCGA.EA.A1QT.01 3 0.0000 1.000 0.00 0.00 1 0.00 0.00
#> TCGA.VS.A9UY.01 1 0.4767 0.577 0.56 0.00 0 0.02 0.42
#> TCGA.C5.A1BL.01 2 0.0609 0.868 0.00 0.98 0 0.00 0.02
#> TCGA.ZJ.AAXI.01 4 0.1216 0.000 0.00 0.02 0 0.96 0.02
#> TCGA.VS.A950.01 2 0.1043 0.860 0.00 0.96 0 0.00 0.04
#> TCGA.VS.A9UI.01 5 0.4360 0.000 0.02 0.30 0 0.00 0.68
#> TCGA.C5.A1M5.01 2 0.1410 0.847 0.00 0.94 0 0.00 0.06
cbind(get_classes(res, k = 6), get_membership(res, k = 6))
#> class entropy silhouette p1 p2 p3 p4 p5 p6
#> TCGA.IR.A3LK.01 6 0.5144 0.000 0.00 0.34 0.00 0.10 0.00 0.56
#> TCGA.JW.AAVH.01 3 0.0547 0.984 0.00 0.00 0.98 0.00 0.00 0.02
#> TCGA.EK.A2PG.01 2 0.2581 0.729 0.00 0.86 0.00 0.00 0.02 0.12
#> TCGA.FU.A3HY.01 2 0.0937 0.821 0.00 0.96 0.00 0.00 0.00 0.04
#> TCGA.EK.A2RA.01 2 0.6001 0.184 0.00 0.58 0.00 0.04 0.20 0.18
#> TCGA.Q1.A5R2.01 2 0.0000 0.838 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.JW.A5VL.01 1 0.0000 0.459 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.EK.A2RB.01 2 0.0547 0.838 0.00 0.98 0.00 0.00 0.00 0.02
#> TCGA.C5.A1MN.01 2 0.0547 0.834 0.00 0.98 0.00 0.00 0.00 0.02
#> TCGA.EA.A1QT.01 3 0.0000 0.984 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.VS.A9UY.01 1 0.5888 0.367 0.46 0.00 0.00 0.00 0.22 0.32
#> TCGA.C5.A1BL.01 2 0.0547 0.838 0.00 0.98 0.00 0.00 0.00 0.02
#> TCGA.ZJ.AAXI.01 4 0.0000 0.000 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.VS.A950.01 2 0.1807 0.806 0.00 0.92 0.00 0.00 0.06 0.02
#> TCGA.VS.A9UI.01 5 0.0547 0.000 0.00 0.02 0.00 0.00 0.98 0.00
#> TCGA.C5.A1M5.01 2 0.3045 0.749 0.00 0.86 0.00 0.02 0.06 0.06
cbind(get_classes(res, k = 7), get_membership(res, k = 7))
#> class entropy silhouette p1 p2 p3 p4 p5 p6 p7
#> TCGA.IR.A3LK.01 6 0.362 0.000 0.00 0.16 0.0 0.08 0.00 0.76 0.00
#> TCGA.JW.AAVH.01 3 0.000 0.916 0.00 0.00 1.0 0.00 0.00 0.00 0.00
#> TCGA.EK.A2PG.01 2 0.334 0.764 0.00 0.82 0.0 0.00 0.04 0.10 0.04
#> TCGA.FU.A3HY.01 2 0.117 0.828 0.00 0.94 0.0 0.00 0.00 0.06 0.00
#> TCGA.EK.A2RA.01 2 0.598 0.380 0.00 0.52 0.0 0.00 0.22 0.20 0.06
#> TCGA.Q1.A5R2.01 2 0.000 0.851 0.00 1.00 0.0 0.00 0.00 0.00 0.00
#> TCGA.JW.A5VL.01 1 0.000 0.000 1.00 0.00 0.0 0.00 0.00 0.00 0.00
#> TCGA.EK.A2RB.01 2 0.000 0.851 0.00 1.00 0.0 0.00 0.00 0.00 0.00
#> TCGA.C5.A1MN.01 2 0.000 0.851 0.00 1.00 0.0 0.00 0.00 0.00 0.00
#> TCGA.EA.A1QT.01 3 0.216 0.916 0.00 0.00 0.9 0.00 0.02 0.06 0.02
#> TCGA.VS.A9UY.01 7 0.143 0.000 0.08 0.00 0.0 0.00 0.00 0.00 0.92
#> TCGA.C5.A1BL.01 2 0.151 0.846 0.00 0.94 0.0 0.00 0.02 0.02 0.02
#> TCGA.ZJ.AAXI.01 4 0.000 0.000 0.00 0.00 0.0 1.00 0.00 0.00 0.00
#> TCGA.VS.A950.01 2 0.306 0.771 0.00 0.84 0.0 0.00 0.06 0.08 0.02
#> TCGA.VS.A9UI.01 5 0.117 0.000 0.00 0.00 0.0 0.00 0.94 0.00 0.06
#> TCGA.C5.A1M5.01 2 0.300 0.793 0.00 0.84 0.0 0.00 0.10 0.02 0.04
cbind(get_classes(res, k = 8), get_membership(res, k = 8))
#> class entropy silhouette p1 p2 p3 p4 p5 p6 p7 p8
#> TCGA.IR.A3LK.01 6 0.0808 0.000 0 0.04 0.00 0 0.00 0.96 0 0.00
#> TCGA.JW.AAVH.01 3 0.0000 0.898 0 0.00 1.00 0 0.00 0.00 0 0.00
#> TCGA.EK.A2PG.01 2 0.2856 0.649 0 0.78 0.00 0 0.02 0.00 0 0.20
#> TCGA.FU.A3HY.01 2 0.0808 0.830 0 0.96 0.00 0 0.00 0.00 0 0.04
#> TCGA.EK.A2RA.01 8 0.3178 0.000 0 0.14 0.00 0 0.04 0.02 0 0.80
#> TCGA.Q1.A5R2.01 2 0.0000 0.843 0 1.00 0.00 0 0.00 0.00 0 0.00
#> TCGA.JW.A5VL.01 1 0.0000 0.000 1 0.00 0.00 0 0.00 0.00 0 0.00
#> TCGA.EK.A2RB.01 2 0.0000 0.843 0 1.00 0.00 0 0.00 0.00 0 0.00
#> TCGA.C5.A1MN.01 2 0.0000 0.843 0 1.00 0.00 0 0.00 0.00 0 0.00
#> TCGA.EA.A1QT.01 3 0.2132 0.898 0 0.00 0.88 0 0.00 0.04 0 0.08
#> TCGA.VS.A9UY.01 7 0.0000 0.000 0 0.00 0.00 0 0.00 0.00 1 0.00
#> TCGA.C5.A1BL.01 2 0.1091 0.828 0 0.94 0.00 0 0.00 0.00 0 0.06
#> TCGA.ZJ.AAXI.01 4 0.0000 0.000 0 0.00 0.00 1 0.00 0.00 0 0.00
#> TCGA.VS.A950.01 2 0.3660 0.519 0 0.70 0.00 0 0.06 0.00 0 0.24
#> TCGA.VS.A9UI.01 5 0.0000 0.000 0 0.00 0.00 0 1.00 0.00 0 0.00
#> TCGA.C5.A1M5.01 2 0.3991 0.571 0 0.70 0.00 0 0.02 0.06 0 0.22
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)
consensus_heatmap(res, k = 7)
consensus_heatmap(res, k = 8)
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)
membership_heatmap(res, k = 7)
membership_heatmap(res, k = 8)
As soon as the classes for columns are determined, the signatures that are significantly different between subgroups can be looked for. Following are the heatmaps for signatures.
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)
get_signatures(res, k = 7)
get_signatures(res, k = 8)
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 (which is done by automatically selecting number of clusters).If there are too many signatures, top_signatures = ... can be set to only show the
signatures with the highest FDRs:
# code only for demonstration
# e.g. to show the top 500 most significant rows
tb = get_signature(res, k = ..., top_signatures = 500)
If the signatures are defined as these which are uniquely high in current group, diff_method argument
can be set to "uniquely_high_in_one_group":
# code only for demonstration
tb = get_signature(res, k = ..., diff_method = "uniquely_high_in_one_group")
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")
dimension_reduction(res, k = 7, method = "UMAP")
dimension_reduction(res, k = 8, method = "UMAP")
Following heatmap shows how subgroups are split when increasing k:
collect_classes(res)
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.
Parent node: Node02. Child nodes: Node0111 , Node0112-leaf , Node0113 , Node0121 , Node0122-leaf , Node0123-leaf , Node0131 , Node0132-leaf , Node0133-leaf , Node0134-leaf , Node0211 , Node0212-leaf , Node0221-leaf , Node0222 , Node0231-leaf , Node0232-leaf , Node0233-leaf , Node0311 , Node0312-leaf , Node0313-leaf .
The object with results only for a single top-value method and a single partitioning method can be extracted as:
res = res_rh["023"]
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, 7, 8.
#> On a matrix with 30000 rows and 28 columns.
#> Top rows (1000) are extracted by 'ATC' method.
#> Subgroups are detected by 'skmeans' method.
#> Performed in total 350 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_partitions"
#> [7] "compare_signatures" "consensus_heatmap" "dimension_reduction"
#> [10] "functional_enrichment" "get_anno_col" "get_anno"
#> [13] "get_classes" "get_consensus" "get_matrix"
#> [16] "get_membership" "get_param" "get_signatures"
#> [19] "get_stats" "is_best_k" "is_stable_k"
#> [22] "membership_heatmap" "ncol" "nrow"
#> [25] "plot_ecdf" "predict_classes" "rownames"
#> [28] "select_partition_number" "show" "suggest_best_k"
#> [31] "test_to_known_factors" "top_rows_heatmap"
collect_plots() function collects all the plots made from res for all k (number of subgroups)
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, higher 1-PAC score, higher mean silhouette score or higher
concordance corresponds to better partition. Rand index and Jaccard index
measure how similar the current partition is compared to partition with k-1.
If they are too similar, we won't accept k is better than k-1.
select_partition_number(res)
The numeric values for all these statistics can be obtained by get_stats().
get_stats(res)
#> k 1-PAC mean_silhouette concordance area_increased Rand Jaccard
#> 2 2 1.000 1.000 1.000 0.4767 0.524 0.524
#> 3 3 1.000 0.997 0.999 0.3828 0.791 0.611
#> 4 4 0.809 0.864 0.880 0.1003 0.963 0.891
#> 5 5 0.803 0.761 0.886 0.0887 0.889 0.635
#> 6 6 0.889 0.859 0.919 0.0443 0.910 0.605
#> 7 7 0.858 0.828 0.892 0.0204 1.000 1.000
#> 8 8 0.818 0.706 0.859 0.0147 0.984 0.909
suggest_best_k() suggests the best \(k\) based on these statistics. The rules are as follows:
suggest_best_k(res)
#> [1] 3
#> attr(,"optional")
#> [1] 2
There is also optional best \(k\) = 2 that is worth to check.
Following is 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 subgroup
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
#> TCGA.GH.A9DA.01 1 0 1 1 0
#> TCGA.ZJ.A8QQ.01 1 0 1 1 0
#> TCGA.EK.A3GJ.01 2 0 1 0 1
#> TCGA.C5.A902.01 2 0 1 0 1
#> TCGA.C5.A3HD.01 2 0 1 0 1
#> TCGA.IR.A3LH.01 1 0 1 1 0
#> TCGA.IR.A3LL.01 2 0 1 0 1
#> TCGA.MY.A5BF.01 2 0 1 0 1
#> TCGA.VS.A8EL.01 1 0 1 1 0
#> TCGA.UC.A7PF.01 2 0 1 0 1
#> TCGA.VS.A8Q9.01 1 0 1 1 0
#> TCGA.C5.A8XH.01 2 0 1 0 1
#> TCGA.VS.A8EI.01 1 0 1 1 0
#> TCGA.C5.A8XI.01 2 0 1 0 1
#> TCGA.DS.A7WI.01 1 0 1 1 0
#> TCGA.EA.A3QD.01 2 0 1 0 1
#> TCGA.C5.A7X5.01 2 0 1 0 1
#> TCGA.EK.A2H0.01 1 0 1 1 0
#> TCGA.FU.A3NI.01 2 0 1 0 1
#> TCGA.EX.A69M.01 2 0 1 0 1
#> TCGA.VS.A9UD.01 2 0 1 0 1
#> TCGA.EA.A78R.01 2 0 1 0 1
#> TCGA.DS.A1OC.01 2 0 1 0 1
#> TCGA.ZJ.AAXJ.01 2 0 1 0 1
#> TCGA.EA.A43B.01 1 0 1 1 0
#> TCGA.C5.A1MQ.01 1 0 1 1 0
#> TCGA.VS.A9UU.01 2 0 1 0 1
#> TCGA.C5.A7CK.01 2 0 1 0 1
cbind(get_classes(res, k = 3), get_membership(res, k = 3))
#> class entropy silhouette p1 p2 p3
#> TCGA.GH.A9DA.01 1 0.0000 1.000 1.00 0.00 0.00
#> TCGA.ZJ.A8QQ.01 1 0.0000 1.000 1.00 0.00 0.00
#> TCGA.EK.A3GJ.01 3 0.0000 0.996 0.00 0.00 1.00
#> TCGA.C5.A902.01 2 0.0892 0.980 0.00 0.98 0.02
#> TCGA.C5.A3HD.01 3 0.0000 0.996 0.00 0.00 1.00
#> TCGA.IR.A3LH.01 1 0.0000 1.000 1.00 0.00 0.00
#> TCGA.IR.A3LL.01 2 0.0000 0.998 0.00 1.00 0.00
#> TCGA.MY.A5BF.01 2 0.0000 0.998 0.00 1.00 0.00
#> TCGA.VS.A8EL.01 1 0.0000 1.000 1.00 0.00 0.00
#> TCGA.UC.A7PF.01 2 0.0000 0.998 0.00 1.00 0.00
#> TCGA.VS.A8Q9.01 1 0.0000 1.000 1.00 0.00 0.00
#> TCGA.C5.A8XH.01 3 0.0000 0.996 0.00 0.00 1.00
#> TCGA.VS.A8EI.01 1 0.0000 1.000 1.00 0.00 0.00
#> TCGA.C5.A8XI.01 2 0.0000 0.998 0.00 1.00 0.00
#> TCGA.DS.A7WI.01 3 0.0892 0.979 0.02 0.00 0.98
#> TCGA.EA.A3QD.01 2 0.0000 0.998 0.00 1.00 0.00
#> TCGA.C5.A7X5.01 3 0.0000 0.996 0.00 0.00 1.00
#> TCGA.EK.A2H0.01 1 0.0000 1.000 1.00 0.00 0.00
#> TCGA.FU.A3NI.01 2 0.0000 0.998 0.00 1.00 0.00
#> TCGA.EX.A69M.01 2 0.0000 0.998 0.00 1.00 0.00
#> TCGA.VS.A9UD.01 2 0.0000 0.998 0.00 1.00 0.00
#> TCGA.EA.A78R.01 2 0.0000 0.998 0.00 1.00 0.00
#> TCGA.DS.A1OC.01 3 0.0000 0.996 0.00 0.00 1.00
#> TCGA.ZJ.AAXJ.01 2 0.0000 0.998 0.00 1.00 0.00
#> TCGA.EA.A43B.01 1 0.0000 1.000 1.00 0.00 0.00
#> TCGA.C5.A1MQ.01 1 0.0000 1.000 1.00 0.00 0.00
#> TCGA.VS.A9UU.01 2 0.0000 0.998 0.00 1.00 0.00
#> TCGA.C5.A7CK.01 2 0.0000 0.998 0.00 1.00 0.00
cbind(get_classes(res, k = 4), get_membership(res, k = 4))
#> class entropy silhouette p1 p2 p3 p4
#> TCGA.GH.A9DA.01 1 0.1637 0.912 0.94 0.00 0.00 0.06
#> TCGA.ZJ.A8QQ.01 4 0.4907 1.000 0.42 0.00 0.00 0.58
#> TCGA.EK.A3GJ.01 3 0.0000 0.943 0.00 0.00 1.00 0.00
#> TCGA.C5.A902.01 2 0.6976 0.513 0.00 0.58 0.24 0.18
#> TCGA.C5.A3HD.01 3 0.0000 0.943 0.00 0.00 1.00 0.00
#> TCGA.IR.A3LH.01 1 0.0000 0.979 1.00 0.00 0.00 0.00
#> TCGA.IR.A3LL.01 2 0.3610 0.794 0.00 0.80 0.00 0.20
#> TCGA.MY.A5BF.01 2 0.3400 0.775 0.00 0.82 0.00 0.18
#> TCGA.VS.A8EL.01 1 0.0000 0.979 1.00 0.00 0.00 0.00
#> TCGA.UC.A7PF.01 2 0.3610 0.794 0.00 0.80 0.00 0.20
#> TCGA.VS.A8Q9.01 1 0.0707 0.959 0.98 0.00 0.00 0.02
#> TCGA.C5.A8XH.01 3 0.0000 0.943 0.00 0.00 1.00 0.00
#> TCGA.VS.A8EI.01 1 0.0000 0.979 1.00 0.00 0.00 0.00
#> TCGA.C5.A8XI.01 2 0.2345 0.813 0.00 0.90 0.00 0.10
#> TCGA.DS.A7WI.01 3 0.4755 0.660 0.20 0.00 0.76 0.04
#> TCGA.EA.A3QD.01 2 0.3610 0.794 0.00 0.80 0.00 0.20
#> TCGA.C5.A7X5.01 3 0.0000 0.943 0.00 0.00 1.00 0.00
#> TCGA.EK.A2H0.01 4 0.4907 1.000 0.42 0.00 0.00 0.58
#> TCGA.FU.A3NI.01 2 0.5291 0.718 0.00 0.74 0.08 0.18
#> TCGA.EX.A69M.01 2 0.2345 0.813 0.00 0.90 0.00 0.10
#> TCGA.VS.A9UD.01 2 0.0000 0.823 0.00 1.00 0.00 0.00
#> TCGA.EA.A78R.01 2 0.3610 0.794 0.00 0.80 0.00 0.20
#> TCGA.DS.A1OC.01 3 0.0000 0.943 0.00 0.00 1.00 0.00
#> TCGA.ZJ.AAXJ.01 2 0.2345 0.813 0.00 0.90 0.00 0.10
#> TCGA.EA.A43B.01 1 0.0000 0.979 1.00 0.00 0.00 0.00
#> TCGA.C5.A1MQ.01 1 0.0000 0.979 1.00 0.00 0.00 0.00
#> TCGA.VS.A9UU.01 2 0.3610 0.794 0.00 0.80 0.00 0.20
#> TCGA.C5.A7CK.01 2 0.0707 0.823 0.00 0.98 0.00 0.02
cbind(get_classes(res, k = 5), get_membership(res, k = 5))
#> class entropy silhouette p1 p2 p3 p4 p5
#> TCGA.GH.A9DA.01 1 0.3697 0.785 0.82 0.00 0.00 0.1 0.08
#> TCGA.ZJ.A8QQ.01 4 0.2020 1.000 0.10 0.00 0.00 0.9 0.00
#> TCGA.EK.A3GJ.01 3 0.0000 0.932 0.00 0.00 1.00 0.0 0.00
#> TCGA.C5.A902.01 5 0.2732 0.649 0.00 0.00 0.16 0.0 0.84
#> TCGA.C5.A3HD.01 3 0.1410 0.901 0.00 0.00 0.94 0.0 0.06
#> TCGA.IR.A3LH.01 1 0.0000 0.958 1.00 0.00 0.00 0.0 0.00
#> TCGA.IR.A3LL.01 2 0.0000 0.766 0.00 1.00 0.00 0.0 0.00
#> TCGA.MY.A5BF.01 5 0.2732 0.741 0.00 0.16 0.00 0.0 0.84
#> TCGA.VS.A8EL.01 1 0.0609 0.948 0.98 0.02 0.00 0.0 0.00
#> TCGA.UC.A7PF.01 2 0.0000 0.766 0.00 1.00 0.00 0.0 0.00
#> TCGA.VS.A8Q9.01 1 0.0000 0.958 1.00 0.00 0.00 0.0 0.00
#> TCGA.C5.A8XH.01 3 0.0000 0.932 0.00 0.00 1.00 0.0 0.00
#> TCGA.VS.A8EI.01 1 0.0609 0.948 0.98 0.02 0.00 0.0 0.00
#> TCGA.C5.A8XI.01 5 0.3895 0.717 0.00 0.32 0.00 0.0 0.68
#> TCGA.DS.A7WI.01 3 0.5604 0.690 0.04 0.00 0.70 0.1 0.16
#> TCGA.EA.A3QD.01 2 0.0000 0.766 0.00 1.00 0.00 0.0 0.00
#> TCGA.C5.A7X5.01 3 0.0000 0.932 0.00 0.00 1.00 0.0 0.00
#> TCGA.EK.A2H0.01 4 0.2020 1.000 0.10 0.00 0.00 0.9 0.00
#> TCGA.FU.A3NI.01 5 0.3390 0.707 0.00 0.06 0.10 0.0 0.84
#> TCGA.EX.A69M.01 5 0.3895 0.717 0.00 0.32 0.00 0.0 0.68
#> TCGA.VS.A9UD.01 2 0.4307 -0.318 0.00 0.50 0.00 0.0 0.50
#> TCGA.EA.A78R.01 2 0.0000 0.766 0.00 1.00 0.00 0.0 0.00
#> TCGA.DS.A1OC.01 3 0.0000 0.932 0.00 0.00 1.00 0.0 0.00
#> TCGA.ZJ.AAXJ.01 5 0.3895 0.717 0.00 0.32 0.00 0.0 0.68
#> TCGA.EA.A43B.01 1 0.0000 0.958 1.00 0.00 0.00 0.0 0.00
#> TCGA.C5.A1MQ.01 1 0.0000 0.958 1.00 0.00 0.00 0.0 0.00
#> TCGA.VS.A9UU.01 2 0.0000 0.766 0.00 1.00 0.00 0.0 0.00
#> TCGA.C5.A7CK.01 2 0.4302 -0.281 0.00 0.52 0.00 0.0 0.48
cbind(get_classes(res, k = 6), get_membership(res, k = 6))
#> class entropy silhouette p1 p2 p3 p4 p5 p6
#> TCGA.GH.A9DA.01 6 0.3309 0.615 0.28 0.00 0.00 0 0.00 0.72
#> TCGA.ZJ.A8QQ.01 4 0.0000 1.000 0.00 0.00 0.00 1 0.00 0.00
#> TCGA.EK.A3GJ.01 3 0.0547 0.946 0.00 0.00 0.98 0 0.00 0.02
#> TCGA.C5.A902.01 5 0.1807 0.735 0.00 0.00 0.06 0 0.92 0.02
#> TCGA.C5.A3HD.01 3 0.2981 0.835 0.00 0.00 0.82 0 0.02 0.16
#> TCGA.IR.A3LH.01 1 0.0547 0.967 0.98 0.02 0.00 0 0.00 0.00
#> TCGA.IR.A3LL.01 2 0.0547 0.985 0.00 0.98 0.00 0 0.02 0.00
#> TCGA.MY.A5BF.01 5 0.1092 0.770 0.00 0.02 0.00 0 0.96 0.02
#> TCGA.VS.A8EL.01 1 0.0937 0.972 0.96 0.04 0.00 0 0.00 0.00
#> TCGA.UC.A7PF.01 2 0.0547 0.985 0.00 0.98 0.00 0 0.02 0.00
#> TCGA.VS.A8Q9.01 1 0.0937 0.941 0.96 0.00 0.00 0 0.00 0.04
#> TCGA.C5.A8XH.01 3 0.0547 0.946 0.00 0.00 0.98 0 0.00 0.02
#> TCGA.VS.A8EI.01 1 0.0937 0.972 0.96 0.04 0.00 0 0.00 0.00
#> TCGA.C5.A8XI.01 5 0.2581 0.804 0.00 0.12 0.00 0 0.86 0.02
#> TCGA.DS.A7WI.01 6 0.0937 0.597 0.00 0.00 0.04 0 0.00 0.96
#> TCGA.EA.A3QD.01 2 0.0547 0.985 0.00 0.98 0.00 0 0.02 0.00
#> TCGA.C5.A7X5.01 3 0.0937 0.946 0.00 0.00 0.96 0 0.00 0.04
#> TCGA.EK.A2H0.01 4 0.0000 1.000 0.00 0.00 0.00 1 0.00 0.00
#> TCGA.FU.A3NI.01 5 0.1480 0.752 0.00 0.00 0.04 0 0.94 0.02
#> TCGA.EX.A69M.01 5 0.2048 0.804 0.00 0.12 0.00 0 0.88 0.00
#> TCGA.VS.A9UD.01 5 0.4310 0.417 0.00 0.44 0.00 0 0.54 0.02
#> TCGA.EA.A78R.01 2 0.0000 0.977 0.00 1.00 0.00 0 0.00 0.00
#> TCGA.DS.A1OC.01 3 0.0000 0.942 0.00 0.00 1.00 0 0.00 0.00
#> TCGA.ZJ.AAXJ.01 5 0.2581 0.804 0.00 0.12 0.00 0 0.86 0.02
#> TCGA.EA.A43B.01 1 0.0000 0.958 1.00 0.00 0.00 0 0.00 0.00
#> TCGA.C5.A1MQ.01 1 0.0937 0.972 0.96 0.04 0.00 0 0.00 0.00
#> TCGA.VS.A9UU.01 2 0.0000 0.977 0.00 1.00 0.00 0 0.00 0.00
#> TCGA.C5.A7CK.01 5 0.4282 0.453 0.00 0.42 0.00 0 0.56 0.02
cbind(get_classes(res, k = 7), get_membership(res, k = 7))
#> class entropy silhouette p1 p2 p3 p4 p5 p6 p7
#> TCGA.GH.A9DA.01 6 0.4505 0.587 0.06 0.00 0.00 0 0.44 0.50 0.00
#> TCGA.ZJ.A8QQ.01 4 0.0000 1.000 0.00 0.00 0.00 1 0.00 0.00 0.00
#> TCGA.EK.A3GJ.01 3 0.0863 0.856 0.00 0.00 0.96 0 0.00 0.04 0.00
#> TCGA.C5.A902.01 7 0.2313 0.565 0.00 0.00 0.06 0 0.06 0.00 0.88
#> TCGA.C5.A3HD.01 3 0.4970 0.517 0.00 0.00 0.58 0 0.24 0.18 0.00
#> TCGA.IR.A3LH.01 1 0.0000 0.979 1.00 0.00 0.00 0 0.00 0.00 0.00
#> TCGA.IR.A3LL.01 2 0.0000 1.000 0.00 1.00 0.00 0 0.00 0.00 0.00
#> TCGA.MY.A5BF.01 7 0.0000 0.640 0.00 0.00 0.00 0 0.00 0.00 1.00
#> TCGA.VS.A8EL.01 1 0.0504 0.974 0.98 0.00 0.00 0 0.02 0.00 0.00
#> TCGA.UC.A7PF.01 2 0.0000 1.000 0.00 1.00 0.00 0 0.00 0.00 0.00
#> TCGA.VS.A8Q9.01 1 0.1363 0.932 0.94 0.00 0.00 0 0.04 0.02 0.00
#> TCGA.C5.A8XH.01 3 0.0504 0.857 0.00 0.00 0.98 0 0.00 0.00 0.02
#> TCGA.VS.A8EI.01 1 0.0504 0.974 0.98 0.00 0.00 0 0.02 0.00 0.00
#> TCGA.C5.A8XI.01 7 0.4348 0.750 0.00 0.14 0.00 0 0.18 0.00 0.68
#> TCGA.DS.A7WI.01 6 0.0000 0.588 0.00 0.00 0.00 0 0.00 1.00 0.00
#> TCGA.EA.A3QD.01 2 0.0000 1.000 0.00 1.00 0.00 0 0.00 0.00 0.00
#> TCGA.C5.A7X5.01 3 0.0863 0.858 0.00 0.00 0.96 0 0.04 0.00 0.00
#> TCGA.EK.A2H0.01 4 0.0000 1.000 0.00 0.00 0.00 1 0.00 0.00 0.00
#> TCGA.FU.A3NI.01 7 0.1664 0.600 0.00 0.00 0.02 0 0.06 0.00 0.92
#> TCGA.EX.A69M.01 7 0.4348 0.750 0.00 0.14 0.00 0 0.18 0.00 0.68
#> TCGA.VS.A9UD.01 7 0.5173 0.589 0.00 0.34 0.00 0 0.16 0.00 0.50
#> TCGA.EA.A78R.01 2 0.0000 1.000 0.00 1.00 0.00 0 0.00 0.00 0.00
#> TCGA.DS.A1OC.01 3 0.1433 0.839 0.00 0.00 0.92 0 0.08 0.00 0.00
#> TCGA.ZJ.AAXJ.01 7 0.4348 0.750 0.00 0.14 0.00 0 0.18 0.00 0.68
#> TCGA.EA.A43B.01 1 0.0000 0.979 1.00 0.00 0.00 0 0.00 0.00 0.00
#> TCGA.C5.A1MQ.01 1 0.0000 0.979 1.00 0.00 0.00 0 0.00 0.00 0.00
#> TCGA.VS.A9UU.01 2 0.0000 1.000 0.00 1.00 0.00 0 0.00 0.00 0.00
#> TCGA.C5.A7CK.01 7 0.5241 0.609 0.00 0.32 0.00 0 0.18 0.00 0.50
cbind(get_classes(res, k = 8), get_membership(res, k = 8))
#> class entropy silhouette p1 p2 p3 p4 p5 p6 p7 p8
#> TCGA.GH.A9DA.01 8 0.0000 0.000 0.00 0.00 0.00 0 0.00 0.00 0.00 1.00
#> TCGA.ZJ.A8QQ.01 4 0.0000 1.000 0.00 0.00 0.00 1 0.00 0.00 0.00 0.00
#> TCGA.EK.A3GJ.01 3 0.0471 0.791 0.00 0.00 0.98 0 0.02 0.00 0.00 0.00
#> TCGA.C5.A902.01 7 0.3690 0.423 0.00 0.00 0.02 0 0.00 0.42 0.56 0.00
#> TCGA.C5.A3HD.01 5 0.3237 -0.310 0.00 0.00 0.40 0 0.60 0.00 0.00 0.00
#> TCGA.IR.A3LH.01 1 0.0000 0.974 1.00 0.00 0.00 0 0.00 0.00 0.00 0.00
#> TCGA.IR.A3LL.01 2 0.0000 1.000 0.00 1.00 0.00 0 0.00 0.00 0.00 0.00
#> TCGA.MY.A5BF.01 7 0.2534 0.583 0.00 0.00 0.00 0 0.00 0.22 0.78 0.00
#> TCGA.VS.A8EL.01 1 0.0000 0.974 1.00 0.00 0.00 0 0.00 0.00 0.00 0.00
#> TCGA.UC.A7PF.01 2 0.0000 1.000 0.00 1.00 0.00 0 0.00 0.00 0.00 0.00
#> TCGA.VS.A8Q9.01 1 0.1887 0.905 0.90 0.00 0.00 0 0.00 0.04 0.00 0.06
#> TCGA.C5.A8XH.01 3 0.1804 0.794 0.00 0.00 0.90 0 0.02 0.08 0.00 0.00
#> TCGA.VS.A8EI.01 1 0.0000 0.974 1.00 0.00 0.00 0 0.00 0.00 0.00 0.00
#> TCGA.C5.A8XI.01 7 0.1765 0.712 0.00 0.12 0.00 0 0.00 0.00 0.88 0.00
#> TCGA.DS.A7WI.01 5 0.5203 -0.382 0.00 0.00 0.00 0 0.42 0.28 0.00 0.30
#> TCGA.EA.A3QD.01 2 0.0000 1.000 0.00 1.00 0.00 0 0.00 0.00 0.00 0.00
#> TCGA.C5.A7X5.01 3 0.2224 0.716 0.00 0.00 0.86 0 0.12 0.02 0.00 0.00
#> TCGA.EK.A2H0.01 4 0.0000 1.000 0.00 0.00 0.00 1 0.00 0.00 0.00 0.00
#> TCGA.FU.A3NI.01 7 0.3193 0.478 0.00 0.00 0.00 0 0.00 0.38 0.62 0.00
#> TCGA.EX.A69M.01 7 0.1765 0.712 0.00 0.12 0.00 0 0.00 0.00 0.88 0.00
#> TCGA.VS.A9UD.01 7 0.3083 0.529 0.00 0.34 0.00 0 0.00 0.00 0.66 0.00
#> TCGA.EA.A78R.01 2 0.0000 1.000 0.00 1.00 0.00 0 0.00 0.00 0.00 0.00
#> TCGA.DS.A1OC.01 3 0.3198 0.629 0.00 0.00 0.72 0 0.02 0.26 0.00 0.00
#> TCGA.ZJ.AAXJ.01 7 0.1765 0.712 0.00 0.12 0.00 0 0.00 0.00 0.88 0.00
#> TCGA.EA.A43B.01 1 0.0941 0.956 0.96 0.00 0.00 0 0.00 0.02 0.00 0.02
#> TCGA.C5.A1MQ.01 1 0.0000 0.974 1.00 0.00 0.00 0 0.00 0.00 0.00 0.00
#> TCGA.VS.A9UU.01 2 0.0000 1.000 0.00 1.00 0.00 0 0.00 0.00 0.00 0.00
#> TCGA.C5.A7CK.01 7 0.2852 0.611 0.00 0.28 0.00 0 0.00 0.00 0.72 0.00
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)
consensus_heatmap(res, k = 7)
consensus_heatmap(res, k = 8)
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)
membership_heatmap(res, k = 7)
membership_heatmap(res, k = 8)
As soon as the classes for columns are determined, the signatures that are significantly different between subgroups can be looked for. Following are the heatmaps for signatures.
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)
get_signatures(res, k = 7)
get_signatures(res, k = 8)
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 (which is done by automatically selecting number of clusters).If there are too many signatures, top_signatures = ... can be set to only show the
signatures with the highest FDRs:
# code only for demonstration
# e.g. to show the top 500 most significant rows
tb = get_signature(res, k = ..., top_signatures = 500)
If the signatures are defined as these which are uniquely high in current group, diff_method argument
can be set to "uniquely_high_in_one_group":
# code only for demonstration
tb = get_signature(res, k = ..., diff_method = "uniquely_high_in_one_group")
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")
dimension_reduction(res, k = 7, method = "UMAP")
dimension_reduction(res, k = 8, method = "UMAP")
Following heatmap shows how subgroups are split when increasing k:
collect_classes(res)
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.
Parent node: Node0. Child nodes: Node011 , Node012 , Node013 , Node021 , Node022 , Node023 , Node031 , Node032-leaf .
The object with results only for a single top-value method and a single partitioning method can be extracted as:
res = res_rh["03"]
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, 7, 8.
#> On a matrix with 30000 rows and 41 columns.
#> Top rows (1000) are extracted by 'ATC' method.
#> Subgroups are detected by 'kmeans' method.
#> Performed in total 350 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_partitions"
#> [7] "compare_signatures" "consensus_heatmap" "dimension_reduction"
#> [10] "functional_enrichment" "get_anno_col" "get_anno"
#> [13] "get_classes" "get_consensus" "get_matrix"
#> [16] "get_membership" "get_param" "get_signatures"
#> [19] "get_stats" "is_best_k" "is_stable_k"
#> [22] "membership_heatmap" "ncol" "nrow"
#> [25] "plot_ecdf" "predict_classes" "rownames"
#> [28] "select_partition_number" "show" "suggest_best_k"
#> [31] "test_to_known_factors" "top_rows_heatmap"
collect_plots() function collects all the plots made from res for all k (number of subgroups)
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, higher 1-PAC score, higher mean silhouette score or higher
concordance corresponds to better partition. Rand index and Jaccard index
measure how similar the current partition is compared to partition with k-1.
If they are too similar, we won't accept k is better than k-1.
select_partition_number(res)
The numeric values for all these statistics can be obtained by get_stats().
get_stats(res)
#> k 1-PAC mean_silhouette concordance area_increased Rand Jaccard
#> 2 2 1.000 0.999 1.000 0.4885 0.512 0.512
#> 3 3 0.710 0.847 0.820 0.3278 0.810 0.629
#> 4 4 0.816 0.826 0.911 0.1511 0.894 0.689
#> 5 5 0.800 0.664 0.812 0.0653 0.955 0.828
#> 6 6 0.799 0.606 0.758 0.0384 0.906 0.611
#> 7 7 0.791 0.627 0.798 0.0273 0.929 0.626
#> 8 8 0.823 0.572 0.781 0.0214 0.972 0.820
suggest_best_k() suggests the best \(k\) based on these statistics. The rules are as follows:
suggest_best_k(res)
#> [1] 2
Following is 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 subgroup
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
#> TCGA.DS.A7WF.01 1 0.000 0.999 1.00 0.00
#> TCGA.FU.A3EO.01 1 0.000 0.999 1.00 0.00
#> TCGA.VS.A8QA.01 1 0.000 0.999 1.00 0.00
#> TCGA.MY.A5BD.01 1 0.000 0.999 1.00 0.00
#> TCGA.VS.A952.01 1 0.000 0.999 1.00 0.00
#> TCGA.IR.A3LI.01 1 0.000 0.999 1.00 0.00
#> TCGA.DS.A7WH.01 2 0.000 1.000 0.00 1.00
#> TCGA.EK.A2RL.01 1 0.000 0.999 1.00 0.00
#> TCGA.Q1.A5R1.01 1 0.000 0.999 1.00 0.00
#> TCGA.C5.A2LS.01 1 0.000 0.999 1.00 0.00
#> TCGA.C5.A7X8.01 2 0.000 1.000 0.00 1.00
#> TCGA.LP.A7HU.01 1 0.000 0.999 1.00 0.00
#> TCGA.DG.A2KK.01 1 0.000 0.999 1.00 0.00
#> TCGA.Q1.A73R.01 1 0.000 0.999 1.00 0.00
#> TCGA.C5.A2M1.01 1 0.000 0.999 1.00 0.00
#> TCGA.C5.A3HE.01 2 0.000 1.000 0.00 1.00
#> TCGA.IR.A3LF.01 1 0.000 0.999 1.00 0.00
#> TCGA.EX.A1H6.01 2 0.000 1.000 0.00 1.00
#> TCGA.JX.A3Q8.01 1 0.000 0.999 1.00 0.00
#> TCGA.C5.A2M2.01 1 0.000 0.999 1.00 0.00
#> TCGA.FU.A770.01 2 0.000 1.000 0.00 1.00
#> TCGA.EA.A5FO.01 1 0.000 0.999 1.00 0.00
#> TCGA.Q1.A6DV.01 2 0.000 1.000 0.00 1.00
#> TCGA.VS.A9UO.01 2 0.000 1.000 0.00 1.00
#> TCGA.C5.A1MJ.01 2 0.000 1.000 0.00 1.00
#> TCGA.EX.A449.01 1 0.000 0.999 1.00 0.00
#> TCGA.VS.A9UQ.01 1 0.000 0.999 1.00 0.00
#> TCGA.IR.A3LB.01 2 0.000 1.000 0.00 1.00
#> TCGA.C5.A1ME.01 2 0.000 1.000 0.00 1.00
#> TCGA.VS.A9V5.01 1 0.000 0.999 1.00 0.00
#> TCGA.JW.A69B.01 1 0.000 0.999 1.00 0.00
#> TCGA.VS.A9UZ.01 1 0.000 0.999 1.00 0.00
#> TCGA.Q1.A73P.01 1 0.000 0.999 1.00 0.00
#> TCGA.VS.A9UR.01 2 0.000 1.000 0.00 1.00
#> TCGA.VS.A9V1.01 2 0.000 1.000 0.00 1.00
#> TCGA.UC.A7PI.01 2 0.000 1.000 0.00 1.00
#> TCGA.VS.A9UL.01 2 0.000 1.000 0.00 1.00
#> TCGA.FU.A40J.01 1 0.141 0.980 0.98 0.02
#> TCGA.MA.AA43.01 2 0.000 1.000 0.00 1.00
#> TCGA.FU.A23K.01 2 0.000 1.000 0.00 1.00
#> TCGA.C5.A1M9.01 1 0.000 0.999 1.00 0.00
cbind(get_classes(res, k = 3), get_membership(res, k = 3))
#> class entropy silhouette p1 p2 p3
#> TCGA.DS.A7WF.01 3 0.604 1.000000 0.38 0.00 0.62
#> TCGA.FU.A3EO.01 1 0.000 0.853292 1.00 0.00 0.00
#> TCGA.VS.A8QA.01 3 0.604 1.000000 0.38 0.00 0.62
#> TCGA.MY.A5BD.01 3 0.604 1.000000 0.38 0.00 0.62
#> TCGA.VS.A952.01 3 0.604 1.000000 0.38 0.00 0.62
#> TCGA.IR.A3LI.01 3 0.604 1.000000 0.38 0.00 0.62
#> TCGA.DS.A7WH.01 2 0.721 0.794430 0.04 0.62 0.34
#> TCGA.EK.A2RL.01 1 0.000 0.853292 1.00 0.00 0.00
#> TCGA.Q1.A5R1.01 1 0.000 0.853292 1.00 0.00 0.00
#> TCGA.C5.A2LS.01 1 0.583 -0.000351 0.66 0.00 0.34
#> TCGA.C5.A7X8.01 2 0.000 0.837581 0.00 1.00 0.00
#> TCGA.LP.A7HU.01 3 0.604 1.000000 0.38 0.00 0.62
#> TCGA.DG.A2KK.01 3 0.604 1.000000 0.38 0.00 0.62
#> TCGA.Q1.A73R.01 3 0.604 1.000000 0.38 0.00 0.62
#> TCGA.C5.A2M1.01 1 0.000 0.853292 1.00 0.00 0.00
#> TCGA.C5.A3HE.01 2 0.000 0.837581 0.00 1.00 0.00
#> TCGA.IR.A3LF.01 1 0.000 0.853292 1.00 0.00 0.00
#> TCGA.EX.A1H6.01 2 0.000 0.837581 0.00 1.00 0.00
#> TCGA.JX.A3Q8.01 3 0.604 1.000000 0.38 0.00 0.62
#> TCGA.C5.A2M2.01 3 0.604 1.000000 0.38 0.00 0.62
#> TCGA.FU.A770.01 2 0.000 0.837581 0.00 1.00 0.00
#> TCGA.EA.A5FO.01 3 0.604 1.000000 0.38 0.00 0.62
#> TCGA.Q1.A6DV.01 2 0.604 0.809809 0.00 0.62 0.38
#> TCGA.VS.A9UO.01 2 0.000 0.837581 0.00 1.00 0.00
#> TCGA.C5.A1MJ.01 2 0.540 0.827102 0.00 0.72 0.28
#> TCGA.EX.A449.01 3 0.604 1.000000 0.38 0.00 0.62
#> TCGA.VS.A9UQ.01 1 0.583 0.505729 0.66 0.00 0.34
#> TCGA.IR.A3LB.01 2 0.000 0.837581 0.00 1.00 0.00
#> TCGA.C5.A1ME.01 2 0.000 0.837581 0.00 1.00 0.00
#> TCGA.VS.A9V5.01 1 0.000 0.853292 1.00 0.00 0.00
#> TCGA.JW.A69B.01 1 0.000 0.853292 1.00 0.00 0.00
#> TCGA.VS.A9UZ.01 1 0.000 0.853292 1.00 0.00 0.00
#> TCGA.Q1.A73P.01 1 0.000 0.853292 1.00 0.00 0.00
#> TCGA.VS.A9UR.01 2 0.604 0.809809 0.00 0.62 0.38
#> TCGA.VS.A9V1.01 2 0.000 0.837581 0.00 1.00 0.00
#> TCGA.UC.A7PI.01 2 0.583 0.817725 0.00 0.66 0.34
#> TCGA.VS.A9UL.01 2 0.604 0.809809 0.00 0.62 0.38
#> TCGA.FU.A40J.01 1 0.583 0.505729 0.66 0.00 0.34
#> TCGA.MA.AA43.01 2 0.595 0.816016 0.00 0.64 0.36
#> TCGA.FU.A23K.01 2 0.604 0.809809 0.00 0.62 0.38
#> TCGA.C5.A1M9.01 1 0.000 0.853292 1.00 0.00 0.00
cbind(get_classes(res, k = 4), get_membership(res, k = 4))
#> class entropy silhouette p1 p2 p3 p4
#> TCGA.DS.A7WF.01 3 0.0000 0.9483 0.00 0.00 1.00 0.00
#> TCGA.FU.A3EO.01 1 0.3400 0.8494 0.82 0.00 0.00 0.18
#> TCGA.VS.A8QA.01 3 0.0707 0.9427 0.00 0.00 0.98 0.02
#> TCGA.MY.A5BD.01 3 0.0000 0.9483 0.00 0.00 1.00 0.00
#> TCGA.VS.A952.01 3 0.0707 0.9427 0.00 0.00 0.98 0.02
#> TCGA.IR.A3LI.01 3 0.0000 0.9483 0.00 0.00 1.00 0.00
#> TCGA.DS.A7WH.01 1 0.4491 0.6970 0.80 0.06 0.00 0.14
#> TCGA.EK.A2RL.01 1 0.3400 0.8494 0.82 0.00 0.00 0.18
#> TCGA.Q1.A5R1.01 1 0.3172 0.8617 0.84 0.00 0.00 0.16
#> TCGA.C5.A2LS.01 4 0.7497 0.0543 0.26 0.00 0.24 0.50
#> TCGA.C5.A7X8.01 2 0.0000 0.8821 0.00 1.00 0.00 0.00
#> TCGA.LP.A7HU.01 3 0.0000 0.9483 0.00 0.00 1.00 0.00
#> TCGA.DG.A2KK.01 3 0.0707 0.9427 0.00 0.00 0.98 0.02
#> TCGA.Q1.A73R.01 3 0.0000 0.9483 0.00 0.00 1.00 0.00
#> TCGA.C5.A2M1.01 1 0.3172 0.8617 0.84 0.00 0.00 0.16
#> TCGA.C5.A3HE.01 2 0.0000 0.8821 0.00 1.00 0.00 0.00
#> TCGA.IR.A3LF.01 1 0.0000 0.9175 1.00 0.00 0.00 0.00
#> TCGA.EX.A1H6.01 2 0.0000 0.8821 0.00 1.00 0.00 0.00
#> TCGA.JX.A3Q8.01 3 0.0000 0.9483 0.00 0.00 1.00 0.00
#> TCGA.C5.A2M2.01 3 0.4949 0.7421 0.06 0.00 0.76 0.18
#> TCGA.FU.A770.01 2 0.0000 0.8821 0.00 1.00 0.00 0.00
#> TCGA.EA.A5FO.01 3 0.0000 0.9483 0.00 0.00 1.00 0.00
#> TCGA.Q1.A6DV.01 4 0.3400 0.7747 0.00 0.18 0.00 0.82
#> TCGA.VS.A9UO.01 2 0.0000 0.8821 0.00 1.00 0.00 0.00
#> TCGA.C5.A1MJ.01 2 0.3610 0.6942 0.00 0.80 0.00 0.20
#> TCGA.EX.A449.01 3 0.4949 0.7421 0.06 0.00 0.76 0.18
#> TCGA.VS.A9UQ.01 1 0.0000 0.9175 1.00 0.00 0.00 0.00
#> TCGA.IR.A3LB.01 2 0.0000 0.8821 0.00 1.00 0.00 0.00
#> TCGA.C5.A1ME.01 2 0.0000 0.8821 0.00 1.00 0.00 0.00
#> TCGA.VS.A9V5.01 1 0.0000 0.9175 1.00 0.00 0.00 0.00
#> TCGA.JW.A69B.01 1 0.0000 0.9175 1.00 0.00 0.00 0.00
#> TCGA.VS.A9UZ.01 1 0.1637 0.9029 0.94 0.00 0.00 0.06
#> TCGA.Q1.A73P.01 1 0.0000 0.9175 1.00 0.00 0.00 0.00
#> TCGA.VS.A9UR.01 4 0.3400 0.7747 0.00 0.18 0.00 0.82
#> TCGA.VS.A9V1.01 2 0.0000 0.8821 0.00 1.00 0.00 0.00
#> TCGA.UC.A7PI.01 2 0.4134 0.6101 0.00 0.74 0.00 0.26
#> TCGA.VS.A9UL.01 4 0.3400 0.7747 0.00 0.18 0.00 0.82
#> TCGA.FU.A40J.01 1 0.0000 0.9175 1.00 0.00 0.00 0.00
#> TCGA.MA.AA43.01 2 0.5000 -0.0420 0.00 0.50 0.00 0.50
#> TCGA.FU.A23K.01 4 0.3400 0.7747 0.00 0.18 0.00 0.82
#> TCGA.C5.A1M9.01 1 0.0000 0.9175 1.00 0.00 0.00 0.00
cbind(get_classes(res, k = 5), get_membership(res, k = 5))
#> class entropy silhouette p1 p2 p3 p4 p5
#> TCGA.DS.A7WF.01 3 0.000 0.8901 0.00 0.00 1.00 0.00 0.00
#> TCGA.FU.A3EO.01 1 0.389 0.6633 0.68 0.00 0.00 0.00 0.32
#> TCGA.VS.A8QA.01 3 0.000 0.8901 0.00 0.00 1.00 0.00 0.00
#> TCGA.MY.A5BD.01 3 0.000 0.8901 0.00 0.00 1.00 0.00 0.00
#> TCGA.VS.A952.01 3 0.104 0.8627 0.00 0.00 0.96 0.00 0.04
#> TCGA.IR.A3LI.01 3 0.000 0.8901 0.00 0.00 1.00 0.00 0.00
#> TCGA.DS.A7WH.01 5 0.389 0.4493 0.32 0.00 0.00 0.00 0.68
#> TCGA.EK.A2RL.01 1 0.406 0.6666 0.64 0.00 0.00 0.00 0.36
#> TCGA.Q1.A5R1.01 1 0.389 0.6949 0.68 0.00 0.00 0.00 0.32
#> TCGA.C5.A2LS.01 4 0.730 0.1978 0.06 0.00 0.16 0.48 0.30
#> TCGA.C5.A7X8.01 2 0.000 0.8634 0.00 1.00 0.00 0.00 0.00
#> TCGA.LP.A7HU.01 3 0.000 0.8901 0.00 0.00 1.00 0.00 0.00
#> TCGA.DG.A2KK.01 3 0.000 0.8901 0.00 0.00 1.00 0.00 0.00
#> TCGA.Q1.A73R.01 3 0.000 0.8901 0.00 0.00 1.00 0.00 0.00
#> TCGA.C5.A2M1.01 1 0.389 0.6949 0.68 0.00 0.00 0.00 0.32
#> TCGA.C5.A3HE.01 2 0.000 0.8634 0.00 1.00 0.00 0.00 0.00
#> TCGA.IR.A3LF.01 1 0.104 0.7739 0.96 0.00 0.00 0.00 0.04
#> TCGA.EX.A1H6.01 2 0.000 0.8634 0.00 1.00 0.00 0.00 0.00
#> TCGA.JX.A3Q8.01 3 0.000 0.8901 0.00 0.00 1.00 0.00 0.00
#> TCGA.C5.A2M2.01 3 0.645 0.2903 0.20 0.00 0.48 0.00 0.32
#> TCGA.FU.A770.01 2 0.000 0.8634 0.00 1.00 0.00 0.00 0.00
#> TCGA.EA.A5FO.01 3 0.000 0.8901 0.00 0.00 1.00 0.00 0.00
#> TCGA.Q1.A6DV.01 4 0.000 0.6313 0.00 0.00 0.00 1.00 0.00
#> TCGA.VS.A9UO.01 2 0.000 0.8634 0.00 1.00 0.00 0.00 0.00
#> TCGA.C5.A1MJ.01 2 0.516 0.0836 0.00 0.52 0.00 0.04 0.44
#> TCGA.EX.A449.01 3 0.645 0.2903 0.20 0.00 0.48 0.00 0.32
#> TCGA.VS.A9UQ.01 1 0.368 0.4688 0.72 0.00 0.00 0.00 0.28
#> TCGA.IR.A3LB.01 2 0.423 0.2515 0.00 0.58 0.00 0.00 0.42
#> TCGA.C5.A1ME.01 2 0.000 0.8634 0.00 1.00 0.00 0.00 0.00
#> TCGA.VS.A9V5.01 1 0.104 0.7655 0.96 0.00 0.00 0.00 0.04
#> TCGA.JW.A69B.01 1 0.000 0.7694 1.00 0.00 0.00 0.00 0.00
#> TCGA.VS.A9UZ.01 1 0.202 0.7721 0.90 0.00 0.00 0.00 0.10
#> TCGA.Q1.A73P.01 1 0.000 0.7694 1.00 0.00 0.00 0.00 0.00
#> TCGA.VS.A9UR.01 4 0.000 0.6313 0.00 0.00 0.00 1.00 0.00
#> TCGA.VS.A9V1.01 2 0.000 0.8634 0.00 1.00 0.00 0.00 0.00
#> TCGA.UC.A7PI.01 5 0.600 0.3353 0.02 0.18 0.00 0.16 0.64
#> TCGA.VS.A9UL.01 4 0.000 0.6313 0.00 0.00 0.00 1.00 0.00
#> TCGA.FU.A40J.01 1 0.368 0.4688 0.72 0.00 0.00 0.00 0.28
#> TCGA.MA.AA43.01 4 0.610 0.0415 0.00 0.14 0.00 0.52 0.34
#> TCGA.FU.A23K.01 4 0.418 0.1929 0.00 0.00 0.00 0.60 0.40
#> TCGA.C5.A1M9.01 1 0.000 0.7694 1.00 0.00 0.00 0.00 0.00
cbind(get_classes(res, k = 6), get_membership(res, k = 6))
#> class entropy silhouette p1 p2 p3 p4 p5 p6
#> TCGA.DS.A7WF.01 3 0.0000 0.96117 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.FU.A3EO.01 6 0.1556 0.60859 0.08 0.00 0.00 0.00 0.00 0.92
#> TCGA.VS.A8QA.01 3 0.1865 0.92815 0.00 0.00 0.92 0.00 0.04 0.04
#> TCGA.MY.A5BD.01 3 0.0000 0.96117 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.VS.A952.01 3 0.3351 0.81310 0.00 0.00 0.80 0.00 0.04 0.16
#> TCGA.IR.A3LI.01 3 0.0000 0.96117 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.DS.A7WH.01 5 0.4078 -0.00267 0.34 0.00 0.00 0.00 0.64 0.02
#> TCGA.EK.A2RL.01 6 0.0000 0.62666 0.00 0.00 0.00 0.00 0.00 1.00
#> TCGA.Q1.A5R1.01 6 0.3270 0.55262 0.12 0.00 0.00 0.00 0.06 0.82
#> TCGA.C5.A2LS.01 4 0.7113 0.20344 0.26 0.00 0.00 0.44 0.12 0.18
#> TCGA.C5.A7X8.01 2 0.0000 0.88845 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.LP.A7HU.01 3 0.0547 0.95487 0.00 0.00 0.98 0.00 0.02 0.00
#> TCGA.DG.A2KK.01 3 0.1865 0.92815 0.00 0.00 0.92 0.00 0.04 0.04
#> TCGA.Q1.A73R.01 3 0.0000 0.96117 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.C5.A2M1.01 6 0.3270 0.55262 0.12 0.00 0.00 0.00 0.06 0.82
#> TCGA.C5.A3HE.01 2 0.0000 0.88845 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.IR.A3LF.01 1 0.3797 0.46663 0.58 0.00 0.00 0.00 0.00 0.42
#> TCGA.EX.A1H6.01 2 0.0547 0.88269 0.02 0.98 0.00 0.00 0.00 0.00
#> TCGA.JX.A3Q8.01 3 0.0000 0.96117 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.C5.A2M2.01 6 0.2793 0.55175 0.00 0.00 0.20 0.00 0.00 0.80
#> TCGA.FU.A770.01 2 0.0547 0.88269 0.02 0.98 0.00 0.00 0.00 0.00
#> TCGA.EA.A5FO.01 3 0.0000 0.96117 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.Q1.A6DV.01 4 0.2793 0.43263 0.00 0.00 0.00 0.80 0.20 0.00
#> TCGA.VS.A9UO.01 2 0.0000 0.88845 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.C5.A1MJ.01 2 0.5106 0.17758 0.04 0.50 0.00 0.02 0.44 0.00
#> TCGA.EX.A449.01 6 0.2793 0.55175 0.00 0.00 0.20 0.00 0.00 0.80
#> TCGA.VS.A9UQ.01 1 0.5447 0.23590 0.46 0.00 0.00 0.00 0.42 0.12
#> TCGA.IR.A3LB.01 2 0.3409 0.59470 0.00 0.70 0.00 0.00 0.30 0.00
#> TCGA.C5.A1ME.01 2 0.0000 0.88845 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.VS.A9V5.01 1 0.4700 0.56607 0.60 0.00 0.00 0.00 0.06 0.34
#> TCGA.JW.A69B.01 1 0.3578 0.61226 0.66 0.00 0.00 0.00 0.00 0.34
#> TCGA.VS.A9UZ.01 6 0.4845 -0.25975 0.40 0.00 0.00 0.00 0.06 0.54
#> TCGA.Q1.A73P.01 1 0.3499 0.61584 0.68 0.00 0.00 0.00 0.00 0.32
#> TCGA.VS.A9UR.01 4 0.2260 0.46562 0.14 0.00 0.00 0.86 0.00 0.00
#> TCGA.VS.A9V1.01 2 0.0000 0.88845 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.UC.A7PI.01 5 0.2403 0.32676 0.04 0.04 0.00 0.02 0.90 0.00
#> TCGA.VS.A9UL.01 4 0.2793 0.43263 0.00 0.00 0.00 0.80 0.20 0.00
#> TCGA.FU.A40J.01 1 0.5447 0.23590 0.46 0.00 0.00 0.00 0.42 0.12
#> TCGA.MA.AA43.01 5 0.6053 0.09255 0.04 0.10 0.00 0.42 0.44 0.00
#> TCGA.FU.A23K.01 5 0.4651 0.01082 0.04 0.00 0.00 0.48 0.48 0.00
#> TCGA.C5.A1M9.01 1 0.3578 0.61226 0.66 0.00 0.00 0.00 0.00 0.34
cbind(get_classes(res, k = 7), get_membership(res, k = 7))
#> class entropy silhouette p1 p2 p3 p4 p5 p6 p7
#> TCGA.DS.A7WF.01 3 0.0000 0.942 0.00 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.FU.A3EO.01 6 0.3221 0.579 0.32 0.00 0.00 0.00 0.00 0.68 0.00
#> TCGA.VS.A8QA.01 3 0.2278 0.890 0.00 0.00 0.88 0.00 0.00 0.08 0.04
#> TCGA.MY.A5BD.01 3 0.0000 0.942 0.00 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.VS.A952.01 3 0.3519 0.732 0.00 0.00 0.74 0.00 0.00 0.22 0.04
#> TCGA.IR.A3LI.01 3 0.0000 0.942 0.00 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.DS.A7WH.01 5 0.1363 0.261 0.02 0.00 0.00 0.00 0.94 0.00 0.04
#> TCGA.EK.A2RL.01 6 0.2259 0.651 0.16 0.00 0.00 0.00 0.00 0.84 0.00
#> TCGA.Q1.A5R1.01 6 0.5027 0.432 0.32 0.00 0.00 0.00 0.04 0.58 0.06
#> TCGA.C5.A2LS.01 7 0.6930 -0.193 0.00 0.00 0.00 0.18 0.20 0.26 0.36
#> TCGA.C5.A7X8.01 2 0.0000 0.929 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.LP.A7HU.01 3 0.0863 0.929 0.00 0.00 0.96 0.00 0.00 0.00 0.04
#> TCGA.DG.A2KK.01 3 0.2278 0.890 0.00 0.00 0.88 0.00 0.00 0.08 0.04
#> TCGA.Q1.A73R.01 3 0.0000 0.942 0.00 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.C5.A2M1.01 6 0.5027 0.432 0.32 0.00 0.00 0.00 0.04 0.58 0.06
#> TCGA.C5.A3HE.01 2 0.0000 0.929 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.IR.A3LF.01 1 0.0000 0.829 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.EX.A1H6.01 2 0.2906 0.805 0.00 0.80 0.00 0.00 0.02 0.00 0.18
#> TCGA.JX.A3Q8.01 3 0.0000 0.942 0.00 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.C5.A2M2.01 6 0.3985 0.625 0.10 0.00 0.18 0.00 0.00 0.72 0.00
#> TCGA.FU.A770.01 2 0.2906 0.805 0.00 0.80 0.00 0.00 0.02 0.00 0.18
#> TCGA.EA.A5FO.01 3 0.0000 0.942 0.00 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.Q1.A6DV.01 4 0.0000 0.603 0.00 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.VS.A9UO.01 2 0.0000 0.929 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.C5.A1MJ.01 7 0.5467 -0.273 0.00 0.26 0.00 0.00 0.28 0.00 0.46
#> TCGA.EX.A449.01 6 0.3985 0.625 0.10 0.00 0.18 0.00 0.00 0.72 0.00
#> TCGA.VS.A9UQ.01 5 0.4789 0.281 0.26 0.00 0.00 0.00 0.60 0.14 0.00
#> TCGA.IR.A3LB.01 5 0.5997 -0.307 0.00 0.28 0.00 0.00 0.38 0.02 0.32
#> TCGA.C5.A1ME.01 2 0.0000 0.929 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.VS.A9V5.01 1 0.3548 0.691 0.80 0.00 0.00 0.00 0.04 0.12 0.04
#> TCGA.JW.A69B.01 1 0.1166 0.812 0.94 0.00 0.00 0.00 0.00 0.00 0.06
#> TCGA.VS.A9UZ.01 1 0.4589 0.522 0.68 0.00 0.00 0.00 0.04 0.22 0.06
#> TCGA.Q1.A73P.01 1 0.0000 0.829 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.VS.A9UR.01 4 0.4353 0.295 0.00 0.00 0.00 0.66 0.00 0.10 0.24
#> TCGA.VS.A9V1.01 2 0.0000 0.929 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.UC.A7PI.01 5 0.3517 0.127 0.00 0.00 0.00 0.00 0.70 0.02 0.28
#> TCGA.VS.A9UL.01 4 0.0000 0.603 0.00 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.FU.A40J.01 5 0.4789 0.281 0.26 0.00 0.00 0.00 0.60 0.14 0.00
#> TCGA.MA.AA43.01 4 0.5129 0.415 0.00 0.04 0.00 0.54 0.06 0.00 0.36
#> TCGA.FU.A23K.01 4 0.4597 0.443 0.00 0.00 0.00 0.56 0.08 0.00 0.36
#> TCGA.C5.A1M9.01 1 0.1166 0.812 0.94 0.00 0.00 0.00 0.00 0.00 0.06
cbind(get_classes(res, k = 8), get_membership(res, k = 8))
#> class entropy silhouette p1 p2 p3 p4 p5 p6 p7 p8
#> TCGA.DS.A7WF.01 8 0.0000 0.89357 0.00 0.00 0.00 0.00 0.00 0.00 0.00 1.00
#> TCGA.FU.A3EO.01 6 0.4538 0.63410 0.12 0.00 0.32 0.00 0.00 0.56 0.00 0.00
#> TCGA.VS.A8QA.01 8 0.2534 0.79621 0.00 0.00 0.22 0.00 0.00 0.00 0.00 0.78
#> TCGA.MY.A5BD.01 8 0.0471 0.88408 0.00 0.00 0.00 0.00 0.02 0.00 0.00 0.98
#> TCGA.VS.A952.01 8 0.3690 0.51987 0.00 0.00 0.42 0.00 0.00 0.02 0.00 0.56
#> TCGA.IR.A3LI.01 8 0.0000 0.89357 0.00 0.00 0.00 0.00 0.00 0.00 0.00 1.00
#> TCGA.DS.A7WH.01 5 0.0808 0.37747 0.00 0.00 0.00 0.04 0.96 0.00 0.00 0.00
#> TCGA.EK.A2RL.01 6 0.4302 0.63148 0.08 0.00 0.36 0.00 0.00 0.56 0.00 0.00
#> TCGA.Q1.A5R1.01 6 0.1765 0.47536 0.12 0.00 0.00 0.00 0.00 0.88 0.00 0.00
#> TCGA.C5.A2LS.01 7 0.6225 0.16639 0.00 0.00 0.24 0.00 0.12 0.22 0.42 0.00
#> TCGA.C5.A7X8.01 2 0.0000 0.95620 0.00 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.LP.A7HU.01 8 0.1341 0.86836 0.00 0.00 0.08 0.00 0.00 0.00 0.00 0.92
#> TCGA.DG.A2KK.01 8 0.2534 0.79621 0.00 0.00 0.22 0.00 0.00 0.00 0.00 0.78
#> TCGA.Q1.A73R.01 8 0.0000 0.89357 0.00 0.00 0.00 0.00 0.00 0.00 0.00 1.00
#> TCGA.C5.A2M1.01 6 0.1765 0.47536 0.12 0.00 0.00 0.00 0.00 0.88 0.00 0.00
#> TCGA.C5.A3HE.01 2 0.0000 0.95620 0.00 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.IR.A3LF.01 1 0.1341 0.83832 0.92 0.00 0.00 0.00 0.00 0.08 0.00 0.00
#> TCGA.EX.A1H6.01 2 0.2350 0.88481 0.00 0.86 0.10 0.00 0.00 0.00 0.04 0.00
#> TCGA.JX.A3Q8.01 8 0.0000 0.89357 0.00 0.00 0.00 0.00 0.00 0.00 0.00 1.00
#> TCGA.C5.A2M2.01 6 0.4657 0.59516 0.04 0.00 0.42 0.00 0.00 0.50 0.00 0.04
#> TCGA.FU.A770.01 2 0.2350 0.88481 0.00 0.86 0.10 0.00 0.00 0.00 0.04 0.00
#> TCGA.EA.A5FO.01 8 0.0000 0.89357 0.00 0.00 0.00 0.00 0.00 0.00 0.00 1.00
#> TCGA.Q1.A6DV.01 7 0.3333 -0.20137 0.00 0.00 0.00 0.50 0.00 0.00 0.50 0.00
#> TCGA.VS.A9UO.01 2 0.0000 0.95620 0.00 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.C5.A1MJ.01 4 0.6190 -0.13776 0.00 0.16 0.08 0.46 0.28 0.00 0.02 0.00
#> TCGA.EX.A449.01 6 0.4657 0.59516 0.04 0.00 0.42 0.00 0.00 0.50 0.00 0.04
#> TCGA.VS.A9UQ.01 5 0.4644 0.33647 0.16 0.00 0.02 0.00 0.64 0.18 0.00 0.00
#> TCGA.IR.A3LB.01 5 0.6910 -0.11056 0.00 0.20 0.20 0.26 0.32 0.00 0.02 0.00
#> TCGA.C5.A1ME.01 2 0.0000 0.95620 0.00 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.VS.A9V5.01 1 0.3193 0.51890 0.62 0.00 0.00 0.00 0.00 0.38 0.00 0.00
#> TCGA.JW.A69B.01 1 0.0471 0.82547 0.98 0.00 0.02 0.00 0.00 0.00 0.00 0.00
#> TCGA.VS.A9UZ.01 6 0.3318 -0.34799 0.46 0.00 0.00 0.00 0.00 0.54 0.00 0.00
#> TCGA.Q1.A73P.01 1 0.1563 0.83282 0.90 0.00 0.00 0.00 0.00 0.10 0.00 0.00
#> TCGA.VS.A9UR.01 7 0.0808 0.34563 0.00 0.00 0.00 0.04 0.00 0.00 0.96 0.00
#> TCGA.VS.A9V1.01 2 0.0000 0.95620 0.00 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.UC.A7PI.01 5 0.4759 0.00808 0.00 0.00 0.14 0.36 0.50 0.00 0.00 0.00
#> TCGA.VS.A9UL.01 4 0.3333 -0.37393 0.00 0.00 0.00 0.50 0.00 0.00 0.50 0.00
#> TCGA.FU.A40J.01 5 0.4644 0.33647 0.16 0.00 0.02 0.00 0.64 0.18 0.00 0.00
#> TCGA.MA.AA43.01 4 0.0000 0.47062 0.00 0.00 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.FU.A23K.01 4 0.0000 0.47062 0.00 0.00 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.C5.A1M9.01 1 0.0471 0.82547 0.98 0.00 0.02 0.00 0.00 0.00 0.00 0.00
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)
consensus_heatmap(res, k = 7)
consensus_heatmap(res, k = 8)
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)
membership_heatmap(res, k = 7)
membership_heatmap(res, k = 8)
As soon as the classes for columns are determined, the signatures that are significantly different between subgroups can be looked for. Following are the heatmaps for signatures.
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)
get_signatures(res, k = 7)
get_signatures(res, k = 8)
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 (which is done by automatically selecting number of clusters).If there are too many signatures, top_signatures = ... can be set to only show the
signatures with the highest FDRs:
# code only for demonstration
# e.g. to show the top 500 most significant rows
tb = get_signature(res, k = ..., top_signatures = 500)
If the signatures are defined as these which are uniquely high in current group, diff_method argument
can be set to "uniquely_high_in_one_group":
# code only for demonstration
tb = get_signature(res, k = ..., diff_method = "uniquely_high_in_one_group")
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")
dimension_reduction(res, k = 7, method = "UMAP")
dimension_reduction(res, k = 8, method = "UMAP")
Following heatmap shows how subgroups are split when increasing k:
collect_classes(res)
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.
Parent node: Node03. Child nodes: Node0111 , Node0112-leaf , Node0113 , Node0121 , Node0122-leaf , Node0123-leaf , Node0131 , Node0132-leaf , Node0133-leaf , Node0134-leaf , Node0211 , Node0212-leaf , Node0221-leaf , Node0222 , Node0231-leaf , Node0232-leaf , Node0233-leaf , Node0311 , Node0312-leaf , Node0313-leaf .
The object with results only for a single top-value method and a single partitioning method can be extracted as:
res = res_rh["031"]
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, 7, 8.
#> On a matrix with 30000 rows and 25 columns.
#> Top rows (1000) are extracted by 'ATC' method.
#> Subgroups are detected by 'kmeans' method.
#> Performed in total 350 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_partitions"
#> [7] "compare_signatures" "consensus_heatmap" "dimension_reduction"
#> [10] "functional_enrichment" "get_anno_col" "get_anno"
#> [13] "get_classes" "get_consensus" "get_matrix"
#> [16] "get_membership" "get_param" "get_signatures"
#> [19] "get_stats" "is_best_k" "is_stable_k"
#> [22] "membership_heatmap" "ncol" "nrow"
#> [25] "plot_ecdf" "predict_classes" "rownames"
#> [28] "select_partition_number" "show" "suggest_best_k"
#> [31] "test_to_known_factors" "top_rows_heatmap"
collect_plots() function collects all the plots made from res for all k (number of subgroups)
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, higher 1-PAC score, higher mean silhouette score or higher
concordance corresponds to better partition. Rand index and Jaccard index
measure how similar the current partition is compared to partition with k-1.
If they are too similar, we won't accept k is better than k-1.
select_partition_number(res)
The numeric values for all these statistics can be obtained by get_stats().
get_stats(res)
#> k 1-PAC mean_silhouette concordance area_increased Rand Jaccard
#> 2 2 1.000 1.000 1.000 0.3806 0.620 0.620
#> 3 3 1.000 0.954 0.985 0.5825 0.733 0.581
#> 4 4 0.759 0.708 0.848 0.1767 0.837 0.592
#> 5 5 0.802 0.935 0.934 0.0845 0.893 0.624
#> 6 6 0.779 0.862 0.890 0.0126 0.993 0.968
#> 7 7 0.885 0.844 0.936 0.0519 0.980 0.902
#> 8 8 0.834 0.735 0.866 0.0183 0.970 0.836
suggest_best_k() suggests the best \(k\) based on these statistics. The rules are as follows:
suggest_best_k(res)
#> [1] 3
#> attr(,"optional")
#> [1] 2
There is also optional best \(k\) = 2 that is worth to check.
Following is 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 subgroup
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
#> TCGA.DS.A7WF.01 2 0 1 0 1
#> TCGA.FU.A3EO.01 1 0 1 1 0
#> TCGA.VS.A8QA.01 1 0 1 1 0
#> TCGA.MY.A5BD.01 2 0 1 0 1
#> TCGA.VS.A952.01 1 0 1 1 0
#> TCGA.IR.A3LI.01 2 0 1 0 1
#> TCGA.EK.A2RL.01 1 0 1 1 0
#> TCGA.Q1.A5R1.01 1 0 1 1 0
#> TCGA.C5.A2LS.01 1 0 1 1 0
#> TCGA.LP.A7HU.01 2 0 1 0 1
#> TCGA.DG.A2KK.01 1 0 1 1 0
#> TCGA.Q1.A73R.01 2 0 1 0 1
#> TCGA.C5.A2M1.01 1 0 1 1 0
#> TCGA.IR.A3LF.01 1 0 1 1 0
#> TCGA.JX.A3Q8.01 1 0 1 1 0
#> TCGA.C5.A2M2.01 1 0 1 1 0
#> TCGA.EA.A5FO.01 2 0 1 0 1
#> TCGA.EX.A449.01 1 0 1 1 0
#> TCGA.VS.A9UQ.01 1 0 1 1 0
#> TCGA.VS.A9V5.01 1 0 1 1 0
#> TCGA.JW.A69B.01 1 0 1 1 0
#> TCGA.VS.A9UZ.01 1 0 1 1 0
#> TCGA.Q1.A73P.01 1 0 1 1 0
#> TCGA.FU.A40J.01 1 0 1 1 0
#> TCGA.C5.A1M9.01 1 0 1 1 0
cbind(get_classes(res, k = 3), get_membership(res, k = 3))
#> class entropy silhouette p1 p2 p3
#> TCGA.DS.A7WF.01 2 0.000 1.000 0.00 1 0.00
#> TCGA.FU.A3EO.01 1 0.000 1.000 1.00 0 0.00
#> TCGA.VS.A8QA.01 3 0.000 0.895 0.00 0 1.00
#> TCGA.MY.A5BD.01 2 0.000 1.000 0.00 1 0.00
#> TCGA.VS.A952.01 3 0.604 0.387 0.38 0 0.62
#> TCGA.IR.A3LI.01 3 0.000 0.895 0.00 0 1.00
#> TCGA.EK.A2RL.01 1 0.000 1.000 1.00 0 0.00
#> TCGA.Q1.A5R1.01 1 0.000 1.000 1.00 0 0.00
#> TCGA.C5.A2LS.01 3 0.000 0.895 0.00 0 1.00
#> TCGA.LP.A7HU.01 2 0.000 1.000 0.00 1 0.00
#> TCGA.DG.A2KK.01 3 0.000 0.895 0.00 0 1.00
#> TCGA.Q1.A73R.01 2 0.000 1.000 0.00 1 0.00
#> TCGA.C5.A2M1.01 1 0.000 1.000 1.00 0 0.00
#> TCGA.IR.A3LF.01 1 0.000 1.000 1.00 0 0.00
#> TCGA.JX.A3Q8.01 3 0.000 0.895 0.00 0 1.00
#> TCGA.C5.A2M2.01 1 0.000 1.000 1.00 0 0.00
#> TCGA.EA.A5FO.01 2 0.000 1.000 0.00 1 0.00
#> TCGA.EX.A449.01 1 0.000 1.000 1.00 0 0.00
#> TCGA.VS.A9UQ.01 1 0.000 1.000 1.00 0 0.00
#> TCGA.VS.A9V5.01 1 0.000 1.000 1.00 0 0.00
#> TCGA.JW.A69B.01 1 0.000 1.000 1.00 0 0.00
#> TCGA.VS.A9UZ.01 1 0.000 1.000 1.00 0 0.00
#> TCGA.Q1.A73P.01 1 0.000 1.000 1.00 0 0.00
#> TCGA.FU.A40J.01 1 0.000 1.000 1.00 0 0.00
#> TCGA.C5.A1M9.01 1 0.000 1.000 1.00 0 0.00
cbind(get_classes(res, k = 4), get_membership(res, k = 4))
#> class entropy silhouette p1 p2 p3 p4
#> TCGA.DS.A7WF.01 2 0.000 1.000 0.00 1 0.00 0.00
#> TCGA.FU.A3EO.01 1 0.000 0.835 1.00 0 0.00 0.00
#> TCGA.VS.A8QA.01 3 0.000 0.835 0.00 0 1.00 0.00
#> TCGA.MY.A5BD.01 2 0.000 1.000 0.00 1 0.00 0.00
#> TCGA.VS.A952.01 4 0.637 0.409 0.10 0 0.28 0.62
#> TCGA.IR.A3LI.01 3 0.471 0.758 0.00 0 0.64 0.36
#> TCGA.EK.A2RL.01 4 0.500 0.576 0.50 0 0.00 0.50
#> TCGA.Q1.A5R1.01 1 0.491 -0.452 0.58 0 0.00 0.42
#> TCGA.C5.A2LS.01 3 0.485 0.757 0.00 0 0.60 0.40
#> TCGA.LP.A7HU.01 2 0.000 1.000 0.00 1 0.00 0.00
#> TCGA.DG.A2KK.01 3 0.000 0.835 0.00 0 1.00 0.00
#> TCGA.Q1.A73R.01 2 0.000 1.000 0.00 1 0.00 0.00
#> TCGA.C5.A2M1.01 4 0.648 0.644 0.30 0 0.10 0.60
#> TCGA.IR.A3LF.01 1 0.000 0.835 1.00 0 0.00 0.00
#> TCGA.JX.A3Q8.01 3 0.234 0.800 0.00 0 0.90 0.10
#> TCGA.C5.A2M2.01 4 0.498 0.661 0.46 0 0.00 0.54
#> TCGA.EA.A5FO.01 2 0.000 1.000 0.00 1 0.00 0.00
#> TCGA.EX.A449.01 1 0.000 0.835 1.00 0 0.00 0.00
#> TCGA.VS.A9UQ.01 4 0.498 0.661 0.46 0 0.00 0.54
#> TCGA.VS.A9V5.01 1 0.000 0.835 1.00 0 0.00 0.00
#> TCGA.JW.A69B.01 1 0.000 0.835 1.00 0 0.00 0.00
#> TCGA.VS.A9UZ.01 1 0.000 0.835 1.00 0 0.00 0.00
#> TCGA.Q1.A73P.01 1 0.000 0.835 1.00 0 0.00 0.00
#> TCGA.FU.A40J.01 1 0.491 -0.452 0.58 0 0.00 0.42
#> TCGA.C5.A1M9.01 1 0.000 0.835 1.00 0 0.00 0.00
cbind(get_classes(res, k = 5), get_membership(res, k = 5))
#> class entropy silhouette p1 p2 p3 p4 p5
#> TCGA.DS.A7WF.01 2 0.0000 0.987 0.00 1.00 0.00 0.00 0.00
#> TCGA.FU.A3EO.01 1 0.0000 1.000 1.00 0.00 0.00 0.00 0.00
#> TCGA.VS.A8QA.01 3 0.3037 0.923 0.00 0.00 0.86 0.04 0.10
#> TCGA.MY.A5BD.01 2 0.1043 0.965 0.00 0.96 0.00 0.04 0.00
#> TCGA.VS.A952.01 4 0.2249 0.762 0.02 0.00 0.02 0.92 0.04
#> TCGA.IR.A3LI.01 5 0.1410 1.000 0.00 0.00 0.06 0.00 0.94
#> TCGA.EK.A2RL.01 4 0.3274 0.854 0.22 0.00 0.00 0.78 0.00
#> TCGA.Q1.A5R1.01 4 0.3684 0.819 0.28 0.00 0.00 0.72 0.00
#> TCGA.C5.A2LS.01 5 0.1410 1.000 0.00 0.00 0.06 0.00 0.94
#> TCGA.LP.A7HU.01 2 0.0609 0.978 0.00 0.98 0.00 0.00 0.02
#> TCGA.DG.A2KK.01 3 0.3037 0.923 0.00 0.00 0.86 0.04 0.10
#> TCGA.Q1.A73R.01 2 0.0000 0.987 0.00 1.00 0.00 0.00 0.00
#> TCGA.C5.A2M1.01 4 0.1648 0.795 0.04 0.00 0.00 0.94 0.02
#> TCGA.IR.A3LF.01 1 0.0000 1.000 1.00 0.00 0.00 0.00 0.00
#> TCGA.JX.A3Q8.01 3 0.0000 0.850 0.00 0.00 1.00 0.00 0.00
#> TCGA.C5.A2M2.01 4 0.2516 0.866 0.14 0.00 0.00 0.86 0.00
#> TCGA.EA.A5FO.01 2 0.0000 0.987 0.00 1.00 0.00 0.00 0.00
#> TCGA.EX.A449.01 1 0.0000 1.000 1.00 0.00 0.00 0.00 0.00
#> TCGA.VS.A9UQ.01 4 0.2516 0.866 0.14 0.00 0.00 0.86 0.00
#> TCGA.VS.A9V5.01 1 0.0000 1.000 1.00 0.00 0.00 0.00 0.00
#> TCGA.JW.A69B.01 1 0.0000 1.000 1.00 0.00 0.00 0.00 0.00
#> TCGA.VS.A9UZ.01 1 0.0000 1.000 1.00 0.00 0.00 0.00 0.00
#> TCGA.Q1.A73P.01 1 0.0000 1.000 1.00 0.00 0.00 0.00 0.00
#> TCGA.FU.A40J.01 4 0.3684 0.819 0.28 0.00 0.00 0.72 0.00
#> TCGA.C5.A1M9.01 1 0.0000 1.000 1.00 0.00 0.00 0.00 0.00
cbind(get_classes(res, k = 6), get_membership(res, k = 6))
#> class entropy silhouette p1 p2 p3 p4 p5 p6
#> TCGA.DS.A7WF.01 2 0.0000 0.931 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.FU.A3EO.01 1 0.0000 0.991 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.VS.A8QA.01 3 0.0000 1.000 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.MY.A5BD.01 2 0.4213 0.794 0.00 0.78 0.00 0.10 0.04 0.08
#> TCGA.VS.A952.01 4 0.6367 0.305 0.02 0.00 0.08 0.58 0.08 0.24
#> TCGA.IR.A3LI.01 5 0.2454 0.948 0.00 0.00 0.16 0.00 0.84 0.00
#> TCGA.EK.A2RL.01 4 0.2941 0.855 0.22 0.00 0.00 0.78 0.00 0.00
#> TCGA.Q1.A5R1.01 4 0.3076 0.847 0.24 0.00 0.00 0.76 0.00 0.00
#> TCGA.C5.A2LS.01 5 0.2048 0.948 0.00 0.00 0.12 0.00 0.88 0.00
#> TCGA.LP.A7HU.01 2 0.1814 0.891 0.00 0.90 0.00 0.00 0.00 0.10
#> TCGA.DG.A2KK.01 3 0.0000 1.000 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.Q1.A73R.01 2 0.0000 0.931 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.C5.A2M1.01 4 0.2725 0.719 0.06 0.00 0.04 0.88 0.00 0.02
#> TCGA.IR.A3LF.01 1 0.0000 0.991 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.JX.A3Q8.01 6 0.5020 0.000 0.00 0.00 0.38 0.02 0.04 0.56
#> TCGA.C5.A2M2.01 4 0.2793 0.856 0.20 0.00 0.00 0.80 0.00 0.00
#> TCGA.EA.A5FO.01 2 0.0000 0.931 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.EX.A449.01 1 0.0000 0.991 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.VS.A9UQ.01 4 0.2793 0.856 0.20 0.00 0.00 0.80 0.00 0.00
#> TCGA.VS.A9V5.01 1 0.0547 0.985 0.98 0.00 0.00 0.00 0.00 0.02
#> TCGA.JW.A69B.01 1 0.0547 0.985 0.98 0.00 0.00 0.00 0.00 0.02
#> TCGA.VS.A9UZ.01 1 0.0000 0.991 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.Q1.A73P.01 1 0.0000 0.991 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.FU.A40J.01 4 0.3592 0.837 0.24 0.00 0.00 0.74 0.00 0.02
#> TCGA.C5.A1M9.01 1 0.0547 0.985 0.98 0.00 0.00 0.00 0.00 0.02
cbind(get_classes(res, k = 7), get_membership(res, k = 7))
#> class entropy silhouette p1 p2 p3 p4 p5 p6 p7
#> TCGA.DS.A7WF.01 2 0.0000 0.937 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.FU.A3EO.01 1 0.0000 0.974 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.VS.A8QA.01 3 0.1166 1.000 0.00 0.00 0.94 0.00 0.06 0.00 0.00
#> TCGA.MY.A5BD.01 2 0.3086 0.796 0.00 0.80 0.00 0.00 0.00 0.04 0.16
#> TCGA.VS.A952.01 7 0.2572 0.000 0.00 0.00 0.00 0.20 0.00 0.00 0.80
#> TCGA.IR.A3LI.01 5 0.1363 0.935 0.00 0.00 0.04 0.00 0.94 0.00 0.02
#> TCGA.EK.A2RL.01 4 0.0000 0.865 0.00 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.Q1.A5R1.01 4 0.2376 0.783 0.12 0.00 0.00 0.86 0.00 0.02 0.00
#> TCGA.C5.A2LS.01 5 0.0000 0.934 0.00 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.LP.A7HU.01 2 0.1166 0.917 0.00 0.94 0.00 0.00 0.00 0.06 0.00
#> TCGA.DG.A2KK.01 3 0.1166 1.000 0.00 0.00 0.94 0.00 0.06 0.00 0.00
#> TCGA.Q1.A73R.01 2 0.0504 0.933 0.00 0.98 0.00 0.00 0.00 0.00 0.02
#> TCGA.C5.A2M1.01 4 0.2857 0.827 0.00 0.00 0.04 0.86 0.00 0.06 0.04
#> TCGA.IR.A3LF.01 1 0.0000 0.974 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.JX.A3Q8.01 6 0.3388 0.000 0.00 0.00 0.20 0.00 0.04 0.76 0.00
#> TCGA.C5.A2M2.01 4 0.0863 0.844 0.00 0.00 0.00 0.96 0.00 0.04 0.00
#> TCGA.EA.A5FO.01 2 0.0000 0.937 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.EX.A449.01 1 0.0000 0.974 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.VS.A9UQ.01 4 0.0000 0.865 0.00 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.VS.A9V5.01 1 0.1363 0.956 0.94 0.00 0.02 0.00 0.00 0.04 0.00
#> TCGA.JW.A69B.01 1 0.1363 0.956 0.94 0.00 0.02 0.00 0.00 0.04 0.00
#> TCGA.VS.A9UZ.01 1 0.0000 0.974 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.Q1.A73P.01 1 0.0000 0.974 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.FU.A40J.01 4 0.3630 0.787 0.04 0.00 0.06 0.80 0.00 0.10 0.00
#> TCGA.C5.A1M9.01 1 0.1363 0.956 0.94 0.00 0.02 0.00 0.00 0.04 0.00
cbind(get_classes(res, k = 8), get_membership(res, k = 8))
#> class entropy silhouette p1 p2 p3 p4 p5 p6 p7 p8
#> TCGA.DS.A7WF.01 2 0.0000 0.897 0.00 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.FU.A3EO.01 1 0.0000 0.955 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.VS.A8QA.01 3 0.2025 0.980 0.00 0.00 0.88 0.02 0.10 0.00 0.00 0.00
#> TCGA.MY.A5BD.01 2 0.4355 0.719 0.00 0.72 0.02 0.04 0.00 0.06 0.16 0.00
#> TCGA.VS.A952.01 7 0.2404 0.000 0.00 0.00 0.00 0.02 0.00 0.00 0.84 0.14
#> TCGA.IR.A3LI.01 5 0.0000 0.967 0.00 0.00 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.EK.A2RL.01 4 0.5171 0.723 0.02 0.00 0.06 0.54 0.00 0.04 0.00 0.34
#> TCGA.Q1.A5R1.01 8 0.4433 0.106 0.34 0.00 0.00 0.10 0.00 0.00 0.00 0.56
#> TCGA.C5.A2LS.01 5 0.0808 0.967 0.00 0.00 0.00 0.04 0.96 0.00 0.00 0.00
#> TCGA.LP.A7HU.01 2 0.2267 0.811 0.00 0.82 0.00 0.18 0.00 0.00 0.00 0.00
#> TCGA.DG.A2KK.01 3 0.1563 0.980 0.00 0.00 0.90 0.00 0.10 0.00 0.00 0.00
#> TCGA.Q1.A73R.01 2 0.0000 0.897 0.00 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.C5.A2M1.01 8 0.1275 0.262 0.00 0.00 0.00 0.04 0.00 0.00 0.02 0.94
#> TCGA.IR.A3LF.01 1 0.0000 0.955 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.JX.A3Q8.01 6 0.2114 0.000 0.00 0.00 0.16 0.00 0.00 0.84 0.00 0.00
#> TCGA.C5.A2M2.01 4 0.4074 0.669 0.02 0.00 0.02 0.68 0.00 0.02 0.00 0.26
#> TCGA.EA.A5FO.01 2 0.0000 0.897 0.00 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.EX.A449.01 1 0.0000 0.955 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.VS.A9UQ.01 4 0.3729 0.690 0.02 0.00 0.00 0.52 0.00 0.00 0.00 0.46
#> TCGA.VS.A9V5.01 1 0.1557 0.924 0.92 0.00 0.02 0.00 0.00 0.00 0.00 0.06
#> TCGA.JW.A69B.01 1 0.1557 0.924 0.92 0.00 0.02 0.00 0.00 0.00 0.00 0.06
#> TCGA.VS.A9UZ.01 1 0.0000 0.955 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.Q1.A73P.01 1 0.0000 0.955 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.FU.A40J.01 8 0.3185 0.329 0.04 0.00 0.06 0.00 0.00 0.08 0.00 0.82
#> TCGA.C5.A1M9.01 1 0.2624 0.871 0.86 0.00 0.06 0.00 0.00 0.02 0.00 0.06
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)
consensus_heatmap(res, k = 7)
consensus_heatmap(res, k = 8)
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)
membership_heatmap(res, k = 7)
membership_heatmap(res, k = 8)
As soon as the classes for columns are determined, the signatures that are significantly different between subgroups can be looked for. Following are the heatmaps for signatures.
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)
get_signatures(res, k = 7)
get_signatures(res, k = 8)
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 (which is done by automatically selecting number of clusters).If there are too many signatures, top_signatures = ... can be set to only show the
signatures with the highest FDRs:
# code only for demonstration
# e.g. to show the top 500 most significant rows
tb = get_signature(res, k = ..., top_signatures = 500)
If the signatures are defined as these which are uniquely high in current group, diff_method argument
can be set to "uniquely_high_in_one_group":
# code only for demonstration
tb = get_signature(res, k = ..., diff_method = "uniquely_high_in_one_group")
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")
dimension_reduction(res, k = 7, method = "UMAP")
dimension_reduction(res, k = 8, method = "UMAP")
Following heatmap shows how subgroups are split when increasing k:
collect_classes(res)
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.
Parent node: Node031. Child nodes: Node01111-leaf , Node01112-leaf , Node01113-leaf , Node01131-leaf , Node01132-leaf , Node01133-leaf , Node01211-leaf , Node01212-leaf , Node01311-leaf , Node01312-leaf , Node01313-leaf , Node02111 , Node02112-leaf , Node02221 , Node02222-leaf , Node03111-leaf , Node03112 .
The object with results only for a single top-value method and a single partitioning method can be extracted as:
res = res_rh["0311"]
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, 7, 8.
#> On a matrix with 30000 rows and 14 columns.
#> Top rows (1000) are extracted by 'ATC' method.
#> Subgroups are detected by 'skmeans' method.
#> Performed in total 350 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_partitions"
#> [7] "compare_signatures" "consensus_heatmap" "dimension_reduction"
#> [10] "functional_enrichment" "get_anno_col" "get_anno"
#> [13] "get_classes" "get_consensus" "get_matrix"
#> [16] "get_membership" "get_param" "get_signatures"
#> [19] "get_stats" "is_best_k" "is_stable_k"
#> [22] "membership_heatmap" "ncol" "nrow"
#> [25] "plot_ecdf" "predict_classes" "rownames"
#> [28] "select_partition_number" "show" "suggest_best_k"
#> [31] "test_to_known_factors" "top_rows_heatmap"
collect_plots() function collects all the plots made from res for all k (number of subgroups)
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, higher 1-PAC score, higher mean silhouette score or higher
concordance corresponds to better partition. Rand index and Jaccard index
measure how similar the current partition is compared to partition with k-1.
If they are too similar, we won't accept k is better than k-1.
select_partition_number(res)
The numeric values for all these statistics can be obtained by get_stats().
get_stats(res)
#> k 1-PAC mean_silhouette concordance area_increased Rand Jaccard
#> 2 2 1.000 1.000 1.000 0.2645 0.736 0.736
#> 3 3 0.615 0.931 0.953 1.2252 0.648 0.522
#> 4 4 0.758 0.803 0.914 0.1370 0.923 0.800
#> 5 5 0.967 0.816 0.979 0.0801 0.967 0.893
#> 6 6 0.956 0.732 0.960 0.0313 0.978 0.920
#> 7 7 0.978 0.621 0.984 0.0188 0.989 0.957
#> 8 8 0.923 0.450 0.956 0.0365 0.989 0.955
suggest_best_k() suggests the best \(k\) based on these statistics. The rules are as follows:
suggest_best_k(res)
#> [1] 2
Following is 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 subgroup
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
#> TCGA.FU.A3EO.01 2 0 1 0 1
#> TCGA.EK.A2RL.01 2 0 1 0 1
#> TCGA.Q1.A5R1.01 2 0 1 0 1
#> TCGA.C5.A2M1.01 2 0 1 0 1
#> TCGA.IR.A3LF.01 2 0 1 0 1
#> TCGA.C5.A2M2.01 2 0 1 0 1
#> TCGA.EX.A449.01 2 0 1 0 1
#> TCGA.VS.A9UQ.01 2 0 1 0 1
#> TCGA.VS.A9V5.01 1 0 1 1 0
#> TCGA.JW.A69B.01 2 0 1 0 1
#> TCGA.VS.A9UZ.01 2 0 1 0 1
#> TCGA.Q1.A73P.01 2 0 1 0 1
#> TCGA.FU.A40J.01 1 0 1 1 0
#> TCGA.C5.A1M9.01 2 0 1 0 1
cbind(get_classes(res, k = 3), get_membership(res, k = 3))
#> class entropy silhouette p1 p2 p3
#> TCGA.FU.A3EO.01 2 0.0000 0.967 0.00 1.00 0.00
#> TCGA.EK.A2RL.01 3 0.3686 0.926 0.00 0.14 0.86
#> TCGA.Q1.A5R1.01 2 0.0000 0.967 0.00 1.00 0.00
#> TCGA.C5.A2M1.01 2 0.5147 0.712 0.02 0.80 0.18
#> TCGA.IR.A3LF.01 2 0.0000 0.967 0.00 1.00 0.00
#> TCGA.C5.A2M2.01 2 0.0000 0.967 0.00 1.00 0.00
#> TCGA.EX.A449.01 2 0.0000 0.967 0.00 1.00 0.00
#> TCGA.VS.A9UQ.01 3 0.3686 0.926 0.00 0.14 0.86
#> TCGA.VS.A9V5.01 1 0.0000 1.000 1.00 0.00 0.00
#> TCGA.JW.A69B.01 3 0.4002 0.911 0.00 0.16 0.84
#> TCGA.VS.A9UZ.01 2 0.0000 0.967 0.00 1.00 0.00
#> TCGA.Q1.A73P.01 2 0.0000 0.967 0.00 1.00 0.00
#> TCGA.FU.A40J.01 1 0.0000 1.000 1.00 0.00 0.00
#> TCGA.C5.A1M9.01 3 0.0892 0.787 0.00 0.02 0.98
cbind(get_classes(res, k = 4), get_membership(res, k = 4))
#> class entropy silhouette p1 p2 p3 p4
#> TCGA.FU.A3EO.01 2 0.000 1.000 0.00 1.00 0.00 0.00
#> TCGA.EK.A2RL.01 3 0.164 0.682 0.00 0.06 0.94 0.00
#> TCGA.Q1.A5R1.01 2 0.000 1.000 0.00 1.00 0.00 0.00
#> TCGA.C5.A2M1.01 4 0.720 0.000 0.00 0.18 0.28 0.54
#> TCGA.IR.A3LF.01 2 0.000 1.000 0.00 1.00 0.00 0.00
#> TCGA.C5.A2M2.01 2 0.000 1.000 0.00 1.00 0.00 0.00
#> TCGA.EX.A449.01 2 0.000 1.000 0.00 1.00 0.00 0.00
#> TCGA.VS.A9UQ.01 3 0.164 0.682 0.00 0.06 0.94 0.00
#> TCGA.VS.A9V5.01 1 0.498 1.000 0.54 0.00 0.00 0.46
#> TCGA.JW.A69B.01 3 0.385 0.558 0.02 0.16 0.82 0.00
#> TCGA.VS.A9UZ.01 2 0.000 1.000 0.00 1.00 0.00 0.00
#> TCGA.Q1.A73P.01 2 0.000 1.000 0.00 1.00 0.00 0.00
#> TCGA.FU.A40J.01 1 0.498 1.000 0.54 0.00 0.00 0.46
#> TCGA.C5.A1M9.01 3 0.498 0.323 0.46 0.00 0.54 0.00
cbind(get_classes(res, k = 5), get_membership(res, k = 5))
#> class entropy silhouette p1 p2 p3 p4 p5
#> TCGA.FU.A3EO.01 2 0.0000 0.997 0.00 1.00 0.00 0.00 0.00
#> TCGA.EK.A2RL.01 3 0.0609 0.879 0.00 0.00 0.98 0.02 0.00
#> TCGA.Q1.A5R1.01 2 0.0609 0.980 0.00 0.98 0.00 0.02 0.00
#> TCGA.C5.A2M1.01 4 0.0609 0.000 0.00 0.00 0.02 0.98 0.00
#> TCGA.IR.A3LF.01 2 0.0000 0.997 0.00 1.00 0.00 0.00 0.00
#> TCGA.C5.A2M2.01 2 0.0000 0.997 0.00 1.00 0.00 0.00 0.00
#> TCGA.EX.A449.01 2 0.0000 0.997 0.00 1.00 0.00 0.00 0.00
#> TCGA.VS.A9UQ.01 3 0.0000 0.882 0.00 0.00 1.00 0.00 0.00
#> TCGA.VS.A9V5.01 1 0.0000 0.967 1.00 0.00 0.00 0.00 0.00
#> TCGA.JW.A69B.01 3 0.3697 0.765 0.00 0.08 0.82 0.00 0.10
#> TCGA.VS.A9UZ.01 2 0.0000 0.997 0.00 1.00 0.00 0.00 0.00
#> TCGA.Q1.A73P.01 2 0.0000 0.997 0.00 1.00 0.00 0.00 0.00
#> TCGA.FU.A40J.01 1 0.1216 0.967 0.96 0.00 0.00 0.02 0.02
#> TCGA.C5.A1M9.01 5 0.0609 0.000 0.00 0.00 0.02 0.00 0.98
cbind(get_classes(res, k = 6), get_membership(res, k = 6))
#> class entropy silhouette p1 p2 p3 p4 p5 p6
#> TCGA.FU.A3EO.01 2 0.0000 0.997 0.0 1.00 0.00 0.00 0 0.00
#> TCGA.EK.A2RL.01 3 0.0547 0.824 0.0 0.00 0.98 0.00 0 0.02
#> TCGA.Q1.A5R1.01 2 0.0547 0.979 0.0 0.98 0.00 0.02 0 0.00
#> TCGA.C5.A2M1.01 4 0.0000 0.000 0.0 0.00 0.00 1.00 0 0.00
#> TCGA.IR.A3LF.01 2 0.0000 0.997 0.0 1.00 0.00 0.00 0 0.00
#> TCGA.C5.A2M2.01 2 0.0000 0.997 0.0 1.00 0.00 0.00 0 0.00
#> TCGA.EX.A449.01 2 0.0000 0.997 0.0 1.00 0.00 0.00 0 0.00
#> TCGA.VS.A9UQ.01 3 0.2048 0.814 0.0 0.00 0.88 0.00 0 0.12
#> TCGA.VS.A9V5.01 1 0.0000 0.826 1.0 0.00 0.00 0.00 0 0.00
#> TCGA.JW.A69B.01 6 0.3156 0.000 0.0 0.02 0.18 0.00 0 0.80
#> TCGA.VS.A9UZ.01 2 0.0000 0.997 0.0 1.00 0.00 0.00 0 0.00
#> TCGA.Q1.A73P.01 2 0.0000 0.997 0.0 1.00 0.00 0.00 0 0.00
#> TCGA.FU.A40J.01 1 0.2793 0.826 0.8 0.00 0.00 0.00 0 0.20
#> TCGA.C5.A1M9.01 5 0.0000 0.000 0.0 0.00 0.00 0.00 1 0.00
cbind(get_classes(res, k = 7), get_membership(res, k = 7))
#> class entropy silhouette p1 p2 p3 p4 p5 p6 p7
#> TCGA.FU.A3EO.01 2 0.0000 0.997 0.00 1.00 0.00 0 0 0.00 0.00
#> TCGA.EK.A2RL.01 3 0.1363 0.867 0.00 0.00 0.94 0 0 0.02 0.04
#> TCGA.Q1.A5R1.01 2 0.0504 0.981 0.00 0.98 0.00 0 0 0.02 0.00
#> TCGA.C5.A2M1.01 4 0.0000 0.000 0.00 0.00 0.00 1 0 0.00 0.00
#> TCGA.IR.A3LF.01 2 0.0000 0.997 0.00 1.00 0.00 0 0 0.00 0.00
#> TCGA.C5.A2M2.01 2 0.0000 0.997 0.00 1.00 0.00 0 0 0.00 0.00
#> TCGA.EX.A449.01 2 0.0000 0.997 0.00 1.00 0.00 0 0 0.00 0.00
#> TCGA.VS.A9UQ.01 3 0.1433 0.863 0.00 0.00 0.92 0 0 0.08 0.00
#> TCGA.VS.A9V5.01 1 0.0000 0.000 1.00 0.00 0.00 0 0 0.00 0.00
#> TCGA.JW.A69B.01 6 0.0504 0.000 0.00 0.00 0.02 0 0 0.98 0.00
#> TCGA.VS.A9UZ.01 2 0.0000 0.997 0.00 1.00 0.00 0 0 0.00 0.00
#> TCGA.Q1.A73P.01 2 0.0000 0.997 0.00 1.00 0.00 0 0 0.00 0.00
#> TCGA.FU.A40J.01 7 0.0863 0.000 0.04 0.00 0.00 0 0 0.00 0.96
#> TCGA.C5.A1M9.01 5 0.0000 0.000 0.00 0.00 0.00 0 1 0.00 0.00
cbind(get_classes(res, k = 8), get_membership(res, k = 8))
#> class entropy silhouette p1 p2 p3 p4 p5 p6 p7 p8
#> TCGA.FU.A3EO.01 2 0.000 0.948 0 1.00 0.0 0 0 0 0 0.00
#> TCGA.EK.A2RL.01 3 0.294 0.000 0 0.00 0.7 0 0 0 0 0.30
#> TCGA.Q1.A5R1.01 2 0.337 0.612 0 0.68 0.3 0 0 0 0 0.02
#> TCGA.C5.A2M1.01 4 0.000 0.000 0 0.00 0.0 1 0 0 0 0.00
#> TCGA.IR.A3LF.01 2 0.000 0.948 0 1.00 0.0 0 0 0 0 0.00
#> TCGA.C5.A2M2.01 2 0.000 0.948 0 1.00 0.0 0 0 0 0 0.00
#> TCGA.EX.A449.01 2 0.000 0.948 0 1.00 0.0 0 0 0 0 0.00
#> TCGA.VS.A9UQ.01 8 0.000 0.000 0 0.00 0.0 0 0 0 0 1.00
#> TCGA.VS.A9V5.01 1 0.000 0.000 1 0.00 0.0 0 0 0 0 0.00
#> TCGA.JW.A69B.01 6 0.000 0.000 0 0.00 0.0 0 0 1 0 0.00
#> TCGA.VS.A9UZ.01 2 0.000 0.948 0 1.00 0.0 0 0 0 0 0.00
#> TCGA.Q1.A73P.01 2 0.000 0.948 0 1.00 0.0 0 0 0 0 0.00
#> TCGA.FU.A40J.01 7 0.000 0.000 0 0.00 0.0 0 0 0 1 0.00
#> TCGA.C5.A1M9.01 5 0.000 0.000 0 0.00 0.0 0 1 0 0 0.00
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)
consensus_heatmap(res, k = 7)
consensus_heatmap(res, k = 8)
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)
membership_heatmap(res, k = 7)
membership_heatmap(res, k = 8)
As soon as the classes for columns are determined, the signatures that are significantly different between subgroups can be looked for. Following are the heatmaps for signatures.
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)
get_signatures(res, k = 7)
get_signatures(res, k = 8)
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 (which is done by automatically selecting number of clusters).If there are too many signatures, top_signatures = ... can be set to only show the
signatures with the highest FDRs:
# code only for demonstration
# e.g. to show the top 500 most significant rows
tb = get_signature(res, k = ..., top_signatures = 500)
If the signatures are defined as these which are uniquely high in current group, diff_method argument
can be set to "uniquely_high_in_one_group":
# code only for demonstration
tb = get_signature(res, k = ..., diff_method = "uniquely_high_in_one_group")
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")
dimension_reduction(res, k = 7, method = "UMAP")
dimension_reduction(res, k = 8, method = "UMAP")
Following heatmap shows how subgroups are split when increasing k:
collect_classes(res)
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.
Parent node: Node0311. Child nodes: Node021111-leaf , Node021112-leaf , Node021113-leaf , Node021114-leaf , Node022211-leaf , Node022212-leaf , Node022213-leaf , Node031121-leaf , Node031122-leaf .
The object with results only for a single top-value method and a single partitioning method can be extracted as:
res = res_rh["03112"]
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, 7, 8.
#> On a matrix with 30000 rows and 12 columns.
#> Top rows (1000) are extracted by 'ATC' method.
#> Subgroups are detected by 'skmeans' method.
#> Performed in total 350 partitions by row resampling.
#> Best k for subgroups seems to be 7.
#>
#> Following methods can be applied to this 'ConsensusPartition' object:
#> [1] "cola_report" "collect_classes" "collect_plots"
#> [4] "collect_stats" "colnames" "compare_partitions"
#> [7] "compare_signatures" "consensus_heatmap" "dimension_reduction"
#> [10] "functional_enrichment" "get_anno_col" "get_anno"
#> [13] "get_classes" "get_consensus" "get_matrix"
#> [16] "get_membership" "get_param" "get_signatures"
#> [19] "get_stats" "is_best_k" "is_stable_k"
#> [22] "membership_heatmap" "ncol" "nrow"
#> [25] "plot_ecdf" "predict_classes" "rownames"
#> [28] "select_partition_number" "show" "suggest_best_k"
#> [31] "test_to_known_factors" "top_rows_heatmap"
collect_plots() function collects all the plots made from res for all k (number of subgroups)
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, higher 1-PAC score, higher mean silhouette score or higher
concordance corresponds to better partition. Rand index and Jaccard index
measure how similar the current partition is compared to partition with k-1.
If they are too similar, we won't accept k is better than k-1.
select_partition_number(res)
The numeric values for all these statistics can be obtained by get_stats().
get_stats(res)
#> k 1-PAC mean_silhouette concordance area_increased Rand Jaccard
#> 2 2 1.000 1.000 1.000 0.3037 0.697 0.697
#> 3 3 1.000 1.000 1.000 1.0465 0.682 0.543
#> 4 4 0.803 0.743 0.913 0.0939 0.985 0.960
#> 5 5 0.758 0.788 0.940 0.1698 0.818 0.500
#> 6 6 0.818 0.677 0.962 0.0616 0.970 0.833
#> 7 7 0.924 0.588 0.942 0.0492 0.955 0.700
#> 8 8 1.000 0.493 0.997 0.0269 0.985 0.857
suggest_best_k() suggests the best \(k\) based on these statistics. The rules are as follows:
suggest_best_k(res)
#> [1] 7
#> attr(,"optional")
#> [1] 2 3
There is also optional best \(k\) = 2 3 that is worth to check.
Following is 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 subgroup
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
#> TCGA.FU.A3EO.01 2 0 1 0 1
#> TCGA.EK.A2RL.01 2 0 1 0 1
#> TCGA.Q1.A5R1.01 2 0 1 0 1
#> TCGA.C5.A2M1.01 2 0 1 0 1
#> TCGA.IR.A3LF.01 2 0 1 0 1
#> TCGA.C5.A2M2.01 2 0 1 0 1
#> TCGA.EX.A449.01 2 0 1 0 1
#> TCGA.VS.A9UQ.01 2 0 1 0 1
#> TCGA.JW.A69B.01 1 0 1 1 0
#> TCGA.VS.A9UZ.01 2 0 1 0 1
#> TCGA.Q1.A73P.01 2 0 1 0 1
#> TCGA.C5.A1M9.01 1 0 1 1 0
cbind(get_classes(res, k = 3), get_membership(res, k = 3))
#> class entropy silhouette p1 p2 p3
#> TCGA.FU.A3EO.01 2 0 1 0 1 0
#> TCGA.EK.A2RL.01 3 0 1 0 0 1
#> TCGA.Q1.A5R1.01 2 0 1 0 1 0
#> TCGA.C5.A2M1.01 2 0 1 0 1 0
#> TCGA.IR.A3LF.01 2 0 1 0 1 0
#> TCGA.C5.A2M2.01 3 0 1 0 0 1
#> TCGA.EX.A449.01 2 0 1 0 1 0
#> TCGA.VS.A9UQ.01 3 0 1 0 0 1
#> TCGA.JW.A69B.01 1 0 1 1 0 0
#> TCGA.VS.A9UZ.01 2 0 1 0 1 0
#> TCGA.Q1.A73P.01 2 0 1 0 1 0
#> TCGA.C5.A1M9.01 1 0 1 1 0 0
cbind(get_classes(res, k = 4), get_membership(res, k = 4))
#> class entropy silhouette p1 p2 p3 p4
#> TCGA.FU.A3EO.01 2 0.413 0.817 0.26 0.74 0 0.00
#> TCGA.EK.A2RL.01 3 0.000 1.000 0.00 0.00 1 0.00
#> TCGA.Q1.A5R1.01 2 0.000 0.867 0.00 1.00 0 0.00
#> TCGA.C5.A2M1.01 2 0.000 0.867 0.00 1.00 0 0.00
#> TCGA.IR.A3LF.01 2 0.000 0.867 0.00 1.00 0 0.00
#> TCGA.C5.A2M2.01 3 0.000 1.000 0.00 0.00 1 0.00
#> TCGA.EX.A449.01 2 0.413 0.817 0.26 0.74 0 0.00
#> TCGA.VS.A9UQ.01 3 0.000 1.000 0.00 0.00 1 0.00
#> TCGA.JW.A69B.01 1 0.413 0.000 0.74 0.00 0 0.26
#> TCGA.VS.A9UZ.01 2 0.413 0.817 0.26 0.74 0 0.00
#> TCGA.Q1.A73P.01 2 0.000 0.867 0.00 1.00 0 0.00
#> TCGA.C5.A1M9.01 4 0.000 0.000 0.00 0.00 0 1.00
cbind(get_classes(res, k = 5), get_membership(res, k = 5))
#> class entropy silhouette p1 p2 p3 p4 p5
#> TCGA.FU.A3EO.01 5 0.252 1.000 0 0.14 0.00 0 0.86
#> TCGA.EK.A2RL.01 3 0.000 0.937 0 0.00 1.00 0 0.00
#> TCGA.Q1.A5R1.01 2 0.141 0.932 0 0.94 0.00 0 0.06
#> TCGA.C5.A2M1.01 2 0.202 0.901 0 0.90 0.00 0 0.10
#> TCGA.IR.A3LF.01 2 0.000 0.938 0 1.00 0.00 0 0.00
#> TCGA.C5.A2M2.01 3 0.252 0.870 0 0.00 0.86 0 0.14
#> TCGA.EX.A449.01 5 0.252 1.000 0 0.14 0.00 0 0.86
#> TCGA.VS.A9UQ.01 3 0.000 0.937 0 0.00 1.00 0 0.00
#> TCGA.JW.A69B.01 1 0.000 0.000 1 0.00 0.00 0 0.00
#> TCGA.VS.A9UZ.01 5 0.252 1.000 0 0.14 0.00 0 0.86
#> TCGA.Q1.A73P.01 2 0.000 0.938 0 1.00 0.00 0 0.00
#> TCGA.C5.A1M9.01 4 0.000 0.000 0 0.00 0.00 1 0.00
cbind(get_classes(res, k = 6), get_membership(res, k = 6))
#> class entropy silhouette p1 p2 p3 p4 p5 p6
#> TCGA.FU.A3EO.01 5 0.000 1.000 0 0.00 0.00 0 1.00 0.00
#> TCGA.EK.A2RL.01 3 0.245 0.810 0 0.00 0.84 0 0.00 0.16
#> TCGA.Q1.A5R1.01 2 0.226 0.875 0 0.86 0.00 0 0.14 0.00
#> TCGA.C5.A2M1.01 2 0.245 0.862 0 0.84 0.00 0 0.16 0.00
#> TCGA.IR.A3LF.01 2 0.000 0.877 0 1.00 0.00 0 0.00 0.00
#> TCGA.C5.A2M2.01 6 0.000 0.000 0 0.00 0.00 0 0.00 1.00
#> TCGA.EX.A449.01 5 0.000 1.000 0 0.00 0.00 0 1.00 0.00
#> TCGA.VS.A9UQ.01 3 0.000 0.823 0 0.00 1.00 0 0.00 0.00
#> TCGA.JW.A69B.01 1 0.000 0.000 1 0.00 0.00 0 0.00 0.00
#> TCGA.VS.A9UZ.01 5 0.000 1.000 0 0.00 0.00 0 1.00 0.00
#> TCGA.Q1.A73P.01 2 0.000 0.877 0 1.00 0.00 0 0.00 0.00
#> TCGA.C5.A1M9.01 4 0.000 0.000 0 0.00 0.00 1 0.00 0.00
cbind(get_classes(res, k = 7), get_membership(res, k = 7))
#> class entropy silhouette p1 p2 p3 p4 p5 p6 p7
#> TCGA.FU.A3EO.01 5 0.000 1.000 0 0.00 0.0 0 1.00 0.00 0.00
#> TCGA.EK.A2RL.01 3 0.479 0.570 0 0.00 0.6 0 0.00 0.14 0.26
#> TCGA.Q1.A5R1.01 2 0.101 0.939 0 0.96 0.0 0 0.02 0.00 0.02
#> TCGA.C5.A2M1.01 7 0.331 0.000 0 0.24 0.0 0 0.02 0.00 0.74
#> TCGA.IR.A3LF.01 2 0.000 0.971 0 1.00 0.0 0 0.00 0.00 0.00
#> TCGA.C5.A2M2.01 6 0.000 0.000 0 0.00 0.0 0 0.00 1.00 0.00
#> TCGA.EX.A449.01 5 0.000 1.000 0 0.00 0.0 0 1.00 0.00 0.00
#> TCGA.VS.A9UQ.01 3 0.000 0.608 0 0.00 1.0 0 0.00 0.00 0.00
#> TCGA.JW.A69B.01 1 0.000 0.000 1 0.00 0.0 0 0.00 0.00 0.00
#> TCGA.VS.A9UZ.01 5 0.000 1.000 0 0.00 0.0 0 1.00 0.00 0.00
#> TCGA.Q1.A73P.01 2 0.000 0.971 0 1.00 0.0 0 0.00 0.00 0.00
#> TCGA.C5.A1M9.01 4 0.000 0.000 0 0.00 0.0 1 0.00 0.00 0.00
cbind(get_classes(res, k = 8), get_membership(res, k = 8))
#> class entropy silhouette p1 p2 p3 p4 p5 p6 p7 p8
#> TCGA.FU.A3EO.01 5 0.0000 1.000 0 0.00 0 0 1 0 0.00 0
#> TCGA.EK.A2RL.01 3 0.0000 0.000 0 0.00 1 0 0 0 0.00 0
#> TCGA.Q1.A5R1.01 2 0.0808 0.958 0 0.96 0 0 0 0 0.04 0
#> TCGA.C5.A2M1.01 7 0.0000 0.000 0 0.00 0 0 0 0 1.00 0
#> TCGA.IR.A3LF.01 2 0.0000 0.980 0 1.00 0 0 0 0 0.00 0
#> TCGA.C5.A2M2.01 6 0.0000 0.000 0 0.00 0 0 0 1 0.00 0
#> TCGA.EX.A449.01 5 0.0000 1.000 0 0.00 0 0 1 0 0.00 0
#> TCGA.VS.A9UQ.01 8 0.0000 0.000 0 0.00 0 0 0 0 0.00 1
#> TCGA.JW.A69B.01 1 0.0000 0.000 1 0.00 0 0 0 0 0.00 0
#> TCGA.VS.A9UZ.01 5 0.0000 1.000 0 0.00 0 0 1 0 0.00 0
#> TCGA.Q1.A73P.01 2 0.0000 0.980 0 1.00 0 0 0 0 0.00 0
#> TCGA.C5.A1M9.01 4 0.0000 0.000 0 0.00 0 1 0 0 0.00 0
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)
consensus_heatmap(res, k = 7)
consensus_heatmap(res, k = 8)
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)
membership_heatmap(res, k = 7)
membership_heatmap(res, k = 8)
As soon as the classes for columns are determined, the signatures that are significantly different between subgroups can be looked for. Following are the heatmaps for signatures.
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)
get_signatures(res, k = 7)
get_signatures(res, k = 8)
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 (which is done by automatically selecting number of clusters).If there are too many signatures, top_signatures = ... can be set to only show the
signatures with the highest FDRs:
# code only for demonstration
# e.g. to show the top 500 most significant rows
tb = get_signature(res, k = ..., top_signatures = 500)
If the signatures are defined as these which are uniquely high in current group, diff_method argument
can be set to "uniquely_high_in_one_group":
# code only for demonstration
tb = get_signature(res, k = ..., diff_method = "uniquely_high_in_one_group")
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")
dimension_reduction(res, k = 7, method = "UMAP")
dimension_reduction(res, k = 8, method = "UMAP")
Following heatmap shows how subgroups are split when increasing k:
collect_classes(res)
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 4.1.0 (2021-05-18)
#> Platform: x86_64-pc-linux-gnu (64-bit)
#> Running under: CentOS Linux 7 (Core)
#>
#> Matrix products: default
#> BLAS/LAPACK: /usr/lib64/libopenblas-r0.3.3.so
#>
#> locale:
#> [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C LC_TIME=en_US.UTF-8
#> [4] LC_COLLATE=en_US.UTF-8 LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8
#> [7] LC_PAPER=en_US.UTF-8 LC_NAME=C LC_ADDRESS=C
#> [10] LC_TELEPHONE=C LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C
#>
#> attached base packages:
#> [1] grid stats graphics grDevices utils datasets methods base
#>
#> other attached packages:
#> [1] genefilter_1.74.0 ComplexHeatmap_2.8.0 markdown_1.1 knitr_1.33
#> [5] matrixStats_0.59.0 cola_1.9.4
#>
#> loaded via a namespace (and not attached):
#> [1] bitops_1.0-7 bit64_4.0.5 doParallel_1.0.16 RColorBrewer_1.1-2
#> [5] httr_1.4.2 GenomeInfoDb_1.28.1 data.tree_1.0.0 tools_4.1.0
#> [9] utf8_1.2.1 R6_2.5.0 irlba_2.3.3 DBI_1.1.1
#> [13] BiocGenerics_0.38.0 colorspace_2.0-2 GetoptLong_1.0.5 gridExtra_2.3
#> [17] tidyselect_1.1.1 bit_4.0.4 compiler_4.1.0 Biobase_2.52.0
#> [21] Cairo_1.5-12.2 xml2_1.3.2 microbenchmark_1.4-7 slam_0.1-48
#> [25] scales_1.1.1 askpass_1.1 stringr_1.4.0 digest_0.6.27
#> [29] XVector_0.32.0 pkgconfig_2.0.3 umap_0.2.7.0 fastmap_1.1.0
#> [33] highr_0.9 rlang_0.4.11 GlobalOptions_0.1.2 rstudioapi_0.13
#> [37] RSQLite_2.2.7 impute_1.66.0 generics_0.1.0 shape_1.4.6
#> [41] jsonlite_1.7.2 mclust_5.4.7 dplyr_1.0.7 dendextend_1.15.1
#> [45] RCurl_1.98-1.3 magrittr_2.0.1 GenomeInfoDbData_1.2.6 Matrix_1.3-4
#> [49] fansi_0.5.0 Rcpp_1.0.7 munsell_0.5.0 S4Vectors_0.30.0
#> [53] viridis_0.6.1 reticulate_1.20 lifecycle_1.0.0 scatterplot3d_0.3-41
#> [57] stringi_1.7.3 zlibbioc_1.38.0 blob_1.2.1 parallel_4.1.0
#> [61] crayon_1.4.1 lattice_0.20-44 Biostrings_2.60.1 splines_4.1.0
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#> [77] vctrs_0.3.8 foreach_1.5.1 polyclip_1.10-0 purrr_0.3.4
#> [81] gtable_0.3.0 openssl_1.4.4 assertthat_0.2.1 clue_0.3-59
#> [85] cachem_1.0.5 ggplot2_3.3.5 xfun_0.24 eulerr_6.1.0
#> [89] xtable_1.8-4 skmeans_0.2-13 RSpectra_0.16-0 viridisLite_0.4.0
#> [93] survival_3.2-11 tibble_3.1.2 Polychrome_1.3.1 iterators_1.0.13
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