Date: 2021-07-22 18:26:29 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 375975 rows and 480 columns.
#> Performed in total 82600 partitions.
#> There are 42 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, 480 cols
#> |-- 01, 108 cols, 4521 signatures
#> | |-- 011, 36 cols, 2 signatures (c)
#> | |-- 012, 37 cols, 373 signatures (c)
#> | |-- 013, 8 cols (b)
#> | `-- 014, 27 cols, 1256 signatures
#> | |-- 0141, 15 cols, 7 signatures (c)
#> | |-- 0142, 7 cols (b)
#> | |-- 0143, 2 cols (b)
#> | `-- 0144, 3 cols (b)
#> |-- 02, 112 cols, 3997 signatures
#> | |-- 021, 42 cols, 3886 signatures
#> | | |-- 0211, 13 cols, 516 signatures (c)
#> | | |-- 0212, 12 cols, 304 signatures (c)
#> | | `-- 0213, 17 cols, 4193 signatures
#> | | |-- 02131, 9 cols (b)
#> | | |-- 02132, 3 cols (b)
#> | | `-- 02133, 5 cols (b)
#> | |-- 022, 47 cols, 261 signatures (c)
#> | `-- 023, 23 cols, 2035 signatures
#> | |-- 0231, 10 cols (b)
#> | |-- 0232, 9 cols (b)
#> | `-- 0233, 4 cols (b)
#> |-- 03, 10 cols (b)
#> |-- 04, 129 cols, 3674 signatures
#> | |-- 041, 50 cols, 3386 signatures
#> | | |-- 0411, 15 cols, 1744 signatures
#> | | | |-- 04111, 6 cols (b)
#> | | | |-- 04112, 5 cols (b)
#> | | | |-- 04113, 2 cols (b)
#> | | | `-- 04114, 2 cols (b)
#> | | |-- 0412, 13 cols, 1 signatures (c)
#> | | `-- 0413, 22 cols, 176 signatures (c)
#> | |-- 042, 43 cols, 133 signatures (c)
#> | `-- 043, 36 cols, 1947 signatures
#> | |-- 0431, 17 cols, 54 signatures (c)
#> | |-- 0432, 12 cols, 34 signatures (c)
#> | `-- 0433, 7 cols (b)
#> |-- 05, 52 cols, 14438 signatures
#> | |-- 051, 21 cols, 3246 signatures
#> | | |-- 0511, 10 cols (b)
#> | | `-- 0512, 11 cols (b)
#> | |-- 052, 11 cols (b)
#> | |-- 053, 2 cols (b)
#> | `-- 054, 18 cols, 3555 signatures
#> | |-- 0541, 9 cols (b)
#> | |-- 0542, 6 cols (b)
#> | `-- 0543, 3 cols (b)
#> |-- 06, 55 cols, 4860 signatures
#> | |-- 061, 23 cols, 185 signatures (c)
#> | |-- 062, 29 cols, 1144 signatures
#> | | |-- 0621, 14 cols, 4 signatures (c)
#> | | |-- 0622, 7 cols (b)
#> | | `-- 0623, 8 cols (b)
#> | `-- 063, 3 cols (b)
#> `-- 07, 14 cols, 5214 signatures
#> |-- 071, 6 cols (b)
#> |-- 072, 6 cols (b)
#> `-- 073, 2 cols (b)
#> 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] 375975 480
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" "012" "013" "014" "0141" "0142" "0143" "0144" "02" "021"
#> [13] "0211" "0212" "0213" "02131" "02132" "02133" "022" "023" "0231" "0232" "0233" "03"
#> [25] "04" "041" "0411" "04111" "04112" "04113" "04114" "0412" "0413" "042" "043" "0431"
#> [37] "0432" "0433" "05" "051" "0511" "0512" "052" "053" "054" "0541" "0542" "0543"
#> [49] "06" "061" "062" "0621" "0622" "0623" "063" "07" "071" "072" "073"
all_leaves(res_rh)
#> [1] "011" "012" "013" "0141" "0142" "0143" "0144" "0211" "0212" "02131" "02132" "02133"
#> [13] "022" "0231" "0232" "0233" "03" "04111" "04112" "04113" "04114" "0412" "0413" "042"
#> [25] "0431" "0432" "0433" "0511" "0512" "052" "053" "0541" "0542" "0543" "061" "0621"
#> [37] "0622" "0623" "063" "071" "072" "073"
node_info(res_rh)
#> id best_method depth best_k n_columns n_signatures p_signatures is_leaf
#> 1 0 ATC:skmeans 1 7 480 28962 7.70e-02 FALSE
#> 2 01 ATC:skmeans 2 4 108 4521 1.20e-02 FALSE
#> 3 011 ATC:skmeans 3 3 36 2 5.32e-06 TRUE
#> 4 012 ATC:kmeans 3 3 37 373 9.92e-04 TRUE
#> 5 013 not applied 3 NA 8 NA NA TRUE
#> 6 014 ATC:skmeans 3 4 27 1256 3.34e-03 FALSE
#> 7 0141 ATC:skmeans 4 2 15 7 1.86e-05 TRUE
#> 8 0142 not applied 4 NA 7 NA NA TRUE
#> 9 0143 not applied 4 NA 2 NA NA TRUE
#> 10 0144 not applied 4 NA 3 NA NA TRUE
#> 11 02 SD:skmeans 2 3 112 3997 1.06e-02 FALSE
#> 12 021 ATC:kmeans 3 3 42 3886 1.03e-02 FALSE
#> 13 0211 SD:kmeans 4 3 13 516 1.37e-03 TRUE
#> 14 0212 ATC:skmeans 4 3 12 304 8.09e-04 TRUE
#> 15 0213 ATC:skmeans 4 3 17 4193 1.12e-02 FALSE
#> 16 02131 not applied 5 NA 9 NA NA TRUE
#> 17 02132 not applied 5 NA 3 NA NA TRUE
#> 18 02133 not applied 5 NA 5 NA NA TRUE
#> 19 022 ATC:kmeans 3 2 47 261 6.94e-04 TRUE
#> 20 023 ATC:skmeans 3 3 23 2035 5.41e-03 FALSE
#> 21 0231 not applied 4 NA 10 NA NA TRUE
#> 22 0232 not applied 4 NA 9 NA NA TRUE
#> 23 0233 not applied 4 NA 4 NA NA TRUE
#> 24 03 not applied 2 NA 10 NA NA TRUE
#> 25 04 SD:skmeans 2 3 129 3674 9.77e-03 FALSE
#> 26 041 ATC:skmeans 3 3 50 3386 9.01e-03 FALSE
#> 27 0411 ATC:kmeans 4 4 15 1744 4.64e-03 FALSE
#> 28 04111 not applied 5 NA 6 NA NA TRUE
#> 29 04112 not applied 5 NA 5 NA NA TRUE
#> 30 04113 not applied 5 NA 2 NA NA TRUE
#> 31 04114 not applied 5 NA 2 NA NA TRUE
#> 32 0412 ATC:kmeans 4 3 13 1 2.66e-06 TRUE
#> 33 0413 ATC:kmeans 4 2 22 176 4.68e-04 TRUE
#> 34 042 ATC:skmeans 3 2 43 133 3.54e-04 TRUE
#> 35 043 ATC:kmeans 3 3 36 1947 5.18e-03 FALSE
#> 36 0431 ATC:kmeans 4 2 17 54 1.44e-04 TRUE
#> 37 0432 ATC:skmeans 4 3 12 34 9.04e-05 TRUE
#> 38 0433 not applied 4 NA 7 NA NA TRUE
#> 39 05 ATC:skmeans 2 4 52 14438 3.84e-02 FALSE
#> 40 051 SD:kmeans 3 2 21 3246 8.63e-03 FALSE
#> 41 0511 not applied 4 NA 10 NA NA TRUE
#> 42 0512 not applied 4 NA 11 NA NA TRUE
#> 43 052 not applied 3 NA 11 NA NA TRUE
#> 44 053 not applied 3 NA 2 NA NA TRUE
#> 45 054 ATC:kmeans 3 3 18 3555 9.46e-03 FALSE
#> 46 0541 not applied 4 NA 9 NA NA TRUE
#> 47 0542 not applied 4 NA 6 NA NA TRUE
#> 48 0543 not applied 4 NA 3 NA NA TRUE
#> 49 06 ATC:skmeans 2 3 55 4860 1.29e-02 FALSE
#> 50 061 ATC:kmeans 3 3 23 185 4.92e-04 TRUE
#> 51 062 ATC:skmeans 3 3 29 1144 3.04e-03 FALSE
#> 52 0621 ATC:skmeans 4 3 14 4 1.06e-05 TRUE
#> 53 0622 not applied 4 NA 7 NA NA TRUE
#> 54 0623 not applied 4 NA 8 NA NA TRUE
#> 55 063 not applied 3 NA 3 NA NA TRUE
#> 56 07 SD:skmeans 2 3 14 5214 1.39e-02 FALSE
#> 57 071 not applied 3 NA 6 NA NA TRUE
#> 58 072 not applied 3 NA 6 NA NA TRUE
#> 59 073 not applied 3 NA 2 NA NA 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 | ATC:skmeans | 8 | 0.91 | 0.88 | 0.92 | 480 | * | |
| Node01 | ATC:skmeans | 5 | 1.00 | 0.98 | 0.99 | 108 | ** | |
| Node011-leaf | ATC:skmeans | ✓ (c) | 3 | 1.00 | 1.00 | 1.00 | 36 | ** |
| Node012-leaf | ATC:kmeans | ✓ (c) | 3 | 1.00 | 1.00 | 1.00 | 37 | ** |
| Node013-leaf | not applied | ✓ (b) | 8 | |||||
| Node014 | ATC:skmeans | 6 | 0.90 | 0.90 | 0.96 | 27 | * | |
| Node0141-leaf | ATC:skmeans | ✓ (c) | 3 | 0.90 | 0.94 | 0.97 | 15 | * |
| Node0142-leaf | not applied | ✓ (b) | 7 | |||||
| Node0143-leaf | not applied | ✓ (b) | 2 | |||||
| Node0144-leaf | not applied | ✓ (b) | 3 | |||||
| Node02 | SD:skmeans | 3 | 1.00 | 0.99 | 1.00 | 112 | ** | |
| Node021 | ATC:kmeans | 3 | 1.00 | 0.97 | 0.99 | 42 | ** | |
| Node0211-leaf | SD:kmeans | ✓ (c) | 3 | 0.97 | 0.96 | 0.97 | 13 | ** |
| Node0212-leaf | ATC:skmeans | ✓ (c) | 3 | 1.00 | 0.92 | 1.00 | 12 | ** |
| Node0213 | ATC:skmeans | 3 | 1.00 | 1.00 | 1.00 | 17 | ** | |
| Node02131-leaf | not applied | ✓ (b) | 9 | |||||
| Node02132-leaf | not applied | ✓ (b) | 3 | |||||
| Node02133-leaf | not applied | ✓ (b) | 5 | |||||
| Node022-leaf | ATC:kmeans | ✓ (c) | 2 | 1.00 | 0.98 | 0.99 | 47 | ** |
| Node023 | ATC:skmeans | 3 | 1.00 | 0.96 | 0.98 | 23 | ** | |
| Node0231-leaf | not applied | ✓ (b) | 10 | |||||
| Node0232-leaf | not applied | ✓ (b) | 9 | |||||
| Node0233-leaf | not applied | ✓ (b) | 4 | |||||
| Node03-leaf | not applied | ✓ (b) | 10 | |||||
| Node04 | SD:skmeans | 3 | 0.99 | 0.95 | 0.98 | 129 | ** | |
| Node041 | ATC:skmeans | 4 | 0.92 | 0.93 | 0.97 | 50 | * | |
| Node0411 | ATC:kmeans | 6 | 0.91 | 0.73 | 0.94 | 15 | * | |
| Node04111-leaf | not applied | ✓ (b) | 6 | |||||
| Node04112-leaf | not applied | ✓ (b) | 5 | |||||
| Node04113-leaf | not applied | ✓ (b) | 2 | |||||
| Node04114-leaf | not applied | ✓ (b) | 2 | |||||
| Node0412-leaf | ATC:kmeans | ✓ (c) | 8 | 0.91 | 0.54 | 0.95 | 13 | * |
| Node0413-leaf | ATC:kmeans | ✓ (c) | 2 | 1.00 | 0.96 | 0.98 | 22 | ** |
| Node042-leaf | ATC:skmeans | ✓ (c) | 2 | 1.00 | 1.00 | 1.00 | 43 | ** |
| Node043 | ATC:kmeans | 3 | 1.00 | 0.99 | 0.98 | 36 | ** | |
| Node0431-leaf | ATC:kmeans | ✓ (c) | 3 | 1.00 | 0.94 | 1.00 | 17 | ** |
| Node0432-leaf | ATC:skmeans | ✓ (c) | 5 | 0.92 | 0.85 | 0.98 | 12 | * |
| Node0433-leaf | not applied | ✓ (b) | 7 | |||||
| Node05 | ATC:skmeans | 4 | 1.00 | 1.00 | 1.00 | 52 | ** | |
| Node051 | SD:kmeans | 2 | 1.00 | 1.00 | 1.00 | 21 | ** | |
| Node0511-leaf | not applied | ✓ (b) | 10 | |||||
| Node0512-leaf | not applied | ✓ (b) | 11 | |||||
| Node052-leaf | not applied | ✓ (b) | 11 | |||||
| Node053-leaf | not applied | ✓ (b) | 2 | |||||
| Node054 | ATC:kmeans | 3 | 0.95 | 0.99 | 0.99 | 18 | * | |
| Node0541-leaf | not applied | ✓ (b) | 9 | |||||
| Node0542-leaf | not applied | ✓ (b) | 6 | |||||
| Node0543-leaf | not applied | ✓ (b) | 3 | |||||
| Node06 | ATC:skmeans | 8 | 0.92 | 0.81 | 0.95 | 55 | * | |
| Node061-leaf | ATC:kmeans | ✓ (c) | 6 | 0.91 | 0.87 | 0.91 | 23 | * |
| Node062 | ATC:skmeans | 3 | 1.00 | 0.97 | 0.98 | 29 | ** | |
| Node0621-leaf | ATC:skmeans | ✓ (c) | 7 | 0.96 | 0.61 | 0.97 | 14 | ** |
| Node0622-leaf | not applied | ✓ (b) | 7 | |||||
| Node0623-leaf | not applied | ✓ (b) | 8 | |||||
| Node063-leaf | not applied | ✓ (b) | 3 | |||||
| Node07 | SD:skmeans | 2 | 1.00 | 1.00 | 1.00 | 14 | ** | |
| Node071-leaf | not applied | ✓ (b) | 6 | |||||
| Node072-leaf | not applied | ✓ (b) | 6 | |||||
| Node073-leaf | not applied | ✓ (b) | 2 |
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 = 1144))
collect_classes(res_rh, merge_node = merge_node_param(min_n_signatures = 1256))
collect_classes(res_rh, merge_node = merge_node_param(min_n_signatures = 1744))
collect_classes(res_rh, merge_node = merge_node_param(min_n_signatures = 1947))
collect_classes(res_rh, merge_node = merge_node_param(min_n_signatures = 2035))
collect_classes(res_rh, merge_node = merge_node_param(min_n_signatures = 3246))
collect_classes(res_rh, merge_node = merge_node_param(min_n_signatures = 3386))
collect_classes(res_rh, merge_node = merge_node_param(min_n_signatures = 3555))
collect_classes(res_rh, merge_node = merge_node_param(min_n_signatures = 3674))
collect_classes(res_rh, merge_node = merge_node_param(min_n_signatures = 3886))
collect_classes(res_rh, merge_node = merge_node_param(min_n_signatures = 3997))
collect_classes(res_rh, merge_node = merge_node_param(min_n_signatures = 4193))
collect_classes(res_rh, merge_node = merge_node_param(min_n_signatures = 4521))
collect_classes(res_rh, merge_node = merge_node_param(min_n_signatures = 4860))
collect_classes(res_rh, merge_node = merge_node_param(min_n_signatures = 5214))
collect_classes(res_rh, merge_node = merge_node_param(min_n_signatures = 14438))
collect_classes(res_rh, merge_node = merge_node_param(min_n_signatures = 28962))
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 = 1144))
#> TCGA.CZ.4863.01 TCGA.CJ.4904.11 TCGA.B0.4827.11 TCGA.CJ.4902.01 TCGA.B0.4823.01 TCGA.CW.6087.01
#> "0412" "011" "0543" "0431" "061" "0433"
#> TCGA.B0.5098.01 TCGA.B0.5113.01 TCGA.DV.5566.01 TCGA.BP.5175.11 TCGA.BP.5181.01 TCGA.B0.4706.11
#> "073" "0233" "04112" "012" "0621" "012"
#> TCGA.B0.5117.01 TCGA.MM.A564.01 TCGA.B0.4821.11 TCGA.CZ.5463.11 TCGA.BP.5182.11 TCGA.DV.5574.01
#> "013" "02133" "072" "0512" "012" "061"
#> TCGA.B0.5094.11 TCGA.MM.A84U.01 TCGA.B0.5100.11 TCGA.B4.5844.01 TCGA.CZ.5459.01 TCGA.B0.4694.01
#> "0144" "0413" "0141" "04111" "042" "0432"
#> TCGA.CZ.5468.11 TCGA.CJ.4916.11 TCGA.B4.5836.01 TCGA.B0.5095.01 TCGA.B0.4846.11 TCGA.AK.3434.01
#> "0512" "011" "0413" "0432" "011" "022"
#> TCGA.B4.5377.01 TCGA.B0.4696.11 TCGA.BP.5187.11 TCGA.B0.4690.01 TCGA.CZ.5466.01 TCGA.B0.4844.11
#> "0622" "0142" "0141" "0433" "0432" "052"
#> TCGA.CZ.5464.11 TCGA.B0.4701.11 TCGA.BP.5194.11 TCGA.B0.4707.01 TCGA.CZ.5467.11 TCGA.B0.5705.01
#> "012" "011" "012" "02131" "0511" "0622"
#> TCGA.CW.5588.01 TCGA.CJ.6031.01 TCGA.B8.A54J.01 TCGA.BP.5192.11 TCGA.CZ.5462.01 TCGA.B8.A54H.01
#> "0413" "0431" "042" "052" "0432" "0413"
#> TCGA.CZ.5470.11 TCGA.BP.4177.11 TCGA.CZ.5469.11 TCGA.CJ.6028.01 TCGA.G6.A8L6.01 TCGA.B8.5551.01
#> "0511" "052" "0512" "0432" "042" "0412"
#> TCGA.CZ.5456.01 TCGA.A3.A8OU.01 TCGA.BP.5186.01 TCGA.A3.A6NI.01 TCGA.BP.4782.01 TCGA.CZ.5454.11
#> "0211" "0413" "0623" "042" "0413" "0541"
#> TCGA.B0.4691.11 TCGA.CZ.5452.01 TCGA.EU.5904.01 TCGA.BP.5201.01 TCGA.CJ.5677.01 TCGA.BP.5170.11
#> "012" "02131" "0621" "022" "0232" "0541"
#> TCGA.B0.4710.11 TCGA.AK.3425.01 TCGA.B0.4841.11 TCGA.B0.4849.01 TCGA.BP.5182.01 TCGA.B0.5711.11
#> "0511" "02131" "0142" "042" "063" "052"
#> TCGA.BP.5180.01 TCGA.BP.5176.01 TCGA.CZ.5984.01 TCGA.CZ.5460.11 TCGA.BP.5190.01 TCGA.BP.4795.11
#> "0212" "0413" "0212" "012" "022" "011"
#> TCGA.B0.4813.11 TCGA.B0.4713.01 TCGA.B0.4841.01 TCGA.B8.5546.01 TCGA.CW.5591.01 TCGA.B0.4698.11
#> "0542" "0232" "022" "072" "0431" "0141"
#> TCGA.B0.5713.11 TCGA.B0.5108.11 TCGA.B0.5083.01 TCGA.B0.5699.01 TCGA.CZ.5453.11 TCGA.BP.5202.01
#> "011" "012" "013" "022" "0512" "022"
#> TCGA.BP.5173.11 TCGA.CW.5581.01 TCGA.B0.4848.11 TCGA.B0.4814.01 TCGA.BP.5178.11 TCGA.CJ.4907.01
#> "013" "042" "0142" "022" "0144" "042"
#> TCGA.A3.3387.01 TCGA.B0.4821.01 TCGA.B0.5712.01 TCGA.B0.5695.01 TCGA.BP.5184.11 TCGA.B2.A4SR.01
#> "042" "0232" "0231" "0622" "012" "042"
#> TCGA.BP.5191.11 TCGA.CJ.4920.01 TCGA.BP.4801.01 TCGA.DV.A4W0.01 TCGA.BP.5177.11 TCGA.B0.4847.11
#> "0143" "0231" "042" "022" "011" "052"
#> TCGA.B0.5100.01 TCGA.CJ.4903.01 TCGA.CJ.4912.01 TCGA.B0.5107.11 TCGA.AK.3453.01 TCGA.B0.5691.01
#> "0431" "022" "0212" "011" "013" "0621"
#> TCGA.BP.5195.11 TCGA.B0.5400.01 TCGA.A3.3376.11 TCGA.B0.4845.01 TCGA.B0.4699.01 TCGA.B0.4818.01
#> "0541" "0412" "071" "022" "071" "0413"
#> TCGA.BP.5174.11 TCGA.CJ.4901.11 TCGA.B8.A54D.01 TCGA.BP.4770.11 TCGA.CW.6093.01 TCGA.BP.5010.11
#> "011" "012" "022" "011" "061" "0541"
#> TCGA.AK.3431.01 TCGA.BP.4770.01 TCGA.BP.5189.01 TCGA.B0.4703.11 TCGA.B8.5163.01 TCGA.CJ.5683.01
#> "0413" "0412" "0431" "0142" "0412" "042"
#> TCGA.CZ.4856.11 TCGA.BP.4760.01 TCGA.B0.5692.01 TCGA.B0.5106.01 TCGA.B0.4843.01 TCGA.CZ.4866.11
#> "0511" "03" "0231" "0212" "0431" "0511"
#> TCGA.B0.5104.11 TCGA.B0.4827.01 TCGA.CJ.4902.11 TCGA.B8.A54G.01 TCGA.B0.5703.01 TCGA.CJ.5672.01
#> "011" "0232" "0541" "042" "042" "042"
#> TCGA.B0.5098.11 TCGA.B0.5113.11 TCGA.CJ.4882.11 TCGA.CZ.5465.11 TCGA.B0.5102.01 TCGA.CW.5585.01
#> "013" "011" "012" "0511" "04112" "042"
#> TCGA.B0.4824.01 TCGA.B0.5115.01 TCGA.B0.4706.01 TCGA.B0.5117.11 TCGA.CZ.4859.11 TCGA.AK.3450.01
#> "0413" "022" "022" "012" "0543" "0413"
#> TCGA.B8.A54I.01 TCGA.CZ.5463.01 TCGA.DV.5568.01 TCGA.CZ.5459.11 TCGA.CJ.4918.11 TCGA.DV.5565.01
#> "0212" "022" "0431" "0141" "0144" "042"
#> TCGA.B0.5119.01 TCGA.B0.4811.01 TCGA.A3.3367.11 TCGA.CJ.4916.01 TCGA.B0.5693.01 TCGA.CZ.4863.11
#> "0622" "042" "0141" "0412" "04112" "0511"
#> TCGA.G6.A5PC.01 TCGA.B8.5550.01 TCGA.DV.A4W0.05 TCGA.B0.4696.01 TCGA.BP.5187.01 TCGA.CZ.5466.11
#> "0231" "0431" "03" "0212" "0431" "0141"
#> TCGA.CW.6097.01 TCGA.CJ.4905.11 TCGA.CZ.5989.01 TCGA.BP.5194.01 TCGA.B0.4707.11 TCGA.CZ.5467.01
#> "0433" "052" "042" "042" "0142" "04112"
#> TCGA.BP.5185.11 TCGA.BP.5183.11 TCGA.BP.5192.01 TCGA.CZ.5462.11 TCGA.BP.4177.01 TCGA.CZ.5469.01
#> "012" "012" "061" "0512" "03" "0211"
#> TCGA.B2.5641.01 TCGA.BP.5196.11 TCGA.CZ.5460.01 TCGA.B0.4712.01 TCGA.B8.A54K.01 TCGA.B0.5707.01
#> "0212" "012" "022" "0211" "03" "0623"
#> TCGA.BP.5186.11 TCGA.EU.5906.01 TCGA.CZ.5461.11 TCGA.CW.5590.01 TCGA.B0.5698.01 TCGA.CW.5580.01
#> "011" "061" "0541" "022" "022" "0231"
#> TCGA.CZ.5454.01 TCGA.B0.4815.01 TCGA.B0.5710.11 TCGA.CJ.4908.11 TCGA.BP.5201.11 TCGA.B0.5694.01
#> "022" "0211" "012" "0541" "012" "022"
#> TCGA.BP.5170.01 TCGA.DV.5575.01 TCGA.CJ.5686.01 TCGA.A3.3357.01 TCGA.A3.3373.01 TCGA.B0.5690.01
#> "042" "0621" "0412" "022" "04113" "0621"
#> TCGA.B8.4622.01 TCGA.AK.3433.01 TCGA.B0.5110.01 TCGA.BP.5180.11 TCGA.CJ.4913.01 TCGA.CJ.4908.01
#> "022" "053" "0623" "012" "0231" "042"
#> TCGA.BP.4795.01 TCGA.CJ.4897.11 TCGA.B2.5636.01 TCGA.CJ.4923.11 TCGA.B0.4819.01 TCGA.B2.5633.01
#> "03" "011" "03" "0141" "0412" "0431"
#> TCGA.CJ.6033.01 TCGA.BP.5181.11 TCGA.B0.4698.01 TCGA.B0.5083.11 TCGA.CZ.4864.11 TCGA.B0.4688.01
#> "0232" "011" "02132" "012" "0141" "02132"
#> TCGA.BP.5168.01 TCGA.BP.5198.11 TCGA.B8.5162.01 TCGA.B0.5096.01 TCGA.BP.5178.01 TCGA.B0.5099.11
#> "042" "0141" "0432" "0232" "0211" "011"
#> TCGA.B0.4842.01 TCGA.BP.5169.11 TCGA.B0.5109.11 TCGA.CJ.4920.11 TCGA.B0.5080.11 TCGA.B0.5700.01
#> "0412" "0141" "071" "0542" "012" "061"
#> TCGA.B0.4847.01 TCGA.B0.5702.01 TCGA.CJ.4905.01 TCGA.B2.5635.01 TCGA.B0.5107.01 TCGA.CW.5584.01
#> "022" "071" "04111" "042" "0232" "022"
#> TCGA.B4.5838.01 TCGA.BP.5199.01 TCGA.A3.3376.01 TCGA.B0.4845.11 TCGA.B0.4699.11 TCGA.BP.5174.01
#> "042" "022" "061" "0542" "0143" "0621"
#> TCGA.CZ.5986.01 TCGA.CJ.4901.01 TCGA.AK.3461.01 TCGA.AK.3460.01 TCGA.AK.3454.01 TCGA.CZ.4859.01
#> "061" "02131" "042" "042" "061" "0622"
#> TCGA.B0.5812.01 TCGA.B0.5116.11 TCGA.B8.A54F.01 TCGA.CW.6090.01 TCGA.CZ.5458.11 TCGA.B0.5106.11
#> "042" "071" "0413" "022" "0512" "012"
#> TCGA.CZ.4866.01 TCGA.B0.4828.01 TCGA.AK.3440.01 TCGA.MM.A563.01 TCGA.B0.4697.01 TCGA.AK.3458.01
#> "0231" "022" "053" "022" "0412" "022"
#> TCGA.CJ.5676.01 TCGA.B0.5402.11 TCGA.CJ.5681.01 TCGA.A3.3370.11 TCGA.A3.A6NL.01 TCGA.B0.4693.01
#> "02133" "0141" "073" "052" "0621" "0231"
#> TCGA.A3.3358.01 TCGA.B0.4710.01 TCGA.CZ.4853.11 TCGA.B4.5835.01 TCGA.CJ.4882.01 TCGA.CZ.5465.01
#> "0413" "0231" "0541" "0623" "0432" "0233"
#> TCGA.B0.5102.11 TCGA.B0.4824.11 TCGA.CJ.5675.01 TCGA.B0.4700.01 TCGA.B0.5092.01 TCGA.B0.5115.11
#> "011" "011" "022" "0433" "0412" "012"
#> TCGA.B0.4945.11 TCGA.B8.5158.01 TCGA.CJ.6030.01 TCGA.B8.A54E.01 TCGA.CJ.6032.01 TCGA.B0.4852.11
#> "011" "02131" "02131" "072" "04111" "011"
#> TCGA.B0.4817.01 TCGA.B8.5159.01 TCGA.A3.A8OW.01 TCGA.B0.4822.01 TCGA.B0.5696.01 TCGA.B0.5706.01
#> "0433" "0233" "061" "0432" "042" "0212"
#> TCGA.CJ.4918.01 TCGA.B0.5119.11 TCGA.BP.5200.11 TCGA.B0.4811.11 TCGA.A3.3367.01 TCGA.B0.5097.01
#> "0431" "0511" "012" "0141" "022" "0412"
#> TCGA.6D.AA2E.01 TCGA.DV.A4VX.01 TCGA.B0.4816.11 TCGA.A3.3385.11 TCGA.DV.5569.01 TCGA.EU.5907.01
#> "072" "022" "0541" "011" "0621" "022"
#> TCGA.CZ.5455.01 TCGA.B8.5545.01 TCGA.DV.5567.01 TCGA.CZ.5451.01 TCGA.CJ.4869.01 TCGA.CJ.5678.01
#> "042" "061" "03" "042" "0432" "022"
#> TCGA.B8.4153.01 TCGA.B0.5121.11 TCGA.B8.4146.01 TCGA.BP.5183.01 TCGA.B0.5399.01 TCGA.B0.4810.11
#> "022" "012" "04113" "022" "042" "052"
#> TCGA.AK.3445.01 TCGA.B4.5378.01 TCGA.BP.5196.01 TCGA.CZ.4865.11 TCGA.B0.5709.01 TCGA.B0.4712.11
#> "0211" "03" "02131" "0511" "0623" "0512"
#> TCGA.B0.4714.01 TCGA.B8.5549.01 TCGA.CZ.5461.01 TCGA.CZ.5457.01 TCGA.A3.A8CQ.01 TCGA.DV.5573.01
#> "022" "022" "0211" "063" "0622" "061"
#> TCGA.B0.4815.11 TCGA.B0.5710.01 TCGA.B8.5165.01 TCGA.B0.4718.01 TCGA.B2.5639.01 TCGA.CW.5583.01
#> "0141" "022" "061" "022" "0431" "0621"
#> TCGA.GK.A6C7.01 TCGA.A3.3357.11 TCGA.B8.5552.01 TCGA.B0.5120.01 TCGA.A3.3373.11 TCGA.BP.5185.01
#> "0623" "012" "0621" "0413" "0543" "042"
#> TCGA.B0.4846.01 TCGA.CJ.4904.01 TCGA.CJ.4913.11 TCGA.BP.4993.11 TCGA.B0.4823.11 TCGA.CJ.4897.01
#> "0413" "0621" "011" "012" "013" "04112"
#> TCGA.BP.4993.01 TCGA.B4.5843.01 TCGA.DV.5576.01 TCGA.CJ.4923.01 TCGA.B0.4819.11 TCGA.BP.5175.01
#> "061" "061" "03" "0432" "011" "0212"
#> TCGA.CZ.5987.01 TCGA.CZ.4864.01 TCGA.B0.4688.11 TCGA.BP.5168.11 TCGA.BP.5198.01 TCGA.B8.A7U6.01
#> "02133" "061" "0542" "0141" "0211" "0413"
#> TCGA.B0.5094.01 TCGA.T7.A92I.01 TCGA.B0.5096.11 TCGA.B0.5400.11 TCGA.B0.4694.11 TCGA.B0.5099.01
#> "0211" "072" "011" "011" "052" "04114"
#> TCGA.CZ.5468.01 TCGA.B0.4842.11 TCGA.CZ.5988.01 TCGA.BP.5169.01 TCGA.B0.5109.01 TCGA.B4.5834.01
#> "02132" "011" "042" "0211" "0433" "061"
#> TCGA.B0.5095.11 TCGA.B0.5080.01 TCGA.CJ.5680.01 TCGA.CZ.5470.01 TCGA.CZ.4865.01 TCGA.A3.A8OX.01
#> "013" "0432" "0231" "0232" "0413" "072"
#> TCGA.B0.4690.11 TCGA.CJ.5684.01 TCGA.B0.4844.01 TCGA.CZ.5464.01 TCGA.B0.4701.01 TCGA.B0.5701.01
#> "013" "042" "02133" "0212" "0412" "0212"
#> TCGA.BP.5199.11 TCGA.CJ.5671.01 TCGA.A3.A8OV.01 TCGA.CZ.5456.11 TCGA.B0.5116.01 TCGA.CZ.5458.01
#> "012" "02131" "061" "0512" "022" "042"
#> TCGA.CZ.5982.01 TCGA.B0.4828.11 TCGA.CJ.5679.01 TCGA.CJ.5682.01 TCGA.B0.5697.01 TCGA.B0.4697.11
#> "04111" "0542" "0211" "022" "042" "0511"
#> TCGA.BP.4782.11 TCGA.G6.A8L8.01 TCGA.A3.A6NJ.01 TCGA.A3.3370.01 TCGA.B0.4691.01 TCGA.CZ.5452.11
#> "011" "0233" "0623" "0621" "0211" "0512"
#> TCGA.B0.4693.11 TCGA.B0.4945.01 TCGA.CZ.4853.01 TCGA.B0.5092.11 TCGA.B0.5402.01 TCGA.B0.4849.11
#> "011" "0621" "022" "011" "022" "012"
#> TCGA.A3.A6NN.01 TCGA.B0.4852.01 TCGA.B0.4817.11 TCGA.BP.5176.11 TCGA.CW.5589.01 TCGA.CJ.5689.01
#> "042" "04114" "0142" "011" "061" "042"
#> TCGA.B0.4822.11 TCGA.BP.5190.11 TCGA.B0.4813.01 TCGA.BP.5200.01 TCGA.G6.A8L7.01 TCGA.B2.4101.01
#> "052" "012" "022" "042" "0232" "0431"
#> TCGA.B0.4713.11 TCGA.B0.4816.01 TCGA.A3.3385.01 TCGA.B2.3924.01 TCGA.CZ.5455.11 TCGA.B0.5713.01
#> "011" "0431" "0622" "042" "0512" "04111"
#> TCGA.B0.5108.01 TCGA.B0.5711.01 TCGA.CZ.5453.01 TCGA.BP.5202.11 TCGA.BP.5173.01 TCGA.CZ.5451.11
#> "0431" "042" "061" "071" "061" "012"
#> TCGA.B8.A8YJ.01 TCGA.B0.4848.01 TCGA.DV.A4VZ.01 TCGA.B0.4814.11 TCGA.CJ.4869.11 TCGA.CJ.4907.11
#> "0623" "02131" "03" "012" "012" "012"
#> TCGA.B8.5553.01 TCGA.MW.A4EC.01 TCGA.B0.5712.11 TCGA.EU.5905.01 TCGA.CZ.5985.01 TCGA.CZ.4856.01
#> "0413" "04111" "011" "0413" "02133" "0413"
#> TCGA.BP.5184.01 TCGA.B0.5121.01 TCGA.BP.5191.01 TCGA.BP.4801.11 TCGA.BP.5177.01 TCGA.B0.5110.11
#> "042" "022" "0212" "012" "0621" "011"
#> TCGA.B0.4810.01 TCGA.CJ.4903.11 TCGA.CJ.4912.11 TCGA.B8.4621.01 TCGA.B4.5832.01 TCGA.CW.6088.01
#> "022" "012" "0542" "063" "0433" "061"
#> TCGA.AK.3428.01 TCGA.B8.5164.01 TCGA.BP.5195.01 TCGA.CJ.6027.01 TCGA.3Z.A93Z.01 TCGA.B0.4714.11
#> "022" "042" "0431" "0211" "061" "0142"
#> TCGA.B0.4818.11 TCGA.CZ.5457.11 TCGA.BP.5010.01 TCGA.BP.5189.11 TCGA.B0.4703.01 TCGA.B0.4718.11
#> "011" "0512" "0431" "012" "0432" "052"
#> TCGA.B0.5097.11 TCGA.BP.4760.11 TCGA.B0.5120.11 TCGA.B0.4843.11 TCGA.B0.5104.01 TCGA.CW.5587.01
#> "011" "0141" "011" "012" "0413" "0413"
get_classes(res_rh, merge_node = merge_node_param(min_n_signatures = 1256))
#> TCGA.CZ.4863.01 TCGA.CJ.4904.11 TCGA.B0.4827.11 TCGA.CJ.4902.01 TCGA.B0.4823.01 TCGA.CW.6087.01
#> "0412" "011" "0543" "0431" "061" "0433"
#> TCGA.B0.5098.01 TCGA.B0.5113.01 TCGA.DV.5566.01 TCGA.BP.5175.11 TCGA.BP.5181.01 TCGA.B0.4706.11
#> "073" "0233" "04112" "012" "062" "012"
#> TCGA.B0.5117.01 TCGA.MM.A564.01 TCGA.B0.4821.11 TCGA.CZ.5463.11 TCGA.BP.5182.11 TCGA.DV.5574.01
#> "013" "02133" "072" "0512" "012" "061"
#> TCGA.B0.5094.11 TCGA.MM.A84U.01 TCGA.B0.5100.11 TCGA.B4.5844.01 TCGA.CZ.5459.01 TCGA.B0.4694.01
#> "0144" "0413" "0141" "04111" "042" "0432"
#> TCGA.CZ.5468.11 TCGA.CJ.4916.11 TCGA.B4.5836.01 TCGA.B0.5095.01 TCGA.B0.4846.11 TCGA.AK.3434.01
#> "0512" "011" "0413" "0432" "011" "022"
#> TCGA.B4.5377.01 TCGA.B0.4696.11 TCGA.BP.5187.11 TCGA.B0.4690.01 TCGA.CZ.5466.01 TCGA.B0.4844.11
#> "062" "0142" "0141" "0433" "0432" "052"
#> TCGA.CZ.5464.11 TCGA.B0.4701.11 TCGA.BP.5194.11 TCGA.B0.4707.01 TCGA.CZ.5467.11 TCGA.B0.5705.01
#> "012" "011" "012" "02131" "0511" "062"
#> TCGA.CW.5588.01 TCGA.CJ.6031.01 TCGA.B8.A54J.01 TCGA.BP.5192.11 TCGA.CZ.5462.01 TCGA.B8.A54H.01
#> "0413" "0431" "042" "052" "0432" "0413"
#> TCGA.CZ.5470.11 TCGA.BP.4177.11 TCGA.CZ.5469.11 TCGA.CJ.6028.01 TCGA.G6.A8L6.01 TCGA.B8.5551.01
#> "0511" "052" "0512" "0432" "042" "0412"
#> TCGA.CZ.5456.01 TCGA.A3.A8OU.01 TCGA.BP.5186.01 TCGA.A3.A6NI.01 TCGA.BP.4782.01 TCGA.CZ.5454.11
#> "0211" "0413" "062" "042" "0413" "0541"
#> TCGA.B0.4691.11 TCGA.CZ.5452.01 TCGA.EU.5904.01 TCGA.BP.5201.01 TCGA.CJ.5677.01 TCGA.BP.5170.11
#> "012" "02131" "062" "022" "0232" "0541"
#> TCGA.B0.4710.11 TCGA.AK.3425.01 TCGA.B0.4841.11 TCGA.B0.4849.01 TCGA.BP.5182.01 TCGA.B0.5711.11
#> "0511" "02131" "0142" "042" "063" "052"
#> TCGA.BP.5180.01 TCGA.BP.5176.01 TCGA.CZ.5984.01 TCGA.CZ.5460.11 TCGA.BP.5190.01 TCGA.BP.4795.11
#> "0212" "0413" "0212" "012" "022" "011"
#> TCGA.B0.4813.11 TCGA.B0.4713.01 TCGA.B0.4841.01 TCGA.B8.5546.01 TCGA.CW.5591.01 TCGA.B0.4698.11
#> "0542" "0232" "022" "072" "0431" "0141"
#> TCGA.B0.5713.11 TCGA.B0.5108.11 TCGA.B0.5083.01 TCGA.B0.5699.01 TCGA.CZ.5453.11 TCGA.BP.5202.01
#> "011" "012" "013" "022" "0512" "022"
#> TCGA.BP.5173.11 TCGA.CW.5581.01 TCGA.B0.4848.11 TCGA.B0.4814.01 TCGA.BP.5178.11 TCGA.CJ.4907.01
#> "013" "042" "0142" "022" "0144" "042"
#> TCGA.A3.3387.01 TCGA.B0.4821.01 TCGA.B0.5712.01 TCGA.B0.5695.01 TCGA.BP.5184.11 TCGA.B2.A4SR.01
#> "042" "0232" "0231" "062" "012" "042"
#> TCGA.BP.5191.11 TCGA.CJ.4920.01 TCGA.BP.4801.01 TCGA.DV.A4W0.01 TCGA.BP.5177.11 TCGA.B0.4847.11
#> "0143" "0231" "042" "022" "011" "052"
#> TCGA.B0.5100.01 TCGA.CJ.4903.01 TCGA.CJ.4912.01 TCGA.B0.5107.11 TCGA.AK.3453.01 TCGA.B0.5691.01
#> "0431" "022" "0212" "011" "013" "062"
#> TCGA.BP.5195.11 TCGA.B0.5400.01 TCGA.A3.3376.11 TCGA.B0.4845.01 TCGA.B0.4699.01 TCGA.B0.4818.01
#> "0541" "0412" "071" "022" "071" "0413"
#> TCGA.BP.5174.11 TCGA.CJ.4901.11 TCGA.B8.A54D.01 TCGA.BP.4770.11 TCGA.CW.6093.01 TCGA.BP.5010.11
#> "011" "012" "022" "011" "061" "0541"
#> TCGA.AK.3431.01 TCGA.BP.4770.01 TCGA.BP.5189.01 TCGA.B0.4703.11 TCGA.B8.5163.01 TCGA.CJ.5683.01
#> "0413" "0412" "0431" "0142" "0412" "042"
#> TCGA.CZ.4856.11 TCGA.BP.4760.01 TCGA.B0.5692.01 TCGA.B0.5106.01 TCGA.B0.4843.01 TCGA.CZ.4866.11
#> "0511" "03" "0231" "0212" "0431" "0511"
#> TCGA.B0.5104.11 TCGA.B0.4827.01 TCGA.CJ.4902.11 TCGA.B8.A54G.01 TCGA.B0.5703.01 TCGA.CJ.5672.01
#> "011" "0232" "0541" "042" "042" "042"
#> TCGA.B0.5098.11 TCGA.B0.5113.11 TCGA.CJ.4882.11 TCGA.CZ.5465.11 TCGA.B0.5102.01 TCGA.CW.5585.01
#> "013" "011" "012" "0511" "04112" "042"
#> TCGA.B0.4824.01 TCGA.B0.5115.01 TCGA.B0.4706.01 TCGA.B0.5117.11 TCGA.CZ.4859.11 TCGA.AK.3450.01
#> "0413" "022" "022" "012" "0543" "0413"
#> TCGA.B8.A54I.01 TCGA.CZ.5463.01 TCGA.DV.5568.01 TCGA.CZ.5459.11 TCGA.CJ.4918.11 TCGA.DV.5565.01
#> "0212" "022" "0431" "0141" "0144" "042"
#> TCGA.B0.5119.01 TCGA.B0.4811.01 TCGA.A3.3367.11 TCGA.CJ.4916.01 TCGA.B0.5693.01 TCGA.CZ.4863.11
#> "062" "042" "0141" "0412" "04112" "0511"
#> TCGA.G6.A5PC.01 TCGA.B8.5550.01 TCGA.DV.A4W0.05 TCGA.B0.4696.01 TCGA.BP.5187.01 TCGA.CZ.5466.11
#> "0231" "0431" "03" "0212" "0431" "0141"
#> TCGA.CW.6097.01 TCGA.CJ.4905.11 TCGA.CZ.5989.01 TCGA.BP.5194.01 TCGA.B0.4707.11 TCGA.CZ.5467.01
#> "0433" "052" "042" "042" "0142" "04112"
#> TCGA.BP.5185.11 TCGA.BP.5183.11 TCGA.BP.5192.01 TCGA.CZ.5462.11 TCGA.BP.4177.01 TCGA.CZ.5469.01
#> "012" "012" "061" "0512" "03" "0211"
#> TCGA.B2.5641.01 TCGA.BP.5196.11 TCGA.CZ.5460.01 TCGA.B0.4712.01 TCGA.B8.A54K.01 TCGA.B0.5707.01
#> "0212" "012" "022" "0211" "03" "062"
#> TCGA.BP.5186.11 TCGA.EU.5906.01 TCGA.CZ.5461.11 TCGA.CW.5590.01 TCGA.B0.5698.01 TCGA.CW.5580.01
#> "011" "061" "0541" "022" "022" "0231"
#> TCGA.CZ.5454.01 TCGA.B0.4815.01 TCGA.B0.5710.11 TCGA.CJ.4908.11 TCGA.BP.5201.11 TCGA.B0.5694.01
#> "022" "0211" "012" "0541" "012" "022"
#> TCGA.BP.5170.01 TCGA.DV.5575.01 TCGA.CJ.5686.01 TCGA.A3.3357.01 TCGA.A3.3373.01 TCGA.B0.5690.01
#> "042" "062" "0412" "022" "04113" "062"
#> TCGA.B8.4622.01 TCGA.AK.3433.01 TCGA.B0.5110.01 TCGA.BP.5180.11 TCGA.CJ.4913.01 TCGA.CJ.4908.01
#> "022" "053" "062" "012" "0231" "042"
#> TCGA.BP.4795.01 TCGA.CJ.4897.11 TCGA.B2.5636.01 TCGA.CJ.4923.11 TCGA.B0.4819.01 TCGA.B2.5633.01
#> "03" "011" "03" "0141" "0412" "0431"
#> TCGA.CJ.6033.01 TCGA.BP.5181.11 TCGA.B0.4698.01 TCGA.B0.5083.11 TCGA.CZ.4864.11 TCGA.B0.4688.01
#> "0232" "011" "02132" "012" "0141" "02132"
#> TCGA.BP.5168.01 TCGA.BP.5198.11 TCGA.B8.5162.01 TCGA.B0.5096.01 TCGA.BP.5178.01 TCGA.B0.5099.11
#> "042" "0141" "0432" "0232" "0211" "011"
#> TCGA.B0.4842.01 TCGA.BP.5169.11 TCGA.B0.5109.11 TCGA.CJ.4920.11 TCGA.B0.5080.11 TCGA.B0.5700.01
#> "0412" "0141" "071" "0542" "012" "061"
#> TCGA.B0.4847.01 TCGA.B0.5702.01 TCGA.CJ.4905.01 TCGA.B2.5635.01 TCGA.B0.5107.01 TCGA.CW.5584.01
#> "022" "071" "04111" "042" "0232" "022"
#> TCGA.B4.5838.01 TCGA.BP.5199.01 TCGA.A3.3376.01 TCGA.B0.4845.11 TCGA.B0.4699.11 TCGA.BP.5174.01
#> "042" "022" "061" "0542" "0143" "062"
#> TCGA.CZ.5986.01 TCGA.CJ.4901.01 TCGA.AK.3461.01 TCGA.AK.3460.01 TCGA.AK.3454.01 TCGA.CZ.4859.01
#> "061" "02131" "042" "042" "061" "062"
#> TCGA.B0.5812.01 TCGA.B0.5116.11 TCGA.B8.A54F.01 TCGA.CW.6090.01 TCGA.CZ.5458.11 TCGA.B0.5106.11
#> "042" "071" "0413" "022" "0512" "012"
#> TCGA.CZ.4866.01 TCGA.B0.4828.01 TCGA.AK.3440.01 TCGA.MM.A563.01 TCGA.B0.4697.01 TCGA.AK.3458.01
#> "0231" "022" "053" "022" "0412" "022"
#> TCGA.CJ.5676.01 TCGA.B0.5402.11 TCGA.CJ.5681.01 TCGA.A3.3370.11 TCGA.A3.A6NL.01 TCGA.B0.4693.01
#> "02133" "0141" "073" "052" "062" "0231"
#> TCGA.A3.3358.01 TCGA.B0.4710.01 TCGA.CZ.4853.11 TCGA.B4.5835.01 TCGA.CJ.4882.01 TCGA.CZ.5465.01
#> "0413" "0231" "0541" "062" "0432" "0233"
#> TCGA.B0.5102.11 TCGA.B0.4824.11 TCGA.CJ.5675.01 TCGA.B0.4700.01 TCGA.B0.5092.01 TCGA.B0.5115.11
#> "011" "011" "022" "0433" "0412" "012"
#> TCGA.B0.4945.11 TCGA.B8.5158.01 TCGA.CJ.6030.01 TCGA.B8.A54E.01 TCGA.CJ.6032.01 TCGA.B0.4852.11
#> "011" "02131" "02131" "072" "04111" "011"
#> TCGA.B0.4817.01 TCGA.B8.5159.01 TCGA.A3.A8OW.01 TCGA.B0.4822.01 TCGA.B0.5696.01 TCGA.B0.5706.01
#> "0433" "0233" "061" "0432" "042" "0212"
#> TCGA.CJ.4918.01 TCGA.B0.5119.11 TCGA.BP.5200.11 TCGA.B0.4811.11 TCGA.A3.3367.01 TCGA.B0.5097.01
#> "0431" "0511" "012" "0141" "022" "0412"
#> TCGA.6D.AA2E.01 TCGA.DV.A4VX.01 TCGA.B0.4816.11 TCGA.A3.3385.11 TCGA.DV.5569.01 TCGA.EU.5907.01
#> "072" "022" "0541" "011" "062" "022"
#> TCGA.CZ.5455.01 TCGA.B8.5545.01 TCGA.DV.5567.01 TCGA.CZ.5451.01 TCGA.CJ.4869.01 TCGA.CJ.5678.01
#> "042" "061" "03" "042" "0432" "022"
#> TCGA.B8.4153.01 TCGA.B0.5121.11 TCGA.B8.4146.01 TCGA.BP.5183.01 TCGA.B0.5399.01 TCGA.B0.4810.11
#> "022" "012" "04113" "022" "042" "052"
#> TCGA.AK.3445.01 TCGA.B4.5378.01 TCGA.BP.5196.01 TCGA.CZ.4865.11 TCGA.B0.5709.01 TCGA.B0.4712.11
#> "0211" "03" "02131" "0511" "062" "0512"
#> TCGA.B0.4714.01 TCGA.B8.5549.01 TCGA.CZ.5461.01 TCGA.CZ.5457.01 TCGA.A3.A8CQ.01 TCGA.DV.5573.01
#> "022" "022" "0211" "063" "062" "061"
#> TCGA.B0.4815.11 TCGA.B0.5710.01 TCGA.B8.5165.01 TCGA.B0.4718.01 TCGA.B2.5639.01 TCGA.CW.5583.01
#> "0141" "022" "061" "022" "0431" "062"
#> TCGA.GK.A6C7.01 TCGA.A3.3357.11 TCGA.B8.5552.01 TCGA.B0.5120.01 TCGA.A3.3373.11 TCGA.BP.5185.01
#> "062" "012" "062" "0413" "0543" "042"
#> TCGA.B0.4846.01 TCGA.CJ.4904.01 TCGA.CJ.4913.11 TCGA.BP.4993.11 TCGA.B0.4823.11 TCGA.CJ.4897.01
#> "0413" "062" "011" "012" "013" "04112"
#> TCGA.BP.4993.01 TCGA.B4.5843.01 TCGA.DV.5576.01 TCGA.CJ.4923.01 TCGA.B0.4819.11 TCGA.BP.5175.01
#> "061" "061" "03" "0432" "011" "0212"
#> TCGA.CZ.5987.01 TCGA.CZ.4864.01 TCGA.B0.4688.11 TCGA.BP.5168.11 TCGA.BP.5198.01 TCGA.B8.A7U6.01
#> "02133" "061" "0542" "0141" "0211" "0413"
#> TCGA.B0.5094.01 TCGA.T7.A92I.01 TCGA.B0.5096.11 TCGA.B0.5400.11 TCGA.B0.4694.11 TCGA.B0.5099.01
#> "0211" "072" "011" "011" "052" "04114"
#> TCGA.CZ.5468.01 TCGA.B0.4842.11 TCGA.CZ.5988.01 TCGA.BP.5169.01 TCGA.B0.5109.01 TCGA.B4.5834.01
#> "02132" "011" "042" "0211" "0433" "061"
#> TCGA.B0.5095.11 TCGA.B0.5080.01 TCGA.CJ.5680.01 TCGA.CZ.5470.01 TCGA.CZ.4865.01 TCGA.A3.A8OX.01
#> "013" "0432" "0231" "0232" "0413" "072"
#> TCGA.B0.4690.11 TCGA.CJ.5684.01 TCGA.B0.4844.01 TCGA.CZ.5464.01 TCGA.B0.4701.01 TCGA.B0.5701.01
#> "013" "042" "02133" "0212" "0412" "0212"
#> TCGA.BP.5199.11 TCGA.CJ.5671.01 TCGA.A3.A8OV.01 TCGA.CZ.5456.11 TCGA.B0.5116.01 TCGA.CZ.5458.01
#> "012" "02131" "061" "0512" "022" "042"
#> TCGA.CZ.5982.01 TCGA.B0.4828.11 TCGA.CJ.5679.01 TCGA.CJ.5682.01 TCGA.B0.5697.01 TCGA.B0.4697.11
#> "04111" "0542" "0211" "022" "042" "0511"
#> TCGA.BP.4782.11 TCGA.G6.A8L8.01 TCGA.A3.A6NJ.01 TCGA.A3.3370.01 TCGA.B0.4691.01 TCGA.CZ.5452.11
#> "011" "0233" "062" "062" "0211" "0512"
#> TCGA.B0.4693.11 TCGA.B0.4945.01 TCGA.CZ.4853.01 TCGA.B0.5092.11 TCGA.B0.5402.01 TCGA.B0.4849.11
#> "011" "062" "022" "011" "022" "012"
#> TCGA.A3.A6NN.01 TCGA.B0.4852.01 TCGA.B0.4817.11 TCGA.BP.5176.11 TCGA.CW.5589.01 TCGA.CJ.5689.01
#> "042" "04114" "0142" "011" "061" "042"
#> TCGA.B0.4822.11 TCGA.BP.5190.11 TCGA.B0.4813.01 TCGA.BP.5200.01 TCGA.G6.A8L7.01 TCGA.B2.4101.01
#> "052" "012" "022" "042" "0232" "0431"
#> TCGA.B0.4713.11 TCGA.B0.4816.01 TCGA.A3.3385.01 TCGA.B2.3924.01 TCGA.CZ.5455.11 TCGA.B0.5713.01
#> "011" "0431" "062" "042" "0512" "04111"
#> TCGA.B0.5108.01 TCGA.B0.5711.01 TCGA.CZ.5453.01 TCGA.BP.5202.11 TCGA.BP.5173.01 TCGA.CZ.5451.11
#> "0431" "042" "061" "071" "061" "012"
#> TCGA.B8.A8YJ.01 TCGA.B0.4848.01 TCGA.DV.A4VZ.01 TCGA.B0.4814.11 TCGA.CJ.4869.11 TCGA.CJ.4907.11
#> "062" "02131" "03" "012" "012" "012"
#> TCGA.B8.5553.01 TCGA.MW.A4EC.01 TCGA.B0.5712.11 TCGA.EU.5905.01 TCGA.CZ.5985.01 TCGA.CZ.4856.01
#> "0413" "04111" "011" "0413" "02133" "0413"
#> TCGA.BP.5184.01 TCGA.B0.5121.01 TCGA.BP.5191.01 TCGA.BP.4801.11 TCGA.BP.5177.01 TCGA.B0.5110.11
#> "042" "022" "0212" "012" "062" "011"
#> TCGA.B0.4810.01 TCGA.CJ.4903.11 TCGA.CJ.4912.11 TCGA.B8.4621.01 TCGA.B4.5832.01 TCGA.CW.6088.01
#> "022" "012" "0542" "063" "0433" "061"
#> TCGA.AK.3428.01 TCGA.B8.5164.01 TCGA.BP.5195.01 TCGA.CJ.6027.01 TCGA.3Z.A93Z.01 TCGA.B0.4714.11
#> "022" "042" "0431" "0211" "061" "0142"
#> TCGA.B0.4818.11 TCGA.CZ.5457.11 TCGA.BP.5010.01 TCGA.BP.5189.11 TCGA.B0.4703.01 TCGA.B0.4718.11
#> "011" "0512" "0431" "012" "0432" "052"
#> TCGA.B0.5097.11 TCGA.BP.4760.11 TCGA.B0.5120.11 TCGA.B0.4843.11 TCGA.B0.5104.01 TCGA.CW.5587.01
#> "011" "0141" "011" "012" "0413" "0413"
get_classes(res_rh, merge_node = merge_node_param(min_n_signatures = 1744))
#> TCGA.CZ.4863.01 TCGA.CJ.4904.11 TCGA.B0.4827.11 TCGA.CJ.4902.01 TCGA.B0.4823.01 TCGA.CW.6087.01
#> "0412" "011" "0543" "0431" "061" "0433"
#> TCGA.B0.5098.01 TCGA.B0.5113.01 TCGA.DV.5566.01 TCGA.BP.5175.11 TCGA.BP.5181.01 TCGA.B0.4706.11
#> "073" "0233" "04112" "012" "062" "012"
#> TCGA.B0.5117.01 TCGA.MM.A564.01 TCGA.B0.4821.11 TCGA.CZ.5463.11 TCGA.BP.5182.11 TCGA.DV.5574.01
#> "013" "02133" "072" "0512" "012" "061"
#> TCGA.B0.5094.11 TCGA.MM.A84U.01 TCGA.B0.5100.11 TCGA.B4.5844.01 TCGA.CZ.5459.01 TCGA.B0.4694.01
#> "014" "0413" "014" "04111" "042" "0432"
#> TCGA.CZ.5468.11 TCGA.CJ.4916.11 TCGA.B4.5836.01 TCGA.B0.5095.01 TCGA.B0.4846.11 TCGA.AK.3434.01
#> "0512" "011" "0413" "0432" "011" "022"
#> TCGA.B4.5377.01 TCGA.B0.4696.11 TCGA.BP.5187.11 TCGA.B0.4690.01 TCGA.CZ.5466.01 TCGA.B0.4844.11
#> "062" "014" "014" "0433" "0432" "052"
#> TCGA.CZ.5464.11 TCGA.B0.4701.11 TCGA.BP.5194.11 TCGA.B0.4707.01 TCGA.CZ.5467.11 TCGA.B0.5705.01
#> "012" "011" "012" "02131" "0511" "062"
#> TCGA.CW.5588.01 TCGA.CJ.6031.01 TCGA.B8.A54J.01 TCGA.BP.5192.11 TCGA.CZ.5462.01 TCGA.B8.A54H.01
#> "0413" "0431" "042" "052" "0432" "0413"
#> TCGA.CZ.5470.11 TCGA.BP.4177.11 TCGA.CZ.5469.11 TCGA.CJ.6028.01 TCGA.G6.A8L6.01 TCGA.B8.5551.01
#> "0511" "052" "0512" "0432" "042" "0412"
#> TCGA.CZ.5456.01 TCGA.A3.A8OU.01 TCGA.BP.5186.01 TCGA.A3.A6NI.01 TCGA.BP.4782.01 TCGA.CZ.5454.11
#> "0211" "0413" "062" "042" "0413" "0541"
#> TCGA.B0.4691.11 TCGA.CZ.5452.01 TCGA.EU.5904.01 TCGA.BP.5201.01 TCGA.CJ.5677.01 TCGA.BP.5170.11
#> "012" "02131" "062" "022" "0232" "0541"
#> TCGA.B0.4710.11 TCGA.AK.3425.01 TCGA.B0.4841.11 TCGA.B0.4849.01 TCGA.BP.5182.01 TCGA.B0.5711.11
#> "0511" "02131" "014" "042" "063" "052"
#> TCGA.BP.5180.01 TCGA.BP.5176.01 TCGA.CZ.5984.01 TCGA.CZ.5460.11 TCGA.BP.5190.01 TCGA.BP.4795.11
#> "0212" "0413" "0212" "012" "022" "011"
#> TCGA.B0.4813.11 TCGA.B0.4713.01 TCGA.B0.4841.01 TCGA.B8.5546.01 TCGA.CW.5591.01 TCGA.B0.4698.11
#> "0542" "0232" "022" "072" "0431" "014"
#> TCGA.B0.5713.11 TCGA.B0.5108.11 TCGA.B0.5083.01 TCGA.B0.5699.01 TCGA.CZ.5453.11 TCGA.BP.5202.01
#> "011" "012" "013" "022" "0512" "022"
#> TCGA.BP.5173.11 TCGA.CW.5581.01 TCGA.B0.4848.11 TCGA.B0.4814.01 TCGA.BP.5178.11 TCGA.CJ.4907.01
#> "013" "042" "014" "022" "014" "042"
#> TCGA.A3.3387.01 TCGA.B0.4821.01 TCGA.B0.5712.01 TCGA.B0.5695.01 TCGA.BP.5184.11 TCGA.B2.A4SR.01
#> "042" "0232" "0231" "062" "012" "042"
#> TCGA.BP.5191.11 TCGA.CJ.4920.01 TCGA.BP.4801.01 TCGA.DV.A4W0.01 TCGA.BP.5177.11 TCGA.B0.4847.11
#> "014" "0231" "042" "022" "011" "052"
#> TCGA.B0.5100.01 TCGA.CJ.4903.01 TCGA.CJ.4912.01 TCGA.B0.5107.11 TCGA.AK.3453.01 TCGA.B0.5691.01
#> "0431" "022" "0212" "011" "013" "062"
#> TCGA.BP.5195.11 TCGA.B0.5400.01 TCGA.A3.3376.11 TCGA.B0.4845.01 TCGA.B0.4699.01 TCGA.B0.4818.01
#> "0541" "0412" "071" "022" "071" "0413"
#> TCGA.BP.5174.11 TCGA.CJ.4901.11 TCGA.B8.A54D.01 TCGA.BP.4770.11 TCGA.CW.6093.01 TCGA.BP.5010.11
#> "011" "012" "022" "011" "061" "0541"
#> TCGA.AK.3431.01 TCGA.BP.4770.01 TCGA.BP.5189.01 TCGA.B0.4703.11 TCGA.B8.5163.01 TCGA.CJ.5683.01
#> "0413" "0412" "0431" "014" "0412" "042"
#> TCGA.CZ.4856.11 TCGA.BP.4760.01 TCGA.B0.5692.01 TCGA.B0.5106.01 TCGA.B0.4843.01 TCGA.CZ.4866.11
#> "0511" "03" "0231" "0212" "0431" "0511"
#> TCGA.B0.5104.11 TCGA.B0.4827.01 TCGA.CJ.4902.11 TCGA.B8.A54G.01 TCGA.B0.5703.01 TCGA.CJ.5672.01
#> "011" "0232" "0541" "042" "042" "042"
#> TCGA.B0.5098.11 TCGA.B0.5113.11 TCGA.CJ.4882.11 TCGA.CZ.5465.11 TCGA.B0.5102.01 TCGA.CW.5585.01
#> "013" "011" "012" "0511" "04112" "042"
#> TCGA.B0.4824.01 TCGA.B0.5115.01 TCGA.B0.4706.01 TCGA.B0.5117.11 TCGA.CZ.4859.11 TCGA.AK.3450.01
#> "0413" "022" "022" "012" "0543" "0413"
#> TCGA.B8.A54I.01 TCGA.CZ.5463.01 TCGA.DV.5568.01 TCGA.CZ.5459.11 TCGA.CJ.4918.11 TCGA.DV.5565.01
#> "0212" "022" "0431" "014" "014" "042"
#> TCGA.B0.5119.01 TCGA.B0.4811.01 TCGA.A3.3367.11 TCGA.CJ.4916.01 TCGA.B0.5693.01 TCGA.CZ.4863.11
#> "062" "042" "014" "0412" "04112" "0511"
#> TCGA.G6.A5PC.01 TCGA.B8.5550.01 TCGA.DV.A4W0.05 TCGA.B0.4696.01 TCGA.BP.5187.01 TCGA.CZ.5466.11
#> "0231" "0431" "03" "0212" "0431" "014"
#> TCGA.CW.6097.01 TCGA.CJ.4905.11 TCGA.CZ.5989.01 TCGA.BP.5194.01 TCGA.B0.4707.11 TCGA.CZ.5467.01
#> "0433" "052" "042" "042" "014" "04112"
#> TCGA.BP.5185.11 TCGA.BP.5183.11 TCGA.BP.5192.01 TCGA.CZ.5462.11 TCGA.BP.4177.01 TCGA.CZ.5469.01
#> "012" "012" "061" "0512" "03" "0211"
#> TCGA.B2.5641.01 TCGA.BP.5196.11 TCGA.CZ.5460.01 TCGA.B0.4712.01 TCGA.B8.A54K.01 TCGA.B0.5707.01
#> "0212" "012" "022" "0211" "03" "062"
#> TCGA.BP.5186.11 TCGA.EU.5906.01 TCGA.CZ.5461.11 TCGA.CW.5590.01 TCGA.B0.5698.01 TCGA.CW.5580.01
#> "011" "061" "0541" "022" "022" "0231"
#> TCGA.CZ.5454.01 TCGA.B0.4815.01 TCGA.B0.5710.11 TCGA.CJ.4908.11 TCGA.BP.5201.11 TCGA.B0.5694.01
#> "022" "0211" "012" "0541" "012" "022"
#> TCGA.BP.5170.01 TCGA.DV.5575.01 TCGA.CJ.5686.01 TCGA.A3.3357.01 TCGA.A3.3373.01 TCGA.B0.5690.01
#> "042" "062" "0412" "022" "04113" "062"
#> TCGA.B8.4622.01 TCGA.AK.3433.01 TCGA.B0.5110.01 TCGA.BP.5180.11 TCGA.CJ.4913.01 TCGA.CJ.4908.01
#> "022" "053" "062" "012" "0231" "042"
#> TCGA.BP.4795.01 TCGA.CJ.4897.11 TCGA.B2.5636.01 TCGA.CJ.4923.11 TCGA.B0.4819.01 TCGA.B2.5633.01
#> "03" "011" "03" "014" "0412" "0431"
#> TCGA.CJ.6033.01 TCGA.BP.5181.11 TCGA.B0.4698.01 TCGA.B0.5083.11 TCGA.CZ.4864.11 TCGA.B0.4688.01
#> "0232" "011" "02132" "012" "014" "02132"
#> TCGA.BP.5168.01 TCGA.BP.5198.11 TCGA.B8.5162.01 TCGA.B0.5096.01 TCGA.BP.5178.01 TCGA.B0.5099.11
#> "042" "014" "0432" "0232" "0211" "011"
#> TCGA.B0.4842.01 TCGA.BP.5169.11 TCGA.B0.5109.11 TCGA.CJ.4920.11 TCGA.B0.5080.11 TCGA.B0.5700.01
#> "0412" "014" "071" "0542" "012" "061"
#> TCGA.B0.4847.01 TCGA.B0.5702.01 TCGA.CJ.4905.01 TCGA.B2.5635.01 TCGA.B0.5107.01 TCGA.CW.5584.01
#> "022" "071" "04111" "042" "0232" "022"
#> TCGA.B4.5838.01 TCGA.BP.5199.01 TCGA.A3.3376.01 TCGA.B0.4845.11 TCGA.B0.4699.11 TCGA.BP.5174.01
#> "042" "022" "061" "0542" "014" "062"
#> TCGA.CZ.5986.01 TCGA.CJ.4901.01 TCGA.AK.3461.01 TCGA.AK.3460.01 TCGA.AK.3454.01 TCGA.CZ.4859.01
#> "061" "02131" "042" "042" "061" "062"
#> TCGA.B0.5812.01 TCGA.B0.5116.11 TCGA.B8.A54F.01 TCGA.CW.6090.01 TCGA.CZ.5458.11 TCGA.B0.5106.11
#> "042" "071" "0413" "022" "0512" "012"
#> TCGA.CZ.4866.01 TCGA.B0.4828.01 TCGA.AK.3440.01 TCGA.MM.A563.01 TCGA.B0.4697.01 TCGA.AK.3458.01
#> "0231" "022" "053" "022" "0412" "022"
#> TCGA.CJ.5676.01 TCGA.B0.5402.11 TCGA.CJ.5681.01 TCGA.A3.3370.11 TCGA.A3.A6NL.01 TCGA.B0.4693.01
#> "02133" "014" "073" "052" "062" "0231"
#> TCGA.A3.3358.01 TCGA.B0.4710.01 TCGA.CZ.4853.11 TCGA.B4.5835.01 TCGA.CJ.4882.01 TCGA.CZ.5465.01
#> "0413" "0231" "0541" "062" "0432" "0233"
#> TCGA.B0.5102.11 TCGA.B0.4824.11 TCGA.CJ.5675.01 TCGA.B0.4700.01 TCGA.B0.5092.01 TCGA.B0.5115.11
#> "011" "011" "022" "0433" "0412" "012"
#> TCGA.B0.4945.11 TCGA.B8.5158.01 TCGA.CJ.6030.01 TCGA.B8.A54E.01 TCGA.CJ.6032.01 TCGA.B0.4852.11
#> "011" "02131" "02131" "072" "04111" "011"
#> TCGA.B0.4817.01 TCGA.B8.5159.01 TCGA.A3.A8OW.01 TCGA.B0.4822.01 TCGA.B0.5696.01 TCGA.B0.5706.01
#> "0433" "0233" "061" "0432" "042" "0212"
#> TCGA.CJ.4918.01 TCGA.B0.5119.11 TCGA.BP.5200.11 TCGA.B0.4811.11 TCGA.A3.3367.01 TCGA.B0.5097.01
#> "0431" "0511" "012" "014" "022" "0412"
#> TCGA.6D.AA2E.01 TCGA.DV.A4VX.01 TCGA.B0.4816.11 TCGA.A3.3385.11 TCGA.DV.5569.01 TCGA.EU.5907.01
#> "072" "022" "0541" "011" "062" "022"
#> TCGA.CZ.5455.01 TCGA.B8.5545.01 TCGA.DV.5567.01 TCGA.CZ.5451.01 TCGA.CJ.4869.01 TCGA.CJ.5678.01
#> "042" "061" "03" "042" "0432" "022"
#> TCGA.B8.4153.01 TCGA.B0.5121.11 TCGA.B8.4146.01 TCGA.BP.5183.01 TCGA.B0.5399.01 TCGA.B0.4810.11
#> "022" "012" "04113" "022" "042" "052"
#> TCGA.AK.3445.01 TCGA.B4.5378.01 TCGA.BP.5196.01 TCGA.CZ.4865.11 TCGA.B0.5709.01 TCGA.B0.4712.11
#> "0211" "03" "02131" "0511" "062" "0512"
#> TCGA.B0.4714.01 TCGA.B8.5549.01 TCGA.CZ.5461.01 TCGA.CZ.5457.01 TCGA.A3.A8CQ.01 TCGA.DV.5573.01
#> "022" "022" "0211" "063" "062" "061"
#> TCGA.B0.4815.11 TCGA.B0.5710.01 TCGA.B8.5165.01 TCGA.B0.4718.01 TCGA.B2.5639.01 TCGA.CW.5583.01
#> "014" "022" "061" "022" "0431" "062"
#> TCGA.GK.A6C7.01 TCGA.A3.3357.11 TCGA.B8.5552.01 TCGA.B0.5120.01 TCGA.A3.3373.11 TCGA.BP.5185.01
#> "062" "012" "062" "0413" "0543" "042"
#> TCGA.B0.4846.01 TCGA.CJ.4904.01 TCGA.CJ.4913.11 TCGA.BP.4993.11 TCGA.B0.4823.11 TCGA.CJ.4897.01
#> "0413" "062" "011" "012" "013" "04112"
#> TCGA.BP.4993.01 TCGA.B4.5843.01 TCGA.DV.5576.01 TCGA.CJ.4923.01 TCGA.B0.4819.11 TCGA.BP.5175.01
#> "061" "061" "03" "0432" "011" "0212"
#> TCGA.CZ.5987.01 TCGA.CZ.4864.01 TCGA.B0.4688.11 TCGA.BP.5168.11 TCGA.BP.5198.01 TCGA.B8.A7U6.01
#> "02133" "061" "0542" "014" "0211" "0413"
#> TCGA.B0.5094.01 TCGA.T7.A92I.01 TCGA.B0.5096.11 TCGA.B0.5400.11 TCGA.B0.4694.11 TCGA.B0.5099.01
#> "0211" "072" "011" "011" "052" "04114"
#> TCGA.CZ.5468.01 TCGA.B0.4842.11 TCGA.CZ.5988.01 TCGA.BP.5169.01 TCGA.B0.5109.01 TCGA.B4.5834.01
#> "02132" "011" "042" "0211" "0433" "061"
#> TCGA.B0.5095.11 TCGA.B0.5080.01 TCGA.CJ.5680.01 TCGA.CZ.5470.01 TCGA.CZ.4865.01 TCGA.A3.A8OX.01
#> "013" "0432" "0231" "0232" "0413" "072"
#> TCGA.B0.4690.11 TCGA.CJ.5684.01 TCGA.B0.4844.01 TCGA.CZ.5464.01 TCGA.B0.4701.01 TCGA.B0.5701.01
#> "013" "042" "02133" "0212" "0412" "0212"
#> TCGA.BP.5199.11 TCGA.CJ.5671.01 TCGA.A3.A8OV.01 TCGA.CZ.5456.11 TCGA.B0.5116.01 TCGA.CZ.5458.01
#> "012" "02131" "061" "0512" "022" "042"
#> TCGA.CZ.5982.01 TCGA.B0.4828.11 TCGA.CJ.5679.01 TCGA.CJ.5682.01 TCGA.B0.5697.01 TCGA.B0.4697.11
#> "04111" "0542" "0211" "022" "042" "0511"
#> TCGA.BP.4782.11 TCGA.G6.A8L8.01 TCGA.A3.A6NJ.01 TCGA.A3.3370.01 TCGA.B0.4691.01 TCGA.CZ.5452.11
#> "011" "0233" "062" "062" "0211" "0512"
#> TCGA.B0.4693.11 TCGA.B0.4945.01 TCGA.CZ.4853.01 TCGA.B0.5092.11 TCGA.B0.5402.01 TCGA.B0.4849.11
#> "011" "062" "022" "011" "022" "012"
#> TCGA.A3.A6NN.01 TCGA.B0.4852.01 TCGA.B0.4817.11 TCGA.BP.5176.11 TCGA.CW.5589.01 TCGA.CJ.5689.01
#> "042" "04114" "014" "011" "061" "042"
#> TCGA.B0.4822.11 TCGA.BP.5190.11 TCGA.B0.4813.01 TCGA.BP.5200.01 TCGA.G6.A8L7.01 TCGA.B2.4101.01
#> "052" "012" "022" "042" "0232" "0431"
#> TCGA.B0.4713.11 TCGA.B0.4816.01 TCGA.A3.3385.01 TCGA.B2.3924.01 TCGA.CZ.5455.11 TCGA.B0.5713.01
#> "011" "0431" "062" "042" "0512" "04111"
#> TCGA.B0.5108.01 TCGA.B0.5711.01 TCGA.CZ.5453.01 TCGA.BP.5202.11 TCGA.BP.5173.01 TCGA.CZ.5451.11
#> "0431" "042" "061" "071" "061" "012"
#> TCGA.B8.A8YJ.01 TCGA.B0.4848.01 TCGA.DV.A4VZ.01 TCGA.B0.4814.11 TCGA.CJ.4869.11 TCGA.CJ.4907.11
#> "062" "02131" "03" "012" "012" "012"
#> TCGA.B8.5553.01 TCGA.MW.A4EC.01 TCGA.B0.5712.11 TCGA.EU.5905.01 TCGA.CZ.5985.01 TCGA.CZ.4856.01
#> "0413" "04111" "011" "0413" "02133" "0413"
#> TCGA.BP.5184.01 TCGA.B0.5121.01 TCGA.BP.5191.01 TCGA.BP.4801.11 TCGA.BP.5177.01 TCGA.B0.5110.11
#> "042" "022" "0212" "012" "062" "011"
#> TCGA.B0.4810.01 TCGA.CJ.4903.11 TCGA.CJ.4912.11 TCGA.B8.4621.01 TCGA.B4.5832.01 TCGA.CW.6088.01
#> "022" "012" "0542" "063" "0433" "061"
#> TCGA.AK.3428.01 TCGA.B8.5164.01 TCGA.BP.5195.01 TCGA.CJ.6027.01 TCGA.3Z.A93Z.01 TCGA.B0.4714.11
#> "022" "042" "0431" "0211" "061" "014"
#> TCGA.B0.4818.11 TCGA.CZ.5457.11 TCGA.BP.5010.01 TCGA.BP.5189.11 TCGA.B0.4703.01 TCGA.B0.4718.11
#> "011" "0512" "0431" "012" "0432" "052"
#> TCGA.B0.5097.11 TCGA.BP.4760.11 TCGA.B0.5120.11 TCGA.B0.4843.11 TCGA.B0.5104.01 TCGA.CW.5587.01
#> "011" "014" "011" "012" "0413" "0413"
get_classes(res_rh, merge_node = merge_node_param(min_n_signatures = 1947))
#> TCGA.CZ.4863.01 TCGA.CJ.4904.11 TCGA.B0.4827.11 TCGA.CJ.4902.01 TCGA.B0.4823.01 TCGA.CW.6087.01
#> "0412" "011" "0543" "0431" "061" "0433"
#> TCGA.B0.5098.01 TCGA.B0.5113.01 TCGA.DV.5566.01 TCGA.BP.5175.11 TCGA.BP.5181.01 TCGA.B0.4706.11
#> "073" "0233" "0411" "012" "062" "012"
#> TCGA.B0.5117.01 TCGA.MM.A564.01 TCGA.B0.4821.11 TCGA.CZ.5463.11 TCGA.BP.5182.11 TCGA.DV.5574.01
#> "013" "02133" "072" "0512" "012" "061"
#> TCGA.B0.5094.11 TCGA.MM.A84U.01 TCGA.B0.5100.11 TCGA.B4.5844.01 TCGA.CZ.5459.01 TCGA.B0.4694.01
#> "014" "0413" "014" "0411" "042" "0432"
#> TCGA.CZ.5468.11 TCGA.CJ.4916.11 TCGA.B4.5836.01 TCGA.B0.5095.01 TCGA.B0.4846.11 TCGA.AK.3434.01
#> "0512" "011" "0413" "0432" "011" "022"
#> TCGA.B4.5377.01 TCGA.B0.4696.11 TCGA.BP.5187.11 TCGA.B0.4690.01 TCGA.CZ.5466.01 TCGA.B0.4844.11
#> "062" "014" "014" "0433" "0432" "052"
#> TCGA.CZ.5464.11 TCGA.B0.4701.11 TCGA.BP.5194.11 TCGA.B0.4707.01 TCGA.CZ.5467.11 TCGA.B0.5705.01
#> "012" "011" "012" "02131" "0511" "062"
#> TCGA.CW.5588.01 TCGA.CJ.6031.01 TCGA.B8.A54J.01 TCGA.BP.5192.11 TCGA.CZ.5462.01 TCGA.B8.A54H.01
#> "0413" "0431" "042" "052" "0432" "0413"
#> TCGA.CZ.5470.11 TCGA.BP.4177.11 TCGA.CZ.5469.11 TCGA.CJ.6028.01 TCGA.G6.A8L6.01 TCGA.B8.5551.01
#> "0511" "052" "0512" "0432" "042" "0412"
#> TCGA.CZ.5456.01 TCGA.A3.A8OU.01 TCGA.BP.5186.01 TCGA.A3.A6NI.01 TCGA.BP.4782.01 TCGA.CZ.5454.11
#> "0211" "0413" "062" "042" "0413" "0541"
#> TCGA.B0.4691.11 TCGA.CZ.5452.01 TCGA.EU.5904.01 TCGA.BP.5201.01 TCGA.CJ.5677.01 TCGA.BP.5170.11
#> "012" "02131" "062" "022" "0232" "0541"
#> TCGA.B0.4710.11 TCGA.AK.3425.01 TCGA.B0.4841.11 TCGA.B0.4849.01 TCGA.BP.5182.01 TCGA.B0.5711.11
#> "0511" "02131" "014" "042" "063" "052"
#> TCGA.BP.5180.01 TCGA.BP.5176.01 TCGA.CZ.5984.01 TCGA.CZ.5460.11 TCGA.BP.5190.01 TCGA.BP.4795.11
#> "0212" "0413" "0212" "012" "022" "011"
#> TCGA.B0.4813.11 TCGA.B0.4713.01 TCGA.B0.4841.01 TCGA.B8.5546.01 TCGA.CW.5591.01 TCGA.B0.4698.11
#> "0542" "0232" "022" "072" "0431" "014"
#> TCGA.B0.5713.11 TCGA.B0.5108.11 TCGA.B0.5083.01 TCGA.B0.5699.01 TCGA.CZ.5453.11 TCGA.BP.5202.01
#> "011" "012" "013" "022" "0512" "022"
#> TCGA.BP.5173.11 TCGA.CW.5581.01 TCGA.B0.4848.11 TCGA.B0.4814.01 TCGA.BP.5178.11 TCGA.CJ.4907.01
#> "013" "042" "014" "022" "014" "042"
#> TCGA.A3.3387.01 TCGA.B0.4821.01 TCGA.B0.5712.01 TCGA.B0.5695.01 TCGA.BP.5184.11 TCGA.B2.A4SR.01
#> "042" "0232" "0231" "062" "012" "042"
#> TCGA.BP.5191.11 TCGA.CJ.4920.01 TCGA.BP.4801.01 TCGA.DV.A4W0.01 TCGA.BP.5177.11 TCGA.B0.4847.11
#> "014" "0231" "042" "022" "011" "052"
#> TCGA.B0.5100.01 TCGA.CJ.4903.01 TCGA.CJ.4912.01 TCGA.B0.5107.11 TCGA.AK.3453.01 TCGA.B0.5691.01
#> "0431" "022" "0212" "011" "013" "062"
#> TCGA.BP.5195.11 TCGA.B0.5400.01 TCGA.A3.3376.11 TCGA.B0.4845.01 TCGA.B0.4699.01 TCGA.B0.4818.01
#> "0541" "0412" "071" "022" "071" "0413"
#> TCGA.BP.5174.11 TCGA.CJ.4901.11 TCGA.B8.A54D.01 TCGA.BP.4770.11 TCGA.CW.6093.01 TCGA.BP.5010.11
#> "011" "012" "022" "011" "061" "0541"
#> TCGA.AK.3431.01 TCGA.BP.4770.01 TCGA.BP.5189.01 TCGA.B0.4703.11 TCGA.B8.5163.01 TCGA.CJ.5683.01
#> "0413" "0412" "0431" "014" "0412" "042"
#> TCGA.CZ.4856.11 TCGA.BP.4760.01 TCGA.B0.5692.01 TCGA.B0.5106.01 TCGA.B0.4843.01 TCGA.CZ.4866.11
#> "0511" "03" "0231" "0212" "0431" "0511"
#> TCGA.B0.5104.11 TCGA.B0.4827.01 TCGA.CJ.4902.11 TCGA.B8.A54G.01 TCGA.B0.5703.01 TCGA.CJ.5672.01
#> "011" "0232" "0541" "042" "042" "042"
#> TCGA.B0.5098.11 TCGA.B0.5113.11 TCGA.CJ.4882.11 TCGA.CZ.5465.11 TCGA.B0.5102.01 TCGA.CW.5585.01
#> "013" "011" "012" "0511" "0411" "042"
#> TCGA.B0.4824.01 TCGA.B0.5115.01 TCGA.B0.4706.01 TCGA.B0.5117.11 TCGA.CZ.4859.11 TCGA.AK.3450.01
#> "0413" "022" "022" "012" "0543" "0413"
#> TCGA.B8.A54I.01 TCGA.CZ.5463.01 TCGA.DV.5568.01 TCGA.CZ.5459.11 TCGA.CJ.4918.11 TCGA.DV.5565.01
#> "0212" "022" "0431" "014" "014" "042"
#> TCGA.B0.5119.01 TCGA.B0.4811.01 TCGA.A3.3367.11 TCGA.CJ.4916.01 TCGA.B0.5693.01 TCGA.CZ.4863.11
#> "062" "042" "014" "0412" "0411" "0511"
#> TCGA.G6.A5PC.01 TCGA.B8.5550.01 TCGA.DV.A4W0.05 TCGA.B0.4696.01 TCGA.BP.5187.01 TCGA.CZ.5466.11
#> "0231" "0431" "03" "0212" "0431" "014"
#> TCGA.CW.6097.01 TCGA.CJ.4905.11 TCGA.CZ.5989.01 TCGA.BP.5194.01 TCGA.B0.4707.11 TCGA.CZ.5467.01
#> "0433" "052" "042" "042" "014" "0411"
#> TCGA.BP.5185.11 TCGA.BP.5183.11 TCGA.BP.5192.01 TCGA.CZ.5462.11 TCGA.BP.4177.01 TCGA.CZ.5469.01
#> "012" "012" "061" "0512" "03" "0211"
#> TCGA.B2.5641.01 TCGA.BP.5196.11 TCGA.CZ.5460.01 TCGA.B0.4712.01 TCGA.B8.A54K.01 TCGA.B0.5707.01
#> "0212" "012" "022" "0211" "03" "062"
#> TCGA.BP.5186.11 TCGA.EU.5906.01 TCGA.CZ.5461.11 TCGA.CW.5590.01 TCGA.B0.5698.01 TCGA.CW.5580.01
#> "011" "061" "0541" "022" "022" "0231"
#> TCGA.CZ.5454.01 TCGA.B0.4815.01 TCGA.B0.5710.11 TCGA.CJ.4908.11 TCGA.BP.5201.11 TCGA.B0.5694.01
#> "022" "0211" "012" "0541" "012" "022"
#> TCGA.BP.5170.01 TCGA.DV.5575.01 TCGA.CJ.5686.01 TCGA.A3.3357.01 TCGA.A3.3373.01 TCGA.B0.5690.01
#> "042" "062" "0412" "022" "0411" "062"
#> TCGA.B8.4622.01 TCGA.AK.3433.01 TCGA.B0.5110.01 TCGA.BP.5180.11 TCGA.CJ.4913.01 TCGA.CJ.4908.01
#> "022" "053" "062" "012" "0231" "042"
#> TCGA.BP.4795.01 TCGA.CJ.4897.11 TCGA.B2.5636.01 TCGA.CJ.4923.11 TCGA.B0.4819.01 TCGA.B2.5633.01
#> "03" "011" "03" "014" "0412" "0431"
#> TCGA.CJ.6033.01 TCGA.BP.5181.11 TCGA.B0.4698.01 TCGA.B0.5083.11 TCGA.CZ.4864.11 TCGA.B0.4688.01
#> "0232" "011" "02132" "012" "014" "02132"
#> TCGA.BP.5168.01 TCGA.BP.5198.11 TCGA.B8.5162.01 TCGA.B0.5096.01 TCGA.BP.5178.01 TCGA.B0.5099.11
#> "042" "014" "0432" "0232" "0211" "011"
#> TCGA.B0.4842.01 TCGA.BP.5169.11 TCGA.B0.5109.11 TCGA.CJ.4920.11 TCGA.B0.5080.11 TCGA.B0.5700.01
#> "0412" "014" "071" "0542" "012" "061"
#> TCGA.B0.4847.01 TCGA.B0.5702.01 TCGA.CJ.4905.01 TCGA.B2.5635.01 TCGA.B0.5107.01 TCGA.CW.5584.01
#> "022" "071" "0411" "042" "0232" "022"
#> TCGA.B4.5838.01 TCGA.BP.5199.01 TCGA.A3.3376.01 TCGA.B0.4845.11 TCGA.B0.4699.11 TCGA.BP.5174.01
#> "042" "022" "061" "0542" "014" "062"
#> TCGA.CZ.5986.01 TCGA.CJ.4901.01 TCGA.AK.3461.01 TCGA.AK.3460.01 TCGA.AK.3454.01 TCGA.CZ.4859.01
#> "061" "02131" "042" "042" "061" "062"
#> TCGA.B0.5812.01 TCGA.B0.5116.11 TCGA.B8.A54F.01 TCGA.CW.6090.01 TCGA.CZ.5458.11 TCGA.B0.5106.11
#> "042" "071" "0413" "022" "0512" "012"
#> TCGA.CZ.4866.01 TCGA.B0.4828.01 TCGA.AK.3440.01 TCGA.MM.A563.01 TCGA.B0.4697.01 TCGA.AK.3458.01
#> "0231" "022" "053" "022" "0412" "022"
#> TCGA.CJ.5676.01 TCGA.B0.5402.11 TCGA.CJ.5681.01 TCGA.A3.3370.11 TCGA.A3.A6NL.01 TCGA.B0.4693.01
#> "02133" "014" "073" "052" "062" "0231"
#> TCGA.A3.3358.01 TCGA.B0.4710.01 TCGA.CZ.4853.11 TCGA.B4.5835.01 TCGA.CJ.4882.01 TCGA.CZ.5465.01
#> "0413" "0231" "0541" "062" "0432" "0233"
#> TCGA.B0.5102.11 TCGA.B0.4824.11 TCGA.CJ.5675.01 TCGA.B0.4700.01 TCGA.B0.5092.01 TCGA.B0.5115.11
#> "011" "011" "022" "0433" "0412" "012"
#> TCGA.B0.4945.11 TCGA.B8.5158.01 TCGA.CJ.6030.01 TCGA.B8.A54E.01 TCGA.CJ.6032.01 TCGA.B0.4852.11
#> "011" "02131" "02131" "072" "0411" "011"
#> TCGA.B0.4817.01 TCGA.B8.5159.01 TCGA.A3.A8OW.01 TCGA.B0.4822.01 TCGA.B0.5696.01 TCGA.B0.5706.01
#> "0433" "0233" "061" "0432" "042" "0212"
#> TCGA.CJ.4918.01 TCGA.B0.5119.11 TCGA.BP.5200.11 TCGA.B0.4811.11 TCGA.A3.3367.01 TCGA.B0.5097.01
#> "0431" "0511" "012" "014" "022" "0412"
#> TCGA.6D.AA2E.01 TCGA.DV.A4VX.01 TCGA.B0.4816.11 TCGA.A3.3385.11 TCGA.DV.5569.01 TCGA.EU.5907.01
#> "072" "022" "0541" "011" "062" "022"
#> TCGA.CZ.5455.01 TCGA.B8.5545.01 TCGA.DV.5567.01 TCGA.CZ.5451.01 TCGA.CJ.4869.01 TCGA.CJ.5678.01
#> "042" "061" "03" "042" "0432" "022"
#> TCGA.B8.4153.01 TCGA.B0.5121.11 TCGA.B8.4146.01 TCGA.BP.5183.01 TCGA.B0.5399.01 TCGA.B0.4810.11
#> "022" "012" "0411" "022" "042" "052"
#> TCGA.AK.3445.01 TCGA.B4.5378.01 TCGA.BP.5196.01 TCGA.CZ.4865.11 TCGA.B0.5709.01 TCGA.B0.4712.11
#> "0211" "03" "02131" "0511" "062" "0512"
#> TCGA.B0.4714.01 TCGA.B8.5549.01 TCGA.CZ.5461.01 TCGA.CZ.5457.01 TCGA.A3.A8CQ.01 TCGA.DV.5573.01
#> "022" "022" "0211" "063" "062" "061"
#> TCGA.B0.4815.11 TCGA.B0.5710.01 TCGA.B8.5165.01 TCGA.B0.4718.01 TCGA.B2.5639.01 TCGA.CW.5583.01
#> "014" "022" "061" "022" "0431" "062"
#> TCGA.GK.A6C7.01 TCGA.A3.3357.11 TCGA.B8.5552.01 TCGA.B0.5120.01 TCGA.A3.3373.11 TCGA.BP.5185.01
#> "062" "012" "062" "0413" "0543" "042"
#> TCGA.B0.4846.01 TCGA.CJ.4904.01 TCGA.CJ.4913.11 TCGA.BP.4993.11 TCGA.B0.4823.11 TCGA.CJ.4897.01
#> "0413" "062" "011" "012" "013" "0411"
#> TCGA.BP.4993.01 TCGA.B4.5843.01 TCGA.DV.5576.01 TCGA.CJ.4923.01 TCGA.B0.4819.11 TCGA.BP.5175.01
#> "061" "061" "03" "0432" "011" "0212"
#> TCGA.CZ.5987.01 TCGA.CZ.4864.01 TCGA.B0.4688.11 TCGA.BP.5168.11 TCGA.BP.5198.01 TCGA.B8.A7U6.01
#> "02133" "061" "0542" "014" "0211" "0413"
#> TCGA.B0.5094.01 TCGA.T7.A92I.01 TCGA.B0.5096.11 TCGA.B0.5400.11 TCGA.B0.4694.11 TCGA.B0.5099.01
#> "0211" "072" "011" "011" "052" "0411"
#> TCGA.CZ.5468.01 TCGA.B0.4842.11 TCGA.CZ.5988.01 TCGA.BP.5169.01 TCGA.B0.5109.01 TCGA.B4.5834.01
#> "02132" "011" "042" "0211" "0433" "061"
#> TCGA.B0.5095.11 TCGA.B0.5080.01 TCGA.CJ.5680.01 TCGA.CZ.5470.01 TCGA.CZ.4865.01 TCGA.A3.A8OX.01
#> "013" "0432" "0231" "0232" "0413" "072"
#> TCGA.B0.4690.11 TCGA.CJ.5684.01 TCGA.B0.4844.01 TCGA.CZ.5464.01 TCGA.B0.4701.01 TCGA.B0.5701.01
#> "013" "042" "02133" "0212" "0412" "0212"
#> TCGA.BP.5199.11 TCGA.CJ.5671.01 TCGA.A3.A8OV.01 TCGA.CZ.5456.11 TCGA.B0.5116.01 TCGA.CZ.5458.01
#> "012" "02131" "061" "0512" "022" "042"
#> TCGA.CZ.5982.01 TCGA.B0.4828.11 TCGA.CJ.5679.01 TCGA.CJ.5682.01 TCGA.B0.5697.01 TCGA.B0.4697.11
#> "0411" "0542" "0211" "022" "042" "0511"
#> TCGA.BP.4782.11 TCGA.G6.A8L8.01 TCGA.A3.A6NJ.01 TCGA.A3.3370.01 TCGA.B0.4691.01 TCGA.CZ.5452.11
#> "011" "0233" "062" "062" "0211" "0512"
#> TCGA.B0.4693.11 TCGA.B0.4945.01 TCGA.CZ.4853.01 TCGA.B0.5092.11 TCGA.B0.5402.01 TCGA.B0.4849.11
#> "011" "062" "022" "011" "022" "012"
#> TCGA.A3.A6NN.01 TCGA.B0.4852.01 TCGA.B0.4817.11 TCGA.BP.5176.11 TCGA.CW.5589.01 TCGA.CJ.5689.01
#> "042" "0411" "014" "011" "061" "042"
#> TCGA.B0.4822.11 TCGA.BP.5190.11 TCGA.B0.4813.01 TCGA.BP.5200.01 TCGA.G6.A8L7.01 TCGA.B2.4101.01
#> "052" "012" "022" "042" "0232" "0431"
#> TCGA.B0.4713.11 TCGA.B0.4816.01 TCGA.A3.3385.01 TCGA.B2.3924.01 TCGA.CZ.5455.11 TCGA.B0.5713.01
#> "011" "0431" "062" "042" "0512" "0411"
#> TCGA.B0.5108.01 TCGA.B0.5711.01 TCGA.CZ.5453.01 TCGA.BP.5202.11 TCGA.BP.5173.01 TCGA.CZ.5451.11
#> "0431" "042" "061" "071" "061" "012"
#> TCGA.B8.A8YJ.01 TCGA.B0.4848.01 TCGA.DV.A4VZ.01 TCGA.B0.4814.11 TCGA.CJ.4869.11 TCGA.CJ.4907.11
#> "062" "02131" "03" "012" "012" "012"
#> TCGA.B8.5553.01 TCGA.MW.A4EC.01 TCGA.B0.5712.11 TCGA.EU.5905.01 TCGA.CZ.5985.01 TCGA.CZ.4856.01
#> "0413" "0411" "011" "0413" "02133" "0413"
#> TCGA.BP.5184.01 TCGA.B0.5121.01 TCGA.BP.5191.01 TCGA.BP.4801.11 TCGA.BP.5177.01 TCGA.B0.5110.11
#> "042" "022" "0212" "012" "062" "011"
#> TCGA.B0.4810.01 TCGA.CJ.4903.11 TCGA.CJ.4912.11 TCGA.B8.4621.01 TCGA.B4.5832.01 TCGA.CW.6088.01
#> "022" "012" "0542" "063" "0433" "061"
#> TCGA.AK.3428.01 TCGA.B8.5164.01 TCGA.BP.5195.01 TCGA.CJ.6027.01 TCGA.3Z.A93Z.01 TCGA.B0.4714.11
#> "022" "042" "0431" "0211" "061" "014"
#> TCGA.B0.4818.11 TCGA.CZ.5457.11 TCGA.BP.5010.01 TCGA.BP.5189.11 TCGA.B0.4703.01 TCGA.B0.4718.11
#> "011" "0512" "0431" "012" "0432" "052"
#> TCGA.B0.5097.11 TCGA.BP.4760.11 TCGA.B0.5120.11 TCGA.B0.4843.11 TCGA.B0.5104.01 TCGA.CW.5587.01
#> "011" "014" "011" "012" "0413" "0413"
get_classes(res_rh, merge_node = merge_node_param(min_n_signatures = 2035))
#> TCGA.CZ.4863.01 TCGA.CJ.4904.11 TCGA.B0.4827.11 TCGA.CJ.4902.01 TCGA.B0.4823.01 TCGA.CW.6087.01
#> "0412" "011" "0543" "043" "061" "043"
#> TCGA.B0.5098.01 TCGA.B0.5113.01 TCGA.DV.5566.01 TCGA.BP.5175.11 TCGA.BP.5181.01 TCGA.B0.4706.11
#> "073" "0233" "0411" "012" "062" "012"
#> TCGA.B0.5117.01 TCGA.MM.A564.01 TCGA.B0.4821.11 TCGA.CZ.5463.11 TCGA.BP.5182.11 TCGA.DV.5574.01
#> "013" "02133" "072" "0512" "012" "061"
#> TCGA.B0.5094.11 TCGA.MM.A84U.01 TCGA.B0.5100.11 TCGA.B4.5844.01 TCGA.CZ.5459.01 TCGA.B0.4694.01
#> "014" "0413" "014" "0411" "042" "043"
#> TCGA.CZ.5468.11 TCGA.CJ.4916.11 TCGA.B4.5836.01 TCGA.B0.5095.01 TCGA.B0.4846.11 TCGA.AK.3434.01
#> "0512" "011" "0413" "043" "011" "022"
#> TCGA.B4.5377.01 TCGA.B0.4696.11 TCGA.BP.5187.11 TCGA.B0.4690.01 TCGA.CZ.5466.01 TCGA.B0.4844.11
#> "062" "014" "014" "043" "043" "052"
#> TCGA.CZ.5464.11 TCGA.B0.4701.11 TCGA.BP.5194.11 TCGA.B0.4707.01 TCGA.CZ.5467.11 TCGA.B0.5705.01
#> "012" "011" "012" "02131" "0511" "062"
#> TCGA.CW.5588.01 TCGA.CJ.6031.01 TCGA.B8.A54J.01 TCGA.BP.5192.11 TCGA.CZ.5462.01 TCGA.B8.A54H.01
#> "0413" "043" "042" "052" "043" "0413"
#> TCGA.CZ.5470.11 TCGA.BP.4177.11 TCGA.CZ.5469.11 TCGA.CJ.6028.01 TCGA.G6.A8L6.01 TCGA.B8.5551.01
#> "0511" "052" "0512" "043" "042" "0412"
#> TCGA.CZ.5456.01 TCGA.A3.A8OU.01 TCGA.BP.5186.01 TCGA.A3.A6NI.01 TCGA.BP.4782.01 TCGA.CZ.5454.11
#> "0211" "0413" "062" "042" "0413" "0541"
#> TCGA.B0.4691.11 TCGA.CZ.5452.01 TCGA.EU.5904.01 TCGA.BP.5201.01 TCGA.CJ.5677.01 TCGA.BP.5170.11
#> "012" "02131" "062" "022" "0232" "0541"
#> TCGA.B0.4710.11 TCGA.AK.3425.01 TCGA.B0.4841.11 TCGA.B0.4849.01 TCGA.BP.5182.01 TCGA.B0.5711.11
#> "0511" "02131" "014" "042" "063" "052"
#> TCGA.BP.5180.01 TCGA.BP.5176.01 TCGA.CZ.5984.01 TCGA.CZ.5460.11 TCGA.BP.5190.01 TCGA.BP.4795.11
#> "0212" "0413" "0212" "012" "022" "011"
#> TCGA.B0.4813.11 TCGA.B0.4713.01 TCGA.B0.4841.01 TCGA.B8.5546.01 TCGA.CW.5591.01 TCGA.B0.4698.11
#> "0542" "0232" "022" "072" "043" "014"
#> TCGA.B0.5713.11 TCGA.B0.5108.11 TCGA.B0.5083.01 TCGA.B0.5699.01 TCGA.CZ.5453.11 TCGA.BP.5202.01
#> "011" "012" "013" "022" "0512" "022"
#> TCGA.BP.5173.11 TCGA.CW.5581.01 TCGA.B0.4848.11 TCGA.B0.4814.01 TCGA.BP.5178.11 TCGA.CJ.4907.01
#> "013" "042" "014" "022" "014" "042"
#> TCGA.A3.3387.01 TCGA.B0.4821.01 TCGA.B0.5712.01 TCGA.B0.5695.01 TCGA.BP.5184.11 TCGA.B2.A4SR.01
#> "042" "0232" "0231" "062" "012" "042"
#> TCGA.BP.5191.11 TCGA.CJ.4920.01 TCGA.BP.4801.01 TCGA.DV.A4W0.01 TCGA.BP.5177.11 TCGA.B0.4847.11
#> "014" "0231" "042" "022" "011" "052"
#> TCGA.B0.5100.01 TCGA.CJ.4903.01 TCGA.CJ.4912.01 TCGA.B0.5107.11 TCGA.AK.3453.01 TCGA.B0.5691.01
#> "043" "022" "0212" "011" "013" "062"
#> TCGA.BP.5195.11 TCGA.B0.5400.01 TCGA.A3.3376.11 TCGA.B0.4845.01 TCGA.B0.4699.01 TCGA.B0.4818.01
#> "0541" "0412" "071" "022" "071" "0413"
#> TCGA.BP.5174.11 TCGA.CJ.4901.11 TCGA.B8.A54D.01 TCGA.BP.4770.11 TCGA.CW.6093.01 TCGA.BP.5010.11
#> "011" "012" "022" "011" "061" "0541"
#> TCGA.AK.3431.01 TCGA.BP.4770.01 TCGA.BP.5189.01 TCGA.B0.4703.11 TCGA.B8.5163.01 TCGA.CJ.5683.01
#> "0413" "0412" "043" "014" "0412" "042"
#> TCGA.CZ.4856.11 TCGA.BP.4760.01 TCGA.B0.5692.01 TCGA.B0.5106.01 TCGA.B0.4843.01 TCGA.CZ.4866.11
#> "0511" "03" "0231" "0212" "043" "0511"
#> TCGA.B0.5104.11 TCGA.B0.4827.01 TCGA.CJ.4902.11 TCGA.B8.A54G.01 TCGA.B0.5703.01 TCGA.CJ.5672.01
#> "011" "0232" "0541" "042" "042" "042"
#> TCGA.B0.5098.11 TCGA.B0.5113.11 TCGA.CJ.4882.11 TCGA.CZ.5465.11 TCGA.B0.5102.01 TCGA.CW.5585.01
#> "013" "011" "012" "0511" "0411" "042"
#> TCGA.B0.4824.01 TCGA.B0.5115.01 TCGA.B0.4706.01 TCGA.B0.5117.11 TCGA.CZ.4859.11 TCGA.AK.3450.01
#> "0413" "022" "022" "012" "0543" "0413"
#> TCGA.B8.A54I.01 TCGA.CZ.5463.01 TCGA.DV.5568.01 TCGA.CZ.5459.11 TCGA.CJ.4918.11 TCGA.DV.5565.01
#> "0212" "022" "043" "014" "014" "042"
#> TCGA.B0.5119.01 TCGA.B0.4811.01 TCGA.A3.3367.11 TCGA.CJ.4916.01 TCGA.B0.5693.01 TCGA.CZ.4863.11
#> "062" "042" "014" "0412" "0411" "0511"
#> TCGA.G6.A5PC.01 TCGA.B8.5550.01 TCGA.DV.A4W0.05 TCGA.B0.4696.01 TCGA.BP.5187.01 TCGA.CZ.5466.11
#> "0231" "043" "03" "0212" "043" "014"
#> TCGA.CW.6097.01 TCGA.CJ.4905.11 TCGA.CZ.5989.01 TCGA.BP.5194.01 TCGA.B0.4707.11 TCGA.CZ.5467.01
#> "043" "052" "042" "042" "014" "0411"
#> TCGA.BP.5185.11 TCGA.BP.5183.11 TCGA.BP.5192.01 TCGA.CZ.5462.11 TCGA.BP.4177.01 TCGA.CZ.5469.01
#> "012" "012" "061" "0512" "03" "0211"
#> TCGA.B2.5641.01 TCGA.BP.5196.11 TCGA.CZ.5460.01 TCGA.B0.4712.01 TCGA.B8.A54K.01 TCGA.B0.5707.01
#> "0212" "012" "022" "0211" "03" "062"
#> TCGA.BP.5186.11 TCGA.EU.5906.01 TCGA.CZ.5461.11 TCGA.CW.5590.01 TCGA.B0.5698.01 TCGA.CW.5580.01
#> "011" "061" "0541" "022" "022" "0231"
#> TCGA.CZ.5454.01 TCGA.B0.4815.01 TCGA.B0.5710.11 TCGA.CJ.4908.11 TCGA.BP.5201.11 TCGA.B0.5694.01
#> "022" "0211" "012" "0541" "012" "022"
#> TCGA.BP.5170.01 TCGA.DV.5575.01 TCGA.CJ.5686.01 TCGA.A3.3357.01 TCGA.A3.3373.01 TCGA.B0.5690.01
#> "042" "062" "0412" "022" "0411" "062"
#> TCGA.B8.4622.01 TCGA.AK.3433.01 TCGA.B0.5110.01 TCGA.BP.5180.11 TCGA.CJ.4913.01 TCGA.CJ.4908.01
#> "022" "053" "062" "012" "0231" "042"
#> TCGA.BP.4795.01 TCGA.CJ.4897.11 TCGA.B2.5636.01 TCGA.CJ.4923.11 TCGA.B0.4819.01 TCGA.B2.5633.01
#> "03" "011" "03" "014" "0412" "043"
#> TCGA.CJ.6033.01 TCGA.BP.5181.11 TCGA.B0.4698.01 TCGA.B0.5083.11 TCGA.CZ.4864.11 TCGA.B0.4688.01
#> "0232" "011" "02132" "012" "014" "02132"
#> TCGA.BP.5168.01 TCGA.BP.5198.11 TCGA.B8.5162.01 TCGA.B0.5096.01 TCGA.BP.5178.01 TCGA.B0.5099.11
#> "042" "014" "043" "0232" "0211" "011"
#> TCGA.B0.4842.01 TCGA.BP.5169.11 TCGA.B0.5109.11 TCGA.CJ.4920.11 TCGA.B0.5080.11 TCGA.B0.5700.01
#> "0412" "014" "071" "0542" "012" "061"
#> TCGA.B0.4847.01 TCGA.B0.5702.01 TCGA.CJ.4905.01 TCGA.B2.5635.01 TCGA.B0.5107.01 TCGA.CW.5584.01
#> "022" "071" "0411" "042" "0232" "022"
#> TCGA.B4.5838.01 TCGA.BP.5199.01 TCGA.A3.3376.01 TCGA.B0.4845.11 TCGA.B0.4699.11 TCGA.BP.5174.01
#> "042" "022" "061" "0542" "014" "062"
#> TCGA.CZ.5986.01 TCGA.CJ.4901.01 TCGA.AK.3461.01 TCGA.AK.3460.01 TCGA.AK.3454.01 TCGA.CZ.4859.01
#> "061" "02131" "042" "042" "061" "062"
#> TCGA.B0.5812.01 TCGA.B0.5116.11 TCGA.B8.A54F.01 TCGA.CW.6090.01 TCGA.CZ.5458.11 TCGA.B0.5106.11
#> "042" "071" "0413" "022" "0512" "012"
#> TCGA.CZ.4866.01 TCGA.B0.4828.01 TCGA.AK.3440.01 TCGA.MM.A563.01 TCGA.B0.4697.01 TCGA.AK.3458.01
#> "0231" "022" "053" "022" "0412" "022"
#> TCGA.CJ.5676.01 TCGA.B0.5402.11 TCGA.CJ.5681.01 TCGA.A3.3370.11 TCGA.A3.A6NL.01 TCGA.B0.4693.01
#> "02133" "014" "073" "052" "062" "0231"
#> TCGA.A3.3358.01 TCGA.B0.4710.01 TCGA.CZ.4853.11 TCGA.B4.5835.01 TCGA.CJ.4882.01 TCGA.CZ.5465.01
#> "0413" "0231" "0541" "062" "043" "0233"
#> TCGA.B0.5102.11 TCGA.B0.4824.11 TCGA.CJ.5675.01 TCGA.B0.4700.01 TCGA.B0.5092.01 TCGA.B0.5115.11
#> "011" "011" "022" "043" "0412" "012"
#> TCGA.B0.4945.11 TCGA.B8.5158.01 TCGA.CJ.6030.01 TCGA.B8.A54E.01 TCGA.CJ.6032.01 TCGA.B0.4852.11
#> "011" "02131" "02131" "072" "0411" "011"
#> TCGA.B0.4817.01 TCGA.B8.5159.01 TCGA.A3.A8OW.01 TCGA.B0.4822.01 TCGA.B0.5696.01 TCGA.B0.5706.01
#> "043" "0233" "061" "043" "042" "0212"
#> TCGA.CJ.4918.01 TCGA.B0.5119.11 TCGA.BP.5200.11 TCGA.B0.4811.11 TCGA.A3.3367.01 TCGA.B0.5097.01
#> "043" "0511" "012" "014" "022" "0412"
#> TCGA.6D.AA2E.01 TCGA.DV.A4VX.01 TCGA.B0.4816.11 TCGA.A3.3385.11 TCGA.DV.5569.01 TCGA.EU.5907.01
#> "072" "022" "0541" "011" "062" "022"
#> TCGA.CZ.5455.01 TCGA.B8.5545.01 TCGA.DV.5567.01 TCGA.CZ.5451.01 TCGA.CJ.4869.01 TCGA.CJ.5678.01
#> "042" "061" "03" "042" "043" "022"
#> TCGA.B8.4153.01 TCGA.B0.5121.11 TCGA.B8.4146.01 TCGA.BP.5183.01 TCGA.B0.5399.01 TCGA.B0.4810.11
#> "022" "012" "0411" "022" "042" "052"
#> TCGA.AK.3445.01 TCGA.B4.5378.01 TCGA.BP.5196.01 TCGA.CZ.4865.11 TCGA.B0.5709.01 TCGA.B0.4712.11
#> "0211" "03" "02131" "0511" "062" "0512"
#> TCGA.B0.4714.01 TCGA.B8.5549.01 TCGA.CZ.5461.01 TCGA.CZ.5457.01 TCGA.A3.A8CQ.01 TCGA.DV.5573.01
#> "022" "022" "0211" "063" "062" "061"
#> TCGA.B0.4815.11 TCGA.B0.5710.01 TCGA.B8.5165.01 TCGA.B0.4718.01 TCGA.B2.5639.01 TCGA.CW.5583.01
#> "014" "022" "061" "022" "043" "062"
#> TCGA.GK.A6C7.01 TCGA.A3.3357.11 TCGA.B8.5552.01 TCGA.B0.5120.01 TCGA.A3.3373.11 TCGA.BP.5185.01
#> "062" "012" "062" "0413" "0543" "042"
#> TCGA.B0.4846.01 TCGA.CJ.4904.01 TCGA.CJ.4913.11 TCGA.BP.4993.11 TCGA.B0.4823.11 TCGA.CJ.4897.01
#> "0413" "062" "011" "012" "013" "0411"
#> TCGA.BP.4993.01 TCGA.B4.5843.01 TCGA.DV.5576.01 TCGA.CJ.4923.01 TCGA.B0.4819.11 TCGA.BP.5175.01
#> "061" "061" "03" "043" "011" "0212"
#> TCGA.CZ.5987.01 TCGA.CZ.4864.01 TCGA.B0.4688.11 TCGA.BP.5168.11 TCGA.BP.5198.01 TCGA.B8.A7U6.01
#> "02133" "061" "0542" "014" "0211" "0413"
#> TCGA.B0.5094.01 TCGA.T7.A92I.01 TCGA.B0.5096.11 TCGA.B0.5400.11 TCGA.B0.4694.11 TCGA.B0.5099.01
#> "0211" "072" "011" "011" "052" "0411"
#> TCGA.CZ.5468.01 TCGA.B0.4842.11 TCGA.CZ.5988.01 TCGA.BP.5169.01 TCGA.B0.5109.01 TCGA.B4.5834.01
#> "02132" "011" "042" "0211" "043" "061"
#> TCGA.B0.5095.11 TCGA.B0.5080.01 TCGA.CJ.5680.01 TCGA.CZ.5470.01 TCGA.CZ.4865.01 TCGA.A3.A8OX.01
#> "013" "043" "0231" "0232" "0413" "072"
#> TCGA.B0.4690.11 TCGA.CJ.5684.01 TCGA.B0.4844.01 TCGA.CZ.5464.01 TCGA.B0.4701.01 TCGA.B0.5701.01
#> "013" "042" "02133" "0212" "0412" "0212"
#> TCGA.BP.5199.11 TCGA.CJ.5671.01 TCGA.A3.A8OV.01 TCGA.CZ.5456.11 TCGA.B0.5116.01 TCGA.CZ.5458.01
#> "012" "02131" "061" "0512" "022" "042"
#> TCGA.CZ.5982.01 TCGA.B0.4828.11 TCGA.CJ.5679.01 TCGA.CJ.5682.01 TCGA.B0.5697.01 TCGA.B0.4697.11
#> "0411" "0542" "0211" "022" "042" "0511"
#> TCGA.BP.4782.11 TCGA.G6.A8L8.01 TCGA.A3.A6NJ.01 TCGA.A3.3370.01 TCGA.B0.4691.01 TCGA.CZ.5452.11
#> "011" "0233" "062" "062" "0211" "0512"
#> TCGA.B0.4693.11 TCGA.B0.4945.01 TCGA.CZ.4853.01 TCGA.B0.5092.11 TCGA.B0.5402.01 TCGA.B0.4849.11
#> "011" "062" "022" "011" "022" "012"
#> TCGA.A3.A6NN.01 TCGA.B0.4852.01 TCGA.B0.4817.11 TCGA.BP.5176.11 TCGA.CW.5589.01 TCGA.CJ.5689.01
#> "042" "0411" "014" "011" "061" "042"
#> TCGA.B0.4822.11 TCGA.BP.5190.11 TCGA.B0.4813.01 TCGA.BP.5200.01 TCGA.G6.A8L7.01 TCGA.B2.4101.01
#> "052" "012" "022" "042" "0232" "043"
#> TCGA.B0.4713.11 TCGA.B0.4816.01 TCGA.A3.3385.01 TCGA.B2.3924.01 TCGA.CZ.5455.11 TCGA.B0.5713.01
#> "011" "043" "062" "042" "0512" "0411"
#> TCGA.B0.5108.01 TCGA.B0.5711.01 TCGA.CZ.5453.01 TCGA.BP.5202.11 TCGA.BP.5173.01 TCGA.CZ.5451.11
#> "043" "042" "061" "071" "061" "012"
#> TCGA.B8.A8YJ.01 TCGA.B0.4848.01 TCGA.DV.A4VZ.01 TCGA.B0.4814.11 TCGA.CJ.4869.11 TCGA.CJ.4907.11
#> "062" "02131" "03" "012" "012" "012"
#> TCGA.B8.5553.01 TCGA.MW.A4EC.01 TCGA.B0.5712.11 TCGA.EU.5905.01 TCGA.CZ.5985.01 TCGA.CZ.4856.01
#> "0413" "0411" "011" "0413" "02133" "0413"
#> TCGA.BP.5184.01 TCGA.B0.5121.01 TCGA.BP.5191.01 TCGA.BP.4801.11 TCGA.BP.5177.01 TCGA.B0.5110.11
#> "042" "022" "0212" "012" "062" "011"
#> TCGA.B0.4810.01 TCGA.CJ.4903.11 TCGA.CJ.4912.11 TCGA.B8.4621.01 TCGA.B4.5832.01 TCGA.CW.6088.01
#> "022" "012" "0542" "063" "043" "061"
#> TCGA.AK.3428.01 TCGA.B8.5164.01 TCGA.BP.5195.01 TCGA.CJ.6027.01 TCGA.3Z.A93Z.01 TCGA.B0.4714.11
#> "022" "042" "043" "0211" "061" "014"
#> TCGA.B0.4818.11 TCGA.CZ.5457.11 TCGA.BP.5010.01 TCGA.BP.5189.11 TCGA.B0.4703.01 TCGA.B0.4718.11
#> "011" "0512" "043" "012" "043" "052"
#> TCGA.B0.5097.11 TCGA.BP.4760.11 TCGA.B0.5120.11 TCGA.B0.4843.11 TCGA.B0.5104.01 TCGA.CW.5587.01
#> "011" "014" "011" "012" "0413" "0413"
get_classes(res_rh, merge_node = merge_node_param(min_n_signatures = 3246))
#> TCGA.CZ.4863.01 TCGA.CJ.4904.11 TCGA.B0.4827.11 TCGA.CJ.4902.01 TCGA.B0.4823.01 TCGA.CW.6087.01
#> "0412" "011" "0543" "043" "061" "043"
#> TCGA.B0.5098.01 TCGA.B0.5113.01 TCGA.DV.5566.01 TCGA.BP.5175.11 TCGA.BP.5181.01 TCGA.B0.4706.11
#> "073" "023" "0411" "012" "062" "012"
#> TCGA.B0.5117.01 TCGA.MM.A564.01 TCGA.B0.4821.11 TCGA.CZ.5463.11 TCGA.BP.5182.11 TCGA.DV.5574.01
#> "013" "02133" "072" "0512" "012" "061"
#> TCGA.B0.5094.11 TCGA.MM.A84U.01 TCGA.B0.5100.11 TCGA.B4.5844.01 TCGA.CZ.5459.01 TCGA.B0.4694.01
#> "014" "0413" "014" "0411" "042" "043"
#> TCGA.CZ.5468.11 TCGA.CJ.4916.11 TCGA.B4.5836.01 TCGA.B0.5095.01 TCGA.B0.4846.11 TCGA.AK.3434.01
#> "0512" "011" "0413" "043" "011" "022"
#> TCGA.B4.5377.01 TCGA.B0.4696.11 TCGA.BP.5187.11 TCGA.B0.4690.01 TCGA.CZ.5466.01 TCGA.B0.4844.11
#> "062" "014" "014" "043" "043" "052"
#> TCGA.CZ.5464.11 TCGA.B0.4701.11 TCGA.BP.5194.11 TCGA.B0.4707.01 TCGA.CZ.5467.11 TCGA.B0.5705.01
#> "012" "011" "012" "02131" "0511" "062"
#> TCGA.CW.5588.01 TCGA.CJ.6031.01 TCGA.B8.A54J.01 TCGA.BP.5192.11 TCGA.CZ.5462.01 TCGA.B8.A54H.01
#> "0413" "043" "042" "052" "043" "0413"
#> TCGA.CZ.5470.11 TCGA.BP.4177.11 TCGA.CZ.5469.11 TCGA.CJ.6028.01 TCGA.G6.A8L6.01 TCGA.B8.5551.01
#> "0511" "052" "0512" "043" "042" "0412"
#> TCGA.CZ.5456.01 TCGA.A3.A8OU.01 TCGA.BP.5186.01 TCGA.A3.A6NI.01 TCGA.BP.4782.01 TCGA.CZ.5454.11
#> "0211" "0413" "062" "042" "0413" "0541"
#> TCGA.B0.4691.11 TCGA.CZ.5452.01 TCGA.EU.5904.01 TCGA.BP.5201.01 TCGA.CJ.5677.01 TCGA.BP.5170.11
#> "012" "02131" "062" "022" "023" "0541"
#> TCGA.B0.4710.11 TCGA.AK.3425.01 TCGA.B0.4841.11 TCGA.B0.4849.01 TCGA.BP.5182.01 TCGA.B0.5711.11
#> "0511" "02131" "014" "042" "063" "052"
#> TCGA.BP.5180.01 TCGA.BP.5176.01 TCGA.CZ.5984.01 TCGA.CZ.5460.11 TCGA.BP.5190.01 TCGA.BP.4795.11
#> "0212" "0413" "0212" "012" "022" "011"
#> TCGA.B0.4813.11 TCGA.B0.4713.01 TCGA.B0.4841.01 TCGA.B8.5546.01 TCGA.CW.5591.01 TCGA.B0.4698.11
#> "0542" "023" "022" "072" "043" "014"
#> TCGA.B0.5713.11 TCGA.B0.5108.11 TCGA.B0.5083.01 TCGA.B0.5699.01 TCGA.CZ.5453.11 TCGA.BP.5202.01
#> "011" "012" "013" "022" "0512" "022"
#> TCGA.BP.5173.11 TCGA.CW.5581.01 TCGA.B0.4848.11 TCGA.B0.4814.01 TCGA.BP.5178.11 TCGA.CJ.4907.01
#> "013" "042" "014" "022" "014" "042"
#> TCGA.A3.3387.01 TCGA.B0.4821.01 TCGA.B0.5712.01 TCGA.B0.5695.01 TCGA.BP.5184.11 TCGA.B2.A4SR.01
#> "042" "023" "023" "062" "012" "042"
#> TCGA.BP.5191.11 TCGA.CJ.4920.01 TCGA.BP.4801.01 TCGA.DV.A4W0.01 TCGA.BP.5177.11 TCGA.B0.4847.11
#> "014" "023" "042" "022" "011" "052"
#> TCGA.B0.5100.01 TCGA.CJ.4903.01 TCGA.CJ.4912.01 TCGA.B0.5107.11 TCGA.AK.3453.01 TCGA.B0.5691.01
#> "043" "022" "0212" "011" "013" "062"
#> TCGA.BP.5195.11 TCGA.B0.5400.01 TCGA.A3.3376.11 TCGA.B0.4845.01 TCGA.B0.4699.01 TCGA.B0.4818.01
#> "0541" "0412" "071" "022" "071" "0413"
#> TCGA.BP.5174.11 TCGA.CJ.4901.11 TCGA.B8.A54D.01 TCGA.BP.4770.11 TCGA.CW.6093.01 TCGA.BP.5010.11
#> "011" "012" "022" "011" "061" "0541"
#> TCGA.AK.3431.01 TCGA.BP.4770.01 TCGA.BP.5189.01 TCGA.B0.4703.11 TCGA.B8.5163.01 TCGA.CJ.5683.01
#> "0413" "0412" "043" "014" "0412" "042"
#> TCGA.CZ.4856.11 TCGA.BP.4760.01 TCGA.B0.5692.01 TCGA.B0.5106.01 TCGA.B0.4843.01 TCGA.CZ.4866.11
#> "0511" "03" "023" "0212" "043" "0511"
#> TCGA.B0.5104.11 TCGA.B0.4827.01 TCGA.CJ.4902.11 TCGA.B8.A54G.01 TCGA.B0.5703.01 TCGA.CJ.5672.01
#> "011" "023" "0541" "042" "042" "042"
#> TCGA.B0.5098.11 TCGA.B0.5113.11 TCGA.CJ.4882.11 TCGA.CZ.5465.11 TCGA.B0.5102.01 TCGA.CW.5585.01
#> "013" "011" "012" "0511" "0411" "042"
#> TCGA.B0.4824.01 TCGA.B0.5115.01 TCGA.B0.4706.01 TCGA.B0.5117.11 TCGA.CZ.4859.11 TCGA.AK.3450.01
#> "0413" "022" "022" "012" "0543" "0413"
#> TCGA.B8.A54I.01 TCGA.CZ.5463.01 TCGA.DV.5568.01 TCGA.CZ.5459.11 TCGA.CJ.4918.11 TCGA.DV.5565.01
#> "0212" "022" "043" "014" "014" "042"
#> TCGA.B0.5119.01 TCGA.B0.4811.01 TCGA.A3.3367.11 TCGA.CJ.4916.01 TCGA.B0.5693.01 TCGA.CZ.4863.11
#> "062" "042" "014" "0412" "0411" "0511"
#> TCGA.G6.A5PC.01 TCGA.B8.5550.01 TCGA.DV.A4W0.05 TCGA.B0.4696.01 TCGA.BP.5187.01 TCGA.CZ.5466.11
#> "023" "043" "03" "0212" "043" "014"
#> TCGA.CW.6097.01 TCGA.CJ.4905.11 TCGA.CZ.5989.01 TCGA.BP.5194.01 TCGA.B0.4707.11 TCGA.CZ.5467.01
#> "043" "052" "042" "042" "014" "0411"
#> TCGA.BP.5185.11 TCGA.BP.5183.11 TCGA.BP.5192.01 TCGA.CZ.5462.11 TCGA.BP.4177.01 TCGA.CZ.5469.01
#> "012" "012" "061" "0512" "03" "0211"
#> TCGA.B2.5641.01 TCGA.BP.5196.11 TCGA.CZ.5460.01 TCGA.B0.4712.01 TCGA.B8.A54K.01 TCGA.B0.5707.01
#> "0212" "012" "022" "0211" "03" "062"
#> TCGA.BP.5186.11 TCGA.EU.5906.01 TCGA.CZ.5461.11 TCGA.CW.5590.01 TCGA.B0.5698.01 TCGA.CW.5580.01
#> "011" "061" "0541" "022" "022" "023"
#> TCGA.CZ.5454.01 TCGA.B0.4815.01 TCGA.B0.5710.11 TCGA.CJ.4908.11 TCGA.BP.5201.11 TCGA.B0.5694.01
#> "022" "0211" "012" "0541" "012" "022"
#> TCGA.BP.5170.01 TCGA.DV.5575.01 TCGA.CJ.5686.01 TCGA.A3.3357.01 TCGA.A3.3373.01 TCGA.B0.5690.01
#> "042" "062" "0412" "022" "0411" "062"
#> TCGA.B8.4622.01 TCGA.AK.3433.01 TCGA.B0.5110.01 TCGA.BP.5180.11 TCGA.CJ.4913.01 TCGA.CJ.4908.01
#> "022" "053" "062" "012" "023" "042"
#> TCGA.BP.4795.01 TCGA.CJ.4897.11 TCGA.B2.5636.01 TCGA.CJ.4923.11 TCGA.B0.4819.01 TCGA.B2.5633.01
#> "03" "011" "03" "014" "0412" "043"
#> TCGA.CJ.6033.01 TCGA.BP.5181.11 TCGA.B0.4698.01 TCGA.B0.5083.11 TCGA.CZ.4864.11 TCGA.B0.4688.01
#> "023" "011" "02132" "012" "014" "02132"
#> TCGA.BP.5168.01 TCGA.BP.5198.11 TCGA.B8.5162.01 TCGA.B0.5096.01 TCGA.BP.5178.01 TCGA.B0.5099.11
#> "042" "014" "043" "023" "0211" "011"
#> TCGA.B0.4842.01 TCGA.BP.5169.11 TCGA.B0.5109.11 TCGA.CJ.4920.11 TCGA.B0.5080.11 TCGA.B0.5700.01
#> "0412" "014" "071" "0542" "012" "061"
#> TCGA.B0.4847.01 TCGA.B0.5702.01 TCGA.CJ.4905.01 TCGA.B2.5635.01 TCGA.B0.5107.01 TCGA.CW.5584.01
#> "022" "071" "0411" "042" "023" "022"
#> TCGA.B4.5838.01 TCGA.BP.5199.01 TCGA.A3.3376.01 TCGA.B0.4845.11 TCGA.B0.4699.11 TCGA.BP.5174.01
#> "042" "022" "061" "0542" "014" "062"
#> TCGA.CZ.5986.01 TCGA.CJ.4901.01 TCGA.AK.3461.01 TCGA.AK.3460.01 TCGA.AK.3454.01 TCGA.CZ.4859.01
#> "061" "02131" "042" "042" "061" "062"
#> TCGA.B0.5812.01 TCGA.B0.5116.11 TCGA.B8.A54F.01 TCGA.CW.6090.01 TCGA.CZ.5458.11 TCGA.B0.5106.11
#> "042" "071" "0413" "022" "0512" "012"
#> TCGA.CZ.4866.01 TCGA.B0.4828.01 TCGA.AK.3440.01 TCGA.MM.A563.01 TCGA.B0.4697.01 TCGA.AK.3458.01
#> "023" "022" "053" "022" "0412" "022"
#> TCGA.CJ.5676.01 TCGA.B0.5402.11 TCGA.CJ.5681.01 TCGA.A3.3370.11 TCGA.A3.A6NL.01 TCGA.B0.4693.01
#> "02133" "014" "073" "052" "062" "023"
#> TCGA.A3.3358.01 TCGA.B0.4710.01 TCGA.CZ.4853.11 TCGA.B4.5835.01 TCGA.CJ.4882.01 TCGA.CZ.5465.01
#> "0413" "023" "0541" "062" "043" "023"
#> TCGA.B0.5102.11 TCGA.B0.4824.11 TCGA.CJ.5675.01 TCGA.B0.4700.01 TCGA.B0.5092.01 TCGA.B0.5115.11
#> "011" "011" "022" "043" "0412" "012"
#> TCGA.B0.4945.11 TCGA.B8.5158.01 TCGA.CJ.6030.01 TCGA.B8.A54E.01 TCGA.CJ.6032.01 TCGA.B0.4852.11
#> "011" "02131" "02131" "072" "0411" "011"
#> TCGA.B0.4817.01 TCGA.B8.5159.01 TCGA.A3.A8OW.01 TCGA.B0.4822.01 TCGA.B0.5696.01 TCGA.B0.5706.01
#> "043" "023" "061" "043" "042" "0212"
#> TCGA.CJ.4918.01 TCGA.B0.5119.11 TCGA.BP.5200.11 TCGA.B0.4811.11 TCGA.A3.3367.01 TCGA.B0.5097.01
#> "043" "0511" "012" "014" "022" "0412"
#> TCGA.6D.AA2E.01 TCGA.DV.A4VX.01 TCGA.B0.4816.11 TCGA.A3.3385.11 TCGA.DV.5569.01 TCGA.EU.5907.01
#> "072" "022" "0541" "011" "062" "022"
#> TCGA.CZ.5455.01 TCGA.B8.5545.01 TCGA.DV.5567.01 TCGA.CZ.5451.01 TCGA.CJ.4869.01 TCGA.CJ.5678.01
#> "042" "061" "03" "042" "043" "022"
#> TCGA.B8.4153.01 TCGA.B0.5121.11 TCGA.B8.4146.01 TCGA.BP.5183.01 TCGA.B0.5399.01 TCGA.B0.4810.11
#> "022" "012" "0411" "022" "042" "052"
#> TCGA.AK.3445.01 TCGA.B4.5378.01 TCGA.BP.5196.01 TCGA.CZ.4865.11 TCGA.B0.5709.01 TCGA.B0.4712.11
#> "0211" "03" "02131" "0511" "062" "0512"
#> TCGA.B0.4714.01 TCGA.B8.5549.01 TCGA.CZ.5461.01 TCGA.CZ.5457.01 TCGA.A3.A8CQ.01 TCGA.DV.5573.01
#> "022" "022" "0211" "063" "062" "061"
#> TCGA.B0.4815.11 TCGA.B0.5710.01 TCGA.B8.5165.01 TCGA.B0.4718.01 TCGA.B2.5639.01 TCGA.CW.5583.01
#> "014" "022" "061" "022" "043" "062"
#> TCGA.GK.A6C7.01 TCGA.A3.3357.11 TCGA.B8.5552.01 TCGA.B0.5120.01 TCGA.A3.3373.11 TCGA.BP.5185.01
#> "062" "012" "062" "0413" "0543" "042"
#> TCGA.B0.4846.01 TCGA.CJ.4904.01 TCGA.CJ.4913.11 TCGA.BP.4993.11 TCGA.B0.4823.11 TCGA.CJ.4897.01
#> "0413" "062" "011" "012" "013" "0411"
#> TCGA.BP.4993.01 TCGA.B4.5843.01 TCGA.DV.5576.01 TCGA.CJ.4923.01 TCGA.B0.4819.11 TCGA.BP.5175.01
#> "061" "061" "03" "043" "011" "0212"
#> TCGA.CZ.5987.01 TCGA.CZ.4864.01 TCGA.B0.4688.11 TCGA.BP.5168.11 TCGA.BP.5198.01 TCGA.B8.A7U6.01
#> "02133" "061" "0542" "014" "0211" "0413"
#> TCGA.B0.5094.01 TCGA.T7.A92I.01 TCGA.B0.5096.11 TCGA.B0.5400.11 TCGA.B0.4694.11 TCGA.B0.5099.01
#> "0211" "072" "011" "011" "052" "0411"
#> TCGA.CZ.5468.01 TCGA.B0.4842.11 TCGA.CZ.5988.01 TCGA.BP.5169.01 TCGA.B0.5109.01 TCGA.B4.5834.01
#> "02132" "011" "042" "0211" "043" "061"
#> TCGA.B0.5095.11 TCGA.B0.5080.01 TCGA.CJ.5680.01 TCGA.CZ.5470.01 TCGA.CZ.4865.01 TCGA.A3.A8OX.01
#> "013" "043" "023" "023" "0413" "072"
#> TCGA.B0.4690.11 TCGA.CJ.5684.01 TCGA.B0.4844.01 TCGA.CZ.5464.01 TCGA.B0.4701.01 TCGA.B0.5701.01
#> "013" "042" "02133" "0212" "0412" "0212"
#> TCGA.BP.5199.11 TCGA.CJ.5671.01 TCGA.A3.A8OV.01 TCGA.CZ.5456.11 TCGA.B0.5116.01 TCGA.CZ.5458.01
#> "012" "02131" "061" "0512" "022" "042"
#> TCGA.CZ.5982.01 TCGA.B0.4828.11 TCGA.CJ.5679.01 TCGA.CJ.5682.01 TCGA.B0.5697.01 TCGA.B0.4697.11
#> "0411" "0542" "0211" "022" "042" "0511"
#> TCGA.BP.4782.11 TCGA.G6.A8L8.01 TCGA.A3.A6NJ.01 TCGA.A3.3370.01 TCGA.B0.4691.01 TCGA.CZ.5452.11
#> "011" "023" "062" "062" "0211" "0512"
#> TCGA.B0.4693.11 TCGA.B0.4945.01 TCGA.CZ.4853.01 TCGA.B0.5092.11 TCGA.B0.5402.01 TCGA.B0.4849.11
#> "011" "062" "022" "011" "022" "012"
#> TCGA.A3.A6NN.01 TCGA.B0.4852.01 TCGA.B0.4817.11 TCGA.BP.5176.11 TCGA.CW.5589.01 TCGA.CJ.5689.01
#> "042" "0411" "014" "011" "061" "042"
#> TCGA.B0.4822.11 TCGA.BP.5190.11 TCGA.B0.4813.01 TCGA.BP.5200.01 TCGA.G6.A8L7.01 TCGA.B2.4101.01
#> "052" "012" "022" "042" "023" "043"
#> TCGA.B0.4713.11 TCGA.B0.4816.01 TCGA.A3.3385.01 TCGA.B2.3924.01 TCGA.CZ.5455.11 TCGA.B0.5713.01
#> "011" "043" "062" "042" "0512" "0411"
#> TCGA.B0.5108.01 TCGA.B0.5711.01 TCGA.CZ.5453.01 TCGA.BP.5202.11 TCGA.BP.5173.01 TCGA.CZ.5451.11
#> "043" "042" "061" "071" "061" "012"
#> TCGA.B8.A8YJ.01 TCGA.B0.4848.01 TCGA.DV.A4VZ.01 TCGA.B0.4814.11 TCGA.CJ.4869.11 TCGA.CJ.4907.11
#> "062" "02131" "03" "012" "012" "012"
#> TCGA.B8.5553.01 TCGA.MW.A4EC.01 TCGA.B0.5712.11 TCGA.EU.5905.01 TCGA.CZ.5985.01 TCGA.CZ.4856.01
#> "0413" "0411" "011" "0413" "02133" "0413"
#> TCGA.BP.5184.01 TCGA.B0.5121.01 TCGA.BP.5191.01 TCGA.BP.4801.11 TCGA.BP.5177.01 TCGA.B0.5110.11
#> "042" "022" "0212" "012" "062" "011"
#> TCGA.B0.4810.01 TCGA.CJ.4903.11 TCGA.CJ.4912.11 TCGA.B8.4621.01 TCGA.B4.5832.01 TCGA.CW.6088.01
#> "022" "012" "0542" "063" "043" "061"
#> TCGA.AK.3428.01 TCGA.B8.5164.01 TCGA.BP.5195.01 TCGA.CJ.6027.01 TCGA.3Z.A93Z.01 TCGA.B0.4714.11
#> "022" "042" "043" "0211" "061" "014"
#> TCGA.B0.4818.11 TCGA.CZ.5457.11 TCGA.BP.5010.01 TCGA.BP.5189.11 TCGA.B0.4703.01 TCGA.B0.4718.11
#> "011" "0512" "043" "012" "043" "052"
#> TCGA.B0.5097.11 TCGA.BP.4760.11 TCGA.B0.5120.11 TCGA.B0.4843.11 TCGA.B0.5104.01 TCGA.CW.5587.01
#> "011" "014" "011" "012" "0413" "0413"
get_classes(res_rh, merge_node = merge_node_param(min_n_signatures = 3386))
#> TCGA.CZ.4863.01 TCGA.CJ.4904.11 TCGA.B0.4827.11 TCGA.CJ.4902.01 TCGA.B0.4823.01 TCGA.CW.6087.01
#> "0412" "011" "0543" "043" "061" "043"
#> TCGA.B0.5098.01 TCGA.B0.5113.01 TCGA.DV.5566.01 TCGA.BP.5175.11 TCGA.BP.5181.01 TCGA.B0.4706.11
#> "073" "023" "0411" "012" "062" "012"
#> TCGA.B0.5117.01 TCGA.MM.A564.01 TCGA.B0.4821.11 TCGA.CZ.5463.11 TCGA.BP.5182.11 TCGA.DV.5574.01
#> "013" "02133" "072" "051" "012" "061"
#> TCGA.B0.5094.11 TCGA.MM.A84U.01 TCGA.B0.5100.11 TCGA.B4.5844.01 TCGA.CZ.5459.01 TCGA.B0.4694.01
#> "014" "0413" "014" "0411" "042" "043"
#> TCGA.CZ.5468.11 TCGA.CJ.4916.11 TCGA.B4.5836.01 TCGA.B0.5095.01 TCGA.B0.4846.11 TCGA.AK.3434.01
#> "051" "011" "0413" "043" "011" "022"
#> TCGA.B4.5377.01 TCGA.B0.4696.11 TCGA.BP.5187.11 TCGA.B0.4690.01 TCGA.CZ.5466.01 TCGA.B0.4844.11
#> "062" "014" "014" "043" "043" "052"
#> TCGA.CZ.5464.11 TCGA.B0.4701.11 TCGA.BP.5194.11 TCGA.B0.4707.01 TCGA.CZ.5467.11 TCGA.B0.5705.01
#> "012" "011" "012" "02131" "051" "062"
#> TCGA.CW.5588.01 TCGA.CJ.6031.01 TCGA.B8.A54J.01 TCGA.BP.5192.11 TCGA.CZ.5462.01 TCGA.B8.A54H.01
#> "0413" "043" "042" "052" "043" "0413"
#> TCGA.CZ.5470.11 TCGA.BP.4177.11 TCGA.CZ.5469.11 TCGA.CJ.6028.01 TCGA.G6.A8L6.01 TCGA.B8.5551.01
#> "051" "052" "051" "043" "042" "0412"
#> TCGA.CZ.5456.01 TCGA.A3.A8OU.01 TCGA.BP.5186.01 TCGA.A3.A6NI.01 TCGA.BP.4782.01 TCGA.CZ.5454.11
#> "0211" "0413" "062" "042" "0413" "0541"
#> TCGA.B0.4691.11 TCGA.CZ.5452.01 TCGA.EU.5904.01 TCGA.BP.5201.01 TCGA.CJ.5677.01 TCGA.BP.5170.11
#> "012" "02131" "062" "022" "023" "0541"
#> TCGA.B0.4710.11 TCGA.AK.3425.01 TCGA.B0.4841.11 TCGA.B0.4849.01 TCGA.BP.5182.01 TCGA.B0.5711.11
#> "051" "02131" "014" "042" "063" "052"
#> TCGA.BP.5180.01 TCGA.BP.5176.01 TCGA.CZ.5984.01 TCGA.CZ.5460.11 TCGA.BP.5190.01 TCGA.BP.4795.11
#> "0212" "0413" "0212" "012" "022" "011"
#> TCGA.B0.4813.11 TCGA.B0.4713.01 TCGA.B0.4841.01 TCGA.B8.5546.01 TCGA.CW.5591.01 TCGA.B0.4698.11
#> "0542" "023" "022" "072" "043" "014"
#> TCGA.B0.5713.11 TCGA.B0.5108.11 TCGA.B0.5083.01 TCGA.B0.5699.01 TCGA.CZ.5453.11 TCGA.BP.5202.01
#> "011" "012" "013" "022" "051" "022"
#> TCGA.BP.5173.11 TCGA.CW.5581.01 TCGA.B0.4848.11 TCGA.B0.4814.01 TCGA.BP.5178.11 TCGA.CJ.4907.01
#> "013" "042" "014" "022" "014" "042"
#> TCGA.A3.3387.01 TCGA.B0.4821.01 TCGA.B0.5712.01 TCGA.B0.5695.01 TCGA.BP.5184.11 TCGA.B2.A4SR.01
#> "042" "023" "023" "062" "012" "042"
#> TCGA.BP.5191.11 TCGA.CJ.4920.01 TCGA.BP.4801.01 TCGA.DV.A4W0.01 TCGA.BP.5177.11 TCGA.B0.4847.11
#> "014" "023" "042" "022" "011" "052"
#> TCGA.B0.5100.01 TCGA.CJ.4903.01 TCGA.CJ.4912.01 TCGA.B0.5107.11 TCGA.AK.3453.01 TCGA.B0.5691.01
#> "043" "022" "0212" "011" "013" "062"
#> TCGA.BP.5195.11 TCGA.B0.5400.01 TCGA.A3.3376.11 TCGA.B0.4845.01 TCGA.B0.4699.01 TCGA.B0.4818.01
#> "0541" "0412" "071" "022" "071" "0413"
#> TCGA.BP.5174.11 TCGA.CJ.4901.11 TCGA.B8.A54D.01 TCGA.BP.4770.11 TCGA.CW.6093.01 TCGA.BP.5010.11
#> "011" "012" "022" "011" "061" "0541"
#> TCGA.AK.3431.01 TCGA.BP.4770.01 TCGA.BP.5189.01 TCGA.B0.4703.11 TCGA.B8.5163.01 TCGA.CJ.5683.01
#> "0413" "0412" "043" "014" "0412" "042"
#> TCGA.CZ.4856.11 TCGA.BP.4760.01 TCGA.B0.5692.01 TCGA.B0.5106.01 TCGA.B0.4843.01 TCGA.CZ.4866.11
#> "051" "03" "023" "0212" "043" "051"
#> TCGA.B0.5104.11 TCGA.B0.4827.01 TCGA.CJ.4902.11 TCGA.B8.A54G.01 TCGA.B0.5703.01 TCGA.CJ.5672.01
#> "011" "023" "0541" "042" "042" "042"
#> TCGA.B0.5098.11 TCGA.B0.5113.11 TCGA.CJ.4882.11 TCGA.CZ.5465.11 TCGA.B0.5102.01 TCGA.CW.5585.01
#> "013" "011" "012" "051" "0411" "042"
#> TCGA.B0.4824.01 TCGA.B0.5115.01 TCGA.B0.4706.01 TCGA.B0.5117.11 TCGA.CZ.4859.11 TCGA.AK.3450.01
#> "0413" "022" "022" "012" "0543" "0413"
#> TCGA.B8.A54I.01 TCGA.CZ.5463.01 TCGA.DV.5568.01 TCGA.CZ.5459.11 TCGA.CJ.4918.11 TCGA.DV.5565.01
#> "0212" "022" "043" "014" "014" "042"
#> TCGA.B0.5119.01 TCGA.B0.4811.01 TCGA.A3.3367.11 TCGA.CJ.4916.01 TCGA.B0.5693.01 TCGA.CZ.4863.11
#> "062" "042" "014" "0412" "0411" "051"
#> TCGA.G6.A5PC.01 TCGA.B8.5550.01 TCGA.DV.A4W0.05 TCGA.B0.4696.01 TCGA.BP.5187.01 TCGA.CZ.5466.11
#> "023" "043" "03" "0212" "043" "014"
#> TCGA.CW.6097.01 TCGA.CJ.4905.11 TCGA.CZ.5989.01 TCGA.BP.5194.01 TCGA.B0.4707.11 TCGA.CZ.5467.01
#> "043" "052" "042" "042" "014" "0411"
#> TCGA.BP.5185.11 TCGA.BP.5183.11 TCGA.BP.5192.01 TCGA.CZ.5462.11 TCGA.BP.4177.01 TCGA.CZ.5469.01
#> "012" "012" "061" "051" "03" "0211"
#> TCGA.B2.5641.01 TCGA.BP.5196.11 TCGA.CZ.5460.01 TCGA.B0.4712.01 TCGA.B8.A54K.01 TCGA.B0.5707.01
#> "0212" "012" "022" "0211" "03" "062"
#> TCGA.BP.5186.11 TCGA.EU.5906.01 TCGA.CZ.5461.11 TCGA.CW.5590.01 TCGA.B0.5698.01 TCGA.CW.5580.01
#> "011" "061" "0541" "022" "022" "023"
#> TCGA.CZ.5454.01 TCGA.B0.4815.01 TCGA.B0.5710.11 TCGA.CJ.4908.11 TCGA.BP.5201.11 TCGA.B0.5694.01
#> "022" "0211" "012" "0541" "012" "022"
#> TCGA.BP.5170.01 TCGA.DV.5575.01 TCGA.CJ.5686.01 TCGA.A3.3357.01 TCGA.A3.3373.01 TCGA.B0.5690.01
#> "042" "062" "0412" "022" "0411" "062"
#> TCGA.B8.4622.01 TCGA.AK.3433.01 TCGA.B0.5110.01 TCGA.BP.5180.11 TCGA.CJ.4913.01 TCGA.CJ.4908.01
#> "022" "053" "062" "012" "023" "042"
#> TCGA.BP.4795.01 TCGA.CJ.4897.11 TCGA.B2.5636.01 TCGA.CJ.4923.11 TCGA.B0.4819.01 TCGA.B2.5633.01
#> "03" "011" "03" "014" "0412" "043"
#> TCGA.CJ.6033.01 TCGA.BP.5181.11 TCGA.B0.4698.01 TCGA.B0.5083.11 TCGA.CZ.4864.11 TCGA.B0.4688.01
#> "023" "011" "02132" "012" "014" "02132"
#> TCGA.BP.5168.01 TCGA.BP.5198.11 TCGA.B8.5162.01 TCGA.B0.5096.01 TCGA.BP.5178.01 TCGA.B0.5099.11
#> "042" "014" "043" "023" "0211" "011"
#> TCGA.B0.4842.01 TCGA.BP.5169.11 TCGA.B0.5109.11 TCGA.CJ.4920.11 TCGA.B0.5080.11 TCGA.B0.5700.01
#> "0412" "014" "071" "0542" "012" "061"
#> TCGA.B0.4847.01 TCGA.B0.5702.01 TCGA.CJ.4905.01 TCGA.B2.5635.01 TCGA.B0.5107.01 TCGA.CW.5584.01
#> "022" "071" "0411" "042" "023" "022"
#> TCGA.B4.5838.01 TCGA.BP.5199.01 TCGA.A3.3376.01 TCGA.B0.4845.11 TCGA.B0.4699.11 TCGA.BP.5174.01
#> "042" "022" "061" "0542" "014" "062"
#> TCGA.CZ.5986.01 TCGA.CJ.4901.01 TCGA.AK.3461.01 TCGA.AK.3460.01 TCGA.AK.3454.01 TCGA.CZ.4859.01
#> "061" "02131" "042" "042" "061" "062"
#> TCGA.B0.5812.01 TCGA.B0.5116.11 TCGA.B8.A54F.01 TCGA.CW.6090.01 TCGA.CZ.5458.11 TCGA.B0.5106.11
#> "042" "071" "0413" "022" "051" "012"
#> TCGA.CZ.4866.01 TCGA.B0.4828.01 TCGA.AK.3440.01 TCGA.MM.A563.01 TCGA.B0.4697.01 TCGA.AK.3458.01
#> "023" "022" "053" "022" "0412" "022"
#> TCGA.CJ.5676.01 TCGA.B0.5402.11 TCGA.CJ.5681.01 TCGA.A3.3370.11 TCGA.A3.A6NL.01 TCGA.B0.4693.01
#> "02133" "014" "073" "052" "062" "023"
#> TCGA.A3.3358.01 TCGA.B0.4710.01 TCGA.CZ.4853.11 TCGA.B4.5835.01 TCGA.CJ.4882.01 TCGA.CZ.5465.01
#> "0413" "023" "0541" "062" "043" "023"
#> TCGA.B0.5102.11 TCGA.B0.4824.11 TCGA.CJ.5675.01 TCGA.B0.4700.01 TCGA.B0.5092.01 TCGA.B0.5115.11
#> "011" "011" "022" "043" "0412" "012"
#> TCGA.B0.4945.11 TCGA.B8.5158.01 TCGA.CJ.6030.01 TCGA.B8.A54E.01 TCGA.CJ.6032.01 TCGA.B0.4852.11
#> "011" "02131" "02131" "072" "0411" "011"
#> TCGA.B0.4817.01 TCGA.B8.5159.01 TCGA.A3.A8OW.01 TCGA.B0.4822.01 TCGA.B0.5696.01 TCGA.B0.5706.01
#> "043" "023" "061" "043" "042" "0212"
#> TCGA.CJ.4918.01 TCGA.B0.5119.11 TCGA.BP.5200.11 TCGA.B0.4811.11 TCGA.A3.3367.01 TCGA.B0.5097.01
#> "043" "051" "012" "014" "022" "0412"
#> TCGA.6D.AA2E.01 TCGA.DV.A4VX.01 TCGA.B0.4816.11 TCGA.A3.3385.11 TCGA.DV.5569.01 TCGA.EU.5907.01
#> "072" "022" "0541" "011" "062" "022"
#> TCGA.CZ.5455.01 TCGA.B8.5545.01 TCGA.DV.5567.01 TCGA.CZ.5451.01 TCGA.CJ.4869.01 TCGA.CJ.5678.01
#> "042" "061" "03" "042" "043" "022"
#> TCGA.B8.4153.01 TCGA.B0.5121.11 TCGA.B8.4146.01 TCGA.BP.5183.01 TCGA.B0.5399.01 TCGA.B0.4810.11
#> "022" "012" "0411" "022" "042" "052"
#> TCGA.AK.3445.01 TCGA.B4.5378.01 TCGA.BP.5196.01 TCGA.CZ.4865.11 TCGA.B0.5709.01 TCGA.B0.4712.11
#> "0211" "03" "02131" "051" "062" "051"
#> TCGA.B0.4714.01 TCGA.B8.5549.01 TCGA.CZ.5461.01 TCGA.CZ.5457.01 TCGA.A3.A8CQ.01 TCGA.DV.5573.01
#> "022" "022" "0211" "063" "062" "061"
#> TCGA.B0.4815.11 TCGA.B0.5710.01 TCGA.B8.5165.01 TCGA.B0.4718.01 TCGA.B2.5639.01 TCGA.CW.5583.01
#> "014" "022" "061" "022" "043" "062"
#> TCGA.GK.A6C7.01 TCGA.A3.3357.11 TCGA.B8.5552.01 TCGA.B0.5120.01 TCGA.A3.3373.11 TCGA.BP.5185.01
#> "062" "012" "062" "0413" "0543" "042"
#> TCGA.B0.4846.01 TCGA.CJ.4904.01 TCGA.CJ.4913.11 TCGA.BP.4993.11 TCGA.B0.4823.11 TCGA.CJ.4897.01
#> "0413" "062" "011" "012" "013" "0411"
#> TCGA.BP.4993.01 TCGA.B4.5843.01 TCGA.DV.5576.01 TCGA.CJ.4923.01 TCGA.B0.4819.11 TCGA.BP.5175.01
#> "061" "061" "03" "043" "011" "0212"
#> TCGA.CZ.5987.01 TCGA.CZ.4864.01 TCGA.B0.4688.11 TCGA.BP.5168.11 TCGA.BP.5198.01 TCGA.B8.A7U6.01
#> "02133" "061" "0542" "014" "0211" "0413"
#> TCGA.B0.5094.01 TCGA.T7.A92I.01 TCGA.B0.5096.11 TCGA.B0.5400.11 TCGA.B0.4694.11 TCGA.B0.5099.01
#> "0211" "072" "011" "011" "052" "0411"
#> TCGA.CZ.5468.01 TCGA.B0.4842.11 TCGA.CZ.5988.01 TCGA.BP.5169.01 TCGA.B0.5109.01 TCGA.B4.5834.01
#> "02132" "011" "042" "0211" "043" "061"
#> TCGA.B0.5095.11 TCGA.B0.5080.01 TCGA.CJ.5680.01 TCGA.CZ.5470.01 TCGA.CZ.4865.01 TCGA.A3.A8OX.01
#> "013" "043" "023" "023" "0413" "072"
#> TCGA.B0.4690.11 TCGA.CJ.5684.01 TCGA.B0.4844.01 TCGA.CZ.5464.01 TCGA.B0.4701.01 TCGA.B0.5701.01
#> "013" "042" "02133" "0212" "0412" "0212"
#> TCGA.BP.5199.11 TCGA.CJ.5671.01 TCGA.A3.A8OV.01 TCGA.CZ.5456.11 TCGA.B0.5116.01 TCGA.CZ.5458.01
#> "012" "02131" "061" "051" "022" "042"
#> TCGA.CZ.5982.01 TCGA.B0.4828.11 TCGA.CJ.5679.01 TCGA.CJ.5682.01 TCGA.B0.5697.01 TCGA.B0.4697.11
#> "0411" "0542" "0211" "022" "042" "051"
#> TCGA.BP.4782.11 TCGA.G6.A8L8.01 TCGA.A3.A6NJ.01 TCGA.A3.3370.01 TCGA.B0.4691.01 TCGA.CZ.5452.11
#> "011" "023" "062" "062" "0211" "051"
#> TCGA.B0.4693.11 TCGA.B0.4945.01 TCGA.CZ.4853.01 TCGA.B0.5092.11 TCGA.B0.5402.01 TCGA.B0.4849.11
#> "011" "062" "022" "011" "022" "012"
#> TCGA.A3.A6NN.01 TCGA.B0.4852.01 TCGA.B0.4817.11 TCGA.BP.5176.11 TCGA.CW.5589.01 TCGA.CJ.5689.01
#> "042" "0411" "014" "011" "061" "042"
#> TCGA.B0.4822.11 TCGA.BP.5190.11 TCGA.B0.4813.01 TCGA.BP.5200.01 TCGA.G6.A8L7.01 TCGA.B2.4101.01
#> "052" "012" "022" "042" "023" "043"
#> TCGA.B0.4713.11 TCGA.B0.4816.01 TCGA.A3.3385.01 TCGA.B2.3924.01 TCGA.CZ.5455.11 TCGA.B0.5713.01
#> "011" "043" "062" "042" "051" "0411"
#> TCGA.B0.5108.01 TCGA.B0.5711.01 TCGA.CZ.5453.01 TCGA.BP.5202.11 TCGA.BP.5173.01 TCGA.CZ.5451.11
#> "043" "042" "061" "071" "061" "012"
#> TCGA.B8.A8YJ.01 TCGA.B0.4848.01 TCGA.DV.A4VZ.01 TCGA.B0.4814.11 TCGA.CJ.4869.11 TCGA.CJ.4907.11
#> "062" "02131" "03" "012" "012" "012"
#> TCGA.B8.5553.01 TCGA.MW.A4EC.01 TCGA.B0.5712.11 TCGA.EU.5905.01 TCGA.CZ.5985.01 TCGA.CZ.4856.01
#> "0413" "0411" "011" "0413" "02133" "0413"
#> TCGA.BP.5184.01 TCGA.B0.5121.01 TCGA.BP.5191.01 TCGA.BP.4801.11 TCGA.BP.5177.01 TCGA.B0.5110.11
#> "042" "022" "0212" "012" "062" "011"
#> TCGA.B0.4810.01 TCGA.CJ.4903.11 TCGA.CJ.4912.11 TCGA.B8.4621.01 TCGA.B4.5832.01 TCGA.CW.6088.01
#> "022" "012" "0542" "063" "043" "061"
#> TCGA.AK.3428.01 TCGA.B8.5164.01 TCGA.BP.5195.01 TCGA.CJ.6027.01 TCGA.3Z.A93Z.01 TCGA.B0.4714.11
#> "022" "042" "043" "0211" "061" "014"
#> TCGA.B0.4818.11 TCGA.CZ.5457.11 TCGA.BP.5010.01 TCGA.BP.5189.11 TCGA.B0.4703.01 TCGA.B0.4718.11
#> "011" "051" "043" "012" "043" "052"
#> TCGA.B0.5097.11 TCGA.BP.4760.11 TCGA.B0.5120.11 TCGA.B0.4843.11 TCGA.B0.5104.01 TCGA.CW.5587.01
#> "011" "014" "011" "012" "0413" "0413"
get_classes(res_rh, merge_node = merge_node_param(min_n_signatures = 3555))
#> TCGA.CZ.4863.01 TCGA.CJ.4904.11 TCGA.B0.4827.11 TCGA.CJ.4902.01 TCGA.B0.4823.01 TCGA.CW.6087.01
#> "041" "011" "0543" "043" "061" "043"
#> TCGA.B0.5098.01 TCGA.B0.5113.01 TCGA.DV.5566.01 TCGA.BP.5175.11 TCGA.BP.5181.01 TCGA.B0.4706.11
#> "073" "023" "041" "012" "062" "012"
#> TCGA.B0.5117.01 TCGA.MM.A564.01 TCGA.B0.4821.11 TCGA.CZ.5463.11 TCGA.BP.5182.11 TCGA.DV.5574.01
#> "013" "02133" "072" "051" "012" "061"
#> TCGA.B0.5094.11 TCGA.MM.A84U.01 TCGA.B0.5100.11 TCGA.B4.5844.01 TCGA.CZ.5459.01 TCGA.B0.4694.01
#> "014" "041" "014" "041" "042" "043"
#> TCGA.CZ.5468.11 TCGA.CJ.4916.11 TCGA.B4.5836.01 TCGA.B0.5095.01 TCGA.B0.4846.11 TCGA.AK.3434.01
#> "051" "011" "041" "043" "011" "022"
#> TCGA.B4.5377.01 TCGA.B0.4696.11 TCGA.BP.5187.11 TCGA.B0.4690.01 TCGA.CZ.5466.01 TCGA.B0.4844.11
#> "062" "014" "014" "043" "043" "052"
#> TCGA.CZ.5464.11 TCGA.B0.4701.11 TCGA.BP.5194.11 TCGA.B0.4707.01 TCGA.CZ.5467.11 TCGA.B0.5705.01
#> "012" "011" "012" "02131" "051" "062"
#> TCGA.CW.5588.01 TCGA.CJ.6031.01 TCGA.B8.A54J.01 TCGA.BP.5192.11 TCGA.CZ.5462.01 TCGA.B8.A54H.01
#> "041" "043" "042" "052" "043" "041"
#> TCGA.CZ.5470.11 TCGA.BP.4177.11 TCGA.CZ.5469.11 TCGA.CJ.6028.01 TCGA.G6.A8L6.01 TCGA.B8.5551.01
#> "051" "052" "051" "043" "042" "041"
#> TCGA.CZ.5456.01 TCGA.A3.A8OU.01 TCGA.BP.5186.01 TCGA.A3.A6NI.01 TCGA.BP.4782.01 TCGA.CZ.5454.11
#> "0211" "041" "062" "042" "041" "0541"
#> TCGA.B0.4691.11 TCGA.CZ.5452.01 TCGA.EU.5904.01 TCGA.BP.5201.01 TCGA.CJ.5677.01 TCGA.BP.5170.11
#> "012" "02131" "062" "022" "023" "0541"
#> TCGA.B0.4710.11 TCGA.AK.3425.01 TCGA.B0.4841.11 TCGA.B0.4849.01 TCGA.BP.5182.01 TCGA.B0.5711.11
#> "051" "02131" "014" "042" "063" "052"
#> TCGA.BP.5180.01 TCGA.BP.5176.01 TCGA.CZ.5984.01 TCGA.CZ.5460.11 TCGA.BP.5190.01 TCGA.BP.4795.11
#> "0212" "041" "0212" "012" "022" "011"
#> TCGA.B0.4813.11 TCGA.B0.4713.01 TCGA.B0.4841.01 TCGA.B8.5546.01 TCGA.CW.5591.01 TCGA.B0.4698.11
#> "0542" "023" "022" "072" "043" "014"
#> TCGA.B0.5713.11 TCGA.B0.5108.11 TCGA.B0.5083.01 TCGA.B0.5699.01 TCGA.CZ.5453.11 TCGA.BP.5202.01
#> "011" "012" "013" "022" "051" "022"
#> TCGA.BP.5173.11 TCGA.CW.5581.01 TCGA.B0.4848.11 TCGA.B0.4814.01 TCGA.BP.5178.11 TCGA.CJ.4907.01
#> "013" "042" "014" "022" "014" "042"
#> TCGA.A3.3387.01 TCGA.B0.4821.01 TCGA.B0.5712.01 TCGA.B0.5695.01 TCGA.BP.5184.11 TCGA.B2.A4SR.01
#> "042" "023" "023" "062" "012" "042"
#> TCGA.BP.5191.11 TCGA.CJ.4920.01 TCGA.BP.4801.01 TCGA.DV.A4W0.01 TCGA.BP.5177.11 TCGA.B0.4847.11
#> "014" "023" "042" "022" "011" "052"
#> TCGA.B0.5100.01 TCGA.CJ.4903.01 TCGA.CJ.4912.01 TCGA.B0.5107.11 TCGA.AK.3453.01 TCGA.B0.5691.01
#> "043" "022" "0212" "011" "013" "062"
#> TCGA.BP.5195.11 TCGA.B0.5400.01 TCGA.A3.3376.11 TCGA.B0.4845.01 TCGA.B0.4699.01 TCGA.B0.4818.01
#> "0541" "041" "071" "022" "071" "041"
#> TCGA.BP.5174.11 TCGA.CJ.4901.11 TCGA.B8.A54D.01 TCGA.BP.4770.11 TCGA.CW.6093.01 TCGA.BP.5010.11
#> "011" "012" "022" "011" "061" "0541"
#> TCGA.AK.3431.01 TCGA.BP.4770.01 TCGA.BP.5189.01 TCGA.B0.4703.11 TCGA.B8.5163.01 TCGA.CJ.5683.01
#> "041" "041" "043" "014" "041" "042"
#> TCGA.CZ.4856.11 TCGA.BP.4760.01 TCGA.B0.5692.01 TCGA.B0.5106.01 TCGA.B0.4843.01 TCGA.CZ.4866.11
#> "051" "03" "023" "0212" "043" "051"
#> TCGA.B0.5104.11 TCGA.B0.4827.01 TCGA.CJ.4902.11 TCGA.B8.A54G.01 TCGA.B0.5703.01 TCGA.CJ.5672.01
#> "011" "023" "0541" "042" "042" "042"
#> TCGA.B0.5098.11 TCGA.B0.5113.11 TCGA.CJ.4882.11 TCGA.CZ.5465.11 TCGA.B0.5102.01 TCGA.CW.5585.01
#> "013" "011" "012" "051" "041" "042"
#> TCGA.B0.4824.01 TCGA.B0.5115.01 TCGA.B0.4706.01 TCGA.B0.5117.11 TCGA.CZ.4859.11 TCGA.AK.3450.01
#> "041" "022" "022" "012" "0543" "041"
#> TCGA.B8.A54I.01 TCGA.CZ.5463.01 TCGA.DV.5568.01 TCGA.CZ.5459.11 TCGA.CJ.4918.11 TCGA.DV.5565.01
#> "0212" "022" "043" "014" "014" "042"
#> TCGA.B0.5119.01 TCGA.B0.4811.01 TCGA.A3.3367.11 TCGA.CJ.4916.01 TCGA.B0.5693.01 TCGA.CZ.4863.11
#> "062" "042" "014" "041" "041" "051"
#> TCGA.G6.A5PC.01 TCGA.B8.5550.01 TCGA.DV.A4W0.05 TCGA.B0.4696.01 TCGA.BP.5187.01 TCGA.CZ.5466.11
#> "023" "043" "03" "0212" "043" "014"
#> TCGA.CW.6097.01 TCGA.CJ.4905.11 TCGA.CZ.5989.01 TCGA.BP.5194.01 TCGA.B0.4707.11 TCGA.CZ.5467.01
#> "043" "052" "042" "042" "014" "041"
#> TCGA.BP.5185.11 TCGA.BP.5183.11 TCGA.BP.5192.01 TCGA.CZ.5462.11 TCGA.BP.4177.01 TCGA.CZ.5469.01
#> "012" "012" "061" "051" "03" "0211"
#> TCGA.B2.5641.01 TCGA.BP.5196.11 TCGA.CZ.5460.01 TCGA.B0.4712.01 TCGA.B8.A54K.01 TCGA.B0.5707.01
#> "0212" "012" "022" "0211" "03" "062"
#> TCGA.BP.5186.11 TCGA.EU.5906.01 TCGA.CZ.5461.11 TCGA.CW.5590.01 TCGA.B0.5698.01 TCGA.CW.5580.01
#> "011" "061" "0541" "022" "022" "023"
#> TCGA.CZ.5454.01 TCGA.B0.4815.01 TCGA.B0.5710.11 TCGA.CJ.4908.11 TCGA.BP.5201.11 TCGA.B0.5694.01
#> "022" "0211" "012" "0541" "012" "022"
#> TCGA.BP.5170.01 TCGA.DV.5575.01 TCGA.CJ.5686.01 TCGA.A3.3357.01 TCGA.A3.3373.01 TCGA.B0.5690.01
#> "042" "062" "041" "022" "041" "062"
#> TCGA.B8.4622.01 TCGA.AK.3433.01 TCGA.B0.5110.01 TCGA.BP.5180.11 TCGA.CJ.4913.01 TCGA.CJ.4908.01
#> "022" "053" "062" "012" "023" "042"
#> TCGA.BP.4795.01 TCGA.CJ.4897.11 TCGA.B2.5636.01 TCGA.CJ.4923.11 TCGA.B0.4819.01 TCGA.B2.5633.01
#> "03" "011" "03" "014" "041" "043"
#> TCGA.CJ.6033.01 TCGA.BP.5181.11 TCGA.B0.4698.01 TCGA.B0.5083.11 TCGA.CZ.4864.11 TCGA.B0.4688.01
#> "023" "011" "02132" "012" "014" "02132"
#> TCGA.BP.5168.01 TCGA.BP.5198.11 TCGA.B8.5162.01 TCGA.B0.5096.01 TCGA.BP.5178.01 TCGA.B0.5099.11
#> "042" "014" "043" "023" "0211" "011"
#> TCGA.B0.4842.01 TCGA.BP.5169.11 TCGA.B0.5109.11 TCGA.CJ.4920.11 TCGA.B0.5080.11 TCGA.B0.5700.01
#> "041" "014" "071" "0542" "012" "061"
#> TCGA.B0.4847.01 TCGA.B0.5702.01 TCGA.CJ.4905.01 TCGA.B2.5635.01 TCGA.B0.5107.01 TCGA.CW.5584.01
#> "022" "071" "041" "042" "023" "022"
#> TCGA.B4.5838.01 TCGA.BP.5199.01 TCGA.A3.3376.01 TCGA.B0.4845.11 TCGA.B0.4699.11 TCGA.BP.5174.01
#> "042" "022" "061" "0542" "014" "062"
#> TCGA.CZ.5986.01 TCGA.CJ.4901.01 TCGA.AK.3461.01 TCGA.AK.3460.01 TCGA.AK.3454.01 TCGA.CZ.4859.01
#> "061" "02131" "042" "042" "061" "062"
#> TCGA.B0.5812.01 TCGA.B0.5116.11 TCGA.B8.A54F.01 TCGA.CW.6090.01 TCGA.CZ.5458.11 TCGA.B0.5106.11
#> "042" "071" "041" "022" "051" "012"
#> TCGA.CZ.4866.01 TCGA.B0.4828.01 TCGA.AK.3440.01 TCGA.MM.A563.01 TCGA.B0.4697.01 TCGA.AK.3458.01
#> "023" "022" "053" "022" "041" "022"
#> TCGA.CJ.5676.01 TCGA.B0.5402.11 TCGA.CJ.5681.01 TCGA.A3.3370.11 TCGA.A3.A6NL.01 TCGA.B0.4693.01
#> "02133" "014" "073" "052" "062" "023"
#> TCGA.A3.3358.01 TCGA.B0.4710.01 TCGA.CZ.4853.11 TCGA.B4.5835.01 TCGA.CJ.4882.01 TCGA.CZ.5465.01
#> "041" "023" "0541" "062" "043" "023"
#> TCGA.B0.5102.11 TCGA.B0.4824.11 TCGA.CJ.5675.01 TCGA.B0.4700.01 TCGA.B0.5092.01 TCGA.B0.5115.11
#> "011" "011" "022" "043" "041" "012"
#> TCGA.B0.4945.11 TCGA.B8.5158.01 TCGA.CJ.6030.01 TCGA.B8.A54E.01 TCGA.CJ.6032.01 TCGA.B0.4852.11
#> "011" "02131" "02131" "072" "041" "011"
#> TCGA.B0.4817.01 TCGA.B8.5159.01 TCGA.A3.A8OW.01 TCGA.B0.4822.01 TCGA.B0.5696.01 TCGA.B0.5706.01
#> "043" "023" "061" "043" "042" "0212"
#> TCGA.CJ.4918.01 TCGA.B0.5119.11 TCGA.BP.5200.11 TCGA.B0.4811.11 TCGA.A3.3367.01 TCGA.B0.5097.01
#> "043" "051" "012" "014" "022" "041"
#> TCGA.6D.AA2E.01 TCGA.DV.A4VX.01 TCGA.B0.4816.11 TCGA.A3.3385.11 TCGA.DV.5569.01 TCGA.EU.5907.01
#> "072" "022" "0541" "011" "062" "022"
#> TCGA.CZ.5455.01 TCGA.B8.5545.01 TCGA.DV.5567.01 TCGA.CZ.5451.01 TCGA.CJ.4869.01 TCGA.CJ.5678.01
#> "042" "061" "03" "042" "043" "022"
#> TCGA.B8.4153.01 TCGA.B0.5121.11 TCGA.B8.4146.01 TCGA.BP.5183.01 TCGA.B0.5399.01 TCGA.B0.4810.11
#> "022" "012" "041" "022" "042" "052"
#> TCGA.AK.3445.01 TCGA.B4.5378.01 TCGA.BP.5196.01 TCGA.CZ.4865.11 TCGA.B0.5709.01 TCGA.B0.4712.11
#> "0211" "03" "02131" "051" "062" "051"
#> TCGA.B0.4714.01 TCGA.B8.5549.01 TCGA.CZ.5461.01 TCGA.CZ.5457.01 TCGA.A3.A8CQ.01 TCGA.DV.5573.01
#> "022" "022" "0211" "063" "062" "061"
#> TCGA.B0.4815.11 TCGA.B0.5710.01 TCGA.B8.5165.01 TCGA.B0.4718.01 TCGA.B2.5639.01 TCGA.CW.5583.01
#> "014" "022" "061" "022" "043" "062"
#> TCGA.GK.A6C7.01 TCGA.A3.3357.11 TCGA.B8.5552.01 TCGA.B0.5120.01 TCGA.A3.3373.11 TCGA.BP.5185.01
#> "062" "012" "062" "041" "0543" "042"
#> TCGA.B0.4846.01 TCGA.CJ.4904.01 TCGA.CJ.4913.11 TCGA.BP.4993.11 TCGA.B0.4823.11 TCGA.CJ.4897.01
#> "041" "062" "011" "012" "013" "041"
#> TCGA.BP.4993.01 TCGA.B4.5843.01 TCGA.DV.5576.01 TCGA.CJ.4923.01 TCGA.B0.4819.11 TCGA.BP.5175.01
#> "061" "061" "03" "043" "011" "0212"
#> TCGA.CZ.5987.01 TCGA.CZ.4864.01 TCGA.B0.4688.11 TCGA.BP.5168.11 TCGA.BP.5198.01 TCGA.B8.A7U6.01
#> "02133" "061" "0542" "014" "0211" "041"
#> TCGA.B0.5094.01 TCGA.T7.A92I.01 TCGA.B0.5096.11 TCGA.B0.5400.11 TCGA.B0.4694.11 TCGA.B0.5099.01
#> "0211" "072" "011" "011" "052" "041"
#> TCGA.CZ.5468.01 TCGA.B0.4842.11 TCGA.CZ.5988.01 TCGA.BP.5169.01 TCGA.B0.5109.01 TCGA.B4.5834.01
#> "02132" "011" "042" "0211" "043" "061"
#> TCGA.B0.5095.11 TCGA.B0.5080.01 TCGA.CJ.5680.01 TCGA.CZ.5470.01 TCGA.CZ.4865.01 TCGA.A3.A8OX.01
#> "013" "043" "023" "023" "041" "072"
#> TCGA.B0.4690.11 TCGA.CJ.5684.01 TCGA.B0.4844.01 TCGA.CZ.5464.01 TCGA.B0.4701.01 TCGA.B0.5701.01
#> "013" "042" "02133" "0212" "041" "0212"
#> TCGA.BP.5199.11 TCGA.CJ.5671.01 TCGA.A3.A8OV.01 TCGA.CZ.5456.11 TCGA.B0.5116.01 TCGA.CZ.5458.01
#> "012" "02131" "061" "051" "022" "042"
#> TCGA.CZ.5982.01 TCGA.B0.4828.11 TCGA.CJ.5679.01 TCGA.CJ.5682.01 TCGA.B0.5697.01 TCGA.B0.4697.11
#> "041" "0542" "0211" "022" "042" "051"
#> TCGA.BP.4782.11 TCGA.G6.A8L8.01 TCGA.A3.A6NJ.01 TCGA.A3.3370.01 TCGA.B0.4691.01 TCGA.CZ.5452.11
#> "011" "023" "062" "062" "0211" "051"
#> TCGA.B0.4693.11 TCGA.B0.4945.01 TCGA.CZ.4853.01 TCGA.B0.5092.11 TCGA.B0.5402.01 TCGA.B0.4849.11
#> "011" "062" "022" "011" "022" "012"
#> TCGA.A3.A6NN.01 TCGA.B0.4852.01 TCGA.B0.4817.11 TCGA.BP.5176.11 TCGA.CW.5589.01 TCGA.CJ.5689.01
#> "042" "041" "014" "011" "061" "042"
#> TCGA.B0.4822.11 TCGA.BP.5190.11 TCGA.B0.4813.01 TCGA.BP.5200.01 TCGA.G6.A8L7.01 TCGA.B2.4101.01
#> "052" "012" "022" "042" "023" "043"
#> TCGA.B0.4713.11 TCGA.B0.4816.01 TCGA.A3.3385.01 TCGA.B2.3924.01 TCGA.CZ.5455.11 TCGA.B0.5713.01
#> "011" "043" "062" "042" "051" "041"
#> TCGA.B0.5108.01 TCGA.B0.5711.01 TCGA.CZ.5453.01 TCGA.BP.5202.11 TCGA.BP.5173.01 TCGA.CZ.5451.11
#> "043" "042" "061" "071" "061" "012"
#> TCGA.B8.A8YJ.01 TCGA.B0.4848.01 TCGA.DV.A4VZ.01 TCGA.B0.4814.11 TCGA.CJ.4869.11 TCGA.CJ.4907.11
#> "062" "02131" "03" "012" "012" "012"
#> TCGA.B8.5553.01 TCGA.MW.A4EC.01 TCGA.B0.5712.11 TCGA.EU.5905.01 TCGA.CZ.5985.01 TCGA.CZ.4856.01
#> "041" "041" "011" "041" "02133" "041"
#> TCGA.BP.5184.01 TCGA.B0.5121.01 TCGA.BP.5191.01 TCGA.BP.4801.11 TCGA.BP.5177.01 TCGA.B0.5110.11
#> "042" "022" "0212" "012" "062" "011"
#> TCGA.B0.4810.01 TCGA.CJ.4903.11 TCGA.CJ.4912.11 TCGA.B8.4621.01 TCGA.B4.5832.01 TCGA.CW.6088.01
#> "022" "012" "0542" "063" "043" "061"
#> TCGA.AK.3428.01 TCGA.B8.5164.01 TCGA.BP.5195.01 TCGA.CJ.6027.01 TCGA.3Z.A93Z.01 TCGA.B0.4714.11
#> "022" "042" "043" "0211" "061" "014"
#> TCGA.B0.4818.11 TCGA.CZ.5457.11 TCGA.BP.5010.01 TCGA.BP.5189.11 TCGA.B0.4703.01 TCGA.B0.4718.11
#> "011" "051" "043" "012" "043" "052"
#> TCGA.B0.5097.11 TCGA.BP.4760.11 TCGA.B0.5120.11 TCGA.B0.4843.11 TCGA.B0.5104.01 TCGA.CW.5587.01
#> "011" "014" "011" "012" "041" "041"
get_classes(res_rh, merge_node = merge_node_param(min_n_signatures = 3674))
#> TCGA.CZ.4863.01 TCGA.CJ.4904.11 TCGA.B0.4827.11 TCGA.CJ.4902.01 TCGA.B0.4823.01 TCGA.CW.6087.01
#> "041" "011" "054" "043" "061" "043"
#> TCGA.B0.5098.01 TCGA.B0.5113.01 TCGA.DV.5566.01 TCGA.BP.5175.11 TCGA.BP.5181.01 TCGA.B0.4706.11
#> "073" "023" "041" "012" "062" "012"
#> TCGA.B0.5117.01 TCGA.MM.A564.01 TCGA.B0.4821.11 TCGA.CZ.5463.11 TCGA.BP.5182.11 TCGA.DV.5574.01
#> "013" "02133" "072" "051" "012" "061"
#> TCGA.B0.5094.11 TCGA.MM.A84U.01 TCGA.B0.5100.11 TCGA.B4.5844.01 TCGA.CZ.5459.01 TCGA.B0.4694.01
#> "014" "041" "014" "041" "042" "043"
#> TCGA.CZ.5468.11 TCGA.CJ.4916.11 TCGA.B4.5836.01 TCGA.B0.5095.01 TCGA.B0.4846.11 TCGA.AK.3434.01
#> "051" "011" "041" "043" "011" "022"
#> TCGA.B4.5377.01 TCGA.B0.4696.11 TCGA.BP.5187.11 TCGA.B0.4690.01 TCGA.CZ.5466.01 TCGA.B0.4844.11
#> "062" "014" "014" "043" "043" "052"
#> TCGA.CZ.5464.11 TCGA.B0.4701.11 TCGA.BP.5194.11 TCGA.B0.4707.01 TCGA.CZ.5467.11 TCGA.B0.5705.01
#> "012" "011" "012" "02131" "051" "062"
#> TCGA.CW.5588.01 TCGA.CJ.6031.01 TCGA.B8.A54J.01 TCGA.BP.5192.11 TCGA.CZ.5462.01 TCGA.B8.A54H.01
#> "041" "043" "042" "052" "043" "041"
#> TCGA.CZ.5470.11 TCGA.BP.4177.11 TCGA.CZ.5469.11 TCGA.CJ.6028.01 TCGA.G6.A8L6.01 TCGA.B8.5551.01
#> "051" "052" "051" "043" "042" "041"
#> TCGA.CZ.5456.01 TCGA.A3.A8OU.01 TCGA.BP.5186.01 TCGA.A3.A6NI.01 TCGA.BP.4782.01 TCGA.CZ.5454.11
#> "0211" "041" "062" "042" "041" "054"
#> TCGA.B0.4691.11 TCGA.CZ.5452.01 TCGA.EU.5904.01 TCGA.BP.5201.01 TCGA.CJ.5677.01 TCGA.BP.5170.11
#> "012" "02131" "062" "022" "023" "054"
#> TCGA.B0.4710.11 TCGA.AK.3425.01 TCGA.B0.4841.11 TCGA.B0.4849.01 TCGA.BP.5182.01 TCGA.B0.5711.11
#> "051" "02131" "014" "042" "063" "052"
#> TCGA.BP.5180.01 TCGA.BP.5176.01 TCGA.CZ.5984.01 TCGA.CZ.5460.11 TCGA.BP.5190.01 TCGA.BP.4795.11
#> "0212" "041" "0212" "012" "022" "011"
#> TCGA.B0.4813.11 TCGA.B0.4713.01 TCGA.B0.4841.01 TCGA.B8.5546.01 TCGA.CW.5591.01 TCGA.B0.4698.11
#> "054" "023" "022" "072" "043" "014"
#> TCGA.B0.5713.11 TCGA.B0.5108.11 TCGA.B0.5083.01 TCGA.B0.5699.01 TCGA.CZ.5453.11 TCGA.BP.5202.01
#> "011" "012" "013" "022" "051" "022"
#> TCGA.BP.5173.11 TCGA.CW.5581.01 TCGA.B0.4848.11 TCGA.B0.4814.01 TCGA.BP.5178.11 TCGA.CJ.4907.01
#> "013" "042" "014" "022" "014" "042"
#> TCGA.A3.3387.01 TCGA.B0.4821.01 TCGA.B0.5712.01 TCGA.B0.5695.01 TCGA.BP.5184.11 TCGA.B2.A4SR.01
#> "042" "023" "023" "062" "012" "042"
#> TCGA.BP.5191.11 TCGA.CJ.4920.01 TCGA.BP.4801.01 TCGA.DV.A4W0.01 TCGA.BP.5177.11 TCGA.B0.4847.11
#> "014" "023" "042" "022" "011" "052"
#> TCGA.B0.5100.01 TCGA.CJ.4903.01 TCGA.CJ.4912.01 TCGA.B0.5107.11 TCGA.AK.3453.01 TCGA.B0.5691.01
#> "043" "022" "0212" "011" "013" "062"
#> TCGA.BP.5195.11 TCGA.B0.5400.01 TCGA.A3.3376.11 TCGA.B0.4845.01 TCGA.B0.4699.01 TCGA.B0.4818.01
#> "054" "041" "071" "022" "071" "041"
#> TCGA.BP.5174.11 TCGA.CJ.4901.11 TCGA.B8.A54D.01 TCGA.BP.4770.11 TCGA.CW.6093.01 TCGA.BP.5010.11
#> "011" "012" "022" "011" "061" "054"
#> TCGA.AK.3431.01 TCGA.BP.4770.01 TCGA.BP.5189.01 TCGA.B0.4703.11 TCGA.B8.5163.01 TCGA.CJ.5683.01
#> "041" "041" "043" "014" "041" "042"
#> TCGA.CZ.4856.11 TCGA.BP.4760.01 TCGA.B0.5692.01 TCGA.B0.5106.01 TCGA.B0.4843.01 TCGA.CZ.4866.11
#> "051" "03" "023" "0212" "043" "051"
#> TCGA.B0.5104.11 TCGA.B0.4827.01 TCGA.CJ.4902.11 TCGA.B8.A54G.01 TCGA.B0.5703.01 TCGA.CJ.5672.01
#> "011" "023" "054" "042" "042" "042"
#> TCGA.B0.5098.11 TCGA.B0.5113.11 TCGA.CJ.4882.11 TCGA.CZ.5465.11 TCGA.B0.5102.01 TCGA.CW.5585.01
#> "013" "011" "012" "051" "041" "042"
#> TCGA.B0.4824.01 TCGA.B0.5115.01 TCGA.B0.4706.01 TCGA.B0.5117.11 TCGA.CZ.4859.11 TCGA.AK.3450.01
#> "041" "022" "022" "012" "054" "041"
#> TCGA.B8.A54I.01 TCGA.CZ.5463.01 TCGA.DV.5568.01 TCGA.CZ.5459.11 TCGA.CJ.4918.11 TCGA.DV.5565.01
#> "0212" "022" "043" "014" "014" "042"
#> TCGA.B0.5119.01 TCGA.B0.4811.01 TCGA.A3.3367.11 TCGA.CJ.4916.01 TCGA.B0.5693.01 TCGA.CZ.4863.11
#> "062" "042" "014" "041" "041" "051"
#> TCGA.G6.A5PC.01 TCGA.B8.5550.01 TCGA.DV.A4W0.05 TCGA.B0.4696.01 TCGA.BP.5187.01 TCGA.CZ.5466.11
#> "023" "043" "03" "0212" "043" "014"
#> TCGA.CW.6097.01 TCGA.CJ.4905.11 TCGA.CZ.5989.01 TCGA.BP.5194.01 TCGA.B0.4707.11 TCGA.CZ.5467.01
#> "043" "052" "042" "042" "014" "041"
#> TCGA.BP.5185.11 TCGA.BP.5183.11 TCGA.BP.5192.01 TCGA.CZ.5462.11 TCGA.BP.4177.01 TCGA.CZ.5469.01
#> "012" "012" "061" "051" "03" "0211"
#> TCGA.B2.5641.01 TCGA.BP.5196.11 TCGA.CZ.5460.01 TCGA.B0.4712.01 TCGA.B8.A54K.01 TCGA.B0.5707.01
#> "0212" "012" "022" "0211" "03" "062"
#> TCGA.BP.5186.11 TCGA.EU.5906.01 TCGA.CZ.5461.11 TCGA.CW.5590.01 TCGA.B0.5698.01 TCGA.CW.5580.01
#> "011" "061" "054" "022" "022" "023"
#> TCGA.CZ.5454.01 TCGA.B0.4815.01 TCGA.B0.5710.11 TCGA.CJ.4908.11 TCGA.BP.5201.11 TCGA.B0.5694.01
#> "022" "0211" "012" "054" "012" "022"
#> TCGA.BP.5170.01 TCGA.DV.5575.01 TCGA.CJ.5686.01 TCGA.A3.3357.01 TCGA.A3.3373.01 TCGA.B0.5690.01
#> "042" "062" "041" "022" "041" "062"
#> TCGA.B8.4622.01 TCGA.AK.3433.01 TCGA.B0.5110.01 TCGA.BP.5180.11 TCGA.CJ.4913.01 TCGA.CJ.4908.01
#> "022" "053" "062" "012" "023" "042"
#> TCGA.BP.4795.01 TCGA.CJ.4897.11 TCGA.B2.5636.01 TCGA.CJ.4923.11 TCGA.B0.4819.01 TCGA.B2.5633.01
#> "03" "011" "03" "014" "041" "043"
#> TCGA.CJ.6033.01 TCGA.BP.5181.11 TCGA.B0.4698.01 TCGA.B0.5083.11 TCGA.CZ.4864.11 TCGA.B0.4688.01
#> "023" "011" "02132" "012" "014" "02132"
#> TCGA.BP.5168.01 TCGA.BP.5198.11 TCGA.B8.5162.01 TCGA.B0.5096.01 TCGA.BP.5178.01 TCGA.B0.5099.11
#> "042" "014" "043" "023" "0211" "011"
#> TCGA.B0.4842.01 TCGA.BP.5169.11 TCGA.B0.5109.11 TCGA.CJ.4920.11 TCGA.B0.5080.11 TCGA.B0.5700.01
#> "041" "014" "071" "054" "012" "061"
#> TCGA.B0.4847.01 TCGA.B0.5702.01 TCGA.CJ.4905.01 TCGA.B2.5635.01 TCGA.B0.5107.01 TCGA.CW.5584.01
#> "022" "071" "041" "042" "023" "022"
#> TCGA.B4.5838.01 TCGA.BP.5199.01 TCGA.A3.3376.01 TCGA.B0.4845.11 TCGA.B0.4699.11 TCGA.BP.5174.01
#> "042" "022" "061" "054" "014" "062"
#> TCGA.CZ.5986.01 TCGA.CJ.4901.01 TCGA.AK.3461.01 TCGA.AK.3460.01 TCGA.AK.3454.01 TCGA.CZ.4859.01
#> "061" "02131" "042" "042" "061" "062"
#> TCGA.B0.5812.01 TCGA.B0.5116.11 TCGA.B8.A54F.01 TCGA.CW.6090.01 TCGA.CZ.5458.11 TCGA.B0.5106.11
#> "042" "071" "041" "022" "051" "012"
#> TCGA.CZ.4866.01 TCGA.B0.4828.01 TCGA.AK.3440.01 TCGA.MM.A563.01 TCGA.B0.4697.01 TCGA.AK.3458.01
#> "023" "022" "053" "022" "041" "022"
#> TCGA.CJ.5676.01 TCGA.B0.5402.11 TCGA.CJ.5681.01 TCGA.A3.3370.11 TCGA.A3.A6NL.01 TCGA.B0.4693.01
#> "02133" "014" "073" "052" "062" "023"
#> TCGA.A3.3358.01 TCGA.B0.4710.01 TCGA.CZ.4853.11 TCGA.B4.5835.01 TCGA.CJ.4882.01 TCGA.CZ.5465.01
#> "041" "023" "054" "062" "043" "023"
#> TCGA.B0.5102.11 TCGA.B0.4824.11 TCGA.CJ.5675.01 TCGA.B0.4700.01 TCGA.B0.5092.01 TCGA.B0.5115.11
#> "011" "011" "022" "043" "041" "012"
#> TCGA.B0.4945.11 TCGA.B8.5158.01 TCGA.CJ.6030.01 TCGA.B8.A54E.01 TCGA.CJ.6032.01 TCGA.B0.4852.11
#> "011" "02131" "02131" "072" "041" "011"
#> TCGA.B0.4817.01 TCGA.B8.5159.01 TCGA.A3.A8OW.01 TCGA.B0.4822.01 TCGA.B0.5696.01 TCGA.B0.5706.01
#> "043" "023" "061" "043" "042" "0212"
#> TCGA.CJ.4918.01 TCGA.B0.5119.11 TCGA.BP.5200.11 TCGA.B0.4811.11 TCGA.A3.3367.01 TCGA.B0.5097.01
#> "043" "051" "012" "014" "022" "041"
#> TCGA.6D.AA2E.01 TCGA.DV.A4VX.01 TCGA.B0.4816.11 TCGA.A3.3385.11 TCGA.DV.5569.01 TCGA.EU.5907.01
#> "072" "022" "054" "011" "062" "022"
#> TCGA.CZ.5455.01 TCGA.B8.5545.01 TCGA.DV.5567.01 TCGA.CZ.5451.01 TCGA.CJ.4869.01 TCGA.CJ.5678.01
#> "042" "061" "03" "042" "043" "022"
#> TCGA.B8.4153.01 TCGA.B0.5121.11 TCGA.B8.4146.01 TCGA.BP.5183.01 TCGA.B0.5399.01 TCGA.B0.4810.11
#> "022" "012" "041" "022" "042" "052"
#> TCGA.AK.3445.01 TCGA.B4.5378.01 TCGA.BP.5196.01 TCGA.CZ.4865.11 TCGA.B0.5709.01 TCGA.B0.4712.11
#> "0211" "03" "02131" "051" "062" "051"
#> TCGA.B0.4714.01 TCGA.B8.5549.01 TCGA.CZ.5461.01 TCGA.CZ.5457.01 TCGA.A3.A8CQ.01 TCGA.DV.5573.01
#> "022" "022" "0211" "063" "062" "061"
#> TCGA.B0.4815.11 TCGA.B0.5710.01 TCGA.B8.5165.01 TCGA.B0.4718.01 TCGA.B2.5639.01 TCGA.CW.5583.01
#> "014" "022" "061" "022" "043" "062"
#> TCGA.GK.A6C7.01 TCGA.A3.3357.11 TCGA.B8.5552.01 TCGA.B0.5120.01 TCGA.A3.3373.11 TCGA.BP.5185.01
#> "062" "012" "062" "041" "054" "042"
#> TCGA.B0.4846.01 TCGA.CJ.4904.01 TCGA.CJ.4913.11 TCGA.BP.4993.11 TCGA.B0.4823.11 TCGA.CJ.4897.01
#> "041" "062" "011" "012" "013" "041"
#> TCGA.BP.4993.01 TCGA.B4.5843.01 TCGA.DV.5576.01 TCGA.CJ.4923.01 TCGA.B0.4819.11 TCGA.BP.5175.01
#> "061" "061" "03" "043" "011" "0212"
#> TCGA.CZ.5987.01 TCGA.CZ.4864.01 TCGA.B0.4688.11 TCGA.BP.5168.11 TCGA.BP.5198.01 TCGA.B8.A7U6.01
#> "02133" "061" "054" "014" "0211" "041"
#> TCGA.B0.5094.01 TCGA.T7.A92I.01 TCGA.B0.5096.11 TCGA.B0.5400.11 TCGA.B0.4694.11 TCGA.B0.5099.01
#> "0211" "072" "011" "011" "052" "041"
#> TCGA.CZ.5468.01 TCGA.B0.4842.11 TCGA.CZ.5988.01 TCGA.BP.5169.01 TCGA.B0.5109.01 TCGA.B4.5834.01
#> "02132" "011" "042" "0211" "043" "061"
#> TCGA.B0.5095.11 TCGA.B0.5080.01 TCGA.CJ.5680.01 TCGA.CZ.5470.01 TCGA.CZ.4865.01 TCGA.A3.A8OX.01
#> "013" "043" "023" "023" "041" "072"
#> TCGA.B0.4690.11 TCGA.CJ.5684.01 TCGA.B0.4844.01 TCGA.CZ.5464.01 TCGA.B0.4701.01 TCGA.B0.5701.01
#> "013" "042" "02133" "0212" "041" "0212"
#> TCGA.BP.5199.11 TCGA.CJ.5671.01 TCGA.A3.A8OV.01 TCGA.CZ.5456.11 TCGA.B0.5116.01 TCGA.CZ.5458.01
#> "012" "02131" "061" "051" "022" "042"
#> TCGA.CZ.5982.01 TCGA.B0.4828.11 TCGA.CJ.5679.01 TCGA.CJ.5682.01 TCGA.B0.5697.01 TCGA.B0.4697.11
#> "041" "054" "0211" "022" "042" "051"
#> TCGA.BP.4782.11 TCGA.G6.A8L8.01 TCGA.A3.A6NJ.01 TCGA.A3.3370.01 TCGA.B0.4691.01 TCGA.CZ.5452.11
#> "011" "023" "062" "062" "0211" "051"
#> TCGA.B0.4693.11 TCGA.B0.4945.01 TCGA.CZ.4853.01 TCGA.B0.5092.11 TCGA.B0.5402.01 TCGA.B0.4849.11
#> "011" "062" "022" "011" "022" "012"
#> TCGA.A3.A6NN.01 TCGA.B0.4852.01 TCGA.B0.4817.11 TCGA.BP.5176.11 TCGA.CW.5589.01 TCGA.CJ.5689.01
#> "042" "041" "014" "011" "061" "042"
#> TCGA.B0.4822.11 TCGA.BP.5190.11 TCGA.B0.4813.01 TCGA.BP.5200.01 TCGA.G6.A8L7.01 TCGA.B2.4101.01
#> "052" "012" "022" "042" "023" "043"
#> TCGA.B0.4713.11 TCGA.B0.4816.01 TCGA.A3.3385.01 TCGA.B2.3924.01 TCGA.CZ.5455.11 TCGA.B0.5713.01
#> "011" "043" "062" "042" "051" "041"
#> TCGA.B0.5108.01 TCGA.B0.5711.01 TCGA.CZ.5453.01 TCGA.BP.5202.11 TCGA.BP.5173.01 TCGA.CZ.5451.11
#> "043" "042" "061" "071" "061" "012"
#> TCGA.B8.A8YJ.01 TCGA.B0.4848.01 TCGA.DV.A4VZ.01 TCGA.B0.4814.11 TCGA.CJ.4869.11 TCGA.CJ.4907.11
#> "062" "02131" "03" "012" "012" "012"
#> TCGA.B8.5553.01 TCGA.MW.A4EC.01 TCGA.B0.5712.11 TCGA.EU.5905.01 TCGA.CZ.5985.01 TCGA.CZ.4856.01
#> "041" "041" "011" "041" "02133" "041"
#> TCGA.BP.5184.01 TCGA.B0.5121.01 TCGA.BP.5191.01 TCGA.BP.4801.11 TCGA.BP.5177.01 TCGA.B0.5110.11
#> "042" "022" "0212" "012" "062" "011"
#> TCGA.B0.4810.01 TCGA.CJ.4903.11 TCGA.CJ.4912.11 TCGA.B8.4621.01 TCGA.B4.5832.01 TCGA.CW.6088.01
#> "022" "012" "054" "063" "043" "061"
#> TCGA.AK.3428.01 TCGA.B8.5164.01 TCGA.BP.5195.01 TCGA.CJ.6027.01 TCGA.3Z.A93Z.01 TCGA.B0.4714.11
#> "022" "042" "043" "0211" "061" "014"
#> TCGA.B0.4818.11 TCGA.CZ.5457.11 TCGA.BP.5010.01 TCGA.BP.5189.11 TCGA.B0.4703.01 TCGA.B0.4718.11
#> "011" "051" "043" "012" "043" "052"
#> TCGA.B0.5097.11 TCGA.BP.4760.11 TCGA.B0.5120.11 TCGA.B0.4843.11 TCGA.B0.5104.01 TCGA.CW.5587.01
#> "011" "014" "011" "012" "041" "041"
get_classes(res_rh, merge_node = merge_node_param(min_n_signatures = 3886))
#> TCGA.CZ.4863.01 TCGA.CJ.4904.11 TCGA.B0.4827.11 TCGA.CJ.4902.01 TCGA.B0.4823.01 TCGA.CW.6087.01
#> "04" "011" "054" "04" "061" "04"
#> TCGA.B0.5098.01 TCGA.B0.5113.01 TCGA.DV.5566.01 TCGA.BP.5175.11 TCGA.BP.5181.01 TCGA.B0.4706.11
#> "073" "023" "04" "012" "062" "012"
#> TCGA.B0.5117.01 TCGA.MM.A564.01 TCGA.B0.4821.11 TCGA.CZ.5463.11 TCGA.BP.5182.11 TCGA.DV.5574.01
#> "013" "02133" "072" "051" "012" "061"
#> TCGA.B0.5094.11 TCGA.MM.A84U.01 TCGA.B0.5100.11 TCGA.B4.5844.01 TCGA.CZ.5459.01 TCGA.B0.4694.01
#> "014" "04" "014" "04" "04" "04"
#> TCGA.CZ.5468.11 TCGA.CJ.4916.11 TCGA.B4.5836.01 TCGA.B0.5095.01 TCGA.B0.4846.11 TCGA.AK.3434.01
#> "051" "011" "04" "04" "011" "022"
#> TCGA.B4.5377.01 TCGA.B0.4696.11 TCGA.BP.5187.11 TCGA.B0.4690.01 TCGA.CZ.5466.01 TCGA.B0.4844.11
#> "062" "014" "014" "04" "04" "052"
#> TCGA.CZ.5464.11 TCGA.B0.4701.11 TCGA.BP.5194.11 TCGA.B0.4707.01 TCGA.CZ.5467.11 TCGA.B0.5705.01
#> "012" "011" "012" "02131" "051" "062"
#> TCGA.CW.5588.01 TCGA.CJ.6031.01 TCGA.B8.A54J.01 TCGA.BP.5192.11 TCGA.CZ.5462.01 TCGA.B8.A54H.01
#> "04" "04" "04" "052" "04" "04"
#> TCGA.CZ.5470.11 TCGA.BP.4177.11 TCGA.CZ.5469.11 TCGA.CJ.6028.01 TCGA.G6.A8L6.01 TCGA.B8.5551.01
#> "051" "052" "051" "04" "04" "04"
#> TCGA.CZ.5456.01 TCGA.A3.A8OU.01 TCGA.BP.5186.01 TCGA.A3.A6NI.01 TCGA.BP.4782.01 TCGA.CZ.5454.11
#> "0211" "04" "062" "04" "04" "054"
#> TCGA.B0.4691.11 TCGA.CZ.5452.01 TCGA.EU.5904.01 TCGA.BP.5201.01 TCGA.CJ.5677.01 TCGA.BP.5170.11
#> "012" "02131" "062" "022" "023" "054"
#> TCGA.B0.4710.11 TCGA.AK.3425.01 TCGA.B0.4841.11 TCGA.B0.4849.01 TCGA.BP.5182.01 TCGA.B0.5711.11
#> "051" "02131" "014" "04" "063" "052"
#> TCGA.BP.5180.01 TCGA.BP.5176.01 TCGA.CZ.5984.01 TCGA.CZ.5460.11 TCGA.BP.5190.01 TCGA.BP.4795.11
#> "0212" "04" "0212" "012" "022" "011"
#> TCGA.B0.4813.11 TCGA.B0.4713.01 TCGA.B0.4841.01 TCGA.B8.5546.01 TCGA.CW.5591.01 TCGA.B0.4698.11
#> "054" "023" "022" "072" "04" "014"
#> TCGA.B0.5713.11 TCGA.B0.5108.11 TCGA.B0.5083.01 TCGA.B0.5699.01 TCGA.CZ.5453.11 TCGA.BP.5202.01
#> "011" "012" "013" "022" "051" "022"
#> TCGA.BP.5173.11 TCGA.CW.5581.01 TCGA.B0.4848.11 TCGA.B0.4814.01 TCGA.BP.5178.11 TCGA.CJ.4907.01
#> "013" "04" "014" "022" "014" "04"
#> TCGA.A3.3387.01 TCGA.B0.4821.01 TCGA.B0.5712.01 TCGA.B0.5695.01 TCGA.BP.5184.11 TCGA.B2.A4SR.01
#> "04" "023" "023" "062" "012" "04"
#> TCGA.BP.5191.11 TCGA.CJ.4920.01 TCGA.BP.4801.01 TCGA.DV.A4W0.01 TCGA.BP.5177.11 TCGA.B0.4847.11
#> "014" "023" "04" "022" "011" "052"
#> TCGA.B0.5100.01 TCGA.CJ.4903.01 TCGA.CJ.4912.01 TCGA.B0.5107.11 TCGA.AK.3453.01 TCGA.B0.5691.01
#> "04" "022" "0212" "011" "013" "062"
#> TCGA.BP.5195.11 TCGA.B0.5400.01 TCGA.A3.3376.11 TCGA.B0.4845.01 TCGA.B0.4699.01 TCGA.B0.4818.01
#> "054" "04" "071" "022" "071" "04"
#> TCGA.BP.5174.11 TCGA.CJ.4901.11 TCGA.B8.A54D.01 TCGA.BP.4770.11 TCGA.CW.6093.01 TCGA.BP.5010.11
#> "011" "012" "022" "011" "061" "054"
#> TCGA.AK.3431.01 TCGA.BP.4770.01 TCGA.BP.5189.01 TCGA.B0.4703.11 TCGA.B8.5163.01 TCGA.CJ.5683.01
#> "04" "04" "04" "014" "04" "04"
#> TCGA.CZ.4856.11 TCGA.BP.4760.01 TCGA.B0.5692.01 TCGA.B0.5106.01 TCGA.B0.4843.01 TCGA.CZ.4866.11
#> "051" "03" "023" "0212" "04" "051"
#> TCGA.B0.5104.11 TCGA.B0.4827.01 TCGA.CJ.4902.11 TCGA.B8.A54G.01 TCGA.B0.5703.01 TCGA.CJ.5672.01
#> "011" "023" "054" "04" "04" "04"
#> TCGA.B0.5098.11 TCGA.B0.5113.11 TCGA.CJ.4882.11 TCGA.CZ.5465.11 TCGA.B0.5102.01 TCGA.CW.5585.01
#> "013" "011" "012" "051" "04" "04"
#> TCGA.B0.4824.01 TCGA.B0.5115.01 TCGA.B0.4706.01 TCGA.B0.5117.11 TCGA.CZ.4859.11 TCGA.AK.3450.01
#> "04" "022" "022" "012" "054" "04"
#> TCGA.B8.A54I.01 TCGA.CZ.5463.01 TCGA.DV.5568.01 TCGA.CZ.5459.11 TCGA.CJ.4918.11 TCGA.DV.5565.01
#> "0212" "022" "04" "014" "014" "04"
#> TCGA.B0.5119.01 TCGA.B0.4811.01 TCGA.A3.3367.11 TCGA.CJ.4916.01 TCGA.B0.5693.01 TCGA.CZ.4863.11
#> "062" "04" "014" "04" "04" "051"
#> TCGA.G6.A5PC.01 TCGA.B8.5550.01 TCGA.DV.A4W0.05 TCGA.B0.4696.01 TCGA.BP.5187.01 TCGA.CZ.5466.11
#> "023" "04" "03" "0212" "04" "014"
#> TCGA.CW.6097.01 TCGA.CJ.4905.11 TCGA.CZ.5989.01 TCGA.BP.5194.01 TCGA.B0.4707.11 TCGA.CZ.5467.01
#> "04" "052" "04" "04" "014" "04"
#> TCGA.BP.5185.11 TCGA.BP.5183.11 TCGA.BP.5192.01 TCGA.CZ.5462.11 TCGA.BP.4177.01 TCGA.CZ.5469.01
#> "012" "012" "061" "051" "03" "0211"
#> TCGA.B2.5641.01 TCGA.BP.5196.11 TCGA.CZ.5460.01 TCGA.B0.4712.01 TCGA.B8.A54K.01 TCGA.B0.5707.01
#> "0212" "012" "022" "0211" "03" "062"
#> TCGA.BP.5186.11 TCGA.EU.5906.01 TCGA.CZ.5461.11 TCGA.CW.5590.01 TCGA.B0.5698.01 TCGA.CW.5580.01
#> "011" "061" "054" "022" "022" "023"
#> TCGA.CZ.5454.01 TCGA.B0.4815.01 TCGA.B0.5710.11 TCGA.CJ.4908.11 TCGA.BP.5201.11 TCGA.B0.5694.01
#> "022" "0211" "012" "054" "012" "022"
#> TCGA.BP.5170.01 TCGA.DV.5575.01 TCGA.CJ.5686.01 TCGA.A3.3357.01 TCGA.A3.3373.01 TCGA.B0.5690.01
#> "04" "062" "04" "022" "04" "062"
#> TCGA.B8.4622.01 TCGA.AK.3433.01 TCGA.B0.5110.01 TCGA.BP.5180.11 TCGA.CJ.4913.01 TCGA.CJ.4908.01
#> "022" "053" "062" "012" "023" "04"
#> TCGA.BP.4795.01 TCGA.CJ.4897.11 TCGA.B2.5636.01 TCGA.CJ.4923.11 TCGA.B0.4819.01 TCGA.B2.5633.01
#> "03" "011" "03" "014" "04" "04"
#> TCGA.CJ.6033.01 TCGA.BP.5181.11 TCGA.B0.4698.01 TCGA.B0.5083.11 TCGA.CZ.4864.11 TCGA.B0.4688.01
#> "023" "011" "02132" "012" "014" "02132"
#> TCGA.BP.5168.01 TCGA.BP.5198.11 TCGA.B8.5162.01 TCGA.B0.5096.01 TCGA.BP.5178.01 TCGA.B0.5099.11
#> "04" "014" "04" "023" "0211" "011"
#> TCGA.B0.4842.01 TCGA.BP.5169.11 TCGA.B0.5109.11 TCGA.CJ.4920.11 TCGA.B0.5080.11 TCGA.B0.5700.01
#> "04" "014" "071" "054" "012" "061"
#> TCGA.B0.4847.01 TCGA.B0.5702.01 TCGA.CJ.4905.01 TCGA.B2.5635.01 TCGA.B0.5107.01 TCGA.CW.5584.01
#> "022" "071" "04" "04" "023" "022"
#> TCGA.B4.5838.01 TCGA.BP.5199.01 TCGA.A3.3376.01 TCGA.B0.4845.11 TCGA.B0.4699.11 TCGA.BP.5174.01
#> "04" "022" "061" "054" "014" "062"
#> TCGA.CZ.5986.01 TCGA.CJ.4901.01 TCGA.AK.3461.01 TCGA.AK.3460.01 TCGA.AK.3454.01 TCGA.CZ.4859.01
#> "061" "02131" "04" "04" "061" "062"
#> TCGA.B0.5812.01 TCGA.B0.5116.11 TCGA.B8.A54F.01 TCGA.CW.6090.01 TCGA.CZ.5458.11 TCGA.B0.5106.11
#> "04" "071" "04" "022" "051" "012"
#> TCGA.CZ.4866.01 TCGA.B0.4828.01 TCGA.AK.3440.01 TCGA.MM.A563.01 TCGA.B0.4697.01 TCGA.AK.3458.01
#> "023" "022" "053" "022" "04" "022"
#> TCGA.CJ.5676.01 TCGA.B0.5402.11 TCGA.CJ.5681.01 TCGA.A3.3370.11 TCGA.A3.A6NL.01 TCGA.B0.4693.01
#> "02133" "014" "073" "052" "062" "023"
#> TCGA.A3.3358.01 TCGA.B0.4710.01 TCGA.CZ.4853.11 TCGA.B4.5835.01 TCGA.CJ.4882.01 TCGA.CZ.5465.01
#> "04" "023" "054" "062" "04" "023"
#> TCGA.B0.5102.11 TCGA.B0.4824.11 TCGA.CJ.5675.01 TCGA.B0.4700.01 TCGA.B0.5092.01 TCGA.B0.5115.11
#> "011" "011" "022" "04" "04" "012"
#> TCGA.B0.4945.11 TCGA.B8.5158.01 TCGA.CJ.6030.01 TCGA.B8.A54E.01 TCGA.CJ.6032.01 TCGA.B0.4852.11
#> "011" "02131" "02131" "072" "04" "011"
#> TCGA.B0.4817.01 TCGA.B8.5159.01 TCGA.A3.A8OW.01 TCGA.B0.4822.01 TCGA.B0.5696.01 TCGA.B0.5706.01
#> "04" "023" "061" "04" "04" "0212"
#> TCGA.CJ.4918.01 TCGA.B0.5119.11 TCGA.BP.5200.11 TCGA.B0.4811.11 TCGA.A3.3367.01 TCGA.B0.5097.01
#> "04" "051" "012" "014" "022" "04"
#> TCGA.6D.AA2E.01 TCGA.DV.A4VX.01 TCGA.B0.4816.11 TCGA.A3.3385.11 TCGA.DV.5569.01 TCGA.EU.5907.01
#> "072" "022" "054" "011" "062" "022"
#> TCGA.CZ.5455.01 TCGA.B8.5545.01 TCGA.DV.5567.01 TCGA.CZ.5451.01 TCGA.CJ.4869.01 TCGA.CJ.5678.01
#> "04" "061" "03" "04" "04" "022"
#> TCGA.B8.4153.01 TCGA.B0.5121.11 TCGA.B8.4146.01 TCGA.BP.5183.01 TCGA.B0.5399.01 TCGA.B0.4810.11
#> "022" "012" "04" "022" "04" "052"
#> TCGA.AK.3445.01 TCGA.B4.5378.01 TCGA.BP.5196.01 TCGA.CZ.4865.11 TCGA.B0.5709.01 TCGA.B0.4712.11
#> "0211" "03" "02131" "051" "062" "051"
#> TCGA.B0.4714.01 TCGA.B8.5549.01 TCGA.CZ.5461.01 TCGA.CZ.5457.01 TCGA.A3.A8CQ.01 TCGA.DV.5573.01
#> "022" "022" "0211" "063" "062" "061"
#> TCGA.B0.4815.11 TCGA.B0.5710.01 TCGA.B8.5165.01 TCGA.B0.4718.01 TCGA.B2.5639.01 TCGA.CW.5583.01
#> "014" "022" "061" "022" "04" "062"
#> TCGA.GK.A6C7.01 TCGA.A3.3357.11 TCGA.B8.5552.01 TCGA.B0.5120.01 TCGA.A3.3373.11 TCGA.BP.5185.01
#> "062" "012" "062" "04" "054" "04"
#> TCGA.B0.4846.01 TCGA.CJ.4904.01 TCGA.CJ.4913.11 TCGA.BP.4993.11 TCGA.B0.4823.11 TCGA.CJ.4897.01
#> "04" "062" "011" "012" "013" "04"
#> TCGA.BP.4993.01 TCGA.B4.5843.01 TCGA.DV.5576.01 TCGA.CJ.4923.01 TCGA.B0.4819.11 TCGA.BP.5175.01
#> "061" "061" "03" "04" "011" "0212"
#> TCGA.CZ.5987.01 TCGA.CZ.4864.01 TCGA.B0.4688.11 TCGA.BP.5168.11 TCGA.BP.5198.01 TCGA.B8.A7U6.01
#> "02133" "061" "054" "014" "0211" "04"
#> TCGA.B0.5094.01 TCGA.T7.A92I.01 TCGA.B0.5096.11 TCGA.B0.5400.11 TCGA.B0.4694.11 TCGA.B0.5099.01
#> "0211" "072" "011" "011" "052" "04"
#> TCGA.CZ.5468.01 TCGA.B0.4842.11 TCGA.CZ.5988.01 TCGA.BP.5169.01 TCGA.B0.5109.01 TCGA.B4.5834.01
#> "02132" "011" "04" "0211" "04" "061"
#> TCGA.B0.5095.11 TCGA.B0.5080.01 TCGA.CJ.5680.01 TCGA.CZ.5470.01 TCGA.CZ.4865.01 TCGA.A3.A8OX.01
#> "013" "04" "023" "023" "04" "072"
#> TCGA.B0.4690.11 TCGA.CJ.5684.01 TCGA.B0.4844.01 TCGA.CZ.5464.01 TCGA.B0.4701.01 TCGA.B0.5701.01
#> "013" "04" "02133" "0212" "04" "0212"
#> TCGA.BP.5199.11 TCGA.CJ.5671.01 TCGA.A3.A8OV.01 TCGA.CZ.5456.11 TCGA.B0.5116.01 TCGA.CZ.5458.01
#> "012" "02131" "061" "051" "022" "04"
#> TCGA.CZ.5982.01 TCGA.B0.4828.11 TCGA.CJ.5679.01 TCGA.CJ.5682.01 TCGA.B0.5697.01 TCGA.B0.4697.11
#> "04" "054" "0211" "022" "04" "051"
#> TCGA.BP.4782.11 TCGA.G6.A8L8.01 TCGA.A3.A6NJ.01 TCGA.A3.3370.01 TCGA.B0.4691.01 TCGA.CZ.5452.11
#> "011" "023" "062" "062" "0211" "051"
#> TCGA.B0.4693.11 TCGA.B0.4945.01 TCGA.CZ.4853.01 TCGA.B0.5092.11 TCGA.B0.5402.01 TCGA.B0.4849.11
#> "011" "062" "022" "011" "022" "012"
#> TCGA.A3.A6NN.01 TCGA.B0.4852.01 TCGA.B0.4817.11 TCGA.BP.5176.11 TCGA.CW.5589.01 TCGA.CJ.5689.01
#> "04" "04" "014" "011" "061" "04"
#> TCGA.B0.4822.11 TCGA.BP.5190.11 TCGA.B0.4813.01 TCGA.BP.5200.01 TCGA.G6.A8L7.01 TCGA.B2.4101.01
#> "052" "012" "022" "04" "023" "04"
#> TCGA.B0.4713.11 TCGA.B0.4816.01 TCGA.A3.3385.01 TCGA.B2.3924.01 TCGA.CZ.5455.11 TCGA.B0.5713.01
#> "011" "04" "062" "04" "051" "04"
#> TCGA.B0.5108.01 TCGA.B0.5711.01 TCGA.CZ.5453.01 TCGA.BP.5202.11 TCGA.BP.5173.01 TCGA.CZ.5451.11
#> "04" "04" "061" "071" "061" "012"
#> TCGA.B8.A8YJ.01 TCGA.B0.4848.01 TCGA.DV.A4VZ.01 TCGA.B0.4814.11 TCGA.CJ.4869.11 TCGA.CJ.4907.11
#> "062" "02131" "03" "012" "012" "012"
#> TCGA.B8.5553.01 TCGA.MW.A4EC.01 TCGA.B0.5712.11 TCGA.EU.5905.01 TCGA.CZ.5985.01 TCGA.CZ.4856.01
#> "04" "04" "011" "04" "02133" "04"
#> TCGA.BP.5184.01 TCGA.B0.5121.01 TCGA.BP.5191.01 TCGA.BP.4801.11 TCGA.BP.5177.01 TCGA.B0.5110.11
#> "04" "022" "0212" "012" "062" "011"
#> TCGA.B0.4810.01 TCGA.CJ.4903.11 TCGA.CJ.4912.11 TCGA.B8.4621.01 TCGA.B4.5832.01 TCGA.CW.6088.01
#> "022" "012" "054" "063" "04" "061"
#> TCGA.AK.3428.01 TCGA.B8.5164.01 TCGA.BP.5195.01 TCGA.CJ.6027.01 TCGA.3Z.A93Z.01 TCGA.B0.4714.11
#> "022" "04" "04" "0211" "061" "014"
#> TCGA.B0.4818.11 TCGA.CZ.5457.11 TCGA.BP.5010.01 TCGA.BP.5189.11 TCGA.B0.4703.01 TCGA.B0.4718.11
#> "011" "051" "04" "012" "04" "052"
#> TCGA.B0.5097.11 TCGA.BP.4760.11 TCGA.B0.5120.11 TCGA.B0.4843.11 TCGA.B0.5104.01 TCGA.CW.5587.01
#> "011" "014" "011" "012" "04" "04"
get_classes(res_rh, merge_node = merge_node_param(min_n_signatures = 3997))
#> TCGA.CZ.4863.01 TCGA.CJ.4904.11 TCGA.B0.4827.11 TCGA.CJ.4902.01 TCGA.B0.4823.01 TCGA.CW.6087.01
#> "04" "011" "054" "04" "061" "04"
#> TCGA.B0.5098.01 TCGA.B0.5113.01 TCGA.DV.5566.01 TCGA.BP.5175.11 TCGA.BP.5181.01 TCGA.B0.4706.11
#> "073" "023" "04" "012" "062" "012"
#> TCGA.B0.5117.01 TCGA.MM.A564.01 TCGA.B0.4821.11 TCGA.CZ.5463.11 TCGA.BP.5182.11 TCGA.DV.5574.01
#> "013" "021" "072" "051" "012" "061"
#> TCGA.B0.5094.11 TCGA.MM.A84U.01 TCGA.B0.5100.11 TCGA.B4.5844.01 TCGA.CZ.5459.01 TCGA.B0.4694.01
#> "014" "04" "014" "04" "04" "04"
#> TCGA.CZ.5468.11 TCGA.CJ.4916.11 TCGA.B4.5836.01 TCGA.B0.5095.01 TCGA.B0.4846.11 TCGA.AK.3434.01
#> "051" "011" "04" "04" "011" "022"
#> TCGA.B4.5377.01 TCGA.B0.4696.11 TCGA.BP.5187.11 TCGA.B0.4690.01 TCGA.CZ.5466.01 TCGA.B0.4844.11
#> "062" "014" "014" "04" "04" "052"
#> TCGA.CZ.5464.11 TCGA.B0.4701.11 TCGA.BP.5194.11 TCGA.B0.4707.01 TCGA.CZ.5467.11 TCGA.B0.5705.01
#> "012" "011" "012" "021" "051" "062"
#> TCGA.CW.5588.01 TCGA.CJ.6031.01 TCGA.B8.A54J.01 TCGA.BP.5192.11 TCGA.CZ.5462.01 TCGA.B8.A54H.01
#> "04" "04" "04" "052" "04" "04"
#> TCGA.CZ.5470.11 TCGA.BP.4177.11 TCGA.CZ.5469.11 TCGA.CJ.6028.01 TCGA.G6.A8L6.01 TCGA.B8.5551.01
#> "051" "052" "051" "04" "04" "04"
#> TCGA.CZ.5456.01 TCGA.A3.A8OU.01 TCGA.BP.5186.01 TCGA.A3.A6NI.01 TCGA.BP.4782.01 TCGA.CZ.5454.11
#> "021" "04" "062" "04" "04" "054"
#> TCGA.B0.4691.11 TCGA.CZ.5452.01 TCGA.EU.5904.01 TCGA.BP.5201.01 TCGA.CJ.5677.01 TCGA.BP.5170.11
#> "012" "021" "062" "022" "023" "054"
#> TCGA.B0.4710.11 TCGA.AK.3425.01 TCGA.B0.4841.11 TCGA.B0.4849.01 TCGA.BP.5182.01 TCGA.B0.5711.11
#> "051" "021" "014" "04" "063" "052"
#> TCGA.BP.5180.01 TCGA.BP.5176.01 TCGA.CZ.5984.01 TCGA.CZ.5460.11 TCGA.BP.5190.01 TCGA.BP.4795.11
#> "021" "04" "021" "012" "022" "011"
#> TCGA.B0.4813.11 TCGA.B0.4713.01 TCGA.B0.4841.01 TCGA.B8.5546.01 TCGA.CW.5591.01 TCGA.B0.4698.11
#> "054" "023" "022" "072" "04" "014"
#> TCGA.B0.5713.11 TCGA.B0.5108.11 TCGA.B0.5083.01 TCGA.B0.5699.01 TCGA.CZ.5453.11 TCGA.BP.5202.01
#> "011" "012" "013" "022" "051" "022"
#> TCGA.BP.5173.11 TCGA.CW.5581.01 TCGA.B0.4848.11 TCGA.B0.4814.01 TCGA.BP.5178.11 TCGA.CJ.4907.01
#> "013" "04" "014" "022" "014" "04"
#> TCGA.A3.3387.01 TCGA.B0.4821.01 TCGA.B0.5712.01 TCGA.B0.5695.01 TCGA.BP.5184.11 TCGA.B2.A4SR.01
#> "04" "023" "023" "062" "012" "04"
#> TCGA.BP.5191.11 TCGA.CJ.4920.01 TCGA.BP.4801.01 TCGA.DV.A4W0.01 TCGA.BP.5177.11 TCGA.B0.4847.11
#> "014" "023" "04" "022" "011" "052"
#> TCGA.B0.5100.01 TCGA.CJ.4903.01 TCGA.CJ.4912.01 TCGA.B0.5107.11 TCGA.AK.3453.01 TCGA.B0.5691.01
#> "04" "022" "021" "011" "013" "062"
#> TCGA.BP.5195.11 TCGA.B0.5400.01 TCGA.A3.3376.11 TCGA.B0.4845.01 TCGA.B0.4699.01 TCGA.B0.4818.01
#> "054" "04" "071" "022" "071" "04"
#> TCGA.BP.5174.11 TCGA.CJ.4901.11 TCGA.B8.A54D.01 TCGA.BP.4770.11 TCGA.CW.6093.01 TCGA.BP.5010.11
#> "011" "012" "022" "011" "061" "054"
#> TCGA.AK.3431.01 TCGA.BP.4770.01 TCGA.BP.5189.01 TCGA.B0.4703.11 TCGA.B8.5163.01 TCGA.CJ.5683.01
#> "04" "04" "04" "014" "04" "04"
#> TCGA.CZ.4856.11 TCGA.BP.4760.01 TCGA.B0.5692.01 TCGA.B0.5106.01 TCGA.B0.4843.01 TCGA.CZ.4866.11
#> "051" "03" "023" "021" "04" "051"
#> TCGA.B0.5104.11 TCGA.B0.4827.01 TCGA.CJ.4902.11 TCGA.B8.A54G.01 TCGA.B0.5703.01 TCGA.CJ.5672.01
#> "011" "023" "054" "04" "04" "04"
#> TCGA.B0.5098.11 TCGA.B0.5113.11 TCGA.CJ.4882.11 TCGA.CZ.5465.11 TCGA.B0.5102.01 TCGA.CW.5585.01
#> "013" "011" "012" "051" "04" "04"
#> TCGA.B0.4824.01 TCGA.B0.5115.01 TCGA.B0.4706.01 TCGA.B0.5117.11 TCGA.CZ.4859.11 TCGA.AK.3450.01
#> "04" "022" "022" "012" "054" "04"
#> TCGA.B8.A54I.01 TCGA.CZ.5463.01 TCGA.DV.5568.01 TCGA.CZ.5459.11 TCGA.CJ.4918.11 TCGA.DV.5565.01
#> "021" "022" "04" "014" "014" "04"
#> TCGA.B0.5119.01 TCGA.B0.4811.01 TCGA.A3.3367.11 TCGA.CJ.4916.01 TCGA.B0.5693.01 TCGA.CZ.4863.11
#> "062" "04" "014" "04" "04" "051"
#> TCGA.G6.A5PC.01 TCGA.B8.5550.01 TCGA.DV.A4W0.05 TCGA.B0.4696.01 TCGA.BP.5187.01 TCGA.CZ.5466.11
#> "023" "04" "03" "021" "04" "014"
#> TCGA.CW.6097.01 TCGA.CJ.4905.11 TCGA.CZ.5989.01 TCGA.BP.5194.01 TCGA.B0.4707.11 TCGA.CZ.5467.01
#> "04" "052" "04" "04" "014" "04"
#> TCGA.BP.5185.11 TCGA.BP.5183.11 TCGA.BP.5192.01 TCGA.CZ.5462.11 TCGA.BP.4177.01 TCGA.CZ.5469.01
#> "012" "012" "061" "051" "03" "021"
#> TCGA.B2.5641.01 TCGA.BP.5196.11 TCGA.CZ.5460.01 TCGA.B0.4712.01 TCGA.B8.A54K.01 TCGA.B0.5707.01
#> "021" "012" "022" "021" "03" "062"
#> TCGA.BP.5186.11 TCGA.EU.5906.01 TCGA.CZ.5461.11 TCGA.CW.5590.01 TCGA.B0.5698.01 TCGA.CW.5580.01
#> "011" "061" "054" "022" "022" "023"
#> TCGA.CZ.5454.01 TCGA.B0.4815.01 TCGA.B0.5710.11 TCGA.CJ.4908.11 TCGA.BP.5201.11 TCGA.B0.5694.01
#> "022" "021" "012" "054" "012" "022"
#> TCGA.BP.5170.01 TCGA.DV.5575.01 TCGA.CJ.5686.01 TCGA.A3.3357.01 TCGA.A3.3373.01 TCGA.B0.5690.01
#> "04" "062" "04" "022" "04" "062"
#> TCGA.B8.4622.01 TCGA.AK.3433.01 TCGA.B0.5110.01 TCGA.BP.5180.11 TCGA.CJ.4913.01 TCGA.CJ.4908.01
#> "022" "053" "062" "012" "023" "04"
#> TCGA.BP.4795.01 TCGA.CJ.4897.11 TCGA.B2.5636.01 TCGA.CJ.4923.11 TCGA.B0.4819.01 TCGA.B2.5633.01
#> "03" "011" "03" "014" "04" "04"
#> TCGA.CJ.6033.01 TCGA.BP.5181.11 TCGA.B0.4698.01 TCGA.B0.5083.11 TCGA.CZ.4864.11 TCGA.B0.4688.01
#> "023" "011" "021" "012" "014" "021"
#> TCGA.BP.5168.01 TCGA.BP.5198.11 TCGA.B8.5162.01 TCGA.B0.5096.01 TCGA.BP.5178.01 TCGA.B0.5099.11
#> "04" "014" "04" "023" "021" "011"
#> TCGA.B0.4842.01 TCGA.BP.5169.11 TCGA.B0.5109.11 TCGA.CJ.4920.11 TCGA.B0.5080.11 TCGA.B0.5700.01
#> "04" "014" "071" "054" "012" "061"
#> TCGA.B0.4847.01 TCGA.B0.5702.01 TCGA.CJ.4905.01 TCGA.B2.5635.01 TCGA.B0.5107.01 TCGA.CW.5584.01
#> "022" "071" "04" "04" "023" "022"
#> TCGA.B4.5838.01 TCGA.BP.5199.01 TCGA.A3.3376.01 TCGA.B0.4845.11 TCGA.B0.4699.11 TCGA.BP.5174.01
#> "04" "022" "061" "054" "014" "062"
#> TCGA.CZ.5986.01 TCGA.CJ.4901.01 TCGA.AK.3461.01 TCGA.AK.3460.01 TCGA.AK.3454.01 TCGA.CZ.4859.01
#> "061" "021" "04" "04" "061" "062"
#> TCGA.B0.5812.01 TCGA.B0.5116.11 TCGA.B8.A54F.01 TCGA.CW.6090.01 TCGA.CZ.5458.11 TCGA.B0.5106.11
#> "04" "071" "04" "022" "051" "012"
#> TCGA.CZ.4866.01 TCGA.B0.4828.01 TCGA.AK.3440.01 TCGA.MM.A563.01 TCGA.B0.4697.01 TCGA.AK.3458.01
#> "023" "022" "053" "022" "04" "022"
#> TCGA.CJ.5676.01 TCGA.B0.5402.11 TCGA.CJ.5681.01 TCGA.A3.3370.11 TCGA.A3.A6NL.01 TCGA.B0.4693.01
#> "021" "014" "073" "052" "062" "023"
#> TCGA.A3.3358.01 TCGA.B0.4710.01 TCGA.CZ.4853.11 TCGA.B4.5835.01 TCGA.CJ.4882.01 TCGA.CZ.5465.01
#> "04" "023" "054" "062" "04" "023"
#> TCGA.B0.5102.11 TCGA.B0.4824.11 TCGA.CJ.5675.01 TCGA.B0.4700.01 TCGA.B0.5092.01 TCGA.B0.5115.11
#> "011" "011" "022" "04" "04" "012"
#> TCGA.B0.4945.11 TCGA.B8.5158.01 TCGA.CJ.6030.01 TCGA.B8.A54E.01 TCGA.CJ.6032.01 TCGA.B0.4852.11
#> "011" "021" "021" "072" "04" "011"
#> TCGA.B0.4817.01 TCGA.B8.5159.01 TCGA.A3.A8OW.01 TCGA.B0.4822.01 TCGA.B0.5696.01 TCGA.B0.5706.01
#> "04" "023" "061" "04" "04" "021"
#> TCGA.CJ.4918.01 TCGA.B0.5119.11 TCGA.BP.5200.11 TCGA.B0.4811.11 TCGA.A3.3367.01 TCGA.B0.5097.01
#> "04" "051" "012" "014" "022" "04"
#> TCGA.6D.AA2E.01 TCGA.DV.A4VX.01 TCGA.B0.4816.11 TCGA.A3.3385.11 TCGA.DV.5569.01 TCGA.EU.5907.01
#> "072" "022" "054" "011" "062" "022"
#> TCGA.CZ.5455.01 TCGA.B8.5545.01 TCGA.DV.5567.01 TCGA.CZ.5451.01 TCGA.CJ.4869.01 TCGA.CJ.5678.01
#> "04" "061" "03" "04" "04" "022"
#> TCGA.B8.4153.01 TCGA.B0.5121.11 TCGA.B8.4146.01 TCGA.BP.5183.01 TCGA.B0.5399.01 TCGA.B0.4810.11
#> "022" "012" "04" "022" "04" "052"
#> TCGA.AK.3445.01 TCGA.B4.5378.01 TCGA.BP.5196.01 TCGA.CZ.4865.11 TCGA.B0.5709.01 TCGA.B0.4712.11
#> "021" "03" "021" "051" "062" "051"
#> TCGA.B0.4714.01 TCGA.B8.5549.01 TCGA.CZ.5461.01 TCGA.CZ.5457.01 TCGA.A3.A8CQ.01 TCGA.DV.5573.01
#> "022" "022" "021" "063" "062" "061"
#> TCGA.B0.4815.11 TCGA.B0.5710.01 TCGA.B8.5165.01 TCGA.B0.4718.01 TCGA.B2.5639.01 TCGA.CW.5583.01
#> "014" "022" "061" "022" "04" "062"
#> TCGA.GK.A6C7.01 TCGA.A3.3357.11 TCGA.B8.5552.01 TCGA.B0.5120.01 TCGA.A3.3373.11 TCGA.BP.5185.01
#> "062" "012" "062" "04" "054" "04"
#> TCGA.B0.4846.01 TCGA.CJ.4904.01 TCGA.CJ.4913.11 TCGA.BP.4993.11 TCGA.B0.4823.11 TCGA.CJ.4897.01
#> "04" "062" "011" "012" "013" "04"
#> TCGA.BP.4993.01 TCGA.B4.5843.01 TCGA.DV.5576.01 TCGA.CJ.4923.01 TCGA.B0.4819.11 TCGA.BP.5175.01
#> "061" "061" "03" "04" "011" "021"
#> TCGA.CZ.5987.01 TCGA.CZ.4864.01 TCGA.B0.4688.11 TCGA.BP.5168.11 TCGA.BP.5198.01 TCGA.B8.A7U6.01
#> "021" "061" "054" "014" "021" "04"
#> TCGA.B0.5094.01 TCGA.T7.A92I.01 TCGA.B0.5096.11 TCGA.B0.5400.11 TCGA.B0.4694.11 TCGA.B0.5099.01
#> "021" "072" "011" "011" "052" "04"
#> TCGA.CZ.5468.01 TCGA.B0.4842.11 TCGA.CZ.5988.01 TCGA.BP.5169.01 TCGA.B0.5109.01 TCGA.B4.5834.01
#> "021" "011" "04" "021" "04" "061"
#> TCGA.B0.5095.11 TCGA.B0.5080.01 TCGA.CJ.5680.01 TCGA.CZ.5470.01 TCGA.CZ.4865.01 TCGA.A3.A8OX.01
#> "013" "04" "023" "023" "04" "072"
#> TCGA.B0.4690.11 TCGA.CJ.5684.01 TCGA.B0.4844.01 TCGA.CZ.5464.01 TCGA.B0.4701.01 TCGA.B0.5701.01
#> "013" "04" "021" "021" "04" "021"
#> TCGA.BP.5199.11 TCGA.CJ.5671.01 TCGA.A3.A8OV.01 TCGA.CZ.5456.11 TCGA.B0.5116.01 TCGA.CZ.5458.01
#> "012" "021" "061" "051" "022" "04"
#> TCGA.CZ.5982.01 TCGA.B0.4828.11 TCGA.CJ.5679.01 TCGA.CJ.5682.01 TCGA.B0.5697.01 TCGA.B0.4697.11
#> "04" "054" "021" "022" "04" "051"
#> TCGA.BP.4782.11 TCGA.G6.A8L8.01 TCGA.A3.A6NJ.01 TCGA.A3.3370.01 TCGA.B0.4691.01 TCGA.CZ.5452.11
#> "011" "023" "062" "062" "021" "051"
#> TCGA.B0.4693.11 TCGA.B0.4945.01 TCGA.CZ.4853.01 TCGA.B0.5092.11 TCGA.B0.5402.01 TCGA.B0.4849.11
#> "011" "062" "022" "011" "022" "012"
#> TCGA.A3.A6NN.01 TCGA.B0.4852.01 TCGA.B0.4817.11 TCGA.BP.5176.11 TCGA.CW.5589.01 TCGA.CJ.5689.01
#> "04" "04" "014" "011" "061" "04"
#> TCGA.B0.4822.11 TCGA.BP.5190.11 TCGA.B0.4813.01 TCGA.BP.5200.01 TCGA.G6.A8L7.01 TCGA.B2.4101.01
#> "052" "012" "022" "04" "023" "04"
#> TCGA.B0.4713.11 TCGA.B0.4816.01 TCGA.A3.3385.01 TCGA.B2.3924.01 TCGA.CZ.5455.11 TCGA.B0.5713.01
#> "011" "04" "062" "04" "051" "04"
#> TCGA.B0.5108.01 TCGA.B0.5711.01 TCGA.CZ.5453.01 TCGA.BP.5202.11 TCGA.BP.5173.01 TCGA.CZ.5451.11
#> "04" "04" "061" "071" "061" "012"
#> TCGA.B8.A8YJ.01 TCGA.B0.4848.01 TCGA.DV.A4VZ.01 TCGA.B0.4814.11 TCGA.CJ.4869.11 TCGA.CJ.4907.11
#> "062" "021" "03" "012" "012" "012"
#> TCGA.B8.5553.01 TCGA.MW.A4EC.01 TCGA.B0.5712.11 TCGA.EU.5905.01 TCGA.CZ.5985.01 TCGA.CZ.4856.01
#> "04" "04" "011" "04" "021" "04"
#> TCGA.BP.5184.01 TCGA.B0.5121.01 TCGA.BP.5191.01 TCGA.BP.4801.11 TCGA.BP.5177.01 TCGA.B0.5110.11
#> "04" "022" "021" "012" "062" "011"
#> TCGA.B0.4810.01 TCGA.CJ.4903.11 TCGA.CJ.4912.11 TCGA.B8.4621.01 TCGA.B4.5832.01 TCGA.CW.6088.01
#> "022" "012" "054" "063" "04" "061"
#> TCGA.AK.3428.01 TCGA.B8.5164.01 TCGA.BP.5195.01 TCGA.CJ.6027.01 TCGA.3Z.A93Z.01 TCGA.B0.4714.11
#> "022" "04" "04" "021" "061" "014"
#> TCGA.B0.4818.11 TCGA.CZ.5457.11 TCGA.BP.5010.01 TCGA.BP.5189.11 TCGA.B0.4703.01 TCGA.B0.4718.11
#> "011" "051" "04" "012" "04" "052"
#> TCGA.B0.5097.11 TCGA.BP.4760.11 TCGA.B0.5120.11 TCGA.B0.4843.11 TCGA.B0.5104.01 TCGA.CW.5587.01
#> "011" "014" "011" "012" "04" "04"
get_classes(res_rh, merge_node = merge_node_param(min_n_signatures = 4193))
#> TCGA.CZ.4863.01 TCGA.CJ.4904.11 TCGA.B0.4827.11 TCGA.CJ.4902.01 TCGA.B0.4823.01 TCGA.CW.6087.01
#> "04" "011" "054" "04" "061" "04"
#> TCGA.B0.5098.01 TCGA.B0.5113.01 TCGA.DV.5566.01 TCGA.BP.5175.11 TCGA.BP.5181.01 TCGA.B0.4706.11
#> "073" "02" "04" "012" "062" "012"
#> TCGA.B0.5117.01 TCGA.MM.A564.01 TCGA.B0.4821.11 TCGA.CZ.5463.11 TCGA.BP.5182.11 TCGA.DV.5574.01
#> "013" "02" "072" "051" "012" "061"
#> TCGA.B0.5094.11 TCGA.MM.A84U.01 TCGA.B0.5100.11 TCGA.B4.5844.01 TCGA.CZ.5459.01 TCGA.B0.4694.01
#> "014" "04" "014" "04" "04" "04"
#> TCGA.CZ.5468.11 TCGA.CJ.4916.11 TCGA.B4.5836.01 TCGA.B0.5095.01 TCGA.B0.4846.11 TCGA.AK.3434.01
#> "051" "011" "04" "04" "011" "02"
#> TCGA.B4.5377.01 TCGA.B0.4696.11 TCGA.BP.5187.11 TCGA.B0.4690.01 TCGA.CZ.5466.01 TCGA.B0.4844.11
#> "062" "014" "014" "04" "04" "052"
#> TCGA.CZ.5464.11 TCGA.B0.4701.11 TCGA.BP.5194.11 TCGA.B0.4707.01 TCGA.CZ.5467.11 TCGA.B0.5705.01
#> "012" "011" "012" "02" "051" "062"
#> TCGA.CW.5588.01 TCGA.CJ.6031.01 TCGA.B8.A54J.01 TCGA.BP.5192.11 TCGA.CZ.5462.01 TCGA.B8.A54H.01
#> "04" "04" "04" "052" "04" "04"
#> TCGA.CZ.5470.11 TCGA.BP.4177.11 TCGA.CZ.5469.11 TCGA.CJ.6028.01 TCGA.G6.A8L6.01 TCGA.B8.5551.01
#> "051" "052" "051" "04" "04" "04"
#> TCGA.CZ.5456.01 TCGA.A3.A8OU.01 TCGA.BP.5186.01 TCGA.A3.A6NI.01 TCGA.BP.4782.01 TCGA.CZ.5454.11
#> "02" "04" "062" "04" "04" "054"
#> TCGA.B0.4691.11 TCGA.CZ.5452.01 TCGA.EU.5904.01 TCGA.BP.5201.01 TCGA.CJ.5677.01 TCGA.BP.5170.11
#> "012" "02" "062" "02" "02" "054"
#> TCGA.B0.4710.11 TCGA.AK.3425.01 TCGA.B0.4841.11 TCGA.B0.4849.01 TCGA.BP.5182.01 TCGA.B0.5711.11
#> "051" "02" "014" "04" "063" "052"
#> TCGA.BP.5180.01 TCGA.BP.5176.01 TCGA.CZ.5984.01 TCGA.CZ.5460.11 TCGA.BP.5190.01 TCGA.BP.4795.11
#> "02" "04" "02" "012" "02" "011"
#> TCGA.B0.4813.11 TCGA.B0.4713.01 TCGA.B0.4841.01 TCGA.B8.5546.01 TCGA.CW.5591.01 TCGA.B0.4698.11
#> "054" "02" "02" "072" "04" "014"
#> TCGA.B0.5713.11 TCGA.B0.5108.11 TCGA.B0.5083.01 TCGA.B0.5699.01 TCGA.CZ.5453.11 TCGA.BP.5202.01
#> "011" "012" "013" "02" "051" "02"
#> TCGA.BP.5173.11 TCGA.CW.5581.01 TCGA.B0.4848.11 TCGA.B0.4814.01 TCGA.BP.5178.11 TCGA.CJ.4907.01
#> "013" "04" "014" "02" "014" "04"
#> TCGA.A3.3387.01 TCGA.B0.4821.01 TCGA.B0.5712.01 TCGA.B0.5695.01 TCGA.BP.5184.11 TCGA.B2.A4SR.01
#> "04" "02" "02" "062" "012" "04"
#> TCGA.BP.5191.11 TCGA.CJ.4920.01 TCGA.BP.4801.01 TCGA.DV.A4W0.01 TCGA.BP.5177.11 TCGA.B0.4847.11
#> "014" "02" "04" "02" "011" "052"
#> TCGA.B0.5100.01 TCGA.CJ.4903.01 TCGA.CJ.4912.01 TCGA.B0.5107.11 TCGA.AK.3453.01 TCGA.B0.5691.01
#> "04" "02" "02" "011" "013" "062"
#> TCGA.BP.5195.11 TCGA.B0.5400.01 TCGA.A3.3376.11 TCGA.B0.4845.01 TCGA.B0.4699.01 TCGA.B0.4818.01
#> "054" "04" "071" "02" "071" "04"
#> TCGA.BP.5174.11 TCGA.CJ.4901.11 TCGA.B8.A54D.01 TCGA.BP.4770.11 TCGA.CW.6093.01 TCGA.BP.5010.11
#> "011" "012" "02" "011" "061" "054"
#> TCGA.AK.3431.01 TCGA.BP.4770.01 TCGA.BP.5189.01 TCGA.B0.4703.11 TCGA.B8.5163.01 TCGA.CJ.5683.01
#> "04" "04" "04" "014" "04" "04"
#> TCGA.CZ.4856.11 TCGA.BP.4760.01 TCGA.B0.5692.01 TCGA.B0.5106.01 TCGA.B0.4843.01 TCGA.CZ.4866.11
#> "051" "03" "02" "02" "04" "051"
#> TCGA.B0.5104.11 TCGA.B0.4827.01 TCGA.CJ.4902.11 TCGA.B8.A54G.01 TCGA.B0.5703.01 TCGA.CJ.5672.01
#> "011" "02" "054" "04" "04" "04"
#> TCGA.B0.5098.11 TCGA.B0.5113.11 TCGA.CJ.4882.11 TCGA.CZ.5465.11 TCGA.B0.5102.01 TCGA.CW.5585.01
#> "013" "011" "012" "051" "04" "04"
#> TCGA.B0.4824.01 TCGA.B0.5115.01 TCGA.B0.4706.01 TCGA.B0.5117.11 TCGA.CZ.4859.11 TCGA.AK.3450.01
#> "04" "02" "02" "012" "054" "04"
#> TCGA.B8.A54I.01 TCGA.CZ.5463.01 TCGA.DV.5568.01 TCGA.CZ.5459.11 TCGA.CJ.4918.11 TCGA.DV.5565.01
#> "02" "02" "04" "014" "014" "04"
#> TCGA.B0.5119.01 TCGA.B0.4811.01 TCGA.A3.3367.11 TCGA.CJ.4916.01 TCGA.B0.5693.01 TCGA.CZ.4863.11
#> "062" "04" "014" "04" "04" "051"
#> TCGA.G6.A5PC.01 TCGA.B8.5550.01 TCGA.DV.A4W0.05 TCGA.B0.4696.01 TCGA.BP.5187.01 TCGA.CZ.5466.11
#> "02" "04" "03" "02" "04" "014"
#> TCGA.CW.6097.01 TCGA.CJ.4905.11 TCGA.CZ.5989.01 TCGA.BP.5194.01 TCGA.B0.4707.11 TCGA.CZ.5467.01
#> "04" "052" "04" "04" "014" "04"
#> TCGA.BP.5185.11 TCGA.BP.5183.11 TCGA.BP.5192.01 TCGA.CZ.5462.11 TCGA.BP.4177.01 TCGA.CZ.5469.01
#> "012" "012" "061" "051" "03" "02"
#> TCGA.B2.5641.01 TCGA.BP.5196.11 TCGA.CZ.5460.01 TCGA.B0.4712.01 TCGA.B8.A54K.01 TCGA.B0.5707.01
#> "02" "012" "02" "02" "03" "062"
#> TCGA.BP.5186.11 TCGA.EU.5906.01 TCGA.CZ.5461.11 TCGA.CW.5590.01 TCGA.B0.5698.01 TCGA.CW.5580.01
#> "011" "061" "054" "02" "02" "02"
#> TCGA.CZ.5454.01 TCGA.B0.4815.01 TCGA.B0.5710.11 TCGA.CJ.4908.11 TCGA.BP.5201.11 TCGA.B0.5694.01
#> "02" "02" "012" "054" "012" "02"
#> TCGA.BP.5170.01 TCGA.DV.5575.01 TCGA.CJ.5686.01 TCGA.A3.3357.01 TCGA.A3.3373.01 TCGA.B0.5690.01
#> "04" "062" "04" "02" "04" "062"
#> TCGA.B8.4622.01 TCGA.AK.3433.01 TCGA.B0.5110.01 TCGA.BP.5180.11 TCGA.CJ.4913.01 TCGA.CJ.4908.01
#> "02" "053" "062" "012" "02" "04"
#> TCGA.BP.4795.01 TCGA.CJ.4897.11 TCGA.B2.5636.01 TCGA.CJ.4923.11 TCGA.B0.4819.01 TCGA.B2.5633.01
#> "03" "011" "03" "014" "04" "04"
#> TCGA.CJ.6033.01 TCGA.BP.5181.11 TCGA.B0.4698.01 TCGA.B0.5083.11 TCGA.CZ.4864.11 TCGA.B0.4688.01
#> "02" "011" "02" "012" "014" "02"
#> TCGA.BP.5168.01 TCGA.BP.5198.11 TCGA.B8.5162.01 TCGA.B0.5096.01 TCGA.BP.5178.01 TCGA.B0.5099.11
#> "04" "014" "04" "02" "02" "011"
#> TCGA.B0.4842.01 TCGA.BP.5169.11 TCGA.B0.5109.11 TCGA.CJ.4920.11 TCGA.B0.5080.11 TCGA.B0.5700.01
#> "04" "014" "071" "054" "012" "061"
#> TCGA.B0.4847.01 TCGA.B0.5702.01 TCGA.CJ.4905.01 TCGA.B2.5635.01 TCGA.B0.5107.01 TCGA.CW.5584.01
#> "02" "071" "04" "04" "02" "02"
#> TCGA.B4.5838.01 TCGA.BP.5199.01 TCGA.A3.3376.01 TCGA.B0.4845.11 TCGA.B0.4699.11 TCGA.BP.5174.01
#> "04" "02" "061" "054" "014" "062"
#> TCGA.CZ.5986.01 TCGA.CJ.4901.01 TCGA.AK.3461.01 TCGA.AK.3460.01 TCGA.AK.3454.01 TCGA.CZ.4859.01
#> "061" "02" "04" "04" "061" "062"
#> TCGA.B0.5812.01 TCGA.B0.5116.11 TCGA.B8.A54F.01 TCGA.CW.6090.01 TCGA.CZ.5458.11 TCGA.B0.5106.11
#> "04" "071" "04" "02" "051" "012"
#> TCGA.CZ.4866.01 TCGA.B0.4828.01 TCGA.AK.3440.01 TCGA.MM.A563.01 TCGA.B0.4697.01 TCGA.AK.3458.01
#> "02" "02" "053" "02" "04" "02"
#> TCGA.CJ.5676.01 TCGA.B0.5402.11 TCGA.CJ.5681.01 TCGA.A3.3370.11 TCGA.A3.A6NL.01 TCGA.B0.4693.01
#> "02" "014" "073" "052" "062" "02"
#> TCGA.A3.3358.01 TCGA.B0.4710.01 TCGA.CZ.4853.11 TCGA.B4.5835.01 TCGA.CJ.4882.01 TCGA.CZ.5465.01
#> "04" "02" "054" "062" "04" "02"
#> TCGA.B0.5102.11 TCGA.B0.4824.11 TCGA.CJ.5675.01 TCGA.B0.4700.01 TCGA.B0.5092.01 TCGA.B0.5115.11
#> "011" "011" "02" "04" "04" "012"
#> TCGA.B0.4945.11 TCGA.B8.5158.01 TCGA.CJ.6030.01 TCGA.B8.A54E.01 TCGA.CJ.6032.01 TCGA.B0.4852.11
#> "011" "02" "02" "072" "04" "011"
#> TCGA.B0.4817.01 TCGA.B8.5159.01 TCGA.A3.A8OW.01 TCGA.B0.4822.01 TCGA.B0.5696.01 TCGA.B0.5706.01
#> "04" "02" "061" "04" "04" "02"
#> TCGA.CJ.4918.01 TCGA.B0.5119.11 TCGA.BP.5200.11 TCGA.B0.4811.11 TCGA.A3.3367.01 TCGA.B0.5097.01
#> "04" "051" "012" "014" "02" "04"
#> TCGA.6D.AA2E.01 TCGA.DV.A4VX.01 TCGA.B0.4816.11 TCGA.A3.3385.11 TCGA.DV.5569.01 TCGA.EU.5907.01
#> "072" "02" "054" "011" "062" "02"
#> TCGA.CZ.5455.01 TCGA.B8.5545.01 TCGA.DV.5567.01 TCGA.CZ.5451.01 TCGA.CJ.4869.01 TCGA.CJ.5678.01
#> "04" "061" "03" "04" "04" "02"
#> TCGA.B8.4153.01 TCGA.B0.5121.11 TCGA.B8.4146.01 TCGA.BP.5183.01 TCGA.B0.5399.01 TCGA.B0.4810.11
#> "02" "012" "04" "02" "04" "052"
#> TCGA.AK.3445.01 TCGA.B4.5378.01 TCGA.BP.5196.01 TCGA.CZ.4865.11 TCGA.B0.5709.01 TCGA.B0.4712.11
#> "02" "03" "02" "051" "062" "051"
#> TCGA.B0.4714.01 TCGA.B8.5549.01 TCGA.CZ.5461.01 TCGA.CZ.5457.01 TCGA.A3.A8CQ.01 TCGA.DV.5573.01
#> "02" "02" "02" "063" "062" "061"
#> TCGA.B0.4815.11 TCGA.B0.5710.01 TCGA.B8.5165.01 TCGA.B0.4718.01 TCGA.B2.5639.01 TCGA.CW.5583.01
#> "014" "02" "061" "02" "04" "062"
#> TCGA.GK.A6C7.01 TCGA.A3.3357.11 TCGA.B8.5552.01 TCGA.B0.5120.01 TCGA.A3.3373.11 TCGA.BP.5185.01
#> "062" "012" "062" "04" "054" "04"
#> TCGA.B0.4846.01 TCGA.CJ.4904.01 TCGA.CJ.4913.11 TCGA.BP.4993.11 TCGA.B0.4823.11 TCGA.CJ.4897.01
#> "04" "062" "011" "012" "013" "04"
#> TCGA.BP.4993.01 TCGA.B4.5843.01 TCGA.DV.5576.01 TCGA.CJ.4923.01 TCGA.B0.4819.11 TCGA.BP.5175.01
#> "061" "061" "03" "04" "011" "02"
#> TCGA.CZ.5987.01 TCGA.CZ.4864.01 TCGA.B0.4688.11 TCGA.BP.5168.11 TCGA.BP.5198.01 TCGA.B8.A7U6.01
#> "02" "061" "054" "014" "02" "04"
#> TCGA.B0.5094.01 TCGA.T7.A92I.01 TCGA.B0.5096.11 TCGA.B0.5400.11 TCGA.B0.4694.11 TCGA.B0.5099.01
#> "02" "072" "011" "011" "052" "04"
#> TCGA.CZ.5468.01 TCGA.B0.4842.11 TCGA.CZ.5988.01 TCGA.BP.5169.01 TCGA.B0.5109.01 TCGA.B4.5834.01
#> "02" "011" "04" "02" "04" "061"
#> TCGA.B0.5095.11 TCGA.B0.5080.01 TCGA.CJ.5680.01 TCGA.CZ.5470.01 TCGA.CZ.4865.01 TCGA.A3.A8OX.01
#> "013" "04" "02" "02" "04" "072"
#> TCGA.B0.4690.11 TCGA.CJ.5684.01 TCGA.B0.4844.01 TCGA.CZ.5464.01 TCGA.B0.4701.01 TCGA.B0.5701.01
#> "013" "04" "02" "02" "04" "02"
#> TCGA.BP.5199.11 TCGA.CJ.5671.01 TCGA.A3.A8OV.01 TCGA.CZ.5456.11 TCGA.B0.5116.01 TCGA.CZ.5458.01
#> "012" "02" "061" "051" "02" "04"
#> TCGA.CZ.5982.01 TCGA.B0.4828.11 TCGA.CJ.5679.01 TCGA.CJ.5682.01 TCGA.B0.5697.01 TCGA.B0.4697.11
#> "04" "054" "02" "02" "04" "051"
#> TCGA.BP.4782.11 TCGA.G6.A8L8.01 TCGA.A3.A6NJ.01 TCGA.A3.3370.01 TCGA.B0.4691.01 TCGA.CZ.5452.11
#> "011" "02" "062" "062" "02" "051"
#> TCGA.B0.4693.11 TCGA.B0.4945.01 TCGA.CZ.4853.01 TCGA.B0.5092.11 TCGA.B0.5402.01 TCGA.B0.4849.11
#> "011" "062" "02" "011" "02" "012"
#> TCGA.A3.A6NN.01 TCGA.B0.4852.01 TCGA.B0.4817.11 TCGA.BP.5176.11 TCGA.CW.5589.01 TCGA.CJ.5689.01
#> "04" "04" "014" "011" "061" "04"
#> TCGA.B0.4822.11 TCGA.BP.5190.11 TCGA.B0.4813.01 TCGA.BP.5200.01 TCGA.G6.A8L7.01 TCGA.B2.4101.01
#> "052" "012" "02" "04" "02" "04"
#> TCGA.B0.4713.11 TCGA.B0.4816.01 TCGA.A3.3385.01 TCGA.B2.3924.01 TCGA.CZ.5455.11 TCGA.B0.5713.01
#> "011" "04" "062" "04" "051" "04"
#> TCGA.B0.5108.01 TCGA.B0.5711.01 TCGA.CZ.5453.01 TCGA.BP.5202.11 TCGA.BP.5173.01 TCGA.CZ.5451.11
#> "04" "04" "061" "071" "061" "012"
#> TCGA.B8.A8YJ.01 TCGA.B0.4848.01 TCGA.DV.A4VZ.01 TCGA.B0.4814.11 TCGA.CJ.4869.11 TCGA.CJ.4907.11
#> "062" "02" "03" "012" "012" "012"
#> TCGA.B8.5553.01 TCGA.MW.A4EC.01 TCGA.B0.5712.11 TCGA.EU.5905.01 TCGA.CZ.5985.01 TCGA.CZ.4856.01
#> "04" "04" "011" "04" "02" "04"
#> TCGA.BP.5184.01 TCGA.B0.5121.01 TCGA.BP.5191.01 TCGA.BP.4801.11 TCGA.BP.5177.01 TCGA.B0.5110.11
#> "04" "02" "02" "012" "062" "011"
#> TCGA.B0.4810.01 TCGA.CJ.4903.11 TCGA.CJ.4912.11 TCGA.B8.4621.01 TCGA.B4.5832.01 TCGA.CW.6088.01
#> "02" "012" "054" "063" "04" "061"
#> TCGA.AK.3428.01 TCGA.B8.5164.01 TCGA.BP.5195.01 TCGA.CJ.6027.01 TCGA.3Z.A93Z.01 TCGA.B0.4714.11
#> "02" "04" "04" "02" "061" "014"
#> TCGA.B0.4818.11 TCGA.CZ.5457.11 TCGA.BP.5010.01 TCGA.BP.5189.11 TCGA.B0.4703.01 TCGA.B0.4718.11
#> "011" "051" "04" "012" "04" "052"
#> TCGA.B0.5097.11 TCGA.BP.4760.11 TCGA.B0.5120.11 TCGA.B0.4843.11 TCGA.B0.5104.01 TCGA.CW.5587.01
#> "011" "014" "011" "012" "04" "04"
get_classes(res_rh, merge_node = merge_node_param(min_n_signatures = 4521))
#> TCGA.CZ.4863.01 TCGA.CJ.4904.11 TCGA.B0.4827.11 TCGA.CJ.4902.01 TCGA.B0.4823.01 TCGA.CW.6087.01
#> "04" "011" "054" "04" "061" "04"
#> TCGA.B0.5098.01 TCGA.B0.5113.01 TCGA.DV.5566.01 TCGA.BP.5175.11 TCGA.BP.5181.01 TCGA.B0.4706.11
#> "073" "02" "04" "012" "062" "012"
#> TCGA.B0.5117.01 TCGA.MM.A564.01 TCGA.B0.4821.11 TCGA.CZ.5463.11 TCGA.BP.5182.11 TCGA.DV.5574.01
#> "013" "02" "072" "051" "012" "061"
#> TCGA.B0.5094.11 TCGA.MM.A84U.01 TCGA.B0.5100.11 TCGA.B4.5844.01 TCGA.CZ.5459.01 TCGA.B0.4694.01
#> "014" "04" "014" "04" "04" "04"
#> TCGA.CZ.5468.11 TCGA.CJ.4916.11 TCGA.B4.5836.01 TCGA.B0.5095.01 TCGA.B0.4846.11 TCGA.AK.3434.01
#> "051" "011" "04" "04" "011" "02"
#> TCGA.B4.5377.01 TCGA.B0.4696.11 TCGA.BP.5187.11 TCGA.B0.4690.01 TCGA.CZ.5466.01 TCGA.B0.4844.11
#> "062" "014" "014" "04" "04" "052"
#> TCGA.CZ.5464.11 TCGA.B0.4701.11 TCGA.BP.5194.11 TCGA.B0.4707.01 TCGA.CZ.5467.11 TCGA.B0.5705.01
#> "012" "011" "012" "02" "051" "062"
#> TCGA.CW.5588.01 TCGA.CJ.6031.01 TCGA.B8.A54J.01 TCGA.BP.5192.11 TCGA.CZ.5462.01 TCGA.B8.A54H.01
#> "04" "04" "04" "052" "04" "04"
#> TCGA.CZ.5470.11 TCGA.BP.4177.11 TCGA.CZ.5469.11 TCGA.CJ.6028.01 TCGA.G6.A8L6.01 TCGA.B8.5551.01
#> "051" "052" "051" "04" "04" "04"
#> TCGA.CZ.5456.01 TCGA.A3.A8OU.01 TCGA.BP.5186.01 TCGA.A3.A6NI.01 TCGA.BP.4782.01 TCGA.CZ.5454.11
#> "02" "04" "062" "04" "04" "054"
#> TCGA.B0.4691.11 TCGA.CZ.5452.01 TCGA.EU.5904.01 TCGA.BP.5201.01 TCGA.CJ.5677.01 TCGA.BP.5170.11
#> "012" "02" "062" "02" "02" "054"
#> TCGA.B0.4710.11 TCGA.AK.3425.01 TCGA.B0.4841.11 TCGA.B0.4849.01 TCGA.BP.5182.01 TCGA.B0.5711.11
#> "051" "02" "014" "04" "063" "052"
#> TCGA.BP.5180.01 TCGA.BP.5176.01 TCGA.CZ.5984.01 TCGA.CZ.5460.11 TCGA.BP.5190.01 TCGA.BP.4795.11
#> "02" "04" "02" "012" "02" "011"
#> TCGA.B0.4813.11 TCGA.B0.4713.01 TCGA.B0.4841.01 TCGA.B8.5546.01 TCGA.CW.5591.01 TCGA.B0.4698.11
#> "054" "02" "02" "072" "04" "014"
#> TCGA.B0.5713.11 TCGA.B0.5108.11 TCGA.B0.5083.01 TCGA.B0.5699.01 TCGA.CZ.5453.11 TCGA.BP.5202.01
#> "011" "012" "013" "02" "051" "02"
#> TCGA.BP.5173.11 TCGA.CW.5581.01 TCGA.B0.4848.11 TCGA.B0.4814.01 TCGA.BP.5178.11 TCGA.CJ.4907.01
#> "013" "04" "014" "02" "014" "04"
#> TCGA.A3.3387.01 TCGA.B0.4821.01 TCGA.B0.5712.01 TCGA.B0.5695.01 TCGA.BP.5184.11 TCGA.B2.A4SR.01
#> "04" "02" "02" "062" "012" "04"
#> TCGA.BP.5191.11 TCGA.CJ.4920.01 TCGA.BP.4801.01 TCGA.DV.A4W0.01 TCGA.BP.5177.11 TCGA.B0.4847.11
#> "014" "02" "04" "02" "011" "052"
#> TCGA.B0.5100.01 TCGA.CJ.4903.01 TCGA.CJ.4912.01 TCGA.B0.5107.11 TCGA.AK.3453.01 TCGA.B0.5691.01
#> "04" "02" "02" "011" "013" "062"
#> TCGA.BP.5195.11 TCGA.B0.5400.01 TCGA.A3.3376.11 TCGA.B0.4845.01 TCGA.B0.4699.01 TCGA.B0.4818.01
#> "054" "04" "071" "02" "071" "04"
#> TCGA.BP.5174.11 TCGA.CJ.4901.11 TCGA.B8.A54D.01 TCGA.BP.4770.11 TCGA.CW.6093.01 TCGA.BP.5010.11
#> "011" "012" "02" "011" "061" "054"
#> TCGA.AK.3431.01 TCGA.BP.4770.01 TCGA.BP.5189.01 TCGA.B0.4703.11 TCGA.B8.5163.01 TCGA.CJ.5683.01
#> "04" "04" "04" "014" "04" "04"
#> TCGA.CZ.4856.11 TCGA.BP.4760.01 TCGA.B0.5692.01 TCGA.B0.5106.01 TCGA.B0.4843.01 TCGA.CZ.4866.11
#> "051" "03" "02" "02" "04" "051"
#> TCGA.B0.5104.11 TCGA.B0.4827.01 TCGA.CJ.4902.11 TCGA.B8.A54G.01 TCGA.B0.5703.01 TCGA.CJ.5672.01
#> "011" "02" "054" "04" "04" "04"
#> TCGA.B0.5098.11 TCGA.B0.5113.11 TCGA.CJ.4882.11 TCGA.CZ.5465.11 TCGA.B0.5102.01 TCGA.CW.5585.01
#> "013" "011" "012" "051" "04" "04"
#> TCGA.B0.4824.01 TCGA.B0.5115.01 TCGA.B0.4706.01 TCGA.B0.5117.11 TCGA.CZ.4859.11 TCGA.AK.3450.01
#> "04" "02" "02" "012" "054" "04"
#> TCGA.B8.A54I.01 TCGA.CZ.5463.01 TCGA.DV.5568.01 TCGA.CZ.5459.11 TCGA.CJ.4918.11 TCGA.DV.5565.01
#> "02" "02" "04" "014" "014" "04"
#> TCGA.B0.5119.01 TCGA.B0.4811.01 TCGA.A3.3367.11 TCGA.CJ.4916.01 TCGA.B0.5693.01 TCGA.CZ.4863.11
#> "062" "04" "014" "04" "04" "051"
#> TCGA.G6.A5PC.01 TCGA.B8.5550.01 TCGA.DV.A4W0.05 TCGA.B0.4696.01 TCGA.BP.5187.01 TCGA.CZ.5466.11
#> "02" "04" "03" "02" "04" "014"
#> TCGA.CW.6097.01 TCGA.CJ.4905.11 TCGA.CZ.5989.01 TCGA.BP.5194.01 TCGA.B0.4707.11 TCGA.CZ.5467.01
#> "04" "052" "04" "04" "014" "04"
#> TCGA.BP.5185.11 TCGA.BP.5183.11 TCGA.BP.5192.01 TCGA.CZ.5462.11 TCGA.BP.4177.01 TCGA.CZ.5469.01
#> "012" "012" "061" "051" "03" "02"
#> TCGA.B2.5641.01 TCGA.BP.5196.11 TCGA.CZ.5460.01 TCGA.B0.4712.01 TCGA.B8.A54K.01 TCGA.B0.5707.01
#> "02" "012" "02" "02" "03" "062"
#> TCGA.BP.5186.11 TCGA.EU.5906.01 TCGA.CZ.5461.11 TCGA.CW.5590.01 TCGA.B0.5698.01 TCGA.CW.5580.01
#> "011" "061" "054" "02" "02" "02"
#> TCGA.CZ.5454.01 TCGA.B0.4815.01 TCGA.B0.5710.11 TCGA.CJ.4908.11 TCGA.BP.5201.11 TCGA.B0.5694.01
#> "02" "02" "012" "054" "012" "02"
#> TCGA.BP.5170.01 TCGA.DV.5575.01 TCGA.CJ.5686.01 TCGA.A3.3357.01 TCGA.A3.3373.01 TCGA.B0.5690.01
#> "04" "062" "04" "02" "04" "062"
#> TCGA.B8.4622.01 TCGA.AK.3433.01 TCGA.B0.5110.01 TCGA.BP.5180.11 TCGA.CJ.4913.01 TCGA.CJ.4908.01
#> "02" "053" "062" "012" "02" "04"
#> TCGA.BP.4795.01 TCGA.CJ.4897.11 TCGA.B2.5636.01 TCGA.CJ.4923.11 TCGA.B0.4819.01 TCGA.B2.5633.01
#> "03" "011" "03" "014" "04" "04"
#> TCGA.CJ.6033.01 TCGA.BP.5181.11 TCGA.B0.4698.01 TCGA.B0.5083.11 TCGA.CZ.4864.11 TCGA.B0.4688.01
#> "02" "011" "02" "012" "014" "02"
#> TCGA.BP.5168.01 TCGA.BP.5198.11 TCGA.B8.5162.01 TCGA.B0.5096.01 TCGA.BP.5178.01 TCGA.B0.5099.11
#> "04" "014" "04" "02" "02" "011"
#> TCGA.B0.4842.01 TCGA.BP.5169.11 TCGA.B0.5109.11 TCGA.CJ.4920.11 TCGA.B0.5080.11 TCGA.B0.5700.01
#> "04" "014" "071" "054" "012" "061"
#> TCGA.B0.4847.01 TCGA.B0.5702.01 TCGA.CJ.4905.01 TCGA.B2.5635.01 TCGA.B0.5107.01 TCGA.CW.5584.01
#> "02" "071" "04" "04" "02" "02"
#> TCGA.B4.5838.01 TCGA.BP.5199.01 TCGA.A3.3376.01 TCGA.B0.4845.11 TCGA.B0.4699.11 TCGA.BP.5174.01
#> "04" "02" "061" "054" "014" "062"
#> TCGA.CZ.5986.01 TCGA.CJ.4901.01 TCGA.AK.3461.01 TCGA.AK.3460.01 TCGA.AK.3454.01 TCGA.CZ.4859.01
#> "061" "02" "04" "04" "061" "062"
#> TCGA.B0.5812.01 TCGA.B0.5116.11 TCGA.B8.A54F.01 TCGA.CW.6090.01 TCGA.CZ.5458.11 TCGA.B0.5106.11
#> "04" "071" "04" "02" "051" "012"
#> TCGA.CZ.4866.01 TCGA.B0.4828.01 TCGA.AK.3440.01 TCGA.MM.A563.01 TCGA.B0.4697.01 TCGA.AK.3458.01
#> "02" "02" "053" "02" "04" "02"
#> TCGA.CJ.5676.01 TCGA.B0.5402.11 TCGA.CJ.5681.01 TCGA.A3.3370.11 TCGA.A3.A6NL.01 TCGA.B0.4693.01
#> "02" "014" "073" "052" "062" "02"
#> TCGA.A3.3358.01 TCGA.B0.4710.01 TCGA.CZ.4853.11 TCGA.B4.5835.01 TCGA.CJ.4882.01 TCGA.CZ.5465.01
#> "04" "02" "054" "062" "04" "02"
#> TCGA.B0.5102.11 TCGA.B0.4824.11 TCGA.CJ.5675.01 TCGA.B0.4700.01 TCGA.B0.5092.01 TCGA.B0.5115.11
#> "011" "011" "02" "04" "04" "012"
#> TCGA.B0.4945.11 TCGA.B8.5158.01 TCGA.CJ.6030.01 TCGA.B8.A54E.01 TCGA.CJ.6032.01 TCGA.B0.4852.11
#> "011" "02" "02" "072" "04" "011"
#> TCGA.B0.4817.01 TCGA.B8.5159.01 TCGA.A3.A8OW.01 TCGA.B0.4822.01 TCGA.B0.5696.01 TCGA.B0.5706.01
#> "04" "02" "061" "04" "04" "02"
#> TCGA.CJ.4918.01 TCGA.B0.5119.11 TCGA.BP.5200.11 TCGA.B0.4811.11 TCGA.A3.3367.01 TCGA.B0.5097.01
#> "04" "051" "012" "014" "02" "04"
#> TCGA.6D.AA2E.01 TCGA.DV.A4VX.01 TCGA.B0.4816.11 TCGA.A3.3385.11 TCGA.DV.5569.01 TCGA.EU.5907.01
#> "072" "02" "054" "011" "062" "02"
#> TCGA.CZ.5455.01 TCGA.B8.5545.01 TCGA.DV.5567.01 TCGA.CZ.5451.01 TCGA.CJ.4869.01 TCGA.CJ.5678.01
#> "04" "061" "03" "04" "04" "02"
#> TCGA.B8.4153.01 TCGA.B0.5121.11 TCGA.B8.4146.01 TCGA.BP.5183.01 TCGA.B0.5399.01 TCGA.B0.4810.11
#> "02" "012" "04" "02" "04" "052"
#> TCGA.AK.3445.01 TCGA.B4.5378.01 TCGA.BP.5196.01 TCGA.CZ.4865.11 TCGA.B0.5709.01 TCGA.B0.4712.11
#> "02" "03" "02" "051" "062" "051"
#> TCGA.B0.4714.01 TCGA.B8.5549.01 TCGA.CZ.5461.01 TCGA.CZ.5457.01 TCGA.A3.A8CQ.01 TCGA.DV.5573.01
#> "02" "02" "02" "063" "062" "061"
#> TCGA.B0.4815.11 TCGA.B0.5710.01 TCGA.B8.5165.01 TCGA.B0.4718.01 TCGA.B2.5639.01 TCGA.CW.5583.01
#> "014" "02" "061" "02" "04" "062"
#> TCGA.GK.A6C7.01 TCGA.A3.3357.11 TCGA.B8.5552.01 TCGA.B0.5120.01 TCGA.A3.3373.11 TCGA.BP.5185.01
#> "062" "012" "062" "04" "054" "04"
#> TCGA.B0.4846.01 TCGA.CJ.4904.01 TCGA.CJ.4913.11 TCGA.BP.4993.11 TCGA.B0.4823.11 TCGA.CJ.4897.01
#> "04" "062" "011" "012" "013" "04"
#> TCGA.BP.4993.01 TCGA.B4.5843.01 TCGA.DV.5576.01 TCGA.CJ.4923.01 TCGA.B0.4819.11 TCGA.BP.5175.01
#> "061" "061" "03" "04" "011" "02"
#> TCGA.CZ.5987.01 TCGA.CZ.4864.01 TCGA.B0.4688.11 TCGA.BP.5168.11 TCGA.BP.5198.01 TCGA.B8.A7U6.01
#> "02" "061" "054" "014" "02" "04"
#> TCGA.B0.5094.01 TCGA.T7.A92I.01 TCGA.B0.5096.11 TCGA.B0.5400.11 TCGA.B0.4694.11 TCGA.B0.5099.01
#> "02" "072" "011" "011" "052" "04"
#> TCGA.CZ.5468.01 TCGA.B0.4842.11 TCGA.CZ.5988.01 TCGA.BP.5169.01 TCGA.B0.5109.01 TCGA.B4.5834.01
#> "02" "011" "04" "02" "04" "061"
#> TCGA.B0.5095.11 TCGA.B0.5080.01 TCGA.CJ.5680.01 TCGA.CZ.5470.01 TCGA.CZ.4865.01 TCGA.A3.A8OX.01
#> "013" "04" "02" "02" "04" "072"
#> TCGA.B0.4690.11 TCGA.CJ.5684.01 TCGA.B0.4844.01 TCGA.CZ.5464.01 TCGA.B0.4701.01 TCGA.B0.5701.01
#> "013" "04" "02" "02" "04" "02"
#> TCGA.BP.5199.11 TCGA.CJ.5671.01 TCGA.A3.A8OV.01 TCGA.CZ.5456.11 TCGA.B0.5116.01 TCGA.CZ.5458.01
#> "012" "02" "061" "051" "02" "04"
#> TCGA.CZ.5982.01 TCGA.B0.4828.11 TCGA.CJ.5679.01 TCGA.CJ.5682.01 TCGA.B0.5697.01 TCGA.B0.4697.11
#> "04" "054" "02" "02" "04" "051"
#> TCGA.BP.4782.11 TCGA.G6.A8L8.01 TCGA.A3.A6NJ.01 TCGA.A3.3370.01 TCGA.B0.4691.01 TCGA.CZ.5452.11
#> "011" "02" "062" "062" "02" "051"
#> TCGA.B0.4693.11 TCGA.B0.4945.01 TCGA.CZ.4853.01 TCGA.B0.5092.11 TCGA.B0.5402.01 TCGA.B0.4849.11
#> "011" "062" "02" "011" "02" "012"
#> TCGA.A3.A6NN.01 TCGA.B0.4852.01 TCGA.B0.4817.11 TCGA.BP.5176.11 TCGA.CW.5589.01 TCGA.CJ.5689.01
#> "04" "04" "014" "011" "061" "04"
#> TCGA.B0.4822.11 TCGA.BP.5190.11 TCGA.B0.4813.01 TCGA.BP.5200.01 TCGA.G6.A8L7.01 TCGA.B2.4101.01
#> "052" "012" "02" "04" "02" "04"
#> TCGA.B0.4713.11 TCGA.B0.4816.01 TCGA.A3.3385.01 TCGA.B2.3924.01 TCGA.CZ.5455.11 TCGA.B0.5713.01
#> "011" "04" "062" "04" "051" "04"
#> TCGA.B0.5108.01 TCGA.B0.5711.01 TCGA.CZ.5453.01 TCGA.BP.5202.11 TCGA.BP.5173.01 TCGA.CZ.5451.11
#> "04" "04" "061" "071" "061" "012"
#> TCGA.B8.A8YJ.01 TCGA.B0.4848.01 TCGA.DV.A4VZ.01 TCGA.B0.4814.11 TCGA.CJ.4869.11 TCGA.CJ.4907.11
#> "062" "02" "03" "012" "012" "012"
#> TCGA.B8.5553.01 TCGA.MW.A4EC.01 TCGA.B0.5712.11 TCGA.EU.5905.01 TCGA.CZ.5985.01 TCGA.CZ.4856.01
#> "04" "04" "011" "04" "02" "04"
#> TCGA.BP.5184.01 TCGA.B0.5121.01 TCGA.BP.5191.01 TCGA.BP.4801.11 TCGA.BP.5177.01 TCGA.B0.5110.11
#> "04" "02" "02" "012" "062" "011"
#> TCGA.B0.4810.01 TCGA.CJ.4903.11 TCGA.CJ.4912.11 TCGA.B8.4621.01 TCGA.B4.5832.01 TCGA.CW.6088.01
#> "02" "012" "054" "063" "04" "061"
#> TCGA.AK.3428.01 TCGA.B8.5164.01 TCGA.BP.5195.01 TCGA.CJ.6027.01 TCGA.3Z.A93Z.01 TCGA.B0.4714.11
#> "02" "04" "04" "02" "061" "014"
#> TCGA.B0.4818.11 TCGA.CZ.5457.11 TCGA.BP.5010.01 TCGA.BP.5189.11 TCGA.B0.4703.01 TCGA.B0.4718.11
#> "011" "051" "04" "012" "04" "052"
#> TCGA.B0.5097.11 TCGA.BP.4760.11 TCGA.B0.5120.11 TCGA.B0.4843.11 TCGA.B0.5104.01 TCGA.CW.5587.01
#> "011" "014" "011" "012" "04" "04"
get_classes(res_rh, merge_node = merge_node_param(min_n_signatures = 4860))
#> TCGA.CZ.4863.01 TCGA.CJ.4904.11 TCGA.B0.4827.11 TCGA.CJ.4902.01 TCGA.B0.4823.01 TCGA.CW.6087.01
#> "04" "01" "054" "04" "061" "04"
#> TCGA.B0.5098.01 TCGA.B0.5113.01 TCGA.DV.5566.01 TCGA.BP.5175.11 TCGA.BP.5181.01 TCGA.B0.4706.11
#> "073" "02" "04" "01" "062" "01"
#> TCGA.B0.5117.01 TCGA.MM.A564.01 TCGA.B0.4821.11 TCGA.CZ.5463.11 TCGA.BP.5182.11 TCGA.DV.5574.01
#> "01" "02" "072" "051" "01" "061"
#> TCGA.B0.5094.11 TCGA.MM.A84U.01 TCGA.B0.5100.11 TCGA.B4.5844.01 TCGA.CZ.5459.01 TCGA.B0.4694.01
#> "01" "04" "01" "04" "04" "04"
#> TCGA.CZ.5468.11 TCGA.CJ.4916.11 TCGA.B4.5836.01 TCGA.B0.5095.01 TCGA.B0.4846.11 TCGA.AK.3434.01
#> "051" "01" "04" "04" "01" "02"
#> TCGA.B4.5377.01 TCGA.B0.4696.11 TCGA.BP.5187.11 TCGA.B0.4690.01 TCGA.CZ.5466.01 TCGA.B0.4844.11
#> "062" "01" "01" "04" "04" "052"
#> TCGA.CZ.5464.11 TCGA.B0.4701.11 TCGA.BP.5194.11 TCGA.B0.4707.01 TCGA.CZ.5467.11 TCGA.B0.5705.01
#> "01" "01" "01" "02" "051" "062"
#> TCGA.CW.5588.01 TCGA.CJ.6031.01 TCGA.B8.A54J.01 TCGA.BP.5192.11 TCGA.CZ.5462.01 TCGA.B8.A54H.01
#> "04" "04" "04" "052" "04" "04"
#> TCGA.CZ.5470.11 TCGA.BP.4177.11 TCGA.CZ.5469.11 TCGA.CJ.6028.01 TCGA.G6.A8L6.01 TCGA.B8.5551.01
#> "051" "052" "051" "04" "04" "04"
#> TCGA.CZ.5456.01 TCGA.A3.A8OU.01 TCGA.BP.5186.01 TCGA.A3.A6NI.01 TCGA.BP.4782.01 TCGA.CZ.5454.11
#> "02" "04" "062" "04" "04" "054"
#> TCGA.B0.4691.11 TCGA.CZ.5452.01 TCGA.EU.5904.01 TCGA.BP.5201.01 TCGA.CJ.5677.01 TCGA.BP.5170.11
#> "01" "02" "062" "02" "02" "054"
#> TCGA.B0.4710.11 TCGA.AK.3425.01 TCGA.B0.4841.11 TCGA.B0.4849.01 TCGA.BP.5182.01 TCGA.B0.5711.11
#> "051" "02" "01" "04" "063" "052"
#> TCGA.BP.5180.01 TCGA.BP.5176.01 TCGA.CZ.5984.01 TCGA.CZ.5460.11 TCGA.BP.5190.01 TCGA.BP.4795.11
#> "02" "04" "02" "01" "02" "01"
#> TCGA.B0.4813.11 TCGA.B0.4713.01 TCGA.B0.4841.01 TCGA.B8.5546.01 TCGA.CW.5591.01 TCGA.B0.4698.11
#> "054" "02" "02" "072" "04" "01"
#> TCGA.B0.5713.11 TCGA.B0.5108.11 TCGA.B0.5083.01 TCGA.B0.5699.01 TCGA.CZ.5453.11 TCGA.BP.5202.01
#> "01" "01" "01" "02" "051" "02"
#> TCGA.BP.5173.11 TCGA.CW.5581.01 TCGA.B0.4848.11 TCGA.B0.4814.01 TCGA.BP.5178.11 TCGA.CJ.4907.01
#> "01" "04" "01" "02" "01" "04"
#> TCGA.A3.3387.01 TCGA.B0.4821.01 TCGA.B0.5712.01 TCGA.B0.5695.01 TCGA.BP.5184.11 TCGA.B2.A4SR.01
#> "04" "02" "02" "062" "01" "04"
#> TCGA.BP.5191.11 TCGA.CJ.4920.01 TCGA.BP.4801.01 TCGA.DV.A4W0.01 TCGA.BP.5177.11 TCGA.B0.4847.11
#> "01" "02" "04" "02" "01" "052"
#> TCGA.B0.5100.01 TCGA.CJ.4903.01 TCGA.CJ.4912.01 TCGA.B0.5107.11 TCGA.AK.3453.01 TCGA.B0.5691.01
#> "04" "02" "02" "01" "01" "062"
#> TCGA.BP.5195.11 TCGA.B0.5400.01 TCGA.A3.3376.11 TCGA.B0.4845.01 TCGA.B0.4699.01 TCGA.B0.4818.01
#> "054" "04" "071" "02" "071" "04"
#> TCGA.BP.5174.11 TCGA.CJ.4901.11 TCGA.B8.A54D.01 TCGA.BP.4770.11 TCGA.CW.6093.01 TCGA.BP.5010.11
#> "01" "01" "02" "01" "061" "054"
#> TCGA.AK.3431.01 TCGA.BP.4770.01 TCGA.BP.5189.01 TCGA.B0.4703.11 TCGA.B8.5163.01 TCGA.CJ.5683.01
#> "04" "04" "04" "01" "04" "04"
#> TCGA.CZ.4856.11 TCGA.BP.4760.01 TCGA.B0.5692.01 TCGA.B0.5106.01 TCGA.B0.4843.01 TCGA.CZ.4866.11
#> "051" "03" "02" "02" "04" "051"
#> TCGA.B0.5104.11 TCGA.B0.4827.01 TCGA.CJ.4902.11 TCGA.B8.A54G.01 TCGA.B0.5703.01 TCGA.CJ.5672.01
#> "01" "02" "054" "04" "04" "04"
#> TCGA.B0.5098.11 TCGA.B0.5113.11 TCGA.CJ.4882.11 TCGA.CZ.5465.11 TCGA.B0.5102.01 TCGA.CW.5585.01
#> "01" "01" "01" "051" "04" "04"
#> TCGA.B0.4824.01 TCGA.B0.5115.01 TCGA.B0.4706.01 TCGA.B0.5117.11 TCGA.CZ.4859.11 TCGA.AK.3450.01
#> "04" "02" "02" "01" "054" "04"
#> TCGA.B8.A54I.01 TCGA.CZ.5463.01 TCGA.DV.5568.01 TCGA.CZ.5459.11 TCGA.CJ.4918.11 TCGA.DV.5565.01
#> "02" "02" "04" "01" "01" "04"
#> TCGA.B0.5119.01 TCGA.B0.4811.01 TCGA.A3.3367.11 TCGA.CJ.4916.01 TCGA.B0.5693.01 TCGA.CZ.4863.11
#> "062" "04" "01" "04" "04" "051"
#> TCGA.G6.A5PC.01 TCGA.B8.5550.01 TCGA.DV.A4W0.05 TCGA.B0.4696.01 TCGA.BP.5187.01 TCGA.CZ.5466.11
#> "02" "04" "03" "02" "04" "01"
#> TCGA.CW.6097.01 TCGA.CJ.4905.11 TCGA.CZ.5989.01 TCGA.BP.5194.01 TCGA.B0.4707.11 TCGA.CZ.5467.01
#> "04" "052" "04" "04" "01" "04"
#> TCGA.BP.5185.11 TCGA.BP.5183.11 TCGA.BP.5192.01 TCGA.CZ.5462.11 TCGA.BP.4177.01 TCGA.CZ.5469.01
#> "01" "01" "061" "051" "03" "02"
#> TCGA.B2.5641.01 TCGA.BP.5196.11 TCGA.CZ.5460.01 TCGA.B0.4712.01 TCGA.B8.A54K.01 TCGA.B0.5707.01
#> "02" "01" "02" "02" "03" "062"
#> TCGA.BP.5186.11 TCGA.EU.5906.01 TCGA.CZ.5461.11 TCGA.CW.5590.01 TCGA.B0.5698.01 TCGA.CW.5580.01
#> "01" "061" "054" "02" "02" "02"
#> TCGA.CZ.5454.01 TCGA.B0.4815.01 TCGA.B0.5710.11 TCGA.CJ.4908.11 TCGA.BP.5201.11 TCGA.B0.5694.01
#> "02" "02" "01" "054" "01" "02"
#> TCGA.BP.5170.01 TCGA.DV.5575.01 TCGA.CJ.5686.01 TCGA.A3.3357.01 TCGA.A3.3373.01 TCGA.B0.5690.01
#> "04" "062" "04" "02" "04" "062"
#> TCGA.B8.4622.01 TCGA.AK.3433.01 TCGA.B0.5110.01 TCGA.BP.5180.11 TCGA.CJ.4913.01 TCGA.CJ.4908.01
#> "02" "053" "062" "01" "02" "04"
#> TCGA.BP.4795.01 TCGA.CJ.4897.11 TCGA.B2.5636.01 TCGA.CJ.4923.11 TCGA.B0.4819.01 TCGA.B2.5633.01
#> "03" "01" "03" "01" "04" "04"
#> TCGA.CJ.6033.01 TCGA.BP.5181.11 TCGA.B0.4698.01 TCGA.B0.5083.11 TCGA.CZ.4864.11 TCGA.B0.4688.01
#> "02" "01" "02" "01" "01" "02"
#> TCGA.BP.5168.01 TCGA.BP.5198.11 TCGA.B8.5162.01 TCGA.B0.5096.01 TCGA.BP.5178.01 TCGA.B0.5099.11
#> "04" "01" "04" "02" "02" "01"
#> TCGA.B0.4842.01 TCGA.BP.5169.11 TCGA.B0.5109.11 TCGA.CJ.4920.11 TCGA.B0.5080.11 TCGA.B0.5700.01
#> "04" "01" "071" "054" "01" "061"
#> TCGA.B0.4847.01 TCGA.B0.5702.01 TCGA.CJ.4905.01 TCGA.B2.5635.01 TCGA.B0.5107.01 TCGA.CW.5584.01
#> "02" "071" "04" "04" "02" "02"
#> TCGA.B4.5838.01 TCGA.BP.5199.01 TCGA.A3.3376.01 TCGA.B0.4845.11 TCGA.B0.4699.11 TCGA.BP.5174.01
#> "04" "02" "061" "054" "01" "062"
#> TCGA.CZ.5986.01 TCGA.CJ.4901.01 TCGA.AK.3461.01 TCGA.AK.3460.01 TCGA.AK.3454.01 TCGA.CZ.4859.01
#> "061" "02" "04" "04" "061" "062"
#> TCGA.B0.5812.01 TCGA.B0.5116.11 TCGA.B8.A54F.01 TCGA.CW.6090.01 TCGA.CZ.5458.11 TCGA.B0.5106.11
#> "04" "071" "04" "02" "051" "01"
#> TCGA.CZ.4866.01 TCGA.B0.4828.01 TCGA.AK.3440.01 TCGA.MM.A563.01 TCGA.B0.4697.01 TCGA.AK.3458.01
#> "02" "02" "053" "02" "04" "02"
#> TCGA.CJ.5676.01 TCGA.B0.5402.11 TCGA.CJ.5681.01 TCGA.A3.3370.11 TCGA.A3.A6NL.01 TCGA.B0.4693.01
#> "02" "01" "073" "052" "062" "02"
#> TCGA.A3.3358.01 TCGA.B0.4710.01 TCGA.CZ.4853.11 TCGA.B4.5835.01 TCGA.CJ.4882.01 TCGA.CZ.5465.01
#> "04" "02" "054" "062" "04" "02"
#> TCGA.B0.5102.11 TCGA.B0.4824.11 TCGA.CJ.5675.01 TCGA.B0.4700.01 TCGA.B0.5092.01 TCGA.B0.5115.11
#> "01" "01" "02" "04" "04" "01"
#> TCGA.B0.4945.11 TCGA.B8.5158.01 TCGA.CJ.6030.01 TCGA.B8.A54E.01 TCGA.CJ.6032.01 TCGA.B0.4852.11
#> "01" "02" "02" "072" "04" "01"
#> TCGA.B0.4817.01 TCGA.B8.5159.01 TCGA.A3.A8OW.01 TCGA.B0.4822.01 TCGA.B0.5696.01 TCGA.B0.5706.01
#> "04" "02" "061" "04" "04" "02"
#> TCGA.CJ.4918.01 TCGA.B0.5119.11 TCGA.BP.5200.11 TCGA.B0.4811.11 TCGA.A3.3367.01 TCGA.B0.5097.01
#> "04" "051" "01" "01" "02" "04"
#> TCGA.6D.AA2E.01 TCGA.DV.A4VX.01 TCGA.B0.4816.11 TCGA.A3.3385.11 TCGA.DV.5569.01 TCGA.EU.5907.01
#> "072" "02" "054" "01" "062" "02"
#> TCGA.CZ.5455.01 TCGA.B8.5545.01 TCGA.DV.5567.01 TCGA.CZ.5451.01 TCGA.CJ.4869.01 TCGA.CJ.5678.01
#> "04" "061" "03" "04" "04" "02"
#> TCGA.B8.4153.01 TCGA.B0.5121.11 TCGA.B8.4146.01 TCGA.BP.5183.01 TCGA.B0.5399.01 TCGA.B0.4810.11
#> "02" "01" "04" "02" "04" "052"
#> TCGA.AK.3445.01 TCGA.B4.5378.01 TCGA.BP.5196.01 TCGA.CZ.4865.11 TCGA.B0.5709.01 TCGA.B0.4712.11
#> "02" "03" "02" "051" "062" "051"
#> TCGA.B0.4714.01 TCGA.B8.5549.01 TCGA.CZ.5461.01 TCGA.CZ.5457.01 TCGA.A3.A8CQ.01 TCGA.DV.5573.01
#> "02" "02" "02" "063" "062" "061"
#> TCGA.B0.4815.11 TCGA.B0.5710.01 TCGA.B8.5165.01 TCGA.B0.4718.01 TCGA.B2.5639.01 TCGA.CW.5583.01
#> "01" "02" "061" "02" "04" "062"
#> TCGA.GK.A6C7.01 TCGA.A3.3357.11 TCGA.B8.5552.01 TCGA.B0.5120.01 TCGA.A3.3373.11 TCGA.BP.5185.01
#> "062" "01" "062" "04" "054" "04"
#> TCGA.B0.4846.01 TCGA.CJ.4904.01 TCGA.CJ.4913.11 TCGA.BP.4993.11 TCGA.B0.4823.11 TCGA.CJ.4897.01
#> "04" "062" "01" "01" "01" "04"
#> TCGA.BP.4993.01 TCGA.B4.5843.01 TCGA.DV.5576.01 TCGA.CJ.4923.01 TCGA.B0.4819.11 TCGA.BP.5175.01
#> "061" "061" "03" "04" "01" "02"
#> TCGA.CZ.5987.01 TCGA.CZ.4864.01 TCGA.B0.4688.11 TCGA.BP.5168.11 TCGA.BP.5198.01 TCGA.B8.A7U6.01
#> "02" "061" "054" "01" "02" "04"
#> TCGA.B0.5094.01 TCGA.T7.A92I.01 TCGA.B0.5096.11 TCGA.B0.5400.11 TCGA.B0.4694.11 TCGA.B0.5099.01
#> "02" "072" "01" "01" "052" "04"
#> TCGA.CZ.5468.01 TCGA.B0.4842.11 TCGA.CZ.5988.01 TCGA.BP.5169.01 TCGA.B0.5109.01 TCGA.B4.5834.01
#> "02" "01" "04" "02" "04" "061"
#> TCGA.B0.5095.11 TCGA.B0.5080.01 TCGA.CJ.5680.01 TCGA.CZ.5470.01 TCGA.CZ.4865.01 TCGA.A3.A8OX.01
#> "01" "04" "02" "02" "04" "072"
#> TCGA.B0.4690.11 TCGA.CJ.5684.01 TCGA.B0.4844.01 TCGA.CZ.5464.01 TCGA.B0.4701.01 TCGA.B0.5701.01
#> "01" "04" "02" "02" "04" "02"
#> TCGA.BP.5199.11 TCGA.CJ.5671.01 TCGA.A3.A8OV.01 TCGA.CZ.5456.11 TCGA.B0.5116.01 TCGA.CZ.5458.01
#> "01" "02" "061" "051" "02" "04"
#> TCGA.CZ.5982.01 TCGA.B0.4828.11 TCGA.CJ.5679.01 TCGA.CJ.5682.01 TCGA.B0.5697.01 TCGA.B0.4697.11
#> "04" "054" "02" "02" "04" "051"
#> TCGA.BP.4782.11 TCGA.G6.A8L8.01 TCGA.A3.A6NJ.01 TCGA.A3.3370.01 TCGA.B0.4691.01 TCGA.CZ.5452.11
#> "01" "02" "062" "062" "02" "051"
#> TCGA.B0.4693.11 TCGA.B0.4945.01 TCGA.CZ.4853.01 TCGA.B0.5092.11 TCGA.B0.5402.01 TCGA.B0.4849.11
#> "01" "062" "02" "01" "02" "01"
#> TCGA.A3.A6NN.01 TCGA.B0.4852.01 TCGA.B0.4817.11 TCGA.BP.5176.11 TCGA.CW.5589.01 TCGA.CJ.5689.01
#> "04" "04" "01" "01" "061" "04"
#> TCGA.B0.4822.11 TCGA.BP.5190.11 TCGA.B0.4813.01 TCGA.BP.5200.01 TCGA.G6.A8L7.01 TCGA.B2.4101.01
#> "052" "01" "02" "04" "02" "04"
#> TCGA.B0.4713.11 TCGA.B0.4816.01 TCGA.A3.3385.01 TCGA.B2.3924.01 TCGA.CZ.5455.11 TCGA.B0.5713.01
#> "01" "04" "062" "04" "051" "04"
#> TCGA.B0.5108.01 TCGA.B0.5711.01 TCGA.CZ.5453.01 TCGA.BP.5202.11 TCGA.BP.5173.01 TCGA.CZ.5451.11
#> "04" "04" "061" "071" "061" "01"
#> TCGA.B8.A8YJ.01 TCGA.B0.4848.01 TCGA.DV.A4VZ.01 TCGA.B0.4814.11 TCGA.CJ.4869.11 TCGA.CJ.4907.11
#> "062" "02" "03" "01" "01" "01"
#> TCGA.B8.5553.01 TCGA.MW.A4EC.01 TCGA.B0.5712.11 TCGA.EU.5905.01 TCGA.CZ.5985.01 TCGA.CZ.4856.01
#> "04" "04" "01" "04" "02" "04"
#> TCGA.BP.5184.01 TCGA.B0.5121.01 TCGA.BP.5191.01 TCGA.BP.4801.11 TCGA.BP.5177.01 TCGA.B0.5110.11
#> "04" "02" "02" "01" "062" "01"
#> TCGA.B0.4810.01 TCGA.CJ.4903.11 TCGA.CJ.4912.11 TCGA.B8.4621.01 TCGA.B4.5832.01 TCGA.CW.6088.01
#> "02" "01" "054" "063" "04" "061"
#> TCGA.AK.3428.01 TCGA.B8.5164.01 TCGA.BP.5195.01 TCGA.CJ.6027.01 TCGA.3Z.A93Z.01 TCGA.B0.4714.11
#> "02" "04" "04" "02" "061" "01"
#> TCGA.B0.4818.11 TCGA.CZ.5457.11 TCGA.BP.5010.01 TCGA.BP.5189.11 TCGA.B0.4703.01 TCGA.B0.4718.11
#> "01" "051" "04" "01" "04" "052"
#> TCGA.B0.5097.11 TCGA.BP.4760.11 TCGA.B0.5120.11 TCGA.B0.4843.11 TCGA.B0.5104.01 TCGA.CW.5587.01
#> "01" "01" "01" "01" "04" "04"
get_classes(res_rh, merge_node = merge_node_param(min_n_signatures = 5214))
#> TCGA.CZ.4863.01 TCGA.CJ.4904.11 TCGA.B0.4827.11 TCGA.CJ.4902.01 TCGA.B0.4823.01 TCGA.CW.6087.01
#> "04" "01" "054" "04" "06" "04"
#> TCGA.B0.5098.01 TCGA.B0.5113.01 TCGA.DV.5566.01 TCGA.BP.5175.11 TCGA.BP.5181.01 TCGA.B0.4706.11
#> "073" "02" "04" "01" "06" "01"
#> TCGA.B0.5117.01 TCGA.MM.A564.01 TCGA.B0.4821.11 TCGA.CZ.5463.11 TCGA.BP.5182.11 TCGA.DV.5574.01
#> "01" "02" "072" "051" "01" "06"
#> TCGA.B0.5094.11 TCGA.MM.A84U.01 TCGA.B0.5100.11 TCGA.B4.5844.01 TCGA.CZ.5459.01 TCGA.B0.4694.01
#> "01" "04" "01" "04" "04" "04"
#> TCGA.CZ.5468.11 TCGA.CJ.4916.11 TCGA.B4.5836.01 TCGA.B0.5095.01 TCGA.B0.4846.11 TCGA.AK.3434.01
#> "051" "01" "04" "04" "01" "02"
#> TCGA.B4.5377.01 TCGA.B0.4696.11 TCGA.BP.5187.11 TCGA.B0.4690.01 TCGA.CZ.5466.01 TCGA.B0.4844.11
#> "06" "01" "01" "04" "04" "052"
#> TCGA.CZ.5464.11 TCGA.B0.4701.11 TCGA.BP.5194.11 TCGA.B0.4707.01 TCGA.CZ.5467.11 TCGA.B0.5705.01
#> "01" "01" "01" "02" "051" "06"
#> TCGA.CW.5588.01 TCGA.CJ.6031.01 TCGA.B8.A54J.01 TCGA.BP.5192.11 TCGA.CZ.5462.01 TCGA.B8.A54H.01
#> "04" "04" "04" "052" "04" "04"
#> TCGA.CZ.5470.11 TCGA.BP.4177.11 TCGA.CZ.5469.11 TCGA.CJ.6028.01 TCGA.G6.A8L6.01 TCGA.B8.5551.01
#> "051" "052" "051" "04" "04" "04"
#> TCGA.CZ.5456.01 TCGA.A3.A8OU.01 TCGA.BP.5186.01 TCGA.A3.A6NI.01 TCGA.BP.4782.01 TCGA.CZ.5454.11
#> "02" "04" "06" "04" "04" "054"
#> TCGA.B0.4691.11 TCGA.CZ.5452.01 TCGA.EU.5904.01 TCGA.BP.5201.01 TCGA.CJ.5677.01 TCGA.BP.5170.11
#> "01" "02" "06" "02" "02" "054"
#> TCGA.B0.4710.11 TCGA.AK.3425.01 TCGA.B0.4841.11 TCGA.B0.4849.01 TCGA.BP.5182.01 TCGA.B0.5711.11
#> "051" "02" "01" "04" "06" "052"
#> TCGA.BP.5180.01 TCGA.BP.5176.01 TCGA.CZ.5984.01 TCGA.CZ.5460.11 TCGA.BP.5190.01 TCGA.BP.4795.11
#> "02" "04" "02" "01" "02" "01"
#> TCGA.B0.4813.11 TCGA.B0.4713.01 TCGA.B0.4841.01 TCGA.B8.5546.01 TCGA.CW.5591.01 TCGA.B0.4698.11
#> "054" "02" "02" "072" "04" "01"
#> TCGA.B0.5713.11 TCGA.B0.5108.11 TCGA.B0.5083.01 TCGA.B0.5699.01 TCGA.CZ.5453.11 TCGA.BP.5202.01
#> "01" "01" "01" "02" "051" "02"
#> TCGA.BP.5173.11 TCGA.CW.5581.01 TCGA.B0.4848.11 TCGA.B0.4814.01 TCGA.BP.5178.11 TCGA.CJ.4907.01
#> "01" "04" "01" "02" "01" "04"
#> TCGA.A3.3387.01 TCGA.B0.4821.01 TCGA.B0.5712.01 TCGA.B0.5695.01 TCGA.BP.5184.11 TCGA.B2.A4SR.01
#> "04" "02" "02" "06" "01" "04"
#> TCGA.BP.5191.11 TCGA.CJ.4920.01 TCGA.BP.4801.01 TCGA.DV.A4W0.01 TCGA.BP.5177.11 TCGA.B0.4847.11
#> "01" "02" "04" "02" "01" "052"
#> TCGA.B0.5100.01 TCGA.CJ.4903.01 TCGA.CJ.4912.01 TCGA.B0.5107.11 TCGA.AK.3453.01 TCGA.B0.5691.01
#> "04" "02" "02" "01" "01" "06"
#> TCGA.BP.5195.11 TCGA.B0.5400.01 TCGA.A3.3376.11 TCGA.B0.4845.01 TCGA.B0.4699.01 TCGA.B0.4818.01
#> "054" "04" "071" "02" "071" "04"
#> TCGA.BP.5174.11 TCGA.CJ.4901.11 TCGA.B8.A54D.01 TCGA.BP.4770.11 TCGA.CW.6093.01 TCGA.BP.5010.11
#> "01" "01" "02" "01" "06" "054"
#> TCGA.AK.3431.01 TCGA.BP.4770.01 TCGA.BP.5189.01 TCGA.B0.4703.11 TCGA.B8.5163.01 TCGA.CJ.5683.01
#> "04" "04" "04" "01" "04" "04"
#> TCGA.CZ.4856.11 TCGA.BP.4760.01 TCGA.B0.5692.01 TCGA.B0.5106.01 TCGA.B0.4843.01 TCGA.CZ.4866.11
#> "051" "03" "02" "02" "04" "051"
#> TCGA.B0.5104.11 TCGA.B0.4827.01 TCGA.CJ.4902.11 TCGA.B8.A54G.01 TCGA.B0.5703.01 TCGA.CJ.5672.01
#> "01" "02" "054" "04" "04" "04"
#> TCGA.B0.5098.11 TCGA.B0.5113.11 TCGA.CJ.4882.11 TCGA.CZ.5465.11 TCGA.B0.5102.01 TCGA.CW.5585.01
#> "01" "01" "01" "051" "04" "04"
#> TCGA.B0.4824.01 TCGA.B0.5115.01 TCGA.B0.4706.01 TCGA.B0.5117.11 TCGA.CZ.4859.11 TCGA.AK.3450.01
#> "04" "02" "02" "01" "054" "04"
#> TCGA.B8.A54I.01 TCGA.CZ.5463.01 TCGA.DV.5568.01 TCGA.CZ.5459.11 TCGA.CJ.4918.11 TCGA.DV.5565.01
#> "02" "02" "04" "01" "01" "04"
#> TCGA.B0.5119.01 TCGA.B0.4811.01 TCGA.A3.3367.11 TCGA.CJ.4916.01 TCGA.B0.5693.01 TCGA.CZ.4863.11
#> "06" "04" "01" "04" "04" "051"
#> TCGA.G6.A5PC.01 TCGA.B8.5550.01 TCGA.DV.A4W0.05 TCGA.B0.4696.01 TCGA.BP.5187.01 TCGA.CZ.5466.11
#> "02" "04" "03" "02" "04" "01"
#> TCGA.CW.6097.01 TCGA.CJ.4905.11 TCGA.CZ.5989.01 TCGA.BP.5194.01 TCGA.B0.4707.11 TCGA.CZ.5467.01
#> "04" "052" "04" "04" "01" "04"
#> TCGA.BP.5185.11 TCGA.BP.5183.11 TCGA.BP.5192.01 TCGA.CZ.5462.11 TCGA.BP.4177.01 TCGA.CZ.5469.01
#> "01" "01" "06" "051" "03" "02"
#> TCGA.B2.5641.01 TCGA.BP.5196.11 TCGA.CZ.5460.01 TCGA.B0.4712.01 TCGA.B8.A54K.01 TCGA.B0.5707.01
#> "02" "01" "02" "02" "03" "06"
#> TCGA.BP.5186.11 TCGA.EU.5906.01 TCGA.CZ.5461.11 TCGA.CW.5590.01 TCGA.B0.5698.01 TCGA.CW.5580.01
#> "01" "06" "054" "02" "02" "02"
#> TCGA.CZ.5454.01 TCGA.B0.4815.01 TCGA.B0.5710.11 TCGA.CJ.4908.11 TCGA.BP.5201.11 TCGA.B0.5694.01
#> "02" "02" "01" "054" "01" "02"
#> TCGA.BP.5170.01 TCGA.DV.5575.01 TCGA.CJ.5686.01 TCGA.A3.3357.01 TCGA.A3.3373.01 TCGA.B0.5690.01
#> "04" "06" "04" "02" "04" "06"
#> TCGA.B8.4622.01 TCGA.AK.3433.01 TCGA.B0.5110.01 TCGA.BP.5180.11 TCGA.CJ.4913.01 TCGA.CJ.4908.01
#> "02" "053" "06" "01" "02" "04"
#> TCGA.BP.4795.01 TCGA.CJ.4897.11 TCGA.B2.5636.01 TCGA.CJ.4923.11 TCGA.B0.4819.01 TCGA.B2.5633.01
#> "03" "01" "03" "01" "04" "04"
#> TCGA.CJ.6033.01 TCGA.BP.5181.11 TCGA.B0.4698.01 TCGA.B0.5083.11 TCGA.CZ.4864.11 TCGA.B0.4688.01
#> "02" "01" "02" "01" "01" "02"
#> TCGA.BP.5168.01 TCGA.BP.5198.11 TCGA.B8.5162.01 TCGA.B0.5096.01 TCGA.BP.5178.01 TCGA.B0.5099.11
#> "04" "01" "04" "02" "02" "01"
#> TCGA.B0.4842.01 TCGA.BP.5169.11 TCGA.B0.5109.11 TCGA.CJ.4920.11 TCGA.B0.5080.11 TCGA.B0.5700.01
#> "04" "01" "071" "054" "01" "06"
#> TCGA.B0.4847.01 TCGA.B0.5702.01 TCGA.CJ.4905.01 TCGA.B2.5635.01 TCGA.B0.5107.01 TCGA.CW.5584.01
#> "02" "071" "04" "04" "02" "02"
#> TCGA.B4.5838.01 TCGA.BP.5199.01 TCGA.A3.3376.01 TCGA.B0.4845.11 TCGA.B0.4699.11 TCGA.BP.5174.01
#> "04" "02" "06" "054" "01" "06"
#> TCGA.CZ.5986.01 TCGA.CJ.4901.01 TCGA.AK.3461.01 TCGA.AK.3460.01 TCGA.AK.3454.01 TCGA.CZ.4859.01
#> "06" "02" "04" "04" "06" "06"
#> TCGA.B0.5812.01 TCGA.B0.5116.11 TCGA.B8.A54F.01 TCGA.CW.6090.01 TCGA.CZ.5458.11 TCGA.B0.5106.11
#> "04" "071" "04" "02" "051" "01"
#> TCGA.CZ.4866.01 TCGA.B0.4828.01 TCGA.AK.3440.01 TCGA.MM.A563.01 TCGA.B0.4697.01 TCGA.AK.3458.01
#> "02" "02" "053" "02" "04" "02"
#> TCGA.CJ.5676.01 TCGA.B0.5402.11 TCGA.CJ.5681.01 TCGA.A3.3370.11 TCGA.A3.A6NL.01 TCGA.B0.4693.01
#> "02" "01" "073" "052" "06" "02"
#> TCGA.A3.3358.01 TCGA.B0.4710.01 TCGA.CZ.4853.11 TCGA.B4.5835.01 TCGA.CJ.4882.01 TCGA.CZ.5465.01
#> "04" "02" "054" "06" "04" "02"
#> TCGA.B0.5102.11 TCGA.B0.4824.11 TCGA.CJ.5675.01 TCGA.B0.4700.01 TCGA.B0.5092.01 TCGA.B0.5115.11
#> "01" "01" "02" "04" "04" "01"
#> TCGA.B0.4945.11 TCGA.B8.5158.01 TCGA.CJ.6030.01 TCGA.B8.A54E.01 TCGA.CJ.6032.01 TCGA.B0.4852.11
#> "01" "02" "02" "072" "04" "01"
#> TCGA.B0.4817.01 TCGA.B8.5159.01 TCGA.A3.A8OW.01 TCGA.B0.4822.01 TCGA.B0.5696.01 TCGA.B0.5706.01
#> "04" "02" "06" "04" "04" "02"
#> TCGA.CJ.4918.01 TCGA.B0.5119.11 TCGA.BP.5200.11 TCGA.B0.4811.11 TCGA.A3.3367.01 TCGA.B0.5097.01
#> "04" "051" "01" "01" "02" "04"
#> TCGA.6D.AA2E.01 TCGA.DV.A4VX.01 TCGA.B0.4816.11 TCGA.A3.3385.11 TCGA.DV.5569.01 TCGA.EU.5907.01
#> "072" "02" "054" "01" "06" "02"
#> TCGA.CZ.5455.01 TCGA.B8.5545.01 TCGA.DV.5567.01 TCGA.CZ.5451.01 TCGA.CJ.4869.01 TCGA.CJ.5678.01
#> "04" "06" "03" "04" "04" "02"
#> TCGA.B8.4153.01 TCGA.B0.5121.11 TCGA.B8.4146.01 TCGA.BP.5183.01 TCGA.B0.5399.01 TCGA.B0.4810.11
#> "02" "01" "04" "02" "04" "052"
#> TCGA.AK.3445.01 TCGA.B4.5378.01 TCGA.BP.5196.01 TCGA.CZ.4865.11 TCGA.B0.5709.01 TCGA.B0.4712.11
#> "02" "03" "02" "051" "06" "051"
#> TCGA.B0.4714.01 TCGA.B8.5549.01 TCGA.CZ.5461.01 TCGA.CZ.5457.01 TCGA.A3.A8CQ.01 TCGA.DV.5573.01
#> "02" "02" "02" "06" "06" "06"
#> TCGA.B0.4815.11 TCGA.B0.5710.01 TCGA.B8.5165.01 TCGA.B0.4718.01 TCGA.B2.5639.01 TCGA.CW.5583.01
#> "01" "02" "06" "02" "04" "06"
#> TCGA.GK.A6C7.01 TCGA.A3.3357.11 TCGA.B8.5552.01 TCGA.B0.5120.01 TCGA.A3.3373.11 TCGA.BP.5185.01
#> "06" "01" "06" "04" "054" "04"
#> TCGA.B0.4846.01 TCGA.CJ.4904.01 TCGA.CJ.4913.11 TCGA.BP.4993.11 TCGA.B0.4823.11 TCGA.CJ.4897.01
#> "04" "06" "01" "01" "01" "04"
#> TCGA.BP.4993.01 TCGA.B4.5843.01 TCGA.DV.5576.01 TCGA.CJ.4923.01 TCGA.B0.4819.11 TCGA.BP.5175.01
#> "06" "06" "03" "04" "01" "02"
#> TCGA.CZ.5987.01 TCGA.CZ.4864.01 TCGA.B0.4688.11 TCGA.BP.5168.11 TCGA.BP.5198.01 TCGA.B8.A7U6.01
#> "02" "06" "054" "01" "02" "04"
#> TCGA.B0.5094.01 TCGA.T7.A92I.01 TCGA.B0.5096.11 TCGA.B0.5400.11 TCGA.B0.4694.11 TCGA.B0.5099.01
#> "02" "072" "01" "01" "052" "04"
#> TCGA.CZ.5468.01 TCGA.B0.4842.11 TCGA.CZ.5988.01 TCGA.BP.5169.01 TCGA.B0.5109.01 TCGA.B4.5834.01
#> "02" "01" "04" "02" "04" "06"
#> TCGA.B0.5095.11 TCGA.B0.5080.01 TCGA.CJ.5680.01 TCGA.CZ.5470.01 TCGA.CZ.4865.01 TCGA.A3.A8OX.01
#> "01" "04" "02" "02" "04" "072"
#> TCGA.B0.4690.11 TCGA.CJ.5684.01 TCGA.B0.4844.01 TCGA.CZ.5464.01 TCGA.B0.4701.01 TCGA.B0.5701.01
#> "01" "04" "02" "02" "04" "02"
#> TCGA.BP.5199.11 TCGA.CJ.5671.01 TCGA.A3.A8OV.01 TCGA.CZ.5456.11 TCGA.B0.5116.01 TCGA.CZ.5458.01
#> "01" "02" "06" "051" "02" "04"
#> TCGA.CZ.5982.01 TCGA.B0.4828.11 TCGA.CJ.5679.01 TCGA.CJ.5682.01 TCGA.B0.5697.01 TCGA.B0.4697.11
#> "04" "054" "02" "02" "04" "051"
#> TCGA.BP.4782.11 TCGA.G6.A8L8.01 TCGA.A3.A6NJ.01 TCGA.A3.3370.01 TCGA.B0.4691.01 TCGA.CZ.5452.11
#> "01" "02" "06" "06" "02" "051"
#> TCGA.B0.4693.11 TCGA.B0.4945.01 TCGA.CZ.4853.01 TCGA.B0.5092.11 TCGA.B0.5402.01 TCGA.B0.4849.11
#> "01" "06" "02" "01" "02" "01"
#> TCGA.A3.A6NN.01 TCGA.B0.4852.01 TCGA.B0.4817.11 TCGA.BP.5176.11 TCGA.CW.5589.01 TCGA.CJ.5689.01
#> "04" "04" "01" "01" "06" "04"
#> TCGA.B0.4822.11 TCGA.BP.5190.11 TCGA.B0.4813.01 TCGA.BP.5200.01 TCGA.G6.A8L7.01 TCGA.B2.4101.01
#> "052" "01" "02" "04" "02" "04"
#> TCGA.B0.4713.11 TCGA.B0.4816.01 TCGA.A3.3385.01 TCGA.B2.3924.01 TCGA.CZ.5455.11 TCGA.B0.5713.01
#> "01" "04" "06" "04" "051" "04"
#> TCGA.B0.5108.01 TCGA.B0.5711.01 TCGA.CZ.5453.01 TCGA.BP.5202.11 TCGA.BP.5173.01 TCGA.CZ.5451.11
#> "04" "04" "06" "071" "06" "01"
#> TCGA.B8.A8YJ.01 TCGA.B0.4848.01 TCGA.DV.A4VZ.01 TCGA.B0.4814.11 TCGA.CJ.4869.11 TCGA.CJ.4907.11
#> "06" "02" "03" "01" "01" "01"
#> TCGA.B8.5553.01 TCGA.MW.A4EC.01 TCGA.B0.5712.11 TCGA.EU.5905.01 TCGA.CZ.5985.01 TCGA.CZ.4856.01
#> "04" "04" "01" "04" "02" "04"
#> TCGA.BP.5184.01 TCGA.B0.5121.01 TCGA.BP.5191.01 TCGA.BP.4801.11 TCGA.BP.5177.01 TCGA.B0.5110.11
#> "04" "02" "02" "01" "06" "01"
#> TCGA.B0.4810.01 TCGA.CJ.4903.11 TCGA.CJ.4912.11 TCGA.B8.4621.01 TCGA.B4.5832.01 TCGA.CW.6088.01
#> "02" "01" "054" "06" "04" "06"
#> TCGA.AK.3428.01 TCGA.B8.5164.01 TCGA.BP.5195.01 TCGA.CJ.6027.01 TCGA.3Z.A93Z.01 TCGA.B0.4714.11
#> "02" "04" "04" "02" "06" "01"
#> TCGA.B0.4818.11 TCGA.CZ.5457.11 TCGA.BP.5010.01 TCGA.BP.5189.11 TCGA.B0.4703.01 TCGA.B0.4718.11
#> "01" "051" "04" "01" "04" "052"
#> TCGA.B0.5097.11 TCGA.BP.4760.11 TCGA.B0.5120.11 TCGA.B0.4843.11 TCGA.B0.5104.01 TCGA.CW.5587.01
#> "01" "01" "01" "01" "04" "04"
get_classes(res_rh, merge_node = merge_node_param(min_n_signatures = 14438))
#> TCGA.CZ.4863.01 TCGA.CJ.4904.11 TCGA.B0.4827.11 TCGA.CJ.4902.01 TCGA.B0.4823.01 TCGA.CW.6087.01
#> "04" "01" "054" "04" "06" "04"
#> TCGA.B0.5098.01 TCGA.B0.5113.01 TCGA.DV.5566.01 TCGA.BP.5175.11 TCGA.BP.5181.01 TCGA.B0.4706.11
#> "07" "02" "04" "01" "06" "01"
#> TCGA.B0.5117.01 TCGA.MM.A564.01 TCGA.B0.4821.11 TCGA.CZ.5463.11 TCGA.BP.5182.11 TCGA.DV.5574.01
#> "01" "02" "07" "051" "01" "06"
#> TCGA.B0.5094.11 TCGA.MM.A84U.01 TCGA.B0.5100.11 TCGA.B4.5844.01 TCGA.CZ.5459.01 TCGA.B0.4694.01
#> "01" "04" "01" "04" "04" "04"
#> TCGA.CZ.5468.11 TCGA.CJ.4916.11 TCGA.B4.5836.01 TCGA.B0.5095.01 TCGA.B0.4846.11 TCGA.AK.3434.01
#> "051" "01" "04" "04" "01" "02"
#> TCGA.B4.5377.01 TCGA.B0.4696.11 TCGA.BP.5187.11 TCGA.B0.4690.01 TCGA.CZ.5466.01 TCGA.B0.4844.11
#> "06" "01" "01" "04" "04" "052"
#> TCGA.CZ.5464.11 TCGA.B0.4701.11 TCGA.BP.5194.11 TCGA.B0.4707.01 TCGA.CZ.5467.11 TCGA.B0.5705.01
#> "01" "01" "01" "02" "051" "06"
#> TCGA.CW.5588.01 TCGA.CJ.6031.01 TCGA.B8.A54J.01 TCGA.BP.5192.11 TCGA.CZ.5462.01 TCGA.B8.A54H.01
#> "04" "04" "04" "052" "04" "04"
#> TCGA.CZ.5470.11 TCGA.BP.4177.11 TCGA.CZ.5469.11 TCGA.CJ.6028.01 TCGA.G6.A8L6.01 TCGA.B8.5551.01
#> "051" "052" "051" "04" "04" "04"
#> TCGA.CZ.5456.01 TCGA.A3.A8OU.01 TCGA.BP.5186.01 TCGA.A3.A6NI.01 TCGA.BP.4782.01 TCGA.CZ.5454.11
#> "02" "04" "06" "04" "04" "054"
#> TCGA.B0.4691.11 TCGA.CZ.5452.01 TCGA.EU.5904.01 TCGA.BP.5201.01 TCGA.CJ.5677.01 TCGA.BP.5170.11
#> "01" "02" "06" "02" "02" "054"
#> TCGA.B0.4710.11 TCGA.AK.3425.01 TCGA.B0.4841.11 TCGA.B0.4849.01 TCGA.BP.5182.01 TCGA.B0.5711.11
#> "051" "02" "01" "04" "06" "052"
#> TCGA.BP.5180.01 TCGA.BP.5176.01 TCGA.CZ.5984.01 TCGA.CZ.5460.11 TCGA.BP.5190.01 TCGA.BP.4795.11
#> "02" "04" "02" "01" "02" "01"
#> TCGA.B0.4813.11 TCGA.B0.4713.01 TCGA.B0.4841.01 TCGA.B8.5546.01 TCGA.CW.5591.01 TCGA.B0.4698.11
#> "054" "02" "02" "07" "04" "01"
#> TCGA.B0.5713.11 TCGA.B0.5108.11 TCGA.B0.5083.01 TCGA.B0.5699.01 TCGA.CZ.5453.11 TCGA.BP.5202.01
#> "01" "01" "01" "02" "051" "02"
#> TCGA.BP.5173.11 TCGA.CW.5581.01 TCGA.B0.4848.11 TCGA.B0.4814.01 TCGA.BP.5178.11 TCGA.CJ.4907.01
#> "01" "04" "01" "02" "01" "04"
#> TCGA.A3.3387.01 TCGA.B0.4821.01 TCGA.B0.5712.01 TCGA.B0.5695.01 TCGA.BP.5184.11 TCGA.B2.A4SR.01
#> "04" "02" "02" "06" "01" "04"
#> TCGA.BP.5191.11 TCGA.CJ.4920.01 TCGA.BP.4801.01 TCGA.DV.A4W0.01 TCGA.BP.5177.11 TCGA.B0.4847.11
#> "01" "02" "04" "02" "01" "052"
#> TCGA.B0.5100.01 TCGA.CJ.4903.01 TCGA.CJ.4912.01 TCGA.B0.5107.11 TCGA.AK.3453.01 TCGA.B0.5691.01
#> "04" "02" "02" "01" "01" "06"
#> TCGA.BP.5195.11 TCGA.B0.5400.01 TCGA.A3.3376.11 TCGA.B0.4845.01 TCGA.B0.4699.01 TCGA.B0.4818.01
#> "054" "04" "07" "02" "07" "04"
#> TCGA.BP.5174.11 TCGA.CJ.4901.11 TCGA.B8.A54D.01 TCGA.BP.4770.11 TCGA.CW.6093.01 TCGA.BP.5010.11
#> "01" "01" "02" "01" "06" "054"
#> TCGA.AK.3431.01 TCGA.BP.4770.01 TCGA.BP.5189.01 TCGA.B0.4703.11 TCGA.B8.5163.01 TCGA.CJ.5683.01
#> "04" "04" "04" "01" "04" "04"
#> TCGA.CZ.4856.11 TCGA.BP.4760.01 TCGA.B0.5692.01 TCGA.B0.5106.01 TCGA.B0.4843.01 TCGA.CZ.4866.11
#> "051" "03" "02" "02" "04" "051"
#> TCGA.B0.5104.11 TCGA.B0.4827.01 TCGA.CJ.4902.11 TCGA.B8.A54G.01 TCGA.B0.5703.01 TCGA.CJ.5672.01
#> "01" "02" "054" "04" "04" "04"
#> TCGA.B0.5098.11 TCGA.B0.5113.11 TCGA.CJ.4882.11 TCGA.CZ.5465.11 TCGA.B0.5102.01 TCGA.CW.5585.01
#> "01" "01" "01" "051" "04" "04"
#> TCGA.B0.4824.01 TCGA.B0.5115.01 TCGA.B0.4706.01 TCGA.B0.5117.11 TCGA.CZ.4859.11 TCGA.AK.3450.01
#> "04" "02" "02" "01" "054" "04"
#> TCGA.B8.A54I.01 TCGA.CZ.5463.01 TCGA.DV.5568.01 TCGA.CZ.5459.11 TCGA.CJ.4918.11 TCGA.DV.5565.01
#> "02" "02" "04" "01" "01" "04"
#> TCGA.B0.5119.01 TCGA.B0.4811.01 TCGA.A3.3367.11 TCGA.CJ.4916.01 TCGA.B0.5693.01 TCGA.CZ.4863.11
#> "06" "04" "01" "04" "04" "051"
#> TCGA.G6.A5PC.01 TCGA.B8.5550.01 TCGA.DV.A4W0.05 TCGA.B0.4696.01 TCGA.BP.5187.01 TCGA.CZ.5466.11
#> "02" "04" "03" "02" "04" "01"
#> TCGA.CW.6097.01 TCGA.CJ.4905.11 TCGA.CZ.5989.01 TCGA.BP.5194.01 TCGA.B0.4707.11 TCGA.CZ.5467.01
#> "04" "052" "04" "04" "01" "04"
#> TCGA.BP.5185.11 TCGA.BP.5183.11 TCGA.BP.5192.01 TCGA.CZ.5462.11 TCGA.BP.4177.01 TCGA.CZ.5469.01
#> "01" "01" "06" "051" "03" "02"
#> TCGA.B2.5641.01 TCGA.BP.5196.11 TCGA.CZ.5460.01 TCGA.B0.4712.01 TCGA.B8.A54K.01 TCGA.B0.5707.01
#> "02" "01" "02" "02" "03" "06"
#> TCGA.BP.5186.11 TCGA.EU.5906.01 TCGA.CZ.5461.11 TCGA.CW.5590.01 TCGA.B0.5698.01 TCGA.CW.5580.01
#> "01" "06" "054" "02" "02" "02"
#> TCGA.CZ.5454.01 TCGA.B0.4815.01 TCGA.B0.5710.11 TCGA.CJ.4908.11 TCGA.BP.5201.11 TCGA.B0.5694.01
#> "02" "02" "01" "054" "01" "02"
#> TCGA.BP.5170.01 TCGA.DV.5575.01 TCGA.CJ.5686.01 TCGA.A3.3357.01 TCGA.A3.3373.01 TCGA.B0.5690.01
#> "04" "06" "04" "02" "04" "06"
#> TCGA.B8.4622.01 TCGA.AK.3433.01 TCGA.B0.5110.01 TCGA.BP.5180.11 TCGA.CJ.4913.01 TCGA.CJ.4908.01
#> "02" "053" "06" "01" "02" "04"
#> TCGA.BP.4795.01 TCGA.CJ.4897.11 TCGA.B2.5636.01 TCGA.CJ.4923.11 TCGA.B0.4819.01 TCGA.B2.5633.01
#> "03" "01" "03" "01" "04" "04"
#> TCGA.CJ.6033.01 TCGA.BP.5181.11 TCGA.B0.4698.01 TCGA.B0.5083.11 TCGA.CZ.4864.11 TCGA.B0.4688.01
#> "02" "01" "02" "01" "01" "02"
#> TCGA.BP.5168.01 TCGA.BP.5198.11 TCGA.B8.5162.01 TCGA.B0.5096.01 TCGA.BP.5178.01 TCGA.B0.5099.11
#> "04" "01" "04" "02" "02" "01"
#> TCGA.B0.4842.01 TCGA.BP.5169.11 TCGA.B0.5109.11 TCGA.CJ.4920.11 TCGA.B0.5080.11 TCGA.B0.5700.01
#> "04" "01" "07" "054" "01" "06"
#> TCGA.B0.4847.01 TCGA.B0.5702.01 TCGA.CJ.4905.01 TCGA.B2.5635.01 TCGA.B0.5107.01 TCGA.CW.5584.01
#> "02" "07" "04" "04" "02" "02"
#> TCGA.B4.5838.01 TCGA.BP.5199.01 TCGA.A3.3376.01 TCGA.B0.4845.11 TCGA.B0.4699.11 TCGA.BP.5174.01
#> "04" "02" "06" "054" "01" "06"
#> TCGA.CZ.5986.01 TCGA.CJ.4901.01 TCGA.AK.3461.01 TCGA.AK.3460.01 TCGA.AK.3454.01 TCGA.CZ.4859.01
#> "06" "02" "04" "04" "06" "06"
#> TCGA.B0.5812.01 TCGA.B0.5116.11 TCGA.B8.A54F.01 TCGA.CW.6090.01 TCGA.CZ.5458.11 TCGA.B0.5106.11
#> "04" "07" "04" "02" "051" "01"
#> TCGA.CZ.4866.01 TCGA.B0.4828.01 TCGA.AK.3440.01 TCGA.MM.A563.01 TCGA.B0.4697.01 TCGA.AK.3458.01
#> "02" "02" "053" "02" "04" "02"
#> TCGA.CJ.5676.01 TCGA.B0.5402.11 TCGA.CJ.5681.01 TCGA.A3.3370.11 TCGA.A3.A6NL.01 TCGA.B0.4693.01
#> "02" "01" "07" "052" "06" "02"
#> TCGA.A3.3358.01 TCGA.B0.4710.01 TCGA.CZ.4853.11 TCGA.B4.5835.01 TCGA.CJ.4882.01 TCGA.CZ.5465.01
#> "04" "02" "054" "06" "04" "02"
#> TCGA.B0.5102.11 TCGA.B0.4824.11 TCGA.CJ.5675.01 TCGA.B0.4700.01 TCGA.B0.5092.01 TCGA.B0.5115.11
#> "01" "01" "02" "04" "04" "01"
#> TCGA.B0.4945.11 TCGA.B8.5158.01 TCGA.CJ.6030.01 TCGA.B8.A54E.01 TCGA.CJ.6032.01 TCGA.B0.4852.11
#> "01" "02" "02" "07" "04" "01"
#> TCGA.B0.4817.01 TCGA.B8.5159.01 TCGA.A3.A8OW.01 TCGA.B0.4822.01 TCGA.B0.5696.01 TCGA.B0.5706.01
#> "04" "02" "06" "04" "04" "02"
#> TCGA.CJ.4918.01 TCGA.B0.5119.11 TCGA.BP.5200.11 TCGA.B0.4811.11 TCGA.A3.3367.01 TCGA.B0.5097.01
#> "04" "051" "01" "01" "02" "04"
#> TCGA.6D.AA2E.01 TCGA.DV.A4VX.01 TCGA.B0.4816.11 TCGA.A3.3385.11 TCGA.DV.5569.01 TCGA.EU.5907.01
#> "07" "02" "054" "01" "06" "02"
#> TCGA.CZ.5455.01 TCGA.B8.5545.01 TCGA.DV.5567.01 TCGA.CZ.5451.01 TCGA.CJ.4869.01 TCGA.CJ.5678.01
#> "04" "06" "03" "04" "04" "02"
#> TCGA.B8.4153.01 TCGA.B0.5121.11 TCGA.B8.4146.01 TCGA.BP.5183.01 TCGA.B0.5399.01 TCGA.B0.4810.11
#> "02" "01" "04" "02" "04" "052"
#> TCGA.AK.3445.01 TCGA.B4.5378.01 TCGA.BP.5196.01 TCGA.CZ.4865.11 TCGA.B0.5709.01 TCGA.B0.4712.11
#> "02" "03" "02" "051" "06" "051"
#> TCGA.B0.4714.01 TCGA.B8.5549.01 TCGA.CZ.5461.01 TCGA.CZ.5457.01 TCGA.A3.A8CQ.01 TCGA.DV.5573.01
#> "02" "02" "02" "06" "06" "06"
#> TCGA.B0.4815.11 TCGA.B0.5710.01 TCGA.B8.5165.01 TCGA.B0.4718.01 TCGA.B2.5639.01 TCGA.CW.5583.01
#> "01" "02" "06" "02" "04" "06"
#> TCGA.GK.A6C7.01 TCGA.A3.3357.11 TCGA.B8.5552.01 TCGA.B0.5120.01 TCGA.A3.3373.11 TCGA.BP.5185.01
#> "06" "01" "06" "04" "054" "04"
#> TCGA.B0.4846.01 TCGA.CJ.4904.01 TCGA.CJ.4913.11 TCGA.BP.4993.11 TCGA.B0.4823.11 TCGA.CJ.4897.01
#> "04" "06" "01" "01" "01" "04"
#> TCGA.BP.4993.01 TCGA.B4.5843.01 TCGA.DV.5576.01 TCGA.CJ.4923.01 TCGA.B0.4819.11 TCGA.BP.5175.01
#> "06" "06" "03" "04" "01" "02"
#> TCGA.CZ.5987.01 TCGA.CZ.4864.01 TCGA.B0.4688.11 TCGA.BP.5168.11 TCGA.BP.5198.01 TCGA.B8.A7U6.01
#> "02" "06" "054" "01" "02" "04"
#> TCGA.B0.5094.01 TCGA.T7.A92I.01 TCGA.B0.5096.11 TCGA.B0.5400.11 TCGA.B0.4694.11 TCGA.B0.5099.01
#> "02" "07" "01" "01" "052" "04"
#> TCGA.CZ.5468.01 TCGA.B0.4842.11 TCGA.CZ.5988.01 TCGA.BP.5169.01 TCGA.B0.5109.01 TCGA.B4.5834.01
#> "02" "01" "04" "02" "04" "06"
#> TCGA.B0.5095.11 TCGA.B0.5080.01 TCGA.CJ.5680.01 TCGA.CZ.5470.01 TCGA.CZ.4865.01 TCGA.A3.A8OX.01
#> "01" "04" "02" "02" "04" "07"
#> TCGA.B0.4690.11 TCGA.CJ.5684.01 TCGA.B0.4844.01 TCGA.CZ.5464.01 TCGA.B0.4701.01 TCGA.B0.5701.01
#> "01" "04" "02" "02" "04" "02"
#> TCGA.BP.5199.11 TCGA.CJ.5671.01 TCGA.A3.A8OV.01 TCGA.CZ.5456.11 TCGA.B0.5116.01 TCGA.CZ.5458.01
#> "01" "02" "06" "051" "02" "04"
#> TCGA.CZ.5982.01 TCGA.B0.4828.11 TCGA.CJ.5679.01 TCGA.CJ.5682.01 TCGA.B0.5697.01 TCGA.B0.4697.11
#> "04" "054" "02" "02" "04" "051"
#> TCGA.BP.4782.11 TCGA.G6.A8L8.01 TCGA.A3.A6NJ.01 TCGA.A3.3370.01 TCGA.B0.4691.01 TCGA.CZ.5452.11
#> "01" "02" "06" "06" "02" "051"
#> TCGA.B0.4693.11 TCGA.B0.4945.01 TCGA.CZ.4853.01 TCGA.B0.5092.11 TCGA.B0.5402.01 TCGA.B0.4849.11
#> "01" "06" "02" "01" "02" "01"
#> TCGA.A3.A6NN.01 TCGA.B0.4852.01 TCGA.B0.4817.11 TCGA.BP.5176.11 TCGA.CW.5589.01 TCGA.CJ.5689.01
#> "04" "04" "01" "01" "06" "04"
#> TCGA.B0.4822.11 TCGA.BP.5190.11 TCGA.B0.4813.01 TCGA.BP.5200.01 TCGA.G6.A8L7.01 TCGA.B2.4101.01
#> "052" "01" "02" "04" "02" "04"
#> TCGA.B0.4713.11 TCGA.B0.4816.01 TCGA.A3.3385.01 TCGA.B2.3924.01 TCGA.CZ.5455.11 TCGA.B0.5713.01
#> "01" "04" "06" "04" "051" "04"
#> TCGA.B0.5108.01 TCGA.B0.5711.01 TCGA.CZ.5453.01 TCGA.BP.5202.11 TCGA.BP.5173.01 TCGA.CZ.5451.11
#> "04" "04" "06" "07" "06" "01"
#> TCGA.B8.A8YJ.01 TCGA.B0.4848.01 TCGA.DV.A4VZ.01 TCGA.B0.4814.11 TCGA.CJ.4869.11 TCGA.CJ.4907.11
#> "06" "02" "03" "01" "01" "01"
#> TCGA.B8.5553.01 TCGA.MW.A4EC.01 TCGA.B0.5712.11 TCGA.EU.5905.01 TCGA.CZ.5985.01 TCGA.CZ.4856.01
#> "04" "04" "01" "04" "02" "04"
#> TCGA.BP.5184.01 TCGA.B0.5121.01 TCGA.BP.5191.01 TCGA.BP.4801.11 TCGA.BP.5177.01 TCGA.B0.5110.11
#> "04" "02" "02" "01" "06" "01"
#> TCGA.B0.4810.01 TCGA.CJ.4903.11 TCGA.CJ.4912.11 TCGA.B8.4621.01 TCGA.B4.5832.01 TCGA.CW.6088.01
#> "02" "01" "054" "06" "04" "06"
#> TCGA.AK.3428.01 TCGA.B8.5164.01 TCGA.BP.5195.01 TCGA.CJ.6027.01 TCGA.3Z.A93Z.01 TCGA.B0.4714.11
#> "02" "04" "04" "02" "06" "01"
#> TCGA.B0.4818.11 TCGA.CZ.5457.11 TCGA.BP.5010.01 TCGA.BP.5189.11 TCGA.B0.4703.01 TCGA.B0.4718.11
#> "01" "051" "04" "01" "04" "052"
#> TCGA.B0.5097.11 TCGA.BP.4760.11 TCGA.B0.5120.11 TCGA.B0.4843.11 TCGA.B0.5104.01 TCGA.CW.5587.01
#> "01" "01" "01" "01" "04" "04"
get_classes(res_rh, merge_node = merge_node_param(min_n_signatures = 28962))
#> TCGA.CZ.4863.01 TCGA.CJ.4904.11 TCGA.B0.4827.11 TCGA.CJ.4902.01 TCGA.B0.4823.01 TCGA.CW.6087.01
#> "04" "01" "05" "04" "06" "04"
#> TCGA.B0.5098.01 TCGA.B0.5113.01 TCGA.DV.5566.01 TCGA.BP.5175.11 TCGA.BP.5181.01 TCGA.B0.4706.11
#> "07" "02" "04" "01" "06" "01"
#> TCGA.B0.5117.01 TCGA.MM.A564.01 TCGA.B0.4821.11 TCGA.CZ.5463.11 TCGA.BP.5182.11 TCGA.DV.5574.01
#> "01" "02" "07" "05" "01" "06"
#> TCGA.B0.5094.11 TCGA.MM.A84U.01 TCGA.B0.5100.11 TCGA.B4.5844.01 TCGA.CZ.5459.01 TCGA.B0.4694.01
#> "01" "04" "01" "04" "04" "04"
#> TCGA.CZ.5468.11 TCGA.CJ.4916.11 TCGA.B4.5836.01 TCGA.B0.5095.01 TCGA.B0.4846.11 TCGA.AK.3434.01
#> "05" "01" "04" "04" "01" "02"
#> TCGA.B4.5377.01 TCGA.B0.4696.11 TCGA.BP.5187.11 TCGA.B0.4690.01 TCGA.CZ.5466.01 TCGA.B0.4844.11
#> "06" "01" "01" "04" "04" "05"
#> TCGA.CZ.5464.11 TCGA.B0.4701.11 TCGA.BP.5194.11 TCGA.B0.4707.01 TCGA.CZ.5467.11 TCGA.B0.5705.01
#> "01" "01" "01" "02" "05" "06"
#> TCGA.CW.5588.01 TCGA.CJ.6031.01 TCGA.B8.A54J.01 TCGA.BP.5192.11 TCGA.CZ.5462.01 TCGA.B8.A54H.01
#> "04" "04" "04" "05" "04" "04"
#> TCGA.CZ.5470.11 TCGA.BP.4177.11 TCGA.CZ.5469.11 TCGA.CJ.6028.01 TCGA.G6.A8L6.01 TCGA.B8.5551.01
#> "05" "05" "05" "04" "04" "04"
#> TCGA.CZ.5456.01 TCGA.A3.A8OU.01 TCGA.BP.5186.01 TCGA.A3.A6NI.01 TCGA.BP.4782.01 TCGA.CZ.5454.11
#> "02" "04" "06" "04" "04" "05"
#> TCGA.B0.4691.11 TCGA.CZ.5452.01 TCGA.EU.5904.01 TCGA.BP.5201.01 TCGA.CJ.5677.01 TCGA.BP.5170.11
#> "01" "02" "06" "02" "02" "05"
#> TCGA.B0.4710.11 TCGA.AK.3425.01 TCGA.B0.4841.11 TCGA.B0.4849.01 TCGA.BP.5182.01 TCGA.B0.5711.11
#> "05" "02" "01" "04" "06" "05"
#> TCGA.BP.5180.01 TCGA.BP.5176.01 TCGA.CZ.5984.01 TCGA.CZ.5460.11 TCGA.BP.5190.01 TCGA.BP.4795.11
#> "02" "04" "02" "01" "02" "01"
#> TCGA.B0.4813.11 TCGA.B0.4713.01 TCGA.B0.4841.01 TCGA.B8.5546.01 TCGA.CW.5591.01 TCGA.B0.4698.11
#> "05" "02" "02" "07" "04" "01"
#> TCGA.B0.5713.11 TCGA.B0.5108.11 TCGA.B0.5083.01 TCGA.B0.5699.01 TCGA.CZ.5453.11 TCGA.BP.5202.01
#> "01" "01" "01" "02" "05" "02"
#> TCGA.BP.5173.11 TCGA.CW.5581.01 TCGA.B0.4848.11 TCGA.B0.4814.01 TCGA.BP.5178.11 TCGA.CJ.4907.01
#> "01" "04" "01" "02" "01" "04"
#> TCGA.A3.3387.01 TCGA.B0.4821.01 TCGA.B0.5712.01 TCGA.B0.5695.01 TCGA.BP.5184.11 TCGA.B2.A4SR.01
#> "04" "02" "02" "06" "01" "04"
#> TCGA.BP.5191.11 TCGA.CJ.4920.01 TCGA.BP.4801.01 TCGA.DV.A4W0.01 TCGA.BP.5177.11 TCGA.B0.4847.11
#> "01" "02" "04" "02" "01" "05"
#> TCGA.B0.5100.01 TCGA.CJ.4903.01 TCGA.CJ.4912.01 TCGA.B0.5107.11 TCGA.AK.3453.01 TCGA.B0.5691.01
#> "04" "02" "02" "01" "01" "06"
#> TCGA.BP.5195.11 TCGA.B0.5400.01 TCGA.A3.3376.11 TCGA.B0.4845.01 TCGA.B0.4699.01 TCGA.B0.4818.01
#> "05" "04" "07" "02" "07" "04"
#> TCGA.BP.5174.11 TCGA.CJ.4901.11 TCGA.B8.A54D.01 TCGA.BP.4770.11 TCGA.CW.6093.01 TCGA.BP.5010.11
#> "01" "01" "02" "01" "06" "05"
#> TCGA.AK.3431.01 TCGA.BP.4770.01 TCGA.BP.5189.01 TCGA.B0.4703.11 TCGA.B8.5163.01 TCGA.CJ.5683.01
#> "04" "04" "04" "01" "04" "04"
#> TCGA.CZ.4856.11 TCGA.BP.4760.01 TCGA.B0.5692.01 TCGA.B0.5106.01 TCGA.B0.4843.01 TCGA.CZ.4866.11
#> "05" "03" "02" "02" "04" "05"
#> TCGA.B0.5104.11 TCGA.B0.4827.01 TCGA.CJ.4902.11 TCGA.B8.A54G.01 TCGA.B0.5703.01 TCGA.CJ.5672.01
#> "01" "02" "05" "04" "04" "04"
#> TCGA.B0.5098.11 TCGA.B0.5113.11 TCGA.CJ.4882.11 TCGA.CZ.5465.11 TCGA.B0.5102.01 TCGA.CW.5585.01
#> "01" "01" "01" "05" "04" "04"
#> TCGA.B0.4824.01 TCGA.B0.5115.01 TCGA.B0.4706.01 TCGA.B0.5117.11 TCGA.CZ.4859.11 TCGA.AK.3450.01
#> "04" "02" "02" "01" "05" "04"
#> TCGA.B8.A54I.01 TCGA.CZ.5463.01 TCGA.DV.5568.01 TCGA.CZ.5459.11 TCGA.CJ.4918.11 TCGA.DV.5565.01
#> "02" "02" "04" "01" "01" "04"
#> TCGA.B0.5119.01 TCGA.B0.4811.01 TCGA.A3.3367.11 TCGA.CJ.4916.01 TCGA.B0.5693.01 TCGA.CZ.4863.11
#> "06" "04" "01" "04" "04" "05"
#> TCGA.G6.A5PC.01 TCGA.B8.5550.01 TCGA.DV.A4W0.05 TCGA.B0.4696.01 TCGA.BP.5187.01 TCGA.CZ.5466.11
#> "02" "04" "03" "02" "04" "01"
#> TCGA.CW.6097.01 TCGA.CJ.4905.11 TCGA.CZ.5989.01 TCGA.BP.5194.01 TCGA.B0.4707.11 TCGA.CZ.5467.01
#> "04" "05" "04" "04" "01" "04"
#> TCGA.BP.5185.11 TCGA.BP.5183.11 TCGA.BP.5192.01 TCGA.CZ.5462.11 TCGA.BP.4177.01 TCGA.CZ.5469.01
#> "01" "01" "06" "05" "03" "02"
#> TCGA.B2.5641.01 TCGA.BP.5196.11 TCGA.CZ.5460.01 TCGA.B0.4712.01 TCGA.B8.A54K.01 TCGA.B0.5707.01
#> "02" "01" "02" "02" "03" "06"
#> TCGA.BP.5186.11 TCGA.EU.5906.01 TCGA.CZ.5461.11 TCGA.CW.5590.01 TCGA.B0.5698.01 TCGA.CW.5580.01
#> "01" "06" "05" "02" "02" "02"
#> TCGA.CZ.5454.01 TCGA.B0.4815.01 TCGA.B0.5710.11 TCGA.CJ.4908.11 TCGA.BP.5201.11 TCGA.B0.5694.01
#> "02" "02" "01" "05" "01" "02"
#> TCGA.BP.5170.01 TCGA.DV.5575.01 TCGA.CJ.5686.01 TCGA.A3.3357.01 TCGA.A3.3373.01 TCGA.B0.5690.01
#> "04" "06" "04" "02" "04" "06"
#> TCGA.B8.4622.01 TCGA.AK.3433.01 TCGA.B0.5110.01 TCGA.BP.5180.11 TCGA.CJ.4913.01 TCGA.CJ.4908.01
#> "02" "05" "06" "01" "02" "04"
#> TCGA.BP.4795.01 TCGA.CJ.4897.11 TCGA.B2.5636.01 TCGA.CJ.4923.11 TCGA.B0.4819.01 TCGA.B2.5633.01
#> "03" "01" "03" "01" "04" "04"
#> TCGA.CJ.6033.01 TCGA.BP.5181.11 TCGA.B0.4698.01 TCGA.B0.5083.11 TCGA.CZ.4864.11 TCGA.B0.4688.01
#> "02" "01" "02" "01" "01" "02"
#> TCGA.BP.5168.01 TCGA.BP.5198.11 TCGA.B8.5162.01 TCGA.B0.5096.01 TCGA.BP.5178.01 TCGA.B0.5099.11
#> "04" "01" "04" "02" "02" "01"
#> TCGA.B0.4842.01 TCGA.BP.5169.11 TCGA.B0.5109.11 TCGA.CJ.4920.11 TCGA.B0.5080.11 TCGA.B0.5700.01
#> "04" "01" "07" "05" "01" "06"
#> TCGA.B0.4847.01 TCGA.B0.5702.01 TCGA.CJ.4905.01 TCGA.B2.5635.01 TCGA.B0.5107.01 TCGA.CW.5584.01
#> "02" "07" "04" "04" "02" "02"
#> TCGA.B4.5838.01 TCGA.BP.5199.01 TCGA.A3.3376.01 TCGA.B0.4845.11 TCGA.B0.4699.11 TCGA.BP.5174.01
#> "04" "02" "06" "05" "01" "06"
#> TCGA.CZ.5986.01 TCGA.CJ.4901.01 TCGA.AK.3461.01 TCGA.AK.3460.01 TCGA.AK.3454.01 TCGA.CZ.4859.01
#> "06" "02" "04" "04" "06" "06"
#> TCGA.B0.5812.01 TCGA.B0.5116.11 TCGA.B8.A54F.01 TCGA.CW.6090.01 TCGA.CZ.5458.11 TCGA.B0.5106.11
#> "04" "07" "04" "02" "05" "01"
#> TCGA.CZ.4866.01 TCGA.B0.4828.01 TCGA.AK.3440.01 TCGA.MM.A563.01 TCGA.B0.4697.01 TCGA.AK.3458.01
#> "02" "02" "05" "02" "04" "02"
#> TCGA.CJ.5676.01 TCGA.B0.5402.11 TCGA.CJ.5681.01 TCGA.A3.3370.11 TCGA.A3.A6NL.01 TCGA.B0.4693.01
#> "02" "01" "07" "05" "06" "02"
#> TCGA.A3.3358.01 TCGA.B0.4710.01 TCGA.CZ.4853.11 TCGA.B4.5835.01 TCGA.CJ.4882.01 TCGA.CZ.5465.01
#> "04" "02" "05" "06" "04" "02"
#> TCGA.B0.5102.11 TCGA.B0.4824.11 TCGA.CJ.5675.01 TCGA.B0.4700.01 TCGA.B0.5092.01 TCGA.B0.5115.11
#> "01" "01" "02" "04" "04" "01"
#> TCGA.B0.4945.11 TCGA.B8.5158.01 TCGA.CJ.6030.01 TCGA.B8.A54E.01 TCGA.CJ.6032.01 TCGA.B0.4852.11
#> "01" "02" "02" "07" "04" "01"
#> TCGA.B0.4817.01 TCGA.B8.5159.01 TCGA.A3.A8OW.01 TCGA.B0.4822.01 TCGA.B0.5696.01 TCGA.B0.5706.01
#> "04" "02" "06" "04" "04" "02"
#> TCGA.CJ.4918.01 TCGA.B0.5119.11 TCGA.BP.5200.11 TCGA.B0.4811.11 TCGA.A3.3367.01 TCGA.B0.5097.01
#> "04" "05" "01" "01" "02" "04"
#> TCGA.6D.AA2E.01 TCGA.DV.A4VX.01 TCGA.B0.4816.11 TCGA.A3.3385.11 TCGA.DV.5569.01 TCGA.EU.5907.01
#> "07" "02" "05" "01" "06" "02"
#> TCGA.CZ.5455.01 TCGA.B8.5545.01 TCGA.DV.5567.01 TCGA.CZ.5451.01 TCGA.CJ.4869.01 TCGA.CJ.5678.01
#> "04" "06" "03" "04" "04" "02"
#> TCGA.B8.4153.01 TCGA.B0.5121.11 TCGA.B8.4146.01 TCGA.BP.5183.01 TCGA.B0.5399.01 TCGA.B0.4810.11
#> "02" "01" "04" "02" "04" "05"
#> TCGA.AK.3445.01 TCGA.B4.5378.01 TCGA.BP.5196.01 TCGA.CZ.4865.11 TCGA.B0.5709.01 TCGA.B0.4712.11
#> "02" "03" "02" "05" "06" "05"
#> TCGA.B0.4714.01 TCGA.B8.5549.01 TCGA.CZ.5461.01 TCGA.CZ.5457.01 TCGA.A3.A8CQ.01 TCGA.DV.5573.01
#> "02" "02" "02" "06" "06" "06"
#> TCGA.B0.4815.11 TCGA.B0.5710.01 TCGA.B8.5165.01 TCGA.B0.4718.01 TCGA.B2.5639.01 TCGA.CW.5583.01
#> "01" "02" "06" "02" "04" "06"
#> TCGA.GK.A6C7.01 TCGA.A3.3357.11 TCGA.B8.5552.01 TCGA.B0.5120.01 TCGA.A3.3373.11 TCGA.BP.5185.01
#> "06" "01" "06" "04" "05" "04"
#> TCGA.B0.4846.01 TCGA.CJ.4904.01 TCGA.CJ.4913.11 TCGA.BP.4993.11 TCGA.B0.4823.11 TCGA.CJ.4897.01
#> "04" "06" "01" "01" "01" "04"
#> TCGA.BP.4993.01 TCGA.B4.5843.01 TCGA.DV.5576.01 TCGA.CJ.4923.01 TCGA.B0.4819.11 TCGA.BP.5175.01
#> "06" "06" "03" "04" "01" "02"
#> TCGA.CZ.5987.01 TCGA.CZ.4864.01 TCGA.B0.4688.11 TCGA.BP.5168.11 TCGA.BP.5198.01 TCGA.B8.A7U6.01
#> "02" "06" "05" "01" "02" "04"
#> TCGA.B0.5094.01 TCGA.T7.A92I.01 TCGA.B0.5096.11 TCGA.B0.5400.11 TCGA.B0.4694.11 TCGA.B0.5099.01
#> "02" "07" "01" "01" "05" "04"
#> TCGA.CZ.5468.01 TCGA.B0.4842.11 TCGA.CZ.5988.01 TCGA.BP.5169.01 TCGA.B0.5109.01 TCGA.B4.5834.01
#> "02" "01" "04" "02" "04" "06"
#> TCGA.B0.5095.11 TCGA.B0.5080.01 TCGA.CJ.5680.01 TCGA.CZ.5470.01 TCGA.CZ.4865.01 TCGA.A3.A8OX.01
#> "01" "04" "02" "02" "04" "07"
#> TCGA.B0.4690.11 TCGA.CJ.5684.01 TCGA.B0.4844.01 TCGA.CZ.5464.01 TCGA.B0.4701.01 TCGA.B0.5701.01
#> "01" "04" "02" "02" "04" "02"
#> TCGA.BP.5199.11 TCGA.CJ.5671.01 TCGA.A3.A8OV.01 TCGA.CZ.5456.11 TCGA.B0.5116.01 TCGA.CZ.5458.01
#> "01" "02" "06" "05" "02" "04"
#> TCGA.CZ.5982.01 TCGA.B0.4828.11 TCGA.CJ.5679.01 TCGA.CJ.5682.01 TCGA.B0.5697.01 TCGA.B0.4697.11
#> "04" "05" "02" "02" "04" "05"
#> TCGA.BP.4782.11 TCGA.G6.A8L8.01 TCGA.A3.A6NJ.01 TCGA.A3.3370.01 TCGA.B0.4691.01 TCGA.CZ.5452.11
#> "01" "02" "06" "06" "02" "05"
#> TCGA.B0.4693.11 TCGA.B0.4945.01 TCGA.CZ.4853.01 TCGA.B0.5092.11 TCGA.B0.5402.01 TCGA.B0.4849.11
#> "01" "06" "02" "01" "02" "01"
#> TCGA.A3.A6NN.01 TCGA.B0.4852.01 TCGA.B0.4817.11 TCGA.BP.5176.11 TCGA.CW.5589.01 TCGA.CJ.5689.01
#> "04" "04" "01" "01" "06" "04"
#> TCGA.B0.4822.11 TCGA.BP.5190.11 TCGA.B0.4813.01 TCGA.BP.5200.01 TCGA.G6.A8L7.01 TCGA.B2.4101.01
#> "05" "01" "02" "04" "02" "04"
#> TCGA.B0.4713.11 TCGA.B0.4816.01 TCGA.A3.3385.01 TCGA.B2.3924.01 TCGA.CZ.5455.11 TCGA.B0.5713.01
#> "01" "04" "06" "04" "05" "04"
#> TCGA.B0.5108.01 TCGA.B0.5711.01 TCGA.CZ.5453.01 TCGA.BP.5202.11 TCGA.BP.5173.01 TCGA.CZ.5451.11
#> "04" "04" "06" "07" "06" "01"
#> TCGA.B8.A8YJ.01 TCGA.B0.4848.01 TCGA.DV.A4VZ.01 TCGA.B0.4814.11 TCGA.CJ.4869.11 TCGA.CJ.4907.11
#> "06" "02" "03" "01" "01" "01"
#> TCGA.B8.5553.01 TCGA.MW.A4EC.01 TCGA.B0.5712.11 TCGA.EU.5905.01 TCGA.CZ.5985.01 TCGA.CZ.4856.01
#> "04" "04" "01" "04" "02" "04"
#> TCGA.BP.5184.01 TCGA.B0.5121.01 TCGA.BP.5191.01 TCGA.BP.4801.11 TCGA.BP.5177.01 TCGA.B0.5110.11
#> "04" "02" "02" "01" "06" "01"
#> TCGA.B0.4810.01 TCGA.CJ.4903.11 TCGA.CJ.4912.11 TCGA.B8.4621.01 TCGA.B4.5832.01 TCGA.CW.6088.01
#> "02" "01" "05" "06" "04" "06"
#> TCGA.AK.3428.01 TCGA.B8.5164.01 TCGA.BP.5195.01 TCGA.CJ.6027.01 TCGA.3Z.A93Z.01 TCGA.B0.4714.11
#> "02" "04" "04" "02" "06" "01"
#> TCGA.B0.4818.11 TCGA.CZ.5457.11 TCGA.BP.5010.01 TCGA.BP.5189.11 TCGA.B0.4703.01 TCGA.B0.4718.11
#> "01" "05" "04" "01" "04" "05"
#> TCGA.B0.5097.11 TCGA.BP.4760.11 TCGA.B0.5120.11 TCGA.B0.4843.11 TCGA.B0.5104.01 TCGA.CW.5587.01
#> "01" "01" "01" "01" "04" "04"
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 = 1144),
method = "UMAP", top_value_method = "SD", top_n = 40000, scale_rows = FALSE)
dimension_reduction(res_rh, merge_node = merge_node_param(min_n_signatures = 1144),
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 = 1256),
method = "UMAP", top_value_method = "SD", top_n = 40000, scale_rows = FALSE)
dimension_reduction(res_rh, merge_node = merge_node_param(min_n_signatures = 1256),
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 = 1744),
method = "UMAP", top_value_method = "SD", top_n = 40000, scale_rows = FALSE)
dimension_reduction(res_rh, merge_node = merge_node_param(min_n_signatures = 1744),
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 = 1947),
method = "UMAP", top_value_method = "SD", top_n = 40000, scale_rows = FALSE)
dimension_reduction(res_rh, merge_node = merge_node_param(min_n_signatures = 1947),
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 = 2035),
method = "UMAP", top_value_method = "SD", top_n = 40000, scale_rows = FALSE)
dimension_reduction(res_rh, merge_node = merge_node_param(min_n_signatures = 2035),
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 = 3246),
method = "UMAP", top_value_method = "SD", top_n = 40000, scale_rows = FALSE)
dimension_reduction(res_rh, merge_node = merge_node_param(min_n_signatures = 3246),
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 = 3386),
method = "UMAP", top_value_method = "SD", top_n = 40000, scale_rows = FALSE)
dimension_reduction(res_rh, merge_node = merge_node_param(min_n_signatures = 3386),
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 = 3555),
method = "UMAP", top_value_method = "SD", top_n = 40000, scale_rows = FALSE)
dimension_reduction(res_rh, merge_node = merge_node_param(min_n_signatures = 3555),
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 = 3674),
method = "UMAP", top_value_method = "SD", top_n = 40000, scale_rows = FALSE)
dimension_reduction(res_rh, merge_node = merge_node_param(min_n_signatures = 3674),
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 = 3886),
method = "UMAP", top_value_method = "SD", top_n = 40000, scale_rows = FALSE)
dimension_reduction(res_rh, merge_node = merge_node_param(min_n_signatures = 3886),
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 = 3997),
method = "UMAP", top_value_method = "SD", top_n = 40000, scale_rows = FALSE)
dimension_reduction(res_rh, merge_node = merge_node_param(min_n_signatures = 3997),
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 = 4193),
method = "UMAP", top_value_method = "SD", top_n = 40000, scale_rows = FALSE)
dimension_reduction(res_rh, merge_node = merge_node_param(min_n_signatures = 4193),
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 = 4521),
method = "UMAP", top_value_method = "SD", top_n = 40000, scale_rows = FALSE)
dimension_reduction(res_rh, merge_node = merge_node_param(min_n_signatures = 4521),
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 = 4860),
method = "UMAP", top_value_method = "SD", top_n = 40000, scale_rows = FALSE)
dimension_reduction(res_rh, merge_node = merge_node_param(min_n_signatures = 4860),
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 = 5214),
method = "UMAP", top_value_method = "SD", top_n = 40000, scale_rows = FALSE)
dimension_reduction(res_rh, merge_node = merge_node_param(min_n_signatures = 5214),
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 = 14438),
method = "UMAP", top_value_method = "SD", top_n = 40000, scale_rows = FALSE)
dimension_reduction(res_rh, merge_node = merge_node_param(min_n_signatures = 14438),
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 = 28962),
method = "UMAP", top_value_method = "SD", top_n = 40000, scale_rows = FALSE)
dimension_reduction(res_rh, merge_node = merge_node_param(min_n_signatures = 28962),
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 = 1144))
get_signatures(res_rh, merge_node = merge_node_param(min_n_signatures = 1256))
get_signatures(res_rh, merge_node = merge_node_param(min_n_signatures = 1744))
get_signatures(res_rh, merge_node = merge_node_param(min_n_signatures = 1947))
get_signatures(res_rh, merge_node = merge_node_param(min_n_signatures = 2035))
get_signatures(res_rh, merge_node = merge_node_param(min_n_signatures = 3246))
get_signatures(res_rh, merge_node = merge_node_param(min_n_signatures = 3386))
get_signatures(res_rh, merge_node = merge_node_param(min_n_signatures = 3555))
get_signatures(res_rh, merge_node = merge_node_param(min_n_signatures = 3674))
get_signatures(res_rh, merge_node = merge_node_param(min_n_signatures = 3886))
get_signatures(res_rh, merge_node = merge_node_param(min_n_signatures = 3997))
get_signatures(res_rh, merge_node = merge_node_param(min_n_signatures = 4193))
get_signatures(res_rh, merge_node = merge_node_param(min_n_signatures = 4521))
get_signatures(res_rh, merge_node = merge_node_param(min_n_signatures = 4860))
get_signatures(res_rh, merge_node = merge_node_param(min_n_signatures = 5214))
get_signatures(res_rh, merge_node = merge_node_param(min_n_signatures = 14438))
get_signatures(res_rh, merge_node = merge_node_param(min_n_signatures = 28962))
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-leaf , Node04 , Node05 , Node06 , Node07 .
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 480 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 8.
#>
#> 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 0.4671 0.533 0.533
#> 3 3 0.796 0.916 0.941 0.1682 0.950 0.906
#> 4 4 1.000 0.969 0.988 0.2843 0.813 0.615
#> 5 5 0.907 0.904 0.951 0.0393 0.898 0.698
#> 6 6 0.958 0.920 0.970 0.0551 0.898 0.665
#> 7 7 0.999 0.951 0.981 0.0387 0.900 0.624
#> 8 8 0.913 0.877 0.924 0.0300 0.968 0.847
suggest_best_k() suggests the best \(k\) based on these statistics. The rules are as follows:
suggest_best_k(res)
#> [1] 8
#> attr(,"optional")
#> [1] 2 4 5 6 7
There is also optional best \(k\) = 2 4 5 6 7 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.CZ.4863.01 2 0 1 0 1
#> TCGA.CJ.4904.11 1 0 1 1 0
#> TCGA.B0.4827.11 1 0 1 1 0
#> TCGA.CJ.4902.01 2 0 1 0 1
#> TCGA.B0.4823.01 2 0 1 0 1
#> TCGA.CW.6087.01 2 0 1 0 1
#> TCGA.B0.5098.01 2 0 1 0 1
#> TCGA.B0.5113.01 2 0 1 0 1
#> TCGA.DV.5566.01 2 0 1 0 1
#> TCGA.BP.5175.11 1 0 1 1 0
#> TCGA.BP.5181.01 2 0 1 0 1
#> TCGA.B0.4706.11 1 0 1 1 0
#> TCGA.B0.5117.01 1 0 1 1 0
#> TCGA.MM.A564.01 2 0 1 0 1
#> TCGA.B0.4821.11 1 0 1 1 0
#> TCGA.CZ.5463.11 1 0 1 1 0
#> TCGA.BP.5182.11 1 0 1 1 0
#> TCGA.DV.5574.01 2 0 1 0 1
#> TCGA.B0.5094.11 1 0 1 1 0
#> TCGA.MM.A84U.01 2 0 1 0 1
#> TCGA.B0.5100.11 1 0 1 1 0
#> TCGA.B4.5844.01 2 0 1 0 1
#> TCGA.CZ.5459.01 2 0 1 0 1
#> TCGA.B0.4694.01 2 0 1 0 1
#> TCGA.CZ.5468.11 1 0 1 1 0
#> TCGA.CJ.4916.11 1 0 1 1 0
#> TCGA.B4.5836.01 2 0 1 0 1
#> TCGA.B0.5095.01 2 0 1 0 1
#> TCGA.B0.4846.11 1 0 1 1 0
#> TCGA.AK.3434.01 2 0 1 0 1
#> TCGA.B4.5377.01 2 0 1 0 1
#> TCGA.B0.4696.11 1 0 1 1 0
#> TCGA.BP.5187.11 1 0 1 1 0
#> TCGA.B0.4690.01 2 0 1 0 1
#> TCGA.CZ.5466.01 2 0 1 0 1
#> TCGA.B0.4844.11 1 0 1 1 0
#> TCGA.CZ.5464.11 1 0 1 1 0
#> TCGA.B0.4701.11 1 0 1 1 0
#> TCGA.BP.5194.11 1 0 1 1 0
#> TCGA.B0.4707.01 2 0 1 0 1
#> TCGA.CZ.5467.11 1 0 1 1 0
#> TCGA.B0.5705.01 2 0 1 0 1
#> TCGA.CW.5588.01 2 0 1 0 1
#> TCGA.CJ.6031.01 2 0 1 0 1
#> TCGA.B8.A54J.01 2 0 1 0 1
#> TCGA.BP.5192.11 1 0 1 1 0
#> TCGA.CZ.5462.01 2 0 1 0 1
#> TCGA.B8.A54H.01 2 0 1 0 1
#> TCGA.CZ.5470.11 1 0 1 1 0
#> TCGA.BP.4177.11 1 0 1 1 0
#> TCGA.CZ.5469.11 1 0 1 1 0
#> TCGA.CJ.6028.01 2 0 1 0 1
#> TCGA.G6.A8L6.01 2 0 1 0 1
#> TCGA.B8.5551.01 2 0 1 0 1
#> TCGA.CZ.5456.01 2 0 1 0 1
#> TCGA.A3.A8OU.01 2 0 1 0 1
#> TCGA.BP.5186.01 2 0 1 0 1
#> TCGA.A3.A6NI.01 2 0 1 0 1
#> TCGA.BP.4782.01 2 0 1 0 1
#> TCGA.CZ.5454.11 1 0 1 1 0
#> TCGA.B0.4691.11 1 0 1 1 0
#> TCGA.CZ.5452.01 2 0 1 0 1
#> TCGA.EU.5904.01 2 0 1 0 1
#> TCGA.BP.5201.01 2 0 1 0 1
#> TCGA.CJ.5677.01 2 0 1 0 1
#> TCGA.BP.5170.11 1 0 1 1 0
#> TCGA.B0.4710.11 1 0 1 1 0
#> TCGA.AK.3425.01 2 0 1 0 1
#> TCGA.B0.4841.11 1 0 1 1 0
#> TCGA.B0.4849.01 2 0 1 0 1
#> TCGA.BP.5182.01 2 0 1 0 1
#> TCGA.B0.5711.11 1 0 1 1 0
#> TCGA.BP.5180.01 2 0 1 0 1
#> TCGA.BP.5176.01 2 0 1 0 1
#> TCGA.CZ.5984.01 2 0 1 0 1
#> TCGA.CZ.5460.11 1 0 1 1 0
#> TCGA.BP.5190.01 2 0 1 0 1
#> TCGA.BP.4795.11 1 0 1 1 0
#> TCGA.B0.4813.11 1 0 1 1 0
#> TCGA.B0.4713.01 2 0 1 0 1
#> TCGA.B0.4841.01 2 0 1 0 1
#> TCGA.B8.5546.01 1 0 1 1 0
#> TCGA.CW.5591.01 2 0 1 0 1
#> TCGA.B0.4698.11 1 0 1 1 0
#> TCGA.B0.5713.11 1 0 1 1 0
#> TCGA.B0.5108.11 1 0 1 1 0
#> TCGA.B0.5083.01 1 0 1 1 0
#> TCGA.B0.5699.01 2 0 1 0 1
#> TCGA.CZ.5453.11 1 0 1 1 0
#> TCGA.BP.5202.01 2 0 1 0 1
#> TCGA.BP.5173.11 1 0 1 1 0
#> TCGA.CW.5581.01 2 0 1 0 1
#> TCGA.B0.4848.11 1 0 1 1 0
#> TCGA.B0.4814.01 2 0 1 0 1
#> TCGA.BP.5178.11 1 0 1 1 0
#> TCGA.CJ.4907.01 2 0 1 0 1
#> TCGA.A3.3387.01 2 0 1 0 1
#> TCGA.B0.4821.01 2 0 1 0 1
#> TCGA.B0.5712.01 2 0 1 0 1
#> TCGA.B0.5695.01 2 0 1 0 1
#> TCGA.BP.5184.11 1 0 1 1 0
#> TCGA.B2.A4SR.01 2 0 1 0 1
#> TCGA.BP.5191.11 1 0 1 1 0
#> TCGA.CJ.4920.01 2 0 1 0 1
#> TCGA.BP.4801.01 2 0 1 0 1
#> TCGA.DV.A4W0.01 2 0 1 0 1
#> TCGA.BP.5177.11 1 0 1 1 0
#> TCGA.B0.4847.11 1 0 1 1 0
#> TCGA.B0.5100.01 2 0 1 0 1
#> TCGA.CJ.4903.01 2 0 1 0 1
#> TCGA.CJ.4912.01 2 0 1 0 1
#> TCGA.B0.5107.11 1 0 1 1 0
#> TCGA.AK.3453.01 1 0 1 1 0
#> TCGA.B0.5691.01 2 0 1 0 1
#> TCGA.BP.5195.11 1 0 1 1 0
#> TCGA.B0.5400.01 2 0 1 0 1
#> TCGA.A3.3376.11 1 0 1 1 0
#> TCGA.B0.4845.01 2 0 1 0 1
#> TCGA.B0.4699.01 1 0 1 1 0
#> TCGA.B0.4818.01 2 0 1 0 1
#> TCGA.BP.5174.11 1 0 1 1 0
#> TCGA.CJ.4901.11 1 0 1 1 0
#> TCGA.B8.A54D.01 2 0 1 0 1
#> TCGA.BP.4770.11 1 0 1 1 0
#> TCGA.CW.6093.01 2 0 1 0 1
#> TCGA.BP.5010.11 1 0 1 1 0
#> TCGA.AK.3431.01 2 0 1 0 1
#> TCGA.BP.4770.01 2 0 1 0 1
#> TCGA.BP.5189.01 2 0 1 0 1
#> TCGA.B0.4703.11 1 0 1 1 0
#> TCGA.B8.5163.01 2 0 1 0 1
#> TCGA.CJ.5683.01 2 0 1 0 1
#> TCGA.CZ.4856.11 1 0 1 1 0
#> TCGA.BP.4760.01 1 0 1 1 0
#> TCGA.B0.5692.01 2 0 1 0 1
#> TCGA.B0.5106.01 2 0 1 0 1
#> TCGA.B0.4843.01 2 0 1 0 1
#> TCGA.CZ.4866.11 1 0 1 1 0
#> TCGA.B0.5104.11 1 0 1 1 0
#> TCGA.B0.4827.01 2 0 1 0 1
#> TCGA.CJ.4902.11 1 0 1 1 0
#> TCGA.B8.A54G.01 2 0 1 0 1
#> TCGA.B0.5703.01 2 0 1 0 1
#> TCGA.CJ.5672.01 2 0 1 0 1
#> TCGA.B0.5098.11 1 0 1 1 0
#> TCGA.B0.5113.11 1 0 1 1 0
#> TCGA.CJ.4882.11 1 0 1 1 0
#> TCGA.CZ.5465.11 1 0 1 1 0
#> TCGA.B0.5102.01 2 0 1 0 1
#> TCGA.CW.5585.01 2 0 1 0 1
#> TCGA.B0.4824.01 2 0 1 0 1
#> TCGA.B0.5115.01 2 0 1 0 1
#> TCGA.B0.4706.01 2 0 1 0 1
#> TCGA.B0.5117.11 1 0 1 1 0
#> TCGA.CZ.4859.11 1 0 1 1 0
#> TCGA.AK.3450.01 2 0 1 0 1
#> TCGA.B8.A54I.01 2 0 1 0 1
#> TCGA.CZ.5463.01 2 0 1 0 1
#> TCGA.DV.5568.01 2 0 1 0 1
#> TCGA.CZ.5459.11 1 0 1 1 0
#> TCGA.CJ.4918.11 1 0 1 1 0
#> TCGA.DV.5565.01 2 0 1 0 1
#> TCGA.B0.5119.01 2 0 1 0 1
#> TCGA.B0.4811.01 2 0 1 0 1
#> TCGA.A3.3367.11 1 0 1 1 0
#> TCGA.CJ.4916.01 2 0 1 0 1
#> TCGA.B0.5693.01 2 0 1 0 1
#> TCGA.CZ.4863.11 1 0 1 1 0
#> TCGA.G6.A5PC.01 2 0 1 0 1
#> TCGA.B8.5550.01 2 0 1 0 1
#> TCGA.DV.A4W0.05 1 0 1 1 0
#> TCGA.B0.4696.01 2 0 1 0 1
#> TCGA.BP.5187.01 2 0 1 0 1
#> TCGA.CZ.5466.11 1 0 1 1 0
#> TCGA.CW.6097.01 2 0 1 0 1
#> TCGA.CJ.4905.11 1 0 1 1 0
#> TCGA.CZ.5989.01 2 0 1 0 1
#> TCGA.BP.5194.01 2 0 1 0 1
#> TCGA.B0.4707.11 1 0 1 1 0
#> TCGA.CZ.5467.01 2 0 1 0 1
#> TCGA.BP.5185.11 1 0 1 1 0
#> TCGA.BP.5183.11 1 0 1 1 0
#> TCGA.BP.5192.01 2 0 1 0 1
#> TCGA.CZ.5462.11 1 0 1 1 0
#> TCGA.BP.4177.01 1 0 1 1 0
#> TCGA.CZ.5469.01 2 0 1 0 1
#> TCGA.B2.5641.01 2 0 1 0 1
#> TCGA.BP.5196.11 1 0 1 1 0
#> TCGA.CZ.5460.01 2 0 1 0 1
#> TCGA.B0.4712.01 2 0 1 0 1
#> TCGA.B8.A54K.01 1 0 1 1 0
#> TCGA.B0.5707.01 2 0 1 0 1
#> TCGA.BP.5186.11 1 0 1 1 0
#> TCGA.EU.5906.01 2 0 1 0 1
#> TCGA.CZ.5461.11 1 0 1 1 0
#> TCGA.CW.5590.01 2 0 1 0 1
#> TCGA.B0.5698.01 2 0 1 0 1
#> TCGA.CW.5580.01 2 0 1 0 1
#> TCGA.CZ.5454.01 2 0 1 0 1
#> TCGA.B0.4815.01 2 0 1 0 1
#> TCGA.B0.5710.11 1 0 1 1 0
#> TCGA.CJ.4908.11 1 0 1 1 0
#> TCGA.BP.5201.11 1 0 1 1 0
#> TCGA.B0.5694.01 2 0 1 0 1
#> TCGA.BP.5170.01 2 0 1 0 1
#> TCGA.DV.5575.01 2 0 1 0 1
#> TCGA.CJ.5686.01 2 0 1 0 1
#> TCGA.A3.3357.01 2 0 1 0 1
#> TCGA.A3.3373.01 2 0 1 0 1
#> TCGA.B0.5690.01 2 0 1 0 1
#> TCGA.B8.4622.01 2 0 1 0 1
#> TCGA.AK.3433.01 1 0 1 1 0
#> TCGA.B0.5110.01 2 0 1 0 1
#> TCGA.BP.5180.11 1 0 1 1 0
#> TCGA.CJ.4913.01 2 0 1 0 1
#> TCGA.CJ.4908.01 2 0 1 0 1
#> TCGA.BP.4795.01 1 0 1 1 0
#> TCGA.CJ.4897.11 1 0 1 1 0
#> TCGA.B2.5636.01 1 0 1 1 0
#> TCGA.CJ.4923.11 1 0 1 1 0
#> TCGA.B0.4819.01 2 0 1 0 1
#> TCGA.B2.5633.01 2 0 1 0 1
#> TCGA.CJ.6033.01 2 0 1 0 1
#> TCGA.BP.5181.11 1 0 1 1 0
#> TCGA.B0.4698.01 2 0 1 0 1
#> TCGA.B0.5083.11 1 0 1 1 0
#> TCGA.CZ.4864.11 1 0 1 1 0
#> TCGA.B0.4688.01 2 0 1 0 1
#> TCGA.BP.5168.01 2 0 1 0 1
#> TCGA.BP.5198.11 1 0 1 1 0
#> TCGA.B8.5162.01 2 0 1 0 1
#> TCGA.B0.5096.01 2 0 1 0 1
#> TCGA.BP.5178.01 2 0 1 0 1
#> TCGA.B0.5099.11 1 0 1 1 0
#> TCGA.B0.4842.01 2 0 1 0 1
#> TCGA.BP.5169.11 1 0 1 1 0
#> TCGA.B0.5109.11 1 0 1 1 0
#> TCGA.CJ.4920.11 1 0 1 1 0
#> TCGA.B0.5080.11 1 0 1 1 0
#> TCGA.B0.5700.01 2 0 1 0 1
#> TCGA.B0.4847.01 2 0 1 0 1
#> TCGA.B0.5702.01 2 0 1 0 1
#> TCGA.CJ.4905.01 2 0 1 0 1
#> TCGA.B2.5635.01 2 0 1 0 1
#> TCGA.B0.5107.01 2 0 1 0 1
#> TCGA.CW.5584.01 2 0 1 0 1
#> TCGA.B4.5838.01 2 0 1 0 1
#> TCGA.BP.5199.01 2 0 1 0 1
#> TCGA.A3.3376.01 2 0 1 0 1
#> TCGA.B0.4845.11 1 0 1 1 0
#> TCGA.B0.4699.11 1 0 1 1 0
#> TCGA.BP.5174.01 2 0 1 0 1
#> TCGA.CZ.5986.01 2 0 1 0 1
#> TCGA.CJ.4901.01 2 0 1 0 1
#> TCGA.AK.3461.01 2 0 1 0 1
#> TCGA.AK.3460.01 2 0 1 0 1
#> TCGA.AK.3454.01 2 0 1 0 1
#> TCGA.CZ.4859.01 2 0 1 0 1
#> TCGA.B0.5812.01 2 0 1 0 1
#> TCGA.B0.5116.11 1 0 1 1 0
#> TCGA.B8.A54F.01 2 0 1 0 1
#> TCGA.CW.6090.01 2 0 1 0 1
#> TCGA.CZ.5458.11 1 0 1 1 0
#> TCGA.B0.5106.11 1 0 1 1 0
#> TCGA.CZ.4866.01 2 0 1 0 1
#> TCGA.B0.4828.01 2 0 1 0 1
#> TCGA.AK.3440.01 1 0 1 1 0
#> TCGA.MM.A563.01 2 0 1 0 1
#> TCGA.B0.4697.01 2 0 1 0 1
#> TCGA.AK.3458.01 2 0 1 0 1
#> TCGA.CJ.5676.01 2 0 1 0 1
#> TCGA.B0.5402.11 1 0 1 1 0
#> TCGA.CJ.5681.01 2 0 1 0 1
#> TCGA.A3.3370.11 1 0 1 1 0
#> TCGA.A3.A6NL.01 2 0 1 0 1
#> TCGA.B0.4693.01 2 0 1 0 1
#> TCGA.A3.3358.01 2 0 1 0 1
#> TCGA.B0.4710.01 2 0 1 0 1
#> TCGA.CZ.4853.11 1 0 1 1 0
#> TCGA.B4.5835.01 2 0 1 0 1
#> TCGA.CJ.4882.01 2 0 1 0 1
#> TCGA.CZ.5465.01 2 0 1 0 1
#> TCGA.B0.5102.11 1 0 1 1 0
#> TCGA.B0.4824.11 1 0 1 1 0
#> TCGA.CJ.5675.01 2 0 1 0 1
#> TCGA.B0.4700.01 2 0 1 0 1
#> TCGA.B0.5092.01 2 0 1 0 1
#> TCGA.B0.5115.11 1 0 1 1 0
#> TCGA.B0.4945.11 1 0 1 1 0
#> TCGA.B8.5158.01 2 0 1 0 1
#> TCGA.CJ.6030.01 2 0 1 0 1
#> TCGA.B8.A54E.01 2 0 1 0 1
#> TCGA.CJ.6032.01 2 0 1 0 1
#> TCGA.B0.4852.11 1 0 1 1 0
#> TCGA.B0.4817.01 2 0 1 0 1
#> TCGA.B8.5159.01 2 0 1 0 1
#> TCGA.A3.A8OW.01 2 0 1 0 1
#> TCGA.B0.4822.01 2 0 1 0 1
#> TCGA.B0.5696.01 2 0 1 0 1
#> TCGA.B0.5706.01 2 0 1 0 1
#> TCGA.CJ.4918.01 2 0 1 0 1
#> TCGA.B0.5119.11 1 0 1 1 0
#> TCGA.BP.5200.11 1 0 1 1 0
#> TCGA.B0.4811.11 1 0 1 1 0
#> TCGA.A3.3367.01 2 0 1 0 1
#> TCGA.B0.5097.01 2 0 1 0 1
#> TCGA.6D.AA2E.01 2 0 1 0 1
#> TCGA.DV.A4VX.01 2 0 1 0 1
#> TCGA.B0.4816.11 1 0 1 1 0
#> TCGA.A3.3385.11 1 0 1 1 0
#> TCGA.DV.5569.01 2 0 1 0 1
#> TCGA.EU.5907.01 2 0 1 0 1
#> TCGA.CZ.5455.01 2 0 1 0 1
#> TCGA.B8.5545.01 2 0 1 0 1
#> TCGA.DV.5567.01 1 0 1 1 0
#> TCGA.CZ.5451.01 2 0 1 0 1
#> TCGA.CJ.4869.01 2 0 1 0 1
#> TCGA.CJ.5678.01 2 0 1 0 1
#> TCGA.B8.4153.01 2 0 1 0 1
#> TCGA.B0.5121.11 1 0 1 1 0
#> TCGA.B8.4146.01 2 0 1 0 1
#> TCGA.BP.5183.01 2 0 1 0 1
#> TCGA.B0.5399.01 2 0 1 0 1
#> TCGA.B0.4810.11 1 0 1 1 0
#> TCGA.AK.3445.01 2 0 1 0 1
#> TCGA.B4.5378.01 1 0 1 1 0
#> TCGA.BP.5196.01 2 0 1 0 1
#> TCGA.CZ.4865.11 1 0 1 1 0
#> TCGA.B0.5709.01 2 0 1 0 1
#> TCGA.B0.4712.11 1 0 1 1 0
#> TCGA.B0.4714.01 2 0 1 0 1
#> TCGA.B8.5549.01 2 0 1 0 1
#> TCGA.CZ.5461.01 2 0 1 0 1
#> TCGA.CZ.5457.01 2 0 1 0 1
#> TCGA.A3.A8CQ.01 2 0 1 0 1
#> TCGA.DV.5573.01 2 0 1 0 1
#> TCGA.B0.4815.11 1 0 1 1 0
#> TCGA.B0.5710.01 2 0 1 0 1
#> TCGA.B8.5165.01 2 0 1 0 1
#> TCGA.B0.4718.01 2 0 1 0 1
#> TCGA.B2.5639.01 2 0 1 0 1
#> TCGA.CW.5583.01 2 0 1 0 1
#> TCGA.GK.A6C7.01 2 0 1 0 1
#> TCGA.A3.3357.11 1 0 1 1 0
#> TCGA.B8.5552.01 2 0 1 0 1
#> TCGA.B0.5120.01 2 0 1 0 1
#> TCGA.A3.3373.11 1 0 1 1 0
#> TCGA.BP.5185.01 2 0 1 0 1
#> TCGA.B0.4846.01 2 0 1 0 1
#> TCGA.CJ.4904.01 2 0 1 0 1
#> TCGA.CJ.4913.11 1 0 1 1 0
#> TCGA.BP.4993.11 1 0 1 1 0
#> TCGA.B0.4823.11 1 0 1 1 0
#> TCGA.CJ.4897.01 2 0 1 0 1
#> TCGA.BP.4993.01 2 0 1 0 1
#> TCGA.B4.5843.01 2 0 1 0 1
#> TCGA.DV.5576.01 1 0 1 1 0
#> TCGA.CJ.4923.01 2 0 1 0 1
#> TCGA.B0.4819.11 1 0 1 1 0
#> TCGA.BP.5175.01 2 0 1 0 1
#> TCGA.CZ.5987.01 2 0 1 0 1
#> TCGA.CZ.4864.01 2 0 1 0 1
#> TCGA.B0.4688.11 1 0 1 1 0
#> TCGA.BP.5168.11 1 0 1 1 0
#> TCGA.BP.5198.01 2 0 1 0 1
#> TCGA.B8.A7U6.01 2 0 1 0 1
#> TCGA.B0.5094.01 2 0 1 0 1
#> TCGA.T7.A92I.01 2 0 1 0 1
#> TCGA.B0.5096.11 1 0 1 1 0
#> TCGA.B0.5400.11 1 0 1 1 0
#> TCGA.B0.4694.11 1 0 1 1 0
#> TCGA.B0.5099.01 2 0 1 0 1
#> TCGA.CZ.5468.01 2 0 1 0 1
#> TCGA.B0.4842.11 1 0 1 1 0
#> TCGA.CZ.5988.01 2 0 1 0 1
#> TCGA.BP.5169.01 2 0 1 0 1
#> TCGA.B0.5109.01 2 0 1 0 1
#> TCGA.B4.5834.01 2 0 1 0 1
#> TCGA.B0.5095.11 1 0 1 1 0
#> TCGA.B0.5080.01 2 0 1 0 1
#> TCGA.CJ.5680.01 2 0 1 0 1
#> TCGA.CZ.5470.01 2 0 1 0 1
#> TCGA.CZ.4865.01 2 0 1 0 1
#> TCGA.A3.A8OX.01 2 0 1 0 1
#> TCGA.B0.4690.11 1 0 1 1 0
#> TCGA.CJ.5684.01 2 0 1 0 1
#> TCGA.B0.4844.01 2 0 1 0 1
#> TCGA.CZ.5464.01 2 0 1 0 1
#> TCGA.B0.4701.01 2 0 1 0 1
#> TCGA.B0.5701.01 2 0 1 0 1
#> TCGA.BP.5199.11 1 0 1 1 0
#> TCGA.CJ.5671.01 2 0 1 0 1
#> TCGA.A3.A8OV.01 2 0 1 0 1
#> TCGA.CZ.5456.11 1 0 1 1 0
#> TCGA.B0.5116.01 2 0 1 0 1
#> TCGA.CZ.5458.01 2 0 1 0 1
#> TCGA.CZ.5982.01 2 0 1 0 1
#> TCGA.B0.4828.11 1 0 1 1 0
#> TCGA.CJ.5679.01 2 0 1 0 1
#> TCGA.CJ.5682.01 2 0 1 0 1
#> TCGA.B0.5697.01 2 0 1 0 1
#> TCGA.B0.4697.11 1 0 1 1 0
#> TCGA.BP.4782.11 1 0 1 1 0
#> TCGA.G6.A8L8.01 2 0 1 0 1
#> TCGA.A3.A6NJ.01 2 0 1 0 1
#> TCGA.A3.3370.01 2 0 1 0 1
#> TCGA.B0.4691.01 2 0 1 0 1
#> TCGA.CZ.5452.11 1 0 1 1 0
#> TCGA.B0.4693.11 1 0 1 1 0
#> TCGA.B0.4945.01 2 0 1 0 1
#> TCGA.CZ.4853.01 2 0 1 0 1
#> TCGA.B0.5092.11 1 0 1 1 0
#> TCGA.B0.5402.01 2 0 1 0 1
#> TCGA.B0.4849.11 1 0 1 1 0
#> TCGA.A3.A6NN.01 2 0 1 0 1
#> TCGA.B0.4852.01 2 0 1 0 1
#> TCGA.B0.4817.11 1 0 1 1 0
#> TCGA.BP.5176.11 1 0 1 1 0
#> TCGA.CW.5589.01 2 0 1 0 1
#> TCGA.CJ.5689.01 2 0 1 0 1
#> TCGA.B0.4822.11 1 0 1 1 0
#> TCGA.BP.5190.11 1 0 1 1 0
#> TCGA.B0.4813.01 2 0 1 0 1
#> TCGA.BP.5200.01 2 0 1 0 1
#> TCGA.G6.A8L7.01 2 0 1 0 1
#> TCGA.B2.4101.01 2 0 1 0 1
#> TCGA.B0.4713.11 1 0 1 1 0
#> TCGA.B0.4816.01 2 0 1 0 1
#> TCGA.A3.3385.01 2 0 1 0 1
#> TCGA.B2.3924.01 2 0 1 0 1
#> TCGA.CZ.5455.11 1 0 1 1 0
#> TCGA.B0.5713.01 2 0 1 0 1
#> TCGA.B0.5108.01 2 0 1 0 1
#> TCGA.B0.5711.01 2 0 1 0 1
#> TCGA.CZ.5453.01 2 0 1 0 1
#> TCGA.BP.5202.11 1 0 1 1 0
#> TCGA.BP.5173.01 2 0 1 0 1
#> TCGA.CZ.5451.11 1 0 1 1 0
#> TCGA.B8.A8YJ.01 2 0 1 0 1
#> TCGA.B0.4848.01 2 0 1 0 1
#> TCGA.DV.A4VZ.01 1 0 1 1 0
#> TCGA.B0.4814.11 1 0 1 1 0
#> TCGA.CJ.4869.11 1 0 1 1 0
#> TCGA.CJ.4907.11 1 0 1 1 0
#> TCGA.B8.5553.01 2 0 1 0 1
#> TCGA.MW.A4EC.01 2 0 1 0 1
#> TCGA.B0.5712.11 1 0 1 1 0
#> TCGA.EU.5905.01 2 0 1 0 1
#> TCGA.CZ.5985.01 2 0 1 0 1
#> TCGA.CZ.4856.01 2 0 1 0 1
#> TCGA.BP.5184.01 2 0 1 0 1
#> TCGA.B0.5121.01 2 0 1 0 1
#> TCGA.BP.5191.01 2 0 1 0 1
#> TCGA.BP.4801.11 1 0 1 1 0
#> TCGA.BP.5177.01 2 0 1 0 1
#> TCGA.B0.5110.11 1 0 1 1 0
#> TCGA.B0.4810.01 2 0 1 0 1
#> TCGA.CJ.4903.11 1 0 1 1 0
#> TCGA.CJ.4912.11 1 0 1 1 0
#> TCGA.B8.4621.01 2 0 1 0 1
#> TCGA.B4.5832.01 2 0 1 0 1
#> TCGA.CW.6088.01 2 0 1 0 1
#> TCGA.AK.3428.01 2 0 1 0 1
#> TCGA.B8.5164.01 2 0 1 0 1
#> TCGA.BP.5195.01 2 0 1 0 1
#> TCGA.CJ.6027.01 2 0 1 0 1
#> TCGA.3Z.A93Z.01 2 0 1 0 1
#> TCGA.B0.4714.11 1 0 1 1 0
#> TCGA.B0.4818.11 1 0 1 1 0
#> TCGA.CZ.5457.11 1 0 1 1 0
#> TCGA.BP.5010.01 2 0 1 0 1
#> TCGA.BP.5189.11 1 0 1 1 0
#> TCGA.B0.4703.01 2 0 1 0 1
#> TCGA.B0.4718.11 1 0 1 1 0
#> TCGA.B0.5097.11 1 0 1 1 0
#> TCGA.BP.4760.11 1 0 1 1 0
#> TCGA.B0.5120.11 1 0 1 1 0
#> TCGA.B0.4843.11 1 0 1 1 0
#> TCGA.B0.5104.01 2 0 1 0 1
#> TCGA.CW.5587.01 2 0 1 0 1
cbind(get_classes(res, k = 3), get_membership(res, k = 3))
#> class entropy silhouette p1 p2 p3
#> TCGA.CZ.4863.01 2 0.4796 0.833 0.00 0.78 0.22
#> TCGA.CJ.4904.11 1 0.0000 0.994 1.00 0.00 0.00
#> TCGA.B0.4827.11 1 0.0000 0.994 1.00 0.00 0.00
#> TCGA.CJ.4902.01 2 0.0000 0.921 0.00 1.00 0.00
#> TCGA.B0.4823.01 2 0.4796 0.833 0.00 0.78 0.22
#> TCGA.CW.6087.01 2 0.0000 0.921 0.00 1.00 0.00
#> TCGA.B0.5098.01 3 0.0000 0.789 0.00 0.00 1.00
#> TCGA.B0.5113.01 2 0.0000 0.921 0.00 1.00 0.00
#> TCGA.DV.5566.01 2 0.1529 0.908 0.00 0.96 0.04
#> TCGA.BP.5175.11 1 0.0000 0.994 1.00 0.00 0.00
#> TCGA.BP.5181.01 2 0.4796 0.833 0.00 0.78 0.22
#> TCGA.B0.4706.11 1 0.0000 0.994 1.00 0.00 0.00
#> TCGA.B0.5117.01 1 0.0000 0.994 1.00 0.00 0.00
#> TCGA.MM.A564.01 2 0.0000 0.921 0.00 1.00 0.00
#> TCGA.B0.4821.11 3 0.4796 0.854 0.22 0.00 0.78
#> TCGA.CZ.5463.11 1 0.0000 0.994 1.00 0.00 0.00
#> TCGA.BP.5182.11 1 0.0000 0.994 1.00 0.00 0.00
#> TCGA.DV.5574.01 2 0.4796 0.833 0.00 0.78 0.22
#> TCGA.B0.5094.11 1 0.0000 0.994 1.00 0.00 0.00
#> TCGA.MM.A84U.01 2 0.0000 0.921 0.00 1.00 0.00
#> TCGA.B0.5100.11 3 0.5835 0.709 0.34 0.00 0.66
#> TCGA.B4.5844.01 2 0.0000 0.921 0.00 1.00 0.00
#> TCGA.CZ.5459.01 2 0.0000 0.921 0.00 1.00 0.00
#> TCGA.B0.4694.01 2 0.0000 0.921 0.00 1.00 0.00
#> TCGA.CZ.5468.11 1 0.0000 0.994 1.00 0.00 0.00
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#> TCGA.B4.5836.01 2 0.4555 0.842 0.00 0.80 0.20
#> TCGA.B0.5095.01 2 0.0000 0.921 0.00 1.00 0.00
#> TCGA.B0.4846.11 1 0.0000 0.994 1.00 0.00 0.00
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#> TCGA.B4.5377.01 2 0.4796 0.833 0.00 0.78 0.22
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#> TCGA.CZ.5467.11 1 0.0000 0.994 1.00 0.00 0.00
#> TCGA.B0.5705.01 2 0.4796 0.833 0.00 0.78 0.22
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#> TCGA.CZ.5454.11 1 0.0000 0.994 1.00 0.00 0.00
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#> TCGA.BP.5182.01 2 0.4796 0.833 0.00 0.78 0.22
#> TCGA.B0.5711.11 1 0.0000 0.994 1.00 0.00 0.00
#> TCGA.BP.5180.01 2 0.0000 0.921 0.00 1.00 0.00
#> TCGA.BP.5176.01 2 0.4796 0.833 0.00 0.78 0.22
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#> TCGA.B0.4713.01 2 0.0000 0.921 0.00 1.00 0.00
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#> TCGA.B0.4698.11 1 0.0000 0.994 1.00 0.00 0.00
#> TCGA.B0.5713.11 1 0.0000 0.994 1.00 0.00 0.00
#> TCGA.B0.5108.11 1 0.0000 0.994 1.00 0.00 0.00
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#> TCGA.B0.5699.01 2 0.0000 0.921 0.00 1.00 0.00
#> TCGA.CZ.5453.11 1 0.0000 0.994 1.00 0.00 0.00
#> TCGA.BP.5202.01 2 0.0000 0.921 0.00 1.00 0.00
#> TCGA.BP.5173.11 1 0.0000 0.994 1.00 0.00 0.00
#> TCGA.CW.5581.01 2 0.0000 0.921 0.00 1.00 0.00
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#> TCGA.B0.4814.01 2 0.0000 0.921 0.00 1.00 0.00
#> TCGA.BP.5178.11 1 0.0000 0.994 1.00 0.00 0.00
#> TCGA.CJ.4907.01 2 0.0000 0.921 0.00 1.00 0.00
#> TCGA.A3.3387.01 2 0.0000 0.921 0.00 1.00 0.00
#> TCGA.B0.4821.01 2 0.0000 0.921 0.00 1.00 0.00
#> TCGA.B0.5712.01 2 0.0000 0.921 0.00 1.00 0.00
#> TCGA.B0.5695.01 2 0.4796 0.833 0.00 0.78 0.22
#> TCGA.BP.5184.11 1 0.0000 0.994 1.00 0.00 0.00
#> TCGA.B2.A4SR.01 2 0.4291 0.851 0.00 0.82 0.18
#> TCGA.BP.5191.11 3 0.5397 0.796 0.28 0.00 0.72
#> TCGA.CJ.4920.01 2 0.0000 0.921 0.00 1.00 0.00
#> TCGA.BP.4801.01 2 0.4796 0.833 0.00 0.78 0.22
#> TCGA.DV.A4W0.01 2 0.0000 0.921 0.00 1.00 0.00
#> TCGA.BP.5177.11 1 0.0000 0.994 1.00 0.00 0.00
#> TCGA.B0.4847.11 1 0.0000 0.994 1.00 0.00 0.00
#> TCGA.B0.5100.01 2 0.4002 0.860 0.00 0.84 0.16
#> TCGA.CJ.4903.01 2 0.0000 0.921 0.00 1.00 0.00
#> TCGA.CJ.4912.01 2 0.0000 0.921 0.00 1.00 0.00
#> TCGA.B0.5107.11 1 0.0000 0.994 1.00 0.00 0.00
#> TCGA.AK.3453.01 1 0.0000 0.994 1.00 0.00 0.00
#> TCGA.B0.5691.01 2 0.6192 0.558 0.00 0.58 0.42
#> TCGA.BP.5195.11 1 0.0000 0.994 1.00 0.00 0.00
#> TCGA.B0.5400.01 2 0.4796 0.833 0.00 0.78 0.22
#> TCGA.A3.3376.11 3 0.4796 0.854 0.22 0.00 0.78
#> TCGA.B0.4845.01 2 0.0000 0.921 0.00 1.00 0.00
#> TCGA.B0.4699.01 3 0.4796 0.854 0.22 0.00 0.78
#> TCGA.B0.4818.01 2 0.0000 0.921 0.00 1.00 0.00
#> TCGA.BP.5174.11 1 0.0000 0.994 1.00 0.00 0.00
#> TCGA.CJ.4901.11 1 0.0000 0.994 1.00 0.00 0.00
#> TCGA.B8.A54D.01 2 0.0000 0.921 0.00 1.00 0.00
#> TCGA.BP.4770.11 1 0.0000 0.994 1.00 0.00 0.00
#> TCGA.CW.6093.01 2 0.4796 0.833 0.00 0.78 0.22
#> TCGA.BP.5010.11 1 0.0000 0.994 1.00 0.00 0.00
#> TCGA.AK.3431.01 2 0.3686 0.869 0.00 0.86 0.14
#> TCGA.BP.4770.01 2 0.4796 0.833 0.00 0.78 0.22
#> TCGA.BP.5189.01 2 0.0000 0.921 0.00 1.00 0.00
#> TCGA.B0.4703.11 1 0.0000 0.994 1.00 0.00 0.00
#> TCGA.B8.5163.01 2 0.0000 0.921 0.00 1.00 0.00
#> TCGA.CJ.5683.01 2 0.4796 0.833 0.00 0.78 0.22
#> TCGA.CZ.4856.11 1 0.0000 0.994 1.00 0.00 0.00
#> TCGA.BP.4760.01 3 0.4796 0.854 0.22 0.00 0.78
#> TCGA.B0.5692.01 2 0.0000 0.921 0.00 1.00 0.00
#> TCGA.B0.5106.01 2 0.0000 0.921 0.00 1.00 0.00
#> TCGA.B0.4843.01 2 0.0000 0.921 0.00 1.00 0.00
#> TCGA.CZ.4866.11 1 0.0000 0.994 1.00 0.00 0.00
#> TCGA.B0.5104.11 1 0.0000 0.994 1.00 0.00 0.00
#> TCGA.B0.4827.01 2 0.0000 0.921 0.00 1.00 0.00
#> TCGA.CJ.4902.11 1 0.0000 0.994 1.00 0.00 0.00
#> TCGA.B8.A54G.01 2 0.0000 0.921 0.00 1.00 0.00
#> TCGA.B0.5703.01 2 0.0000 0.921 0.00 1.00 0.00
#> TCGA.CJ.5672.01 2 0.0000 0.921 0.00 1.00 0.00
#> TCGA.B0.5098.11 3 0.5397 0.796 0.28 0.00 0.72
#> TCGA.B0.5113.11 1 0.0000 0.994 1.00 0.00 0.00
#> TCGA.CJ.4882.11 1 0.0000 0.994 1.00 0.00 0.00
#> TCGA.CZ.5465.11 1 0.0000 0.994 1.00 0.00 0.00
#> TCGA.B0.5102.01 2 0.4796 0.833 0.00 0.78 0.22
#> TCGA.CW.5585.01 2 0.0000 0.921 0.00 1.00 0.00
#> TCGA.B0.4824.01 2 0.4796 0.833 0.00 0.78 0.22
#> TCGA.B0.5115.01 2 0.0000 0.921 0.00 1.00 0.00
#> TCGA.B0.4706.01 2 0.0000 0.921 0.00 1.00 0.00
#> TCGA.B0.5117.11 1 0.0000 0.994 1.00 0.00 0.00
#> TCGA.CZ.4859.11 1 0.0000 0.994 1.00 0.00 0.00
#> TCGA.AK.3450.01 2 0.0000 0.921 0.00 1.00 0.00
#> TCGA.B8.A54I.01 2 0.0000 0.921 0.00 1.00 0.00
#> TCGA.CZ.5463.01 2 0.0000 0.921 0.00 1.00 0.00
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#> TCGA.CZ.5459.11 1 0.0000 0.994 1.00 0.00 0.00
#> TCGA.CJ.4918.11 1 0.0000 0.994 1.00 0.00 0.00
#> TCGA.DV.5565.01 2 0.0000 0.921 0.00 1.00 0.00
#> TCGA.B0.5119.01 2 0.4796 0.833 0.00 0.78 0.22
#> TCGA.B0.4811.01 2 0.0000 0.921 0.00 1.00 0.00
#> TCGA.A3.3367.11 1 0.0000 0.994 1.00 0.00 0.00
#> TCGA.CJ.4916.01 2 0.0000 0.921 0.00 1.00 0.00
#> TCGA.B0.5693.01 2 0.4796 0.833 0.00 0.78 0.22
#> TCGA.CZ.4863.11 1 0.0000 0.994 1.00 0.00 0.00
#> TCGA.G6.A5PC.01 2 0.0000 0.921 0.00 1.00 0.00
#> TCGA.B8.5550.01 2 0.4796 0.833 0.00 0.78 0.22
#> TCGA.DV.A4W0.05 3 0.4796 0.854 0.22 0.00 0.78
#> TCGA.B0.4696.01 2 0.0000 0.921 0.00 1.00 0.00
#> TCGA.BP.5187.01 2 0.4796 0.833 0.00 0.78 0.22
#> TCGA.CZ.5466.11 1 0.0000 0.994 1.00 0.00 0.00
#> TCGA.CW.6097.01 2 0.4796 0.833 0.00 0.78 0.22
#> TCGA.CJ.4905.11 1 0.0000 0.994 1.00 0.00 0.00
#> TCGA.CZ.5989.01 2 0.4796 0.833 0.00 0.78 0.22
#> TCGA.BP.5194.01 2 0.4796 0.833 0.00 0.78 0.22
#> TCGA.B0.4707.11 1 0.0000 0.994 1.00 0.00 0.00
#> TCGA.CZ.5467.01 2 0.0000 0.921 0.00 1.00 0.00
#> TCGA.BP.5185.11 1 0.0000 0.994 1.00 0.00 0.00
#> TCGA.BP.5183.11 1 0.0000 0.994 1.00 0.00 0.00
#> TCGA.BP.5192.01 2 0.4796 0.833 0.00 0.78 0.22
#> TCGA.CZ.5462.11 1 0.0000 0.994 1.00 0.00 0.00
#> TCGA.BP.4177.01 3 0.4796 0.854 0.22 0.00 0.78
#> TCGA.CZ.5469.01 2 0.0000 0.921 0.00 1.00 0.00
#> TCGA.B2.5641.01 2 0.0000 0.921 0.00 1.00 0.00
#> TCGA.BP.5196.11 1 0.0000 0.994 1.00 0.00 0.00
#> TCGA.CZ.5460.01 2 0.0000 0.921 0.00 1.00 0.00
#> TCGA.B0.4712.01 2 0.0000 0.921 0.00 1.00 0.00
#> TCGA.B8.A54K.01 3 0.4796 0.854 0.22 0.00 0.78
#> TCGA.B0.5707.01 2 0.4796 0.833 0.00 0.78 0.22
#> TCGA.BP.5186.11 1 0.0000 0.994 1.00 0.00 0.00
#> TCGA.EU.5906.01 2 0.4796 0.833 0.00 0.78 0.22
#> TCGA.CZ.5461.11 1 0.0000 0.994 1.00 0.00 0.00
#> TCGA.CW.5590.01 2 0.0000 0.921 0.00 1.00 0.00
#> TCGA.B0.5698.01 2 0.0000 0.921 0.00 1.00 0.00
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#> TCGA.CZ.5454.01 2 0.0000 0.921 0.00 1.00 0.00
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#> TCGA.B0.5710.11 1 0.0000 0.994 1.00 0.00 0.00
#> TCGA.CJ.4908.11 1 0.0000 0.994 1.00 0.00 0.00
#> TCGA.BP.5201.11 1 0.0000 0.994 1.00 0.00 0.00
#> TCGA.B0.5694.01 2 0.0000 0.921 0.00 1.00 0.00
#> TCGA.BP.5170.01 2 0.3340 0.877 0.00 0.88 0.12
#> TCGA.DV.5575.01 2 0.4796 0.833 0.00 0.78 0.22
#> TCGA.CJ.5686.01 2 0.4796 0.833 0.00 0.78 0.22
#> TCGA.A3.3357.01 2 0.0000 0.921 0.00 1.00 0.00
#> TCGA.A3.3373.01 2 0.4796 0.833 0.00 0.78 0.22
#> TCGA.B0.5690.01 2 0.4796 0.833 0.00 0.78 0.22
#> TCGA.B8.4622.01 2 0.0000 0.921 0.00 1.00 0.00
#> TCGA.AK.3433.01 1 0.0000 0.994 1.00 0.00 0.00
#> TCGA.B0.5110.01 2 0.4796 0.833 0.00 0.78 0.22
#> TCGA.BP.5180.11 1 0.0000 0.994 1.00 0.00 0.00
#> TCGA.CJ.4913.01 2 0.0000 0.921 0.00 1.00 0.00
#> TCGA.CJ.4908.01 2 0.4796 0.833 0.00 0.78 0.22
#> TCGA.BP.4795.01 3 0.4796 0.854 0.22 0.00 0.78
#> TCGA.CJ.4897.11 1 0.0000 0.994 1.00 0.00 0.00
#> TCGA.B2.5636.01 3 0.0892 0.795 0.02 0.00 0.98
#> TCGA.CJ.4923.11 1 0.0000 0.994 1.00 0.00 0.00
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#> TCGA.B2.5633.01 2 0.0000 0.921 0.00 1.00 0.00
#> TCGA.CJ.6033.01 2 0.0000 0.921 0.00 1.00 0.00
#> TCGA.BP.5181.11 1 0.0000 0.994 1.00 0.00 0.00
#> TCGA.B0.4698.01 2 0.0000 0.921 0.00 1.00 0.00
#> TCGA.B0.5083.11 1 0.0000 0.994 1.00 0.00 0.00
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#> TCGA.B8.5162.01 2 0.4796 0.833 0.00 0.78 0.22
#> TCGA.B0.5096.01 2 0.0000 0.921 0.00 1.00 0.00
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#> TCGA.BP.5169.11 1 0.0000 0.994 1.00 0.00 0.00
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#> TCGA.B0.5700.01 2 0.4796 0.833 0.00 0.78 0.22
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#> TCGA.B0.5702.01 3 0.0000 0.789 0.00 0.00 1.00
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#> TCGA.BP.5174.01 2 0.4796 0.833 0.00 0.78 0.22
#> TCGA.CZ.5986.01 2 0.4796 0.833 0.00 0.78 0.22
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#> TCGA.AK.3460.01 2 0.4796 0.833 0.00 0.78 0.22
#> TCGA.AK.3454.01 2 0.4796 0.833 0.00 0.78 0.22
#> TCGA.CZ.4859.01 2 0.4796 0.833 0.00 0.78 0.22
#> TCGA.B0.5812.01 2 0.4796 0.833 0.00 0.78 0.22
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#> TCGA.CW.6090.01 2 0.0000 0.921 0.00 1.00 0.00
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#> TCGA.CZ.4866.01 2 0.0000 0.921 0.00 1.00 0.00
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#> TCGA.AK.3440.01 1 0.0000 0.994 1.00 0.00 0.00
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#> TCGA.B0.4697.01 2 0.0000 0.921 0.00 1.00 0.00
#> TCGA.AK.3458.01 2 0.0000 0.921 0.00 1.00 0.00
#> TCGA.CJ.5676.01 2 0.0000 0.921 0.00 1.00 0.00
#> TCGA.B0.5402.11 3 0.5835 0.709 0.34 0.00 0.66
#> TCGA.CJ.5681.01 3 0.0000 0.789 0.00 0.00 1.00
#> TCGA.A3.3370.11 1 0.0000 0.994 1.00 0.00 0.00
#> TCGA.A3.A6NL.01 2 0.4796 0.833 0.00 0.78 0.22
#> TCGA.B0.4693.01 2 0.0000 0.921 0.00 1.00 0.00
#> TCGA.A3.3358.01 2 0.0000 0.921 0.00 1.00 0.00
#> TCGA.B0.4710.01 2 0.0000 0.921 0.00 1.00 0.00
#> TCGA.CZ.4853.11 1 0.0000 0.994 1.00 0.00 0.00
#> TCGA.B4.5835.01 2 0.4796 0.833 0.00 0.78 0.22
#> TCGA.CJ.4882.01 2 0.0000 0.921 0.00 1.00 0.00
#> TCGA.CZ.5465.01 2 0.0000 0.921 0.00 1.00 0.00
#> TCGA.B0.5102.11 1 0.0000 0.994 1.00 0.00 0.00
#> TCGA.B0.4824.11 1 0.0000 0.994 1.00 0.00 0.00
#> TCGA.CJ.5675.01 2 0.0000 0.921 0.00 1.00 0.00
#> TCGA.B0.4700.01 2 0.4555 0.842 0.00 0.80 0.20
#> TCGA.B0.5092.01 2 0.0000 0.921 0.00 1.00 0.00
#> TCGA.B0.5115.11 1 0.0000 0.994 1.00 0.00 0.00
#> TCGA.B0.4945.11 1 0.0000 0.994 1.00 0.00 0.00
#> TCGA.B8.5158.01 2 0.0000 0.921 0.00 1.00 0.00
#> TCGA.CJ.6030.01 2 0.0000 0.921 0.00 1.00 0.00
#> TCGA.B8.A54E.01 3 0.0000 0.789 0.00 0.00 1.00
#> TCGA.CJ.6032.01 2 0.0000 0.921 0.00 1.00 0.00
#> TCGA.B0.4852.11 1 0.0000 0.994 1.00 0.00 0.00
#> TCGA.B0.4817.01 2 0.4796 0.833 0.00 0.78 0.22
#> TCGA.B8.5159.01 2 0.0000 0.921 0.00 1.00 0.00
#> TCGA.A3.A8OW.01 2 0.4796 0.833 0.00 0.78 0.22
#> TCGA.B0.4822.01 2 0.0000 0.921 0.00 1.00 0.00
#> TCGA.B0.5696.01 2 0.0000 0.921 0.00 1.00 0.00
#> TCGA.B0.5706.01 2 0.0000 0.921 0.00 1.00 0.00
#> TCGA.CJ.4918.01 2 0.4796 0.833 0.00 0.78 0.22
#> TCGA.B0.5119.11 1 0.0000 0.994 1.00 0.00 0.00
#> TCGA.BP.5200.11 1 0.0000 0.994 1.00 0.00 0.00
#> TCGA.B0.4811.11 3 0.5835 0.709 0.34 0.00 0.66
#> TCGA.A3.3367.01 2 0.0000 0.921 0.00 1.00 0.00
#> TCGA.B0.5097.01 2 0.0000 0.921 0.00 1.00 0.00
#> TCGA.6D.AA2E.01 3 0.0000 0.789 0.00 0.00 1.00
#> TCGA.DV.A4VX.01 2 0.0000 0.921 0.00 1.00 0.00
#> TCGA.B0.4816.11 1 0.0000 0.994 1.00 0.00 0.00
#> TCGA.A3.3385.11 1 0.0000 0.994 1.00 0.00 0.00
#> TCGA.DV.5569.01 2 0.4796 0.833 0.00 0.78 0.22
#> TCGA.EU.5907.01 2 0.0000 0.921 0.00 1.00 0.00
#> TCGA.CZ.5455.01 2 0.0000 0.921 0.00 1.00 0.00
#> TCGA.B8.5545.01 2 0.5560 0.750 0.00 0.70 0.30
#> TCGA.DV.5567.01 3 0.4796 0.854 0.22 0.00 0.78
#> TCGA.CZ.5451.01 2 0.0000 0.921 0.00 1.00 0.00
#> TCGA.CJ.4869.01 2 0.0000 0.921 0.00 1.00 0.00
#> TCGA.CJ.5678.01 2 0.0000 0.921 0.00 1.00 0.00
#> TCGA.B8.4153.01 2 0.0000 0.921 0.00 1.00 0.00
#> TCGA.B0.5121.11 1 0.0000 0.994 1.00 0.00 0.00
#> TCGA.B8.4146.01 2 0.2066 0.900 0.00 0.94 0.06
#> TCGA.BP.5183.01 2 0.0000 0.921 0.00 1.00 0.00
#> TCGA.B0.5399.01 2 0.0000 0.921 0.00 1.00 0.00
#> TCGA.B0.4810.11 1 0.0000 0.994 1.00 0.00 0.00
#> TCGA.AK.3445.01 2 0.0000 0.921 0.00 1.00 0.00
#> TCGA.B4.5378.01 3 0.4796 0.854 0.22 0.00 0.78
#> TCGA.BP.5196.01 2 0.0000 0.921 0.00 1.00 0.00
#> TCGA.CZ.4865.11 1 0.0000 0.994 1.00 0.00 0.00
#> TCGA.B0.5709.01 2 0.4796 0.833 0.00 0.78 0.22
#> TCGA.B0.4712.11 1 0.0000 0.994 1.00 0.00 0.00
#> TCGA.B0.4714.01 2 0.0000 0.921 0.00 1.00 0.00
#> TCGA.B8.5549.01 2 0.0000 0.921 0.00 1.00 0.00
#> TCGA.CZ.5461.01 2 0.0000 0.921 0.00 1.00 0.00
#> TCGA.CZ.5457.01 2 0.4796 0.833 0.00 0.78 0.22
#> TCGA.A3.A8CQ.01 2 0.4796 0.833 0.00 0.78 0.22
#> TCGA.DV.5573.01 2 0.4796 0.833 0.00 0.78 0.22
#> TCGA.B0.4815.11 1 0.0000 0.994 1.00 0.00 0.00
#> TCGA.B0.5710.01 2 0.0000 0.921 0.00 1.00 0.00
#> TCGA.B8.5165.01 2 0.5397 0.774 0.00 0.72 0.28
#> TCGA.B0.4718.01 2 0.0000 0.921 0.00 1.00 0.00
#> TCGA.B2.5639.01 2 0.0000 0.921 0.00 1.00 0.00
#> TCGA.CW.5583.01 2 0.4796 0.833 0.00 0.78 0.22
#> TCGA.GK.A6C7.01 2 0.4796 0.833 0.00 0.78 0.22
#> TCGA.A3.3357.11 1 0.0000 0.994 1.00 0.00 0.00
#> TCGA.B8.5552.01 2 0.4796 0.833 0.00 0.78 0.22
#> TCGA.B0.5120.01 2 0.3340 0.877 0.00 0.88 0.12
#> TCGA.A3.3373.11 1 0.0000 0.994 1.00 0.00 0.00
#> TCGA.BP.5185.01 2 0.0000 0.921 0.00 1.00 0.00
#> TCGA.B0.4846.01 2 0.4796 0.833 0.00 0.78 0.22
#> TCGA.CJ.4904.01 2 0.4796 0.833 0.00 0.78 0.22
#> TCGA.CJ.4913.11 1 0.0000 0.994 1.00 0.00 0.00
#> TCGA.BP.4993.11 1 0.0000 0.994 1.00 0.00 0.00
#> TCGA.B0.4823.11 1 0.0000 0.994 1.00 0.00 0.00
#> TCGA.CJ.4897.01 2 0.0000 0.921 0.00 1.00 0.00
#> TCGA.BP.4993.01 2 0.4796 0.833 0.00 0.78 0.22
#> TCGA.B4.5843.01 2 0.4796 0.833 0.00 0.78 0.22
#> TCGA.DV.5576.01 3 0.4796 0.854 0.22 0.00 0.78
#> TCGA.CJ.4923.01 2 0.0000 0.921 0.00 1.00 0.00
#> TCGA.B0.4819.11 1 0.0000 0.994 1.00 0.00 0.00
#> TCGA.BP.5175.01 2 0.0000 0.921 0.00 1.00 0.00
#> TCGA.CZ.5987.01 2 0.0000 0.921 0.00 1.00 0.00
#> TCGA.CZ.4864.01 2 0.4796 0.833 0.00 0.78 0.22
#> TCGA.B0.4688.11 1 0.0000 0.994 1.00 0.00 0.00
#> TCGA.BP.5168.11 1 0.0000 0.994 1.00 0.00 0.00
#> TCGA.BP.5198.01 2 0.0000 0.921 0.00 1.00 0.00
#> TCGA.B8.A7U6.01 2 0.4796 0.833 0.00 0.78 0.22
#> TCGA.B0.5094.01 2 0.0000 0.921 0.00 1.00 0.00
#> TCGA.T7.A92I.01 3 0.0000 0.789 0.00 0.00 1.00
#> TCGA.B0.5096.11 1 0.0000 0.994 1.00 0.00 0.00
#> TCGA.B0.5400.11 1 0.4555 0.684 0.80 0.00 0.20
#> TCGA.B0.4694.11 1 0.0000 0.994 1.00 0.00 0.00
#> TCGA.B0.5099.01 2 0.0000 0.921 0.00 1.00 0.00
#> TCGA.CZ.5468.01 2 0.0000 0.921 0.00 1.00 0.00
#> TCGA.B0.4842.11 1 0.0000 0.994 1.00 0.00 0.00
#> TCGA.CZ.5988.01 2 0.0000 0.921 0.00 1.00 0.00
#> TCGA.BP.5169.01 2 0.0000 0.921 0.00 1.00 0.00
#> TCGA.B0.5109.01 2 0.4796 0.833 0.00 0.78 0.22
#> TCGA.B4.5834.01 2 0.4796 0.833 0.00 0.78 0.22
#> TCGA.B0.5095.11 1 0.5016 0.597 0.76 0.00 0.24
#> TCGA.B0.5080.01 2 0.0000 0.921 0.00 1.00 0.00
#> TCGA.CJ.5680.01 2 0.0000 0.921 0.00 1.00 0.00
#> TCGA.CZ.5470.01 2 0.0000 0.921 0.00 1.00 0.00
#> TCGA.CZ.4865.01 2 0.0000 0.921 0.00 1.00 0.00
#> TCGA.A3.A8OX.01 3 0.0000 0.789 0.00 0.00 1.00
#> TCGA.B0.4690.11 1 0.0000 0.994 1.00 0.00 0.00
#> TCGA.CJ.5684.01 2 0.0000 0.921 0.00 1.00 0.00
#> TCGA.B0.4844.01 2 0.0000 0.921 0.00 1.00 0.00
#> TCGA.CZ.5464.01 2 0.0000 0.921 0.00 1.00 0.00
#> TCGA.B0.4701.01 2 0.0000 0.921 0.00 1.00 0.00
#> TCGA.B0.5701.01 2 0.0000 0.921 0.00 1.00 0.00
#> TCGA.BP.5199.11 1 0.0000 0.994 1.00 0.00 0.00
#> TCGA.CJ.5671.01 2 0.0000 0.921 0.00 1.00 0.00
#> TCGA.A3.A8OV.01 2 0.4796 0.833 0.00 0.78 0.22
#> TCGA.CZ.5456.11 1 0.0000 0.994 1.00 0.00 0.00
#> TCGA.B0.5116.01 2 0.0000 0.921 0.00 1.00 0.00
#> TCGA.CZ.5458.01 2 0.0000 0.921 0.00 1.00 0.00
#> TCGA.CZ.5982.01 2 0.0000 0.921 0.00 1.00 0.00
#> TCGA.B0.4828.11 1 0.0000 0.994 1.00 0.00 0.00
#> TCGA.CJ.5679.01 2 0.0000 0.921 0.00 1.00 0.00
#> TCGA.CJ.5682.01 2 0.0000 0.921 0.00 1.00 0.00
#> TCGA.B0.5697.01 2 0.4796 0.833 0.00 0.78 0.22
#> TCGA.B0.4697.11 1 0.0000 0.994 1.00 0.00 0.00
#> TCGA.BP.4782.11 1 0.0000 0.994 1.00 0.00 0.00
#> TCGA.G6.A8L8.01 2 0.0000 0.921 0.00 1.00 0.00
#> TCGA.A3.A6NJ.01 2 0.4796 0.833 0.00 0.78 0.22
#> TCGA.A3.3370.01 2 0.5706 0.724 0.00 0.68 0.32
#> TCGA.B0.4691.01 2 0.0000 0.921 0.00 1.00 0.00
#> TCGA.CZ.5452.11 1 0.0000 0.994 1.00 0.00 0.00
#> TCGA.B0.4693.11 1 0.0000 0.994 1.00 0.00 0.00
#> TCGA.B0.4945.01 2 0.4796 0.833 0.00 0.78 0.22
#> TCGA.CZ.4853.01 2 0.0000 0.921 0.00 1.00 0.00
#> TCGA.B0.5092.11 1 0.0000 0.994 1.00 0.00 0.00
#> TCGA.B0.5402.01 2 0.0000 0.921 0.00 1.00 0.00
#> TCGA.B0.4849.11 1 0.0000 0.994 1.00 0.00 0.00
#> TCGA.A3.A6NN.01 2 0.0000 0.921 0.00 1.00 0.00
#> TCGA.B0.4852.01 2 0.0000 0.921 0.00 1.00 0.00
#> TCGA.B0.4817.11 1 0.0000 0.994 1.00 0.00 0.00
#> TCGA.BP.5176.11 1 0.0000 0.994 1.00 0.00 0.00
#> TCGA.CW.5589.01 2 0.4796 0.833 0.00 0.78 0.22
#> TCGA.CJ.5689.01 2 0.0000 0.921 0.00 1.00 0.00
#> TCGA.B0.4822.11 1 0.0000 0.994 1.00 0.00 0.00
#> TCGA.BP.5190.11 1 0.0000 0.994 1.00 0.00 0.00
#> TCGA.B0.4813.01 2 0.0000 0.921 0.00 1.00 0.00
#> TCGA.BP.5200.01 2 0.2537 0.893 0.00 0.92 0.08
#> TCGA.G6.A8L7.01 2 0.0000 0.921 0.00 1.00 0.00
#> TCGA.B2.4101.01 2 0.0000 0.921 0.00 1.00 0.00
#> TCGA.B0.4713.11 1 0.0000 0.994 1.00 0.00 0.00
#> TCGA.B0.4816.01 2 0.0000 0.921 0.00 1.00 0.00
#> TCGA.A3.3385.01 2 0.4796 0.833 0.00 0.78 0.22
#> TCGA.B2.3924.01 2 0.4796 0.833 0.00 0.78 0.22
#> TCGA.CZ.5455.11 1 0.0000 0.994 1.00 0.00 0.00
#> TCGA.B0.5713.01 2 0.0000 0.921 0.00 1.00 0.00
#> TCGA.B0.5108.01 2 0.0000 0.921 0.00 1.00 0.00
#> TCGA.B0.5711.01 2 0.0892 0.915 0.00 0.98 0.02
#> TCGA.CZ.5453.01 2 0.4796 0.833 0.00 0.78 0.22
#> TCGA.BP.5202.11 3 0.4796 0.854 0.22 0.00 0.78
#> TCGA.BP.5173.01 2 0.4796 0.833 0.00 0.78 0.22
#> TCGA.CZ.5451.11 1 0.0000 0.994 1.00 0.00 0.00
#> TCGA.B8.A8YJ.01 2 0.4796 0.833 0.00 0.78 0.22
#> TCGA.B0.4848.01 2 0.0000 0.921 0.00 1.00 0.00
#> TCGA.DV.A4VZ.01 3 0.4796 0.854 0.22 0.00 0.78
#> TCGA.B0.4814.11 1 0.0000 0.994 1.00 0.00 0.00
#> TCGA.CJ.4869.11 1 0.0000 0.994 1.00 0.00 0.00
#> TCGA.CJ.4907.11 1 0.0000 0.994 1.00 0.00 0.00
#> TCGA.B8.5553.01 2 0.4796 0.833 0.00 0.78 0.22
#> TCGA.MW.A4EC.01 2 0.4796 0.833 0.00 0.78 0.22
#> TCGA.B0.5712.11 3 0.5397 0.796 0.28 0.00 0.72
#> TCGA.EU.5905.01 2 0.0000 0.921 0.00 1.00 0.00
#> TCGA.CZ.5985.01 2 0.0000 0.921 0.00 1.00 0.00
#> TCGA.CZ.4856.01 2 0.4796 0.833 0.00 0.78 0.22
#> TCGA.BP.5184.01 2 0.4796 0.833 0.00 0.78 0.22
#> TCGA.B0.5121.01 2 0.0000 0.921 0.00 1.00 0.00
#> TCGA.BP.5191.01 2 0.0000 0.921 0.00 1.00 0.00
#> TCGA.BP.4801.11 1 0.0000 0.994 1.00 0.00 0.00
#> TCGA.BP.5177.01 2 0.4796 0.833 0.00 0.78 0.22
#> TCGA.B0.5110.11 1 0.0000 0.994 1.00 0.00 0.00
#> TCGA.B0.4810.01 2 0.0000 0.921 0.00 1.00 0.00
#> TCGA.CJ.4903.11 1 0.0000 0.994 1.00 0.00 0.00
#> TCGA.CJ.4912.11 1 0.0000 0.994 1.00 0.00 0.00
#> TCGA.B8.4621.01 2 0.4796 0.833 0.00 0.78 0.22
#> TCGA.B4.5832.01 2 0.4555 0.842 0.00 0.80 0.20
#> TCGA.CW.6088.01 2 0.4796 0.833 0.00 0.78 0.22
#> TCGA.AK.3428.01 2 0.0000 0.921 0.00 1.00 0.00
#> TCGA.B8.5164.01 2 0.4796 0.833 0.00 0.78 0.22
#> TCGA.BP.5195.01 2 0.0000 0.921 0.00 1.00 0.00
#> TCGA.CJ.6027.01 2 0.0000 0.921 0.00 1.00 0.00
#> TCGA.3Z.A93Z.01 2 0.4796 0.833 0.00 0.78 0.22
#> TCGA.B0.4714.11 1 0.0000 0.994 1.00 0.00 0.00
#> TCGA.B0.4818.11 1 0.0000 0.994 1.00 0.00 0.00
#> TCGA.CZ.5457.11 1 0.0000 0.994 1.00 0.00 0.00
#> TCGA.BP.5010.01 2 0.0000 0.921 0.00 1.00 0.00
#> TCGA.BP.5189.11 1 0.0000 0.994 1.00 0.00 0.00
#> TCGA.B0.4703.01 2 0.0000 0.921 0.00 1.00 0.00
#> TCGA.B0.4718.11 1 0.0000 0.994 1.00 0.00 0.00
#> TCGA.B0.5097.11 1 0.0000 0.994 1.00 0.00 0.00
#> TCGA.BP.4760.11 1 0.0000 0.994 1.00 0.00 0.00
#> TCGA.B0.5120.11 1 0.0000 0.994 1.00 0.00 0.00
#> TCGA.B0.4843.11 1 0.0000 0.994 1.00 0.00 0.00
#> TCGA.B0.5104.01 2 0.4796 0.833 0.00 0.78 0.22
#> TCGA.CW.5587.01 2 0.4796 0.833 0.00 0.78 0.22
cbind(get_classes(res, k = 4), get_membership(res, k = 4))
#> class entropy silhouette p1 p2 p3 p4
#> TCGA.CZ.4863.01 4 0.0000 0.9687 0.00 0.00 0.00 1.00
#> TCGA.CJ.4904.11 1 0.0000 0.9971 1.00 0.00 0.00 0.00
#> TCGA.B0.4827.11 1 0.0000 0.9971 1.00 0.00 0.00 0.00
#> TCGA.CJ.4902.01 2 0.0000 0.9858 0.00 1.00 0.00 0.00
#> TCGA.B0.4823.01 4 0.0000 0.9687 0.00 0.00 0.00 1.00
#> TCGA.CW.6087.01 2 0.2011 0.8946 0.00 0.92 0.00 0.08
#> TCGA.B0.5098.01 3 0.0707 0.9786 0.00 0.00 0.98 0.02
#> TCGA.B0.5113.01 2 0.0000 0.9858 0.00 1.00 0.00 0.00
#> TCGA.DV.5566.01 4 0.0000 0.9687 0.00 0.00 0.00 1.00
#> TCGA.BP.5175.11 1 0.0000 0.9971 1.00 0.00 0.00 0.00
#> TCGA.BP.5181.01 4 0.0000 0.9687 0.00 0.00 0.00 1.00
#> TCGA.B0.4706.11 1 0.0000 0.9971 1.00 0.00 0.00 0.00
#> TCGA.B0.5117.01 1 0.0000 0.9971 1.00 0.00 0.00 0.00
#> TCGA.MM.A564.01 2 0.0000 0.9858 0.00 1.00 0.00 0.00
#> TCGA.B0.4821.11 3 0.0707 0.9793 0.02 0.00 0.98 0.00
#> TCGA.CZ.5463.11 1 0.0000 0.9971 1.00 0.00 0.00 0.00
#> TCGA.BP.5182.11 1 0.0000 0.9971 1.00 0.00 0.00 0.00
#> TCGA.DV.5574.01 4 0.0000 0.9687 0.00 0.00 0.00 1.00
#> TCGA.B0.5094.11 1 0.0000 0.9971 1.00 0.00 0.00 0.00
#> TCGA.MM.A84U.01 2 0.0000 0.9858 0.00 1.00 0.00 0.00
#> TCGA.B0.5100.11 3 0.1637 0.9445 0.06 0.00 0.94 0.00
#> TCGA.B4.5844.01 2 0.0000 0.9858 0.00 1.00 0.00 0.00
#> TCGA.CZ.5459.01 2 0.0000 0.9858 0.00 1.00 0.00 0.00
#> TCGA.B0.4694.01 2 0.0000 0.9858 0.00 1.00 0.00 0.00
#> TCGA.CZ.5468.11 1 0.0000 0.9971 1.00 0.00 0.00 0.00
#> TCGA.CJ.4916.11 1 0.2921 0.8370 0.86 0.00 0.14 0.00
#> TCGA.B4.5836.01 4 0.0000 0.9687 0.00 0.00 0.00 1.00
#> TCGA.B0.5095.01 4 0.1637 0.9026 0.00 0.06 0.00 0.94
#> TCGA.B0.4846.11 1 0.0000 0.9971 1.00 0.00 0.00 0.00
#> TCGA.AK.3434.01 2 0.0000 0.9858 0.00 1.00 0.00 0.00
#> TCGA.B4.5377.01 4 0.0000 0.9687 0.00 0.00 0.00 1.00
#> TCGA.B0.4696.11 1 0.0000 0.9971 1.00 0.00 0.00 0.00
#> TCGA.BP.5187.11 1 0.0000 0.9971 1.00 0.00 0.00 0.00
#> TCGA.B0.4690.01 2 0.0000 0.9858 0.00 1.00 0.00 0.00
#> TCGA.CZ.5466.01 2 0.0000 0.9858 0.00 1.00 0.00 0.00
#> TCGA.B0.4844.11 1 0.0000 0.9971 1.00 0.00 0.00 0.00
#> TCGA.CZ.5464.11 1 0.0000 0.9971 1.00 0.00 0.00 0.00
#> TCGA.B0.4701.11 1 0.0000 0.9971 1.00 0.00 0.00 0.00
#> TCGA.BP.5194.11 1 0.0000 0.9971 1.00 0.00 0.00 0.00
#> TCGA.B0.4707.01 2 0.0000 0.9858 0.00 1.00 0.00 0.00
#> TCGA.CZ.5467.11 1 0.0000 0.9971 1.00 0.00 0.00 0.00
#> TCGA.B0.5705.01 4 0.0000 0.9687 0.00 0.00 0.00 1.00
#> TCGA.CW.5588.01 4 0.1211 0.9259 0.00 0.04 0.00 0.96
#> TCGA.CJ.6031.01 4 0.3801 0.6714 0.00 0.22 0.00 0.78
#> TCGA.B8.A54J.01 4 0.0000 0.9687 0.00 0.00 0.00 1.00
#> TCGA.BP.5192.11 1 0.0000 0.9971 1.00 0.00 0.00 0.00
#> TCGA.CZ.5462.01 2 0.0000 0.9858 0.00 1.00 0.00 0.00
#> TCGA.B8.A54H.01 4 0.0000 0.9687 0.00 0.00 0.00 1.00
#> TCGA.CZ.5470.11 1 0.0000 0.9971 1.00 0.00 0.00 0.00
#> TCGA.BP.4177.11 1 0.0000 0.9971 1.00 0.00 0.00 0.00
#> TCGA.CZ.5469.11 1 0.0000 0.9971 1.00 0.00 0.00 0.00
#> TCGA.CJ.6028.01 2 0.0000 0.9858 0.00 1.00 0.00 0.00
#> TCGA.G6.A8L6.01 2 0.1211 0.9426 0.00 0.96 0.00 0.04
#> TCGA.B8.5551.01 2 0.0000 0.9858 0.00 1.00 0.00 0.00
#> TCGA.CZ.5456.01 2 0.0000 0.9858 0.00 1.00 0.00 0.00
#> TCGA.A3.A8OU.01 4 0.3400 0.7332 0.00 0.18 0.00 0.82
#> TCGA.BP.5186.01 4 0.0000 0.9687 0.00 0.00 0.00 1.00
#> TCGA.A3.A6NI.01 2 0.4624 0.4808 0.00 0.66 0.00 0.34
#> TCGA.BP.4782.01 4 0.0000 0.9687 0.00 0.00 0.00 1.00
#> TCGA.CZ.5454.11 1 0.0000 0.9971 1.00 0.00 0.00 0.00
#> TCGA.B0.4691.11 1 0.0000 0.9971 1.00 0.00 0.00 0.00
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#> TCGA.B0.5696.01 2 0.0000 0.9858 0.00 1.00 0.00 0.00
#> TCGA.B0.5706.01 2 0.0000 0.9858 0.00 1.00 0.00 0.00
#> TCGA.CJ.4918.01 4 0.0000 0.9687 0.00 0.00 0.00 1.00
#> TCGA.B0.5119.11 1 0.0000 0.9971 1.00 0.00 0.00 0.00
#> TCGA.BP.5200.11 1 0.0000 0.9971 1.00 0.00 0.00 0.00
#> TCGA.B0.4811.11 3 0.1637 0.9445 0.06 0.00 0.94 0.00
#> TCGA.A3.3367.01 2 0.0000 0.9858 0.00 1.00 0.00 0.00
#> TCGA.B0.5097.01 2 0.0000 0.9858 0.00 1.00 0.00 0.00
#> TCGA.6D.AA2E.01 3 0.0707 0.9786 0.00 0.00 0.98 0.02
#> TCGA.DV.A4VX.01 2 0.0000 0.9858 0.00 1.00 0.00 0.00
#> TCGA.B0.4816.11 1 0.0000 0.9971 1.00 0.00 0.00 0.00
#> TCGA.A3.3385.11 1 0.0000 0.9971 1.00 0.00 0.00 0.00
#> TCGA.DV.5569.01 4 0.0000 0.9687 0.00 0.00 0.00 1.00
#> TCGA.EU.5907.01 2 0.0000 0.9858 0.00 1.00 0.00 0.00
#> TCGA.CZ.5455.01 2 0.0000 0.9858 0.00 1.00 0.00 0.00
#> TCGA.B8.5545.01 4 0.0000 0.9687 0.00 0.00 0.00 1.00
#> TCGA.DV.5567.01 3 0.0000 0.9815 0.00 0.00 1.00 0.00
#> TCGA.CZ.5451.01 2 0.0000 0.9858 0.00 1.00 0.00 0.00
#> TCGA.CJ.4869.01 2 0.0000 0.9858 0.00 1.00 0.00 0.00
#> TCGA.CJ.5678.01 2 0.0000 0.9858 0.00 1.00 0.00 0.00
#> TCGA.B8.4153.01 2 0.0000 0.9858 0.00 1.00 0.00 0.00
#> TCGA.B0.5121.11 1 0.0000 0.9971 1.00 0.00 0.00 0.00
#> TCGA.B8.4146.01 4 0.1637 0.9024 0.00 0.06 0.00 0.94
#> TCGA.BP.5183.01 2 0.0000 0.9858 0.00 1.00 0.00 0.00
#> TCGA.B0.5399.01 4 0.2011 0.8781 0.00 0.08 0.00 0.92
#> TCGA.B0.4810.11 1 0.0000 0.9971 1.00 0.00 0.00 0.00
#> TCGA.AK.3445.01 2 0.0000 0.9858 0.00 1.00 0.00 0.00
#> TCGA.B4.5378.01 3 0.0000 0.9815 0.00 0.00 1.00 0.00
#> TCGA.BP.5196.01 2 0.0000 0.9858 0.00 1.00 0.00 0.00
#> TCGA.CZ.4865.11 1 0.0000 0.9971 1.00 0.00 0.00 0.00
#> TCGA.B0.5709.01 4 0.0000 0.9687 0.00 0.00 0.00 1.00
#> TCGA.B0.4712.11 1 0.0000 0.9971 1.00 0.00 0.00 0.00
#> TCGA.B0.4714.01 2 0.0000 0.9858 0.00 1.00 0.00 0.00
#> TCGA.B8.5549.01 2 0.0000 0.9858 0.00 1.00 0.00 0.00
#> TCGA.CZ.5461.01 2 0.0000 0.9858 0.00 1.00 0.00 0.00
#> TCGA.CZ.5457.01 4 0.0000 0.9687 0.00 0.00 0.00 1.00
#> TCGA.A3.A8CQ.01 4 0.0000 0.9687 0.00 0.00 0.00 1.00
#> TCGA.DV.5573.01 4 0.0000 0.9687 0.00 0.00 0.00 1.00
#> TCGA.B0.4815.11 1 0.0000 0.9971 1.00 0.00 0.00 0.00
#> TCGA.B0.5710.01 2 0.0000 0.9858 0.00 1.00 0.00 0.00
#> TCGA.B8.5165.01 4 0.0000 0.9687 0.00 0.00 0.00 1.00
#> TCGA.B0.4718.01 2 0.0000 0.9858 0.00 1.00 0.00 0.00
#> TCGA.B2.5639.01 2 0.0000 0.9858 0.00 1.00 0.00 0.00
#> TCGA.CW.5583.01 4 0.0000 0.9687 0.00 0.00 0.00 1.00
#> TCGA.GK.A6C7.01 4 0.0000 0.9687 0.00 0.00 0.00 1.00
#> TCGA.A3.3357.11 1 0.0000 0.9971 1.00 0.00 0.00 0.00
#> TCGA.B8.5552.01 4 0.0000 0.9687 0.00 0.00 0.00 1.00
#> TCGA.B0.5120.01 4 0.0000 0.9687 0.00 0.00 0.00 1.00
#> TCGA.A3.3373.11 1 0.0000 0.9971 1.00 0.00 0.00 0.00
#> TCGA.BP.5185.01 4 0.4855 0.3505 0.00 0.40 0.00 0.60
#> TCGA.B0.4846.01 4 0.0000 0.9687 0.00 0.00 0.00 1.00
#> TCGA.CJ.4904.01 4 0.0000 0.9687 0.00 0.00 0.00 1.00
#> TCGA.CJ.4913.11 1 0.0000 0.9971 1.00 0.00 0.00 0.00
#> TCGA.BP.4993.11 1 0.0000 0.9971 1.00 0.00 0.00 0.00
#> TCGA.B0.4823.11 1 0.0000 0.9971 1.00 0.00 0.00 0.00
#> TCGA.CJ.4897.01 2 0.4134 0.6274 0.00 0.74 0.00 0.26
#> TCGA.BP.4993.01 4 0.0000 0.9687 0.00 0.00 0.00 1.00
#> TCGA.B4.5843.01 4 0.0000 0.9687 0.00 0.00 0.00 1.00
#> TCGA.DV.5576.01 3 0.0000 0.9815 0.00 0.00 1.00 0.00
#> TCGA.CJ.4923.01 4 0.0000 0.9687 0.00 0.00 0.00 1.00
#> TCGA.B0.4819.11 1 0.0000 0.9971 1.00 0.00 0.00 0.00
#> TCGA.BP.5175.01 2 0.0000 0.9858 0.00 1.00 0.00 0.00
#> TCGA.CZ.5987.01 2 0.0000 0.9858 0.00 1.00 0.00 0.00
#> TCGA.CZ.4864.01 4 0.0000 0.9687 0.00 0.00 0.00 1.00
#> TCGA.B0.4688.11 1 0.0000 0.9971 1.00 0.00 0.00 0.00
#> TCGA.BP.5168.11 1 0.0000 0.9971 1.00 0.00 0.00 0.00
#> TCGA.BP.5198.01 2 0.0000 0.9858 0.00 1.00 0.00 0.00
#> TCGA.B8.A7U6.01 4 0.0000 0.9687 0.00 0.00 0.00 1.00
#> TCGA.B0.5094.01 2 0.0000 0.9858 0.00 1.00 0.00 0.00
#> TCGA.T7.A92I.01 3 0.0707 0.9786 0.00 0.00 0.98 0.02
#> TCGA.B0.5096.11 1 0.0000 0.9971 1.00 0.00 0.00 0.00
#> TCGA.B0.5400.11 1 0.2647 0.8630 0.88 0.00 0.12 0.00
#> TCGA.B0.4694.11 1 0.0000 0.9971 1.00 0.00 0.00 0.00
#> TCGA.B0.5099.01 2 0.4522 0.5197 0.00 0.68 0.00 0.32
#> TCGA.CZ.5468.01 2 0.0000 0.9858 0.00 1.00 0.00 0.00
#> TCGA.B0.4842.11 1 0.0000 0.9971 1.00 0.00 0.00 0.00
#> TCGA.CZ.5988.01 2 0.1211 0.9428 0.00 0.96 0.00 0.04
#> TCGA.BP.5169.01 2 0.0000 0.9858 0.00 1.00 0.00 0.00
#> TCGA.B0.5109.01 4 0.0000 0.9687 0.00 0.00 0.00 1.00
#> TCGA.B4.5834.01 4 0.0000 0.9687 0.00 0.00 0.00 1.00
#> TCGA.B0.5095.11 1 0.3172 0.8093 0.84 0.00 0.16 0.00
#> TCGA.B0.5080.01 4 0.0000 0.9687 0.00 0.00 0.00 1.00
#> TCGA.CJ.5680.01 2 0.0000 0.9858 0.00 1.00 0.00 0.00
#> TCGA.CZ.5470.01 2 0.0000 0.9858 0.00 1.00 0.00 0.00
#> TCGA.CZ.4865.01 2 0.1211 0.9427 0.00 0.96 0.00 0.04
#> TCGA.A3.A8OX.01 3 0.0707 0.9786 0.00 0.00 0.98 0.02
#> TCGA.B0.4690.11 1 0.0000 0.9971 1.00 0.00 0.00 0.00
#> TCGA.CJ.5684.01 4 0.1211 0.9257 0.00 0.04 0.00 0.96
#> TCGA.B0.4844.01 2 0.0000 0.9858 0.00 1.00 0.00 0.00
#> TCGA.CZ.5464.01 2 0.0000 0.9858 0.00 1.00 0.00 0.00
#> TCGA.B0.4701.01 2 0.0000 0.9858 0.00 1.00 0.00 0.00
#> TCGA.B0.5701.01 2 0.0000 0.9858 0.00 1.00 0.00 0.00
#> TCGA.BP.5199.11 1 0.0000 0.9971 1.00 0.00 0.00 0.00
#> TCGA.CJ.5671.01 2 0.0000 0.9858 0.00 1.00 0.00 0.00
#> TCGA.A3.A8OV.01 4 0.0000 0.9687 0.00 0.00 0.00 1.00
#> TCGA.CZ.5456.11 1 0.0000 0.9971 1.00 0.00 0.00 0.00
#> TCGA.B0.5116.01 2 0.0000 0.9858 0.00 1.00 0.00 0.00
#> TCGA.CZ.5458.01 2 0.1637 0.9191 0.00 0.94 0.00 0.06
#> TCGA.CZ.5982.01 2 0.0000 0.9858 0.00 1.00 0.00 0.00
#> TCGA.B0.4828.11 1 0.0000 0.9971 1.00 0.00 0.00 0.00
#> TCGA.CJ.5679.01 2 0.0000 0.9858 0.00 1.00 0.00 0.00
#> TCGA.CJ.5682.01 2 0.0000 0.9858 0.00 1.00 0.00 0.00
#> TCGA.B0.5697.01 4 0.0000 0.9687 0.00 0.00 0.00 1.00
#> TCGA.B0.4697.11 1 0.0000 0.9971 1.00 0.00 0.00 0.00
#> TCGA.BP.4782.11 1 0.0000 0.9971 1.00 0.00 0.00 0.00
#> TCGA.G6.A8L8.01 2 0.0000 0.9858 0.00 1.00 0.00 0.00
#> TCGA.A3.A6NJ.01 4 0.0000 0.9687 0.00 0.00 0.00 1.00
#> TCGA.A3.3370.01 4 0.0000 0.9687 0.00 0.00 0.00 1.00
#> TCGA.B0.4691.01 2 0.0000 0.9858 0.00 1.00 0.00 0.00
#> TCGA.CZ.5452.11 1 0.0000 0.9971 1.00 0.00 0.00 0.00
#> TCGA.B0.4693.11 1 0.0000 0.9971 1.00 0.00 0.00 0.00
#> TCGA.B0.4945.01 4 0.0000 0.9687 0.00 0.00 0.00 1.00
#> TCGA.CZ.4853.01 2 0.0000 0.9858 0.00 1.00 0.00 0.00
#> TCGA.B0.5092.11 1 0.0000 0.9971 1.00 0.00 0.00 0.00
#> TCGA.B0.5402.01 2 0.0000 0.9858 0.00 1.00 0.00 0.00
#> TCGA.B0.4849.11 1 0.0000 0.9971 1.00 0.00 0.00 0.00
#> TCGA.A3.A6NN.01 2 0.0000 0.9858 0.00 1.00 0.00 0.00
#> TCGA.B0.4852.01 4 0.2345 0.8524 0.00 0.10 0.00 0.90
#> TCGA.B0.4817.11 1 0.0000 0.9971 1.00 0.00 0.00 0.00
#> TCGA.BP.5176.11 1 0.0000 0.9971 1.00 0.00 0.00 0.00
#> TCGA.CW.5589.01 4 0.0000 0.9687 0.00 0.00 0.00 1.00
#> TCGA.CJ.5689.01 4 0.0707 0.9472 0.00 0.02 0.00 0.98
#> TCGA.B0.4822.11 1 0.0000 0.9971 1.00 0.00 0.00 0.00
#> TCGA.BP.5190.11 1 0.0000 0.9971 1.00 0.00 0.00 0.00
#> TCGA.B0.4813.01 2 0.0000 0.9858 0.00 1.00 0.00 0.00
#> TCGA.BP.5200.01 4 0.0000 0.9687 0.00 0.00 0.00 1.00
#> TCGA.G6.A8L7.01 2 0.0000 0.9858 0.00 1.00 0.00 0.00
#> TCGA.B2.4101.01 2 0.0000 0.9858 0.00 1.00 0.00 0.00
#> TCGA.B0.4713.11 1 0.0000 0.9971 1.00 0.00 0.00 0.00
#> TCGA.B0.4816.01 4 0.4994 0.0941 0.00 0.48 0.00 0.52
#> TCGA.A3.3385.01 4 0.0000 0.9687 0.00 0.00 0.00 1.00
#> TCGA.B2.3924.01 4 0.0000 0.9687 0.00 0.00 0.00 1.00
#> TCGA.CZ.5455.11 1 0.0000 0.9971 1.00 0.00 0.00 0.00
#> TCGA.B0.5713.01 2 0.0707 0.9647 0.00 0.98 0.00 0.02
#> TCGA.B0.5108.01 2 0.0000 0.9858 0.00 1.00 0.00 0.00
#> TCGA.B0.5711.01 4 0.0000 0.9687 0.00 0.00 0.00 1.00
#> TCGA.CZ.5453.01 4 0.0000 0.9687 0.00 0.00 0.00 1.00
#> TCGA.BP.5202.11 3 0.0707 0.9793 0.02 0.00 0.98 0.00
#> TCGA.BP.5173.01 4 0.0000 0.9687 0.00 0.00 0.00 1.00
#> TCGA.CZ.5451.11 1 0.0000 0.9971 1.00 0.00 0.00 0.00
#> TCGA.B8.A8YJ.01 4 0.0000 0.9687 0.00 0.00 0.00 1.00
#> TCGA.B0.4848.01 2 0.0000 0.9858 0.00 1.00 0.00 0.00
#> TCGA.DV.A4VZ.01 3 0.0000 0.9815 0.00 0.00 1.00 0.00
#> TCGA.B0.4814.11 1 0.0000 0.9971 1.00 0.00 0.00 0.00
#> TCGA.CJ.4869.11 1 0.0000 0.9971 1.00 0.00 0.00 0.00
#> TCGA.CJ.4907.11 1 0.0000 0.9971 1.00 0.00 0.00 0.00
#> TCGA.B8.5553.01 4 0.0000 0.9687 0.00 0.00 0.00 1.00
#> TCGA.MW.A4EC.01 4 0.0000 0.9687 0.00 0.00 0.00 1.00
#> TCGA.B0.5712.11 3 0.0707 0.9793 0.02 0.00 0.98 0.00
#> TCGA.EU.5905.01 2 0.2647 0.8410 0.00 0.88 0.00 0.12
#> TCGA.CZ.5985.01 2 0.0000 0.9858 0.00 1.00 0.00 0.00
#> TCGA.CZ.4856.01 4 0.0000 0.9687 0.00 0.00 0.00 1.00
#> TCGA.BP.5184.01 4 0.0000 0.9687 0.00 0.00 0.00 1.00
#> TCGA.B0.5121.01 2 0.0000 0.9858 0.00 1.00 0.00 0.00
#> TCGA.BP.5191.01 2 0.0000 0.9858 0.00 1.00 0.00 0.00
#> TCGA.BP.4801.11 1 0.0000 0.9971 1.00 0.00 0.00 0.00
#> TCGA.BP.5177.01 4 0.0000 0.9687 0.00 0.00 0.00 1.00
#> TCGA.B0.5110.11 1 0.0000 0.9971 1.00 0.00 0.00 0.00
#> TCGA.B0.4810.01 2 0.0000 0.9858 0.00 1.00 0.00 0.00
#> TCGA.CJ.4903.11 1 0.0000 0.9971 1.00 0.00 0.00 0.00
#> TCGA.CJ.4912.11 1 0.0000 0.9971 1.00 0.00 0.00 0.00
#> TCGA.B8.4621.01 4 0.0000 0.9687 0.00 0.00 0.00 1.00
#> TCGA.B4.5832.01 4 0.0000 0.9687 0.00 0.00 0.00 1.00
#> TCGA.CW.6088.01 4 0.0000 0.9687 0.00 0.00 0.00 1.00
#> TCGA.AK.3428.01 2 0.0000 0.9858 0.00 1.00 0.00 0.00
#> TCGA.B8.5164.01 4 0.0000 0.9687 0.00 0.00 0.00 1.00
#> TCGA.BP.5195.01 4 0.0000 0.9687 0.00 0.00 0.00 1.00
#> TCGA.CJ.6027.01 2 0.0000 0.9858 0.00 1.00 0.00 0.00
#> TCGA.3Z.A93Z.01 4 0.0000 0.9687 0.00 0.00 0.00 1.00
#> TCGA.B0.4714.11 1 0.0000 0.9971 1.00 0.00 0.00 0.00
#> TCGA.B0.4818.11 1 0.0000 0.9971 1.00 0.00 0.00 0.00
#> TCGA.CZ.5457.11 1 0.0000 0.9971 1.00 0.00 0.00 0.00
#> TCGA.BP.5010.01 2 0.0000 0.9858 0.00 1.00 0.00 0.00
#> TCGA.BP.5189.11 1 0.0000 0.9971 1.00 0.00 0.00 0.00
#> TCGA.B0.4703.01 2 0.0000 0.9858 0.00 1.00 0.00 0.00
#> TCGA.B0.4718.11 1 0.0000 0.9971 1.00 0.00 0.00 0.00
#> TCGA.B0.5097.11 1 0.0000 0.9971 1.00 0.00 0.00 0.00
#> TCGA.BP.4760.11 1 0.0000 0.9971 1.00 0.00 0.00 0.00
#> TCGA.B0.5120.11 1 0.0000 0.9971 1.00 0.00 0.00 0.00
#> TCGA.B0.4843.11 1 0.0000 0.9971 1.00 0.00 0.00 0.00
#> TCGA.B0.5104.01 4 0.0000 0.9687 0.00 0.00 0.00 1.00
#> TCGA.CW.5587.01 4 0.0000 0.9687 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.CZ.4863.01 4 0.0000 0.9168 0.00 0.00 0.00 1.00 0.00
#> TCGA.CJ.4904.11 1 0.1043 0.9250 0.96 0.00 0.00 0.00 0.04
#> TCGA.B0.4827.11 5 0.2020 0.9964 0.10 0.00 0.00 0.00 0.90
#> TCGA.CJ.4902.01 2 0.0000 0.9571 0.00 1.00 0.00 0.00 0.00
#> TCGA.B0.4823.01 4 0.0000 0.9168 0.00 0.00 0.00 1.00 0.00
#> TCGA.CW.6087.01 2 0.2020 0.8658 0.00 0.90 0.00 0.10 0.00
#> TCGA.B0.5098.01 4 0.5579 0.3743 0.00 0.00 0.30 0.60 0.10
#> TCGA.B0.5113.01 2 0.0000 0.9571 0.00 1.00 0.00 0.00 0.00
#> TCGA.DV.5566.01 4 0.2020 0.7997 0.00 0.10 0.00 0.90 0.00
#> TCGA.BP.5175.11 1 0.0000 0.9609 1.00 0.00 0.00 0.00 0.00
#> TCGA.BP.5181.01 4 0.0000 0.9168 0.00 0.00 0.00 1.00 0.00
#> TCGA.B0.4706.11 1 0.0000 0.9609 1.00 0.00 0.00 0.00 0.00
#> TCGA.B0.5117.01 1 0.3424 0.6369 0.76 0.00 0.00 0.00 0.24
#> TCGA.MM.A564.01 2 0.0000 0.9571 0.00 1.00 0.00 0.00 0.00
#> TCGA.B0.4821.11 1 0.2797 0.8685 0.88 0.00 0.06 0.00 0.06
#> TCGA.CZ.5463.11 5 0.2020 0.9964 0.10 0.00 0.00 0.00 0.90
#> TCGA.BP.5182.11 1 0.0000 0.9609 1.00 0.00 0.00 0.00 0.00
#> TCGA.DV.5574.01 4 0.1043 0.8995 0.00 0.00 0.00 0.96 0.04
#> TCGA.B0.5094.11 1 0.1410 0.9203 0.94 0.00 0.00 0.00 0.06
#> TCGA.MM.A84U.01 2 0.0609 0.9427 0.00 0.98 0.00 0.02 0.00
#> TCGA.B0.5100.11 1 0.1410 0.9203 0.94 0.00 0.00 0.00 0.06
#> TCGA.B4.5844.01 2 0.0000 0.9571 0.00 1.00 0.00 0.00 0.00
#> TCGA.CZ.5459.01 2 0.0000 0.9571 0.00 1.00 0.00 0.00 0.00
#> TCGA.B0.4694.01 2 0.0000 0.9571 0.00 1.00 0.00 0.00 0.00
#> TCGA.CZ.5468.11 5 0.2020 0.9964 0.10 0.00 0.00 0.00 0.90
#> TCGA.CJ.4916.11 1 0.1410 0.9203 0.94 0.00 0.00 0.00 0.06
#> TCGA.B4.5836.01 4 0.0000 0.9168 0.00 0.00 0.00 1.00 0.00
#> TCGA.B0.5095.01 4 0.4302 0.0304 0.00 0.48 0.00 0.52 0.00
#> TCGA.B0.4846.11 1 0.0000 0.9609 1.00 0.00 0.00 0.00 0.00
#> TCGA.AK.3434.01 2 0.0000 0.9571 0.00 1.00 0.00 0.00 0.00
#> TCGA.B4.5377.01 4 0.0000 0.9168 0.00 0.00 0.00 1.00 0.00
#> TCGA.B0.4696.11 1 0.0000 0.9609 1.00 0.00 0.00 0.00 0.00
#> TCGA.BP.5187.11 1 0.0000 0.9609 1.00 0.00 0.00 0.00 0.00
#> TCGA.B0.4690.01 2 0.0000 0.9571 0.00 1.00 0.00 0.00 0.00
#> TCGA.CZ.5466.01 2 0.0000 0.9571 0.00 1.00 0.00 0.00 0.00
#> TCGA.B0.4844.11 5 0.2280 0.9677 0.12 0.00 0.00 0.00 0.88
#> TCGA.CZ.5464.11 1 0.0609 0.9500 0.98 0.00 0.00 0.00 0.02
#> TCGA.B0.4701.11 5 0.2929 0.8709 0.18 0.00 0.00 0.00 0.82
#> TCGA.BP.5194.11 1 0.1043 0.9250 0.96 0.00 0.00 0.00 0.04
#> TCGA.B0.4707.01 2 0.0000 0.9571 0.00 1.00 0.00 0.00 0.00
#> TCGA.CZ.5467.11 5 0.2020 0.9964 0.10 0.00 0.00 0.00 0.90
#> TCGA.B0.5705.01 4 0.0000 0.9168 0.00 0.00 0.00 1.00 0.00
#> TCGA.CW.5588.01 2 0.4287 0.1914 0.00 0.54 0.00 0.46 0.00
#> TCGA.CJ.6031.01 2 0.3983 0.5132 0.00 0.66 0.00 0.34 0.00
#> TCGA.B8.A54J.01 4 0.0000 0.9168 0.00 0.00 0.00 1.00 0.00
#> TCGA.BP.5192.11 5 0.2020 0.9964 0.10 0.00 0.00 0.00 0.90
#> TCGA.CZ.5462.01 2 0.0000 0.9571 0.00 1.00 0.00 0.00 0.00
#> TCGA.B8.A54H.01 4 0.1410 0.8539 0.00 0.06 0.00 0.94 0.00
#> TCGA.CZ.5470.11 5 0.2020 0.9964 0.10 0.00 0.00 0.00 0.90
#> TCGA.BP.4177.11 5 0.2020 0.9964 0.10 0.00 0.00 0.00 0.90
#> TCGA.CZ.5469.11 5 0.2020 0.9964 0.10 0.00 0.00 0.00 0.90
#> TCGA.CJ.6028.01 2 0.0000 0.9571 0.00 1.00 0.00 0.00 0.00
#> TCGA.G6.A8L6.01 2 0.1043 0.9270 0.00 0.96 0.00 0.04 0.00
#> TCGA.B8.5551.01 2 0.0000 0.9571 0.00 1.00 0.00 0.00 0.00
#> TCGA.CZ.5456.01 2 0.0000 0.9571 0.00 1.00 0.00 0.00 0.00
#> TCGA.A3.A8OU.01 2 0.4060 0.4719 0.00 0.64 0.00 0.36 0.00
#> TCGA.BP.5186.01 4 0.1043 0.8995 0.00 0.00 0.00 0.96 0.04
#> TCGA.A3.A6NI.01 2 0.2516 0.8169 0.00 0.86 0.00 0.14 0.00
#> TCGA.BP.4782.01 4 0.0000 0.9168 0.00 0.00 0.00 1.00 0.00
#> TCGA.CZ.5454.11 5 0.2020 0.9964 0.10 0.00 0.00 0.00 0.90
#> TCGA.B0.4691.11 1 0.0000 0.9609 1.00 0.00 0.00 0.00 0.00
#> TCGA.CZ.5452.01 2 0.0000 0.9571 0.00 1.00 0.00 0.00 0.00
#> TCGA.EU.5904.01 4 0.0000 0.9168 0.00 0.00 0.00 1.00 0.00
#> TCGA.BP.5201.01 2 0.0000 0.9571 0.00 1.00 0.00 0.00 0.00
#> TCGA.CJ.5677.01 2 0.0000 0.9571 0.00 1.00 0.00 0.00 0.00
#> TCGA.BP.5170.11 5 0.2020 0.9964 0.10 0.00 0.00 0.00 0.90
#> TCGA.B0.4710.11 5 0.2020 0.9964 0.10 0.00 0.00 0.00 0.90
#> TCGA.AK.3425.01 2 0.0000 0.9571 0.00 1.00 0.00 0.00 0.00
#> TCGA.B0.4841.11 1 0.0000 0.9609 1.00 0.00 0.00 0.00 0.00
#> TCGA.B0.4849.01 2 0.1043 0.9270 0.00 0.96 0.00 0.04 0.00
#> TCGA.BP.5182.01 4 0.0000 0.9168 0.00 0.00 0.00 1.00 0.00
#> TCGA.B0.5711.11 5 0.2020 0.9964 0.10 0.00 0.00 0.00 0.90
#> TCGA.BP.5180.01 2 0.0000 0.9571 0.00 1.00 0.00 0.00 0.00
#> TCGA.BP.5176.01 4 0.0000 0.9168 0.00 0.00 0.00 1.00 0.00
#> TCGA.CZ.5984.01 2 0.0000 0.9571 0.00 1.00 0.00 0.00 0.00
#> TCGA.CZ.5460.11 1 0.0000 0.9609 1.00 0.00 0.00 0.00 0.00
#> TCGA.BP.5190.01 2 0.0000 0.9571 0.00 1.00 0.00 0.00 0.00
#> TCGA.BP.4795.11 1 0.0000 0.9609 1.00 0.00 0.00 0.00 0.00
#> TCGA.B0.4813.11 5 0.2020 0.9964 0.10 0.00 0.00 0.00 0.90
#> TCGA.B0.4713.01 2 0.0000 0.9571 0.00 1.00 0.00 0.00 0.00
#> TCGA.B0.4841.01 2 0.0000 0.9571 0.00 1.00 0.00 0.00 0.00
#> TCGA.B8.5546.01 1 0.6791 0.2454 0.54 0.00 0.30 0.06 0.10
#> TCGA.CW.5591.01 2 0.0000 0.9571 0.00 1.00 0.00 0.00 0.00
#> TCGA.B0.4698.11 1 0.0000 0.9609 1.00 0.00 0.00 0.00 0.00
#> TCGA.B0.5713.11 1 0.0000 0.9609 1.00 0.00 0.00 0.00 0.00
#> TCGA.B0.5108.11 1 0.0000 0.9609 1.00 0.00 0.00 0.00 0.00
#> TCGA.B0.5083.01 1 0.0609 0.9500 0.98 0.00 0.00 0.00 0.02
#> TCGA.B0.5699.01 2 0.0000 0.9571 0.00 1.00 0.00 0.00 0.00
#> TCGA.CZ.5453.11 5 0.2020 0.9964 0.10 0.00 0.00 0.00 0.90
#> TCGA.BP.5202.01 2 0.0000 0.9571 0.00 1.00 0.00 0.00 0.00
#> TCGA.BP.5173.11 1 0.0000 0.9609 1.00 0.00 0.00 0.00 0.00
#> TCGA.CW.5581.01 2 0.2020 0.8660 0.00 0.90 0.00 0.10 0.00
#> TCGA.B0.4848.11 1 0.0609 0.9500 0.98 0.00 0.00 0.00 0.02
#> TCGA.B0.4814.01 2 0.0000 0.9571 0.00 1.00 0.00 0.00 0.00
#> TCGA.BP.5178.11 1 0.0000 0.9609 1.00 0.00 0.00 0.00 0.00
#> TCGA.CJ.4907.01 2 0.1043 0.9270 0.00 0.96 0.00 0.04 0.00
#> TCGA.A3.3387.01 4 0.3895 0.4463 0.00 0.32 0.00 0.68 0.00
#> TCGA.B0.4821.01 2 0.0000 0.9571 0.00 1.00 0.00 0.00 0.00
#> TCGA.B0.5712.01 2 0.0000 0.9571 0.00 1.00 0.00 0.00 0.00
#> TCGA.B0.5695.01 4 0.0000 0.9168 0.00 0.00 0.00 1.00 0.00
#> TCGA.BP.5184.11 1 0.0000 0.9609 1.00 0.00 0.00 0.00 0.00
#> TCGA.B2.A4SR.01 4 0.0000 0.9168 0.00 0.00 0.00 1.00 0.00
#> TCGA.BP.5191.11 1 0.1410 0.9203 0.94 0.00 0.00 0.00 0.06
#> TCGA.CJ.4920.01 2 0.0000 0.9571 0.00 1.00 0.00 0.00 0.00
#> TCGA.BP.4801.01 4 0.0000 0.9168 0.00 0.00 0.00 1.00 0.00
#> TCGA.DV.A4W0.01 2 0.0000 0.9571 0.00 1.00 0.00 0.00 0.00
#> TCGA.BP.5177.11 1 0.0000 0.9609 1.00 0.00 0.00 0.00 0.00
#> TCGA.B0.4847.11 5 0.2020 0.9964 0.10 0.00 0.00 0.00 0.90
#> TCGA.B0.5100.01 4 0.3561 0.5482 0.00 0.26 0.00 0.74 0.00
#> TCGA.CJ.4903.01 2 0.0000 0.9571 0.00 1.00 0.00 0.00 0.00
#> TCGA.CJ.4912.01 2 0.0000 0.9571 0.00 1.00 0.00 0.00 0.00
#> TCGA.B0.5107.11 1 0.0000 0.9609 1.00 0.00 0.00 0.00 0.00
#> TCGA.AK.3453.01 1 0.0000 0.9609 1.00 0.00 0.00 0.00 0.00
#> TCGA.B0.5691.01 4 0.1043 0.8995 0.00 0.00 0.00 0.96 0.04
#> TCGA.BP.5195.11 5 0.2020 0.9964 0.10 0.00 0.00 0.00 0.90
#> TCGA.B0.5400.01 4 0.0000 0.9168 0.00 0.00 0.00 1.00 0.00
#> TCGA.A3.3376.11 1 0.5068 0.4922 0.64 0.00 0.30 0.00 0.06
#> TCGA.B0.4845.01 2 0.0000 0.9571 0.00 1.00 0.00 0.00 0.00
#> TCGA.B0.4699.01 1 0.5068 0.4922 0.64 0.00 0.30 0.00 0.06
#> TCGA.B0.4818.01 2 0.4060 0.4725 0.00 0.64 0.00 0.36 0.00
#> TCGA.BP.5174.11 1 0.0000 0.9609 1.00 0.00 0.00 0.00 0.00
#> TCGA.CJ.4901.11 1 0.0000 0.9609 1.00 0.00 0.00 0.00 0.00
#> TCGA.B8.A54D.01 2 0.0000 0.9571 0.00 1.00 0.00 0.00 0.00
#> TCGA.BP.4770.11 1 0.0609 0.9500 0.98 0.00 0.00 0.00 0.02
#> TCGA.CW.6093.01 4 0.1043 0.8995 0.00 0.00 0.00 0.96 0.04
#> TCGA.BP.5010.11 5 0.2020 0.9964 0.10 0.00 0.00 0.00 0.90
#> TCGA.AK.3431.01 4 0.0609 0.9000 0.00 0.02 0.00 0.98 0.00
#> TCGA.BP.4770.01 4 0.0609 0.8998 0.00 0.02 0.00 0.98 0.00
#> TCGA.BP.5189.01 2 0.0000 0.9571 0.00 1.00 0.00 0.00 0.00
#> TCGA.B0.4703.11 1 0.0000 0.9609 1.00 0.00 0.00 0.00 0.00
#> TCGA.B8.5163.01 2 0.1043 0.9270 0.00 0.96 0.00 0.04 0.00
#> TCGA.CJ.5683.01 4 0.0000 0.9168 0.00 0.00 0.00 1.00 0.00
#> TCGA.CZ.4856.11 5 0.2020 0.9964 0.10 0.00 0.00 0.00 0.90
#> TCGA.BP.4760.01 3 0.0000 1.0000 0.00 0.00 1.00 0.00 0.00
#> TCGA.B0.5692.01 2 0.0000 0.9571 0.00 1.00 0.00 0.00 0.00
#> TCGA.B0.5106.01 2 0.0000 0.9571 0.00 1.00 0.00 0.00 0.00
#> TCGA.B0.4843.01 2 0.1043 0.9270 0.00 0.96 0.00 0.04 0.00
#> TCGA.CZ.4866.11 5 0.2020 0.9964 0.10 0.00 0.00 0.00 0.90
#> TCGA.B0.5104.11 1 0.0000 0.9609 1.00 0.00 0.00 0.00 0.00
#> TCGA.B0.4827.01 2 0.0000 0.9571 0.00 1.00 0.00 0.00 0.00
#> TCGA.CJ.4902.11 5 0.2020 0.9964 0.10 0.00 0.00 0.00 0.90
#> TCGA.B8.A54G.01 2 0.0000 0.9571 0.00 1.00 0.00 0.00 0.00
#> TCGA.B0.5703.01 2 0.1043 0.9270 0.00 0.96 0.00 0.04 0.00
#> TCGA.CJ.5672.01 2 0.0000 0.9571 0.00 1.00 0.00 0.00 0.00
#> TCGA.B0.5098.11 1 0.1410 0.9203 0.94 0.00 0.00 0.00 0.06
#> TCGA.B0.5113.11 1 0.0000 0.9609 1.00 0.00 0.00 0.00 0.00
#> TCGA.CJ.4882.11 1 0.0000 0.9609 1.00 0.00 0.00 0.00 0.00
#> TCGA.CZ.5465.11 5 0.2020 0.9964 0.10 0.00 0.00 0.00 0.90
#> TCGA.B0.5102.01 4 0.0000 0.9168 0.00 0.00 0.00 1.00 0.00
#> TCGA.CW.5585.01 2 0.3424 0.6773 0.00 0.76 0.00 0.24 0.00
#> TCGA.B0.4824.01 4 0.0000 0.9168 0.00 0.00 0.00 1.00 0.00
#> TCGA.B0.5115.01 2 0.0000 0.9571 0.00 1.00 0.00 0.00 0.00
#> TCGA.B0.4706.01 2 0.0000 0.9571 0.00 1.00 0.00 0.00 0.00
#> TCGA.B0.5117.11 1 0.0000 0.9609 1.00 0.00 0.00 0.00 0.00
#> TCGA.CZ.4859.11 5 0.2020 0.9964 0.10 0.00 0.00 0.00 0.90
#> TCGA.AK.3450.01 2 0.3684 0.6143 0.00 0.72 0.00 0.28 0.00
#> TCGA.B8.A54I.01 2 0.0000 0.9571 0.00 1.00 0.00 0.00 0.00
#> TCGA.CZ.5463.01 2 0.0000 0.9571 0.00 1.00 0.00 0.00 0.00
#> TCGA.DV.5568.01 2 0.0000 0.9571 0.00 1.00 0.00 0.00 0.00
#> TCGA.CZ.5459.11 1 0.1410 0.9203 0.94 0.00 0.00 0.00 0.06
#> TCGA.CJ.4918.11 1 0.0000 0.9609 1.00 0.00 0.00 0.00 0.00
#> TCGA.DV.5565.01 2 0.0609 0.9427 0.00 0.98 0.00 0.02 0.00
#> TCGA.B0.5119.01 4 0.0000 0.9168 0.00 0.00 0.00 1.00 0.00
#> TCGA.B0.4811.01 2 0.0609 0.9427 0.00 0.98 0.00 0.02 0.00
#> TCGA.A3.3367.11 1 0.0000 0.9609 1.00 0.00 0.00 0.00 0.00
#> TCGA.CJ.4916.01 2 0.0000 0.9571 0.00 1.00 0.00 0.00 0.00
#> TCGA.B0.5693.01 4 0.0000 0.9168 0.00 0.00 0.00 1.00 0.00
#> TCGA.CZ.4863.11 5 0.2020 0.9964 0.10 0.00 0.00 0.00 0.90
#> TCGA.G6.A5PC.01 2 0.0000 0.9571 0.00 1.00 0.00 0.00 0.00
#> TCGA.B8.5550.01 4 0.0000 0.9168 0.00 0.00 0.00 1.00 0.00
#> TCGA.DV.A4W0.05 3 0.0000 1.0000 0.00 0.00 1.00 0.00 0.00
#> TCGA.B0.4696.01 2 0.0000 0.9571 0.00 1.00 0.00 0.00 0.00
#> TCGA.BP.5187.01 4 0.0000 0.9168 0.00 0.00 0.00 1.00 0.00
#> TCGA.CZ.5466.11 1 0.1410 0.9203 0.94 0.00 0.00 0.00 0.06
#> TCGA.CW.6097.01 4 0.0000 0.9168 0.00 0.00 0.00 1.00 0.00
#> TCGA.CJ.4905.11 5 0.2020 0.9964 0.10 0.00 0.00 0.00 0.90
#> TCGA.CZ.5989.01 4 0.0000 0.9168 0.00 0.00 0.00 1.00 0.00
#> TCGA.BP.5194.01 4 0.0000 0.9168 0.00 0.00 0.00 1.00 0.00
#> TCGA.B0.4707.11 1 0.0000 0.9609 1.00 0.00 0.00 0.00 0.00
#> TCGA.CZ.5467.01 2 0.1043 0.9270 0.00 0.96 0.00 0.04 0.00
#> TCGA.BP.5185.11 1 0.1410 0.9203 0.94 0.00 0.00 0.00 0.06
#> TCGA.BP.5183.11 1 0.0000 0.9609 1.00 0.00 0.00 0.00 0.00
#> TCGA.BP.5192.01 4 0.0000 0.9168 0.00 0.00 0.00 1.00 0.00
#> TCGA.CZ.5462.11 5 0.2020 0.9964 0.10 0.00 0.00 0.00 0.90
#> TCGA.BP.4177.01 3 0.0000 1.0000 0.00 0.00 1.00 0.00 0.00
#> TCGA.CZ.5469.01 2 0.0000 0.9571 0.00 1.00 0.00 0.00 0.00
#> TCGA.B2.5641.01 2 0.0000 0.9571 0.00 1.00 0.00 0.00 0.00
#> TCGA.BP.5196.11 1 0.0000 0.9609 1.00 0.00 0.00 0.00 0.00
#> TCGA.CZ.5460.01 2 0.0000 0.9571 0.00 1.00 0.00 0.00 0.00
#> TCGA.B0.4712.01 2 0.0000 0.9571 0.00 1.00 0.00 0.00 0.00
#> TCGA.B8.A54K.01 3 0.0000 1.0000 0.00 0.00 1.00 0.00 0.00
#> TCGA.B0.5707.01 4 0.1043 0.8995 0.00 0.00 0.00 0.96 0.04
#> TCGA.BP.5186.11 1 0.4126 0.2743 0.62 0.00 0.00 0.00 0.38
#> TCGA.EU.5906.01 4 0.0609 0.9089 0.00 0.00 0.00 0.98 0.02
#> TCGA.CZ.5461.11 5 0.2020 0.9964 0.10 0.00 0.00 0.00 0.90
#> TCGA.CW.5590.01 2 0.0000 0.9571 0.00 1.00 0.00 0.00 0.00
#> TCGA.B0.5698.01 2 0.0000 0.9571 0.00 1.00 0.00 0.00 0.00
#> TCGA.CW.5580.01 2 0.0000 0.9571 0.00 1.00 0.00 0.00 0.00
#> TCGA.CZ.5454.01 2 0.0000 0.9571 0.00 1.00 0.00 0.00 0.00
#> TCGA.B0.4815.01 2 0.0000 0.9571 0.00 1.00 0.00 0.00 0.00
#> TCGA.B0.5710.11 1 0.0000 0.9609 1.00 0.00 0.00 0.00 0.00
#> TCGA.CJ.4908.11 5 0.2020 0.9964 0.10 0.00 0.00 0.00 0.90
#> TCGA.BP.5201.11 1 0.0000 0.9609 1.00 0.00 0.00 0.00 0.00
#> TCGA.B0.5694.01 2 0.0000 0.9571 0.00 1.00 0.00 0.00 0.00
#> TCGA.BP.5170.01 4 0.1043 0.8783 0.00 0.04 0.00 0.96 0.00
#> TCGA.DV.5575.01 4 0.1043 0.8995 0.00 0.00 0.00 0.96 0.04
#> TCGA.CJ.5686.01 4 0.0000 0.9168 0.00 0.00 0.00 1.00 0.00
#> TCGA.A3.3357.01 2 0.0000 0.9571 0.00 1.00 0.00 0.00 0.00
#> TCGA.A3.3373.01 4 0.0000 0.9168 0.00 0.00 0.00 1.00 0.00
#> TCGA.B0.5690.01 4 0.0000 0.9168 0.00 0.00 0.00 1.00 0.00
#> TCGA.B8.4622.01 2 0.0000 0.9571 0.00 1.00 0.00 0.00 0.00
#> TCGA.AK.3433.01 5 0.2020 0.9964 0.10 0.00 0.00 0.00 0.90
#> TCGA.B0.5110.01 4 0.0000 0.9168 0.00 0.00 0.00 1.00 0.00
#> TCGA.BP.5180.11 1 0.0000 0.9609 1.00 0.00 0.00 0.00 0.00
#> TCGA.CJ.4913.01 2 0.0000 0.9571 0.00 1.00 0.00 0.00 0.00
#> TCGA.CJ.4908.01 4 0.0000 0.9168 0.00 0.00 0.00 1.00 0.00
#> TCGA.BP.4795.01 3 0.0000 1.0000 0.00 0.00 1.00 0.00 0.00
#> TCGA.CJ.4897.11 1 0.0000 0.9609 1.00 0.00 0.00 0.00 0.00
#> TCGA.B2.5636.01 3 0.0000 1.0000 0.00 0.00 1.00 0.00 0.00
#> TCGA.CJ.4923.11 1 0.0000 0.9609 1.00 0.00 0.00 0.00 0.00
#> TCGA.B0.4819.01 2 0.1732 0.8877 0.00 0.92 0.00 0.08 0.00
#> TCGA.B2.5633.01 4 0.2516 0.7407 0.00 0.14 0.00 0.86 0.00
#> TCGA.CJ.6033.01 2 0.0000 0.9571 0.00 1.00 0.00 0.00 0.00
#> TCGA.BP.5181.11 1 0.0000 0.9609 1.00 0.00 0.00 0.00 0.00
#> TCGA.B0.4698.01 2 0.0000 0.9571 0.00 1.00 0.00 0.00 0.00
#> TCGA.B0.5083.11 1 0.0000 0.9609 1.00 0.00 0.00 0.00 0.00
#> TCGA.CZ.4864.11 1 0.0000 0.9609 1.00 0.00 0.00 0.00 0.00
#> TCGA.B0.4688.01 2 0.0000 0.9571 0.00 1.00 0.00 0.00 0.00
#> TCGA.BP.5168.01 2 0.1410 0.9085 0.00 0.94 0.00 0.06 0.00
#> TCGA.BP.5198.11 1 0.0609 0.9500 0.98 0.00 0.00 0.00 0.02
#> TCGA.B8.5162.01 4 0.0000 0.9168 0.00 0.00 0.00 1.00 0.00
#> TCGA.B0.5096.01 2 0.0000 0.9571 0.00 1.00 0.00 0.00 0.00
#> TCGA.BP.5178.01 2 0.0000 0.9571 0.00 1.00 0.00 0.00 0.00
#> TCGA.B0.5099.11 1 0.0000 0.9609 1.00 0.00 0.00 0.00 0.00
#> TCGA.B0.4842.01 2 0.0000 0.9571 0.00 1.00 0.00 0.00 0.00
#> TCGA.BP.5169.11 1 0.0000 0.9609 1.00 0.00 0.00 0.00 0.00
#> TCGA.B0.5109.11 1 0.3110 0.8469 0.86 0.00 0.08 0.00 0.06
#> TCGA.CJ.4920.11 5 0.2020 0.9964 0.10 0.00 0.00 0.00 0.90
#> TCGA.B0.5080.11 1 0.0609 0.9500 0.98 0.00 0.00 0.00 0.02
#> TCGA.B0.5700.01 4 0.1043 0.8995 0.00 0.00 0.00 0.96 0.04
#> TCGA.B0.4847.01 2 0.0000 0.9571 0.00 1.00 0.00 0.00 0.00
#> TCGA.B0.5702.01 4 0.5579 0.3743 0.00 0.00 0.30 0.60 0.10
#> TCGA.CJ.4905.01 4 0.0609 0.9000 0.00 0.02 0.00 0.98 0.00
#> TCGA.B2.5635.01 2 0.4060 0.4719 0.00 0.64 0.00 0.36 0.00
#> TCGA.B0.5107.01 2 0.0000 0.9571 0.00 1.00 0.00 0.00 0.00
#> TCGA.CW.5584.01 2 0.0000 0.9571 0.00 1.00 0.00 0.00 0.00
#> TCGA.B4.5838.01 2 0.0000 0.9571 0.00 1.00 0.00 0.00 0.00
#> TCGA.BP.5199.01 2 0.0000 0.9571 0.00 1.00 0.00 0.00 0.00
#> TCGA.A3.3376.01 4 0.1043 0.8995 0.00 0.00 0.00 0.96 0.04
#> TCGA.B0.4845.11 5 0.2020 0.9964 0.10 0.00 0.00 0.00 0.90
#> TCGA.B0.4699.11 1 0.0000 0.9609 1.00 0.00 0.00 0.00 0.00
#> TCGA.BP.5174.01 4 0.0000 0.9168 0.00 0.00 0.00 1.00 0.00
#> TCGA.CZ.5986.01 4 0.1043 0.8995 0.00 0.00 0.00 0.96 0.04
#> TCGA.CJ.4901.01 2 0.0000 0.9571 0.00 1.00 0.00 0.00 0.00
#> TCGA.AK.3461.01 4 0.0000 0.9168 0.00 0.00 0.00 1.00 0.00
#> TCGA.AK.3460.01 4 0.0000 0.9168 0.00 0.00 0.00 1.00 0.00
#> TCGA.AK.3454.01 4 0.0000 0.9168 0.00 0.00 0.00 1.00 0.00
#> TCGA.CZ.4859.01 4 0.1043 0.8995 0.00 0.00 0.00 0.96 0.04
#> TCGA.B0.5812.01 4 0.0000 0.9168 0.00 0.00 0.00 1.00 0.00
#> TCGA.B0.5116.11 4 0.7605 -0.0065 0.14 0.00 0.30 0.46 0.10
#> TCGA.B8.A54F.01 4 0.0000 0.9168 0.00 0.00 0.00 1.00 0.00
#> TCGA.CW.6090.01 2 0.0000 0.9571 0.00 1.00 0.00 0.00 0.00
#> TCGA.CZ.5458.11 5 0.2020 0.9964 0.10 0.00 0.00 0.00 0.90
#> TCGA.B0.5106.11 1 0.0000 0.9609 1.00 0.00 0.00 0.00 0.00
#> TCGA.CZ.4866.01 2 0.0000 0.9571 0.00 1.00 0.00 0.00 0.00
#> TCGA.B0.4828.01 2 0.0000 0.9571 0.00 1.00 0.00 0.00 0.00
#> TCGA.AK.3440.01 5 0.2020 0.9964 0.10 0.00 0.00 0.00 0.90
#> TCGA.MM.A563.01 2 0.0000 0.9571 0.00 1.00 0.00 0.00 0.00
#> TCGA.B0.4697.01 2 0.4287 0.1875 0.00 0.54 0.00 0.46 0.00
#> TCGA.AK.3458.01 2 0.0000 0.9571 0.00 1.00 0.00 0.00 0.00
#> TCGA.CJ.5676.01 2 0.0000 0.9571 0.00 1.00 0.00 0.00 0.00
#> TCGA.B0.5402.11 1 0.1410 0.9203 0.94 0.00 0.00 0.00 0.06
#> TCGA.CJ.5681.01 4 0.5579 0.3743 0.00 0.00 0.30 0.60 0.10
#> TCGA.A3.3370.11 5 0.2020 0.9964 0.10 0.00 0.00 0.00 0.90
#> TCGA.A3.A6NL.01 4 0.0609 0.9089 0.00 0.00 0.00 0.98 0.02
#> TCGA.B0.4693.01 2 0.0000 0.9571 0.00 1.00 0.00 0.00 0.00
#> TCGA.A3.3358.01 2 0.0609 0.9427 0.00 0.98 0.00 0.02 0.00
#> TCGA.B0.4710.01 2 0.0000 0.9571 0.00 1.00 0.00 0.00 0.00
#> TCGA.CZ.4853.11 5 0.2020 0.9964 0.10 0.00 0.00 0.00 0.90
#> TCGA.B4.5835.01 4 0.1043 0.8995 0.00 0.00 0.00 0.96 0.04
#> TCGA.CJ.4882.01 2 0.4287 0.1869 0.00 0.54 0.00 0.46 0.00
#> TCGA.CZ.5465.01 2 0.0000 0.9571 0.00 1.00 0.00 0.00 0.00
#> TCGA.B0.5102.11 1 0.0000 0.9609 1.00 0.00 0.00 0.00 0.00
#> TCGA.B0.4824.11 1 0.0000 0.9609 1.00 0.00 0.00 0.00 0.00
#> TCGA.CJ.5675.01 2 0.0000 0.9571 0.00 1.00 0.00 0.00 0.00
#> TCGA.B0.4700.01 4 0.0000 0.9168 0.00 0.00 0.00 1.00 0.00
#> TCGA.B0.5092.01 2 0.1043 0.9270 0.00 0.96 0.00 0.04 0.00
#> TCGA.B0.5115.11 1 0.0000 0.9609 1.00 0.00 0.00 0.00 0.00
#> TCGA.B0.4945.11 1 0.0000 0.9609 1.00 0.00 0.00 0.00 0.00
#> TCGA.B8.5158.01 2 0.0000 0.9571 0.00 1.00 0.00 0.00 0.00
#> TCGA.CJ.6030.01 2 0.0000 0.9571 0.00 1.00 0.00 0.00 0.00
#> TCGA.B8.A54E.01 4 0.5579 0.3743 0.00 0.00 0.30 0.60 0.10
#> TCGA.CJ.6032.01 2 0.0000 0.9571 0.00 1.00 0.00 0.00 0.00
#> TCGA.B0.4852.11 1 0.0000 0.9609 1.00 0.00 0.00 0.00 0.00
#> TCGA.B0.4817.01 4 0.0000 0.9168 0.00 0.00 0.00 1.00 0.00
#> TCGA.B8.5159.01 2 0.0000 0.9571 0.00 1.00 0.00 0.00 0.00
#> TCGA.A3.A8OW.01 4 0.0000 0.9168 0.00 0.00 0.00 1.00 0.00
#> TCGA.B0.4822.01 2 0.0000 0.9571 0.00 1.00 0.00 0.00 0.00
#> TCGA.B0.5696.01 2 0.1043 0.9270 0.00 0.96 0.00 0.04 0.00
#> TCGA.B0.5706.01 2 0.0000 0.9571 0.00 1.00 0.00 0.00 0.00
#> TCGA.CJ.4918.01 4 0.0000 0.9168 0.00 0.00 0.00 1.00 0.00
#> TCGA.B0.5119.11 5 0.2020 0.9964 0.10 0.00 0.00 0.00 0.90
#> TCGA.BP.5200.11 1 0.0000 0.9609 1.00 0.00 0.00 0.00 0.00
#> TCGA.B0.4811.11 1 0.1410 0.9203 0.94 0.00 0.00 0.00 0.06
#> TCGA.A3.3367.01 2 0.0000 0.9571 0.00 1.00 0.00 0.00 0.00
#> TCGA.B0.5097.01 2 0.0000 0.9571 0.00 1.00 0.00 0.00 0.00
#> TCGA.6D.AA2E.01 4 0.5579 0.3743 0.00 0.00 0.30 0.60 0.10
#> TCGA.DV.A4VX.01 2 0.0000 0.9571 0.00 1.00 0.00 0.00 0.00
#> TCGA.B0.4816.11 5 0.2020 0.9964 0.10 0.00 0.00 0.00 0.90
#> TCGA.A3.3385.11 1 0.0000 0.9609 1.00 0.00 0.00 0.00 0.00
#> TCGA.DV.5569.01 4 0.1043 0.8995 0.00 0.00 0.00 0.96 0.04
#> TCGA.EU.5907.01 2 0.0000 0.9571 0.00 1.00 0.00 0.00 0.00
#> TCGA.CZ.5455.01 2 0.0000 0.9571 0.00 1.00 0.00 0.00 0.00
#> TCGA.B8.5545.01 4 0.1043 0.8995 0.00 0.00 0.00 0.96 0.04
#> TCGA.DV.5567.01 3 0.0000 1.0000 0.00 0.00 1.00 0.00 0.00
#> TCGA.CZ.5451.01 2 0.0000 0.9571 0.00 1.00 0.00 0.00 0.00
#> TCGA.CJ.4869.01 2 0.0000 0.9571 0.00 1.00 0.00 0.00 0.00
#> TCGA.CJ.5678.01 2 0.0000 0.9571 0.00 1.00 0.00 0.00 0.00
#> TCGA.B8.4153.01 2 0.0000 0.9571 0.00 1.00 0.00 0.00 0.00
#> TCGA.B0.5121.11 1 0.0000 0.9609 1.00 0.00 0.00 0.00 0.00
#> TCGA.B8.4146.01 4 0.4182 0.3076 0.00 0.40 0.00 0.60 0.00
#> TCGA.BP.5183.01 2 0.0000 0.9571 0.00 1.00 0.00 0.00 0.00
#> TCGA.B0.5399.01 2 0.4060 0.4726 0.00 0.64 0.00 0.36 0.00
#> TCGA.B0.4810.11 5 0.2020 0.9964 0.10 0.00 0.00 0.00 0.90
#> TCGA.AK.3445.01 2 0.0000 0.9571 0.00 1.00 0.00 0.00 0.00
#> TCGA.B4.5378.01 3 0.0000 1.0000 0.00 0.00 1.00 0.00 0.00
#> TCGA.BP.5196.01 2 0.0000 0.9571 0.00 1.00 0.00 0.00 0.00
#> TCGA.CZ.4865.11 5 0.2020 0.9964 0.10 0.00 0.00 0.00 0.90
#> TCGA.B0.5709.01 4 0.1043 0.8995 0.00 0.00 0.00 0.96 0.04
#> TCGA.B0.4712.11 5 0.2020 0.9964 0.10 0.00 0.00 0.00 0.90
#> TCGA.B0.4714.01 2 0.0000 0.9571 0.00 1.00 0.00 0.00 0.00
#> TCGA.B8.5549.01 2 0.0000 0.9571 0.00 1.00 0.00 0.00 0.00
#> TCGA.CZ.5461.01 2 0.0000 0.9571 0.00 1.00 0.00 0.00 0.00
#> TCGA.CZ.5457.01 4 0.1043 0.8995 0.00 0.00 0.00 0.96 0.04
#> TCGA.A3.A8CQ.01 4 0.1043 0.8995 0.00 0.00 0.00 0.96 0.04
#> TCGA.DV.5573.01 4 0.0000 0.9168 0.00 0.00 0.00 1.00 0.00
#> TCGA.B0.4815.11 1 0.0609 0.9500 0.98 0.00 0.00 0.00 0.02
#> TCGA.B0.5710.01 2 0.0000 0.9571 0.00 1.00 0.00 0.00 0.00
#> TCGA.B8.5165.01 4 0.1043 0.8995 0.00 0.00 0.00 0.96 0.04
#> TCGA.B0.4718.01 2 0.0000 0.9571 0.00 1.00 0.00 0.00 0.00
#> TCGA.B2.5639.01 2 0.0000 0.9571 0.00 1.00 0.00 0.00 0.00
#> TCGA.CW.5583.01 4 0.1043 0.8995 0.00 0.00 0.00 0.96 0.04
#> TCGA.GK.A6C7.01 4 0.0000 0.9168 0.00 0.00 0.00 1.00 0.00
#> TCGA.A3.3357.11 1 0.0000 0.9609 1.00 0.00 0.00 0.00 0.00
#> TCGA.B8.5552.01 4 0.1043 0.8995 0.00 0.00 0.00 0.96 0.04
#> TCGA.B0.5120.01 4 0.1043 0.8782 0.00 0.04 0.00 0.96 0.00
#> TCGA.A3.3373.11 5 0.2020 0.9964 0.10 0.00 0.00 0.00 0.90
#> TCGA.BP.5185.01 2 0.3274 0.7071 0.00 0.78 0.00 0.22 0.00
#> TCGA.B0.4846.01 4 0.0000 0.9168 0.00 0.00 0.00 1.00 0.00
#> TCGA.CJ.4904.01 4 0.0000 0.9168 0.00 0.00 0.00 1.00 0.00
#> TCGA.CJ.4913.11 1 0.0000 0.9609 1.00 0.00 0.00 0.00 0.00
#> TCGA.BP.4993.11 1 0.0000 0.9609 1.00 0.00 0.00 0.00 0.00
#> TCGA.B0.4823.11 1 0.0000 0.9609 1.00 0.00 0.00 0.00 0.00
#> TCGA.CJ.4897.01 2 0.2280 0.8415 0.00 0.88 0.00 0.12 0.00
#> TCGA.BP.4993.01 4 0.0000 0.9168 0.00 0.00 0.00 1.00 0.00
#> TCGA.B4.5843.01 4 0.1043 0.8995 0.00 0.00 0.00 0.96 0.04
#> TCGA.DV.5576.01 3 0.0000 1.0000 0.00 0.00 1.00 0.00 0.00
#> TCGA.CJ.4923.01 4 0.4182 0.3038 0.00 0.40 0.00 0.60 0.00
#> TCGA.B0.4819.11 1 0.0000 0.9609 1.00 0.00 0.00 0.00 0.00
#> TCGA.BP.5175.01 2 0.0000 0.9571 0.00 1.00 0.00 0.00 0.00
#> TCGA.CZ.5987.01 2 0.0000 0.9571 0.00 1.00 0.00 0.00 0.00
#> TCGA.CZ.4864.01 4 0.0000 0.9168 0.00 0.00 0.00 1.00 0.00
#> TCGA.B0.4688.11 5 0.2020 0.9964 0.10 0.00 0.00 0.00 0.90
#> TCGA.BP.5168.11 1 0.1410 0.9203 0.94 0.00 0.00 0.00 0.06
#> TCGA.BP.5198.01 2 0.0000 0.9571 0.00 1.00 0.00 0.00 0.00
#> TCGA.B8.A7U6.01 4 0.0000 0.9168 0.00 0.00 0.00 1.00 0.00
#> TCGA.B0.5094.01 2 0.0000 0.9571 0.00 1.00 0.00 0.00 0.00
#> TCGA.T7.A92I.01 4 0.5579 0.3743 0.00 0.00 0.30 0.60 0.10
#> TCGA.B0.5096.11 1 0.0000 0.9609 1.00 0.00 0.00 0.00 0.00
#> TCGA.B0.5400.11 1 0.1410 0.9203 0.94 0.00 0.00 0.00 0.06
#> TCGA.B0.4694.11 5 0.2280 0.9677 0.12 0.00 0.00 0.00 0.88
#> TCGA.B0.5099.01 2 0.2516 0.8162 0.00 0.86 0.00 0.14 0.00
#> TCGA.CZ.5468.01 2 0.0000 0.9571 0.00 1.00 0.00 0.00 0.00
#> TCGA.B0.4842.11 1 0.0000 0.9609 1.00 0.00 0.00 0.00 0.00
#> TCGA.CZ.5988.01 2 0.1043 0.9270 0.00 0.96 0.00 0.04 0.00
#> TCGA.BP.5169.01 2 0.0000 0.9571 0.00 1.00 0.00 0.00 0.00
#> TCGA.B0.5109.01 4 0.0000 0.9168 0.00 0.00 0.00 1.00 0.00
#> TCGA.B4.5834.01 4 0.1043 0.8995 0.00 0.00 0.00 0.96 0.04
#> TCGA.B0.5095.11 1 0.1410 0.9203 0.94 0.00 0.00 0.00 0.06
#> TCGA.B0.5080.01 4 0.3424 0.5811 0.00 0.24 0.00 0.76 0.00
#> TCGA.CJ.5680.01 2 0.0000 0.9571 0.00 1.00 0.00 0.00 0.00
#> TCGA.CZ.5470.01 2 0.0000 0.9571 0.00 1.00 0.00 0.00 0.00
#> TCGA.CZ.4865.01 2 0.1043 0.9270 0.00 0.96 0.00 0.04 0.00
#> TCGA.A3.A8OX.01 4 0.5579 0.3743 0.00 0.00 0.30 0.60 0.10
#> TCGA.B0.4690.11 1 0.1410 0.9203 0.94 0.00 0.00 0.00 0.06
#> TCGA.CJ.5684.01 2 0.4262 0.2581 0.00 0.56 0.00 0.44 0.00
#> TCGA.B0.4844.01 2 0.0000 0.9571 0.00 1.00 0.00 0.00 0.00
#> TCGA.CZ.5464.01 2 0.0000 0.9571 0.00 1.00 0.00 0.00 0.00
#> TCGA.B0.4701.01 2 0.0000 0.9571 0.00 1.00 0.00 0.00 0.00
#> TCGA.B0.5701.01 2 0.0000 0.9571 0.00 1.00 0.00 0.00 0.00
#> TCGA.BP.5199.11 1 0.0000 0.9609 1.00 0.00 0.00 0.00 0.00
#> TCGA.CJ.5671.01 2 0.0000 0.9571 0.00 1.00 0.00 0.00 0.00
#> TCGA.A3.A8OV.01 4 0.0000 0.9168 0.00 0.00 0.00 1.00 0.00
#> TCGA.CZ.5456.11 5 0.2020 0.9964 0.10 0.00 0.00 0.00 0.90
#> TCGA.B0.5116.01 2 0.0000 0.9571 0.00 1.00 0.00 0.00 0.00
#> TCGA.CZ.5458.01 2 0.1043 0.9270 0.00 0.96 0.00 0.04 0.00
#> TCGA.CZ.5982.01 2 0.0000 0.9571 0.00 1.00 0.00 0.00 0.00
#> TCGA.B0.4828.11 5 0.2020 0.9964 0.10 0.00 0.00 0.00 0.90
#> TCGA.CJ.5679.01 2 0.0000 0.9571 0.00 1.00 0.00 0.00 0.00
#> TCGA.CJ.5682.01 2 0.0000 0.9571 0.00 1.00 0.00 0.00 0.00
#> TCGA.B0.5697.01 4 0.0000 0.9168 0.00 0.00 0.00 1.00 0.00
#> TCGA.B0.4697.11 5 0.2020 0.9964 0.10 0.00 0.00 0.00 0.90
#> TCGA.BP.4782.11 1 0.1410 0.9203 0.94 0.00 0.00 0.00 0.06
#> TCGA.G6.A8L8.01 2 0.0000 0.9571 0.00 1.00 0.00 0.00 0.00
#> TCGA.A3.A6NJ.01 4 0.0000 0.9168 0.00 0.00 0.00 1.00 0.00
#> TCGA.A3.3370.01 4 0.1043 0.8995 0.00 0.00 0.00 0.96 0.04
#> TCGA.B0.4691.01 2 0.0000 0.9571 0.00 1.00 0.00 0.00 0.00
#> TCGA.CZ.5452.11 5 0.2020 0.9964 0.10 0.00 0.00 0.00 0.90
#> TCGA.B0.4693.11 1 0.0000 0.9609 1.00 0.00 0.00 0.00 0.00
#> TCGA.B0.4945.01 4 0.0000 0.9168 0.00 0.00 0.00 1.00 0.00
#> TCGA.CZ.4853.01 2 0.0000 0.9571 0.00 1.00 0.00 0.00 0.00
#> TCGA.B0.5092.11 1 0.0000 0.9609 1.00 0.00 0.00 0.00 0.00
#> TCGA.B0.5402.01 2 0.0000 0.9571 0.00 1.00 0.00 0.00 0.00
#> TCGA.B0.4849.11 1 0.1043 0.9250 0.96 0.00 0.00 0.00 0.04
#> TCGA.A3.A6NN.01 2 0.0000 0.9571 0.00 1.00 0.00 0.00 0.00
#> TCGA.B0.4852.01 2 0.3983 0.5153 0.00 0.66 0.00 0.34 0.00
#> TCGA.B0.4817.11 1 0.0000 0.9609 1.00 0.00 0.00 0.00 0.00
#> TCGA.BP.5176.11 1 0.0609 0.9500 0.98 0.00 0.00 0.00 0.02
#> TCGA.CW.5589.01 4 0.1043 0.8995 0.00 0.00 0.00 0.96 0.04
#> TCGA.CJ.5689.01 4 0.4302 0.0236 0.00 0.48 0.00 0.52 0.00
#> TCGA.B0.4822.11 5 0.2020 0.9964 0.10 0.00 0.00 0.00 0.90
#> TCGA.BP.5190.11 1 0.0000 0.9609 1.00 0.00 0.00 0.00 0.00
#> TCGA.B0.4813.01 2 0.0000 0.9571 0.00 1.00 0.00 0.00 0.00
#> TCGA.BP.5200.01 4 0.1043 0.8788 0.00 0.04 0.00 0.96 0.00
#> TCGA.G6.A8L7.01 2 0.0000 0.9571 0.00 1.00 0.00 0.00 0.00
#> TCGA.B2.4101.01 2 0.0000 0.9571 0.00 1.00 0.00 0.00 0.00
#> TCGA.B0.4713.11 1 0.1410 0.9203 0.94 0.00 0.00 0.00 0.06
#> TCGA.B0.4816.01 2 0.3424 0.6754 0.00 0.76 0.00 0.24 0.00
#> TCGA.A3.3385.01 4 0.1043 0.8995 0.00 0.00 0.00 0.96 0.04
#> TCGA.B2.3924.01 4 0.0000 0.9168 0.00 0.00 0.00 1.00 0.00
#> TCGA.CZ.5455.11 5 0.2020 0.9964 0.10 0.00 0.00 0.00 0.90
#> TCGA.B0.5713.01 2 0.1043 0.9270 0.00 0.96 0.00 0.04 0.00
#> TCGA.B0.5108.01 2 0.0609 0.9427 0.00 0.98 0.00 0.02 0.00
#> TCGA.B0.5711.01 4 0.2020 0.8000 0.00 0.10 0.00 0.90 0.00
#> TCGA.CZ.5453.01 4 0.0000 0.9168 0.00 0.00 0.00 1.00 0.00
#> TCGA.BP.5202.11 1 0.3641 0.7987 0.82 0.00 0.12 0.00 0.06
#> TCGA.BP.5173.01 4 0.0000 0.9168 0.00 0.00 0.00 1.00 0.00
#> TCGA.CZ.5451.11 1 0.0000 0.9609 1.00 0.00 0.00 0.00 0.00
#> TCGA.B8.A8YJ.01 4 0.1043 0.8995 0.00 0.00 0.00 0.96 0.04
#> TCGA.B0.4848.01 2 0.0000 0.9571 0.00 1.00 0.00 0.00 0.00
#> TCGA.DV.A4VZ.01 3 0.0000 1.0000 0.00 0.00 1.00 0.00 0.00
#> TCGA.B0.4814.11 1 0.0000 0.9609 1.00 0.00 0.00 0.00 0.00
#> TCGA.CJ.4869.11 1 0.0000 0.9609 1.00 0.00 0.00 0.00 0.00
#> TCGA.CJ.4907.11 1 0.0000 0.9609 1.00 0.00 0.00 0.00 0.00
#> TCGA.B8.5553.01 4 0.0000 0.9168 0.00 0.00 0.00 1.00 0.00
#> TCGA.MW.A4EC.01 4 0.0000 0.9168 0.00 0.00 0.00 1.00 0.00
#> TCGA.B0.5712.11 1 0.1410 0.9203 0.94 0.00 0.00 0.00 0.06
#> TCGA.EU.5905.01 2 0.2020 0.8657 0.00 0.90 0.00 0.10 0.00
#> TCGA.CZ.5985.01 2 0.0000 0.9571 0.00 1.00 0.00 0.00 0.00
#> TCGA.CZ.4856.01 4 0.0000 0.9168 0.00 0.00 0.00 1.00 0.00
#> TCGA.BP.5184.01 4 0.0000 0.9168 0.00 0.00 0.00 1.00 0.00
#> TCGA.B0.5121.01 2 0.0000 0.9571 0.00 1.00 0.00 0.00 0.00
#> TCGA.BP.5191.01 2 0.0000 0.9571 0.00 1.00 0.00 0.00 0.00
#> TCGA.BP.4801.11 1 0.0000 0.9609 1.00 0.00 0.00 0.00 0.00
#> TCGA.BP.5177.01 4 0.0000 0.9168 0.00 0.00 0.00 1.00 0.00
#> TCGA.B0.5110.11 1 0.0609 0.9500 0.98 0.00 0.00 0.00 0.02
#> TCGA.B0.4810.01 2 0.0000 0.9571 0.00 1.00 0.00 0.00 0.00
#> TCGA.CJ.4903.11 1 0.0000 0.9609 1.00 0.00 0.00 0.00 0.00
#> TCGA.CJ.4912.11 5 0.2020 0.9964 0.10 0.00 0.00 0.00 0.90
#> TCGA.B8.4621.01 4 0.1043 0.8995 0.00 0.00 0.00 0.96 0.04
#> TCGA.B4.5832.01 4 0.0000 0.9168 0.00 0.00 0.00 1.00 0.00
#> TCGA.CW.6088.01 4 0.0000 0.9168 0.00 0.00 0.00 1.00 0.00
#> TCGA.AK.3428.01 2 0.0000 0.9571 0.00 1.00 0.00 0.00 0.00
#> TCGA.B8.5164.01 4 0.0000 0.9168 0.00 0.00 0.00 1.00 0.00
#> TCGA.BP.5195.01 4 0.3274 0.6139 0.00 0.22 0.00 0.78 0.00
#> TCGA.CJ.6027.01 2 0.0000 0.9571 0.00 1.00 0.00 0.00 0.00
#> TCGA.3Z.A93Z.01 4 0.0609 0.9089 0.00 0.00 0.00 0.98 0.02
#> TCGA.B0.4714.11 1 0.0000 0.9609 1.00 0.00 0.00 0.00 0.00
#> TCGA.B0.4818.11 1 0.4126 0.2740 0.62 0.00 0.00 0.00 0.38
#> TCGA.CZ.5457.11 5 0.2020 0.9964 0.10 0.00 0.00 0.00 0.90
#> TCGA.BP.5010.01 2 0.0609 0.9427 0.00 0.98 0.00 0.02 0.00
#> TCGA.BP.5189.11 1 0.0000 0.9609 1.00 0.00 0.00 0.00 0.00
#> TCGA.B0.4703.01 2 0.1043 0.9270 0.00 0.96 0.00 0.04 0.00
#> TCGA.B0.4718.11 5 0.2020 0.9964 0.10 0.00 0.00 0.00 0.90
#> TCGA.B0.5097.11 1 0.0000 0.9609 1.00 0.00 0.00 0.00 0.00
#> TCGA.BP.4760.11 1 0.0000 0.9609 1.00 0.00 0.00 0.00 0.00
#> TCGA.B0.5120.11 1 0.0000 0.9609 1.00 0.00 0.00 0.00 0.00
#> TCGA.B0.4843.11 1 0.0000 0.9609 1.00 0.00 0.00 0.00 0.00
#> TCGA.B0.5104.01 4 0.0000 0.9168 0.00 0.00 0.00 1.00 0.00
#> TCGA.CW.5587.01 4 0.0000 0.9168 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.CZ.4863.01 4 0.0000 0.9313 0.00 0.00 0 1.00 0.00 0.00
#> TCGA.CJ.4904.11 1 0.0000 0.9888 1.00 0.00 0 0.00 0.00 0.00
#> TCGA.B0.4827.11 5 0.0000 0.9994 0.00 0.00 0 0.00 1.00 0.00
#> TCGA.CJ.4902.01 2 0.1267 0.9108 0.00 0.94 0 0.06 0.00 0.00
#> TCGA.B0.4823.01 4 0.0000 0.9313 0.00 0.00 0 1.00 0.00 0.00
#> TCGA.CW.6087.01 4 0.2631 0.7154 0.00 0.18 0 0.82 0.00 0.00
#> TCGA.B0.5098.01 6 0.0000 0.8336 0.00 0.00 0 0.00 0.00 1.00
#> TCGA.B0.5113.01 2 0.0000 0.9648 0.00 1.00 0 0.00 0.00 0.00
#> TCGA.DV.5566.01 4 0.0000 0.9313 0.00 0.00 0 1.00 0.00 0.00
#> TCGA.BP.5175.11 1 0.0000 0.9888 1.00 0.00 0 0.00 0.00 0.00
#> TCGA.BP.5181.01 4 0.0937 0.8937 0.00 0.00 0 0.96 0.00 0.04
#> TCGA.B0.4706.11 1 0.0000 0.9888 1.00 0.00 0 0.00 0.00 0.00
#> TCGA.B0.5117.01 1 0.2260 0.8109 0.86 0.00 0 0.00 0.14 0.00
#> TCGA.MM.A564.01 2 0.0000 0.9648 0.00 1.00 0 0.00 0.00 0.00
#> TCGA.B0.4821.11 1 0.0547 0.9707 0.98 0.00 0 0.00 0.00 0.02
#> TCGA.CZ.5463.11 5 0.0000 0.9994 0.00 0.00 0 0.00 1.00 0.00
#> TCGA.BP.5182.11 1 0.0000 0.9888 1.00 0.00 0 0.00 0.00 0.00
#> TCGA.DV.5574.01 4 0.3499 0.4501 0.00 0.00 0 0.68 0.00 0.32
#> TCGA.B0.5094.11 1 0.0000 0.9888 1.00 0.00 0 0.00 0.00 0.00
#> TCGA.MM.A84U.01 4 0.3851 0.1538 0.00 0.46 0 0.54 0.00 0.00
#> TCGA.B0.5100.11 1 0.0000 0.9888 1.00 0.00 0 0.00 0.00 0.00
#> TCGA.B4.5844.01 2 0.2793 0.7174 0.00 0.80 0 0.20 0.00 0.00
#> TCGA.CZ.5459.01 2 0.0937 0.9317 0.00 0.96 0 0.04 0.00 0.00
#> TCGA.B0.4694.01 2 0.0937 0.9318 0.00 0.96 0 0.04 0.00 0.00
#> TCGA.CZ.5468.11 5 0.0000 0.9994 0.00 0.00 0 0.00 1.00 0.00
#> TCGA.CJ.4916.11 1 0.0000 0.9888 1.00 0.00 0 0.00 0.00 0.00
#> TCGA.B4.5836.01 4 0.0000 0.9313 0.00 0.00 0 1.00 0.00 0.00
#> TCGA.B0.5095.01 4 0.0000 0.9313 0.00 0.00 0 1.00 0.00 0.00
#> TCGA.B0.4846.11 1 0.0000 0.9888 1.00 0.00 0 0.00 0.00 0.00
#> TCGA.AK.3434.01 2 0.0000 0.9648 0.00 1.00 0 0.00 0.00 0.00
#> TCGA.B4.5377.01 4 0.0000 0.9313 0.00 0.00 0 1.00 0.00 0.00
#> TCGA.B0.4696.11 1 0.0000 0.9888 1.00 0.00 0 0.00 0.00 0.00
#> TCGA.BP.5187.11 1 0.0000 0.9888 1.00 0.00 0 0.00 0.00 0.00
#> TCGA.B0.4690.01 2 0.0937 0.9318 0.00 0.96 0 0.04 0.00 0.00
#> TCGA.CZ.5466.01 2 0.0937 0.9318 0.00 0.96 0 0.04 0.00 0.00
#> TCGA.B0.4844.11 5 0.0000 0.9994 0.00 0.00 0 0.00 1.00 0.00
#> TCGA.CZ.5464.11 1 0.0000 0.9888 1.00 0.00 0 0.00 0.00 0.00
#> TCGA.B0.4701.11 5 0.0547 0.9672 0.02 0.00 0 0.00 0.98 0.00
#> TCGA.BP.5194.11 1 0.0000 0.9888 1.00 0.00 0 0.00 0.00 0.00
#> TCGA.B0.4707.01 2 0.0000 0.9648 0.00 1.00 0 0.00 0.00 0.00
#> TCGA.CZ.5467.11 5 0.0000 0.9994 0.00 0.00 0 0.00 1.00 0.00
#> TCGA.B0.5705.01 4 0.0000 0.9313 0.00 0.00 0 1.00 0.00 0.00
#> TCGA.CW.5588.01 4 0.0000 0.9313 0.00 0.00 0 1.00 0.00 0.00
#> TCGA.CJ.6031.01 4 0.0000 0.9313 0.00 0.00 0 1.00 0.00 0.00
#> TCGA.B8.A54J.01 4 0.0000 0.9313 0.00 0.00 0 1.00 0.00 0.00
#> TCGA.BP.5192.11 5 0.0000 0.9994 0.00 0.00 0 0.00 1.00 0.00
#> TCGA.CZ.5462.01 2 0.1267 0.9108 0.00 0.94 0 0.06 0.00 0.00
#> TCGA.B8.A54H.01 4 0.0000 0.9313 0.00 0.00 0 1.00 0.00 0.00
#> TCGA.CZ.5470.11 5 0.0000 0.9994 0.00 0.00 0 0.00 1.00 0.00
#> TCGA.BP.4177.11 5 0.0000 0.9994 0.00 0.00 0 0.00 1.00 0.00
#> TCGA.CZ.5469.11 5 0.0000 0.9994 0.00 0.00 0 0.00 1.00 0.00
#> TCGA.CJ.6028.01 2 0.0937 0.9318 0.00 0.96 0 0.04 0.00 0.00
#> TCGA.G6.A8L6.01 4 0.1267 0.8702 0.00 0.06 0 0.94 0.00 0.00
#> TCGA.B8.5551.01 2 0.0937 0.9318 0.00 0.96 0 0.04 0.00 0.00
#> TCGA.CZ.5456.01 2 0.0000 0.9648 0.00 1.00 0 0.00 0.00 0.00
#> TCGA.A3.A8OU.01 4 0.0000 0.9313 0.00 0.00 0 1.00 0.00 0.00
#> TCGA.BP.5186.01 6 0.3076 0.6890 0.00 0.00 0 0.24 0.00 0.76
#> TCGA.A3.A6NI.01 4 0.0000 0.9313 0.00 0.00 0 1.00 0.00 0.00
#> TCGA.BP.4782.01 4 0.0000 0.9313 0.00 0.00 0 1.00 0.00 0.00
#> TCGA.CZ.5454.11 5 0.0000 0.9994 0.00 0.00 0 0.00 1.00 0.00
#> TCGA.B0.4691.11 1 0.0000 0.9888 1.00 0.00 0 0.00 0.00 0.00
#> TCGA.CZ.5452.01 2 0.0000 0.9648 0.00 1.00 0 0.00 0.00 0.00
#> TCGA.EU.5904.01 4 0.0000 0.9313 0.00 0.00 0 1.00 0.00 0.00
#> TCGA.BP.5201.01 2 0.0000 0.9648 0.00 1.00 0 0.00 0.00 0.00
#> TCGA.CJ.5677.01 2 0.0000 0.9648 0.00 1.00 0 0.00 0.00 0.00
#> TCGA.BP.5170.11 5 0.0000 0.9994 0.00 0.00 0 0.00 1.00 0.00
#> TCGA.B0.4710.11 5 0.0000 0.9994 0.00 0.00 0 0.00 1.00 0.00
#> TCGA.AK.3425.01 2 0.0000 0.9648 0.00 1.00 0 0.00 0.00 0.00
#> TCGA.B0.4841.11 1 0.0000 0.9888 1.00 0.00 0 0.00 0.00 0.00
#> TCGA.B0.4849.01 4 0.1267 0.8708 0.00 0.06 0 0.94 0.00 0.00
#> TCGA.BP.5182.01 4 0.0937 0.8937 0.00 0.00 0 0.96 0.00 0.04
#> TCGA.B0.5711.11 5 0.0000 0.9994 0.00 0.00 0 0.00 1.00 0.00
#> TCGA.BP.5180.01 2 0.0000 0.9648 0.00 1.00 0 0.00 0.00 0.00
#> TCGA.BP.5176.01 4 0.0000 0.9313 0.00 0.00 0 1.00 0.00 0.00
#> TCGA.CZ.5984.01 2 0.0000 0.9648 0.00 1.00 0 0.00 0.00 0.00
#> TCGA.CZ.5460.11 1 0.0000 0.9888 1.00 0.00 0 0.00 0.00 0.00
#> TCGA.BP.5190.01 2 0.0000 0.9648 0.00 1.00 0 0.00 0.00 0.00
#> TCGA.BP.4795.11 1 0.0000 0.9888 1.00 0.00 0 0.00 0.00 0.00
#> TCGA.B0.4813.11 5 0.0000 0.9994 0.00 0.00 0 0.00 1.00 0.00
#> TCGA.B0.4713.01 2 0.0000 0.9648 0.00 1.00 0 0.00 0.00 0.00
#> TCGA.B0.4841.01 2 0.0000 0.9648 0.00 1.00 0 0.00 0.00 0.00
#> TCGA.B8.5546.01 6 0.0000 0.8336 0.00 0.00 0 0.00 0.00 1.00
#> TCGA.CW.5591.01 2 0.1267 0.9108 0.00 0.94 0 0.06 0.00 0.00
#> TCGA.B0.4698.11 1 0.0000 0.9888 1.00 0.00 0 0.00 0.00 0.00
#> TCGA.B0.5713.11 1 0.0000 0.9888 1.00 0.00 0 0.00 0.00 0.00
#> TCGA.B0.5108.11 1 0.0000 0.9888 1.00 0.00 0 0.00 0.00 0.00
#> TCGA.B0.5083.01 1 0.0000 0.9888 1.00 0.00 0 0.00 0.00 0.00
#> TCGA.B0.5699.01 2 0.0000 0.9648 0.00 1.00 0 0.00 0.00 0.00
#> TCGA.CZ.5453.11 5 0.0000 0.9994 0.00 0.00 0 0.00 1.00 0.00
#> TCGA.BP.5202.01 2 0.0000 0.9648 0.00 1.00 0 0.00 0.00 0.00
#> TCGA.BP.5173.11 1 0.0000 0.9888 1.00 0.00 0 0.00 0.00 0.00
#> TCGA.CW.5581.01 4 0.0547 0.9124 0.00 0.02 0 0.98 0.00 0.00
#> TCGA.B0.4848.11 1 0.0000 0.9888 1.00 0.00 0 0.00 0.00 0.00
#> TCGA.B0.4814.01 2 0.0000 0.9648 0.00 1.00 0 0.00 0.00 0.00
#> TCGA.BP.5178.11 1 0.0000 0.9888 1.00 0.00 0 0.00 0.00 0.00
#> TCGA.CJ.4907.01 4 0.3578 0.4502 0.00 0.34 0 0.66 0.00 0.00
#> TCGA.A3.3387.01 4 0.0000 0.9313 0.00 0.00 0 1.00 0.00 0.00
#> TCGA.B0.4821.01 2 0.0000 0.9648 0.00 1.00 0 0.00 0.00 0.00
#> TCGA.B0.5712.01 2 0.0000 0.9648 0.00 1.00 0 0.00 0.00 0.00
#> TCGA.B0.5695.01 4 0.0000 0.9313 0.00 0.00 0 1.00 0.00 0.00
#> TCGA.BP.5184.11 1 0.0000 0.9888 1.00 0.00 0 0.00 0.00 0.00
#> TCGA.B2.A4SR.01 4 0.0000 0.9313 0.00 0.00 0 1.00 0.00 0.00
#> TCGA.BP.5191.11 1 0.0000 0.9888 1.00 0.00 0 0.00 0.00 0.00
#> TCGA.CJ.4920.01 2 0.0000 0.9648 0.00 1.00 0 0.00 0.00 0.00
#> TCGA.BP.4801.01 4 0.0000 0.9313 0.00 0.00 0 1.00 0.00 0.00
#> TCGA.DV.A4W0.01 2 0.0000 0.9648 0.00 1.00 0 0.00 0.00 0.00
#> TCGA.BP.5177.11 1 0.0000 0.9888 1.00 0.00 0 0.00 0.00 0.00
#> TCGA.B0.4847.11 5 0.0000 0.9994 0.00 0.00 0 0.00 1.00 0.00
#> TCGA.B0.5100.01 4 0.0547 0.9126 0.00 0.02 0 0.98 0.00 0.00
#> TCGA.CJ.4903.01 2 0.0000 0.9648 0.00 1.00 0 0.00 0.00 0.00
#> TCGA.CJ.4912.01 2 0.0000 0.9648 0.00 1.00 0 0.00 0.00 0.00
#> TCGA.B0.5107.11 1 0.0000 0.9888 1.00 0.00 0 0.00 0.00 0.00
#> TCGA.AK.3453.01 1 0.0000 0.9888 1.00 0.00 0 0.00 0.00 0.00
#> TCGA.B0.5691.01 6 0.0000 0.8336 0.00 0.00 0 0.00 0.00 1.00
#> TCGA.BP.5195.11 5 0.0000 0.9994 0.00 0.00 0 0.00 1.00 0.00
#> TCGA.B0.5400.01 4 0.0000 0.9313 0.00 0.00 0 1.00 0.00 0.00
#> TCGA.A3.3376.11 1 0.0547 0.9707 0.98 0.00 0 0.00 0.00 0.02
#> TCGA.B0.4845.01 2 0.0000 0.9648 0.00 1.00 0 0.00 0.00 0.00
#> TCGA.B0.4699.01 1 0.0547 0.9707 0.98 0.00 0 0.00 0.00 0.02
#> TCGA.B0.4818.01 4 0.0000 0.9313 0.00 0.00 0 1.00 0.00 0.00
#> TCGA.BP.5174.11 1 0.0000 0.9888 1.00 0.00 0 0.00 0.00 0.00
#> TCGA.CJ.4901.11 1 0.0000 0.9888 1.00 0.00 0 0.00 0.00 0.00
#> TCGA.B8.A54D.01 2 0.0000 0.9648 0.00 1.00 0 0.00 0.00 0.00
#> TCGA.BP.4770.11 1 0.0000 0.9888 1.00 0.00 0 0.00 0.00 0.00
#> TCGA.CW.6093.01 6 0.3076 0.6890 0.00 0.00 0 0.24 0.00 0.76
#> TCGA.BP.5010.11 5 0.0000 0.9994 0.00 0.00 0 0.00 1.00 0.00
#> TCGA.AK.3431.01 4 0.0000 0.9313 0.00 0.00 0 1.00 0.00 0.00
#> TCGA.BP.4770.01 4 0.0000 0.9313 0.00 0.00 0 1.00 0.00 0.00
#> TCGA.BP.5189.01 2 0.0000 0.9648 0.00 1.00 0 0.00 0.00 0.00
#> TCGA.B0.4703.11 1 0.0000 0.9888 1.00 0.00 0 0.00 0.00 0.00
#> TCGA.B8.5163.01 4 0.3647 0.4170 0.00 0.36 0 0.64 0.00 0.00
#> TCGA.CJ.5683.01 4 0.0000 0.9313 0.00 0.00 0 1.00 0.00 0.00
#> TCGA.CZ.4856.11 5 0.0000 0.9994 0.00 0.00 0 0.00 1.00 0.00
#> TCGA.BP.4760.01 3 0.0000 1.0000 0.00 0.00 1 0.00 0.00 0.00
#> TCGA.B0.5692.01 2 0.0000 0.9648 0.00 1.00 0 0.00 0.00 0.00
#> TCGA.B0.5106.01 2 0.0000 0.9648 0.00 1.00 0 0.00 0.00 0.00
#> TCGA.B0.4843.01 4 0.3309 0.5530 0.00 0.28 0 0.72 0.00 0.00
#> TCGA.CZ.4866.11 5 0.0000 0.9994 0.00 0.00 0 0.00 1.00 0.00
#> TCGA.B0.5104.11 1 0.0000 0.9888 1.00 0.00 0 0.00 0.00 0.00
#> TCGA.B0.4827.01 2 0.0000 0.9648 0.00 1.00 0 0.00 0.00 0.00
#> TCGA.CJ.4902.11 5 0.0000 0.9994 0.00 0.00 0 0.00 1.00 0.00
#> TCGA.B8.A54G.01 2 0.0937 0.9318 0.00 0.96 0 0.04 0.00 0.00
#> TCGA.B0.5703.01 2 0.3756 0.3416 0.00 0.60 0 0.40 0.00 0.00
#> TCGA.CJ.5672.01 2 0.1267 0.9108 0.00 0.94 0 0.06 0.00 0.00
#> TCGA.B0.5098.11 1 0.0000 0.9888 1.00 0.00 0 0.00 0.00 0.00
#> TCGA.B0.5113.11 1 0.0000 0.9888 1.00 0.00 0 0.00 0.00 0.00
#> TCGA.CJ.4882.11 1 0.0000 0.9888 1.00 0.00 0 0.00 0.00 0.00
#> TCGA.CZ.5465.11 5 0.0000 0.9994 0.00 0.00 0 0.00 1.00 0.00
#> TCGA.B0.5102.01 4 0.0000 0.9313 0.00 0.00 0 1.00 0.00 0.00
#> TCGA.CW.5585.01 4 0.0000 0.9313 0.00 0.00 0 1.00 0.00 0.00
#> TCGA.B0.4824.01 4 0.0000 0.9313 0.00 0.00 0 1.00 0.00 0.00
#> TCGA.B0.5115.01 2 0.0000 0.9648 0.00 1.00 0 0.00 0.00 0.00
#> TCGA.B0.4706.01 2 0.0000 0.9648 0.00 1.00 0 0.00 0.00 0.00
#> TCGA.B0.5117.11 1 0.0000 0.9888 1.00 0.00 0 0.00 0.00 0.00
#> TCGA.CZ.4859.11 5 0.0000 0.9994 0.00 0.00 0 0.00 1.00 0.00
#> TCGA.AK.3450.01 4 0.0000 0.9313 0.00 0.00 0 1.00 0.00 0.00
#> TCGA.B8.A54I.01 2 0.0000 0.9648 0.00 1.00 0 0.00 0.00 0.00
#> TCGA.CZ.5463.01 2 0.0000 0.9648 0.00 1.00 0 0.00 0.00 0.00
#> TCGA.DV.5568.01 2 0.2793 0.7187 0.00 0.80 0 0.20 0.00 0.00
#> TCGA.CZ.5459.11 1 0.0000 0.9888 1.00 0.00 0 0.00 0.00 0.00
#> TCGA.CJ.4918.11 1 0.0000 0.9888 1.00 0.00 0 0.00 0.00 0.00
#> TCGA.DV.5565.01 2 0.3797 0.2852 0.00 0.58 0 0.42 0.00 0.00
#> TCGA.B0.5119.01 4 0.0000 0.9313 0.00 0.00 0 1.00 0.00 0.00
#> TCGA.B0.4811.01 4 0.3864 0.0723 0.00 0.48 0 0.52 0.00 0.00
#> TCGA.A3.3367.11 1 0.0000 0.9888 1.00 0.00 0 0.00 0.00 0.00
#> TCGA.CJ.4916.01 2 0.1267 0.9108 0.00 0.94 0 0.06 0.00 0.00
#> TCGA.B0.5693.01 4 0.0000 0.9313 0.00 0.00 0 1.00 0.00 0.00
#> TCGA.CZ.4863.11 5 0.0000 0.9994 0.00 0.00 0 0.00 1.00 0.00
#> TCGA.G6.A5PC.01 2 0.0000 0.9648 0.00 1.00 0 0.00 0.00 0.00
#> TCGA.B8.5550.01 4 0.0000 0.9313 0.00 0.00 0 1.00 0.00 0.00
#> TCGA.DV.A4W0.05 3 0.0000 1.0000 0.00 0.00 1 0.00 0.00 0.00
#> TCGA.B0.4696.01 2 0.0547 0.9490 0.00 0.98 0 0.02 0.00 0.00
#> TCGA.BP.5187.01 4 0.0000 0.9313 0.00 0.00 0 1.00 0.00 0.00
#> TCGA.CZ.5466.11 1 0.0000 0.9888 1.00 0.00 0 0.00 0.00 0.00
#> TCGA.CW.6097.01 4 0.0000 0.9313 0.00 0.00 0 1.00 0.00 0.00
#> TCGA.CJ.4905.11 5 0.0000 0.9994 0.00 0.00 0 0.00 1.00 0.00
#> TCGA.CZ.5989.01 4 0.0000 0.9313 0.00 0.00 0 1.00 0.00 0.00
#> TCGA.BP.5194.01 4 0.0000 0.9313 0.00 0.00 0 1.00 0.00 0.00
#> TCGA.B0.4707.11 1 0.0000 0.9888 1.00 0.00 0 0.00 0.00 0.00
#> TCGA.CZ.5467.01 4 0.2454 0.7436 0.00 0.16 0 0.84 0.00 0.00
#> TCGA.BP.5185.11 1 0.0000 0.9888 1.00 0.00 0 0.00 0.00 0.00
#> TCGA.BP.5183.11 1 0.0000 0.9888 1.00 0.00 0 0.00 0.00 0.00
#> TCGA.BP.5192.01 4 0.0000 0.9313 0.00 0.00 0 1.00 0.00 0.00
#> TCGA.CZ.5462.11 5 0.0000 0.9994 0.00 0.00 0 0.00 1.00 0.00
#> TCGA.BP.4177.01 3 0.0000 1.0000 0.00 0.00 1 0.00 0.00 0.00
#> TCGA.CZ.5469.01 2 0.0000 0.9648 0.00 1.00 0 0.00 0.00 0.00
#> TCGA.B2.5641.01 2 0.0000 0.9648 0.00 1.00 0 0.00 0.00 0.00
#> TCGA.BP.5196.11 1 0.0000 0.9888 1.00 0.00 0 0.00 0.00 0.00
#> TCGA.CZ.5460.01 2 0.0000 0.9648 0.00 1.00 0 0.00 0.00 0.00
#> TCGA.B0.4712.01 2 0.0000 0.9648 0.00 1.00 0 0.00 0.00 0.00
#> TCGA.B8.A54K.01 3 0.0000 1.0000 0.00 0.00 1 0.00 0.00 0.00
#> TCGA.B0.5707.01 6 0.0547 0.8475 0.00 0.00 0 0.02 0.00 0.98
#> TCGA.BP.5186.11 1 0.3797 0.2823 0.58 0.00 0 0.00 0.42 0.00
#> TCGA.EU.5906.01 4 0.2941 0.6590 0.00 0.00 0 0.78 0.00 0.22
#> TCGA.CZ.5461.11 5 0.0000 0.9994 0.00 0.00 0 0.00 1.00 0.00
#> TCGA.CW.5590.01 2 0.0000 0.9648 0.00 1.00 0 0.00 0.00 0.00
#> TCGA.B0.5698.01 2 0.0000 0.9648 0.00 1.00 0 0.00 0.00 0.00
#> TCGA.CW.5580.01 2 0.0000 0.9648 0.00 1.00 0 0.00 0.00 0.00
#> TCGA.CZ.5454.01 2 0.0000 0.9648 0.00 1.00 0 0.00 0.00 0.00
#> TCGA.B0.4815.01 2 0.0000 0.9648 0.00 1.00 0 0.00 0.00 0.00
#> TCGA.B0.5710.11 1 0.0000 0.9888 1.00 0.00 0 0.00 0.00 0.00
#> TCGA.CJ.4908.11 5 0.0000 0.9994 0.00 0.00 0 0.00 1.00 0.00
#> TCGA.BP.5201.11 1 0.0000 0.9888 1.00 0.00 0 0.00 0.00 0.00
#> TCGA.B0.5694.01 2 0.0000 0.9648 0.00 1.00 0 0.00 0.00 0.00
#> TCGA.BP.5170.01 4 0.0000 0.9313 0.00 0.00 0 1.00 0.00 0.00
#> TCGA.DV.5575.01 6 0.0547 0.8475 0.00 0.00 0 0.02 0.00 0.98
#> TCGA.CJ.5686.01 4 0.0000 0.9313 0.00 0.00 0 1.00 0.00 0.00
#> TCGA.A3.3357.01 2 0.0000 0.9648 0.00 1.00 0 0.00 0.00 0.00
#> TCGA.A3.3373.01 4 0.0000 0.9313 0.00 0.00 0 1.00 0.00 0.00
#> TCGA.B0.5690.01 4 0.0000 0.9313 0.00 0.00 0 1.00 0.00 0.00
#> TCGA.B8.4622.01 2 0.0000 0.9648 0.00 1.00 0 0.00 0.00 0.00
#> TCGA.AK.3433.01 5 0.0000 0.9994 0.00 0.00 0 0.00 1.00 0.00
#> TCGA.B0.5110.01 4 0.0000 0.9313 0.00 0.00 0 1.00 0.00 0.00
#> TCGA.BP.5180.11 1 0.0000 0.9888 1.00 0.00 0 0.00 0.00 0.00
#> TCGA.CJ.4913.01 2 0.0000 0.9648 0.00 1.00 0 0.00 0.00 0.00
#> TCGA.CJ.4908.01 4 0.0000 0.9313 0.00 0.00 0 1.00 0.00 0.00
#> TCGA.BP.4795.01 3 0.0000 1.0000 0.00 0.00 1 0.00 0.00 0.00
#> TCGA.CJ.4897.11 1 0.0000 0.9888 1.00 0.00 0 0.00 0.00 0.00
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#> TCGA.CZ.5455.11 5 0.0000 0.9994 0.00 0.00 0 0.00 1.00 0.00
#> TCGA.B0.5713.01 4 0.2454 0.7430 0.00 0.16 0 0.84 0.00 0.00
#> TCGA.B0.5108.01 2 0.3499 0.5107 0.00 0.68 0 0.32 0.00 0.00
#> TCGA.B0.5711.01 4 0.0000 0.9313 0.00 0.00 0 1.00 0.00 0.00
#> TCGA.CZ.5453.01 4 0.0937 0.8937 0.00 0.00 0 0.96 0.00 0.04
#> TCGA.BP.5202.11 1 0.0547 0.9707 0.98 0.00 0 0.00 0.00 0.02
#> TCGA.BP.5173.01 4 0.0000 0.9313 0.00 0.00 0 1.00 0.00 0.00
#> TCGA.CZ.5451.11 1 0.0000 0.9888 1.00 0.00 0 0.00 0.00 0.00
#> TCGA.B8.A8YJ.01 6 0.1267 0.8256 0.00 0.00 0 0.06 0.00 0.94
#> TCGA.B0.4848.01 2 0.0000 0.9648 0.00 1.00 0 0.00 0.00 0.00
#> TCGA.DV.A4VZ.01 3 0.0000 1.0000 0.00 0.00 1 0.00 0.00 0.00
#> TCGA.B0.4814.11 1 0.0000 0.9888 1.00 0.00 0 0.00 0.00 0.00
#> TCGA.CJ.4869.11 1 0.0000 0.9888 1.00 0.00 0 0.00 0.00 0.00
#> TCGA.CJ.4907.11 1 0.0000 0.9888 1.00 0.00 0 0.00 0.00 0.00
#> TCGA.B8.5553.01 4 0.0000 0.9313 0.00 0.00 0 1.00 0.00 0.00
#> TCGA.MW.A4EC.01 4 0.0000 0.9313 0.00 0.00 0 1.00 0.00 0.00
#> TCGA.B0.5712.11 1 0.0000 0.9888 1.00 0.00 0 0.00 0.00 0.00
#> TCGA.EU.5905.01 4 0.0937 0.8922 0.00 0.04 0 0.96 0.00 0.00
#> TCGA.CZ.5985.01 2 0.0000 0.9648 0.00 1.00 0 0.00 0.00 0.00
#> TCGA.CZ.4856.01 4 0.0000 0.9313 0.00 0.00 0 1.00 0.00 0.00
#> TCGA.BP.5184.01 4 0.0000 0.9313 0.00 0.00 0 1.00 0.00 0.00
#> TCGA.B0.5121.01 2 0.0000 0.9648 0.00 1.00 0 0.00 0.00 0.00
#> TCGA.BP.5191.01 2 0.0000 0.9648 0.00 1.00 0 0.00 0.00 0.00
#> TCGA.BP.4801.11 1 0.0000 0.9888 1.00 0.00 0 0.00 0.00 0.00
#> TCGA.BP.5177.01 4 0.2048 0.8056 0.00 0.00 0 0.88 0.00 0.12
#> TCGA.B0.5110.11 1 0.0000 0.9888 1.00 0.00 0 0.00 0.00 0.00
#> TCGA.B0.4810.01 2 0.0000 0.9648 0.00 1.00 0 0.00 0.00 0.00
#> TCGA.CJ.4903.11 1 0.0000 0.9888 1.00 0.00 0 0.00 0.00 0.00
#> TCGA.CJ.4912.11 5 0.0000 0.9994 0.00 0.00 0 0.00 1.00 0.00
#> TCGA.B8.4621.01 4 0.3864 -0.1000 0.00 0.00 0 0.52 0.00 0.48
#> TCGA.B4.5832.01 4 0.0000 0.9313 0.00 0.00 0 1.00 0.00 0.00
#> TCGA.CW.6088.01 4 0.0000 0.9313 0.00 0.00 0 1.00 0.00 0.00
#> TCGA.AK.3428.01 2 0.0000 0.9648 0.00 1.00 0 0.00 0.00 0.00
#> TCGA.B8.5164.01 4 0.0000 0.9313 0.00 0.00 0 1.00 0.00 0.00
#> TCGA.BP.5195.01 4 0.0000 0.9313 0.00 0.00 0 1.00 0.00 0.00
#> TCGA.CJ.6027.01 2 0.0000 0.9648 0.00 1.00 0 0.00 0.00 0.00
#> TCGA.3Z.A93Z.01 4 0.3578 0.3981 0.00 0.00 0 0.66 0.00 0.34
#> TCGA.B0.4714.11 1 0.0000 0.9888 1.00 0.00 0 0.00 0.00 0.00
#> TCGA.B0.4818.11 1 0.3797 0.2829 0.58 0.00 0 0.00 0.42 0.00
#> TCGA.CZ.5457.11 5 0.0000 0.9994 0.00 0.00 0 0.00 1.00 0.00
#> TCGA.BP.5010.01 2 0.3864 0.0688 0.00 0.52 0 0.48 0.00 0.00
#> TCGA.BP.5189.11 1 0.0000 0.9888 1.00 0.00 0 0.00 0.00 0.00
#> TCGA.B0.4703.01 4 0.2454 0.7441 0.00 0.16 0 0.84 0.00 0.00
#> TCGA.B0.4718.11 5 0.0000 0.9994 0.00 0.00 0 0.00 1.00 0.00
#> TCGA.B0.5097.11 1 0.0000 0.9888 1.00 0.00 0 0.00 0.00 0.00
#> TCGA.BP.4760.11 1 0.0000 0.9888 1.00 0.00 0 0.00 0.00 0.00
#> TCGA.B0.5120.11 1 0.0000 0.9888 1.00 0.00 0 0.00 0.00 0.00
#> TCGA.B0.4843.11 1 0.0000 0.9888 1.00 0.00 0 0.00 0.00 0.00
#> TCGA.B0.5104.01 4 0.0000 0.9313 0.00 0.00 0 1.00 0.00 0.00
#> TCGA.CW.5587.01 4 0.0000 0.9313 0.00 0.00 0 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.CZ.4863.01 4 0.0000 0.9623 0.00 0.00 0 1.00 0.00 0.00 0.00
#> TCGA.CJ.4904.11 1 0.0000 0.9880 1.00 0.00 0 0.00 0.00 0.00 0.00
#> TCGA.B0.4827.11 5 0.0000 0.9946 0.00 0.00 0 0.00 1.00 0.00 0.00
#> TCGA.CJ.4902.01 4 0.0504 0.9523 0.00 0.02 0 0.98 0.00 0.00 0.00
#> TCGA.B0.4823.01 6 0.0504 0.9344 0.00 0.00 0 0.02 0.00 0.98 0.00
#> TCGA.CW.6087.01 4 0.0000 0.9623 0.00 0.00 0 1.00 0.00 0.00 0.00
#> TCGA.B0.5098.01 7 0.0504 0.9683 0.00 0.00 0 0.00 0.00 0.02 0.98
#> TCGA.B0.5113.01 2 0.0000 0.9870 0.00 1.00 0 0.00 0.00 0.00 0.00
#> TCGA.DV.5566.01 4 0.0000 0.9623 0.00 0.00 0 1.00 0.00 0.00 0.00
#> TCGA.BP.5175.11 1 0.0000 0.9880 1.00 0.00 0 0.00 0.00 0.00 0.00
#> TCGA.BP.5181.01 6 0.0504 0.9344 0.00 0.00 0 0.02 0.00 0.98 0.00
#> TCGA.B0.4706.11 1 0.0000 0.9880 1.00 0.00 0 0.00 0.00 0.00 0.00
#> TCGA.B0.5117.01 1 0.3413 0.3825 0.62 0.00 0 0.00 0.38 0.00 0.00
#> TCGA.MM.A564.01 2 0.0000 0.9870 0.00 1.00 0 0.00 0.00 0.00 0.00
#> TCGA.B0.4821.11 7 0.1886 0.7114 0.12 0.00 0 0.00 0.00 0.00 0.88
#> TCGA.CZ.5463.11 5 0.0000 0.9946 0.00 0.00 0 0.00 1.00 0.00 0.00
#> TCGA.BP.5182.11 1 0.0000 0.9880 1.00 0.00 0 0.00 0.00 0.00 0.00
#> TCGA.DV.5574.01 6 0.0504 0.9344 0.00 0.00 0 0.02 0.00 0.98 0.00
#> TCGA.B0.5094.11 1 0.0504 0.9790 0.98 0.00 0 0.00 0.00 0.00 0.02
#> TCGA.MM.A84U.01 4 0.0504 0.9523 0.00 0.02 0 0.98 0.00 0.00 0.00
#> TCGA.B0.5100.11 1 0.0504 0.9790 0.98 0.00 0 0.00 0.00 0.00 0.02
#> TCGA.B4.5844.01 4 0.1166 0.9126 0.00 0.06 0 0.94 0.00 0.00 0.00
#> TCGA.CZ.5459.01 4 0.2945 0.6026 0.00 0.26 0 0.74 0.00 0.00 0.00
#> TCGA.B0.4694.01 4 0.0504 0.9523 0.00 0.02 0 0.98 0.00 0.00 0.00
#> TCGA.CZ.5468.11 5 0.0000 0.9946 0.00 0.00 0 0.00 1.00 0.00 0.00
#> TCGA.CJ.4916.11 1 0.0504 0.9790 0.98 0.00 0 0.00 0.00 0.00 0.02
#> TCGA.B4.5836.01 4 0.0000 0.9623 0.00 0.00 0 1.00 0.00 0.00 0.00
#> TCGA.B0.5095.01 4 0.0000 0.9623 0.00 0.00 0 1.00 0.00 0.00 0.00
#> TCGA.B0.4846.11 1 0.0000 0.9880 1.00 0.00 0 0.00 0.00 0.00 0.00
#> TCGA.AK.3434.01 2 0.0000 0.9870 0.00 1.00 0 0.00 0.00 0.00 0.00
#> TCGA.B4.5377.01 6 0.3525 0.2543 0.00 0.00 0 0.44 0.00 0.56 0.00
#> TCGA.B0.4696.11 1 0.0000 0.9880 1.00 0.00 0 0.00 0.00 0.00 0.00
#> TCGA.BP.5187.11 1 0.0000 0.9880 1.00 0.00 0 0.00 0.00 0.00 0.00
#> TCGA.B0.4690.01 4 0.0504 0.9523 0.00 0.02 0 0.98 0.00 0.00 0.00
#> TCGA.CZ.5466.01 4 0.0504 0.9523 0.00 0.02 0 0.98 0.00 0.00 0.00
#> TCGA.B0.4844.11 5 0.1671 0.8370 0.10 0.00 0 0.00 0.90 0.00 0.00
#> TCGA.CZ.5464.11 1 0.0504 0.9790 0.98 0.00 0 0.00 0.00 0.00 0.02
#> TCGA.B0.4701.11 1 0.2708 0.6877 0.78 0.00 0 0.00 0.22 0.00 0.00
#> TCGA.BP.5194.11 1 0.0000 0.9880 1.00 0.00 0 0.00 0.00 0.00 0.00
#> TCGA.B0.4707.01 2 0.0000 0.9870 0.00 1.00 0 0.00 0.00 0.00 0.00
#> TCGA.CZ.5467.11 5 0.0000 0.9946 0.00 0.00 0 0.00 1.00 0.00 0.00
#> TCGA.B0.5705.01 6 0.0504 0.9344 0.00 0.00 0 0.02 0.00 0.98 0.00
#> TCGA.CW.5588.01 4 0.0000 0.9623 0.00 0.00 0 1.00 0.00 0.00 0.00
#> TCGA.CJ.6031.01 4 0.0000 0.9623 0.00 0.00 0 1.00 0.00 0.00 0.00
#> TCGA.B8.A54J.01 4 0.0000 0.9623 0.00 0.00 0 1.00 0.00 0.00 0.00
#> TCGA.BP.5192.11 5 0.0000 0.9946 0.00 0.00 0 0.00 1.00 0.00 0.00
#> TCGA.CZ.5462.01 4 0.0504 0.9523 0.00 0.02 0 0.98 0.00 0.00 0.00
#> TCGA.B8.A54H.01 4 0.0000 0.9623 0.00 0.00 0 1.00 0.00 0.00 0.00
#> TCGA.CZ.5470.11 5 0.0000 0.9946 0.00 0.00 0 0.00 1.00 0.00 0.00
#> TCGA.BP.4177.11 5 0.0000 0.9946 0.00 0.00 0 0.00 1.00 0.00 0.00
#> TCGA.CZ.5469.11 5 0.0000 0.9946 0.00 0.00 0 0.00 1.00 0.00 0.00
#> TCGA.CJ.6028.01 4 0.0504 0.9523 0.00 0.02 0 0.98 0.00 0.00 0.00
#> TCGA.G6.A8L6.01 4 0.0000 0.9623 0.00 0.00 0 1.00 0.00 0.00 0.00
#> TCGA.B8.5551.01 4 0.0504 0.9523 0.00 0.02 0 0.98 0.00 0.00 0.00
#> TCGA.CZ.5456.01 2 0.0000 0.9870 0.00 1.00 0 0.00 0.00 0.00 0.00
#> TCGA.A3.A8OU.01 4 0.0000 0.9623 0.00 0.00 0 1.00 0.00 0.00 0.00
#> TCGA.BP.5186.01 6 0.0504 0.9344 0.00 0.00 0 0.02 0.00 0.98 0.00
#> TCGA.A3.A6NI.01 4 0.0000 0.9623 0.00 0.00 0 1.00 0.00 0.00 0.00
#> TCGA.BP.4782.01 4 0.3558 0.0159 0.00 0.00 0 0.52 0.00 0.48 0.00
#> TCGA.CZ.5454.11 5 0.0000 0.9946 0.00 0.00 0 0.00 1.00 0.00 0.00
#> TCGA.B0.4691.11 1 0.0000 0.9880 1.00 0.00 0 0.00 0.00 0.00 0.00
#> TCGA.CZ.5452.01 2 0.0000 0.9870 0.00 1.00 0 0.00 0.00 0.00 0.00
#> TCGA.EU.5904.01 6 0.0504 0.9344 0.00 0.00 0 0.02 0.00 0.98 0.00
#> TCGA.BP.5201.01 2 0.0000 0.9870 0.00 1.00 0 0.00 0.00 0.00 0.00
#> TCGA.CJ.5677.01 2 0.0000 0.9870 0.00 1.00 0 0.00 0.00 0.00 0.00
#> TCGA.BP.5170.11 5 0.0000 0.9946 0.00 0.00 0 0.00 1.00 0.00 0.00
#> TCGA.B0.4710.11 5 0.0000 0.9946 0.00 0.00 0 0.00 1.00 0.00 0.00
#> TCGA.AK.3425.01 2 0.0000 0.9870 0.00 1.00 0 0.00 0.00 0.00 0.00
#> TCGA.B0.4841.11 1 0.0000 0.9880 1.00 0.00 0 0.00 0.00 0.00 0.00
#> TCGA.B0.4849.01 4 0.0000 0.9623 0.00 0.00 0 1.00 0.00 0.00 0.00
#> TCGA.BP.5182.01 6 0.0504 0.9344 0.00 0.00 0 0.02 0.00 0.98 0.00
#> TCGA.B0.5711.11 5 0.0000 0.9946 0.00 0.00 0 0.00 1.00 0.00 0.00
#> TCGA.BP.5180.01 2 0.0000 0.9870 0.00 1.00 0 0.00 0.00 0.00 0.00
#> TCGA.BP.5176.01 4 0.0000 0.9623 0.00 0.00 0 1.00 0.00 0.00 0.00
#> TCGA.CZ.5984.01 2 0.0000 0.9870 0.00 1.00 0 0.00 0.00 0.00 0.00
#> TCGA.CZ.5460.11 1 0.0000 0.9880 1.00 0.00 0 0.00 0.00 0.00 0.00
#> TCGA.BP.5190.01 2 0.0000 0.9870 0.00 1.00 0 0.00 0.00 0.00 0.00
#> TCGA.BP.4795.11 1 0.0504 0.9790 0.98 0.00 0 0.00 0.00 0.00 0.02
#> TCGA.B0.4813.11 5 0.0000 0.9946 0.00 0.00 0 0.00 1.00 0.00 0.00
#> TCGA.B0.4713.01 2 0.0000 0.9870 0.00 1.00 0 0.00 0.00 0.00 0.00
#> TCGA.B0.4841.01 2 0.0000 0.9870 0.00 1.00 0 0.00 0.00 0.00 0.00
#> TCGA.B8.5546.01 7 0.0504 0.9683 0.00 0.00 0 0.00 0.00 0.02 0.98
#> TCGA.CW.5591.01 4 0.0504 0.9523 0.00 0.02 0 0.98 0.00 0.00 0.00
#> TCGA.B0.4698.11 1 0.0000 0.9880 1.00 0.00 0 0.00 0.00 0.00 0.00
#> TCGA.B0.5713.11 1 0.0000 0.9880 1.00 0.00 0 0.00 0.00 0.00 0.00
#> TCGA.B0.5108.11 1 0.0000 0.9880 1.00 0.00 0 0.00 0.00 0.00 0.00
#> TCGA.B0.5083.01 1 0.0504 0.9790 0.98 0.00 0 0.00 0.00 0.00 0.02
#> TCGA.B0.5699.01 2 0.0000 0.9870 0.00 1.00 0 0.00 0.00 0.00 0.00
#> TCGA.CZ.5453.11 5 0.0000 0.9946 0.00 0.00 0 0.00 1.00 0.00 0.00
#> TCGA.BP.5202.01 2 0.1433 0.8780 0.00 0.92 0 0.08 0.00 0.00 0.00
#> TCGA.BP.5173.11 1 0.0000 0.9880 1.00 0.00 0 0.00 0.00 0.00 0.00
#> TCGA.CW.5581.01 4 0.0000 0.9623 0.00 0.00 0 1.00 0.00 0.00 0.00
#> TCGA.B0.4848.11 1 0.0504 0.9790 0.98 0.00 0 0.00 0.00 0.00 0.02
#> TCGA.B0.4814.01 2 0.0000 0.9870 0.00 1.00 0 0.00 0.00 0.00 0.00
#> TCGA.BP.5178.11 1 0.0000 0.9880 1.00 0.00 0 0.00 0.00 0.00 0.00
#> TCGA.CJ.4907.01 4 0.0504 0.9523 0.00 0.02 0 0.98 0.00 0.00 0.00
#> TCGA.A3.3387.01 4 0.0000 0.9623 0.00 0.00 0 1.00 0.00 0.00 0.00
#> TCGA.B0.4821.01 2 0.0000 0.9870 0.00 1.00 0 0.00 0.00 0.00 0.00
#> TCGA.B0.5712.01 2 0.0000 0.9870 0.00 1.00 0 0.00 0.00 0.00 0.00
#> TCGA.B0.5695.01 6 0.3562 0.0454 0.00 0.00 0 0.50 0.00 0.50 0.00
#> TCGA.BP.5184.11 1 0.0000 0.9880 1.00 0.00 0 0.00 0.00 0.00 0.00
#> TCGA.B2.A4SR.01 4 0.0000 0.9623 0.00 0.00 0 1.00 0.00 0.00 0.00
#> TCGA.BP.5191.11 1 0.0504 0.9790 0.98 0.00 0 0.00 0.00 0.00 0.02
#> TCGA.CJ.4920.01 2 0.0000 0.9870 0.00 1.00 0 0.00 0.00 0.00 0.00
#> TCGA.BP.4801.01 4 0.0000 0.9623 0.00 0.00 0 1.00 0.00 0.00 0.00
#> TCGA.DV.A4W0.01 2 0.0000 0.9870 0.00 1.00 0 0.00 0.00 0.00 0.00
#> TCGA.BP.5177.11 1 0.0000 0.9880 1.00 0.00 0 0.00 0.00 0.00 0.00
#> TCGA.B0.4847.11 5 0.0000 0.9946 0.00 0.00 0 0.00 1.00 0.00 0.00
#> TCGA.B0.5100.01 4 0.0000 0.9623 0.00 0.00 0 1.00 0.00 0.00 0.00
#> TCGA.CJ.4903.01 2 0.0000 0.9870 0.00 1.00 0 0.00 0.00 0.00 0.00
#> TCGA.CJ.4912.01 2 0.0000 0.9870 0.00 1.00 0 0.00 0.00 0.00 0.00
#> TCGA.B0.5107.11 1 0.0000 0.9880 1.00 0.00 0 0.00 0.00 0.00 0.00
#> TCGA.AK.3453.01 1 0.0000 0.9880 1.00 0.00 0 0.00 0.00 0.00 0.00
#> TCGA.B0.5691.01 6 0.0000 0.9221 0.00 0.00 0 0.00 0.00 1.00 0.00
#> TCGA.BP.5195.11 5 0.0000 0.9946 0.00 0.00 0 0.00 1.00 0.00 0.00
#> TCGA.B0.5400.01 4 0.0000 0.9623 0.00 0.00 0 1.00 0.00 0.00 0.00
#> TCGA.A3.3376.11 7 0.0000 0.9571 0.00 0.00 0 0.00 0.00 0.00 1.00
#> TCGA.B0.4845.01 2 0.0000 0.9870 0.00 1.00 0 0.00 0.00 0.00 0.00
#> TCGA.B0.4699.01 7 0.0000 0.9571 0.00 0.00 0 0.00 0.00 0.00 1.00
#> TCGA.B0.4818.01 4 0.0000 0.9623 0.00 0.00 0 1.00 0.00 0.00 0.00
#> TCGA.BP.5174.11 1 0.0000 0.9880 1.00 0.00 0 0.00 0.00 0.00 0.00
#> TCGA.CJ.4901.11 1 0.0000 0.9880 1.00 0.00 0 0.00 0.00 0.00 0.00
#> TCGA.B8.A54D.01 2 0.0000 0.9870 0.00 1.00 0 0.00 0.00 0.00 0.00
#> TCGA.BP.4770.11 1 0.0504 0.9790 0.98 0.00 0 0.00 0.00 0.00 0.02
#> TCGA.CW.6093.01 6 0.0504 0.9344 0.00 0.00 0 0.02 0.00 0.98 0.00
#> TCGA.BP.5010.11 5 0.0000 0.9946 0.00 0.00 0 0.00 1.00 0.00 0.00
#> TCGA.AK.3431.01 4 0.0000 0.9623 0.00 0.00 0 1.00 0.00 0.00 0.00
#> TCGA.BP.4770.01 4 0.0000 0.9623 0.00 0.00 0 1.00 0.00 0.00 0.00
#> TCGA.BP.5189.01 4 0.0504 0.9523 0.00 0.02 0 0.98 0.00 0.00 0.00
#> TCGA.B0.4703.11 1 0.0000 0.9880 1.00 0.00 0 0.00 0.00 0.00 0.00
#> TCGA.B8.5163.01 4 0.0504 0.9523 0.00 0.02 0 0.98 0.00 0.00 0.00
#> TCGA.CJ.5683.01 4 0.0000 0.9623 0.00 0.00 0 1.00 0.00 0.00 0.00
#> TCGA.CZ.4856.11 5 0.0000 0.9946 0.00 0.00 0 0.00 1.00 0.00 0.00
#> TCGA.BP.4760.01 3 0.0000 1.0000 0.00 0.00 1 0.00 0.00 0.00 0.00
#> TCGA.B0.5692.01 2 0.0000 0.9870 0.00 1.00 0 0.00 0.00 0.00 0.00
#> TCGA.B0.5106.01 2 0.0000 0.9870 0.00 1.00 0 0.00 0.00 0.00 0.00
#> TCGA.B0.4843.01 4 0.0504 0.9523 0.00 0.02 0 0.98 0.00 0.00 0.00
#> TCGA.CZ.4866.11 5 0.0000 0.9946 0.00 0.00 0 0.00 1.00 0.00 0.00
#> TCGA.B0.5104.11 1 0.0000 0.9880 1.00 0.00 0 0.00 0.00 0.00 0.00
#> TCGA.B0.4827.01 2 0.0000 0.9870 0.00 1.00 0 0.00 0.00 0.00 0.00
#> TCGA.CJ.4902.11 5 0.0000 0.9946 0.00 0.00 0 0.00 1.00 0.00 0.00
#> TCGA.B8.A54G.01 4 0.0504 0.9523 0.00 0.02 0 0.98 0.00 0.00 0.00
#> TCGA.B0.5703.01 4 0.0863 0.9346 0.00 0.04 0 0.96 0.00 0.00 0.00
#> TCGA.CJ.5672.01 4 0.0504 0.9523 0.00 0.02 0 0.98 0.00 0.00 0.00
#> TCGA.B0.5098.11 1 0.0504 0.9790 0.98 0.00 0 0.00 0.00 0.00 0.02
#> TCGA.B0.5113.11 1 0.0000 0.9880 1.00 0.00 0 0.00 0.00 0.00 0.00
#> TCGA.CJ.4882.11 1 0.0000 0.9880 1.00 0.00 0 0.00 0.00 0.00 0.00
#> TCGA.CZ.5465.11 5 0.0000 0.9946 0.00 0.00 0 0.00 1.00 0.00 0.00
#> TCGA.B0.5102.01 4 0.1166 0.9097 0.00 0.00 0 0.94 0.00 0.06 0.00
#> TCGA.CW.5585.01 4 0.0504 0.9498 0.00 0.02 0 0.98 0.00 0.00 0.00
#> TCGA.B0.4824.01 4 0.0000 0.9623 0.00 0.00 0 1.00 0.00 0.00 0.00
#> TCGA.B0.5115.01 2 0.1886 0.8161 0.00 0.88 0 0.12 0.00 0.00 0.00
#> TCGA.B0.4706.01 2 0.0000 0.9870 0.00 1.00 0 0.00 0.00 0.00 0.00
#> TCGA.B0.5117.11 1 0.0000 0.9880 1.00 0.00 0 0.00 0.00 0.00 0.00
#> TCGA.CZ.4859.11 5 0.0000 0.9946 0.00 0.00 0 0.00 1.00 0.00 0.00
#> TCGA.AK.3450.01 4 0.0000 0.9623 0.00 0.00 0 1.00 0.00 0.00 0.00
#> TCGA.B8.A54I.01 2 0.0000 0.9870 0.00 1.00 0 0.00 0.00 0.00 0.00
#> TCGA.CZ.5463.01 2 0.0000 0.9870 0.00 1.00 0 0.00 0.00 0.00 0.00
#> TCGA.DV.5568.01 4 0.0504 0.9523 0.00 0.02 0 0.98 0.00 0.00 0.00
#> TCGA.CZ.5459.11 1 0.0504 0.9790 0.98 0.00 0 0.00 0.00 0.00 0.02
#> TCGA.CJ.4918.11 1 0.0000 0.9880 1.00 0.00 0 0.00 0.00 0.00 0.00
#> TCGA.DV.5565.01 4 0.1166 0.9126 0.00 0.06 0 0.94 0.00 0.00 0.00
#> TCGA.B0.5119.01 6 0.0504 0.9344 0.00 0.00 0 0.02 0.00 0.98 0.00
#> TCGA.B0.4811.01 4 0.0504 0.9523 0.00 0.02 0 0.98 0.00 0.00 0.00
#> TCGA.A3.3367.11 1 0.0000 0.9880 1.00 0.00 0 0.00 0.00 0.00 0.00
#> TCGA.CJ.4916.01 4 0.0504 0.9523 0.00 0.02 0 0.98 0.00 0.00 0.00
#> TCGA.B0.5693.01 4 0.0863 0.9299 0.00 0.00 0 0.96 0.00 0.04 0.00
#> TCGA.CZ.4863.11 5 0.0000 0.9946 0.00 0.00 0 0.00 1.00 0.00 0.00
#> TCGA.G6.A5PC.01 2 0.0000 0.9870 0.00 1.00 0 0.00 0.00 0.00 0.00
#> TCGA.B8.5550.01 4 0.0000 0.9623 0.00 0.00 0 1.00 0.00 0.00 0.00
#> TCGA.DV.A4W0.05 3 0.0000 1.0000 0.00 0.00 1 0.00 0.00 0.00 0.00
#> TCGA.B0.4696.01 2 0.3221 0.4503 0.00 0.68 0 0.32 0.00 0.00 0.00
#> TCGA.BP.5187.01 4 0.0000 0.9623 0.00 0.00 0 1.00 0.00 0.00 0.00
#> TCGA.CZ.5466.11 1 0.0504 0.9790 0.98 0.00 0 0.00 0.00 0.00 0.02
#> TCGA.CW.6097.01 4 0.0000 0.9623 0.00 0.00 0 1.00 0.00 0.00 0.00
#> TCGA.CJ.4905.11 5 0.0000 0.9946 0.00 0.00 0 0.00 1.00 0.00 0.00
#> TCGA.CZ.5989.01 4 0.1886 0.8370 0.00 0.00 0 0.88 0.00 0.12 0.00
#> TCGA.BP.5194.01 4 0.1886 0.8377 0.00 0.00 0 0.88 0.00 0.12 0.00
#> TCGA.B0.4707.11 1 0.0000 0.9880 1.00 0.00 0 0.00 0.00 0.00 0.00
#> TCGA.CZ.5467.01 4 0.0000 0.9623 0.00 0.00 0 1.00 0.00 0.00 0.00
#> TCGA.BP.5185.11 1 0.0504 0.9790 0.98 0.00 0 0.00 0.00 0.00 0.02
#> TCGA.BP.5183.11 1 0.0000 0.9880 1.00 0.00 0 0.00 0.00 0.00 0.00
#> TCGA.BP.5192.01 6 0.0504 0.9344 0.00 0.00 0 0.02 0.00 0.98 0.00
#> TCGA.CZ.5462.11 5 0.0000 0.9946 0.00 0.00 0 0.00 1.00 0.00 0.00
#> TCGA.BP.4177.01 3 0.0000 1.0000 0.00 0.00 1 0.00 0.00 0.00 0.00
#> TCGA.CZ.5469.01 2 0.0000 0.9870 0.00 1.00 0 0.00 0.00 0.00 0.00
#> TCGA.B2.5641.01 2 0.0000 0.9870 0.00 1.00 0 0.00 0.00 0.00 0.00
#> TCGA.BP.5196.11 1 0.0000 0.9880 1.00 0.00 0 0.00 0.00 0.00 0.00
#> TCGA.CZ.5460.01 2 0.0000 0.9870 0.00 1.00 0 0.00 0.00 0.00 0.00
#> TCGA.B0.4712.01 2 0.0000 0.9870 0.00 1.00 0 0.00 0.00 0.00 0.00
#> TCGA.B8.A54K.01 3 0.0000 1.0000 0.00 0.00 1 0.00 0.00 0.00 0.00
#> TCGA.B0.5707.01 6 0.0000 0.9221 0.00 0.00 0 0.00 0.00 1.00 0.00
#> TCGA.BP.5186.11 1 0.0000 0.9880 1.00 0.00 0 0.00 0.00 0.00 0.00
#> TCGA.EU.5906.01 6 0.0504 0.9344 0.00 0.00 0 0.02 0.00 0.98 0.00
#> TCGA.CZ.5461.11 5 0.0000 0.9946 0.00 0.00 0 0.00 1.00 0.00 0.00
#> TCGA.CW.5590.01 2 0.0000 0.9870 0.00 1.00 0 0.00 0.00 0.00 0.00
#> TCGA.B0.5698.01 2 0.0000 0.9870 0.00 1.00 0 0.00 0.00 0.00 0.00
#> TCGA.CW.5580.01 2 0.0000 0.9870 0.00 1.00 0 0.00 0.00 0.00 0.00
#> TCGA.CZ.5454.01 2 0.0000 0.9870 0.00 1.00 0 0.00 0.00 0.00 0.00
#> TCGA.B0.4815.01 2 0.0000 0.9870 0.00 1.00 0 0.00 0.00 0.00 0.00
#> TCGA.B0.5710.11 1 0.0000 0.9880 1.00 0.00 0 0.00 0.00 0.00 0.00
#> TCGA.CJ.4908.11 5 0.0000 0.9946 0.00 0.00 0 0.00 1.00 0.00 0.00
#> TCGA.BP.5201.11 1 0.0000 0.9880 1.00 0.00 0 0.00 0.00 0.00 0.00
#> TCGA.B0.5694.01 2 0.0000 0.9870 0.00 1.00 0 0.00 0.00 0.00 0.00
#> TCGA.BP.5170.01 4 0.0000 0.9623 0.00 0.00 0 1.00 0.00 0.00 0.00
#> TCGA.DV.5575.01 6 0.0000 0.9221 0.00 0.00 0 0.00 0.00 1.00 0.00
#> TCGA.CJ.5686.01 4 0.0000 0.9623 0.00 0.00 0 1.00 0.00 0.00 0.00
#> TCGA.A3.3357.01 2 0.0000 0.9870 0.00 1.00 0 0.00 0.00 0.00 0.00
#> TCGA.A3.3373.01 4 0.3546 0.0877 0.00 0.00 0 0.54 0.00 0.46 0.00
#> TCGA.B0.5690.01 6 0.0504 0.9344 0.00 0.00 0 0.02 0.00 0.98 0.00
#> TCGA.B8.4622.01 2 0.0000 0.9870 0.00 1.00 0 0.00 0.00 0.00 0.00
#> TCGA.AK.3433.01 5 0.0000 0.9946 0.00 0.00 0 0.00 1.00 0.00 0.00
#> TCGA.B0.5110.01 6 0.0504 0.9344 0.00 0.00 0 0.02 0.00 0.98 0.00
#> TCGA.BP.5180.11 1 0.0000 0.9880 1.00 0.00 0 0.00 0.00 0.00 0.00
#> TCGA.CJ.4913.01 2 0.0000 0.9870 0.00 1.00 0 0.00 0.00 0.00 0.00
#> TCGA.CJ.4908.01 4 0.0000 0.9623 0.00 0.00 0 1.00 0.00 0.00 0.00
#> TCGA.BP.4795.01 3 0.0000 1.0000 0.00 0.00 1 0.00 0.00 0.00 0.00
#> TCGA.CJ.4897.11 1 0.0000 0.9880 1.00 0.00 0 0.00 0.00 0.00 0.00
#> TCGA.B2.5636.01 3 0.0000 1.0000 0.00 0.00 1 0.00 0.00 0.00 0.00
#> TCGA.CJ.4923.11 1 0.0000 0.9880 1.00 0.00 0 0.00 0.00 0.00 0.00
#> TCGA.B0.4819.01 4 0.0000 0.9623 0.00 0.00 0 1.00 0.00 0.00 0.00
#> TCGA.B2.5633.01 4 0.0000 0.9623 0.00 0.00 0 1.00 0.00 0.00 0.00
#> TCGA.CJ.6033.01 2 0.0000 0.9870 0.00 1.00 0 0.00 0.00 0.00 0.00
#> TCGA.BP.5181.11 1 0.0504 0.9790 0.98 0.00 0 0.00 0.00 0.00 0.02
#> TCGA.B0.4698.01 2 0.0000 0.9870 0.00 1.00 0 0.00 0.00 0.00 0.00
#> TCGA.B0.5083.11 1 0.0000 0.9880 1.00 0.00 0 0.00 0.00 0.00 0.00
#> TCGA.CZ.4864.11 1 0.0504 0.9790 0.98 0.00 0 0.00 0.00 0.00 0.02
#> TCGA.B0.4688.01 2 0.0000 0.9870 0.00 1.00 0 0.00 0.00 0.00 0.00
#> TCGA.BP.5168.01 4 0.0000 0.9623 0.00 0.00 0 1.00 0.00 0.00 0.00
#> TCGA.BP.5198.11 1 0.0504 0.9790 0.98 0.00 0 0.00 0.00 0.00 0.02
#> TCGA.B8.5162.01 4 0.0000 0.9623 0.00 0.00 0 1.00 0.00 0.00 0.00
#> TCGA.B0.5096.01 2 0.0000 0.9870 0.00 1.00 0 0.00 0.00 0.00 0.00
#> TCGA.BP.5178.01 2 0.0000 0.9870 0.00 1.00 0 0.00 0.00 0.00 0.00
#> TCGA.B0.5099.11 1 0.0000 0.9880 1.00 0.00 0 0.00 0.00 0.00 0.00
#> TCGA.B0.4842.01 4 0.0504 0.9523 0.00 0.02 0 0.98 0.00 0.00 0.00
#> TCGA.BP.5169.11 1 0.0000 0.9880 1.00 0.00 0 0.00 0.00 0.00 0.00
#> TCGA.B0.5109.11 7 0.0000 0.9571 0.00 0.00 0 0.00 0.00 0.00 1.00
#> TCGA.CJ.4920.11 5 0.0000 0.9946 0.00 0.00 0 0.00 1.00 0.00 0.00
#> TCGA.B0.5080.11 1 0.0504 0.9790 0.98 0.00 0 0.00 0.00 0.00 0.02
#> TCGA.B0.5700.01 6 0.0504 0.9344 0.00 0.00 0 0.02 0.00 0.98 0.00
#> TCGA.B0.4847.01 2 0.0000 0.9870 0.00 1.00 0 0.00 0.00 0.00 0.00
#> TCGA.B0.5702.01 7 0.0504 0.9683 0.00 0.00 0 0.00 0.00 0.02 0.98
#> TCGA.CJ.4905.01 4 0.0000 0.9623 0.00 0.00 0 1.00 0.00 0.00 0.00
#> TCGA.B2.5635.01 4 0.0000 0.9623 0.00 0.00 0 1.00 0.00 0.00 0.00
#> TCGA.B0.5107.01 2 0.0000 0.9870 0.00 1.00 0 0.00 0.00 0.00 0.00
#> TCGA.CW.5584.01 2 0.0000 0.9870 0.00 1.00 0 0.00 0.00 0.00 0.00
#> TCGA.B4.5838.01 4 0.3294 0.4576 0.00 0.34 0 0.66 0.00 0.00 0.00
#> TCGA.BP.5199.01 2 0.1671 0.8479 0.00 0.90 0 0.10 0.00 0.00 0.00
#> TCGA.A3.3376.01 6 0.0504 0.9344 0.00 0.00 0 0.02 0.00 0.98 0.00
#> TCGA.B0.4845.11 5 0.0000 0.9946 0.00 0.00 0 0.00 1.00 0.00 0.00
#> TCGA.B0.4699.11 1 0.0000 0.9880 1.00 0.00 0 0.00 0.00 0.00 0.00
#> TCGA.BP.5174.01 6 0.0504 0.9344 0.00 0.00 0 0.02 0.00 0.98 0.00
#> TCGA.CZ.5986.01 6 0.0000 0.9221 0.00 0.00 0 0.00 0.00 1.00 0.00
#> TCGA.CJ.4901.01 2 0.0000 0.9870 0.00 1.00 0 0.00 0.00 0.00 0.00
#> TCGA.AK.3461.01 4 0.0000 0.9623 0.00 0.00 0 1.00 0.00 0.00 0.00
#> TCGA.AK.3460.01 4 0.0000 0.9623 0.00 0.00 0 1.00 0.00 0.00 0.00
#> TCGA.AK.3454.01 6 0.0504 0.9344 0.00 0.00 0 0.02 0.00 0.98 0.00
#> TCGA.CZ.4859.01 6 0.0000 0.9221 0.00 0.00 0 0.00 0.00 1.00 0.00
#> TCGA.B0.5812.01 4 0.0000 0.9623 0.00 0.00 0 1.00 0.00 0.00 0.00
#> TCGA.B0.5116.11 7 0.0504 0.9683 0.00 0.00 0 0.00 0.00 0.02 0.98
#> TCGA.B8.A54F.01 4 0.0000 0.9623 0.00 0.00 0 1.00 0.00 0.00 0.00
#> TCGA.CW.6090.01 2 0.0000 0.9870 0.00 1.00 0 0.00 0.00 0.00 0.00
#> TCGA.CZ.5458.11 5 0.0000 0.9946 0.00 0.00 0 0.00 1.00 0.00 0.00
#> TCGA.B0.5106.11 1 0.0000 0.9880 1.00 0.00 0 0.00 0.00 0.00 0.00
#> TCGA.CZ.4866.01 2 0.0000 0.9870 0.00 1.00 0 0.00 0.00 0.00 0.00
#> TCGA.B0.4828.01 2 0.0000 0.9870 0.00 1.00 0 0.00 0.00 0.00 0.00
#> TCGA.AK.3440.01 5 0.0000 0.9946 0.00 0.00 0 0.00 1.00 0.00 0.00
#> TCGA.MM.A563.01 2 0.0000 0.9870 0.00 1.00 0 0.00 0.00 0.00 0.00
#> TCGA.B0.4697.01 4 0.0000 0.9623 0.00 0.00 0 1.00 0.00 0.00 0.00
#> TCGA.AK.3458.01 2 0.0000 0.9870 0.00 1.00 0 0.00 0.00 0.00 0.00
#> TCGA.CJ.5676.01 2 0.0000 0.9870 0.00 1.00 0 0.00 0.00 0.00 0.00
#> TCGA.B0.5402.11 1 0.0504 0.9790 0.98 0.00 0 0.00 0.00 0.00 0.02
#> TCGA.CJ.5681.01 7 0.0504 0.9683 0.00 0.00 0 0.00 0.00 0.02 0.98
#> TCGA.A3.3370.11 5 0.0504 0.9678 0.02 0.00 0 0.00 0.98 0.00 0.00
#> TCGA.A3.A6NL.01 6 0.0504 0.9344 0.00 0.00 0 0.02 0.00 0.98 0.00
#> TCGA.B0.4693.01 2 0.0000 0.9870 0.00 1.00 0 0.00 0.00 0.00 0.00
#> TCGA.A3.3358.01 4 0.0504 0.9523 0.00 0.02 0 0.98 0.00 0.00 0.00
#> TCGA.B0.4710.01 2 0.0000 0.9870 0.00 1.00 0 0.00 0.00 0.00 0.00
#> TCGA.CZ.4853.11 5 0.0000 0.9946 0.00 0.00 0 0.00 1.00 0.00 0.00
#> TCGA.B4.5835.01 6 0.0000 0.9221 0.00 0.00 0 0.00 0.00 1.00 0.00
#> TCGA.CJ.4882.01 4 0.0000 0.9623 0.00 0.00 0 1.00 0.00 0.00 0.00
#> TCGA.CZ.5465.01 2 0.0000 0.9870 0.00 1.00 0 0.00 0.00 0.00 0.00
#> TCGA.B0.5102.11 1 0.0000 0.9880 1.00 0.00 0 0.00 0.00 0.00 0.00
#> TCGA.B0.4824.11 1 0.0000 0.9880 1.00 0.00 0 0.00 0.00 0.00 0.00
#> TCGA.CJ.5675.01 2 0.0000 0.9870 0.00 1.00 0 0.00 0.00 0.00 0.00
#> TCGA.B0.4700.01 4 0.0000 0.9623 0.00 0.00 0 1.00 0.00 0.00 0.00
#> TCGA.B0.5092.01 4 0.0000 0.9623 0.00 0.00 0 1.00 0.00 0.00 0.00
#> TCGA.B0.5115.11 1 0.0000 0.9880 1.00 0.00 0 0.00 0.00 0.00 0.00
#> TCGA.B0.4945.11 1 0.0000 0.9880 1.00 0.00 0 0.00 0.00 0.00 0.00
#> TCGA.B8.5158.01 2 0.3294 0.4110 0.00 0.66 0 0.34 0.00 0.00 0.00
#> TCGA.CJ.6030.01 2 0.0000 0.9870 0.00 1.00 0 0.00 0.00 0.00 0.00
#> TCGA.B8.A54E.01 7 0.0504 0.9683 0.00 0.00 0 0.00 0.00 0.02 0.98
#> TCGA.CJ.6032.01 4 0.0863 0.9346 0.00 0.04 0 0.96 0.00 0.00 0.00
#> TCGA.B0.4852.11 1 0.0000 0.9880 1.00 0.00 0 0.00 0.00 0.00 0.00
#> TCGA.B0.4817.01 4 0.0000 0.9623 0.00 0.00 0 1.00 0.00 0.00 0.00
#> TCGA.B8.5159.01 2 0.0000 0.9870 0.00 1.00 0 0.00 0.00 0.00 0.00
#> TCGA.A3.A8OW.01 6 0.0504 0.9344 0.00 0.00 0 0.02 0.00 0.98 0.00
#> TCGA.B0.4822.01 4 0.0504 0.9523 0.00 0.02 0 0.98 0.00 0.00 0.00
#> TCGA.B0.5696.01 4 0.0000 0.9623 0.00 0.00 0 1.00 0.00 0.00 0.00
#> TCGA.B0.5706.01 2 0.0000 0.9870 0.00 1.00 0 0.00 0.00 0.00 0.00
#> TCGA.CJ.4918.01 4 0.0000 0.9623 0.00 0.00 0 1.00 0.00 0.00 0.00
#> TCGA.B0.5119.11 5 0.0000 0.9946 0.00 0.00 0 0.00 1.00 0.00 0.00
#> TCGA.BP.5200.11 1 0.0000 0.9880 1.00 0.00 0 0.00 0.00 0.00 0.00
#> TCGA.B0.4811.11 1 0.0504 0.9790 0.98 0.00 0 0.00 0.00 0.00 0.02
#> TCGA.A3.3367.01 2 0.0000 0.9870 0.00 1.00 0 0.00 0.00 0.00 0.00
#> TCGA.B0.5097.01 4 0.1166 0.9119 0.00 0.06 0 0.94 0.00 0.00 0.00
#> TCGA.6D.AA2E.01 7 0.0504 0.9683 0.00 0.00 0 0.00 0.00 0.02 0.98
#> TCGA.DV.A4VX.01 2 0.0000 0.9870 0.00 1.00 0 0.00 0.00 0.00 0.00
#> TCGA.B0.4816.11 5 0.0000 0.9946 0.00 0.00 0 0.00 1.00 0.00 0.00
#> TCGA.A3.3385.11 1 0.0000 0.9880 1.00 0.00 0 0.00 0.00 0.00 0.00
#> TCGA.DV.5569.01 6 0.0504 0.9344 0.00 0.00 0 0.02 0.00 0.98 0.00
#> TCGA.EU.5907.01 2 0.0000 0.9870 0.00 1.00 0 0.00 0.00 0.00 0.00
#> TCGA.CZ.5455.01 4 0.0504 0.9523 0.00 0.02 0 0.98 0.00 0.00 0.00
#> TCGA.B8.5545.01 6 0.0000 0.9221 0.00 0.00 0 0.00 0.00 1.00 0.00
#> TCGA.DV.5567.01 3 0.0000 1.0000 0.00 0.00 1 0.00 0.00 0.00 0.00
#> TCGA.CZ.5451.01 4 0.2259 0.7764 0.00 0.16 0 0.84 0.00 0.00 0.00
#> TCGA.CJ.4869.01 4 0.0504 0.9523 0.00 0.02 0 0.98 0.00 0.00 0.00
#> TCGA.CJ.5678.01 2 0.0000 0.9870 0.00 1.00 0 0.00 0.00 0.00 0.00
#> TCGA.B8.4153.01 2 0.0000 0.9870 0.00 1.00 0 0.00 0.00 0.00 0.00
#> TCGA.B0.5121.11 1 0.0000 0.9880 1.00 0.00 0 0.00 0.00 0.00 0.00
#> TCGA.B8.4146.01 4 0.1433 0.8878 0.00 0.00 0 0.92 0.00 0.08 0.00
#> TCGA.BP.5183.01 2 0.0000 0.9870 0.00 1.00 0 0.00 0.00 0.00 0.00
#> TCGA.B0.5399.01 4 0.0000 0.9623 0.00 0.00 0 1.00 0.00 0.00 0.00
#> TCGA.B0.4810.11 5 0.0000 0.9946 0.00 0.00 0 0.00 1.00 0.00 0.00
#> TCGA.AK.3445.01 2 0.0000 0.9870 0.00 1.00 0 0.00 0.00 0.00 0.00
#> TCGA.B4.5378.01 3 0.0000 1.0000 0.00 0.00 1 0.00 0.00 0.00 0.00
#> TCGA.BP.5196.01 2 0.0000 0.9870 0.00 1.00 0 0.00 0.00 0.00 0.00
#> TCGA.CZ.4865.11 5 0.0000 0.9946 0.00 0.00 0 0.00 1.00 0.00 0.00
#> TCGA.B0.5709.01 6 0.0000 0.9221 0.00 0.00 0 0.00 0.00 1.00 0.00
#> TCGA.B0.4712.11 5 0.0000 0.9946 0.00 0.00 0 0.00 1.00 0.00 0.00
#> TCGA.B0.4714.01 2 0.0000 0.9870 0.00 1.00 0 0.00 0.00 0.00 0.00
#> TCGA.B8.5549.01 2 0.0000 0.9870 0.00 1.00 0 0.00 0.00 0.00 0.00
#> TCGA.CZ.5461.01 2 0.0000 0.9870 0.00 1.00 0 0.00 0.00 0.00 0.00
#> TCGA.CZ.5457.01 6 0.0000 0.9221 0.00 0.00 0 0.00 0.00 1.00 0.00
#> TCGA.A3.A8CQ.01 6 0.0000 0.9221 0.00 0.00 0 0.00 0.00 1.00 0.00
#> TCGA.DV.5573.01 6 0.3496 0.3001 0.00 0.00 0 0.42 0.00 0.58 0.00
#> TCGA.B0.4815.11 1 0.0504 0.9790 0.98 0.00 0 0.00 0.00 0.00 0.02
#> TCGA.B0.5710.01 2 0.0000 0.9870 0.00 1.00 0 0.00 0.00 0.00 0.00
#> TCGA.B8.5165.01 6 0.0000 0.9221 0.00 0.00 0 0.00 0.00 1.00 0.00
#> TCGA.B0.4718.01 2 0.0000 0.9870 0.00 1.00 0 0.00 0.00 0.00 0.00
#> TCGA.B2.5639.01 4 0.1433 0.8873 0.00 0.08 0 0.92 0.00 0.00 0.00
#> TCGA.CW.5583.01 6 0.0504 0.9344 0.00 0.00 0 0.02 0.00 0.98 0.00
#> TCGA.GK.A6C7.01 6 0.0504 0.9344 0.00 0.00 0 0.02 0.00 0.98 0.00
#> TCGA.A3.3357.11 1 0.0000 0.9880 1.00 0.00 0 0.00 0.00 0.00 0.00
#> TCGA.B8.5552.01 6 0.0000 0.9221 0.00 0.00 0 0.00 0.00 1.00 0.00
#> TCGA.B0.5120.01 4 0.0000 0.9623 0.00 0.00 0 1.00 0.00 0.00 0.00
#> TCGA.A3.3373.11 5 0.0000 0.9946 0.00 0.00 0 0.00 1.00 0.00 0.00
#> TCGA.BP.5185.01 4 0.0504 0.9498 0.00 0.02 0 0.98 0.00 0.00 0.00
#> TCGA.B0.4846.01 4 0.0000 0.9623 0.00 0.00 0 1.00 0.00 0.00 0.00
#> TCGA.CJ.4904.01 6 0.0504 0.9344 0.00 0.00 0 0.02 0.00 0.98 0.00
#> TCGA.CJ.4913.11 1 0.0000 0.9880 1.00 0.00 0 0.00 0.00 0.00 0.00
#> TCGA.BP.4993.11 1 0.0000 0.9880 1.00 0.00 0 0.00 0.00 0.00 0.00
#> TCGA.B0.4823.11 1 0.0000 0.9880 1.00 0.00 0 0.00 0.00 0.00 0.00
#> TCGA.CJ.4897.01 4 0.0000 0.9623 0.00 0.00 0 1.00 0.00 0.00 0.00
#> TCGA.BP.4993.01 6 0.0504 0.9344 0.00 0.00 0 0.02 0.00 0.98 0.00
#> TCGA.B4.5843.01 6 0.0504 0.9344 0.00 0.00 0 0.02 0.00 0.98 0.00
#> TCGA.DV.5576.01 3 0.0000 1.0000 0.00 0.00 1 0.00 0.00 0.00 0.00
#> TCGA.CJ.4923.01 4 0.0000 0.9623 0.00 0.00 0 1.00 0.00 0.00 0.00
#> TCGA.B0.4819.11 1 0.0000 0.9880 1.00 0.00 0 0.00 0.00 0.00 0.00
#> TCGA.BP.5175.01 2 0.0000 0.9870 0.00 1.00 0 0.00 0.00 0.00 0.00
#> TCGA.CZ.5987.01 2 0.0000 0.9870 0.00 1.00 0 0.00 0.00 0.00 0.00
#> TCGA.CZ.4864.01 6 0.3546 0.1899 0.00 0.00 0 0.46 0.00 0.54 0.00
#> TCGA.B0.4688.11 5 0.0000 0.9946 0.00 0.00 0 0.00 1.00 0.00 0.00
#> TCGA.BP.5168.11 1 0.0504 0.9790 0.98 0.00 0 0.00 0.00 0.00 0.02
#> TCGA.BP.5198.01 2 0.0000 0.9870 0.00 1.00 0 0.00 0.00 0.00 0.00
#> TCGA.B8.A7U6.01 4 0.0000 0.9623 0.00 0.00 0 1.00 0.00 0.00 0.00
#> TCGA.B0.5094.01 2 0.0000 0.9870 0.00 1.00 0 0.00 0.00 0.00 0.00
#> TCGA.T7.A92I.01 7 0.0504 0.9683 0.00 0.00 0 0.00 0.00 0.02 0.98
#> TCGA.B0.5096.11 1 0.0000 0.9880 1.00 0.00 0 0.00 0.00 0.00 0.00
#> TCGA.B0.5400.11 1 0.0504 0.9790 0.98 0.00 0 0.00 0.00 0.00 0.02
#> TCGA.B0.4694.11 5 0.1166 0.9058 0.06 0.00 0 0.00 0.94 0.00 0.00
#> TCGA.B0.5099.01 4 0.0504 0.9498 0.00 0.02 0 0.98 0.00 0.00 0.00
#> TCGA.CZ.5468.01 2 0.0000 0.9870 0.00 1.00 0 0.00 0.00 0.00 0.00
#> TCGA.B0.4842.11 1 0.0000 0.9880 1.00 0.00 0 0.00 0.00 0.00 0.00
#> TCGA.CZ.5988.01 4 0.0000 0.9623 0.00 0.00 0 1.00 0.00 0.00 0.00
#> TCGA.BP.5169.01 2 0.0000 0.9870 0.00 1.00 0 0.00 0.00 0.00 0.00
#> TCGA.B0.5109.01 4 0.0000 0.9623 0.00 0.00 0 1.00 0.00 0.00 0.00
#> TCGA.B4.5834.01 6 0.0504 0.9344 0.00 0.00 0 0.02 0.00 0.98 0.00
#> TCGA.B0.5095.11 1 0.0504 0.9790 0.98 0.00 0 0.00 0.00 0.00 0.02
#> TCGA.B0.5080.01 4 0.0000 0.9623 0.00 0.00 0 1.00 0.00 0.00 0.00
#> TCGA.CJ.5680.01 2 0.0000 0.9870 0.00 1.00 0 0.00 0.00 0.00 0.00
#> TCGA.CZ.5470.01 2 0.0000 0.9870 0.00 1.00 0 0.00 0.00 0.00 0.00
#> TCGA.CZ.4865.01 4 0.0000 0.9623 0.00 0.00 0 1.00 0.00 0.00 0.00
#> TCGA.A3.A8OX.01 7 0.0504 0.9683 0.00 0.00 0 0.00 0.00 0.02 0.98
#> TCGA.B0.4690.11 1 0.0504 0.9790 0.98 0.00 0 0.00 0.00 0.00 0.02
#> TCGA.CJ.5684.01 4 0.0000 0.9623 0.00 0.00 0 1.00 0.00 0.00 0.00
#> TCGA.B0.4844.01 2 0.0000 0.9870 0.00 1.00 0 0.00 0.00 0.00 0.00
#> TCGA.CZ.5464.01 2 0.0000 0.9870 0.00 1.00 0 0.00 0.00 0.00 0.00
#> TCGA.B0.4701.01 4 0.0504 0.9523 0.00 0.02 0 0.98 0.00 0.00 0.00
#> TCGA.B0.5701.01 2 0.0000 0.9870 0.00 1.00 0 0.00 0.00 0.00 0.00
#> TCGA.BP.5199.11 1 0.0000 0.9880 1.00 0.00 0 0.00 0.00 0.00 0.00
#> TCGA.CJ.5671.01 2 0.0863 0.9361 0.00 0.96 0 0.04 0.00 0.00 0.00
#> TCGA.A3.A8OV.01 6 0.0504 0.9344 0.00 0.00 0 0.02 0.00 0.98 0.00
#> TCGA.CZ.5456.11 5 0.0000 0.9946 0.00 0.00 0 0.00 1.00 0.00 0.00
#> TCGA.B0.5116.01 2 0.0000 0.9870 0.00 1.00 0 0.00 0.00 0.00 0.00
#> TCGA.CZ.5458.01 4 0.0000 0.9623 0.00 0.00 0 1.00 0.00 0.00 0.00
#> TCGA.CZ.5982.01 4 0.3358 0.4170 0.00 0.36 0 0.64 0.00 0.00 0.00
#> TCGA.B0.4828.11 5 0.0000 0.9946 0.00 0.00 0 0.00 1.00 0.00 0.00
#> TCGA.CJ.5679.01 2 0.0000 0.9870 0.00 1.00 0 0.00 0.00 0.00 0.00
#> TCGA.CJ.5682.01 2 0.0000 0.9870 0.00 1.00 0 0.00 0.00 0.00 0.00
#> TCGA.B0.5697.01 4 0.0000 0.9623 0.00 0.00 0 1.00 0.00 0.00 0.00
#> TCGA.B0.4697.11 5 0.0000 0.9946 0.00 0.00 0 0.00 1.00 0.00 0.00
#> TCGA.BP.4782.11 1 0.0504 0.9790 0.98 0.00 0 0.00 0.00 0.00 0.02
#> TCGA.G6.A8L8.01 2 0.0000 0.9870 0.00 1.00 0 0.00 0.00 0.00 0.00
#> TCGA.A3.A6NJ.01 6 0.0504 0.9344 0.00 0.00 0 0.02 0.00 0.98 0.00
#> TCGA.A3.3370.01 6 0.0000 0.9221 0.00 0.00 0 0.00 0.00 1.00 0.00
#> TCGA.B0.4691.01 2 0.0000 0.9870 0.00 1.00 0 0.00 0.00 0.00 0.00
#> TCGA.CZ.5452.11 5 0.0000 0.9946 0.00 0.00 0 0.00 1.00 0.00 0.00
#> TCGA.B0.4693.11 1 0.0000 0.9880 1.00 0.00 0 0.00 0.00 0.00 0.00
#> TCGA.B0.4945.01 6 0.0504 0.9344 0.00 0.00 0 0.02 0.00 0.98 0.00
#> TCGA.CZ.4853.01 2 0.0000 0.9870 0.00 1.00 0 0.00 0.00 0.00 0.00
#> TCGA.B0.5092.11 1 0.0000 0.9880 1.00 0.00 0 0.00 0.00 0.00 0.00
#> TCGA.B0.5402.01 2 0.0000 0.9870 0.00 1.00 0 0.00 0.00 0.00 0.00
#> TCGA.B0.4849.11 1 0.0000 0.9880 1.00 0.00 0 0.00 0.00 0.00 0.00
#> TCGA.A3.A6NN.01 4 0.2081 0.8061 0.00 0.14 0 0.86 0.00 0.00 0.00
#> TCGA.B0.4852.01 4 0.0000 0.9623 0.00 0.00 0 1.00 0.00 0.00 0.00
#> TCGA.B0.4817.11 1 0.0000 0.9880 1.00 0.00 0 0.00 0.00 0.00 0.00
#> TCGA.BP.5176.11 1 0.0504 0.9790 0.98 0.00 0 0.00 0.00 0.00 0.02
#> TCGA.CW.5589.01 6 0.0000 0.9221 0.00 0.00 0 0.00 0.00 1.00 0.00
#> TCGA.CJ.5689.01 4 0.0000 0.9623 0.00 0.00 0 1.00 0.00 0.00 0.00
#> TCGA.B0.4822.11 5 0.0000 0.9946 0.00 0.00 0 0.00 1.00 0.00 0.00
#> TCGA.BP.5190.11 1 0.0000 0.9880 1.00 0.00 0 0.00 0.00 0.00 0.00
#> TCGA.B0.4813.01 2 0.0000 0.9870 0.00 1.00 0 0.00 0.00 0.00 0.00
#> TCGA.BP.5200.01 4 0.0000 0.9623 0.00 0.00 0 1.00 0.00 0.00 0.00
#> TCGA.G6.A8L7.01 2 0.0863 0.9353 0.00 0.96 0 0.04 0.00 0.00 0.00
#> TCGA.B2.4101.01 4 0.0504 0.9523 0.00 0.02 0 0.98 0.00 0.00 0.00
#> TCGA.B0.4713.11 1 0.0504 0.9790 0.98 0.00 0 0.00 0.00 0.00 0.02
#> TCGA.B0.4816.01 4 0.0000 0.9623 0.00 0.00 0 1.00 0.00 0.00 0.00
#> TCGA.A3.3385.01 6 0.0000 0.9221 0.00 0.00 0 0.00 0.00 1.00 0.00
#> TCGA.B2.3924.01 4 0.0504 0.9472 0.00 0.00 0 0.98 0.00 0.02 0.00
#> TCGA.CZ.5455.11 5 0.0000 0.9946 0.00 0.00 0 0.00 1.00 0.00 0.00
#> TCGA.B0.5713.01 4 0.0504 0.9523 0.00 0.02 0 0.98 0.00 0.00 0.00
#> TCGA.B0.5108.01 4 0.0504 0.9523 0.00 0.02 0 0.98 0.00 0.00 0.00
#> TCGA.B0.5711.01 4 0.0000 0.9623 0.00 0.00 0 1.00 0.00 0.00 0.00
#> TCGA.CZ.5453.01 6 0.0504 0.9344 0.00 0.00 0 0.02 0.00 0.98 0.00
#> TCGA.BP.5202.11 7 0.0000 0.9571 0.00 0.00 0 0.00 0.00 0.00 1.00
#> TCGA.BP.5173.01 6 0.0863 0.9086 0.00 0.00 0 0.04 0.00 0.96 0.00
#> TCGA.CZ.5451.11 1 0.0000 0.9880 1.00 0.00 0 0.00 0.00 0.00 0.00
#> TCGA.B8.A8YJ.01 6 0.0000 0.9221 0.00 0.00 0 0.00 0.00 1.00 0.00
#> TCGA.B0.4848.01 2 0.0000 0.9870 0.00 1.00 0 0.00 0.00 0.00 0.00
#> TCGA.DV.A4VZ.01 3 0.0000 1.0000 0.00 0.00 1 0.00 0.00 0.00 0.00
#> TCGA.B0.4814.11 1 0.0000 0.9880 1.00 0.00 0 0.00 0.00 0.00 0.00
#> TCGA.CJ.4869.11 1 0.0000 0.9880 1.00 0.00 0 0.00 0.00 0.00 0.00
#> TCGA.CJ.4907.11 1 0.0000 0.9880 1.00 0.00 0 0.00 0.00 0.00 0.00
#> TCGA.B8.5553.01 4 0.0000 0.9623 0.00 0.00 0 1.00 0.00 0.00 0.00
#> TCGA.MW.A4EC.01 4 0.2945 0.6292 0.00 0.00 0 0.74 0.00 0.26 0.00
#> TCGA.B0.5712.11 1 0.0504 0.9790 0.98 0.00 0 0.00 0.00 0.00 0.02
#> TCGA.EU.5905.01 4 0.0000 0.9623 0.00 0.00 0 1.00 0.00 0.00 0.00
#> TCGA.CZ.5985.01 2 0.0000 0.9870 0.00 1.00 0 0.00 0.00 0.00 0.00
#> TCGA.CZ.4856.01 4 0.0000 0.9623 0.00 0.00 0 1.00 0.00 0.00 0.00
#> TCGA.BP.5184.01 4 0.0000 0.9623 0.00 0.00 0 1.00 0.00 0.00 0.00
#> TCGA.B0.5121.01 2 0.0000 0.9870 0.00 1.00 0 0.00 0.00 0.00 0.00
#> TCGA.BP.5191.01 2 0.0000 0.9870 0.00 1.00 0 0.00 0.00 0.00 0.00
#> TCGA.BP.4801.11 1 0.0000 0.9880 1.00 0.00 0 0.00 0.00 0.00 0.00
#> TCGA.BP.5177.01 6 0.0504 0.9344 0.00 0.00 0 0.02 0.00 0.98 0.00
#> TCGA.B0.5110.11 1 0.0504 0.9790 0.98 0.00 0 0.00 0.00 0.00 0.02
#> TCGA.B0.4810.01 2 0.0000 0.9870 0.00 1.00 0 0.00 0.00 0.00 0.00
#> TCGA.CJ.4903.11 1 0.0000 0.9880 1.00 0.00 0 0.00 0.00 0.00 0.00
#> TCGA.CJ.4912.11 5 0.0000 0.9946 0.00 0.00 0 0.00 1.00 0.00 0.00
#> TCGA.B8.4621.01 6 0.0504 0.9344 0.00 0.00 0 0.02 0.00 0.98 0.00
#> TCGA.B4.5832.01 4 0.0000 0.9623 0.00 0.00 0 1.00 0.00 0.00 0.00
#> TCGA.CW.6088.01 6 0.1166 0.8794 0.00 0.00 0 0.06 0.00 0.94 0.00
#> TCGA.AK.3428.01 2 0.0000 0.9870 0.00 1.00 0 0.00 0.00 0.00 0.00
#> TCGA.B8.5164.01 4 0.0000 0.9623 0.00 0.00 0 1.00 0.00 0.00 0.00
#> TCGA.BP.5195.01 4 0.0000 0.9623 0.00 0.00 0 1.00 0.00 0.00 0.00
#> TCGA.CJ.6027.01 2 0.0000 0.9870 0.00 1.00 0 0.00 0.00 0.00 0.00
#> TCGA.3Z.A93Z.01 6 0.0504 0.9344 0.00 0.00 0 0.02 0.00 0.98 0.00
#> TCGA.B0.4714.11 1 0.0000 0.9880 1.00 0.00 0 0.00 0.00 0.00 0.00
#> TCGA.B0.4818.11 1 0.0000 0.9880 1.00 0.00 0 0.00 0.00 0.00 0.00
#> TCGA.CZ.5457.11 5 0.0000 0.9946 0.00 0.00 0 0.00 1.00 0.00 0.00
#> TCGA.BP.5010.01 4 0.0504 0.9523 0.00 0.02 0 0.98 0.00 0.00 0.00
#> TCGA.BP.5189.11 1 0.0000 0.9880 1.00 0.00 0 0.00 0.00 0.00 0.00
#> TCGA.B0.4703.01 4 0.0000 0.9623 0.00 0.00 0 1.00 0.00 0.00 0.00
#> TCGA.B0.4718.11 5 0.0000 0.9946 0.00 0.00 0 0.00 1.00 0.00 0.00
#> TCGA.B0.5097.11 1 0.0000 0.9880 1.00 0.00 0 0.00 0.00 0.00 0.00
#> TCGA.BP.4760.11 1 0.0000 0.9880 1.00 0.00 0 0.00 0.00 0.00 0.00
#> TCGA.B0.5120.11 1 0.0000 0.9880 1.00 0.00 0 0.00 0.00 0.00 0.00
#> TCGA.B0.4843.11 1 0.0000 0.9880 1.00 0.00 0 0.00 0.00 0.00 0.00
#> TCGA.B0.5104.01 4 0.0000 0.9623 0.00 0.00 0 1.00 0.00 0.00 0.00
#> TCGA.CW.5587.01 4 0.0000 0.9623 0.00 0.00 0 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.CZ.4863.01 4 0.1765 0.8252 0.00 0.00 0 0.88 0.00 0.00 0.00 0.12
#> TCGA.CJ.4904.11 1 0.0000 0.9635 1.00 0.00 0 0.00 0.00 0.00 0.00 0.00
#> TCGA.B0.4827.11 5 0.0000 0.9975 0.00 0.00 0 0.00 1.00 0.00 0.00 0.00
#> TCGA.CJ.4902.01 4 0.0000 0.8626 0.00 0.00 0 1.00 0.00 0.00 0.00 0.00
#> TCGA.B0.4823.01 6 0.0808 0.8187 0.00 0.00 0 0.00 0.00 0.96 0.00 0.04
#> TCGA.CW.6087.01 4 0.0000 0.8626 0.00 0.00 0 1.00 0.00 0.00 0.00 0.00
#> TCGA.B0.5098.01 7 0.0000 0.9339 0.00 0.00 0 0.00 0.00 0.00 1.00 0.00
#> TCGA.B0.5113.01 2 0.0471 0.9659 0.00 0.98 0 0.00 0.00 0.00 0.00 0.02
#> TCGA.DV.5566.01 4 0.1765 0.8274 0.00 0.00 0 0.88 0.00 0.00 0.00 0.12
#> TCGA.BP.5175.11 1 0.0000 0.9635 1.00 0.00 0 0.00 0.00 0.00 0.00 0.00
#> TCGA.BP.5181.01 6 0.1341 0.8067 0.00 0.00 0 0.00 0.00 0.92 0.00 0.08
#> TCGA.B0.4706.11 1 0.0000 0.9635 1.00 0.00 0 0.00 0.00 0.00 0.00 0.00
#> TCGA.B0.5117.01 1 0.4004 0.1106 0.50 0.00 0 0.00 0.46 0.00 0.00 0.04
#> TCGA.MM.A564.01 2 0.0000 0.9851 0.00 1.00 0 0.00 0.00 0.00 0.00 0.00
#> TCGA.B0.4821.11 8 0.3095 0.4906 0.02 0.00 0 0.00 0.00 0.00 0.24 0.74
#> TCGA.CZ.5463.11 5 0.0000 0.9975 0.00 0.00 0 0.00 1.00 0.00 0.00 0.00
#> TCGA.BP.5182.11 1 0.0000 0.9635 1.00 0.00 0 0.00 0.00 0.00 0.00 0.00
#> TCGA.DV.5574.01 6 0.0000 0.8265 0.00 0.00 0 0.00 0.00 1.00 0.00 0.00
#> TCGA.B0.5094.11 8 0.2756 0.9385 0.26 0.00 0 0.00 0.00 0.00 0.00 0.74
#> TCGA.MM.A84U.01 4 0.0000 0.8626 0.00 0.00 0 1.00 0.00 0.00 0.00 0.00
#> TCGA.B0.5100.11 8 0.2756 0.9385 0.26 0.00 0 0.00 0.00 0.00 0.00 0.74
#> TCGA.B4.5844.01 4 0.3970 0.6996 0.00 0.10 0 0.68 0.00 0.00 0.00 0.22
#> TCGA.CZ.5459.01 4 0.3015 0.5216 0.00 0.32 0 0.68 0.00 0.00 0.00 0.00
#> TCGA.B0.4694.01 4 0.0471 0.8523 0.00 0.02 0 0.98 0.00 0.00 0.00 0.00
#> TCGA.CZ.5468.11 5 0.0000 0.9975 0.00 0.00 0 0.00 1.00 0.00 0.00 0.00
#> TCGA.CJ.4916.11 8 0.2756 0.9385 0.26 0.00 0 0.00 0.00 0.00 0.00 0.74
#> TCGA.B4.5836.01 4 0.1091 0.8499 0.00 0.00 0 0.94 0.00 0.00 0.00 0.06
#> TCGA.B0.5095.01 4 0.0000 0.8626 0.00 0.00 0 1.00 0.00 0.00 0.00 0.00
#> TCGA.B0.4846.11 1 0.0000 0.9635 1.00 0.00 0 0.00 0.00 0.00 0.00 0.00
#> TCGA.AK.3434.01 2 0.0000 0.9851 0.00 1.00 0 0.00 0.00 0.00 0.00 0.00
#> TCGA.B4.5377.01 6 0.4998 0.4059 0.00 0.00 0 0.24 0.00 0.50 0.00 0.26
#> TCGA.B0.4696.11 1 0.0000 0.9635 1.00 0.00 0 0.00 0.00 0.00 0.00 0.00
#> TCGA.BP.5187.11 1 0.0000 0.9635 1.00 0.00 0 0.00 0.00 0.00 0.00 0.00
#> TCGA.B0.4690.01 4 0.0471 0.8523 0.00 0.02 0 0.98 0.00 0.00 0.00 0.00
#> TCGA.CZ.5466.01 4 0.0471 0.8523 0.00 0.02 0 0.98 0.00 0.00 0.00 0.00
#> TCGA.B0.4844.11 1 0.2650 0.6089 0.76 0.00 0 0.00 0.24 0.00 0.00 0.00
#> TCGA.CZ.5464.11 8 0.2852 0.9129 0.28 0.00 0 0.00 0.00 0.00 0.00 0.72
#> TCGA.B0.4701.11 1 0.0808 0.9099 0.96 0.00 0 0.00 0.04 0.00 0.00 0.00
#> TCGA.BP.5194.11 1 0.0000 0.9635 1.00 0.00 0 0.00 0.00 0.00 0.00 0.00
#> TCGA.B0.4707.01 2 0.0000 0.9851 0.00 1.00 0 0.00 0.00 0.00 0.00 0.00
#> TCGA.CZ.5467.11 5 0.0000 0.9975 0.00 0.00 0 0.00 1.00 0.00 0.00 0.00
#> TCGA.B0.5705.01 6 0.3198 0.6942 0.00 0.00 0 0.02 0.00 0.72 0.00 0.26
#> TCGA.CW.5588.01 4 0.0000 0.8626 0.00 0.00 0 1.00 0.00 0.00 0.00 0.00
#> TCGA.CJ.6031.01 4 0.0000 0.8626 0.00 0.00 0 1.00 0.00 0.00 0.00 0.00
#> TCGA.B8.A54J.01 4 0.3095 0.7526 0.00 0.00 0 0.74 0.00 0.02 0.00 0.24
#> TCGA.BP.5192.11 5 0.0000 0.9975 0.00 0.00 0 0.00 1.00 0.00 0.00 0.00
#> TCGA.CZ.5462.01 4 0.0471 0.8523 0.00 0.02 0 0.98 0.00 0.00 0.00 0.00
#> TCGA.B8.A54H.01 4 0.3095 0.7526 0.00 0.00 0 0.74 0.00 0.02 0.00 0.24
#> TCGA.CZ.5470.11 5 0.0000 0.9975 0.00 0.00 0 0.00 1.00 0.00 0.00 0.00
#> TCGA.BP.4177.11 5 0.0000 0.9975 0.00 0.00 0 0.00 1.00 0.00 0.00 0.00
#> TCGA.CZ.5469.11 5 0.0000 0.9975 0.00 0.00 0 0.00 1.00 0.00 0.00 0.00
#> TCGA.CJ.6028.01 4 0.0471 0.8523 0.00 0.02 0 0.98 0.00 0.00 0.00 0.00
#> TCGA.G6.A8L6.01 4 0.2534 0.7772 0.00 0.00 0 0.78 0.00 0.00 0.00 0.22
#> TCGA.B8.5551.01 4 0.0471 0.8523 0.00 0.02 0 0.98 0.00 0.00 0.00 0.00
#> TCGA.CZ.5456.01 2 0.0000 0.9851 0.00 1.00 0 0.00 0.00 0.00 0.00 0.00
#> TCGA.A3.A8OU.01 4 0.0000 0.8626 0.00 0.00 0 1.00 0.00 0.00 0.00 0.00
#> TCGA.BP.5186.01 6 0.0000 0.8265 0.00 0.00 0 0.00 0.00 1.00 0.00 0.00
#> TCGA.A3.A6NI.01 4 0.0808 0.8554 0.00 0.00 0 0.96 0.00 0.00 0.00 0.04
#> TCGA.BP.4782.01 6 0.3757 0.5104 0.00 0.00 0 0.26 0.00 0.68 0.00 0.06
#> TCGA.CZ.5454.11 5 0.0000 0.9975 0.00 0.00 0 0.00 1.00 0.00 0.00 0.00
#> TCGA.B0.4691.11 1 0.0000 0.9635 1.00 0.00 0 0.00 0.00 0.00 0.00 0.00
#> TCGA.CZ.5452.01 2 0.0808 0.9439 0.00 0.96 0 0.04 0.00 0.00 0.00 0.00
#> TCGA.EU.5904.01 6 0.1091 0.8129 0.00 0.00 0 0.00 0.00 0.94 0.00 0.06
#> TCGA.BP.5201.01 2 0.0000 0.9851 0.00 1.00 0 0.00 0.00 0.00 0.00 0.00
#> TCGA.CJ.5677.01 2 0.0000 0.9851 0.00 1.00 0 0.00 0.00 0.00 0.00 0.00
#> TCGA.BP.5170.11 5 0.0000 0.9975 0.00 0.00 0 0.00 1.00 0.00 0.00 0.00
#> TCGA.B0.4710.11 5 0.0000 0.9975 0.00 0.00 0 0.00 1.00 0.00 0.00 0.00
#> TCGA.AK.3425.01 2 0.0000 0.9851 0.00 1.00 0 0.00 0.00 0.00 0.00 0.00
#> TCGA.B0.4841.11 1 0.0000 0.9635 1.00 0.00 0 0.00 0.00 0.00 0.00 0.00
#> TCGA.B0.4849.01 4 0.0808 0.8554 0.00 0.00 0 0.96 0.00 0.00 0.00 0.04
#> TCGA.BP.5182.01 6 0.2756 0.7093 0.00 0.00 0 0.00 0.00 0.74 0.00 0.26
#> TCGA.B0.5711.11 5 0.0000 0.9975 0.00 0.00 0 0.00 1.00 0.00 0.00 0.00
#> TCGA.BP.5180.01 2 0.0000 0.9851 0.00 1.00 0 0.00 0.00 0.00 0.00 0.00
#> TCGA.BP.5176.01 4 0.3504 0.7226 0.00 0.00 0 0.70 0.00 0.04 0.00 0.26
#> TCGA.CZ.5984.01 2 0.0000 0.9851 0.00 1.00 0 0.00 0.00 0.00 0.00 0.00
#> TCGA.CZ.5460.11 1 0.0000 0.9635 1.00 0.00 0 0.00 0.00 0.00 0.00 0.00
#> TCGA.BP.5190.01 2 0.0000 0.9851 0.00 1.00 0 0.00 0.00 0.00 0.00 0.00
#> TCGA.BP.4795.11 8 0.2852 0.9129 0.28 0.00 0 0.00 0.00 0.00 0.00 0.72
#> TCGA.B0.4813.11 5 0.0000 0.9975 0.00 0.00 0 0.00 1.00 0.00 0.00 0.00
#> TCGA.B0.4713.01 2 0.0000 0.9851 0.00 1.00 0 0.00 0.00 0.00 0.00 0.00
#> TCGA.B0.4841.01 2 0.0808 0.9448 0.00 0.96 0 0.00 0.00 0.00 0.00 0.04
#> TCGA.B8.5546.01 7 0.0000 0.9339 0.00 0.00 0 0.00 0.00 0.00 1.00 0.00
#> TCGA.CW.5591.01 4 0.0000 0.8626 0.00 0.00 0 1.00 0.00 0.00 0.00 0.00
#> TCGA.B0.4698.11 1 0.0000 0.9635 1.00 0.00 0 0.00 0.00 0.00 0.00 0.00
#> TCGA.B0.5713.11 1 0.0000 0.9635 1.00 0.00 0 0.00 0.00 0.00 0.00 0.00
#> TCGA.B0.5108.11 1 0.0000 0.9635 1.00 0.00 0 0.00 0.00 0.00 0.00 0.00
#> TCGA.B0.5083.01 8 0.2756 0.9385 0.26 0.00 0 0.00 0.00 0.00 0.00 0.74
#> TCGA.B0.5699.01 2 0.0000 0.9851 0.00 1.00 0 0.00 0.00 0.00 0.00 0.00
#> TCGA.CZ.5453.11 5 0.0000 0.9975 0.00 0.00 0 0.00 1.00 0.00 0.00 0.00
#> TCGA.BP.5202.01 2 0.0941 0.9451 0.00 0.96 0 0.02 0.00 0.00 0.00 0.02
#> TCGA.BP.5173.11 1 0.3154 0.6486 0.78 0.00 0 0.00 0.16 0.00 0.00 0.06
#> TCGA.CW.5581.01 4 0.2650 0.7649 0.00 0.00 0 0.76 0.00 0.00 0.00 0.24
#> TCGA.B0.4848.11 8 0.2756 0.9385 0.26 0.00 0 0.00 0.00 0.00 0.00 0.74
#> TCGA.B0.4814.01 2 0.0000 0.9851 0.00 1.00 0 0.00 0.00 0.00 0.00 0.00
#> TCGA.BP.5178.11 1 0.0000 0.9635 1.00 0.00 0 0.00 0.00 0.00 0.00 0.00
#> TCGA.CJ.4907.01 4 0.0000 0.8626 0.00 0.00 0 1.00 0.00 0.00 0.00 0.00
#> TCGA.A3.3387.01 4 0.0000 0.8626 0.00 0.00 0 1.00 0.00 0.00 0.00 0.00
#> TCGA.B0.4821.01 2 0.0000 0.9851 0.00 1.00 0 0.00 0.00 0.00 0.00 0.00
#> TCGA.B0.5712.01 2 0.0000 0.9851 0.00 1.00 0 0.00 0.00 0.00 0.00 0.00
#> TCGA.B0.5695.01 6 0.5190 0.2142 0.00 0.00 0 0.32 0.00 0.42 0.00 0.26
#> TCGA.BP.5184.11 1 0.0000 0.9635 1.00 0.00 0 0.00 0.00 0.00 0.00 0.00
#> TCGA.B2.A4SR.01 4 0.3293 0.7538 0.00 0.00 0 0.74 0.00 0.04 0.00 0.22
#> TCGA.BP.5191.11 8 0.3293 0.8888 0.22 0.00 0 0.00 0.00 0.00 0.04 0.74
#> TCGA.CJ.4920.01 2 0.0000 0.9851 0.00 1.00 0 0.00 0.00 0.00 0.00 0.00
#> TCGA.BP.4801.01 4 0.3095 0.7526 0.00 0.00 0 0.74 0.00 0.02 0.00 0.24
#> TCGA.DV.A4W0.01 2 0.0000 0.9851 0.00 1.00 0 0.00 0.00 0.00 0.00 0.00
#> TCGA.BP.5177.11 1 0.0000 0.9635 1.00 0.00 0 0.00 0.00 0.00 0.00 0.00
#> TCGA.B0.4847.11 5 0.0000 0.9975 0.00 0.00 0 0.00 1.00 0.00 0.00 0.00
#> TCGA.B0.5100.01 4 0.0000 0.8626 0.00 0.00 0 1.00 0.00 0.00 0.00 0.00
#> TCGA.CJ.4903.01 2 0.0000 0.9851 0.00 1.00 0 0.00 0.00 0.00 0.00 0.00
#> TCGA.CJ.4912.01 2 0.0000 0.9851 0.00 1.00 0 0.00 0.00 0.00 0.00 0.00
#> TCGA.B0.5107.11 1 0.0000 0.9635 1.00 0.00 0 0.00 0.00 0.00 0.00 0.00
#> TCGA.AK.3453.01 1 0.0000 0.9635 1.00 0.00 0 0.00 0.00 0.00 0.00 0.00
#> TCGA.B0.5691.01 6 0.2938 0.4530 0.00 0.00 0 0.00 0.00 0.70 0.30 0.00
#> TCGA.BP.5195.11 5 0.0000 0.9975 0.00 0.00 0 0.00 1.00 0.00 0.00 0.00
#> TCGA.B0.5400.01 4 0.0000 0.8626 0.00 0.00 0 1.00 0.00 0.00 0.00 0.00
#> TCGA.A3.3376.11 8 0.2756 0.4376 0.00 0.00 0 0.00 0.00 0.00 0.26 0.74
#> TCGA.B0.4845.01 2 0.0000 0.9851 0.00 1.00 0 0.00 0.00 0.00 0.00 0.00
#> TCGA.B0.4699.01 7 0.3237 0.3564 0.00 0.00 0 0.00 0.00 0.00 0.60 0.40
#> TCGA.B0.4818.01 4 0.2650 0.7649 0.00 0.00 0 0.76 0.00 0.00 0.00 0.24
#> TCGA.BP.5174.11 1 0.0000 0.9635 1.00 0.00 0 0.00 0.00 0.00 0.00 0.00
#> TCGA.CJ.4901.11 1 0.0000 0.9635 1.00 0.00 0 0.00 0.00 0.00 0.00 0.00
#> TCGA.B8.A54D.01 2 0.0000 0.9851 0.00 1.00 0 0.00 0.00 0.00 0.00 0.00
#> TCGA.BP.4770.11 8 0.2756 0.9385 0.26 0.00 0 0.00 0.00 0.00 0.00 0.74
#> TCGA.CW.6093.01 6 0.0000 0.8265 0.00 0.00 0 0.00 0.00 1.00 0.00 0.00
#> TCGA.BP.5010.11 5 0.0000 0.9975 0.00 0.00 0 0.00 1.00 0.00 0.00 0.00
#> TCGA.AK.3431.01 4 0.2650 0.7649 0.00 0.00 0 0.76 0.00 0.00 0.00 0.24
#> TCGA.BP.4770.01 4 0.0000 0.8626 0.00 0.00 0 1.00 0.00 0.00 0.00 0.00
#> TCGA.BP.5189.01 4 0.0471 0.8523 0.00 0.02 0 0.98 0.00 0.00 0.00 0.00
#> TCGA.B0.4703.11 1 0.0000 0.9635 1.00 0.00 0 0.00 0.00 0.00 0.00 0.00
#> TCGA.B8.5163.01 4 0.0000 0.8626 0.00 0.00 0 1.00 0.00 0.00 0.00 0.00
#> TCGA.CJ.5683.01 4 0.3880 0.7011 0.00 0.00 0 0.68 0.00 0.08 0.00 0.24
#> TCGA.CZ.4856.11 5 0.0000 0.9975 0.00 0.00 0 0.00 1.00 0.00 0.00 0.00
#> TCGA.BP.4760.01 3 0.0000 1.0000 0.00 0.00 1 0.00 0.00 0.00 0.00 0.00
#> TCGA.B0.5692.01 2 0.0000 0.9851 0.00 1.00 0 0.00 0.00 0.00 0.00 0.00
#> TCGA.B0.5106.01 2 0.0000 0.9851 0.00 1.00 0 0.00 0.00 0.00 0.00 0.00
#> TCGA.B0.4843.01 4 0.0000 0.8626 0.00 0.00 0 1.00 0.00 0.00 0.00 0.00
#> TCGA.CZ.4866.11 5 0.0000 0.9975 0.00 0.00 0 0.00 1.00 0.00 0.00 0.00
#> TCGA.B0.5104.11 1 0.0000 0.9635 1.00 0.00 0 0.00 0.00 0.00 0.00 0.00
#> TCGA.B0.4827.01 2 0.0471 0.9657 0.00 0.98 0 0.02 0.00 0.00 0.00 0.00
#> TCGA.CJ.4902.11 5 0.0000 0.9975 0.00 0.00 0 0.00 1.00 0.00 0.00 0.00
#> TCGA.B8.A54G.01 4 0.0471 0.8523 0.00 0.02 0 0.98 0.00 0.00 0.00 0.00
#> TCGA.B0.5703.01 4 0.3757 0.7078 0.00 0.06 0 0.68 0.00 0.00 0.00 0.26
#> TCGA.CJ.5672.01 4 0.0808 0.8435 0.00 0.04 0 0.96 0.00 0.00 0.00 0.00
#> TCGA.B0.5098.11 8 0.2756 0.9385 0.26 0.00 0 0.00 0.00 0.00 0.00 0.74
#> TCGA.B0.5113.11 1 0.0000 0.9635 1.00 0.00 0 0.00 0.00 0.00 0.00 0.00
#> TCGA.CJ.4882.11 1 0.0000 0.9635 1.00 0.00 0 0.00 0.00 0.00 0.00 0.00
#> TCGA.CZ.5465.11 5 0.0000 0.9975 0.00 0.00 0 0.00 1.00 0.00 0.00 0.00
#> TCGA.B0.5102.01 4 0.4482 0.5968 0.00 0.00 0 0.60 0.00 0.14 0.00 0.26
#> TCGA.CW.5585.01 4 0.4406 0.6650 0.00 0.02 0 0.64 0.00 0.08 0.00 0.26
#> TCGA.B0.4824.01 4 0.4333 0.6282 0.00 0.00 0 0.62 0.00 0.12 0.00 0.26
#> TCGA.B0.5115.01 2 0.1804 0.8619 0.00 0.90 0 0.08 0.00 0.00 0.00 0.02
#> TCGA.B0.4706.01 2 0.0000 0.9851 0.00 1.00 0 0.00 0.00 0.00 0.00 0.00
#> TCGA.B0.5117.11 1 0.0000 0.9635 1.00 0.00 0 0.00 0.00 0.00 0.00 0.00
#> TCGA.CZ.4859.11 5 0.0000 0.9975 0.00 0.00 0 0.00 1.00 0.00 0.00 0.00
#> TCGA.AK.3450.01 4 0.0808 0.8554 0.00 0.00 0 0.96 0.00 0.00 0.00 0.04
#> TCGA.B8.A54I.01 2 0.0000 0.9851 0.00 1.00 0 0.00 0.00 0.00 0.00 0.00
#> TCGA.CZ.5463.01 2 0.0000 0.9851 0.00 1.00 0 0.00 0.00 0.00 0.00 0.00
#> TCGA.DV.5568.01 4 0.0000 0.8626 0.00 0.00 0 1.00 0.00 0.00 0.00 0.00
#> TCGA.CZ.5459.11 8 0.2756 0.9385 0.26 0.00 0 0.00 0.00 0.00 0.00 0.74
#> TCGA.CJ.4918.11 1 0.0000 0.9635 1.00 0.00 0 0.00 0.00 0.00 0.00 0.00
#> TCGA.DV.5565.01 4 0.3975 0.6864 0.00 0.08 0 0.66 0.00 0.00 0.00 0.26
#> TCGA.B0.5119.01 6 0.3198 0.6942 0.00 0.00 0 0.02 0.00 0.72 0.00 0.26
#> TCGA.B0.4811.01 4 0.2267 0.7976 0.00 0.00 0 0.82 0.00 0.00 0.00 0.18
#> TCGA.A3.3367.11 1 0.0000 0.9635 1.00 0.00 0 0.00 0.00 0.00 0.00 0.00
#> TCGA.CJ.4916.01 4 0.0471 0.8523 0.00 0.02 0 0.98 0.00 0.00 0.00 0.00
#> TCGA.B0.5693.01 4 0.4165 0.6557 0.00 0.00 0 0.64 0.00 0.10 0.00 0.26
#> TCGA.CZ.4863.11 5 0.0000 0.9975 0.00 0.00 0 0.00 1.00 0.00 0.00 0.00
#> TCGA.G6.A5PC.01 2 0.0000 0.9851 0.00 1.00 0 0.00 0.00 0.00 0.00 0.00
#> TCGA.B8.5550.01 4 0.0000 0.8626 0.00 0.00 0 1.00 0.00 0.00 0.00 0.00
#> TCGA.DV.A4W0.05 3 0.0000 1.0000 0.00 0.00 1 0.00 0.00 0.00 0.00 0.00
#> TCGA.B0.4696.01 4 0.3299 0.2302 0.00 0.44 0 0.56 0.00 0.00 0.00 0.00
#> TCGA.BP.5187.01 4 0.0000 0.8626 0.00 0.00 0 1.00 0.00 0.00 0.00 0.00
#> TCGA.CZ.5466.11 8 0.2756 0.9385 0.26 0.00 0 0.00 0.00 0.00 0.00 0.74
#> TCGA.CW.6097.01 4 0.0000 0.8626 0.00 0.00 0 1.00 0.00 0.00 0.00 0.00
#> TCGA.CJ.4905.11 5 0.0471 0.9692 0.02 0.00 0 0.00 0.98 0.00 0.00 0.00
#> TCGA.CZ.5989.01 4 0.3291 0.5891 0.00 0.00 0 0.70 0.00 0.28 0.00 0.02
#> TCGA.BP.5194.01 4 0.5063 0.3328 0.00 0.00 0 0.48 0.00 0.26 0.00 0.26
#> TCGA.B0.4707.11 1 0.0000 0.9635 1.00 0.00 0 0.00 0.00 0.00 0.00 0.00
#> TCGA.CZ.5467.01 4 0.3154 0.7793 0.00 0.06 0 0.78 0.00 0.00 0.00 0.16
#> TCGA.BP.5185.11 8 0.2756 0.9385 0.26 0.00 0 0.00 0.00 0.00 0.00 0.74
#> TCGA.BP.5183.11 1 0.0000 0.9635 1.00 0.00 0 0.00 0.00 0.00 0.00 0.00
#> TCGA.BP.5192.01 6 0.3198 0.6942 0.00 0.00 0 0.02 0.00 0.72 0.00 0.26
#> TCGA.CZ.5462.11 5 0.0000 0.9975 0.00 0.00 0 0.00 1.00 0.00 0.00 0.00
#> TCGA.BP.4177.01 3 0.0000 1.0000 0.00 0.00 1 0.00 0.00 0.00 0.00 0.00
#> TCGA.CZ.5469.01 2 0.0000 0.9851 0.00 1.00 0 0.00 0.00 0.00 0.00 0.00
#> TCGA.B2.5641.01 2 0.1091 0.9196 0.00 0.94 0 0.06 0.00 0.00 0.00 0.00
#> TCGA.BP.5196.11 1 0.0000 0.9635 1.00 0.00 0 0.00 0.00 0.00 0.00 0.00
#> TCGA.CZ.5460.01 2 0.0000 0.9851 0.00 1.00 0 0.00 0.00 0.00 0.00 0.00
#> TCGA.B0.4712.01 2 0.0000 0.9851 0.00 1.00 0 0.00 0.00 0.00 0.00 0.00
#> TCGA.B8.A54K.01 3 0.0000 1.0000 0.00 0.00 1 0.00 0.00 0.00 0.00 0.00
#> TCGA.B0.5707.01 6 0.0471 0.8149 0.00 0.00 0 0.00 0.00 0.98 0.02 0.00
#> TCGA.BP.5186.11 1 0.0000 0.9635 1.00 0.00 0 0.00 0.00 0.00 0.00 0.00
#> TCGA.EU.5906.01 6 0.0000 0.8265 0.00 0.00 0 0.00 0.00 1.00 0.00 0.00
#> TCGA.CZ.5461.11 5 0.0000 0.9975 0.00 0.00 0 0.00 1.00 0.00 0.00 0.00
#> TCGA.CW.5590.01 2 0.0000 0.9851 0.00 1.00 0 0.00 0.00 0.00 0.00 0.00
#> TCGA.B0.5698.01 2 0.0000 0.9851 0.00 1.00 0 0.00 0.00 0.00 0.00 0.00
#> TCGA.CW.5580.01 2 0.0000 0.9851 0.00 1.00 0 0.00 0.00 0.00 0.00 0.00
#> TCGA.CZ.5454.01 2 0.0000 0.9851 0.00 1.00 0 0.00 0.00 0.00 0.00 0.00
#> TCGA.B0.4815.01 2 0.0471 0.9657 0.00 0.98 0 0.02 0.00 0.00 0.00 0.00
#> TCGA.B0.5710.11 1 0.0000 0.9635 1.00 0.00 0 0.00 0.00 0.00 0.00 0.00
#> TCGA.CJ.4908.11 5 0.0000 0.9975 0.00 0.00 0 0.00 1.00 0.00 0.00 0.00
#> TCGA.BP.5201.11 1 0.0000 0.9635 1.00 0.00 0 0.00 0.00 0.00 0.00 0.00
#> TCGA.B0.5694.01 2 0.0000 0.9851 0.00 1.00 0 0.00 0.00 0.00 0.00 0.00
#> TCGA.BP.5170.01 4 0.0000 0.8626 0.00 0.00 0 1.00 0.00 0.00 0.00 0.00
#> TCGA.DV.5575.01 6 0.0471 0.8149 0.00 0.00 0 0.00 0.00 0.98 0.02 0.00
#> TCGA.CJ.5686.01 4 0.0000 0.8626 0.00 0.00 0 1.00 0.00 0.00 0.00 0.00
#> TCGA.A3.3357.01 2 0.0000 0.9851 0.00 1.00 0 0.00 0.00 0.00 0.00 0.00
#> TCGA.A3.3373.01 6 0.5158 0.2819 0.00 0.00 0 0.30 0.00 0.44 0.00 0.26
#> TCGA.B0.5690.01 6 0.0000 0.8265 0.00 0.00 0 0.00 0.00 1.00 0.00 0.00
#> TCGA.B8.4622.01 2 0.0000 0.9851 0.00 1.00 0 0.00 0.00 0.00 0.00 0.00
#> TCGA.AK.3433.01 5 0.0000 0.9975 0.00 0.00 0 0.00 1.00 0.00 0.00 0.00
#> TCGA.B0.5110.01 6 0.3198 0.6942 0.00 0.00 0 0.02 0.00 0.72 0.00 0.26
#> TCGA.BP.5180.11 1 0.0000 0.9635 1.00 0.00 0 0.00 0.00 0.00 0.00 0.00
#> TCGA.CJ.4913.01 2 0.0000 0.9851 0.00 1.00 0 0.00 0.00 0.00 0.00 0.00
#> TCGA.CJ.4908.01 4 0.0808 0.8554 0.00 0.00 0 0.96 0.00 0.00 0.00 0.04
#> TCGA.BP.4795.01 3 0.0000 1.0000 0.00 0.00 1 0.00 0.00 0.00 0.00 0.00
#> TCGA.CJ.4897.11 1 0.0000 0.9635 1.00 0.00 0 0.00 0.00 0.00 0.00 0.00
#> TCGA.B2.5636.01 3 0.0000 1.0000 0.00 0.00 1 0.00 0.00 0.00 0.00 0.00
#> TCGA.CJ.4923.11 1 0.0000 0.9635 1.00 0.00 0 0.00 0.00 0.00 0.00 0.00
#> TCGA.B0.4819.01 4 0.0000 0.8626 0.00 0.00 0 1.00 0.00 0.00 0.00 0.00
#> TCGA.B2.5633.01 4 0.0000 0.8626 0.00 0.00 0 1.00 0.00 0.00 0.00 0.00
#> TCGA.CJ.6033.01 2 0.0808 0.9443 0.00 0.96 0 0.04 0.00 0.00 0.00 0.00
#> TCGA.BP.5181.11 8 0.2756 0.9385 0.26 0.00 0 0.00 0.00 0.00 0.00 0.74
#> TCGA.B0.4698.01 2 0.2114 0.7764 0.00 0.84 0 0.16 0.00 0.00 0.00 0.00
#> TCGA.B0.5083.11 1 0.0000 0.9635 1.00 0.00 0 0.00 0.00 0.00 0.00 0.00
#> TCGA.CZ.4864.11 8 0.2852 0.9129 0.28 0.00 0 0.00 0.00 0.00 0.00 0.72
#> TCGA.B0.4688.01 2 0.0000 0.9851 0.00 1.00 0 0.00 0.00 0.00 0.00 0.00
#> TCGA.BP.5168.01 4 0.2267 0.7990 0.00 0.00 0 0.82 0.00 0.00 0.00 0.18
#> TCGA.BP.5198.11 8 0.2756 0.9385 0.26 0.00 0 0.00 0.00 0.00 0.00 0.74
#> TCGA.B8.5162.01 4 0.0000 0.8626 0.00 0.00 0 1.00 0.00 0.00 0.00 0.00
#> TCGA.B0.5096.01 2 0.0000 0.9851 0.00 1.00 0 0.00 0.00 0.00 0.00 0.00
#> TCGA.BP.5178.01 2 0.0000 0.9851 0.00 1.00 0 0.00 0.00 0.00 0.00 0.00
#> TCGA.B0.5099.11 1 0.0000 0.9635 1.00 0.00 0 0.00 0.00 0.00 0.00 0.00
#> TCGA.B0.4842.01 4 0.0471 0.8523 0.00 0.02 0 0.98 0.00 0.00 0.00 0.00
#> TCGA.BP.5169.11 1 0.0000 0.9635 1.00 0.00 0 0.00 0.00 0.00 0.00 0.00
#> TCGA.B0.5109.11 8 0.2756 0.4376 0.00 0.00 0 0.00 0.00 0.00 0.26 0.74
#> TCGA.CJ.4920.11 5 0.1091 0.9074 0.06 0.00 0 0.00 0.94 0.00 0.00 0.00
#> TCGA.B0.5080.11 8 0.2756 0.9385 0.26 0.00 0 0.00 0.00 0.00 0.00 0.74
#> TCGA.B0.5700.01 6 0.0000 0.8265 0.00 0.00 0 0.00 0.00 1.00 0.00 0.00
#> TCGA.B0.4847.01 2 0.0000 0.9851 0.00 1.00 0 0.00 0.00 0.00 0.00 0.00
#> TCGA.B0.5702.01 7 0.0000 0.9339 0.00 0.00 0 0.00 0.00 0.00 1.00 0.00
#> TCGA.CJ.4905.01 4 0.3504 0.7226 0.00 0.00 0 0.70 0.00 0.04 0.00 0.26
#> TCGA.B2.5635.01 4 0.0000 0.8626 0.00 0.00 0 1.00 0.00 0.00 0.00 0.00
#> TCGA.B0.5107.01 2 0.0000 0.9851 0.00 1.00 0 0.00 0.00 0.00 0.00 0.00
#> TCGA.CW.5584.01 2 0.0000 0.9851 0.00 1.00 0 0.00 0.00 0.00 0.00 0.00
#> TCGA.B4.5838.01 4 0.3299 0.3148 0.00 0.44 0 0.56 0.00 0.00 0.00 0.00
#> TCGA.BP.5199.01 2 0.1091 0.9121 0.00 0.94 0 0.06 0.00 0.00 0.00 0.00
#> TCGA.A3.3376.01 6 0.0000 0.8265 0.00 0.00 0 0.00 0.00 1.00 0.00 0.00
#> TCGA.B0.4845.11 5 0.0000 0.9975 0.00 0.00 0 0.00 1.00 0.00 0.00 0.00
#> TCGA.B0.4699.11 1 0.0000 0.9635 1.00 0.00 0 0.00 0.00 0.00 0.00 0.00
#> TCGA.BP.5174.01 6 0.1557 0.8048 0.00 0.00 0 0.02 0.00 0.92 0.00 0.06
#> TCGA.CZ.5986.01 6 0.0471 0.8149 0.00 0.00 0 0.00 0.00 0.98 0.02 0.00
#> TCGA.CJ.4901.01 2 0.0000 0.9851 0.00 1.00 0 0.00 0.00 0.00 0.00 0.00
#> TCGA.AK.3461.01 4 0.3095 0.7526 0.00 0.00 0 0.74 0.00 0.02 0.00 0.24
#> TCGA.AK.3460.01 4 0.4333 0.6278 0.00 0.00 0 0.62 0.00 0.12 0.00 0.26
#> TCGA.AK.3454.01 6 0.0000 0.8265 0.00 0.00 0 0.00 0.00 1.00 0.00 0.00
#> TCGA.CZ.4859.01 6 0.0471 0.8149 0.00 0.00 0 0.00 0.00 0.98 0.02 0.00
#> TCGA.B0.5812.01 4 0.3551 0.7385 0.00 0.00 0 0.72 0.00 0.06 0.00 0.22
#> TCGA.B0.5116.11 7 0.0000 0.9339 0.00 0.00 0 0.00 0.00 0.00 1.00 0.00
#> TCGA.B8.A54F.01 4 0.1275 0.8497 0.00 0.00 0 0.94 0.00 0.02 0.00 0.04
#> TCGA.CW.6090.01 2 0.0000 0.9851 0.00 1.00 0 0.00 0.00 0.00 0.00 0.00
#> TCGA.CZ.5458.11 5 0.0000 0.9975 0.00 0.00 0 0.00 1.00 0.00 0.00 0.00
#> TCGA.B0.5106.11 1 0.0000 0.9635 1.00 0.00 0 0.00 0.00 0.00 0.00 0.00
#> TCGA.CZ.4866.01 2 0.0000 0.9851 0.00 1.00 0 0.00 0.00 0.00 0.00 0.00
#> TCGA.B0.4828.01 2 0.0000 0.9851 0.00 1.00 0 0.00 0.00 0.00 0.00 0.00
#> TCGA.AK.3440.01 5 0.0000 0.9975 0.00 0.00 0 0.00 1.00 0.00 0.00 0.00
#> TCGA.MM.A563.01 2 0.0000 0.9851 0.00 1.00 0 0.00 0.00 0.00 0.00 0.00
#> TCGA.B0.4697.01 4 0.0000 0.8626 0.00 0.00 0 1.00 0.00 0.00 0.00 0.00
#> TCGA.AK.3458.01 2 0.0471 0.9628 0.00 0.98 0 0.02 0.00 0.00 0.00 0.00
#> TCGA.CJ.5676.01 2 0.0000 0.9851 0.00 1.00 0 0.00 0.00 0.00 0.00 0.00
#> TCGA.B0.5402.11 8 0.2756 0.9385 0.26 0.00 0 0.00 0.00 0.00 0.00 0.74
#> TCGA.CJ.5681.01 7 0.0000 0.9339 0.00 0.00 0 0.00 0.00 0.00 1.00 0.00
#> TCGA.A3.3370.11 1 0.2756 0.5777 0.74 0.00 0 0.00 0.26 0.00 0.00 0.00
#> TCGA.A3.A6NL.01 6 0.0000 0.8265 0.00 0.00 0 0.00 0.00 1.00 0.00 0.00
#> TCGA.B0.4693.01 2 0.0000 0.9851 0.00 1.00 0 0.00 0.00 0.00 0.00 0.00
#> TCGA.A3.3358.01 4 0.0000 0.8626 0.00 0.00 0 1.00 0.00 0.00 0.00 0.00
#> TCGA.B0.4710.01 2 0.0000 0.9851 0.00 1.00 0 0.00 0.00 0.00 0.00 0.00
#> TCGA.CZ.4853.11 5 0.0000 0.9975 0.00 0.00 0 0.00 1.00 0.00 0.00 0.00
#> TCGA.B4.5835.01 6 0.3333 -0.1123 0.00 0.00 0 0.00 0.00 0.50 0.50 0.00
#> TCGA.CJ.4882.01 4 0.0000 0.8626 0.00 0.00 0 1.00 0.00 0.00 0.00 0.00
#> TCGA.CZ.5465.01 2 0.0000 0.9851 0.00 1.00 0 0.00 0.00 0.00 0.00 0.00
#> TCGA.B0.5102.11 1 0.0000 0.9635 1.00 0.00 0 0.00 0.00 0.00 0.00 0.00
#> TCGA.B0.4824.11 1 0.0000 0.9635 1.00 0.00 0 0.00 0.00 0.00 0.00 0.00
#> TCGA.CJ.5675.01 2 0.0000 0.9851 0.00 1.00 0 0.00 0.00 0.00 0.00 0.00
#> TCGA.B0.4700.01 4 0.0000 0.8626 0.00 0.00 0 1.00 0.00 0.00 0.00 0.00
#> TCGA.B0.5092.01 4 0.0000 0.8626 0.00 0.00 0 1.00 0.00 0.00 0.00 0.00
#> TCGA.B0.5115.11 1 0.0000 0.9635 1.00 0.00 0 0.00 0.00 0.00 0.00 0.00
#> TCGA.B0.4945.11 1 0.0000 0.9635 1.00 0.00 0 0.00 0.00 0.00 0.00 0.00
#> TCGA.B8.5158.01 4 0.3193 0.3044 0.00 0.38 0 0.62 0.00 0.00 0.00 0.00
#> TCGA.CJ.6030.01 2 0.0808 0.9443 0.00 0.96 0 0.04 0.00 0.00 0.00 0.00
#> TCGA.B8.A54E.01 7 0.0000 0.9339 0.00 0.00 0 0.00 0.00 0.00 1.00 0.00
#> TCGA.CJ.6032.01 4 0.3404 0.7417 0.00 0.04 0 0.72 0.00 0.00 0.00 0.24
#> TCGA.B0.4852.11 1 0.0000 0.9635 1.00 0.00 0 0.00 0.00 0.00 0.00 0.00
#> TCGA.B0.4817.01 4 0.0000 0.8626 0.00 0.00 0 1.00 0.00 0.00 0.00 0.00
#> TCGA.B8.5159.01 2 0.0000 0.9851 0.00 1.00 0 0.00 0.00 0.00 0.00 0.00
#> TCGA.A3.A8OW.01 6 0.1341 0.8067 0.00 0.00 0 0.00 0.00 0.92 0.00 0.08
#> TCGA.B0.4822.01 4 0.0471 0.8523 0.00 0.02 0 0.98 0.00 0.00 0.00 0.00
#> TCGA.B0.5696.01 4 0.0000 0.8626 0.00 0.00 0 1.00 0.00 0.00 0.00 0.00
#> TCGA.B0.5706.01 2 0.0000 0.9851 0.00 1.00 0 0.00 0.00 0.00 0.00 0.00
#> TCGA.CJ.4918.01 4 0.0000 0.8626 0.00 0.00 0 1.00 0.00 0.00 0.00 0.00
#> TCGA.B0.5119.11 5 0.0000 0.9975 0.00 0.00 0 0.00 1.00 0.00 0.00 0.00
#> TCGA.BP.5200.11 1 0.0000 0.9635 1.00 0.00 0 0.00 0.00 0.00 0.00 0.00
#> TCGA.B0.4811.11 8 0.2756 0.9385 0.26 0.00 0 0.00 0.00 0.00 0.00 0.74
#> TCGA.A3.3367.01 2 0.0000 0.9851 0.00 1.00 0 0.00 0.00 0.00 0.00 0.00
#> TCGA.B0.5097.01 4 0.0808 0.8373 0.00 0.04 0 0.96 0.00 0.00 0.00 0.00
#> TCGA.6D.AA2E.01 7 0.0000 0.9339 0.00 0.00 0 0.00 0.00 0.00 1.00 0.00
#> TCGA.DV.A4VX.01 2 0.0000 0.9851 0.00 1.00 0 0.00 0.00 0.00 0.00 0.00
#> TCGA.B0.4816.11 5 0.0000 0.9975 0.00 0.00 0 0.00 1.00 0.00 0.00 0.00
#> TCGA.A3.3385.11 1 0.0000 0.9635 1.00 0.00 0 0.00 0.00 0.00 0.00 0.00
#> TCGA.DV.5569.01 6 0.0000 0.8265 0.00 0.00 0 0.00 0.00 1.00 0.00 0.00
#> TCGA.EU.5907.01 2 0.0000 0.9851 0.00 1.00 0 0.00 0.00 0.00 0.00 0.00
#> TCGA.CZ.5455.01 4 0.1275 0.8530 0.00 0.02 0 0.94 0.00 0.00 0.00 0.04
#> TCGA.B8.5545.01 6 0.0471 0.8149 0.00 0.00 0 0.00 0.00 0.98 0.02 0.00
#> TCGA.DV.5567.01 3 0.0000 1.0000 0.00 0.00 1 0.00 0.00 0.00 0.00 0.00
#> TCGA.CZ.5451.01 4 0.4396 0.6305 0.00 0.14 0 0.62 0.00 0.00 0.00 0.24
#> TCGA.CJ.4869.01 4 0.0471 0.8523 0.00 0.02 0 0.98 0.00 0.00 0.00 0.00
#> TCGA.CJ.5678.01 2 0.0000 0.9851 0.00 1.00 0 0.00 0.00 0.00 0.00 0.00
#> TCGA.B8.4153.01 2 0.0000 0.9851 0.00 1.00 0 0.00 0.00 0.00 0.00 0.00
#> TCGA.B0.5121.11 1 0.0000 0.9635 1.00 0.00 0 0.00 0.00 0.00 0.00 0.00
#> TCGA.B8.4146.01 4 0.4832 0.4816 0.00 0.00 0 0.54 0.00 0.20 0.00 0.26
#> TCGA.BP.5183.01 2 0.0000 0.9851 0.00 1.00 0 0.00 0.00 0.00 0.00 0.00
#> TCGA.B0.5399.01 4 0.1765 0.8273 0.00 0.00 0 0.88 0.00 0.00 0.00 0.12
#> TCGA.B0.4810.11 5 0.0000 0.9975 0.00 0.00 0 0.00 1.00 0.00 0.00 0.00
#> TCGA.AK.3445.01 2 0.0000 0.9851 0.00 1.00 0 0.00 0.00 0.00 0.00 0.00
#> TCGA.B4.5378.01 3 0.0000 1.0000 0.00 0.00 1 0.00 0.00 0.00 0.00 0.00
#> TCGA.BP.5196.01 2 0.0000 0.9851 0.00 1.00 0 0.00 0.00 0.00 0.00 0.00
#> TCGA.CZ.4865.11 5 0.0000 0.9975 0.00 0.00 0 0.00 1.00 0.00 0.00 0.00
#> TCGA.B0.5709.01 6 0.0000 0.8265 0.00 0.00 0 0.00 0.00 1.00 0.00 0.00
#> TCGA.B0.4712.11 5 0.0000 0.9975 0.00 0.00 0 0.00 1.00 0.00 0.00 0.00
#> TCGA.B0.4714.01 2 0.0000 0.9851 0.00 1.00 0 0.00 0.00 0.00 0.00 0.00
#> TCGA.B8.5549.01 2 0.0000 0.9851 0.00 1.00 0 0.00 0.00 0.00 0.00 0.00
#> TCGA.CZ.5461.01 2 0.0000 0.9851 0.00 1.00 0 0.00 0.00 0.00 0.00 0.00
#> TCGA.CZ.5457.01 6 0.2534 0.7307 0.00 0.00 0 0.00 0.00 0.78 0.00 0.22
#> TCGA.A3.A8CQ.01 6 0.0000 0.8265 0.00 0.00 0 0.00 0.00 1.00 0.00 0.00
#> TCGA.DV.5573.01 6 0.4531 0.5339 0.00 0.00 0 0.16 0.00 0.60 0.00 0.24
#> TCGA.B0.4815.11 8 0.2756 0.9385 0.26 0.00 0 0.00 0.00 0.00 0.00 0.74
#> TCGA.B0.5710.01 2 0.0000 0.9851 0.00 1.00 0 0.00 0.00 0.00 0.00 0.00
#> TCGA.B8.5165.01 6 0.0471 0.8149 0.00 0.00 0 0.00 0.00 0.98 0.02 0.00
#> TCGA.B0.4718.01 2 0.0000 0.9851 0.00 1.00 0 0.00 0.00 0.00 0.00 0.00
#> TCGA.B2.5639.01 4 0.2406 0.6961 0.00 0.20 0 0.80 0.00 0.00 0.00 0.00
#> TCGA.CW.5583.01 6 0.0000 0.8265 0.00 0.00 0 0.00 0.00 1.00 0.00 0.00
#> TCGA.GK.A6C7.01 6 0.2406 0.7408 0.00 0.00 0 0.00 0.00 0.80 0.00 0.20
#> TCGA.A3.3357.11 1 0.0000 0.9635 1.00 0.00 0 0.00 0.00 0.00 0.00 0.00
#> TCGA.B8.5552.01 6 0.0471 0.8149 0.00 0.00 0 0.00 0.00 0.98 0.02 0.00
#> TCGA.B0.5120.01 4 0.0000 0.8626 0.00 0.00 0 1.00 0.00 0.00 0.00 0.00
#> TCGA.A3.3373.11 5 0.0000 0.9975 0.00 0.00 0 0.00 1.00 0.00 0.00 0.00
#> TCGA.BP.5185.01 4 0.4593 0.6382 0.00 0.02 0 0.62 0.00 0.10 0.00 0.26
#> TCGA.B0.4846.01 4 0.0808 0.8554 0.00 0.00 0 0.96 0.00 0.00 0.00 0.04
#> TCGA.CJ.4904.01 6 0.0000 0.8265 0.00 0.00 0 0.00 0.00 1.00 0.00 0.00
#> TCGA.CJ.4913.11 1 0.0000 0.9635 1.00 0.00 0 0.00 0.00 0.00 0.00 0.00
#> TCGA.BP.4993.11 1 0.0000 0.9635 1.00 0.00 0 0.00 0.00 0.00 0.00 0.00
#> TCGA.B0.4823.11 1 0.3154 0.6486 0.78 0.00 0 0.00 0.16 0.00 0.00 0.06
#> TCGA.CJ.4897.01 4 0.3198 0.7384 0.00 0.00 0 0.72 0.00 0.02 0.00 0.26
#> TCGA.BP.4993.01 6 0.1563 0.7991 0.00 0.00 0 0.00 0.00 0.90 0.00 0.10
#> TCGA.B4.5843.01 6 0.0000 0.8265 0.00 0.00 0 0.00 0.00 1.00 0.00 0.00
#> TCGA.DV.5576.01 3 0.0000 1.0000 0.00 0.00 1 0.00 0.00 0.00 0.00 0.00
#> TCGA.CJ.4923.01 4 0.0000 0.8626 0.00 0.00 0 1.00 0.00 0.00 0.00 0.00
#> TCGA.B0.4819.11 1 0.0000 0.9635 1.00 0.00 0 0.00 0.00 0.00 0.00 0.00
#> TCGA.BP.5175.01 2 0.0000 0.9851 0.00 1.00 0 0.00 0.00 0.00 0.00 0.00
#> TCGA.CZ.5987.01 2 0.0000 0.9851 0.00 1.00 0 0.00 0.00 0.00 0.00 0.00
#> TCGA.CZ.4864.01 6 0.5063 0.3797 0.00 0.00 0 0.26 0.00 0.48 0.00 0.26
#> TCGA.B0.4688.11 5 0.0000 0.9975 0.00 0.00 0 0.00 1.00 0.00 0.00 0.00
#> TCGA.BP.5168.11 8 0.2756 0.9385 0.26 0.00 0 0.00 0.00 0.00 0.00 0.74
#> TCGA.BP.5198.01 2 0.0000 0.9851 0.00 1.00 0 0.00 0.00 0.00 0.00 0.00
#> TCGA.B8.A7U6.01 4 0.4333 0.6279 0.00 0.00 0 0.62 0.00 0.12 0.00 0.26
#> TCGA.B0.5094.01 2 0.0000 0.9851 0.00 1.00 0 0.00 0.00 0.00 0.00 0.00
#> TCGA.T7.A92I.01 7 0.0000 0.9339 0.00 0.00 0 0.00 0.00 0.00 1.00 0.00
#> TCGA.B0.5096.11 1 0.0000 0.9635 1.00 0.00 0 0.00 0.00 0.00 0.00 0.00
#> TCGA.B0.5400.11 8 0.2756 0.9385 0.26 0.00 0 0.00 0.00 0.00 0.00 0.74
#> TCGA.B0.4694.11 1 0.2650 0.6089 0.76 0.00 0 0.00 0.24 0.00 0.00 0.00
#> TCGA.B0.5099.01 4 0.3504 0.7232 0.00 0.00 0 0.70 0.00 0.04 0.00 0.26
#> TCGA.CZ.5468.01 2 0.0000 0.9851 0.00 1.00 0 0.00 0.00 0.00 0.00 0.00
#> TCGA.B0.4842.11 1 0.0000 0.9635 1.00 0.00 0 0.00 0.00 0.00 0.00 0.00
#> TCGA.CZ.5988.01 4 0.0000 0.8626 0.00 0.00 0 1.00 0.00 0.00 0.00 0.00
#> TCGA.BP.5169.01 2 0.0000 0.9851 0.00 1.00 0 0.00 0.00 0.00 0.00 0.00
#> TCGA.B0.5109.01 4 0.0000 0.8626 0.00 0.00 0 1.00 0.00 0.00 0.00 0.00
#> TCGA.B4.5834.01 6 0.0000 0.8265 0.00 0.00 0 0.00 0.00 1.00 0.00 0.00
#> TCGA.B0.5095.11 8 0.2756 0.9385 0.26 0.00 0 0.00 0.00 0.00 0.00 0.74
#> TCGA.B0.5080.01 4 0.0000 0.8626 0.00 0.00 0 1.00 0.00 0.00 0.00 0.00
#> TCGA.CJ.5680.01 2 0.0000 0.9851 0.00 1.00 0 0.00 0.00 0.00 0.00 0.00
#> TCGA.CZ.5470.01 2 0.0000 0.9851 0.00 1.00 0 0.00 0.00 0.00 0.00 0.00
#> TCGA.CZ.4865.01 4 0.0000 0.8626 0.00 0.00 0 1.00 0.00 0.00 0.00 0.00
#> TCGA.A3.A8OX.01 7 0.0000 0.9339 0.00 0.00 0 0.00 0.00 0.00 1.00 0.00
#> TCGA.B0.4690.11 8 0.2756 0.9385 0.26 0.00 0 0.00 0.00 0.00 0.00 0.74
#> TCGA.CJ.5684.01 4 0.0471 0.8596 0.00 0.00 0 0.98 0.00 0.00 0.00 0.02
#> TCGA.B0.4844.01 2 0.0000 0.9851 0.00 1.00 0 0.00 0.00 0.00 0.00 0.00
#> TCGA.CZ.5464.01 2 0.0000 0.9851 0.00 1.00 0 0.00 0.00 0.00 0.00 0.00
#> TCGA.B0.4701.01 4 0.0471 0.8523 0.00 0.02 0 0.98 0.00 0.00 0.00 0.00
#> TCGA.B0.5701.01 2 0.0000 0.9851 0.00 1.00 0 0.00 0.00 0.00 0.00 0.00
#> TCGA.BP.5199.11 1 0.0000 0.9635 1.00 0.00 0 0.00 0.00 0.00 0.00 0.00
#> TCGA.CJ.5671.01 2 0.3193 0.3715 0.00 0.62 0 0.38 0.00 0.00 0.00 0.00
#> TCGA.A3.A8OV.01 6 0.2756 0.7093 0.00 0.00 0 0.00 0.00 0.74 0.00 0.26
#> TCGA.CZ.5456.11 5 0.0000 0.9975 0.00 0.00 0 0.00 1.00 0.00 0.00 0.00
#> TCGA.B0.5116.01 2 0.0000 0.9851 0.00 1.00 0 0.00 0.00 0.00 0.00 0.00
#> TCGA.CZ.5458.01 4 0.0000 0.8626 0.00 0.00 0 1.00 0.00 0.00 0.00 0.00
#> TCGA.CZ.5982.01 4 0.4723 0.3901 0.00 0.34 0 0.52 0.00 0.00 0.00 0.14
#> TCGA.B0.4828.11 5 0.0000 0.9975 0.00 0.00 0 0.00 1.00 0.00 0.00 0.00
#> TCGA.CJ.5679.01 2 0.0000 0.9851 0.00 1.00 0 0.00 0.00 0.00 0.00 0.00
#> TCGA.CJ.5682.01 2 0.0000 0.9851 0.00 1.00 0 0.00 0.00 0.00 0.00 0.00
#> TCGA.B0.5697.01 4 0.0000 0.8626 0.00 0.00 0 1.00 0.00 0.00 0.00 0.00
#> TCGA.B0.4697.11 5 0.0000 0.9975 0.00 0.00 0 0.00 1.00 0.00 0.00 0.00
#> TCGA.BP.4782.11 8 0.2756 0.9385 0.26 0.00 0 0.00 0.00 0.00 0.00 0.74
#> TCGA.G6.A8L8.01 2 0.2534 0.6947 0.00 0.78 0 0.00 0.00 0.00 0.00 0.22
#> TCGA.A3.A6NJ.01 6 0.2404 0.7710 0.00 0.00 0 0.02 0.00 0.84 0.00 0.14
#> TCGA.A3.3370.01 6 0.0471 0.8149 0.00 0.00 0 0.00 0.00 0.98 0.02 0.00
#> TCGA.B0.4691.01 2 0.0000 0.9851 0.00 1.00 0 0.00 0.00 0.00 0.00 0.00
#> TCGA.CZ.5452.11 5 0.0000 0.9975 0.00 0.00 0 0.00 1.00 0.00 0.00 0.00
#> TCGA.B0.4693.11 1 0.0000 0.9635 1.00 0.00 0 0.00 0.00 0.00 0.00 0.00
#> TCGA.B0.4945.01 6 0.0000 0.8265 0.00 0.00 0 0.00 0.00 1.00 0.00 0.00
#> TCGA.CZ.4853.01 2 0.0000 0.9851 0.00 1.00 0 0.00 0.00 0.00 0.00 0.00
#> TCGA.B0.5092.11 1 0.0000 0.9635 1.00 0.00 0 0.00 0.00 0.00 0.00 0.00
#> TCGA.B0.5402.01 2 0.0000 0.9851 0.00 1.00 0 0.00 0.00 0.00 0.00 0.00
#> TCGA.B0.4849.11 1 0.0000 0.9635 1.00 0.00 0 0.00 0.00 0.00 0.00 0.00
#> TCGA.A3.A6NN.01 4 0.3808 0.4811 0.00 0.34 0 0.62 0.00 0.00 0.00 0.04
#> TCGA.B0.4852.01 4 0.3198 0.7384 0.00 0.00 0 0.72 0.00 0.02 0.00 0.26
#> TCGA.B0.4817.11 1 0.2852 0.4230 0.72 0.00 0 0.00 0.00 0.00 0.00 0.28
#> TCGA.BP.5176.11 8 0.2756 0.9385 0.26 0.00 0 0.00 0.00 0.00 0.00 0.74
#> TCGA.CW.5589.01 6 0.0000 0.8265 0.00 0.00 0 0.00 0.00 1.00 0.00 0.00
#> TCGA.CJ.5689.01 4 0.0000 0.8626 0.00 0.00 0 1.00 0.00 0.00 0.00 0.00
#> TCGA.B0.4822.11 5 0.0000 0.9975 0.00 0.00 0 0.00 1.00 0.00 0.00 0.00
#> TCGA.BP.5190.11 1 0.0000 0.9635 1.00 0.00 0 0.00 0.00 0.00 0.00 0.00
#> TCGA.B0.4813.01 2 0.0000 0.9851 0.00 1.00 0 0.00 0.00 0.00 0.00 0.00
#> TCGA.BP.5200.01 4 0.3975 0.6814 0.00 0.00 0 0.66 0.00 0.08 0.00 0.26
#> TCGA.G6.A8L7.01 2 0.0808 0.9380 0.00 0.96 0 0.04 0.00 0.00 0.00 0.00
#> TCGA.B2.4101.01 4 0.0471 0.8523 0.00 0.02 0 0.98 0.00 0.00 0.00 0.00
#> TCGA.B0.4713.11 8 0.2756 0.9385 0.26 0.00 0 0.00 0.00 0.00 0.00 0.74
#> TCGA.B0.4816.01 4 0.0000 0.8626 0.00 0.00 0 1.00 0.00 0.00 0.00 0.00
#> TCGA.A3.3385.01 6 0.2756 0.7093 0.00 0.00 0 0.00 0.00 0.74 0.00 0.26
#> TCGA.B2.3924.01 4 0.4333 0.6278 0.00 0.00 0 0.62 0.00 0.12 0.00 0.26
#> TCGA.CZ.5455.11 5 0.0000 0.9975 0.00 0.00 0 0.00 1.00 0.00 0.00 0.00
#> TCGA.B0.5713.01 4 0.2756 0.7528 0.00 0.00 0 0.74 0.00 0.00 0.00 0.26
#> TCGA.B0.5108.01 4 0.0000 0.8626 0.00 0.00 0 1.00 0.00 0.00 0.00 0.00
#> TCGA.B0.5711.01 4 0.1563 0.8352 0.00 0.00 0 0.90 0.00 0.00 0.00 0.10
#> TCGA.CZ.5453.01 6 0.2756 0.7093 0.00 0.00 0 0.00 0.00 0.74 0.00 0.26
#> TCGA.BP.5202.11 8 0.2756 0.4376 0.00 0.00 0 0.00 0.00 0.00 0.26 0.74
#> TCGA.BP.5173.01 6 0.3504 0.6732 0.00 0.00 0 0.04 0.00 0.70 0.00 0.26
#> TCGA.CZ.5451.11 1 0.0000 0.9635 1.00 0.00 0 0.00 0.00 0.00 0.00 0.00
#> TCGA.B8.A8YJ.01 6 0.0471 0.8149 0.00 0.00 0 0.00 0.00 0.98 0.02 0.00
#> TCGA.B0.4848.01 2 0.0000 0.9851 0.00 1.00 0 0.00 0.00 0.00 0.00 0.00
#> TCGA.DV.A4VZ.01 3 0.0000 1.0000 0.00 0.00 1 0.00 0.00 0.00 0.00 0.00
#> TCGA.B0.4814.11 1 0.0000 0.9635 1.00 0.00 0 0.00 0.00 0.00 0.00 0.00
#> TCGA.CJ.4869.11 1 0.0000 0.9635 1.00 0.00 0 0.00 0.00 0.00 0.00 0.00
#> TCGA.CJ.4907.11 1 0.0000 0.9635 1.00 0.00 0 0.00 0.00 0.00 0.00 0.00
#> TCGA.B8.5553.01 4 0.0471 0.8596 0.00 0.00 0 0.98 0.00 0.00 0.00 0.02
#> TCGA.MW.A4EC.01 4 0.5211 0.0706 0.00 0.00 0 0.40 0.00 0.34 0.00 0.26
#> TCGA.B0.5712.11 8 0.3293 0.8888 0.22 0.00 0 0.00 0.00 0.00 0.04 0.74
#> TCGA.EU.5905.01 4 0.0000 0.8626 0.00 0.00 0 1.00 0.00 0.00 0.00 0.00
#> TCGA.CZ.5985.01 2 0.0000 0.9851 0.00 1.00 0 0.00 0.00 0.00 0.00 0.00
#> TCGA.CZ.4856.01 4 0.0471 0.8596 0.00 0.00 0 0.98 0.00 0.00 0.00 0.02
#> TCGA.BP.5184.01 4 0.3504 0.7226 0.00 0.00 0 0.70 0.00 0.04 0.00 0.26
#> TCGA.B0.5121.01 2 0.0000 0.9851 0.00 1.00 0 0.00 0.00 0.00 0.00 0.00
#> TCGA.BP.5191.01 2 0.0000 0.9851 0.00 1.00 0 0.00 0.00 0.00 0.00 0.00
#> TCGA.BP.4801.11 1 0.0000 0.9635 1.00 0.00 0 0.00 0.00 0.00 0.00 0.00
#> TCGA.BP.5177.01 6 0.0000 0.8265 0.00 0.00 0 0.00 0.00 1.00 0.00 0.00
#> TCGA.B0.5110.11 8 0.2756 0.9385 0.26 0.00 0 0.00 0.00 0.00 0.00 0.74
#> TCGA.B0.4810.01 2 0.0000 0.9851 0.00 1.00 0 0.00 0.00 0.00 0.00 0.00
#> TCGA.CJ.4903.11 1 0.0000 0.9635 1.00 0.00 0 0.00 0.00 0.00 0.00 0.00
#> TCGA.CJ.4912.11 5 0.0000 0.9975 0.00 0.00 0 0.00 1.00 0.00 0.00 0.00
#> TCGA.B8.4621.01 6 0.0000 0.8265 0.00 0.00 0 0.00 0.00 1.00 0.00 0.00
#> TCGA.B4.5832.01 4 0.0000 0.8626 0.00 0.00 0 1.00 0.00 0.00 0.00 0.00
#> TCGA.CW.6088.01 6 0.2856 0.7361 0.00 0.00 0 0.02 0.00 0.78 0.00 0.20
#> TCGA.AK.3428.01 2 0.0000 0.9851 0.00 1.00 0 0.00 0.00 0.00 0.00 0.00
#> TCGA.B8.5164.01 4 0.0000 0.8626 0.00 0.00 0 1.00 0.00 0.00 0.00 0.00
#> TCGA.BP.5195.01 4 0.0000 0.8626 0.00 0.00 0 1.00 0.00 0.00 0.00 0.00
#> TCGA.CJ.6027.01 2 0.0000 0.9851 0.00 1.00 0 0.00 0.00 0.00 0.00 0.00
#> TCGA.3Z.A93Z.01 6 0.0000 0.8265 0.00 0.00 0 0.00 0.00 1.00 0.00 0.00
#> TCGA.B0.4714.11 1 0.1341 0.8590 0.92 0.00 0 0.00 0.00 0.00 0.00 0.08
#> TCGA.B0.4818.11 1 0.0000 0.9635 1.00 0.00 0 0.00 0.00 0.00 0.00 0.00
#> TCGA.CZ.5457.11 5 0.0000 0.9975 0.00 0.00 0 0.00 1.00 0.00 0.00 0.00
#> TCGA.BP.5010.01 4 0.0000 0.8626 0.00 0.00 0 1.00 0.00 0.00 0.00 0.00
#> TCGA.BP.5189.11 1 0.0000 0.9635 1.00 0.00 0 0.00 0.00 0.00 0.00 0.00
#> TCGA.B0.4703.01 4 0.0000 0.8626 0.00 0.00 0 1.00 0.00 0.00 0.00 0.00
#> TCGA.B0.4718.11 5 0.0000 0.9975 0.00 0.00 0 0.00 1.00 0.00 0.00 0.00
#> TCGA.B0.5097.11 1 0.0000 0.9635 1.00 0.00 0 0.00 0.00 0.00 0.00 0.00
#> TCGA.BP.4760.11 1 0.0000 0.9635 1.00 0.00 0 0.00 0.00 0.00 0.00 0.00
#> TCGA.B0.5120.11 1 0.0000 0.9635 1.00 0.00 0 0.00 0.00 0.00 0.00 0.00
#> TCGA.B0.4843.11 1 0.0000 0.9635 1.00 0.00 0 0.00 0.00 0.00 0.00 0.00
#> TCGA.B0.5104.01 4 0.0808 0.8554 0.00 0.00 0 0.96 0.00 0.00 0.00 0.04
#> TCGA.CW.5587.01 4 0.0471 0.8596 0.00 0.00 0 0.98 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-leaf , Node012-leaf , Node013-leaf , Node014 , Node021 , Node022-leaf , Node023 , Node041 , Node042-leaf , Node043 , Node051 , Node052-leaf , Node053-leaf , Node054 , Node061-leaf , Node062 , Node063-leaf , Node071-leaf , Node072-leaf , Node073-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 108 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 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 0.988 0.996 0.4578 0.545 0.545
#> 3 3 1.000 0.983 0.994 0.2402 0.886 0.792
#> 4 4 1.000 0.991 0.997 0.2508 0.830 0.620
#> 5 5 1.000 0.984 0.994 0.0622 0.955 0.845
#> 6 6 0.860 0.807 0.896 0.0365 0.998 0.992
#> 7 7 0.816 0.745 0.850 0.0309 0.948 0.788
#> 8 8 0.792 0.692 0.787 0.0283 0.957 0.790
suggest_best_k() suggests the best \(k\) based on these statistics. The rules are as follows:
suggest_best_k(res)
#> [1] 5
#> attr(,"optional")
#> [1] 2 3 4
There is also optional best \(k\) = 2 3 4 that is worth to check.
Following 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.CJ.4904.11 1 0.000 1.000 1.00 0.00
#> TCGA.BP.5175.11 2 0.000 0.993 0.00 1.00
#> TCGA.B0.4706.11 2 0.000 0.993 0.00 1.00
#> TCGA.B0.5117.01 2 0.000 0.993 0.00 1.00
#> TCGA.BP.5182.11 2 0.000 0.993 0.00 1.00
#> TCGA.B0.5094.11 2 0.000 0.993 0.00 1.00
#> TCGA.B0.5100.11 2 0.000 0.993 0.00 1.00
#> TCGA.CJ.4916.11 1 0.000 1.000 1.00 0.00
#> TCGA.B0.4846.11 1 0.000 1.000 1.00 0.00
#> TCGA.B0.4696.11 2 0.000 0.993 0.00 1.00
#> TCGA.BP.5187.11 2 0.000 0.993 0.00 1.00
#> TCGA.CZ.5464.11 2 0.000 0.993 0.00 1.00
#> TCGA.B0.4701.11 1 0.000 1.000 1.00 0.00
#> TCGA.BP.5194.11 2 0.000 0.993 0.00 1.00
#> TCGA.B0.4691.11 2 0.000 0.993 0.00 1.00
#> TCGA.B0.4841.11 2 0.000 0.993 0.00 1.00
#> TCGA.CZ.5460.11 2 0.000 0.993 0.00 1.00
#> TCGA.BP.4795.11 1 0.000 1.000 1.00 0.00
#> TCGA.B0.4698.11 2 0.000 0.993 0.00 1.00
#> TCGA.B0.5713.11 1 0.000 1.000 1.00 0.00
#> TCGA.B0.5108.11 2 0.000 0.993 0.00 1.00
#> TCGA.B0.5083.01 2 0.000 0.993 0.00 1.00
#> TCGA.BP.5173.11 2 0.000 0.993 0.00 1.00
#> TCGA.B0.4848.11 2 0.000 0.993 0.00 1.00
#> TCGA.BP.5178.11 2 0.000 0.993 0.00 1.00
#> TCGA.BP.5184.11 2 0.000 0.993 0.00 1.00
#> TCGA.BP.5191.11 2 0.000 0.993 0.00 1.00
#> TCGA.BP.5177.11 1 0.000 1.000 1.00 0.00
#> TCGA.B0.5107.11 1 0.000 1.000 1.00 0.00
#> TCGA.AK.3453.01 2 0.995 0.148 0.46 0.54
#> TCGA.BP.5174.11 1 0.000 1.000 1.00 0.00
#> TCGA.CJ.4901.11 2 0.000 0.993 0.00 1.00
#> TCGA.BP.4770.11 1 0.000 1.000 1.00 0.00
#> TCGA.B0.4703.11 2 0.000 0.993 0.00 1.00
#> TCGA.B0.5104.11 1 0.000 1.000 1.00 0.00
#> TCGA.B0.5098.11 1 0.000 1.000 1.00 0.00
#> TCGA.B0.5113.11 1 0.000 1.000 1.00 0.00
#> TCGA.CJ.4882.11 2 0.000 0.993 0.00 1.00
#> TCGA.B0.5117.11 2 0.000 0.993 0.00 1.00
#> TCGA.CZ.5459.11 2 0.000 0.993 0.00 1.00
#> TCGA.CJ.4918.11 2 0.000 0.993 0.00 1.00
#> TCGA.A3.3367.11 2 0.000 0.993 0.00 1.00
#> TCGA.CZ.5466.11 2 0.000 0.993 0.00 1.00
#> TCGA.B0.4707.11 2 0.000 0.993 0.00 1.00
#> TCGA.BP.5185.11 2 0.000 0.993 0.00 1.00
#> TCGA.BP.5183.11 2 0.000 0.993 0.00 1.00
#> TCGA.BP.5196.11 2 0.000 0.993 0.00 1.00
#> TCGA.BP.5186.11 1 0.000 1.000 1.00 0.00
#> TCGA.B0.5710.11 2 0.000 0.993 0.00 1.00
#> TCGA.BP.5201.11 2 0.000 0.993 0.00 1.00
#> TCGA.BP.5180.11 2 0.000 0.993 0.00 1.00
#> TCGA.CJ.4897.11 1 0.000 1.000 1.00 0.00
#> TCGA.CJ.4923.11 2 0.000 0.993 0.00 1.00
#> TCGA.BP.5181.11 1 0.000 1.000 1.00 0.00
#> TCGA.B0.5083.11 2 0.000 0.993 0.00 1.00
#> TCGA.CZ.4864.11 2 0.000 0.993 0.00 1.00
#> TCGA.BP.5198.11 2 0.000 0.993 0.00 1.00
#> TCGA.B0.5099.11 1 0.000 1.000 1.00 0.00
#> TCGA.BP.5169.11 2 0.000 0.993 0.00 1.00
#> TCGA.B0.5080.11 2 0.000 0.993 0.00 1.00
#> TCGA.B0.4699.11 2 0.000 0.993 0.00 1.00
#> TCGA.B0.5106.11 2 0.000 0.993 0.00 1.00
#> TCGA.B0.5402.11 2 0.000 0.993 0.00 1.00
#> TCGA.B0.5102.11 1 0.000 1.000 1.00 0.00
#> TCGA.B0.4824.11 1 0.000 1.000 1.00 0.00
#> TCGA.B0.5115.11 2 0.000 0.993 0.00 1.00
#> TCGA.B0.4945.11 1 0.000 1.000 1.00 0.00
#> TCGA.B0.4852.11 1 0.000 1.000 1.00 0.00
#> TCGA.BP.5200.11 2 0.000 0.993 0.00 1.00
#> TCGA.B0.4811.11 2 0.000 0.993 0.00 1.00
#> TCGA.A3.3385.11 1 0.000 1.000 1.00 0.00
#> TCGA.B0.5121.11 2 0.000 0.993 0.00 1.00
#> TCGA.B0.4815.11 2 0.000 0.993 0.00 1.00
#> TCGA.A3.3357.11 2 0.000 0.993 0.00 1.00
#> TCGA.CJ.4913.11 1 0.000 1.000 1.00 0.00
#> TCGA.BP.4993.11 2 0.000 0.993 0.00 1.00
#> TCGA.B0.4823.11 2 0.000 0.993 0.00 1.00
#> TCGA.B0.4819.11 1 0.000 1.000 1.00 0.00
#> TCGA.BP.5168.11 2 0.000 0.993 0.00 1.00
#> TCGA.B0.5096.11 1 0.000 1.000 1.00 0.00
#> TCGA.B0.5400.11 1 0.000 1.000 1.00 0.00
#> TCGA.B0.4842.11 1 0.000 1.000 1.00 0.00
#> TCGA.B0.5095.11 2 0.000 0.993 0.00 1.00
#> TCGA.B0.4690.11 2 0.000 0.993 0.00 1.00
#> TCGA.BP.5199.11 2 0.000 0.993 0.00 1.00
#> TCGA.BP.4782.11 1 0.000 1.000 1.00 0.00
#> TCGA.B0.4693.11 1 0.000 1.000 1.00 0.00
#> TCGA.B0.5092.11 1 0.000 1.000 1.00 0.00
#> TCGA.B0.4849.11 2 0.000 0.993 0.00 1.00
#> TCGA.B0.4817.11 2 0.000 0.993 0.00 1.00
#> TCGA.BP.5176.11 1 0.000 1.000 1.00 0.00
#> TCGA.BP.5190.11 2 0.000 0.993 0.00 1.00
#> TCGA.B0.4713.11 1 0.000 1.000 1.00 0.00
#> TCGA.CZ.5451.11 2 0.000 0.993 0.00 1.00
#> TCGA.B0.4814.11 2 0.000 0.993 0.00 1.00
#> TCGA.CJ.4869.11 2 0.000 0.993 0.00 1.00
#> TCGA.CJ.4907.11 2 0.000 0.993 0.00 1.00
#> TCGA.B0.5712.11 1 0.000 1.000 1.00 0.00
#> TCGA.BP.4801.11 2 0.000 0.993 0.00 1.00
#> TCGA.B0.5110.11 1 0.000 1.000 1.00 0.00
#> TCGA.CJ.4903.11 2 0.000 0.993 0.00 1.00
#> TCGA.B0.4714.11 2 0.000 0.993 0.00 1.00
#> TCGA.B0.4818.11 1 0.000 1.000 1.00 0.00
#> TCGA.BP.5189.11 2 0.000 0.993 0.00 1.00
#> TCGA.B0.5097.11 1 0.000 1.000 1.00 0.00
#> TCGA.BP.4760.11 2 0.000 0.993 0.00 1.00
#> TCGA.B0.5120.11 1 0.000 1.000 1.00 0.00
#> TCGA.B0.4843.11 2 0.000 0.993 0.00 1.00
cbind(get_classes(res, k = 3), get_membership(res, k = 3))
#> class entropy silhouette p1 p2 p3
#> TCGA.CJ.4904.11 1 0.000 1.0000 1 0.00 0.00
#> TCGA.BP.5175.11 2 0.000 0.9918 0 1.00 0.00
#> TCGA.B0.4706.11 2 0.000 0.9918 0 1.00 0.00
#> TCGA.B0.5117.01 3 0.000 0.9802 0 0.00 1.00
#> TCGA.BP.5182.11 2 0.000 0.9918 0 1.00 0.00
#> TCGA.B0.5094.11 2 0.000 0.9918 0 1.00 0.00
#> TCGA.B0.5100.11 3 0.254 0.9102 0 0.08 0.92
#> TCGA.CJ.4916.11 1 0.000 1.0000 1 0.00 0.00
#> TCGA.B0.4846.11 1 0.000 1.0000 1 0.00 0.00
#> TCGA.B0.4696.11 2 0.000 0.9918 0 1.00 0.00
#> TCGA.BP.5187.11 2 0.000 0.9918 0 1.00 0.00
#> TCGA.CZ.5464.11 2 0.000 0.9918 0 1.00 0.00
#> TCGA.B0.4701.11 1 0.000 1.0000 1 0.00 0.00
#> TCGA.BP.5194.11 2 0.000 0.9918 0 1.00 0.00
#> TCGA.B0.4691.11 2 0.000 0.9918 0 1.00 0.00
#> TCGA.B0.4841.11 2 0.000 0.9918 0 1.00 0.00
#> TCGA.CZ.5460.11 2 0.000 0.9918 0 1.00 0.00
#> TCGA.BP.4795.11 1 0.000 1.0000 1 0.00 0.00
#> TCGA.B0.4698.11 2 0.000 0.9918 0 1.00 0.00
#> TCGA.B0.5713.11 1 0.000 1.0000 1 0.00 0.00
#> TCGA.B0.5108.11 2 0.000 0.9918 0 1.00 0.00
#> TCGA.B0.5083.01 3 0.000 0.9802 0 0.00 1.00
#> TCGA.BP.5173.11 3 0.000 0.9802 0 0.00 1.00
#> TCGA.B0.4848.11 2 0.000 0.9918 0 1.00 0.00
#> TCGA.BP.5178.11 3 0.000 0.9802 0 0.00 1.00
#> TCGA.BP.5184.11 2 0.000 0.9918 0 1.00 0.00
#> TCGA.BP.5191.11 2 0.000 0.9918 0 1.00 0.00
#> TCGA.BP.5177.11 1 0.000 1.0000 1 0.00 0.00
#> TCGA.B0.5107.11 1 0.000 1.0000 1 0.00 0.00
#> TCGA.AK.3453.01 3 0.000 0.9802 0 0.00 1.00
#> TCGA.BP.5174.11 1 0.000 1.0000 1 0.00 0.00
#> TCGA.CJ.4901.11 2 0.000 0.9918 0 1.00 0.00
#> TCGA.BP.4770.11 1 0.000 1.0000 1 0.00 0.00
#> TCGA.B0.4703.11 2 0.000 0.9918 0 1.00 0.00
#> TCGA.B0.5104.11 1 0.000 1.0000 1 0.00 0.00
#> TCGA.B0.5098.11 3 0.000 0.9802 0 0.00 1.00
#> TCGA.B0.5113.11 1 0.000 1.0000 1 0.00 0.00
#> TCGA.CJ.4882.11 2 0.000 0.9918 0 1.00 0.00
#> TCGA.B0.5117.11 2 0.000 0.9918 0 1.00 0.00
#> TCGA.CZ.5459.11 2 0.000 0.9918 0 1.00 0.00
#> TCGA.CJ.4918.11 2 0.000 0.9918 0 1.00 0.00
#> TCGA.A3.3367.11 3 0.254 0.9102 0 0.08 0.92
#> TCGA.CZ.5466.11 2 0.000 0.9918 0 1.00 0.00
#> TCGA.B0.4707.11 2 0.000 0.9918 0 1.00 0.00
#> TCGA.BP.5185.11 2 0.000 0.9918 0 1.00 0.00
#> TCGA.BP.5183.11 2 0.000 0.9918 0 1.00 0.00
#> TCGA.BP.5196.11 2 0.000 0.9918 0 1.00 0.00
#> TCGA.BP.5186.11 1 0.000 1.0000 1 0.00 0.00
#> TCGA.B0.5710.11 2 0.000 0.9918 0 1.00 0.00
#> TCGA.BP.5201.11 2 0.000 0.9918 0 1.00 0.00
#> TCGA.BP.5180.11 2 0.000 0.9918 0 1.00 0.00
#> TCGA.CJ.4897.11 1 0.000 1.0000 1 0.00 0.00
#> TCGA.CJ.4923.11 2 0.000 0.9918 0 1.00 0.00
#> TCGA.BP.5181.11 1 0.000 1.0000 1 0.00 0.00
#> TCGA.B0.5083.11 2 0.000 0.9918 0 1.00 0.00
#> TCGA.CZ.4864.11 2 0.000 0.9918 0 1.00 0.00
#> TCGA.BP.5198.11 2 0.000 0.9918 0 1.00 0.00
#> TCGA.B0.5099.11 1 0.000 1.0000 1 0.00 0.00
#> TCGA.BP.5169.11 2 0.000 0.9918 0 1.00 0.00
#> TCGA.B0.5080.11 2 0.000 0.9918 0 1.00 0.00
#> TCGA.B0.4699.11 2 0.000 0.9918 0 1.00 0.00
#> TCGA.B0.5106.11 2 0.000 0.9918 0 1.00 0.00
#> TCGA.B0.5402.11 2 0.000 0.9918 0 1.00 0.00
#> TCGA.B0.5102.11 1 0.000 1.0000 1 0.00 0.00
#> TCGA.B0.4824.11 1 0.000 1.0000 1 0.00 0.00
#> TCGA.B0.5115.11 2 0.000 0.9918 0 1.00 0.00
#> TCGA.B0.4945.11 1 0.000 1.0000 1 0.00 0.00
#> TCGA.B0.4852.11 1 0.000 1.0000 1 0.00 0.00
#> TCGA.BP.5200.11 2 0.000 0.9918 0 1.00 0.00
#> TCGA.B0.4811.11 2 0.000 0.9918 0 1.00 0.00
#> TCGA.A3.3385.11 1 0.000 1.0000 1 0.00 0.00
#> TCGA.B0.5121.11 2 0.000 0.9918 0 1.00 0.00
#> TCGA.B0.4815.11 2 0.000 0.9918 0 1.00 0.00
#> TCGA.A3.3357.11 2 0.000 0.9918 0 1.00 0.00
#> TCGA.CJ.4913.11 1 0.000 1.0000 1 0.00 0.00
#> TCGA.BP.4993.11 2 0.000 0.9918 0 1.00 0.00
#> TCGA.B0.4823.11 3 0.000 0.9802 0 0.00 1.00
#> TCGA.B0.4819.11 1 0.000 1.0000 1 0.00 0.00
#> TCGA.BP.5168.11 2 0.000 0.9918 0 1.00 0.00
#> TCGA.B0.5096.11 1 0.000 1.0000 1 0.00 0.00
#> TCGA.B0.5400.11 1 0.000 1.0000 1 0.00 0.00
#> TCGA.B0.4842.11 1 0.000 1.0000 1 0.00 0.00
#> TCGA.B0.5095.11 3 0.000 0.9802 0 0.00 1.00
#> TCGA.B0.4690.11 3 0.000 0.9802 0 0.00 1.00
#> TCGA.BP.5199.11 2 0.000 0.9918 0 1.00 0.00
#> TCGA.BP.4782.11 1 0.000 1.0000 1 0.00 0.00
#> TCGA.B0.4693.11 1 0.000 1.0000 1 0.00 0.00
#> TCGA.B0.5092.11 1 0.000 1.0000 1 0.00 0.00
#> TCGA.B0.4849.11 2 0.000 0.9918 0 1.00 0.00
#> TCGA.B0.4817.11 2 0.000 0.9918 0 1.00 0.00
#> TCGA.BP.5176.11 1 0.000 1.0000 1 0.00 0.00
#> TCGA.BP.5190.11 2 0.000 0.9918 0 1.00 0.00
#> TCGA.B0.4713.11 1 0.000 1.0000 1 0.00 0.00
#> TCGA.CZ.5451.11 2 0.000 0.9918 0 1.00 0.00
#> TCGA.B0.4814.11 2 0.000 0.9918 0 1.00 0.00
#> TCGA.CJ.4869.11 2 0.000 0.9918 0 1.00 0.00
#> TCGA.CJ.4907.11 2 0.000 0.9918 0 1.00 0.00
#> TCGA.B0.5712.11 1 0.000 1.0000 1 0.00 0.00
#> TCGA.BP.4801.11 2 0.000 0.9918 0 1.00 0.00
#> TCGA.B0.5110.11 1 0.000 1.0000 1 0.00 0.00
#> TCGA.CJ.4903.11 2 0.000 0.9918 0 1.00 0.00
#> TCGA.B0.4714.11 2 0.630 0.0445 0 0.52 0.48
#> TCGA.B0.4818.11 1 0.000 1.0000 1 0.00 0.00
#> TCGA.BP.5189.11 2 0.000 0.9918 0 1.00 0.00
#> TCGA.B0.5097.11 1 0.000 1.0000 1 0.00 0.00
#> TCGA.BP.4760.11 2 0.000 0.9918 0 1.00 0.00
#> TCGA.B0.5120.11 1 0.000 1.0000 1 0.00 0.00
#> TCGA.B0.4843.11 2 0.000 0.9918 0 1.00 0.00
cbind(get_classes(res, k = 4), get_membership(res, k = 4))
#> class entropy silhouette p1 p2 p3 p4
#> TCGA.CJ.4904.11 1 0.0000 1.000 1 0.00 0.0 0.00
#> TCGA.BP.5175.11 2 0.0000 1.000 0 1.00 0.0 0.00
#> TCGA.B0.4706.11 2 0.0000 1.000 0 1.00 0.0 0.00
#> TCGA.B0.5117.01 3 0.0000 1.000 0 0.00 1.0 0.00
#> TCGA.BP.5182.11 2 0.0000 1.000 0 1.00 0.0 0.00
#> TCGA.B0.5094.11 4 0.0000 0.982 0 0.00 0.0 1.00
#> TCGA.B0.5100.11 4 0.0000 0.982 0 0.00 0.0 1.00
#> TCGA.CJ.4916.11 1 0.0000 1.000 1 0.00 0.0 0.00
#> TCGA.B0.4846.11 1 0.0000 1.000 1 0.00 0.0 0.00
#> TCGA.B0.4696.11 4 0.0000 0.982 0 0.00 0.0 1.00
#> TCGA.BP.5187.11 4 0.0000 0.982 0 0.00 0.0 1.00
#> TCGA.CZ.5464.11 2 0.0000 1.000 0 1.00 0.0 0.00
#> TCGA.B0.4701.11 1 0.0000 1.000 1 0.00 0.0 0.00
#> TCGA.BP.5194.11 2 0.0000 1.000 0 1.00 0.0 0.00
#> TCGA.B0.4691.11 2 0.0000 1.000 0 1.00 0.0 0.00
#> TCGA.B0.4841.11 4 0.0000 0.982 0 0.00 0.0 1.00
#> TCGA.CZ.5460.11 2 0.0000 1.000 0 1.00 0.0 0.00
#> TCGA.BP.4795.11 1 0.0000 1.000 1 0.00 0.0 0.00
#> TCGA.B0.4698.11 4 0.0000 0.982 0 0.00 0.0 1.00
#> TCGA.B0.5713.11 1 0.0000 1.000 1 0.00 0.0 0.00
#> TCGA.B0.5108.11 2 0.0000 1.000 0 1.00 0.0 0.00
#> TCGA.B0.5083.01 3 0.0000 1.000 0 0.00 1.0 0.00
#> TCGA.BP.5173.11 3 0.0000 1.000 0 0.00 1.0 0.00
#> TCGA.B0.4848.11 4 0.0000 0.982 0 0.00 0.0 1.00
#> TCGA.BP.5178.11 4 0.2345 0.880 0 0.00 0.1 0.90
#> TCGA.BP.5184.11 2 0.0000 1.000 0 1.00 0.0 0.00
#> TCGA.BP.5191.11 4 0.0000 0.982 0 0.00 0.0 1.00
#> TCGA.BP.5177.11 1 0.0000 1.000 1 0.00 0.0 0.00
#> TCGA.B0.5107.11 1 0.0000 1.000 1 0.00 0.0 0.00
#> TCGA.AK.3453.01 3 0.0000 1.000 0 0.00 1.0 0.00
#> TCGA.BP.5174.11 1 0.0000 1.000 1 0.00 0.0 0.00
#> TCGA.CJ.4901.11 2 0.0000 1.000 0 1.00 0.0 0.00
#> TCGA.BP.4770.11 1 0.0000 1.000 1 0.00 0.0 0.00
#> TCGA.B0.4703.11 4 0.0000 0.982 0 0.00 0.0 1.00
#> TCGA.B0.5104.11 1 0.0000 1.000 1 0.00 0.0 0.00
#> TCGA.B0.5098.11 3 0.0000 1.000 0 0.00 1.0 0.00
#> TCGA.B0.5113.11 1 0.0000 1.000 1 0.00 0.0 0.00
#> TCGA.CJ.4882.11 2 0.0000 1.000 0 1.00 0.0 0.00
#> TCGA.B0.5117.11 2 0.0000 1.000 0 1.00 0.0 0.00
#> TCGA.CZ.5459.11 4 0.0000 0.982 0 0.00 0.0 1.00
#> TCGA.CJ.4918.11 4 0.0000 0.982 0 0.00 0.0 1.00
#> TCGA.A3.3367.11 4 0.0000 0.982 0 0.00 0.0 1.00
#> TCGA.CZ.5466.11 4 0.3975 0.626 0 0.24 0.0 0.76
#> TCGA.B0.4707.11 4 0.0000 0.982 0 0.00 0.0 1.00
#> TCGA.BP.5185.11 2 0.0000 1.000 0 1.00 0.0 0.00
#> TCGA.BP.5183.11 2 0.0000 1.000 0 1.00 0.0 0.00
#> TCGA.BP.5196.11 2 0.0000 1.000 0 1.00 0.0 0.00
#> TCGA.BP.5186.11 1 0.0000 1.000 1 0.00 0.0 0.00
#> TCGA.B0.5710.11 2 0.0000 1.000 0 1.00 0.0 0.00
#> TCGA.BP.5201.11 2 0.0000 1.000 0 1.00 0.0 0.00
#> TCGA.BP.5180.11 2 0.0000 1.000 0 1.00 0.0 0.00
#> TCGA.CJ.4897.11 1 0.0000 1.000 1 0.00 0.0 0.00
#> TCGA.CJ.4923.11 4 0.0707 0.959 0 0.02 0.0 0.98
#> TCGA.BP.5181.11 1 0.0000 1.000 1 0.00 0.0 0.00
#> TCGA.B0.5083.11 2 0.0000 1.000 0 1.00 0.0 0.00
#> TCGA.CZ.4864.11 4 0.0000 0.982 0 0.00 0.0 1.00
#> TCGA.BP.5198.11 4 0.0000 0.982 0 0.00 0.0 1.00
#> TCGA.B0.5099.11 1 0.0000 1.000 1 0.00 0.0 0.00
#> TCGA.BP.5169.11 4 0.0000 0.982 0 0.00 0.0 1.00
#> TCGA.B0.5080.11 2 0.0000 1.000 0 1.00 0.0 0.00
#> TCGA.B0.4699.11 4 0.0000 0.982 0 0.00 0.0 1.00
#> TCGA.B0.5106.11 2 0.0000 1.000 0 1.00 0.0 0.00
#> TCGA.B0.5402.11 4 0.0000 0.982 0 0.00 0.0 1.00
#> TCGA.B0.5102.11 1 0.0000 1.000 1 0.00 0.0 0.00
#> TCGA.B0.4824.11 1 0.0000 1.000 1 0.00 0.0 0.00
#> TCGA.B0.5115.11 2 0.0000 1.000 0 1.00 0.0 0.00
#> TCGA.B0.4945.11 1 0.0000 1.000 1 0.00 0.0 0.00
#> TCGA.B0.4852.11 1 0.0000 1.000 1 0.00 0.0 0.00
#> TCGA.BP.5200.11 2 0.0000 1.000 0 1.00 0.0 0.00
#> TCGA.B0.4811.11 4 0.0000 0.982 0 0.00 0.0 1.00
#> TCGA.A3.3385.11 1 0.0000 1.000 1 0.00 0.0 0.00
#> TCGA.B0.5121.11 2 0.0000 1.000 0 1.00 0.0 0.00
#> TCGA.B0.4815.11 4 0.0000 0.982 0 0.00 0.0 1.00
#> TCGA.A3.3357.11 2 0.0000 1.000 0 1.00 0.0 0.00
#> TCGA.CJ.4913.11 1 0.0000 1.000 1 0.00 0.0 0.00
#> TCGA.BP.4993.11 2 0.0000 1.000 0 1.00 0.0 0.00
#> TCGA.B0.4823.11 3 0.0000 1.000 0 0.00 1.0 0.00
#> TCGA.B0.4819.11 1 0.0000 1.000 1 0.00 0.0 0.00
#> TCGA.BP.5168.11 4 0.0000 0.982 0 0.00 0.0 1.00
#> TCGA.B0.5096.11 1 0.0000 1.000 1 0.00 0.0 0.00
#> TCGA.B0.5400.11 1 0.0000 1.000 1 0.00 0.0 0.00
#> TCGA.B0.4842.11 1 0.0000 1.000 1 0.00 0.0 0.00
#> TCGA.B0.5095.11 3 0.0000 1.000 0 0.00 1.0 0.00
#> TCGA.B0.4690.11 3 0.0000 1.000 0 0.00 1.0 0.00
#> TCGA.BP.5199.11 2 0.0000 1.000 0 1.00 0.0 0.00
#> TCGA.BP.4782.11 1 0.0000 1.000 1 0.00 0.0 0.00
#> TCGA.B0.4693.11 1 0.0000 1.000 1 0.00 0.0 0.00
#> TCGA.B0.5092.11 1 0.0000 1.000 1 0.00 0.0 0.00
#> TCGA.B0.4849.11 2 0.0000 1.000 0 1.00 0.0 0.00
#> TCGA.B0.4817.11 4 0.0000 0.982 0 0.00 0.0 1.00
#> TCGA.BP.5176.11 1 0.0000 1.000 1 0.00 0.0 0.00
#> TCGA.BP.5190.11 2 0.0000 1.000 0 1.00 0.0 0.00
#> TCGA.B0.4713.11 1 0.0000 1.000 1 0.00 0.0 0.00
#> TCGA.CZ.5451.11 2 0.0000 1.000 0 1.00 0.0 0.00
#> TCGA.B0.4814.11 2 0.0000 1.000 0 1.00 0.0 0.00
#> TCGA.CJ.4869.11 2 0.0000 1.000 0 1.00 0.0 0.00
#> TCGA.CJ.4907.11 2 0.0000 1.000 0 1.00 0.0 0.00
#> TCGA.B0.5712.11 1 0.0000 1.000 1 0.00 0.0 0.00
#> TCGA.BP.4801.11 2 0.0000 1.000 0 1.00 0.0 0.00
#> TCGA.B0.5110.11 1 0.0000 1.000 1 0.00 0.0 0.00
#> TCGA.CJ.4903.11 2 0.0000 1.000 0 1.00 0.0 0.00
#> TCGA.B0.4714.11 4 0.0000 0.982 0 0.00 0.0 1.00
#> TCGA.B0.4818.11 1 0.0000 1.000 1 0.00 0.0 0.00
#> TCGA.BP.5189.11 2 0.0000 1.000 0 1.00 0.0 0.00
#> TCGA.B0.5097.11 1 0.0000 1.000 1 0.00 0.0 0.00
#> TCGA.BP.4760.11 4 0.0000 0.982 0 0.00 0.0 1.00
#> TCGA.B0.5120.11 1 0.0000 1.000 1 0.00 0.0 0.00
#> TCGA.B0.4843.11 2 0.0000 1.000 0 1.00 0.0 0.00
cbind(get_classes(res, k = 5), get_membership(res, k = 5))
#> class entropy silhouette p1 p2 p3 p4 p5
#> TCGA.CJ.4904.11 1 0.0000 0.998 1.00 0.00 0.00 0.00 0.00
#> TCGA.BP.5175.11 2 0.0000 1.000 0.00 1.00 0.00 0.00 0.00
#> TCGA.B0.4706.11 2 0.0000 1.000 0.00 1.00 0.00 0.00 0.00
#> TCGA.B0.5117.01 3 0.0000 1.000 0.00 0.00 1.00 0.00 0.00
#> TCGA.BP.5182.11 2 0.0000 1.000 0.00 1.00 0.00 0.00 0.00
#> TCGA.B0.5094.11 4 0.0000 0.984 0.00 0.00 0.00 1.00 0.00
#> TCGA.B0.5100.11 4 0.0000 0.984 0.00 0.00 0.00 1.00 0.00
#> TCGA.CJ.4916.11 5 0.0000 0.962 0.00 0.00 0.00 0.00 1.00
#> TCGA.B0.4846.11 5 0.0000 0.962 0.00 0.00 0.00 0.00 1.00
#> TCGA.B0.4696.11 4 0.0000 0.984 0.00 0.00 0.00 1.00 0.00
#> TCGA.BP.5187.11 4 0.0000 0.984 0.00 0.00 0.00 1.00 0.00
#> TCGA.CZ.5464.11 2 0.0000 1.000 0.00 1.00 0.00 0.00 0.00
#> TCGA.B0.4701.11 1 0.1043 0.958 0.96 0.00 0.00 0.00 0.04
#> TCGA.BP.5194.11 2 0.0000 1.000 0.00 1.00 0.00 0.00 0.00
#> TCGA.B0.4691.11 2 0.0000 1.000 0.00 1.00 0.00 0.00 0.00
#> TCGA.B0.4841.11 4 0.0000 0.984 0.00 0.00 0.00 1.00 0.00
#> TCGA.CZ.5460.11 2 0.0000 1.000 0.00 1.00 0.00 0.00 0.00
#> TCGA.BP.4795.11 5 0.0000 0.962 0.00 0.00 0.00 0.00 1.00
#> TCGA.B0.4698.11 4 0.0000 0.984 0.00 0.00 0.00 1.00 0.00
#> TCGA.B0.5713.11 1 0.0000 0.998 1.00 0.00 0.00 0.00 0.00
#> TCGA.B0.5108.11 2 0.0000 1.000 0.00 1.00 0.00 0.00 0.00
#> TCGA.B0.5083.01 3 0.0000 1.000 0.00 0.00 1.00 0.00 0.00
#> TCGA.BP.5173.11 3 0.0000 1.000 0.00 0.00 1.00 0.00 0.00
#> TCGA.B0.4848.11 4 0.0000 0.984 0.00 0.00 0.00 1.00 0.00
#> TCGA.BP.5178.11 4 0.1043 0.945 0.00 0.00 0.04 0.96 0.00
#> TCGA.BP.5184.11 2 0.0000 1.000 0.00 1.00 0.00 0.00 0.00
#> TCGA.BP.5191.11 4 0.0000 0.984 0.00 0.00 0.00 1.00 0.00
#> TCGA.BP.5177.11 5 0.3424 0.637 0.24 0.00 0.00 0.00 0.76
#> TCGA.B0.5107.11 1 0.0000 0.998 1.00 0.00 0.00 0.00 0.00
#> TCGA.AK.3453.01 3 0.0000 1.000 0.00 0.00 1.00 0.00 0.00
#> TCGA.BP.5174.11 1 0.0000 0.998 1.00 0.00 0.00 0.00 0.00
#> TCGA.CJ.4901.11 2 0.0000 1.000 0.00 1.00 0.00 0.00 0.00
#> TCGA.BP.4770.11 5 0.0000 0.962 0.00 0.00 0.00 0.00 1.00
#> TCGA.B0.4703.11 4 0.0000 0.984 0.00 0.00 0.00 1.00 0.00
#> TCGA.B0.5104.11 1 0.0000 0.998 1.00 0.00 0.00 0.00 0.00
#> TCGA.B0.5098.11 3 0.0000 1.000 0.00 0.00 1.00 0.00 0.00
#> TCGA.B0.5113.11 1 0.0609 0.979 0.98 0.00 0.00 0.00 0.02
#> TCGA.CJ.4882.11 2 0.0000 1.000 0.00 1.00 0.00 0.00 0.00
#> TCGA.B0.5117.11 2 0.0000 1.000 0.00 1.00 0.00 0.00 0.00
#> TCGA.CZ.5459.11 4 0.0000 0.984 0.00 0.00 0.00 1.00 0.00
#> TCGA.CJ.4918.11 4 0.0000 0.984 0.00 0.00 0.00 1.00 0.00
#> TCGA.A3.3367.11 4 0.0000 0.984 0.00 0.00 0.00 1.00 0.00
#> TCGA.CZ.5466.11 4 0.3684 0.555 0.00 0.28 0.00 0.72 0.00
#> TCGA.B0.4707.11 4 0.0000 0.984 0.00 0.00 0.00 1.00 0.00
#> TCGA.BP.5185.11 2 0.0000 1.000 0.00 1.00 0.00 0.00 0.00
#> TCGA.BP.5183.11 2 0.0000 1.000 0.00 1.00 0.00 0.00 0.00
#> TCGA.BP.5196.11 2 0.0000 1.000 0.00 1.00 0.00 0.00 0.00
#> TCGA.BP.5186.11 1 0.0000 0.998 1.00 0.00 0.00 0.00 0.00
#> TCGA.B0.5710.11 2 0.0000 1.000 0.00 1.00 0.00 0.00 0.00
#> TCGA.BP.5201.11 2 0.0000 1.000 0.00 1.00 0.00 0.00 0.00
#> TCGA.BP.5180.11 2 0.0000 1.000 0.00 1.00 0.00 0.00 0.00
#> TCGA.CJ.4897.11 1 0.0000 0.998 1.00 0.00 0.00 0.00 0.00
#> TCGA.CJ.4923.11 4 0.0000 0.984 0.00 0.00 0.00 1.00 0.00
#> TCGA.BP.5181.11 5 0.0000 0.962 0.00 0.00 0.00 0.00 1.00
#> TCGA.B0.5083.11 2 0.0000 1.000 0.00 1.00 0.00 0.00 0.00
#> TCGA.CZ.4864.11 4 0.0000 0.984 0.00 0.00 0.00 1.00 0.00
#> TCGA.BP.5198.11 4 0.0000 0.984 0.00 0.00 0.00 1.00 0.00
#> TCGA.B0.5099.11 5 0.0000 0.962 0.00 0.00 0.00 0.00 1.00
#> TCGA.BP.5169.11 4 0.0000 0.984 0.00 0.00 0.00 1.00 0.00
#> TCGA.B0.5080.11 2 0.0000 1.000 0.00 1.00 0.00 0.00 0.00
#> TCGA.B0.4699.11 4 0.0000 0.984 0.00 0.00 0.00 1.00 0.00
#> TCGA.B0.5106.11 2 0.0000 1.000 0.00 1.00 0.00 0.00 0.00
#> TCGA.B0.5402.11 4 0.0000 0.984 0.00 0.00 0.00 1.00 0.00
#> TCGA.B0.5102.11 1 0.0000 0.998 1.00 0.00 0.00 0.00 0.00
#> TCGA.B0.4824.11 1 0.0000 0.998 1.00 0.00 0.00 0.00 0.00
#> TCGA.B0.5115.11 2 0.0000 1.000 0.00 1.00 0.00 0.00 0.00
#> TCGA.B0.4945.11 1 0.0000 0.998 1.00 0.00 0.00 0.00 0.00
#> TCGA.B0.4852.11 1 0.0000 0.998 1.00 0.00 0.00 0.00 0.00
#> TCGA.BP.5200.11 2 0.0000 1.000 0.00 1.00 0.00 0.00 0.00
#> TCGA.B0.4811.11 4 0.0000 0.984 0.00 0.00 0.00 1.00 0.00
#> TCGA.A3.3385.11 1 0.0000 0.998 1.00 0.00 0.00 0.00 0.00
#> TCGA.B0.5121.11 2 0.0000 1.000 0.00 1.00 0.00 0.00 0.00
#> TCGA.B0.4815.11 4 0.0000 0.984 0.00 0.00 0.00 1.00 0.00
#> TCGA.A3.3357.11 2 0.0000 1.000 0.00 1.00 0.00 0.00 0.00
#> TCGA.CJ.4913.11 1 0.0000 0.998 1.00 0.00 0.00 0.00 0.00
#> TCGA.BP.4993.11 2 0.0000 1.000 0.00 1.00 0.00 0.00 0.00
#> TCGA.B0.4823.11 3 0.0000 1.000 0.00 0.00 1.00 0.00 0.00
#> TCGA.B0.4819.11 1 0.0000 0.998 1.00 0.00 0.00 0.00 0.00
#> TCGA.BP.5168.11 4 0.0000 0.984 0.00 0.00 0.00 1.00 0.00
#> TCGA.B0.5096.11 1 0.0000 0.998 1.00 0.00 0.00 0.00 0.00
#> TCGA.B0.5400.11 5 0.0000 0.962 0.00 0.00 0.00 0.00 1.00
#> TCGA.B0.4842.11 1 0.0000 0.998 1.00 0.00 0.00 0.00 0.00
#> TCGA.B0.5095.11 3 0.0000 1.000 0.00 0.00 1.00 0.00 0.00
#> TCGA.B0.4690.11 3 0.0000 1.000 0.00 0.00 1.00 0.00 0.00
#> TCGA.BP.5199.11 2 0.0000 1.000 0.00 1.00 0.00 0.00 0.00
#> TCGA.BP.4782.11 5 0.0000 0.962 0.00 0.00 0.00 0.00 1.00
#> TCGA.B0.4693.11 1 0.0000 0.998 1.00 0.00 0.00 0.00 0.00
#> TCGA.B0.5092.11 1 0.0000 0.998 1.00 0.00 0.00 0.00 0.00
#> TCGA.B0.4849.11 2 0.0000 1.000 0.00 1.00 0.00 0.00 0.00
#> TCGA.B0.4817.11 4 0.0000 0.984 0.00 0.00 0.00 1.00 0.00
#> TCGA.BP.5176.11 1 0.0000 0.998 1.00 0.00 0.00 0.00 0.00
#> TCGA.BP.5190.11 2 0.0000 1.000 0.00 1.00 0.00 0.00 0.00
#> TCGA.B0.4713.11 1 0.0000 0.998 1.00 0.00 0.00 0.00 0.00
#> TCGA.CZ.5451.11 2 0.0000 1.000 0.00 1.00 0.00 0.00 0.00
#> TCGA.B0.4814.11 2 0.0000 1.000 0.00 1.00 0.00 0.00 0.00
#> TCGA.CJ.4869.11 2 0.0000 1.000 0.00 1.00 0.00 0.00 0.00
#> TCGA.CJ.4907.11 2 0.0000 1.000 0.00 1.00 0.00 0.00 0.00
#> TCGA.B0.5712.11 5 0.0000 0.962 0.00 0.00 0.00 0.00 1.00
#> TCGA.BP.4801.11 2 0.0000 1.000 0.00 1.00 0.00 0.00 0.00
#> TCGA.B0.5110.11 1 0.0000 0.998 1.00 0.00 0.00 0.00 0.00
#> TCGA.CJ.4903.11 2 0.0000 1.000 0.00 1.00 0.00 0.00 0.00
#> TCGA.B0.4714.11 4 0.0000 0.984 0.00 0.00 0.00 1.00 0.00
#> TCGA.B0.4818.11 1 0.0000 0.998 1.00 0.00 0.00 0.00 0.00
#> TCGA.BP.5189.11 2 0.0000 1.000 0.00 1.00 0.00 0.00 0.00
#> TCGA.B0.5097.11 1 0.0000 0.998 1.00 0.00 0.00 0.00 0.00
#> TCGA.BP.4760.11 4 0.0000 0.984 0.00 0.00 0.00 1.00 0.00
#> TCGA.B0.5120.11 1 0.0000 0.998 1.00 0.00 0.00 0.00 0.00
#> TCGA.B0.4843.11 2 0.0000 1.000 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.CJ.4904.11 1 0.0547 0.983 0.98 0.00 0.00 0.00 0.00 0.02
#> TCGA.BP.5175.11 2 0.3797 0.716 0.00 0.58 0.00 0.00 0.00 0.42
#> TCGA.B0.4706.11 2 0.3756 0.730 0.00 0.60 0.00 0.00 0.00 0.40
#> TCGA.B0.5117.01 3 0.0000 0.193 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.BP.5182.11 2 0.0000 0.832 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.B0.5094.11 4 0.0937 0.887 0.00 0.00 0.00 0.96 0.00 0.04
#> TCGA.B0.5100.11 4 0.0937 0.887 0.00 0.00 0.00 0.96 0.00 0.04
#> TCGA.CJ.4916.11 5 0.0000 0.965 0.00 0.00 0.00 0.00 1.00 0.00
#> TCGA.B0.4846.11 5 0.0000 0.965 0.00 0.00 0.00 0.00 1.00 0.00
#> TCGA.B0.4696.11 4 0.2941 0.730 0.00 0.22 0.00 0.78 0.00 0.00
#> TCGA.BP.5187.11 4 0.2941 0.730 0.00 0.22 0.00 0.78 0.00 0.00
#> TCGA.CZ.5464.11 2 0.0937 0.803 0.00 0.96 0.00 0.04 0.00 0.00
#> TCGA.B0.4701.11 1 0.1480 0.948 0.94 0.00 0.00 0.00 0.04 0.02
#> TCGA.BP.5194.11 2 0.0000 0.832 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.B0.4691.11 2 0.0937 0.800 0.00 0.96 0.00 0.04 0.00 0.00
#> TCGA.B0.4841.11 4 0.0937 0.887 0.00 0.00 0.00 0.96 0.00 0.04
#> TCGA.CZ.5460.11 2 0.3756 0.730 0.00 0.60 0.00 0.00 0.00 0.40
#> TCGA.BP.4795.11 5 0.0000 0.965 0.00 0.00 0.00 0.00 1.00 0.00
#> TCGA.B0.4698.11 4 0.1556 0.851 0.00 0.08 0.00 0.92 0.00 0.00
#> TCGA.B0.5713.11 1 0.0000 0.991 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.B0.5108.11 2 0.0000 0.832 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.B0.5083.01 3 0.0000 0.193 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.BP.5173.11 3 0.3706 -0.375 0.00 0.00 0.62 0.00 0.00 0.38
#> TCGA.B0.4848.11 4 0.0937 0.887 0.00 0.00 0.00 0.96 0.00 0.04
#> TCGA.BP.5178.11 4 0.5285 -0.034 0.00 0.00 0.10 0.48 0.00 0.42
#> TCGA.BP.5184.11 2 0.0000 0.832 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.BP.5191.11 4 0.0937 0.887 0.00 0.00 0.00 0.96 0.00 0.04
#> TCGA.BP.5177.11 5 0.3156 0.687 0.18 0.00 0.00 0.00 0.80 0.02
#> TCGA.B0.5107.11 1 0.0000 0.991 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.AK.3453.01 6 0.3864 0.920 0.00 0.00 0.48 0.00 0.00 0.52
#> TCGA.BP.5174.11 1 0.0000 0.991 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.CJ.4901.11 2 0.2793 0.818 0.00 0.80 0.00 0.00 0.00 0.20
#> TCGA.BP.4770.11 5 0.0547 0.949 0.00 0.00 0.00 0.00 0.98 0.02
#> TCGA.B0.4703.11 4 0.0937 0.887 0.00 0.00 0.00 0.96 0.00 0.04
#> TCGA.B0.5104.11 1 0.0000 0.991 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.B0.5098.11 6 0.3869 0.918 0.00 0.00 0.50 0.00 0.00 0.50
#> TCGA.B0.5113.11 1 0.1480 0.948 0.94 0.00 0.00 0.00 0.04 0.02
#> TCGA.CJ.4882.11 2 0.2048 0.836 0.00 0.88 0.00 0.00 0.00 0.12
#> TCGA.B0.5117.11 2 0.2048 0.836 0.00 0.88 0.00 0.00 0.00 0.12
#> TCGA.CZ.5459.11 4 0.2631 0.771 0.00 0.18 0.00 0.82 0.00 0.00
#> TCGA.CJ.4918.11 4 0.0937 0.872 0.00 0.04 0.00 0.96 0.00 0.00
#> TCGA.A3.3367.11 4 0.0937 0.887 0.00 0.00 0.00 0.96 0.00 0.04
#> TCGA.CZ.5466.11 4 0.3409 0.626 0.00 0.30 0.00 0.70 0.00 0.00
#> TCGA.B0.4707.11 4 0.0937 0.887 0.00 0.00 0.00 0.96 0.00 0.04
#> TCGA.BP.5185.11 2 0.3797 0.716 0.00 0.58 0.00 0.00 0.00 0.42
#> TCGA.BP.5183.11 2 0.2793 0.818 0.00 0.80 0.00 0.00 0.00 0.20
#> TCGA.BP.5196.11 2 0.3756 0.730 0.00 0.60 0.00 0.00 0.00 0.40
#> TCGA.BP.5186.11 1 0.0000 0.991 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.B0.5710.11 2 0.3797 0.716 0.00 0.58 0.00 0.00 0.00 0.42
#> TCGA.BP.5201.11 2 0.0000 0.832 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.BP.5180.11 2 0.3797 0.716 0.00 0.58 0.00 0.00 0.00 0.42
#> TCGA.CJ.4897.11 1 0.0547 0.983 0.98 0.00 0.00 0.00 0.00 0.02
#> TCGA.CJ.4923.11 4 0.3706 0.503 0.00 0.38 0.00 0.62 0.00 0.00
#> TCGA.BP.5181.11 5 0.0000 0.965 0.00 0.00 0.00 0.00 1.00 0.00
#> TCGA.B0.5083.11 2 0.2048 0.836 0.00 0.88 0.00 0.00 0.00 0.12
#> TCGA.CZ.4864.11 4 0.0000 0.886 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.BP.5198.11 4 0.0000 0.886 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.B0.5099.11 5 0.0000 0.965 0.00 0.00 0.00 0.00 1.00 0.00
#> TCGA.BP.5169.11 4 0.1267 0.863 0.00 0.06 0.00 0.94 0.00 0.00
#> TCGA.B0.5080.11 2 0.3797 0.716 0.00 0.58 0.00 0.00 0.00 0.42
#> TCGA.B0.4699.11 4 0.0937 0.887 0.00 0.00 0.00 0.96 0.00 0.04
#> TCGA.B0.5106.11 2 0.0937 0.838 0.00 0.96 0.00 0.00 0.00 0.04
#> TCGA.B0.5402.11 4 0.0000 0.886 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.B0.5102.11 1 0.0000 0.991 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.B0.4824.11 1 0.0000 0.991 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.B0.5115.11 2 0.0000 0.832 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.B0.4945.11 1 0.0000 0.991 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.B0.4852.11 1 0.0000 0.991 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.BP.5200.11 2 0.3797 0.716 0.00 0.58 0.00 0.00 0.00 0.42
#> TCGA.B0.4811.11 4 0.0000 0.886 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.A3.3385.11 1 0.0000 0.991 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.B0.5121.11 2 0.2631 0.824 0.00 0.82 0.00 0.00 0.00 0.18
#> TCGA.B0.4815.11 4 0.0000 0.886 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.A3.3357.11 2 0.3797 0.716 0.00 0.58 0.00 0.00 0.00 0.42
#> TCGA.CJ.4913.11 1 0.0547 0.983 0.98 0.00 0.00 0.00 0.00 0.02
#> TCGA.BP.4993.11 2 0.0937 0.838 0.00 0.96 0.00 0.00 0.00 0.04
#> TCGA.B0.4823.11 3 0.3706 -0.375 0.00 0.00 0.62 0.00 0.00 0.38
#> TCGA.B0.4819.11 1 0.0000 0.991 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.BP.5168.11 4 0.0000 0.886 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.B0.5096.11 1 0.0000 0.991 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.B0.5400.11 5 0.0000 0.965 0.00 0.00 0.00 0.00 1.00 0.00
#> TCGA.B0.4842.11 1 0.0000 0.991 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.B0.5095.11 3 0.3706 -0.375 0.00 0.00 0.62 0.00 0.00 0.38
#> TCGA.B0.4690.11 3 0.5285 -0.200 0.00 0.00 0.48 0.10 0.00 0.42
#> TCGA.BP.5199.11 2 0.2793 0.818 0.00 0.80 0.00 0.00 0.00 0.20
#> TCGA.BP.4782.11 5 0.0000 0.965 0.00 0.00 0.00 0.00 1.00 0.00
#> TCGA.B0.4693.11 1 0.0547 0.983 0.98 0.00 0.00 0.00 0.00 0.02
#> TCGA.B0.5092.11 1 0.0000 0.991 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.B0.4849.11 2 0.0000 0.832 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.B0.4817.11 4 0.0937 0.887 0.00 0.00 0.00 0.96 0.00 0.04
#> TCGA.BP.5176.11 1 0.0000 0.991 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.BP.5190.11 2 0.0000 0.832 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.B0.4713.11 1 0.0000 0.991 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.CZ.5451.11 2 0.3756 0.730 0.00 0.60 0.00 0.00 0.00 0.40
#> TCGA.B0.4814.11 2 0.0000 0.832 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.CJ.4869.11 2 0.0937 0.838 0.00 0.96 0.00 0.00 0.00 0.04
#> TCGA.CJ.4907.11 2 0.0000 0.832 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.B0.5712.11 5 0.0000 0.965 0.00 0.00 0.00 0.00 1.00 0.00
#> TCGA.BP.4801.11 2 0.1556 0.838 0.00 0.92 0.00 0.00 0.00 0.08
#> TCGA.B0.5110.11 1 0.0000 0.991 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.CJ.4903.11 2 0.2454 0.829 0.00 0.84 0.00 0.00 0.00 0.16
#> TCGA.B0.4714.11 4 0.0937 0.887 0.00 0.00 0.00 0.96 0.00 0.04
#> TCGA.B0.4818.11 1 0.0547 0.983 0.98 0.00 0.00 0.00 0.00 0.02
#> TCGA.BP.5189.11 2 0.0000 0.832 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.B0.5097.11 1 0.0000 0.991 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.BP.4760.11 4 0.2048 0.823 0.00 0.12 0.00 0.88 0.00 0.00
#> TCGA.B0.5120.11 1 0.0547 0.983 0.98 0.00 0.00 0.00 0.00 0.02
#> TCGA.B0.4843.11 2 0.0000 0.832 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.CJ.4904.11 1 0.1928 0.9205 0.90 0.00 0.00 0.00 0.00 0.08 0.02
#> TCGA.BP.5175.11 6 0.5416 0.9824 0.00 0.38 0.00 0.00 0.00 0.42 0.20
#> TCGA.B0.4706.11 6 0.5421 0.9637 0.00 0.40 0.00 0.00 0.00 0.40 0.20
#> TCGA.B0.5117.01 7 0.3294 1.0000 0.00 0.00 0.34 0.00 0.00 0.00 0.66
#> TCGA.BP.5182.11 2 0.0000 0.7403 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.B0.5094.11 4 0.2832 0.7307 0.00 0.00 0.00 0.76 0.00 0.24 0.00
#> TCGA.B0.5100.11 4 0.3047 0.7229 0.00 0.00 0.00 0.72 0.00 0.28 0.00
#> TCGA.CJ.4916.11 5 0.0000 0.9332 0.00 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.B0.4846.11 5 0.0000 0.9332 0.00 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.B0.4696.11 4 0.4615 0.5704 0.00 0.30 0.00 0.60 0.00 0.10 0.00
#> TCGA.BP.5187.11 4 0.3417 0.5909 0.00 0.26 0.00 0.72 0.00 0.02 0.00
#> TCGA.CZ.5464.11 2 0.2832 0.4172 0.00 0.76 0.00 0.24 0.00 0.00 0.00
#> TCGA.B0.4701.11 1 0.3315 0.8482 0.82 0.00 0.00 0.00 0.08 0.08 0.02
#> TCGA.BP.5194.11 2 0.0000 0.7403 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.B0.4691.11 2 0.1433 0.6399 0.00 0.92 0.00 0.00 0.00 0.08 0.00
#> TCGA.B0.4841.11 4 0.3358 0.7145 0.00 0.00 0.00 0.64 0.00 0.36 0.00
#> TCGA.CZ.5460.11 2 0.5416 -0.9225 0.00 0.42 0.00 0.00 0.00 0.38 0.20
#> TCGA.BP.4795.11 5 0.0000 0.9332 0.00 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.B0.4698.11 4 0.2912 0.7069 0.00 0.14 0.00 0.82 0.00 0.04 0.00
#> TCGA.B0.5713.11 1 0.0000 0.9593 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.B0.5108.11 2 0.0504 0.7350 0.00 0.98 0.00 0.00 0.00 0.02 0.00
#> TCGA.B0.5083.01 7 0.3294 1.0000 0.00 0.00 0.34 0.00 0.00 0.00 0.66
#> TCGA.BP.5173.11 3 0.0000 0.6915 0.00 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.B0.4848.11 4 0.3358 0.7145 0.00 0.00 0.00 0.64 0.00 0.36 0.00
#> TCGA.BP.5178.11 3 0.4338 0.4117 0.00 0.00 0.64 0.08 0.00 0.28 0.00
#> TCGA.BP.5184.11 2 0.0000 0.7403 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.BP.5191.11 4 0.2708 0.7370 0.00 0.00 0.00 0.78 0.00 0.22 0.00
#> TCGA.BP.5177.11 5 0.4500 0.4862 0.22 0.00 0.00 0.00 0.68 0.08 0.02
#> TCGA.B0.5107.11 1 0.0000 0.9593 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.AK.3453.01 3 0.4204 0.4061 0.00 0.00 0.70 0.00 0.00 0.14 0.16
#> TCGA.BP.5174.11 1 0.0000 0.9593 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.CJ.4901.11 2 0.3667 0.4376 0.00 0.74 0.00 0.00 0.00 0.20 0.06
#> TCGA.BP.4770.11 5 0.1928 0.8382 0.00 0.00 0.00 0.00 0.90 0.08 0.02
#> TCGA.B0.4703.11 4 0.3815 0.7114 0.00 0.02 0.00 0.62 0.00 0.36 0.00
#> TCGA.B0.5104.11 1 0.0000 0.9593 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.B0.5098.11 3 0.1006 0.6767 0.00 0.00 0.96 0.00 0.00 0.02 0.02
#> TCGA.B0.5113.11 1 0.3061 0.8702 0.84 0.00 0.00 0.00 0.06 0.08 0.02
#> TCGA.CJ.4882.11 2 0.3086 0.5646 0.00 0.80 0.00 0.00 0.00 0.16 0.04
#> TCGA.B0.5117.11 2 0.3526 0.4859 0.00 0.76 0.00 0.00 0.00 0.18 0.06
#> TCGA.CZ.5459.11 4 0.1886 0.7025 0.00 0.12 0.00 0.88 0.00 0.00 0.00
#> TCGA.CJ.4918.11 4 0.1363 0.7512 0.00 0.02 0.00 0.94 0.00 0.04 0.00
#> TCGA.A3.3367.11 4 0.3358 0.7145 0.00 0.00 0.00 0.64 0.00 0.36 0.00
#> TCGA.CZ.5466.11 4 0.1886 0.6979 0.00 0.12 0.00 0.88 0.00 0.00 0.00
#> TCGA.B0.4707.11 4 0.3358 0.7145 0.00 0.00 0.00 0.64 0.00 0.36 0.00
#> TCGA.BP.5185.11 6 0.5416 0.9824 0.00 0.38 0.00 0.00 0.00 0.42 0.20
#> TCGA.BP.5183.11 2 0.3908 0.3779 0.00 0.72 0.00 0.00 0.00 0.20 0.08
#> TCGA.BP.5196.11 6 0.5421 0.9637 0.00 0.40 0.00 0.00 0.00 0.40 0.20
#> TCGA.BP.5186.11 1 0.0000 0.9593 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.B0.5710.11 6 0.5416 0.9824 0.00 0.38 0.00 0.00 0.00 0.42 0.20
#> TCGA.BP.5201.11 2 0.0000 0.7403 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.BP.5180.11 6 0.5416 0.9824 0.00 0.38 0.00 0.00 0.00 0.42 0.20
#> TCGA.CJ.4897.11 1 0.1928 0.9205 0.90 0.00 0.00 0.00 0.00 0.08 0.02
#> TCGA.CJ.4923.11 4 0.4283 0.2269 0.00 0.48 0.00 0.48 0.00 0.04 0.00
#> TCGA.BP.5181.11 5 0.0000 0.9332 0.00 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.B0.5083.11 2 0.2722 0.6282 0.00 0.84 0.00 0.00 0.00 0.12 0.04
#> TCGA.CZ.4864.11 4 0.0000 0.7505 0.00 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.BP.5198.11 4 0.0000 0.7505 0.00 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.B0.5099.11 5 0.0000 0.9332 0.00 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.BP.5169.11 4 0.2163 0.7252 0.00 0.10 0.00 0.88 0.00 0.02 0.00
#> TCGA.B0.5080.11 6 0.5416 0.9824 0.00 0.38 0.00 0.00 0.00 0.42 0.20
#> TCGA.B0.4699.11 4 0.3815 0.7114 0.00 0.02 0.00 0.62 0.00 0.36 0.00
#> TCGA.B0.5106.11 2 0.1928 0.6956 0.00 0.90 0.00 0.00 0.00 0.08 0.02
#> TCGA.B0.5402.11 4 0.0000 0.7505 0.00 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.B0.5102.11 1 0.0000 0.9593 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.B0.4824.11 1 0.0000 0.9593 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.B0.5115.11 2 0.0000 0.7403 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.B0.4945.11 1 0.0000 0.9593 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.B0.4852.11 1 0.0000 0.9593 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.BP.5200.11 6 0.5416 0.9824 0.00 0.38 0.00 0.00 0.00 0.42 0.20
#> TCGA.B0.4811.11 4 0.0000 0.7505 0.00 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.A3.3385.11 1 0.0000 0.9593 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.B0.5121.11 2 0.4108 0.0898 0.00 0.66 0.00 0.00 0.00 0.28 0.06
#> TCGA.B0.4815.11 4 0.0000 0.7505 0.00 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.A3.3357.11 2 0.5421 -0.9688 0.00 0.40 0.00 0.00 0.00 0.40 0.20
#> TCGA.CJ.4913.11 1 0.1928 0.9205 0.90 0.00 0.00 0.00 0.00 0.08 0.02
#> TCGA.BP.4993.11 2 0.2016 0.6968 0.00 0.90 0.00 0.00 0.00 0.06 0.04
#> TCGA.B0.4823.11 3 0.0000 0.6915 0.00 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.B0.4819.11 1 0.1664 0.9295 0.92 0.00 0.00 0.00 0.00 0.06 0.02
#> TCGA.BP.5168.11 4 0.0000 0.7505 0.00 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.B0.5096.11 1 0.0000 0.9593 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.B0.5400.11 5 0.0000 0.9332 0.00 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.B0.4842.11 1 0.0000 0.9593 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.B0.5095.11 3 0.0000 0.6915 0.00 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.B0.4690.11 3 0.2945 0.5126 0.00 0.00 0.74 0.00 0.00 0.26 0.00
#> TCGA.BP.5199.11 2 0.3667 0.4376 0.00 0.74 0.00 0.00 0.00 0.20 0.06
#> TCGA.BP.4782.11 5 0.0000 0.9332 0.00 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.B0.4693.11 1 0.2421 0.9068 0.88 0.00 0.00 0.00 0.02 0.08 0.02
#> TCGA.B0.5092.11 1 0.0000 0.9593 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.B0.4849.11 2 0.0000 0.7403 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.B0.4817.11 4 0.3358 0.7145 0.00 0.00 0.00 0.64 0.00 0.36 0.00
#> TCGA.BP.5176.11 1 0.0000 0.9593 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.BP.5190.11 2 0.0000 0.7403 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.B0.4713.11 1 0.0000 0.9593 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.CZ.5451.11 6 0.5421 0.9637 0.00 0.40 0.00 0.00 0.00 0.40 0.20
#> TCGA.B0.4814.11 2 0.0000 0.7403 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.CJ.4869.11 2 0.1664 0.7080 0.00 0.92 0.00 0.00 0.00 0.06 0.02
#> TCGA.CJ.4907.11 2 0.0000 0.7403 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.B0.5712.11 5 0.0000 0.9332 0.00 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.BP.4801.11 2 0.2163 0.6762 0.00 0.88 0.00 0.00 0.00 0.10 0.02
#> TCGA.B0.5110.11 1 0.0000 0.9593 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.CJ.4903.11 2 0.3795 0.3745 0.00 0.72 0.00 0.00 0.00 0.22 0.06
#> TCGA.B0.4714.11 4 0.3358 0.7145 0.00 0.00 0.00 0.64 0.00 0.36 0.00
#> TCGA.B0.4818.11 1 0.1928 0.9205 0.90 0.00 0.00 0.00 0.00 0.08 0.02
#> TCGA.BP.5189.11 2 0.0000 0.7403 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.B0.5097.11 1 0.0000 0.9593 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.BP.4760.11 4 0.3835 0.6994 0.00 0.16 0.00 0.74 0.00 0.10 0.00
#> TCGA.B0.5120.11 1 0.1928 0.9205 0.90 0.00 0.00 0.00 0.00 0.08 0.02
#> TCGA.B0.4843.11 2 0.0000 0.7403 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.CJ.4904.11 1 0.3630 0.7967 0.78 0.00 0.00 0.00 0.00 0.08 0.04 0.10
#> TCGA.BP.5175.11 6 0.2114 0.9504 0.00 0.16 0.00 0.00 0.00 0.84 0.00 0.00
#> TCGA.B0.4706.11 6 0.2406 0.9427 0.00 0.20 0.00 0.00 0.00 0.80 0.00 0.00
#> TCGA.B0.5117.01 7 0.2938 1.0000 0.00 0.00 0.30 0.00 0.00 0.00 0.70 0.00
#> TCGA.BP.5182.11 2 0.0471 0.7860 0.00 0.98 0.00 0.00 0.00 0.00 0.00 0.02
#> TCGA.B0.5094.11 4 0.3291 -0.2746 0.00 0.00 0.00 0.70 0.00 0.00 0.02 0.28
#> TCGA.B0.5100.11 4 0.3449 -0.4052 0.00 0.00 0.00 0.66 0.00 0.00 0.02 0.32
#> TCGA.CJ.4916.11 5 0.0471 0.8758 0.00 0.00 0.00 0.00 0.98 0.02 0.00 0.00
#> TCGA.B0.4846.11 5 0.0000 0.8842 0.00 0.00 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.B0.4696.11 4 0.6129 0.1218 0.00 0.34 0.00 0.38 0.00 0.02 0.04 0.22
#> TCGA.BP.5187.11 4 0.5365 0.2878 0.00 0.32 0.00 0.52 0.00 0.02 0.02 0.12
#> TCGA.CZ.5464.11 2 0.4239 0.4153 0.00 0.64 0.00 0.30 0.00 0.02 0.02 0.02
#> TCGA.B0.4701.11 1 0.5986 0.5973 0.58 0.00 0.00 0.00 0.14 0.10 0.06 0.12
#> TCGA.BP.5194.11 2 0.0941 0.7752 0.00 0.96 0.00 0.00 0.00 0.02 0.00 0.02
#> TCGA.B0.4691.11 2 0.2680 0.6707 0.00 0.84 0.00 0.00 0.00 0.02 0.02 0.12
#> TCGA.B0.4841.11 8 0.3329 0.9441 0.00 0.00 0.00 0.48 0.00 0.00 0.00 0.52
#> TCGA.CZ.5460.11 6 0.2650 0.9087 0.00 0.24 0.00 0.00 0.00 0.76 0.00 0.00
#> TCGA.BP.4795.11 5 0.0000 0.8842 0.00 0.00 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.B0.4698.11 4 0.4272 0.4153 0.00 0.08 0.00 0.72 0.00 0.02 0.02 0.16
#> TCGA.B0.5713.11 1 0.0000 0.8895 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.B0.5108.11 2 0.1341 0.7767 0.00 0.92 0.00 0.00 0.00 0.08 0.00 0.00
#> TCGA.B0.5083.01 7 0.2938 1.0000 0.00 0.00 0.30 0.00 0.00 0.00 0.70 0.00
#> TCGA.BP.5173.11 3 0.0000 0.6319 0.00 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.B0.4848.11 4 0.3333 -0.9122 0.00 0.00 0.00 0.50 0.00 0.00 0.00 0.50
#> TCGA.BP.5178.11 3 0.4050 0.3963 0.00 0.00 0.60 0.06 0.00 0.00 0.00 0.34
#> TCGA.BP.5184.11 2 0.0471 0.7860 0.00 0.98 0.00 0.00 0.00 0.00 0.00 0.02
#> TCGA.BP.5191.11 4 0.2856 0.0562 0.00 0.00 0.00 0.78 0.00 0.00 0.02 0.20
#> TCGA.BP.5177.11 5 0.6326 0.3319 0.20 0.00 0.00 0.00 0.52 0.10 0.06 0.12
#> TCGA.B0.5107.11 1 0.0000 0.8895 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.AK.3453.01 3 0.5575 0.1877 0.00 0.00 0.46 0.00 0.00 0.04 0.18 0.32
#> TCGA.BP.5174.11 1 0.0000 0.8895 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.CJ.4901.11 2 0.2756 0.6158 0.00 0.74 0.00 0.00 0.00 0.26 0.00 0.00
#> TCGA.BP.4770.11 5 0.3454 0.7295 0.00 0.00 0.00 0.00 0.80 0.08 0.06 0.06
#> TCGA.B0.4703.11 8 0.4137 0.8815 0.00 0.00 0.00 0.46 0.00 0.02 0.02 0.50
#> TCGA.B0.5104.11 1 0.0000 0.8895 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.B0.5098.11 3 0.2680 0.5881 0.00 0.00 0.84 0.00 0.02 0.00 0.12 0.02
#> TCGA.B0.5113.11 1 0.5986 0.5973 0.58 0.00 0.00 0.00 0.14 0.10 0.06 0.12
#> TCGA.CJ.4882.11 2 0.2406 0.6971 0.00 0.80 0.00 0.00 0.00 0.20 0.00 0.00
#> TCGA.B0.5117.11 2 0.2534 0.6712 0.00 0.78 0.00 0.00 0.00 0.22 0.00 0.00
#> TCGA.CZ.5459.11 4 0.2680 0.5098 0.00 0.12 0.00 0.84 0.00 0.00 0.02 0.02
#> TCGA.CJ.4918.11 4 0.3627 0.3659 0.00 0.04 0.00 0.78 0.00 0.02 0.02 0.14
#> TCGA.A3.3367.11 8 0.3729 0.9134 0.00 0.00 0.02 0.46 0.00 0.00 0.00 0.52
#> TCGA.CZ.5466.11 4 0.2859 0.4980 0.00 0.14 0.00 0.82 0.00 0.00 0.02 0.02
#> TCGA.B0.4707.11 8 0.3329 0.9441 0.00 0.00 0.00 0.48 0.00 0.00 0.00 0.52
#> TCGA.BP.5185.11 6 0.2114 0.9504 0.00 0.16 0.00 0.00 0.00 0.84 0.00 0.00
#> TCGA.BP.5183.11 2 0.3015 0.5032 0.00 0.68 0.00 0.00 0.00 0.32 0.00 0.00
#> TCGA.BP.5196.11 6 0.2650 0.9104 0.00 0.24 0.00 0.00 0.00 0.76 0.00 0.00
#> TCGA.BP.5186.11 1 0.0000 0.8895 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.B0.5710.11 6 0.2114 0.9504 0.00 0.16 0.00 0.00 0.00 0.84 0.00 0.00
#> TCGA.BP.5201.11 2 0.0000 0.7884 0.00 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.BP.5180.11 6 0.2114 0.9504 0.00 0.16 0.00 0.00 0.00 0.84 0.00 0.00
#> TCGA.CJ.4897.11 1 0.4280 0.7612 0.72 0.00 0.00 0.00 0.00 0.10 0.06 0.12
#> TCGA.CJ.4923.11 2 0.5180 0.1939 0.00 0.58 0.00 0.26 0.00 0.02 0.02 0.12
#> TCGA.BP.5181.11 5 0.0000 0.8842 0.00 0.00 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.B0.5083.11 2 0.2114 0.7334 0.00 0.84 0.00 0.00 0.00 0.16 0.00 0.00
#> TCGA.CZ.4864.11 4 0.0000 0.5279 0.00 0.00 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.BP.5198.11 4 0.0471 0.5256 0.00 0.00 0.00 0.98 0.00 0.00 0.02 0.00
#> TCGA.B0.5099.11 5 0.0000 0.8842 0.00 0.00 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.BP.5169.11 4 0.3951 0.4525 0.00 0.08 0.00 0.76 0.00 0.02 0.02 0.12
#> TCGA.B0.5080.11 6 0.2114 0.9504 0.00 0.16 0.00 0.00 0.00 0.84 0.00 0.00
#> TCGA.B0.4699.11 8 0.4137 0.8815 0.00 0.00 0.00 0.46 0.00 0.02 0.02 0.50
#> TCGA.B0.5106.11 2 0.1765 0.7615 0.00 0.88 0.00 0.00 0.00 0.12 0.00 0.00
#> TCGA.B0.5402.11 4 0.0471 0.5256 0.00 0.00 0.00 0.98 0.00 0.00 0.02 0.00
#> TCGA.B0.5102.11 1 0.0000 0.8895 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.B0.4824.11 1 0.0000 0.8895 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.B0.5115.11 2 0.0000 0.7884 0.00 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.B0.4945.11 1 0.0000 0.8895 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.B0.4852.11 1 0.0000 0.8895 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.BP.5200.11 6 0.2267 0.9498 0.00 0.18 0.00 0.00 0.00 0.82 0.00 0.00
#> TCGA.B0.4811.11 4 0.0471 0.5256 0.00 0.00 0.00 0.98 0.00 0.00 0.02 0.00
#> TCGA.A3.3385.11 1 0.0000 0.8895 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.B0.5121.11 2 0.3272 0.1638 0.00 0.58 0.00 0.00 0.00 0.42 0.00 0.00
#> TCGA.B0.4815.11 4 0.0471 0.5259 0.00 0.00 0.00 0.98 0.00 0.00 0.02 0.00
#> TCGA.A3.3357.11 6 0.2406 0.9366 0.00 0.20 0.00 0.00 0.00 0.80 0.00 0.00
#> TCGA.CJ.4913.11 1 0.4280 0.7612 0.72 0.00 0.00 0.00 0.00 0.10 0.06 0.12
#> TCGA.BP.4993.11 2 0.1765 0.7629 0.00 0.88 0.00 0.00 0.00 0.12 0.00 0.00
#> TCGA.B0.4823.11 3 0.0000 0.6319 0.00 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.B0.4819.11 1 0.3586 0.7968 0.78 0.00 0.00 0.00 0.00 0.04 0.06 0.12
#> TCGA.BP.5168.11 4 0.0471 0.5256 0.00 0.00 0.00 0.98 0.00 0.00 0.02 0.00
#> TCGA.B0.5096.11 1 0.0000 0.8895 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.B0.5400.11 5 0.0000 0.8842 0.00 0.00 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.B0.4842.11 1 0.0000 0.8895 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.B0.5095.11 3 0.0000 0.6319 0.00 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.B0.4690.11 3 0.3095 0.5218 0.00 0.00 0.74 0.02 0.00 0.00 0.00 0.24
#> TCGA.BP.5199.11 2 0.2852 0.5823 0.00 0.72 0.00 0.00 0.00 0.28 0.00 0.00
#> TCGA.BP.4782.11 5 0.2071 0.8250 0.00 0.00 0.00 0.00 0.90 0.04 0.04 0.02
#> TCGA.B0.4693.11 1 0.4280 0.7612 0.72 0.00 0.00 0.00 0.00 0.10 0.06 0.12
#> TCGA.B0.5092.11 1 0.0000 0.8895 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.B0.4849.11 2 0.0000 0.7884 0.00 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.B0.4817.11 8 0.3329 0.9441 0.00 0.00 0.00 0.48 0.00 0.00 0.00 0.52
#> TCGA.BP.5176.11 1 0.0000 0.8895 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.BP.5190.11 2 0.0471 0.7860 0.00 0.98 0.00 0.00 0.00 0.00 0.00 0.02
#> TCGA.B0.4713.11 1 0.0471 0.8824 0.98 0.00 0.00 0.00 0.00 0.02 0.00 0.00
#> TCGA.CZ.5451.11 6 0.2650 0.9081 0.00 0.24 0.00 0.00 0.00 0.76 0.00 0.00
#> TCGA.B0.4814.11 2 0.1408 0.7642 0.00 0.94 0.00 0.00 0.00 0.02 0.02 0.02
#> TCGA.CJ.4869.11 2 0.1765 0.7615 0.00 0.88 0.00 0.00 0.00 0.12 0.00 0.00
#> TCGA.CJ.4907.11 2 0.1275 0.7666 0.00 0.94 0.00 0.00 0.00 0.02 0.00 0.04
#> TCGA.B0.5712.11 5 0.0000 0.8842 0.00 0.00 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.BP.4801.11 2 0.1947 0.7489 0.00 0.86 0.00 0.00 0.00 0.14 0.00 0.00
#> TCGA.B0.5110.11 1 0.0000 0.8895 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.CJ.4903.11 2 0.3015 0.4984 0.00 0.68 0.00 0.00 0.00 0.32 0.00 0.00
#> TCGA.B0.4714.11 8 0.3329 0.9441 0.00 0.00 0.00 0.48 0.00 0.00 0.00 0.52
#> TCGA.B0.4818.11 1 0.4280 0.7612 0.72 0.00 0.00 0.00 0.00 0.10 0.06 0.12
#> TCGA.BP.5189.11 2 0.0471 0.7860 0.00 0.98 0.00 0.00 0.00 0.00 0.00 0.02
#> TCGA.B0.5097.11 1 0.0000 0.8895 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.BP.4760.11 4 0.5097 0.2352 0.00 0.12 0.00 0.60 0.00 0.02 0.02 0.24
#> TCGA.B0.5120.11 1 0.4280 0.7612 0.72 0.00 0.00 0.00 0.00 0.10 0.06 0.12
#> TCGA.B0.4843.11 2 0.0941 0.7755 0.00 0.96 0.00 0.00 0.00 0.02 0.02 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: Node0141-leaf , Node0142-leaf , Node0143-leaf , Node0144-leaf , Node0211-leaf , Node0212-leaf , Node0213 , Node0231-leaf , Node0232-leaf , Node0233-leaf , Node0411 , Node0412-leaf , Node0413-leaf , Node0431-leaf , Node0432-leaf , Node0433-leaf , Node0511-leaf , Node0512-leaf , Node0541-leaf , Node0542-leaf , Node0543-leaf , Node0621-leaf , Node0622-leaf , Node0623-leaf .
The object with results only for a single top-value method and a single partitioning method can be extracted as:
res = res_rh["014"]
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 27 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 6.
#>
#> 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 0.999 0.4844 0.516 0.516
#> 3 3 0.908 0.968 0.977 0.2229 0.815 0.667
#> 4 4 1.000 0.974 0.986 0.0714 0.926 0.827
#> 5 5 0.860 0.914 0.973 0.0374 0.977 0.939
#> 6 6 0.903 0.900 0.961 0.1067 0.897 0.710
#> 7 7 0.867 0.806 0.847 0.0163 1.000 1.000
#> 8 8 0.877 0.695 0.895 0.0207 0.974 0.898
suggest_best_k() suggests the best \(k\) based on these statistics. The rules are as follows:
suggest_best_k(res)
#> [1] 6
#> attr(,"optional")
#> [1] 2 3 4
There is also optional best \(k\) = 2 3 4 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.B0.5094.11 1 0.000 1.000 1.00 0.00
#> TCGA.B0.5100.11 1 0.000 1.000 1.00 0.00
#> TCGA.B0.4696.11 2 0.000 0.998 0.00 1.00
#> TCGA.BP.5187.11 1 0.000 1.000 1.00 0.00
#> TCGA.B0.4841.11 2 0.000 0.998 0.00 1.00
#> TCGA.B0.4698.11 1 0.000 1.000 1.00 0.00
#> TCGA.B0.4848.11 2 0.000 0.998 0.00 1.00
#> TCGA.BP.5178.11 2 0.141 0.980 0.02 0.98
#> TCGA.BP.5191.11 2 0.000 0.998 0.00 1.00
#> TCGA.B0.4703.11 2 0.000 0.998 0.00 1.00
#> TCGA.CZ.5459.11 1 0.000 1.000 1.00 0.00
#> TCGA.CJ.4918.11 1 0.000 1.000 1.00 0.00
#> TCGA.A3.3367.11 1 0.000 1.000 1.00 0.00
#> TCGA.CZ.5466.11 1 0.000 1.000 1.00 0.00
#> TCGA.B0.4707.11 2 0.000 0.998 0.00 1.00
#> TCGA.CJ.4923.11 1 0.000 1.000 1.00 0.00
#> TCGA.CZ.4864.11 1 0.000 1.000 1.00 0.00
#> TCGA.BP.5198.11 1 0.000 1.000 1.00 0.00
#> TCGA.BP.5169.11 1 0.000 1.000 1.00 0.00
#> TCGA.B0.4699.11 2 0.000 0.998 0.00 1.00
#> TCGA.B0.5402.11 1 0.000 1.000 1.00 0.00
#> TCGA.B0.4811.11 1 0.000 1.000 1.00 0.00
#> TCGA.B0.4815.11 1 0.000 1.000 1.00 0.00
#> TCGA.BP.5168.11 1 0.000 1.000 1.00 0.00
#> TCGA.B0.4817.11 2 0.000 0.998 0.00 1.00
#> TCGA.B0.4714.11 2 0.000 0.998 0.00 1.00
#> TCGA.BP.4760.11 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.B0.5094.11 2 0.2959 0.904 0.00 0.90 0.10
#> TCGA.B0.5100.11 1 0.0000 0.999 1.00 0.00 0.00
#> TCGA.B0.4696.11 2 0.0892 0.949 0.00 0.98 0.02
#> TCGA.BP.5187.11 1 0.0000 0.999 1.00 0.00 0.00
#> TCGA.B0.4841.11 2 0.0000 0.943 0.00 1.00 0.00
#> TCGA.B0.4698.11 1 0.0000 0.999 1.00 0.00 0.00
#> TCGA.B0.4848.11 2 0.0892 0.949 0.00 0.98 0.02
#> TCGA.BP.5178.11 2 0.2959 0.904 0.00 0.90 0.10
#> TCGA.BP.5191.11 3 0.0000 0.888 0.00 0.00 1.00
#> TCGA.B0.4703.11 2 0.0892 0.949 0.00 0.98 0.02
#> TCGA.CZ.5459.11 1 0.0000 0.999 1.00 0.00 0.00
#> TCGA.CJ.4918.11 2 0.2959 0.904 0.00 0.90 0.10
#> TCGA.A3.3367.11 1 0.0892 0.979 0.98 0.02 0.00
#> TCGA.CZ.5466.11 1 0.0000 0.999 1.00 0.00 0.00
#> TCGA.B0.4707.11 2 0.0892 0.949 0.00 0.98 0.02
#> TCGA.CJ.4923.11 1 0.0000 0.999 1.00 0.00 0.00
#> TCGA.CZ.4864.11 1 0.0000 0.999 1.00 0.00 0.00
#> TCGA.BP.5198.11 1 0.0000 0.999 1.00 0.00 0.00
#> TCGA.BP.5169.11 1 0.0000 0.999 1.00 0.00 0.00
#> TCGA.B0.4699.11 3 0.2959 0.943 0.00 0.10 0.90
#> TCGA.B0.5402.11 1 0.0000 0.999 1.00 0.00 0.00
#> TCGA.B0.4811.11 1 0.0000 0.999 1.00 0.00 0.00
#> TCGA.B0.4815.11 1 0.0000 0.999 1.00 0.00 0.00
#> TCGA.BP.5168.11 1 0.0000 0.999 1.00 0.00 0.00
#> TCGA.B0.4817.11 3 0.2959 0.943 0.00 0.10 0.90
#> TCGA.B0.4714.11 2 0.0892 0.949 0.00 0.98 0.02
#> TCGA.BP.4760.11 1 0.0000 0.999 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.B0.5094.11 4 0.0000 1.000 0.0 0.00 0.00 1.00
#> TCGA.B0.5100.11 1 0.0000 0.993 1.0 0.00 0.00 0.00
#> TCGA.B0.4696.11 2 0.0000 0.954 0.0 1.00 0.00 0.00
#> TCGA.BP.5187.11 1 0.0000 0.993 1.0 0.00 0.00 0.00
#> TCGA.B0.4841.11 2 0.2011 0.913 0.0 0.92 0.00 0.08
#> TCGA.B0.4698.11 1 0.0000 0.993 1.0 0.00 0.00 0.00
#> TCGA.B0.4848.11 2 0.0707 0.958 0.0 0.98 0.00 0.02
#> TCGA.BP.5178.11 4 0.0000 1.000 0.0 0.00 0.00 1.00
#> TCGA.BP.5191.11 3 0.0000 0.980 0.0 0.00 1.00 0.00
#> TCGA.B0.4703.11 2 0.0000 0.954 0.0 1.00 0.00 0.00
#> TCGA.CZ.5459.11 1 0.0000 0.993 1.0 0.00 0.00 0.00
#> TCGA.CJ.4918.11 4 0.0000 1.000 0.0 0.00 0.00 1.00
#> TCGA.A3.3367.11 1 0.2345 0.887 0.9 0.00 0.00 0.10
#> TCGA.CZ.5466.11 1 0.0000 0.993 1.0 0.00 0.00 0.00
#> TCGA.B0.4707.11 2 0.0707 0.958 0.0 0.98 0.00 0.02
#> TCGA.CJ.4923.11 1 0.0000 0.993 1.0 0.00 0.00 0.00
#> TCGA.CZ.4864.11 1 0.0000 0.993 1.0 0.00 0.00 0.00
#> TCGA.BP.5198.11 1 0.0000 0.993 1.0 0.00 0.00 0.00
#> TCGA.BP.5169.11 1 0.0000 0.993 1.0 0.00 0.00 0.00
#> TCGA.B0.4699.11 3 0.0707 0.980 0.0 0.02 0.98 0.00
#> TCGA.B0.5402.11 1 0.0000 0.993 1.0 0.00 0.00 0.00
#> TCGA.B0.4811.11 1 0.0000 0.993 1.0 0.00 0.00 0.00
#> TCGA.B0.4815.11 1 0.0000 0.993 1.0 0.00 0.00 0.00
#> TCGA.BP.5168.11 1 0.0000 0.993 1.0 0.00 0.00 0.00
#> TCGA.B0.4817.11 2 0.2647 0.851 0.0 0.88 0.12 0.00
#> TCGA.B0.4714.11 2 0.0707 0.958 0.0 0.98 0.00 0.02
#> TCGA.BP.4760.11 1 0.0000 0.993 1.0 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.B0.5094.11 4 0.0000 1.000 0.00 0.00 0.00 1.00 0.00
#> TCGA.B0.5100.11 1 0.2616 0.889 0.88 0.00 0.02 0.00 0.10
#> TCGA.B0.4696.11 2 0.0000 0.982 0.00 1.00 0.00 0.00 0.00
#> TCGA.BP.5187.11 1 0.0000 0.973 1.00 0.00 0.00 0.00 0.00
#> TCGA.B0.4841.11 2 0.0609 0.968 0.00 0.98 0.00 0.02 0.00
#> TCGA.B0.4698.11 1 0.0000 0.973 1.00 0.00 0.00 0.00 0.00
#> TCGA.B0.4848.11 2 0.0000 0.982 0.00 1.00 0.00 0.00 0.00
#> TCGA.BP.5178.11 4 0.0000 1.000 0.00 0.00 0.00 1.00 0.00
#> TCGA.BP.5191.11 3 0.0609 0.000 0.00 0.00 0.98 0.00 0.02
#> TCGA.B0.4703.11 2 0.1410 0.931 0.00 0.94 0.00 0.00 0.06
#> TCGA.CZ.5459.11 1 0.0000 0.973 1.00 0.00 0.00 0.00 0.00
#> TCGA.CJ.4918.11 4 0.0000 1.000 0.00 0.00 0.00 1.00 0.00
#> TCGA.A3.3367.11 1 0.3209 0.871 0.86 0.00 0.02 0.02 0.10
#> TCGA.CZ.5466.11 1 0.0000 0.973 1.00 0.00 0.00 0.00 0.00
#> TCGA.B0.4707.11 2 0.0000 0.982 0.00 1.00 0.00 0.00 0.00
#> TCGA.CJ.4923.11 1 0.0000 0.973 1.00 0.00 0.00 0.00 0.00
#> TCGA.CZ.4864.11 1 0.0000 0.973 1.00 0.00 0.00 0.00 0.00
#> TCGA.BP.5198.11 1 0.0000 0.973 1.00 0.00 0.00 0.00 0.00
#> TCGA.BP.5169.11 1 0.0000 0.973 1.00 0.00 0.00 0.00 0.00
#> TCGA.B0.4699.11 5 0.2280 0.747 0.00 0.00 0.12 0.00 0.88
#> TCGA.B0.5402.11 1 0.0000 0.973 1.00 0.00 0.00 0.00 0.00
#> TCGA.B0.4811.11 1 0.0000 0.973 1.00 0.00 0.00 0.00 0.00
#> TCGA.B0.4815.11 1 0.0000 0.973 1.00 0.00 0.00 0.00 0.00
#> TCGA.BP.5168.11 1 0.0000 0.973 1.00 0.00 0.00 0.00 0.00
#> TCGA.B0.4817.11 5 0.2280 0.765 0.00 0.12 0.00 0.00 0.88
#> TCGA.B0.4714.11 2 0.0000 0.982 0.00 1.00 0.00 0.00 0.00
#> TCGA.BP.4760.11 1 0.2616 0.889 0.88 0.00 0.02 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.B0.5094.11 4 0.0547 0.970 0.00 0.00 0 0.98 0.00 0.02
#> TCGA.B0.5100.11 6 0.3309 0.702 0.28 0.00 0 0.00 0.00 0.72
#> TCGA.B0.4696.11 2 0.1092 0.950 0.00 0.96 0 0.00 0.02 0.02
#> TCGA.BP.5187.11 1 0.0000 1.000 1.00 0.00 0 0.00 0.00 0.00
#> TCGA.B0.4841.11 2 0.0937 0.950 0.00 0.96 0 0.00 0.00 0.04
#> TCGA.B0.4698.11 1 0.0000 1.000 1.00 0.00 0 0.00 0.00 0.00
#> TCGA.B0.4848.11 2 0.0547 0.959 0.00 0.98 0 0.00 0.00 0.02
#> TCGA.BP.5178.11 4 0.0547 0.972 0.00 0.00 0 0.98 0.00 0.02
#> TCGA.BP.5191.11 3 0.0000 0.000 0.00 0.00 1 0.00 0.00 0.00
#> TCGA.B0.4703.11 2 0.2190 0.908 0.00 0.90 0 0.00 0.06 0.04
#> TCGA.CZ.5459.11 1 0.0000 1.000 1.00 0.00 0 0.00 0.00 0.00
#> TCGA.CJ.4918.11 4 0.0000 0.979 0.00 0.00 0 1.00 0.00 0.00
#> TCGA.A3.3367.11 6 0.2512 0.416 0.06 0.00 0 0.06 0.00 0.88
#> TCGA.CZ.5466.11 1 0.0000 1.000 1.00 0.00 0 0.00 0.00 0.00
#> TCGA.B0.4707.11 2 0.0000 0.963 0.00 1.00 0 0.00 0.00 0.00
#> TCGA.CJ.4923.11 1 0.0000 1.000 1.00 0.00 0 0.00 0.00 0.00
#> TCGA.CZ.4864.11 1 0.0000 1.000 1.00 0.00 0 0.00 0.00 0.00
#> TCGA.BP.5198.11 1 0.0000 1.000 1.00 0.00 0 0.00 0.00 0.00
#> TCGA.BP.5169.11 1 0.0000 1.000 1.00 0.00 0 0.00 0.00 0.00
#> TCGA.B0.4699.11 5 0.0937 0.963 0.00 0.00 0 0.00 0.96 0.04
#> TCGA.B0.5402.11 1 0.0000 1.000 1.00 0.00 0 0.00 0.00 0.00
#> TCGA.B0.4811.11 1 0.0000 1.000 1.00 0.00 0 0.00 0.00 0.00
#> TCGA.B0.4815.11 1 0.0000 1.000 1.00 0.00 0 0.00 0.00 0.00
#> TCGA.BP.5168.11 1 0.0000 1.000 1.00 0.00 0 0.00 0.00 0.00
#> TCGA.B0.4817.11 5 0.0000 0.963 0.00 0.00 0 0.00 1.00 0.00
#> TCGA.B0.4714.11 2 0.0000 0.963 0.00 1.00 0 0.00 0.00 0.00
#> TCGA.BP.4760.11 6 0.3706 0.643 0.38 0.00 0 0.00 0.00 0.62
cbind(get_classes(res, k = 7), get_membership(res, k = 7))
#> class entropy silhouette p1 p2 p3 p4 p5 p6 p7
#> TCGA.B0.5094.11 4 0.0504 0.977 0.00 0.00 0.00 0.98 0.00 0.02 0
#> TCGA.B0.5100.11 6 0.3221 0.597 0.32 0.00 0.00 0.00 0.00 0.68 0
#> TCGA.B0.4696.11 2 0.3294 0.638 0.00 0.66 0.34 0.00 0.00 0.00 0
#> TCGA.BP.5187.11 1 0.0000 1.000 1.00 0.00 0.00 0.00 0.00 0.00 0
#> TCGA.B0.4841.11 2 0.2769 0.742 0.00 0.86 0.08 0.02 0.00 0.04 0
#> TCGA.B0.4698.11 1 0.0000 1.000 1.00 0.00 0.00 0.00 0.00 0.00 0
#> TCGA.B0.4848.11 2 0.1671 0.772 0.00 0.90 0.10 0.00 0.00 0.00 0
#> TCGA.BP.5178.11 4 0.0000 0.989 0.00 0.00 0.00 1.00 0.00 0.00 0
#> TCGA.BP.5191.11 7 0.0000 0.000 0.00 0.00 0.00 0.00 0.00 0.00 1
#> TCGA.B0.4703.11 2 0.3558 0.433 0.00 0.52 0.48 0.00 0.00 0.00 0
#> TCGA.CZ.5459.11 1 0.0000 1.000 1.00 0.00 0.00 0.00 0.00 0.00 0
#> TCGA.CJ.4918.11 4 0.0000 0.989 0.00 0.00 0.00 1.00 0.00 0.00 0
#> TCGA.A3.3367.11 6 0.0000 0.130 0.00 0.00 0.00 0.00 0.00 1.00 0
#> TCGA.CZ.5466.11 1 0.0000 1.000 1.00 0.00 0.00 0.00 0.00 0.00 0
#> TCGA.B0.4707.11 2 0.1166 0.781 0.00 0.94 0.06 0.00 0.00 0.00 0
#> TCGA.CJ.4923.11 1 0.0000 1.000 1.00 0.00 0.00 0.00 0.00 0.00 0
#> TCGA.CZ.4864.11 1 0.0000 1.000 1.00 0.00 0.00 0.00 0.00 0.00 0
#> TCGA.BP.5198.11 1 0.0000 1.000 1.00 0.00 0.00 0.00 0.00 0.00 0
#> TCGA.BP.5169.11 1 0.0000 1.000 1.00 0.00 0.00 0.00 0.00 0.00 0
#> TCGA.B0.4699.11 5 0.0000 0.707 0.00 0.00 0.00 0.00 1.00 0.00 0
#> TCGA.B0.5402.11 1 0.0000 1.000 1.00 0.00 0.00 0.00 0.00 0.00 0
#> TCGA.B0.4811.11 1 0.0000 1.000 1.00 0.00 0.00 0.00 0.00 0.00 0
#> TCGA.B0.4815.11 1 0.0000 1.000 1.00 0.00 0.00 0.00 0.00 0.00 0
#> TCGA.BP.5168.11 1 0.0000 1.000 1.00 0.00 0.00 0.00 0.00 0.00 0
#> TCGA.B0.4817.11 5 0.3221 0.707 0.00 0.00 0.32 0.00 0.68 0.00 0
#> TCGA.B0.4714.11 2 0.0504 0.786 0.00 0.98 0.02 0.00 0.00 0.00 0
#> TCGA.BP.4760.11 6 0.3525 0.510 0.44 0.00 0.00 0.00 0.00 0.56 0
cbind(get_classes(res, k = 8), get_membership(res, k = 8))
#> class entropy silhouette p1 p2 p3 p4 p5 p6 p7 p8
#> TCGA.B0.5094.11 4 0.0471 0.962 0.00 0.02 0.00 0.98 0.00 0.00 0 0.00
#> TCGA.B0.5100.11 6 0.2534 0.649 0.22 0.00 0.00 0.00 0.00 0.78 0 0.00
#> TCGA.B0.4696.11 8 0.5605 0.122 0.00 0.18 0.04 0.00 0.34 0.00 0 0.44
#> TCGA.BP.5187.11 1 0.0000 0.998 1.00 0.00 0.00 0.00 0.00 0.00 0 0.00
#> TCGA.B0.4841.11 2 0.0941 0.559 0.00 0.96 0.00 0.00 0.00 0.02 0 0.02
#> TCGA.B0.4698.11 1 0.0000 0.998 1.00 0.00 0.00 0.00 0.00 0.00 0 0.00
#> TCGA.B0.4848.11 2 0.4672 0.428 0.00 0.62 0.02 0.00 0.12 0.00 0 0.24
#> TCGA.BP.5178.11 4 0.0471 0.962 0.00 0.00 0.00 0.98 0.00 0.00 0 0.02
#> TCGA.BP.5191.11 7 0.0000 0.000 0.00 0.00 0.00 0.00 0.00 0.00 1 0.00
#> TCGA.B0.4703.11 8 0.2888 0.199 0.00 0.16 0.04 0.00 0.00 0.00 0 0.80
#> TCGA.CZ.5459.11 1 0.0000 0.998 1.00 0.00 0.00 0.00 0.00 0.00 0 0.00
#> TCGA.CJ.4918.11 4 0.0808 0.955 0.00 0.00 0.00 0.96 0.00 0.00 0 0.04
#> TCGA.A3.3367.11 6 0.0471 0.393 0.02 0.00 0.00 0.00 0.00 0.98 0 0.00
#> TCGA.CZ.5466.11 1 0.0000 0.998 1.00 0.00 0.00 0.00 0.00 0.00 0 0.00
#> TCGA.B0.4707.11 2 0.3404 0.486 0.00 0.72 0.00 0.00 0.04 0.00 0 0.24
#> TCGA.CJ.4923.11 1 0.0000 0.998 1.00 0.00 0.00 0.00 0.00 0.00 0 0.00
#> TCGA.CZ.4864.11 1 0.0000 0.998 1.00 0.00 0.00 0.00 0.00 0.00 0 0.00
#> TCGA.BP.5198.11 1 0.0000 0.998 1.00 0.00 0.00 0.00 0.00 0.00 0 0.00
#> TCGA.BP.5169.11 1 0.0471 0.973 0.98 0.00 0.00 0.00 0.00 0.02 0 0.00
#> TCGA.B0.4699.11 5 0.3237 0.000 0.00 0.00 0.40 0.00 0.60 0.00 0 0.00
#> TCGA.B0.5402.11 1 0.0000 0.998 1.00 0.00 0.00 0.00 0.00 0.00 0 0.00
#> TCGA.B0.4811.11 1 0.0000 0.998 1.00 0.00 0.00 0.00 0.00 0.00 0 0.00
#> TCGA.B0.4815.11 1 0.0000 0.998 1.00 0.00 0.00 0.00 0.00 0.00 0 0.00
#> TCGA.BP.5168.11 1 0.0000 0.998 1.00 0.00 0.00 0.00 0.00 0.00 0 0.00
#> TCGA.B0.4817.11 3 0.0000 0.000 0.00 0.00 1.00 0.00 0.00 0.00 0 0.00
#> TCGA.B0.4714.11 2 0.3830 0.542 0.00 0.74 0.00 0.00 0.08 0.02 0 0.16
#> TCGA.BP.4760.11 6 0.3193 0.554 0.38 0.00 0.00 0.00 0.00 0.62 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: Node0. Child nodes: Node011-leaf , Node012-leaf , Node013-leaf , Node014 , Node021 , Node022-leaf , Node023 , Node041 , Node042-leaf , Node043 , Node051 , Node052-leaf , Node053-leaf , Node054 , Node061-leaf , Node062 , Node063-leaf , Node071-leaf , Node072-leaf , Node073-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 112 columns.
#> Top rows (1000) are extracted by 'SD' 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 0.496 0.904 0.897 0.4661 0.501 0.501
#> 3 3 1.000 0.986 0.996 0.3893 0.813 0.641
#> 4 4 0.733 0.782 0.866 0.1417 0.883 0.677
#> 5 5 0.733 0.739 0.854 0.0626 0.935 0.755
#> 6 6 0.706 0.663 0.801 0.0210 0.972 0.872
#> 7 7 0.681 0.593 0.748 0.0265 0.958 0.812
#> 8 8 0.684 0.392 0.711 0.0167 0.976 0.882
suggest_best_k() suggests the best \(k\) based on these statistics. The rules are as follows:
suggest_best_k(res)
#> [1] 3
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.B0.5113.01 2 0.722 0.805 0.20 0.80
#> TCGA.MM.A564.01 1 0.722 0.956 0.80 0.20
#> TCGA.AK.3434.01 2 0.000 0.930 0.00 1.00
#> TCGA.B0.4707.01 1 0.722 0.956 0.80 0.20
#> TCGA.CZ.5456.01 1 0.722 0.956 0.80 0.20
#> TCGA.CZ.5452.01 1 0.722 0.956 0.80 0.20
#> TCGA.BP.5201.01 2 0.000 0.930 0.00 1.00
#> TCGA.CJ.5677.01 1 0.000 0.786 1.00 0.00
#> TCGA.AK.3425.01 1 0.722 0.956 0.80 0.20
#> TCGA.BP.5180.01 1 0.855 0.859 0.72 0.28
#> TCGA.CZ.5984.01 1 0.722 0.956 0.80 0.20
#> TCGA.BP.5190.01 2 0.000 0.930 0.00 1.00
#> TCGA.B0.4713.01 1 0.000 0.786 1.00 0.00
#> TCGA.B0.4841.01 2 0.000 0.930 0.00 1.00
#> TCGA.B0.5699.01 2 0.000 0.930 0.00 1.00
#> TCGA.BP.5202.01 2 0.000 0.930 0.00 1.00
#> TCGA.B0.4814.01 2 0.000 0.930 0.00 1.00
#> TCGA.B0.4821.01 1 0.000 0.786 1.00 0.00
#> TCGA.B0.5712.01 2 0.722 0.805 0.20 0.80
#> TCGA.CJ.4920.01 2 0.722 0.805 0.20 0.80
#> TCGA.DV.A4W0.01 2 0.000 0.930 0.00 1.00
#> TCGA.CJ.4903.01 2 0.000 0.930 0.00 1.00
#> TCGA.CJ.4912.01 1 0.722 0.956 0.80 0.20
#> TCGA.B0.4845.01 2 0.000 0.930 0.00 1.00
#> TCGA.B8.A54D.01 2 0.000 0.930 0.00 1.00
#> TCGA.B0.5692.01 2 0.722 0.805 0.20 0.80
#> TCGA.B0.5106.01 1 0.760 0.935 0.78 0.22
#> TCGA.B0.4827.01 1 0.000 0.786 1.00 0.00
#> TCGA.B0.5115.01 2 0.000 0.930 0.00 1.00
#> TCGA.B0.4706.01 2 0.000 0.930 0.00 1.00
#> TCGA.B8.A54I.01 1 0.722 0.956 0.80 0.20
#> TCGA.CZ.5463.01 2 0.000 0.930 0.00 1.00
#> TCGA.G6.A5PC.01 2 0.722 0.805 0.20 0.80
#> TCGA.B0.4696.01 1 0.722 0.956 0.80 0.20
#> TCGA.CZ.5469.01 1 0.722 0.956 0.80 0.20
#> TCGA.B2.5641.01 1 0.722 0.956 0.80 0.20
#> TCGA.CZ.5460.01 2 0.000 0.930 0.00 1.00
#> TCGA.B0.4712.01 1 0.722 0.956 0.80 0.20
#> TCGA.CW.5590.01 2 0.000 0.930 0.00 1.00
#> TCGA.B0.5698.01 2 0.000 0.930 0.00 1.00
#> TCGA.CW.5580.01 2 0.722 0.805 0.20 0.80
#> TCGA.CZ.5454.01 2 0.000 0.930 0.00 1.00
#> TCGA.B0.4815.01 1 0.722 0.956 0.80 0.20
#> TCGA.B0.5694.01 2 0.000 0.930 0.00 1.00
#> TCGA.A3.3357.01 2 0.000 0.930 0.00 1.00
#> TCGA.B8.4622.01 2 0.000 0.930 0.00 1.00
#> TCGA.CJ.4913.01 2 0.722 0.805 0.20 0.80
#> TCGA.CJ.6033.01 1 0.000 0.786 1.00 0.00
#> TCGA.B0.4698.01 1 0.722 0.956 0.80 0.20
#> TCGA.B0.4688.01 1 0.722 0.956 0.80 0.20
#> TCGA.B0.5096.01 1 0.000 0.786 1.00 0.00
#> TCGA.BP.5178.01 1 0.722 0.956 0.80 0.20
#> TCGA.B0.4847.01 2 0.000 0.930 0.00 1.00
#> TCGA.B0.5107.01 1 0.000 0.786 1.00 0.00
#> TCGA.CW.5584.01 2 0.000 0.930 0.00 1.00
#> TCGA.BP.5199.01 2 0.000 0.930 0.00 1.00
#> TCGA.CJ.4901.01 1 0.722 0.956 0.80 0.20
#> TCGA.CW.6090.01 2 0.000 0.930 0.00 1.00
#> TCGA.CZ.4866.01 2 0.722 0.805 0.20 0.80
#> TCGA.B0.4828.01 2 0.000 0.930 0.00 1.00
#> TCGA.MM.A563.01 2 0.000 0.930 0.00 1.00
#> TCGA.AK.3458.01 2 0.000 0.930 0.00 1.00
#> TCGA.CJ.5676.01 1 0.722 0.956 0.80 0.20
#> TCGA.B0.4693.01 2 0.722 0.805 0.20 0.80
#> TCGA.B0.4710.01 2 0.722 0.805 0.20 0.80
#> TCGA.CZ.5465.01 2 0.722 0.805 0.20 0.80
#> TCGA.CJ.5675.01 2 0.000 0.930 0.00 1.00
#> TCGA.B8.5158.01 1 0.722 0.956 0.80 0.20
#> TCGA.CJ.6030.01 1 0.722 0.956 0.80 0.20
#> TCGA.B8.5159.01 2 0.722 0.805 0.20 0.80
#> TCGA.B0.5706.01 1 0.722 0.956 0.80 0.20
#> TCGA.A3.3367.01 2 0.000 0.930 0.00 1.00
#> TCGA.DV.A4VX.01 2 0.943 0.166 0.36 0.64
#> TCGA.EU.5907.01 2 0.000 0.930 0.00 1.00
#> TCGA.CJ.5678.01 2 0.000 0.930 0.00 1.00
#> TCGA.B8.4153.01 2 0.000 0.930 0.00 1.00
#> TCGA.BP.5183.01 2 0.000 0.930 0.00 1.00
#> TCGA.AK.3445.01 1 0.722 0.956 0.80 0.20
#> TCGA.BP.5196.01 1 0.722 0.956 0.80 0.20
#> TCGA.B0.4714.01 2 0.000 0.930 0.00 1.00
#> TCGA.B8.5549.01 2 0.000 0.930 0.00 1.00
#> TCGA.CZ.5461.01 1 0.722 0.956 0.80 0.20
#> TCGA.B0.5710.01 2 0.000 0.930 0.00 1.00
#> TCGA.B0.4718.01 2 0.000 0.930 0.00 1.00
#> TCGA.BP.5175.01 1 0.722 0.956 0.80 0.20
#> TCGA.CZ.5987.01 1 0.722 0.956 0.80 0.20
#> TCGA.BP.5198.01 1 0.722 0.956 0.80 0.20
#> TCGA.B0.5094.01 1 0.722 0.956 0.80 0.20
#> TCGA.CZ.5468.01 1 0.722 0.956 0.80 0.20
#> TCGA.BP.5169.01 1 0.722 0.956 0.80 0.20
#> TCGA.CJ.5680.01 2 0.722 0.805 0.20 0.80
#> TCGA.CZ.5470.01 2 0.881 0.728 0.30 0.70
#> TCGA.B0.4844.01 1 0.722 0.956 0.80 0.20
#> TCGA.CZ.5464.01 1 0.722 0.956 0.80 0.20
#> TCGA.B0.5701.01 1 0.722 0.956 0.80 0.20
#> TCGA.CJ.5671.01 1 0.722 0.956 0.80 0.20
#> TCGA.B0.5116.01 2 0.000 0.930 0.00 1.00
#> TCGA.CJ.5679.01 1 0.722 0.956 0.80 0.20
#> TCGA.CJ.5682.01 2 0.000 0.930 0.00 1.00
#> TCGA.G6.A8L8.01 2 0.722 0.805 0.20 0.80
#> TCGA.B0.4691.01 1 0.722 0.956 0.80 0.20
#> TCGA.CZ.4853.01 2 0.000 0.930 0.00 1.00
#> TCGA.B0.5402.01 2 0.000 0.930 0.00 1.00
#> TCGA.B0.4813.01 2 0.000 0.930 0.00 1.00
#> TCGA.G6.A8L7.01 1 0.000 0.786 1.00 0.00
#> TCGA.B0.4848.01 1 0.722 0.956 0.80 0.20
#> TCGA.CZ.5985.01 1 0.722 0.956 0.80 0.20
#> TCGA.B0.5121.01 2 0.000 0.930 0.00 1.00
#> TCGA.BP.5191.01 1 0.722 0.956 0.80 0.20
#> TCGA.B0.4810.01 2 0.000 0.930 0.00 1.00
#> TCGA.AK.3428.01 2 0.000 0.930 0.00 1.00
#> TCGA.CJ.6027.01 1 0.722 0.956 0.80 0.20
cbind(get_classes(res, k = 3), get_membership(res, k = 3))
#> class entropy silhouette p1 p2 p3
#> TCGA.B0.5113.01 3 0.0000 1.0000 0.00 0.00 1
#> TCGA.MM.A564.01 1 0.0000 0.9994 1.00 0.00 0
#> TCGA.AK.3434.01 2 0.0000 0.9882 0.00 1.00 0
#> TCGA.B0.4707.01 1 0.0000 0.9994 1.00 0.00 0
#> TCGA.CZ.5456.01 1 0.0000 0.9994 1.00 0.00 0
#> TCGA.CZ.5452.01 1 0.0000 0.9994 1.00 0.00 0
#> TCGA.BP.5201.01 2 0.0000 0.9882 0.00 1.00 0
#> TCGA.CJ.5677.01 3 0.0000 1.0000 0.00 0.00 1
#> TCGA.AK.3425.01 1 0.0000 0.9994 1.00 0.00 0
#> TCGA.BP.5180.01 1 0.0892 0.9763 0.98 0.02 0
#> TCGA.CZ.5984.01 1 0.0000 0.9994 1.00 0.00 0
#> TCGA.BP.5190.01 2 0.0000 0.9882 0.00 1.00 0
#> TCGA.B0.4713.01 3 0.0000 1.0000 0.00 0.00 1
#> TCGA.B0.4841.01 2 0.0000 0.9882 0.00 1.00 0
#> TCGA.B0.5699.01 2 0.0000 0.9882 0.00 1.00 0
#> TCGA.BP.5202.01 2 0.0000 0.9882 0.00 1.00 0
#> TCGA.B0.4814.01 2 0.0000 0.9882 0.00 1.00 0
#> TCGA.B0.4821.01 3 0.0000 1.0000 0.00 0.00 1
#> TCGA.B0.5712.01 3 0.0000 1.0000 0.00 0.00 1
#> TCGA.CJ.4920.01 3 0.0000 1.0000 0.00 0.00 1
#> TCGA.DV.A4W0.01 2 0.0000 0.9882 0.00 1.00 0
#> TCGA.CJ.4903.01 2 0.0000 0.9882 0.00 1.00 0
#> TCGA.CJ.4912.01 1 0.0000 0.9994 1.00 0.00 0
#> TCGA.B0.4845.01 2 0.0000 0.9882 0.00 1.00 0
#> TCGA.B8.A54D.01 2 0.0000 0.9882 0.00 1.00 0
#> TCGA.B0.5692.01 3 0.0000 1.0000 0.00 0.00 1
#> TCGA.B0.5106.01 1 0.0000 0.9994 1.00 0.00 0
#> TCGA.B0.4827.01 3 0.0000 1.0000 0.00 0.00 1
#> TCGA.B0.5115.01 2 0.0000 0.9882 0.00 1.00 0
#> TCGA.B0.4706.01 2 0.0000 0.9882 0.00 1.00 0
#> TCGA.B8.A54I.01 1 0.0000 0.9994 1.00 0.00 0
#> TCGA.CZ.5463.01 2 0.0000 0.9882 0.00 1.00 0
#> TCGA.G6.A5PC.01 3 0.0000 1.0000 0.00 0.00 1
#> TCGA.B0.4696.01 1 0.0000 0.9994 1.00 0.00 0
#> TCGA.CZ.5469.01 1 0.0000 0.9994 1.00 0.00 0
#> TCGA.B2.5641.01 1 0.0000 0.9994 1.00 0.00 0
#> TCGA.CZ.5460.01 2 0.0000 0.9882 0.00 1.00 0
#> TCGA.B0.4712.01 1 0.0000 0.9994 1.00 0.00 0
#> TCGA.CW.5590.01 2 0.0000 0.9882 0.00 1.00 0
#> TCGA.B0.5698.01 2 0.0000 0.9882 0.00 1.00 0
#> TCGA.CW.5580.01 3 0.0000 1.0000 0.00 0.00 1
#> TCGA.CZ.5454.01 2 0.0000 0.9882 0.00 1.00 0
#> TCGA.B0.4815.01 1 0.0000 0.9994 1.00 0.00 0
#> TCGA.B0.5694.01 2 0.0000 0.9882 0.00 1.00 0
#> TCGA.A3.3357.01 2 0.0000 0.9882 0.00 1.00 0
#> TCGA.B8.4622.01 2 0.0000 0.9882 0.00 1.00 0
#> TCGA.CJ.4913.01 3 0.0000 1.0000 0.00 0.00 1
#> TCGA.CJ.6033.01 3 0.0000 1.0000 0.00 0.00 1
#> TCGA.B0.4698.01 1 0.0000 0.9994 1.00 0.00 0
#> TCGA.B0.4688.01 1 0.0000 0.9994 1.00 0.00 0
#> TCGA.B0.5096.01 3 0.0000 1.0000 0.00 0.00 1
#> TCGA.BP.5178.01 1 0.0000 0.9994 1.00 0.00 0
#> TCGA.B0.4847.01 2 0.0000 0.9882 0.00 1.00 0
#> TCGA.B0.5107.01 3 0.0000 1.0000 0.00 0.00 1
#> TCGA.CW.5584.01 2 0.0000 0.9882 0.00 1.00 0
#> TCGA.BP.5199.01 2 0.0000 0.9882 0.00 1.00 0
#> TCGA.CJ.4901.01 1 0.0000 0.9994 1.00 0.00 0
#> TCGA.CW.6090.01 2 0.0000 0.9882 0.00 1.00 0
#> TCGA.CZ.4866.01 3 0.0000 1.0000 0.00 0.00 1
#> TCGA.B0.4828.01 2 0.0000 0.9882 0.00 1.00 0
#> TCGA.MM.A563.01 2 0.0000 0.9882 0.00 1.00 0
#> TCGA.AK.3458.01 2 0.0000 0.9882 0.00 1.00 0
#> TCGA.CJ.5676.01 1 0.0000 0.9994 1.00 0.00 0
#> TCGA.B0.4693.01 3 0.0000 1.0000 0.00 0.00 1
#> TCGA.B0.4710.01 3 0.0000 1.0000 0.00 0.00 1
#> TCGA.CZ.5465.01 3 0.0000 1.0000 0.00 0.00 1
#> TCGA.CJ.5675.01 2 0.0000 0.9882 0.00 1.00 0
#> TCGA.B8.5158.01 1 0.0000 0.9994 1.00 0.00 0
#> TCGA.CJ.6030.01 1 0.0000 0.9994 1.00 0.00 0
#> TCGA.B8.5159.01 3 0.0000 1.0000 0.00 0.00 1
#> TCGA.B0.5706.01 1 0.0000 0.9994 1.00 0.00 0
#> TCGA.A3.3367.01 2 0.0000 0.9882 0.00 1.00 0
#> TCGA.DV.A4VX.01 2 0.6302 0.0753 0.48 0.52 0
#> TCGA.EU.5907.01 2 0.0000 0.9882 0.00 1.00 0
#> TCGA.CJ.5678.01 2 0.0000 0.9882 0.00 1.00 0
#> TCGA.B8.4153.01 2 0.0000 0.9882 0.00 1.00 0
#> TCGA.BP.5183.01 2 0.0000 0.9882 0.00 1.00 0
#> TCGA.AK.3445.01 1 0.0000 0.9994 1.00 0.00 0
#> TCGA.BP.5196.01 1 0.0000 0.9994 1.00 0.00 0
#> TCGA.B0.4714.01 2 0.0000 0.9882 0.00 1.00 0
#> TCGA.B8.5549.01 2 0.0000 0.9882 0.00 1.00 0
#> TCGA.CZ.5461.01 1 0.0000 0.9994 1.00 0.00 0
#> TCGA.B0.5710.01 2 0.0000 0.9882 0.00 1.00 0
#> TCGA.B0.4718.01 2 0.0000 0.9882 0.00 1.00 0
#> TCGA.BP.5175.01 1 0.0000 0.9994 1.00 0.00 0
#> TCGA.CZ.5987.01 1 0.0000 0.9994 1.00 0.00 0
#> TCGA.BP.5198.01 1 0.0000 0.9994 1.00 0.00 0
#> TCGA.B0.5094.01 1 0.0000 0.9994 1.00 0.00 0
#> TCGA.CZ.5468.01 1 0.0000 0.9994 1.00 0.00 0
#> TCGA.BP.5169.01 1 0.0000 0.9994 1.00 0.00 0
#> TCGA.CJ.5680.01 3 0.0000 1.0000 0.00 0.00 1
#> TCGA.CZ.5470.01 3 0.0000 1.0000 0.00 0.00 1
#> TCGA.B0.4844.01 1 0.0000 0.9994 1.00 0.00 0
#> TCGA.CZ.5464.01 1 0.0000 0.9994 1.00 0.00 0
#> TCGA.B0.5701.01 1 0.0000 0.9994 1.00 0.00 0
#> TCGA.CJ.5671.01 1 0.0000 0.9994 1.00 0.00 0
#> TCGA.B0.5116.01 2 0.0000 0.9882 0.00 1.00 0
#> TCGA.CJ.5679.01 1 0.0000 0.9994 1.00 0.00 0
#> TCGA.CJ.5682.01 2 0.0000 0.9882 0.00 1.00 0
#> TCGA.G6.A8L8.01 3 0.0000 1.0000 0.00 0.00 1
#> TCGA.B0.4691.01 1 0.0000 0.9994 1.00 0.00 0
#> TCGA.CZ.4853.01 2 0.0000 0.9882 0.00 1.00 0
#> TCGA.B0.5402.01 2 0.0000 0.9882 0.00 1.00 0
#> TCGA.B0.4813.01 2 0.0000 0.9882 0.00 1.00 0
#> TCGA.G6.A8L7.01 3 0.0000 1.0000 0.00 0.00 1
#> TCGA.B0.4848.01 1 0.0000 0.9994 1.00 0.00 0
#> TCGA.CZ.5985.01 1 0.0000 0.9994 1.00 0.00 0
#> TCGA.B0.5121.01 2 0.0000 0.9882 0.00 1.00 0
#> TCGA.BP.5191.01 1 0.0000 0.9994 1.00 0.00 0
#> TCGA.B0.4810.01 2 0.0000 0.9882 0.00 1.00 0
#> TCGA.AK.3428.01 2 0.0000 0.9882 0.00 1.00 0
#> TCGA.CJ.6027.01 1 0.0000 0.9994 1.00 0.00 0
cbind(get_classes(res, k = 4), get_membership(res, k = 4))
#> class entropy silhouette p1 p2 p3 p4
#> TCGA.B0.5113.01 3 0.0000 1.0000 0.00 0.00 1 0.00
#> TCGA.MM.A564.01 4 0.4277 0.6768 0.28 0.00 0 0.72
#> TCGA.AK.3434.01 2 0.4713 0.2585 0.00 0.64 0 0.36
#> TCGA.B0.4707.01 1 0.0000 0.8762 1.00 0.00 0 0.00
#> TCGA.CZ.5456.01 1 0.0000 0.8762 1.00 0.00 0 0.00
#> TCGA.CZ.5452.01 1 0.4522 0.7712 0.68 0.00 0 0.32
#> TCGA.BP.5201.01 2 0.0000 0.8082 0.00 1.00 0 0.00
#> TCGA.CJ.5677.01 3 0.0000 1.0000 0.00 0.00 1 0.00
#> TCGA.AK.3425.01 1 0.1637 0.8678 0.94 0.00 0 0.06
#> TCGA.BP.5180.01 1 0.7427 0.5532 0.50 0.20 0 0.30
#> TCGA.CZ.5984.01 1 0.5173 0.7569 0.66 0.02 0 0.32
#> TCGA.BP.5190.01 2 0.0000 0.8082 0.00 1.00 0 0.00
#> TCGA.B0.4713.01 3 0.0000 1.0000 0.00 0.00 1 0.00
#> TCGA.B0.4841.01 2 0.0000 0.8082 0.00 1.00 0 0.00
#> TCGA.B0.5699.01 2 0.4713 0.2488 0.00 0.64 0 0.36
#> TCGA.BP.5202.01 2 0.0000 0.8082 0.00 1.00 0 0.00
#> TCGA.B0.4814.01 2 0.4522 0.3707 0.00 0.68 0 0.32
#> TCGA.B0.4821.01 3 0.0000 1.0000 0.00 0.00 1 0.00
#> TCGA.B0.5712.01 3 0.0000 1.0000 0.00 0.00 1 0.00
#> TCGA.CJ.4920.01 3 0.0000 1.0000 0.00 0.00 1 0.00
#> TCGA.DV.A4W0.01 4 0.4994 0.3422 0.00 0.48 0 0.52
#> TCGA.CJ.4903.01 2 0.0000 0.8082 0.00 1.00 0 0.00
#> TCGA.CJ.4912.01 1 0.1637 0.8627 0.94 0.00 0 0.06
#> TCGA.B0.4845.01 2 0.4907 0.0241 0.00 0.58 0 0.42
#> TCGA.B8.A54D.01 2 0.3400 0.6702 0.00 0.82 0 0.18
#> TCGA.B0.5692.01 3 0.0000 1.0000 0.00 0.00 1 0.00
#> TCGA.B0.5106.01 1 0.6570 0.6815 0.58 0.10 0 0.32
#> TCGA.B0.4827.01 3 0.0000 1.0000 0.00 0.00 1 0.00
#> TCGA.B0.5115.01 2 0.0000 0.8082 0.00 1.00 0 0.00
#> TCGA.B0.4706.01 2 0.0000 0.8082 0.00 1.00 0 0.00
#> TCGA.B8.A54I.01 1 0.4134 0.8047 0.74 0.00 0 0.26
#> TCGA.CZ.5463.01 2 0.1211 0.7888 0.00 0.96 0 0.04
#> TCGA.G6.A5PC.01 3 0.0000 1.0000 0.00 0.00 1 0.00
#> TCGA.B0.4696.01 1 0.2647 0.8521 0.88 0.00 0 0.12
#> TCGA.CZ.5469.01 1 0.0000 0.8762 1.00 0.00 0 0.00
#> TCGA.B2.5641.01 1 0.4406 0.7840 0.70 0.00 0 0.30
#> TCGA.CZ.5460.01 4 0.4855 0.5333 0.00 0.40 0 0.60
#> TCGA.B0.4712.01 1 0.0000 0.8762 1.00 0.00 0 0.00
#> TCGA.CW.5590.01 4 0.6049 0.7642 0.12 0.20 0 0.68
#> TCGA.B0.5698.01 2 0.0000 0.8082 0.00 1.00 0 0.00
#> TCGA.CW.5580.01 3 0.0000 1.0000 0.00 0.00 1 0.00
#> TCGA.CZ.5454.01 2 0.0000 0.8082 0.00 1.00 0 0.00
#> TCGA.B0.4815.01 1 0.0000 0.8762 1.00 0.00 0 0.00
#> TCGA.B0.5694.01 4 0.5902 0.7729 0.14 0.16 0 0.70
#> TCGA.A3.3357.01 4 0.6122 0.7748 0.16 0.16 0 0.68
#> TCGA.B8.4622.01 4 0.6104 0.7744 0.14 0.18 0 0.68
#> TCGA.CJ.4913.01 3 0.0000 1.0000 0.00 0.00 1 0.00
#> TCGA.CJ.6033.01 3 0.0000 1.0000 0.00 0.00 1 0.00
#> TCGA.B0.4698.01 1 0.2647 0.8521 0.88 0.00 0 0.12
#> TCGA.B0.4688.01 1 0.1637 0.8682 0.94 0.00 0 0.06
#> TCGA.B0.5096.01 3 0.0000 1.0000 0.00 0.00 1 0.00
#> TCGA.BP.5178.01 1 0.0000 0.8762 1.00 0.00 0 0.00
#> TCGA.B0.4847.01 2 0.4907 0.0302 0.00 0.58 0 0.42
#> TCGA.B0.5107.01 3 0.0000 1.0000 0.00 0.00 1 0.00
#> TCGA.CW.5584.01 4 0.4855 0.5319 0.00 0.40 0 0.60
#> TCGA.BP.5199.01 2 0.1211 0.7898 0.00 0.96 0 0.04
#> TCGA.CJ.4901.01 1 0.2647 0.8521 0.88 0.00 0 0.12
#> TCGA.CW.6090.01 4 0.6122 0.7757 0.16 0.16 0 0.68
#> TCGA.CZ.4866.01 3 0.0000 1.0000 0.00 0.00 1 0.00
#> TCGA.B0.4828.01 4 0.4522 0.6465 0.00 0.32 0 0.68
#> TCGA.MM.A563.01 2 0.2345 0.7449 0.00 0.90 0 0.10
#> TCGA.AK.3458.01 2 0.0000 0.8082 0.00 1.00 0 0.00
#> TCGA.CJ.5676.01 4 0.4406 0.6766 0.30 0.00 0 0.70
#> TCGA.B0.4693.01 3 0.0000 1.0000 0.00 0.00 1 0.00
#> TCGA.B0.4710.01 3 0.0000 1.0000 0.00 0.00 1 0.00
#> TCGA.CZ.5465.01 3 0.0000 1.0000 0.00 0.00 1 0.00
#> TCGA.CJ.5675.01 4 0.6122 0.7757 0.16 0.16 0 0.68
#> TCGA.B8.5158.01 1 0.0000 0.8762 1.00 0.00 0 0.00
#> TCGA.CJ.6030.01 1 0.0000 0.8762 1.00 0.00 0 0.00
#> TCGA.B8.5159.01 3 0.0000 1.0000 0.00 0.00 1 0.00
#> TCGA.B0.5706.01 1 0.4406 0.7840 0.70 0.00 0 0.30
#> TCGA.A3.3367.01 2 0.4790 0.1948 0.00 0.62 0 0.38
#> TCGA.DV.A4VX.01 4 0.5962 0.7226 0.26 0.08 0 0.66
#> TCGA.EU.5907.01 2 0.0000 0.8082 0.00 1.00 0 0.00
#> TCGA.CJ.5678.01 4 0.5962 0.7198 0.08 0.26 0 0.66
#> TCGA.B8.4153.01 4 0.4948 0.4467 0.00 0.44 0 0.56
#> TCGA.BP.5183.01 2 0.0707 0.7983 0.00 0.98 0 0.02
#> TCGA.AK.3445.01 1 0.0000 0.8762 1.00 0.00 0 0.00
#> TCGA.BP.5196.01 1 0.4277 0.7952 0.72 0.00 0 0.28
#> TCGA.B0.4714.01 2 0.3801 0.5753 0.00 0.78 0 0.22
#> TCGA.B8.5549.01 2 0.4134 0.5856 0.00 0.74 0 0.26
#> TCGA.CZ.5461.01 4 0.4522 0.6722 0.32 0.00 0 0.68
#> TCGA.B0.5710.01 2 0.0707 0.7993 0.00 0.98 0 0.02
#> TCGA.B0.4718.01 4 0.4522 0.6465 0.00 0.32 0 0.68
#> TCGA.BP.5175.01 1 0.4522 0.7712 0.68 0.00 0 0.32
#> TCGA.CZ.5987.01 1 0.2345 0.8317 0.90 0.00 0 0.10
#> TCGA.BP.5198.01 4 0.4624 0.6463 0.34 0.00 0 0.66
#> TCGA.B0.5094.01 1 0.0000 0.8762 1.00 0.00 0 0.00
#> TCGA.CZ.5468.01 1 0.0000 0.8762 1.00 0.00 0 0.00
#> TCGA.BP.5169.01 1 0.0000 0.8762 1.00 0.00 0 0.00
#> TCGA.CJ.5680.01 3 0.0000 1.0000 0.00 0.00 1 0.00
#> TCGA.CZ.5470.01 3 0.0000 1.0000 0.00 0.00 1 0.00
#> TCGA.B0.4844.01 1 0.0707 0.8737 0.98 0.00 0 0.02
#> TCGA.CZ.5464.01 1 0.5619 0.7417 0.64 0.04 0 0.32
#> TCGA.B0.5701.01 1 0.1211 0.8707 0.96 0.00 0 0.04
#> TCGA.CJ.5671.01 1 0.0000 0.8762 1.00 0.00 0 0.00
#> TCGA.B0.5116.01 4 0.6104 0.7744 0.14 0.18 0 0.68
#> TCGA.CJ.5679.01 1 0.0000 0.8762 1.00 0.00 0 0.00
#> TCGA.CJ.5682.01 4 0.6049 0.7583 0.20 0.12 0 0.68
#> TCGA.G6.A8L8.01 3 0.0000 1.0000 0.00 0.00 1 0.00
#> TCGA.B0.4691.01 1 0.0000 0.8762 1.00 0.00 0 0.00
#> TCGA.CZ.4853.01 2 0.0707 0.7983 0.00 0.98 0 0.02
#> TCGA.B0.5402.01 2 0.2011 0.7519 0.00 0.92 0 0.08
#> TCGA.B0.4813.01 2 0.3037 0.7306 0.02 0.88 0 0.10
#> TCGA.G6.A8L7.01 3 0.0000 1.0000 0.00 0.00 1 0.00
#> TCGA.B0.4848.01 1 0.0000 0.8762 1.00 0.00 0 0.00
#> TCGA.CZ.5985.01 1 0.3975 0.8139 0.76 0.00 0 0.24
#> TCGA.B0.5121.01 4 0.4994 0.3378 0.00 0.48 0 0.52
#> TCGA.BP.5191.01 1 0.4406 0.7840 0.70 0.00 0 0.30
#> TCGA.B0.4810.01 2 0.4277 0.5630 0.00 0.72 0 0.28
#> TCGA.AK.3428.01 2 0.3801 0.5765 0.00 0.78 0 0.22
#> TCGA.CJ.6027.01 1 0.0000 0.8762 1.00 0.00 0 0.00
cbind(get_classes(res, k = 5), get_membership(res, k = 5))
#> class entropy silhouette p1 p2 p3 p4 p5
#> TCGA.B0.5113.01 3 0.0000 0.992 0.00 0.00 1.00 0.00 0.00
#> TCGA.MM.A564.01 4 0.3319 0.708 0.16 0.00 0.00 0.82 0.02
#> TCGA.AK.3434.01 2 0.4990 0.484 0.00 0.60 0.00 0.36 0.04
#> TCGA.B0.4707.01 1 0.2012 0.830 0.92 0.00 0.00 0.06 0.02
#> TCGA.CZ.5456.01 1 0.1043 0.841 0.96 0.00 0.00 0.04 0.00
#> TCGA.CZ.5452.01 5 0.3983 0.735 0.34 0.00 0.00 0.00 0.66
#> TCGA.BP.5201.01 2 0.1410 0.787 0.00 0.94 0.00 0.00 0.06
#> TCGA.CJ.5677.01 3 0.0609 0.990 0.00 0.00 0.98 0.00 0.02
#> TCGA.AK.3425.01 1 0.5013 0.520 0.68 0.00 0.00 0.08 0.24
#> TCGA.BP.5180.01 5 0.4426 0.717 0.22 0.02 0.00 0.02 0.74
#> TCGA.CZ.5984.01 5 0.3561 0.758 0.26 0.00 0.00 0.00 0.74
#> TCGA.BP.5190.01 2 0.0609 0.802 0.00 0.98 0.00 0.02 0.00
#> TCGA.B0.4713.01 3 0.0609 0.990 0.00 0.00 0.98 0.00 0.02
#> TCGA.B0.4841.01 2 0.1043 0.803 0.00 0.96 0.00 0.04 0.00
#> TCGA.B0.5699.01 2 0.3999 0.662 0.00 0.74 0.00 0.24 0.02
#> TCGA.BP.5202.01 2 0.0609 0.802 0.00 0.98 0.00 0.02 0.00
#> TCGA.B0.4814.01 2 0.4360 0.613 0.00 0.68 0.00 0.30 0.02
#> TCGA.B0.4821.01 3 0.0609 0.990 0.00 0.00 0.98 0.00 0.02
#> TCGA.B0.5712.01 3 0.0609 0.990 0.00 0.00 0.98 0.00 0.02
#> TCGA.CJ.4920.01 3 0.0000 0.992 0.00 0.00 1.00 0.00 0.00
#> TCGA.DV.A4W0.01 4 0.4227 0.181 0.00 0.42 0.00 0.58 0.00
#> TCGA.CJ.4903.01 2 0.0609 0.802 0.00 0.98 0.00 0.02 0.00
#> TCGA.CJ.4912.01 1 0.3390 0.777 0.84 0.00 0.00 0.10 0.06
#> TCGA.B0.4845.01 2 0.4726 0.442 0.00 0.58 0.00 0.40 0.02
#> TCGA.B8.A54D.01 2 0.4262 0.187 0.00 0.56 0.00 0.00 0.44
#> TCGA.B0.5692.01 3 0.0000 0.992 0.00 0.00 1.00 0.00 0.00
#> TCGA.B0.5106.01 5 0.3868 0.712 0.14 0.06 0.00 0.00 0.80
#> TCGA.B0.4827.01 3 0.0609 0.990 0.00 0.00 0.98 0.00 0.02
#> TCGA.B0.5115.01 2 0.1732 0.799 0.00 0.92 0.00 0.08 0.00
#> TCGA.B0.4706.01 2 0.1648 0.802 0.00 0.94 0.00 0.04 0.02
#> TCGA.B8.A54I.01 1 0.4287 -0.338 0.54 0.00 0.00 0.00 0.46
#> TCGA.CZ.5463.01 2 0.2873 0.756 0.00 0.86 0.00 0.02 0.12
#> TCGA.G6.A5PC.01 3 0.0000 0.992 0.00 0.00 1.00 0.00 0.00
#> TCGA.B0.4696.01 1 0.3690 0.671 0.78 0.00 0.00 0.02 0.20
#> TCGA.CZ.5469.01 1 0.1043 0.841 0.96 0.00 0.00 0.04 0.00
#> TCGA.B2.5641.01 5 0.4060 0.714 0.36 0.00 0.00 0.00 0.64
#> TCGA.CZ.5460.01 4 0.4613 0.256 0.00 0.36 0.00 0.62 0.02
#> TCGA.B0.4712.01 1 0.0609 0.824 0.98 0.00 0.00 0.00 0.02
#> TCGA.CW.5590.01 4 0.1043 0.796 0.04 0.00 0.00 0.96 0.00
#> TCGA.B0.5698.01 2 0.2020 0.794 0.00 0.90 0.00 0.10 0.00
#> TCGA.CW.5580.01 3 0.0000 0.992 0.00 0.00 1.00 0.00 0.00
#> TCGA.CZ.5454.01 2 0.0609 0.802 0.00 0.98 0.00 0.02 0.00
#> TCGA.B0.4815.01 1 0.0609 0.824 0.98 0.00 0.00 0.00 0.02
#> TCGA.B0.5694.01 4 0.1648 0.793 0.04 0.00 0.00 0.94 0.02
#> TCGA.A3.3357.01 4 0.1648 0.793 0.04 0.00 0.00 0.94 0.02
#> TCGA.B8.4622.01 4 0.1043 0.796 0.04 0.00 0.00 0.96 0.00
#> TCGA.CJ.4913.01 3 0.0000 0.992 0.00 0.00 1.00 0.00 0.00
#> TCGA.CJ.6033.01 3 0.0609 0.990 0.00 0.00 0.98 0.00 0.02
#> TCGA.B0.4698.01 1 0.2873 0.751 0.86 0.00 0.00 0.02 0.12
#> TCGA.B0.4688.01 1 0.3106 0.730 0.84 0.00 0.00 0.02 0.14
#> TCGA.B0.5096.01 3 0.0609 0.990 0.00 0.00 0.98 0.00 0.02
#> TCGA.BP.5178.01 1 0.1648 0.838 0.94 0.00 0.00 0.04 0.02
#> TCGA.B0.4847.01 2 0.4818 0.289 0.00 0.52 0.00 0.46 0.02
#> TCGA.B0.5107.01 3 0.0609 0.990 0.00 0.00 0.98 0.00 0.02
#> TCGA.CW.5584.01 4 0.3561 0.520 0.00 0.26 0.00 0.74 0.00
#> TCGA.BP.5199.01 2 0.3319 0.715 0.00 0.82 0.00 0.02 0.16
#> TCGA.CJ.4901.01 1 0.1043 0.818 0.96 0.00 0.00 0.00 0.04
#> TCGA.CW.6090.01 4 0.1043 0.796 0.04 0.00 0.00 0.96 0.00
#> TCGA.CZ.4866.01 3 0.0000 0.992 0.00 0.00 1.00 0.00 0.00
#> TCGA.B0.4828.01 4 0.2280 0.702 0.00 0.12 0.00 0.88 0.00
#> TCGA.MM.A563.01 2 0.3109 0.663 0.00 0.80 0.00 0.00 0.20
#> TCGA.AK.3458.01 2 0.0609 0.802 0.00 0.98 0.00 0.02 0.00
#> TCGA.CJ.5676.01 4 0.2873 0.750 0.12 0.00 0.00 0.86 0.02
#> TCGA.B0.4693.01 3 0.0000 0.992 0.00 0.00 1.00 0.00 0.00
#> TCGA.B0.4710.01 3 0.0000 0.992 0.00 0.00 1.00 0.00 0.00
#> TCGA.CZ.5465.01 3 0.0000 0.992 0.00 0.00 1.00 0.00 0.00
#> TCGA.CJ.5675.01 4 0.2675 0.776 0.04 0.04 0.00 0.90 0.02
#> TCGA.B8.5158.01 1 0.1216 0.832 0.96 0.00 0.00 0.02 0.02
#> TCGA.CJ.6030.01 1 0.1732 0.831 0.92 0.00 0.00 0.08 0.00
#> TCGA.B8.5159.01 3 0.0000 0.992 0.00 0.00 1.00 0.00 0.00
#> TCGA.B0.5706.01 5 0.4182 0.633 0.40 0.00 0.00 0.00 0.60
#> TCGA.A3.3367.01 2 0.4767 0.398 0.00 0.56 0.00 0.42 0.02
#> TCGA.DV.A4VX.01 4 0.4268 0.669 0.20 0.02 0.00 0.76 0.02
#> TCGA.EU.5907.01 2 0.2438 0.796 0.00 0.90 0.00 0.06 0.04
#> TCGA.CJ.5678.01 4 0.3641 0.738 0.06 0.12 0.00 0.82 0.00
#> TCGA.B8.4153.01 4 0.4818 -0.109 0.00 0.46 0.00 0.52 0.02
#> TCGA.BP.5183.01 2 0.2438 0.801 0.00 0.90 0.00 0.06 0.04
#> TCGA.AK.3445.01 1 0.1648 0.839 0.94 0.00 0.00 0.04 0.02
#> TCGA.BP.5196.01 5 0.4060 0.681 0.36 0.00 0.00 0.00 0.64
#> TCGA.B0.4714.01 2 0.3319 0.758 0.00 0.82 0.00 0.16 0.02
#> TCGA.B8.5549.01 5 0.4227 0.192 0.00 0.42 0.00 0.00 0.58
#> TCGA.CZ.5461.01 4 0.2280 0.757 0.12 0.00 0.00 0.88 0.00
#> TCGA.B0.5710.01 2 0.0609 0.790 0.00 0.98 0.00 0.00 0.02
#> TCGA.B0.4718.01 4 0.3999 0.530 0.00 0.24 0.00 0.74 0.02
#> TCGA.BP.5175.01 5 0.3796 0.751 0.30 0.00 0.00 0.00 0.70
#> TCGA.CZ.5987.01 1 0.5558 0.391 0.56 0.00 0.00 0.36 0.08
#> TCGA.BP.5198.01 4 0.3684 0.530 0.28 0.00 0.00 0.72 0.00
#> TCGA.B0.5094.01 1 0.0609 0.841 0.98 0.00 0.00 0.02 0.00
#> TCGA.CZ.5468.01 1 0.2331 0.782 0.90 0.00 0.00 0.02 0.08
#> TCGA.BP.5169.01 1 0.0609 0.824 0.98 0.00 0.00 0.00 0.02
#> TCGA.CJ.5680.01 3 0.0000 0.992 0.00 0.00 1.00 0.00 0.00
#> TCGA.CZ.5470.01 3 0.0609 0.990 0.00 0.00 0.98 0.00 0.02
#> TCGA.B0.4844.01 1 0.2438 0.823 0.90 0.00 0.00 0.06 0.04
#> TCGA.CZ.5464.01 5 0.4254 0.754 0.22 0.04 0.00 0.00 0.74
#> TCGA.B0.5701.01 1 0.2616 0.799 0.88 0.00 0.00 0.10 0.02
#> TCGA.CJ.5671.01 1 0.2616 0.810 0.88 0.00 0.00 0.10 0.02
#> TCGA.B0.5116.01 4 0.1043 0.796 0.04 0.00 0.00 0.96 0.00
#> TCGA.CJ.5679.01 1 0.2616 0.803 0.88 0.00 0.00 0.10 0.02
#> TCGA.CJ.5682.01 4 0.1043 0.796 0.04 0.00 0.00 0.96 0.00
#> TCGA.G6.A8L8.01 3 0.0000 0.992 0.00 0.00 1.00 0.00 0.00
#> TCGA.B0.4691.01 1 0.1043 0.841 0.96 0.00 0.00 0.04 0.00
#> TCGA.CZ.4853.01 2 0.2438 0.796 0.00 0.90 0.00 0.06 0.04
#> TCGA.B0.5402.01 2 0.2516 0.759 0.00 0.86 0.00 0.14 0.00
#> TCGA.B0.4813.01 2 0.5610 0.571 0.00 0.64 0.00 0.18 0.18
#> TCGA.G6.A8L7.01 3 0.0609 0.990 0.00 0.00 0.98 0.00 0.02
#> TCGA.B0.4848.01 1 0.1732 0.831 0.92 0.00 0.00 0.08 0.00
#> TCGA.CZ.5985.01 1 0.4060 0.227 0.64 0.00 0.00 0.00 0.36
#> TCGA.B0.5121.01 2 0.4767 0.285 0.00 0.56 0.00 0.42 0.02
#> TCGA.BP.5191.01 5 0.3983 0.734 0.34 0.00 0.00 0.00 0.66
#> TCGA.B0.4810.01 5 0.4126 0.293 0.00 0.38 0.00 0.00 0.62
#> TCGA.AK.3428.01 2 0.3109 0.742 0.00 0.80 0.00 0.20 0.00
#> TCGA.CJ.6027.01 1 0.0609 0.841 0.98 0.00 0.00 0.02 0.00
cbind(get_classes(res, k = 6), get_membership(res, k = 6))
#> class entropy silhouette p1 p2 p3 p4 p5 p6
#> TCGA.B0.5113.01 3 0.1480 0.8853 0.00 0.00 0.94 0.00 0.02 0.04
#> TCGA.MM.A564.01 4 0.5679 0.4954 0.18 0.00 0.00 0.64 0.06 0.12
#> TCGA.AK.3434.01 4 0.5523 0.1129 0.00 0.36 0.00 0.50 0.00 0.14
#> TCGA.B0.4707.01 1 0.2020 0.8178 0.92 0.00 0.00 0.02 0.02 0.04
#> TCGA.CZ.5456.01 1 0.0000 0.8417 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.CZ.5452.01 5 0.3797 0.5639 0.42 0.00 0.00 0.00 0.58 0.00
#> TCGA.BP.5201.01 2 0.2190 0.7479 0.00 0.90 0.00 0.04 0.00 0.06
#> TCGA.CJ.5677.01 3 0.2941 0.8765 0.00 0.00 0.78 0.00 0.00 0.22
#> TCGA.AK.3425.01 1 0.3834 0.5765 0.76 0.00 0.00 0.02 0.20 0.02
#> TCGA.BP.5180.01 5 0.5618 0.6245 0.20 0.06 0.00 0.00 0.64 0.10
#> TCGA.CZ.5984.01 5 0.3499 0.6544 0.32 0.00 0.00 0.00 0.68 0.00
#> TCGA.BP.5190.01 2 0.2403 0.7376 0.00 0.90 0.00 0.04 0.02 0.04
#> TCGA.B0.4713.01 3 0.2941 0.8765 0.00 0.00 0.78 0.00 0.00 0.22
#> TCGA.B0.4841.01 2 0.1092 0.7450 0.00 0.96 0.00 0.02 0.00 0.02
#> TCGA.B0.5699.01 2 0.4922 0.5194 0.00 0.66 0.00 0.26 0.04 0.04
#> TCGA.BP.5202.01 2 0.2020 0.7399 0.00 0.92 0.00 0.02 0.02 0.04
#> TCGA.B0.4814.01 2 0.4576 0.2454 0.00 0.56 0.00 0.40 0.00 0.04
#> TCGA.B0.4821.01 3 0.2941 0.8765 0.00 0.00 0.78 0.00 0.00 0.22
#> TCGA.B0.5712.01 3 0.1807 0.8978 0.00 0.00 0.92 0.00 0.02 0.06
#> TCGA.CJ.4920.01 3 0.1480 0.8978 0.00 0.00 0.94 0.00 0.02 0.04
#> TCGA.DV.A4W0.01 4 0.5896 0.1213 0.00 0.40 0.00 0.46 0.02 0.12
#> TCGA.CJ.4903.01 2 0.2020 0.7399 0.00 0.92 0.00 0.02 0.02 0.04
#> TCGA.CJ.4912.01 1 0.5580 0.4909 0.66 0.00 0.00 0.08 0.16 0.10
#> TCGA.B0.4845.01 4 0.4328 0.1287 0.00 0.46 0.00 0.52 0.00 0.02
#> TCGA.B8.A54D.01 2 0.6200 0.3602 0.00 0.46 0.00 0.02 0.34 0.18
#> TCGA.B0.5692.01 3 0.2190 0.8886 0.00 0.00 0.90 0.00 0.04 0.06
#> TCGA.B0.5106.01 5 0.4733 0.6243 0.12 0.06 0.00 0.00 0.74 0.08
#> TCGA.B0.4827.01 3 0.2941 0.8765 0.00 0.00 0.78 0.00 0.00 0.22
#> TCGA.B0.5115.01 2 0.2403 0.7471 0.00 0.90 0.00 0.04 0.02 0.04
#> TCGA.B0.4706.01 2 0.2020 0.7437 0.00 0.92 0.00 0.02 0.02 0.04
#> TCGA.B8.A54I.01 1 0.4172 0.3634 0.68 0.00 0.00 0.00 0.28 0.04
#> TCGA.CZ.5463.01 2 0.5292 0.5999 0.00 0.60 0.00 0.00 0.18 0.22
#> TCGA.G6.A5PC.01 3 0.1865 0.8938 0.00 0.00 0.92 0.00 0.04 0.04
#> TCGA.B0.4696.01 1 0.4864 0.4984 0.66 0.00 0.00 0.02 0.06 0.26
#> TCGA.CZ.5469.01 1 0.0000 0.8417 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.B2.5641.01 5 0.4310 0.5368 0.44 0.00 0.00 0.00 0.54 0.02
#> TCGA.CZ.5460.01 4 0.3829 0.6318 0.00 0.18 0.00 0.76 0.00 0.06
#> TCGA.B0.4712.01 1 0.0000 0.8417 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.CW.5590.01 4 0.0547 0.7336 0.00 0.02 0.00 0.98 0.00 0.00
#> TCGA.B0.5698.01 2 0.3483 0.7338 0.00 0.82 0.00 0.04 0.02 0.12
#> TCGA.CW.5580.01 3 0.0547 0.8955 0.00 0.00 0.98 0.00 0.02 0.00
#> TCGA.CZ.5454.01 2 0.1480 0.7458 0.00 0.94 0.00 0.00 0.02 0.04
#> TCGA.B0.4815.01 1 0.0000 0.8417 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.B0.5694.01 4 0.1480 0.7274 0.00 0.02 0.00 0.94 0.00 0.04
#> TCGA.A3.3357.01 4 0.2020 0.7308 0.02 0.04 0.00 0.92 0.00 0.02
#> TCGA.B8.4622.01 4 0.0937 0.7324 0.00 0.04 0.00 0.96 0.00 0.00
#> TCGA.CJ.4913.01 3 0.1865 0.8842 0.00 0.00 0.92 0.00 0.04 0.04
#> TCGA.CJ.6033.01 3 0.2941 0.8765 0.00 0.00 0.78 0.00 0.00 0.22
#> TCGA.B0.4698.01 1 0.3318 0.7073 0.82 0.00 0.00 0.02 0.02 0.14
#> TCGA.B0.4688.01 1 0.3834 0.6257 0.76 0.00 0.00 0.02 0.02 0.20
#> TCGA.B0.5096.01 3 0.2941 0.8765 0.00 0.00 0.78 0.00 0.00 0.22
#> TCGA.BP.5178.01 1 0.0547 0.8361 0.98 0.00 0.00 0.02 0.00 0.00
#> TCGA.B0.4847.01 2 0.3851 0.0961 0.00 0.54 0.00 0.46 0.00 0.00
#> TCGA.B0.5107.01 3 0.2941 0.8765 0.00 0.00 0.78 0.00 0.00 0.22
#> TCGA.CW.5584.01 4 0.3156 0.6485 0.00 0.18 0.00 0.80 0.00 0.02
#> TCGA.BP.5199.01 2 0.4860 0.6821 0.00 0.72 0.00 0.04 0.14 0.10
#> TCGA.CJ.4901.01 1 0.0937 0.8216 0.96 0.00 0.00 0.00 0.04 0.00
#> TCGA.CW.6090.01 4 0.0547 0.7336 0.00 0.02 0.00 0.98 0.00 0.00
#> TCGA.CZ.4866.01 3 0.2190 0.8877 0.00 0.00 0.90 0.00 0.04 0.06
#> TCGA.B0.4828.01 4 0.2350 0.7101 0.00 0.10 0.00 0.88 0.00 0.02
#> TCGA.MM.A563.01 2 0.5628 0.4963 0.00 0.54 0.00 0.00 0.24 0.22
#> TCGA.AK.3458.01 2 0.2020 0.7399 0.00 0.92 0.00 0.02 0.02 0.04
#> TCGA.CJ.5676.01 4 0.2790 0.6588 0.14 0.00 0.00 0.84 0.00 0.02
#> TCGA.B0.4693.01 3 0.1865 0.8842 0.00 0.00 0.92 0.00 0.04 0.04
#> TCGA.B0.4710.01 3 0.1865 0.8842 0.00 0.00 0.92 0.00 0.04 0.04
#> TCGA.CZ.5465.01 3 0.1480 0.8889 0.00 0.00 0.94 0.00 0.02 0.04
#> TCGA.CJ.5675.01 4 0.0937 0.7320 0.00 0.04 0.00 0.96 0.00 0.00
#> TCGA.B8.5158.01 1 0.0000 0.8417 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.CJ.6030.01 1 0.1807 0.8128 0.92 0.00 0.00 0.06 0.02 0.00
#> TCGA.B8.5159.01 3 0.1865 0.8842 0.00 0.00 0.92 0.00 0.04 0.04
#> TCGA.B0.5706.01 1 0.4337 -0.4365 0.50 0.00 0.00 0.00 0.48 0.02
#> TCGA.A3.3367.01 4 0.4337 0.0258 0.00 0.48 0.00 0.50 0.00 0.02
#> TCGA.DV.A4VX.01 4 0.6669 0.4341 0.26 0.12 0.00 0.54 0.04 0.04
#> TCGA.EU.5907.01 2 0.3873 0.7188 0.00 0.78 0.00 0.02 0.04 0.16
#> TCGA.CJ.5678.01 4 0.4361 0.6538 0.00 0.14 0.00 0.76 0.04 0.06
#> TCGA.B8.4153.01 4 0.5322 0.1687 0.00 0.40 0.00 0.52 0.02 0.06
#> TCGA.BP.5183.01 2 0.4088 0.7022 0.00 0.78 0.00 0.10 0.02 0.10
#> TCGA.AK.3445.01 1 0.0000 0.8417 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.BP.5196.01 5 0.3851 0.4609 0.46 0.00 0.00 0.00 0.54 0.00
#> TCGA.B0.4714.01 2 0.3315 0.6326 0.00 0.78 0.00 0.20 0.00 0.02
#> TCGA.B8.5549.01 5 0.5783 0.0051 0.00 0.28 0.00 0.00 0.50 0.22
#> TCGA.CZ.5461.01 4 0.2048 0.6830 0.12 0.00 0.00 0.88 0.00 0.00
#> TCGA.B0.5710.01 2 0.2048 0.7359 0.00 0.88 0.00 0.00 0.00 0.12
#> TCGA.B0.4718.01 4 0.2790 0.6764 0.00 0.14 0.00 0.84 0.00 0.02
#> TCGA.BP.5175.01 5 0.4078 0.6463 0.34 0.00 0.00 0.00 0.64 0.02
#> TCGA.CZ.5987.01 1 0.5256 0.5054 0.68 0.00 0.00 0.18 0.06 0.08
#> TCGA.BP.5198.01 4 0.3647 0.3704 0.36 0.00 0.00 0.64 0.00 0.00
#> TCGA.B0.5094.01 1 0.0000 0.8417 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.CZ.5468.01 1 0.1092 0.8271 0.96 0.00 0.00 0.02 0.00 0.02
#> TCGA.BP.5169.01 1 0.0000 0.8417 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.CJ.5680.01 3 0.0547 0.8950 0.00 0.00 0.98 0.00 0.00 0.02
#> TCGA.CZ.5470.01 3 0.2793 0.8810 0.00 0.00 0.80 0.00 0.00 0.20
#> TCGA.B0.4844.01 1 0.2784 0.7814 0.88 0.00 0.00 0.04 0.04 0.04
#> TCGA.CZ.5464.01 5 0.4864 0.6591 0.26 0.02 0.00 0.00 0.66 0.06
#> TCGA.B0.5701.01 1 0.3420 0.7548 0.84 0.00 0.00 0.06 0.06 0.04
#> TCGA.CJ.5671.01 1 0.1267 0.8151 0.94 0.00 0.00 0.06 0.00 0.00
#> TCGA.B0.5116.01 4 0.0547 0.7336 0.00 0.02 0.00 0.98 0.00 0.00
#> TCGA.CJ.5679.01 1 0.1480 0.8220 0.94 0.00 0.00 0.04 0.00 0.02
#> TCGA.CJ.5682.01 4 0.0547 0.7336 0.00 0.02 0.00 0.98 0.00 0.00
#> TCGA.G6.A8L8.01 3 0.1807 0.8845 0.00 0.00 0.92 0.00 0.02 0.06
#> TCGA.B0.4691.01 1 0.0000 0.8417 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.CZ.4853.01 2 0.3985 0.7167 0.00 0.76 0.00 0.10 0.00 0.14
#> TCGA.B0.5402.01 2 0.3787 0.7183 0.00 0.78 0.00 0.10 0.00 0.12
#> TCGA.B0.4813.01 2 0.7310 0.2462 0.00 0.32 0.00 0.10 0.26 0.32
#> TCGA.G6.A8L7.01 3 0.2941 0.8765 0.00 0.00 0.78 0.00 0.00 0.22
#> TCGA.B0.4848.01 1 0.0547 0.8357 0.98 0.00 0.00 0.00 0.02 0.00
#> TCGA.CZ.5985.01 1 0.2048 0.7602 0.88 0.00 0.00 0.00 0.12 0.00
#> TCGA.B0.5121.01 2 0.5322 0.1897 0.00 0.52 0.00 0.40 0.02 0.06
#> TCGA.BP.5191.01 5 0.3706 0.6159 0.38 0.00 0.00 0.00 0.62 0.00
#> TCGA.B0.4810.01 5 0.5235 -0.0830 0.00 0.38 0.00 0.00 0.52 0.10
#> TCGA.AK.3428.01 2 0.4420 0.4843 0.00 0.66 0.00 0.30 0.02 0.02
#> TCGA.CJ.6027.01 1 0.0000 0.8417 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.B0.5113.01 3 0.1006 0.859 0.00 0.00 0.96 0.00 0.02 0.00 0.02
#> TCGA.MM.A564.01 4 0.5635 0.592 0.06 0.00 0.00 0.66 0.10 0.12 0.06
#> TCGA.AK.3434.01 2 0.6009 0.334 0.02 0.36 0.00 0.34 0.00 0.00 0.28
#> TCGA.B0.4707.01 6 0.4590 0.679 0.06 0.00 0.00 0.06 0.12 0.74 0.02
#> TCGA.CZ.5456.01 6 0.0504 0.770 0.00 0.00 0.00 0.02 0.00 0.98 0.00
#> TCGA.CZ.5452.01 5 0.3815 0.659 0.00 0.00 0.00 0.00 0.62 0.36 0.02
#> TCGA.BP.5201.01 2 0.4479 0.389 0.02 0.66 0.00 0.06 0.00 0.00 0.26
#> TCGA.CJ.5677.01 3 0.3294 0.786 0.34 0.00 0.66 0.00 0.00 0.00 0.00
#> TCGA.AK.3425.01 6 0.5543 0.533 0.06 0.00 0.00 0.08 0.22 0.62 0.02
#> TCGA.BP.5180.01 5 0.7047 0.207 0.06 0.04 0.00 0.08 0.54 0.10 0.18
#> TCGA.CZ.5984.01 5 0.4466 0.697 0.04 0.00 0.00 0.00 0.70 0.20 0.06
#> TCGA.BP.5190.01 2 0.2654 0.427 0.10 0.86 0.00 0.02 0.00 0.00 0.02
#> TCGA.B0.4713.01 3 0.3294 0.786 0.34 0.00 0.66 0.00 0.00 0.00 0.00
#> TCGA.B0.4841.01 2 0.1671 0.457 0.00 0.90 0.00 0.00 0.00 0.00 0.10
#> TCGA.B0.5699.01 2 0.5469 0.413 0.04 0.56 0.00 0.28 0.00 0.00 0.12
#> TCGA.BP.5202.01 2 0.1166 0.460 0.06 0.94 0.00 0.00 0.00 0.00 0.00
#> TCGA.B0.4814.01 2 0.5695 0.439 0.02 0.50 0.00 0.26 0.00 0.00 0.22
#> TCGA.B0.4821.01 3 0.3294 0.786 0.34 0.00 0.66 0.00 0.00 0.00 0.00
#> TCGA.B0.5712.01 3 0.1671 0.865 0.10 0.00 0.90 0.00 0.00 0.00 0.00
#> TCGA.CJ.4920.01 3 0.0863 0.872 0.04 0.00 0.96 0.00 0.00 0.00 0.00
#> TCGA.DV.A4W0.01 4 0.5922 0.218 0.06 0.26 0.00 0.52 0.00 0.00 0.16
#> TCGA.CJ.4903.01 2 0.1718 0.464 0.04 0.92 0.00 0.00 0.00 0.00 0.04
#> TCGA.CJ.4912.01 6 0.6863 0.364 0.12 0.00 0.00 0.08 0.18 0.52 0.10
#> TCGA.B0.4845.01 2 0.5207 0.355 0.00 0.48 0.00 0.36 0.00 0.00 0.16
#> TCGA.B8.A54D.01 2 0.5893 -0.565 0.02 0.38 0.00 0.00 0.22 0.00 0.38
#> TCGA.B0.5692.01 3 0.1505 0.863 0.02 0.00 0.94 0.00 0.02 0.00 0.02
#> TCGA.B0.5106.01 5 0.5922 0.313 0.16 0.00 0.00 0.00 0.52 0.06 0.26
#> TCGA.B0.4827.01 3 0.3685 0.794 0.32 0.00 0.66 0.00 0.00 0.00 0.02
#> TCGA.B0.5115.01 2 0.3519 0.453 0.00 0.74 0.00 0.04 0.00 0.00 0.22
#> TCGA.B0.4706.01 2 0.1718 0.469 0.04 0.92 0.00 0.00 0.00 0.00 0.04
#> TCGA.B8.A54I.01 6 0.4278 -0.324 0.00 0.00 0.00 0.00 0.46 0.50 0.04
#> TCGA.CZ.5463.01 7 0.4524 0.409 0.02 0.34 0.00 0.04 0.00 0.00 0.60
#> TCGA.G6.A5PC.01 3 0.1363 0.872 0.04 0.00 0.94 0.00 0.00 0.00 0.02
#> TCGA.B0.4696.01 6 0.6259 0.179 0.24 0.00 0.00 0.02 0.20 0.50 0.04
#> TCGA.CZ.5469.01 6 0.1860 0.768 0.04 0.00 0.00 0.02 0.02 0.92 0.00
#> TCGA.B2.5641.01 5 0.3815 0.640 0.02 0.00 0.00 0.00 0.62 0.36 0.00
#> TCGA.CZ.5460.01 4 0.4487 0.260 0.00 0.32 0.00 0.60 0.00 0.00 0.08
#> TCGA.B0.4712.01 6 0.0000 0.769 0.00 0.00 0.00 0.00 0.00 1.00 0.00
#> TCGA.CW.5590.01 4 0.1505 0.726 0.00 0.02 0.00 0.94 0.00 0.02 0.02
#> TCGA.B0.5698.01 2 0.4992 0.391 0.00 0.60 0.00 0.10 0.02 0.00 0.28
#> TCGA.CW.5580.01 3 0.0000 0.869 0.00 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.CZ.5454.01 2 0.2829 0.389 0.08 0.84 0.00 0.00 0.00 0.00 0.08
#> TCGA.B0.4815.01 6 0.0504 0.761 0.00 0.00 0.00 0.00 0.02 0.98 0.00
#> TCGA.B0.5694.01 4 0.4421 0.706 0.02 0.04 0.00 0.78 0.08 0.04 0.04
#> TCGA.A3.3357.01 4 0.3542 0.719 0.02 0.04 0.00 0.84 0.02 0.04 0.04
#> TCGA.B8.4622.01 4 0.3000 0.731 0.02 0.02 0.00 0.86 0.04 0.06 0.00
#> TCGA.CJ.4913.01 3 0.0504 0.866 0.00 0.00 0.98 0.00 0.00 0.00 0.02
#> TCGA.CJ.6033.01 3 0.2422 0.845 0.18 0.00 0.82 0.00 0.00 0.00 0.00
#> TCGA.B0.4698.01 6 0.4145 0.574 0.14 0.00 0.00 0.02 0.10 0.74 0.00
#> TCGA.B0.4688.01 6 0.5482 0.421 0.22 0.00 0.00 0.02 0.10 0.62 0.04
#> TCGA.B0.5096.01 3 0.3294 0.786 0.34 0.00 0.66 0.00 0.00 0.00 0.00
#> TCGA.BP.5178.01 6 0.0504 0.770 0.00 0.00 0.00 0.00 0.00 0.98 0.02
#> TCGA.B0.4847.01 2 0.4787 0.465 0.00 0.58 0.00 0.30 0.00 0.00 0.12
#> TCGA.B0.5107.01 3 0.3294 0.786 0.34 0.00 0.66 0.00 0.00 0.00 0.00
#> TCGA.CW.5584.01 4 0.4884 0.406 0.04 0.28 0.00 0.62 0.00 0.00 0.06
#> TCGA.BP.5199.01 2 0.5566 0.124 0.04 0.60 0.00 0.06 0.04 0.00 0.26
#> TCGA.CJ.4901.01 6 0.2569 0.648 0.02 0.00 0.00 0.00 0.14 0.84 0.00
#> TCGA.CW.6090.01 4 0.1363 0.732 0.00 0.02 0.00 0.94 0.00 0.04 0.00
#> TCGA.CZ.4866.01 3 0.1006 0.870 0.02 0.00 0.96 0.00 0.02 0.00 0.00
#> TCGA.B0.4828.01 4 0.3244 0.605 0.00 0.18 0.00 0.78 0.00 0.00 0.04
#> TCGA.MM.A563.01 7 0.5338 0.558 0.04 0.28 0.00 0.02 0.06 0.00 0.60
#> TCGA.AK.3458.01 2 0.1928 0.448 0.08 0.90 0.00 0.00 0.00 0.00 0.02
#> TCGA.CJ.5676.01 4 0.3680 0.671 0.00 0.00 0.00 0.78 0.06 0.14 0.02
#> TCGA.B0.4693.01 3 0.0504 0.866 0.00 0.00 0.98 0.00 0.00 0.00 0.02
#> TCGA.B0.4710.01 3 0.0504 0.865 0.00 0.00 0.98 0.00 0.00 0.00 0.02
#> TCGA.CZ.5465.01 3 0.0504 0.863 0.00 0.00 0.98 0.02 0.00 0.00 0.00
#> TCGA.CJ.5675.01 4 0.3061 0.701 0.00 0.06 0.00 0.84 0.00 0.02 0.08
#> TCGA.B8.5158.01 6 0.1664 0.756 0.00 0.00 0.00 0.00 0.06 0.92 0.02
#> TCGA.CJ.6030.01 6 0.4770 0.641 0.04 0.00 0.00 0.10 0.12 0.72 0.02
#> TCGA.B8.5159.01 3 0.1006 0.859 0.00 0.00 0.96 0.00 0.02 0.00 0.02
#> TCGA.B0.5706.01 5 0.4175 0.595 0.04 0.00 0.00 0.00 0.58 0.38 0.00
#> TCGA.A3.3367.01 2 0.5312 0.363 0.00 0.46 0.00 0.36 0.00 0.00 0.18
#> TCGA.DV.A4VX.01 4 0.6562 0.539 0.06 0.04 0.00 0.56 0.02 0.20 0.12
#> TCGA.EU.5907.01 2 0.5215 0.342 0.06 0.58 0.00 0.06 0.00 0.00 0.30
#> TCGA.CJ.5678.01 4 0.5027 0.670 0.06 0.08 0.00 0.72 0.00 0.06 0.08
#> TCGA.B8.4153.01 4 0.5166 0.139 0.04 0.38 0.00 0.52 0.00 0.00 0.06
#> TCGA.BP.5183.01 2 0.4248 0.468 0.00 0.66 0.00 0.08 0.00 0.00 0.26
#> TCGA.AK.3445.01 6 0.2003 0.761 0.02 0.00 0.00 0.02 0.02 0.92 0.02
#> TCGA.BP.5196.01 5 0.5223 0.601 0.04 0.00 0.00 0.04 0.58 0.32 0.02
#> TCGA.B0.4714.01 2 0.4812 0.505 0.02 0.66 0.00 0.18 0.00 0.00 0.14
#> TCGA.B8.5549.01 7 0.6057 0.593 0.04 0.26 0.00 0.00 0.24 0.00 0.46
#> TCGA.CZ.5461.01 4 0.2569 0.698 0.00 0.00 0.00 0.84 0.02 0.14 0.00
#> TCGA.B0.5710.01 2 0.3780 0.201 0.02 0.72 0.00 0.00 0.02 0.00 0.24
#> TCGA.B0.4718.01 4 0.3863 0.544 0.02 0.20 0.00 0.74 0.00 0.00 0.04
#> TCGA.BP.5175.01 5 0.3244 0.694 0.00 0.00 0.00 0.00 0.78 0.18 0.04
#> TCGA.CZ.5987.01 6 0.5566 0.494 0.06 0.00 0.00 0.14 0.14 0.64 0.02
#> TCGA.BP.5198.01 4 0.4461 0.420 0.00 0.00 0.00 0.62 0.04 0.32 0.02
#> TCGA.B0.5094.01 6 0.1505 0.767 0.02 0.00 0.00 0.02 0.00 0.94 0.02
#> TCGA.CZ.5468.01 6 0.1860 0.731 0.04 0.00 0.00 0.02 0.02 0.92 0.00
#> TCGA.BP.5169.01 6 0.0000 0.769 0.00 0.00 0.00 0.00 0.00 1.00 0.00
#> TCGA.CJ.5680.01 3 0.0000 0.869 0.00 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.CZ.5470.01 3 0.2945 0.820 0.26 0.00 0.74 0.00 0.00 0.00 0.00
#> TCGA.B0.4844.01 6 0.3922 0.719 0.06 0.00 0.00 0.02 0.06 0.80 0.06
#> TCGA.CZ.5464.01 5 0.4992 0.619 0.04 0.00 0.00 0.00 0.66 0.16 0.14
#> TCGA.B0.5701.01 6 0.4732 0.658 0.04 0.00 0.00 0.08 0.14 0.72 0.02
#> TCGA.CJ.5671.01 6 0.2509 0.752 0.00 0.00 0.00 0.06 0.04 0.88 0.02
#> TCGA.B0.5116.01 4 0.1860 0.732 0.00 0.02 0.00 0.92 0.02 0.04 0.00
#> TCGA.CJ.5679.01 6 0.2213 0.759 0.04 0.00 0.00 0.02 0.04 0.90 0.00
#> TCGA.CJ.5682.01 4 0.2355 0.732 0.02 0.02 0.00 0.90 0.00 0.04 0.02
#> TCGA.G6.A8L8.01 3 0.0000 0.869 0.00 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.B0.4691.01 6 0.0504 0.770 0.02 0.00 0.00 0.00 0.00 0.98 0.00
#> TCGA.CZ.4853.01 2 0.5393 0.418 0.04 0.58 0.00 0.12 0.00 0.00 0.26
#> TCGA.B0.5402.01 2 0.5259 0.428 0.00 0.52 0.00 0.26 0.00 0.00 0.22
#> TCGA.B0.4813.01 7 0.7574 0.499 0.04 0.18 0.00 0.14 0.14 0.04 0.46
#> TCGA.G6.A8L7.01 3 0.3139 0.804 0.30 0.00 0.70 0.00 0.00 0.00 0.00
#> TCGA.B0.4848.01 6 0.2911 0.749 0.02 0.00 0.00 0.02 0.08 0.86 0.02
#> TCGA.CZ.5985.01 6 0.4473 0.621 0.06 0.00 0.00 0.02 0.18 0.72 0.02
#> TCGA.B0.5121.01 2 0.4461 0.428 0.04 0.62 0.00 0.32 0.00 0.00 0.02
#> TCGA.BP.5191.01 5 0.4070 0.711 0.02 0.00 0.00 0.00 0.66 0.30 0.02
#> TCGA.B0.4810.01 7 0.6150 0.585 0.04 0.24 0.00 0.00 0.30 0.00 0.42
#> TCGA.AK.3428.01 2 0.4629 0.496 0.00 0.64 0.00 0.20 0.00 0.00 0.16
#> TCGA.CJ.6027.01 6 0.0000 0.769 0.00 0.00 0.00 0.00 0.00 1.00 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.B0.5113.01 3 0.0000 0.87222 0.00 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.MM.A564.01 4 0.6804 0.31315 0.06 0.00 0.00 0.50 0.04 0.18 0.06 0.16
#> TCGA.AK.3434.01 8 0.6412 0.00000 0.00 0.28 0.00 0.30 0.00 0.00 0.12 0.30
#> TCGA.B0.4707.01 6 0.4711 0.47207 0.02 0.00 0.00 0.02 0.16 0.70 0.02 0.08
#> TCGA.CZ.5456.01 6 0.0941 0.67895 0.00 0.00 0.00 0.02 0.00 0.96 0.02 0.00
#> TCGA.CZ.5452.01 5 0.3690 0.45599 0.02 0.00 0.00 0.00 0.56 0.42 0.00 0.00
#> TCGA.BP.5201.01 2 0.4881 0.35323 0.04 0.68 0.00 0.04 0.00 0.00 0.16 0.08
#> TCGA.CJ.5677.01 3 0.2852 0.82568 0.28 0.00 0.72 0.00 0.00 0.00 0.00 0.00
#> TCGA.AK.3425.01 6 0.7190 -0.01606 0.08 0.00 0.00 0.10 0.24 0.44 0.04 0.10
#> TCGA.BP.5180.01 5 0.8295 0.22517 0.12 0.06 0.00 0.08 0.38 0.18 0.12 0.06
#> TCGA.CZ.5984.01 5 0.3551 0.57665 0.00 0.00 0.00 0.00 0.72 0.22 0.06 0.00
#> TCGA.BP.5190.01 2 0.1557 0.40964 0.02 0.92 0.00 0.00 0.00 0.00 0.06 0.00
#> TCGA.B0.4713.01 3 0.2852 0.82568 0.28 0.00 0.72 0.00 0.00 0.00 0.00 0.00
#> TCGA.B0.4841.01 2 0.4073 0.34779 0.00 0.66 0.00 0.00 0.00 0.00 0.10 0.24
#> TCGA.B0.5699.01 2 0.4314 -0.03973 0.00 0.66 0.00 0.24 0.00 0.00 0.02 0.08
#> TCGA.BP.5202.01 2 0.1887 0.41449 0.00 0.90 0.00 0.00 0.00 0.00 0.06 0.04
#> TCGA.B0.4814.01 2 0.5203 -0.48932 0.00 0.42 0.00 0.28 0.00 0.00 0.00 0.30
#> TCGA.B0.4821.01 3 0.3291 0.81155 0.28 0.00 0.70 0.00 0.00 0.02 0.00 0.00
#> TCGA.B0.5712.01 3 0.1341 0.87365 0.08 0.00 0.92 0.00 0.00 0.00 0.00 0.00
#> TCGA.CJ.4920.01 3 0.1091 0.87367 0.06 0.00 0.94 0.00 0.00 0.00 0.00 0.00
#> TCGA.DV.A4W0.01 4 0.6586 -0.10821 0.02 0.26 0.00 0.46 0.02 0.00 0.10 0.14
#> TCGA.CJ.4903.01 2 0.0471 0.41153 0.00 0.98 0.00 0.00 0.00 0.00 0.00 0.02
#> TCGA.CJ.4912.01 6 0.7182 0.02509 0.06 0.00 0.00 0.08 0.08 0.46 0.10 0.22
#> TCGA.B0.4845.01 2 0.5054 -0.45062 0.00 0.44 0.00 0.36 0.00 0.00 0.00 0.20
#> TCGA.B8.A54D.01 2 0.7030 -0.25205 0.06 0.38 0.00 0.02 0.20 0.00 0.28 0.06
#> TCGA.B0.5692.01 3 0.0471 0.87570 0.02 0.00 0.98 0.00 0.00 0.00 0.00 0.00
#> TCGA.B0.5106.01 5 0.5247 0.25688 0.04 0.00 0.00 0.02 0.58 0.04 0.30 0.02
#> TCGA.B0.4827.01 3 0.2938 0.82237 0.30 0.00 0.70 0.00 0.00 0.00 0.00 0.00
#> TCGA.B0.5115.01 2 0.5137 0.14069 0.00 0.54 0.00 0.08 0.00 0.00 0.06 0.32
#> TCGA.B0.4706.01 2 0.2407 0.41119 0.00 0.86 0.00 0.00 0.00 0.00 0.08 0.06
#> TCGA.B8.A54I.01 6 0.5171 -0.12731 0.04 0.00 0.00 0.00 0.34 0.54 0.02 0.06
#> TCGA.CZ.5463.01 7 0.5914 0.45946 0.02 0.20 0.00 0.02 0.02 0.00 0.52 0.22
#> TCGA.G6.A5PC.01 3 0.0808 0.87648 0.04 0.00 0.96 0.00 0.00 0.00 0.00 0.00
#> TCGA.B0.4696.01 1 0.5983 0.00000 0.46 0.00 0.00 0.00 0.14 0.32 0.02 0.06
#> TCGA.CZ.5469.01 6 0.0808 0.67657 0.00 0.00 0.00 0.00 0.04 0.96 0.00 0.00
#> TCGA.B2.5641.01 5 0.4975 0.50088 0.06 0.00 0.00 0.00 0.64 0.22 0.06 0.02
#> TCGA.CZ.5460.01 4 0.4740 -0.13643 0.00 0.30 0.00 0.58 0.00 0.00 0.02 0.10
#> TCGA.B0.4712.01 6 0.0471 0.67798 0.00 0.00 0.00 0.00 0.00 0.98 0.00 0.02
#> TCGA.CW.5590.01 4 0.0941 0.50972 0.00 0.02 0.00 0.96 0.00 0.00 0.00 0.02
#> TCGA.B0.5698.01 2 0.6235 0.01917 0.02 0.48 0.00 0.10 0.00 0.00 0.16 0.24
#> TCGA.CW.5580.01 3 0.0471 0.86600 0.02 0.00 0.98 0.00 0.00 0.00 0.00 0.00
#> TCGA.CZ.5454.01 2 0.3934 0.36758 0.00 0.70 0.00 0.00 0.00 0.00 0.14 0.16
#> TCGA.B0.4815.01 6 0.1275 0.64855 0.02 0.00 0.00 0.00 0.04 0.94 0.00 0.00
#> TCGA.B0.5694.01 4 0.4921 0.45517 0.04 0.02 0.00 0.72 0.06 0.02 0.02 0.12
#> TCGA.A3.3357.01 4 0.5719 0.40978 0.04 0.06 0.00 0.64 0.08 0.04 0.00 0.14
#> TCGA.B8.4622.01 4 0.4030 0.48594 0.04 0.10 0.00 0.78 0.02 0.00 0.04 0.02
#> TCGA.CJ.4913.01 3 0.0471 0.86600 0.02 0.00 0.98 0.00 0.00 0.00 0.00 0.00
#> TCGA.CJ.6033.01 3 0.2756 0.83411 0.26 0.00 0.74 0.00 0.00 0.00 0.00 0.00
#> TCGA.B0.4698.01 6 0.4747 0.16651 0.18 0.00 0.00 0.00 0.08 0.66 0.00 0.08
#> TCGA.B0.4688.01 6 0.5537 -0.61267 0.34 0.00 0.00 0.00 0.10 0.48 0.00 0.08
#> TCGA.B0.5096.01 3 0.2852 0.82568 0.28 0.00 0.72 0.00 0.00 0.00 0.00 0.00
#> TCGA.BP.5178.01 6 0.0808 0.67748 0.00 0.00 0.00 0.00 0.00 0.96 0.04 0.00
#> TCGA.B0.4847.01 2 0.4914 -0.49327 0.00 0.42 0.00 0.42 0.00 0.00 0.00 0.16
#> TCGA.B0.5107.01 3 0.2852 0.82568 0.28 0.00 0.72 0.00 0.00 0.00 0.00 0.00
#> TCGA.CW.5584.01 4 0.4805 0.00648 0.02 0.16 0.00 0.66 0.00 0.00 0.02 0.14
#> TCGA.BP.5199.01 2 0.5687 0.27771 0.02 0.62 0.00 0.04 0.04 0.00 0.14 0.14
#> TCGA.CJ.4901.01 6 0.2224 0.60736 0.02 0.00 0.00 0.00 0.12 0.86 0.00 0.00
#> TCGA.CW.6090.01 4 0.0941 0.52883 0.00 0.00 0.00 0.96 0.00 0.02 0.00 0.02
#> TCGA.CZ.4866.01 3 0.4004 0.76103 0.08 0.00 0.78 0.02 0.02 0.00 0.02 0.08
#> TCGA.B0.4828.01 4 0.1887 0.47595 0.00 0.04 0.00 0.90 0.00 0.00 0.00 0.06
#> TCGA.MM.A563.01 7 0.5482 0.55748 0.02 0.16 0.00 0.00 0.06 0.00 0.60 0.16
#> TCGA.AK.3458.01 2 0.2025 0.41457 0.00 0.88 0.00 0.00 0.00 0.00 0.10 0.02
#> TCGA.CJ.5676.01 4 0.5050 0.43052 0.02 0.00 0.00 0.66 0.02 0.20 0.04 0.06
#> TCGA.B0.4693.01 3 0.0471 0.87570 0.02 0.00 0.98 0.00 0.00 0.00 0.00 0.00
#> TCGA.B0.4710.01 3 0.0000 0.87222 0.00 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.CZ.5465.01 3 0.0941 0.85679 0.02 0.00 0.96 0.00 0.00 0.00 0.00 0.02
#> TCGA.CJ.5675.01 4 0.4262 0.37626 0.04 0.08 0.00 0.74 0.02 0.00 0.00 0.12
#> TCGA.B8.5158.01 6 0.1563 0.63126 0.00 0.00 0.00 0.00 0.10 0.90 0.00 0.00
#> TCGA.CJ.6030.01 6 0.4604 0.51909 0.06 0.00 0.00 0.12 0.06 0.72 0.00 0.04
#> TCGA.B8.5159.01 3 0.0000 0.87222 0.00 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.B0.5706.01 5 0.4674 0.27868 0.04 0.00 0.00 0.00 0.46 0.46 0.04 0.00
#> TCGA.A3.3367.01 4 0.5123 -0.63066 0.00 0.36 0.00 0.42 0.00 0.00 0.00 0.22
#> TCGA.DV.A4VX.01 4 0.6682 0.34555 0.04 0.10 0.00 0.54 0.02 0.20 0.06 0.04
#> TCGA.EU.5907.01 2 0.5497 0.03811 0.02 0.44 0.00 0.00 0.00 0.00 0.24 0.30
#> TCGA.CJ.5678.01 4 0.5094 0.42542 0.04 0.12 0.00 0.70 0.00 0.04 0.06 0.04
#> TCGA.B8.4153.01 4 0.5244 -0.33937 0.00 0.34 0.00 0.48 0.00 0.00 0.02 0.16
#> TCGA.BP.5183.01 2 0.5602 -0.02342 0.00 0.58 0.00 0.18 0.02 0.00 0.06 0.16
#> TCGA.AK.3445.01 6 0.2399 0.65313 0.04 0.00 0.00 0.04 0.00 0.88 0.00 0.04
#> TCGA.BP.5196.01 5 0.5256 0.47605 0.02 0.00 0.00 0.06 0.62 0.24 0.02 0.04
#> TCGA.B0.4714.01 2 0.5244 -0.15389 0.00 0.52 0.00 0.20 0.00 0.00 0.02 0.26
#> TCGA.B8.5549.01 7 0.6053 0.52676 0.02 0.16 0.00 0.00 0.30 0.00 0.46 0.06
#> TCGA.CZ.5461.01 4 0.3337 0.49828 0.00 0.00 0.00 0.78 0.00 0.16 0.02 0.04
#> TCGA.B0.5710.01 2 0.4821 0.14100 0.02 0.60 0.00 0.00 0.00 0.00 0.24 0.14
#> TCGA.B0.4718.01 4 0.4031 0.19720 0.00 0.16 0.00 0.72 0.00 0.00 0.02 0.10
#> TCGA.BP.5175.01 5 0.3637 0.56298 0.00 0.00 0.00 0.00 0.70 0.26 0.02 0.02
#> TCGA.CZ.5987.01 6 0.6846 0.16571 0.08 0.00 0.00 0.18 0.08 0.52 0.08 0.06
#> TCGA.BP.5198.01 4 0.4125 0.00855 0.00 0.00 0.00 0.52 0.00 0.44 0.02 0.02
#> TCGA.B0.5094.01 6 0.0941 0.67961 0.02 0.00 0.00 0.02 0.00 0.96 0.00 0.00
#> TCGA.CZ.5468.01 6 0.2858 0.61658 0.04 0.00 0.00 0.00 0.04 0.86 0.02 0.04
#> TCGA.BP.5169.01 6 0.0471 0.67071 0.00 0.00 0.00 0.00 0.02 0.98 0.00 0.00
#> TCGA.CJ.5680.01 3 0.0471 0.87570 0.02 0.00 0.98 0.00 0.00 0.00 0.00 0.00
#> TCGA.CZ.5470.01 3 0.2650 0.83901 0.24 0.00 0.76 0.00 0.00 0.00 0.00 0.00
#> TCGA.B0.4844.01 6 0.3585 0.61405 0.02 0.00 0.00 0.06 0.04 0.82 0.02 0.04
#> TCGA.CZ.5464.01 5 0.5051 0.46634 0.04 0.00 0.00 0.00 0.60 0.16 0.20 0.00
#> TCGA.B0.5701.01 6 0.6702 0.28815 0.04 0.00 0.00 0.12 0.12 0.54 0.06 0.12
#> TCGA.CJ.5671.01 6 0.2482 0.66175 0.02 0.00 0.00 0.06 0.02 0.88 0.02 0.00
#> TCGA.B0.5116.01 4 0.0808 0.52546 0.00 0.00 0.00 0.96 0.00 0.00 0.00 0.04
#> TCGA.CJ.5679.01 6 0.3954 0.57636 0.04 0.00 0.00 0.06 0.00 0.78 0.04 0.08
#> TCGA.CJ.5682.01 4 0.0941 0.53096 0.00 0.00 0.00 0.96 0.00 0.02 0.02 0.00
#> TCGA.G6.A8L8.01 3 0.0000 0.87222 0.00 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.B0.4691.01 6 0.0471 0.67742 0.00 0.00 0.00 0.00 0.00 0.98 0.02 0.00
#> TCGA.CZ.4853.01 2 0.5852 -0.03045 0.00 0.42 0.00 0.10 0.00 0.00 0.12 0.36
#> TCGA.B0.5402.01 2 0.6476 -0.13524 0.02 0.42 0.00 0.28 0.00 0.00 0.12 0.16
#> TCGA.B0.4813.01 2 0.8355 -0.13683 0.04 0.28 0.00 0.12 0.16 0.02 0.22 0.16
#> TCGA.G6.A8L7.01 3 0.2852 0.82568 0.28 0.00 0.72 0.00 0.00 0.00 0.00 0.00
#> TCGA.B0.4848.01 6 0.1408 0.68046 0.02 0.00 0.00 0.02 0.02 0.94 0.00 0.00
#> TCGA.CZ.5985.01 6 0.5662 0.27283 0.04 0.00 0.00 0.02 0.22 0.60 0.08 0.04
#> TCGA.B0.5121.01 2 0.4953 -0.15570 0.00 0.54 0.00 0.32 0.00 0.00 0.02 0.12
#> TCGA.BP.5191.01 5 0.2938 0.57191 0.00 0.00 0.00 0.00 0.70 0.30 0.00 0.00
#> TCGA.B0.4810.01 2 0.7036 -0.30605 0.08 0.34 0.00 0.00 0.32 0.00 0.14 0.12
#> TCGA.AK.3428.01 2 0.5210 -0.18774 0.00 0.52 0.00 0.18 0.00 0.00 0.02 0.28
#> TCGA.CJ.6027.01 6 0.0471 0.67581 0.00 0.00 0.00 0.00 0.00 0.98 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: Node02. Child nodes: Node0141-leaf , Node0142-leaf , Node0143-leaf , Node0144-leaf , Node0211-leaf , Node0212-leaf , Node0213 , Node0231-leaf , Node0232-leaf , Node0233-leaf , Node0411 , Node0412-leaf , Node0413-leaf , Node0431-leaf , Node0432-leaf , Node0433-leaf , Node0511-leaf , Node0512-leaf , Node0541-leaf , Node0542-leaf , Node0543-leaf , Node0621-leaf , Node0622-leaf , Node0623-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 42 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 0.997 0.999 0.5112 0.489 0.489
#> 3 3 1.000 0.974 0.988 0.3209 0.669 0.422
#> 4 4 0.815 0.846 0.912 0.1116 0.893 0.683
#> 5 5 0.776 0.713 0.871 0.0449 0.988 0.952
#> 6 6 0.821 0.684 0.806 0.0296 0.988 0.949
#> 7 7 0.815 0.468 0.762 0.0195 0.925 0.677
#> 8 8 0.835 0.701 0.816 0.0223 0.920 0.606
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.MM.A564.01 2 0.000 0.997 0.00 1.00
#> TCGA.B0.4707.01 2 0.000 0.997 0.00 1.00
#> TCGA.CZ.5456.01 1 0.000 1.000 1.00 0.00
#> TCGA.CZ.5452.01 2 0.000 0.997 0.00 1.00
#> TCGA.AK.3425.01 2 0.000 0.997 0.00 1.00
#> TCGA.BP.5180.01 2 0.000 0.997 0.00 1.00
#> TCGA.CZ.5984.01 2 0.000 0.997 0.00 1.00
#> TCGA.CJ.4912.01 2 0.000 0.997 0.00 1.00
#> TCGA.B0.5106.01 2 0.000 0.997 0.00 1.00
#> TCGA.B8.A54I.01 2 0.000 0.997 0.00 1.00
#> TCGA.B0.4696.01 2 0.000 0.997 0.00 1.00
#> TCGA.CZ.5469.01 1 0.000 1.000 1.00 0.00
#> TCGA.B2.5641.01 2 0.000 0.997 0.00 1.00
#> TCGA.B0.4712.01 1 0.000 1.000 1.00 0.00
#> TCGA.B0.4815.01 1 0.000 1.000 1.00 0.00
#> TCGA.B0.4698.01 1 0.000 1.000 1.00 0.00
#> TCGA.B0.4688.01 2 0.141 0.982 0.02 0.98
#> TCGA.BP.5178.01 1 0.000 1.000 1.00 0.00
#> TCGA.CJ.4901.01 1 0.000 1.000 1.00 0.00
#> TCGA.CJ.5676.01 1 0.000 1.000 1.00 0.00
#> TCGA.B8.5158.01 1 0.000 1.000 1.00 0.00
#> TCGA.CJ.6030.01 1 0.000 1.000 1.00 0.00
#> TCGA.B0.5706.01 2 0.000 0.997 0.00 1.00
#> TCGA.AK.3445.01 1 0.000 1.000 1.00 0.00
#> TCGA.BP.5196.01 2 0.000 0.997 0.00 1.00
#> TCGA.CZ.5461.01 1 0.000 1.000 1.00 0.00
#> TCGA.BP.5175.01 2 0.000 0.997 0.00 1.00
#> TCGA.CZ.5987.01 2 0.141 0.982 0.02 0.98
#> TCGA.BP.5198.01 1 0.000 1.000 1.00 0.00
#> TCGA.B0.5094.01 1 0.000 1.000 1.00 0.00
#> TCGA.CZ.5468.01 1 0.000 1.000 1.00 0.00
#> TCGA.BP.5169.01 1 0.000 1.000 1.00 0.00
#> TCGA.B0.4844.01 1 0.000 1.000 1.00 0.00
#> TCGA.CZ.5464.01 2 0.000 0.997 0.00 1.00
#> TCGA.B0.5701.01 2 0.000 0.997 0.00 1.00
#> TCGA.CJ.5671.01 1 0.000 1.000 1.00 0.00
#> TCGA.CJ.5679.01 1 0.000 1.000 1.00 0.00
#> TCGA.B0.4691.01 1 0.000 1.000 1.00 0.00
#> TCGA.B0.4848.01 1 0.000 1.000 1.00 0.00
#> TCGA.CZ.5985.01 2 0.141 0.982 0.02 0.98
#> TCGA.BP.5191.01 2 0.000 0.997 0.00 1.00
#> TCGA.CJ.6027.01 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.MM.A564.01 3 0.334 0.868 0.00 0.12 0.88
#> TCGA.B0.4707.01 3 0.000 0.981 0.00 0.00 1.00
#> TCGA.CZ.5456.01 1 0.000 0.982 1.00 0.00 0.00
#> TCGA.CZ.5452.01 3 0.000 0.981 0.00 0.00 1.00
#> TCGA.AK.3425.01 3 0.000 0.981 0.00 0.00 1.00
#> TCGA.BP.5180.01 2 0.000 1.000 0.00 1.00 0.00
#> TCGA.CZ.5984.01 2 0.000 1.000 0.00 1.00 0.00
#> TCGA.CJ.4912.01 2 0.000 1.000 0.00 1.00 0.00
#> TCGA.B0.5106.01 2 0.000 1.000 0.00 1.00 0.00
#> TCGA.B8.A54I.01 2 0.000 1.000 0.00 1.00 0.00
#> TCGA.B0.4696.01 2 0.000 1.000 0.00 1.00 0.00
#> TCGA.CZ.5469.01 1 0.000 0.982 1.00 0.00 0.00
#> TCGA.B2.5641.01 2 0.000 1.000 0.00 1.00 0.00
#> TCGA.B0.4712.01 1 0.000 0.982 1.00 0.00 0.00
#> TCGA.B0.4815.01 1 0.000 0.982 1.00 0.00 0.00
#> TCGA.B0.4698.01 3 0.000 0.981 0.00 0.00 1.00
#> TCGA.B0.4688.01 3 0.000 0.981 0.00 0.00 1.00
#> TCGA.BP.5178.01 1 0.000 0.982 1.00 0.00 0.00
#> TCGA.CJ.4901.01 3 0.000 0.981 0.00 0.00 1.00
#> TCGA.CJ.5676.01 3 0.000 0.981 0.00 0.00 1.00
#> TCGA.B8.5158.01 3 0.000 0.981 0.00 0.00 1.00
#> TCGA.CJ.6030.01 3 0.000 0.981 0.00 0.00 1.00
#> TCGA.B0.5706.01 2 0.000 1.000 0.00 1.00 0.00
#> TCGA.AK.3445.01 1 0.000 0.982 1.00 0.00 0.00
#> TCGA.BP.5196.01 3 0.207 0.931 0.00 0.06 0.94
#> TCGA.CZ.5461.01 1 0.000 0.982 1.00 0.00 0.00
#> TCGA.BP.5175.01 2 0.000 1.000 0.00 1.00 0.00
#> TCGA.CZ.5987.01 3 0.000 0.981 0.00 0.00 1.00
#> TCGA.BP.5198.01 1 0.000 0.982 1.00 0.00 0.00
#> TCGA.B0.5094.01 1 0.000 0.982 1.00 0.00 0.00
#> TCGA.CZ.5468.01 3 0.000 0.981 0.00 0.00 1.00
#> TCGA.BP.5169.01 1 0.000 0.982 1.00 0.00 0.00
#> TCGA.B0.4844.01 3 0.000 0.981 0.00 0.00 1.00
#> TCGA.CZ.5464.01 2 0.000 1.000 0.00 1.00 0.00
#> TCGA.B0.5701.01 2 0.000 1.000 0.00 1.00 0.00
#> TCGA.CJ.5671.01 3 0.334 0.858 0.12 0.00 0.88
#> TCGA.CJ.5679.01 1 0.000 0.982 1.00 0.00 0.00
#> TCGA.B0.4691.01 1 0.455 0.749 0.80 0.00 0.20
#> TCGA.B0.4848.01 3 0.000 0.981 0.00 0.00 1.00
#> TCGA.CZ.5985.01 3 0.000 0.981 0.00 0.00 1.00
#> TCGA.BP.5191.01 2 0.000 1.000 0.00 1.00 0.00
#> TCGA.CJ.6027.01 1 0.000 0.982 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.MM.A564.01 4 0.0000 0.862 0.00 0.00 0.00 1.00
#> TCGA.B0.4707.01 4 0.0000 0.862 0.00 0.00 0.00 1.00
#> TCGA.CZ.5456.01 1 0.0000 1.000 1.00 0.00 0.00 0.00
#> TCGA.CZ.5452.01 4 0.0707 0.851 0.00 0.00 0.02 0.98
#> TCGA.AK.3425.01 4 0.0000 0.862 0.00 0.00 0.00 1.00
#> TCGA.BP.5180.01 2 0.1211 0.917 0.00 0.96 0.00 0.04
#> TCGA.CZ.5984.01 2 0.3610 0.846 0.00 0.80 0.00 0.20
#> TCGA.CJ.4912.01 2 0.0000 0.917 0.00 1.00 0.00 0.00
#> TCGA.B0.5106.01 2 0.0000 0.917 0.00 1.00 0.00 0.00
#> TCGA.B8.A54I.01 2 0.0707 0.918 0.00 0.98 0.00 0.02
#> TCGA.B0.4696.01 2 0.0000 0.917 0.00 1.00 0.00 0.00
#> TCGA.CZ.5469.01 1 0.0000 1.000 1.00 0.00 0.00 0.00
#> TCGA.B2.5641.01 2 0.3610 0.846 0.00 0.80 0.00 0.20
#> TCGA.B0.4712.01 1 0.0000 1.000 1.00 0.00 0.00 0.00
#> TCGA.B0.4815.01 1 0.0000 1.000 1.00 0.00 0.00 0.00
#> TCGA.B0.4698.01 3 0.0000 0.730 0.00 0.00 1.00 0.00
#> TCGA.B0.4688.01 3 0.0000 0.730 0.00 0.00 1.00 0.00
#> TCGA.BP.5178.01 1 0.0000 1.000 1.00 0.00 0.00 0.00
#> TCGA.CJ.4901.01 3 0.3801 0.765 0.00 0.00 0.78 0.22
#> TCGA.CJ.5676.01 3 0.4855 0.545 0.00 0.00 0.60 0.40
#> TCGA.B8.5158.01 3 0.3801 0.765 0.00 0.00 0.78 0.22
#> TCGA.CJ.6030.01 3 0.4855 0.545 0.00 0.00 0.60 0.40
#> TCGA.B0.5706.01 2 0.3801 0.830 0.00 0.78 0.00 0.22
#> TCGA.AK.3445.01 1 0.0000 1.000 1.00 0.00 0.00 0.00
#> TCGA.BP.5196.01 4 0.0000 0.862 0.00 0.00 0.00 1.00
#> TCGA.CZ.5461.01 1 0.0000 1.000 1.00 0.00 0.00 0.00
#> TCGA.BP.5175.01 2 0.0000 0.917 0.00 1.00 0.00 0.00
#> TCGA.CZ.5987.01 4 0.3610 0.624 0.00 0.00 0.20 0.80
#> TCGA.BP.5198.01 1 0.0000 1.000 1.00 0.00 0.00 0.00
#> TCGA.B0.5094.01 1 0.0000 1.000 1.00 0.00 0.00 0.00
#> TCGA.CZ.5468.01 3 0.0000 0.730 0.00 0.00 1.00 0.00
#> TCGA.BP.5169.01 1 0.0000 1.000 1.00 0.00 0.00 0.00
#> TCGA.B0.4844.01 3 0.4406 0.697 0.00 0.00 0.70 0.30
#> TCGA.CZ.5464.01 2 0.0000 0.917 0.00 1.00 0.00 0.00
#> TCGA.B0.5701.01 2 0.1211 0.917 0.00 0.96 0.00 0.04
#> TCGA.CJ.5671.01 3 0.4841 0.720 0.14 0.00 0.78 0.08
#> TCGA.CJ.5679.01 1 0.0000 1.000 1.00 0.00 0.00 0.00
#> TCGA.B0.4691.01 3 0.3801 0.645 0.22 0.00 0.78 0.00
#> TCGA.B0.4848.01 3 0.3801 0.765 0.00 0.00 0.78 0.22
#> TCGA.CZ.5985.01 4 0.4624 0.279 0.00 0.00 0.34 0.66
#> TCGA.BP.5191.01 2 0.3801 0.830 0.00 0.78 0.00 0.22
#> TCGA.CJ.6027.01 1 0.0000 1.000 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.MM.A564.01 4 0.2012 0.7865 0.00 0.02 0.00 0.92 0.06
#> TCGA.B0.4707.01 4 0.0000 0.7973 0.00 0.00 0.00 1.00 0.00
#> TCGA.CZ.5456.01 1 0.0000 0.9464 1.00 0.00 0.00 0.00 0.00
#> TCGA.CZ.5452.01 4 0.1732 0.7830 0.00 0.00 0.08 0.92 0.00
#> TCGA.AK.3425.01 4 0.0609 0.8032 0.00 0.00 0.02 0.98 0.00
#> TCGA.BP.5180.01 2 0.2754 0.7707 0.00 0.88 0.00 0.08 0.04
#> TCGA.CZ.5984.01 2 0.3424 0.7193 0.00 0.76 0.00 0.24 0.00
#> TCGA.CJ.4912.01 2 0.2929 0.7545 0.00 0.82 0.00 0.00 0.18
#> TCGA.B0.5106.01 2 0.2929 0.7545 0.00 0.82 0.00 0.00 0.18
#> TCGA.B8.A54I.01 2 0.1410 0.7788 0.00 0.94 0.00 0.06 0.00
#> TCGA.B0.4696.01 2 0.2929 0.7545 0.00 0.82 0.00 0.00 0.18
#> TCGA.CZ.5469.01 1 0.0000 0.9464 1.00 0.00 0.00 0.00 0.00
#> TCGA.B2.5641.01 2 0.3424 0.7193 0.00 0.76 0.00 0.24 0.00
#> TCGA.B0.4712.01 1 0.0000 0.9464 1.00 0.00 0.00 0.00 0.00
#> TCGA.B0.4815.01 1 0.0000 0.9464 1.00 0.00 0.00 0.00 0.00
#> TCGA.B0.4698.01 3 0.3983 0.0395 0.00 0.00 0.66 0.00 0.34
#> TCGA.B0.4688.01 5 0.3796 0.0000 0.00 0.00 0.30 0.00 0.70
#> TCGA.BP.5178.01 1 0.0000 0.9464 1.00 0.00 0.00 0.00 0.00
#> TCGA.CJ.4901.01 3 0.0000 0.7350 0.00 0.00 1.00 0.00 0.00
#> TCGA.CJ.5676.01 3 0.4725 0.4931 0.00 0.00 0.72 0.20 0.08
#> TCGA.B8.5158.01 3 0.0000 0.7350 0.00 0.00 1.00 0.00 0.00
#> TCGA.CJ.6030.01 3 0.4725 0.4931 0.00 0.00 0.72 0.20 0.08
#> TCGA.B0.5706.01 2 0.3895 0.6338 0.00 0.68 0.00 0.32 0.00
#> TCGA.AK.3445.01 1 0.0000 0.9464 1.00 0.00 0.00 0.00 0.00
#> TCGA.BP.5196.01 4 0.0000 0.7973 0.00 0.00 0.00 1.00 0.00
#> TCGA.CZ.5461.01 1 0.0000 0.9464 1.00 0.00 0.00 0.00 0.00
#> TCGA.BP.5175.01 2 0.2929 0.7545 0.00 0.82 0.00 0.00 0.18
#> TCGA.CZ.5987.01 4 0.5136 0.5850 0.00 0.00 0.26 0.66 0.08
#> TCGA.BP.5198.01 1 0.0000 0.9464 1.00 0.00 0.00 0.00 0.00
#> TCGA.B0.5094.01 1 0.0000 0.9464 1.00 0.00 0.00 0.00 0.00
#> TCGA.CZ.5468.01 3 0.3983 0.0395 0.00 0.00 0.66 0.00 0.34
#> TCGA.BP.5169.01 1 0.3109 0.7316 0.80 0.00 0.20 0.00 0.00
#> TCGA.B0.4844.01 3 0.2331 0.6782 0.00 0.00 0.90 0.02 0.08
#> TCGA.CZ.5464.01 2 0.2929 0.7545 0.00 0.82 0.00 0.00 0.18
#> TCGA.B0.5701.01 2 0.1732 0.7783 0.00 0.92 0.00 0.08 0.00
#> TCGA.CJ.5671.01 3 0.0000 0.7350 0.00 0.00 1.00 0.00 0.00
#> TCGA.CJ.5679.01 1 0.3796 0.5733 0.70 0.00 0.30 0.00 0.00
#> TCGA.B0.4691.01 3 0.0609 0.7143 0.02 0.00 0.98 0.00 0.00
#> TCGA.B0.4848.01 3 0.0000 0.7350 0.00 0.00 1.00 0.00 0.00
#> TCGA.CZ.5985.01 4 0.5498 0.4438 0.00 0.00 0.34 0.58 0.08
#> TCGA.BP.5191.01 2 0.3983 0.6094 0.00 0.66 0.00 0.34 0.00
#> TCGA.CJ.6027.01 1 0.0000 0.9464 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.MM.A564.01 4 0.4144 -0.105 0.00 0.02 0.00 0.62 0.00 0.36
#> TCGA.B0.4707.01 4 0.0000 0.839 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.CZ.5456.01 1 0.0000 0.938 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.CZ.5452.01 4 0.0547 0.813 0.00 0.00 0.02 0.98 0.00 0.00
#> TCGA.AK.3425.01 4 0.0000 0.839 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.BP.5180.01 2 0.3600 0.722 0.00 0.82 0.00 0.02 0.08 0.08
#> TCGA.CZ.5984.01 2 0.1556 0.762 0.00 0.92 0.00 0.08 0.00 0.00
#> TCGA.CJ.4912.01 2 0.4360 0.738 0.00 0.68 0.00 0.00 0.06 0.26
#> TCGA.B0.5106.01 2 0.4360 0.738 0.00 0.68 0.00 0.00 0.06 0.26
#> TCGA.B8.A54I.01 2 0.0000 0.776 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.B0.4696.01 2 0.4360 0.738 0.00 0.68 0.00 0.00 0.06 0.26
#> TCGA.CZ.5469.01 1 0.0000 0.938 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.B2.5641.01 2 0.1556 0.762 0.00 0.92 0.00 0.08 0.00 0.00
#> TCGA.B0.4712.01 1 0.0000 0.938 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.B0.4815.01 1 0.0000 0.938 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.B0.4698.01 3 0.5071 -0.152 0.00 0.00 0.52 0.00 0.40 0.08
#> TCGA.B0.4688.01 5 0.2260 0.000 0.00 0.00 0.14 0.00 0.86 0.00
#> TCGA.BP.5178.01 1 0.0000 0.938 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.CJ.4901.01 3 0.0937 0.677 0.00 0.00 0.96 0.00 0.00 0.04
#> TCGA.CJ.5676.01 3 0.3679 0.464 0.00 0.00 0.76 0.04 0.00 0.20
#> TCGA.B8.5158.01 3 0.0000 0.691 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.CJ.6030.01 3 0.3679 0.464 0.00 0.00 0.76 0.04 0.00 0.20
#> TCGA.B0.5706.01 2 0.2094 0.753 0.00 0.90 0.00 0.08 0.00 0.02
#> TCGA.AK.3445.01 1 0.0000 0.938 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.BP.5196.01 4 0.0000 0.839 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.CZ.5461.01 1 0.0000 0.938 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.BP.5175.01 2 0.4360 0.738 0.00 0.68 0.00 0.00 0.06 0.26
#> TCGA.CZ.5987.01 6 0.6016 0.940 0.00 0.00 0.24 0.38 0.00 0.38
#> TCGA.BP.5198.01 1 0.0000 0.938 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.B0.5094.01 1 0.0000 0.938 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.CZ.5468.01 3 0.6010 -0.297 0.00 0.00 0.40 0.00 0.36 0.24
#> TCGA.BP.5169.01 1 0.2631 0.744 0.82 0.00 0.18 0.00 0.00 0.00
#> TCGA.B0.4844.01 3 0.3076 0.525 0.00 0.00 0.76 0.00 0.00 0.24
#> TCGA.CZ.5464.01 2 0.4360 0.738 0.00 0.68 0.00 0.00 0.06 0.26
#> TCGA.B0.5701.01 2 0.0547 0.775 0.00 0.98 0.00 0.02 0.00 0.00
#> TCGA.CJ.5671.01 3 0.0000 0.691 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.CJ.5679.01 1 0.5520 0.342 0.56 0.00 0.24 0.00 0.00 0.20
#> TCGA.B0.4691.01 3 0.3076 0.525 0.00 0.00 0.76 0.00 0.00 0.24
#> TCGA.B0.4848.01 3 0.0000 0.691 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.CZ.5985.01 6 0.5945 0.940 0.00 0.00 0.22 0.36 0.00 0.42
#> TCGA.BP.5191.01 2 0.2941 0.635 0.00 0.78 0.00 0.22 0.00 0.00
#> TCGA.CJ.6027.01 1 0.0000 0.938 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.MM.A564.01 4 0.6201 0.2063 0.00 0.04 0.00 0.40 0.00 0.26 0.30
#> TCGA.B0.4707.01 4 0.0504 0.8358 0.00 0.02 0.00 0.98 0.00 0.00 0.00
#> TCGA.CZ.5456.01 1 0.0000 0.9706 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.CZ.5452.01 4 0.0504 0.8161 0.00 0.00 0.02 0.98 0.00 0.00 0.00
#> TCGA.AK.3425.01 4 0.0504 0.8358 0.00 0.02 0.00 0.98 0.00 0.00 0.00
#> TCGA.BP.5180.01 2 0.3526 0.3751 0.00 0.76 0.00 0.00 0.00 0.18 0.06
#> TCGA.CZ.5984.01 2 0.0504 0.5524 0.00 0.98 0.00 0.02 0.00 0.00 0.00
#> TCGA.CJ.4912.01 7 0.3562 1.0000 0.00 0.50 0.00 0.00 0.00 0.00 0.50
#> TCGA.B0.5106.01 2 0.3562 -1.0000 0.00 0.50 0.00 0.00 0.00 0.00 0.50
#> TCGA.B8.A54I.01 2 0.0000 0.5434 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.B0.4696.01 2 0.4278 -0.9327 0.00 0.50 0.00 0.00 0.04 0.00 0.46
#> TCGA.CZ.5469.01 1 0.0000 0.9706 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.B2.5641.01 2 0.0504 0.5524 0.00 0.98 0.00 0.02 0.00 0.00 0.00
#> TCGA.B0.4712.01 1 0.0000 0.9706 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.B0.4815.01 1 0.0000 0.9706 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.B0.4698.01 3 0.6229 0.2896 0.00 0.00 0.44 0.02 0.30 0.22 0.02
#> TCGA.B0.4688.01 5 0.0863 0.0000 0.00 0.00 0.04 0.00 0.96 0.00 0.00
#> TCGA.BP.5178.01 1 0.0000 0.9706 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.CJ.4901.01 3 0.2945 0.3878 0.00 0.00 0.74 0.00 0.00 0.26 0.00
#> TCGA.CJ.5676.01 6 0.4266 0.2823 0.00 0.00 0.44 0.04 0.00 0.52 0.00
#> TCGA.B8.5158.01 3 0.3139 0.3740 0.00 0.00 0.70 0.00 0.00 0.30 0.00
#> TCGA.CJ.6030.01 6 0.4266 0.2823 0.00 0.00 0.44 0.04 0.00 0.52 0.00
#> TCGA.B0.5706.01 2 0.1363 0.5368 0.00 0.94 0.00 0.02 0.00 0.00 0.04
#> TCGA.AK.3445.01 1 0.0000 0.9706 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.BP.5196.01 4 0.0504 0.8358 0.00 0.02 0.00 0.98 0.00 0.00 0.00
#> TCGA.CZ.5461.01 1 0.0000 0.9706 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.BP.5175.01 2 0.3562 -1.0000 0.00 0.50 0.00 0.00 0.00 0.00 0.50
#> TCGA.CZ.5987.01 6 0.6262 0.1733 0.00 0.00 0.10 0.22 0.00 0.50 0.18
#> TCGA.BP.5198.01 1 0.0000 0.9706 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.B0.5094.01 1 0.0000 0.9706 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.CZ.5468.01 3 0.4574 0.0679 0.00 0.00 0.68 0.02 0.24 0.02 0.04
#> TCGA.BP.5169.01 1 0.2832 0.6481 0.76 0.00 0.24 0.00 0.00 0.00 0.00
#> TCGA.B0.4844.01 6 0.3968 0.1922 0.00 0.00 0.44 0.00 0.00 0.54 0.02
#> TCGA.CZ.5464.01 7 0.3562 1.0000 0.00 0.50 0.00 0.00 0.00 0.00 0.50
#> TCGA.B0.5701.01 2 0.0000 0.5434 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.CJ.5671.01 3 0.3139 0.3740 0.00 0.00 0.70 0.00 0.00 0.30 0.00
#> TCGA.CJ.5679.01 3 0.4386 -0.0665 0.42 0.00 0.54 0.00 0.00 0.02 0.02
#> TCGA.B0.4691.01 3 0.1006 0.3466 0.00 0.00 0.96 0.00 0.00 0.02 0.02
#> TCGA.B0.4848.01 3 0.3139 0.3740 0.00 0.00 0.70 0.00 0.00 0.30 0.00
#> TCGA.CZ.5985.01 6 0.6458 0.1544 0.00 0.00 0.10 0.18 0.00 0.44 0.28
#> TCGA.BP.5191.01 2 0.2832 0.3737 0.00 0.76 0.00 0.24 0.00 0.00 0.00
#> TCGA.CJ.6027.01 1 0.0000 0.9706 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.MM.A564.01 6 0.5336 0.5985 0.00 0.10 0.00 0.22 0.00 0.58 0.00 0.10
#> TCGA.B0.4707.01 4 0.0000 1.0000 0.00 0.00 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.CZ.5456.01 1 0.0000 0.9411 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.CZ.5452.01 4 0.0000 1.0000 0.00 0.00 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.AK.3425.01 4 0.0000 1.0000 0.00 0.00 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.BP.5180.01 2 0.4673 0.6817 0.00 0.56 0.00 0.00 0.00 0.02 0.34 0.08
#> TCGA.CZ.5984.01 2 0.4302 0.8459 0.00 0.56 0.00 0.08 0.00 0.00 0.36 0.00
#> TCGA.CJ.4912.01 7 0.0000 0.9777 0.00 0.00 0.00 0.00 0.00 0.00 1.00 0.00
#> TCGA.B0.5106.01 7 0.0000 0.9777 0.00 0.00 0.00 0.00 0.00 0.00 1.00 0.00
#> TCGA.B8.A54I.01 2 0.3299 0.7918 0.00 0.56 0.00 0.00 0.00 0.00 0.44 0.00
#> TCGA.B0.4696.01 7 0.1557 0.9076 0.00 0.00 0.00 0.00 0.00 0.02 0.92 0.06
#> TCGA.CZ.5469.01 1 0.0000 0.9411 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.B2.5641.01 2 0.4302 0.8459 0.00 0.56 0.00 0.08 0.00 0.00 0.36 0.00
#> TCGA.B0.4712.01 1 0.0941 0.9336 0.96 0.02 0.00 0.00 0.00 0.00 0.00 0.02
#> TCGA.B0.4815.01 1 0.0941 0.9336 0.96 0.02 0.00 0.00 0.00 0.00 0.00 0.02
#> TCGA.B0.4698.01 3 0.4437 0.0226 0.00 0.00 0.62 0.00 0.16 0.00 0.00 0.22
#> TCGA.B0.4688.01 5 0.0000 0.0000 0.00 0.00 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.BP.5178.01 1 0.0941 0.9336 0.96 0.02 0.00 0.00 0.00 0.00 0.00 0.02
#> TCGA.CJ.4901.01 3 0.1557 0.4978 0.00 0.02 0.92 0.00 0.00 0.00 0.00 0.06
#> TCGA.CJ.5676.01 3 0.3193 0.3604 0.00 0.00 0.62 0.00 0.00 0.38 0.00 0.00
#> TCGA.B8.5158.01 3 0.0000 0.5587 0.00 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.CJ.6030.01 3 0.2938 0.4607 0.00 0.00 0.70 0.00 0.00 0.30 0.00 0.00
#> TCGA.B0.5706.01 2 0.4255 0.8388 0.00 0.58 0.00 0.08 0.00 0.00 0.34 0.00
#> TCGA.AK.3445.01 1 0.0000 0.9411 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.BP.5196.01 4 0.0000 1.0000 0.00 0.00 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.CZ.5461.01 1 0.0000 0.9411 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.BP.5175.01 7 0.0000 0.9777 0.00 0.00 0.00 0.00 0.00 0.00 1.00 0.00
#> TCGA.CZ.5987.01 6 0.2404 0.6790 0.00 0.00 0.02 0.14 0.00 0.84 0.00 0.00
#> TCGA.BP.5198.01 1 0.0941 0.9336 0.96 0.02 0.00 0.00 0.00 0.00 0.00 0.02
#> TCGA.B0.5094.01 1 0.0000 0.9411 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.CZ.5468.01 8 0.4050 0.4469 0.00 0.00 0.34 0.00 0.06 0.00 0.00 0.60
#> TCGA.BP.5169.01 1 0.4276 0.3574 0.64 0.06 0.28 0.00 0.00 0.00 0.00 0.02
#> TCGA.B0.4844.01 3 0.4680 0.2144 0.00 0.12 0.48 0.00 0.00 0.40 0.00 0.00
#> TCGA.CZ.5464.01 7 0.0000 0.9777 0.00 0.00 0.00 0.00 0.00 0.00 1.00 0.00
#> TCGA.B0.5701.01 2 0.3299 0.7918 0.00 0.56 0.00 0.00 0.00 0.00 0.44 0.00
#> TCGA.CJ.5671.01 3 0.0471 0.5487 0.00 0.02 0.98 0.00 0.00 0.00 0.00 0.00
#> TCGA.CJ.5679.01 8 0.6284 0.5158 0.18 0.08 0.28 0.00 0.00 0.02 0.00 0.44
#> TCGA.B0.4691.01 3 0.4803 -0.5873 0.00 0.08 0.46 0.00 0.00 0.02 0.00 0.44
#> TCGA.B0.4848.01 3 0.0000 0.5587 0.00 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.CZ.5985.01 6 0.4046 0.5614 0.00 0.06 0.02 0.02 0.00 0.74 0.00 0.16
#> TCGA.BP.5191.01 2 0.4757 0.6731 0.00 0.56 0.00 0.24 0.00 0.00 0.20 0.00
#> TCGA.CJ.6027.01 1 0.0000 0.9411 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: Node021. Child nodes: Node02131-leaf , Node02132-leaf , Node02133-leaf , Node04111-leaf , Node04112-leaf , Node04113-leaf , Node04114-leaf .
The object with results only for a single top-value method and a single partitioning method can be extracted as:
res = res_rh["0213"]
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 17 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 0.3095 0.691 0.691
#> 3 3 1.000 1.000 1.000 1.0680 0.669 0.521
#> 4 4 1.000 0.938 0.999 0.0219 0.985 0.959
#> 5 5 0.824 0.641 0.893 0.1532 0.897 0.702
#> 6 6 0.691 0.653 0.865 0.0736 0.875 0.541
#> 7 7 0.691 0.499 0.819 0.0389 0.890 0.483
#> 8 8 0.728 0.430 0.840 0.0362 0.897 0.440
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.MM.A564.01 1 0 1 1 0
#> TCGA.B0.4707.01 1 0 1 1 0
#> TCGA.CZ.5452.01 1 0 1 1 0
#> TCGA.AK.3425.01 1 0 1 1 0
#> TCGA.B0.4698.01 2 0 1 0 1
#> TCGA.B0.4688.01 2 0 1 0 1
#> TCGA.CJ.4901.01 1 0 1 1 0
#> TCGA.CJ.5676.01 1 0 1 1 0
#> TCGA.B8.5158.01 1 0 1 1 0
#> TCGA.CJ.6030.01 1 0 1 1 0
#> TCGA.BP.5196.01 1 0 1 1 0
#> TCGA.CZ.5987.01 1 0 1 1 0
#> TCGA.CZ.5468.01 2 0 1 0 1
#> TCGA.B0.4844.01 1 0 1 1 0
#> TCGA.CJ.5671.01 1 0 1 1 0
#> TCGA.B0.4848.01 1 0 1 1 0
#> TCGA.CZ.5985.01 1 0 1 1 0
cbind(get_classes(res, k = 3), get_membership(res, k = 3))
#> class entropy silhouette p1 p2 p3
#> TCGA.MM.A564.01 3 0 1 0 0 1
#> TCGA.B0.4707.01 1 0 1 1 0 0
#> TCGA.CZ.5452.01 1 0 1 1 0 0
#> TCGA.AK.3425.01 1 0 1 1 0 0
#> TCGA.B0.4698.01 2 0 1 0 1 0
#> TCGA.B0.4688.01 2 0 1 0 1 0
#> TCGA.CJ.4901.01 1 0 1 1 0 0
#> TCGA.CJ.5676.01 3 0 1 0 0 1
#> TCGA.B8.5158.01 1 0 1 1 0 0
#> TCGA.CJ.6030.01 1 0 1 1 0 0
#> TCGA.BP.5196.01 1 0 1 1 0 0
#> TCGA.CZ.5987.01 3 0 1 0 0 1
#> TCGA.CZ.5468.01 2 0 1 0 1 0
#> TCGA.B0.4844.01 3 0 1 0 0 1
#> TCGA.CJ.5671.01 1 0 1 1 0 0
#> TCGA.B0.4848.01 1 0 1 1 0 0
#> TCGA.CZ.5985.01 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.MM.A564.01 3 0.0000 0.992 0.00 0 1.00 0
#> TCGA.B0.4707.01 1 0.0000 1.000 1.00 0 0.00 0
#> TCGA.CZ.5452.01 1 0.0000 1.000 1.00 0 0.00 0
#> TCGA.AK.3425.01 1 0.0000 1.000 1.00 0 0.00 0
#> TCGA.B0.4698.01 2 0.0000 1.000 0.00 1 0.00 0
#> TCGA.B0.4688.01 2 0.0000 1.000 0.00 1 0.00 0
#> TCGA.CJ.4901.01 1 0.0000 1.000 1.00 0 0.00 0
#> TCGA.CJ.5676.01 3 0.0707 0.969 0.02 0 0.98 0
#> TCGA.B8.5158.01 1 0.0000 1.000 1.00 0 0.00 0
#> TCGA.CJ.6030.01 1 0.0000 1.000 1.00 0 0.00 0
#> TCGA.BP.5196.01 1 0.0000 1.000 1.00 0 0.00 0
#> TCGA.CZ.5987.01 3 0.0000 0.992 0.00 0 1.00 0
#> TCGA.CZ.5468.01 4 0.0000 0.000 0.00 0 0.00 1
#> TCGA.B0.4844.01 3 0.0000 0.992 0.00 0 1.00 0
#> TCGA.CJ.5671.01 1 0.0000 1.000 1.00 0 0.00 0
#> TCGA.B0.4848.01 1 0.0000 1.000 1.00 0 0.00 0
#> TCGA.CZ.5985.01 3 0.0000 0.992 0.00 0 1.00 0
cbind(get_classes(res, k = 5), get_membership(res, k = 5))
#> class entropy silhouette p1 p2 p3 p4 p5
#> TCGA.MM.A564.01 3 0.0609 0.9695 0.00 0 0.98 0 0.02
#> TCGA.B0.4707.01 5 0.1410 0.4179 0.06 0 0.00 0 0.94
#> TCGA.CZ.5452.01 1 0.0000 0.6628 1.00 0 0.00 0 0.00
#> TCGA.AK.3425.01 1 0.4227 0.2341 0.58 0 0.00 0 0.42
#> TCGA.B0.4698.01 2 0.0000 1.0000 0.00 1 0.00 0 0.00
#> TCGA.B0.4688.01 2 0.0000 1.0000 0.00 1 0.00 0 0.00
#> TCGA.CJ.4901.01 1 0.0000 0.6628 1.00 0 0.00 0 0.00
#> TCGA.CJ.5676.01 3 0.1043 0.9415 0.00 0 0.96 0 0.04
#> TCGA.B8.5158.01 1 0.0609 0.6693 0.98 0 0.00 0 0.02
#> TCGA.CJ.6030.01 1 0.4126 0.3568 0.62 0 0.00 0 0.38
#> TCGA.BP.5196.01 5 0.4182 0.0361 0.40 0 0.00 0 0.60
#> TCGA.CZ.5987.01 3 0.0000 0.9682 0.00 0 1.00 0 0.00
#> TCGA.CZ.5468.01 4 0.0000 0.0000 0.00 0 0.00 1 0.00
#> TCGA.B0.4844.01 3 0.0609 0.9695 0.00 0 0.98 0 0.02
#> TCGA.CJ.5671.01 1 0.1732 0.6602 0.92 0 0.00 0 0.08
#> TCGA.B0.4848.01 1 0.4060 0.3959 0.64 0 0.00 0 0.36
#> TCGA.CZ.5985.01 3 0.1043 0.9523 0.00 0 0.96 0 0.04
cbind(get_classes(res, k = 6), get_membership(res, k = 6))
#> class entropy silhouette p1 p2 p3 p4 p5 p6
#> TCGA.MM.A564.01 3 0.0000 0.787 0.00 0 1.00 0 0.00 0.00
#> TCGA.B0.4707.01 5 0.3797 0.000 0.42 0 0.00 0 0.58 0.00
#> TCGA.CZ.5452.01 6 0.0547 0.861 0.02 0 0.00 0 0.00 0.98
#> TCGA.AK.3425.01 1 0.1556 0.700 0.92 0 0.00 0 0.00 0.08
#> TCGA.B0.4698.01 2 0.0000 1.000 0.00 1 0.00 0 0.00 0.00
#> TCGA.B0.4688.01 2 0.0000 1.000 0.00 1 0.00 0 0.00 0.00
#> TCGA.CJ.4901.01 6 0.0937 0.872 0.04 0 0.00 0 0.00 0.96
#> TCGA.CJ.5676.01 3 0.3309 0.510 0.28 0 0.72 0 0.00 0.00
#> TCGA.B8.5158.01 6 0.2793 0.716 0.20 0 0.00 0 0.00 0.80
#> TCGA.CJ.6030.01 1 0.2631 0.758 0.82 0 0.00 0 0.00 0.18
#> TCGA.BP.5196.01 1 0.0937 0.491 0.96 0 0.00 0 0.04 0.00
#> TCGA.CZ.5987.01 3 0.1556 0.777 0.00 0 0.92 0 0.08 0.00
#> TCGA.CZ.5468.01 4 0.0000 0.000 0.00 0 0.00 1 0.00 0.00
#> TCGA.B0.4844.01 3 0.0000 0.787 0.00 0 1.00 0 0.00 0.00
#> TCGA.CJ.5671.01 1 0.3647 0.580 0.64 0 0.00 0 0.00 0.36
#> TCGA.B0.4848.01 1 0.2941 0.750 0.78 0 0.00 0 0.00 0.22
#> TCGA.CZ.5985.01 3 0.4282 0.511 0.00 0 0.56 0 0.42 0.02
cbind(get_classes(res, k = 7), get_membership(res, k = 7))
#> class entropy silhouette p1 p2 p3 p4 p5 p6 p7
#> TCGA.MM.A564.01 3 0.0000 0.7342 0.00 0 1.00 0 0.00 0.00 0.00
#> TCGA.B0.4707.01 5 0.3927 0.0000 0.04 0 0.00 0 0.66 0.00 0.30
#> TCGA.CZ.5452.01 6 0.2572 0.7865 0.20 0 0.00 0 0.00 0.80 0.00
#> TCGA.AK.3425.01 1 0.3548 0.6103 0.80 0 0.00 0 0.04 0.04 0.12
#> TCGA.B0.4698.01 2 0.0000 1.0000 0.00 1 0.00 0 0.00 0.00 0.00
#> TCGA.B0.4688.01 2 0.0000 1.0000 0.00 1 0.00 0 0.00 0.00 0.00
#> TCGA.CJ.4901.01 6 0.3294 0.7507 0.34 0 0.00 0 0.00 0.66 0.00
#> TCGA.CJ.5676.01 3 0.4377 0.5539 0.24 0 0.68 0 0.00 0.02 0.06
#> TCGA.B8.5158.01 1 0.3413 0.0424 0.62 0 0.00 0 0.00 0.38 0.00
#> TCGA.CJ.6030.01 1 0.0000 0.7512 1.00 0 0.00 0 0.00 0.00 0.00
#> TCGA.BP.5196.01 7 0.3558 -0.3535 0.48 0 0.00 0 0.00 0.00 0.52
#> TCGA.CZ.5987.01 3 0.5321 0.6174 0.00 0 0.64 0 0.16 0.08 0.12
#> TCGA.CZ.5468.01 4 0.0000 0.0000 0.00 0 0.00 1 0.00 0.00 0.00
#> TCGA.B0.4844.01 3 0.2213 0.7296 0.00 0 0.90 0 0.02 0.04 0.04
#> TCGA.CJ.5671.01 1 0.1671 0.6945 0.90 0 0.00 0 0.00 0.10 0.00
#> TCGA.B0.4848.01 1 0.0504 0.7495 0.98 0 0.00 0 0.00 0.00 0.02
#> TCGA.CZ.5985.01 7 0.6290 -0.1918 0.00 0 0.10 0 0.30 0.14 0.46
cbind(get_classes(res, k = 8), get_membership(res, k = 8))
#> class entropy silhouette p1 p2 p3 p4 p5 p6 p7 p8
#> TCGA.MM.A564.01 3 0.1091 0.761 0.00 0.00 0.94 0 0.00 0.00 0.06 0.0
#> TCGA.B0.4707.01 5 0.0000 0.000 0.00 0.00 0.00 0 1.00 0.00 0.00 0.0
#> TCGA.CZ.5452.01 6 0.1091 0.599 0.06 0.00 0.00 0 0.00 0.94 0.00 0.0
#> TCGA.AK.3425.01 1 0.3299 0.322 0.76 0.00 0.00 0 0.06 0.00 0.18 0.0
#> TCGA.B0.4698.01 2 0.0000 0.898 0.00 1.00 0.00 0 0.00 0.00 0.00 0.0
#> TCGA.B0.4688.01 2 0.1765 0.898 0.00 0.88 0.00 0 0.00 0.00 0.12 0.0
#> TCGA.CJ.4901.01 6 0.3657 0.624 0.20 0.00 0.00 0 0.00 0.72 0.08 0.0
#> TCGA.CJ.5676.01 1 0.6365 -0.168 0.40 0.00 0.36 0 0.00 0.04 0.10 0.1
#> TCGA.B8.5158.01 6 0.3318 0.326 0.46 0.00 0.00 0 0.00 0.54 0.00 0.0
#> TCGA.CJ.6030.01 1 0.0471 0.597 0.98 0.00 0.00 0 0.00 0.00 0.02 0.0
#> TCGA.BP.5196.01 7 0.4593 0.000 0.26 0.00 0.00 0 0.10 0.02 0.62 0.0
#> TCGA.CZ.5987.01 3 0.4593 0.549 0.00 0.00 0.66 0 0.00 0.04 0.10 0.2
#> TCGA.CZ.5468.01 4 0.0000 0.000 0.00 0.00 0.00 1 0.00 0.00 0.00 0.0
#> TCGA.B0.4844.01 3 0.0941 0.761 0.00 0.00 0.96 0 0.00 0.02 0.02 0.0
#> TCGA.CJ.5671.01 1 0.2025 0.536 0.88 0.00 0.00 0 0.00 0.10 0.02 0.0
#> TCGA.B0.4848.01 1 0.0471 0.601 0.98 0.00 0.00 0 0.00 0.02 0.00 0.0
#> TCGA.CZ.5985.01 8 0.0000 0.000 0.00 0.00 0.00 0 0.00 0.00 0.00 1.0
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: Node02. Child nodes: Node0141-leaf , Node0142-leaf , Node0143-leaf , Node0144-leaf , Node0211-leaf , Node0212-leaf , Node0213 , Node0231-leaf , Node0232-leaf , Node0233-leaf , Node0411 , Node0412-leaf , Node0413-leaf , Node0431-leaf , Node0432-leaf , Node0433-leaf , Node0511-leaf , Node0512-leaf , Node0541-leaf , Node0542-leaf , Node0543-leaf , Node0621-leaf , Node0622-leaf , Node0623-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 23 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 0.4985 0.502 0.502
#> 3 3 1.000 0.960 0.977 0.3307 0.842 0.685
#> 4 4 0.800 0.616 0.724 0.1016 0.917 0.759
#> 5 5 0.752 0.636 0.770 0.0395 0.874 0.600
#> 6 6 0.767 0.688 0.837 0.0394 0.964 0.857
#> 7 7 0.724 0.542 0.803 0.0349 0.968 0.855
#> 8 8 0.757 0.460 0.786 0.0230 0.988 0.938
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.B0.5113.01 1 0 1 1 0
#> TCGA.CJ.5677.01 2 0 1 0 1
#> TCGA.B0.4713.01 2 0 1 0 1
#> TCGA.B0.4821.01 2 0 1 0 1
#> TCGA.B0.5712.01 1 0 1 1 0
#> TCGA.CJ.4920.01 1 0 1 1 0
#> TCGA.B0.5692.01 1 0 1 1 0
#> TCGA.B0.4827.01 2 0 1 0 1
#> TCGA.G6.A5PC.01 1 0 1 1 0
#> TCGA.CW.5580.01 1 0 1 1 0
#> TCGA.CJ.4913.01 1 0 1 1 0
#> TCGA.CJ.6033.01 2 0 1 0 1
#> TCGA.B0.5096.01 2 0 1 0 1
#> TCGA.B0.5107.01 2 0 1 0 1
#> TCGA.CZ.4866.01 1 0 1 1 0
#> TCGA.B0.4693.01 1 0 1 1 0
#> TCGA.B0.4710.01 1 0 1 1 0
#> TCGA.CZ.5465.01 1 0 1 1 0
#> TCGA.B8.5159.01 1 0 1 1 0
#> TCGA.CJ.5680.01 1 0 1 1 0
#> TCGA.CZ.5470.01 2 0 1 0 1
#> TCGA.G6.A8L8.01 1 0 1 1 0
#> TCGA.G6.A8L7.01 2 0 1 0 1
cbind(get_classes(res, k = 3), get_membership(res, k = 3))
#> class entropy silhouette p1 p2 p3
#> TCGA.B0.5113.01 3 0.0892 0.985 0.02 0 0.98
#> TCGA.CJ.5677.01 2 0.0000 1.000 0.00 1 0.00
#> TCGA.B0.4713.01 2 0.0000 1.000 0.00 1 0.00
#> TCGA.B0.4821.01 2 0.0000 1.000 0.00 1 0.00
#> TCGA.B0.5712.01 1 0.2959 0.898 0.90 0 0.10
#> TCGA.CJ.4920.01 1 0.0892 0.944 0.98 0 0.02
#> TCGA.B0.5692.01 1 0.0892 0.945 0.98 0 0.02
#> TCGA.B0.4827.01 2 0.0000 1.000 0.00 1 0.00
#> TCGA.G6.A5PC.01 1 0.0000 0.948 1.00 0 0.00
#> TCGA.CW.5580.01 1 0.0892 0.944 0.98 0 0.02
#> TCGA.CJ.4913.01 1 0.0000 0.948 1.00 0 0.00
#> TCGA.CJ.6033.01 2 0.0000 1.000 0.00 1 0.00
#> TCGA.B0.5096.01 2 0.0000 1.000 0.00 1 0.00
#> TCGA.B0.5107.01 2 0.0000 1.000 0.00 1 0.00
#> TCGA.CZ.4866.01 1 0.0000 0.948 1.00 0 0.00
#> TCGA.B0.4693.01 1 0.1529 0.936 0.96 0 0.04
#> TCGA.B0.4710.01 1 0.5397 0.671 0.72 0 0.28
#> TCGA.CZ.5465.01 3 0.0000 0.985 0.00 0 1.00
#> TCGA.B8.5159.01 3 0.0892 0.985 0.02 0 0.98
#> TCGA.CJ.5680.01 1 0.0000 0.948 1.00 0 0.00
#> TCGA.CZ.5470.01 2 0.0000 1.000 0.00 1 0.00
#> TCGA.G6.A8L8.01 3 0.0000 0.985 0.00 0 1.00
#> TCGA.G6.A8L7.01 2 0.0000 1.000 0.00 1 0.00
cbind(get_classes(res, k = 4), get_membership(res, k = 4))
#> class entropy silhouette p1 p2 p3 p4
#> TCGA.B0.5113.01 3 0.5428 0.6111 0.38 0 0.60 0.02
#> TCGA.CJ.5677.01 2 0.0000 1.0000 0.00 1 0.00 0.00
#> TCGA.B0.4713.01 2 0.0000 1.0000 0.00 1 0.00 0.00
#> TCGA.B0.4821.01 2 0.0000 1.0000 0.00 1 0.00 0.00
#> TCGA.B0.5712.01 1 0.4227 0.3171 0.82 0 0.06 0.12
#> TCGA.CJ.4920.01 1 0.5915 0.0143 0.56 0 0.04 0.40
#> TCGA.B0.5692.01 1 0.4713 0.1806 0.64 0 0.00 0.36
#> TCGA.B0.4827.01 2 0.0000 1.0000 0.00 1 0.00 0.00
#> TCGA.G6.A5PC.01 4 0.4277 0.5168 0.28 0 0.00 0.72
#> TCGA.CW.5580.01 1 0.5860 0.0400 0.58 0 0.04 0.38
#> TCGA.CJ.4913.01 1 0.4994 -0.1023 0.52 0 0.00 0.48
#> TCGA.CJ.6033.01 2 0.0000 1.0000 0.00 1 0.00 0.00
#> TCGA.B0.5096.01 2 0.0000 1.0000 0.00 1 0.00 0.00
#> TCGA.B0.5107.01 2 0.0000 1.0000 0.00 1 0.00 0.00
#> TCGA.CZ.4866.01 4 0.1211 0.5819 0.04 0 0.00 0.96
#> TCGA.B0.4693.01 1 0.5713 0.1951 0.62 0 0.04 0.34
#> TCGA.B0.4710.01 1 0.5106 0.1873 0.72 0 0.24 0.04
#> TCGA.CZ.5465.01 3 0.0707 0.6828 0.02 0 0.98 0.00
#> TCGA.B8.5159.01 3 0.5487 0.5893 0.40 0 0.58 0.02
#> TCGA.CJ.5680.01 4 0.3172 0.6810 0.16 0 0.00 0.84
#> TCGA.CZ.5470.01 2 0.0000 1.0000 0.00 1 0.00 0.00
#> TCGA.G6.A8L8.01 3 0.0000 0.6761 0.00 0 1.00 0.00
#> TCGA.G6.A8L7.01 2 0.0000 1.0000 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.B0.5113.01 1 0.492 0.176 0.62 0.00 0.34 0.04 0.00
#> TCGA.CJ.5677.01 2 0.000 0.978 0.00 1.00 0.00 0.00 0.00
#> TCGA.B0.4713.01 2 0.000 0.978 0.00 1.00 0.00 0.00 0.00
#> TCGA.B0.4821.01 2 0.000 0.978 0.00 1.00 0.00 0.00 0.00
#> TCGA.B0.5712.01 5 0.680 0.213 0.40 0.00 0.08 0.06 0.46
#> TCGA.CJ.4920.01 5 0.173 0.552 0.08 0.00 0.00 0.00 0.92
#> TCGA.B0.5692.01 1 0.397 0.499 0.80 0.00 0.00 0.10 0.10
#> TCGA.B0.4827.01 2 0.000 0.978 0.00 1.00 0.00 0.00 0.00
#> TCGA.G6.A5PC.01 1 0.613 0.246 0.54 0.00 0.00 0.16 0.30
#> TCGA.CW.5580.01 5 0.104 0.577 0.04 0.00 0.00 0.00 0.96
#> TCGA.CJ.4913.01 1 0.560 0.380 0.62 0.00 0.00 0.12 0.26
#> TCGA.CJ.6033.01 2 0.202 0.905 0.00 0.90 0.00 0.00 0.10
#> TCGA.B0.5096.01 2 0.000 0.978 0.00 1.00 0.00 0.00 0.00
#> TCGA.B0.5107.01 2 0.000 0.978 0.00 1.00 0.00 0.00 0.00
#> TCGA.CZ.4866.01 4 0.287 0.381 0.02 0.00 0.00 0.86 0.12
#> TCGA.B0.4693.01 1 0.464 0.485 0.74 0.00 0.00 0.10 0.16
#> TCGA.B0.4710.01 1 0.568 0.171 0.70 0.00 0.08 0.06 0.16
#> TCGA.CZ.5465.01 3 0.201 0.871 0.06 0.00 0.92 0.00 0.02
#> TCGA.B8.5159.01 1 0.464 0.255 0.68 0.00 0.28 0.04 0.00
#> TCGA.CJ.5680.01 4 0.653 0.263 0.20 0.00 0.00 0.44 0.36
#> TCGA.CZ.5470.01 2 0.000 0.978 0.00 1.00 0.00 0.00 0.00
#> TCGA.G6.A8L8.01 3 0.165 0.871 0.04 0.00 0.94 0.02 0.00
#> TCGA.G6.A8L7.01 2 0.201 0.927 0.00 0.92 0.00 0.02 0.06
cbind(get_classes(res, k = 6), get_membership(res, k = 6))
#> class entropy silhouette p1 p2 p3 p4 p5 p6
#> TCGA.B0.5113.01 1 0.4632 0.178 0.52 0.00 0.44 0.00 0.00 0.04
#> TCGA.CJ.5677.01 2 0.0000 0.934 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.B0.4713.01 2 0.0000 0.934 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.B0.4821.01 2 0.0000 0.934 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.B0.5712.01 6 0.5774 0.370 0.14 0.00 0.02 0.00 0.28 0.56
#> TCGA.CJ.4920.01 5 0.0547 1.000 0.02 0.00 0.00 0.00 0.98 0.00
#> TCGA.B0.5692.01 1 0.0547 0.579 0.98 0.00 0.00 0.02 0.00 0.00
#> TCGA.B0.4827.01 2 0.1480 0.907 0.00 0.94 0.00 0.00 0.04 0.02
#> TCGA.G6.A5PC.01 1 0.4667 0.392 0.74 0.00 0.00 0.12 0.10 0.04
#> TCGA.CW.5580.01 5 0.0547 1.000 0.02 0.00 0.00 0.00 0.98 0.00
#> TCGA.CJ.4913.01 1 0.3007 0.543 0.86 0.00 0.00 0.08 0.04 0.02
#> TCGA.CJ.6033.01 2 0.3315 0.752 0.00 0.78 0.00 0.02 0.20 0.00
#> TCGA.B0.5096.01 2 0.0000 0.934 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.B0.5107.01 2 0.0000 0.934 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.CZ.4866.01 4 0.1865 0.404 0.04 0.00 0.00 0.92 0.04 0.00
#> TCGA.B0.4693.01 1 0.0000 0.575 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.B0.4710.01 6 0.6676 0.376 0.38 0.00 0.06 0.00 0.16 0.40
#> TCGA.CZ.5465.01 3 0.2094 0.911 0.00 0.00 0.90 0.00 0.02 0.08
#> TCGA.B8.5159.01 1 0.5371 0.230 0.52 0.00 0.36 0.00 0.00 0.12
#> TCGA.CJ.5680.01 4 0.7062 0.351 0.28 0.00 0.00 0.44 0.16 0.12
#> TCGA.CZ.5470.01 2 0.0547 0.926 0.00 0.98 0.00 0.00 0.02 0.00
#> TCGA.G6.A8L8.01 3 0.0000 0.913 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.G6.A8L7.01 2 0.4541 0.740 0.00 0.74 0.00 0.04 0.06 0.16
cbind(get_classes(res, k = 7), get_membership(res, k = 7))
#> class entropy silhouette p1 p2 p3 p4 p5 p6 p7
#> TCGA.B0.5113.01 1 0.5604 0.2475 0.52 0.00 0.20 0.02 0.00 0.26 0.00
#> TCGA.CJ.5677.01 2 0.0000 0.8236 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.B0.4713.01 2 0.0000 0.8236 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.B0.4821.01 2 0.0000 0.8236 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.B0.5712.01 6 0.6990 0.1783 0.12 0.00 0.02 0.02 0.24 0.48 0.12
#> TCGA.CJ.4920.01 5 0.0504 0.9687 0.02 0.00 0.00 0.00 0.98 0.00 0.00
#> TCGA.B0.5692.01 1 0.0863 0.5732 0.96 0.00 0.00 0.00 0.00 0.04 0.00
#> TCGA.B0.4827.01 2 0.3795 0.3376 0.00 0.72 0.00 0.00 0.06 0.00 0.22
#> TCGA.G6.A5PC.01 1 0.4854 0.3897 0.70 0.00 0.00 0.04 0.18 0.04 0.04
#> TCGA.CW.5580.01 5 0.1006 0.9688 0.02 0.00 0.00 0.00 0.96 0.02 0.00
#> TCGA.CJ.4913.01 1 0.2512 0.5391 0.86 0.00 0.00 0.00 0.10 0.00 0.04
#> TCGA.CJ.6033.01 2 0.4045 0.3456 0.00 0.72 0.00 0.00 0.14 0.00 0.14
#> TCGA.B0.5096.01 2 0.2081 0.6714 0.00 0.86 0.00 0.00 0.00 0.00 0.14
#> TCGA.B0.5107.01 2 0.0000 0.8236 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.CZ.4866.01 4 0.1166 0.3421 0.00 0.00 0.00 0.94 0.06 0.00 0.00
#> TCGA.B0.4693.01 1 0.0000 0.5834 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.B0.4710.01 6 0.5279 0.0605 0.34 0.00 0.02 0.00 0.04 0.56 0.04
#> TCGA.CZ.5465.01 3 0.3011 0.8375 0.00 0.00 0.82 0.00 0.00 0.12 0.06
#> TCGA.B8.5159.01 1 0.6148 0.1837 0.48 0.00 0.10 0.02 0.00 0.34 0.06
#> TCGA.CJ.5680.01 4 0.7864 0.2757 0.22 0.00 0.00 0.32 0.20 0.08 0.18
#> TCGA.CZ.5470.01 2 0.0000 0.8236 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.G6.A8L8.01 3 0.0000 0.8413 0.00 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.G6.A8L7.01 7 0.4214 0.0000 0.00 0.40 0.00 0.00 0.04 0.00 0.56
cbind(get_classes(res, k = 8), get_membership(res, k = 8))
#> class entropy silhouette p1 p2 p3 p4 p5 p6 p7 p8
#> TCGA.B0.5113.01 1 0.5589 0.3523 0.56 0.00 0.18 0.00 0.00 0.04 0.02 0.20
#> TCGA.CJ.5677.01 2 0.0000 0.8034 0.00 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.B0.4713.01 2 0.1408 0.7912 0.00 0.94 0.00 0.00 0.02 0.00 0.02 0.02
#> TCGA.B0.4821.01 2 0.0000 0.8034 0.00 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.B0.5712.01 6 0.2569 0.0000 0.02 0.00 0.00 0.00 0.16 0.82 0.00 0.00
#> TCGA.CJ.4920.01 5 0.0471 1.0000 0.02 0.00 0.00 0.00 0.98 0.00 0.00 0.00
#> TCGA.B0.5692.01 1 0.0471 0.5800 0.98 0.00 0.00 0.00 0.00 0.02 0.00 0.00
#> TCGA.B0.4827.01 2 0.4472 0.4560 0.00 0.68 0.00 0.00 0.10 0.00 0.18 0.04
#> TCGA.G6.A5PC.01 1 0.4916 0.2738 0.62 0.00 0.00 0.14 0.04 0.00 0.00 0.20
#> TCGA.CW.5580.01 5 0.0471 1.0000 0.02 0.00 0.00 0.00 0.98 0.00 0.00 0.00
#> TCGA.CJ.4913.01 1 0.3637 0.4942 0.80 0.00 0.00 0.02 0.06 0.04 0.00 0.08
#> TCGA.CJ.6033.01 2 0.4995 0.0418 0.00 0.52 0.00 0.00 0.36 0.00 0.08 0.04
#> TCGA.B0.5096.01 2 0.1091 0.7755 0.00 0.94 0.00 0.00 0.00 0.00 0.06 0.00
#> TCGA.B0.5107.01 2 0.0000 0.8034 0.00 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.CZ.4866.01 4 0.0000 0.0000 0.00 0.00 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.B0.4693.01 1 0.0471 0.5821 0.98 0.00 0.00 0.00 0.00 0.00 0.00 0.02
#> TCGA.B0.4710.01 8 0.8203 -0.1544 0.22 0.00 0.08 0.00 0.10 0.18 0.14 0.28
#> TCGA.CZ.5465.01 3 0.0808 0.5924 0.00 0.00 0.96 0.00 0.04 0.00 0.00 0.00
#> TCGA.B8.5159.01 1 0.5762 0.2862 0.52 0.00 0.18 0.00 0.00 0.04 0.02 0.24
#> TCGA.CJ.5680.01 8 0.5145 -0.2723 0.18 0.00 0.00 0.26 0.02 0.00 0.00 0.54
#> TCGA.CZ.5470.01 2 0.1557 0.7767 0.00 0.92 0.00 0.00 0.06 0.00 0.02 0.00
#> TCGA.G6.A8L8.01 3 0.5155 0.5939 0.00 0.00 0.60 0.00 0.00 0.10 0.22 0.08
#> TCGA.G6.A8L7.01 7 0.4165 0.0000 0.00 0.26 0.00 0.00 0.10 0.00 0.64 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-leaf , Node012-leaf , Node013-leaf , Node014 , Node021 , Node022-leaf , Node023 , Node041 , Node042-leaf , Node043 , Node051 , Node052-leaf , Node053-leaf , Node054 , Node061-leaf , Node062 , Node063-leaf , Node071-leaf , Node072-leaf , Node073-leaf .
The object with results only for a single top-value method and a single partitioning method can be extracted as:
res = res_rh["04"]
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 129 columns.
#> Top rows (1000) are extracted by 'SD' 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 0.4790 0.522 0.522
#> 3 3 0.990 0.951 0.979 0.3866 0.812 0.641
#> 4 4 0.825 0.715 0.855 0.0817 0.919 0.766
#> 5 5 0.734 0.663 0.805 0.0447 0.960 0.864
#> 6 6 0.724 0.611 0.772 0.0291 0.959 0.857
#> 7 7 0.684 0.546 0.707 0.0246 0.967 0.876
#> 8 8 0.669 0.401 0.671 0.0195 0.859 0.493
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.CZ.4863.01 1 0 1 1 0
#> TCGA.CJ.4902.01 2 0 1 0 1
#> TCGA.CW.6087.01 2 0 1 0 1
#> TCGA.DV.5566.01 1 0 1 1 0
#> TCGA.MM.A84U.01 1 0 1 1 0
#> TCGA.B4.5844.01 1 0 1 1 0
#> TCGA.CZ.5459.01 2 0 1 0 1
#> TCGA.B0.4694.01 2 0 1 0 1
#> TCGA.B4.5836.01 1 0 1 1 0
#> TCGA.B0.5095.01 2 0 1 0 1
#> TCGA.B0.4690.01 2 0 1 0 1
#> TCGA.CZ.5466.01 2 0 1 0 1
#> TCGA.CW.5588.01 1 0 1 1 0
#> TCGA.CJ.6031.01 2 0 1 0 1
#> TCGA.B8.A54J.01 2 0 1 0 1
#> TCGA.CZ.5462.01 2 0 1 0 1
#> TCGA.B8.A54H.01 1 0 1 1 0
#> TCGA.CJ.6028.01 2 0 1 0 1
#> TCGA.G6.A8L6.01 2 0 1 0 1
#> TCGA.B8.5551.01 1 0 1 1 0
#> TCGA.A3.A8OU.01 1 0 1 1 0
#> TCGA.A3.A6NI.01 2 0 1 0 1
#> TCGA.BP.4782.01 1 0 1 1 0
#> TCGA.B0.4849.01 2 0 1 0 1
#> TCGA.BP.5176.01 1 0 1 1 0
#> TCGA.CW.5591.01 2 0 1 0 1
#> TCGA.CW.5581.01 2 0 1 0 1
#> TCGA.CJ.4907.01 2 0 1 0 1
#> TCGA.A3.3387.01 2 0 1 0 1
#> TCGA.B2.A4SR.01 2 0 1 0 1
#> TCGA.BP.4801.01 2 0 1 0 1
#> TCGA.B0.5100.01 2 0 1 0 1
#> TCGA.B0.5400.01 1 0 1 1 0
#> TCGA.B0.4818.01 1 0 1 1 0
#> TCGA.AK.3431.01 1 0 1 1 0
#> TCGA.BP.4770.01 1 0 1 1 0
#> TCGA.BP.5189.01 2 0 1 0 1
#> TCGA.B8.5163.01 1 0 1 1 0
#> TCGA.CJ.5683.01 2 0 1 0 1
#> TCGA.B0.4843.01 2 0 1 0 1
#> TCGA.B8.A54G.01 2 0 1 0 1
#> TCGA.B0.5703.01 2 0 1 0 1
#> TCGA.CJ.5672.01 2 0 1 0 1
#> TCGA.B0.5102.01 1 0 1 1 0
#> TCGA.CW.5585.01 2 0 1 0 1
#> TCGA.B0.4824.01 1 0 1 1 0
#> TCGA.AK.3450.01 1 0 1 1 0
#> TCGA.DV.5568.01 2 0 1 0 1
#> TCGA.DV.5565.01 2 0 1 0 1
#> TCGA.B0.4811.01 2 0 1 0 1
#> TCGA.CJ.4916.01 1 0 1 1 0
#> TCGA.B0.5693.01 1 0 1 1 0
#> TCGA.B8.5550.01 2 0 1 0 1
#> TCGA.BP.5187.01 2 0 1 0 1
#> TCGA.CW.6097.01 2 0 1 0 1
#> TCGA.CZ.5989.01 2 0 1 0 1
#> TCGA.BP.5194.01 2 0 1 0 1
#> TCGA.CZ.5467.01 1 0 1 1 0
#> TCGA.BP.5170.01 2 0 1 0 1
#> TCGA.CJ.5686.01 1 0 1 1 0
#> TCGA.A3.3373.01 1 0 1 1 0
#> TCGA.CJ.4908.01 2 0 1 0 1
#> TCGA.B0.4819.01 1 0 1 1 0
#> TCGA.B2.5633.01 2 0 1 0 1
#> TCGA.BP.5168.01 2 0 1 0 1
#> TCGA.B8.5162.01 2 0 1 0 1
#> TCGA.B0.4842.01 1 0 1 1 0
#> TCGA.CJ.4905.01 1 0 1 1 0
#> TCGA.B2.5635.01 2 0 1 0 1
#> TCGA.B4.5838.01 2 0 1 0 1
#> TCGA.AK.3461.01 2 0 1 0 1
#> TCGA.AK.3460.01 2 0 1 0 1
#> TCGA.B0.5812.01 2 0 1 0 1
#> TCGA.B8.A54F.01 1 0 1 1 0
#> TCGA.B0.4697.01 1 0 1 1 0
#> TCGA.A3.3358.01 1 0 1 1 0
#> TCGA.CJ.4882.01 2 0 1 0 1
#> TCGA.B0.4700.01 2 0 1 0 1
#> TCGA.B0.5092.01 1 0 1 1 0
#> TCGA.CJ.6032.01 1 0 1 1 0
#> TCGA.B0.4817.01 2 0 1 0 1
#> TCGA.B0.4822.01 2 0 1 0 1
#> TCGA.B0.5696.01 2 0 1 0 1
#> TCGA.CJ.4918.01 2 0 1 0 1
#> TCGA.B0.5097.01 1 0 1 1 0
#> TCGA.CZ.5455.01 2 0 1 0 1
#> TCGA.CZ.5451.01 2 0 1 0 1
#> TCGA.CJ.4869.01 2 0 1 0 1
#> TCGA.B8.4146.01 1 0 1 1 0
#> TCGA.B0.5399.01 2 0 1 0 1
#> TCGA.B2.5639.01 2 0 1 0 1
#> TCGA.B0.5120.01 1 0 1 1 0
#> TCGA.BP.5185.01 2 0 1 0 1
#> TCGA.B0.4846.01 1 0 1 1 0
#> TCGA.CJ.4897.01 1 0 1 1 0
#> TCGA.CJ.4923.01 2 0 1 0 1
#> TCGA.B8.A7U6.01 1 0 1 1 0
#> TCGA.B0.5099.01 1 0 1 1 0
#> TCGA.CZ.5988.01 2 0 1 0 1
#> TCGA.B0.5109.01 2 0 1 0 1
#> TCGA.B0.5080.01 2 0 1 0 1
#> TCGA.CZ.4865.01 1 0 1 1 0
#> TCGA.CJ.5684.01 2 0 1 0 1
#> TCGA.B0.4701.01 1 0 1 1 0
#> TCGA.CZ.5458.01 2 0 1 0 1
#> TCGA.CZ.5982.01 1 0 1 1 0
#> TCGA.B0.5697.01 2 0 1 0 1
#> TCGA.A3.A6NN.01 2 0 1 0 1
#> TCGA.B0.4852.01 1 0 1 1 0
#> TCGA.CJ.5689.01 2 0 1 0 1
#> TCGA.BP.5200.01 2 0 1 0 1
#> TCGA.B2.4101.01 2 0 1 0 1
#> TCGA.B0.4816.01 2 0 1 0 1
#> TCGA.B2.3924.01 2 0 1 0 1
#> TCGA.B0.5713.01 1 0 1 1 0
#> TCGA.B0.5108.01 2 0 1 0 1
#> TCGA.B0.5711.01 2 0 1 0 1
#> TCGA.B8.5553.01 1 0 1 1 0
#> TCGA.MW.A4EC.01 1 0 1 1 0
#> TCGA.EU.5905.01 1 0 1 1 0
#> TCGA.CZ.4856.01 1 0 1 1 0
#> TCGA.BP.5184.01 2 0 1 0 1
#> TCGA.B4.5832.01 2 0 1 0 1
#> TCGA.B8.5164.01 2 0 1 0 1
#> TCGA.BP.5195.01 2 0 1 0 1
#> TCGA.BP.5010.01 2 0 1 0 1
#> TCGA.B0.4703.01 2 0 1 0 1
#> TCGA.B0.5104.01 1 0 1 1 0
#> TCGA.CW.5587.01 1 0 1 1 0
cbind(get_classes(res, k = 3), get_membership(res, k = 3))
#> class entropy silhouette p1 p2 p3
#> TCGA.CZ.4863.01 1 0.0000 1.000 1 0.00 0.00
#> TCGA.CJ.4902.01 3 0.0000 0.941 0 0.00 1.00
#> TCGA.CW.6087.01 3 0.0000 0.941 0 0.00 1.00
#> TCGA.DV.5566.01 1 0.0000 1.000 1 0.00 0.00
#> TCGA.MM.A84U.01 1 0.0000 1.000 1 0.00 0.00
#> TCGA.B4.5844.01 1 0.0000 1.000 1 0.00 0.00
#> TCGA.CZ.5459.01 2 0.0000 0.982 0 1.00 0.00
#> TCGA.B0.4694.01 3 0.0000 0.941 0 0.00 1.00
#> TCGA.B4.5836.01 1 0.0000 1.000 1 0.00 0.00
#> TCGA.B0.5095.01 3 0.0000 0.941 0 0.00 1.00
#> TCGA.B0.4690.01 3 0.0000 0.941 0 0.00 1.00
#> TCGA.CZ.5466.01 3 0.0000 0.941 0 0.00 1.00
#> TCGA.CW.5588.01 1 0.0000 1.000 1 0.00 0.00
#> TCGA.CJ.6031.01 3 0.0000 0.941 0 0.00 1.00
#> TCGA.B8.A54J.01 2 0.0000 0.982 0 1.00 0.00
#> TCGA.CZ.5462.01 3 0.0000 0.941 0 0.00 1.00
#> TCGA.B8.A54H.01 1 0.0000 1.000 1 0.00 0.00
#> TCGA.CJ.6028.01 3 0.0000 0.941 0 0.00 1.00
#> TCGA.G6.A8L6.01 2 0.0000 0.982 0 1.00 0.00
#> TCGA.B8.5551.01 1 0.0000 1.000 1 0.00 0.00
#> TCGA.A3.A8OU.01 1 0.0000 1.000 1 0.00 0.00
#> TCGA.A3.A6NI.01 2 0.0000 0.982 0 1.00 0.00
#> TCGA.BP.4782.01 1 0.0000 1.000 1 0.00 0.00
#> TCGA.B0.4849.01 2 0.0000 0.982 0 1.00 0.00
#> TCGA.BP.5176.01 1 0.0000 1.000 1 0.00 0.00
#> TCGA.CW.5591.01 3 0.0000 0.941 0 0.00 1.00
#> TCGA.CW.5581.01 2 0.0000 0.982 0 1.00 0.00
#> TCGA.CJ.4907.01 2 0.0000 0.982 0 1.00 0.00
#> TCGA.A3.3387.01 2 0.0000 0.982 0 1.00 0.00
#> TCGA.B2.A4SR.01 2 0.0000 0.982 0 1.00 0.00
#> TCGA.BP.4801.01 2 0.0000 0.982 0 1.00 0.00
#> TCGA.B0.5100.01 3 0.0000 0.941 0 0.00 1.00
#> TCGA.B0.5400.01 1 0.0000 1.000 1 0.00 0.00
#> TCGA.B0.4818.01 1 0.0000 1.000 1 0.00 0.00
#> TCGA.AK.3431.01 1 0.0000 1.000 1 0.00 0.00
#> TCGA.BP.4770.01 1 0.0000 1.000 1 0.00 0.00
#> TCGA.BP.5189.01 3 0.0000 0.941 0 0.00 1.00
#> TCGA.B8.5163.01 1 0.0000 1.000 1 0.00 0.00
#> TCGA.CJ.5683.01 2 0.0000 0.982 0 1.00 0.00
#> TCGA.B0.4843.01 3 0.0000 0.941 0 0.00 1.00
#> TCGA.B8.A54G.01 2 0.2959 0.895 0 0.90 0.10
#> TCGA.B0.5703.01 2 0.2959 0.892 0 0.90 0.10
#> TCGA.CJ.5672.01 2 0.2066 0.936 0 0.94 0.06
#> TCGA.B0.5102.01 1 0.0000 1.000 1 0.00 0.00
#> TCGA.CW.5585.01 2 0.0000 0.982 0 1.00 0.00
#> TCGA.B0.4824.01 1 0.0000 1.000 1 0.00 0.00
#> TCGA.AK.3450.01 1 0.0000 1.000 1 0.00 0.00
#> TCGA.DV.5568.01 3 0.2066 0.893 0 0.06 0.94
#> TCGA.DV.5565.01 2 0.0000 0.982 0 1.00 0.00
#> TCGA.B0.4811.01 2 0.2066 0.937 0 0.94 0.06
#> TCGA.CJ.4916.01 1 0.0000 1.000 1 0.00 0.00
#> TCGA.B0.5693.01 1 0.0000 1.000 1 0.00 0.00
#> TCGA.B8.5550.01 3 0.5948 0.467 0 0.36 0.64
#> TCGA.BP.5187.01 3 0.0892 0.926 0 0.02 0.98
#> TCGA.CW.6097.01 3 0.0000 0.941 0 0.00 1.00
#> TCGA.CZ.5989.01 2 0.0000 0.982 0 1.00 0.00
#> TCGA.BP.5194.01 2 0.0000 0.982 0 1.00 0.00
#> TCGA.CZ.5467.01 1 0.0000 1.000 1 0.00 0.00
#> TCGA.BP.5170.01 2 0.0000 0.982 0 1.00 0.00
#> TCGA.CJ.5686.01 1 0.0000 1.000 1 0.00 0.00
#> TCGA.A3.3373.01 1 0.0000 1.000 1 0.00 0.00
#> TCGA.CJ.4908.01 2 0.0000 0.982 0 1.00 0.00
#> TCGA.B0.4819.01 1 0.0000 1.000 1 0.00 0.00
#> TCGA.B2.5633.01 3 0.6280 0.192 0 0.46 0.54
#> TCGA.BP.5168.01 2 0.0000 0.982 0 1.00 0.00
#> TCGA.B8.5162.01 3 0.6192 0.310 0 0.42 0.58
#> TCGA.B0.4842.01 1 0.0000 1.000 1 0.00 0.00
#> TCGA.CJ.4905.01 1 0.0000 1.000 1 0.00 0.00
#> TCGA.B2.5635.01 2 0.1529 0.955 0 0.96 0.04
#> TCGA.B4.5838.01 2 0.0892 0.968 0 0.98 0.02
#> TCGA.AK.3461.01 2 0.0000 0.982 0 1.00 0.00
#> TCGA.AK.3460.01 2 0.0000 0.982 0 1.00 0.00
#> TCGA.B0.5812.01 2 0.0000 0.982 0 1.00 0.00
#> TCGA.B8.A54F.01 1 0.0000 1.000 1 0.00 0.00
#> TCGA.B0.4697.01 1 0.0000 1.000 1 0.00 0.00
#> TCGA.A3.3358.01 1 0.0000 1.000 1 0.00 0.00
#> TCGA.CJ.4882.01 3 0.0000 0.941 0 0.00 1.00
#> TCGA.B0.4700.01 3 0.0000 0.941 0 0.00 1.00
#> TCGA.B0.5092.01 1 0.0000 1.000 1 0.00 0.00
#> TCGA.CJ.6032.01 1 0.0000 1.000 1 0.00 0.00
#> TCGA.B0.4817.01 3 0.0000 0.941 0 0.00 1.00
#> TCGA.B0.4822.01 3 0.0000 0.941 0 0.00 1.00
#> TCGA.B0.5696.01 2 0.2066 0.937 0 0.94 0.06
#> TCGA.CJ.4918.01 3 0.0000 0.941 0 0.00 1.00
#> TCGA.B0.5097.01 1 0.0000 1.000 1 0.00 0.00
#> TCGA.CZ.5455.01 2 0.0000 0.982 0 1.00 0.00
#> TCGA.CZ.5451.01 2 0.0000 0.982 0 1.00 0.00
#> TCGA.CJ.4869.01 3 0.0000 0.941 0 0.00 1.00
#> TCGA.B8.4146.01 1 0.0000 1.000 1 0.00 0.00
#> TCGA.B0.5399.01 2 0.0000 0.982 0 1.00 0.00
#> TCGA.B2.5639.01 3 0.6126 0.370 0 0.40 0.60
#> TCGA.B0.5120.01 1 0.0000 1.000 1 0.00 0.00
#> TCGA.BP.5185.01 2 0.0000 0.982 0 1.00 0.00
#> TCGA.B0.4846.01 1 0.0000 1.000 1 0.00 0.00
#> TCGA.CJ.4897.01 1 0.0000 1.000 1 0.00 0.00
#> TCGA.CJ.4923.01 3 0.0000 0.941 0 0.00 1.00
#> TCGA.B8.A7U6.01 1 0.0000 1.000 1 0.00 0.00
#> TCGA.B0.5099.01 1 0.0000 1.000 1 0.00 0.00
#> TCGA.CZ.5988.01 2 0.0000 0.982 0 1.00 0.00
#> TCGA.B0.5109.01 3 0.0000 0.941 0 0.00 1.00
#> TCGA.B0.5080.01 3 0.0000 0.941 0 0.00 1.00
#> TCGA.CZ.4865.01 1 0.0000 1.000 1 0.00 0.00
#> TCGA.CJ.5684.01 2 0.0000 0.982 0 1.00 0.00
#> TCGA.B0.4701.01 1 0.0000 1.000 1 0.00 0.00
#> TCGA.CZ.5458.01 2 0.2066 0.936 0 0.94 0.06
#> TCGA.CZ.5982.01 1 0.0000 1.000 1 0.00 0.00
#> TCGA.B0.5697.01 2 0.0000 0.982 0 1.00 0.00
#> TCGA.A3.A6NN.01 2 0.0000 0.982 0 1.00 0.00
#> TCGA.B0.4852.01 1 0.0000 1.000 1 0.00 0.00
#> TCGA.CJ.5689.01 2 0.4002 0.817 0 0.84 0.16
#> TCGA.BP.5200.01 2 0.0000 0.982 0 1.00 0.00
#> TCGA.B2.4101.01 3 0.5216 0.654 0 0.26 0.74
#> TCGA.B0.4816.01 3 0.0000 0.941 0 0.00 1.00
#> TCGA.B2.3924.01 2 0.0000 0.982 0 1.00 0.00
#> TCGA.B0.5713.01 1 0.0000 1.000 1 0.00 0.00
#> TCGA.B0.5108.01 3 0.0000 0.941 0 0.00 1.00
#> TCGA.B0.5711.01 2 0.0000 0.982 0 1.00 0.00
#> TCGA.B8.5553.01 1 0.0000 1.000 1 0.00 0.00
#> TCGA.MW.A4EC.01 1 0.0000 1.000 1 0.00 0.00
#> TCGA.EU.5905.01 1 0.0000 1.000 1 0.00 0.00
#> TCGA.CZ.4856.01 1 0.0000 1.000 1 0.00 0.00
#> TCGA.BP.5184.01 2 0.0000 0.982 0 1.00 0.00
#> TCGA.B4.5832.01 3 0.0000 0.941 0 0.00 1.00
#> TCGA.B8.5164.01 2 0.2066 0.937 0 0.94 0.06
#> TCGA.BP.5195.01 3 0.0000 0.941 0 0.00 1.00
#> TCGA.BP.5010.01 3 0.0000 0.941 0 0.00 1.00
#> TCGA.B0.4703.01 3 0.0000 0.941 0 0.00 1.00
#> TCGA.B0.5104.01 1 0.0000 1.000 1 0.00 0.00
#> TCGA.CW.5587.01 1 0.0000 1.000 1 0.00 0.00
cbind(get_classes(res, k = 4), get_membership(res, k = 4))
#> class entropy silhouette p1 p2 p3 p4
#> TCGA.CZ.4863.01 1 0.0707 0.9771 0.98 0.00 0.00 0.02
#> TCGA.CJ.4902.01 3 0.4949 0.7428 0.00 0.06 0.76 0.18
#> TCGA.CW.6087.01 3 0.0000 0.9037 0.00 0.00 1.00 0.00
#> TCGA.DV.5566.01 1 0.0000 0.9831 1.00 0.00 0.00 0.00
#> TCGA.MM.A84U.01 1 0.1637 0.9636 0.94 0.00 0.00 0.06
#> TCGA.B4.5844.01 1 0.0000 0.9831 1.00 0.00 0.00 0.00
#> TCGA.CZ.5459.01 2 0.4790 0.0547 0.00 0.62 0.00 0.38
#> TCGA.B0.4694.01 3 0.0000 0.9037 0.00 0.00 1.00 0.00
#> TCGA.B4.5836.01 1 0.0000 0.9831 1.00 0.00 0.00 0.00
#> TCGA.B0.5095.01 3 0.0000 0.9037 0.00 0.00 1.00 0.00
#> TCGA.B0.4690.01 3 0.0000 0.9037 0.00 0.00 1.00 0.00
#> TCGA.CZ.5466.01 3 0.0000 0.9037 0.00 0.00 1.00 0.00
#> TCGA.CW.5588.01 1 0.1637 0.9636 0.94 0.00 0.00 0.06
#> TCGA.CJ.6031.01 3 0.4472 0.7332 0.00 0.02 0.76 0.22
#> TCGA.B8.A54J.01 2 0.2345 0.5426 0.00 0.90 0.00 0.10
#> TCGA.CZ.5462.01 3 0.0000 0.9037 0.00 0.00 1.00 0.00
#> TCGA.B8.A54H.01 1 0.0000 0.9831 1.00 0.00 0.00 0.00
#> TCGA.CJ.6028.01 3 0.0000 0.9037 0.00 0.00 1.00 0.00
#> TCGA.G6.A8L6.01 2 0.3400 0.4938 0.00 0.82 0.00 0.18
#> TCGA.B8.5551.01 1 0.1637 0.9636 0.94 0.00 0.00 0.06
#> TCGA.A3.A8OU.01 1 0.0000 0.9831 1.00 0.00 0.00 0.00
#> TCGA.A3.A6NI.01 2 0.2921 0.5318 0.00 0.86 0.00 0.14
#> TCGA.BP.4782.01 1 0.0000 0.9831 1.00 0.00 0.00 0.00
#> TCGA.B0.4849.01 4 0.4977 0.5772 0.00 0.46 0.00 0.54
#> TCGA.BP.5176.01 1 0.0000 0.9831 1.00 0.00 0.00 0.00
#> TCGA.CW.5591.01 3 0.0707 0.8963 0.00 0.00 0.98 0.02
#> TCGA.CW.5581.01 2 0.4624 -0.1080 0.00 0.66 0.00 0.34
#> TCGA.CJ.4907.01 4 0.4522 0.5338 0.00 0.32 0.00 0.68
#> TCGA.A3.3387.01 2 0.1913 0.5457 0.00 0.94 0.04 0.02
#> TCGA.B2.A4SR.01 2 0.4855 0.1059 0.00 0.60 0.00 0.40
#> TCGA.BP.4801.01 2 0.0000 0.5464 0.00 1.00 0.00 0.00
#> TCGA.B0.5100.01 3 0.1637 0.8764 0.00 0.00 0.94 0.06
#> TCGA.B0.5400.01 1 0.1637 0.9636 0.94 0.00 0.00 0.06
#> TCGA.B0.4818.01 1 0.0000 0.9831 1.00 0.00 0.00 0.00
#> TCGA.AK.3431.01 1 0.0000 0.9831 1.00 0.00 0.00 0.00
#> TCGA.BP.4770.01 1 0.1637 0.9636 0.94 0.00 0.00 0.06
#> TCGA.BP.5189.01 3 0.0707 0.8963 0.00 0.00 0.98 0.02
#> TCGA.B8.5163.01 1 0.1637 0.9636 0.94 0.00 0.00 0.06
#> TCGA.CJ.5683.01 2 0.3400 0.5075 0.00 0.82 0.00 0.18
#> TCGA.B0.4843.01 3 0.7414 0.1760 0.00 0.34 0.48 0.18
#> TCGA.B8.A54G.01 2 0.3335 0.5372 0.00 0.86 0.02 0.12
#> TCGA.B0.5703.01 2 0.5077 0.4435 0.00 0.76 0.08 0.16
#> TCGA.CJ.5672.01 4 0.6510 0.2912 0.00 0.38 0.08 0.54
#> TCGA.B0.5102.01 1 0.0000 0.9831 1.00 0.00 0.00 0.00
#> TCGA.CW.5585.01 4 0.4907 0.6071 0.00 0.42 0.00 0.58
#> TCGA.B0.4824.01 1 0.0000 0.9831 1.00 0.00 0.00 0.00
#> TCGA.AK.3450.01 1 0.0000 0.9831 1.00 0.00 0.00 0.00
#> TCGA.DV.5568.01 3 0.6477 0.4028 0.00 0.10 0.60 0.30
#> TCGA.DV.5565.01 2 0.3801 0.4474 0.00 0.78 0.00 0.22
#> TCGA.B0.4811.01 2 0.6074 -0.2179 0.00 0.60 0.06 0.34
#> TCGA.CJ.4916.01 1 0.1637 0.9636 0.94 0.00 0.00 0.06
#> TCGA.B0.5693.01 1 0.0000 0.9831 1.00 0.00 0.00 0.00
#> TCGA.B8.5550.01 2 0.6212 0.2231 0.00 0.56 0.38 0.06
#> TCGA.BP.5187.01 3 0.5291 0.6922 0.00 0.08 0.74 0.18
#> TCGA.CW.6097.01 3 0.0000 0.9037 0.00 0.00 1.00 0.00
#> TCGA.CZ.5989.01 2 0.2345 0.5397 0.00 0.90 0.00 0.10
#> TCGA.BP.5194.01 4 0.4855 0.6223 0.00 0.40 0.00 0.60
#> TCGA.CZ.5467.01 1 0.0000 0.9831 1.00 0.00 0.00 0.00
#> TCGA.BP.5170.01 4 0.5606 0.4191 0.00 0.48 0.02 0.50
#> TCGA.CJ.5686.01 1 0.0000 0.9831 1.00 0.00 0.00 0.00
#> TCGA.A3.3373.01 1 0.0000 0.9831 1.00 0.00 0.00 0.00
#> TCGA.CJ.4908.01 4 0.4713 0.6382 0.00 0.36 0.00 0.64
#> TCGA.B0.4819.01 1 0.1637 0.9636 0.94 0.00 0.00 0.06
#> TCGA.B2.5633.01 2 0.7610 0.1210 0.00 0.46 0.22 0.32
#> TCGA.BP.5168.01 2 0.2345 0.5323 0.00 0.90 0.00 0.10
#> TCGA.B8.5162.01 2 0.7040 0.1434 0.00 0.46 0.42 0.12
#> TCGA.B0.4842.01 1 0.1637 0.9636 0.94 0.00 0.00 0.06
#> TCGA.CJ.4905.01 1 0.0000 0.9831 1.00 0.00 0.00 0.00
#> TCGA.B2.5635.01 4 0.6586 0.1875 0.00 0.42 0.08 0.50
#> TCGA.B4.5838.01 2 0.3606 0.5070 0.00 0.84 0.02 0.14
#> TCGA.AK.3461.01 2 0.2647 0.5248 0.00 0.88 0.00 0.12
#> TCGA.AK.3460.01 2 0.2345 0.5142 0.00 0.90 0.00 0.10
#> TCGA.B0.5812.01 4 0.4790 0.6362 0.00 0.38 0.00 0.62
#> TCGA.B8.A54F.01 1 0.0000 0.9831 1.00 0.00 0.00 0.00
#> TCGA.B0.4697.01 1 0.1637 0.9636 0.94 0.00 0.00 0.06
#> TCGA.A3.3358.01 1 0.0000 0.9831 1.00 0.00 0.00 0.00
#> TCGA.CJ.4882.01 3 0.0707 0.8925 0.00 0.00 0.98 0.02
#> TCGA.B0.4700.01 3 0.0000 0.9037 0.00 0.00 1.00 0.00
#> TCGA.B0.5092.01 1 0.1637 0.9636 0.94 0.00 0.00 0.06
#> TCGA.CJ.6032.01 1 0.0000 0.9831 1.00 0.00 0.00 0.00
#> TCGA.B0.4817.01 3 0.0000 0.9037 0.00 0.00 1.00 0.00
#> TCGA.B0.4822.01 3 0.0000 0.9037 0.00 0.00 1.00 0.00
#> TCGA.B0.5696.01 2 0.7179 -0.1900 0.00 0.48 0.14 0.38
#> TCGA.CJ.4918.01 3 0.0707 0.8946 0.00 0.00 0.98 0.02
#> TCGA.B0.5097.01 1 0.1637 0.9636 0.94 0.00 0.00 0.06
#> TCGA.CZ.5455.01 4 0.6336 0.4757 0.00 0.46 0.06 0.48
#> TCGA.CZ.5451.01 2 0.2921 0.4965 0.00 0.86 0.00 0.14
#> TCGA.CJ.4869.01 3 0.0707 0.8965 0.00 0.00 0.98 0.02
#> TCGA.B8.4146.01 1 0.0000 0.9831 1.00 0.00 0.00 0.00
#> TCGA.B0.5399.01 4 0.4855 0.6388 0.00 0.40 0.00 0.60
#> TCGA.B2.5639.01 3 0.7699 -0.2408 0.00 0.22 0.40 0.38
#> TCGA.B0.5120.01 1 0.0000 0.9831 1.00 0.00 0.00 0.00
#> TCGA.BP.5185.01 2 0.3801 0.4474 0.00 0.78 0.00 0.22
#> TCGA.B0.4846.01 1 0.0000 0.9831 1.00 0.00 0.00 0.00
#> TCGA.CJ.4897.01 1 0.0000 0.9831 1.00 0.00 0.00 0.00
#> TCGA.CJ.4923.01 3 0.0000 0.9037 0.00 0.00 1.00 0.00
#> TCGA.B8.A7U6.01 1 0.0000 0.9831 1.00 0.00 0.00 0.00
#> TCGA.B0.5099.01 1 0.0000 0.9831 1.00 0.00 0.00 0.00
#> TCGA.CZ.5988.01 4 0.4855 0.4889 0.00 0.40 0.00 0.60
#> TCGA.B0.5109.01 3 0.0000 0.9037 0.00 0.00 1.00 0.00
#> TCGA.B0.5080.01 3 0.0000 0.9037 0.00 0.00 1.00 0.00
#> TCGA.CZ.4865.01 1 0.1637 0.9636 0.94 0.00 0.00 0.06
#> TCGA.CJ.5684.01 2 0.4855 -0.3250 0.00 0.60 0.00 0.40
#> TCGA.B0.4701.01 1 0.1637 0.9636 0.94 0.00 0.00 0.06
#> TCGA.CZ.5458.01 4 0.4406 0.5215 0.00 0.30 0.00 0.70
#> TCGA.CZ.5982.01 1 0.0000 0.9831 1.00 0.00 0.00 0.00
#> TCGA.B0.5697.01 2 0.6011 -0.3836 0.00 0.48 0.04 0.48
#> TCGA.A3.A6NN.01 2 0.2921 0.5143 0.00 0.86 0.00 0.14
#> TCGA.B0.4852.01 1 0.0000 0.9831 1.00 0.00 0.00 0.00
#> TCGA.CJ.5689.01 2 0.5902 0.3791 0.00 0.70 0.14 0.16
#> TCGA.BP.5200.01 4 0.4948 0.5106 0.00 0.44 0.00 0.56
#> TCGA.B2.4101.01 4 0.7344 0.1444 0.00 0.16 0.38 0.46
#> TCGA.B0.4816.01 3 0.4642 0.6375 0.00 0.24 0.74 0.02
#> TCGA.B2.3924.01 4 0.4977 0.5441 0.00 0.46 0.00 0.54
#> TCGA.B0.5713.01 1 0.0000 0.9831 1.00 0.00 0.00 0.00
#> TCGA.B0.5108.01 3 0.3853 0.7879 0.00 0.02 0.82 0.16
#> TCGA.B0.5711.01 4 0.4790 0.6362 0.00 0.38 0.00 0.62
#> TCGA.B8.5553.01 1 0.0000 0.9831 1.00 0.00 0.00 0.00
#> TCGA.MW.A4EC.01 1 0.0000 0.9831 1.00 0.00 0.00 0.00
#> TCGA.EU.5905.01 1 0.1637 0.9636 0.94 0.00 0.00 0.06
#> TCGA.CZ.4856.01 1 0.0000 0.9831 1.00 0.00 0.00 0.00
#> TCGA.BP.5184.01 4 0.4855 0.6229 0.00 0.40 0.00 0.60
#> TCGA.B4.5832.01 3 0.0000 0.9037 0.00 0.00 1.00 0.00
#> TCGA.B8.5164.01 2 0.6216 0.3471 0.00 0.66 0.12 0.22
#> TCGA.BP.5195.01 3 0.2011 0.8596 0.00 0.00 0.92 0.08
#> TCGA.BP.5010.01 3 0.0000 0.9037 0.00 0.00 1.00 0.00
#> TCGA.B0.4703.01 3 0.0000 0.9037 0.00 0.00 1.00 0.00
#> TCGA.B0.5104.01 1 0.0000 0.9831 1.00 0.00 0.00 0.00
#> TCGA.CW.5587.01 1 0.1211 0.9706 0.96 0.00 0.00 0.04
cbind(get_classes(res, k = 5), get_membership(res, k = 5))
#> class entropy silhouette p1 p2 p3 p4 p5
#> TCGA.CZ.4863.01 1 0.0000 0.9324 1.00 0.00 0.00 0.00 0.00
#> TCGA.CJ.4902.01 3 0.8001 0.2324 0.00 0.14 0.44 0.24 0.18
#> TCGA.CW.6087.01 3 0.0609 0.8678 0.00 0.00 0.98 0.02 0.00
#> TCGA.DV.5566.01 1 0.0000 0.9324 1.00 0.00 0.00 0.00 0.00
#> TCGA.MM.A84U.01 1 0.3274 0.8469 0.78 0.22 0.00 0.00 0.00
#> TCGA.B4.5844.01 1 0.0000 0.9324 1.00 0.00 0.00 0.00 0.00
#> TCGA.CZ.5459.01 5 0.5972 0.2057 0.00 0.14 0.00 0.30 0.56
#> TCGA.B0.4694.01 3 0.0000 0.8705 0.00 0.00 1.00 0.00 0.00
#> TCGA.B4.5836.01 1 0.0000 0.9324 1.00 0.00 0.00 0.00 0.00
#> TCGA.B0.5095.01 3 0.1648 0.8520 0.00 0.04 0.94 0.02 0.00
#> TCGA.B0.4690.01 3 0.0000 0.8705 0.00 0.00 1.00 0.00 0.00
#> TCGA.CZ.5466.01 3 0.0000 0.8705 0.00 0.00 1.00 0.00 0.00
#> TCGA.CW.5588.01 1 0.3274 0.8469 0.78 0.22 0.00 0.00 0.00
#> TCGA.CJ.6031.01 3 0.5970 0.4535 0.00 0.08 0.58 0.32 0.02
#> TCGA.B8.A54J.01 5 0.3110 0.5585 0.00 0.06 0.00 0.08 0.86
#> TCGA.CZ.5462.01 3 0.0000 0.8705 0.00 0.00 1.00 0.00 0.00
#> TCGA.B8.A54H.01 1 0.0000 0.9324 1.00 0.00 0.00 0.00 0.00
#> TCGA.CJ.6028.01 3 0.0609 0.8678 0.00 0.00 0.98 0.02 0.00
#> TCGA.G6.A8L6.01 5 0.5258 0.4672 0.00 0.14 0.00 0.18 0.68
#> TCGA.B8.5551.01 1 0.3274 0.8469 0.78 0.22 0.00 0.00 0.00
#> TCGA.A3.A8OU.01 1 0.0000 0.9324 1.00 0.00 0.00 0.00 0.00
#> TCGA.A3.A6NI.01 5 0.4433 0.5366 0.00 0.20 0.00 0.06 0.74
#> TCGA.BP.4782.01 1 0.0000 0.9324 1.00 0.00 0.00 0.00 0.00
#> TCGA.B0.4849.01 4 0.5382 0.4746 0.00 0.10 0.00 0.64 0.26
#> TCGA.BP.5176.01 1 0.0000 0.9324 1.00 0.00 0.00 0.00 0.00
#> TCGA.CW.5591.01 3 0.1648 0.8587 0.00 0.02 0.94 0.04 0.00
#> TCGA.CW.5581.01 5 0.3922 0.4511 0.00 0.04 0.00 0.18 0.78
#> TCGA.CJ.4907.01 4 0.5484 0.4408 0.00 0.12 0.00 0.64 0.24
#> TCGA.A3.3387.01 5 0.2610 0.5608 0.00 0.02 0.02 0.06 0.90
#> TCGA.B2.A4SR.01 5 0.5888 0.2212 0.00 0.14 0.00 0.28 0.58
#> TCGA.BP.4801.01 5 0.1216 0.5737 0.00 0.02 0.00 0.02 0.96
#> TCGA.B0.5100.01 3 0.4075 0.7715 0.00 0.16 0.78 0.06 0.00
#> TCGA.B0.5400.01 1 0.3274 0.8469 0.78 0.22 0.00 0.00 0.00
#> TCGA.B0.4818.01 1 0.0000 0.9324 1.00 0.00 0.00 0.00 0.00
#> TCGA.AK.3431.01 1 0.0609 0.9270 0.98 0.02 0.00 0.00 0.00
#> TCGA.BP.4770.01 1 0.3561 0.8174 0.74 0.26 0.00 0.00 0.00
#> TCGA.BP.5189.01 3 0.3641 0.7962 0.00 0.06 0.82 0.12 0.00
#> TCGA.B8.5163.01 1 0.3274 0.8469 0.78 0.22 0.00 0.00 0.00
#> TCGA.CJ.5683.01 5 0.3922 0.5438 0.00 0.18 0.00 0.04 0.78
#> TCGA.B0.4843.01 5 0.7380 0.2451 0.00 0.10 0.28 0.12 0.50
#> TCGA.B8.A54G.01 5 0.6381 0.4588 0.00 0.16 0.04 0.18 0.62
#> TCGA.B0.5703.01 5 0.6596 0.3207 0.00 0.08 0.12 0.18 0.62
#> TCGA.CJ.5672.01 4 0.6541 0.0884 0.00 0.12 0.02 0.48 0.38
#> TCGA.B0.5102.01 1 0.0000 0.9324 1.00 0.00 0.00 0.00 0.00
#> TCGA.CW.5585.01 4 0.5783 0.3675 0.00 0.10 0.00 0.54 0.36
#> TCGA.B0.4824.01 1 0.0000 0.9324 1.00 0.00 0.00 0.00 0.00
#> TCGA.AK.3450.01 1 0.0000 0.9324 1.00 0.00 0.00 0.00 0.00
#> TCGA.DV.5568.01 4 0.6280 -0.0468 0.00 0.04 0.40 0.50 0.06
#> TCGA.DV.5565.01 5 0.5484 0.4448 0.00 0.24 0.00 0.12 0.64
#> TCGA.B0.4811.01 5 0.7001 -0.0626 0.00 0.06 0.10 0.40 0.44
#> TCGA.CJ.4916.01 1 0.3274 0.8469 0.78 0.22 0.00 0.00 0.00
#> TCGA.B0.5693.01 1 0.0000 0.9324 1.00 0.00 0.00 0.00 0.00
#> TCGA.B8.5550.01 5 0.7161 0.2890 0.00 0.14 0.24 0.08 0.54
#> TCGA.BP.5187.01 3 0.7154 0.2660 0.00 0.08 0.48 0.34 0.10
#> TCGA.CW.6097.01 3 0.1732 0.8481 0.00 0.00 0.92 0.08 0.00
#> TCGA.CZ.5989.01 5 0.3037 0.5419 0.00 0.04 0.00 0.10 0.86
#> TCGA.BP.5194.01 4 0.4748 0.4610 0.00 0.04 0.00 0.66 0.30
#> TCGA.CZ.5467.01 1 0.1043 0.9096 0.96 0.04 0.00 0.00 0.00
#> TCGA.BP.5170.01 4 0.5890 0.3841 0.00 0.08 0.02 0.60 0.30
#> TCGA.CJ.5686.01 1 0.0000 0.9324 1.00 0.00 0.00 0.00 0.00
#> TCGA.A3.3373.01 1 0.0000 0.9324 1.00 0.00 0.00 0.00 0.00
#> TCGA.CJ.4908.01 4 0.3690 0.5041 0.00 0.02 0.00 0.78 0.20
#> TCGA.B0.4819.01 1 0.3274 0.8469 0.78 0.22 0.00 0.00 0.00
#> TCGA.B2.5633.01 4 0.8202 -0.0210 0.00 0.16 0.16 0.34 0.34
#> TCGA.BP.5168.01 5 0.2012 0.5702 0.00 0.06 0.00 0.02 0.92
#> TCGA.B8.5162.01 5 0.7724 0.1485 0.00 0.12 0.36 0.12 0.40
#> TCGA.B0.4842.01 1 0.3274 0.8469 0.78 0.22 0.00 0.00 0.00
#> TCGA.CJ.4905.01 1 0.0000 0.9324 1.00 0.00 0.00 0.00 0.00
#> TCGA.B2.5635.01 4 0.7039 0.0536 0.00 0.14 0.04 0.44 0.38
#> TCGA.B4.5838.01 5 0.5247 0.4966 0.00 0.14 0.02 0.12 0.72
#> TCGA.AK.3461.01 5 0.2616 0.5627 0.00 0.02 0.00 0.10 0.88
#> TCGA.AK.3460.01 5 0.3868 0.5265 0.00 0.06 0.00 0.14 0.80
#> TCGA.B0.5812.01 4 0.4644 0.4758 0.00 0.04 0.00 0.68 0.28
#> TCGA.B8.A54F.01 1 0.0000 0.9324 1.00 0.00 0.00 0.00 0.00
#> TCGA.B0.4697.01 1 0.3274 0.8469 0.78 0.22 0.00 0.00 0.00
#> TCGA.A3.3358.01 1 0.0000 0.9324 1.00 0.00 0.00 0.00 0.00
#> TCGA.CJ.4882.01 3 0.1216 0.8602 0.00 0.02 0.96 0.02 0.00
#> TCGA.B0.4700.01 3 0.0609 0.8678 0.00 0.00 0.98 0.02 0.00
#> TCGA.B0.5092.01 1 0.3274 0.8469 0.78 0.22 0.00 0.00 0.00
#> TCGA.CJ.6032.01 1 0.0000 0.9324 1.00 0.00 0.00 0.00 0.00
#> TCGA.B0.4817.01 3 0.0000 0.8705 0.00 0.00 1.00 0.00 0.00
#> TCGA.B0.4822.01 3 0.0000 0.8705 0.00 0.00 1.00 0.00 0.00
#> TCGA.B0.5696.01 4 0.7724 0.0615 0.00 0.12 0.12 0.40 0.36
#> TCGA.CJ.4918.01 3 0.1216 0.8641 0.00 0.02 0.96 0.02 0.00
#> TCGA.B0.5097.01 1 0.3274 0.8469 0.78 0.22 0.00 0.00 0.00
#> TCGA.CZ.5455.01 4 0.5425 0.2938 0.00 0.06 0.00 0.52 0.42
#> TCGA.CZ.5451.01 5 0.4558 0.5168 0.00 0.18 0.00 0.08 0.74
#> TCGA.CJ.4869.01 3 0.4437 0.7389 0.00 0.10 0.76 0.14 0.00
#> TCGA.B8.4146.01 1 0.0000 0.9324 1.00 0.00 0.00 0.00 0.00
#> TCGA.B0.5399.01 4 0.4398 0.4951 0.00 0.04 0.00 0.72 0.24
#> TCGA.B2.5639.01 4 0.7430 0.2208 0.00 0.06 0.30 0.46 0.18
#> TCGA.B0.5120.01 1 0.0000 0.9324 1.00 0.00 0.00 0.00 0.00
#> TCGA.BP.5185.01 5 0.4872 0.4812 0.00 0.16 0.00 0.12 0.72
#> TCGA.B0.4846.01 1 0.0609 0.9270 0.98 0.02 0.00 0.00 0.00
#> TCGA.CJ.4897.01 1 0.0000 0.9324 1.00 0.00 0.00 0.00 0.00
#> TCGA.CJ.4923.01 3 0.0000 0.8705 0.00 0.00 1.00 0.00 0.00
#> TCGA.B8.A7U6.01 1 0.0000 0.9324 1.00 0.00 0.00 0.00 0.00
#> TCGA.B0.5099.01 1 0.0000 0.9324 1.00 0.00 0.00 0.00 0.00
#> TCGA.CZ.5988.01 4 0.5700 0.4024 0.00 0.12 0.00 0.60 0.28
#> TCGA.B0.5109.01 3 0.0609 0.8678 0.00 0.00 0.98 0.02 0.00
#> TCGA.B0.5080.01 3 0.1043 0.8600 0.00 0.00 0.96 0.04 0.00
#> TCGA.CZ.4865.01 1 0.3274 0.8469 0.78 0.22 0.00 0.00 0.00
#> TCGA.CJ.5684.01 4 0.5173 0.2136 0.00 0.04 0.00 0.50 0.46
#> TCGA.B0.4701.01 1 0.3274 0.8469 0.78 0.22 0.00 0.00 0.00
#> TCGA.CZ.5458.01 4 0.5083 0.3921 0.00 0.14 0.00 0.70 0.16
#> TCGA.CZ.5982.01 1 0.0000 0.9324 1.00 0.00 0.00 0.00 0.00
#> TCGA.B0.5697.01 4 0.6406 0.0860 0.00 0.10 0.02 0.44 0.44
#> TCGA.A3.A6NN.01 5 0.4637 0.5349 0.00 0.16 0.00 0.10 0.74
#> TCGA.B0.4852.01 1 0.0000 0.9324 1.00 0.00 0.00 0.00 0.00
#> TCGA.CJ.5689.01 5 0.7260 0.3766 0.00 0.16 0.14 0.14 0.56
#> TCGA.BP.5200.01 4 0.4967 0.4621 0.00 0.06 0.00 0.66 0.28
#> TCGA.B2.4101.01 4 0.6629 0.3451 0.00 0.08 0.16 0.62 0.14
#> TCGA.B0.4816.01 3 0.6985 0.0497 0.00 0.08 0.48 0.08 0.36
#> TCGA.B2.3924.01 4 0.4921 0.4320 0.00 0.04 0.00 0.62 0.34
#> TCGA.B0.5713.01 1 0.0000 0.9324 1.00 0.00 0.00 0.00 0.00
#> TCGA.B0.5108.01 3 0.4725 0.7050 0.00 0.08 0.72 0.20 0.00
#> TCGA.B0.5711.01 4 0.4748 0.4687 0.00 0.04 0.00 0.66 0.30
#> TCGA.B8.5553.01 1 0.0609 0.9270 0.98 0.02 0.00 0.00 0.00
#> TCGA.MW.A4EC.01 1 0.0000 0.9324 1.00 0.00 0.00 0.00 0.00
#> TCGA.EU.5905.01 1 0.2929 0.8655 0.82 0.18 0.00 0.00 0.00
#> TCGA.CZ.4856.01 1 0.0000 0.9324 1.00 0.00 0.00 0.00 0.00
#> TCGA.BP.5184.01 4 0.4644 0.4666 0.00 0.04 0.00 0.68 0.28
#> TCGA.B4.5832.01 3 0.0000 0.8705 0.00 0.00 1.00 0.00 0.00
#> TCGA.B8.5164.01 5 0.6356 0.3745 0.00 0.06 0.14 0.16 0.64
#> TCGA.BP.5195.01 3 0.5692 0.5642 0.00 0.08 0.64 0.26 0.02
#> TCGA.BP.5010.01 3 0.0000 0.8705 0.00 0.00 1.00 0.00 0.00
#> TCGA.B0.4703.01 3 0.0609 0.8658 0.00 0.02 0.98 0.00 0.00
#> TCGA.B0.5104.01 1 0.0000 0.9324 1.00 0.00 0.00 0.00 0.00
#> TCGA.CW.5587.01 1 0.2929 0.8655 0.82 0.18 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.CZ.4863.01 1 0.2260 0.87811 0.86 0.00 0.00 0.00 0.00 0.14
#> TCGA.CJ.4902.01 3 0.6119 0.07467 0.00 0.42 0.44 0.00 0.08 0.06
#> TCGA.CW.6087.01 3 0.1267 0.79161 0.00 0.06 0.94 0.00 0.00 0.00
#> TCGA.DV.5566.01 1 0.0547 0.88307 0.98 0.00 0.00 0.00 0.00 0.02
#> TCGA.MM.A84U.01 1 0.3409 0.80627 0.70 0.00 0.00 0.00 0.00 0.30
#> TCGA.B4.5844.01 1 0.0547 0.88307 0.98 0.00 0.00 0.00 0.00 0.02
#> TCGA.CZ.5459.01 5 0.6035 -0.02662 0.00 0.14 0.00 0.40 0.44 0.02
#> TCGA.B0.4694.01 3 0.0547 0.79390 0.00 0.02 0.98 0.00 0.00 0.00
#> TCGA.B4.5836.01 1 0.0000 0.88693 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.B0.5095.01 3 0.2260 0.74709 0.00 0.14 0.86 0.00 0.00 0.00
#> TCGA.B0.4690.01 3 0.0547 0.79058 0.00 0.02 0.98 0.00 0.00 0.00
#> TCGA.CZ.5466.01 3 0.1556 0.78280 0.00 0.08 0.92 0.00 0.00 0.00
#> TCGA.CW.5588.01 1 0.3409 0.80627 0.70 0.00 0.00 0.00 0.00 0.30
#> TCGA.CJ.6031.01 3 0.5586 0.07299 0.00 0.42 0.44 0.14 0.00 0.00
#> TCGA.B8.A54J.01 5 0.5615 0.51008 0.00 0.14 0.00 0.12 0.66 0.08
#> TCGA.CZ.5462.01 3 0.0937 0.79287 0.00 0.04 0.96 0.00 0.00 0.00
#> TCGA.B8.A54H.01 1 0.0000 0.88693 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.CJ.6028.01 3 0.0000 0.79314 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.G6.A8L6.01 5 0.6022 0.47004 0.00 0.04 0.00 0.26 0.56 0.14
#> TCGA.B8.5551.01 1 0.3409 0.80627 0.70 0.00 0.00 0.00 0.00 0.30
#> TCGA.A3.A8OU.01 1 0.0547 0.88895 0.98 0.00 0.00 0.00 0.00 0.02
#> TCGA.A3.A6NI.01 5 0.5679 0.39241 0.00 0.18 0.00 0.06 0.64 0.12
#> TCGA.BP.4782.01 1 0.1814 0.88187 0.90 0.00 0.00 0.00 0.00 0.10
#> TCGA.B0.4849.01 4 0.3787 0.52813 0.00 0.10 0.00 0.78 0.12 0.00
#> TCGA.BP.5176.01 1 0.0937 0.88656 0.96 0.00 0.00 0.00 0.00 0.04
#> TCGA.CW.5591.01 3 0.0000 0.79314 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.CW.5581.01 5 0.5447 0.07578 0.00 0.12 0.00 0.42 0.46 0.00
#> TCGA.CJ.4907.01 4 0.4913 0.33345 0.00 0.34 0.00 0.60 0.02 0.04
#> TCGA.A3.3387.01 5 0.6063 0.44008 0.00 0.24 0.02 0.10 0.60 0.04
#> TCGA.B2.A4SR.01 4 0.6769 -0.19027 0.00 0.06 0.00 0.38 0.38 0.18
#> TCGA.BP.4801.01 5 0.4088 0.54930 0.00 0.10 0.00 0.10 0.78 0.02
#> TCGA.B0.5100.01 3 0.5841 0.29138 0.00 0.30 0.48 0.00 0.00 0.22
#> TCGA.B0.5400.01 1 0.3499 0.80239 0.68 0.00 0.00 0.00 0.00 0.32
#> TCGA.B0.4818.01 1 0.0000 0.88693 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.AK.3431.01 1 0.0547 0.88895 0.98 0.00 0.00 0.00 0.00 0.02
#> TCGA.BP.4770.01 1 0.3647 0.77256 0.64 0.00 0.00 0.00 0.00 0.36
#> TCGA.BP.5189.01 3 0.1267 0.77634 0.00 0.06 0.94 0.00 0.00 0.00
#> TCGA.B8.5163.01 1 0.3409 0.80627 0.70 0.00 0.00 0.00 0.00 0.30
#> TCGA.CJ.5683.01 5 0.4055 0.53353 0.00 0.04 0.00 0.14 0.78 0.04
#> TCGA.B0.4843.01 2 0.6059 0.14023 0.00 0.38 0.36 0.00 0.26 0.00
#> TCGA.B8.A54G.01 5 0.5935 0.47388 0.00 0.12 0.02 0.08 0.66 0.12
#> TCGA.B0.5703.01 5 0.7209 0.26032 0.00 0.26 0.06 0.22 0.44 0.02
#> TCGA.CJ.5672.01 2 0.7365 0.23800 0.00 0.46 0.04 0.28 0.14 0.08
#> TCGA.B0.5102.01 1 0.0547 0.88307 0.98 0.00 0.00 0.00 0.00 0.02
#> TCGA.CW.5585.01 4 0.3258 0.56584 0.00 0.02 0.00 0.84 0.10 0.04
#> TCGA.B0.4824.01 1 0.0000 0.88693 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.AK.3450.01 1 0.1814 0.88514 0.90 0.00 0.00 0.00 0.00 0.10
#> TCGA.DV.5568.01 3 0.5626 0.23116 0.00 0.10 0.54 0.34 0.00 0.02
#> TCGA.DV.5565.01 5 0.5740 0.48936 0.00 0.06 0.00 0.22 0.62 0.10
#> TCGA.B0.4811.01 4 0.6554 -0.08203 0.00 0.32 0.00 0.34 0.32 0.02
#> TCGA.CJ.4916.01 1 0.3409 0.80627 0.70 0.00 0.00 0.00 0.00 0.30
#> TCGA.B0.5693.01 1 0.0547 0.88307 0.98 0.00 0.00 0.00 0.00 0.02
#> TCGA.B8.5550.01 5 0.7178 -0.09946 0.00 0.30 0.26 0.04 0.38 0.02
#> TCGA.BP.5187.01 3 0.6498 0.28943 0.00 0.32 0.52 0.04 0.08 0.04
#> TCGA.CW.6097.01 3 0.1267 0.78605 0.00 0.06 0.94 0.00 0.00 0.00
#> TCGA.CZ.5989.01 5 0.3928 0.54707 0.00 0.08 0.00 0.16 0.76 0.00
#> TCGA.BP.5194.01 4 0.1635 0.58684 0.00 0.02 0.00 0.94 0.02 0.02
#> TCGA.CZ.5467.01 1 0.1556 0.86776 0.92 0.00 0.00 0.00 0.00 0.08
#> TCGA.BP.5170.01 4 0.6433 0.35535 0.00 0.24 0.00 0.54 0.14 0.08
#> TCGA.CJ.5686.01 1 0.1814 0.88187 0.90 0.00 0.00 0.00 0.00 0.10
#> TCGA.A3.3373.01 1 0.0000 0.88693 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.CJ.4908.01 4 0.2403 0.58578 0.00 0.04 0.00 0.90 0.02 0.04
#> TCGA.B0.4819.01 1 0.3409 0.80627 0.70 0.00 0.00 0.00 0.00 0.30
#> TCGA.B2.5633.01 2 0.4920 0.20116 0.00 0.64 0.02 0.02 0.30 0.02
#> TCGA.BP.5168.01 5 0.4238 0.55562 0.00 0.04 0.00 0.16 0.76 0.04
#> TCGA.B8.5162.01 3 0.6460 -0.02934 0.00 0.16 0.50 0.02 0.30 0.02
#> TCGA.B0.4842.01 1 0.3409 0.80627 0.70 0.00 0.00 0.00 0.00 0.30
#> TCGA.CJ.4905.01 1 0.0547 0.88307 0.98 0.00 0.00 0.00 0.00 0.02
#> TCGA.B2.5635.01 2 0.7712 0.43420 0.00 0.48 0.10 0.14 0.20 0.08
#> TCGA.B4.5838.01 5 0.4172 0.43718 0.00 0.28 0.00 0.04 0.68 0.00
#> TCGA.AK.3461.01 5 0.5618 0.49341 0.00 0.10 0.00 0.20 0.64 0.06
#> TCGA.AK.3460.01 5 0.5274 0.53719 0.00 0.06 0.00 0.22 0.66 0.06
#> TCGA.B0.5812.01 4 0.1092 0.59252 0.00 0.02 0.00 0.96 0.02 0.00
#> TCGA.B8.A54F.01 1 0.0937 0.88955 0.96 0.00 0.00 0.00 0.00 0.04
#> TCGA.B0.4697.01 1 0.3409 0.80627 0.70 0.00 0.00 0.00 0.00 0.30
#> TCGA.A3.3358.01 1 0.2048 0.88110 0.88 0.00 0.00 0.00 0.00 0.12
#> TCGA.CJ.4882.01 3 0.1267 0.79161 0.00 0.06 0.94 0.00 0.00 0.00
#> TCGA.B0.4700.01 3 0.0000 0.79314 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.B0.5092.01 1 0.3409 0.80627 0.70 0.00 0.00 0.00 0.00 0.30
#> TCGA.CJ.6032.01 1 0.0000 0.88693 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.B0.4817.01 3 0.0937 0.79272 0.00 0.04 0.96 0.00 0.00 0.00
#> TCGA.B0.4822.01 3 0.0937 0.79042 0.00 0.04 0.96 0.00 0.00 0.00
#> TCGA.B0.5696.01 4 0.7573 0.05684 0.00 0.26 0.06 0.40 0.24 0.04
#> TCGA.CJ.4918.01 3 0.1480 0.78685 0.00 0.04 0.94 0.00 0.02 0.00
#> TCGA.B0.5097.01 1 0.3409 0.80627 0.70 0.00 0.00 0.00 0.00 0.30
#> TCGA.CZ.5455.01 4 0.6544 0.36423 0.00 0.20 0.08 0.58 0.12 0.02
#> TCGA.CZ.5451.01 5 0.4403 0.52288 0.00 0.04 0.00 0.18 0.74 0.04
#> TCGA.CJ.4869.01 3 0.2581 0.74039 0.00 0.12 0.86 0.00 0.02 0.00
#> TCGA.B8.4146.01 1 0.0547 0.88307 0.98 0.00 0.00 0.00 0.00 0.02
#> TCGA.B0.5399.01 4 0.2728 0.57777 0.00 0.10 0.00 0.86 0.00 0.04
#> TCGA.B2.5639.01 3 0.7837 -0.30267 0.00 0.26 0.34 0.28 0.08 0.04
#> TCGA.B0.5120.01 1 0.0547 0.88926 0.98 0.00 0.00 0.00 0.00 0.02
#> TCGA.BP.5185.01 5 0.5274 0.51375 0.00 0.06 0.00 0.22 0.66 0.06
#> TCGA.B0.4846.01 1 0.2260 0.87195 0.86 0.00 0.00 0.00 0.00 0.14
#> TCGA.CJ.4897.01 1 0.0547 0.88307 0.98 0.00 0.00 0.00 0.00 0.02
#> TCGA.CJ.4923.01 3 0.0000 0.79314 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.B8.A7U6.01 1 0.0000 0.88693 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.B0.5099.01 1 0.0000 0.88693 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.CZ.5988.01 4 0.5991 0.21370 0.00 0.36 0.00 0.50 0.10 0.04
#> TCGA.B0.5109.01 3 0.0000 0.79314 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.B0.5080.01 3 0.0000 0.79314 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.CZ.4865.01 1 0.3409 0.80627 0.70 0.00 0.00 0.00 0.00 0.30
#> TCGA.CJ.5684.01 4 0.6404 0.28197 0.00 0.20 0.00 0.50 0.26 0.04
#> TCGA.B0.4701.01 1 0.3409 0.80627 0.70 0.00 0.00 0.00 0.00 0.30
#> TCGA.CZ.5458.01 4 0.6489 0.00584 0.00 0.40 0.02 0.42 0.02 0.14
#> TCGA.CZ.5982.01 1 0.0000 0.88693 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.B0.5697.01 2 0.7020 0.22945 0.00 0.44 0.02 0.28 0.22 0.04
#> TCGA.A3.A6NN.01 5 0.5529 0.50569 0.00 0.06 0.00 0.16 0.66 0.12
#> TCGA.B0.4852.01 1 0.0000 0.88693 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.CJ.5689.01 5 0.7081 0.11880 0.00 0.36 0.06 0.08 0.44 0.06
#> TCGA.BP.5200.01 4 0.2882 0.57439 0.00 0.02 0.00 0.86 0.10 0.02
#> TCGA.B2.4101.01 4 0.6610 0.03021 0.00 0.30 0.22 0.44 0.04 0.00
#> TCGA.B0.4816.01 3 0.5509 0.19510 0.00 0.16 0.54 0.00 0.30 0.00
#> TCGA.B2.3924.01 4 0.4361 0.51965 0.00 0.04 0.00 0.76 0.14 0.06
#> TCGA.B0.5713.01 1 0.0000 0.88693 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.B0.5108.01 3 0.5077 0.49232 0.00 0.26 0.66 0.02 0.02 0.04
#> TCGA.B0.5711.01 4 0.2512 0.58508 0.00 0.06 0.00 0.88 0.06 0.00
#> TCGA.B8.5553.01 1 0.1556 0.88683 0.92 0.00 0.00 0.00 0.00 0.08
#> TCGA.MW.A4EC.01 1 0.0547 0.88307 0.98 0.00 0.00 0.00 0.00 0.02
#> TCGA.EU.5905.01 1 0.3409 0.81488 0.70 0.00 0.00 0.00 0.00 0.30
#> TCGA.CZ.4856.01 1 0.1814 0.88447 0.90 0.00 0.00 0.00 0.00 0.10
#> TCGA.BP.5184.01 4 0.0000 0.59020 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.B4.5832.01 3 0.0547 0.79058 0.00 0.02 0.98 0.00 0.00 0.00
#> TCGA.B8.5164.01 5 0.6549 0.10857 0.00 0.32 0.12 0.08 0.48 0.00
#> TCGA.BP.5195.01 3 0.4067 0.52344 0.00 0.04 0.70 0.26 0.00 0.00
#> TCGA.BP.5010.01 3 0.1267 0.78853 0.00 0.06 0.94 0.00 0.00 0.00
#> TCGA.B0.4703.01 3 0.1556 0.78271 0.00 0.08 0.92 0.00 0.00 0.00
#> TCGA.B0.5104.01 1 0.1267 0.88813 0.94 0.00 0.00 0.00 0.00 0.06
#> TCGA.CW.5587.01 1 0.3076 0.83433 0.76 0.00 0.00 0.00 0.00 0.24
cbind(get_classes(res, k = 7), get_membership(res, k = 7))
#> class entropy silhouette p1 p2 p3 p4 p5 p6 p7
#> TCGA.CZ.4863.01 1 0.2081 0.83442 0.86 0.00 0.00 0.00 0.14 0.00 0.00
#> TCGA.CJ.4902.01 2 0.5679 -0.06548 0.00 0.48 0.40 0.04 0.04 0.04 0.00
#> TCGA.CW.6087.01 3 0.0504 0.71128 0.00 0.02 0.98 0.00 0.00 0.00 0.00
#> TCGA.DV.5566.01 1 0.0504 0.83081 0.98 0.00 0.00 0.00 0.02 0.00 0.00
#> TCGA.MM.A84U.01 1 0.3413 0.74034 0.62 0.00 0.00 0.00 0.38 0.00 0.00
#> TCGA.B4.5844.01 1 0.0000 0.83281 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.CZ.5459.01 6 0.6973 0.13269 0.00 0.26 0.00 0.24 0.06 0.40 0.04
#> TCGA.B0.4694.01 3 0.1928 0.70943 0.00 0.08 0.90 0.00 0.00 0.00 0.02
#> TCGA.B4.5836.01 1 0.0504 0.83802 0.98 0.00 0.00 0.00 0.02 0.00 0.00
#> TCGA.B0.5095.01 3 0.2159 0.68720 0.00 0.06 0.90 0.00 0.00 0.02 0.02
#> TCGA.B0.4690.01 3 0.0863 0.70093 0.00 0.00 0.96 0.00 0.04 0.00 0.00
#> TCGA.CZ.5466.01 3 0.1860 0.70824 0.00 0.04 0.92 0.00 0.02 0.00 0.02
#> TCGA.CW.5588.01 1 0.3459 0.71787 0.60 0.00 0.00 0.00 0.40 0.00 0.00
#> TCGA.CJ.6031.01 3 0.4941 -0.11439 0.00 0.46 0.46 0.06 0.00 0.00 0.02
#> TCGA.B8.A54J.01 6 0.5600 0.53827 0.00 0.10 0.00 0.12 0.08 0.66 0.04
#> TCGA.CZ.5462.01 3 0.0863 0.71051 0.00 0.04 0.96 0.00 0.00 0.00 0.00
#> TCGA.B8.A54H.01 1 0.0504 0.82858 0.98 0.00 0.00 0.00 0.02 0.00 0.00
#> TCGA.CJ.6028.01 3 0.0863 0.71359 0.00 0.04 0.96 0.00 0.00 0.00 0.00
#> TCGA.G6.A8L6.01 6 0.5303 0.47235 0.00 0.02 0.00 0.18 0.08 0.66 0.06
#> TCGA.B8.5551.01 1 0.3459 0.71787 0.60 0.00 0.00 0.00 0.40 0.00 0.00
#> TCGA.A3.A8OU.01 1 0.1166 0.83592 0.94 0.00 0.00 0.00 0.06 0.00 0.00
#> TCGA.A3.A6NI.01 6 0.6682 0.44182 0.00 0.14 0.00 0.10 0.16 0.54 0.06
#> TCGA.BP.4782.01 1 0.2422 0.82535 0.82 0.00 0.00 0.00 0.18 0.00 0.00
#> TCGA.B0.4849.01 4 0.5036 0.56494 0.00 0.08 0.00 0.68 0.02 0.18 0.04
#> TCGA.BP.5176.01 1 0.0863 0.83091 0.96 0.00 0.00 0.00 0.04 0.00 0.00
#> TCGA.CW.5591.01 3 0.2572 0.69814 0.00 0.08 0.86 0.00 0.00 0.00 0.06
#> TCGA.CW.5581.01 6 0.7026 0.22915 0.00 0.20 0.00 0.26 0.08 0.42 0.04
#> TCGA.CJ.4907.01 2 0.5429 -0.08387 0.00 0.48 0.00 0.40 0.00 0.06 0.06
#> TCGA.A3.3387.01 6 0.5355 0.45061 0.00 0.24 0.04 0.04 0.02 0.64 0.02
#> TCGA.B2.A4SR.01 6 0.6458 0.26734 0.00 0.06 0.00 0.32 0.08 0.48 0.06
#> TCGA.BP.4801.01 6 0.4092 0.50343 0.00 0.16 0.00 0.08 0.00 0.74 0.02
#> TCGA.B0.5100.01 7 0.5293 0.00000 0.00 0.12 0.32 0.00 0.00 0.02 0.54
#> TCGA.B0.5400.01 1 0.3496 0.71531 0.58 0.00 0.00 0.00 0.42 0.00 0.00
#> TCGA.B0.4818.01 1 0.0504 0.82858 0.98 0.00 0.00 0.00 0.02 0.00 0.00
#> TCGA.AK.3431.01 1 0.1671 0.83855 0.90 0.00 0.00 0.00 0.10 0.00 0.00
#> TCGA.BP.4770.01 1 0.3985 0.65854 0.52 0.00 0.00 0.00 0.46 0.00 0.02
#> TCGA.BP.5189.01 3 0.4565 0.48266 0.00 0.16 0.72 0.08 0.02 0.00 0.02
#> TCGA.B8.5163.01 1 0.3459 0.71787 0.60 0.00 0.00 0.00 0.40 0.00 0.00
#> TCGA.CJ.5683.01 6 0.5423 0.49885 0.00 0.04 0.00 0.04 0.10 0.66 0.16
#> TCGA.B0.4843.01 2 0.6922 0.05940 0.00 0.42 0.24 0.00 0.04 0.24 0.06
#> TCGA.B8.A54G.01 6 0.6133 0.42300 0.00 0.18 0.04 0.04 0.08 0.62 0.04
#> TCGA.B0.5703.01 6 0.7621 0.09260 0.00 0.22 0.12 0.20 0.04 0.40 0.02
#> TCGA.CJ.5672.01 2 0.5936 0.27044 0.00 0.60 0.02 0.10 0.04 0.22 0.02
#> TCGA.B0.5102.01 1 0.1166 0.83679 0.94 0.00 0.00 0.00 0.06 0.00 0.00
#> TCGA.CW.5585.01 4 0.4311 0.54545 0.00 0.06 0.00 0.76 0.04 0.12 0.02
#> TCGA.B0.4824.01 1 0.0504 0.82858 0.98 0.00 0.00 0.00 0.02 0.00 0.00
#> TCGA.AK.3450.01 1 0.1671 0.83948 0.90 0.00 0.00 0.00 0.10 0.00 0.00
#> TCGA.DV.5568.01 2 0.7332 0.06669 0.00 0.36 0.26 0.26 0.02 0.02 0.08
#> TCGA.DV.5565.01 6 0.5853 0.46628 0.00 0.02 0.00 0.10 0.08 0.60 0.20
#> TCGA.B0.4811.01 4 0.7115 -0.06607 0.00 0.30 0.10 0.32 0.00 0.26 0.02
#> TCGA.CJ.4916.01 1 0.3496 0.71531 0.58 0.00 0.00 0.00 0.42 0.00 0.00
#> TCGA.B0.5693.01 1 0.0504 0.83081 0.98 0.00 0.00 0.00 0.02 0.00 0.00
#> TCGA.B8.5550.01 6 0.7052 -0.14522 0.00 0.30 0.30 0.02 0.02 0.32 0.04
#> TCGA.BP.5187.01 3 0.8002 -0.25960 0.00 0.28 0.36 0.16 0.06 0.08 0.06
#> TCGA.CW.6097.01 3 0.2163 0.67433 0.00 0.10 0.88 0.00 0.00 0.00 0.02
#> TCGA.CZ.5989.01 6 0.5370 0.50230 0.00 0.22 0.00 0.04 0.06 0.64 0.04
#> TCGA.BP.5194.01 4 0.1860 0.60125 0.00 0.02 0.00 0.92 0.02 0.04 0.00
#> TCGA.CZ.5467.01 1 0.2829 0.76115 0.84 0.00 0.00 0.00 0.08 0.00 0.08
#> TCGA.BP.5170.01 4 0.6385 0.25890 0.00 0.28 0.00 0.46 0.04 0.20 0.02
#> TCGA.CJ.5686.01 1 0.1671 0.83907 0.90 0.00 0.00 0.00 0.10 0.00 0.00
#> TCGA.A3.3373.01 1 0.0504 0.82858 0.98 0.00 0.00 0.00 0.02 0.00 0.00
#> TCGA.CJ.4908.01 4 0.3876 0.56527 0.00 0.14 0.00 0.78 0.02 0.04 0.02
#> TCGA.B0.4819.01 1 0.3459 0.71787 0.60 0.00 0.00 0.00 0.40 0.00 0.00
#> TCGA.B2.5633.01 2 0.6848 0.26502 0.00 0.54 0.14 0.06 0.02 0.18 0.06
#> TCGA.BP.5168.01 6 0.4171 0.55346 0.00 0.08 0.00 0.06 0.06 0.78 0.02
#> TCGA.B8.5162.01 3 0.7411 -0.36808 0.00 0.28 0.32 0.00 0.06 0.26 0.08
#> TCGA.B0.4842.01 1 0.3459 0.71787 0.60 0.00 0.00 0.00 0.40 0.00 0.00
#> TCGA.CJ.4905.01 1 0.0504 0.83081 0.98 0.00 0.00 0.00 0.02 0.00 0.00
#> TCGA.B2.5635.01 2 0.6023 0.37923 0.00 0.64 0.04 0.08 0.08 0.14 0.02
#> TCGA.B4.5838.01 6 0.4431 0.45754 0.00 0.24 0.00 0.00 0.04 0.68 0.04
#> TCGA.AK.3461.01 6 0.5448 0.53184 0.00 0.10 0.00 0.14 0.08 0.66 0.02
#> TCGA.AK.3460.01 6 0.5094 0.55086 0.00 0.06 0.00 0.14 0.04 0.70 0.06
#> TCGA.B0.5812.01 4 0.2509 0.62042 0.00 0.04 0.00 0.88 0.02 0.06 0.00
#> TCGA.B8.A54F.01 1 0.2081 0.83655 0.86 0.00 0.00 0.00 0.14 0.00 0.00
#> TCGA.B0.4697.01 1 0.3459 0.71787 0.60 0.00 0.00 0.00 0.40 0.00 0.00
#> TCGA.A3.3358.01 1 0.2081 0.83622 0.86 0.00 0.00 0.00 0.14 0.00 0.00
#> TCGA.CJ.4882.01 3 0.1928 0.70881 0.00 0.08 0.90 0.00 0.00 0.00 0.02
#> TCGA.B0.4700.01 3 0.0000 0.70930 0.00 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.B0.5092.01 1 0.3459 0.71787 0.60 0.00 0.00 0.00 0.40 0.00 0.00
#> TCGA.CJ.6032.01 1 0.1166 0.83679 0.94 0.00 0.00 0.00 0.06 0.00 0.00
#> TCGA.B0.4817.01 3 0.0863 0.71284 0.00 0.04 0.96 0.00 0.00 0.00 0.00
#> TCGA.B0.4822.01 3 0.1860 0.70583 0.00 0.04 0.92 0.00 0.02 0.00 0.02
#> TCGA.B0.5696.01 4 0.7372 0.11137 0.00 0.32 0.08 0.38 0.02 0.16 0.04
#> TCGA.CJ.4918.01 3 0.2569 0.66131 0.00 0.14 0.84 0.00 0.00 0.00 0.02
#> TCGA.B0.5097.01 1 0.3496 0.71441 0.58 0.00 0.00 0.00 0.42 0.00 0.00
#> TCGA.CZ.5455.01 4 0.6577 0.37488 0.00 0.24 0.00 0.50 0.06 0.16 0.04
#> TCGA.CZ.5451.01 6 0.5562 0.50758 0.00 0.04 0.00 0.08 0.08 0.66 0.14
#> TCGA.CJ.4869.01 3 0.5338 0.32449 0.00 0.28 0.60 0.02 0.00 0.04 0.06
#> TCGA.B8.4146.01 1 0.0504 0.83081 0.98 0.00 0.00 0.00 0.02 0.00 0.00
#> TCGA.B0.5399.01 4 0.4222 0.58883 0.00 0.08 0.00 0.76 0.02 0.12 0.02
#> TCGA.B2.5639.01 2 0.8001 0.12130 0.00 0.32 0.24 0.26 0.04 0.08 0.06
#> TCGA.B0.5120.01 1 0.1886 0.83718 0.88 0.00 0.00 0.00 0.12 0.00 0.00
#> TCGA.BP.5185.01 6 0.4696 0.51650 0.00 0.00 0.00 0.06 0.08 0.70 0.16
#> TCGA.B0.4846.01 1 0.2572 0.82105 0.80 0.00 0.00 0.00 0.20 0.00 0.00
#> TCGA.CJ.4897.01 1 0.0504 0.82858 0.98 0.00 0.00 0.00 0.02 0.00 0.00
#> TCGA.CJ.4923.01 3 0.0863 0.71359 0.00 0.04 0.96 0.00 0.00 0.00 0.00
#> TCGA.B8.A7U6.01 1 0.0504 0.82858 0.98 0.00 0.00 0.00 0.02 0.00 0.00
#> TCGA.B0.5099.01 1 0.0504 0.82858 0.98 0.00 0.00 0.00 0.02 0.00 0.00
#> TCGA.CZ.5988.01 2 0.7016 0.04392 0.00 0.38 0.00 0.34 0.06 0.16 0.06
#> TCGA.B0.5109.01 3 0.0863 0.71284 0.00 0.04 0.96 0.00 0.00 0.00 0.00
#> TCGA.B0.5080.01 3 0.2313 0.69671 0.00 0.06 0.88 0.00 0.00 0.00 0.06
#> TCGA.CZ.4865.01 1 0.3496 0.71531 0.58 0.00 0.00 0.00 0.42 0.00 0.00
#> TCGA.CJ.5684.01 4 0.6559 0.31497 0.00 0.26 0.00 0.46 0.06 0.20 0.02
#> TCGA.B0.4701.01 1 0.3459 0.71787 0.60 0.00 0.00 0.00 0.40 0.00 0.00
#> TCGA.CZ.5458.01 2 0.6161 0.26297 0.00 0.58 0.00 0.20 0.10 0.04 0.08
#> TCGA.CZ.5982.01 1 0.0863 0.82703 0.96 0.00 0.00 0.00 0.04 0.00 0.00
#> TCGA.B0.5697.01 2 0.7236 0.27636 0.00 0.46 0.04 0.22 0.08 0.18 0.02
#> TCGA.A3.A6NN.01 6 0.4575 0.53874 0.00 0.02 0.00 0.04 0.10 0.74 0.10
#> TCGA.B0.4852.01 1 0.0504 0.82858 0.98 0.00 0.00 0.00 0.02 0.00 0.00
#> TCGA.CJ.5689.01 6 0.6225 0.10913 0.00 0.36 0.14 0.04 0.00 0.44 0.02
#> TCGA.BP.5200.01 4 0.3292 0.60820 0.00 0.06 0.00 0.84 0.02 0.06 0.02
#> TCGA.B2.4101.01 4 0.7258 -0.00579 0.00 0.26 0.20 0.42 0.02 0.06 0.04
#> TCGA.B0.4816.01 3 0.6970 -0.16374 0.00 0.16 0.42 0.00 0.06 0.30 0.06
#> TCGA.B2.3924.01 4 0.3566 0.58152 0.00 0.04 0.00 0.78 0.02 0.16 0.00
#> TCGA.B0.5713.01 1 0.0504 0.82858 0.98 0.00 0.00 0.00 0.02 0.00 0.00
#> TCGA.B0.5108.01 2 0.5987 -0.14142 0.00 0.44 0.40 0.02 0.10 0.00 0.04
#> TCGA.B0.5711.01 4 0.3257 0.61228 0.00 0.04 0.00 0.84 0.02 0.08 0.02
#> TCGA.B8.5553.01 1 0.2081 0.83421 0.86 0.00 0.00 0.00 0.14 0.00 0.00
#> TCGA.MW.A4EC.01 1 0.0504 0.83081 0.98 0.00 0.00 0.00 0.02 0.00 0.00
#> TCGA.EU.5905.01 1 0.3459 0.72411 0.60 0.00 0.00 0.00 0.40 0.00 0.00
#> TCGA.CZ.4856.01 1 0.1886 0.84055 0.88 0.00 0.00 0.00 0.12 0.00 0.00
#> TCGA.BP.5184.01 4 0.1860 0.61158 0.00 0.02 0.00 0.92 0.02 0.04 0.00
#> TCGA.B4.5832.01 3 0.0504 0.70570 0.00 0.00 0.98 0.00 0.02 0.00 0.00
#> TCGA.B8.5164.01 6 0.7281 -0.06837 0.00 0.32 0.18 0.06 0.04 0.38 0.02
#> TCGA.BP.5195.01 3 0.6706 -0.11056 0.00 0.22 0.48 0.20 0.04 0.00 0.06
#> TCGA.BP.5010.01 3 0.1928 0.70788 0.00 0.08 0.90 0.00 0.00 0.00 0.02
#> TCGA.B0.4703.01 3 0.1363 0.71389 0.00 0.04 0.94 0.00 0.02 0.00 0.00
#> TCGA.B0.5104.01 1 0.1363 0.82969 0.94 0.00 0.00 0.00 0.04 0.00 0.02
#> TCGA.CW.5587.01 1 0.3358 0.74764 0.64 0.00 0.00 0.00 0.36 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.CZ.4863.01 1 0.3658 -0.3072 0.58 0.00 0.00 0.00 0.40 0.00 0.02 0.00
#> TCGA.CJ.4902.01 3 0.5508 0.0686 0.00 0.20 0.54 0.00 0.00 0.20 0.06 0.00
#> TCGA.CW.6087.01 3 0.1741 0.6709 0.00 0.04 0.92 0.00 0.00 0.02 0.02 0.00
#> TCGA.DV.5566.01 5 0.3570 0.9067 0.36 0.00 0.00 0.00 0.62 0.00 0.02 0.00
#> TCGA.MM.A84U.01 1 0.0808 0.6637 0.96 0.00 0.00 0.00 0.04 0.00 0.00 0.00
#> TCGA.B4.5844.01 5 0.3193 0.9245 0.38 0.00 0.00 0.00 0.62 0.00 0.00 0.00
#> TCGA.CZ.5459.01 4 0.7167 -0.2311 0.00 0.26 0.00 0.28 0.00 0.22 0.04 0.20
#> TCGA.B0.4694.01 3 0.2348 0.6314 0.00 0.06 0.88 0.00 0.00 0.04 0.00 0.02
#> TCGA.B4.5836.01 5 0.3237 0.8978 0.40 0.00 0.00 0.00 0.60 0.00 0.00 0.00
#> TCGA.B0.5095.01 3 0.2864 0.5893 0.00 0.00 0.84 0.02 0.00 0.08 0.06 0.00
#> TCGA.B0.4690.01 3 0.0941 0.6655 0.00 0.02 0.96 0.00 0.00 0.00 0.02 0.00
#> TCGA.CZ.5466.01 3 0.2204 0.6330 0.00 0.02 0.90 0.00 0.00 0.02 0.04 0.02
#> TCGA.CW.5588.01 1 0.0471 0.6691 0.98 0.00 0.00 0.00 0.02 0.00 0.00 0.00
#> TCGA.CJ.6031.01 3 0.5823 0.1132 0.00 0.26 0.54 0.10 0.00 0.06 0.04 0.00
#> TCGA.B8.A54J.01 6 0.5583 0.1722 0.00 0.04 0.00 0.12 0.00 0.58 0.04 0.22
#> TCGA.CZ.5462.01 3 0.1607 0.6639 0.00 0.04 0.92 0.00 0.00 0.00 0.04 0.00
#> TCGA.B8.A54H.01 5 0.3193 0.9245 0.38 0.00 0.00 0.00 0.62 0.00 0.00 0.00
#> TCGA.CJ.6028.01 3 0.1408 0.6774 0.00 0.02 0.94 0.00 0.00 0.02 0.02 0.00
#> TCGA.G6.A8L6.01 6 0.6049 0.0317 0.00 0.02 0.00 0.20 0.00 0.42 0.04 0.32
#> TCGA.B8.5551.01 1 0.0000 0.6673 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.A3.A8OU.01 5 0.3237 0.8987 0.40 0.00 0.00 0.00 0.60 0.00 0.00 0.00
#> TCGA.A3.A6NI.01 8 0.7249 0.1160 0.00 0.04 0.00 0.06 0.08 0.32 0.14 0.36
#> TCGA.BP.4782.01 1 0.3272 -0.2945 0.58 0.00 0.00 0.00 0.42 0.00 0.00 0.00
#> TCGA.B0.4849.01 4 0.4074 0.4706 0.00 0.02 0.00 0.68 0.00 0.26 0.02 0.02
#> TCGA.BP.5176.01 5 0.3193 0.9245 0.38 0.00 0.00 0.00 0.62 0.00 0.00 0.00
#> TCGA.CW.5591.01 3 0.1557 0.6595 0.00 0.06 0.92 0.00 0.00 0.00 0.02 0.00
#> TCGA.CW.5581.01 6 0.5806 0.0666 0.00 0.08 0.00 0.36 0.02 0.48 0.02 0.04
#> TCGA.CJ.4907.01 4 0.6023 0.1438 0.00 0.32 0.00 0.42 0.00 0.16 0.10 0.00
#> TCGA.A3.3387.01 6 0.4713 0.3312 0.00 0.08 0.04 0.06 0.00 0.74 0.04 0.04
#> TCGA.B2.A4SR.01 4 0.6260 -0.1998 0.00 0.00 0.00 0.38 0.04 0.18 0.04 0.36
#> TCGA.BP.4801.01 6 0.3924 0.0680 0.00 0.04 0.00 0.04 0.00 0.72 0.00 0.20
#> TCGA.B0.5100.01 7 0.3943 0.0000 0.00 0.04 0.40 0.00 0.00 0.00 0.56 0.00
#> TCGA.B0.5400.01 1 0.0000 0.6673 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.B0.4818.01 5 0.3193 0.9245 0.38 0.00 0.00 0.00 0.62 0.00 0.00 0.00
#> TCGA.AK.3431.01 5 0.3318 0.7743 0.46 0.00 0.00 0.00 0.54 0.00 0.00 0.00
#> TCGA.BP.4770.01 1 0.1341 0.5825 0.92 0.00 0.00 0.00 0.08 0.00 0.00 0.00
#> TCGA.BP.5189.01 3 0.4188 0.4605 0.00 0.14 0.72 0.00 0.00 0.04 0.10 0.00
#> TCGA.B8.5163.01 1 0.0471 0.6703 0.98 0.00 0.00 0.00 0.02 0.00 0.00 0.00
#> TCGA.CJ.5683.01 6 0.5829 -0.4288 0.00 0.04 0.00 0.08 0.02 0.46 0.02 0.38
#> TCGA.B0.4843.01 6 0.6558 -0.0115 0.00 0.14 0.28 0.00 0.00 0.44 0.08 0.06
#> TCGA.B8.A54G.01 6 0.5900 0.1481 0.00 0.02 0.06 0.04 0.00 0.58 0.08 0.22
#> TCGA.B0.5703.01 6 0.5230 0.2244 0.00 0.04 0.04 0.18 0.02 0.66 0.00 0.06
#> TCGA.CJ.5672.01 2 0.5815 0.3001 0.00 0.52 0.02 0.06 0.00 0.32 0.04 0.04
#> TCGA.B0.5102.01 5 0.3690 0.8187 0.42 0.00 0.00 0.00 0.56 0.00 0.02 0.00
#> TCGA.CW.5585.01 4 0.3903 0.5242 0.00 0.06 0.00 0.78 0.00 0.06 0.02 0.08
#> TCGA.B0.4824.01 5 0.3193 0.9245 0.38 0.00 0.00 0.00 0.62 0.00 0.00 0.00
#> TCGA.AK.3450.01 1 0.3272 -0.2906 0.58 0.00 0.00 0.00 0.42 0.00 0.00 0.00
#> TCGA.DV.5568.01 3 0.7245 -0.1618 0.00 0.20 0.42 0.22 0.02 0.08 0.04 0.02
#> TCGA.DV.5565.01 8 0.7189 0.3916 0.00 0.06 0.00 0.18 0.02 0.24 0.10 0.40
#> TCGA.B0.4811.01 6 0.7163 0.1663 0.00 0.14 0.08 0.26 0.00 0.42 0.06 0.04
#> TCGA.CJ.4916.01 1 0.0471 0.6691 0.98 0.00 0.00 0.00 0.02 0.00 0.00 0.00
#> TCGA.B0.5693.01 5 0.3570 0.9067 0.36 0.00 0.00 0.00 0.62 0.00 0.02 0.00
#> TCGA.B8.5550.01 6 0.2725 0.3110 0.00 0.04 0.14 0.00 0.00 0.82 0.00 0.00
#> TCGA.BP.5187.01 3 0.6910 -0.1193 0.00 0.16 0.44 0.10 0.00 0.20 0.10 0.00
#> TCGA.CW.6097.01 3 0.2404 0.6257 0.00 0.14 0.84 0.00 0.00 0.02 0.00 0.00
#> TCGA.CZ.5989.01 6 0.5861 -0.1547 0.00 0.12 0.00 0.14 0.00 0.50 0.00 0.24
#> TCGA.BP.5194.01 4 0.2204 0.5690 0.00 0.02 0.00 0.90 0.00 0.02 0.02 0.04
#> TCGA.CZ.5467.01 5 0.3537 0.6227 0.24 0.00 0.00 0.00 0.72 0.00 0.02 0.02
#> TCGA.BP.5170.01 4 0.7285 0.0337 0.00 0.14 0.02 0.36 0.00 0.30 0.10 0.08
#> TCGA.CJ.5686.01 1 0.3193 -0.1129 0.62 0.00 0.00 0.00 0.38 0.00 0.00 0.00
#> TCGA.A3.3373.01 5 0.3193 0.9245 0.38 0.00 0.00 0.00 0.62 0.00 0.00 0.00
#> TCGA.CJ.4908.01 4 0.3530 0.5871 0.00 0.02 0.00 0.80 0.00 0.10 0.02 0.06
#> TCGA.B0.4819.01 1 0.0000 0.6673 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.B2.5633.01 6 0.6435 0.1407 0.00 0.28 0.06 0.06 0.00 0.50 0.06 0.04
#> TCGA.BP.5168.01 6 0.6147 -0.1897 0.00 0.06 0.00 0.18 0.00 0.44 0.02 0.30
#> TCGA.B8.5162.01 6 0.5371 0.0272 0.00 0.24 0.16 0.00 0.00 0.56 0.02 0.02
#> TCGA.B0.4842.01 1 0.0000 0.6673 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.CJ.4905.01 5 0.3142 0.9160 0.36 0.00 0.00 0.00 0.64 0.00 0.00 0.00
#> TCGA.B2.5635.01 2 0.5548 0.3693 0.00 0.52 0.06 0.08 0.00 0.32 0.00 0.02
#> TCGA.B4.5838.01 6 0.3850 0.1737 0.00 0.12 0.00 0.06 0.00 0.76 0.00 0.06
#> TCGA.AK.3461.01 6 0.5818 0.0911 0.00 0.06 0.00 0.12 0.00 0.56 0.04 0.22
#> TCGA.AK.3460.01 6 0.5897 -0.3441 0.00 0.06 0.00 0.20 0.00 0.38 0.00 0.36
#> TCGA.B0.5812.01 4 0.1408 0.5811 0.00 0.02 0.00 0.94 0.00 0.02 0.00 0.02
#> TCGA.B8.A54F.01 1 0.3329 -0.5905 0.52 0.00 0.00 0.00 0.48 0.00 0.00 0.00
#> TCGA.B0.4697.01 1 0.0000 0.6673 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.A3.3358.01 1 0.3142 -0.0138 0.64 0.00 0.00 0.00 0.36 0.00 0.00 0.00
#> TCGA.CJ.4882.01 3 0.1557 0.6712 0.00 0.06 0.92 0.00 0.00 0.00 0.02 0.00
#> TCGA.B0.4700.01 3 0.0471 0.6721 0.00 0.02 0.98 0.00 0.00 0.00 0.00 0.00
#> TCGA.B0.5092.01 1 0.0000 0.6673 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.CJ.6032.01 5 0.3318 0.7545 0.46 0.00 0.00 0.00 0.54 0.00 0.00 0.00
#> TCGA.B0.4817.01 3 0.0941 0.6748 0.00 0.02 0.96 0.00 0.00 0.02 0.00 0.00
#> TCGA.B0.4822.01 3 0.2532 0.6156 0.00 0.02 0.88 0.00 0.00 0.04 0.04 0.02
#> TCGA.B0.5696.01 6 0.7214 0.0957 0.00 0.20 0.06 0.28 0.02 0.38 0.02 0.04
#> TCGA.CJ.4918.01 3 0.3710 0.5400 0.00 0.10 0.76 0.00 0.00 0.12 0.02 0.00
#> TCGA.B0.5097.01 1 0.0471 0.6703 0.98 0.00 0.00 0.00 0.02 0.00 0.00 0.00
#> TCGA.CZ.5455.01 6 0.5976 0.0124 0.00 0.08 0.02 0.40 0.02 0.44 0.02 0.02
#> TCGA.CZ.5451.01 8 0.6102 0.3307 0.00 0.08 0.00 0.12 0.02 0.38 0.00 0.40
#> TCGA.CJ.4869.01 3 0.4367 0.4264 0.00 0.14 0.70 0.04 0.00 0.12 0.00 0.00
#> TCGA.B8.4146.01 5 0.3570 0.9067 0.36 0.00 0.00 0.00 0.62 0.00 0.02 0.00
#> TCGA.B0.5399.01 4 0.4202 0.5679 0.00 0.06 0.00 0.74 0.00 0.14 0.04 0.02
#> TCGA.B2.5639.01 3 0.7354 -0.3069 0.00 0.12 0.30 0.26 0.00 0.22 0.10 0.00
#> TCGA.B0.5120.01 1 0.3299 -0.3931 0.56 0.00 0.00 0.00 0.44 0.00 0.00 0.00
#> TCGA.BP.5185.01 8 0.5030 0.3717 0.00 0.00 0.00 0.20 0.00 0.34 0.00 0.46
#> TCGA.B0.4846.01 1 0.3142 -0.0186 0.64 0.00 0.00 0.00 0.36 0.00 0.00 0.00
#> TCGA.CJ.4897.01 5 0.3142 0.9160 0.36 0.00 0.00 0.00 0.64 0.00 0.00 0.00
#> TCGA.CJ.4923.01 3 0.0941 0.6743 0.00 0.02 0.96 0.00 0.00 0.00 0.02 0.00
#> TCGA.B8.A7U6.01 5 0.3142 0.9160 0.36 0.00 0.00 0.00 0.64 0.00 0.00 0.00
#> TCGA.B0.5099.01 5 0.3193 0.9245 0.38 0.00 0.00 0.00 0.62 0.00 0.00 0.00
#> TCGA.CZ.5988.01 4 0.5593 -0.0179 0.00 0.34 0.00 0.38 0.00 0.26 0.00 0.02
#> TCGA.B0.5109.01 3 0.0941 0.6748 0.00 0.02 0.96 0.00 0.00 0.02 0.00 0.00
#> TCGA.B0.5080.01 3 0.1275 0.6683 0.00 0.04 0.94 0.00 0.00 0.02 0.00 0.00
#> TCGA.CZ.4865.01 1 0.0808 0.6625 0.96 0.00 0.00 0.00 0.04 0.00 0.00 0.00
#> TCGA.CJ.5684.01 6 0.5715 0.2095 0.00 0.10 0.00 0.32 0.00 0.50 0.06 0.02
#> TCGA.B0.4701.01 1 0.0471 0.6703 0.98 0.00 0.00 0.00 0.02 0.00 0.00 0.00
#> TCGA.CZ.5458.01 2 0.4881 0.2992 0.00 0.68 0.00 0.16 0.04 0.08 0.04 0.00
#> TCGA.CZ.5982.01 5 0.3142 0.9160 0.36 0.00 0.00 0.00 0.64 0.00 0.00 0.00
#> TCGA.B0.5697.01 2 0.6410 0.1564 0.00 0.40 0.02 0.16 0.00 0.32 0.00 0.10
#> TCGA.A3.A6NN.01 6 0.5937 -0.0146 0.00 0.00 0.00 0.10 0.02 0.46 0.08 0.34
#> TCGA.B0.4852.01 5 0.3193 0.9245 0.38 0.00 0.00 0.00 0.62 0.00 0.00 0.00
#> TCGA.CJ.5689.01 6 0.3895 0.3463 0.00 0.12 0.00 0.12 0.00 0.74 0.02 0.00
#> TCGA.BP.5200.01 4 0.4488 0.4994 0.00 0.02 0.00 0.72 0.02 0.06 0.02 0.16
#> TCGA.B2.4101.01 4 0.6968 -0.0155 0.00 0.20 0.20 0.38 0.00 0.18 0.04 0.00
#> TCGA.B0.4816.01 6 0.4621 0.0927 0.00 0.08 0.32 0.00 0.00 0.58 0.02 0.00
#> TCGA.B2.3924.01 4 0.3830 0.5057 0.00 0.00 0.00 0.74 0.00 0.16 0.02 0.08
#> TCGA.B0.5713.01 5 0.3193 0.9245 0.38 0.00 0.00 0.00 0.62 0.00 0.00 0.00
#> TCGA.B0.5108.01 2 0.5061 -0.3789 0.00 0.48 0.42 0.00 0.00 0.04 0.04 0.02
#> TCGA.B0.5711.01 4 0.1887 0.5941 0.00 0.04 0.00 0.90 0.00 0.06 0.00 0.00
#> TCGA.B8.5553.01 1 0.3299 -0.3814 0.56 0.00 0.00 0.00 0.44 0.00 0.00 0.00
#> TCGA.MW.A4EC.01 5 0.3570 0.9067 0.36 0.00 0.00 0.00 0.62 0.00 0.02 0.00
#> TCGA.EU.5905.01 1 0.1947 0.5729 0.86 0.00 0.00 0.00 0.14 0.00 0.00 0.00
#> TCGA.CZ.4856.01 1 0.3272 -0.2886 0.58 0.00 0.00 0.00 0.42 0.00 0.00 0.00
#> TCGA.BP.5184.01 4 0.2482 0.5910 0.00 0.00 0.00 0.88 0.02 0.06 0.02 0.02
#> TCGA.B4.5832.01 3 0.1408 0.6564 0.00 0.02 0.94 0.00 0.00 0.00 0.02 0.02
#> TCGA.B8.5164.01 6 0.2680 0.3044 0.00 0.12 0.00 0.02 0.00 0.84 0.00 0.02
#> TCGA.BP.5195.01 3 0.4804 0.3433 0.00 0.14 0.68 0.12 0.00 0.02 0.04 0.00
#> TCGA.BP.5010.01 3 0.1275 0.6707 0.00 0.04 0.94 0.00 0.00 0.00 0.02 0.00
#> TCGA.B0.4703.01 3 0.1607 0.6742 0.00 0.04 0.92 0.00 0.00 0.04 0.00 0.00
#> TCGA.B0.5104.01 5 0.3318 0.7775 0.46 0.00 0.00 0.00 0.54 0.00 0.00 0.00
#> TCGA.CW.5587.01 1 0.1947 0.5689 0.86 0.00 0.00 0.00 0.14 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: Node04. Child nodes: Node0141-leaf , Node0142-leaf , Node0143-leaf , Node0144-leaf , Node0211-leaf , Node0212-leaf , Node0213 , Node0231-leaf , Node0232-leaf , Node0233-leaf , Node0411 , Node0412-leaf , Node0413-leaf , Node0431-leaf , Node0432-leaf , Node0433-leaf , Node0511-leaf , Node0512-leaf , Node0541-leaf , Node0542-leaf , Node0543-leaf , Node0621-leaf , Node0622-leaf , Node0623-leaf .
The object with results only for a single top-value method and a single partitioning method can be extracted as:
res = res_rh["041"]
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 50 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 0.983 0.992 0.4928 0.510 0.510
#> 3 3 1.000 0.994 0.997 0.3459 0.656 0.423
#> 4 4 0.923 0.930 0.969 0.1460 0.812 0.509
#> 5 5 0.803 0.781 0.908 0.0231 0.993 0.969
#> 6 6 0.784 0.659 0.813 0.0355 1.000 1.000
#> 7 7 0.780 0.524 0.774 0.0283 0.943 0.757
#> 8 8 0.748 0.670 0.827 0.0279 0.922 0.623
suggest_best_k() suggests the best \(k\) based on these statistics. The rules are as follows:
suggest_best_k(res)
#> [1] 4
#> attr(,"optional")
#> [1] 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.CZ.4863.01 2 0.000 1.000 0.00 1.00
#> TCGA.DV.5566.01 1 0.000 0.987 1.00 0.00
#> TCGA.MM.A84U.01 2 0.000 1.000 0.00 1.00
#> TCGA.B4.5844.01 1 0.000 0.987 1.00 0.00
#> TCGA.B4.5836.01 1 0.000 0.987 1.00 0.00
#> TCGA.CW.5588.01 2 0.000 1.000 0.00 1.00
#> TCGA.B8.A54H.01 1 0.000 0.987 1.00 0.00
#> TCGA.B8.5551.01 2 0.000 1.000 0.00 1.00
#> TCGA.A3.A8OU.01 1 0.000 0.987 1.00 0.00
#> TCGA.BP.4782.01 2 0.000 1.000 0.00 1.00
#> TCGA.BP.5176.01 1 0.000 0.987 1.00 0.00
#> TCGA.B0.5400.01 2 0.000 1.000 0.00 1.00
#> TCGA.B0.4818.01 1 0.000 0.987 1.00 0.00
#> TCGA.AK.3431.01 1 0.000 0.987 1.00 0.00
#> TCGA.BP.4770.01 2 0.000 1.000 0.00 1.00
#> TCGA.B8.5163.01 2 0.000 1.000 0.00 1.00
#> TCGA.B0.5102.01 1 0.000 0.987 1.00 0.00
#> TCGA.B0.4824.01 1 0.000 0.987 1.00 0.00
#> TCGA.AK.3450.01 1 0.000 0.987 1.00 0.00
#> TCGA.CJ.4916.01 2 0.000 1.000 0.00 1.00
#> TCGA.B0.5693.01 1 0.000 0.987 1.00 0.00
#> TCGA.CZ.5467.01 1 0.000 0.987 1.00 0.00
#> TCGA.CJ.5686.01 2 0.000 1.000 0.00 1.00
#> TCGA.A3.3373.01 1 0.000 0.987 1.00 0.00
#> TCGA.B0.4819.01 2 0.000 1.000 0.00 1.00
#> TCGA.B0.4842.01 2 0.000 1.000 0.00 1.00
#> TCGA.CJ.4905.01 1 0.000 0.987 1.00 0.00
#> TCGA.B8.A54F.01 1 0.000 0.987 1.00 0.00
#> TCGA.B0.4697.01 2 0.000 1.000 0.00 1.00
#> TCGA.A3.3358.01 2 0.000 1.000 0.00 1.00
#> TCGA.B0.5092.01 2 0.000 1.000 0.00 1.00
#> TCGA.CJ.6032.01 1 0.000 0.987 1.00 0.00
#> TCGA.B0.5097.01 2 0.000 1.000 0.00 1.00
#> TCGA.B8.4146.01 1 0.000 0.987 1.00 0.00
#> TCGA.B0.5120.01 1 0.000 0.987 1.00 0.00
#> TCGA.B0.4846.01 1 0.000 0.987 1.00 0.00
#> TCGA.CJ.4897.01 1 0.000 0.987 1.00 0.00
#> TCGA.B8.A7U6.01 1 0.000 0.987 1.00 0.00
#> TCGA.B0.5099.01 1 0.000 0.987 1.00 0.00
#> TCGA.CZ.4865.01 2 0.000 1.000 0.00 1.00
#> TCGA.B0.4701.01 2 0.000 1.000 0.00 1.00
#> TCGA.CZ.5982.01 1 0.000 0.987 1.00 0.00
#> TCGA.B0.4852.01 1 0.000 0.987 1.00 0.00
#> TCGA.B0.5713.01 1 0.000 0.987 1.00 0.00
#> TCGA.B8.5553.01 2 0.000 1.000 0.00 1.00
#> TCGA.MW.A4EC.01 1 0.000 0.987 1.00 0.00
#> TCGA.EU.5905.01 1 0.760 0.727 0.78 0.22
#> TCGA.CZ.4856.01 1 0.634 0.813 0.84 0.16
#> TCGA.B0.5104.01 1 0.000 0.987 1.00 0.00
#> TCGA.CW.5587.01 2 0.000 1.000 0.00 1.00
cbind(get_classes(res, k = 3), get_membership(res, k = 3))
#> class entropy silhouette p1 p2 p3
#> TCGA.CZ.4863.01 2 0.000 1.000 0 1.00 0.00
#> TCGA.DV.5566.01 1 0.000 1.000 1 0.00 0.00
#> TCGA.MM.A84U.01 3 0.369 0.837 0 0.14 0.86
#> TCGA.B4.5844.01 1 0.000 1.000 1 0.00 0.00
#> TCGA.B4.5836.01 3 0.000 0.993 0 0.00 1.00
#> TCGA.CW.5588.01 3 0.000 0.993 0 0.00 1.00
#> TCGA.B8.A54H.01 3 0.000 0.993 0 0.00 1.00
#> TCGA.B8.5551.01 2 0.000 1.000 0 1.00 0.00
#> TCGA.A3.A8OU.01 3 0.000 0.993 0 0.00 1.00
#> TCGA.BP.4782.01 3 0.000 0.993 0 0.00 1.00
#> TCGA.BP.5176.01 3 0.000 0.993 0 0.00 1.00
#> TCGA.B0.5400.01 2 0.000 1.000 0 1.00 0.00
#> TCGA.B0.4818.01 3 0.000 0.993 0 0.00 1.00
#> TCGA.AK.3431.01 3 0.000 0.993 0 0.00 1.00
#> TCGA.BP.4770.01 2 0.000 1.000 0 1.00 0.00
#> TCGA.B8.5163.01 2 0.000 1.000 0 1.00 0.00
#> TCGA.B0.5102.01 1 0.000 1.000 1 0.00 0.00
#> TCGA.B0.4824.01 3 0.000 0.993 0 0.00 1.00
#> TCGA.AK.3450.01 3 0.000 0.993 0 0.00 1.00
#> TCGA.CJ.4916.01 2 0.000 1.000 0 1.00 0.00
#> TCGA.B0.5693.01 1 0.000 1.000 1 0.00 0.00
#> TCGA.CZ.5467.01 1 0.000 1.000 1 0.00 0.00
#> TCGA.CJ.5686.01 2 0.000 1.000 0 1.00 0.00
#> TCGA.A3.3373.01 1 0.000 1.000 1 0.00 0.00
#> TCGA.B0.4819.01 2 0.000 1.000 0 1.00 0.00
#> TCGA.B0.4842.01 2 0.000 1.000 0 1.00 0.00
#> TCGA.CJ.4905.01 1 0.000 1.000 1 0.00 0.00
#> TCGA.B8.A54F.01 3 0.000 0.993 0 0.00 1.00
#> TCGA.B0.4697.01 2 0.000 1.000 0 1.00 0.00
#> TCGA.A3.3358.01 3 0.000 0.993 0 0.00 1.00
#> TCGA.B0.5092.01 2 0.000 1.000 0 1.00 0.00
#> TCGA.CJ.6032.01 1 0.000 1.000 1 0.00 0.00
#> TCGA.B0.5097.01 2 0.000 1.000 0 1.00 0.00
#> TCGA.B8.4146.01 1 0.000 1.000 1 0.00 0.00
#> TCGA.B0.5120.01 3 0.000 0.993 0 0.00 1.00
#> TCGA.B0.4846.01 3 0.000 0.993 0 0.00 1.00
#> TCGA.CJ.4897.01 1 0.000 1.000 1 0.00 0.00
#> TCGA.B8.A7U6.01 3 0.000 0.993 0 0.00 1.00
#> TCGA.B0.5099.01 1 0.000 1.000 1 0.00 0.00
#> TCGA.CZ.4865.01 3 0.000 0.993 0 0.00 1.00
#> TCGA.B0.4701.01 2 0.000 1.000 0 1.00 0.00
#> TCGA.CZ.5982.01 1 0.000 1.000 1 0.00 0.00
#> TCGA.B0.4852.01 1 0.000 1.000 1 0.00 0.00
#> TCGA.B0.5713.01 1 0.000 1.000 1 0.00 0.00
#> TCGA.B8.5553.01 3 0.000 0.993 0 0.00 1.00
#> TCGA.MW.A4EC.01 1 0.000 1.000 1 0.00 0.00
#> TCGA.EU.5905.01 3 0.000 0.993 0 0.00 1.00
#> TCGA.CZ.4856.01 3 0.000 0.993 0 0.00 1.00
#> TCGA.B0.5104.01 3 0.000 0.993 0 0.00 1.00
#> TCGA.CW.5587.01 3 0.000 0.993 0 0.00 1.00
cbind(get_classes(res, k = 4), get_membership(res, k = 4))
#> class entropy silhouette p1 p2 p3 p4
#> TCGA.CZ.4863.01 4 0.164 0.871 0.00 0.06 0.00 0.94
#> TCGA.DV.5566.01 3 0.265 0.844 0.12 0.00 0.88 0.00
#> TCGA.MM.A84U.01 4 0.000 0.920 0.00 0.00 0.00 1.00
#> TCGA.B4.5844.01 1 0.000 1.000 1.00 0.00 0.00 0.00
#> TCGA.B4.5836.01 4 0.471 0.514 0.00 0.00 0.36 0.64
#> TCGA.CW.5588.01 4 0.000 0.920 0.00 0.00 0.00 1.00
#> TCGA.B8.A54H.01 3 0.000 0.959 0.00 0.00 1.00 0.00
#> TCGA.B8.5551.01 2 0.000 0.974 0.00 1.00 0.00 0.00
#> TCGA.A3.A8OU.01 3 0.000 0.959 0.00 0.00 1.00 0.00
#> TCGA.BP.4782.01 4 0.000 0.920 0.00 0.00 0.00 1.00
#> TCGA.BP.5176.01 3 0.000 0.959 0.00 0.00 1.00 0.00
#> TCGA.B0.5400.01 2 0.000 0.974 0.00 1.00 0.00 0.00
#> TCGA.B0.4818.01 3 0.000 0.959 0.00 0.00 1.00 0.00
#> TCGA.AK.3431.01 3 0.000 0.959 0.00 0.00 1.00 0.00
#> TCGA.BP.4770.01 2 0.000 0.974 0.00 1.00 0.00 0.00
#> TCGA.B8.5163.01 2 0.000 0.974 0.00 1.00 0.00 0.00
#> TCGA.B0.5102.01 1 0.000 1.000 1.00 0.00 0.00 0.00
#> TCGA.B0.4824.01 3 0.000 0.959 0.00 0.00 1.00 0.00
#> TCGA.AK.3450.01 3 0.000 0.959 0.00 0.00 1.00 0.00
#> TCGA.CJ.4916.01 2 0.234 0.898 0.00 0.90 0.00 0.10
#> TCGA.B0.5693.01 1 0.000 1.000 1.00 0.00 0.00 0.00
#> TCGA.CZ.5467.01 1 0.000 1.000 1.00 0.00 0.00 0.00
#> TCGA.CJ.5686.01 4 0.000 0.920 0.00 0.00 0.00 1.00
#> TCGA.A3.3373.01 1 0.000 1.000 1.00 0.00 0.00 0.00
#> TCGA.B0.4819.01 2 0.000 0.974 0.00 1.00 0.00 0.00
#> TCGA.B0.4842.01 2 0.000 0.974 0.00 1.00 0.00 0.00
#> TCGA.CJ.4905.01 1 0.000 1.000 1.00 0.00 0.00 0.00
#> TCGA.B8.A54F.01 3 0.000 0.959 0.00 0.00 1.00 0.00
#> TCGA.B0.4697.01 2 0.000 0.974 0.00 1.00 0.00 0.00
#> TCGA.A3.3358.01 4 0.000 0.920 0.00 0.00 0.00 1.00
#> TCGA.B0.5092.01 2 0.000 0.974 0.00 1.00 0.00 0.00
#> TCGA.CJ.6032.01 1 0.000 1.000 1.00 0.00 0.00 0.00
#> TCGA.B0.5097.01 2 0.292 0.857 0.00 0.86 0.00 0.14
#> TCGA.B8.4146.01 1 0.000 1.000 1.00 0.00 0.00 0.00
#> TCGA.B0.5120.01 3 0.000 0.959 0.00 0.00 1.00 0.00
#> TCGA.B0.4846.01 3 0.000 0.959 0.00 0.00 1.00 0.00
#> TCGA.CJ.4897.01 1 0.000 1.000 1.00 0.00 0.00 0.00
#> TCGA.B8.A7U6.01 3 0.000 0.959 0.00 0.00 1.00 0.00
#> TCGA.B0.5099.01 1 0.000 1.000 1.00 0.00 0.00 0.00
#> TCGA.CZ.4865.01 4 0.000 0.920 0.00 0.00 0.00 1.00
#> TCGA.B0.4701.01 4 0.000 0.920 0.00 0.00 0.00 1.00
#> TCGA.CZ.5982.01 1 0.000 1.000 1.00 0.00 0.00 0.00
#> TCGA.B0.4852.01 3 0.462 0.489 0.34 0.00 0.66 0.00
#> TCGA.B0.5713.01 1 0.000 1.000 1.00 0.00 0.00 0.00
#> TCGA.B8.5553.01 4 0.000 0.920 0.00 0.00 0.00 1.00
#> TCGA.MW.A4EC.01 1 0.000 1.000 1.00 0.00 0.00 0.00
#> TCGA.EU.5905.01 4 0.265 0.839 0.00 0.00 0.12 0.88
#> TCGA.CZ.4856.01 4 0.452 0.589 0.00 0.00 0.32 0.68
#> TCGA.B0.5104.01 3 0.000 0.959 0.00 0.00 1.00 0.00
#> TCGA.CW.5587.01 4 0.000 0.920 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.CZ.4863.01 4 0.560 0.518 0.00 0.20 0.00 0.64 0.16
#> TCGA.DV.5566.01 3 0.498 0.533 0.20 0.00 0.70 0.00 0.10
#> TCGA.MM.A84U.01 4 0.273 0.731 0.00 0.00 0.00 0.84 0.16
#> TCGA.B4.5844.01 1 0.000 0.954 1.00 0.00 0.00 0.00 0.00
#> TCGA.B4.5836.01 4 0.406 0.406 0.00 0.00 0.36 0.64 0.00
#> TCGA.CW.5588.01 4 0.000 0.776 0.00 0.00 0.00 1.00 0.00
#> TCGA.B8.A54H.01 3 0.104 0.852 0.00 0.00 0.96 0.00 0.04
#> TCGA.B8.5551.01 2 0.000 0.901 0.00 1.00 0.00 0.00 0.00
#> TCGA.A3.A8OU.01 3 0.000 0.879 0.00 0.00 1.00 0.00 0.00
#> TCGA.BP.4782.01 4 0.000 0.776 0.00 0.00 0.00 1.00 0.00
#> TCGA.BP.5176.01 3 0.000 0.879 0.00 0.00 1.00 0.00 0.00
#> TCGA.B0.5400.01 2 0.000 0.901 0.00 1.00 0.00 0.00 0.00
#> TCGA.B0.4818.01 3 0.327 0.661 0.00 0.00 0.78 0.22 0.00
#> TCGA.AK.3431.01 3 0.000 0.879 0.00 0.00 1.00 0.00 0.00
#> TCGA.BP.4770.01 5 0.380 0.000 0.00 0.30 0.00 0.00 0.70
#> TCGA.B8.5163.01 2 0.000 0.901 0.00 1.00 0.00 0.00 0.00
#> TCGA.B0.5102.01 1 0.202 0.935 0.90 0.00 0.00 0.00 0.10
#> TCGA.B0.4824.01 3 0.000 0.879 0.00 0.00 1.00 0.00 0.00
#> TCGA.AK.3450.01 3 0.000 0.879 0.00 0.00 1.00 0.00 0.00
#> TCGA.CJ.4916.01 2 0.273 0.708 0.00 0.84 0.00 0.00 0.16
#> TCGA.B0.5693.01 1 0.000 0.954 1.00 0.00 0.00 0.00 0.00
#> TCGA.CZ.5467.01 1 0.000 0.954 1.00 0.00 0.00 0.00 0.00
#> TCGA.CJ.5686.01 4 0.332 0.719 0.00 0.02 0.00 0.82 0.16
#> TCGA.A3.3373.01 1 0.202 0.935 0.90 0.00 0.00 0.00 0.10
#> TCGA.B0.4819.01 2 0.000 0.901 0.00 1.00 0.00 0.00 0.00
#> TCGA.B0.4842.01 2 0.000 0.901 0.00 1.00 0.00 0.00 0.00
#> TCGA.CJ.4905.01 1 0.000 0.954 1.00 0.00 0.00 0.00 0.00
#> TCGA.B8.A54F.01 3 0.000 0.879 0.00 0.00 1.00 0.00 0.00
#> TCGA.B0.4697.01 2 0.000 0.901 0.00 1.00 0.00 0.00 0.00
#> TCGA.A3.3358.01 4 0.228 0.747 0.00 0.00 0.00 0.88 0.12
#> TCGA.B0.5092.01 2 0.000 0.901 0.00 1.00 0.00 0.00 0.00
#> TCGA.CJ.6032.01 1 0.202 0.935 0.90 0.00 0.00 0.00 0.10
#> TCGA.B0.5097.01 2 0.508 0.469 0.00 0.70 0.00 0.14 0.16
#> TCGA.B8.4146.01 1 0.202 0.935 0.90 0.00 0.00 0.00 0.10
#> TCGA.B0.5120.01 3 0.252 0.757 0.00 0.00 0.86 0.14 0.00
#> TCGA.B0.4846.01 3 0.000 0.879 0.00 0.00 1.00 0.00 0.00
#> TCGA.CJ.4897.01 1 0.000 0.954 1.00 0.00 0.00 0.00 0.00
#> TCGA.B8.A7U6.01 3 0.000 0.879 0.00 0.00 1.00 0.00 0.00
#> TCGA.B0.5099.01 1 0.000 0.954 1.00 0.00 0.00 0.00 0.00
#> TCGA.CZ.4865.01 4 0.000 0.776 0.00 0.00 0.00 1.00 0.00
#> TCGA.B0.4701.01 4 0.544 0.548 0.00 0.18 0.00 0.66 0.16
#> TCGA.CZ.5982.01 1 0.000 0.954 1.00 0.00 0.00 0.00 0.00
#> TCGA.B0.4852.01 3 0.588 0.036 0.42 0.00 0.48 0.00 0.10
#> TCGA.B0.5713.01 1 0.202 0.935 0.90 0.00 0.00 0.00 0.10
#> TCGA.B8.5553.01 4 0.000 0.776 0.00 0.00 0.00 1.00 0.00
#> TCGA.MW.A4EC.01 1 0.104 0.949 0.96 0.00 0.00 0.00 0.04
#> TCGA.EU.5905.01 4 0.352 0.655 0.00 0.00 0.14 0.82 0.04
#> TCGA.CZ.4856.01 4 0.418 0.314 0.00 0.00 0.40 0.60 0.00
#> TCGA.B0.5104.01 3 0.000 0.879 0.00 0.00 1.00 0.00 0.00
#> TCGA.CW.5587.01 4 0.000 0.776 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.CZ.4863.01 6 0.5569 0.510 0.00 0.10 0.00 0.32 0.02 0.56
#> TCGA.DV.5566.01 3 0.5692 0.291 0.18 0.00 0.50 0.32 0.00 0.00
#> TCGA.MM.A84U.01 6 0.4078 0.595 0.00 0.00 0.00 0.34 0.02 0.64
#> TCGA.B4.5844.01 1 0.0547 0.808 0.98 0.00 0.00 0.02 0.00 0.00
#> TCGA.B4.5836.01 6 0.3706 0.249 0.00 0.00 0.38 0.00 0.00 0.62
#> TCGA.CW.5588.01 6 0.1556 0.661 0.00 0.00 0.00 0.08 0.00 0.92
#> TCGA.B8.A54H.01 3 0.3592 0.642 0.00 0.00 0.74 0.24 0.00 0.02
#> TCGA.B8.5551.01 2 0.0000 0.863 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.A3.A8OU.01 3 0.0547 0.785 0.00 0.00 0.98 0.00 0.00 0.02
#> TCGA.BP.4782.01 6 0.0937 0.650 0.00 0.00 0.04 0.00 0.00 0.96
#> TCGA.BP.5176.01 3 0.0937 0.784 0.00 0.00 0.96 0.04 0.00 0.00
#> TCGA.B0.5400.01 2 0.0000 0.863 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.B0.4818.01 3 0.3756 0.301 0.00 0.00 0.60 0.00 0.00 0.40
#> TCGA.AK.3431.01 3 0.0547 0.785 0.00 0.00 0.98 0.00 0.00 0.02
#> TCGA.BP.4770.01 5 0.0937 0.000 0.00 0.04 0.00 0.00 0.96 0.00
#> TCGA.B8.5163.01 2 0.0000 0.863 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.B0.5102.01 1 0.3578 0.743 0.66 0.00 0.00 0.34 0.00 0.00
#> TCGA.B0.4824.01 3 0.1556 0.772 0.00 0.00 0.92 0.08 0.00 0.00
#> TCGA.AK.3450.01 3 0.0547 0.788 0.00 0.00 0.98 0.02 0.00 0.00
#> TCGA.CJ.4916.01 2 0.4675 0.515 0.00 0.66 0.00 0.28 0.02 0.04
#> TCGA.B0.5693.01 1 0.0937 0.795 0.96 0.00 0.00 0.04 0.00 0.00
#> TCGA.CZ.5467.01 1 0.0937 0.795 0.96 0.00 0.00 0.04 0.00 0.00
#> TCGA.CJ.5686.01 6 0.4502 0.586 0.00 0.02 0.00 0.32 0.02 0.64
#> TCGA.A3.3373.01 1 0.4078 0.719 0.64 0.00 0.02 0.34 0.00 0.00
#> TCGA.B0.4819.01 2 0.0000 0.863 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.B0.4842.01 2 0.0000 0.863 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.CJ.4905.01 1 0.0000 0.805 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.B8.A54F.01 3 0.2790 0.709 0.00 0.00 0.84 0.14 0.02 0.00
#> TCGA.B0.4697.01 2 0.0000 0.863 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.A3.3358.01 6 0.3916 0.607 0.00 0.00 0.00 0.30 0.02 0.68
#> TCGA.B0.5092.01 2 0.0000 0.863 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.CJ.6032.01 1 0.3647 0.726 0.64 0.00 0.00 0.36 0.00 0.00
#> TCGA.B0.5097.01 2 0.6042 0.291 0.00 0.50 0.00 0.32 0.02 0.16
#> TCGA.B8.4146.01 1 0.3499 0.753 0.68 0.00 0.00 0.32 0.00 0.00
#> TCGA.B0.5120.01 3 0.3315 0.618 0.00 0.00 0.78 0.02 0.00 0.20
#> TCGA.B0.4846.01 3 0.0000 0.786 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.CJ.4897.01 1 0.0937 0.795 0.96 0.00 0.00 0.04 0.00 0.00
#> TCGA.B8.A7U6.01 3 0.0547 0.785 0.00 0.00 0.98 0.00 0.00 0.02
#> TCGA.B0.5099.01 1 0.1267 0.788 0.94 0.00 0.00 0.06 0.00 0.00
#> TCGA.CZ.4865.01 6 0.0937 0.669 0.00 0.00 0.00 0.04 0.00 0.96
#> TCGA.B0.4701.01 6 0.5124 0.556 0.00 0.06 0.00 0.32 0.02 0.60
#> TCGA.CZ.5982.01 1 0.0000 0.805 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.B0.4852.01 3 0.5922 0.176 0.22 0.00 0.44 0.34 0.00 0.00
#> TCGA.B0.5713.01 1 0.3647 0.726 0.64 0.00 0.00 0.36 0.00 0.00
#> TCGA.B8.5553.01 6 0.0000 0.666 0.00 0.00 0.00 0.00 0.00 1.00
#> TCGA.MW.A4EC.01 1 0.2793 0.786 0.80 0.00 0.00 0.20 0.00 0.00
#> TCGA.EU.5905.01 6 0.4754 0.402 0.00 0.00 0.06 0.24 0.02 0.68
#> TCGA.CZ.4856.01 6 0.3706 0.246 0.00 0.00 0.38 0.00 0.00 0.62
#> TCGA.B0.5104.01 3 0.0937 0.784 0.00 0.00 0.96 0.04 0.00 0.00
#> TCGA.CW.5587.01 6 0.0000 0.666 0.00 0.00 0.00 0.00 0.00 1.00
cbind(get_classes(res, k = 7), get_membership(res, k = 7))
#> class entropy silhouette p1 p2 p3 p4 p5 p6 p7
#> TCGA.CZ.4863.01 6 0.4266 0.433026 0.00 0.04 0.00 0.00 0.44 0.52 0.00
#> TCGA.DV.5566.01 7 0.4901 -0.133673 0.06 0.00 0.40 0.02 0.00 0.00 0.52
#> TCGA.MM.A84U.01 6 0.5016 0.382852 0.00 0.00 0.00 0.12 0.42 0.46 0.00
#> TCGA.B4.5844.01 1 0.1886 0.735222 0.88 0.00 0.00 0.00 0.00 0.00 0.12
#> TCGA.B4.5836.01 6 0.3358 -0.188805 0.00 0.00 0.36 0.00 0.00 0.64 0.00
#> TCGA.CW.5588.01 6 0.2422 0.044632 0.00 0.00 0.00 0.18 0.00 0.82 0.00
#> TCGA.B8.A54H.01 3 0.3525 0.369277 0.00 0.00 0.56 0.00 0.00 0.00 0.44
#> TCGA.B8.5551.01 2 0.0000 0.840291 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.A3.A8OU.01 3 0.0504 0.766586 0.00 0.00 0.98 0.00 0.00 0.00 0.02
#> TCGA.BP.4782.01 6 0.0504 0.341386 0.00 0.00 0.02 0.00 0.00 0.98 0.00
#> TCGA.BP.5176.01 3 0.2512 0.757542 0.00 0.00 0.86 0.04 0.00 0.00 0.10
#> TCGA.B0.5400.01 2 0.0000 0.840291 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.B0.4818.01 3 0.3525 0.005332 0.00 0.00 0.56 0.00 0.00 0.44 0.00
#> TCGA.AK.3431.01 3 0.0504 0.761283 0.00 0.00 0.98 0.00 0.00 0.00 0.02
#> TCGA.BP.4770.01 5 0.4214 0.000000 0.00 0.00 0.00 0.40 0.56 0.00 0.04
#> TCGA.B8.5163.01 2 0.0000 0.840291 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.B0.5102.01 7 0.3909 0.678108 0.40 0.00 0.00 0.02 0.00 0.00 0.58
#> TCGA.B0.4824.01 3 0.2722 0.753452 0.00 0.00 0.84 0.04 0.00 0.00 0.12
#> TCGA.AK.3450.01 3 0.1886 0.762285 0.00 0.00 0.88 0.00 0.00 0.00 0.12
#> TCGA.CJ.4916.01 2 0.3968 0.366346 0.00 0.54 0.00 0.00 0.44 0.02 0.00
#> TCGA.B0.5693.01 1 0.0000 0.811070 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.CZ.5467.01 1 0.0000 0.811070 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.CJ.5686.01 6 0.3525 0.464376 0.00 0.00 0.00 0.00 0.44 0.56 0.00
#> TCGA.A3.3373.01 7 0.3459 0.675481 0.40 0.00 0.00 0.00 0.00 0.00 0.60
#> TCGA.B0.4819.01 2 0.0000 0.840291 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.B0.4842.01 2 0.0000 0.840291 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.CJ.4905.01 1 0.1166 0.800487 0.94 0.00 0.00 0.00 0.00 0.00 0.06
#> TCGA.B8.A54F.01 3 0.4121 0.636147 0.00 0.00 0.70 0.20 0.00 0.00 0.10
#> TCGA.B0.4697.01 2 0.0000 0.840291 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.A3.3358.01 6 0.3294 0.473610 0.00 0.00 0.00 0.00 0.34 0.66 0.00
#> TCGA.B0.5092.01 2 0.0000 0.840291 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.CJ.6032.01 7 0.3294 0.707996 0.34 0.00 0.00 0.00 0.00 0.00 0.66
#> TCGA.B0.5097.01 2 0.5020 0.232873 0.00 0.44 0.00 0.00 0.44 0.12 0.00
#> TCGA.B8.4146.01 7 0.3496 0.659780 0.42 0.00 0.00 0.00 0.00 0.00 0.58
#> TCGA.B0.5120.01 3 0.3055 0.629645 0.00 0.00 0.82 0.02 0.00 0.14 0.02
#> TCGA.B0.4846.01 3 0.0504 0.761283 0.00 0.00 0.98 0.00 0.00 0.00 0.02
#> TCGA.CJ.4897.01 1 0.0000 0.811070 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.B8.A7U6.01 3 0.0504 0.761283 0.00 0.00 0.98 0.00 0.00 0.00 0.02
#> TCGA.B0.5099.01 1 0.2832 0.547236 0.76 0.00 0.00 0.00 0.00 0.00 0.24
#> TCGA.CZ.4865.01 6 0.1006 0.371286 0.00 0.00 0.00 0.02 0.02 0.96 0.00
#> TCGA.B0.4701.01 6 0.3525 0.464376 0.00 0.00 0.00 0.00 0.44 0.56 0.00
#> TCGA.CZ.5982.01 1 0.1166 0.800487 0.94 0.00 0.00 0.00 0.00 0.00 0.06
#> TCGA.B0.4852.01 3 0.5931 -0.005453 0.12 0.00 0.42 0.06 0.00 0.00 0.40
#> TCGA.B0.5713.01 7 0.3358 0.715133 0.36 0.00 0.00 0.00 0.00 0.00 0.64
#> TCGA.B8.5553.01 6 0.0504 0.390380 0.00 0.00 0.00 0.00 0.02 0.98 0.00
#> TCGA.MW.A4EC.01 1 0.3358 0.000932 0.64 0.00 0.00 0.00 0.00 0.00 0.36
#> TCGA.EU.5905.01 4 0.4487 0.000000 0.00 0.00 0.06 0.52 0.00 0.42 0.00
#> TCGA.CZ.4856.01 6 0.3413 -0.203138 0.00 0.00 0.38 0.00 0.00 0.62 0.00
#> TCGA.B0.5104.01 3 0.1718 0.763574 0.00 0.00 0.92 0.04 0.00 0.00 0.04
#> TCGA.CW.5587.01 6 0.0504 0.390380 0.00 0.00 0.00 0.00 0.02 0.98 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.CZ.4863.01 8 0.0000 0.7444 0.00 0.00 0.00 0.00 0 0.00 0.00 1.00
#> TCGA.DV.5566.01 3 0.4137 0.4039 0.00 0.00 0.50 0.02 0 0.02 0.46 0.00
#> TCGA.MM.A84U.01 8 0.3503 0.6011 0.00 0.00 0.00 0.12 0 0.08 0.02 0.78
#> TCGA.B4.5844.01 1 0.1947 0.7534 0.86 0.00 0.00 0.00 0 0.00 0.14 0.00
#> TCGA.B4.5836.01 6 0.3078 0.6012 0.00 0.00 0.10 0.00 0 0.82 0.02 0.06
#> TCGA.CW.5588.01 6 0.5180 0.3868 0.00 0.00 0.00 0.22 0 0.54 0.02 0.22
#> TCGA.B8.A54H.01 3 0.4680 0.4023 0.00 0.00 0.48 0.00 0 0.12 0.40 0.00
#> TCGA.B8.5551.01 2 0.0000 1.0000 0.00 1.00 0.00 0.00 0 0.00 0.00 0.00
#> TCGA.A3.A8OU.01 3 0.1275 0.7530 0.00 0.00 0.94 0.02 0 0.04 0.00 0.00
#> TCGA.BP.4782.01 6 0.2267 0.6878 0.00 0.00 0.00 0.00 0 0.82 0.00 0.18
#> TCGA.BP.5176.01 3 0.2348 0.7555 0.00 0.00 0.88 0.06 0 0.04 0.02 0.00
#> TCGA.B0.5400.01 2 0.0000 1.0000 0.00 1.00 0.00 0.00 0 0.00 0.00 0.00
#> TCGA.B0.4818.01 6 0.3198 0.3769 0.00 0.00 0.26 0.00 0 0.72 0.02 0.00
#> TCGA.AK.3431.01 3 0.1275 0.7549 0.00 0.00 0.94 0.00 0 0.04 0.02 0.00
#> TCGA.BP.4770.01 5 0.0000 0.0000 0.00 0.00 0.00 0.00 1 0.00 0.00 0.00
#> TCGA.B8.5163.01 2 0.0000 1.0000 0.00 1.00 0.00 0.00 0 0.00 0.00 0.00
#> TCGA.B0.5102.01 7 0.4096 0.8052 0.24 0.00 0.00 0.02 0 0.06 0.68 0.00
#> TCGA.B0.4824.01 3 0.3270 0.7259 0.00 0.00 0.80 0.02 0 0.06 0.12 0.00
#> TCGA.AK.3450.01 3 0.3102 0.7443 0.00 0.00 0.82 0.02 0 0.08 0.08 0.00
#> TCGA.CJ.4916.01 8 0.2756 0.5474 0.00 0.26 0.00 0.00 0 0.00 0.00 0.74
#> TCGA.B0.5693.01 1 0.0000 0.7909 1.00 0.00 0.00 0.00 0 0.00 0.00 0.00
#> TCGA.CZ.5467.01 1 0.0000 0.7909 1.00 0.00 0.00 0.00 0 0.00 0.00 0.00
#> TCGA.CJ.5686.01 8 0.0000 0.7444 0.00 0.00 0.00 0.00 0 0.00 0.00 1.00
#> TCGA.A3.3373.01 7 0.2756 0.8908 0.26 0.00 0.00 0.00 0 0.00 0.74 0.00
#> TCGA.B0.4819.01 2 0.0000 1.0000 0.00 1.00 0.00 0.00 0 0.00 0.00 0.00
#> TCGA.B0.4842.01 2 0.0000 1.0000 0.00 1.00 0.00 0.00 0 0.00 0.00 0.00
#> TCGA.CJ.4905.01 1 0.1765 0.7724 0.88 0.00 0.00 0.00 0 0.00 0.12 0.00
#> TCGA.B8.A54F.01 3 0.2981 0.6644 0.00 0.00 0.76 0.22 0 0.00 0.02 0.00
#> TCGA.B0.4697.01 2 0.0000 1.0000 0.00 1.00 0.00 0.00 0 0.00 0.00 0.00
#> TCGA.A3.3358.01 8 0.3015 0.2411 0.00 0.00 0.00 0.00 0 0.32 0.00 0.68
#> TCGA.B0.5092.01 2 0.0000 1.0000 0.00 1.00 0.00 0.00 0 0.00 0.00 0.00
#> TCGA.CJ.6032.01 7 0.2981 0.8868 0.22 0.00 0.00 0.00 0 0.02 0.76 0.00
#> TCGA.B0.5097.01 8 0.2650 0.5804 0.00 0.24 0.00 0.00 0 0.00 0.00 0.76
#> TCGA.B8.4146.01 7 0.3095 0.8663 0.24 0.00 0.00 0.02 0 0.00 0.74 0.00
#> TCGA.B0.5120.01 3 0.4100 0.2661 0.00 0.00 0.58 0.06 0 0.36 0.00 0.00
#> TCGA.B0.4846.01 3 0.0471 0.7549 0.00 0.00 0.98 0.00 0 0.02 0.00 0.00
#> TCGA.CJ.4897.01 1 0.0000 0.7909 1.00 0.00 0.00 0.00 0 0.00 0.00 0.00
#> TCGA.B8.A7U6.01 3 0.1557 0.7510 0.00 0.00 0.92 0.00 0 0.06 0.02 0.00
#> TCGA.B0.5099.01 1 0.4079 0.5282 0.74 0.00 0.00 0.08 0 0.06 0.12 0.00
#> TCGA.CZ.4865.01 6 0.3015 0.6267 0.00 0.00 0.00 0.00 0 0.68 0.00 0.32
#> TCGA.B0.4701.01 8 0.0000 0.7444 0.00 0.00 0.00 0.00 0 0.00 0.00 1.00
#> TCGA.CZ.5982.01 1 0.1765 0.7724 0.88 0.00 0.00 0.00 0 0.00 0.12 0.00
#> TCGA.B0.4852.01 3 0.5712 0.4247 0.12 0.00 0.50 0.10 0 0.00 0.28 0.00
#> TCGA.B0.5713.01 7 0.2534 0.8917 0.22 0.00 0.00 0.00 0 0.00 0.78 0.00
#> TCGA.B8.5553.01 6 0.2756 0.6869 0.00 0.00 0.00 0.00 0 0.74 0.00 0.26
#> TCGA.MW.A4EC.01 1 0.3272 -0.0347 0.58 0.00 0.00 0.00 0 0.00 0.42 0.00
#> TCGA.EU.5905.01 4 0.2981 0.0000 0.00 0.00 0.02 0.76 0 0.22 0.00 0.00
#> TCGA.CZ.4856.01 6 0.3154 0.5929 0.00 0.00 0.16 0.00 0 0.78 0.00 0.06
#> TCGA.B0.5104.01 3 0.1557 0.7502 0.00 0.00 0.92 0.06 0 0.00 0.02 0.00
#> TCGA.CW.5587.01 6 0.2756 0.6869 0.00 0.00 0.00 0.00 0 0.74 0.00 0.26
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: Node041. Child nodes: Node02131-leaf , Node02132-leaf , Node02133-leaf , Node04111-leaf , Node04112-leaf , Node04113-leaf , Node04114-leaf .
The object with results only for a single top-value method and a single partitioning method can be extracted as:
res = res_rh["0411"]
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 6.
#>
#> 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 0.792 0.899 0.2182 0.867 0.720
#> 4 4 1.000 1.000 1.000 0.1428 0.905 0.730
#> 5 5 1.000 0.859 0.992 0.0151 0.990 0.963
#> 6 6 0.914 0.732 0.939 0.0550 0.952 0.808
#> 7 7 0.848 0.602 0.912 0.0466 0.962 0.810
#> 8 8 0.848 0.585 0.929 0.0460 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] 6
#> attr(,"optional")
#> [1] 2 4
There is also optional best \(k\) = 2 4 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.DV.5566.01 2 0 1 0 1
#> TCGA.B4.5844.01 1 0 1 1 0
#> TCGA.B0.5102.01 2 0 1 0 1
#> TCGA.B0.5693.01 2 0 1 0 1
#> TCGA.CZ.5467.01 2 0 1 0 1
#> TCGA.A3.3373.01 2 0 1 0 1
#> TCGA.CJ.4905.01 1 0 1 1 0
#> TCGA.CJ.6032.01 1 0 1 1 0
#> TCGA.B8.4146.01 1 0 1 1 0
#> TCGA.CJ.4897.01 2 0 1 0 1
#> TCGA.B0.5099.01 2 0 1 0 1
#> TCGA.CZ.5982.01 1 0 1 1 0
#> TCGA.B0.4852.01 2 0 1 0 1
#> TCGA.B0.5713.01 1 0 1 1 0
#> TCGA.MW.A4EC.01 1 0 1 1 0
cbind(get_classes(res, k = 3), get_membership(res, k = 3))
#> class entropy silhouette p1 p2 p3
#> TCGA.DV.5566.01 2 0.000 0.846 0.0 1.00 0.00
#> TCGA.B4.5844.01 1 0.000 1.000 1.0 0.00 0.00
#> TCGA.B0.5102.01 2 0.000 0.846 0.0 1.00 0.00
#> TCGA.B0.5693.01 2 0.000 0.846 0.0 1.00 0.00
#> TCGA.CZ.5467.01 2 0.000 0.846 0.0 1.00 0.00
#> TCGA.A3.3373.01 3 0.571 0.288 0.0 0.32 0.68
#> TCGA.CJ.4905.01 1 0.000 1.000 1.0 0.00 0.00
#> TCGA.CJ.6032.01 1 0.000 1.000 1.0 0.00 0.00
#> TCGA.B8.4146.01 3 0.613 0.208 0.4 0.00 0.60
#> TCGA.CJ.4897.01 2 0.000 0.846 0.0 1.00 0.00
#> TCGA.B0.5099.01 2 0.613 0.576 0.0 0.60 0.40
#> TCGA.CZ.5982.01 1 0.000 1.000 1.0 0.00 0.00
#> TCGA.B0.4852.01 2 0.613 0.576 0.0 0.60 0.40
#> TCGA.B0.5713.01 1 0.000 1.000 1.0 0.00 0.00
#> TCGA.MW.A4EC.01 1 0.000 1.000 1.0 0.00 0.00
cbind(get_classes(res, k = 4), get_membership(res, k = 4))
#> class entropy silhouette p1 p2 p3 p4
#> TCGA.DV.5566.01 2 0 1 0 1 0 0
#> TCGA.B4.5844.01 1 0 1 1 0 0 0
#> TCGA.B0.5102.01 2 0 1 0 1 0 0
#> TCGA.B0.5693.01 2 0 1 0 1 0 0
#> TCGA.CZ.5467.01 2 0 1 0 1 0 0
#> TCGA.A3.3373.01 3 0 1 0 0 1 0
#> TCGA.CJ.4905.01 1 0 1 1 0 0 0
#> TCGA.CJ.6032.01 1 0 1 1 0 0 0
#> TCGA.B8.4146.01 3 0 1 0 0 1 0
#> TCGA.CJ.4897.01 2 0 1 0 1 0 0
#> TCGA.B0.5099.01 4 0 1 0 0 0 1
#> TCGA.CZ.5982.01 1 0 1 1 0 0 0
#> TCGA.B0.4852.01 4 0 1 0 0 0 1
#> TCGA.B0.5713.01 1 0 1 1 0 0 0
#> TCGA.MW.A4EC.01 1 0 1 1 0 0 0
cbind(get_classes(res, k = 5), get_membership(res, k = 5))
#> class entropy silhouette p1 p2 p3 p4 p5
#> TCGA.DV.5566.01 2 0.000 0.986 0 1.00 0.00 0 0.00
#> TCGA.B4.5844.01 1 0.000 1.000 1 0.00 0.00 0 0.00
#> TCGA.B0.5102.01 2 0.141 0.943 0 0.94 0.00 0 0.06
#> TCGA.B0.5693.01 2 0.000 0.986 0 1.00 0.00 0 0.00
#> TCGA.CZ.5467.01 2 0.000 0.986 0 1.00 0.00 0 0.00
#> TCGA.A3.3373.01 3 0.000 0.000 0 0.00 1.00 0 0.00
#> TCGA.CJ.4905.01 1 0.000 1.000 1 0.00 0.00 0 0.00
#> TCGA.CJ.6032.01 1 0.000 1.000 1 0.00 0.00 0 0.00
#> TCGA.B8.4146.01 5 0.141 0.000 0 0.00 0.06 0 0.94
#> TCGA.CJ.4897.01 2 0.000 0.986 0 1.00 0.00 0 0.00
#> TCGA.B0.5099.01 4 0.000 1.000 0 0.00 0.00 1 0.00
#> TCGA.CZ.5982.01 1 0.000 1.000 1 0.00 0.00 0 0.00
#> TCGA.B0.4852.01 4 0.000 1.000 0 0.00 0.00 1 0.00
#> TCGA.B0.5713.01 1 0.000 1.000 1 0.00 0.00 0 0.00
#> TCGA.MW.A4EC.01 1 0.000 1.000 1 0.00 0.00 0 0.00
cbind(get_classes(res, k = 6), get_membership(res, k = 6))
#> class entropy silhouette p1 p2 p3 p4 p5 p6
#> TCGA.DV.5566.01 2 0.000 0.888 0.00 1.00 0 0.00 0 0.00
#> TCGA.B4.5844.01 1 0.000 1.000 1.00 0.00 0 0.00 0 0.00
#> TCGA.B0.5102.01 2 0.385 0.422 0.00 0.54 0 0.46 0 0.00
#> TCGA.B0.5693.01 2 0.000 0.888 0.00 1.00 0 0.00 0 0.00
#> TCGA.CZ.5467.01 2 0.000 0.888 0.00 1.00 0 0.00 0 0.00
#> TCGA.A3.3373.01 3 0.000 0.000 0.00 0.00 1 0.00 0 0.00
#> TCGA.CJ.4905.01 6 0.385 0.000 0.46 0.00 0 0.00 0 0.54
#> TCGA.CJ.6032.01 1 0.000 1.000 1.00 0.00 0 0.00 0 0.00
#> TCGA.B8.4146.01 5 0.000 0.000 0.00 0.00 0 0.00 1 0.00
#> TCGA.CJ.4897.01 2 0.000 0.888 0.00 1.00 0 0.00 0 0.00
#> TCGA.B0.5099.01 4 0.385 1.000 0.00 0.00 0 0.54 0 0.46
#> TCGA.CZ.5982.01 1 0.000 1.000 1.00 0.00 0 0.00 0 0.00
#> TCGA.B0.4852.01 4 0.385 1.000 0.00 0.00 0 0.54 0 0.46
#> TCGA.B0.5713.01 1 0.000 1.000 1.00 0.00 0 0.00 0 0.00
#> TCGA.MW.A4EC.01 1 0.000 1.000 1.00 0.00 0 0.00 0 0.00
cbind(get_classes(res, k = 7), get_membership(res, k = 7))
#> class entropy silhouette p1 p2 p3 p4 p5 p6 p7
#> TCGA.DV.5566.01 2 0.208 0.735 0.00 0.86 0 0.00 0 0.14 0.00
#> TCGA.B4.5844.01 1 0.000 0.871 1.00 0.00 0 0.00 0 0.00 0.00
#> TCGA.B0.5102.01 7 0.350 0.000 0.00 0.42 0 0.00 0 0.00 0.58
#> TCGA.B0.5693.01 2 0.000 0.879 0.00 1.00 0 0.00 0 0.00 0.00
#> TCGA.CZ.5467.01 2 0.143 0.813 0.00 0.92 0 0.00 0 0.08 0.00
#> TCGA.A3.3373.01 3 0.000 0.000 0.00 0.00 1 0.00 0 0.00 0.00
#> TCGA.CJ.4905.01 6 0.283 0.000 0.24 0.00 0 0.00 0 0.76 0.00
#> TCGA.CJ.6032.01 1 0.000 0.871 1.00 0.00 0 0.00 0 0.00 0.00
#> TCGA.B8.4146.01 5 0.000 0.000 0.00 0.00 0 0.00 1 0.00 0.00
#> TCGA.CJ.4897.01 2 0.000 0.879 0.00 1.00 0 0.00 0 0.00 0.00
#> TCGA.B0.5099.01 4 0.000 0.967 0.00 0.00 0 1.00 0 0.00 0.00
#> TCGA.CZ.5982.01 1 0.000 0.871 1.00 0.00 0 0.00 0 0.00 0.00
#> TCGA.B0.4852.01 4 0.101 0.967 0.00 0.00 0 0.96 0 0.02 0.02
#> TCGA.B0.5713.01 1 0.000 0.871 1.00 0.00 0 0.00 0 0.00 0.00
#> TCGA.MW.A4EC.01 1 0.346 0.309 0.60 0.00 0 0.00 0 0.00 0.40
cbind(get_classes(res, k = 8), get_membership(res, k = 8))
#> class entropy silhouette p1 p2 p3 p4 p5 p6 p7 p8
#> TCGA.DV.5566.01 2 0.2981 0.685 0.00 0.76 0.00 0.00 0 0.00 0.02 0.22
#> TCGA.B4.5844.01 1 0.1341 0.869 0.92 0.00 0.00 0.00 0 0.00 0.08 0.00
#> TCGA.B0.5102.01 7 0.2267 0.000 0.00 0.18 0.00 0.00 0 0.00 0.82 0.00
#> TCGA.B0.5693.01 2 0.0000 0.869 0.00 1.00 0.00 0.00 0 0.00 0.00 0.00
#> TCGA.CZ.5467.01 2 0.2020 0.817 0.00 0.90 0.00 0.00 0 0.02 0.02 0.06
#> TCGA.A3.3373.01 3 0.0471 0.000 0.00 0.02 0.98 0.00 0 0.00 0.00 0.00
#> TCGA.CJ.4905.01 6 0.0808 0.000 0.04 0.00 0.00 0.00 0 0.96 0.00 0.00
#> TCGA.CJ.6032.01 1 0.0000 0.922 1.00 0.00 0.00 0.00 0 0.00 0.00 0.00
#> TCGA.B8.4146.01 5 0.0000 0.000 0.00 0.00 0.00 0.00 1 0.00 0.00 0.00
#> TCGA.CJ.4897.01 2 0.0000 0.869 0.00 1.00 0.00 0.00 0 0.00 0.00 0.00
#> TCGA.B0.5099.01 4 0.0000 0.984 0.00 0.00 0.00 1.00 0 0.00 0.00 0.00
#> TCGA.CZ.5982.01 1 0.1804 0.849 0.90 0.00 0.02 0.00 0 0.00 0.08 0.00
#> TCGA.B0.4852.01 4 0.0471 0.984 0.00 0.00 0.00 0.98 0 0.02 0.00 0.00
#> TCGA.B0.5713.01 1 0.0000 0.922 1.00 0.00 0.00 0.00 0 0.00 0.00 0.00
#> TCGA.MW.A4EC.01 8 0.2852 0.000 0.28 0.00 0.00 0.00 0 0.00 0.00 0.72
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: Node04. Child nodes: Node0141-leaf , Node0142-leaf , Node0143-leaf , Node0144-leaf , Node0211-leaf , Node0212-leaf , Node0213 , Node0231-leaf , Node0232-leaf , Node0233-leaf , Node0411 , Node0412-leaf , Node0413-leaf , Node0431-leaf , Node0432-leaf , Node0433-leaf , Node0511-leaf , Node0512-leaf , Node0541-leaf , Node0542-leaf , Node0543-leaf , Node0621-leaf , Node0622-leaf , Node0623-leaf .
The object with results only for a single top-value method and a single partitioning method can be extracted as:
res = res_rh["043"]
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 '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 0.754 0.905 0.953 0.5051 0.487 0.487
#> 3 3 1.000 0.990 0.979 0.2619 0.867 0.726
#> 4 4 0.836 0.823 0.881 0.1154 1.000 1.000
#> 5 5 0.745 0.743 0.821 0.0737 0.895 0.704
#> 6 6 0.711 0.681 0.824 0.0471 0.943 0.772
#> 7 7 0.756 0.668 0.819 0.0327 0.946 0.752
#> 8 8 0.781 0.684 0.833 0.0327 0.963 0.803
suggest_best_k() suggests the best \(k\) based on these statistics. The rules are as follows:
suggest_best_k(res)
#> [1] 3
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.CJ.4902.01 1 0.000 1.000 1.00 0.00
#> TCGA.CW.6087.01 2 0.000 0.899 0.00 1.00
#> TCGA.B0.4694.01 2 0.925 0.599 0.34 0.66
#> TCGA.B0.5095.01 2 0.925 0.599 0.34 0.66
#> TCGA.B0.4690.01 2 0.000 0.899 0.00 1.00
#> TCGA.CZ.5466.01 2 0.000 0.899 0.00 1.00
#> TCGA.CJ.6031.01 1 0.000 1.000 1.00 0.00
#> TCGA.CZ.5462.01 2 0.000 0.899 0.00 1.00
#> TCGA.CJ.6028.01 2 0.000 0.899 0.00 1.00
#> TCGA.CW.5591.01 1 0.000 1.000 1.00 0.00
#> TCGA.B0.5100.01 1 0.000 1.000 1.00 0.00
#> TCGA.BP.5189.01 1 0.000 1.000 1.00 0.00
#> TCGA.B0.4843.01 1 0.000 1.000 1.00 0.00
#> TCGA.DV.5568.01 1 0.000 1.000 1.00 0.00
#> TCGA.B8.5550.01 1 0.000 1.000 1.00 0.00
#> TCGA.BP.5187.01 1 0.000 1.000 1.00 0.00
#> TCGA.CW.6097.01 2 0.000 0.899 0.00 1.00
#> TCGA.B2.5633.01 1 0.000 1.000 1.00 0.00
#> TCGA.B8.5162.01 2 0.000 0.899 0.00 1.00
#> TCGA.CJ.4882.01 2 0.000 0.899 0.00 1.00
#> TCGA.B0.4700.01 2 0.000 0.899 0.00 1.00
#> TCGA.B0.4817.01 2 0.000 0.899 0.00 1.00
#> TCGA.B0.4822.01 2 0.925 0.599 0.34 0.66
#> TCGA.CJ.4918.01 1 0.000 1.000 1.00 0.00
#> TCGA.CJ.4869.01 2 0.925 0.599 0.34 0.66
#> TCGA.B2.5639.01 1 0.000 1.000 1.00 0.00
#> TCGA.CJ.4923.01 2 0.000 0.899 0.00 1.00
#> TCGA.B0.5109.01 2 0.000 0.899 0.00 1.00
#> TCGA.B0.5080.01 2 0.925 0.599 0.34 0.66
#> TCGA.B2.4101.01 1 0.000 1.000 1.00 0.00
#> TCGA.B0.4816.01 1 0.000 1.000 1.00 0.00
#> TCGA.B0.5108.01 1 0.000 1.000 1.00 0.00
#> TCGA.B4.5832.01 2 0.000 0.899 0.00 1.00
#> TCGA.BP.5195.01 1 0.000 1.000 1.00 0.00
#> TCGA.BP.5010.01 1 0.000 1.000 1.00 0.00
#> TCGA.B0.4703.01 2 0.000 0.899 0.00 1.00
cbind(get_classes(res, k = 3), get_membership(res, k = 3))
#> class entropy silhouette p1 p2 p3
#> TCGA.CJ.4902.01 1 0.0000 0.996 1.00 0.00 0.00
#> TCGA.CW.6087.01 3 0.2537 0.996 0.00 0.08 0.92
#> TCGA.B0.4694.01 2 0.0892 0.981 0.02 0.98 0.00
#> TCGA.B0.5095.01 2 0.0892 0.981 0.02 0.98 0.00
#> TCGA.B0.4690.01 3 0.2537 0.996 0.00 0.08 0.92
#> TCGA.CZ.5466.01 2 0.0000 0.987 0.00 1.00 0.00
#> TCGA.CJ.6031.01 1 0.0000 0.996 1.00 0.00 0.00
#> TCGA.CZ.5462.01 2 0.0000 0.987 0.00 1.00 0.00
#> TCGA.CJ.6028.01 2 0.0000 0.987 0.00 1.00 0.00
#> TCGA.CW.5591.01 1 0.0000 0.996 1.00 0.00 0.00
#> TCGA.B0.5100.01 1 0.2537 0.928 0.92 0.00 0.08
#> TCGA.BP.5189.01 1 0.0000 0.996 1.00 0.00 0.00
#> TCGA.B0.4843.01 1 0.0000 0.996 1.00 0.00 0.00
#> TCGA.DV.5568.01 1 0.0000 0.996 1.00 0.00 0.00
#> TCGA.B8.5550.01 1 0.0000 0.996 1.00 0.00 0.00
#> TCGA.BP.5187.01 1 0.0000 0.996 1.00 0.00 0.00
#> TCGA.CW.6097.01 3 0.2959 0.978 0.00 0.10 0.90
#> TCGA.B2.5633.01 1 0.0000 0.996 1.00 0.00 0.00
#> TCGA.B8.5162.01 2 0.0000 0.987 0.00 1.00 0.00
#> TCGA.CJ.4882.01 2 0.0000 0.987 0.00 1.00 0.00
#> TCGA.B0.4700.01 3 0.2537 0.996 0.00 0.08 0.92
#> TCGA.B0.4817.01 3 0.2537 0.996 0.00 0.08 0.92
#> TCGA.B0.4822.01 2 0.0892 0.981 0.02 0.98 0.00
#> TCGA.CJ.4918.01 1 0.0000 0.996 1.00 0.00 0.00
#> TCGA.CJ.4869.01 2 0.0892 0.981 0.02 0.98 0.00
#> TCGA.B2.5639.01 1 0.0000 0.996 1.00 0.00 0.00
#> TCGA.CJ.4923.01 2 0.0000 0.987 0.00 1.00 0.00
#> TCGA.B0.5109.01 3 0.2537 0.996 0.00 0.08 0.92
#> TCGA.B0.5080.01 2 0.0892 0.981 0.02 0.98 0.00
#> TCGA.B2.4101.01 1 0.0000 0.996 1.00 0.00 0.00
#> TCGA.B0.4816.01 1 0.0000 0.996 1.00 0.00 0.00
#> TCGA.B0.5108.01 1 0.0000 0.996 1.00 0.00 0.00
#> TCGA.B4.5832.01 3 0.2537 0.996 0.00 0.08 0.92
#> TCGA.BP.5195.01 1 0.0000 0.996 1.00 0.00 0.00
#> TCGA.BP.5010.01 1 0.0000 0.996 1.00 0.00 0.00
#> TCGA.B0.4703.01 2 0.0000 0.987 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.CJ.4902.01 4 0.0000 0.653 0.00 0.00 0.00 1.00
#> TCGA.CW.6087.01 3 0.0000 0.935 0.00 0.00 1.00 0.00
#> TCGA.B0.4694.01 2 0.0707 0.875 0.02 0.98 0.00 0.00
#> TCGA.B0.5095.01 2 0.3610 0.825 0.20 0.80 0.00 0.00
#> TCGA.B0.4690.01 3 0.0000 0.935 0.00 0.00 1.00 0.00
#> TCGA.CZ.5466.01 2 0.1637 0.870 0.06 0.94 0.00 0.00
#> TCGA.CJ.6031.01 4 0.4907 0.868 0.42 0.00 0.00 0.58
#> TCGA.CZ.5462.01 2 0.4134 0.749 0.26 0.74 0.00 0.00
#> TCGA.CJ.6028.01 2 0.1637 0.870 0.06 0.94 0.00 0.00
#> TCGA.CW.5591.01 4 0.4907 0.868 0.42 0.00 0.00 0.58
#> TCGA.B0.5100.01 4 0.2647 0.534 0.12 0.00 0.00 0.88
#> TCGA.BP.5189.01 4 0.4907 0.868 0.42 0.00 0.00 0.58
#> TCGA.B0.4843.01 4 0.0000 0.653 0.00 0.00 0.00 1.00
#> TCGA.DV.5568.01 4 0.0000 0.653 0.00 0.00 0.00 1.00
#> TCGA.B8.5550.01 4 0.5987 0.825 0.44 0.04 0.00 0.52
#> TCGA.BP.5187.01 4 0.4907 0.868 0.42 0.00 0.00 0.58
#> TCGA.CW.6097.01 3 0.7249 0.465 0.26 0.20 0.54 0.00
#> TCGA.B2.5633.01 4 0.0000 0.653 0.00 0.00 0.00 1.00
#> TCGA.B8.5162.01 2 0.4134 0.749 0.26 0.74 0.00 0.00
#> TCGA.CJ.4882.01 2 0.0000 0.876 0.00 1.00 0.00 0.00
#> TCGA.B0.4700.01 3 0.0000 0.935 0.00 0.00 1.00 0.00
#> TCGA.B0.4817.01 3 0.0000 0.935 0.00 0.00 1.00 0.00
#> TCGA.B0.4822.01 2 0.3610 0.825 0.20 0.80 0.00 0.00
#> TCGA.CJ.4918.01 4 0.4907 0.868 0.42 0.00 0.00 0.58
#> TCGA.CJ.4869.01 2 0.0707 0.875 0.02 0.98 0.00 0.00
#> TCGA.B2.5639.01 4 0.4907 0.868 0.42 0.00 0.00 0.58
#> TCGA.CJ.4923.01 2 0.1637 0.870 0.06 0.94 0.00 0.00
#> TCGA.B0.5109.01 3 0.0000 0.935 0.00 0.00 1.00 0.00
#> TCGA.B0.5080.01 2 0.3610 0.825 0.20 0.80 0.00 0.00
#> TCGA.B2.4101.01 4 0.4907 0.868 0.42 0.00 0.00 0.58
#> TCGA.B0.4816.01 4 0.4907 0.868 0.42 0.00 0.00 0.58
#> TCGA.B0.5108.01 4 0.4907 0.868 0.42 0.00 0.00 0.58
#> TCGA.B4.5832.01 3 0.0000 0.935 0.00 0.00 1.00 0.00
#> TCGA.BP.5195.01 4 0.4907 0.868 0.42 0.00 0.00 0.58
#> TCGA.BP.5010.01 4 0.4907 0.868 0.42 0.00 0.00 0.58
#> TCGA.B0.4703.01 2 0.3801 0.835 0.22 0.78 0.00 0.00
cbind(get_classes(res, k = 5), get_membership(res, k = 5))
#> class entropy silhouette p1 p2 p3 p4 p5
#> TCGA.CJ.4902.01 5 0.3684 0.9133 0.00 0.00 0.00 0.28 0.72
#> TCGA.CW.6087.01 3 0.0609 0.9861 0.00 0.00 0.98 0.00 0.02
#> TCGA.B0.4694.01 2 0.1216 0.6709 0.02 0.96 0.00 0.00 0.02
#> TCGA.B0.5095.01 2 0.5425 0.5621 0.32 0.60 0.00 0.00 0.08
#> TCGA.B0.4690.01 3 0.0000 0.9861 0.00 0.00 1.00 0.00 0.00
#> TCGA.CZ.5466.01 2 0.1410 0.6459 0.06 0.94 0.00 0.00 0.00
#> TCGA.CJ.6031.01 4 0.0000 0.9027 0.00 0.00 0.00 1.00 0.00
#> TCGA.CZ.5462.01 2 0.5048 -0.0133 0.38 0.58 0.00 0.00 0.04
#> TCGA.CJ.6028.01 2 0.1410 0.6459 0.06 0.94 0.00 0.00 0.00
#> TCGA.CW.5591.01 4 0.3971 0.7880 0.10 0.00 0.00 0.80 0.10
#> TCGA.B0.5100.01 5 0.4872 0.7003 0.12 0.00 0.00 0.16 0.72
#> TCGA.BP.5189.01 4 0.3521 0.7906 0.04 0.00 0.00 0.82 0.14
#> TCGA.B0.4843.01 5 0.3684 0.9133 0.00 0.00 0.00 0.28 0.72
#> TCGA.DV.5568.01 5 0.4644 0.8830 0.04 0.00 0.00 0.28 0.68
#> TCGA.B8.5550.01 4 0.1648 0.8435 0.02 0.00 0.00 0.94 0.04
#> TCGA.BP.5187.01 4 0.0000 0.9027 0.00 0.00 0.00 1.00 0.00
#> TCGA.CW.6097.01 1 0.6705 0.0000 0.42 0.26 0.32 0.00 0.00
#> TCGA.B2.5633.01 5 0.3684 0.9133 0.00 0.00 0.00 0.28 0.72
#> TCGA.B8.5162.01 2 0.4227 -0.0298 0.42 0.58 0.00 0.00 0.00
#> TCGA.CJ.4882.01 2 0.0609 0.6705 0.00 0.98 0.00 0.00 0.02
#> TCGA.B0.4700.01 3 0.0609 0.9861 0.00 0.00 0.98 0.00 0.02
#> TCGA.B0.4817.01 3 0.0609 0.9861 0.00 0.00 0.98 0.00 0.02
#> TCGA.B0.4822.01 2 0.4456 0.5894 0.32 0.66 0.00 0.00 0.02
#> TCGA.CJ.4918.01 4 0.0000 0.9027 0.00 0.00 0.00 1.00 0.00
#> TCGA.CJ.4869.01 2 0.1820 0.6660 0.02 0.94 0.00 0.02 0.02
#> TCGA.B2.5639.01 4 0.4170 0.7648 0.14 0.00 0.00 0.78 0.08
#> TCGA.CJ.4923.01 2 0.1410 0.6459 0.06 0.94 0.00 0.00 0.00
#> TCGA.B0.5109.01 3 0.0000 0.9861 0.00 0.00 1.00 0.00 0.00
#> TCGA.B0.5080.01 2 0.6124 0.5560 0.30 0.58 0.00 0.02 0.10
#> TCGA.B2.4101.01 4 0.2754 0.8494 0.04 0.00 0.00 0.88 0.08
#> TCGA.B0.4816.01 4 0.0000 0.9027 0.00 0.00 0.00 1.00 0.00
#> TCGA.B0.5108.01 4 0.0000 0.9027 0.00 0.00 0.00 1.00 0.00
#> TCGA.B4.5832.01 3 0.0000 0.9861 0.00 0.00 1.00 0.00 0.00
#> TCGA.BP.5195.01 4 0.0609 0.8985 0.00 0.00 0.00 0.98 0.02
#> TCGA.BP.5010.01 4 0.1410 0.8844 0.00 0.00 0.00 0.94 0.06
#> TCGA.B0.4703.01 2 0.5068 0.5779 0.30 0.64 0.00 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.CJ.4902.01 5 0.2941 0.859 0.00 0.00 0.00 0.22 0.78 0.00
#> TCGA.CW.6087.01 3 0.0000 0.996 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.B0.4694.01 2 0.4265 0.560 0.08 0.76 0.00 0.00 0.02 0.14
#> TCGA.B0.5095.01 6 0.2631 0.826 0.00 0.18 0.00 0.00 0.00 0.82
#> TCGA.B0.4690.01 3 0.0000 0.996 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.CZ.5466.01 2 0.0000 0.542 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.CJ.6031.01 4 0.0000 0.837 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.CZ.5462.01 2 0.5871 -0.787 0.38 0.50 0.00 0.00 0.06 0.06
#> TCGA.CJ.6028.01 2 0.0000 0.542 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.CW.5591.01 4 0.4903 0.630 0.14 0.00 0.00 0.70 0.14 0.02
#> TCGA.B0.5100.01 5 0.6193 0.490 0.22 0.00 0.00 0.10 0.58 0.10
#> TCGA.BP.5189.01 4 0.4873 0.334 0.08 0.00 0.00 0.60 0.32 0.00
#> TCGA.B0.4843.01 5 0.2941 0.859 0.00 0.00 0.00 0.22 0.78 0.00
#> TCGA.DV.5568.01 5 0.4380 0.797 0.08 0.00 0.00 0.22 0.70 0.00
#> TCGA.B8.5550.01 4 0.3258 0.697 0.04 0.00 0.00 0.84 0.02 0.10
#> TCGA.BP.5187.01 4 0.0000 0.837 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.CW.6097.01 1 0.5734 0.754 0.48 0.40 0.10 0.00 0.02 0.00
#> TCGA.B2.5633.01 5 0.2941 0.859 0.00 0.00 0.00 0.22 0.78 0.00
#> TCGA.B8.5162.01 1 0.3869 0.719 0.50 0.50 0.00 0.00 0.00 0.00
#> TCGA.CJ.4882.01 2 0.3997 0.575 0.06 0.78 0.00 0.00 0.02 0.14
#> TCGA.B0.4700.01 3 0.0000 0.996 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.B0.4817.01 3 0.0547 0.982 0.00 0.00 0.98 0.00 0.02 0.00
#> TCGA.B0.4822.01 2 0.3869 -0.497 0.00 0.50 0.00 0.00 0.00 0.50
#> TCGA.CJ.4918.01 4 0.0547 0.834 0.02 0.00 0.00 0.98 0.00 0.00
#> TCGA.CJ.4869.01 2 0.4607 0.525 0.08 0.72 0.00 0.00 0.02 0.18
#> TCGA.B2.5639.01 4 0.4495 0.659 0.20 0.00 0.00 0.72 0.06 0.02
#> TCGA.CJ.4923.01 2 0.0000 0.542 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.B0.5109.01 3 0.0000 0.996 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.B0.5080.01 6 0.4607 0.784 0.08 0.18 0.00 0.00 0.02 0.72
#> TCGA.B2.4101.01 4 0.3073 0.759 0.08 0.00 0.00 0.84 0.08 0.00
#> TCGA.B0.4816.01 4 0.0547 0.834 0.02 0.00 0.00 0.98 0.00 0.00
#> TCGA.B0.5108.01 4 0.0547 0.834 0.02 0.00 0.00 0.98 0.00 0.00
#> TCGA.B4.5832.01 3 0.0000 0.996 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.BP.5195.01 4 0.0000 0.837 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.BP.5010.01 4 0.1814 0.788 0.00 0.00 0.00 0.90 0.10 0.00
#> TCGA.B0.4703.01 6 0.3499 0.731 0.00 0.32 0.00 0.00 0.00 0.68
cbind(get_classes(res, k = 7), get_membership(res, k = 7))
#> class entropy silhouette p1 p2 p3 p4 p5 p6 p7
#> TCGA.CJ.4902.01 5 0.1671 0.7696 0.00 0.00 0.00 0.10 0.90 0.00 0.00
#> TCGA.CW.6087.01 3 0.0000 0.9963 0.00 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.B0.4694.01 2 0.0000 0.5275 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.B0.5095.01 6 0.3294 0.8801 0.00 0.34 0.00 0.00 0.00 0.66 0.00
#> TCGA.B0.4690.01 3 0.0000 0.9963 0.00 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.CZ.5466.01 2 0.5755 0.5100 0.16 0.58 0.00 0.00 0.00 0.08 0.18
#> TCGA.CJ.6031.01 4 0.0000 0.8307 0.00 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.CZ.5462.01 7 0.4712 0.8154 0.08 0.18 0.00 0.00 0.02 0.02 0.70
#> TCGA.CJ.6028.01 2 0.5455 0.5309 0.12 0.62 0.00 0.00 0.00 0.08 0.18
#> TCGA.CW.5591.01 4 0.6261 0.3657 0.32 0.00 0.00 0.48 0.12 0.06 0.02
#> TCGA.B0.5100.01 5 0.6739 0.2442 0.22 0.00 0.00 0.02 0.48 0.12 0.16
#> TCGA.BP.5189.01 5 0.4705 0.0182 0.08 0.00 0.00 0.44 0.48 0.00 0.00
#> TCGA.B0.4843.01 5 0.1671 0.7696 0.00 0.00 0.00 0.10 0.90 0.00 0.00
#> TCGA.DV.5568.01 5 0.2803 0.7464 0.06 0.00 0.00 0.10 0.84 0.00 0.00
#> TCGA.B8.5550.01 4 0.2769 0.7671 0.08 0.04 0.00 0.86 0.00 0.02 0.00
#> TCGA.BP.5187.01 4 0.0000 0.8307 0.00 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.CW.6097.01 7 0.3541 0.7825 0.02 0.08 0.10 0.00 0.00 0.00 0.80
#> TCGA.B2.5633.01 5 0.1671 0.7696 0.00 0.00 0.00 0.10 0.90 0.00 0.00
#> TCGA.B8.5162.01 7 0.2422 0.8381 0.00 0.18 0.00 0.00 0.00 0.00 0.82
#> TCGA.CJ.4882.01 2 0.0000 0.5275 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.B0.4700.01 3 0.0000 0.9963 0.00 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.B0.4817.01 3 0.0504 0.9813 0.02 0.00 0.98 0.00 0.00 0.00 0.00
#> TCGA.B0.4822.01 2 0.5055 0.2170 0.18 0.56 0.00 0.00 0.00 0.26 0.00
#> TCGA.CJ.4918.01 4 0.0000 0.8307 0.00 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.CJ.4869.01 2 0.0000 0.5275 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.B2.5639.01 4 0.5635 0.2786 0.42 0.00 0.00 0.44 0.08 0.06 0.00
#> TCGA.CJ.4923.01 2 0.5455 0.5309 0.12 0.62 0.00 0.00 0.00 0.08 0.18
#> TCGA.B0.5109.01 3 0.0000 0.9963 0.00 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.B0.5080.01 2 0.3525 -0.6028 0.00 0.56 0.00 0.00 0.00 0.44 0.00
#> TCGA.B2.4101.01 4 0.3617 0.6412 0.08 0.00 0.00 0.76 0.16 0.00 0.00
#> TCGA.B0.4816.01 4 0.0000 0.8307 0.00 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.B0.5108.01 4 0.0000 0.8307 0.00 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.B4.5832.01 3 0.0000 0.9963 0.00 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.BP.5195.01 4 0.0000 0.8307 0.00 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.BP.5010.01 4 0.3289 0.7495 0.10 0.00 0.00 0.82 0.06 0.02 0.00
#> TCGA.B0.4703.01 6 0.3047 0.8795 0.00 0.28 0.00 0.00 0.00 0.72 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.CJ.4902.01 5 0.0471 0.813 0.00 0.00 0.00 0.02 0.98 0.00 0.00 0.00
#> TCGA.CW.6087.01 3 0.0941 0.974 0.00 0.00 0.96 0.00 0.00 0.02 0.00 0.02
#> TCGA.B0.4694.01 2 0.0000 0.542 0.00 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.B0.5095.01 6 0.2267 0.836 0.00 0.18 0.00 0.00 0.00 0.82 0.00 0.00
#> TCGA.B0.4690.01 3 0.0000 0.976 0.00 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.CZ.5466.01 2 0.6537 0.495 0.10 0.50 0.00 0.00 0.00 0.10 0.10 0.20
#> TCGA.CJ.6031.01 4 0.0000 0.849 0.00 0.00 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.CZ.5462.01 7 0.4627 0.841 0.10 0.14 0.00 0.00 0.02 0.00 0.70 0.04
#> TCGA.CJ.6028.01 2 0.6188 0.512 0.08 0.56 0.00 0.00 0.00 0.10 0.14 0.12
#> TCGA.CW.5591.01 8 0.6313 0.652 0.00 0.00 0.00 0.32 0.10 0.02 0.14 0.42
#> TCGA.B0.5100.01 1 0.2756 0.000 0.74 0.00 0.00 0.00 0.26 0.00 0.00 0.00
#> TCGA.BP.5189.01 5 0.4919 0.401 0.00 0.00 0.00 0.16 0.64 0.00 0.06 0.14
#> TCGA.B0.4843.01 5 0.0471 0.813 0.00 0.00 0.00 0.02 0.98 0.00 0.00 0.00
#> TCGA.DV.5568.01 5 0.2224 0.755 0.00 0.00 0.00 0.02 0.86 0.00 0.00 0.12
#> TCGA.B8.5550.01 4 0.1741 0.793 0.02 0.00 0.00 0.92 0.00 0.04 0.02 0.00
#> TCGA.BP.5187.01 4 0.0941 0.837 0.00 0.00 0.00 0.96 0.00 0.02 0.00 0.02
#> TCGA.CW.6097.01 7 0.2350 0.869 0.00 0.10 0.04 0.00 0.00 0.00 0.86 0.00
#> TCGA.B2.5633.01 5 0.0471 0.813 0.00 0.00 0.00 0.02 0.98 0.00 0.00 0.00
#> TCGA.B8.5162.01 7 0.1947 0.889 0.00 0.14 0.00 0.00 0.00 0.00 0.86 0.00
#> TCGA.CJ.4882.01 2 0.0000 0.542 0.00 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.B0.4700.01 3 0.0941 0.974 0.00 0.00 0.96 0.00 0.00 0.02 0.00 0.02
#> TCGA.B0.4817.01 3 0.1275 0.964 0.00 0.00 0.94 0.00 0.00 0.04 0.00 0.02
#> TCGA.B0.4822.01 2 0.6313 0.213 0.14 0.38 0.00 0.00 0.00 0.30 0.00 0.18
#> TCGA.CJ.4918.01 4 0.0000 0.849 0.00 0.00 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.CJ.4869.01 2 0.0000 0.542 0.00 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.B2.5639.01 8 0.3551 0.659 0.00 0.00 0.00 0.22 0.06 0.00 0.00 0.72
#> TCGA.CJ.4923.01 2 0.6188 0.512 0.08 0.56 0.00 0.00 0.00 0.10 0.14 0.12
#> TCGA.B0.5109.01 3 0.0000 0.976 0.00 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.B0.5080.01 2 0.3318 -0.397 0.00 0.54 0.00 0.00 0.00 0.46 0.00 0.00
#> TCGA.B2.4101.01 4 0.5153 0.262 0.00 0.00 0.00 0.64 0.10 0.02 0.06 0.18
#> TCGA.B0.4816.01 4 0.0471 0.846 0.00 0.00 0.00 0.98 0.00 0.02 0.00 0.00
#> TCGA.B0.5108.01 4 0.0000 0.849 0.00 0.00 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.B4.5832.01 3 0.0000 0.976 0.00 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.BP.5195.01 4 0.2071 0.799 0.00 0.00 0.00 0.90 0.04 0.02 0.00 0.04
#> TCGA.BP.5010.01 4 0.4396 0.552 0.02 0.00 0.00 0.74 0.12 0.02 0.08 0.02
#> TCGA.B0.4703.01 6 0.2025 0.834 0.00 0.10 0.00 0.00 0.00 0.88 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-leaf , Node012-leaf , Node013-leaf , Node014 , Node021 , Node022-leaf , Node023 , Node041 , Node042-leaf , Node043 , Node051 , Node052-leaf , Node053-leaf , Node054 , Node061-leaf , Node062 , Node063-leaf , Node071-leaf , Node072-leaf , Node073-leaf .
The object with results only for a single top-value method and a single partitioning method can be extracted as:
res = res_rh["05"]
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 52 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 0.3830 0.618 0.618
#> 3 3 0.673 0.694 0.814 0.3400 0.983 0.973
#> 4 4 1.000 0.998 0.999 0.3334 0.715 0.526
#> 5 5 0.865 0.850 0.896 0.0475 1.000 1.000
#> 6 6 0.763 0.626 0.827 0.0377 0.986 0.957
#> 7 7 0.746 0.657 0.798 0.0481 0.876 0.616
#> 8 8 0.702 0.716 0.823 0.0389 0.925 0.672
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.B0.4827.11 1 0 1 1 0
#> TCGA.CZ.5463.11 1 0 1 1 0
#> TCGA.CZ.5468.11 1 0 1 1 0
#> TCGA.B0.4844.11 2 0 1 0 1
#> TCGA.CZ.5467.11 1 0 1 1 0
#> TCGA.BP.5192.11 2 0 1 0 1
#> TCGA.CZ.5470.11 1 0 1 1 0
#> TCGA.BP.4177.11 2 0 1 0 1
#> TCGA.CZ.5469.11 1 0 1 1 0
#> TCGA.CZ.5454.11 1 0 1 1 0
#> TCGA.BP.5170.11 1 0 1 1 0
#> TCGA.B0.4710.11 1 0 1 1 0
#> TCGA.B0.5711.11 2 0 1 0 1
#> TCGA.B0.4813.11 1 0 1 1 0
#> TCGA.CZ.5453.11 1 0 1 1 0
#> TCGA.B0.4847.11 2 0 1 0 1
#> TCGA.BP.5195.11 1 0 1 1 0
#> TCGA.BP.5010.11 1 0 1 1 0
#> TCGA.CZ.4856.11 1 0 1 1 0
#> TCGA.CZ.4866.11 1 0 1 1 0
#> TCGA.CJ.4902.11 1 0 1 1 0
#> TCGA.CZ.5465.11 1 0 1 1 0
#> TCGA.CZ.4859.11 1 0 1 1 0
#> TCGA.CZ.4863.11 1 0 1 1 0
#> TCGA.CJ.4905.11 2 0 1 0 1
#> TCGA.CZ.5462.11 1 0 1 1 0
#> TCGA.CZ.5461.11 1 0 1 1 0
#> TCGA.CJ.4908.11 1 0 1 1 0
#> TCGA.AK.3433.01 2 0 1 0 1
#> TCGA.CJ.4920.11 1 0 1 1 0
#> TCGA.B0.4845.11 1 0 1 1 0
#> TCGA.CZ.5458.11 1 0 1 1 0
#> TCGA.AK.3440.01 2 0 1 0 1
#> TCGA.A3.3370.11 2 0 1 0 1
#> TCGA.CZ.4853.11 1 0 1 1 0
#> TCGA.B0.5119.11 1 0 1 1 0
#> TCGA.B0.4816.11 1 0 1 1 0
#> TCGA.B0.4810.11 2 0 1 0 1
#> TCGA.CZ.4865.11 1 0 1 1 0
#> TCGA.B0.4712.11 1 0 1 1 0
#> TCGA.A3.3373.11 1 0 1 1 0
#> TCGA.B0.4688.11 1 0 1 1 0
#> TCGA.B0.4694.11 2 0 1 0 1
#> TCGA.CZ.5456.11 1 0 1 1 0
#> TCGA.B0.4828.11 1 0 1 1 0
#> TCGA.B0.4697.11 1 0 1 1 0
#> TCGA.CZ.5452.11 1 0 1 1 0
#> TCGA.B0.4822.11 2 0 1 0 1
#> TCGA.CZ.5455.11 1 0 1 1 0
#> TCGA.CJ.4912.11 1 0 1 1 0
#> TCGA.CZ.5457.11 1 0 1 1 0
#> TCGA.B0.4718.11 2 0 1 0 1
cbind(get_classes(res, k = 3), get_membership(res, k = 3))
#> class entropy silhouette p1 p2 p3
#> TCGA.B0.4827.11 1 0.628 0.646 0.54 0.00 0.46
#> TCGA.CZ.5463.11 1 0.000 0.776 1.00 0.00 0.00
#> TCGA.CZ.5468.11 1 0.000 0.776 1.00 0.00 0.00
#> TCGA.B0.4844.11 2 0.000 0.618 0.00 1.00 0.00
#> TCGA.CZ.5467.11 1 0.000 0.776 1.00 0.00 0.00
#> TCGA.BP.5192.11 2 0.000 0.618 0.00 1.00 0.00
#> TCGA.CZ.5470.11 1 0.000 0.776 1.00 0.00 0.00
#> TCGA.BP.4177.11 2 0.000 0.618 0.00 1.00 0.00
#> TCGA.CZ.5469.11 1 0.000 0.776 1.00 0.00 0.00
#> TCGA.CZ.5454.11 1 0.000 0.776 1.00 0.00 0.00
#> TCGA.BP.5170.11 1 0.628 0.646 0.54 0.00 0.46
#> TCGA.B0.4710.11 1 0.000 0.776 1.00 0.00 0.00
#> TCGA.B0.5711.11 2 0.628 0.318 0.00 0.54 0.46
#> TCGA.B0.4813.11 1 0.628 0.646 0.54 0.00 0.46
#> TCGA.CZ.5453.11 1 0.000 0.776 1.00 0.00 0.00
#> TCGA.B0.4847.11 2 0.628 0.318 0.00 0.54 0.46
#> TCGA.BP.5195.11 1 0.628 0.646 0.54 0.00 0.46
#> TCGA.BP.5010.11 1 0.628 0.646 0.54 0.00 0.46
#> TCGA.CZ.4856.11 1 0.000 0.776 1.00 0.00 0.00
#> TCGA.CZ.4866.11 1 0.000 0.776 1.00 0.00 0.00
#> TCGA.CJ.4902.11 1 0.000 0.776 1.00 0.00 0.00
#> TCGA.CZ.5465.11 1 0.000 0.776 1.00 0.00 0.00
#> TCGA.CZ.4859.11 1 0.628 0.646 0.54 0.00 0.46
#> TCGA.CZ.4863.11 1 0.000 0.776 1.00 0.00 0.00
#> TCGA.CJ.4905.11 2 0.000 0.618 0.00 1.00 0.00
#> TCGA.CZ.5462.11 1 0.000 0.776 1.00 0.00 0.00
#> TCGA.CZ.5461.11 1 0.628 0.646 0.54 0.00 0.46
#> TCGA.CJ.4908.11 1 0.628 0.646 0.54 0.00 0.46
#> TCGA.AK.3433.01 3 0.628 1.000 0.00 0.46 0.54
#> TCGA.CJ.4920.11 1 0.628 0.646 0.54 0.00 0.46
#> TCGA.B0.4845.11 1 0.628 0.646 0.54 0.00 0.46
#> TCGA.CZ.5458.11 1 0.000 0.776 1.00 0.00 0.00
#> TCGA.AK.3440.01 3 0.628 1.000 0.00 0.46 0.54
#> TCGA.A3.3370.11 2 0.000 0.618 0.00 1.00 0.00
#> TCGA.CZ.4853.11 1 0.628 0.646 0.54 0.00 0.46
#> TCGA.B0.5119.11 1 0.000 0.776 1.00 0.00 0.00
#> TCGA.B0.4816.11 1 0.628 0.646 0.54 0.00 0.46
#> TCGA.B0.4810.11 2 0.000 0.618 0.00 1.00 0.00
#> TCGA.CZ.4865.11 1 0.000 0.776 1.00 0.00 0.00
#> TCGA.B0.4712.11 1 0.000 0.776 1.00 0.00 0.00
#> TCGA.A3.3373.11 1 0.628 0.646 0.54 0.00 0.46
#> TCGA.B0.4688.11 1 0.628 0.646 0.54 0.00 0.46
#> TCGA.B0.4694.11 2 0.000 0.618 0.00 1.00 0.00
#> TCGA.CZ.5456.11 1 0.000 0.776 1.00 0.00 0.00
#> TCGA.B0.4828.11 1 0.628 0.646 0.54 0.00 0.46
#> TCGA.B0.4697.11 1 0.000 0.776 1.00 0.00 0.00
#> TCGA.CZ.5452.11 1 0.000 0.776 1.00 0.00 0.00
#> TCGA.B0.4822.11 2 0.000 0.618 0.00 1.00 0.00
#> TCGA.CZ.5455.11 1 0.000 0.776 1.00 0.00 0.00
#> TCGA.CJ.4912.11 1 0.628 0.646 0.54 0.00 0.46
#> TCGA.CZ.5457.11 1 0.000 0.776 1.00 0.00 0.00
#> TCGA.B0.4718.11 2 0.628 0.318 0.00 0.54 0.46
cbind(get_classes(res, k = 4), get_membership(res, k = 4))
#> class entropy silhouette p1 p2 p3 p4
#> TCGA.B0.4827.11 4 0.0000 0.998 0.00 0 0 1.00
#> TCGA.CZ.5463.11 1 0.0000 0.999 1.00 0 0 0.00
#> TCGA.CZ.5468.11 1 0.0000 0.999 1.00 0 0 0.00
#> TCGA.B0.4844.11 2 0.0000 1.000 0.00 1 0 0.00
#> TCGA.CZ.5467.11 1 0.0000 0.999 1.00 0 0 0.00
#> TCGA.BP.5192.11 2 0.0000 1.000 0.00 1 0 0.00
#> TCGA.CZ.5470.11 1 0.0707 0.974 0.98 0 0 0.02
#> TCGA.BP.4177.11 2 0.0000 1.000 0.00 1 0 0.00
#> TCGA.CZ.5469.11 1 0.0000 0.999 1.00 0 0 0.00
#> TCGA.CZ.5454.11 4 0.0707 0.972 0.02 0 0 0.98
#> TCGA.BP.5170.11 4 0.0000 0.998 0.00 0 0 1.00
#> TCGA.B0.4710.11 1 0.0000 0.999 1.00 0 0 0.00
#> TCGA.B0.5711.11 2 0.0000 1.000 0.00 1 0 0.00
#> TCGA.B0.4813.11 4 0.0000 0.998 0.00 0 0 1.00
#> TCGA.CZ.5453.11 1 0.0000 0.999 1.00 0 0 0.00
#> TCGA.B0.4847.11 2 0.0000 1.000 0.00 1 0 0.00
#> TCGA.BP.5195.11 4 0.0000 0.998 0.00 0 0 1.00
#> TCGA.BP.5010.11 4 0.0000 0.998 0.00 0 0 1.00
#> TCGA.CZ.4856.11 1 0.0000 0.999 1.00 0 0 0.00
#> TCGA.CZ.4866.11 1 0.0000 0.999 1.00 0 0 0.00
#> TCGA.CJ.4902.11 4 0.0000 0.998 0.00 0 0 1.00
#> TCGA.CZ.5465.11 1 0.0000 0.999 1.00 0 0 0.00
#> TCGA.CZ.4859.11 4 0.0000 0.998 0.00 0 0 1.00
#> TCGA.CZ.4863.11 1 0.0000 0.999 1.00 0 0 0.00
#> TCGA.CJ.4905.11 2 0.0000 1.000 0.00 1 0 0.00
#> TCGA.CZ.5462.11 1 0.0000 0.999 1.00 0 0 0.00
#> TCGA.CZ.5461.11 4 0.0000 0.998 0.00 0 0 1.00
#> TCGA.CJ.4908.11 4 0.0000 0.998 0.00 0 0 1.00
#> TCGA.AK.3433.01 3 0.0000 1.000 0.00 0 1 0.00
#> TCGA.CJ.4920.11 4 0.0000 0.998 0.00 0 0 1.00
#> TCGA.B0.4845.11 4 0.0000 0.998 0.00 0 0 1.00
#> TCGA.CZ.5458.11 1 0.0000 0.999 1.00 0 0 0.00
#> TCGA.AK.3440.01 3 0.0000 1.000 0.00 0 1 0.00
#> TCGA.A3.3370.11 2 0.0000 1.000 0.00 1 0 0.00
#> TCGA.CZ.4853.11 4 0.0000 0.998 0.00 0 0 1.00
#> TCGA.B0.5119.11 1 0.0000 0.999 1.00 0 0 0.00
#> TCGA.B0.4816.11 4 0.0000 0.998 0.00 0 0 1.00
#> TCGA.B0.4810.11 2 0.0000 1.000 0.00 1 0 0.00
#> TCGA.CZ.4865.11 1 0.0000 0.999 1.00 0 0 0.00
#> TCGA.B0.4712.11 1 0.0000 0.999 1.00 0 0 0.00
#> TCGA.A3.3373.11 4 0.0000 0.998 0.00 0 0 1.00
#> TCGA.B0.4688.11 4 0.0000 0.998 0.00 0 0 1.00
#> TCGA.B0.4694.11 2 0.0000 1.000 0.00 1 0 0.00
#> TCGA.CZ.5456.11 1 0.0000 0.999 1.00 0 0 0.00
#> TCGA.B0.4828.11 4 0.0000 0.998 0.00 0 0 1.00
#> TCGA.B0.4697.11 1 0.0000 0.999 1.00 0 0 0.00
#> TCGA.CZ.5452.11 1 0.0000 0.999 1.00 0 0 0.00
#> TCGA.B0.4822.11 2 0.0000 1.000 0.00 1 0 0.00
#> TCGA.CZ.5455.11 1 0.0000 0.999 1.00 0 0 0.00
#> TCGA.CJ.4912.11 4 0.0000 0.998 0.00 0 0 1.00
#> TCGA.CZ.5457.11 1 0.0000 0.999 1.00 0 0 0.00
#> TCGA.B0.4718.11 2 0.0000 1.000 0.00 1 0 0.00
cbind(get_classes(res, k = 5), get_membership(res, k = 5))
#> class entropy silhouette p1 p2 p3 p4 p5
#> TCGA.B0.4827.11 4 0.327 0.840 0.00 0.22 0.00 0.78 0.00
#> TCGA.CZ.5463.11 1 0.104 0.919 0.96 0.04 0.00 0.00 0.00
#> TCGA.CZ.5468.11 1 0.000 0.930 1.00 0.00 0.00 0.00 0.00
#> TCGA.B0.4844.11 5 0.000 0.850 0.00 0.00 0.00 0.00 1.00
#> TCGA.CZ.5467.11 1 0.104 0.919 0.96 0.04 0.00 0.00 0.00
#> TCGA.BP.5192.11 5 0.000 0.850 0.00 0.00 0.00 0.00 1.00
#> TCGA.CZ.5470.11 1 0.413 0.637 0.72 0.26 0.00 0.02 0.00
#> TCGA.BP.4177.11 5 0.000 0.850 0.00 0.00 0.00 0.00 1.00
#> TCGA.CZ.5469.11 1 0.000 0.930 1.00 0.00 0.00 0.00 0.00
#> TCGA.CZ.5454.11 4 0.636 0.479 0.22 0.26 0.00 0.52 0.00
#> TCGA.BP.5170.11 4 0.327 0.840 0.00 0.22 0.00 0.78 0.00
#> TCGA.B0.4710.11 1 0.000 0.930 1.00 0.00 0.00 0.00 0.00
#> TCGA.B0.5711.11 5 0.605 0.605 0.00 0.28 0.00 0.16 0.56
#> TCGA.B0.4813.11 4 0.000 0.856 0.00 0.00 0.00 1.00 0.00
#> TCGA.CZ.5453.11 1 0.356 0.669 0.74 0.26 0.00 0.00 0.00
#> TCGA.B0.4847.11 5 0.368 0.791 0.00 0.28 0.00 0.00 0.72
#> TCGA.BP.5195.11 4 0.000 0.856 0.00 0.00 0.00 1.00 0.00
#> TCGA.BP.5010.11 4 0.293 0.846 0.00 0.18 0.00 0.82 0.00
#> TCGA.CZ.4856.11 1 0.173 0.910 0.92 0.08 0.00 0.00 0.00
#> TCGA.CZ.4866.11 1 0.000 0.930 1.00 0.00 0.00 0.00 0.00
#> TCGA.CJ.4902.11 4 0.356 0.809 0.00 0.26 0.00 0.74 0.00
#> TCGA.CZ.5465.11 1 0.000 0.930 1.00 0.00 0.00 0.00 0.00
#> TCGA.CZ.4859.11 4 0.000 0.856 0.00 0.00 0.00 1.00 0.00
#> TCGA.CZ.4863.11 1 0.173 0.910 0.92 0.08 0.00 0.00 0.00
#> TCGA.CJ.4905.11 5 0.000 0.850 0.00 0.00 0.00 0.00 1.00
#> TCGA.CZ.5462.11 1 0.104 0.919 0.96 0.04 0.00 0.00 0.00
#> TCGA.CZ.5461.11 4 0.327 0.840 0.00 0.22 0.00 0.78 0.00
#> TCGA.CJ.4908.11 4 0.000 0.856 0.00 0.00 0.00 1.00 0.00
#> TCGA.AK.3433.01 3 0.000 0.824 0.00 0.00 1.00 0.00 0.00
#> TCGA.CJ.4920.11 4 0.000 0.856 0.00 0.00 0.00 1.00 0.00
#> TCGA.B0.4845.11 4 0.000 0.856 0.00 0.00 0.00 1.00 0.00
#> TCGA.CZ.5458.11 1 0.104 0.919 0.96 0.04 0.00 0.00 0.00
#> TCGA.AK.3440.01 3 0.413 0.824 0.00 0.38 0.62 0.00 0.00
#> TCGA.A3.3370.11 5 0.000 0.850 0.00 0.00 0.00 0.00 1.00
#> TCGA.CZ.4853.11 4 0.327 0.840 0.00 0.22 0.00 0.78 0.00
#> TCGA.B0.5119.11 1 0.173 0.910 0.92 0.08 0.00 0.00 0.00
#> TCGA.B0.4816.11 4 0.327 0.840 0.00 0.22 0.00 0.78 0.00
#> TCGA.B0.4810.11 5 0.000 0.850 0.00 0.00 0.00 0.00 1.00
#> TCGA.CZ.4865.11 1 0.173 0.910 0.92 0.08 0.00 0.00 0.00
#> TCGA.B0.4712.11 1 0.000 0.930 1.00 0.00 0.00 0.00 0.00
#> TCGA.A3.3373.11 4 0.000 0.856 0.00 0.00 0.00 1.00 0.00
#> TCGA.B0.4688.11 4 0.327 0.840 0.00 0.22 0.00 0.78 0.00
#> TCGA.B0.4694.11 5 0.342 0.807 0.00 0.24 0.00 0.00 0.76
#> TCGA.CZ.5456.11 1 0.173 0.910 0.92 0.08 0.00 0.00 0.00
#> TCGA.B0.4828.11 4 0.000 0.856 0.00 0.00 0.00 1.00 0.00
#> TCGA.B0.4697.11 1 0.173 0.910 0.92 0.08 0.00 0.00 0.00
#> TCGA.CZ.5452.11 1 0.104 0.919 0.96 0.04 0.00 0.00 0.00
#> TCGA.B0.4822.11 5 0.356 0.801 0.00 0.26 0.00 0.00 0.74
#> TCGA.CZ.5455.11 1 0.000 0.930 1.00 0.00 0.00 0.00 0.00
#> TCGA.CJ.4912.11 4 0.000 0.856 0.00 0.00 0.00 1.00 0.00
#> TCGA.CZ.5457.11 1 0.173 0.910 0.92 0.08 0.00 0.00 0.00
#> TCGA.B0.4718.11 5 0.368 0.791 0.00 0.28 0.00 0.00 0.72
cbind(get_classes(res, k = 6), get_membership(res, k = 6))
#> class entropy silhouette p1 p2 p3 p4 p5 p6
#> TCGA.B0.4827.11 4 0.3578 0.4187 0.00 0.34 0.00 0.66 0.00 0.00
#> TCGA.CZ.5463.11 1 0.1556 0.8385 0.92 0.08 0.00 0.00 0.00 0.00
#> TCGA.CZ.5468.11 1 0.0000 0.8654 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.B0.4844.11 5 0.1814 0.6817 0.00 0.10 0.00 0.00 0.90 0.00
#> TCGA.CZ.5467.11 1 0.1556 0.8385 0.92 0.08 0.00 0.00 0.00 0.00
#> TCGA.BP.5192.11 5 0.0000 0.7587 0.00 0.00 0.00 0.00 1.00 0.00
#> TCGA.CZ.5470.11 1 0.3797 0.2097 0.58 0.42 0.00 0.00 0.00 0.00
#> TCGA.BP.4177.11 5 0.0000 0.7587 0.00 0.00 0.00 0.00 1.00 0.00
#> TCGA.CZ.5469.11 1 0.0000 0.8654 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.CZ.5454.11 2 0.5882 0.0000 0.20 0.42 0.00 0.38 0.00 0.00
#> TCGA.BP.5170.11 4 0.3578 0.4187 0.00 0.34 0.00 0.66 0.00 0.00
#> TCGA.B0.4710.11 1 0.0000 0.8654 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.B0.5711.11 5 0.6791 0.4845 0.00 0.36 0.12 0.10 0.42 0.00
#> TCGA.B0.4813.11 4 0.0547 0.6342 0.00 0.02 0.00 0.98 0.00 0.00
#> TCGA.CZ.5453.11 1 0.3706 0.3341 0.62 0.38 0.00 0.00 0.00 0.00
#> TCGA.B0.4847.11 5 0.5371 0.6081 0.00 0.36 0.12 0.00 0.52 0.00
#> TCGA.BP.5195.11 4 0.0000 0.6393 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.BP.5010.11 4 0.3309 0.4878 0.00 0.28 0.00 0.72 0.00 0.00
#> TCGA.CZ.4856.11 1 0.3567 0.7977 0.80 0.10 0.00 0.00 0.00 0.10
#> TCGA.CZ.4866.11 1 0.0000 0.8654 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.CJ.4902.11 4 0.4282 -0.0923 0.02 0.42 0.00 0.56 0.00 0.00
#> TCGA.CZ.5465.11 1 0.0000 0.8654 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.CZ.4859.11 4 0.0937 0.6468 0.00 0.04 0.00 0.96 0.00 0.00
#> TCGA.CZ.4863.11 1 0.3567 0.7977 0.80 0.10 0.00 0.00 0.00 0.10
#> TCGA.CJ.4905.11 5 0.0000 0.7587 0.00 0.00 0.00 0.00 1.00 0.00
#> TCGA.CZ.5462.11 1 0.1556 0.8385 0.92 0.08 0.00 0.00 0.00 0.00
#> TCGA.CZ.5461.11 4 0.3578 0.4187 0.00 0.34 0.00 0.66 0.00 0.00
#> TCGA.CJ.4908.11 4 0.0937 0.6165 0.00 0.04 0.00 0.96 0.00 0.00
#> TCGA.AK.3433.01 3 0.2048 0.0000 0.00 0.00 0.88 0.00 0.00 0.12
#> TCGA.CJ.4920.11 4 0.0937 0.6468 0.00 0.04 0.00 0.96 0.00 0.00
#> TCGA.B0.4845.11 4 0.1814 0.5548 0.00 0.10 0.00 0.90 0.00 0.00
#> TCGA.CZ.5458.11 1 0.1556 0.8385 0.92 0.08 0.00 0.00 0.00 0.00
#> TCGA.AK.3440.01 6 0.1814 0.0000 0.00 0.00 0.10 0.00 0.00 0.90
#> TCGA.A3.3370.11 5 0.0000 0.7587 0.00 0.00 0.00 0.00 1.00 0.00
#> TCGA.CZ.4853.11 4 0.3578 0.4187 0.00 0.34 0.00 0.66 0.00 0.00
#> TCGA.B0.5119.11 1 0.3567 0.7977 0.80 0.10 0.00 0.00 0.00 0.10
#> TCGA.B0.4816.11 4 0.3578 0.4187 0.00 0.34 0.00 0.66 0.00 0.00
#> TCGA.B0.4810.11 5 0.0000 0.7587 0.00 0.00 0.00 0.00 1.00 0.00
#> TCGA.CZ.4865.11 1 0.3567 0.7977 0.80 0.10 0.00 0.00 0.00 0.10
#> TCGA.B0.4712.11 1 0.0000 0.8654 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.A3.3373.11 4 0.0937 0.6468 0.00 0.04 0.00 0.96 0.00 0.00
#> TCGA.B0.4688.11 4 0.3578 0.4313 0.00 0.34 0.00 0.66 0.00 0.00
#> TCGA.B0.4694.11 5 0.4475 0.7026 0.00 0.20 0.10 0.00 0.70 0.00
#> TCGA.CZ.5456.11 1 0.1814 0.8396 0.90 0.10 0.00 0.00 0.00 0.00
#> TCGA.B0.4828.11 4 0.0547 0.6342 0.00 0.02 0.00 0.98 0.00 0.00
#> TCGA.B0.4697.11 1 0.3567 0.7977 0.80 0.10 0.00 0.00 0.00 0.10
#> TCGA.CZ.5452.11 1 0.1556 0.8385 0.92 0.08 0.00 0.00 0.00 0.00
#> TCGA.B0.4822.11 5 0.5029 0.6724 0.00 0.26 0.12 0.00 0.62 0.00
#> TCGA.CZ.5455.11 1 0.0000 0.8654 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.CJ.4912.11 4 0.1556 0.5783 0.00 0.08 0.00 0.92 0.00 0.00
#> TCGA.CZ.5457.11 1 0.1814 0.8396 0.90 0.10 0.00 0.00 0.00 0.00
#> TCGA.B0.4718.11 5 0.5267 0.6398 0.00 0.32 0.12 0.00 0.56 0.00
cbind(get_classes(res, k = 7), get_membership(res, k = 7))
#> class entropy silhouette p1 p2 p3 p4 p5 p6 p7
#> TCGA.B0.4827.11 2 0.0863 0.5764 0.00 0.96 0.00 0.04 0.00 0.00 0.00
#> TCGA.CZ.5463.11 1 0.2376 0.7614 0.86 0.02 0.00 0.00 0.00 0.12 0.00
#> TCGA.CZ.5468.11 1 0.0000 0.8271 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.B0.4844.11 5 0.4502 0.4032 0.00 0.00 0.00 0.16 0.66 0.00 0.18
#> TCGA.CZ.5467.11 1 0.1886 0.7752 0.88 0.00 0.00 0.00 0.00 0.12 0.00
#> TCGA.BP.5192.11 5 0.0000 0.7456 0.00 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.CZ.5470.11 2 0.4630 0.3544 0.26 0.62 0.00 0.00 0.00 0.12 0.00
#> TCGA.BP.4177.11 5 0.0504 0.7297 0.00 0.00 0.00 0.00 0.98 0.00 0.02
#> TCGA.CZ.5469.11 1 0.0000 0.8271 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.CZ.5454.11 2 0.4535 0.3809 0.24 0.64 0.00 0.00 0.00 0.12 0.00
#> TCGA.BP.5170.11 2 0.0000 0.5842 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.B0.4710.11 1 0.0000 0.8271 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.B0.5711.11 7 0.4426 0.9007 0.00 0.00 0.00 0.06 0.38 0.00 0.56
#> TCGA.B0.4813.11 4 0.3546 0.8820 0.00 0.46 0.00 0.54 0.00 0.00 0.00
#> TCGA.CZ.5453.11 2 0.5016 0.0834 0.42 0.46 0.00 0.00 0.00 0.12 0.00
#> TCGA.B0.4847.11 7 0.4214 0.9274 0.00 0.00 0.00 0.04 0.40 0.00 0.56
#> TCGA.BP.5195.11 4 0.3459 0.9229 0.00 0.40 0.00 0.60 0.00 0.00 0.00
#> TCGA.BP.5010.11 2 0.2945 -0.0829 0.00 0.74 0.00 0.26 0.00 0.00 0.00
#> TCGA.CZ.4856.11 1 0.4479 0.6774 0.66 0.00 0.00 0.06 0.00 0.02 0.26
#> TCGA.CZ.4866.11 1 0.0000 0.8271 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.CJ.4902.11 2 0.2376 0.5629 0.02 0.86 0.00 0.00 0.00 0.12 0.00
#> TCGA.CZ.5465.11 1 0.0000 0.8271 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.CZ.4859.11 4 0.3546 0.8880 0.00 0.46 0.00 0.54 0.00 0.00 0.00
#> TCGA.CZ.4863.11 1 0.4479 0.6774 0.66 0.00 0.00 0.06 0.00 0.02 0.26
#> TCGA.CJ.4905.11 5 0.0504 0.7297 0.00 0.00 0.00 0.00 0.98 0.00 0.02
#> TCGA.CZ.5462.11 1 0.2722 0.7433 0.84 0.04 0.00 0.00 0.00 0.12 0.00
#> TCGA.CZ.5461.11 2 0.1166 0.5580 0.00 0.94 0.00 0.06 0.00 0.00 0.00
#> TCGA.CJ.4908.11 4 0.3358 0.9120 0.00 0.36 0.00 0.64 0.00 0.00 0.00
#> TCGA.AK.3433.01 3 0.0000 0.0000 0.00 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.CJ.4920.11 4 0.3525 0.9111 0.00 0.44 0.00 0.56 0.00 0.00 0.00
#> TCGA.B0.4845.11 4 0.3294 0.8962 0.00 0.34 0.00 0.66 0.00 0.00 0.00
#> TCGA.CZ.5458.11 1 0.2376 0.7614 0.86 0.02 0.00 0.00 0.00 0.12 0.00
#> TCGA.AK.3440.01 6 0.2376 0.0000 0.00 0.00 0.02 0.12 0.00 0.86 0.00
#> TCGA.A3.3370.11 5 0.0000 0.7456 0.00 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.CZ.4853.11 2 0.0863 0.5764 0.00 0.96 0.00 0.04 0.00 0.00 0.00
#> TCGA.B0.5119.11 1 0.4479 0.6774 0.66 0.00 0.00 0.06 0.00 0.02 0.26
#> TCGA.B0.4816.11 2 0.1433 0.5308 0.00 0.92 0.00 0.08 0.00 0.00 0.00
#> TCGA.B0.4810.11 5 0.0000 0.7456 0.00 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.CZ.4865.11 1 0.4479 0.6774 0.66 0.00 0.00 0.06 0.00 0.02 0.26
#> TCGA.B0.4712.11 1 0.0000 0.8271 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.A3.3373.11 4 0.3525 0.9111 0.00 0.44 0.00 0.56 0.00 0.00 0.00
#> TCGA.B0.4688.11 2 0.1886 0.4511 0.00 0.88 0.00 0.12 0.00 0.00 0.00
#> TCGA.B0.4694.11 5 0.3558 -0.7989 0.00 0.00 0.00 0.00 0.52 0.00 0.48
#> TCGA.CZ.5456.11 1 0.3370 0.7504 0.78 0.00 0.00 0.06 0.00 0.00 0.16
#> TCGA.B0.4828.11 4 0.3413 0.9200 0.00 0.38 0.00 0.62 0.00 0.00 0.00
#> TCGA.B0.4697.11 1 0.4479 0.6774 0.66 0.00 0.00 0.06 0.00 0.02 0.26
#> TCGA.CZ.5452.11 1 0.1671 0.7870 0.90 0.00 0.00 0.00 0.00 0.10 0.00
#> TCGA.B0.4822.11 7 0.3546 0.8698 0.00 0.00 0.00 0.00 0.46 0.00 0.54
#> TCGA.CZ.5455.11 1 0.0504 0.8216 0.98 0.00 0.00 0.00 0.00 0.02 0.00
#> TCGA.CJ.4912.11 4 0.3294 0.8962 0.00 0.34 0.00 0.66 0.00 0.00 0.00
#> TCGA.CZ.5457.11 1 0.3011 0.7670 0.82 0.00 0.00 0.06 0.00 0.00 0.12
#> TCGA.B0.4718.11 7 0.3943 0.9259 0.00 0.00 0.00 0.02 0.42 0.00 0.56
cbind(get_classes(res, k = 8), get_membership(res, k = 8))
#> class entropy silhouette p1 p2 p3 p4 p5 p6 p7 p8
#> TCGA.B0.4827.11 2 0.3015 0.6211 0.00 0.68 0.00 0.32 0.00 0.00 0.00 0.00
#> TCGA.CZ.5463.11 1 0.3036 0.6886 0.78 0.18 0.00 0.00 0.00 0.00 0.00 0.04
#> TCGA.CZ.5468.11 1 0.0000 0.8357 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.B0.4844.11 5 0.4588 0.0193 0.00 0.12 0.00 0.00 0.54 0.00 0.00 0.34
#> TCGA.CZ.5467.11 1 0.2132 0.7763 0.88 0.08 0.00 0.00 0.00 0.00 0.00 0.04
#> TCGA.BP.5192.11 5 0.2267 0.8195 0.00 0.00 0.00 0.00 0.82 0.00 0.18 0.00
#> TCGA.CZ.5470.11 2 0.3036 0.4871 0.18 0.78 0.00 0.00 0.00 0.00 0.00 0.04
#> TCGA.BP.4177.11 5 0.2650 0.7886 0.00 0.00 0.00 0.00 0.76 0.00 0.24 0.00
#> TCGA.CZ.5469.11 1 0.0000 0.8357 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.CZ.5454.11 2 0.2547 0.5423 0.12 0.84 0.00 0.00 0.00 0.00 0.00 0.04
#> TCGA.BP.5170.11 2 0.2406 0.6656 0.00 0.80 0.00 0.20 0.00 0.00 0.00 0.00
#> TCGA.B0.4710.11 1 0.0000 0.8357 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.B0.5711.11 7 0.0471 0.8406 0.00 0.00 0.00 0.02 0.00 0.00 0.98 0.00
#> TCGA.B0.4813.11 4 0.2071 0.8251 0.00 0.04 0.00 0.90 0.00 0.02 0.00 0.04
#> TCGA.CZ.5453.11 2 0.3293 0.4372 0.22 0.74 0.00 0.00 0.00 0.00 0.00 0.04
#> TCGA.B0.4847.11 7 0.0471 0.8758 0.00 0.00 0.00 0.00 0.02 0.00 0.98 0.00
#> TCGA.BP.5195.11 4 0.0471 0.8540 0.00 0.00 0.00 0.98 0.00 0.00 0.00 0.02
#> TCGA.BP.5010.11 4 0.3142 0.2197 0.00 0.36 0.00 0.64 0.00 0.00 0.00 0.00
#> TCGA.CZ.4856.11 8 0.3299 1.0000 0.44 0.00 0.00 0.00 0.00 0.00 0.00 0.56
#> TCGA.CZ.4866.11 1 0.0000 0.8357 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.CJ.4902.11 2 0.2547 0.6407 0.00 0.84 0.00 0.12 0.00 0.00 0.00 0.04
#> TCGA.CZ.5465.11 1 0.0000 0.8357 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.CZ.4859.11 4 0.2265 0.8327 0.00 0.08 0.00 0.88 0.00 0.02 0.00 0.02
#> TCGA.CZ.4863.11 8 0.3299 1.0000 0.44 0.00 0.00 0.00 0.00 0.00 0.00 0.56
#> TCGA.CJ.4905.11 5 0.2406 0.8218 0.00 0.00 0.00 0.00 0.80 0.00 0.20 0.00
#> TCGA.CZ.5462.11 1 0.3036 0.6886 0.78 0.18 0.00 0.00 0.00 0.00 0.00 0.04
#> TCGA.CZ.5461.11 2 0.3514 0.5951 0.00 0.64 0.00 0.34 0.00 0.02 0.00 0.00
#> TCGA.CJ.4908.11 4 0.1741 0.8432 0.00 0.00 0.00 0.92 0.00 0.02 0.04 0.02
#> TCGA.AK.3433.01 3 0.0000 0.0000 0.00 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.CJ.4920.11 4 0.1804 0.8312 0.00 0.08 0.00 0.90 0.00 0.00 0.00 0.02
#> TCGA.B0.4845.11 4 0.1275 0.8414 0.00 0.00 0.00 0.94 0.00 0.00 0.04 0.02
#> TCGA.CZ.5458.11 1 0.3036 0.6886 0.78 0.18 0.00 0.00 0.00 0.00 0.00 0.04
#> TCGA.AK.3440.01 6 0.0808 0.0000 0.00 0.00 0.04 0.00 0.00 0.96 0.00 0.00
#> TCGA.A3.3370.11 5 0.2406 0.8218 0.00 0.00 0.00 0.00 0.80 0.00 0.20 0.00
#> TCGA.CZ.4853.11 2 0.3083 0.6092 0.00 0.66 0.00 0.34 0.00 0.00 0.00 0.00
#> TCGA.B0.5119.11 8 0.3299 1.0000 0.44 0.00 0.00 0.00 0.00 0.00 0.00 0.56
#> TCGA.B0.4816.11 2 0.3570 0.5659 0.00 0.62 0.00 0.36 0.00 0.02 0.00 0.00
#> TCGA.B0.4810.11 5 0.2267 0.8110 0.00 0.00 0.00 0.00 0.82 0.00 0.18 0.00
#> TCGA.CZ.4865.11 8 0.3299 1.0000 0.44 0.00 0.00 0.00 0.00 0.00 0.00 0.56
#> TCGA.B0.4712.11 1 0.0000 0.8357 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.A3.3373.11 4 0.1804 0.8296 0.00 0.08 0.00 0.90 0.00 0.02 0.00 0.00
#> TCGA.B0.4688.11 2 0.4125 0.3722 0.00 0.52 0.00 0.44 0.00 0.02 0.00 0.02
#> TCGA.B0.4694.11 7 0.2534 0.7122 0.00 0.00 0.00 0.00 0.22 0.00 0.78 0.00
#> TCGA.CZ.5456.11 1 0.1765 0.6276 0.88 0.00 0.00 0.00 0.00 0.00 0.00 0.12
#> TCGA.B0.4828.11 4 0.1408 0.8433 0.00 0.02 0.00 0.94 0.00 0.02 0.00 0.02
#> TCGA.B0.4697.11 8 0.3299 1.0000 0.44 0.00 0.00 0.00 0.00 0.00 0.00 0.56
#> TCGA.CZ.5452.11 1 0.1557 0.8048 0.92 0.06 0.00 0.00 0.00 0.00 0.00 0.02
#> TCGA.B0.4822.11 7 0.1765 0.8414 0.00 0.00 0.00 0.00 0.12 0.00 0.88 0.00
#> TCGA.CZ.5455.11 1 0.0471 0.8322 0.98 0.02 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.CJ.4912.11 4 0.1804 0.8125 0.00 0.00 0.00 0.90 0.00 0.00 0.08 0.02
#> TCGA.CZ.5457.11 1 0.1765 0.6276 0.88 0.00 0.00 0.00 0.00 0.00 0.00 0.12
#> TCGA.B0.4718.11 7 0.0808 0.8795 0.00 0.00 0.00 0.00 0.04 0.00 0.96 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: Node05. Child nodes: Node0141-leaf , Node0142-leaf , Node0143-leaf , Node0144-leaf , Node0211-leaf , Node0212-leaf , Node0213 , Node0231-leaf , Node0232-leaf , Node0233-leaf , Node0411 , Node0412-leaf , Node0413-leaf , Node0431-leaf , Node0432-leaf , Node0433-leaf , Node0511-leaf , Node0512-leaf , Node0541-leaf , Node0542-leaf , Node0543-leaf , Node0621-leaf , Node0622-leaf , Node0623-leaf .
The object with results only for a single top-value method and a single partitioning method can be extracted as:
res = res_rh["051"]
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 21 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 1.000 1.000 0.5243 0.476 0.476
#> 3 3 0.689 0.760 0.799 0.2330 0.857 0.700
#> 4 4 0.563 0.727 0.785 0.1240 0.838 0.553
#> 5 5 0.642 0.565 0.749 0.0803 0.971 0.875
#> 6 6 0.563 0.411 0.598 0.0391 0.933 0.689
#> 7 7 0.626 0.348 0.691 0.0364 0.919 0.595
#> 8 8 0.684 0.326 0.700 0.0380 0.914 0.526
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.CZ.5463.11 2 0 1 0 1
#> TCGA.CZ.5468.11 2 0 1 0 1
#> TCGA.CZ.5467.11 1 0 1 1 0
#> TCGA.CZ.5470.11 1 0 1 1 0
#> TCGA.CZ.5469.11 2 0 1 0 1
#> TCGA.B0.4710.11 1 0 1 1 0
#> TCGA.CZ.5453.11 2 0 1 0 1
#> TCGA.CZ.4856.11 1 0 1 1 0
#> TCGA.CZ.4866.11 1 0 1 1 0
#> TCGA.CZ.5465.11 1 0 1 1 0
#> TCGA.CZ.4863.11 1 0 1 1 0
#> TCGA.CZ.5462.11 2 0 1 0 1
#> TCGA.CZ.5458.11 2 0 1 0 1
#> TCGA.B0.5119.11 1 0 1 1 0
#> TCGA.CZ.4865.11 1 0 1 1 0
#> TCGA.B0.4712.11 2 0 1 0 1
#> TCGA.CZ.5456.11 2 0 1 0 1
#> TCGA.B0.4697.11 1 0 1 1 0
#> TCGA.CZ.5452.11 2 0 1 0 1
#> TCGA.CZ.5455.11 2 0 1 0 1
#> TCGA.CZ.5457.11 2 0 1 0 1
cbind(get_classes(res, k = 3), get_membership(res, k = 3))
#> class entropy silhouette p1 p2 p3
#> TCGA.CZ.5463.11 2 0.6045 0.886 0.00 0.62 0.38
#> TCGA.CZ.5468.11 2 0.6244 0.887 0.00 0.56 0.44
#> TCGA.CZ.5467.11 1 0.0892 0.874 0.98 0.02 0.00
#> TCGA.CZ.5470.11 1 0.2066 0.871 0.94 0.06 0.00
#> TCGA.CZ.5469.11 3 0.6192 -0.416 0.00 0.42 0.58
#> TCGA.B0.4710.11 1 0.0000 0.872 1.00 0.00 0.00
#> TCGA.CZ.5453.11 2 0.6045 0.886 0.00 0.62 0.38
#> TCGA.CZ.4856.11 1 0.5560 0.816 0.70 0.30 0.00
#> TCGA.CZ.4866.11 1 0.0000 0.872 1.00 0.00 0.00
#> TCGA.CZ.5465.11 1 0.0892 0.873 0.98 0.02 0.00
#> TCGA.CZ.4863.11 1 0.0000 0.872 1.00 0.00 0.00
#> TCGA.CZ.5462.11 3 0.2959 0.688 0.00 0.10 0.90
#> TCGA.CZ.5458.11 2 0.6302 0.833 0.00 0.52 0.48
#> TCGA.B0.5119.11 1 0.6045 0.781 0.62 0.38 0.00
#> TCGA.CZ.4865.11 1 0.6045 0.781 0.62 0.38 0.00
#> TCGA.B0.4712.11 3 0.3686 0.597 0.00 0.14 0.86
#> TCGA.CZ.5456.11 2 0.6302 0.837 0.00 0.52 0.48
#> TCGA.B0.4697.11 1 0.5397 0.819 0.72 0.28 0.00
#> TCGA.CZ.5452.11 3 0.0000 0.715 0.00 0.00 1.00
#> TCGA.CZ.5455.11 3 0.0000 0.715 0.00 0.00 1.00
#> TCGA.CZ.5457.11 2 0.6126 0.897 0.00 0.60 0.40
cbind(get_classes(res, k = 4), get_membership(res, k = 4))
#> class entropy silhouette p1 p2 p3 p4
#> TCGA.CZ.5463.11 2 0.433 0.720 0.16 0.80 0.04 0.00
#> TCGA.CZ.5468.11 2 0.164 0.737 0.06 0.94 0.00 0.00
#> TCGA.CZ.5467.11 1 0.452 0.862 0.68 0.00 0.00 0.32
#> TCGA.CZ.5470.11 1 0.645 0.687 0.56 0.00 0.08 0.36
#> TCGA.CZ.5469.11 2 0.702 0.167 0.14 0.54 0.32 0.00
#> TCGA.B0.4710.11 1 0.413 0.874 0.74 0.00 0.00 0.26
#> TCGA.CZ.5453.11 2 0.317 0.735 0.16 0.84 0.00 0.00
#> TCGA.CZ.4856.11 4 0.292 0.729 0.14 0.00 0.00 0.86
#> TCGA.CZ.4866.11 1 0.471 0.811 0.64 0.00 0.00 0.36
#> TCGA.CZ.5465.11 1 0.494 0.853 0.70 0.00 0.02 0.28
#> TCGA.CZ.4863.11 1 0.413 0.872 0.74 0.00 0.00 0.26
#> TCGA.CZ.5462.11 3 0.577 0.782 0.06 0.28 0.66 0.00
#> TCGA.CZ.5458.11 2 0.394 0.671 0.06 0.84 0.10 0.00
#> TCGA.B0.5119.11 4 0.292 0.711 0.00 0.00 0.14 0.86
#> TCGA.CZ.4865.11 4 0.283 0.763 0.04 0.00 0.06 0.90
#> TCGA.B0.4712.11 3 0.601 0.536 0.04 0.46 0.50 0.00
#> TCGA.CZ.5456.11 2 0.353 0.715 0.04 0.86 0.10 0.00
#> TCGA.B0.4697.11 4 0.408 0.644 0.18 0.00 0.02 0.80
#> TCGA.CZ.5452.11 3 0.464 0.821 0.02 0.24 0.74 0.00
#> TCGA.CZ.5455.11 3 0.398 0.822 0.00 0.24 0.76 0.00
#> TCGA.CZ.5457.11 2 0.191 0.761 0.04 0.94 0.02 0.00
cbind(get_classes(res, k = 5), get_membership(res, k = 5))
#> class entropy silhouette p1 p2 p3 p4 p5
#> TCGA.CZ.5463.11 2 0.5330 0.1266 0.00 0.52 0.02 0.02 0.44
#> TCGA.CZ.5468.11 2 0.0000 0.5132 0.00 1.00 0.00 0.00 0.00
#> TCGA.CZ.5467.11 1 0.1043 0.8817 0.96 0.00 0.00 0.04 0.00
#> TCGA.CZ.5470.11 1 0.4158 0.7541 0.82 0.00 0.06 0.06 0.06
#> TCGA.CZ.5469.11 5 0.7052 0.0000 0.00 0.22 0.22 0.04 0.52
#> TCGA.B0.4710.11 1 0.0609 0.8943 0.98 0.00 0.00 0.00 0.02
#> TCGA.CZ.5453.11 2 0.5293 0.4007 0.00 0.68 0.02 0.06 0.24
#> TCGA.CZ.4856.11 4 0.5558 0.7298 0.36 0.00 0.00 0.56 0.08
#> TCGA.CZ.4866.11 1 0.2754 0.8266 0.88 0.00 0.00 0.08 0.04
#> TCGA.CZ.5465.11 1 0.1648 0.8904 0.94 0.00 0.02 0.00 0.04
#> TCGA.CZ.4863.11 1 0.0609 0.8940 0.98 0.00 0.00 0.00 0.02
#> TCGA.CZ.5462.11 3 0.5347 0.4956 0.00 0.08 0.72 0.04 0.16
#> TCGA.CZ.5458.11 2 0.3390 0.4567 0.00 0.86 0.02 0.06 0.06
#> TCGA.B0.5119.11 4 0.5597 0.6740 0.20 0.00 0.00 0.64 0.16
#> TCGA.CZ.4865.11 4 0.3424 0.7597 0.24 0.00 0.00 0.76 0.00
#> TCGA.B0.4712.11 3 0.7241 0.0892 0.00 0.34 0.44 0.04 0.18
#> TCGA.CZ.5456.11 2 0.5470 0.0386 0.00 0.60 0.02 0.04 0.34
#> TCGA.B0.4697.11 4 0.5783 0.7172 0.36 0.00 0.00 0.54 0.10
#> TCGA.CZ.5452.11 3 0.2012 0.6621 0.00 0.06 0.92 0.00 0.02
#> TCGA.CZ.5455.11 3 0.1410 0.6621 0.00 0.06 0.94 0.00 0.00
#> TCGA.CZ.5457.11 2 0.4748 0.3888 0.00 0.66 0.00 0.04 0.30
cbind(get_classes(res, k = 6), get_membership(res, k = 6))
#> class entropy silhouette p1 p2 p3 p4 p5 p6
#> TCGA.CZ.5463.11 2 0.581 0.439108 0.00 0.62 0.12 0.02 0.02 0.22
#> TCGA.CZ.5468.11 6 0.706 0.000000 0.00 0.14 0.12 0.00 0.36 0.38
#> TCGA.CZ.5467.11 1 0.273 0.766275 0.88 0.04 0.00 0.02 0.00 0.06
#> TCGA.CZ.5470.11 1 0.661 0.321532 0.46 0.00 0.00 0.10 0.10 0.34
#> TCGA.CZ.5469.11 2 0.436 0.204747 0.00 0.68 0.26 0.00 0.06 0.00
#> TCGA.B0.4710.11 1 0.000 0.776512 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.CZ.5453.11 2 0.543 0.351401 0.00 0.48 0.12 0.00 0.00 0.40
#> TCGA.CZ.4856.11 4 0.450 0.646110 0.20 0.02 0.00 0.72 0.00 0.06
#> TCGA.CZ.4866.11 1 0.370 0.718370 0.82 0.08 0.00 0.04 0.00 0.06
#> TCGA.CZ.5465.11 1 0.432 0.708962 0.78 0.06 0.00 0.02 0.02 0.12
#> TCGA.CZ.4863.11 1 0.181 0.771834 0.92 0.00 0.00 0.02 0.00 0.06
#> TCGA.CZ.5462.11 3 0.477 0.373571 0.00 0.30 0.64 0.04 0.00 0.02
#> TCGA.CZ.5458.11 5 0.757 -0.743969 0.00 0.14 0.14 0.02 0.40 0.30
#> TCGA.B0.5119.11 4 0.580 0.532190 0.08 0.00 0.00 0.52 0.36 0.04
#> TCGA.CZ.4865.11 4 0.380 0.682624 0.12 0.00 0.00 0.80 0.06 0.02
#> TCGA.B0.4712.11 3 0.465 0.000568 0.00 0.04 0.50 0.00 0.46 0.00
#> TCGA.CZ.5456.11 5 0.694 -0.001339 0.00 0.34 0.18 0.00 0.40 0.08
#> TCGA.B0.4697.11 4 0.648 0.597792 0.20 0.04 0.00 0.60 0.08 0.08
#> TCGA.CZ.5452.11 3 0.202 0.616691 0.00 0.02 0.92 0.00 0.04 0.02
#> TCGA.CZ.5455.11 3 0.000 0.632383 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.CZ.5457.11 2 0.675 0.231689 0.00 0.54 0.12 0.02 0.08 0.24
cbind(get_classes(res, k = 7), get_membership(res, k = 7))
#> class entropy silhouette p1 p2 p3 p4 p5 p6 p7
#> TCGA.CZ.5463.11 2 0.6216 -0.1054 0.00 0.42 0.00 0.02 0.34 0.02 0.20
#> TCGA.CZ.5468.11 5 0.0000 0.4459 0.00 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.CZ.5467.11 1 0.2857 0.6197 0.86 0.04 0.00 0.00 0.00 0.04 0.06
#> TCGA.CZ.5470.11 7 0.4783 0.0000 0.36 0.00 0.00 0.00 0.00 0.10 0.54
#> TCGA.CZ.5469.11 2 0.3835 0.1742 0.00 0.74 0.16 0.00 0.10 0.00 0.00
#> TCGA.B0.4710.11 1 0.0000 0.7106 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.CZ.5453.11 5 0.5735 -0.0743 0.00 0.18 0.00 0.02 0.44 0.00 0.36
#> TCGA.CZ.4856.11 6 0.2708 0.5364 0.22 0.00 0.00 0.00 0.00 0.78 0.00
#> TCGA.CZ.4866.11 1 0.4331 0.5802 0.72 0.18 0.00 0.04 0.00 0.06 0.00
#> TCGA.CZ.5465.11 1 0.5525 0.4798 0.70 0.10 0.04 0.04 0.00 0.06 0.06
#> TCGA.CZ.4863.11 1 0.0863 0.6957 0.96 0.00 0.00 0.00 0.00 0.00 0.04
#> TCGA.CZ.5462.11 3 0.6372 0.1145 0.00 0.38 0.46 0.04 0.04 0.04 0.04
#> TCGA.CZ.5458.11 5 0.3530 0.3810 0.00 0.02 0.00 0.20 0.76 0.00 0.02
#> TCGA.B0.5119.11 6 0.5413 0.2657 0.08 0.00 0.00 0.44 0.00 0.44 0.04
#> TCGA.CZ.4865.11 6 0.3914 0.5276 0.10 0.00 0.00 0.06 0.00 0.78 0.06
#> TCGA.B0.4712.11 3 0.6611 0.0450 0.00 0.08 0.34 0.30 0.28 0.00 0.00
#> TCGA.CZ.5456.11 5 0.4939 0.1699 0.00 0.30 0.00 0.14 0.56 0.00 0.00
#> TCGA.B0.4697.11 6 0.5512 0.4343 0.26 0.02 0.00 0.06 0.00 0.60 0.06
#> TCGA.CZ.5452.11 3 0.2509 0.5263 0.00 0.00 0.88 0.06 0.04 0.00 0.02
#> TCGA.CZ.5455.11 3 0.1363 0.5395 0.00 0.02 0.94 0.00 0.04 0.00 0.00
#> TCGA.CZ.5457.11 5 0.5898 0.2341 0.00 0.24 0.02 0.02 0.58 0.02 0.12
cbind(get_classes(res, k = 8), get_membership(res, k = 8))
#> class entropy silhouette p1 p2 p3 p4 p5 p6 p7 p8
#> TCGA.CZ.5463.11 4 0.4975 0.219 0.00 0.28 0.00 0.56 0.14 0.02 0.00 0.00
#> TCGA.CZ.5468.11 5 0.3830 0.119 0.00 0.00 0.00 0.16 0.74 0.02 0.00 0.08
#> TCGA.CZ.5467.11 1 0.1557 0.605 0.92 0.00 0.00 0.00 0.00 0.02 0.06 0.00
#> TCGA.CZ.5470.11 7 0.4758 0.000 0.26 0.00 0.00 0.00 0.00 0.12 0.60 0.02
#> TCGA.CZ.5469.11 2 0.4460 0.000 0.00 0.70 0.12 0.12 0.06 0.00 0.00 0.00
#> TCGA.B0.4710.11 1 0.0471 0.649 0.98 0.00 0.00 0.02 0.00 0.00 0.00 0.00
#> TCGA.CZ.5453.11 4 0.2569 0.495 0.00 0.00 0.00 0.82 0.16 0.00 0.00 0.02
#> TCGA.CZ.4856.11 6 0.1563 0.511 0.10 0.00 0.00 0.00 0.00 0.90 0.00 0.00
#> TCGA.CZ.4866.11 1 0.5241 0.515 0.66 0.04 0.00 0.10 0.00 0.08 0.12 0.00
#> TCGA.CZ.5465.11 1 0.6306 0.311 0.48 0.16 0.00 0.02 0.00 0.12 0.22 0.00
#> TCGA.CZ.4863.11 1 0.1607 0.628 0.92 0.00 0.00 0.00 0.00 0.04 0.04 0.00
#> TCGA.CZ.5462.11 3 0.5708 0.279 0.00 0.20 0.56 0.16 0.02 0.00 0.06 0.00
#> TCGA.CZ.5458.11 5 0.2624 0.319 0.00 0.00 0.00 0.06 0.86 0.02 0.06 0.00
#> TCGA.B0.5119.11 8 0.3095 0.000 0.02 0.00 0.00 0.00 0.00 0.24 0.00 0.74
#> TCGA.CZ.4865.11 6 0.4750 0.202 0.06 0.00 0.02 0.02 0.00 0.68 0.02 0.20
#> TCGA.B0.4712.11 5 0.6219 0.125 0.00 0.12 0.30 0.00 0.48 0.02 0.06 0.02
#> TCGA.CZ.5456.11 5 0.4541 -0.081 0.00 0.46 0.02 0.00 0.48 0.02 0.00 0.02
#> TCGA.B0.4697.11 6 0.6509 0.424 0.18 0.08 0.02 0.02 0.00 0.54 0.02 0.14
#> TCGA.CZ.5452.11 3 0.3454 0.614 0.00 0.02 0.80 0.02 0.04 0.00 0.12 0.00
#> TCGA.CZ.5455.11 3 0.1275 0.656 0.00 0.02 0.94 0.00 0.04 0.00 0.00 0.00
#> TCGA.CZ.5457.11 4 0.5984 0.266 0.00 0.10 0.00 0.44 0.38 0.02 0.02 0.04
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: Node05. Child nodes: Node0141-leaf , Node0142-leaf , Node0143-leaf , Node0144-leaf , Node0211-leaf , Node0212-leaf , Node0213 , Node0231-leaf , Node0232-leaf , Node0233-leaf , Node0411 , Node0412-leaf , Node0413-leaf , Node0431-leaf , Node0432-leaf , Node0433-leaf , Node0511-leaf , Node0512-leaf , Node0541-leaf , Node0542-leaf , Node0543-leaf , Node0621-leaf , Node0622-leaf , Node0623-leaf .
The object with results only for a single top-value method and a single partitioning method can be extracted as:
res = res_rh["054"]
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 18 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 0.477 0.928 0.933 0.4635 0.529 0.529
#> 3 3 0.948 0.988 0.994 0.3997 0.824 0.667
#> 4 4 0.791 0.690 0.868 0.1238 0.967 0.907
#> 5 5 0.778 0.868 0.933 0.0769 0.837 0.519
#> 6 6 0.850 0.782 0.912 0.0486 1.000 1.000
#> 7 7 0.876 0.657 0.857 0.0377 0.954 0.774
#> 8 8 0.850 0.632 0.874 0.0225 0.928 0.593
suggest_best_k() suggests the best \(k\) based on these statistics. The rules are as follows:
suggest_best_k(res)
#> [1] 3
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.B0.4827.11 1 0.722 0.824 0.80 0.20
#> TCGA.CZ.5454.11 1 0.000 0.946 1.00 0.00
#> TCGA.BP.5170.11 1 0.000 0.946 1.00 0.00
#> TCGA.B0.4813.11 2 0.529 0.971 0.12 0.88
#> TCGA.BP.5195.11 1 0.000 0.946 1.00 0.00
#> TCGA.BP.5010.11 1 0.000 0.946 1.00 0.00
#> TCGA.CJ.4902.11 1 0.000 0.946 1.00 0.00
#> TCGA.CZ.4859.11 1 0.722 0.824 0.80 0.20
#> TCGA.CZ.5461.11 1 0.000 0.946 1.00 0.00
#> TCGA.CJ.4908.11 1 0.000 0.946 1.00 0.00
#> TCGA.CJ.4920.11 2 0.000 0.861 0.00 1.00
#> TCGA.B0.4845.11 2 0.529 0.971 0.12 0.88
#> TCGA.CZ.4853.11 1 0.000 0.946 1.00 0.00
#> TCGA.B0.4816.11 1 0.000 0.946 1.00 0.00
#> TCGA.A3.3373.11 1 0.722 0.824 0.80 0.20
#> TCGA.B0.4688.11 2 0.529 0.971 0.12 0.88
#> TCGA.B0.4828.11 2 0.529 0.971 0.12 0.88
#> TCGA.CJ.4912.11 2 0.529 0.971 0.12 0.88
cbind(get_classes(res, k = 3), get_membership(res, k = 3))
#> class entropy silhouette p1 p2 p3
#> TCGA.B0.4827.11 3 0.000 1.000 0 0.0 1.0
#> TCGA.CZ.5454.11 1 0.000 1.000 1 0.0 0.0
#> TCGA.BP.5170.11 1 0.000 1.000 1 0.0 0.0
#> TCGA.B0.4813.11 2 0.000 0.980 0 1.0 0.0
#> TCGA.BP.5195.11 1 0.000 1.000 1 0.0 0.0
#> TCGA.BP.5010.11 1 0.000 1.000 1 0.0 0.0
#> TCGA.CJ.4902.11 1 0.000 1.000 1 0.0 0.0
#> TCGA.CZ.4859.11 3 0.000 1.000 0 0.0 1.0
#> TCGA.CZ.5461.11 1 0.000 1.000 1 0.0 0.0
#> TCGA.CJ.4908.11 1 0.000 1.000 1 0.0 0.0
#> TCGA.CJ.4920.11 2 0.296 0.889 0 0.9 0.1
#> TCGA.B0.4845.11 2 0.000 0.980 0 1.0 0.0
#> TCGA.CZ.4853.11 1 0.000 1.000 1 0.0 0.0
#> TCGA.B0.4816.11 1 0.000 1.000 1 0.0 0.0
#> TCGA.A3.3373.11 3 0.000 1.000 0 0.0 1.0
#> TCGA.B0.4688.11 2 0.000 0.980 0 1.0 0.0
#> TCGA.B0.4828.11 2 0.000 0.980 0 1.0 0.0
#> TCGA.CJ.4912.11 2 0.000 0.980 0 1.0 0.0
cbind(get_classes(res, k = 4), get_membership(res, k = 4))
#> class entropy silhouette p1 p2 p3 p4
#> TCGA.B0.4827.11 3 0.000 1.000 0.00 0.00 1 0.00
#> TCGA.CZ.5454.11 1 0.000 0.796 1.00 0.00 0 0.00
#> TCGA.BP.5170.11 1 0.000 0.796 1.00 0.00 0 0.00
#> TCGA.B0.4813.11 2 0.234 0.689 0.00 0.90 0 0.10
#> TCGA.BP.5195.11 1 0.499 0.392 0.52 0.00 0 0.48
#> TCGA.BP.5010.11 1 0.499 0.392 0.52 0.00 0 0.48
#> TCGA.CJ.4902.11 1 0.000 0.796 1.00 0.00 0 0.00
#> TCGA.CZ.4859.11 3 0.000 1.000 0.00 0.00 1 0.00
#> TCGA.CZ.5461.11 1 0.000 0.796 1.00 0.00 0 0.00
#> TCGA.CJ.4908.11 1 0.000 0.796 1.00 0.00 0 0.00
#> TCGA.CJ.4920.11 2 0.491 0.377 0.00 0.58 0 0.42
#> TCGA.B0.4845.11 4 0.491 0.000 0.00 0.42 0 0.58
#> TCGA.CZ.4853.11 1 0.499 0.392 0.52 0.00 0 0.48
#> TCGA.B0.4816.11 1 0.000 0.796 1.00 0.00 0 0.00
#> TCGA.A3.3373.11 3 0.000 1.000 0.00 0.00 1 0.00
#> TCGA.B0.4688.11 2 0.000 0.799 0.00 1.00 0 0.00
#> TCGA.B0.4828.11 2 0.000 0.799 0.00 1.00 0 0.00
#> TCGA.CJ.4912.11 2 0.000 0.799 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.B0.4827.11 3 0.202 0.910 0.00 0.00 0.9 0.10 0.00
#> TCGA.CZ.5454.11 1 0.000 0.985 1.00 0.00 0.0 0.00 0.00
#> TCGA.BP.5170.11 1 0.173 0.920 0.92 0.00 0.0 0.00 0.08
#> TCGA.B0.4813.11 2 0.262 0.851 0.00 0.88 0.0 0.10 0.02
#> TCGA.BP.5195.11 4 0.311 0.880 0.20 0.00 0.0 0.80 0.00
#> TCGA.BP.5010.11 4 0.410 0.865 0.20 0.00 0.0 0.76 0.04
#> TCGA.CJ.4902.11 1 0.000 0.985 1.00 0.00 0.0 0.00 0.00
#> TCGA.CZ.4859.11 3 0.000 0.956 0.00 0.00 1.0 0.00 0.00
#> TCGA.CZ.5461.11 1 0.000 0.985 1.00 0.00 0.0 0.00 0.00
#> TCGA.CJ.4908.11 1 0.000 0.985 1.00 0.00 0.0 0.00 0.00
#> TCGA.CJ.4920.11 5 0.252 0.000 0.00 0.14 0.0 0.00 0.86
#> TCGA.B0.4845.11 4 0.262 0.631 0.00 0.10 0.0 0.88 0.02
#> TCGA.CZ.4853.11 4 0.311 0.880 0.20 0.00 0.0 0.80 0.00
#> TCGA.B0.4816.11 1 0.000 0.985 1.00 0.00 0.0 0.00 0.00
#> TCGA.A3.3373.11 3 0.000 0.956 0.00 0.00 1.0 0.00 0.00
#> TCGA.B0.4688.11 2 0.000 0.952 0.00 1.00 0.0 0.00 0.00
#> TCGA.B0.4828.11 2 0.000 0.952 0.00 1.00 0.0 0.00 0.00
#> TCGA.CJ.4912.11 2 0.000 0.952 0.00 1.00 0.0 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.B0.4827.11 3 0.1814 0.909 0.10 0.0 0.9 0.00 0.00 0.00
#> TCGA.CZ.5454.11 6 0.0000 0.977 0.00 0.0 0.0 0.00 0.00 1.00
#> TCGA.BP.5170.11 6 0.2725 0.874 0.02 0.0 0.0 0.06 0.04 0.88
#> TCGA.B0.4813.11 2 0.4482 0.423 0.36 0.6 0.0 0.04 0.00 0.00
#> TCGA.BP.5195.11 4 0.0937 0.875 0.00 0.0 0.0 0.96 0.00 0.04
#> TCGA.BP.5010.11 4 0.4162 0.799 0.12 0.0 0.0 0.78 0.06 0.04
#> TCGA.CJ.4902.11 6 0.0000 0.977 0.00 0.0 0.0 0.00 0.00 1.00
#> TCGA.CZ.4859.11 3 0.0000 0.956 0.00 0.0 1.0 0.00 0.00 0.00
#> TCGA.CZ.5461.11 6 0.0000 0.977 0.00 0.0 0.0 0.00 0.00 1.00
#> TCGA.CJ.4908.11 6 0.0000 0.977 0.00 0.0 0.0 0.00 0.00 1.00
#> TCGA.CJ.4920.11 5 0.1814 0.000 0.00 0.1 0.0 0.00 0.90 0.00
#> TCGA.B0.4845.11 4 0.2454 0.762 0.16 0.0 0.0 0.84 0.00 0.00
#> TCGA.CZ.4853.11 4 0.0937 0.875 0.00 0.0 0.0 0.96 0.00 0.04
#> TCGA.B0.4816.11 6 0.0000 0.977 0.00 0.0 0.0 0.00 0.00 1.00
#> TCGA.A3.3373.11 3 0.0000 0.956 0.00 0.0 1.0 0.00 0.00 0.00
#> TCGA.B0.4688.11 2 0.0000 0.692 0.00 1.0 0.0 0.00 0.00 0.00
#> TCGA.B0.4828.11 2 0.0000 0.692 0.00 1.0 0.0 0.00 0.00 0.00
#> TCGA.CJ.4912.11 2 0.3756 0.387 0.40 0.6 0.0 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.B0.4827.11 3 0.2376 0.870 0.00 0.02 0.86 0.00 0.00 0.00 0.12
#> TCGA.CZ.5454.11 6 0.0000 0.882 0.00 0.00 0.00 0.00 0.00 1.00 0.00
#> TCGA.BP.5170.11 6 0.5002 0.193 0.00 0.12 0.00 0.40 0.00 0.48 0.00
#> TCGA.B0.4813.11 7 0.4177 0.306 0.18 0.12 0.00 0.00 0.00 0.00 0.70
#> TCGA.BP.5195.11 4 0.0000 0.712 0.00 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.BP.5010.11 4 0.3546 0.336 0.00 0.46 0.00 0.54 0.00 0.00 0.00
#> TCGA.CJ.4902.11 6 0.0000 0.882 0.00 0.00 0.00 0.00 0.00 1.00 0.00
#> TCGA.CZ.4859.11 3 0.0000 0.937 0.00 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.CZ.5461.11 6 0.0000 0.882 0.00 0.00 0.00 0.00 0.00 1.00 0.00
#> TCGA.CJ.4908.11 6 0.0863 0.861 0.00 0.00 0.00 0.00 0.04 0.96 0.00
#> TCGA.CJ.4920.11 5 0.0863 0.000 0.04 0.00 0.00 0.00 0.96 0.00 0.00
#> TCGA.B0.4845.11 7 0.3459 0.108 0.00 0.00 0.00 0.40 0.00 0.00 0.60
#> TCGA.CZ.4853.11 4 0.0000 0.712 0.00 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.B0.4816.11 6 0.0000 0.882 0.00 0.00 0.00 0.00 0.00 1.00 0.00
#> TCGA.A3.3373.11 3 0.0000 0.937 0.00 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.B0.4688.11 1 0.0000 0.840 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.B0.4828.11 1 0.0000 0.840 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.CJ.4912.11 1 0.3841 0.650 0.68 0.28 0.00 0.00 0.00 0.00 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.B0.4827.11 3 0.414 0.672 0.00 0.22 0.66 0.00 0 0.00 0.00 0.12
#> TCGA.CZ.5454.11 6 0.000 0.977 0.00 0.00 0.00 0.00 0 1.00 0.00 0.00
#> TCGA.BP.5170.11 4 0.544 0.309 0.00 0.08 0.00 0.56 0 0.28 0.02 0.06
#> TCGA.B0.4813.11 7 0.343 0.478 0.14 0.10 0.00 0.00 0 0.00 0.76 0.00
#> TCGA.BP.5195.11 4 0.000 0.540 0.00 0.00 0.00 1.00 0 0.00 0.00 0.00
#> TCGA.BP.5010.11 2 0.324 0.000 0.00 0.60 0.00 0.40 0 0.00 0.00 0.00
#> TCGA.CJ.4902.11 6 0.000 0.977 0.00 0.00 0.00 0.00 0 1.00 0.00 0.00
#> TCGA.CZ.4859.11 3 0.000 0.824 0.00 0.00 1.00 0.00 0 0.00 0.00 0.00
#> TCGA.CZ.5461.11 6 0.000 0.977 0.00 0.00 0.00 0.00 0 1.00 0.00 0.00
#> TCGA.CJ.4908.11 6 0.156 0.903 0.00 0.00 0.00 0.00 0 0.90 0.00 0.10
#> TCGA.CJ.4920.11 5 0.000 0.000 0.00 0.00 0.00 0.00 1 0.00 0.00 0.00
#> TCGA.B0.4845.11 7 0.377 0.388 0.00 0.00 0.00 0.22 0 0.00 0.70 0.08
#> TCGA.CZ.4853.11 4 0.000 0.540 0.00 0.00 0.00 1.00 0 0.00 0.00 0.00
#> TCGA.B0.4816.11 6 0.000 0.977 0.00 0.00 0.00 0.00 0 1.00 0.00 0.00
#> TCGA.A3.3373.11 3 0.128 0.824 0.00 0.00 0.94 0.00 0 0.00 0.04 0.02
#> TCGA.B0.4688.11 1 0.000 1.000 1.00 0.00 0.00 0.00 0 0.00 0.00 0.00
#> TCGA.B0.4828.11 1 0.000 1.000 1.00 0.00 0.00 0.00 0 0.00 0.00 0.00
#> TCGA.CJ.4912.11 8 0.319 0.000 0.38 0.00 0.00 0.00 0 0.00 0.00 0.62
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-leaf , Node012-leaf , Node013-leaf , Node014 , Node021 , Node022-leaf , Node023 , Node041 , Node042-leaf , Node043 , Node051 , Node052-leaf , Node053-leaf , Node054 , Node061-leaf , Node062 , Node063-leaf , Node071-leaf , Node072-leaf , Node073-leaf .
The object with results only for a single top-value method and a single partitioning method can be extracted as:
res = res_rh["06"]
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 55 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 8.
#>
#> 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 0.50824 0.492 0.492
#> 3 3 0.968 0.965 0.985 0.08860 0.954 0.906
#> 4 4 0.940 0.896 0.968 0.04805 0.982 0.961
#> 5 5 0.913 0.894 0.960 0.03476 0.970 0.931
#> 6 6 0.934 0.856 0.951 0.02664 0.999 0.997
#> 7 7 0.928 0.849 0.955 0.00729 0.999 0.998
#> 8 8 0.922 0.812 0.947 0.02890 0.966 0.915
suggest_best_k() suggests the best \(k\) based on these statistics. The rules are as follows:
suggest_best_k(res)
#> [1] 8
#> 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.B0.4823.01 1 0 1 1 0
#> TCGA.BP.5181.01 2 0 1 0 1
#> TCGA.DV.5574.01 1 0 1 1 0
#> TCGA.B4.5377.01 2 0 1 0 1
#> TCGA.B0.5705.01 2 0 1 0 1
#> TCGA.BP.5186.01 2 0 1 0 1
#> TCGA.EU.5904.01 2 0 1 0 1
#> TCGA.BP.5182.01 1 0 1 1 0
#> TCGA.B0.5695.01 2 0 1 0 1
#> TCGA.B0.5691.01 2 0 1 0 1
#> TCGA.CW.6093.01 1 0 1 1 0
#> TCGA.B0.5119.01 2 0 1 0 1
#> TCGA.BP.5192.01 1 0 1 1 0
#> TCGA.B0.5707.01 2 0 1 0 1
#> TCGA.EU.5906.01 1 0 1 1 0
#> TCGA.DV.5575.01 2 0 1 0 1
#> TCGA.B0.5690.01 2 0 1 0 1
#> TCGA.B0.5110.01 2 0 1 0 1
#> TCGA.B0.5700.01 1 0 1 1 0
#> TCGA.A3.3376.01 1 0 1 1 0
#> TCGA.BP.5174.01 2 0 1 0 1
#> TCGA.CZ.5986.01 1 0 1 1 0
#> TCGA.AK.3454.01 1 0 1 1 0
#> TCGA.CZ.4859.01 2 0 1 0 1
#> TCGA.A3.A6NL.01 2 0 1 0 1
#> TCGA.B4.5835.01 2 0 1 0 1
#> TCGA.A3.A8OW.01 1 0 1 1 0
#> TCGA.DV.5569.01 2 0 1 0 1
#> TCGA.B8.5545.01 1 0 1 1 0
#> TCGA.B0.5709.01 2 0 1 0 1
#> TCGA.CZ.5457.01 1 0 1 1 0
#> TCGA.A3.A8CQ.01 2 0 1 0 1
#> TCGA.DV.5573.01 1 0 1 1 0
#> TCGA.B8.5165.01 1 0 1 1 0
#> TCGA.CW.5583.01 2 0 1 0 1
#> TCGA.GK.A6C7.01 2 0 1 0 1
#> TCGA.B8.5552.01 2 0 1 0 1
#> TCGA.CJ.4904.01 2 0 1 0 1
#> TCGA.BP.4993.01 1 0 1 1 0
#> TCGA.B4.5843.01 1 0 1 1 0
#> TCGA.CZ.4864.01 1 0 1 1 0
#> TCGA.B4.5834.01 1 0 1 1 0
#> TCGA.A3.A8OV.01 1 0 1 1 0
#> TCGA.A3.A6NJ.01 2 0 1 0 1
#> TCGA.A3.3370.01 2 0 1 0 1
#> TCGA.B0.4945.01 2 0 1 0 1
#> TCGA.CW.5589.01 1 0 1 1 0
#> TCGA.A3.3385.01 2 0 1 0 1
#> TCGA.CZ.5453.01 1 0 1 1 0
#> TCGA.BP.5173.01 1 0 1 1 0
#> TCGA.B8.A8YJ.01 2 0 1 0 1
#> TCGA.BP.5177.01 2 0 1 0 1
#> TCGA.B8.4621.01 1 0 1 1 0
#> TCGA.CW.6088.01 1 0 1 1 0
#> TCGA.3Z.A93Z.01 1 0 1 1 0
cbind(get_classes(res, k = 3), get_membership(res, k = 3))
#> class entropy silhouette p1 p2 p3
#> TCGA.B0.4823.01 1 0.000 0.978 1.00 0 0.00
#> TCGA.BP.5181.01 2 0.000 1.000 0.00 1 0.00
#> TCGA.DV.5574.01 1 0.000 0.978 1.00 0 0.00
#> TCGA.B4.5377.01 2 0.000 1.000 0.00 1 0.00
#> TCGA.B0.5705.01 2 0.000 1.000 0.00 1 0.00
#> TCGA.BP.5186.01 2 0.000 1.000 0.00 1 0.00
#> TCGA.EU.5904.01 2 0.000 1.000 0.00 1 0.00
#> TCGA.BP.5182.01 3 0.480 0.853 0.22 0 0.78
#> TCGA.B0.5695.01 2 0.000 1.000 0.00 1 0.00
#> TCGA.B0.5691.01 2 0.000 1.000 0.00 1 0.00
#> TCGA.CW.6093.01 1 0.000 0.978 1.00 0 0.00
#> TCGA.B0.5119.01 2 0.000 1.000 0.00 1 0.00
#> TCGA.BP.5192.01 1 0.000 0.978 1.00 0 0.00
#> TCGA.B0.5707.01 2 0.000 1.000 0.00 1 0.00
#> TCGA.EU.5906.01 1 0.000 0.978 1.00 0 0.00
#> TCGA.DV.5575.01 2 0.000 1.000 0.00 1 0.00
#> TCGA.B0.5690.01 2 0.000 1.000 0.00 1 0.00
#> TCGA.B0.5110.01 2 0.000 1.000 0.00 1 0.00
#> TCGA.B0.5700.01 1 0.000 0.978 1.00 0 0.00
#> TCGA.A3.3376.01 1 0.000 0.978 1.00 0 0.00
#> TCGA.BP.5174.01 2 0.000 1.000 0.00 1 0.00
#> TCGA.CZ.5986.01 1 0.613 0.103 0.60 0 0.40
#> TCGA.AK.3454.01 1 0.000 0.978 1.00 0 0.00
#> TCGA.CZ.4859.01 2 0.000 1.000 0.00 1 0.00
#> TCGA.A3.A6NL.01 2 0.000 1.000 0.00 1 0.00
#> TCGA.B4.5835.01 2 0.000 1.000 0.00 1 0.00
#> TCGA.A3.A8OW.01 1 0.000 0.978 1.00 0 0.00
#> TCGA.DV.5569.01 2 0.000 1.000 0.00 1 0.00
#> TCGA.B8.5545.01 1 0.000 0.978 1.00 0 0.00
#> TCGA.B0.5709.01 2 0.000 1.000 0.00 1 0.00
#> TCGA.CZ.5457.01 3 0.000 0.765 0.00 0 1.00
#> TCGA.A3.A8CQ.01 2 0.000 1.000 0.00 1 0.00
#> TCGA.DV.5573.01 1 0.000 0.978 1.00 0 0.00
#> TCGA.B8.5165.01 1 0.000 0.978 1.00 0 0.00
#> TCGA.CW.5583.01 2 0.000 1.000 0.00 1 0.00
#> TCGA.GK.A6C7.01 2 0.000 1.000 0.00 1 0.00
#> TCGA.B8.5552.01 2 0.000 1.000 0.00 1 0.00
#> TCGA.CJ.4904.01 2 0.000 1.000 0.00 1 0.00
#> TCGA.BP.4993.01 1 0.000 0.978 1.00 0 0.00
#> TCGA.B4.5843.01 1 0.000 0.978 1.00 0 0.00
#> TCGA.CZ.4864.01 1 0.000 0.978 1.00 0 0.00
#> TCGA.B4.5834.01 1 0.000 0.978 1.00 0 0.00
#> TCGA.A3.A8OV.01 1 0.000 0.978 1.00 0 0.00
#> TCGA.A3.A6NJ.01 2 0.000 1.000 0.00 1 0.00
#> TCGA.A3.3370.01 2 0.000 1.000 0.00 1 0.00
#> TCGA.B0.4945.01 2 0.000 1.000 0.00 1 0.00
#> TCGA.CW.5589.01 1 0.000 0.978 1.00 0 0.00
#> TCGA.A3.3385.01 2 0.000 1.000 0.00 1 0.00
#> TCGA.CZ.5453.01 1 0.000 0.978 1.00 0 0.00
#> TCGA.BP.5173.01 1 0.000 0.978 1.00 0 0.00
#> TCGA.B8.A8YJ.01 2 0.000 1.000 0.00 1 0.00
#> TCGA.BP.5177.01 2 0.000 1.000 0.00 1 0.00
#> TCGA.B8.4621.01 3 0.480 0.853 0.22 0 0.78
#> TCGA.CW.6088.01 1 0.000 0.978 1.00 0 0.00
#> TCGA.3Z.A93Z.01 1 0.000 0.978 1.00 0 0.00
cbind(get_classes(res, k = 4), get_membership(res, k = 4))
#> class entropy silhouette p1 p2 p3 p4
#> TCGA.B0.4823.01 1 0.0000 0.921 1.00 0 0.00 0
#> TCGA.BP.5181.01 2 0.0000 1.000 0.00 1 0.00 0
#> TCGA.DV.5574.01 1 0.4624 0.512 0.66 0 0.34 0
#> TCGA.B4.5377.01 2 0.0000 1.000 0.00 1 0.00 0
#> TCGA.B0.5705.01 2 0.0000 1.000 0.00 1 0.00 0
#> TCGA.BP.5186.01 2 0.0000 1.000 0.00 1 0.00 0
#> TCGA.EU.5904.01 2 0.0000 1.000 0.00 1 0.00 0
#> TCGA.BP.5182.01 3 0.0000 0.614 0.00 0 1.00 0
#> TCGA.B0.5695.01 2 0.0000 1.000 0.00 1 0.00 0
#> TCGA.B0.5691.01 2 0.0000 1.000 0.00 1 0.00 0
#> TCGA.CW.6093.01 1 0.1211 0.895 0.96 0 0.04 0
#> TCGA.B0.5119.01 2 0.0000 1.000 0.00 1 0.00 0
#> TCGA.BP.5192.01 1 0.0000 0.921 1.00 0 0.00 0
#> TCGA.B0.5707.01 2 0.0000 1.000 0.00 1 0.00 0
#> TCGA.EU.5906.01 1 0.0000 0.921 1.00 0 0.00 0
#> TCGA.DV.5575.01 2 0.0000 1.000 0.00 1 0.00 0
#> TCGA.B0.5690.01 2 0.0000 1.000 0.00 1 0.00 0
#> TCGA.B0.5110.01 2 0.0000 1.000 0.00 1 0.00 0
#> TCGA.B0.5700.01 1 0.4624 0.485 0.66 0 0.34 0
#> TCGA.A3.3376.01 1 0.0000 0.921 1.00 0 0.00 0
#> TCGA.BP.5174.01 2 0.0000 1.000 0.00 1 0.00 0
#> TCGA.CZ.5986.01 3 0.4522 0.380 0.32 0 0.68 0
#> TCGA.AK.3454.01 1 0.0000 0.921 1.00 0 0.00 0
#> TCGA.CZ.4859.01 2 0.0000 1.000 0.00 1 0.00 0
#> TCGA.A3.A6NL.01 2 0.0000 1.000 0.00 1 0.00 0
#> TCGA.B4.5835.01 2 0.0000 1.000 0.00 1 0.00 0
#> TCGA.A3.A8OW.01 1 0.0000 0.921 1.00 0 0.00 0
#> TCGA.DV.5569.01 2 0.0000 1.000 0.00 1 0.00 0
#> TCGA.B8.5545.01 1 0.0000 0.921 1.00 0 0.00 0
#> TCGA.B0.5709.01 2 0.0000 1.000 0.00 1 0.00 0
#> TCGA.CZ.5457.01 4 0.0000 0.000 0.00 0 0.00 1
#> TCGA.A3.A8CQ.01 2 0.0000 1.000 0.00 1 0.00 0
#> TCGA.DV.5573.01 1 0.3400 0.768 0.82 0 0.18 0
#> TCGA.B8.5165.01 1 0.0000 0.921 1.00 0 0.00 0
#> TCGA.CW.5583.01 2 0.0000 1.000 0.00 1 0.00 0
#> TCGA.GK.A6C7.01 2 0.0000 1.000 0.00 1 0.00 0
#> TCGA.B8.5552.01 2 0.0000 1.000 0.00 1 0.00 0
#> TCGA.CJ.4904.01 2 0.0000 1.000 0.00 1 0.00 0
#> TCGA.BP.4993.01 1 0.0000 0.921 1.00 0 0.00 0
#> TCGA.B4.5843.01 1 0.0000 0.921 1.00 0 0.00 0
#> TCGA.CZ.4864.01 1 0.4624 0.501 0.66 0 0.34 0
#> TCGA.B4.5834.01 1 0.0000 0.921 1.00 0 0.00 0
#> TCGA.A3.A8OV.01 1 0.0000 0.921 1.00 0 0.00 0
#> TCGA.A3.A6NJ.01 2 0.0000 1.000 0.00 1 0.00 0
#> TCGA.A3.3370.01 2 0.0000 1.000 0.00 1 0.00 0
#> TCGA.B0.4945.01 2 0.0000 1.000 0.00 1 0.00 0
#> TCGA.CW.5589.01 1 0.0000 0.921 1.00 0 0.00 0
#> TCGA.A3.3385.01 2 0.0000 1.000 0.00 1 0.00 0
#> TCGA.CZ.5453.01 1 0.0707 0.909 0.98 0 0.02 0
#> TCGA.BP.5173.01 1 0.3400 0.769 0.82 0 0.18 0
#> TCGA.B8.A8YJ.01 2 0.0000 1.000 0.00 1 0.00 0
#> TCGA.BP.5177.01 2 0.0000 1.000 0.00 1 0.00 0
#> TCGA.B8.4621.01 3 0.0000 0.614 0.00 0 1.00 0
#> TCGA.CW.6088.01 1 0.0000 0.921 1.00 0 0.00 0
#> TCGA.3Z.A93Z.01 1 0.0000 0.921 1.00 0 0.00 0
cbind(get_classes(res, k = 5), get_membership(res, k = 5))
#> class entropy silhouette p1 p2 p3 p4 p5
#> TCGA.B0.4823.01 1 0.0000 0.906 1.00 0 0.00 0 0.00
#> TCGA.BP.5181.01 2 0.0000 1.000 0.00 1 0.00 0 0.00
#> TCGA.DV.5574.01 1 0.5733 0.348 0.62 0 0.22 0 0.16
#> TCGA.B4.5377.01 2 0.0000 1.000 0.00 1 0.00 0 0.00
#> TCGA.B0.5705.01 2 0.0000 1.000 0.00 1 0.00 0 0.00
#> TCGA.BP.5186.01 2 0.0000 1.000 0.00 1 0.00 0 0.00
#> TCGA.EU.5904.01 2 0.0000 1.000 0.00 1 0.00 0 0.00
#> TCGA.BP.5182.01 3 0.0000 1.000 0.00 0 1.00 0 0.00
#> TCGA.B0.5695.01 2 0.0000 1.000 0.00 1 0.00 0 0.00
#> TCGA.B0.5691.01 2 0.0000 1.000 0.00 1 0.00 0 0.00
#> TCGA.CW.6093.01 1 0.3274 0.683 0.78 0 0.00 0 0.22
#> TCGA.B0.5119.01 2 0.0000 1.000 0.00 1 0.00 0 0.00
#> TCGA.BP.5192.01 1 0.0000 0.906 1.00 0 0.00 0 0.00
#> TCGA.B0.5707.01 2 0.0000 1.000 0.00 1 0.00 0 0.00
#> TCGA.EU.5906.01 1 0.0609 0.896 0.98 0 0.00 0 0.02
#> TCGA.DV.5575.01 2 0.0000 1.000 0.00 1 0.00 0 0.00
#> TCGA.B0.5690.01 2 0.0000 1.000 0.00 1 0.00 0 0.00
#> TCGA.B0.5110.01 2 0.0000 1.000 0.00 1 0.00 0 0.00
#> TCGA.B0.5700.01 5 0.3852 0.615 0.22 0 0.02 0 0.76
#> TCGA.A3.3376.01 1 0.0000 0.906 1.00 0 0.00 0 0.00
#> TCGA.BP.5174.01 2 0.0000 1.000 0.00 1 0.00 0 0.00
#> TCGA.CZ.5986.01 5 0.3421 0.390 0.08 0 0.08 0 0.84
#> TCGA.AK.3454.01 1 0.0000 0.906 1.00 0 0.00 0 0.00
#> TCGA.CZ.4859.01 2 0.0000 1.000 0.00 1 0.00 0 0.00
#> TCGA.A3.A6NL.01 2 0.0000 1.000 0.00 1 0.00 0 0.00
#> TCGA.B4.5835.01 2 0.0000 1.000 0.00 1 0.00 0 0.00
#> TCGA.A3.A8OW.01 1 0.0000 0.906 1.00 0 0.00 0 0.00
#> TCGA.DV.5569.01 2 0.0000 1.000 0.00 1 0.00 0 0.00
#> TCGA.B8.5545.01 1 0.0000 0.906 1.00 0 0.00 0 0.00
#> TCGA.B0.5709.01 2 0.0000 1.000 0.00 1 0.00 0 0.00
#> TCGA.CZ.5457.01 4 0.0000 0.000 0.00 0 0.00 1 0.00
#> TCGA.A3.A8CQ.01 2 0.0000 1.000 0.00 1 0.00 0 0.00
#> TCGA.DV.5573.01 1 0.4437 0.669 0.76 0 0.10 0 0.14
#> TCGA.B8.5165.01 1 0.0000 0.906 1.00 0 0.00 0 0.00
#> TCGA.CW.5583.01 2 0.0000 1.000 0.00 1 0.00 0 0.00
#> TCGA.GK.A6C7.01 2 0.0000 1.000 0.00 1 0.00 0 0.00
#> TCGA.B8.5552.01 2 0.0000 1.000 0.00 1 0.00 0 0.00
#> TCGA.CJ.4904.01 2 0.0000 1.000 0.00 1 0.00 0 0.00
#> TCGA.BP.4993.01 1 0.0000 0.906 1.00 0 0.00 0 0.00
#> TCGA.B4.5843.01 1 0.0000 0.906 1.00 0 0.00 0 0.00
#> TCGA.CZ.4864.01 5 0.4990 0.509 0.36 0 0.04 0 0.60
#> TCGA.B4.5834.01 1 0.0000 0.906 1.00 0 0.00 0 0.00
#> TCGA.A3.A8OV.01 1 0.0000 0.906 1.00 0 0.00 0 0.00
#> TCGA.A3.A6NJ.01 2 0.0000 1.000 0.00 1 0.00 0 0.00
#> TCGA.A3.3370.01 2 0.0000 1.000 0.00 1 0.00 0 0.00
#> TCGA.B0.4945.01 2 0.0000 1.000 0.00 1 0.00 0 0.00
#> TCGA.CW.5589.01 1 0.2020 0.831 0.90 0 0.00 0 0.10
#> TCGA.A3.3385.01 2 0.0000 1.000 0.00 1 0.00 0 0.00
#> TCGA.CZ.5453.01 1 0.2929 0.748 0.82 0 0.00 0 0.18
#> TCGA.BP.5173.01 1 0.4170 0.703 0.78 0 0.08 0 0.14
#> TCGA.B8.A8YJ.01 2 0.0000 1.000 0.00 1 0.00 0 0.00
#> TCGA.BP.5177.01 2 0.0000 1.000 0.00 1 0.00 0 0.00
#> TCGA.B8.4621.01 3 0.0000 1.000 0.00 0 1.00 0 0.00
#> TCGA.CW.6088.01 1 0.0609 0.896 0.98 0 0.00 0 0.02
#> TCGA.3Z.A93Z.01 1 0.0000 0.906 1.00 0 0.00 0 0.00
cbind(get_classes(res, k = 6), get_membership(res, k = 6))
#> class entropy silhouette p1 p2 p3 p4 p5 p6
#> TCGA.B0.4823.01 1 0.0547 0.865 0.98 0 0.00 0 0.02 0.00
#> TCGA.BP.5181.01 2 0.0000 1.000 0.00 1 0.00 0 0.00 0.00
#> TCGA.DV.5574.01 1 0.6554 0.274 0.50 0 0.18 0 0.06 0.26
#> TCGA.B4.5377.01 2 0.0000 1.000 0.00 1 0.00 0 0.00 0.00
#> TCGA.B0.5705.01 2 0.0000 1.000 0.00 1 0.00 0 0.00 0.00
#> TCGA.BP.5186.01 2 0.0000 1.000 0.00 1 0.00 0 0.00 0.00
#> TCGA.EU.5904.01 2 0.0000 1.000 0.00 1 0.00 0 0.00 0.00
#> TCGA.BP.5182.01 3 0.0000 1.000 0.00 0 1.00 0 0.00 0.00
#> TCGA.B0.5695.01 2 0.0000 1.000 0.00 1 0.00 0 0.00 0.00
#> TCGA.B0.5691.01 2 0.0000 1.000 0.00 1 0.00 0 0.00 0.00
#> TCGA.CW.6093.01 1 0.4834 0.546 0.64 0 0.00 0 0.10 0.26
#> TCGA.B0.5119.01 2 0.0000 1.000 0.00 1 0.00 0 0.00 0.00
#> TCGA.BP.5192.01 1 0.0000 0.873 1.00 0 0.00 0 0.00 0.00
#> TCGA.B0.5707.01 2 0.0000 1.000 0.00 1 0.00 0 0.00 0.00
#> TCGA.EU.5906.01 1 0.1865 0.836 0.92 0 0.00 0 0.04 0.04
#> TCGA.DV.5575.01 2 0.0000 1.000 0.00 1 0.00 0 0.00 0.00
#> TCGA.B0.5690.01 2 0.0000 1.000 0.00 1 0.00 0 0.00 0.00
#> TCGA.B0.5110.01 2 0.0000 1.000 0.00 1 0.00 0 0.00 0.00
#> TCGA.B0.5700.01 5 0.3647 0.286 0.00 0 0.00 0 0.64 0.36
#> TCGA.A3.3376.01 1 0.0000 0.873 1.00 0 0.00 0 0.00 0.00
#> TCGA.BP.5174.01 2 0.0000 1.000 0.00 1 0.00 0 0.00 0.00
#> TCGA.CZ.5986.01 5 0.2403 0.428 0.02 0 0.04 0 0.90 0.04
#> TCGA.AK.3454.01 1 0.0000 0.873 1.00 0 0.00 0 0.00 0.00
#> TCGA.CZ.4859.01 2 0.0000 1.000 0.00 1 0.00 0 0.00 0.00
#> TCGA.A3.A6NL.01 2 0.0000 1.000 0.00 1 0.00 0 0.00 0.00
#> TCGA.B4.5835.01 2 0.0000 1.000 0.00 1 0.00 0 0.00 0.00
#> TCGA.A3.A8OW.01 1 0.0000 0.873 1.00 0 0.00 0 0.00 0.00
#> TCGA.DV.5569.01 2 0.0000 1.000 0.00 1 0.00 0 0.00 0.00
#> TCGA.B8.5545.01 1 0.0000 0.873 1.00 0 0.00 0 0.00 0.00
#> TCGA.B0.5709.01 2 0.0000 1.000 0.00 1 0.00 0 0.00 0.00
#> TCGA.CZ.5457.01 4 0.0000 0.000 0.00 0 0.00 1 0.00 0.00
#> TCGA.A3.A8CQ.01 2 0.0000 1.000 0.00 1 0.00 0 0.00 0.00
#> TCGA.DV.5573.01 1 0.5735 0.486 0.60 0 0.08 0 0.06 0.26
#> TCGA.B8.5165.01 1 0.0000 0.873 1.00 0 0.00 0 0.00 0.00
#> TCGA.CW.5583.01 2 0.0000 1.000 0.00 1 0.00 0 0.00 0.00
#> TCGA.GK.A6C7.01 2 0.0000 1.000 0.00 1 0.00 0 0.00 0.00
#> TCGA.B8.5552.01 2 0.0000 1.000 0.00 1 0.00 0 0.00 0.00
#> TCGA.CJ.4904.01 2 0.0000 1.000 0.00 1 0.00 0 0.00 0.00
#> TCGA.BP.4993.01 1 0.0000 0.873 1.00 0 0.00 0 0.00 0.00
#> TCGA.B4.5843.01 1 0.0000 0.873 1.00 0 0.00 0 0.00 0.00
#> TCGA.CZ.4864.01 6 0.1807 0.000 0.06 0 0.00 0 0.02 0.92
#> TCGA.B4.5834.01 1 0.0000 0.873 1.00 0 0.00 0 0.00 0.00
#> TCGA.A3.A8OV.01 1 0.0000 0.873 1.00 0 0.00 0 0.00 0.00
#> TCGA.A3.A6NJ.01 2 0.0000 1.000 0.00 1 0.00 0 0.00 0.00
#> TCGA.A3.3370.01 2 0.0000 1.000 0.00 1 0.00 0 0.00 0.00
#> TCGA.B0.4945.01 2 0.0000 1.000 0.00 1 0.00 0 0.00 0.00
#> TCGA.CW.5589.01 1 0.2474 0.805 0.88 0 0.00 0 0.04 0.08
#> TCGA.A3.3385.01 2 0.0000 1.000 0.00 1 0.00 0 0.00 0.00
#> TCGA.CZ.5453.01 1 0.3829 0.695 0.76 0 0.00 0 0.06 0.18
#> TCGA.BP.5173.01 1 0.6129 0.413 0.56 0 0.12 0 0.06 0.26
#> TCGA.B8.A8YJ.01 2 0.0000 1.000 0.00 1 0.00 0 0.00 0.00
#> TCGA.BP.5177.01 2 0.0000 1.000 0.00 1 0.00 0 0.00 0.00
#> TCGA.B8.4621.01 3 0.0000 1.000 0.00 0 1.00 0 0.00 0.00
#> TCGA.CW.6088.01 1 0.0547 0.866 0.98 0 0.00 0 0.00 0.02
#> TCGA.3Z.A93Z.01 1 0.0000 0.873 1.00 0 0.00 0 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.B0.4823.01 1 0.1363 0.864 0.94 0 0.00 0 0.04 0.02 0.00
#> TCGA.BP.5181.01 2 0.0000 1.000 0.00 1 0.00 0 0.00 0.00 0.00
#> TCGA.DV.5574.01 1 0.6502 0.275 0.44 0 0.12 0 0.28 0.16 0.00
#> TCGA.B4.5377.01 2 0.0000 1.000 0.00 1 0.00 0 0.00 0.00 0.00
#> TCGA.B0.5705.01 2 0.0000 1.000 0.00 1 0.00 0 0.00 0.00 0.00
#> TCGA.BP.5186.01 2 0.0000 1.000 0.00 1 0.00 0 0.00 0.00 0.00
#> TCGA.EU.5904.01 2 0.0000 1.000 0.00 1 0.00 0 0.00 0.00 0.00
#> TCGA.BP.5182.01 3 0.0000 1.000 0.00 0 1.00 0 0.00 0.00 0.00
#> TCGA.B0.5695.01 2 0.0000 1.000 0.00 1 0.00 0 0.00 0.00 0.00
#> TCGA.B0.5691.01 2 0.0000 1.000 0.00 1 0.00 0 0.00 0.00 0.00
#> TCGA.CW.6093.01 1 0.3985 0.697 0.72 0 0.00 0 0.18 0.10 0.00
#> TCGA.B0.5119.01 2 0.0000 1.000 0.00 1 0.00 0 0.00 0.00 0.00
#> TCGA.BP.5192.01 1 0.0000 0.879 1.00 0 0.00 0 0.00 0.00 0.00
#> TCGA.B0.5707.01 2 0.0000 1.000 0.00 1 0.00 0 0.00 0.00 0.00
#> TCGA.EU.5906.01 1 0.1166 0.864 0.94 0 0.00 0 0.06 0.00 0.00
#> TCGA.DV.5575.01 2 0.0000 1.000 0.00 1 0.00 0 0.00 0.00 0.00
#> TCGA.B0.5690.01 2 0.0000 1.000 0.00 1 0.00 0 0.00 0.00 0.00
#> TCGA.B0.5110.01 2 0.0000 1.000 0.00 1 0.00 0 0.00 0.00 0.00
#> TCGA.B0.5700.01 5 0.2081 0.000 0.00 0 0.00 0 0.86 0.00 0.14
#> TCGA.A3.3376.01 1 0.0863 0.872 0.96 0 0.00 0 0.04 0.00 0.00
#> TCGA.BP.5174.01 2 0.0000 1.000 0.00 1 0.00 0 0.00 0.00 0.00
#> TCGA.CZ.5986.01 7 0.0000 0.000 0.00 0 0.00 0 0.00 0.00 1.00
#> TCGA.AK.3454.01 1 0.0000 0.879 1.00 0 0.00 0 0.00 0.00 0.00
#> TCGA.CZ.4859.01 2 0.0000 1.000 0.00 1 0.00 0 0.00 0.00 0.00
#> TCGA.A3.A6NL.01 2 0.0000 1.000 0.00 1 0.00 0 0.00 0.00 0.00
#> TCGA.B4.5835.01 2 0.0000 1.000 0.00 1 0.00 0 0.00 0.00 0.00
#> TCGA.A3.A8OW.01 1 0.0000 0.879 1.00 0 0.00 0 0.00 0.00 0.00
#> TCGA.DV.5569.01 2 0.0000 1.000 0.00 1 0.00 0 0.00 0.00 0.00
#> TCGA.B8.5545.01 1 0.0863 0.872 0.96 0 0.00 0 0.04 0.00 0.00
#> TCGA.B0.5709.01 2 0.0000 1.000 0.00 1 0.00 0 0.00 0.00 0.00
#> TCGA.CZ.5457.01 4 0.0000 0.000 0.00 0 0.00 1 0.00 0.00 0.00
#> TCGA.A3.A8CQ.01 2 0.0000 1.000 0.00 1 0.00 0 0.00 0.00 0.00
#> TCGA.DV.5573.01 1 0.6187 0.363 0.48 0 0.08 0 0.28 0.16 0.00
#> TCGA.B8.5165.01 1 0.0504 0.875 0.98 0 0.00 0 0.02 0.00 0.00
#> TCGA.CW.5583.01 2 0.0000 1.000 0.00 1 0.00 0 0.00 0.00 0.00
#> TCGA.GK.A6C7.01 2 0.0000 1.000 0.00 1 0.00 0 0.00 0.00 0.00
#> TCGA.B8.5552.01 2 0.0000 1.000 0.00 1 0.00 0 0.00 0.00 0.00
#> TCGA.CJ.4904.01 2 0.0000 1.000 0.00 1 0.00 0 0.00 0.00 0.00
#> TCGA.BP.4993.01 1 0.0000 0.879 1.00 0 0.00 0 0.00 0.00 0.00
#> TCGA.B4.5843.01 1 0.0000 0.879 1.00 0 0.00 0 0.00 0.00 0.00
#> TCGA.CZ.4864.01 6 0.0504 0.000 0.00 0 0.00 0 0.00 0.98 0.02
#> TCGA.B4.5834.01 1 0.0000 0.879 1.00 0 0.00 0 0.00 0.00 0.00
#> TCGA.A3.A8OV.01 1 0.0000 0.879 1.00 0 0.00 0 0.00 0.00 0.00
#> TCGA.A3.A6NJ.01 2 0.0000 1.000 0.00 1 0.00 0 0.00 0.00 0.00
#> TCGA.A3.3370.01 2 0.0000 1.000 0.00 1 0.00 0 0.00 0.00 0.00
#> TCGA.B0.4945.01 2 0.0000 1.000 0.00 1 0.00 0 0.00 0.00 0.00
#> TCGA.CW.5589.01 1 0.2512 0.816 0.86 0 0.00 0 0.10 0.04 0.00
#> TCGA.A3.3385.01 2 0.0000 1.000 0.00 1 0.00 0 0.00 0.00 0.00
#> TCGA.CZ.5453.01 1 0.3011 0.779 0.82 0 0.00 0 0.12 0.06 0.00
#> TCGA.BP.5173.01 1 0.5775 0.503 0.56 0 0.08 0 0.24 0.12 0.00
#> TCGA.B8.A8YJ.01 2 0.0000 1.000 0.00 1 0.00 0 0.00 0.00 0.00
#> TCGA.BP.5177.01 2 0.0000 1.000 0.00 1 0.00 0 0.00 0.00 0.00
#> TCGA.B8.4621.01 3 0.0000 1.000 0.00 0 1.00 0 0.00 0.00 0.00
#> TCGA.CW.6088.01 1 0.0000 0.879 1.00 0 0.00 0 0.00 0.00 0.00
#> TCGA.3Z.A93Z.01 1 0.0000 0.879 1.00 0 0.00 0 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.B0.4823.01 1 0.1947 0.7488 0.86 0 0.00 0 0.00 0.00 0.00 0.14
#> TCGA.BP.5181.01 2 0.0000 1.0000 0.00 1 0.00 0 0.00 0.00 0.00 0.00
#> TCGA.DV.5574.01 8 0.2856 0.8269 0.20 0 0.02 0 0.00 0.00 0.00 0.78
#> TCGA.B4.5377.01 2 0.0000 1.0000 0.00 1 0.00 0 0.00 0.00 0.00 0.00
#> TCGA.B0.5705.01 2 0.0000 1.0000 0.00 1 0.00 0 0.00 0.00 0.00 0.00
#> TCGA.BP.5186.01 2 0.0000 1.0000 0.00 1 0.00 0 0.00 0.00 0.00 0.00
#> TCGA.EU.5904.01 2 0.0000 1.0000 0.00 1 0.00 0 0.00 0.00 0.00 0.00
#> TCGA.BP.5182.01 3 0.2224 0.8638 0.00 0 0.86 0 0.00 0.02 0.00 0.12
#> TCGA.B0.5695.01 2 0.0000 1.0000 0.00 1 0.00 0 0.00 0.00 0.00 0.00
#> TCGA.B0.5691.01 2 0.0000 1.0000 0.00 1 0.00 0 0.00 0.00 0.00 0.00
#> TCGA.CW.6093.01 1 0.4403 -0.4244 0.48 0 0.00 0 0.08 0.00 0.00 0.44
#> TCGA.B0.5119.01 2 0.0000 1.0000 0.00 1 0.00 0 0.00 0.00 0.00 0.00
#> TCGA.BP.5192.01 1 0.0000 0.8354 1.00 0 0.00 0 0.00 0.00 0.00 0.00
#> TCGA.B0.5707.01 2 0.0000 1.0000 0.00 1 0.00 0 0.00 0.00 0.00 0.00
#> TCGA.EU.5906.01 1 0.2267 0.7040 0.82 0 0.00 0 0.00 0.00 0.00 0.18
#> TCGA.DV.5575.01 2 0.0000 1.0000 0.00 1 0.00 0 0.00 0.00 0.00 0.00
#> TCGA.B0.5690.01 2 0.0000 1.0000 0.00 1 0.00 0 0.00 0.00 0.00 0.00
#> TCGA.B0.5110.01 2 0.0000 1.0000 0.00 1 0.00 0 0.00 0.00 0.00 0.00
#> TCGA.B0.5700.01 5 0.0471 0.0000 0.00 0 0.00 0 0.98 0.00 0.00 0.02
#> TCGA.A3.3376.01 1 0.1765 0.7716 0.88 0 0.00 0 0.00 0.00 0.00 0.12
#> TCGA.BP.5174.01 2 0.0000 1.0000 0.00 1 0.00 0 0.00 0.00 0.00 0.00
#> TCGA.CZ.5986.01 7 0.0000 0.0000 0.00 0 0.00 0 0.00 0.00 1.00 0.00
#> TCGA.AK.3454.01 1 0.0000 0.8354 1.00 0 0.00 0 0.00 0.00 0.00 0.00
#> TCGA.CZ.4859.01 2 0.0000 1.0000 0.00 1 0.00 0 0.00 0.00 0.00 0.00
#> TCGA.A3.A6NL.01 2 0.0000 1.0000 0.00 1 0.00 0 0.00 0.00 0.00 0.00
#> TCGA.B4.5835.01 2 0.0000 1.0000 0.00 1 0.00 0 0.00 0.00 0.00 0.00
#> TCGA.A3.A8OW.01 1 0.0000 0.8354 1.00 0 0.00 0 0.00 0.00 0.00 0.00
#> TCGA.DV.5569.01 2 0.0000 1.0000 0.00 1 0.00 0 0.00 0.00 0.00 0.00
#> TCGA.B8.5545.01 1 0.1765 0.7688 0.88 0 0.00 0 0.00 0.00 0.00 0.12
#> TCGA.B0.5709.01 2 0.0000 1.0000 0.00 1 0.00 0 0.00 0.00 0.00 0.00
#> TCGA.CZ.5457.01 4 0.0000 0.0000 0.00 0 0.00 1 0.00 0.00 0.00 0.00
#> TCGA.A3.A8CQ.01 2 0.0000 1.0000 0.00 1 0.00 0 0.00 0.00 0.00 0.00
#> TCGA.DV.5573.01 8 0.2756 0.8756 0.26 0 0.00 0 0.00 0.00 0.00 0.74
#> TCGA.B8.5165.01 1 0.0000 0.8354 1.00 0 0.00 0 0.00 0.00 0.00 0.00
#> TCGA.CW.5583.01 2 0.0000 1.0000 0.00 1 0.00 0 0.00 0.00 0.00 0.00
#> TCGA.GK.A6C7.01 2 0.0000 1.0000 0.00 1 0.00 0 0.00 0.00 0.00 0.00
#> TCGA.B8.5552.01 2 0.0000 1.0000 0.00 1 0.00 0 0.00 0.00 0.00 0.00
#> TCGA.CJ.4904.01 2 0.0000 1.0000 0.00 1 0.00 0 0.00 0.00 0.00 0.00
#> TCGA.BP.4993.01 1 0.0000 0.8354 1.00 0 0.00 0 0.00 0.00 0.00 0.00
#> TCGA.B4.5843.01 1 0.0000 0.8354 1.00 0 0.00 0 0.00 0.00 0.00 0.00
#> TCGA.CZ.4864.01 6 0.0471 0.0000 0.00 0 0.00 0 0.00 0.98 0.00 0.02
#> TCGA.B4.5834.01 1 0.0000 0.8354 1.00 0 0.00 0 0.00 0.00 0.00 0.00
#> TCGA.A3.A8OV.01 1 0.0000 0.8354 1.00 0 0.00 0 0.00 0.00 0.00 0.00
#> TCGA.A3.A6NJ.01 2 0.0000 1.0000 0.00 1 0.00 0 0.00 0.00 0.00 0.00
#> TCGA.A3.3370.01 2 0.0000 1.0000 0.00 1 0.00 0 0.00 0.00 0.00 0.00
#> TCGA.B0.4945.01 2 0.0000 1.0000 0.00 1 0.00 0 0.00 0.00 0.00 0.00
#> TCGA.CW.5589.01 1 0.2981 0.5801 0.76 0 0.00 0 0.02 0.00 0.00 0.22
#> TCGA.A3.3385.01 2 0.0000 1.0000 0.00 1 0.00 0 0.00 0.00 0.00 0.00
#> TCGA.CZ.5453.01 1 0.5403 -0.0273 0.50 0 0.02 0 0.08 0.00 0.04 0.36
#> TCGA.BP.5173.01 8 0.3015 0.8142 0.32 0 0.00 0 0.00 0.00 0.00 0.68
#> TCGA.B8.A8YJ.01 2 0.0000 1.0000 0.00 1 0.00 0 0.00 0.00 0.00 0.00
#> TCGA.BP.5177.01 2 0.0000 1.0000 0.00 1 0.00 0 0.00 0.00 0.00 0.00
#> TCGA.B8.4621.01 3 0.0471 0.8631 0.00 0 0.98 0 0.00 0.00 0.00 0.02
#> TCGA.CW.6088.01 1 0.1091 0.8126 0.94 0 0.00 0 0.00 0.00 0.00 0.06
#> TCGA.3Z.A93Z.01 1 0.0808 0.8087 0.96 0 0.00 0 0.00 0.00 0.00 0.04
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: Node06. Child nodes: Node0141-leaf , Node0142-leaf , Node0143-leaf , Node0144-leaf , Node0211-leaf , Node0212-leaf , Node0213 , Node0231-leaf , Node0232-leaf , Node0233-leaf , Node0411 , Node0412-leaf , Node0413-leaf , Node0431-leaf , Node0432-leaf , Node0433-leaf , Node0511-leaf , Node0512-leaf , Node0541-leaf , Node0542-leaf , Node0543-leaf , Node0621-leaf , Node0622-leaf , Node0623-leaf .
The object with results only for a single top-value method and a single partitioning method can be extracted as:
res = res_rh["062"]
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 29 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 0.952 0.983 0.4560 0.557 0.557
#> 3 3 1.000 0.971 0.983 0.4414 0.729 0.538
#> 4 4 0.755 0.784 0.894 0.0494 0.946 0.848
#> 5 5 0.712 0.698 0.864 0.1250 0.823 0.497
#> 6 6 0.712 0.631 0.832 0.0509 0.857 0.473
#> 7 7 0.701 0.513 0.683 0.0167 0.865 0.427
#> 8 8 0.718 0.471 0.779 0.0205 0.889 0.451
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.BP.5181.01 1 0.000 0.973 1.00 0.00
#> TCGA.B4.5377.01 2 0.000 1.000 0.00 1.00
#> TCGA.B0.5705.01 2 0.000 1.000 0.00 1.00
#> TCGA.BP.5186.01 1 0.000 0.973 1.00 0.00
#> TCGA.EU.5904.01 1 0.000 0.973 1.00 0.00
#> TCGA.B0.5695.01 2 0.000 1.000 0.00 1.00
#> TCGA.B0.5691.01 1 0.000 0.973 1.00 0.00
#> TCGA.B0.5119.01 2 0.000 1.000 0.00 1.00
#> TCGA.B0.5707.01 1 0.000 0.973 1.00 0.00
#> TCGA.DV.5575.01 1 0.000 0.973 1.00 0.00
#> TCGA.B0.5690.01 1 0.000 0.973 1.00 0.00
#> TCGA.B0.5110.01 1 0.995 0.156 0.54 0.46
#> TCGA.BP.5174.01 1 0.000 0.973 1.00 0.00
#> TCGA.CZ.4859.01 2 0.000 1.000 0.00 1.00
#> TCGA.A3.A6NL.01 1 0.000 0.973 1.00 0.00
#> TCGA.B4.5835.01 2 0.000 1.000 0.00 1.00
#> TCGA.DV.5569.01 1 0.000 0.973 1.00 0.00
#> TCGA.B0.5709.01 1 0.242 0.936 0.96 0.04
#> TCGA.A3.A8CQ.01 2 0.000 1.000 0.00 1.00
#> TCGA.CW.5583.01 1 0.000 0.973 1.00 0.00
#> TCGA.GK.A6C7.01 2 0.000 1.000 0.00 1.00
#> TCGA.B8.5552.01 1 0.000 0.973 1.00 0.00
#> TCGA.CJ.4904.01 1 0.000 0.973 1.00 0.00
#> TCGA.A3.A6NJ.01 1 0.000 0.973 1.00 0.00
#> TCGA.A3.3370.01 1 0.000 0.973 1.00 0.00
#> TCGA.B0.4945.01 1 0.000 0.973 1.00 0.00
#> TCGA.A3.3385.01 2 0.000 1.000 0.00 1.00
#> TCGA.B8.A8YJ.01 1 0.000 0.973 1.00 0.00
#> TCGA.BP.5177.01 1 0.000 0.973 1.00 0.00
cbind(get_classes(res, k = 3), get_membership(res, k = 3))
#> class entropy silhouette p1 p2 p3
#> TCGA.BP.5181.01 1 0.0000 0.970 1.00 0.00 0.00
#> TCGA.B4.5377.01 2 0.0000 0.994 0.00 1.00 0.00
#> TCGA.B0.5705.01 2 0.0000 0.994 0.00 1.00 0.00
#> TCGA.BP.5186.01 3 0.0892 0.976 0.02 0.00 0.98
#> TCGA.EU.5904.01 1 0.0000 0.970 1.00 0.00 0.00
#> TCGA.B0.5695.01 2 0.0000 0.994 0.00 1.00 0.00
#> TCGA.B0.5691.01 1 0.0000 0.970 1.00 0.00 0.00
#> TCGA.B0.5119.01 2 0.0000 0.994 0.00 1.00 0.00
#> TCGA.B0.5707.01 3 0.0000 0.993 0.00 0.00 1.00
#> TCGA.DV.5575.01 1 0.0000 0.970 1.00 0.00 0.00
#> TCGA.B0.5690.01 1 0.2066 0.942 0.94 0.00 0.06
#> TCGA.B0.5110.01 3 0.0000 0.993 0.00 0.00 1.00
#> TCGA.BP.5174.01 1 0.2537 0.927 0.92 0.00 0.08
#> TCGA.CZ.4859.01 2 0.0892 0.984 0.00 0.98 0.02
#> TCGA.A3.A6NL.01 1 0.0000 0.970 1.00 0.00 0.00
#> TCGA.B4.5835.01 3 0.0000 0.993 0.00 0.00 1.00
#> TCGA.DV.5569.01 1 0.0000 0.970 1.00 0.00 0.00
#> TCGA.B0.5709.01 3 0.0000 0.993 0.00 0.00 1.00
#> TCGA.A3.A8CQ.01 2 0.0892 0.984 0.00 0.98 0.02
#> TCGA.CW.5583.01 1 0.0000 0.970 1.00 0.00 0.00
#> TCGA.GK.A6C7.01 3 0.0000 0.993 0.00 0.00 1.00
#> TCGA.B8.5552.01 1 0.1529 0.954 0.96 0.00 0.04
#> TCGA.CJ.4904.01 1 0.4291 0.810 0.82 0.00 0.18
#> TCGA.A3.A6NJ.01 3 0.0000 0.993 0.00 0.00 1.00
#> TCGA.A3.3370.01 1 0.1529 0.954 0.96 0.00 0.04
#> TCGA.B0.4945.01 1 0.0000 0.970 1.00 0.00 0.00
#> TCGA.A3.3385.01 2 0.0000 0.994 0.00 1.00 0.00
#> TCGA.B8.A8YJ.01 3 0.0892 0.976 0.02 0.00 0.98
#> TCGA.BP.5177.01 1 0.0000 0.970 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.BP.5181.01 1 0.0000 0.875 1.00 0.00 0.00 0.00
#> TCGA.B4.5377.01 2 0.0707 0.872 0.00 0.98 0.00 0.02
#> TCGA.B0.5705.01 2 0.4134 0.648 0.00 0.74 0.00 0.26
#> TCGA.BP.5186.01 3 0.7095 0.392 0.26 0.18 0.56 0.00
#> TCGA.EU.5904.01 1 0.0000 0.875 1.00 0.00 0.00 0.00
#> TCGA.B0.5695.01 4 0.0707 1.000 0.00 0.02 0.00 0.98
#> TCGA.B0.5691.01 1 0.1637 0.863 0.94 0.00 0.06 0.00
#> TCGA.B0.5119.01 2 0.1637 0.854 0.00 0.94 0.00 0.06
#> TCGA.B0.5707.01 3 0.0707 0.789 0.00 0.00 0.98 0.02
#> TCGA.DV.5575.01 1 0.1211 0.869 0.96 0.00 0.04 0.00
#> TCGA.B0.5690.01 1 0.4134 0.747 0.74 0.00 0.26 0.00
#> TCGA.B0.5110.01 3 0.4994 0.113 0.00 0.48 0.52 0.00
#> TCGA.BP.5174.01 1 0.4522 0.665 0.68 0.00 0.32 0.00
#> TCGA.CZ.4859.01 2 0.0000 0.873 0.00 1.00 0.00 0.00
#> TCGA.A3.A6NL.01 1 0.0000 0.875 1.00 0.00 0.00 0.00
#> TCGA.B4.5835.01 3 0.2335 0.747 0.00 0.06 0.92 0.02
#> TCGA.DV.5569.01 1 0.0000 0.875 1.00 0.00 0.00 0.00
#> TCGA.B0.5709.01 3 0.0707 0.789 0.00 0.00 0.98 0.02
#> TCGA.A3.A8CQ.01 2 0.0000 0.873 0.00 1.00 0.00 0.00
#> TCGA.CW.5583.01 1 0.0000 0.875 1.00 0.00 0.00 0.00
#> TCGA.GK.A6C7.01 2 0.4079 0.675 0.00 0.80 0.18 0.02
#> TCGA.B8.5552.01 1 0.3975 0.767 0.76 0.00 0.24 0.00
#> TCGA.CJ.4904.01 1 0.4797 0.731 0.72 0.02 0.26 0.00
#> TCGA.A3.A6NJ.01 3 0.0000 0.789 0.00 0.00 1.00 0.00
#> TCGA.A3.3370.01 1 0.3975 0.767 0.76 0.00 0.24 0.00
#> TCGA.B0.4945.01 1 0.0000 0.875 1.00 0.00 0.00 0.00
#> TCGA.A3.3385.01 4 0.0707 1.000 0.00 0.02 0.00 0.98
#> TCGA.B8.A8YJ.01 3 0.0000 0.789 0.00 0.00 1.00 0.00
#> TCGA.BP.5177.01 1 0.0000 0.875 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.BP.5181.01 1 0.0000 0.809 1.00 0.00 0.00 0.00 0.00
#> TCGA.B4.5377.01 2 0.0609 0.826 0.00 0.98 0.00 0.00 0.02
#> TCGA.B0.5705.01 2 0.4126 0.395 0.00 0.62 0.00 0.38 0.00
#> TCGA.BP.5186.01 5 0.1043 0.679 0.00 0.00 0.04 0.00 0.96
#> TCGA.EU.5904.01 1 0.0000 0.809 1.00 0.00 0.00 0.00 0.00
#> TCGA.B0.5695.01 4 0.0000 1.000 0.00 0.00 0.00 1.00 0.00
#> TCGA.B0.5691.01 1 0.4227 0.305 0.58 0.00 0.00 0.00 0.42
#> TCGA.B0.5119.01 2 0.1216 0.819 0.00 0.96 0.00 0.02 0.02
#> TCGA.B0.5707.01 3 0.0609 0.896 0.00 0.00 0.98 0.00 0.02
#> TCGA.DV.5575.01 1 0.4182 0.363 0.60 0.00 0.00 0.00 0.40
#> TCGA.B0.5690.01 5 0.2732 0.687 0.16 0.00 0.00 0.00 0.84
#> TCGA.B0.5110.01 5 0.5414 0.340 0.00 0.20 0.14 0.00 0.66
#> TCGA.BP.5174.01 5 0.3922 0.682 0.18 0.00 0.04 0.00 0.78
#> TCGA.CZ.4859.01 2 0.0000 0.828 0.00 1.00 0.00 0.00 0.00
#> TCGA.A3.A6NL.01 1 0.1410 0.798 0.94 0.00 0.00 0.00 0.06
#> TCGA.B4.5835.01 3 0.0000 0.898 0.00 0.00 1.00 0.00 0.00
#> TCGA.DV.5569.01 1 0.0000 0.809 1.00 0.00 0.00 0.00 0.00
#> TCGA.B0.5709.01 3 0.0000 0.898 0.00 0.00 1.00 0.00 0.00
#> TCGA.A3.A8CQ.01 2 0.0000 0.828 0.00 1.00 0.00 0.00 0.00
#> TCGA.CW.5583.01 1 0.0000 0.809 1.00 0.00 0.00 0.00 0.00
#> TCGA.GK.A6C7.01 2 0.5245 0.528 0.00 0.64 0.08 0.00 0.28
#> TCGA.B8.5552.01 5 0.3983 0.437 0.34 0.00 0.00 0.00 0.66
#> TCGA.CJ.4904.01 5 0.1043 0.709 0.04 0.00 0.00 0.00 0.96
#> TCGA.A3.A6NJ.01 5 0.3684 0.460 0.00 0.00 0.28 0.00 0.72
#> TCGA.A3.3370.01 5 0.3895 0.483 0.32 0.00 0.00 0.00 0.68
#> TCGA.B0.4945.01 1 0.1043 0.805 0.96 0.00 0.00 0.00 0.04
#> TCGA.A3.3385.01 4 0.0000 1.000 0.00 0.00 0.00 1.00 0.00
#> TCGA.B8.A8YJ.01 3 0.3109 0.727 0.00 0.00 0.80 0.00 0.20
#> TCGA.BP.5177.01 1 0.3561 0.618 0.74 0.00 0.00 0.00 0.26
cbind(get_classes(res, k = 6), get_membership(res, k = 6))
#> class entropy silhouette p1 p2 p3 p4 p5 p6
#> TCGA.BP.5181.01 1 0.0000 0.9048 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.B4.5377.01 2 0.0000 0.8525 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.B0.5705.01 4 0.4731 0.2592 0.00 0.40 0.02 0.56 0.02 0.00
#> TCGA.BP.5186.01 5 0.4310 -0.0189 0.00 0.00 0.02 0.00 0.54 0.44
#> TCGA.EU.5904.01 1 0.0000 0.9048 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.B0.5695.01 4 0.0000 0.7565 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.B0.5691.01 5 0.3309 0.5011 0.28 0.00 0.00 0.00 0.72 0.00
#> TCGA.B0.5119.01 2 0.3382 0.7419 0.00 0.84 0.00 0.04 0.04 0.08
#> TCGA.B0.5707.01 3 0.0547 0.8515 0.00 0.00 0.98 0.00 0.02 0.00
#> TCGA.DV.5575.01 5 0.3578 0.4189 0.34 0.00 0.00 0.00 0.66 0.00
#> TCGA.B0.5690.01 5 0.2956 0.5452 0.04 0.00 0.00 0.00 0.84 0.12
#> TCGA.B0.5110.01 6 0.5356 0.7291 0.00 0.08 0.08 0.00 0.16 0.68
#> TCGA.BP.5174.01 5 0.2094 0.6205 0.08 0.00 0.00 0.00 0.90 0.02
#> TCGA.CZ.4859.01 2 0.2350 0.8668 0.00 0.88 0.00 0.00 0.02 0.10
#> TCGA.A3.A6NL.01 1 0.2941 0.6971 0.78 0.00 0.00 0.00 0.22 0.00
#> TCGA.B4.5835.01 3 0.0000 0.8549 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.DV.5569.01 1 0.0547 0.8995 0.98 0.00 0.00 0.00 0.02 0.00
#> TCGA.B0.5709.01 3 0.0000 0.8549 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.A3.A8CQ.01 2 0.2350 0.8668 0.00 0.88 0.00 0.00 0.02 0.10
#> TCGA.CW.5583.01 1 0.0000 0.9048 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.GK.A6C7.01 6 0.2794 0.7279 0.00 0.08 0.06 0.00 0.00 0.86
#> TCGA.B8.5552.01 5 0.2048 0.6322 0.12 0.00 0.00 0.00 0.88 0.00
#> TCGA.CJ.4904.01 5 0.3851 0.0137 0.00 0.00 0.00 0.00 0.54 0.46
#> TCGA.A3.A6NJ.01 5 0.5769 -0.1995 0.00 0.00 0.18 0.00 0.46 0.36
#> TCGA.A3.3370.01 5 0.1814 0.6312 0.10 0.00 0.00 0.00 0.90 0.00
#> TCGA.B0.4945.01 1 0.2260 0.8201 0.86 0.00 0.00 0.00 0.14 0.00
#> TCGA.A3.3385.01 4 0.0000 0.7565 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.B8.A8YJ.01 3 0.3409 0.5638 0.00 0.00 0.70 0.00 0.30 0.00
#> TCGA.BP.5177.01 5 0.3706 0.3322 0.38 0.00 0.00 0.00 0.62 0.00
cbind(get_classes(res, k = 7), get_membership(res, k = 7))
#> class entropy silhouette p1 p2 p3 p4 p5 p6 p7
#> TCGA.BP.5181.01 1 0.2832 0.8919 0.76 0.00 0.00 0.00 0.24 0.00 0.00
#> TCGA.B4.5377.01 2 0.3841 0.0606 0.04 0.68 0.00 0.00 0.00 0.00 0.28
#> TCGA.B0.5705.01 4 0.5622 0.0664 0.00 0.22 0.00 0.52 0.00 0.02 0.24
#> TCGA.BP.5186.01 6 0.2081 0.6877 0.00 0.00 0.00 0.00 0.14 0.86 0.00
#> TCGA.EU.5904.01 1 0.3755 0.8466 0.64 0.00 0.00 0.00 0.34 0.00 0.02
#> TCGA.B0.5695.01 4 0.0000 0.7182 0.00 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.B0.5691.01 5 0.0863 0.6685 0.04 0.00 0.00 0.00 0.96 0.00 0.00
#> TCGA.B0.5119.01 7 0.4175 0.0000 0.00 0.38 0.00 0.04 0.00 0.00 0.58
#> TCGA.B0.5707.01 3 0.0000 0.7909 0.00 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.DV.5575.01 5 0.0863 0.6684 0.04 0.00 0.00 0.00 0.96 0.00 0.00
#> TCGA.B0.5690.01 6 0.3909 0.4203 0.00 0.00 0.00 0.00 0.40 0.58 0.02
#> TCGA.B0.5110.01 6 0.3346 0.5790 0.02 0.04 0.04 0.00 0.00 0.84 0.06
#> TCGA.BP.5174.01 5 0.3887 0.3049 0.02 0.00 0.00 0.00 0.70 0.26 0.02
#> TCGA.CZ.4859.01 2 0.1664 0.5429 0.02 0.92 0.00 0.00 0.00 0.06 0.00
#> TCGA.A3.A6NL.01 5 0.3459 -0.1532 0.40 0.00 0.00 0.00 0.60 0.00 0.00
#> TCGA.B4.5835.01 3 0.0000 0.7909 0.00 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.DV.5569.01 1 0.3221 0.8784 0.68 0.00 0.00 0.00 0.32 0.00 0.00
#> TCGA.B0.5709.01 3 0.0000 0.7909 0.00 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.A3.A8CQ.01 2 0.3061 0.4715 0.06 0.84 0.00 0.00 0.00 0.02 0.08
#> TCGA.CW.5583.01 1 0.2832 0.8919 0.76 0.00 0.00 0.00 0.24 0.00 0.00
#> TCGA.GK.A6C7.01 6 0.5917 0.1914 0.08 0.10 0.00 0.00 0.00 0.48 0.34
#> TCGA.B8.5552.01 5 0.1363 0.6583 0.02 0.00 0.00 0.00 0.94 0.04 0.00
#> TCGA.CJ.4904.01 6 0.2422 0.6890 0.00 0.00 0.00 0.00 0.18 0.82 0.00
#> TCGA.A3.A6NJ.01 6 0.5218 0.5715 0.02 0.00 0.18 0.00 0.20 0.60 0.00
#> TCGA.A3.3370.01 5 0.0863 0.6671 0.00 0.00 0.00 0.00 0.96 0.04 0.00
#> TCGA.B0.4945.01 5 0.3546 -0.3791 0.46 0.00 0.00 0.00 0.54 0.00 0.00
#> TCGA.A3.3385.01 4 0.0000 0.7182 0.00 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.B8.A8YJ.01 3 0.4408 0.2690 0.02 0.00 0.52 0.00 0.44 0.02 0.00
#> TCGA.BP.5177.01 5 0.2081 0.5747 0.14 0.00 0.00 0.00 0.86 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.BP.5181.01 1 0.1275 0.6272 0.94 0.00 0.00 0.00 0.00 0.00 0.02 0.04
#> TCGA.B4.5377.01 2 0.5244 0.1539 0.00 0.48 0.00 0.00 0.00 0.02 0.34 0.16
#> TCGA.B0.5705.01 4 0.6362 0.0781 0.00 0.20 0.02 0.42 0.00 0.00 0.28 0.08
#> TCGA.BP.5186.01 6 0.3198 0.5762 0.00 0.02 0.00 0.00 0.26 0.72 0.00 0.00
#> TCGA.EU.5904.01 1 0.2534 0.7321 0.78 0.00 0.00 0.00 0.22 0.00 0.00 0.00
#> TCGA.B0.5695.01 4 0.0000 0.6891 0.00 0.00 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.B0.5691.01 5 0.2114 0.5649 0.16 0.00 0.00 0.00 0.84 0.00 0.00 0.00
#> TCGA.B0.5119.01 7 0.1563 0.0000 0.00 0.10 0.00 0.00 0.00 0.00 0.90 0.00
#> TCGA.B0.5707.01 3 0.0471 0.9645 0.00 0.00 0.98 0.00 0.02 0.00 0.00 0.00
#> TCGA.DV.5575.01 5 0.2114 0.5580 0.16 0.00 0.00 0.00 0.84 0.00 0.00 0.00
#> TCGA.B0.5690.01 5 0.3299 -0.2684 0.00 0.00 0.00 0.00 0.56 0.44 0.00 0.00
#> TCGA.B0.5110.01 6 0.2624 0.0172 0.00 0.00 0.06 0.00 0.00 0.86 0.02 0.06
#> TCGA.BP.5174.01 5 0.2888 0.4515 0.00 0.00 0.00 0.00 0.80 0.16 0.00 0.04
#> TCGA.CZ.4859.01 2 0.0471 0.5239 0.00 0.98 0.00 0.00 0.00 0.00 0.02 0.00
#> TCGA.A3.A6NL.01 1 0.3299 0.4261 0.56 0.00 0.00 0.00 0.44 0.00 0.00 0.00
#> TCGA.B4.5835.01 3 0.0471 0.9579 0.00 0.00 0.98 0.00 0.00 0.02 0.00 0.00
#> TCGA.DV.5569.01 1 0.2406 0.7375 0.80 0.00 0.00 0.00 0.20 0.00 0.00 0.00
#> TCGA.B0.5709.01 3 0.1408 0.9633 0.00 0.00 0.94 0.00 0.02 0.02 0.00 0.02
#> TCGA.A3.A8CQ.01 2 0.4443 0.4612 0.00 0.70 0.00 0.00 0.00 0.06 0.10 0.14
#> TCGA.CW.5583.01 1 0.0808 0.6453 0.96 0.00 0.00 0.00 0.00 0.00 0.00 0.04
#> TCGA.GK.A6C7.01 8 0.3943 0.0000 0.00 0.04 0.00 0.00 0.00 0.40 0.00 0.56
#> TCGA.B8.5552.01 5 0.0471 0.6374 0.02 0.00 0.00 0.00 0.98 0.00 0.00 0.00
#> TCGA.CJ.4904.01 6 0.2938 0.5859 0.00 0.00 0.00 0.00 0.30 0.70 0.00 0.00
#> TCGA.A3.A6NJ.01 6 0.5674 0.4328 0.00 0.00 0.20 0.00 0.24 0.50 0.00 0.06
#> TCGA.A3.3370.01 5 0.0808 0.6399 0.04 0.00 0.00 0.00 0.96 0.00 0.00 0.00
#> TCGA.B0.4945.01 1 0.3015 0.6553 0.68 0.00 0.00 0.00 0.32 0.00 0.00 0.00
#> TCGA.A3.3385.01 4 0.0000 0.6891 0.00 0.00 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.B8.A8YJ.01 5 0.4886 -0.1098 0.00 0.00 0.44 0.00 0.46 0.04 0.00 0.06
#> TCGA.BP.5177.01 5 0.3374 0.2714 0.30 0.00 0.00 0.00 0.68 0.02 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-leaf , Node012-leaf , Node013-leaf , Node014 , Node021 , Node022-leaf , Node023 , Node041 , Node042-leaf , Node043 , Node051 , Node052-leaf , Node053-leaf , Node054 , Node061-leaf , Node062 , Node063-leaf , Node071-leaf , Node072-leaf , Node073-leaf .
The object with results only for a single top-value method and a single partitioning method can be extracted as:
res = res_rh["07"]
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 'SD' 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 0.5279 0.473 0.473
#> 3 3 0.813 0.962 0.943 0.2129 0.868 0.721
#> 4 4 0.857 0.818 0.957 0.1128 0.945 0.839
#> 5 5 0.879 0.743 0.906 0.0658 1.000 1.000
#> 6 6 0.835 0.633 0.920 0.0449 0.934 0.769
#> 7 7 0.868 0.528 0.933 0.0515 0.956 0.800
#> 8 8 0.879 0.470 0.920 0.0390 0.967 0.812
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.B0.5098.01 2 0 1 0 1
#> TCGA.B0.4821.11 2 0 1 0 1
#> TCGA.B8.5546.01 2 0 1 0 1
#> TCGA.A3.3376.11 1 0 1 1 0
#> TCGA.B0.4699.01 1 0 1 1 0
#> TCGA.B0.5109.11 1 0 1 1 0
#> TCGA.B0.5702.01 1 0 1 1 0
#> TCGA.B0.5116.11 1 0 1 1 0
#> TCGA.CJ.5681.01 2 0 1 0 1
#> TCGA.B8.A54E.01 2 0 1 0 1
#> TCGA.6D.AA2E.01 2 0 1 0 1
#> TCGA.T7.A92I.01 2 0 1 0 1
#> TCGA.A3.A8OX.01 2 0 1 0 1
#> TCGA.BP.5202.11 1 0 1 1 0
cbind(get_classes(res, k = 3), get_membership(res, k = 3))
#> class entropy silhouette p1 p2 p3
#> TCGA.B0.5098.01 3 0.5216 1.000 0.00 0.26 0.74
#> TCGA.B0.4821.11 2 0.0000 0.995 0.00 1.00 0.00
#> TCGA.B8.5546.01 2 0.0892 0.972 0.00 0.98 0.02
#> TCGA.A3.3376.11 1 0.0000 0.955 1.00 0.00 0.00
#> TCGA.B0.4699.01 1 0.5216 0.743 0.74 0.00 0.26
#> TCGA.B0.5109.11 1 0.0000 0.955 1.00 0.00 0.00
#> TCGA.B0.5702.01 1 0.0000 0.955 1.00 0.00 0.00
#> TCGA.B0.5116.11 1 0.0000 0.955 1.00 0.00 0.00
#> TCGA.CJ.5681.01 3 0.5216 1.000 0.00 0.26 0.74
#> TCGA.B8.A54E.01 2 0.0000 0.995 0.00 1.00 0.00
#> TCGA.6D.AA2E.01 2 0.0000 0.995 0.00 1.00 0.00
#> TCGA.T7.A92I.01 2 0.0000 0.995 0.00 1.00 0.00
#> TCGA.A3.A8OX.01 2 0.0000 0.995 0.00 1.00 0.00
#> TCGA.BP.5202.11 1 0.0000 0.955 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.B0.5098.01 3 0.3975 0.611 0.00 0.24 0.76 0.00
#> TCGA.B0.4821.11 2 0.0000 0.933 0.00 1.00 0.00 0.00
#> TCGA.B8.5546.01 2 0.4134 0.642 0.00 0.74 0.26 0.00
#> TCGA.A3.3376.11 1 0.0000 0.995 1.00 0.00 0.00 0.00
#> TCGA.B0.4699.01 4 0.0707 0.000 0.02 0.00 0.00 0.98
#> TCGA.B0.5109.11 1 0.0000 0.995 1.00 0.00 0.00 0.00
#> TCGA.B0.5702.01 1 0.0707 0.979 0.98 0.00 0.00 0.02
#> TCGA.B0.5116.11 1 0.0000 0.995 1.00 0.00 0.00 0.00
#> TCGA.CJ.5681.01 3 0.0707 0.586 0.00 0.00 0.98 0.02
#> TCGA.B8.A54E.01 2 0.0000 0.933 0.00 1.00 0.00 0.00
#> TCGA.6D.AA2E.01 2 0.0707 0.930 0.00 0.98 0.02 0.00
#> TCGA.T7.A92I.01 2 0.0707 0.930 0.00 0.98 0.02 0.00
#> TCGA.A3.A8OX.01 2 0.0000 0.933 0.00 1.00 0.00 0.00
#> TCGA.BP.5202.11 1 0.0000 0.995 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.B0.5098.01 3 0.4262 0.574 0.00 0.00 0.56 0.00 0.44
#> TCGA.B0.4821.11 2 0.0000 0.871 0.00 1.00 0.00 0.00 0.00
#> TCGA.B8.5546.01 2 0.6459 0.212 0.00 0.42 0.18 0.40 0.00
#> TCGA.A3.3376.11 1 0.1732 0.928 0.92 0.00 0.00 0.00 0.08
#> TCGA.B0.4699.01 4 0.4182 0.000 0.00 0.00 0.00 0.60 0.40
#> TCGA.B0.5109.11 1 0.0000 0.957 1.00 0.00 0.00 0.00 0.00
#> TCGA.B0.5702.01 1 0.2280 0.899 0.88 0.00 0.00 0.00 0.12
#> TCGA.B0.5116.11 1 0.0000 0.957 1.00 0.00 0.00 0.00 0.00
#> TCGA.CJ.5681.01 3 0.0000 0.577 0.00 0.00 1.00 0.00 0.00
#> TCGA.B8.A54E.01 2 0.0609 0.870 0.00 0.98 0.00 0.02 0.00
#> TCGA.6D.AA2E.01 2 0.0609 0.870 0.00 0.98 0.00 0.02 0.00
#> TCGA.T7.A92I.01 2 0.1410 0.858 0.00 0.94 0.00 0.06 0.00
#> TCGA.A3.A8OX.01 2 0.0000 0.871 0.00 1.00 0.00 0.00 0.00
#> TCGA.BP.5202.11 1 0.0000 0.957 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.B0.5098.01 3 0.331 0.000 0.00 0.00 0.72 0 0.28 0.00
#> TCGA.B0.4821.11 2 0.000 0.975 0.00 1.00 0.00 0 0.00 0.00
#> TCGA.B8.5546.01 6 0.335 0.000 0.00 0.16 0.00 0 0.04 0.80
#> TCGA.A3.3376.11 1 0.279 0.830 0.86 0.00 0.08 0 0.00 0.06
#> TCGA.B0.4699.01 4 0.000 0.000 0.00 0.00 0.00 1 0.00 0.00
#> TCGA.B0.5109.11 1 0.000 0.870 1.00 0.00 0.00 0 0.00 0.00
#> TCGA.B0.5702.01 1 0.472 0.675 0.68 0.00 0.18 0 0.00 0.14
#> TCGA.B0.5116.11 1 0.000 0.870 1.00 0.00 0.00 0 0.00 0.00
#> TCGA.CJ.5681.01 5 0.000 0.000 0.00 0.00 0.00 0 1.00 0.00
#> TCGA.B8.A54E.01 2 0.000 0.975 0.00 1.00 0.00 0 0.00 0.00
#> TCGA.6D.AA2E.01 2 0.000 0.975 0.00 1.00 0.00 0 0.00 0.00
#> TCGA.T7.A92I.01 2 0.156 0.895 0.00 0.92 0.00 0 0.00 0.08
#> TCGA.A3.A8OX.01 2 0.000 0.975 0.00 1.00 0.00 0 0.00 0.00
#> TCGA.BP.5202.11 1 0.219 0.826 0.90 0.00 0.06 0 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.B0.5098.01 3 0.0000 0.000 0.00 0.00 1.00 0 0.00 0.00 0.00
#> TCGA.B0.4821.11 2 0.0000 0.955 0.00 1.00 0.00 0 0.00 0.00 0.00
#> TCGA.B8.5546.01 6 0.0863 0.000 0.00 0.04 0.00 0 0.00 0.96 0.00
#> TCGA.A3.3376.11 1 0.4772 0.357 0.60 0.00 0.00 0 0.04 0.04 0.32
#> TCGA.B0.4699.01 4 0.0000 0.000 0.00 0.00 0.00 1 0.00 0.00 0.00
#> TCGA.B0.5109.11 1 0.0000 0.805 1.00 0.00 0.00 0 0.00 0.00 0.00
#> TCGA.B0.5702.01 7 0.2422 0.000 0.18 0.00 0.00 0 0.00 0.00 0.82
#> TCGA.B0.5116.11 1 0.0000 0.805 1.00 0.00 0.00 0 0.00 0.00 0.00
#> TCGA.CJ.5681.01 5 0.1166 0.000 0.00 0.00 0.06 0 0.94 0.00 0.00
#> TCGA.B8.A54E.01 2 0.0000 0.955 0.00 1.00 0.00 0 0.00 0.00 0.00
#> TCGA.6D.AA2E.01 2 0.1006 0.941 0.00 0.96 0.00 0 0.02 0.02 0.00
#> TCGA.T7.A92I.01 2 0.2376 0.855 0.00 0.86 0.00 0 0.02 0.12 0.00
#> TCGA.A3.A8OX.01 2 0.0000 0.955 0.00 1.00 0.00 0 0.00 0.00 0.00
#> TCGA.BP.5202.11 1 0.1433 0.763 0.92 0.00 0.00 0 0.00 0.00 0.08
cbind(get_classes(res, k = 8), get_membership(res, k = 8))
#> class entropy silhouette p1 p2 p3 p4 p5 p6 p7 p8
#> TCGA.B0.5098.01 3 0.0471 0.000 0.00 0.00 0.98 0 0.02 0.00 0.00 0.00
#> TCGA.B0.4821.11 2 0.0471 0.883 0.00 0.98 0.00 0 0.00 0.02 0.00 0.00
#> TCGA.B8.5546.01 6 0.0471 0.000 0.00 0.02 0.00 0 0.00 0.98 0.00 0.00
#> TCGA.A3.3376.11 8 0.3922 0.000 0.30 0.00 0.00 0 0.00 0.00 0.06 0.64
#> TCGA.B0.4699.01 4 0.0000 0.000 0.00 0.00 0.00 1 0.00 0.00 0.00 0.00
#> TCGA.B0.5109.11 1 0.0000 0.810 1.00 0.00 0.00 0 0.00 0.00 0.00 0.00
#> TCGA.B0.5702.01 7 0.0471 0.000 0.02 0.00 0.00 0 0.00 0.00 0.98 0.00
#> TCGA.B0.5116.11 1 0.0471 0.814 0.98 0.00 0.00 0 0.00 0.00 0.02 0.00
#> TCGA.CJ.5681.01 5 0.0000 0.000 0.00 0.00 0.00 0 1.00 0.00 0.00 0.00
#> TCGA.B8.A54E.01 2 0.0000 0.891 0.00 1.00 0.00 0 0.00 0.00 0.00 0.00
#> TCGA.6D.AA2E.01 2 0.2725 0.837 0.00 0.82 0.00 0 0.00 0.04 0.00 0.14
#> TCGA.T7.A92I.01 2 0.3299 0.797 0.00 0.76 0.00 0 0.00 0.06 0.00 0.18
#> TCGA.A3.A8OX.01 2 0.0000 0.891 0.00 1.00 0.00 0 0.00 0.00 0.00 0.00
#> TCGA.BP.5202.11 1 0.3928 0.664 0.74 0.00 0.02 0 0.00 0.02 0.04 0.18
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
#> [65] annotate_1.70.0 circlize_0.4.13 KEGGREST_1.32.0 polylabelr_0.2.0
#> [69] pillar_1.6.1 rjson_0.2.20 codetools_0.2-18 stats4_4.1.0
#> [73] XML_3.99-0.6 glue_1.4.2 evaluate_0.14 png_0.1-7
#> [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
#> [97] AnnotationDbi_1.54.1 memoise_2.0.0 IRanges_2.26.0 cluster_2.1.2
#> [101] ellipsis_0.3.2 brew_1.0-6