Date: 2021-07-22 16:14:45 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 375938 rows and 571 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, 571 cols
#> |-- 01, 175 cols, 5878 signatures
#> | |-- 011, 58 cols, 1595 signatures
#> | | |-- 0111, 16 cols, 49 signatures (c)
#> | | |-- 0112, 17 cols, 5 signatures (c)
#> | | |-- 0113, 9 cols (b)
#> | | `-- 0114, 16 cols, 137 signatures (c)
#> | |-- 012, 24 cols, 385 signatures (c)
#> | |-- 013, 40 cols, 2027 signatures
#> | | |-- 0131, 19 cols, 41 signatures (c)
#> | | |-- 0132, 3 cols (b)
#> | | `-- 0133, 18 cols, 100 signatures (c)
#> | |-- 014, 17 cols, 2606 signatures
#> | | |-- 0141, 2 cols (b)
#> | | |-- 0142, 9 cols (b)
#> | | `-- 0143, 6 cols (b)
#> | `-- 015, 36 cols, 96 signatures (c)
#> |-- 02, 209 cols, 11281 signatures
#> | |-- 021, 43 cols, 3180 signatures
#> | | |-- 0211, 31 cols, 43 signatures (c)
#> | | `-- 0212, 12 cols, 0 signatures (c)
#> | |-- 022, 45 cols, 4441 signatures
#> | | |-- 0221, 9 cols (b)
#> | | |-- 0222, 22 cols, 33 signatures (c)
#> | | |-- 0223, 11 cols (b)
#> | | `-- 0224, 3 cols (b)
#> | |-- 023, 32 cols, 8600 signatures
#> | | |-- 0231, 9 cols (b)
#> | | |-- 0232, 13 cols, 3187 signatures
#> | | | |-- 02321, 11 cols (b)
#> | | | `-- 02322, 2 cols (b)
#> | | |-- 0233, 8 cols (b)
#> | | `-- 0234, 2 cols (b)
#> | |-- 024, 41 cols, 6634 signatures
#> | | |-- 0241, 21 cols, 3269 signatures
#> | | | |-- 02411, 8 cols (b)
#> | | | |-- 02412, 4 cols (b)
#> | | | |-- 02413, 5 cols (b)
#> | | | `-- 02414, 4 cols (b)
#> | | |-- 0242, 9 cols (b)
#> | | |-- 0243, 6 cols (b)
#> | | `-- 0244, 5 cols (b)
#> | `-- 025, 48 cols, 3159 signatures
#> | |-- 0251, 12 cols (a)
#> | `-- 0252, 36 cols, 341 signatures (c)
#> `-- 03, 187 cols, 3641 signatures
#> |-- 031, 54 cols, 1289 signatures
#> | |-- 0311, 23 cols, 1291 signatures
#> | | |-- 03111, 2 cols (b)
#> | | |-- 03112, 13 cols, 21 signatures (c)
#> | | `-- 03113, 8 cols (b)
#> | |-- 0312, 13 cols, 79 signatures (c)
#> | `-- 0313, 18 cols, 15 signatures (c)
#> |-- 032, 65 cols, 842 signatures (c)
#> |-- 033, 65 cols, 1662 signatures
#> | |-- 0331, 28 cols, 181 signatures (c)
#> | |-- 0332, 9 cols (b)
#> | `-- 0333, 28 cols, 295 signatures (c)
#> `-- 034, 3 cols (b)
#> Stop reason:
#> a) Mean silhouette score was too small
#> 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] 375938 571
All the methods that were tried:
res_rh@param$combination_method
#> [[1]]
#> [1] "SD" "kmeans"
#>
#> [[2]]
#> [1] "ATC" "kmeans"
#>
#> [[3]]
#> [1] "SD" "skmeans"
#>
#> [[4]]
#> [1] "ATC" "skmeans"
The density distribution for each sample is visualized as one column in the following heatmap. The clustering is based on the distance which is the Kolmogorov-Smirnov statistic between two distributions.
library(ComplexHeatmap)
densityHeatmap(mat, ylab = "value", cluster_columns = TRUE, show_column_names = FALSE,
mc.cores = 1)
Some values about the hierarchy:
all_nodes(res_rh)
#> [1] "0" "01" "011" "0111" "0112" "0113" "0114" "012" "013" "0131" "0132" "0133"
#> [13] "014" "0141" "0142" "0143" "015" "02" "021" "0211" "0212" "022" "0221" "0222"
#> [25] "0223" "0224" "023" "0231" "0232" "02321" "02322" "0233" "0234" "024" "0241" "02411"
#> [37] "02412" "02413" "02414" "0242" "0243" "0244" "025" "0251" "0252" "03" "031" "0311"
#> [49] "03111" "03112" "03113" "0312" "0313" "032" "033" "0331" "0332" "0333" "034"
all_leaves(res_rh)
#> [1] "0111" "0112" "0113" "0114" "012" "0131" "0132" "0133" "0141" "0142" "0143" "015"
#> [13] "0211" "0212" "0221" "0222" "0223" "0224" "0231" "02321" "02322" "0233" "0234" "02411"
#> [25] "02412" "02413" "02414" "0242" "0243" "0244" "0251" "0252" "03111" "03112" "03113" "0312"
#> [37] "0313" "032" "0331" "0332" "0333" "034"
node_info(res_rh)
#> id best_method depth best_k n_columns n_signatures p_signatures is_leaf
#> 1 0 SD:skmeans 1 3 571 3511 9.34e-03 FALSE
#> 2 01 ATC:skmeans 2 5 175 5878 1.56e-02 FALSE
#> 3 011 ATC:skmeans 3 4 58 1595 4.24e-03 FALSE
#> 4 0111 ATC:kmeans 4 2 16 49 1.30e-04 TRUE
#> 5 0112 ATC:skmeans 4 2 17 5 1.33e-05 TRUE
#> 6 0113 not applied 4 NA 9 NA NA TRUE
#> 7 0114 ATC:skmeans 4 2 16 137 3.64e-04 TRUE
#> 8 012 ATC:kmeans 3 2 24 385 1.02e-03 TRUE
#> 9 013 ATC:skmeans 3 3 40 2027 5.39e-03 FALSE
#> 10 0131 ATC:skmeans 4 2 19 41 1.09e-04 TRUE
#> 11 0132 not applied 4 NA 3 NA NA TRUE
#> 12 0133 ATC:kmeans 4 2 18 100 2.66e-04 TRUE
#> 13 014 ATC:skmeans 3 3 17 2606 6.93e-03 FALSE
#> 14 0141 not applied 4 NA 2 NA NA TRUE
#> 15 0142 not applied 4 NA 9 NA NA TRUE
#> 16 0143 not applied 4 NA 6 NA NA TRUE
#> 17 015 ATC:kmeans 3 2 36 96 2.55e-04 TRUE
#> 18 02 ATC:skmeans 2 5 209 11281 3.00e-02 FALSE
#> 19 021 ATC:kmeans 3 2 43 3180 8.46e-03 FALSE
#> 20 0211 ATC:skmeans 4 3 31 43 1.14e-04 TRUE
#> 21 0212 SD:kmeans 4 2 12 0 0.00e+00 TRUE
#> 22 022 ATC:kmeans 3 4 45 4441 1.18e-02 FALSE
#> 23 0221 not applied 4 NA 9 NA NA TRUE
#> 24 0222 ATC:skmeans 4 2 22 33 8.78e-05 TRUE
#> 25 0223 not applied 4 NA 11 NA NA TRUE
#> 26 0224 not applied 4 NA 3 NA NA TRUE
#> 27 023 ATC:skmeans 3 4 32 8600 2.29e-02 FALSE
#> 28 0231 not applied 4 NA 9 NA NA TRUE
#> 29 0232 SD:kmeans 4 2 13 3187 8.48e-03 FALSE
#> 30 02321 not applied 5 NA 11 NA NA TRUE
#> 31 02322 not applied 5 NA 2 NA NA TRUE
#> 32 0233 not applied 4 NA 8 NA NA TRUE
#> 33 0234 not applied 4 NA 2 NA NA TRUE
#> 34 024 ATC:skmeans 3 4 41 6634 1.76e-02 FALSE
#> 35 0241 ATC:kmeans 4 4 21 3269 8.70e-03 FALSE
#> 36 02411 not applied 5 NA 8 NA NA TRUE
#> 37 02412 not applied 5 NA 4 NA NA TRUE
#> 38 02413 not applied 5 NA 5 NA NA TRUE
#> 39 02414 not applied 5 NA 4 NA NA TRUE
#> 40 0242 not applied 4 NA 9 NA NA TRUE
#> 41 0243 not applied 4 NA 6 NA NA TRUE
#> 42 0244 not applied 4 NA 5 NA NA TRUE
#> 43 025 ATC:kmeans 3 2 48 3159 8.40e-03 FALSE
#> 44 0251 ATC:skmeans 4 2 12 NA NA TRUE
#> 45 0252 ATC:kmeans 4 2 36 341 9.07e-04 TRUE
#> 46 03 ATC:kmeans 2 4 187 3641 9.69e-03 FALSE
#> 47 031 ATC:skmeans 3 3 54 1289 3.43e-03 FALSE
#> 48 0311 ATC:skmeans 4 3 23 1291 3.43e-03 FALSE
#> 49 03111 not applied 5 NA 2 NA NA TRUE
#> 50 03112 ATC:kmeans 5 2 13 21 5.59e-05 TRUE
#> 51 03113 not applied 5 NA 8 NA NA TRUE
#> 52 0312 ATC:skmeans 4 2 13 79 2.10e-04 TRUE
#> 53 0313 ATC:skmeans 4 2 18 15 3.99e-05 TRUE
#> 54 032 ATC:skmeans 3 3 65 842 2.24e-03 TRUE
#> 55 033 ATC:skmeans 3 3 65 1662 4.42e-03 FALSE
#> 56 0331 ATC:kmeans 4 3 28 181 4.81e-04 TRUE
#> 57 0332 not applied 4 NA 9 NA NA TRUE
#> 58 0333 ATC:kmeans 4 3 28 295 7.85e-04 TRUE
#> 59 034 not applied 3 NA 3 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 | SD:skmeans | 7 | 0.93 | 0.85 | 0.91 | 571 | * | |
| Node01 | ATC:skmeans | 6 | 0.94 | 0.88 | 0.94 | 175 | * | |
| Node011 | ATC:skmeans | 4 | 1.00 | 0.97 | 0.98 | 58 | ** | |
| Node0111-leaf | ATC:kmeans | 2 | 1.00 | 1.00 | 1.00 | 16 | ** | |
| Node0112-leaf | ATC:skmeans | 2 | 0.76 | 0.92 | 0.96 | 17 | ||
| Node0113-leaf | not applied | 9 | ||||||
| Node0114-leaf | ATC:skmeans | 2 | 1.00 | 1.00 | 1.00 | 16 | ** | |
| Node012-leaf | ATC:kmeans | 2 | 1.00 | 1.00 | 1.00 | 24 | ** | |
| Node013 | ATC:skmeans | 3 | 0.99 | 0.97 | 0.98 | 40 | ** | |
| Node0131-leaf | ATC:skmeans | 2 | 0.72 | 0.98 | 0.97 | 19 | ||
| Node0132-leaf | not applied | 3 | ||||||
| Node0133-leaf | ATC:kmeans | 2 | 1.00 | 1.00 | 1.00 | 18 | ** | |
| Node014 | ATC:skmeans | 4 | 0.90 | 0.92 | 0.99 | 17 | * | |
| Node0141-leaf | not applied | 2 | ||||||
| Node0142-leaf | not applied | 9 | ||||||
| Node0143-leaf | not applied | 6 | ||||||
| Node015-leaf | ATC:kmeans | 2 | 0.65 | 0.96 | 0.96 | 36 | ||
| Node02 | ATC:skmeans | 5 | 1.00 | 0.98 | 0.99 | 209 | ** | |
| Node021 | ATC:kmeans | 2 | 1.00 | 1.00 | 1.00 | 43 | ** | |
| Node0211-leaf | ATC:skmeans | 3 | 1.00 | 0.96 | 0.98 | 31 | ** | |
| Node0212-leaf | SD:kmeans | 6 | 0.68 | 0.57 | 0.84 | 12 | ||
| Node022 | ATC:kmeans | 2 | 1.00 | 1.00 | 1.00 | 45 | ** | |
| Node0221-leaf | not applied | 9 | ||||||
| Node0222-leaf | ATC:skmeans | 2 | 1.00 | 1.00 | 1.00 | 22 | ** | |
| Node0223-leaf | not applied | 11 | ||||||
| Node0224-leaf | not applied | 3 | ||||||
| Node023 | ATC:skmeans | 3 | 1.00 | 1.00 | 1.00 | 32 | ** | |
| Node0231-leaf | not applied | 9 | ||||||
| Node0232 | SD:kmeans | 2 | 1.00 | 1.00 | 1.00 | 13 | ** | |
| Node02321-leaf | not applied | 11 | ||||||
| Node02322-leaf | not applied | 2 | ||||||
| Node0233-leaf | not applied | 8 | ||||||
| Node0234-leaf | not applied | 2 | ||||||
| Node024 | ATC:skmeans | 4 | 1.00 | 0.99 | 0.99 | 41 | ** | |
| Node0241 | ATC:kmeans | 6 | 0.92 | 0.84 | 0.94 | 21 | * | |
| Node02411-leaf | not applied | 8 | ||||||
| Node02412-leaf | not applied | 4 | ||||||
| Node02413-leaf | not applied | 5 | ||||||
| Node02414-leaf | not applied | 4 | ||||||
| Node0242-leaf | not applied | 9 | ||||||
| Node0243-leaf | not applied | 6 | ||||||
| Node0244-leaf | not applied | 5 | ||||||
| Node025 | ATC:kmeans | 2 | 1.00 | 1.00 | 1.00 | 48 | ** | |
| Node0251-leaf | ATC:skmeans | 8 | 0.98 | 0.48 | 0.98 | 12 | ** | |
| Node0252-leaf | ATC:kmeans | 2 | 0.94 | 0.96 | 0.98 | 36 | * | |
| Node03 | ATC:kmeans | 2 | 1.00 | 1.00 | 1.00 | 187 | ** | |
| Node031 | ATC:skmeans | 3 | 1.00 | 0.97 | 0.99 | 54 | ** | |
| Node0311 | ATC:skmeans | 3 | 1.00 | 0.99 | 0.99 | 23 | ** | |
| Node03111-leaf | not applied | 2 | ||||||
| Node03112-leaf | ATC:kmeans | 7 | 0.94 | 0.16 | 0.64 | 13 | * | |
| Node03113-leaf | not applied | 8 | ||||||
| Node0312-leaf | ATC:skmeans | 2 | 1.00 | 0.99 | 1.00 | 13 | ** | |
| Node0313-leaf | ATC:skmeans | 2 | 1.00 | 1.00 | 1.00 | 18 | ** | |
| Node032-leaf | ATC:skmeans | 3 | 1.00 | 0.98 | 0.99 | 65 | ** | |
| Node033 | ATC:skmeans | 3 | 1.00 | 0.99 | 1.00 | 65 | ** | |
| Node0331-leaf | ATC:kmeans | 2 | 0.59 | 0.95 | 0.93 | 28 | ||
| Node0332-leaf | not applied | 9 | ||||||
| Node0333-leaf | ATC:kmeans | 3 | 1.00 | 0.98 | 0.99 | 28 | ** | |
| Node034-leaf | not applied | 3 |
Stop reason: a) Mean silhouette score was too small 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 = 1289))
collect_classes(res_rh, merge_node = merge_node_param(min_n_signatures = 1291))
collect_classes(res_rh, merge_node = merge_node_param(min_n_signatures = 1595))
collect_classes(res_rh, merge_node = merge_node_param(min_n_signatures = 1662))
collect_classes(res_rh, merge_node = merge_node_param(min_n_signatures = 2027))
collect_classes(res_rh, merge_node = merge_node_param(min_n_signatures = 2606))
collect_classes(res_rh, merge_node = merge_node_param(min_n_signatures = 3159))
collect_classes(res_rh, merge_node = merge_node_param(min_n_signatures = 3180))
collect_classes(res_rh, merge_node = merge_node_param(min_n_signatures = 3187))
collect_classes(res_rh, merge_node = merge_node_param(min_n_signatures = 3269))
collect_classes(res_rh, merge_node = merge_node_param(min_n_signatures = 3511))
collect_classes(res_rh, merge_node = merge_node_param(min_n_signatures = 3641))
#> Error in lt[[hierarchy[i, 1]]]$AddChildNode({: attempt to apply non-function
collect_classes(res_rh, merge_node = merge_node_param(min_n_signatures = 4441))
#> Error in lt[[hierarchy[i, 1]]]$AddChildNode({: attempt to apply non-function
collect_classes(res_rh, merge_node = merge_node_param(min_n_signatures = 5878))
#> Error in lt[[hierarchy[i, 1]]]$AddChildNode({: attempt to apply non-function
collect_classes(res_rh, merge_node = merge_node_param(min_n_signatures = 6634))
#> Error in lt[[hierarchy[i, 1]]]$AddChildNode({: attempt to apply non-function
collect_classes(res_rh, merge_node = merge_node_param(min_n_signatures = 8600))
#> Error in lt[[hierarchy[i, 1]]]$AddChildNode({: attempt to apply non-function
collect_classes(res_rh, merge_node = merge_node_param(min_n_signatures = 11281))
#> Error in max(children_height): invalid 'type' (list) of argument
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 = 1289))
#> TCGA.E8.A416.01 TCGA.E8.A433.01 TCGA.EL.A4K9.01 TCGA.DJ.A3V9.01 TCGA.EL.A3ZO.11 TCGA.EL.A3ZN.01
#> "0211" "015" "03113" "0114" "0211" "0113"
#> TCGA.KS.A41F.01 TCGA.EL.A3ZK.01 TCGA.ET.A40R.01 TCGA.EL.A3ZM.01 TCGA.ET.A2N3.01 TCGA.EL.A3ZQ.01
#> "032" "015" "015" "0312" "02411" "032"
#> TCGA.ET.A40T.01 TCGA.DE.A4MA.01 TCGA.EM.A4FU.01 TCGA.E8.A418.01 TCGA.DJ.A3VD.01 TCGA.DJ.A3VM.01
#> "032" "032" "0251" "032" "0131" "0244"
#> TCGA.EL.A3ZG.01 TCGA.EM.A4FV.01 TCGA.E8.A413.01 TCGA.DJ.A3VG.01 TCGA.EL.A4K2.01 TCGA.IM.A420.01
#> "012" "015" "015" "0251" "0222" "0133"
#> TCGA.KS.A41J.01 TCGA.EL.A3ZK.11 TCGA.J8.A3O2.01 TCGA.E8.A415.01 TCGA.FY.A40M.01 TCGA.DJ.A3VB.01
#> "032" "02321" "012" "0114" "0252" "0313"
#> TCGA.KS.A41I.01 TCGA.DJ.A3VL.01 TCGA.ET.A4KQ.01 TCGA.H2.A421.01 TCGA.EL.A3ZO.01 TCGA.KS.A4I3.01
#> "0252" "0234" "0252" "032" "032" "012"
#> TCGA.DJ.A4UT.01 TCGA.DE.A4MD.01 TCGA.EL.A4JW.01 TCGA.DJ.A3VI.01 TCGA.DJ.A3VA.01 TCGA.L6.A4ET.01
#> "0131" "0312" "015" "032" "032" "0333"
#> TCGA.E8.A419.01 TCGA.DJ.A4V0.01 TCGA.DJ.A4V2.01 TCGA.ET.A40Q.01 TCGA.EL.A3ZS.01 TCGA.KS.A4ID.01
#> "0133" "02321" "0331" "0313" "0131" "0133"
#> TCGA.EL.A3ZL.11 TCGA.J8.A3YE.01 TCGA.EL.A4K7.01 TCGA.DJ.A3VF.01 TCGA.EM.A4FH.01 TCGA.E8.A432.01
#> "0211" "0112" "0313" "0133" "0221" "015"
#> TCGA.J8.A3O2.06 TCGA.ET.A2MX.01 TCGA.ET.A40S.01 TCGA.DE.A4M8.01 TCGA.IM.A41Z.01 TCGA.EL.A4KD.01
#> "0313" "012" "0142" "0131" "02412" "012"
#> TCGA.DJ.A3V7.01 TCGA.FY.A40L.01 TCGA.DE.A4M9.01 TCGA.J8.A42S.01 TCGA.KS.A41L.01 TCGA.EM.A4FN.01
#> "032" "015" "0221" "012" "0224" "0331"
#> TCGA.EL.A4K1.01 TCGA.KS.A4IC.01 TCGA.E8.A414.01 TCGA.H2.A422.01 TCGA.J8.A3YF.01 TCGA.EL.A4KI.01
#> "0331" "0112" "015" "032" "0312" "0243"
#> TCGA.EM.A4G1.01 TCGA.DJ.A3VJ.01 TCGA.DE.A4MD.06 TCGA.EL.A3ZP.01 TCGA.EM.A4FQ.01 TCGA.EL.A3ZT.01
#> "0252" "03113" "0141" "03112" "0331" "03112"
#> TCGA.DJ.A4V4.01 TCGA.FY.A40K.01 TCGA.L6.A4EQ.01 TCGA.DJ.A3VE.01 TCGA.E8.A434.01 TCGA.EL.A3ZH.01
#> "0112" "0111" "0313" "03113" "0222" "0222"
#> TCGA.EM.A4FR.01 TCGA.EL.A3ZH.11 TCGA.EL.A3ZR.01 TCGA.DJ.A3V8.01 TCGA.EL.A3ZG.11 TCGA.ET.A40P.01
#> "012" "0211" "0252" "015" "0212" "0252"
#> TCGA.DE.A4MB.01 TCGA.MK.A4N6.01 TCGA.DJ.A3VK.01 TCGA.E8.A417.01 TCGA.L6.A4EU.01 TCGA.J8.A4HY.01
#> "032" "0313" "0251" "032" "032" "0112"
#> TCGA.EL.A3ZL.01 TCGA.EL.A3ZP.11 TCGA.FY.A40N.01 TCGA.J8.A4HW.01 TCGA.BJ.A45J.01 TCGA.CE.A482.01
#> "032" "02322" "0114" "032" "032" "032"
#> TCGA.DJ.A2Q6.01 TCGA.DJ.A2PX.01 TCGA.DJ.A4UL.01 TCGA.EL.A4JX.01 TCGA.BJ.A2N8.11 TCGA.DJ.A2Q5.01
#> "032" "015" "0333" "0131" "0211" "0143"
#> TCGA.EL.A4KG.01 TCGA.DJ.A4UP.01 TCGA.E8.A438.01 TCGA.EL.A3H2.01 TCGA.EM.A3AP.01 TCGA.DJ.A2PQ.01
#> "0333" "015" "0113" "0221" "0252" "03113"
#> TCGA.L6.A4EP.01 TCGA.FY.A4B4.01 TCGA.EL.A4KH.01 TCGA.BJ.A45E.01 TCGA.DJ.A4V5.01 TCGA.DE.A4MC.01
#> "0333" "032" "0111" "0231" "0143" "0332"
#> TCGA.E8.A44M.01 TCGA.BJ.A45K.01 TCGA.E3.A3DZ.01 TCGA.E3.A3E2.01 TCGA.BJ.A45H.01 TCGA.E8.A44K.01
#> "0131" "0242" "0252" "032" "012" "015"
#> TCGA.ET.A2MY.01 TCGA.EL.A3H8.01 TCGA.BJ.A45C.01 TCGA.BJ.A45G.01 TCGA.EL.A4JZ.01 TCGA.CE.A481.01
#> "032" "0333" "0242" "0252" "0332" "015"
#> TCGA.KS.A4I9.01 TCGA.EL.A3MW.01 TCGA.E8.A436.01 TCGA.E3.A3DY.01 TCGA.DJ.A2Q3.01 TCGA.BJ.A2P4.01
#> "0331" "0333" "015" "0313" "0133" "0252"
#> TCGA.CE.A484.01 TCGA.ET.A2N1.01 TCGA.DJ.A2Q4.01 TCGA.DJ.A2PZ.01 TCGA.BJ.A45F.01 TCGA.IM.A4EB.01
#> "0252" "0113" "03112" "012" "0252" "0143"
#> TCGA.EM.A4FO.01 TCGA.FY.A4B3.01 TCGA.FY.A4B0.01 TCGA.BJ.A45I.01 TCGA.E3.A3E3.01 TCGA.EM.A3AQ.01
#> "0142" "03112" "0242" "0133" "0331" "034"
#> TCGA.EL.A3N3.01 TCGA.DJ.A2Q9.01 TCGA.EM.A4FM.01 TCGA.EL.A4K6.01 TCGA.MK.A4N9.01 TCGA.KS.A4I1.01
#> "0133" "0231" "0332" "0243" "0333" "032"
#> TCGA.DJ.A2PS.01 TCGA.CE.A3MD.01 TCGA.E3.A3E5.01 TCGA.EL.A3CN.01 TCGA.J8.A4HW.06 TCGA.EM.A4FK.01
#> "0114" "012" "0313" "015" "0131" "02412"
#> TCGA.E8.A437.01 TCGA.BJ.A4O8.01 TCGA.EL.A3MW.11 TCGA.E3.A3E0.01 TCGA.BJ.A45D.01 TCGA.CE.A483.01
#> "0114" "03113" "0211" "0333" "0251" "0112"
#> TCGA.CE.A485.01 TCGA.DJ.A4UR.01 TCGA.IM.A41Y.01 TCGA.ET.A4KN.01 TCGA.KS.A4I5.01 TCGA.DJ.A4UQ.01
#> "012" "0244" "032" "0133" "0333" "012"
#> TCGA.KS.A4IB.01 TCGA.EL.A3N2.11 TCGA.BJ.A2N9.01 TCGA.DJ.A4UW.01 TCGA.EL.A3GZ.11 TCGA.EM.A3AR.01
#> "0331" "0211" "0222" "0114" "0211" "0212"
#> TCGA.EL.A3N3.11 TCGA.DE.A3KN.01 TCGA.DJ.A2QA.01 TCGA.EL.A4JV.01 TCGA.EM.A4FF.01 TCGA.EL.A4K0.01
#> "02321" "0113" "0114" "0252" "0331" "0333"
#> TCGA.FK.A4UB.01 TCGA.BJ.A4O9.01 TCGA.BJ.A2N7.01 TCGA.DE.A2OL.01 TCGA.CE.A3ME.01 TCGA.MK.A4N7.01
#> "03113" "0112" "0252" "02411" "0112" "032"
#> TCGA.EL.A3H2.11 TCGA.EL.A4K4.01 TCGA.EL.A3GS.01 TCGA.EL.A3GZ.01 TCGA.E3.A3E1.01 TCGA.DJ.A2Q8.01
#> "0212" "0331" "0331" "032" "0112" "015"
#> TCGA.EL.A3N2.01 TCGA.KS.A4I7.01 TCGA.MK.A84Z.01 TCGA.ET.A3DP.11 TCGA.EL.A3MX.11 TCGA.ET.A25G.01
#> "0331" "032" "0251" "0211" "0211" "032"
#> TCGA.EM.A3FK.01 TCGA.EM.A2CS.01 TCGA.FE.A23A.01 TCGA.BJ.A28T.11 TCGA.EM.A22J.01 TCGA.EL.A3MX.01
#> "034" "032" "0133" "0211" "02412" "0332"
#> TCGA.FY.A3I4.01 TCGA.BJ.A28W.11 TCGA.ET.A25R.01 TCGA.BJ.A2N8.01 TCGA.FY.A76V.01 TCGA.EM.A3FN.01
#> "0114" "02321" "032" "0252" "0251" "02413"
#> TCGA.QD.A8IV.01 TCGA.EM.A3FJ.01 TCGA.ET.A2MY.11 TCGA.EM.A3FQ.06 TCGA.ET.A25P.01 TCGA.ET.A2N0.01
#> "0252" "0333" "02413" "0333" "0252" "015"
#> TCGA.EM.A2CT.01 TCGA.FE.A235.01 TCGA.ET.A25M.01 TCGA.EL.A3MY.01 TCGA.DE.A7U5.01 TCGA.E8.A2JQ.11
#> "0222" "0333" "0313" "0312" "0331" "0231"
#> TCGA.ET.A3DP.01 TCGA.EM.A2CL.01 TCGA.ET.A2N5.01 TCGA.ET.A25J.11 TCGA.DE.A69J.01 TCGA.BJ.A28R.11
#> "0111" "0242" "0252" "0211" "0333" "02321"
#> TCGA.ET.A25K.01 TCGA.EL.A3GV.01 TCGA.GE.A2C6.01 TCGA.EM.A3FM.01 TCGA.EL.A3H7.11 TCGA.FE.A22Z.01
#> "032" "0111" "0133" "0313" "0211" "0332"
#> TCGA.H2.A2K9.01 TCGA.EM.A22Q.01 TCGA.EM.A3FP.01 TCGA.GE.A2C6.11 TCGA.EL.A3MZ.01 TCGA.DJ.A2PT.01
#> "0243" "0242" "0252" "02321" "0312" "0133"
#> TCGA.E8.A242.01 TCGA.ET.A25L.01 TCGA.CE.A27D.01 TCGA.EL.A3H1.11 TCGA.BJ.A2N7.11 TCGA.DJ.A2Q7.01
#> "0133" "032" "0233" "0233" "0211" "0333"
#> TCGA.J8.A3O1.01 TCGA.EM.A2CR.01 TCGA.DE.A69K.01 TCGA.EM.A2CQ.01 TCGA.FE.A238.01 TCGA.EL.A3H1.01
#> "0113" "0114" "0333" "0222" "015" "02411"
#> TCGA.BJ.A28W.01 TCGA.BJ.A28T.01 TCGA.EM.A2CJ.01 TCGA.EM.A3FQ.01 TCGA.4C.A93U.01 TCGA.EM.A22M.01
#> "0231" "02321" "0223" "015" "0332" "0142"
#> TCGA.J8.A3NZ.01 TCGA.EM.A22K.01 TCGA.FE.A236.01 TCGA.BJ.A28R.01 TCGA.EM.A2CU.01 TCGA.ET.A25N.01
#> "0112" "0252" "012" "015" "015" "0333"
#> TCGA.EL.A3H7.01 TCGA.FY.A3NM.01 TCGA.EM.A3FO.01 TCGA.EM.A22L.01 TCGA.BJ.A2N9.11 TCGA.BJ.A291.01
#> "0331" "0223" "03112" "0252" "0231" "0222"
#> TCGA.ET.A2N5.11 TCGA.ET.A25N.11 TCGA.J8.A3O0.01 TCGA.FE.A237.01 TCGA.DJ.A2QC.01 TCGA.ET.A25O.01
#> "0211" "0211" "0243" "0112" "0111" "0331"
#> TCGA.EL.A3GU.01 TCGA.EL.A3MY.11 TCGA.DJ.A2PY.01 TCGA.EM.A2CS.06 TCGA.FY.A3NP.01 TCGA.ET.A25I.01
#> "0332" "0221" "0331" "0114" "0251" "0222"
#> TCGA.H2.A26U.01 TCGA.BJ.A290.11 TCGA.EM.A22I.01 TCGA.FE.A239.01 TCGA.BJ.A28Z.01 TCGA.DE.A0XZ.01
#> "0133" "0212" "0331" "0242" "0131" "0333"
#> TCGA.ET.A25J.01 TCGA.EM.A22N.01 TCGA.EM.A2CM.01 TCGA.FY.A3NN.01 TCGA.EM.A3FL.01 TCGA.H2.A2K9.11
#> "0112" "0222" "0244" "0112" "0223" "0233"
#> TCGA.EL.A3H3.01 TCGA.EL.A3H4.01 TCGA.EM.A2OX.01 TCGA.EM.A3SX.01 TCGA.BJ.A0Z3.01 TCGA.BJ.A28X.01
#> "015" "032" "0313" "032" "0131" "0131"
#> TCGA.EL.A3CT.01 TCGA.EL.A3CR.01 TCGA.FY.A3TY.01 TCGA.J8.A3YG.01 TCGA.DJ.A3V6.01 TCGA.EM.A3SZ.01
#> "0132" "032" "0233" "015" "0312" "015"
#> TCGA.EM.A2OW.01 TCGA.DO.A1JZ.11 TCGA.EL.A3D5.01 TCGA.EM.A2P0.01 TCGA.E8.A2JQ.01 TCGA.BJ.A18Z.01
#> "0222" "0211" "0252" "012" "0131" "0313"
#> TCGA.DJ.A3V0.01 TCGA.EL.A3GW.01 TCGA.DJ.A3UW.01 TCGA.DJ.A3V3.01 TCGA.EL.A3T1.11 TCGA.BJ.A0ZC.01
#> "0313" "0252" "0131" "015" "02321" "0221"
#> TCGA.EM.A2OV.01 TCGA.EL.A3GY.01 TCGA.EM.A3SY.01 TCGA.EM.A3AI.01 TCGA.EM.A2OY.01 TCGA.EL.A3T8.01
#> "0222" "0331" "0212" "0222" "0223" "03113"
#> TCGA.BJ.A18Y.01 TCGA.EL.A3GP.01 TCGA.EM.A2CK.01 TCGA.EL.A3T7.11 TCGA.BJ.A192.01 TCGA.BJ.A191.01
#> "0251" "0141" "0251" "0211" "0223" "0113"
#> TCGA.EM.A2CP.01 TCGA.EM.A22O.01 TCGA.EM.A2P1.01 TCGA.J8.A3YH.01 TCGA.DJ.A3UZ.01 TCGA.IM.A3EB.01
#> "0231" "0312" "0142" "03111" "0222" "0133"
#> TCGA.BJ.A3F0.01 TCGA.EL.A3GX.01 TCGA.EM.A3AK.01 TCGA.DO.A1JZ.01 TCGA.FY.A3YR.01 TCGA.DO.A1K0.01
#> "02414" "0331" "0114" "0333" "032" "0331"
#> TCGA.DJ.A3V5.01 TCGA.EM.A3AJ.01 TCGA.IM.A3ED.01 TCGA.EM.A3AO.01 TCGA.EM.A2P1.06 TCGA.EM.A1CW.01
#> "032" "02322" "0333" "012" "0142" "0222"
#> TCGA.FK.A3SE.01 TCGA.EL.A3T7.01 TCGA.EM.A2P2.01 TCGA.EM.A1CU.11 TCGA.EL.A3T0.11 TCGA.E8.A3X7.01
#> "032" "032" "0251" "0212" "0211" "032"
#> TCGA.ET.A3BQ.01 TCGA.EM.A1CS.01 TCGA.EL.A3GQ.01 TCGA.EL.A3H5.01 TCGA.DJ.A3V4.01 TCGA.EM.A2P3.01
#> "0333" "0111" "0111" "0332" "0112" "0331"
#> TCGA.FY.A3WA.01 TCGA.DJ.A3V2.01 TCGA.FY.A3TY.11 TCGA.BJ.A290.01 TCGA.EM.A3SU.01 TCGA.EL.A3D0.01
#> "0223" "0131" "0211" "012" "015" "0312"
#> TCGA.EM.A1CT.11 TCGA.EL.A3GR.01 TCGA.J8.A3YH.06 TCGA.EM.A3ST.11 TCGA.ET.A3DV.01 TCGA.BJ.A3EZ.01
#> "0212" "0114" "03111" "0211" "02411" "0312"
#> TCGA.J8.A3YD.01 TCGA.EM.A3SU.06 TCGA.EM.A3AL.01 TCGA.DJ.A3US.01 TCGA.EM.A1CS.11 TCGA.EM.A1CW.11
#> "0222" "0131" "02411" "015" "0211" "0211"
#> TCGA.BJ.A190.01 TCGA.EM.A2OZ.01 TCGA.EM.A1CV.11 TCGA.EM.A1CU.01 TCGA.EM.A3AN.01 TCGA.E8.A2EA.01
#> "0221" "012" "0211" "03112" "032" "0133"
#> TCGA.EM.A1CV.01 TCGA.EM.A1CT.01 TCGA.EM.A3ST.01 TCGA.ET.A3BS.01 TCGA.EL.A3GO.01 TCGA.DJ.A2Q0.01
#> "0111" "012" "0244" "0143" "02411" "0223"
#> TCGA.EL.A3D6.01 TCGA.DJ.A3UN.01 TCGA.DJ.A3UU.01 TCGA.FK.A3SD.01 TCGA.DJ.A2PO.01 TCGA.DJ.A3UQ.01
#> "032" "032" "0114" "02413" "012" "015"
#> TCGA.EM.A1YE.11 TCGA.EL.A3T2.11 TCGA.EL.A3CL.01 TCGA.EM.A1YC.01 TCGA.DJ.A3UP.01 TCGA.EL.A3T0.01
#> "0211" "0211" "0333" "0223" "0252" "0114"
#> TCGA.IM.A3U2.01 TCGA.IM.A3U3.01 TCGA.DJ.A3UX.01 TCGA.ET.A3BW.01 TCGA.ET.A39S.01 TCGA.ET.A3BP.01
#> "032" "032" "015" "0111" "0114" "0112"
#> TCGA.DJ.A1QE.01 TCGA.EL.A3D4.01 TCGA.FK.A3SB.01 TCGA.EL.A3CW.01 TCGA.ET.A39L.01 TCGA.DJ.A2PW.01
#> "0331" "012" "0333" "02321" "0252" "03112"
#> TCGA.EM.A2CO.01 TCGA.FE.A232.01 TCGA.DJ.A3UR.01 TCGA.DJ.A2PP.01 TCGA.ET.A3DQ.01 TCGA.ET.A3DS.01
#> "0222" "0112" "0111" "0242" "02321" "0222"
#> TCGA.FY.A3W9.01 TCGA.FK.A3S3.01 TCGA.ET.A2MZ.01 TCGA.BJ.A2NA.11 TCGA.DJ.A1QL.01 TCGA.EL.A3CS.01
#> "0244" "0114" "03113" "0233" "0242" "015"
#> TCGA.FE.A233.01 TCGA.EM.A1YD.11 TCGA.ET.A3DW.11 TCGA.EL.A3T9.01 TCGA.DJ.A3UM.01 TCGA.DO.A2HM.01
#> "0331" "0211" "0212" "032" "032" "0142"
#> TCGA.FY.A3BL.01 TCGA.EL.A3TA.11 TCGA.ET.A3BX.01 TCGA.DJ.A1QQ.01 TCGA.DJ.A1QF.01 TCGA.DJ.A1QO.01
#> "012" "0212" "0313" "03112" "0112" "0312"
#> TCGA.BJ.A2NA.01 TCGA.EM.A1YE.01 TCGA.FY.A2QD.01 TCGA.ET.A39J.01 TCGA.ET.A3DU.01 TCGA.EL.A3CM.01
#> "0313" "0223" "02413" "034" "0133" "032"
#> TCGA.DJ.A3UO.01 TCGA.ET.A39P.01 TCGA.DJ.A2Q2.01 TCGA.BJ.A28V.01 TCGA.ET.A3BO.01 TCGA.EL.A3T1.01
#> "0313" "0331" "0222" "02411" "032" "015"
#> TCGA.DJ.A1QI.01 TCGA.EL.A3TB.01 TCGA.BJ.A28X.11 TCGA.DJ.A1QN.01 TCGA.FE.A230.01 TCGA.FE.A234.01
#> "0333" "032" "0231" "0333" "015" "0331"
#> TCGA.ET.A39R.01 TCGA.DJ.A1QG.01 TCGA.EL.A3CV.01 TCGA.FE.A231.01 TCGA.EL.A3TA.01 TCGA.DJ.A3UY.01
#> "015" "0251" "0142" "0312" "012" "015"
#> TCGA.DJ.A2Q1.01 TCGA.EL.A3CU.01 TCGA.EL.A3TB.11 TCGA.ET.A39I.01 TCGA.EM.A1YB.01 TCGA.DJ.A3UV.01
#> "0131" "0133" "0211" "0252" "02414" "0113"
#> TCGA.DJ.A3UT.01 TCGA.ET.A3DW.01 TCGA.ET.A3BT.01 TCGA.EL.A3T3.01 TCGA.DJ.A1QM.01 TCGA.EL.A3CY.01
#> "0252" "0312" "032" "032" "0212" "0231"
#> TCGA.ET.A39O.01 TCGA.EM.A1YC.11 TCGA.DJ.A1QH.01 TCGA.EL.A3T3.11 TCGA.EL.A3CX.01 TCGA.EL.A3T2.01
#> "0313" "0211" "0332" "0211" "0113" "0252"
#> TCGA.EM.A22P.01 TCGA.EL.A3T8.11 TCGA.DJ.A2PU.01 TCGA.DJ.A3UK.01 TCGA.ET.A3DO.01 TCGA.EM.A1YA.01
#> "0142" "0212" "0333" "0111" "0131" "0223"
#> TCGA.ET.A3BV.01 TCGA.EL.A3CO.01 TCGA.DJ.A2PN.01 TCGA.FK.A3SG.01 TCGA.FK.A3SH.01 TCGA.EM.A1YD.01
#> "0131" "0233" "0333" "032" "032" "0223"
#> TCGA.DJ.A1QD.01 TCGA.EL.A3CZ.01 TCGA.BJ.A0Z9.01 TCGA.CE.A13K.01 TCGA.EM.A3FR.01 TCGA.EM.A3O8.01
#> "0331" "0222" "0132" "032" "02413" "0252"
#> TCGA.FY.A3R6.01 TCGA.FY.A3R9.01 TCGA.EL.A3D1.01 TCGA.EM.A3O6.01 TCGA.BJ.A0Z5.01 TCGA.BJ.A28S.01
#> "0131" "0222" "03112" "0222" "012" "0251"
#> TCGA.BJ.A0ZH.01 TCGA.ET.A3DT.01 TCGA.H2.A3RI.11 TCGA.DJ.A13W.01 TCGA.DJ.A13T.01 TCGA.BJ.A0ZA.01
#> "032" "0131" "0211" "02411" "032" "02414"
#> TCGA.BJ.A3PT.01 TCGA.FE.A3PD.01 TCGA.BJ.A0ZF.01 TCGA.ET.A39M.01 TCGA.BJ.A0ZJ.01 TCGA.BJ.A0YZ.01
#> "0252" "032" "0224" "0143" "0143" "0221"
#> TCGA.FE.A3PC.01 TCGA.DJ.A2QB.01 TCGA.EM.A3OB.01 TCGA.H2.A3RH.01 TCGA.ET.A39T.01 TCGA.DJ.A2PV.01
#> "032" "0252" "0252" "0252" "0112" "0111"
#> TCGA.BJ.A3PR.11 TCGA.EL.A3T6.11 TCGA.DJ.A13X.01 TCGA.BJ.A0ZG.01 TCGA.EL.A3T6.01 TCGA.BJ.A0Z0.01
#> "02321" "0233" "0111" "0221" "0133" "0242"
#> TCGA.ET.A39K.01 TCGA.EM.A3O9.01 TCGA.BJ.A3PU.01 TCGA.BJ.A3PR.01 TCGA.EM.A3O3.01 TCGA.BJ.A0ZB.01
#> "032" "0234" "0313" "0231" "0132" "0312"
#> TCGA.EM.A3OA.01 TCGA.DJ.A2PR.01 TCGA.DJ.A13L.01 TCGA.FY.A3ON.01 TCGA.DJ.A13V.01 TCGA.FY.A3R8.01
#> "02412" "03112" "0142" "03112" "032" "032"
#> TCGA.EL.A3CP.01 TCGA.DJ.A13U.01 TCGA.DE.A0Y3.01 TCGA.ET.A2N4.01 TCGA.DJ.A13P.01 TCGA.BJ.A0ZE.01
#> "0333" "012" "032" "0111" "0111" "0252"
#> TCGA.EM.A3O7.01 TCGA.DJ.A13O.01 TCGA.FY.A3RA.01 TCGA.DJ.A13M.01 TCGA.DJ.A13R.01 TCGA.ET.A3DR.01
#> "0111" "0233" "0331" "0252" "0221" "0113"
#> TCGA.FE.A3PB.01 TCGA.ET.A3BN.01 TCGA.H2.A3RI.01 TCGA.ET.A39N.01 TCGA.BJ.A3PU.11 TCGA.FY.A3R7.01
#> "015" "0331" "032" "0224" "0212" "0222"
#> TCGA.FE.A3PA.01 TCGA.EM.A2CN.01 TCGA.BJ.A0Z2.01 TCGA.FY.A3I5.01 TCGA.DJ.A13S.01 TCGA.DE.A0Y2.01
#> "03112" "0243" "0243" "02414" "0252" "0331"
#> TCGA.ET.A3BU.01
#> "03112"
get_classes(res_rh, merge_node = merge_node_param(min_n_signatures = 1291))
#> TCGA.E8.A416.01 TCGA.E8.A433.01 TCGA.EL.A4K9.01 TCGA.DJ.A3V9.01 TCGA.EL.A3ZO.11 TCGA.EL.A3ZN.01
#> "0211" "015" "031" "0114" "0211" "0113"
#> TCGA.KS.A41F.01 TCGA.EL.A3ZK.01 TCGA.ET.A40R.01 TCGA.EL.A3ZM.01 TCGA.ET.A2N3.01 TCGA.EL.A3ZQ.01
#> "032" "015" "015" "031" "02411" "032"
#> TCGA.ET.A40T.01 TCGA.DE.A4MA.01 TCGA.EM.A4FU.01 TCGA.E8.A418.01 TCGA.DJ.A3VD.01 TCGA.DJ.A3VM.01
#> "032" "032" "0251" "032" "0131" "0244"
#> TCGA.EL.A3ZG.01 TCGA.EM.A4FV.01 TCGA.E8.A413.01 TCGA.DJ.A3VG.01 TCGA.EL.A4K2.01 TCGA.IM.A420.01
#> "012" "015" "015" "0251" "0222" "0133"
#> TCGA.KS.A41J.01 TCGA.EL.A3ZK.11 TCGA.J8.A3O2.01 TCGA.E8.A415.01 TCGA.FY.A40M.01 TCGA.DJ.A3VB.01
#> "032" "02321" "012" "0114" "0252" "031"
#> TCGA.KS.A41I.01 TCGA.DJ.A3VL.01 TCGA.ET.A4KQ.01 TCGA.H2.A421.01 TCGA.EL.A3ZO.01 TCGA.KS.A4I3.01
#> "0252" "0234" "0252" "032" "032" "012"
#> TCGA.DJ.A4UT.01 TCGA.DE.A4MD.01 TCGA.EL.A4JW.01 TCGA.DJ.A3VI.01 TCGA.DJ.A3VA.01 TCGA.L6.A4ET.01
#> "0131" "031" "015" "032" "032" "0333"
#> TCGA.E8.A419.01 TCGA.DJ.A4V0.01 TCGA.DJ.A4V2.01 TCGA.ET.A40Q.01 TCGA.EL.A3ZS.01 TCGA.KS.A4ID.01
#> "0133" "02321" "0331" "031" "0131" "0133"
#> TCGA.EL.A3ZL.11 TCGA.J8.A3YE.01 TCGA.EL.A4K7.01 TCGA.DJ.A3VF.01 TCGA.EM.A4FH.01 TCGA.E8.A432.01
#> "0211" "0112" "031" "0133" "0221" "015"
#> TCGA.J8.A3O2.06 TCGA.ET.A2MX.01 TCGA.ET.A40S.01 TCGA.DE.A4M8.01 TCGA.IM.A41Z.01 TCGA.EL.A4KD.01
#> "031" "012" "0142" "0131" "02412" "012"
#> TCGA.DJ.A3V7.01 TCGA.FY.A40L.01 TCGA.DE.A4M9.01 TCGA.J8.A42S.01 TCGA.KS.A41L.01 TCGA.EM.A4FN.01
#> "032" "015" "0221" "012" "0224" "0331"
#> TCGA.EL.A4K1.01 TCGA.KS.A4IC.01 TCGA.E8.A414.01 TCGA.H2.A422.01 TCGA.J8.A3YF.01 TCGA.EL.A4KI.01
#> "0331" "0112" "015" "032" "031" "0243"
#> TCGA.EM.A4G1.01 TCGA.DJ.A3VJ.01 TCGA.DE.A4MD.06 TCGA.EL.A3ZP.01 TCGA.EM.A4FQ.01 TCGA.EL.A3ZT.01
#> "0252" "031" "0141" "031" "0331" "031"
#> TCGA.DJ.A4V4.01 TCGA.FY.A40K.01 TCGA.L6.A4EQ.01 TCGA.DJ.A3VE.01 TCGA.E8.A434.01 TCGA.EL.A3ZH.01
#> "0112" "0111" "031" "031" "0222" "0222"
#> TCGA.EM.A4FR.01 TCGA.EL.A3ZH.11 TCGA.EL.A3ZR.01 TCGA.DJ.A3V8.01 TCGA.EL.A3ZG.11 TCGA.ET.A40P.01
#> "012" "0211" "0252" "015" "0212" "0252"
#> TCGA.DE.A4MB.01 TCGA.MK.A4N6.01 TCGA.DJ.A3VK.01 TCGA.E8.A417.01 TCGA.L6.A4EU.01 TCGA.J8.A4HY.01
#> "032" "031" "0251" "032" "032" "0112"
#> TCGA.EL.A3ZL.01 TCGA.EL.A3ZP.11 TCGA.FY.A40N.01 TCGA.J8.A4HW.01 TCGA.BJ.A45J.01 TCGA.CE.A482.01
#> "032" "02322" "0114" "032" "032" "032"
#> TCGA.DJ.A2Q6.01 TCGA.DJ.A2PX.01 TCGA.DJ.A4UL.01 TCGA.EL.A4JX.01 TCGA.BJ.A2N8.11 TCGA.DJ.A2Q5.01
#> "032" "015" "0333" "0131" "0211" "0143"
#> TCGA.EL.A4KG.01 TCGA.DJ.A4UP.01 TCGA.E8.A438.01 TCGA.EL.A3H2.01 TCGA.EM.A3AP.01 TCGA.DJ.A2PQ.01
#> "0333" "015" "0113" "0221" "0252" "031"
#> TCGA.L6.A4EP.01 TCGA.FY.A4B4.01 TCGA.EL.A4KH.01 TCGA.BJ.A45E.01 TCGA.DJ.A4V5.01 TCGA.DE.A4MC.01
#> "0333" "032" "0111" "0231" "0143" "0332"
#> TCGA.E8.A44M.01 TCGA.BJ.A45K.01 TCGA.E3.A3DZ.01 TCGA.E3.A3E2.01 TCGA.BJ.A45H.01 TCGA.E8.A44K.01
#> "0131" "0242" "0252" "032" "012" "015"
#> TCGA.ET.A2MY.01 TCGA.EL.A3H8.01 TCGA.BJ.A45C.01 TCGA.BJ.A45G.01 TCGA.EL.A4JZ.01 TCGA.CE.A481.01
#> "032" "0333" "0242" "0252" "0332" "015"
#> TCGA.KS.A4I9.01 TCGA.EL.A3MW.01 TCGA.E8.A436.01 TCGA.E3.A3DY.01 TCGA.DJ.A2Q3.01 TCGA.BJ.A2P4.01
#> "0331" "0333" "015" "031" "0133" "0252"
#> TCGA.CE.A484.01 TCGA.ET.A2N1.01 TCGA.DJ.A2Q4.01 TCGA.DJ.A2PZ.01 TCGA.BJ.A45F.01 TCGA.IM.A4EB.01
#> "0252" "0113" "031" "012" "0252" "0143"
#> TCGA.EM.A4FO.01 TCGA.FY.A4B3.01 TCGA.FY.A4B0.01 TCGA.BJ.A45I.01 TCGA.E3.A3E3.01 TCGA.EM.A3AQ.01
#> "0142" "031" "0242" "0133" "0331" "034"
#> TCGA.EL.A3N3.01 TCGA.DJ.A2Q9.01 TCGA.EM.A4FM.01 TCGA.EL.A4K6.01 TCGA.MK.A4N9.01 TCGA.KS.A4I1.01
#> "0133" "0231" "0332" "0243" "0333" "032"
#> TCGA.DJ.A2PS.01 TCGA.CE.A3MD.01 TCGA.E3.A3E5.01 TCGA.EL.A3CN.01 TCGA.J8.A4HW.06 TCGA.EM.A4FK.01
#> "0114" "012" "031" "015" "0131" "02412"
#> TCGA.E8.A437.01 TCGA.BJ.A4O8.01 TCGA.EL.A3MW.11 TCGA.E3.A3E0.01 TCGA.BJ.A45D.01 TCGA.CE.A483.01
#> "0114" "031" "0211" "0333" "0251" "0112"
#> TCGA.CE.A485.01 TCGA.DJ.A4UR.01 TCGA.IM.A41Y.01 TCGA.ET.A4KN.01 TCGA.KS.A4I5.01 TCGA.DJ.A4UQ.01
#> "012" "0244" "032" "0133" "0333" "012"
#> TCGA.KS.A4IB.01 TCGA.EL.A3N2.11 TCGA.BJ.A2N9.01 TCGA.DJ.A4UW.01 TCGA.EL.A3GZ.11 TCGA.EM.A3AR.01
#> "0331" "0211" "0222" "0114" "0211" "0212"
#> TCGA.EL.A3N3.11 TCGA.DE.A3KN.01 TCGA.DJ.A2QA.01 TCGA.EL.A4JV.01 TCGA.EM.A4FF.01 TCGA.EL.A4K0.01
#> "02321" "0113" "0114" "0252" "0331" "0333"
#> TCGA.FK.A4UB.01 TCGA.BJ.A4O9.01 TCGA.BJ.A2N7.01 TCGA.DE.A2OL.01 TCGA.CE.A3ME.01 TCGA.MK.A4N7.01
#> "031" "0112" "0252" "02411" "0112" "032"
#> TCGA.EL.A3H2.11 TCGA.EL.A4K4.01 TCGA.EL.A3GS.01 TCGA.EL.A3GZ.01 TCGA.E3.A3E1.01 TCGA.DJ.A2Q8.01
#> "0212" "0331" "0331" "032" "0112" "015"
#> TCGA.EL.A3N2.01 TCGA.KS.A4I7.01 TCGA.MK.A84Z.01 TCGA.ET.A3DP.11 TCGA.EL.A3MX.11 TCGA.ET.A25G.01
#> "0331" "032" "0251" "0211" "0211" "032"
#> TCGA.EM.A3FK.01 TCGA.EM.A2CS.01 TCGA.FE.A23A.01 TCGA.BJ.A28T.11 TCGA.EM.A22J.01 TCGA.EL.A3MX.01
#> "034" "032" "0133" "0211" "02412" "0332"
#> TCGA.FY.A3I4.01 TCGA.BJ.A28W.11 TCGA.ET.A25R.01 TCGA.BJ.A2N8.01 TCGA.FY.A76V.01 TCGA.EM.A3FN.01
#> "0114" "02321" "032" "0252" "0251" "02413"
#> TCGA.QD.A8IV.01 TCGA.EM.A3FJ.01 TCGA.ET.A2MY.11 TCGA.EM.A3FQ.06 TCGA.ET.A25P.01 TCGA.ET.A2N0.01
#> "0252" "0333" "02413" "0333" "0252" "015"
#> TCGA.EM.A2CT.01 TCGA.FE.A235.01 TCGA.ET.A25M.01 TCGA.EL.A3MY.01 TCGA.DE.A7U5.01 TCGA.E8.A2JQ.11
#> "0222" "0333" "031" "031" "0331" "0231"
#> TCGA.ET.A3DP.01 TCGA.EM.A2CL.01 TCGA.ET.A2N5.01 TCGA.ET.A25J.11 TCGA.DE.A69J.01 TCGA.BJ.A28R.11
#> "0111" "0242" "0252" "0211" "0333" "02321"
#> TCGA.ET.A25K.01 TCGA.EL.A3GV.01 TCGA.GE.A2C6.01 TCGA.EM.A3FM.01 TCGA.EL.A3H7.11 TCGA.FE.A22Z.01
#> "032" "0111" "0133" "031" "0211" "0332"
#> TCGA.H2.A2K9.01 TCGA.EM.A22Q.01 TCGA.EM.A3FP.01 TCGA.GE.A2C6.11 TCGA.EL.A3MZ.01 TCGA.DJ.A2PT.01
#> "0243" "0242" "0252" "02321" "031" "0133"
#> TCGA.E8.A242.01 TCGA.ET.A25L.01 TCGA.CE.A27D.01 TCGA.EL.A3H1.11 TCGA.BJ.A2N7.11 TCGA.DJ.A2Q7.01
#> "0133" "032" "0233" "0233" "0211" "0333"
#> TCGA.J8.A3O1.01 TCGA.EM.A2CR.01 TCGA.DE.A69K.01 TCGA.EM.A2CQ.01 TCGA.FE.A238.01 TCGA.EL.A3H1.01
#> "0113" "0114" "0333" "0222" "015" "02411"
#> TCGA.BJ.A28W.01 TCGA.BJ.A28T.01 TCGA.EM.A2CJ.01 TCGA.EM.A3FQ.01 TCGA.4C.A93U.01 TCGA.EM.A22M.01
#> "0231" "02321" "0223" "015" "0332" "0142"
#> TCGA.J8.A3NZ.01 TCGA.EM.A22K.01 TCGA.FE.A236.01 TCGA.BJ.A28R.01 TCGA.EM.A2CU.01 TCGA.ET.A25N.01
#> "0112" "0252" "012" "015" "015" "0333"
#> TCGA.EL.A3H7.01 TCGA.FY.A3NM.01 TCGA.EM.A3FO.01 TCGA.EM.A22L.01 TCGA.BJ.A2N9.11 TCGA.BJ.A291.01
#> "0331" "0223" "031" "0252" "0231" "0222"
#> TCGA.ET.A2N5.11 TCGA.ET.A25N.11 TCGA.J8.A3O0.01 TCGA.FE.A237.01 TCGA.DJ.A2QC.01 TCGA.ET.A25O.01
#> "0211" "0211" "0243" "0112" "0111" "0331"
#> TCGA.EL.A3GU.01 TCGA.EL.A3MY.11 TCGA.DJ.A2PY.01 TCGA.EM.A2CS.06 TCGA.FY.A3NP.01 TCGA.ET.A25I.01
#> "0332" "0221" "0331" "0114" "0251" "0222"
#> TCGA.H2.A26U.01 TCGA.BJ.A290.11 TCGA.EM.A22I.01 TCGA.FE.A239.01 TCGA.BJ.A28Z.01 TCGA.DE.A0XZ.01
#> "0133" "0212" "0331" "0242" "0131" "0333"
#> TCGA.ET.A25J.01 TCGA.EM.A22N.01 TCGA.EM.A2CM.01 TCGA.FY.A3NN.01 TCGA.EM.A3FL.01 TCGA.H2.A2K9.11
#> "0112" "0222" "0244" "0112" "0223" "0233"
#> TCGA.EL.A3H3.01 TCGA.EL.A3H4.01 TCGA.EM.A2OX.01 TCGA.EM.A3SX.01 TCGA.BJ.A0Z3.01 TCGA.BJ.A28X.01
#> "015" "032" "031" "032" "0131" "0131"
#> TCGA.EL.A3CT.01 TCGA.EL.A3CR.01 TCGA.FY.A3TY.01 TCGA.J8.A3YG.01 TCGA.DJ.A3V6.01 TCGA.EM.A3SZ.01
#> "0132" "032" "0233" "015" "031" "015"
#> TCGA.EM.A2OW.01 TCGA.DO.A1JZ.11 TCGA.EL.A3D5.01 TCGA.EM.A2P0.01 TCGA.E8.A2JQ.01 TCGA.BJ.A18Z.01
#> "0222" "0211" "0252" "012" "0131" "031"
#> TCGA.DJ.A3V0.01 TCGA.EL.A3GW.01 TCGA.DJ.A3UW.01 TCGA.DJ.A3V3.01 TCGA.EL.A3T1.11 TCGA.BJ.A0ZC.01
#> "031" "0252" "0131" "015" "02321" "0221"
#> TCGA.EM.A2OV.01 TCGA.EL.A3GY.01 TCGA.EM.A3SY.01 TCGA.EM.A3AI.01 TCGA.EM.A2OY.01 TCGA.EL.A3T8.01
#> "0222" "0331" "0212" "0222" "0223" "031"
#> TCGA.BJ.A18Y.01 TCGA.EL.A3GP.01 TCGA.EM.A2CK.01 TCGA.EL.A3T7.11 TCGA.BJ.A192.01 TCGA.BJ.A191.01
#> "0251" "0141" "0251" "0211" "0223" "0113"
#> TCGA.EM.A2CP.01 TCGA.EM.A22O.01 TCGA.EM.A2P1.01 TCGA.J8.A3YH.01 TCGA.DJ.A3UZ.01 TCGA.IM.A3EB.01
#> "0231" "031" "0142" "031" "0222" "0133"
#> TCGA.BJ.A3F0.01 TCGA.EL.A3GX.01 TCGA.EM.A3AK.01 TCGA.DO.A1JZ.01 TCGA.FY.A3YR.01 TCGA.DO.A1K0.01
#> "02414" "0331" "0114" "0333" "032" "0331"
#> TCGA.DJ.A3V5.01 TCGA.EM.A3AJ.01 TCGA.IM.A3ED.01 TCGA.EM.A3AO.01 TCGA.EM.A2P1.06 TCGA.EM.A1CW.01
#> "032" "02322" "0333" "012" "0142" "0222"
#> TCGA.FK.A3SE.01 TCGA.EL.A3T7.01 TCGA.EM.A2P2.01 TCGA.EM.A1CU.11 TCGA.EL.A3T0.11 TCGA.E8.A3X7.01
#> "032" "032" "0251" "0212" "0211" "032"
#> TCGA.ET.A3BQ.01 TCGA.EM.A1CS.01 TCGA.EL.A3GQ.01 TCGA.EL.A3H5.01 TCGA.DJ.A3V4.01 TCGA.EM.A2P3.01
#> "0333" "0111" "0111" "0332" "0112" "0331"
#> TCGA.FY.A3WA.01 TCGA.DJ.A3V2.01 TCGA.FY.A3TY.11 TCGA.BJ.A290.01 TCGA.EM.A3SU.01 TCGA.EL.A3D0.01
#> "0223" "0131" "0211" "012" "015" "031"
#> TCGA.EM.A1CT.11 TCGA.EL.A3GR.01 TCGA.J8.A3YH.06 TCGA.EM.A3ST.11 TCGA.ET.A3DV.01 TCGA.BJ.A3EZ.01
#> "0212" "0114" "031" "0211" "02411" "031"
#> TCGA.J8.A3YD.01 TCGA.EM.A3SU.06 TCGA.EM.A3AL.01 TCGA.DJ.A3US.01 TCGA.EM.A1CS.11 TCGA.EM.A1CW.11
#> "0222" "0131" "02411" "015" "0211" "0211"
#> TCGA.BJ.A190.01 TCGA.EM.A2OZ.01 TCGA.EM.A1CV.11 TCGA.EM.A1CU.01 TCGA.EM.A3AN.01 TCGA.E8.A2EA.01
#> "0221" "012" "0211" "031" "032" "0133"
#> TCGA.EM.A1CV.01 TCGA.EM.A1CT.01 TCGA.EM.A3ST.01 TCGA.ET.A3BS.01 TCGA.EL.A3GO.01 TCGA.DJ.A2Q0.01
#> "0111" "012" "0244" "0143" "02411" "0223"
#> TCGA.EL.A3D6.01 TCGA.DJ.A3UN.01 TCGA.DJ.A3UU.01 TCGA.FK.A3SD.01 TCGA.DJ.A2PO.01 TCGA.DJ.A3UQ.01
#> "032" "032" "0114" "02413" "012" "015"
#> TCGA.EM.A1YE.11 TCGA.EL.A3T2.11 TCGA.EL.A3CL.01 TCGA.EM.A1YC.01 TCGA.DJ.A3UP.01 TCGA.EL.A3T0.01
#> "0211" "0211" "0333" "0223" "0252" "0114"
#> TCGA.IM.A3U2.01 TCGA.IM.A3U3.01 TCGA.DJ.A3UX.01 TCGA.ET.A3BW.01 TCGA.ET.A39S.01 TCGA.ET.A3BP.01
#> "032" "032" "015" "0111" "0114" "0112"
#> TCGA.DJ.A1QE.01 TCGA.EL.A3D4.01 TCGA.FK.A3SB.01 TCGA.EL.A3CW.01 TCGA.ET.A39L.01 TCGA.DJ.A2PW.01
#> "0331" "012" "0333" "02321" "0252" "031"
#> TCGA.EM.A2CO.01 TCGA.FE.A232.01 TCGA.DJ.A3UR.01 TCGA.DJ.A2PP.01 TCGA.ET.A3DQ.01 TCGA.ET.A3DS.01
#> "0222" "0112" "0111" "0242" "02321" "0222"
#> TCGA.FY.A3W9.01 TCGA.FK.A3S3.01 TCGA.ET.A2MZ.01 TCGA.BJ.A2NA.11 TCGA.DJ.A1QL.01 TCGA.EL.A3CS.01
#> "0244" "0114" "031" "0233" "0242" "015"
#> TCGA.FE.A233.01 TCGA.EM.A1YD.11 TCGA.ET.A3DW.11 TCGA.EL.A3T9.01 TCGA.DJ.A3UM.01 TCGA.DO.A2HM.01
#> "0331" "0211" "0212" "032" "032" "0142"
#> TCGA.FY.A3BL.01 TCGA.EL.A3TA.11 TCGA.ET.A3BX.01 TCGA.DJ.A1QQ.01 TCGA.DJ.A1QF.01 TCGA.DJ.A1QO.01
#> "012" "0212" "031" "031" "0112" "031"
#> TCGA.BJ.A2NA.01 TCGA.EM.A1YE.01 TCGA.FY.A2QD.01 TCGA.ET.A39J.01 TCGA.ET.A3DU.01 TCGA.EL.A3CM.01
#> "031" "0223" "02413" "034" "0133" "032"
#> TCGA.DJ.A3UO.01 TCGA.ET.A39P.01 TCGA.DJ.A2Q2.01 TCGA.BJ.A28V.01 TCGA.ET.A3BO.01 TCGA.EL.A3T1.01
#> "031" "0331" "0222" "02411" "032" "015"
#> TCGA.DJ.A1QI.01 TCGA.EL.A3TB.01 TCGA.BJ.A28X.11 TCGA.DJ.A1QN.01 TCGA.FE.A230.01 TCGA.FE.A234.01
#> "0333" "032" "0231" "0333" "015" "0331"
#> TCGA.ET.A39R.01 TCGA.DJ.A1QG.01 TCGA.EL.A3CV.01 TCGA.FE.A231.01 TCGA.EL.A3TA.01 TCGA.DJ.A3UY.01
#> "015" "0251" "0142" "031" "012" "015"
#> TCGA.DJ.A2Q1.01 TCGA.EL.A3CU.01 TCGA.EL.A3TB.11 TCGA.ET.A39I.01 TCGA.EM.A1YB.01 TCGA.DJ.A3UV.01
#> "0131" "0133" "0211" "0252" "02414" "0113"
#> TCGA.DJ.A3UT.01 TCGA.ET.A3DW.01 TCGA.ET.A3BT.01 TCGA.EL.A3T3.01 TCGA.DJ.A1QM.01 TCGA.EL.A3CY.01
#> "0252" "031" "032" "032" "0212" "0231"
#> TCGA.ET.A39O.01 TCGA.EM.A1YC.11 TCGA.DJ.A1QH.01 TCGA.EL.A3T3.11 TCGA.EL.A3CX.01 TCGA.EL.A3T2.01
#> "031" "0211" "0332" "0211" "0113" "0252"
#> TCGA.EM.A22P.01 TCGA.EL.A3T8.11 TCGA.DJ.A2PU.01 TCGA.DJ.A3UK.01 TCGA.ET.A3DO.01 TCGA.EM.A1YA.01
#> "0142" "0212" "0333" "0111" "0131" "0223"
#> TCGA.ET.A3BV.01 TCGA.EL.A3CO.01 TCGA.DJ.A2PN.01 TCGA.FK.A3SG.01 TCGA.FK.A3SH.01 TCGA.EM.A1YD.01
#> "0131" "0233" "0333" "032" "032" "0223"
#> TCGA.DJ.A1QD.01 TCGA.EL.A3CZ.01 TCGA.BJ.A0Z9.01 TCGA.CE.A13K.01 TCGA.EM.A3FR.01 TCGA.EM.A3O8.01
#> "0331" "0222" "0132" "032" "02413" "0252"
#> TCGA.FY.A3R6.01 TCGA.FY.A3R9.01 TCGA.EL.A3D1.01 TCGA.EM.A3O6.01 TCGA.BJ.A0Z5.01 TCGA.BJ.A28S.01
#> "0131" "0222" "031" "0222" "012" "0251"
#> TCGA.BJ.A0ZH.01 TCGA.ET.A3DT.01 TCGA.H2.A3RI.11 TCGA.DJ.A13W.01 TCGA.DJ.A13T.01 TCGA.BJ.A0ZA.01
#> "032" "0131" "0211" "02411" "032" "02414"
#> TCGA.BJ.A3PT.01 TCGA.FE.A3PD.01 TCGA.BJ.A0ZF.01 TCGA.ET.A39M.01 TCGA.BJ.A0ZJ.01 TCGA.BJ.A0YZ.01
#> "0252" "032" "0224" "0143" "0143" "0221"
#> TCGA.FE.A3PC.01 TCGA.DJ.A2QB.01 TCGA.EM.A3OB.01 TCGA.H2.A3RH.01 TCGA.ET.A39T.01 TCGA.DJ.A2PV.01
#> "032" "0252" "0252" "0252" "0112" "0111"
#> TCGA.BJ.A3PR.11 TCGA.EL.A3T6.11 TCGA.DJ.A13X.01 TCGA.BJ.A0ZG.01 TCGA.EL.A3T6.01 TCGA.BJ.A0Z0.01
#> "02321" "0233" "0111" "0221" "0133" "0242"
#> TCGA.ET.A39K.01 TCGA.EM.A3O9.01 TCGA.BJ.A3PU.01 TCGA.BJ.A3PR.01 TCGA.EM.A3O3.01 TCGA.BJ.A0ZB.01
#> "032" "0234" "031" "0231" "0132" "031"
#> TCGA.EM.A3OA.01 TCGA.DJ.A2PR.01 TCGA.DJ.A13L.01 TCGA.FY.A3ON.01 TCGA.DJ.A13V.01 TCGA.FY.A3R8.01
#> "02412" "031" "0142" "031" "032" "032"
#> TCGA.EL.A3CP.01 TCGA.DJ.A13U.01 TCGA.DE.A0Y3.01 TCGA.ET.A2N4.01 TCGA.DJ.A13P.01 TCGA.BJ.A0ZE.01
#> "0333" "012" "032" "0111" "0111" "0252"
#> TCGA.EM.A3O7.01 TCGA.DJ.A13O.01 TCGA.FY.A3RA.01 TCGA.DJ.A13M.01 TCGA.DJ.A13R.01 TCGA.ET.A3DR.01
#> "0111" "0233" "0331" "0252" "0221" "0113"
#> TCGA.FE.A3PB.01 TCGA.ET.A3BN.01 TCGA.H2.A3RI.01 TCGA.ET.A39N.01 TCGA.BJ.A3PU.11 TCGA.FY.A3R7.01
#> "015" "0331" "032" "0224" "0212" "0222"
#> TCGA.FE.A3PA.01 TCGA.EM.A2CN.01 TCGA.BJ.A0Z2.01 TCGA.FY.A3I5.01 TCGA.DJ.A13S.01 TCGA.DE.A0Y2.01
#> "031" "0243" "0243" "02414" "0252" "0331"
#> TCGA.ET.A3BU.01
#> "031"
get_classes(res_rh, merge_node = merge_node_param(min_n_signatures = 1595))
#> TCGA.E8.A416.01 TCGA.E8.A433.01 TCGA.EL.A4K9.01 TCGA.DJ.A3V9.01 TCGA.EL.A3ZO.11 TCGA.EL.A3ZN.01
#> "0211" "015" "031" "0114" "0211" "0113"
#> TCGA.KS.A41F.01 TCGA.EL.A3ZK.01 TCGA.ET.A40R.01 TCGA.EL.A3ZM.01 TCGA.ET.A2N3.01 TCGA.EL.A3ZQ.01
#> "032" "015" "015" "031" "02411" "032"
#> TCGA.ET.A40T.01 TCGA.DE.A4MA.01 TCGA.EM.A4FU.01 TCGA.E8.A418.01 TCGA.DJ.A3VD.01 TCGA.DJ.A3VM.01
#> "032" "032" "0251" "032" "0131" "0244"
#> TCGA.EL.A3ZG.01 TCGA.EM.A4FV.01 TCGA.E8.A413.01 TCGA.DJ.A3VG.01 TCGA.EL.A4K2.01 TCGA.IM.A420.01
#> "012" "015" "015" "0251" "0222" "0133"
#> TCGA.KS.A41J.01 TCGA.EL.A3ZK.11 TCGA.J8.A3O2.01 TCGA.E8.A415.01 TCGA.FY.A40M.01 TCGA.DJ.A3VB.01
#> "032" "02321" "012" "0114" "0252" "031"
#> TCGA.KS.A41I.01 TCGA.DJ.A3VL.01 TCGA.ET.A4KQ.01 TCGA.H2.A421.01 TCGA.EL.A3ZO.01 TCGA.KS.A4I3.01
#> "0252" "0234" "0252" "032" "032" "012"
#> TCGA.DJ.A4UT.01 TCGA.DE.A4MD.01 TCGA.EL.A4JW.01 TCGA.DJ.A3VI.01 TCGA.DJ.A3VA.01 TCGA.L6.A4ET.01
#> "0131" "031" "015" "032" "032" "0333"
#> TCGA.E8.A419.01 TCGA.DJ.A4V0.01 TCGA.DJ.A4V2.01 TCGA.ET.A40Q.01 TCGA.EL.A3ZS.01 TCGA.KS.A4ID.01
#> "0133" "02321" "0331" "031" "0131" "0133"
#> TCGA.EL.A3ZL.11 TCGA.J8.A3YE.01 TCGA.EL.A4K7.01 TCGA.DJ.A3VF.01 TCGA.EM.A4FH.01 TCGA.E8.A432.01
#> "0211" "0112" "031" "0133" "0221" "015"
#> TCGA.J8.A3O2.06 TCGA.ET.A2MX.01 TCGA.ET.A40S.01 TCGA.DE.A4M8.01 TCGA.IM.A41Z.01 TCGA.EL.A4KD.01
#> "031" "012" "0142" "0131" "02412" "012"
#> TCGA.DJ.A3V7.01 TCGA.FY.A40L.01 TCGA.DE.A4M9.01 TCGA.J8.A42S.01 TCGA.KS.A41L.01 TCGA.EM.A4FN.01
#> "032" "015" "0221" "012" "0224" "0331"
#> TCGA.EL.A4K1.01 TCGA.KS.A4IC.01 TCGA.E8.A414.01 TCGA.H2.A422.01 TCGA.J8.A3YF.01 TCGA.EL.A4KI.01
#> "0331" "0112" "015" "032" "031" "0243"
#> TCGA.EM.A4G1.01 TCGA.DJ.A3VJ.01 TCGA.DE.A4MD.06 TCGA.EL.A3ZP.01 TCGA.EM.A4FQ.01 TCGA.EL.A3ZT.01
#> "0252" "031" "0141" "031" "0331" "031"
#> TCGA.DJ.A4V4.01 TCGA.FY.A40K.01 TCGA.L6.A4EQ.01 TCGA.DJ.A3VE.01 TCGA.E8.A434.01 TCGA.EL.A3ZH.01
#> "0112" "0111" "031" "031" "0222" "0222"
#> TCGA.EM.A4FR.01 TCGA.EL.A3ZH.11 TCGA.EL.A3ZR.01 TCGA.DJ.A3V8.01 TCGA.EL.A3ZG.11 TCGA.ET.A40P.01
#> "012" "0211" "0252" "015" "0212" "0252"
#> TCGA.DE.A4MB.01 TCGA.MK.A4N6.01 TCGA.DJ.A3VK.01 TCGA.E8.A417.01 TCGA.L6.A4EU.01 TCGA.J8.A4HY.01
#> "032" "031" "0251" "032" "032" "0112"
#> TCGA.EL.A3ZL.01 TCGA.EL.A3ZP.11 TCGA.FY.A40N.01 TCGA.J8.A4HW.01 TCGA.BJ.A45J.01 TCGA.CE.A482.01
#> "032" "02322" "0114" "032" "032" "032"
#> TCGA.DJ.A2Q6.01 TCGA.DJ.A2PX.01 TCGA.DJ.A4UL.01 TCGA.EL.A4JX.01 TCGA.BJ.A2N8.11 TCGA.DJ.A2Q5.01
#> "032" "015" "0333" "0131" "0211" "0143"
#> TCGA.EL.A4KG.01 TCGA.DJ.A4UP.01 TCGA.E8.A438.01 TCGA.EL.A3H2.01 TCGA.EM.A3AP.01 TCGA.DJ.A2PQ.01
#> "0333" "015" "0113" "0221" "0252" "031"
#> TCGA.L6.A4EP.01 TCGA.FY.A4B4.01 TCGA.EL.A4KH.01 TCGA.BJ.A45E.01 TCGA.DJ.A4V5.01 TCGA.DE.A4MC.01
#> "0333" "032" "0111" "0231" "0143" "0332"
#> TCGA.E8.A44M.01 TCGA.BJ.A45K.01 TCGA.E3.A3DZ.01 TCGA.E3.A3E2.01 TCGA.BJ.A45H.01 TCGA.E8.A44K.01
#> "0131" "0242" "0252" "032" "012" "015"
#> TCGA.ET.A2MY.01 TCGA.EL.A3H8.01 TCGA.BJ.A45C.01 TCGA.BJ.A45G.01 TCGA.EL.A4JZ.01 TCGA.CE.A481.01
#> "032" "0333" "0242" "0252" "0332" "015"
#> TCGA.KS.A4I9.01 TCGA.EL.A3MW.01 TCGA.E8.A436.01 TCGA.E3.A3DY.01 TCGA.DJ.A2Q3.01 TCGA.BJ.A2P4.01
#> "0331" "0333" "015" "031" "0133" "0252"
#> TCGA.CE.A484.01 TCGA.ET.A2N1.01 TCGA.DJ.A2Q4.01 TCGA.DJ.A2PZ.01 TCGA.BJ.A45F.01 TCGA.IM.A4EB.01
#> "0252" "0113" "031" "012" "0252" "0143"
#> TCGA.EM.A4FO.01 TCGA.FY.A4B3.01 TCGA.FY.A4B0.01 TCGA.BJ.A45I.01 TCGA.E3.A3E3.01 TCGA.EM.A3AQ.01
#> "0142" "031" "0242" "0133" "0331" "034"
#> TCGA.EL.A3N3.01 TCGA.DJ.A2Q9.01 TCGA.EM.A4FM.01 TCGA.EL.A4K6.01 TCGA.MK.A4N9.01 TCGA.KS.A4I1.01
#> "0133" "0231" "0332" "0243" "0333" "032"
#> TCGA.DJ.A2PS.01 TCGA.CE.A3MD.01 TCGA.E3.A3E5.01 TCGA.EL.A3CN.01 TCGA.J8.A4HW.06 TCGA.EM.A4FK.01
#> "0114" "012" "031" "015" "0131" "02412"
#> TCGA.E8.A437.01 TCGA.BJ.A4O8.01 TCGA.EL.A3MW.11 TCGA.E3.A3E0.01 TCGA.BJ.A45D.01 TCGA.CE.A483.01
#> "0114" "031" "0211" "0333" "0251" "0112"
#> TCGA.CE.A485.01 TCGA.DJ.A4UR.01 TCGA.IM.A41Y.01 TCGA.ET.A4KN.01 TCGA.KS.A4I5.01 TCGA.DJ.A4UQ.01
#> "012" "0244" "032" "0133" "0333" "012"
#> TCGA.KS.A4IB.01 TCGA.EL.A3N2.11 TCGA.BJ.A2N9.01 TCGA.DJ.A4UW.01 TCGA.EL.A3GZ.11 TCGA.EM.A3AR.01
#> "0331" "0211" "0222" "0114" "0211" "0212"
#> TCGA.EL.A3N3.11 TCGA.DE.A3KN.01 TCGA.DJ.A2QA.01 TCGA.EL.A4JV.01 TCGA.EM.A4FF.01 TCGA.EL.A4K0.01
#> "02321" "0113" "0114" "0252" "0331" "0333"
#> TCGA.FK.A4UB.01 TCGA.BJ.A4O9.01 TCGA.BJ.A2N7.01 TCGA.DE.A2OL.01 TCGA.CE.A3ME.01 TCGA.MK.A4N7.01
#> "031" "0112" "0252" "02411" "0112" "032"
#> TCGA.EL.A3H2.11 TCGA.EL.A4K4.01 TCGA.EL.A3GS.01 TCGA.EL.A3GZ.01 TCGA.E3.A3E1.01 TCGA.DJ.A2Q8.01
#> "0212" "0331" "0331" "032" "0112" "015"
#> TCGA.EL.A3N2.01 TCGA.KS.A4I7.01 TCGA.MK.A84Z.01 TCGA.ET.A3DP.11 TCGA.EL.A3MX.11 TCGA.ET.A25G.01
#> "0331" "032" "0251" "0211" "0211" "032"
#> TCGA.EM.A3FK.01 TCGA.EM.A2CS.01 TCGA.FE.A23A.01 TCGA.BJ.A28T.11 TCGA.EM.A22J.01 TCGA.EL.A3MX.01
#> "034" "032" "0133" "0211" "02412" "0332"
#> TCGA.FY.A3I4.01 TCGA.BJ.A28W.11 TCGA.ET.A25R.01 TCGA.BJ.A2N8.01 TCGA.FY.A76V.01 TCGA.EM.A3FN.01
#> "0114" "02321" "032" "0252" "0251" "02413"
#> TCGA.QD.A8IV.01 TCGA.EM.A3FJ.01 TCGA.ET.A2MY.11 TCGA.EM.A3FQ.06 TCGA.ET.A25P.01 TCGA.ET.A2N0.01
#> "0252" "0333" "02413" "0333" "0252" "015"
#> TCGA.EM.A2CT.01 TCGA.FE.A235.01 TCGA.ET.A25M.01 TCGA.EL.A3MY.01 TCGA.DE.A7U5.01 TCGA.E8.A2JQ.11
#> "0222" "0333" "031" "031" "0331" "0231"
#> TCGA.ET.A3DP.01 TCGA.EM.A2CL.01 TCGA.ET.A2N5.01 TCGA.ET.A25J.11 TCGA.DE.A69J.01 TCGA.BJ.A28R.11
#> "0111" "0242" "0252" "0211" "0333" "02321"
#> TCGA.ET.A25K.01 TCGA.EL.A3GV.01 TCGA.GE.A2C6.01 TCGA.EM.A3FM.01 TCGA.EL.A3H7.11 TCGA.FE.A22Z.01
#> "032" "0111" "0133" "031" "0211" "0332"
#> TCGA.H2.A2K9.01 TCGA.EM.A22Q.01 TCGA.EM.A3FP.01 TCGA.GE.A2C6.11 TCGA.EL.A3MZ.01 TCGA.DJ.A2PT.01
#> "0243" "0242" "0252" "02321" "031" "0133"
#> TCGA.E8.A242.01 TCGA.ET.A25L.01 TCGA.CE.A27D.01 TCGA.EL.A3H1.11 TCGA.BJ.A2N7.11 TCGA.DJ.A2Q7.01
#> "0133" "032" "0233" "0233" "0211" "0333"
#> TCGA.J8.A3O1.01 TCGA.EM.A2CR.01 TCGA.DE.A69K.01 TCGA.EM.A2CQ.01 TCGA.FE.A238.01 TCGA.EL.A3H1.01
#> "0113" "0114" "0333" "0222" "015" "02411"
#> TCGA.BJ.A28W.01 TCGA.BJ.A28T.01 TCGA.EM.A2CJ.01 TCGA.EM.A3FQ.01 TCGA.4C.A93U.01 TCGA.EM.A22M.01
#> "0231" "02321" "0223" "015" "0332" "0142"
#> TCGA.J8.A3NZ.01 TCGA.EM.A22K.01 TCGA.FE.A236.01 TCGA.BJ.A28R.01 TCGA.EM.A2CU.01 TCGA.ET.A25N.01
#> "0112" "0252" "012" "015" "015" "0333"
#> TCGA.EL.A3H7.01 TCGA.FY.A3NM.01 TCGA.EM.A3FO.01 TCGA.EM.A22L.01 TCGA.BJ.A2N9.11 TCGA.BJ.A291.01
#> "0331" "0223" "031" "0252" "0231" "0222"
#> TCGA.ET.A2N5.11 TCGA.ET.A25N.11 TCGA.J8.A3O0.01 TCGA.FE.A237.01 TCGA.DJ.A2QC.01 TCGA.ET.A25O.01
#> "0211" "0211" "0243" "0112" "0111" "0331"
#> TCGA.EL.A3GU.01 TCGA.EL.A3MY.11 TCGA.DJ.A2PY.01 TCGA.EM.A2CS.06 TCGA.FY.A3NP.01 TCGA.ET.A25I.01
#> "0332" "0221" "0331" "0114" "0251" "0222"
#> TCGA.H2.A26U.01 TCGA.BJ.A290.11 TCGA.EM.A22I.01 TCGA.FE.A239.01 TCGA.BJ.A28Z.01 TCGA.DE.A0XZ.01
#> "0133" "0212" "0331" "0242" "0131" "0333"
#> TCGA.ET.A25J.01 TCGA.EM.A22N.01 TCGA.EM.A2CM.01 TCGA.FY.A3NN.01 TCGA.EM.A3FL.01 TCGA.H2.A2K9.11
#> "0112" "0222" "0244" "0112" "0223" "0233"
#> TCGA.EL.A3H3.01 TCGA.EL.A3H4.01 TCGA.EM.A2OX.01 TCGA.EM.A3SX.01 TCGA.BJ.A0Z3.01 TCGA.BJ.A28X.01
#> "015" "032" "031" "032" "0131" "0131"
#> TCGA.EL.A3CT.01 TCGA.EL.A3CR.01 TCGA.FY.A3TY.01 TCGA.J8.A3YG.01 TCGA.DJ.A3V6.01 TCGA.EM.A3SZ.01
#> "0132" "032" "0233" "015" "031" "015"
#> TCGA.EM.A2OW.01 TCGA.DO.A1JZ.11 TCGA.EL.A3D5.01 TCGA.EM.A2P0.01 TCGA.E8.A2JQ.01 TCGA.BJ.A18Z.01
#> "0222" "0211" "0252" "012" "0131" "031"
#> TCGA.DJ.A3V0.01 TCGA.EL.A3GW.01 TCGA.DJ.A3UW.01 TCGA.DJ.A3V3.01 TCGA.EL.A3T1.11 TCGA.BJ.A0ZC.01
#> "031" "0252" "0131" "015" "02321" "0221"
#> TCGA.EM.A2OV.01 TCGA.EL.A3GY.01 TCGA.EM.A3SY.01 TCGA.EM.A3AI.01 TCGA.EM.A2OY.01 TCGA.EL.A3T8.01
#> "0222" "0331" "0212" "0222" "0223" "031"
#> TCGA.BJ.A18Y.01 TCGA.EL.A3GP.01 TCGA.EM.A2CK.01 TCGA.EL.A3T7.11 TCGA.BJ.A192.01 TCGA.BJ.A191.01
#> "0251" "0141" "0251" "0211" "0223" "0113"
#> TCGA.EM.A2CP.01 TCGA.EM.A22O.01 TCGA.EM.A2P1.01 TCGA.J8.A3YH.01 TCGA.DJ.A3UZ.01 TCGA.IM.A3EB.01
#> "0231" "031" "0142" "031" "0222" "0133"
#> TCGA.BJ.A3F0.01 TCGA.EL.A3GX.01 TCGA.EM.A3AK.01 TCGA.DO.A1JZ.01 TCGA.FY.A3YR.01 TCGA.DO.A1K0.01
#> "02414" "0331" "0114" "0333" "032" "0331"
#> TCGA.DJ.A3V5.01 TCGA.EM.A3AJ.01 TCGA.IM.A3ED.01 TCGA.EM.A3AO.01 TCGA.EM.A2P1.06 TCGA.EM.A1CW.01
#> "032" "02322" "0333" "012" "0142" "0222"
#> TCGA.FK.A3SE.01 TCGA.EL.A3T7.01 TCGA.EM.A2P2.01 TCGA.EM.A1CU.11 TCGA.EL.A3T0.11 TCGA.E8.A3X7.01
#> "032" "032" "0251" "0212" "0211" "032"
#> TCGA.ET.A3BQ.01 TCGA.EM.A1CS.01 TCGA.EL.A3GQ.01 TCGA.EL.A3H5.01 TCGA.DJ.A3V4.01 TCGA.EM.A2P3.01
#> "0333" "0111" "0111" "0332" "0112" "0331"
#> TCGA.FY.A3WA.01 TCGA.DJ.A3V2.01 TCGA.FY.A3TY.11 TCGA.BJ.A290.01 TCGA.EM.A3SU.01 TCGA.EL.A3D0.01
#> "0223" "0131" "0211" "012" "015" "031"
#> TCGA.EM.A1CT.11 TCGA.EL.A3GR.01 TCGA.J8.A3YH.06 TCGA.EM.A3ST.11 TCGA.ET.A3DV.01 TCGA.BJ.A3EZ.01
#> "0212" "0114" "031" "0211" "02411" "031"
#> TCGA.J8.A3YD.01 TCGA.EM.A3SU.06 TCGA.EM.A3AL.01 TCGA.DJ.A3US.01 TCGA.EM.A1CS.11 TCGA.EM.A1CW.11
#> "0222" "0131" "02411" "015" "0211" "0211"
#> TCGA.BJ.A190.01 TCGA.EM.A2OZ.01 TCGA.EM.A1CV.11 TCGA.EM.A1CU.01 TCGA.EM.A3AN.01 TCGA.E8.A2EA.01
#> "0221" "012" "0211" "031" "032" "0133"
#> TCGA.EM.A1CV.01 TCGA.EM.A1CT.01 TCGA.EM.A3ST.01 TCGA.ET.A3BS.01 TCGA.EL.A3GO.01 TCGA.DJ.A2Q0.01
#> "0111" "012" "0244" "0143" "02411" "0223"
#> TCGA.EL.A3D6.01 TCGA.DJ.A3UN.01 TCGA.DJ.A3UU.01 TCGA.FK.A3SD.01 TCGA.DJ.A2PO.01 TCGA.DJ.A3UQ.01
#> "032" "032" "0114" "02413" "012" "015"
#> TCGA.EM.A1YE.11 TCGA.EL.A3T2.11 TCGA.EL.A3CL.01 TCGA.EM.A1YC.01 TCGA.DJ.A3UP.01 TCGA.EL.A3T0.01
#> "0211" "0211" "0333" "0223" "0252" "0114"
#> TCGA.IM.A3U2.01 TCGA.IM.A3U3.01 TCGA.DJ.A3UX.01 TCGA.ET.A3BW.01 TCGA.ET.A39S.01 TCGA.ET.A3BP.01
#> "032" "032" "015" "0111" "0114" "0112"
#> TCGA.DJ.A1QE.01 TCGA.EL.A3D4.01 TCGA.FK.A3SB.01 TCGA.EL.A3CW.01 TCGA.ET.A39L.01 TCGA.DJ.A2PW.01
#> "0331" "012" "0333" "02321" "0252" "031"
#> TCGA.EM.A2CO.01 TCGA.FE.A232.01 TCGA.DJ.A3UR.01 TCGA.DJ.A2PP.01 TCGA.ET.A3DQ.01 TCGA.ET.A3DS.01
#> "0222" "0112" "0111" "0242" "02321" "0222"
#> TCGA.FY.A3W9.01 TCGA.FK.A3S3.01 TCGA.ET.A2MZ.01 TCGA.BJ.A2NA.11 TCGA.DJ.A1QL.01 TCGA.EL.A3CS.01
#> "0244" "0114" "031" "0233" "0242" "015"
#> TCGA.FE.A233.01 TCGA.EM.A1YD.11 TCGA.ET.A3DW.11 TCGA.EL.A3T9.01 TCGA.DJ.A3UM.01 TCGA.DO.A2HM.01
#> "0331" "0211" "0212" "032" "032" "0142"
#> TCGA.FY.A3BL.01 TCGA.EL.A3TA.11 TCGA.ET.A3BX.01 TCGA.DJ.A1QQ.01 TCGA.DJ.A1QF.01 TCGA.DJ.A1QO.01
#> "012" "0212" "031" "031" "0112" "031"
#> TCGA.BJ.A2NA.01 TCGA.EM.A1YE.01 TCGA.FY.A2QD.01 TCGA.ET.A39J.01 TCGA.ET.A3DU.01 TCGA.EL.A3CM.01
#> "031" "0223" "02413" "034" "0133" "032"
#> TCGA.DJ.A3UO.01 TCGA.ET.A39P.01 TCGA.DJ.A2Q2.01 TCGA.BJ.A28V.01 TCGA.ET.A3BO.01 TCGA.EL.A3T1.01
#> "031" "0331" "0222" "02411" "032" "015"
#> TCGA.DJ.A1QI.01 TCGA.EL.A3TB.01 TCGA.BJ.A28X.11 TCGA.DJ.A1QN.01 TCGA.FE.A230.01 TCGA.FE.A234.01
#> "0333" "032" "0231" "0333" "015" "0331"
#> TCGA.ET.A39R.01 TCGA.DJ.A1QG.01 TCGA.EL.A3CV.01 TCGA.FE.A231.01 TCGA.EL.A3TA.01 TCGA.DJ.A3UY.01
#> "015" "0251" "0142" "031" "012" "015"
#> TCGA.DJ.A2Q1.01 TCGA.EL.A3CU.01 TCGA.EL.A3TB.11 TCGA.ET.A39I.01 TCGA.EM.A1YB.01 TCGA.DJ.A3UV.01
#> "0131" "0133" "0211" "0252" "02414" "0113"
#> TCGA.DJ.A3UT.01 TCGA.ET.A3DW.01 TCGA.ET.A3BT.01 TCGA.EL.A3T3.01 TCGA.DJ.A1QM.01 TCGA.EL.A3CY.01
#> "0252" "031" "032" "032" "0212" "0231"
#> TCGA.ET.A39O.01 TCGA.EM.A1YC.11 TCGA.DJ.A1QH.01 TCGA.EL.A3T3.11 TCGA.EL.A3CX.01 TCGA.EL.A3T2.01
#> "031" "0211" "0332" "0211" "0113" "0252"
#> TCGA.EM.A22P.01 TCGA.EL.A3T8.11 TCGA.DJ.A2PU.01 TCGA.DJ.A3UK.01 TCGA.ET.A3DO.01 TCGA.EM.A1YA.01
#> "0142" "0212" "0333" "0111" "0131" "0223"
#> TCGA.ET.A3BV.01 TCGA.EL.A3CO.01 TCGA.DJ.A2PN.01 TCGA.FK.A3SG.01 TCGA.FK.A3SH.01 TCGA.EM.A1YD.01
#> "0131" "0233" "0333" "032" "032" "0223"
#> TCGA.DJ.A1QD.01 TCGA.EL.A3CZ.01 TCGA.BJ.A0Z9.01 TCGA.CE.A13K.01 TCGA.EM.A3FR.01 TCGA.EM.A3O8.01
#> "0331" "0222" "0132" "032" "02413" "0252"
#> TCGA.FY.A3R6.01 TCGA.FY.A3R9.01 TCGA.EL.A3D1.01 TCGA.EM.A3O6.01 TCGA.BJ.A0Z5.01 TCGA.BJ.A28S.01
#> "0131" "0222" "031" "0222" "012" "0251"
#> TCGA.BJ.A0ZH.01 TCGA.ET.A3DT.01 TCGA.H2.A3RI.11 TCGA.DJ.A13W.01 TCGA.DJ.A13T.01 TCGA.BJ.A0ZA.01
#> "032" "0131" "0211" "02411" "032" "02414"
#> TCGA.BJ.A3PT.01 TCGA.FE.A3PD.01 TCGA.BJ.A0ZF.01 TCGA.ET.A39M.01 TCGA.BJ.A0ZJ.01 TCGA.BJ.A0YZ.01
#> "0252" "032" "0224" "0143" "0143" "0221"
#> TCGA.FE.A3PC.01 TCGA.DJ.A2QB.01 TCGA.EM.A3OB.01 TCGA.H2.A3RH.01 TCGA.ET.A39T.01 TCGA.DJ.A2PV.01
#> "032" "0252" "0252" "0252" "0112" "0111"
#> TCGA.BJ.A3PR.11 TCGA.EL.A3T6.11 TCGA.DJ.A13X.01 TCGA.BJ.A0ZG.01 TCGA.EL.A3T6.01 TCGA.BJ.A0Z0.01
#> "02321" "0233" "0111" "0221" "0133" "0242"
#> TCGA.ET.A39K.01 TCGA.EM.A3O9.01 TCGA.BJ.A3PU.01 TCGA.BJ.A3PR.01 TCGA.EM.A3O3.01 TCGA.BJ.A0ZB.01
#> "032" "0234" "031" "0231" "0132" "031"
#> TCGA.EM.A3OA.01 TCGA.DJ.A2PR.01 TCGA.DJ.A13L.01 TCGA.FY.A3ON.01 TCGA.DJ.A13V.01 TCGA.FY.A3R8.01
#> "02412" "031" "0142" "031" "032" "032"
#> TCGA.EL.A3CP.01 TCGA.DJ.A13U.01 TCGA.DE.A0Y3.01 TCGA.ET.A2N4.01 TCGA.DJ.A13P.01 TCGA.BJ.A0ZE.01
#> "0333" "012" "032" "0111" "0111" "0252"
#> TCGA.EM.A3O7.01 TCGA.DJ.A13O.01 TCGA.FY.A3RA.01 TCGA.DJ.A13M.01 TCGA.DJ.A13R.01 TCGA.ET.A3DR.01
#> "0111" "0233" "0331" "0252" "0221" "0113"
#> TCGA.FE.A3PB.01 TCGA.ET.A3BN.01 TCGA.H2.A3RI.01 TCGA.ET.A39N.01 TCGA.BJ.A3PU.11 TCGA.FY.A3R7.01
#> "015" "0331" "032" "0224" "0212" "0222"
#> TCGA.FE.A3PA.01 TCGA.EM.A2CN.01 TCGA.BJ.A0Z2.01 TCGA.FY.A3I5.01 TCGA.DJ.A13S.01 TCGA.DE.A0Y2.01
#> "031" "0243" "0243" "02414" "0252" "0331"
#> TCGA.ET.A3BU.01
#> "031"
get_classes(res_rh, merge_node = merge_node_param(min_n_signatures = 1662))
#> TCGA.E8.A416.01 TCGA.E8.A433.01 TCGA.EL.A4K9.01 TCGA.DJ.A3V9.01 TCGA.EL.A3ZO.11 TCGA.EL.A3ZN.01
#> "0211" "015" "031" "011" "0211" "011"
#> TCGA.KS.A41F.01 TCGA.EL.A3ZK.01 TCGA.ET.A40R.01 TCGA.EL.A3ZM.01 TCGA.ET.A2N3.01 TCGA.EL.A3ZQ.01
#> "032" "015" "015" "031" "02411" "032"
#> TCGA.ET.A40T.01 TCGA.DE.A4MA.01 TCGA.EM.A4FU.01 TCGA.E8.A418.01 TCGA.DJ.A3VD.01 TCGA.DJ.A3VM.01
#> "032" "032" "0251" "032" "0131" "0244"
#> TCGA.EL.A3ZG.01 TCGA.EM.A4FV.01 TCGA.E8.A413.01 TCGA.DJ.A3VG.01 TCGA.EL.A4K2.01 TCGA.IM.A420.01
#> "012" "015" "015" "0251" "0222" "0133"
#> TCGA.KS.A41J.01 TCGA.EL.A3ZK.11 TCGA.J8.A3O2.01 TCGA.E8.A415.01 TCGA.FY.A40M.01 TCGA.DJ.A3VB.01
#> "032" "02321" "012" "011" "0252" "031"
#> TCGA.KS.A41I.01 TCGA.DJ.A3VL.01 TCGA.ET.A4KQ.01 TCGA.H2.A421.01 TCGA.EL.A3ZO.01 TCGA.KS.A4I3.01
#> "0252" "0234" "0252" "032" "032" "012"
#> TCGA.DJ.A4UT.01 TCGA.DE.A4MD.01 TCGA.EL.A4JW.01 TCGA.DJ.A3VI.01 TCGA.DJ.A3VA.01 TCGA.L6.A4ET.01
#> "0131" "031" "015" "032" "032" "0333"
#> TCGA.E8.A419.01 TCGA.DJ.A4V0.01 TCGA.DJ.A4V2.01 TCGA.ET.A40Q.01 TCGA.EL.A3ZS.01 TCGA.KS.A4ID.01
#> "0133" "02321" "0331" "031" "0131" "0133"
#> TCGA.EL.A3ZL.11 TCGA.J8.A3YE.01 TCGA.EL.A4K7.01 TCGA.DJ.A3VF.01 TCGA.EM.A4FH.01 TCGA.E8.A432.01
#> "0211" "011" "031" "0133" "0221" "015"
#> TCGA.J8.A3O2.06 TCGA.ET.A2MX.01 TCGA.ET.A40S.01 TCGA.DE.A4M8.01 TCGA.IM.A41Z.01 TCGA.EL.A4KD.01
#> "031" "012" "0142" "0131" "02412" "012"
#> TCGA.DJ.A3V7.01 TCGA.FY.A40L.01 TCGA.DE.A4M9.01 TCGA.J8.A42S.01 TCGA.KS.A41L.01 TCGA.EM.A4FN.01
#> "032" "015" "0221" "012" "0224" "0331"
#> TCGA.EL.A4K1.01 TCGA.KS.A4IC.01 TCGA.E8.A414.01 TCGA.H2.A422.01 TCGA.J8.A3YF.01 TCGA.EL.A4KI.01
#> "0331" "011" "015" "032" "031" "0243"
#> TCGA.EM.A4G1.01 TCGA.DJ.A3VJ.01 TCGA.DE.A4MD.06 TCGA.EL.A3ZP.01 TCGA.EM.A4FQ.01 TCGA.EL.A3ZT.01
#> "0252" "031" "0141" "031" "0331" "031"
#> TCGA.DJ.A4V4.01 TCGA.FY.A40K.01 TCGA.L6.A4EQ.01 TCGA.DJ.A3VE.01 TCGA.E8.A434.01 TCGA.EL.A3ZH.01
#> "011" "011" "031" "031" "0222" "0222"
#> TCGA.EM.A4FR.01 TCGA.EL.A3ZH.11 TCGA.EL.A3ZR.01 TCGA.DJ.A3V8.01 TCGA.EL.A3ZG.11 TCGA.ET.A40P.01
#> "012" "0211" "0252" "015" "0212" "0252"
#> TCGA.DE.A4MB.01 TCGA.MK.A4N6.01 TCGA.DJ.A3VK.01 TCGA.E8.A417.01 TCGA.L6.A4EU.01 TCGA.J8.A4HY.01
#> "032" "031" "0251" "032" "032" "011"
#> TCGA.EL.A3ZL.01 TCGA.EL.A3ZP.11 TCGA.FY.A40N.01 TCGA.J8.A4HW.01 TCGA.BJ.A45J.01 TCGA.CE.A482.01
#> "032" "02322" "011" "032" "032" "032"
#> TCGA.DJ.A2Q6.01 TCGA.DJ.A2PX.01 TCGA.DJ.A4UL.01 TCGA.EL.A4JX.01 TCGA.BJ.A2N8.11 TCGA.DJ.A2Q5.01
#> "032" "015" "0333" "0131" "0211" "0143"
#> TCGA.EL.A4KG.01 TCGA.DJ.A4UP.01 TCGA.E8.A438.01 TCGA.EL.A3H2.01 TCGA.EM.A3AP.01 TCGA.DJ.A2PQ.01
#> "0333" "015" "011" "0221" "0252" "031"
#> TCGA.L6.A4EP.01 TCGA.FY.A4B4.01 TCGA.EL.A4KH.01 TCGA.BJ.A45E.01 TCGA.DJ.A4V5.01 TCGA.DE.A4MC.01
#> "0333" "032" "011" "0231" "0143" "0332"
#> TCGA.E8.A44M.01 TCGA.BJ.A45K.01 TCGA.E3.A3DZ.01 TCGA.E3.A3E2.01 TCGA.BJ.A45H.01 TCGA.E8.A44K.01
#> "0131" "0242" "0252" "032" "012" "015"
#> TCGA.ET.A2MY.01 TCGA.EL.A3H8.01 TCGA.BJ.A45C.01 TCGA.BJ.A45G.01 TCGA.EL.A4JZ.01 TCGA.CE.A481.01
#> "032" "0333" "0242" "0252" "0332" "015"
#> TCGA.KS.A4I9.01 TCGA.EL.A3MW.01 TCGA.E8.A436.01 TCGA.E3.A3DY.01 TCGA.DJ.A2Q3.01 TCGA.BJ.A2P4.01
#> "0331" "0333" "015" "031" "0133" "0252"
#> TCGA.CE.A484.01 TCGA.ET.A2N1.01 TCGA.DJ.A2Q4.01 TCGA.DJ.A2PZ.01 TCGA.BJ.A45F.01 TCGA.IM.A4EB.01
#> "0252" "011" "031" "012" "0252" "0143"
#> TCGA.EM.A4FO.01 TCGA.FY.A4B3.01 TCGA.FY.A4B0.01 TCGA.BJ.A45I.01 TCGA.E3.A3E3.01 TCGA.EM.A3AQ.01
#> "0142" "031" "0242" "0133" "0331" "034"
#> TCGA.EL.A3N3.01 TCGA.DJ.A2Q9.01 TCGA.EM.A4FM.01 TCGA.EL.A4K6.01 TCGA.MK.A4N9.01 TCGA.KS.A4I1.01
#> "0133" "0231" "0332" "0243" "0333" "032"
#> TCGA.DJ.A2PS.01 TCGA.CE.A3MD.01 TCGA.E3.A3E5.01 TCGA.EL.A3CN.01 TCGA.J8.A4HW.06 TCGA.EM.A4FK.01
#> "011" "012" "031" "015" "0131" "02412"
#> TCGA.E8.A437.01 TCGA.BJ.A4O8.01 TCGA.EL.A3MW.11 TCGA.E3.A3E0.01 TCGA.BJ.A45D.01 TCGA.CE.A483.01
#> "011" "031" "0211" "0333" "0251" "011"
#> TCGA.CE.A485.01 TCGA.DJ.A4UR.01 TCGA.IM.A41Y.01 TCGA.ET.A4KN.01 TCGA.KS.A4I5.01 TCGA.DJ.A4UQ.01
#> "012" "0244" "032" "0133" "0333" "012"
#> TCGA.KS.A4IB.01 TCGA.EL.A3N2.11 TCGA.BJ.A2N9.01 TCGA.DJ.A4UW.01 TCGA.EL.A3GZ.11 TCGA.EM.A3AR.01
#> "0331" "0211" "0222" "011" "0211" "0212"
#> TCGA.EL.A3N3.11 TCGA.DE.A3KN.01 TCGA.DJ.A2QA.01 TCGA.EL.A4JV.01 TCGA.EM.A4FF.01 TCGA.EL.A4K0.01
#> "02321" "011" "011" "0252" "0331" "0333"
#> TCGA.FK.A4UB.01 TCGA.BJ.A4O9.01 TCGA.BJ.A2N7.01 TCGA.DE.A2OL.01 TCGA.CE.A3ME.01 TCGA.MK.A4N7.01
#> "031" "011" "0252" "02411" "011" "032"
#> TCGA.EL.A3H2.11 TCGA.EL.A4K4.01 TCGA.EL.A3GS.01 TCGA.EL.A3GZ.01 TCGA.E3.A3E1.01 TCGA.DJ.A2Q8.01
#> "0212" "0331" "0331" "032" "011" "015"
#> TCGA.EL.A3N2.01 TCGA.KS.A4I7.01 TCGA.MK.A84Z.01 TCGA.ET.A3DP.11 TCGA.EL.A3MX.11 TCGA.ET.A25G.01
#> "0331" "032" "0251" "0211" "0211" "032"
#> TCGA.EM.A3FK.01 TCGA.EM.A2CS.01 TCGA.FE.A23A.01 TCGA.BJ.A28T.11 TCGA.EM.A22J.01 TCGA.EL.A3MX.01
#> "034" "032" "0133" "0211" "02412" "0332"
#> TCGA.FY.A3I4.01 TCGA.BJ.A28W.11 TCGA.ET.A25R.01 TCGA.BJ.A2N8.01 TCGA.FY.A76V.01 TCGA.EM.A3FN.01
#> "011" "02321" "032" "0252" "0251" "02413"
#> TCGA.QD.A8IV.01 TCGA.EM.A3FJ.01 TCGA.ET.A2MY.11 TCGA.EM.A3FQ.06 TCGA.ET.A25P.01 TCGA.ET.A2N0.01
#> "0252" "0333" "02413" "0333" "0252" "015"
#> TCGA.EM.A2CT.01 TCGA.FE.A235.01 TCGA.ET.A25M.01 TCGA.EL.A3MY.01 TCGA.DE.A7U5.01 TCGA.E8.A2JQ.11
#> "0222" "0333" "031" "031" "0331" "0231"
#> TCGA.ET.A3DP.01 TCGA.EM.A2CL.01 TCGA.ET.A2N5.01 TCGA.ET.A25J.11 TCGA.DE.A69J.01 TCGA.BJ.A28R.11
#> "011" "0242" "0252" "0211" "0333" "02321"
#> TCGA.ET.A25K.01 TCGA.EL.A3GV.01 TCGA.GE.A2C6.01 TCGA.EM.A3FM.01 TCGA.EL.A3H7.11 TCGA.FE.A22Z.01
#> "032" "011" "0133" "031" "0211" "0332"
#> TCGA.H2.A2K9.01 TCGA.EM.A22Q.01 TCGA.EM.A3FP.01 TCGA.GE.A2C6.11 TCGA.EL.A3MZ.01 TCGA.DJ.A2PT.01
#> "0243" "0242" "0252" "02321" "031" "0133"
#> TCGA.E8.A242.01 TCGA.ET.A25L.01 TCGA.CE.A27D.01 TCGA.EL.A3H1.11 TCGA.BJ.A2N7.11 TCGA.DJ.A2Q7.01
#> "0133" "032" "0233" "0233" "0211" "0333"
#> TCGA.J8.A3O1.01 TCGA.EM.A2CR.01 TCGA.DE.A69K.01 TCGA.EM.A2CQ.01 TCGA.FE.A238.01 TCGA.EL.A3H1.01
#> "011" "011" "0333" "0222" "015" "02411"
#> TCGA.BJ.A28W.01 TCGA.BJ.A28T.01 TCGA.EM.A2CJ.01 TCGA.EM.A3FQ.01 TCGA.4C.A93U.01 TCGA.EM.A22M.01
#> "0231" "02321" "0223" "015" "0332" "0142"
#> TCGA.J8.A3NZ.01 TCGA.EM.A22K.01 TCGA.FE.A236.01 TCGA.BJ.A28R.01 TCGA.EM.A2CU.01 TCGA.ET.A25N.01
#> "011" "0252" "012" "015" "015" "0333"
#> TCGA.EL.A3H7.01 TCGA.FY.A3NM.01 TCGA.EM.A3FO.01 TCGA.EM.A22L.01 TCGA.BJ.A2N9.11 TCGA.BJ.A291.01
#> "0331" "0223" "031" "0252" "0231" "0222"
#> TCGA.ET.A2N5.11 TCGA.ET.A25N.11 TCGA.J8.A3O0.01 TCGA.FE.A237.01 TCGA.DJ.A2QC.01 TCGA.ET.A25O.01
#> "0211" "0211" "0243" "011" "011" "0331"
#> TCGA.EL.A3GU.01 TCGA.EL.A3MY.11 TCGA.DJ.A2PY.01 TCGA.EM.A2CS.06 TCGA.FY.A3NP.01 TCGA.ET.A25I.01
#> "0332" "0221" "0331" "011" "0251" "0222"
#> TCGA.H2.A26U.01 TCGA.BJ.A290.11 TCGA.EM.A22I.01 TCGA.FE.A239.01 TCGA.BJ.A28Z.01 TCGA.DE.A0XZ.01
#> "0133" "0212" "0331" "0242" "0131" "0333"
#> TCGA.ET.A25J.01 TCGA.EM.A22N.01 TCGA.EM.A2CM.01 TCGA.FY.A3NN.01 TCGA.EM.A3FL.01 TCGA.H2.A2K9.11
#> "011" "0222" "0244" "011" "0223" "0233"
#> TCGA.EL.A3H3.01 TCGA.EL.A3H4.01 TCGA.EM.A2OX.01 TCGA.EM.A3SX.01 TCGA.BJ.A0Z3.01 TCGA.BJ.A28X.01
#> "015" "032" "031" "032" "0131" "0131"
#> TCGA.EL.A3CT.01 TCGA.EL.A3CR.01 TCGA.FY.A3TY.01 TCGA.J8.A3YG.01 TCGA.DJ.A3V6.01 TCGA.EM.A3SZ.01
#> "0132" "032" "0233" "015" "031" "015"
#> TCGA.EM.A2OW.01 TCGA.DO.A1JZ.11 TCGA.EL.A3D5.01 TCGA.EM.A2P0.01 TCGA.E8.A2JQ.01 TCGA.BJ.A18Z.01
#> "0222" "0211" "0252" "012" "0131" "031"
#> TCGA.DJ.A3V0.01 TCGA.EL.A3GW.01 TCGA.DJ.A3UW.01 TCGA.DJ.A3V3.01 TCGA.EL.A3T1.11 TCGA.BJ.A0ZC.01
#> "031" "0252" "0131" "015" "02321" "0221"
#> TCGA.EM.A2OV.01 TCGA.EL.A3GY.01 TCGA.EM.A3SY.01 TCGA.EM.A3AI.01 TCGA.EM.A2OY.01 TCGA.EL.A3T8.01
#> "0222" "0331" "0212" "0222" "0223" "031"
#> TCGA.BJ.A18Y.01 TCGA.EL.A3GP.01 TCGA.EM.A2CK.01 TCGA.EL.A3T7.11 TCGA.BJ.A192.01 TCGA.BJ.A191.01
#> "0251" "0141" "0251" "0211" "0223" "011"
#> TCGA.EM.A2CP.01 TCGA.EM.A22O.01 TCGA.EM.A2P1.01 TCGA.J8.A3YH.01 TCGA.DJ.A3UZ.01 TCGA.IM.A3EB.01
#> "0231" "031" "0142" "031" "0222" "0133"
#> TCGA.BJ.A3F0.01 TCGA.EL.A3GX.01 TCGA.EM.A3AK.01 TCGA.DO.A1JZ.01 TCGA.FY.A3YR.01 TCGA.DO.A1K0.01
#> "02414" "0331" "011" "0333" "032" "0331"
#> TCGA.DJ.A3V5.01 TCGA.EM.A3AJ.01 TCGA.IM.A3ED.01 TCGA.EM.A3AO.01 TCGA.EM.A2P1.06 TCGA.EM.A1CW.01
#> "032" "02322" "0333" "012" "0142" "0222"
#> TCGA.FK.A3SE.01 TCGA.EL.A3T7.01 TCGA.EM.A2P2.01 TCGA.EM.A1CU.11 TCGA.EL.A3T0.11 TCGA.E8.A3X7.01
#> "032" "032" "0251" "0212" "0211" "032"
#> TCGA.ET.A3BQ.01 TCGA.EM.A1CS.01 TCGA.EL.A3GQ.01 TCGA.EL.A3H5.01 TCGA.DJ.A3V4.01 TCGA.EM.A2P3.01
#> "0333" "011" "011" "0332" "011" "0331"
#> TCGA.FY.A3WA.01 TCGA.DJ.A3V2.01 TCGA.FY.A3TY.11 TCGA.BJ.A290.01 TCGA.EM.A3SU.01 TCGA.EL.A3D0.01
#> "0223" "0131" "0211" "012" "015" "031"
#> TCGA.EM.A1CT.11 TCGA.EL.A3GR.01 TCGA.J8.A3YH.06 TCGA.EM.A3ST.11 TCGA.ET.A3DV.01 TCGA.BJ.A3EZ.01
#> "0212" "011" "031" "0211" "02411" "031"
#> TCGA.J8.A3YD.01 TCGA.EM.A3SU.06 TCGA.EM.A3AL.01 TCGA.DJ.A3US.01 TCGA.EM.A1CS.11 TCGA.EM.A1CW.11
#> "0222" "0131" "02411" "015" "0211" "0211"
#> TCGA.BJ.A190.01 TCGA.EM.A2OZ.01 TCGA.EM.A1CV.11 TCGA.EM.A1CU.01 TCGA.EM.A3AN.01 TCGA.E8.A2EA.01
#> "0221" "012" "0211" "031" "032" "0133"
#> TCGA.EM.A1CV.01 TCGA.EM.A1CT.01 TCGA.EM.A3ST.01 TCGA.ET.A3BS.01 TCGA.EL.A3GO.01 TCGA.DJ.A2Q0.01
#> "011" "012" "0244" "0143" "02411" "0223"
#> TCGA.EL.A3D6.01 TCGA.DJ.A3UN.01 TCGA.DJ.A3UU.01 TCGA.FK.A3SD.01 TCGA.DJ.A2PO.01 TCGA.DJ.A3UQ.01
#> "032" "032" "011" "02413" "012" "015"
#> TCGA.EM.A1YE.11 TCGA.EL.A3T2.11 TCGA.EL.A3CL.01 TCGA.EM.A1YC.01 TCGA.DJ.A3UP.01 TCGA.EL.A3T0.01
#> "0211" "0211" "0333" "0223" "0252" "011"
#> TCGA.IM.A3U2.01 TCGA.IM.A3U3.01 TCGA.DJ.A3UX.01 TCGA.ET.A3BW.01 TCGA.ET.A39S.01 TCGA.ET.A3BP.01
#> "032" "032" "015" "011" "011" "011"
#> TCGA.DJ.A1QE.01 TCGA.EL.A3D4.01 TCGA.FK.A3SB.01 TCGA.EL.A3CW.01 TCGA.ET.A39L.01 TCGA.DJ.A2PW.01
#> "0331" "012" "0333" "02321" "0252" "031"
#> TCGA.EM.A2CO.01 TCGA.FE.A232.01 TCGA.DJ.A3UR.01 TCGA.DJ.A2PP.01 TCGA.ET.A3DQ.01 TCGA.ET.A3DS.01
#> "0222" "011" "011" "0242" "02321" "0222"
#> TCGA.FY.A3W9.01 TCGA.FK.A3S3.01 TCGA.ET.A2MZ.01 TCGA.BJ.A2NA.11 TCGA.DJ.A1QL.01 TCGA.EL.A3CS.01
#> "0244" "011" "031" "0233" "0242" "015"
#> TCGA.FE.A233.01 TCGA.EM.A1YD.11 TCGA.ET.A3DW.11 TCGA.EL.A3T9.01 TCGA.DJ.A3UM.01 TCGA.DO.A2HM.01
#> "0331" "0211" "0212" "032" "032" "0142"
#> TCGA.FY.A3BL.01 TCGA.EL.A3TA.11 TCGA.ET.A3BX.01 TCGA.DJ.A1QQ.01 TCGA.DJ.A1QF.01 TCGA.DJ.A1QO.01
#> "012" "0212" "031" "031" "011" "031"
#> TCGA.BJ.A2NA.01 TCGA.EM.A1YE.01 TCGA.FY.A2QD.01 TCGA.ET.A39J.01 TCGA.ET.A3DU.01 TCGA.EL.A3CM.01
#> "031" "0223" "02413" "034" "0133" "032"
#> TCGA.DJ.A3UO.01 TCGA.ET.A39P.01 TCGA.DJ.A2Q2.01 TCGA.BJ.A28V.01 TCGA.ET.A3BO.01 TCGA.EL.A3T1.01
#> "031" "0331" "0222" "02411" "032" "015"
#> TCGA.DJ.A1QI.01 TCGA.EL.A3TB.01 TCGA.BJ.A28X.11 TCGA.DJ.A1QN.01 TCGA.FE.A230.01 TCGA.FE.A234.01
#> "0333" "032" "0231" "0333" "015" "0331"
#> TCGA.ET.A39R.01 TCGA.DJ.A1QG.01 TCGA.EL.A3CV.01 TCGA.FE.A231.01 TCGA.EL.A3TA.01 TCGA.DJ.A3UY.01
#> "015" "0251" "0142" "031" "012" "015"
#> TCGA.DJ.A2Q1.01 TCGA.EL.A3CU.01 TCGA.EL.A3TB.11 TCGA.ET.A39I.01 TCGA.EM.A1YB.01 TCGA.DJ.A3UV.01
#> "0131" "0133" "0211" "0252" "02414" "011"
#> TCGA.DJ.A3UT.01 TCGA.ET.A3DW.01 TCGA.ET.A3BT.01 TCGA.EL.A3T3.01 TCGA.DJ.A1QM.01 TCGA.EL.A3CY.01
#> "0252" "031" "032" "032" "0212" "0231"
#> TCGA.ET.A39O.01 TCGA.EM.A1YC.11 TCGA.DJ.A1QH.01 TCGA.EL.A3T3.11 TCGA.EL.A3CX.01 TCGA.EL.A3T2.01
#> "031" "0211" "0332" "0211" "011" "0252"
#> TCGA.EM.A22P.01 TCGA.EL.A3T8.11 TCGA.DJ.A2PU.01 TCGA.DJ.A3UK.01 TCGA.ET.A3DO.01 TCGA.EM.A1YA.01
#> "0142" "0212" "0333" "011" "0131" "0223"
#> TCGA.ET.A3BV.01 TCGA.EL.A3CO.01 TCGA.DJ.A2PN.01 TCGA.FK.A3SG.01 TCGA.FK.A3SH.01 TCGA.EM.A1YD.01
#> "0131" "0233" "0333" "032" "032" "0223"
#> TCGA.DJ.A1QD.01 TCGA.EL.A3CZ.01 TCGA.BJ.A0Z9.01 TCGA.CE.A13K.01 TCGA.EM.A3FR.01 TCGA.EM.A3O8.01
#> "0331" "0222" "0132" "032" "02413" "0252"
#> TCGA.FY.A3R6.01 TCGA.FY.A3R9.01 TCGA.EL.A3D1.01 TCGA.EM.A3O6.01 TCGA.BJ.A0Z5.01 TCGA.BJ.A28S.01
#> "0131" "0222" "031" "0222" "012" "0251"
#> TCGA.BJ.A0ZH.01 TCGA.ET.A3DT.01 TCGA.H2.A3RI.11 TCGA.DJ.A13W.01 TCGA.DJ.A13T.01 TCGA.BJ.A0ZA.01
#> "032" "0131" "0211" "02411" "032" "02414"
#> TCGA.BJ.A3PT.01 TCGA.FE.A3PD.01 TCGA.BJ.A0ZF.01 TCGA.ET.A39M.01 TCGA.BJ.A0ZJ.01 TCGA.BJ.A0YZ.01
#> "0252" "032" "0224" "0143" "0143" "0221"
#> TCGA.FE.A3PC.01 TCGA.DJ.A2QB.01 TCGA.EM.A3OB.01 TCGA.H2.A3RH.01 TCGA.ET.A39T.01 TCGA.DJ.A2PV.01
#> "032" "0252" "0252" "0252" "011" "011"
#> TCGA.BJ.A3PR.11 TCGA.EL.A3T6.11 TCGA.DJ.A13X.01 TCGA.BJ.A0ZG.01 TCGA.EL.A3T6.01 TCGA.BJ.A0Z0.01
#> "02321" "0233" "011" "0221" "0133" "0242"
#> TCGA.ET.A39K.01 TCGA.EM.A3O9.01 TCGA.BJ.A3PU.01 TCGA.BJ.A3PR.01 TCGA.EM.A3O3.01 TCGA.BJ.A0ZB.01
#> "032" "0234" "031" "0231" "0132" "031"
#> TCGA.EM.A3OA.01 TCGA.DJ.A2PR.01 TCGA.DJ.A13L.01 TCGA.FY.A3ON.01 TCGA.DJ.A13V.01 TCGA.FY.A3R8.01
#> "02412" "031" "0142" "031" "032" "032"
#> TCGA.EL.A3CP.01 TCGA.DJ.A13U.01 TCGA.DE.A0Y3.01 TCGA.ET.A2N4.01 TCGA.DJ.A13P.01 TCGA.BJ.A0ZE.01
#> "0333" "012" "032" "011" "011" "0252"
#> TCGA.EM.A3O7.01 TCGA.DJ.A13O.01 TCGA.FY.A3RA.01 TCGA.DJ.A13M.01 TCGA.DJ.A13R.01 TCGA.ET.A3DR.01
#> "011" "0233" "0331" "0252" "0221" "011"
#> TCGA.FE.A3PB.01 TCGA.ET.A3BN.01 TCGA.H2.A3RI.01 TCGA.ET.A39N.01 TCGA.BJ.A3PU.11 TCGA.FY.A3R7.01
#> "015" "0331" "032" "0224" "0212" "0222"
#> TCGA.FE.A3PA.01 TCGA.EM.A2CN.01 TCGA.BJ.A0Z2.01 TCGA.FY.A3I5.01 TCGA.DJ.A13S.01 TCGA.DE.A0Y2.01
#> "031" "0243" "0243" "02414" "0252" "0331"
#> TCGA.ET.A3BU.01
#> "031"
get_classes(res_rh, merge_node = merge_node_param(min_n_signatures = 2027))
#> TCGA.E8.A416.01 TCGA.E8.A433.01 TCGA.EL.A4K9.01 TCGA.DJ.A3V9.01 TCGA.EL.A3ZO.11 TCGA.EL.A3ZN.01
#> "0211" "015" "031" "011" "0211" "011"
#> TCGA.KS.A41F.01 TCGA.EL.A3ZK.01 TCGA.ET.A40R.01 TCGA.EL.A3ZM.01 TCGA.ET.A2N3.01 TCGA.EL.A3ZQ.01
#> "032" "015" "015" "031" "02411" "032"
#> TCGA.ET.A40T.01 TCGA.DE.A4MA.01 TCGA.EM.A4FU.01 TCGA.E8.A418.01 TCGA.DJ.A3VD.01 TCGA.DJ.A3VM.01
#> "032" "032" "0251" "032" "0131" "0244"
#> TCGA.EL.A3ZG.01 TCGA.EM.A4FV.01 TCGA.E8.A413.01 TCGA.DJ.A3VG.01 TCGA.EL.A4K2.01 TCGA.IM.A420.01
#> "012" "015" "015" "0251" "0222" "0133"
#> TCGA.KS.A41J.01 TCGA.EL.A3ZK.11 TCGA.J8.A3O2.01 TCGA.E8.A415.01 TCGA.FY.A40M.01 TCGA.DJ.A3VB.01
#> "032" "02321" "012" "011" "0252" "031"
#> TCGA.KS.A41I.01 TCGA.DJ.A3VL.01 TCGA.ET.A4KQ.01 TCGA.H2.A421.01 TCGA.EL.A3ZO.01 TCGA.KS.A4I3.01
#> "0252" "0234" "0252" "032" "032" "012"
#> TCGA.DJ.A4UT.01 TCGA.DE.A4MD.01 TCGA.EL.A4JW.01 TCGA.DJ.A3VI.01 TCGA.DJ.A3VA.01 TCGA.L6.A4ET.01
#> "0131" "031" "015" "032" "032" "033"
#> TCGA.E8.A419.01 TCGA.DJ.A4V0.01 TCGA.DJ.A4V2.01 TCGA.ET.A40Q.01 TCGA.EL.A3ZS.01 TCGA.KS.A4ID.01
#> "0133" "02321" "033" "031" "0131" "0133"
#> TCGA.EL.A3ZL.11 TCGA.J8.A3YE.01 TCGA.EL.A4K7.01 TCGA.DJ.A3VF.01 TCGA.EM.A4FH.01 TCGA.E8.A432.01
#> "0211" "011" "031" "0133" "0221" "015"
#> TCGA.J8.A3O2.06 TCGA.ET.A2MX.01 TCGA.ET.A40S.01 TCGA.DE.A4M8.01 TCGA.IM.A41Z.01 TCGA.EL.A4KD.01
#> "031" "012" "0142" "0131" "02412" "012"
#> TCGA.DJ.A3V7.01 TCGA.FY.A40L.01 TCGA.DE.A4M9.01 TCGA.J8.A42S.01 TCGA.KS.A41L.01 TCGA.EM.A4FN.01
#> "032" "015" "0221" "012" "0224" "033"
#> TCGA.EL.A4K1.01 TCGA.KS.A4IC.01 TCGA.E8.A414.01 TCGA.H2.A422.01 TCGA.J8.A3YF.01 TCGA.EL.A4KI.01
#> "033" "011" "015" "032" "031" "0243"
#> TCGA.EM.A4G1.01 TCGA.DJ.A3VJ.01 TCGA.DE.A4MD.06 TCGA.EL.A3ZP.01 TCGA.EM.A4FQ.01 TCGA.EL.A3ZT.01
#> "0252" "031" "0141" "031" "033" "031"
#> TCGA.DJ.A4V4.01 TCGA.FY.A40K.01 TCGA.L6.A4EQ.01 TCGA.DJ.A3VE.01 TCGA.E8.A434.01 TCGA.EL.A3ZH.01
#> "011" "011" "031" "031" "0222" "0222"
#> TCGA.EM.A4FR.01 TCGA.EL.A3ZH.11 TCGA.EL.A3ZR.01 TCGA.DJ.A3V8.01 TCGA.EL.A3ZG.11 TCGA.ET.A40P.01
#> "012" "0211" "0252" "015" "0212" "0252"
#> TCGA.DE.A4MB.01 TCGA.MK.A4N6.01 TCGA.DJ.A3VK.01 TCGA.E8.A417.01 TCGA.L6.A4EU.01 TCGA.J8.A4HY.01
#> "032" "031" "0251" "032" "032" "011"
#> TCGA.EL.A3ZL.01 TCGA.EL.A3ZP.11 TCGA.FY.A40N.01 TCGA.J8.A4HW.01 TCGA.BJ.A45J.01 TCGA.CE.A482.01
#> "032" "02322" "011" "032" "032" "032"
#> TCGA.DJ.A2Q6.01 TCGA.DJ.A2PX.01 TCGA.DJ.A4UL.01 TCGA.EL.A4JX.01 TCGA.BJ.A2N8.11 TCGA.DJ.A2Q5.01
#> "032" "015" "033" "0131" "0211" "0143"
#> TCGA.EL.A4KG.01 TCGA.DJ.A4UP.01 TCGA.E8.A438.01 TCGA.EL.A3H2.01 TCGA.EM.A3AP.01 TCGA.DJ.A2PQ.01
#> "033" "015" "011" "0221" "0252" "031"
#> TCGA.L6.A4EP.01 TCGA.FY.A4B4.01 TCGA.EL.A4KH.01 TCGA.BJ.A45E.01 TCGA.DJ.A4V5.01 TCGA.DE.A4MC.01
#> "033" "032" "011" "0231" "0143" "033"
#> TCGA.E8.A44M.01 TCGA.BJ.A45K.01 TCGA.E3.A3DZ.01 TCGA.E3.A3E2.01 TCGA.BJ.A45H.01 TCGA.E8.A44K.01
#> "0131" "0242" "0252" "032" "012" "015"
#> TCGA.ET.A2MY.01 TCGA.EL.A3H8.01 TCGA.BJ.A45C.01 TCGA.BJ.A45G.01 TCGA.EL.A4JZ.01 TCGA.CE.A481.01
#> "032" "033" "0242" "0252" "033" "015"
#> TCGA.KS.A4I9.01 TCGA.EL.A3MW.01 TCGA.E8.A436.01 TCGA.E3.A3DY.01 TCGA.DJ.A2Q3.01 TCGA.BJ.A2P4.01
#> "033" "033" "015" "031" "0133" "0252"
#> TCGA.CE.A484.01 TCGA.ET.A2N1.01 TCGA.DJ.A2Q4.01 TCGA.DJ.A2PZ.01 TCGA.BJ.A45F.01 TCGA.IM.A4EB.01
#> "0252" "011" "031" "012" "0252" "0143"
#> TCGA.EM.A4FO.01 TCGA.FY.A4B3.01 TCGA.FY.A4B0.01 TCGA.BJ.A45I.01 TCGA.E3.A3E3.01 TCGA.EM.A3AQ.01
#> "0142" "031" "0242" "0133" "033" "034"
#> TCGA.EL.A3N3.01 TCGA.DJ.A2Q9.01 TCGA.EM.A4FM.01 TCGA.EL.A4K6.01 TCGA.MK.A4N9.01 TCGA.KS.A4I1.01
#> "0133" "0231" "033" "0243" "033" "032"
#> TCGA.DJ.A2PS.01 TCGA.CE.A3MD.01 TCGA.E3.A3E5.01 TCGA.EL.A3CN.01 TCGA.J8.A4HW.06 TCGA.EM.A4FK.01
#> "011" "012" "031" "015" "0131" "02412"
#> TCGA.E8.A437.01 TCGA.BJ.A4O8.01 TCGA.EL.A3MW.11 TCGA.E3.A3E0.01 TCGA.BJ.A45D.01 TCGA.CE.A483.01
#> "011" "031" "0211" "033" "0251" "011"
#> TCGA.CE.A485.01 TCGA.DJ.A4UR.01 TCGA.IM.A41Y.01 TCGA.ET.A4KN.01 TCGA.KS.A4I5.01 TCGA.DJ.A4UQ.01
#> "012" "0244" "032" "0133" "033" "012"
#> TCGA.KS.A4IB.01 TCGA.EL.A3N2.11 TCGA.BJ.A2N9.01 TCGA.DJ.A4UW.01 TCGA.EL.A3GZ.11 TCGA.EM.A3AR.01
#> "033" "0211" "0222" "011" "0211" "0212"
#> TCGA.EL.A3N3.11 TCGA.DE.A3KN.01 TCGA.DJ.A2QA.01 TCGA.EL.A4JV.01 TCGA.EM.A4FF.01 TCGA.EL.A4K0.01
#> "02321" "011" "011" "0252" "033" "033"
#> TCGA.FK.A4UB.01 TCGA.BJ.A4O9.01 TCGA.BJ.A2N7.01 TCGA.DE.A2OL.01 TCGA.CE.A3ME.01 TCGA.MK.A4N7.01
#> "031" "011" "0252" "02411" "011" "032"
#> TCGA.EL.A3H2.11 TCGA.EL.A4K4.01 TCGA.EL.A3GS.01 TCGA.EL.A3GZ.01 TCGA.E3.A3E1.01 TCGA.DJ.A2Q8.01
#> "0212" "033" "033" "032" "011" "015"
#> TCGA.EL.A3N2.01 TCGA.KS.A4I7.01 TCGA.MK.A84Z.01 TCGA.ET.A3DP.11 TCGA.EL.A3MX.11 TCGA.ET.A25G.01
#> "033" "032" "0251" "0211" "0211" "032"
#> TCGA.EM.A3FK.01 TCGA.EM.A2CS.01 TCGA.FE.A23A.01 TCGA.BJ.A28T.11 TCGA.EM.A22J.01 TCGA.EL.A3MX.01
#> "034" "032" "0133" "0211" "02412" "033"
#> TCGA.FY.A3I4.01 TCGA.BJ.A28W.11 TCGA.ET.A25R.01 TCGA.BJ.A2N8.01 TCGA.FY.A76V.01 TCGA.EM.A3FN.01
#> "011" "02321" "032" "0252" "0251" "02413"
#> TCGA.QD.A8IV.01 TCGA.EM.A3FJ.01 TCGA.ET.A2MY.11 TCGA.EM.A3FQ.06 TCGA.ET.A25P.01 TCGA.ET.A2N0.01
#> "0252" "033" "02413" "033" "0252" "015"
#> TCGA.EM.A2CT.01 TCGA.FE.A235.01 TCGA.ET.A25M.01 TCGA.EL.A3MY.01 TCGA.DE.A7U5.01 TCGA.E8.A2JQ.11
#> "0222" "033" "031" "031" "033" "0231"
#> TCGA.ET.A3DP.01 TCGA.EM.A2CL.01 TCGA.ET.A2N5.01 TCGA.ET.A25J.11 TCGA.DE.A69J.01 TCGA.BJ.A28R.11
#> "011" "0242" "0252" "0211" "033" "02321"
#> TCGA.ET.A25K.01 TCGA.EL.A3GV.01 TCGA.GE.A2C6.01 TCGA.EM.A3FM.01 TCGA.EL.A3H7.11 TCGA.FE.A22Z.01
#> "032" "011" "0133" "031" "0211" "033"
#> TCGA.H2.A2K9.01 TCGA.EM.A22Q.01 TCGA.EM.A3FP.01 TCGA.GE.A2C6.11 TCGA.EL.A3MZ.01 TCGA.DJ.A2PT.01
#> "0243" "0242" "0252" "02321" "031" "0133"
#> TCGA.E8.A242.01 TCGA.ET.A25L.01 TCGA.CE.A27D.01 TCGA.EL.A3H1.11 TCGA.BJ.A2N7.11 TCGA.DJ.A2Q7.01
#> "0133" "032" "0233" "0233" "0211" "033"
#> TCGA.J8.A3O1.01 TCGA.EM.A2CR.01 TCGA.DE.A69K.01 TCGA.EM.A2CQ.01 TCGA.FE.A238.01 TCGA.EL.A3H1.01
#> "011" "011" "033" "0222" "015" "02411"
#> TCGA.BJ.A28W.01 TCGA.BJ.A28T.01 TCGA.EM.A2CJ.01 TCGA.EM.A3FQ.01 TCGA.4C.A93U.01 TCGA.EM.A22M.01
#> "0231" "02321" "0223" "015" "033" "0142"
#> TCGA.J8.A3NZ.01 TCGA.EM.A22K.01 TCGA.FE.A236.01 TCGA.BJ.A28R.01 TCGA.EM.A2CU.01 TCGA.ET.A25N.01
#> "011" "0252" "012" "015" "015" "033"
#> TCGA.EL.A3H7.01 TCGA.FY.A3NM.01 TCGA.EM.A3FO.01 TCGA.EM.A22L.01 TCGA.BJ.A2N9.11 TCGA.BJ.A291.01
#> "033" "0223" "031" "0252" "0231" "0222"
#> TCGA.ET.A2N5.11 TCGA.ET.A25N.11 TCGA.J8.A3O0.01 TCGA.FE.A237.01 TCGA.DJ.A2QC.01 TCGA.ET.A25O.01
#> "0211" "0211" "0243" "011" "011" "033"
#> TCGA.EL.A3GU.01 TCGA.EL.A3MY.11 TCGA.DJ.A2PY.01 TCGA.EM.A2CS.06 TCGA.FY.A3NP.01 TCGA.ET.A25I.01
#> "033" "0221" "033" "011" "0251" "0222"
#> TCGA.H2.A26U.01 TCGA.BJ.A290.11 TCGA.EM.A22I.01 TCGA.FE.A239.01 TCGA.BJ.A28Z.01 TCGA.DE.A0XZ.01
#> "0133" "0212" "033" "0242" "0131" "033"
#> TCGA.ET.A25J.01 TCGA.EM.A22N.01 TCGA.EM.A2CM.01 TCGA.FY.A3NN.01 TCGA.EM.A3FL.01 TCGA.H2.A2K9.11
#> "011" "0222" "0244" "011" "0223" "0233"
#> TCGA.EL.A3H3.01 TCGA.EL.A3H4.01 TCGA.EM.A2OX.01 TCGA.EM.A3SX.01 TCGA.BJ.A0Z3.01 TCGA.BJ.A28X.01
#> "015" "032" "031" "032" "0131" "0131"
#> TCGA.EL.A3CT.01 TCGA.EL.A3CR.01 TCGA.FY.A3TY.01 TCGA.J8.A3YG.01 TCGA.DJ.A3V6.01 TCGA.EM.A3SZ.01
#> "0132" "032" "0233" "015" "031" "015"
#> TCGA.EM.A2OW.01 TCGA.DO.A1JZ.11 TCGA.EL.A3D5.01 TCGA.EM.A2P0.01 TCGA.E8.A2JQ.01 TCGA.BJ.A18Z.01
#> "0222" "0211" "0252" "012" "0131" "031"
#> TCGA.DJ.A3V0.01 TCGA.EL.A3GW.01 TCGA.DJ.A3UW.01 TCGA.DJ.A3V3.01 TCGA.EL.A3T1.11 TCGA.BJ.A0ZC.01
#> "031" "0252" "0131" "015" "02321" "0221"
#> TCGA.EM.A2OV.01 TCGA.EL.A3GY.01 TCGA.EM.A3SY.01 TCGA.EM.A3AI.01 TCGA.EM.A2OY.01 TCGA.EL.A3T8.01
#> "0222" "033" "0212" "0222" "0223" "031"
#> TCGA.BJ.A18Y.01 TCGA.EL.A3GP.01 TCGA.EM.A2CK.01 TCGA.EL.A3T7.11 TCGA.BJ.A192.01 TCGA.BJ.A191.01
#> "0251" "0141" "0251" "0211" "0223" "011"
#> TCGA.EM.A2CP.01 TCGA.EM.A22O.01 TCGA.EM.A2P1.01 TCGA.J8.A3YH.01 TCGA.DJ.A3UZ.01 TCGA.IM.A3EB.01
#> "0231" "031" "0142" "031" "0222" "0133"
#> TCGA.BJ.A3F0.01 TCGA.EL.A3GX.01 TCGA.EM.A3AK.01 TCGA.DO.A1JZ.01 TCGA.FY.A3YR.01 TCGA.DO.A1K0.01
#> "02414" "033" "011" "033" "032" "033"
#> TCGA.DJ.A3V5.01 TCGA.EM.A3AJ.01 TCGA.IM.A3ED.01 TCGA.EM.A3AO.01 TCGA.EM.A2P1.06 TCGA.EM.A1CW.01
#> "032" "02322" "033" "012" "0142" "0222"
#> TCGA.FK.A3SE.01 TCGA.EL.A3T7.01 TCGA.EM.A2P2.01 TCGA.EM.A1CU.11 TCGA.EL.A3T0.11 TCGA.E8.A3X7.01
#> "032" "032" "0251" "0212" "0211" "032"
#> TCGA.ET.A3BQ.01 TCGA.EM.A1CS.01 TCGA.EL.A3GQ.01 TCGA.EL.A3H5.01 TCGA.DJ.A3V4.01 TCGA.EM.A2P3.01
#> "033" "011" "011" "033" "011" "033"
#> TCGA.FY.A3WA.01 TCGA.DJ.A3V2.01 TCGA.FY.A3TY.11 TCGA.BJ.A290.01 TCGA.EM.A3SU.01 TCGA.EL.A3D0.01
#> "0223" "0131" "0211" "012" "015" "031"
#> TCGA.EM.A1CT.11 TCGA.EL.A3GR.01 TCGA.J8.A3YH.06 TCGA.EM.A3ST.11 TCGA.ET.A3DV.01 TCGA.BJ.A3EZ.01
#> "0212" "011" "031" "0211" "02411" "031"
#> TCGA.J8.A3YD.01 TCGA.EM.A3SU.06 TCGA.EM.A3AL.01 TCGA.DJ.A3US.01 TCGA.EM.A1CS.11 TCGA.EM.A1CW.11
#> "0222" "0131" "02411" "015" "0211" "0211"
#> TCGA.BJ.A190.01 TCGA.EM.A2OZ.01 TCGA.EM.A1CV.11 TCGA.EM.A1CU.01 TCGA.EM.A3AN.01 TCGA.E8.A2EA.01
#> "0221" "012" "0211" "031" "032" "0133"
#> TCGA.EM.A1CV.01 TCGA.EM.A1CT.01 TCGA.EM.A3ST.01 TCGA.ET.A3BS.01 TCGA.EL.A3GO.01 TCGA.DJ.A2Q0.01
#> "011" "012" "0244" "0143" "02411" "0223"
#> TCGA.EL.A3D6.01 TCGA.DJ.A3UN.01 TCGA.DJ.A3UU.01 TCGA.FK.A3SD.01 TCGA.DJ.A2PO.01 TCGA.DJ.A3UQ.01
#> "032" "032" "011" "02413" "012" "015"
#> TCGA.EM.A1YE.11 TCGA.EL.A3T2.11 TCGA.EL.A3CL.01 TCGA.EM.A1YC.01 TCGA.DJ.A3UP.01 TCGA.EL.A3T0.01
#> "0211" "0211" "033" "0223" "0252" "011"
#> TCGA.IM.A3U2.01 TCGA.IM.A3U3.01 TCGA.DJ.A3UX.01 TCGA.ET.A3BW.01 TCGA.ET.A39S.01 TCGA.ET.A3BP.01
#> "032" "032" "015" "011" "011" "011"
#> TCGA.DJ.A1QE.01 TCGA.EL.A3D4.01 TCGA.FK.A3SB.01 TCGA.EL.A3CW.01 TCGA.ET.A39L.01 TCGA.DJ.A2PW.01
#> "033" "012" "033" "02321" "0252" "031"
#> TCGA.EM.A2CO.01 TCGA.FE.A232.01 TCGA.DJ.A3UR.01 TCGA.DJ.A2PP.01 TCGA.ET.A3DQ.01 TCGA.ET.A3DS.01
#> "0222" "011" "011" "0242" "02321" "0222"
#> TCGA.FY.A3W9.01 TCGA.FK.A3S3.01 TCGA.ET.A2MZ.01 TCGA.BJ.A2NA.11 TCGA.DJ.A1QL.01 TCGA.EL.A3CS.01
#> "0244" "011" "031" "0233" "0242" "015"
#> TCGA.FE.A233.01 TCGA.EM.A1YD.11 TCGA.ET.A3DW.11 TCGA.EL.A3T9.01 TCGA.DJ.A3UM.01 TCGA.DO.A2HM.01
#> "033" "0211" "0212" "032" "032" "0142"
#> TCGA.FY.A3BL.01 TCGA.EL.A3TA.11 TCGA.ET.A3BX.01 TCGA.DJ.A1QQ.01 TCGA.DJ.A1QF.01 TCGA.DJ.A1QO.01
#> "012" "0212" "031" "031" "011" "031"
#> TCGA.BJ.A2NA.01 TCGA.EM.A1YE.01 TCGA.FY.A2QD.01 TCGA.ET.A39J.01 TCGA.ET.A3DU.01 TCGA.EL.A3CM.01
#> "031" "0223" "02413" "034" "0133" "032"
#> TCGA.DJ.A3UO.01 TCGA.ET.A39P.01 TCGA.DJ.A2Q2.01 TCGA.BJ.A28V.01 TCGA.ET.A3BO.01 TCGA.EL.A3T1.01
#> "031" "033" "0222" "02411" "032" "015"
#> TCGA.DJ.A1QI.01 TCGA.EL.A3TB.01 TCGA.BJ.A28X.11 TCGA.DJ.A1QN.01 TCGA.FE.A230.01 TCGA.FE.A234.01
#> "033" "032" "0231" "033" "015" "033"
#> TCGA.ET.A39R.01 TCGA.DJ.A1QG.01 TCGA.EL.A3CV.01 TCGA.FE.A231.01 TCGA.EL.A3TA.01 TCGA.DJ.A3UY.01
#> "015" "0251" "0142" "031" "012" "015"
#> TCGA.DJ.A2Q1.01 TCGA.EL.A3CU.01 TCGA.EL.A3TB.11 TCGA.ET.A39I.01 TCGA.EM.A1YB.01 TCGA.DJ.A3UV.01
#> "0131" "0133" "0211" "0252" "02414" "011"
#> TCGA.DJ.A3UT.01 TCGA.ET.A3DW.01 TCGA.ET.A3BT.01 TCGA.EL.A3T3.01 TCGA.DJ.A1QM.01 TCGA.EL.A3CY.01
#> "0252" "031" "032" "032" "0212" "0231"
#> TCGA.ET.A39O.01 TCGA.EM.A1YC.11 TCGA.DJ.A1QH.01 TCGA.EL.A3T3.11 TCGA.EL.A3CX.01 TCGA.EL.A3T2.01
#> "031" "0211" "033" "0211" "011" "0252"
#> TCGA.EM.A22P.01 TCGA.EL.A3T8.11 TCGA.DJ.A2PU.01 TCGA.DJ.A3UK.01 TCGA.ET.A3DO.01 TCGA.EM.A1YA.01
#> "0142" "0212" "033" "011" "0131" "0223"
#> TCGA.ET.A3BV.01 TCGA.EL.A3CO.01 TCGA.DJ.A2PN.01 TCGA.FK.A3SG.01 TCGA.FK.A3SH.01 TCGA.EM.A1YD.01
#> "0131" "0233" "033" "032" "032" "0223"
#> TCGA.DJ.A1QD.01 TCGA.EL.A3CZ.01 TCGA.BJ.A0Z9.01 TCGA.CE.A13K.01 TCGA.EM.A3FR.01 TCGA.EM.A3O8.01
#> "033" "0222" "0132" "032" "02413" "0252"
#> TCGA.FY.A3R6.01 TCGA.FY.A3R9.01 TCGA.EL.A3D1.01 TCGA.EM.A3O6.01 TCGA.BJ.A0Z5.01 TCGA.BJ.A28S.01
#> "0131" "0222" "031" "0222" "012" "0251"
#> TCGA.BJ.A0ZH.01 TCGA.ET.A3DT.01 TCGA.H2.A3RI.11 TCGA.DJ.A13W.01 TCGA.DJ.A13T.01 TCGA.BJ.A0ZA.01
#> "032" "0131" "0211" "02411" "032" "02414"
#> TCGA.BJ.A3PT.01 TCGA.FE.A3PD.01 TCGA.BJ.A0ZF.01 TCGA.ET.A39M.01 TCGA.BJ.A0ZJ.01 TCGA.BJ.A0YZ.01
#> "0252" "032" "0224" "0143" "0143" "0221"
#> TCGA.FE.A3PC.01 TCGA.DJ.A2QB.01 TCGA.EM.A3OB.01 TCGA.H2.A3RH.01 TCGA.ET.A39T.01 TCGA.DJ.A2PV.01
#> "032" "0252" "0252" "0252" "011" "011"
#> TCGA.BJ.A3PR.11 TCGA.EL.A3T6.11 TCGA.DJ.A13X.01 TCGA.BJ.A0ZG.01 TCGA.EL.A3T6.01 TCGA.BJ.A0Z0.01
#> "02321" "0233" "011" "0221" "0133" "0242"
#> TCGA.ET.A39K.01 TCGA.EM.A3O9.01 TCGA.BJ.A3PU.01 TCGA.BJ.A3PR.01 TCGA.EM.A3O3.01 TCGA.BJ.A0ZB.01
#> "032" "0234" "031" "0231" "0132" "031"
#> TCGA.EM.A3OA.01 TCGA.DJ.A2PR.01 TCGA.DJ.A13L.01 TCGA.FY.A3ON.01 TCGA.DJ.A13V.01 TCGA.FY.A3R8.01
#> "02412" "031" "0142" "031" "032" "032"
#> TCGA.EL.A3CP.01 TCGA.DJ.A13U.01 TCGA.DE.A0Y3.01 TCGA.ET.A2N4.01 TCGA.DJ.A13P.01 TCGA.BJ.A0ZE.01
#> "033" "012" "032" "011" "011" "0252"
#> TCGA.EM.A3O7.01 TCGA.DJ.A13O.01 TCGA.FY.A3RA.01 TCGA.DJ.A13M.01 TCGA.DJ.A13R.01 TCGA.ET.A3DR.01
#> "011" "0233" "033" "0252" "0221" "011"
#> TCGA.FE.A3PB.01 TCGA.ET.A3BN.01 TCGA.H2.A3RI.01 TCGA.ET.A39N.01 TCGA.BJ.A3PU.11 TCGA.FY.A3R7.01
#> "015" "033" "032" "0224" "0212" "0222"
#> TCGA.FE.A3PA.01 TCGA.EM.A2CN.01 TCGA.BJ.A0Z2.01 TCGA.FY.A3I5.01 TCGA.DJ.A13S.01 TCGA.DE.A0Y2.01
#> "031" "0243" "0243" "02414" "0252" "033"
#> TCGA.ET.A3BU.01
#> "031"
get_classes(res_rh, merge_node = merge_node_param(min_n_signatures = 2606))
#> TCGA.E8.A416.01 TCGA.E8.A433.01 TCGA.EL.A4K9.01 TCGA.DJ.A3V9.01 TCGA.EL.A3ZO.11 TCGA.EL.A3ZN.01
#> "0211" "015" "031" "011" "0211" "011"
#> TCGA.KS.A41F.01 TCGA.EL.A3ZK.01 TCGA.ET.A40R.01 TCGA.EL.A3ZM.01 TCGA.ET.A2N3.01 TCGA.EL.A3ZQ.01
#> "032" "015" "015" "031" "02411" "032"
#> TCGA.ET.A40T.01 TCGA.DE.A4MA.01 TCGA.EM.A4FU.01 TCGA.E8.A418.01 TCGA.DJ.A3VD.01 TCGA.DJ.A3VM.01
#> "032" "032" "0251" "032" "013" "0244"
#> TCGA.EL.A3ZG.01 TCGA.EM.A4FV.01 TCGA.E8.A413.01 TCGA.DJ.A3VG.01 TCGA.EL.A4K2.01 TCGA.IM.A420.01
#> "012" "015" "015" "0251" "0222" "013"
#> TCGA.KS.A41J.01 TCGA.EL.A3ZK.11 TCGA.J8.A3O2.01 TCGA.E8.A415.01 TCGA.FY.A40M.01 TCGA.DJ.A3VB.01
#> "032" "02321" "012" "011" "0252" "031"
#> TCGA.KS.A41I.01 TCGA.DJ.A3VL.01 TCGA.ET.A4KQ.01 TCGA.H2.A421.01 TCGA.EL.A3ZO.01 TCGA.KS.A4I3.01
#> "0252" "0234" "0252" "032" "032" "012"
#> TCGA.DJ.A4UT.01 TCGA.DE.A4MD.01 TCGA.EL.A4JW.01 TCGA.DJ.A3VI.01 TCGA.DJ.A3VA.01 TCGA.L6.A4ET.01
#> "013" "031" "015" "032" "032" "033"
#> TCGA.E8.A419.01 TCGA.DJ.A4V0.01 TCGA.DJ.A4V2.01 TCGA.ET.A40Q.01 TCGA.EL.A3ZS.01 TCGA.KS.A4ID.01
#> "013" "02321" "033" "031" "013" "013"
#> TCGA.EL.A3ZL.11 TCGA.J8.A3YE.01 TCGA.EL.A4K7.01 TCGA.DJ.A3VF.01 TCGA.EM.A4FH.01 TCGA.E8.A432.01
#> "0211" "011" "031" "013" "0221" "015"
#> TCGA.J8.A3O2.06 TCGA.ET.A2MX.01 TCGA.ET.A40S.01 TCGA.DE.A4M8.01 TCGA.IM.A41Z.01 TCGA.EL.A4KD.01
#> "031" "012" "0142" "013" "02412" "012"
#> TCGA.DJ.A3V7.01 TCGA.FY.A40L.01 TCGA.DE.A4M9.01 TCGA.J8.A42S.01 TCGA.KS.A41L.01 TCGA.EM.A4FN.01
#> "032" "015" "0221" "012" "0224" "033"
#> TCGA.EL.A4K1.01 TCGA.KS.A4IC.01 TCGA.E8.A414.01 TCGA.H2.A422.01 TCGA.J8.A3YF.01 TCGA.EL.A4KI.01
#> "033" "011" "015" "032" "031" "0243"
#> TCGA.EM.A4G1.01 TCGA.DJ.A3VJ.01 TCGA.DE.A4MD.06 TCGA.EL.A3ZP.01 TCGA.EM.A4FQ.01 TCGA.EL.A3ZT.01
#> "0252" "031" "0141" "031" "033" "031"
#> TCGA.DJ.A4V4.01 TCGA.FY.A40K.01 TCGA.L6.A4EQ.01 TCGA.DJ.A3VE.01 TCGA.E8.A434.01 TCGA.EL.A3ZH.01
#> "011" "011" "031" "031" "0222" "0222"
#> TCGA.EM.A4FR.01 TCGA.EL.A3ZH.11 TCGA.EL.A3ZR.01 TCGA.DJ.A3V8.01 TCGA.EL.A3ZG.11 TCGA.ET.A40P.01
#> "012" "0211" "0252" "015" "0212" "0252"
#> TCGA.DE.A4MB.01 TCGA.MK.A4N6.01 TCGA.DJ.A3VK.01 TCGA.E8.A417.01 TCGA.L6.A4EU.01 TCGA.J8.A4HY.01
#> "032" "031" "0251" "032" "032" "011"
#> TCGA.EL.A3ZL.01 TCGA.EL.A3ZP.11 TCGA.FY.A40N.01 TCGA.J8.A4HW.01 TCGA.BJ.A45J.01 TCGA.CE.A482.01
#> "032" "02322" "011" "032" "032" "032"
#> TCGA.DJ.A2Q6.01 TCGA.DJ.A2PX.01 TCGA.DJ.A4UL.01 TCGA.EL.A4JX.01 TCGA.BJ.A2N8.11 TCGA.DJ.A2Q5.01
#> "032" "015" "033" "013" "0211" "0143"
#> TCGA.EL.A4KG.01 TCGA.DJ.A4UP.01 TCGA.E8.A438.01 TCGA.EL.A3H2.01 TCGA.EM.A3AP.01 TCGA.DJ.A2PQ.01
#> "033" "015" "011" "0221" "0252" "031"
#> TCGA.L6.A4EP.01 TCGA.FY.A4B4.01 TCGA.EL.A4KH.01 TCGA.BJ.A45E.01 TCGA.DJ.A4V5.01 TCGA.DE.A4MC.01
#> "033" "032" "011" "0231" "0143" "033"
#> TCGA.E8.A44M.01 TCGA.BJ.A45K.01 TCGA.E3.A3DZ.01 TCGA.E3.A3E2.01 TCGA.BJ.A45H.01 TCGA.E8.A44K.01
#> "013" "0242" "0252" "032" "012" "015"
#> TCGA.ET.A2MY.01 TCGA.EL.A3H8.01 TCGA.BJ.A45C.01 TCGA.BJ.A45G.01 TCGA.EL.A4JZ.01 TCGA.CE.A481.01
#> "032" "033" "0242" "0252" "033" "015"
#> TCGA.KS.A4I9.01 TCGA.EL.A3MW.01 TCGA.E8.A436.01 TCGA.E3.A3DY.01 TCGA.DJ.A2Q3.01 TCGA.BJ.A2P4.01
#> "033" "033" "015" "031" "013" "0252"
#> TCGA.CE.A484.01 TCGA.ET.A2N1.01 TCGA.DJ.A2Q4.01 TCGA.DJ.A2PZ.01 TCGA.BJ.A45F.01 TCGA.IM.A4EB.01
#> "0252" "011" "031" "012" "0252" "0143"
#> TCGA.EM.A4FO.01 TCGA.FY.A4B3.01 TCGA.FY.A4B0.01 TCGA.BJ.A45I.01 TCGA.E3.A3E3.01 TCGA.EM.A3AQ.01
#> "0142" "031" "0242" "013" "033" "034"
#> TCGA.EL.A3N3.01 TCGA.DJ.A2Q9.01 TCGA.EM.A4FM.01 TCGA.EL.A4K6.01 TCGA.MK.A4N9.01 TCGA.KS.A4I1.01
#> "013" "0231" "033" "0243" "033" "032"
#> TCGA.DJ.A2PS.01 TCGA.CE.A3MD.01 TCGA.E3.A3E5.01 TCGA.EL.A3CN.01 TCGA.J8.A4HW.06 TCGA.EM.A4FK.01
#> "011" "012" "031" "015" "013" "02412"
#> TCGA.E8.A437.01 TCGA.BJ.A4O8.01 TCGA.EL.A3MW.11 TCGA.E3.A3E0.01 TCGA.BJ.A45D.01 TCGA.CE.A483.01
#> "011" "031" "0211" "033" "0251" "011"
#> TCGA.CE.A485.01 TCGA.DJ.A4UR.01 TCGA.IM.A41Y.01 TCGA.ET.A4KN.01 TCGA.KS.A4I5.01 TCGA.DJ.A4UQ.01
#> "012" "0244" "032" "013" "033" "012"
#> TCGA.KS.A4IB.01 TCGA.EL.A3N2.11 TCGA.BJ.A2N9.01 TCGA.DJ.A4UW.01 TCGA.EL.A3GZ.11 TCGA.EM.A3AR.01
#> "033" "0211" "0222" "011" "0211" "0212"
#> TCGA.EL.A3N3.11 TCGA.DE.A3KN.01 TCGA.DJ.A2QA.01 TCGA.EL.A4JV.01 TCGA.EM.A4FF.01 TCGA.EL.A4K0.01
#> "02321" "011" "011" "0252" "033" "033"
#> TCGA.FK.A4UB.01 TCGA.BJ.A4O9.01 TCGA.BJ.A2N7.01 TCGA.DE.A2OL.01 TCGA.CE.A3ME.01 TCGA.MK.A4N7.01
#> "031" "011" "0252" "02411" "011" "032"
#> TCGA.EL.A3H2.11 TCGA.EL.A4K4.01 TCGA.EL.A3GS.01 TCGA.EL.A3GZ.01 TCGA.E3.A3E1.01 TCGA.DJ.A2Q8.01
#> "0212" "033" "033" "032" "011" "015"
#> TCGA.EL.A3N2.01 TCGA.KS.A4I7.01 TCGA.MK.A84Z.01 TCGA.ET.A3DP.11 TCGA.EL.A3MX.11 TCGA.ET.A25G.01
#> "033" "032" "0251" "0211" "0211" "032"
#> TCGA.EM.A3FK.01 TCGA.EM.A2CS.01 TCGA.FE.A23A.01 TCGA.BJ.A28T.11 TCGA.EM.A22J.01 TCGA.EL.A3MX.01
#> "034" "032" "013" "0211" "02412" "033"
#> TCGA.FY.A3I4.01 TCGA.BJ.A28W.11 TCGA.ET.A25R.01 TCGA.BJ.A2N8.01 TCGA.FY.A76V.01 TCGA.EM.A3FN.01
#> "011" "02321" "032" "0252" "0251" "02413"
#> TCGA.QD.A8IV.01 TCGA.EM.A3FJ.01 TCGA.ET.A2MY.11 TCGA.EM.A3FQ.06 TCGA.ET.A25P.01 TCGA.ET.A2N0.01
#> "0252" "033" "02413" "033" "0252" "015"
#> TCGA.EM.A2CT.01 TCGA.FE.A235.01 TCGA.ET.A25M.01 TCGA.EL.A3MY.01 TCGA.DE.A7U5.01 TCGA.E8.A2JQ.11
#> "0222" "033" "031" "031" "033" "0231"
#> TCGA.ET.A3DP.01 TCGA.EM.A2CL.01 TCGA.ET.A2N5.01 TCGA.ET.A25J.11 TCGA.DE.A69J.01 TCGA.BJ.A28R.11
#> "011" "0242" "0252" "0211" "033" "02321"
#> TCGA.ET.A25K.01 TCGA.EL.A3GV.01 TCGA.GE.A2C6.01 TCGA.EM.A3FM.01 TCGA.EL.A3H7.11 TCGA.FE.A22Z.01
#> "032" "011" "013" "031" "0211" "033"
#> TCGA.H2.A2K9.01 TCGA.EM.A22Q.01 TCGA.EM.A3FP.01 TCGA.GE.A2C6.11 TCGA.EL.A3MZ.01 TCGA.DJ.A2PT.01
#> "0243" "0242" "0252" "02321" "031" "013"
#> TCGA.E8.A242.01 TCGA.ET.A25L.01 TCGA.CE.A27D.01 TCGA.EL.A3H1.11 TCGA.BJ.A2N7.11 TCGA.DJ.A2Q7.01
#> "013" "032" "0233" "0233" "0211" "033"
#> TCGA.J8.A3O1.01 TCGA.EM.A2CR.01 TCGA.DE.A69K.01 TCGA.EM.A2CQ.01 TCGA.FE.A238.01 TCGA.EL.A3H1.01
#> "011" "011" "033" "0222" "015" "02411"
#> TCGA.BJ.A28W.01 TCGA.BJ.A28T.01 TCGA.EM.A2CJ.01 TCGA.EM.A3FQ.01 TCGA.4C.A93U.01 TCGA.EM.A22M.01
#> "0231" "02321" "0223" "015" "033" "0142"
#> TCGA.J8.A3NZ.01 TCGA.EM.A22K.01 TCGA.FE.A236.01 TCGA.BJ.A28R.01 TCGA.EM.A2CU.01 TCGA.ET.A25N.01
#> "011" "0252" "012" "015" "015" "033"
#> TCGA.EL.A3H7.01 TCGA.FY.A3NM.01 TCGA.EM.A3FO.01 TCGA.EM.A22L.01 TCGA.BJ.A2N9.11 TCGA.BJ.A291.01
#> "033" "0223" "031" "0252" "0231" "0222"
#> TCGA.ET.A2N5.11 TCGA.ET.A25N.11 TCGA.J8.A3O0.01 TCGA.FE.A237.01 TCGA.DJ.A2QC.01 TCGA.ET.A25O.01
#> "0211" "0211" "0243" "011" "011" "033"
#> TCGA.EL.A3GU.01 TCGA.EL.A3MY.11 TCGA.DJ.A2PY.01 TCGA.EM.A2CS.06 TCGA.FY.A3NP.01 TCGA.ET.A25I.01
#> "033" "0221" "033" "011" "0251" "0222"
#> TCGA.H2.A26U.01 TCGA.BJ.A290.11 TCGA.EM.A22I.01 TCGA.FE.A239.01 TCGA.BJ.A28Z.01 TCGA.DE.A0XZ.01
#> "013" "0212" "033" "0242" "013" "033"
#> TCGA.ET.A25J.01 TCGA.EM.A22N.01 TCGA.EM.A2CM.01 TCGA.FY.A3NN.01 TCGA.EM.A3FL.01 TCGA.H2.A2K9.11
#> "011" "0222" "0244" "011" "0223" "0233"
#> TCGA.EL.A3H3.01 TCGA.EL.A3H4.01 TCGA.EM.A2OX.01 TCGA.EM.A3SX.01 TCGA.BJ.A0Z3.01 TCGA.BJ.A28X.01
#> "015" "032" "031" "032" "013" "013"
#> TCGA.EL.A3CT.01 TCGA.EL.A3CR.01 TCGA.FY.A3TY.01 TCGA.J8.A3YG.01 TCGA.DJ.A3V6.01 TCGA.EM.A3SZ.01
#> "013" "032" "0233" "015" "031" "015"
#> TCGA.EM.A2OW.01 TCGA.DO.A1JZ.11 TCGA.EL.A3D5.01 TCGA.EM.A2P0.01 TCGA.E8.A2JQ.01 TCGA.BJ.A18Z.01
#> "0222" "0211" "0252" "012" "013" "031"
#> TCGA.DJ.A3V0.01 TCGA.EL.A3GW.01 TCGA.DJ.A3UW.01 TCGA.DJ.A3V3.01 TCGA.EL.A3T1.11 TCGA.BJ.A0ZC.01
#> "031" "0252" "013" "015" "02321" "0221"
#> TCGA.EM.A2OV.01 TCGA.EL.A3GY.01 TCGA.EM.A3SY.01 TCGA.EM.A3AI.01 TCGA.EM.A2OY.01 TCGA.EL.A3T8.01
#> "0222" "033" "0212" "0222" "0223" "031"
#> TCGA.BJ.A18Y.01 TCGA.EL.A3GP.01 TCGA.EM.A2CK.01 TCGA.EL.A3T7.11 TCGA.BJ.A192.01 TCGA.BJ.A191.01
#> "0251" "0141" "0251" "0211" "0223" "011"
#> TCGA.EM.A2CP.01 TCGA.EM.A22O.01 TCGA.EM.A2P1.01 TCGA.J8.A3YH.01 TCGA.DJ.A3UZ.01 TCGA.IM.A3EB.01
#> "0231" "031" "0142" "031" "0222" "013"
#> TCGA.BJ.A3F0.01 TCGA.EL.A3GX.01 TCGA.EM.A3AK.01 TCGA.DO.A1JZ.01 TCGA.FY.A3YR.01 TCGA.DO.A1K0.01
#> "02414" "033" "011" "033" "032" "033"
#> TCGA.DJ.A3V5.01 TCGA.EM.A3AJ.01 TCGA.IM.A3ED.01 TCGA.EM.A3AO.01 TCGA.EM.A2P1.06 TCGA.EM.A1CW.01
#> "032" "02322" "033" "012" "0142" "0222"
#> TCGA.FK.A3SE.01 TCGA.EL.A3T7.01 TCGA.EM.A2P2.01 TCGA.EM.A1CU.11 TCGA.EL.A3T0.11 TCGA.E8.A3X7.01
#> "032" "032" "0251" "0212" "0211" "032"
#> TCGA.ET.A3BQ.01 TCGA.EM.A1CS.01 TCGA.EL.A3GQ.01 TCGA.EL.A3H5.01 TCGA.DJ.A3V4.01 TCGA.EM.A2P3.01
#> "033" "011" "011" "033" "011" "033"
#> TCGA.FY.A3WA.01 TCGA.DJ.A3V2.01 TCGA.FY.A3TY.11 TCGA.BJ.A290.01 TCGA.EM.A3SU.01 TCGA.EL.A3D0.01
#> "0223" "013" "0211" "012" "015" "031"
#> TCGA.EM.A1CT.11 TCGA.EL.A3GR.01 TCGA.J8.A3YH.06 TCGA.EM.A3ST.11 TCGA.ET.A3DV.01 TCGA.BJ.A3EZ.01
#> "0212" "011" "031" "0211" "02411" "031"
#> TCGA.J8.A3YD.01 TCGA.EM.A3SU.06 TCGA.EM.A3AL.01 TCGA.DJ.A3US.01 TCGA.EM.A1CS.11 TCGA.EM.A1CW.11
#> "0222" "013" "02411" "015" "0211" "0211"
#> TCGA.BJ.A190.01 TCGA.EM.A2OZ.01 TCGA.EM.A1CV.11 TCGA.EM.A1CU.01 TCGA.EM.A3AN.01 TCGA.E8.A2EA.01
#> "0221" "012" "0211" "031" "032" "013"
#> TCGA.EM.A1CV.01 TCGA.EM.A1CT.01 TCGA.EM.A3ST.01 TCGA.ET.A3BS.01 TCGA.EL.A3GO.01 TCGA.DJ.A2Q0.01
#> "011" "012" "0244" "0143" "02411" "0223"
#> TCGA.EL.A3D6.01 TCGA.DJ.A3UN.01 TCGA.DJ.A3UU.01 TCGA.FK.A3SD.01 TCGA.DJ.A2PO.01 TCGA.DJ.A3UQ.01
#> "032" "032" "011" "02413" "012" "015"
#> TCGA.EM.A1YE.11 TCGA.EL.A3T2.11 TCGA.EL.A3CL.01 TCGA.EM.A1YC.01 TCGA.DJ.A3UP.01 TCGA.EL.A3T0.01
#> "0211" "0211" "033" "0223" "0252" "011"
#> TCGA.IM.A3U2.01 TCGA.IM.A3U3.01 TCGA.DJ.A3UX.01 TCGA.ET.A3BW.01 TCGA.ET.A39S.01 TCGA.ET.A3BP.01
#> "032" "032" "015" "011" "011" "011"
#> TCGA.DJ.A1QE.01 TCGA.EL.A3D4.01 TCGA.FK.A3SB.01 TCGA.EL.A3CW.01 TCGA.ET.A39L.01 TCGA.DJ.A2PW.01
#> "033" "012" "033" "02321" "0252" "031"
#> TCGA.EM.A2CO.01 TCGA.FE.A232.01 TCGA.DJ.A3UR.01 TCGA.DJ.A2PP.01 TCGA.ET.A3DQ.01 TCGA.ET.A3DS.01
#> "0222" "011" "011" "0242" "02321" "0222"
#> TCGA.FY.A3W9.01 TCGA.FK.A3S3.01 TCGA.ET.A2MZ.01 TCGA.BJ.A2NA.11 TCGA.DJ.A1QL.01 TCGA.EL.A3CS.01
#> "0244" "011" "031" "0233" "0242" "015"
#> TCGA.FE.A233.01 TCGA.EM.A1YD.11 TCGA.ET.A3DW.11 TCGA.EL.A3T9.01 TCGA.DJ.A3UM.01 TCGA.DO.A2HM.01
#> "033" "0211" "0212" "032" "032" "0142"
#> TCGA.FY.A3BL.01 TCGA.EL.A3TA.11 TCGA.ET.A3BX.01 TCGA.DJ.A1QQ.01 TCGA.DJ.A1QF.01 TCGA.DJ.A1QO.01
#> "012" "0212" "031" "031" "011" "031"
#> TCGA.BJ.A2NA.01 TCGA.EM.A1YE.01 TCGA.FY.A2QD.01 TCGA.ET.A39J.01 TCGA.ET.A3DU.01 TCGA.EL.A3CM.01
#> "031" "0223" "02413" "034" "013" "032"
#> TCGA.DJ.A3UO.01 TCGA.ET.A39P.01 TCGA.DJ.A2Q2.01 TCGA.BJ.A28V.01 TCGA.ET.A3BO.01 TCGA.EL.A3T1.01
#> "031" "033" "0222" "02411" "032" "015"
#> TCGA.DJ.A1QI.01 TCGA.EL.A3TB.01 TCGA.BJ.A28X.11 TCGA.DJ.A1QN.01 TCGA.FE.A230.01 TCGA.FE.A234.01
#> "033" "032" "0231" "033" "015" "033"
#> TCGA.ET.A39R.01 TCGA.DJ.A1QG.01 TCGA.EL.A3CV.01 TCGA.FE.A231.01 TCGA.EL.A3TA.01 TCGA.DJ.A3UY.01
#> "015" "0251" "0142" "031" "012" "015"
#> TCGA.DJ.A2Q1.01 TCGA.EL.A3CU.01 TCGA.EL.A3TB.11 TCGA.ET.A39I.01 TCGA.EM.A1YB.01 TCGA.DJ.A3UV.01
#> "013" "013" "0211" "0252" "02414" "011"
#> TCGA.DJ.A3UT.01 TCGA.ET.A3DW.01 TCGA.ET.A3BT.01 TCGA.EL.A3T3.01 TCGA.DJ.A1QM.01 TCGA.EL.A3CY.01
#> "0252" "031" "032" "032" "0212" "0231"
#> TCGA.ET.A39O.01 TCGA.EM.A1YC.11 TCGA.DJ.A1QH.01 TCGA.EL.A3T3.11 TCGA.EL.A3CX.01 TCGA.EL.A3T2.01
#> "031" "0211" "033" "0211" "011" "0252"
#> TCGA.EM.A22P.01 TCGA.EL.A3T8.11 TCGA.DJ.A2PU.01 TCGA.DJ.A3UK.01 TCGA.ET.A3DO.01 TCGA.EM.A1YA.01
#> "0142" "0212" "033" "011" "013" "0223"
#> TCGA.ET.A3BV.01 TCGA.EL.A3CO.01 TCGA.DJ.A2PN.01 TCGA.FK.A3SG.01 TCGA.FK.A3SH.01 TCGA.EM.A1YD.01
#> "013" "0233" "033" "032" "032" "0223"
#> TCGA.DJ.A1QD.01 TCGA.EL.A3CZ.01 TCGA.BJ.A0Z9.01 TCGA.CE.A13K.01 TCGA.EM.A3FR.01 TCGA.EM.A3O8.01
#> "033" "0222" "013" "032" "02413" "0252"
#> TCGA.FY.A3R6.01 TCGA.FY.A3R9.01 TCGA.EL.A3D1.01 TCGA.EM.A3O6.01 TCGA.BJ.A0Z5.01 TCGA.BJ.A28S.01
#> "013" "0222" "031" "0222" "012" "0251"
#> TCGA.BJ.A0ZH.01 TCGA.ET.A3DT.01 TCGA.H2.A3RI.11 TCGA.DJ.A13W.01 TCGA.DJ.A13T.01 TCGA.BJ.A0ZA.01
#> "032" "013" "0211" "02411" "032" "02414"
#> TCGA.BJ.A3PT.01 TCGA.FE.A3PD.01 TCGA.BJ.A0ZF.01 TCGA.ET.A39M.01 TCGA.BJ.A0ZJ.01 TCGA.BJ.A0YZ.01
#> "0252" "032" "0224" "0143" "0143" "0221"
#> TCGA.FE.A3PC.01 TCGA.DJ.A2QB.01 TCGA.EM.A3OB.01 TCGA.H2.A3RH.01 TCGA.ET.A39T.01 TCGA.DJ.A2PV.01
#> "032" "0252" "0252" "0252" "011" "011"
#> TCGA.BJ.A3PR.11 TCGA.EL.A3T6.11 TCGA.DJ.A13X.01 TCGA.BJ.A0ZG.01 TCGA.EL.A3T6.01 TCGA.BJ.A0Z0.01
#> "02321" "0233" "011" "0221" "013" "0242"
#> TCGA.ET.A39K.01 TCGA.EM.A3O9.01 TCGA.BJ.A3PU.01 TCGA.BJ.A3PR.01 TCGA.EM.A3O3.01 TCGA.BJ.A0ZB.01
#> "032" "0234" "031" "0231" "013" "031"
#> TCGA.EM.A3OA.01 TCGA.DJ.A2PR.01 TCGA.DJ.A13L.01 TCGA.FY.A3ON.01 TCGA.DJ.A13V.01 TCGA.FY.A3R8.01
#> "02412" "031" "0142" "031" "032" "032"
#> TCGA.EL.A3CP.01 TCGA.DJ.A13U.01 TCGA.DE.A0Y3.01 TCGA.ET.A2N4.01 TCGA.DJ.A13P.01 TCGA.BJ.A0ZE.01
#> "033" "012" "032" "011" "011" "0252"
#> TCGA.EM.A3O7.01 TCGA.DJ.A13O.01 TCGA.FY.A3RA.01 TCGA.DJ.A13M.01 TCGA.DJ.A13R.01 TCGA.ET.A3DR.01
#> "011" "0233" "033" "0252" "0221" "011"
#> TCGA.FE.A3PB.01 TCGA.ET.A3BN.01 TCGA.H2.A3RI.01 TCGA.ET.A39N.01 TCGA.BJ.A3PU.11 TCGA.FY.A3R7.01
#> "015" "033" "032" "0224" "0212" "0222"
#> TCGA.FE.A3PA.01 TCGA.EM.A2CN.01 TCGA.BJ.A0Z2.01 TCGA.FY.A3I5.01 TCGA.DJ.A13S.01 TCGA.DE.A0Y2.01
#> "031" "0243" "0243" "02414" "0252" "033"
#> TCGA.ET.A3BU.01
#> "031"
get_classes(res_rh, merge_node = merge_node_param(min_n_signatures = 3159))
#> TCGA.E8.A416.01 TCGA.E8.A433.01 TCGA.EL.A4K9.01 TCGA.DJ.A3V9.01 TCGA.EL.A3ZO.11 TCGA.EL.A3ZN.01
#> "0211" "015" "031" "011" "0211" "011"
#> TCGA.KS.A41F.01 TCGA.EL.A3ZK.01 TCGA.ET.A40R.01 TCGA.EL.A3ZM.01 TCGA.ET.A2N3.01 TCGA.EL.A3ZQ.01
#> "032" "015" "015" "031" "02411" "032"
#> TCGA.ET.A40T.01 TCGA.DE.A4MA.01 TCGA.EM.A4FU.01 TCGA.E8.A418.01 TCGA.DJ.A3VD.01 TCGA.DJ.A3VM.01
#> "032" "032" "0251" "032" "013" "0244"
#> TCGA.EL.A3ZG.01 TCGA.EM.A4FV.01 TCGA.E8.A413.01 TCGA.DJ.A3VG.01 TCGA.EL.A4K2.01 TCGA.IM.A420.01
#> "012" "015" "015" "0251" "0222" "013"
#> TCGA.KS.A41J.01 TCGA.EL.A3ZK.11 TCGA.J8.A3O2.01 TCGA.E8.A415.01 TCGA.FY.A40M.01 TCGA.DJ.A3VB.01
#> "032" "02321" "012" "011" "0252" "031"
#> TCGA.KS.A41I.01 TCGA.DJ.A3VL.01 TCGA.ET.A4KQ.01 TCGA.H2.A421.01 TCGA.EL.A3ZO.01 TCGA.KS.A4I3.01
#> "0252" "0234" "0252" "032" "032" "012"
#> TCGA.DJ.A4UT.01 TCGA.DE.A4MD.01 TCGA.EL.A4JW.01 TCGA.DJ.A3VI.01 TCGA.DJ.A3VA.01 TCGA.L6.A4ET.01
#> "013" "031" "015" "032" "032" "033"
#> TCGA.E8.A419.01 TCGA.DJ.A4V0.01 TCGA.DJ.A4V2.01 TCGA.ET.A40Q.01 TCGA.EL.A3ZS.01 TCGA.KS.A4ID.01
#> "013" "02321" "033" "031" "013" "013"
#> TCGA.EL.A3ZL.11 TCGA.J8.A3YE.01 TCGA.EL.A4K7.01 TCGA.DJ.A3VF.01 TCGA.EM.A4FH.01 TCGA.E8.A432.01
#> "0211" "011" "031" "013" "0221" "015"
#> TCGA.J8.A3O2.06 TCGA.ET.A2MX.01 TCGA.ET.A40S.01 TCGA.DE.A4M8.01 TCGA.IM.A41Z.01 TCGA.EL.A4KD.01
#> "031" "012" "014" "013" "02412" "012"
#> TCGA.DJ.A3V7.01 TCGA.FY.A40L.01 TCGA.DE.A4M9.01 TCGA.J8.A42S.01 TCGA.KS.A41L.01 TCGA.EM.A4FN.01
#> "032" "015" "0221" "012" "0224" "033"
#> TCGA.EL.A4K1.01 TCGA.KS.A4IC.01 TCGA.E8.A414.01 TCGA.H2.A422.01 TCGA.J8.A3YF.01 TCGA.EL.A4KI.01
#> "033" "011" "015" "032" "031" "0243"
#> TCGA.EM.A4G1.01 TCGA.DJ.A3VJ.01 TCGA.DE.A4MD.06 TCGA.EL.A3ZP.01 TCGA.EM.A4FQ.01 TCGA.EL.A3ZT.01
#> "0252" "031" "014" "031" "033" "031"
#> TCGA.DJ.A4V4.01 TCGA.FY.A40K.01 TCGA.L6.A4EQ.01 TCGA.DJ.A3VE.01 TCGA.E8.A434.01 TCGA.EL.A3ZH.01
#> "011" "011" "031" "031" "0222" "0222"
#> TCGA.EM.A4FR.01 TCGA.EL.A3ZH.11 TCGA.EL.A3ZR.01 TCGA.DJ.A3V8.01 TCGA.EL.A3ZG.11 TCGA.ET.A40P.01
#> "012" "0211" "0252" "015" "0212" "0252"
#> TCGA.DE.A4MB.01 TCGA.MK.A4N6.01 TCGA.DJ.A3VK.01 TCGA.E8.A417.01 TCGA.L6.A4EU.01 TCGA.J8.A4HY.01
#> "032" "031" "0251" "032" "032" "011"
#> TCGA.EL.A3ZL.01 TCGA.EL.A3ZP.11 TCGA.FY.A40N.01 TCGA.J8.A4HW.01 TCGA.BJ.A45J.01 TCGA.CE.A482.01
#> "032" "02322" "011" "032" "032" "032"
#> TCGA.DJ.A2Q6.01 TCGA.DJ.A2PX.01 TCGA.DJ.A4UL.01 TCGA.EL.A4JX.01 TCGA.BJ.A2N8.11 TCGA.DJ.A2Q5.01
#> "032" "015" "033" "013" "0211" "014"
#> TCGA.EL.A4KG.01 TCGA.DJ.A4UP.01 TCGA.E8.A438.01 TCGA.EL.A3H2.01 TCGA.EM.A3AP.01 TCGA.DJ.A2PQ.01
#> "033" "015" "011" "0221" "0252" "031"
#> TCGA.L6.A4EP.01 TCGA.FY.A4B4.01 TCGA.EL.A4KH.01 TCGA.BJ.A45E.01 TCGA.DJ.A4V5.01 TCGA.DE.A4MC.01
#> "033" "032" "011" "0231" "014" "033"
#> TCGA.E8.A44M.01 TCGA.BJ.A45K.01 TCGA.E3.A3DZ.01 TCGA.E3.A3E2.01 TCGA.BJ.A45H.01 TCGA.E8.A44K.01
#> "013" "0242" "0252" "032" "012" "015"
#> TCGA.ET.A2MY.01 TCGA.EL.A3H8.01 TCGA.BJ.A45C.01 TCGA.BJ.A45G.01 TCGA.EL.A4JZ.01 TCGA.CE.A481.01
#> "032" "033" "0242" "0252" "033" "015"
#> TCGA.KS.A4I9.01 TCGA.EL.A3MW.01 TCGA.E8.A436.01 TCGA.E3.A3DY.01 TCGA.DJ.A2Q3.01 TCGA.BJ.A2P4.01
#> "033" "033" "015" "031" "013" "0252"
#> TCGA.CE.A484.01 TCGA.ET.A2N1.01 TCGA.DJ.A2Q4.01 TCGA.DJ.A2PZ.01 TCGA.BJ.A45F.01 TCGA.IM.A4EB.01
#> "0252" "011" "031" "012" "0252" "014"
#> TCGA.EM.A4FO.01 TCGA.FY.A4B3.01 TCGA.FY.A4B0.01 TCGA.BJ.A45I.01 TCGA.E3.A3E3.01 TCGA.EM.A3AQ.01
#> "014" "031" "0242" "013" "033" "034"
#> TCGA.EL.A3N3.01 TCGA.DJ.A2Q9.01 TCGA.EM.A4FM.01 TCGA.EL.A4K6.01 TCGA.MK.A4N9.01 TCGA.KS.A4I1.01
#> "013" "0231" "033" "0243" "033" "032"
#> TCGA.DJ.A2PS.01 TCGA.CE.A3MD.01 TCGA.E3.A3E5.01 TCGA.EL.A3CN.01 TCGA.J8.A4HW.06 TCGA.EM.A4FK.01
#> "011" "012" "031" "015" "013" "02412"
#> TCGA.E8.A437.01 TCGA.BJ.A4O8.01 TCGA.EL.A3MW.11 TCGA.E3.A3E0.01 TCGA.BJ.A45D.01 TCGA.CE.A483.01
#> "011" "031" "0211" "033" "0251" "011"
#> TCGA.CE.A485.01 TCGA.DJ.A4UR.01 TCGA.IM.A41Y.01 TCGA.ET.A4KN.01 TCGA.KS.A4I5.01 TCGA.DJ.A4UQ.01
#> "012" "0244" "032" "013" "033" "012"
#> TCGA.KS.A4IB.01 TCGA.EL.A3N2.11 TCGA.BJ.A2N9.01 TCGA.DJ.A4UW.01 TCGA.EL.A3GZ.11 TCGA.EM.A3AR.01
#> "033" "0211" "0222" "011" "0211" "0212"
#> TCGA.EL.A3N3.11 TCGA.DE.A3KN.01 TCGA.DJ.A2QA.01 TCGA.EL.A4JV.01 TCGA.EM.A4FF.01 TCGA.EL.A4K0.01
#> "02321" "011" "011" "0252" "033" "033"
#> TCGA.FK.A4UB.01 TCGA.BJ.A4O9.01 TCGA.BJ.A2N7.01 TCGA.DE.A2OL.01 TCGA.CE.A3ME.01 TCGA.MK.A4N7.01
#> "031" "011" "0252" "02411" "011" "032"
#> TCGA.EL.A3H2.11 TCGA.EL.A4K4.01 TCGA.EL.A3GS.01 TCGA.EL.A3GZ.01 TCGA.E3.A3E1.01 TCGA.DJ.A2Q8.01
#> "0212" "033" "033" "032" "011" "015"
#> TCGA.EL.A3N2.01 TCGA.KS.A4I7.01 TCGA.MK.A84Z.01 TCGA.ET.A3DP.11 TCGA.EL.A3MX.11 TCGA.ET.A25G.01
#> "033" "032" "0251" "0211" "0211" "032"
#> TCGA.EM.A3FK.01 TCGA.EM.A2CS.01 TCGA.FE.A23A.01 TCGA.BJ.A28T.11 TCGA.EM.A22J.01 TCGA.EL.A3MX.01
#> "034" "032" "013" "0211" "02412" "033"
#> TCGA.FY.A3I4.01 TCGA.BJ.A28W.11 TCGA.ET.A25R.01 TCGA.BJ.A2N8.01 TCGA.FY.A76V.01 TCGA.EM.A3FN.01
#> "011" "02321" "032" "0252" "0251" "02413"
#> TCGA.QD.A8IV.01 TCGA.EM.A3FJ.01 TCGA.ET.A2MY.11 TCGA.EM.A3FQ.06 TCGA.ET.A25P.01 TCGA.ET.A2N0.01
#> "0252" "033" "02413" "033" "0252" "015"
#> TCGA.EM.A2CT.01 TCGA.FE.A235.01 TCGA.ET.A25M.01 TCGA.EL.A3MY.01 TCGA.DE.A7U5.01 TCGA.E8.A2JQ.11
#> "0222" "033" "031" "031" "033" "0231"
#> TCGA.ET.A3DP.01 TCGA.EM.A2CL.01 TCGA.ET.A2N5.01 TCGA.ET.A25J.11 TCGA.DE.A69J.01 TCGA.BJ.A28R.11
#> "011" "0242" "0252" "0211" "033" "02321"
#> TCGA.ET.A25K.01 TCGA.EL.A3GV.01 TCGA.GE.A2C6.01 TCGA.EM.A3FM.01 TCGA.EL.A3H7.11 TCGA.FE.A22Z.01
#> "032" "011" "013" "031" "0211" "033"
#> TCGA.H2.A2K9.01 TCGA.EM.A22Q.01 TCGA.EM.A3FP.01 TCGA.GE.A2C6.11 TCGA.EL.A3MZ.01 TCGA.DJ.A2PT.01
#> "0243" "0242" "0252" "02321" "031" "013"
#> TCGA.E8.A242.01 TCGA.ET.A25L.01 TCGA.CE.A27D.01 TCGA.EL.A3H1.11 TCGA.BJ.A2N7.11 TCGA.DJ.A2Q7.01
#> "013" "032" "0233" "0233" "0211" "033"
#> TCGA.J8.A3O1.01 TCGA.EM.A2CR.01 TCGA.DE.A69K.01 TCGA.EM.A2CQ.01 TCGA.FE.A238.01 TCGA.EL.A3H1.01
#> "011" "011" "033" "0222" "015" "02411"
#> TCGA.BJ.A28W.01 TCGA.BJ.A28T.01 TCGA.EM.A2CJ.01 TCGA.EM.A3FQ.01 TCGA.4C.A93U.01 TCGA.EM.A22M.01
#> "0231" "02321" "0223" "015" "033" "014"
#> TCGA.J8.A3NZ.01 TCGA.EM.A22K.01 TCGA.FE.A236.01 TCGA.BJ.A28R.01 TCGA.EM.A2CU.01 TCGA.ET.A25N.01
#> "011" "0252" "012" "015" "015" "033"
#> TCGA.EL.A3H7.01 TCGA.FY.A3NM.01 TCGA.EM.A3FO.01 TCGA.EM.A22L.01 TCGA.BJ.A2N9.11 TCGA.BJ.A291.01
#> "033" "0223" "031" "0252" "0231" "0222"
#> TCGA.ET.A2N5.11 TCGA.ET.A25N.11 TCGA.J8.A3O0.01 TCGA.FE.A237.01 TCGA.DJ.A2QC.01 TCGA.ET.A25O.01
#> "0211" "0211" "0243" "011" "011" "033"
#> TCGA.EL.A3GU.01 TCGA.EL.A3MY.11 TCGA.DJ.A2PY.01 TCGA.EM.A2CS.06 TCGA.FY.A3NP.01 TCGA.ET.A25I.01
#> "033" "0221" "033" "011" "0251" "0222"
#> TCGA.H2.A26U.01 TCGA.BJ.A290.11 TCGA.EM.A22I.01 TCGA.FE.A239.01 TCGA.BJ.A28Z.01 TCGA.DE.A0XZ.01
#> "013" "0212" "033" "0242" "013" "033"
#> TCGA.ET.A25J.01 TCGA.EM.A22N.01 TCGA.EM.A2CM.01 TCGA.FY.A3NN.01 TCGA.EM.A3FL.01 TCGA.H2.A2K9.11
#> "011" "0222" "0244" "011" "0223" "0233"
#> TCGA.EL.A3H3.01 TCGA.EL.A3H4.01 TCGA.EM.A2OX.01 TCGA.EM.A3SX.01 TCGA.BJ.A0Z3.01 TCGA.BJ.A28X.01
#> "015" "032" "031" "032" "013" "013"
#> TCGA.EL.A3CT.01 TCGA.EL.A3CR.01 TCGA.FY.A3TY.01 TCGA.J8.A3YG.01 TCGA.DJ.A3V6.01 TCGA.EM.A3SZ.01
#> "013" "032" "0233" "015" "031" "015"
#> TCGA.EM.A2OW.01 TCGA.DO.A1JZ.11 TCGA.EL.A3D5.01 TCGA.EM.A2P0.01 TCGA.E8.A2JQ.01 TCGA.BJ.A18Z.01
#> "0222" "0211" "0252" "012" "013" "031"
#> TCGA.DJ.A3V0.01 TCGA.EL.A3GW.01 TCGA.DJ.A3UW.01 TCGA.DJ.A3V3.01 TCGA.EL.A3T1.11 TCGA.BJ.A0ZC.01
#> "031" "0252" "013" "015" "02321" "0221"
#> TCGA.EM.A2OV.01 TCGA.EL.A3GY.01 TCGA.EM.A3SY.01 TCGA.EM.A3AI.01 TCGA.EM.A2OY.01 TCGA.EL.A3T8.01
#> "0222" "033" "0212" "0222" "0223" "031"
#> TCGA.BJ.A18Y.01 TCGA.EL.A3GP.01 TCGA.EM.A2CK.01 TCGA.EL.A3T7.11 TCGA.BJ.A192.01 TCGA.BJ.A191.01
#> "0251" "014" "0251" "0211" "0223" "011"
#> TCGA.EM.A2CP.01 TCGA.EM.A22O.01 TCGA.EM.A2P1.01 TCGA.J8.A3YH.01 TCGA.DJ.A3UZ.01 TCGA.IM.A3EB.01
#> "0231" "031" "014" "031" "0222" "013"
#> TCGA.BJ.A3F0.01 TCGA.EL.A3GX.01 TCGA.EM.A3AK.01 TCGA.DO.A1JZ.01 TCGA.FY.A3YR.01 TCGA.DO.A1K0.01
#> "02414" "033" "011" "033" "032" "033"
#> TCGA.DJ.A3V5.01 TCGA.EM.A3AJ.01 TCGA.IM.A3ED.01 TCGA.EM.A3AO.01 TCGA.EM.A2P1.06 TCGA.EM.A1CW.01
#> "032" "02322" "033" "012" "014" "0222"
#> TCGA.FK.A3SE.01 TCGA.EL.A3T7.01 TCGA.EM.A2P2.01 TCGA.EM.A1CU.11 TCGA.EL.A3T0.11 TCGA.E8.A3X7.01
#> "032" "032" "0251" "0212" "0211" "032"
#> TCGA.ET.A3BQ.01 TCGA.EM.A1CS.01 TCGA.EL.A3GQ.01 TCGA.EL.A3H5.01 TCGA.DJ.A3V4.01 TCGA.EM.A2P3.01
#> "033" "011" "011" "033" "011" "033"
#> TCGA.FY.A3WA.01 TCGA.DJ.A3V2.01 TCGA.FY.A3TY.11 TCGA.BJ.A290.01 TCGA.EM.A3SU.01 TCGA.EL.A3D0.01
#> "0223" "013" "0211" "012" "015" "031"
#> TCGA.EM.A1CT.11 TCGA.EL.A3GR.01 TCGA.J8.A3YH.06 TCGA.EM.A3ST.11 TCGA.ET.A3DV.01 TCGA.BJ.A3EZ.01
#> "0212" "011" "031" "0211" "02411" "031"
#> TCGA.J8.A3YD.01 TCGA.EM.A3SU.06 TCGA.EM.A3AL.01 TCGA.DJ.A3US.01 TCGA.EM.A1CS.11 TCGA.EM.A1CW.11
#> "0222" "013" "02411" "015" "0211" "0211"
#> TCGA.BJ.A190.01 TCGA.EM.A2OZ.01 TCGA.EM.A1CV.11 TCGA.EM.A1CU.01 TCGA.EM.A3AN.01 TCGA.E8.A2EA.01
#> "0221" "012" "0211" "031" "032" "013"
#> TCGA.EM.A1CV.01 TCGA.EM.A1CT.01 TCGA.EM.A3ST.01 TCGA.ET.A3BS.01 TCGA.EL.A3GO.01 TCGA.DJ.A2Q0.01
#> "011" "012" "0244" "014" "02411" "0223"
#> TCGA.EL.A3D6.01 TCGA.DJ.A3UN.01 TCGA.DJ.A3UU.01 TCGA.FK.A3SD.01 TCGA.DJ.A2PO.01 TCGA.DJ.A3UQ.01
#> "032" "032" "011" "02413" "012" "015"
#> TCGA.EM.A1YE.11 TCGA.EL.A3T2.11 TCGA.EL.A3CL.01 TCGA.EM.A1YC.01 TCGA.DJ.A3UP.01 TCGA.EL.A3T0.01
#> "0211" "0211" "033" "0223" "0252" "011"
#> TCGA.IM.A3U2.01 TCGA.IM.A3U3.01 TCGA.DJ.A3UX.01 TCGA.ET.A3BW.01 TCGA.ET.A39S.01 TCGA.ET.A3BP.01
#> "032" "032" "015" "011" "011" "011"
#> TCGA.DJ.A1QE.01 TCGA.EL.A3D4.01 TCGA.FK.A3SB.01 TCGA.EL.A3CW.01 TCGA.ET.A39L.01 TCGA.DJ.A2PW.01
#> "033" "012" "033" "02321" "0252" "031"
#> TCGA.EM.A2CO.01 TCGA.FE.A232.01 TCGA.DJ.A3UR.01 TCGA.DJ.A2PP.01 TCGA.ET.A3DQ.01 TCGA.ET.A3DS.01
#> "0222" "011" "011" "0242" "02321" "0222"
#> TCGA.FY.A3W9.01 TCGA.FK.A3S3.01 TCGA.ET.A2MZ.01 TCGA.BJ.A2NA.11 TCGA.DJ.A1QL.01 TCGA.EL.A3CS.01
#> "0244" "011" "031" "0233" "0242" "015"
#> TCGA.FE.A233.01 TCGA.EM.A1YD.11 TCGA.ET.A3DW.11 TCGA.EL.A3T9.01 TCGA.DJ.A3UM.01 TCGA.DO.A2HM.01
#> "033" "0211" "0212" "032" "032" "014"
#> TCGA.FY.A3BL.01 TCGA.EL.A3TA.11 TCGA.ET.A3BX.01 TCGA.DJ.A1QQ.01 TCGA.DJ.A1QF.01 TCGA.DJ.A1QO.01
#> "012" "0212" "031" "031" "011" "031"
#> TCGA.BJ.A2NA.01 TCGA.EM.A1YE.01 TCGA.FY.A2QD.01 TCGA.ET.A39J.01 TCGA.ET.A3DU.01 TCGA.EL.A3CM.01
#> "031" "0223" "02413" "034" "013" "032"
#> TCGA.DJ.A3UO.01 TCGA.ET.A39P.01 TCGA.DJ.A2Q2.01 TCGA.BJ.A28V.01 TCGA.ET.A3BO.01 TCGA.EL.A3T1.01
#> "031" "033" "0222" "02411" "032" "015"
#> TCGA.DJ.A1QI.01 TCGA.EL.A3TB.01 TCGA.BJ.A28X.11 TCGA.DJ.A1QN.01 TCGA.FE.A230.01 TCGA.FE.A234.01
#> "033" "032" "0231" "033" "015" "033"
#> TCGA.ET.A39R.01 TCGA.DJ.A1QG.01 TCGA.EL.A3CV.01 TCGA.FE.A231.01 TCGA.EL.A3TA.01 TCGA.DJ.A3UY.01
#> "015" "0251" "014" "031" "012" "015"
#> TCGA.DJ.A2Q1.01 TCGA.EL.A3CU.01 TCGA.EL.A3TB.11 TCGA.ET.A39I.01 TCGA.EM.A1YB.01 TCGA.DJ.A3UV.01
#> "013" "013" "0211" "0252" "02414" "011"
#> TCGA.DJ.A3UT.01 TCGA.ET.A3DW.01 TCGA.ET.A3BT.01 TCGA.EL.A3T3.01 TCGA.DJ.A1QM.01 TCGA.EL.A3CY.01
#> "0252" "031" "032" "032" "0212" "0231"
#> TCGA.ET.A39O.01 TCGA.EM.A1YC.11 TCGA.DJ.A1QH.01 TCGA.EL.A3T3.11 TCGA.EL.A3CX.01 TCGA.EL.A3T2.01
#> "031" "0211" "033" "0211" "011" "0252"
#> TCGA.EM.A22P.01 TCGA.EL.A3T8.11 TCGA.DJ.A2PU.01 TCGA.DJ.A3UK.01 TCGA.ET.A3DO.01 TCGA.EM.A1YA.01
#> "014" "0212" "033" "011" "013" "0223"
#> TCGA.ET.A3BV.01 TCGA.EL.A3CO.01 TCGA.DJ.A2PN.01 TCGA.FK.A3SG.01 TCGA.FK.A3SH.01 TCGA.EM.A1YD.01
#> "013" "0233" "033" "032" "032" "0223"
#> TCGA.DJ.A1QD.01 TCGA.EL.A3CZ.01 TCGA.BJ.A0Z9.01 TCGA.CE.A13K.01 TCGA.EM.A3FR.01 TCGA.EM.A3O8.01
#> "033" "0222" "013" "032" "02413" "0252"
#> TCGA.FY.A3R6.01 TCGA.FY.A3R9.01 TCGA.EL.A3D1.01 TCGA.EM.A3O6.01 TCGA.BJ.A0Z5.01 TCGA.BJ.A28S.01
#> "013" "0222" "031" "0222" "012" "0251"
#> TCGA.BJ.A0ZH.01 TCGA.ET.A3DT.01 TCGA.H2.A3RI.11 TCGA.DJ.A13W.01 TCGA.DJ.A13T.01 TCGA.BJ.A0ZA.01
#> "032" "013" "0211" "02411" "032" "02414"
#> TCGA.BJ.A3PT.01 TCGA.FE.A3PD.01 TCGA.BJ.A0ZF.01 TCGA.ET.A39M.01 TCGA.BJ.A0ZJ.01 TCGA.BJ.A0YZ.01
#> "0252" "032" "0224" "014" "014" "0221"
#> TCGA.FE.A3PC.01 TCGA.DJ.A2QB.01 TCGA.EM.A3OB.01 TCGA.H2.A3RH.01 TCGA.ET.A39T.01 TCGA.DJ.A2PV.01
#> "032" "0252" "0252" "0252" "011" "011"
#> TCGA.BJ.A3PR.11 TCGA.EL.A3T6.11 TCGA.DJ.A13X.01 TCGA.BJ.A0ZG.01 TCGA.EL.A3T6.01 TCGA.BJ.A0Z0.01
#> "02321" "0233" "011" "0221" "013" "0242"
#> TCGA.ET.A39K.01 TCGA.EM.A3O9.01 TCGA.BJ.A3PU.01 TCGA.BJ.A3PR.01 TCGA.EM.A3O3.01 TCGA.BJ.A0ZB.01
#> "032" "0234" "031" "0231" "013" "031"
#> TCGA.EM.A3OA.01 TCGA.DJ.A2PR.01 TCGA.DJ.A13L.01 TCGA.FY.A3ON.01 TCGA.DJ.A13V.01 TCGA.FY.A3R8.01
#> "02412" "031" "014" "031" "032" "032"
#> TCGA.EL.A3CP.01 TCGA.DJ.A13U.01 TCGA.DE.A0Y3.01 TCGA.ET.A2N4.01 TCGA.DJ.A13P.01 TCGA.BJ.A0ZE.01
#> "033" "012" "032" "011" "011" "0252"
#> TCGA.EM.A3O7.01 TCGA.DJ.A13O.01 TCGA.FY.A3RA.01 TCGA.DJ.A13M.01 TCGA.DJ.A13R.01 TCGA.ET.A3DR.01
#> "011" "0233" "033" "0252" "0221" "011"
#> TCGA.FE.A3PB.01 TCGA.ET.A3BN.01 TCGA.H2.A3RI.01 TCGA.ET.A39N.01 TCGA.BJ.A3PU.11 TCGA.FY.A3R7.01
#> "015" "033" "032" "0224" "0212" "0222"
#> TCGA.FE.A3PA.01 TCGA.EM.A2CN.01 TCGA.BJ.A0Z2.01 TCGA.FY.A3I5.01 TCGA.DJ.A13S.01 TCGA.DE.A0Y2.01
#> "031" "0243" "0243" "02414" "0252" "033"
#> TCGA.ET.A3BU.01
#> "031"
get_classes(res_rh, merge_node = merge_node_param(min_n_signatures = 3180))
#> TCGA.E8.A416.01 TCGA.E8.A433.01 TCGA.EL.A4K9.01 TCGA.DJ.A3V9.01 TCGA.EL.A3ZO.11 TCGA.EL.A3ZN.01
#> "0211" "015" "031" "011" "0211" "011"
#> TCGA.KS.A41F.01 TCGA.EL.A3ZK.01 TCGA.ET.A40R.01 TCGA.EL.A3ZM.01 TCGA.ET.A2N3.01 TCGA.EL.A3ZQ.01
#> "032" "015" "015" "031" "02411" "032"
#> TCGA.ET.A40T.01 TCGA.DE.A4MA.01 TCGA.EM.A4FU.01 TCGA.E8.A418.01 TCGA.DJ.A3VD.01 TCGA.DJ.A3VM.01
#> "032" "032" "025" "032" "013" "0244"
#> TCGA.EL.A3ZG.01 TCGA.EM.A4FV.01 TCGA.E8.A413.01 TCGA.DJ.A3VG.01 TCGA.EL.A4K2.01 TCGA.IM.A420.01
#> "012" "015" "015" "025" "0222" "013"
#> TCGA.KS.A41J.01 TCGA.EL.A3ZK.11 TCGA.J8.A3O2.01 TCGA.E8.A415.01 TCGA.FY.A40M.01 TCGA.DJ.A3VB.01
#> "032" "02321" "012" "011" "025" "031"
#> TCGA.KS.A41I.01 TCGA.DJ.A3VL.01 TCGA.ET.A4KQ.01 TCGA.H2.A421.01 TCGA.EL.A3ZO.01 TCGA.KS.A4I3.01
#> "025" "0234" "025" "032" "032" "012"
#> TCGA.DJ.A4UT.01 TCGA.DE.A4MD.01 TCGA.EL.A4JW.01 TCGA.DJ.A3VI.01 TCGA.DJ.A3VA.01 TCGA.L6.A4ET.01
#> "013" "031" "015" "032" "032" "033"
#> TCGA.E8.A419.01 TCGA.DJ.A4V0.01 TCGA.DJ.A4V2.01 TCGA.ET.A40Q.01 TCGA.EL.A3ZS.01 TCGA.KS.A4ID.01
#> "013" "02321" "033" "031" "013" "013"
#> TCGA.EL.A3ZL.11 TCGA.J8.A3YE.01 TCGA.EL.A4K7.01 TCGA.DJ.A3VF.01 TCGA.EM.A4FH.01 TCGA.E8.A432.01
#> "0211" "011" "031" "013" "0221" "015"
#> TCGA.J8.A3O2.06 TCGA.ET.A2MX.01 TCGA.ET.A40S.01 TCGA.DE.A4M8.01 TCGA.IM.A41Z.01 TCGA.EL.A4KD.01
#> "031" "012" "014" "013" "02412" "012"
#> TCGA.DJ.A3V7.01 TCGA.FY.A40L.01 TCGA.DE.A4M9.01 TCGA.J8.A42S.01 TCGA.KS.A41L.01 TCGA.EM.A4FN.01
#> "032" "015" "0221" "012" "0224" "033"
#> TCGA.EL.A4K1.01 TCGA.KS.A4IC.01 TCGA.E8.A414.01 TCGA.H2.A422.01 TCGA.J8.A3YF.01 TCGA.EL.A4KI.01
#> "033" "011" "015" "032" "031" "0243"
#> TCGA.EM.A4G1.01 TCGA.DJ.A3VJ.01 TCGA.DE.A4MD.06 TCGA.EL.A3ZP.01 TCGA.EM.A4FQ.01 TCGA.EL.A3ZT.01
#> "025" "031" "014" "031" "033" "031"
#> TCGA.DJ.A4V4.01 TCGA.FY.A40K.01 TCGA.L6.A4EQ.01 TCGA.DJ.A3VE.01 TCGA.E8.A434.01 TCGA.EL.A3ZH.01
#> "011" "011" "031" "031" "0222" "0222"
#> TCGA.EM.A4FR.01 TCGA.EL.A3ZH.11 TCGA.EL.A3ZR.01 TCGA.DJ.A3V8.01 TCGA.EL.A3ZG.11 TCGA.ET.A40P.01
#> "012" "0211" "025" "015" "0212" "025"
#> TCGA.DE.A4MB.01 TCGA.MK.A4N6.01 TCGA.DJ.A3VK.01 TCGA.E8.A417.01 TCGA.L6.A4EU.01 TCGA.J8.A4HY.01
#> "032" "031" "025" "032" "032" "011"
#> TCGA.EL.A3ZL.01 TCGA.EL.A3ZP.11 TCGA.FY.A40N.01 TCGA.J8.A4HW.01 TCGA.BJ.A45J.01 TCGA.CE.A482.01
#> "032" "02322" "011" "032" "032" "032"
#> TCGA.DJ.A2Q6.01 TCGA.DJ.A2PX.01 TCGA.DJ.A4UL.01 TCGA.EL.A4JX.01 TCGA.BJ.A2N8.11 TCGA.DJ.A2Q5.01
#> "032" "015" "033" "013" "0211" "014"
#> TCGA.EL.A4KG.01 TCGA.DJ.A4UP.01 TCGA.E8.A438.01 TCGA.EL.A3H2.01 TCGA.EM.A3AP.01 TCGA.DJ.A2PQ.01
#> "033" "015" "011" "0221" "025" "031"
#> TCGA.L6.A4EP.01 TCGA.FY.A4B4.01 TCGA.EL.A4KH.01 TCGA.BJ.A45E.01 TCGA.DJ.A4V5.01 TCGA.DE.A4MC.01
#> "033" "032" "011" "0231" "014" "033"
#> TCGA.E8.A44M.01 TCGA.BJ.A45K.01 TCGA.E3.A3DZ.01 TCGA.E3.A3E2.01 TCGA.BJ.A45H.01 TCGA.E8.A44K.01
#> "013" "0242" "025" "032" "012" "015"
#> TCGA.ET.A2MY.01 TCGA.EL.A3H8.01 TCGA.BJ.A45C.01 TCGA.BJ.A45G.01 TCGA.EL.A4JZ.01 TCGA.CE.A481.01
#> "032" "033" "0242" "025" "033" "015"
#> TCGA.KS.A4I9.01 TCGA.EL.A3MW.01 TCGA.E8.A436.01 TCGA.E3.A3DY.01 TCGA.DJ.A2Q3.01 TCGA.BJ.A2P4.01
#> "033" "033" "015" "031" "013" "025"
#> TCGA.CE.A484.01 TCGA.ET.A2N1.01 TCGA.DJ.A2Q4.01 TCGA.DJ.A2PZ.01 TCGA.BJ.A45F.01 TCGA.IM.A4EB.01
#> "025" "011" "031" "012" "025" "014"
#> TCGA.EM.A4FO.01 TCGA.FY.A4B3.01 TCGA.FY.A4B0.01 TCGA.BJ.A45I.01 TCGA.E3.A3E3.01 TCGA.EM.A3AQ.01
#> "014" "031" "0242" "013" "033" "034"
#> TCGA.EL.A3N3.01 TCGA.DJ.A2Q9.01 TCGA.EM.A4FM.01 TCGA.EL.A4K6.01 TCGA.MK.A4N9.01 TCGA.KS.A4I1.01
#> "013" "0231" "033" "0243" "033" "032"
#> TCGA.DJ.A2PS.01 TCGA.CE.A3MD.01 TCGA.E3.A3E5.01 TCGA.EL.A3CN.01 TCGA.J8.A4HW.06 TCGA.EM.A4FK.01
#> "011" "012" "031" "015" "013" "02412"
#> TCGA.E8.A437.01 TCGA.BJ.A4O8.01 TCGA.EL.A3MW.11 TCGA.E3.A3E0.01 TCGA.BJ.A45D.01 TCGA.CE.A483.01
#> "011" "031" "0211" "033" "025" "011"
#> TCGA.CE.A485.01 TCGA.DJ.A4UR.01 TCGA.IM.A41Y.01 TCGA.ET.A4KN.01 TCGA.KS.A4I5.01 TCGA.DJ.A4UQ.01
#> "012" "0244" "032" "013" "033" "012"
#> TCGA.KS.A4IB.01 TCGA.EL.A3N2.11 TCGA.BJ.A2N9.01 TCGA.DJ.A4UW.01 TCGA.EL.A3GZ.11 TCGA.EM.A3AR.01
#> "033" "0211" "0222" "011" "0211" "0212"
#> TCGA.EL.A3N3.11 TCGA.DE.A3KN.01 TCGA.DJ.A2QA.01 TCGA.EL.A4JV.01 TCGA.EM.A4FF.01 TCGA.EL.A4K0.01
#> "02321" "011" "011" "025" "033" "033"
#> TCGA.FK.A4UB.01 TCGA.BJ.A4O9.01 TCGA.BJ.A2N7.01 TCGA.DE.A2OL.01 TCGA.CE.A3ME.01 TCGA.MK.A4N7.01
#> "031" "011" "025" "02411" "011" "032"
#> TCGA.EL.A3H2.11 TCGA.EL.A4K4.01 TCGA.EL.A3GS.01 TCGA.EL.A3GZ.01 TCGA.E3.A3E1.01 TCGA.DJ.A2Q8.01
#> "0212" "033" "033" "032" "011" "015"
#> TCGA.EL.A3N2.01 TCGA.KS.A4I7.01 TCGA.MK.A84Z.01 TCGA.ET.A3DP.11 TCGA.EL.A3MX.11 TCGA.ET.A25G.01
#> "033" "032" "025" "0211" "0211" "032"
#> TCGA.EM.A3FK.01 TCGA.EM.A2CS.01 TCGA.FE.A23A.01 TCGA.BJ.A28T.11 TCGA.EM.A22J.01 TCGA.EL.A3MX.01
#> "034" "032" "013" "0211" "02412" "033"
#> TCGA.FY.A3I4.01 TCGA.BJ.A28W.11 TCGA.ET.A25R.01 TCGA.BJ.A2N8.01 TCGA.FY.A76V.01 TCGA.EM.A3FN.01
#> "011" "02321" "032" "025" "025" "02413"
#> TCGA.QD.A8IV.01 TCGA.EM.A3FJ.01 TCGA.ET.A2MY.11 TCGA.EM.A3FQ.06 TCGA.ET.A25P.01 TCGA.ET.A2N0.01
#> "025" "033" "02413" "033" "025" "015"
#> TCGA.EM.A2CT.01 TCGA.FE.A235.01 TCGA.ET.A25M.01 TCGA.EL.A3MY.01 TCGA.DE.A7U5.01 TCGA.E8.A2JQ.11
#> "0222" "033" "031" "031" "033" "0231"
#> TCGA.ET.A3DP.01 TCGA.EM.A2CL.01 TCGA.ET.A2N5.01 TCGA.ET.A25J.11 TCGA.DE.A69J.01 TCGA.BJ.A28R.11
#> "011" "0242" "025" "0211" "033" "02321"
#> TCGA.ET.A25K.01 TCGA.EL.A3GV.01 TCGA.GE.A2C6.01 TCGA.EM.A3FM.01 TCGA.EL.A3H7.11 TCGA.FE.A22Z.01
#> "032" "011" "013" "031" "0211" "033"
#> TCGA.H2.A2K9.01 TCGA.EM.A22Q.01 TCGA.EM.A3FP.01 TCGA.GE.A2C6.11 TCGA.EL.A3MZ.01 TCGA.DJ.A2PT.01
#> "0243" "0242" "025" "02321" "031" "013"
#> TCGA.E8.A242.01 TCGA.ET.A25L.01 TCGA.CE.A27D.01 TCGA.EL.A3H1.11 TCGA.BJ.A2N7.11 TCGA.DJ.A2Q7.01
#> "013" "032" "0233" "0233" "0211" "033"
#> TCGA.J8.A3O1.01 TCGA.EM.A2CR.01 TCGA.DE.A69K.01 TCGA.EM.A2CQ.01 TCGA.FE.A238.01 TCGA.EL.A3H1.01
#> "011" "011" "033" "0222" "015" "02411"
#> TCGA.BJ.A28W.01 TCGA.BJ.A28T.01 TCGA.EM.A2CJ.01 TCGA.EM.A3FQ.01 TCGA.4C.A93U.01 TCGA.EM.A22M.01
#> "0231" "02321" "0223" "015" "033" "014"
#> TCGA.J8.A3NZ.01 TCGA.EM.A22K.01 TCGA.FE.A236.01 TCGA.BJ.A28R.01 TCGA.EM.A2CU.01 TCGA.ET.A25N.01
#> "011" "025" "012" "015" "015" "033"
#> TCGA.EL.A3H7.01 TCGA.FY.A3NM.01 TCGA.EM.A3FO.01 TCGA.EM.A22L.01 TCGA.BJ.A2N9.11 TCGA.BJ.A291.01
#> "033" "0223" "031" "025" "0231" "0222"
#> TCGA.ET.A2N5.11 TCGA.ET.A25N.11 TCGA.J8.A3O0.01 TCGA.FE.A237.01 TCGA.DJ.A2QC.01 TCGA.ET.A25O.01
#> "0211" "0211" "0243" "011" "011" "033"
#> TCGA.EL.A3GU.01 TCGA.EL.A3MY.11 TCGA.DJ.A2PY.01 TCGA.EM.A2CS.06 TCGA.FY.A3NP.01 TCGA.ET.A25I.01
#> "033" "0221" "033" "011" "025" "0222"
#> TCGA.H2.A26U.01 TCGA.BJ.A290.11 TCGA.EM.A22I.01 TCGA.FE.A239.01 TCGA.BJ.A28Z.01 TCGA.DE.A0XZ.01
#> "013" "0212" "033" "0242" "013" "033"
#> TCGA.ET.A25J.01 TCGA.EM.A22N.01 TCGA.EM.A2CM.01 TCGA.FY.A3NN.01 TCGA.EM.A3FL.01 TCGA.H2.A2K9.11
#> "011" "0222" "0244" "011" "0223" "0233"
#> TCGA.EL.A3H3.01 TCGA.EL.A3H4.01 TCGA.EM.A2OX.01 TCGA.EM.A3SX.01 TCGA.BJ.A0Z3.01 TCGA.BJ.A28X.01
#> "015" "032" "031" "032" "013" "013"
#> TCGA.EL.A3CT.01 TCGA.EL.A3CR.01 TCGA.FY.A3TY.01 TCGA.J8.A3YG.01 TCGA.DJ.A3V6.01 TCGA.EM.A3SZ.01
#> "013" "032" "0233" "015" "031" "015"
#> TCGA.EM.A2OW.01 TCGA.DO.A1JZ.11 TCGA.EL.A3D5.01 TCGA.EM.A2P0.01 TCGA.E8.A2JQ.01 TCGA.BJ.A18Z.01
#> "0222" "0211" "025" "012" "013" "031"
#> TCGA.DJ.A3V0.01 TCGA.EL.A3GW.01 TCGA.DJ.A3UW.01 TCGA.DJ.A3V3.01 TCGA.EL.A3T1.11 TCGA.BJ.A0ZC.01
#> "031" "025" "013" "015" "02321" "0221"
#> TCGA.EM.A2OV.01 TCGA.EL.A3GY.01 TCGA.EM.A3SY.01 TCGA.EM.A3AI.01 TCGA.EM.A2OY.01 TCGA.EL.A3T8.01
#> "0222" "033" "0212" "0222" "0223" "031"
#> TCGA.BJ.A18Y.01 TCGA.EL.A3GP.01 TCGA.EM.A2CK.01 TCGA.EL.A3T7.11 TCGA.BJ.A192.01 TCGA.BJ.A191.01
#> "025" "014" "025" "0211" "0223" "011"
#> TCGA.EM.A2CP.01 TCGA.EM.A22O.01 TCGA.EM.A2P1.01 TCGA.J8.A3YH.01 TCGA.DJ.A3UZ.01 TCGA.IM.A3EB.01
#> "0231" "031" "014" "031" "0222" "013"
#> TCGA.BJ.A3F0.01 TCGA.EL.A3GX.01 TCGA.EM.A3AK.01 TCGA.DO.A1JZ.01 TCGA.FY.A3YR.01 TCGA.DO.A1K0.01
#> "02414" "033" "011" "033" "032" "033"
#> TCGA.DJ.A3V5.01 TCGA.EM.A3AJ.01 TCGA.IM.A3ED.01 TCGA.EM.A3AO.01 TCGA.EM.A2P1.06 TCGA.EM.A1CW.01
#> "032" "02322" "033" "012" "014" "0222"
#> TCGA.FK.A3SE.01 TCGA.EL.A3T7.01 TCGA.EM.A2P2.01 TCGA.EM.A1CU.11 TCGA.EL.A3T0.11 TCGA.E8.A3X7.01
#> "032" "032" "025" "0212" "0211" "032"
#> TCGA.ET.A3BQ.01 TCGA.EM.A1CS.01 TCGA.EL.A3GQ.01 TCGA.EL.A3H5.01 TCGA.DJ.A3V4.01 TCGA.EM.A2P3.01
#> "033" "011" "011" "033" "011" "033"
#> TCGA.FY.A3WA.01 TCGA.DJ.A3V2.01 TCGA.FY.A3TY.11 TCGA.BJ.A290.01 TCGA.EM.A3SU.01 TCGA.EL.A3D0.01
#> "0223" "013" "0211" "012" "015" "031"
#> TCGA.EM.A1CT.11 TCGA.EL.A3GR.01 TCGA.J8.A3YH.06 TCGA.EM.A3ST.11 TCGA.ET.A3DV.01 TCGA.BJ.A3EZ.01
#> "0212" "011" "031" "0211" "02411" "031"
#> TCGA.J8.A3YD.01 TCGA.EM.A3SU.06 TCGA.EM.A3AL.01 TCGA.DJ.A3US.01 TCGA.EM.A1CS.11 TCGA.EM.A1CW.11
#> "0222" "013" "02411" "015" "0211" "0211"
#> TCGA.BJ.A190.01 TCGA.EM.A2OZ.01 TCGA.EM.A1CV.11 TCGA.EM.A1CU.01 TCGA.EM.A3AN.01 TCGA.E8.A2EA.01
#> "0221" "012" "0211" "031" "032" "013"
#> TCGA.EM.A1CV.01 TCGA.EM.A1CT.01 TCGA.EM.A3ST.01 TCGA.ET.A3BS.01 TCGA.EL.A3GO.01 TCGA.DJ.A2Q0.01
#> "011" "012" "0244" "014" "02411" "0223"
#> TCGA.EL.A3D6.01 TCGA.DJ.A3UN.01 TCGA.DJ.A3UU.01 TCGA.FK.A3SD.01 TCGA.DJ.A2PO.01 TCGA.DJ.A3UQ.01
#> "032" "032" "011" "02413" "012" "015"
#> TCGA.EM.A1YE.11 TCGA.EL.A3T2.11 TCGA.EL.A3CL.01 TCGA.EM.A1YC.01 TCGA.DJ.A3UP.01 TCGA.EL.A3T0.01
#> "0211" "0211" "033" "0223" "025" "011"
#> TCGA.IM.A3U2.01 TCGA.IM.A3U3.01 TCGA.DJ.A3UX.01 TCGA.ET.A3BW.01 TCGA.ET.A39S.01 TCGA.ET.A3BP.01
#> "032" "032" "015" "011" "011" "011"
#> TCGA.DJ.A1QE.01 TCGA.EL.A3D4.01 TCGA.FK.A3SB.01 TCGA.EL.A3CW.01 TCGA.ET.A39L.01 TCGA.DJ.A2PW.01
#> "033" "012" "033" "02321" "025" "031"
#> TCGA.EM.A2CO.01 TCGA.FE.A232.01 TCGA.DJ.A3UR.01 TCGA.DJ.A2PP.01 TCGA.ET.A3DQ.01 TCGA.ET.A3DS.01
#> "0222" "011" "011" "0242" "02321" "0222"
#> TCGA.FY.A3W9.01 TCGA.FK.A3S3.01 TCGA.ET.A2MZ.01 TCGA.BJ.A2NA.11 TCGA.DJ.A1QL.01 TCGA.EL.A3CS.01
#> "0244" "011" "031" "0233" "0242" "015"
#> TCGA.FE.A233.01 TCGA.EM.A1YD.11 TCGA.ET.A3DW.11 TCGA.EL.A3T9.01 TCGA.DJ.A3UM.01 TCGA.DO.A2HM.01
#> "033" "0211" "0212" "032" "032" "014"
#> TCGA.FY.A3BL.01 TCGA.EL.A3TA.11 TCGA.ET.A3BX.01 TCGA.DJ.A1QQ.01 TCGA.DJ.A1QF.01 TCGA.DJ.A1QO.01
#> "012" "0212" "031" "031" "011" "031"
#> TCGA.BJ.A2NA.01 TCGA.EM.A1YE.01 TCGA.FY.A2QD.01 TCGA.ET.A39J.01 TCGA.ET.A3DU.01 TCGA.EL.A3CM.01
#> "031" "0223" "02413" "034" "013" "032"
#> TCGA.DJ.A3UO.01 TCGA.ET.A39P.01 TCGA.DJ.A2Q2.01 TCGA.BJ.A28V.01 TCGA.ET.A3BO.01 TCGA.EL.A3T1.01
#> "031" "033" "0222" "02411" "032" "015"
#> TCGA.DJ.A1QI.01 TCGA.EL.A3TB.01 TCGA.BJ.A28X.11 TCGA.DJ.A1QN.01 TCGA.FE.A230.01 TCGA.FE.A234.01
#> "033" "032" "0231" "033" "015" "033"
#> TCGA.ET.A39R.01 TCGA.DJ.A1QG.01 TCGA.EL.A3CV.01 TCGA.FE.A231.01 TCGA.EL.A3TA.01 TCGA.DJ.A3UY.01
#> "015" "025" "014" "031" "012" "015"
#> TCGA.DJ.A2Q1.01 TCGA.EL.A3CU.01 TCGA.EL.A3TB.11 TCGA.ET.A39I.01 TCGA.EM.A1YB.01 TCGA.DJ.A3UV.01
#> "013" "013" "0211" "025" "02414" "011"
#> TCGA.DJ.A3UT.01 TCGA.ET.A3DW.01 TCGA.ET.A3BT.01 TCGA.EL.A3T3.01 TCGA.DJ.A1QM.01 TCGA.EL.A3CY.01
#> "025" "031" "032" "032" "0212" "0231"
#> TCGA.ET.A39O.01 TCGA.EM.A1YC.11 TCGA.DJ.A1QH.01 TCGA.EL.A3T3.11 TCGA.EL.A3CX.01 TCGA.EL.A3T2.01
#> "031" "0211" "033" "0211" "011" "025"
#> TCGA.EM.A22P.01 TCGA.EL.A3T8.11 TCGA.DJ.A2PU.01 TCGA.DJ.A3UK.01 TCGA.ET.A3DO.01 TCGA.EM.A1YA.01
#> "014" "0212" "033" "011" "013" "0223"
#> TCGA.ET.A3BV.01 TCGA.EL.A3CO.01 TCGA.DJ.A2PN.01 TCGA.FK.A3SG.01 TCGA.FK.A3SH.01 TCGA.EM.A1YD.01
#> "013" "0233" "033" "032" "032" "0223"
#> TCGA.DJ.A1QD.01 TCGA.EL.A3CZ.01 TCGA.BJ.A0Z9.01 TCGA.CE.A13K.01 TCGA.EM.A3FR.01 TCGA.EM.A3O8.01
#> "033" "0222" "013" "032" "02413" "025"
#> TCGA.FY.A3R6.01 TCGA.FY.A3R9.01 TCGA.EL.A3D1.01 TCGA.EM.A3O6.01 TCGA.BJ.A0Z5.01 TCGA.BJ.A28S.01
#> "013" "0222" "031" "0222" "012" "025"
#> TCGA.BJ.A0ZH.01 TCGA.ET.A3DT.01 TCGA.H2.A3RI.11 TCGA.DJ.A13W.01 TCGA.DJ.A13T.01 TCGA.BJ.A0ZA.01
#> "032" "013" "0211" "02411" "032" "02414"
#> TCGA.BJ.A3PT.01 TCGA.FE.A3PD.01 TCGA.BJ.A0ZF.01 TCGA.ET.A39M.01 TCGA.BJ.A0ZJ.01 TCGA.BJ.A0YZ.01
#> "025" "032" "0224" "014" "014" "0221"
#> TCGA.FE.A3PC.01 TCGA.DJ.A2QB.01 TCGA.EM.A3OB.01 TCGA.H2.A3RH.01 TCGA.ET.A39T.01 TCGA.DJ.A2PV.01
#> "032" "025" "025" "025" "011" "011"
#> TCGA.BJ.A3PR.11 TCGA.EL.A3T6.11 TCGA.DJ.A13X.01 TCGA.BJ.A0ZG.01 TCGA.EL.A3T6.01 TCGA.BJ.A0Z0.01
#> "02321" "0233" "011" "0221" "013" "0242"
#> TCGA.ET.A39K.01 TCGA.EM.A3O9.01 TCGA.BJ.A3PU.01 TCGA.BJ.A3PR.01 TCGA.EM.A3O3.01 TCGA.BJ.A0ZB.01
#> "032" "0234" "031" "0231" "013" "031"
#> TCGA.EM.A3OA.01 TCGA.DJ.A2PR.01 TCGA.DJ.A13L.01 TCGA.FY.A3ON.01 TCGA.DJ.A13V.01 TCGA.FY.A3R8.01
#> "02412" "031" "014" "031" "032" "032"
#> TCGA.EL.A3CP.01 TCGA.DJ.A13U.01 TCGA.DE.A0Y3.01 TCGA.ET.A2N4.01 TCGA.DJ.A13P.01 TCGA.BJ.A0ZE.01
#> "033" "012" "032" "011" "011" "025"
#> TCGA.EM.A3O7.01 TCGA.DJ.A13O.01 TCGA.FY.A3RA.01 TCGA.DJ.A13M.01 TCGA.DJ.A13R.01 TCGA.ET.A3DR.01
#> "011" "0233" "033" "025" "0221" "011"
#> TCGA.FE.A3PB.01 TCGA.ET.A3BN.01 TCGA.H2.A3RI.01 TCGA.ET.A39N.01 TCGA.BJ.A3PU.11 TCGA.FY.A3R7.01
#> "015" "033" "032" "0224" "0212" "0222"
#> TCGA.FE.A3PA.01 TCGA.EM.A2CN.01 TCGA.BJ.A0Z2.01 TCGA.FY.A3I5.01 TCGA.DJ.A13S.01 TCGA.DE.A0Y2.01
#> "031" "0243" "0243" "02414" "025" "033"
#> TCGA.ET.A3BU.01
#> "031"
get_classes(res_rh, merge_node = merge_node_param(min_n_signatures = 3187))
#> TCGA.E8.A416.01 TCGA.E8.A433.01 TCGA.EL.A4K9.01 TCGA.DJ.A3V9.01 TCGA.EL.A3ZO.11 TCGA.EL.A3ZN.01
#> "021" "015" "031" "011" "021" "011"
#> TCGA.KS.A41F.01 TCGA.EL.A3ZK.01 TCGA.ET.A40R.01 TCGA.EL.A3ZM.01 TCGA.ET.A2N3.01 TCGA.EL.A3ZQ.01
#> "032" "015" "015" "031" "02411" "032"
#> TCGA.ET.A40T.01 TCGA.DE.A4MA.01 TCGA.EM.A4FU.01 TCGA.E8.A418.01 TCGA.DJ.A3VD.01 TCGA.DJ.A3VM.01
#> "032" "032" "025" "032" "013" "0244"
#> TCGA.EL.A3ZG.01 TCGA.EM.A4FV.01 TCGA.E8.A413.01 TCGA.DJ.A3VG.01 TCGA.EL.A4K2.01 TCGA.IM.A420.01
#> "012" "015" "015" "025" "0222" "013"
#> TCGA.KS.A41J.01 TCGA.EL.A3ZK.11 TCGA.J8.A3O2.01 TCGA.E8.A415.01 TCGA.FY.A40M.01 TCGA.DJ.A3VB.01
#> "032" "02321" "012" "011" "025" "031"
#> TCGA.KS.A41I.01 TCGA.DJ.A3VL.01 TCGA.ET.A4KQ.01 TCGA.H2.A421.01 TCGA.EL.A3ZO.01 TCGA.KS.A4I3.01
#> "025" "0234" "025" "032" "032" "012"
#> TCGA.DJ.A4UT.01 TCGA.DE.A4MD.01 TCGA.EL.A4JW.01 TCGA.DJ.A3VI.01 TCGA.DJ.A3VA.01 TCGA.L6.A4ET.01
#> "013" "031" "015" "032" "032" "033"
#> TCGA.E8.A419.01 TCGA.DJ.A4V0.01 TCGA.DJ.A4V2.01 TCGA.ET.A40Q.01 TCGA.EL.A3ZS.01 TCGA.KS.A4ID.01
#> "013" "02321" "033" "031" "013" "013"
#> TCGA.EL.A3ZL.11 TCGA.J8.A3YE.01 TCGA.EL.A4K7.01 TCGA.DJ.A3VF.01 TCGA.EM.A4FH.01 TCGA.E8.A432.01
#> "021" "011" "031" "013" "0221" "015"
#> TCGA.J8.A3O2.06 TCGA.ET.A2MX.01 TCGA.ET.A40S.01 TCGA.DE.A4M8.01 TCGA.IM.A41Z.01 TCGA.EL.A4KD.01
#> "031" "012" "014" "013" "02412" "012"
#> TCGA.DJ.A3V7.01 TCGA.FY.A40L.01 TCGA.DE.A4M9.01 TCGA.J8.A42S.01 TCGA.KS.A41L.01 TCGA.EM.A4FN.01
#> "032" "015" "0221" "012" "0224" "033"
#> TCGA.EL.A4K1.01 TCGA.KS.A4IC.01 TCGA.E8.A414.01 TCGA.H2.A422.01 TCGA.J8.A3YF.01 TCGA.EL.A4KI.01
#> "033" "011" "015" "032" "031" "0243"
#> TCGA.EM.A4G1.01 TCGA.DJ.A3VJ.01 TCGA.DE.A4MD.06 TCGA.EL.A3ZP.01 TCGA.EM.A4FQ.01 TCGA.EL.A3ZT.01
#> "025" "031" "014" "031" "033" "031"
#> TCGA.DJ.A4V4.01 TCGA.FY.A40K.01 TCGA.L6.A4EQ.01 TCGA.DJ.A3VE.01 TCGA.E8.A434.01 TCGA.EL.A3ZH.01
#> "011" "011" "031" "031" "0222" "0222"
#> TCGA.EM.A4FR.01 TCGA.EL.A3ZH.11 TCGA.EL.A3ZR.01 TCGA.DJ.A3V8.01 TCGA.EL.A3ZG.11 TCGA.ET.A40P.01
#> "012" "021" "025" "015" "021" "025"
#> TCGA.DE.A4MB.01 TCGA.MK.A4N6.01 TCGA.DJ.A3VK.01 TCGA.E8.A417.01 TCGA.L6.A4EU.01 TCGA.J8.A4HY.01
#> "032" "031" "025" "032" "032" "011"
#> TCGA.EL.A3ZL.01 TCGA.EL.A3ZP.11 TCGA.FY.A40N.01 TCGA.J8.A4HW.01 TCGA.BJ.A45J.01 TCGA.CE.A482.01
#> "032" "02322" "011" "032" "032" "032"
#> TCGA.DJ.A2Q6.01 TCGA.DJ.A2PX.01 TCGA.DJ.A4UL.01 TCGA.EL.A4JX.01 TCGA.BJ.A2N8.11 TCGA.DJ.A2Q5.01
#> "032" "015" "033" "013" "021" "014"
#> TCGA.EL.A4KG.01 TCGA.DJ.A4UP.01 TCGA.E8.A438.01 TCGA.EL.A3H2.01 TCGA.EM.A3AP.01 TCGA.DJ.A2PQ.01
#> "033" "015" "011" "0221" "025" "031"
#> TCGA.L6.A4EP.01 TCGA.FY.A4B4.01 TCGA.EL.A4KH.01 TCGA.BJ.A45E.01 TCGA.DJ.A4V5.01 TCGA.DE.A4MC.01
#> "033" "032" "011" "0231" "014" "033"
#> TCGA.E8.A44M.01 TCGA.BJ.A45K.01 TCGA.E3.A3DZ.01 TCGA.E3.A3E2.01 TCGA.BJ.A45H.01 TCGA.E8.A44K.01
#> "013" "0242" "025" "032" "012" "015"
#> TCGA.ET.A2MY.01 TCGA.EL.A3H8.01 TCGA.BJ.A45C.01 TCGA.BJ.A45G.01 TCGA.EL.A4JZ.01 TCGA.CE.A481.01
#> "032" "033" "0242" "025" "033" "015"
#> TCGA.KS.A4I9.01 TCGA.EL.A3MW.01 TCGA.E8.A436.01 TCGA.E3.A3DY.01 TCGA.DJ.A2Q3.01 TCGA.BJ.A2P4.01
#> "033" "033" "015" "031" "013" "025"
#> TCGA.CE.A484.01 TCGA.ET.A2N1.01 TCGA.DJ.A2Q4.01 TCGA.DJ.A2PZ.01 TCGA.BJ.A45F.01 TCGA.IM.A4EB.01
#> "025" "011" "031" "012" "025" "014"
#> TCGA.EM.A4FO.01 TCGA.FY.A4B3.01 TCGA.FY.A4B0.01 TCGA.BJ.A45I.01 TCGA.E3.A3E3.01 TCGA.EM.A3AQ.01
#> "014" "031" "0242" "013" "033" "034"
#> TCGA.EL.A3N3.01 TCGA.DJ.A2Q9.01 TCGA.EM.A4FM.01 TCGA.EL.A4K6.01 TCGA.MK.A4N9.01 TCGA.KS.A4I1.01
#> "013" "0231" "033" "0243" "033" "032"
#> TCGA.DJ.A2PS.01 TCGA.CE.A3MD.01 TCGA.E3.A3E5.01 TCGA.EL.A3CN.01 TCGA.J8.A4HW.06 TCGA.EM.A4FK.01
#> "011" "012" "031" "015" "013" "02412"
#> TCGA.E8.A437.01 TCGA.BJ.A4O8.01 TCGA.EL.A3MW.11 TCGA.E3.A3E0.01 TCGA.BJ.A45D.01 TCGA.CE.A483.01
#> "011" "031" "021" "033" "025" "011"
#> TCGA.CE.A485.01 TCGA.DJ.A4UR.01 TCGA.IM.A41Y.01 TCGA.ET.A4KN.01 TCGA.KS.A4I5.01 TCGA.DJ.A4UQ.01
#> "012" "0244" "032" "013" "033" "012"
#> TCGA.KS.A4IB.01 TCGA.EL.A3N2.11 TCGA.BJ.A2N9.01 TCGA.DJ.A4UW.01 TCGA.EL.A3GZ.11 TCGA.EM.A3AR.01
#> "033" "021" "0222" "011" "021" "021"
#> TCGA.EL.A3N3.11 TCGA.DE.A3KN.01 TCGA.DJ.A2QA.01 TCGA.EL.A4JV.01 TCGA.EM.A4FF.01 TCGA.EL.A4K0.01
#> "02321" "011" "011" "025" "033" "033"
#> TCGA.FK.A4UB.01 TCGA.BJ.A4O9.01 TCGA.BJ.A2N7.01 TCGA.DE.A2OL.01 TCGA.CE.A3ME.01 TCGA.MK.A4N7.01
#> "031" "011" "025" "02411" "011" "032"
#> TCGA.EL.A3H2.11 TCGA.EL.A4K4.01 TCGA.EL.A3GS.01 TCGA.EL.A3GZ.01 TCGA.E3.A3E1.01 TCGA.DJ.A2Q8.01
#> "021" "033" "033" "032" "011" "015"
#> TCGA.EL.A3N2.01 TCGA.KS.A4I7.01 TCGA.MK.A84Z.01 TCGA.ET.A3DP.11 TCGA.EL.A3MX.11 TCGA.ET.A25G.01
#> "033" "032" "025" "021" "021" "032"
#> TCGA.EM.A3FK.01 TCGA.EM.A2CS.01 TCGA.FE.A23A.01 TCGA.BJ.A28T.11 TCGA.EM.A22J.01 TCGA.EL.A3MX.01
#> "034" "032" "013" "021" "02412" "033"
#> TCGA.FY.A3I4.01 TCGA.BJ.A28W.11 TCGA.ET.A25R.01 TCGA.BJ.A2N8.01 TCGA.FY.A76V.01 TCGA.EM.A3FN.01
#> "011" "02321" "032" "025" "025" "02413"
#> TCGA.QD.A8IV.01 TCGA.EM.A3FJ.01 TCGA.ET.A2MY.11 TCGA.EM.A3FQ.06 TCGA.ET.A25P.01 TCGA.ET.A2N0.01
#> "025" "033" "02413" "033" "025" "015"
#> TCGA.EM.A2CT.01 TCGA.FE.A235.01 TCGA.ET.A25M.01 TCGA.EL.A3MY.01 TCGA.DE.A7U5.01 TCGA.E8.A2JQ.11
#> "0222" "033" "031" "031" "033" "0231"
#> TCGA.ET.A3DP.01 TCGA.EM.A2CL.01 TCGA.ET.A2N5.01 TCGA.ET.A25J.11 TCGA.DE.A69J.01 TCGA.BJ.A28R.11
#> "011" "0242" "025" "021" "033" "02321"
#> TCGA.ET.A25K.01 TCGA.EL.A3GV.01 TCGA.GE.A2C6.01 TCGA.EM.A3FM.01 TCGA.EL.A3H7.11 TCGA.FE.A22Z.01
#> "032" "011" "013" "031" "021" "033"
#> TCGA.H2.A2K9.01 TCGA.EM.A22Q.01 TCGA.EM.A3FP.01 TCGA.GE.A2C6.11 TCGA.EL.A3MZ.01 TCGA.DJ.A2PT.01
#> "0243" "0242" "025" "02321" "031" "013"
#> TCGA.E8.A242.01 TCGA.ET.A25L.01 TCGA.CE.A27D.01 TCGA.EL.A3H1.11 TCGA.BJ.A2N7.11 TCGA.DJ.A2Q7.01
#> "013" "032" "0233" "0233" "021" "033"
#> TCGA.J8.A3O1.01 TCGA.EM.A2CR.01 TCGA.DE.A69K.01 TCGA.EM.A2CQ.01 TCGA.FE.A238.01 TCGA.EL.A3H1.01
#> "011" "011" "033" "0222" "015" "02411"
#> TCGA.BJ.A28W.01 TCGA.BJ.A28T.01 TCGA.EM.A2CJ.01 TCGA.EM.A3FQ.01 TCGA.4C.A93U.01 TCGA.EM.A22M.01
#> "0231" "02321" "0223" "015" "033" "014"
#> TCGA.J8.A3NZ.01 TCGA.EM.A22K.01 TCGA.FE.A236.01 TCGA.BJ.A28R.01 TCGA.EM.A2CU.01 TCGA.ET.A25N.01
#> "011" "025" "012" "015" "015" "033"
#> TCGA.EL.A3H7.01 TCGA.FY.A3NM.01 TCGA.EM.A3FO.01 TCGA.EM.A22L.01 TCGA.BJ.A2N9.11 TCGA.BJ.A291.01
#> "033" "0223" "031" "025" "0231" "0222"
#> TCGA.ET.A2N5.11 TCGA.ET.A25N.11 TCGA.J8.A3O0.01 TCGA.FE.A237.01 TCGA.DJ.A2QC.01 TCGA.ET.A25O.01
#> "021" "021" "0243" "011" "011" "033"
#> TCGA.EL.A3GU.01 TCGA.EL.A3MY.11 TCGA.DJ.A2PY.01 TCGA.EM.A2CS.06 TCGA.FY.A3NP.01 TCGA.ET.A25I.01
#> "033" "0221" "033" "011" "025" "0222"
#> TCGA.H2.A26U.01 TCGA.BJ.A290.11 TCGA.EM.A22I.01 TCGA.FE.A239.01 TCGA.BJ.A28Z.01 TCGA.DE.A0XZ.01
#> "013" "021" "033" "0242" "013" "033"
#> TCGA.ET.A25J.01 TCGA.EM.A22N.01 TCGA.EM.A2CM.01 TCGA.FY.A3NN.01 TCGA.EM.A3FL.01 TCGA.H2.A2K9.11
#> "011" "0222" "0244" "011" "0223" "0233"
#> TCGA.EL.A3H3.01 TCGA.EL.A3H4.01 TCGA.EM.A2OX.01 TCGA.EM.A3SX.01 TCGA.BJ.A0Z3.01 TCGA.BJ.A28X.01
#> "015" "032" "031" "032" "013" "013"
#> TCGA.EL.A3CT.01 TCGA.EL.A3CR.01 TCGA.FY.A3TY.01 TCGA.J8.A3YG.01 TCGA.DJ.A3V6.01 TCGA.EM.A3SZ.01
#> "013" "032" "0233" "015" "031" "015"
#> TCGA.EM.A2OW.01 TCGA.DO.A1JZ.11 TCGA.EL.A3D5.01 TCGA.EM.A2P0.01 TCGA.E8.A2JQ.01 TCGA.BJ.A18Z.01
#> "0222" "021" "025" "012" "013" "031"
#> TCGA.DJ.A3V0.01 TCGA.EL.A3GW.01 TCGA.DJ.A3UW.01 TCGA.DJ.A3V3.01 TCGA.EL.A3T1.11 TCGA.BJ.A0ZC.01
#> "031" "025" "013" "015" "02321" "0221"
#> TCGA.EM.A2OV.01 TCGA.EL.A3GY.01 TCGA.EM.A3SY.01 TCGA.EM.A3AI.01 TCGA.EM.A2OY.01 TCGA.EL.A3T8.01
#> "0222" "033" "021" "0222" "0223" "031"
#> TCGA.BJ.A18Y.01 TCGA.EL.A3GP.01 TCGA.EM.A2CK.01 TCGA.EL.A3T7.11 TCGA.BJ.A192.01 TCGA.BJ.A191.01
#> "025" "014" "025" "021" "0223" "011"
#> TCGA.EM.A2CP.01 TCGA.EM.A22O.01 TCGA.EM.A2P1.01 TCGA.J8.A3YH.01 TCGA.DJ.A3UZ.01 TCGA.IM.A3EB.01
#> "0231" "031" "014" "031" "0222" "013"
#> TCGA.BJ.A3F0.01 TCGA.EL.A3GX.01 TCGA.EM.A3AK.01 TCGA.DO.A1JZ.01 TCGA.FY.A3YR.01 TCGA.DO.A1K0.01
#> "02414" "033" "011" "033" "032" "033"
#> TCGA.DJ.A3V5.01 TCGA.EM.A3AJ.01 TCGA.IM.A3ED.01 TCGA.EM.A3AO.01 TCGA.EM.A2P1.06 TCGA.EM.A1CW.01
#> "032" "02322" "033" "012" "014" "0222"
#> TCGA.FK.A3SE.01 TCGA.EL.A3T7.01 TCGA.EM.A2P2.01 TCGA.EM.A1CU.11 TCGA.EL.A3T0.11 TCGA.E8.A3X7.01
#> "032" "032" "025" "021" "021" "032"
#> TCGA.ET.A3BQ.01 TCGA.EM.A1CS.01 TCGA.EL.A3GQ.01 TCGA.EL.A3H5.01 TCGA.DJ.A3V4.01 TCGA.EM.A2P3.01
#> "033" "011" "011" "033" "011" "033"
#> TCGA.FY.A3WA.01 TCGA.DJ.A3V2.01 TCGA.FY.A3TY.11 TCGA.BJ.A290.01 TCGA.EM.A3SU.01 TCGA.EL.A3D0.01
#> "0223" "013" "021" "012" "015" "031"
#> TCGA.EM.A1CT.11 TCGA.EL.A3GR.01 TCGA.J8.A3YH.06 TCGA.EM.A3ST.11 TCGA.ET.A3DV.01 TCGA.BJ.A3EZ.01
#> "021" "011" "031" "021" "02411" "031"
#> TCGA.J8.A3YD.01 TCGA.EM.A3SU.06 TCGA.EM.A3AL.01 TCGA.DJ.A3US.01 TCGA.EM.A1CS.11 TCGA.EM.A1CW.11
#> "0222" "013" "02411" "015" "021" "021"
#> TCGA.BJ.A190.01 TCGA.EM.A2OZ.01 TCGA.EM.A1CV.11 TCGA.EM.A1CU.01 TCGA.EM.A3AN.01 TCGA.E8.A2EA.01
#> "0221" "012" "021" "031" "032" "013"
#> TCGA.EM.A1CV.01 TCGA.EM.A1CT.01 TCGA.EM.A3ST.01 TCGA.ET.A3BS.01 TCGA.EL.A3GO.01 TCGA.DJ.A2Q0.01
#> "011" "012" "0244" "014" "02411" "0223"
#> TCGA.EL.A3D6.01 TCGA.DJ.A3UN.01 TCGA.DJ.A3UU.01 TCGA.FK.A3SD.01 TCGA.DJ.A2PO.01 TCGA.DJ.A3UQ.01
#> "032" "032" "011" "02413" "012" "015"
#> TCGA.EM.A1YE.11 TCGA.EL.A3T2.11 TCGA.EL.A3CL.01 TCGA.EM.A1YC.01 TCGA.DJ.A3UP.01 TCGA.EL.A3T0.01
#> "021" "021" "033" "0223" "025" "011"
#> TCGA.IM.A3U2.01 TCGA.IM.A3U3.01 TCGA.DJ.A3UX.01 TCGA.ET.A3BW.01 TCGA.ET.A39S.01 TCGA.ET.A3BP.01
#> "032" "032" "015" "011" "011" "011"
#> TCGA.DJ.A1QE.01 TCGA.EL.A3D4.01 TCGA.FK.A3SB.01 TCGA.EL.A3CW.01 TCGA.ET.A39L.01 TCGA.DJ.A2PW.01
#> "033" "012" "033" "02321" "025" "031"
#> TCGA.EM.A2CO.01 TCGA.FE.A232.01 TCGA.DJ.A3UR.01 TCGA.DJ.A2PP.01 TCGA.ET.A3DQ.01 TCGA.ET.A3DS.01
#> "0222" "011" "011" "0242" "02321" "0222"
#> TCGA.FY.A3W9.01 TCGA.FK.A3S3.01 TCGA.ET.A2MZ.01 TCGA.BJ.A2NA.11 TCGA.DJ.A1QL.01 TCGA.EL.A3CS.01
#> "0244" "011" "031" "0233" "0242" "015"
#> TCGA.FE.A233.01 TCGA.EM.A1YD.11 TCGA.ET.A3DW.11 TCGA.EL.A3T9.01 TCGA.DJ.A3UM.01 TCGA.DO.A2HM.01
#> "033" "021" "021" "032" "032" "014"
#> TCGA.FY.A3BL.01 TCGA.EL.A3TA.11 TCGA.ET.A3BX.01 TCGA.DJ.A1QQ.01 TCGA.DJ.A1QF.01 TCGA.DJ.A1QO.01
#> "012" "021" "031" "031" "011" "031"
#> TCGA.BJ.A2NA.01 TCGA.EM.A1YE.01 TCGA.FY.A2QD.01 TCGA.ET.A39J.01 TCGA.ET.A3DU.01 TCGA.EL.A3CM.01
#> "031" "0223" "02413" "034" "013" "032"
#> TCGA.DJ.A3UO.01 TCGA.ET.A39P.01 TCGA.DJ.A2Q2.01 TCGA.BJ.A28V.01 TCGA.ET.A3BO.01 TCGA.EL.A3T1.01
#> "031" "033" "0222" "02411" "032" "015"
#> TCGA.DJ.A1QI.01 TCGA.EL.A3TB.01 TCGA.BJ.A28X.11 TCGA.DJ.A1QN.01 TCGA.FE.A230.01 TCGA.FE.A234.01
#> "033" "032" "0231" "033" "015" "033"
#> TCGA.ET.A39R.01 TCGA.DJ.A1QG.01 TCGA.EL.A3CV.01 TCGA.FE.A231.01 TCGA.EL.A3TA.01 TCGA.DJ.A3UY.01
#> "015" "025" "014" "031" "012" "015"
#> TCGA.DJ.A2Q1.01 TCGA.EL.A3CU.01 TCGA.EL.A3TB.11 TCGA.ET.A39I.01 TCGA.EM.A1YB.01 TCGA.DJ.A3UV.01
#> "013" "013" "021" "025" "02414" "011"
#> TCGA.DJ.A3UT.01 TCGA.ET.A3DW.01 TCGA.ET.A3BT.01 TCGA.EL.A3T3.01 TCGA.DJ.A1QM.01 TCGA.EL.A3CY.01
#> "025" "031" "032" "032" "021" "0231"
#> TCGA.ET.A39O.01 TCGA.EM.A1YC.11 TCGA.DJ.A1QH.01 TCGA.EL.A3T3.11 TCGA.EL.A3CX.01 TCGA.EL.A3T2.01
#> "031" "021" "033" "021" "011" "025"
#> TCGA.EM.A22P.01 TCGA.EL.A3T8.11 TCGA.DJ.A2PU.01 TCGA.DJ.A3UK.01 TCGA.ET.A3DO.01 TCGA.EM.A1YA.01
#> "014" "021" "033" "011" "013" "0223"
#> TCGA.ET.A3BV.01 TCGA.EL.A3CO.01 TCGA.DJ.A2PN.01 TCGA.FK.A3SG.01 TCGA.FK.A3SH.01 TCGA.EM.A1YD.01
#> "013" "0233" "033" "032" "032" "0223"
#> TCGA.DJ.A1QD.01 TCGA.EL.A3CZ.01 TCGA.BJ.A0Z9.01 TCGA.CE.A13K.01 TCGA.EM.A3FR.01 TCGA.EM.A3O8.01
#> "033" "0222" "013" "032" "02413" "025"
#> TCGA.FY.A3R6.01 TCGA.FY.A3R9.01 TCGA.EL.A3D1.01 TCGA.EM.A3O6.01 TCGA.BJ.A0Z5.01 TCGA.BJ.A28S.01
#> "013" "0222" "031" "0222" "012" "025"
#> TCGA.BJ.A0ZH.01 TCGA.ET.A3DT.01 TCGA.H2.A3RI.11 TCGA.DJ.A13W.01 TCGA.DJ.A13T.01 TCGA.BJ.A0ZA.01
#> "032" "013" "021" "02411" "032" "02414"
#> TCGA.BJ.A3PT.01 TCGA.FE.A3PD.01 TCGA.BJ.A0ZF.01 TCGA.ET.A39M.01 TCGA.BJ.A0ZJ.01 TCGA.BJ.A0YZ.01
#> "025" "032" "0224" "014" "014" "0221"
#> TCGA.FE.A3PC.01 TCGA.DJ.A2QB.01 TCGA.EM.A3OB.01 TCGA.H2.A3RH.01 TCGA.ET.A39T.01 TCGA.DJ.A2PV.01
#> "032" "025" "025" "025" "011" "011"
#> TCGA.BJ.A3PR.11 TCGA.EL.A3T6.11 TCGA.DJ.A13X.01 TCGA.BJ.A0ZG.01 TCGA.EL.A3T6.01 TCGA.BJ.A0Z0.01
#> "02321" "0233" "011" "0221" "013" "0242"
#> TCGA.ET.A39K.01 TCGA.EM.A3O9.01 TCGA.BJ.A3PU.01 TCGA.BJ.A3PR.01 TCGA.EM.A3O3.01 TCGA.BJ.A0ZB.01
#> "032" "0234" "031" "0231" "013" "031"
#> TCGA.EM.A3OA.01 TCGA.DJ.A2PR.01 TCGA.DJ.A13L.01 TCGA.FY.A3ON.01 TCGA.DJ.A13V.01 TCGA.FY.A3R8.01
#> "02412" "031" "014" "031" "032" "032"
#> TCGA.EL.A3CP.01 TCGA.DJ.A13U.01 TCGA.DE.A0Y3.01 TCGA.ET.A2N4.01 TCGA.DJ.A13P.01 TCGA.BJ.A0ZE.01
#> "033" "012" "032" "011" "011" "025"
#> TCGA.EM.A3O7.01 TCGA.DJ.A13O.01 TCGA.FY.A3RA.01 TCGA.DJ.A13M.01 TCGA.DJ.A13R.01 TCGA.ET.A3DR.01
#> "011" "0233" "033" "025" "0221" "011"
#> TCGA.FE.A3PB.01 TCGA.ET.A3BN.01 TCGA.H2.A3RI.01 TCGA.ET.A39N.01 TCGA.BJ.A3PU.11 TCGA.FY.A3R7.01
#> "015" "033" "032" "0224" "021" "0222"
#> TCGA.FE.A3PA.01 TCGA.EM.A2CN.01 TCGA.BJ.A0Z2.01 TCGA.FY.A3I5.01 TCGA.DJ.A13S.01 TCGA.DE.A0Y2.01
#> "031" "0243" "0243" "02414" "025" "033"
#> TCGA.ET.A3BU.01
#> "031"
get_classes(res_rh, merge_node = merge_node_param(min_n_signatures = 3269))
#> TCGA.E8.A416.01 TCGA.E8.A433.01 TCGA.EL.A4K9.01 TCGA.DJ.A3V9.01 TCGA.EL.A3ZO.11 TCGA.EL.A3ZN.01
#> "021" "015" "031" "011" "021" "011"
#> TCGA.KS.A41F.01 TCGA.EL.A3ZK.01 TCGA.ET.A40R.01 TCGA.EL.A3ZM.01 TCGA.ET.A2N3.01 TCGA.EL.A3ZQ.01
#> "032" "015" "015" "031" "02411" "032"
#> TCGA.ET.A40T.01 TCGA.DE.A4MA.01 TCGA.EM.A4FU.01 TCGA.E8.A418.01 TCGA.DJ.A3VD.01 TCGA.DJ.A3VM.01
#> "032" "032" "025" "032" "013" "0244"
#> TCGA.EL.A3ZG.01 TCGA.EM.A4FV.01 TCGA.E8.A413.01 TCGA.DJ.A3VG.01 TCGA.EL.A4K2.01 TCGA.IM.A420.01
#> "012" "015" "015" "025" "0222" "013"
#> TCGA.KS.A41J.01 TCGA.EL.A3ZK.11 TCGA.J8.A3O2.01 TCGA.E8.A415.01 TCGA.FY.A40M.01 TCGA.DJ.A3VB.01
#> "032" "0232" "012" "011" "025" "031"
#> TCGA.KS.A41I.01 TCGA.DJ.A3VL.01 TCGA.ET.A4KQ.01 TCGA.H2.A421.01 TCGA.EL.A3ZO.01 TCGA.KS.A4I3.01
#> "025" "0234" "025" "032" "032" "012"
#> TCGA.DJ.A4UT.01 TCGA.DE.A4MD.01 TCGA.EL.A4JW.01 TCGA.DJ.A3VI.01 TCGA.DJ.A3VA.01 TCGA.L6.A4ET.01
#> "013" "031" "015" "032" "032" "033"
#> TCGA.E8.A419.01 TCGA.DJ.A4V0.01 TCGA.DJ.A4V2.01 TCGA.ET.A40Q.01 TCGA.EL.A3ZS.01 TCGA.KS.A4ID.01
#> "013" "0232" "033" "031" "013" "013"
#> TCGA.EL.A3ZL.11 TCGA.J8.A3YE.01 TCGA.EL.A4K7.01 TCGA.DJ.A3VF.01 TCGA.EM.A4FH.01 TCGA.E8.A432.01
#> "021" "011" "031" "013" "0221" "015"
#> TCGA.J8.A3O2.06 TCGA.ET.A2MX.01 TCGA.ET.A40S.01 TCGA.DE.A4M8.01 TCGA.IM.A41Z.01 TCGA.EL.A4KD.01
#> "031" "012" "014" "013" "02412" "012"
#> TCGA.DJ.A3V7.01 TCGA.FY.A40L.01 TCGA.DE.A4M9.01 TCGA.J8.A42S.01 TCGA.KS.A41L.01 TCGA.EM.A4FN.01
#> "032" "015" "0221" "012" "0224" "033"
#> TCGA.EL.A4K1.01 TCGA.KS.A4IC.01 TCGA.E8.A414.01 TCGA.H2.A422.01 TCGA.J8.A3YF.01 TCGA.EL.A4KI.01
#> "033" "011" "015" "032" "031" "0243"
#> TCGA.EM.A4G1.01 TCGA.DJ.A3VJ.01 TCGA.DE.A4MD.06 TCGA.EL.A3ZP.01 TCGA.EM.A4FQ.01 TCGA.EL.A3ZT.01
#> "025" "031" "014" "031" "033" "031"
#> TCGA.DJ.A4V4.01 TCGA.FY.A40K.01 TCGA.L6.A4EQ.01 TCGA.DJ.A3VE.01 TCGA.E8.A434.01 TCGA.EL.A3ZH.01
#> "011" "011" "031" "031" "0222" "0222"
#> TCGA.EM.A4FR.01 TCGA.EL.A3ZH.11 TCGA.EL.A3ZR.01 TCGA.DJ.A3V8.01 TCGA.EL.A3ZG.11 TCGA.ET.A40P.01
#> "012" "021" "025" "015" "021" "025"
#> TCGA.DE.A4MB.01 TCGA.MK.A4N6.01 TCGA.DJ.A3VK.01 TCGA.E8.A417.01 TCGA.L6.A4EU.01 TCGA.J8.A4HY.01
#> "032" "031" "025" "032" "032" "011"
#> TCGA.EL.A3ZL.01 TCGA.EL.A3ZP.11 TCGA.FY.A40N.01 TCGA.J8.A4HW.01 TCGA.BJ.A45J.01 TCGA.CE.A482.01
#> "032" "0232" "011" "032" "032" "032"
#> TCGA.DJ.A2Q6.01 TCGA.DJ.A2PX.01 TCGA.DJ.A4UL.01 TCGA.EL.A4JX.01 TCGA.BJ.A2N8.11 TCGA.DJ.A2Q5.01
#> "032" "015" "033" "013" "021" "014"
#> TCGA.EL.A4KG.01 TCGA.DJ.A4UP.01 TCGA.E8.A438.01 TCGA.EL.A3H2.01 TCGA.EM.A3AP.01 TCGA.DJ.A2PQ.01
#> "033" "015" "011" "0221" "025" "031"
#> TCGA.L6.A4EP.01 TCGA.FY.A4B4.01 TCGA.EL.A4KH.01 TCGA.BJ.A45E.01 TCGA.DJ.A4V5.01 TCGA.DE.A4MC.01
#> "033" "032" "011" "0231" "014" "033"
#> TCGA.E8.A44M.01 TCGA.BJ.A45K.01 TCGA.E3.A3DZ.01 TCGA.E3.A3E2.01 TCGA.BJ.A45H.01 TCGA.E8.A44K.01
#> "013" "0242" "025" "032" "012" "015"
#> TCGA.ET.A2MY.01 TCGA.EL.A3H8.01 TCGA.BJ.A45C.01 TCGA.BJ.A45G.01 TCGA.EL.A4JZ.01 TCGA.CE.A481.01
#> "032" "033" "0242" "025" "033" "015"
#> TCGA.KS.A4I9.01 TCGA.EL.A3MW.01 TCGA.E8.A436.01 TCGA.E3.A3DY.01 TCGA.DJ.A2Q3.01 TCGA.BJ.A2P4.01
#> "033" "033" "015" "031" "013" "025"
#> TCGA.CE.A484.01 TCGA.ET.A2N1.01 TCGA.DJ.A2Q4.01 TCGA.DJ.A2PZ.01 TCGA.BJ.A45F.01 TCGA.IM.A4EB.01
#> "025" "011" "031" "012" "025" "014"
#> TCGA.EM.A4FO.01 TCGA.FY.A4B3.01 TCGA.FY.A4B0.01 TCGA.BJ.A45I.01 TCGA.E3.A3E3.01 TCGA.EM.A3AQ.01
#> "014" "031" "0242" "013" "033" "034"
#> TCGA.EL.A3N3.01 TCGA.DJ.A2Q9.01 TCGA.EM.A4FM.01 TCGA.EL.A4K6.01 TCGA.MK.A4N9.01 TCGA.KS.A4I1.01
#> "013" "0231" "033" "0243" "033" "032"
#> TCGA.DJ.A2PS.01 TCGA.CE.A3MD.01 TCGA.E3.A3E5.01 TCGA.EL.A3CN.01 TCGA.J8.A4HW.06 TCGA.EM.A4FK.01
#> "011" "012" "031" "015" "013" "02412"
#> TCGA.E8.A437.01 TCGA.BJ.A4O8.01 TCGA.EL.A3MW.11 TCGA.E3.A3E0.01 TCGA.BJ.A45D.01 TCGA.CE.A483.01
#> "011" "031" "021" "033" "025" "011"
#> TCGA.CE.A485.01 TCGA.DJ.A4UR.01 TCGA.IM.A41Y.01 TCGA.ET.A4KN.01 TCGA.KS.A4I5.01 TCGA.DJ.A4UQ.01
#> "012" "0244" "032" "013" "033" "012"
#> TCGA.KS.A4IB.01 TCGA.EL.A3N2.11 TCGA.BJ.A2N9.01 TCGA.DJ.A4UW.01 TCGA.EL.A3GZ.11 TCGA.EM.A3AR.01
#> "033" "021" "0222" "011" "021" "021"
#> TCGA.EL.A3N3.11 TCGA.DE.A3KN.01 TCGA.DJ.A2QA.01 TCGA.EL.A4JV.01 TCGA.EM.A4FF.01 TCGA.EL.A4K0.01
#> "0232" "011" "011" "025" "033" "033"
#> TCGA.FK.A4UB.01 TCGA.BJ.A4O9.01 TCGA.BJ.A2N7.01 TCGA.DE.A2OL.01 TCGA.CE.A3ME.01 TCGA.MK.A4N7.01
#> "031" "011" "025" "02411" "011" "032"
#> TCGA.EL.A3H2.11 TCGA.EL.A4K4.01 TCGA.EL.A3GS.01 TCGA.EL.A3GZ.01 TCGA.E3.A3E1.01 TCGA.DJ.A2Q8.01
#> "021" "033" "033" "032" "011" "015"
#> TCGA.EL.A3N2.01 TCGA.KS.A4I7.01 TCGA.MK.A84Z.01 TCGA.ET.A3DP.11 TCGA.EL.A3MX.11 TCGA.ET.A25G.01
#> "033" "032" "025" "021" "021" "032"
#> TCGA.EM.A3FK.01 TCGA.EM.A2CS.01 TCGA.FE.A23A.01 TCGA.BJ.A28T.11 TCGA.EM.A22J.01 TCGA.EL.A3MX.01
#> "034" "032" "013" "021" "02412" "033"
#> TCGA.FY.A3I4.01 TCGA.BJ.A28W.11 TCGA.ET.A25R.01 TCGA.BJ.A2N8.01 TCGA.FY.A76V.01 TCGA.EM.A3FN.01
#> "011" "0232" "032" "025" "025" "02413"
#> TCGA.QD.A8IV.01 TCGA.EM.A3FJ.01 TCGA.ET.A2MY.11 TCGA.EM.A3FQ.06 TCGA.ET.A25P.01 TCGA.ET.A2N0.01
#> "025" "033" "02413" "033" "025" "015"
#> TCGA.EM.A2CT.01 TCGA.FE.A235.01 TCGA.ET.A25M.01 TCGA.EL.A3MY.01 TCGA.DE.A7U5.01 TCGA.E8.A2JQ.11
#> "0222" "033" "031" "031" "033" "0231"
#> TCGA.ET.A3DP.01 TCGA.EM.A2CL.01 TCGA.ET.A2N5.01 TCGA.ET.A25J.11 TCGA.DE.A69J.01 TCGA.BJ.A28R.11
#> "011" "0242" "025" "021" "033" "0232"
#> TCGA.ET.A25K.01 TCGA.EL.A3GV.01 TCGA.GE.A2C6.01 TCGA.EM.A3FM.01 TCGA.EL.A3H7.11 TCGA.FE.A22Z.01
#> "032" "011" "013" "031" "021" "033"
#> TCGA.H2.A2K9.01 TCGA.EM.A22Q.01 TCGA.EM.A3FP.01 TCGA.GE.A2C6.11 TCGA.EL.A3MZ.01 TCGA.DJ.A2PT.01
#> "0243" "0242" "025" "0232" "031" "013"
#> TCGA.E8.A242.01 TCGA.ET.A25L.01 TCGA.CE.A27D.01 TCGA.EL.A3H1.11 TCGA.BJ.A2N7.11 TCGA.DJ.A2Q7.01
#> "013" "032" "0233" "0233" "021" "033"
#> TCGA.J8.A3O1.01 TCGA.EM.A2CR.01 TCGA.DE.A69K.01 TCGA.EM.A2CQ.01 TCGA.FE.A238.01 TCGA.EL.A3H1.01
#> "011" "011" "033" "0222" "015" "02411"
#> TCGA.BJ.A28W.01 TCGA.BJ.A28T.01 TCGA.EM.A2CJ.01 TCGA.EM.A3FQ.01 TCGA.4C.A93U.01 TCGA.EM.A22M.01
#> "0231" "0232" "0223" "015" "033" "014"
#> TCGA.J8.A3NZ.01 TCGA.EM.A22K.01 TCGA.FE.A236.01 TCGA.BJ.A28R.01 TCGA.EM.A2CU.01 TCGA.ET.A25N.01
#> "011" "025" "012" "015" "015" "033"
#> TCGA.EL.A3H7.01 TCGA.FY.A3NM.01 TCGA.EM.A3FO.01 TCGA.EM.A22L.01 TCGA.BJ.A2N9.11 TCGA.BJ.A291.01
#> "033" "0223" "031" "025" "0231" "0222"
#> TCGA.ET.A2N5.11 TCGA.ET.A25N.11 TCGA.J8.A3O0.01 TCGA.FE.A237.01 TCGA.DJ.A2QC.01 TCGA.ET.A25O.01
#> "021" "021" "0243" "011" "011" "033"
#> TCGA.EL.A3GU.01 TCGA.EL.A3MY.11 TCGA.DJ.A2PY.01 TCGA.EM.A2CS.06 TCGA.FY.A3NP.01 TCGA.ET.A25I.01
#> "033" "0221" "033" "011" "025" "0222"
#> TCGA.H2.A26U.01 TCGA.BJ.A290.11 TCGA.EM.A22I.01 TCGA.FE.A239.01 TCGA.BJ.A28Z.01 TCGA.DE.A0XZ.01
#> "013" "021" "033" "0242" "013" "033"
#> TCGA.ET.A25J.01 TCGA.EM.A22N.01 TCGA.EM.A2CM.01 TCGA.FY.A3NN.01 TCGA.EM.A3FL.01 TCGA.H2.A2K9.11
#> "011" "0222" "0244" "011" "0223" "0233"
#> TCGA.EL.A3H3.01 TCGA.EL.A3H4.01 TCGA.EM.A2OX.01 TCGA.EM.A3SX.01 TCGA.BJ.A0Z3.01 TCGA.BJ.A28X.01
#> "015" "032" "031" "032" "013" "013"
#> TCGA.EL.A3CT.01 TCGA.EL.A3CR.01 TCGA.FY.A3TY.01 TCGA.J8.A3YG.01 TCGA.DJ.A3V6.01 TCGA.EM.A3SZ.01
#> "013" "032" "0233" "015" "031" "015"
#> TCGA.EM.A2OW.01 TCGA.DO.A1JZ.11 TCGA.EL.A3D5.01 TCGA.EM.A2P0.01 TCGA.E8.A2JQ.01 TCGA.BJ.A18Z.01
#> "0222" "021" "025" "012" "013" "031"
#> TCGA.DJ.A3V0.01 TCGA.EL.A3GW.01 TCGA.DJ.A3UW.01 TCGA.DJ.A3V3.01 TCGA.EL.A3T1.11 TCGA.BJ.A0ZC.01
#> "031" "025" "013" "015" "0232" "0221"
#> TCGA.EM.A2OV.01 TCGA.EL.A3GY.01 TCGA.EM.A3SY.01 TCGA.EM.A3AI.01 TCGA.EM.A2OY.01 TCGA.EL.A3T8.01
#> "0222" "033" "021" "0222" "0223" "031"
#> TCGA.BJ.A18Y.01 TCGA.EL.A3GP.01 TCGA.EM.A2CK.01 TCGA.EL.A3T7.11 TCGA.BJ.A192.01 TCGA.BJ.A191.01
#> "025" "014" "025" "021" "0223" "011"
#> TCGA.EM.A2CP.01 TCGA.EM.A22O.01 TCGA.EM.A2P1.01 TCGA.J8.A3YH.01 TCGA.DJ.A3UZ.01 TCGA.IM.A3EB.01
#> "0231" "031" "014" "031" "0222" "013"
#> TCGA.BJ.A3F0.01 TCGA.EL.A3GX.01 TCGA.EM.A3AK.01 TCGA.DO.A1JZ.01 TCGA.FY.A3YR.01 TCGA.DO.A1K0.01
#> "02414" "033" "011" "033" "032" "033"
#> TCGA.DJ.A3V5.01 TCGA.EM.A3AJ.01 TCGA.IM.A3ED.01 TCGA.EM.A3AO.01 TCGA.EM.A2P1.06 TCGA.EM.A1CW.01
#> "032" "0232" "033" "012" "014" "0222"
#> TCGA.FK.A3SE.01 TCGA.EL.A3T7.01 TCGA.EM.A2P2.01 TCGA.EM.A1CU.11 TCGA.EL.A3T0.11 TCGA.E8.A3X7.01
#> "032" "032" "025" "021" "021" "032"
#> TCGA.ET.A3BQ.01 TCGA.EM.A1CS.01 TCGA.EL.A3GQ.01 TCGA.EL.A3H5.01 TCGA.DJ.A3V4.01 TCGA.EM.A2P3.01
#> "033" "011" "011" "033" "011" "033"
#> TCGA.FY.A3WA.01 TCGA.DJ.A3V2.01 TCGA.FY.A3TY.11 TCGA.BJ.A290.01 TCGA.EM.A3SU.01 TCGA.EL.A3D0.01
#> "0223" "013" "021" "012" "015" "031"
#> TCGA.EM.A1CT.11 TCGA.EL.A3GR.01 TCGA.J8.A3YH.06 TCGA.EM.A3ST.11 TCGA.ET.A3DV.01 TCGA.BJ.A3EZ.01
#> "021" "011" "031" "021" "02411" "031"
#> TCGA.J8.A3YD.01 TCGA.EM.A3SU.06 TCGA.EM.A3AL.01 TCGA.DJ.A3US.01 TCGA.EM.A1CS.11 TCGA.EM.A1CW.11
#> "0222" "013" "02411" "015" "021" "021"
#> TCGA.BJ.A190.01 TCGA.EM.A2OZ.01 TCGA.EM.A1CV.11 TCGA.EM.A1CU.01 TCGA.EM.A3AN.01 TCGA.E8.A2EA.01
#> "0221" "012" "021" "031" "032" "013"
#> TCGA.EM.A1CV.01 TCGA.EM.A1CT.01 TCGA.EM.A3ST.01 TCGA.ET.A3BS.01 TCGA.EL.A3GO.01 TCGA.DJ.A2Q0.01
#> "011" "012" "0244" "014" "02411" "0223"
#> TCGA.EL.A3D6.01 TCGA.DJ.A3UN.01 TCGA.DJ.A3UU.01 TCGA.FK.A3SD.01 TCGA.DJ.A2PO.01 TCGA.DJ.A3UQ.01
#> "032" "032" "011" "02413" "012" "015"
#> TCGA.EM.A1YE.11 TCGA.EL.A3T2.11 TCGA.EL.A3CL.01 TCGA.EM.A1YC.01 TCGA.DJ.A3UP.01 TCGA.EL.A3T0.01
#> "021" "021" "033" "0223" "025" "011"
#> TCGA.IM.A3U2.01 TCGA.IM.A3U3.01 TCGA.DJ.A3UX.01 TCGA.ET.A3BW.01 TCGA.ET.A39S.01 TCGA.ET.A3BP.01
#> "032" "032" "015" "011" "011" "011"
#> TCGA.DJ.A1QE.01 TCGA.EL.A3D4.01 TCGA.FK.A3SB.01 TCGA.EL.A3CW.01 TCGA.ET.A39L.01 TCGA.DJ.A2PW.01
#> "033" "012" "033" "0232" "025" "031"
#> TCGA.EM.A2CO.01 TCGA.FE.A232.01 TCGA.DJ.A3UR.01 TCGA.DJ.A2PP.01 TCGA.ET.A3DQ.01 TCGA.ET.A3DS.01
#> "0222" "011" "011" "0242" "0232" "0222"
#> TCGA.FY.A3W9.01 TCGA.FK.A3S3.01 TCGA.ET.A2MZ.01 TCGA.BJ.A2NA.11 TCGA.DJ.A1QL.01 TCGA.EL.A3CS.01
#> "0244" "011" "031" "0233" "0242" "015"
#> TCGA.FE.A233.01 TCGA.EM.A1YD.11 TCGA.ET.A3DW.11 TCGA.EL.A3T9.01 TCGA.DJ.A3UM.01 TCGA.DO.A2HM.01
#> "033" "021" "021" "032" "032" "014"
#> TCGA.FY.A3BL.01 TCGA.EL.A3TA.11 TCGA.ET.A3BX.01 TCGA.DJ.A1QQ.01 TCGA.DJ.A1QF.01 TCGA.DJ.A1QO.01
#> "012" "021" "031" "031" "011" "031"
#> TCGA.BJ.A2NA.01 TCGA.EM.A1YE.01 TCGA.FY.A2QD.01 TCGA.ET.A39J.01 TCGA.ET.A3DU.01 TCGA.EL.A3CM.01
#> "031" "0223" "02413" "034" "013" "032"
#> TCGA.DJ.A3UO.01 TCGA.ET.A39P.01 TCGA.DJ.A2Q2.01 TCGA.BJ.A28V.01 TCGA.ET.A3BO.01 TCGA.EL.A3T1.01
#> "031" "033" "0222" "02411" "032" "015"
#> TCGA.DJ.A1QI.01 TCGA.EL.A3TB.01 TCGA.BJ.A28X.11 TCGA.DJ.A1QN.01 TCGA.FE.A230.01 TCGA.FE.A234.01
#> "033" "032" "0231" "033" "015" "033"
#> TCGA.ET.A39R.01 TCGA.DJ.A1QG.01 TCGA.EL.A3CV.01 TCGA.FE.A231.01 TCGA.EL.A3TA.01 TCGA.DJ.A3UY.01
#> "015" "025" "014" "031" "012" "015"
#> TCGA.DJ.A2Q1.01 TCGA.EL.A3CU.01 TCGA.EL.A3TB.11 TCGA.ET.A39I.01 TCGA.EM.A1YB.01 TCGA.DJ.A3UV.01
#> "013" "013" "021" "025" "02414" "011"
#> TCGA.DJ.A3UT.01 TCGA.ET.A3DW.01 TCGA.ET.A3BT.01 TCGA.EL.A3T3.01 TCGA.DJ.A1QM.01 TCGA.EL.A3CY.01
#> "025" "031" "032" "032" "021" "0231"
#> TCGA.ET.A39O.01 TCGA.EM.A1YC.11 TCGA.DJ.A1QH.01 TCGA.EL.A3T3.11 TCGA.EL.A3CX.01 TCGA.EL.A3T2.01
#> "031" "021" "033" "021" "011" "025"
#> TCGA.EM.A22P.01 TCGA.EL.A3T8.11 TCGA.DJ.A2PU.01 TCGA.DJ.A3UK.01 TCGA.ET.A3DO.01 TCGA.EM.A1YA.01
#> "014" "021" "033" "011" "013" "0223"
#> TCGA.ET.A3BV.01 TCGA.EL.A3CO.01 TCGA.DJ.A2PN.01 TCGA.FK.A3SG.01 TCGA.FK.A3SH.01 TCGA.EM.A1YD.01
#> "013" "0233" "033" "032" "032" "0223"
#> TCGA.DJ.A1QD.01 TCGA.EL.A3CZ.01 TCGA.BJ.A0Z9.01 TCGA.CE.A13K.01 TCGA.EM.A3FR.01 TCGA.EM.A3O8.01
#> "033" "0222" "013" "032" "02413" "025"
#> TCGA.FY.A3R6.01 TCGA.FY.A3R9.01 TCGA.EL.A3D1.01 TCGA.EM.A3O6.01 TCGA.BJ.A0Z5.01 TCGA.BJ.A28S.01
#> "013" "0222" "031" "0222" "012" "025"
#> TCGA.BJ.A0ZH.01 TCGA.ET.A3DT.01 TCGA.H2.A3RI.11 TCGA.DJ.A13W.01 TCGA.DJ.A13T.01 TCGA.BJ.A0ZA.01
#> "032" "013" "021" "02411" "032" "02414"
#> TCGA.BJ.A3PT.01 TCGA.FE.A3PD.01 TCGA.BJ.A0ZF.01 TCGA.ET.A39M.01 TCGA.BJ.A0ZJ.01 TCGA.BJ.A0YZ.01
#> "025" "032" "0224" "014" "014" "0221"
#> TCGA.FE.A3PC.01 TCGA.DJ.A2QB.01 TCGA.EM.A3OB.01 TCGA.H2.A3RH.01 TCGA.ET.A39T.01 TCGA.DJ.A2PV.01
#> "032" "025" "025" "025" "011" "011"
#> TCGA.BJ.A3PR.11 TCGA.EL.A3T6.11 TCGA.DJ.A13X.01 TCGA.BJ.A0ZG.01 TCGA.EL.A3T6.01 TCGA.BJ.A0Z0.01
#> "0232" "0233" "011" "0221" "013" "0242"
#> TCGA.ET.A39K.01 TCGA.EM.A3O9.01 TCGA.BJ.A3PU.01 TCGA.BJ.A3PR.01 TCGA.EM.A3O3.01 TCGA.BJ.A0ZB.01
#> "032" "0234" "031" "0231" "013" "031"
#> TCGA.EM.A3OA.01 TCGA.DJ.A2PR.01 TCGA.DJ.A13L.01 TCGA.FY.A3ON.01 TCGA.DJ.A13V.01 TCGA.FY.A3R8.01
#> "02412" "031" "014" "031" "032" "032"
#> TCGA.EL.A3CP.01 TCGA.DJ.A13U.01 TCGA.DE.A0Y3.01 TCGA.ET.A2N4.01 TCGA.DJ.A13P.01 TCGA.BJ.A0ZE.01
#> "033" "012" "032" "011" "011" "025"
#> TCGA.EM.A3O7.01 TCGA.DJ.A13O.01 TCGA.FY.A3RA.01 TCGA.DJ.A13M.01 TCGA.DJ.A13R.01 TCGA.ET.A3DR.01
#> "011" "0233" "033" "025" "0221" "011"
#> TCGA.FE.A3PB.01 TCGA.ET.A3BN.01 TCGA.H2.A3RI.01 TCGA.ET.A39N.01 TCGA.BJ.A3PU.11 TCGA.FY.A3R7.01
#> "015" "033" "032" "0224" "021" "0222"
#> TCGA.FE.A3PA.01 TCGA.EM.A2CN.01 TCGA.BJ.A0Z2.01 TCGA.FY.A3I5.01 TCGA.DJ.A13S.01 TCGA.DE.A0Y2.01
#> "031" "0243" "0243" "02414" "025" "033"
#> TCGA.ET.A3BU.01
#> "031"
get_classes(res_rh, merge_node = merge_node_param(min_n_signatures = 3511))
#> TCGA.E8.A416.01 TCGA.E8.A433.01 TCGA.EL.A4K9.01 TCGA.DJ.A3V9.01 TCGA.EL.A3ZO.11 TCGA.EL.A3ZN.01
#> "021" "015" "031" "011" "021" "011"
#> TCGA.KS.A41F.01 TCGA.EL.A3ZK.01 TCGA.ET.A40R.01 TCGA.EL.A3ZM.01 TCGA.ET.A2N3.01 TCGA.EL.A3ZQ.01
#> "032" "015" "015" "031" "0241" "032"
#> TCGA.ET.A40T.01 TCGA.DE.A4MA.01 TCGA.EM.A4FU.01 TCGA.E8.A418.01 TCGA.DJ.A3VD.01 TCGA.DJ.A3VM.01
#> "032" "032" "025" "032" "013" "0244"
#> TCGA.EL.A3ZG.01 TCGA.EM.A4FV.01 TCGA.E8.A413.01 TCGA.DJ.A3VG.01 TCGA.EL.A4K2.01 TCGA.IM.A420.01
#> "012" "015" "015" "025" "0222" "013"
#> TCGA.KS.A41J.01 TCGA.EL.A3ZK.11 TCGA.J8.A3O2.01 TCGA.E8.A415.01 TCGA.FY.A40M.01 TCGA.DJ.A3VB.01
#> "032" "0232" "012" "011" "025" "031"
#> TCGA.KS.A41I.01 TCGA.DJ.A3VL.01 TCGA.ET.A4KQ.01 TCGA.H2.A421.01 TCGA.EL.A3ZO.01 TCGA.KS.A4I3.01
#> "025" "0234" "025" "032" "032" "012"
#> TCGA.DJ.A4UT.01 TCGA.DE.A4MD.01 TCGA.EL.A4JW.01 TCGA.DJ.A3VI.01 TCGA.DJ.A3VA.01 TCGA.L6.A4ET.01
#> "013" "031" "015" "032" "032" "033"
#> TCGA.E8.A419.01 TCGA.DJ.A4V0.01 TCGA.DJ.A4V2.01 TCGA.ET.A40Q.01 TCGA.EL.A3ZS.01 TCGA.KS.A4ID.01
#> "013" "0232" "033" "031" "013" "013"
#> TCGA.EL.A3ZL.11 TCGA.J8.A3YE.01 TCGA.EL.A4K7.01 TCGA.DJ.A3VF.01 TCGA.EM.A4FH.01 TCGA.E8.A432.01
#> "021" "011" "031" "013" "0221" "015"
#> TCGA.J8.A3O2.06 TCGA.ET.A2MX.01 TCGA.ET.A40S.01 TCGA.DE.A4M8.01 TCGA.IM.A41Z.01 TCGA.EL.A4KD.01
#> "031" "012" "014" "013" "0241" "012"
#> TCGA.DJ.A3V7.01 TCGA.FY.A40L.01 TCGA.DE.A4M9.01 TCGA.J8.A42S.01 TCGA.KS.A41L.01 TCGA.EM.A4FN.01
#> "032" "015" "0221" "012" "0224" "033"
#> TCGA.EL.A4K1.01 TCGA.KS.A4IC.01 TCGA.E8.A414.01 TCGA.H2.A422.01 TCGA.J8.A3YF.01 TCGA.EL.A4KI.01
#> "033" "011" "015" "032" "031" "0243"
#> TCGA.EM.A4G1.01 TCGA.DJ.A3VJ.01 TCGA.DE.A4MD.06 TCGA.EL.A3ZP.01 TCGA.EM.A4FQ.01 TCGA.EL.A3ZT.01
#> "025" "031" "014" "031" "033" "031"
#> TCGA.DJ.A4V4.01 TCGA.FY.A40K.01 TCGA.L6.A4EQ.01 TCGA.DJ.A3VE.01 TCGA.E8.A434.01 TCGA.EL.A3ZH.01
#> "011" "011" "031" "031" "0222" "0222"
#> TCGA.EM.A4FR.01 TCGA.EL.A3ZH.11 TCGA.EL.A3ZR.01 TCGA.DJ.A3V8.01 TCGA.EL.A3ZG.11 TCGA.ET.A40P.01
#> "012" "021" "025" "015" "021" "025"
#> TCGA.DE.A4MB.01 TCGA.MK.A4N6.01 TCGA.DJ.A3VK.01 TCGA.E8.A417.01 TCGA.L6.A4EU.01 TCGA.J8.A4HY.01
#> "032" "031" "025" "032" "032" "011"
#> TCGA.EL.A3ZL.01 TCGA.EL.A3ZP.11 TCGA.FY.A40N.01 TCGA.J8.A4HW.01 TCGA.BJ.A45J.01 TCGA.CE.A482.01
#> "032" "0232" "011" "032" "032" "032"
#> TCGA.DJ.A2Q6.01 TCGA.DJ.A2PX.01 TCGA.DJ.A4UL.01 TCGA.EL.A4JX.01 TCGA.BJ.A2N8.11 TCGA.DJ.A2Q5.01
#> "032" "015" "033" "013" "021" "014"
#> TCGA.EL.A4KG.01 TCGA.DJ.A4UP.01 TCGA.E8.A438.01 TCGA.EL.A3H2.01 TCGA.EM.A3AP.01 TCGA.DJ.A2PQ.01
#> "033" "015" "011" "0221" "025" "031"
#> TCGA.L6.A4EP.01 TCGA.FY.A4B4.01 TCGA.EL.A4KH.01 TCGA.BJ.A45E.01 TCGA.DJ.A4V5.01 TCGA.DE.A4MC.01
#> "033" "032" "011" "0231" "014" "033"
#> TCGA.E8.A44M.01 TCGA.BJ.A45K.01 TCGA.E3.A3DZ.01 TCGA.E3.A3E2.01 TCGA.BJ.A45H.01 TCGA.E8.A44K.01
#> "013" "0242" "025" "032" "012" "015"
#> TCGA.ET.A2MY.01 TCGA.EL.A3H8.01 TCGA.BJ.A45C.01 TCGA.BJ.A45G.01 TCGA.EL.A4JZ.01 TCGA.CE.A481.01
#> "032" "033" "0242" "025" "033" "015"
#> TCGA.KS.A4I9.01 TCGA.EL.A3MW.01 TCGA.E8.A436.01 TCGA.E3.A3DY.01 TCGA.DJ.A2Q3.01 TCGA.BJ.A2P4.01
#> "033" "033" "015" "031" "013" "025"
#> TCGA.CE.A484.01 TCGA.ET.A2N1.01 TCGA.DJ.A2Q4.01 TCGA.DJ.A2PZ.01 TCGA.BJ.A45F.01 TCGA.IM.A4EB.01
#> "025" "011" "031" "012" "025" "014"
#> TCGA.EM.A4FO.01 TCGA.FY.A4B3.01 TCGA.FY.A4B0.01 TCGA.BJ.A45I.01 TCGA.E3.A3E3.01 TCGA.EM.A3AQ.01
#> "014" "031" "0242" "013" "033" "034"
#> TCGA.EL.A3N3.01 TCGA.DJ.A2Q9.01 TCGA.EM.A4FM.01 TCGA.EL.A4K6.01 TCGA.MK.A4N9.01 TCGA.KS.A4I1.01
#> "013" "0231" "033" "0243" "033" "032"
#> TCGA.DJ.A2PS.01 TCGA.CE.A3MD.01 TCGA.E3.A3E5.01 TCGA.EL.A3CN.01 TCGA.J8.A4HW.06 TCGA.EM.A4FK.01
#> "011" "012" "031" "015" "013" "0241"
#> TCGA.E8.A437.01 TCGA.BJ.A4O8.01 TCGA.EL.A3MW.11 TCGA.E3.A3E0.01 TCGA.BJ.A45D.01 TCGA.CE.A483.01
#> "011" "031" "021" "033" "025" "011"
#> TCGA.CE.A485.01 TCGA.DJ.A4UR.01 TCGA.IM.A41Y.01 TCGA.ET.A4KN.01 TCGA.KS.A4I5.01 TCGA.DJ.A4UQ.01
#> "012" "0244" "032" "013" "033" "012"
#> TCGA.KS.A4IB.01 TCGA.EL.A3N2.11 TCGA.BJ.A2N9.01 TCGA.DJ.A4UW.01 TCGA.EL.A3GZ.11 TCGA.EM.A3AR.01
#> "033" "021" "0222" "011" "021" "021"
#> TCGA.EL.A3N3.11 TCGA.DE.A3KN.01 TCGA.DJ.A2QA.01 TCGA.EL.A4JV.01 TCGA.EM.A4FF.01 TCGA.EL.A4K0.01
#> "0232" "011" "011" "025" "033" "033"
#> TCGA.FK.A4UB.01 TCGA.BJ.A4O9.01 TCGA.BJ.A2N7.01 TCGA.DE.A2OL.01 TCGA.CE.A3ME.01 TCGA.MK.A4N7.01
#> "031" "011" "025" "0241" "011" "032"
#> TCGA.EL.A3H2.11 TCGA.EL.A4K4.01 TCGA.EL.A3GS.01 TCGA.EL.A3GZ.01 TCGA.E3.A3E1.01 TCGA.DJ.A2Q8.01
#> "021" "033" "033" "032" "011" "015"
#> TCGA.EL.A3N2.01 TCGA.KS.A4I7.01 TCGA.MK.A84Z.01 TCGA.ET.A3DP.11 TCGA.EL.A3MX.11 TCGA.ET.A25G.01
#> "033" "032" "025" "021" "021" "032"
#> TCGA.EM.A3FK.01 TCGA.EM.A2CS.01 TCGA.FE.A23A.01 TCGA.BJ.A28T.11 TCGA.EM.A22J.01 TCGA.EL.A3MX.01
#> "034" "032" "013" "021" "0241" "033"
#> TCGA.FY.A3I4.01 TCGA.BJ.A28W.11 TCGA.ET.A25R.01 TCGA.BJ.A2N8.01 TCGA.FY.A76V.01 TCGA.EM.A3FN.01
#> "011" "0232" "032" "025" "025" "0241"
#> TCGA.QD.A8IV.01 TCGA.EM.A3FJ.01 TCGA.ET.A2MY.11 TCGA.EM.A3FQ.06 TCGA.ET.A25P.01 TCGA.ET.A2N0.01
#> "025" "033" "0241" "033" "025" "015"
#> TCGA.EM.A2CT.01 TCGA.FE.A235.01 TCGA.ET.A25M.01 TCGA.EL.A3MY.01 TCGA.DE.A7U5.01 TCGA.E8.A2JQ.11
#> "0222" "033" "031" "031" "033" "0231"
#> TCGA.ET.A3DP.01 TCGA.EM.A2CL.01 TCGA.ET.A2N5.01 TCGA.ET.A25J.11 TCGA.DE.A69J.01 TCGA.BJ.A28R.11
#> "011" "0242" "025" "021" "033" "0232"
#> TCGA.ET.A25K.01 TCGA.EL.A3GV.01 TCGA.GE.A2C6.01 TCGA.EM.A3FM.01 TCGA.EL.A3H7.11 TCGA.FE.A22Z.01
#> "032" "011" "013" "031" "021" "033"
#> TCGA.H2.A2K9.01 TCGA.EM.A22Q.01 TCGA.EM.A3FP.01 TCGA.GE.A2C6.11 TCGA.EL.A3MZ.01 TCGA.DJ.A2PT.01
#> "0243" "0242" "025" "0232" "031" "013"
#> TCGA.E8.A242.01 TCGA.ET.A25L.01 TCGA.CE.A27D.01 TCGA.EL.A3H1.11 TCGA.BJ.A2N7.11 TCGA.DJ.A2Q7.01
#> "013" "032" "0233" "0233" "021" "033"
#> TCGA.J8.A3O1.01 TCGA.EM.A2CR.01 TCGA.DE.A69K.01 TCGA.EM.A2CQ.01 TCGA.FE.A238.01 TCGA.EL.A3H1.01
#> "011" "011" "033" "0222" "015" "0241"
#> TCGA.BJ.A28W.01 TCGA.BJ.A28T.01 TCGA.EM.A2CJ.01 TCGA.EM.A3FQ.01 TCGA.4C.A93U.01 TCGA.EM.A22M.01
#> "0231" "0232" "0223" "015" "033" "014"
#> TCGA.J8.A3NZ.01 TCGA.EM.A22K.01 TCGA.FE.A236.01 TCGA.BJ.A28R.01 TCGA.EM.A2CU.01 TCGA.ET.A25N.01
#> "011" "025" "012" "015" "015" "033"
#> TCGA.EL.A3H7.01 TCGA.FY.A3NM.01 TCGA.EM.A3FO.01 TCGA.EM.A22L.01 TCGA.BJ.A2N9.11 TCGA.BJ.A291.01
#> "033" "0223" "031" "025" "0231" "0222"
#> TCGA.ET.A2N5.11 TCGA.ET.A25N.11 TCGA.J8.A3O0.01 TCGA.FE.A237.01 TCGA.DJ.A2QC.01 TCGA.ET.A25O.01
#> "021" "021" "0243" "011" "011" "033"
#> TCGA.EL.A3GU.01 TCGA.EL.A3MY.11 TCGA.DJ.A2PY.01 TCGA.EM.A2CS.06 TCGA.FY.A3NP.01 TCGA.ET.A25I.01
#> "033" "0221" "033" "011" "025" "0222"
#> TCGA.H2.A26U.01 TCGA.BJ.A290.11 TCGA.EM.A22I.01 TCGA.FE.A239.01 TCGA.BJ.A28Z.01 TCGA.DE.A0XZ.01
#> "013" "021" "033" "0242" "013" "033"
#> TCGA.ET.A25J.01 TCGA.EM.A22N.01 TCGA.EM.A2CM.01 TCGA.FY.A3NN.01 TCGA.EM.A3FL.01 TCGA.H2.A2K9.11
#> "011" "0222" "0244" "011" "0223" "0233"
#> TCGA.EL.A3H3.01 TCGA.EL.A3H4.01 TCGA.EM.A2OX.01 TCGA.EM.A3SX.01 TCGA.BJ.A0Z3.01 TCGA.BJ.A28X.01
#> "015" "032" "031" "032" "013" "013"
#> TCGA.EL.A3CT.01 TCGA.EL.A3CR.01 TCGA.FY.A3TY.01 TCGA.J8.A3YG.01 TCGA.DJ.A3V6.01 TCGA.EM.A3SZ.01
#> "013" "032" "0233" "015" "031" "015"
#> TCGA.EM.A2OW.01 TCGA.DO.A1JZ.11 TCGA.EL.A3D5.01 TCGA.EM.A2P0.01 TCGA.E8.A2JQ.01 TCGA.BJ.A18Z.01
#> "0222" "021" "025" "012" "013" "031"
#> TCGA.DJ.A3V0.01 TCGA.EL.A3GW.01 TCGA.DJ.A3UW.01 TCGA.DJ.A3V3.01 TCGA.EL.A3T1.11 TCGA.BJ.A0ZC.01
#> "031" "025" "013" "015" "0232" "0221"
#> TCGA.EM.A2OV.01 TCGA.EL.A3GY.01 TCGA.EM.A3SY.01 TCGA.EM.A3AI.01 TCGA.EM.A2OY.01 TCGA.EL.A3T8.01
#> "0222" "033" "021" "0222" "0223" "031"
#> TCGA.BJ.A18Y.01 TCGA.EL.A3GP.01 TCGA.EM.A2CK.01 TCGA.EL.A3T7.11 TCGA.BJ.A192.01 TCGA.BJ.A191.01
#> "025" "014" "025" "021" "0223" "011"
#> TCGA.EM.A2CP.01 TCGA.EM.A22O.01 TCGA.EM.A2P1.01 TCGA.J8.A3YH.01 TCGA.DJ.A3UZ.01 TCGA.IM.A3EB.01
#> "0231" "031" "014" "031" "0222" "013"
#> TCGA.BJ.A3F0.01 TCGA.EL.A3GX.01 TCGA.EM.A3AK.01 TCGA.DO.A1JZ.01 TCGA.FY.A3YR.01 TCGA.DO.A1K0.01
#> "0241" "033" "011" "033" "032" "033"
#> TCGA.DJ.A3V5.01 TCGA.EM.A3AJ.01 TCGA.IM.A3ED.01 TCGA.EM.A3AO.01 TCGA.EM.A2P1.06 TCGA.EM.A1CW.01
#> "032" "0232" "033" "012" "014" "0222"
#> TCGA.FK.A3SE.01 TCGA.EL.A3T7.01 TCGA.EM.A2P2.01 TCGA.EM.A1CU.11 TCGA.EL.A3T0.11 TCGA.E8.A3X7.01
#> "032" "032" "025" "021" "021" "032"
#> TCGA.ET.A3BQ.01 TCGA.EM.A1CS.01 TCGA.EL.A3GQ.01 TCGA.EL.A3H5.01 TCGA.DJ.A3V4.01 TCGA.EM.A2P3.01
#> "033" "011" "011" "033" "011" "033"
#> TCGA.FY.A3WA.01 TCGA.DJ.A3V2.01 TCGA.FY.A3TY.11 TCGA.BJ.A290.01 TCGA.EM.A3SU.01 TCGA.EL.A3D0.01
#> "0223" "013" "021" "012" "015" "031"
#> TCGA.EM.A1CT.11 TCGA.EL.A3GR.01 TCGA.J8.A3YH.06 TCGA.EM.A3ST.11 TCGA.ET.A3DV.01 TCGA.BJ.A3EZ.01
#> "021" "011" "031" "021" "0241" "031"
#> TCGA.J8.A3YD.01 TCGA.EM.A3SU.06 TCGA.EM.A3AL.01 TCGA.DJ.A3US.01 TCGA.EM.A1CS.11 TCGA.EM.A1CW.11
#> "0222" "013" "0241" "015" "021" "021"
#> TCGA.BJ.A190.01 TCGA.EM.A2OZ.01 TCGA.EM.A1CV.11 TCGA.EM.A1CU.01 TCGA.EM.A3AN.01 TCGA.E8.A2EA.01
#> "0221" "012" "021" "031" "032" "013"
#> TCGA.EM.A1CV.01 TCGA.EM.A1CT.01 TCGA.EM.A3ST.01 TCGA.ET.A3BS.01 TCGA.EL.A3GO.01 TCGA.DJ.A2Q0.01
#> "011" "012" "0244" "014" "0241" "0223"
#> TCGA.EL.A3D6.01 TCGA.DJ.A3UN.01 TCGA.DJ.A3UU.01 TCGA.FK.A3SD.01 TCGA.DJ.A2PO.01 TCGA.DJ.A3UQ.01
#> "032" "032" "011" "0241" "012" "015"
#> TCGA.EM.A1YE.11 TCGA.EL.A3T2.11 TCGA.EL.A3CL.01 TCGA.EM.A1YC.01 TCGA.DJ.A3UP.01 TCGA.EL.A3T0.01
#> "021" "021" "033" "0223" "025" "011"
#> TCGA.IM.A3U2.01 TCGA.IM.A3U3.01 TCGA.DJ.A3UX.01 TCGA.ET.A3BW.01 TCGA.ET.A39S.01 TCGA.ET.A3BP.01
#> "032" "032" "015" "011" "011" "011"
#> TCGA.DJ.A1QE.01 TCGA.EL.A3D4.01 TCGA.FK.A3SB.01 TCGA.EL.A3CW.01 TCGA.ET.A39L.01 TCGA.DJ.A2PW.01
#> "033" "012" "033" "0232" "025" "031"
#> TCGA.EM.A2CO.01 TCGA.FE.A232.01 TCGA.DJ.A3UR.01 TCGA.DJ.A2PP.01 TCGA.ET.A3DQ.01 TCGA.ET.A3DS.01
#> "0222" "011" "011" "0242" "0232" "0222"
#> TCGA.FY.A3W9.01 TCGA.FK.A3S3.01 TCGA.ET.A2MZ.01 TCGA.BJ.A2NA.11 TCGA.DJ.A1QL.01 TCGA.EL.A3CS.01
#> "0244" "011" "031" "0233" "0242" "015"
#> TCGA.FE.A233.01 TCGA.EM.A1YD.11 TCGA.ET.A3DW.11 TCGA.EL.A3T9.01 TCGA.DJ.A3UM.01 TCGA.DO.A2HM.01
#> "033" "021" "021" "032" "032" "014"
#> TCGA.FY.A3BL.01 TCGA.EL.A3TA.11 TCGA.ET.A3BX.01 TCGA.DJ.A1QQ.01 TCGA.DJ.A1QF.01 TCGA.DJ.A1QO.01
#> "012" "021" "031" "031" "011" "031"
#> TCGA.BJ.A2NA.01 TCGA.EM.A1YE.01 TCGA.FY.A2QD.01 TCGA.ET.A39J.01 TCGA.ET.A3DU.01 TCGA.EL.A3CM.01
#> "031" "0223" "0241" "034" "013" "032"
#> TCGA.DJ.A3UO.01 TCGA.ET.A39P.01 TCGA.DJ.A2Q2.01 TCGA.BJ.A28V.01 TCGA.ET.A3BO.01 TCGA.EL.A3T1.01
#> "031" "033" "0222" "0241" "032" "015"
#> TCGA.DJ.A1QI.01 TCGA.EL.A3TB.01 TCGA.BJ.A28X.11 TCGA.DJ.A1QN.01 TCGA.FE.A230.01 TCGA.FE.A234.01
#> "033" "032" "0231" "033" "015" "033"
#> TCGA.ET.A39R.01 TCGA.DJ.A1QG.01 TCGA.EL.A3CV.01 TCGA.FE.A231.01 TCGA.EL.A3TA.01 TCGA.DJ.A3UY.01
#> "015" "025" "014" "031" "012" "015"
#> TCGA.DJ.A2Q1.01 TCGA.EL.A3CU.01 TCGA.EL.A3TB.11 TCGA.ET.A39I.01 TCGA.EM.A1YB.01 TCGA.DJ.A3UV.01
#> "013" "013" "021" "025" "0241" "011"
#> TCGA.DJ.A3UT.01 TCGA.ET.A3DW.01 TCGA.ET.A3BT.01 TCGA.EL.A3T3.01 TCGA.DJ.A1QM.01 TCGA.EL.A3CY.01
#> "025" "031" "032" "032" "021" "0231"
#> TCGA.ET.A39O.01 TCGA.EM.A1YC.11 TCGA.DJ.A1QH.01 TCGA.EL.A3T3.11 TCGA.EL.A3CX.01 TCGA.EL.A3T2.01
#> "031" "021" "033" "021" "011" "025"
#> TCGA.EM.A22P.01 TCGA.EL.A3T8.11 TCGA.DJ.A2PU.01 TCGA.DJ.A3UK.01 TCGA.ET.A3DO.01 TCGA.EM.A1YA.01
#> "014" "021" "033" "011" "013" "0223"
#> TCGA.ET.A3BV.01 TCGA.EL.A3CO.01 TCGA.DJ.A2PN.01 TCGA.FK.A3SG.01 TCGA.FK.A3SH.01 TCGA.EM.A1YD.01
#> "013" "0233" "033" "032" "032" "0223"
#> TCGA.DJ.A1QD.01 TCGA.EL.A3CZ.01 TCGA.BJ.A0Z9.01 TCGA.CE.A13K.01 TCGA.EM.A3FR.01 TCGA.EM.A3O8.01
#> "033" "0222" "013" "032" "0241" "025"
#> TCGA.FY.A3R6.01 TCGA.FY.A3R9.01 TCGA.EL.A3D1.01 TCGA.EM.A3O6.01 TCGA.BJ.A0Z5.01 TCGA.BJ.A28S.01
#> "013" "0222" "031" "0222" "012" "025"
#> TCGA.BJ.A0ZH.01 TCGA.ET.A3DT.01 TCGA.H2.A3RI.11 TCGA.DJ.A13W.01 TCGA.DJ.A13T.01 TCGA.BJ.A0ZA.01
#> "032" "013" "021" "0241" "032" "0241"
#> TCGA.BJ.A3PT.01 TCGA.FE.A3PD.01 TCGA.BJ.A0ZF.01 TCGA.ET.A39M.01 TCGA.BJ.A0ZJ.01 TCGA.BJ.A0YZ.01
#> "025" "032" "0224" "014" "014" "0221"
#> TCGA.FE.A3PC.01 TCGA.DJ.A2QB.01 TCGA.EM.A3OB.01 TCGA.H2.A3RH.01 TCGA.ET.A39T.01 TCGA.DJ.A2PV.01
#> "032" "025" "025" "025" "011" "011"
#> TCGA.BJ.A3PR.11 TCGA.EL.A3T6.11 TCGA.DJ.A13X.01 TCGA.BJ.A0ZG.01 TCGA.EL.A3T6.01 TCGA.BJ.A0Z0.01
#> "0232" "0233" "011" "0221" "013" "0242"
#> TCGA.ET.A39K.01 TCGA.EM.A3O9.01 TCGA.BJ.A3PU.01 TCGA.BJ.A3PR.01 TCGA.EM.A3O3.01 TCGA.BJ.A0ZB.01
#> "032" "0234" "031" "0231" "013" "031"
#> TCGA.EM.A3OA.01 TCGA.DJ.A2PR.01 TCGA.DJ.A13L.01 TCGA.FY.A3ON.01 TCGA.DJ.A13V.01 TCGA.FY.A3R8.01
#> "0241" "031" "014" "031" "032" "032"
#> TCGA.EL.A3CP.01 TCGA.DJ.A13U.01 TCGA.DE.A0Y3.01 TCGA.ET.A2N4.01 TCGA.DJ.A13P.01 TCGA.BJ.A0ZE.01
#> "033" "012" "032" "011" "011" "025"
#> TCGA.EM.A3O7.01 TCGA.DJ.A13O.01 TCGA.FY.A3RA.01 TCGA.DJ.A13M.01 TCGA.DJ.A13R.01 TCGA.ET.A3DR.01
#> "011" "0233" "033" "025" "0221" "011"
#> TCGA.FE.A3PB.01 TCGA.ET.A3BN.01 TCGA.H2.A3RI.01 TCGA.ET.A39N.01 TCGA.BJ.A3PU.11 TCGA.FY.A3R7.01
#> "015" "033" "032" "0224" "021" "0222"
#> TCGA.FE.A3PA.01 TCGA.EM.A2CN.01 TCGA.BJ.A0Z2.01 TCGA.FY.A3I5.01 TCGA.DJ.A13S.01 TCGA.DE.A0Y2.01
#> "031" "0243" "0243" "0241" "025" "033"
#> TCGA.ET.A3BU.01
#> "031"
get_classes(res_rh, merge_node = merge_node_param(min_n_signatures = 3641))
#> TCGA.E8.A416.01 TCGA.E8.A433.01 TCGA.EL.A4K9.01 TCGA.DJ.A3V9.01 TCGA.EL.A3ZO.11 TCGA.EL.A3ZN.01
#> NA NA NA NA NA NA
#> TCGA.KS.A41F.01 TCGA.EL.A3ZK.01 TCGA.ET.A40R.01 TCGA.EL.A3ZM.01 TCGA.ET.A2N3.01 TCGA.EL.A3ZQ.01
#> NA NA NA NA "0241" NA
#> TCGA.ET.A40T.01 TCGA.DE.A4MA.01 TCGA.EM.A4FU.01 TCGA.E8.A418.01 TCGA.DJ.A3VD.01 TCGA.DJ.A3VM.01
#> NA NA NA NA NA "0244"
#> TCGA.EL.A3ZG.01 TCGA.EM.A4FV.01 TCGA.E8.A413.01 TCGA.DJ.A3VG.01 TCGA.EL.A4K2.01 TCGA.IM.A420.01
#> NA NA NA NA "0222" NA
#> TCGA.KS.A41J.01 TCGA.EL.A3ZK.11 TCGA.J8.A3O2.01 TCGA.E8.A415.01 TCGA.FY.A40M.01 TCGA.DJ.A3VB.01
#> NA "0232" NA NA NA NA
#> TCGA.KS.A41I.01 TCGA.DJ.A3VL.01 TCGA.ET.A4KQ.01 TCGA.H2.A421.01 TCGA.EL.A3ZO.01 TCGA.KS.A4I3.01
#> NA "0234" NA NA NA NA
#> TCGA.DJ.A4UT.01 TCGA.DE.A4MD.01 TCGA.EL.A4JW.01 TCGA.DJ.A3VI.01 TCGA.DJ.A3VA.01 TCGA.L6.A4ET.01
#> NA NA NA NA NA NA
#> TCGA.E8.A419.01 TCGA.DJ.A4V0.01 TCGA.DJ.A4V2.01 TCGA.ET.A40Q.01 TCGA.EL.A3ZS.01 TCGA.KS.A4ID.01
#> NA "0232" NA NA NA NA
#> TCGA.EL.A3ZL.11 TCGA.J8.A3YE.01 TCGA.EL.A4K7.01 TCGA.DJ.A3VF.01 TCGA.EM.A4FH.01 TCGA.E8.A432.01
#> NA NA NA NA "0221" NA
#> TCGA.J8.A3O2.06 TCGA.ET.A2MX.01 TCGA.ET.A40S.01 TCGA.DE.A4M8.01 TCGA.IM.A41Z.01 TCGA.EL.A4KD.01
#> NA NA NA NA "0241" NA
#> TCGA.DJ.A3V7.01 TCGA.FY.A40L.01 TCGA.DE.A4M9.01 TCGA.J8.A42S.01 TCGA.KS.A41L.01 TCGA.EM.A4FN.01
#> NA NA "0221" NA "0224" NA
#> TCGA.EL.A4K1.01 TCGA.KS.A4IC.01 TCGA.E8.A414.01 TCGA.H2.A422.01 TCGA.J8.A3YF.01 TCGA.EL.A4KI.01
#> NA NA NA NA NA "0243"
#> TCGA.EM.A4G1.01 TCGA.DJ.A3VJ.01 TCGA.DE.A4MD.06 TCGA.EL.A3ZP.01 TCGA.EM.A4FQ.01 TCGA.EL.A3ZT.01
#> NA NA NA NA NA NA
#> TCGA.DJ.A4V4.01 TCGA.FY.A40K.01 TCGA.L6.A4EQ.01 TCGA.DJ.A3VE.01 TCGA.E8.A434.01 TCGA.EL.A3ZH.01
#> NA NA NA NA "0222" "0222"
#> TCGA.EM.A4FR.01 TCGA.EL.A3ZH.11 TCGA.EL.A3ZR.01 TCGA.DJ.A3V8.01 TCGA.EL.A3ZG.11 TCGA.ET.A40P.01
#> NA NA NA NA NA NA
#> TCGA.DE.A4MB.01 TCGA.MK.A4N6.01 TCGA.DJ.A3VK.01 TCGA.E8.A417.01 TCGA.L6.A4EU.01 TCGA.J8.A4HY.01
#> NA NA NA NA NA NA
#> TCGA.EL.A3ZL.01 TCGA.EL.A3ZP.11 TCGA.FY.A40N.01 TCGA.J8.A4HW.01 TCGA.BJ.A45J.01 TCGA.CE.A482.01
#> NA "0232" NA NA NA NA
#> TCGA.DJ.A2Q6.01 TCGA.DJ.A2PX.01 TCGA.DJ.A4UL.01 TCGA.EL.A4JX.01 TCGA.BJ.A2N8.11 TCGA.DJ.A2Q5.01
#> NA NA NA NA NA NA
#> TCGA.EL.A4KG.01 TCGA.DJ.A4UP.01 TCGA.E8.A438.01 TCGA.EL.A3H2.01 TCGA.EM.A3AP.01 TCGA.DJ.A2PQ.01
#> NA NA NA "0221" NA NA
#> TCGA.L6.A4EP.01 TCGA.FY.A4B4.01 TCGA.EL.A4KH.01 TCGA.BJ.A45E.01 TCGA.DJ.A4V5.01 TCGA.DE.A4MC.01
#> NA NA NA "0231" NA NA
#> TCGA.E8.A44M.01 TCGA.BJ.A45K.01 TCGA.E3.A3DZ.01 TCGA.E3.A3E2.01 TCGA.BJ.A45H.01 TCGA.E8.A44K.01
#> NA "0242" NA NA NA NA
#> TCGA.ET.A2MY.01 TCGA.EL.A3H8.01 TCGA.BJ.A45C.01 TCGA.BJ.A45G.01 TCGA.EL.A4JZ.01 TCGA.CE.A481.01
#> NA NA "0242" NA NA NA
#> TCGA.KS.A4I9.01 TCGA.EL.A3MW.01 TCGA.E8.A436.01 TCGA.E3.A3DY.01 TCGA.DJ.A2Q3.01 TCGA.BJ.A2P4.01
#> NA NA NA NA NA NA
#> TCGA.CE.A484.01 TCGA.ET.A2N1.01 TCGA.DJ.A2Q4.01 TCGA.DJ.A2PZ.01 TCGA.BJ.A45F.01 TCGA.IM.A4EB.01
#> NA NA NA NA NA NA
#> TCGA.EM.A4FO.01 TCGA.FY.A4B3.01 TCGA.FY.A4B0.01 TCGA.BJ.A45I.01 TCGA.E3.A3E3.01 TCGA.EM.A3AQ.01
#> NA NA "0242" NA NA NA
#> TCGA.EL.A3N3.01 TCGA.DJ.A2Q9.01 TCGA.EM.A4FM.01 TCGA.EL.A4K6.01 TCGA.MK.A4N9.01 TCGA.KS.A4I1.01
#> NA "0231" NA "0243" NA NA
#> TCGA.DJ.A2PS.01 TCGA.CE.A3MD.01 TCGA.E3.A3E5.01 TCGA.EL.A3CN.01 TCGA.J8.A4HW.06 TCGA.EM.A4FK.01
#> NA NA NA NA NA "0241"
#> TCGA.E8.A437.01 TCGA.BJ.A4O8.01 TCGA.EL.A3MW.11 TCGA.E3.A3E0.01 TCGA.BJ.A45D.01 TCGA.CE.A483.01
#> NA NA NA NA NA NA
#> TCGA.CE.A485.01 TCGA.DJ.A4UR.01 TCGA.IM.A41Y.01 TCGA.ET.A4KN.01 TCGA.KS.A4I5.01 TCGA.DJ.A4UQ.01
#> NA "0244" NA NA NA NA
#> TCGA.KS.A4IB.01 TCGA.EL.A3N2.11 TCGA.BJ.A2N9.01 TCGA.DJ.A4UW.01 TCGA.EL.A3GZ.11 TCGA.EM.A3AR.01
#> NA NA "0222" NA NA NA
#> TCGA.EL.A3N3.11 TCGA.DE.A3KN.01 TCGA.DJ.A2QA.01 TCGA.EL.A4JV.01 TCGA.EM.A4FF.01 TCGA.EL.A4K0.01
#> "0232" NA NA NA NA NA
#> TCGA.FK.A4UB.01 TCGA.BJ.A4O9.01 TCGA.BJ.A2N7.01 TCGA.DE.A2OL.01 TCGA.CE.A3ME.01 TCGA.MK.A4N7.01
#> NA NA NA "0241" NA NA
#> TCGA.EL.A3H2.11 TCGA.EL.A4K4.01 TCGA.EL.A3GS.01 TCGA.EL.A3GZ.01 TCGA.E3.A3E1.01 TCGA.DJ.A2Q8.01
#> NA NA NA NA NA NA
#> TCGA.EL.A3N2.01 TCGA.KS.A4I7.01 TCGA.MK.A84Z.01 TCGA.ET.A3DP.11 TCGA.EL.A3MX.11 TCGA.ET.A25G.01
#> NA NA NA NA NA NA
#> TCGA.EM.A3FK.01 TCGA.EM.A2CS.01 TCGA.FE.A23A.01 TCGA.BJ.A28T.11 TCGA.EM.A22J.01 TCGA.EL.A3MX.01
#> NA NA NA NA "0241" NA
#> TCGA.FY.A3I4.01 TCGA.BJ.A28W.11 TCGA.ET.A25R.01 TCGA.BJ.A2N8.01 TCGA.FY.A76V.01 TCGA.EM.A3FN.01
#> NA "0232" NA NA NA "0241"
#> TCGA.QD.A8IV.01 TCGA.EM.A3FJ.01 TCGA.ET.A2MY.11 TCGA.EM.A3FQ.06 TCGA.ET.A25P.01 TCGA.ET.A2N0.01
#> NA NA "0241" NA NA NA
#> TCGA.EM.A2CT.01 TCGA.FE.A235.01 TCGA.ET.A25M.01 TCGA.EL.A3MY.01 TCGA.DE.A7U5.01 TCGA.E8.A2JQ.11
#> "0222" NA NA NA NA "0231"
#> TCGA.ET.A3DP.01 TCGA.EM.A2CL.01 TCGA.ET.A2N5.01 TCGA.ET.A25J.11 TCGA.DE.A69J.01 TCGA.BJ.A28R.11
#> NA "0242" NA NA NA "0232"
#> TCGA.ET.A25K.01 TCGA.EL.A3GV.01 TCGA.GE.A2C6.01 TCGA.EM.A3FM.01 TCGA.EL.A3H7.11 TCGA.FE.A22Z.01
#> NA NA NA NA NA NA
#> TCGA.H2.A2K9.01 TCGA.EM.A22Q.01 TCGA.EM.A3FP.01 TCGA.GE.A2C6.11 TCGA.EL.A3MZ.01 TCGA.DJ.A2PT.01
#> "0243" "0242" NA "0232" NA NA
#> TCGA.E8.A242.01 TCGA.ET.A25L.01 TCGA.CE.A27D.01 TCGA.EL.A3H1.11 TCGA.BJ.A2N7.11 TCGA.DJ.A2Q7.01
#> NA NA "0233" "0233" NA NA
#> TCGA.J8.A3O1.01 TCGA.EM.A2CR.01 TCGA.DE.A69K.01 TCGA.EM.A2CQ.01 TCGA.FE.A238.01 TCGA.EL.A3H1.01
#> NA NA NA "0222" NA "0241"
#> TCGA.BJ.A28W.01 TCGA.BJ.A28T.01 TCGA.EM.A2CJ.01 TCGA.EM.A3FQ.01 TCGA.4C.A93U.01 TCGA.EM.A22M.01
#> "0231" "0232" "0223" NA NA NA
#> TCGA.J8.A3NZ.01 TCGA.EM.A22K.01 TCGA.FE.A236.01 TCGA.BJ.A28R.01 TCGA.EM.A2CU.01 TCGA.ET.A25N.01
#> NA NA NA NA NA NA
#> TCGA.EL.A3H7.01 TCGA.FY.A3NM.01 TCGA.EM.A3FO.01 TCGA.EM.A22L.01 TCGA.BJ.A2N9.11 TCGA.BJ.A291.01
#> NA "0223" NA NA "0231" "0222"
#> TCGA.ET.A2N5.11 TCGA.ET.A25N.11 TCGA.J8.A3O0.01 TCGA.FE.A237.01 TCGA.DJ.A2QC.01 TCGA.ET.A25O.01
#> NA NA "0243" NA NA NA
#> TCGA.EL.A3GU.01 TCGA.EL.A3MY.11 TCGA.DJ.A2PY.01 TCGA.EM.A2CS.06 TCGA.FY.A3NP.01 TCGA.ET.A25I.01
#> NA "0221" NA NA NA "0222"
#> TCGA.H2.A26U.01 TCGA.BJ.A290.11 TCGA.EM.A22I.01 TCGA.FE.A239.01 TCGA.BJ.A28Z.01 TCGA.DE.A0XZ.01
#> NA NA NA "0242" NA NA
#> TCGA.ET.A25J.01 TCGA.EM.A22N.01 TCGA.EM.A2CM.01 TCGA.FY.A3NN.01 TCGA.EM.A3FL.01 TCGA.H2.A2K9.11
#> NA "0222" "0244" NA "0223" "0233"
#> TCGA.EL.A3H3.01 TCGA.EL.A3H4.01 TCGA.EM.A2OX.01 TCGA.EM.A3SX.01 TCGA.BJ.A0Z3.01 TCGA.BJ.A28X.01
#> NA NA NA NA NA NA
#> TCGA.EL.A3CT.01 TCGA.EL.A3CR.01 TCGA.FY.A3TY.01 TCGA.J8.A3YG.01 TCGA.DJ.A3V6.01 TCGA.EM.A3SZ.01
#> NA NA "0233" NA NA NA
#> TCGA.EM.A2OW.01 TCGA.DO.A1JZ.11 TCGA.EL.A3D5.01 TCGA.EM.A2P0.01 TCGA.E8.A2JQ.01 TCGA.BJ.A18Z.01
#> "0222" NA NA NA NA NA
#> TCGA.DJ.A3V0.01 TCGA.EL.A3GW.01 TCGA.DJ.A3UW.01 TCGA.DJ.A3V3.01 TCGA.EL.A3T1.11 TCGA.BJ.A0ZC.01
#> NA NA NA NA "0232" "0221"
#> TCGA.EM.A2OV.01 TCGA.EL.A3GY.01 TCGA.EM.A3SY.01 TCGA.EM.A3AI.01 TCGA.EM.A2OY.01 TCGA.EL.A3T8.01
#> "0222" NA NA "0222" "0223" NA
#> TCGA.BJ.A18Y.01 TCGA.EL.A3GP.01 TCGA.EM.A2CK.01 TCGA.EL.A3T7.11 TCGA.BJ.A192.01 TCGA.BJ.A191.01
#> NA NA NA NA "0223" NA
#> TCGA.EM.A2CP.01 TCGA.EM.A22O.01 TCGA.EM.A2P1.01 TCGA.J8.A3YH.01 TCGA.DJ.A3UZ.01 TCGA.IM.A3EB.01
#> "0231" NA NA NA "0222" NA
#> TCGA.BJ.A3F0.01 TCGA.EL.A3GX.01 TCGA.EM.A3AK.01 TCGA.DO.A1JZ.01 TCGA.FY.A3YR.01 TCGA.DO.A1K0.01
#> "0241" NA NA NA NA NA
#> TCGA.DJ.A3V5.01 TCGA.EM.A3AJ.01 TCGA.IM.A3ED.01 TCGA.EM.A3AO.01 TCGA.EM.A2P1.06 TCGA.EM.A1CW.01
#> NA "0232" NA NA NA "0222"
#> TCGA.FK.A3SE.01 TCGA.EL.A3T7.01 TCGA.EM.A2P2.01 TCGA.EM.A1CU.11 TCGA.EL.A3T0.11 TCGA.E8.A3X7.01
#> NA NA NA NA NA NA
#> TCGA.ET.A3BQ.01 TCGA.EM.A1CS.01 TCGA.EL.A3GQ.01 TCGA.EL.A3H5.01 TCGA.DJ.A3V4.01 TCGA.EM.A2P3.01
#> NA NA NA NA NA NA
#> TCGA.FY.A3WA.01 TCGA.DJ.A3V2.01 TCGA.FY.A3TY.11 TCGA.BJ.A290.01 TCGA.EM.A3SU.01 TCGA.EL.A3D0.01
#> "0223" NA NA NA NA NA
#> TCGA.EM.A1CT.11 TCGA.EL.A3GR.01 TCGA.J8.A3YH.06 TCGA.EM.A3ST.11 TCGA.ET.A3DV.01 TCGA.BJ.A3EZ.01
#> NA NA NA NA "0241" NA
#> TCGA.J8.A3YD.01 TCGA.EM.A3SU.06 TCGA.EM.A3AL.01 TCGA.DJ.A3US.01 TCGA.EM.A1CS.11 TCGA.EM.A1CW.11
#> "0222" NA "0241" NA NA NA
#> TCGA.BJ.A190.01 TCGA.EM.A2OZ.01 TCGA.EM.A1CV.11 TCGA.EM.A1CU.01 TCGA.EM.A3AN.01 TCGA.E8.A2EA.01
#> "0221" NA NA NA NA NA
#> TCGA.EM.A1CV.01 TCGA.EM.A1CT.01 TCGA.EM.A3ST.01 TCGA.ET.A3BS.01 TCGA.EL.A3GO.01 TCGA.DJ.A2Q0.01
#> NA NA "0244" NA "0241" "0223"
#> TCGA.EL.A3D6.01 TCGA.DJ.A3UN.01 TCGA.DJ.A3UU.01 TCGA.FK.A3SD.01 TCGA.DJ.A2PO.01 TCGA.DJ.A3UQ.01
#> NA NA NA "0241" NA NA
#> TCGA.EM.A1YE.11 TCGA.EL.A3T2.11 TCGA.EL.A3CL.01 TCGA.EM.A1YC.01 TCGA.DJ.A3UP.01 TCGA.EL.A3T0.01
#> NA NA NA "0223" NA NA
#> TCGA.IM.A3U2.01 TCGA.IM.A3U3.01 TCGA.DJ.A3UX.01 TCGA.ET.A3BW.01 TCGA.ET.A39S.01 TCGA.ET.A3BP.01
#> NA NA NA NA NA NA
#> TCGA.DJ.A1QE.01 TCGA.EL.A3D4.01 TCGA.FK.A3SB.01 TCGA.EL.A3CW.01 TCGA.ET.A39L.01 TCGA.DJ.A2PW.01
#> NA NA NA "0232" NA NA
#> TCGA.EM.A2CO.01 TCGA.FE.A232.01 TCGA.DJ.A3UR.01 TCGA.DJ.A2PP.01 TCGA.ET.A3DQ.01 TCGA.ET.A3DS.01
#> "0222" NA NA "0242" "0232" "0222"
#> TCGA.FY.A3W9.01 TCGA.FK.A3S3.01 TCGA.ET.A2MZ.01 TCGA.BJ.A2NA.11 TCGA.DJ.A1QL.01 TCGA.EL.A3CS.01
#> "0244" NA NA "0233" "0242" NA
#> TCGA.FE.A233.01 TCGA.EM.A1YD.11 TCGA.ET.A3DW.11 TCGA.EL.A3T9.01 TCGA.DJ.A3UM.01 TCGA.DO.A2HM.01
#> NA NA NA NA NA NA
#> TCGA.FY.A3BL.01 TCGA.EL.A3TA.11 TCGA.ET.A3BX.01 TCGA.DJ.A1QQ.01 TCGA.DJ.A1QF.01 TCGA.DJ.A1QO.01
#> NA NA NA NA NA NA
#> TCGA.BJ.A2NA.01 TCGA.EM.A1YE.01 TCGA.FY.A2QD.01 TCGA.ET.A39J.01 TCGA.ET.A3DU.01 TCGA.EL.A3CM.01
#> NA "0223" "0241" NA NA NA
#> TCGA.DJ.A3UO.01 TCGA.ET.A39P.01 TCGA.DJ.A2Q2.01 TCGA.BJ.A28V.01 TCGA.ET.A3BO.01 TCGA.EL.A3T1.01
#> NA NA "0222" "0241" NA NA
#> TCGA.DJ.A1QI.01 TCGA.EL.A3TB.01 TCGA.BJ.A28X.11 TCGA.DJ.A1QN.01 TCGA.FE.A230.01 TCGA.FE.A234.01
#> NA NA "0231" NA NA NA
#> TCGA.ET.A39R.01 TCGA.DJ.A1QG.01 TCGA.EL.A3CV.01 TCGA.FE.A231.01 TCGA.EL.A3TA.01 TCGA.DJ.A3UY.01
#> NA NA NA NA NA NA
#> TCGA.DJ.A2Q1.01 TCGA.EL.A3CU.01 TCGA.EL.A3TB.11 TCGA.ET.A39I.01 TCGA.EM.A1YB.01 TCGA.DJ.A3UV.01
#> NA NA NA NA "0241" NA
#> TCGA.DJ.A3UT.01 TCGA.ET.A3DW.01 TCGA.ET.A3BT.01 TCGA.EL.A3T3.01 TCGA.DJ.A1QM.01 TCGA.EL.A3CY.01
#> NA NA NA NA NA "0231"
#> TCGA.ET.A39O.01 TCGA.EM.A1YC.11 TCGA.DJ.A1QH.01 TCGA.EL.A3T3.11 TCGA.EL.A3CX.01 TCGA.EL.A3T2.01
#> NA NA NA NA NA NA
#> TCGA.EM.A22P.01 TCGA.EL.A3T8.11 TCGA.DJ.A2PU.01 TCGA.DJ.A3UK.01 TCGA.ET.A3DO.01 TCGA.EM.A1YA.01
#> NA NA NA NA NA "0223"
#> TCGA.ET.A3BV.01 TCGA.EL.A3CO.01 TCGA.DJ.A2PN.01 TCGA.FK.A3SG.01 TCGA.FK.A3SH.01 TCGA.EM.A1YD.01
#> NA "0233" NA NA NA "0223"
#> TCGA.DJ.A1QD.01 TCGA.EL.A3CZ.01 TCGA.BJ.A0Z9.01 TCGA.CE.A13K.01 TCGA.EM.A3FR.01 TCGA.EM.A3O8.01
#> NA "0222" NA NA "0241" NA
#> TCGA.FY.A3R6.01 TCGA.FY.A3R9.01 TCGA.EL.A3D1.01 TCGA.EM.A3O6.01 TCGA.BJ.A0Z5.01 TCGA.BJ.A28S.01
#> NA "0222" NA "0222" NA NA
#> TCGA.BJ.A0ZH.01 TCGA.ET.A3DT.01 TCGA.H2.A3RI.11 TCGA.DJ.A13W.01 TCGA.DJ.A13T.01 TCGA.BJ.A0ZA.01
#> NA NA NA "0241" NA "0241"
#> TCGA.BJ.A3PT.01 TCGA.FE.A3PD.01 TCGA.BJ.A0ZF.01 TCGA.ET.A39M.01 TCGA.BJ.A0ZJ.01 TCGA.BJ.A0YZ.01
#> NA NA "0224" NA NA "0221"
#> TCGA.FE.A3PC.01 TCGA.DJ.A2QB.01 TCGA.EM.A3OB.01 TCGA.H2.A3RH.01 TCGA.ET.A39T.01 TCGA.DJ.A2PV.01
#> NA NA NA NA NA NA
#> TCGA.BJ.A3PR.11 TCGA.EL.A3T6.11 TCGA.DJ.A13X.01 TCGA.BJ.A0ZG.01 TCGA.EL.A3T6.01 TCGA.BJ.A0Z0.01
#> "0232" "0233" NA "0221" NA "0242"
#> TCGA.ET.A39K.01 TCGA.EM.A3O9.01 TCGA.BJ.A3PU.01 TCGA.BJ.A3PR.01 TCGA.EM.A3O3.01 TCGA.BJ.A0ZB.01
#> NA "0234" NA "0231" NA NA
#> TCGA.EM.A3OA.01 TCGA.DJ.A2PR.01 TCGA.DJ.A13L.01 TCGA.FY.A3ON.01 TCGA.DJ.A13V.01 TCGA.FY.A3R8.01
#> "0241" NA NA NA NA NA
#> TCGA.EL.A3CP.01 TCGA.DJ.A13U.01 TCGA.DE.A0Y3.01 TCGA.ET.A2N4.01 TCGA.DJ.A13P.01 TCGA.BJ.A0ZE.01
#> NA NA NA NA NA NA
#> TCGA.EM.A3O7.01 TCGA.DJ.A13O.01 TCGA.FY.A3RA.01 TCGA.DJ.A13M.01 TCGA.DJ.A13R.01 TCGA.ET.A3DR.01
#> NA "0233" NA NA "0221" NA
#> TCGA.FE.A3PB.01 TCGA.ET.A3BN.01 TCGA.H2.A3RI.01 TCGA.ET.A39N.01 TCGA.BJ.A3PU.11 TCGA.FY.A3R7.01
#> NA NA NA "0224" NA "0222"
#> TCGA.FE.A3PA.01 TCGA.EM.A2CN.01 TCGA.BJ.A0Z2.01 TCGA.FY.A3I5.01 TCGA.DJ.A13S.01 TCGA.DE.A0Y2.01
#> NA "0243" "0243" "0241" NA NA
#> TCGA.ET.A3BU.01
#> NA
get_classes(res_rh, merge_node = merge_node_param(min_n_signatures = 4441))
#> TCGA.E8.A416.01 TCGA.E8.A433.01 TCGA.EL.A4K9.01 TCGA.DJ.A3V9.01 TCGA.EL.A3ZO.11 TCGA.EL.A3ZN.01
#> NA NA NA NA NA NA
#> TCGA.KS.A41F.01 TCGA.EL.A3ZK.01 TCGA.ET.A40R.01 TCGA.EL.A3ZM.01 TCGA.ET.A2N3.01 TCGA.EL.A3ZQ.01
#> NA NA NA NA "0241" NA
#> TCGA.ET.A40T.01 TCGA.DE.A4MA.01 TCGA.EM.A4FU.01 TCGA.E8.A418.01 TCGA.DJ.A3VD.01 TCGA.DJ.A3VM.01
#> NA NA NA NA NA "0244"
#> TCGA.EL.A3ZG.01 TCGA.EM.A4FV.01 TCGA.E8.A413.01 TCGA.DJ.A3VG.01 TCGA.EL.A4K2.01 TCGA.IM.A420.01
#> NA NA NA NA "0222" NA
#> TCGA.KS.A41J.01 TCGA.EL.A3ZK.11 TCGA.J8.A3O2.01 TCGA.E8.A415.01 TCGA.FY.A40M.01 TCGA.DJ.A3VB.01
#> NA "0232" NA NA NA NA
#> TCGA.KS.A41I.01 TCGA.DJ.A3VL.01 TCGA.ET.A4KQ.01 TCGA.H2.A421.01 TCGA.EL.A3ZO.01 TCGA.KS.A4I3.01
#> NA "0234" NA NA NA NA
#> TCGA.DJ.A4UT.01 TCGA.DE.A4MD.01 TCGA.EL.A4JW.01 TCGA.DJ.A3VI.01 TCGA.DJ.A3VA.01 TCGA.L6.A4ET.01
#> NA NA NA NA NA NA
#> TCGA.E8.A419.01 TCGA.DJ.A4V0.01 TCGA.DJ.A4V2.01 TCGA.ET.A40Q.01 TCGA.EL.A3ZS.01 TCGA.KS.A4ID.01
#> NA "0232" NA NA NA NA
#> TCGA.EL.A3ZL.11 TCGA.J8.A3YE.01 TCGA.EL.A4K7.01 TCGA.DJ.A3VF.01 TCGA.EM.A4FH.01 TCGA.E8.A432.01
#> NA NA NA NA "0221" NA
#> TCGA.J8.A3O2.06 TCGA.ET.A2MX.01 TCGA.ET.A40S.01 TCGA.DE.A4M8.01 TCGA.IM.A41Z.01 TCGA.EL.A4KD.01
#> NA NA NA NA "0241" NA
#> TCGA.DJ.A3V7.01 TCGA.FY.A40L.01 TCGA.DE.A4M9.01 TCGA.J8.A42S.01 TCGA.KS.A41L.01 TCGA.EM.A4FN.01
#> NA NA "0221" NA "0224" NA
#> TCGA.EL.A4K1.01 TCGA.KS.A4IC.01 TCGA.E8.A414.01 TCGA.H2.A422.01 TCGA.J8.A3YF.01 TCGA.EL.A4KI.01
#> NA NA NA NA NA "0243"
#> TCGA.EM.A4G1.01 TCGA.DJ.A3VJ.01 TCGA.DE.A4MD.06 TCGA.EL.A3ZP.01 TCGA.EM.A4FQ.01 TCGA.EL.A3ZT.01
#> NA NA NA NA NA NA
#> TCGA.DJ.A4V4.01 TCGA.FY.A40K.01 TCGA.L6.A4EQ.01 TCGA.DJ.A3VE.01 TCGA.E8.A434.01 TCGA.EL.A3ZH.01
#> NA NA NA NA "0222" "0222"
#> TCGA.EM.A4FR.01 TCGA.EL.A3ZH.11 TCGA.EL.A3ZR.01 TCGA.DJ.A3V8.01 TCGA.EL.A3ZG.11 TCGA.ET.A40P.01
#> NA NA NA NA NA NA
#> TCGA.DE.A4MB.01 TCGA.MK.A4N6.01 TCGA.DJ.A3VK.01 TCGA.E8.A417.01 TCGA.L6.A4EU.01 TCGA.J8.A4HY.01
#> NA NA NA NA NA NA
#> TCGA.EL.A3ZL.01 TCGA.EL.A3ZP.11 TCGA.FY.A40N.01 TCGA.J8.A4HW.01 TCGA.BJ.A45J.01 TCGA.CE.A482.01
#> NA "0232" NA NA NA NA
#> TCGA.DJ.A2Q6.01 TCGA.DJ.A2PX.01 TCGA.DJ.A4UL.01 TCGA.EL.A4JX.01 TCGA.BJ.A2N8.11 TCGA.DJ.A2Q5.01
#> NA NA NA NA NA NA
#> TCGA.EL.A4KG.01 TCGA.DJ.A4UP.01 TCGA.E8.A438.01 TCGA.EL.A3H2.01 TCGA.EM.A3AP.01 TCGA.DJ.A2PQ.01
#> NA NA NA "0221" NA NA
#> TCGA.L6.A4EP.01 TCGA.FY.A4B4.01 TCGA.EL.A4KH.01 TCGA.BJ.A45E.01 TCGA.DJ.A4V5.01 TCGA.DE.A4MC.01
#> NA NA NA "0231" NA NA
#> TCGA.E8.A44M.01 TCGA.BJ.A45K.01 TCGA.E3.A3DZ.01 TCGA.E3.A3E2.01 TCGA.BJ.A45H.01 TCGA.E8.A44K.01
#> NA "0242" NA NA NA NA
#> TCGA.ET.A2MY.01 TCGA.EL.A3H8.01 TCGA.BJ.A45C.01 TCGA.BJ.A45G.01 TCGA.EL.A4JZ.01 TCGA.CE.A481.01
#> NA NA "0242" NA NA NA
#> TCGA.KS.A4I9.01 TCGA.EL.A3MW.01 TCGA.E8.A436.01 TCGA.E3.A3DY.01 TCGA.DJ.A2Q3.01 TCGA.BJ.A2P4.01
#> NA NA NA NA NA NA
#> TCGA.CE.A484.01 TCGA.ET.A2N1.01 TCGA.DJ.A2Q4.01 TCGA.DJ.A2PZ.01 TCGA.BJ.A45F.01 TCGA.IM.A4EB.01
#> NA NA NA NA NA NA
#> TCGA.EM.A4FO.01 TCGA.FY.A4B3.01 TCGA.FY.A4B0.01 TCGA.BJ.A45I.01 TCGA.E3.A3E3.01 TCGA.EM.A3AQ.01
#> NA NA "0242" NA NA NA
#> TCGA.EL.A3N3.01 TCGA.DJ.A2Q9.01 TCGA.EM.A4FM.01 TCGA.EL.A4K6.01 TCGA.MK.A4N9.01 TCGA.KS.A4I1.01
#> NA "0231" NA "0243" NA NA
#> TCGA.DJ.A2PS.01 TCGA.CE.A3MD.01 TCGA.E3.A3E5.01 TCGA.EL.A3CN.01 TCGA.J8.A4HW.06 TCGA.EM.A4FK.01
#> NA NA NA NA NA "0241"
#> TCGA.E8.A437.01 TCGA.BJ.A4O8.01 TCGA.EL.A3MW.11 TCGA.E3.A3E0.01 TCGA.BJ.A45D.01 TCGA.CE.A483.01
#> NA NA NA NA NA NA
#> TCGA.CE.A485.01 TCGA.DJ.A4UR.01 TCGA.IM.A41Y.01 TCGA.ET.A4KN.01 TCGA.KS.A4I5.01 TCGA.DJ.A4UQ.01
#> NA "0244" NA NA NA NA
#> TCGA.KS.A4IB.01 TCGA.EL.A3N2.11 TCGA.BJ.A2N9.01 TCGA.DJ.A4UW.01 TCGA.EL.A3GZ.11 TCGA.EM.A3AR.01
#> NA NA "0222" NA NA NA
#> TCGA.EL.A3N3.11 TCGA.DE.A3KN.01 TCGA.DJ.A2QA.01 TCGA.EL.A4JV.01 TCGA.EM.A4FF.01 TCGA.EL.A4K0.01
#> "0232" NA NA NA NA NA
#> TCGA.FK.A4UB.01 TCGA.BJ.A4O9.01 TCGA.BJ.A2N7.01 TCGA.DE.A2OL.01 TCGA.CE.A3ME.01 TCGA.MK.A4N7.01
#> NA NA NA "0241" NA NA
#> TCGA.EL.A3H2.11 TCGA.EL.A4K4.01 TCGA.EL.A3GS.01 TCGA.EL.A3GZ.01 TCGA.E3.A3E1.01 TCGA.DJ.A2Q8.01
#> NA NA NA NA NA NA
#> TCGA.EL.A3N2.01 TCGA.KS.A4I7.01 TCGA.MK.A84Z.01 TCGA.ET.A3DP.11 TCGA.EL.A3MX.11 TCGA.ET.A25G.01
#> NA NA NA NA NA NA
#> TCGA.EM.A3FK.01 TCGA.EM.A2CS.01 TCGA.FE.A23A.01 TCGA.BJ.A28T.11 TCGA.EM.A22J.01 TCGA.EL.A3MX.01
#> NA NA NA NA "0241" NA
#> TCGA.FY.A3I4.01 TCGA.BJ.A28W.11 TCGA.ET.A25R.01 TCGA.BJ.A2N8.01 TCGA.FY.A76V.01 TCGA.EM.A3FN.01
#> NA "0232" NA NA NA "0241"
#> TCGA.QD.A8IV.01 TCGA.EM.A3FJ.01 TCGA.ET.A2MY.11 TCGA.EM.A3FQ.06 TCGA.ET.A25P.01 TCGA.ET.A2N0.01
#> NA NA "0241" NA NA NA
#> TCGA.EM.A2CT.01 TCGA.FE.A235.01 TCGA.ET.A25M.01 TCGA.EL.A3MY.01 TCGA.DE.A7U5.01 TCGA.E8.A2JQ.11
#> "0222" NA NA NA NA "0231"
#> TCGA.ET.A3DP.01 TCGA.EM.A2CL.01 TCGA.ET.A2N5.01 TCGA.ET.A25J.11 TCGA.DE.A69J.01 TCGA.BJ.A28R.11
#> NA "0242" NA NA NA "0232"
#> TCGA.ET.A25K.01 TCGA.EL.A3GV.01 TCGA.GE.A2C6.01 TCGA.EM.A3FM.01 TCGA.EL.A3H7.11 TCGA.FE.A22Z.01
#> NA NA NA NA NA NA
#> TCGA.H2.A2K9.01 TCGA.EM.A22Q.01 TCGA.EM.A3FP.01 TCGA.GE.A2C6.11 TCGA.EL.A3MZ.01 TCGA.DJ.A2PT.01
#> "0243" "0242" NA "0232" NA NA
#> TCGA.E8.A242.01 TCGA.ET.A25L.01 TCGA.CE.A27D.01 TCGA.EL.A3H1.11 TCGA.BJ.A2N7.11 TCGA.DJ.A2Q7.01
#> NA NA "0233" "0233" NA NA
#> TCGA.J8.A3O1.01 TCGA.EM.A2CR.01 TCGA.DE.A69K.01 TCGA.EM.A2CQ.01 TCGA.FE.A238.01 TCGA.EL.A3H1.01
#> NA NA NA "0222" NA "0241"
#> TCGA.BJ.A28W.01 TCGA.BJ.A28T.01 TCGA.EM.A2CJ.01 TCGA.EM.A3FQ.01 TCGA.4C.A93U.01 TCGA.EM.A22M.01
#> "0231" "0232" "0223" NA NA NA
#> TCGA.J8.A3NZ.01 TCGA.EM.A22K.01 TCGA.FE.A236.01 TCGA.BJ.A28R.01 TCGA.EM.A2CU.01 TCGA.ET.A25N.01
#> NA NA NA NA NA NA
#> TCGA.EL.A3H7.01 TCGA.FY.A3NM.01 TCGA.EM.A3FO.01 TCGA.EM.A22L.01 TCGA.BJ.A2N9.11 TCGA.BJ.A291.01
#> NA "0223" NA NA "0231" "0222"
#> TCGA.ET.A2N5.11 TCGA.ET.A25N.11 TCGA.J8.A3O0.01 TCGA.FE.A237.01 TCGA.DJ.A2QC.01 TCGA.ET.A25O.01
#> NA NA "0243" NA NA NA
#> TCGA.EL.A3GU.01 TCGA.EL.A3MY.11 TCGA.DJ.A2PY.01 TCGA.EM.A2CS.06 TCGA.FY.A3NP.01 TCGA.ET.A25I.01
#> NA "0221" NA NA NA "0222"
#> TCGA.H2.A26U.01 TCGA.BJ.A290.11 TCGA.EM.A22I.01 TCGA.FE.A239.01 TCGA.BJ.A28Z.01 TCGA.DE.A0XZ.01
#> NA NA NA "0242" NA NA
#> TCGA.ET.A25J.01 TCGA.EM.A22N.01 TCGA.EM.A2CM.01 TCGA.FY.A3NN.01 TCGA.EM.A3FL.01 TCGA.H2.A2K9.11
#> NA "0222" "0244" NA "0223" "0233"
#> TCGA.EL.A3H3.01 TCGA.EL.A3H4.01 TCGA.EM.A2OX.01 TCGA.EM.A3SX.01 TCGA.BJ.A0Z3.01 TCGA.BJ.A28X.01
#> NA NA NA NA NA NA
#> TCGA.EL.A3CT.01 TCGA.EL.A3CR.01 TCGA.FY.A3TY.01 TCGA.J8.A3YG.01 TCGA.DJ.A3V6.01 TCGA.EM.A3SZ.01
#> NA NA "0233" NA NA NA
#> TCGA.EM.A2OW.01 TCGA.DO.A1JZ.11 TCGA.EL.A3D5.01 TCGA.EM.A2P0.01 TCGA.E8.A2JQ.01 TCGA.BJ.A18Z.01
#> "0222" NA NA NA NA NA
#> TCGA.DJ.A3V0.01 TCGA.EL.A3GW.01 TCGA.DJ.A3UW.01 TCGA.DJ.A3V3.01 TCGA.EL.A3T1.11 TCGA.BJ.A0ZC.01
#> NA NA NA NA "0232" "0221"
#> TCGA.EM.A2OV.01 TCGA.EL.A3GY.01 TCGA.EM.A3SY.01 TCGA.EM.A3AI.01 TCGA.EM.A2OY.01 TCGA.EL.A3T8.01
#> "0222" NA NA "0222" "0223" NA
#> TCGA.BJ.A18Y.01 TCGA.EL.A3GP.01 TCGA.EM.A2CK.01 TCGA.EL.A3T7.11 TCGA.BJ.A192.01 TCGA.BJ.A191.01
#> NA NA NA NA "0223" NA
#> TCGA.EM.A2CP.01 TCGA.EM.A22O.01 TCGA.EM.A2P1.01 TCGA.J8.A3YH.01 TCGA.DJ.A3UZ.01 TCGA.IM.A3EB.01
#> "0231" NA NA NA "0222" NA
#> TCGA.BJ.A3F0.01 TCGA.EL.A3GX.01 TCGA.EM.A3AK.01 TCGA.DO.A1JZ.01 TCGA.FY.A3YR.01 TCGA.DO.A1K0.01
#> "0241" NA NA NA NA NA
#> TCGA.DJ.A3V5.01 TCGA.EM.A3AJ.01 TCGA.IM.A3ED.01 TCGA.EM.A3AO.01 TCGA.EM.A2P1.06 TCGA.EM.A1CW.01
#> NA "0232" NA NA NA "0222"
#> TCGA.FK.A3SE.01 TCGA.EL.A3T7.01 TCGA.EM.A2P2.01 TCGA.EM.A1CU.11 TCGA.EL.A3T0.11 TCGA.E8.A3X7.01
#> NA NA NA NA NA NA
#> TCGA.ET.A3BQ.01 TCGA.EM.A1CS.01 TCGA.EL.A3GQ.01 TCGA.EL.A3H5.01 TCGA.DJ.A3V4.01 TCGA.EM.A2P3.01
#> NA NA NA NA NA NA
#> TCGA.FY.A3WA.01 TCGA.DJ.A3V2.01 TCGA.FY.A3TY.11 TCGA.BJ.A290.01 TCGA.EM.A3SU.01 TCGA.EL.A3D0.01
#> "0223" NA NA NA NA NA
#> TCGA.EM.A1CT.11 TCGA.EL.A3GR.01 TCGA.J8.A3YH.06 TCGA.EM.A3ST.11 TCGA.ET.A3DV.01 TCGA.BJ.A3EZ.01
#> NA NA NA NA "0241" NA
#> TCGA.J8.A3YD.01 TCGA.EM.A3SU.06 TCGA.EM.A3AL.01 TCGA.DJ.A3US.01 TCGA.EM.A1CS.11 TCGA.EM.A1CW.11
#> "0222" NA "0241" NA NA NA
#> TCGA.BJ.A190.01 TCGA.EM.A2OZ.01 TCGA.EM.A1CV.11 TCGA.EM.A1CU.01 TCGA.EM.A3AN.01 TCGA.E8.A2EA.01
#> "0221" NA NA NA NA NA
#> TCGA.EM.A1CV.01 TCGA.EM.A1CT.01 TCGA.EM.A3ST.01 TCGA.ET.A3BS.01 TCGA.EL.A3GO.01 TCGA.DJ.A2Q0.01
#> NA NA "0244" NA "0241" "0223"
#> TCGA.EL.A3D6.01 TCGA.DJ.A3UN.01 TCGA.DJ.A3UU.01 TCGA.FK.A3SD.01 TCGA.DJ.A2PO.01 TCGA.DJ.A3UQ.01
#> NA NA NA "0241" NA NA
#> TCGA.EM.A1YE.11 TCGA.EL.A3T2.11 TCGA.EL.A3CL.01 TCGA.EM.A1YC.01 TCGA.DJ.A3UP.01 TCGA.EL.A3T0.01
#> NA NA NA "0223" NA NA
#> TCGA.IM.A3U2.01 TCGA.IM.A3U3.01 TCGA.DJ.A3UX.01 TCGA.ET.A3BW.01 TCGA.ET.A39S.01 TCGA.ET.A3BP.01
#> NA NA NA NA NA NA
#> TCGA.DJ.A1QE.01 TCGA.EL.A3D4.01 TCGA.FK.A3SB.01 TCGA.EL.A3CW.01 TCGA.ET.A39L.01 TCGA.DJ.A2PW.01
#> NA NA NA "0232" NA NA
#> TCGA.EM.A2CO.01 TCGA.FE.A232.01 TCGA.DJ.A3UR.01 TCGA.DJ.A2PP.01 TCGA.ET.A3DQ.01 TCGA.ET.A3DS.01
#> "0222" NA NA "0242" "0232" "0222"
#> TCGA.FY.A3W9.01 TCGA.FK.A3S3.01 TCGA.ET.A2MZ.01 TCGA.BJ.A2NA.11 TCGA.DJ.A1QL.01 TCGA.EL.A3CS.01
#> "0244" NA NA "0233" "0242" NA
#> TCGA.FE.A233.01 TCGA.EM.A1YD.11 TCGA.ET.A3DW.11 TCGA.EL.A3T9.01 TCGA.DJ.A3UM.01 TCGA.DO.A2HM.01
#> NA NA NA NA NA NA
#> TCGA.FY.A3BL.01 TCGA.EL.A3TA.11 TCGA.ET.A3BX.01 TCGA.DJ.A1QQ.01 TCGA.DJ.A1QF.01 TCGA.DJ.A1QO.01
#> NA NA NA NA NA NA
#> TCGA.BJ.A2NA.01 TCGA.EM.A1YE.01 TCGA.FY.A2QD.01 TCGA.ET.A39J.01 TCGA.ET.A3DU.01 TCGA.EL.A3CM.01
#> NA "0223" "0241" NA NA NA
#> TCGA.DJ.A3UO.01 TCGA.ET.A39P.01 TCGA.DJ.A2Q2.01 TCGA.BJ.A28V.01 TCGA.ET.A3BO.01 TCGA.EL.A3T1.01
#> NA NA "0222" "0241" NA NA
#> TCGA.DJ.A1QI.01 TCGA.EL.A3TB.01 TCGA.BJ.A28X.11 TCGA.DJ.A1QN.01 TCGA.FE.A230.01 TCGA.FE.A234.01
#> NA NA "0231" NA NA NA
#> TCGA.ET.A39R.01 TCGA.DJ.A1QG.01 TCGA.EL.A3CV.01 TCGA.FE.A231.01 TCGA.EL.A3TA.01 TCGA.DJ.A3UY.01
#> NA NA NA NA NA NA
#> TCGA.DJ.A2Q1.01 TCGA.EL.A3CU.01 TCGA.EL.A3TB.11 TCGA.ET.A39I.01 TCGA.EM.A1YB.01 TCGA.DJ.A3UV.01
#> NA NA NA NA "0241" NA
#> TCGA.DJ.A3UT.01 TCGA.ET.A3DW.01 TCGA.ET.A3BT.01 TCGA.EL.A3T3.01 TCGA.DJ.A1QM.01 TCGA.EL.A3CY.01
#> NA NA NA NA NA "0231"
#> TCGA.ET.A39O.01 TCGA.EM.A1YC.11 TCGA.DJ.A1QH.01 TCGA.EL.A3T3.11 TCGA.EL.A3CX.01 TCGA.EL.A3T2.01
#> NA NA NA NA NA NA
#> TCGA.EM.A22P.01 TCGA.EL.A3T8.11 TCGA.DJ.A2PU.01 TCGA.DJ.A3UK.01 TCGA.ET.A3DO.01 TCGA.EM.A1YA.01
#> NA NA NA NA NA "0223"
#> TCGA.ET.A3BV.01 TCGA.EL.A3CO.01 TCGA.DJ.A2PN.01 TCGA.FK.A3SG.01 TCGA.FK.A3SH.01 TCGA.EM.A1YD.01
#> NA "0233" NA NA NA "0223"
#> TCGA.DJ.A1QD.01 TCGA.EL.A3CZ.01 TCGA.BJ.A0Z9.01 TCGA.CE.A13K.01 TCGA.EM.A3FR.01 TCGA.EM.A3O8.01
#> NA "0222" NA NA "0241" NA
#> TCGA.FY.A3R6.01 TCGA.FY.A3R9.01 TCGA.EL.A3D1.01 TCGA.EM.A3O6.01 TCGA.BJ.A0Z5.01 TCGA.BJ.A28S.01
#> NA "0222" NA "0222" NA NA
#> TCGA.BJ.A0ZH.01 TCGA.ET.A3DT.01 TCGA.H2.A3RI.11 TCGA.DJ.A13W.01 TCGA.DJ.A13T.01 TCGA.BJ.A0ZA.01
#> NA NA NA "0241" NA "0241"
#> TCGA.BJ.A3PT.01 TCGA.FE.A3PD.01 TCGA.BJ.A0ZF.01 TCGA.ET.A39M.01 TCGA.BJ.A0ZJ.01 TCGA.BJ.A0YZ.01
#> NA NA "0224" NA NA "0221"
#> TCGA.FE.A3PC.01 TCGA.DJ.A2QB.01 TCGA.EM.A3OB.01 TCGA.H2.A3RH.01 TCGA.ET.A39T.01 TCGA.DJ.A2PV.01
#> NA NA NA NA NA NA
#> TCGA.BJ.A3PR.11 TCGA.EL.A3T6.11 TCGA.DJ.A13X.01 TCGA.BJ.A0ZG.01 TCGA.EL.A3T6.01 TCGA.BJ.A0Z0.01
#> "0232" "0233" NA "0221" NA "0242"
#> TCGA.ET.A39K.01 TCGA.EM.A3O9.01 TCGA.BJ.A3PU.01 TCGA.BJ.A3PR.01 TCGA.EM.A3O3.01 TCGA.BJ.A0ZB.01
#> NA "0234" NA "0231" NA NA
#> TCGA.EM.A3OA.01 TCGA.DJ.A2PR.01 TCGA.DJ.A13L.01 TCGA.FY.A3ON.01 TCGA.DJ.A13V.01 TCGA.FY.A3R8.01
#> "0241" NA NA NA NA NA
#> TCGA.EL.A3CP.01 TCGA.DJ.A13U.01 TCGA.DE.A0Y3.01 TCGA.ET.A2N4.01 TCGA.DJ.A13P.01 TCGA.BJ.A0ZE.01
#> NA NA NA NA NA NA
#> TCGA.EM.A3O7.01 TCGA.DJ.A13O.01 TCGA.FY.A3RA.01 TCGA.DJ.A13M.01 TCGA.DJ.A13R.01 TCGA.ET.A3DR.01
#> NA "0233" NA NA "0221" NA
#> TCGA.FE.A3PB.01 TCGA.ET.A3BN.01 TCGA.H2.A3RI.01 TCGA.ET.A39N.01 TCGA.BJ.A3PU.11 TCGA.FY.A3R7.01
#> NA NA NA "0224" NA "0222"
#> TCGA.FE.A3PA.01 TCGA.EM.A2CN.01 TCGA.BJ.A0Z2.01 TCGA.FY.A3I5.01 TCGA.DJ.A13S.01 TCGA.DE.A0Y2.01
#> NA "0243" "0243" "0241" NA NA
#> TCGA.ET.A3BU.01
#> NA
get_classes(res_rh, merge_node = merge_node_param(min_n_signatures = 5878))
#> TCGA.E8.A416.01 TCGA.E8.A433.01 TCGA.EL.A4K9.01 TCGA.DJ.A3V9.01 TCGA.EL.A3ZO.11 TCGA.EL.A3ZN.01
#> NA NA NA NA NA NA
#> TCGA.KS.A41F.01 TCGA.EL.A3ZK.01 TCGA.ET.A40R.01 TCGA.EL.A3ZM.01 TCGA.ET.A2N3.01 TCGA.EL.A3ZQ.01
#> NA NA NA NA "0241" NA
#> TCGA.ET.A40T.01 TCGA.DE.A4MA.01 TCGA.EM.A4FU.01 TCGA.E8.A418.01 TCGA.DJ.A3VD.01 TCGA.DJ.A3VM.01
#> NA NA NA NA NA "0244"
#> TCGA.EL.A3ZG.01 TCGA.EM.A4FV.01 TCGA.E8.A413.01 TCGA.DJ.A3VG.01 TCGA.EL.A4K2.01 TCGA.IM.A420.01
#> NA NA NA NA NA NA
#> TCGA.KS.A41J.01 TCGA.EL.A3ZK.11 TCGA.J8.A3O2.01 TCGA.E8.A415.01 TCGA.FY.A40M.01 TCGA.DJ.A3VB.01
#> NA "0232" NA NA NA NA
#> TCGA.KS.A41I.01 TCGA.DJ.A3VL.01 TCGA.ET.A4KQ.01 TCGA.H2.A421.01 TCGA.EL.A3ZO.01 TCGA.KS.A4I3.01
#> NA "0234" NA NA NA NA
#> TCGA.DJ.A4UT.01 TCGA.DE.A4MD.01 TCGA.EL.A4JW.01 TCGA.DJ.A3VI.01 TCGA.DJ.A3VA.01 TCGA.L6.A4ET.01
#> NA NA NA NA NA NA
#> TCGA.E8.A419.01 TCGA.DJ.A4V0.01 TCGA.DJ.A4V2.01 TCGA.ET.A40Q.01 TCGA.EL.A3ZS.01 TCGA.KS.A4ID.01
#> NA "0232" NA NA NA NA
#> TCGA.EL.A3ZL.11 TCGA.J8.A3YE.01 TCGA.EL.A4K7.01 TCGA.DJ.A3VF.01 TCGA.EM.A4FH.01 TCGA.E8.A432.01
#> NA NA NA NA NA NA
#> TCGA.J8.A3O2.06 TCGA.ET.A2MX.01 TCGA.ET.A40S.01 TCGA.DE.A4M8.01 TCGA.IM.A41Z.01 TCGA.EL.A4KD.01
#> NA NA NA NA "0241" NA
#> TCGA.DJ.A3V7.01 TCGA.FY.A40L.01 TCGA.DE.A4M9.01 TCGA.J8.A42S.01 TCGA.KS.A41L.01 TCGA.EM.A4FN.01
#> NA NA NA NA NA NA
#> TCGA.EL.A4K1.01 TCGA.KS.A4IC.01 TCGA.E8.A414.01 TCGA.H2.A422.01 TCGA.J8.A3YF.01 TCGA.EL.A4KI.01
#> NA NA NA NA NA "0243"
#> TCGA.EM.A4G1.01 TCGA.DJ.A3VJ.01 TCGA.DE.A4MD.06 TCGA.EL.A3ZP.01 TCGA.EM.A4FQ.01 TCGA.EL.A3ZT.01
#> NA NA NA NA NA NA
#> TCGA.DJ.A4V4.01 TCGA.FY.A40K.01 TCGA.L6.A4EQ.01 TCGA.DJ.A3VE.01 TCGA.E8.A434.01 TCGA.EL.A3ZH.01
#> NA NA NA NA NA NA
#> TCGA.EM.A4FR.01 TCGA.EL.A3ZH.11 TCGA.EL.A3ZR.01 TCGA.DJ.A3V8.01 TCGA.EL.A3ZG.11 TCGA.ET.A40P.01
#> NA NA NA NA NA NA
#> TCGA.DE.A4MB.01 TCGA.MK.A4N6.01 TCGA.DJ.A3VK.01 TCGA.E8.A417.01 TCGA.L6.A4EU.01 TCGA.J8.A4HY.01
#> NA NA NA NA NA NA
#> TCGA.EL.A3ZL.01 TCGA.EL.A3ZP.11 TCGA.FY.A40N.01 TCGA.J8.A4HW.01 TCGA.BJ.A45J.01 TCGA.CE.A482.01
#> NA "0232" NA NA NA NA
#> TCGA.DJ.A2Q6.01 TCGA.DJ.A2PX.01 TCGA.DJ.A4UL.01 TCGA.EL.A4JX.01 TCGA.BJ.A2N8.11 TCGA.DJ.A2Q5.01
#> NA NA NA NA NA NA
#> TCGA.EL.A4KG.01 TCGA.DJ.A4UP.01 TCGA.E8.A438.01 TCGA.EL.A3H2.01 TCGA.EM.A3AP.01 TCGA.DJ.A2PQ.01
#> NA NA NA NA NA NA
#> TCGA.L6.A4EP.01 TCGA.FY.A4B4.01 TCGA.EL.A4KH.01 TCGA.BJ.A45E.01 TCGA.DJ.A4V5.01 TCGA.DE.A4MC.01
#> NA NA NA "0231" NA NA
#> TCGA.E8.A44M.01 TCGA.BJ.A45K.01 TCGA.E3.A3DZ.01 TCGA.E3.A3E2.01 TCGA.BJ.A45H.01 TCGA.E8.A44K.01
#> NA "0242" NA NA NA NA
#> TCGA.ET.A2MY.01 TCGA.EL.A3H8.01 TCGA.BJ.A45C.01 TCGA.BJ.A45G.01 TCGA.EL.A4JZ.01 TCGA.CE.A481.01
#> NA NA "0242" NA NA NA
#> TCGA.KS.A4I9.01 TCGA.EL.A3MW.01 TCGA.E8.A436.01 TCGA.E3.A3DY.01 TCGA.DJ.A2Q3.01 TCGA.BJ.A2P4.01
#> NA NA NA NA NA NA
#> TCGA.CE.A484.01 TCGA.ET.A2N1.01 TCGA.DJ.A2Q4.01 TCGA.DJ.A2PZ.01 TCGA.BJ.A45F.01 TCGA.IM.A4EB.01
#> NA NA NA NA NA NA
#> TCGA.EM.A4FO.01 TCGA.FY.A4B3.01 TCGA.FY.A4B0.01 TCGA.BJ.A45I.01 TCGA.E3.A3E3.01 TCGA.EM.A3AQ.01
#> NA NA "0242" NA NA NA
#> TCGA.EL.A3N3.01 TCGA.DJ.A2Q9.01 TCGA.EM.A4FM.01 TCGA.EL.A4K6.01 TCGA.MK.A4N9.01 TCGA.KS.A4I1.01
#> NA "0231" NA "0243" NA NA
#> TCGA.DJ.A2PS.01 TCGA.CE.A3MD.01 TCGA.E3.A3E5.01 TCGA.EL.A3CN.01 TCGA.J8.A4HW.06 TCGA.EM.A4FK.01
#> NA NA NA NA NA "0241"
#> TCGA.E8.A437.01 TCGA.BJ.A4O8.01 TCGA.EL.A3MW.11 TCGA.E3.A3E0.01 TCGA.BJ.A45D.01 TCGA.CE.A483.01
#> NA NA NA NA NA NA
#> TCGA.CE.A485.01 TCGA.DJ.A4UR.01 TCGA.IM.A41Y.01 TCGA.ET.A4KN.01 TCGA.KS.A4I5.01 TCGA.DJ.A4UQ.01
#> NA "0244" NA NA NA NA
#> TCGA.KS.A4IB.01 TCGA.EL.A3N2.11 TCGA.BJ.A2N9.01 TCGA.DJ.A4UW.01 TCGA.EL.A3GZ.11 TCGA.EM.A3AR.01
#> NA NA NA NA NA NA
#> TCGA.EL.A3N3.11 TCGA.DE.A3KN.01 TCGA.DJ.A2QA.01 TCGA.EL.A4JV.01 TCGA.EM.A4FF.01 TCGA.EL.A4K0.01
#> "0232" NA NA NA NA NA
#> TCGA.FK.A4UB.01 TCGA.BJ.A4O9.01 TCGA.BJ.A2N7.01 TCGA.DE.A2OL.01 TCGA.CE.A3ME.01 TCGA.MK.A4N7.01
#> NA NA NA "0241" NA NA
#> TCGA.EL.A3H2.11 TCGA.EL.A4K4.01 TCGA.EL.A3GS.01 TCGA.EL.A3GZ.01 TCGA.E3.A3E1.01 TCGA.DJ.A2Q8.01
#> NA NA NA NA NA NA
#> TCGA.EL.A3N2.01 TCGA.KS.A4I7.01 TCGA.MK.A84Z.01 TCGA.ET.A3DP.11 TCGA.EL.A3MX.11 TCGA.ET.A25G.01
#> NA NA NA NA NA NA
#> TCGA.EM.A3FK.01 TCGA.EM.A2CS.01 TCGA.FE.A23A.01 TCGA.BJ.A28T.11 TCGA.EM.A22J.01 TCGA.EL.A3MX.01
#> NA NA NA NA "0241" NA
#> TCGA.FY.A3I4.01 TCGA.BJ.A28W.11 TCGA.ET.A25R.01 TCGA.BJ.A2N8.01 TCGA.FY.A76V.01 TCGA.EM.A3FN.01
#> NA "0232" NA NA NA "0241"
#> TCGA.QD.A8IV.01 TCGA.EM.A3FJ.01 TCGA.ET.A2MY.11 TCGA.EM.A3FQ.06 TCGA.ET.A25P.01 TCGA.ET.A2N0.01
#> NA NA "0241" NA NA NA
#> TCGA.EM.A2CT.01 TCGA.FE.A235.01 TCGA.ET.A25M.01 TCGA.EL.A3MY.01 TCGA.DE.A7U5.01 TCGA.E8.A2JQ.11
#> NA NA NA NA NA "0231"
#> TCGA.ET.A3DP.01 TCGA.EM.A2CL.01 TCGA.ET.A2N5.01 TCGA.ET.A25J.11 TCGA.DE.A69J.01 TCGA.BJ.A28R.11
#> NA "0242" NA NA NA "0232"
#> TCGA.ET.A25K.01 TCGA.EL.A3GV.01 TCGA.GE.A2C6.01 TCGA.EM.A3FM.01 TCGA.EL.A3H7.11 TCGA.FE.A22Z.01
#> NA NA NA NA NA NA
#> TCGA.H2.A2K9.01 TCGA.EM.A22Q.01 TCGA.EM.A3FP.01 TCGA.GE.A2C6.11 TCGA.EL.A3MZ.01 TCGA.DJ.A2PT.01
#> "0243" "0242" NA "0232" NA NA
#> TCGA.E8.A242.01 TCGA.ET.A25L.01 TCGA.CE.A27D.01 TCGA.EL.A3H1.11 TCGA.BJ.A2N7.11 TCGA.DJ.A2Q7.01
#> NA NA "0233" "0233" NA NA
#> TCGA.J8.A3O1.01 TCGA.EM.A2CR.01 TCGA.DE.A69K.01 TCGA.EM.A2CQ.01 TCGA.FE.A238.01 TCGA.EL.A3H1.01
#> NA NA NA NA NA "0241"
#> TCGA.BJ.A28W.01 TCGA.BJ.A28T.01 TCGA.EM.A2CJ.01 TCGA.EM.A3FQ.01 TCGA.4C.A93U.01 TCGA.EM.A22M.01
#> "0231" "0232" NA NA NA NA
#> TCGA.J8.A3NZ.01 TCGA.EM.A22K.01 TCGA.FE.A236.01 TCGA.BJ.A28R.01 TCGA.EM.A2CU.01 TCGA.ET.A25N.01
#> NA NA NA NA NA NA
#> TCGA.EL.A3H7.01 TCGA.FY.A3NM.01 TCGA.EM.A3FO.01 TCGA.EM.A22L.01 TCGA.BJ.A2N9.11 TCGA.BJ.A291.01
#> NA NA NA NA "0231" NA
#> TCGA.ET.A2N5.11 TCGA.ET.A25N.11 TCGA.J8.A3O0.01 TCGA.FE.A237.01 TCGA.DJ.A2QC.01 TCGA.ET.A25O.01
#> NA NA "0243" NA NA NA
#> TCGA.EL.A3GU.01 TCGA.EL.A3MY.11 TCGA.DJ.A2PY.01 TCGA.EM.A2CS.06 TCGA.FY.A3NP.01 TCGA.ET.A25I.01
#> NA NA NA NA NA NA
#> TCGA.H2.A26U.01 TCGA.BJ.A290.11 TCGA.EM.A22I.01 TCGA.FE.A239.01 TCGA.BJ.A28Z.01 TCGA.DE.A0XZ.01
#> NA NA NA "0242" NA NA
#> TCGA.ET.A25J.01 TCGA.EM.A22N.01 TCGA.EM.A2CM.01 TCGA.FY.A3NN.01 TCGA.EM.A3FL.01 TCGA.H2.A2K9.11
#> NA NA "0244" NA NA "0233"
#> TCGA.EL.A3H3.01 TCGA.EL.A3H4.01 TCGA.EM.A2OX.01 TCGA.EM.A3SX.01 TCGA.BJ.A0Z3.01 TCGA.BJ.A28X.01
#> NA NA NA NA NA NA
#> TCGA.EL.A3CT.01 TCGA.EL.A3CR.01 TCGA.FY.A3TY.01 TCGA.J8.A3YG.01 TCGA.DJ.A3V6.01 TCGA.EM.A3SZ.01
#> NA NA "0233" NA NA NA
#> TCGA.EM.A2OW.01 TCGA.DO.A1JZ.11 TCGA.EL.A3D5.01 TCGA.EM.A2P0.01 TCGA.E8.A2JQ.01 TCGA.BJ.A18Z.01
#> NA NA NA NA NA NA
#> TCGA.DJ.A3V0.01 TCGA.EL.A3GW.01 TCGA.DJ.A3UW.01 TCGA.DJ.A3V3.01 TCGA.EL.A3T1.11 TCGA.BJ.A0ZC.01
#> NA NA NA NA "0232" NA
#> TCGA.EM.A2OV.01 TCGA.EL.A3GY.01 TCGA.EM.A3SY.01 TCGA.EM.A3AI.01 TCGA.EM.A2OY.01 TCGA.EL.A3T8.01
#> NA NA NA NA NA NA
#> TCGA.BJ.A18Y.01 TCGA.EL.A3GP.01 TCGA.EM.A2CK.01 TCGA.EL.A3T7.11 TCGA.BJ.A192.01 TCGA.BJ.A191.01
#> NA NA NA NA NA NA
#> TCGA.EM.A2CP.01 TCGA.EM.A22O.01 TCGA.EM.A2P1.01 TCGA.J8.A3YH.01 TCGA.DJ.A3UZ.01 TCGA.IM.A3EB.01
#> "0231" NA NA NA NA NA
#> TCGA.BJ.A3F0.01 TCGA.EL.A3GX.01 TCGA.EM.A3AK.01 TCGA.DO.A1JZ.01 TCGA.FY.A3YR.01 TCGA.DO.A1K0.01
#> "0241" NA NA NA NA NA
#> TCGA.DJ.A3V5.01 TCGA.EM.A3AJ.01 TCGA.IM.A3ED.01 TCGA.EM.A3AO.01 TCGA.EM.A2P1.06 TCGA.EM.A1CW.01
#> NA "0232" NA NA NA NA
#> TCGA.FK.A3SE.01 TCGA.EL.A3T7.01 TCGA.EM.A2P2.01 TCGA.EM.A1CU.11 TCGA.EL.A3T0.11 TCGA.E8.A3X7.01
#> NA NA NA NA NA NA
#> TCGA.ET.A3BQ.01 TCGA.EM.A1CS.01 TCGA.EL.A3GQ.01 TCGA.EL.A3H5.01 TCGA.DJ.A3V4.01 TCGA.EM.A2P3.01
#> NA NA NA NA NA NA
#> TCGA.FY.A3WA.01 TCGA.DJ.A3V2.01 TCGA.FY.A3TY.11 TCGA.BJ.A290.01 TCGA.EM.A3SU.01 TCGA.EL.A3D0.01
#> NA NA NA NA NA NA
#> TCGA.EM.A1CT.11 TCGA.EL.A3GR.01 TCGA.J8.A3YH.06 TCGA.EM.A3ST.11 TCGA.ET.A3DV.01 TCGA.BJ.A3EZ.01
#> NA NA NA NA "0241" NA
#> TCGA.J8.A3YD.01 TCGA.EM.A3SU.06 TCGA.EM.A3AL.01 TCGA.DJ.A3US.01 TCGA.EM.A1CS.11 TCGA.EM.A1CW.11
#> NA NA "0241" NA NA NA
#> TCGA.BJ.A190.01 TCGA.EM.A2OZ.01 TCGA.EM.A1CV.11 TCGA.EM.A1CU.01 TCGA.EM.A3AN.01 TCGA.E8.A2EA.01
#> NA NA NA NA NA NA
#> TCGA.EM.A1CV.01 TCGA.EM.A1CT.01 TCGA.EM.A3ST.01 TCGA.ET.A3BS.01 TCGA.EL.A3GO.01 TCGA.DJ.A2Q0.01
#> NA NA "0244" NA "0241" NA
#> TCGA.EL.A3D6.01 TCGA.DJ.A3UN.01 TCGA.DJ.A3UU.01 TCGA.FK.A3SD.01 TCGA.DJ.A2PO.01 TCGA.DJ.A3UQ.01
#> NA NA NA "0241" NA NA
#> TCGA.EM.A1YE.11 TCGA.EL.A3T2.11 TCGA.EL.A3CL.01 TCGA.EM.A1YC.01 TCGA.DJ.A3UP.01 TCGA.EL.A3T0.01
#> NA NA NA NA NA NA
#> TCGA.IM.A3U2.01 TCGA.IM.A3U3.01 TCGA.DJ.A3UX.01 TCGA.ET.A3BW.01 TCGA.ET.A39S.01 TCGA.ET.A3BP.01
#> NA NA NA NA NA NA
#> TCGA.DJ.A1QE.01 TCGA.EL.A3D4.01 TCGA.FK.A3SB.01 TCGA.EL.A3CW.01 TCGA.ET.A39L.01 TCGA.DJ.A2PW.01
#> NA NA NA "0232" NA NA
#> TCGA.EM.A2CO.01 TCGA.FE.A232.01 TCGA.DJ.A3UR.01 TCGA.DJ.A2PP.01 TCGA.ET.A3DQ.01 TCGA.ET.A3DS.01
#> NA NA NA "0242" "0232" NA
#> TCGA.FY.A3W9.01 TCGA.FK.A3S3.01 TCGA.ET.A2MZ.01 TCGA.BJ.A2NA.11 TCGA.DJ.A1QL.01 TCGA.EL.A3CS.01
#> "0244" NA NA "0233" "0242" NA
#> TCGA.FE.A233.01 TCGA.EM.A1YD.11 TCGA.ET.A3DW.11 TCGA.EL.A3T9.01 TCGA.DJ.A3UM.01 TCGA.DO.A2HM.01
#> NA NA NA NA NA NA
#> TCGA.FY.A3BL.01 TCGA.EL.A3TA.11 TCGA.ET.A3BX.01 TCGA.DJ.A1QQ.01 TCGA.DJ.A1QF.01 TCGA.DJ.A1QO.01
#> NA NA NA NA NA NA
#> TCGA.BJ.A2NA.01 TCGA.EM.A1YE.01 TCGA.FY.A2QD.01 TCGA.ET.A39J.01 TCGA.ET.A3DU.01 TCGA.EL.A3CM.01
#> NA NA "0241" NA NA NA
#> TCGA.DJ.A3UO.01 TCGA.ET.A39P.01 TCGA.DJ.A2Q2.01 TCGA.BJ.A28V.01 TCGA.ET.A3BO.01 TCGA.EL.A3T1.01
#> NA NA NA "0241" NA NA
#> TCGA.DJ.A1QI.01 TCGA.EL.A3TB.01 TCGA.BJ.A28X.11 TCGA.DJ.A1QN.01 TCGA.FE.A230.01 TCGA.FE.A234.01
#> NA NA "0231" NA NA NA
#> TCGA.ET.A39R.01 TCGA.DJ.A1QG.01 TCGA.EL.A3CV.01 TCGA.FE.A231.01 TCGA.EL.A3TA.01 TCGA.DJ.A3UY.01
#> NA NA NA NA NA NA
#> TCGA.DJ.A2Q1.01 TCGA.EL.A3CU.01 TCGA.EL.A3TB.11 TCGA.ET.A39I.01 TCGA.EM.A1YB.01 TCGA.DJ.A3UV.01
#> NA NA NA NA "0241" NA
#> TCGA.DJ.A3UT.01 TCGA.ET.A3DW.01 TCGA.ET.A3BT.01 TCGA.EL.A3T3.01 TCGA.DJ.A1QM.01 TCGA.EL.A3CY.01
#> NA NA NA NA NA "0231"
#> TCGA.ET.A39O.01 TCGA.EM.A1YC.11 TCGA.DJ.A1QH.01 TCGA.EL.A3T3.11 TCGA.EL.A3CX.01 TCGA.EL.A3T2.01
#> NA NA NA NA NA NA
#> TCGA.EM.A22P.01 TCGA.EL.A3T8.11 TCGA.DJ.A2PU.01 TCGA.DJ.A3UK.01 TCGA.ET.A3DO.01 TCGA.EM.A1YA.01
#> NA NA NA NA NA NA
#> TCGA.ET.A3BV.01 TCGA.EL.A3CO.01 TCGA.DJ.A2PN.01 TCGA.FK.A3SG.01 TCGA.FK.A3SH.01 TCGA.EM.A1YD.01
#> NA "0233" NA NA NA NA
#> TCGA.DJ.A1QD.01 TCGA.EL.A3CZ.01 TCGA.BJ.A0Z9.01 TCGA.CE.A13K.01 TCGA.EM.A3FR.01 TCGA.EM.A3O8.01
#> NA NA NA NA "0241" NA
#> TCGA.FY.A3R6.01 TCGA.FY.A3R9.01 TCGA.EL.A3D1.01 TCGA.EM.A3O6.01 TCGA.BJ.A0Z5.01 TCGA.BJ.A28S.01
#> NA NA NA NA NA NA
#> TCGA.BJ.A0ZH.01 TCGA.ET.A3DT.01 TCGA.H2.A3RI.11 TCGA.DJ.A13W.01 TCGA.DJ.A13T.01 TCGA.BJ.A0ZA.01
#> NA NA NA "0241" NA "0241"
#> TCGA.BJ.A3PT.01 TCGA.FE.A3PD.01 TCGA.BJ.A0ZF.01 TCGA.ET.A39M.01 TCGA.BJ.A0ZJ.01 TCGA.BJ.A0YZ.01
#> NA NA NA NA NA NA
#> TCGA.FE.A3PC.01 TCGA.DJ.A2QB.01 TCGA.EM.A3OB.01 TCGA.H2.A3RH.01 TCGA.ET.A39T.01 TCGA.DJ.A2PV.01
#> NA NA NA NA NA NA
#> TCGA.BJ.A3PR.11 TCGA.EL.A3T6.11 TCGA.DJ.A13X.01 TCGA.BJ.A0ZG.01 TCGA.EL.A3T6.01 TCGA.BJ.A0Z0.01
#> "0232" "0233" NA NA NA "0242"
#> TCGA.ET.A39K.01 TCGA.EM.A3O9.01 TCGA.BJ.A3PU.01 TCGA.BJ.A3PR.01 TCGA.EM.A3O3.01 TCGA.BJ.A0ZB.01
#> NA "0234" NA "0231" NA NA
#> TCGA.EM.A3OA.01 TCGA.DJ.A2PR.01 TCGA.DJ.A13L.01 TCGA.FY.A3ON.01 TCGA.DJ.A13V.01 TCGA.FY.A3R8.01
#> "0241" NA NA NA NA NA
#> TCGA.EL.A3CP.01 TCGA.DJ.A13U.01 TCGA.DE.A0Y3.01 TCGA.ET.A2N4.01 TCGA.DJ.A13P.01 TCGA.BJ.A0ZE.01
#> NA NA NA NA NA NA
#> TCGA.EM.A3O7.01 TCGA.DJ.A13O.01 TCGA.FY.A3RA.01 TCGA.DJ.A13M.01 TCGA.DJ.A13R.01 TCGA.ET.A3DR.01
#> NA "0233" NA NA NA NA
#> TCGA.FE.A3PB.01 TCGA.ET.A3BN.01 TCGA.H2.A3RI.01 TCGA.ET.A39N.01 TCGA.BJ.A3PU.11 TCGA.FY.A3R7.01
#> NA NA NA NA NA NA
#> TCGA.FE.A3PA.01 TCGA.EM.A2CN.01 TCGA.BJ.A0Z2.01 TCGA.FY.A3I5.01 TCGA.DJ.A13S.01 TCGA.DE.A0Y2.01
#> NA "0243" "0243" "0241" NA NA
#> TCGA.ET.A3BU.01
#> NA
get_classes(res_rh, merge_node = merge_node_param(min_n_signatures = 6634))
#> TCGA.E8.A416.01 TCGA.E8.A433.01 TCGA.EL.A4K9.01 TCGA.DJ.A3V9.01 TCGA.EL.A3ZO.11 TCGA.EL.A3ZN.01
#> NA NA NA NA NA NA
#> TCGA.KS.A41F.01 TCGA.EL.A3ZK.01 TCGA.ET.A40R.01 TCGA.EL.A3ZM.01 TCGA.ET.A2N3.01 TCGA.EL.A3ZQ.01
#> NA NA NA NA "0241" NA
#> TCGA.ET.A40T.01 TCGA.DE.A4MA.01 TCGA.EM.A4FU.01 TCGA.E8.A418.01 TCGA.DJ.A3VD.01 TCGA.DJ.A3VM.01
#> NA NA NA NA NA "0244"
#> TCGA.EL.A3ZG.01 TCGA.EM.A4FV.01 TCGA.E8.A413.01 TCGA.DJ.A3VG.01 TCGA.EL.A4K2.01 TCGA.IM.A420.01
#> NA NA NA NA NA NA
#> TCGA.KS.A41J.01 TCGA.EL.A3ZK.11 TCGA.J8.A3O2.01 TCGA.E8.A415.01 TCGA.FY.A40M.01 TCGA.DJ.A3VB.01
#> NA "0232" NA NA NA NA
#> TCGA.KS.A41I.01 TCGA.DJ.A3VL.01 TCGA.ET.A4KQ.01 TCGA.H2.A421.01 TCGA.EL.A3ZO.01 TCGA.KS.A4I3.01
#> NA "0234" NA NA NA NA
#> TCGA.DJ.A4UT.01 TCGA.DE.A4MD.01 TCGA.EL.A4JW.01 TCGA.DJ.A3VI.01 TCGA.DJ.A3VA.01 TCGA.L6.A4ET.01
#> NA NA NA NA NA NA
#> TCGA.E8.A419.01 TCGA.DJ.A4V0.01 TCGA.DJ.A4V2.01 TCGA.ET.A40Q.01 TCGA.EL.A3ZS.01 TCGA.KS.A4ID.01
#> NA "0232" NA NA NA NA
#> TCGA.EL.A3ZL.11 TCGA.J8.A3YE.01 TCGA.EL.A4K7.01 TCGA.DJ.A3VF.01 TCGA.EM.A4FH.01 TCGA.E8.A432.01
#> NA NA NA NA NA NA
#> TCGA.J8.A3O2.06 TCGA.ET.A2MX.01 TCGA.ET.A40S.01 TCGA.DE.A4M8.01 TCGA.IM.A41Z.01 TCGA.EL.A4KD.01
#> NA NA NA NA "0241" NA
#> TCGA.DJ.A3V7.01 TCGA.FY.A40L.01 TCGA.DE.A4M9.01 TCGA.J8.A42S.01 TCGA.KS.A41L.01 TCGA.EM.A4FN.01
#> NA NA NA NA NA NA
#> TCGA.EL.A4K1.01 TCGA.KS.A4IC.01 TCGA.E8.A414.01 TCGA.H2.A422.01 TCGA.J8.A3YF.01 TCGA.EL.A4KI.01
#> NA NA NA NA NA "0243"
#> TCGA.EM.A4G1.01 TCGA.DJ.A3VJ.01 TCGA.DE.A4MD.06 TCGA.EL.A3ZP.01 TCGA.EM.A4FQ.01 TCGA.EL.A3ZT.01
#> NA NA NA NA NA NA
#> TCGA.DJ.A4V4.01 TCGA.FY.A40K.01 TCGA.L6.A4EQ.01 TCGA.DJ.A3VE.01 TCGA.E8.A434.01 TCGA.EL.A3ZH.01
#> NA NA NA NA NA NA
#> TCGA.EM.A4FR.01 TCGA.EL.A3ZH.11 TCGA.EL.A3ZR.01 TCGA.DJ.A3V8.01 TCGA.EL.A3ZG.11 TCGA.ET.A40P.01
#> NA NA NA NA NA NA
#> TCGA.DE.A4MB.01 TCGA.MK.A4N6.01 TCGA.DJ.A3VK.01 TCGA.E8.A417.01 TCGA.L6.A4EU.01 TCGA.J8.A4HY.01
#> NA NA NA NA NA NA
#> TCGA.EL.A3ZL.01 TCGA.EL.A3ZP.11 TCGA.FY.A40N.01 TCGA.J8.A4HW.01 TCGA.BJ.A45J.01 TCGA.CE.A482.01
#> NA "0232" NA NA NA NA
#> TCGA.DJ.A2Q6.01 TCGA.DJ.A2PX.01 TCGA.DJ.A4UL.01 TCGA.EL.A4JX.01 TCGA.BJ.A2N8.11 TCGA.DJ.A2Q5.01
#> NA NA NA NA NA NA
#> TCGA.EL.A4KG.01 TCGA.DJ.A4UP.01 TCGA.E8.A438.01 TCGA.EL.A3H2.01 TCGA.EM.A3AP.01 TCGA.DJ.A2PQ.01
#> NA NA NA NA NA NA
#> TCGA.L6.A4EP.01 TCGA.FY.A4B4.01 TCGA.EL.A4KH.01 TCGA.BJ.A45E.01 TCGA.DJ.A4V5.01 TCGA.DE.A4MC.01
#> NA NA NA "0231" NA NA
#> TCGA.E8.A44M.01 TCGA.BJ.A45K.01 TCGA.E3.A3DZ.01 TCGA.E3.A3E2.01 TCGA.BJ.A45H.01 TCGA.E8.A44K.01
#> NA "0242" NA NA NA NA
#> TCGA.ET.A2MY.01 TCGA.EL.A3H8.01 TCGA.BJ.A45C.01 TCGA.BJ.A45G.01 TCGA.EL.A4JZ.01 TCGA.CE.A481.01
#> NA NA "0242" NA NA NA
#> TCGA.KS.A4I9.01 TCGA.EL.A3MW.01 TCGA.E8.A436.01 TCGA.E3.A3DY.01 TCGA.DJ.A2Q3.01 TCGA.BJ.A2P4.01
#> NA NA NA NA NA NA
#> TCGA.CE.A484.01 TCGA.ET.A2N1.01 TCGA.DJ.A2Q4.01 TCGA.DJ.A2PZ.01 TCGA.BJ.A45F.01 TCGA.IM.A4EB.01
#> NA NA NA NA NA NA
#> TCGA.EM.A4FO.01 TCGA.FY.A4B3.01 TCGA.FY.A4B0.01 TCGA.BJ.A45I.01 TCGA.E3.A3E3.01 TCGA.EM.A3AQ.01
#> NA NA "0242" NA NA NA
#> TCGA.EL.A3N3.01 TCGA.DJ.A2Q9.01 TCGA.EM.A4FM.01 TCGA.EL.A4K6.01 TCGA.MK.A4N9.01 TCGA.KS.A4I1.01
#> NA "0231" NA "0243" NA NA
#> TCGA.DJ.A2PS.01 TCGA.CE.A3MD.01 TCGA.E3.A3E5.01 TCGA.EL.A3CN.01 TCGA.J8.A4HW.06 TCGA.EM.A4FK.01
#> NA NA NA NA NA "0241"
#> TCGA.E8.A437.01 TCGA.BJ.A4O8.01 TCGA.EL.A3MW.11 TCGA.E3.A3E0.01 TCGA.BJ.A45D.01 TCGA.CE.A483.01
#> NA NA NA NA NA NA
#> TCGA.CE.A485.01 TCGA.DJ.A4UR.01 TCGA.IM.A41Y.01 TCGA.ET.A4KN.01 TCGA.KS.A4I5.01 TCGA.DJ.A4UQ.01
#> NA "0244" NA NA NA NA
#> TCGA.KS.A4IB.01 TCGA.EL.A3N2.11 TCGA.BJ.A2N9.01 TCGA.DJ.A4UW.01 TCGA.EL.A3GZ.11 TCGA.EM.A3AR.01
#> NA NA NA NA NA NA
#> TCGA.EL.A3N3.11 TCGA.DE.A3KN.01 TCGA.DJ.A2QA.01 TCGA.EL.A4JV.01 TCGA.EM.A4FF.01 TCGA.EL.A4K0.01
#> "0232" NA NA NA NA NA
#> TCGA.FK.A4UB.01 TCGA.BJ.A4O9.01 TCGA.BJ.A2N7.01 TCGA.DE.A2OL.01 TCGA.CE.A3ME.01 TCGA.MK.A4N7.01
#> NA NA NA "0241" NA NA
#> TCGA.EL.A3H2.11 TCGA.EL.A4K4.01 TCGA.EL.A3GS.01 TCGA.EL.A3GZ.01 TCGA.E3.A3E1.01 TCGA.DJ.A2Q8.01
#> NA NA NA NA NA NA
#> TCGA.EL.A3N2.01 TCGA.KS.A4I7.01 TCGA.MK.A84Z.01 TCGA.ET.A3DP.11 TCGA.EL.A3MX.11 TCGA.ET.A25G.01
#> NA NA NA NA NA NA
#> TCGA.EM.A3FK.01 TCGA.EM.A2CS.01 TCGA.FE.A23A.01 TCGA.BJ.A28T.11 TCGA.EM.A22J.01 TCGA.EL.A3MX.01
#> NA NA NA NA "0241" NA
#> TCGA.FY.A3I4.01 TCGA.BJ.A28W.11 TCGA.ET.A25R.01 TCGA.BJ.A2N8.01 TCGA.FY.A76V.01 TCGA.EM.A3FN.01
#> NA "0232" NA NA NA "0241"
#> TCGA.QD.A8IV.01 TCGA.EM.A3FJ.01 TCGA.ET.A2MY.11 TCGA.EM.A3FQ.06 TCGA.ET.A25P.01 TCGA.ET.A2N0.01
#> NA NA "0241" NA NA NA
#> TCGA.EM.A2CT.01 TCGA.FE.A235.01 TCGA.ET.A25M.01 TCGA.EL.A3MY.01 TCGA.DE.A7U5.01 TCGA.E8.A2JQ.11
#> NA NA NA NA NA "0231"
#> TCGA.ET.A3DP.01 TCGA.EM.A2CL.01 TCGA.ET.A2N5.01 TCGA.ET.A25J.11 TCGA.DE.A69J.01 TCGA.BJ.A28R.11
#> NA "0242" NA NA NA "0232"
#> TCGA.ET.A25K.01 TCGA.EL.A3GV.01 TCGA.GE.A2C6.01 TCGA.EM.A3FM.01 TCGA.EL.A3H7.11 TCGA.FE.A22Z.01
#> NA NA NA NA NA NA
#> TCGA.H2.A2K9.01 TCGA.EM.A22Q.01 TCGA.EM.A3FP.01 TCGA.GE.A2C6.11 TCGA.EL.A3MZ.01 TCGA.DJ.A2PT.01
#> "0243" "0242" NA "0232" NA NA
#> TCGA.E8.A242.01 TCGA.ET.A25L.01 TCGA.CE.A27D.01 TCGA.EL.A3H1.11 TCGA.BJ.A2N7.11 TCGA.DJ.A2Q7.01
#> NA NA "0233" "0233" NA NA
#> TCGA.J8.A3O1.01 TCGA.EM.A2CR.01 TCGA.DE.A69K.01 TCGA.EM.A2CQ.01 TCGA.FE.A238.01 TCGA.EL.A3H1.01
#> NA NA NA NA NA "0241"
#> TCGA.BJ.A28W.01 TCGA.BJ.A28T.01 TCGA.EM.A2CJ.01 TCGA.EM.A3FQ.01 TCGA.4C.A93U.01 TCGA.EM.A22M.01
#> "0231" "0232" NA NA NA NA
#> TCGA.J8.A3NZ.01 TCGA.EM.A22K.01 TCGA.FE.A236.01 TCGA.BJ.A28R.01 TCGA.EM.A2CU.01 TCGA.ET.A25N.01
#> NA NA NA NA NA NA
#> TCGA.EL.A3H7.01 TCGA.FY.A3NM.01 TCGA.EM.A3FO.01 TCGA.EM.A22L.01 TCGA.BJ.A2N9.11 TCGA.BJ.A291.01
#> NA NA NA NA "0231" NA
#> TCGA.ET.A2N5.11 TCGA.ET.A25N.11 TCGA.J8.A3O0.01 TCGA.FE.A237.01 TCGA.DJ.A2QC.01 TCGA.ET.A25O.01
#> NA NA "0243" NA NA NA
#> TCGA.EL.A3GU.01 TCGA.EL.A3MY.11 TCGA.DJ.A2PY.01 TCGA.EM.A2CS.06 TCGA.FY.A3NP.01 TCGA.ET.A25I.01
#> NA NA NA NA NA NA
#> TCGA.H2.A26U.01 TCGA.BJ.A290.11 TCGA.EM.A22I.01 TCGA.FE.A239.01 TCGA.BJ.A28Z.01 TCGA.DE.A0XZ.01
#> NA NA NA "0242" NA NA
#> TCGA.ET.A25J.01 TCGA.EM.A22N.01 TCGA.EM.A2CM.01 TCGA.FY.A3NN.01 TCGA.EM.A3FL.01 TCGA.H2.A2K9.11
#> NA NA "0244" NA NA "0233"
#> TCGA.EL.A3H3.01 TCGA.EL.A3H4.01 TCGA.EM.A2OX.01 TCGA.EM.A3SX.01 TCGA.BJ.A0Z3.01 TCGA.BJ.A28X.01
#> NA NA NA NA NA NA
#> TCGA.EL.A3CT.01 TCGA.EL.A3CR.01 TCGA.FY.A3TY.01 TCGA.J8.A3YG.01 TCGA.DJ.A3V6.01 TCGA.EM.A3SZ.01
#> NA NA "0233" NA NA NA
#> TCGA.EM.A2OW.01 TCGA.DO.A1JZ.11 TCGA.EL.A3D5.01 TCGA.EM.A2P0.01 TCGA.E8.A2JQ.01 TCGA.BJ.A18Z.01
#> NA NA NA NA NA NA
#> TCGA.DJ.A3V0.01 TCGA.EL.A3GW.01 TCGA.DJ.A3UW.01 TCGA.DJ.A3V3.01 TCGA.EL.A3T1.11 TCGA.BJ.A0ZC.01
#> NA NA NA NA "0232" NA
#> TCGA.EM.A2OV.01 TCGA.EL.A3GY.01 TCGA.EM.A3SY.01 TCGA.EM.A3AI.01 TCGA.EM.A2OY.01 TCGA.EL.A3T8.01
#> NA NA NA NA NA NA
#> TCGA.BJ.A18Y.01 TCGA.EL.A3GP.01 TCGA.EM.A2CK.01 TCGA.EL.A3T7.11 TCGA.BJ.A192.01 TCGA.BJ.A191.01
#> NA NA NA NA NA NA
#> TCGA.EM.A2CP.01 TCGA.EM.A22O.01 TCGA.EM.A2P1.01 TCGA.J8.A3YH.01 TCGA.DJ.A3UZ.01 TCGA.IM.A3EB.01
#> "0231" NA NA NA NA NA
#> TCGA.BJ.A3F0.01 TCGA.EL.A3GX.01 TCGA.EM.A3AK.01 TCGA.DO.A1JZ.01 TCGA.FY.A3YR.01 TCGA.DO.A1K0.01
#> "0241" NA NA NA NA NA
#> TCGA.DJ.A3V5.01 TCGA.EM.A3AJ.01 TCGA.IM.A3ED.01 TCGA.EM.A3AO.01 TCGA.EM.A2P1.06 TCGA.EM.A1CW.01
#> NA "0232" NA NA NA NA
#> TCGA.FK.A3SE.01 TCGA.EL.A3T7.01 TCGA.EM.A2P2.01 TCGA.EM.A1CU.11 TCGA.EL.A3T0.11 TCGA.E8.A3X7.01
#> NA NA NA NA NA NA
#> TCGA.ET.A3BQ.01 TCGA.EM.A1CS.01 TCGA.EL.A3GQ.01 TCGA.EL.A3H5.01 TCGA.DJ.A3V4.01 TCGA.EM.A2P3.01
#> NA NA NA NA NA NA
#> TCGA.FY.A3WA.01 TCGA.DJ.A3V2.01 TCGA.FY.A3TY.11 TCGA.BJ.A290.01 TCGA.EM.A3SU.01 TCGA.EL.A3D0.01
#> NA NA NA NA NA NA
#> TCGA.EM.A1CT.11 TCGA.EL.A3GR.01 TCGA.J8.A3YH.06 TCGA.EM.A3ST.11 TCGA.ET.A3DV.01 TCGA.BJ.A3EZ.01
#> NA NA NA NA "0241" NA
#> TCGA.J8.A3YD.01 TCGA.EM.A3SU.06 TCGA.EM.A3AL.01 TCGA.DJ.A3US.01 TCGA.EM.A1CS.11 TCGA.EM.A1CW.11
#> NA NA "0241" NA NA NA
#> TCGA.BJ.A190.01 TCGA.EM.A2OZ.01 TCGA.EM.A1CV.11 TCGA.EM.A1CU.01 TCGA.EM.A3AN.01 TCGA.E8.A2EA.01
#> NA NA NA NA NA NA
#> TCGA.EM.A1CV.01 TCGA.EM.A1CT.01 TCGA.EM.A3ST.01 TCGA.ET.A3BS.01 TCGA.EL.A3GO.01 TCGA.DJ.A2Q0.01
#> NA NA "0244" NA "0241" NA
#> TCGA.EL.A3D6.01 TCGA.DJ.A3UN.01 TCGA.DJ.A3UU.01 TCGA.FK.A3SD.01 TCGA.DJ.A2PO.01 TCGA.DJ.A3UQ.01
#> NA NA NA "0241" NA NA
#> TCGA.EM.A1YE.11 TCGA.EL.A3T2.11 TCGA.EL.A3CL.01 TCGA.EM.A1YC.01 TCGA.DJ.A3UP.01 TCGA.EL.A3T0.01
#> NA NA NA NA NA NA
#> TCGA.IM.A3U2.01 TCGA.IM.A3U3.01 TCGA.DJ.A3UX.01 TCGA.ET.A3BW.01 TCGA.ET.A39S.01 TCGA.ET.A3BP.01
#> NA NA NA NA NA NA
#> TCGA.DJ.A1QE.01 TCGA.EL.A3D4.01 TCGA.FK.A3SB.01 TCGA.EL.A3CW.01 TCGA.ET.A39L.01 TCGA.DJ.A2PW.01
#> NA NA NA "0232" NA NA
#> TCGA.EM.A2CO.01 TCGA.FE.A232.01 TCGA.DJ.A3UR.01 TCGA.DJ.A2PP.01 TCGA.ET.A3DQ.01 TCGA.ET.A3DS.01
#> NA NA NA "0242" "0232" NA
#> TCGA.FY.A3W9.01 TCGA.FK.A3S3.01 TCGA.ET.A2MZ.01 TCGA.BJ.A2NA.11 TCGA.DJ.A1QL.01 TCGA.EL.A3CS.01
#> "0244" NA NA "0233" "0242" NA
#> TCGA.FE.A233.01 TCGA.EM.A1YD.11 TCGA.ET.A3DW.11 TCGA.EL.A3T9.01 TCGA.DJ.A3UM.01 TCGA.DO.A2HM.01
#> NA NA NA NA NA NA
#> TCGA.FY.A3BL.01 TCGA.EL.A3TA.11 TCGA.ET.A3BX.01 TCGA.DJ.A1QQ.01 TCGA.DJ.A1QF.01 TCGA.DJ.A1QO.01
#> NA NA NA NA NA NA
#> TCGA.BJ.A2NA.01 TCGA.EM.A1YE.01 TCGA.FY.A2QD.01 TCGA.ET.A39J.01 TCGA.ET.A3DU.01 TCGA.EL.A3CM.01
#> NA NA "0241" NA NA NA
#> TCGA.DJ.A3UO.01 TCGA.ET.A39P.01 TCGA.DJ.A2Q2.01 TCGA.BJ.A28V.01 TCGA.ET.A3BO.01 TCGA.EL.A3T1.01
#> NA NA NA "0241" NA NA
#> TCGA.DJ.A1QI.01 TCGA.EL.A3TB.01 TCGA.BJ.A28X.11 TCGA.DJ.A1QN.01 TCGA.FE.A230.01 TCGA.FE.A234.01
#> NA NA "0231" NA NA NA
#> TCGA.ET.A39R.01 TCGA.DJ.A1QG.01 TCGA.EL.A3CV.01 TCGA.FE.A231.01 TCGA.EL.A3TA.01 TCGA.DJ.A3UY.01
#> NA NA NA NA NA NA
#> TCGA.DJ.A2Q1.01 TCGA.EL.A3CU.01 TCGA.EL.A3TB.11 TCGA.ET.A39I.01 TCGA.EM.A1YB.01 TCGA.DJ.A3UV.01
#> NA NA NA NA "0241" NA
#> TCGA.DJ.A3UT.01 TCGA.ET.A3DW.01 TCGA.ET.A3BT.01 TCGA.EL.A3T3.01 TCGA.DJ.A1QM.01 TCGA.EL.A3CY.01
#> NA NA NA NA NA "0231"
#> TCGA.ET.A39O.01 TCGA.EM.A1YC.11 TCGA.DJ.A1QH.01 TCGA.EL.A3T3.11 TCGA.EL.A3CX.01 TCGA.EL.A3T2.01
#> NA NA NA NA NA NA
#> TCGA.EM.A22P.01 TCGA.EL.A3T8.11 TCGA.DJ.A2PU.01 TCGA.DJ.A3UK.01 TCGA.ET.A3DO.01 TCGA.EM.A1YA.01
#> NA NA NA NA NA NA
#> TCGA.ET.A3BV.01 TCGA.EL.A3CO.01 TCGA.DJ.A2PN.01 TCGA.FK.A3SG.01 TCGA.FK.A3SH.01 TCGA.EM.A1YD.01
#> NA "0233" NA NA NA NA
#> TCGA.DJ.A1QD.01 TCGA.EL.A3CZ.01 TCGA.BJ.A0Z9.01 TCGA.CE.A13K.01 TCGA.EM.A3FR.01 TCGA.EM.A3O8.01
#> NA NA NA NA "0241" NA
#> TCGA.FY.A3R6.01 TCGA.FY.A3R9.01 TCGA.EL.A3D1.01 TCGA.EM.A3O6.01 TCGA.BJ.A0Z5.01 TCGA.BJ.A28S.01
#> NA NA NA NA NA NA
#> TCGA.BJ.A0ZH.01 TCGA.ET.A3DT.01 TCGA.H2.A3RI.11 TCGA.DJ.A13W.01 TCGA.DJ.A13T.01 TCGA.BJ.A0ZA.01
#> NA NA NA "0241" NA "0241"
#> TCGA.BJ.A3PT.01 TCGA.FE.A3PD.01 TCGA.BJ.A0ZF.01 TCGA.ET.A39M.01 TCGA.BJ.A0ZJ.01 TCGA.BJ.A0YZ.01
#> NA NA NA NA NA NA
#> TCGA.FE.A3PC.01 TCGA.DJ.A2QB.01 TCGA.EM.A3OB.01 TCGA.H2.A3RH.01 TCGA.ET.A39T.01 TCGA.DJ.A2PV.01
#> NA NA NA NA NA NA
#> TCGA.BJ.A3PR.11 TCGA.EL.A3T6.11 TCGA.DJ.A13X.01 TCGA.BJ.A0ZG.01 TCGA.EL.A3T6.01 TCGA.BJ.A0Z0.01
#> "0232" "0233" NA NA NA "0242"
#> TCGA.ET.A39K.01 TCGA.EM.A3O9.01 TCGA.BJ.A3PU.01 TCGA.BJ.A3PR.01 TCGA.EM.A3O3.01 TCGA.BJ.A0ZB.01
#> NA "0234" NA "0231" NA NA
#> TCGA.EM.A3OA.01 TCGA.DJ.A2PR.01 TCGA.DJ.A13L.01 TCGA.FY.A3ON.01 TCGA.DJ.A13V.01 TCGA.FY.A3R8.01
#> "0241" NA NA NA NA NA
#> TCGA.EL.A3CP.01 TCGA.DJ.A13U.01 TCGA.DE.A0Y3.01 TCGA.ET.A2N4.01 TCGA.DJ.A13P.01 TCGA.BJ.A0ZE.01
#> NA NA NA NA NA NA
#> TCGA.EM.A3O7.01 TCGA.DJ.A13O.01 TCGA.FY.A3RA.01 TCGA.DJ.A13M.01 TCGA.DJ.A13R.01 TCGA.ET.A3DR.01
#> NA "0233" NA NA NA NA
#> TCGA.FE.A3PB.01 TCGA.ET.A3BN.01 TCGA.H2.A3RI.01 TCGA.ET.A39N.01 TCGA.BJ.A3PU.11 TCGA.FY.A3R7.01
#> NA NA NA NA NA NA
#> TCGA.FE.A3PA.01 TCGA.EM.A2CN.01 TCGA.BJ.A0Z2.01 TCGA.FY.A3I5.01 TCGA.DJ.A13S.01 TCGA.DE.A0Y2.01
#> NA "0243" "0243" "0241" NA NA
#> TCGA.ET.A3BU.01
#> NA
get_classes(res_rh, merge_node = merge_node_param(min_n_signatures = 8600))
#> TCGA.E8.A416.01 TCGA.E8.A433.01 TCGA.EL.A4K9.01 TCGA.DJ.A3V9.01 TCGA.EL.A3ZO.11 TCGA.EL.A3ZN.01
#> NA NA NA NA NA NA
#> TCGA.KS.A41F.01 TCGA.EL.A3ZK.01 TCGA.ET.A40R.01 TCGA.EL.A3ZM.01 TCGA.ET.A2N3.01 TCGA.EL.A3ZQ.01
#> NA NA NA NA NA NA
#> TCGA.ET.A40T.01 TCGA.DE.A4MA.01 TCGA.EM.A4FU.01 TCGA.E8.A418.01 TCGA.DJ.A3VD.01 TCGA.DJ.A3VM.01
#> NA NA NA NA NA NA
#> TCGA.EL.A3ZG.01 TCGA.EM.A4FV.01 TCGA.E8.A413.01 TCGA.DJ.A3VG.01 TCGA.EL.A4K2.01 TCGA.IM.A420.01
#> NA NA NA NA NA NA
#> TCGA.KS.A41J.01 TCGA.EL.A3ZK.11 TCGA.J8.A3O2.01 TCGA.E8.A415.01 TCGA.FY.A40M.01 TCGA.DJ.A3VB.01
#> NA "0232" NA NA NA NA
#> TCGA.KS.A41I.01 TCGA.DJ.A3VL.01 TCGA.ET.A4KQ.01 TCGA.H2.A421.01 TCGA.EL.A3ZO.01 TCGA.KS.A4I3.01
#> NA "0234" NA NA NA NA
#> TCGA.DJ.A4UT.01 TCGA.DE.A4MD.01 TCGA.EL.A4JW.01 TCGA.DJ.A3VI.01 TCGA.DJ.A3VA.01 TCGA.L6.A4ET.01
#> NA NA NA NA NA NA
#> TCGA.E8.A419.01 TCGA.DJ.A4V0.01 TCGA.DJ.A4V2.01 TCGA.ET.A40Q.01 TCGA.EL.A3ZS.01 TCGA.KS.A4ID.01
#> NA "0232" NA NA NA NA
#> TCGA.EL.A3ZL.11 TCGA.J8.A3YE.01 TCGA.EL.A4K7.01 TCGA.DJ.A3VF.01 TCGA.EM.A4FH.01 TCGA.E8.A432.01
#> NA NA NA NA NA NA
#> TCGA.J8.A3O2.06 TCGA.ET.A2MX.01 TCGA.ET.A40S.01 TCGA.DE.A4M8.01 TCGA.IM.A41Z.01 TCGA.EL.A4KD.01
#> NA NA NA NA NA NA
#> TCGA.DJ.A3V7.01 TCGA.FY.A40L.01 TCGA.DE.A4M9.01 TCGA.J8.A42S.01 TCGA.KS.A41L.01 TCGA.EM.A4FN.01
#> NA NA NA NA NA NA
#> TCGA.EL.A4K1.01 TCGA.KS.A4IC.01 TCGA.E8.A414.01 TCGA.H2.A422.01 TCGA.J8.A3YF.01 TCGA.EL.A4KI.01
#> NA NA NA NA NA NA
#> TCGA.EM.A4G1.01 TCGA.DJ.A3VJ.01 TCGA.DE.A4MD.06 TCGA.EL.A3ZP.01 TCGA.EM.A4FQ.01 TCGA.EL.A3ZT.01
#> NA NA NA NA NA NA
#> TCGA.DJ.A4V4.01 TCGA.FY.A40K.01 TCGA.L6.A4EQ.01 TCGA.DJ.A3VE.01 TCGA.E8.A434.01 TCGA.EL.A3ZH.01
#> NA NA NA NA NA NA
#> TCGA.EM.A4FR.01 TCGA.EL.A3ZH.11 TCGA.EL.A3ZR.01 TCGA.DJ.A3V8.01 TCGA.EL.A3ZG.11 TCGA.ET.A40P.01
#> NA NA NA NA NA NA
#> TCGA.DE.A4MB.01 TCGA.MK.A4N6.01 TCGA.DJ.A3VK.01 TCGA.E8.A417.01 TCGA.L6.A4EU.01 TCGA.J8.A4HY.01
#> NA NA NA NA NA NA
#> TCGA.EL.A3ZL.01 TCGA.EL.A3ZP.11 TCGA.FY.A40N.01 TCGA.J8.A4HW.01 TCGA.BJ.A45J.01 TCGA.CE.A482.01
#> NA "0232" NA NA NA NA
#> TCGA.DJ.A2Q6.01 TCGA.DJ.A2PX.01 TCGA.DJ.A4UL.01 TCGA.EL.A4JX.01 TCGA.BJ.A2N8.11 TCGA.DJ.A2Q5.01
#> NA NA NA NA NA NA
#> TCGA.EL.A4KG.01 TCGA.DJ.A4UP.01 TCGA.E8.A438.01 TCGA.EL.A3H2.01 TCGA.EM.A3AP.01 TCGA.DJ.A2PQ.01
#> NA NA NA NA NA NA
#> TCGA.L6.A4EP.01 TCGA.FY.A4B4.01 TCGA.EL.A4KH.01 TCGA.BJ.A45E.01 TCGA.DJ.A4V5.01 TCGA.DE.A4MC.01
#> NA NA NA "0231" NA NA
#> TCGA.E8.A44M.01 TCGA.BJ.A45K.01 TCGA.E3.A3DZ.01 TCGA.E3.A3E2.01 TCGA.BJ.A45H.01 TCGA.E8.A44K.01
#> NA NA NA NA NA NA
#> TCGA.ET.A2MY.01 TCGA.EL.A3H8.01 TCGA.BJ.A45C.01 TCGA.BJ.A45G.01 TCGA.EL.A4JZ.01 TCGA.CE.A481.01
#> NA NA NA NA NA NA
#> TCGA.KS.A4I9.01 TCGA.EL.A3MW.01 TCGA.E8.A436.01 TCGA.E3.A3DY.01 TCGA.DJ.A2Q3.01 TCGA.BJ.A2P4.01
#> NA NA NA NA NA NA
#> TCGA.CE.A484.01 TCGA.ET.A2N1.01 TCGA.DJ.A2Q4.01 TCGA.DJ.A2PZ.01 TCGA.BJ.A45F.01 TCGA.IM.A4EB.01
#> NA NA NA NA NA NA
#> TCGA.EM.A4FO.01 TCGA.FY.A4B3.01 TCGA.FY.A4B0.01 TCGA.BJ.A45I.01 TCGA.E3.A3E3.01 TCGA.EM.A3AQ.01
#> NA NA NA NA NA NA
#> TCGA.EL.A3N3.01 TCGA.DJ.A2Q9.01 TCGA.EM.A4FM.01 TCGA.EL.A4K6.01 TCGA.MK.A4N9.01 TCGA.KS.A4I1.01
#> NA "0231" NA NA NA NA
#> TCGA.DJ.A2PS.01 TCGA.CE.A3MD.01 TCGA.E3.A3E5.01 TCGA.EL.A3CN.01 TCGA.J8.A4HW.06 TCGA.EM.A4FK.01
#> NA NA NA NA NA NA
#> TCGA.E8.A437.01 TCGA.BJ.A4O8.01 TCGA.EL.A3MW.11 TCGA.E3.A3E0.01 TCGA.BJ.A45D.01 TCGA.CE.A483.01
#> NA NA NA NA NA NA
#> TCGA.CE.A485.01 TCGA.DJ.A4UR.01 TCGA.IM.A41Y.01 TCGA.ET.A4KN.01 TCGA.KS.A4I5.01 TCGA.DJ.A4UQ.01
#> NA NA NA NA NA NA
#> TCGA.KS.A4IB.01 TCGA.EL.A3N2.11 TCGA.BJ.A2N9.01 TCGA.DJ.A4UW.01 TCGA.EL.A3GZ.11 TCGA.EM.A3AR.01
#> NA NA NA NA NA NA
#> TCGA.EL.A3N3.11 TCGA.DE.A3KN.01 TCGA.DJ.A2QA.01 TCGA.EL.A4JV.01 TCGA.EM.A4FF.01 TCGA.EL.A4K0.01
#> "0232" NA NA NA NA NA
#> TCGA.FK.A4UB.01 TCGA.BJ.A4O9.01 TCGA.BJ.A2N7.01 TCGA.DE.A2OL.01 TCGA.CE.A3ME.01 TCGA.MK.A4N7.01
#> NA NA NA NA NA NA
#> TCGA.EL.A3H2.11 TCGA.EL.A4K4.01 TCGA.EL.A3GS.01 TCGA.EL.A3GZ.01 TCGA.E3.A3E1.01 TCGA.DJ.A2Q8.01
#> NA NA NA NA NA NA
#> TCGA.EL.A3N2.01 TCGA.KS.A4I7.01 TCGA.MK.A84Z.01 TCGA.ET.A3DP.11 TCGA.EL.A3MX.11 TCGA.ET.A25G.01
#> NA NA NA NA NA NA
#> TCGA.EM.A3FK.01 TCGA.EM.A2CS.01 TCGA.FE.A23A.01 TCGA.BJ.A28T.11 TCGA.EM.A22J.01 TCGA.EL.A3MX.01
#> NA NA NA NA NA NA
#> TCGA.FY.A3I4.01 TCGA.BJ.A28W.11 TCGA.ET.A25R.01 TCGA.BJ.A2N8.01 TCGA.FY.A76V.01 TCGA.EM.A3FN.01
#> NA "0232" NA NA NA NA
#> TCGA.QD.A8IV.01 TCGA.EM.A3FJ.01 TCGA.ET.A2MY.11 TCGA.EM.A3FQ.06 TCGA.ET.A25P.01 TCGA.ET.A2N0.01
#> NA NA NA NA NA NA
#> TCGA.EM.A2CT.01 TCGA.FE.A235.01 TCGA.ET.A25M.01 TCGA.EL.A3MY.01 TCGA.DE.A7U5.01 TCGA.E8.A2JQ.11
#> NA NA NA NA NA "0231"
#> TCGA.ET.A3DP.01 TCGA.EM.A2CL.01 TCGA.ET.A2N5.01 TCGA.ET.A25J.11 TCGA.DE.A69J.01 TCGA.BJ.A28R.11
#> NA NA NA NA NA "0232"
#> TCGA.ET.A25K.01 TCGA.EL.A3GV.01 TCGA.GE.A2C6.01 TCGA.EM.A3FM.01 TCGA.EL.A3H7.11 TCGA.FE.A22Z.01
#> NA NA NA NA NA NA
#> TCGA.H2.A2K9.01 TCGA.EM.A22Q.01 TCGA.EM.A3FP.01 TCGA.GE.A2C6.11 TCGA.EL.A3MZ.01 TCGA.DJ.A2PT.01
#> NA NA NA "0232" NA NA
#> TCGA.E8.A242.01 TCGA.ET.A25L.01 TCGA.CE.A27D.01 TCGA.EL.A3H1.11 TCGA.BJ.A2N7.11 TCGA.DJ.A2Q7.01
#> NA NA "0233" "0233" NA NA
#> TCGA.J8.A3O1.01 TCGA.EM.A2CR.01 TCGA.DE.A69K.01 TCGA.EM.A2CQ.01 TCGA.FE.A238.01 TCGA.EL.A3H1.01
#> NA NA NA NA NA NA
#> TCGA.BJ.A28W.01 TCGA.BJ.A28T.01 TCGA.EM.A2CJ.01 TCGA.EM.A3FQ.01 TCGA.4C.A93U.01 TCGA.EM.A22M.01
#> "0231" "0232" NA NA NA NA
#> TCGA.J8.A3NZ.01 TCGA.EM.A22K.01 TCGA.FE.A236.01 TCGA.BJ.A28R.01 TCGA.EM.A2CU.01 TCGA.ET.A25N.01
#> NA NA NA NA NA NA
#> TCGA.EL.A3H7.01 TCGA.FY.A3NM.01 TCGA.EM.A3FO.01 TCGA.EM.A22L.01 TCGA.BJ.A2N9.11 TCGA.BJ.A291.01
#> NA NA NA NA "0231" NA
#> TCGA.ET.A2N5.11 TCGA.ET.A25N.11 TCGA.J8.A3O0.01 TCGA.FE.A237.01 TCGA.DJ.A2QC.01 TCGA.ET.A25O.01
#> NA NA NA NA NA NA
#> TCGA.EL.A3GU.01 TCGA.EL.A3MY.11 TCGA.DJ.A2PY.01 TCGA.EM.A2CS.06 TCGA.FY.A3NP.01 TCGA.ET.A25I.01
#> NA NA NA NA NA NA
#> TCGA.H2.A26U.01 TCGA.BJ.A290.11 TCGA.EM.A22I.01 TCGA.FE.A239.01 TCGA.BJ.A28Z.01 TCGA.DE.A0XZ.01
#> NA NA NA NA NA NA
#> TCGA.ET.A25J.01 TCGA.EM.A22N.01 TCGA.EM.A2CM.01 TCGA.FY.A3NN.01 TCGA.EM.A3FL.01 TCGA.H2.A2K9.11
#> NA NA NA NA NA "0233"
#> TCGA.EL.A3H3.01 TCGA.EL.A3H4.01 TCGA.EM.A2OX.01 TCGA.EM.A3SX.01 TCGA.BJ.A0Z3.01 TCGA.BJ.A28X.01
#> NA NA NA NA NA NA
#> TCGA.EL.A3CT.01 TCGA.EL.A3CR.01 TCGA.FY.A3TY.01 TCGA.J8.A3YG.01 TCGA.DJ.A3V6.01 TCGA.EM.A3SZ.01
#> NA NA "0233" NA NA NA
#> TCGA.EM.A2OW.01 TCGA.DO.A1JZ.11 TCGA.EL.A3D5.01 TCGA.EM.A2P0.01 TCGA.E8.A2JQ.01 TCGA.BJ.A18Z.01
#> NA NA NA NA NA NA
#> TCGA.DJ.A3V0.01 TCGA.EL.A3GW.01 TCGA.DJ.A3UW.01 TCGA.DJ.A3V3.01 TCGA.EL.A3T1.11 TCGA.BJ.A0ZC.01
#> NA NA NA NA "0232" NA
#> TCGA.EM.A2OV.01 TCGA.EL.A3GY.01 TCGA.EM.A3SY.01 TCGA.EM.A3AI.01 TCGA.EM.A2OY.01 TCGA.EL.A3T8.01
#> NA NA NA NA NA NA
#> TCGA.BJ.A18Y.01 TCGA.EL.A3GP.01 TCGA.EM.A2CK.01 TCGA.EL.A3T7.11 TCGA.BJ.A192.01 TCGA.BJ.A191.01
#> NA NA NA NA NA NA
#> TCGA.EM.A2CP.01 TCGA.EM.A22O.01 TCGA.EM.A2P1.01 TCGA.J8.A3YH.01 TCGA.DJ.A3UZ.01 TCGA.IM.A3EB.01
#> "0231" NA NA NA NA NA
#> TCGA.BJ.A3F0.01 TCGA.EL.A3GX.01 TCGA.EM.A3AK.01 TCGA.DO.A1JZ.01 TCGA.FY.A3YR.01 TCGA.DO.A1K0.01
#> NA NA NA NA NA NA
#> TCGA.DJ.A3V5.01 TCGA.EM.A3AJ.01 TCGA.IM.A3ED.01 TCGA.EM.A3AO.01 TCGA.EM.A2P1.06 TCGA.EM.A1CW.01
#> NA "0232" NA NA NA NA
#> TCGA.FK.A3SE.01 TCGA.EL.A3T7.01 TCGA.EM.A2P2.01 TCGA.EM.A1CU.11 TCGA.EL.A3T0.11 TCGA.E8.A3X7.01
#> NA NA NA NA NA NA
#> TCGA.ET.A3BQ.01 TCGA.EM.A1CS.01 TCGA.EL.A3GQ.01 TCGA.EL.A3H5.01 TCGA.DJ.A3V4.01 TCGA.EM.A2P3.01
#> NA NA NA NA NA NA
#> TCGA.FY.A3WA.01 TCGA.DJ.A3V2.01 TCGA.FY.A3TY.11 TCGA.BJ.A290.01 TCGA.EM.A3SU.01 TCGA.EL.A3D0.01
#> NA NA NA NA NA NA
#> TCGA.EM.A1CT.11 TCGA.EL.A3GR.01 TCGA.J8.A3YH.06 TCGA.EM.A3ST.11 TCGA.ET.A3DV.01 TCGA.BJ.A3EZ.01
#> NA NA NA NA NA NA
#> TCGA.J8.A3YD.01 TCGA.EM.A3SU.06 TCGA.EM.A3AL.01 TCGA.DJ.A3US.01 TCGA.EM.A1CS.11 TCGA.EM.A1CW.11
#> NA NA NA NA NA NA
#> TCGA.BJ.A190.01 TCGA.EM.A2OZ.01 TCGA.EM.A1CV.11 TCGA.EM.A1CU.01 TCGA.EM.A3AN.01 TCGA.E8.A2EA.01
#> NA NA NA NA NA NA
#> TCGA.EM.A1CV.01 TCGA.EM.A1CT.01 TCGA.EM.A3ST.01 TCGA.ET.A3BS.01 TCGA.EL.A3GO.01 TCGA.DJ.A2Q0.01
#> NA NA NA NA NA NA
#> TCGA.EL.A3D6.01 TCGA.DJ.A3UN.01 TCGA.DJ.A3UU.01 TCGA.FK.A3SD.01 TCGA.DJ.A2PO.01 TCGA.DJ.A3UQ.01
#> NA NA NA NA NA NA
#> TCGA.EM.A1YE.11 TCGA.EL.A3T2.11 TCGA.EL.A3CL.01 TCGA.EM.A1YC.01 TCGA.DJ.A3UP.01 TCGA.EL.A3T0.01
#> NA NA NA NA NA NA
#> TCGA.IM.A3U2.01 TCGA.IM.A3U3.01 TCGA.DJ.A3UX.01 TCGA.ET.A3BW.01 TCGA.ET.A39S.01 TCGA.ET.A3BP.01
#> NA NA NA NA NA NA
#> TCGA.DJ.A1QE.01 TCGA.EL.A3D4.01 TCGA.FK.A3SB.01 TCGA.EL.A3CW.01 TCGA.ET.A39L.01 TCGA.DJ.A2PW.01
#> NA NA NA "0232" NA NA
#> TCGA.EM.A2CO.01 TCGA.FE.A232.01 TCGA.DJ.A3UR.01 TCGA.DJ.A2PP.01 TCGA.ET.A3DQ.01 TCGA.ET.A3DS.01
#> NA NA NA NA "0232" NA
#> TCGA.FY.A3W9.01 TCGA.FK.A3S3.01 TCGA.ET.A2MZ.01 TCGA.BJ.A2NA.11 TCGA.DJ.A1QL.01 TCGA.EL.A3CS.01
#> NA NA NA "0233" NA NA
#> TCGA.FE.A233.01 TCGA.EM.A1YD.11 TCGA.ET.A3DW.11 TCGA.EL.A3T9.01 TCGA.DJ.A3UM.01 TCGA.DO.A2HM.01
#> NA NA NA NA NA NA
#> TCGA.FY.A3BL.01 TCGA.EL.A3TA.11 TCGA.ET.A3BX.01 TCGA.DJ.A1QQ.01 TCGA.DJ.A1QF.01 TCGA.DJ.A1QO.01
#> NA NA NA NA NA NA
#> TCGA.BJ.A2NA.01 TCGA.EM.A1YE.01 TCGA.FY.A2QD.01 TCGA.ET.A39J.01 TCGA.ET.A3DU.01 TCGA.EL.A3CM.01
#> NA NA NA NA NA NA
#> TCGA.DJ.A3UO.01 TCGA.ET.A39P.01 TCGA.DJ.A2Q2.01 TCGA.BJ.A28V.01 TCGA.ET.A3BO.01 TCGA.EL.A3T1.01
#> NA NA NA NA NA NA
#> TCGA.DJ.A1QI.01 TCGA.EL.A3TB.01 TCGA.BJ.A28X.11 TCGA.DJ.A1QN.01 TCGA.FE.A230.01 TCGA.FE.A234.01
#> NA NA "0231" NA NA NA
#> TCGA.ET.A39R.01 TCGA.DJ.A1QG.01 TCGA.EL.A3CV.01 TCGA.FE.A231.01 TCGA.EL.A3TA.01 TCGA.DJ.A3UY.01
#> NA NA NA NA NA NA
#> TCGA.DJ.A2Q1.01 TCGA.EL.A3CU.01 TCGA.EL.A3TB.11 TCGA.ET.A39I.01 TCGA.EM.A1YB.01 TCGA.DJ.A3UV.01
#> NA NA NA NA NA NA
#> TCGA.DJ.A3UT.01 TCGA.ET.A3DW.01 TCGA.ET.A3BT.01 TCGA.EL.A3T3.01 TCGA.DJ.A1QM.01 TCGA.EL.A3CY.01
#> NA NA NA NA NA "0231"
#> TCGA.ET.A39O.01 TCGA.EM.A1YC.11 TCGA.DJ.A1QH.01 TCGA.EL.A3T3.11 TCGA.EL.A3CX.01 TCGA.EL.A3T2.01
#> NA NA NA NA NA NA
#> TCGA.EM.A22P.01 TCGA.EL.A3T8.11 TCGA.DJ.A2PU.01 TCGA.DJ.A3UK.01 TCGA.ET.A3DO.01 TCGA.EM.A1YA.01
#> NA NA NA NA NA NA
#> TCGA.ET.A3BV.01 TCGA.EL.A3CO.01 TCGA.DJ.A2PN.01 TCGA.FK.A3SG.01 TCGA.FK.A3SH.01 TCGA.EM.A1YD.01
#> NA "0233" NA NA NA NA
#> TCGA.DJ.A1QD.01 TCGA.EL.A3CZ.01 TCGA.BJ.A0Z9.01 TCGA.CE.A13K.01 TCGA.EM.A3FR.01 TCGA.EM.A3O8.01
#> NA NA NA NA NA NA
#> TCGA.FY.A3R6.01 TCGA.FY.A3R9.01 TCGA.EL.A3D1.01 TCGA.EM.A3O6.01 TCGA.BJ.A0Z5.01 TCGA.BJ.A28S.01
#> NA NA NA NA NA NA
#> TCGA.BJ.A0ZH.01 TCGA.ET.A3DT.01 TCGA.H2.A3RI.11 TCGA.DJ.A13W.01 TCGA.DJ.A13T.01 TCGA.BJ.A0ZA.01
#> NA NA NA NA NA NA
#> TCGA.BJ.A3PT.01 TCGA.FE.A3PD.01 TCGA.BJ.A0ZF.01 TCGA.ET.A39M.01 TCGA.BJ.A0ZJ.01 TCGA.BJ.A0YZ.01
#> NA NA NA NA NA NA
#> TCGA.FE.A3PC.01 TCGA.DJ.A2QB.01 TCGA.EM.A3OB.01 TCGA.H2.A3RH.01 TCGA.ET.A39T.01 TCGA.DJ.A2PV.01
#> NA NA NA NA NA NA
#> TCGA.BJ.A3PR.11 TCGA.EL.A3T6.11 TCGA.DJ.A13X.01 TCGA.BJ.A0ZG.01 TCGA.EL.A3T6.01 TCGA.BJ.A0Z0.01
#> "0232" "0233" NA NA NA NA
#> TCGA.ET.A39K.01 TCGA.EM.A3O9.01 TCGA.BJ.A3PU.01 TCGA.BJ.A3PR.01 TCGA.EM.A3O3.01 TCGA.BJ.A0ZB.01
#> NA "0234" NA "0231" NA NA
#> TCGA.EM.A3OA.01 TCGA.DJ.A2PR.01 TCGA.DJ.A13L.01 TCGA.FY.A3ON.01 TCGA.DJ.A13V.01 TCGA.FY.A3R8.01
#> NA NA NA NA NA NA
#> TCGA.EL.A3CP.01 TCGA.DJ.A13U.01 TCGA.DE.A0Y3.01 TCGA.ET.A2N4.01 TCGA.DJ.A13P.01 TCGA.BJ.A0ZE.01
#> NA NA NA NA NA NA
#> TCGA.EM.A3O7.01 TCGA.DJ.A13O.01 TCGA.FY.A3RA.01 TCGA.DJ.A13M.01 TCGA.DJ.A13R.01 TCGA.ET.A3DR.01
#> NA "0233" NA NA NA NA
#> TCGA.FE.A3PB.01 TCGA.ET.A3BN.01 TCGA.H2.A3RI.01 TCGA.ET.A39N.01 TCGA.BJ.A3PU.11 TCGA.FY.A3R7.01
#> NA NA NA NA NA NA
#> TCGA.FE.A3PA.01 TCGA.EM.A2CN.01 TCGA.BJ.A0Z2.01 TCGA.FY.A3I5.01 TCGA.DJ.A13S.01 TCGA.DE.A0Y2.01
#> NA NA NA NA NA NA
#> TCGA.ET.A3BU.01
#> NA
get_classes(res_rh, merge_node = merge_node_param(min_n_signatures = 11281))
#> TCGA.E8.A416.01 TCGA.E8.A433.01 TCGA.EL.A4K9.01 TCGA.DJ.A3V9.01 TCGA.EL.A3ZO.11 TCGA.EL.A3ZN.01
#> NA NA NA NA NA NA
#> TCGA.KS.A41F.01 TCGA.EL.A3ZK.01 TCGA.ET.A40R.01 TCGA.EL.A3ZM.01 TCGA.ET.A2N3.01 TCGA.EL.A3ZQ.01
#> NA NA NA NA NA NA
#> TCGA.ET.A40T.01 TCGA.DE.A4MA.01 TCGA.EM.A4FU.01 TCGA.E8.A418.01 TCGA.DJ.A3VD.01 TCGA.DJ.A3VM.01
#> NA NA NA NA NA NA
#> TCGA.EL.A3ZG.01 TCGA.EM.A4FV.01 TCGA.E8.A413.01 TCGA.DJ.A3VG.01 TCGA.EL.A4K2.01 TCGA.IM.A420.01
#> NA NA NA NA NA NA
#> TCGA.KS.A41J.01 TCGA.EL.A3ZK.11 TCGA.J8.A3O2.01 TCGA.E8.A415.01 TCGA.FY.A40M.01 TCGA.DJ.A3VB.01
#> NA NA NA NA NA NA
#> TCGA.KS.A41I.01 TCGA.DJ.A3VL.01 TCGA.ET.A4KQ.01 TCGA.H2.A421.01 TCGA.EL.A3ZO.01 TCGA.KS.A4I3.01
#> NA NA NA NA NA NA
#> TCGA.DJ.A4UT.01 TCGA.DE.A4MD.01 TCGA.EL.A4JW.01 TCGA.DJ.A3VI.01 TCGA.DJ.A3VA.01 TCGA.L6.A4ET.01
#> NA NA NA NA NA NA
#> TCGA.E8.A419.01 TCGA.DJ.A4V0.01 TCGA.DJ.A4V2.01 TCGA.ET.A40Q.01 TCGA.EL.A3ZS.01 TCGA.KS.A4ID.01
#> NA NA NA NA NA NA
#> TCGA.EL.A3ZL.11 TCGA.J8.A3YE.01 TCGA.EL.A4K7.01 TCGA.DJ.A3VF.01 TCGA.EM.A4FH.01 TCGA.E8.A432.01
#> NA NA NA NA NA NA
#> TCGA.J8.A3O2.06 TCGA.ET.A2MX.01 TCGA.ET.A40S.01 TCGA.DE.A4M8.01 TCGA.IM.A41Z.01 TCGA.EL.A4KD.01
#> NA NA NA NA NA NA
#> TCGA.DJ.A3V7.01 TCGA.FY.A40L.01 TCGA.DE.A4M9.01 TCGA.J8.A42S.01 TCGA.KS.A41L.01 TCGA.EM.A4FN.01
#> NA NA NA NA NA NA
#> TCGA.EL.A4K1.01 TCGA.KS.A4IC.01 TCGA.E8.A414.01 TCGA.H2.A422.01 TCGA.J8.A3YF.01 TCGA.EL.A4KI.01
#> NA NA NA NA NA NA
#> TCGA.EM.A4G1.01 TCGA.DJ.A3VJ.01 TCGA.DE.A4MD.06 TCGA.EL.A3ZP.01 TCGA.EM.A4FQ.01 TCGA.EL.A3ZT.01
#> NA NA NA NA NA NA
#> TCGA.DJ.A4V4.01 TCGA.FY.A40K.01 TCGA.L6.A4EQ.01 TCGA.DJ.A3VE.01 TCGA.E8.A434.01 TCGA.EL.A3ZH.01
#> NA NA NA NA NA NA
#> TCGA.EM.A4FR.01 TCGA.EL.A3ZH.11 TCGA.EL.A3ZR.01 TCGA.DJ.A3V8.01 TCGA.EL.A3ZG.11 TCGA.ET.A40P.01
#> NA NA NA NA NA NA
#> TCGA.DE.A4MB.01 TCGA.MK.A4N6.01 TCGA.DJ.A3VK.01 TCGA.E8.A417.01 TCGA.L6.A4EU.01 TCGA.J8.A4HY.01
#> NA NA NA NA NA NA
#> TCGA.EL.A3ZL.01 TCGA.EL.A3ZP.11 TCGA.FY.A40N.01 TCGA.J8.A4HW.01 TCGA.BJ.A45J.01 TCGA.CE.A482.01
#> NA NA NA NA NA NA
#> TCGA.DJ.A2Q6.01 TCGA.DJ.A2PX.01 TCGA.DJ.A4UL.01 TCGA.EL.A4JX.01 TCGA.BJ.A2N8.11 TCGA.DJ.A2Q5.01
#> NA NA NA NA NA NA
#> TCGA.EL.A4KG.01 TCGA.DJ.A4UP.01 TCGA.E8.A438.01 TCGA.EL.A3H2.01 TCGA.EM.A3AP.01 TCGA.DJ.A2PQ.01
#> NA NA NA NA NA NA
#> TCGA.L6.A4EP.01 TCGA.FY.A4B4.01 TCGA.EL.A4KH.01 TCGA.BJ.A45E.01 TCGA.DJ.A4V5.01 TCGA.DE.A4MC.01
#> NA NA NA NA NA NA
#> TCGA.E8.A44M.01 TCGA.BJ.A45K.01 TCGA.E3.A3DZ.01 TCGA.E3.A3E2.01 TCGA.BJ.A45H.01 TCGA.E8.A44K.01
#> NA NA NA NA NA NA
#> TCGA.ET.A2MY.01 TCGA.EL.A3H8.01 TCGA.BJ.A45C.01 TCGA.BJ.A45G.01 TCGA.EL.A4JZ.01 TCGA.CE.A481.01
#> NA NA NA NA NA NA
#> TCGA.KS.A4I9.01 TCGA.EL.A3MW.01 TCGA.E8.A436.01 TCGA.E3.A3DY.01 TCGA.DJ.A2Q3.01 TCGA.BJ.A2P4.01
#> NA NA NA NA NA NA
#> TCGA.CE.A484.01 TCGA.ET.A2N1.01 TCGA.DJ.A2Q4.01 TCGA.DJ.A2PZ.01 TCGA.BJ.A45F.01 TCGA.IM.A4EB.01
#> NA NA NA NA NA NA
#> TCGA.EM.A4FO.01 TCGA.FY.A4B3.01 TCGA.FY.A4B0.01 TCGA.BJ.A45I.01 TCGA.E3.A3E3.01 TCGA.EM.A3AQ.01
#> NA NA NA NA NA NA
#> TCGA.EL.A3N3.01 TCGA.DJ.A2Q9.01 TCGA.EM.A4FM.01 TCGA.EL.A4K6.01 TCGA.MK.A4N9.01 TCGA.KS.A4I1.01
#> NA NA NA NA NA NA
#> TCGA.DJ.A2PS.01 TCGA.CE.A3MD.01 TCGA.E3.A3E5.01 TCGA.EL.A3CN.01 TCGA.J8.A4HW.06 TCGA.EM.A4FK.01
#> NA NA NA NA NA NA
#> TCGA.E8.A437.01 TCGA.BJ.A4O8.01 TCGA.EL.A3MW.11 TCGA.E3.A3E0.01 TCGA.BJ.A45D.01 TCGA.CE.A483.01
#> NA NA NA NA NA NA
#> TCGA.CE.A485.01 TCGA.DJ.A4UR.01 TCGA.IM.A41Y.01 TCGA.ET.A4KN.01 TCGA.KS.A4I5.01 TCGA.DJ.A4UQ.01
#> NA NA NA NA NA NA
#> TCGA.KS.A4IB.01 TCGA.EL.A3N2.11 TCGA.BJ.A2N9.01 TCGA.DJ.A4UW.01 TCGA.EL.A3GZ.11 TCGA.EM.A3AR.01
#> NA NA NA NA NA NA
#> TCGA.EL.A3N3.11 TCGA.DE.A3KN.01 TCGA.DJ.A2QA.01 TCGA.EL.A4JV.01 TCGA.EM.A4FF.01 TCGA.EL.A4K0.01
#> NA NA NA NA NA NA
#> TCGA.FK.A4UB.01 TCGA.BJ.A4O9.01 TCGA.BJ.A2N7.01 TCGA.DE.A2OL.01 TCGA.CE.A3ME.01 TCGA.MK.A4N7.01
#> NA NA NA NA NA NA
#> TCGA.EL.A3H2.11 TCGA.EL.A4K4.01 TCGA.EL.A3GS.01 TCGA.EL.A3GZ.01 TCGA.E3.A3E1.01 TCGA.DJ.A2Q8.01
#> NA NA NA NA NA NA
#> TCGA.EL.A3N2.01 TCGA.KS.A4I7.01 TCGA.MK.A84Z.01 TCGA.ET.A3DP.11 TCGA.EL.A3MX.11 TCGA.ET.A25G.01
#> NA NA NA NA NA NA
#> TCGA.EM.A3FK.01 TCGA.EM.A2CS.01 TCGA.FE.A23A.01 TCGA.BJ.A28T.11 TCGA.EM.A22J.01 TCGA.EL.A3MX.01
#> NA NA NA NA NA NA
#> TCGA.FY.A3I4.01 TCGA.BJ.A28W.11 TCGA.ET.A25R.01 TCGA.BJ.A2N8.01 TCGA.FY.A76V.01 TCGA.EM.A3FN.01
#> NA NA NA NA NA NA
#> TCGA.QD.A8IV.01 TCGA.EM.A3FJ.01 TCGA.ET.A2MY.11 TCGA.EM.A3FQ.06 TCGA.ET.A25P.01 TCGA.ET.A2N0.01
#> NA NA NA NA NA NA
#> TCGA.EM.A2CT.01 TCGA.FE.A235.01 TCGA.ET.A25M.01 TCGA.EL.A3MY.01 TCGA.DE.A7U5.01 TCGA.E8.A2JQ.11
#> NA NA NA NA NA NA
#> TCGA.ET.A3DP.01 TCGA.EM.A2CL.01 TCGA.ET.A2N5.01 TCGA.ET.A25J.11 TCGA.DE.A69J.01 TCGA.BJ.A28R.11
#> NA NA NA NA NA NA
#> TCGA.ET.A25K.01 TCGA.EL.A3GV.01 TCGA.GE.A2C6.01 TCGA.EM.A3FM.01 TCGA.EL.A3H7.11 TCGA.FE.A22Z.01
#> NA NA NA NA NA NA
#> TCGA.H2.A2K9.01 TCGA.EM.A22Q.01 TCGA.EM.A3FP.01 TCGA.GE.A2C6.11 TCGA.EL.A3MZ.01 TCGA.DJ.A2PT.01
#> NA NA NA NA NA NA
#> TCGA.E8.A242.01 TCGA.ET.A25L.01 TCGA.CE.A27D.01 TCGA.EL.A3H1.11 TCGA.BJ.A2N7.11 TCGA.DJ.A2Q7.01
#> NA NA NA NA NA NA
#> TCGA.J8.A3O1.01 TCGA.EM.A2CR.01 TCGA.DE.A69K.01 TCGA.EM.A2CQ.01 TCGA.FE.A238.01 TCGA.EL.A3H1.01
#> NA NA NA NA NA NA
#> TCGA.BJ.A28W.01 TCGA.BJ.A28T.01 TCGA.EM.A2CJ.01 TCGA.EM.A3FQ.01 TCGA.4C.A93U.01 TCGA.EM.A22M.01
#> NA NA NA NA NA NA
#> TCGA.J8.A3NZ.01 TCGA.EM.A22K.01 TCGA.FE.A236.01 TCGA.BJ.A28R.01 TCGA.EM.A2CU.01 TCGA.ET.A25N.01
#> NA NA NA NA NA NA
#> TCGA.EL.A3H7.01 TCGA.FY.A3NM.01 TCGA.EM.A3FO.01 TCGA.EM.A22L.01 TCGA.BJ.A2N9.11 TCGA.BJ.A291.01
#> NA NA NA NA NA NA
#> TCGA.ET.A2N5.11 TCGA.ET.A25N.11 TCGA.J8.A3O0.01 TCGA.FE.A237.01 TCGA.DJ.A2QC.01 TCGA.ET.A25O.01
#> NA NA NA NA NA NA
#> TCGA.EL.A3GU.01 TCGA.EL.A3MY.11 TCGA.DJ.A2PY.01 TCGA.EM.A2CS.06 TCGA.FY.A3NP.01 TCGA.ET.A25I.01
#> NA NA NA NA NA NA
#> TCGA.H2.A26U.01 TCGA.BJ.A290.11 TCGA.EM.A22I.01 TCGA.FE.A239.01 TCGA.BJ.A28Z.01 TCGA.DE.A0XZ.01
#> NA NA NA NA NA NA
#> TCGA.ET.A25J.01 TCGA.EM.A22N.01 TCGA.EM.A2CM.01 TCGA.FY.A3NN.01 TCGA.EM.A3FL.01 TCGA.H2.A2K9.11
#> NA NA NA NA NA NA
#> TCGA.EL.A3H3.01 TCGA.EL.A3H4.01 TCGA.EM.A2OX.01 TCGA.EM.A3SX.01 TCGA.BJ.A0Z3.01 TCGA.BJ.A28X.01
#> NA NA NA NA NA NA
#> TCGA.EL.A3CT.01 TCGA.EL.A3CR.01 TCGA.FY.A3TY.01 TCGA.J8.A3YG.01 TCGA.DJ.A3V6.01 TCGA.EM.A3SZ.01
#> NA NA NA NA NA NA
#> TCGA.EM.A2OW.01 TCGA.DO.A1JZ.11 TCGA.EL.A3D5.01 TCGA.EM.A2P0.01 TCGA.E8.A2JQ.01 TCGA.BJ.A18Z.01
#> NA NA NA NA NA NA
#> TCGA.DJ.A3V0.01 TCGA.EL.A3GW.01 TCGA.DJ.A3UW.01 TCGA.DJ.A3V3.01 TCGA.EL.A3T1.11 TCGA.BJ.A0ZC.01
#> NA NA NA NA NA NA
#> TCGA.EM.A2OV.01 TCGA.EL.A3GY.01 TCGA.EM.A3SY.01 TCGA.EM.A3AI.01 TCGA.EM.A2OY.01 TCGA.EL.A3T8.01
#> NA NA NA NA NA NA
#> TCGA.BJ.A18Y.01 TCGA.EL.A3GP.01 TCGA.EM.A2CK.01 TCGA.EL.A3T7.11 TCGA.BJ.A192.01 TCGA.BJ.A191.01
#> NA NA NA NA NA NA
#> TCGA.EM.A2CP.01 TCGA.EM.A22O.01 TCGA.EM.A2P1.01 TCGA.J8.A3YH.01 TCGA.DJ.A3UZ.01 TCGA.IM.A3EB.01
#> NA NA NA NA NA NA
#> TCGA.BJ.A3F0.01 TCGA.EL.A3GX.01 TCGA.EM.A3AK.01 TCGA.DO.A1JZ.01 TCGA.FY.A3YR.01 TCGA.DO.A1K0.01
#> NA NA NA NA NA NA
#> TCGA.DJ.A3V5.01 TCGA.EM.A3AJ.01 TCGA.IM.A3ED.01 TCGA.EM.A3AO.01 TCGA.EM.A2P1.06 TCGA.EM.A1CW.01
#> NA NA NA NA NA NA
#> TCGA.FK.A3SE.01 TCGA.EL.A3T7.01 TCGA.EM.A2P2.01 TCGA.EM.A1CU.11 TCGA.EL.A3T0.11 TCGA.E8.A3X7.01
#> NA NA NA NA NA NA
#> TCGA.ET.A3BQ.01 TCGA.EM.A1CS.01 TCGA.EL.A3GQ.01 TCGA.EL.A3H5.01 TCGA.DJ.A3V4.01 TCGA.EM.A2P3.01
#> NA NA NA NA NA NA
#> TCGA.FY.A3WA.01 TCGA.DJ.A3V2.01 TCGA.FY.A3TY.11 TCGA.BJ.A290.01 TCGA.EM.A3SU.01 TCGA.EL.A3D0.01
#> NA NA NA NA NA NA
#> TCGA.EM.A1CT.11 TCGA.EL.A3GR.01 TCGA.J8.A3YH.06 TCGA.EM.A3ST.11 TCGA.ET.A3DV.01 TCGA.BJ.A3EZ.01
#> NA NA NA NA NA NA
#> TCGA.J8.A3YD.01 TCGA.EM.A3SU.06 TCGA.EM.A3AL.01 TCGA.DJ.A3US.01 TCGA.EM.A1CS.11 TCGA.EM.A1CW.11
#> NA NA NA NA NA NA
#> TCGA.BJ.A190.01 TCGA.EM.A2OZ.01 TCGA.EM.A1CV.11 TCGA.EM.A1CU.01 TCGA.EM.A3AN.01 TCGA.E8.A2EA.01
#> NA NA NA NA NA NA
#> TCGA.EM.A1CV.01 TCGA.EM.A1CT.01 TCGA.EM.A3ST.01 TCGA.ET.A3BS.01 TCGA.EL.A3GO.01 TCGA.DJ.A2Q0.01
#> NA NA NA NA NA NA
#> TCGA.EL.A3D6.01 TCGA.DJ.A3UN.01 TCGA.DJ.A3UU.01 TCGA.FK.A3SD.01 TCGA.DJ.A2PO.01 TCGA.DJ.A3UQ.01
#> NA NA NA NA NA NA
#> TCGA.EM.A1YE.11 TCGA.EL.A3T2.11 TCGA.EL.A3CL.01 TCGA.EM.A1YC.01 TCGA.DJ.A3UP.01 TCGA.EL.A3T0.01
#> NA NA NA NA NA NA
#> TCGA.IM.A3U2.01 TCGA.IM.A3U3.01 TCGA.DJ.A3UX.01 TCGA.ET.A3BW.01 TCGA.ET.A39S.01 TCGA.ET.A3BP.01
#> NA NA NA NA NA NA
#> TCGA.DJ.A1QE.01 TCGA.EL.A3D4.01 TCGA.FK.A3SB.01 TCGA.EL.A3CW.01 TCGA.ET.A39L.01 TCGA.DJ.A2PW.01
#> NA NA NA NA NA NA
#> TCGA.EM.A2CO.01 TCGA.FE.A232.01 TCGA.DJ.A3UR.01 TCGA.DJ.A2PP.01 TCGA.ET.A3DQ.01 TCGA.ET.A3DS.01
#> NA NA NA NA NA NA
#> TCGA.FY.A3W9.01 TCGA.FK.A3S3.01 TCGA.ET.A2MZ.01 TCGA.BJ.A2NA.11 TCGA.DJ.A1QL.01 TCGA.EL.A3CS.01
#> NA NA NA NA NA NA
#> TCGA.FE.A233.01 TCGA.EM.A1YD.11 TCGA.ET.A3DW.11 TCGA.EL.A3T9.01 TCGA.DJ.A3UM.01 TCGA.DO.A2HM.01
#> NA NA NA NA NA NA
#> TCGA.FY.A3BL.01 TCGA.EL.A3TA.11 TCGA.ET.A3BX.01 TCGA.DJ.A1QQ.01 TCGA.DJ.A1QF.01 TCGA.DJ.A1QO.01
#> NA NA NA NA NA NA
#> TCGA.BJ.A2NA.01 TCGA.EM.A1YE.01 TCGA.FY.A2QD.01 TCGA.ET.A39J.01 TCGA.ET.A3DU.01 TCGA.EL.A3CM.01
#> NA NA NA NA NA NA
#> TCGA.DJ.A3UO.01 TCGA.ET.A39P.01 TCGA.DJ.A2Q2.01 TCGA.BJ.A28V.01 TCGA.ET.A3BO.01 TCGA.EL.A3T1.01
#> NA NA NA NA NA NA
#> TCGA.DJ.A1QI.01 TCGA.EL.A3TB.01 TCGA.BJ.A28X.11 TCGA.DJ.A1QN.01 TCGA.FE.A230.01 TCGA.FE.A234.01
#> NA NA NA NA NA NA
#> TCGA.ET.A39R.01 TCGA.DJ.A1QG.01 TCGA.EL.A3CV.01 TCGA.FE.A231.01 TCGA.EL.A3TA.01 TCGA.DJ.A3UY.01
#> NA NA NA NA NA NA
#> TCGA.DJ.A2Q1.01 TCGA.EL.A3CU.01 TCGA.EL.A3TB.11 TCGA.ET.A39I.01 TCGA.EM.A1YB.01 TCGA.DJ.A3UV.01
#> NA NA NA NA NA NA
#> TCGA.DJ.A3UT.01 TCGA.ET.A3DW.01 TCGA.ET.A3BT.01 TCGA.EL.A3T3.01 TCGA.DJ.A1QM.01 TCGA.EL.A3CY.01
#> NA NA NA NA NA NA
#> TCGA.ET.A39O.01 TCGA.EM.A1YC.11 TCGA.DJ.A1QH.01 TCGA.EL.A3T3.11 TCGA.EL.A3CX.01 TCGA.EL.A3T2.01
#> NA NA NA NA NA NA
#> TCGA.EM.A22P.01 TCGA.EL.A3T8.11 TCGA.DJ.A2PU.01 TCGA.DJ.A3UK.01 TCGA.ET.A3DO.01 TCGA.EM.A1YA.01
#> NA NA NA NA NA NA
#> TCGA.ET.A3BV.01 TCGA.EL.A3CO.01 TCGA.DJ.A2PN.01 TCGA.FK.A3SG.01 TCGA.FK.A3SH.01 TCGA.EM.A1YD.01
#> NA NA NA NA NA NA
#> TCGA.DJ.A1QD.01 TCGA.EL.A3CZ.01 TCGA.BJ.A0Z9.01 TCGA.CE.A13K.01 TCGA.EM.A3FR.01 TCGA.EM.A3O8.01
#> NA NA NA NA NA NA
#> TCGA.FY.A3R6.01 TCGA.FY.A3R9.01 TCGA.EL.A3D1.01 TCGA.EM.A3O6.01 TCGA.BJ.A0Z5.01 TCGA.BJ.A28S.01
#> NA NA NA NA NA NA
#> TCGA.BJ.A0ZH.01 TCGA.ET.A3DT.01 TCGA.H2.A3RI.11 TCGA.DJ.A13W.01 TCGA.DJ.A13T.01 TCGA.BJ.A0ZA.01
#> NA NA NA NA NA NA
#> TCGA.BJ.A3PT.01 TCGA.FE.A3PD.01 TCGA.BJ.A0ZF.01 TCGA.ET.A39M.01 TCGA.BJ.A0ZJ.01 TCGA.BJ.A0YZ.01
#> NA NA NA NA NA NA
#> TCGA.FE.A3PC.01 TCGA.DJ.A2QB.01 TCGA.EM.A3OB.01 TCGA.H2.A3RH.01 TCGA.ET.A39T.01 TCGA.DJ.A2PV.01
#> NA NA NA NA NA NA
#> TCGA.BJ.A3PR.11 TCGA.EL.A3T6.11 TCGA.DJ.A13X.01 TCGA.BJ.A0ZG.01 TCGA.EL.A3T6.01 TCGA.BJ.A0Z0.01
#> NA NA NA NA NA NA
#> TCGA.ET.A39K.01 TCGA.EM.A3O9.01 TCGA.BJ.A3PU.01 TCGA.BJ.A3PR.01 TCGA.EM.A3O3.01 TCGA.BJ.A0ZB.01
#> NA NA NA NA NA NA
#> TCGA.EM.A3OA.01 TCGA.DJ.A2PR.01 TCGA.DJ.A13L.01 TCGA.FY.A3ON.01 TCGA.DJ.A13V.01 TCGA.FY.A3R8.01
#> NA NA NA NA NA NA
#> TCGA.EL.A3CP.01 TCGA.DJ.A13U.01 TCGA.DE.A0Y3.01 TCGA.ET.A2N4.01 TCGA.DJ.A13P.01 TCGA.BJ.A0ZE.01
#> NA NA NA NA NA NA
#> TCGA.EM.A3O7.01 TCGA.DJ.A13O.01 TCGA.FY.A3RA.01 TCGA.DJ.A13M.01 TCGA.DJ.A13R.01 TCGA.ET.A3DR.01
#> NA NA NA NA NA NA
#> TCGA.FE.A3PB.01 TCGA.ET.A3BN.01 TCGA.H2.A3RI.01 TCGA.ET.A39N.01 TCGA.BJ.A3PU.11 TCGA.FY.A3R7.01
#> NA NA NA NA NA NA
#> TCGA.FE.A3PA.01 TCGA.EM.A2CN.01 TCGA.BJ.A0Z2.01 TCGA.FY.A3I5.01 TCGA.DJ.A13S.01 TCGA.DE.A0Y2.01
#> NA NA NA NA NA NA
#> TCGA.ET.A3BU.01
#> NA
Heatmaps of the top rows:
top_rows_heatmap(res_rh)
#> Error in UseMethod("height", x) :
#> 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 = 1289),
method = "UMAP", top_value_method = "SD", top_n = 40000, scale_rows = FALSE)
dimension_reduction(res_rh, merge_node = merge_node_param(min_n_signatures = 1289),
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 = 1291),
method = "UMAP", top_value_method = "SD", top_n = 40000, scale_rows = FALSE)
dimension_reduction(res_rh, merge_node = merge_node_param(min_n_signatures = 1291),
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 = 1595),
method = "UMAP", top_value_method = "SD", top_n = 40000, scale_rows = FALSE)
dimension_reduction(res_rh, merge_node = merge_node_param(min_n_signatures = 1595),
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 = 1662),
method = "UMAP", top_value_method = "SD", top_n = 40000, scale_rows = FALSE)
dimension_reduction(res_rh, merge_node = merge_node_param(min_n_signatures = 1662),
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 = 2027),
method = "UMAP", top_value_method = "SD", top_n = 40000, scale_rows = FALSE)
dimension_reduction(res_rh, merge_node = merge_node_param(min_n_signatures = 2027),
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 = 2606),
method = "UMAP", top_value_method = "SD", top_n = 40000, scale_rows = FALSE)
dimension_reduction(res_rh, merge_node = merge_node_param(min_n_signatures = 2606),
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 = 3159),
method = "UMAP", top_value_method = "SD", top_n = 40000, scale_rows = FALSE)
dimension_reduction(res_rh, merge_node = merge_node_param(min_n_signatures = 3159),
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 = 3180),
method = "UMAP", top_value_method = "SD", top_n = 40000, scale_rows = FALSE)
dimension_reduction(res_rh, merge_node = merge_node_param(min_n_signatures = 3180),
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 = 3187),
method = "UMAP", top_value_method = "SD", top_n = 40000, scale_rows = FALSE)
dimension_reduction(res_rh, merge_node = merge_node_param(min_n_signatures = 3187),
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 = 3269),
method = "UMAP", top_value_method = "SD", top_n = 40000, scale_rows = FALSE)
dimension_reduction(res_rh, merge_node = merge_node_param(min_n_signatures = 3269),
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 = 3511),
method = "UMAP", top_value_method = "SD", top_n = 40000, scale_rows = FALSE)
dimension_reduction(res_rh, merge_node = merge_node_param(min_n_signatures = 3511),
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 = 3641),
method = "UMAP", top_value_method = "SD", top_n = 40000, scale_rows = FALSE)
dimension_reduction(res_rh, merge_node = merge_node_param(min_n_signatures = 3641),
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 = 4441),
method = "UMAP", top_value_method = "SD", top_n = 40000, scale_rows = FALSE)
dimension_reduction(res_rh, merge_node = merge_node_param(min_n_signatures = 4441),
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 = 5878),
method = "UMAP", top_value_method = "SD", top_n = 40000, scale_rows = FALSE)
dimension_reduction(res_rh, merge_node = merge_node_param(min_n_signatures = 5878),
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 = 6634),
method = "UMAP", top_value_method = "SD", top_n = 40000, scale_rows = FALSE)
dimension_reduction(res_rh, merge_node = merge_node_param(min_n_signatures = 6634),
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 = 8600),
method = "UMAP", top_value_method = "SD", top_n = 40000, scale_rows = FALSE)
dimension_reduction(res_rh, merge_node = merge_node_param(min_n_signatures = 8600),
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 = 11281),
method = "UMAP", top_value_method = "SD", top_n = 40000, scale_rows = FALSE)
dimension_reduction(res_rh, merge_node = merge_node_param(min_n_signatures = 11281),
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 = 1289))
get_signatures(res_rh, merge_node = merge_node_param(min_n_signatures = 1291))
get_signatures(res_rh, merge_node = merge_node_param(min_n_signatures = 1595))
get_signatures(res_rh, merge_node = merge_node_param(min_n_signatures = 1662))
get_signatures(res_rh, merge_node = merge_node_param(min_n_signatures = 2027))
get_signatures(res_rh, merge_node = merge_node_param(min_n_signatures = 2606))
get_signatures(res_rh, merge_node = merge_node_param(min_n_signatures = 3159))
get_signatures(res_rh, merge_node = merge_node_param(min_n_signatures = 3180))
get_signatures(res_rh, merge_node = merge_node_param(min_n_signatures = 3187))
get_signatures(res_rh, merge_node = merge_node_param(min_n_signatures = 3269))
get_signatures(res_rh, merge_node = merge_node_param(min_n_signatures = 3511))
get_signatures(res_rh, merge_node = merge_node_param(min_n_signatures = 3641))
#> Error in lt[[hierarchy[i, 1]]]$AddChildNode({: attempt to apply non-function
get_signatures(res_rh, merge_node = merge_node_param(min_n_signatures = 4441))
#> Error in lt[[hierarchy[i, 1]]]$AddChildNode({: attempt to apply non-function
get_signatures(res_rh, merge_node = merge_node_param(min_n_signatures = 5878))
#> Error in lt[[hierarchy[i, 1]]]$AddChildNode({: attempt to apply non-function
get_signatures(res_rh, merge_node = merge_node_param(min_n_signatures = 6634))
#> Error in lt[[hierarchy[i, 1]]]$AddChildNode({: attempt to apply non-function
get_signatures(res_rh, merge_node = merge_node_param(min_n_signatures = 8600))
#> Error in lt[[hierarchy[i, 1]]]$AddChildNode({: attempt to apply non-function
get_signatures(res_rh, merge_node = merge_node_param(min_n_signatures = 11281))
#> Error in names(x) <- value: 'names' attribute [1] must be the same length as the vector [0]
Compare signatures from different nodes:
compare_signatures(res_rh, verbose = FALSE)
If there are too many signatures, top_signatures = ... can be set to only show the
signatures with the highest FDRs. Note it only works on every node and the final signatures
are the union of all signatures of all nodes.
# code only for demonstration
# e.g. to show the top 500 most significant rows on each node.
tb = get_signature(res_rh, top_signatures = 500)
Child nodes: Node01 , Node02 , Node03 .
The object with results only for a single top-value method and a single partitioning method can be extracted as:
res = res_rh["0"]
A summary of res and all the functions that can be applied to it:
res
#> A 'DownSamplingConsensusPartition' object with k = 2, 3, 4, 5, 6, 7, 8.
#> On a matrix with 375938 rows and 500 columns, randomly sampled from 571 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 7.
#>
#> Following methods can be applied to this 'DownSamplingConsensusPartition' object:
#> [1] "cola_report" "collect_classes" "collect_plots"
#> [4] "collect_stats" "colnames" "compare_partitions"
#> [7] "compare_signatures" "consensus_heatmap" "dimension_reduction"
#> [10] "functional_enrichment" "get_anno_col" "get_anno"
#> [13] "get_classes" "get_consensus" "get_matrix"
#> [16] "get_membership" "get_param" "get_signatures"
#> [19] "get_stats" "is_best_k" "is_stable_k"
#> [22] "membership_heatmap" "ncol" "nrow"
#> [25] "plot_ecdf" "predict_classes" "rownames"
#> [28] "select_partition_number" "show" "suggest_best_k"
#> [31] "test_to_known_factors" "top_rows_heatmap"
collect_plots() function collects all the plots made from res for all k (number of subgroups)
into one single page to provide an easy and fast comparison between different k.
collect_plots(res)
The plots are:
k and the heatmap of
predicted classes for each k.k.k.k.All the plots in panels can be made by individual functions and they are plotted later in this section.
select_partition_number() produces several plots showing different
statistics for choosing “optimized” k. There are following statistics:
k;k, the area increased is defined as \(A_k - A_{k-1}\).The detailed explanations of these statistics can be found in the cola vignette.
Generally speaking, higher 1-PAC score, higher mean silhouette score or higher
concordance corresponds to better partition. Rand index and Jaccard index
measure how similar the current partition is compared to partition with k-1.
If they are too similar, we won't accept k is better than k-1.
select_partition_number(res)
The numeric values for all these statistics can be obtained by get_stats().
get_stats(res)
#> k 1-PAC mean_silhouette concordance area_increased Rand Jaccard
#> 2 2 1.000 0.991 0.996 0.4800 0.521 0.521
#> 3 3 1.000 0.988 0.996 0.2994 0.848 0.710
#> 4 4 0.984 0.949 0.978 0.1725 0.867 0.658
#> 5 5 0.949 0.903 0.950 0.0479 0.932 0.761
#> 6 6 0.877 0.893 0.933 0.0634 0.925 0.696
#> 7 7 0.935 0.847 0.912 0.0231 0.974 0.861
#> 8 8 0.853 0.805 0.867 0.0197 0.981 0.888
suggest_best_k() suggests the best \(k\) based on these statistics. The rules are as follows:
suggest_best_k(res)
#> [1] 7
#> attr(,"optional")
#> [1] 2 3 4 5
There is also optional best \(k\) = 2 3 4 5 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.
get_classes(res, k = 2)
#> class p
#> TCGA.E8.A416.01 2 0.000
#> TCGA.E8.A433.01 1 0.000
#> TCGA.EL.A4K9.01 1 0.000
#> TCGA.DJ.A3V9.01 1 0.000
#> TCGA.EL.A3ZO.11 2 0.000
#> TCGA.EL.A3ZN.01 1 0.000
#> TCGA.KS.A41F.01 1 0.000
#> TCGA.EL.A3ZK.01 1 0.000
#> TCGA.ET.A40R.01 1 0.000
#> TCGA.EL.A3ZM.01 1 0.000
#> TCGA.ET.A2N3.01 2 0.000
#> TCGA.EL.A3ZQ.01 1 0.000
#> TCGA.ET.A40T.01 1 0.000
#> TCGA.DE.A4MA.01 1 0.000
#> TCGA.EM.A4FU.01 2 0.000
#> TCGA.E8.A418.01 1 0.000
#> TCGA.DJ.A3VD.01 1 0.000
#> TCGA.DJ.A3VM.01 2 0.000
#> TCGA.EL.A3ZG.01 1 0.000
#> TCGA.EM.A4FV.01 1 0.000
#> TCGA.E8.A413.01 1 0.000
#> TCGA.DJ.A3VG.01 2 0.000
#> TCGA.EL.A4K2.01 2 0.000
#> TCGA.IM.A420.01 1 0.000
#> TCGA.KS.A41J.01 1 0.000
#> TCGA.EL.A3ZK.11 2 0.000
#> TCGA.J8.A3O2.01 1 0.000
#> TCGA.E8.A415.01 1 0.000
#> TCGA.FY.A40M.01 2 0.000
#> TCGA.DJ.A3VB.01 1 0.000
#> TCGA.KS.A41I.01 2 0.000
#> TCGA.DJ.A3VL.01 2 0.000
#> TCGA.ET.A4KQ.01 2 0.000
#> TCGA.H2.A421.01 1 0.000
#> TCGA.EL.A3ZO.01 1 0.000
#> TCGA.KS.A4I3.01 1 0.000
#> TCGA.DJ.A4UT.01 1 0.000
#> TCGA.DE.A4MD.01 1 0.000
#> TCGA.EL.A4JW.01 1 0.000
#> TCGA.DJ.A3VI.01 1 0.000
#> TCGA.DJ.A3VA.01 1 0.000
#> TCGA.L6.A4ET.01 1 0.000
#> TCGA.E8.A419.01 1 0.000
#> TCGA.DJ.A4V0.01 2 0.000
#> TCGA.DJ.A4V2.01 1 0.000
#> TCGA.ET.A40Q.01 1 0.000
#> TCGA.EL.A3ZS.01 1 0.000
#> TCGA.KS.A4ID.01 1 0.000
#> TCGA.EL.A3ZL.11 2 0.000
#> TCGA.J8.A3YE.01 1 0.000
#> TCGA.EL.A4K7.01 1 0.000
#> TCGA.DJ.A3VF.01 1 0.000
#> TCGA.EM.A4FH.01 2 0.000
#> TCGA.E8.A432.01 1 0.000
#> TCGA.J8.A3O2.06 1 0.000
#> TCGA.ET.A2MX.01 1 0.000
#> TCGA.ET.A40S.01 1 0.000
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#> TCGA.FK.A3SG.01 1 0.000
#> TCGA.FK.A3SH.01 1 0.000
#> TCGA.EM.A1YD.01 2 0.000
#> TCGA.DJ.A1QD.01 1 0.000
#> TCGA.EL.A3CZ.01 2 0.000
#> TCGA.BJ.A0Z9.01 1 0.000
#> TCGA.CE.A13K.01 1 0.000
#> TCGA.EM.A3FR.01 2 0.000
#> TCGA.EM.A3O8.01 2 0.000
#> TCGA.FY.A3R6.01 1 0.000
#> TCGA.FY.A3R9.01 2 0.000
#> TCGA.EL.A3D1.01 1 0.000
#> TCGA.EM.A3O6.01 2 0.000
#> TCGA.BJ.A0Z5.01 1 0.000
#> TCGA.BJ.A28S.01 2 0.000
#> TCGA.BJ.A0ZH.01 1 0.000
#> TCGA.ET.A3DT.01 1 0.000
#> TCGA.H2.A3RI.11 2 0.000
#> TCGA.DJ.A13W.01 2 0.000
#> TCGA.DJ.A13T.01 1 0.000
#> TCGA.BJ.A0ZA.01 2 0.000
#> TCGA.BJ.A3PT.01 2 0.000
#> TCGA.FE.A3PD.01 1 0.000
#> TCGA.BJ.A0ZF.01 2 0.000
#> TCGA.ET.A39M.01 1 0.000
#> TCGA.BJ.A0ZJ.01 1 0.000
#> TCGA.BJ.A0YZ.01 2 0.000
#> TCGA.FE.A3PC.01 1 0.000
#> TCGA.DJ.A2QB.01 2 0.000
#> TCGA.EM.A3OB.01 2 0.000
#> TCGA.H2.A3RH.01 2 0.000
#> TCGA.ET.A39T.01 1 0.000
#> TCGA.DJ.A2PV.01 1 0.000
#> TCGA.BJ.A3PR.11 2 0.000
#> TCGA.EL.A3T6.11 2 0.000
#> TCGA.DJ.A13X.01 1 0.000
#> TCGA.BJ.A0ZG.01 2 0.000
#> TCGA.EL.A3T6.01 1 0.000
#> TCGA.BJ.A0Z0.01 2 0.000
#> TCGA.ET.A39K.01 1 0.000
#> TCGA.EM.A3O9.01 2 0.000
#> TCGA.BJ.A3PU.01 1 0.000
#> TCGA.BJ.A3PR.01 2 0.000
#> TCGA.EM.A3O3.01 1 0.000
#> TCGA.BJ.A0ZB.01 1 0.000
#> TCGA.EM.A3OA.01 2 0.000
#> TCGA.DJ.A2PR.01 1 0.000
#> TCGA.DJ.A13L.01 1 0.000
#> TCGA.FY.A3ON.01 1 0.000
#> TCGA.DJ.A13V.01 1 0.000
#> TCGA.FY.A3R8.01 1 0.000
#> TCGA.EL.A3CP.01 1 0.000
#> TCGA.DJ.A13U.01 1 0.000
#> TCGA.DE.A0Y3.01 1 0.000
#> TCGA.ET.A2N4.01 1 0.000
#> TCGA.DJ.A13P.01 1 0.000
#> TCGA.BJ.A0ZE.01 2 0.000
#> TCGA.EM.A3O7.01 1 0.000
#> TCGA.DJ.A13O.01 2 0.000
#> TCGA.FY.A3RA.01 1 0.000
#> TCGA.DJ.A13M.01 2 0.000
#> TCGA.DJ.A13R.01 2 0.000
#> TCGA.ET.A3DR.01 1 0.000
#> TCGA.FE.A3PB.01 1 0.000
#> TCGA.ET.A3BN.01 1 0.000
#> TCGA.H2.A3RI.01 1 0.000
#> TCGA.ET.A39N.01 2 0.000
#> TCGA.BJ.A3PU.11 2 0.000
#> TCGA.FY.A3R7.01 2 0.000
#> TCGA.FE.A3PA.01 1 0.000
#> TCGA.EM.A2CN.01 2 0.000
#> TCGA.BJ.A0Z2.01 2 0.000
#> TCGA.FY.A3I5.01 2 0.000
#> TCGA.DJ.A13S.01 2 0.000
#> TCGA.DE.A0Y2.01 1 0.000
#> TCGA.ET.A3BU.01 1 0.000
get_classes(res, k = 3)
#> class p
#> TCGA.E8.A416.01 2 0.000
#> TCGA.E8.A433.01 1 0.000
#> TCGA.EL.A4K9.01 3 0.000
#> TCGA.DJ.A3V9.01 1 0.000
#> TCGA.EL.A3ZO.11 2 0.000
#> TCGA.EL.A3ZN.01 1 0.000
#> TCGA.KS.A41F.01 3 0.000
#> TCGA.EL.A3ZK.01 1 0.000
#> TCGA.ET.A40R.01 1 0.000
#> TCGA.EL.A3ZM.01 3 0.000
#> TCGA.ET.A2N3.01 2 0.000
#> TCGA.EL.A3ZQ.01 3 0.498
#> TCGA.ET.A40T.01 3 1.000
#> TCGA.DE.A4MA.01 3 0.000
#> TCGA.EM.A4FU.01 2 0.000
#> TCGA.E8.A418.01 3 0.000
#> TCGA.DJ.A3VD.01 1 0.000
#> TCGA.DJ.A3VM.01 2 0.000
#> TCGA.EL.A3ZG.01 1 0.249
#> TCGA.EM.A4FV.01 1 0.000
#> TCGA.E8.A413.01 1 0.000
#> TCGA.DJ.A3VG.01 2 0.000
#> TCGA.EL.A4K2.01 2 0.000
#> TCGA.IM.A420.01 1 0.000
#> TCGA.KS.A41J.01 3 0.000
#> TCGA.EL.A3ZK.11 2 0.000
#> TCGA.J8.A3O2.01 1 0.000
#> TCGA.E8.A415.01 1 0.000
#> TCGA.FY.A40M.01 2 0.000
#> TCGA.DJ.A3VB.01 3 0.000
#> TCGA.KS.A41I.01 2 0.000
#> TCGA.DJ.A3VL.01 2 0.000
#> TCGA.ET.A4KQ.01 2 0.000
#> TCGA.H2.A421.01 3 1.000
#> TCGA.EL.A3ZO.01 3 0.000
#> TCGA.KS.A4I3.01 1 0.000
#> TCGA.DJ.A4UT.01 1 0.000
#> TCGA.DE.A4MD.01 3 0.000
#> TCGA.EL.A4JW.01 1 0.000
#> TCGA.DJ.A3VI.01 3 0.000
#> TCGA.DJ.A3VA.01 3 0.000
#> TCGA.L6.A4ET.01 3 0.000
#> TCGA.E8.A419.01 1 0.000
#> TCGA.DJ.A4V0.01 2 0.000
#> TCGA.DJ.A4V2.01 3 0.000
#> TCGA.ET.A40Q.01 3 0.000
#> TCGA.EL.A3ZS.01 1 0.000
#> TCGA.KS.A4ID.01 1 0.000
#> TCGA.EL.A3ZL.11 2 0.000
#> TCGA.J8.A3YE.01 1 0.000
#> TCGA.EL.A4K7.01 3 0.000
#> TCGA.DJ.A3VF.01 1 0.000
#> TCGA.EM.A4FH.01 2 0.000
#> TCGA.E8.A432.01 1 0.000
#> TCGA.J8.A3O2.06 3 0.000
#> TCGA.ET.A2MX.01 1 1.000
#> TCGA.ET.A40S.01 1 0.000
#> TCGA.DE.A4M8.01 1 0.000
#> TCGA.IM.A41Z.01 2 0.000
#> TCGA.EL.A4KD.01 1 1.000
#> TCGA.DJ.A3V7.01 3 0.000
#> TCGA.FY.A40L.01 1 0.000
#> TCGA.DE.A4M9.01 2 0.000
#> TCGA.J8.A42S.01 1 0.000
#> TCGA.KS.A41L.01 2 0.000
#> TCGA.EM.A4FN.01 3 0.000
#> TCGA.EL.A4K1.01 3 0.000
#> TCGA.KS.A4IC.01 1 0.000
#> TCGA.E8.A414.01 1 0.000
#> TCGA.H2.A422.01 3 0.249
#> TCGA.J8.A3YF.01 3 0.000
#> TCGA.EL.A4KI.01 2 0.000
#> TCGA.EM.A4G1.01 2 0.000
#> TCGA.DJ.A3VJ.01 3 1.000
#> TCGA.DE.A4MD.06 1 1.000
#> TCGA.EL.A3ZP.01 3 0.000
#> TCGA.EM.A4FQ.01 3 0.000
#> TCGA.EL.A3ZT.01 3 0.000
#> TCGA.DJ.A4V4.01 1 0.000
#> TCGA.FY.A40K.01 1 0.000
#> TCGA.L6.A4EQ.01 3 0.000
#> TCGA.DJ.A3VE.01 3 0.000
#> TCGA.E8.A434.01 2 0.000
#> TCGA.EL.A3ZH.01 2 0.000
#> TCGA.EM.A4FR.01 1 0.498
#> TCGA.EL.A3ZH.11 2 0.000
#> TCGA.EL.A3ZR.01 2 0.000
#> TCGA.DJ.A3V8.01 1 0.000
#> TCGA.EL.A3ZG.11 2 0.000
#> TCGA.ET.A40P.01 2 0.000
#> TCGA.DE.A4MB.01 3 0.000
#> TCGA.MK.A4N6.01 3 0.000
#> TCGA.DJ.A3VK.01 2 0.000
#> TCGA.E8.A417.01 3 0.000
#> TCGA.L6.A4EU.01 3 0.253
#> TCGA.J8.A4HY.01 1 0.000
#> TCGA.EL.A3ZL.01 3 0.000
#> TCGA.EL.A3ZP.11 2 0.000
#> TCGA.FY.A40N.01 1 0.000
#> TCGA.J8.A4HW.01 3 0.000
#> TCGA.BJ.A45J.01 3 0.000
#> TCGA.CE.A482.01 3 0.000
#> TCGA.DJ.A2Q6.01 3 0.000
#> TCGA.DJ.A2PX.01 1 0.000
#> TCGA.DJ.A4UL.01 3 0.000
#> TCGA.EL.A4JX.01 1 0.000
#> TCGA.BJ.A2N8.11 2 0.000
#> TCGA.DJ.A2Q5.01 1 0.000
#> TCGA.EL.A4KG.01 3 0.000
#> TCGA.DJ.A4UP.01 1 0.000
#> TCGA.E8.A438.01 1 0.249
#> TCGA.EL.A3H2.01 2 0.000
#> TCGA.EM.A3AP.01 2 0.000
#> TCGA.DJ.A2PQ.01 3 0.000
#> TCGA.L6.A4EP.01 3 0.000
#> TCGA.FY.A4B4.01 3 0.000
#> TCGA.EL.A4KH.01 1 0.000
#> TCGA.BJ.A45E.01 2 0.000
#> TCGA.DJ.A4V5.01 1 0.000
#> TCGA.DE.A4MC.01 3 0.000
#> TCGA.E8.A44M.01 1 0.000
#> TCGA.BJ.A45K.01 2 0.000
#> TCGA.E3.A3DZ.01 2 0.000
#> TCGA.E3.A3E2.01 3 0.000
#> TCGA.BJ.A45H.01 1 0.000
#> TCGA.E8.A44K.01 1 0.000
#> TCGA.ET.A2MY.01 3 0.000
#> TCGA.EL.A3H8.01 3 0.000
#> TCGA.BJ.A45C.01 2 0.000
#> TCGA.BJ.A45G.01 2 0.000
#> TCGA.EL.A4JZ.01 3 0.000
#> TCGA.CE.A481.01 1 0.000
#> TCGA.KS.A4I9.01 3 0.000
#> TCGA.EL.A3MW.01 3 0.751
#> TCGA.E8.A436.01 1 0.000
#> TCGA.E3.A3DY.01 3 0.000
#> TCGA.DJ.A2Q3.01 1 0.000
#> TCGA.BJ.A2P4.01 2 0.000
#> TCGA.CE.A484.01 2 0.000
#> TCGA.ET.A2N1.01 1 0.000
#> TCGA.DJ.A2Q4.01 3 0.000
#> TCGA.DJ.A2PZ.01 1 0.000
#> TCGA.BJ.A45F.01 2 0.000
#> TCGA.IM.A4EB.01 1 0.000
#> TCGA.EM.A4FO.01 1 0.000
#> TCGA.FY.A4B3.01 3 0.000
#> TCGA.FY.A4B0.01 2 0.000
#> TCGA.BJ.A45I.01 1 0.000
#> TCGA.E3.A3E3.01 3 0.000
#> TCGA.EM.A3AQ.01 3 0.000
#> TCGA.EL.A3N3.01 1 0.000
#> TCGA.DJ.A2Q9.01 2 0.000
#> TCGA.EM.A4FM.01 3 0.000
#> TCGA.EL.A4K6.01 2 0.000
#> TCGA.MK.A4N9.01 3 0.000
#> TCGA.KS.A4I1.01 3 0.000
#> TCGA.DJ.A2PS.01 1 0.000
#> TCGA.CE.A3MD.01 1 1.000
#> TCGA.E3.A3E5.01 3 0.000
#> TCGA.EL.A3CN.01 1 0.000
#> TCGA.J8.A4HW.06 1 0.000
#> TCGA.EM.A4FK.01 2 0.000
#> TCGA.E8.A437.01 1 0.000
#> TCGA.BJ.A4O8.01 3 0.000
#> TCGA.EL.A3MW.11 2 0.000
#> TCGA.E3.A3E0.01 3 1.000
#> TCGA.BJ.A45D.01 2 0.000
#> TCGA.CE.A483.01 1 0.000
#> TCGA.CE.A485.01 1 0.000
#> TCGA.DJ.A4UR.01 2 0.000
#> TCGA.IM.A41Y.01 3 0.000
#> TCGA.ET.A4KN.01 1 0.000
#> TCGA.KS.A4I5.01 3 0.000
#> TCGA.DJ.A4UQ.01 1 0.000
#> TCGA.KS.A4IB.01 3 0.000
#> TCGA.EL.A3N2.11 2 0.000
#> TCGA.BJ.A2N9.01 2 0.000
#> TCGA.DJ.A4UW.01 1 0.000
#> TCGA.EL.A3GZ.11 2 0.000
#> TCGA.EM.A3AR.01 2 0.000
#> TCGA.EL.A3N3.11 2 0.000
#> TCGA.DE.A3KN.01 1 0.000
#> TCGA.DJ.A2QA.01 1 0.000
#> TCGA.EL.A4JV.01 2 0.000
#> TCGA.EM.A4FF.01 3 0.000
#> TCGA.EL.A4K0.01 3 0.000
#> TCGA.FK.A4UB.01 3 0.000
#> TCGA.BJ.A4O9.01 1 0.249
#> TCGA.BJ.A2N7.01 2 0.000
#> TCGA.DE.A2OL.01 2 0.000
#> TCGA.CE.A3ME.01 1 0.000
#> TCGA.MK.A4N7.01 3 0.000
#> TCGA.EL.A3H2.11 2 0.000
#> TCGA.EL.A4K4.01 3 0.000
#> TCGA.EL.A3GS.01 3 0.000
#> TCGA.EL.A3GZ.01 3 0.000
#> TCGA.E3.A3E1.01 1 0.000
#> TCGA.DJ.A2Q8.01 1 0.000
#> TCGA.EL.A3N2.01 3 0.000
#> TCGA.KS.A4I7.01 3 0.000
#> TCGA.MK.A84Z.01 2 0.000
#> TCGA.ET.A3DP.11 2 0.000
#> TCGA.EL.A3MX.11 2 0.000
#> TCGA.ET.A25G.01 3 0.000
#> TCGA.EM.A3FK.01 3 0.000
#> TCGA.EM.A2CS.01 3 0.000
#> TCGA.FE.A23A.01 1 0.000
#> TCGA.BJ.A28T.11 2 0.000
#> TCGA.EM.A22J.01 2 0.000
#> TCGA.EL.A3MX.01 3 0.000
#> TCGA.FY.A3I4.01 1 0.000
#> TCGA.BJ.A28W.11 2 0.000
#> TCGA.ET.A25R.01 3 0.000
#> TCGA.BJ.A2N8.01 2 0.000
#> TCGA.FY.A76V.01 2 0.000
#> TCGA.EM.A3FN.01 2 0.000
#> TCGA.QD.A8IV.01 2 0.000
#> TCGA.EM.A3FJ.01 3 0.000
#> TCGA.ET.A2MY.11 2 0.000
#> TCGA.EM.A3FQ.06 3 0.000
#> TCGA.ET.A25P.01 2 0.000
#> TCGA.ET.A2N0.01 1 0.000
#> TCGA.EM.A2CT.01 2 0.000
#> TCGA.FE.A235.01 3 0.000
#> TCGA.ET.A25M.01 3 0.000
#> TCGA.EL.A3MY.01 3 0.000
#> TCGA.DE.A7U5.01 3 0.502
#> TCGA.E8.A2JQ.11 2 0.000
#> TCGA.ET.A3DP.01 1 0.000
#> TCGA.EM.A2CL.01 2 0.000
#> TCGA.ET.A2N5.01 2 0.000
#> TCGA.ET.A25J.11 2 0.000
#> TCGA.DE.A69J.01 3 0.000
#> TCGA.BJ.A28R.11 2 0.000
#> TCGA.ET.A25K.01 3 0.000
#> TCGA.EL.A3GV.01 1 0.000
#> TCGA.GE.A2C6.01 1 0.000
#> TCGA.EM.A3FM.01 3 0.000
#> TCGA.EL.A3H7.11 2 0.000
#> TCGA.FE.A22Z.01 3 0.000
#> TCGA.H2.A2K9.01 2 0.000
#> TCGA.EM.A22Q.01 2 0.000
#> TCGA.EM.A3FP.01 2 0.000
#> TCGA.GE.A2C6.11 2 0.000
#> TCGA.EL.A3MZ.01 3 0.000
#> TCGA.DJ.A2PT.01 1 0.000
#> TCGA.E8.A242.01 1 0.000
#> TCGA.ET.A25L.01 3 0.000
#> TCGA.CE.A27D.01 2 0.000
#> TCGA.EL.A3H1.11 2 0.000
#> TCGA.BJ.A2N7.11 2 0.000
#> TCGA.DJ.A2Q7.01 3 0.000
#> TCGA.J8.A3O1.01 1 0.249
#> TCGA.EM.A2CR.01 1 0.249
#> TCGA.DE.A69K.01 3 0.000
#> TCGA.EM.A2CQ.01 2 0.000
#> TCGA.FE.A238.01 1 0.000
#> TCGA.EL.A3H1.01 2 0.000
#> TCGA.BJ.A28W.01 2 0.000
#> TCGA.BJ.A28T.01 2 0.000
#> TCGA.EM.A2CJ.01 2 0.000
#> TCGA.EM.A3FQ.01 1 0.000
#> TCGA.4C.A93U.01 3 0.000
#> TCGA.EM.A22M.01 1 0.000
#> TCGA.J8.A3NZ.01 1 0.000
#> TCGA.EM.A22K.01 2 0.000
#> TCGA.FE.A236.01 1 1.000
#> TCGA.BJ.A28R.01 1 0.000
#> TCGA.EM.A2CU.01 1 0.000
#> TCGA.ET.A25N.01 3 0.000
#> TCGA.EL.A3H7.01 3 0.000
#> TCGA.FY.A3NM.01 2 0.000
#> TCGA.EM.A3FO.01 3 0.000
#> TCGA.EM.A22L.01 2 0.000
#> TCGA.BJ.A2N9.11 2 0.000
#> TCGA.BJ.A291.01 2 0.000
#> TCGA.ET.A2N5.11 2 0.000
#> TCGA.ET.A25N.11 2 0.000
#> TCGA.J8.A3O0.01 2 0.000
#> TCGA.FE.A237.01 1 0.000
#> TCGA.DJ.A2QC.01 1 0.000
#> TCGA.ET.A25O.01 3 0.000
#> TCGA.EL.A3GU.01 3 0.000
#> TCGA.EL.A3MY.11 2 0.000
#> TCGA.DJ.A2PY.01 3 0.000
#> TCGA.EM.A2CS.06 1 0.000
#> TCGA.FY.A3NP.01 2 0.000
#> TCGA.ET.A25I.01 2 0.000
#> TCGA.H2.A26U.01 1 0.000
#> TCGA.BJ.A290.11 2 0.000
#> TCGA.EM.A22I.01 3 0.000
#> TCGA.FE.A239.01 2 0.000
#> TCGA.BJ.A28Z.01 1 0.000
#> TCGA.DE.A0XZ.01 3 0.000
#> TCGA.ET.A25J.01 1 0.000
#> TCGA.EM.A22N.01 2 0.000
#> TCGA.EM.A2CM.01 2 0.000
#> TCGA.FY.A3NN.01 1 0.000
#> TCGA.EM.A3FL.01 2 0.000
#> TCGA.H2.A2K9.11 2 0.000
#> TCGA.EL.A3H3.01 1 1.000
#> TCGA.EL.A3H4.01 3 0.000
#> TCGA.EM.A2OX.01 3 0.000
#> TCGA.EM.A3SX.01 3 0.000
#> TCGA.BJ.A0Z3.01 1 0.000
#> TCGA.BJ.A28X.01 1 0.000
#> TCGA.EL.A3CT.01 1 0.000
#> TCGA.EL.A3CR.01 3 0.000
#> TCGA.FY.A3TY.01 2 0.000
#> TCGA.J8.A3YG.01 1 0.000
#> TCGA.DJ.A3V6.01 3 0.000
#> TCGA.EM.A3SZ.01 1 0.000
#> TCGA.EM.A2OW.01 2 0.000
#> TCGA.DO.A1JZ.11 2 0.000
#> TCGA.EL.A3D5.01 2 0.000
#> TCGA.EM.A2P0.01 1 0.000
#> TCGA.E8.A2JQ.01 1 0.000
#> TCGA.BJ.A18Z.01 3 0.000
#> TCGA.DJ.A3V0.01 3 0.000
#> TCGA.EL.A3GW.01 2 0.000
#> TCGA.DJ.A3UW.01 1 0.000
#> TCGA.DJ.A3V3.01 1 0.000
#> TCGA.EL.A3T1.11 2 0.000
#> TCGA.BJ.A0ZC.01 2 0.000
#> TCGA.EM.A2OV.01 2 0.000
#> TCGA.EL.A3GY.01 3 0.000
#> TCGA.EM.A3SY.01 2 0.000
#> TCGA.EM.A3AI.01 2 0.000
#> TCGA.EM.A2OY.01 2 0.000
#> TCGA.EL.A3T8.01 3 0.000
#> TCGA.BJ.A18Y.01 2 0.000
#> TCGA.EL.A3GP.01 1 1.000
#> TCGA.EM.A2CK.01 2 0.000
#> TCGA.EL.A3T7.11 2 0.000
#> TCGA.BJ.A192.01 2 0.000
#> TCGA.BJ.A191.01 1 0.000
#> TCGA.EM.A2CP.01 2 0.000
#> TCGA.EM.A22O.01 3 1.000
#> TCGA.EM.A2P1.01 1 0.000
#> TCGA.J8.A3YH.01 3 0.000
#> TCGA.DJ.A3UZ.01 2 0.000
#> TCGA.IM.A3EB.01 1 0.000
#> TCGA.BJ.A3F0.01 2 0.000
#> TCGA.EL.A3GX.01 3 0.000
#> TCGA.EM.A3AK.01 1 1.000
#> TCGA.DO.A1JZ.01 3 0.000
#> TCGA.FY.A3YR.01 3 0.000
#> TCGA.DO.A1K0.01 3 0.000
#> TCGA.DJ.A3V5.01 3 0.000
#> TCGA.EM.A3AJ.01 2 0.000
#> TCGA.IM.A3ED.01 3 0.000
#> TCGA.EM.A3AO.01 1 1.000
#> TCGA.EM.A2P1.06 1 0.000
#> TCGA.EM.A1CW.01 2 0.000
#> TCGA.FK.A3SE.01 3 0.000
#> TCGA.EL.A3T7.01 3 0.000
#> TCGA.EM.A2P2.01 2 0.000
#> TCGA.EM.A1CU.11 2 0.000
#> TCGA.EL.A3T0.11 2 0.000
#> TCGA.E8.A3X7.01 3 0.000
#> TCGA.ET.A3BQ.01 3 0.000
#> TCGA.EM.A1CS.01 1 0.000
#> TCGA.EL.A3GQ.01 1 0.000
#> TCGA.EL.A3H5.01 3 0.000
#> TCGA.DJ.A3V4.01 1 0.000
#> TCGA.EM.A2P3.01 3 0.000
#> TCGA.FY.A3WA.01 2 0.000
#> TCGA.DJ.A3V2.01 1 0.000
#> TCGA.FY.A3TY.11 2 0.000
#> TCGA.BJ.A290.01 1 1.000
#> TCGA.EM.A3SU.01 1 0.000
#> TCGA.EL.A3D0.01 3 0.000
#> TCGA.EM.A1CT.11 2 0.000
#> TCGA.EL.A3GR.01 1 0.000
#> TCGA.J8.A3YH.06 3 1.000
#> TCGA.EM.A3ST.11 2 0.000
#> TCGA.ET.A3DV.01 2 0.000
#> TCGA.BJ.A3EZ.01 3 0.000
#> TCGA.J8.A3YD.01 2 0.000
#> TCGA.EM.A3SU.06 1 0.000
#> TCGA.EM.A3AL.01 2 0.000
#> TCGA.DJ.A3US.01 1 0.000
#> TCGA.EM.A1CS.11 2 0.000
#> TCGA.EM.A1CW.11 2 0.000
#> TCGA.BJ.A190.01 2 0.000
#> TCGA.EM.A2OZ.01 1 0.000
#> TCGA.EM.A1CV.11 2 0.000
#> TCGA.EM.A1CU.01 3 0.000
#> TCGA.EM.A3AN.01 3 0.000
#> TCGA.E8.A2EA.01 1 0.000
#> TCGA.EM.A1CV.01 1 0.249
#> TCGA.EM.A1CT.01 1 1.000
#> TCGA.EM.A3ST.01 2 0.000
#> TCGA.ET.A3BS.01 1 1.000
#> TCGA.EL.A3GO.01 2 0.000
#> TCGA.DJ.A2Q0.01 2 0.000
#> TCGA.EL.A3D6.01 3 0.000
#> TCGA.DJ.A3UN.01 3 0.000
#> TCGA.DJ.A3UU.01 1 0.000
#> TCGA.FK.A3SD.01 2 0.000
#> TCGA.DJ.A2PO.01 1 0.000
#> TCGA.DJ.A3UQ.01 1 0.000
#> TCGA.EM.A1YE.11 2 0.000
#> TCGA.EL.A3T2.11 2 0.000
#> TCGA.EL.A3CL.01 3 0.000
#> TCGA.EM.A1YC.01 2 0.000
#> TCGA.DJ.A3UP.01 2 0.000
#> TCGA.EL.A3T0.01 1 0.000
#> TCGA.IM.A3U2.01 3 0.000
#> TCGA.IM.A3U3.01 3 0.000
#> TCGA.DJ.A3UX.01 1 0.000
#> TCGA.ET.A3BW.01 1 0.000
#> TCGA.ET.A39S.01 1 0.000
#> TCGA.ET.A3BP.01 1 0.249
#> TCGA.DJ.A1QE.01 3 0.000
#> TCGA.EL.A3D4.01 1 0.249
#> TCGA.FK.A3SB.01 3 0.000
#> TCGA.EL.A3CW.01 2 0.000
#> TCGA.ET.A39L.01 2 0.000
#> TCGA.DJ.A2PW.01 3 0.000
#> TCGA.EM.A2CO.01 2 0.000
#> TCGA.FE.A232.01 1 0.000
#> TCGA.DJ.A3UR.01 1 0.000
#> TCGA.DJ.A2PP.01 2 0.000
#> TCGA.ET.A3DQ.01 2 0.000
#> TCGA.ET.A3DS.01 2 0.000
#> TCGA.FY.A3W9.01 2 0.000
#> TCGA.FK.A3S3.01 1 0.000
#> TCGA.ET.A2MZ.01 3 0.249
#> TCGA.BJ.A2NA.11 2 0.000
#> TCGA.DJ.A1QL.01 2 0.000
#> TCGA.EL.A3CS.01 1 0.751
#> TCGA.FE.A233.01 3 1.000
#> TCGA.EM.A1YD.11 2 0.000
#> TCGA.ET.A3DW.11 2 0.000
#> TCGA.EL.A3T9.01 3 0.000
#> TCGA.DJ.A3UM.01 3 0.000
#> TCGA.DO.A2HM.01 1 0.000
#> TCGA.FY.A3BL.01 1 0.000
#> TCGA.EL.A3TA.11 2 0.000
#> TCGA.ET.A3BX.01 3 0.000
#> TCGA.DJ.A1QQ.01 3 0.000
#> TCGA.DJ.A1QF.01 1 0.000
#> TCGA.DJ.A1QO.01 3 0.000
#> TCGA.BJ.A2NA.01 3 0.000
#> TCGA.EM.A1YE.01 2 0.000
#> TCGA.FY.A2QD.01 2 0.000
#> TCGA.ET.A39J.01 3 0.000
#> TCGA.ET.A3DU.01 1 0.000
#> TCGA.EL.A3CM.01 3 0.000
#> TCGA.DJ.A3UO.01 3 0.000
#> TCGA.ET.A39P.01 3 0.000
#> TCGA.DJ.A2Q2.01 2 0.000
#> TCGA.BJ.A28V.01 2 0.000
#> TCGA.ET.A3BO.01 3 0.000
#> TCGA.EL.A3T1.01 1 0.000
#> TCGA.DJ.A1QI.01 3 0.000
#> TCGA.EL.A3TB.01 3 0.000
#> TCGA.BJ.A28X.11 2 0.000
#> TCGA.DJ.A1QN.01 3 0.000
#> TCGA.FE.A230.01 1 0.000
#> TCGA.FE.A234.01 3 0.000
#> TCGA.ET.A39R.01 1 0.000
#> TCGA.DJ.A1QG.01 2 0.000
#> TCGA.EL.A3CV.01 1 0.000
#> TCGA.FE.A231.01 3 0.000
#> TCGA.EL.A3TA.01 1 0.000
#> TCGA.DJ.A3UY.01 1 0.000
#> TCGA.DJ.A2Q1.01 1 0.000
#> TCGA.EL.A3CU.01 1 0.000
#> TCGA.EL.A3TB.11 2 0.000
#> TCGA.ET.A39I.01 2 0.000
#> TCGA.EM.A1YB.01 2 0.000
#> TCGA.DJ.A3UV.01 1 1.000
#> TCGA.DJ.A3UT.01 2 0.000
#> TCGA.ET.A3DW.01 3 0.000
#> TCGA.ET.A3BT.01 3 0.000
#> TCGA.EL.A3T3.01 3 0.000
#> TCGA.DJ.A1QM.01 2 0.000
#> TCGA.EL.A3CY.01 2 0.000
#> TCGA.ET.A39O.01 3 0.000
#> TCGA.EM.A1YC.11 2 0.000
#> TCGA.DJ.A1QH.01 3 0.000
#> TCGA.EL.A3T3.11 2 0.000
#> TCGA.EL.A3CX.01 1 0.000
#> TCGA.EL.A3T2.01 2 0.000
#> TCGA.EM.A22P.01 1 0.000
#> TCGA.EL.A3T8.11 2 0.000
#> TCGA.DJ.A2PU.01 3 0.000
#> TCGA.DJ.A3UK.01 1 0.249
#> TCGA.ET.A3DO.01 1 0.000
#> TCGA.EM.A1YA.01 2 0.000
#> TCGA.ET.A3BV.01 1 0.000
#> TCGA.EL.A3CO.01 2 0.000
#> TCGA.DJ.A2PN.01 3 0.000
#> TCGA.FK.A3SG.01 3 0.000
#> TCGA.FK.A3SH.01 3 0.000
#> TCGA.EM.A1YD.01 2 0.000
#> TCGA.DJ.A1QD.01 3 0.000
#> TCGA.EL.A3CZ.01 2 0.000
#> TCGA.BJ.A0Z9.01 1 0.000
#> TCGA.CE.A13K.01 3 1.000
#> TCGA.EM.A3FR.01 2 0.000
#> TCGA.EM.A3O8.01 2 0.000
#> TCGA.FY.A3R6.01 1 0.000
#> TCGA.FY.A3R9.01 2 0.000
#> TCGA.EL.A3D1.01 3 0.000
#> TCGA.EM.A3O6.01 2 0.000
#> TCGA.BJ.A0Z5.01 1 1.000
#> TCGA.BJ.A28S.01 2 0.000
#> TCGA.BJ.A0ZH.01 3 0.000
#> TCGA.ET.A3DT.01 1 0.000
#> TCGA.H2.A3RI.11 2 0.000
#> TCGA.DJ.A13W.01 2 0.000
#> TCGA.DJ.A13T.01 3 0.000
#> TCGA.BJ.A0ZA.01 2 0.000
#> TCGA.BJ.A3PT.01 2 0.000
#> TCGA.FE.A3PD.01 3 0.000
#> TCGA.BJ.A0ZF.01 2 0.000
#> TCGA.ET.A39M.01 1 0.000
#> TCGA.BJ.A0ZJ.01 1 0.000
#> TCGA.BJ.A0YZ.01 2 0.000
#> TCGA.FE.A3PC.01 3 0.000
#> TCGA.DJ.A2QB.01 2 0.000
#> TCGA.EM.A3OB.01 2 0.000
#> TCGA.H2.A3RH.01 2 0.000
#> TCGA.ET.A39T.01 1 0.000
#> TCGA.DJ.A2PV.01 1 0.000
#> TCGA.BJ.A3PR.11 2 0.000
#> TCGA.EL.A3T6.11 2 0.000
#> TCGA.DJ.A13X.01 1 0.000
#> TCGA.BJ.A0ZG.01 2 0.000
#> TCGA.EL.A3T6.01 1 0.000
#> TCGA.BJ.A0Z0.01 2 0.000
#> TCGA.ET.A39K.01 3 0.000
#> TCGA.EM.A3O9.01 2 0.000
#> TCGA.BJ.A3PU.01 3 0.000
#> TCGA.BJ.A3PR.01 2 0.000
#> TCGA.EM.A3O3.01 1 1.000
#> TCGA.BJ.A0ZB.01 3 0.000
#> TCGA.EM.A3OA.01 2 0.000
#> TCGA.DJ.A2PR.01 3 0.000
#> TCGA.DJ.A13L.01 1 0.000
#> TCGA.FY.A3ON.01 3 0.000
#> TCGA.DJ.A13V.01 3 0.000
#> TCGA.FY.A3R8.01 3 0.000
#> TCGA.EL.A3CP.01 3 0.000
#> TCGA.DJ.A13U.01 1 1.000
#> TCGA.DE.A0Y3.01 3 0.000
#> TCGA.ET.A2N4.01 1 0.000
#> TCGA.DJ.A13P.01 1 0.249
#> TCGA.BJ.A0ZE.01 2 0.000
#> TCGA.EM.A3O7.01 1 0.000
#> TCGA.DJ.A13O.01 2 0.000
#> TCGA.FY.A3RA.01 3 0.253
#> TCGA.DJ.A13M.01 2 0.000
#> TCGA.DJ.A13R.01 2 0.000
#> TCGA.ET.A3DR.01 1 0.000
#> TCGA.FE.A3PB.01 1 0.000
#> TCGA.ET.A3BN.01 3 0.000
#> TCGA.H2.A3RI.01 3 0.000
#> TCGA.ET.A39N.01 2 0.000
#> TCGA.BJ.A3PU.11 2 0.000
#> TCGA.FY.A3R7.01 2 1.000
#> TCGA.FE.A3PA.01 3 0.000
#> TCGA.EM.A2CN.01 2 0.000
#> TCGA.BJ.A0Z2.01 2 0.000
#> TCGA.FY.A3I5.01 2 0.000
#> TCGA.DJ.A13S.01 2 0.000
#> TCGA.DE.A0Y2.01 3 0.000
#> TCGA.ET.A3BU.01 3 0.000
get_classes(res, k = 4)
#> class p
#> TCGA.E8.A416.01 2 0.000
#> TCGA.E8.A433.01 3 0.000
#> TCGA.EL.A4K9.01 1 0.000
#> TCGA.DJ.A3V9.01 3 0.000
#> TCGA.EL.A3ZO.11 2 0.000
#> TCGA.EL.A3ZN.01 4 0.000
#> TCGA.KS.A41F.01 1 0.751
#> TCGA.EL.A3ZK.01 3 0.000
#> TCGA.ET.A40R.01 3 0.000
#> TCGA.EL.A3ZM.01 1 0.000
#> TCGA.ET.A2N3.01 2 0.000
#> TCGA.EL.A3ZQ.01 3 0.000
#> TCGA.ET.A40T.01 3 0.000
#> TCGA.DE.A4MA.01 1 0.000
#> TCGA.EM.A4FU.01 2 0.000
#> TCGA.E8.A418.01 1 0.000
#> TCGA.DJ.A3VD.01 4 0.000
#> TCGA.DJ.A3VM.01 2 0.000
#> TCGA.EL.A3ZG.01 4 0.000
#> TCGA.EM.A4FV.01 4 1.000
#> TCGA.E8.A413.01 4 0.000
#> TCGA.DJ.A3VG.01 2 0.000
#> TCGA.EL.A4K2.01 2 0.000
#> TCGA.IM.A420.01 3 0.000
#> TCGA.KS.A41J.01 1 0.000
#> TCGA.EL.A3ZK.11 2 0.000
#> TCGA.J8.A3O2.01 4 0.000
#> TCGA.E8.A415.01 4 0.000
#> TCGA.FY.A40M.01 4 0.000
#> TCGA.DJ.A3VB.01 1 0.000
#> TCGA.KS.A41I.01 2 0.000
#> TCGA.DJ.A3VL.01 2 0.000
#> TCGA.ET.A4KQ.01 2 0.000
#> TCGA.H2.A421.01 3 0.000
#> TCGA.EL.A3ZO.01 1 0.000
#> TCGA.KS.A4I3.01 4 0.000
#> TCGA.DJ.A4UT.01 4 0.000
#> TCGA.DE.A4MD.01 1 1.000
#> TCGA.EL.A4JW.01 4 0.000
#> TCGA.DJ.A3VI.01 1 0.000
#> TCGA.DJ.A3VA.01 1 0.000
#> TCGA.L6.A4ET.01 3 1.000
#> TCGA.E8.A419.01 3 0.000
#> TCGA.DJ.A4V0.01 4 0.000
#> TCGA.DJ.A4V2.01 1 0.000
#> TCGA.ET.A40Q.01 3 1.000
#> TCGA.EL.A3ZS.01 4 0.000
#> TCGA.KS.A4ID.01 4 0.000
#> TCGA.EL.A3ZL.11 2 0.000
#> TCGA.J8.A3YE.01 4 0.000
#> TCGA.EL.A4K7.01 1 0.000
#> TCGA.DJ.A3VF.01 3 0.000
#> TCGA.EM.A4FH.01 2 0.000
#> TCGA.E8.A432.01 4 0.000
#> TCGA.J8.A3O2.06 1 0.000
#> TCGA.ET.A2MX.01 3 0.000
#> TCGA.ET.A40S.01 4 0.000
#> TCGA.DE.A4M8.01 4 0.000
#> TCGA.IM.A41Z.01 2 0.000
#> TCGA.EL.A4KD.01 4 0.000
#> TCGA.DJ.A3V7.01 1 0.000
#> TCGA.FY.A40L.01 3 0.000
#> TCGA.DE.A4M9.01 2 0.000
#> TCGA.J8.A42S.01 3 0.000
#> TCGA.KS.A41L.01 2 0.000
#> TCGA.EM.A4FN.01 1 0.000
#> TCGA.EL.A4K1.01 1 0.000
#> TCGA.KS.A4IC.01 3 0.000
#> TCGA.E8.A414.01 4 0.000
#> TCGA.H2.A422.01 1 0.000
#> TCGA.J8.A3YF.01 3 1.000
#> TCGA.EL.A4KI.01 2 0.000
#> TCGA.EM.A4G1.01 2 0.000
#> TCGA.DJ.A3VJ.01 3 0.000
#> TCGA.DE.A4MD.06 4 0.000
#> TCGA.EL.A3ZP.01 1 1.000
#> TCGA.EM.A4FQ.01 1 0.000
#> TCGA.EL.A3ZT.01 1 0.000
#> TCGA.DJ.A4V4.01 3 1.000
#> TCGA.FY.A40K.01 3 0.000
#> TCGA.L6.A4EQ.01 3 0.000
#> TCGA.DJ.A3VE.01 1 0.000
#> TCGA.E8.A434.01 4 0.000
#> TCGA.EL.A3ZH.01 2 0.000
#> TCGA.EM.A4FR.01 4 0.000
#> TCGA.EL.A3ZH.11 2 0.000
#> TCGA.EL.A3ZR.01 2 0.000
#> TCGA.DJ.A3V8.01 3 0.000
#> TCGA.EL.A3ZG.11 2 0.000
#> TCGA.ET.A40P.01 2 0.000
#> TCGA.DE.A4MB.01 1 0.000
#> TCGA.MK.A4N6.01 1 0.000
#> TCGA.DJ.A3VK.01 2 0.000
#> TCGA.E8.A417.01 1 0.000
#> TCGA.L6.A4EU.01 1 0.000
#> TCGA.J8.A4HY.01 4 0.000
#> TCGA.EL.A3ZL.01 1 0.000
#> TCGA.EL.A3ZP.11 2 0.000
#> TCGA.FY.A40N.01 4 0.000
#> TCGA.J8.A4HW.01 1 0.000
#> TCGA.BJ.A45J.01 1 0.000
#> TCGA.CE.A482.01 3 0.000
#> TCGA.DJ.A2Q6.01 1 0.000
#> TCGA.DJ.A2PX.01 4 0.000
#> TCGA.DJ.A4UL.01 1 0.000
#> TCGA.EL.A4JX.01 4 0.000
#> TCGA.BJ.A2N8.11 2 0.000
#> TCGA.DJ.A2Q5.01 3 0.000
#> TCGA.EL.A4KG.01 1 0.000
#> TCGA.DJ.A4UP.01 4 0.000
#> TCGA.E8.A438.01 4 0.000
#> TCGA.EL.A3H2.01 2 0.000
#> TCGA.EM.A3AP.01 2 0.000
#> TCGA.DJ.A2PQ.01 1 0.000
#> TCGA.L6.A4EP.01 1 0.000
#> TCGA.FY.A4B4.01 1 0.000
#> TCGA.EL.A4KH.01 3 0.000
#> TCGA.BJ.A45E.01 2 1.000
#> TCGA.DJ.A4V5.01 3 0.000
#> TCGA.DE.A4MC.01 1 0.000
#> TCGA.E8.A44M.01 4 0.000
#> TCGA.BJ.A45K.01 2 0.000
#> TCGA.E3.A3DZ.01 2 0.000
#> TCGA.E3.A3E2.01 1 1.000
#> TCGA.BJ.A45H.01 4 0.000
#> TCGA.E8.A44K.01 3 0.000
#> TCGA.ET.A2MY.01 1 0.000
#> TCGA.EL.A3H8.01 1 0.000
#> TCGA.BJ.A45C.01 2 0.000
#> TCGA.BJ.A45G.01 2 0.000
#> TCGA.EL.A4JZ.01 1 0.000
#> TCGA.CE.A481.01 4 0.000
#> TCGA.KS.A4I9.01 1 0.000
#> TCGA.EL.A3MW.01 3 0.000
#> TCGA.E8.A436.01 4 0.000
#> TCGA.E3.A3DY.01 1 0.000
#> TCGA.DJ.A2Q3.01 4 0.000
#> TCGA.BJ.A2P4.01 2 0.000
#> TCGA.CE.A484.01 2 0.000
#> TCGA.ET.A2N1.01 4 0.000
#> TCGA.DJ.A2Q4.01 1 0.000
#> TCGA.DJ.A2PZ.01 3 0.000
#> TCGA.BJ.A45F.01 2 0.000
#> TCGA.IM.A4EB.01 3 0.000
#> TCGA.EM.A4FO.01 4 0.000
#> TCGA.FY.A4B3.01 1 0.000
#> TCGA.FY.A4B0.01 2 0.000
#> TCGA.BJ.A45I.01 3 0.000
#> TCGA.E3.A3E3.01 1 0.000
#> TCGA.EM.A3AQ.01 3 0.000
#> TCGA.EL.A3N3.01 3 0.000
#> TCGA.DJ.A2Q9.01 4 0.000
#> TCGA.EM.A4FM.01 1 0.000
#> TCGA.EL.A4K6.01 2 0.000
#> TCGA.MK.A4N9.01 1 0.000
#> TCGA.KS.A4I1.01 1 0.000
#> TCGA.DJ.A2PS.01 4 0.000
#> TCGA.CE.A3MD.01 4 1.000
#> TCGA.E3.A3E5.01 3 0.000
#> TCGA.EL.A3CN.01 3 0.000
#> TCGA.J8.A4HW.06 4 0.000
#> TCGA.EM.A4FK.01 2 0.000
#> TCGA.E8.A437.01 4 0.000
#> TCGA.BJ.A4O8.01 1 0.000
#> TCGA.EL.A3MW.11 2 0.000
#> TCGA.E3.A3E0.01 3 0.000
#> TCGA.BJ.A45D.01 2 0.000
#> TCGA.CE.A483.01 3 0.253
#> TCGA.CE.A485.01 4 0.000
#> TCGA.DJ.A4UR.01 2 1.000
#> TCGA.IM.A41Y.01 1 0.000
#> TCGA.ET.A4KN.01 3 0.000
#> TCGA.KS.A4I5.01 1 0.000
#> TCGA.DJ.A4UQ.01 3 0.000
#> TCGA.KS.A4IB.01 3 0.249
#> TCGA.EL.A3N2.11 2 0.000
#> TCGA.BJ.A2N9.01 2 0.000
#> TCGA.DJ.A4UW.01 3 0.000
#> TCGA.EL.A3GZ.11 2 0.000
#> TCGA.EM.A3AR.01 2 0.000
#> TCGA.EL.A3N3.11 2 0.000
#> TCGA.DE.A3KN.01 4 0.000
#> TCGA.DJ.A2QA.01 4 0.000
#> TCGA.EL.A4JV.01 2 0.000
#> TCGA.EM.A4FF.01 1 0.000
#> TCGA.EL.A4K0.01 1 0.000
#> TCGA.FK.A4UB.01 1 0.000
#> TCGA.BJ.A4O9.01 4 0.000
#> TCGA.BJ.A2N7.01 2 0.000
#> TCGA.DE.A2OL.01 2 0.000
#> TCGA.CE.A3ME.01 4 0.000
#> TCGA.MK.A4N7.01 1 0.000
#> TCGA.EL.A3H2.11 2 0.000
#> TCGA.EL.A4K4.01 1 0.000
#> TCGA.EL.A3GS.01 1 0.000
#> TCGA.EL.A3GZ.01 1 0.000
#> TCGA.E3.A3E1.01 4 0.000
#> TCGA.DJ.A2Q8.01 3 0.000
#> TCGA.EL.A3N2.01 1 0.000
#> TCGA.KS.A4I7.01 1 0.000
#> TCGA.MK.A84Z.01 2 0.000
#> TCGA.ET.A3DP.11 2 0.000
#> TCGA.EL.A3MX.11 2 0.000
#> TCGA.ET.A25G.01 1 0.000
#> TCGA.EM.A3FK.01 1 0.000
#> TCGA.EM.A2CS.01 1 0.000
#> TCGA.FE.A23A.01 3 0.000
#> TCGA.BJ.A28T.11 2 0.000
#> TCGA.EM.A22J.01 2 0.000
#> TCGA.EL.A3MX.01 1 0.000
#> TCGA.FY.A3I4.01 4 0.000
#> TCGA.BJ.A28W.11 2 0.000
#> TCGA.ET.A25R.01 1 0.000
#> TCGA.BJ.A2N8.01 2 0.000
#> TCGA.FY.A76V.01 2 0.000
#> TCGA.EM.A3FN.01 2 0.000
#> TCGA.QD.A8IV.01 2 0.000
#> TCGA.EM.A3FJ.01 1 0.000
#> TCGA.ET.A2MY.11 2 0.000
#> TCGA.EM.A3FQ.06 3 1.000
#> TCGA.ET.A25P.01 4 0.000
#> TCGA.ET.A2N0.01 3 0.000
#> TCGA.EM.A2CT.01 2 0.000
#> TCGA.FE.A235.01 3 1.000
#> TCGA.ET.A25M.01 1 0.000
#> TCGA.EL.A3MY.01 3 1.000
#> TCGA.DE.A7U5.01 1 1.000
#> TCGA.E8.A2JQ.11 2 0.000
#> TCGA.ET.A3DP.01 3 0.000
#> TCGA.EM.A2CL.01 2 0.000
#> TCGA.ET.A2N5.01 2 0.000
#> TCGA.ET.A25J.11 2 0.000
#> TCGA.DE.A69J.01 1 0.000
#> TCGA.BJ.A28R.11 2 0.000
#> TCGA.ET.A25K.01 3 0.000
#> TCGA.EL.A3GV.01 3 0.000
#> TCGA.GE.A2C6.01 4 0.000
#> TCGA.EM.A3FM.01 1 0.000
#> TCGA.EL.A3H7.11 2 0.000
#> TCGA.FE.A22Z.01 1 0.000
#> TCGA.H2.A2K9.01 2 0.000
#> TCGA.EM.A22Q.01 2 0.000
#> TCGA.EM.A3FP.01 2 0.000
#> TCGA.GE.A2C6.11 2 0.000
#> TCGA.EL.A3MZ.01 1 0.000
#> TCGA.DJ.A2PT.01 4 1.000
#> TCGA.E8.A242.01 3 0.000
#> TCGA.ET.A25L.01 1 0.000
#> TCGA.CE.A27D.01 2 0.000
#> TCGA.EL.A3H1.11 2 0.000
#> TCGA.BJ.A2N7.11 2 0.000
#> TCGA.DJ.A2Q7.01 3 1.000
#> TCGA.J8.A3O1.01 4 0.000
#> TCGA.EM.A2CR.01 4 0.000
#> TCGA.DE.A69K.01 1 1.000
#> TCGA.EM.A2CQ.01 2 0.000
#> TCGA.FE.A238.01 3 0.000
#> TCGA.EL.A3H1.01 2 0.000
#> TCGA.BJ.A28W.01 2 0.000
#> TCGA.BJ.A28T.01 2 0.000
#> TCGA.EM.A2CJ.01 2 0.000
#> TCGA.EM.A3FQ.01 4 0.000
#> TCGA.4C.A93U.01 1 0.000
#> TCGA.EM.A22M.01 3 0.000
#> TCGA.J8.A3NZ.01 1 1.000
#> TCGA.EM.A22K.01 2 0.000
#> TCGA.FE.A236.01 4 0.000
#> TCGA.BJ.A28R.01 3 0.000
#> TCGA.EM.A2CU.01 4 0.000
#> TCGA.ET.A25N.01 1 0.000
#> TCGA.EL.A3H7.01 1 0.000
#> TCGA.FY.A3NM.01 2 0.000
#> TCGA.EM.A3FO.01 1 0.000
#> TCGA.EM.A22L.01 2 0.000
#> TCGA.BJ.A2N9.11 2 0.000
#> TCGA.BJ.A291.01 2 0.000
#> TCGA.ET.A2N5.11 2 0.000
#> TCGA.ET.A25N.11 2 0.000
#> TCGA.J8.A3O0.01 2 0.000
#> TCGA.FE.A237.01 4 0.000
#> TCGA.DJ.A2QC.01 4 0.000
#> TCGA.ET.A25O.01 1 0.000
#> TCGA.EL.A3GU.01 1 0.000
#> TCGA.EL.A3MY.11 2 0.000
#> TCGA.DJ.A2PY.01 1 0.000
#> TCGA.EM.A2CS.06 4 0.000
#> TCGA.FY.A3NP.01 2 0.000
#> TCGA.ET.A25I.01 2 0.000
#> TCGA.H2.A26U.01 3 0.751
#> TCGA.BJ.A290.11 2 0.000
#> TCGA.EM.A22I.01 1 0.000
#> TCGA.FE.A239.01 2 0.000
#> TCGA.BJ.A28Z.01 4 0.000
#> TCGA.DE.A0XZ.01 1 0.000
#> TCGA.ET.A25J.01 3 0.000
#> TCGA.EM.A22N.01 2 0.000
#> TCGA.EM.A2CM.01 2 0.000
#> TCGA.FY.A3NN.01 4 0.000
#> TCGA.EM.A3FL.01 2 0.000
#> TCGA.H2.A2K9.11 2 0.000
#> TCGA.EL.A3H3.01 1 0.751
#> TCGA.EL.A3H4.01 1 0.000
#> TCGA.EM.A2OX.01 1 0.000
#> TCGA.EM.A3SX.01 1 1.000
#> TCGA.BJ.A0Z3.01 4 0.000
#> TCGA.BJ.A28X.01 4 0.000
#> TCGA.EL.A3CT.01 3 0.000
#> TCGA.EL.A3CR.01 1 0.000
#> TCGA.FY.A3TY.01 2 0.000
#> TCGA.J8.A3YG.01 4 0.000
#> TCGA.DJ.A3V6.01 1 0.000
#> TCGA.EM.A3SZ.01 1 0.000
#> TCGA.EM.A2OW.01 2 0.000
#> TCGA.DO.A1JZ.11 2 0.000
#> TCGA.EL.A3D5.01 2 0.000
#> TCGA.EM.A2P0.01 3 0.000
#> TCGA.E8.A2JQ.01 4 0.000
#> TCGA.BJ.A18Z.01 1 0.000
#> TCGA.DJ.A3V0.01 3 0.000
#> TCGA.EL.A3GW.01 2 0.000
#> TCGA.DJ.A3UW.01 4 0.000
#> TCGA.DJ.A3V3.01 3 0.000
#> TCGA.EL.A3T1.11 2 0.000
#> TCGA.BJ.A0ZC.01 2 0.000
#> TCGA.EM.A2OV.01 2 0.000
#> TCGA.EL.A3GY.01 1 0.000
#> TCGA.EM.A3SY.01 2 0.000
#> TCGA.EM.A3AI.01 2 0.000
#> TCGA.EM.A2OY.01 2 0.000
#> TCGA.EL.A3T8.01 1 0.000
#> TCGA.BJ.A18Y.01 2 0.000
#> TCGA.EL.A3GP.01 4 0.000
#> TCGA.EM.A2CK.01 2 0.000
#> TCGA.EL.A3T7.11 2 0.000
#> TCGA.BJ.A192.01 2 0.000
#> TCGA.BJ.A191.01 4 0.000
#> TCGA.EM.A2CP.01 2 0.000
#> TCGA.EM.A22O.01 4 1.000
#> TCGA.EM.A2P1.01 4 0.000
#> TCGA.J8.A3YH.01 1 1.000
#> TCGA.DJ.A3UZ.01 4 0.000
#> TCGA.IM.A3EB.01 3 0.000
#> TCGA.BJ.A3F0.01 2 0.000
#> TCGA.EL.A3GX.01 1 0.000
#> TCGA.EM.A3AK.01 3 0.000
#> TCGA.DO.A1JZ.01 1 0.253
#> TCGA.FY.A3YR.01 1 0.000
#> TCGA.DO.A1K0.01 1 0.000
#> TCGA.DJ.A3V5.01 1 0.000
#> TCGA.EM.A3AJ.01 2 0.000
#> TCGA.IM.A3ED.01 1 0.000
#> TCGA.EM.A3AO.01 3 0.000
#> TCGA.EM.A2P1.06 4 0.000
#> TCGA.EM.A1CW.01 2 0.000
#> TCGA.FK.A3SE.01 1 1.000
#> TCGA.EL.A3T7.01 1 0.000
#> TCGA.EM.A2P2.01 2 0.000
#> TCGA.EM.A1CU.11 2 0.000
#> TCGA.EL.A3T0.11 2 0.000
#> TCGA.E8.A3X7.01 1 0.000
#> TCGA.ET.A3BQ.01 1 0.000
#> TCGA.EM.A1CS.01 3 0.000
#> TCGA.EL.A3GQ.01 3 0.000
#> TCGA.EL.A3H5.01 1 0.000
#> TCGA.DJ.A3V4.01 4 0.000
#> TCGA.EM.A2P3.01 1 0.000
#> TCGA.FY.A3WA.01 2 0.000
#> TCGA.DJ.A3V2.01 3 0.000
#> TCGA.FY.A3TY.11 2 0.000
#> TCGA.BJ.A290.01 4 0.000
#> TCGA.EM.A3SU.01 3 0.000
#> TCGA.EL.A3D0.01 1 0.000
#> TCGA.EM.A1CT.11 2 0.000
#> TCGA.EL.A3GR.01 3 0.000
#> TCGA.J8.A3YH.06 3 0.000
#> TCGA.EM.A3ST.11 2 0.000
#> TCGA.ET.A3DV.01 2 0.000
#> TCGA.BJ.A3EZ.01 1 0.000
#> TCGA.J8.A3YD.01 2 0.000
#> TCGA.EM.A3SU.06 4 0.000
#> TCGA.EM.A3AL.01 2 0.000
#> TCGA.DJ.A3US.01 4 0.000
#> TCGA.EM.A1CS.11 2 0.000
#> TCGA.EM.A1CW.11 2 0.000
#> TCGA.BJ.A190.01 2 0.000
#> TCGA.EM.A2OZ.01 4 0.000
#> TCGA.EM.A1CV.11 2 0.000
#> TCGA.EM.A1CU.01 1 0.000
#> TCGA.EM.A3AN.01 1 0.000
#> TCGA.E8.A2EA.01 4 0.000
#> TCGA.EM.A1CV.01 4 1.000
#> TCGA.EM.A1CT.01 3 0.000
#> TCGA.EM.A3ST.01 2 0.000
#> TCGA.ET.A3BS.01 3 0.000
#> TCGA.EL.A3GO.01 2 0.000
#> TCGA.DJ.A2Q0.01 2 0.000
#> TCGA.EL.A3D6.01 1 0.000
#> TCGA.DJ.A3UN.01 3 0.000
#> TCGA.DJ.A3UU.01 3 0.000
#> TCGA.FK.A3SD.01 2 0.000
#> TCGA.DJ.A2PO.01 4 0.000
#> TCGA.DJ.A3UQ.01 3 0.000
#> TCGA.EM.A1YE.11 2 0.000
#> TCGA.EL.A3T2.11 2 0.000
#> TCGA.EL.A3CL.01 1 0.000
#> TCGA.EM.A1YC.01 2 0.000
#> TCGA.DJ.A3UP.01 2 0.000
#> TCGA.EL.A3T0.01 4 0.000
#> TCGA.IM.A3U2.01 1 0.000
#> TCGA.IM.A3U3.01 1 0.000
#> TCGA.DJ.A3UX.01 4 0.000
#> TCGA.ET.A3BW.01 3 0.000
#> TCGA.ET.A39S.01 4 0.000
#> TCGA.ET.A3BP.01 4 0.000
#> TCGA.DJ.A1QE.01 1 0.000
#> TCGA.EL.A3D4.01 4 0.000
#> TCGA.FK.A3SB.01 1 0.000
#> TCGA.EL.A3CW.01 2 0.000
#> TCGA.ET.A39L.01 4 0.000
#> TCGA.DJ.A2PW.01 1 0.000
#> TCGA.EM.A2CO.01 2 0.000
#> TCGA.FE.A232.01 4 0.000
#> TCGA.DJ.A3UR.01 4 0.000
#> TCGA.DJ.A2PP.01 2 0.000
#> TCGA.ET.A3DQ.01 4 0.000
#> TCGA.ET.A3DS.01 2 0.000
#> TCGA.FY.A3W9.01 2 0.000
#> TCGA.FK.A3S3.01 3 1.000
#> TCGA.ET.A2MZ.01 3 0.000
#> TCGA.BJ.A2NA.11 2 0.000
#> TCGA.DJ.A1QL.01 2 0.000
#> TCGA.EL.A3CS.01 4 0.000
#> TCGA.FE.A233.01 3 0.000
#> TCGA.EM.A1YD.11 2 0.000
#> TCGA.ET.A3DW.11 2 0.000
#> TCGA.EL.A3T9.01 1 0.000
#> TCGA.DJ.A3UM.01 1 0.000
#> TCGA.DO.A2HM.01 4 0.000
#> TCGA.FY.A3BL.01 4 0.000
#> TCGA.EL.A3TA.11 2 0.000
#> TCGA.ET.A3BX.01 1 0.000
#> TCGA.DJ.A1QQ.01 1 0.000
#> TCGA.DJ.A1QF.01 4 0.000
#> TCGA.DJ.A1QO.01 1 0.000
#> TCGA.BJ.A2NA.01 1 0.000
#> TCGA.EM.A1YE.01 2 0.000
#> TCGA.FY.A2QD.01 2 0.000
#> TCGA.ET.A39J.01 3 1.000
#> TCGA.ET.A3DU.01 4 0.000
#> TCGA.EL.A3CM.01 3 0.000
#> TCGA.DJ.A3UO.01 3 1.000
#> TCGA.ET.A39P.01 1 0.000
#> TCGA.DJ.A2Q2.01 2 0.000
#> TCGA.BJ.A28V.01 2 0.000
#> TCGA.ET.A3BO.01 1 0.000
#> TCGA.EL.A3T1.01 3 0.000
#> TCGA.DJ.A1QI.01 1 0.000
#> TCGA.EL.A3TB.01 1 0.000
#> TCGA.BJ.A28X.11 2 0.000
#> TCGA.DJ.A1QN.01 3 0.000
#> TCGA.FE.A230.01 4 0.000
#> TCGA.FE.A234.01 1 0.000
#> TCGA.ET.A39R.01 3 0.000
#> TCGA.DJ.A1QG.01 2 0.000
#> TCGA.EL.A3CV.01 4 0.000
#> TCGA.FE.A231.01 1 0.000
#> TCGA.EL.A3TA.01 4 0.000
#> TCGA.DJ.A3UY.01 4 0.000
#> TCGA.DJ.A2Q1.01 3 0.000
#> TCGA.EL.A3CU.01 3 0.000
#> TCGA.EL.A3TB.11 2 0.000
#> TCGA.ET.A39I.01 2 0.000
#> TCGA.EM.A1YB.01 2 0.000
#> TCGA.DJ.A3UV.01 4 0.000
#> TCGA.DJ.A3UT.01 2 0.000
#> TCGA.ET.A3DW.01 1 0.000
#> TCGA.ET.A3BT.01 1 0.000
#> TCGA.EL.A3T3.01 1 0.000
#> TCGA.DJ.A1QM.01 2 0.000
#> TCGA.EL.A3CY.01 4 0.000
#> TCGA.ET.A39O.01 1 0.000
#> TCGA.EM.A1YC.11 2 0.000
#> TCGA.DJ.A1QH.01 1 0.000
#> TCGA.EL.A3T3.11 2 0.000
#> TCGA.EL.A3CX.01 4 0.000
#> TCGA.EL.A3T2.01 2 0.000
#> TCGA.EM.A22P.01 4 0.000
#> TCGA.EL.A3T8.11 2 0.000
#> TCGA.DJ.A2PU.01 3 1.000
#> TCGA.DJ.A3UK.01 3 0.000
#> TCGA.ET.A3DO.01 3 0.000
#> TCGA.EM.A1YA.01 2 0.000
#> TCGA.ET.A3BV.01 3 0.000
#> TCGA.EL.A3CO.01 2 0.000
#> TCGA.DJ.A2PN.01 1 0.000
#> TCGA.FK.A3SG.01 3 0.000
#> TCGA.FK.A3SH.01 1 0.000
#> TCGA.EM.A1YD.01 2 0.000
#> TCGA.DJ.A1QD.01 3 0.000
#> TCGA.EL.A3CZ.01 2 0.000
#> TCGA.BJ.A0Z9.01 3 1.000
#> TCGA.CE.A13K.01 3 0.000
#> TCGA.EM.A3FR.01 2 0.000
#> TCGA.EM.A3O8.01 2 0.000
#> TCGA.FY.A3R6.01 4 0.000
#> TCGA.FY.A3R9.01 2 0.000
#> TCGA.EL.A3D1.01 1 0.000
#> TCGA.EM.A3O6.01 2 0.000
#> TCGA.BJ.A0Z5.01 4 0.000
#> TCGA.BJ.A28S.01 2 0.000
#> TCGA.BJ.A0ZH.01 3 0.000
#> TCGA.ET.A3DT.01 4 0.000
#> TCGA.H2.A3RI.11 2 0.000
#> TCGA.DJ.A13W.01 2 0.000
#> TCGA.DJ.A13T.01 1 0.000
#> TCGA.BJ.A0ZA.01 2 0.000
#> TCGA.BJ.A3PT.01 2 0.000
#> TCGA.FE.A3PD.01 1 0.000
#> TCGA.BJ.A0ZF.01 2 0.000
#> TCGA.ET.A39M.01 3 0.000
#> TCGA.BJ.A0ZJ.01 4 0.000
#> TCGA.BJ.A0YZ.01 2 0.000
#> TCGA.FE.A3PC.01 1 0.000
#> TCGA.DJ.A2QB.01 2 0.000
#> TCGA.EM.A3OB.01 2 0.000
#> TCGA.H2.A3RH.01 4 0.000
#> TCGA.ET.A39T.01 4 0.000
#> TCGA.DJ.A2PV.01 3 0.000
#> TCGA.BJ.A3PR.11 2 0.000
#> TCGA.EL.A3T6.11 2 0.000
#> TCGA.DJ.A13X.01 4 1.000
#> TCGA.BJ.A0ZG.01 2 0.000
#> TCGA.EL.A3T6.01 3 0.000
#> TCGA.BJ.A0Z0.01 2 0.000
#> TCGA.ET.A39K.01 1 0.000
#> TCGA.EM.A3O9.01 2 0.000
#> TCGA.BJ.A3PU.01 1 0.000
#> TCGA.BJ.A3PR.01 4 0.000
#> TCGA.EM.A3O3.01 1 1.000
#> TCGA.BJ.A0ZB.01 1 0.000
#> TCGA.EM.A3OA.01 2 0.000
#> TCGA.DJ.A2PR.01 1 0.000
#> TCGA.DJ.A13L.01 3 1.000
#> TCGA.FY.A3ON.01 1 0.000
#> TCGA.DJ.A13V.01 1 0.000
#> TCGA.FY.A3R8.01 1 0.000
#> TCGA.EL.A3CP.01 1 0.000
#> TCGA.DJ.A13U.01 4 0.751
#> TCGA.DE.A0Y3.01 1 0.000
#> TCGA.ET.A2N4.01 4 0.000
#> TCGA.DJ.A13P.01 4 0.000
#> TCGA.BJ.A0ZE.01 2 0.000
#> TCGA.EM.A3O7.01 4 0.000
#> TCGA.DJ.A13O.01 4 0.000
#> TCGA.FY.A3RA.01 1 1.000
#> TCGA.DJ.A13M.01 2 0.000
#> TCGA.DJ.A13R.01 2 0.000
#> TCGA.ET.A3DR.01 3 0.000
#> TCGA.FE.A3PB.01 3 0.000
#> TCGA.ET.A3BN.01 1 0.000
#> TCGA.H2.A3RI.01 1 0.000
#> TCGA.ET.A39N.01 2 0.000
#> TCGA.BJ.A3PU.11 2 0.000
#> TCGA.FY.A3R7.01 4 0.000
#> TCGA.FE.A3PA.01 3 0.000
#> TCGA.EM.A2CN.01 2 0.000
#> TCGA.BJ.A0Z2.01 2 0.000
#> TCGA.FY.A3I5.01 2 0.000
#> TCGA.DJ.A13S.01 2 0.000
#> TCGA.DE.A0Y2.01 1 0.000
#> TCGA.ET.A3BU.01 1 0.000
get_classes(res, k = 5)
#> class p
#> TCGA.E8.A416.01 2 0.000
#> TCGA.E8.A433.01 3 0.000
#> TCGA.EL.A4K9.01 1 0.000
#> TCGA.DJ.A3V9.01 3 0.000
#> TCGA.EL.A3ZO.11 2 0.000
#> TCGA.EL.A3ZN.01 4 0.000
#> TCGA.KS.A41F.01 1 0.000
#> TCGA.EL.A3ZK.01 5 1.000
#> TCGA.ET.A40R.01 3 0.000
#> TCGA.EL.A3ZM.01 1 0.000
#> TCGA.ET.A2N3.01 2 0.000
#> TCGA.EL.A3ZQ.01 3 0.000
#> TCGA.ET.A40T.01 3 0.000
#> TCGA.DE.A4MA.01 1 0.000
#> TCGA.EM.A4FU.01 2 0.000
#> TCGA.E8.A418.01 1 0.000
#> TCGA.DJ.A3VD.01 5 0.000
#> TCGA.DJ.A3VM.01 2 0.000
#> TCGA.EL.A3ZG.01 4 0.000
#> TCGA.EM.A4FV.01 3 1.000
#> TCGA.E8.A413.01 4 0.000
#> TCGA.DJ.A3VG.01 2 0.000
#> TCGA.EL.A4K2.01 2 0.000
#> TCGA.IM.A420.01 3 0.000
#> TCGA.KS.A41J.01 1 0.000
#> TCGA.EL.A3ZK.11 2 0.000
#> TCGA.J8.A3O2.01 5 1.000
#> TCGA.E8.A415.01 4 0.000
#> TCGA.FY.A40M.01 4 0.000
#> TCGA.DJ.A3VB.01 1 0.000
#> TCGA.KS.A41I.01 2 0.000
#> TCGA.DJ.A3VL.01 2 0.000
#> TCGA.ET.A4KQ.01 2 0.000
#> TCGA.H2.A421.01 3 0.000
#> TCGA.EL.A3ZO.01 3 0.751
#> TCGA.KS.A4I3.01 4 0.000
#> TCGA.DJ.A4UT.01 5 0.000
#> TCGA.DE.A4MD.01 1 0.000
#> TCGA.EL.A4JW.01 5 0.000
#> TCGA.DJ.A3VI.01 1 0.000
#> TCGA.DJ.A3VA.01 1 0.000
#> TCGA.L6.A4ET.01 1 1.000
#> TCGA.E8.A419.01 5 0.000
#> TCGA.DJ.A4V0.01 2 0.502
#> TCGA.DJ.A4V2.01 1 0.000
#> TCGA.ET.A40Q.01 3 0.000
#> TCGA.EL.A3ZS.01 5 0.000
#> TCGA.KS.A4ID.01 5 0.000
#> TCGA.EL.A3ZL.11 2 0.000
#> TCGA.J8.A3YE.01 4 0.000
#> TCGA.EL.A4K7.01 1 0.000
#> TCGA.DJ.A3VF.01 3 0.000
#> TCGA.EM.A4FH.01 2 0.000
#> TCGA.E8.A432.01 5 0.000
#> TCGA.J8.A3O2.06 1 0.000
#> TCGA.ET.A2MX.01 3 0.249
#> TCGA.ET.A40S.01 5 0.000
#> TCGA.DE.A4M8.01 5 0.000
#> TCGA.IM.A41Z.01 2 0.000
#> TCGA.EL.A4KD.01 5 0.000
#> TCGA.DJ.A3V7.01 1 0.000
#> TCGA.FY.A40L.01 3 0.000
#> TCGA.DE.A4M9.01 2 0.000
#> TCGA.J8.A42S.01 3 0.000
#> TCGA.KS.A41L.01 2 0.000
#> TCGA.EM.A4FN.01 1 0.000
#> TCGA.EL.A4K1.01 1 0.000
#> TCGA.KS.A4IC.01 3 0.000
#> TCGA.E8.A414.01 5 0.000
#> TCGA.H2.A422.01 1 0.000
#> TCGA.J8.A3YF.01 3 0.000
#> TCGA.EL.A4KI.01 2 0.000
#> TCGA.EM.A4G1.01 2 0.000
#> TCGA.DJ.A3VJ.01 3 0.000
#> TCGA.DE.A4MD.06 5 0.000
#> TCGA.EL.A3ZP.01 3 0.000
#> TCGA.EM.A4FQ.01 1 0.000
#> TCGA.EL.A3ZT.01 1 0.000
#> TCGA.DJ.A4V4.01 5 1.000
#> TCGA.FY.A40K.01 3 0.000
#> TCGA.L6.A4EQ.01 4 0.000
#> TCGA.DJ.A3VE.01 1 0.000
#> TCGA.E8.A434.01 4 0.000
#> TCGA.EL.A3ZH.01 2 0.000
#> TCGA.EM.A4FR.01 4 0.000
#> TCGA.EL.A3ZH.11 2 0.000
#> TCGA.EL.A3ZR.01 2 0.000
#> TCGA.DJ.A3V8.01 3 0.000
#> TCGA.EL.A3ZG.11 2 0.000
#> TCGA.ET.A40P.01 2 0.000
#> TCGA.DE.A4MB.01 1 0.000
#> TCGA.MK.A4N6.01 1 0.000
#> TCGA.DJ.A3VK.01 2 0.000
#> TCGA.E8.A417.01 1 0.000
#> TCGA.L6.A4EU.01 3 1.000
#> TCGA.J8.A4HY.01 5 0.000
#> TCGA.EL.A3ZL.01 1 0.000
#> TCGA.EL.A3ZP.11 2 0.000
#> TCGA.FY.A40N.01 4 0.000
#> TCGA.J8.A4HW.01 1 0.000
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#> TCGA.BJ.A3PR.01 5 0.000
#> TCGA.EM.A3O3.01 3 0.000
#> TCGA.BJ.A0ZB.01 1 0.000
#> TCGA.EM.A3OA.01 2 0.000
#> TCGA.DJ.A2PR.01 1 0.000
#> TCGA.DJ.A13L.01 5 0.000
#> TCGA.FY.A3ON.01 1 0.000
#> TCGA.DJ.A13V.01 1 0.000
#> TCGA.FY.A3R8.01 1 0.000
#> TCGA.EL.A3CP.01 1 0.000
#> TCGA.DJ.A13U.01 4 0.000
#> TCGA.DE.A0Y3.01 1 0.000
#> TCGA.ET.A2N4.01 4 0.000
#> TCGA.DJ.A13P.01 4 0.000
#> TCGA.BJ.A0ZE.01 2 0.000
#> TCGA.EM.A3O7.01 4 0.000
#> TCGA.DJ.A13O.01 5 1.000
#> TCGA.FY.A3RA.01 1 0.000
#> TCGA.DJ.A13M.01 2 0.000
#> TCGA.DJ.A13R.01 2 0.000
#> TCGA.ET.A3DR.01 3 0.000
#> TCGA.FE.A3PB.01 3 0.000
#> TCGA.ET.A3BN.01 1 0.000
#> TCGA.H2.A3RI.01 1 0.000
#> TCGA.ET.A39N.01 2 0.000
#> TCGA.BJ.A3PU.11 2 0.000
#> TCGA.FY.A3R7.01 4 0.000
#> TCGA.FE.A3PA.01 3 0.000
#> TCGA.EM.A2CN.01 2 0.000
#> TCGA.BJ.A0Z2.01 2 0.000
#> TCGA.FY.A3I5.01 2 0.000
#> TCGA.DJ.A13S.01 2 0.000
#> TCGA.DE.A0Y2.01 1 0.000
#> TCGA.ET.A3BU.01 1 0.000
get_classes(res, k = 6)
#> class p
#> TCGA.E8.A416.01 2 0.000
#> TCGA.E8.A433.01 5 0.000
#> TCGA.EL.A4K9.01 3 0.000
#> TCGA.DJ.A3V9.01 5 0.498
#> TCGA.EL.A3ZO.11 2 0.000
#> TCGA.EL.A3ZN.01 5 0.000
#> TCGA.KS.A41F.01 1 0.751
#> TCGA.EL.A3ZK.01 5 0.000
#> TCGA.ET.A40R.01 5 0.000
#> TCGA.EL.A3ZM.01 3 0.000
#> TCGA.ET.A2N3.01 2 0.000
#> TCGA.EL.A3ZQ.01 5 0.000
#> TCGA.ET.A40T.01 5 0.498
#> TCGA.DE.A4MA.01 1 0.249
#> TCGA.EM.A4FU.01 6 0.000
#> TCGA.E8.A418.01 1 0.751
#> TCGA.DJ.A3VD.01 5 0.000
#> TCGA.DJ.A3VM.01 2 0.000
#> TCGA.EL.A3ZG.01 3 0.000
#> TCGA.EM.A4FV.01 5 0.498
#> TCGA.E8.A413.01 5 0.000
#> TCGA.DJ.A3VG.01 6 0.000
#> TCGA.EL.A4K2.01 2 0.000
#> TCGA.IM.A420.01 5 0.000
#> TCGA.KS.A41J.01 1 0.498
#> TCGA.EL.A3ZK.11 2 0.000
#> TCGA.J8.A3O2.01 3 0.000
#> TCGA.E8.A415.01 5 0.000
#> TCGA.FY.A40M.01 2 0.000
#> TCGA.DJ.A3VB.01 3 0.000
#> TCGA.KS.A41I.01 2 0.000
#> TCGA.DJ.A3VL.01 6 0.000
#> TCGA.ET.A4KQ.01 2 0.000
#> TCGA.H2.A421.01 5 0.502
#> TCGA.EL.A3ZO.01 5 0.000
#> TCGA.KS.A4I3.01 3 0.000
#> TCGA.DJ.A4UT.01 1 0.751
#> TCGA.DE.A4MD.01 3 0.000
#> TCGA.EL.A4JW.01 5 0.498
#> TCGA.DJ.A3VI.01 1 0.000
#> TCGA.DJ.A3VA.01 5 0.498
#> TCGA.L6.A4ET.01 4 1.000
#> TCGA.E8.A419.01 5 0.000
#> TCGA.DJ.A4V0.01 5 0.000
#> TCGA.DJ.A4V2.01 4 1.000
#> TCGA.ET.A40Q.01 3 0.000
#> TCGA.EL.A3ZS.01 5 0.000
#> TCGA.KS.A4ID.01 4 1.000
#> TCGA.EL.A3ZL.11 2 0.000
#> TCGA.J8.A3YE.01 4 0.502
#> TCGA.EL.A4K7.01 3 0.000
#> TCGA.DJ.A3VF.01 5 0.000
#> TCGA.EM.A4FH.01 6 0.000
#> TCGA.E8.A432.01 5 0.000
#> TCGA.J8.A3O2.06 3 0.000
#> TCGA.ET.A2MX.01 3 0.000
#> TCGA.ET.A40S.01 3 0.000
#> TCGA.DE.A4M8.01 5 0.000
#> TCGA.IM.A41Z.01 2 0.000
#> TCGA.EL.A4KD.01 3 0.000
#> TCGA.DJ.A3V7.01 1 0.249
#> TCGA.FY.A40L.01 5 0.000
#> TCGA.DE.A4M9.01 6 0.000
#> TCGA.J8.A42S.01 3 0.000
#> TCGA.KS.A41L.01 2 0.000
#> TCGA.EM.A4FN.01 4 1.000
#> TCGA.EL.A4K1.01 1 0.000
#> TCGA.KS.A4IC.01 4 0.249
#> TCGA.E8.A414.01 5 0.000
#> TCGA.H2.A422.01 1 0.000
#> TCGA.J8.A3YF.01 3 0.000
#> TCGA.EL.A4KI.01 6 0.000
#> TCGA.EM.A4G1.01 2 0.000
#> TCGA.DJ.A3VJ.01 3 0.000
#> TCGA.DE.A4MD.06 3 0.000
#> TCGA.EL.A3ZP.01 3 0.000
#> TCGA.EM.A4FQ.01 4 1.000
#> TCGA.EL.A3ZT.01 3 0.000
#> TCGA.DJ.A4V4.01 4 0.000
#> TCGA.FY.A40K.01 5 0.000
#> TCGA.L6.A4EQ.01 3 0.000
#> TCGA.DJ.A3VE.01 3 0.000
#> TCGA.E8.A434.01 5 0.000
#> TCGA.EL.A3ZH.01 2 0.000
#> TCGA.EM.A4FR.01 3 0.000
#> TCGA.EL.A3ZH.11 2 0.000
#> TCGA.EL.A3ZR.01 2 0.000
#> TCGA.DJ.A3V8.01 5 0.000
#> TCGA.EL.A3ZG.11 6 0.000
#> TCGA.ET.A40P.01 2 0.000
#> TCGA.DE.A4MB.01 5 0.747
#> TCGA.MK.A4N6.01 3 0.000
#> TCGA.DJ.A3VK.01 6 0.000
#> TCGA.E8.A417.01 1 1.000
#> TCGA.L6.A4EU.01 1 0.498
#> TCGA.J8.A4HY.01 5 0.000
#> TCGA.EL.A3ZL.01 1 0.249
#> TCGA.EL.A3ZP.11 6 0.000
#> TCGA.FY.A40N.01 5 0.000
#> TCGA.J8.A4HW.01 1 0.000
#> TCGA.BJ.A45J.01 5 0.000
#> TCGA.CE.A482.01 5 0.000
#> TCGA.DJ.A2Q6.01 1 0.000
#> TCGA.DJ.A2PX.01 5 0.000
#> TCGA.DJ.A4UL.01 4 1.000
#> TCGA.EL.A4JX.01 5 0.000
#> TCGA.BJ.A2N8.11 2 0.000
#> TCGA.DJ.A2Q5.01 3 0.000
#> TCGA.EL.A4KG.01 4 0.747
#> TCGA.DJ.A4UP.01 5 0.000
#> TCGA.E8.A438.01 5 0.000
#> TCGA.EL.A3H2.01 6 0.000
#> TCGA.EM.A3AP.01 2 0.000
#> TCGA.DJ.A2PQ.01 3 0.000
#> TCGA.L6.A4EP.01 1 0.751
#> TCGA.FY.A4B4.01 1 0.751
#> TCGA.EL.A4KH.01 4 0.000
#> TCGA.BJ.A45E.01 5 0.000
#> TCGA.DJ.A4V5.01 3 0.000
#> TCGA.DE.A4MC.01 4 1.000
#> TCGA.E8.A44M.01 5 0.000
#> TCGA.BJ.A45K.01 6 0.000
#> TCGA.E3.A3DZ.01 2 0.000
#> TCGA.E3.A3E2.01 5 0.249
#> TCGA.BJ.A45H.01 3 0.000
#> TCGA.E8.A44K.01 5 0.000
#> TCGA.ET.A2MY.01 5 0.747
#> TCGA.EL.A3H8.01 1 0.502
#> TCGA.BJ.A45C.01 6 0.000
#> TCGA.BJ.A45G.01 2 0.000
#> TCGA.EL.A4JZ.01 1 0.751
#> TCGA.CE.A481.01 5 0.000
#> TCGA.KS.A4I9.01 1 1.000
#> TCGA.EL.A3MW.01 4 1.000
#> TCGA.E8.A436.01 5 0.000
#> TCGA.E3.A3DY.01 3 0.000
#> TCGA.DJ.A2Q3.01 5 0.000
#> TCGA.BJ.A2P4.01 2 0.000
#> TCGA.CE.A484.01 2 0.000
#> TCGA.ET.A2N1.01 5 0.000
#> TCGA.DJ.A2Q4.01 3 0.000
#> TCGA.DJ.A2PZ.01 3 0.000
#> TCGA.BJ.A45F.01 2 0.000
#> TCGA.IM.A4EB.01 3 0.000
#> TCGA.EM.A4FO.01 3 0.000
#> TCGA.FY.A4B3.01 3 0.000
#> TCGA.FY.A4B0.01 6 0.000
#> TCGA.BJ.A45I.01 5 0.000
#> TCGA.E3.A3E3.01 4 0.751
#> TCGA.EM.A3AQ.01 3 1.000
#> TCGA.EL.A3N3.01 1 0.249
#> TCGA.DJ.A2Q9.01 5 0.000
#> TCGA.EM.A4FM.01 1 0.000
#> TCGA.EL.A4K6.01 6 0.000
#> TCGA.MK.A4N9.01 1 0.253
#> TCGA.KS.A4I1.01 1 0.000
#> TCGA.DJ.A2PS.01 5 0.000
#> TCGA.CE.A3MD.01 3 0.000
#> TCGA.E3.A3E5.01 3 0.000
#> TCGA.EL.A3CN.01 4 0.751
#> TCGA.J8.A4HW.06 5 0.000
#> TCGA.EM.A4FK.01 2 0.000
#> TCGA.E8.A437.01 5 0.000
#> TCGA.BJ.A4O8.01 3 0.000
#> TCGA.EL.A3MW.11 2 0.000
#> TCGA.E3.A3E0.01 4 1.000
#> TCGA.BJ.A45D.01 6 0.000
#> TCGA.CE.A483.01 1 0.747
#> TCGA.CE.A485.01 3 0.000
#> TCGA.DJ.A4UR.01 2 0.000
#> TCGA.IM.A41Y.01 1 0.498
#> TCGA.ET.A4KN.01 5 0.000
#> TCGA.KS.A4I5.01 1 0.000
#> TCGA.DJ.A4UQ.01 3 0.000
#> TCGA.KS.A4IB.01 1 0.000
#> TCGA.EL.A3N2.11 2 0.000
#> TCGA.BJ.A2N9.01 2 0.000
#> TCGA.DJ.A4UW.01 1 1.000
#> TCGA.EL.A3GZ.11 2 0.000
#> TCGA.EM.A3AR.01 6 0.000
#> TCGA.EL.A3N3.11 2 0.000
#> TCGA.DE.A3KN.01 4 0.751
#> TCGA.DJ.A2QA.01 5 0.000
#> TCGA.EL.A4JV.01 2 0.000
#> TCGA.EM.A4FF.01 1 0.000
#> TCGA.EL.A4K0.01 4 1.000
#> TCGA.FK.A4UB.01 3 0.000
#> TCGA.BJ.A4O9.01 4 0.253
#> TCGA.BJ.A2N7.01 2 0.000
#> TCGA.DE.A2OL.01 2 0.000
#> TCGA.CE.A3ME.01 4 0.000
#> TCGA.MK.A4N7.01 1 0.000
#> TCGA.EL.A3H2.11 6 0.000
#> TCGA.EL.A4K4.01 1 0.000
#> TCGA.EL.A3GS.01 1 0.751
#> TCGA.EL.A3GZ.01 1 0.000
#> TCGA.E3.A3E1.01 1 0.751
#> TCGA.DJ.A2Q8.01 5 0.000
#> TCGA.EL.A3N2.01 1 0.502
#> TCGA.KS.A4I7.01 1 0.000
#> TCGA.MK.A84Z.01 6 0.000
#> TCGA.ET.A3DP.11 2 0.000
#> TCGA.EL.A3MX.11 2 0.000
#> TCGA.ET.A25G.01 1 0.249
#> TCGA.EM.A3FK.01 4 1.000
#> TCGA.EM.A2CS.01 1 0.751
#> TCGA.FE.A23A.01 5 0.751
#> TCGA.BJ.A28T.11 2 0.000
#> TCGA.EM.A22J.01 2 0.000
#> TCGA.EL.A3MX.01 1 1.000
#> TCGA.FY.A3I4.01 4 0.249
#> TCGA.BJ.A28W.11 2 0.000
#> TCGA.ET.A25R.01 1 0.000
#> TCGA.BJ.A2N8.01 2 0.000
#> TCGA.FY.A76V.01 6 0.000
#> TCGA.EM.A3FN.01 2 0.000
#> TCGA.QD.A8IV.01 2 0.000
#> TCGA.EM.A3FJ.01 4 1.000
#> TCGA.ET.A2MY.11 2 0.000
#> TCGA.EM.A3FQ.06 1 1.000
#> TCGA.ET.A25P.01 2 0.000
#> TCGA.ET.A2N0.01 4 0.249
#> TCGA.EM.A2CT.01 2 0.000
#> TCGA.FE.A235.01 1 0.000
#> TCGA.ET.A25M.01 3 0.000
#> TCGA.EL.A3MY.01 3 0.000
#> TCGA.DE.A7U5.01 1 0.751
#> TCGA.E8.A2JQ.11 2 0.000
#> TCGA.ET.A3DP.01 4 0.000
#> TCGA.EM.A2CL.01 6 0.000
#> TCGA.ET.A2N5.01 2 0.000
#> TCGA.ET.A25J.11 2 0.000
#> TCGA.DE.A69J.01 4 1.000
#> TCGA.BJ.A28R.11 2 0.000
#> TCGA.ET.A25K.01 1 0.502
#> TCGA.EL.A3GV.01 4 0.249
#> TCGA.GE.A2C6.01 5 0.000
#> TCGA.EM.A3FM.01 3 0.000
#> TCGA.EL.A3H7.11 2 0.000
#> TCGA.FE.A22Z.01 1 0.000
#> TCGA.H2.A2K9.01 6 0.000
#> TCGA.EM.A22Q.01 6 0.000
#> TCGA.EM.A3FP.01 2 0.000
#> TCGA.GE.A2C6.11 2 0.000
#> TCGA.EL.A3MZ.01 3 0.000
#> TCGA.DJ.A2PT.01 5 0.000
#> TCGA.E8.A242.01 5 0.000
#> TCGA.ET.A25L.01 5 0.249
#> TCGA.CE.A27D.01 2 0.000
#> TCGA.EL.A3H1.11 2 0.000
#> TCGA.BJ.A2N7.11 2 0.000
#> TCGA.DJ.A2Q7.01 1 0.751
#> TCGA.J8.A3O1.01 4 0.000
#> TCGA.EM.A2CR.01 4 0.000
#> TCGA.DE.A69K.01 4 1.000
#> TCGA.EM.A2CQ.01 2 0.000
#> TCGA.FE.A238.01 5 0.000
#> TCGA.EL.A3H1.01 2 0.000
#> TCGA.BJ.A28W.01 2 0.000
#> TCGA.BJ.A28T.01 2 0.000
#> TCGA.EM.A2CJ.01 2 0.000
#> TCGA.EM.A3FQ.01 4 1.000
#> TCGA.4C.A93U.01 4 0.751
#> TCGA.EM.A22M.01 3 0.000
#> TCGA.J8.A3NZ.01 4 1.000
#> TCGA.EM.A22K.01 2 0.000
#> TCGA.FE.A236.01 3 0.000
#> TCGA.BJ.A28R.01 1 0.502
#> TCGA.EM.A2CU.01 5 1.000
#> TCGA.ET.A25N.01 1 1.000
#> TCGA.EL.A3H7.01 1 0.000
#> TCGA.FY.A3NM.01 2 0.000
#> TCGA.EM.A3FO.01 3 0.000
#> TCGA.EM.A22L.01 4 1.000
#> TCGA.BJ.A2N9.11 2 0.000
#> TCGA.BJ.A291.01 2 0.000
#> TCGA.ET.A2N5.11 2 0.000
#> TCGA.ET.A25N.11 2 0.000
#> TCGA.J8.A3O0.01 6 0.000
#> TCGA.FE.A237.01 4 1.000
#> TCGA.DJ.A2QC.01 5 0.000
#> TCGA.ET.A25O.01 4 1.000
#> TCGA.EL.A3GU.01 1 0.000
#> TCGA.EL.A3MY.11 6 0.000
#> TCGA.DJ.A2PY.01 4 0.502
#> TCGA.EM.A2CS.06 5 0.000
#> TCGA.FY.A3NP.01 6 0.000
#> TCGA.ET.A25I.01 2 0.000
#> TCGA.H2.A26U.01 5 0.000
#> TCGA.BJ.A290.11 6 0.000
#> TCGA.EM.A22I.01 1 0.000
#> TCGA.FE.A239.01 6 0.000
#> TCGA.BJ.A28Z.01 5 0.000
#> TCGA.DE.A0XZ.01 1 0.249
#> TCGA.ET.A25J.01 4 0.498
#> TCGA.EM.A22N.01 2 0.000
#> TCGA.EM.A2CM.01 2 0.000
#> TCGA.FY.A3NN.01 4 0.000
#> TCGA.EM.A3FL.01 2 0.000
#> TCGA.H2.A2K9.11 6 0.000
#> TCGA.EL.A3H3.01 1 0.747
#> TCGA.EL.A3H4.01 1 0.000
#> TCGA.EM.A2OX.01 3 0.000
#> TCGA.EM.A3SX.01 5 1.000
#> TCGA.BJ.A0Z3.01 5 0.249
#> TCGA.BJ.A28X.01 5 0.000
#> TCGA.EL.A3CT.01 5 1.000
#> TCGA.EL.A3CR.01 1 0.000
#> TCGA.FY.A3TY.01 2 0.000
#> TCGA.J8.A3YG.01 5 0.249
#> TCGA.DJ.A3V6.01 3 0.000
#> TCGA.EM.A3SZ.01 5 0.000
#> TCGA.EM.A2OW.01 2 0.000
#> TCGA.DO.A1JZ.11 2 0.000
#> TCGA.EL.A3D5.01 2 0.000
#> TCGA.EM.A2P0.01 3 0.000
#> TCGA.E8.A2JQ.01 5 0.000
#> TCGA.BJ.A18Z.01 3 0.000
#> TCGA.DJ.A3V0.01 3 0.000
#> TCGA.EL.A3GW.01 2 0.000
#> TCGA.DJ.A3UW.01 5 0.000
#> TCGA.DJ.A3V3.01 5 0.498
#> TCGA.EL.A3T1.11 2 0.000
#> TCGA.BJ.A0ZC.01 6 0.000
#> TCGA.EM.A2OV.01 2 0.000
#> TCGA.EL.A3GY.01 1 0.249
#> TCGA.EM.A3SY.01 6 0.000
#> TCGA.EM.A3AI.01 2 0.000
#> TCGA.EM.A2OY.01 2 0.000
#> TCGA.EL.A3T8.01 3 0.000
#> TCGA.BJ.A18Y.01 6 0.000
#> TCGA.EL.A3GP.01 3 0.000
#> TCGA.EM.A2CK.01 6 0.000
#> TCGA.EL.A3T7.11 2 0.000
#> TCGA.BJ.A192.01 2 0.000
#> TCGA.BJ.A191.01 4 0.751
#> TCGA.EM.A2CP.01 2 0.000
#> TCGA.EM.A22O.01 3 0.000
#> TCGA.EM.A2P1.01 3 0.000
#> TCGA.J8.A3YH.01 3 0.000
#> TCGA.DJ.A3UZ.01 2 1.000
#> TCGA.IM.A3EB.01 1 0.751
#> TCGA.BJ.A3F0.01 2 0.000
#> TCGA.EL.A3GX.01 1 0.249
#> TCGA.EM.A3AK.01 4 1.000
#> TCGA.DO.A1JZ.01 4 1.000
#> TCGA.FY.A3YR.01 1 0.000
#> TCGA.DO.A1K0.01 4 0.751
#> TCGA.DJ.A3V5.01 5 0.000
#> TCGA.EM.A3AJ.01 6 0.000
#> TCGA.IM.A3ED.01 1 0.751
#> TCGA.EM.A3AO.01 3 0.000
#> TCGA.EM.A2P1.06 3 0.000
#> TCGA.EM.A1CW.01 2 0.000
#> TCGA.FK.A3SE.01 1 0.000
#> TCGA.EL.A3T7.01 1 0.000
#> TCGA.EM.A2P2.01 6 0.000
#> TCGA.EM.A1CU.11 6 0.000
#> TCGA.EL.A3T0.11 2 0.000
#> TCGA.E8.A3X7.01 5 0.000
#> TCGA.ET.A3BQ.01 4 1.000
#> TCGA.EM.A1CS.01 4 0.000
#> TCGA.EL.A3GQ.01 4 0.000
#> TCGA.EL.A3H5.01 1 1.000
#> TCGA.DJ.A3V4.01 5 0.000
#> TCGA.EM.A2P3.01 1 0.000
#> TCGA.FY.A3WA.01 2 0.000
#> TCGA.DJ.A3V2.01 5 0.000
#> TCGA.FY.A3TY.11 2 0.000
#> TCGA.BJ.A290.01 3 0.000
#> TCGA.EM.A3SU.01 5 0.000
#> TCGA.EL.A3D0.01 3 0.000
#> TCGA.EM.A1CT.11 6 0.000
#> TCGA.EL.A3GR.01 4 0.249
#> TCGA.J8.A3YH.06 3 0.000
#> TCGA.EM.A3ST.11 2 0.000
#> TCGA.ET.A3DV.01 2 0.000
#> TCGA.BJ.A3EZ.01 3 0.000
#> TCGA.J8.A3YD.01 2 0.000
#> TCGA.EM.A3SU.06 5 0.000
#> TCGA.EM.A3AL.01 2 0.000
#> TCGA.DJ.A3US.01 5 0.000
#> TCGA.EM.A1CS.11 2 0.000
#> TCGA.EM.A1CW.11 2 0.000
#> TCGA.BJ.A190.01 6 0.000
#> TCGA.EM.A2OZ.01 3 0.000
#> TCGA.EM.A1CV.11 2 0.000
#> TCGA.EM.A1CU.01 3 0.000
#> TCGA.EM.A3AN.01 1 0.000
#> TCGA.E8.A2EA.01 5 0.000
#> TCGA.EM.A1CV.01 4 0.000
#> TCGA.EM.A1CT.01 3 0.000
#> TCGA.EM.A3ST.01 2 0.000
#> TCGA.ET.A3BS.01 3 0.000
#> TCGA.EL.A3GO.01 2 0.000
#> TCGA.DJ.A2Q0.01 2 0.000
#> TCGA.EL.A3D6.01 5 0.498
#> TCGA.DJ.A3UN.01 1 1.000
#> TCGA.DJ.A3UU.01 5 0.000
#> TCGA.FK.A3SD.01 2 0.000
#> TCGA.DJ.A2PO.01 3 0.000
#> TCGA.DJ.A3UQ.01 5 0.000
#> TCGA.EM.A1YE.11 2 0.000
#> TCGA.EL.A3T2.11 2 0.000
#> TCGA.EL.A3CL.01 1 0.000
#> TCGA.EM.A1YC.01 2 1.000
#> TCGA.DJ.A3UP.01 2 0.000
#> TCGA.EL.A3T0.01 5 0.000
#> TCGA.IM.A3U2.01 5 0.498
#> TCGA.IM.A3U3.01 1 0.751
#> TCGA.DJ.A3UX.01 5 0.000
#> TCGA.ET.A3BW.01 4 0.751
#> TCGA.ET.A39S.01 5 0.000
#> TCGA.ET.A3BP.01 1 0.502
#> TCGA.DJ.A1QE.01 4 1.000
#> TCGA.EL.A3D4.01 3 0.000
#> TCGA.FK.A3SB.01 1 1.000
#> TCGA.EL.A3CW.01 2 0.000
#> TCGA.ET.A39L.01 5 0.000
#> TCGA.DJ.A2PW.01 3 0.000
#> TCGA.EM.A2CO.01 2 0.000
#> TCGA.FE.A232.01 4 0.000
#> TCGA.DJ.A3UR.01 1 0.000
#> TCGA.DJ.A2PP.01 6 0.000
#> TCGA.ET.A3DQ.01 2 0.000
#> TCGA.ET.A3DS.01 2 0.000
#> TCGA.FY.A3W9.01 2 0.000
#> TCGA.FK.A3S3.01 1 1.000
#> TCGA.ET.A2MZ.01 3 0.000
#> TCGA.BJ.A2NA.11 6 0.000
#> TCGA.DJ.A1QL.01 6 0.000
#> TCGA.EL.A3CS.01 1 0.498
#> TCGA.FE.A233.01 4 1.000
#> TCGA.EM.A1YD.11 2 0.000
#> TCGA.ET.A3DW.11 6 0.000
#> TCGA.EL.A3T9.01 5 0.000
#> TCGA.DJ.A3UM.01 5 0.751
#> TCGA.DO.A2HM.01 3 1.000
#> TCGA.FY.A3BL.01 3 0.000
#> TCGA.EL.A3TA.11 6 0.000
#> TCGA.ET.A3BX.01 3 0.000
#> TCGA.DJ.A1QQ.01 3 0.000
#> TCGA.DJ.A1QF.01 4 0.000
#> TCGA.DJ.A1QO.01 3 0.000
#> TCGA.BJ.A2NA.01 3 0.000
#> TCGA.EM.A1YE.01 2 0.000
#> TCGA.FY.A2QD.01 2 0.000
#> TCGA.ET.A39J.01 4 0.000
#> TCGA.ET.A3DU.01 5 0.000
#> TCGA.EL.A3CM.01 5 0.000
#> TCGA.DJ.A3UO.01 3 0.000
#> TCGA.ET.A39P.01 1 0.498
#> TCGA.DJ.A2Q2.01 2 0.000
#> TCGA.BJ.A28V.01 2 0.000
#> TCGA.ET.A3BO.01 1 0.498
#> TCGA.EL.A3T1.01 5 0.498
#> TCGA.DJ.A1QI.01 4 0.000
#> TCGA.EL.A3TB.01 5 0.751
#> TCGA.BJ.A28X.11 2 0.000
#> TCGA.DJ.A1QN.01 4 0.000
#> TCGA.FE.A230.01 4 0.000
#> TCGA.FE.A234.01 4 0.249
#> TCGA.ET.A39R.01 5 0.249
#> TCGA.DJ.A1QG.01 6 0.000
#> TCGA.EL.A3CV.01 3 0.000
#> TCGA.FE.A231.01 3 0.000
#> TCGA.EL.A3TA.01 3 0.000
#> TCGA.DJ.A3UY.01 5 0.000
#> TCGA.DJ.A2Q1.01 5 0.000
#> TCGA.EL.A3CU.01 5 0.000
#> TCGA.EL.A3TB.11 2 0.000
#> TCGA.ET.A39I.01 2 0.000
#> TCGA.EM.A1YB.01 2 0.000
#> TCGA.DJ.A3UV.01 5 0.000
#> TCGA.DJ.A3UT.01 2 0.000
#> TCGA.ET.A3DW.01 3 0.000
#> TCGA.ET.A3BT.01 5 0.249
#> TCGA.EL.A3T3.01 1 0.000
#> TCGA.DJ.A1QM.01 6 0.000
#> TCGA.EL.A3CY.01 3 1.000
#> TCGA.ET.A39O.01 3 0.000
#> TCGA.EM.A1YC.11 2 0.000
#> TCGA.DJ.A1QH.01 4 1.000
#> TCGA.EL.A3T3.11 2 0.000
#> TCGA.EL.A3CX.01 5 0.000
#> TCGA.EL.A3T2.01 2 0.000
#> TCGA.EM.A22P.01 3 0.000
#> TCGA.EL.A3T8.11 6 0.000
#> TCGA.DJ.A2PU.01 4 0.000
#> TCGA.DJ.A3UK.01 1 1.000
#> TCGA.ET.A3DO.01 5 0.000
#> TCGA.EM.A1YA.01 2 0.502
#> TCGA.ET.A3BV.01 5 0.000
#> TCGA.EL.A3CO.01 6 0.000
#> TCGA.DJ.A2PN.01 1 0.502
#> TCGA.FK.A3SG.01 1 1.000
#> TCGA.FK.A3SH.01 5 0.249
#> TCGA.EM.A1YD.01 2 0.000
#> TCGA.DJ.A1QD.01 4 0.000
#> TCGA.EL.A3CZ.01 2 0.000
#> TCGA.BJ.A0Z9.01 5 0.000
#> TCGA.CE.A13K.01 1 0.747
#> TCGA.EM.A3FR.01 2 0.000
#> TCGA.EM.A3O8.01 2 0.000
#> TCGA.FY.A3R6.01 5 0.000
#> TCGA.FY.A3R9.01 2 0.000
#> TCGA.EL.A3D1.01 3 0.000
#> TCGA.EM.A3O6.01 2 0.000
#> TCGA.BJ.A0Z5.01 3 0.000
#> TCGA.BJ.A28S.01 6 0.000
#> TCGA.BJ.A0ZH.01 1 0.249
#> TCGA.ET.A3DT.01 5 0.000
#> TCGA.H2.A3RI.11 2 0.000
#> TCGA.DJ.A13W.01 2 0.000
#> TCGA.DJ.A13T.01 1 0.000
#> TCGA.BJ.A0ZA.01 2 0.000
#> TCGA.BJ.A3PT.01 2 0.000
#> TCGA.FE.A3PD.01 5 1.000
#> TCGA.BJ.A0ZF.01 2 0.000
#> TCGA.ET.A39M.01 3 0.000
#> TCGA.BJ.A0ZJ.01 3 0.000
#> TCGA.BJ.A0YZ.01 6 0.000
#> TCGA.FE.A3PC.01 1 0.498
#> TCGA.DJ.A2QB.01 2 0.000
#> TCGA.EM.A3OB.01 2 0.000
#> TCGA.H2.A3RH.01 2 0.000
#> TCGA.ET.A39T.01 4 1.000
#> TCGA.DJ.A2PV.01 1 0.000
#> TCGA.BJ.A3PR.11 2 0.000
#> TCGA.EL.A3T6.11 2 0.000
#> TCGA.DJ.A13X.01 1 0.751
#> TCGA.BJ.A0ZG.01 6 0.000
#> TCGA.EL.A3T6.01 5 0.747
#> TCGA.BJ.A0Z0.01 6 0.000
#> TCGA.ET.A39K.01 1 0.249
#> TCGA.EM.A3O9.01 6 0.000
#> TCGA.BJ.A3PU.01 3 0.000
#> TCGA.BJ.A3PR.01 5 0.000
#> TCGA.EM.A3O3.01 4 0.000
#> TCGA.BJ.A0ZB.01 3 0.000
#> TCGA.EM.A3OA.01 2 0.000
#> TCGA.DJ.A2PR.01 3 0.000
#> TCGA.DJ.A13L.01 3 0.000
#> TCGA.FY.A3ON.01 3 0.000
#> TCGA.DJ.A13V.01 1 0.249
#> TCGA.FY.A3R8.01 1 0.000
#> TCGA.EL.A3CP.01 1 0.498
#> TCGA.DJ.A13U.01 3 0.000
#> TCGA.DE.A0Y3.01 1 0.000
#> TCGA.ET.A2N4.01 1 0.249
#> TCGA.DJ.A13P.01 5 0.747
#> TCGA.BJ.A0ZE.01 2 0.000
#> TCGA.EM.A3O7.01 4 1.000
#> TCGA.DJ.A13O.01 6 0.000
#> TCGA.FY.A3RA.01 1 0.498
#> TCGA.DJ.A13M.01 2 0.000
#> TCGA.DJ.A13R.01 6 0.000
#> TCGA.ET.A3DR.01 5 0.502
#> TCGA.FE.A3PB.01 5 0.000
#> TCGA.ET.A3BN.01 1 1.000
#> TCGA.H2.A3RI.01 1 0.747
#> TCGA.ET.A39N.01 2 0.000
#> TCGA.BJ.A3PU.11 6 0.000
#> TCGA.FY.A3R7.01 5 0.747
#> TCGA.FE.A3PA.01 3 0.000
#> TCGA.EM.A2CN.01 6 0.000
#> TCGA.BJ.A0Z2.01 6 0.000
#> TCGA.FY.A3I5.01 2 0.000
#> TCGA.DJ.A13S.01 2 0.000
#> TCGA.DE.A0Y2.01 1 0.000
#> TCGA.ET.A3BU.01 3 0.000
get_classes(res, k = 7)
#> class p
#> TCGA.E8.A416.01 2 0.000
#> TCGA.E8.A433.01 5 1.000
#> TCGA.EL.A4K9.01 3 0.000
#> TCGA.DJ.A3V9.01 5 0.747
#> TCGA.EL.A3ZO.11 2 0.000
#> TCGA.EL.A3ZN.01 7 1.000
#> TCGA.KS.A41F.01 1 0.000
#> TCGA.EL.A3ZK.01 5 0.000
#> TCGA.ET.A40R.01 5 0.498
#> TCGA.EL.A3ZM.01 3 0.000
#> TCGA.ET.A2N3.01 2 0.000
#> TCGA.EL.A3ZQ.01 1 1.000
#> TCGA.ET.A40T.01 5 0.747
#> TCGA.DE.A4MA.01 1 0.000
#> TCGA.EM.A4FU.01 6 0.000
#> TCGA.E8.A418.01 1 0.000
#> TCGA.DJ.A3VD.01 5 1.000
#> TCGA.DJ.A3VM.01 2 0.000
#> TCGA.EL.A3ZG.01 3 0.000
#> TCGA.EM.A4FV.01 5 0.747
#> TCGA.E8.A413.01 7 1.000
#> TCGA.DJ.A3VG.01 6 0.000
#> TCGA.EL.A4K2.01 2 0.000
#> TCGA.IM.A420.01 5 0.747
#> TCGA.KS.A41J.01 1 0.000
#> TCGA.EL.A3ZK.11 2 0.000
#> TCGA.J8.A3O2.01 3 0.000
#> TCGA.E8.A415.01 7 1.000
#> TCGA.FY.A40M.01 7 1.000
#> TCGA.DJ.A3VB.01 3 0.000
#> TCGA.KS.A41I.01 2 0.000
#> TCGA.DJ.A3VL.01 6 0.000
#> TCGA.ET.A4KQ.01 2 0.000
#> TCGA.H2.A421.01 5 0.747
#> TCGA.EL.A3ZO.01 5 1.000
#> TCGA.KS.A4I3.01 3 0.000
#> TCGA.DJ.A4UT.01 5 0.000
#> TCGA.DE.A4MD.01 3 0.000
#> TCGA.EL.A4JW.01 5 0.000
#> TCGA.DJ.A3VI.01 1 0.000
#> TCGA.DJ.A3VA.01 1 0.498
#> TCGA.L6.A4ET.01 4 0.253
#> TCGA.E8.A419.01 5 0.000
#> TCGA.DJ.A4V0.01 7 0.000
#> TCGA.DJ.A4V2.01 1 0.000
#> TCGA.ET.A40Q.01 3 0.000
#> TCGA.EL.A3ZS.01 5 0.000
#> TCGA.KS.A4ID.01 5 0.000
#> TCGA.EL.A3ZL.11 2 0.000
#> TCGA.J8.A3YE.01 4 0.249
#> TCGA.EL.A4K7.01 3 0.000
#> TCGA.DJ.A3VF.01 5 0.498
#> TCGA.EM.A4FH.01 6 0.000
#> TCGA.E8.A432.01 5 0.000
#> TCGA.J8.A3O2.06 3 0.000
#> TCGA.ET.A2MX.01 3 0.000
#> TCGA.ET.A40S.01 3 0.000
#> TCGA.DE.A4M8.01 5 0.000
#> TCGA.IM.A41Z.01 2 0.000
#> TCGA.EL.A4KD.01 3 0.000
#> TCGA.DJ.A3V7.01 1 0.000
#> TCGA.FY.A40L.01 1 0.747
#> TCGA.DE.A4M9.01 6 0.000
#> TCGA.J8.A42S.01 3 0.000
#> TCGA.KS.A41L.01 2 0.000
#> TCGA.EM.A4FN.01 4 1.000
#> TCGA.EL.A4K1.01 1 0.000
#> TCGA.KS.A4IC.01 4 0.000
#> TCGA.E8.A414.01 5 1.000
#> TCGA.H2.A422.01 1 0.000
#> TCGA.J8.A3YF.01 3 0.000
#> TCGA.EL.A4KI.01 6 0.000
#> TCGA.EM.A4G1.01 2 0.000
#> TCGA.DJ.A3VJ.01 3 0.000
#> TCGA.DE.A4MD.06 3 0.000
#> TCGA.EL.A3ZP.01 3 0.000
#> TCGA.EM.A4FQ.01 1 0.253
#> TCGA.EL.A3ZT.01 3 0.000
#> TCGA.DJ.A4V4.01 5 1.000
#> TCGA.FY.A40K.01 1 1.000
#> TCGA.L6.A4EQ.01 3 0.000
#> TCGA.DJ.A3VE.01 3 0.000
#> TCGA.E8.A434.01 7 0.000
#> TCGA.EL.A3ZH.01 2 0.000
#> TCGA.EM.A4FR.01 3 0.000
#> TCGA.EL.A3ZH.11 2 0.000
#> TCGA.EL.A3ZR.01 2 0.000
#> TCGA.DJ.A3V8.01 5 1.000
#> TCGA.EL.A3ZG.11 6 0.000
#> TCGA.ET.A40P.01 2 0.000
#> TCGA.DE.A4MB.01 1 0.000
#> TCGA.MK.A4N6.01 3 0.000
#> TCGA.DJ.A3VK.01 6 0.000
#> TCGA.E8.A417.01 1 0.000
#> TCGA.L6.A4EU.01 1 0.747
#> TCGA.J8.A4HY.01 5 0.000
#> TCGA.EL.A3ZL.01 1 0.000
#> TCGA.EL.A3ZP.11 6 0.000
#> TCGA.FY.A40N.01 5 1.000
#> TCGA.J8.A4HW.01 1 0.000
#> TCGA.BJ.A45J.01 1 0.747
#> TCGA.CE.A482.01 5 1.000
#> TCGA.DJ.A2Q6.01 1 0.498
#> TCGA.DJ.A2PX.01 5 0.000
#> TCGA.DJ.A4UL.01 1 0.751
#> TCGA.EL.A4JX.01 5 0.000
#> TCGA.BJ.A2N8.11 2 0.000
#> TCGA.DJ.A2Q5.01 3 0.000
#> TCGA.EL.A4KG.01 4 0.502
#> TCGA.DJ.A4UP.01 7 0.498
#> TCGA.E8.A438.01 5 0.000
#> TCGA.EL.A3H2.01 6 0.000
#> TCGA.EM.A3AP.01 2 1.000
#> TCGA.DJ.A2PQ.01 3 0.000
#> TCGA.L6.A4EP.01 1 0.000
#> TCGA.FY.A4B4.01 1 0.498
#> TCGA.EL.A4KH.01 4 0.000
#> TCGA.BJ.A45E.01 7 0.000
#> TCGA.DJ.A4V5.01 3 0.000
#> TCGA.DE.A4MC.01 1 0.502
#> TCGA.E8.A44M.01 5 1.000
#> TCGA.BJ.A45K.01 6 0.000
#> TCGA.E3.A3DZ.01 2 0.000
#> TCGA.E3.A3E2.01 1 0.747
#> TCGA.BJ.A45H.01 3 0.000
#> TCGA.E8.A44K.01 5 0.747
#> TCGA.ET.A2MY.01 1 0.000
#> TCGA.EL.A3H8.01 1 0.000
#> TCGA.BJ.A45C.01 6 0.000
#> TCGA.BJ.A45G.01 2 0.000
#> TCGA.EL.A4JZ.01 1 0.249
#> TCGA.CE.A481.01 5 1.000
#> TCGA.KS.A4I9.01 1 0.000
#> TCGA.EL.A3MW.01 1 0.502
#> TCGA.E8.A436.01 7 1.000
#> TCGA.E3.A3DY.01 3 0.000
#> TCGA.DJ.A2Q3.01 5 0.000
#> TCGA.BJ.A2P4.01 2 0.000
#> TCGA.CE.A484.01 7 1.000
#> TCGA.ET.A2N1.01 7 1.000
#> TCGA.DJ.A2Q4.01 3 0.000
#> TCGA.DJ.A2PZ.01 3 0.000
#> TCGA.BJ.A45F.01 2 0.000
#> TCGA.IM.A4EB.01 3 0.000
#> TCGA.EM.A4FO.01 3 0.000
#> TCGA.FY.A4B3.01 3 0.000
#> TCGA.FY.A4B0.01 6 0.000
#> TCGA.BJ.A45I.01 5 0.747
#> TCGA.E3.A3E3.01 4 1.000
#> TCGA.EM.A3AQ.01 3 0.000
#> TCGA.EL.A3N3.01 5 0.747
#> TCGA.DJ.A2Q9.01 7 0.000
#> TCGA.EM.A4FM.01 1 0.000
#> TCGA.EL.A4K6.01 6 0.000
#> TCGA.MK.A4N9.01 1 0.000
#> TCGA.KS.A4I1.01 1 0.000
#> TCGA.DJ.A2PS.01 5 1.000
#> TCGA.CE.A3MD.01 3 0.000
#> TCGA.E3.A3E5.01 3 0.000
#> TCGA.EL.A3CN.01 1 0.498
#> TCGA.J8.A4HW.06 5 0.000
#> TCGA.EM.A4FK.01 2 0.000
#> TCGA.E8.A437.01 5 0.000
#> TCGA.BJ.A4O8.01 3 0.000
#> TCGA.EL.A3MW.11 2 0.000
#> TCGA.E3.A3E0.01 1 0.747
#> TCGA.BJ.A45D.01 6 0.000
#> TCGA.CE.A483.01 1 0.498
#> TCGA.CE.A485.01 3 0.000
#> TCGA.DJ.A4UR.01 2 0.249
#> TCGA.IM.A41Y.01 1 0.000
#> TCGA.ET.A4KN.01 5 0.000
#> TCGA.KS.A4I5.01 1 0.000
#> TCGA.DJ.A4UQ.01 3 0.000
#> TCGA.KS.A4IB.01 1 0.000
#> TCGA.EL.A3N2.11 2 0.000
#> TCGA.BJ.A2N9.01 2 0.000
#> TCGA.DJ.A4UW.01 5 1.000
#> TCGA.EL.A3GZ.11 2 0.000
#> TCGA.EM.A3AR.01 6 0.000
#> TCGA.EL.A3N3.11 2 0.000
#> TCGA.DE.A3KN.01 5 0.000
#> TCGA.DJ.A2QA.01 5 0.000
#> TCGA.EL.A4JV.01 2 0.000
#> TCGA.EM.A4FF.01 1 0.000
#> TCGA.EL.A4K0.01 1 0.498
#> TCGA.FK.A4UB.01 3 0.000
#> TCGA.BJ.A4O9.01 4 0.000
#> TCGA.BJ.A2N7.01 2 0.000
#> TCGA.DE.A2OL.01 2 0.000
#> TCGA.CE.A3ME.01 4 0.000
#> TCGA.MK.A4N7.01 1 0.000
#> TCGA.EL.A3H2.11 6 0.000
#> TCGA.EL.A4K4.01 1 0.000
#> TCGA.EL.A3GS.01 1 0.000
#> TCGA.EL.A3GZ.01 1 0.000
#> TCGA.E3.A3E1.01 5 0.747
#> TCGA.DJ.A2Q8.01 5 0.000
#> TCGA.EL.A3N2.01 1 0.000
#> TCGA.KS.A4I7.01 1 0.000
#> TCGA.MK.A84Z.01 6 0.000
#> TCGA.ET.A3DP.11 2 0.000
#> TCGA.EL.A3MX.11 2 0.000
#> TCGA.ET.A25G.01 1 0.249
#> TCGA.EM.A3FK.01 4 1.000
#> TCGA.EM.A2CS.01 1 0.000
#> TCGA.FE.A23A.01 5 0.747
#> TCGA.BJ.A28T.11 2 0.000
#> TCGA.EM.A22J.01 2 0.000
#> TCGA.EL.A3MX.01 1 0.000
#> TCGA.FY.A3I4.01 7 0.000
#> TCGA.BJ.A28W.11 2 0.000
#> TCGA.ET.A25R.01 1 0.000
#> TCGA.BJ.A2N8.01 2 0.000
#> TCGA.FY.A76V.01 6 0.000
#> TCGA.EM.A3FN.01 2 0.000
#> TCGA.QD.A8IV.01 2 0.000
#> TCGA.EM.A3FJ.01 4 1.000
#> TCGA.ET.A2MY.11 2 0.000
#> TCGA.EM.A3FQ.06 1 0.000
#> TCGA.ET.A25P.01 2 1.000
#> TCGA.ET.A2N0.01 4 0.000
#> TCGA.EM.A2CT.01 2 0.000
#> TCGA.FE.A235.01 1 0.000
#> TCGA.ET.A25M.01 3 0.000
#> TCGA.EL.A3MY.01 3 0.000
#> TCGA.DE.A7U5.01 1 0.249
#> TCGA.E8.A2JQ.11 2 1.000
#> TCGA.ET.A3DP.01 4 0.000
#> TCGA.EM.A2CL.01 6 0.000
#> TCGA.ET.A2N5.01 2 0.000
#> TCGA.ET.A25J.11 2 0.000
#> TCGA.DE.A69J.01 1 0.000
#> TCGA.BJ.A28R.11 2 0.000
#> TCGA.ET.A25K.01 1 0.249
#> TCGA.EL.A3GV.01 4 0.000
#> TCGA.GE.A2C6.01 5 0.000
#> TCGA.EM.A3FM.01 3 0.000
#> TCGA.EL.A3H7.11 2 0.000
#> TCGA.FE.A22Z.01 1 0.000
#> TCGA.H2.A2K9.01 6 0.000
#> TCGA.EM.A22Q.01 6 0.000
#> TCGA.EM.A3FP.01 2 0.000
#> TCGA.GE.A2C6.11 2 0.000
#> TCGA.EL.A3MZ.01 3 0.000
#> TCGA.DJ.A2PT.01 5 0.000
#> TCGA.E8.A242.01 5 0.000
#> TCGA.ET.A25L.01 1 0.747
#> TCGA.CE.A27D.01 2 1.000
#> TCGA.EL.A3H1.11 2 0.000
#> TCGA.BJ.A2N7.11 2 0.000
#> TCGA.DJ.A2Q7.01 1 0.498
#> TCGA.J8.A3O1.01 4 0.751
#> TCGA.EM.A2CR.01 7 0.000
#> TCGA.DE.A69K.01 1 0.751
#> TCGA.EM.A2CQ.01 2 0.000
#> TCGA.FE.A238.01 5 0.000
#> TCGA.EL.A3H1.01 2 0.000
#> TCGA.BJ.A28W.01 2 1.000
#> TCGA.BJ.A28T.01 2 1.000
#> TCGA.EM.A2CJ.01 2 0.000
#> TCGA.EM.A3FQ.01 5 0.000
#> TCGA.4C.A93U.01 1 0.000
#> TCGA.EM.A22M.01 3 0.000
#> TCGA.J8.A3NZ.01 4 1.000
#> TCGA.EM.A22K.01 2 0.000
#> TCGA.FE.A236.01 3 0.000
#> TCGA.BJ.A28R.01 1 0.000
#> TCGA.EM.A2CU.01 5 0.249
#> TCGA.ET.A25N.01 1 0.000
#> TCGA.EL.A3H7.01 1 0.000
#> TCGA.FY.A3NM.01 2 0.000
#> TCGA.EM.A3FO.01 3 0.000
#> TCGA.EM.A22L.01 2 0.000
#> TCGA.BJ.A2N9.11 2 0.000
#> TCGA.BJ.A291.01 2 0.000
#> TCGA.ET.A2N5.11 2 0.000
#> TCGA.ET.A25N.11 2 0.000
#> TCGA.J8.A3O0.01 6 0.000
#> TCGA.FE.A237.01 5 0.498
#> TCGA.DJ.A2QC.01 5 1.000
#> TCGA.ET.A25O.01 4 0.502
#> TCGA.EL.A3GU.01 1 0.000
#> TCGA.EL.A3MY.11 6 0.000
#> TCGA.DJ.A2PY.01 4 0.751
#> TCGA.EM.A2CS.06 5 0.000
#> TCGA.FY.A3NP.01 6 0.000
#> TCGA.ET.A25I.01 2 0.000
#> TCGA.H2.A26U.01 5 0.000
#> TCGA.BJ.A290.11 6 0.000
#> TCGA.EM.A22I.01 1 0.000
#> TCGA.FE.A239.01 6 0.000
#> TCGA.BJ.A28Z.01 5 0.000
#> TCGA.DE.A0XZ.01 1 0.000
#> TCGA.ET.A25J.01 4 0.747
#> TCGA.EM.A22N.01 2 0.000
#> TCGA.EM.A2CM.01 2 0.000
#> TCGA.FY.A3NN.01 4 0.000
#> TCGA.EM.A3FL.01 2 0.000
#> TCGA.H2.A2K9.11 6 0.000
#> TCGA.EL.A3H3.01 1 0.249
#> TCGA.EL.A3H4.01 1 0.000
#> TCGA.EM.A2OX.01 3 0.000
#> TCGA.EM.A3SX.01 1 0.000
#> TCGA.BJ.A0Z3.01 5 0.000
#> TCGA.BJ.A28X.01 5 0.000
#> TCGA.EL.A3CT.01 5 0.000
#> TCGA.EL.A3CR.01 1 0.000
#> TCGA.FY.A3TY.01 7 1.000
#> TCGA.J8.A3YG.01 5 0.000
#> TCGA.DJ.A3V6.01 3 0.000
#> TCGA.EM.A3SZ.01 5 1.000
#> TCGA.EM.A2OW.01 2 0.000
#> TCGA.DO.A1JZ.11 2 0.000
#> TCGA.EL.A3D5.01 2 0.000
#> TCGA.EM.A2P0.01 3 0.000
#> TCGA.E8.A2JQ.01 5 0.000
#> TCGA.BJ.A18Z.01 3 0.000
#> TCGA.DJ.A3V0.01 3 0.000
#> TCGA.EL.A3GW.01 2 0.000
#> TCGA.DJ.A3UW.01 5 0.000
#> TCGA.DJ.A3V3.01 5 0.747
#> TCGA.EL.A3T1.11 2 0.502
#> TCGA.BJ.A0ZC.01 6 0.000
#> TCGA.EM.A2OV.01 2 0.000
#> TCGA.EL.A3GY.01 1 0.000
#> TCGA.EM.A3SY.01 6 0.000
#> TCGA.EM.A3AI.01 2 0.000
#> TCGA.EM.A2OY.01 2 0.000
#> TCGA.EL.A3T8.01 3 0.000
#> TCGA.BJ.A18Y.01 6 0.000
#> TCGA.EL.A3GP.01 3 0.000
#> TCGA.EM.A2CK.01 6 0.000
#> TCGA.EL.A3T7.11 2 0.000
#> TCGA.BJ.A192.01 2 0.000
#> TCGA.BJ.A191.01 7 0.498
#> TCGA.EM.A2CP.01 2 1.000
#> TCGA.EM.A22O.01 3 0.000
#> TCGA.EM.A2P1.01 3 0.000
#> TCGA.J8.A3YH.01 3 0.000
#> TCGA.DJ.A3UZ.01 7 0.000
#> TCGA.IM.A3EB.01 1 0.000
#> TCGA.BJ.A3F0.01 2 0.000
#> TCGA.EL.A3GX.01 1 0.000
#> TCGA.EM.A3AK.01 4 0.502
#> TCGA.DO.A1JZ.01 1 0.000
#> TCGA.FY.A3YR.01 1 0.000
#> TCGA.DO.A1K0.01 1 0.502
#> TCGA.DJ.A3V5.01 1 1.000
#> TCGA.EM.A3AJ.01 6 0.000
#> TCGA.IM.A3ED.01 1 0.249
#> TCGA.EM.A3AO.01 3 0.000
#> TCGA.EM.A2P1.06 3 0.000
#> TCGA.EM.A1CW.01 2 0.000
#> TCGA.FK.A3SE.01 1 0.000
#> TCGA.EL.A3T7.01 1 0.000
#> TCGA.EM.A2P2.01 6 0.000
#> TCGA.EM.A1CU.11 6 0.000
#> TCGA.EL.A3T0.11 2 0.000
#> TCGA.E8.A3X7.01 1 1.000
#> TCGA.ET.A3BQ.01 1 0.000
#> TCGA.EM.A1CS.01 4 0.000
#> TCGA.EL.A3GQ.01 4 0.000
#> TCGA.EL.A3H5.01 1 0.000
#> TCGA.DJ.A3V4.01 5 0.498
#> TCGA.EM.A2P3.01 1 0.000
#> TCGA.FY.A3WA.01 2 0.000
#> TCGA.DJ.A3V2.01 5 0.747
#> TCGA.FY.A3TY.11 2 0.000
#> TCGA.BJ.A290.01 3 0.000
#> TCGA.EM.A3SU.01 5 0.747
#> TCGA.EL.A3D0.01 3 0.000
#> TCGA.EM.A1CT.11 6 0.000
#> TCGA.EL.A3GR.01 4 0.747
#> TCGA.J8.A3YH.06 3 0.000
#> TCGA.EM.A3ST.11 2 0.000
#> TCGA.ET.A3DV.01 2 0.000
#> TCGA.BJ.A3EZ.01 3 0.000
#> TCGA.J8.A3YD.01 2 1.000
#> TCGA.EM.A3SU.06 5 1.000
#> TCGA.EM.A3AL.01 2 0.000
#> TCGA.DJ.A3US.01 7 0.747
#> TCGA.EM.A1CS.11 2 0.000
#> TCGA.EM.A1CW.11 2 0.000
#> TCGA.BJ.A190.01 6 0.000
#> TCGA.EM.A2OZ.01 3 0.000
#> TCGA.EM.A1CV.11 2 0.000
#> TCGA.EM.A1CU.01 3 0.000
#> TCGA.EM.A3AN.01 1 0.000
#> TCGA.E8.A2EA.01 5 0.000
#> TCGA.EM.A1CV.01 4 0.000
#> TCGA.EM.A1CT.01 3 0.000
#> TCGA.EM.A3ST.01 2 0.000
#> TCGA.ET.A3BS.01 3 0.000
#> TCGA.EL.A3GO.01 2 0.000
#> TCGA.DJ.A2Q0.01 2 0.000
#> TCGA.EL.A3D6.01 1 0.747
#> TCGA.DJ.A3UN.01 1 0.249
#> TCGA.DJ.A3UU.01 5 1.000
#> TCGA.FK.A3SD.01 2 0.000
#> TCGA.DJ.A2PO.01 3 0.000
#> TCGA.DJ.A3UQ.01 5 0.747
#> TCGA.EM.A1YE.11 2 0.000
#> TCGA.EL.A3T2.11 2 0.000
#> TCGA.EL.A3CL.01 1 0.000
#> TCGA.EM.A1YC.01 2 0.000
#> TCGA.DJ.A3UP.01 2 0.000
#> TCGA.EL.A3T0.01 7 1.000
#> TCGA.IM.A3U2.01 1 0.000
#> TCGA.IM.A3U3.01 1 0.000
#> TCGA.DJ.A3UX.01 7 0.000
#> TCGA.ET.A3BW.01 1 0.498
#> TCGA.ET.A39S.01 5 0.000
#> TCGA.ET.A3BP.01 4 1.000
#> TCGA.DJ.A1QE.01 1 1.000
#> TCGA.EL.A3D4.01 3 0.000
#> TCGA.FK.A3SB.01 1 0.249
#> TCGA.EL.A3CW.01 2 1.000
#> TCGA.ET.A39L.01 7 1.000
#> TCGA.DJ.A2PW.01 3 0.000
#> TCGA.EM.A2CO.01 2 0.000
#> TCGA.FE.A232.01 4 0.000
#> TCGA.DJ.A3UR.01 4 1.000
#> TCGA.DJ.A2PP.01 6 0.000
#> TCGA.ET.A3DQ.01 7 0.000
#> TCGA.ET.A3DS.01 2 0.000
#> TCGA.FY.A3W9.01 2 0.000
#> TCGA.FK.A3S3.01 1 1.000
#> TCGA.ET.A2MZ.01 3 0.000
#> TCGA.BJ.A2NA.11 6 0.000
#> TCGA.DJ.A1QL.01 6 0.000
#> TCGA.EL.A3CS.01 5 0.747
#> TCGA.FE.A233.01 4 0.502
#> TCGA.EM.A1YD.11 2 0.000
#> TCGA.ET.A3DW.11 6 0.000
#> TCGA.EL.A3T9.01 5 0.498
#> TCGA.DJ.A3UM.01 1 0.249
#> TCGA.DO.A2HM.01 3 1.000
#> TCGA.FY.A3BL.01 3 0.000
#> TCGA.EL.A3TA.11 6 0.000
#> TCGA.ET.A3BX.01 3 0.000
#> TCGA.DJ.A1QQ.01 3 0.000
#> TCGA.DJ.A1QF.01 4 0.000
#> TCGA.DJ.A1QO.01 3 0.000
#> TCGA.BJ.A2NA.01 3 0.000
#> TCGA.EM.A1YE.01 2 0.000
#> TCGA.FY.A2QD.01 2 0.000
#> TCGA.ET.A39J.01 4 0.000
#> TCGA.ET.A3DU.01 5 0.000
#> TCGA.EL.A3CM.01 5 0.747
#> TCGA.DJ.A3UO.01 3 0.000
#> TCGA.ET.A39P.01 1 0.000
#> TCGA.DJ.A2Q2.01 2 0.000
#> TCGA.BJ.A28V.01 2 0.000
#> TCGA.ET.A3BO.01 1 0.249
#> TCGA.EL.A3T1.01 1 0.747
#> TCGA.DJ.A1QI.01 4 0.253
#> TCGA.EL.A3TB.01 1 0.498
#> TCGA.BJ.A28X.11 7 1.000
#> TCGA.DJ.A1QN.01 4 0.000
#> TCGA.FE.A230.01 4 0.000
#> TCGA.FE.A234.01 4 1.000
#> TCGA.ET.A39R.01 5 0.747
#> TCGA.DJ.A1QG.01 6 0.000
#> TCGA.EL.A3CV.01 3 0.000
#> TCGA.FE.A231.01 3 0.000
#> TCGA.EL.A3TA.01 3 0.000
#> TCGA.DJ.A3UY.01 5 0.747
#> TCGA.DJ.A2Q1.01 5 0.000
#> TCGA.EL.A3CU.01 5 0.249
#> TCGA.EL.A3TB.11 2 0.000
#> TCGA.ET.A39I.01 2 0.000
#> TCGA.EM.A1YB.01 2 0.000
#> TCGA.DJ.A3UV.01 7 0.000
#> TCGA.DJ.A3UT.01 2 0.000
#> TCGA.ET.A3DW.01 3 0.000
#> TCGA.ET.A3BT.01 1 0.000
#> TCGA.EL.A3T3.01 1 0.000
#> TCGA.DJ.A1QM.01 6 0.000
#> TCGA.EL.A3CY.01 6 1.000
#> TCGA.ET.A39O.01 3 0.000
#> TCGA.EM.A1YC.11 2 0.000
#> TCGA.DJ.A1QH.01 4 1.000
#> TCGA.EL.A3T3.11 2 0.000
#> TCGA.EL.A3CX.01 7 0.000
#> TCGA.EL.A3T2.01 2 0.000
#> TCGA.EM.A22P.01 3 0.000
#> TCGA.EL.A3T8.11 6 0.000
#> TCGA.DJ.A2PU.01 4 0.000
#> TCGA.DJ.A3UK.01 1 0.000
#> TCGA.ET.A3DO.01 5 0.000
#> TCGA.EM.A1YA.01 2 0.000
#> TCGA.ET.A3BV.01 5 0.000
#> TCGA.EL.A3CO.01 6 0.000
#> TCGA.DJ.A2PN.01 1 0.000
#> TCGA.FK.A3SG.01 1 0.498
#> TCGA.FK.A3SH.01 1 0.000
#> TCGA.EM.A1YD.01 2 0.000
#> TCGA.DJ.A1QD.01 4 0.000
#> TCGA.EL.A3CZ.01 2 0.000
#> TCGA.BJ.A0Z9.01 5 0.498
#> TCGA.CE.A13K.01 1 1.000
#> TCGA.EM.A3FR.01 2 0.000
#> TCGA.EM.A3O8.01 2 0.000
#> TCGA.FY.A3R6.01 7 1.000
#> TCGA.FY.A3R9.01 2 0.000
#> TCGA.EL.A3D1.01 3 0.000
#> TCGA.EM.A3O6.01 2 0.000
#> TCGA.BJ.A0Z5.01 3 0.000
#> TCGA.BJ.A28S.01 6 0.000
#> TCGA.BJ.A0ZH.01 1 0.000
#> TCGA.ET.A3DT.01 5 0.000
#> TCGA.H2.A3RI.11 2 0.000
#> TCGA.DJ.A13W.01 2 0.000
#> TCGA.DJ.A13T.01 1 0.000
#> TCGA.BJ.A0ZA.01 2 0.000
#> TCGA.BJ.A3PT.01 2 0.000
#> TCGA.FE.A3PD.01 1 0.747
#> TCGA.BJ.A0ZF.01 2 0.000
#> TCGA.ET.A39M.01 3 0.000
#> TCGA.BJ.A0ZJ.01 3 0.000
#> TCGA.BJ.A0YZ.01 6 0.000
#> TCGA.FE.A3PC.01 1 0.000
#> TCGA.DJ.A2QB.01 2 0.000
#> TCGA.EM.A3OB.01 2 0.000
#> TCGA.H2.A3RH.01 7 1.000
#> TCGA.ET.A39T.01 4 0.747
#> TCGA.DJ.A2PV.01 1 0.747
#> TCGA.BJ.A3PR.11 2 0.000
#> TCGA.EL.A3T6.11 2 1.000
#> TCGA.DJ.A13X.01 1 1.000
#> TCGA.BJ.A0ZG.01 6 0.000
#> TCGA.EL.A3T6.01 1 1.000
#> TCGA.BJ.A0Z0.01 6 0.000
#> TCGA.ET.A39K.01 1 0.000
#> TCGA.EM.A3O9.01 6 0.000
#> TCGA.BJ.A3PU.01 3 0.000
#> TCGA.BJ.A3PR.01 7 0.000
#> TCGA.EM.A3O3.01 4 0.000
#> TCGA.BJ.A0ZB.01 3 0.000
#> TCGA.EM.A3OA.01 2 0.000
#> TCGA.DJ.A2PR.01 3 0.000
#> TCGA.DJ.A13L.01 3 0.000
#> TCGA.FY.A3ON.01 3 0.000
#> TCGA.DJ.A13V.01 1 0.000
#> TCGA.FY.A3R8.01 1 0.000
#> TCGA.EL.A3CP.01 1 0.000
#> TCGA.DJ.A13U.01 3 0.000
#> TCGA.DE.A0Y3.01 1 0.000
#> TCGA.ET.A2N4.01 4 0.747
#> TCGA.DJ.A13P.01 1 1.000
#> TCGA.BJ.A0ZE.01 2 0.000
#> TCGA.EM.A3O7.01 4 0.249
#> TCGA.DJ.A13O.01 6 1.000
#> TCGA.FY.A3RA.01 1 0.000
#> TCGA.DJ.A13M.01 2 0.000
#> TCGA.DJ.A13R.01 6 0.000
#> TCGA.ET.A3DR.01 5 1.000
#> TCGA.FE.A3PB.01 5 0.498
#> TCGA.ET.A3BN.01 1 0.249
#> TCGA.H2.A3RI.01 1 0.000
#> TCGA.ET.A39N.01 2 0.000
#> TCGA.BJ.A3PU.11 6 0.000
#> TCGA.FY.A3R7.01 7 0.000
#> TCGA.FE.A3PA.01 3 0.000
#> TCGA.EM.A2CN.01 6 0.000
#> TCGA.BJ.A0Z2.01 6 0.000
#> TCGA.FY.A3I5.01 2 0.000
#> TCGA.DJ.A13S.01 2 0.000
#> TCGA.DE.A0Y2.01 1 0.000
#> TCGA.ET.A3BU.01 3 0.000
get_classes(res, k = 8)
#> class p
#> TCGA.E8.A416.01 2 0.000
#> TCGA.E8.A433.01 5 1.000
#> TCGA.EL.A4K9.01 3 0.000
#> TCGA.DJ.A3V9.01 5 1.000
#> TCGA.EL.A3ZO.11 2 0.000
#> TCGA.EL.A3ZN.01 7 1.000
#> TCGA.KS.A41F.01 1 0.000
#> TCGA.EL.A3ZK.01 5 0.000
#> TCGA.ET.A40R.01 5 1.000
#> TCGA.EL.A3ZM.01 3 0.000
#> TCGA.ET.A2N3.01 2 0.000
#> TCGA.EL.A3ZQ.01 1 1.000
#> TCGA.ET.A40T.01 1 1.000
#> TCGA.DE.A4MA.01 1 0.000
#> TCGA.EM.A4FU.01 6 0.000
#> TCGA.E8.A418.01 1 0.000
#> TCGA.DJ.A3VD.01 7 1.000
#> TCGA.DJ.A3VM.01 2 0.000
#> TCGA.EL.A3ZG.01 8 0.000
#> TCGA.EM.A4FV.01 5 0.747
#> TCGA.E8.A413.01 7 1.000
#> TCGA.DJ.A3VG.01 6 0.000
#> TCGA.EL.A4K2.01 2 0.000
#> TCGA.IM.A420.01 5 1.000
#> TCGA.KS.A41J.01 1 0.000
#> TCGA.EL.A3ZK.11 2 0.000
#> TCGA.J8.A3O2.01 8 0.000
#> TCGA.E8.A415.01 7 1.000
#> TCGA.FY.A40M.01 2 1.000
#> TCGA.DJ.A3VB.01 3 0.000
#> TCGA.KS.A41I.01 2 0.000
#> TCGA.DJ.A3VL.01 6 0.000
#> TCGA.ET.A4KQ.01 2 0.000
#> TCGA.H2.A421.01 5 1.000
#> TCGA.EL.A3ZO.01 1 1.000
#> TCGA.KS.A4I3.01 8 1.000
#> TCGA.DJ.A4UT.01 5 0.000
#> TCGA.DE.A4MD.01 3 0.000
#> TCGA.EL.A4JW.01 5 0.000
#> TCGA.DJ.A3VI.01 1 0.000
#> TCGA.DJ.A3VA.01 1 0.000
#> TCGA.L6.A4ET.01 4 0.502
#> TCGA.E8.A419.01 5 0.000
#> TCGA.DJ.A4V0.01 7 0.000
#> TCGA.DJ.A4V2.01 1 0.000
#> TCGA.ET.A40Q.01 3 0.000
#> TCGA.EL.A3ZS.01 5 0.751
#> TCGA.KS.A4ID.01 5 0.000
#> TCGA.EL.A3ZL.11 2 0.000
#> TCGA.J8.A3YE.01 4 1.000
#> TCGA.EL.A4K7.01 3 0.000
#> TCGA.DJ.A3VF.01 5 0.498
#> TCGA.EM.A4FH.01 6 0.000
#> TCGA.E8.A432.01 5 0.000
#> TCGA.J8.A3O2.06 3 0.000
#> TCGA.ET.A2MX.01 8 0.000
#> TCGA.ET.A40S.01 8 0.000
#> TCGA.DE.A4M8.01 5 0.000
#> TCGA.IM.A41Z.01 2 0.000
#> TCGA.EL.A4KD.01 8 0.000
#> TCGA.DJ.A3V7.01 1 0.000
#> TCGA.FY.A40L.01 1 0.498
#> TCGA.DE.A4M9.01 6 0.000
#> TCGA.J8.A42S.01 3 0.000
#> TCGA.KS.A41L.01 2 0.000
#> TCGA.EM.A4FN.01 1 1.000
#> TCGA.EL.A4K1.01 1 0.000
#> TCGA.KS.A4IC.01 4 0.502
#> TCGA.E8.A414.01 7 1.000
#> TCGA.H2.A422.01 1 0.000
#> TCGA.J8.A3YF.01 3 1.000
#> TCGA.EL.A4KI.01 6 0.000
#> TCGA.EM.A4G1.01 2 0.000
#> TCGA.DJ.A3VJ.01 3 1.000
#> TCGA.DE.A4MD.06 8 0.000
#> TCGA.EL.A3ZP.01 3 0.000
#> TCGA.EM.A4FQ.01 1 0.000
#> TCGA.EL.A3ZT.01 3 0.000
#> TCGA.DJ.A4V4.01 5 1.000
#> TCGA.FY.A40K.01 1 1.000
#> TCGA.L6.A4EQ.01 3 0.000
#> TCGA.DJ.A3VE.01 3 0.000
#> TCGA.E8.A434.01 7 0.000
#> TCGA.EL.A3ZH.01 2 0.000
#> TCGA.EM.A4FR.01 8 0.000
#> TCGA.EL.A3ZH.11 2 0.000
#> TCGA.EL.A3ZR.01 2 0.000
#> TCGA.DJ.A3V8.01 1 1.000
#> TCGA.EL.A3ZG.11 6 0.000
#> TCGA.ET.A40P.01 2 0.000
#> TCGA.DE.A4MB.01 1 0.000
#> TCGA.MK.A4N6.01 3 0.000
#> TCGA.DJ.A3VK.01 6 0.000
#> TCGA.E8.A417.01 1 0.000
#> TCGA.L6.A4EU.01 1 1.000
#> TCGA.J8.A4HY.01 5 0.253
#> TCGA.EL.A3ZL.01 1 0.000
#> TCGA.EL.A3ZP.11 6 0.000
#> TCGA.FY.A40N.01 7 0.498
#> TCGA.J8.A4HW.01 1 0.000
#> TCGA.BJ.A45J.01 1 0.000
#> TCGA.CE.A482.01 1 1.000
#> TCGA.DJ.A2Q6.01 1 0.000
#> TCGA.DJ.A2PX.01 5 0.000
#> TCGA.DJ.A4UL.01 1 0.000
#> TCGA.EL.A4JX.01 5 0.000
#> TCGA.BJ.A2N8.11 2 0.000
#> TCGA.DJ.A2Q5.01 8 0.000
#> TCGA.EL.A4KG.01 1 0.502
#> TCGA.DJ.A4UP.01 7 0.000
#> TCGA.E8.A438.01 5 0.498
#> TCGA.EL.A3H2.01 6 0.000
#> TCGA.EM.A3AP.01 7 0.751
#> TCGA.DJ.A2PQ.01 3 0.000
#> TCGA.L6.A4EP.01 1 0.000
#> TCGA.FY.A4B4.01 1 0.000
#> TCGA.EL.A4KH.01 4 0.000
#> TCGA.BJ.A45E.01 7 0.000
#> TCGA.DJ.A4V5.01 8 0.502
#> TCGA.DE.A4MC.01 1 0.000
#> TCGA.E8.A44M.01 7 1.000
#> TCGA.BJ.A45K.01 6 0.000
#> TCGA.E3.A3DZ.01 2 0.000
#> TCGA.E3.A3E2.01 1 1.000
#> TCGA.BJ.A45H.01 8 0.000
#> TCGA.E8.A44K.01 5 1.000
#> TCGA.ET.A2MY.01 1 0.000
#> TCGA.EL.A3H8.01 1 0.000
#> TCGA.BJ.A45C.01 6 0.000
#> TCGA.BJ.A45G.01 2 1.000
#> TCGA.EL.A4JZ.01 1 0.249
#> TCGA.CE.A481.01 5 1.000
#> TCGA.KS.A4I9.01 1 0.000
#> TCGA.EL.A3MW.01 1 0.000
#> TCGA.E8.A436.01 7 1.000
#> TCGA.E3.A3DY.01 3 0.000
#> TCGA.DJ.A2Q3.01 5 1.000
#> TCGA.BJ.A2P4.01 2 0.000
#> TCGA.CE.A484.01 7 1.000
#> TCGA.ET.A2N1.01 7 0.498
#> TCGA.DJ.A2Q4.01 3 0.000
#> TCGA.DJ.A2PZ.01 3 0.000
#> TCGA.BJ.A45F.01 2 0.000
#> TCGA.IM.A4EB.01 8 0.000
#> TCGA.EM.A4FO.01 8 0.000
#> TCGA.FY.A4B3.01 3 0.000
#> TCGA.FY.A4B0.01 6 0.000
#> TCGA.BJ.A45I.01 5 1.000
#> TCGA.E3.A3E3.01 4 1.000
#> TCGA.EM.A3AQ.01 8 1.000
#> TCGA.EL.A3N3.01 5 1.000
#> TCGA.DJ.A2Q9.01 7 0.000
#> TCGA.EM.A4FM.01 1 0.000
#> TCGA.EL.A4K6.01 6 0.000
#> TCGA.MK.A4N9.01 1 0.000
#> TCGA.KS.A4I1.01 1 0.000
#> TCGA.DJ.A2PS.01 7 1.000
#> TCGA.CE.A3MD.01 8 0.000
#> TCGA.E3.A3E5.01 3 0.000
#> TCGA.EL.A3CN.01 1 0.747
#> TCGA.J8.A4HW.06 5 0.000
#> TCGA.EM.A4FK.01 2 0.000
#> TCGA.E8.A437.01 5 0.000
#> TCGA.BJ.A4O8.01 3 0.000
#> TCGA.EL.A3MW.11 2 0.000
#> TCGA.E3.A3E0.01 1 1.000
#> TCGA.BJ.A45D.01 6 0.000
#> TCGA.CE.A483.01 1 0.000
#> TCGA.CE.A485.01 8 0.000
#> TCGA.DJ.A4UR.01 7 1.000
#> TCGA.IM.A41Y.01 1 0.000
#> TCGA.ET.A4KN.01 5 0.000
#> TCGA.KS.A4I5.01 1 0.000
#> TCGA.DJ.A4UQ.01 3 0.253
#> TCGA.KS.A4IB.01 1 0.000
#> TCGA.EL.A3N2.11 2 0.000
#> TCGA.BJ.A2N9.01 2 0.000
#> TCGA.DJ.A4UW.01 5 1.000
#> TCGA.EL.A3GZ.11 2 0.000
#> TCGA.EM.A3AR.01 6 0.000
#> TCGA.EL.A3N3.11 2 0.000
#> TCGA.DE.A3KN.01 5 0.000
#> TCGA.DJ.A2QA.01 5 0.000
#> TCGA.EL.A4JV.01 2 0.000
#> TCGA.EM.A4FF.01 1 0.000
#> TCGA.EL.A4K0.01 1 0.000
#> TCGA.FK.A4UB.01 3 0.000
#> TCGA.BJ.A4O9.01 4 0.000
#> TCGA.BJ.A2N7.01 2 0.000
#> TCGA.DE.A2OL.01 2 0.000
#> TCGA.CE.A3ME.01 4 1.000
#> TCGA.MK.A4N7.01 1 0.000
#> TCGA.EL.A3H2.11 6 0.000
#> TCGA.EL.A4K4.01 1 0.000
#> TCGA.EL.A3GS.01 1 0.000
#> TCGA.EL.A3GZ.01 1 0.000
#> TCGA.E3.A3E1.01 5 1.000
#> TCGA.DJ.A2Q8.01 5 0.000
#> TCGA.EL.A3N2.01 1 0.000
#> TCGA.KS.A4I7.01 1 0.000
#> TCGA.MK.A84Z.01 6 0.000
#> TCGA.ET.A3DP.11 2 0.000
#> TCGA.EL.A3MX.11 2 0.000
#> TCGA.ET.A25G.01 1 0.000
#> TCGA.EM.A3FK.01 4 1.000
#> TCGA.EM.A2CS.01 1 0.000
#> TCGA.FE.A23A.01 5 1.000
#> TCGA.BJ.A28T.11 2 0.000
#> TCGA.EM.A22J.01 2 0.000
#> TCGA.EL.A3MX.01 1 0.000
#> TCGA.FY.A3I4.01 7 0.751
#> TCGA.BJ.A28W.11 2 0.000
#> TCGA.ET.A25R.01 1 0.000
#> TCGA.BJ.A2N8.01 2 0.000
#> TCGA.FY.A76V.01 6 0.000
#> TCGA.EM.A3FN.01 2 0.000
#> TCGA.QD.A8IV.01 2 0.000
#> TCGA.EM.A3FJ.01 1 0.502
#> TCGA.ET.A2MY.11 2 0.000
#> TCGA.EM.A3FQ.06 1 0.000
#> TCGA.ET.A25P.01 7 0.751
#> TCGA.ET.A2N0.01 4 1.000
#> TCGA.EM.A2CT.01 2 0.000
#> TCGA.FE.A235.01 1 0.000
#> TCGA.ET.A25M.01 3 0.000
#> TCGA.EL.A3MY.01 3 0.000
#> TCGA.DE.A7U5.01 5 1.000
#> TCGA.E8.A2JQ.11 2 0.000
#> TCGA.ET.A3DP.01 4 0.000
#> TCGA.EM.A2CL.01 6 0.000
#> TCGA.ET.A2N5.01 2 0.000
#> TCGA.ET.A25J.11 2 0.000
#> TCGA.DE.A69J.01 1 0.000
#> TCGA.BJ.A28R.11 2 0.000
#> TCGA.ET.A25K.01 1 0.000
#> TCGA.EL.A3GV.01 4 0.000
#> TCGA.GE.A2C6.01 5 0.000
#> TCGA.EM.A3FM.01 3 0.000
#> TCGA.EL.A3H7.11 2 0.000
#> TCGA.FE.A22Z.01 1 0.000
#> TCGA.H2.A2K9.01 6 0.000
#> TCGA.EM.A22Q.01 6 0.000
#> TCGA.EM.A3FP.01 2 0.000
#> TCGA.GE.A2C6.11 2 0.000
#> TCGA.EL.A3MZ.01 3 0.000
#> TCGA.DJ.A2PT.01 5 0.000
#> TCGA.E8.A242.01 5 0.000
#> TCGA.ET.A25L.01 1 0.000
#> TCGA.CE.A27D.01 2 1.000
#> TCGA.EL.A3H1.11 2 0.000
#> TCGA.BJ.A2N7.11 2 0.000
#> TCGA.DJ.A2Q7.01 1 0.498
#> TCGA.J8.A3O1.01 7 0.000
#> TCGA.EM.A2CR.01 7 0.000
#> TCGA.DE.A69K.01 1 0.000
#> TCGA.EM.A2CQ.01 2 0.000
#> TCGA.FE.A238.01 5 1.000
#> TCGA.EL.A3H1.01 2 0.000
#> TCGA.BJ.A28W.01 2 1.000
#> TCGA.BJ.A28T.01 2 1.000
#> TCGA.EM.A2CJ.01 2 0.000
#> TCGA.EM.A3FQ.01 5 0.000
#> TCGA.4C.A93U.01 1 0.000
#> TCGA.EM.A22M.01 8 0.000
#> TCGA.J8.A3NZ.01 1 0.502
#> TCGA.EM.A22K.01 2 0.000
#> TCGA.FE.A236.01 8 0.000
#> TCGA.BJ.A28R.01 1 0.000
#> TCGA.EM.A2CU.01 5 0.000
#> TCGA.ET.A25N.01 1 0.000
#> TCGA.EL.A3H7.01 1 0.000
#> TCGA.FY.A3NM.01 2 0.000
#> TCGA.EM.A3FO.01 3 0.000
#> TCGA.EM.A22L.01 2 0.000
#> TCGA.BJ.A2N9.11 2 0.000
#> TCGA.BJ.A291.01 2 0.000
#> TCGA.ET.A2N5.11 2 0.000
#> TCGA.ET.A25N.11 2 0.000
#> TCGA.J8.A3O0.01 6 0.000
#> TCGA.FE.A237.01 5 1.000
#> TCGA.DJ.A2QC.01 5 1.000
#> TCGA.ET.A25O.01 1 0.498
#> TCGA.EL.A3GU.01 1 0.000
#> TCGA.EL.A3MY.11 6 0.000
#> TCGA.DJ.A2PY.01 1 0.000
#> TCGA.EM.A2CS.06 5 0.000
#> TCGA.FY.A3NP.01 6 0.000
#> TCGA.ET.A25I.01 2 0.000
#> TCGA.H2.A26U.01 5 0.000
#> TCGA.BJ.A290.11 6 0.000
#> TCGA.EM.A22I.01 1 0.000
#> TCGA.FE.A239.01 6 0.000
#> TCGA.BJ.A28Z.01 5 0.000
#> TCGA.DE.A0XZ.01 1 0.000
#> TCGA.ET.A25J.01 1 0.747
#> TCGA.EM.A22N.01 2 0.000
#> TCGA.EM.A2CM.01 2 0.000
#> TCGA.FY.A3NN.01 4 0.000
#> TCGA.EM.A3FL.01 2 0.000
#> TCGA.H2.A2K9.11 6 0.000
#> TCGA.EL.A3H3.01 1 1.000
#> TCGA.EL.A3H4.01 1 0.000
#> TCGA.EM.A2OX.01 3 0.000
#> TCGA.EM.A3SX.01 1 0.000
#> TCGA.BJ.A0Z3.01 5 0.000
#> TCGA.BJ.A28X.01 5 0.000
#> TCGA.EL.A3CT.01 5 0.000
#> TCGA.EL.A3CR.01 1 0.000
#> TCGA.FY.A3TY.01 7 0.751
#> TCGA.J8.A3YG.01 5 0.000
#> TCGA.DJ.A3V6.01 3 0.000
#> TCGA.EM.A3SZ.01 1 1.000
#> TCGA.EM.A2OW.01 2 0.000
#> TCGA.DO.A1JZ.11 2 0.000
#> TCGA.EL.A3D5.01 2 0.000
#> TCGA.EM.A2P0.01 3 0.000
#> TCGA.E8.A2JQ.01 5 0.000
#> TCGA.BJ.A18Z.01 3 0.000
#> TCGA.DJ.A3V0.01 3 0.000
#> TCGA.EL.A3GW.01 2 0.498
#> TCGA.DJ.A3UW.01 5 0.000
#> TCGA.DJ.A3V3.01 5 1.000
#> TCGA.EL.A3T1.11 2 0.751
#> TCGA.BJ.A0ZC.01 6 0.000
#> TCGA.EM.A2OV.01 2 0.000
#> TCGA.EL.A3GY.01 1 0.000
#> TCGA.EM.A3SY.01 6 0.000
#> TCGA.EM.A3AI.01 2 0.000
#> TCGA.EM.A2OY.01 2 0.000
#> TCGA.EL.A3T8.01 3 0.000
#> TCGA.BJ.A18Y.01 6 0.000
#> TCGA.EL.A3GP.01 8 0.000
#> TCGA.EM.A2CK.01 6 0.000
#> TCGA.EL.A3T7.11 2 0.000
#> TCGA.BJ.A192.01 2 0.000
#> TCGA.BJ.A191.01 7 0.000
#> TCGA.EM.A2CP.01 2 1.000
#> TCGA.EM.A22O.01 3 1.000
#> TCGA.EM.A2P1.01 8 0.000
#> TCGA.J8.A3YH.01 3 0.000
#> TCGA.DJ.A3UZ.01 7 0.000
#> TCGA.IM.A3EB.01 1 0.000
#> TCGA.BJ.A3F0.01 2 0.000
#> TCGA.EL.A3GX.01 1 0.000
#> TCGA.EM.A3AK.01 1 0.747
#> TCGA.DO.A1JZ.01 1 0.000
#> TCGA.FY.A3YR.01 1 0.000
#> TCGA.DO.A1K0.01 1 0.249
#> TCGA.DJ.A3V5.01 1 0.747
#> TCGA.EM.A3AJ.01 6 0.000
#> TCGA.IM.A3ED.01 1 0.000
#> TCGA.EM.A3AO.01 8 1.000
#> TCGA.EM.A2P1.06 8 0.000
#> TCGA.EM.A1CW.01 2 0.000
#> TCGA.FK.A3SE.01 1 0.000
#> TCGA.EL.A3T7.01 1 0.000
#> TCGA.EM.A2P2.01 6 0.000
#> TCGA.EM.A1CU.11 6 0.000
#> TCGA.EL.A3T0.11 2 0.000
#> TCGA.E8.A3X7.01 1 1.000
#> TCGA.ET.A3BQ.01 1 0.000
#> TCGA.EM.A1CS.01 4 0.000
#> TCGA.EL.A3GQ.01 4 0.000
#> TCGA.EL.A3H5.01 1 0.000
#> TCGA.DJ.A3V4.01 5 0.249
#> TCGA.EM.A2P3.01 1 0.000
#> TCGA.FY.A3WA.01 2 0.000
#> TCGA.DJ.A3V2.01 5 1.000
#> TCGA.FY.A3TY.11 2 0.000
#> TCGA.BJ.A290.01 3 0.253
#> TCGA.EM.A3SU.01 5 1.000
#> TCGA.EL.A3D0.01 3 0.000
#> TCGA.EM.A1CT.11 6 0.000
#> TCGA.EL.A3GR.01 1 1.000
#> TCGA.J8.A3YH.06 3 0.751
#> TCGA.EM.A3ST.11 2 0.000
#> TCGA.ET.A3DV.01 2 0.000
#> TCGA.BJ.A3EZ.01 3 0.000
#> TCGA.J8.A3YD.01 2 1.000
#> TCGA.EM.A3SU.06 5 1.000
#> TCGA.EM.A3AL.01 2 0.000
#> TCGA.DJ.A3US.01 7 0.000
#> TCGA.EM.A1CS.11 2 0.000
#> TCGA.EM.A1CW.11 2 0.000
#> TCGA.BJ.A190.01 6 0.000
#> TCGA.EM.A2OZ.01 8 0.000
#> TCGA.EM.A1CV.11 2 0.000
#> TCGA.EM.A1CU.01 3 0.000
#> TCGA.EM.A3AN.01 1 0.000
#> TCGA.E8.A2EA.01 5 0.000
#> TCGA.EM.A1CV.01 4 0.000
#> TCGA.EM.A1CT.01 3 0.000
#> TCGA.EM.A3ST.01 2 0.000
#> TCGA.ET.A3BS.01 3 0.000
#> TCGA.EL.A3GO.01 2 0.000
#> TCGA.DJ.A2Q0.01 2 0.000
#> TCGA.EL.A3D6.01 1 1.000
#> TCGA.DJ.A3UN.01 1 0.000
#> TCGA.DJ.A3UU.01 5 1.000
#> TCGA.FK.A3SD.01 2 0.000
#> TCGA.DJ.A2PO.01 8 0.000
#> TCGA.DJ.A3UQ.01 5 1.000
#> TCGA.EM.A1YE.11 2 0.000
#> TCGA.EL.A3T2.11 2 0.000
#> TCGA.EL.A3CL.01 1 0.000
#> TCGA.EM.A1YC.01 2 0.000
#> TCGA.DJ.A3UP.01 2 1.000
#> TCGA.EL.A3T0.01 7 0.498
#> TCGA.IM.A3U2.01 1 0.000
#> TCGA.IM.A3U3.01 1 0.000
#> TCGA.DJ.A3UX.01 7 0.000
#> TCGA.ET.A3BW.01 1 1.000
#> TCGA.ET.A39S.01 5 0.000
#> TCGA.ET.A3BP.01 1 1.000
#> TCGA.DJ.A1QE.01 1 0.000
#> TCGA.EL.A3D4.01 8 0.000
#> TCGA.FK.A3SB.01 1 0.000
#> TCGA.EL.A3CW.01 2 1.000
#> TCGA.ET.A39L.01 7 1.000
#> TCGA.DJ.A2PW.01 3 0.000
#> TCGA.EM.A2CO.01 2 0.000
#> TCGA.FE.A232.01 4 0.000
#> TCGA.DJ.A3UR.01 1 1.000
#> TCGA.DJ.A2PP.01 6 0.000
#> TCGA.ET.A3DQ.01 7 0.000
#> TCGA.ET.A3DS.01 2 0.000
#> TCGA.FY.A3W9.01 2 0.000
#> TCGA.FK.A3S3.01 5 1.000
#> TCGA.ET.A2MZ.01 3 0.000
#> TCGA.BJ.A2NA.11 6 0.000
#> TCGA.DJ.A1QL.01 6 0.000
#> TCGA.EL.A3CS.01 5 1.000
#> TCGA.FE.A233.01 4 0.498
#> TCGA.EM.A1YD.11 2 0.000
#> TCGA.ET.A3DW.11 6 0.000
#> TCGA.EL.A3T9.01 5 0.498
#> TCGA.DJ.A3UM.01 1 0.000
#> TCGA.DO.A2HM.01 8 0.000
#> TCGA.FY.A3BL.01 3 0.000
#> TCGA.EL.A3TA.11 6 0.000
#> TCGA.ET.A3BX.01 3 0.000
#> TCGA.DJ.A1QQ.01 3 0.000
#> TCGA.DJ.A1QF.01 4 0.000
#> TCGA.DJ.A1QO.01 3 0.000
#> TCGA.BJ.A2NA.01 3 0.000
#> TCGA.EM.A1YE.01 2 0.000
#> TCGA.FY.A2QD.01 2 0.000
#> TCGA.ET.A39J.01 4 0.000
#> TCGA.ET.A3DU.01 5 0.000
#> TCGA.EL.A3CM.01 1 1.000
#> TCGA.DJ.A3UO.01 3 0.000
#> TCGA.ET.A39P.01 1 0.000
#> TCGA.DJ.A2Q2.01 2 0.000
#> TCGA.BJ.A28V.01 2 0.000
#> TCGA.ET.A3BO.01 1 0.000
#> TCGA.EL.A3T1.01 1 1.000
#> TCGA.DJ.A1QI.01 4 1.000
#> TCGA.EL.A3TB.01 1 0.000
#> TCGA.BJ.A28X.11 7 1.000
#> TCGA.DJ.A1QN.01 4 0.000
#> TCGA.FE.A230.01 4 0.000
#> TCGA.FE.A234.01 1 0.751
#> TCGA.ET.A39R.01 5 1.000
#> TCGA.DJ.A1QG.01 6 0.000
#> TCGA.EL.A3CV.01 8 0.000
#> TCGA.FE.A231.01 3 0.000
#> TCGA.EL.A3TA.01 8 0.000
#> TCGA.DJ.A3UY.01 7 1.000
#> TCGA.DJ.A2Q1.01 5 0.000
#> TCGA.EL.A3CU.01 5 0.000
#> TCGA.EL.A3TB.11 2 0.000
#> TCGA.ET.A39I.01 2 0.000
#> TCGA.EM.A1YB.01 2 0.249
#> TCGA.DJ.A3UV.01 7 0.000
#> TCGA.DJ.A3UT.01 2 0.000
#> TCGA.ET.A3DW.01 3 0.000
#> TCGA.ET.A3BT.01 1 0.000
#> TCGA.EL.A3T3.01 1 0.000
#> TCGA.DJ.A1QM.01 6 0.000
#> TCGA.EL.A3CY.01 8 0.000
#> TCGA.ET.A39O.01 3 0.000
#> TCGA.EM.A1YC.11 2 0.000
#> TCGA.DJ.A1QH.01 1 0.000
#> TCGA.EL.A3T3.11 2 0.000
#> TCGA.EL.A3CX.01 7 0.249
#> TCGA.EL.A3T2.01 2 0.000
#> TCGA.EM.A22P.01 8 0.000
#> TCGA.EL.A3T8.11 6 0.000
#> TCGA.DJ.A2PU.01 4 0.000
#> TCGA.DJ.A3UK.01 1 0.249
#> TCGA.ET.A3DO.01 5 0.000
#> TCGA.EM.A1YA.01 2 0.000
#> TCGA.ET.A3BV.01 5 0.000
#> TCGA.EL.A3CO.01 6 0.000
#> TCGA.DJ.A2PN.01 1 0.000
#> TCGA.FK.A3SG.01 1 0.249
#> TCGA.FK.A3SH.01 1 0.000
#> TCGA.EM.A1YD.01 2 0.000
#> TCGA.DJ.A1QD.01 4 0.000
#> TCGA.EL.A3CZ.01 2 0.000
#> TCGA.BJ.A0Z9.01 5 0.000
#> TCGA.CE.A13K.01 1 1.000
#> TCGA.EM.A3FR.01 2 0.000
#> TCGA.EM.A3O8.01 2 0.000
#> TCGA.FY.A3R6.01 7 1.000
#> TCGA.FY.A3R9.01 2 0.000
#> TCGA.EL.A3D1.01 3 0.000
#> TCGA.EM.A3O6.01 2 0.000
#> TCGA.BJ.A0Z5.01 3 1.000
#> TCGA.BJ.A28S.01 6 0.000
#> TCGA.BJ.A0ZH.01 1 0.000
#> TCGA.ET.A3DT.01 5 0.000
#> TCGA.H2.A3RI.11 2 0.000
#> TCGA.DJ.A13W.01 2 0.000
#> TCGA.DJ.A13T.01 1 0.000
#> TCGA.BJ.A0ZA.01 2 0.000
#> TCGA.BJ.A3PT.01 2 0.000
#> TCGA.FE.A3PD.01 1 0.000
#> TCGA.BJ.A0ZF.01 2 0.000
#> TCGA.ET.A39M.01 8 0.000
#> TCGA.BJ.A0ZJ.01 8 0.000
#> TCGA.BJ.A0YZ.01 6 0.000
#> TCGA.FE.A3PC.01 1 0.000
#> TCGA.DJ.A2QB.01 2 0.000
#> TCGA.EM.A3OB.01 2 0.000
#> TCGA.H2.A3RH.01 7 0.000
#> TCGA.ET.A39T.01 5 1.000
#> TCGA.DJ.A2PV.01 1 1.000
#> TCGA.BJ.A3PR.11 2 0.000
#> TCGA.EL.A3T6.11 2 1.000
#> TCGA.DJ.A13X.01 1 1.000
#> TCGA.BJ.A0ZG.01 6 0.000
#> TCGA.EL.A3T6.01 5 1.000
#> TCGA.BJ.A0Z0.01 6 0.000
#> TCGA.ET.A39K.01 1 0.000
#> TCGA.EM.A3O9.01 6 0.000
#> TCGA.BJ.A3PU.01 3 0.000
#> TCGA.BJ.A3PR.01 7 0.000
#> TCGA.EM.A3O3.01 4 0.000
#> TCGA.BJ.A0ZB.01 3 0.000
#> TCGA.EM.A3OA.01 2 0.000
#> TCGA.DJ.A2PR.01 3 0.000
#> TCGA.DJ.A13L.01 8 0.000
#> TCGA.FY.A3ON.01 3 0.000
#> TCGA.DJ.A13V.01 1 0.000
#> TCGA.FY.A3R8.01 1 0.000
#> TCGA.EL.A3CP.01 1 0.000
#> TCGA.DJ.A13U.01 8 0.253
#> TCGA.DE.A0Y3.01 1 0.000
#> TCGA.ET.A2N4.01 1 1.000
#> TCGA.DJ.A13P.01 1 1.000
#> TCGA.BJ.A0ZE.01 2 0.000
#> TCGA.EM.A3O7.01 4 1.000
#> TCGA.DJ.A13O.01 8 0.000
#> TCGA.FY.A3RA.01 1 0.000
#> TCGA.DJ.A13M.01 2 0.000
#> TCGA.DJ.A13R.01 6 0.000
#> TCGA.ET.A3DR.01 5 1.000
#> TCGA.FE.A3PB.01 5 1.000
#> TCGA.ET.A3BN.01 1 0.000
#> TCGA.H2.A3RI.01 1 0.000
#> TCGA.ET.A39N.01 2 0.502
#> TCGA.BJ.A3PU.11 6 0.000
#> TCGA.FY.A3R7.01 7 0.000
#> TCGA.FE.A3PA.01 3 0.000
#> TCGA.EM.A2CN.01 6 0.000
#> TCGA.BJ.A0Z2.01 6 0.000
#> TCGA.FY.A3I5.01 2 0.000
#> TCGA.DJ.A13S.01 2 0.000
#> TCGA.DE.A0Y2.01 1 0.000
#> TCGA.ET.A3BU.01 3 0.000
Heatmaps for the consensus matrix. It visualizes the probability of two samples to be in a same group.
consensus_heatmap(res, k = 2)
consensus_heatmap(res, k = 3)
consensus_heatmap(res, k = 4)
consensus_heatmap(res, k = 5)
consensus_heatmap(res, k = 6)
consensus_heatmap(res, k = 7)
consensus_heatmap(res, k = 8)
Heatmaps for the membership of samples in all partitions to see how consistent they are:
membership_heatmap(res, k = 2)
membership_heatmap(res, k = 3)
membership_heatmap(res, k = 4)
membership_heatmap(res, k = 5)
membership_heatmap(res, k = 6)
membership_heatmap(res, k = 7)
membership_heatmap(res, k = 8)
As soon as the classes for columns are determined, the signatures that are significantly different between subgroups can be looked for. Following are the heatmaps for signatures.
get_signatures(res, k = 2)
get_signatures(res, k = 3)
get_signatures(res, k = 4)
get_signatures(res, k = 5)
get_signatures(res, k = 6)
get_signatures(res, k = 7)
get_signatures(res, k = 8)
Compare the overlap of signatures from different k:
compare_signatures(res)
get_signature() returns a data frame invisibly. To get the list of signatures, the function
call should be assigned to a variable explicitly. In following code, if plot argument is set
to FALSE, no heatmap is plotted while only the differential analysis is performed.
# code only for demonstration
tb = get_signature(res, k = ..., plot = FALSE)
An example of the output of tb is:
#> which_row fdr mean_1 mean_2 scaled_mean_1 scaled_mean_2 km
#> 1 38 0.042760348 8.373488 9.131774 -0.5533452 0.5164555 1
#> 2 40 0.018707592 7.106213 8.469186 -0.6173731 0.5762149 1
#> 3 55 0.019134737 10.221463 11.207825 -0.6159697 0.5749050 1
#> 4 59 0.006059896 5.921854 7.869574 -0.6899429 0.6439467 1
#> 5 60 0.018055526 8.928898 10.211722 -0.6204761 0.5791110 1
#> 6 98 0.009384629 15.714769 14.887706 0.6635654 -0.6193277 2
...
The columns in tb are:
which_row: row indices corresponding to the input matrix.fdr: FDR for the differential test. mean_x: The mean value in group x.scaled_mean_x: The mean value in group x after rows are scaled.km: Row groups if k-means clustering is applied to rows (which is done by automatically selecting number of clusters).If there are too many signatures, top_signatures = ... can be set to only show the
signatures with the highest FDRs:
# code only for demonstration
# e.g. to show the top 500 most significant rows
tb = get_signature(res, k = ..., top_signatures = 500)
If the signatures are defined as these which are uniquely high in current group, diff_method argument
can be set to "uniquely_high_in_one_group":
# code only for demonstration
tb = get_signature(res, k = ..., diff_method = "uniquely_high_in_one_group")
UMAP plot which shows how samples are separated.
dimension_reduction(res, k = 2, method = "UMAP")
dimension_reduction(res, k = 3, method = "UMAP")
dimension_reduction(res, k = 4, method = "UMAP")
dimension_reduction(res, k = 5, method = "UMAP")
dimension_reduction(res, k = 6, method = "UMAP")
dimension_reduction(res, k = 7, method = "UMAP")
dimension_reduction(res, k = 8, method = "UMAP")
Following heatmap shows how subgroups are split when increasing k:
collect_classes(res)
If matrix rows can be associated to genes, consider to use functional_enrichment(res,
...) to perform function enrichment for the signature genes. See this vignette for more detailed explanations.
Parent node: Node0. Child nodes: Node011 , Node012-leaf , Node013 , Node014 , Node015-leaf , Node021 , Node022 , Node023 , Node024 , Node025 , Node031 , Node032-leaf , Node033 , Node034-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 175 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 1.000 1.000 0.36149 0.639 0.639
#> 3 3 1.000 0.992 0.997 0.80166 0.710 0.547
#> 4 4 1.000 0.974 0.979 0.04718 0.973 0.923
#> 5 5 0.959 0.950 0.976 0.13197 0.863 0.601
#> 6 6 0.943 0.878 0.937 0.06016 0.876 0.532
#> 7 7 0.869 0.768 0.886 0.02462 0.964 0.813
#> 8 8 0.819 0.511 0.806 0.00994 0.970 0.832
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 5
There is also optional best \(k\) = 2 3 4 5 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.E8.A433.01 1 0 1 1 0
#> TCGA.DJ.A3V9.01 1 0 1 1 0
#> TCGA.EL.A3ZN.01 1 0 1 1 0
#> TCGA.EL.A3ZK.01 1 0 1 1 0
#> TCGA.ET.A40R.01 1 0 1 1 0
#> TCGA.DJ.A3VD.01 1 0 1 1 0
#> TCGA.EL.A3ZG.01 2 0 1 0 1
#> TCGA.EM.A4FV.01 1 0 1 1 0
#> TCGA.E8.A413.01 1 0 1 1 0
#> TCGA.IM.A420.01 1 0 1 1 0
#> TCGA.J8.A3O2.01 2 0 1 0 1
#> TCGA.E8.A415.01 1 0 1 1 0
#> TCGA.KS.A4I3.01 2 0 1 0 1
#> TCGA.DJ.A4UT.01 1 0 1 1 0
#> TCGA.EL.A4JW.01 1 0 1 1 0
#> TCGA.E8.A419.01 1 0 1 1 0
#> TCGA.EL.A3ZS.01 1 0 1 1 0
#> TCGA.KS.A4ID.01 1 0 1 1 0
#> TCGA.J8.A3YE.01 1 0 1 1 0
#> TCGA.DJ.A3VF.01 1 0 1 1 0
#> TCGA.E8.A432.01 1 0 1 1 0
#> TCGA.ET.A2MX.01 2 0 1 0 1
#> TCGA.ET.A40S.01 2 0 1 0 1
#> TCGA.DE.A4M8.01 1 0 1 1 0
#> TCGA.EL.A4KD.01 2 0 1 0 1
#> TCGA.FY.A40L.01 1 0 1 1 0
#> TCGA.J8.A42S.01 2 0 1 0 1
#> TCGA.KS.A4IC.01 1 0 1 1 0
#> TCGA.E8.A414.01 1 0 1 1 0
#> TCGA.DE.A4MD.06 2 0 1 0 1
#> TCGA.DJ.A4V4.01 1 0 1 1 0
#> TCGA.FY.A40K.01 1 0 1 1 0
#> TCGA.EM.A4FR.01 2 0 1 0 1
#> TCGA.DJ.A3V8.01 1 0 1 1 0
#> TCGA.J8.A4HY.01 1 0 1 1 0
#> TCGA.FY.A40N.01 1 0 1 1 0
#> TCGA.DJ.A2PX.01 1 0 1 1 0
#> TCGA.EL.A4JX.01 1 0 1 1 0
#> TCGA.DJ.A2Q5.01 2 0 1 0 1
#> TCGA.DJ.A4UP.01 1 0 1 1 0
#> TCGA.E8.A438.01 1 0 1 1 0
#> TCGA.EL.A4KH.01 1 0 1 1 0
#> TCGA.DJ.A4V5.01 2 0 1 0 1
#> TCGA.E8.A44M.01 1 0 1 1 0
#> TCGA.BJ.A45H.01 2 0 1 0 1
#> TCGA.E8.A44K.01 1 0 1 1 0
#> TCGA.CE.A481.01 1 0 1 1 0
#> TCGA.E8.A436.01 1 0 1 1 0
#> TCGA.DJ.A2Q3.01 1 0 1 1 0
#> TCGA.ET.A2N1.01 1 0 1 1 0
#> TCGA.DJ.A2PZ.01 2 0 1 0 1
#> TCGA.IM.A4EB.01 2 0 1 0 1
#> TCGA.EM.A4FO.01 2 0 1 0 1
#> TCGA.BJ.A45I.01 1 0 1 1 0
#> TCGA.EL.A3N3.01 1 0 1 1 0
#> TCGA.DJ.A2PS.01 1 0 1 1 0
#> TCGA.CE.A3MD.01 2 0 1 0 1
#> TCGA.EL.A3CN.01 1 0 1 1 0
#> TCGA.J8.A4HW.06 1 0 1 1 0
#> TCGA.E8.A437.01 1 0 1 1 0
#> TCGA.CE.A483.01 1 0 1 1 0
#> TCGA.CE.A485.01 2 0 1 0 1
#> TCGA.ET.A4KN.01 1 0 1 1 0
#> TCGA.DJ.A4UQ.01 2 0 1 0 1
#> TCGA.DJ.A4UW.01 1 0 1 1 0
#> TCGA.DE.A3KN.01 1 0 1 1 0
#> TCGA.DJ.A2QA.01 1 0 1 1 0
#> TCGA.BJ.A4O9.01 1 0 1 1 0
#> TCGA.CE.A3ME.01 1 0 1 1 0
#> TCGA.E3.A3E1.01 1 0 1 1 0
#> TCGA.DJ.A2Q8.01 1 0 1 1 0
#> TCGA.FE.A23A.01 1 0 1 1 0
#> TCGA.FY.A3I4.01 1 0 1 1 0
#> TCGA.ET.A2N0.01 1 0 1 1 0
#> TCGA.ET.A3DP.01 1 0 1 1 0
#> TCGA.EL.A3GV.01 1 0 1 1 0
#> TCGA.GE.A2C6.01 1 0 1 1 0
#> TCGA.DJ.A2PT.01 1 0 1 1 0
#> TCGA.E8.A242.01 1 0 1 1 0
#> TCGA.J8.A3O1.01 1 0 1 1 0
#> TCGA.EM.A2CR.01 1 0 1 1 0
#> TCGA.FE.A238.01 1 0 1 1 0
#> TCGA.EM.A3FQ.01 1 0 1 1 0
#> TCGA.EM.A22M.01 2 0 1 0 1
#> TCGA.J8.A3NZ.01 1 0 1 1 0
#> TCGA.FE.A236.01 2 0 1 0 1
#> TCGA.BJ.A28R.01 1 0 1 1 0
#> TCGA.EM.A2CU.01 1 0 1 1 0
#> TCGA.FE.A237.01 1 0 1 1 0
#> TCGA.DJ.A2QC.01 1 0 1 1 0
#> TCGA.EM.A2CS.06 1 0 1 1 0
#> TCGA.H2.A26U.01 1 0 1 1 0
#> TCGA.BJ.A28Z.01 1 0 1 1 0
#> TCGA.ET.A25J.01 1 0 1 1 0
#> TCGA.FY.A3NN.01 1 0 1 1 0
#> TCGA.EL.A3H3.01 1 0 1 1 0
#> TCGA.BJ.A0Z3.01 1 0 1 1 0
#> TCGA.BJ.A28X.01 1 0 1 1 0
#> TCGA.EL.A3CT.01 1 0 1 1 0
#> TCGA.J8.A3YG.01 1 0 1 1 0
#> TCGA.EM.A3SZ.01 1 0 1 1 0
#> TCGA.EM.A2P0.01 2 0 1 0 1
#> TCGA.E8.A2JQ.01 1 0 1 1 0
#> TCGA.DJ.A3UW.01 1 0 1 1 0
#> TCGA.DJ.A3V3.01 1 0 1 1 0
#> TCGA.EL.A3GP.01 2 0 1 0 1
#> TCGA.BJ.A191.01 1 0 1 1 0
#> TCGA.EM.A2P1.01 2 0 1 0 1
#> TCGA.IM.A3EB.01 1 0 1 1 0
#> TCGA.EM.A3AK.01 1 0 1 1 0
#> TCGA.EM.A3AO.01 2 0 1 0 1
#> TCGA.EM.A2P1.06 2 0 1 0 1
#> TCGA.EM.A1CS.01 1 0 1 1 0
#> TCGA.EL.A3GQ.01 1 0 1 1 0
#> TCGA.DJ.A3V4.01 1 0 1 1 0
#> TCGA.DJ.A3V2.01 1 0 1 1 0
#> TCGA.BJ.A290.01 2 0 1 0 1
#> TCGA.EM.A3SU.01 1 0 1 1 0
#> TCGA.EL.A3GR.01 1 0 1 1 0
#> TCGA.EM.A3SU.06 1 0 1 1 0
#> TCGA.DJ.A3US.01 1 0 1 1 0
#> TCGA.EM.A2OZ.01 2 0 1 0 1
#> TCGA.E8.A2EA.01 1 0 1 1 0
#> TCGA.EM.A1CV.01 1 0 1 1 0
#> TCGA.EM.A1CT.01 2 0 1 0 1
#> TCGA.ET.A3BS.01 2 0 1 0 1
#> TCGA.DJ.A3UU.01 1 0 1 1 0
#> TCGA.DJ.A2PO.01 2 0 1 0 1
#> TCGA.DJ.A3UQ.01 1 0 1 1 0
#> TCGA.EL.A3T0.01 1 0 1 1 0
#> TCGA.DJ.A3UX.01 1 0 1 1 0
#> TCGA.ET.A3BW.01 1 0 1 1 0
#> TCGA.ET.A39S.01 1 0 1 1 0
#> TCGA.ET.A3BP.01 1 0 1 1 0
#> TCGA.EL.A3D4.01 2 0 1 0 1
#> TCGA.FE.A232.01 1 0 1 1 0
#> TCGA.DJ.A3UR.01 1 0 1 1 0
#> TCGA.FK.A3S3.01 1 0 1 1 0
#> TCGA.EL.A3CS.01 1 0 1 1 0
#> TCGA.DO.A2HM.01 2 0 1 0 1
#> TCGA.FY.A3BL.01 2 0 1 0 1
#> TCGA.DJ.A1QF.01 1 0 1 1 0
#> TCGA.ET.A3DU.01 1 0 1 1 0
#> TCGA.EL.A3T1.01 1 0 1 1 0
#> TCGA.FE.A230.01 1 0 1 1 0
#> TCGA.ET.A39R.01 1 0 1 1 0
#> TCGA.EL.A3CV.01 2 0 1 0 1
#> TCGA.EL.A3TA.01 2 0 1 0 1
#> TCGA.DJ.A3UY.01 1 0 1 1 0
#> TCGA.DJ.A2Q1.01 1 0 1 1 0
#> TCGA.EL.A3CU.01 1 0 1 1 0
#> TCGA.DJ.A3UV.01 1 0 1 1 0
#> TCGA.EL.A3CX.01 1 0 1 1 0
#> TCGA.EM.A22P.01 2 0 1 0 1
#> TCGA.DJ.A3UK.01 1 0 1 1 0
#> TCGA.ET.A3DO.01 1 0 1 1 0
#> TCGA.ET.A3BV.01 1 0 1 1 0
#> TCGA.BJ.A0Z9.01 1 0 1 1 0
#> TCGA.FY.A3R6.01 1 0 1 1 0
#> TCGA.BJ.A0Z5.01 2 0 1 0 1
#> TCGA.ET.A3DT.01 1 0 1 1 0
#> TCGA.ET.A39M.01 2 0 1 0 1
#> TCGA.BJ.A0ZJ.01 2 0 1 0 1
#> TCGA.ET.A39T.01 1 0 1 1 0
#> TCGA.DJ.A2PV.01 1 0 1 1 0
#> TCGA.DJ.A13X.01 1 0 1 1 0
#> TCGA.EL.A3T6.01 1 0 1 1 0
#> TCGA.EM.A3O3.01 1 0 1 1 0
#> TCGA.DJ.A13L.01 2 0 1 0 1
#> TCGA.DJ.A13U.01 2 0 1 0 1
#> TCGA.ET.A2N4.01 1 0 1 1 0
#> TCGA.DJ.A13P.01 1 0 1 1 0
#> TCGA.EM.A3O7.01 1 0 1 1 0
#> TCGA.ET.A3DR.01 1 0 1 1 0
#> TCGA.FE.A3PB.01 1 0 1 1 0
cbind(get_classes(res, k = 3), get_membership(res, k = 3))
#> class entropy silhouette p1 p2 p3
#> TCGA.E8.A433.01 1 0.000 0.993 1.00 0 0.00
#> TCGA.DJ.A3V9.01 1 0.000 0.993 1.00 0 0.00
#> TCGA.EL.A3ZN.01 1 0.000 0.993 1.00 0 0.00
#> TCGA.EL.A3ZK.01 3 0.000 1.000 0.00 0 1.00
#> TCGA.ET.A40R.01 1 0.000 0.993 1.00 0 0.00
#> TCGA.DJ.A3VD.01 3 0.000 1.000 0.00 0 1.00
#> TCGA.EL.A3ZG.01 2 0.000 1.000 0.00 1 0.00
#> TCGA.EM.A4FV.01 1 0.000 0.993 1.00 0 0.00
#> TCGA.E8.A413.01 1 0.000 0.993 1.00 0 0.00
#> TCGA.IM.A420.01 3 0.000 1.000 0.00 0 1.00
#> TCGA.J8.A3O2.01 2 0.000 1.000 0.00 1 0.00
#> TCGA.E8.A415.01 1 0.000 0.993 1.00 0 0.00
#> TCGA.KS.A4I3.01 2 0.000 1.000 0.00 1 0.00
#> TCGA.DJ.A4UT.01 3 0.000 1.000 0.00 0 1.00
#> TCGA.EL.A4JW.01 1 0.369 0.835 0.86 0 0.14
#> TCGA.E8.A419.01 3 0.000 1.000 0.00 0 1.00
#> TCGA.EL.A3ZS.01 3 0.000 1.000 0.00 0 1.00
#> TCGA.KS.A4ID.01 3 0.000 1.000 0.00 0 1.00
#> TCGA.J8.A3YE.01 1 0.000 0.993 1.00 0 0.00
#> TCGA.DJ.A3VF.01 3 0.000 1.000 0.00 0 1.00
#> TCGA.E8.A432.01 1 0.000 0.993 1.00 0 0.00
#> TCGA.ET.A2MX.01 2 0.000 1.000 0.00 1 0.00
#> TCGA.ET.A40S.01 2 0.000 1.000 0.00 1 0.00
#> TCGA.DE.A4M8.01 3 0.000 1.000 0.00 0 1.00
#> TCGA.EL.A4KD.01 2 0.000 1.000 0.00 1 0.00
#> TCGA.FY.A40L.01 1 0.000 0.993 1.00 0 0.00
#> TCGA.J8.A42S.01 2 0.000 1.000 0.00 1 0.00
#> TCGA.KS.A4IC.01 1 0.000 0.993 1.00 0 0.00
#> TCGA.E8.A414.01 3 0.000 1.000 0.00 0 1.00
#> TCGA.DE.A4MD.06 2 0.000 1.000 0.00 1 0.00
#> TCGA.DJ.A4V4.01 1 0.000 0.993 1.00 0 0.00
#> TCGA.FY.A40K.01 1 0.000 0.993 1.00 0 0.00
#> TCGA.EM.A4FR.01 2 0.000 1.000 0.00 1 0.00
#> TCGA.DJ.A3V8.01 1 0.000 0.993 1.00 0 0.00
#> TCGA.J8.A4HY.01 1 0.000 0.993 1.00 0 0.00
#> TCGA.FY.A40N.01 1 0.000 0.993 1.00 0 0.00
#> TCGA.DJ.A2PX.01 3 0.000 1.000 0.00 0 1.00
#> TCGA.EL.A4JX.01 3 0.000 1.000 0.00 0 1.00
#> TCGA.DJ.A2Q5.01 2 0.000 1.000 0.00 1 0.00
#> TCGA.DJ.A4UP.01 3 0.000 1.000 0.00 0 1.00
#> TCGA.E8.A438.01 1 0.000 0.993 1.00 0 0.00
#> TCGA.EL.A4KH.01 1 0.000 0.993 1.00 0 0.00
#> TCGA.DJ.A4V5.01 2 0.000 1.000 0.00 1 0.00
#> TCGA.E8.A44M.01 3 0.000 1.000 0.00 0 1.00
#> TCGA.BJ.A45H.01 2 0.000 1.000 0.00 1 0.00
#> TCGA.E8.A44K.01 1 0.000 0.993 1.00 0 0.00
#> TCGA.CE.A481.01 3 0.000 1.000 0.00 0 1.00
#> TCGA.E8.A436.01 1 0.000 0.993 1.00 0 0.00
#> TCGA.DJ.A2Q3.01 3 0.000 1.000 0.00 0 1.00
#> TCGA.ET.A2N1.01 1 0.000 0.993 1.00 0 0.00
#> TCGA.DJ.A2PZ.01 2 0.000 1.000 0.00 1 0.00
#> TCGA.IM.A4EB.01 2 0.000 1.000 0.00 1 0.00
#> TCGA.EM.A4FO.01 2 0.000 1.000 0.00 1 0.00
#> TCGA.BJ.A45I.01 3 0.000 1.000 0.00 0 1.00
#> TCGA.EL.A3N3.01 3 0.000 1.000 0.00 0 1.00
#> TCGA.DJ.A2PS.01 1 0.000 0.993 1.00 0 0.00
#> TCGA.CE.A3MD.01 2 0.000 1.000 0.00 1 0.00
#> TCGA.EL.A3CN.01 3 0.000 1.000 0.00 0 1.00
#> TCGA.J8.A4HW.06 3 0.000 1.000 0.00 0 1.00
#> TCGA.E8.A437.01 1 0.000 0.993 1.00 0 0.00
#> TCGA.CE.A483.01 1 0.000 0.993 1.00 0 0.00
#> TCGA.CE.A485.01 2 0.000 1.000 0.00 1 0.00
#> TCGA.ET.A4KN.01 3 0.000 1.000 0.00 0 1.00
#> TCGA.DJ.A4UQ.01 2 0.000 1.000 0.00 1 0.00
#> TCGA.DJ.A4UW.01 1 0.000 0.993 1.00 0 0.00
#> TCGA.DE.A3KN.01 1 0.000 0.993 1.00 0 0.00
#> TCGA.DJ.A2QA.01 1 0.000 0.993 1.00 0 0.00
#> TCGA.BJ.A4O9.01 1 0.000 0.993 1.00 0 0.00
#> TCGA.CE.A3ME.01 1 0.000 0.993 1.00 0 0.00
#> TCGA.E3.A3E1.01 1 0.000 0.993 1.00 0 0.00
#> TCGA.DJ.A2Q8.01 1 0.000 0.993 1.00 0 0.00
#> TCGA.FE.A23A.01 3 0.000 1.000 0.00 0 1.00
#> TCGA.FY.A3I4.01 1 0.000 0.993 1.00 0 0.00
#> TCGA.ET.A2N0.01 1 0.000 0.993 1.00 0 0.00
#> TCGA.ET.A3DP.01 1 0.000 0.993 1.00 0 0.00
#> TCGA.EL.A3GV.01 1 0.000 0.993 1.00 0 0.00
#> TCGA.GE.A2C6.01 3 0.000 1.000 0.00 0 1.00
#> TCGA.DJ.A2PT.01 3 0.000 1.000 0.00 0 1.00
#> TCGA.E8.A242.01 3 0.000 1.000 0.00 0 1.00
#> TCGA.J8.A3O1.01 1 0.000 0.993 1.00 0 0.00
#> TCGA.EM.A2CR.01 1 0.000 0.993 1.00 0 0.00
#> TCGA.FE.A238.01 1 0.000 0.993 1.00 0 0.00
#> TCGA.EM.A3FQ.01 3 0.000 1.000 0.00 0 1.00
#> TCGA.EM.A22M.01 2 0.000 1.000 0.00 1 0.00
#> TCGA.J8.A3NZ.01 1 0.000 0.993 1.00 0 0.00
#> TCGA.FE.A236.01 2 0.000 1.000 0.00 1 0.00
#> TCGA.BJ.A28R.01 1 0.604 0.392 0.62 0 0.38
#> TCGA.EM.A2CU.01 1 0.000 0.993 1.00 0 0.00
#> TCGA.FE.A237.01 1 0.000 0.993 1.00 0 0.00
#> TCGA.DJ.A2QC.01 1 0.000 0.993 1.00 0 0.00
#> TCGA.EM.A2CS.06 1 0.000 0.993 1.00 0 0.00
#> TCGA.H2.A26U.01 3 0.000 1.000 0.00 0 1.00
#> TCGA.BJ.A28Z.01 3 0.000 1.000 0.00 0 1.00
#> TCGA.ET.A25J.01 1 0.000 0.993 1.00 0 0.00
#> TCGA.FY.A3NN.01 1 0.000 0.993 1.00 0 0.00
#> TCGA.EL.A3H3.01 3 0.000 1.000 0.00 0 1.00
#> TCGA.BJ.A0Z3.01 3 0.000 1.000 0.00 0 1.00
#> TCGA.BJ.A28X.01 3 0.000 1.000 0.00 0 1.00
#> TCGA.EL.A3CT.01 3 0.000 1.000 0.00 0 1.00
#> TCGA.J8.A3YG.01 3 0.000 1.000 0.00 0 1.00
#> TCGA.EM.A3SZ.01 3 0.000 1.000 0.00 0 1.00
#> TCGA.EM.A2P0.01 2 0.000 1.000 0.00 1 0.00
#> TCGA.E8.A2JQ.01 3 0.000 1.000 0.00 0 1.00
#> TCGA.DJ.A3UW.01 3 0.000 1.000 0.00 0 1.00
#> TCGA.DJ.A3V3.01 3 0.000 1.000 0.00 0 1.00
#> TCGA.EL.A3GP.01 2 0.000 1.000 0.00 1 0.00
#> TCGA.BJ.A191.01 1 0.000 0.993 1.00 0 0.00
#> TCGA.EM.A2P1.01 2 0.000 1.000 0.00 1 0.00
#> TCGA.IM.A3EB.01 3 0.000 1.000 0.00 0 1.00
#> TCGA.EM.A3AK.01 1 0.000 0.993 1.00 0 0.00
#> TCGA.EM.A3AO.01 2 0.000 1.000 0.00 1 0.00
#> TCGA.EM.A2P1.06 2 0.000 1.000 0.00 1 0.00
#> TCGA.EM.A1CS.01 1 0.000 0.993 1.00 0 0.00
#> TCGA.EL.A3GQ.01 1 0.000 0.993 1.00 0 0.00
#> TCGA.DJ.A3V4.01 1 0.000 0.993 1.00 0 0.00
#> TCGA.DJ.A3V2.01 3 0.000 1.000 0.00 0 1.00
#> TCGA.BJ.A290.01 2 0.000 1.000 0.00 1 0.00
#> TCGA.EM.A3SU.01 3 0.000 1.000 0.00 0 1.00
#> TCGA.EL.A3GR.01 1 0.000 0.993 1.00 0 0.00
#> TCGA.EM.A3SU.06 3 0.000 1.000 0.00 0 1.00
#> TCGA.DJ.A3US.01 3 0.000 1.000 0.00 0 1.00
#> TCGA.EM.A2OZ.01 2 0.000 1.000 0.00 1 0.00
#> TCGA.E8.A2EA.01 3 0.000 1.000 0.00 0 1.00
#> TCGA.EM.A1CV.01 1 0.000 0.993 1.00 0 0.00
#> TCGA.EM.A1CT.01 2 0.000 1.000 0.00 1 0.00
#> TCGA.ET.A3BS.01 2 0.000 1.000 0.00 1 0.00
#> TCGA.DJ.A3UU.01 1 0.000 0.993 1.00 0 0.00
#> TCGA.DJ.A2PO.01 2 0.000 1.000 0.00 1 0.00
#> TCGA.DJ.A3UQ.01 3 0.000 1.000 0.00 0 1.00
#> TCGA.EL.A3T0.01 1 0.000 0.993 1.00 0 0.00
#> TCGA.DJ.A3UX.01 1 0.000 0.993 1.00 0 0.00
#> TCGA.ET.A3BW.01 1 0.000 0.993 1.00 0 0.00
#> TCGA.ET.A39S.01 1 0.000 0.993 1.00 0 0.00
#> TCGA.ET.A3BP.01 1 0.000 0.993 1.00 0 0.00
#> TCGA.EL.A3D4.01 2 0.000 1.000 0.00 1 0.00
#> TCGA.FE.A232.01 1 0.000 0.993 1.00 0 0.00
#> TCGA.DJ.A3UR.01 1 0.000 0.993 1.00 0 0.00
#> TCGA.FK.A3S3.01 1 0.000 0.993 1.00 0 0.00
#> TCGA.EL.A3CS.01 1 0.000 0.993 1.00 0 0.00
#> TCGA.DO.A2HM.01 2 0.000 1.000 0.00 1 0.00
#> TCGA.FY.A3BL.01 2 0.000 1.000 0.00 1 0.00
#> TCGA.DJ.A1QF.01 1 0.000 0.993 1.00 0 0.00
#> TCGA.ET.A3DU.01 3 0.000 1.000 0.00 0 1.00
#> TCGA.EL.A3T1.01 3 0.000 1.000 0.00 0 1.00
#> TCGA.FE.A230.01 3 0.000 1.000 0.00 0 1.00
#> TCGA.ET.A39R.01 3 0.000 1.000 0.00 0 1.00
#> TCGA.EL.A3CV.01 2 0.000 1.000 0.00 1 0.00
#> TCGA.EL.A3TA.01 2 0.000 1.000 0.00 1 0.00
#> TCGA.DJ.A3UY.01 1 0.000 0.993 1.00 0 0.00
#> TCGA.DJ.A2Q1.01 3 0.000 1.000 0.00 0 1.00
#> TCGA.EL.A3CU.01 3 0.000 1.000 0.00 0 1.00
#> TCGA.DJ.A3UV.01 1 0.000 0.993 1.00 0 0.00
#> TCGA.EL.A3CX.01 1 0.000 0.993 1.00 0 0.00
#> TCGA.EM.A22P.01 2 0.000 1.000 0.00 1 0.00
#> TCGA.DJ.A3UK.01 1 0.000 0.993 1.00 0 0.00
#> TCGA.ET.A3DO.01 3 0.000 1.000 0.00 0 1.00
#> TCGA.ET.A3BV.01 3 0.000 1.000 0.00 0 1.00
#> TCGA.BJ.A0Z9.01 3 0.000 1.000 0.00 0 1.00
#> TCGA.FY.A3R6.01 3 0.000 1.000 0.00 0 1.00
#> TCGA.BJ.A0Z5.01 2 0.000 1.000 0.00 1 0.00
#> TCGA.ET.A3DT.01 3 0.000 1.000 0.00 0 1.00
#> TCGA.ET.A39M.01 2 0.000 1.000 0.00 1 0.00
#> TCGA.BJ.A0ZJ.01 2 0.000 1.000 0.00 1 0.00
#> TCGA.ET.A39T.01 1 0.000 0.993 1.00 0 0.00
#> TCGA.DJ.A2PV.01 1 0.000 0.993 1.00 0 0.00
#> TCGA.DJ.A13X.01 1 0.000 0.993 1.00 0 0.00
#> TCGA.EL.A3T6.01 3 0.000 1.000 0.00 0 1.00
#> TCGA.EM.A3O3.01 3 0.000 1.000 0.00 0 1.00
#> TCGA.DJ.A13L.01 2 0.000 1.000 0.00 1 0.00
#> TCGA.DJ.A13U.01 2 0.000 1.000 0.00 1 0.00
#> TCGA.ET.A2N4.01 1 0.000 0.993 1.00 0 0.00
#> TCGA.DJ.A13P.01 1 0.000 0.993 1.00 0 0.00
#> TCGA.EM.A3O7.01 1 0.000 0.993 1.00 0 0.00
#> TCGA.ET.A3DR.01 1 0.000 0.993 1.00 0 0.00
#> TCGA.FE.A3PB.01 3 0.000 1.000 0.00 0 1.00
cbind(get_classes(res, k = 4), get_membership(res, k = 4))
#> class entropy silhouette p1 p2 p3 p4
#> TCGA.E8.A433.01 1 0.1637 0.944 0.94 0.00 0.00 0.06
#> TCGA.DJ.A3V9.01 1 0.0000 0.978 1.00 0.00 0.00 0.00
#> TCGA.EL.A3ZN.01 1 0.0000 0.978 1.00 0.00 0.00 0.00
#> TCGA.EL.A3ZK.01 3 0.1637 0.956 0.00 0.00 0.94 0.06
#> TCGA.ET.A40R.01 1 0.1637 0.944 0.94 0.00 0.00 0.06
#> TCGA.DJ.A3VD.01 3 0.0000 0.981 0.00 0.00 1.00 0.00
#> TCGA.EL.A3ZG.01 2 0.0000 1.000 0.00 1.00 0.00 0.00
#> TCGA.EM.A4FV.01 1 0.1637 0.944 0.94 0.00 0.00 0.06
#> TCGA.E8.A413.01 1 0.1637 0.944 0.94 0.00 0.00 0.06
#> TCGA.IM.A420.01 3 0.0000 0.981 0.00 0.00 1.00 0.00
#> TCGA.J8.A3O2.01 2 0.0000 1.000 0.00 1.00 0.00 0.00
#> TCGA.E8.A415.01 1 0.0000 0.978 1.00 0.00 0.00 0.00
#> TCGA.KS.A4I3.01 2 0.0000 1.000 0.00 1.00 0.00 0.00
#> TCGA.DJ.A4UT.01 3 0.0000 0.981 0.00 0.00 1.00 0.00
#> TCGA.EL.A4JW.01 1 0.4227 0.798 0.82 0.00 0.12 0.06
#> TCGA.E8.A419.01 3 0.0000 0.981 0.00 0.00 1.00 0.00
#> TCGA.EL.A3ZS.01 3 0.0000 0.981 0.00 0.00 1.00 0.00
#> TCGA.KS.A4ID.01 3 0.0000 0.981 0.00 0.00 1.00 0.00
#> TCGA.J8.A3YE.01 1 0.0000 0.978 1.00 0.00 0.00 0.00
#> TCGA.DJ.A3VF.01 3 0.0000 0.981 0.00 0.00 1.00 0.00
#> TCGA.E8.A432.01 1 0.1211 0.956 0.96 0.00 0.00 0.04
#> TCGA.ET.A2MX.01 2 0.0000 1.000 0.00 1.00 0.00 0.00
#> TCGA.ET.A40S.01 4 0.1637 1.000 0.00 0.06 0.00 0.94
#> TCGA.DE.A4M8.01 3 0.0000 0.981 0.00 0.00 1.00 0.00
#> TCGA.EL.A4KD.01 2 0.0000 1.000 0.00 1.00 0.00 0.00
#> TCGA.FY.A40L.01 1 0.1637 0.944 0.94 0.00 0.00 0.06
#> TCGA.J8.A42S.01 2 0.0000 1.000 0.00 1.00 0.00 0.00
#> TCGA.KS.A4IC.01 1 0.0000 0.978 1.00 0.00 0.00 0.00
#> TCGA.E8.A414.01 3 0.1637 0.956 0.00 0.00 0.94 0.06
#> TCGA.DE.A4MD.06 4 0.1637 1.000 0.00 0.06 0.00 0.94
#> TCGA.DJ.A4V4.01 1 0.0000 0.978 1.00 0.00 0.00 0.00
#> TCGA.FY.A40K.01 1 0.0000 0.978 1.00 0.00 0.00 0.00
#> TCGA.EM.A4FR.01 2 0.0000 1.000 0.00 1.00 0.00 0.00
#> TCGA.DJ.A3V8.01 1 0.1637 0.944 0.94 0.00 0.00 0.06
#> TCGA.J8.A4HY.01 1 0.0000 0.978 1.00 0.00 0.00 0.00
#> TCGA.FY.A40N.01 1 0.0000 0.978 1.00 0.00 0.00 0.00
#> TCGA.DJ.A2PX.01 3 0.1637 0.956 0.00 0.00 0.94 0.06
#> TCGA.EL.A4JX.01 3 0.0000 0.981 0.00 0.00 1.00 0.00
#> TCGA.DJ.A2Q5.01 4 0.1637 1.000 0.00 0.06 0.00 0.94
#> TCGA.DJ.A4UP.01 3 0.1211 0.965 0.00 0.00 0.96 0.04
#> TCGA.E8.A438.01 1 0.0000 0.978 1.00 0.00 0.00 0.00
#> TCGA.EL.A4KH.01 1 0.0000 0.978 1.00 0.00 0.00 0.00
#> TCGA.DJ.A4V5.01 4 0.1637 1.000 0.00 0.06 0.00 0.94
#> TCGA.E8.A44M.01 3 0.0000 0.981 0.00 0.00 1.00 0.00
#> TCGA.BJ.A45H.01 2 0.0000 1.000 0.00 1.00 0.00 0.00
#> TCGA.E8.A44K.01 1 0.1637 0.944 0.94 0.00 0.00 0.06
#> TCGA.CE.A481.01 3 0.1637 0.956 0.00 0.00 0.94 0.06
#> TCGA.E8.A436.01 1 0.1637 0.944 0.94 0.00 0.00 0.06
#> TCGA.DJ.A2Q3.01 3 0.0000 0.981 0.00 0.00 1.00 0.00
#> TCGA.ET.A2N1.01 1 0.0000 0.978 1.00 0.00 0.00 0.00
#> TCGA.DJ.A2PZ.01 2 0.0000 1.000 0.00 1.00 0.00 0.00
#> TCGA.IM.A4EB.01 4 0.1637 1.000 0.00 0.06 0.00 0.94
#> TCGA.EM.A4FO.01 4 0.1637 1.000 0.00 0.06 0.00 0.94
#> TCGA.BJ.A45I.01 3 0.0000 0.981 0.00 0.00 1.00 0.00
#> TCGA.EL.A3N3.01 3 0.0000 0.981 0.00 0.00 1.00 0.00
#> TCGA.DJ.A2PS.01 1 0.0000 0.978 1.00 0.00 0.00 0.00
#> TCGA.CE.A3MD.01 2 0.0000 1.000 0.00 1.00 0.00 0.00
#> TCGA.EL.A3CN.01 3 0.1637 0.956 0.00 0.00 0.94 0.06
#> TCGA.J8.A4HW.06 3 0.0000 0.981 0.00 0.00 1.00 0.00
#> TCGA.E8.A437.01 1 0.0000 0.978 1.00 0.00 0.00 0.00
#> TCGA.CE.A483.01 1 0.0000 0.978 1.00 0.00 0.00 0.00
#> TCGA.CE.A485.01 2 0.0000 1.000 0.00 1.00 0.00 0.00
#> TCGA.ET.A4KN.01 3 0.0000 0.981 0.00 0.00 1.00 0.00
#> TCGA.DJ.A4UQ.01 2 0.0000 1.000 0.00 1.00 0.00 0.00
#> TCGA.DJ.A4UW.01 1 0.0000 0.978 1.00 0.00 0.00 0.00
#> TCGA.DE.A3KN.01 1 0.0000 0.978 1.00 0.00 0.00 0.00
#> TCGA.DJ.A2QA.01 1 0.0000 0.978 1.00 0.00 0.00 0.00
#> TCGA.BJ.A4O9.01 1 0.0000 0.978 1.00 0.00 0.00 0.00
#> TCGA.CE.A3ME.01 1 0.0000 0.978 1.00 0.00 0.00 0.00
#> TCGA.E3.A3E1.01 1 0.0000 0.978 1.00 0.00 0.00 0.00
#> TCGA.DJ.A2Q8.01 1 0.1637 0.944 0.94 0.00 0.00 0.06
#> TCGA.FE.A23A.01 3 0.0000 0.981 0.00 0.00 1.00 0.00
#> TCGA.FY.A3I4.01 1 0.0000 0.978 1.00 0.00 0.00 0.00
#> TCGA.ET.A2N0.01 1 0.1637 0.944 0.94 0.00 0.00 0.06
#> TCGA.ET.A3DP.01 1 0.0000 0.978 1.00 0.00 0.00 0.00
#> TCGA.EL.A3GV.01 1 0.0000 0.978 1.00 0.00 0.00 0.00
#> TCGA.GE.A2C6.01 3 0.0000 0.981 0.00 0.00 1.00 0.00
#> TCGA.DJ.A2PT.01 3 0.0000 0.981 0.00 0.00 1.00 0.00
#> TCGA.E8.A242.01 3 0.0000 0.981 0.00 0.00 1.00 0.00
#> TCGA.J8.A3O1.01 1 0.0000 0.978 1.00 0.00 0.00 0.00
#> TCGA.EM.A2CR.01 1 0.0000 0.978 1.00 0.00 0.00 0.00
#> TCGA.FE.A238.01 1 0.1637 0.944 0.94 0.00 0.00 0.06
#> TCGA.EM.A3FQ.01 3 0.1637 0.956 0.00 0.00 0.94 0.06
#> TCGA.EM.A22M.01 4 0.1637 1.000 0.00 0.06 0.00 0.94
#> TCGA.J8.A3NZ.01 1 0.0000 0.978 1.00 0.00 0.00 0.00
#> TCGA.FE.A236.01 2 0.0000 1.000 0.00 1.00 0.00 0.00
#> TCGA.BJ.A28R.01 1 0.6150 0.360 0.58 0.00 0.36 0.06
#> TCGA.EM.A2CU.01 1 0.1637 0.944 0.94 0.00 0.00 0.06
#> TCGA.FE.A237.01 1 0.0000 0.978 1.00 0.00 0.00 0.00
#> TCGA.DJ.A2QC.01 1 0.0000 0.978 1.00 0.00 0.00 0.00
#> TCGA.EM.A2CS.06 1 0.0000 0.978 1.00 0.00 0.00 0.00
#> TCGA.H2.A26U.01 3 0.0000 0.981 0.00 0.00 1.00 0.00
#> TCGA.BJ.A28Z.01 3 0.0000 0.981 0.00 0.00 1.00 0.00
#> TCGA.ET.A25J.01 1 0.0000 0.978 1.00 0.00 0.00 0.00
#> TCGA.FY.A3NN.01 1 0.0000 0.978 1.00 0.00 0.00 0.00
#> TCGA.EL.A3H3.01 3 0.1637 0.956 0.00 0.00 0.94 0.06
#> TCGA.BJ.A0Z3.01 3 0.0000 0.981 0.00 0.00 1.00 0.00
#> TCGA.BJ.A28X.01 3 0.0000 0.981 0.00 0.00 1.00 0.00
#> TCGA.EL.A3CT.01 3 0.0000 0.981 0.00 0.00 1.00 0.00
#> TCGA.J8.A3YG.01 3 0.1637 0.956 0.00 0.00 0.94 0.06
#> TCGA.EM.A3SZ.01 3 0.1637 0.956 0.00 0.00 0.94 0.06
#> TCGA.EM.A2P0.01 2 0.0000 1.000 0.00 1.00 0.00 0.00
#> TCGA.E8.A2JQ.01 3 0.0000 0.981 0.00 0.00 1.00 0.00
#> TCGA.DJ.A3UW.01 3 0.0000 0.981 0.00 0.00 1.00 0.00
#> TCGA.DJ.A3V3.01 3 0.1637 0.956 0.00 0.00 0.94 0.06
#> TCGA.EL.A3GP.01 4 0.1637 1.000 0.00 0.06 0.00 0.94
#> TCGA.BJ.A191.01 1 0.0000 0.978 1.00 0.00 0.00 0.00
#> TCGA.EM.A2P1.01 4 0.1637 1.000 0.00 0.06 0.00 0.94
#> TCGA.IM.A3EB.01 3 0.0000 0.981 0.00 0.00 1.00 0.00
#> TCGA.EM.A3AK.01 1 0.0000 0.978 1.00 0.00 0.00 0.00
#> TCGA.EM.A3AO.01 2 0.0000 1.000 0.00 1.00 0.00 0.00
#> TCGA.EM.A2P1.06 4 0.1637 1.000 0.00 0.06 0.00 0.94
#> TCGA.EM.A1CS.01 1 0.0000 0.978 1.00 0.00 0.00 0.00
#> TCGA.EL.A3GQ.01 1 0.0000 0.978 1.00 0.00 0.00 0.00
#> TCGA.DJ.A3V4.01 1 0.0000 0.978 1.00 0.00 0.00 0.00
#> TCGA.DJ.A3V2.01 3 0.0000 0.981 0.00 0.00 1.00 0.00
#> TCGA.BJ.A290.01 2 0.0000 1.000 0.00 1.00 0.00 0.00
#> TCGA.EM.A3SU.01 3 0.1637 0.956 0.00 0.00 0.94 0.06
#> TCGA.EL.A3GR.01 1 0.0000 0.978 1.00 0.00 0.00 0.00
#> TCGA.EM.A3SU.06 3 0.0000 0.981 0.00 0.00 1.00 0.00
#> TCGA.DJ.A3US.01 3 0.1637 0.956 0.00 0.00 0.94 0.06
#> TCGA.EM.A2OZ.01 2 0.0000 1.000 0.00 1.00 0.00 0.00
#> TCGA.E8.A2EA.01 3 0.0000 0.981 0.00 0.00 1.00 0.00
#> TCGA.EM.A1CV.01 1 0.0000 0.978 1.00 0.00 0.00 0.00
#> TCGA.EM.A1CT.01 2 0.0000 1.000 0.00 1.00 0.00 0.00
#> TCGA.ET.A3BS.01 4 0.1637 1.000 0.00 0.06 0.00 0.94
#> TCGA.DJ.A3UU.01 1 0.0000 0.978 1.00 0.00 0.00 0.00
#> TCGA.DJ.A2PO.01 2 0.0000 1.000 0.00 1.00 0.00 0.00
#> TCGA.DJ.A3UQ.01 3 0.1637 0.956 0.00 0.00 0.94 0.06
#> TCGA.EL.A3T0.01 1 0.0000 0.978 1.00 0.00 0.00 0.00
#> TCGA.DJ.A3UX.01 1 0.1637 0.944 0.94 0.00 0.00 0.06
#> TCGA.ET.A3BW.01 1 0.0000 0.978 1.00 0.00 0.00 0.00
#> TCGA.ET.A39S.01 1 0.0000 0.978 1.00 0.00 0.00 0.00
#> TCGA.ET.A3BP.01 1 0.0000 0.978 1.00 0.00 0.00 0.00
#> TCGA.EL.A3D4.01 2 0.0000 1.000 0.00 1.00 0.00 0.00
#> TCGA.FE.A232.01 1 0.0000 0.978 1.00 0.00 0.00 0.00
#> TCGA.DJ.A3UR.01 1 0.0000 0.978 1.00 0.00 0.00 0.00
#> TCGA.FK.A3S3.01 1 0.0000 0.978 1.00 0.00 0.00 0.00
#> TCGA.EL.A3CS.01 1 0.1637 0.944 0.94 0.00 0.00 0.06
#> TCGA.DO.A2HM.01 4 0.1637 1.000 0.00 0.06 0.00 0.94
#> TCGA.FY.A3BL.01 2 0.0000 1.000 0.00 1.00 0.00 0.00
#> TCGA.DJ.A1QF.01 1 0.0000 0.978 1.00 0.00 0.00 0.00
#> TCGA.ET.A3DU.01 3 0.0000 0.981 0.00 0.00 1.00 0.00
#> TCGA.EL.A3T1.01 3 0.1637 0.956 0.00 0.00 0.94 0.06
#> TCGA.FE.A230.01 3 0.1637 0.956 0.00 0.00 0.94 0.06
#> TCGA.ET.A39R.01 3 0.1637 0.956 0.00 0.00 0.94 0.06
#> TCGA.EL.A3CV.01 4 0.1637 1.000 0.00 0.06 0.00 0.94
#> TCGA.EL.A3TA.01 2 0.0000 1.000 0.00 1.00 0.00 0.00
#> TCGA.DJ.A3UY.01 1 0.1637 0.944 0.94 0.00 0.00 0.06
#> TCGA.DJ.A2Q1.01 3 0.0000 0.981 0.00 0.00 1.00 0.00
#> TCGA.EL.A3CU.01 3 0.0000 0.981 0.00 0.00 1.00 0.00
#> TCGA.DJ.A3UV.01 1 0.0000 0.978 1.00 0.00 0.00 0.00
#> TCGA.EL.A3CX.01 1 0.0707 0.967 0.98 0.00 0.00 0.02
#> TCGA.EM.A22P.01 4 0.1637 1.000 0.00 0.06 0.00 0.94
#> TCGA.DJ.A3UK.01 1 0.0000 0.978 1.00 0.00 0.00 0.00
#> TCGA.ET.A3DO.01 3 0.0000 0.981 0.00 0.00 1.00 0.00
#> TCGA.ET.A3BV.01 3 0.0000 0.981 0.00 0.00 1.00 0.00
#> TCGA.BJ.A0Z9.01 3 0.0000 0.981 0.00 0.00 1.00 0.00
#> TCGA.FY.A3R6.01 3 0.0000 0.981 0.00 0.00 1.00 0.00
#> TCGA.BJ.A0Z5.01 2 0.0000 1.000 0.00 1.00 0.00 0.00
#> TCGA.ET.A3DT.01 3 0.0000 0.981 0.00 0.00 1.00 0.00
#> TCGA.ET.A39M.01 4 0.1637 1.000 0.00 0.06 0.00 0.94
#> TCGA.BJ.A0ZJ.01 4 0.1637 1.000 0.00 0.06 0.00 0.94
#> TCGA.ET.A39T.01 1 0.0000 0.978 1.00 0.00 0.00 0.00
#> TCGA.DJ.A2PV.01 1 0.0000 0.978 1.00 0.00 0.00 0.00
#> TCGA.DJ.A13X.01 1 0.0000 0.978 1.00 0.00 0.00 0.00
#> TCGA.EL.A3T6.01 3 0.0000 0.981 0.00 0.00 1.00 0.00
#> TCGA.EM.A3O3.01 3 0.0000 0.981 0.00 0.00 1.00 0.00
#> TCGA.DJ.A13L.01 4 0.1637 1.000 0.00 0.06 0.00 0.94
#> TCGA.DJ.A13U.01 2 0.0000 1.000 0.00 1.00 0.00 0.00
#> TCGA.ET.A2N4.01 1 0.0000 0.978 1.00 0.00 0.00 0.00
#> TCGA.DJ.A13P.01 1 0.0000 0.978 1.00 0.00 0.00 0.00
#> TCGA.EM.A3O7.01 1 0.0000 0.978 1.00 0.00 0.00 0.00
#> TCGA.ET.A3DR.01 1 0.0000 0.978 1.00 0.00 0.00 0.00
#> TCGA.FE.A3PB.01 3 0.1637 0.956 0.00 0.00 0.94 0.06
cbind(get_classes(res, k = 5), get_membership(res, k = 5))
#> class entropy silhouette p1 p2 p3 p4 p5
#> TCGA.E8.A433.01 5 0.3274 0.659 0.22 0 0.00 0 0.78
#> TCGA.DJ.A3V9.01 1 0.2020 0.916 0.90 0 0.00 0 0.10
#> TCGA.EL.A3ZN.01 1 0.1410 0.941 0.94 0 0.00 0 0.06
#> TCGA.EL.A3ZK.01 5 0.0000 0.929 0.00 0 0.00 0 1.00
#> TCGA.ET.A40R.01 5 0.0000 0.929 0.00 0 0.00 0 1.00
#> TCGA.DJ.A3VD.01 3 0.0000 0.992 0.00 0 1.00 0 0.00
#> TCGA.EL.A3ZG.01 2 0.0000 1.000 0.00 1 0.00 0 0.00
#> TCGA.EM.A4FV.01 5 0.0000 0.929 0.00 0 0.00 0 1.00
#> TCGA.E8.A413.01 5 0.0000 0.929 0.00 0 0.00 0 1.00
#> TCGA.IM.A420.01 3 0.0000 0.992 0.00 0 1.00 0 0.00
#> TCGA.J8.A3O2.01 2 0.0000 1.000 0.00 1 0.00 0 0.00
#> TCGA.E8.A415.01 1 0.1043 0.951 0.96 0 0.00 0 0.04
#> TCGA.KS.A4I3.01 2 0.0000 1.000 0.00 1 0.00 0 0.00
#> TCGA.DJ.A4UT.01 3 0.0000 0.992 0.00 0 1.00 0 0.00
#> TCGA.EL.A4JW.01 5 0.0000 0.929 0.00 0 0.00 0 1.00
#> TCGA.E8.A419.01 3 0.0000 0.992 0.00 0 1.00 0 0.00
#> TCGA.EL.A3ZS.01 3 0.0000 0.992 0.00 0 1.00 0 0.00
#> TCGA.KS.A4ID.01 3 0.0000 0.992 0.00 0 1.00 0 0.00
#> TCGA.J8.A3YE.01 1 0.0000 0.964 1.00 0 0.00 0 0.00
#> TCGA.DJ.A3VF.01 3 0.2020 0.882 0.00 0 0.90 0 0.10
#> TCGA.E8.A432.01 5 0.4262 0.122 0.44 0 0.00 0 0.56
#> TCGA.ET.A2MX.01 2 0.0000 1.000 0.00 1 0.00 0 0.00
#> TCGA.ET.A40S.01 4 0.0000 1.000 0.00 0 0.00 1 0.00
#> TCGA.DE.A4M8.01 3 0.0000 0.992 0.00 0 1.00 0 0.00
#> TCGA.EL.A4KD.01 2 0.0000 1.000 0.00 1 0.00 0 0.00
#> TCGA.FY.A40L.01 5 0.0000 0.929 0.00 0 0.00 0 1.00
#> TCGA.J8.A42S.01 2 0.0000 1.000 0.00 1 0.00 0 0.00
#> TCGA.KS.A4IC.01 1 0.0000 0.964 1.00 0 0.00 0 0.00
#> TCGA.E8.A414.01 5 0.2516 0.821 0.00 0 0.14 0 0.86
#> TCGA.DE.A4MD.06 4 0.0000 1.000 0.00 0 0.00 1 0.00
#> TCGA.DJ.A4V4.01 1 0.0000 0.964 1.00 0 0.00 0 0.00
#> TCGA.FY.A40K.01 1 0.0000 0.964 1.00 0 0.00 0 0.00
#> TCGA.EM.A4FR.01 2 0.0000 1.000 0.00 1 0.00 0 0.00
#> TCGA.DJ.A3V8.01 5 0.0609 0.911 0.02 0 0.00 0 0.98
#> TCGA.J8.A4HY.01 1 0.0000 0.964 1.00 0 0.00 0 0.00
#> TCGA.FY.A40N.01 1 0.0000 0.964 1.00 0 0.00 0 0.00
#> TCGA.DJ.A2PX.01 5 0.1410 0.892 0.00 0 0.06 0 0.94
#> TCGA.EL.A4JX.01 3 0.0000 0.992 0.00 0 1.00 0 0.00
#> TCGA.DJ.A2Q5.01 4 0.0000 1.000 0.00 0 0.00 1 0.00
#> TCGA.DJ.A4UP.01 5 0.4126 0.419 0.00 0 0.38 0 0.62
#> TCGA.E8.A438.01 1 0.2020 0.916 0.90 0 0.00 0 0.10
#> TCGA.EL.A4KH.01 1 0.0000 0.964 1.00 0 0.00 0 0.00
#> TCGA.DJ.A4V5.01 4 0.0000 1.000 0.00 0 0.00 1 0.00
#> TCGA.E8.A44M.01 3 0.0000 0.992 0.00 0 1.00 0 0.00
#> TCGA.BJ.A45H.01 2 0.0000 1.000 0.00 1 0.00 0 0.00
#> TCGA.E8.A44K.01 5 0.0000 0.929 0.00 0 0.00 0 1.00
#> TCGA.CE.A481.01 5 0.0000 0.929 0.00 0 0.00 0 1.00
#> TCGA.E8.A436.01 5 0.0000 0.929 0.00 0 0.00 0 1.00
#> TCGA.DJ.A2Q3.01 3 0.0000 0.992 0.00 0 1.00 0 0.00
#> TCGA.ET.A2N1.01 1 0.0000 0.964 1.00 0 0.00 0 0.00
#> TCGA.DJ.A2PZ.01 2 0.0000 1.000 0.00 1 0.00 0 0.00
#> TCGA.IM.A4EB.01 4 0.0000 1.000 0.00 0 0.00 1 0.00
#> TCGA.EM.A4FO.01 4 0.0000 1.000 0.00 0 0.00 1 0.00
#> TCGA.BJ.A45I.01 3 0.0000 0.992 0.00 0 1.00 0 0.00
#> TCGA.EL.A3N3.01 3 0.0000 0.992 0.00 0 1.00 0 0.00
#> TCGA.DJ.A2PS.01 1 0.2020 0.916 0.90 0 0.00 0 0.10
#> TCGA.CE.A3MD.01 2 0.0000 1.000 0.00 1 0.00 0 0.00
#> TCGA.EL.A3CN.01 5 0.2516 0.821 0.00 0 0.14 0 0.86
#> TCGA.J8.A4HW.06 3 0.0000 0.992 0.00 0 1.00 0 0.00
#> TCGA.E8.A437.01 1 0.0000 0.964 1.00 0 0.00 0 0.00
#> TCGA.CE.A483.01 1 0.0000 0.964 1.00 0 0.00 0 0.00
#> TCGA.CE.A485.01 2 0.0000 1.000 0.00 1 0.00 0 0.00
#> TCGA.ET.A4KN.01 3 0.0000 0.992 0.00 0 1.00 0 0.00
#> TCGA.DJ.A4UQ.01 2 0.0000 1.000 0.00 1 0.00 0 0.00
#> TCGA.DJ.A4UW.01 1 0.0000 0.964 1.00 0 0.00 0 0.00
#> TCGA.DE.A3KN.01 1 0.1410 0.941 0.94 0 0.00 0 0.06
#> TCGA.DJ.A2QA.01 1 0.0000 0.964 1.00 0 0.00 0 0.00
#> TCGA.BJ.A4O9.01 1 0.0000 0.964 1.00 0 0.00 0 0.00
#> TCGA.CE.A3ME.01 1 0.1732 0.930 0.92 0 0.00 0 0.08
#> TCGA.E3.A3E1.01 1 0.1732 0.930 0.92 0 0.00 0 0.08
#> TCGA.DJ.A2Q8.01 5 0.0000 0.929 0.00 0 0.00 0 1.00
#> TCGA.FE.A23A.01 3 0.0000 0.992 0.00 0 1.00 0 0.00
#> TCGA.FY.A3I4.01 1 0.1043 0.951 0.96 0 0.00 0 0.04
#> TCGA.ET.A2N0.01 5 0.0000 0.929 0.00 0 0.00 0 1.00
#> TCGA.ET.A3DP.01 1 0.1732 0.930 0.92 0 0.00 0 0.08
#> TCGA.EL.A3GV.01 1 0.1732 0.930 0.92 0 0.00 0 0.08
#> TCGA.GE.A2C6.01 3 0.0000 0.992 0.00 0 1.00 0 0.00
#> TCGA.DJ.A2PT.01 3 0.0000 0.992 0.00 0 1.00 0 0.00
#> TCGA.E8.A242.01 3 0.0000 0.992 0.00 0 1.00 0 0.00
#> TCGA.J8.A3O1.01 1 0.0000 0.964 1.00 0 0.00 0 0.00
#> TCGA.EM.A2CR.01 1 0.0000 0.964 1.00 0 0.00 0 0.00
#> TCGA.FE.A238.01 5 0.0000 0.929 0.00 0 0.00 0 1.00
#> TCGA.EM.A3FQ.01 5 0.2516 0.821 0.00 0 0.14 0 0.86
#> TCGA.EM.A22M.01 4 0.0000 1.000 0.00 0 0.00 1 0.00
#> TCGA.J8.A3NZ.01 1 0.0000 0.964 1.00 0 0.00 0 0.00
#> TCGA.FE.A236.01 2 0.0000 1.000 0.00 1 0.00 0 0.00
#> TCGA.BJ.A28R.01 5 0.0000 0.929 0.00 0 0.00 0 1.00
#> TCGA.EM.A2CU.01 5 0.0000 0.929 0.00 0 0.00 0 1.00
#> TCGA.FE.A237.01 1 0.1732 0.930 0.92 0 0.00 0 0.08
#> TCGA.DJ.A2QC.01 1 0.0000 0.964 1.00 0 0.00 0 0.00
#> TCGA.EM.A2CS.06 1 0.0000 0.964 1.00 0 0.00 0 0.00
#> TCGA.H2.A26U.01 3 0.0000 0.992 0.00 0 1.00 0 0.00
#> TCGA.BJ.A28Z.01 3 0.0000 0.992 0.00 0 1.00 0 0.00
#> TCGA.ET.A25J.01 1 0.0000 0.964 1.00 0 0.00 0 0.00
#> TCGA.FY.A3NN.01 1 0.0000 0.964 1.00 0 0.00 0 0.00
#> TCGA.EL.A3H3.01 5 0.0000 0.929 0.00 0 0.00 0 1.00
#> TCGA.BJ.A0Z3.01 3 0.0000 0.992 0.00 0 1.00 0 0.00
#> TCGA.BJ.A28X.01 3 0.0000 0.992 0.00 0 1.00 0 0.00
#> TCGA.EL.A3CT.01 3 0.0000 0.992 0.00 0 1.00 0 0.00
#> TCGA.J8.A3YG.01 5 0.0000 0.929 0.00 0 0.00 0 1.00
#> TCGA.EM.A3SZ.01 5 0.1410 0.892 0.00 0 0.06 0 0.94
#> TCGA.EM.A2P0.01 2 0.0000 1.000 0.00 1 0.00 0 0.00
#> TCGA.E8.A2JQ.01 3 0.0000 0.992 0.00 0 1.00 0 0.00
#> TCGA.DJ.A3UW.01 3 0.0000 0.992 0.00 0 1.00 0 0.00
#> TCGA.DJ.A3V3.01 5 0.0000 0.929 0.00 0 0.00 0 1.00
#> TCGA.EL.A3GP.01 4 0.0000 1.000 0.00 0 0.00 1 0.00
#> TCGA.BJ.A191.01 1 0.1043 0.951 0.96 0 0.00 0 0.04
#> TCGA.EM.A2P1.01 4 0.0000 1.000 0.00 0 0.00 1 0.00
#> TCGA.IM.A3EB.01 3 0.0000 0.992 0.00 0 1.00 0 0.00
#> TCGA.EM.A3AK.01 1 0.1410 0.941 0.94 0 0.00 0 0.06
#> TCGA.EM.A3AO.01 2 0.0000 1.000 0.00 1 0.00 0 0.00
#> TCGA.EM.A2P1.06 4 0.0000 1.000 0.00 0 0.00 1 0.00
#> TCGA.EM.A1CS.01 1 0.0000 0.964 1.00 0 0.00 0 0.00
#> TCGA.EL.A3GQ.01 1 0.0000 0.964 1.00 0 0.00 0 0.00
#> TCGA.DJ.A3V4.01 1 0.2020 0.916 0.90 0 0.00 0 0.10
#> TCGA.DJ.A3V2.01 3 0.2516 0.832 0.00 0 0.86 0 0.14
#> TCGA.BJ.A290.01 2 0.0000 1.000 0.00 1 0.00 0 0.00
#> TCGA.EM.A3SU.01 5 0.0000 0.929 0.00 0 0.00 0 1.00
#> TCGA.EL.A3GR.01 1 0.2020 0.916 0.90 0 0.00 0 0.10
#> TCGA.EM.A3SU.06 3 0.0000 0.992 0.00 0 1.00 0 0.00
#> TCGA.DJ.A3US.01 5 0.1732 0.876 0.00 0 0.08 0 0.92
#> TCGA.EM.A2OZ.01 2 0.0000 1.000 0.00 1 0.00 0 0.00
#> TCGA.E8.A2EA.01 3 0.0000 0.992 0.00 0 1.00 0 0.00
#> TCGA.EM.A1CV.01 1 0.0000 0.964 1.00 0 0.00 0 0.00
#> TCGA.EM.A1CT.01 2 0.0000 1.000 0.00 1 0.00 0 0.00
#> TCGA.ET.A3BS.01 4 0.0000 1.000 0.00 0 0.00 1 0.00
#> TCGA.DJ.A3UU.01 1 0.2020 0.916 0.90 0 0.00 0 0.10
#> TCGA.DJ.A2PO.01 2 0.0000 1.000 0.00 1 0.00 0 0.00
#> TCGA.DJ.A3UQ.01 5 0.0000 0.929 0.00 0 0.00 0 1.00
#> TCGA.EL.A3T0.01 1 0.2020 0.916 0.90 0 0.00 0 0.10
#> TCGA.DJ.A3UX.01 5 0.0000 0.929 0.00 0 0.00 0 1.00
#> TCGA.ET.A3BW.01 1 0.0000 0.964 1.00 0 0.00 0 0.00
#> TCGA.ET.A39S.01 1 0.0000 0.964 1.00 0 0.00 0 0.00
#> TCGA.ET.A3BP.01 1 0.0000 0.964 1.00 0 0.00 0 0.00
#> TCGA.EL.A3D4.01 2 0.0000 1.000 0.00 1 0.00 0 0.00
#> TCGA.FE.A232.01 1 0.1043 0.951 0.96 0 0.00 0 0.04
#> TCGA.DJ.A3UR.01 1 0.0000 0.964 1.00 0 0.00 0 0.00
#> TCGA.FK.A3S3.01 1 0.0000 0.964 1.00 0 0.00 0 0.00
#> TCGA.EL.A3CS.01 5 0.0000 0.929 0.00 0 0.00 0 1.00
#> TCGA.DO.A2HM.01 4 0.0000 1.000 0.00 0 0.00 1 0.00
#> TCGA.FY.A3BL.01 2 0.0000 1.000 0.00 1 0.00 0 0.00
#> TCGA.DJ.A1QF.01 1 0.0000 0.964 1.00 0 0.00 0 0.00
#> TCGA.ET.A3DU.01 3 0.0000 0.992 0.00 0 1.00 0 0.00
#> TCGA.EL.A3T1.01 5 0.1732 0.876 0.00 0 0.08 0 0.92
#> TCGA.FE.A230.01 5 0.0000 0.929 0.00 0 0.00 0 1.00
#> TCGA.ET.A39R.01 5 0.2020 0.858 0.00 0 0.10 0 0.90
#> TCGA.EL.A3CV.01 4 0.0000 1.000 0.00 0 0.00 1 0.00
#> TCGA.EL.A3TA.01 2 0.0000 1.000 0.00 1 0.00 0 0.00
#> TCGA.DJ.A3UY.01 5 0.0000 0.929 0.00 0 0.00 0 1.00
#> TCGA.DJ.A2Q1.01 3 0.0000 0.992 0.00 0 1.00 0 0.00
#> TCGA.EL.A3CU.01 3 0.0000 0.992 0.00 0 1.00 0 0.00
#> TCGA.DJ.A3UV.01 1 0.2020 0.916 0.90 0 0.00 0 0.10
#> TCGA.EL.A3CX.01 1 0.4227 0.348 0.58 0 0.00 0 0.42
#> TCGA.EM.A22P.01 4 0.0000 1.000 0.00 0 0.00 1 0.00
#> TCGA.DJ.A3UK.01 1 0.0000 0.964 1.00 0 0.00 0 0.00
#> TCGA.ET.A3DO.01 3 0.0000 0.992 0.00 0 1.00 0 0.00
#> TCGA.ET.A3BV.01 3 0.0000 0.992 0.00 0 1.00 0 0.00
#> TCGA.BJ.A0Z9.01 3 0.0609 0.972 0.00 0 0.98 0 0.02
#> TCGA.FY.A3R6.01 3 0.0000 0.992 0.00 0 1.00 0 0.00
#> TCGA.BJ.A0Z5.01 2 0.0000 1.000 0.00 1 0.00 0 0.00
#> TCGA.ET.A3DT.01 3 0.0000 0.992 0.00 0 1.00 0 0.00
#> TCGA.ET.A39M.01 4 0.0000 1.000 0.00 0 0.00 1 0.00
#> TCGA.BJ.A0ZJ.01 4 0.0000 1.000 0.00 0 0.00 1 0.00
#> TCGA.ET.A39T.01 1 0.0000 0.964 1.00 0 0.00 0 0.00
#> TCGA.DJ.A2PV.01 1 0.0000 0.964 1.00 0 0.00 0 0.00
#> TCGA.DJ.A13X.01 1 0.0000 0.964 1.00 0 0.00 0 0.00
#> TCGA.EL.A3T6.01 3 0.0000 0.992 0.00 0 1.00 0 0.00
#> TCGA.EM.A3O3.01 3 0.0000 0.992 0.00 0 1.00 0 0.00
#> TCGA.DJ.A13L.01 4 0.0000 1.000 0.00 0 0.00 1 0.00
#> TCGA.DJ.A13U.01 2 0.0000 1.000 0.00 1 0.00 0 0.00
#> TCGA.ET.A2N4.01 1 0.0000 0.964 1.00 0 0.00 0 0.00
#> TCGA.DJ.A13P.01 1 0.0000 0.964 1.00 0 0.00 0 0.00
#> TCGA.EM.A3O7.01 1 0.0000 0.964 1.00 0 0.00 0 0.00
#> TCGA.ET.A3DR.01 1 0.0000 0.964 1.00 0 0.00 0 0.00
#> TCGA.FE.A3PB.01 5 0.1410 0.892 0.00 0 0.06 0 0.94
cbind(get_classes(res, k = 6), get_membership(res, k = 6))
#> class entropy silhouette p1 p2 p3 p4 p5 p6
#> TCGA.E8.A433.01 1 0.0937 0.8960 0.96 0.00 0.00 0 0.04 0.00
#> TCGA.DJ.A3V9.01 1 0.1092 0.9016 0.96 0.00 0.00 0 0.02 0.02
#> TCGA.EL.A3ZN.01 1 0.1556 0.8987 0.92 0.00 0.00 0 0.00 0.08
#> TCGA.EL.A3ZK.01 5 0.0937 0.9244 0.04 0.00 0.00 0 0.96 0.00
#> TCGA.ET.A40R.01 1 0.2941 0.6899 0.78 0.00 0.00 0 0.22 0.00
#> TCGA.DJ.A3VD.01 3 0.0000 0.9572 0.00 0.00 1.00 0 0.00 0.00
#> TCGA.EL.A3ZG.01 2 0.0000 0.9718 0.00 1.00 0.00 0 0.00 0.00
#> TCGA.EM.A4FV.01 1 0.3797 0.2303 0.58 0.00 0.00 0 0.42 0.00
#> TCGA.E8.A413.01 1 0.0937 0.8960 0.96 0.00 0.00 0 0.04 0.00
#> TCGA.IM.A420.01 3 0.3797 0.2543 0.00 0.00 0.58 0 0.42 0.00
#> TCGA.J8.A3O2.01 2 0.1865 0.9651 0.04 0.92 0.00 0 0.04 0.00
#> TCGA.E8.A415.01 1 0.1556 0.8987 0.92 0.00 0.00 0 0.00 0.08
#> TCGA.KS.A4I3.01 2 0.0000 0.9718 0.00 1.00 0.00 0 0.00 0.00
#> TCGA.DJ.A4UT.01 3 0.0000 0.9572 0.00 0.00 1.00 0 0.00 0.00
#> TCGA.EL.A4JW.01 5 0.2048 0.8489 0.12 0.00 0.00 0 0.88 0.00
#> TCGA.E8.A419.01 3 0.0000 0.9572 0.00 0.00 1.00 0 0.00 0.00
#> TCGA.EL.A3ZS.01 3 0.0000 0.9572 0.00 0.00 1.00 0 0.00 0.00
#> TCGA.KS.A4ID.01 3 0.0000 0.9572 0.00 0.00 1.00 0 0.00 0.00
#> TCGA.J8.A3YE.01 6 0.0000 0.8929 0.00 0.00 0.00 0 0.00 1.00
#> TCGA.DJ.A3VF.01 5 0.1556 0.9024 0.00 0.00 0.08 0 0.92 0.00
#> TCGA.E8.A432.01 1 0.0937 0.8960 0.96 0.00 0.00 0 0.04 0.00
#> TCGA.ET.A2MX.01 2 0.0000 0.9718 0.00 1.00 0.00 0 0.00 0.00
#> TCGA.ET.A40S.01 4 0.0000 1.0000 0.00 0.00 0.00 1 0.00 0.00
#> TCGA.DE.A4M8.01 3 0.0000 0.9572 0.00 0.00 1.00 0 0.00 0.00
#> TCGA.EL.A4KD.01 2 0.1865 0.9651 0.04 0.92 0.00 0 0.04 0.00
#> TCGA.FY.A40L.01 1 0.0937 0.8960 0.96 0.00 0.00 0 0.04 0.00
#> TCGA.J8.A42S.01 2 0.0000 0.9718 0.00 1.00 0.00 0 0.00 0.00
#> TCGA.KS.A4IC.01 6 0.3797 0.2668 0.42 0.00 0.00 0 0.00 0.58
#> TCGA.E8.A414.01 5 0.1267 0.9175 0.00 0.00 0.06 0 0.94 0.00
#> TCGA.DE.A4MD.06 4 0.0000 1.0000 0.00 0.00 0.00 1 0.00 0.00
#> TCGA.DJ.A4V4.01 6 0.3797 0.2671 0.42 0.00 0.00 0 0.00 0.58
#> TCGA.FY.A40K.01 1 0.3578 0.5169 0.66 0.00 0.00 0 0.00 0.34
#> TCGA.EM.A4FR.01 2 0.0000 0.9718 0.00 1.00 0.00 0 0.00 0.00
#> TCGA.DJ.A3V8.01 1 0.0937 0.8960 0.96 0.00 0.00 0 0.04 0.00
#> TCGA.J8.A4HY.01 1 0.2631 0.8038 0.82 0.00 0.00 0 0.00 0.18
#> TCGA.FY.A40N.01 6 0.3828 0.1929 0.44 0.00 0.00 0 0.00 0.56
#> TCGA.DJ.A2PX.01 5 0.1092 0.9266 0.02 0.00 0.02 0 0.96 0.00
#> TCGA.EL.A4JX.01 3 0.0000 0.9572 0.00 0.00 1.00 0 0.00 0.00
#> TCGA.DJ.A2Q5.01 4 0.0000 1.0000 0.00 0.00 0.00 1 0.00 0.00
#> TCGA.DJ.A4UP.01 5 0.1267 0.9175 0.00 0.00 0.06 0 0.94 0.00
#> TCGA.E8.A438.01 1 0.0937 0.9057 0.96 0.00 0.00 0 0.00 0.04
#> TCGA.EL.A4KH.01 6 0.0000 0.8929 0.00 0.00 0.00 0 0.00 1.00
#> TCGA.DJ.A4V5.01 4 0.0000 1.0000 0.00 0.00 0.00 1 0.00 0.00
#> TCGA.E8.A44M.01 3 0.0000 0.9572 0.00 0.00 1.00 0 0.00 0.00
#> TCGA.BJ.A45H.01 2 0.1865 0.9651 0.04 0.92 0.00 0 0.04 0.00
#> TCGA.E8.A44K.01 5 0.3797 0.2908 0.42 0.00 0.00 0 0.58 0.00
#> TCGA.CE.A481.01 5 0.0937 0.9244 0.04 0.00 0.00 0 0.96 0.00
#> TCGA.E8.A436.01 1 0.0937 0.8960 0.96 0.00 0.00 0 0.04 0.00
#> TCGA.DJ.A2Q3.01 3 0.0000 0.9572 0.00 0.00 1.00 0 0.00 0.00
#> TCGA.ET.A2N1.01 6 0.0000 0.8929 0.00 0.00 0.00 0 0.00 1.00
#> TCGA.DJ.A2PZ.01 2 0.1092 0.9697 0.02 0.96 0.00 0 0.02 0.00
#> TCGA.IM.A4EB.01 4 0.0000 1.0000 0.00 0.00 0.00 1 0.00 0.00
#> TCGA.EM.A4FO.01 4 0.0000 1.0000 0.00 0.00 0.00 1 0.00 0.00
#> TCGA.BJ.A45I.01 5 0.1556 0.9024 0.00 0.00 0.08 0 0.92 0.00
#> TCGA.EL.A3N3.01 3 0.3864 0.0537 0.00 0.00 0.52 0 0.48 0.00
#> TCGA.DJ.A2PS.01 1 0.0937 0.9057 0.96 0.00 0.00 0 0.00 0.04
#> TCGA.CE.A3MD.01 2 0.1865 0.9651 0.04 0.92 0.00 0 0.04 0.00
#> TCGA.EL.A3CN.01 5 0.1267 0.9175 0.00 0.00 0.06 0 0.94 0.00
#> TCGA.J8.A4HW.06 3 0.0000 0.9572 0.00 0.00 1.00 0 0.00 0.00
#> TCGA.E8.A437.01 1 0.2048 0.8714 0.88 0.00 0.00 0 0.00 0.12
#> TCGA.CE.A483.01 6 0.0000 0.8929 0.00 0.00 0.00 0 0.00 1.00
#> TCGA.CE.A485.01 2 0.1865 0.9651 0.04 0.92 0.00 0 0.04 0.00
#> TCGA.ET.A4KN.01 3 0.0000 0.9572 0.00 0.00 1.00 0 0.00 0.00
#> TCGA.DJ.A4UQ.01 2 0.1865 0.9651 0.04 0.92 0.00 0 0.04 0.00
#> TCGA.DJ.A4UW.01 1 0.2048 0.8714 0.88 0.00 0.00 0 0.00 0.12
#> TCGA.DE.A3KN.01 1 0.1556 0.8987 0.92 0.00 0.00 0 0.00 0.08
#> TCGA.DJ.A2QA.01 6 0.0000 0.8929 0.00 0.00 0.00 0 0.00 1.00
#> TCGA.BJ.A4O9.01 6 0.0000 0.8929 0.00 0.00 0.00 0 0.00 1.00
#> TCGA.CE.A3ME.01 1 0.0937 0.9057 0.96 0.00 0.00 0 0.00 0.04
#> TCGA.E3.A3E1.01 1 0.1267 0.9048 0.94 0.00 0.00 0 0.00 0.06
#> TCGA.DJ.A2Q8.01 1 0.0937 0.8960 0.96 0.00 0.00 0 0.04 0.00
#> TCGA.FE.A23A.01 3 0.0000 0.9572 0.00 0.00 1.00 0 0.00 0.00
#> TCGA.FY.A3I4.01 1 0.1556 0.8987 0.92 0.00 0.00 0 0.00 0.08
#> TCGA.ET.A2N0.01 1 0.0937 0.8960 0.96 0.00 0.00 0 0.04 0.00
#> TCGA.ET.A3DP.01 1 0.1556 0.8987 0.92 0.00 0.00 0 0.00 0.08
#> TCGA.EL.A3GV.01 1 0.1556 0.8987 0.92 0.00 0.00 0 0.00 0.08
#> TCGA.GE.A2C6.01 3 0.0000 0.9572 0.00 0.00 1.00 0 0.00 0.00
#> TCGA.DJ.A2PT.01 3 0.0000 0.9572 0.00 0.00 1.00 0 0.00 0.00
#> TCGA.E8.A242.01 3 0.0000 0.9572 0.00 0.00 1.00 0 0.00 0.00
#> TCGA.J8.A3O1.01 6 0.0000 0.8929 0.00 0.00 0.00 0 0.00 1.00
#> TCGA.EM.A2CR.01 6 0.0000 0.8929 0.00 0.00 0.00 0 0.00 1.00
#> TCGA.FE.A238.01 1 0.1267 0.8821 0.94 0.00 0.00 0 0.06 0.00
#> TCGA.EM.A3FQ.01 5 0.1267 0.9175 0.00 0.00 0.06 0 0.94 0.00
#> TCGA.EM.A22M.01 4 0.0000 1.0000 0.00 0.00 0.00 1 0.00 0.00
#> TCGA.J8.A3NZ.01 1 0.3828 0.2302 0.56 0.00 0.00 0 0.00 0.44
#> TCGA.FE.A236.01 2 0.0547 0.9712 0.00 0.98 0.00 0 0.02 0.00
#> TCGA.BJ.A28R.01 5 0.0937 0.9244 0.04 0.00 0.00 0 0.96 0.00
#> TCGA.EM.A2CU.01 1 0.0937 0.8960 0.96 0.00 0.00 0 0.04 0.00
#> TCGA.FE.A237.01 1 0.1267 0.9048 0.94 0.00 0.00 0 0.00 0.06
#> TCGA.DJ.A2QC.01 6 0.3756 0.3239 0.40 0.00 0.00 0 0.00 0.60
#> TCGA.EM.A2CS.06 1 0.2048 0.8714 0.88 0.00 0.00 0 0.00 0.12
#> TCGA.H2.A26U.01 3 0.0000 0.9572 0.00 0.00 1.00 0 0.00 0.00
#> TCGA.BJ.A28Z.01 3 0.0000 0.9572 0.00 0.00 1.00 0 0.00 0.00
#> TCGA.ET.A25J.01 6 0.2631 0.7242 0.18 0.00 0.00 0 0.00 0.82
#> TCGA.FY.A3NN.01 6 0.0000 0.8929 0.00 0.00 0.00 0 0.00 1.00
#> TCGA.EL.A3H3.01 5 0.0937 0.9244 0.04 0.00 0.00 0 0.96 0.00
#> TCGA.BJ.A0Z3.01 3 0.0000 0.9572 0.00 0.00 1.00 0 0.00 0.00
#> TCGA.BJ.A28X.01 3 0.0000 0.9572 0.00 0.00 1.00 0 0.00 0.00
#> TCGA.EL.A3CT.01 3 0.0000 0.9572 0.00 0.00 1.00 0 0.00 0.00
#> TCGA.J8.A3YG.01 5 0.0937 0.9244 0.04 0.00 0.00 0 0.96 0.00
#> TCGA.EM.A3SZ.01 5 0.1092 0.9266 0.02 0.00 0.02 0 0.96 0.00
#> TCGA.EM.A2P0.01 2 0.0000 0.9718 0.00 1.00 0.00 0 0.00 0.00
#> TCGA.E8.A2JQ.01 3 0.0000 0.9572 0.00 0.00 1.00 0 0.00 0.00
#> TCGA.DJ.A3UW.01 3 0.0000 0.9572 0.00 0.00 1.00 0 0.00 0.00
#> TCGA.DJ.A3V3.01 5 0.0937 0.9244 0.04 0.00 0.00 0 0.96 0.00
#> TCGA.EL.A3GP.01 4 0.0000 1.0000 0.00 0.00 0.00 1 0.00 0.00
#> TCGA.BJ.A191.01 1 0.2260 0.8521 0.86 0.00 0.00 0 0.00 0.14
#> TCGA.EM.A2P1.01 4 0.0000 1.0000 0.00 0.00 0.00 1 0.00 0.00
#> TCGA.IM.A3EB.01 5 0.1556 0.9024 0.00 0.00 0.08 0 0.92 0.00
#> TCGA.EM.A3AK.01 1 0.1556 0.8987 0.92 0.00 0.00 0 0.00 0.08
#> TCGA.EM.A3AO.01 2 0.1865 0.9651 0.04 0.92 0.00 0 0.04 0.00
#> TCGA.EM.A2P1.06 4 0.0000 1.0000 0.00 0.00 0.00 1 0.00 0.00
#> TCGA.EM.A1CS.01 6 0.0000 0.8929 0.00 0.00 0.00 0 0.00 1.00
#> TCGA.EL.A3GQ.01 6 0.0000 0.8929 0.00 0.00 0.00 0 0.00 1.00
#> TCGA.DJ.A3V4.01 1 0.1267 0.9048 0.94 0.00 0.00 0 0.00 0.06
#> TCGA.DJ.A3V2.01 5 0.1556 0.9024 0.00 0.00 0.08 0 0.92 0.00
#> TCGA.BJ.A290.01 2 0.0000 0.9718 0.00 1.00 0.00 0 0.00 0.00
#> TCGA.EM.A3SU.01 5 0.0937 0.9244 0.04 0.00 0.00 0 0.96 0.00
#> TCGA.EL.A3GR.01 1 0.0937 0.9057 0.96 0.00 0.00 0 0.00 0.04
#> TCGA.EM.A3SU.06 3 0.0000 0.9572 0.00 0.00 1.00 0 0.00 0.00
#> TCGA.DJ.A3US.01 5 0.0937 0.9248 0.00 0.00 0.04 0 0.96 0.00
#> TCGA.EM.A2OZ.01 2 0.0000 0.9718 0.00 1.00 0.00 0 0.00 0.00
#> TCGA.E8.A2EA.01 3 0.3828 0.1915 0.00 0.00 0.56 0 0.44 0.00
#> TCGA.EM.A1CV.01 6 0.0000 0.8929 0.00 0.00 0.00 0 0.00 1.00
#> TCGA.EM.A1CT.01 2 0.0000 0.9718 0.00 1.00 0.00 0 0.00 0.00
#> TCGA.ET.A3BS.01 4 0.0000 1.0000 0.00 0.00 0.00 1 0.00 0.00
#> TCGA.DJ.A3UU.01 1 0.1267 0.9048 0.94 0.00 0.00 0 0.00 0.06
#> TCGA.DJ.A2PO.01 2 0.1865 0.9651 0.04 0.92 0.00 0 0.04 0.00
#> TCGA.DJ.A3UQ.01 5 0.0937 0.9244 0.04 0.00 0.00 0 0.96 0.00
#> TCGA.EL.A3T0.01 1 0.0937 0.9057 0.96 0.00 0.00 0 0.00 0.04
#> TCGA.DJ.A3UX.01 1 0.0937 0.8960 0.96 0.00 0.00 0 0.04 0.00
#> TCGA.ET.A3BW.01 6 0.0000 0.8929 0.00 0.00 0.00 0 0.00 1.00
#> TCGA.ET.A39S.01 6 0.3756 0.3246 0.40 0.00 0.00 0 0.00 0.60
#> TCGA.ET.A3BP.01 6 0.0000 0.8929 0.00 0.00 0.00 0 0.00 1.00
#> TCGA.EL.A3D4.01 2 0.1865 0.9651 0.04 0.92 0.00 0 0.04 0.00
#> TCGA.FE.A232.01 1 0.1556 0.8987 0.92 0.00 0.00 0 0.00 0.08
#> TCGA.DJ.A3UR.01 6 0.0000 0.8929 0.00 0.00 0.00 0 0.00 1.00
#> TCGA.FK.A3S3.01 1 0.3828 0.2344 0.56 0.00 0.00 0 0.00 0.44
#> TCGA.EL.A3CS.01 1 0.0937 0.8960 0.96 0.00 0.00 0 0.04 0.00
#> TCGA.DO.A2HM.01 4 0.0000 1.0000 0.00 0.00 0.00 1 0.00 0.00
#> TCGA.FY.A3BL.01 2 0.0000 0.9718 0.00 1.00 0.00 0 0.00 0.00
#> TCGA.DJ.A1QF.01 6 0.0000 0.8929 0.00 0.00 0.00 0 0.00 1.00
#> TCGA.ET.A3DU.01 3 0.0000 0.9572 0.00 0.00 1.00 0 0.00 0.00
#> TCGA.EL.A3T1.01 5 0.0937 0.9248 0.00 0.00 0.04 0 0.96 0.00
#> TCGA.FE.A230.01 5 0.0937 0.9244 0.04 0.00 0.00 0 0.96 0.00
#> TCGA.ET.A39R.01 5 0.0937 0.9248 0.00 0.00 0.04 0 0.96 0.00
#> TCGA.EL.A3CV.01 4 0.0000 1.0000 0.00 0.00 0.00 1 0.00 0.00
#> TCGA.EL.A3TA.01 2 0.1865 0.9651 0.04 0.92 0.00 0 0.04 0.00
#> TCGA.DJ.A3UY.01 1 0.0937 0.8960 0.96 0.00 0.00 0 0.04 0.00
#> TCGA.DJ.A2Q1.01 3 0.0000 0.9572 0.00 0.00 1.00 0 0.00 0.00
#> TCGA.EL.A3CU.01 3 0.0000 0.9572 0.00 0.00 1.00 0 0.00 0.00
#> TCGA.DJ.A3UV.01 1 0.1267 0.9048 0.94 0.00 0.00 0 0.00 0.06
#> TCGA.EL.A3CX.01 1 0.0937 0.8960 0.96 0.00 0.00 0 0.04 0.00
#> TCGA.EM.A22P.01 4 0.0000 1.0000 0.00 0.00 0.00 1 0.00 0.00
#> TCGA.DJ.A3UK.01 6 0.0000 0.8929 0.00 0.00 0.00 0 0.00 1.00
#> TCGA.ET.A3DO.01 3 0.0000 0.9572 0.00 0.00 1.00 0 0.00 0.00
#> TCGA.ET.A3BV.01 3 0.0000 0.9572 0.00 0.00 1.00 0 0.00 0.00
#> TCGA.BJ.A0Z9.01 5 0.3309 0.6181 0.00 0.00 0.28 0 0.72 0.00
#> TCGA.FY.A3R6.01 3 0.0000 0.9572 0.00 0.00 1.00 0 0.00 0.00
#> TCGA.BJ.A0Z5.01 2 0.0000 0.9718 0.00 1.00 0.00 0 0.00 0.00
#> TCGA.ET.A3DT.01 3 0.0000 0.9572 0.00 0.00 1.00 0 0.00 0.00
#> TCGA.ET.A39M.01 4 0.0000 1.0000 0.00 0.00 0.00 1 0.00 0.00
#> TCGA.BJ.A0ZJ.01 4 0.0000 1.0000 0.00 0.00 0.00 1 0.00 0.00
#> TCGA.ET.A39T.01 6 0.0000 0.8929 0.00 0.00 0.00 0 0.00 1.00
#> TCGA.DJ.A2PV.01 1 0.2048 0.8714 0.88 0.00 0.00 0 0.00 0.12
#> TCGA.DJ.A13X.01 6 0.0000 0.8929 0.00 0.00 0.00 0 0.00 1.00
#> TCGA.EL.A3T6.01 3 0.0000 0.9572 0.00 0.00 1.00 0 0.00 0.00
#> TCGA.EM.A3O3.01 3 0.0000 0.9572 0.00 0.00 1.00 0 0.00 0.00
#> TCGA.DJ.A13L.01 4 0.0000 1.0000 0.00 0.00 0.00 1 0.00 0.00
#> TCGA.DJ.A13U.01 2 0.0000 0.9718 0.00 1.00 0.00 0 0.00 0.00
#> TCGA.ET.A2N4.01 6 0.0000 0.8929 0.00 0.00 0.00 0 0.00 1.00
#> TCGA.DJ.A13P.01 6 0.0000 0.8929 0.00 0.00 0.00 0 0.00 1.00
#> TCGA.EM.A3O7.01 6 0.0000 0.8929 0.00 0.00 0.00 0 0.00 1.00
#> TCGA.ET.A3DR.01 1 0.1814 0.8863 0.90 0.00 0.00 0 0.00 0.10
#> TCGA.FE.A3PB.01 5 0.0937 0.9244 0.04 0.00 0.00 0 0.96 0.00
cbind(get_classes(res, k = 7), get_membership(res, k = 7))
#> class entropy silhouette p1 p2 p3 p4 p5 p6 p7
#> TCGA.E8.A433.01 1 0.0504 0.7475 0.98 0.00 0.00 0.00 0.00 0.00 0.02
#> TCGA.DJ.A3V9.01 1 0.3047 0.8275 0.72 0.00 0.00 0.00 0.00 0.00 0.28
#> TCGA.EL.A3ZN.01 1 0.3047 0.8275 0.72 0.00 0.00 0.00 0.00 0.00 0.28
#> TCGA.EL.A3ZK.01 5 0.1928 0.8477 0.08 0.00 0.00 0.00 0.90 0.00 0.02
#> TCGA.ET.A40R.01 1 0.1363 0.7006 0.94 0.00 0.00 0.00 0.04 0.00 0.02
#> TCGA.DJ.A3VD.01 3 0.0000 0.9752 0.00 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.EL.A3ZG.01 2 0.0000 0.7133 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.EM.A4FV.01 1 0.3307 0.3805 0.74 0.00 0.00 0.00 0.24 0.00 0.02
#> TCGA.E8.A413.01 1 0.0504 0.7290 0.98 0.00 0.00 0.00 0.00 0.00 0.02
#> TCGA.IM.A420.01 5 0.3413 0.3691 0.00 0.00 0.38 0.00 0.62 0.00 0.00
#> TCGA.J8.A3O2.01 7 0.3558 1.0000 0.00 0.48 0.00 0.00 0.00 0.00 0.52
#> TCGA.E8.A415.01 1 0.3047 0.8275 0.72 0.00 0.00 0.00 0.00 0.00 0.28
#> TCGA.KS.A4I3.01 2 0.0504 0.7093 0.00 0.98 0.00 0.00 0.00 0.00 0.02
#> TCGA.DJ.A4UT.01 3 0.1166 0.9538 0.00 0.00 0.94 0.00 0.06 0.00 0.00
#> TCGA.EL.A4JW.01 5 0.3968 0.4487 0.44 0.00 0.00 0.00 0.54 0.00 0.02
#> TCGA.E8.A419.01 3 0.0000 0.9752 0.00 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.EL.A3ZS.01 3 0.2081 0.8677 0.00 0.00 0.86 0.00 0.14 0.00 0.00
#> TCGA.KS.A4ID.01 3 0.1166 0.9538 0.00 0.00 0.94 0.00 0.06 0.00 0.00
#> TCGA.J8.A3YE.01 6 0.1671 0.7678 0.00 0.00 0.00 0.00 0.00 0.90 0.10
#> TCGA.DJ.A3VF.01 5 0.0000 0.8867 0.00 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.E8.A432.01 1 0.3047 0.8275 0.72 0.00 0.00 0.00 0.00 0.00 0.28
#> TCGA.ET.A2MX.01 2 0.0863 0.6778 0.00 0.96 0.00 0.00 0.00 0.00 0.04
#> TCGA.ET.A40S.01 4 0.1886 0.9132 0.00 0.00 0.00 0.88 0.00 0.00 0.12
#> TCGA.DE.A4M8.01 3 0.0000 0.9752 0.00 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.EL.A4KD.01 2 0.3294 -0.1666 0.00 0.66 0.00 0.00 0.00 0.00 0.34
#> TCGA.FY.A40L.01 1 0.0504 0.7290 0.98 0.00 0.00 0.00 0.00 0.00 0.02
#> TCGA.J8.A42S.01 2 0.0000 0.7133 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.KS.A4IC.01 6 0.5467 0.1454 0.26 0.00 0.00 0.00 0.00 0.46 0.28
#> TCGA.E8.A414.01 5 0.0000 0.8867 0.00 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.DE.A4MD.06 4 0.0000 0.9666 0.00 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.DJ.A4V4.01 6 0.5007 0.3905 0.16 0.00 0.00 0.00 0.00 0.56 0.28
#> TCGA.FY.A40K.01 6 0.5589 -0.0782 0.32 0.00 0.00 0.00 0.00 0.40 0.28
#> TCGA.EM.A4FR.01 2 0.0000 0.7133 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.DJ.A3V8.01 1 0.0000 0.7387 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.J8.A4HY.01 1 0.5520 0.4277 0.44 0.00 0.00 0.00 0.00 0.28 0.28
#> TCGA.FY.A40N.01 6 0.4970 0.4208 0.18 0.00 0.00 0.00 0.00 0.58 0.24
#> TCGA.DJ.A2PX.01 5 0.0000 0.8867 0.00 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.EL.A4JX.01 3 0.0000 0.9752 0.00 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.DJ.A2Q5.01 4 0.0000 0.9666 0.00 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.DJ.A4UP.01 5 0.0000 0.8867 0.00 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.E8.A438.01 1 0.3047 0.8275 0.72 0.00 0.00 0.00 0.00 0.00 0.28
#> TCGA.EL.A4KH.01 6 0.0000 0.8126 0.00 0.00 0.00 0.00 0.00 1.00 0.00
#> TCGA.DJ.A4V5.01 4 0.2259 0.8813 0.00 0.00 0.00 0.84 0.00 0.00 0.16
#> TCGA.E8.A44M.01 3 0.0000 0.9752 0.00 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.BJ.A45H.01 2 0.3358 -0.2771 0.00 0.64 0.00 0.00 0.00 0.00 0.36
#> TCGA.E8.A44K.01 1 0.3755 0.1072 0.64 0.00 0.00 0.00 0.34 0.00 0.02
#> TCGA.CE.A481.01 5 0.1363 0.8663 0.04 0.00 0.00 0.00 0.94 0.00 0.02
#> TCGA.E8.A436.01 1 0.0504 0.7290 0.98 0.00 0.00 0.00 0.00 0.00 0.02
#> TCGA.DJ.A2Q3.01 3 0.1166 0.9538 0.00 0.00 0.94 0.00 0.06 0.00 0.00
#> TCGA.ET.A2N1.01 6 0.0504 0.8047 0.00 0.00 0.00 0.00 0.00 0.98 0.02
#> TCGA.DJ.A2PZ.01 2 0.2945 0.2216 0.00 0.74 0.00 0.00 0.00 0.00 0.26
#> TCGA.IM.A4EB.01 4 0.1433 0.9345 0.00 0.00 0.00 0.92 0.00 0.00 0.08
#> TCGA.EM.A4FO.01 4 0.0000 0.9666 0.00 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.BJ.A45I.01 5 0.0000 0.8867 0.00 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.EL.A3N3.01 5 0.3221 0.5074 0.00 0.00 0.32 0.00 0.68 0.00 0.00
#> TCGA.DJ.A2PS.01 1 0.3047 0.8275 0.72 0.00 0.00 0.00 0.00 0.00 0.28
#> TCGA.CE.A3MD.01 2 0.3294 -0.1666 0.00 0.66 0.00 0.00 0.00 0.00 0.34
#> TCGA.EL.A3CN.01 5 0.0000 0.8867 0.00 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.J8.A4HW.06 3 0.0000 0.9752 0.00 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.E8.A437.01 1 0.5233 0.5965 0.52 0.00 0.00 0.00 0.00 0.20 0.28
#> TCGA.CE.A483.01 6 0.0000 0.8126 0.00 0.00 0.00 0.00 0.00 1.00 0.00
#> TCGA.CE.A485.01 7 0.3558 1.0000 0.00 0.48 0.00 0.00 0.00 0.00 0.52
#> TCGA.ET.A4KN.01 3 0.0000 0.9752 0.00 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.DJ.A4UQ.01 2 0.3358 -0.2771 0.00 0.64 0.00 0.00 0.00 0.00 0.36
#> TCGA.DJ.A4UW.01 1 0.4714 0.7198 0.60 0.00 0.00 0.00 0.00 0.12 0.28
#> TCGA.DE.A3KN.01 1 0.3047 0.8275 0.72 0.00 0.00 0.00 0.00 0.00 0.28
#> TCGA.DJ.A2QA.01 6 0.0000 0.8126 0.00 0.00 0.00 0.00 0.00 1.00 0.00
#> TCGA.BJ.A4O9.01 6 0.1886 0.7538 0.00 0.00 0.00 0.00 0.00 0.88 0.12
#> TCGA.CE.A3ME.01 1 0.2081 0.6750 0.86 0.00 0.00 0.00 0.00 0.00 0.14
#> TCGA.E3.A3E1.01 1 0.3047 0.8275 0.72 0.00 0.00 0.00 0.00 0.00 0.28
#> TCGA.DJ.A2Q8.01 1 0.2945 0.8250 0.74 0.00 0.00 0.00 0.00 0.00 0.26
#> TCGA.FE.A23A.01 3 0.1166 0.9538 0.00 0.00 0.94 0.00 0.06 0.00 0.00
#> TCGA.FY.A3I4.01 1 0.3047 0.8275 0.72 0.00 0.00 0.00 0.00 0.00 0.28
#> TCGA.ET.A2N0.01 1 0.0504 0.7290 0.98 0.00 0.00 0.00 0.00 0.00 0.02
#> TCGA.ET.A3DP.01 1 0.3047 0.8275 0.72 0.00 0.00 0.00 0.00 0.00 0.28
#> TCGA.EL.A3GV.01 1 0.3047 0.8275 0.72 0.00 0.00 0.00 0.00 0.00 0.28
#> TCGA.GE.A2C6.01 3 0.1166 0.9538 0.00 0.00 0.94 0.00 0.06 0.00 0.00
#> TCGA.DJ.A2PT.01 3 0.0504 0.9703 0.00 0.00 0.98 0.00 0.02 0.00 0.00
#> TCGA.E8.A242.01 3 0.0000 0.9752 0.00 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.J8.A3O1.01 6 0.1433 0.7788 0.00 0.00 0.00 0.00 0.00 0.92 0.08
#> TCGA.EM.A2CR.01 6 0.0000 0.8126 0.00 0.00 0.00 0.00 0.00 1.00 0.00
#> TCGA.FE.A238.01 1 0.1363 0.6965 0.94 0.00 0.00 0.00 0.04 0.00 0.02
#> TCGA.EM.A3FQ.01 5 0.0000 0.8867 0.00 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.EM.A22M.01 4 0.0000 0.9666 0.00 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.J8.A3NZ.01 6 0.5606 -0.1466 0.34 0.00 0.00 0.00 0.00 0.38 0.28
#> TCGA.FE.A236.01 2 0.1886 0.6029 0.00 0.88 0.00 0.00 0.00 0.00 0.12
#> TCGA.BJ.A28R.01 5 0.3517 0.6673 0.28 0.00 0.00 0.00 0.70 0.00 0.02
#> TCGA.EM.A2CU.01 1 0.0504 0.7290 0.98 0.00 0.00 0.00 0.00 0.00 0.02
#> TCGA.FE.A237.01 1 0.3047 0.8275 0.72 0.00 0.00 0.00 0.00 0.00 0.28
#> TCGA.DJ.A2QC.01 6 0.4870 0.4295 0.14 0.00 0.00 0.00 0.00 0.58 0.28
#> TCGA.EM.A2CS.06 1 0.4714 0.7198 0.60 0.00 0.00 0.00 0.00 0.12 0.28
#> TCGA.H2.A26U.01 3 0.0000 0.9752 0.00 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.BJ.A28Z.01 3 0.0000 0.9752 0.00 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.ET.A25J.01 6 0.3770 0.6665 0.08 0.00 0.00 0.00 0.00 0.74 0.18
#> TCGA.FY.A3NN.01 6 0.0000 0.8126 0.00 0.00 0.00 0.00 0.00 1.00 0.00
#> TCGA.EL.A3H3.01 5 0.1363 0.8663 0.04 0.00 0.00 0.00 0.94 0.00 0.02
#> TCGA.BJ.A0Z3.01 3 0.1166 0.9538 0.00 0.00 0.94 0.00 0.06 0.00 0.00
#> TCGA.BJ.A28X.01 3 0.0000 0.9752 0.00 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.EL.A3CT.01 3 0.1166 0.9538 0.00 0.00 0.94 0.00 0.06 0.00 0.00
#> TCGA.J8.A3YG.01 5 0.2745 0.7882 0.16 0.00 0.00 0.00 0.82 0.00 0.02
#> TCGA.EM.A3SZ.01 5 0.0000 0.8867 0.00 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.EM.A2P0.01 2 0.0000 0.7133 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.E8.A2JQ.01 3 0.0000 0.9752 0.00 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.DJ.A3UW.01 3 0.0000 0.9752 0.00 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.DJ.A3V3.01 5 0.1363 0.8663 0.04 0.00 0.00 0.00 0.94 0.00 0.02
#> TCGA.EL.A3GP.01 4 0.0000 0.9666 0.00 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.BJ.A191.01 1 0.5007 0.6705 0.56 0.00 0.00 0.00 0.00 0.16 0.28
#> TCGA.EM.A2P1.01 4 0.0000 0.9666 0.00 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.IM.A3EB.01 5 0.0000 0.8867 0.00 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.EM.A3AK.01 1 0.3047 0.8275 0.72 0.00 0.00 0.00 0.00 0.00 0.28
#> TCGA.EM.A3AO.01 7 0.3558 1.0000 0.00 0.48 0.00 0.00 0.00 0.00 0.52
#> TCGA.EM.A2P1.06 4 0.0000 0.9666 0.00 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.EM.A1CS.01 6 0.0000 0.8126 0.00 0.00 0.00 0.00 0.00 1.00 0.00
#> TCGA.EL.A3GQ.01 6 0.0000 0.8126 0.00 0.00 0.00 0.00 0.00 1.00 0.00
#> TCGA.DJ.A3V4.01 1 0.3047 0.8275 0.72 0.00 0.00 0.00 0.00 0.00 0.28
#> TCGA.DJ.A3V2.01 5 0.0000 0.8867 0.00 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.BJ.A290.01 2 0.0504 0.7083 0.00 0.98 0.00 0.00 0.00 0.00 0.02
#> TCGA.EM.A3SU.01 5 0.1006 0.8741 0.02 0.00 0.00 0.00 0.96 0.00 0.02
#> TCGA.EL.A3GR.01 1 0.3047 0.8275 0.72 0.00 0.00 0.00 0.00 0.00 0.28
#> TCGA.EM.A3SU.06 3 0.0000 0.9752 0.00 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.DJ.A3US.01 5 0.0000 0.8867 0.00 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.EM.A2OZ.01 2 0.0504 0.7093 0.00 0.98 0.00 0.00 0.00 0.00 0.02
#> TCGA.E8.A2EA.01 5 0.3358 0.4225 0.00 0.00 0.36 0.00 0.64 0.00 0.00
#> TCGA.EM.A1CV.01 6 0.0000 0.8126 0.00 0.00 0.00 0.00 0.00 1.00 0.00
#> TCGA.EM.A1CT.01 2 0.1886 0.6029 0.00 0.88 0.00 0.00 0.00 0.00 0.12
#> TCGA.ET.A3BS.01 4 0.1886 0.9132 0.00 0.00 0.00 0.88 0.00 0.00 0.12
#> TCGA.DJ.A3UU.01 1 0.3047 0.8275 0.72 0.00 0.00 0.00 0.00 0.00 0.28
#> TCGA.DJ.A2PO.01 7 0.3558 1.0000 0.00 0.48 0.00 0.00 0.00 0.00 0.52
#> TCGA.DJ.A3UQ.01 5 0.1928 0.8473 0.08 0.00 0.00 0.00 0.90 0.00 0.02
#> TCGA.EL.A3T0.01 1 0.3047 0.8275 0.72 0.00 0.00 0.00 0.00 0.00 0.28
#> TCGA.DJ.A3UX.01 1 0.0504 0.7480 0.98 0.00 0.00 0.00 0.00 0.00 0.02
#> TCGA.ET.A3BW.01 6 0.0000 0.8126 0.00 0.00 0.00 0.00 0.00 1.00 0.00
#> TCGA.ET.A39S.01 6 0.5128 0.3479 0.18 0.00 0.00 0.00 0.00 0.54 0.28
#> TCGA.ET.A3BP.01 6 0.0000 0.8126 0.00 0.00 0.00 0.00 0.00 1.00 0.00
#> TCGA.EL.A3D4.01 2 0.3294 -0.1666 0.00 0.66 0.00 0.00 0.00 0.00 0.34
#> TCGA.FE.A232.01 1 0.2945 0.8172 0.74 0.00 0.00 0.00 0.00 0.00 0.26
#> TCGA.DJ.A3UR.01 6 0.0000 0.8126 0.00 0.00 0.00 0.00 0.00 1.00 0.00
#> TCGA.FK.A3S3.01 6 0.5402 0.1877 0.24 0.00 0.00 0.00 0.00 0.48 0.28
#> TCGA.EL.A3CS.01 1 0.2081 0.6386 0.86 0.00 0.00 0.00 0.00 0.00 0.14
#> TCGA.DO.A2HM.01 4 0.0000 0.9666 0.00 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.FY.A3BL.01 2 0.0863 0.6782 0.00 0.96 0.00 0.00 0.00 0.00 0.04
#> TCGA.DJ.A1QF.01 6 0.1166 0.7882 0.00 0.00 0.00 0.00 0.00 0.94 0.06
#> TCGA.ET.A3DU.01 3 0.0000 0.9752 0.00 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.EL.A3T1.01 5 0.0000 0.8867 0.00 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.FE.A230.01 5 0.2376 0.8207 0.12 0.00 0.00 0.00 0.86 0.00 0.02
#> TCGA.ET.A39R.01 5 0.0000 0.8867 0.00 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.EL.A3CV.01 4 0.0000 0.9666 0.00 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.EL.A3TA.01 7 0.3558 1.0000 0.00 0.48 0.00 0.00 0.00 0.00 0.52
#> TCGA.DJ.A3UY.01 1 0.0504 0.7290 0.98 0.00 0.00 0.00 0.00 0.00 0.02
#> TCGA.DJ.A2Q1.01 3 0.0504 0.9703 0.00 0.00 0.98 0.00 0.02 0.00 0.00
#> TCGA.EL.A3CU.01 3 0.1166 0.9538 0.00 0.00 0.94 0.00 0.06 0.00 0.00
#> TCGA.DJ.A3UV.01 1 0.3047 0.8275 0.72 0.00 0.00 0.00 0.00 0.00 0.28
#> TCGA.EL.A3CX.01 1 0.2832 0.8212 0.76 0.00 0.00 0.00 0.00 0.00 0.24
#> TCGA.EM.A22P.01 4 0.0000 0.9666 0.00 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.DJ.A3UK.01 6 0.0000 0.8126 0.00 0.00 0.00 0.00 0.00 1.00 0.00
#> TCGA.ET.A3DO.01 3 0.0000 0.9752 0.00 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.ET.A3BV.01 3 0.0504 0.9703 0.00 0.00 0.98 0.00 0.02 0.00 0.00
#> TCGA.BJ.A0Z9.01 5 0.1671 0.8063 0.00 0.00 0.10 0.00 0.90 0.00 0.00
#> TCGA.FY.A3R6.01 3 0.0000 0.9752 0.00 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.BJ.A0Z5.01 2 0.0863 0.6782 0.00 0.96 0.00 0.00 0.00 0.00 0.04
#> TCGA.ET.A3DT.01 3 0.0000 0.9752 0.00 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.ET.A39M.01 4 0.0504 0.9601 0.00 0.00 0.00 0.98 0.00 0.00 0.02
#> TCGA.BJ.A0ZJ.01 4 0.1886 0.9132 0.00 0.00 0.00 0.88 0.00 0.00 0.12
#> TCGA.ET.A39T.01 6 0.0000 0.8126 0.00 0.00 0.00 0.00 0.00 1.00 0.00
#> TCGA.DJ.A2PV.01 1 0.4714 0.7198 0.60 0.00 0.00 0.00 0.00 0.12 0.28
#> TCGA.DJ.A13X.01 6 0.0000 0.8126 0.00 0.00 0.00 0.00 0.00 1.00 0.00
#> TCGA.EL.A3T6.01 3 0.1166 0.9538 0.00 0.00 0.94 0.00 0.06 0.00 0.00
#> TCGA.EM.A3O3.01 3 0.0000 0.9752 0.00 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.DJ.A13L.01 4 0.0000 0.9666 0.00 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.DJ.A13U.01 2 0.0000 0.7133 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.ET.A2N4.01 6 0.0000 0.8126 0.00 0.00 0.00 0.00 0.00 1.00 0.00
#> TCGA.DJ.A13P.01 6 0.0000 0.8126 0.00 0.00 0.00 0.00 0.00 1.00 0.00
#> TCGA.EM.A3O7.01 6 0.0000 0.8126 0.00 0.00 0.00 0.00 0.00 1.00 0.00
#> TCGA.ET.A3DR.01 1 0.4338 0.7632 0.64 0.00 0.00 0.00 0.00 0.08 0.28
#> TCGA.FE.A3PB.01 5 0.0000 0.8867 0.00 0.00 0.00 0.00 1.00 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.E8.A433.01 1 0.1947 0.3624 0.86 0.00 0.00 0.00 0.00 0.00 0.00 0.14
#> TCGA.DJ.A3V9.01 1 0.3299 0.2679 0.56 0.00 0.00 0.00 0.00 0.00 0.00 0.44
#> TCGA.EL.A3ZN.01 1 0.3299 0.2679 0.56 0.00 0.00 0.00 0.00 0.00 0.00 0.44
#> TCGA.EL.A3ZK.01 5 0.2534 0.7536 0.22 0.00 0.00 0.00 0.78 0.00 0.00 0.00
#> TCGA.ET.A40R.01 1 0.1887 0.3526 0.90 0.00 0.00 0.00 0.06 0.00 0.00 0.04
#> TCGA.DJ.A3VD.01 3 0.0000 0.9532 0.00 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.EL.A3ZG.01 2 0.3329 -0.8826 0.00 0.52 0.00 0.00 0.00 0.00 0.48 0.00
#> TCGA.EM.A4FV.01 1 0.2650 0.2322 0.76 0.00 0.00 0.00 0.24 0.00 0.00 0.00
#> TCGA.E8.A413.01 1 0.0808 0.3793 0.96 0.00 0.00 0.00 0.00 0.00 0.00 0.04
#> TCGA.IM.A420.01 5 0.3318 0.0235 0.00 0.00 0.46 0.00 0.54 0.00 0.00 0.00
#> TCGA.J8.A3O2.01 2 0.3193 0.3258 0.00 0.62 0.00 0.00 0.00 0.00 0.38 0.00
#> TCGA.E8.A415.01 1 0.3299 0.2679 0.56 0.00 0.00 0.00 0.00 0.00 0.00 0.44
#> TCGA.KS.A4I3.01 2 0.3237 -0.6781 0.00 0.60 0.00 0.00 0.00 0.00 0.40 0.00
#> TCGA.DJ.A4UT.01 3 0.1947 0.8800 0.00 0.00 0.86 0.00 0.14 0.00 0.00 0.00
#> TCGA.EL.A4JW.01 1 0.3333 -0.4961 0.50 0.00 0.00 0.00 0.50 0.00 0.00 0.00
#> TCGA.E8.A419.01 3 0.0000 0.9532 0.00 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.EL.A3ZS.01 3 0.2650 0.7522 0.00 0.00 0.76 0.00 0.24 0.00 0.00 0.00
#> TCGA.KS.A4ID.01 3 0.1765 0.8974 0.00 0.00 0.88 0.00 0.12 0.00 0.00 0.00
#> TCGA.J8.A3YE.01 6 0.3170 0.7037 0.00 0.00 0.00 0.00 0.00 0.76 0.04 0.20
#> TCGA.DJ.A3VF.01 5 0.0000 0.8418 0.00 0.00 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.E8.A432.01 1 0.3299 0.2679 0.56 0.00 0.00 0.00 0.00 0.00 0.00 0.44
#> TCGA.ET.A2MX.01 7 0.3737 0.0000 0.00 0.48 0.00 0.00 0.00 0.00 0.50 0.02
#> TCGA.ET.A40S.01 4 0.2650 0.8192 0.00 0.00 0.00 0.76 0.00 0.00 0.24 0.00
#> TCGA.DE.A4M8.01 3 0.0000 0.9532 0.00 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.EL.A4KD.01 2 0.0000 0.2915 0.00 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.FY.A40L.01 1 0.0000 0.3723 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.J8.A42S.01 2 0.3329 -0.8826 0.00 0.52 0.00 0.00 0.00 0.00 0.48 0.00
#> TCGA.KS.A4IC.01 8 0.4804 0.5561 0.14 0.00 0.00 0.00 0.00 0.40 0.00 0.46
#> TCGA.E8.A414.01 5 0.0000 0.8418 0.00 0.00 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.DE.A4MD.06 4 0.0000 0.9302 0.00 0.00 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.DJ.A4V4.01 6 0.4216 -0.3706 0.06 0.00 0.00 0.00 0.00 0.50 0.00 0.44
#> TCGA.FY.A40K.01 8 0.4990 0.5995 0.18 0.00 0.00 0.00 0.00 0.38 0.00 0.44
#> TCGA.EM.A4FR.01 2 0.3329 -0.8826 0.00 0.52 0.00 0.00 0.00 0.00 0.48 0.00
#> TCGA.DJ.A3V8.01 1 0.2114 0.3606 0.84 0.00 0.00 0.00 0.00 0.00 0.00 0.16
#> TCGA.J8.A4HY.01 8 0.4693 0.3962 0.42 0.00 0.00 0.00 0.00 0.12 0.00 0.46
#> TCGA.FY.A40N.01 6 0.4370 -0.3204 0.08 0.00 0.00 0.00 0.00 0.52 0.00 0.40
#> TCGA.DJ.A2PX.01 5 0.0000 0.8418 0.00 0.00 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.EL.A4JX.01 3 0.0000 0.9532 0.00 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.DJ.A2Q5.01 4 0.0000 0.9302 0.00 0.00 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.DJ.A4UP.01 5 0.0000 0.8418 0.00 0.00 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.E8.A438.01 1 0.3299 0.2679 0.56 0.00 0.00 0.00 0.00 0.00 0.00 0.44
#> TCGA.EL.A4KH.01 6 0.0000 0.8468 0.00 0.00 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.DJ.A4V5.01 4 0.3083 0.7236 0.00 0.00 0.00 0.66 0.00 0.00 0.34 0.00
#> TCGA.E8.A44M.01 3 0.0000 0.9532 0.00 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.BJ.A45H.01 2 0.0808 0.3082 0.00 0.96 0.00 0.00 0.00 0.00 0.04 0.00
#> TCGA.E8.A44K.01 1 0.3083 -0.0630 0.66 0.00 0.00 0.00 0.34 0.00 0.00 0.00
#> TCGA.CE.A481.01 5 0.2406 0.7667 0.20 0.00 0.00 0.00 0.80 0.00 0.00 0.00
#> TCGA.E8.A436.01 1 0.0471 0.3765 0.98 0.00 0.00 0.00 0.00 0.00 0.00 0.02
#> TCGA.DJ.A2Q3.01 3 0.1563 0.9109 0.00 0.00 0.90 0.00 0.10 0.00 0.00 0.00
#> TCGA.ET.A2N1.01 6 0.0808 0.8232 0.00 0.00 0.00 0.00 0.00 0.96 0.00 0.04
#> TCGA.DJ.A2PZ.01 2 0.1765 0.1302 0.00 0.88 0.00 0.00 0.00 0.00 0.12 0.00
#> TCGA.IM.A4EB.01 4 0.2267 0.8569 0.00 0.00 0.00 0.82 0.00 0.00 0.18 0.00
#> TCGA.EM.A4FO.01 4 0.0000 0.9302 0.00 0.00 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.BJ.A45I.01 5 0.0000 0.8418 0.00 0.00 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.EL.A3N3.01 5 0.3142 0.3419 0.00 0.00 0.36 0.00 0.64 0.00 0.00 0.00
#> TCGA.DJ.A2PS.01 1 0.3299 0.2679 0.56 0.00 0.00 0.00 0.00 0.00 0.00 0.44
#> TCGA.CE.A3MD.01 2 0.0000 0.2915 0.00 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.EL.A3CN.01 5 0.0000 0.8418 0.00 0.00 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.J8.A4HW.06 3 0.0000 0.9532 0.00 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.E8.A437.01 8 0.4813 0.4396 0.42 0.00 0.00 0.00 0.00 0.14 0.00 0.44
#> TCGA.CE.A483.01 6 0.0000 0.8468 0.00 0.00 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.CE.A485.01 2 0.3193 0.3258 0.00 0.62 0.00 0.00 0.00 0.00 0.38 0.00
#> TCGA.ET.A4KN.01 3 0.0000 0.9532 0.00 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.DJ.A4UQ.01 2 0.0808 0.3082 0.00 0.96 0.00 0.00 0.00 0.00 0.04 0.00
#> TCGA.DJ.A4UW.01 1 0.4562 -0.3654 0.46 0.00 0.00 0.00 0.00 0.10 0.00 0.44
#> TCGA.DE.A3KN.01 1 0.3299 0.2679 0.56 0.00 0.00 0.00 0.00 0.00 0.00 0.44
#> TCGA.DJ.A2QA.01 6 0.1091 0.8055 0.00 0.00 0.00 0.00 0.00 0.94 0.00 0.06
#> TCGA.BJ.A4O9.01 6 0.3843 0.6478 0.02 0.00 0.00 0.00 0.00 0.70 0.04 0.24
#> TCGA.CE.A3ME.01 1 0.3862 0.1867 0.60 0.00 0.00 0.00 0.00 0.00 0.04 0.36
#> TCGA.E3.A3E1.01 1 0.3272 0.2648 0.58 0.00 0.00 0.00 0.00 0.00 0.00 0.42
#> TCGA.DJ.A2Q8.01 1 0.3299 0.2679 0.56 0.00 0.00 0.00 0.00 0.00 0.00 0.44
#> TCGA.FE.A23A.01 3 0.1765 0.8974 0.00 0.00 0.88 0.00 0.12 0.00 0.00 0.00
#> TCGA.FY.A3I4.01 1 0.3299 0.2679 0.56 0.00 0.00 0.00 0.00 0.00 0.00 0.44
#> TCGA.ET.A2N0.01 1 0.0000 0.3723 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.ET.A3DP.01 1 0.3299 0.2679 0.56 0.00 0.00 0.00 0.00 0.00 0.00 0.44
#> TCGA.EL.A3GV.01 1 0.3299 0.2679 0.56 0.00 0.00 0.00 0.00 0.00 0.00 0.44
#> TCGA.GE.A2C6.01 3 0.1947 0.8800 0.00 0.00 0.86 0.00 0.14 0.00 0.00 0.00
#> TCGA.DJ.A2PT.01 3 0.0471 0.9479 0.00 0.00 0.98 0.00 0.02 0.00 0.00 0.00
#> TCGA.E8.A242.01 3 0.0000 0.9532 0.00 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.J8.A3O1.01 6 0.1947 0.7737 0.00 0.00 0.00 0.00 0.00 0.86 0.00 0.14
#> TCGA.EM.A2CR.01 6 0.0808 0.8224 0.00 0.00 0.00 0.00 0.00 0.96 0.00 0.04
#> TCGA.FE.A238.01 1 0.0000 0.3723 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.EM.A3FQ.01 5 0.0000 0.8418 0.00 0.00 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.EM.A22M.01 4 0.0000 0.9302 0.00 0.00 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.J8.A3NZ.01 8 0.5165 0.6044 0.28 0.00 0.00 0.00 0.00 0.28 0.00 0.44
#> TCGA.FE.A236.01 2 0.2650 -0.1800 0.00 0.76 0.00 0.00 0.00 0.00 0.24 0.00
#> TCGA.BJ.A28R.01 5 0.3299 0.5365 0.44 0.00 0.00 0.00 0.56 0.00 0.00 0.00
#> TCGA.EM.A2CU.01 1 0.1091 0.3759 0.94 0.00 0.00 0.00 0.00 0.00 0.00 0.06
#> TCGA.FE.A237.01 1 0.3272 0.2728 0.58 0.00 0.00 0.00 0.00 0.00 0.00 0.42
#> TCGA.DJ.A2QC.01 6 0.4216 -0.3706 0.06 0.00 0.00 0.00 0.00 0.50 0.00 0.44
#> TCGA.EM.A2CS.06 1 0.4698 -0.4566 0.44 0.00 0.00 0.00 0.00 0.12 0.00 0.44
#> TCGA.H2.A26U.01 3 0.0000 0.9532 0.00 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.BJ.A28Z.01 3 0.0000 0.9532 0.00 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.ET.A25J.01 6 0.3198 0.5631 0.00 0.00 0.00 0.00 0.00 0.72 0.02 0.26
#> TCGA.FY.A3NN.01 6 0.0808 0.8299 0.00 0.00 0.00 0.00 0.00 0.96 0.00 0.04
#> TCGA.EL.A3H3.01 5 0.2406 0.7667 0.20 0.00 0.00 0.00 0.80 0.00 0.00 0.00
#> TCGA.BJ.A0Z3.01 3 0.2114 0.8591 0.00 0.00 0.84 0.00 0.16 0.00 0.00 0.00
#> TCGA.BJ.A28X.01 3 0.0000 0.9532 0.00 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.EL.A3CT.01 3 0.1765 0.8976 0.00 0.00 0.88 0.00 0.12 0.00 0.00 0.00
#> TCGA.J8.A3YG.01 5 0.2534 0.7520 0.22 0.00 0.00 0.00 0.78 0.00 0.00 0.00
#> TCGA.EM.A3SZ.01 5 0.0000 0.8418 0.00 0.00 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.EM.A2P0.01 2 0.3329 -0.8826 0.00 0.52 0.00 0.00 0.00 0.00 0.48 0.00
#> TCGA.E8.A2JQ.01 3 0.0000 0.9532 0.00 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.DJ.A3UW.01 3 0.0000 0.9532 0.00 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.DJ.A3V3.01 5 0.2114 0.7849 0.16 0.00 0.00 0.00 0.84 0.00 0.00 0.00
#> TCGA.EL.A3GP.01 4 0.0471 0.9253 0.00 0.00 0.00 0.98 0.00 0.00 0.02 0.00
#> TCGA.BJ.A191.01 8 0.4562 0.3081 0.44 0.00 0.00 0.00 0.00 0.10 0.00 0.46
#> TCGA.EM.A2P1.01 4 0.0000 0.9302 0.00 0.00 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.IM.A3EB.01 5 0.0000 0.8418 0.00 0.00 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.EM.A3AK.01 1 0.3299 0.2679 0.56 0.00 0.00 0.00 0.00 0.00 0.00 0.44
#> TCGA.EM.A3AO.01 2 0.3193 0.3258 0.00 0.62 0.00 0.00 0.00 0.00 0.38 0.00
#> TCGA.EM.A2P1.06 4 0.0000 0.9302 0.00 0.00 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.EM.A1CS.01 6 0.0000 0.8468 0.00 0.00 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.EL.A3GQ.01 6 0.0000 0.8468 0.00 0.00 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.DJ.A3V4.01 1 0.3299 0.2679 0.56 0.00 0.00 0.00 0.00 0.00 0.00 0.44
#> TCGA.DJ.A3V2.01 5 0.0000 0.8418 0.00 0.00 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.BJ.A290.01 2 0.5230 -0.2783 0.00 0.40 0.00 0.00 0.00 0.00 0.32 0.28
#> TCGA.EM.A3SU.01 5 0.1947 0.7910 0.14 0.00 0.00 0.00 0.86 0.00 0.00 0.00
#> TCGA.EL.A3GR.01 1 0.3299 0.2679 0.56 0.00 0.00 0.00 0.00 0.00 0.00 0.44
#> TCGA.EM.A3SU.06 3 0.0000 0.9532 0.00 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.DJ.A3US.01 5 0.0000 0.8418 0.00 0.00 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.EM.A2OZ.01 2 0.3237 -0.6781 0.00 0.60 0.00 0.00 0.00 0.00 0.40 0.00
#> TCGA.E8.A2EA.01 5 0.3329 -0.0548 0.00 0.00 0.48 0.00 0.52 0.00 0.00 0.00
#> TCGA.EM.A1CV.01 6 0.0000 0.8468 0.00 0.00 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.EM.A1CT.01 2 0.2852 -0.2005 0.00 0.72 0.00 0.00 0.00 0.00 0.28 0.00
#> TCGA.ET.A3BS.01 4 0.2406 0.8455 0.00 0.00 0.00 0.80 0.00 0.00 0.20 0.00
#> TCGA.DJ.A3UU.01 1 0.3299 0.2679 0.56 0.00 0.00 0.00 0.00 0.00 0.00 0.44
#> TCGA.DJ.A2PO.01 2 0.3193 0.3258 0.00 0.62 0.00 0.00 0.00 0.00 0.38 0.00
#> TCGA.DJ.A3UQ.01 5 0.2534 0.7536 0.22 0.00 0.00 0.00 0.78 0.00 0.00 0.00
#> TCGA.EL.A3T0.01 1 0.3299 0.2679 0.56 0.00 0.00 0.00 0.00 0.00 0.00 0.44
#> TCGA.DJ.A3UX.01 1 0.1765 0.3721 0.88 0.00 0.00 0.00 0.00 0.00 0.00 0.12
#> TCGA.ET.A3BW.01 6 0.0000 0.8468 0.00 0.00 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.ET.A39S.01 6 0.4216 -0.3706 0.06 0.00 0.00 0.00 0.00 0.50 0.00 0.44
#> TCGA.ET.A3BP.01 6 0.0000 0.8468 0.00 0.00 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.EL.A3D4.01 2 0.0000 0.2915 0.00 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.FE.A232.01 1 0.3690 0.1584 0.56 0.00 0.00 0.00 0.00 0.00 0.02 0.42
#> TCGA.DJ.A3UR.01 6 0.0000 0.8468 0.00 0.00 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.FK.A3S3.01 8 0.4990 0.5992 0.18 0.00 0.00 0.00 0.00 0.38 0.00 0.44
#> TCGA.EL.A3CS.01 1 0.3293 0.2121 0.74 0.00 0.00 0.00 0.00 0.00 0.04 0.22
#> TCGA.DO.A2HM.01 4 0.0000 0.9302 0.00 0.00 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.FY.A3BL.01 2 0.3329 -0.8826 0.00 0.52 0.00 0.00 0.00 0.00 0.48 0.00
#> TCGA.DJ.A1QF.01 6 0.1887 0.8034 0.00 0.00 0.00 0.00 0.00 0.90 0.04 0.06
#> TCGA.ET.A3DU.01 3 0.0000 0.9532 0.00 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.EL.A3T1.01 5 0.0000 0.8418 0.00 0.00 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.FE.A230.01 5 0.2406 0.7651 0.20 0.00 0.00 0.00 0.80 0.00 0.00 0.00
#> TCGA.ET.A39R.01 5 0.0000 0.8418 0.00 0.00 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.EL.A3CV.01 4 0.0000 0.9302 0.00 0.00 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.EL.A3TA.01 2 0.3193 0.3258 0.00 0.62 0.00 0.00 0.00 0.00 0.38 0.00
#> TCGA.DJ.A3UY.01 1 0.0000 0.3723 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.DJ.A2Q1.01 3 0.0808 0.9418 0.00 0.00 0.96 0.00 0.04 0.00 0.00 0.00
#> TCGA.EL.A3CU.01 3 0.1563 0.9109 0.00 0.00 0.90 0.00 0.10 0.00 0.00 0.00
#> TCGA.DJ.A3UV.01 1 0.3299 0.2679 0.56 0.00 0.00 0.00 0.00 0.00 0.00 0.44
#> TCGA.EL.A3CX.01 1 0.3272 0.2717 0.58 0.00 0.00 0.00 0.00 0.00 0.00 0.42
#> TCGA.EM.A22P.01 4 0.0000 0.9302 0.00 0.00 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.DJ.A3UK.01 6 0.0000 0.8468 0.00 0.00 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.ET.A3DO.01 3 0.0000 0.9532 0.00 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.ET.A3BV.01 3 0.0808 0.9418 0.00 0.00 0.96 0.00 0.04 0.00 0.00 0.00
#> TCGA.BJ.A0Z9.01 5 0.2114 0.7022 0.00 0.00 0.16 0.00 0.84 0.00 0.00 0.00
#> TCGA.FY.A3R6.01 3 0.0000 0.9532 0.00 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.BJ.A0Z5.01 2 0.3329 -0.8826 0.00 0.52 0.00 0.00 0.00 0.00 0.48 0.00
#> TCGA.ET.A3DT.01 3 0.0000 0.9532 0.00 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.ET.A39M.01 4 0.1091 0.9120 0.00 0.00 0.00 0.94 0.00 0.00 0.06 0.00
#> TCGA.BJ.A0ZJ.01 4 0.2650 0.8192 0.00 0.00 0.00 0.76 0.00 0.00 0.24 0.00
#> TCGA.ET.A39T.01 6 0.0000 0.8468 0.00 0.00 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.DJ.A2PV.01 8 0.4698 0.3690 0.44 0.00 0.00 0.00 0.00 0.12 0.00 0.44
#> TCGA.DJ.A13X.01 6 0.0000 0.8468 0.00 0.00 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.EL.A3T6.01 3 0.1091 0.9326 0.00 0.00 0.94 0.00 0.06 0.00 0.00 0.00
#> TCGA.EM.A3O3.01 3 0.0000 0.9532 0.00 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.DJ.A13L.01 4 0.0000 0.9302 0.00 0.00 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.DJ.A13U.01 2 0.3329 -0.8826 0.00 0.52 0.00 0.00 0.00 0.00 0.48 0.00
#> TCGA.ET.A2N4.01 6 0.0000 0.8468 0.00 0.00 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.DJ.A13P.01 6 0.0000 0.8468 0.00 0.00 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.EM.A3O7.01 6 0.0000 0.8468 0.00 0.00 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.ET.A3DR.01 1 0.3992 0.0301 0.52 0.00 0.00 0.00 0.00 0.04 0.00 0.44
#> TCGA.FE.A3PB.01 5 0.0000 0.8418 0.00 0.00 0.00 0.00 1.00 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: Node01. Child nodes: Node0111-leaf , Node0112-leaf , Node0113-leaf , Node0114-leaf , Node0131-leaf , Node0132-leaf , Node0133-leaf , Node0141-leaf , Node0142-leaf , Node0143-leaf , Node0211-leaf , Node0212-leaf , Node0221-leaf , Node0222-leaf , Node0223-leaf , Node0224-leaf , Node0231-leaf , Node0232 , Node0233-leaf , Node0234-leaf , Node0241 , Node0242-leaf , Node0243-leaf , Node0244-leaf , Node0251-leaf , Node0252-leaf , Node0311 , Node0312-leaf , Node0313-leaf , Node0331-leaf , Node0332-leaf , Node0333-leaf .
The object with results only for a single top-value method and a single partitioning method can be extracted as:
res = res_rh["011"]
A summary of res and all the functions that can be applied to it:
res
#> A 'ConsensusPartition' object with k = 2, 3, 4, 5, 6, 7, 8.
#> On a matrix with 30000 rows and 58 columns.
#> Top rows (1000) are extracted by 'ATC' method.
#> Subgroups are detected by '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 0.4996 0.501 0.501
#> 3 3 1.000 1.000 1.000 0.3048 0.652 0.418
#> 4 4 1.000 0.973 0.984 0.1507 0.828 0.553
#> 5 5 0.896 0.867 0.938 0.0233 0.969 0.876
#> 6 6 0.829 0.749 0.876 0.0277 0.999 0.995
#> 7 7 0.815 0.690 0.852 0.0188 0.991 0.960
#> 8 8 0.780 0.555 0.781 0.0240 0.962 0.833
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.DJ.A3V9.01 2 0 1 0 1
#> TCGA.EL.A3ZN.01 2 0 1 0 1
#> TCGA.E8.A415.01 2 0 1 0 1
#> TCGA.J8.A3YE.01 2 0 1 0 1
#> TCGA.KS.A4IC.01 1 0 1 1 0
#> TCGA.DJ.A4V4.01 2 0 1 0 1
#> TCGA.FY.A40K.01 1 0 1 1 0
#> TCGA.J8.A4HY.01 2 0 1 0 1
#> TCGA.FY.A40N.01 2 0 1 0 1
#> TCGA.E8.A438.01 2 0 1 0 1
#> TCGA.EL.A4KH.01 1 0 1 1 0
#> TCGA.ET.A2N1.01 2 0 1 0 1
#> TCGA.DJ.A2PS.01 2 0 1 0 1
#> TCGA.E8.A437.01 2 0 1 0 1
#> TCGA.CE.A483.01 1 0 1 1 0
#> TCGA.DJ.A4UW.01 2 0 1 0 1
#> TCGA.DE.A3KN.01 2 0 1 0 1
#> TCGA.DJ.A2QA.01 2 0 1 0 1
#> TCGA.BJ.A4O9.01 1 0 1 1 0
#> TCGA.CE.A3ME.01 2 0 1 0 1
#> TCGA.E3.A3E1.01 2 0 1 0 1
#> TCGA.FY.A3I4.01 2 0 1 0 1
#> TCGA.ET.A3DP.01 1 0 1 1 0
#> TCGA.EL.A3GV.01 1 0 1 1 0
#> TCGA.J8.A3O1.01 2 0 1 0 1
#> TCGA.EM.A2CR.01 2 0 1 0 1
#> TCGA.J8.A3NZ.01 2 0 1 0 1
#> TCGA.FE.A237.01 1 0 1 1 0
#> TCGA.DJ.A2QC.01 1 0 1 1 0
#> TCGA.EM.A2CS.06 2 0 1 0 1
#> TCGA.ET.A25J.01 2 0 1 0 1
#> TCGA.FY.A3NN.01 1 0 1 1 0
#> TCGA.BJ.A191.01 2 0 1 0 1
#> TCGA.EM.A3AK.01 1 0 1 1 0
#> TCGA.EM.A1CS.01 1 0 1 1 0
#> TCGA.EL.A3GQ.01 1 0 1 1 0
#> TCGA.DJ.A3V4.01 2 0 1 0 1
#> TCGA.EL.A3GR.01 2 0 1 0 1
#> TCGA.EM.A1CV.01 1 0 1 1 0
#> TCGA.DJ.A3UU.01 2 0 1 0 1
#> TCGA.EL.A3T0.01 2 0 1 0 1
#> TCGA.ET.A3BW.01 1 0 1 1 0
#> TCGA.ET.A39S.01 2 0 1 0 1
#> TCGA.ET.A3BP.01 1 0 1 1 0
#> TCGA.FE.A232.01 2 0 1 0 1
#> TCGA.DJ.A3UR.01 1 0 1 1 0
#> TCGA.FK.A3S3.01 2 0 1 0 1
#> TCGA.DJ.A1QF.01 1 0 1 1 0
#> TCGA.DJ.A3UV.01 2 0 1 0 1
#> TCGA.EL.A3CX.01 2 0 1 0 1
#> TCGA.DJ.A3UK.01 1 0 1 1 0
#> TCGA.ET.A39T.01 1 0 1 1 0
#> TCGA.DJ.A2PV.01 1 0 1 1 0
#> TCGA.DJ.A13X.01 1 0 1 1 0
#> TCGA.ET.A2N4.01 1 0 1 1 0
#> TCGA.DJ.A13P.01 1 0 1 1 0
#> TCGA.EM.A3O7.01 1 0 1 1 0
#> TCGA.ET.A3DR.01 2 0 1 0 1
cbind(get_classes(res, k = 3), get_membership(res, k = 3))
#> class entropy silhouette p1 p2 p3
#> TCGA.DJ.A3V9.01 2 0 1 0 1 0
#> TCGA.EL.A3ZN.01 3 0 1 0 0 1
#> TCGA.E8.A415.01 2 0 1 0 1 0
#> TCGA.J8.A3YE.01 2 0 1 0 1 0
#> TCGA.KS.A4IC.01 2 0 1 0 1 0
#> TCGA.DJ.A4V4.01 2 0 1 0 1 0
#> TCGA.FY.A40K.01 1 0 1 1 0 0
#> TCGA.J8.A4HY.01 2 0 1 0 1 0
#> TCGA.FY.A40N.01 3 0 1 0 0 1
#> TCGA.E8.A438.01 3 0 1 0 0 1
#> TCGA.EL.A4KH.01 1 0 1 1 0 0
#> TCGA.ET.A2N1.01 3 0 1 0 0 1
#> TCGA.DJ.A2PS.01 2 0 1 0 1 0
#> TCGA.E8.A437.01 2 0 1 0 1 0
#> TCGA.CE.A483.01 2 0 1 0 1 0
#> TCGA.DJ.A4UW.01 2 0 1 0 1 0
#> TCGA.DE.A3KN.01 3 0 1 0 0 1
#> TCGA.DJ.A2QA.01 2 0 1 0 1 0
#> TCGA.BJ.A4O9.01 2 0 1 0 1 0
#> TCGA.CE.A3ME.01 2 0 1 0 1 0
#> TCGA.E3.A3E1.01 2 0 1 0 1 0
#> TCGA.FY.A3I4.01 3 0 1 0 0 1
#> TCGA.ET.A3DP.01 1 0 1 1 0 0
#> TCGA.EL.A3GV.01 1 0 1 1 0 0
#> TCGA.J8.A3O1.01 3 0 1 0 0 1
#> TCGA.EM.A2CR.01 3 0 1 0 0 1
#> TCGA.J8.A3NZ.01 2 0 1 0 1 0
#> TCGA.FE.A237.01 2 0 1 0 1 0
#> TCGA.DJ.A2QC.01 1 0 1 1 0 0
#> TCGA.EM.A2CS.06 2 0 1 0 1 0
#> TCGA.ET.A25J.01 2 0 1 0 1 0
#> TCGA.FY.A3NN.01 2 0 1 0 1 0
#> TCGA.BJ.A191.01 3 0 1 0 0 1
#> TCGA.EM.A3AK.01 2 0 1 0 1 0
#> TCGA.EM.A1CS.01 1 0 1 1 0 0
#> TCGA.EL.A3GQ.01 1 0 1 1 0 0
#> TCGA.DJ.A3V4.01 2 0 1 0 1 0
#> TCGA.EL.A3GR.01 3 0 1 0 0 1
#> TCGA.EM.A1CV.01 1 0 1 1 0 0
#> TCGA.DJ.A3UU.01 2 0 1 0 1 0
#> TCGA.EL.A3T0.01 3 0 1 0 0 1
#> TCGA.ET.A3BW.01 1 0 1 1 0 0
#> TCGA.ET.A39S.01 2 0 1 0 1 0
#> TCGA.ET.A3BP.01 2 0 1 0 1 0
#> TCGA.FE.A232.01 2 0 1 0 1 0
#> TCGA.DJ.A3UR.01 1 0 1 1 0 0
#> TCGA.FK.A3S3.01 3 0 1 0 0 1
#> TCGA.DJ.A1QF.01 2 0 1 0 1 0
#> TCGA.DJ.A3UV.01 3 0 1 0 0 1
#> TCGA.EL.A3CX.01 3 0 1 0 0 1
#> TCGA.DJ.A3UK.01 1 0 1 1 0 0
#> TCGA.ET.A39T.01 2 0 1 0 1 0
#> TCGA.DJ.A2PV.01 1 0 1 1 0 0
#> TCGA.DJ.A13X.01 1 0 1 1 0 0
#> TCGA.ET.A2N4.01 1 0 1 1 0 0
#> TCGA.DJ.A13P.01 1 0 1 1 0 0
#> TCGA.EM.A3O7.01 1 0 1 1 0 0
#> TCGA.ET.A3DR.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.DJ.A3V9.01 4 0.0707 0.963 0 0.02 0.00 0.98
#> TCGA.EL.A3ZN.01 3 0.0000 0.973 0 0.00 1.00 0.00
#> TCGA.E8.A415.01 4 0.0707 0.963 0 0.02 0.00 0.98
#> TCGA.J8.A3YE.01 2 0.0000 1.000 0 1.00 0.00 0.00
#> TCGA.KS.A4IC.01 2 0.0000 1.000 0 1.00 0.00 0.00
#> TCGA.DJ.A4V4.01 2 0.0000 1.000 0 1.00 0.00 0.00
#> TCGA.FY.A40K.01 1 0.0000 1.000 1 0.00 0.00 0.00
#> TCGA.J8.A4HY.01 2 0.0000 1.000 0 1.00 0.00 0.00
#> TCGA.FY.A40N.01 4 0.0707 0.953 0 0.00 0.02 0.98
#> TCGA.E8.A438.01 3 0.0000 0.973 0 0.00 1.00 0.00
#> TCGA.EL.A4KH.01 1 0.0000 1.000 1 0.00 0.00 0.00
#> TCGA.ET.A2N1.01 3 0.0000 0.973 0 0.00 1.00 0.00
#> TCGA.DJ.A2PS.01 4 0.0707 0.963 0 0.02 0.00 0.98
#> TCGA.E8.A437.01 4 0.0707 0.963 0 0.02 0.00 0.98
#> TCGA.CE.A483.01 2 0.0000 1.000 0 1.00 0.00 0.00
#> TCGA.DJ.A4UW.01 4 0.0707 0.963 0 0.02 0.00 0.98
#> TCGA.DE.A3KN.01 3 0.0000 0.973 0 0.00 1.00 0.00
#> TCGA.DJ.A2QA.01 4 0.0707 0.963 0 0.02 0.00 0.98
#> TCGA.BJ.A4O9.01 2 0.0000 1.000 0 1.00 0.00 0.00
#> TCGA.CE.A3ME.01 2 0.0000 1.000 0 1.00 0.00 0.00
#> TCGA.E3.A3E1.01 2 0.0000 1.000 0 1.00 0.00 0.00
#> TCGA.FY.A3I4.01 4 0.0000 0.952 0 0.00 0.00 1.00
#> TCGA.ET.A3DP.01 1 0.0000 1.000 1 0.00 0.00 0.00
#> TCGA.EL.A3GV.01 1 0.0000 1.000 1 0.00 0.00 0.00
#> TCGA.J8.A3O1.01 3 0.0000 0.973 0 0.00 1.00 0.00
#> TCGA.EM.A2CR.01 4 0.0707 0.953 0 0.00 0.02 0.98
#> TCGA.J8.A3NZ.01 2 0.0000 1.000 0 1.00 0.00 0.00
#> TCGA.FE.A237.01 2 0.0000 1.000 0 1.00 0.00 0.00
#> TCGA.DJ.A2QC.01 1 0.0000 1.000 1 0.00 0.00 0.00
#> TCGA.EM.A2CS.06 4 0.0707 0.963 0 0.02 0.00 0.98
#> TCGA.ET.A25J.01 2 0.0000 1.000 0 1.00 0.00 0.00
#> TCGA.FY.A3NN.01 2 0.0000 1.000 0 1.00 0.00 0.00
#> TCGA.BJ.A191.01 3 0.0707 0.963 0 0.00 0.98 0.02
#> TCGA.EM.A3AK.01 4 0.0707 0.963 0 0.02 0.00 0.98
#> TCGA.EM.A1CS.01 1 0.0000 1.000 1 0.00 0.00 0.00
#> TCGA.EL.A3GQ.01 1 0.0000 1.000 1 0.00 0.00 0.00
#> TCGA.DJ.A3V4.01 2 0.0000 1.000 0 1.00 0.00 0.00
#> TCGA.EL.A3GR.01 4 0.4406 0.536 0 0.00 0.30 0.70
#> TCGA.EM.A1CV.01 1 0.0000 1.000 1 0.00 0.00 0.00
#> TCGA.DJ.A3UU.01 4 0.0707 0.963 0 0.02 0.00 0.98
#> TCGA.EL.A3T0.01 4 0.0707 0.953 0 0.00 0.02 0.98
#> TCGA.ET.A3BW.01 1 0.0000 1.000 1 0.00 0.00 0.00
#> TCGA.ET.A39S.01 4 0.0707 0.963 0 0.02 0.00 0.98
#> TCGA.ET.A3BP.01 2 0.0000 1.000 0 1.00 0.00 0.00
#> TCGA.FE.A232.01 2 0.0000 1.000 0 1.00 0.00 0.00
#> TCGA.DJ.A3UR.01 1 0.0000 1.000 1 0.00 0.00 0.00
#> TCGA.FK.A3S3.01 4 0.2647 0.860 0 0.00 0.12 0.88
#> TCGA.DJ.A1QF.01 2 0.0000 1.000 0 1.00 0.00 0.00
#> TCGA.DJ.A3UV.01 3 0.2921 0.834 0 0.00 0.86 0.14
#> TCGA.EL.A3CX.01 3 0.0000 0.973 0 0.00 1.00 0.00
#> TCGA.DJ.A3UK.01 1 0.0000 1.000 1 0.00 0.00 0.00
#> TCGA.ET.A39T.01 2 0.0000 1.000 0 1.00 0.00 0.00
#> TCGA.DJ.A2PV.01 1 0.0000 1.000 1 0.00 0.00 0.00
#> TCGA.DJ.A13X.01 1 0.0000 1.000 1 0.00 0.00 0.00
#> TCGA.ET.A2N4.01 1 0.0000 1.000 1 0.00 0.00 0.00
#> TCGA.DJ.A13P.01 1 0.0000 1.000 1 0.00 0.00 0.00
#> TCGA.EM.A3O7.01 1 0.0000 1.000 1 0.00 0.00 0.00
#> TCGA.ET.A3DR.01 3 0.1637 0.942 0 0.00 0.94 0.06
cbind(get_classes(res, k = 5), get_membership(res, k = 5))
#> class entropy silhouette p1 p2 p3 p4 p5
#> TCGA.DJ.A3V9.01 4 0.1043 0.8702 0.00 0.00 0.00 0.96 0.04
#> TCGA.EL.A3ZN.01 3 0.0000 0.8229 0.00 0.00 1.00 0.00 0.00
#> TCGA.E8.A415.01 4 0.2873 0.7658 0.00 0.12 0.00 0.86 0.02
#> TCGA.J8.A3YE.01 2 0.0000 0.9725 0.00 1.00 0.00 0.00 0.00
#> TCGA.KS.A4IC.01 2 0.1043 0.9726 0.00 0.96 0.00 0.00 0.04
#> TCGA.DJ.A4V4.01 2 0.0609 0.9596 0.00 0.98 0.00 0.00 0.02
#> TCGA.FY.A40K.01 1 0.0000 1.0000 1.00 0.00 0.00 0.00 0.00
#> TCGA.J8.A4HY.01 2 0.0000 0.9725 0.00 1.00 0.00 0.00 0.00
#> TCGA.FY.A40N.01 4 0.2438 0.8339 0.00 0.00 0.04 0.90 0.06
#> TCGA.E8.A438.01 3 0.0000 0.8229 0.00 0.00 1.00 0.00 0.00
#> TCGA.EL.A4KH.01 1 0.0000 1.0000 1.00 0.00 0.00 0.00 0.00
#> TCGA.ET.A2N1.01 3 0.0000 0.8229 0.00 0.00 1.00 0.00 0.00
#> TCGA.DJ.A2PS.01 4 0.0000 0.8820 0.00 0.00 0.00 1.00 0.00
#> TCGA.E8.A437.01 4 0.2754 0.8077 0.00 0.08 0.00 0.88 0.04
#> TCGA.CE.A483.01 2 0.1043 0.9726 0.00 0.96 0.00 0.00 0.04
#> TCGA.DJ.A4UW.01 4 0.0000 0.8820 0.00 0.00 0.00 1.00 0.00
#> TCGA.DE.A3KN.01 3 0.0000 0.8229 0.00 0.00 1.00 0.00 0.00
#> TCGA.DJ.A2QA.01 4 0.0000 0.8820 0.00 0.00 0.00 1.00 0.00
#> TCGA.BJ.A4O9.01 2 0.1043 0.9726 0.00 0.96 0.00 0.00 0.04
#> TCGA.CE.A3ME.01 2 0.0000 0.9725 0.00 1.00 0.00 0.00 0.00
#> TCGA.E3.A3E1.01 2 0.0000 0.9725 0.00 1.00 0.00 0.00 0.00
#> TCGA.FY.A3I4.01 4 0.4588 0.5551 0.00 0.00 0.06 0.72 0.22
#> TCGA.ET.A3DP.01 1 0.0000 1.0000 1.00 0.00 0.00 0.00 0.00
#> TCGA.EL.A3GV.01 1 0.0000 1.0000 1.00 0.00 0.00 0.00 0.00
#> TCGA.J8.A3O1.01 3 0.1410 0.7945 0.00 0.00 0.94 0.00 0.06
#> TCGA.EM.A2CR.01 4 0.3037 0.7899 0.00 0.00 0.10 0.86 0.04
#> TCGA.J8.A3NZ.01 2 0.0000 0.9725 0.00 1.00 0.00 0.00 0.00
#> TCGA.FE.A237.01 2 0.1043 0.9726 0.00 0.96 0.00 0.00 0.04
#> TCGA.DJ.A2QC.01 1 0.0000 1.0000 1.00 0.00 0.00 0.00 0.00
#> TCGA.EM.A2CS.06 4 0.0000 0.8820 0.00 0.00 0.00 1.00 0.00
#> TCGA.ET.A25J.01 2 0.0000 0.9725 0.00 1.00 0.00 0.00 0.00
#> TCGA.FY.A3NN.01 2 0.1043 0.9726 0.00 0.96 0.00 0.00 0.04
#> TCGA.BJ.A191.01 5 0.3109 0.3123 0.00 0.00 0.20 0.00 0.80
#> TCGA.EM.A3AK.01 4 0.2675 0.8033 0.04 0.02 0.00 0.90 0.04
#> TCGA.EM.A1CS.01 1 0.0000 1.0000 1.00 0.00 0.00 0.00 0.00
#> TCGA.EL.A3GQ.01 1 0.0000 1.0000 1.00 0.00 0.00 0.00 0.00
#> TCGA.DJ.A3V4.01 2 0.2438 0.8716 0.00 0.90 0.00 0.06 0.04
#> TCGA.EL.A3GR.01 5 0.6219 0.2142 0.00 0.00 0.14 0.42 0.44
#> TCGA.EM.A1CV.01 1 0.0000 1.0000 1.00 0.00 0.00 0.00 0.00
#> TCGA.DJ.A3UU.01 4 0.1043 0.8702 0.00 0.00 0.00 0.96 0.04
#> TCGA.EL.A3T0.01 4 0.3106 0.7665 0.00 0.00 0.14 0.84 0.02
#> TCGA.ET.A3BW.01 1 0.0000 1.0000 1.00 0.00 0.00 0.00 0.00
#> TCGA.ET.A39S.01 4 0.0000 0.8820 0.00 0.00 0.00 1.00 0.00
#> TCGA.ET.A3BP.01 2 0.1043 0.9726 0.00 0.96 0.00 0.00 0.04
#> TCGA.FE.A232.01 2 0.0000 0.9725 0.00 1.00 0.00 0.00 0.00
#> TCGA.DJ.A3UR.01 1 0.0000 1.0000 1.00 0.00 0.00 0.00 0.00
#> TCGA.FK.A3S3.01 3 0.4990 0.0942 0.00 0.00 0.60 0.36 0.04
#> TCGA.DJ.A1QF.01 2 0.1043 0.9726 0.00 0.96 0.00 0.00 0.04
#> TCGA.DJ.A3UV.01 3 0.3731 0.5440 0.00 0.00 0.80 0.16 0.04
#> TCGA.EL.A3CX.01 3 0.1732 0.7804 0.00 0.00 0.92 0.00 0.08
#> TCGA.DJ.A3UK.01 1 0.0000 1.0000 1.00 0.00 0.00 0.00 0.00
#> TCGA.ET.A39T.01 2 0.1043 0.9726 0.00 0.96 0.00 0.00 0.04
#> TCGA.DJ.A2PV.01 1 0.0000 1.0000 1.00 0.00 0.00 0.00 0.00
#> TCGA.DJ.A13X.01 1 0.0000 1.0000 1.00 0.00 0.00 0.00 0.00
#> TCGA.ET.A2N4.01 1 0.0000 1.0000 1.00 0.00 0.00 0.00 0.00
#> TCGA.DJ.A13P.01 1 0.0000 1.0000 1.00 0.00 0.00 0.00 0.00
#> TCGA.EM.A3O7.01 1 0.0000 1.0000 1.00 0.00 0.00 0.00 0.00
#> TCGA.ET.A3DR.01 5 0.6447 0.3725 0.00 0.00 0.38 0.18 0.44
cbind(get_classes(res, k = 6), get_membership(res, k = 6))
#> class entropy silhouette p1 p2 p3 p4 p5 p6
#> TCGA.DJ.A3V9.01 4 0.0937 0.7248 0.00 0.00 0.00 0.96 0.04 0.00
#> TCGA.EL.A3ZN.01 3 0.0000 0.7693 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.E8.A415.01 4 0.5111 0.4505 0.00 0.02 0.00 0.66 0.22 0.10
#> TCGA.J8.A3YE.01 2 0.2793 0.8604 0.00 0.80 0.00 0.00 0.00 0.20
#> TCGA.KS.A4IC.01 2 0.0000 0.8565 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.DJ.A4V4.01 2 0.4475 0.7751 0.00 0.70 0.00 0.10 0.00 0.20
#> TCGA.FY.A40K.01 1 0.0000 0.9831 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.J8.A4HY.01 2 0.2793 0.8604 0.00 0.80 0.00 0.00 0.00 0.20
#> TCGA.FY.A40N.01 4 0.3499 0.4883 0.00 0.00 0.00 0.68 0.32 0.00
#> TCGA.E8.A438.01 3 0.0000 0.7693 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.EL.A4KH.01 1 0.0000 0.9831 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.ET.A2N1.01 3 0.0000 0.7693 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.DJ.A2PS.01 4 0.0000 0.7323 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.E8.A437.01 4 0.5043 0.3969 0.00 0.02 0.00 0.68 0.12 0.18
#> TCGA.CE.A483.01 2 0.0547 0.8442 0.00 0.98 0.00 0.02 0.00 0.00
#> TCGA.DJ.A4UW.01 4 0.0000 0.7323 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.DE.A3KN.01 3 0.0000 0.7693 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.DJ.A2QA.01 4 0.0000 0.7323 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.BJ.A4O9.01 2 0.0000 0.8565 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.CE.A3ME.01 2 0.2793 0.8604 0.00 0.80 0.00 0.00 0.00 0.20
#> TCGA.E3.A3E1.01 2 0.2793 0.8604 0.00 0.80 0.00 0.00 0.00 0.20
#> TCGA.FY.A3I4.01 4 0.3828 0.0540 0.00 0.00 0.00 0.56 0.44 0.00
#> TCGA.ET.A3DP.01 1 0.1092 0.9740 0.96 0.00 0.00 0.00 0.02 0.02
#> TCGA.EL.A3GV.01 1 0.1092 0.9740 0.96 0.00 0.00 0.00 0.02 0.02
#> TCGA.J8.A3O1.01 3 0.0937 0.7509 0.00 0.00 0.96 0.00 0.04 0.00
#> TCGA.EM.A2CR.01 4 0.4420 0.4694 0.00 0.00 0.02 0.66 0.30 0.02
#> TCGA.J8.A3NZ.01 2 0.2793 0.8604 0.00 0.80 0.00 0.00 0.00 0.20
#> TCGA.FE.A237.01 2 0.0000 0.8565 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.DJ.A2QC.01 1 0.1092 0.9740 0.96 0.00 0.00 0.00 0.02 0.02
#> TCGA.EM.A2CS.06 4 0.0937 0.7169 0.00 0.00 0.00 0.96 0.04 0.00
#> TCGA.ET.A25J.01 2 0.2793 0.8604 0.00 0.80 0.00 0.00 0.00 0.20
#> TCGA.FY.A3NN.01 2 0.0000 0.8565 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.BJ.A191.01 6 0.4067 0.0000 0.00 0.00 0.04 0.00 0.26 0.70
#> TCGA.EM.A3AK.01 4 0.4947 0.4484 0.12 0.02 0.00 0.74 0.08 0.04
#> TCGA.EM.A1CS.01 1 0.0000 0.9831 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.EL.A3GQ.01 1 0.0547 0.9803 0.98 0.00 0.00 0.00 0.00 0.02
#> TCGA.DJ.A3V4.01 2 0.6575 0.5408 0.00 0.54 0.00 0.10 0.16 0.20
#> TCGA.EL.A3GR.01 5 0.5189 0.6205 0.00 0.00 0.06 0.34 0.58 0.02
#> TCGA.EM.A1CV.01 1 0.0000 0.9831 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.DJ.A3UU.01 4 0.1480 0.7098 0.00 0.00 0.00 0.94 0.04 0.02
#> TCGA.EL.A3T0.01 4 0.3198 0.5617 0.00 0.00 0.00 0.74 0.26 0.00
#> TCGA.ET.A3BW.01 1 0.0547 0.9682 0.98 0.02 0.00 0.00 0.00 0.00
#> TCGA.ET.A39S.01 4 0.0547 0.7260 0.00 0.00 0.00 0.98 0.02 0.00
#> TCGA.ET.A3BP.01 2 0.0000 0.8565 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.FE.A232.01 2 0.2793 0.8604 0.00 0.80 0.00 0.00 0.00 0.20
#> TCGA.DJ.A3UR.01 1 0.0000 0.9831 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.FK.A3S3.01 3 0.6157 0.1378 0.00 0.00 0.50 0.28 0.20 0.02
#> TCGA.DJ.A1QF.01 2 0.0000 0.8565 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.DJ.A3UV.01 3 0.5569 -0.0757 0.00 0.00 0.54 0.18 0.28 0.00
#> TCGA.EL.A3CX.01 3 0.4121 0.5683 0.00 0.00 0.72 0.00 0.22 0.06
#> TCGA.DJ.A3UK.01 1 0.0000 0.9831 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.ET.A39T.01 2 0.0000 0.8565 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.DJ.A2PV.01 1 0.1092 0.9740 0.96 0.00 0.00 0.00 0.02 0.02
#> TCGA.DJ.A13X.01 1 0.0547 0.9803 0.98 0.00 0.00 0.00 0.00 0.02
#> TCGA.ET.A2N4.01 1 0.1092 0.9740 0.96 0.00 0.00 0.00 0.02 0.02
#> TCGA.DJ.A13P.01 1 0.0000 0.9831 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.EM.A3O7.01 1 0.0000 0.9831 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.ET.A3DR.01 5 0.5782 0.5825 0.00 0.00 0.22 0.18 0.58 0.02
cbind(get_classes(res, k = 7), get_membership(res, k = 7))
#> class entropy silhouette p1 p2 p3 p4 p5 p6 p7
#> TCGA.DJ.A3V9.01 4 0.1433 0.5998 0.00 0.00 0.00 0.92 0.08 0.00 0.00
#> TCGA.EL.A3ZN.01 3 0.0000 0.7495 0.00 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.E8.A415.01 4 0.4783 0.0666 0.00 0.00 0.00 0.54 0.36 0.00 0.10
#> TCGA.J8.A3YE.01 7 0.0000 0.8518 0.00 0.00 0.00 0.00 0.00 0.00 1.00
#> TCGA.KS.A4IC.01 7 0.2259 0.8438 0.00 0.00 0.00 0.00 0.00 0.16 0.84
#> TCGA.DJ.A4V4.01 7 0.1928 0.7839 0.00 0.02 0.00 0.08 0.00 0.00 0.90
#> TCGA.FY.A40K.01 1 0.0000 0.9578 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.J8.A4HY.01 7 0.0504 0.8472 0.00 0.02 0.00 0.00 0.00 0.00 0.98
#> TCGA.FY.A40N.01 4 0.5272 0.0811 0.00 0.02 0.06 0.54 0.36 0.02 0.00
#> TCGA.E8.A438.01 3 0.0000 0.7495 0.00 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.EL.A4KH.01 1 0.1006 0.9520 0.96 0.02 0.00 0.00 0.00 0.02 0.00
#> TCGA.ET.A2N1.01 3 0.0000 0.7495 0.00 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.DJ.A2PS.01 4 0.0000 0.6428 0.00 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.E8.A437.01 4 0.5293 0.1546 0.00 0.02 0.00 0.58 0.24 0.00 0.16
#> TCGA.CE.A483.01 7 0.3661 0.8086 0.00 0.00 0.00 0.02 0.02 0.22 0.74
#> TCGA.DJ.A4UW.01 4 0.0000 0.6428 0.00 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.DE.A3KN.01 3 0.0000 0.7495 0.00 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.DJ.A2QA.01 4 0.0000 0.6428 0.00 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.BJ.A4O9.01 7 0.1886 0.8502 0.00 0.00 0.00 0.00 0.00 0.12 0.88
#> TCGA.CE.A3ME.01 7 0.0000 0.8518 0.00 0.00 0.00 0.00 0.00 0.00 1.00
#> TCGA.E3.A3E1.01 7 0.0504 0.8472 0.00 0.02 0.00 0.00 0.00 0.00 0.98
#> TCGA.FY.A3I4.01 5 0.3968 0.0339 0.00 0.00 0.02 0.44 0.54 0.00 0.00
#> TCGA.ET.A3DP.01 1 0.1166 0.9455 0.94 0.06 0.00 0.00 0.00 0.00 0.00
#> TCGA.EL.A3GV.01 1 0.0863 0.9523 0.96 0.04 0.00 0.00 0.00 0.00 0.00
#> TCGA.J8.A3O1.01 3 0.2745 0.6516 0.00 0.16 0.82 0.00 0.02 0.00 0.00
#> TCGA.EM.A2CR.01 4 0.6428 0.2204 0.00 0.18 0.08 0.52 0.20 0.02 0.00
#> TCGA.J8.A3NZ.01 7 0.0504 0.8472 0.00 0.02 0.00 0.00 0.00 0.00 0.98
#> TCGA.FE.A237.01 7 0.2832 0.8171 0.00 0.00 0.00 0.00 0.00 0.24 0.76
#> TCGA.DJ.A2QC.01 1 0.1166 0.9454 0.94 0.06 0.00 0.00 0.00 0.00 0.00
#> TCGA.EM.A2CS.06 4 0.0504 0.6355 0.00 0.02 0.00 0.98 0.00 0.00 0.00
#> TCGA.ET.A25J.01 7 0.0504 0.8472 0.00 0.02 0.00 0.00 0.00 0.00 0.98
#> TCGA.FY.A3NN.01 7 0.2832 0.8171 0.00 0.00 0.00 0.00 0.00 0.24 0.76
#> TCGA.BJ.A191.01 6 0.4177 0.0000 0.00 0.12 0.00 0.00 0.18 0.70 0.00
#> TCGA.EM.A3AK.01 4 0.5159 0.3172 0.04 0.24 0.00 0.64 0.02 0.06 0.00
#> TCGA.EM.A1CS.01 1 0.1006 0.9520 0.96 0.02 0.00 0.00 0.00 0.02 0.00
#> TCGA.EL.A3GQ.01 1 0.0863 0.9519 0.96 0.04 0.00 0.00 0.00 0.00 0.00
#> TCGA.DJ.A3V4.01 7 0.4378 0.5065 0.00 0.02 0.00 0.08 0.20 0.00 0.70
#> TCGA.EL.A3GR.01 5 0.5282 0.6174 0.00 0.04 0.08 0.22 0.64 0.02 0.00
#> TCGA.EM.A1CV.01 1 0.0000 0.9578 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.DJ.A3UU.01 4 0.3186 0.4200 0.00 0.02 0.00 0.76 0.22 0.00 0.00
#> TCGA.EL.A3T0.01 4 0.4872 0.2512 0.00 0.02 0.08 0.60 0.30 0.00 0.00
#> TCGA.ET.A3BW.01 1 0.1363 0.9407 0.94 0.02 0.00 0.00 0.00 0.04 0.00
#> TCGA.ET.A39S.01 4 0.0000 0.6428 0.00 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.ET.A3BP.01 7 0.2945 0.8062 0.00 0.00 0.00 0.00 0.00 0.26 0.74
#> TCGA.FE.A232.01 7 0.0504 0.8541 0.00 0.00 0.00 0.00 0.00 0.02 0.98
#> TCGA.DJ.A3UR.01 1 0.1006 0.9520 0.96 0.02 0.00 0.00 0.00 0.02 0.00
#> TCGA.FK.A3S3.01 3 0.5536 0.4100 0.00 0.16 0.60 0.18 0.06 0.00 0.00
#> TCGA.DJ.A1QF.01 7 0.2945 0.8062 0.00 0.00 0.00 0.00 0.00 0.26 0.74
#> TCGA.DJ.A3UV.01 3 0.4737 0.1817 0.00 0.00 0.56 0.10 0.34 0.00 0.00
#> TCGA.EL.A3CX.01 3 0.4710 0.2948 0.00 0.46 0.46 0.00 0.08 0.00 0.00
#> TCGA.DJ.A3UK.01 1 0.0504 0.9564 0.98 0.00 0.00 0.00 0.00 0.02 0.00
#> TCGA.ET.A39T.01 7 0.2708 0.8252 0.00 0.00 0.00 0.00 0.00 0.22 0.78
#> TCGA.DJ.A2PV.01 1 0.1166 0.9454 0.94 0.06 0.00 0.00 0.00 0.00 0.00
#> TCGA.DJ.A13X.01 1 0.1166 0.9454 0.94 0.06 0.00 0.00 0.00 0.00 0.00
#> TCGA.ET.A2N4.01 1 0.1928 0.9192 0.90 0.08 0.00 0.00 0.00 0.02 0.00
#> TCGA.DJ.A13P.01 1 0.1006 0.9520 0.96 0.02 0.00 0.00 0.00 0.02 0.00
#> TCGA.EM.A3O7.01 1 0.0504 0.9564 0.98 0.00 0.00 0.00 0.00 0.02 0.00
#> TCGA.ET.A3DR.01 5 0.5453 0.5499 0.00 0.04 0.16 0.14 0.64 0.02 0.00
cbind(get_classes(res, k = 8), get_membership(res, k = 8))
#> class entropy silhouette p1 p2 p3 p4 p5 p6 p7 p8
#> TCGA.DJ.A3V9.01 4 0.1741 0.58524 0.00 0.02 0.00 0.92 0.02 0.00 0.00 0.04
#> TCGA.EL.A3ZN.01 3 0.0000 0.67759 0.00 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.E8.A415.01 4 0.5656 -0.28177 0.00 0.00 0.00 0.42 0.38 0.00 0.06 0.14
#> TCGA.J8.A3YE.01 7 0.3015 0.62683 0.00 0.00 0.00 0.00 0.00 0.00 0.68 0.32
#> TCGA.KS.A4IC.01 7 0.1091 0.69527 0.00 0.00 0.00 0.00 0.00 0.00 0.94 0.06
#> TCGA.DJ.A4V4.01 7 0.4174 0.47982 0.00 0.00 0.00 0.06 0.00 0.00 0.54 0.40
#> TCGA.FY.A40K.01 1 0.0471 0.90674 0.98 0.00 0.00 0.00 0.00 0.02 0.00 0.00
#> TCGA.J8.A4HY.01 7 0.3618 0.57567 0.00 0.00 0.00 0.02 0.00 0.00 0.60 0.38
#> TCGA.FY.A40N.01 5 0.4399 0.42771 0.00 0.00 0.04 0.44 0.50 0.00 0.00 0.02
#> TCGA.E8.A438.01 3 0.0000 0.67759 0.00 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.EL.A4KH.01 1 0.2114 0.87781 0.84 0.00 0.00 0.00 0.00 0.16 0.00 0.00
#> TCGA.ET.A2N1.01 3 0.0000 0.67759 0.00 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.DJ.A2PS.01 4 0.1091 0.59739 0.00 0.00 0.00 0.94 0.06 0.00 0.00 0.00
#> TCGA.E8.A437.01 4 0.5493 0.12336 0.00 0.00 0.00 0.48 0.12 0.00 0.06 0.34
#> TCGA.CE.A483.01 7 0.2864 0.65382 0.00 0.00 0.00 0.06 0.00 0.02 0.84 0.08
#> TCGA.DJ.A4UW.01 4 0.0471 0.61957 0.00 0.00 0.00 0.98 0.02 0.00 0.00 0.00
#> TCGA.DE.A3KN.01 3 0.0000 0.67759 0.00 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.DJ.A2QA.01 4 0.0471 0.61940 0.00 0.00 0.00 0.98 0.02 0.00 0.00 0.00
#> TCGA.BJ.A4O9.01 7 0.0471 0.69501 0.00 0.00 0.00 0.00 0.00 0.00 0.98 0.02
#> TCGA.CE.A3ME.01 7 0.2650 0.66809 0.00 0.00 0.00 0.00 0.00 0.00 0.76 0.24
#> TCGA.E3.A3E1.01 7 0.3618 0.57567 0.00 0.00 0.00 0.02 0.00 0.00 0.60 0.38
#> TCGA.FY.A3I4.01 5 0.5273 0.42922 0.00 0.04 0.00 0.34 0.50 0.00 0.00 0.12
#> TCGA.ET.A3DP.01 1 0.1607 0.87771 0.92 0.00 0.00 0.00 0.04 0.00 0.00 0.04
#> TCGA.EL.A3GV.01 1 0.0941 0.90610 0.96 0.00 0.00 0.00 0.02 0.02 0.00 0.00
#> TCGA.J8.A3O1.01 3 0.4031 0.31653 0.00 0.16 0.72 0.00 0.00 0.02 0.00 0.10
#> TCGA.EM.A2CR.01 5 0.5242 0.31608 0.00 0.04 0.06 0.38 0.50 0.00 0.00 0.02
#> TCGA.J8.A3NZ.01 7 0.3907 0.54780 0.00 0.00 0.00 0.04 0.00 0.00 0.58 0.38
#> TCGA.FE.A237.01 7 0.0941 0.67588 0.00 0.00 0.00 0.00 0.00 0.02 0.96 0.02
#> TCGA.DJ.A2QC.01 1 0.1275 0.88647 0.94 0.00 0.00 0.00 0.02 0.00 0.00 0.04
#> TCGA.EM.A2CS.06 4 0.2224 0.53387 0.00 0.00 0.00 0.86 0.12 0.00 0.00 0.02
#> TCGA.ET.A25J.01 7 0.3618 0.57567 0.00 0.00 0.00 0.02 0.00 0.00 0.60 0.38
#> TCGA.FY.A3NN.01 7 0.0941 0.67588 0.00 0.00 0.00 0.00 0.00 0.02 0.96 0.02
#> TCGA.BJ.A191.01 6 0.3320 0.00000 0.00 0.04 0.00 0.00 0.12 0.80 0.00 0.04
#> TCGA.EM.A3AK.01 4 0.5612 0.27883 0.14 0.04 0.00 0.64 0.10 0.00 0.02 0.06
#> TCGA.EM.A1CS.01 1 0.2114 0.87781 0.84 0.00 0.00 0.00 0.00 0.16 0.00 0.00
#> TCGA.EL.A3GQ.01 1 0.0000 0.90427 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.DJ.A3V4.01 8 0.5273 -0.55573 0.00 0.00 0.00 0.08 0.06 0.00 0.42 0.44
#> TCGA.EL.A3GR.01 5 0.6835 -0.00324 0.00 0.10 0.08 0.12 0.36 0.00 0.00 0.34
#> TCGA.EM.A1CV.01 1 0.0941 0.90718 0.96 0.00 0.00 0.00 0.02 0.02 0.00 0.00
#> TCGA.DJ.A3UU.01 4 0.3303 0.46975 0.00 0.02 0.00 0.76 0.02 0.00 0.00 0.20
#> TCGA.EL.A3T0.01 5 0.4216 0.43294 0.00 0.00 0.06 0.44 0.50 0.00 0.00 0.00
#> TCGA.ET.A3BW.01 1 0.4034 0.82252 0.76 0.04 0.00 0.00 0.06 0.12 0.00 0.02
#> TCGA.ET.A39S.01 4 0.0471 0.61891 0.00 0.00 0.00 0.98 0.02 0.00 0.00 0.00
#> TCGA.ET.A3BP.01 7 0.1887 0.62801 0.00 0.00 0.00 0.00 0.00 0.06 0.90 0.04
#> TCGA.FE.A232.01 7 0.2852 0.65819 0.00 0.00 0.00 0.00 0.00 0.00 0.72 0.28
#> TCGA.DJ.A3UR.01 1 0.2114 0.87781 0.84 0.00 0.00 0.00 0.00 0.16 0.00 0.00
#> TCGA.FK.A3S3.01 3 0.5069 0.24410 0.00 0.02 0.56 0.18 0.24 0.00 0.00 0.00
#> TCGA.DJ.A1QF.01 7 0.1275 0.66249 0.00 0.00 0.00 0.00 0.00 0.02 0.94 0.04
#> TCGA.DJ.A3UV.01 3 0.5189 0.03565 0.00 0.00 0.48 0.10 0.38 0.00 0.00 0.04
#> TCGA.EL.A3CX.01 2 0.2534 0.00000 0.00 0.78 0.22 0.00 0.00 0.00 0.00 0.00
#> TCGA.DJ.A3UK.01 1 0.1091 0.90549 0.94 0.00 0.00 0.00 0.00 0.06 0.00 0.00
#> TCGA.ET.A39T.01 7 0.0471 0.68435 0.00 0.00 0.00 0.00 0.00 0.02 0.98 0.00
#> TCGA.DJ.A2PV.01 1 0.1607 0.87685 0.92 0.00 0.00 0.00 0.04 0.00 0.00 0.04
#> TCGA.DJ.A13X.01 1 0.0471 0.90081 0.98 0.00 0.00 0.00 0.00 0.00 0.00 0.02
#> TCGA.ET.A2N4.01 1 0.3402 0.82804 0.82 0.04 0.00 0.00 0.06 0.02 0.00 0.06
#> TCGA.DJ.A13P.01 1 0.2569 0.87114 0.82 0.00 0.00 0.00 0.02 0.16 0.00 0.00
#> TCGA.EM.A3O7.01 1 0.1765 0.89085 0.88 0.00 0.00 0.00 0.00 0.12 0.00 0.00
#> TCGA.ET.A3DR.01 8 0.7056 -0.52550 0.00 0.10 0.14 0.10 0.32 0.00 0.00 0.34
Heatmaps for the consensus matrix. It visualizes the probability of two samples to be in a same group.
consensus_heatmap(res, k = 2)
consensus_heatmap(res, k = 3)
consensus_heatmap(res, k = 4)
consensus_heatmap(res, k = 5)
consensus_heatmap(res, k = 6)
consensus_heatmap(res, k = 7)
consensus_heatmap(res, k = 8)
Heatmaps for the membership of samples in all partitions to see how consistent they are:
membership_heatmap(res, k = 2)
membership_heatmap(res, k = 3)
membership_heatmap(res, k = 4)
membership_heatmap(res, k = 5)
membership_heatmap(res, k = 6)
membership_heatmap(res, k = 7)
membership_heatmap(res, k = 8)
As soon as the classes for columns are determined, the signatures that are significantly different between subgroups can be looked for. Following are the heatmaps for signatures.
get_signatures(res, k = 2)
get_signatures(res, k = 3)
get_signatures(res, k = 4)
get_signatures(res, k = 5)
get_signatures(res, k = 6)
get_signatures(res, k = 7)
get_signatures(res, k = 8)
Compare the overlap of signatures from different k:
compare_signatures(res)
get_signature() returns a data frame invisibly. To get the list of signatures, the function
call should be assigned to a variable explicitly. In following code, if plot argument is set
to FALSE, no heatmap is plotted while only the differential analysis is performed.
# code only for demonstration
tb = get_signature(res, k = ..., plot = FALSE)
An example of the output of tb is:
#> which_row fdr mean_1 mean_2 scaled_mean_1 scaled_mean_2 km
#> 1 38 0.042760348 8.373488 9.131774 -0.5533452 0.5164555 1
#> 2 40 0.018707592 7.106213 8.469186 -0.6173731 0.5762149 1
#> 3 55 0.019134737 10.221463 11.207825 -0.6159697 0.5749050 1
#> 4 59 0.006059896 5.921854 7.869574 -0.6899429 0.6439467 1
#> 5 60 0.018055526 8.928898 10.211722 -0.6204761 0.5791110 1
#> 6 98 0.009384629 15.714769 14.887706 0.6635654 -0.6193277 2
...
The columns in tb are:
which_row: row indices corresponding to the input matrix.fdr: FDR for the differential test. mean_x: The mean value in group x.scaled_mean_x: The mean value in group x after rows are scaled.km: Row groups if k-means clustering is applied to rows (which is done by automatically selecting number of clusters).If there are too many signatures, top_signatures = ... can be set to only show the
signatures with the highest FDRs:
# code only for demonstration
# e.g. to show the top 500 most significant rows
tb = get_signature(res, k = ..., top_signatures = 500)
If the signatures are defined as these which are uniquely high in current group, diff_method argument
can be set to "uniquely_high_in_one_group":
# code only for demonstration
tb = get_signature(res, k = ..., diff_method = "uniquely_high_in_one_group")
UMAP plot which shows how samples are separated.
dimension_reduction(res, k = 2, method = "UMAP")
dimension_reduction(res, k = 3, method = "UMAP")
dimension_reduction(res, k = 4, method = "UMAP")
dimension_reduction(res, k = 5, method = "UMAP")
dimension_reduction(res, k = 6, method = "UMAP")
dimension_reduction(res, k = 7, method = "UMAP")
dimension_reduction(res, k = 8, method = "UMAP")
Following heatmap shows how subgroups are split when increasing k:
collect_classes(res)
If matrix rows can be associated to genes, consider to use functional_enrichment(res,
...) to perform function enrichment for the signature genes. See this vignette for more detailed explanations.
Parent node: Node01. Child nodes: Node0111-leaf , Node0112-leaf , Node0113-leaf , Node0114-leaf , Node0131-leaf , Node0132-leaf , Node0133-leaf , Node0141-leaf , Node0142-leaf , Node0143-leaf , Node0211-leaf , Node0212-leaf , Node0221-leaf , Node0222-leaf , Node0223-leaf , Node0224-leaf , Node0231-leaf , Node0232 , Node0233-leaf , Node0234-leaf , Node0241 , Node0242-leaf , Node0243-leaf , Node0244-leaf , Node0251-leaf , Node0252-leaf , Node0311 , Node0312-leaf , Node0313-leaf , Node0331-leaf , Node0332-leaf , Node0333-leaf .
The object with results only for a single top-value method and a single partitioning method can be extracted as:
res = res_rh["013"]
A summary of res and all the functions that can be applied to it:
res
#> A 'ConsensusPartition' object with k = 2, 3, 4, 5, 6, 7, 8.
#> On a matrix with 30000 rows and 40 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 0.985 0.993 0.2632 0.738 0.738
#> 3 3 0.991 0.974 0.985 1.1866 0.565 0.454
#> 4 4 0.521 0.751 0.834 0.1390 0.942 0.862
#> 5 5 0.519 0.569 0.732 0.1141 0.845 0.593
#> 6 6 0.475 0.462 0.720 0.0278 0.991 0.963
#> 7 7 0.509 0.351 0.645 0.0388 0.865 0.545
#> 8 8 0.508 0.391 0.665 0.0350 0.919 0.691
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.DJ.A3VD.01 1 0.000 0.995 1.00 0.00
#> TCGA.IM.A420.01 2 0.529 0.862 0.12 0.88
#> TCGA.DJ.A4UT.01 1 0.000 0.995 1.00 0.00
#> TCGA.E8.A419.01 1 0.000 0.995 1.00 0.00
#> TCGA.EL.A3ZS.01 1 0.000 0.995 1.00 0.00
#> TCGA.KS.A4ID.01 1 0.000 0.995 1.00 0.00
#> TCGA.DJ.A3VF.01 1 0.000 0.995 1.00 0.00
#> TCGA.DE.A4M8.01 1 0.000 0.995 1.00 0.00
#> TCGA.EL.A4JX.01 1 0.000 0.995 1.00 0.00
#> TCGA.E8.A44M.01 1 0.000 0.995 1.00 0.00
#> TCGA.DJ.A2Q3.01 1 0.000 0.995 1.00 0.00
#> TCGA.BJ.A45I.01 1 0.469 0.889 0.90 0.10
#> TCGA.EL.A3N3.01 1 0.000 0.995 1.00 0.00
#> TCGA.J8.A4HW.06 1 0.000 0.995 1.00 0.00
#> TCGA.ET.A4KN.01 1 0.000 0.995 1.00 0.00
#> TCGA.FE.A23A.01 1 0.000 0.995 1.00 0.00
#> TCGA.GE.A2C6.01 1 0.000 0.995 1.00 0.00
#> TCGA.DJ.A2PT.01 1 0.000 0.995 1.00 0.00
#> TCGA.E8.A242.01 1 0.327 0.935 0.94 0.06
#> TCGA.H2.A26U.01 1 0.000 0.995 1.00 0.00
#> TCGA.BJ.A28Z.01 1 0.000 0.995 1.00 0.00
#> TCGA.BJ.A0Z3.01 1 0.000 0.995 1.00 0.00
#> TCGA.BJ.A28X.01 1 0.000 0.995 1.00 0.00
#> TCGA.EL.A3CT.01 2 0.000 0.976 0.00 1.00
#> TCGA.E8.A2JQ.01 1 0.000 0.995 1.00 0.00
#> TCGA.DJ.A3UW.01 1 0.000 0.995 1.00 0.00
#> TCGA.IM.A3EB.01 2 0.000 0.976 0.00 1.00
#> TCGA.DJ.A3V2.01 1 0.000 0.995 1.00 0.00
#> TCGA.EM.A3SU.06 1 0.000 0.995 1.00 0.00
#> TCGA.E8.A2EA.01 1 0.000 0.995 1.00 0.00
#> TCGA.ET.A3DU.01 1 0.000 0.995 1.00 0.00
#> TCGA.DJ.A2Q1.01 1 0.000 0.995 1.00 0.00
#> TCGA.EL.A3CU.01 1 0.000 0.995 1.00 0.00
#> TCGA.ET.A3DO.01 1 0.000 0.995 1.00 0.00
#> TCGA.ET.A3BV.01 1 0.000 0.995 1.00 0.00
#> TCGA.BJ.A0Z9.01 2 0.000 0.976 0.00 1.00
#> TCGA.FY.A3R6.01 1 0.000 0.995 1.00 0.00
#> TCGA.ET.A3DT.01 1 0.000 0.995 1.00 0.00
#> TCGA.EL.A3T6.01 2 0.000 0.976 0.00 1.00
#> TCGA.EM.A3O3.01 2 0.000 0.976 0.00 1.00
cbind(get_classes(res, k = 3), get_membership(res, k = 3))
#> class entropy silhouette p1 p2 p3
#> TCGA.DJ.A3VD.01 1 0.000 1.000 1.00 0 0.00
#> TCGA.IM.A420.01 3 0.000 0.953 0.00 0 1.00
#> TCGA.DJ.A4UT.01 1 0.000 1.000 1.00 0 0.00
#> TCGA.E8.A419.01 3 0.207 0.943 0.06 0 0.94
#> TCGA.EL.A3ZS.01 1 0.000 1.000 1.00 0 0.00
#> TCGA.KS.A4ID.01 3 0.153 0.955 0.04 0 0.96
#> TCGA.DJ.A3VF.01 3 0.153 0.955 0.04 0 0.96
#> TCGA.DE.A4M8.01 1 0.000 1.000 1.00 0 0.00
#> TCGA.EL.A4JX.01 1 0.000 1.000 1.00 0 0.00
#> TCGA.E8.A44M.01 1 0.000 1.000 1.00 0 0.00
#> TCGA.DJ.A2Q3.01 3 0.000 0.953 0.00 0 1.00
#> TCGA.BJ.A45I.01 3 0.000 0.953 0.00 0 1.00
#> TCGA.EL.A3N3.01 3 0.000 0.953 0.00 0 1.00
#> TCGA.J8.A4HW.06 1 0.000 1.000 1.00 0 0.00
#> TCGA.ET.A4KN.01 3 0.254 0.924 0.08 0 0.92
#> TCGA.FE.A23A.01 3 0.153 0.955 0.04 0 0.96
#> TCGA.GE.A2C6.01 3 0.207 0.942 0.06 0 0.94
#> TCGA.DJ.A2PT.01 3 0.153 0.955 0.04 0 0.96
#> TCGA.E8.A242.01 3 0.000 0.953 0.00 0 1.00
#> TCGA.H2.A26U.01 3 0.000 0.953 0.00 0 1.00
#> TCGA.BJ.A28Z.01 1 0.000 1.000 1.00 0 0.00
#> TCGA.BJ.A0Z3.01 1 0.000 1.000 1.00 0 0.00
#> TCGA.BJ.A28X.01 1 0.000 1.000 1.00 0 0.00
#> TCGA.EL.A3CT.01 2 0.000 1.000 0.00 1 0.00
#> TCGA.E8.A2JQ.01 1 0.000 1.000 1.00 0 0.00
#> TCGA.DJ.A3UW.01 1 0.000 1.000 1.00 0 0.00
#> TCGA.IM.A3EB.01 3 0.000 0.953 0.00 0 1.00
#> TCGA.DJ.A3V2.01 1 0.000 1.000 1.00 0 0.00
#> TCGA.EM.A3SU.06 1 0.000 1.000 1.00 0 0.00
#> TCGA.E8.A2EA.01 3 0.153 0.955 0.04 0 0.96
#> TCGA.ET.A3DU.01 3 0.400 0.821 0.16 0 0.84
#> TCGA.DJ.A2Q1.01 1 0.000 1.000 1.00 0 0.00
#> TCGA.EL.A3CU.01 3 0.207 0.924 0.06 0 0.94
#> TCGA.ET.A3DO.01 1 0.000 1.000 1.00 0 0.00
#> TCGA.ET.A3BV.01 1 0.000 1.000 1.00 0 0.00
#> TCGA.BJ.A0Z9.01 2 0.000 1.000 0.00 1 0.00
#> TCGA.FY.A3R6.01 1 0.000 1.000 1.00 0 0.00
#> TCGA.ET.A3DT.01 1 0.000 1.000 1.00 0 0.00
#> TCGA.EL.A3T6.01 3 0.000 0.953 0.00 0 1.00
#> TCGA.EM.A3O3.01 2 0.000 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.DJ.A3VD.01 1 0.5428 0.777 0.74 0 0.14 0.12
#> TCGA.IM.A420.01 4 0.4855 0.813 0.00 0 0.40 0.60
#> TCGA.DJ.A4UT.01 1 0.3198 0.738 0.88 0 0.04 0.08
#> TCGA.E8.A419.01 3 0.3525 0.708 0.04 0 0.86 0.10
#> TCGA.EL.A3ZS.01 1 0.2011 0.734 0.92 0 0.00 0.08
#> TCGA.KS.A4ID.01 3 0.2335 0.747 0.02 0 0.92 0.06
#> TCGA.DJ.A3VF.01 3 0.3525 0.717 0.04 0 0.86 0.10
#> TCGA.DE.A4M8.01 1 0.5902 0.762 0.70 0 0.14 0.16
#> TCGA.EL.A4JX.01 1 0.6921 0.652 0.58 0 0.26 0.16
#> TCGA.E8.A44M.01 1 0.5151 0.780 0.76 0 0.14 0.10
#> TCGA.DJ.A2Q3.01 3 0.2011 0.740 0.00 0 0.92 0.08
#> TCGA.BJ.A45I.01 3 0.3610 0.520 0.00 0 0.80 0.20
#> TCGA.EL.A3N3.01 3 0.2921 0.649 0.00 0 0.86 0.14
#> TCGA.J8.A4HW.06 1 0.0707 0.753 0.98 0 0.00 0.02
#> TCGA.ET.A4KN.01 3 0.4731 0.640 0.06 0 0.78 0.16
#> TCGA.FE.A23A.01 3 0.2335 0.773 0.02 0 0.92 0.06
#> TCGA.GE.A2C6.01 3 0.1211 0.776 0.00 0 0.96 0.04
#> TCGA.DJ.A2PT.01 3 0.1211 0.776 0.00 0 0.96 0.04
#> TCGA.E8.A242.01 3 0.2345 0.714 0.00 0 0.90 0.10
#> TCGA.H2.A26U.01 3 0.2011 0.740 0.00 0 0.92 0.08
#> TCGA.BJ.A28Z.01 1 0.7121 0.587 0.54 0 0.30 0.16
#> TCGA.BJ.A0Z3.01 1 0.1637 0.739 0.94 0 0.00 0.06
#> TCGA.BJ.A28X.01 1 0.5784 0.757 0.70 0 0.20 0.10
#> TCGA.EL.A3CT.01 2 0.0000 1.000 0.00 1 0.00 0.00
#> TCGA.E8.A2JQ.01 1 0.7016 0.577 0.54 0 0.32 0.14
#> TCGA.DJ.A3UW.01 1 0.5428 0.777 0.74 0 0.14 0.12
#> TCGA.IM.A3EB.01 4 0.4406 0.919 0.00 0 0.30 0.70
#> TCGA.DJ.A3V2.01 1 0.2345 0.724 0.90 0 0.00 0.10
#> TCGA.EM.A3SU.06 1 0.0000 0.759 1.00 0 0.00 0.00
#> TCGA.E8.A2EA.01 3 0.1637 0.767 0.00 0 0.94 0.06
#> TCGA.ET.A3DU.01 3 0.4731 0.642 0.06 0 0.78 0.16
#> TCGA.DJ.A2Q1.01 1 0.1637 0.739 0.94 0 0.00 0.06
#> TCGA.EL.A3CU.01 3 0.4939 0.604 0.04 0 0.74 0.22
#> TCGA.ET.A3DO.01 1 0.5594 0.778 0.72 0 0.18 0.10
#> TCGA.ET.A3BV.01 1 0.2345 0.724 0.90 0 0.00 0.10
#> TCGA.BJ.A0Z9.01 2 0.0000 1.000 0.00 1 0.00 0.00
#> TCGA.FY.A3R6.01 1 0.5956 0.740 0.68 0 0.22 0.10
#> TCGA.ET.A3DT.01 1 0.1913 0.772 0.94 0 0.04 0.02
#> TCGA.EL.A3T6.01 4 0.4406 0.919 0.00 0 0.30 0.70
#> TCGA.EM.A3O3.01 2 0.0000 1.000 0.00 1 0.00 0.00
cbind(get_classes(res, k = 5), get_membership(res, k = 5))
#> class entropy silhouette p1 p2 p3 p4 p5
#> TCGA.DJ.A3VD.01 1 0.426 0.2786 0.56 0 0.00 0.00 0.44
#> TCGA.IM.A420.01 4 0.413 0.6998 0.00 0 0.26 0.72 0.02
#> TCGA.DJ.A4UT.01 1 0.526 0.4323 0.66 0 0.10 0.00 0.24
#> TCGA.E8.A419.01 3 0.454 0.5968 0.02 0 0.64 0.00 0.34
#> TCGA.EL.A3ZS.01 1 0.352 0.5968 0.82 0 0.04 0.00 0.14
#> TCGA.KS.A4ID.01 3 0.400 0.6929 0.00 0 0.74 0.02 0.24
#> TCGA.DJ.A3VF.01 3 0.335 0.7777 0.02 0 0.86 0.04 0.08
#> TCGA.DE.A4M8.01 5 0.430 -0.0911 0.48 0 0.00 0.00 0.52
#> TCGA.EL.A4JX.01 5 0.356 0.4496 0.26 0 0.00 0.00 0.74
#> TCGA.E8.A44M.01 1 0.468 0.3845 0.60 0 0.02 0.00 0.38
#> TCGA.DJ.A2Q3.01 3 0.165 0.7814 0.00 0 0.94 0.04 0.02
#> TCGA.BJ.A45I.01 3 0.440 0.5672 0.00 0 0.72 0.24 0.04
#> TCGA.EL.A3N3.01 3 0.417 0.7177 0.00 0 0.78 0.14 0.08
#> TCGA.J8.A4HW.06 1 0.173 0.6289 0.92 0 0.00 0.00 0.08
#> TCGA.ET.A4KN.01 5 0.425 0.2219 0.02 0 0.28 0.00 0.70
#> TCGA.FE.A23A.01 3 0.346 0.7815 0.02 0 0.84 0.02 0.12
#> TCGA.GE.A2C6.01 3 0.506 0.7277 0.04 0 0.74 0.06 0.16
#> TCGA.DJ.A2PT.01 3 0.311 0.7881 0.00 0 0.84 0.02 0.14
#> TCGA.E8.A242.01 3 0.339 0.7281 0.00 0 0.84 0.10 0.06
#> TCGA.H2.A26U.01 3 0.201 0.7780 0.00 0 0.92 0.02 0.06
#> TCGA.BJ.A28Z.01 5 0.385 0.4883 0.22 0 0.02 0.00 0.76
#> TCGA.BJ.A0Z3.01 1 0.000 0.6090 1.00 0 0.00 0.00 0.00
#> TCGA.BJ.A28X.01 1 0.482 0.2028 0.52 0 0.02 0.00 0.46
#> TCGA.EL.A3CT.01 2 0.000 1.0000 0.00 1 0.00 0.00 0.00
#> TCGA.E8.A2JQ.01 5 0.505 0.1402 0.38 0 0.04 0.00 0.58
#> TCGA.DJ.A3UW.01 1 0.426 0.2859 0.56 0 0.00 0.00 0.44
#> TCGA.IM.A3EB.01 4 0.141 0.8418 0.00 0 0.06 0.94 0.00
#> TCGA.DJ.A3V2.01 1 0.122 0.5959 0.96 0 0.00 0.02 0.02
#> TCGA.EM.A3SU.06 1 0.273 0.6156 0.84 0 0.00 0.00 0.16
#> TCGA.E8.A2EA.01 3 0.369 0.7491 0.02 0 0.82 0.02 0.14
#> TCGA.ET.A3DU.01 5 0.422 0.5173 0.10 0 0.12 0.00 0.78
#> TCGA.DJ.A2Q1.01 1 0.104 0.6059 0.96 0 0.00 0.00 0.04
#> TCGA.EL.A3CU.01 5 0.490 0.4316 0.04 0 0.18 0.04 0.74
#> TCGA.ET.A3DO.01 1 0.509 0.3226 0.56 0 0.04 0.00 0.40
#> TCGA.ET.A3BV.01 1 0.104 0.6059 0.96 0 0.00 0.00 0.04
#> TCGA.BJ.A0Z9.01 2 0.000 1.0000 0.00 1 0.00 0.00 0.00
#> TCGA.FY.A3R6.01 5 0.589 -0.1479 0.44 0 0.10 0.00 0.46
#> TCGA.ET.A3DT.01 1 0.380 0.5242 0.70 0 0.00 0.00 0.30
#> TCGA.EL.A3T6.01 4 0.173 0.8520 0.00 0 0.08 0.92 0.00
#> TCGA.EM.A3O3.01 2 0.000 1.0000 0.00 1 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.DJ.A3VD.01 1 0.4328 0.0941 0.52 0.00 0.02 0.00 0.46 0.00
#> TCGA.IM.A420.01 4 0.5797 0.3684 0.00 0.00 0.36 0.52 0.04 0.08
#> TCGA.DJ.A4UT.01 1 0.6211 0.3267 0.64 0.00 0.14 0.04 0.12 0.06
#> TCGA.E8.A419.01 3 0.4812 0.5299 0.04 0.00 0.68 0.00 0.24 0.04
#> TCGA.EL.A3ZS.01 1 0.2882 0.5526 0.86 0.00 0.00 0.02 0.10 0.02
#> TCGA.KS.A4ID.01 3 0.7361 0.2922 0.08 0.00 0.48 0.04 0.24 0.16
#> TCGA.DJ.A3VF.01 3 0.5305 0.6636 0.04 0.00 0.72 0.04 0.08 0.12
#> TCGA.DE.A4M8.01 5 0.4337 -0.1600 0.48 0.00 0.00 0.00 0.50 0.02
#> TCGA.EL.A4JX.01 5 0.3916 0.4042 0.30 0.00 0.02 0.00 0.68 0.00
#> TCGA.E8.A44M.01 1 0.5402 0.2570 0.58 0.00 0.04 0.02 0.34 0.02
#> TCGA.DJ.A2Q3.01 3 0.3942 0.6793 0.00 0.00 0.80 0.04 0.06 0.10
#> TCGA.BJ.A45I.01 3 0.4703 0.4592 0.00 0.00 0.72 0.18 0.04 0.06
#> TCGA.EL.A3N3.01 3 0.3258 0.6079 0.00 0.00 0.84 0.10 0.02 0.04
#> TCGA.J8.A4HW.06 1 0.1267 0.5576 0.94 0.00 0.00 0.00 0.06 0.00
#> TCGA.ET.A4KN.01 5 0.5316 -0.0160 0.04 0.00 0.24 0.04 0.66 0.02
#> TCGA.FE.A23A.01 3 0.5477 0.6150 0.02 0.00 0.70 0.06 0.12 0.10
#> TCGA.GE.A2C6.01 3 0.4221 0.6494 0.06 0.00 0.80 0.02 0.08 0.04
#> TCGA.DJ.A2PT.01 3 0.3942 0.6716 0.06 0.00 0.80 0.00 0.10 0.04
#> TCGA.E8.A242.01 3 0.3324 0.6232 0.00 0.00 0.84 0.08 0.06 0.02
#> TCGA.H2.A26U.01 3 0.2725 0.6492 0.00 0.00 0.88 0.04 0.06 0.02
#> TCGA.BJ.A28Z.01 5 0.4475 0.5134 0.20 0.00 0.10 0.00 0.70 0.00
#> TCGA.BJ.A0Z3.01 1 0.0547 0.5498 0.98 0.00 0.00 0.00 0.00 0.02
#> TCGA.BJ.A28X.01 1 0.5424 0.2135 0.56 0.00 0.08 0.02 0.34 0.00
#> TCGA.EL.A3CT.01 2 0.0547 0.9730 0.00 0.98 0.00 0.00 0.00 0.02
#> TCGA.E8.A2JQ.01 5 0.6267 0.4733 0.22 0.00 0.18 0.02 0.56 0.02
#> TCGA.DJ.A3UW.01 1 0.3797 0.1616 0.58 0.00 0.00 0.00 0.42 0.00
#> TCGA.IM.A3EB.01 4 0.2350 0.7021 0.00 0.00 0.10 0.88 0.00 0.02
#> TCGA.DJ.A3V2.01 1 0.3970 0.5050 0.80 0.00 0.00 0.04 0.08 0.08
#> TCGA.EM.A3SU.06 1 0.3315 0.5112 0.78 0.00 0.02 0.00 0.20 0.00
#> TCGA.E8.A2EA.01 3 0.5916 0.6272 0.02 0.00 0.66 0.08 0.14 0.10
#> TCGA.ET.A3DU.01 5 0.4962 0.1808 0.06 0.00 0.28 0.00 0.64 0.02
#> TCGA.DJ.A2Q1.01 1 0.2956 0.4851 0.84 0.00 0.00 0.00 0.04 0.12
#> TCGA.EL.A3CU.01 6 0.5837 0.0000 0.00 0.00 0.20 0.00 0.34 0.46
#> TCGA.ET.A3DO.01 1 0.6084 0.1708 0.50 0.00 0.06 0.02 0.38 0.04
#> TCGA.ET.A3BV.01 1 0.3523 0.4697 0.78 0.00 0.00 0.00 0.04 0.18
#> TCGA.BJ.A0Z9.01 2 0.1092 0.9652 0.00 0.96 0.00 0.00 0.02 0.02
#> TCGA.FY.A3R6.01 5 0.6654 0.0811 0.40 0.00 0.12 0.02 0.42 0.04
#> TCGA.ET.A3DT.01 1 0.4002 0.3924 0.66 0.00 0.02 0.00 0.32 0.00
#> TCGA.EL.A3T6.01 4 0.2474 0.6903 0.00 0.00 0.08 0.88 0.00 0.04
#> TCGA.EM.A3O3.01 2 0.0000 0.9771 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.DJ.A3VD.01 5 0.439 0.1477 0.42 0.00 0.02 0.00 0.54 0.02 0.00
#> TCGA.IM.A420.01 7 0.534 0.0000 0.00 0.00 0.24 0.26 0.00 0.00 0.50
#> TCGA.DJ.A4UT.01 1 0.696 0.0542 0.40 0.00 0.16 0.00 0.32 0.04 0.08
#> TCGA.E8.A419.01 5 0.605 -0.3159 0.02 0.00 0.40 0.00 0.44 0.06 0.08
#> TCGA.EL.A3ZS.01 1 0.524 0.2683 0.56 0.00 0.00 0.00 0.32 0.04 0.08
#> TCGA.KS.A4ID.01 3 0.573 0.2681 0.00 0.00 0.44 0.00 0.36 0.02 0.18
#> TCGA.DJ.A3VF.01 3 0.414 0.5017 0.02 0.00 0.78 0.00 0.04 0.08 0.08
#> TCGA.DE.A4M8.01 5 0.480 0.1757 0.40 0.00 0.02 0.00 0.54 0.02 0.02
#> TCGA.EL.A4JX.01 5 0.431 0.4163 0.16 0.00 0.00 0.00 0.72 0.10 0.02
#> TCGA.E8.A44M.01 5 0.453 0.3303 0.30 0.00 0.02 0.00 0.64 0.02 0.02
#> TCGA.DJ.A2Q3.01 3 0.404 0.5167 0.00 0.00 0.76 0.02 0.04 0.02 0.16
#> TCGA.BJ.A45I.01 3 0.558 0.0444 0.00 0.00 0.60 0.04 0.02 0.10 0.24
#> TCGA.EL.A3N3.01 3 0.339 0.3305 0.00 0.00 0.76 0.04 0.00 0.00 0.20
#> TCGA.J8.A4HW.06 1 0.257 0.5778 0.84 0.00 0.00 0.00 0.14 0.00 0.02
#> TCGA.ET.A4KN.01 5 0.568 -0.0724 0.00 0.00 0.16 0.00 0.54 0.26 0.04
#> TCGA.FE.A23A.01 3 0.602 0.4203 0.00 0.00 0.54 0.00 0.14 0.10 0.22
#> TCGA.GE.A2C6.01 3 0.582 0.3412 0.04 0.00 0.58 0.00 0.26 0.06 0.06
#> TCGA.DJ.A2PT.01 3 0.385 0.5257 0.00 0.00 0.76 0.00 0.16 0.02 0.06
#> TCGA.E8.A242.01 3 0.344 0.4260 0.00 0.00 0.82 0.00 0.06 0.06 0.06
#> TCGA.H2.A26U.01 3 0.238 0.5104 0.00 0.00 0.86 0.00 0.12 0.00 0.02
#> TCGA.BJ.A28Z.01 5 0.424 0.4351 0.10 0.00 0.02 0.00 0.76 0.10 0.02
#> TCGA.BJ.A0Z3.01 1 0.193 0.6002 0.90 0.00 0.00 0.00 0.08 0.02 0.00
#> TCGA.BJ.A28X.01 5 0.541 0.2643 0.30 0.00 0.06 0.00 0.58 0.04 0.02
#> TCGA.EL.A3CT.01 2 0.000 0.9752 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.E8.A2JQ.01 5 0.582 0.3740 0.12 0.00 0.12 0.00 0.64 0.06 0.06
#> TCGA.DJ.A3UW.01 5 0.523 0.2548 0.34 0.00 0.02 0.00 0.56 0.06 0.02
#> TCGA.IM.A3EB.01 4 0.291 0.3944 0.00 0.00 0.04 0.82 0.00 0.00 0.14
#> TCGA.DJ.A3V2.01 1 0.402 0.5448 0.78 0.00 0.02 0.00 0.10 0.02 0.08
#> TCGA.EM.A3SU.06 1 0.322 0.3533 0.68 0.00 0.00 0.00 0.32 0.00 0.00
#> TCGA.E8.A2EA.01 3 0.550 0.3575 0.00 0.00 0.54 0.00 0.18 0.02 0.26
#> TCGA.ET.A3DU.01 5 0.481 0.0623 0.00 0.00 0.14 0.00 0.66 0.18 0.02
#> TCGA.DJ.A2Q1.01 1 0.101 0.5709 0.96 0.00 0.00 0.00 0.00 0.02 0.02
#> TCGA.EL.A3CU.01 6 0.369 0.0000 0.00 0.00 0.12 0.00 0.12 0.76 0.00
#> TCGA.ET.A3DO.01 5 0.553 0.1573 0.34 0.00 0.02 0.00 0.54 0.04 0.06
#> TCGA.ET.A3BV.01 1 0.306 0.5590 0.84 0.00 0.00 0.00 0.06 0.02 0.08
#> TCGA.BJ.A0Z9.01 2 0.136 0.9497 0.00 0.94 0.00 0.00 0.00 0.02 0.04
#> TCGA.FY.A3R6.01 5 0.667 0.2619 0.28 0.00 0.10 0.00 0.48 0.04 0.10
#> TCGA.ET.A3DT.01 1 0.441 0.0294 0.52 0.00 0.02 0.00 0.44 0.00 0.02
#> TCGA.EL.A3T6.01 4 0.418 0.4593 0.00 0.00 0.04 0.74 0.00 0.06 0.16
#> TCGA.EM.A3O3.01 2 0.000 0.9752 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.DJ.A3VD.01 1 0.3737 0.09076 0.50 0.00 0.02 0.00 0.48 0.00 0.00 0.00
#> TCGA.IM.A420.01 7 0.6733 0.28713 0.00 0.00 0.18 0.10 0.00 0.04 0.36 0.32
#> TCGA.DJ.A4UT.01 1 0.6298 0.27701 0.52 0.00 0.04 0.16 0.16 0.00 0.00 0.12
#> TCGA.E8.A419.01 8 0.5936 0.17691 0.02 0.00 0.04 0.16 0.38 0.00 0.00 0.40
#> TCGA.EL.A3ZS.01 1 0.5376 0.46233 0.62 0.00 0.06 0.08 0.20 0.00 0.00 0.04
#> TCGA.KS.A4ID.01 8 0.6006 0.36003 0.02 0.00 0.00 0.16 0.28 0.06 0.00 0.48
#> TCGA.DJ.A3VF.01 8 0.5117 0.43357 0.04 0.00 0.02 0.36 0.02 0.02 0.00 0.54
#> TCGA.DE.A4M8.01 5 0.3942 0.14472 0.34 0.00 0.02 0.00 0.62 0.02 0.00 0.00
#> TCGA.EL.A4JX.01 5 0.3771 0.48595 0.06 0.00 0.02 0.08 0.80 0.02 0.00 0.02
#> TCGA.E8.A44M.01 1 0.4407 0.05819 0.48 0.00 0.00 0.02 0.46 0.00 0.00 0.04
#> TCGA.DJ.A2Q3.01 8 0.2818 0.55849 0.00 0.00 0.00 0.12 0.06 0.00 0.00 0.82
#> TCGA.BJ.A45I.01 8 0.4787 0.43035 0.00 0.00 0.04 0.06 0.02 0.04 0.12 0.72
#> TCGA.EL.A3N3.01 8 0.3897 0.46820 0.00 0.00 0.04 0.04 0.00 0.04 0.10 0.78
#> TCGA.J8.A4HW.06 1 0.2404 0.56600 0.84 0.00 0.02 0.00 0.14 0.00 0.00 0.00
#> TCGA.ET.A4KN.01 5 0.5906 0.07496 0.00 0.00 0.00 0.16 0.54 0.08 0.02 0.20
#> TCGA.FE.A23A.01 8 0.6117 0.47266 0.04 0.00 0.02 0.28 0.06 0.04 0.02 0.54
#> TCGA.GE.A2C6.01 8 0.6601 0.36553 0.04 0.00 0.00 0.22 0.24 0.04 0.02 0.44
#> TCGA.DJ.A2PT.01 8 0.4967 0.54492 0.02 0.00 0.02 0.20 0.08 0.00 0.02 0.66
#> TCGA.E8.A242.01 8 0.4511 0.48639 0.00 0.00 0.00 0.14 0.04 0.04 0.06 0.72
#> TCGA.H2.A26U.01 8 0.3744 0.49898 0.00 0.00 0.00 0.18 0.02 0.00 0.06 0.74
#> TCGA.BJ.A28Z.01 5 0.3502 0.48316 0.02 0.00 0.02 0.08 0.82 0.04 0.00 0.02
#> TCGA.BJ.A0Z3.01 1 0.0941 0.57607 0.96 0.00 0.00 0.00 0.02 0.02 0.00 0.00
#> TCGA.BJ.A28X.01 5 0.4995 0.07974 0.36 0.00 0.00 0.08 0.52 0.00 0.00 0.04
#> TCGA.EL.A3CT.01 2 0.0941 0.85435 0.00 0.96 0.02 0.02 0.00 0.00 0.00 0.00
#> TCGA.E8.A2JQ.01 5 0.4998 0.47782 0.10 0.00 0.00 0.16 0.64 0.00 0.00 0.10
#> TCGA.DJ.A3UW.01 5 0.3995 0.00852 0.36 0.00 0.02 0.00 0.60 0.02 0.00 0.00
#> TCGA.IM.A3EB.01 7 0.0808 0.44409 0.00 0.00 0.00 0.00 0.00 0.00 0.96 0.04
#> TCGA.DJ.A3V2.01 1 0.4134 0.53169 0.76 0.00 0.06 0.08 0.08 0.02 0.00 0.00
#> TCGA.EM.A3SU.06 1 0.3374 0.43542 0.68 0.00 0.02 0.00 0.30 0.00 0.00 0.00
#> TCGA.E8.A2EA.01 8 0.5535 0.45698 0.02 0.00 0.04 0.14 0.12 0.04 0.00 0.64
#> TCGA.ET.A3DU.01 5 0.5412 0.24058 0.00 0.00 0.04 0.12 0.64 0.08 0.00 0.12
#> TCGA.DJ.A2Q1.01 1 0.2864 0.54058 0.84 0.00 0.08 0.06 0.02 0.00 0.00 0.00
#> TCGA.EL.A3CU.01 6 0.2404 0.00000 0.00 0.00 0.00 0.00 0.14 0.84 0.00 0.02
#> TCGA.ET.A3DO.01 5 0.5189 0.01563 0.38 0.00 0.00 0.10 0.48 0.04 0.00 0.00
#> TCGA.ET.A3BV.01 1 0.5043 0.48514 0.70 0.00 0.12 0.06 0.04 0.06 0.00 0.02
#> TCGA.BJ.A0Z9.01 2 0.2994 0.78295 0.00 0.80 0.14 0.00 0.00 0.06 0.00 0.00
#> TCGA.FY.A3R6.01 5 0.5639 0.31023 0.20 0.00 0.02 0.08 0.58 0.00 0.00 0.12
#> TCGA.ET.A3DT.01 1 0.3374 0.43522 0.68 0.00 0.02 0.00 0.30 0.00 0.00 0.00
#> TCGA.EL.A3T6.01 7 0.4717 0.40822 0.00 0.00 0.36 0.00 0.00 0.02 0.54 0.08
#> TCGA.EM.A3O3.01 2 0.1341 0.84283 0.00 0.92 0.08 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: Node01. Child nodes: Node0111-leaf , Node0112-leaf , Node0113-leaf , Node0114-leaf , Node0131-leaf , Node0132-leaf , Node0133-leaf , Node0141-leaf , Node0142-leaf , Node0143-leaf , Node0211-leaf , Node0212-leaf , Node0221-leaf , Node0222-leaf , Node0223-leaf , Node0224-leaf , Node0231-leaf , Node0232 , Node0233-leaf , Node0234-leaf , Node0241 , Node0242-leaf , Node0243-leaf , Node0244-leaf , Node0251-leaf , Node0252-leaf , Node0311 , Node0312-leaf , Node0313-leaf , Node0331-leaf , Node0332-leaf , Node0333-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 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 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 0.2214 0.779 0.779
#> 3 3 1.000 0.995 0.991 1.7677 0.603 0.491
#> 4 4 0.904 0.922 0.992 0.1087 0.941 0.846
#> 5 5 0.831 0.790 0.955 0.0821 0.949 0.841
#> 6 6 0.801 0.678 0.932 0.0542 0.956 0.838
#> 7 7 0.728 0.563 0.865 0.0590 0.919 0.703
#> 8 8 0.743 0.331 0.836 0.0461 0.926 0.688
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.ET.A40S.01 2 0 1 0 1
#> TCGA.DE.A4MD.06 1 0 1 1 0
#> TCGA.DJ.A2Q5.01 2 0 1 0 1
#> TCGA.DJ.A4V5.01 2 0 1 0 1
#> TCGA.IM.A4EB.01 2 0 1 0 1
#> TCGA.EM.A4FO.01 2 0 1 0 1
#> TCGA.EM.A22M.01 2 0 1 0 1
#> TCGA.EL.A3GP.01 1 0 1 1 0
#> TCGA.EM.A2P1.01 2 0 1 0 1
#> TCGA.EM.A2P1.06 2 0 1 0 1
#> TCGA.ET.A3BS.01 2 0 1 0 1
#> TCGA.DO.A2HM.01 2 0 1 0 1
#> TCGA.EL.A3CV.01 2 0 1 0 1
#> TCGA.EM.A22P.01 2 0 1 0 1
#> TCGA.ET.A39M.01 2 0 1 0 1
#> TCGA.BJ.A0ZJ.01 2 0 1 0 1
#> TCGA.DJ.A13L.01 2 0 1 0 1
cbind(get_classes(res, k = 3), get_membership(res, k = 3))
#> class entropy silhouette p1 p2 p3
#> TCGA.ET.A40S.01 2 0.0892 0.975 0 0.98 0.02
#> TCGA.DE.A4MD.06 1 0.0000 1.000 1 0.00 0.00
#> TCGA.DJ.A2Q5.01 3 0.0892 1.000 0 0.02 0.98
#> TCGA.DJ.A4V5.01 3 0.0892 1.000 0 0.02 0.98
#> TCGA.IM.A4EB.01 3 0.0892 1.000 0 0.02 0.98
#> TCGA.EM.A4FO.01 2 0.0892 0.975 0 0.98 0.02
#> TCGA.EM.A22M.01 2 0.0000 0.994 0 1.00 0.00
#> TCGA.EL.A3GP.01 1 0.0000 1.000 1 0.00 0.00
#> TCGA.EM.A2P1.01 2 0.0000 0.994 0 1.00 0.00
#> TCGA.EM.A2P1.06 2 0.0000 0.994 0 1.00 0.00
#> TCGA.ET.A3BS.01 3 0.0892 1.000 0 0.02 0.98
#> TCGA.DO.A2HM.01 2 0.0000 0.994 0 1.00 0.00
#> TCGA.EL.A3CV.01 2 0.0000 0.994 0 1.00 0.00
#> TCGA.EM.A22P.01 2 0.0000 0.994 0 1.00 0.00
#> TCGA.ET.A39M.01 3 0.0892 1.000 0 0.02 0.98
#> TCGA.BJ.A0ZJ.01 3 0.0892 1.000 0 0.02 0.98
#> TCGA.DJ.A13L.01 2 0.0000 0.994 0 1.00 0.00
cbind(get_classes(res, k = 4), get_membership(res, k = 4))
#> class entropy silhouette p1 p2 p3 p4
#> TCGA.ET.A40S.01 4 0.000 0.000 0 0.00 0.0 1.00
#> TCGA.DE.A4MD.06 1 0.000 1.000 1 0.00 0.0 0.00
#> TCGA.DJ.A2Q5.01 3 0.000 1.000 0 0.00 1.0 0.00
#> TCGA.DJ.A4V5.01 3 0.000 1.000 0 0.00 1.0 0.00
#> TCGA.IM.A4EB.01 3 0.000 1.000 0 0.00 1.0 0.00
#> TCGA.EM.A4FO.01 2 0.234 0.865 0 0.90 0.1 0.00
#> TCGA.EM.A22M.01 2 0.121 0.946 0 0.96 0.0 0.04
#> TCGA.EL.A3GP.01 1 0.000 1.000 1 0.00 0.0 0.00
#> TCGA.EM.A2P1.01 2 0.000 0.976 0 1.00 0.0 0.00
#> TCGA.EM.A2P1.06 2 0.000 0.976 0 1.00 0.0 0.00
#> TCGA.ET.A3BS.01 3 0.000 1.000 0 0.00 1.0 0.00
#> TCGA.DO.A2HM.01 2 0.000 0.976 0 1.00 0.0 0.00
#> TCGA.EL.A3CV.01 2 0.000 0.976 0 1.00 0.0 0.00
#> TCGA.EM.A22P.01 2 0.000 0.976 0 1.00 0.0 0.00
#> TCGA.ET.A39M.01 3 0.000 1.000 0 0.00 1.0 0.00
#> TCGA.BJ.A0ZJ.01 3 0.000 1.000 0 0.00 1.0 0.00
#> TCGA.DJ.A13L.01 2 0.000 0.976 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.ET.A40S.01 4 0.0000 0.000 0 0.00 0.00 1 0.00
#> TCGA.DE.A4MD.06 1 0.0000 1.000 1 0.00 0.00 0 0.00
#> TCGA.DJ.A2Q5.01 3 0.0000 0.976 0 0.00 1.00 0 0.00
#> TCGA.DJ.A4V5.01 3 0.1410 0.958 0 0.00 0.94 0 0.06
#> TCGA.IM.A4EB.01 3 0.1410 0.958 0 0.00 0.94 0 0.06
#> TCGA.EM.A4FO.01 2 0.3895 0.459 0 0.68 0.32 0 0.00
#> TCGA.EM.A22M.01 5 0.2020 0.000 0 0.10 0.00 0 0.90
#> TCGA.EL.A3GP.01 1 0.0000 1.000 1 0.00 0.00 0 0.00
#> TCGA.EM.A2P1.01 2 0.0000 0.884 0 1.00 0.00 0 0.00
#> TCGA.EM.A2P1.06 2 0.0000 0.884 0 1.00 0.00 0 0.00
#> TCGA.ET.A3BS.01 3 0.0000 0.976 0 0.00 1.00 0 0.00
#> TCGA.DO.A2HM.01 2 0.0000 0.884 0 1.00 0.00 0 0.00
#> TCGA.EL.A3CV.01 2 0.0000 0.884 0 1.00 0.00 0 0.00
#> TCGA.EM.A22P.01 2 0.2732 0.745 0 0.84 0.00 0 0.16
#> TCGA.ET.A39M.01 3 0.0000 0.976 0 0.00 1.00 0 0.00
#> TCGA.BJ.A0ZJ.01 3 0.0609 0.974 0 0.00 0.98 0 0.02
#> TCGA.DJ.A13L.01 2 0.1043 0.866 0 0.96 0.00 0 0.04
cbind(get_classes(res, k = 6), get_membership(res, k = 6))
#> class entropy silhouette p1 p2 p3 p4 p5 p6
#> TCGA.ET.A40S.01 4 0.0000 0.000 0 0.00 0.00 1 0.00 0.00
#> TCGA.DE.A4MD.06 1 0.0000 1.000 1 0.00 0.00 0 0.00 0.00
#> TCGA.DJ.A2Q5.01 3 0.0000 0.968 0 0.00 1.00 0 0.00 0.00
#> TCGA.DJ.A4V5.01 3 0.2260 0.866 0 0.00 0.86 0 0.00 0.14
#> TCGA.IM.A4EB.01 3 0.0937 0.950 0 0.00 0.96 0 0.00 0.04
#> TCGA.EM.A4FO.01 2 0.4787 0.159 0 0.52 0.44 0 0.02 0.02
#> TCGA.EM.A22M.01 5 0.0000 0.000 0 0.00 0.00 0 1.00 0.00
#> TCGA.EL.A3GP.01 1 0.0000 1.000 1 0.00 0.00 0 0.00 0.00
#> TCGA.EM.A2P1.01 2 0.0000 0.779 0 1.00 0.00 0 0.00 0.00
#> TCGA.EM.A2P1.06 2 0.0000 0.779 0 1.00 0.00 0 0.00 0.00
#> TCGA.ET.A3BS.01 3 0.0000 0.968 0 0.00 1.00 0 0.00 0.00
#> TCGA.DO.A2HM.01 2 0.0000 0.779 0 1.00 0.00 0 0.00 0.00
#> TCGA.EL.A3CV.01 2 0.0547 0.770 0 0.98 0.00 0 0.00 0.02
#> TCGA.EM.A22P.01 6 0.3679 0.000 0 0.20 0.00 0 0.04 0.76
#> TCGA.ET.A39M.01 3 0.0000 0.968 0 0.00 1.00 0 0.00 0.00
#> TCGA.BJ.A0ZJ.01 3 0.0000 0.968 0 0.00 1.00 0 0.00 0.00
#> TCGA.DJ.A13L.01 2 0.4004 0.580 0 0.76 0.00 0 0.12 0.12
cbind(get_classes(res, k = 7), get_membership(res, k = 7))
#> class entropy silhouette p1 p2 p3 p4 p5 p6 p7
#> TCGA.ET.A40S.01 4 0.0000 0.0000 0 0.00 0.00 1 0.00 0.00 0.00
#> TCGA.DE.A4MD.06 1 0.0000 1.0000 1 0.00 0.00 0 0.00 0.00 0.00
#> TCGA.DJ.A2Q5.01 3 0.2016 0.7218 0 0.00 0.90 0 0.06 0.04 0.00
#> TCGA.DJ.A4V5.01 3 0.4108 0.5406 0 0.00 0.66 0 0.28 0.06 0.00
#> TCGA.IM.A4EB.01 3 0.3841 0.6225 0 0.00 0.68 0 0.28 0.04 0.00
#> TCGA.EM.A4FO.01 3 0.5791 -0.0139 0 0.40 0.44 0 0.10 0.06 0.00
#> TCGA.EM.A22M.01 7 0.0000 0.0000 0 0.00 0.00 0 0.00 0.00 1.00
#> TCGA.EL.A3GP.01 1 0.0000 1.0000 1 0.00 0.00 0 0.00 0.00 0.00
#> TCGA.EM.A2P1.01 2 0.0000 0.8240 0 1.00 0.00 0 0.00 0.00 0.00
#> TCGA.EM.A2P1.06 2 0.0000 0.8240 0 1.00 0.00 0 0.00 0.00 0.00
#> TCGA.ET.A3BS.01 3 0.2912 0.6891 0 0.00 0.82 0 0.14 0.04 0.00
#> TCGA.DO.A2HM.01 2 0.0504 0.8202 0 0.98 0.00 0 0.00 0.02 0.00
#> TCGA.EL.A3CV.01 2 0.2512 0.7389 0 0.86 0.00 0 0.10 0.04 0.00
#> TCGA.EM.A22P.01 6 0.1886 0.0000 0 0.12 0.00 0 0.00 0.88 0.00
#> TCGA.ET.A39M.01 3 0.0863 0.7355 0 0.00 0.96 0 0.04 0.00 0.00
#> TCGA.BJ.A0ZJ.01 3 0.0504 0.7362 0 0.00 0.98 0 0.02 0.00 0.00
#> TCGA.DJ.A13L.01 2 0.5293 0.3319 0 0.54 0.00 0 0.32 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.ET.A40S.01 4 0.0000 0.0000 0 0.00 0.00 1 0.00 0.00 0.00 0.00
#> TCGA.DE.A4MD.06 1 0.0000 1.0000 1 0.00 0.00 0 0.00 0.00 0.00 0.00
#> TCGA.DJ.A2Q5.01 3 0.3483 0.1997 0 0.02 0.76 0 0.18 0.00 0.00 0.04
#> TCGA.DJ.A4V5.01 3 0.5206 0.0482 0 0.00 0.50 0 0.32 0.02 0.00 0.16
#> TCGA.IM.A4EB.01 5 0.3318 0.0000 0 0.00 0.46 0 0.54 0.00 0.00 0.00
#> TCGA.EM.A4FO.01 3 0.5295 0.0449 0 0.36 0.50 0 0.10 0.02 0.00 0.02
#> TCGA.EM.A22M.01 7 0.0000 0.0000 0 0.00 0.00 0 0.00 0.00 1.00 0.00
#> TCGA.EL.A3GP.01 1 0.0000 1.0000 1 0.00 0.00 0 0.00 0.00 0.00 0.00
#> TCGA.EM.A2P1.01 2 0.0000 0.9087 0 1.00 0.00 0 0.00 0.00 0.00 0.00
#> TCGA.EM.A2P1.06 2 0.0000 0.9087 0 1.00 0.00 0 0.00 0.00 0.00 0.00
#> TCGA.ET.A3BS.01 3 0.3618 -0.3935 0 0.00 0.60 0 0.38 0.00 0.00 0.02
#> TCGA.DO.A2HM.01 2 0.2484 0.8442 0 0.86 0.00 0 0.02 0.02 0.00 0.10
#> TCGA.EL.A3CV.01 2 0.2348 0.8538 0 0.88 0.00 0 0.06 0.02 0.00 0.04
#> TCGA.EM.A22P.01 6 0.0941 0.0000 0 0.02 0.00 0 0.00 0.96 0.02 0.00
#> TCGA.ET.A39M.01 3 0.0471 0.1822 0 0.00 0.98 0 0.02 0.00 0.00 0.00
#> TCGA.BJ.A0ZJ.01 3 0.2224 0.0262 0 0.00 0.86 0 0.12 0.00 0.00 0.02
#> TCGA.DJ.A13L.01 8 0.3444 0.0000 0 0.14 0.00 0 0.00 0.02 0.06 0.78
Heatmaps for the consensus matrix. It visualizes the probability of two samples to be in a same group.
consensus_heatmap(res, k = 2)
consensus_heatmap(res, k = 3)
consensus_heatmap(res, k = 4)
consensus_heatmap(res, k = 5)
consensus_heatmap(res, k = 6)
consensus_heatmap(res, k = 7)
consensus_heatmap(res, k = 8)
Heatmaps for the membership of samples in all partitions to see how consistent they are:
membership_heatmap(res, k = 2)
membership_heatmap(res, k = 3)
membership_heatmap(res, k = 4)
membership_heatmap(res, k = 5)
membership_heatmap(res, k = 6)
membership_heatmap(res, k = 7)
membership_heatmap(res, k = 8)
As soon as the classes for columns are determined, the signatures that are significantly different between subgroups can be looked for. Following are the heatmaps for signatures.
get_signatures(res, k = 2)
get_signatures(res, k = 3)
get_signatures(res, k = 4)
get_signatures(res, k = 5)
get_signatures(res, k = 6)
get_signatures(res, k = 7)
get_signatures(res, k = 8)
Compare the overlap of signatures from different k:
compare_signatures(res)
get_signature() returns a data frame invisibly. To get the list of signatures, the function
call should be assigned to a variable explicitly. In following code, if plot argument is set
to FALSE, no heatmap is plotted while only the differential analysis is performed.
# code only for demonstration
tb = get_signature(res, k = ..., plot = FALSE)
An example of the output of tb is:
#> which_row fdr mean_1 mean_2 scaled_mean_1 scaled_mean_2 km
#> 1 38 0.042760348 8.373488 9.131774 -0.5533452 0.5164555 1
#> 2 40 0.018707592 7.106213 8.469186 -0.6173731 0.5762149 1
#> 3 55 0.019134737 10.221463 11.207825 -0.6159697 0.5749050 1
#> 4 59 0.006059896 5.921854 7.869574 -0.6899429 0.6439467 1
#> 5 60 0.018055526 8.928898 10.211722 -0.6204761 0.5791110 1
#> 6 98 0.009384629 15.714769 14.887706 0.6635654 -0.6193277 2
...
The columns in tb are:
which_row: row indices corresponding to the input matrix.fdr: FDR for the differential test. mean_x: The mean value in group x.scaled_mean_x: The mean value in group x after rows are scaled.km: Row groups if k-means clustering is applied to rows (which is done by automatically selecting number of clusters).If there are too many signatures, top_signatures = ... can be set to only show the
signatures with the highest FDRs:
# code only for demonstration
# e.g. to show the top 500 most significant rows
tb = get_signature(res, k = ..., top_signatures = 500)
If the signatures are defined as these which are uniquely high in current group, diff_method argument
can be set to "uniquely_high_in_one_group":
# code only for demonstration
tb = get_signature(res, k = ..., diff_method = "uniquely_high_in_one_group")
UMAP plot which shows how samples are separated.
dimension_reduction(res, k = 2, method = "UMAP")
dimension_reduction(res, k = 3, method = "UMAP")
dimension_reduction(res, k = 4, method = "UMAP")
dimension_reduction(res, k = 5, method = "UMAP")
dimension_reduction(res, k = 6, method = "UMAP")
dimension_reduction(res, k = 7, method = "UMAP")
dimension_reduction(res, k = 8, method = "UMAP")
Following heatmap shows how subgroups are split when increasing k:
collect_classes(res)
If matrix rows can be associated to genes, consider to use functional_enrichment(res,
...) to perform function enrichment for the signature genes. See this vignette for more detailed explanations.
Parent node: Node0. Child nodes: Node011 , Node012-leaf , Node013 , Node014 , Node015-leaf , Node021 , Node022 , Node023 , Node024 , Node025 , Node031 , Node032-leaf , Node033 , Node034-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 209 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 0.931 0.947 0.978 0.4859 0.513 0.513
#> 3 3 0.726 0.897 0.927 0.1960 0.877 0.769
#> 4 4 0.988 0.953 0.981 0.2466 0.772 0.511
#> 5 5 1.000 0.985 0.994 0.1053 0.878 0.590
#> 6 6 0.920 0.870 0.925 0.0243 0.991 0.954
#> 7 7 0.875 0.758 0.870 0.0224 0.976 0.873
#> 8 8 0.856 0.680 0.831 0.0155 0.977 0.867
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 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.E8.A416.01 1 0.000 0.972 1.00 0.00
#> TCGA.EL.A3ZO.11 1 0.000 0.972 1.00 0.00
#> TCGA.ET.A2N3.01 2 0.000 0.980 0.00 1.00
#> TCGA.EM.A4FU.01 2 0.000 0.980 0.00 1.00
#> TCGA.DJ.A3VM.01 2 0.000 0.980 0.00 1.00
#> TCGA.DJ.A3VG.01 2 0.000 0.980 0.00 1.00
#> TCGA.EL.A4K2.01 1 0.881 0.586 0.70 0.30
#> TCGA.EL.A3ZK.11 1 0.000 0.972 1.00 0.00
#> TCGA.FY.A40M.01 2 0.000 0.980 0.00 1.00
#> TCGA.KS.A41I.01 2 0.000 0.980 0.00 1.00
#> TCGA.DJ.A3VL.01 1 0.000 0.972 1.00 0.00
#> TCGA.ET.A4KQ.01 1 0.981 0.292 0.58 0.42
#> TCGA.DJ.A4V0.01 1 0.000 0.972 1.00 0.00
#> TCGA.EL.A3ZL.11 1 0.000 0.972 1.00 0.00
#> TCGA.EM.A4FH.01 2 0.000 0.980 0.00 1.00
#> TCGA.IM.A41Z.01 2 0.000 0.980 0.00 1.00
#> TCGA.DE.A4M9.01 2 0.000 0.980 0.00 1.00
#> TCGA.KS.A41L.01 2 0.000 0.980 0.00 1.00
#> TCGA.EL.A4KI.01 2 0.000 0.980 0.00 1.00
#> TCGA.EM.A4G1.01 2 0.000 0.980 0.00 1.00
#> TCGA.E8.A434.01 1 0.680 0.784 0.82 0.18
#> TCGA.EL.A3ZH.01 2 0.000 0.980 0.00 1.00
#> TCGA.EL.A3ZH.11 1 0.000 0.972 1.00 0.00
#> TCGA.EL.A3ZR.01 2 0.000 0.980 0.00 1.00
#> TCGA.EL.A3ZG.11 1 0.000 0.972 1.00 0.00
#> TCGA.ET.A40P.01 2 0.000 0.980 0.00 1.00
#> TCGA.DJ.A3VK.01 2 0.000 0.980 0.00 1.00
#> TCGA.EL.A3ZP.11 1 0.000 0.972 1.00 0.00
#> TCGA.BJ.A2N8.11 1 0.000 0.972 1.00 0.00
#> TCGA.EL.A3H2.01 2 0.000 0.980 0.00 1.00
#> TCGA.EM.A3AP.01 2 0.000 0.980 0.00 1.00
#> TCGA.BJ.A45E.01 1 0.000 0.972 1.00 0.00
#> TCGA.BJ.A45K.01 2 0.000 0.980 0.00 1.00
#> TCGA.E3.A3DZ.01 2 0.000 0.980 0.00 1.00
#> TCGA.BJ.A45C.01 2 0.000 0.980 0.00 1.00
#> TCGA.BJ.A45G.01 2 0.000 0.980 0.00 1.00
#> TCGA.BJ.A2P4.01 2 0.000 0.980 0.00 1.00
#> TCGA.CE.A484.01 2 0.000 0.980 0.00 1.00
#> TCGA.BJ.A45F.01 2 0.000 0.980 0.00 1.00
#> TCGA.FY.A4B0.01 2 0.000 0.980 0.00 1.00
#> TCGA.DJ.A2Q9.01 1 0.000 0.972 1.00 0.00
#> TCGA.EL.A4K6.01 2 0.000 0.980 0.00 1.00
#> TCGA.EM.A4FK.01 2 0.000 0.980 0.00 1.00
#> TCGA.EL.A3MW.11 1 0.000 0.972 1.00 0.00
#> TCGA.BJ.A45D.01 2 0.634 0.801 0.16 0.84
#> TCGA.DJ.A4UR.01 2 0.000 0.980 0.00 1.00
#> TCGA.EL.A3N2.11 1 0.000 0.972 1.00 0.00
#> TCGA.BJ.A2N9.01 2 0.000 0.980 0.00 1.00
#> TCGA.EL.A3GZ.11 1 0.000 0.972 1.00 0.00
#> TCGA.EM.A3AR.01 1 0.000 0.972 1.00 0.00
#> TCGA.EL.A3N3.11 1 0.000 0.972 1.00 0.00
#> TCGA.EL.A4JV.01 2 0.000 0.980 0.00 1.00
#> TCGA.BJ.A2N7.01 2 0.000 0.980 0.00 1.00
#> TCGA.DE.A2OL.01 2 0.000 0.980 0.00 1.00
#> TCGA.EL.A3H2.11 1 0.000 0.972 1.00 0.00
#> TCGA.MK.A84Z.01 2 0.000 0.980 0.00 1.00
#> TCGA.ET.A3DP.11 1 0.000 0.972 1.00 0.00
#> TCGA.EL.A3MX.11 1 0.000 0.972 1.00 0.00
#> TCGA.BJ.A28T.11 1 0.000 0.972 1.00 0.00
#> TCGA.EM.A22J.01 2 0.000 0.980 0.00 1.00
#> TCGA.BJ.A28W.11 2 0.000 0.980 0.00 1.00
#> TCGA.BJ.A2N8.01 2 0.000 0.980 0.00 1.00
#> TCGA.FY.A76V.01 2 0.000 0.980 0.00 1.00
#> TCGA.EM.A3FN.01 2 0.000 0.980 0.00 1.00
#> TCGA.QD.A8IV.01 2 0.000 0.980 0.00 1.00
#> TCGA.ET.A2MY.11 2 0.000 0.980 0.00 1.00
#> TCGA.ET.A25P.01 2 0.000 0.980 0.00 1.00
#> TCGA.EM.A2CT.01 2 0.000 0.980 0.00 1.00
#> TCGA.E8.A2JQ.11 1 0.000 0.972 1.00 0.00
#> TCGA.EM.A2CL.01 2 0.000 0.980 0.00 1.00
#> TCGA.ET.A2N5.01 2 0.000 0.980 0.00 1.00
#> TCGA.ET.A25J.11 1 0.000 0.972 1.00 0.00
#> TCGA.BJ.A28R.11 1 0.000 0.972 1.00 0.00
#> TCGA.EL.A3H7.11 1 0.000 0.972 1.00 0.00
#> TCGA.H2.A2K9.01 2 0.000 0.980 0.00 1.00
#> TCGA.EM.A22Q.01 2 0.000 0.980 0.00 1.00
#> TCGA.EM.A3FP.01 2 0.327 0.921 0.06 0.94
#> TCGA.GE.A2C6.11 1 0.000 0.972 1.00 0.00
#> TCGA.CE.A27D.01 1 0.000 0.972 1.00 0.00
#> TCGA.EL.A3H1.11 1 0.000 0.972 1.00 0.00
#> TCGA.BJ.A2N7.11 1 0.000 0.972 1.00 0.00
#> TCGA.EM.A2CQ.01 2 0.000 0.980 0.00 1.00
#> TCGA.EL.A3H1.01 2 0.000 0.980 0.00 1.00
#> TCGA.BJ.A28W.01 1 0.000 0.972 1.00 0.00
#> TCGA.BJ.A28T.01 1 0.000 0.972 1.00 0.00
#> TCGA.EM.A2CJ.01 2 0.000 0.980 0.00 1.00
#> TCGA.EM.A22K.01 2 0.000 0.980 0.00 1.00
#> TCGA.FY.A3NM.01 2 0.000 0.980 0.00 1.00
#> TCGA.EM.A22L.01 2 0.000 0.980 0.00 1.00
#> TCGA.BJ.A2N9.11 1 0.000 0.972 1.00 0.00
#> TCGA.BJ.A291.01 1 0.634 0.810 0.84 0.16
#> TCGA.ET.A2N5.11 1 0.000 0.972 1.00 0.00
#> TCGA.ET.A25N.11 1 0.000 0.972 1.00 0.00
#> TCGA.J8.A3O0.01 2 0.000 0.980 0.00 1.00
#> TCGA.EL.A3MY.11 1 0.760 0.727 0.78 0.22
#> TCGA.FY.A3NP.01 2 0.000 0.980 0.00 1.00
#> TCGA.ET.A25I.01 2 0.000 0.980 0.00 1.00
#> TCGA.BJ.A290.11 1 0.000 0.972 1.00 0.00
#> TCGA.FE.A239.01 2 0.000 0.980 0.00 1.00
#> TCGA.EM.A22N.01 2 0.958 0.379 0.38 0.62
#> TCGA.EM.A2CM.01 2 0.000 0.980 0.00 1.00
#> TCGA.EM.A3FL.01 2 0.000 0.980 0.00 1.00
#> TCGA.H2.A2K9.11 1 0.000 0.972 1.00 0.00
#> TCGA.FY.A3TY.01 1 0.000 0.972 1.00 0.00
#> TCGA.EM.A2OW.01 2 0.943 0.431 0.36 0.64
#> TCGA.DO.A1JZ.11 1 0.000 0.972 1.00 0.00
#> TCGA.EL.A3D5.01 2 0.000 0.980 0.00 1.00
#> TCGA.EL.A3GW.01 2 0.000 0.980 0.00 1.00
#> TCGA.EL.A3T1.11 1 0.000 0.972 1.00 0.00
#> TCGA.BJ.A0ZC.01 2 0.000 0.980 0.00 1.00
#> TCGA.EM.A2OV.01 2 0.000 0.980 0.00 1.00
#> TCGA.EM.A3SY.01 1 0.000 0.972 1.00 0.00
#> TCGA.EM.A3AI.01 1 0.469 0.880 0.90 0.10
#> TCGA.EM.A2OY.01 2 0.000 0.980 0.00 1.00
#> TCGA.BJ.A18Y.01 2 0.000 0.980 0.00 1.00
#> TCGA.EM.A2CK.01 1 0.943 0.455 0.64 0.36
#> TCGA.EL.A3T7.11 1 0.000 0.972 1.00 0.00
#> TCGA.BJ.A192.01 2 0.000 0.980 0.00 1.00
#> TCGA.EM.A2CP.01 1 0.000 0.972 1.00 0.00
#> TCGA.DJ.A3UZ.01 2 0.855 0.605 0.28 0.72
#> TCGA.BJ.A3F0.01 2 0.000 0.980 0.00 1.00
#> TCGA.EM.A3AJ.01 2 0.000 0.980 0.00 1.00
#> TCGA.EM.A1CW.01 2 0.000 0.980 0.00 1.00
#> TCGA.EM.A2P2.01 2 0.000 0.980 0.00 1.00
#> TCGA.EM.A1CU.11 1 0.000 0.972 1.00 0.00
#> TCGA.EL.A3T0.11 1 0.000 0.972 1.00 0.00
#> TCGA.FY.A3WA.01 2 0.000 0.980 0.00 1.00
#> TCGA.FY.A3TY.11 1 0.000 0.972 1.00 0.00
#> TCGA.EM.A1CT.11 1 0.000 0.972 1.00 0.00
#> TCGA.EM.A3ST.11 1 0.000 0.972 1.00 0.00
#> TCGA.ET.A3DV.01 2 0.000 0.980 0.00 1.00
#> TCGA.J8.A3YD.01 1 0.529 0.858 0.88 0.12
#> TCGA.EM.A3AL.01 2 0.000 0.980 0.00 1.00
#> TCGA.EM.A1CS.11 1 0.000 0.972 1.00 0.00
#> TCGA.EM.A1CW.11 1 0.000 0.972 1.00 0.00
#> TCGA.BJ.A190.01 1 0.000 0.972 1.00 0.00
#> TCGA.EM.A1CV.11 1 0.000 0.972 1.00 0.00
#> TCGA.EM.A3ST.01 2 0.000 0.980 0.00 1.00
#> TCGA.EL.A3GO.01 2 0.000 0.980 0.00 1.00
#> TCGA.DJ.A2Q0.01 2 0.584 0.827 0.14 0.86
#> TCGA.FK.A3SD.01 2 0.000 0.980 0.00 1.00
#> TCGA.EM.A1YE.11 1 0.000 0.972 1.00 0.00
#> TCGA.EL.A3T2.11 1 0.000 0.972 1.00 0.00
#> TCGA.EM.A1YC.01 1 0.469 0.880 0.90 0.10
#> TCGA.DJ.A3UP.01 2 0.000 0.980 0.00 1.00
#> TCGA.EL.A3CW.01 1 0.000 0.972 1.00 0.00
#> TCGA.ET.A39L.01 2 0.981 0.263 0.42 0.58
#> TCGA.EM.A2CO.01 2 0.000 0.980 0.00 1.00
#> TCGA.DJ.A2PP.01 2 0.000 0.980 0.00 1.00
#> TCGA.ET.A3DQ.01 1 0.000 0.972 1.00 0.00
#> TCGA.ET.A3DS.01 1 0.141 0.956 0.98 0.02
#> TCGA.FY.A3W9.01 2 0.000 0.980 0.00 1.00
#> TCGA.BJ.A2NA.11 1 0.000 0.972 1.00 0.00
#> TCGA.DJ.A1QL.01 2 0.000 0.980 0.00 1.00
#> TCGA.EM.A1YD.11 1 0.000 0.972 1.00 0.00
#> TCGA.ET.A3DW.11 1 0.000 0.972 1.00 0.00
#> TCGA.EL.A3TA.11 1 0.000 0.972 1.00 0.00
#> TCGA.EM.A1YE.01 2 0.000 0.980 0.00 1.00
#> TCGA.FY.A2QD.01 2 0.000 0.980 0.00 1.00
#> TCGA.DJ.A2Q2.01 2 0.000 0.980 0.00 1.00
#> TCGA.BJ.A28V.01 2 0.000 0.980 0.00 1.00
#> TCGA.BJ.A28X.11 1 0.000 0.972 1.00 0.00
#> TCGA.DJ.A1QG.01 2 0.000 0.980 0.00 1.00
#> TCGA.EL.A3TB.11 1 0.000 0.972 1.00 0.00
#> TCGA.ET.A39I.01 2 0.000 0.980 0.00 1.00
#> TCGA.EM.A1YB.01 2 0.000 0.980 0.00 1.00
#> TCGA.DJ.A3UT.01 2 0.000 0.980 0.00 1.00
#> TCGA.DJ.A1QM.01 1 0.000 0.972 1.00 0.00
#> TCGA.EL.A3CY.01 1 0.000 0.972 1.00 0.00
#> TCGA.EM.A1YC.11 1 0.000 0.972 1.00 0.00
#> TCGA.EL.A3T3.11 1 0.000 0.972 1.00 0.00
#> TCGA.EL.A3T2.01 2 0.000 0.980 0.00 1.00
#> TCGA.EL.A3T8.11 1 0.000 0.972 1.00 0.00
#> TCGA.EM.A1YA.01 2 0.000 0.980 0.00 1.00
#> TCGA.EL.A3CO.01 1 0.000 0.972 1.00 0.00
#> TCGA.EM.A1YD.01 1 0.141 0.956 0.98 0.02
#> TCGA.EL.A3CZ.01 2 0.000 0.980 0.00 1.00
#> TCGA.EM.A3FR.01 2 0.000 0.980 0.00 1.00
#> TCGA.EM.A3O8.01 2 0.971 0.324 0.40 0.60
#> TCGA.FY.A3R9.01 2 0.000 0.980 0.00 1.00
#> TCGA.EM.A3O6.01 2 0.000 0.980 0.00 1.00
#> TCGA.BJ.A28S.01 2 0.000 0.980 0.00 1.00
#> TCGA.H2.A3RI.11 1 0.000 0.972 1.00 0.00
#> TCGA.DJ.A13W.01 2 0.000 0.980 0.00 1.00
#> TCGA.BJ.A0ZA.01 2 0.000 0.980 0.00 1.00
#> TCGA.BJ.A3PT.01 2 0.000 0.980 0.00 1.00
#> TCGA.BJ.A0ZF.01 2 0.000 0.980 0.00 1.00
#> TCGA.BJ.A0YZ.01 2 0.000 0.980 0.00 1.00
#> TCGA.DJ.A2QB.01 2 0.000 0.980 0.00 1.00
#> TCGA.EM.A3OB.01 2 0.000 0.980 0.00 1.00
#> TCGA.H2.A3RH.01 2 0.000 0.980 0.00 1.00
#> TCGA.BJ.A3PR.11 1 0.000 0.972 1.00 0.00
#> TCGA.EL.A3T6.11 1 0.000 0.972 1.00 0.00
#> TCGA.BJ.A0ZG.01 1 0.881 0.587 0.70 0.30
#> TCGA.BJ.A0Z0.01 2 0.000 0.980 0.00 1.00
#> TCGA.EM.A3O9.01 1 0.000 0.972 1.00 0.00
#> TCGA.BJ.A3PR.01 1 0.000 0.972 1.00 0.00
#> TCGA.EM.A3OA.01 2 0.000 0.980 0.00 1.00
#> TCGA.BJ.A0ZE.01 2 0.000 0.980 0.00 1.00
#> TCGA.DJ.A13O.01 1 0.000 0.972 1.00 0.00
#> TCGA.DJ.A13M.01 2 0.000 0.980 0.00 1.00
#> TCGA.DJ.A13R.01 2 0.000 0.980 0.00 1.00
#> TCGA.ET.A39N.01 2 0.000 0.980 0.00 1.00
#> TCGA.BJ.A3PU.11 1 0.000 0.972 1.00 0.00
#> TCGA.FY.A3R7.01 2 0.529 0.853 0.12 0.88
#> TCGA.EM.A2CN.01 2 0.000 0.980 0.00 1.00
#> TCGA.BJ.A0Z2.01 2 0.000 0.980 0.00 1.00
#> TCGA.FY.A3I5.01 2 0.000 0.980 0.00 1.00
#> TCGA.DJ.A13S.01 2 0.000 0.980 0.00 1.00
cbind(get_classes(res, k = 3), get_membership(res, k = 3))
#> class entropy silhouette p1 p2 p3
#> TCGA.E8.A416.01 1 0.3340 0.9056 0.88 0.00 0.12
#> TCGA.EL.A3ZO.11 1 0.3340 0.9056 0.88 0.00 0.12
#> TCGA.ET.A2N3.01 2 0.0000 0.9263 0.00 1.00 0.00
#> TCGA.EM.A4FU.01 2 0.0000 0.9263 0.00 1.00 0.00
#> TCGA.DJ.A3VM.01 2 0.0000 0.9263 0.00 1.00 0.00
#> TCGA.DJ.A3VG.01 2 0.3340 0.9345 0.12 0.88 0.00
#> TCGA.EL.A4K2.01 2 0.6280 0.3865 0.46 0.54 0.00
#> TCGA.EL.A3ZK.11 3 0.0000 0.9792 0.00 0.00 1.00
#> TCGA.FY.A40M.01 2 0.2537 0.9331 0.08 0.92 0.00
#> TCGA.KS.A41I.01 2 0.3340 0.9345 0.12 0.88 0.00
#> TCGA.DJ.A3VL.01 3 0.3340 0.8297 0.12 0.00 0.88
#> TCGA.ET.A4KQ.01 1 0.6045 0.1536 0.62 0.38 0.00
#> TCGA.DJ.A4V0.01 3 0.0000 0.9792 0.00 0.00 1.00
#> TCGA.EL.A3ZL.11 1 0.3340 0.9056 0.88 0.00 0.12
#> TCGA.EM.A4FH.01 2 0.3340 0.9345 0.12 0.88 0.00
#> TCGA.IM.A41Z.01 2 0.0000 0.9263 0.00 1.00 0.00
#> TCGA.DE.A4M9.01 2 0.3340 0.9345 0.12 0.88 0.00
#> TCGA.KS.A41L.01 2 0.3340 0.9345 0.12 0.88 0.00
#> TCGA.EL.A4KI.01 2 0.0000 0.9263 0.00 1.00 0.00
#> TCGA.EM.A4G1.01 2 0.3340 0.9345 0.12 0.88 0.00
#> TCGA.E8.A434.01 2 0.6280 0.3861 0.46 0.54 0.00
#> TCGA.EL.A3ZH.01 2 0.3340 0.9345 0.12 0.88 0.00
#> TCGA.EL.A3ZH.11 1 0.3340 0.9056 0.88 0.00 0.12
#> TCGA.EL.A3ZR.01 2 0.3340 0.9345 0.12 0.88 0.00
#> TCGA.EL.A3ZG.11 1 0.3340 0.9056 0.88 0.00 0.12
#> TCGA.ET.A40P.01 2 0.3340 0.9345 0.12 0.88 0.00
#> TCGA.DJ.A3VK.01 2 0.3340 0.9345 0.12 0.88 0.00
#> TCGA.EL.A3ZP.11 3 0.0000 0.9792 0.00 0.00 1.00
#> TCGA.BJ.A2N8.11 1 0.3340 0.9056 0.88 0.00 0.12
#> TCGA.EL.A3H2.01 2 0.3340 0.9345 0.12 0.88 0.00
#> TCGA.EM.A3AP.01 2 0.3340 0.9345 0.12 0.88 0.00
#> TCGA.BJ.A45E.01 3 0.0000 0.9792 0.00 0.00 1.00
#> TCGA.BJ.A45K.01 2 0.0000 0.9263 0.00 1.00 0.00
#> TCGA.E3.A3DZ.01 2 0.3340 0.9345 0.12 0.88 0.00
#> TCGA.BJ.A45C.01 2 0.0000 0.9263 0.00 1.00 0.00
#> TCGA.BJ.A45G.01 2 0.2537 0.9331 0.08 0.92 0.00
#> TCGA.BJ.A2P4.01 2 0.3340 0.9345 0.12 0.88 0.00
#> TCGA.CE.A484.01 2 0.0000 0.9263 0.00 1.00 0.00
#> TCGA.BJ.A45F.01 2 0.3340 0.9345 0.12 0.88 0.00
#> TCGA.FY.A4B0.01 2 0.0000 0.9263 0.00 1.00 0.00
#> TCGA.DJ.A2Q9.01 3 0.0000 0.9792 0.00 0.00 1.00
#> TCGA.EL.A4K6.01 2 0.0000 0.9263 0.00 1.00 0.00
#> TCGA.EM.A4FK.01 2 0.0000 0.9263 0.00 1.00 0.00
#> TCGA.EL.A3MW.11 1 0.3340 0.9056 0.88 0.00 0.12
#> TCGA.BJ.A45D.01 2 0.3340 0.9345 0.12 0.88 0.00
#> TCGA.DJ.A4UR.01 2 0.0000 0.9263 0.00 1.00 0.00
#> TCGA.EL.A3N2.11 1 0.3340 0.9056 0.88 0.00 0.12
#> TCGA.BJ.A2N9.01 2 0.3340 0.9345 0.12 0.88 0.00
#> TCGA.EL.A3GZ.11 1 0.3340 0.9056 0.88 0.00 0.12
#> TCGA.EM.A3AR.01 1 0.3340 0.9056 0.88 0.00 0.12
#> TCGA.EL.A3N3.11 3 0.0000 0.9792 0.00 0.00 1.00
#> TCGA.EL.A4JV.01 2 0.3340 0.9345 0.12 0.88 0.00
#> TCGA.BJ.A2N7.01 2 0.3340 0.9345 0.12 0.88 0.00
#> TCGA.DE.A2OL.01 2 0.0000 0.9263 0.00 1.00 0.00
#> TCGA.EL.A3H2.11 1 0.3340 0.9056 0.88 0.00 0.12
#> TCGA.MK.A84Z.01 2 0.0000 0.9263 0.00 1.00 0.00
#> TCGA.ET.A3DP.11 1 0.3340 0.9056 0.88 0.00 0.12
#> TCGA.EL.A3MX.11 1 0.3340 0.9056 0.88 0.00 0.12
#> TCGA.BJ.A28T.11 1 0.3340 0.9056 0.88 0.00 0.12
#> TCGA.EM.A22J.01 2 0.0000 0.9263 0.00 1.00 0.00
#> TCGA.BJ.A28W.11 3 0.3340 0.8297 0.12 0.00 0.88
#> TCGA.BJ.A2N8.01 2 0.3340 0.9345 0.12 0.88 0.00
#> TCGA.FY.A76V.01 2 0.3340 0.9345 0.12 0.88 0.00
#> TCGA.EM.A3FN.01 2 0.0000 0.9263 0.00 1.00 0.00
#> TCGA.QD.A8IV.01 2 0.3340 0.9345 0.12 0.88 0.00
#> TCGA.ET.A2MY.11 2 0.0000 0.9263 0.00 1.00 0.00
#> TCGA.ET.A25P.01 2 0.3340 0.9345 0.12 0.88 0.00
#> TCGA.EM.A2CT.01 2 0.3340 0.9345 0.12 0.88 0.00
#> TCGA.E8.A2JQ.11 3 0.0000 0.9792 0.00 0.00 1.00
#> TCGA.EM.A2CL.01 2 0.0000 0.9263 0.00 1.00 0.00
#> TCGA.ET.A2N5.01 2 0.3340 0.9345 0.12 0.88 0.00
#> TCGA.ET.A25J.11 1 0.3340 0.9056 0.88 0.00 0.12
#> TCGA.BJ.A28R.11 3 0.0000 0.9792 0.00 0.00 1.00
#> TCGA.EL.A3H7.11 1 0.3340 0.9056 0.88 0.00 0.12
#> TCGA.H2.A2K9.01 2 0.0000 0.9263 0.00 1.00 0.00
#> TCGA.EM.A22Q.01 2 0.0000 0.9263 0.00 1.00 0.00
#> TCGA.EM.A3FP.01 2 0.8683 0.4425 0.12 0.54 0.34
#> TCGA.GE.A2C6.11 3 0.0000 0.9792 0.00 0.00 1.00
#> TCGA.CE.A27D.01 3 0.0000 0.9792 0.00 0.00 1.00
#> TCGA.EL.A3H1.11 3 0.0000 0.9792 0.00 0.00 1.00
#> TCGA.BJ.A2N7.11 1 0.3340 0.9056 0.88 0.00 0.12
#> TCGA.EM.A2CQ.01 2 0.3340 0.9345 0.12 0.88 0.00
#> TCGA.EL.A3H1.01 2 0.0000 0.9263 0.00 1.00 0.00
#> TCGA.BJ.A28W.01 3 0.0000 0.9792 0.00 0.00 1.00
#> TCGA.BJ.A28T.01 3 0.0000 0.9792 0.00 0.00 1.00
#> TCGA.EM.A2CJ.01 2 0.3340 0.9345 0.12 0.88 0.00
#> TCGA.EM.A22K.01 2 0.3340 0.9345 0.12 0.88 0.00
#> TCGA.FY.A3NM.01 2 0.3340 0.9345 0.12 0.88 0.00
#> TCGA.EM.A22L.01 2 0.3340 0.9345 0.12 0.88 0.00
#> TCGA.BJ.A2N9.11 3 0.0000 0.9792 0.00 0.00 1.00
#> TCGA.BJ.A291.01 1 0.4002 0.6048 0.84 0.16 0.00
#> TCGA.ET.A2N5.11 1 0.3340 0.9056 0.88 0.00 0.12
#> TCGA.ET.A25N.11 1 0.3340 0.9056 0.88 0.00 0.12
#> TCGA.J8.A3O0.01 2 0.0000 0.9263 0.00 1.00 0.00
#> TCGA.EL.A3MY.11 1 0.0000 0.8017 1.00 0.00 0.00
#> TCGA.FY.A3NP.01 2 0.3340 0.9345 0.12 0.88 0.00
#> TCGA.ET.A25I.01 2 0.3340 0.9345 0.12 0.88 0.00
#> TCGA.BJ.A290.11 1 0.3340 0.9056 0.88 0.00 0.12
#> TCGA.FE.A239.01 2 0.0000 0.9263 0.00 1.00 0.00
#> TCGA.EM.A22N.01 2 0.3340 0.9345 0.12 0.88 0.00
#> TCGA.EM.A2CM.01 2 0.0000 0.9263 0.00 1.00 0.00
#> TCGA.EM.A3FL.01 2 0.3340 0.9345 0.12 0.88 0.00
#> TCGA.H2.A2K9.11 3 0.0000 0.9792 0.00 0.00 1.00
#> TCGA.FY.A3TY.01 3 0.0000 0.9792 0.00 0.00 1.00
#> TCGA.EM.A2OW.01 2 0.3340 0.9345 0.12 0.88 0.00
#> TCGA.DO.A1JZ.11 1 0.3340 0.9056 0.88 0.00 0.12
#> TCGA.EL.A3D5.01 2 0.0000 0.9263 0.00 1.00 0.00
#> TCGA.EL.A3GW.01 2 0.0000 0.9263 0.00 1.00 0.00
#> TCGA.EL.A3T1.11 3 0.0000 0.9792 0.00 0.00 1.00
#> TCGA.BJ.A0ZC.01 2 0.3340 0.9345 0.12 0.88 0.00
#> TCGA.EM.A2OV.01 2 0.3340 0.9345 0.12 0.88 0.00
#> TCGA.EM.A3SY.01 1 0.3340 0.9056 0.88 0.00 0.12
#> TCGA.EM.A3AI.01 1 0.0000 0.8017 1.00 0.00 0.00
#> TCGA.EM.A2OY.01 2 0.3340 0.9345 0.12 0.88 0.00
#> TCGA.BJ.A18Y.01 2 0.3340 0.9345 0.12 0.88 0.00
#> TCGA.EM.A2CK.01 1 0.2959 0.6856 0.90 0.10 0.00
#> TCGA.EL.A3T7.11 1 0.3340 0.9056 0.88 0.00 0.12
#> TCGA.BJ.A192.01 2 0.2537 0.9331 0.08 0.92 0.00
#> TCGA.EM.A2CP.01 3 0.0000 0.9792 0.00 0.00 1.00
#> TCGA.DJ.A3UZ.01 2 0.7633 0.7170 0.12 0.68 0.20
#> TCGA.BJ.A3F0.01 2 0.0000 0.9263 0.00 1.00 0.00
#> TCGA.EM.A3AJ.01 3 0.5334 0.7596 0.12 0.06 0.82
#> TCGA.EM.A1CW.01 2 0.3340 0.9345 0.12 0.88 0.00
#> TCGA.EM.A2P2.01 2 0.0000 0.9263 0.00 1.00 0.00
#> TCGA.EM.A1CU.11 1 0.3340 0.9056 0.88 0.00 0.12
#> TCGA.EL.A3T0.11 1 0.3340 0.9056 0.88 0.00 0.12
#> TCGA.FY.A3WA.01 2 0.0000 0.9263 0.00 1.00 0.00
#> TCGA.FY.A3TY.11 1 0.3340 0.9056 0.88 0.00 0.12
#> TCGA.EM.A1CT.11 1 0.3340 0.9056 0.88 0.00 0.12
#> TCGA.EM.A3ST.11 1 0.3340 0.9056 0.88 0.00 0.12
#> TCGA.ET.A3DV.01 2 0.0000 0.9263 0.00 1.00 0.00
#> TCGA.J8.A3YD.01 1 0.0000 0.8017 1.00 0.00 0.00
#> TCGA.EM.A3AL.01 2 0.0000 0.9263 0.00 1.00 0.00
#> TCGA.EM.A1CS.11 1 0.3340 0.9056 0.88 0.00 0.12
#> TCGA.EM.A1CW.11 1 0.3340 0.9056 0.88 0.00 0.12
#> TCGA.BJ.A190.01 1 0.0000 0.8017 1.00 0.00 0.00
#> TCGA.EM.A1CV.11 1 0.3340 0.9056 0.88 0.00 0.12
#> TCGA.EM.A3ST.01 2 0.0000 0.9263 0.00 1.00 0.00
#> TCGA.EL.A3GO.01 2 0.0000 0.9263 0.00 1.00 0.00
#> TCGA.DJ.A2Q0.01 2 0.3340 0.9345 0.12 0.88 0.00
#> TCGA.FK.A3SD.01 2 0.0000 0.9263 0.00 1.00 0.00
#> TCGA.EM.A1YE.11 1 0.3340 0.9056 0.88 0.00 0.12
#> TCGA.EL.A3T2.11 1 0.3340 0.9056 0.88 0.00 0.12
#> TCGA.EM.A1YC.01 1 0.0000 0.8017 1.00 0.00 0.00
#> TCGA.DJ.A3UP.01 2 0.0000 0.9263 0.00 1.00 0.00
#> TCGA.EL.A3CW.01 3 0.0000 0.9792 0.00 0.00 1.00
#> TCGA.ET.A39L.01 1 0.6302 -0.2213 0.52 0.48 0.00
#> TCGA.EM.A2CO.01 2 0.3340 0.9345 0.12 0.88 0.00
#> TCGA.DJ.A2PP.01 2 0.0000 0.9263 0.00 1.00 0.00
#> TCGA.ET.A3DQ.01 3 0.0892 0.9555 0.02 0.00 0.98
#> TCGA.ET.A3DS.01 1 0.0000 0.8017 1.00 0.00 0.00
#> TCGA.FY.A3W9.01 2 0.0000 0.9263 0.00 1.00 0.00
#> TCGA.BJ.A2NA.11 3 0.0000 0.9792 0.00 0.00 1.00
#> TCGA.DJ.A1QL.01 2 0.0000 0.9263 0.00 1.00 0.00
#> TCGA.EM.A1YD.11 1 0.3340 0.9056 0.88 0.00 0.12
#> TCGA.ET.A3DW.11 1 0.3340 0.9056 0.88 0.00 0.12
#> TCGA.EL.A3TA.11 1 0.3340 0.9056 0.88 0.00 0.12
#> TCGA.EM.A1YE.01 2 0.3340 0.9345 0.12 0.88 0.00
#> TCGA.FY.A2QD.01 2 0.0000 0.9263 0.00 1.00 0.00
#> TCGA.DJ.A2Q2.01 2 0.3340 0.9345 0.12 0.88 0.00
#> TCGA.BJ.A28V.01 2 0.0000 0.9263 0.00 1.00 0.00
#> TCGA.BJ.A28X.11 3 0.0000 0.9792 0.00 0.00 1.00
#> TCGA.DJ.A1QG.01 2 0.0892 0.9283 0.02 0.98 0.00
#> TCGA.EL.A3TB.11 1 0.3340 0.9056 0.88 0.00 0.12
#> TCGA.ET.A39I.01 2 0.3340 0.9345 0.12 0.88 0.00
#> TCGA.EM.A1YB.01 2 0.0000 0.9263 0.00 1.00 0.00
#> TCGA.DJ.A3UT.01 2 0.3340 0.9345 0.12 0.88 0.00
#> TCGA.DJ.A1QM.01 1 0.3340 0.9056 0.88 0.00 0.12
#> TCGA.EL.A3CY.01 3 0.0000 0.9792 0.00 0.00 1.00
#> TCGA.EM.A1YC.11 1 0.3340 0.9056 0.88 0.00 0.12
#> TCGA.EL.A3T3.11 1 0.3340 0.9056 0.88 0.00 0.12
#> TCGA.EL.A3T2.01 2 0.3340 0.9345 0.12 0.88 0.00
#> TCGA.EL.A3T8.11 1 0.3340 0.9056 0.88 0.00 0.12
#> TCGA.EM.A1YA.01 2 0.3340 0.9345 0.12 0.88 0.00
#> TCGA.EL.A3CO.01 3 0.0000 0.9792 0.00 0.00 1.00
#> TCGA.EM.A1YD.01 1 0.0000 0.8017 1.00 0.00 0.00
#> TCGA.EL.A3CZ.01 2 0.3340 0.9345 0.12 0.88 0.00
#> TCGA.EM.A3FR.01 2 0.0000 0.9263 0.00 1.00 0.00
#> TCGA.EM.A3O8.01 1 0.6126 0.0820 0.60 0.40 0.00
#> TCGA.FY.A3R9.01 2 0.3340 0.9345 0.12 0.88 0.00
#> TCGA.EM.A3O6.01 2 0.3340 0.9345 0.12 0.88 0.00
#> TCGA.BJ.A28S.01 2 0.0000 0.9263 0.00 1.00 0.00
#> TCGA.H2.A3RI.11 1 0.3340 0.9056 0.88 0.00 0.12
#> TCGA.DJ.A13W.01 2 0.0000 0.9263 0.00 1.00 0.00
#> TCGA.BJ.A0ZA.01 2 0.0000 0.9263 0.00 1.00 0.00
#> TCGA.BJ.A3PT.01 2 0.3340 0.9345 0.12 0.88 0.00
#> TCGA.BJ.A0ZF.01 2 0.3340 0.9345 0.12 0.88 0.00
#> TCGA.BJ.A0YZ.01 2 0.3340 0.9345 0.12 0.88 0.00
#> TCGA.DJ.A2QB.01 2 0.3340 0.9345 0.12 0.88 0.00
#> TCGA.EM.A3OB.01 2 0.3340 0.9345 0.12 0.88 0.00
#> TCGA.H2.A3RH.01 2 0.0000 0.9263 0.00 1.00 0.00
#> TCGA.BJ.A3PR.11 3 0.0000 0.9792 0.00 0.00 1.00
#> TCGA.EL.A3T6.11 3 0.0000 0.9792 0.00 0.00 1.00
#> TCGA.BJ.A0ZG.01 1 0.6126 0.0816 0.60 0.40 0.00
#> TCGA.BJ.A0Z0.01 2 0.0000 0.9263 0.00 1.00 0.00
#> TCGA.EM.A3O9.01 3 0.0000 0.9792 0.00 0.00 1.00
#> TCGA.BJ.A3PR.01 3 0.0000 0.9792 0.00 0.00 1.00
#> TCGA.EM.A3OA.01 2 0.0000 0.9263 0.00 1.00 0.00
#> TCGA.BJ.A0ZE.01 2 0.0000 0.9263 0.00 1.00 0.00
#> TCGA.DJ.A13O.01 3 0.0000 0.9792 0.00 0.00 1.00
#> TCGA.DJ.A13M.01 2 0.3340 0.9345 0.12 0.88 0.00
#> TCGA.DJ.A13R.01 2 0.2537 0.9331 0.08 0.92 0.00
#> TCGA.ET.A39N.01 2 0.0892 0.9285 0.02 0.98 0.00
#> TCGA.BJ.A3PU.11 1 0.3340 0.9056 0.88 0.00 0.12
#> TCGA.FY.A3R7.01 2 0.3340 0.9345 0.12 0.88 0.00
#> TCGA.EM.A2CN.01 2 0.0000 0.9263 0.00 1.00 0.00
#> TCGA.BJ.A0Z2.01 2 0.0000 0.9263 0.00 1.00 0.00
#> TCGA.FY.A3I5.01 2 0.0000 0.9263 0.00 1.00 0.00
#> TCGA.DJ.A13S.01 2 0.3340 0.9345 0.12 0.88 0.00
cbind(get_classes(res, k = 4), get_membership(res, k = 4))
#> class entropy silhouette p1 p2 p3 p4
#> TCGA.E8.A416.01 1 0.0000 0.99941 1.00 0.00 0.00 0.00
#> TCGA.EL.A3ZO.11 1 0.0000 0.99941 1.00 0.00 0.00 0.00
#> TCGA.ET.A2N3.01 4 0.0000 0.94977 0.00 0.00 0.00 1.00
#> TCGA.EM.A4FU.01 4 0.1211 0.91703 0.00 0.04 0.00 0.96
#> TCGA.DJ.A3VM.01 4 0.0000 0.94977 0.00 0.00 0.00 1.00
#> TCGA.DJ.A3VG.01 2 0.0000 0.97657 0.00 1.00 0.00 0.00
#> TCGA.EL.A4K2.01 2 0.0000 0.97657 0.00 1.00 0.00 0.00
#> TCGA.EL.A3ZK.11 3 0.0000 0.99845 0.00 0.00 1.00 0.00
#> TCGA.FY.A40M.01 2 0.2921 0.82493 0.00 0.86 0.00 0.14
#> TCGA.KS.A41I.01 2 0.0000 0.97657 0.00 1.00 0.00 0.00
#> TCGA.DJ.A3VL.01 3 0.1211 0.95133 0.00 0.04 0.96 0.00
#> TCGA.ET.A4KQ.01 2 0.0000 0.97657 0.00 1.00 0.00 0.00
#> TCGA.DJ.A4V0.01 3 0.0000 0.99845 0.00 0.00 1.00 0.00
#> TCGA.EL.A3ZL.11 1 0.0000 0.99941 1.00 0.00 0.00 0.00
#> TCGA.EM.A4FH.01 2 0.0000 0.97657 0.00 1.00 0.00 0.00
#> TCGA.IM.A41Z.01 4 0.0000 0.94977 0.00 0.00 0.00 1.00
#> TCGA.DE.A4M9.01 2 0.0000 0.97657 0.00 1.00 0.00 0.00
#> TCGA.KS.A41L.01 2 0.0000 0.97657 0.00 1.00 0.00 0.00
#> TCGA.EL.A4KI.01 4 0.0000 0.94977 0.00 0.00 0.00 1.00
#> TCGA.EM.A4G1.01 2 0.0000 0.97657 0.00 1.00 0.00 0.00
#> TCGA.E8.A434.01 2 0.0000 0.97657 0.00 1.00 0.00 0.00
#> TCGA.EL.A3ZH.01 2 0.0000 0.97657 0.00 1.00 0.00 0.00
#> TCGA.EL.A3ZH.11 1 0.0000 0.99941 1.00 0.00 0.00 0.00
#> TCGA.EL.A3ZR.01 2 0.0000 0.97657 0.00 1.00 0.00 0.00
#> TCGA.EL.A3ZG.11 1 0.0000 0.99941 1.00 0.00 0.00 0.00
#> TCGA.ET.A40P.01 2 0.0000 0.97657 0.00 1.00 0.00 0.00
#> TCGA.DJ.A3VK.01 2 0.0000 0.97657 0.00 1.00 0.00 0.00
#> TCGA.EL.A3ZP.11 3 0.0000 0.99845 0.00 0.00 1.00 0.00
#> TCGA.BJ.A2N8.11 1 0.0000 0.99941 1.00 0.00 0.00 0.00
#> TCGA.EL.A3H2.01 2 0.0000 0.97657 0.00 1.00 0.00 0.00
#> TCGA.EM.A3AP.01 2 0.0000 0.97657 0.00 1.00 0.00 0.00
#> TCGA.BJ.A45E.01 3 0.0000 0.99845 0.00 0.00 1.00 0.00
#> TCGA.BJ.A45K.01 4 0.0000 0.94977 0.00 0.00 0.00 1.00
#> TCGA.E3.A3DZ.01 2 0.0000 0.97657 0.00 1.00 0.00 0.00
#> TCGA.BJ.A45C.01 4 0.0000 0.94977 0.00 0.00 0.00 1.00
#> TCGA.BJ.A45G.01 2 0.3172 0.79728 0.00 0.84 0.00 0.16
#> TCGA.BJ.A2P4.01 2 0.0000 0.97657 0.00 1.00 0.00 0.00
#> TCGA.CE.A484.01 4 0.4522 0.56204 0.00 0.32 0.00 0.68
#> TCGA.BJ.A45F.01 2 0.0000 0.97657 0.00 1.00 0.00 0.00
#> TCGA.FY.A4B0.01 4 0.0000 0.94977 0.00 0.00 0.00 1.00
#> TCGA.DJ.A2Q9.01 3 0.0000 0.99845 0.00 0.00 1.00 0.00
#> TCGA.EL.A4K6.01 4 0.0000 0.94977 0.00 0.00 0.00 1.00
#> TCGA.EM.A4FK.01 4 0.0000 0.94977 0.00 0.00 0.00 1.00
#> TCGA.EL.A3MW.11 1 0.0000 0.99941 1.00 0.00 0.00 0.00
#> TCGA.BJ.A45D.01 2 0.0000 0.97657 0.00 1.00 0.00 0.00
#> TCGA.DJ.A4UR.01 4 0.0000 0.94977 0.00 0.00 0.00 1.00
#> TCGA.EL.A3N2.11 1 0.0000 0.99941 1.00 0.00 0.00 0.00
#> TCGA.BJ.A2N9.01 2 0.0000 0.97657 0.00 1.00 0.00 0.00
#> TCGA.EL.A3GZ.11 1 0.0000 0.99941 1.00 0.00 0.00 0.00
#> TCGA.EM.A3AR.01 1 0.0000 0.99941 1.00 0.00 0.00 0.00
#> TCGA.EL.A3N3.11 3 0.0000 0.99845 0.00 0.00 1.00 0.00
#> TCGA.EL.A4JV.01 2 0.0000 0.97657 0.00 1.00 0.00 0.00
#> TCGA.BJ.A2N7.01 2 0.0000 0.97657 0.00 1.00 0.00 0.00
#> TCGA.DE.A2OL.01 4 0.0000 0.94977 0.00 0.00 0.00 1.00
#> TCGA.EL.A3H2.11 1 0.0000 0.99941 1.00 0.00 0.00 0.00
#> TCGA.MK.A84Z.01 4 0.1211 0.91703 0.00 0.04 0.00 0.96
#> TCGA.ET.A3DP.11 1 0.0000 0.99941 1.00 0.00 0.00 0.00
#> TCGA.EL.A3MX.11 1 0.0000 0.99941 1.00 0.00 0.00 0.00
#> TCGA.BJ.A28T.11 1 0.0000 0.99941 1.00 0.00 0.00 0.00
#> TCGA.EM.A22J.01 4 0.0000 0.94977 0.00 0.00 0.00 1.00
#> TCGA.BJ.A28W.11 3 0.0000 0.99845 0.00 0.00 1.00 0.00
#> TCGA.BJ.A2N8.01 2 0.0000 0.97657 0.00 1.00 0.00 0.00
#> TCGA.FY.A76V.01 2 0.0000 0.97657 0.00 1.00 0.00 0.00
#> TCGA.EM.A3FN.01 4 0.0000 0.94977 0.00 0.00 0.00 1.00
#> TCGA.QD.A8IV.01 2 0.0000 0.97657 0.00 1.00 0.00 0.00
#> TCGA.ET.A2MY.11 4 0.0000 0.94977 0.00 0.00 0.00 1.00
#> TCGA.ET.A25P.01 2 0.0000 0.97657 0.00 1.00 0.00 0.00
#> TCGA.EM.A2CT.01 2 0.2011 0.89992 0.00 0.92 0.00 0.08
#> TCGA.E8.A2JQ.11 3 0.0000 0.99845 0.00 0.00 1.00 0.00
#> TCGA.EM.A2CL.01 4 0.0000 0.94977 0.00 0.00 0.00 1.00
#> TCGA.ET.A2N5.01 2 0.0000 0.97657 0.00 1.00 0.00 0.00
#> TCGA.ET.A25J.11 1 0.0000 0.99941 1.00 0.00 0.00 0.00
#> TCGA.BJ.A28R.11 3 0.0000 0.99845 0.00 0.00 1.00 0.00
#> TCGA.EL.A3H7.11 1 0.0000 0.99941 1.00 0.00 0.00 0.00
#> TCGA.H2.A2K9.01 4 0.0000 0.94977 0.00 0.00 0.00 1.00
#> TCGA.EM.A22Q.01 4 0.0000 0.94977 0.00 0.00 0.00 1.00
#> TCGA.EM.A3FP.01 2 0.0000 0.97657 0.00 1.00 0.00 0.00
#> TCGA.GE.A2C6.11 3 0.0000 0.99845 0.00 0.00 1.00 0.00
#> TCGA.CE.A27D.01 3 0.0000 0.99845 0.00 0.00 1.00 0.00
#> TCGA.EL.A3H1.11 3 0.0000 0.99845 0.00 0.00 1.00 0.00
#> TCGA.BJ.A2N7.11 1 0.0000 0.99941 1.00 0.00 0.00 0.00
#> TCGA.EM.A2CQ.01 2 0.0000 0.97657 0.00 1.00 0.00 0.00
#> TCGA.EL.A3H1.01 4 0.0000 0.94977 0.00 0.00 0.00 1.00
#> TCGA.BJ.A28W.01 3 0.0000 0.99845 0.00 0.00 1.00 0.00
#> TCGA.BJ.A28T.01 3 0.0000 0.99845 0.00 0.00 1.00 0.00
#> TCGA.EM.A2CJ.01 2 0.0000 0.97657 0.00 1.00 0.00 0.00
#> TCGA.EM.A22K.01 2 0.0000 0.97657 0.00 1.00 0.00 0.00
#> TCGA.FY.A3NM.01 2 0.0000 0.97657 0.00 1.00 0.00 0.00
#> TCGA.EM.A22L.01 2 0.0000 0.97657 0.00 1.00 0.00 0.00
#> TCGA.BJ.A2N9.11 3 0.0000 0.99845 0.00 0.00 1.00 0.00
#> TCGA.BJ.A291.01 2 0.0000 0.97657 0.00 1.00 0.00 0.00
#> TCGA.ET.A2N5.11 1 0.0000 0.99941 1.00 0.00 0.00 0.00
#> TCGA.ET.A25N.11 1 0.0000 0.99941 1.00 0.00 0.00 0.00
#> TCGA.J8.A3O0.01 4 0.0000 0.94977 0.00 0.00 0.00 1.00
#> TCGA.EL.A3MY.11 2 0.0000 0.97657 0.00 1.00 0.00 0.00
#> TCGA.FY.A3NP.01 2 0.0000 0.97657 0.00 1.00 0.00 0.00
#> TCGA.ET.A25I.01 2 0.0000 0.97657 0.00 1.00 0.00 0.00
#> TCGA.BJ.A290.11 1 0.0000 0.99941 1.00 0.00 0.00 0.00
#> TCGA.FE.A239.01 4 0.0000 0.94977 0.00 0.00 0.00 1.00
#> TCGA.EM.A22N.01 2 0.0000 0.97657 0.00 1.00 0.00 0.00
#> TCGA.EM.A2CM.01 4 0.0000 0.94977 0.00 0.00 0.00 1.00
#> TCGA.EM.A3FL.01 2 0.0000 0.97657 0.00 1.00 0.00 0.00
#> TCGA.H2.A2K9.11 3 0.0000 0.99845 0.00 0.00 1.00 0.00
#> TCGA.FY.A3TY.01 3 0.0000 0.99845 0.00 0.00 1.00 0.00
#> TCGA.EM.A2OW.01 2 0.0000 0.97657 0.00 1.00 0.00 0.00
#> TCGA.DO.A1JZ.11 1 0.0000 0.99941 1.00 0.00 0.00 0.00
#> TCGA.EL.A3D5.01 4 0.1637 0.89904 0.00 0.06 0.00 0.94
#> TCGA.EL.A3GW.01 4 0.4713 0.47846 0.00 0.36 0.00 0.64
#> TCGA.EL.A3T1.11 3 0.0000 0.99845 0.00 0.00 1.00 0.00
#> TCGA.BJ.A0ZC.01 2 0.0000 0.97657 0.00 1.00 0.00 0.00
#> TCGA.EM.A2OV.01 2 0.0000 0.97657 0.00 1.00 0.00 0.00
#> TCGA.EM.A3SY.01 1 0.0000 0.99941 1.00 0.00 0.00 0.00
#> TCGA.EM.A3AI.01 2 0.0000 0.97657 0.00 1.00 0.00 0.00
#> TCGA.EM.A2OY.01 2 0.0000 0.97657 0.00 1.00 0.00 0.00
#> TCGA.BJ.A18Y.01 2 0.0000 0.97657 0.00 1.00 0.00 0.00
#> TCGA.EM.A2CK.01 2 0.0000 0.97657 0.00 1.00 0.00 0.00
#> TCGA.EL.A3T7.11 1 0.0000 0.99941 1.00 0.00 0.00 0.00
#> TCGA.BJ.A192.01 2 0.2921 0.83265 0.00 0.86 0.00 0.14
#> TCGA.EM.A2CP.01 3 0.0000 0.99845 0.00 0.00 1.00 0.00
#> TCGA.DJ.A3UZ.01 2 0.0000 0.97657 0.00 1.00 0.00 0.00
#> TCGA.BJ.A3F0.01 4 0.0000 0.94977 0.00 0.00 0.00 1.00
#> TCGA.EM.A3AJ.01 3 0.0000 0.99845 0.00 0.00 1.00 0.00
#> TCGA.EM.A1CW.01 2 0.0000 0.97657 0.00 1.00 0.00 0.00
#> TCGA.EM.A2P2.01 4 0.3400 0.77127 0.00 0.18 0.00 0.82
#> TCGA.EM.A1CU.11 1 0.0000 0.99941 1.00 0.00 0.00 0.00
#> TCGA.EL.A3T0.11 1 0.0000 0.99941 1.00 0.00 0.00 0.00
#> TCGA.FY.A3WA.01 4 0.1637 0.89872 0.00 0.06 0.00 0.94
#> TCGA.FY.A3TY.11 1 0.0000 0.99941 1.00 0.00 0.00 0.00
#> TCGA.EM.A1CT.11 1 0.0000 0.99941 1.00 0.00 0.00 0.00
#> TCGA.EM.A3ST.11 1 0.0000 0.99941 1.00 0.00 0.00 0.00
#> TCGA.ET.A3DV.01 4 0.0000 0.94977 0.00 0.00 0.00 1.00
#> TCGA.J8.A3YD.01 2 0.0000 0.97657 0.00 1.00 0.00 0.00
#> TCGA.EM.A3AL.01 4 0.0000 0.94977 0.00 0.00 0.00 1.00
#> TCGA.EM.A1CS.11 1 0.0000 0.99941 1.00 0.00 0.00 0.00
#> TCGA.EM.A1CW.11 1 0.0000 0.99941 1.00 0.00 0.00 0.00
#> TCGA.BJ.A190.01 1 0.0707 0.97436 0.98 0.02 0.00 0.00
#> TCGA.EM.A1CV.11 1 0.0000 0.99941 1.00 0.00 0.00 0.00
#> TCGA.EM.A3ST.01 4 0.0000 0.94977 0.00 0.00 0.00 1.00
#> TCGA.EL.A3GO.01 4 0.0000 0.94977 0.00 0.00 0.00 1.00
#> TCGA.DJ.A2Q0.01 2 0.0000 0.97657 0.00 1.00 0.00 0.00
#> TCGA.FK.A3SD.01 4 0.0000 0.94977 0.00 0.00 0.00 1.00
#> TCGA.EM.A1YE.11 1 0.0000 0.99941 1.00 0.00 0.00 0.00
#> TCGA.EL.A3T2.11 1 0.0000 0.99941 1.00 0.00 0.00 0.00
#> TCGA.EM.A1YC.01 2 0.0707 0.95783 0.02 0.98 0.00 0.00
#> TCGA.DJ.A3UP.01 4 0.2345 0.85918 0.00 0.10 0.00 0.90
#> TCGA.EL.A3CW.01 3 0.0000 0.99845 0.00 0.00 1.00 0.00
#> TCGA.ET.A39L.01 2 0.0000 0.97657 0.00 1.00 0.00 0.00
#> TCGA.EM.A2CO.01 2 0.0000 0.97657 0.00 1.00 0.00 0.00
#> TCGA.DJ.A2PP.01 4 0.0000 0.94977 0.00 0.00 0.00 1.00
#> TCGA.ET.A3DQ.01 3 0.0000 0.99845 0.00 0.00 1.00 0.00
#> TCGA.ET.A3DS.01 2 0.0000 0.97657 0.00 1.00 0.00 0.00
#> TCGA.FY.A3W9.01 4 0.0000 0.94977 0.00 0.00 0.00 1.00
#> TCGA.BJ.A2NA.11 3 0.0000 0.99845 0.00 0.00 1.00 0.00
#> TCGA.DJ.A1QL.01 4 0.0000 0.94977 0.00 0.00 0.00 1.00
#> TCGA.EM.A1YD.11 1 0.0000 0.99941 1.00 0.00 0.00 0.00
#> TCGA.ET.A3DW.11 1 0.0000 0.99941 1.00 0.00 0.00 0.00
#> TCGA.EL.A3TA.11 1 0.0000 0.99941 1.00 0.00 0.00 0.00
#> TCGA.EM.A1YE.01 2 0.0000 0.97657 0.00 1.00 0.00 0.00
#> TCGA.FY.A2QD.01 4 0.0000 0.94977 0.00 0.00 0.00 1.00
#> TCGA.DJ.A2Q2.01 2 0.2011 0.89977 0.00 0.92 0.00 0.08
#> TCGA.BJ.A28V.01 4 0.0000 0.94977 0.00 0.00 0.00 1.00
#> TCGA.BJ.A28X.11 3 0.0000 0.99845 0.00 0.00 1.00 0.00
#> TCGA.DJ.A1QG.01 2 0.4994 0.00539 0.00 0.52 0.00 0.48
#> TCGA.EL.A3TB.11 1 0.0000 0.99941 1.00 0.00 0.00 0.00
#> TCGA.ET.A39I.01 2 0.0000 0.97657 0.00 1.00 0.00 0.00
#> TCGA.EM.A1YB.01 4 0.0000 0.94977 0.00 0.00 0.00 1.00
#> TCGA.DJ.A3UT.01 2 0.0000 0.97657 0.00 1.00 0.00 0.00
#> TCGA.DJ.A1QM.01 1 0.0000 0.99941 1.00 0.00 0.00 0.00
#> TCGA.EL.A3CY.01 3 0.0000 0.99845 0.00 0.00 1.00 0.00
#> TCGA.EM.A1YC.11 1 0.0000 0.99941 1.00 0.00 0.00 0.00
#> TCGA.EL.A3T3.11 1 0.0000 0.99941 1.00 0.00 0.00 0.00
#> TCGA.EL.A3T2.01 2 0.0000 0.97657 0.00 1.00 0.00 0.00
#> TCGA.EL.A3T8.11 1 0.0000 0.99941 1.00 0.00 0.00 0.00
#> TCGA.EM.A1YA.01 2 0.3400 0.77867 0.00 0.82 0.00 0.18
#> TCGA.EL.A3CO.01 3 0.0000 0.99845 0.00 0.00 1.00 0.00
#> TCGA.EM.A1YD.01 2 0.0000 0.97657 0.00 1.00 0.00 0.00
#> TCGA.EL.A3CZ.01 2 0.0000 0.97657 0.00 1.00 0.00 0.00
#> TCGA.EM.A3FR.01 4 0.0000 0.94977 0.00 0.00 0.00 1.00
#> TCGA.EM.A3O8.01 2 0.0000 0.97657 0.00 1.00 0.00 0.00
#> TCGA.FY.A3R9.01 2 0.0000 0.97657 0.00 1.00 0.00 0.00
#> TCGA.EM.A3O6.01 2 0.0000 0.97657 0.00 1.00 0.00 0.00
#> TCGA.BJ.A28S.01 4 0.4790 0.42972 0.00 0.38 0.00 0.62
#> TCGA.H2.A3RI.11 1 0.0000 0.99941 1.00 0.00 0.00 0.00
#> TCGA.DJ.A13W.01 4 0.0000 0.94977 0.00 0.00 0.00 1.00
#> TCGA.BJ.A0ZA.01 4 0.0000 0.94977 0.00 0.00 0.00 1.00
#> TCGA.BJ.A3PT.01 2 0.0000 0.97657 0.00 1.00 0.00 0.00
#> TCGA.BJ.A0ZF.01 2 0.0000 0.97657 0.00 1.00 0.00 0.00
#> TCGA.BJ.A0YZ.01 2 0.0000 0.97657 0.00 1.00 0.00 0.00
#> TCGA.DJ.A2QB.01 2 0.0000 0.97657 0.00 1.00 0.00 0.00
#> TCGA.EM.A3OB.01 2 0.0000 0.97657 0.00 1.00 0.00 0.00
#> TCGA.H2.A3RH.01 4 0.4624 0.52267 0.00 0.34 0.00 0.66
#> TCGA.BJ.A3PR.11 3 0.0000 0.99845 0.00 0.00 1.00 0.00
#> TCGA.EL.A3T6.11 3 0.0000 0.99845 0.00 0.00 1.00 0.00
#> TCGA.BJ.A0ZG.01 2 0.0000 0.97657 0.00 1.00 0.00 0.00
#> TCGA.BJ.A0Z0.01 4 0.0000 0.94977 0.00 0.00 0.00 1.00
#> TCGA.EM.A3O9.01 3 0.0000 0.99845 0.00 0.00 1.00 0.00
#> TCGA.BJ.A3PR.01 3 0.0000 0.99845 0.00 0.00 1.00 0.00
#> TCGA.EM.A3OA.01 4 0.0000 0.94977 0.00 0.00 0.00 1.00
#> TCGA.BJ.A0ZE.01 4 0.0000 0.94977 0.00 0.00 0.00 1.00
#> TCGA.DJ.A13O.01 3 0.0000 0.99845 0.00 0.00 1.00 0.00
#> TCGA.DJ.A13M.01 2 0.0000 0.97657 0.00 1.00 0.00 0.00
#> TCGA.DJ.A13R.01 4 0.5902 0.63897 0.00 0.14 0.16 0.70
#> TCGA.ET.A39N.01 2 0.4948 0.17514 0.00 0.56 0.00 0.44
#> TCGA.BJ.A3PU.11 1 0.0000 0.99941 1.00 0.00 0.00 0.00
#> TCGA.FY.A3R7.01 2 0.0000 0.97657 0.00 1.00 0.00 0.00
#> TCGA.EM.A2CN.01 4 0.0000 0.94977 0.00 0.00 0.00 1.00
#> TCGA.BJ.A0Z2.01 4 0.0000 0.94977 0.00 0.00 0.00 1.00
#> TCGA.FY.A3I5.01 4 0.0000 0.94977 0.00 0.00 0.00 1.00
#> TCGA.DJ.A13S.01 2 0.0000 0.97657 0.00 1.00 0.00 0.00
cbind(get_classes(res, k = 5), get_membership(res, k = 5))
#> class entropy silhouette p1 p2 p3 p4 p5
#> TCGA.E8.A416.01 1 0.0000 0.999 1.00 0.00 0 0.00 0.00
#> TCGA.EL.A3ZO.11 1 0.0000 0.999 1.00 0.00 0 0.00 0.00
#> TCGA.ET.A2N3.01 4 0.0000 0.995 0.00 0.00 0 1.00 0.00
#> TCGA.EM.A4FU.01 5 0.0000 0.993 0.00 0.00 0 0.00 1.00
#> TCGA.DJ.A3VM.01 4 0.0000 0.995 0.00 0.00 0 1.00 0.00
#> TCGA.DJ.A3VG.01 5 0.0000 0.993 0.00 0.00 0 0.00 1.00
#> TCGA.EL.A4K2.01 2 0.1043 0.944 0.00 0.96 0 0.00 0.04
#> TCGA.EL.A3ZK.11 3 0.0000 1.000 0.00 0.00 1 0.00 0.00
#> TCGA.FY.A40M.01 5 0.0000 0.993 0.00 0.00 0 0.00 1.00
#> TCGA.KS.A41I.01 5 0.0000 0.993 0.00 0.00 0 0.00 1.00
#> TCGA.DJ.A3VL.01 3 0.0000 1.000 0.00 0.00 1 0.00 0.00
#> TCGA.ET.A4KQ.01 5 0.0000 0.993 0.00 0.00 0 0.00 1.00
#> TCGA.DJ.A4V0.01 3 0.0000 1.000 0.00 0.00 1 0.00 0.00
#> TCGA.EL.A3ZL.11 1 0.0000 0.999 1.00 0.00 0 0.00 0.00
#> TCGA.EM.A4FH.01 2 0.0000 0.980 0.00 1.00 0 0.00 0.00
#> TCGA.IM.A41Z.01 4 0.0000 0.995 0.00 0.00 0 1.00 0.00
#> TCGA.DE.A4M9.01 2 0.0000 0.980 0.00 1.00 0 0.00 0.00
#> TCGA.KS.A41L.01 2 0.0000 0.980 0.00 1.00 0 0.00 0.00
#> TCGA.EL.A4KI.01 4 0.0000 0.995 0.00 0.00 0 1.00 0.00
#> TCGA.EM.A4G1.01 5 0.1043 0.953 0.00 0.04 0 0.00 0.96
#> TCGA.E8.A434.01 2 0.0000 0.980 0.00 1.00 0 0.00 0.00
#> TCGA.EL.A3ZH.01 2 0.2280 0.857 0.00 0.88 0 0.00 0.12
#> TCGA.EL.A3ZH.11 1 0.0000 0.999 1.00 0.00 0 0.00 0.00
#> TCGA.EL.A3ZR.01 5 0.0000 0.993 0.00 0.00 0 0.00 1.00
#> TCGA.EL.A3ZG.11 1 0.0000 0.999 1.00 0.00 0 0.00 0.00
#> TCGA.ET.A40P.01 5 0.0000 0.993 0.00 0.00 0 0.00 1.00
#> TCGA.DJ.A3VK.01 5 0.0000 0.993 0.00 0.00 0 0.00 1.00
#> TCGA.EL.A3ZP.11 3 0.0000 1.000 0.00 0.00 1 0.00 0.00
#> TCGA.BJ.A2N8.11 1 0.0000 0.999 1.00 0.00 0 0.00 0.00
#> TCGA.EL.A3H2.01 2 0.0000 0.980 0.00 1.00 0 0.00 0.00
#> TCGA.EM.A3AP.01 5 0.0000 0.993 0.00 0.00 0 0.00 1.00
#> TCGA.BJ.A45E.01 3 0.0000 1.000 0.00 0.00 1 0.00 0.00
#> TCGA.BJ.A45K.01 4 0.0000 0.995 0.00 0.00 0 1.00 0.00
#> TCGA.E3.A3DZ.01 5 0.0000 0.993 0.00 0.00 0 0.00 1.00
#> TCGA.BJ.A45C.01 4 0.1043 0.954 0.00 0.04 0 0.96 0.00
#> TCGA.BJ.A45G.01 5 0.0000 0.993 0.00 0.00 0 0.00 1.00
#> TCGA.BJ.A2P4.01 5 0.0000 0.993 0.00 0.00 0 0.00 1.00
#> TCGA.CE.A484.01 5 0.0000 0.993 0.00 0.00 0 0.00 1.00
#> TCGA.BJ.A45F.01 5 0.0000 0.993 0.00 0.00 0 0.00 1.00
#> TCGA.FY.A4B0.01 4 0.0000 0.995 0.00 0.00 0 1.00 0.00
#> TCGA.DJ.A2Q9.01 3 0.0000 1.000 0.00 0.00 1 0.00 0.00
#> TCGA.EL.A4K6.01 4 0.0000 0.995 0.00 0.00 0 1.00 0.00
#> TCGA.EM.A4FK.01 4 0.0000 0.995 0.00 0.00 0 1.00 0.00
#> TCGA.EL.A3MW.11 1 0.0000 0.999 1.00 0.00 0 0.00 0.00
#> TCGA.BJ.A45D.01 5 0.0000 0.993 0.00 0.00 0 0.00 1.00
#> TCGA.DJ.A4UR.01 4 0.0000 0.995 0.00 0.00 0 1.00 0.00
#> TCGA.EL.A3N2.11 1 0.0000 0.999 1.00 0.00 0 0.00 0.00
#> TCGA.BJ.A2N9.01 2 0.0000 0.980 0.00 1.00 0 0.00 0.00
#> TCGA.EL.A3GZ.11 1 0.0000 0.999 1.00 0.00 0 0.00 0.00
#> TCGA.EM.A3AR.01 1 0.0000 0.999 1.00 0.00 0 0.00 0.00
#> TCGA.EL.A3N3.11 3 0.0000 1.000 0.00 0.00 1 0.00 0.00
#> TCGA.EL.A4JV.01 5 0.0000 0.993 0.00 0.00 0 0.00 1.00
#> TCGA.BJ.A2N7.01 5 0.0000 0.993 0.00 0.00 0 0.00 1.00
#> TCGA.DE.A2OL.01 4 0.0000 0.995 0.00 0.00 0 1.00 0.00
#> TCGA.EL.A3H2.11 1 0.0000 0.999 1.00 0.00 0 0.00 0.00
#> TCGA.MK.A84Z.01 5 0.0000 0.993 0.00 0.00 0 0.00 1.00
#> TCGA.ET.A3DP.11 1 0.0000 0.999 1.00 0.00 0 0.00 0.00
#> TCGA.EL.A3MX.11 1 0.0000 0.999 1.00 0.00 0 0.00 0.00
#> TCGA.BJ.A28T.11 1 0.0000 0.999 1.00 0.00 0 0.00 0.00
#> TCGA.EM.A22J.01 4 0.0000 0.995 0.00 0.00 0 1.00 0.00
#> TCGA.BJ.A28W.11 3 0.0000 1.000 0.00 0.00 1 0.00 0.00
#> TCGA.BJ.A2N8.01 5 0.0000 0.993 0.00 0.00 0 0.00 1.00
#> TCGA.FY.A76V.01 5 0.0000 0.993 0.00 0.00 0 0.00 1.00
#> TCGA.EM.A3FN.01 4 0.0000 0.995 0.00 0.00 0 1.00 0.00
#> TCGA.QD.A8IV.01 5 0.0000 0.993 0.00 0.00 0 0.00 1.00
#> TCGA.ET.A2MY.11 4 0.0609 0.975 0.00 0.02 0 0.98 0.00
#> TCGA.ET.A25P.01 5 0.0000 0.993 0.00 0.00 0 0.00 1.00
#> TCGA.EM.A2CT.01 2 0.0000 0.980 0.00 1.00 0 0.00 0.00
#> TCGA.E8.A2JQ.11 3 0.0000 1.000 0.00 0.00 1 0.00 0.00
#> TCGA.EM.A2CL.01 4 0.0000 0.995 0.00 0.00 0 1.00 0.00
#> TCGA.ET.A2N5.01 5 0.0000 0.993 0.00 0.00 0 0.00 1.00
#> TCGA.ET.A25J.11 1 0.0000 0.999 1.00 0.00 0 0.00 0.00
#> TCGA.BJ.A28R.11 3 0.0000 1.000 0.00 0.00 1 0.00 0.00
#> TCGA.EL.A3H7.11 1 0.0000 0.999 1.00 0.00 0 0.00 0.00
#> TCGA.H2.A2K9.01 4 0.0000 0.995 0.00 0.00 0 1.00 0.00
#> TCGA.EM.A22Q.01 4 0.0000 0.995 0.00 0.00 0 1.00 0.00
#> TCGA.EM.A3FP.01 5 0.0000 0.993 0.00 0.00 0 0.00 1.00
#> TCGA.GE.A2C6.11 3 0.0000 1.000 0.00 0.00 1 0.00 0.00
#> TCGA.CE.A27D.01 3 0.0000 1.000 0.00 0.00 1 0.00 0.00
#> TCGA.EL.A3H1.11 3 0.0000 1.000 0.00 0.00 1 0.00 0.00
#> TCGA.BJ.A2N7.11 1 0.0000 0.999 1.00 0.00 0 0.00 0.00
#> TCGA.EM.A2CQ.01 2 0.0000 0.980 0.00 1.00 0 0.00 0.00
#> TCGA.EL.A3H1.01 4 0.0000 0.995 0.00 0.00 0 1.00 0.00
#> TCGA.BJ.A28W.01 3 0.0000 1.000 0.00 0.00 1 0.00 0.00
#> TCGA.BJ.A28T.01 3 0.0000 1.000 0.00 0.00 1 0.00 0.00
#> TCGA.EM.A2CJ.01 2 0.0000 0.980 0.00 1.00 0 0.00 0.00
#> TCGA.EM.A22K.01 5 0.0000 0.993 0.00 0.00 0 0.00 1.00
#> TCGA.FY.A3NM.01 2 0.0000 0.980 0.00 1.00 0 0.00 0.00
#> TCGA.EM.A22L.01 5 0.0000 0.993 0.00 0.00 0 0.00 1.00
#> TCGA.BJ.A2N9.11 3 0.0000 1.000 0.00 0.00 1 0.00 0.00
#> TCGA.BJ.A291.01 2 0.0000 0.980 0.00 1.00 0 0.00 0.00
#> TCGA.ET.A2N5.11 1 0.0000 0.999 1.00 0.00 0 0.00 0.00
#> TCGA.ET.A25N.11 1 0.0000 0.999 1.00 0.00 0 0.00 0.00
#> TCGA.J8.A3O0.01 4 0.0000 0.995 0.00 0.00 0 1.00 0.00
#> TCGA.EL.A3MY.11 2 0.0000 0.980 0.00 1.00 0 0.00 0.00
#> TCGA.FY.A3NP.01 5 0.0000 0.993 0.00 0.00 0 0.00 1.00
#> TCGA.ET.A25I.01 2 0.2020 0.881 0.00 0.90 0 0.00 0.10
#> TCGA.BJ.A290.11 1 0.0000 0.999 1.00 0.00 0 0.00 0.00
#> TCGA.FE.A239.01 4 0.0000 0.995 0.00 0.00 0 1.00 0.00
#> TCGA.EM.A22N.01 2 0.0000 0.980 0.00 1.00 0 0.00 0.00
#> TCGA.EM.A2CM.01 4 0.0000 0.995 0.00 0.00 0 1.00 0.00
#> TCGA.EM.A3FL.01 2 0.0000 0.980 0.00 1.00 0 0.00 0.00
#> TCGA.H2.A2K9.11 3 0.0000 1.000 0.00 0.00 1 0.00 0.00
#> TCGA.FY.A3TY.01 3 0.0000 1.000 0.00 0.00 1 0.00 0.00
#> TCGA.EM.A2OW.01 2 0.0000 0.980 0.00 1.00 0 0.00 0.00
#> TCGA.DO.A1JZ.11 1 0.0000 0.999 1.00 0.00 0 0.00 0.00
#> TCGA.EL.A3D5.01 5 0.3274 0.717 0.00 0.00 0 0.22 0.78
#> TCGA.EL.A3GW.01 5 0.0000 0.993 0.00 0.00 0 0.00 1.00
#> TCGA.EL.A3T1.11 3 0.0000 1.000 0.00 0.00 1 0.00 0.00
#> TCGA.BJ.A0ZC.01 2 0.0000 0.980 0.00 1.00 0 0.00 0.00
#> TCGA.EM.A2OV.01 2 0.0000 0.980 0.00 1.00 0 0.00 0.00
#> TCGA.EM.A3SY.01 1 0.1043 0.956 0.96 0.04 0 0.00 0.00
#> TCGA.EM.A3AI.01 2 0.0000 0.980 0.00 1.00 0 0.00 0.00
#> TCGA.EM.A2OY.01 2 0.0000 0.980 0.00 1.00 0 0.00 0.00
#> TCGA.BJ.A18Y.01 5 0.0000 0.993 0.00 0.00 0 0.00 1.00
#> TCGA.EM.A2CK.01 5 0.0000 0.993 0.00 0.00 0 0.00 1.00
#> TCGA.EL.A3T7.11 1 0.0000 0.999 1.00 0.00 0 0.00 0.00
#> TCGA.BJ.A192.01 2 0.0000 0.980 0.00 1.00 0 0.00 0.00
#> TCGA.EM.A2CP.01 3 0.0000 1.000 0.00 0.00 1 0.00 0.00
#> TCGA.DJ.A3UZ.01 2 0.0000 0.980 0.00 1.00 0 0.00 0.00
#> TCGA.BJ.A3F0.01 4 0.0000 0.995 0.00 0.00 0 1.00 0.00
#> TCGA.EM.A3AJ.01 3 0.0000 1.000 0.00 0.00 1 0.00 0.00
#> TCGA.EM.A1CW.01 2 0.0000 0.980 0.00 1.00 0 0.00 0.00
#> TCGA.EM.A2P2.01 5 0.0000 0.993 0.00 0.00 0 0.00 1.00
#> TCGA.EM.A1CU.11 1 0.0000 0.999 1.00 0.00 0 0.00 0.00
#> TCGA.EL.A3T0.11 1 0.0000 0.999 1.00 0.00 0 0.00 0.00
#> TCGA.FY.A3WA.01 2 0.4262 0.213 0.00 0.56 0 0.44 0.00
#> TCGA.FY.A3TY.11 1 0.0000 0.999 1.00 0.00 0 0.00 0.00
#> TCGA.EM.A1CT.11 1 0.0000 0.999 1.00 0.00 0 0.00 0.00
#> TCGA.EM.A3ST.11 1 0.0000 0.999 1.00 0.00 0 0.00 0.00
#> TCGA.ET.A3DV.01 4 0.0000 0.995 0.00 0.00 0 1.00 0.00
#> TCGA.J8.A3YD.01 2 0.0000 0.980 0.00 1.00 0 0.00 0.00
#> TCGA.EM.A3AL.01 4 0.0000 0.995 0.00 0.00 0 1.00 0.00
#> TCGA.EM.A1CS.11 1 0.0000 0.999 1.00 0.00 0 0.00 0.00
#> TCGA.EM.A1CW.11 1 0.0000 0.999 1.00 0.00 0 0.00 0.00
#> TCGA.BJ.A190.01 2 0.1410 0.923 0.06 0.94 0 0.00 0.00
#> TCGA.EM.A1CV.11 1 0.0000 0.999 1.00 0.00 0 0.00 0.00
#> TCGA.EM.A3ST.01 4 0.0000 0.995 0.00 0.00 0 1.00 0.00
#> TCGA.EL.A3GO.01 4 0.0000 0.995 0.00 0.00 0 1.00 0.00
#> TCGA.DJ.A2Q0.01 2 0.0000 0.980 0.00 1.00 0 0.00 0.00
#> TCGA.FK.A3SD.01 4 0.0000 0.995 0.00 0.00 0 1.00 0.00
#> TCGA.EM.A1YE.11 1 0.0000 0.999 1.00 0.00 0 0.00 0.00
#> TCGA.EL.A3T2.11 1 0.0000 0.999 1.00 0.00 0 0.00 0.00
#> TCGA.EM.A1YC.01 2 0.0000 0.980 0.00 1.00 0 0.00 0.00
#> TCGA.DJ.A3UP.01 5 0.0000 0.993 0.00 0.00 0 0.00 1.00
#> TCGA.EL.A3CW.01 3 0.0000 1.000 0.00 0.00 1 0.00 0.00
#> TCGA.ET.A39L.01 5 0.0000 0.993 0.00 0.00 0 0.00 1.00
#> TCGA.EM.A2CO.01 2 0.0000 0.980 0.00 1.00 0 0.00 0.00
#> TCGA.DJ.A2PP.01 4 0.0000 0.995 0.00 0.00 0 1.00 0.00
#> TCGA.ET.A3DQ.01 3 0.0000 1.000 0.00 0.00 1 0.00 0.00
#> TCGA.ET.A3DS.01 2 0.0000 0.980 0.00 1.00 0 0.00 0.00
#> TCGA.FY.A3W9.01 4 0.0000 0.995 0.00 0.00 0 1.00 0.00
#> TCGA.BJ.A2NA.11 3 0.0000 1.000 0.00 0.00 1 0.00 0.00
#> TCGA.DJ.A1QL.01 4 0.0000 0.995 0.00 0.00 0 1.00 0.00
#> TCGA.EM.A1YD.11 1 0.0000 0.999 1.00 0.00 0 0.00 0.00
#> TCGA.ET.A3DW.11 1 0.0000 0.999 1.00 0.00 0 0.00 0.00
#> TCGA.EL.A3TA.11 1 0.0000 0.999 1.00 0.00 0 0.00 0.00
#> TCGA.EM.A1YE.01 2 0.0000 0.980 0.00 1.00 0 0.00 0.00
#> TCGA.FY.A2QD.01 4 0.0000 0.995 0.00 0.00 0 1.00 0.00
#> TCGA.DJ.A2Q2.01 2 0.0000 0.980 0.00 1.00 0 0.00 0.00
#> TCGA.BJ.A28V.01 4 0.0000 0.995 0.00 0.00 0 1.00 0.00
#> TCGA.BJ.A28X.11 3 0.0000 1.000 0.00 0.00 1 0.00 0.00
#> TCGA.DJ.A1QG.01 5 0.0000 0.993 0.00 0.00 0 0.00 1.00
#> TCGA.EL.A3TB.11 1 0.0000 0.999 1.00 0.00 0 0.00 0.00
#> TCGA.ET.A39I.01 5 0.0000 0.993 0.00 0.00 0 0.00 1.00
#> TCGA.EM.A1YB.01 4 0.0000 0.995 0.00 0.00 0 1.00 0.00
#> TCGA.DJ.A3UT.01 5 0.0000 0.993 0.00 0.00 0 0.00 1.00
#> TCGA.DJ.A1QM.01 1 0.0000 0.999 1.00 0.00 0 0.00 0.00
#> TCGA.EL.A3CY.01 3 0.0000 1.000 0.00 0.00 1 0.00 0.00
#> TCGA.EM.A1YC.11 1 0.0000 0.999 1.00 0.00 0 0.00 0.00
#> TCGA.EL.A3T3.11 1 0.0000 0.999 1.00 0.00 0 0.00 0.00
#> TCGA.EL.A3T2.01 5 0.0000 0.993 0.00 0.00 0 0.00 1.00
#> TCGA.EL.A3T8.11 1 0.0000 0.999 1.00 0.00 0 0.00 0.00
#> TCGA.EM.A1YA.01 2 0.0000 0.980 0.00 1.00 0 0.00 0.00
#> TCGA.EL.A3CO.01 3 0.0000 1.000 0.00 0.00 1 0.00 0.00
#> TCGA.EM.A1YD.01 2 0.0000 0.980 0.00 1.00 0 0.00 0.00
#> TCGA.EL.A3CZ.01 2 0.1043 0.944 0.00 0.96 0 0.00 0.04
#> TCGA.EM.A3FR.01 4 0.0000 0.995 0.00 0.00 0 1.00 0.00
#> TCGA.EM.A3O8.01 5 0.0000 0.993 0.00 0.00 0 0.00 1.00
#> TCGA.FY.A3R9.01 2 0.0000 0.980 0.00 1.00 0 0.00 0.00
#> TCGA.EM.A3O6.01 2 0.0000 0.980 0.00 1.00 0 0.00 0.00
#> TCGA.BJ.A28S.01 5 0.0000 0.993 0.00 0.00 0 0.00 1.00
#> TCGA.H2.A3RI.11 1 0.0000 0.999 1.00 0.00 0 0.00 0.00
#> TCGA.DJ.A13W.01 4 0.0000 0.995 0.00 0.00 0 1.00 0.00
#> TCGA.BJ.A0ZA.01 4 0.2516 0.835 0.00 0.00 0 0.86 0.14
#> TCGA.BJ.A3PT.01 5 0.0000 0.993 0.00 0.00 0 0.00 1.00
#> TCGA.BJ.A0ZF.01 2 0.0000 0.980 0.00 1.00 0 0.00 0.00
#> TCGA.BJ.A0YZ.01 2 0.0000 0.980 0.00 1.00 0 0.00 0.00
#> TCGA.DJ.A2QB.01 5 0.0000 0.993 0.00 0.00 0 0.00 1.00
#> TCGA.EM.A3OB.01 5 0.0000 0.993 0.00 0.00 0 0.00 1.00
#> TCGA.H2.A3RH.01 5 0.0000 0.993 0.00 0.00 0 0.00 1.00
#> TCGA.BJ.A3PR.11 3 0.0000 1.000 0.00 0.00 1 0.00 0.00
#> TCGA.EL.A3T6.11 3 0.0000 1.000 0.00 0.00 1 0.00 0.00
#> TCGA.BJ.A0ZG.01 2 0.0000 0.980 0.00 1.00 0 0.00 0.00
#> TCGA.BJ.A0Z0.01 4 0.0000 0.995 0.00 0.00 0 1.00 0.00
#> TCGA.EM.A3O9.01 3 0.0000 1.000 0.00 0.00 1 0.00 0.00
#> TCGA.BJ.A3PR.01 3 0.0000 1.000 0.00 0.00 1 0.00 0.00
#> TCGA.EM.A3OA.01 4 0.0000 0.995 0.00 0.00 0 1.00 0.00
#> TCGA.BJ.A0ZE.01 5 0.1043 0.954 0.00 0.00 0 0.04 0.96
#> TCGA.DJ.A13O.01 3 0.0000 1.000 0.00 0.00 1 0.00 0.00
#> TCGA.DJ.A13M.01 5 0.0000 0.993 0.00 0.00 0 0.00 1.00
#> TCGA.DJ.A13R.01 2 0.0000 0.980 0.00 1.00 0 0.00 0.00
#> TCGA.ET.A39N.01 2 0.0000 0.980 0.00 1.00 0 0.00 0.00
#> TCGA.BJ.A3PU.11 1 0.0000 0.999 1.00 0.00 0 0.00 0.00
#> TCGA.FY.A3R7.01 2 0.0000 0.980 0.00 1.00 0 0.00 0.00
#> TCGA.EM.A2CN.01 4 0.0000 0.995 0.00 0.00 0 1.00 0.00
#> TCGA.BJ.A0Z2.01 4 0.0000 0.995 0.00 0.00 0 1.00 0.00
#> TCGA.FY.A3I5.01 4 0.0000 0.995 0.00 0.00 0 1.00 0.00
#> TCGA.DJ.A13S.01 5 0.0000 0.993 0.00 0.00 0 0.00 1.00
cbind(get_classes(res, k = 6), get_membership(res, k = 6))
#> class entropy silhouette p1 p2 p3 p4 p5 p6
#> TCGA.E8.A416.01 1 0.0000 0.995 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.EL.A3ZO.11 1 0.0000 0.995 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.ET.A2N3.01 4 0.0000 0.977 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.EM.A4FU.01 5 0.0547 0.887 0.00 0.00 0.00 0.00 0.98 0.02
#> TCGA.DJ.A3VM.01 4 0.0000 0.977 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.DJ.A3VG.01 5 0.0547 0.887 0.00 0.00 0.00 0.00 0.98 0.02
#> TCGA.EL.A4K2.01 2 0.3982 0.468 0.00 0.74 0.00 0.00 0.06 0.20
#> TCGA.EL.A3ZK.11 3 0.0000 0.939 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.FY.A40M.01 5 0.3409 0.584 0.00 0.00 0.00 0.00 0.70 0.30
#> TCGA.KS.A41I.01 5 0.2260 0.842 0.00 0.00 0.00 0.00 0.86 0.14
#> TCGA.DJ.A3VL.01 3 0.4482 0.608 0.00 0.00 0.60 0.00 0.04 0.36
#> TCGA.ET.A4KQ.01 5 0.3076 0.829 0.00 0.00 0.00 0.00 0.76 0.24
#> TCGA.DJ.A4V0.01 3 0.0937 0.935 0.00 0.00 0.96 0.00 0.00 0.04
#> TCGA.EL.A3ZL.11 1 0.0000 0.995 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.EM.A4FH.01 2 0.1267 0.757 0.00 0.94 0.00 0.00 0.00 0.06
#> TCGA.IM.A41Z.01 4 0.0937 0.952 0.00 0.00 0.00 0.96 0.00 0.04
#> TCGA.DE.A4M9.01 6 0.4328 0.706 0.00 0.46 0.00 0.00 0.02 0.52
#> TCGA.KS.A41L.01 2 0.3851 -0.662 0.00 0.54 0.00 0.00 0.00 0.46
#> TCGA.EL.A4KI.01 4 0.0000 0.977 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.EM.A4G1.01 5 0.3544 0.827 0.00 0.08 0.00 0.00 0.80 0.12
#> TCGA.E8.A434.01 2 0.2048 0.734 0.00 0.88 0.00 0.00 0.00 0.12
#> TCGA.EL.A3ZH.01 2 0.3916 0.202 0.00 0.68 0.00 0.00 0.30 0.02
#> TCGA.EL.A3ZH.11 1 0.0000 0.995 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.EL.A3ZR.01 5 0.0547 0.890 0.00 0.00 0.00 0.00 0.98 0.02
#> TCGA.EL.A3ZG.11 1 0.0000 0.995 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.ET.A40P.01 5 0.0000 0.890 0.00 0.00 0.00 0.00 1.00 0.00
#> TCGA.DJ.A3VK.01 5 0.2260 0.872 0.00 0.00 0.00 0.00 0.86 0.14
#> TCGA.EL.A3ZP.11 3 0.0000 0.939 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.BJ.A2N8.11 1 0.0000 0.995 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.EL.A3H2.01 2 0.1556 0.733 0.00 0.92 0.00 0.00 0.00 0.08
#> TCGA.EM.A3AP.01 5 0.0000 0.890 0.00 0.00 0.00 0.00 1.00 0.00
#> TCGA.BJ.A45E.01 3 0.0000 0.939 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.BJ.A45K.01 4 0.0000 0.977 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.E3.A3DZ.01 5 0.0547 0.887 0.00 0.00 0.00 0.00 0.98 0.02
#> TCGA.BJ.A45C.01 4 0.1807 0.917 0.00 0.02 0.00 0.92 0.00 0.06
#> TCGA.BJ.A45G.01 5 0.0547 0.887 0.00 0.00 0.00 0.00 0.98 0.02
#> TCGA.BJ.A2P4.01 5 0.1814 0.881 0.00 0.00 0.00 0.00 0.90 0.10
#> TCGA.CE.A484.01 5 0.0547 0.887 0.00 0.00 0.00 0.00 0.98 0.02
#> TCGA.BJ.A45F.01 5 0.2631 0.859 0.00 0.00 0.00 0.00 0.82 0.18
#> TCGA.FY.A4B0.01 4 0.0000 0.977 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.DJ.A2Q9.01 3 0.0000 0.939 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.EL.A4K6.01 4 0.0000 0.977 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.EM.A4FK.01 4 0.0937 0.952 0.00 0.00 0.00 0.96 0.00 0.04
#> TCGA.EL.A3MW.11 1 0.0000 0.995 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.BJ.A45D.01 5 0.3198 0.816 0.00 0.00 0.00 0.00 0.74 0.26
#> TCGA.DJ.A4UR.01 4 0.0937 0.944 0.00 0.00 0.00 0.96 0.04 0.00
#> TCGA.EL.A3N2.11 1 0.0000 0.995 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.BJ.A2N9.01 2 0.1556 0.795 0.00 0.92 0.00 0.00 0.00 0.08
#> TCGA.EL.A3GZ.11 1 0.0000 0.995 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.EM.A3AR.01 1 0.0000 0.995 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.EL.A3N3.11 3 0.0937 0.935 0.00 0.00 0.96 0.00 0.00 0.04
#> TCGA.EL.A4JV.01 5 0.2631 0.859 0.00 0.00 0.00 0.00 0.82 0.18
#> TCGA.BJ.A2N7.01 5 0.2631 0.859 0.00 0.00 0.00 0.00 0.82 0.18
#> TCGA.DE.A2OL.01 4 0.0000 0.977 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.EL.A3H2.11 1 0.0000 0.995 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.MK.A84Z.01 5 0.0547 0.887 0.00 0.00 0.00 0.00 0.98 0.02
#> TCGA.ET.A3DP.11 1 0.0000 0.995 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.EL.A3MX.11 1 0.0000 0.995 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.BJ.A28T.11 1 0.0000 0.995 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.EM.A22J.01 4 0.1556 0.915 0.00 0.00 0.00 0.92 0.00 0.08
#> TCGA.BJ.A28W.11 3 0.2793 0.850 0.00 0.00 0.80 0.00 0.00 0.20
#> TCGA.BJ.A2N8.01 5 0.2048 0.877 0.00 0.00 0.00 0.00 0.88 0.12
#> TCGA.FY.A76V.01 5 0.3076 0.829 0.00 0.00 0.00 0.00 0.76 0.24
#> TCGA.EM.A3FN.01 4 0.0547 0.966 0.00 0.00 0.00 0.98 0.00 0.02
#> TCGA.QD.A8IV.01 5 0.0547 0.887 0.00 0.00 0.00 0.00 0.98 0.02
#> TCGA.ET.A2MY.11 4 0.1480 0.931 0.00 0.02 0.00 0.94 0.00 0.04
#> TCGA.ET.A25P.01 5 0.2454 0.865 0.00 0.00 0.00 0.00 0.84 0.16
#> TCGA.EM.A2CT.01 2 0.1814 0.785 0.00 0.90 0.00 0.00 0.00 0.10
#> TCGA.E8.A2JQ.11 3 0.0000 0.939 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.EM.A2CL.01 4 0.0547 0.966 0.00 0.00 0.00 0.98 0.00 0.02
#> TCGA.ET.A2N5.01 5 0.0000 0.890 0.00 0.00 0.00 0.00 1.00 0.00
#> TCGA.ET.A25J.11 1 0.0000 0.995 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.BJ.A28R.11 3 0.0000 0.939 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.EL.A3H7.11 1 0.0000 0.995 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.H2.A2K9.01 4 0.0000 0.977 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.EM.A22Q.01 4 0.0000 0.977 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.EM.A3FP.01 5 0.3706 0.682 0.00 0.00 0.00 0.00 0.62 0.38
#> TCGA.GE.A2C6.11 3 0.0000 0.939 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.CE.A27D.01 3 0.0937 0.935 0.00 0.00 0.96 0.00 0.00 0.04
#> TCGA.EL.A3H1.11 3 0.0937 0.935 0.00 0.00 0.96 0.00 0.00 0.04
#> TCGA.BJ.A2N7.11 1 0.0000 0.995 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.EM.A2CQ.01 2 0.1814 0.785 0.00 0.90 0.00 0.00 0.00 0.10
#> TCGA.EL.A3H1.01 4 0.0000 0.977 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.BJ.A28W.01 3 0.0000 0.939 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.BJ.A28T.01 3 0.0000 0.939 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.EM.A2CJ.01 2 0.0937 0.790 0.00 0.96 0.00 0.00 0.00 0.04
#> TCGA.EM.A22K.01 5 0.1556 0.883 0.00 0.00 0.00 0.00 0.92 0.08
#> TCGA.FY.A3NM.01 2 0.0547 0.797 0.00 0.98 0.00 0.00 0.00 0.02
#> TCGA.EM.A22L.01 5 0.1814 0.881 0.00 0.00 0.00 0.00 0.90 0.10
#> TCGA.BJ.A2N9.11 3 0.0000 0.939 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.BJ.A291.01 2 0.1814 0.736 0.00 0.90 0.00 0.00 0.00 0.10
#> TCGA.ET.A2N5.11 1 0.0000 0.995 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.ET.A25N.11 1 0.0000 0.995 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.J8.A3O0.01 4 0.2094 0.877 0.00 0.00 0.00 0.90 0.08 0.02
#> TCGA.EL.A3MY.11 2 0.0000 0.798 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.FY.A3NP.01 5 0.0000 0.890 0.00 0.00 0.00 0.00 1.00 0.00
#> TCGA.ET.A25I.01 2 0.4552 0.386 0.00 0.64 0.00 0.00 0.06 0.30
#> TCGA.BJ.A290.11 1 0.0000 0.995 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.FE.A239.01 4 0.0000 0.977 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.EM.A22N.01 2 0.1556 0.795 0.00 0.92 0.00 0.00 0.00 0.08
#> TCGA.EM.A2CM.01 4 0.0000 0.977 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.EM.A3FL.01 2 0.1814 0.785 0.00 0.90 0.00 0.00 0.00 0.10
#> TCGA.H2.A2K9.11 3 0.0547 0.929 0.02 0.00 0.98 0.00 0.00 0.00
#> TCGA.FY.A3TY.01 3 0.0937 0.935 0.00 0.00 0.96 0.00 0.00 0.04
#> TCGA.EM.A2OW.01 2 0.1814 0.775 0.00 0.90 0.00 0.00 0.00 0.10
#> TCGA.DO.A1JZ.11 1 0.0000 0.995 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.EL.A3D5.01 5 0.5628 0.253 0.00 0.00 0.00 0.22 0.54 0.24
#> TCGA.EL.A3GW.01 5 0.0547 0.887 0.00 0.00 0.00 0.00 0.98 0.02
#> TCGA.EL.A3T1.11 3 0.0000 0.939 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.BJ.A0ZC.01 2 0.1267 0.776 0.00 0.94 0.00 0.00 0.00 0.06
#> TCGA.EM.A2OV.01 2 0.1267 0.798 0.00 0.94 0.00 0.00 0.00 0.06
#> TCGA.EM.A3SY.01 1 0.3475 0.738 0.80 0.14 0.00 0.00 0.00 0.06
#> TCGA.EM.A3AI.01 2 0.0000 0.798 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.EM.A2OY.01 2 0.0937 0.799 0.00 0.96 0.00 0.00 0.00 0.04
#> TCGA.BJ.A18Y.01 5 0.1814 0.881 0.00 0.00 0.00 0.00 0.90 0.10
#> TCGA.EM.A2CK.01 5 0.3076 0.829 0.00 0.00 0.00 0.00 0.76 0.24
#> TCGA.EL.A3T7.11 1 0.0000 0.995 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.BJ.A192.01 2 0.1556 0.790 0.00 0.92 0.00 0.00 0.00 0.08
#> TCGA.EM.A2CP.01 3 0.0000 0.939 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.DJ.A3UZ.01 2 0.3076 0.588 0.00 0.76 0.00 0.00 0.00 0.24
#> TCGA.BJ.A3F0.01 4 0.0000 0.977 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.EM.A3AJ.01 3 0.2941 0.833 0.00 0.00 0.78 0.00 0.00 0.22
#> TCGA.EM.A1CW.01 2 0.3198 0.600 0.00 0.74 0.00 0.00 0.00 0.26
#> TCGA.EM.A2P2.01 5 0.0547 0.887 0.00 0.00 0.00 0.00 0.98 0.02
#> TCGA.EM.A1CU.11 1 0.0000 0.995 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.EL.A3T0.11 1 0.0000 0.995 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.FY.A3WA.01 6 0.6525 0.451 0.00 0.20 0.00 0.30 0.04 0.46
#> TCGA.FY.A3TY.11 1 0.0000 0.995 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.EM.A1CT.11 1 0.0000 0.995 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.EM.A3ST.11 1 0.0000 0.995 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.ET.A3DV.01 4 0.0000 0.977 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.J8.A3YD.01 2 0.0000 0.798 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.EM.A3AL.01 4 0.0000 0.977 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.EM.A1CS.11 1 0.0000 0.995 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.EM.A1CW.11 1 0.0000 0.995 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.BJ.A190.01 2 0.2454 0.524 0.16 0.84 0.00 0.00 0.00 0.00
#> TCGA.EM.A1CV.11 1 0.0000 0.995 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.EM.A3ST.01 4 0.0000 0.977 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.EL.A3GO.01 4 0.0000 0.977 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.DJ.A2Q0.01 2 0.0000 0.798 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.FK.A3SD.01 4 0.0000 0.977 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.EM.A1YE.11 1 0.0000 0.995 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.EL.A3T2.11 1 0.0000 0.995 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.EM.A1YC.01 2 0.0000 0.798 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.DJ.A3UP.01 5 0.0547 0.887 0.00 0.00 0.00 0.00 0.98 0.02
#> TCGA.EL.A3CW.01 3 0.0937 0.935 0.00 0.00 0.96 0.00 0.00 0.04
#> TCGA.ET.A39L.01 5 0.3076 0.829 0.00 0.00 0.00 0.00 0.76 0.24
#> TCGA.EM.A2CO.01 2 0.1556 0.795 0.00 0.92 0.00 0.00 0.00 0.08
#> TCGA.DJ.A2PP.01 4 0.0000 0.977 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.ET.A3DQ.01 3 0.2454 0.879 0.00 0.00 0.84 0.00 0.00 0.16
#> TCGA.ET.A3DS.01 2 0.1556 0.757 0.00 0.92 0.00 0.00 0.00 0.08
#> TCGA.FY.A3W9.01 4 0.0000 0.977 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.BJ.A2NA.11 3 0.0937 0.935 0.00 0.00 0.96 0.00 0.00 0.04
#> TCGA.DJ.A1QL.01 4 0.0000 0.977 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.EM.A1YD.11 1 0.0000 0.995 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.ET.A3DW.11 1 0.0000 0.995 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.EL.A3TA.11 1 0.0000 0.995 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.EM.A1YE.01 2 0.2941 0.452 0.00 0.78 0.00 0.00 0.00 0.22
#> TCGA.FY.A2QD.01 4 0.0000 0.977 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.DJ.A2Q2.01 2 0.1814 0.785 0.00 0.90 0.00 0.00 0.00 0.10
#> TCGA.BJ.A28V.01 4 0.0000 0.977 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.BJ.A28X.11 3 0.0000 0.939 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.DJ.A1QG.01 5 0.0547 0.887 0.00 0.00 0.00 0.00 0.98 0.02
#> TCGA.EL.A3TB.11 1 0.0000 0.995 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.ET.A39I.01 5 0.0547 0.887 0.00 0.00 0.00 0.00 0.98 0.02
#> TCGA.EM.A1YB.01 4 0.1556 0.915 0.00 0.00 0.00 0.92 0.00 0.08
#> TCGA.DJ.A3UT.01 5 0.2941 0.837 0.00 0.00 0.00 0.00 0.78 0.22
#> TCGA.DJ.A1QM.01 1 0.0000 0.995 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.EL.A3CY.01 3 0.0000 0.939 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.EM.A1YC.11 1 0.0000 0.995 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.EL.A3T3.11 1 0.0000 0.995 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.EL.A3T2.01 5 0.0547 0.887 0.00 0.00 0.00 0.00 0.98 0.02
#> TCGA.EL.A3T8.11 1 0.0000 0.995 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.EM.A1YA.01 2 0.1814 0.785 0.00 0.90 0.00 0.00 0.00 0.10
#> TCGA.EL.A3CO.01 3 0.2631 0.866 0.00 0.00 0.82 0.00 0.00 0.18
#> TCGA.EM.A1YD.01 2 0.0000 0.798 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.EL.A3CZ.01 2 0.3321 0.573 0.00 0.82 0.00 0.00 0.10 0.08
#> TCGA.EM.A3FR.01 4 0.0000 0.977 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.EM.A3O8.01 5 0.3076 0.829 0.00 0.00 0.00 0.00 0.76 0.24
#> TCGA.FY.A3R9.01 2 0.0547 0.801 0.00 0.98 0.00 0.00 0.00 0.02
#> TCGA.EM.A3O6.01 2 0.0547 0.797 0.00 0.98 0.00 0.00 0.00 0.02
#> TCGA.BJ.A28S.01 5 0.0547 0.887 0.00 0.00 0.00 0.00 0.98 0.02
#> TCGA.H2.A3RI.11 1 0.0000 0.995 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.DJ.A13W.01 4 0.0000 0.977 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.BJ.A0ZA.01 4 0.3523 0.715 0.00 0.00 0.00 0.78 0.18 0.04
#> TCGA.BJ.A3PT.01 5 0.3499 0.749 0.00 0.00 0.00 0.00 0.68 0.32
#> TCGA.BJ.A0ZF.01 6 0.3869 0.656 0.00 0.50 0.00 0.00 0.00 0.50
#> TCGA.BJ.A0YZ.01 6 0.3864 0.678 0.00 0.48 0.00 0.00 0.00 0.52
#> TCGA.DJ.A2QB.01 5 0.3076 0.814 0.00 0.00 0.00 0.00 0.76 0.24
#> TCGA.EM.A3OB.01 5 0.0000 0.890 0.00 0.00 0.00 0.00 1.00 0.00
#> TCGA.H2.A3RH.01 5 0.0547 0.887 0.00 0.00 0.00 0.00 0.98 0.02
#> TCGA.BJ.A3PR.11 3 0.2631 0.866 0.00 0.00 0.82 0.00 0.00 0.18
#> TCGA.EL.A3T6.11 3 0.2454 0.879 0.00 0.00 0.84 0.00 0.00 0.16
#> TCGA.BJ.A0ZG.01 2 0.0000 0.798 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.BJ.A0Z0.01 4 0.0547 0.964 0.00 0.00 0.00 0.98 0.00 0.02
#> TCGA.EM.A3O9.01 3 0.2454 0.879 0.00 0.00 0.84 0.00 0.00 0.16
#> TCGA.BJ.A3PR.01 3 0.0000 0.939 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.EM.A3OA.01 4 0.0000 0.977 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.BJ.A0ZE.01 5 0.1480 0.861 0.00 0.00 0.00 0.04 0.94 0.02
#> TCGA.DJ.A13O.01 3 0.2454 0.879 0.00 0.00 0.84 0.00 0.00 0.16
#> TCGA.DJ.A13M.01 5 0.0547 0.889 0.00 0.00 0.00 0.00 0.98 0.02
#> TCGA.DJ.A13R.01 2 0.3198 0.600 0.00 0.74 0.00 0.00 0.00 0.26
#> TCGA.ET.A39N.01 6 0.4845 0.692 0.00 0.40 0.00 0.00 0.06 0.54
#> TCGA.BJ.A3PU.11 1 0.0000 0.995 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.FY.A3R7.01 2 0.2793 0.630 0.00 0.80 0.00 0.00 0.00 0.20
#> TCGA.EM.A2CN.01 4 0.0547 0.964 0.00 0.00 0.00 0.98 0.00 0.02
#> TCGA.BJ.A0Z2.01 4 0.0000 0.977 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.FY.A3I5.01 4 0.0000 0.977 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.DJ.A13S.01 5 0.2631 0.859 0.00 0.00 0.00 0.00 0.82 0.18
cbind(get_classes(res, k = 7), get_membership(res, k = 7))
#> class entropy silhouette p1 p2 p3 p4 p5 p6 p7
#> TCGA.E8.A416.01 1 0.0000 0.98868 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.EL.A3ZO.11 1 0.0000 0.98868 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.ET.A2N3.01 4 0.0000 0.94705 0.00 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.EM.A4FU.01 5 0.1363 0.76256 0.00 0.00 0.00 0.00 0.94 0.04 0.02
#> TCGA.DJ.A3VM.01 4 0.0504 0.93630 0.00 0.00 0.00 0.98 0.02 0.00 0.00
#> TCGA.DJ.A3VG.01 5 0.0504 0.76491 0.00 0.00 0.00 0.00 0.98 0.00 0.02
#> TCGA.EL.A4K2.01 7 0.5128 0.14401 0.00 0.24 0.00 0.00 0.04 0.10 0.62
#> TCGA.EL.A3ZK.11 3 0.0000 0.92202 0.00 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.FY.A40M.01 5 0.3617 0.56960 0.00 0.00 0.00 0.00 0.76 0.16 0.08
#> TCGA.KS.A41I.01 5 0.4597 -0.00126 0.00 0.00 0.00 0.00 0.56 0.08 0.36
#> TCGA.DJ.A3VL.01 7 0.4328 -0.01169 0.00 0.00 0.34 0.00 0.00 0.06 0.60
#> TCGA.ET.A4KQ.01 7 0.3413 0.46547 0.00 0.00 0.00 0.00 0.38 0.00 0.62
#> TCGA.DJ.A4V0.01 3 0.0504 0.92002 0.00 0.00 0.98 0.00 0.00 0.02 0.00
#> TCGA.EL.A3ZL.11 1 0.0000 0.98868 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.EM.A4FH.01 2 0.4121 0.54309 0.00 0.70 0.00 0.00 0.00 0.20 0.10
#> TCGA.IM.A41Z.01 4 0.2509 0.86697 0.00 0.04 0.00 0.88 0.00 0.02 0.06
#> TCGA.DE.A4M9.01 6 0.3294 0.76384 0.00 0.34 0.00 0.00 0.00 0.66 0.00
#> TCGA.KS.A41L.01 6 0.3909 0.57205 0.00 0.40 0.00 0.00 0.00 0.58 0.02
#> TCGA.EL.A4KI.01 4 0.0000 0.94705 0.00 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.EM.A4G1.01 5 0.5639 0.11562 0.00 0.20 0.00 0.00 0.56 0.04 0.20
#> TCGA.E8.A434.01 2 0.4939 0.43596 0.00 0.56 0.00 0.00 0.00 0.14 0.30
#> TCGA.EL.A3ZH.01 2 0.5844 0.27569 0.00 0.54 0.00 0.00 0.16 0.06 0.24
#> TCGA.EL.A3ZH.11 1 0.0000 0.98868 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.EL.A3ZR.01 5 0.1363 0.75854 0.00 0.00 0.00 0.00 0.94 0.02 0.04
#> TCGA.EL.A3ZG.11 1 0.0000 0.98868 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.ET.A40P.01 5 0.1928 0.74407 0.00 0.00 0.00 0.00 0.90 0.02 0.08
#> TCGA.DJ.A3VK.01 5 0.3517 0.52519 0.00 0.00 0.00 0.00 0.70 0.02 0.28
#> TCGA.EL.A3ZP.11 3 0.0000 0.92202 0.00 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.BJ.A2N8.11 1 0.0000 0.98868 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.EL.A3H2.01 2 0.4033 0.55007 0.00 0.70 0.00 0.00 0.00 0.22 0.08
#> TCGA.EM.A3AP.01 5 0.1928 0.74354 0.00 0.00 0.00 0.00 0.90 0.02 0.08
#> TCGA.BJ.A45E.01 3 0.0000 0.92202 0.00 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.BJ.A45K.01 4 0.0000 0.94705 0.00 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.E3.A3DZ.01 5 0.1671 0.75408 0.00 0.00 0.00 0.00 0.90 0.00 0.10
#> TCGA.BJ.A45C.01 4 0.3541 0.77353 0.00 0.08 0.00 0.80 0.00 0.10 0.02
#> TCGA.BJ.A45G.01 5 0.1006 0.75690 0.00 0.00 0.00 0.00 0.96 0.02 0.02
#> TCGA.BJ.A2P4.01 5 0.2906 0.66483 0.00 0.00 0.00 0.00 0.80 0.02 0.18
#> TCGA.CE.A484.01 5 0.1363 0.75078 0.00 0.00 0.00 0.00 0.94 0.04 0.02
#> TCGA.BJ.A45F.01 5 0.3867 0.19629 0.00 0.00 0.00 0.00 0.60 0.02 0.38
#> TCGA.FY.A4B0.01 4 0.0000 0.94705 0.00 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.DJ.A2Q9.01 3 0.0000 0.92202 0.00 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.EL.A4K6.01 4 0.0000 0.94705 0.00 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.EM.A4FK.01 4 0.2804 0.84588 0.00 0.06 0.00 0.86 0.00 0.02 0.06
#> TCGA.EL.A3MW.11 1 0.0000 0.98868 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.BJ.A45D.01 7 0.3496 0.41627 0.00 0.00 0.00 0.00 0.42 0.00 0.58
#> TCGA.DJ.A4UR.01 4 0.1928 0.87083 0.00 0.00 0.00 0.90 0.08 0.02 0.00
#> TCGA.EL.A3N2.11 1 0.0000 0.98868 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.BJ.A2N9.01 2 0.1718 0.66117 0.00 0.92 0.00 0.00 0.00 0.04 0.04
#> TCGA.EL.A3GZ.11 1 0.0000 0.98868 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.EM.A3AR.01 1 0.0000 0.98868 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.EL.A3N3.11 3 0.1718 0.90847 0.00 0.00 0.92 0.00 0.00 0.04 0.04
#> TCGA.EL.A4JV.01 5 0.3221 0.43777 0.00 0.00 0.00 0.00 0.68 0.00 0.32
#> TCGA.BJ.A2N7.01 5 0.3047 0.52304 0.00 0.00 0.00 0.00 0.72 0.00 0.28
#> TCGA.DE.A2OL.01 4 0.0000 0.94705 0.00 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.EL.A3H2.11 1 0.0504 0.97198 0.98 0.00 0.00 0.00 0.00 0.00 0.02
#> TCGA.MK.A84Z.01 5 0.0504 0.75949 0.00 0.00 0.00 0.00 0.98 0.02 0.00
#> TCGA.ET.A3DP.11 1 0.0000 0.98868 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.EL.A3MX.11 1 0.0000 0.98868 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.BJ.A28T.11 1 0.1006 0.95343 0.96 0.00 0.02 0.00 0.00 0.02 0.00
#> TCGA.EM.A22J.01 4 0.3061 0.82446 0.00 0.08 0.00 0.84 0.00 0.02 0.06
#> TCGA.BJ.A28W.11 3 0.4965 0.71319 0.00 0.04 0.66 0.00 0.00 0.12 0.18
#> TCGA.BJ.A2N8.01 5 0.2259 0.69537 0.00 0.00 0.00 0.00 0.84 0.00 0.16
#> TCGA.FY.A76V.01 7 0.3546 0.31144 0.00 0.00 0.00 0.00 0.46 0.00 0.54
#> TCGA.EM.A3FN.01 4 0.0504 0.93881 0.00 0.00 0.00 0.98 0.00 0.00 0.02
#> TCGA.QD.A8IV.01 5 0.0504 0.76312 0.00 0.00 0.00 0.00 0.98 0.00 0.02
#> TCGA.ET.A2MY.11 4 0.3000 0.81526 0.00 0.10 0.00 0.84 0.00 0.04 0.02
#> TCGA.ET.A25P.01 5 0.3968 -0.07213 0.00 0.00 0.00 0.00 0.54 0.02 0.44
#> TCGA.EM.A2CT.01 2 0.3263 0.60203 0.00 0.80 0.00 0.00 0.00 0.12 0.08
#> TCGA.E8.A2JQ.11 3 0.0000 0.92202 0.00 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.EM.A2CL.01 4 0.0504 0.93881 0.00 0.00 0.00 0.98 0.00 0.00 0.02
#> TCGA.ET.A2N5.01 5 0.0504 0.76312 0.00 0.00 0.00 0.00 0.98 0.00 0.02
#> TCGA.ET.A25J.11 1 0.0000 0.98868 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.BJ.A28R.11 3 0.0000 0.92202 0.00 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.EL.A3H7.11 1 0.0504 0.97301 0.98 0.00 0.00 0.00 0.00 0.02 0.00
#> TCGA.H2.A2K9.01 4 0.0000 0.94705 0.00 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.EM.A22Q.01 4 0.0000 0.94705 0.00 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.EM.A3FP.01 7 0.4353 0.50928 0.00 0.00 0.00 0.00 0.24 0.10 0.66
#> TCGA.GE.A2C6.11 3 0.0000 0.92202 0.00 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.CE.A27D.01 3 0.1718 0.90847 0.00 0.00 0.92 0.00 0.00 0.04 0.04
#> TCGA.EL.A3H1.11 3 0.1718 0.90847 0.00 0.00 0.92 0.00 0.00 0.04 0.04
#> TCGA.BJ.A2N7.11 1 0.0000 0.98868 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.EM.A2CQ.01 2 0.2313 0.63772 0.00 0.88 0.00 0.00 0.00 0.06 0.06
#> TCGA.EL.A3H1.01 4 0.0000 0.94705 0.00 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.BJ.A28W.01 3 0.0000 0.92202 0.00 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.BJ.A28T.01 3 0.0000 0.92202 0.00 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.EM.A2CJ.01 2 0.3263 0.64255 0.00 0.80 0.00 0.00 0.00 0.12 0.08
#> TCGA.EM.A22K.01 5 0.2745 0.68626 0.00 0.00 0.00 0.00 0.82 0.02 0.16
#> TCGA.FY.A3NM.01 2 0.2278 0.66583 0.00 0.88 0.00 0.00 0.00 0.08 0.04
#> TCGA.EM.A22L.01 5 0.2745 0.68494 0.00 0.00 0.00 0.00 0.82 0.02 0.16
#> TCGA.BJ.A2N9.11 3 0.0000 0.92202 0.00 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.BJ.A291.01 2 0.4502 0.57031 0.00 0.66 0.00 0.00 0.00 0.18 0.16
#> TCGA.ET.A2N5.11 1 0.0504 0.97198 0.98 0.00 0.00 0.00 0.00 0.00 0.02
#> TCGA.ET.A25N.11 1 0.0000 0.98868 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.J8.A3O0.01 4 0.2803 0.80717 0.00 0.00 0.00 0.84 0.10 0.06 0.00
#> TCGA.EL.A3MY.11 2 0.3670 0.60291 0.00 0.76 0.00 0.00 0.00 0.14 0.10
#> TCGA.FY.A3NP.01 5 0.1363 0.75993 0.00 0.00 0.00 0.00 0.94 0.02 0.04
#> TCGA.ET.A25I.01 2 0.4820 0.31005 0.00 0.52 0.00 0.00 0.00 0.10 0.38
#> TCGA.BJ.A290.11 1 0.0000 0.98868 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.FE.A239.01 4 0.0000 0.94705 0.00 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.EM.A22N.01 2 0.1718 0.66117 0.00 0.92 0.00 0.00 0.00 0.04 0.04
#> TCGA.EM.A2CM.01 4 0.0000 0.94705 0.00 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.EM.A3FL.01 2 0.0863 0.67001 0.00 0.96 0.00 0.00 0.00 0.04 0.00
#> TCGA.H2.A2K9.11 3 0.0504 0.91820 0.00 0.00 0.98 0.00 0.00 0.02 0.00
#> TCGA.FY.A3TY.01 3 0.2313 0.89454 0.00 0.00 0.88 0.00 0.00 0.06 0.06
#> TCGA.EM.A2OW.01 2 0.2803 0.64071 0.00 0.84 0.00 0.00 0.00 0.10 0.06
#> TCGA.DO.A1JZ.11 1 0.0000 0.98868 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.EL.A3D5.01 5 0.3908 0.40947 0.00 0.00 0.00 0.20 0.72 0.08 0.00
#> TCGA.EL.A3GW.01 5 0.1166 0.74308 0.00 0.00 0.00 0.00 0.94 0.06 0.00
#> TCGA.EL.A3T1.11 3 0.0000 0.92202 0.00 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.BJ.A0ZC.01 2 0.1671 0.65235 0.00 0.90 0.00 0.00 0.00 0.10 0.00
#> TCGA.EM.A2OV.01 2 0.1363 0.66297 0.00 0.94 0.00 0.00 0.00 0.04 0.02
#> TCGA.EM.A3SY.01 1 0.5190 0.54197 0.66 0.10 0.00 0.00 0.00 0.10 0.14
#> TCGA.EM.A3AI.01 2 0.3867 0.61743 0.00 0.74 0.00 0.00 0.00 0.14 0.12
#> TCGA.EM.A2OY.01 2 0.0504 0.67424 0.00 0.98 0.00 0.00 0.00 0.02 0.00
#> TCGA.BJ.A18Y.01 5 0.3307 0.58792 0.00 0.00 0.00 0.00 0.74 0.02 0.24
#> TCGA.EM.A2CK.01 7 0.3867 0.47115 0.00 0.00 0.00 0.00 0.38 0.02 0.60
#> TCGA.EL.A3T7.11 1 0.0000 0.98868 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.BJ.A192.01 2 0.2016 0.64506 0.00 0.90 0.00 0.00 0.00 0.04 0.06
#> TCGA.EM.A2CP.01 3 0.0000 0.92202 0.00 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.DJ.A3UZ.01 7 0.5416 -0.43486 0.00 0.38 0.00 0.00 0.00 0.20 0.42
#> TCGA.BJ.A3F0.01 4 0.0000 0.94705 0.00 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.EM.A3AJ.01 3 0.5731 0.59717 0.00 0.08 0.58 0.00 0.00 0.14 0.20
#> TCGA.EM.A1CW.01 2 0.4842 0.37532 0.00 0.60 0.00 0.00 0.00 0.16 0.24
#> TCGA.EM.A2P2.01 5 0.1166 0.74308 0.00 0.00 0.00 0.00 0.94 0.06 0.00
#> TCGA.EM.A1CU.11 1 0.0000 0.98868 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.EL.A3T0.11 1 0.0504 0.97301 0.98 0.00 0.00 0.00 0.00 0.02 0.00
#> TCGA.FY.A3WA.01 6 0.5723 0.42134 0.00 0.20 0.00 0.30 0.02 0.48 0.00
#> TCGA.FY.A3TY.11 1 0.0000 0.98868 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.EM.A1CT.11 1 0.0000 0.98868 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.EM.A3ST.11 1 0.0000 0.98868 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.ET.A3DV.01 4 0.0000 0.94705 0.00 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.J8.A3YD.01 2 0.3449 0.64380 0.00 0.78 0.00 0.00 0.00 0.08 0.14
#> TCGA.EM.A3AL.01 4 0.0000 0.94705 0.00 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.EM.A1CS.11 1 0.0000 0.98868 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.EM.A1CW.11 1 0.0000 0.98868 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.BJ.A190.01 2 0.5652 0.39510 0.10 0.60 0.00 0.00 0.00 0.18 0.12
#> TCGA.EM.A1CV.11 1 0.0000 0.98868 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.EM.A3ST.01 4 0.0000 0.94705 0.00 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.EL.A3GO.01 4 0.0000 0.94705 0.00 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.DJ.A2Q0.01 2 0.2512 0.67058 0.00 0.86 0.00 0.00 0.00 0.10 0.04
#> TCGA.FK.A3SD.01 4 0.0000 0.94705 0.00 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.EM.A1YE.11 1 0.0000 0.98868 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.EL.A3T2.11 1 0.0000 0.98868 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.EM.A1YC.01 2 0.4177 0.56494 0.00 0.70 0.00 0.00 0.00 0.18 0.12
#> TCGA.DJ.A3UP.01 5 0.1664 0.73712 0.00 0.00 0.00 0.00 0.92 0.06 0.02
#> TCGA.EL.A3CW.01 3 0.1363 0.91230 0.00 0.00 0.94 0.00 0.00 0.02 0.04
#> TCGA.ET.A39L.01 7 0.3525 0.36975 0.00 0.00 0.00 0.00 0.44 0.00 0.56
#> TCGA.EM.A2CO.01 2 0.1363 0.66498 0.00 0.94 0.00 0.00 0.00 0.02 0.04
#> TCGA.DJ.A2PP.01 4 0.0863 0.92970 0.00 0.00 0.00 0.96 0.00 0.00 0.04
#> TCGA.ET.A3DQ.01 3 0.3199 0.84730 0.00 0.00 0.80 0.00 0.00 0.06 0.14
#> TCGA.ET.A3DS.01 2 0.4842 0.48355 0.00 0.60 0.00 0.00 0.00 0.16 0.24
#> TCGA.FY.A3W9.01 4 0.0000 0.94705 0.00 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.BJ.A2NA.11 3 0.2313 0.89454 0.00 0.00 0.88 0.00 0.00 0.06 0.06
#> TCGA.DJ.A1QL.01 4 0.0000 0.94705 0.00 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.EM.A1YD.11 1 0.0000 0.98868 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.ET.A3DW.11 1 0.0000 0.98868 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.EL.A3TA.11 1 0.0000 0.98868 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.EM.A1YE.01 2 0.3186 0.50074 0.00 0.76 0.00 0.00 0.00 0.22 0.02
#> TCGA.FY.A2QD.01 4 0.0000 0.94705 0.00 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.DJ.A2Q2.01 2 0.2572 0.62798 0.00 0.86 0.00 0.00 0.00 0.08 0.06
#> TCGA.BJ.A28V.01 4 0.0000 0.94705 0.00 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.BJ.A28X.11 3 0.0000 0.92202 0.00 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.DJ.A1QG.01 5 0.1363 0.76256 0.00 0.00 0.00 0.00 0.94 0.04 0.02
#> TCGA.EL.A3TB.11 1 0.0000 0.98868 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.ET.A39I.01 5 0.0504 0.76312 0.00 0.00 0.00 0.00 0.98 0.00 0.02
#> TCGA.EM.A1YB.01 4 0.3541 0.77632 0.00 0.10 0.00 0.80 0.00 0.02 0.08
#> TCGA.DJ.A3UT.01 7 0.3685 0.51666 0.00 0.00 0.00 0.00 0.32 0.02 0.66
#> TCGA.DJ.A1QM.01 1 0.0000 0.98868 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.EL.A3CY.01 3 0.0000 0.92202 0.00 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.EM.A1YC.11 1 0.0504 0.97198 0.98 0.00 0.00 0.00 0.00 0.00 0.02
#> TCGA.EL.A3T3.11 1 0.0000 0.98868 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.EL.A3T2.01 5 0.1363 0.75956 0.00 0.00 0.00 0.00 0.94 0.02 0.04
#> TCGA.EL.A3T8.11 1 0.0000 0.98868 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.EM.A1YA.01 2 0.2016 0.64506 0.00 0.90 0.00 0.00 0.00 0.04 0.06
#> TCGA.EL.A3CO.01 3 0.4145 0.79680 0.00 0.02 0.74 0.00 0.00 0.10 0.14
#> TCGA.EM.A1YD.01 2 0.3487 0.64673 0.00 0.78 0.00 0.00 0.00 0.12 0.10
#> TCGA.EL.A3CZ.01 2 0.5652 0.33889 0.00 0.58 0.00 0.00 0.06 0.16 0.20
#> TCGA.EM.A3FR.01 4 0.0000 0.94705 0.00 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.EM.A3O8.01 7 0.4461 0.51197 0.00 0.02 0.00 0.00 0.32 0.04 0.62
#> TCGA.FY.A3R9.01 2 0.2016 0.68308 0.00 0.90 0.00 0.00 0.00 0.06 0.04
#> TCGA.EM.A3O6.01 2 0.1363 0.67311 0.00 0.94 0.00 0.00 0.00 0.04 0.02
#> TCGA.BJ.A28S.01 5 0.1363 0.75078 0.00 0.00 0.00 0.00 0.94 0.04 0.02
#> TCGA.H2.A3RI.11 1 0.0000 0.98868 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.DJ.A13W.01 4 0.0000 0.94705 0.00 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.BJ.A0ZA.01 4 0.4524 0.41612 0.00 0.00 0.00 0.60 0.34 0.04 0.02
#> TCGA.BJ.A3PT.01 7 0.4681 0.49264 0.00 0.00 0.00 0.00 0.32 0.10 0.58
#> TCGA.BJ.A0ZF.01 6 0.3755 0.75820 0.00 0.34 0.00 0.00 0.00 0.64 0.02
#> TCGA.BJ.A0YZ.01 6 0.3294 0.76384 0.00 0.34 0.00 0.00 0.00 0.66 0.00
#> TCGA.DJ.A2QB.01 5 0.5577 -0.14593 0.00 0.08 0.00 0.00 0.50 0.06 0.36
#> TCGA.EM.A3OB.01 5 0.0504 0.76312 0.00 0.00 0.00 0.00 0.98 0.00 0.02
#> TCGA.H2.A3RH.01 5 0.1664 0.73712 0.00 0.00 0.00 0.00 0.92 0.06 0.02
#> TCGA.BJ.A3PR.11 3 0.3449 0.83266 0.00 0.00 0.78 0.00 0.00 0.08 0.14
#> TCGA.EL.A3T6.11 3 0.3263 0.85198 0.00 0.00 0.80 0.00 0.00 0.08 0.12
#> TCGA.BJ.A0ZG.01 2 0.3687 0.62144 0.00 0.76 0.00 0.00 0.00 0.12 0.12
#> TCGA.BJ.A0Z0.01 4 0.1006 0.92462 0.00 0.00 0.00 0.96 0.02 0.02 0.00
#> TCGA.EM.A3O9.01 3 0.3487 0.84273 0.00 0.00 0.78 0.00 0.00 0.10 0.12
#> TCGA.BJ.A3PR.01 3 0.0000 0.92202 0.00 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.EM.A3OA.01 4 0.0863 0.92970 0.00 0.00 0.00 0.96 0.00 0.00 0.04
#> TCGA.BJ.A0ZE.01 5 0.1718 0.72983 0.00 0.00 0.00 0.04 0.92 0.04 0.00
#> TCGA.DJ.A13O.01 3 0.3199 0.84730 0.00 0.00 0.80 0.00 0.00 0.06 0.14
#> TCGA.DJ.A13M.01 5 0.1928 0.74450 0.00 0.00 0.00 0.00 0.90 0.02 0.08
#> TCGA.DJ.A13R.01 2 0.5363 0.33446 0.00 0.60 0.00 0.04 0.00 0.14 0.22
#> TCGA.ET.A39N.01 6 0.3745 0.70924 0.00 0.26 0.00 0.00 0.04 0.70 0.00
#> TCGA.BJ.A3PU.11 1 0.0000 0.98868 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.FY.A3R7.01 2 0.5115 0.32133 0.00 0.48 0.00 0.00 0.00 0.14 0.38
#> TCGA.EM.A2CN.01 4 0.1363 0.90902 0.00 0.00 0.00 0.94 0.04 0.02 0.00
#> TCGA.BJ.A0Z2.01 4 0.1006 0.92462 0.00 0.00 0.00 0.96 0.02 0.02 0.00
#> TCGA.FY.A3I5.01 4 0.0863 0.92970 0.00 0.00 0.00 0.96 0.00 0.00 0.04
#> TCGA.DJ.A13S.01 5 0.3943 0.08432 0.00 0.00 0.00 0.00 0.56 0.02 0.42
cbind(get_classes(res, k = 8), get_membership(res, k = 8))
#> class entropy silhouette p1 p2 p3 p4 p5 p6 p7 p8
#> TCGA.E8.A416.01 1 0.0000 0.97912 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.EL.A3ZO.11 1 0.0000 0.97912 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.ET.A2N3.01 4 0.0000 0.90380 0.00 0.00 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.EM.A4FU.01 5 0.0941 0.72680 0.00 0.00 0.00 0.02 0.96 0.00 0.00 0.02
#> TCGA.DJ.A3VM.01 4 0.0471 0.89176 0.00 0.00 0.00 0.98 0.02 0.00 0.00 0.00
#> TCGA.DJ.A3VG.01 5 0.0808 0.74578 0.00 0.00 0.00 0.00 0.96 0.00 0.04 0.00
#> TCGA.EL.A4K2.01 2 0.6431 -0.07778 0.00 0.40 0.00 0.00 0.04 0.06 0.32 0.18
#> TCGA.EL.A3ZK.11 3 0.0471 0.86096 0.00 0.00 0.98 0.00 0.00 0.02 0.00 0.00
#> TCGA.FY.A40M.01 5 0.3314 0.61951 0.00 0.00 0.00 0.00 0.80 0.08 0.02 0.10
#> TCGA.KS.A41I.01 5 0.5512 0.15636 0.00 0.02 0.00 0.00 0.52 0.02 0.16 0.28
#> TCGA.DJ.A3VL.01 8 0.4144 0.32244 0.00 0.00 0.12 0.00 0.00 0.00 0.22 0.66
#> TCGA.ET.A4KQ.01 7 0.5857 0.53144 0.00 0.02 0.00 0.00 0.24 0.04 0.50 0.20
#> TCGA.DJ.A4V0.01 3 0.0808 0.85146 0.00 0.00 0.96 0.00 0.00 0.00 0.00 0.04
#> TCGA.EL.A3ZL.11 1 0.0000 0.97912 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.EM.A4FH.01 2 0.2547 0.59025 0.00 0.84 0.00 0.00 0.00 0.12 0.04 0.00
#> TCGA.IM.A41Z.01 4 0.4028 0.61571 0.00 0.00 0.00 0.66 0.00 0.04 0.28 0.02
#> TCGA.DE.A4M9.01 6 0.2719 0.75930 0.00 0.18 0.00 0.00 0.02 0.80 0.00 0.00
#> TCGA.KS.A41L.01 6 0.3737 0.27464 0.00 0.48 0.00 0.00 0.00 0.50 0.02 0.00
#> TCGA.EL.A4KI.01 4 0.0000 0.90380 0.00 0.00 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.EM.A4G1.01 5 0.5393 0.28479 0.00 0.10 0.00 0.00 0.54 0.00 0.28 0.08
#> TCGA.E8.A434.01 2 0.3374 0.46310 0.00 0.68 0.00 0.00 0.00 0.00 0.02 0.30
#> TCGA.EL.A3ZH.01 2 0.6199 0.22352 0.00 0.54 0.00 0.00 0.20 0.08 0.08 0.10
#> TCGA.EL.A3ZH.11 1 0.0000 0.97912 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.EL.A3ZR.01 5 0.1563 0.73546 0.00 0.00 0.00 0.00 0.90 0.00 0.10 0.00
#> TCGA.EL.A3ZG.11 1 0.0000 0.97912 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.ET.A40P.01 5 0.2224 0.71977 0.00 0.00 0.00 0.00 0.86 0.02 0.12 0.00
#> TCGA.DJ.A3VK.01 5 0.3922 0.47757 0.00 0.00 0.00 0.00 0.64 0.00 0.30 0.06
#> TCGA.EL.A3ZP.11 3 0.0000 0.86486 0.00 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.BJ.A2N8.11 1 0.0000 0.97912 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.EL.A3H2.01 2 0.2623 0.58801 0.00 0.84 0.00 0.00 0.00 0.10 0.00 0.06
#> TCGA.EM.A3AP.01 5 0.1557 0.73907 0.00 0.00 0.00 0.00 0.92 0.02 0.06 0.00
#> TCGA.BJ.A45E.01 3 0.0000 0.86486 0.00 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.BJ.A45K.01 4 0.0000 0.90380 0.00 0.00 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.E3.A3DZ.01 5 0.3483 0.65091 0.00 0.02 0.00 0.00 0.76 0.00 0.18 0.04
#> TCGA.BJ.A45C.01 4 0.4841 0.50233 0.00 0.06 0.00 0.64 0.00 0.20 0.10 0.00
#> TCGA.BJ.A45G.01 5 0.1091 0.72692 0.00 0.00 0.00 0.00 0.94 0.00 0.00 0.06
#> TCGA.BJ.A2P4.01 5 0.2938 0.58004 0.00 0.00 0.00 0.00 0.70 0.00 0.30 0.00
#> TCGA.CE.A484.01 5 0.1275 0.73021 0.00 0.00 0.00 0.00 0.94 0.02 0.00 0.04
#> TCGA.BJ.A45F.01 5 0.5277 0.32332 0.00 0.00 0.00 0.00 0.56 0.04 0.20 0.20
#> TCGA.FY.A4B0.01 4 0.0000 0.90380 0.00 0.00 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.DJ.A2Q9.01 3 0.0000 0.86486 0.00 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.EL.A4K6.01 4 0.0000 0.90380 0.00 0.00 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.EM.A4FK.01 4 0.3941 0.64134 0.00 0.00 0.00 0.68 0.00 0.04 0.26 0.02
#> TCGA.EL.A3MW.11 1 0.0000 0.97912 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.BJ.A45D.01 7 0.5653 0.52535 0.00 0.00 0.00 0.00 0.22 0.04 0.46 0.28
#> TCGA.DJ.A4UR.01 4 0.2406 0.71165 0.00 0.00 0.00 0.80 0.20 0.00 0.00 0.00
#> TCGA.EL.A3N2.11 1 0.0000 0.97912 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.BJ.A2N9.01 2 0.4096 0.59368 0.00 0.68 0.00 0.00 0.00 0.06 0.24 0.02
#> TCGA.EL.A3GZ.11 1 0.0000 0.97912 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.EM.A3AR.01 1 0.0000 0.97912 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.EL.A3N3.11 3 0.2569 0.77064 0.00 0.00 0.82 0.00 0.00 0.02 0.00 0.16
#> TCGA.EL.A4JV.01 5 0.3618 0.41798 0.00 0.00 0.00 0.00 0.60 0.00 0.38 0.02
#> TCGA.BJ.A2N7.01 5 0.3570 0.45897 0.00 0.00 0.00 0.00 0.62 0.00 0.36 0.02
#> TCGA.DE.A2OL.01 4 0.0000 0.90380 0.00 0.00 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.EL.A3H2.11 1 0.0000 0.97912 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.MK.A84Z.01 5 0.0471 0.73432 0.00 0.00 0.00 0.00 0.98 0.00 0.00 0.02
#> TCGA.ET.A3DP.11 1 0.0000 0.97912 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.EL.A3MX.11 1 0.0000 0.97912 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.BJ.A28T.11 1 0.1804 0.88153 0.90 0.00 0.00 0.00 0.00 0.02 0.00 0.08
#> TCGA.EM.A22J.01 4 0.4401 0.55720 0.00 0.00 0.00 0.62 0.00 0.04 0.30 0.04
#> TCGA.BJ.A28W.11 8 0.4588 0.29349 0.00 0.00 0.34 0.00 0.00 0.00 0.12 0.54
#> TCGA.BJ.A2N8.01 5 0.2938 0.57702 0.00 0.00 0.00 0.00 0.70 0.00 0.30 0.00
#> TCGA.FY.A76V.01 7 0.5273 0.31690 0.00 0.00 0.00 0.00 0.36 0.02 0.46 0.16
#> TCGA.EM.A3FN.01 4 0.2025 0.83617 0.00 0.00 0.00 0.88 0.00 0.02 0.10 0.00
#> TCGA.QD.A8IV.01 5 0.1741 0.74069 0.00 0.00 0.00 0.00 0.92 0.02 0.04 0.02
#> TCGA.ET.A2MY.11 4 0.4700 0.51202 0.00 0.04 0.00 0.62 0.00 0.08 0.26 0.00
#> TCGA.ET.A25P.01 5 0.5019 0.44674 0.00 0.00 0.00 0.00 0.60 0.04 0.22 0.14
#> TCGA.EM.A2CT.01 7 0.5735 -0.49804 0.00 0.38 0.00 0.00 0.00 0.10 0.42 0.10
#> TCGA.E8.A2JQ.11 3 0.0000 0.86486 0.00 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.EM.A2CL.01 4 0.1275 0.87352 0.00 0.00 0.00 0.94 0.00 0.02 0.04 0.00
#> TCGA.ET.A2N5.01 5 0.1091 0.74480 0.00 0.00 0.00 0.00 0.94 0.00 0.06 0.00
#> TCGA.ET.A25J.11 1 0.0000 0.97912 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.BJ.A28R.11 3 0.0471 0.86096 0.00 0.00 0.98 0.00 0.00 0.02 0.00 0.00
#> TCGA.EL.A3H7.11 1 0.0471 0.96173 0.98 0.00 0.00 0.00 0.00 0.02 0.00 0.00
#> TCGA.H2.A2K9.01 4 0.0000 0.90380 0.00 0.00 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.EM.A22Q.01 4 0.0000 0.90380 0.00 0.00 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.EM.A3FP.01 8 0.4953 -0.20418 0.00 0.00 0.00 0.00 0.16 0.02 0.24 0.58
#> TCGA.GE.A2C6.11 3 0.0000 0.86486 0.00 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.CE.A27D.01 3 0.2569 0.77064 0.00 0.00 0.82 0.00 0.00 0.02 0.00 0.16
#> TCGA.EL.A3H1.11 3 0.2719 0.75210 0.00 0.00 0.80 0.00 0.00 0.02 0.00 0.18
#> TCGA.BJ.A2N7.11 1 0.0000 0.97912 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.EM.A2CQ.01 2 0.4621 0.52501 0.00 0.58 0.00 0.00 0.00 0.08 0.32 0.02
#> TCGA.EL.A3H1.01 4 0.0000 0.90380 0.00 0.00 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.BJ.A28W.01 3 0.0000 0.86486 0.00 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.BJ.A28T.01 3 0.0000 0.86486 0.00 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.EM.A2CJ.01 2 0.3385 0.55559 0.00 0.76 0.00 0.00 0.00 0.16 0.08 0.00
#> TCGA.EM.A22K.01 5 0.3021 0.69572 0.00 0.00 0.00 0.00 0.80 0.02 0.16 0.02
#> TCGA.FY.A3NM.01 2 0.2407 0.64757 0.00 0.86 0.00 0.00 0.00 0.06 0.08 0.00
#> TCGA.EM.A22L.01 5 0.2650 0.64451 0.00 0.00 0.00 0.00 0.76 0.00 0.24 0.00
#> TCGA.BJ.A2N9.11 3 0.0000 0.86486 0.00 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.BJ.A291.01 2 0.2680 0.63111 0.00 0.84 0.00 0.00 0.00 0.02 0.02 0.12
#> TCGA.ET.A2N5.11 1 0.0471 0.96059 0.98 0.02 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.ET.A25N.11 1 0.0000 0.97912 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.J8.A3O0.01 4 0.2719 0.71751 0.00 0.00 0.00 0.80 0.18 0.00 0.00 0.02
#> TCGA.EL.A3MY.11 2 0.1275 0.63752 0.00 0.94 0.00 0.00 0.00 0.02 0.04 0.00
#> TCGA.FY.A3NP.01 5 0.1091 0.74419 0.00 0.00 0.00 0.00 0.94 0.00 0.06 0.00
#> TCGA.ET.A25I.01 8 0.5802 0.10855 0.00 0.24 0.00 0.00 0.02 0.02 0.26 0.46
#> TCGA.BJ.A290.11 1 0.0000 0.97912 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.FE.A239.01 4 0.0000 0.90380 0.00 0.00 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.EM.A22N.01 2 0.4880 0.54881 0.00 0.58 0.00 0.00 0.00 0.06 0.30 0.06
#> TCGA.EM.A2CM.01 4 0.0000 0.90380 0.00 0.00 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.EM.A3FL.01 2 0.4529 0.59487 0.00 0.68 0.00 0.00 0.00 0.08 0.18 0.06
#> TCGA.H2.A2K9.11 3 0.1408 0.84147 0.02 0.00 0.94 0.00 0.00 0.02 0.00 0.02
#> TCGA.FY.A3TY.01 3 0.2981 0.70591 0.00 0.00 0.76 0.00 0.00 0.02 0.00 0.22
#> TCGA.EM.A2OW.01 2 0.5019 0.58050 0.00 0.60 0.00 0.00 0.00 0.04 0.22 0.14
#> TCGA.DO.A1JZ.11 1 0.0000 0.97912 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.EL.A3D5.01 5 0.3970 0.43423 0.00 0.00 0.00 0.18 0.72 0.08 0.00 0.02
#> TCGA.EL.A3GW.01 5 0.0471 0.73432 0.00 0.00 0.00 0.00 0.98 0.00 0.00 0.02
#> TCGA.EL.A3T1.11 3 0.0471 0.86096 0.00 0.00 0.98 0.00 0.00 0.02 0.00 0.00
#> TCGA.BJ.A0ZC.01 2 0.4096 0.51025 0.00 0.68 0.00 0.00 0.00 0.24 0.06 0.02
#> TCGA.EM.A2OV.01 2 0.3991 0.60449 0.00 0.70 0.00 0.00 0.00 0.06 0.22 0.02
#> TCGA.EM.A3SY.01 1 0.6877 -0.09046 0.40 0.20 0.00 0.00 0.00 0.06 0.10 0.24
#> TCGA.EM.A3AI.01 2 0.1741 0.64314 0.00 0.92 0.00 0.00 0.00 0.02 0.02 0.04
#> TCGA.EM.A2OY.01 2 0.2856 0.64652 0.00 0.78 0.00 0.00 0.00 0.02 0.20 0.00
#> TCGA.BJ.A18Y.01 5 0.3015 0.56199 0.00 0.00 0.00 0.00 0.68 0.00 0.32 0.00
#> TCGA.EM.A2CK.01 7 0.6342 0.52744 0.00 0.04 0.00 0.00 0.24 0.08 0.48 0.16
#> TCGA.EL.A3T7.11 1 0.0000 0.97912 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.BJ.A192.01 2 0.4999 0.45444 0.00 0.52 0.00 0.00 0.00 0.12 0.34 0.02
#> TCGA.EM.A2CP.01 3 0.0000 0.86486 0.00 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.DJ.A3UZ.01 8 0.2888 0.36553 0.00 0.16 0.00 0.00 0.00 0.00 0.04 0.80
#> TCGA.BJ.A3F0.01 4 0.0000 0.90380 0.00 0.00 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.EM.A3AJ.01 8 0.5257 0.36241 0.00 0.00 0.28 0.00 0.00 0.04 0.14 0.54
#> TCGA.EM.A1CW.01 7 0.5554 -0.35510 0.00 0.16 0.00 0.00 0.00 0.04 0.40 0.40
#> TCGA.EM.A2P2.01 5 0.0941 0.73606 0.00 0.00 0.00 0.00 0.96 0.00 0.02 0.02
#> TCGA.EM.A1CU.11 1 0.0000 0.97912 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.EL.A3T0.11 1 0.1275 0.92539 0.94 0.00 0.00 0.00 0.00 0.02 0.00 0.04
#> TCGA.FY.A3WA.01 6 0.5491 0.40582 0.00 0.10 0.00 0.32 0.04 0.52 0.02 0.00
#> TCGA.FY.A3TY.11 1 0.0000 0.97912 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.EM.A1CT.11 1 0.0000 0.97912 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.EM.A3ST.11 1 0.0000 0.97912 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.ET.A3DV.01 4 0.0000 0.90380 0.00 0.00 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.J8.A3YD.01 2 0.1765 0.62772 0.00 0.88 0.00 0.00 0.00 0.00 0.00 0.12
#> TCGA.EM.A3AL.01 4 0.0000 0.90380 0.00 0.00 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.EM.A1CS.11 1 0.0000 0.97912 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.EM.A1CW.11 1 0.0000 0.97912 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.BJ.A190.01 2 0.3131 0.58633 0.06 0.84 0.00 0.00 0.00 0.04 0.04 0.02
#> TCGA.EM.A1CV.11 1 0.0000 0.97912 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.EM.A3ST.01 4 0.0000 0.90380 0.00 0.00 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.EL.A3GO.01 4 0.0000 0.90380 0.00 0.00 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.DJ.A2Q0.01 2 0.2071 0.66067 0.00 0.90 0.00 0.00 0.00 0.04 0.02 0.04
#> TCGA.FK.A3SD.01 4 0.0000 0.90380 0.00 0.00 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.EM.A1YE.11 1 0.0000 0.97912 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.EL.A3T2.11 1 0.0000 0.97912 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.EM.A1YC.01 2 0.3128 0.57936 0.00 0.82 0.00 0.00 0.00 0.10 0.04 0.04
#> TCGA.DJ.A3UP.01 5 0.0471 0.73432 0.00 0.00 0.00 0.00 0.98 0.00 0.00 0.02
#> TCGA.EL.A3CW.01 3 0.2224 0.79840 0.00 0.00 0.86 0.00 0.00 0.02 0.00 0.12
#> TCGA.ET.A39L.01 7 0.5693 0.43023 0.00 0.00 0.00 0.00 0.32 0.06 0.46 0.16
#> TCGA.EM.A2CO.01 2 0.3922 0.57612 0.00 0.64 0.00 0.00 0.00 0.06 0.30 0.00
#> TCGA.DJ.A2PP.01 4 0.2725 0.79435 0.00 0.00 0.00 0.82 0.00 0.04 0.14 0.00
#> TCGA.ET.A3DQ.01 3 0.3329 0.17078 0.00 0.00 0.52 0.00 0.00 0.00 0.00 0.48
#> TCGA.ET.A3DS.01 2 0.3444 0.55394 0.00 0.78 0.00 0.00 0.00 0.06 0.02 0.14
#> TCGA.FY.A3W9.01 4 0.0000 0.90380 0.00 0.00 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.BJ.A2NA.11 3 0.2856 0.73115 0.00 0.00 0.78 0.00 0.00 0.02 0.00 0.20
#> TCGA.DJ.A1QL.01 4 0.0000 0.90380 0.00 0.00 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.EM.A1YD.11 1 0.0000 0.97912 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.ET.A3DW.11 1 0.0000 0.97912 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.EL.A3TA.11 1 0.0000 0.97912 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.EM.A1YE.01 2 0.4276 0.46484 0.00 0.64 0.00 0.00 0.00 0.28 0.06 0.02
#> TCGA.FY.A2QD.01 4 0.0000 0.90380 0.00 0.00 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.DJ.A2Q2.01 2 0.5566 0.38890 0.00 0.46 0.00 0.00 0.00 0.08 0.36 0.10
#> TCGA.BJ.A28V.01 4 0.0000 0.90380 0.00 0.00 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.BJ.A28X.11 3 0.0000 0.86486 0.00 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.DJ.A1QG.01 5 0.0471 0.73680 0.00 0.00 0.00 0.02 0.98 0.00 0.00 0.00
#> TCGA.EL.A3TB.11 1 0.0000 0.97912 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.ET.A39I.01 5 0.0941 0.74367 0.00 0.00 0.00 0.00 0.96 0.02 0.02 0.00
#> TCGA.EM.A1YB.01 4 0.4415 0.51926 0.00 0.00 0.00 0.60 0.00 0.06 0.32 0.02
#> TCGA.DJ.A3UT.01 7 0.6884 0.46288 0.00 0.08 0.00 0.00 0.26 0.06 0.36 0.24
#> TCGA.DJ.A1QM.01 1 0.0000 0.97912 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.EL.A3CY.01 3 0.0000 0.86486 0.00 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.EM.A1YC.11 1 0.1557 0.90317 0.92 0.06 0.00 0.00 0.00 0.00 0.00 0.02
#> TCGA.EL.A3T3.11 1 0.0000 0.97912 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.EL.A3T2.01 5 0.2025 0.73115 0.00 0.00 0.00 0.00 0.88 0.02 0.10 0.00
#> TCGA.EL.A3T8.11 1 0.0000 0.97912 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.EM.A1YA.01 2 0.5162 0.43875 0.00 0.50 0.00 0.00 0.00 0.10 0.36 0.04
#> TCGA.EL.A3CO.01 8 0.3570 0.22145 0.00 0.00 0.36 0.00 0.00 0.00 0.02 0.62
#> TCGA.EM.A1YD.01 2 0.2265 0.63496 0.00 0.88 0.00 0.00 0.00 0.02 0.02 0.08
#> TCGA.EL.A3CZ.01 2 0.5322 0.35637 0.00 0.64 0.00 0.00 0.06 0.16 0.10 0.04
#> TCGA.EM.A3FR.01 4 0.0000 0.90380 0.00 0.00 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.EM.A3O8.01 7 0.6670 0.53577 0.00 0.06 0.00 0.00 0.20 0.08 0.44 0.22
#> TCGA.FY.A3R9.01 2 0.1275 0.65765 0.00 0.94 0.00 0.00 0.00 0.00 0.02 0.04
#> TCGA.EM.A3O6.01 2 0.3054 0.63474 0.00 0.80 0.00 0.00 0.00 0.08 0.12 0.00
#> TCGA.BJ.A28S.01 5 0.1408 0.73916 0.00 0.00 0.00 0.00 0.94 0.02 0.02 0.02
#> TCGA.H2.A3RI.11 1 0.0000 0.97912 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.DJ.A13W.01 4 0.0000 0.90380 0.00 0.00 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.BJ.A0ZA.01 5 0.3992 0.06658 0.00 0.00 0.00 0.44 0.52 0.00 0.04 0.00
#> TCGA.BJ.A3PT.01 8 0.5088 -0.24151 0.00 0.00 0.00 0.00 0.22 0.02 0.20 0.56
#> TCGA.BJ.A0ZF.01 6 0.2406 0.74147 0.00 0.20 0.00 0.00 0.00 0.80 0.00 0.00
#> TCGA.BJ.A0YZ.01 6 0.3169 0.75577 0.00 0.18 0.00 0.00 0.02 0.78 0.00 0.02
#> TCGA.DJ.A2QB.01 5 0.6355 -0.22138 0.00 0.06 0.00 0.00 0.38 0.02 0.26 0.28
#> TCGA.EM.A3OB.01 5 0.1275 0.74432 0.00 0.00 0.00 0.00 0.94 0.02 0.04 0.00
#> TCGA.H2.A3RH.01 5 0.0471 0.73432 0.00 0.00 0.00 0.00 0.98 0.00 0.00 0.02
#> TCGA.BJ.A3PR.11 8 0.3299 -0.00416 0.00 0.00 0.44 0.00 0.00 0.00 0.00 0.56
#> TCGA.EL.A3T6.11 3 0.3737 0.15213 0.00 0.00 0.50 0.00 0.00 0.02 0.00 0.48
#> TCGA.BJ.A0ZG.01 2 0.2071 0.65351 0.00 0.90 0.00 0.00 0.00 0.02 0.04 0.04
#> TCGA.BJ.A0Z0.01 4 0.0471 0.89169 0.00 0.00 0.00 0.98 0.02 0.00 0.00 0.00
#> TCGA.EM.A3O9.01 8 0.5019 -0.11808 0.00 0.02 0.44 0.00 0.00 0.02 0.06 0.46
#> TCGA.BJ.A3PR.01 3 0.0000 0.86486 0.00 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.EM.A3OA.01 4 0.2547 0.81086 0.00 0.00 0.00 0.84 0.00 0.04 0.12 0.00
#> TCGA.BJ.A0ZE.01 5 0.1091 0.70292 0.00 0.00 0.00 0.06 0.94 0.00 0.00 0.00
#> TCGA.DJ.A13O.01 3 0.3729 0.20473 0.00 0.00 0.52 0.00 0.00 0.02 0.00 0.46
#> TCGA.DJ.A13M.01 5 0.1563 0.73669 0.00 0.00 0.00 0.00 0.90 0.00 0.10 0.00
#> TCGA.DJ.A13R.01 8 0.5554 0.10796 0.00 0.16 0.00 0.00 0.00 0.04 0.40 0.40
#> TCGA.ET.A39N.01 6 0.2888 0.74817 0.00 0.16 0.00 0.00 0.04 0.80 0.00 0.00
#> TCGA.BJ.A3PU.11 1 0.0000 0.97912 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.FY.A3R7.01 8 0.3318 -0.08490 0.00 0.46 0.00 0.00 0.00 0.00 0.00 0.54
#> TCGA.EM.A2CN.01 4 0.1563 0.82500 0.00 0.00 0.00 0.90 0.10 0.00 0.00 0.00
#> TCGA.BJ.A0Z2.01 4 0.0808 0.87771 0.00 0.00 0.00 0.96 0.04 0.00 0.00 0.00
#> TCGA.FY.A3I5.01 4 0.2725 0.79435 0.00 0.00 0.00 0.82 0.00 0.04 0.14 0.00
#> TCGA.DJ.A13S.01 5 0.4537 0.11815 0.00 0.00 0.00 0.00 0.50 0.00 0.40 0.10
Heatmaps for the consensus matrix. It visualizes the probability of two samples to be in a same group.
consensus_heatmap(res, k = 2)
consensus_heatmap(res, k = 3)
consensus_heatmap(res, k = 4)
consensus_heatmap(res, k = 5)
consensus_heatmap(res, k = 6)
consensus_heatmap(res, k = 7)
consensus_heatmap(res, k = 8)
Heatmaps for the membership of samples in all partitions to see how consistent they are:
membership_heatmap(res, k = 2)
membership_heatmap(res, k = 3)
membership_heatmap(res, k = 4)
membership_heatmap(res, k = 5)
membership_heatmap(res, k = 6)
membership_heatmap(res, k = 7)
membership_heatmap(res, k = 8)
As soon as the classes for columns are determined, the signatures that are significantly different between subgroups can be looked for. Following are the heatmaps for signatures.
get_signatures(res, k = 2)
get_signatures(res, k = 3)
get_signatures(res, k = 4)
get_signatures(res, k = 5)
get_signatures(res, k = 6)
get_signatures(res, k = 7)
get_signatures(res, k = 8)
Compare the overlap of signatures from different k:
compare_signatures(res)
get_signature() returns a data frame invisibly. To get the list of signatures, the function
call should be assigned to a variable explicitly. In following code, if plot argument is set
to FALSE, no heatmap is plotted while only the differential analysis is performed.
# code only for demonstration
tb = get_signature(res, k = ..., plot = FALSE)
An example of the output of tb is:
#> which_row fdr mean_1 mean_2 scaled_mean_1 scaled_mean_2 km
#> 1 38 0.042760348 8.373488 9.131774 -0.5533452 0.5164555 1
#> 2 40 0.018707592 7.106213 8.469186 -0.6173731 0.5762149 1
#> 3 55 0.019134737 10.221463 11.207825 -0.6159697 0.5749050 1
#> 4 59 0.006059896 5.921854 7.869574 -0.6899429 0.6439467 1
#> 5 60 0.018055526 8.928898 10.211722 -0.6204761 0.5791110 1
#> 6 98 0.009384629 15.714769 14.887706 0.6635654 -0.6193277 2
...
The columns in tb are:
which_row: row indices corresponding to the input matrix.fdr: FDR for the differential test. mean_x: The mean value in group x.scaled_mean_x: The mean value in group x after rows are scaled.km: Row groups if k-means clustering is applied to rows (which is done by automatically selecting number of clusters).If there are too many signatures, top_signatures = ... can be set to only show the
signatures with the highest FDRs:
# code only for demonstration
# e.g. to show the top 500 most significant rows
tb = get_signature(res, k = ..., top_signatures = 500)
If the signatures are defined as these which are uniquely high in current group, diff_method argument
can be set to "uniquely_high_in_one_group":
# code only for demonstration
tb = get_signature(res, k = ..., diff_method = "uniquely_high_in_one_group")
UMAP plot which shows how samples are separated.
dimension_reduction(res, k = 2, method = "UMAP")
dimension_reduction(res, k = 3, method = "UMAP")
dimension_reduction(res, k = 4, method = "UMAP")
dimension_reduction(res, k = 5, method = "UMAP")
dimension_reduction(res, k = 6, method = "UMAP")
dimension_reduction(res, k = 7, method = "UMAP")
dimension_reduction(res, k = 8, method = "UMAP")
Following heatmap shows how subgroups are split when increasing k:
collect_classes(res)
If matrix rows can be associated to genes, consider to use functional_enrichment(res,
...) to perform function enrichment for the signature genes. See this vignette for more detailed explanations.
Parent node: Node02. Child nodes: Node0111-leaf , Node0112-leaf , Node0113-leaf , Node0114-leaf , Node0131-leaf , Node0132-leaf , Node0133-leaf , Node0141-leaf , Node0142-leaf , Node0143-leaf , Node0211-leaf , Node0212-leaf , Node0221-leaf , Node0222-leaf , Node0223-leaf , Node0224-leaf , Node0231-leaf , Node0232 , Node0233-leaf , Node0234-leaf , Node0241 , Node0242-leaf , Node0243-leaf , Node0244-leaf , Node0251-leaf , Node0252-leaf , Node0311 , Node0312-leaf , Node0313-leaf , Node0331-leaf , Node0332-leaf , Node0333-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 43 columns.
#> Top rows (1000) are extracted by 'ATC' method.
#> Subgroups are detected by 'kmeans' method.
#> Performed in total 350 partitions by row resampling.
#> Best k for subgroups seems to be 2.
#>
#> Following methods can be applied to this 'ConsensusPartition' object:
#> [1] "cola_report" "collect_classes" "collect_plots"
#> [4] "collect_stats" "colnames" "compare_partitions"
#> [7] "compare_signatures" "consensus_heatmap" "dimension_reduction"
#> [10] "functional_enrichment" "get_anno_col" "get_anno"
#> [13] "get_classes" "get_consensus" "get_matrix"
#> [16] "get_membership" "get_param" "get_signatures"
#> [19] "get_stats" "is_best_k" "is_stable_k"
#> [22] "membership_heatmap" "ncol" "nrow"
#> [25] "plot_ecdf" "predict_classes" "rownames"
#> [28] "select_partition_number" "show" "suggest_best_k"
#> [31] "test_to_known_factors" "top_rows_heatmap"
collect_plots() function collects all the plots made from res for all k (number of subgroups)
into one single page to provide an easy and fast comparison between different k.
collect_plots(res)
The plots are:
k and the heatmap of
predicted classes for each k.k.k.k.All the plots in panels can be made by individual functions and they are plotted later in this section.
select_partition_number() produces several plots showing different
statistics for choosing “optimized” k. There are following statistics:
k;k, the area increased is defined as \(A_k - A_{k-1}\).The detailed explanations of these statistics can be found in the cola vignette.
Generally speaking, higher 1-PAC score, higher mean silhouette score or higher
concordance corresponds to better partition. Rand index and Jaccard index
measure how similar the current partition is compared to partition with k-1.
If they are too similar, we won't accept k is better than k-1.
select_partition_number(res)
The numeric values for all these statistics can be obtained by get_stats().
get_stats(res)
#> k 1-PAC mean_silhouette concordance area_increased Rand Jaccard
#> 2 2 1.000 1.000 1.000 0.4125 0.588 0.588
#> 3 3 0.661 0.812 0.906 0.4738 0.796 0.653
#> 4 4 0.709 0.753 0.857 0.1741 0.887 0.706
#> 5 5 0.719 0.487 0.799 0.0588 0.935 0.775
#> 6 6 0.711 0.640 0.801 0.0468 0.926 0.718
#> 7 7 0.832 0.736 0.832 0.0467 0.935 0.712
#> 8 8 0.851 0.654 0.798 0.0178 0.955 0.763
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.E8.A416.01 1 0 1 1 0
#> TCGA.EL.A3ZO.11 1 0 1 1 0
#> TCGA.EL.A3ZL.11 1 0 1 1 0
#> TCGA.EL.A3ZH.11 1 0 1 1 0
#> TCGA.EL.A3ZG.11 2 0 1 0 1
#> TCGA.BJ.A2N8.11 1 0 1 1 0
#> TCGA.EL.A3MW.11 1 0 1 1 0
#> TCGA.EL.A3N2.11 1 0 1 1 0
#> TCGA.EL.A3GZ.11 1 0 1 1 0
#> TCGA.EM.A3AR.01 2 0 1 0 1
#> TCGA.EL.A3H2.11 2 0 1 0 1
#> TCGA.ET.A3DP.11 1 0 1 1 0
#> TCGA.EL.A3MX.11 1 0 1 1 0
#> TCGA.BJ.A28T.11 1 0 1 1 0
#> TCGA.ET.A25J.11 1 0 1 1 0
#> TCGA.EL.A3H7.11 1 0 1 1 0
#> TCGA.BJ.A2N7.11 1 0 1 1 0
#> TCGA.ET.A2N5.11 1 0 1 1 0
#> TCGA.ET.A25N.11 1 0 1 1 0
#> TCGA.BJ.A290.11 2 0 1 0 1
#> TCGA.DO.A1JZ.11 1 0 1 1 0
#> TCGA.EM.A3SY.01 2 0 1 0 1
#> TCGA.EL.A3T7.11 1 0 1 1 0
#> TCGA.EM.A1CU.11 2 0 1 0 1
#> TCGA.EL.A3T0.11 1 0 1 1 0
#> TCGA.FY.A3TY.11 1 0 1 1 0
#> TCGA.EM.A1CT.11 2 0 1 0 1
#> TCGA.EM.A3ST.11 1 0 1 1 0
#> TCGA.EM.A1CS.11 1 0 1 1 0
#> TCGA.EM.A1CW.11 1 0 1 1 0
#> TCGA.EM.A1CV.11 1 0 1 1 0
#> TCGA.EM.A1YE.11 1 0 1 1 0
#> TCGA.EL.A3T2.11 1 0 1 1 0
#> TCGA.EM.A1YD.11 1 0 1 1 0
#> TCGA.ET.A3DW.11 2 0 1 0 1
#> TCGA.EL.A3TA.11 2 0 1 0 1
#> TCGA.EL.A3TB.11 1 0 1 1 0
#> TCGA.DJ.A1QM.01 2 0 1 0 1
#> TCGA.EM.A1YC.11 1 0 1 1 0
#> TCGA.EL.A3T3.11 1 0 1 1 0
#> TCGA.EL.A3T8.11 2 0 1 0 1
#> TCGA.H2.A3RI.11 1 0 1 1 0
#> TCGA.BJ.A3PU.11 2 0 1 0 1
cbind(get_classes(res, k = 3), get_membership(res, k = 3))
#> class entropy silhouette p1 p2 p3
#> TCGA.E8.A416.01 1 0.000 0.856 1.00 0.00 0.00
#> TCGA.EL.A3ZO.11 1 0.000 0.856 1.00 0.00 0.00
#> TCGA.EL.A3ZL.11 1 0.000 0.856 1.00 0.00 0.00
#> TCGA.EL.A3ZH.11 1 0.000 0.856 1.00 0.00 0.00
#> TCGA.EL.A3ZG.11 2 0.000 0.988 0.00 1.00 0.00
#> TCGA.BJ.A2N8.11 1 0.000 0.856 1.00 0.00 0.00
#> TCGA.EL.A3MW.11 3 0.429 1.000 0.18 0.00 0.82
#> TCGA.EL.A3N2.11 1 0.630 -0.106 0.52 0.00 0.48
#> TCGA.EL.A3GZ.11 1 0.630 -0.106 0.52 0.00 0.48
#> TCGA.EM.A3AR.01 2 0.000 0.988 0.00 1.00 0.00
#> TCGA.EL.A3H2.11 2 0.000 0.988 0.00 1.00 0.00
#> TCGA.ET.A3DP.11 1 0.000 0.856 1.00 0.00 0.00
#> TCGA.EL.A3MX.11 3 0.429 1.000 0.18 0.00 0.82
#> TCGA.BJ.A28T.11 1 0.000 0.856 1.00 0.00 0.00
#> TCGA.ET.A25J.11 1 0.000 0.856 1.00 0.00 0.00
#> TCGA.EL.A3H7.11 1 0.429 0.662 0.82 0.00 0.18
#> TCGA.BJ.A2N7.11 1 0.000 0.856 1.00 0.00 0.00
#> TCGA.ET.A2N5.11 1 0.000 0.856 1.00 0.00 0.00
#> TCGA.ET.A25N.11 1 0.000 0.856 1.00 0.00 0.00
#> TCGA.BJ.A290.11 2 0.000 0.988 0.00 1.00 0.00
#> TCGA.DO.A1JZ.11 3 0.429 1.000 0.18 0.00 0.82
#> TCGA.EM.A3SY.01 2 0.429 0.857 0.00 0.82 0.18
#> TCGA.EL.A3T7.11 1 0.000 0.856 1.00 0.00 0.00
#> TCGA.EM.A1CU.11 2 0.000 0.988 0.00 1.00 0.00
#> TCGA.EL.A3T0.11 1 0.000 0.856 1.00 0.00 0.00
#> TCGA.FY.A3TY.11 1 0.000 0.856 1.00 0.00 0.00
#> TCGA.EM.A1CT.11 2 0.000 0.988 0.00 1.00 0.00
#> TCGA.EM.A3ST.11 1 0.000 0.856 1.00 0.00 0.00
#> TCGA.EM.A1CS.11 3 0.429 1.000 0.18 0.00 0.82
#> TCGA.EM.A1CW.11 1 0.630 -0.106 0.52 0.00 0.48
#> TCGA.EM.A1CV.11 3 0.429 1.000 0.18 0.00 0.82
#> TCGA.EM.A1YE.11 3 0.429 1.000 0.18 0.00 0.82
#> TCGA.EL.A3T2.11 1 0.000 0.856 1.00 0.00 0.00
#> TCGA.EM.A1YD.11 3 0.429 1.000 0.18 0.00 0.82
#> TCGA.ET.A3DW.11 2 0.000 0.988 0.00 1.00 0.00
#> TCGA.EL.A3TA.11 2 0.000 0.988 0.00 1.00 0.00
#> TCGA.EL.A3TB.11 1 0.000 0.856 1.00 0.00 0.00
#> TCGA.DJ.A1QM.01 2 0.000 0.988 0.00 1.00 0.00
#> TCGA.EM.A1YC.11 3 0.429 1.000 0.18 0.00 0.82
#> TCGA.EL.A3T3.11 1 0.571 0.408 0.68 0.00 0.32
#> TCGA.EL.A3T8.11 2 0.000 0.988 0.00 1.00 0.00
#> TCGA.H2.A3RI.11 1 0.630 -0.106 0.52 0.00 0.48
#> TCGA.BJ.A3PU.11 2 0.000 0.988 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.E8.A416.01 1 0.0000 0.7406 1.00 0.00 0.00 0.00
#> TCGA.EL.A3ZO.11 1 0.2647 0.6376 0.88 0.00 0.00 0.12
#> TCGA.EL.A3ZL.11 1 0.0000 0.7406 1.00 0.00 0.00 0.00
#> TCGA.EL.A3ZH.11 1 0.0000 0.7406 1.00 0.00 0.00 0.00
#> TCGA.EL.A3ZG.11 2 0.0000 0.9737 0.00 1.00 0.00 0.00
#> TCGA.BJ.A2N8.11 1 0.3610 0.6927 0.80 0.00 0.00 0.20
#> TCGA.EL.A3MW.11 3 0.4642 0.6521 0.02 0.00 0.74 0.24
#> TCGA.EL.A3N2.11 4 0.6286 0.9249 0.20 0.00 0.14 0.66
#> TCGA.EL.A3GZ.11 4 0.6286 0.9249 0.20 0.00 0.14 0.66
#> TCGA.EM.A3AR.01 2 0.0707 0.9644 0.00 0.98 0.02 0.00
#> TCGA.EL.A3H2.11 2 0.0000 0.9737 0.00 1.00 0.00 0.00
#> TCGA.ET.A3DP.11 1 0.4948 0.1962 0.56 0.00 0.00 0.44
#> TCGA.EL.A3MX.11 3 0.5606 0.0914 0.02 0.00 0.50 0.48
#> TCGA.BJ.A28T.11 1 0.0000 0.7406 1.00 0.00 0.00 0.00
#> TCGA.ET.A25J.11 1 0.3610 0.6927 0.80 0.00 0.00 0.20
#> TCGA.EL.A3H7.11 4 0.5173 0.7274 0.32 0.00 0.02 0.66
#> TCGA.BJ.A2N7.11 1 0.3610 0.6927 0.80 0.00 0.00 0.20
#> TCGA.ET.A2N5.11 1 0.3610 0.6927 0.80 0.00 0.00 0.20
#> TCGA.ET.A25N.11 1 0.4948 0.1962 0.56 0.00 0.00 0.44
#> TCGA.BJ.A290.11 2 0.0000 0.9737 0.00 1.00 0.00 0.00
#> TCGA.DO.A1JZ.11 3 0.0707 0.8838 0.02 0.00 0.98 0.00
#> TCGA.EM.A3SY.01 2 0.4522 0.6952 0.00 0.68 0.00 0.32
#> TCGA.EL.A3T7.11 1 0.4994 -0.4097 0.52 0.00 0.00 0.48
#> TCGA.EM.A1CU.11 2 0.0000 0.9737 0.00 1.00 0.00 0.00
#> TCGA.EL.A3T0.11 1 0.0000 0.7406 1.00 0.00 0.00 0.00
#> TCGA.FY.A3TY.11 1 0.3610 0.6927 0.80 0.00 0.00 0.20
#> TCGA.EM.A1CT.11 2 0.0000 0.9737 0.00 1.00 0.00 0.00
#> TCGA.EM.A3ST.11 1 0.0000 0.7406 1.00 0.00 0.00 0.00
#> TCGA.EM.A1CS.11 3 0.0707 0.8838 0.02 0.00 0.98 0.00
#> TCGA.EM.A1CW.11 4 0.6286 0.9249 0.20 0.00 0.14 0.66
#> TCGA.EM.A1CV.11 3 0.0707 0.8838 0.02 0.00 0.98 0.00
#> TCGA.EM.A1YE.11 3 0.0707 0.8838 0.02 0.00 0.98 0.00
#> TCGA.EL.A3T2.11 1 0.4790 0.3880 0.62 0.00 0.00 0.38
#> TCGA.EM.A1YD.11 3 0.0707 0.8838 0.02 0.00 0.98 0.00
#> TCGA.ET.A3DW.11 2 0.0000 0.9737 0.00 1.00 0.00 0.00
#> TCGA.EL.A3TA.11 2 0.0000 0.9737 0.00 1.00 0.00 0.00
#> TCGA.EL.A3TB.11 1 0.0000 0.7406 1.00 0.00 0.00 0.00
#> TCGA.DJ.A1QM.01 2 0.0707 0.9644 0.00 0.98 0.02 0.00
#> TCGA.EM.A1YC.11 3 0.0707 0.8838 0.02 0.00 0.98 0.00
#> TCGA.EL.A3T3.11 4 0.5962 0.8613 0.26 0.00 0.08 0.66
#> TCGA.EL.A3T8.11 2 0.0000 0.9737 0.00 1.00 0.00 0.00
#> TCGA.H2.A3RI.11 4 0.6286 0.9249 0.20 0.00 0.14 0.66
#> TCGA.BJ.A3PU.11 2 0.0000 0.9737 0.00 1.00 0.00 0.00
cbind(get_classes(res, k = 5), get_membership(res, k = 5))
#> class entropy silhouette p1 p2 p3 p4 p5
#> TCGA.E8.A416.01 1 0.3895 0.6943 0.68 0.00 0.00 0.32 0.00
#> TCGA.EL.A3ZO.11 4 0.4540 -0.2342 0.34 0.00 0.00 0.64 0.02
#> TCGA.EL.A3ZL.11 1 0.3895 0.6943 0.68 0.00 0.00 0.32 0.00
#> TCGA.EL.A3ZH.11 1 0.4287 0.5927 0.54 0.00 0.00 0.46 0.00
#> TCGA.EL.A3ZG.11 2 0.0000 0.9397 0.00 1.00 0.00 0.00 0.00
#> TCGA.BJ.A2N8.11 1 0.0000 0.7217 1.00 0.00 0.00 0.00 0.00
#> TCGA.EL.A3MW.11 3 0.7288 -0.4653 0.02 0.00 0.34 0.30 0.34
#> TCGA.EL.A3N2.11 4 0.7492 -0.8395 0.24 0.00 0.04 0.38 0.34
#> TCGA.EL.A3GZ.11 4 0.7492 -0.8395 0.24 0.00 0.04 0.38 0.34
#> TCGA.EM.A3AR.01 2 0.2732 0.8594 0.00 0.84 0.00 0.16 0.00
#> TCGA.EL.A3H2.11 2 0.0000 0.9397 0.00 1.00 0.00 0.00 0.00
#> TCGA.ET.A3DP.11 1 0.2331 0.6321 0.90 0.00 0.00 0.08 0.02
#> TCGA.EL.A3MX.11 4 0.7226 -0.2598 0.02 0.00 0.26 0.38 0.34
#> TCGA.BJ.A28T.11 1 0.3895 0.6943 0.68 0.00 0.00 0.32 0.00
#> TCGA.ET.A25J.11 1 0.0609 0.7120 0.98 0.00 0.00 0.00 0.02
#> TCGA.EL.A3H7.11 4 0.7226 -0.7904 0.26 0.00 0.02 0.38 0.34
#> TCGA.BJ.A2N7.11 1 0.0000 0.7217 1.00 0.00 0.00 0.00 0.00
#> TCGA.ET.A2N5.11 1 0.0000 0.7217 1.00 0.00 0.00 0.00 0.00
#> TCGA.ET.A25N.11 1 0.2331 0.6321 0.90 0.00 0.00 0.08 0.02
#> TCGA.BJ.A290.11 2 0.0000 0.9397 0.00 1.00 0.00 0.00 0.00
#> TCGA.DO.A1JZ.11 3 0.2331 0.8393 0.02 0.00 0.90 0.00 0.08
#> TCGA.EM.A3SY.01 2 0.4287 0.5368 0.00 0.54 0.00 0.00 0.46
#> TCGA.EL.A3T7.11 4 0.5273 -0.0614 0.16 0.00 0.00 0.68 0.16
#> TCGA.EM.A1CU.11 2 0.0609 0.9346 0.00 0.98 0.02 0.00 0.00
#> TCGA.EL.A3T0.11 1 0.4287 0.5927 0.54 0.00 0.00 0.46 0.00
#> TCGA.FY.A3TY.11 1 0.0000 0.7217 1.00 0.00 0.00 0.00 0.00
#> TCGA.EM.A1CT.11 2 0.0609 0.9346 0.00 0.98 0.02 0.00 0.00
#> TCGA.EM.A3ST.11 1 0.3895 0.6943 0.68 0.00 0.00 0.32 0.00
#> TCGA.EM.A1CS.11 3 0.2012 0.8388 0.02 0.00 0.92 0.00 0.06
#> TCGA.EM.A1CW.11 4 0.7540 -0.5196 0.34 0.00 0.04 0.36 0.26
#> TCGA.EM.A1CV.11 3 0.2331 0.8393 0.02 0.00 0.90 0.00 0.08
#> TCGA.EM.A1YE.11 3 0.2012 0.8225 0.02 0.00 0.92 0.00 0.06
#> TCGA.EL.A3T2.11 1 0.1410 0.6720 0.94 0.00 0.00 0.06 0.00
#> TCGA.EM.A1YD.11 3 0.2012 0.8291 0.02 0.00 0.92 0.00 0.06
#> TCGA.ET.A3DW.11 2 0.0000 0.9397 0.00 1.00 0.00 0.00 0.00
#> TCGA.EL.A3TA.11 2 0.0000 0.9397 0.00 1.00 0.00 0.00 0.00
#> TCGA.EL.A3TB.11 1 0.4287 0.5927 0.54 0.00 0.00 0.46 0.00
#> TCGA.DJ.A1QM.01 2 0.2732 0.8594 0.00 0.84 0.00 0.16 0.00
#> TCGA.EM.A1YC.11 3 0.0609 0.8375 0.02 0.00 0.98 0.00 0.00
#> TCGA.EL.A3T3.11 5 0.7492 0.0000 0.24 0.00 0.04 0.34 0.38
#> TCGA.EL.A3T8.11 2 0.0000 0.9397 0.00 1.00 0.00 0.00 0.00
#> TCGA.H2.A3RI.11 4 0.7492 -0.8395 0.24 0.00 0.04 0.38 0.34
#> TCGA.BJ.A3PU.11 2 0.0000 0.9397 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.E8.A416.01 1 0.4534 -0.269 0.58 0.00 0.00 0.04 0.38 0.00
#> TCGA.EL.A3ZO.11 5 0.6208 0.671 0.28 0.00 0.00 0.06 0.54 0.12
#> TCGA.EL.A3ZL.11 1 0.4534 -0.269 0.58 0.00 0.00 0.04 0.38 0.00
#> TCGA.EL.A3ZH.11 5 0.5655 0.702 0.36 0.00 0.00 0.16 0.48 0.00
#> TCGA.EL.A3ZG.11 2 0.0937 0.894 0.00 0.96 0.00 0.00 0.00 0.04
#> TCGA.BJ.A2N8.11 1 0.0000 0.580 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.EL.A3MW.11 6 0.3647 0.353 0.00 0.00 0.36 0.00 0.00 0.64
#> TCGA.EL.A3N2.11 6 0.2790 0.819 0.14 0.00 0.02 0.00 0.00 0.84
#> TCGA.EL.A3GZ.11 6 0.2790 0.819 0.14 0.00 0.02 0.00 0.00 0.84
#> TCGA.EM.A3AR.01 2 0.3309 0.772 0.00 0.72 0.00 0.28 0.00 0.00
#> TCGA.EL.A3H2.11 2 0.1092 0.895 0.00 0.96 0.02 0.00 0.00 0.02
#> TCGA.ET.A3DP.11 1 0.4380 0.405 0.70 0.00 0.00 0.08 0.00 0.22
#> TCGA.EL.A3MX.11 6 0.2260 0.704 0.00 0.00 0.14 0.00 0.00 0.86
#> TCGA.BJ.A28T.11 1 0.3797 -0.331 0.58 0.00 0.00 0.00 0.42 0.00
#> TCGA.ET.A25J.11 1 0.1267 0.557 0.94 0.00 0.00 0.06 0.00 0.00
#> TCGA.EL.A3H7.11 6 0.2454 0.806 0.16 0.00 0.00 0.00 0.00 0.84
#> TCGA.BJ.A2N7.11 1 0.0000 0.580 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.ET.A2N5.11 1 0.0000 0.580 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.ET.A25N.11 1 0.3982 0.437 0.74 0.00 0.00 0.06 0.00 0.20
#> TCGA.BJ.A290.11 2 0.1092 0.895 0.00 0.96 0.02 0.00 0.00 0.02
#> TCGA.DO.A1JZ.11 3 0.0547 0.920 0.00 0.00 0.98 0.00 0.00 0.02
#> TCGA.EM.A3SY.01 2 0.6642 0.433 0.00 0.44 0.00 0.16 0.34 0.06
#> TCGA.EL.A3T7.11 6 0.6209 0.242 0.10 0.00 0.00 0.06 0.34 0.50
#> TCGA.EM.A1CU.11 2 0.1267 0.891 0.00 0.94 0.00 0.00 0.00 0.06
#> TCGA.EL.A3T0.11 5 0.3706 0.780 0.38 0.00 0.00 0.00 0.62 0.00
#> TCGA.FY.A3TY.11 1 0.0000 0.580 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.EM.A1CT.11 2 0.1092 0.895 0.00 0.96 0.02 0.00 0.00 0.02
#> TCGA.EM.A3ST.11 1 0.4534 -0.269 0.58 0.00 0.00 0.04 0.38 0.00
#> TCGA.EM.A1CS.11 3 0.0547 0.920 0.00 0.00 0.98 0.00 0.00 0.02
#> TCGA.EM.A1CW.11 6 0.4887 0.703 0.22 0.00 0.02 0.08 0.00 0.68
#> TCGA.EM.A1CV.11 3 0.0547 0.920 0.00 0.00 0.98 0.00 0.00 0.02
#> TCGA.EM.A1YE.11 3 0.3679 0.885 0.00 0.00 0.76 0.20 0.00 0.04
#> TCGA.EL.A3T2.11 1 0.2454 0.496 0.84 0.00 0.00 0.00 0.00 0.16
#> TCGA.EM.A1YD.11 3 0.3523 0.894 0.00 0.00 0.78 0.18 0.00 0.04
#> TCGA.ET.A3DW.11 2 0.0000 0.896 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.EL.A3TA.11 2 0.0937 0.894 0.00 0.96 0.00 0.00 0.00 0.04
#> TCGA.EL.A3TB.11 5 0.3706 0.780 0.38 0.00 0.00 0.00 0.62 0.00
#> TCGA.DJ.A1QM.01 2 0.3309 0.772 0.00 0.72 0.00 0.28 0.00 0.00
#> TCGA.EM.A1YC.11 3 0.2728 0.912 0.00 0.00 0.86 0.10 0.00 0.04
#> TCGA.EL.A3T3.11 6 0.4165 0.779 0.16 0.00 0.00 0.10 0.00 0.74
#> TCGA.EL.A3T8.11 2 0.1092 0.895 0.00 0.96 0.02 0.00 0.00 0.02
#> TCGA.H2.A3RI.11 6 0.2790 0.819 0.14 0.00 0.02 0.00 0.00 0.84
#> TCGA.BJ.A3PU.11 2 0.0937 0.894 0.00 0.96 0.00 0.00 0.00 0.04
cbind(get_classes(res, k = 7), get_membership(res, k = 7))
#> class entropy silhouette p1 p2 p3 p4 p5 p6 p7
#> TCGA.E8.A416.01 5 0.2572 0.625 0.00 0.00 0.00 0.20 0.80 0.00 0.00
#> TCGA.EL.A3ZO.11 5 0.5293 0.516 0.24 0.00 0.00 0.02 0.58 0.16 0.00
#> TCGA.EL.A3ZL.11 5 0.2832 0.596 0.00 0.00 0.00 0.24 0.76 0.00 0.00
#> TCGA.EL.A3ZH.11 5 0.5130 0.580 0.18 0.00 0.00 0.04 0.64 0.00 0.14
#> TCGA.EL.A3ZG.11 2 0.0000 0.908 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.BJ.A2N8.11 4 0.2708 0.803 0.00 0.00 0.00 0.78 0.22 0.00 0.00
#> TCGA.EL.A3MW.11 6 0.1664 0.787 0.00 0.00 0.06 0.00 0.00 0.92 0.02
#> TCGA.EL.A3N2.11 6 0.0000 0.832 0.00 0.00 0.00 0.00 0.00 1.00 0.00
#> TCGA.EL.A3GZ.11 6 0.0863 0.828 0.04 0.00 0.00 0.00 0.00 0.96 0.00
#> TCGA.EM.A3AR.01 2 0.3186 0.589 0.22 0.76 0.00 0.02 0.00 0.00 0.00
#> TCGA.EL.A3H2.11 2 0.0504 0.907 0.00 0.98 0.00 0.00 0.02 0.00 0.00
#> TCGA.ET.A3DP.11 4 0.3058 0.655 0.10 0.00 0.00 0.82 0.00 0.08 0.00
#> TCGA.EL.A3MX.11 6 0.0000 0.832 0.00 0.00 0.00 0.00 0.00 1.00 0.00
#> TCGA.BJ.A28T.11 5 0.4121 0.631 0.10 0.00 0.00 0.20 0.70 0.00 0.00
#> TCGA.ET.A25J.11 4 0.1860 0.731 0.04 0.00 0.00 0.92 0.02 0.02 0.00
#> TCGA.EL.A3H7.11 6 0.0000 0.832 0.00 0.00 0.00 0.00 0.00 1.00 0.00
#> TCGA.BJ.A2N7.11 4 0.2708 0.803 0.00 0.00 0.00 0.78 0.22 0.00 0.00
#> TCGA.ET.A2N5.11 4 0.2708 0.803 0.00 0.00 0.00 0.78 0.22 0.00 0.00
#> TCGA.ET.A25N.11 4 0.2278 0.695 0.04 0.00 0.00 0.88 0.00 0.08 0.00
#> TCGA.BJ.A290.11 2 0.0504 0.907 0.00 0.98 0.00 0.00 0.02 0.00 0.00
#> TCGA.DO.A1JZ.11 3 0.0000 0.844 0.00 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.EM.A3SY.01 7 0.4783 0.000 0.10 0.36 0.00 0.00 0.00 0.00 0.54
#> TCGA.EL.A3T7.11 6 0.5128 0.344 0.28 0.00 0.00 0.00 0.18 0.54 0.00
#> TCGA.EM.A1CU.11 2 0.0504 0.903 0.00 0.98 0.00 0.00 0.02 0.00 0.00
#> TCGA.EL.A3T0.11 5 0.3519 0.677 0.22 0.00 0.00 0.04 0.74 0.00 0.00
#> TCGA.FY.A3TY.11 4 0.2708 0.803 0.00 0.00 0.00 0.78 0.22 0.00 0.00
#> TCGA.EM.A1CT.11 2 0.0863 0.902 0.00 0.96 0.00 0.00 0.04 0.00 0.00
#> TCGA.EM.A3ST.11 5 0.2832 0.596 0.00 0.00 0.00 0.24 0.76 0.00 0.00
#> TCGA.EM.A1CS.11 3 0.0504 0.844 0.00 0.00 0.98 0.00 0.00 0.00 0.02
#> TCGA.EM.A1CW.11 6 0.5086 0.319 0.14 0.00 0.00 0.36 0.00 0.50 0.00
#> TCGA.EM.A1CV.11 3 0.0000 0.844 0.00 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.EM.A1YE.11 3 0.4569 0.784 0.06 0.00 0.64 0.02 0.00 0.00 0.28
#> TCGA.EL.A3T2.11 4 0.3388 0.798 0.00 0.00 0.00 0.76 0.20 0.04 0.00
#> TCGA.EM.A1YD.11 3 0.2945 0.832 0.00 0.00 0.74 0.00 0.00 0.00 0.26
#> TCGA.ET.A3DW.11 2 0.0000 0.908 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.EL.A3TA.11 2 0.0000 0.908 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.EL.A3TB.11 5 0.3519 0.677 0.22 0.00 0.00 0.04 0.74 0.00 0.00
#> TCGA.DJ.A1QM.01 2 0.3186 0.589 0.22 0.76 0.00 0.02 0.00 0.00 0.00
#> TCGA.EM.A1YC.11 3 0.3047 0.830 0.00 0.00 0.72 0.00 0.00 0.00 0.28
#> TCGA.EL.A3T3.11 6 0.2422 0.760 0.18 0.00 0.00 0.00 0.00 0.82 0.00
#> TCGA.EL.A3T8.11 2 0.0504 0.907 0.00 0.98 0.00 0.00 0.02 0.00 0.00
#> TCGA.H2.A3RI.11 6 0.0863 0.828 0.04 0.00 0.00 0.00 0.00 0.96 0.00
#> TCGA.BJ.A3PU.11 2 0.0504 0.903 0.00 0.98 0.00 0.00 0.02 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.E8.A416.01 5 0.2132 0.5720 0.00 0.00 0.00 0.00 0.88 0.04 0.00 0.08
#> TCGA.EL.A3ZO.11 8 0.4174 0.5105 0.06 0.00 0.00 0.00 0.40 0.00 0.00 0.54
#> TCGA.EL.A3ZL.11 5 0.0000 0.6283 0.00 0.00 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.EL.A3ZH.11 5 0.5698 -0.0755 0.00 0.00 0.00 0.00 0.40 0.04 0.20 0.36
#> TCGA.EL.A3ZG.11 2 0.0000 0.8587 0.00 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.BJ.A2N8.11 4 0.3272 0.6376 0.00 0.00 0.00 0.58 0.42 0.00 0.00 0.00
#> TCGA.EL.A3MW.11 1 0.1804 0.8394 0.90 0.00 0.08 0.00 0.00 0.00 0.00 0.02
#> TCGA.EL.A3N2.11 1 0.0941 0.9112 0.96 0.00 0.00 0.02 0.02 0.00 0.00 0.00
#> TCGA.EL.A3GZ.11 1 0.1408 0.9103 0.94 0.00 0.00 0.02 0.02 0.00 0.02 0.00
#> TCGA.EM.A3AR.01 2 0.4213 0.4199 0.00 0.66 0.00 0.00 0.00 0.18 0.00 0.16
#> TCGA.EL.A3H2.11 2 0.1557 0.8484 0.02 0.92 0.00 0.00 0.00 0.06 0.00 0.00
#> TCGA.ET.A3DP.11 4 0.4202 0.5371 0.04 0.00 0.00 0.74 0.06 0.14 0.02 0.00
#> TCGA.EL.A3MX.11 1 0.0941 0.8843 0.96 0.00 0.02 0.00 0.00 0.00 0.00 0.02
#> TCGA.BJ.A28T.11 5 0.4241 0.3068 0.00 0.00 0.00 0.04 0.66 0.04 0.00 0.26
#> TCGA.ET.A25J.11 4 0.2484 0.6022 0.00 0.00 0.00 0.86 0.10 0.02 0.02 0.00
#> TCGA.EL.A3H7.11 1 0.0941 0.9112 0.96 0.00 0.00 0.02 0.02 0.00 0.00 0.00
#> TCGA.BJ.A2N7.11 4 0.3272 0.6376 0.00 0.00 0.00 0.58 0.42 0.00 0.00 0.00
#> TCGA.ET.A2N5.11 4 0.3237 0.6521 0.00 0.00 0.00 0.60 0.40 0.00 0.00 0.00
#> TCGA.ET.A25N.11 4 0.2807 0.5980 0.04 0.00 0.00 0.86 0.06 0.02 0.02 0.00
#> TCGA.BJ.A290.11 2 0.1557 0.8484 0.00 0.92 0.00 0.02 0.00 0.06 0.00 0.00
#> TCGA.DO.A1JZ.11 3 0.3095 0.8477 0.02 0.00 0.74 0.00 0.00 0.24 0.00 0.00
#> TCGA.EM.A3SY.01 7 0.3015 0.0000 0.00 0.32 0.00 0.00 0.00 0.00 0.68 0.00
#> TCGA.EL.A3T7.11 8 0.4556 0.1107 0.38 0.00 0.00 0.00 0.06 0.02 0.00 0.54
#> TCGA.EM.A1CU.11 2 0.0471 0.8519 0.00 0.98 0.00 0.02 0.00 0.00 0.00 0.00
#> TCGA.EL.A3T0.11 8 0.3971 0.5168 0.00 0.00 0.00 0.00 0.42 0.04 0.00 0.54
#> TCGA.FY.A3TY.11 4 0.3237 0.6521 0.00 0.00 0.00 0.60 0.40 0.00 0.00 0.00
#> TCGA.EM.A1CT.11 2 0.1557 0.8449 0.00 0.92 0.00 0.02 0.00 0.06 0.00 0.00
#> TCGA.EM.A3ST.11 5 0.0000 0.6283 0.00 0.00 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.EM.A1CS.11 3 0.2981 0.8473 0.02 0.00 0.76 0.00 0.00 0.22 0.00 0.00
#> TCGA.EM.A1CW.11 4 0.5582 -0.1003 0.38 0.00 0.00 0.44 0.02 0.14 0.02 0.00
#> TCGA.EM.A1CV.11 3 0.3095 0.8477 0.02 0.00 0.74 0.00 0.00 0.24 0.00 0.00
#> TCGA.EM.A1YE.11 3 0.2025 0.7733 0.00 0.00 0.88 0.02 0.00 0.10 0.00 0.00
#> TCGA.EL.A3T2.11 4 0.3862 0.6532 0.04 0.00 0.00 0.60 0.36 0.00 0.00 0.00
#> TCGA.EM.A1YD.11 3 0.0941 0.8196 0.00 0.00 0.96 0.00 0.00 0.02 0.00 0.02
#> TCGA.ET.A3DW.11 2 0.0000 0.8587 0.00 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.EL.A3TA.11 2 0.0471 0.8577 0.00 0.98 0.00 0.00 0.00 0.02 0.00 0.00
#> TCGA.EL.A3TB.11 8 0.3971 0.5168 0.00 0.00 0.00 0.00 0.42 0.04 0.00 0.54
#> TCGA.DJ.A1QM.01 2 0.4190 0.4199 0.00 0.66 0.00 0.00 0.00 0.20 0.00 0.14
#> TCGA.EM.A1YC.11 3 0.0941 0.8336 0.02 0.00 0.96 0.00 0.00 0.00 0.00 0.02
#> TCGA.EL.A3T3.11 1 0.5121 0.7063 0.68 0.00 0.00 0.06 0.02 0.14 0.08 0.02
#> TCGA.EL.A3T8.11 2 0.1341 0.8479 0.00 0.92 0.00 0.00 0.00 0.08 0.00 0.00
#> TCGA.H2.A3RI.11 1 0.1408 0.9103 0.94 0.00 0.00 0.02 0.02 0.00 0.02 0.00
#> TCGA.BJ.A3PU.11 2 0.0000 0.8587 0.00 1.00 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: Node02. Child nodes: Node0111-leaf , Node0112-leaf , Node0113-leaf , Node0114-leaf , Node0131-leaf , Node0132-leaf , Node0133-leaf , Node0141-leaf , Node0142-leaf , Node0143-leaf , Node0211-leaf , Node0212-leaf , Node0221-leaf , Node0222-leaf , Node0223-leaf , Node0224-leaf , Node0231-leaf , Node0232 , Node0233-leaf , Node0234-leaf , Node0241 , Node0242-leaf , Node0243-leaf , Node0244-leaf , Node0251-leaf , Node0252-leaf , Node0311 , Node0312-leaf , Node0313-leaf , Node0331-leaf , Node0332-leaf , Node0333-leaf .
The object with results only for a single top-value method and a single partitioning method can be extracted as:
res = res_rh["022"]
A summary of res and all the functions that can be applied to it:
res
#> A 'ConsensusPartition' object with k = 2, 3, 4, 5, 6, 7, 8.
#> On a matrix with 30000 rows and 45 columns.
#> Top rows (1000) are extracted by 'ATC' method.
#> Subgroups are detected by 'kmeans' method.
#> Performed in total 350 partitions by row resampling.
#> Best k for subgroups seems to be 2.
#>
#> Following methods can be applied to this 'ConsensusPartition' object:
#> [1] "cola_report" "collect_classes" "collect_plots"
#> [4] "collect_stats" "colnames" "compare_partitions"
#> [7] "compare_signatures" "consensus_heatmap" "dimension_reduction"
#> [10] "functional_enrichment" "get_anno_col" "get_anno"
#> [13] "get_classes" "get_consensus" "get_matrix"
#> [16] "get_membership" "get_param" "get_signatures"
#> [19] "get_stats" "is_best_k" "is_stable_k"
#> [22] "membership_heatmap" "ncol" "nrow"
#> [25] "plot_ecdf" "predict_classes" "rownames"
#> [28] "select_partition_number" "show" "suggest_best_k"
#> [31] "test_to_known_factors" "top_rows_heatmap"
collect_plots() function collects all the plots made from res for all k (number of subgroups)
into one single page to provide an easy and fast comparison between different k.
collect_plots(res)
The plots are:
k and the heatmap of
predicted classes for each k.k.k.k.All the plots in panels can be made by individual functions and they are plotted later in this section.
select_partition_number() produces several plots showing different
statistics for choosing “optimized” k. There are following statistics:
k;k, the area increased is defined as \(A_k - A_{k-1}\).The detailed explanations of these statistics can be found in the cola vignette.
Generally speaking, higher 1-PAC score, higher mean silhouette score or higher
concordance corresponds to better partition. Rand index and Jaccard index
measure how similar the current partition is compared to partition with k-1.
If they are too similar, we won't accept k is better than k-1.
select_partition_number(res)
The numeric values for all these statistics can be obtained by get_stats().
get_stats(res)
#> k 1-PAC mean_silhouette concordance area_increased Rand Jaccard
#> 2 2 1.000 1.000 1.000 0.3279 0.673 0.673
#> 3 3 0.746 0.900 0.898 0.7040 0.689 0.538
#> 4 4 0.726 0.953 0.934 0.1398 0.967 0.908
#> 5 5 0.984 0.916 0.952 0.0684 0.998 0.994
#> 6 6 0.931 0.859 0.921 0.0300 0.990 0.969
#> 7 7 0.801 0.826 0.903 0.0288 0.991 0.971
#> 8 8 0.800 0.720 0.865 0.0115 0.992 0.974
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.EL.A4K2.01 2 0 1 0 1
#> TCGA.EM.A4FH.01 1 0 1 1 0
#> TCGA.DE.A4M9.01 1 0 1 1 0
#> TCGA.KS.A41L.01 2 0 1 0 1
#> TCGA.E8.A434.01 2 0 1 0 1
#> TCGA.EL.A3ZH.01 2 0 1 0 1
#> TCGA.EL.A3H2.01 1 0 1 1 0
#> TCGA.BJ.A2N9.01 2 0 1 0 1
#> TCGA.EM.A2CT.01 2 0 1 0 1
#> TCGA.EM.A2CQ.01 2 0 1 0 1
#> TCGA.EM.A2CJ.01 2 0 1 0 1
#> TCGA.FY.A3NM.01 2 0 1 0 1
#> TCGA.BJ.A291.01 2 0 1 0 1
#> TCGA.EL.A3MY.11 1 0 1 1 0
#> TCGA.ET.A25I.01 2 0 1 0 1
#> TCGA.EM.A22N.01 2 0 1 0 1
#> TCGA.EM.A3FL.01 2 0 1 0 1
#> TCGA.EM.A2OW.01 2 0 1 0 1
#> TCGA.BJ.A0ZC.01 1 0 1 1 0
#> TCGA.EM.A2OV.01 2 0 1 0 1
#> TCGA.EM.A3AI.01 2 0 1 0 1
#> TCGA.EM.A2OY.01 2 0 1 0 1
#> TCGA.BJ.A192.01 2 0 1 0 1
#> TCGA.DJ.A3UZ.01 2 0 1 0 1
#> TCGA.EM.A1CW.01 2 0 1 0 1
#> TCGA.FY.A3WA.01 2 0 1 0 1
#> TCGA.J8.A3YD.01 2 0 1 0 1
#> TCGA.BJ.A190.01 1 0 1 1 0
#> TCGA.DJ.A2Q0.01 2 0 1 0 1
#> TCGA.EM.A1YC.01 2 0 1 0 1
#> TCGA.EM.A2CO.01 2 0 1 0 1
#> TCGA.ET.A3DS.01 2 0 1 0 1
#> TCGA.EM.A1YE.01 2 0 1 0 1
#> TCGA.DJ.A2Q2.01 2 0 1 0 1
#> TCGA.EM.A1YA.01 2 0 1 0 1
#> TCGA.EM.A1YD.01 2 0 1 0 1
#> TCGA.EL.A3CZ.01 2 0 1 0 1
#> TCGA.FY.A3R9.01 2 0 1 0 1
#> TCGA.EM.A3O6.01 2 0 1 0 1
#> TCGA.BJ.A0ZF.01 2 0 1 0 1
#> TCGA.BJ.A0YZ.01 1 0 1 1 0
#> TCGA.BJ.A0ZG.01 1 0 1 1 0
#> TCGA.DJ.A13R.01 1 0 1 1 0
#> TCGA.ET.A39N.01 2 0 1 0 1
#> TCGA.FY.A3R7.01 2 0 1 0 1
cbind(get_classes(res, k = 3), get_membership(res, k = 3))
#> class entropy silhouette p1 p2 p3
#> TCGA.EL.A4K2.01 2 0.628 1.000 0.00 0.54 0.46
#> TCGA.EM.A4FH.01 1 0.604 0.989 0.62 0.38 0.00
#> TCGA.DE.A4M9.01 1 0.624 0.966 0.56 0.44 0.00
#> TCGA.KS.A41L.01 3 0.604 0.635 0.38 0.00 0.62
#> TCGA.E8.A434.01 2 0.628 1.000 0.00 0.54 0.46
#> TCGA.EL.A3ZH.01 2 0.628 1.000 0.00 0.54 0.46
#> TCGA.EL.A3H2.01 1 0.604 0.989 0.62 0.38 0.00
#> TCGA.BJ.A2N9.01 2 0.628 1.000 0.00 0.54 0.46
#> TCGA.EM.A2CT.01 2 0.628 1.000 0.00 0.54 0.46
#> TCGA.EM.A2CQ.01 2 0.628 1.000 0.00 0.54 0.46
#> TCGA.EM.A2CJ.01 3 0.000 0.718 0.00 0.00 1.00
#> TCGA.FY.A3NM.01 3 0.000 0.718 0.00 0.00 1.00
#> TCGA.BJ.A291.01 2 0.628 1.000 0.00 0.54 0.46
#> TCGA.EL.A3MY.11 1 0.604 0.989 0.62 0.38 0.00
#> TCGA.ET.A25I.01 2 0.628 1.000 0.00 0.54 0.46
#> TCGA.EM.A22N.01 2 0.628 1.000 0.00 0.54 0.46
#> TCGA.EM.A3FL.01 3 0.000 0.718 0.00 0.00 1.00
#> TCGA.EM.A2OW.01 2 0.628 1.000 0.00 0.54 0.46
#> TCGA.BJ.A0ZC.01 1 0.604 0.989 0.62 0.38 0.00
#> TCGA.EM.A2OV.01 2 0.628 1.000 0.00 0.54 0.46
#> TCGA.EM.A3AI.01 2 0.628 1.000 0.00 0.54 0.46
#> TCGA.EM.A2OY.01 3 0.000 0.718 0.00 0.00 1.00
#> TCGA.BJ.A192.01 3 0.296 0.719 0.10 0.00 0.90
#> TCGA.DJ.A3UZ.01 2 0.628 1.000 0.00 0.54 0.46
#> TCGA.EM.A1CW.01 2 0.628 1.000 0.00 0.54 0.46
#> TCGA.FY.A3WA.01 3 0.604 0.635 0.38 0.00 0.62
#> TCGA.J8.A3YD.01 2 0.628 1.000 0.00 0.54 0.46
#> TCGA.BJ.A190.01 1 0.604 0.989 0.62 0.38 0.00
#> TCGA.DJ.A2Q0.01 3 0.000 0.718 0.00 0.00 1.00
#> TCGA.EM.A1YC.01 3 0.604 0.635 0.38 0.00 0.62
#> TCGA.EM.A2CO.01 2 0.628 1.000 0.00 0.54 0.46
#> TCGA.ET.A3DS.01 2 0.628 1.000 0.00 0.54 0.46
#> TCGA.EM.A1YE.01 3 0.000 0.718 0.00 0.00 1.00
#> TCGA.DJ.A2Q2.01 2 0.628 1.000 0.00 0.54 0.46
#> TCGA.EM.A1YA.01 3 0.000 0.718 0.00 0.00 1.00
#> TCGA.EM.A1YD.01 3 0.000 0.718 0.00 0.00 1.00
#> TCGA.EL.A3CZ.01 2 0.628 1.000 0.00 0.54 0.46
#> TCGA.FY.A3R9.01 2 0.628 1.000 0.00 0.54 0.46
#> TCGA.EM.A3O6.01 2 0.628 1.000 0.00 0.54 0.46
#> TCGA.BJ.A0ZF.01 3 0.604 0.635 0.38 0.00 0.62
#> TCGA.BJ.A0YZ.01 1 0.624 0.966 0.56 0.44 0.00
#> TCGA.BJ.A0ZG.01 1 0.604 0.989 0.62 0.38 0.00
#> TCGA.DJ.A13R.01 1 0.613 0.981 0.60 0.40 0.00
#> TCGA.ET.A39N.01 3 0.604 0.635 0.38 0.00 0.62
#> TCGA.FY.A3R7.01 2 0.628 1.000 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.EL.A4K2.01 2 0.0000 0.991 0.00 1.00 0.00 0.00
#> TCGA.EM.A4FH.01 1 0.0000 0.960 1.00 0.00 0.00 0.00
#> TCGA.DE.A4M9.01 1 0.2921 0.891 0.86 0.00 0.00 0.14
#> TCGA.KS.A41L.01 4 0.5512 0.922 0.00 0.04 0.30 0.66
#> TCGA.E8.A434.01 2 0.0000 0.991 0.00 1.00 0.00 0.00
#> TCGA.EL.A3ZH.01 2 0.0000 0.991 0.00 1.00 0.00 0.00
#> TCGA.EL.A3H2.01 1 0.0000 0.960 1.00 0.00 0.00 0.00
#> TCGA.BJ.A2N9.01 2 0.0707 0.989 0.00 0.98 0.00 0.02
#> TCGA.EM.A2CT.01 2 0.0707 0.989 0.00 0.98 0.00 0.02
#> TCGA.EM.A2CQ.01 2 0.0707 0.989 0.00 0.98 0.00 0.02
#> TCGA.EM.A2CJ.01 3 0.2921 0.926 0.00 0.14 0.86 0.00
#> TCGA.FY.A3NM.01 3 0.3172 0.943 0.00 0.16 0.84 0.00
#> TCGA.BJ.A291.01 2 0.0000 0.991 0.00 1.00 0.00 0.00
#> TCGA.EL.A3MY.11 1 0.0000 0.960 1.00 0.00 0.00 0.00
#> TCGA.ET.A25I.01 2 0.0707 0.989 0.00 0.98 0.00 0.02
#> TCGA.EM.A22N.01 2 0.0707 0.989 0.00 0.98 0.00 0.02
#> TCGA.EM.A3FL.01 3 0.3172 0.943 0.00 0.16 0.84 0.00
#> TCGA.EM.A2OW.01 2 0.0707 0.989 0.00 0.98 0.00 0.02
#> TCGA.BJ.A0ZC.01 1 0.0000 0.960 1.00 0.00 0.00 0.00
#> TCGA.EM.A2OV.01 2 0.0000 0.991 0.00 1.00 0.00 0.00
#> TCGA.EM.A3AI.01 2 0.0707 0.989 0.00 0.98 0.00 0.02
#> TCGA.EM.A2OY.01 3 0.3172 0.943 0.00 0.16 0.84 0.00
#> TCGA.BJ.A192.01 3 0.2921 0.926 0.00 0.14 0.86 0.00
#> TCGA.DJ.A3UZ.01 2 0.0000 0.991 0.00 1.00 0.00 0.00
#> TCGA.EM.A1CW.01 2 0.0707 0.989 0.00 0.98 0.00 0.02
#> TCGA.FY.A3WA.01 3 0.1913 0.753 0.00 0.04 0.94 0.02
#> TCGA.J8.A3YD.01 2 0.0000 0.991 0.00 1.00 0.00 0.00
#> TCGA.BJ.A190.01 1 0.0000 0.960 1.00 0.00 0.00 0.00
#> TCGA.DJ.A2Q0.01 3 0.3172 0.943 0.00 0.16 0.84 0.00
#> TCGA.EM.A1YC.01 3 0.1913 0.754 0.00 0.04 0.94 0.02
#> TCGA.EM.A2CO.01 2 0.0707 0.989 0.00 0.98 0.00 0.02
#> TCGA.ET.A3DS.01 2 0.0000 0.991 0.00 1.00 0.00 0.00
#> TCGA.EM.A1YE.01 3 0.3172 0.943 0.00 0.16 0.84 0.00
#> TCGA.DJ.A2Q2.01 2 0.0707 0.989 0.00 0.98 0.00 0.02
#> TCGA.EM.A1YA.01 3 0.3172 0.943 0.00 0.16 0.84 0.00
#> TCGA.EM.A1YD.01 3 0.3172 0.943 0.00 0.16 0.84 0.00
#> TCGA.EL.A3CZ.01 2 0.0000 0.991 0.00 1.00 0.00 0.00
#> TCGA.FY.A3R9.01 2 0.0000 0.991 0.00 1.00 0.00 0.00
#> TCGA.EM.A3O6.01 2 0.0000 0.991 0.00 1.00 0.00 0.00
#> TCGA.BJ.A0ZF.01 4 0.5512 0.922 0.00 0.04 0.30 0.66
#> TCGA.BJ.A0YZ.01 1 0.2921 0.891 0.86 0.00 0.00 0.14
#> TCGA.BJ.A0ZG.01 1 0.0000 0.960 1.00 0.00 0.00 0.00
#> TCGA.DJ.A13R.01 1 0.2830 0.908 0.90 0.00 0.04 0.06
#> TCGA.ET.A39N.01 4 0.4755 0.858 0.00 0.04 0.20 0.76
#> TCGA.FY.A3R7.01 2 0.0000 0.991 0.00 1.00 0.00 0.00
cbind(get_classes(res, k = 5), get_membership(res, k = 5))
#> class entropy silhouette p1 p2 p3 p4 p5
#> TCGA.EL.A4K2.01 2 0.0000 0.991 0.00 1.00 0.00 0.00 0.00
#> TCGA.EM.A4FH.01 1 0.0609 0.941 0.98 0.00 0.00 0.00 0.02
#> TCGA.DE.A4M9.01 1 0.3109 0.821 0.80 0.00 0.00 0.20 0.00
#> TCGA.KS.A41L.01 4 0.5689 1.000 0.00 0.00 0.08 0.48 0.44
#> TCGA.E8.A434.01 2 0.0000 0.991 0.00 1.00 0.00 0.00 0.00
#> TCGA.EL.A3ZH.01 2 0.0609 0.989 0.00 0.98 0.00 0.02 0.00
#> TCGA.EL.A3H2.01 1 0.0000 0.942 1.00 0.00 0.00 0.00 0.00
#> TCGA.BJ.A2N9.01 2 0.0000 0.991 0.00 1.00 0.00 0.00 0.00
#> TCGA.EM.A2CT.01 2 0.0609 0.989 0.00 0.98 0.00 0.02 0.00
#> TCGA.EM.A2CQ.01 2 0.0609 0.989 0.00 0.98 0.00 0.02 0.00
#> TCGA.EM.A2CJ.01 3 0.1648 0.906 0.00 0.02 0.94 0.04 0.00
#> TCGA.FY.A3NM.01 3 0.0609 0.922 0.00 0.02 0.98 0.00 0.00
#> TCGA.BJ.A291.01 2 0.0000 0.991 0.00 1.00 0.00 0.00 0.00
#> TCGA.EL.A3MY.11 1 0.0000 0.942 1.00 0.00 0.00 0.00 0.00
#> TCGA.ET.A25I.01 2 0.0609 0.989 0.00 0.98 0.00 0.02 0.00
#> TCGA.EM.A22N.01 2 0.0609 0.989 0.00 0.98 0.00 0.02 0.00
#> TCGA.EM.A3FL.01 3 0.0609 0.922 0.00 0.02 0.98 0.00 0.00
#> TCGA.EM.A2OW.01 2 0.0000 0.991 0.00 1.00 0.00 0.00 0.00
#> TCGA.BJ.A0ZC.01 1 0.0609 0.941 0.98 0.00 0.00 0.00 0.02
#> TCGA.EM.A2OV.01 2 0.0000 0.991 0.00 1.00 0.00 0.00 0.00
#> TCGA.EM.A3AI.01 2 0.0609 0.989 0.00 0.98 0.00 0.02 0.00
#> TCGA.EM.A2OY.01 3 0.1648 0.906 0.00 0.02 0.94 0.04 0.00
#> TCGA.BJ.A192.01 3 0.0000 0.903 0.00 0.00 1.00 0.00 0.00
#> TCGA.DJ.A3UZ.01 2 0.0000 0.991 0.00 1.00 0.00 0.00 0.00
#> TCGA.EM.A1CW.01 2 0.0000 0.991 0.00 1.00 0.00 0.00 0.00
#> TCGA.FY.A3WA.01 3 0.4287 0.219 0.00 0.00 0.54 0.46 0.00
#> TCGA.J8.A3YD.01 2 0.0000 0.991 0.00 1.00 0.00 0.00 0.00
#> TCGA.BJ.A190.01 1 0.0609 0.941 0.98 0.00 0.00 0.00 0.02
#> TCGA.DJ.A2Q0.01 3 0.0609 0.922 0.00 0.02 0.98 0.00 0.00
#> TCGA.EM.A1YC.01 3 0.2732 0.782 0.00 0.00 0.84 0.16 0.00
#> TCGA.EM.A2CO.01 2 0.0000 0.991 0.00 1.00 0.00 0.00 0.00
#> TCGA.ET.A3DS.01 2 0.0609 0.989 0.00 0.98 0.00 0.02 0.00
#> TCGA.EM.A1YE.01 3 0.0609 0.922 0.00 0.02 0.98 0.00 0.00
#> TCGA.DJ.A2Q2.01 2 0.0609 0.989 0.00 0.98 0.00 0.02 0.00
#> TCGA.EM.A1YA.01 3 0.0609 0.922 0.00 0.02 0.98 0.00 0.00
#> TCGA.EM.A1YD.01 3 0.0609 0.922 0.00 0.02 0.98 0.00 0.00
#> TCGA.EL.A3CZ.01 2 0.0000 0.991 0.00 1.00 0.00 0.00 0.00
#> TCGA.FY.A3R9.01 2 0.0609 0.989 0.00 0.98 0.00 0.02 0.00
#> TCGA.EM.A3O6.01 2 0.0609 0.989 0.00 0.98 0.00 0.02 0.00
#> TCGA.BJ.A0ZF.01 4 0.5689 1.000 0.00 0.00 0.08 0.48 0.44
#> TCGA.BJ.A0YZ.01 1 0.3109 0.821 0.80 0.00 0.00 0.20 0.00
#> TCGA.BJ.A0ZG.01 1 0.0000 0.942 1.00 0.00 0.00 0.00 0.00
#> TCGA.DJ.A13R.01 1 0.1043 0.922 0.96 0.00 0.00 0.04 0.00
#> TCGA.ET.A39N.01 5 0.0609 0.000 0.00 0.00 0.02 0.00 0.98
#> TCGA.FY.A3R7.01 2 0.0000 0.991 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.EL.A4K2.01 2 0.0937 0.9641 0.00 0.96 0.00 0.00 0.00 0.04
#> TCGA.EM.A4FH.01 1 0.0000 0.9084 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.DE.A4M9.01 1 0.3409 0.7081 0.70 0.00 0.00 0.00 0.30 0.00
#> TCGA.KS.A41L.01 4 0.1556 1.0000 0.00 0.00 0.08 0.92 0.00 0.00
#> TCGA.E8.A434.01 2 0.0547 0.9629 0.00 0.98 0.00 0.00 0.00 0.02
#> TCGA.EL.A3ZH.01 2 0.0937 0.9621 0.00 0.96 0.00 0.00 0.00 0.04
#> TCGA.EL.A3H2.01 1 0.0547 0.9084 0.98 0.00 0.00 0.00 0.00 0.02
#> TCGA.BJ.A2N9.01 2 0.1480 0.9584 0.00 0.94 0.00 0.00 0.02 0.04
#> TCGA.EM.A2CT.01 2 0.1807 0.9516 0.00 0.92 0.00 0.00 0.02 0.06
#> TCGA.EM.A2CQ.01 2 0.1807 0.9516 0.00 0.92 0.00 0.00 0.02 0.06
#> TCGA.EM.A2CJ.01 3 0.2728 0.7460 0.00 0.00 0.86 0.00 0.04 0.10
#> TCGA.FY.A3NM.01 3 0.0000 0.8897 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.BJ.A291.01 2 0.2094 0.9545 0.00 0.90 0.00 0.00 0.02 0.08
#> TCGA.EL.A3MY.11 1 0.0547 0.9084 0.98 0.00 0.00 0.00 0.00 0.02
#> TCGA.ET.A25I.01 2 0.1807 0.9516 0.00 0.92 0.00 0.00 0.02 0.06
#> TCGA.EM.A22N.01 2 0.1480 0.9600 0.00 0.94 0.00 0.00 0.02 0.04
#> TCGA.EM.A3FL.01 3 0.0000 0.8897 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.EM.A2OW.01 2 0.0547 0.9647 0.00 0.98 0.00 0.00 0.00 0.02
#> TCGA.BJ.A0ZC.01 1 0.0000 0.9084 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.EM.A2OV.01 2 0.0547 0.9647 0.00 0.98 0.00 0.00 0.00 0.02
#> TCGA.EM.A3AI.01 2 0.1480 0.9546 0.00 0.94 0.00 0.00 0.02 0.04
#> TCGA.EM.A2OY.01 3 0.2728 0.7460 0.00 0.00 0.86 0.00 0.04 0.10
#> TCGA.BJ.A192.01 3 0.0000 0.8897 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.DJ.A3UZ.01 2 0.0547 0.9629 0.00 0.98 0.00 0.00 0.00 0.02
#> TCGA.EM.A1CW.01 2 0.0547 0.9647 0.00 0.98 0.00 0.00 0.00 0.02
#> TCGA.FY.A3WA.01 6 0.5569 0.0000 0.00 0.00 0.28 0.18 0.00 0.54
#> TCGA.J8.A3YD.01 2 0.0547 0.9629 0.00 0.98 0.00 0.00 0.00 0.02
#> TCGA.BJ.A190.01 1 0.0000 0.9084 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.DJ.A2Q0.01 3 0.0000 0.8897 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.EM.A1YC.01 3 0.5120 0.0989 0.00 0.00 0.60 0.00 0.12 0.28
#> TCGA.EM.A2CO.01 2 0.0547 0.9647 0.00 0.98 0.00 0.00 0.00 0.02
#> TCGA.ET.A3DS.01 2 0.0000 0.9647 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.EM.A1YE.01 3 0.0000 0.8897 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.DJ.A2Q2.01 2 0.1092 0.9614 0.00 0.96 0.00 0.00 0.02 0.02
#> TCGA.EM.A1YA.01 3 0.0000 0.8897 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.EM.A1YD.01 3 0.0000 0.8897 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.EL.A3CZ.01 2 0.1807 0.9536 0.00 0.92 0.00 0.00 0.02 0.06
#> TCGA.FY.A3R9.01 2 0.0547 0.9629 0.00 0.98 0.00 0.00 0.00 0.02
#> TCGA.EM.A3O6.01 2 0.0547 0.9629 0.00 0.98 0.00 0.00 0.00 0.02
#> TCGA.BJ.A0ZF.01 4 0.1556 1.0000 0.00 0.00 0.08 0.92 0.00 0.00
#> TCGA.BJ.A0YZ.01 1 0.3819 0.7081 0.70 0.00 0.00 0.00 0.28 0.02
#> TCGA.BJ.A0ZG.01 1 0.0547 0.9084 0.98 0.00 0.00 0.00 0.00 0.02
#> TCGA.DJ.A13R.01 1 0.2725 0.8436 0.88 0.00 0.00 0.04 0.02 0.06
#> TCGA.ET.A39N.01 5 0.5708 0.0000 0.00 0.00 0.02 0.38 0.50 0.10
#> TCGA.FY.A3R7.01 2 0.0547 0.9629 0.00 0.98 0.00 0.00 0.00 0.02
cbind(get_classes(res, k = 7), get_membership(res, k = 7))
#> class entropy silhouette p1 p2 p3 p4 p5 p6 p7
#> TCGA.EL.A4K2.01 2 0.1166 0.936 0.00 0.94 0.00 0.0 0.00 0.06 0.00
#> TCGA.EM.A4FH.01 1 0.0504 0.860 0.98 0.00 0.00 0.0 0.00 0.00 0.02
#> TCGA.DE.A4M9.01 1 0.3558 0.460 0.52 0.00 0.00 0.0 0.48 0.00 0.00
#> TCGA.KS.A41L.01 4 0.0000 1.000 0.00 0.00 0.00 1.0 0.00 0.00 0.00
#> TCGA.E8.A434.01 2 0.0863 0.925 0.00 0.96 0.00 0.0 0.00 0.04 0.00
#> TCGA.EL.A3ZH.01 2 0.1671 0.933 0.00 0.90 0.00 0.0 0.00 0.10 0.00
#> TCGA.EL.A3H2.01 1 0.0000 0.861 1.00 0.00 0.00 0.0 0.00 0.00 0.00
#> TCGA.BJ.A2N9.01 2 0.2376 0.921 0.00 0.86 0.00 0.0 0.00 0.12 0.02
#> TCGA.EM.A2CT.01 2 0.2081 0.921 0.00 0.86 0.00 0.0 0.00 0.14 0.00
#> TCGA.EM.A2CQ.01 2 0.1886 0.925 0.00 0.88 0.00 0.0 0.00 0.12 0.00
#> TCGA.EM.A2CJ.01 3 0.3208 0.721 0.00 0.00 0.82 0.0 0.04 0.02 0.12
#> TCGA.FY.A3NM.01 3 0.0000 0.923 0.00 0.00 1.00 0.0 0.00 0.00 0.00
#> TCGA.BJ.A291.01 2 0.2081 0.931 0.00 0.86 0.00 0.0 0.00 0.14 0.00
#> TCGA.EL.A3MY.11 1 0.0000 0.861 1.00 0.00 0.00 0.0 0.00 0.00 0.00
#> TCGA.ET.A25I.01 2 0.2081 0.921 0.00 0.86 0.00 0.0 0.00 0.14 0.00
#> TCGA.EM.A22N.01 2 0.1886 0.925 0.00 0.88 0.00 0.0 0.00 0.12 0.00
#> TCGA.EM.A3FL.01 3 0.0504 0.908 0.00 0.00 0.98 0.0 0.00 0.00 0.02
#> TCGA.EM.A2OW.01 2 0.1433 0.929 0.00 0.92 0.00 0.0 0.00 0.08 0.00
#> TCGA.BJ.A0ZC.01 1 0.0504 0.860 0.98 0.00 0.00 0.0 0.00 0.00 0.02
#> TCGA.EM.A2OV.01 2 0.1166 0.933 0.00 0.94 0.00 0.0 0.00 0.06 0.00
#> TCGA.EM.A3AI.01 2 0.1928 0.926 0.00 0.90 0.00 0.0 0.00 0.08 0.02
#> TCGA.EM.A2OY.01 3 0.3208 0.721 0.00 0.00 0.82 0.0 0.04 0.02 0.12
#> TCGA.BJ.A192.01 3 0.0000 0.923 0.00 0.00 1.00 0.0 0.00 0.00 0.00
#> TCGA.DJ.A3UZ.01 2 0.0863 0.925 0.00 0.96 0.00 0.0 0.00 0.04 0.00
#> TCGA.EM.A1CW.01 2 0.1671 0.928 0.00 0.90 0.00 0.0 0.00 0.10 0.00
#> TCGA.FY.A3WA.01 6 0.5990 0.000 0.00 0.00 0.14 0.1 0.02 0.60 0.14
#> TCGA.J8.A3YD.01 2 0.0863 0.925 0.00 0.96 0.00 0.0 0.00 0.04 0.00
#> TCGA.BJ.A190.01 1 0.0504 0.860 0.98 0.00 0.00 0.0 0.00 0.00 0.02
#> TCGA.DJ.A2Q0.01 3 0.0000 0.923 0.00 0.00 1.00 0.0 0.00 0.00 0.00
#> TCGA.EM.A1YC.01 7 0.3459 0.000 0.00 0.00 0.40 0.0 0.00 0.00 0.60
#> TCGA.EM.A2CO.01 2 0.1433 0.929 0.00 0.92 0.00 0.0 0.00 0.08 0.00
#> TCGA.ET.A3DS.01 2 0.1363 0.928 0.00 0.94 0.00 0.0 0.00 0.04 0.02
#> TCGA.EM.A1YE.01 3 0.0000 0.923 0.00 0.00 1.00 0.0 0.00 0.00 0.00
#> TCGA.DJ.A2Q2.01 2 0.1928 0.926 0.00 0.90 0.00 0.0 0.00 0.08 0.02
#> TCGA.EM.A1YA.01 3 0.0000 0.923 0.00 0.00 1.00 0.0 0.00 0.00 0.00
#> TCGA.EM.A1YD.01 3 0.0000 0.923 0.00 0.00 1.00 0.0 0.00 0.00 0.00
#> TCGA.EL.A3CZ.01 2 0.1433 0.927 0.00 0.92 0.00 0.0 0.00 0.08 0.00
#> TCGA.FY.A3R9.01 2 0.1166 0.929 0.00 0.94 0.00 0.0 0.00 0.06 0.00
#> TCGA.EM.A3O6.01 2 0.1433 0.930 0.00 0.92 0.00 0.0 0.00 0.08 0.00
#> TCGA.BJ.A0ZF.01 4 0.0000 1.000 0.00 0.00 0.00 1.0 0.00 0.00 0.00
#> TCGA.BJ.A0YZ.01 1 0.3558 0.460 0.52 0.00 0.00 0.0 0.48 0.00 0.00
#> TCGA.BJ.A0ZG.01 1 0.0000 0.861 1.00 0.00 0.00 0.0 0.00 0.00 0.00
#> TCGA.DJ.A13R.01 1 0.1928 0.809 0.90 0.00 0.00 0.0 0.00 0.02 0.08
#> TCGA.ET.A39N.01 5 0.6559 0.000 0.00 0.00 0.00 0.2 0.46 0.20 0.14
#> TCGA.FY.A3R7.01 2 0.0863 0.925 0.00 0.96 0.00 0.0 0.00 0.04 0.00
cbind(get_classes(res, k = 8), get_membership(res, k = 8))
#> class entropy silhouette p1 p2 p3 p4 p5 p6 p7 p8
#> TCGA.EL.A4K2.01 2 0.1341 0.913 0.00 0.92 0.00 0.00 0.00 0.00 0.08 0.00
#> TCGA.EM.A4FH.01 1 0.0941 0.721 0.96 0.00 0.00 0.00 0.02 0.02 0.00 0.00
#> TCGA.DE.A4M9.01 1 0.4403 -0.916 0.48 0.00 0.00 0.00 0.08 0.00 0.00 0.44
#> TCGA.KS.A41L.01 4 0.2265 0.891 0.00 0.00 0.02 0.88 0.00 0.00 0.02 0.08
#> TCGA.E8.A434.01 2 0.0000 0.908 0.00 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.EL.A3ZH.01 2 0.1091 0.908 0.00 0.94 0.00 0.00 0.00 0.00 0.06 0.00
#> TCGA.EL.A3H2.01 1 0.1408 0.726 0.94 0.00 0.00 0.02 0.02 0.02 0.00 0.00
#> TCGA.BJ.A2N9.01 2 0.2406 0.899 0.00 0.80 0.00 0.00 0.00 0.00 0.20 0.00
#> TCGA.EM.A2CT.01 2 0.2406 0.899 0.00 0.80 0.00 0.00 0.00 0.00 0.20 0.00
#> TCGA.EM.A2CQ.01 2 0.2406 0.899 0.00 0.80 0.00 0.00 0.00 0.00 0.20 0.00
#> TCGA.EM.A2CJ.01 3 0.3880 0.468 0.00 0.00 0.64 0.00 0.02 0.02 0.00 0.32
#> TCGA.FY.A3NM.01 3 0.2265 0.749 0.00 0.00 0.88 0.00 0.02 0.02 0.00 0.08
#> TCGA.BJ.A291.01 2 0.0471 0.910 0.00 0.98 0.00 0.00 0.00 0.00 0.02 0.00
#> TCGA.EL.A3MY.11 1 0.1408 0.726 0.94 0.00 0.00 0.02 0.02 0.02 0.00 0.00
#> TCGA.ET.A25I.01 2 0.2406 0.899 0.00 0.80 0.00 0.00 0.00 0.00 0.20 0.00
#> TCGA.EM.A22N.01 2 0.2406 0.899 0.00 0.80 0.00 0.00 0.00 0.00 0.20 0.00
#> TCGA.EM.A3FL.01 3 0.0471 0.841 0.00 0.00 0.98 0.00 0.00 0.00 0.00 0.02
#> TCGA.EM.A2OW.01 2 0.1947 0.908 0.00 0.86 0.00 0.00 0.00 0.00 0.14 0.00
#> TCGA.BJ.A0ZC.01 1 0.0941 0.721 0.96 0.00 0.00 0.00 0.02 0.02 0.00 0.00
#> TCGA.EM.A2OV.01 2 0.1563 0.916 0.00 0.90 0.00 0.00 0.00 0.00 0.10 0.00
#> TCGA.EM.A3AI.01 2 0.2114 0.908 0.00 0.84 0.00 0.00 0.00 0.00 0.16 0.00
#> TCGA.EM.A2OY.01 3 0.3808 0.500 0.00 0.00 0.66 0.00 0.02 0.02 0.00 0.30
#> TCGA.BJ.A192.01 3 0.0471 0.841 0.00 0.00 0.98 0.00 0.00 0.02 0.00 0.00
#> TCGA.DJ.A3UZ.01 2 0.0000 0.908 0.00 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.EM.A1CW.01 2 0.2406 0.899 0.00 0.80 0.00 0.00 0.00 0.00 0.20 0.00
#> TCGA.FY.A3WA.01 6 0.2350 0.000 0.00 0.00 0.10 0.04 0.00 0.86 0.00 0.00
#> TCGA.J8.A3YD.01 2 0.0000 0.908 0.00 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.BJ.A190.01 1 0.0941 0.721 0.96 0.00 0.00 0.00 0.02 0.02 0.00 0.00
#> TCGA.DJ.A2Q0.01 3 0.0000 0.849 0.00 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.EM.A1YC.01 7 0.4489 0.000 0.00 0.00 0.26 0.00 0.04 0.06 0.64 0.00
#> TCGA.EM.A2CO.01 2 0.1947 0.908 0.00 0.86 0.00 0.00 0.00 0.00 0.14 0.00
#> TCGA.ET.A3DS.01 2 0.0000 0.908 0.00 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.EM.A1YE.01 3 0.0000 0.849 0.00 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.DJ.A2Q2.01 2 0.1947 0.910 0.00 0.86 0.00 0.00 0.00 0.00 0.14 0.00
#> TCGA.EM.A1YA.01 3 0.0471 0.841 0.00 0.00 0.98 0.00 0.00 0.02 0.00 0.00
#> TCGA.EM.A1YD.01 3 0.0000 0.849 0.00 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.EL.A3CZ.01 2 0.0000 0.908 0.00 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.FY.A3R9.01 2 0.0000 0.908 0.00 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.EM.A3O6.01 2 0.1091 0.908 0.00 0.94 0.00 0.00 0.00 0.00 0.06 0.00
#> TCGA.BJ.A0ZF.01 4 0.0471 0.891 0.00 0.00 0.02 0.98 0.00 0.00 0.00 0.00
#> TCGA.BJ.A0YZ.01 8 0.3737 0.000 0.48 0.00 0.00 0.00 0.00 0.00 0.02 0.50
#> TCGA.BJ.A0ZG.01 1 0.1408 0.726 0.94 0.00 0.00 0.02 0.02 0.02 0.00 0.00
#> TCGA.DJ.A13R.01 1 0.3720 0.445 0.78 0.00 0.00 0.00 0.02 0.06 0.12 0.02
#> TCGA.ET.A39N.01 5 0.2534 0.000 0.00 0.00 0.00 0.22 0.78 0.00 0.00 0.00
#> TCGA.FY.A3R7.01 2 0.0000 0.908 0.00 1.00 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: Node02. Child nodes: Node0111-leaf , Node0112-leaf , Node0113-leaf , Node0114-leaf , Node0131-leaf , Node0132-leaf , Node0133-leaf , Node0141-leaf , Node0142-leaf , Node0143-leaf , Node0211-leaf , Node0212-leaf , Node0221-leaf , Node0222-leaf , Node0223-leaf , Node0224-leaf , Node0231-leaf , Node0232 , Node0233-leaf , Node0234-leaf , Node0241 , Node0242-leaf , Node0243-leaf , Node0244-leaf , Node0251-leaf , Node0252-leaf , Node0311 , Node0312-leaf , Node0313-leaf , Node0331-leaf , Node0332-leaf , Node0333-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 32 columns.
#> Top rows (1000) are extracted by 'ATC' method.
#> Subgroups are detected by 'skmeans' method.
#> Performed in total 350 partitions by row resampling.
#> Best k for subgroups seems to be 3.
#>
#> Following methods can be applied to this 'ConsensusPartition' object:
#> [1] "cola_report" "collect_classes" "collect_plots"
#> [4] "collect_stats" "colnames" "compare_partitions"
#> [7] "compare_signatures" "consensus_heatmap" "dimension_reduction"
#> [10] "functional_enrichment" "get_anno_col" "get_anno"
#> [13] "get_classes" "get_consensus" "get_matrix"
#> [16] "get_membership" "get_param" "get_signatures"
#> [19] "get_stats" "is_best_k" "is_stable_k"
#> [22] "membership_heatmap" "ncol" "nrow"
#> [25] "plot_ecdf" "predict_classes" "rownames"
#> [28] "select_partition_number" "show" "suggest_best_k"
#> [31] "test_to_known_factors" "top_rows_heatmap"
collect_plots() function collects all the plots made from res for all k (number of subgroups)
into one single page to provide an easy and fast comparison between different k.
collect_plots(res)
The plots are:
k and the heatmap of
predicted classes for each k.k.k.k.All the plots in panels can be made by individual functions and they are plotted later in this section.
select_partition_number() produces several plots showing different
statistics for choosing “optimized” k. There are following statistics:
k;k, the area increased is defined as \(A_k - A_{k-1}\).The detailed explanations of these statistics can be found in the cola vignette.
Generally speaking, higher 1-PAC score, higher mean silhouette score or higher
concordance corresponds to better partition. Rand index and Jaccard index
measure how similar the current partition is compared to partition with k-1.
If they are too similar, we won't accept k is better than k-1.
select_partition_number(res)
The numeric values for all these statistics can be obtained by get_stats().
get_stats(res)
#> k 1-PAC mean_silhouette concordance area_increased Rand Jaccard
#> 2 2 1.000 1.000 1.000 0.4663 0.534 0.534
#> 3 3 1.000 1.000 1.000 0.4579 0.698 0.477
#> 4 4 1.000 0.994 0.997 0.0479 0.968 0.899
#> 5 5 0.880 0.806 0.900 0.0443 0.976 0.916
#> 6 6 0.855 0.841 0.911 0.0306 0.958 0.844
#> 7 7 0.865 0.742 0.856 0.0468 0.935 0.729
#> 8 8 0.843 0.785 0.891 0.0337 0.970 0.833
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.EL.A3ZK.11 2 0 1 0 1
#> TCGA.DJ.A3VL.01 2 0 1 0 1
#> TCGA.DJ.A4V0.01 2 0 1 0 1
#> TCGA.EL.A3ZP.11 2 0 1 0 1
#> TCGA.BJ.A45E.01 1 0 1 1 0
#> TCGA.DJ.A2Q9.01 1 0 1 1 0
#> TCGA.EL.A3N3.11 2 0 1 0 1
#> TCGA.BJ.A28W.11 1 0 1 1 0
#> TCGA.E8.A2JQ.11 1 0 1 1 0
#> TCGA.BJ.A28R.11 2 0 1 0 1
#> TCGA.GE.A2C6.11 1 0 1 1 0
#> TCGA.CE.A27D.01 2 0 1 0 1
#> TCGA.EL.A3H1.11 2 0 1 0 1
#> TCGA.BJ.A28W.01 1 0 1 1 0
#> TCGA.BJ.A28T.01 2 0 1 0 1
#> TCGA.BJ.A2N9.11 1 0 1 1 0
#> TCGA.H2.A2K9.11 2 0 1 0 1
#> TCGA.FY.A3TY.01 2 0 1 0 1
#> TCGA.EL.A3T1.11 2 0 1 0 1
#> TCGA.EM.A2CP.01 1 0 1 1 0
#> TCGA.EM.A3AJ.01 2 0 1 0 1
#> TCGA.EL.A3CW.01 2 0 1 0 1
#> TCGA.ET.A3DQ.01 2 0 1 0 1
#> TCGA.BJ.A2NA.11 2 0 1 0 1
#> TCGA.BJ.A28X.11 1 0 1 1 0
#> TCGA.EL.A3CY.01 1 0 1 1 0
#> TCGA.EL.A3CO.01 2 0 1 0 1
#> TCGA.BJ.A3PR.11 2 0 1 0 1
#> TCGA.EL.A3T6.11 2 0 1 0 1
#> TCGA.EM.A3O9.01 2 0 1 0 1
#> TCGA.BJ.A3PR.01 1 0 1 1 0
#> TCGA.DJ.A13O.01 2 0 1 0 1
cbind(get_classes(res, k = 3), get_membership(res, k = 3))
#> class entropy silhouette p1 p2 p3
#> TCGA.EL.A3ZK.11 2 0 1 0 1 0
#> TCGA.DJ.A3VL.01 3 0 1 0 0 1
#> TCGA.DJ.A4V0.01 2 0 1 0 1 0
#> TCGA.EL.A3ZP.11 2 0 1 0 1 0
#> TCGA.BJ.A45E.01 1 0 1 1 0 0
#> TCGA.DJ.A2Q9.01 1 0 1 1 0 0
#> TCGA.EL.A3N3.11 2 0 1 0 1 0
#> TCGA.BJ.A28W.11 2 0 1 0 1 0
#> TCGA.E8.A2JQ.11 1 0 1 1 0 0
#> TCGA.BJ.A28R.11 2 0 1 0 1 0
#> TCGA.GE.A2C6.11 2 0 1 0 1 0
#> TCGA.CE.A27D.01 3 0 1 0 0 1
#> TCGA.EL.A3H1.11 3 0 1 0 0 1
#> TCGA.BJ.A28W.01 1 0 1 1 0 0
#> TCGA.BJ.A28T.01 2 0 1 0 1 0
#> TCGA.BJ.A2N9.11 1 0 1 1 0 0
#> TCGA.H2.A2K9.11 3 0 1 0 0 1
#> TCGA.FY.A3TY.01 3 0 1 0 0 1
#> TCGA.EL.A3T1.11 2 0 1 0 1 0
#> TCGA.EM.A2CP.01 1 0 1 1 0 0
#> TCGA.EM.A3AJ.01 2 0 1 0 1 0
#> TCGA.EL.A3CW.01 2 0 1 0 1 0
#> TCGA.ET.A3DQ.01 2 0 1 0 1 0
#> TCGA.BJ.A2NA.11 3 0 1 0 0 1
#> TCGA.BJ.A28X.11 1 0 1 1 0 0
#> TCGA.EL.A3CY.01 1 0 1 1 0 0
#> TCGA.EL.A3CO.01 3 0 1 0 0 1
#> TCGA.BJ.A3PR.11 2 0 1 0 1 0
#> TCGA.EL.A3T6.11 3 0 1 0 0 1
#> TCGA.EM.A3O9.01 3 0 1 0 0 1
#> TCGA.BJ.A3PR.01 1 0 1 1 0 0
#> TCGA.DJ.A13O.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.EL.A3ZK.11 2 0.0000 1.000 0 1 0.00 0.00
#> TCGA.DJ.A3VL.01 4 0.0707 0.979 0 0 0.02 0.98
#> TCGA.DJ.A4V0.01 2 0.0000 1.000 0 1 0.00 0.00
#> TCGA.EL.A3ZP.11 2 0.0000 1.000 0 1 0.00 0.00
#> TCGA.BJ.A45E.01 1 0.0000 1.000 1 0 0.00 0.00
#> TCGA.DJ.A2Q9.01 1 0.0000 1.000 1 0 0.00 0.00
#> TCGA.EL.A3N3.11 2 0.0000 1.000 0 1 0.00 0.00
#> TCGA.BJ.A28W.11 2 0.0000 1.000 0 1 0.00 0.00
#> TCGA.E8.A2JQ.11 1 0.0000 1.000 1 0 0.00 0.00
#> TCGA.BJ.A28R.11 2 0.0000 1.000 0 1 0.00 0.00
#> TCGA.GE.A2C6.11 2 0.0000 1.000 0 1 0.00 0.00
#> TCGA.CE.A27D.01 3 0.0000 0.988 0 0 1.00 0.00
#> TCGA.EL.A3H1.11 3 0.0000 0.988 0 0 1.00 0.00
#> TCGA.BJ.A28W.01 1 0.0000 1.000 1 0 0.00 0.00
#> TCGA.BJ.A28T.01 2 0.0000 1.000 0 1 0.00 0.00
#> TCGA.BJ.A2N9.11 1 0.0000 1.000 1 0 0.00 0.00
#> TCGA.H2.A2K9.11 3 0.0000 0.988 0 0 1.00 0.00
#> TCGA.FY.A3TY.01 3 0.0000 0.988 0 0 1.00 0.00
#> TCGA.EL.A3T1.11 2 0.0000 1.000 0 1 0.00 0.00
#> TCGA.EM.A2CP.01 1 0.0000 1.000 1 0 0.00 0.00
#> TCGA.EM.A3AJ.01 2 0.0000 1.000 0 1 0.00 0.00
#> TCGA.EL.A3CW.01 2 0.0000 1.000 0 1 0.00 0.00
#> TCGA.ET.A3DQ.01 2 0.0000 1.000 0 1 0.00 0.00
#> TCGA.BJ.A2NA.11 3 0.0000 0.988 0 0 1.00 0.00
#> TCGA.BJ.A28X.11 1 0.0000 1.000 1 0 0.00 0.00
#> TCGA.EL.A3CY.01 1 0.0000 1.000 1 0 0.00 0.00
#> TCGA.EL.A3CO.01 3 0.1211 0.964 0 0 0.96 0.04
#> TCGA.BJ.A3PR.11 2 0.0000 1.000 0 1 0.00 0.00
#> TCGA.EL.A3T6.11 3 0.0000 0.988 0 0 1.00 0.00
#> TCGA.EM.A3O9.01 4 0.0000 0.979 0 0 0.00 1.00
#> TCGA.BJ.A3PR.01 1 0.0000 1.000 1 0 0.00 0.00
#> TCGA.DJ.A13O.01 3 0.1211 0.964 0 0 0.96 0.04
cbind(get_classes(res, k = 5), get_membership(res, k = 5))
#> class entropy silhouette p1 p2 p3 p4 p5
#> TCGA.EL.A3ZK.11 2 0.2280 0.852 0 0.88 0.00 0.00 0.12
#> TCGA.DJ.A3VL.01 4 0.2280 0.352 0 0.00 0.12 0.88 0.00
#> TCGA.DJ.A4V0.01 2 0.0609 0.875 0 0.98 0.00 0.00 0.02
#> TCGA.EL.A3ZP.11 2 0.0000 0.874 0 1.00 0.00 0.00 0.00
#> TCGA.BJ.A45E.01 1 0.0000 1.000 1 0.00 0.00 0.00 0.00
#> TCGA.DJ.A2Q9.01 1 0.0000 1.000 1 0.00 0.00 0.00 0.00
#> TCGA.EL.A3N3.11 2 0.2280 0.852 0 0.88 0.00 0.00 0.12
#> TCGA.BJ.A28W.11 5 0.4302 0.000 0 0.48 0.00 0.00 0.52
#> TCGA.E8.A2JQ.11 1 0.0000 1.000 1 0.00 0.00 0.00 0.00
#> TCGA.BJ.A28R.11 2 0.0000 0.874 0 1.00 0.00 0.00 0.00
#> TCGA.GE.A2C6.11 2 0.1732 0.751 0 0.92 0.00 0.00 0.08
#> TCGA.CE.A27D.01 3 0.0000 0.736 0 0.00 1.00 0.00 0.00
#> TCGA.EL.A3H1.11 3 0.0000 0.736 0 0.00 1.00 0.00 0.00
#> TCGA.BJ.A28W.01 1 0.0000 1.000 1 0.00 0.00 0.00 0.00
#> TCGA.BJ.A28T.01 2 0.0609 0.853 0 0.98 0.00 0.00 0.02
#> TCGA.BJ.A2N9.11 1 0.0000 1.000 1 0.00 0.00 0.00 0.00
#> TCGA.H2.A2K9.11 3 0.4060 0.708 0 0.00 0.64 0.36 0.00
#> TCGA.FY.A3TY.01 3 0.0000 0.736 0 0.00 1.00 0.00 0.00
#> TCGA.EL.A3T1.11 2 0.2280 0.852 0 0.88 0.00 0.00 0.12
#> TCGA.EM.A2CP.01 1 0.0000 1.000 1 0.00 0.00 0.00 0.00
#> TCGA.EM.A3AJ.01 2 0.0000 0.874 0 1.00 0.00 0.00 0.00
#> TCGA.EL.A3CW.01 2 0.0000 0.874 0 1.00 0.00 0.00 0.00
#> TCGA.ET.A3DQ.01 2 0.2280 0.852 0 0.88 0.00 0.00 0.12
#> TCGA.BJ.A2NA.11 3 0.4060 0.708 0 0.00 0.64 0.36 0.00
#> TCGA.BJ.A28X.11 1 0.0000 1.000 1 0.00 0.00 0.00 0.00
#> TCGA.EL.A3CY.01 1 0.0000 1.000 1 0.00 0.00 0.00 0.00
#> TCGA.EL.A3CO.01 3 0.4060 0.708 0 0.00 0.64 0.36 0.00
#> TCGA.BJ.A3PR.11 2 0.2280 0.852 0 0.88 0.00 0.00 0.12
#> TCGA.EL.A3T6.11 3 0.0000 0.736 0 0.00 1.00 0.00 0.00
#> TCGA.EM.A3O9.01 4 0.4060 0.441 0 0.00 0.00 0.64 0.36
#> TCGA.BJ.A3PR.01 1 0.0000 1.000 1 0.00 0.00 0.00 0.00
#> TCGA.DJ.A13O.01 3 0.4060 0.708 0 0.00 0.64 0.36 0.00
cbind(get_classes(res, k = 6), get_membership(res, k = 6))
#> class entropy silhouette p1 p2 p3 p4 p5 p6
#> TCGA.EL.A3ZK.11 2 0.1480 0.904 0 0.94 0.00 0.02 0.04 0.00
#> TCGA.DJ.A3VL.01 3 0.0000 0.274 0 0.00 1.00 0.00 0.00 0.00
#> TCGA.DJ.A4V0.01 2 0.0547 0.909 0 0.98 0.00 0.00 0.02 0.00
#> TCGA.EL.A3ZP.11 2 0.1092 0.905 0 0.96 0.00 0.02 0.02 0.00
#> TCGA.BJ.A45E.01 1 0.0000 1.000 1 0.00 0.00 0.00 0.00 0.00
#> TCGA.DJ.A2Q9.01 1 0.0000 1.000 1 0.00 0.00 0.00 0.00 0.00
#> TCGA.EL.A3N3.11 2 0.2190 0.897 0 0.90 0.00 0.06 0.04 0.00
#> TCGA.BJ.A28W.11 5 0.0937 0.000 0 0.04 0.00 0.00 0.96 0.00
#> TCGA.E8.A2JQ.11 1 0.0000 1.000 1 0.00 0.00 0.00 0.00 0.00
#> TCGA.BJ.A28R.11 2 0.0547 0.909 0 0.98 0.00 0.00 0.02 0.00
#> TCGA.GE.A2C6.11 2 0.2941 0.732 0 0.78 0.00 0.00 0.22 0.00
#> TCGA.CE.A27D.01 6 0.0000 1.000 0 0.00 0.00 0.00 0.00 1.00
#> TCGA.EL.A3H1.11 6 0.0000 1.000 0 0.00 0.00 0.00 0.00 1.00
#> TCGA.BJ.A28W.01 1 0.0000 1.000 1 0.00 0.00 0.00 0.00 0.00
#> TCGA.BJ.A28T.01 2 0.2048 0.850 0 0.88 0.00 0.00 0.12 0.00
#> TCGA.BJ.A2N9.11 1 0.0000 1.000 1 0.00 0.00 0.00 0.00 0.00
#> TCGA.H2.A2K9.11 3 0.3828 0.771 0 0.00 0.56 0.00 0.00 0.44
#> TCGA.FY.A3TY.01 6 0.0000 1.000 0 0.00 0.00 0.00 0.00 1.00
#> TCGA.EL.A3T1.11 2 0.2190 0.897 0 0.90 0.00 0.06 0.04 0.00
#> TCGA.EM.A2CP.01 1 0.0000 1.000 1 0.00 0.00 0.00 0.00 0.00
#> TCGA.EM.A3AJ.01 2 0.1865 0.902 0 0.92 0.00 0.04 0.04 0.00
#> TCGA.EL.A3CW.01 2 0.0937 0.903 0 0.96 0.00 0.00 0.04 0.00
#> TCGA.ET.A3DQ.01 2 0.2190 0.897 0 0.90 0.00 0.06 0.04 0.00
#> TCGA.BJ.A2NA.11 3 0.3851 0.745 0 0.00 0.54 0.00 0.00 0.46
#> TCGA.BJ.A28X.11 1 0.0000 1.000 1 0.00 0.00 0.00 0.00 0.00
#> TCGA.EL.A3CY.01 1 0.0000 1.000 1 0.00 0.00 0.00 0.00 0.00
#> TCGA.EL.A3CO.01 3 0.3828 0.771 0 0.00 0.56 0.00 0.00 0.44
#> TCGA.BJ.A3PR.11 2 0.2190 0.897 0 0.90 0.00 0.06 0.04 0.00
#> TCGA.EL.A3T6.11 6 0.0000 1.000 0 0.00 0.00 0.00 0.00 1.00
#> TCGA.EM.A3O9.01 4 0.1556 0.000 0 0.00 0.08 0.92 0.00 0.00
#> TCGA.BJ.A3PR.01 1 0.0000 1.000 1 0.00 0.00 0.00 0.00 0.00
#> TCGA.DJ.A13O.01 3 0.3706 0.752 0 0.00 0.62 0.00 0.00 0.38
cbind(get_classes(res, k = 7), get_membership(res, k = 7))
#> class entropy silhouette p1 p2 p3 p4 p5 p6 p7
#> TCGA.EL.A3ZK.11 2 0.3496 -0.741 0.00 0.58 0.00 0.00 0.00 0.00 0.42
#> TCGA.DJ.A3VL.01 3 0.3517 0.188 0.00 0.00 0.70 0.02 0.00 0.00 0.28
#> TCGA.DJ.A4V0.01 2 0.2259 0.458 0.00 0.84 0.00 0.00 0.00 0.00 0.16
#> TCGA.EL.A3ZP.11 2 0.0000 0.691 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.BJ.A45E.01 1 0.0000 0.980 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.DJ.A2Q9.01 1 0.0000 0.980 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.EL.A3N3.11 7 0.3558 1.000 0.00 0.48 0.00 0.00 0.00 0.00 0.52
#> TCGA.BJ.A28W.11 5 0.0504 0.000 0.00 0.02 0.00 0.00 0.98 0.00 0.00
#> TCGA.E8.A2JQ.11 1 0.1006 0.975 0.96 0.00 0.00 0.00 0.02 0.00 0.02
#> TCGA.BJ.A28R.11 2 0.0863 0.680 0.00 0.96 0.00 0.00 0.00 0.00 0.04
#> TCGA.GE.A2C6.11 2 0.1664 0.662 0.00 0.92 0.00 0.00 0.06 0.00 0.02
#> TCGA.CE.A27D.01 6 0.0000 1.000 0.00 0.00 0.00 0.00 0.00 1.00 0.00
#> TCGA.EL.A3H1.11 6 0.0000 1.000 0.00 0.00 0.00 0.00 0.00 1.00 0.00
#> TCGA.BJ.A28W.01 1 0.0000 0.980 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.BJ.A28T.01 2 0.1166 0.677 0.00 0.94 0.00 0.00 0.06 0.00 0.00
#> TCGA.BJ.A2N9.11 1 0.1006 0.975 0.96 0.00 0.00 0.00 0.02 0.00 0.02
#> TCGA.H2.A2K9.11 3 0.3139 0.802 0.00 0.00 0.70 0.00 0.00 0.30 0.00
#> TCGA.FY.A3TY.01 6 0.0000 1.000 0.00 0.00 0.00 0.00 0.00 1.00 0.00
#> TCGA.EL.A3T1.11 7 0.3558 1.000 0.00 0.48 0.00 0.00 0.00 0.00 0.52
#> TCGA.EM.A2CP.01 1 0.1006 0.975 0.96 0.00 0.00 0.00 0.02 0.00 0.02
#> TCGA.EM.A3AJ.01 2 0.3307 0.446 0.00 0.74 0.02 0.00 0.00 0.00 0.24
#> TCGA.EL.A3CW.01 2 0.1166 0.663 0.00 0.94 0.00 0.00 0.00 0.00 0.06
#> TCGA.ET.A3DQ.01 7 0.3558 1.000 0.00 0.48 0.00 0.00 0.00 0.00 0.52
#> TCGA.BJ.A2NA.11 3 0.3139 0.802 0.00 0.00 0.70 0.00 0.00 0.30 0.00
#> TCGA.BJ.A28X.11 1 0.1006 0.975 0.96 0.00 0.00 0.00 0.02 0.00 0.02
#> TCGA.EL.A3CY.01 1 0.0000 0.980 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.EL.A3CO.01 3 0.3047 0.808 0.00 0.00 0.72 0.00 0.00 0.28 0.00
#> TCGA.BJ.A3PR.11 7 0.3558 1.000 0.00 0.48 0.00 0.00 0.00 0.00 0.52
#> TCGA.EL.A3T6.11 6 0.0000 1.000 0.00 0.00 0.00 0.00 0.00 1.00 0.00
#> TCGA.EM.A3O9.01 4 0.0000 0.000 0.00 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.BJ.A3PR.01 1 0.0000 0.980 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.DJ.A13O.01 3 0.2832 0.795 0.00 0.00 0.76 0.00 0.00 0.24 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.EL.A3ZK.11 7 0.3318 0.667 0.00 0.46 0.00 0.00 0.00 0.00 0.54 0.00
#> TCGA.DJ.A3VL.01 8 0.2404 0.000 0.00 0.00 0.14 0.02 0.00 0.00 0.00 0.84
#> TCGA.DJ.A4V0.01 2 0.2756 0.332 0.00 0.74 0.00 0.00 0.00 0.00 0.26 0.00
#> TCGA.EL.A3ZP.11 2 0.1275 0.781 0.00 0.94 0.00 0.00 0.02 0.00 0.04 0.00
#> TCGA.BJ.A45E.01 1 0.0000 0.940 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.DJ.A2Q9.01 1 0.0000 0.940 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.EL.A3N3.11 7 0.2852 0.876 0.00 0.28 0.00 0.00 0.00 0.00 0.72 0.00
#> TCGA.BJ.A28W.11 5 0.0808 0.000 0.00 0.04 0.00 0.00 0.96 0.00 0.00 0.00
#> TCGA.E8.A2JQ.11 1 0.2165 0.924 0.88 0.00 0.00 0.00 0.00 0.00 0.06 0.06
#> TCGA.BJ.A28R.11 2 0.0808 0.777 0.00 0.96 0.00 0.00 0.00 0.00 0.04 0.00
#> TCGA.GE.A2C6.11 2 0.1557 0.748 0.00 0.92 0.00 0.00 0.06 0.00 0.02 0.00
#> TCGA.CE.A27D.01 6 0.1341 1.000 0.00 0.00 0.08 0.00 0.00 0.92 0.00 0.00
#> TCGA.EL.A3H1.11 6 0.1341 1.000 0.00 0.00 0.08 0.00 0.00 0.92 0.00 0.00
#> TCGA.BJ.A28W.01 1 0.0000 0.940 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.BJ.A28T.01 2 0.0000 0.792 0.00 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.BJ.A2N9.11 1 0.2165 0.924 0.88 0.00 0.00 0.00 0.00 0.00 0.06 0.06
#> TCGA.H2.A2K9.11 3 0.0000 1.000 0.00 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.FY.A3TY.01 6 0.1341 1.000 0.00 0.00 0.08 0.00 0.00 0.92 0.00 0.00
#> TCGA.EL.A3T1.11 7 0.2852 0.876 0.00 0.28 0.00 0.00 0.00 0.00 0.72 0.00
#> TCGA.EM.A2CP.01 1 0.2165 0.924 0.88 0.00 0.00 0.00 0.00 0.00 0.06 0.06
#> TCGA.EM.A3AJ.01 2 0.5569 0.420 0.00 0.58 0.00 0.00 0.04 0.08 0.24 0.06
#> TCGA.EL.A3CW.01 2 0.0471 0.788 0.00 0.98 0.00 0.00 0.00 0.00 0.02 0.00
#> TCGA.ET.A3DQ.01 7 0.3504 0.835 0.00 0.26 0.00 0.00 0.00 0.00 0.70 0.04
#> TCGA.BJ.A2NA.11 3 0.0000 1.000 0.00 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.BJ.A28X.11 1 0.2165 0.924 0.88 0.00 0.00 0.00 0.00 0.00 0.06 0.06
#> TCGA.EL.A3CY.01 1 0.0000 0.940 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.EL.A3CO.01 3 0.0000 1.000 0.00 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.BJ.A3PR.11 7 0.3142 0.831 0.00 0.36 0.00 0.00 0.00 0.00 0.64 0.00
#> TCGA.EL.A3T6.11 6 0.1341 1.000 0.00 0.00 0.08 0.00 0.00 0.92 0.00 0.00
#> TCGA.EM.A3O9.01 4 0.0000 0.000 0.00 0.00 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.BJ.A3PR.01 1 0.0000 0.940 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.DJ.A13O.01 3 0.0000 1.000 0.00 0.00 1.00 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: Node023. Child nodes: Node02321-leaf , Node02322-leaf , Node02411-leaf , Node02412-leaf , Node02413-leaf , Node02414-leaf , Node03111-leaf , Node03112-leaf , Node03113-leaf .
The object with results only for a single top-value method and a single partitioning method can be extracted as:
res = res_rh["0232"]
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 13 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 0.2828 0.718 0.718
#> 3 3 0.667 0.916 0.938 1.0711 0.641 0.500
#> 4 4 0.513 0.640 0.848 0.1783 0.962 0.893
#> 5 5 0.590 0.505 0.820 0.1543 0.821 0.481
#> 6 6 0.667 0.423 0.760 0.0550 0.859 0.389
#> 7 7 0.692 0.310 0.726 0.0473 0.897 0.429
#> 8 8 0.769 0.305 0.771 0.0361 0.910 0.417
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.EL.A3ZK.11 1 0 1 1 0
#> TCGA.DJ.A4V0.01 1 0 1 1 0
#> TCGA.EL.A3ZP.11 2 0 1 0 1
#> TCGA.EL.A3N3.11 1 0 1 1 0
#> TCGA.BJ.A28W.11 1 0 1 1 0
#> TCGA.BJ.A28R.11 1 0 1 1 0
#> TCGA.GE.A2C6.11 1 0 1 1 0
#> TCGA.BJ.A28T.01 1 0 1 1 0
#> TCGA.EL.A3T1.11 1 0 1 1 0
#> TCGA.EM.A3AJ.01 2 0 1 0 1
#> TCGA.EL.A3CW.01 1 0 1 1 0
#> TCGA.ET.A3DQ.01 1 0 1 1 0
#> TCGA.BJ.A3PR.11 1 0 1 1 0
cbind(get_classes(res, k = 3), get_membership(res, k = 3))
#> class entropy silhouette p1 p2 p3
#> TCGA.EL.A3ZK.11 1 0.000 1.000 1.00 0 0.00
#> TCGA.DJ.A4V0.01 3 0.480 0.822 0.22 0 0.78
#> TCGA.EL.A3ZP.11 2 0.000 1.000 0.00 1 0.00
#> TCGA.EL.A3N3.11 1 0.000 1.000 1.00 0 0.00
#> TCGA.BJ.A28W.11 3 0.000 0.613 0.00 0 1.00
#> TCGA.BJ.A28R.11 1 0.000 1.000 1.00 0 0.00
#> TCGA.GE.A2C6.11 1 0.000 1.000 1.00 0 0.00
#> TCGA.BJ.A28T.01 1 0.000 1.000 1.00 0 0.00
#> TCGA.EL.A3T1.11 1 0.000 1.000 1.00 0 0.00
#> TCGA.EM.A3AJ.01 2 0.000 1.000 0.00 1 0.00
#> TCGA.EL.A3CW.01 1 0.000 1.000 1.00 0 0.00
#> TCGA.ET.A3DQ.01 3 0.480 0.822 0.22 0 0.78
#> TCGA.BJ.A3PR.11 3 0.595 0.650 0.36 0 0.64
cbind(get_classes(res, k = 4), get_membership(res, k = 4))
#> class entropy silhouette p1 p2 p3 p4
#> TCGA.EL.A3ZK.11 1 0.320 0.7891 0.88 0.00 0.04 0.08
#> TCGA.DJ.A4V0.01 3 0.121 0.5184 0.04 0.00 0.96 0.00
#> TCGA.EL.A3ZP.11 2 0.201 0.9345 0.00 0.92 0.00 0.08
#> TCGA.EL.A3N3.11 1 0.191 0.8040 0.94 0.00 0.04 0.02
#> TCGA.BJ.A28W.11 4 0.361 0.0000 0.00 0.00 0.20 0.80
#> TCGA.BJ.A28R.11 1 0.385 0.7624 0.82 0.00 0.16 0.02
#> TCGA.GE.A2C6.11 1 0.265 0.7840 0.88 0.00 0.12 0.00
#> TCGA.BJ.A28T.01 1 0.141 0.8107 0.96 0.00 0.02 0.02
#> TCGA.EL.A3T1.11 1 0.461 0.7417 0.80 0.00 0.10 0.10
#> TCGA.EM.A3AJ.01 2 0.000 0.9345 0.00 1.00 0.00 0.00
#> TCGA.EL.A3CW.01 1 0.549 0.6615 0.70 0.00 0.24 0.06
#> TCGA.ET.A3DQ.01 3 0.164 0.5136 0.06 0.00 0.94 0.00
#> TCGA.BJ.A3PR.11 3 0.760 0.0613 0.38 0.00 0.42 0.20
cbind(get_classes(res, k = 5), get_membership(res, k = 5))
#> class entropy silhouette p1 p2 p3 p4 p5
#> TCGA.EL.A3ZK.11 1 0.4126 0.0347 0.62 0.00 0.00 0.00 0.38
#> TCGA.DJ.A4V0.01 3 0.1043 0.9770 0.04 0.00 0.96 0.00 0.00
#> TCGA.EL.A3ZP.11 2 0.0000 0.9329 0.00 1.00 0.00 0.00 0.00
#> TCGA.EL.A3N3.11 1 0.4060 0.2749 0.64 0.00 0.00 0.00 0.36
#> TCGA.BJ.A28W.11 4 0.0000 0.0000 0.00 0.00 0.00 1.00 0.00
#> TCGA.BJ.A28R.11 1 0.3421 0.5740 0.84 0.00 0.08 0.00 0.08
#> TCGA.GE.A2C6.11 1 0.3110 0.6037 0.86 0.00 0.06 0.00 0.08
#> TCGA.BJ.A28T.01 1 0.0609 0.6016 0.98 0.00 0.00 0.00 0.02
#> TCGA.EL.A3T1.11 5 0.5048 0.1675 0.38 0.00 0.04 0.00 0.58
#> TCGA.EM.A3AJ.01 2 0.2012 0.9329 0.00 0.92 0.02 0.00 0.06
#> TCGA.EL.A3CW.01 5 0.5864 0.0870 0.32 0.00 0.12 0.00 0.56
#> TCGA.ET.A3DQ.01 3 0.1648 0.9770 0.04 0.00 0.94 0.00 0.02
#> TCGA.BJ.A3PR.11 5 0.2616 0.4078 0.00 0.00 0.10 0.02 0.88
cbind(get_classes(res, k = 6), get_membership(res, k = 6))
#> class entropy silhouette p1 p2 p3 p4 p5 p6
#> TCGA.EL.A3ZK.11 6 0.558 0.111 0.40 0.00 0.00 0.00 0.14 0.46
#> TCGA.DJ.A4V0.01 3 0.425 0.862 0.06 0.00 0.78 0.00 0.06 0.10
#> TCGA.EL.A3ZP.11 2 0.342 0.862 0.00 0.84 0.06 0.00 0.06 0.04
#> TCGA.EL.A3N3.11 6 0.308 0.284 0.24 0.00 0.00 0.00 0.00 0.76
#> TCGA.BJ.A28W.11 4 0.000 0.000 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.BJ.A28R.11 1 0.000 0.479 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.GE.A2C6.11 1 0.181 0.464 0.90 0.00 0.00 0.00 0.00 0.10
#> TCGA.BJ.A28T.01 1 0.308 0.217 0.76 0.00 0.00 0.00 0.00 0.24
#> TCGA.EL.A3T1.11 5 0.407 0.374 0.26 0.00 0.00 0.00 0.70 0.04
#> TCGA.EM.A3AJ.01 2 0.000 0.862 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.EL.A3CW.01 1 0.602 -0.262 0.46 0.00 0.02 0.00 0.14 0.38
#> TCGA.ET.A3DQ.01 3 0.127 0.862 0.06 0.00 0.94 0.00 0.00 0.00
#> TCGA.BJ.A3PR.11 5 0.518 0.380 0.04 0.00 0.02 0.02 0.64 0.28
cbind(get_classes(res, k = 7), get_membership(res, k = 7))
#> class entropy silhouette p1 p2 p3 p4 p5 p6 p7
#> TCGA.EL.A3ZK.11 1 0.536 -0.1184 0.60 0.0 0.04 0 0.14 0.22 0.00
#> TCGA.DJ.A4V0.01 7 0.393 0.6915 0.00 0.0 0.30 0 0.00 0.04 0.66
#> TCGA.EL.A3ZP.11 2 0.000 0.7311 0.00 1.0 0.00 0 0.00 0.00 0.00
#> TCGA.EL.A3N3.11 6 0.595 0.0618 0.36 0.0 0.10 0 0.08 0.46 0.00
#> TCGA.BJ.A28W.11 4 0.000 0.0000 0.00 0.0 0.00 1 0.00 0.00 0.00
#> TCGA.BJ.A28R.11 1 0.382 0.3485 0.62 0.0 0.00 0 0.00 0.36 0.02
#> TCGA.GE.A2C6.11 1 0.399 0.2415 0.50 0.0 0.00 0 0.00 0.48 0.02
#> TCGA.BJ.A28T.01 1 0.000 0.2885 1.00 0.0 0.00 0 0.00 0.00 0.00
#> TCGA.EL.A3T1.11 5 0.681 0.2520 0.20 0.0 0.30 0 0.36 0.14 0.00
#> TCGA.EM.A3AJ.01 2 0.314 0.7311 0.00 0.7 0.30 0 0.00 0.00 0.00
#> TCGA.EL.A3CW.01 6 0.482 -0.0996 0.12 0.0 0.00 0 0.16 0.68 0.04
#> TCGA.ET.A3DQ.01 7 0.000 0.6913 0.00 0.0 0.00 0 0.00 0.00 1.00
#> TCGA.BJ.A3PR.11 5 0.143 0.2044 0.00 0.0 0.00 0 0.92 0.08 0.00
cbind(get_classes(res, k = 8), get_membership(res, k = 8))
#> class entropy silhouette p1 p2 p3 p4 p5 p6 p7 p8
#> TCGA.EL.A3ZK.11 6 0.7351 0.264 0.16 0.00 0.26 0 0.20 0.30 0.00 0.08
#> TCGA.DJ.A4V0.01 7 0.0471 0.000 0.02 0.00 0.00 0 0.00 0.00 0.98 0.00
#> TCGA.EL.A3ZP.11 2 0.0000 0.672 0.00 1.00 0.00 0 0.00 0.00 0.00 0.00
#> TCGA.EL.A3N3.11 6 0.1275 0.230 0.04 0.00 0.00 0 0.00 0.94 0.00 0.02
#> TCGA.BJ.A28W.11 4 0.0000 0.000 0.00 0.00 0.00 1 0.00 0.00 0.00 0.00
#> TCGA.BJ.A28R.11 1 0.0808 0.700 0.96 0.00 0.00 0 0.04 0.00 0.00 0.00
#> TCGA.GE.A2C6.11 1 0.1887 0.637 0.90 0.00 0.06 0 0.00 0.04 0.00 0.00
#> TCGA.BJ.A28T.01 1 0.4472 0.498 0.68 0.00 0.10 0 0.04 0.18 0.00 0.00
#> TCGA.EL.A3T1.11 5 0.1563 0.000 0.00 0.00 0.00 0 0.90 0.00 0.00 0.10
#> TCGA.EM.A3AJ.01 2 0.5612 0.672 0.00 0.64 0.14 0 0.10 0.06 0.02 0.04
#> TCGA.EL.A3CW.01 6 0.7177 0.287 0.28 0.00 0.24 0 0.08 0.30 0.00 0.10
#> TCGA.ET.A3DQ.01 3 0.3272 0.000 0.00 0.00 0.58 0 0.00 0.00 0.42 0.00
#> TCGA.BJ.A3PR.11 8 0.0808 0.000 0.00 0.00 0.00 0 0.00 0.04 0.00 0.96
Heatmaps for the consensus matrix. It visualizes the probability of two samples to be in a same group.
consensus_heatmap(res, k = 2)
consensus_heatmap(res, k = 3)
consensus_heatmap(res, k = 4)
consensus_heatmap(res, k = 5)
consensus_heatmap(res, k = 6)
consensus_heatmap(res, k = 7)
consensus_heatmap(res, k = 8)
Heatmaps for the membership of samples in all partitions to see how consistent they are:
membership_heatmap(res, k = 2)
membership_heatmap(res, k = 3)
membership_heatmap(res, k = 4)
membership_heatmap(res, k = 5)
membership_heatmap(res, k = 6)
membership_heatmap(res, k = 7)
membership_heatmap(res, k = 8)
As soon as the classes for columns are determined, the signatures that are significantly different between subgroups can be looked for. Following are the heatmaps for signatures.
get_signatures(res, k = 2)
get_signatures(res, k = 3)
get_signatures(res, k = 4)
get_signatures(res, k = 5)
get_signatures(res, k = 6)
get_signatures(res, k = 7)
get_signatures(res, k = 8)
Compare the overlap of signatures from different k:
compare_signatures(res)
get_signature() returns a data frame invisibly. To get the list of signatures, the function
call should be assigned to a variable explicitly. In following code, if plot argument is set
to FALSE, no heatmap is plotted while only the differential analysis is performed.
# code only for demonstration
tb = get_signature(res, k = ..., plot = FALSE)
An example of the output of tb is:
#> which_row fdr mean_1 mean_2 scaled_mean_1 scaled_mean_2 km
#> 1 38 0.042760348 8.373488 9.131774 -0.5533452 0.5164555 1
#> 2 40 0.018707592 7.106213 8.469186 -0.6173731 0.5762149 1
#> 3 55 0.019134737 10.221463 11.207825 -0.6159697 0.5749050 1
#> 4 59 0.006059896 5.921854 7.869574 -0.6899429 0.6439467 1
#> 5 60 0.018055526 8.928898 10.211722 -0.6204761 0.5791110 1
#> 6 98 0.009384629 15.714769 14.887706 0.6635654 -0.6193277 2
...
The columns in tb are:
which_row: row indices corresponding to the input matrix.fdr: FDR for the differential test. mean_x: The mean value in group x.scaled_mean_x: The mean value in group x after rows are scaled.km: Row groups if k-means clustering is applied to rows (which is done by automatically selecting number of clusters).If there are too many signatures, top_signatures = ... can be set to only show the
signatures with the highest FDRs:
# code only for demonstration
# e.g. to show the top 500 most significant rows
tb = get_signature(res, k = ..., top_signatures = 500)
If the signatures are defined as these which are uniquely high in current group, diff_method argument
can be set to "uniquely_high_in_one_group":
# code only for demonstration
tb = get_signature(res, k = ..., diff_method = "uniquely_high_in_one_group")
UMAP plot which shows how samples are separated.
dimension_reduction(res, k = 2, method = "UMAP")
dimension_reduction(res, k = 3, method = "UMAP")
dimension_reduction(res, k = 4, method = "UMAP")
dimension_reduction(res, k = 5, method = "UMAP")
dimension_reduction(res, k = 6, method = "UMAP")
dimension_reduction(res, k = 7, method = "UMAP")
dimension_reduction(res, k = 8, method = "UMAP")
Following heatmap shows how subgroups are split when increasing k:
collect_classes(res)
If matrix rows can be associated to genes, consider to use functional_enrichment(res,
...) to perform function enrichment for the signature genes. See this vignette for more detailed explanations.
Parent node: Node02. Child nodes: Node0111-leaf , Node0112-leaf , Node0113-leaf , Node0114-leaf , Node0131-leaf , Node0132-leaf , Node0133-leaf , Node0141-leaf , Node0142-leaf , Node0143-leaf , Node0211-leaf , Node0212-leaf , Node0221-leaf , Node0222-leaf , Node0223-leaf , Node0224-leaf , Node0231-leaf , Node0232 , Node0233-leaf , Node0234-leaf , Node0241 , Node0242-leaf , Node0243-leaf , Node0244-leaf , Node0251-leaf , Node0252-leaf , Node0311 , Node0312-leaf , Node0313-leaf , Node0331-leaf , Node0332-leaf , Node0333-leaf .
The object with results only for a single top-value method and a single partitioning method can be extracted as:
res = res_rh["024"]
A summary of res and all the functions that can be applied to it:
res
#> A 'ConsensusPartition' object with k = 2, 3, 4, 5, 6, 7, 8.
#> On a matrix with 30000 rows and 41 columns.
#> Top rows (1000) are extracted by 'ATC' method.
#> Subgroups are detected by '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 0.4761 0.524 0.524
#> 3 3 0.818 0.980 0.972 0.1525 0.934 0.874
#> 4 4 1.000 0.988 0.994 0.2281 0.872 0.721
#> 5 5 0.883 0.922 0.949 0.0513 0.983 0.948
#> 6 6 0.839 0.904 0.914 0.0724 0.890 0.650
#> 7 7 0.891 0.866 0.942 0.0321 0.994 0.970
#> 8 8 0.936 0.809 0.940 0.0191 0.990 0.953
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.ET.A2N3.01 1 0 1 1 0
#> TCGA.DJ.A3VM.01 1 0 1 1 0
#> TCGA.IM.A41Z.01 1 0 1 1 0
#> TCGA.EL.A4KI.01 2 0 1 0 1
#> TCGA.BJ.A45K.01 2 0 1 0 1
#> TCGA.BJ.A45C.01 2 0 1 0 1
#> TCGA.FY.A4B0.01 2 0 1 0 1
#> TCGA.EL.A4K6.01 2 0 1 0 1
#> TCGA.EM.A4FK.01 1 0 1 1 0
#> TCGA.DJ.A4UR.01 1 0 1 1 0
#> TCGA.DE.A2OL.01 1 0 1 1 0
#> TCGA.EM.A22J.01 1 0 1 1 0
#> TCGA.EM.A3FN.01 1 0 1 1 0
#> TCGA.ET.A2MY.11 1 0 1 1 0
#> TCGA.EM.A2CL.01 2 0 1 0 1
#> TCGA.H2.A2K9.01 2 0 1 0 1
#> TCGA.EM.A22Q.01 2 0 1 0 1
#> TCGA.EL.A3H1.01 1 0 1 1 0
#> TCGA.J8.A3O0.01 2 0 1 0 1
#> TCGA.FE.A239.01 2 0 1 0 1
#> TCGA.EM.A2CM.01 1 0 1 1 0
#> TCGA.BJ.A3F0.01 1 0 1 1 0
#> TCGA.ET.A3DV.01 1 0 1 1 0
#> TCGA.EM.A3AL.01 1 0 1 1 0
#> TCGA.EM.A3ST.01 1 0 1 1 0
#> TCGA.EL.A3GO.01 1 0 1 1 0
#> TCGA.FK.A3SD.01 1 0 1 1 0
#> TCGA.DJ.A2PP.01 2 0 1 0 1
#> TCGA.FY.A3W9.01 1 0 1 1 0
#> TCGA.DJ.A1QL.01 2 0 1 0 1
#> TCGA.FY.A2QD.01 1 0 1 1 0
#> TCGA.BJ.A28V.01 1 0 1 1 0
#> TCGA.EM.A1YB.01 1 0 1 1 0
#> TCGA.EM.A3FR.01 1 0 1 1 0
#> TCGA.DJ.A13W.01 1 0 1 1 0
#> TCGA.BJ.A0ZA.01 1 0 1 1 0
#> TCGA.BJ.A0Z0.01 2 0 1 0 1
#> TCGA.EM.A3OA.01 1 0 1 1 0
#> TCGA.EM.A2CN.01 2 0 1 0 1
#> TCGA.BJ.A0Z2.01 2 0 1 0 1
#> TCGA.FY.A3I5.01 1 0 1 1 0
cbind(get_classes(res, k = 3), get_membership(res, k = 3))
#> class entropy silhouette p1 p2 p3
#> TCGA.ET.A2N3.01 1 0.0000 0.981 1.00 0.0 0.00
#> TCGA.DJ.A3VM.01 1 0.2959 0.923 0.90 0.0 0.10
#> TCGA.IM.A41Z.01 1 0.0000 0.981 1.00 0.0 0.00
#> TCGA.EL.A4KI.01 3 0.2959 1.000 0.00 0.1 0.90
#> TCGA.BJ.A45K.01 2 0.0000 1.000 0.00 1.0 0.00
#> TCGA.BJ.A45C.01 2 0.0000 1.000 0.00 1.0 0.00
#> TCGA.FY.A4B0.01 2 0.0000 1.000 0.00 1.0 0.00
#> TCGA.EL.A4K6.01 3 0.2959 1.000 0.00 0.1 0.90
#> TCGA.EM.A4FK.01 1 0.0000 0.981 1.00 0.0 0.00
#> TCGA.DJ.A4UR.01 1 0.2959 0.923 0.90 0.0 0.10
#> TCGA.DE.A2OL.01 1 0.0000 0.981 1.00 0.0 0.00
#> TCGA.EM.A22J.01 1 0.0000 0.981 1.00 0.0 0.00
#> TCGA.EM.A3FN.01 1 0.0000 0.981 1.00 0.0 0.00
#> TCGA.ET.A2MY.11 1 0.0000 0.981 1.00 0.0 0.00
#> TCGA.EM.A2CL.01 2 0.0000 1.000 0.00 1.0 0.00
#> TCGA.H2.A2K9.01 3 0.2959 1.000 0.00 0.1 0.90
#> TCGA.EM.A22Q.01 2 0.0000 1.000 0.00 1.0 0.00
#> TCGA.EL.A3H1.01 1 0.0000 0.981 1.00 0.0 0.00
#> TCGA.J8.A3O0.01 3 0.2959 1.000 0.00 0.1 0.90
#> TCGA.FE.A239.01 2 0.0000 1.000 0.00 1.0 0.00
#> TCGA.EM.A2CM.01 1 0.2959 0.923 0.90 0.0 0.10
#> TCGA.BJ.A3F0.01 1 0.0000 0.981 1.00 0.0 0.00
#> TCGA.ET.A3DV.01 1 0.0000 0.981 1.00 0.0 0.00
#> TCGA.EM.A3AL.01 1 0.0000 0.981 1.00 0.0 0.00
#> TCGA.EM.A3ST.01 1 0.2959 0.923 0.90 0.0 0.10
#> TCGA.EL.A3GO.01 1 0.0892 0.971 0.98 0.0 0.02
#> TCGA.FK.A3SD.01 1 0.0000 0.981 1.00 0.0 0.00
#> TCGA.DJ.A2PP.01 2 0.0000 1.000 0.00 1.0 0.00
#> TCGA.FY.A3W9.01 1 0.2959 0.923 0.90 0.0 0.10
#> TCGA.DJ.A1QL.01 2 0.0000 1.000 0.00 1.0 0.00
#> TCGA.FY.A2QD.01 1 0.0000 0.981 1.00 0.0 0.00
#> TCGA.BJ.A28V.01 1 0.0000 0.981 1.00 0.0 0.00
#> TCGA.EM.A1YB.01 1 0.0000 0.981 1.00 0.0 0.00
#> TCGA.EM.A3FR.01 1 0.0000 0.981 1.00 0.0 0.00
#> TCGA.DJ.A13W.01 1 0.0000 0.981 1.00 0.0 0.00
#> TCGA.BJ.A0ZA.01 1 0.0892 0.971 0.98 0.0 0.02
#> TCGA.BJ.A0Z0.01 2 0.0000 1.000 0.00 1.0 0.00
#> TCGA.EM.A3OA.01 1 0.0000 0.981 1.00 0.0 0.00
#> TCGA.EM.A2CN.01 3 0.2959 1.000 0.00 0.1 0.90
#> TCGA.BJ.A0Z2.01 3 0.2959 1.000 0.00 0.1 0.90
#> TCGA.FY.A3I5.01 1 0.0000 0.981 1.00 0.0 0.00
cbind(get_classes(res, k = 4), get_membership(res, k = 4))
#> class entropy silhouette p1 p2 p3 p4
#> TCGA.ET.A2N3.01 1 0.000 0.988 1.00 0 0 0.00
#> TCGA.DJ.A3VM.01 4 0.000 1.000 0.00 0 0 1.00
#> TCGA.IM.A41Z.01 1 0.000 0.988 1.00 0 0 0.00
#> TCGA.EL.A4KI.01 3 0.000 1.000 0.00 0 1 0.00
#> TCGA.BJ.A45K.01 2 0.000 1.000 0.00 1 0 0.00
#> TCGA.BJ.A45C.01 2 0.000 1.000 0.00 1 0 0.00
#> TCGA.FY.A4B0.01 2 0.000 1.000 0.00 1 0 0.00
#> TCGA.EL.A4K6.01 3 0.000 1.000 0.00 0 1 0.00
#> TCGA.EM.A4FK.01 1 0.000 0.988 1.00 0 0 0.00
#> TCGA.DJ.A4UR.01 4 0.000 1.000 0.00 0 0 1.00
#> TCGA.DE.A2OL.01 1 0.000 0.988 1.00 0 0 0.00
#> TCGA.EM.A22J.01 1 0.000 0.988 1.00 0 0 0.00
#> TCGA.EM.A3FN.01 1 0.000 0.988 1.00 0 0 0.00
#> TCGA.ET.A2MY.11 1 0.000 0.988 1.00 0 0 0.00
#> TCGA.EM.A2CL.01 2 0.000 1.000 0.00 1 0 0.00
#> TCGA.H2.A2K9.01 3 0.000 1.000 0.00 0 1 0.00
#> TCGA.EM.A22Q.01 2 0.000 1.000 0.00 1 0 0.00
#> TCGA.EL.A3H1.01 1 0.000 0.988 1.00 0 0 0.00
#> TCGA.J8.A3O0.01 3 0.000 1.000 0.00 0 1 0.00
#> TCGA.FE.A239.01 2 0.000 1.000 0.00 1 0 0.00
#> TCGA.EM.A2CM.01 4 0.000 1.000 0.00 0 0 1.00
#> TCGA.BJ.A3F0.01 1 0.000 0.988 1.00 0 0 0.00
#> TCGA.ET.A3DV.01 1 0.000 0.988 1.00 0 0 0.00
#> TCGA.EM.A3AL.01 1 0.000 0.988 1.00 0 0 0.00
#> TCGA.EM.A3ST.01 4 0.000 1.000 0.00 0 0 1.00
#> TCGA.EL.A3GO.01 1 0.265 0.870 0.88 0 0 0.12
#> TCGA.FK.A3SD.01 1 0.000 0.988 1.00 0 0 0.00
#> TCGA.DJ.A2PP.01 2 0.000 1.000 0.00 1 0 0.00
#> TCGA.FY.A3W9.01 4 0.000 1.000 0.00 0 0 1.00
#> TCGA.DJ.A1QL.01 2 0.000 1.000 0.00 1 0 0.00
#> TCGA.FY.A2QD.01 1 0.000 0.988 1.00 0 0 0.00
#> TCGA.BJ.A28V.01 1 0.000 0.988 1.00 0 0 0.00
#> TCGA.EM.A1YB.01 1 0.000 0.988 1.00 0 0 0.00
#> TCGA.EM.A3FR.01 1 0.000 0.988 1.00 0 0 0.00
#> TCGA.DJ.A13W.01 1 0.000 0.988 1.00 0 0 0.00
#> TCGA.BJ.A0ZA.01 1 0.265 0.870 0.88 0 0 0.12
#> TCGA.BJ.A0Z0.01 2 0.000 1.000 0.00 1 0 0.00
#> TCGA.EM.A3OA.01 1 0.000 0.988 1.00 0 0 0.00
#> TCGA.EM.A2CN.01 3 0.000 1.000 0.00 0 1 0.00
#> TCGA.BJ.A0Z2.01 3 0.000 1.000 0.00 0 1 0.00
#> TCGA.FY.A3I5.01 1 0.000 0.988 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.ET.A2N3.01 1 0.000 0.933 1.00 0.00 0.00 0.00 0.00
#> TCGA.DJ.A3VM.01 4 0.000 1.000 0.00 0.00 0.00 1.00 0.00
#> TCGA.IM.A41Z.01 1 0.273 0.846 0.84 0.00 0.00 0.00 0.16
#> TCGA.EL.A4KI.01 3 0.000 0.950 0.00 0.00 1.00 0.00 0.00
#> TCGA.BJ.A45K.01 2 0.000 1.000 0.00 1.00 0.00 0.00 0.00
#> TCGA.BJ.A45C.01 2 0.000 1.000 0.00 1.00 0.00 0.00 0.00
#> TCGA.FY.A4B0.01 2 0.000 1.000 0.00 1.00 0.00 0.00 0.00
#> TCGA.EL.A4K6.01 3 0.000 0.950 0.00 0.00 1.00 0.00 0.00
#> TCGA.EM.A4FK.01 1 0.000 0.933 1.00 0.00 0.00 0.00 0.00
#> TCGA.DJ.A4UR.01 4 0.000 1.000 0.00 0.00 0.00 1.00 0.00
#> TCGA.DE.A2OL.01 1 0.000 0.933 1.00 0.00 0.00 0.00 0.00
#> TCGA.EM.A22J.01 1 0.273 0.846 0.84 0.00 0.00 0.00 0.16
#> TCGA.EM.A3FN.01 1 0.000 0.933 1.00 0.00 0.00 0.00 0.00
#> TCGA.ET.A2MY.11 1 0.000 0.933 1.00 0.00 0.00 0.00 0.00
#> TCGA.EM.A2CL.01 2 0.000 1.000 0.00 1.00 0.00 0.00 0.00
#> TCGA.H2.A2K9.01 3 0.228 0.892 0.00 0.00 0.88 0.00 0.12
#> TCGA.EM.A22Q.01 5 0.380 0.801 0.00 0.30 0.00 0.00 0.70
#> TCGA.EL.A3H1.01 1 0.000 0.933 1.00 0.00 0.00 0.00 0.00
#> TCGA.J8.A3O0.01 3 0.228 0.892 0.00 0.00 0.88 0.00 0.12
#> TCGA.FE.A239.01 2 0.000 1.000 0.00 1.00 0.00 0.00 0.00
#> TCGA.EM.A2CM.01 4 0.000 1.000 0.00 0.00 0.00 1.00 0.00
#> TCGA.BJ.A3F0.01 1 0.273 0.846 0.84 0.00 0.00 0.00 0.16
#> TCGA.ET.A3DV.01 1 0.000 0.933 1.00 0.00 0.00 0.00 0.00
#> TCGA.EM.A3AL.01 1 0.000 0.933 1.00 0.00 0.00 0.00 0.00
#> TCGA.EM.A3ST.01 4 0.000 1.000 0.00 0.00 0.00 1.00 0.00
#> TCGA.EL.A3GO.01 1 0.544 0.648 0.66 0.00 0.00 0.18 0.16
#> TCGA.FK.A3SD.01 1 0.000 0.933 1.00 0.00 0.00 0.00 0.00
#> TCGA.DJ.A2PP.01 2 0.000 1.000 0.00 1.00 0.00 0.00 0.00
#> TCGA.FY.A3W9.01 4 0.000 1.000 0.00 0.00 0.00 1.00 0.00
#> TCGA.DJ.A1QL.01 2 0.000 1.000 0.00 1.00 0.00 0.00 0.00
#> TCGA.FY.A2QD.01 1 0.000 0.933 1.00 0.00 0.00 0.00 0.00
#> TCGA.BJ.A28V.01 1 0.000 0.933 1.00 0.00 0.00 0.00 0.00
#> TCGA.EM.A1YB.01 1 0.273 0.846 0.84 0.00 0.00 0.00 0.16
#> TCGA.EM.A3FR.01 1 0.000 0.933 1.00 0.00 0.00 0.00 0.00
#> TCGA.DJ.A13W.01 1 0.000 0.933 1.00 0.00 0.00 0.00 0.00
#> TCGA.BJ.A0ZA.01 1 0.585 0.549 0.60 0.00 0.00 0.24 0.16
#> TCGA.BJ.A0Z0.01 5 0.273 0.828 0.00 0.16 0.00 0.00 0.84
#> TCGA.EM.A3OA.01 1 0.000 0.933 1.00 0.00 0.00 0.00 0.00
#> TCGA.EM.A2CN.01 3 0.000 0.950 0.00 0.00 1.00 0.00 0.00
#> TCGA.BJ.A0Z2.01 3 0.000 0.950 0.00 0.00 1.00 0.00 0.00
#> TCGA.FY.A3I5.01 1 0.000 0.933 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.ET.A2N3.01 1 0.0000 1.000 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.DJ.A3VM.01 4 0.0000 0.974 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.IM.A41Z.01 6 0.3756 0.808 0.40 0.00 0.00 0.00 0.00 0.60
#> TCGA.EL.A4KI.01 3 0.0000 0.897 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.BJ.A45K.01 2 0.0000 1.000 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.BJ.A45C.01 2 0.0000 1.000 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.FY.A4B0.01 2 0.0000 1.000 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.EL.A4K6.01 3 0.0000 0.897 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.EM.A4FK.01 1 0.0000 1.000 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.DJ.A4UR.01 4 0.0000 0.974 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.DE.A2OL.01 1 0.0000 1.000 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.EM.A22J.01 6 0.3647 0.828 0.36 0.00 0.00 0.00 0.00 0.64
#> TCGA.EM.A3FN.01 1 0.0000 1.000 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.ET.A2MY.11 1 0.0000 1.000 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.EM.A2CL.01 2 0.0000 1.000 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.H2.A2K9.01 3 0.4929 0.614 0.00 0.00 0.62 0.00 0.10 0.28
#> TCGA.EM.A22Q.01 5 0.5095 0.281 0.00 0.42 0.00 0.00 0.50 0.08
#> TCGA.EL.A3H1.01 1 0.0000 1.000 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.J8.A3O0.01 3 0.3321 0.796 0.00 0.00 0.82 0.00 0.10 0.08
#> TCGA.FE.A239.01 2 0.0000 1.000 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.EM.A2CM.01 4 0.0937 0.947 0.00 0.00 0.00 0.96 0.00 0.04
#> TCGA.BJ.A3F0.01 6 0.3869 0.630 0.50 0.00 0.00 0.00 0.00 0.50
#> TCGA.ET.A3DV.01 1 0.0000 1.000 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.EM.A3AL.01 1 0.0000 1.000 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.EM.A3ST.01 4 0.1267 0.932 0.00 0.00 0.00 0.94 0.00 0.06
#> TCGA.EL.A3GO.01 6 0.4863 0.702 0.20 0.00 0.00 0.14 0.00 0.66
#> TCGA.FK.A3SD.01 1 0.0000 1.000 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.DJ.A2PP.01 2 0.0000 1.000 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.FY.A3W9.01 4 0.0000 0.974 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.DJ.A1QL.01 2 0.0000 1.000 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.FY.A2QD.01 1 0.0000 1.000 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.BJ.A28V.01 1 0.0000 1.000 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.EM.A1YB.01 6 0.3706 0.824 0.38 0.00 0.00 0.00 0.00 0.62
#> TCGA.EM.A3FR.01 1 0.0000 1.000 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.DJ.A13W.01 1 0.0000 1.000 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.BJ.A0ZA.01 6 0.4863 0.702 0.20 0.00 0.00 0.14 0.00 0.66
#> TCGA.BJ.A0Z0.01 5 0.0937 0.474 0.00 0.04 0.00 0.00 0.96 0.00
#> TCGA.EM.A3OA.01 1 0.0000 1.000 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.EM.A2CN.01 3 0.0000 0.897 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.BJ.A0Z2.01 3 0.0000 0.897 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.FY.A3I5.01 1 0.0000 1.000 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.ET.A2N3.01 1 0.0000 1.000 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.DJ.A3VM.01 4 0.0000 0.947 0.00 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.IM.A41Z.01 6 0.2832 0.799 0.24 0.00 0.00 0.00 0.00 0.76 0.00
#> TCGA.EL.A4KI.01 3 0.0000 0.918 0.00 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.BJ.A45K.01 2 0.0000 0.989 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.BJ.A45C.01 2 0.0000 0.989 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.FY.A4B0.01 2 0.0504 0.986 0.00 0.98 0.00 0.00 0.00 0.00 0.02
#> TCGA.EL.A4K6.01 3 0.0000 0.918 0.00 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.EM.A4FK.01 1 0.0000 1.000 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.DJ.A4UR.01 4 0.0000 0.947 0.00 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.DE.A2OL.01 1 0.0000 1.000 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.EM.A22J.01 6 0.2708 0.809 0.22 0.00 0.00 0.00 0.00 0.78 0.00
#> TCGA.EM.A3FN.01 1 0.0000 1.000 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.ET.A2MY.11 1 0.0000 1.000 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.EM.A2CL.01 2 0.0000 0.989 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.H2.A2K9.01 7 0.1664 0.000 0.00 0.00 0.06 0.00 0.02 0.00 0.92
#> TCGA.EM.A22Q.01 5 0.5467 0.191 0.00 0.28 0.00 0.00 0.46 0.00 0.26
#> TCGA.EL.A3H1.01 1 0.0000 1.000 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.J8.A3O0.01 3 0.3795 0.571 0.00 0.00 0.72 0.00 0.06 0.00 0.22
#> TCGA.FE.A239.01 2 0.0504 0.986 0.00 0.98 0.00 0.00 0.00 0.00 0.02
#> TCGA.EM.A2CM.01 4 0.1886 0.865 0.00 0.00 0.00 0.88 0.00 0.12 0.00
#> TCGA.BJ.A3F0.01 6 0.3358 0.656 0.36 0.00 0.00 0.00 0.00 0.64 0.00
#> TCGA.ET.A3DV.01 1 0.0000 1.000 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.EM.A3AL.01 1 0.0000 1.000 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.EM.A3ST.01 4 0.1363 0.913 0.00 0.00 0.00 0.94 0.00 0.04 0.02
#> TCGA.EL.A3GO.01 6 0.1363 0.561 0.00 0.00 0.00 0.04 0.00 0.94 0.02
#> TCGA.FK.A3SD.01 1 0.0000 1.000 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.DJ.A2PP.01 2 0.0504 0.986 0.00 0.98 0.00 0.00 0.00 0.00 0.02
#> TCGA.FY.A3W9.01 4 0.0504 0.943 0.00 0.00 0.00 0.98 0.00 0.02 0.00
#> TCGA.DJ.A1QL.01 2 0.0000 0.989 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.FY.A2QD.01 1 0.0000 1.000 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.BJ.A28V.01 1 0.0000 1.000 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.EM.A1YB.01 6 0.2708 0.809 0.22 0.00 0.00 0.00 0.00 0.78 0.00
#> TCGA.EM.A3FR.01 1 0.0000 1.000 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.DJ.A13W.01 1 0.0000 1.000 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.BJ.A0ZA.01 6 0.2016 0.671 0.06 0.00 0.00 0.04 0.00 0.90 0.00
#> TCGA.BJ.A0Z0.01 5 0.0000 0.227 0.00 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.EM.A3OA.01 1 0.0000 1.000 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.EM.A2CN.01 3 0.0000 0.918 0.00 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.BJ.A0Z2.01 3 0.0000 0.918 0.00 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.FY.A3I5.01 1 0.0000 1.000 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.ET.A2N3.01 1 0.0000 0.997 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.DJ.A3VM.01 8 0.0000 0.871 0.00 0.00 0.00 0.00 0.00 0.00 0.00 1.00
#> TCGA.IM.A41Z.01 6 0.1563 0.825 0.10 0.00 0.00 0.00 0.00 0.90 0.00 0.00
#> TCGA.EL.A4KI.01 3 0.0000 0.903 0.00 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.BJ.A45K.01 2 0.0000 0.892 0.00 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.BJ.A45C.01 2 0.0000 0.892 0.00 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.FY.A4B0.01 2 0.0000 0.892 0.00 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.EL.A4K6.01 3 0.0000 0.903 0.00 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.EM.A4FK.01 1 0.0808 0.955 0.96 0.00 0.00 0.00 0.00 0.04 0.00 0.00
#> TCGA.DJ.A4UR.01 8 0.0000 0.871 0.00 0.00 0.00 0.00 0.00 0.00 0.00 1.00
#> TCGA.DE.A2OL.01 1 0.0000 0.997 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.EM.A22J.01 6 0.1341 0.835 0.08 0.00 0.00 0.00 0.00 0.92 0.00 0.00
#> TCGA.EM.A3FN.01 1 0.0000 0.997 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.ET.A2MY.11 1 0.0000 0.997 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.EM.A2CL.01 2 0.0000 0.892 0.00 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.H2.A2K9.01 7 0.0000 0.000 0.00 0.00 0.00 0.00 0.00 0.00 1.00 0.00
#> TCGA.EM.A22Q.01 2 0.6655 -0.398 0.00 0.26 0.00 0.26 0.26 0.00 0.22 0.00
#> TCGA.EL.A3H1.01 1 0.0000 0.997 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.J8.A3O0.01 3 0.4489 0.464 0.00 0.00 0.64 0.04 0.06 0.00 0.26 0.00
#> TCGA.FE.A239.01 2 0.0000 0.892 0.00 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.EM.A2CM.01 8 0.1275 0.835 0.00 0.00 0.00 0.02 0.00 0.04 0.00 0.94
#> TCGA.BJ.A3F0.01 6 0.2650 0.650 0.24 0.00 0.00 0.00 0.00 0.76 0.00 0.00
#> TCGA.ET.A3DV.01 1 0.0000 0.997 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.EM.A3AL.01 1 0.0000 0.997 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.EM.A3ST.01 8 0.3318 0.425 0.00 0.00 0.00 0.46 0.00 0.00 0.00 0.54
#> TCGA.EL.A3GO.01 6 0.2852 0.545 0.00 0.00 0.00 0.28 0.00 0.72 0.00 0.00
#> TCGA.FK.A3SD.01 1 0.0000 0.997 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.DJ.A2PP.01 2 0.0000 0.892 0.00 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.FY.A3W9.01 8 0.0000 0.871 0.00 0.00 0.00 0.00 0.00 0.00 0.00 1.00
#> TCGA.DJ.A1QL.01 2 0.0000 0.892 0.00 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.FY.A2QD.01 1 0.0000 0.997 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.BJ.A28V.01 1 0.0000 0.997 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.EM.A1YB.01 6 0.1091 0.831 0.06 0.00 0.00 0.00 0.00 0.94 0.00 0.00
#> TCGA.EM.A3FR.01 1 0.0000 0.997 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.DJ.A13W.01 1 0.0000 0.997 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.BJ.A0ZA.01 6 0.0941 0.794 0.02 0.00 0.00 0.00 0.00 0.96 0.00 0.02
#> TCGA.BJ.A0Z0.01 5 0.0000 0.000 0.00 0.00 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.EM.A3OA.01 1 0.0000 0.997 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.EM.A2CN.01 3 0.0000 0.903 0.00 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.BJ.A0Z2.01 3 0.0000 0.903 0.00 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.FY.A3I5.01 1 0.0000 0.997 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: Node024. Child nodes: Node02321-leaf , Node02322-leaf , Node02411-leaf , Node02412-leaf , Node02413-leaf , Node02414-leaf , Node03111-leaf , Node03112-leaf , Node03113-leaf .
The object with results only for a single top-value method and a single partitioning method can be extracted as:
res = res_rh["0241"]
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 '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 0.4957 0.505 0.505
#> 3 3 0.648 0.724 0.738 0.3064 0.857 0.717
#> 4 4 0.916 0.985 0.954 0.1529 0.819 0.537
#> 5 5 0.963 0.916 0.947 0.0461 1.000 1.000
#> 6 6 0.924 0.841 0.938 0.0372 0.948 0.780
#> 7 7 0.838 0.723 0.890 0.0308 0.986 0.923
#> 8 8 0.833 0.653 0.865 0.0179 1.000 1.000
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.ET.A2N3.01 1 0 1 1 0
#> TCGA.IM.A41Z.01 2 0 1 0 1
#> TCGA.EM.A4FK.01 2 0 1 0 1
#> TCGA.DE.A2OL.01 1 0 1 1 0
#> TCGA.EM.A22J.01 2 0 1 0 1
#> TCGA.EM.A3FN.01 1 0 1 1 0
#> TCGA.ET.A2MY.11 1 0 1 1 0
#> TCGA.EL.A3H1.01 1 0 1 1 0
#> TCGA.BJ.A3F0.01 2 0 1 0 1
#> TCGA.ET.A3DV.01 1 0 1 1 0
#> TCGA.EM.A3AL.01 1 0 1 1 0
#> TCGA.EL.A3GO.01 1 0 1 1 0
#> TCGA.FK.A3SD.01 1 0 1 1 0
#> TCGA.FY.A2QD.01 1 0 1 1 0
#> TCGA.BJ.A28V.01 1 0 1 1 0
#> TCGA.EM.A1YB.01 2 0 1 0 1
#> TCGA.EM.A3FR.01 1 0 1 1 0
#> TCGA.DJ.A13W.01 1 0 1 1 0
#> TCGA.BJ.A0ZA.01 2 0 1 0 1
#> TCGA.EM.A3OA.01 2 0 1 0 1
#> TCGA.FY.A3I5.01 2 0 1 0 1
cbind(get_classes(res, k = 3), get_membership(res, k = 3))
#> class entropy silhouette p1 p2 p3
#> TCGA.ET.A2N3.01 1 0.000 0.876 1.00 0.00 0.00
#> TCGA.IM.A41Z.01 2 0.540 0.714 0.00 0.72 0.28
#> TCGA.EM.A4FK.01 2 0.540 0.714 0.00 0.72 0.28
#> TCGA.DE.A2OL.01 1 0.000 0.876 1.00 0.00 0.00
#> TCGA.EM.A22J.01 2 0.540 0.714 0.00 0.72 0.28
#> TCGA.EM.A3FN.01 3 0.540 1.000 0.28 0.00 0.72
#> TCGA.ET.A2MY.11 3 0.540 1.000 0.28 0.00 0.72
#> TCGA.EL.A3H1.01 1 0.000 0.876 1.00 0.00 0.00
#> TCGA.BJ.A3F0.01 2 0.583 0.489 0.00 0.66 0.34
#> TCGA.ET.A3DV.01 1 0.000 0.876 1.00 0.00 0.00
#> TCGA.EM.A3AL.01 1 0.000 0.876 1.00 0.00 0.00
#> TCGA.EL.A3GO.01 1 0.000 0.876 1.00 0.00 0.00
#> TCGA.FK.A3SD.01 1 0.604 0.105 0.62 0.00 0.38
#> TCGA.FY.A2QD.01 1 0.604 0.105 0.62 0.00 0.38
#> TCGA.BJ.A28V.01 1 0.000 0.876 1.00 0.00 0.00
#> TCGA.EM.A1YB.01 2 0.000 0.667 0.00 1.00 0.00
#> TCGA.EM.A3FR.01 3 0.540 1.000 0.28 0.00 0.72
#> TCGA.DJ.A13W.01 1 0.000 0.876 1.00 0.00 0.00
#> TCGA.BJ.A0ZA.01 2 0.583 0.489 0.00 0.66 0.34
#> TCGA.EM.A3OA.01 2 0.540 0.714 0.00 0.72 0.28
#> TCGA.FY.A3I5.01 2 0.583 0.489 0.00 0.66 0.34
cbind(get_classes(res, k = 4), get_membership(res, k = 4))
#> class entropy silhouette p1 p2 p3 p4
#> TCGA.ET.A2N3.01 1 0.000 0.986 1.00 0.00 0.00 0.00
#> TCGA.IM.A41Z.01 2 0.265 1.000 0.00 0.88 0.00 0.12
#> TCGA.EM.A4FK.01 2 0.265 1.000 0.00 0.88 0.00 0.12
#> TCGA.DE.A2OL.01 1 0.000 0.986 1.00 0.00 0.00 0.00
#> TCGA.EM.A22J.01 2 0.265 1.000 0.00 0.88 0.00 0.12
#> TCGA.EM.A3FN.01 3 0.164 1.000 0.06 0.00 0.94 0.00
#> TCGA.ET.A2MY.11 3 0.164 1.000 0.06 0.00 0.94 0.00
#> TCGA.EL.A3H1.01 1 0.000 0.986 1.00 0.00 0.00 0.00
#> TCGA.BJ.A3F0.01 4 0.000 0.984 0.00 0.00 0.00 1.00
#> TCGA.ET.A3DV.01 1 0.000 0.986 1.00 0.00 0.00 0.00
#> TCGA.EM.A3AL.01 1 0.000 0.986 1.00 0.00 0.00 0.00
#> TCGA.EL.A3GO.01 1 0.265 0.893 0.88 0.12 0.00 0.00
#> TCGA.FK.A3SD.01 3 0.164 1.000 0.06 0.00 0.94 0.00
#> TCGA.FY.A2QD.01 3 0.164 1.000 0.06 0.00 0.94 0.00
#> TCGA.BJ.A28V.01 1 0.000 0.986 1.00 0.00 0.00 0.00
#> TCGA.EM.A1YB.01 4 0.164 0.951 0.00 0.00 0.06 0.94
#> TCGA.EM.A3FR.01 3 0.164 1.000 0.06 0.00 0.94 0.00
#> TCGA.DJ.A13W.01 1 0.000 0.986 1.00 0.00 0.00 0.00
#> TCGA.BJ.A0ZA.01 4 0.000 0.984 0.00 0.00 0.00 1.00
#> TCGA.EM.A3OA.01 2 0.265 1.000 0.00 0.88 0.00 0.12
#> TCGA.FY.A3I5.01 4 0.000 0.984 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.ET.A2N3.01 1 0.0000 0.958 1.00 0.00 0.00 0.00 0.00
#> TCGA.IM.A41Z.01 5 0.0000 0.995 0.00 0.00 0.00 0.00 1.00
#> TCGA.EM.A4FK.01 5 0.0000 0.995 0.00 0.00 0.00 0.00 1.00
#> TCGA.DE.A2OL.01 1 0.0000 0.958 1.00 0.00 0.00 0.00 0.00
#> TCGA.EM.A22J.01 5 0.0609 0.985 0.00 0.00 0.02 0.00 0.98
#> TCGA.EM.A3FN.01 3 0.0609 0.935 0.02 0.00 0.98 0.00 0.00
#> TCGA.ET.A2MY.11 3 0.0609 0.935 0.02 0.00 0.98 0.00 0.00
#> TCGA.EL.A3H1.01 1 0.0000 0.958 1.00 0.00 0.00 0.00 0.00
#> TCGA.BJ.A3F0.01 4 0.0000 0.917 0.00 0.00 0.00 1.00 0.00
#> TCGA.ET.A3DV.01 1 0.0000 0.958 1.00 0.00 0.00 0.00 0.00
#> TCGA.EM.A3AL.01 1 0.0000 0.958 1.00 0.00 0.00 0.00 0.00
#> TCGA.EL.A3GO.01 1 0.3983 0.642 0.66 0.34 0.00 0.00 0.00
#> TCGA.FK.A3SD.01 3 0.0609 0.935 0.02 0.00 0.98 0.00 0.00
#> TCGA.FY.A2QD.01 3 0.0609 0.935 0.02 0.00 0.98 0.00 0.00
#> TCGA.BJ.A28V.01 1 0.0000 0.958 1.00 0.00 0.00 0.00 0.00
#> TCGA.EM.A1YB.01 4 0.3983 0.728 0.00 0.34 0.00 0.66 0.00
#> TCGA.EM.A3FR.01 3 0.4456 0.708 0.02 0.32 0.66 0.00 0.00
#> TCGA.DJ.A13W.01 1 0.0000 0.958 1.00 0.00 0.00 0.00 0.00
#> TCGA.BJ.A0ZA.01 4 0.0000 0.917 0.00 0.00 0.00 1.00 0.00
#> TCGA.EM.A3OA.01 5 0.0000 0.995 0.00 0.00 0.00 0.00 1.00
#> TCGA.FY.A3I5.01 4 0.0000 0.917 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.ET.A2N3.01 1 0.0000 0.974 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.IM.A41Z.01 5 0.0000 0.988 0.00 0.00 0.00 0.00 1.00 0.00
#> TCGA.EM.A4FK.01 5 0.0000 0.988 0.00 0.00 0.00 0.00 1.00 0.00
#> TCGA.DE.A2OL.01 1 0.0000 0.974 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.EM.A22J.01 5 0.0937 0.965 0.00 0.00 0.00 0.00 0.96 0.04
#> TCGA.EM.A3FN.01 3 0.1267 0.922 0.00 0.06 0.94 0.00 0.00 0.00
#> TCGA.ET.A2MY.11 3 0.1267 0.922 0.00 0.06 0.94 0.00 0.00 0.00
#> TCGA.EL.A3H1.01 1 0.0937 0.965 0.96 0.00 0.00 0.00 0.00 0.04
#> TCGA.BJ.A3F0.01 4 0.0000 0.882 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.ET.A3DV.01 1 0.0000 0.974 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.EM.A3AL.01 1 0.0937 0.965 0.96 0.00 0.00 0.00 0.00 0.04
#> TCGA.EL.A3GO.01 2 0.3198 0.000 0.26 0.74 0.00 0.00 0.00 0.00
#> TCGA.FK.A3SD.01 3 0.0547 0.917 0.00 0.00 0.98 0.00 0.00 0.02
#> TCGA.FY.A2QD.01 3 0.0937 0.906 0.00 0.00 0.96 0.00 0.00 0.04
#> TCGA.BJ.A28V.01 1 0.0937 0.965 0.96 0.00 0.00 0.00 0.00 0.04
#> TCGA.EM.A1YB.01 4 0.5027 0.634 0.00 0.20 0.00 0.64 0.00 0.16
#> TCGA.EM.A3FR.01 6 0.3409 0.000 0.00 0.00 0.30 0.00 0.00 0.70
#> TCGA.DJ.A13W.01 1 0.0000 0.974 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.BJ.A0ZA.01 4 0.0000 0.882 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.EM.A3OA.01 5 0.0000 0.988 0.00 0.00 0.00 0.00 1.00 0.00
#> TCGA.FY.A3I5.01 4 0.0937 0.873 0.00 0.00 0.00 0.96 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.ET.A2N3.01 1 0.3770 0.825 0.74 0.00 0.00 0.00 0.00 0.08 0.18
#> TCGA.IM.A41Z.01 5 0.0504 0.944 0.00 0.00 0.00 0.00 0.98 0.02 0.00
#> TCGA.EM.A4FK.01 5 0.0000 0.948 0.00 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.DE.A2OL.01 1 0.3770 0.825 0.74 0.00 0.00 0.00 0.00 0.08 0.18
#> TCGA.EM.A22J.01 5 0.2803 0.853 0.00 0.10 0.00 0.00 0.84 0.06 0.00
#> TCGA.EM.A3FN.01 3 0.0000 0.806 0.00 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.ET.A2MY.11 3 0.0504 0.802 0.00 0.02 0.98 0.00 0.00 0.00 0.00
#> TCGA.EL.A3H1.01 1 0.0000 0.755 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.BJ.A3F0.01 4 0.0000 0.946 0.00 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.ET.A3DV.01 1 0.3770 0.825 0.74 0.00 0.00 0.00 0.00 0.08 0.18
#> TCGA.EM.A3AL.01 1 0.0000 0.755 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.EL.A3GO.01 2 0.2708 0.000 0.22 0.78 0.00 0.00 0.00 0.00 0.00
#> TCGA.FK.A3SD.01 3 0.3289 0.792 0.00 0.06 0.82 0.00 0.00 0.02 0.10
#> TCGA.FY.A2QD.01 3 0.4457 0.732 0.00 0.06 0.72 0.00 0.00 0.06 0.16
#> TCGA.BJ.A28V.01 1 0.0000 0.755 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.EM.A1YB.01 7 0.3294 0.000 0.00 0.00 0.00 0.34 0.00 0.00 0.66
#> TCGA.EM.A3FR.01 6 0.2832 0.000 0.00 0.00 0.24 0.00 0.00 0.76 0.00
#> TCGA.DJ.A13W.01 1 0.3770 0.825 0.74 0.00 0.00 0.00 0.00 0.08 0.18
#> TCGA.BJ.A0ZA.01 4 0.0504 0.939 0.00 0.02 0.00 0.98 0.00 0.00 0.00
#> TCGA.EM.A3OA.01 5 0.0000 0.948 0.00 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.FY.A3I5.01 4 0.1363 0.911 0.00 0.02 0.00 0.94 0.00 0.04 0.00
cbind(get_classes(res, k = 8), get_membership(res, k = 8))
#> class entropy silhouette p1 p2 p3 p4 p5 p6 p7 p8
#> TCGA.ET.A2N3.01 1 0.3619 0.834 0.74 0.00 0.00 0.00 0.00 0.00 0.12 0.14
#> TCGA.IM.A41Z.01 5 0.0000 0.915 0.00 0.00 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.EM.A4FK.01 5 0.0471 0.910 0.00 0.02 0.00 0.00 0.98 0.00 0.00 0.00
#> TCGA.DE.A2OL.01 1 0.3619 0.834 0.74 0.00 0.00 0.00 0.00 0.00 0.12 0.14
#> TCGA.EM.A22J.01 5 0.4098 0.735 0.00 0.10 0.00 0.00 0.74 0.06 0.00 0.10
#> TCGA.EM.A3FN.01 3 0.3142 0.661 0.00 0.00 0.64 0.00 0.00 0.00 0.00 0.36
#> TCGA.ET.A2MY.11 3 0.3318 0.636 0.00 0.00 0.54 0.00 0.00 0.00 0.00 0.46
#> TCGA.EL.A3H1.01 1 0.0000 0.769 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.BJ.A3F0.01 4 0.0000 0.780 0.00 0.00 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.ET.A3DV.01 1 0.3619 0.834 0.74 0.00 0.00 0.00 0.00 0.00 0.12 0.14
#> TCGA.EM.A3AL.01 1 0.0000 0.769 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.EL.A3GO.01 2 0.2267 0.000 0.18 0.82 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.FK.A3SD.01 3 0.0000 0.648 0.00 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.FY.A2QD.01 3 0.2350 0.593 0.00 0.04 0.86 0.00 0.00 0.00 0.10 0.00
#> TCGA.BJ.A28V.01 1 0.0000 0.769 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.EM.A1YB.01 7 0.2534 0.000 0.00 0.00 0.00 0.22 0.00 0.00 0.78 0.00
#> TCGA.EM.A3FR.01 6 0.1563 0.000 0.00 0.00 0.10 0.00 0.00 0.90 0.00 0.00
#> TCGA.DJ.A13W.01 1 0.3619 0.834 0.74 0.00 0.00 0.00 0.00 0.00 0.12 0.14
#> TCGA.BJ.A0ZA.01 4 0.0000 0.780 0.00 0.00 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.EM.A3OA.01 5 0.0000 0.915 0.00 0.00 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.FY.A3I5.01 4 0.4106 0.502 0.00 0.02 0.00 0.64 0.00 0.04 0.00 0.30
Heatmaps for the consensus matrix. It visualizes the probability of two samples to be in a same group.
consensus_heatmap(res, k = 2)
consensus_heatmap(res, k = 3)
consensus_heatmap(res, k = 4)
consensus_heatmap(res, k = 5)
consensus_heatmap(res, k = 6)
consensus_heatmap(res, k = 7)
consensus_heatmap(res, k = 8)
Heatmaps for the membership of samples in all partitions to see how consistent they are:
membership_heatmap(res, k = 2)
membership_heatmap(res, k = 3)
membership_heatmap(res, k = 4)
membership_heatmap(res, k = 5)
membership_heatmap(res, k = 6)
membership_heatmap(res, k = 7)
membership_heatmap(res, k = 8)
As soon as the classes for columns are determined, the signatures that are significantly different between subgroups can be looked for. Following are the heatmaps for signatures.
get_signatures(res, k = 2)
get_signatures(res, k = 3)
get_signatures(res, k = 4)
get_signatures(res, k = 5)
get_signatures(res, k = 6)
get_signatures(res, k = 7)
get_signatures(res, k = 8)
Compare the overlap of signatures from different k:
compare_signatures(res)
get_signature() returns a data frame invisibly. To get the list of signatures, the function
call should be assigned to a variable explicitly. In following code, if plot argument is set
to FALSE, no heatmap is plotted while only the differential analysis is performed.
# code only for demonstration
tb = get_signature(res, k = ..., plot = FALSE)
An example of the output of tb is:
#> which_row fdr mean_1 mean_2 scaled_mean_1 scaled_mean_2 km
#> 1 38 0.042760348 8.373488 9.131774 -0.5533452 0.5164555 1
#> 2 40 0.018707592 7.106213 8.469186 -0.6173731 0.5762149 1
#> 3 55 0.019134737 10.221463 11.207825 -0.6159697 0.5749050 1
#> 4 59 0.006059896 5.921854 7.869574 -0.6899429 0.6439467 1
#> 5 60 0.018055526 8.928898 10.211722 -0.6204761 0.5791110 1
#> 6 98 0.009384629 15.714769 14.887706 0.6635654 -0.6193277 2
...
The columns in tb are:
which_row: row indices corresponding to the input matrix.fdr: FDR for the differential test. mean_x: The mean value in group x.scaled_mean_x: The mean value in group x after rows are scaled.km: Row groups if k-means clustering is applied to rows (which is done by automatically selecting number of clusters).If there are too many signatures, top_signatures = ... can be set to only show the
signatures with the highest FDRs:
# code only for demonstration
# e.g. to show the top 500 most significant rows
tb = get_signature(res, k = ..., top_signatures = 500)
If the signatures are defined as these which are uniquely high in current group, diff_method argument
can be set to "uniquely_high_in_one_group":
# code only for demonstration
tb = get_signature(res, k = ..., diff_method = "uniquely_high_in_one_group")
UMAP plot which shows how samples are separated.
dimension_reduction(res, k = 2, method = "UMAP")
dimension_reduction(res, k = 3, method = "UMAP")
dimension_reduction(res, k = 4, method = "UMAP")
dimension_reduction(res, k = 5, method = "UMAP")
dimension_reduction(res, k = 6, method = "UMAP")
dimension_reduction(res, k = 7, method = "UMAP")
dimension_reduction(res, k = 8, method = "UMAP")
Following heatmap shows how subgroups are split when increasing k:
collect_classes(res)
If matrix rows can be associated to genes, consider to use functional_enrichment(res,
...) to perform function enrichment for the signature genes. See this vignette for more detailed explanations.
Parent node: Node02. Child nodes: Node0111-leaf , Node0112-leaf , Node0113-leaf , Node0114-leaf , Node0131-leaf , Node0132-leaf , Node0133-leaf , Node0141-leaf , Node0142-leaf , Node0143-leaf , Node0211-leaf , Node0212-leaf , Node0221-leaf , Node0222-leaf , Node0223-leaf , Node0224-leaf , Node0231-leaf , Node0232 , Node0233-leaf , Node0234-leaf , Node0241 , Node0242-leaf , Node0243-leaf , Node0244-leaf , Node0251-leaf , Node0252-leaf , Node0311 , Node0312-leaf , Node0313-leaf , Node0331-leaf , Node0332-leaf , Node0333-leaf .
The object with results only for a single top-value method and a single partitioning method can be extracted as:
res = res_rh["025"]
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 48 columns.
#> Top rows (1000) are extracted by 'ATC' method.
#> Subgroups are detected by 'kmeans' method.
#> Performed in total 350 partitions by row resampling.
#> Best k for subgroups seems to be 2.
#>
#> Following methods can be applied to this 'ConsensusPartition' object:
#> [1] "cola_report" "collect_classes" "collect_plots"
#> [4] "collect_stats" "colnames" "compare_partitions"
#> [7] "compare_signatures" "consensus_heatmap" "dimension_reduction"
#> [10] "functional_enrichment" "get_anno_col" "get_anno"
#> [13] "get_classes" "get_consensus" "get_matrix"
#> [16] "get_membership" "get_param" "get_signatures"
#> [19] "get_stats" "is_best_k" "is_stable_k"
#> [22] "membership_heatmap" "ncol" "nrow"
#> [25] "plot_ecdf" "predict_classes" "rownames"
#> [28] "select_partition_number" "show" "suggest_best_k"
#> [31] "test_to_known_factors" "top_rows_heatmap"
collect_plots() function collects all the plots made from res for all k (number of subgroups)
into one single page to provide an easy and fast comparison between different k.
collect_plots(res)
The plots are:
k and the heatmap of
predicted classes for each k.k.k.k.All the plots in panels can be made by individual functions and they are plotted later in this section.
select_partition_number() produces several plots showing different
statistics for choosing “optimized” k. There are following statistics:
k;k, the area increased is defined as \(A_k - A_{k-1}\).The detailed explanations of these statistics can be found in the cola vignette.
Generally speaking, higher 1-PAC score, higher mean silhouette score or higher
concordance corresponds to better partition. Rand index and Jaccard index
measure how similar the current partition is compared to partition with k-1.
If they are too similar, we won't accept k is better than k-1.
select_partition_number(res)
The numeric values for all these statistics can be obtained by get_stats().
get_stats(res)
#> k 1-PAC mean_silhouette concordance area_increased Rand Jaccard
#> 2 2 1.000 1.000 1.000 0.3836 0.617 0.617
#> 3 3 0.784 0.845 0.935 0.2567 0.969 0.950
#> 4 4 0.742 0.939 0.929 0.2411 0.766 0.601
#> 5 5 0.780 0.869 0.921 0.0994 1.000 1.000
#> 6 6 0.773 0.801 0.909 0.0314 0.980 0.942
#> 7 7 0.652 0.712 0.853 0.0415 0.984 0.952
#> 8 8 0.624 0.553 0.805 0.0433 0.935 0.798
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.EM.A4FU.01 1 0 1 1 0
#> TCGA.DJ.A3VG.01 1 0 1 1 0
#> TCGA.FY.A40M.01 2 0 1 0 1
#> TCGA.KS.A41I.01 2 0 1 0 1
#> TCGA.ET.A4KQ.01 2 0 1 0 1
#> TCGA.EM.A4G1.01 2 0 1 0 1
#> TCGA.EL.A3ZR.01 2 0 1 0 1
#> TCGA.ET.A40P.01 2 0 1 0 1
#> TCGA.DJ.A3VK.01 1 0 1 1 0
#> TCGA.EM.A3AP.01 2 0 1 0 1
#> TCGA.E3.A3DZ.01 2 0 1 0 1
#> TCGA.BJ.A45G.01 2 0 1 0 1
#> TCGA.BJ.A2P4.01 2 0 1 0 1
#> TCGA.CE.A484.01 2 0 1 0 1
#> TCGA.BJ.A45F.01 2 0 1 0 1
#> TCGA.BJ.A45D.01 1 0 1 1 0
#> TCGA.EL.A4JV.01 2 0 1 0 1
#> TCGA.BJ.A2N7.01 2 0 1 0 1
#> TCGA.MK.A84Z.01 1 0 1 1 0
#> TCGA.BJ.A2N8.01 2 0 1 0 1
#> TCGA.FY.A76V.01 1 0 1 1 0
#> TCGA.QD.A8IV.01 2 0 1 0 1
#> TCGA.ET.A25P.01 2 0 1 0 1
#> TCGA.ET.A2N5.01 2 0 1 0 1
#> TCGA.EM.A3FP.01 2 0 1 0 1
#> TCGA.EM.A22K.01 2 0 1 0 1
#> TCGA.EM.A22L.01 2 0 1 0 1
#> TCGA.FY.A3NP.01 1 0 1 1 0
#> TCGA.EL.A3D5.01 2 0 1 0 1
#> TCGA.EL.A3GW.01 2 0 1 0 1
#> TCGA.BJ.A18Y.01 1 0 1 1 0
#> TCGA.EM.A2CK.01 1 0 1 1 0
#> TCGA.EM.A2P2.01 1 0 1 1 0
#> TCGA.DJ.A3UP.01 2 0 1 0 1
#> TCGA.ET.A39L.01 2 0 1 0 1
#> TCGA.DJ.A1QG.01 1 0 1 1 0
#> TCGA.ET.A39I.01 2 0 1 0 1
#> TCGA.DJ.A3UT.01 2 0 1 0 1
#> TCGA.EL.A3T2.01 2 0 1 0 1
#> TCGA.EM.A3O8.01 2 0 1 0 1
#> TCGA.BJ.A28S.01 1 0 1 1 0
#> TCGA.BJ.A3PT.01 2 0 1 0 1
#> TCGA.DJ.A2QB.01 2 0 1 0 1
#> TCGA.EM.A3OB.01 2 0 1 0 1
#> TCGA.H2.A3RH.01 2 0 1 0 1
#> TCGA.BJ.A0ZE.01 2 0 1 0 1
#> TCGA.DJ.A13M.01 2 0 1 0 1
#> TCGA.DJ.A13S.01 2 0 1 0 1
cbind(get_classes(res, k = 3), get_membership(res, k = 3))
#> class entropy silhouette p1 p2 p3
#> TCGA.EM.A4FU.01 1 0.0000 0.995 1.00 0.00 0.00
#> TCGA.DJ.A3VG.01 1 0.0000 0.995 1.00 0.00 0.00
#> TCGA.FY.A40M.01 2 0.0000 0.896 0.00 1.00 0.00
#> TCGA.KS.A41I.01 2 0.0000 0.896 0.00 1.00 0.00
#> TCGA.ET.A4KQ.01 2 0.5706 0.619 0.00 0.68 0.32
#> TCGA.EM.A4G1.01 2 0.5835 0.596 0.00 0.66 0.34
#> TCGA.EL.A3ZR.01 2 0.5835 0.596 0.00 0.66 0.34
#> TCGA.ET.A40P.01 2 0.0000 0.896 0.00 1.00 0.00
#> TCGA.DJ.A3VK.01 1 0.0000 0.995 1.00 0.00 0.00
#> TCGA.EM.A3AP.01 2 0.0000 0.896 0.00 1.00 0.00
#> TCGA.E3.A3DZ.01 2 0.0000 0.896 0.00 1.00 0.00
#> TCGA.BJ.A45G.01 2 0.0000 0.896 0.00 1.00 0.00
#> TCGA.BJ.A2P4.01 2 0.0000 0.896 0.00 1.00 0.00
#> TCGA.CE.A484.01 2 0.0000 0.896 0.00 1.00 0.00
#> TCGA.BJ.A45F.01 2 0.0000 0.896 0.00 1.00 0.00
#> TCGA.BJ.A45D.01 1 0.0000 0.995 1.00 0.00 0.00
#> TCGA.EL.A4JV.01 2 0.5835 0.596 0.00 0.66 0.34
#> TCGA.BJ.A2N7.01 2 0.5835 0.596 0.00 0.66 0.34
#> TCGA.MK.A84Z.01 1 0.0892 0.985 0.98 0.00 0.02
#> TCGA.BJ.A2N8.01 2 0.0000 0.896 0.00 1.00 0.00
#> TCGA.FY.A76V.01 1 0.0892 0.985 0.98 0.00 0.02
#> TCGA.QD.A8IV.01 2 0.5835 0.596 0.00 0.66 0.34
#> TCGA.ET.A25P.01 2 0.0000 0.896 0.00 1.00 0.00
#> TCGA.ET.A2N5.01 2 0.0000 0.896 0.00 1.00 0.00
#> TCGA.EM.A3FP.01 2 0.0000 0.896 0.00 1.00 0.00
#> TCGA.EM.A22K.01 2 0.5835 0.596 0.00 0.66 0.34
#> TCGA.EM.A22L.01 3 0.0892 0.000 0.00 0.02 0.98
#> TCGA.FY.A3NP.01 1 0.0000 0.995 1.00 0.00 0.00
#> TCGA.EL.A3D5.01 2 0.5835 0.596 0.00 0.66 0.34
#> TCGA.EL.A3GW.01 2 0.5835 0.596 0.00 0.66 0.34
#> TCGA.BJ.A18Y.01 1 0.0892 0.985 0.98 0.00 0.02
#> TCGA.EM.A2CK.01 1 0.0000 0.995 1.00 0.00 0.00
#> TCGA.EM.A2P2.01 1 0.0000 0.995 1.00 0.00 0.00
#> TCGA.DJ.A3UP.01 2 0.0000 0.896 0.00 1.00 0.00
#> TCGA.ET.A39L.01 2 0.0000 0.896 0.00 1.00 0.00
#> TCGA.DJ.A1QG.01 1 0.0000 0.995 1.00 0.00 0.00
#> TCGA.ET.A39I.01 2 0.0000 0.896 0.00 1.00 0.00
#> TCGA.DJ.A3UT.01 2 0.0000 0.896 0.00 1.00 0.00
#> TCGA.EL.A3T2.01 2 0.0000 0.896 0.00 1.00 0.00
#> TCGA.EM.A3O8.01 2 0.0000 0.896 0.00 1.00 0.00
#> TCGA.BJ.A28S.01 1 0.0000 0.995 1.00 0.00 0.00
#> TCGA.BJ.A3PT.01 2 0.0000 0.896 0.00 1.00 0.00
#> TCGA.DJ.A2QB.01 2 0.0000 0.896 0.00 1.00 0.00
#> TCGA.EM.A3OB.01 2 0.0000 0.896 0.00 1.00 0.00
#> TCGA.H2.A3RH.01 2 0.0000 0.896 0.00 1.00 0.00
#> TCGA.BJ.A0ZE.01 2 0.0000 0.896 0.00 1.00 0.00
#> TCGA.DJ.A13M.01 2 0.0892 0.884 0.00 0.98 0.02
#> TCGA.DJ.A13S.01 2 0.0000 0.896 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.EM.A4FU.01 1 0.0000 0.957 1.00 0.00 0.00 0.00
#> TCGA.DJ.A3VG.01 1 0.0000 0.957 1.00 0.00 0.00 0.00
#> TCGA.FY.A40M.01 2 0.0707 0.976 0.00 0.98 0.02 0.00
#> TCGA.KS.A41I.01 2 0.0000 0.997 0.00 1.00 0.00 0.00
#> TCGA.ET.A4KQ.01 4 0.3975 0.943 0.00 0.24 0.00 0.76
#> TCGA.EM.A4G1.01 4 0.3610 0.909 0.00 0.20 0.00 0.80
#> TCGA.EL.A3ZR.01 4 0.4284 0.904 0.00 0.20 0.02 0.78
#> TCGA.ET.A40P.01 2 0.0000 0.997 0.00 1.00 0.00 0.00
#> TCGA.DJ.A3VK.01 1 0.0000 0.957 1.00 0.00 0.00 0.00
#> TCGA.EM.A3AP.01 2 0.0000 0.997 0.00 1.00 0.00 0.00
#> TCGA.E3.A3DZ.01 2 0.0000 0.997 0.00 1.00 0.00 0.00
#> TCGA.BJ.A45G.01 2 0.0000 0.997 0.00 1.00 0.00 0.00
#> TCGA.BJ.A2P4.01 2 0.0707 0.974 0.00 0.98 0.00 0.02
#> TCGA.CE.A484.01 2 0.0000 0.997 0.00 1.00 0.00 0.00
#> TCGA.BJ.A45F.01 2 0.0000 0.997 0.00 1.00 0.00 0.00
#> TCGA.BJ.A45D.01 1 0.2011 0.932 0.92 0.00 0.00 0.08
#> TCGA.EL.A4JV.01 4 0.3975 0.943 0.00 0.24 0.00 0.76
#> TCGA.BJ.A2N7.01 4 0.3975 0.943 0.00 0.24 0.00 0.76
#> TCGA.MK.A84Z.01 1 0.2647 0.912 0.88 0.00 0.00 0.12
#> TCGA.BJ.A2N8.01 2 0.0000 0.997 0.00 1.00 0.00 0.00
#> TCGA.FY.A76V.01 1 0.3400 0.862 0.82 0.00 0.00 0.18
#> TCGA.QD.A8IV.01 4 0.3975 0.943 0.00 0.24 0.00 0.76
#> TCGA.ET.A25P.01 2 0.0000 0.997 0.00 1.00 0.00 0.00
#> TCGA.ET.A2N5.01 2 0.0707 0.974 0.00 0.98 0.00 0.02
#> TCGA.EM.A3FP.01 2 0.0000 0.997 0.00 1.00 0.00 0.00
#> TCGA.EM.A22K.01 4 0.3610 0.909 0.00 0.20 0.00 0.80
#> TCGA.EM.A22L.01 3 0.0707 0.000 0.00 0.00 0.98 0.02
#> TCGA.FY.A3NP.01 1 0.0000 0.957 1.00 0.00 0.00 0.00
#> TCGA.EL.A3D5.01 4 0.3975 0.943 0.00 0.24 0.00 0.76
#> TCGA.EL.A3GW.01 4 0.3975 0.943 0.00 0.24 0.00 0.76
#> TCGA.BJ.A18Y.01 1 0.1637 0.940 0.94 0.00 0.00 0.06
#> TCGA.EM.A2CK.01 1 0.0000 0.957 1.00 0.00 0.00 0.00
#> TCGA.EM.A2P2.01 1 0.0000 0.957 1.00 0.00 0.00 0.00
#> TCGA.DJ.A3UP.01 2 0.0000 0.997 0.00 1.00 0.00 0.00
#> TCGA.ET.A39L.01 2 0.0000 0.997 0.00 1.00 0.00 0.00
#> TCGA.DJ.A1QG.01 1 0.0000 0.957 1.00 0.00 0.00 0.00
#> TCGA.ET.A39I.01 2 0.0000 0.997 0.00 1.00 0.00 0.00
#> TCGA.DJ.A3UT.01 2 0.0000 0.997 0.00 1.00 0.00 0.00
#> TCGA.EL.A3T2.01 2 0.0000 0.997 0.00 1.00 0.00 0.00
#> TCGA.EM.A3O8.01 2 0.0000 0.997 0.00 1.00 0.00 0.00
#> TCGA.BJ.A28S.01 1 0.2345 0.925 0.90 0.00 0.00 0.10
#> TCGA.BJ.A3PT.01 2 0.0000 0.997 0.00 1.00 0.00 0.00
#> TCGA.DJ.A2QB.01 2 0.0000 0.997 0.00 1.00 0.00 0.00
#> TCGA.EM.A3OB.01 2 0.0000 0.997 0.00 1.00 0.00 0.00
#> TCGA.H2.A3RH.01 2 0.0000 0.997 0.00 1.00 0.00 0.00
#> TCGA.BJ.A0ZE.01 4 0.5570 0.615 0.00 0.44 0.02 0.54
#> TCGA.DJ.A13M.01 4 0.4642 0.933 0.00 0.24 0.02 0.74
#> TCGA.DJ.A13S.01 2 0.0000 0.997 0.00 1.00 0.00 0.00
cbind(get_classes(res, k = 5), get_membership(res, k = 5))
#> class entropy silhouette p1 p2 p3 p4 p5
#> TCGA.EM.A4FU.01 1 0.0000 0.918 1.00 0.00 0 0.00 0.00
#> TCGA.DJ.A3VG.01 1 0.1648 0.903 0.94 0.00 0 0.02 0.04
#> TCGA.FY.A40M.01 2 0.4060 0.489 0.00 0.64 0 0.00 0.36
#> TCGA.KS.A41I.01 2 0.0000 0.934 0.00 1.00 0 0.00 0.00
#> TCGA.ET.A4KQ.01 4 0.1410 0.915 0.00 0.06 0 0.94 0.00
#> TCGA.EM.A4G1.01 4 0.2012 0.901 0.00 0.06 0 0.92 0.02
#> TCGA.EL.A3ZR.01 4 0.4433 0.766 0.00 0.06 0 0.74 0.20
#> TCGA.ET.A40P.01 2 0.0000 0.934 0.00 1.00 0 0.00 0.00
#> TCGA.DJ.A3VK.01 1 0.0609 0.914 0.98 0.00 0 0.00 0.02
#> TCGA.EM.A3AP.01 2 0.0609 0.932 0.00 0.98 0 0.02 0.00
#> TCGA.E3.A3DZ.01 2 0.2280 0.882 0.00 0.88 0 0.12 0.00
#> TCGA.BJ.A45G.01 2 0.0609 0.933 0.00 0.98 0 0.00 0.02
#> TCGA.BJ.A2P4.01 2 0.2280 0.882 0.00 0.88 0 0.12 0.00
#> TCGA.CE.A484.01 2 0.0609 0.933 0.00 0.98 0 0.00 0.02
#> TCGA.BJ.A45F.01 2 0.0609 0.933 0.00 0.98 0 0.00 0.02
#> TCGA.BJ.A45D.01 1 0.0609 0.919 0.98 0.00 0 0.00 0.02
#> TCGA.EL.A4JV.01 4 0.1410 0.915 0.00 0.06 0 0.94 0.00
#> TCGA.BJ.A2N7.01 4 0.1410 0.915 0.00 0.06 0 0.94 0.00
#> TCGA.MK.A84Z.01 1 0.2929 0.862 0.82 0.00 0 0.00 0.18
#> TCGA.BJ.A2N8.01 2 0.0609 0.932 0.00 0.98 0 0.02 0.00
#> TCGA.FY.A76V.01 1 0.3796 0.752 0.70 0.00 0 0.00 0.30
#> TCGA.QD.A8IV.01 4 0.1410 0.915 0.00 0.06 0 0.94 0.00
#> TCGA.ET.A25P.01 2 0.0609 0.933 0.00 0.98 0 0.00 0.02
#> TCGA.ET.A2N5.01 2 0.2280 0.882 0.00 0.88 0 0.12 0.00
#> TCGA.EM.A3FP.01 2 0.2020 0.897 0.00 0.90 0 0.10 0.00
#> TCGA.EM.A22K.01 4 0.4433 0.758 0.00 0.06 0 0.74 0.20
#> TCGA.EM.A22L.01 3 0.0000 0.000 0.00 0.00 1 0.00 0.00
#> TCGA.FY.A3NP.01 1 0.0609 0.919 0.98 0.00 0 0.00 0.02
#> TCGA.EL.A3D5.01 4 0.1410 0.915 0.00 0.06 0 0.94 0.00
#> TCGA.EL.A3GW.01 4 0.1410 0.915 0.00 0.06 0 0.94 0.00
#> TCGA.BJ.A18Y.01 1 0.2929 0.862 0.82 0.00 0 0.00 0.18
#> TCGA.EM.A2CK.01 1 0.1732 0.904 0.92 0.00 0 0.00 0.08
#> TCGA.EM.A2P2.01 1 0.0000 0.918 1.00 0.00 0 0.00 0.00
#> TCGA.DJ.A3UP.01 2 0.0609 0.933 0.00 0.98 0 0.00 0.02
#> TCGA.ET.A39L.01 2 0.0609 0.933 0.00 0.98 0 0.00 0.02
#> TCGA.DJ.A1QG.01 1 0.0609 0.914 0.98 0.00 0 0.00 0.02
#> TCGA.ET.A39I.01 2 0.2280 0.882 0.00 0.88 0 0.12 0.00
#> TCGA.DJ.A3UT.01 2 0.0609 0.933 0.00 0.98 0 0.00 0.02
#> TCGA.EL.A3T2.01 2 0.0609 0.932 0.00 0.98 0 0.02 0.00
#> TCGA.EM.A3O8.01 2 0.0609 0.933 0.00 0.98 0 0.00 0.02
#> TCGA.BJ.A28S.01 1 0.3291 0.875 0.84 0.00 0 0.04 0.12
#> TCGA.BJ.A3PT.01 2 0.2020 0.897 0.00 0.90 0 0.10 0.00
#> TCGA.DJ.A2QB.01 2 0.0609 0.932 0.00 0.98 0 0.02 0.00
#> TCGA.EM.A3OB.01 2 0.2020 0.897 0.00 0.90 0 0.10 0.00
#> TCGA.H2.A3RH.01 2 0.0609 0.933 0.00 0.98 0 0.00 0.02
#> TCGA.BJ.A0ZE.01 4 0.3796 0.580 0.00 0.30 0 0.70 0.00
#> TCGA.DJ.A13M.01 4 0.1732 0.899 0.00 0.08 0 0.92 0.00
#> TCGA.DJ.A13S.01 2 0.0000 0.934 0.00 1.00 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.EM.A4FU.01 1 0.0000 0.923 1.00 0.00 0.00 0.00 0.00 0
#> TCGA.DJ.A3VG.01 1 0.1480 0.909 0.94 0.00 0.04 0.02 0.00 0
#> TCGA.FY.A40M.01 5 0.3309 0.000 0.00 0.28 0.00 0.00 0.72 0
#> TCGA.KS.A41I.01 2 0.0000 0.917 0.00 1.00 0.00 0.00 0.00 0
#> TCGA.ET.A4KQ.01 4 0.1267 0.834 0.00 0.06 0.00 0.94 0.00 0
#> TCGA.EM.A4G1.01 4 0.1092 0.798 0.00 0.02 0.02 0.96 0.00 0
#> TCGA.EL.A3ZR.01 4 0.4801 0.285 0.00 0.02 0.46 0.50 0.02 0
#> TCGA.ET.A40P.01 2 0.0547 0.917 0.00 0.98 0.02 0.00 0.00 0
#> TCGA.DJ.A3VK.01 1 0.0937 0.915 0.96 0.00 0.04 0.00 0.00 0
#> TCGA.EM.A3AP.01 2 0.0547 0.914 0.00 0.98 0.02 0.00 0.00 0
#> TCGA.E3.A3DZ.01 2 0.2350 0.831 0.00 0.88 0.02 0.10 0.00 0
#> TCGA.BJ.A45G.01 2 0.0547 0.917 0.00 0.98 0.02 0.00 0.00 0
#> TCGA.BJ.A2P4.01 2 0.4042 0.645 0.00 0.76 0.04 0.18 0.02 0
#> TCGA.CE.A484.01 2 0.0547 0.917 0.00 0.98 0.02 0.00 0.00 0
#> TCGA.BJ.A45F.01 2 0.0547 0.917 0.00 0.98 0.02 0.00 0.00 0
#> TCGA.BJ.A45D.01 1 0.0547 0.921 0.98 0.00 0.00 0.00 0.02 0
#> TCGA.EL.A4JV.01 4 0.1807 0.831 0.00 0.06 0.02 0.92 0.00 0
#> TCGA.BJ.A2N7.01 4 0.2725 0.815 0.00 0.06 0.04 0.88 0.02 0
#> TCGA.MK.A84Z.01 1 0.1807 0.897 0.92 0.00 0.02 0.00 0.06 0
#> TCGA.BJ.A2N8.01 2 0.0547 0.914 0.00 0.98 0.02 0.00 0.00 0
#> TCGA.FY.A76V.01 1 0.4723 0.677 0.68 0.00 0.14 0.00 0.18 0
#> TCGA.QD.A8IV.01 4 0.1807 0.833 0.00 0.06 0.02 0.92 0.00 0
#> TCGA.ET.A25P.01 2 0.0547 0.917 0.00 0.98 0.02 0.00 0.00 0
#> TCGA.ET.A2N5.01 2 0.3873 0.685 0.00 0.78 0.04 0.16 0.02 0
#> TCGA.EM.A3FP.01 2 0.2350 0.831 0.00 0.88 0.02 0.10 0.00 0
#> TCGA.EM.A22K.01 4 0.4420 0.521 0.00 0.02 0.30 0.66 0.02 0
#> TCGA.EM.A22L.01 6 0.0000 0.000 0.00 0.00 0.00 0.00 0.00 1
#> TCGA.FY.A3NP.01 1 0.0000 0.923 1.00 0.00 0.00 0.00 0.00 0
#> TCGA.EL.A3D5.01 4 0.1807 0.833 0.00 0.06 0.02 0.92 0.00 0
#> TCGA.EL.A3GW.01 4 0.2190 0.832 0.00 0.06 0.04 0.90 0.00 0
#> TCGA.BJ.A18Y.01 1 0.1480 0.905 0.94 0.00 0.02 0.00 0.04 0
#> TCGA.EM.A2CK.01 1 0.0000 0.923 1.00 0.00 0.00 0.00 0.00 0
#> TCGA.EM.A2P2.01 1 0.0000 0.923 1.00 0.00 0.00 0.00 0.00 0
#> TCGA.DJ.A3UP.01 2 0.0547 0.917 0.00 0.98 0.02 0.00 0.00 0
#> TCGA.ET.A39L.01 2 0.0000 0.917 0.00 1.00 0.00 0.00 0.00 0
#> TCGA.DJ.A1QG.01 1 0.0937 0.915 0.96 0.00 0.04 0.00 0.00 0
#> TCGA.ET.A39I.01 2 0.2350 0.831 0.00 0.88 0.02 0.10 0.00 0
#> TCGA.DJ.A3UT.01 2 0.0547 0.917 0.00 0.98 0.02 0.00 0.00 0
#> TCGA.EL.A3T2.01 2 0.1480 0.893 0.00 0.94 0.02 0.04 0.00 0
#> TCGA.EM.A3O8.01 2 0.0547 0.917 0.00 0.98 0.02 0.00 0.00 0
#> TCGA.BJ.A28S.01 1 0.4380 0.677 0.70 0.00 0.22 0.00 0.08 0
#> TCGA.BJ.A3PT.01 2 0.0547 0.914 0.00 0.98 0.02 0.00 0.00 0
#> TCGA.DJ.A2QB.01 2 0.0547 0.914 0.00 0.98 0.02 0.00 0.00 0
#> TCGA.EM.A3OB.01 2 0.2094 0.857 0.00 0.90 0.02 0.08 0.00 0
#> TCGA.H2.A3RH.01 2 0.0547 0.917 0.00 0.98 0.02 0.00 0.00 0
#> TCGA.BJ.A0ZE.01 4 0.5107 0.336 0.00 0.30 0.04 0.62 0.04 0
#> TCGA.DJ.A13M.01 4 0.3103 0.812 0.00 0.06 0.04 0.86 0.04 0
#> TCGA.DJ.A13S.01 2 0.0547 0.912 0.00 0.98 0.00 0.02 0.00 0
cbind(get_classes(res, k = 7), get_membership(res, k = 7))
#> class entropy silhouette p1 p2 p3 p4 p5 p6 p7
#> TCGA.EM.A4FU.01 1 0.0000 0.846 1.00 0.00 0.00 0.00 0.00 0 0.00
#> TCGA.DJ.A3VG.01 1 0.1006 0.842 0.96 0.00 0.00 0.00 0.02 0 0.02
#> TCGA.FY.A40M.01 3 0.2422 0.000 0.00 0.18 0.82 0.00 0.00 0 0.00
#> TCGA.KS.A41I.01 2 0.0504 0.829 0.00 0.98 0.00 0.00 0.02 0 0.00
#> TCGA.ET.A4KQ.01 4 0.0863 0.801 0.00 0.04 0.00 0.96 0.00 0 0.00
#> TCGA.EM.A4G1.01 4 0.3055 0.305 0.00 0.00 0.02 0.82 0.02 0 0.14
#> TCGA.EL.A3ZR.01 7 0.5579 0.535 0.00 0.00 0.00 0.36 0.26 0 0.38
#> TCGA.ET.A40P.01 2 0.0504 0.831 0.00 0.98 0.00 0.00 0.02 0 0.00
#> TCGA.DJ.A3VK.01 1 0.0000 0.846 1.00 0.00 0.00 0.00 0.00 0 0.00
#> TCGA.EM.A3AP.01 2 0.2081 0.807 0.00 0.86 0.00 0.14 0.00 0 0.00
#> TCGA.E3.A3DZ.01 2 0.3307 0.725 0.00 0.74 0.00 0.24 0.02 0 0.00
#> TCGA.BJ.A45G.01 2 0.0504 0.831 0.00 0.98 0.00 0.00 0.02 0 0.00
#> TCGA.BJ.A2P4.01 2 0.4783 0.402 0.00 0.54 0.00 0.36 0.10 0 0.00
#> TCGA.CE.A484.01 2 0.0504 0.831 0.00 0.98 0.00 0.00 0.02 0 0.00
#> TCGA.BJ.A45F.01 2 0.0504 0.831 0.00 0.98 0.00 0.00 0.02 0 0.00
#> TCGA.BJ.A45D.01 1 0.3061 0.808 0.84 0.00 0.06 0.00 0.08 0 0.02
#> TCGA.EL.A4JV.01 4 0.0863 0.801 0.00 0.04 0.00 0.96 0.00 0 0.00
#> TCGA.BJ.A2N7.01 4 0.1363 0.767 0.00 0.02 0.00 0.94 0.04 0 0.00
#> TCGA.MK.A84Z.01 1 0.3991 0.747 0.72 0.00 0.02 0.00 0.22 0 0.04
#> TCGA.BJ.A2N8.01 2 0.1671 0.819 0.00 0.90 0.00 0.10 0.00 0 0.00
#> TCGA.FY.A76V.01 1 0.3562 0.489 0.50 0.00 0.00 0.00 0.50 0 0.00
#> TCGA.QD.A8IV.01 4 0.1363 0.802 0.00 0.04 0.02 0.94 0.00 0 0.00
#> TCGA.ET.A25P.01 2 0.0504 0.831 0.00 0.98 0.00 0.00 0.02 0 0.00
#> TCGA.ET.A2N5.01 2 0.4681 0.484 0.00 0.58 0.00 0.32 0.10 0 0.00
#> TCGA.EM.A3FP.01 2 0.2708 0.755 0.00 0.78 0.00 0.22 0.00 0 0.00
#> TCGA.EM.A22K.01 7 0.3546 0.542 0.00 0.00 0.00 0.46 0.00 0 0.54
#> TCGA.EM.A22L.01 6 0.0000 0.000 0.00 0.00 0.00 0.00 0.00 1 0.00
#> TCGA.FY.A3NP.01 1 0.0504 0.846 0.98 0.00 0.00 0.00 0.02 0 0.00
#> TCGA.EL.A3D5.01 4 0.1363 0.802 0.00 0.04 0.02 0.94 0.00 0 0.00
#> TCGA.EL.A3GW.01 4 0.1860 0.782 0.00 0.04 0.02 0.92 0.00 0 0.02
#> TCGA.BJ.A18Y.01 1 0.3086 0.797 0.80 0.00 0.00 0.00 0.16 0 0.04
#> TCGA.EM.A2CK.01 1 0.1166 0.844 0.94 0.00 0.00 0.00 0.06 0 0.00
#> TCGA.EM.A2P2.01 1 0.1718 0.834 0.92 0.00 0.04 0.00 0.04 0 0.00
#> TCGA.DJ.A3UP.01 2 0.0504 0.831 0.00 0.98 0.00 0.00 0.02 0 0.00
#> TCGA.ET.A39L.01 2 0.0504 0.831 0.00 0.98 0.00 0.00 0.02 0 0.00
#> TCGA.DJ.A1QG.01 1 0.0504 0.847 0.98 0.00 0.02 0.00 0.00 0 0.00
#> TCGA.ET.A39I.01 2 0.3307 0.725 0.00 0.74 0.00 0.24 0.02 0 0.00
#> TCGA.DJ.A3UT.01 2 0.0504 0.831 0.00 0.98 0.00 0.00 0.02 0 0.00
#> TCGA.EL.A3T2.01 2 0.2745 0.788 0.00 0.82 0.00 0.16 0.02 0 0.00
#> TCGA.EM.A3O8.01 2 0.0504 0.831 0.00 0.98 0.00 0.00 0.02 0 0.00
#> TCGA.BJ.A28S.01 1 0.6357 0.359 0.46 0.00 0.10 0.00 0.16 0 0.28
#> TCGA.BJ.A3PT.01 2 0.2745 0.785 0.00 0.82 0.00 0.16 0.02 0 0.00
#> TCGA.DJ.A2QB.01 2 0.1671 0.819 0.00 0.90 0.00 0.10 0.00 0 0.00
#> TCGA.EM.A3OB.01 2 0.3388 0.748 0.00 0.76 0.00 0.20 0.04 0 0.00
#> TCGA.H2.A3RH.01 2 0.0504 0.831 0.00 0.98 0.00 0.00 0.02 0 0.00
#> TCGA.BJ.A0ZE.01 4 0.4813 0.389 0.00 0.24 0.00 0.64 0.10 0 0.02
#> TCGA.DJ.A13M.01 4 0.3772 0.696 0.00 0.06 0.02 0.80 0.10 0 0.02
#> TCGA.DJ.A13S.01 2 0.1006 0.828 0.00 0.96 0.00 0.02 0.02 0 0.00
cbind(get_classes(res, k = 8), get_membership(res, k = 8))
#> class entropy silhouette p1 p2 p3 p4 p5 p6 p7 p8
#> TCGA.EM.A4FU.01 1 0.0000 0.84059 1.00 0.00 0.00 0.00 0.00 0 0.00 0.00
#> TCGA.DJ.A3VG.01 1 0.1741 0.82125 0.92 0.00 0.04 0.00 0.02 0 0.00 0.02
#> TCGA.FY.A40M.01 3 0.1765 0.00000 0.00 0.12 0.88 0.00 0.00 0 0.00 0.00
#> TCGA.KS.A41I.01 2 0.0471 0.76017 0.00 0.98 0.00 0.00 0.00 0 0.00 0.02
#> TCGA.ET.A4KQ.01 4 0.2025 0.71365 0.00 0.02 0.00 0.88 0.00 0 0.00 0.10
#> TCGA.EM.A4G1.01 4 0.3830 0.45769 0.00 0.02 0.00 0.74 0.08 0 0.00 0.16
#> TCGA.EL.A3ZR.01 7 0.6737 -0.46376 0.00 0.02 0.04 0.10 0.34 0 0.40 0.10
#> TCGA.ET.A40P.01 2 0.0471 0.75923 0.00 0.98 0.00 0.02 0.00 0 0.00 0.00
#> TCGA.DJ.A3VK.01 1 0.0471 0.84010 0.98 0.00 0.02 0.00 0.00 0 0.00 0.00
#> TCGA.EM.A3AP.01 2 0.3434 0.65025 0.00 0.76 0.00 0.14 0.00 0 0.00 0.10
#> TCGA.E3.A3DZ.01 2 0.4759 0.08116 0.00 0.50 0.00 0.36 0.00 0 0.00 0.14
#> TCGA.BJ.A45G.01 2 0.0000 0.76325 0.00 1.00 0.00 0.00 0.00 0 0.00 0.00
#> TCGA.BJ.A2P4.01 8 0.5270 0.55287 0.00 0.30 0.00 0.34 0.00 0 0.00 0.36
#> TCGA.CE.A484.01 2 0.0000 0.76325 0.00 1.00 0.00 0.00 0.00 0 0.00 0.00
#> TCGA.BJ.A45F.01 2 0.0000 0.76325 0.00 1.00 0.00 0.00 0.00 0 0.00 0.00
#> TCGA.BJ.A45D.01 1 0.2020 0.80038 0.90 0.00 0.00 0.02 0.00 0 0.06 0.02
#> TCGA.EL.A4JV.01 4 0.1275 0.81579 0.00 0.02 0.00 0.94 0.00 0 0.00 0.04
#> TCGA.BJ.A2N7.01 4 0.2025 0.76409 0.00 0.02 0.00 0.88 0.00 0 0.00 0.10
#> TCGA.MK.A84Z.01 1 0.4211 0.59412 0.68 0.00 0.00 0.02 0.00 0 0.22 0.08
#> TCGA.BJ.A2N8.01 2 0.3263 0.66805 0.00 0.78 0.00 0.12 0.00 0 0.00 0.10
#> TCGA.FY.A76V.01 7 0.3329 -0.47307 0.48 0.00 0.00 0.00 0.00 0 0.52 0.00
#> TCGA.QD.A8IV.01 4 0.0471 0.84701 0.00 0.02 0.00 0.98 0.00 0 0.00 0.00
#> TCGA.ET.A25P.01 2 0.0000 0.76325 0.00 1.00 0.00 0.00 0.00 0 0.00 0.00
#> TCGA.ET.A2N5.01 8 0.5276 0.52044 0.00 0.32 0.00 0.32 0.00 0 0.00 0.36
#> TCGA.EM.A3FP.01 2 0.4677 0.22197 0.00 0.54 0.00 0.32 0.00 0 0.00 0.14
#> TCGA.EM.A22K.01 5 0.3198 0.00000 0.00 0.02 0.00 0.26 0.72 0 0.00 0.00
#> TCGA.EM.A22L.01 6 0.0000 0.00000 0.00 0.00 0.00 0.00 0.00 1 0.00 0.00
#> TCGA.FY.A3NP.01 1 0.1408 0.83460 0.94 0.00 0.02 0.00 0.00 0 0.02 0.02
#> TCGA.EL.A3D5.01 4 0.0471 0.84701 0.00 0.02 0.00 0.98 0.00 0 0.00 0.00
#> TCGA.EL.A3GW.01 4 0.0941 0.83382 0.00 0.02 0.00 0.96 0.02 0 0.00 0.00
#> TCGA.BJ.A18Y.01 1 0.3601 0.68724 0.76 0.00 0.02 0.00 0.00 0 0.16 0.06
#> TCGA.EM.A2CK.01 1 0.0941 0.83982 0.96 0.00 0.00 0.00 0.00 0 0.02 0.02
#> TCGA.EM.A2P2.01 1 0.0471 0.84039 0.98 0.00 0.02 0.00 0.00 0 0.00 0.00
#> TCGA.DJ.A3UP.01 2 0.0000 0.76325 0.00 1.00 0.00 0.00 0.00 0 0.00 0.00
#> TCGA.ET.A39L.01 2 0.0000 0.76325 0.00 1.00 0.00 0.00 0.00 0 0.00 0.00
#> TCGA.DJ.A1QG.01 1 0.0941 0.84202 0.96 0.00 0.02 0.00 0.02 0 0.00 0.00
#> TCGA.ET.A39I.01 2 0.4873 0.00648 0.00 0.48 0.00 0.36 0.00 0 0.00 0.16
#> TCGA.DJ.A3UT.01 2 0.0000 0.76325 0.00 1.00 0.00 0.00 0.00 0 0.00 0.00
#> TCGA.EL.A3T2.01 2 0.3909 0.58227 0.00 0.70 0.00 0.12 0.00 0 0.00 0.18
#> TCGA.EM.A3O8.01 2 0.0000 0.76325 0.00 1.00 0.00 0.00 0.00 0 0.00 0.00
#> TCGA.BJ.A28S.01 1 0.5252 0.33886 0.56 0.00 0.02 0.00 0.02 0 0.12 0.28
#> TCGA.BJ.A3PT.01 2 0.3434 0.64895 0.00 0.76 0.00 0.10 0.00 0 0.00 0.14
#> TCGA.DJ.A2QB.01 2 0.3434 0.65025 0.00 0.76 0.00 0.14 0.00 0 0.00 0.10
#> TCGA.EM.A3OB.01 2 0.5033 -0.02417 0.00 0.48 0.00 0.30 0.00 0 0.00 0.22
#> TCGA.H2.A3RH.01 2 0.0000 0.76325 0.00 1.00 0.00 0.00 0.00 0 0.00 0.00
#> TCGA.BJ.A0ZE.01 8 0.5535 0.39952 0.00 0.16 0.00 0.36 0.00 0 0.04 0.44
#> TCGA.DJ.A13M.01 8 0.4794 -0.10726 0.00 0.02 0.00 0.42 0.00 0 0.08 0.48
#> TCGA.DJ.A13S.01 2 0.2569 0.69089 0.00 0.82 0.00 0.02 0.00 0 0.00 0.16
Heatmaps for the consensus matrix. It visualizes the probability of two samples to be in a same group.
consensus_heatmap(res, k = 2)
consensus_heatmap(res, k = 3)
consensus_heatmap(res, k = 4)
consensus_heatmap(res, k = 5)
consensus_heatmap(res, k = 6)
consensus_heatmap(res, k = 7)
consensus_heatmap(res, k = 8)
Heatmaps for the membership of samples in all partitions to see how consistent they are:
membership_heatmap(res, k = 2)
membership_heatmap(res, k = 3)
membership_heatmap(res, k = 4)
membership_heatmap(res, k = 5)
membership_heatmap(res, k = 6)
membership_heatmap(res, k = 7)
membership_heatmap(res, k = 8)
As soon as the classes for columns are determined, the signatures that are significantly different between subgroups can be looked for. Following are the heatmaps for signatures.
get_signatures(res, k = 2)
get_signatures(res, k = 3)
get_signatures(res, k = 4)
get_signatures(res, k = 5)
get_signatures(res, k = 6)
get_signatures(res, k = 7)
get_signatures(res, k = 8)
Compare the overlap of signatures from different k:
compare_signatures(res)
get_signature() returns a data frame invisibly. To get the list of signatures, the function
call should be assigned to a variable explicitly. In following code, if plot argument is set
to FALSE, no heatmap is plotted while only the differential analysis is performed.
# code only for demonstration
tb = get_signature(res, k = ..., plot = FALSE)
An example of the output of tb is:
#> which_row fdr mean_1 mean_2 scaled_mean_1 scaled_mean_2 km
#> 1 38 0.042760348 8.373488 9.131774 -0.5533452 0.5164555 1
#> 2 40 0.018707592 7.106213 8.469186 -0.6173731 0.5762149 1
#> 3 55 0.019134737 10.221463 11.207825 -0.6159697 0.5749050 1
#> 4 59 0.006059896 5.921854 7.869574 -0.6899429 0.6439467 1
#> 5 60 0.018055526 8.928898 10.211722 -0.6204761 0.5791110 1
#> 6 98 0.009384629 15.714769 14.887706 0.6635654 -0.6193277 2
...
The columns in tb are:
which_row: row indices corresponding to the input matrix.fdr: FDR for the differential test. mean_x: The mean value in group x.scaled_mean_x: The mean value in group x after rows are scaled.km: Row groups if k-means clustering is applied to rows (which is done by automatically selecting number of clusters).If there are too many signatures, top_signatures = ... can be set to only show the
signatures with the highest FDRs:
# code only for demonstration
# e.g. to show the top 500 most significant rows
tb = get_signature(res, k = ..., top_signatures = 500)
If the signatures are defined as these which are uniquely high in current group, diff_method argument
can be set to "uniquely_high_in_one_group":
# code only for demonstration
tb = get_signature(res, k = ..., diff_method = "uniquely_high_in_one_group")
UMAP plot which shows how samples are separated.
dimension_reduction(res, k = 2, method = "UMAP")
dimension_reduction(res, k = 3, method = "UMAP")
dimension_reduction(res, k = 4, method = "UMAP")
dimension_reduction(res, k = 5, method = "UMAP")
dimension_reduction(res, k = 6, method = "UMAP")
dimension_reduction(res, k = 7, method = "UMAP")
dimension_reduction(res, k = 8, method = "UMAP")
Following heatmap shows how subgroups are split when increasing k:
collect_classes(res)
If matrix rows can be associated to genes, consider to use functional_enrichment(res,
...) to perform function enrichment for the signature genes. See this vignette for more detailed explanations.
Parent node: Node0. Child nodes: Node011 , Node012-leaf , Node013 , Node014 , Node015-leaf , Node021 , Node022 , Node023 , Node024 , Node025 , Node031 , Node032-leaf , Node033 , Node034-leaf .
The object with results only for a single top-value method and a single partitioning method can be extracted as:
res = res_rh["03"]
A summary of res and all the functions that can be applied to it:
res
#> A 'ConsensusPartition' object with k = 2, 3, 4, 5, 6, 7, 8.
#> On a matrix with 30000 rows and 187 columns.
#> Top rows (1000) are extracted by 'ATC' method.
#> Subgroups are detected by 'kmeans' method.
#> Performed in total 350 partitions by row resampling.
#> Best k for subgroups seems to be 2.
#>
#> Following methods can be applied to this 'ConsensusPartition' object:
#> [1] "cola_report" "collect_classes" "collect_plots"
#> [4] "collect_stats" "colnames" "compare_partitions"
#> [7] "compare_signatures" "consensus_heatmap" "dimension_reduction"
#> [10] "functional_enrichment" "get_anno_col" "get_anno"
#> [13] "get_classes" "get_consensus" "get_matrix"
#> [16] "get_membership" "get_param" "get_signatures"
#> [19] "get_stats" "is_best_k" "is_stable_k"
#> [22] "membership_heatmap" "ncol" "nrow"
#> [25] "plot_ecdf" "predict_classes" "rownames"
#> [28] "select_partition_number" "show" "suggest_best_k"
#> [31] "test_to_known_factors" "top_rows_heatmap"
collect_plots() function collects all the plots made from res for all k (number of subgroups)
into one single page to provide an easy and fast comparison between different k.
collect_plots(res)
The plots are:
k and the heatmap of
predicted classes for each k.k.k.k.All the plots in panels can be made by individual functions and they are plotted later in this section.
select_partition_number() produces several plots showing different
statistics for choosing “optimized” k. There are following statistics:
k;k, the area increased is defined as \(A_k - A_{k-1}\).The detailed explanations of these statistics can be found in the cola vignette.
Generally speaking, higher 1-PAC score, higher mean silhouette score or higher
concordance corresponds to better partition. Rand index and Jaccard index
measure how similar the current partition is compared to partition with k-1.
If they are too similar, we won't accept k is better than k-1.
select_partition_number(res)
The numeric values for all these statistics can be obtained by get_stats().
get_stats(res)
#> k 1-PAC mean_silhouette concordance area_increased Rand Jaccard
#> 2 2 1.000 1.000 1.000 0.4180 0.583 0.583
#> 3 3 0.699 0.627 0.867 0.3581 0.828 0.705
#> 4 4 0.750 0.960 0.922 0.1216 0.793 0.559
#> 5 5 0.842 0.805 0.909 0.0872 0.930 0.797
#> 6 6 0.826 0.838 0.895 0.0487 0.971 0.905
#> 7 7 0.799 0.770 0.877 0.0426 0.964 0.875
#> 8 8 0.768 0.762 0.856 0.0187 0.983 0.934
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.EL.A4K9.01 1 0 1 1 0
#> TCGA.KS.A41F.01 2 0 1 0 1
#> TCGA.EL.A3ZM.01 1 0 1 1 0
#> TCGA.EL.A3ZQ.01 2 0 1 0 1
#> TCGA.ET.A40T.01 2 0 1 0 1
#> TCGA.DE.A4MA.01 2 0 1 0 1
#> TCGA.E8.A418.01 2 0 1 0 1
#> TCGA.KS.A41J.01 2 0 1 0 1
#> TCGA.DJ.A3VB.01 1 0 1 1 0
#> TCGA.H2.A421.01 2 0 1 0 1
#> TCGA.EL.A3ZO.01 2 0 1 0 1
#> TCGA.DE.A4MD.01 1 0 1 1 0
#> TCGA.DJ.A3VI.01 2 0 1 0 1
#> TCGA.DJ.A3VA.01 2 0 1 0 1
#> TCGA.L6.A4ET.01 2 0 1 0 1
#> TCGA.DJ.A4V2.01 2 0 1 0 1
#> TCGA.ET.A40Q.01 1 0 1 1 0
#> TCGA.EL.A4K7.01 1 0 1 1 0
#> TCGA.J8.A3O2.06 1 0 1 1 0
#> TCGA.DJ.A3V7.01 2 0 1 0 1
#> TCGA.EM.A4FN.01 2 0 1 0 1
#> TCGA.EL.A4K1.01 2 0 1 0 1
#> TCGA.H2.A422.01 2 0 1 0 1
#> TCGA.J8.A3YF.01 1 0 1 1 0
#> TCGA.DJ.A3VJ.01 1 0 1 1 0
#> TCGA.EL.A3ZP.01 1 0 1 1 0
#> TCGA.EM.A4FQ.01 2 0 1 0 1
#> TCGA.EL.A3ZT.01 1 0 1 1 0
#> TCGA.L6.A4EQ.01 1 0 1 1 0
#> TCGA.DJ.A3VE.01 1 0 1 1 0
#> TCGA.DE.A4MB.01 2 0 1 0 1
#> TCGA.MK.A4N6.01 1 0 1 1 0
#> TCGA.E8.A417.01 2 0 1 0 1
#> TCGA.L6.A4EU.01 2 0 1 0 1
#> TCGA.EL.A3ZL.01 2 0 1 0 1
#> TCGA.J8.A4HW.01 2 0 1 0 1
#> TCGA.BJ.A45J.01 2 0 1 0 1
#> TCGA.CE.A482.01 2 0 1 0 1
#> TCGA.DJ.A2Q6.01 2 0 1 0 1
#> TCGA.DJ.A4UL.01 2 0 1 0 1
#> TCGA.EL.A4KG.01 2 0 1 0 1
#> TCGA.DJ.A2PQ.01 1 0 1 1 0
#> TCGA.L6.A4EP.01 2 0 1 0 1
#> TCGA.FY.A4B4.01 2 0 1 0 1
#> TCGA.DE.A4MC.01 2 0 1 0 1
#> TCGA.E3.A3E2.01 2 0 1 0 1
#> TCGA.ET.A2MY.01 2 0 1 0 1
#> TCGA.EL.A3H8.01 2 0 1 0 1
#> TCGA.EL.A4JZ.01 2 0 1 0 1
#> TCGA.KS.A4I9.01 2 0 1 0 1
#> TCGA.EL.A3MW.01 2 0 1 0 1
#> TCGA.E3.A3DY.01 1 0 1 1 0
#> TCGA.DJ.A2Q4.01 1 0 1 1 0
#> TCGA.FY.A4B3.01 1 0 1 1 0
#> TCGA.E3.A3E3.01 2 0 1 0 1
#> TCGA.EM.A3AQ.01 1 0 1 1 0
#> TCGA.EM.A4FM.01 2 0 1 0 1
#> TCGA.MK.A4N9.01 2 0 1 0 1
#> TCGA.KS.A4I1.01 2 0 1 0 1
#> TCGA.E3.A3E5.01 1 0 1 1 0
#> TCGA.BJ.A4O8.01 1 0 1 1 0
#> TCGA.E3.A3E0.01 2 0 1 0 1
#> TCGA.IM.A41Y.01 2 0 1 0 1
#> TCGA.KS.A4I5.01 2 0 1 0 1
#> TCGA.KS.A4IB.01 2 0 1 0 1
#> TCGA.EM.A4FF.01 2 0 1 0 1
#> TCGA.EL.A4K0.01 2 0 1 0 1
#> TCGA.FK.A4UB.01 1 0 1 1 0
#> TCGA.MK.A4N7.01 2 0 1 0 1
#> TCGA.EL.A4K4.01 2 0 1 0 1
#> TCGA.EL.A3GS.01 2 0 1 0 1
#> TCGA.EL.A3GZ.01 2 0 1 0 1
#> TCGA.EL.A3N2.01 2 0 1 0 1
#> TCGA.KS.A4I7.01 2 0 1 0 1
#> TCGA.ET.A25G.01 2 0 1 0 1
#> TCGA.EM.A3FK.01 2 0 1 0 1
#> TCGA.EM.A2CS.01 2 0 1 0 1
#> TCGA.EL.A3MX.01 2 0 1 0 1
#> TCGA.ET.A25R.01 2 0 1 0 1
#> TCGA.EM.A3FJ.01 2 0 1 0 1
#> TCGA.EM.A3FQ.06 2 0 1 0 1
#> TCGA.FE.A235.01 2 0 1 0 1
#> TCGA.ET.A25M.01 1 0 1 1 0
#> TCGA.EL.A3MY.01 1 0 1 1 0
#> TCGA.DE.A7U5.01 2 0 1 0 1
#> TCGA.DE.A69J.01 2 0 1 0 1
#> TCGA.ET.A25K.01 2 0 1 0 1
#> TCGA.EM.A3FM.01 1 0 1 1 0
#> TCGA.FE.A22Z.01 2 0 1 0 1
#> TCGA.EL.A3MZ.01 1 0 1 1 0
#> TCGA.ET.A25L.01 2 0 1 0 1
#> TCGA.DJ.A2Q7.01 2 0 1 0 1
#> TCGA.DE.A69K.01 2 0 1 0 1
#> TCGA.4C.A93U.01 2 0 1 0 1
#> TCGA.ET.A25N.01 2 0 1 0 1
#> TCGA.EL.A3H7.01 2 0 1 0 1
#> TCGA.EM.A3FO.01 1 0 1 1 0
#> TCGA.ET.A25O.01 2 0 1 0 1
#> TCGA.EL.A3GU.01 2 0 1 0 1
#> TCGA.DJ.A2PY.01 2 0 1 0 1
#> TCGA.EM.A22I.01 2 0 1 0 1
#> TCGA.DE.A0XZ.01 2 0 1 0 1
#> TCGA.EL.A3H4.01 2 0 1 0 1
#> TCGA.EM.A2OX.01 1 0 1 1 0
#> TCGA.EM.A3SX.01 2 0 1 0 1
#> TCGA.EL.A3CR.01 2 0 1 0 1
#> TCGA.DJ.A3V6.01 1 0 1 1 0
#> TCGA.BJ.A18Z.01 1 0 1 1 0
#> TCGA.DJ.A3V0.01 1 0 1 1 0
#> TCGA.EL.A3GY.01 2 0 1 0 1
#> TCGA.EL.A3T8.01 1 0 1 1 0
#> TCGA.EM.A22O.01 1 0 1 1 0
#> TCGA.J8.A3YH.01 1 0 1 1 0
#> TCGA.EL.A3GX.01 2 0 1 0 1
#> TCGA.DO.A1JZ.01 2 0 1 0 1
#> TCGA.FY.A3YR.01 2 0 1 0 1
#> TCGA.DO.A1K0.01 2 0 1 0 1
#> TCGA.DJ.A3V5.01 2 0 1 0 1
#> TCGA.IM.A3ED.01 2 0 1 0 1
#> TCGA.FK.A3SE.01 2 0 1 0 1
#> TCGA.EL.A3T7.01 2 0 1 0 1
#> TCGA.E8.A3X7.01 2 0 1 0 1
#> TCGA.ET.A3BQ.01 2 0 1 0 1
#> TCGA.EL.A3H5.01 2 0 1 0 1
#> TCGA.EM.A2P3.01 2 0 1 0 1
#> TCGA.EL.A3D0.01 1 0 1 1 0
#> TCGA.J8.A3YH.06 1 0 1 1 0
#> TCGA.BJ.A3EZ.01 1 0 1 1 0
#> TCGA.EM.A1CU.01 1 0 1 1 0
#> TCGA.EM.A3AN.01 2 0 1 0 1
#> TCGA.EL.A3D6.01 2 0 1 0 1
#> TCGA.DJ.A3UN.01 2 0 1 0 1
#> TCGA.EL.A3CL.01 2 0 1 0 1
#> TCGA.IM.A3U2.01 2 0 1 0 1
#> TCGA.IM.A3U3.01 2 0 1 0 1
#> TCGA.DJ.A1QE.01 2 0 1 0 1
#> TCGA.FK.A3SB.01 2 0 1 0 1
#> TCGA.DJ.A2PW.01 1 0 1 1 0
#> TCGA.ET.A2MZ.01 1 0 1 1 0
#> TCGA.FE.A233.01 2 0 1 0 1
#> TCGA.EL.A3T9.01 2 0 1 0 1
#> TCGA.DJ.A3UM.01 2 0 1 0 1
#> TCGA.ET.A3BX.01 1 0 1 1 0
#> TCGA.DJ.A1QQ.01 1 0 1 1 0
#> TCGA.DJ.A1QO.01 1 0 1 1 0
#> TCGA.BJ.A2NA.01 1 0 1 1 0
#> TCGA.ET.A39J.01 2 0 1 0 1
#> TCGA.EL.A3CM.01 2 0 1 0 1
#> TCGA.DJ.A3UO.01 1 0 1 1 0
#> TCGA.ET.A39P.01 2 0 1 0 1
#> TCGA.ET.A3BO.01 2 0 1 0 1
#> TCGA.DJ.A1QI.01 2 0 1 0 1
#> TCGA.EL.A3TB.01 2 0 1 0 1
#> TCGA.DJ.A1QN.01 2 0 1 0 1
#> TCGA.FE.A234.01 2 0 1 0 1
#> TCGA.FE.A231.01 1 0 1 1 0
#> TCGA.ET.A3DW.01 1 0 1 1 0
#> TCGA.ET.A3BT.01 2 0 1 0 1
#> TCGA.EL.A3T3.01 2 0 1 0 1
#> TCGA.ET.A39O.01 1 0 1 1 0
#> TCGA.DJ.A1QH.01 2 0 1 0 1
#> TCGA.DJ.A2PU.01 2 0 1 0 1
#> TCGA.DJ.A2PN.01 2 0 1 0 1
#> TCGA.FK.A3SG.01 2 0 1 0 1
#> TCGA.FK.A3SH.01 2 0 1 0 1
#> TCGA.DJ.A1QD.01 2 0 1 0 1
#> TCGA.CE.A13K.01 2 0 1 0 1
#> TCGA.EL.A3D1.01 1 0 1 1 0
#> TCGA.BJ.A0ZH.01 2 0 1 0 1
#> TCGA.DJ.A13T.01 2 0 1 0 1
#> TCGA.FE.A3PD.01 2 0 1 0 1
#> TCGA.FE.A3PC.01 2 0 1 0 1
#> TCGA.ET.A39K.01 2 0 1 0 1
#> TCGA.BJ.A3PU.01 1 0 1 1 0
#> TCGA.BJ.A0ZB.01 1 0 1 1 0
#> TCGA.DJ.A2PR.01 1 0 1 1 0
#> TCGA.FY.A3ON.01 1 0 1 1 0
#> TCGA.DJ.A13V.01 2 0 1 0 1
#> TCGA.FY.A3R8.01 2 0 1 0 1
#> TCGA.EL.A3CP.01 2 0 1 0 1
#> TCGA.DE.A0Y3.01 2 0 1 0 1
#> TCGA.FY.A3RA.01 2 0 1 0 1
#> TCGA.ET.A3BN.01 2 0 1 0 1
#> TCGA.H2.A3RI.01 2 0 1 0 1
#> TCGA.FE.A3PA.01 1 0 1 1 0
#> TCGA.DE.A0Y2.01 2 0 1 0 1
#> TCGA.ET.A3BU.01 1 0 1 1 0
cbind(get_classes(res, k = 3), get_membership(res, k = 3))
#> class entropy silhouette p1 p2 p3
#> TCGA.EL.A4K9.01 1 0.0000 0.996 1.0 0.00 0.00
#> TCGA.KS.A41F.01 2 0.0000 0.754 0.0 1.00 0.00
#> TCGA.EL.A3ZM.01 1 0.0000 0.996 1.0 0.00 0.00
#> TCGA.EL.A3ZQ.01 2 0.0000 0.754 0.0 1.00 0.00
#> TCGA.ET.A40T.01 2 0.0000 0.754 0.0 1.00 0.00
#> TCGA.DE.A4MA.01 2 0.0000 0.754 0.0 1.00 0.00
#> TCGA.E8.A418.01 2 0.0000 0.754 0.0 1.00 0.00
#> TCGA.KS.A41J.01 2 0.0000 0.754 0.0 1.00 0.00
#> TCGA.DJ.A3VB.01 1 0.0000 0.996 1.0 0.00 0.00
#> TCGA.H2.A421.01 2 0.0000 0.754 0.0 1.00 0.00
#> TCGA.EL.A3ZO.01 2 0.0000 0.754 0.0 1.00 0.00
#> TCGA.DE.A4MD.01 1 0.0000 0.996 1.0 0.00 0.00
#> TCGA.DJ.A3VI.01 2 0.0000 0.754 0.0 1.00 0.00
#> TCGA.DJ.A3VA.01 2 0.0000 0.754 0.0 1.00 0.00
#> TCGA.L6.A4ET.01 3 0.5706 0.790 0.0 0.32 0.68
#> TCGA.DJ.A4V2.01 2 0.6309 -0.585 0.0 0.50 0.50
#> TCGA.ET.A40Q.01 1 0.0000 0.996 1.0 0.00 0.00
#> TCGA.EL.A4K7.01 1 0.0000 0.996 1.0 0.00 0.00
#> TCGA.J8.A3O2.06 1 0.0000 0.996 1.0 0.00 0.00
#> TCGA.DJ.A3V7.01 2 0.0000 0.754 0.0 1.00 0.00
#> TCGA.EM.A4FN.01 3 0.5560 0.793 0.0 0.30 0.70
#> TCGA.EL.A4K1.01 2 0.4796 0.416 0.0 0.78 0.22
#> TCGA.H2.A422.01 2 0.0000 0.754 0.0 1.00 0.00
#> TCGA.J8.A3YF.01 1 0.0000 0.996 1.0 0.00 0.00
#> TCGA.DJ.A3VJ.01 1 0.0000 0.996 1.0 0.00 0.00
#> TCGA.EL.A3ZP.01 1 0.0000 0.996 1.0 0.00 0.00
#> TCGA.EM.A4FQ.01 3 0.6280 0.663 0.0 0.46 0.54
#> TCGA.EL.A3ZT.01 1 0.0000 0.996 1.0 0.00 0.00
#> TCGA.L6.A4EQ.01 1 0.0000 0.996 1.0 0.00 0.00
#> TCGA.DJ.A3VE.01 1 0.0000 0.996 1.0 0.00 0.00
#> TCGA.DE.A4MB.01 2 0.0000 0.754 0.0 1.00 0.00
#> TCGA.MK.A4N6.01 1 0.0000 0.996 1.0 0.00 0.00
#> TCGA.E8.A417.01 2 0.0000 0.754 0.0 1.00 0.00
#> TCGA.L6.A4EU.01 2 0.0000 0.754 0.0 1.00 0.00
#> TCGA.EL.A3ZL.01 2 0.0000 0.754 0.0 1.00 0.00
#> TCGA.J8.A4HW.01 2 0.0000 0.754 0.0 1.00 0.00
#> TCGA.BJ.A45J.01 2 0.0000 0.754 0.0 1.00 0.00
#> TCGA.CE.A482.01 2 0.0000 0.754 0.0 1.00 0.00
#> TCGA.DJ.A2Q6.01 2 0.0000 0.754 0.0 1.00 0.00
#> TCGA.DJ.A4UL.01 3 0.5560 0.793 0.0 0.30 0.70
#> TCGA.EL.A4KG.01 3 0.5560 0.793 0.0 0.30 0.70
#> TCGA.DJ.A2PQ.01 1 0.0000 0.996 1.0 0.00 0.00
#> TCGA.L6.A4EP.01 2 0.6045 -0.147 0.0 0.62 0.38
#> TCGA.FY.A4B4.01 2 0.0000 0.754 0.0 1.00 0.00
#> TCGA.DE.A4MC.01 3 0.6280 0.663 0.0 0.46 0.54
#> TCGA.E3.A3E2.01 2 0.0000 0.754 0.0 1.00 0.00
#> TCGA.ET.A2MY.01 2 0.0000 0.754 0.0 1.00 0.00
#> TCGA.EL.A3H8.01 2 0.5016 0.365 0.0 0.76 0.24
#> TCGA.EL.A4JZ.01 2 0.6126 -0.223 0.0 0.60 0.40
#> TCGA.KS.A4I9.01 2 0.6280 -0.439 0.0 0.54 0.46
#> TCGA.EL.A3MW.01 2 0.6280 -0.439 0.0 0.54 0.46
#> TCGA.E3.A3DY.01 1 0.0000 0.996 1.0 0.00 0.00
#> TCGA.DJ.A2Q4.01 1 0.0000 0.996 1.0 0.00 0.00
#> TCGA.FY.A4B3.01 1 0.0000 0.996 1.0 0.00 0.00
#> TCGA.E3.A3E3.01 3 0.5560 0.793 0.0 0.30 0.70
#> TCGA.EM.A3AQ.01 1 0.5560 0.746 0.7 0.00 0.30
#> TCGA.EM.A4FM.01 2 0.6192 -0.295 0.0 0.58 0.42
#> TCGA.MK.A4N9.01 2 0.6126 -0.223 0.0 0.60 0.40
#> TCGA.KS.A4I1.01 2 0.0000 0.754 0.0 1.00 0.00
#> TCGA.E3.A3E5.01 1 0.0000 0.996 1.0 0.00 0.00
#> TCGA.BJ.A4O8.01 1 0.0000 0.996 1.0 0.00 0.00
#> TCGA.E3.A3E0.01 2 0.6126 -0.227 0.0 0.60 0.40
#> TCGA.IM.A41Y.01 2 0.0000 0.754 0.0 1.00 0.00
#> TCGA.KS.A4I5.01 2 0.6280 -0.439 0.0 0.54 0.46
#> TCGA.KS.A4IB.01 2 0.6244 -0.380 0.0 0.56 0.44
#> TCGA.EM.A4FF.01 2 0.0892 0.735 0.0 0.98 0.02
#> TCGA.EL.A4K0.01 3 0.6309 0.566 0.0 0.50 0.50
#> TCGA.FK.A4UB.01 1 0.0000 0.996 1.0 0.00 0.00
#> TCGA.MK.A4N7.01 2 0.0000 0.754 0.0 1.00 0.00
#> TCGA.EL.A4K4.01 2 0.0892 0.735 0.0 0.98 0.02
#> TCGA.EL.A3GS.01 2 0.6302 -0.514 0.0 0.52 0.48
#> TCGA.EL.A3GZ.01 2 0.0000 0.754 0.0 1.00 0.00
#> TCGA.EL.A3N2.01 2 0.6280 -0.439 0.0 0.54 0.46
#> TCGA.KS.A4I7.01 2 0.0000 0.754 0.0 1.00 0.00
#> TCGA.ET.A25G.01 2 0.0000 0.754 0.0 1.00 0.00
#> TCGA.EM.A3FK.01 3 0.0000 0.472 0.0 0.00 1.00
#> TCGA.EM.A2CS.01 2 0.0000 0.754 0.0 1.00 0.00
#> TCGA.EL.A3MX.01 2 0.6045 -0.146 0.0 0.62 0.38
#> TCGA.ET.A25R.01 2 0.0000 0.754 0.0 1.00 0.00
#> TCGA.EM.A3FJ.01 3 0.6280 0.663 0.0 0.46 0.54
#> TCGA.EM.A3FQ.06 3 0.6280 0.663 0.0 0.46 0.54
#> TCGA.FE.A235.01 2 0.2066 0.692 0.0 0.94 0.06
#> TCGA.ET.A25M.01 1 0.0000 0.996 1.0 0.00 0.00
#> TCGA.EL.A3MY.01 1 0.0000 0.996 1.0 0.00 0.00
#> TCGA.DE.A7U5.01 2 0.6244 -0.367 0.0 0.56 0.44
#> TCGA.DE.A69J.01 3 0.6302 0.622 0.0 0.48 0.52
#> TCGA.ET.A25K.01 2 0.0000 0.754 0.0 1.00 0.00
#> TCGA.EM.A3FM.01 1 0.0000 0.996 1.0 0.00 0.00
#> TCGA.FE.A22Z.01 2 0.6192 -0.295 0.0 0.58 0.42
#> TCGA.EL.A3MZ.01 1 0.0000 0.996 1.0 0.00 0.00
#> TCGA.ET.A25L.01 2 0.0000 0.754 0.0 1.00 0.00
#> TCGA.DJ.A2Q7.01 2 0.6302 -0.514 0.0 0.52 0.48
#> TCGA.DE.A69K.01 3 0.5835 0.780 0.0 0.34 0.66
#> TCGA.4C.A93U.01 3 0.6302 0.622 0.0 0.48 0.52
#> TCGA.ET.A25N.01 2 0.6280 -0.439 0.0 0.54 0.46
#> TCGA.EL.A3H7.01 2 0.5560 0.179 0.0 0.70 0.30
#> TCGA.EM.A3FO.01 1 0.0000 0.996 1.0 0.00 0.00
#> TCGA.ET.A25O.01 3 0.5560 0.793 0.0 0.30 0.70
#> TCGA.EL.A3GU.01 2 0.3686 0.576 0.0 0.86 0.14
#> TCGA.DJ.A2PY.01 3 0.5706 0.790 0.0 0.32 0.68
#> TCGA.EM.A22I.01 2 0.6045 -0.146 0.0 0.62 0.38
#> TCGA.DE.A0XZ.01 2 0.6244 -0.367 0.0 0.56 0.44
#> TCGA.EL.A3H4.01 2 0.0000 0.754 0.0 1.00 0.00
#> TCGA.EM.A2OX.01 1 0.0000 0.996 1.0 0.00 0.00
#> TCGA.EM.A3SX.01 2 0.0000 0.754 0.0 1.00 0.00
#> TCGA.EL.A3CR.01 2 0.0000 0.754 0.0 1.00 0.00
#> TCGA.DJ.A3V6.01 1 0.0000 0.996 1.0 0.00 0.00
#> TCGA.BJ.A18Z.01 1 0.0000 0.996 1.0 0.00 0.00
#> TCGA.DJ.A3V0.01 1 0.0000 0.996 1.0 0.00 0.00
#> TCGA.EL.A3GY.01 2 0.6280 -0.439 0.0 0.54 0.46
#> TCGA.EL.A3T8.01 1 0.0000 0.996 1.0 0.00 0.00
#> TCGA.EM.A22O.01 1 0.0000 0.996 1.0 0.00 0.00
#> TCGA.J8.A3YH.01 1 0.0000 0.996 1.0 0.00 0.00
#> TCGA.EL.A3GX.01 2 0.6192 -0.295 0.0 0.58 0.42
#> TCGA.DO.A1JZ.01 3 0.6309 0.566 0.0 0.50 0.50
#> TCGA.FY.A3YR.01 2 0.0000 0.754 0.0 1.00 0.00
#> TCGA.DO.A1K0.01 3 0.6302 0.621 0.0 0.48 0.52
#> TCGA.DJ.A3V5.01 2 0.0000 0.754 0.0 1.00 0.00
#> TCGA.IM.A3ED.01 2 0.6244 -0.367 0.0 0.56 0.44
#> TCGA.FK.A3SE.01 2 0.0000 0.754 0.0 1.00 0.00
#> TCGA.EL.A3T7.01 2 0.0000 0.754 0.0 1.00 0.00
#> TCGA.E8.A3X7.01 2 0.0000 0.754 0.0 1.00 0.00
#> TCGA.ET.A3BQ.01 2 0.6302 -0.514 0.0 0.52 0.48
#> TCGA.EL.A3H5.01 2 0.6244 -0.367 0.0 0.56 0.44
#> TCGA.EM.A2P3.01 2 0.6280 -0.439 0.0 0.54 0.46
#> TCGA.EL.A3D0.01 1 0.0000 0.996 1.0 0.00 0.00
#> TCGA.J8.A3YH.06 1 0.0000 0.996 1.0 0.00 0.00
#> TCGA.BJ.A3EZ.01 1 0.0000 0.996 1.0 0.00 0.00
#> TCGA.EM.A1CU.01 1 0.0000 0.996 1.0 0.00 0.00
#> TCGA.EM.A3AN.01 2 0.0000 0.754 0.0 1.00 0.00
#> TCGA.EL.A3D6.01 2 0.0000 0.754 0.0 1.00 0.00
#> TCGA.DJ.A3UN.01 2 0.0000 0.754 0.0 1.00 0.00
#> TCGA.EL.A3CL.01 2 0.6192 -0.295 0.0 0.58 0.42
#> TCGA.IM.A3U2.01 2 0.0000 0.754 0.0 1.00 0.00
#> TCGA.IM.A3U3.01 2 0.0000 0.754 0.0 1.00 0.00
#> TCGA.DJ.A1QE.01 3 0.6126 0.732 0.0 0.40 0.60
#> TCGA.FK.A3SB.01 2 0.6280 -0.439 0.0 0.54 0.46
#> TCGA.DJ.A2PW.01 1 0.0000 0.996 1.0 0.00 0.00
#> TCGA.ET.A2MZ.01 1 0.0000 0.996 1.0 0.00 0.00
#> TCGA.FE.A233.01 3 0.5560 0.793 0.0 0.30 0.70
#> TCGA.EL.A3T9.01 2 0.0000 0.754 0.0 1.00 0.00
#> TCGA.DJ.A3UM.01 2 0.0000 0.754 0.0 1.00 0.00
#> TCGA.ET.A3BX.01 1 0.0000 0.996 1.0 0.00 0.00
#> TCGA.DJ.A1QQ.01 1 0.0000 0.996 1.0 0.00 0.00
#> TCGA.DJ.A1QO.01 1 0.0000 0.996 1.0 0.00 0.00
#> TCGA.BJ.A2NA.01 1 0.0000 0.996 1.0 0.00 0.00
#> TCGA.ET.A39J.01 3 0.0000 0.472 0.0 0.00 1.00
#> TCGA.EL.A3CM.01 2 0.0000 0.754 0.0 1.00 0.00
#> TCGA.DJ.A3UO.01 1 0.0000 0.996 1.0 0.00 0.00
#> TCGA.ET.A39P.01 3 0.6309 0.566 0.0 0.50 0.50
#> TCGA.ET.A3BO.01 2 0.0000 0.754 0.0 1.00 0.00
#> TCGA.DJ.A1QI.01 3 0.5560 0.793 0.0 0.30 0.70
#> TCGA.EL.A3TB.01 2 0.0000 0.754 0.0 1.00 0.00
#> TCGA.DJ.A1QN.01 3 0.5560 0.793 0.0 0.30 0.70
#> TCGA.FE.A234.01 3 0.5560 0.793 0.0 0.30 0.70
#> TCGA.FE.A231.01 1 0.0000 0.996 1.0 0.00 0.00
#> TCGA.ET.A3DW.01 1 0.0000 0.996 1.0 0.00 0.00
#> TCGA.ET.A3BT.01 2 0.0000 0.754 0.0 1.00 0.00
#> TCGA.EL.A3T3.01 2 0.0000 0.754 0.0 1.00 0.00
#> TCGA.ET.A39O.01 1 0.0000 0.996 1.0 0.00 0.00
#> TCGA.DJ.A1QH.01 3 0.5706 0.790 0.0 0.32 0.68
#> TCGA.DJ.A2PU.01 3 0.5560 0.793 0.0 0.30 0.70
#> TCGA.DJ.A2PN.01 2 0.6244 -0.367 0.0 0.56 0.44
#> TCGA.FK.A3SG.01 2 0.0000 0.754 0.0 1.00 0.00
#> TCGA.FK.A3SH.01 2 0.0000 0.754 0.0 1.00 0.00
#> TCGA.DJ.A1QD.01 3 0.5560 0.793 0.0 0.30 0.70
#> TCGA.CE.A13K.01 2 0.0000 0.754 0.0 1.00 0.00
#> TCGA.EL.A3D1.01 1 0.0000 0.996 1.0 0.00 0.00
#> TCGA.BJ.A0ZH.01 2 0.0000 0.754 0.0 1.00 0.00
#> TCGA.DJ.A13T.01 2 0.0000 0.754 0.0 1.00 0.00
#> TCGA.FE.A3PD.01 2 0.0000 0.754 0.0 1.00 0.00
#> TCGA.FE.A3PC.01 2 0.0000 0.754 0.0 1.00 0.00
#> TCGA.ET.A39K.01 2 0.0000 0.754 0.0 1.00 0.00
#> TCGA.BJ.A3PU.01 1 0.0000 0.996 1.0 0.00 0.00
#> TCGA.BJ.A0ZB.01 1 0.0000 0.996 1.0 0.00 0.00
#> TCGA.DJ.A2PR.01 1 0.0000 0.996 1.0 0.00 0.00
#> TCGA.FY.A3ON.01 1 0.0000 0.996 1.0 0.00 0.00
#> TCGA.DJ.A13V.01 2 0.0000 0.754 0.0 1.00 0.00
#> TCGA.FY.A3R8.01 2 0.0000 0.754 0.0 1.00 0.00
#> TCGA.EL.A3CP.01 2 0.6244 -0.367 0.0 0.56 0.44
#> TCGA.DE.A0Y3.01 2 0.0000 0.754 0.0 1.00 0.00
#> TCGA.FY.A3RA.01 3 0.6309 0.566 0.0 0.50 0.50
#> TCGA.ET.A3BN.01 2 0.6302 -0.514 0.0 0.52 0.48
#> TCGA.H2.A3RI.01 2 0.0000 0.754 0.0 1.00 0.00
#> TCGA.FE.A3PA.01 1 0.0000 0.996 1.0 0.00 0.00
#> TCGA.DE.A0Y2.01 2 0.2537 0.666 0.0 0.92 0.08
#> TCGA.ET.A3BU.01 1 0.0000 0.996 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.EL.A4K9.01 1 0.0000 0.987 1.00 0.00 0.00 0.00
#> TCGA.KS.A41F.01 2 0.3400 0.969 0.00 0.82 0.18 0.00
#> TCGA.EL.A3ZM.01 1 0.2647 0.883 0.88 0.12 0.00 0.00
#> TCGA.EL.A3ZQ.01 2 0.3400 0.969 0.00 0.82 0.18 0.00
#> TCGA.ET.A40T.01 2 0.3400 0.969 0.00 0.82 0.18 0.00
#> TCGA.DE.A4MA.01 2 0.3400 0.969 0.00 0.82 0.18 0.00
#> TCGA.E8.A418.01 2 0.3400 0.969 0.00 0.82 0.18 0.00
#> TCGA.KS.A41J.01 2 0.3400 0.969 0.00 0.82 0.18 0.00
#> TCGA.DJ.A3VB.01 1 0.0000 0.987 1.00 0.00 0.00 0.00
#> TCGA.H2.A421.01 2 0.3400 0.969 0.00 0.82 0.18 0.00
#> TCGA.EL.A3ZO.01 2 0.3400 0.969 0.00 0.82 0.18 0.00
#> TCGA.DE.A4MD.01 1 0.2921 0.862 0.86 0.14 0.00 0.00
#> TCGA.DJ.A3VI.01 2 0.3801 0.925 0.00 0.78 0.22 0.00
#> TCGA.DJ.A3VA.01 2 0.3400 0.969 0.00 0.82 0.18 0.00
#> TCGA.L6.A4ET.01 3 0.0000 0.986 0.00 0.00 1.00 0.00
#> TCGA.DJ.A4V2.01 3 0.0000 0.986 0.00 0.00 1.00 0.00
#> TCGA.ET.A40Q.01 1 0.0000 0.987 1.00 0.00 0.00 0.00
#> TCGA.EL.A4K7.01 1 0.0000 0.987 1.00 0.00 0.00 0.00
#> TCGA.J8.A3O2.06 1 0.0000 0.987 1.00 0.00 0.00 0.00
#> TCGA.DJ.A3V7.01 2 0.3400 0.969 0.00 0.82 0.18 0.00
#> TCGA.EM.A4FN.01 3 0.0000 0.986 0.00 0.00 1.00 0.00
#> TCGA.EL.A4K1.01 3 0.0000 0.986 0.00 0.00 1.00 0.00
#> TCGA.H2.A422.01 2 0.5000 0.378 0.00 0.50 0.50 0.00
#> TCGA.J8.A3YF.01 1 0.2647 0.883 0.88 0.12 0.00 0.00
#> TCGA.DJ.A3VJ.01 1 0.0000 0.987 1.00 0.00 0.00 0.00
#> TCGA.EL.A3ZP.01 1 0.0000 0.987 1.00 0.00 0.00 0.00
#> TCGA.EM.A4FQ.01 3 0.0000 0.986 0.00 0.00 1.00 0.00
#> TCGA.EL.A3ZT.01 1 0.0000 0.987 1.00 0.00 0.00 0.00
#> TCGA.L6.A4EQ.01 1 0.0000 0.987 1.00 0.00 0.00 0.00
#> TCGA.DJ.A3VE.01 1 0.0000 0.987 1.00 0.00 0.00 0.00
#> TCGA.DE.A4MB.01 2 0.3400 0.969 0.00 0.82 0.18 0.00
#> TCGA.MK.A4N6.01 1 0.0707 0.971 0.98 0.02 0.00 0.00
#> TCGA.E8.A417.01 2 0.3400 0.969 0.00 0.82 0.18 0.00
#> TCGA.L6.A4EU.01 2 0.3400 0.969 0.00 0.82 0.18 0.00
#> TCGA.EL.A3ZL.01 2 0.3400 0.969 0.00 0.82 0.18 0.00
#> TCGA.J8.A4HW.01 2 0.4977 0.497 0.00 0.54 0.46 0.00
#> TCGA.BJ.A45J.01 2 0.3400 0.969 0.00 0.82 0.18 0.00
#> TCGA.CE.A482.01 2 0.3400 0.969 0.00 0.82 0.18 0.00
#> TCGA.DJ.A2Q6.01 2 0.3400 0.969 0.00 0.82 0.18 0.00
#> TCGA.DJ.A4UL.01 3 0.0000 0.986 0.00 0.00 1.00 0.00
#> TCGA.EL.A4KG.01 3 0.0000 0.986 0.00 0.00 1.00 0.00
#> TCGA.DJ.A2PQ.01 1 0.0000 0.987 1.00 0.00 0.00 0.00
#> TCGA.L6.A4EP.01 3 0.0000 0.986 0.00 0.00 1.00 0.00
#> TCGA.FY.A4B4.01 2 0.3400 0.969 0.00 0.82 0.18 0.00
#> TCGA.DE.A4MC.01 3 0.0000 0.986 0.00 0.00 1.00 0.00
#> TCGA.E3.A3E2.01 2 0.3400 0.969 0.00 0.82 0.18 0.00
#> TCGA.ET.A2MY.01 2 0.3400 0.969 0.00 0.82 0.18 0.00
#> TCGA.EL.A3H8.01 3 0.0707 0.964 0.00 0.02 0.98 0.00
#> TCGA.EL.A4JZ.01 3 0.0000 0.986 0.00 0.00 1.00 0.00
#> TCGA.KS.A4I9.01 3 0.0000 0.986 0.00 0.00 1.00 0.00
#> TCGA.EL.A3MW.01 3 0.0000 0.986 0.00 0.00 1.00 0.00
#> TCGA.E3.A3DY.01 1 0.0000 0.987 1.00 0.00 0.00 0.00
#> TCGA.DJ.A2Q4.01 1 0.0000 0.987 1.00 0.00 0.00 0.00
#> TCGA.FY.A4B3.01 1 0.0000 0.987 1.00 0.00 0.00 0.00
#> TCGA.E3.A3E3.01 3 0.0000 0.986 0.00 0.00 1.00 0.00
#> TCGA.EM.A3AQ.01 4 0.0000 0.995 0.00 0.00 0.00 1.00
#> TCGA.EM.A4FM.01 3 0.0000 0.986 0.00 0.00 1.00 0.00
#> TCGA.MK.A4N9.01 3 0.0000 0.986 0.00 0.00 1.00 0.00
#> TCGA.KS.A4I1.01 2 0.3400 0.969 0.00 0.82 0.18 0.00
#> TCGA.E3.A3E5.01 1 0.0000 0.987 1.00 0.00 0.00 0.00
#> TCGA.BJ.A4O8.01 1 0.0000 0.987 1.00 0.00 0.00 0.00
#> TCGA.E3.A3E0.01 3 0.0000 0.986 0.00 0.00 1.00 0.00
#> TCGA.IM.A41Y.01 2 0.3400 0.969 0.00 0.82 0.18 0.00
#> TCGA.KS.A4I5.01 3 0.0000 0.986 0.00 0.00 1.00 0.00
#> TCGA.KS.A4IB.01 3 0.0707 0.964 0.00 0.02 0.98 0.00
#> TCGA.EM.A4FF.01 3 0.3172 0.759 0.00 0.16 0.84 0.00
#> TCGA.EL.A4K0.01 3 0.0000 0.986 0.00 0.00 1.00 0.00
#> TCGA.FK.A4UB.01 1 0.0000 0.987 1.00 0.00 0.00 0.00
#> TCGA.MK.A4N7.01 2 0.3400 0.969 0.00 0.82 0.18 0.00
#> TCGA.EL.A4K4.01 3 0.3172 0.759 0.00 0.16 0.84 0.00
#> TCGA.EL.A3GS.01 3 0.0000 0.986 0.00 0.00 1.00 0.00
#> TCGA.EL.A3GZ.01 2 0.4134 0.878 0.00 0.74 0.26 0.00
#> TCGA.EL.A3N2.01 3 0.0000 0.986 0.00 0.00 1.00 0.00
#> TCGA.KS.A4I7.01 2 0.4790 0.687 0.00 0.62 0.38 0.00
#> TCGA.ET.A25G.01 2 0.3400 0.969 0.00 0.82 0.18 0.00
#> TCGA.EM.A3FK.01 4 0.1211 0.991 0.00 0.04 0.00 0.96
#> TCGA.EM.A2CS.01 2 0.3400 0.969 0.00 0.82 0.18 0.00
#> TCGA.EL.A3MX.01 3 0.0707 0.964 0.00 0.02 0.98 0.00
#> TCGA.ET.A25R.01 2 0.3400 0.969 0.00 0.82 0.18 0.00
#> TCGA.EM.A3FJ.01 3 0.0000 0.986 0.00 0.00 1.00 0.00
#> TCGA.EM.A3FQ.06 3 0.0000 0.986 0.00 0.00 1.00 0.00
#> TCGA.FE.A235.01 3 0.2921 0.794 0.00 0.14 0.86 0.00
#> TCGA.ET.A25M.01 1 0.0000 0.987 1.00 0.00 0.00 0.00
#> TCGA.EL.A3MY.01 1 0.2345 0.903 0.90 0.10 0.00 0.00
#> TCGA.DE.A7U5.01 3 0.0000 0.986 0.00 0.00 1.00 0.00
#> TCGA.DE.A69J.01 3 0.0000 0.986 0.00 0.00 1.00 0.00
#> TCGA.ET.A25K.01 2 0.3400 0.969 0.00 0.82 0.18 0.00
#> TCGA.EM.A3FM.01 1 0.0000 0.987 1.00 0.00 0.00 0.00
#> TCGA.FE.A22Z.01 3 0.0000 0.986 0.00 0.00 1.00 0.00
#> TCGA.EL.A3MZ.01 1 0.2647 0.883 0.88 0.12 0.00 0.00
#> TCGA.ET.A25L.01 2 0.3400 0.969 0.00 0.82 0.18 0.00
#> TCGA.DJ.A2Q7.01 3 0.0000 0.986 0.00 0.00 1.00 0.00
#> TCGA.DE.A69K.01 3 0.0000 0.986 0.00 0.00 1.00 0.00
#> TCGA.4C.A93U.01 3 0.0000 0.986 0.00 0.00 1.00 0.00
#> TCGA.ET.A25N.01 3 0.0000 0.986 0.00 0.00 1.00 0.00
#> TCGA.EL.A3H7.01 3 0.0000 0.986 0.00 0.00 1.00 0.00
#> TCGA.EM.A3FO.01 1 0.0000 0.987 1.00 0.00 0.00 0.00
#> TCGA.ET.A25O.01 3 0.0000 0.986 0.00 0.00 1.00 0.00
#> TCGA.EL.A3GU.01 3 0.1637 0.915 0.00 0.06 0.94 0.00
#> TCGA.DJ.A2PY.01 3 0.0000 0.986 0.00 0.00 1.00 0.00
#> TCGA.EM.A22I.01 3 0.0000 0.986 0.00 0.00 1.00 0.00
#> TCGA.DE.A0XZ.01 3 0.0000 0.986 0.00 0.00 1.00 0.00
#> TCGA.EL.A3H4.01 2 0.3400 0.969 0.00 0.82 0.18 0.00
#> TCGA.EM.A2OX.01 1 0.0000 0.987 1.00 0.00 0.00 0.00
#> TCGA.EM.A3SX.01 2 0.3400 0.969 0.00 0.82 0.18 0.00
#> TCGA.EL.A3CR.01 2 0.3400 0.969 0.00 0.82 0.18 0.00
#> TCGA.DJ.A3V6.01 1 0.0000 0.987 1.00 0.00 0.00 0.00
#> TCGA.BJ.A18Z.01 1 0.0000 0.987 1.00 0.00 0.00 0.00
#> TCGA.DJ.A3V0.01 1 0.0000 0.987 1.00 0.00 0.00 0.00
#> TCGA.EL.A3GY.01 3 0.0000 0.986 0.00 0.00 1.00 0.00
#> TCGA.EL.A3T8.01 1 0.0000 0.987 1.00 0.00 0.00 0.00
#> TCGA.EM.A22O.01 1 0.2345 0.903 0.90 0.10 0.00 0.00
#> TCGA.J8.A3YH.01 1 0.0000 0.987 1.00 0.00 0.00 0.00
#> TCGA.EL.A3GX.01 3 0.0000 0.986 0.00 0.00 1.00 0.00
#> TCGA.DO.A1JZ.01 3 0.0000 0.986 0.00 0.00 1.00 0.00
#> TCGA.FY.A3YR.01 2 0.4994 0.444 0.00 0.52 0.48 0.00
#> TCGA.DO.A1K0.01 3 0.0000 0.986 0.00 0.00 1.00 0.00
#> TCGA.DJ.A3V5.01 2 0.3400 0.969 0.00 0.82 0.18 0.00
#> TCGA.IM.A3ED.01 3 0.0000 0.986 0.00 0.00 1.00 0.00
#> TCGA.FK.A3SE.01 2 0.3400 0.969 0.00 0.82 0.18 0.00
#> TCGA.EL.A3T7.01 2 0.3400 0.969 0.00 0.82 0.18 0.00
#> TCGA.E8.A3X7.01 2 0.3400 0.969 0.00 0.82 0.18 0.00
#> TCGA.ET.A3BQ.01 3 0.0000 0.986 0.00 0.00 1.00 0.00
#> TCGA.EL.A3H5.01 3 0.0000 0.986 0.00 0.00 1.00 0.00
#> TCGA.EM.A2P3.01 3 0.0000 0.986 0.00 0.00 1.00 0.00
#> TCGA.EL.A3D0.01 1 0.0000 0.987 1.00 0.00 0.00 0.00
#> TCGA.J8.A3YH.06 1 0.0000 0.987 1.00 0.00 0.00 0.00
#> TCGA.BJ.A3EZ.01 1 0.0000 0.987 1.00 0.00 0.00 0.00
#> TCGA.EM.A1CU.01 1 0.0000 0.987 1.00 0.00 0.00 0.00
#> TCGA.EM.A3AN.01 2 0.3400 0.969 0.00 0.82 0.18 0.00
#> TCGA.EL.A3D6.01 2 0.3400 0.969 0.00 0.82 0.18 0.00
#> TCGA.DJ.A3UN.01 2 0.3400 0.969 0.00 0.82 0.18 0.00
#> TCGA.EL.A3CL.01 3 0.0000 0.986 0.00 0.00 1.00 0.00
#> TCGA.IM.A3U2.01 2 0.3400 0.969 0.00 0.82 0.18 0.00
#> TCGA.IM.A3U3.01 2 0.3400 0.969 0.00 0.82 0.18 0.00
#> TCGA.DJ.A1QE.01 3 0.0000 0.986 0.00 0.00 1.00 0.00
#> TCGA.FK.A3SB.01 3 0.0000 0.986 0.00 0.00 1.00 0.00
#> TCGA.DJ.A2PW.01 1 0.0000 0.987 1.00 0.00 0.00 0.00
#> TCGA.ET.A2MZ.01 1 0.0000 0.987 1.00 0.00 0.00 0.00
#> TCGA.FE.A233.01 3 0.0000 0.986 0.00 0.00 1.00 0.00
#> TCGA.EL.A3T9.01 2 0.3400 0.969 0.00 0.82 0.18 0.00
#> TCGA.DJ.A3UM.01 2 0.3400 0.969 0.00 0.82 0.18 0.00
#> TCGA.ET.A3BX.01 1 0.0000 0.987 1.00 0.00 0.00 0.00
#> TCGA.DJ.A1QQ.01 1 0.0000 0.987 1.00 0.00 0.00 0.00
#> TCGA.DJ.A1QO.01 1 0.0000 0.987 1.00 0.00 0.00 0.00
#> TCGA.BJ.A2NA.01 1 0.0000 0.987 1.00 0.00 0.00 0.00
#> TCGA.ET.A39J.01 4 0.0000 0.995 0.00 0.00 0.00 1.00
#> TCGA.EL.A3CM.01 2 0.3400 0.969 0.00 0.82 0.18 0.00
#> TCGA.DJ.A3UO.01 1 0.0000 0.987 1.00 0.00 0.00 0.00
#> TCGA.ET.A39P.01 3 0.0000 0.986 0.00 0.00 1.00 0.00
#> TCGA.ET.A3BO.01 2 0.3400 0.969 0.00 0.82 0.18 0.00
#> TCGA.DJ.A1QI.01 3 0.0000 0.986 0.00 0.00 1.00 0.00
#> TCGA.EL.A3TB.01 2 0.3400 0.969 0.00 0.82 0.18 0.00
#> TCGA.DJ.A1QN.01 3 0.0000 0.986 0.00 0.00 1.00 0.00
#> TCGA.FE.A234.01 3 0.0000 0.986 0.00 0.00 1.00 0.00
#> TCGA.FE.A231.01 1 0.0000 0.987 1.00 0.00 0.00 0.00
#> TCGA.ET.A3DW.01 1 0.0000 0.987 1.00 0.00 0.00 0.00
#> TCGA.ET.A3BT.01 2 0.3400 0.969 0.00 0.82 0.18 0.00
#> TCGA.EL.A3T3.01 2 0.3400 0.969 0.00 0.82 0.18 0.00
#> TCGA.ET.A39O.01 1 0.0000 0.987 1.00 0.00 0.00 0.00
#> TCGA.DJ.A1QH.01 3 0.0000 0.986 0.00 0.00 1.00 0.00
#> TCGA.DJ.A2PU.01 3 0.0000 0.986 0.00 0.00 1.00 0.00
#> TCGA.DJ.A2PN.01 3 0.0000 0.986 0.00 0.00 1.00 0.00
#> TCGA.FK.A3SG.01 2 0.3400 0.969 0.00 0.82 0.18 0.00
#> TCGA.FK.A3SH.01 2 0.3400 0.969 0.00 0.82 0.18 0.00
#> TCGA.DJ.A1QD.01 3 0.0000 0.986 0.00 0.00 1.00 0.00
#> TCGA.CE.A13K.01 2 0.3400 0.969 0.00 0.82 0.18 0.00
#> TCGA.EL.A3D1.01 1 0.0000 0.987 1.00 0.00 0.00 0.00
#> TCGA.BJ.A0ZH.01 2 0.3400 0.969 0.00 0.82 0.18 0.00
#> TCGA.DJ.A13T.01 2 0.4134 0.877 0.00 0.74 0.26 0.00
#> TCGA.FE.A3PD.01 2 0.3400 0.969 0.00 0.82 0.18 0.00
#> TCGA.FE.A3PC.01 2 0.3400 0.969 0.00 0.82 0.18 0.00
#> TCGA.ET.A39K.01 2 0.3400 0.969 0.00 0.82 0.18 0.00
#> TCGA.BJ.A3PU.01 1 0.0000 0.987 1.00 0.00 0.00 0.00
#> TCGA.BJ.A0ZB.01 1 0.0000 0.987 1.00 0.00 0.00 0.00
#> TCGA.DJ.A2PR.01 1 0.0000 0.987 1.00 0.00 0.00 0.00
#> TCGA.FY.A3ON.01 1 0.0000 0.987 1.00 0.00 0.00 0.00
#> TCGA.DJ.A13V.01 2 0.3400 0.969 0.00 0.82 0.18 0.00
#> TCGA.FY.A3R8.01 2 0.4624 0.762 0.00 0.66 0.34 0.00
#> TCGA.EL.A3CP.01 3 0.0000 0.986 0.00 0.00 1.00 0.00
#> TCGA.DE.A0Y3.01 2 0.3400 0.969 0.00 0.82 0.18 0.00
#> TCGA.FY.A3RA.01 3 0.0000 0.986 0.00 0.00 1.00 0.00
#> TCGA.ET.A3BN.01 3 0.0000 0.986 0.00 0.00 1.00 0.00
#> TCGA.H2.A3RI.01 2 0.3400 0.969 0.00 0.82 0.18 0.00
#> TCGA.FE.A3PA.01 1 0.0000 0.987 1.00 0.00 0.00 0.00
#> TCGA.DE.A0Y2.01 3 0.2345 0.859 0.00 0.10 0.90 0.00
#> TCGA.ET.A3BU.01 1 0.0000 0.987 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.EL.A4K9.01 1 0.0000 0.9754 1.00 0.00 0.00 0.00 0.00
#> TCGA.KS.A41F.01 2 0.1410 0.9530 0.00 0.94 0.06 0.00 0.00
#> TCGA.EL.A3ZM.01 1 0.3109 0.7933 0.80 0.00 0.00 0.00 0.20
#> TCGA.EL.A3ZQ.01 2 0.1410 0.9530 0.00 0.94 0.06 0.00 0.00
#> TCGA.ET.A40T.01 2 0.1410 0.9530 0.00 0.94 0.06 0.00 0.00
#> TCGA.DE.A4MA.01 2 0.1410 0.9530 0.00 0.94 0.06 0.00 0.00
#> TCGA.E8.A418.01 2 0.1410 0.9530 0.00 0.94 0.06 0.00 0.00
#> TCGA.KS.A41J.01 2 0.1410 0.9530 0.00 0.94 0.06 0.00 0.00
#> TCGA.DJ.A3VB.01 1 0.0000 0.9754 1.00 0.00 0.00 0.00 0.00
#> TCGA.H2.A421.01 2 0.1410 0.9530 0.00 0.94 0.06 0.00 0.00
#> TCGA.EL.A3ZO.01 2 0.1410 0.9530 0.00 0.94 0.06 0.00 0.00
#> TCGA.DE.A4MD.01 1 0.4096 0.7392 0.76 0.04 0.00 0.00 0.20
#> TCGA.DJ.A3VI.01 2 0.5351 0.3774 0.00 0.56 0.38 0.00 0.06
#> TCGA.DJ.A3VA.01 2 0.1410 0.9530 0.00 0.94 0.06 0.00 0.00
#> TCGA.L6.A4ET.01 5 0.4287 0.8402 0.00 0.00 0.46 0.00 0.54
#> TCGA.DJ.A4V2.01 3 0.0000 0.7837 0.00 0.00 1.00 0.00 0.00
#> TCGA.ET.A40Q.01 1 0.0000 0.9754 1.00 0.00 0.00 0.00 0.00
#> TCGA.EL.A4K7.01 1 0.0000 0.9754 1.00 0.00 0.00 0.00 0.00
#> TCGA.J8.A3O2.06 1 0.0000 0.9754 1.00 0.00 0.00 0.00 0.00
#> TCGA.DJ.A3V7.01 2 0.1410 0.9530 0.00 0.94 0.06 0.00 0.00
#> TCGA.EM.A4FN.01 3 0.4287 -0.8188 0.00 0.00 0.54 0.00 0.46
#> TCGA.EL.A4K1.01 3 0.0609 0.7696 0.00 0.00 0.98 0.00 0.02
#> TCGA.H2.A422.01 3 0.5659 0.1694 0.00 0.32 0.58 0.00 0.10
#> TCGA.J8.A3YF.01 1 0.3109 0.7933 0.80 0.00 0.00 0.00 0.20
#> TCGA.DJ.A3VJ.01 1 0.0000 0.9754 1.00 0.00 0.00 0.00 0.00
#> TCGA.EL.A3ZP.01 1 0.0000 0.9754 1.00 0.00 0.00 0.00 0.00
#> TCGA.EM.A4FQ.01 3 0.0000 0.7837 0.00 0.00 1.00 0.00 0.00
#> TCGA.EL.A3ZT.01 1 0.0000 0.9754 1.00 0.00 0.00 0.00 0.00
#> TCGA.L6.A4EQ.01 1 0.0000 0.9754 1.00 0.00 0.00 0.00 0.00
#> TCGA.DJ.A3VE.01 1 0.0000 0.9754 1.00 0.00 0.00 0.00 0.00
#> TCGA.DE.A4MB.01 2 0.1410 0.9530 0.00 0.94 0.06 0.00 0.00
#> TCGA.MK.A4N6.01 1 0.2280 0.8782 0.88 0.00 0.00 0.00 0.12
#> TCGA.E8.A417.01 2 0.1410 0.9530 0.00 0.94 0.06 0.00 0.00
#> TCGA.L6.A4EU.01 2 0.1410 0.9530 0.00 0.94 0.06 0.00 0.00
#> TCGA.EL.A3ZL.01 2 0.1410 0.9530 0.00 0.94 0.06 0.00 0.00
#> TCGA.J8.A4HW.01 3 0.4132 0.3377 0.00 0.26 0.72 0.00 0.02
#> TCGA.BJ.A45J.01 2 0.1410 0.9530 0.00 0.94 0.06 0.00 0.00
#> TCGA.CE.A482.01 2 0.1410 0.9530 0.00 0.94 0.06 0.00 0.00
#> TCGA.DJ.A2Q6.01 2 0.1410 0.9530 0.00 0.94 0.06 0.00 0.00
#> TCGA.DJ.A4UL.01 5 0.4262 0.8810 0.00 0.00 0.44 0.00 0.56
#> TCGA.EL.A4KG.01 3 0.4302 -0.8557 0.00 0.00 0.52 0.00 0.48
#> TCGA.DJ.A2PQ.01 1 0.0000 0.9754 1.00 0.00 0.00 0.00 0.00
#> TCGA.L6.A4EP.01 3 0.0609 0.7698 0.00 0.00 0.98 0.00 0.02
#> TCGA.FY.A4B4.01 2 0.1410 0.9530 0.00 0.94 0.06 0.00 0.00
#> TCGA.DE.A4MC.01 3 0.0000 0.7837 0.00 0.00 1.00 0.00 0.00
#> TCGA.E3.A3E2.01 2 0.1410 0.9530 0.00 0.94 0.06 0.00 0.00
#> TCGA.ET.A2MY.01 2 0.1410 0.9530 0.00 0.94 0.06 0.00 0.00
#> TCGA.EL.A3H8.01 3 0.0000 0.7837 0.00 0.00 1.00 0.00 0.00
#> TCGA.EL.A4JZ.01 3 0.0000 0.7837 0.00 0.00 1.00 0.00 0.00
#> TCGA.KS.A4I9.01 3 0.0000 0.7837 0.00 0.00 1.00 0.00 0.00
#> TCGA.EL.A3MW.01 3 0.0000 0.7837 0.00 0.00 1.00 0.00 0.00
#> TCGA.E3.A3DY.01 1 0.0000 0.9754 1.00 0.00 0.00 0.00 0.00
#> TCGA.DJ.A2Q4.01 1 0.0000 0.9754 1.00 0.00 0.00 0.00 0.00
#> TCGA.FY.A4B3.01 1 0.0000 0.9754 1.00 0.00 0.00 0.00 0.00
#> TCGA.E3.A3E3.01 3 0.4307 -0.8881 0.00 0.00 0.50 0.00 0.50
#> TCGA.EM.A3AQ.01 4 0.1043 0.9227 0.04 0.00 0.00 0.96 0.00
#> TCGA.EM.A4FM.01 3 0.0000 0.7837 0.00 0.00 1.00 0.00 0.00
#> TCGA.MK.A4N9.01 3 0.0000 0.7837 0.00 0.00 1.00 0.00 0.00
#> TCGA.KS.A4I1.01 2 0.5095 0.3623 0.00 0.56 0.40 0.00 0.04
#> TCGA.E3.A3E5.01 1 0.0000 0.9754 1.00 0.00 0.00 0.00 0.00
#> TCGA.BJ.A4O8.01 1 0.0000 0.9754 1.00 0.00 0.00 0.00 0.00
#> TCGA.E3.A3E0.01 3 0.0609 0.7696 0.00 0.00 0.98 0.00 0.02
#> TCGA.IM.A41Y.01 2 0.1410 0.9530 0.00 0.94 0.06 0.00 0.00
#> TCGA.KS.A4I5.01 3 0.0000 0.7837 0.00 0.00 1.00 0.00 0.00
#> TCGA.KS.A4IB.01 3 0.2873 0.6384 0.00 0.02 0.86 0.00 0.12
#> TCGA.EM.A4FF.01 3 0.2438 0.6740 0.00 0.06 0.90 0.00 0.04
#> TCGA.EL.A4K0.01 3 0.1410 0.7376 0.00 0.00 0.94 0.00 0.06
#> TCGA.FK.A4UB.01 1 0.0000 0.9754 1.00 0.00 0.00 0.00 0.00
#> TCGA.MK.A4N7.01 2 0.4675 0.4471 0.00 0.60 0.38 0.00 0.02
#> TCGA.EL.A4K4.01 3 0.3971 0.5382 0.00 0.10 0.80 0.00 0.10
#> TCGA.EL.A3GS.01 3 0.0000 0.7837 0.00 0.00 1.00 0.00 0.00
#> TCGA.EL.A3GZ.01 3 0.4287 0.0374 0.00 0.46 0.54 0.00 0.00
#> TCGA.EL.A3N2.01 3 0.2020 0.6885 0.00 0.00 0.90 0.00 0.10
#> TCGA.KS.A4I7.01 3 0.5864 0.1563 0.00 0.32 0.56 0.00 0.12
#> TCGA.ET.A25G.01 2 0.5050 0.6957 0.00 0.70 0.18 0.00 0.12
#> TCGA.EM.A3FK.01 4 0.3106 0.9196 0.00 0.02 0.00 0.84 0.14
#> TCGA.EM.A2CS.01 2 0.1410 0.9530 0.00 0.94 0.06 0.00 0.00
#> TCGA.EL.A3MX.01 3 0.0000 0.7837 0.00 0.00 1.00 0.00 0.00
#> TCGA.ET.A25R.01 2 0.2754 0.9031 0.00 0.88 0.08 0.00 0.04
#> TCGA.EM.A3FJ.01 3 0.0000 0.7837 0.00 0.00 1.00 0.00 0.00
#> TCGA.EM.A3FQ.06 3 0.0000 0.7837 0.00 0.00 1.00 0.00 0.00
#> TCGA.FE.A235.01 3 0.3946 0.5446 0.00 0.08 0.80 0.00 0.12
#> TCGA.ET.A25M.01 1 0.0000 0.9754 1.00 0.00 0.00 0.00 0.00
#> TCGA.EL.A3MY.01 1 0.2929 0.8166 0.82 0.00 0.00 0.00 0.18
#> TCGA.DE.A7U5.01 3 0.0000 0.7837 0.00 0.00 1.00 0.00 0.00
#> TCGA.DE.A69J.01 3 0.0000 0.7837 0.00 0.00 1.00 0.00 0.00
#> TCGA.ET.A25K.01 2 0.3106 0.8542 0.00 0.84 0.14 0.00 0.02
#> TCGA.EM.A3FM.01 1 0.0000 0.9754 1.00 0.00 0.00 0.00 0.00
#> TCGA.FE.A22Z.01 3 0.0000 0.7837 0.00 0.00 1.00 0.00 0.00
#> TCGA.EL.A3MZ.01 1 0.2732 0.8381 0.84 0.00 0.00 0.00 0.16
#> TCGA.ET.A25L.01 2 0.1410 0.9530 0.00 0.94 0.06 0.00 0.00
#> TCGA.DJ.A2Q7.01 3 0.1732 0.7098 0.00 0.00 0.92 0.00 0.08
#> TCGA.DE.A69K.01 3 0.2732 0.4464 0.00 0.00 0.84 0.00 0.16
#> TCGA.4C.A93U.01 3 0.0000 0.7837 0.00 0.00 1.00 0.00 0.00
#> TCGA.ET.A25N.01 3 0.2280 0.6608 0.00 0.00 0.88 0.00 0.12
#> TCGA.EL.A3H7.01 3 0.0000 0.7837 0.00 0.00 1.00 0.00 0.00
#> TCGA.EM.A3FO.01 1 0.0000 0.9754 1.00 0.00 0.00 0.00 0.00
#> TCGA.ET.A25O.01 5 0.4126 0.8422 0.00 0.00 0.38 0.00 0.62
#> TCGA.EL.A3GU.01 3 0.0000 0.7837 0.00 0.00 1.00 0.00 0.00
#> TCGA.DJ.A2PY.01 3 0.2280 0.5642 0.00 0.00 0.88 0.00 0.12
#> TCGA.EM.A22I.01 3 0.0000 0.7837 0.00 0.00 1.00 0.00 0.00
#> TCGA.DE.A0XZ.01 3 0.0000 0.7837 0.00 0.00 1.00 0.00 0.00
#> TCGA.EL.A3H4.01 2 0.1410 0.9530 0.00 0.94 0.06 0.00 0.00
#> TCGA.EM.A2OX.01 1 0.0000 0.9754 1.00 0.00 0.00 0.00 0.00
#> TCGA.EM.A3SX.01 2 0.1410 0.9530 0.00 0.94 0.06 0.00 0.00
#> TCGA.EL.A3CR.01 2 0.3561 0.7003 0.00 0.74 0.26 0.00 0.00
#> TCGA.DJ.A3V6.01 1 0.0000 0.9754 1.00 0.00 0.00 0.00 0.00
#> TCGA.BJ.A18Z.01 1 0.0000 0.9754 1.00 0.00 0.00 0.00 0.00
#> TCGA.DJ.A3V0.01 1 0.0000 0.9754 1.00 0.00 0.00 0.00 0.00
#> TCGA.EL.A3GY.01 3 0.0000 0.7837 0.00 0.00 1.00 0.00 0.00
#> TCGA.EL.A3T8.01 1 0.0000 0.9754 1.00 0.00 0.00 0.00 0.00
#> TCGA.EM.A22O.01 1 0.2732 0.8382 0.84 0.00 0.00 0.00 0.16
#> TCGA.J8.A3YH.01 1 0.0000 0.9754 1.00 0.00 0.00 0.00 0.00
#> TCGA.EL.A3GX.01 3 0.0609 0.7698 0.00 0.00 0.98 0.00 0.02
#> TCGA.DO.A1JZ.01 3 0.0000 0.7837 0.00 0.00 1.00 0.00 0.00
#> TCGA.FY.A3YR.01 3 0.5355 0.2977 0.00 0.22 0.66 0.00 0.12
#> TCGA.DO.A1K0.01 3 0.0000 0.7837 0.00 0.00 1.00 0.00 0.00
#> TCGA.DJ.A3V5.01 2 0.1410 0.9530 0.00 0.94 0.06 0.00 0.00
#> TCGA.IM.A3ED.01 3 0.0000 0.7837 0.00 0.00 1.00 0.00 0.00
#> TCGA.FK.A3SE.01 2 0.2280 0.8922 0.00 0.88 0.12 0.00 0.00
#> TCGA.EL.A3T7.01 2 0.4132 0.6851 0.00 0.72 0.26 0.00 0.02
#> TCGA.E8.A3X7.01 2 0.1410 0.9530 0.00 0.94 0.06 0.00 0.00
#> TCGA.ET.A3BQ.01 3 0.0000 0.7837 0.00 0.00 1.00 0.00 0.00
#> TCGA.EL.A3H5.01 3 0.0000 0.7837 0.00 0.00 1.00 0.00 0.00
#> TCGA.EM.A2P3.01 3 0.0000 0.7837 0.00 0.00 1.00 0.00 0.00
#> TCGA.EL.A3D0.01 1 0.0000 0.9754 1.00 0.00 0.00 0.00 0.00
#> TCGA.J8.A3YH.06 1 0.0000 0.9754 1.00 0.00 0.00 0.00 0.00
#> TCGA.BJ.A3EZ.01 1 0.0000 0.9754 1.00 0.00 0.00 0.00 0.00
#> TCGA.EM.A1CU.01 1 0.0000 0.9754 1.00 0.00 0.00 0.00 0.00
#> TCGA.EM.A3AN.01 2 0.1410 0.9530 0.00 0.94 0.06 0.00 0.00
#> TCGA.EL.A3D6.01 2 0.1410 0.9530 0.00 0.94 0.06 0.00 0.00
#> TCGA.DJ.A3UN.01 2 0.1410 0.9530 0.00 0.94 0.06 0.00 0.00
#> TCGA.EL.A3CL.01 3 0.0000 0.7837 0.00 0.00 1.00 0.00 0.00
#> TCGA.IM.A3U2.01 2 0.1410 0.9530 0.00 0.94 0.06 0.00 0.00
#> TCGA.IM.A3U3.01 2 0.1410 0.9530 0.00 0.94 0.06 0.00 0.00
#> TCGA.DJ.A1QE.01 3 0.0000 0.7837 0.00 0.00 1.00 0.00 0.00
#> TCGA.FK.A3SB.01 3 0.0609 0.7698 0.00 0.00 0.98 0.00 0.02
#> TCGA.DJ.A2PW.01 1 0.0000 0.9754 1.00 0.00 0.00 0.00 0.00
#> TCGA.ET.A2MZ.01 1 0.0000 0.9754 1.00 0.00 0.00 0.00 0.00
#> TCGA.FE.A233.01 3 0.4307 -0.8881 0.00 0.00 0.50 0.00 0.50
#> TCGA.EL.A3T9.01 2 0.1410 0.9530 0.00 0.94 0.06 0.00 0.00
#> TCGA.DJ.A3UM.01 2 0.1410 0.9530 0.00 0.94 0.06 0.00 0.00
#> TCGA.ET.A3BX.01 1 0.0000 0.9754 1.00 0.00 0.00 0.00 0.00
#> TCGA.DJ.A1QQ.01 1 0.0000 0.9754 1.00 0.00 0.00 0.00 0.00
#> TCGA.DJ.A1QO.01 1 0.0000 0.9754 1.00 0.00 0.00 0.00 0.00
#> TCGA.BJ.A2NA.01 1 0.0000 0.9754 1.00 0.00 0.00 0.00 0.00
#> TCGA.ET.A39J.01 4 0.1043 0.9315 0.00 0.00 0.00 0.96 0.04
#> TCGA.EL.A3CM.01 2 0.1410 0.9530 0.00 0.94 0.06 0.00 0.00
#> TCGA.DJ.A3UO.01 1 0.0000 0.9754 1.00 0.00 0.00 0.00 0.00
#> TCGA.ET.A39P.01 3 0.0000 0.7837 0.00 0.00 1.00 0.00 0.00
#> TCGA.ET.A3BO.01 2 0.1410 0.9530 0.00 0.94 0.06 0.00 0.00
#> TCGA.DJ.A1QI.01 5 0.4307 0.8674 0.00 0.00 0.50 0.00 0.50
#> TCGA.EL.A3TB.01 2 0.1410 0.9530 0.00 0.94 0.06 0.00 0.00
#> TCGA.DJ.A1QN.01 5 0.4307 0.8674 0.00 0.00 0.50 0.00 0.50
#> TCGA.FE.A234.01 3 0.2020 0.6144 0.00 0.00 0.90 0.00 0.10
#> TCGA.FE.A231.01 1 0.0000 0.9754 1.00 0.00 0.00 0.00 0.00
#> TCGA.ET.A3DW.01 1 0.0000 0.9754 1.00 0.00 0.00 0.00 0.00
#> TCGA.ET.A3BT.01 2 0.1410 0.9530 0.00 0.94 0.06 0.00 0.00
#> TCGA.EL.A3T3.01 2 0.1410 0.9530 0.00 0.94 0.06 0.00 0.00
#> TCGA.ET.A39O.01 1 0.0000 0.9754 1.00 0.00 0.00 0.00 0.00
#> TCGA.DJ.A1QH.01 3 0.1410 0.6937 0.00 0.00 0.94 0.00 0.06
#> TCGA.DJ.A2PU.01 5 0.4182 0.8668 0.00 0.00 0.40 0.00 0.60
#> TCGA.DJ.A2PN.01 3 0.0000 0.7837 0.00 0.00 1.00 0.00 0.00
#> TCGA.FK.A3SG.01 2 0.1410 0.9530 0.00 0.94 0.06 0.00 0.00
#> TCGA.FK.A3SH.01 2 0.1410 0.9530 0.00 0.94 0.06 0.00 0.00
#> TCGA.DJ.A1QD.01 5 0.4307 0.8674 0.00 0.00 0.50 0.00 0.50
#> TCGA.CE.A13K.01 2 0.1410 0.9530 0.00 0.94 0.06 0.00 0.00
#> TCGA.EL.A3D1.01 1 0.0000 0.9754 1.00 0.00 0.00 0.00 0.00
#> TCGA.BJ.A0ZH.01 2 0.1410 0.9530 0.00 0.94 0.06 0.00 0.00
#> TCGA.DJ.A13T.01 3 0.5864 0.1587 0.00 0.32 0.56 0.00 0.12
#> TCGA.FE.A3PD.01 2 0.1410 0.9530 0.00 0.94 0.06 0.00 0.00
#> TCGA.FE.A3PC.01 2 0.2732 0.8457 0.00 0.84 0.16 0.00 0.00
#> TCGA.ET.A39K.01 2 0.1410 0.9530 0.00 0.94 0.06 0.00 0.00
#> TCGA.BJ.A3PU.01 1 0.1410 0.9301 0.94 0.00 0.00 0.00 0.06
#> TCGA.BJ.A0ZB.01 1 0.0609 0.9610 0.98 0.00 0.00 0.00 0.02
#> TCGA.DJ.A2PR.01 1 0.0000 0.9754 1.00 0.00 0.00 0.00 0.00
#> TCGA.FY.A3ON.01 1 0.0000 0.9754 1.00 0.00 0.00 0.00 0.00
#> TCGA.DJ.A13V.01 2 0.1410 0.9530 0.00 0.94 0.06 0.00 0.00
#> TCGA.FY.A3R8.01 3 0.4227 0.1325 0.00 0.42 0.58 0.00 0.00
#> TCGA.EL.A3CP.01 3 0.1410 0.7333 0.00 0.00 0.94 0.00 0.06
#> TCGA.DE.A0Y3.01 2 0.1410 0.9530 0.00 0.94 0.06 0.00 0.00
#> TCGA.FY.A3RA.01 3 0.2020 0.6910 0.00 0.00 0.90 0.00 0.10
#> TCGA.ET.A3BN.01 3 0.0000 0.7837 0.00 0.00 1.00 0.00 0.00
#> TCGA.H2.A3RI.01 2 0.1410 0.9530 0.00 0.94 0.06 0.00 0.00
#> TCGA.FE.A3PA.01 1 0.0000 0.9754 1.00 0.00 0.00 0.00 0.00
#> TCGA.DE.A0Y2.01 3 0.4216 0.5020 0.00 0.10 0.78 0.00 0.12
#> TCGA.ET.A3BU.01 1 0.0000 0.9754 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.EL.A4K9.01 1 0.0547 0.953 0.98 0.02 0.00 0.00 0.00 0.00
#> TCGA.KS.A41F.01 6 0.0547 0.930 0.00 0.00 0.02 0.00 0.00 0.98
#> TCGA.EL.A3ZM.01 1 0.3315 0.814 0.78 0.20 0.00 0.00 0.02 0.00
#> TCGA.EL.A3ZQ.01 6 0.0547 0.930 0.00 0.00 0.02 0.00 0.00 0.98
#> TCGA.ET.A40T.01 6 0.0547 0.930 0.00 0.00 0.02 0.00 0.00 0.98
#> TCGA.DE.A4MA.01 6 0.1092 0.924 0.00 0.02 0.02 0.00 0.00 0.96
#> TCGA.E8.A418.01 6 0.1807 0.903 0.00 0.06 0.02 0.00 0.00 0.92
#> TCGA.KS.A41J.01 6 0.0547 0.930 0.00 0.00 0.02 0.00 0.00 0.98
#> TCGA.DJ.A3VB.01 1 0.1092 0.946 0.96 0.02 0.00 0.00 0.02 0.00
#> TCGA.H2.A421.01 6 0.1092 0.924 0.00 0.02 0.02 0.00 0.00 0.96
#> TCGA.EL.A3ZO.01 6 0.0547 0.930 0.00 0.00 0.02 0.00 0.00 0.98
#> TCGA.DE.A4MD.01 1 0.4328 0.717 0.72 0.18 0.00 0.00 0.10 0.00
#> TCGA.DJ.A3VI.01 3 0.5569 0.284 0.00 0.16 0.52 0.00 0.00 0.32
#> TCGA.DJ.A3VA.01 6 0.0547 0.930 0.00 0.00 0.02 0.00 0.00 0.98
#> TCGA.L6.A4ET.01 5 0.3711 0.845 0.00 0.02 0.26 0.00 0.72 0.00
#> TCGA.DJ.A4V2.01 3 0.1092 0.812 0.00 0.02 0.96 0.00 0.02 0.00
#> TCGA.ET.A40Q.01 1 0.0547 0.953 0.98 0.02 0.00 0.00 0.00 0.00
#> TCGA.EL.A4K7.01 1 0.1480 0.938 0.94 0.04 0.00 0.00 0.02 0.00
#> TCGA.J8.A3O2.06 1 0.0547 0.953 0.98 0.02 0.00 0.00 0.00 0.00
#> TCGA.DJ.A3V7.01 6 0.1092 0.924 0.00 0.02 0.02 0.00 0.00 0.96
#> TCGA.EM.A4FN.01 5 0.3198 0.941 0.00 0.00 0.26 0.00 0.74 0.00
#> TCGA.EL.A4K1.01 3 0.0547 0.809 0.00 0.02 0.98 0.00 0.00 0.00
#> TCGA.H2.A422.01 3 0.5985 0.444 0.00 0.20 0.60 0.00 0.06 0.14
#> TCGA.J8.A3YF.01 1 0.2793 0.823 0.80 0.20 0.00 0.00 0.00 0.00
#> TCGA.DJ.A3VJ.01 1 0.0547 0.953 0.98 0.02 0.00 0.00 0.00 0.00
#> TCGA.EL.A3ZP.01 1 0.0547 0.953 0.98 0.02 0.00 0.00 0.00 0.00
#> TCGA.EM.A4FQ.01 3 0.1807 0.797 0.00 0.06 0.92 0.00 0.02 0.00
#> TCGA.EL.A3ZT.01 1 0.1480 0.949 0.94 0.04 0.00 0.00 0.02 0.00
#> TCGA.L6.A4EQ.01 1 0.1480 0.938 0.94 0.04 0.00 0.00 0.02 0.00
#> TCGA.DJ.A3VE.01 1 0.1480 0.938 0.94 0.04 0.00 0.00 0.02 0.00
#> TCGA.DE.A4MB.01 6 0.0547 0.930 0.00 0.00 0.02 0.00 0.00 0.98
#> TCGA.MK.A4N6.01 1 0.1556 0.924 0.92 0.08 0.00 0.00 0.00 0.00
#> TCGA.E8.A417.01 6 0.0547 0.930 0.00 0.00 0.02 0.00 0.00 0.98
#> TCGA.L6.A4EU.01 6 0.1480 0.912 0.00 0.02 0.04 0.00 0.00 0.94
#> TCGA.EL.A3ZL.01 6 0.0547 0.930 0.00 0.00 0.02 0.00 0.00 0.98
#> TCGA.J8.A4HW.01 3 0.4380 0.528 0.00 0.08 0.70 0.00 0.00 0.22
#> TCGA.BJ.A45J.01 6 0.0547 0.930 0.00 0.00 0.02 0.00 0.00 0.98
#> TCGA.CE.A482.01 6 0.0547 0.930 0.00 0.00 0.02 0.00 0.00 0.98
#> TCGA.DJ.A2Q6.01 6 0.1092 0.924 0.00 0.02 0.02 0.00 0.00 0.96
#> TCGA.DJ.A4UL.01 5 0.3076 0.908 0.00 0.00 0.24 0.00 0.76 0.00
#> TCGA.EL.A4KG.01 5 0.3309 0.929 0.00 0.00 0.28 0.00 0.72 0.00
#> TCGA.DJ.A2PQ.01 1 0.1480 0.938 0.94 0.04 0.00 0.00 0.02 0.00
#> TCGA.L6.A4EP.01 3 0.0547 0.811 0.00 0.02 0.98 0.00 0.00 0.00
#> TCGA.FY.A4B4.01 6 0.2190 0.884 0.00 0.04 0.06 0.00 0.00 0.90
#> TCGA.DE.A4MC.01 3 0.1807 0.797 0.00 0.06 0.92 0.00 0.02 0.00
#> TCGA.E3.A3E2.01 6 0.0547 0.930 0.00 0.00 0.02 0.00 0.00 0.98
#> TCGA.ET.A2MY.01 6 0.0547 0.930 0.00 0.00 0.02 0.00 0.00 0.98
#> TCGA.EL.A3H8.01 3 0.0000 0.811 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.EL.A4JZ.01 3 0.1480 0.804 0.00 0.04 0.94 0.00 0.02 0.00
#> TCGA.KS.A4I9.01 3 0.1480 0.804 0.00 0.04 0.94 0.00 0.02 0.00
#> TCGA.EL.A3MW.01 3 0.0000 0.811 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.E3.A3DY.01 1 0.0000 0.954 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.DJ.A2Q4.01 1 0.0547 0.953 0.98 0.02 0.00 0.00 0.00 0.00
#> TCGA.FY.A4B3.01 1 0.1865 0.929 0.92 0.04 0.00 0.00 0.04 0.00
#> TCGA.E3.A3E3.01 5 0.3198 0.941 0.00 0.00 0.26 0.00 0.74 0.00
#> TCGA.EM.A3AQ.01 4 0.0000 0.888 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.EM.A4FM.01 3 0.2350 0.773 0.00 0.10 0.88 0.00 0.02 0.00
#> TCGA.MK.A4N9.01 3 0.1267 0.802 0.00 0.06 0.94 0.00 0.00 0.00
#> TCGA.KS.A4I1.01 3 0.5682 0.139 0.00 0.16 0.46 0.00 0.00 0.38
#> TCGA.E3.A3E5.01 1 0.0000 0.954 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.BJ.A4O8.01 1 0.0547 0.951 0.98 0.00 0.00 0.00 0.02 0.00
#> TCGA.E3.A3E0.01 3 0.1556 0.794 0.00 0.08 0.92 0.00 0.00 0.00
#> TCGA.IM.A41Y.01 6 0.0547 0.930 0.00 0.00 0.02 0.00 0.00 0.98
#> TCGA.KS.A4I5.01 3 0.0937 0.806 0.00 0.04 0.96 0.00 0.00 0.00
#> TCGA.KS.A4IB.01 3 0.3660 0.662 0.00 0.16 0.78 0.00 0.06 0.00
#> TCGA.EM.A4FF.01 3 0.1807 0.796 0.00 0.06 0.92 0.00 0.00 0.02
#> TCGA.EL.A4K0.01 3 0.1807 0.795 0.00 0.06 0.92 0.00 0.02 0.00
#> TCGA.FK.A4UB.01 1 0.0547 0.953 0.98 0.02 0.00 0.00 0.00 0.00
#> TCGA.MK.A4N7.01 6 0.5428 0.362 0.00 0.14 0.32 0.00 0.00 0.54
#> TCGA.EL.A4K4.01 3 0.4238 0.665 0.00 0.16 0.76 0.00 0.04 0.04
#> TCGA.EL.A3GS.01 3 0.0937 0.806 0.00 0.04 0.96 0.00 0.00 0.00
#> TCGA.EL.A3GZ.01 3 0.4631 0.381 0.00 0.06 0.62 0.00 0.00 0.32
#> TCGA.EL.A3N2.01 3 0.3045 0.736 0.00 0.10 0.84 0.00 0.06 0.00
#> TCGA.KS.A4I7.01 3 0.6381 0.333 0.00 0.18 0.54 0.00 0.06 0.22
#> TCGA.ET.A25G.01 6 0.6273 0.460 0.00 0.18 0.20 0.00 0.06 0.56
#> TCGA.EM.A3FK.01 4 0.5361 0.770 0.00 0.44 0.00 0.48 0.06 0.02
#> TCGA.EM.A2CS.01 6 0.1480 0.914 0.00 0.04 0.02 0.00 0.00 0.94
#> TCGA.EL.A3MX.01 3 0.1807 0.797 0.00 0.06 0.92 0.00 0.02 0.00
#> TCGA.ET.A25R.01 6 0.4328 0.704 0.00 0.18 0.10 0.00 0.00 0.72
#> TCGA.EM.A3FJ.01 3 0.1807 0.797 0.00 0.06 0.92 0.00 0.02 0.00
#> TCGA.EM.A3FQ.06 3 0.1807 0.797 0.00 0.06 0.92 0.00 0.02 0.00
#> TCGA.FE.A235.01 3 0.4703 0.619 0.00 0.18 0.72 0.00 0.06 0.04
#> TCGA.ET.A25M.01 1 0.0547 0.953 0.98 0.02 0.00 0.00 0.00 0.00
#> TCGA.EL.A3MY.01 1 0.2793 0.823 0.80 0.20 0.00 0.00 0.00 0.00
#> TCGA.DE.A7U5.01 3 0.1807 0.797 0.00 0.06 0.92 0.00 0.02 0.00
#> TCGA.DE.A69J.01 3 0.1480 0.804 0.00 0.04 0.94 0.00 0.02 0.00
#> TCGA.ET.A25K.01 6 0.4393 0.699 0.00 0.14 0.14 0.00 0.00 0.72
#> TCGA.EM.A3FM.01 1 0.0547 0.953 0.98 0.02 0.00 0.00 0.00 0.00
#> TCGA.FE.A22Z.01 3 0.2350 0.773 0.00 0.10 0.88 0.00 0.02 0.00
#> TCGA.EL.A3MZ.01 1 0.2793 0.823 0.80 0.20 0.00 0.00 0.00 0.00
#> TCGA.ET.A25L.01 6 0.0547 0.930 0.00 0.00 0.02 0.00 0.00 0.98
#> TCGA.DJ.A2Q7.01 3 0.2474 0.768 0.00 0.08 0.88 0.00 0.04 0.00
#> TCGA.DE.A69K.01 3 0.3679 0.599 0.00 0.04 0.76 0.00 0.20 0.00
#> TCGA.4C.A93U.01 3 0.2350 0.773 0.00 0.10 0.88 0.00 0.02 0.00
#> TCGA.ET.A25N.01 3 0.3660 0.679 0.00 0.16 0.78 0.00 0.06 0.00
#> TCGA.EL.A3H7.01 3 0.1267 0.802 0.00 0.06 0.94 0.00 0.00 0.00
#> TCGA.EM.A3FO.01 1 0.0547 0.950 0.98 0.02 0.00 0.00 0.00 0.00
#> TCGA.ET.A25O.01 5 0.2941 0.884 0.00 0.00 0.22 0.00 0.78 0.00
#> TCGA.EL.A3GU.01 3 0.1807 0.797 0.00 0.06 0.92 0.00 0.02 0.00
#> TCGA.DJ.A2PY.01 3 0.2581 0.717 0.00 0.02 0.86 0.00 0.12 0.00
#> TCGA.EM.A22I.01 3 0.0547 0.811 0.00 0.02 0.98 0.00 0.00 0.00
#> TCGA.DE.A0XZ.01 3 0.1807 0.797 0.00 0.06 0.92 0.00 0.02 0.00
#> TCGA.EL.A3H4.01 6 0.1092 0.924 0.00 0.02 0.02 0.00 0.00 0.96
#> TCGA.EM.A2OX.01 1 0.1092 0.946 0.96 0.02 0.00 0.00 0.02 0.00
#> TCGA.EM.A3SX.01 6 0.0547 0.930 0.00 0.00 0.02 0.00 0.00 0.98
#> TCGA.EL.A3CR.01 6 0.4700 0.407 0.00 0.06 0.34 0.00 0.00 0.60
#> TCGA.DJ.A3V6.01 1 0.0547 0.950 0.98 0.02 0.00 0.00 0.00 0.00
#> TCGA.BJ.A18Z.01 1 0.0000 0.954 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.DJ.A3V0.01 1 0.1092 0.946 0.96 0.02 0.00 0.00 0.02 0.00
#> TCGA.EL.A3GY.01 3 0.1092 0.811 0.00 0.02 0.96 0.00 0.02 0.00
#> TCGA.EL.A3T8.01 1 0.0547 0.951 0.98 0.00 0.00 0.00 0.02 0.00
#> TCGA.EM.A22O.01 1 0.2631 0.844 0.82 0.18 0.00 0.00 0.00 0.00
#> TCGA.J8.A3YH.01 1 0.0000 0.954 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.EL.A3GX.01 3 0.0937 0.806 0.00 0.04 0.96 0.00 0.00 0.00
#> TCGA.DO.A1JZ.01 3 0.1480 0.809 0.00 0.04 0.94 0.00 0.02 0.00
#> TCGA.FY.A3YR.01 3 0.6012 0.445 0.00 0.18 0.60 0.00 0.06 0.16
#> TCGA.DO.A1K0.01 3 0.2094 0.796 0.00 0.08 0.90 0.00 0.02 0.00
#> TCGA.DJ.A3V5.01 6 0.0547 0.930 0.00 0.00 0.02 0.00 0.00 0.98
#> TCGA.IM.A3ED.01 3 0.0937 0.810 0.00 0.04 0.96 0.00 0.00 0.00
#> TCGA.FK.A3SE.01 6 0.4094 0.716 0.00 0.08 0.18 0.00 0.00 0.74
#> TCGA.EL.A3T7.01 6 0.6001 0.492 0.00 0.18 0.20 0.00 0.04 0.58
#> TCGA.E8.A3X7.01 6 0.0547 0.930 0.00 0.00 0.02 0.00 0.00 0.98
#> TCGA.ET.A3BQ.01 3 0.0937 0.806 0.00 0.04 0.96 0.00 0.00 0.00
#> TCGA.EL.A3H5.01 3 0.1807 0.797 0.00 0.06 0.92 0.00 0.02 0.00
#> TCGA.EM.A2P3.01 3 0.0547 0.811 0.00 0.02 0.98 0.00 0.00 0.00
#> TCGA.EL.A3D0.01 1 0.1865 0.929 0.92 0.04 0.00 0.00 0.04 0.00
#> TCGA.J8.A3YH.06 1 0.0547 0.953 0.98 0.02 0.00 0.00 0.00 0.00
#> TCGA.BJ.A3EZ.01 1 0.0547 0.953 0.98 0.02 0.00 0.00 0.00 0.00
#> TCGA.EM.A1CU.01 1 0.0000 0.954 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.EM.A3AN.01 6 0.0937 0.917 0.00 0.00 0.04 0.00 0.00 0.96
#> TCGA.EL.A3D6.01 6 0.0547 0.930 0.00 0.00 0.02 0.00 0.00 0.98
#> TCGA.DJ.A3UN.01 6 0.0547 0.930 0.00 0.00 0.02 0.00 0.00 0.98
#> TCGA.EL.A3CL.01 3 0.1267 0.811 0.00 0.06 0.94 0.00 0.00 0.00
#> TCGA.IM.A3U2.01 6 0.0547 0.930 0.00 0.00 0.02 0.00 0.00 0.98
#> TCGA.IM.A3U3.01 6 0.1092 0.924 0.00 0.02 0.02 0.00 0.00 0.96
#> TCGA.DJ.A1QE.01 3 0.1807 0.797 0.00 0.06 0.92 0.00 0.02 0.00
#> TCGA.FK.A3SB.01 3 0.1267 0.800 0.00 0.06 0.94 0.00 0.00 0.00
#> TCGA.DJ.A2PW.01 1 0.0547 0.953 0.98 0.02 0.00 0.00 0.00 0.00
#> TCGA.ET.A2MZ.01 1 0.1092 0.953 0.96 0.02 0.00 0.00 0.02 0.00
#> TCGA.FE.A233.01 5 0.3198 0.941 0.00 0.00 0.26 0.00 0.74 0.00
#> TCGA.EL.A3T9.01 6 0.0547 0.930 0.00 0.00 0.02 0.00 0.00 0.98
#> TCGA.DJ.A3UM.01 6 0.0547 0.930 0.00 0.00 0.02 0.00 0.00 0.98
#> TCGA.ET.A3BX.01 1 0.0000 0.954 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.DJ.A1QQ.01 1 0.0000 0.954 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.DJ.A1QO.01 1 0.0547 0.953 0.98 0.02 0.00 0.00 0.00 0.00
#> TCGA.BJ.A2NA.01 1 0.0937 0.947 0.96 0.04 0.00 0.00 0.00 0.00
#> TCGA.ET.A39J.01 4 0.0000 0.888 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.EL.A3CM.01 6 0.0547 0.930 0.00 0.00 0.02 0.00 0.00 0.98
#> TCGA.DJ.A3UO.01 1 0.1480 0.938 0.94 0.04 0.00 0.00 0.02 0.00
#> TCGA.ET.A39P.01 3 0.0937 0.806 0.00 0.04 0.96 0.00 0.00 0.00
#> TCGA.ET.A3BO.01 6 0.0547 0.930 0.00 0.00 0.02 0.00 0.00 0.98
#> TCGA.DJ.A1QI.01 5 0.3198 0.941 0.00 0.00 0.26 0.00 0.74 0.00
#> TCGA.EL.A3TB.01 6 0.0547 0.930 0.00 0.00 0.02 0.00 0.00 0.98
#> TCGA.DJ.A1QN.01 5 0.3198 0.941 0.00 0.00 0.26 0.00 0.74 0.00
#> TCGA.FE.A234.01 3 0.4094 0.594 0.00 0.08 0.74 0.00 0.18 0.00
#> TCGA.FE.A231.01 1 0.0000 0.954 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.ET.A3DW.01 1 0.1480 0.939 0.94 0.04 0.00 0.00 0.02 0.00
#> TCGA.ET.A3BT.01 6 0.0547 0.930 0.00 0.00 0.02 0.00 0.00 0.98
#> TCGA.EL.A3T3.01 6 0.1807 0.896 0.00 0.06 0.02 0.00 0.00 0.92
#> TCGA.ET.A39O.01 1 0.0547 0.953 0.98 0.02 0.00 0.00 0.00 0.00
#> TCGA.DJ.A1QH.01 3 0.3045 0.721 0.00 0.06 0.84 0.00 0.10 0.00
#> TCGA.DJ.A2PU.01 5 0.2941 0.884 0.00 0.00 0.22 0.00 0.78 0.00
#> TCGA.DJ.A2PN.01 3 0.1267 0.808 0.00 0.06 0.94 0.00 0.00 0.00
#> TCGA.FK.A3SG.01 6 0.0547 0.930 0.00 0.00 0.02 0.00 0.00 0.98
#> TCGA.FK.A3SH.01 6 0.0547 0.930 0.00 0.00 0.02 0.00 0.00 0.98
#> TCGA.DJ.A1QD.01 5 0.3198 0.941 0.00 0.00 0.26 0.00 0.74 0.00
#> TCGA.CE.A13K.01 6 0.2350 0.871 0.00 0.10 0.02 0.00 0.00 0.88
#> TCGA.EL.A3D1.01 1 0.1092 0.946 0.96 0.02 0.00 0.00 0.02 0.00
#> TCGA.BJ.A0ZH.01 6 0.2190 0.884 0.00 0.04 0.06 0.00 0.00 0.90
#> TCGA.DJ.A13T.01 3 0.6554 0.271 0.00 0.18 0.50 0.00 0.06 0.26
#> TCGA.FE.A3PD.01 6 0.2728 0.853 0.00 0.10 0.04 0.00 0.00 0.86
#> TCGA.FE.A3PC.01 6 0.4566 0.671 0.00 0.14 0.16 0.00 0.00 0.70
#> TCGA.ET.A39K.01 6 0.0547 0.930 0.00 0.00 0.02 0.00 0.00 0.98
#> TCGA.BJ.A3PU.01 1 0.2474 0.902 0.88 0.08 0.00 0.00 0.04 0.00
#> TCGA.BJ.A0ZB.01 1 0.0000 0.954 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.DJ.A2PR.01 1 0.0547 0.953 0.98 0.02 0.00 0.00 0.00 0.00
#> TCGA.FY.A3ON.01 1 0.1480 0.938 0.94 0.04 0.00 0.00 0.02 0.00
#> TCGA.DJ.A13V.01 6 0.1092 0.924 0.00 0.02 0.02 0.00 0.00 0.96
#> TCGA.FY.A3R8.01 3 0.4608 0.520 0.00 0.10 0.68 0.00 0.00 0.22
#> TCGA.EL.A3CP.01 3 0.0937 0.806 0.00 0.04 0.96 0.00 0.00 0.00
#> TCGA.DE.A0Y3.01 6 0.1092 0.924 0.00 0.02 0.02 0.00 0.00 0.96
#> TCGA.FY.A3RA.01 3 0.3270 0.725 0.00 0.12 0.82 0.00 0.06 0.00
#> TCGA.ET.A3BN.01 3 0.1267 0.800 0.00 0.06 0.94 0.00 0.00 0.00
#> TCGA.H2.A3RI.01 6 0.0547 0.930 0.00 0.00 0.02 0.00 0.00 0.98
#> TCGA.FE.A3PA.01 1 0.1092 0.946 0.96 0.02 0.00 0.00 0.02 0.00
#> TCGA.DE.A0Y2.01 3 0.5144 0.569 0.00 0.20 0.68 0.00 0.06 0.06
#> TCGA.ET.A3BU.01 1 0.0937 0.952 0.96 0.04 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.EL.A4K9.01 1 0.0000 0.954 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.KS.A41F.01 6 0.1006 0.897 0.00 0.00 0.00 0.02 0.00 0.96 0.02
#> TCGA.EL.A3ZM.01 1 0.4475 0.722 0.72 0.00 0.00 0.14 0.04 0.00 0.10
#> TCGA.EL.A3ZQ.01 6 0.0000 0.912 0.00 0.00 0.00 0.00 0.00 1.00 0.00
#> TCGA.ET.A40T.01 6 0.0000 0.912 0.00 0.00 0.00 0.00 0.00 1.00 0.00
#> TCGA.DE.A4MA.01 6 0.0504 0.905 0.00 0.00 0.00 0.00 0.00 0.98 0.02
#> TCGA.E8.A418.01 6 0.2016 0.836 0.00 0.00 0.00 0.04 0.00 0.90 0.06
#> TCGA.KS.A41J.01 6 0.0000 0.912 0.00 0.00 0.00 0.00 0.00 1.00 0.00
#> TCGA.DJ.A3VB.01 1 0.0504 0.951 0.98 0.00 0.00 0.00 0.02 0.00 0.00
#> TCGA.H2.A421.01 6 0.0504 0.905 0.00 0.00 0.00 0.00 0.00 0.98 0.02
#> TCGA.EL.A3ZO.01 6 0.0000 0.912 0.00 0.00 0.00 0.00 0.00 1.00 0.00
#> TCGA.DE.A4MD.01 1 0.4338 0.562 0.64 0.00 0.00 0.08 0.00 0.00 0.28
#> TCGA.DJ.A3VI.01 7 0.5750 0.602 0.00 0.00 0.38 0.02 0.00 0.18 0.42
#> TCGA.DJ.A3VA.01 6 0.0000 0.912 0.00 0.00 0.00 0.00 0.00 1.00 0.00
#> TCGA.L6.A4ET.01 5 0.5652 0.611 0.00 0.00 0.18 0.10 0.60 0.00 0.12
#> TCGA.DJ.A4V2.01 3 0.1166 0.761 0.00 0.00 0.94 0.00 0.00 0.00 0.06
#> TCGA.ET.A40Q.01 1 0.0000 0.954 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.EL.A4K7.01 1 0.1433 0.932 0.92 0.00 0.00 0.00 0.08 0.00 0.00
#> TCGA.J8.A3O2.06 1 0.0000 0.954 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.DJ.A3V7.01 6 0.0504 0.903 0.00 0.00 0.00 0.02 0.00 0.98 0.00
#> TCGA.EM.A4FN.01 5 0.2259 0.852 0.00 0.00 0.16 0.00 0.84 0.00 0.00
#> TCGA.EL.A4K1.01 3 0.0504 0.778 0.00 0.00 0.98 0.00 0.00 0.00 0.02
#> TCGA.H2.A422.01 7 0.4278 0.466 0.00 0.00 0.46 0.00 0.00 0.04 0.50
#> TCGA.J8.A3YF.01 1 0.3541 0.813 0.80 0.00 0.00 0.10 0.02 0.00 0.08
#> TCGA.DJ.A3VJ.01 1 0.0000 0.954 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.EL.A3ZP.01 1 0.0000 0.954 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.EM.A4FQ.01 3 0.2159 0.778 0.00 0.00 0.90 0.02 0.02 0.00 0.06
#> TCGA.EL.A3ZT.01 1 0.0863 0.945 0.96 0.00 0.00 0.00 0.04 0.00 0.00
#> TCGA.L6.A4EQ.01 1 0.1433 0.932 0.92 0.00 0.00 0.00 0.08 0.00 0.00
#> TCGA.DJ.A3VE.01 1 0.1433 0.932 0.92 0.00 0.00 0.00 0.08 0.00 0.00
#> TCGA.DE.A4MB.01 6 0.0000 0.912 0.00 0.00 0.00 0.00 0.00 1.00 0.00
#> TCGA.MK.A4N6.01 1 0.1928 0.902 0.90 0.00 0.00 0.08 0.02 0.00 0.00
#> TCGA.E8.A417.01 6 0.0000 0.912 0.00 0.00 0.00 0.00 0.00 1.00 0.00
#> TCGA.L6.A4EU.01 6 0.1664 0.865 0.00 0.00 0.02 0.00 0.00 0.92 0.06
#> TCGA.EL.A3ZL.01 6 0.0000 0.912 0.00 0.00 0.00 0.00 0.00 1.00 0.00
#> TCGA.J8.A4HW.01 3 0.4033 0.367 0.00 0.00 0.70 0.00 0.00 0.08 0.22
#> TCGA.BJ.A45J.01 6 0.0000 0.912 0.00 0.00 0.00 0.00 0.00 1.00 0.00
#> TCGA.CE.A482.01 6 0.0000 0.912 0.00 0.00 0.00 0.00 0.00 1.00 0.00
#> TCGA.DJ.A2Q6.01 6 0.1166 0.880 0.00 0.00 0.00 0.00 0.00 0.94 0.06
#> TCGA.DJ.A4UL.01 5 0.4100 0.840 0.00 0.00 0.10 0.10 0.76 0.00 0.04
#> TCGA.EL.A4KG.01 5 0.1671 0.898 0.00 0.00 0.10 0.00 0.90 0.00 0.00
#> TCGA.DJ.A2PQ.01 1 0.1433 0.932 0.92 0.00 0.00 0.00 0.08 0.00 0.00
#> TCGA.L6.A4EP.01 3 0.1166 0.765 0.00 0.00 0.94 0.00 0.00 0.00 0.06
#> TCGA.FY.A4B4.01 6 0.2376 0.814 0.00 0.00 0.00 0.02 0.00 0.86 0.12
#> TCGA.DE.A4MC.01 3 0.2376 0.756 0.00 0.00 0.86 0.02 0.00 0.00 0.12
#> TCGA.E3.A3E2.01 6 0.0000 0.912 0.00 0.00 0.00 0.00 0.00 1.00 0.00
#> TCGA.ET.A2MY.01 6 0.0000 0.912 0.00 0.00 0.00 0.00 0.00 1.00 0.00
#> TCGA.EL.A3H8.01 3 0.0863 0.773 0.00 0.00 0.96 0.00 0.00 0.00 0.04
#> TCGA.EL.A4JZ.01 3 0.1886 0.771 0.00 0.00 0.88 0.00 0.00 0.00 0.12
#> TCGA.KS.A4I9.01 3 0.0504 0.778 0.00 0.00 0.98 0.00 0.00 0.00 0.02
#> TCGA.EL.A3MW.01 3 0.0000 0.782 0.00 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.E3.A3DY.01 1 0.0000 0.954 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.DJ.A2Q4.01 1 0.0000 0.954 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.FY.A4B3.01 1 0.1433 0.932 0.92 0.00 0.00 0.00 0.08 0.00 0.00
#> TCGA.E3.A3E3.01 5 0.1671 0.898 0.00 0.00 0.10 0.00 0.90 0.00 0.00
#> TCGA.EM.A3AQ.01 4 0.4003 0.735 0.04 0.32 0.00 0.64 0.00 0.00 0.00
#> TCGA.EM.A4FM.01 3 0.2722 0.749 0.00 0.00 0.84 0.04 0.00 0.00 0.12
#> TCGA.MK.A4N9.01 3 0.0863 0.771 0.00 0.00 0.96 0.00 0.00 0.00 0.04
#> TCGA.KS.A4I1.01 7 0.5875 0.559 0.00 0.00 0.24 0.02 0.00 0.30 0.44
#> TCGA.E3.A3E5.01 1 0.0504 0.951 0.98 0.00 0.00 0.00 0.02 0.00 0.00
#> TCGA.BJ.A4O8.01 1 0.0504 0.952 0.98 0.00 0.00 0.00 0.02 0.00 0.00
#> TCGA.E3.A3E0.01 3 0.2376 0.697 0.00 0.00 0.86 0.02 0.00 0.00 0.12
#> TCGA.IM.A41Y.01 6 0.1363 0.883 0.00 0.00 0.00 0.02 0.00 0.94 0.04
#> TCGA.KS.A4I5.01 3 0.0863 0.771 0.00 0.00 0.96 0.00 0.00 0.00 0.04
#> TCGA.KS.A4IB.01 3 0.4278 -0.316 0.00 0.00 0.50 0.04 0.00 0.00 0.46
#> TCGA.EM.A4FF.01 3 0.2081 0.687 0.00 0.00 0.86 0.00 0.00 0.00 0.14
#> TCGA.EL.A4K0.01 3 0.4295 0.563 0.00 0.00 0.74 0.06 0.06 0.00 0.14
#> TCGA.FK.A4UB.01 1 0.0000 0.954 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.MK.A4N7.01 7 0.5342 0.370 0.00 0.00 0.18 0.00 0.00 0.40 0.42
#> TCGA.EL.A4K4.01 3 0.4684 -0.332 0.00 0.00 0.52 0.04 0.00 0.02 0.42
#> TCGA.EL.A3GS.01 3 0.0000 0.782 0.00 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.EL.A3GZ.01 3 0.4348 0.212 0.00 0.00 0.68 0.00 0.00 0.18 0.14
#> TCGA.EL.A3N2.01 3 0.3606 0.326 0.00 0.00 0.68 0.02 0.00 0.00 0.30
#> TCGA.KS.A4I7.01 7 0.5105 0.579 0.00 0.00 0.40 0.02 0.00 0.08 0.50
#> TCGA.ET.A25G.01 7 0.5381 0.436 0.00 0.00 0.12 0.02 0.00 0.36 0.50
#> TCGA.EM.A3FK.01 2 0.0000 0.000 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.EM.A2CS.01 6 0.1166 0.882 0.00 0.00 0.00 0.00 0.00 0.94 0.06
#> TCGA.EL.A3MX.01 3 0.2376 0.756 0.00 0.00 0.86 0.02 0.00 0.00 0.12
#> TCGA.ET.A25R.01 7 0.4266 0.196 0.00 0.00 0.04 0.00 0.00 0.44 0.52
#> TCGA.EM.A3FJ.01 3 0.1433 0.778 0.00 0.00 0.92 0.00 0.00 0.00 0.08
#> TCGA.EM.A3FQ.06 3 0.3228 0.724 0.00 0.00 0.80 0.02 0.02 0.00 0.16
#> TCGA.FE.A235.01 7 0.4283 0.316 0.00 0.00 0.48 0.04 0.00 0.00 0.48
#> TCGA.ET.A25M.01 1 0.0000 0.954 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.EL.A3MY.01 1 0.2654 0.871 0.86 0.00 0.00 0.10 0.02 0.00 0.02
#> TCGA.DE.A7U5.01 3 0.1671 0.771 0.00 0.00 0.90 0.00 0.00 0.00 0.10
#> TCGA.DE.A69J.01 3 0.1166 0.782 0.00 0.00 0.94 0.00 0.00 0.00 0.06
#> TCGA.ET.A25K.01 6 0.4514 -0.180 0.00 0.00 0.06 0.00 0.00 0.48 0.46
#> TCGA.EM.A3FM.01 1 0.0504 0.948 0.98 0.00 0.00 0.00 0.02 0.00 0.00
#> TCGA.FE.A22Z.01 3 0.2722 0.749 0.00 0.00 0.84 0.04 0.00 0.00 0.12
#> TCGA.EL.A3MZ.01 1 0.3315 0.835 0.82 0.00 0.00 0.08 0.02 0.00 0.08
#> TCGA.ET.A25L.01 6 0.0000 0.912 0.00 0.00 0.00 0.00 0.00 1.00 0.00
#> TCGA.DJ.A2Q7.01 3 0.4015 0.391 0.00 0.00 0.68 0.06 0.00 0.00 0.26
#> TCGA.DE.A69K.01 3 0.3770 0.630 0.00 0.00 0.74 0.00 0.18 0.00 0.08
#> TCGA.4C.A93U.01 3 0.2722 0.749 0.00 0.00 0.84 0.04 0.00 0.00 0.12
#> TCGA.ET.A25N.01 3 0.4278 -0.316 0.00 0.00 0.50 0.04 0.00 0.00 0.46
#> TCGA.EL.A3H7.01 3 0.1886 0.764 0.00 0.00 0.88 0.00 0.00 0.00 0.12
#> TCGA.EM.A3FO.01 1 0.0504 0.951 0.98 0.00 0.00 0.00 0.02 0.00 0.00
#> TCGA.ET.A25O.01 5 0.4405 0.818 0.00 0.00 0.08 0.10 0.74 0.00 0.08
#> TCGA.EL.A3GU.01 3 0.2376 0.756 0.00 0.00 0.86 0.02 0.00 0.00 0.12
#> TCGA.DJ.A2PY.01 3 0.3722 0.619 0.00 0.00 0.76 0.02 0.18 0.00 0.04
#> TCGA.EM.A22I.01 3 0.0504 0.778 0.00 0.00 0.98 0.00 0.00 0.00 0.02
#> TCGA.DE.A0XZ.01 3 0.1671 0.771 0.00 0.00 0.90 0.00 0.00 0.00 0.10
#> TCGA.EL.A3H4.01 6 0.0504 0.905 0.00 0.00 0.00 0.00 0.00 0.98 0.02
#> TCGA.EM.A2OX.01 1 0.0863 0.946 0.96 0.00 0.00 0.00 0.04 0.00 0.00
#> TCGA.EM.A3SX.01 6 0.0000 0.912 0.00 0.00 0.00 0.00 0.00 1.00 0.00
#> TCGA.EL.A3CR.01 6 0.5134 -0.212 0.00 0.00 0.40 0.00 0.00 0.46 0.14
#> TCGA.DJ.A3V6.01 1 0.0863 0.946 0.96 0.00 0.00 0.00 0.04 0.00 0.00
#> TCGA.BJ.A18Z.01 1 0.0504 0.948 0.98 0.00 0.00 0.00 0.02 0.00 0.00
#> TCGA.DJ.A3V0.01 1 0.1166 0.939 0.94 0.00 0.00 0.00 0.06 0.00 0.00
#> TCGA.EL.A3GY.01 3 0.0863 0.786 0.00 0.00 0.96 0.00 0.00 0.00 0.04
#> TCGA.EL.A3T8.01 1 0.0504 0.951 0.98 0.00 0.00 0.00 0.02 0.00 0.00
#> TCGA.EM.A22O.01 1 0.3289 0.836 0.82 0.00 0.00 0.10 0.02 0.00 0.06
#> TCGA.J8.A3YH.01 1 0.0000 0.954 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.EL.A3GX.01 3 0.1363 0.768 0.00 0.00 0.94 0.02 0.00 0.00 0.04
#> TCGA.DO.A1JZ.01 3 0.0504 0.785 0.00 0.00 0.98 0.00 0.00 0.00 0.02
#> TCGA.FY.A3YR.01 7 0.4487 0.552 0.00 0.00 0.42 0.00 0.00 0.06 0.52
#> TCGA.DO.A1K0.01 3 0.1363 0.781 0.00 0.00 0.94 0.00 0.04 0.00 0.02
#> TCGA.DJ.A3V5.01 6 0.0000 0.912 0.00 0.00 0.00 0.00 0.00 1.00 0.00
#> TCGA.IM.A3ED.01 3 0.0000 0.782 0.00 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.FK.A3SE.01 6 0.4587 0.510 0.00 0.00 0.10 0.02 0.00 0.68 0.20
#> TCGA.EL.A3T7.01 6 0.5635 -0.132 0.00 0.00 0.12 0.04 0.00 0.50 0.34
#> TCGA.E8.A3X7.01 6 0.0000 0.912 0.00 0.00 0.00 0.00 0.00 1.00 0.00
#> TCGA.ET.A3BQ.01 3 0.2769 0.717 0.00 0.00 0.86 0.04 0.02 0.00 0.08
#> TCGA.EL.A3H5.01 3 0.2376 0.756 0.00 0.00 0.86 0.02 0.00 0.00 0.12
#> TCGA.EM.A2P3.01 3 0.1363 0.783 0.00 0.00 0.94 0.02 0.00 0.00 0.04
#> TCGA.EL.A3D0.01 1 0.1433 0.932 0.92 0.00 0.00 0.00 0.08 0.00 0.00
#> TCGA.J8.A3YH.06 1 0.0000 0.954 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.BJ.A3EZ.01 1 0.0000 0.954 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.EM.A1CU.01 1 0.0000 0.954 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.EM.A3AN.01 6 0.0863 0.895 0.00 0.00 0.00 0.00 0.00 0.96 0.04
#> TCGA.EL.A3D6.01 6 0.0504 0.905 0.00 0.00 0.00 0.00 0.00 0.98 0.02
#> TCGA.DJ.A3UN.01 6 0.0000 0.912 0.00 0.00 0.00 0.00 0.00 1.00 0.00
#> TCGA.EL.A3CL.01 3 0.0863 0.786 0.00 0.00 0.96 0.00 0.00 0.00 0.04
#> TCGA.IM.A3U2.01 6 0.0000 0.912 0.00 0.00 0.00 0.00 0.00 1.00 0.00
#> TCGA.IM.A3U3.01 6 0.0000 0.912 0.00 0.00 0.00 0.00 0.00 1.00 0.00
#> TCGA.DJ.A1QE.01 3 0.2512 0.756 0.00 0.00 0.86 0.00 0.04 0.00 0.10
#> TCGA.FK.A3SB.01 3 0.2745 0.634 0.00 0.00 0.82 0.02 0.00 0.00 0.16
#> TCGA.DJ.A2PW.01 1 0.0000 0.954 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.ET.A2MZ.01 1 0.0504 0.952 0.98 0.00 0.00 0.00 0.02 0.00 0.00
#> TCGA.FE.A233.01 5 0.1671 0.898 0.00 0.00 0.10 0.00 0.90 0.00 0.00
#> TCGA.EL.A3T9.01 6 0.0000 0.912 0.00 0.00 0.00 0.00 0.00 1.00 0.00
#> TCGA.DJ.A3UM.01 6 0.0000 0.912 0.00 0.00 0.00 0.00 0.00 1.00 0.00
#> TCGA.ET.A3BX.01 1 0.0000 0.954 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.DJ.A1QQ.01 1 0.0000 0.954 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.DJ.A1QO.01 1 0.0000 0.954 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.BJ.A2NA.01 1 0.0000 0.954 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.ET.A39J.01 4 0.4003 0.728 0.00 0.32 0.00 0.64 0.04 0.00 0.00
#> TCGA.EL.A3CM.01 6 0.0000 0.912 0.00 0.00 0.00 0.00 0.00 1.00 0.00
#> TCGA.DJ.A3UO.01 1 0.1433 0.932 0.92 0.00 0.00 0.00 0.08 0.00 0.00
#> TCGA.ET.A39P.01 3 0.0504 0.782 0.00 0.00 0.98 0.02 0.00 0.00 0.00
#> TCGA.ET.A3BO.01 6 0.0000 0.912 0.00 0.00 0.00 0.00 0.00 1.00 0.00
#> TCGA.DJ.A1QI.01 5 0.1671 0.898 0.00 0.00 0.10 0.00 0.90 0.00 0.00
#> TCGA.EL.A3TB.01 6 0.0000 0.912 0.00 0.00 0.00 0.00 0.00 1.00 0.00
#> TCGA.DJ.A1QN.01 5 0.1671 0.898 0.00 0.00 0.10 0.00 0.90 0.00 0.00
#> TCGA.FE.A234.01 3 0.4908 0.478 0.00 0.00 0.62 0.02 0.26 0.00 0.10
#> TCGA.FE.A231.01 1 0.0000 0.954 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.ET.A3DW.01 1 0.0863 0.945 0.96 0.00 0.00 0.00 0.04 0.00 0.00
#> TCGA.ET.A3BT.01 6 0.0000 0.912 0.00 0.00 0.00 0.00 0.00 1.00 0.00
#> TCGA.EL.A3T3.01 6 0.2081 0.812 0.00 0.00 0.00 0.00 0.00 0.86 0.14
#> TCGA.ET.A39O.01 1 0.1006 0.939 0.96 0.00 0.00 0.02 0.02 0.00 0.00
#> TCGA.DJ.A1QH.01 3 0.4308 0.628 0.00 0.00 0.72 0.02 0.16 0.00 0.10
#> TCGA.DJ.A2PU.01 5 0.4100 0.840 0.00 0.00 0.10 0.10 0.76 0.00 0.04
#> TCGA.DJ.A2PN.01 3 0.0504 0.785 0.00 0.00 0.98 0.00 0.00 0.00 0.02
#> TCGA.FK.A3SG.01 6 0.0000 0.912 0.00 0.00 0.00 0.00 0.00 1.00 0.00
#> TCGA.FK.A3SH.01 6 0.0000 0.912 0.00 0.00 0.00 0.00 0.00 1.00 0.00
#> TCGA.DJ.A1QD.01 5 0.1671 0.898 0.00 0.00 0.10 0.00 0.90 0.00 0.00
#> TCGA.CE.A13K.01 6 0.2708 0.708 0.00 0.00 0.00 0.00 0.00 0.78 0.22
#> TCGA.EL.A3D1.01 1 0.0504 0.951 0.98 0.00 0.00 0.00 0.02 0.00 0.00
#> TCGA.BJ.A0ZH.01 6 0.2259 0.786 0.00 0.00 0.00 0.00 0.00 0.84 0.16
#> TCGA.DJ.A13T.01 7 0.5483 0.628 0.00 0.00 0.34 0.02 0.00 0.14 0.50
#> TCGA.FE.A3PD.01 6 0.3745 0.588 0.00 0.00 0.00 0.04 0.00 0.70 0.26
#> TCGA.FE.A3PC.01 6 0.4587 0.511 0.00 0.00 0.10 0.02 0.00 0.68 0.20
#> TCGA.ET.A39K.01 6 0.0504 0.905 0.00 0.00 0.00 0.00 0.00 0.98 0.02
#> TCGA.BJ.A3PU.01 1 0.2016 0.917 0.90 0.00 0.00 0.04 0.06 0.00 0.00
#> TCGA.BJ.A0ZB.01 1 0.1006 0.939 0.96 0.00 0.00 0.02 0.02 0.00 0.00
#> TCGA.DJ.A2PR.01 1 0.0000 0.954 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.FY.A3ON.01 1 0.1433 0.932 0.92 0.00 0.00 0.00 0.08 0.00 0.00
#> TCGA.DJ.A13V.01 6 0.1166 0.881 0.00 0.00 0.00 0.00 0.00 0.94 0.06
#> TCGA.FY.A3R8.01 3 0.4587 0.459 0.00 0.00 0.68 0.02 0.00 0.10 0.20
#> TCGA.EL.A3CP.01 3 0.3370 0.611 0.00 0.00 0.78 0.06 0.00 0.00 0.16
#> TCGA.DE.A0Y3.01 6 0.1166 0.880 0.00 0.00 0.00 0.00 0.00 0.94 0.06
#> TCGA.FY.A3RA.01 3 0.4832 0.100 0.00 0.00 0.58 0.04 0.04 0.00 0.34
#> TCGA.ET.A3BN.01 3 0.0504 0.778 0.00 0.00 0.98 0.00 0.00 0.00 0.02
#> TCGA.H2.A3RI.01 6 0.0504 0.904 0.00 0.00 0.00 0.00 0.00 0.98 0.02
#> TCGA.FE.A3PA.01 1 0.0863 0.946 0.96 0.00 0.00 0.00 0.04 0.00 0.00
#> TCGA.DE.A0Y2.01 7 0.4701 0.453 0.00 0.00 0.44 0.04 0.00 0.02 0.50
#> TCGA.ET.A3BU.01 1 0.0000 0.954 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.EL.A4K9.01 1 0.0000 0.92585 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.KS.A41F.01 8 0.2648 0.83909 0.00 0.00 0.00 0.00 0.00 0.08 0.08 0.84
#> TCGA.EL.A3ZM.01 1 0.3514 0.61117 0.64 0.00 0.00 0.00 0.00 0.34 0.02 0.00
#> TCGA.EL.A3ZQ.01 8 0.0000 0.91128 0.00 0.00 0.00 0.00 0.00 0.00 0.00 1.00
#> TCGA.ET.A40T.01 8 0.0000 0.91128 0.00 0.00 0.00 0.00 0.00 0.00 0.00 1.00
#> TCGA.DE.A4MA.01 8 0.0808 0.90074 0.00 0.00 0.00 0.00 0.00 0.00 0.04 0.96
#> TCGA.E8.A418.01 8 0.3601 0.68563 0.00 0.02 0.00 0.00 0.00 0.16 0.06 0.76
#> TCGA.KS.A41J.01 8 0.0000 0.91128 0.00 0.00 0.00 0.00 0.00 0.00 0.00 1.00
#> TCGA.DJ.A3VB.01 1 0.0808 0.91971 0.96 0.00 0.00 0.00 0.00 0.00 0.04 0.00
#> TCGA.H2.A421.01 8 0.1804 0.87396 0.00 0.00 0.00 0.00 0.00 0.02 0.08 0.90
#> TCGA.EL.A3ZO.01 8 0.0000 0.91128 0.00 0.00 0.00 0.00 0.00 0.00 0.00 1.00
#> TCGA.DE.A4MD.01 1 0.6376 0.30032 0.50 0.08 0.00 0.00 0.06 0.22 0.14 0.00
#> TCGA.DJ.A3VI.01 7 0.5839 0.59483 0.00 0.02 0.38 0.00 0.00 0.04 0.42 0.14
#> TCGA.DJ.A3VA.01 8 0.0000 0.91128 0.00 0.00 0.00 0.00 0.00 0.00 0.00 1.00
#> TCGA.L6.A4ET.01 5 0.5451 0.59062 0.00 0.00 0.12 0.00 0.58 0.18 0.12 0.00
#> TCGA.DJ.A4V2.01 3 0.1275 0.76989 0.00 0.00 0.94 0.00 0.00 0.02 0.04 0.00
#> TCGA.ET.A40Q.01 1 0.0941 0.91588 0.96 0.00 0.00 0.00 0.00 0.02 0.02 0.00
#> TCGA.EL.A4K7.01 1 0.1341 0.90196 0.92 0.00 0.00 0.00 0.00 0.00 0.08 0.00
#> TCGA.J8.A3O2.06 1 0.0471 0.92179 0.98 0.00 0.00 0.00 0.00 0.00 0.02 0.00
#> TCGA.DJ.A3V7.01 8 0.1563 0.85173 0.00 0.00 0.00 0.00 0.00 0.10 0.00 0.90
#> TCGA.EM.A4FN.01 5 0.1091 0.85840 0.00 0.00 0.06 0.00 0.94 0.00 0.00 0.00
#> TCGA.EL.A4K1.01 3 0.1091 0.76306 0.00 0.00 0.94 0.00 0.00 0.00 0.06 0.00
#> TCGA.H2.A422.01 7 0.5039 0.62580 0.00 0.02 0.32 0.00 0.00 0.02 0.56 0.08
#> TCGA.J8.A3YF.01 1 0.3142 0.60039 0.64 0.00 0.00 0.00 0.00 0.36 0.00 0.00
#> TCGA.DJ.A3VJ.01 1 0.0471 0.92179 0.98 0.00 0.00 0.00 0.00 0.00 0.02 0.00
#> TCGA.EL.A3ZP.01 1 0.0000 0.92585 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.EM.A4FQ.01 3 0.1275 0.76859 0.00 0.00 0.94 0.00 0.00 0.04 0.02 0.00
#> TCGA.EL.A3ZT.01 1 0.1557 0.90787 0.92 0.00 0.00 0.00 0.00 0.02 0.06 0.00
#> TCGA.L6.A4EQ.01 1 0.1563 0.89443 0.90 0.00 0.00 0.00 0.00 0.00 0.10 0.00
#> TCGA.DJ.A3VE.01 1 0.1341 0.90196 0.92 0.00 0.00 0.00 0.00 0.00 0.08 0.00
#> TCGA.DE.A4MB.01 8 0.0941 0.89528 0.00 0.00 0.00 0.00 0.00 0.02 0.02 0.96
#> TCGA.MK.A4N6.01 1 0.1947 0.85868 0.86 0.00 0.00 0.00 0.00 0.14 0.00 0.00
#> TCGA.E8.A417.01 8 0.0000 0.91128 0.00 0.00 0.00 0.00 0.00 0.00 0.00 1.00
#> TCGA.L6.A4EU.01 8 0.2484 0.84010 0.00 0.00 0.02 0.00 0.00 0.02 0.10 0.86
#> TCGA.EL.A3ZL.01 8 0.0000 0.91128 0.00 0.00 0.00 0.00 0.00 0.00 0.00 1.00
#> TCGA.J8.A4HW.01 3 0.4313 0.37636 0.00 0.02 0.70 0.00 0.00 0.02 0.20 0.06
#> TCGA.BJ.A45J.01 8 0.0000 0.91128 0.00 0.00 0.00 0.00 0.00 0.00 0.00 1.00
#> TCGA.CE.A482.01 8 0.0000 0.91128 0.00 0.00 0.00 0.00 0.00 0.00 0.00 1.00
#> TCGA.DJ.A2Q6.01 8 0.1804 0.87396 0.00 0.00 0.00 0.00 0.00 0.02 0.08 0.90
#> TCGA.DJ.A4UL.01 5 0.5269 0.71077 0.00 0.10 0.06 0.00 0.62 0.20 0.02 0.00
#> TCGA.EL.A4KG.01 5 0.1557 0.85227 0.00 0.00 0.06 0.00 0.92 0.02 0.00 0.00
#> TCGA.DJ.A2PQ.01 1 0.1563 0.89443 0.90 0.00 0.00 0.00 0.00 0.00 0.10 0.00
#> TCGA.L6.A4EP.01 3 0.1765 0.72646 0.00 0.00 0.88 0.00 0.00 0.00 0.12 0.00
#> TCGA.FY.A4B4.01 8 0.2569 0.79656 0.00 0.00 0.02 0.00 0.00 0.00 0.16 0.82
#> TCGA.DE.A4MC.01 3 0.2807 0.72647 0.00 0.02 0.84 0.00 0.00 0.10 0.04 0.00
#> TCGA.E3.A3E2.01 8 0.0471 0.90681 0.00 0.00 0.00 0.00 0.00 0.00 0.02 0.98
#> TCGA.ET.A2MY.01 8 0.0000 0.91128 0.00 0.00 0.00 0.00 0.00 0.00 0.00 1.00
#> TCGA.EL.A3H8.01 3 0.1887 0.75775 0.00 0.00 0.90 0.00 0.00 0.04 0.06 0.00
#> TCGA.EL.A4JZ.01 3 0.1557 0.76230 0.00 0.02 0.92 0.00 0.00 0.00 0.06 0.00
#> TCGA.KS.A4I9.01 3 0.0808 0.76842 0.00 0.00 0.96 0.00 0.00 0.04 0.00 0.00
#> TCGA.EL.A3MW.01 3 0.0808 0.76564 0.00 0.00 0.96 0.00 0.00 0.00 0.04 0.00
#> TCGA.E3.A3DY.01 1 0.0000 0.92585 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.DJ.A2Q4.01 1 0.0000 0.92585 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.FY.A4B3.01 1 0.1563 0.89443 0.90 0.00 0.00 0.00 0.00 0.00 0.10 0.00
#> TCGA.E3.A3E3.01 5 0.1091 0.85840 0.00 0.00 0.06 0.00 0.94 0.00 0.00 0.00
#> TCGA.EM.A3AQ.01 4 0.0000 1.00000 0.00 0.00 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.EM.A4FM.01 3 0.3758 0.67400 0.00 0.04 0.76 0.00 0.00 0.14 0.06 0.00
#> TCGA.MK.A4N9.01 3 0.1804 0.74688 0.00 0.00 0.90 0.00 0.00 0.02 0.08 0.00
#> TCGA.KS.A4I1.01 7 0.5610 0.62193 0.00 0.02 0.32 0.00 0.00 0.02 0.48 0.16
#> TCGA.E3.A3E5.01 1 0.0000 0.92585 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.BJ.A4O8.01 1 0.1341 0.90856 0.92 0.00 0.00 0.00 0.00 0.00 0.08 0.00
#> TCGA.E3.A3E0.01 3 0.2818 0.69030 0.00 0.00 0.82 0.00 0.00 0.06 0.12 0.00
#> TCGA.IM.A41Y.01 8 0.0808 0.90165 0.00 0.00 0.00 0.00 0.00 0.00 0.04 0.96
#> TCGA.KS.A4I5.01 3 0.1607 0.75869 0.00 0.00 0.92 0.00 0.00 0.04 0.04 0.00
#> TCGA.KS.A4IB.01 7 0.4358 0.35280 0.00 0.04 0.40 0.00 0.00 0.02 0.54 0.00
#> TCGA.EM.A4FF.01 3 0.2940 0.71083 0.00 0.02 0.84 0.00 0.00 0.02 0.10 0.02
#> TCGA.EL.A4K0.01 3 0.3314 0.68205 0.00 0.00 0.80 0.00 0.02 0.10 0.08 0.00
#> TCGA.FK.A4UB.01 1 0.0000 0.92585 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.MK.A4N7.01 7 0.6340 0.50393 0.00 0.02 0.24 0.00 0.00 0.06 0.38 0.30
#> TCGA.EL.A4K4.01 3 0.4199 0.29204 0.00 0.00 0.60 0.00 0.00 0.08 0.32 0.00
#> TCGA.EL.A3GS.01 3 0.1557 0.76568 0.00 0.00 0.92 0.00 0.00 0.02 0.06 0.00
#> TCGA.EL.A3GZ.01 3 0.4428 0.49819 0.00 0.02 0.72 0.00 0.00 0.04 0.14 0.08
#> TCGA.EL.A3N2.01 3 0.3293 0.55808 0.00 0.00 0.74 0.00 0.00 0.04 0.22 0.00
#> TCGA.KS.A4I7.01 7 0.4612 0.63673 0.00 0.04 0.24 0.00 0.00 0.00 0.64 0.08
#> TCGA.ET.A25G.01 7 0.4916 0.55076 0.00 0.04 0.14 0.00 0.00 0.00 0.62 0.20
#> TCGA.EM.A3FK.01 2 0.2756 0.00000 0.00 0.74 0.00 0.26 0.00 0.00 0.00 0.00
#> TCGA.EM.A2CS.01 8 0.2025 0.86010 0.00 0.00 0.00 0.00 0.00 0.02 0.10 0.88
#> TCGA.EL.A3MX.01 3 0.3270 0.70378 0.00 0.02 0.80 0.00 0.00 0.12 0.06 0.00
#> TCGA.ET.A25R.01 7 0.4077 0.28284 0.00 0.00 0.02 0.00 0.00 0.02 0.56 0.40
#> TCGA.EM.A3FJ.01 3 0.1091 0.76563 0.00 0.00 0.94 0.00 0.00 0.06 0.00 0.00
#> TCGA.EM.A3FQ.06 3 0.2624 0.74073 0.00 0.02 0.86 0.00 0.00 0.06 0.06 0.00
#> TCGA.FE.A235.01 7 0.4777 0.42877 0.00 0.00 0.40 0.00 0.00 0.08 0.50 0.02
#> TCGA.ET.A25M.01 1 0.0000 0.92585 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.EL.A3MY.01 1 0.3142 0.60039 0.64 0.00 0.00 0.00 0.00 0.36 0.00 0.00
#> TCGA.DE.A7U5.01 3 0.2348 0.74955 0.00 0.02 0.88 0.00 0.00 0.04 0.06 0.00
#> TCGA.DE.A69J.01 3 0.1091 0.76563 0.00 0.00 0.94 0.00 0.00 0.06 0.00 0.00
#> TCGA.ET.A25K.01 7 0.4940 0.33876 0.00 0.00 0.10 0.00 0.00 0.02 0.48 0.40
#> TCGA.EM.A3FM.01 1 0.0000 0.92585 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.FE.A22Z.01 3 0.3758 0.67400 0.00 0.04 0.76 0.00 0.00 0.14 0.06 0.00
#> TCGA.EL.A3MZ.01 1 0.3015 0.65389 0.68 0.00 0.00 0.00 0.00 0.32 0.00 0.00
#> TCGA.ET.A25L.01 8 0.0000 0.91128 0.00 0.00 0.00 0.00 0.00 0.00 0.00 1.00
#> TCGA.DJ.A2Q7.01 3 0.3856 0.57845 0.00 0.00 0.70 0.00 0.00 0.10 0.20 0.00
#> TCGA.DE.A69K.01 3 0.3504 0.55531 0.00 0.00 0.70 0.00 0.26 0.04 0.00 0.00
#> TCGA.4C.A93U.01 3 0.3651 0.66824 0.00 0.04 0.76 0.00 0.00 0.16 0.04 0.00
#> TCGA.ET.A25N.01 3 0.4619 -0.21724 0.00 0.02 0.48 0.00 0.00 0.06 0.44 0.00
#> TCGA.EL.A3H7.01 3 0.3270 0.70378 0.00 0.02 0.80 0.00 0.00 0.12 0.06 0.00
#> TCGA.EM.A3FO.01 1 0.0000 0.92585 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.ET.A25O.01 5 0.5040 0.69277 0.00 0.10 0.06 0.00 0.60 0.24 0.00 0.00
#> TCGA.EL.A3GU.01 3 0.3270 0.70378 0.00 0.02 0.80 0.00 0.00 0.12 0.06 0.00
#> TCGA.DJ.A2PY.01 3 0.5111 0.47766 0.00 0.00 0.60 0.00 0.22 0.12 0.06 0.00
#> TCGA.EM.A22I.01 3 0.1341 0.75736 0.00 0.00 0.92 0.00 0.00 0.00 0.08 0.00
#> TCGA.DE.A0XZ.01 3 0.1408 0.76665 0.00 0.02 0.94 0.00 0.00 0.02 0.02 0.00
#> TCGA.EL.A3H4.01 8 0.1804 0.87396 0.00 0.00 0.00 0.00 0.00 0.02 0.08 0.90
#> TCGA.EM.A2OX.01 1 0.1091 0.91172 0.94 0.00 0.00 0.00 0.00 0.00 0.06 0.00
#> TCGA.EM.A3SX.01 8 0.0000 0.91128 0.00 0.00 0.00 0.00 0.00 0.00 0.00 1.00
#> TCGA.EL.A3CR.01 3 0.5859 -0.07416 0.00 0.02 0.50 0.00 0.00 0.10 0.08 0.30
#> TCGA.DJ.A3V6.01 1 0.1091 0.91172 0.94 0.00 0.00 0.00 0.00 0.00 0.06 0.00
#> TCGA.BJ.A18Z.01 1 0.0808 0.91595 0.96 0.00 0.00 0.00 0.00 0.04 0.00 0.00
#> TCGA.DJ.A3V0.01 1 0.2224 0.87649 0.86 0.00 0.00 0.00 0.00 0.02 0.12 0.00
#> TCGA.EL.A3GY.01 3 0.0000 0.76994 0.00 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.EL.A3T8.01 1 0.0000 0.92585 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.EM.A22O.01 1 0.3746 0.61226 0.64 0.00 0.00 0.00 0.00 0.32 0.04 0.00
#> TCGA.J8.A3YH.01 1 0.0000 0.92585 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.EL.A3GX.01 3 0.2407 0.74270 0.00 0.00 0.86 0.00 0.00 0.08 0.06 0.00
#> TCGA.DO.A1JZ.01 3 0.0808 0.77222 0.00 0.00 0.96 0.00 0.00 0.04 0.00 0.00
#> TCGA.FY.A3YR.01 7 0.3991 0.63143 0.00 0.00 0.32 0.00 0.00 0.00 0.62 0.06
#> TCGA.DO.A1K0.01 3 0.2348 0.76323 0.00 0.00 0.88 0.00 0.04 0.06 0.02 0.00
#> TCGA.DJ.A3V5.01 8 0.0000 0.91128 0.00 0.00 0.00 0.00 0.00 0.00 0.00 1.00
#> TCGA.IM.A3ED.01 3 0.0471 0.76747 0.00 0.00 0.98 0.00 0.00 0.00 0.02 0.00
#> TCGA.FK.A3SE.01 8 0.4757 0.09237 0.00 0.00 0.20 0.00 0.00 0.00 0.24 0.56
#> TCGA.EL.A3T7.01 7 0.5493 0.48152 0.00 0.00 0.12 0.00 0.00 0.06 0.48 0.34
#> TCGA.E8.A3X7.01 8 0.0000 0.91128 0.00 0.00 0.00 0.00 0.00 0.00 0.00 1.00
#> TCGA.ET.A3BQ.01 3 0.2862 0.70365 0.00 0.00 0.82 0.00 0.00 0.10 0.08 0.00
#> TCGA.EL.A3H5.01 3 0.3270 0.70378 0.00 0.02 0.80 0.00 0.00 0.12 0.06 0.00
#> TCGA.EM.A2P3.01 3 0.2020 0.76309 0.00 0.02 0.90 0.00 0.00 0.02 0.06 0.00
#> TCGA.EL.A3D0.01 1 0.1563 0.89443 0.90 0.00 0.00 0.00 0.00 0.00 0.10 0.00
#> TCGA.J8.A3YH.06 1 0.0000 0.92585 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.BJ.A3EZ.01 1 0.0000 0.92585 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.EM.A1CU.01 1 0.0000 0.92585 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.EM.A3AN.01 8 0.2265 0.85744 0.00 0.00 0.02 0.00 0.00 0.02 0.08 0.88
#> TCGA.EL.A3D6.01 8 0.1275 0.89462 0.00 0.00 0.00 0.00 0.00 0.02 0.04 0.94
#> TCGA.DJ.A3UN.01 8 0.0000 0.91128 0.00 0.00 0.00 0.00 0.00 0.00 0.00 1.00
#> TCGA.EL.A3CL.01 3 0.0808 0.76564 0.00 0.00 0.96 0.00 0.00 0.00 0.04 0.00
#> TCGA.IM.A3U2.01 8 0.0471 0.90185 0.00 0.00 0.00 0.00 0.00 0.00 0.02 0.98
#> TCGA.IM.A3U3.01 8 0.0941 0.89752 0.00 0.00 0.00 0.00 0.00 0.02 0.02 0.96
#> TCGA.DJ.A1QE.01 3 0.1887 0.75144 0.00 0.00 0.90 0.00 0.04 0.06 0.00 0.00
#> TCGA.FK.A3SB.01 3 0.3227 0.67570 0.00 0.00 0.78 0.00 0.00 0.08 0.14 0.00
#> TCGA.DJ.A2PW.01 1 0.0000 0.92585 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.ET.A2MZ.01 1 0.1275 0.91229 0.94 0.00 0.00 0.00 0.00 0.02 0.04 0.00
#> TCGA.FE.A233.01 5 0.1557 0.84763 0.00 0.00 0.06 0.00 0.92 0.02 0.00 0.00
#> TCGA.EL.A3T9.01 8 0.0000 0.91128 0.00 0.00 0.00 0.00 0.00 0.00 0.00 1.00
#> TCGA.DJ.A3UM.01 8 0.0000 0.91128 0.00 0.00 0.00 0.00 0.00 0.00 0.00 1.00
#> TCGA.ET.A3BX.01 1 0.0000 0.92585 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.DJ.A1QQ.01 1 0.0000 0.92585 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.DJ.A1QO.01 1 0.0000 0.92585 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.BJ.A2NA.01 1 0.0471 0.92126 0.98 0.00 0.00 0.00 0.00 0.02 0.00 0.00
#> TCGA.ET.A39J.01 4 0.0000 1.00000 0.00 0.00 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.EL.A3CM.01 8 0.0000 0.91128 0.00 0.00 0.00 0.00 0.00 0.00 0.00 1.00
#> TCGA.DJ.A3UO.01 1 0.1563 0.89358 0.90 0.00 0.00 0.00 0.00 0.00 0.10 0.00
#> TCGA.ET.A39P.01 3 0.2132 0.75174 0.00 0.00 0.88 0.00 0.00 0.08 0.04 0.00
#> TCGA.ET.A3BO.01 8 0.0000 0.91128 0.00 0.00 0.00 0.00 0.00 0.00 0.00 1.00
#> TCGA.DJ.A1QI.01 5 0.1091 0.85840 0.00 0.00 0.06 0.00 0.94 0.00 0.00 0.00
#> TCGA.EL.A3TB.01 8 0.0000 0.91128 0.00 0.00 0.00 0.00 0.00 0.00 0.00 1.00
#> TCGA.DJ.A1QN.01 5 0.1091 0.85840 0.00 0.00 0.06 0.00 0.94 0.00 0.00 0.00
#> TCGA.FE.A234.01 3 0.3943 0.28531 0.00 0.00 0.56 0.00 0.40 0.04 0.00 0.00
#> TCGA.FE.A231.01 1 0.0000 0.92585 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.ET.A3DW.01 1 0.1887 0.89040 0.90 0.00 0.00 0.00 0.00 0.06 0.04 0.00
#> TCGA.ET.A3BT.01 8 0.0000 0.91128 0.00 0.00 0.00 0.00 0.00 0.00 0.00 1.00
#> TCGA.EL.A3T3.01 8 0.2569 0.78084 0.00 0.02 0.00 0.00 0.00 0.00 0.16 0.82
#> TCGA.ET.A39O.01 1 0.1275 0.90855 0.94 0.00 0.00 0.00 0.00 0.04 0.02 0.00
#> TCGA.DJ.A1QH.01 3 0.4835 0.50285 0.00 0.02 0.64 0.00 0.22 0.10 0.02 0.00
#> TCGA.DJ.A2PU.01 5 0.5153 0.72472 0.00 0.10 0.06 0.00 0.64 0.18 0.02 0.00
#> TCGA.DJ.A2PN.01 3 0.1275 0.77062 0.00 0.00 0.94 0.00 0.00 0.04 0.02 0.00
#> TCGA.FK.A3SG.01 8 0.0000 0.91128 0.00 0.00 0.00 0.00 0.00 0.00 0.00 1.00
#> TCGA.FK.A3SH.01 8 0.0000 0.91128 0.00 0.00 0.00 0.00 0.00 0.00 0.00 1.00
#> TCGA.DJ.A1QD.01 5 0.1091 0.85840 0.00 0.00 0.06 0.00 0.94 0.00 0.00 0.00
#> TCGA.CE.A13K.01 8 0.2650 0.70744 0.00 0.00 0.00 0.00 0.00 0.00 0.24 0.76
#> TCGA.EL.A3D1.01 1 0.0000 0.92585 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.BJ.A0ZH.01 8 0.2569 0.80324 0.00 0.00 0.00 0.00 0.00 0.02 0.16 0.82
#> TCGA.DJ.A13T.01 7 0.4276 0.64006 0.00 0.02 0.28 0.00 0.00 0.00 0.64 0.06
#> TCGA.FE.A3PD.01 8 0.3594 0.57559 0.00 0.00 0.00 0.00 0.00 0.04 0.28 0.68
#> TCGA.FE.A3PC.01 8 0.5159 -0.00418 0.00 0.00 0.16 0.00 0.00 0.02 0.30 0.52
#> TCGA.ET.A39K.01 8 0.1804 0.87396 0.00 0.00 0.00 0.00 0.00 0.02 0.08 0.90
#> TCGA.BJ.A3PU.01 1 0.3619 0.77805 0.74 0.00 0.00 0.00 0.00 0.14 0.12 0.00
#> TCGA.BJ.A0ZB.01 1 0.0000 0.92585 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.DJ.A2PR.01 1 0.0000 0.92585 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.FY.A3ON.01 1 0.1765 0.88376 0.88 0.00 0.00 0.00 0.00 0.00 0.12 0.00
#> TCGA.DJ.A13V.01 8 0.1563 0.87216 0.00 0.00 0.00 0.00 0.00 0.00 0.10 0.90
#> TCGA.FY.A3R8.01 3 0.5178 0.31507 0.00 0.02 0.64 0.00 0.00 0.08 0.18 0.08
#> TCGA.EL.A3CP.01 3 0.2862 0.69696 0.00 0.00 0.82 0.00 0.00 0.10 0.08 0.00
#> TCGA.DE.A0Y3.01 8 0.1765 0.86287 0.00 0.00 0.00 0.00 0.00 0.00 0.12 0.88
#> TCGA.FY.A3RA.01 3 0.5363 0.19844 0.00 0.00 0.50 0.00 0.04 0.14 0.32 0.00
#> TCGA.ET.A3BN.01 3 0.2648 0.73199 0.00 0.00 0.84 0.00 0.00 0.08 0.08 0.00
#> TCGA.H2.A3RI.01 8 0.1091 0.89286 0.00 0.00 0.00 0.00 0.00 0.00 0.06 0.94
#> TCGA.FE.A3PA.01 1 0.0808 0.91578 0.96 0.00 0.00 0.00 0.00 0.00 0.04 0.00
#> TCGA.DE.A0Y2.01 7 0.4995 0.55811 0.00 0.00 0.36 0.00 0.00 0.08 0.52 0.04
#> TCGA.ET.A3BU.01 1 0.0000 0.92585 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: Node03. Child nodes: Node0111-leaf , Node0112-leaf , Node0113-leaf , Node0114-leaf , Node0131-leaf , Node0132-leaf , Node0133-leaf , Node0141-leaf , Node0142-leaf , Node0143-leaf , Node0211-leaf , Node0212-leaf , Node0221-leaf , Node0222-leaf , Node0223-leaf , Node0224-leaf , Node0231-leaf , Node0232 , Node0233-leaf , Node0234-leaf , Node0241 , Node0242-leaf , Node0243-leaf , Node0244-leaf , Node0251-leaf , Node0252-leaf , Node0311 , Node0312-leaf , Node0313-leaf , Node0331-leaf , Node0332-leaf , Node0333-leaf .
The object with results only for a single top-value method and a single partitioning method can be extracted as:
res = res_rh["031"]
A summary of res and all the functions that can be applied to it:
res
#> A 'ConsensusPartition' object with k = 2, 3, 4, 5, 6, 7, 8.
#> On a matrix with 30000 rows and 54 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 0.999 1.000 0.4398 0.560 0.560
#> 3 3 0.997 0.973 0.987 0.5080 0.700 0.499
#> 4 4 0.736 0.746 0.869 0.1248 0.820 0.528
#> 5 5 0.697 0.617 0.827 0.0453 0.863 0.545
#> 6 6 0.688 0.592 0.798 0.0264 0.907 0.645
#> 7 7 0.678 0.491 0.744 0.0230 0.941 0.742
#> 8 8 0.709 0.397 0.673 0.0215 0.939 0.709
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.EL.A4K9.01 1 0.000 1.000 1.00 0.00
#> TCGA.EL.A3ZM.01 2 0.000 0.999 0.00 1.00
#> TCGA.DJ.A3VB.01 2 0.000 0.999 0.00 1.00
#> TCGA.DE.A4MD.01 2 0.000 0.999 0.00 1.00
#> TCGA.ET.A40Q.01 2 0.141 0.980 0.02 0.98
#> TCGA.EL.A4K7.01 1 0.000 1.000 1.00 0.00
#> TCGA.J8.A3O2.06 1 0.000 1.000 1.00 0.00
#> TCGA.J8.A3YF.01 2 0.000 0.999 0.00 1.00
#> TCGA.DJ.A3VJ.01 1 0.000 1.000 1.00 0.00
#> TCGA.EL.A3ZP.01 1 0.000 1.000 1.00 0.00
#> TCGA.EL.A3ZT.01 1 0.000 1.000 1.00 0.00
#> TCGA.L6.A4EQ.01 1 0.000 1.000 1.00 0.00
#> TCGA.DJ.A3VE.01 1 0.000 1.000 1.00 0.00
#> TCGA.MK.A4N6.01 2 0.000 0.999 0.00 1.00
#> TCGA.DJ.A2PQ.01 1 0.000 1.000 1.00 0.00
#> TCGA.E3.A3DY.01 1 0.000 1.000 1.00 0.00
#> TCGA.DJ.A2Q4.01 1 0.000 1.000 1.00 0.00
#> TCGA.FY.A4B3.01 1 0.000 1.000 1.00 0.00
#> TCGA.E3.A3E5.01 1 0.000 1.000 1.00 0.00
#> TCGA.BJ.A4O8.01 1 0.000 1.000 1.00 0.00
#> TCGA.FK.A4UB.01 1 0.000 1.000 1.00 0.00
#> TCGA.ET.A25M.01 1 0.000 1.000 1.00 0.00
#> TCGA.EL.A3MY.01 2 0.000 0.999 0.00 1.00
#> TCGA.EM.A3FM.01 1 0.000 1.000 1.00 0.00
#> TCGA.EL.A3MZ.01 2 0.000 0.999 0.00 1.00
#> TCGA.EM.A3FO.01 1 0.000 1.000 1.00 0.00
#> TCGA.EM.A2OX.01 1 0.000 1.000 1.00 0.00
#> TCGA.DJ.A3V6.01 2 0.000 0.999 0.00 1.00
#> TCGA.BJ.A18Z.01 1 0.000 1.000 1.00 0.00
#> TCGA.DJ.A3V0.01 2 0.000 0.999 0.00 1.00
#> TCGA.EL.A3T8.01 1 0.000 1.000 1.00 0.00
#> TCGA.EM.A22O.01 2 0.000 0.999 0.00 1.00
#> TCGA.J8.A3YH.01 1 0.000 1.000 1.00 0.00
#> TCGA.EL.A3D0.01 2 0.000 0.999 0.00 1.00
#> TCGA.J8.A3YH.06 1 0.000 1.000 1.00 0.00
#> TCGA.BJ.A3EZ.01 2 0.000 0.999 0.00 1.00
#> TCGA.EM.A1CU.01 1 0.000 1.000 1.00 0.00
#> TCGA.DJ.A2PW.01 1 0.000 1.000 1.00 0.00
#> TCGA.ET.A2MZ.01 1 0.000 1.000 1.00 0.00
#> TCGA.ET.A3BX.01 1 0.000 1.000 1.00 0.00
#> TCGA.DJ.A1QQ.01 1 0.000 1.000 1.00 0.00
#> TCGA.DJ.A1QO.01 2 0.000 0.999 0.00 1.00
#> TCGA.BJ.A2NA.01 1 0.000 1.000 1.00 0.00
#> TCGA.DJ.A3UO.01 1 0.000 1.000 1.00 0.00
#> TCGA.FE.A231.01 2 0.000 0.999 0.00 1.00
#> TCGA.ET.A3DW.01 2 0.000 0.999 0.00 1.00
#> TCGA.ET.A39O.01 1 0.000 1.000 1.00 0.00
#> TCGA.EL.A3D1.01 1 0.000 1.000 1.00 0.00
#> TCGA.BJ.A3PU.01 1 0.000 1.000 1.00 0.00
#> TCGA.BJ.A0ZB.01 2 0.000 0.999 0.00 1.00
#> TCGA.DJ.A2PR.01 1 0.000 1.000 1.00 0.00
#> TCGA.FY.A3ON.01 1 0.000 1.000 1.00 0.00
#> TCGA.FE.A3PA.01 1 0.000 1.000 1.00 0.00
#> TCGA.ET.A3BU.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.EL.A4K9.01 1 0.000 0.976 1.00 0.00 0.00
#> TCGA.EL.A3ZM.01 2 0.000 0.997 0.00 1.00 0.00
#> TCGA.DJ.A3VB.01 3 0.207 0.936 0.00 0.06 0.94
#> TCGA.DE.A4MD.01 2 0.000 0.997 0.00 1.00 0.00
#> TCGA.ET.A40Q.01 3 0.000 0.990 0.00 0.00 1.00
#> TCGA.EL.A4K7.01 3 0.000 0.990 0.00 0.00 1.00
#> TCGA.J8.A3O2.06 3 0.000 0.990 0.00 0.00 1.00
#> TCGA.J8.A3YF.01 2 0.000 0.997 0.00 1.00 0.00
#> TCGA.DJ.A3VJ.01 1 0.000 0.976 1.00 0.00 0.00
#> TCGA.EL.A3ZP.01 1 0.000 0.976 1.00 0.00 0.00
#> TCGA.EL.A3ZT.01 1 0.000 0.976 1.00 0.00 0.00
#> TCGA.L6.A4EQ.01 3 0.000 0.990 0.00 0.00 1.00
#> TCGA.DJ.A3VE.01 1 0.000 0.976 1.00 0.00 0.00
#> TCGA.MK.A4N6.01 3 0.000 0.990 0.00 0.00 1.00
#> TCGA.DJ.A2PQ.01 1 0.369 0.848 0.86 0.00 0.14
#> TCGA.E3.A3DY.01 3 0.000 0.990 0.00 0.00 1.00
#> TCGA.DJ.A2Q4.01 1 0.000 0.976 1.00 0.00 0.00
#> TCGA.FY.A4B3.01 1 0.000 0.976 1.00 0.00 0.00
#> TCGA.E3.A3E5.01 3 0.000 0.990 0.00 0.00 1.00
#> TCGA.BJ.A4O8.01 1 0.480 0.740 0.78 0.00 0.22
#> TCGA.FK.A4UB.01 1 0.000 0.976 1.00 0.00 0.00
#> TCGA.ET.A25M.01 3 0.000 0.990 0.00 0.00 1.00
#> TCGA.EL.A3MY.01 2 0.000 0.997 0.00 1.00 0.00
#> TCGA.EM.A3FM.01 3 0.000 0.990 0.00 0.00 1.00
#> TCGA.EL.A3MZ.01 2 0.000 0.997 0.00 1.00 0.00
#> TCGA.EM.A3FO.01 1 0.000 0.976 1.00 0.00 0.00
#> TCGA.EM.A2OX.01 3 0.000 0.990 0.00 0.00 1.00
#> TCGA.DJ.A3V6.01 2 0.153 0.958 0.00 0.96 0.04
#> TCGA.BJ.A18Z.01 3 0.000 0.990 0.00 0.00 1.00
#> TCGA.DJ.A3V0.01 3 0.207 0.936 0.00 0.06 0.94
#> TCGA.EL.A3T8.01 1 0.000 0.976 1.00 0.00 0.00
#> TCGA.EM.A22O.01 2 0.000 0.997 0.00 1.00 0.00
#> TCGA.J8.A3YH.01 1 0.000 0.976 1.00 0.00 0.00
#> TCGA.EL.A3D0.01 2 0.000 0.997 0.00 1.00 0.00
#> TCGA.J8.A3YH.06 1 0.000 0.976 1.00 0.00 0.00
#> TCGA.BJ.A3EZ.01 2 0.000 0.997 0.00 1.00 0.00
#> TCGA.EM.A1CU.01 1 0.000 0.976 1.00 0.00 0.00
#> TCGA.DJ.A2PW.01 1 0.000 0.976 1.00 0.00 0.00
#> TCGA.ET.A2MZ.01 1 0.000 0.976 1.00 0.00 0.00
#> TCGA.ET.A3BX.01 3 0.000 0.990 0.00 0.00 1.00
#> TCGA.DJ.A1QQ.01 1 0.000 0.976 1.00 0.00 0.00
#> TCGA.DJ.A1QO.01 2 0.000 0.997 0.00 1.00 0.00
#> TCGA.BJ.A2NA.01 3 0.000 0.990 0.00 0.00 1.00
#> TCGA.DJ.A3UO.01 3 0.153 0.950 0.04 0.00 0.96
#> TCGA.FE.A231.01 2 0.000 0.997 0.00 1.00 0.00
#> TCGA.ET.A3DW.01 2 0.000 0.997 0.00 1.00 0.00
#> TCGA.ET.A39O.01 3 0.000 0.990 0.00 0.00 1.00
#> TCGA.EL.A3D1.01 1 0.000 0.976 1.00 0.00 0.00
#> TCGA.BJ.A3PU.01 3 0.000 0.990 0.00 0.00 1.00
#> TCGA.BJ.A0ZB.01 2 0.000 0.997 0.00 1.00 0.00
#> TCGA.DJ.A2PR.01 1 0.000 0.976 1.00 0.00 0.00
#> TCGA.FY.A3ON.01 1 0.000 0.976 1.00 0.00 0.00
#> TCGA.FE.A3PA.01 1 0.369 0.849 0.86 0.00 0.14
#> TCGA.ET.A3BU.01 1 0.000 0.976 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.EL.A4K9.01 1 0.4134 0.73995 0.74 0.00 0.26 0.00
#> TCGA.EL.A3ZM.01 2 0.0000 0.97297 0.00 1.00 0.00 0.00
#> TCGA.DJ.A3VB.01 4 0.0000 0.87469 0.00 0.00 0.00 1.00
#> TCGA.DE.A4MD.01 2 0.0000 0.97297 0.00 1.00 0.00 0.00
#> TCGA.ET.A40Q.01 4 0.0000 0.87469 0.00 0.00 0.00 1.00
#> TCGA.EL.A4K7.01 3 0.4907 0.27967 0.00 0.00 0.58 0.42
#> TCGA.J8.A3O2.06 3 0.4855 0.45593 0.00 0.00 0.60 0.40
#> TCGA.J8.A3YF.01 2 0.0000 0.97297 0.00 1.00 0.00 0.00
#> TCGA.DJ.A3VJ.01 1 0.4624 0.61318 0.66 0.00 0.34 0.00
#> TCGA.EL.A3ZP.01 1 0.0000 0.88022 1.00 0.00 0.00 0.00
#> TCGA.EL.A3ZT.01 1 0.0000 0.88022 1.00 0.00 0.00 0.00
#> TCGA.L6.A4EQ.01 3 0.4948 0.28687 0.00 0.00 0.56 0.44
#> TCGA.DJ.A3VE.01 1 0.3975 0.75661 0.76 0.00 0.24 0.00
#> TCGA.MK.A4N6.01 4 0.0000 0.87469 0.00 0.00 0.00 1.00
#> TCGA.DJ.A2PQ.01 3 0.3335 0.65035 0.12 0.00 0.86 0.02
#> TCGA.E3.A3DY.01 3 0.3037 0.65128 0.02 0.00 0.88 0.10
#> TCGA.DJ.A2Q4.01 1 0.0000 0.88022 1.00 0.00 0.00 0.00
#> TCGA.FY.A4B3.01 1 0.0000 0.88022 1.00 0.00 0.00 0.00
#> TCGA.E3.A3E5.01 3 0.4624 0.52615 0.00 0.00 0.66 0.34
#> TCGA.BJ.A4O8.01 3 0.3606 0.63772 0.14 0.00 0.84 0.02
#> TCGA.FK.A4UB.01 1 0.4134 0.73995 0.74 0.00 0.26 0.00
#> TCGA.ET.A25M.01 3 0.4522 0.55197 0.00 0.00 0.68 0.32
#> TCGA.EL.A3MY.01 2 0.3801 0.71939 0.00 0.78 0.00 0.22
#> TCGA.EM.A3FM.01 3 0.4994 0.31511 0.00 0.00 0.52 0.48
#> TCGA.EL.A3MZ.01 2 0.0000 0.97297 0.00 1.00 0.00 0.00
#> TCGA.EM.A3FO.01 1 0.0707 0.87147 0.98 0.00 0.02 0.00
#> TCGA.EM.A2OX.01 3 0.4790 0.48066 0.00 0.00 0.62 0.38
#> TCGA.DJ.A3V6.01 4 0.4977 0.00742 0.00 0.46 0.00 0.54
#> TCGA.BJ.A18Z.01 4 0.2345 0.81247 0.00 0.00 0.10 0.90
#> TCGA.DJ.A3V0.01 4 0.0707 0.85926 0.00 0.02 0.00 0.98
#> TCGA.EL.A3T8.01 1 0.4134 0.73995 0.74 0.00 0.26 0.00
#> TCGA.EM.A22O.01 2 0.0000 0.97297 0.00 1.00 0.00 0.00
#> TCGA.J8.A3YH.01 3 0.4277 0.42768 0.28 0.00 0.72 0.00
#> TCGA.EL.A3D0.01 2 0.2011 0.91432 0.00 0.92 0.08 0.00
#> TCGA.J8.A3YH.06 3 0.4277 0.42768 0.28 0.00 0.72 0.00
#> TCGA.BJ.A3EZ.01 2 0.0000 0.97297 0.00 1.00 0.00 0.00
#> TCGA.EM.A1CU.01 1 0.0000 0.88022 1.00 0.00 0.00 0.00
#> TCGA.DJ.A2PW.01 1 0.3801 0.77049 0.78 0.00 0.22 0.00
#> TCGA.ET.A2MZ.01 3 0.4713 0.23502 0.36 0.00 0.64 0.00
#> TCGA.ET.A3BX.01 4 0.1211 0.86614 0.00 0.00 0.04 0.96
#> TCGA.DJ.A1QQ.01 1 0.0000 0.88022 1.00 0.00 0.00 0.00
#> TCGA.DJ.A1QO.01 2 0.0000 0.97297 0.00 1.00 0.00 0.00
#> TCGA.BJ.A2NA.01 4 0.2345 0.81247 0.00 0.00 0.10 0.90
#> TCGA.DJ.A3UO.01 3 0.2706 0.65331 0.02 0.00 0.90 0.08
#> TCGA.FE.A231.01 2 0.0000 0.97297 0.00 1.00 0.00 0.00
#> TCGA.ET.A3DW.01 2 0.0000 0.97297 0.00 1.00 0.00 0.00
#> TCGA.ET.A39O.01 4 0.1211 0.86618 0.00 0.00 0.04 0.96
#> TCGA.EL.A3D1.01 1 0.0707 0.87147 0.98 0.00 0.02 0.00
#> TCGA.BJ.A3PU.01 4 0.0707 0.87334 0.00 0.00 0.02 0.98
#> TCGA.BJ.A0ZB.01 2 0.0000 0.97297 0.00 1.00 0.00 0.00
#> TCGA.DJ.A2PR.01 1 0.0707 0.87147 0.98 0.00 0.02 0.00
#> TCGA.FY.A3ON.01 1 0.0000 0.88022 1.00 0.00 0.00 0.00
#> TCGA.FE.A3PA.01 3 0.2921 0.62241 0.14 0.00 0.86 0.00
#> TCGA.ET.A3BU.01 1 0.0000 0.88022 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.EL.A4K9.01 3 0.4818 0.2524 0.46 0.00 0.52 0.00 0.02
#> TCGA.EL.A3ZM.01 2 0.0000 0.8870 0.00 1.00 0.00 0.00 0.00
#> TCGA.DJ.A3VB.01 4 0.2331 0.6335 0.00 0.02 0.00 0.90 0.08
#> TCGA.DE.A4MD.01 2 0.0000 0.8870 0.00 1.00 0.00 0.00 0.00
#> TCGA.ET.A40Q.01 4 0.0000 0.7085 0.00 0.00 0.00 1.00 0.00
#> TCGA.EL.A4K7.01 5 0.4216 0.7262 0.00 0.00 0.12 0.10 0.78
#> TCGA.J8.A3O2.06 4 0.5579 0.3063 0.00 0.00 0.30 0.60 0.10
#> TCGA.J8.A3YF.01 2 0.2280 0.8164 0.00 0.88 0.00 0.00 0.12
#> TCGA.DJ.A3VJ.01 3 0.4613 0.4680 0.36 0.00 0.62 0.00 0.02
#> TCGA.EL.A3ZP.01 1 0.0000 0.8668 1.00 0.00 0.00 0.00 0.00
#> TCGA.EL.A3ZT.01 1 0.1216 0.8564 0.96 0.00 0.02 0.00 0.02
#> TCGA.L6.A4EQ.01 5 0.5888 0.6630 0.00 0.00 0.14 0.28 0.58
#> TCGA.DJ.A3VE.01 1 0.4227 0.0507 0.58 0.00 0.42 0.00 0.00
#> TCGA.MK.A4N6.01 4 0.0609 0.6979 0.00 0.00 0.00 0.98 0.02
#> TCGA.DJ.A2PQ.01 3 0.2754 0.6291 0.08 0.00 0.88 0.04 0.00
#> TCGA.E3.A3DY.01 3 0.2331 0.5177 0.00 0.00 0.90 0.08 0.02
#> TCGA.DJ.A2Q4.01 1 0.0609 0.8575 0.98 0.00 0.02 0.00 0.00
#> TCGA.FY.A4B3.01 1 0.0609 0.8616 0.98 0.00 0.00 0.00 0.02
#> TCGA.E3.A3E5.01 3 0.6455 -0.2846 0.00 0.00 0.48 0.32 0.20
#> TCGA.BJ.A4O8.01 3 0.2438 0.6161 0.06 0.00 0.90 0.04 0.00
#> TCGA.FK.A4UB.01 3 0.4798 0.3176 0.44 0.00 0.54 0.00 0.02
#> TCGA.ET.A25M.01 3 0.5457 -0.3304 0.00 0.00 0.48 0.46 0.06
#> TCGA.EL.A3MY.01 2 0.5444 0.5992 0.00 0.66 0.00 0.18 0.16
#> TCGA.EM.A3FM.01 4 0.4990 0.3243 0.00 0.00 0.36 0.60 0.04
#> TCGA.EL.A3MZ.01 2 0.0000 0.8870 0.00 1.00 0.00 0.00 0.00
#> TCGA.EM.A3FO.01 1 0.3521 0.7639 0.82 0.00 0.04 0.00 0.14
#> TCGA.EM.A2OX.01 4 0.6070 0.0119 0.00 0.00 0.44 0.44 0.12
#> TCGA.DJ.A3V6.01 2 0.6326 0.2295 0.00 0.46 0.00 0.38 0.16
#> TCGA.BJ.A18Z.01 4 0.2754 0.6744 0.00 0.00 0.08 0.88 0.04
#> TCGA.DJ.A3V0.01 4 0.2331 0.6335 0.00 0.02 0.00 0.90 0.08
#> TCGA.EL.A3T8.01 3 0.4675 0.4254 0.38 0.00 0.60 0.00 0.02
#> TCGA.EM.A22O.01 2 0.0000 0.8870 0.00 1.00 0.00 0.00 0.00
#> TCGA.J8.A3YH.01 3 0.3319 0.6577 0.16 0.00 0.82 0.00 0.02
#> TCGA.EL.A3D0.01 2 0.4540 0.5783 0.00 0.64 0.02 0.00 0.34
#> TCGA.J8.A3YH.06 3 0.3319 0.6577 0.16 0.00 0.82 0.00 0.02
#> TCGA.BJ.A3EZ.01 2 0.0000 0.8870 0.00 1.00 0.00 0.00 0.00
#> TCGA.EM.A1CU.01 1 0.0000 0.8668 1.00 0.00 0.00 0.00 0.00
#> TCGA.DJ.A2PW.01 1 0.4182 0.1246 0.60 0.00 0.40 0.00 0.00
#> TCGA.ET.A2MZ.01 3 0.3513 0.6540 0.18 0.00 0.80 0.00 0.02
#> TCGA.ET.A3BX.01 4 0.5741 0.5069 0.06 0.00 0.10 0.70 0.14
#> TCGA.DJ.A1QQ.01 1 0.0000 0.8668 1.00 0.00 0.00 0.00 0.00
#> TCGA.DJ.A1QO.01 2 0.0000 0.8870 0.00 1.00 0.00 0.00 0.00
#> TCGA.BJ.A2NA.01 4 0.2438 0.6864 0.00 0.00 0.06 0.90 0.04
#> TCGA.DJ.A3UO.01 3 0.2754 0.4919 0.00 0.00 0.88 0.04 0.08
#> TCGA.FE.A231.01 2 0.0000 0.8870 0.00 1.00 0.00 0.00 0.00
#> TCGA.ET.A3DW.01 2 0.0000 0.8870 0.00 1.00 0.00 0.00 0.00
#> TCGA.ET.A39O.01 4 0.0609 0.7140 0.00 0.00 0.02 0.98 0.00
#> TCGA.EL.A3D1.01 1 0.2873 0.8001 0.86 0.00 0.02 0.00 0.12
#> TCGA.BJ.A3PU.01 4 0.0609 0.7140 0.00 0.00 0.02 0.98 0.00
#> TCGA.BJ.A0ZB.01 2 0.0000 0.8870 0.00 1.00 0.00 0.00 0.00
#> TCGA.DJ.A2PR.01 1 0.2438 0.8246 0.90 0.00 0.06 0.00 0.04
#> TCGA.FY.A3ON.01 1 0.0000 0.8668 1.00 0.00 0.00 0.00 0.00
#> TCGA.FE.A3PA.01 3 0.3110 0.5638 0.06 0.00 0.86 0.00 0.08
#> TCGA.ET.A3BU.01 1 0.0000 0.8668 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.EL.A4K9.01 1 0.3851 0.16995 0.54 0.00 0.46 0.00 0.00 0.00
#> TCGA.EL.A3ZM.01 2 0.0000 0.90202 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.DJ.A3VB.01 4 0.3506 0.71207 0.00 0.00 0.02 0.80 0.02 0.16
#> TCGA.DE.A4MD.01 2 0.0000 0.90202 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.ET.A40Q.01 4 0.2350 0.74595 0.00 0.00 0.00 0.88 0.02 0.10
#> TCGA.EL.A4K7.01 5 0.3163 0.63069 0.00 0.00 0.04 0.00 0.82 0.14
#> TCGA.J8.A3O2.06 3 0.5797 0.38995 0.00 0.00 0.52 0.36 0.08 0.04
#> TCGA.J8.A3YF.01 2 0.3756 -0.00511 0.00 0.60 0.00 0.00 0.00 0.40
#> TCGA.DJ.A3VJ.01 3 0.3309 0.43313 0.28 0.00 0.72 0.00 0.00 0.00
#> TCGA.EL.A3ZP.01 1 0.0000 0.80657 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.EL.A3ZT.01 1 0.0547 0.80441 0.98 0.00 0.02 0.00 0.00 0.00
#> TCGA.L6.A4EQ.01 5 0.5397 0.63459 0.00 0.00 0.06 0.20 0.66 0.08
#> TCGA.DJ.A3VE.01 1 0.3864 0.11230 0.52 0.00 0.48 0.00 0.00 0.00
#> TCGA.MK.A4N6.01 4 0.3111 0.73134 0.00 0.00 0.02 0.84 0.02 0.12
#> TCGA.DJ.A2PQ.01 3 0.2474 0.63067 0.04 0.00 0.88 0.08 0.00 0.00
#> TCGA.E3.A3DY.01 3 0.2956 0.61162 0.00 0.00 0.84 0.12 0.04 0.00
#> TCGA.DJ.A2Q4.01 1 0.0547 0.80404 0.98 0.00 0.02 0.00 0.00 0.00
#> TCGA.FY.A4B3.01 1 0.1092 0.78924 0.96 0.00 0.00 0.00 0.02 0.02
#> TCGA.E3.A3E5.01 3 0.6702 0.39642 0.00 0.00 0.52 0.20 0.18 0.10
#> TCGA.BJ.A4O8.01 3 0.3045 0.63183 0.06 0.00 0.84 0.10 0.00 0.00
#> TCGA.FK.A4UB.01 3 0.3851 -0.02609 0.46 0.00 0.54 0.00 0.00 0.00
#> TCGA.ET.A25M.01 3 0.4144 0.47259 0.00 0.00 0.62 0.36 0.02 0.00
#> TCGA.EL.A3MY.01 6 0.5747 0.38470 0.00 0.30 0.00 0.20 0.00 0.50
#> TCGA.EM.A3FM.01 3 0.5106 0.36157 0.00 0.00 0.50 0.44 0.02 0.04
#> TCGA.EL.A3MZ.01 2 0.0000 0.90202 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.EM.A3FO.01 1 0.4631 0.61908 0.70 0.00 0.02 0.00 0.06 0.22
#> TCGA.EM.A2OX.01 3 0.6516 0.38020 0.00 0.00 0.52 0.26 0.14 0.08
#> TCGA.DJ.A3V6.01 4 0.5888 -0.27217 0.00 0.20 0.00 0.40 0.00 0.40
#> TCGA.BJ.A18Z.01 4 0.0547 0.74327 0.00 0.00 0.02 0.98 0.00 0.00
#> TCGA.DJ.A3V0.01 4 0.4002 0.54685 0.00 0.00 0.02 0.66 0.00 0.32
#> TCGA.EL.A3T8.01 3 0.3797 0.09719 0.42 0.00 0.58 0.00 0.00 0.00
#> TCGA.EM.A22O.01 2 0.0000 0.90202 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.J8.A3YH.01 3 0.3600 0.61448 0.08 0.00 0.82 0.00 0.08 0.02
#> TCGA.EL.A3D0.01 6 0.5841 0.24056 0.00 0.30 0.00 0.00 0.22 0.48
#> TCGA.J8.A3YH.06 3 0.3600 0.61448 0.08 0.00 0.82 0.00 0.08 0.02
#> TCGA.BJ.A3EZ.01 2 0.0000 0.90202 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.EM.A1CU.01 1 0.0000 0.80657 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.DJ.A2PW.01 1 0.4646 0.05276 0.50 0.00 0.46 0.00 0.04 0.00
#> TCGA.ET.A2MZ.01 3 0.2981 0.58333 0.16 0.00 0.82 0.00 0.02 0.00
#> TCGA.ET.A3BX.01 4 0.4933 0.52571 0.06 0.00 0.06 0.76 0.06 0.06
#> TCGA.DJ.A1QQ.01 1 0.0547 0.80432 0.98 0.00 0.02 0.00 0.00 0.00
#> TCGA.DJ.A1QO.01 2 0.1556 0.82388 0.00 0.92 0.00 0.00 0.00 0.08
#> TCGA.BJ.A2NA.01 4 0.0547 0.74327 0.00 0.00 0.02 0.98 0.00 0.00
#> TCGA.DJ.A3UO.01 3 0.4926 0.55869 0.00 0.00 0.72 0.08 0.14 0.06
#> TCGA.FE.A231.01 2 0.0000 0.90202 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.ET.A3DW.01 2 0.0000 0.90202 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.ET.A39O.01 4 0.0000 0.75512 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.EL.A3D1.01 1 0.3688 0.70467 0.80 0.00 0.02 0.00 0.04 0.14
#> TCGA.BJ.A3PU.01 4 0.0000 0.75512 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.BJ.A0ZB.01 2 0.2048 0.76786 0.00 0.88 0.00 0.00 0.00 0.12
#> TCGA.DJ.A2PR.01 1 0.2512 0.76846 0.88 0.00 0.06 0.00 0.00 0.06
#> TCGA.FY.A3ON.01 1 0.0000 0.80657 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.FE.A3PA.01 3 0.4695 0.57449 0.02 0.00 0.74 0.02 0.16 0.06
#> TCGA.ET.A3BU.01 1 0.0547 0.80033 0.98 0.00 0.00 0.00 0.02 0.00
cbind(get_classes(res, k = 7), get_membership(res, k = 7))
#> class entropy silhouette p1 p2 p3 p4 p5 p6 p7
#> TCGA.EL.A4K9.01 3 0.3459 0.2124 0.40 0.00 0.60 0.00 0.00 0.00 0.00
#> TCGA.EL.A3ZM.01 2 0.0000 0.8801 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.DJ.A3VB.01 4 0.0863 0.6445 0.00 0.00 0.00 0.96 0.00 0.04 0.00
#> TCGA.DE.A4MD.01 2 0.0000 0.8801 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.ET.A40Q.01 4 0.1671 0.6431 0.00 0.00 0.00 0.90 0.00 0.00 0.10
#> TCGA.EL.A4K7.01 5 0.5071 0.6329 0.00 0.00 0.02 0.06 0.68 0.18 0.06
#> TCGA.J8.A3O2.06 7 0.5833 0.6949 0.00 0.00 0.14 0.22 0.08 0.00 0.56
#> TCGA.J8.A3YF.01 2 0.3927 0.1681 0.00 0.66 0.00 0.04 0.00 0.30 0.00
#> TCGA.DJ.A3VJ.01 3 0.4211 0.4425 0.26 0.00 0.68 0.00 0.00 0.02 0.04
#> TCGA.EL.A3ZP.01 1 0.0000 0.7736 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.EL.A3ZT.01 1 0.2421 0.7454 0.88 0.00 0.02 0.00 0.00 0.02 0.08
#> TCGA.L6.A4EQ.01 5 0.2769 0.6567 0.00 0.00 0.02 0.04 0.86 0.00 0.08
#> TCGA.DJ.A3VE.01 1 0.3546 -0.0201 0.54 0.00 0.46 0.00 0.00 0.00 0.00
#> TCGA.MK.A4N6.01 4 0.0504 0.6515 0.00 0.00 0.00 0.98 0.00 0.00 0.02
#> TCGA.DJ.A2PQ.01 3 0.3867 0.1031 0.02 0.00 0.60 0.00 0.00 0.00 0.38
#> TCGA.E3.A3DY.01 3 0.4954 -0.2129 0.00 0.00 0.52 0.04 0.04 0.00 0.40
#> TCGA.DJ.A2Q4.01 1 0.1363 0.7608 0.94 0.00 0.04 0.00 0.00 0.02 0.00
#> TCGA.FY.A4B3.01 1 0.1363 0.7702 0.94 0.00 0.02 0.00 0.00 0.00 0.04
#> TCGA.E3.A3E5.01 3 0.7328 -0.4804 0.00 0.00 0.34 0.10 0.16 0.06 0.34
#> TCGA.BJ.A4O8.01 3 0.3815 0.1200 0.02 0.00 0.62 0.00 0.00 0.00 0.36
#> TCGA.FK.A4UB.01 3 0.3558 0.0901 0.48 0.00 0.52 0.00 0.00 0.00 0.00
#> TCGA.ET.A25M.01 7 0.5190 0.6982 0.00 0.00 0.30 0.18 0.00 0.00 0.52
#> TCGA.EL.A3MY.01 4 0.5606 -0.3733 0.00 0.28 0.00 0.38 0.00 0.34 0.00
#> TCGA.EM.A3FM.01 7 0.5182 0.7499 0.00 0.00 0.24 0.22 0.00 0.00 0.54
#> TCGA.EL.A3MZ.01 2 0.0504 0.8773 0.00 0.98 0.00 0.00 0.00 0.02 0.00
#> TCGA.EM.A3FO.01 1 0.6607 0.4371 0.50 0.00 0.10 0.00 0.02 0.20 0.18
#> TCGA.EM.A2OX.01 7 0.6568 0.5372 0.00 0.00 0.34 0.24 0.08 0.00 0.34
#> TCGA.DJ.A3V6.01 4 0.4587 0.3697 0.00 0.10 0.00 0.68 0.00 0.20 0.02
#> TCGA.BJ.A18Z.01 4 0.3294 0.4329 0.00 0.00 0.00 0.66 0.00 0.00 0.34
#> TCGA.DJ.A3V0.01 4 0.2421 0.5949 0.00 0.02 0.00 0.88 0.00 0.08 0.02
#> TCGA.EL.A3T8.01 3 0.3496 0.1783 0.42 0.00 0.58 0.00 0.00 0.00 0.00
#> TCGA.EM.A22O.01 2 0.0000 0.8801 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.J8.A3YH.01 3 0.2512 0.5012 0.10 0.00 0.86 0.00 0.00 0.00 0.04
#> TCGA.EL.A3D0.01 6 0.5381 0.0000 0.00 0.36 0.00 0.00 0.12 0.50 0.02
#> TCGA.J8.A3YH.06 3 0.2512 0.5012 0.10 0.00 0.86 0.00 0.00 0.00 0.04
#> TCGA.BJ.A3EZ.01 2 0.0504 0.8745 0.00 0.98 0.00 0.00 0.00 0.02 0.00
#> TCGA.EM.A1CU.01 1 0.0863 0.7668 0.96 0.00 0.04 0.00 0.00 0.00 0.00
#> TCGA.DJ.A2PW.01 1 0.4701 0.0789 0.50 0.00 0.44 0.00 0.00 0.04 0.02
#> TCGA.ET.A2MZ.01 3 0.3011 0.5014 0.12 0.00 0.82 0.00 0.00 0.00 0.06
#> TCGA.ET.A3BX.01 4 0.5974 0.3006 0.06 0.00 0.02 0.50 0.00 0.08 0.34
#> TCGA.DJ.A1QQ.01 1 0.0000 0.7736 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.DJ.A1QO.01 2 0.2016 0.8063 0.00 0.90 0.00 0.04 0.00 0.06 0.00
#> TCGA.BJ.A2NA.01 4 0.4070 0.4210 0.00 0.00 0.02 0.66 0.00 0.02 0.30
#> TCGA.DJ.A3UO.01 3 0.4872 -0.0758 0.00 0.00 0.60 0.02 0.08 0.00 0.30
#> TCGA.FE.A231.01 2 0.0000 0.8801 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.ET.A3DW.01 2 0.0504 0.8773 0.00 0.98 0.00 0.00 0.00 0.02 0.00
#> TCGA.ET.A39O.01 4 0.2259 0.6235 0.00 0.00 0.00 0.84 0.00 0.00 0.16
#> TCGA.EL.A3D1.01 1 0.6381 0.4766 0.54 0.00 0.20 0.00 0.02 0.12 0.12
#> TCGA.BJ.A3PU.01 4 0.3186 0.5800 0.00 0.00 0.00 0.76 0.00 0.02 0.22
#> TCGA.BJ.A0ZB.01 2 0.2259 0.6937 0.00 0.84 0.00 0.00 0.00 0.16 0.00
#> TCGA.DJ.A2PR.01 1 0.3386 0.6676 0.78 0.00 0.18 0.00 0.00 0.02 0.02
#> TCGA.FY.A3ON.01 1 0.0000 0.7736 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.FE.A3PA.01 3 0.5998 0.2072 0.04 0.00 0.60 0.00 0.12 0.06 0.18
#> TCGA.ET.A3BU.01 1 0.1363 0.7660 0.94 0.00 0.04 0.00 0.00 0.00 0.02
cbind(get_classes(res, k = 8), get_membership(res, k = 8))
#> class entropy silhouette p1 p2 p3 p4 p5 p6 p7 p8
#> TCGA.EL.A4K9.01 3 0.5342 -0.0746 0.40 0.00 0.44 0.00 0.00 0.00 0.04 0.12
#> TCGA.EL.A3ZM.01 2 0.0808 0.8883 0.00 0.96 0.00 0.00 0.00 0.00 0.04 0.00
#> TCGA.DJ.A3VB.01 4 0.1741 0.6048 0.00 0.00 0.00 0.92 0.02 0.02 0.04 0.00
#> TCGA.DE.A4MD.01 2 0.0808 0.8883 0.00 0.96 0.00 0.00 0.00 0.00 0.04 0.00
#> TCGA.ET.A40Q.01 4 0.0000 0.6042 0.00 0.00 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.EL.A4K7.01 5 0.6367 0.4060 0.00 0.00 0.02 0.02 0.52 0.14 0.20 0.10
#> TCGA.J8.A3O2.06 7 0.6390 0.4634 0.00 0.00 0.32 0.26 0.06 0.02 0.34 0.00
#> TCGA.J8.A3YF.01 2 0.5208 0.3221 0.00 0.60 0.00 0.06 0.04 0.26 0.04 0.00
#> TCGA.DJ.A3VJ.01 3 0.5393 0.2745 0.28 0.00 0.54 0.00 0.00 0.00 0.10 0.08
#> TCGA.EL.A3ZP.01 1 0.0000 0.6342 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.EL.A3ZT.01 1 0.2624 0.5706 0.86 0.00 0.00 0.00 0.00 0.02 0.06 0.06
#> TCGA.L6.A4EQ.01 5 0.3048 0.4123 0.00 0.00 0.02 0.08 0.84 0.04 0.02 0.00
#> TCGA.DJ.A3VE.01 1 0.5039 0.3057 0.56 0.00 0.32 0.00 0.00 0.02 0.02 0.08
#> TCGA.MK.A4N6.01 4 0.0808 0.6075 0.00 0.00 0.00 0.96 0.04 0.00 0.00 0.00
#> TCGA.DJ.A2PQ.01 3 0.2484 0.3280 0.02 0.00 0.86 0.00 0.02 0.00 0.10 0.00
#> TCGA.E3.A3DY.01 3 0.2224 0.2618 0.00 0.00 0.86 0.00 0.02 0.00 0.12 0.00
#> TCGA.DJ.A2Q4.01 1 0.1607 0.6224 0.92 0.00 0.00 0.00 0.00 0.00 0.04 0.04
#> TCGA.FY.A4B3.01 1 0.1341 0.5916 0.92 0.00 0.00 0.00 0.00 0.00 0.00 0.08
#> TCGA.E3.A3E5.01 7 0.7043 0.4557 0.00 0.00 0.30 0.12 0.08 0.02 0.40 0.08
#> TCGA.BJ.A4O8.01 3 0.2265 0.3563 0.02 0.00 0.88 0.00 0.00 0.00 0.08 0.02
#> TCGA.FK.A4UB.01 1 0.5349 0.0498 0.44 0.00 0.42 0.00 0.00 0.02 0.02 0.10
#> TCGA.ET.A25M.01 3 0.5210 -0.4319 0.00 0.00 0.52 0.18 0.02 0.00 0.28 0.00
#> TCGA.EL.A3MY.01 4 0.6731 -0.0377 0.00 0.24 0.00 0.42 0.08 0.20 0.06 0.00
#> TCGA.EM.A3FM.01 3 0.5916 -0.5043 0.00 0.00 0.40 0.24 0.02 0.02 0.32 0.00
#> TCGA.EL.A3MZ.01 2 0.0941 0.8919 0.00 0.96 0.00 0.00 0.00 0.02 0.02 0.00
#> TCGA.EM.A3FO.01 8 0.3570 0.0000 0.36 0.00 0.00 0.00 0.00 0.00 0.02 0.62
#> TCGA.EM.A2OX.01 7 0.5767 0.3415 0.00 0.00 0.32 0.14 0.02 0.00 0.48 0.04
#> TCGA.DJ.A3V6.01 4 0.5675 0.3927 0.00 0.10 0.00 0.62 0.10 0.12 0.06 0.00
#> TCGA.BJ.A18Z.01 4 0.4651 0.0497 0.00 0.00 0.18 0.58 0.00 0.00 0.24 0.00
#> TCGA.DJ.A3V0.01 4 0.3670 0.5609 0.00 0.02 0.00 0.80 0.06 0.06 0.06 0.00
#> TCGA.EL.A3T8.01 3 0.5462 -0.0659 0.38 0.00 0.46 0.00 0.00 0.02 0.02 0.12
#> TCGA.EM.A22O.01 2 0.0000 0.8982 0.00 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.J8.A3YH.01 3 0.4882 0.3721 0.02 0.00 0.60 0.00 0.00 0.00 0.20 0.18
#> TCGA.EL.A3D0.01 6 0.2888 0.0000 0.00 0.16 0.00 0.00 0.04 0.80 0.00 0.00
#> TCGA.J8.A3YH.06 3 0.4760 0.3754 0.02 0.00 0.62 0.00 0.00 0.00 0.20 0.16
#> TCGA.BJ.A3EZ.01 2 0.0000 0.8982 0.00 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.EM.A1CU.01 1 0.1275 0.6282 0.94 0.00 0.02 0.00 0.00 0.00 0.00 0.04
#> TCGA.DJ.A2PW.01 1 0.5582 0.0779 0.44 0.00 0.38 0.00 0.02 0.00 0.02 0.14
#> TCGA.ET.A2MZ.01 3 0.3670 0.4284 0.06 0.00 0.80 0.00 0.00 0.02 0.06 0.06
#> TCGA.ET.A3BX.01 7 0.7690 0.1427 0.08 0.00 0.04 0.30 0.02 0.06 0.34 0.16
#> TCGA.DJ.A1QQ.01 1 0.0471 0.6271 0.98 0.00 0.00 0.00 0.00 0.00 0.02 0.00
#> TCGA.DJ.A1QO.01 2 0.2165 0.8198 0.00 0.88 0.00 0.00 0.00 0.06 0.06 0.00
#> TCGA.BJ.A2NA.01 4 0.5037 -0.0326 0.00 0.00 0.14 0.54 0.02 0.00 0.30 0.00
#> TCGA.DJ.A3UO.01 3 0.4834 0.1240 0.00 0.00 0.52 0.00 0.04 0.00 0.38 0.06
#> TCGA.FE.A231.01 2 0.0471 0.8920 0.00 0.98 0.00 0.00 0.00 0.00 0.02 0.00
#> TCGA.ET.A3DW.01 2 0.0000 0.8982 0.00 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.ET.A39O.01 4 0.2547 0.5111 0.00 0.00 0.04 0.84 0.00 0.00 0.12 0.00
#> TCGA.EL.A3D1.01 1 0.3618 -0.2717 0.60 0.00 0.00 0.00 0.02 0.00 0.00 0.38
#> TCGA.BJ.A3PU.01 4 0.3054 0.4769 0.00 0.00 0.08 0.80 0.00 0.00 0.12 0.00
#> TCGA.BJ.A0ZB.01 2 0.1804 0.8389 0.00 0.90 0.00 0.00 0.00 0.08 0.02 0.00
#> TCGA.DJ.A2PR.01 1 0.2888 0.5185 0.80 0.00 0.04 0.00 0.00 0.00 0.00 0.16
#> TCGA.FY.A3ON.01 1 0.0000 0.6342 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.FE.A3PA.01 3 0.5966 0.1788 0.04 0.00 0.46 0.02 0.02 0.00 0.36 0.10
#> TCGA.ET.A3BU.01 1 0.0808 0.6092 0.96 0.00 0.00 0.00 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: Node031. Child nodes: Node02321-leaf , Node02322-leaf , Node02411-leaf , Node02412-leaf , Node02413-leaf , Node02414-leaf , Node03111-leaf , Node03112-leaf , Node03113-leaf .
The object with results only for a single top-value method and a single partitioning method can be extracted as:
res = res_rh["0311"]
A summary of res and all the functions that can be applied to it:
res
#> A 'ConsensusPartition' object with k = 2, 3, 4, 5, 6, 7, 8.
#> On a matrix with 30000 rows and 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 0.992 0.996 0.1733 0.834 0.834
#> 3 3 1.000 0.986 0.994 2.3446 0.589 0.507
#> 4 4 0.657 0.828 0.882 0.1923 0.881 0.720
#> 5 5 0.638 0.770 0.848 0.0808 1.000 1.000
#> 6 6 0.657 0.597 0.807 0.0482 0.953 0.844
#> 7 7 0.667 0.479 0.768 0.0527 0.921 0.701
#> 8 8 0.690 0.362 0.730 0.0329 0.929 0.684
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.EL.A4K9.01 2 0.141 0.980 0.02 0.98
#> TCGA.DJ.A3VJ.01 2 0.000 0.995 0.00 1.00
#> TCGA.EL.A3ZP.01 2 0.000 0.995 0.00 1.00
#> TCGA.EL.A3ZT.01 2 0.000 0.995 0.00 1.00
#> TCGA.DJ.A3VE.01 2 0.000 0.995 0.00 1.00
#> TCGA.DJ.A2PQ.01 2 0.000 0.995 0.00 1.00
#> TCGA.DJ.A2Q4.01 2 0.000 0.995 0.00 1.00
#> TCGA.FY.A4B3.01 2 0.000 0.995 0.00 1.00
#> TCGA.BJ.A4O8.01 2 0.141 0.980 0.02 0.98
#> TCGA.FK.A4UB.01 2 0.000 0.995 0.00 1.00
#> TCGA.EM.A3FO.01 2 0.000 0.995 0.00 1.00
#> TCGA.EL.A3T8.01 2 0.000 0.995 0.00 1.00
#> TCGA.J8.A3YH.01 1 0.000 1.000 1.00 0.00
#> TCGA.J8.A3YH.06 1 0.000 1.000 1.00 0.00
#> TCGA.EM.A1CU.01 2 0.000 0.995 0.00 1.00
#> TCGA.DJ.A2PW.01 2 0.000 0.995 0.00 1.00
#> TCGA.ET.A2MZ.01 2 0.327 0.941 0.06 0.94
#> TCGA.DJ.A1QQ.01 2 0.000 0.995 0.00 1.00
#> TCGA.EL.A3D1.01 2 0.000 0.995 0.00 1.00
#> TCGA.DJ.A2PR.01 2 0.000 0.995 0.00 1.00
#> TCGA.FY.A3ON.01 2 0.000 0.995 0.00 1.00
#> TCGA.FE.A3PA.01 2 0.000 0.995 0.00 1.00
#> TCGA.ET.A3BU.01 2 0.000 0.995 0.00 1.00
cbind(get_classes(res, k = 3), get_membership(res, k = 3))
#> class entropy silhouette p1 p2 p3
#> TCGA.EL.A4K9.01 3 0.0000 0.997 0.00 0.00 1.00
#> TCGA.DJ.A3VJ.01 3 0.0000 0.997 0.00 0.00 1.00
#> TCGA.EL.A3ZP.01 2 0.0000 0.988 0.00 1.00 0.00
#> TCGA.EL.A3ZT.01 2 0.0000 0.988 0.00 1.00 0.00
#> TCGA.DJ.A3VE.01 3 0.0000 0.997 0.00 0.00 1.00
#> TCGA.DJ.A2PQ.01 3 0.0000 0.997 0.00 0.00 1.00
#> TCGA.DJ.A2Q4.01 2 0.0000 0.988 0.00 1.00 0.00
#> TCGA.FY.A4B3.01 2 0.0000 0.988 0.00 1.00 0.00
#> TCGA.BJ.A4O8.01 3 0.0000 0.997 0.00 0.00 1.00
#> TCGA.FK.A4UB.01 3 0.0000 0.997 0.00 0.00 1.00
#> TCGA.EM.A3FO.01 2 0.0000 0.988 0.00 1.00 0.00
#> TCGA.EL.A3T8.01 3 0.0000 0.997 0.00 0.00 1.00
#> TCGA.J8.A3YH.01 1 0.0000 1.000 1.00 0.00 0.00
#> TCGA.J8.A3YH.06 1 0.0000 1.000 1.00 0.00 0.00
#> TCGA.EM.A1CU.01 2 0.0000 0.988 0.00 1.00 0.00
#> TCGA.DJ.A2PW.01 2 0.0892 0.970 0.00 0.98 0.02
#> TCGA.ET.A2MZ.01 3 0.0892 0.980 0.02 0.00 0.98
#> TCGA.DJ.A1QQ.01 2 0.0000 0.988 0.00 1.00 0.00
#> TCGA.EL.A3D1.01 2 0.0000 0.988 0.00 1.00 0.00
#> TCGA.DJ.A2PR.01 2 0.0000 0.988 0.00 1.00 0.00
#> TCGA.FY.A3ON.01 2 0.0000 0.988 0.00 1.00 0.00
#> TCGA.FE.A3PA.01 2 0.2959 0.876 0.00 0.90 0.10
#> TCGA.ET.A3BU.01 2 0.0000 0.988 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.EL.A4K9.01 3 0.4797 0.719 0 0.02 0.72 0.26
#> TCGA.DJ.A3VJ.01 3 0.5077 0.723 0 0.08 0.76 0.16
#> TCGA.EL.A3ZP.01 2 0.1211 0.895 0 0.96 0.00 0.04
#> TCGA.EL.A3ZT.01 2 0.1211 0.887 0 0.96 0.00 0.04
#> TCGA.DJ.A3VE.01 3 0.2921 0.776 0 0.00 0.86 0.14
#> TCGA.DJ.A2PQ.01 3 0.2011 0.816 0 0.00 0.92 0.08
#> TCGA.DJ.A2Q4.01 2 0.4088 0.751 0 0.82 0.04 0.14
#> TCGA.FY.A4B3.01 2 0.0707 0.894 0 0.98 0.00 0.02
#> TCGA.BJ.A4O8.01 3 0.1211 0.840 0 0.00 0.96 0.04
#> TCGA.FK.A4UB.01 3 0.0707 0.841 0 0.00 0.98 0.02
#> TCGA.EM.A3FO.01 2 0.1211 0.891 0 0.96 0.00 0.04
#> TCGA.EL.A3T8.01 3 0.0707 0.838 0 0.00 0.98 0.02
#> TCGA.J8.A3YH.01 1 0.0000 1.000 1 0.00 0.00 0.00
#> TCGA.J8.A3YH.06 1 0.0000 1.000 1 0.00 0.00 0.00
#> TCGA.EM.A1CU.01 2 0.2411 0.858 0 0.92 0.04 0.04
#> TCGA.DJ.A2PW.01 2 0.5147 0.537 0 0.74 0.20 0.06
#> TCGA.ET.A2MZ.01 3 0.4406 0.709 0 0.00 0.70 0.30
#> TCGA.DJ.A1QQ.01 2 0.0707 0.891 0 0.98 0.00 0.02
#> TCGA.EL.A3D1.01 4 0.4134 0.842 0 0.26 0.00 0.74
#> TCGA.DJ.A2PR.01 4 0.4277 0.831 0 0.28 0.00 0.72
#> TCGA.FY.A3ON.01 2 0.0707 0.894 0 0.98 0.00 0.02
#> TCGA.FE.A3PA.01 4 0.6104 0.724 0 0.18 0.14 0.68
#> TCGA.ET.A3BU.01 2 0.1637 0.880 0 0.94 0.00 0.06
cbind(get_classes(res, k = 5), get_membership(res, k = 5))
#> class entropy silhouette p1 p2 p3 p4 p5
#> TCGA.EL.A4K9.01 5 0.3922 0.755 0 0.00 0.18 0.04 0.78
#> TCGA.DJ.A3VJ.01 5 0.4094 0.757 0 0.02 0.18 0.02 0.78
#> TCGA.EL.A3ZP.01 2 0.0609 0.846 0 0.98 0.00 0.02 0.00
#> TCGA.EL.A3ZT.01 2 0.2012 0.829 0 0.92 0.06 0.02 0.00
#> TCGA.DJ.A3VE.01 5 0.4644 0.574 0 0.04 0.28 0.00 0.68
#> TCGA.DJ.A2PQ.01 5 0.3109 0.699 0 0.00 0.20 0.00 0.80
#> TCGA.DJ.A2Q4.01 2 0.6471 0.516 0 0.62 0.20 0.12 0.06
#> TCGA.FY.A4B3.01 2 0.2797 0.826 0 0.88 0.06 0.06 0.00
#> TCGA.BJ.A4O8.01 5 0.2516 0.780 0 0.00 0.14 0.00 0.86
#> TCGA.FK.A4UB.01 5 0.1732 0.779 0 0.00 0.08 0.00 0.92
#> TCGA.EM.A3FO.01 2 0.4437 0.746 0 0.76 0.14 0.10 0.00
#> TCGA.EL.A3T8.01 5 0.1648 0.775 0 0.00 0.04 0.02 0.94
#> TCGA.J8.A3YH.01 1 0.0000 1.000 1 0.00 0.00 0.00 0.00
#> TCGA.J8.A3YH.06 1 0.0000 1.000 1 0.00 0.00 0.00 0.00
#> TCGA.EM.A1CU.01 2 0.2012 0.823 0 0.92 0.00 0.02 0.06
#> TCGA.DJ.A2PW.01 2 0.5295 0.700 0 0.74 0.06 0.10 0.10
#> TCGA.ET.A2MZ.01 5 0.4456 0.662 0 0.00 0.32 0.02 0.66
#> TCGA.DJ.A1QQ.01 2 0.0000 0.845 0 1.00 0.00 0.00 0.00
#> TCGA.EL.A3D1.01 4 0.2012 0.753 0 0.06 0.02 0.92 0.00
#> TCGA.DJ.A2PR.01 4 0.3627 0.772 0 0.10 0.04 0.84 0.02
#> TCGA.FY.A3ON.01 2 0.0609 0.847 0 0.98 0.02 0.00 0.00
#> TCGA.FE.A3PA.01 4 0.5778 0.636 0 0.04 0.10 0.68 0.18
#> TCGA.ET.A3BU.01 2 0.3521 0.792 0 0.82 0.04 0.14 0.00
cbind(get_classes(res, k = 6), get_membership(res, k = 6))
#> class entropy silhouette p1 p2 p3 p4 p5 p6
#> TCGA.EL.A4K9.01 5 0.3258 0.4276 0 0.02 0.02 0.06 0.86 0.04
#> TCGA.DJ.A3VJ.01 5 0.1480 0.4785 0 0.04 0.00 0.02 0.94 0.00
#> TCGA.EL.A3ZP.01 2 0.0937 0.8243 0 0.96 0.00 0.04 0.00 0.00
#> TCGA.EL.A3ZT.01 2 0.1635 0.8203 0 0.94 0.02 0.02 0.00 0.02
#> TCGA.DJ.A3VE.01 6 0.6276 0.3182 0 0.06 0.00 0.12 0.30 0.52
#> TCGA.DJ.A2PQ.01 6 0.3828 0.0754 0 0.00 0.00 0.00 0.44 0.56
#> TCGA.DJ.A2Q4.01 2 0.5877 0.5168 0 0.58 0.06 0.30 0.04 0.02
#> TCGA.FY.A4B3.01 2 0.2581 0.7820 0 0.86 0.02 0.12 0.00 0.00
#> TCGA.BJ.A4O8.01 5 0.2094 0.4561 0 0.00 0.00 0.02 0.90 0.08
#> TCGA.FK.A4UB.01 5 0.4731 -0.0365 0 0.00 0.02 0.02 0.56 0.40
#> TCGA.EM.A3FO.01 2 0.3578 0.6185 0 0.66 0.00 0.34 0.00 0.00
#> TCGA.EL.A3T8.01 5 0.4731 -0.0354 0 0.00 0.02 0.02 0.56 0.40
#> TCGA.J8.A3YH.01 1 0.0000 1.0000 1 0.00 0.00 0.00 0.00 0.00
#> TCGA.J8.A3YH.06 1 0.0000 1.0000 1 0.00 0.00 0.00 0.00 0.00
#> TCGA.EM.A1CU.01 2 0.3162 0.7858 0 0.86 0.02 0.08 0.02 0.02
#> TCGA.DJ.A2PW.01 2 0.5636 0.4855 0 0.62 0.06 0.08 0.24 0.00
#> TCGA.ET.A2MZ.01 5 0.5679 0.2983 0 0.00 0.06 0.18 0.64 0.12
#> TCGA.DJ.A1QQ.01 2 0.0000 0.8250 0 1.00 0.00 0.00 0.00 0.00
#> TCGA.EL.A3D1.01 3 0.2020 0.8619 0 0.04 0.92 0.00 0.02 0.02
#> TCGA.DJ.A2PR.01 3 0.1807 0.8607 0 0.06 0.92 0.00 0.02 0.00
#> TCGA.FY.A3ON.01 2 0.0000 0.8250 0 1.00 0.00 0.00 0.00 0.00
#> TCGA.FE.A3PA.01 3 0.4947 0.7433 0 0.04 0.74 0.08 0.12 0.02
#> TCGA.ET.A3BU.01 2 0.2725 0.8002 0 0.88 0.06 0.04 0.00 0.02
cbind(get_classes(res, k = 7), get_membership(res, k = 7))
#> class entropy silhouette p1 p2 p3 p4 p5 p6 p7
#> TCGA.EL.A4K9.01 5 0.2569 0.5749 0 0.00 0.00 0.02 0.84 0.00 0.14
#> TCGA.DJ.A3VJ.01 5 0.3396 0.5501 0 0.00 0.02 0.04 0.80 0.00 0.14
#> TCGA.EL.A3ZP.01 2 0.2213 0.5953 0 0.90 0.00 0.04 0.04 0.00 0.02
#> TCGA.EL.A3ZT.01 2 0.2706 0.5858 0 0.88 0.04 0.02 0.04 0.02 0.00
#> TCGA.DJ.A3VE.01 6 0.6470 0.0000 0 0.00 0.00 0.10 0.16 0.38 0.36
#> TCGA.DJ.A2PQ.01 7 0.3315 0.2577 0 0.00 0.00 0.08 0.02 0.08 0.82
#> TCGA.DJ.A2Q4.01 4 0.5429 0.0000 0 0.32 0.10 0.54 0.04 0.00 0.00
#> TCGA.FY.A4B3.01 2 0.1363 0.6110 0 0.94 0.02 0.00 0.00 0.04 0.00
#> TCGA.BJ.A4O8.01 5 0.4649 0.4536 0 0.00 0.00 0.06 0.62 0.02 0.30
#> TCGA.FK.A4UB.01 7 0.4675 0.4315 0 0.00 0.02 0.02 0.26 0.04 0.66
#> TCGA.EM.A3FO.01 2 0.4070 0.2112 0 0.62 0.04 0.00 0.00 0.34 0.00
#> TCGA.EL.A3T8.01 7 0.3417 0.4459 0 0.00 0.02 0.00 0.26 0.00 0.72
#> TCGA.J8.A3YH.01 1 0.0000 1.0000 1 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.J8.A3YH.06 1 0.0000 1.0000 1 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.EM.A1CU.01 2 0.5668 0.2720 0 0.64 0.00 0.12 0.12 0.10 0.02
#> TCGA.DJ.A2PW.01 2 0.5822 -0.0263 0 0.44 0.00 0.14 0.38 0.00 0.04
#> TCGA.ET.A2MZ.01 5 0.5412 0.3578 0 0.00 0.00 0.24 0.60 0.08 0.08
#> TCGA.DJ.A1QQ.01 2 0.2313 0.5793 0 0.88 0.00 0.06 0.00 0.06 0.00
#> TCGA.EL.A3D1.01 3 0.2278 0.7005 0 0.00 0.88 0.04 0.00 0.08 0.00
#> TCGA.DJ.A2PR.01 3 0.1718 0.7344 0 0.04 0.92 0.00 0.04 0.00 0.00
#> TCGA.FY.A3ON.01 2 0.0504 0.6139 0 0.98 0.00 0.02 0.00 0.00 0.00
#> TCGA.FE.A3PA.01 3 0.3984 0.6011 0 0.00 0.68 0.00 0.28 0.02 0.02
#> TCGA.ET.A3BU.01 2 0.4453 0.4657 0 0.76 0.06 0.12 0.02 0.02 0.02
cbind(get_classes(res, k = 8), get_membership(res, k = 8))
#> class entropy silhouette p1 p2 p3 p4 p5 p6 p7 p8
#> TCGA.EL.A4K9.01 5 0.353 0.3943 0 0.00 0.06 0.06 0.82 0.02 0.02 0.02
#> TCGA.DJ.A3VJ.01 5 0.462 0.3805 0 0.02 0.06 0.04 0.76 0.04 0.06 0.02
#> TCGA.EL.A3ZP.01 2 0.213 0.5474 0 0.88 0.00 0.08 0.00 0.00 0.00 0.04
#> TCGA.EL.A3ZT.01 2 0.414 0.5074 0 0.72 0.00 0.08 0.00 0.04 0.00 0.16
#> TCGA.DJ.A3VE.01 6 0.211 0.0000 0 0.00 0.00 0.00 0.16 0.84 0.00 0.00
#> TCGA.DJ.A2PQ.01 7 0.511 0.0000 0 0.00 0.00 0.04 0.14 0.24 0.58 0.00
#> TCGA.DJ.A2Q4.01 4 0.411 0.0000 0 0.30 0.00 0.64 0.04 0.02 0.00 0.00
#> TCGA.FY.A4B3.01 2 0.410 0.3523 0 0.68 0.02 0.06 0.00 0.00 0.00 0.24
#> TCGA.BJ.A4O8.01 5 0.353 0.4090 0 0.00 0.02 0.02 0.80 0.06 0.10 0.00
#> TCGA.FK.A4UB.01 5 0.579 -0.0258 0 0.00 0.00 0.02 0.44 0.20 0.32 0.02
#> TCGA.EM.A3FO.01 8 0.337 0.0000 0 0.30 0.02 0.00 0.00 0.00 0.00 0.68
#> TCGA.EL.A3T8.01 5 0.524 0.0590 0 0.00 0.00 0.00 0.48 0.16 0.34 0.02
#> TCGA.J8.A3YH.01 1 0.000 1.0000 1 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.J8.A3YH.06 1 0.000 1.0000 1 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.EM.A1CU.01 2 0.485 0.3402 0 0.70 0.00 0.06 0.04 0.10 0.00 0.10
#> TCGA.DJ.A2PW.01 2 0.769 -0.1257 0 0.38 0.04 0.10 0.26 0.06 0.02 0.14
#> TCGA.ET.A2MZ.01 5 0.565 0.1905 0 0.00 0.02 0.06 0.46 0.00 0.38 0.08
#> TCGA.DJ.A1QQ.01 2 0.359 0.4778 0 0.78 0.00 0.12 0.00 0.04 0.00 0.06
#> TCGA.EL.A3D1.01 3 0.355 0.6375 0 0.00 0.80 0.08 0.00 0.02 0.02 0.08
#> TCGA.DJ.A2PR.01 3 0.207 0.6493 0 0.04 0.90 0.04 0.00 0.00 0.00 0.02
#> TCGA.FY.A3ON.01 2 0.235 0.5254 0 0.88 0.00 0.04 0.00 0.02 0.00 0.06
#> TCGA.FE.A3PA.01 3 0.524 0.4958 0 0.08 0.62 0.04 0.22 0.00 0.00 0.04
#> TCGA.ET.A3BU.01 2 0.371 0.5150 0 0.76 0.00 0.10 0.00 0.02 0.00 0.12
Heatmaps for the consensus matrix. It visualizes the probability of two samples to be in a same group.
consensus_heatmap(res, k = 2)
consensus_heatmap(res, k = 3)
consensus_heatmap(res, k = 4)
consensus_heatmap(res, k = 5)
consensus_heatmap(res, k = 6)
consensus_heatmap(res, k = 7)
consensus_heatmap(res, k = 8)
Heatmaps for the membership of samples in all partitions to see how consistent they are:
membership_heatmap(res, k = 2)
membership_heatmap(res, k = 3)
membership_heatmap(res, k = 4)
membership_heatmap(res, k = 5)
membership_heatmap(res, k = 6)
membership_heatmap(res, k = 7)
membership_heatmap(res, k = 8)
As soon as the classes for columns are determined, the signatures that are significantly different between subgroups can be looked for. Following are the heatmaps for signatures.
get_signatures(res, k = 2)
get_signatures(res, k = 3)
get_signatures(res, k = 4)
get_signatures(res, k = 5)
get_signatures(res, k = 6)
get_signatures(res, k = 7)
get_signatures(res, k = 8)
Compare the overlap of signatures from different k:
compare_signatures(res)
get_signature() returns a data frame invisibly. To get the list of signatures, the function
call should be assigned to a variable explicitly. In following code, if plot argument is set
to FALSE, no heatmap is plotted while only the differential analysis is performed.
# code only for demonstration
tb = get_signature(res, k = ..., plot = FALSE)
An example of the output of tb is:
#> which_row fdr mean_1 mean_2 scaled_mean_1 scaled_mean_2 km
#> 1 38 0.042760348 8.373488 9.131774 -0.5533452 0.5164555 1
#> 2 40 0.018707592 7.106213 8.469186 -0.6173731 0.5762149 1
#> 3 55 0.019134737 10.221463 11.207825 -0.6159697 0.5749050 1
#> 4 59 0.006059896 5.921854 7.869574 -0.6899429 0.6439467 1
#> 5 60 0.018055526 8.928898 10.211722 -0.6204761 0.5791110 1
#> 6 98 0.009384629 15.714769 14.887706 0.6635654 -0.6193277 2
...
The columns in tb are:
which_row: row indices corresponding to the input matrix.fdr: FDR for the differential test. mean_x: The mean value in group x.scaled_mean_x: The mean value in group x after rows are scaled.km: Row groups if k-means clustering is applied to rows (which is done by automatically selecting number of clusters).If there are too many signatures, top_signatures = ... can be set to only show the
signatures with the highest FDRs:
# code only for demonstration
# e.g. to show the top 500 most significant rows
tb = get_signature(res, k = ..., top_signatures = 500)
If the signatures are defined as these which are uniquely high in current group, diff_method argument
can be set to "uniquely_high_in_one_group":
# code only for demonstration
tb = get_signature(res, k = ..., diff_method = "uniquely_high_in_one_group")
UMAP plot which shows how samples are separated.
dimension_reduction(res, k = 2, method = "UMAP")
dimension_reduction(res, k = 3, method = "UMAP")
dimension_reduction(res, k = 4, method = "UMAP")
dimension_reduction(res, k = 5, method = "UMAP")
dimension_reduction(res, k = 6, method = "UMAP")
dimension_reduction(res, k = 7, method = "UMAP")
dimension_reduction(res, k = 8, method = "UMAP")
Following heatmap shows how subgroups are split when increasing k:
collect_classes(res)
If matrix rows can be associated to genes, consider to use functional_enrichment(res,
...) to perform function enrichment for the signature genes. See this vignette for more detailed explanations.
Parent node: Node03. Child nodes: Node0111-leaf , Node0112-leaf , Node0113-leaf , Node0114-leaf , Node0131-leaf , Node0132-leaf , Node0133-leaf , Node0141-leaf , Node0142-leaf , Node0143-leaf , Node0211-leaf , Node0212-leaf , Node0221-leaf , Node0222-leaf , Node0223-leaf , Node0224-leaf , Node0231-leaf , Node0232 , Node0233-leaf , Node0234-leaf , Node0241 , Node0242-leaf , Node0243-leaf , Node0244-leaf , Node0251-leaf , Node0252-leaf , Node0311 , Node0312-leaf , Node0313-leaf , Node0331-leaf , Node0332-leaf , Node0333-leaf .
The object with results only for a single top-value method and a single partitioning method can be extracted as:
res = res_rh["033"]
A summary of res and all the functions that can be applied to it:
res
#> A 'ConsensusPartition' object with k = 2, 3, 4, 5, 6, 7, 8.
#> On a matrix with 30000 rows and 65 columns.
#> Top rows (1000) are extracted by 'ATC' method.
#> Subgroups are detected by 'skmeans' method.
#> Performed in total 350 partitions by row resampling.
#> Best k for subgroups seems to be 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 0.976 0.990 0.2654 0.736 0.736
#> 3 3 1.000 0.991 0.996 1.3330 0.619 0.491
#> 4 4 0.831 0.820 0.918 0.1688 0.871 0.672
#> 5 5 0.677 0.720 0.834 0.0419 0.968 0.891
#> 6 6 0.622 0.568 0.788 0.0251 0.932 0.776
#> 7 7 0.609 0.567 0.737 0.0220 0.934 0.777
#> 8 8 0.606 0.420 0.666 0.0344 0.903 0.649
suggest_best_k() suggests the best \(k\) based on these statistics. The rules are as follows:
suggest_best_k(res)
#> [1] 3
#> attr(,"optional")
#> [1] 2
There is also optional best \(k\) = 2 that is worth to check.
Following is the table of the partitions (You need to click the show/hide
code output link to see it). The membership matrix (columns with name p*)
is inferred by
clue::cl_consensus()
function with the SE method. Basically the value in the membership matrix
represents the probability to belong to a certain group. The finall subgroup
label for an item is determined with the group with highest probability it
belongs to.
In get_classes() function, the entropy is calculated from the membership
matrix and the silhouette score is calculated from the consensus matrix.
cbind(get_classes(res, k = 2), get_membership(res, k = 2))
#> class entropy silhouette p1 p2
#> TCGA.L6.A4ET.01 1 0.000 0.994 1.00 0.00
#> TCGA.DJ.A4V2.01 1 0.000 0.994 1.00 0.00
#> TCGA.EM.A4FN.01 1 0.000 0.994 1.00 0.00
#> TCGA.EL.A4K1.01 1 0.000 0.994 1.00 0.00
#> TCGA.EM.A4FQ.01 1 0.000 0.994 1.00 0.00
#> TCGA.DJ.A4UL.01 1 0.000 0.994 1.00 0.00
#> TCGA.EL.A4KG.01 1 0.000 0.994 1.00 0.00
#> TCGA.L6.A4EP.01 1 0.000 0.994 1.00 0.00
#> TCGA.DE.A4MC.01 2 0.000 0.966 0.00 1.00
#> TCGA.EL.A3H8.01 1 0.000 0.994 1.00 0.00
#> TCGA.EL.A4JZ.01 2 0.000 0.966 0.00 1.00
#> TCGA.KS.A4I9.01 1 0.000 0.994 1.00 0.00
#> TCGA.EL.A3MW.01 1 0.000 0.994 1.00 0.00
#> TCGA.E3.A3E3.01 1 0.000 0.994 1.00 0.00
#> TCGA.EM.A4FM.01 2 0.000 0.966 0.00 1.00
#> TCGA.MK.A4N9.01 1 0.000 0.994 1.00 0.00
#> TCGA.E3.A3E0.01 1 0.000 0.994 1.00 0.00
#> TCGA.KS.A4I5.01 1 0.000 0.994 1.00 0.00
#> TCGA.KS.A4IB.01 1 0.904 0.510 0.68 0.32
#> TCGA.EM.A4FF.01 1 0.000 0.994 1.00 0.00
#> TCGA.EL.A4K0.01 1 0.000 0.994 1.00 0.00
#> TCGA.EL.A4K4.01 1 0.000 0.994 1.00 0.00
#> TCGA.EL.A3GS.01 1 0.000 0.994 1.00 0.00
#> TCGA.EL.A3N2.01 1 0.000 0.994 1.00 0.00
#> TCGA.EL.A3MX.01 2 0.000 0.966 0.00 1.00
#> TCGA.EM.A3FJ.01 1 0.000 0.994 1.00 0.00
#> TCGA.EM.A3FQ.06 1 0.000 0.994 1.00 0.00
#> TCGA.FE.A235.01 1 0.000 0.994 1.00 0.00
#> TCGA.DE.A7U5.01 1 0.000 0.994 1.00 0.00
#> TCGA.DE.A69J.01 1 0.000 0.994 1.00 0.00
#> TCGA.FE.A22Z.01 2 0.000 0.966 0.00 1.00
#> TCGA.DJ.A2Q7.01 1 0.000 0.994 1.00 0.00
#> TCGA.DE.A69K.01 1 0.000 0.994 1.00 0.00
#> TCGA.4C.A93U.01 2 0.000 0.966 0.00 1.00
#> TCGA.ET.A25N.01 1 0.000 0.994 1.00 0.00
#> TCGA.EL.A3H7.01 1 0.000 0.994 1.00 0.00
#> TCGA.ET.A25O.01 1 0.000 0.994 1.00 0.00
#> TCGA.EL.A3GU.01 2 0.000 0.966 0.00 1.00
#> TCGA.DJ.A2PY.01 1 0.000 0.994 1.00 0.00
#> TCGA.EM.A22I.01 1 0.000 0.994 1.00 0.00
#> TCGA.DE.A0XZ.01 1 0.000 0.994 1.00 0.00
#> TCGA.EL.A3GY.01 1 0.000 0.994 1.00 0.00
#> TCGA.EL.A3GX.01 1 0.000 0.994 1.00 0.00
#> TCGA.DO.A1JZ.01 1 0.000 0.994 1.00 0.00
#> TCGA.DO.A1K0.01 1 0.000 0.994 1.00 0.00
#> TCGA.IM.A3ED.01 1 0.000 0.994 1.00 0.00
#> TCGA.ET.A3BQ.01 1 0.000 0.994 1.00 0.00
#> TCGA.EL.A3H5.01 2 0.000 0.966 0.00 1.00
#> TCGA.EM.A2P3.01 1 0.000 0.994 1.00 0.00
#> TCGA.EL.A3CL.01 2 0.881 0.569 0.30 0.70
#> TCGA.DJ.A1QE.01 1 0.000 0.994 1.00 0.00
#> TCGA.FK.A3SB.01 1 0.000 0.994 1.00 0.00
#> TCGA.FE.A233.01 1 0.000 0.994 1.00 0.00
#> TCGA.ET.A39P.01 1 0.000 0.994 1.00 0.00
#> TCGA.DJ.A1QI.01 1 0.000 0.994 1.00 0.00
#> TCGA.DJ.A1QN.01 1 0.000 0.994 1.00 0.00
#> TCGA.FE.A234.01 1 0.000 0.994 1.00 0.00
#> TCGA.DJ.A1QH.01 2 0.000 0.966 0.00 1.00
#> TCGA.DJ.A2PU.01 1 0.000 0.994 1.00 0.00
#> TCGA.DJ.A2PN.01 1 0.000 0.994 1.00 0.00
#> TCGA.DJ.A1QD.01 1 0.000 0.994 1.00 0.00
#> TCGA.EL.A3CP.01 1 0.000 0.994 1.00 0.00
#> TCGA.FY.A3RA.01 1 0.000 0.994 1.00 0.00
#> TCGA.ET.A3BN.01 1 0.000 0.994 1.00 0.00
#> TCGA.DE.A0Y2.01 1 0.000 0.994 1.00 0.00
cbind(get_classes(res, k = 3), get_membership(res, k = 3))
#> class entropy silhouette p1 p2 p3
#> TCGA.L6.A4ET.01 3 0.0000 0.988 0.00 0.00 1.00
#> TCGA.DJ.A4V2.01 1 0.0000 0.999 1.00 0.00 0.00
#> TCGA.EM.A4FN.01 1 0.0000 0.999 1.00 0.00 0.00
#> TCGA.EL.A4K1.01 1 0.0000 0.999 1.00 0.00 0.00
#> TCGA.EM.A4FQ.01 1 0.0000 0.999 1.00 0.00 0.00
#> TCGA.DJ.A4UL.01 3 0.0000 0.988 0.00 0.00 1.00
#> TCGA.EL.A4KG.01 3 0.0000 0.988 0.00 0.00 1.00
#> TCGA.L6.A4EP.01 3 0.0000 0.988 0.00 0.00 1.00
#> TCGA.DE.A4MC.01 2 0.0000 1.000 0.00 1.00 0.00
#> TCGA.EL.A3H8.01 3 0.0000 0.988 0.00 0.00 1.00
#> TCGA.EL.A4JZ.01 2 0.0000 1.000 0.00 1.00 0.00
#> TCGA.KS.A4I9.01 1 0.0000 0.999 1.00 0.00 0.00
#> TCGA.EL.A3MW.01 3 0.1529 0.954 0.04 0.00 0.96
#> TCGA.E3.A3E3.01 1 0.0000 0.999 1.00 0.00 0.00
#> TCGA.EM.A4FM.01 2 0.0000 1.000 0.00 1.00 0.00
#> TCGA.MK.A4N9.01 3 0.0000 0.988 0.00 0.00 1.00
#> TCGA.E3.A3E0.01 3 0.0000 0.988 0.00 0.00 1.00
#> TCGA.KS.A4I5.01 3 0.0000 0.988 0.00 0.00 1.00
#> TCGA.KS.A4IB.01 1 0.0000 0.999 1.00 0.00 0.00
#> TCGA.EM.A4FF.01 1 0.0000 0.999 1.00 0.00 0.00
#> TCGA.EL.A4K0.01 3 0.0000 0.988 0.00 0.00 1.00
#> TCGA.EL.A4K4.01 1 0.0000 0.999 1.00 0.00 0.00
#> TCGA.EL.A3GS.01 1 0.0000 0.999 1.00 0.00 0.00
#> TCGA.EL.A3N2.01 1 0.0000 0.999 1.00 0.00 0.00
#> TCGA.EL.A3MX.01 2 0.0000 1.000 0.00 1.00 0.00
#> TCGA.EM.A3FJ.01 3 0.2066 0.933 0.06 0.00 0.94
#> TCGA.EM.A3FQ.06 3 0.0000 0.988 0.00 0.00 1.00
#> TCGA.FE.A235.01 3 0.0000 0.988 0.00 0.00 1.00
#> TCGA.DE.A7U5.01 1 0.0000 0.999 1.00 0.00 0.00
#> TCGA.DE.A69J.01 3 0.0892 0.972 0.02 0.00 0.98
#> TCGA.FE.A22Z.01 2 0.0000 1.000 0.00 1.00 0.00
#> TCGA.DJ.A2Q7.01 3 0.0000 0.988 0.00 0.00 1.00
#> TCGA.DE.A69K.01 3 0.0000 0.988 0.00 0.00 1.00
#> TCGA.4C.A93U.01 2 0.0000 1.000 0.00 1.00 0.00
#> TCGA.ET.A25N.01 3 0.0000 0.988 0.00 0.00 1.00
#> TCGA.EL.A3H7.01 1 0.0000 0.999 1.00 0.00 0.00
#> TCGA.ET.A25O.01 1 0.0000 0.999 1.00 0.00 0.00
#> TCGA.EL.A3GU.01 2 0.0000 1.000 0.00 1.00 0.00
#> TCGA.DJ.A2PY.01 1 0.0000 0.999 1.00 0.00 0.00
#> TCGA.EM.A22I.01 1 0.0892 0.975 0.98 0.00 0.02
#> TCGA.DE.A0XZ.01 3 0.0000 0.988 0.00 0.00 1.00
#> TCGA.EL.A3GY.01 1 0.0000 0.999 1.00 0.00 0.00
#> TCGA.EL.A3GX.01 1 0.0000 0.999 1.00 0.00 0.00
#> TCGA.DO.A1JZ.01 3 0.0000 0.988 0.00 0.00 1.00
#> TCGA.DO.A1K0.01 1 0.0000 0.999 1.00 0.00 0.00
#> TCGA.IM.A3ED.01 3 0.0000 0.988 0.00 0.00 1.00
#> TCGA.ET.A3BQ.01 3 0.0000 0.988 0.00 0.00 1.00
#> TCGA.EL.A3H5.01 2 0.0000 1.000 0.00 1.00 0.00
#> TCGA.EM.A2P3.01 1 0.0000 0.999 1.00 0.00 0.00
#> TCGA.EL.A3CL.01 3 0.0892 0.973 0.00 0.02 0.98
#> TCGA.DJ.A1QE.01 1 0.0000 0.999 1.00 0.00 0.00
#> TCGA.FK.A3SB.01 3 0.0000 0.988 0.00 0.00 1.00
#> TCGA.FE.A233.01 1 0.0000 0.999 1.00 0.00 0.00
#> TCGA.ET.A39P.01 1 0.0000 0.999 1.00 0.00 0.00
#> TCGA.DJ.A1QI.01 3 0.0000 0.988 0.00 0.00 1.00
#> TCGA.DJ.A1QN.01 3 0.2066 0.933 0.06 0.00 0.94
#> TCGA.FE.A234.01 1 0.0000 0.999 1.00 0.00 0.00
#> TCGA.DJ.A1QH.01 2 0.0000 1.000 0.00 1.00 0.00
#> TCGA.DJ.A2PU.01 3 0.2066 0.933 0.06 0.00 0.94
#> TCGA.DJ.A2PN.01 3 0.0000 0.988 0.00 0.00 1.00
#> TCGA.DJ.A1QD.01 1 0.0000 0.999 1.00 0.00 0.00
#> TCGA.EL.A3CP.01 3 0.0000 0.988 0.00 0.00 1.00
#> TCGA.FY.A3RA.01 1 0.0000 0.999 1.00 0.00 0.00
#> TCGA.ET.A3BN.01 1 0.0000 0.999 1.00 0.00 0.00
#> TCGA.DE.A0Y2.01 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.L6.A4ET.01 4 0.0000 0.848 0.00 0.00 0.00 1.00
#> TCGA.DJ.A4V2.01 1 0.0000 0.897 1.00 0.00 0.00 0.00
#> TCGA.EM.A4FN.01 1 0.4948 0.292 0.56 0.00 0.00 0.44
#> TCGA.EL.A4K1.01 1 0.0000 0.897 1.00 0.00 0.00 0.00
#> TCGA.EM.A4FQ.01 1 0.0000 0.897 1.00 0.00 0.00 0.00
#> TCGA.DJ.A4UL.01 4 0.0000 0.848 0.00 0.00 0.00 1.00
#> TCGA.EL.A4KG.01 4 0.7357 0.277 0.18 0.00 0.32 0.50
#> TCGA.L6.A4EP.01 3 0.4277 0.718 0.00 0.00 0.72 0.28
#> TCGA.DE.A4MC.01 2 0.0000 0.998 0.00 1.00 0.00 0.00
#> TCGA.EL.A3H8.01 4 0.1211 0.828 0.00 0.00 0.04 0.96
#> TCGA.EL.A4JZ.01 2 0.0000 0.998 0.00 1.00 0.00 0.00
#> TCGA.KS.A4I9.01 1 0.0000 0.897 1.00 0.00 0.00 0.00
#> TCGA.EL.A3MW.01 4 0.0000 0.848 0.00 0.00 0.00 1.00
#> TCGA.E3.A3E3.01 1 0.1211 0.875 0.96 0.00 0.00 0.04
#> TCGA.EM.A4FM.01 2 0.0000 0.998 0.00 1.00 0.00 0.00
#> TCGA.MK.A4N9.01 3 0.2011 0.904 0.00 0.00 0.92 0.08
#> TCGA.E3.A3E0.01 3 0.4624 0.611 0.00 0.00 0.66 0.34
#> TCGA.KS.A4I5.01 3 0.1211 0.915 0.00 0.00 0.96 0.04
#> TCGA.KS.A4IB.01 1 0.0000 0.897 1.00 0.00 0.00 0.00
#> TCGA.EM.A4FF.01 1 0.0000 0.897 1.00 0.00 0.00 0.00
#> TCGA.EL.A4K0.01 3 0.1637 0.913 0.00 0.00 0.94 0.06
#> TCGA.EL.A4K4.01 1 0.0000 0.897 1.00 0.00 0.00 0.00
#> TCGA.EL.A3GS.01 1 0.0000 0.897 1.00 0.00 0.00 0.00
#> TCGA.EL.A3N2.01 1 0.0000 0.897 1.00 0.00 0.00 0.00
#> TCGA.EL.A3MX.01 2 0.0000 0.998 0.00 1.00 0.00 0.00
#> TCGA.EM.A3FJ.01 4 0.0000 0.848 0.00 0.00 0.00 1.00
#> TCGA.EM.A3FQ.06 3 0.1637 0.913 0.00 0.00 0.94 0.06
#> TCGA.FE.A235.01 3 0.0707 0.912 0.00 0.00 0.98 0.02
#> TCGA.DE.A7U5.01 1 0.0000 0.897 1.00 0.00 0.00 0.00
#> TCGA.DE.A69J.01 4 0.0707 0.840 0.00 0.00 0.02 0.98
#> TCGA.FE.A22Z.01 2 0.0000 0.998 0.00 1.00 0.00 0.00
#> TCGA.DJ.A2Q7.01 4 0.2921 0.736 0.00 0.00 0.14 0.86
#> TCGA.DE.A69K.01 3 0.1211 0.915 0.00 0.00 0.96 0.04
#> TCGA.4C.A93U.01 2 0.0000 0.998 0.00 1.00 0.00 0.00
#> TCGA.ET.A25N.01 3 0.0707 0.912 0.00 0.00 0.98 0.02
#> TCGA.EL.A3H7.01 1 0.0000 0.897 1.00 0.00 0.00 0.00
#> TCGA.ET.A25O.01 4 0.4790 0.261 0.38 0.00 0.00 0.62
#> TCGA.EL.A3GU.01 2 0.0000 0.998 0.00 1.00 0.00 0.00
#> TCGA.DJ.A2PY.01 1 0.2647 0.808 0.88 0.00 0.00 0.12
#> TCGA.EM.A22I.01 1 0.1637 0.847 0.94 0.00 0.06 0.00
#> TCGA.DE.A0XZ.01 3 0.0707 0.912 0.00 0.00 0.98 0.02
#> TCGA.EL.A3GY.01 1 0.4277 0.609 0.72 0.00 0.00 0.28
#> TCGA.EL.A3GX.01 1 0.0000 0.897 1.00 0.00 0.00 0.00
#> TCGA.DO.A1JZ.01 3 0.0000 0.899 0.00 0.00 1.00 0.00
#> TCGA.DO.A1K0.01 1 0.4948 0.292 0.56 0.00 0.00 0.44
#> TCGA.IM.A3ED.01 3 0.1637 0.913 0.00 0.00 0.94 0.06
#> TCGA.ET.A3BQ.01 4 0.3610 0.635 0.00 0.00 0.20 0.80
#> TCGA.EL.A3H5.01 2 0.0000 0.998 0.00 1.00 0.00 0.00
#> TCGA.EM.A2P3.01 4 0.4624 0.373 0.34 0.00 0.00 0.66
#> TCGA.EL.A3CL.01 3 0.0000 0.899 0.00 0.00 1.00 0.00
#> TCGA.DJ.A1QE.01 1 0.0000 0.897 1.00 0.00 0.00 0.00
#> TCGA.FK.A3SB.01 3 0.3801 0.796 0.00 0.00 0.78 0.22
#> TCGA.FE.A233.01 1 0.0000 0.897 1.00 0.00 0.00 0.00
#> TCGA.ET.A39P.01 1 0.0000 0.897 1.00 0.00 0.00 0.00
#> TCGA.DJ.A1QI.01 3 0.3801 0.797 0.00 0.00 0.78 0.22
#> TCGA.DJ.A1QN.01 4 0.0000 0.848 0.00 0.00 0.00 1.00
#> TCGA.FE.A234.01 1 0.4907 0.345 0.58 0.00 0.00 0.42
#> TCGA.DJ.A1QH.01 2 0.0707 0.985 0.00 0.98 0.02 0.00
#> TCGA.DJ.A2PU.01 4 0.0000 0.848 0.00 0.00 0.00 1.00
#> TCGA.DJ.A2PN.01 3 0.0707 0.912 0.00 0.00 0.98 0.02
#> TCGA.DJ.A1QD.01 1 0.4790 0.431 0.62 0.00 0.00 0.38
#> TCGA.EL.A3CP.01 4 0.0000 0.848 0.00 0.00 0.00 1.00
#> TCGA.FY.A3RA.01 1 0.1637 0.861 0.94 0.00 0.00 0.06
#> TCGA.ET.A3BN.01 1 0.0000 0.897 1.00 0.00 0.00 0.00
#> TCGA.DE.A0Y2.01 1 0.0000 0.897 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.L6.A4ET.01 4 0.0000 0.82740 0.00 0.00 0.00 1.00 0.00
#> TCGA.DJ.A4V2.01 5 0.0609 0.78805 0.02 0.00 0.00 0.00 0.98
#> TCGA.EM.A4FN.01 5 0.4126 0.35443 0.00 0.00 0.00 0.38 0.62
#> TCGA.EL.A4K1.01 5 0.3424 0.76965 0.24 0.00 0.00 0.00 0.76
#> TCGA.EM.A4FQ.01 5 0.3274 0.77663 0.22 0.00 0.00 0.00 0.78
#> TCGA.DJ.A4UL.01 4 0.0000 0.82740 0.00 0.00 0.00 1.00 0.00
#> TCGA.EL.A4KG.01 3 0.6665 0.00472 0.00 0.00 0.44 0.26 0.30
#> TCGA.L6.A4EP.01 3 0.3424 0.69225 0.00 0.00 0.76 0.24 0.00
#> TCGA.DE.A4MC.01 2 0.3109 0.87137 0.20 0.80 0.00 0.00 0.00
#> TCGA.EL.A3H8.01 4 0.2438 0.79421 0.00 0.00 0.04 0.90 0.06
#> TCGA.EL.A4JZ.01 2 0.1043 0.92290 0.04 0.96 0.00 0.00 0.00
#> TCGA.KS.A4I9.01 5 0.0000 0.78166 0.00 0.00 0.00 0.00 1.00
#> TCGA.EL.A3MW.01 4 0.0000 0.82740 0.00 0.00 0.00 1.00 0.00
#> TCGA.E3.A3E3.01 5 0.1043 0.76637 0.00 0.00 0.00 0.04 0.96
#> TCGA.EM.A4FM.01 2 0.0000 0.92982 0.00 1.00 0.00 0.00 0.00
#> TCGA.MK.A4N9.01 3 0.2012 0.81862 0.02 0.00 0.92 0.06 0.00
#> TCGA.E3.A3E0.01 3 0.3895 0.54759 0.00 0.00 0.68 0.32 0.00
#> TCGA.KS.A4I5.01 3 0.1648 0.81938 0.04 0.00 0.94 0.02 0.00
#> TCGA.KS.A4IB.01 5 0.4302 0.56289 0.48 0.00 0.00 0.00 0.52
#> TCGA.EM.A4FF.01 5 0.0609 0.78860 0.02 0.00 0.00 0.00 0.98
#> TCGA.EL.A4K0.01 3 0.3697 0.79720 0.08 0.00 0.82 0.10 0.00
#> TCGA.EL.A4K4.01 5 0.3424 0.76965 0.24 0.00 0.00 0.00 0.76
#> TCGA.EL.A3GS.01 5 0.3424 0.76965 0.24 0.00 0.00 0.00 0.76
#> TCGA.EL.A3N2.01 5 0.2280 0.79666 0.12 0.00 0.00 0.00 0.88
#> TCGA.EL.A3MX.01 2 0.0000 0.92982 0.00 1.00 0.00 0.00 0.00
#> TCGA.EM.A3FJ.01 4 0.0609 0.82125 0.00 0.00 0.00 0.98 0.02
#> TCGA.EM.A3FQ.06 3 0.3110 0.80976 0.08 0.00 0.86 0.06 0.00
#> TCGA.FE.A235.01 3 0.1732 0.80495 0.08 0.00 0.92 0.00 0.00
#> TCGA.DE.A7U5.01 5 0.3424 0.77127 0.24 0.00 0.00 0.00 0.76
#> TCGA.DE.A69J.01 4 0.5680 0.57107 0.00 0.00 0.14 0.62 0.24
#> TCGA.FE.A22Z.01 2 0.0000 0.92982 0.00 1.00 0.00 0.00 0.00
#> TCGA.DJ.A2Q7.01 4 0.4252 0.52357 0.00 0.00 0.28 0.70 0.02
#> TCGA.DE.A69K.01 3 0.3697 0.80175 0.10 0.00 0.82 0.08 0.00
#> TCGA.4C.A93U.01 2 0.0000 0.92982 0.00 1.00 0.00 0.00 0.00
#> TCGA.ET.A25N.01 3 0.1410 0.81395 0.06 0.00 0.94 0.00 0.00
#> TCGA.EL.A3H7.01 5 0.3424 0.76965 0.24 0.00 0.00 0.00 0.76
#> TCGA.ET.A25O.01 5 0.5425 0.27858 0.06 0.00 0.00 0.42 0.52
#> TCGA.EL.A3GU.01 2 0.2929 0.87814 0.18 0.82 0.00 0.00 0.00
#> TCGA.DJ.A2PY.01 5 0.2929 0.67299 0.00 0.00 0.00 0.18 0.82
#> TCGA.EM.A22I.01 5 0.4263 0.64779 0.06 0.00 0.18 0.00 0.76
#> TCGA.DE.A0XZ.01 3 0.0000 0.81892 0.00 0.00 1.00 0.00 0.00
#> TCGA.EL.A3GY.01 5 0.3109 0.63851 0.00 0.00 0.00 0.20 0.80
#> TCGA.EL.A3GX.01 5 0.3274 0.77614 0.22 0.00 0.00 0.00 0.78
#> TCGA.DO.A1JZ.01 3 0.4060 0.62674 0.36 0.00 0.64 0.00 0.00
#> TCGA.DO.A1K0.01 5 0.3895 0.46462 0.00 0.00 0.00 0.32 0.68
#> TCGA.IM.A3ED.01 3 0.0609 0.82021 0.00 0.00 0.98 0.02 0.00
#> TCGA.ET.A3BQ.01 4 0.4540 0.34641 0.02 0.00 0.34 0.64 0.00
#> TCGA.EL.A3H5.01 2 0.0000 0.92982 0.00 1.00 0.00 0.00 0.00
#> TCGA.EM.A2P3.01 4 0.4262 0.14777 0.00 0.00 0.00 0.56 0.44
#> TCGA.EL.A3CL.01 3 0.4060 0.61677 0.36 0.00 0.64 0.00 0.00
#> TCGA.DJ.A1QE.01 5 0.2020 0.79635 0.10 0.00 0.00 0.00 0.90
#> TCGA.FK.A3SB.01 3 0.3731 0.76741 0.04 0.00 0.80 0.16 0.00
#> TCGA.FE.A233.01 5 0.2516 0.79442 0.14 0.00 0.00 0.00 0.86
#> TCGA.ET.A39P.01 5 0.2020 0.79635 0.10 0.00 0.00 0.00 0.90
#> TCGA.DJ.A1QI.01 3 0.3291 0.78784 0.04 0.00 0.84 0.12 0.00
#> TCGA.DJ.A1QN.01 4 0.0000 0.82740 0.00 0.00 0.00 1.00 0.00
#> TCGA.FE.A234.01 5 0.4126 0.38076 0.00 0.00 0.00 0.38 0.62
#> TCGA.DJ.A1QH.01 2 0.4182 0.74699 0.40 0.60 0.00 0.00 0.00
#> TCGA.DJ.A2PU.01 4 0.0000 0.82740 0.00 0.00 0.00 1.00 0.00
#> TCGA.DJ.A2PN.01 3 0.1410 0.81395 0.06 0.00 0.94 0.00 0.00
#> TCGA.DJ.A1QD.01 5 0.4126 0.35585 0.00 0.00 0.00 0.38 0.62
#> TCGA.EL.A3CP.01 4 0.1216 0.80428 0.02 0.00 0.02 0.96 0.00
#> TCGA.FY.A3RA.01 5 0.1732 0.74500 0.00 0.00 0.00 0.08 0.92
#> TCGA.ET.A3BN.01 5 0.0609 0.78805 0.02 0.00 0.00 0.00 0.98
#> TCGA.DE.A0Y2.01 5 0.2280 0.79666 0.12 0.00 0.00 0.00 0.88
cbind(get_classes(res, k = 6), get_membership(res, k = 6))
#> class entropy silhouette p1 p2 p3 p4 p5 p6
#> TCGA.L6.A4ET.01 4 0.0547 0.7388 0.00 0.00 0.00 0.98 0.00 0.02
#> TCGA.DJ.A4V2.01 5 0.1092 0.6248 0.02 0.00 0.00 0.02 0.96 0.00
#> TCGA.EM.A4FN.01 5 0.4844 0.2900 0.04 0.00 0.00 0.32 0.62 0.02
#> TCGA.EL.A4K1.01 5 0.3499 0.3401 0.32 0.00 0.00 0.00 0.68 0.00
#> TCGA.EM.A4FQ.01 5 0.3460 0.4715 0.22 0.00 0.00 0.00 0.76 0.02
#> TCGA.DJ.A4UL.01 4 0.1480 0.7324 0.00 0.00 0.04 0.94 0.00 0.02
#> TCGA.EL.A4KG.01 3 0.5883 0.2625 0.00 0.00 0.56 0.24 0.18 0.02
#> TCGA.L6.A4EP.01 3 0.3679 0.6592 0.00 0.00 0.76 0.20 0.00 0.04
#> TCGA.DE.A4MC.01 2 0.3351 0.8333 0.16 0.80 0.00 0.00 0.00 0.04
#> TCGA.EL.A3H8.01 4 0.5265 0.1964 0.00 0.00 0.40 0.50 0.10 0.00
#> TCGA.EL.A4JZ.01 2 0.2094 0.8806 0.08 0.90 0.00 0.00 0.00 0.02
#> TCGA.KS.A4I9.01 5 0.1480 0.6171 0.04 0.00 0.00 0.02 0.94 0.00
#> TCGA.EL.A3MW.01 4 0.0547 0.7388 0.00 0.00 0.00 0.98 0.00 0.02
#> TCGA.E3.A3E3.01 5 0.2728 0.5800 0.04 0.00 0.00 0.10 0.86 0.00
#> TCGA.EM.A4FM.01 2 0.0000 0.8977 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.MK.A4N9.01 3 0.4468 0.6572 0.06 0.00 0.76 0.12 0.00 0.06
#> TCGA.E3.A3E0.01 3 0.3315 0.6451 0.00 0.00 0.78 0.20 0.02 0.00
#> TCGA.KS.A4I5.01 3 0.3258 0.6382 0.02 0.00 0.84 0.04 0.00 0.10
#> TCGA.KS.A4IB.01 1 0.4534 0.1733 0.58 0.00 0.00 0.00 0.38 0.04
#> TCGA.EM.A4FF.01 5 0.1480 0.6311 0.04 0.00 0.00 0.02 0.94 0.00
#> TCGA.EL.A4K0.01 3 0.3600 0.6823 0.02 0.00 0.82 0.08 0.00 0.08
#> TCGA.EL.A4K4.01 5 0.3819 0.3787 0.28 0.00 0.00 0.00 0.70 0.02
#> TCGA.EL.A3GS.01 5 0.3076 0.4868 0.24 0.00 0.00 0.00 0.76 0.00
#> TCGA.EL.A3N2.01 5 0.1814 0.6058 0.10 0.00 0.00 0.00 0.90 0.00
#> TCGA.EL.A3MX.01 2 0.0000 0.8977 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.EM.A3FJ.01 4 0.2020 0.7047 0.02 0.00 0.02 0.92 0.04 0.00
#> TCGA.EM.A3FQ.06 3 0.3688 0.6061 0.04 0.00 0.80 0.02 0.00 0.14
#> TCGA.FE.A235.01 3 0.3821 0.4386 0.04 0.00 0.74 0.00 0.00 0.22
#> TCGA.DE.A7U5.01 5 0.4495 0.4394 0.20 0.00 0.02 0.00 0.72 0.06
#> TCGA.DE.A69J.01 4 0.6882 0.3205 0.08 0.00 0.30 0.44 0.18 0.00
#> TCGA.FE.A22Z.01 2 0.0000 0.8977 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.DJ.A2Q7.01 4 0.4764 0.0897 0.02 0.00 0.42 0.54 0.02 0.00
#> TCGA.DE.A69K.01 3 0.4361 0.5983 0.06 0.00 0.76 0.04 0.00 0.14
#> TCGA.4C.A93U.01 2 0.0000 0.8977 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.ET.A25N.01 3 0.3315 0.5123 0.02 0.00 0.78 0.00 0.00 0.20
#> TCGA.EL.A3H7.01 5 0.3156 0.5307 0.18 0.00 0.00 0.00 0.80 0.02
#> TCGA.ET.A25O.01 1 0.6985 0.2382 0.36 0.00 0.00 0.32 0.26 0.06
#> TCGA.EL.A3GU.01 2 0.2581 0.8638 0.12 0.86 0.00 0.00 0.00 0.02
#> TCGA.DJ.A2PY.01 5 0.2956 0.5697 0.04 0.00 0.00 0.12 0.84 0.00
#> TCGA.EM.A22I.01 5 0.5107 0.1093 0.04 0.00 0.30 0.00 0.62 0.04
#> TCGA.DE.A0XZ.01 3 0.3854 0.6116 0.04 0.00 0.80 0.04 0.00 0.12
#> TCGA.EL.A3GY.01 5 0.3829 0.5097 0.06 0.00 0.00 0.18 0.76 0.00
#> TCGA.EL.A3GX.01 5 0.2793 0.5496 0.20 0.00 0.00 0.00 0.80 0.00
#> TCGA.DO.A1JZ.01 6 0.3198 0.8876 0.00 0.00 0.26 0.00 0.00 0.74
#> TCGA.DO.A1K0.01 5 0.4265 0.3536 0.04 0.00 0.00 0.30 0.66 0.00
#> TCGA.IM.A3ED.01 3 0.3045 0.6748 0.02 0.00 0.86 0.06 0.00 0.06
#> TCGA.ET.A3BQ.01 3 0.3828 0.2440 0.00 0.00 0.56 0.44 0.00 0.00
#> TCGA.EL.A3H5.01 2 0.0547 0.8964 0.02 0.98 0.00 0.00 0.00 0.00
#> TCGA.EM.A2P3.01 5 0.4873 0.0926 0.06 0.00 0.00 0.42 0.52 0.00
#> TCGA.EL.A3CL.01 6 0.3409 0.8807 0.00 0.00 0.30 0.00 0.00 0.70
#> TCGA.DJ.A1QE.01 5 0.2048 0.5915 0.12 0.00 0.00 0.00 0.88 0.00
#> TCGA.FK.A3SB.01 3 0.3318 0.6776 0.02 0.00 0.82 0.14 0.00 0.02
#> TCGA.FE.A233.01 5 0.1814 0.6073 0.10 0.00 0.00 0.00 0.90 0.00
#> TCGA.ET.A39P.01 5 0.1807 0.6229 0.06 0.00 0.00 0.02 0.92 0.00
#> TCGA.DJ.A1QI.01 3 0.3483 0.6742 0.02 0.00 0.82 0.12 0.00 0.04
#> TCGA.DJ.A1QN.01 4 0.0547 0.7315 0.02 0.00 0.00 0.98 0.00 0.00
#> TCGA.FE.A234.01 5 0.4360 0.3945 0.06 0.00 0.00 0.26 0.68 0.00
#> TCGA.DJ.A1QH.01 2 0.5682 0.4532 0.38 0.46 0.00 0.00 0.00 0.16
#> TCGA.DJ.A2PU.01 4 0.0000 0.7381 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.DJ.A2PN.01 3 0.3460 0.4754 0.02 0.00 0.76 0.00 0.00 0.22
#> TCGA.DJ.A1QD.01 5 0.4482 0.2476 0.04 0.00 0.00 0.36 0.60 0.00
#> TCGA.EL.A3CP.01 4 0.2882 0.7124 0.02 0.00 0.10 0.86 0.00 0.02
#> TCGA.FY.A3RA.01 5 0.3270 0.5586 0.06 0.00 0.00 0.12 0.82 0.00
#> TCGA.ET.A3BN.01 5 0.1807 0.6276 0.06 0.00 0.00 0.02 0.92 0.00
#> TCGA.DE.A0Y2.01 5 0.2094 0.6222 0.08 0.00 0.00 0.02 0.90 0.00
cbind(get_classes(res, k = 7), get_membership(res, k = 7))
#> class entropy silhouette p1 p2 p3 p4 p5 p6 p7
#> TCGA.L6.A4ET.01 4 0.1006 0.7106 0.02 0.00 0.02 0.96 0.00 0.00 0.00
#> TCGA.DJ.A4V2.01 5 0.2722 0.6183 0.00 0.00 0.00 0.04 0.84 0.00 0.12
#> TCGA.EM.A4FN.01 5 0.5233 0.5698 0.00 0.00 0.00 0.20 0.52 0.00 0.28
#> TCGA.EL.A4K1.01 5 0.3186 0.3836 0.22 0.00 0.00 0.00 0.76 0.00 0.02
#> TCGA.EM.A4FQ.01 5 0.3052 0.4340 0.20 0.00 0.00 0.00 0.78 0.00 0.02
#> TCGA.DJ.A4UL.01 4 0.0863 0.7149 0.00 0.00 0.04 0.96 0.00 0.00 0.00
#> TCGA.EL.A4KG.01 5 0.6947 0.2522 0.00 0.00 0.34 0.10 0.36 0.02 0.18
#> TCGA.L6.A4EP.01 3 0.4249 0.5747 0.02 0.00 0.70 0.24 0.00 0.02 0.02
#> TCGA.DE.A4MC.01 2 0.3685 0.6024 0.32 0.66 0.00 0.00 0.00 0.00 0.02
#> TCGA.EL.A3H8.01 4 0.6405 0.3417 0.00 0.00 0.26 0.46 0.10 0.00 0.18
#> TCGA.EL.A4JZ.01 2 0.1928 0.8569 0.08 0.90 0.00 0.00 0.00 0.00 0.02
#> TCGA.KS.A4I9.01 5 0.3911 0.6231 0.00 0.00 0.00 0.06 0.70 0.00 0.24
#> TCGA.EL.A3MW.01 4 0.0504 0.7240 0.00 0.00 0.00 0.98 0.00 0.00 0.02
#> TCGA.E3.A3E3.01 5 0.4681 0.6034 0.00 0.00 0.00 0.10 0.58 0.00 0.32
#> TCGA.EM.A4FM.01 2 0.0000 0.8886 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.MK.A4N9.01 3 0.3289 0.7226 0.00 0.00 0.82 0.02 0.00 0.10 0.06
#> TCGA.E3.A3E0.01 3 0.3617 0.6440 0.00 0.00 0.76 0.16 0.00 0.00 0.08
#> TCGA.KS.A4I5.01 3 0.2509 0.7116 0.00 0.00 0.88 0.00 0.02 0.04 0.06
#> TCGA.KS.A4IB.01 1 0.4461 0.0768 0.54 0.00 0.00 0.00 0.40 0.00 0.06
#> TCGA.EM.A4FF.01 5 0.3770 0.6264 0.00 0.00 0.00 0.08 0.74 0.00 0.18
#> TCGA.EL.A4K0.01 3 0.3494 0.6982 0.00 0.00 0.80 0.02 0.00 0.12 0.06
#> TCGA.EL.A4K4.01 5 0.3863 0.3427 0.20 0.00 0.00 0.00 0.74 0.04 0.02
#> TCGA.EL.A3GS.01 5 0.2864 0.4650 0.12 0.00 0.00 0.00 0.84 0.02 0.02
#> TCGA.EL.A3N2.01 5 0.3263 0.5635 0.08 0.00 0.00 0.00 0.80 0.00 0.12
#> TCGA.EL.A3MX.01 2 0.0000 0.8886 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.EM.A3FJ.01 4 0.1433 0.7067 0.00 0.00 0.00 0.92 0.00 0.00 0.08
#> TCGA.EM.A3FQ.06 3 0.3011 0.7214 0.00 0.00 0.82 0.00 0.00 0.06 0.12
#> TCGA.FE.A235.01 3 0.3927 0.6014 0.00 0.00 0.76 0.00 0.02 0.14 0.08
#> TCGA.DE.A7U5.01 5 0.3617 0.4205 0.16 0.00 0.00 0.00 0.76 0.00 0.08
#> TCGA.DE.A69J.01 5 0.7431 0.1081 0.02 0.00 0.22 0.28 0.28 0.00 0.20
#> TCGA.FE.A22Z.01 2 0.0000 0.8886 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.DJ.A2Q7.01 4 0.4977 0.1873 0.00 0.00 0.42 0.50 0.00 0.04 0.04
#> TCGA.DE.A69K.01 3 0.4030 0.6596 0.00 0.00 0.72 0.00 0.00 0.12 0.16
#> TCGA.4C.A93U.01 2 0.0000 0.8886 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.ET.A25N.01 3 0.3494 0.6542 0.00 0.00 0.80 0.00 0.02 0.06 0.12
#> TCGA.EL.A3H7.01 5 0.3055 0.4612 0.14 0.00 0.00 0.00 0.82 0.02 0.02
#> TCGA.ET.A25O.01 5 0.6816 0.2254 0.22 0.00 0.00 0.26 0.38 0.00 0.14
#> TCGA.EL.A3GU.01 2 0.3186 0.7360 0.22 0.76 0.00 0.00 0.00 0.00 0.02
#> TCGA.DJ.A2PY.01 5 0.5007 0.5914 0.00 0.00 0.00 0.16 0.56 0.00 0.28
#> TCGA.EM.A22I.01 5 0.5588 0.4543 0.04 0.00 0.18 0.02 0.62 0.00 0.14
#> TCGA.DE.A0XZ.01 3 0.4402 0.6607 0.02 0.00 0.74 0.00 0.02 0.14 0.08
#> TCGA.EL.A3GY.01 5 0.4789 0.5998 0.00 0.00 0.00 0.14 0.60 0.00 0.26
#> TCGA.EL.A3GX.01 5 0.2163 0.5148 0.10 0.00 0.00 0.00 0.88 0.00 0.02
#> TCGA.DO.A1JZ.01 6 0.4825 0.6483 0.02 0.00 0.16 0.00 0.00 0.66 0.16
#> TCGA.DO.A1K0.01 5 0.5291 0.5601 0.00 0.00 0.00 0.20 0.50 0.00 0.30
#> TCGA.IM.A3ED.01 3 0.1664 0.7268 0.00 0.00 0.92 0.00 0.00 0.06 0.02
#> TCGA.ET.A3BQ.01 4 0.5221 -0.1019 0.00 0.00 0.44 0.46 0.00 0.06 0.04
#> TCGA.EL.A3H5.01 2 0.0863 0.8814 0.04 0.96 0.00 0.00 0.00 0.00 0.00
#> TCGA.EM.A2P3.01 5 0.5589 0.4252 0.00 0.00 0.00 0.32 0.40 0.00 0.28
#> TCGA.EL.A3CL.01 6 0.4388 0.6194 0.04 0.00 0.30 0.00 0.00 0.64 0.02
#> TCGA.DJ.A1QE.01 5 0.1928 0.5870 0.02 0.00 0.00 0.00 0.90 0.00 0.08
#> TCGA.FK.A3SB.01 3 0.4492 0.6709 0.00 0.00 0.72 0.12 0.00 0.12 0.04
#> TCGA.FE.A233.01 5 0.2803 0.5519 0.06 0.00 0.00 0.00 0.84 0.00 0.10
#> TCGA.ET.A39P.01 5 0.2722 0.6111 0.04 0.00 0.00 0.00 0.84 0.00 0.12
#> TCGA.DJ.A1QI.01 3 0.4379 0.6628 0.00 0.00 0.74 0.10 0.00 0.06 0.10
#> TCGA.DJ.A1QN.01 4 0.1664 0.7103 0.02 0.00 0.00 0.92 0.00 0.00 0.06
#> TCGA.FE.A234.01 5 0.5341 0.5495 0.00 0.00 0.00 0.24 0.50 0.00 0.26
#> TCGA.DJ.A1QH.01 1 0.4418 -0.2534 0.62 0.30 0.00 0.00 0.00 0.00 0.08
#> TCGA.DJ.A2PU.01 4 0.0504 0.7240 0.00 0.00 0.00 0.98 0.00 0.00 0.02
#> TCGA.DJ.A2PN.01 3 0.4145 0.6005 0.00 0.00 0.74 0.00 0.02 0.10 0.14
#> TCGA.DJ.A1QD.01 5 0.5128 0.5762 0.00 0.00 0.00 0.18 0.54 0.00 0.28
#> TCGA.EL.A3CP.01 4 0.2745 0.6587 0.00 0.00 0.16 0.82 0.00 0.00 0.02
#> TCGA.FY.A3RA.01 5 0.4418 0.5981 0.00 0.00 0.00 0.08 0.62 0.00 0.30
#> TCGA.ET.A3BN.01 5 0.2421 0.5871 0.02 0.00 0.00 0.02 0.88 0.00 0.08
#> TCGA.DE.A0Y2.01 5 0.1433 0.5734 0.00 0.00 0.00 0.00 0.92 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.L6.A4ET.01 4 0.1341 0.714379 0.00 0.00 0.00 0.92 0.08 0.00 0.00 0.00
#> TCGA.DJ.A4V2.01 5 0.4191 0.019367 0.02 0.00 0.00 0.00 0.66 0.00 0.26 0.06
#> TCGA.EM.A4FN.01 5 0.3078 0.471067 0.00 0.00 0.00 0.10 0.82 0.00 0.06 0.02
#> TCGA.EL.A4K1.01 7 0.4100 0.715708 0.06 0.00 0.00 0.00 0.36 0.00 0.58 0.00
#> TCGA.EM.A4FQ.01 7 0.4794 0.662012 0.00 0.00 0.00 0.00 0.42 0.02 0.48 0.08
#> TCGA.DJ.A4UL.01 4 0.2132 0.712788 0.00 0.00 0.04 0.88 0.08 0.00 0.00 0.00
#> TCGA.EL.A4KG.01 5 0.7397 -0.100302 0.00 0.00 0.24 0.12 0.38 0.02 0.08 0.16
#> TCGA.L6.A4EP.01 3 0.5781 0.399645 0.00 0.00 0.52 0.22 0.04 0.00 0.02 0.20
#> TCGA.DE.A4MC.01 2 0.3714 0.403094 0.44 0.54 0.00 0.02 0.00 0.00 0.00 0.00
#> TCGA.EL.A3H8.01 4 0.6700 0.147206 0.00 0.00 0.26 0.36 0.24 0.00 0.02 0.12
#> TCGA.EL.A4JZ.01 2 0.1804 0.825859 0.08 0.90 0.00 0.02 0.00 0.00 0.00 0.00
#> TCGA.KS.A4I9.01 5 0.2025 0.429790 0.00 0.00 0.00 0.00 0.88 0.00 0.10 0.02
#> TCGA.EL.A3MW.01 4 0.1563 0.721040 0.00 0.00 0.00 0.90 0.10 0.00 0.00 0.00
#> TCGA.E3.A3E3.01 5 0.0941 0.482639 0.02 0.00 0.00 0.00 0.96 0.00 0.02 0.00
#> TCGA.EM.A4FM.01 2 0.1275 0.842812 0.04 0.94 0.00 0.02 0.00 0.00 0.00 0.00
#> TCGA.MK.A4N9.01 3 0.5744 0.393002 0.04 0.00 0.60 0.10 0.02 0.04 0.00 0.20
#> TCGA.E3.A3E0.01 3 0.5668 0.370704 0.00 0.00 0.46 0.26 0.04 0.00 0.00 0.24
#> TCGA.KS.A4I5.01 3 0.5345 -0.145819 0.02 0.00 0.52 0.02 0.02 0.06 0.00 0.36
#> TCGA.KS.A4IB.01 1 0.5623 0.262804 0.48 0.00 0.00 0.00 0.08 0.02 0.36 0.06
#> TCGA.EM.A4FF.01 5 0.3337 0.298109 0.04 0.00 0.00 0.00 0.78 0.00 0.16 0.02
#> TCGA.EL.A4K0.01 3 0.2348 0.450310 0.02 0.00 0.88 0.06 0.00 0.04 0.00 0.00
#> TCGA.EL.A4K4.01 7 0.4106 0.688962 0.04 0.00 0.00 0.00 0.30 0.00 0.64 0.02
#> TCGA.EL.A3GS.01 7 0.3880 0.670545 0.02 0.00 0.00 0.00 0.32 0.00 0.64 0.02
#> TCGA.EL.A3N2.01 5 0.3995 -0.142978 0.02 0.00 0.00 0.00 0.60 0.00 0.36 0.02
#> TCGA.EL.A3MX.01 2 0.0000 0.843897 0.00 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.EM.A3FJ.01 4 0.2406 0.674915 0.00 0.00 0.00 0.80 0.20 0.00 0.00 0.00
#> TCGA.EM.A3FQ.06 3 0.5129 0.332547 0.02 0.00 0.60 0.06 0.02 0.02 0.00 0.28
#> TCGA.FE.A235.01 8 0.5801 0.504787 0.02 0.00 0.34 0.00 0.00 0.14 0.04 0.46
#> TCGA.DE.A7U5.01 7 0.4999 0.645972 0.02 0.00 0.00 0.00 0.34 0.00 0.52 0.12
#> TCGA.DE.A69J.01 5 0.6355 0.293444 0.02 0.00 0.12 0.16 0.56 0.00 0.06 0.08
#> TCGA.FE.A22Z.01 2 0.0000 0.843897 0.00 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.DJ.A2Q7.01 4 0.5932 -0.000665 0.02 0.00 0.38 0.42 0.12 0.00 0.00 0.06
#> TCGA.DE.A69K.01 3 0.5793 0.271318 0.02 0.00 0.58 0.10 0.02 0.06 0.00 0.22
#> TCGA.4C.A93U.01 2 0.0000 0.843897 0.00 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.ET.A25N.01 8 0.4106 0.671601 0.00 0.00 0.30 0.00 0.00 0.02 0.04 0.64
#> TCGA.EL.A3H7.01 7 0.4077 0.718366 0.02 0.00 0.00 0.00 0.40 0.00 0.56 0.02
#> TCGA.ET.A25O.01 5 0.8086 -0.014539 0.16 0.00 0.02 0.24 0.30 0.06 0.18 0.04
#> TCGA.EL.A3GU.01 2 0.3015 0.610911 0.32 0.68 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.DJ.A2PY.01 5 0.0808 0.480151 0.00 0.00 0.00 0.00 0.96 0.00 0.04 0.00
#> TCGA.EM.A22I.01 5 0.6272 -0.236960 0.00 0.00 0.12 0.00 0.40 0.00 0.26 0.22
#> TCGA.DE.A0XZ.01 3 0.5959 0.209379 0.00 0.00 0.52 0.02 0.04 0.08 0.04 0.30
#> TCGA.EL.A3GY.01 5 0.2350 0.464362 0.00 0.00 0.00 0.04 0.86 0.00 0.10 0.00
#> TCGA.EL.A3GX.01 7 0.4141 0.603216 0.02 0.00 0.00 0.00 0.48 0.02 0.48 0.00
#> TCGA.DO.A1JZ.01 6 0.3036 0.596599 0.00 0.00 0.04 0.00 0.00 0.78 0.00 0.18
#> TCGA.DO.A1K0.01 5 0.2940 0.489765 0.02 0.00 0.00 0.10 0.84 0.00 0.02 0.02
#> TCGA.IM.A3ED.01 3 0.4828 0.203926 0.04 0.00 0.64 0.02 0.00 0.06 0.00 0.24
#> TCGA.ET.A3BQ.01 4 0.5329 -0.052609 0.00 0.00 0.38 0.46 0.04 0.00 0.00 0.12
#> TCGA.EL.A3H5.01 2 0.1557 0.840079 0.06 0.92 0.00 0.02 0.00 0.00 0.00 0.00
#> TCGA.EM.A2P3.01 5 0.4057 0.401992 0.02 0.00 0.00 0.20 0.72 0.00 0.02 0.04
#> TCGA.EL.A3CL.01 6 0.4299 0.519753 0.00 0.00 0.14 0.00 0.00 0.64 0.00 0.22
#> TCGA.DJ.A1QE.01 5 0.4105 -0.270128 0.02 0.00 0.00 0.00 0.54 0.00 0.42 0.02
#> TCGA.FK.A3SB.01 3 0.3880 0.444609 0.00 0.00 0.68 0.24 0.00 0.00 0.00 0.08
#> TCGA.FE.A233.01 7 0.4491 0.565067 0.02 0.00 0.02 0.00 0.40 0.00 0.54 0.02
#> TCGA.ET.A39P.01 5 0.3728 0.134550 0.02 0.00 0.00 0.00 0.68 0.00 0.28 0.02
#> TCGA.DJ.A1QI.01 3 0.5298 0.383838 0.06 0.00 0.64 0.20 0.00 0.06 0.02 0.02
#> TCGA.DJ.A1QN.01 4 0.2025 0.714983 0.02 0.00 0.00 0.88 0.10 0.00 0.00 0.00
#> TCGA.FE.A234.01 5 0.3270 0.464268 0.02 0.00 0.00 0.12 0.80 0.00 0.00 0.06
#> TCGA.DJ.A1QH.01 1 0.5433 0.177634 0.60 0.20 0.00 0.00 0.00 0.06 0.12 0.02
#> TCGA.DJ.A2PU.01 4 0.2224 0.715915 0.02 0.00 0.00 0.86 0.12 0.00 0.00 0.00
#> TCGA.DJ.A2PN.01 8 0.4570 0.672970 0.00 0.00 0.28 0.00 0.00 0.04 0.06 0.62
#> TCGA.DJ.A1QD.01 5 0.0808 0.494316 0.00 0.00 0.00 0.04 0.96 0.00 0.00 0.00
#> TCGA.EL.A3CP.01 4 0.4230 0.582420 0.02 0.00 0.16 0.74 0.04 0.00 0.02 0.02
#> TCGA.FY.A3RA.01 5 0.3178 0.419015 0.02 0.00 0.00 0.00 0.80 0.00 0.14 0.04
#> TCGA.ET.A3BN.01 5 0.4704 0.006882 0.04 0.00 0.00 0.00 0.58 0.00 0.32 0.06
#> TCGA.DE.A0Y2.01 5 0.4325 -0.228460 0.02 0.00 0.00 0.00 0.56 0.00 0.38 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.
sessionInfo()
#> R version 4.0.0 (2020-04-24)
#> Platform: x86_64-pc-linux-gnu (64-bit)
#> Running under: CentOS Linux 7 (Core)
#>
#> Matrix products: default
#> BLAS: /usr/lib64/libblas.so.3.4.2
#> LAPACK: /usr/lib64/liblapack.so.3.4.2
#>
#> locale:
#> [1] LC_CTYPE=C 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_1.70.0 ComplexHeatmap_2.7.11 markdown_1.1 knitr_1.30
#> [5] matrixStats_0.57.0 cola_1.9.4
#>
#> loaded via a namespace (and not attached):
#> [1] bitops_1.0-6 bit64_4.0.5 doParallel_1.0.15 RColorBrewer_1.1-2
#> [5] httr_1.4.2 data.tree_0.7.11 tools_4.0.0 R6_2.5.0
#> [9] irlba_2.3.3 DBI_1.1.0 BiocGenerics_0.34.0 colorspace_2.0-0
#> [13] GetoptLong_1.0.4 gridExtra_2.3 tidyselect_1.0.0 bit_4.0.4
#> [17] compiler_4.0.0 Biobase_2.48.0 Cairo_1.5-12.2 xml2_1.3.2
#> [21] microbenchmark_1.4-7 slam_0.1-47 scales_1.1.0 askpass_1.1
#> [25] stringr_1.4.0 digest_0.6.27 pkgconfig_2.0.3 umap_0.2.6.0
#> [29] highr_0.8 rlang_0.4.7 GlobalOptions_0.1.2 RSQLite_2.2.0
#> [33] impute_1.62.0 shape_1.4.5 jsonlite_1.7.1 mclust_5.4.7
#> [37] dendextend_1.13.4 dplyr_0.8.5 RCurl_1.98-1.2 magrittr_2.0.1
#> [41] Matrix_1.2-18 Rcpp_1.0.5 munsell_0.5.0 S4Vectors_0.26.1
#> [45] reticulate_1.15 viridis_0.5.1 lifecycle_0.2.0 scatterplot3d_0.3-41
#> [49] stringi_1.5.3 blob_1.2.1 parallel_4.0.0 crayon_1.3.4
#> [53] lattice_0.20-41 splines_4.0.0 annotate_1.65.1 circlize_0.4.12
#> [57] polylabelr_0.2.0 pillar_1.4.3 rjson_0.2.20 codetools_0.2-16
#> [61] stats4_4.0.0 XML_3.99-0.3 glue_1.4.2 evaluate_0.14
#> [65] png_0.1-7 vctrs_0.3.4 foreach_1.5.0 polyclip_1.10-0
#> [69] gtable_0.3.0 openssl_1.4.3 purrr_0.3.4 clue_0.3-57
#> [73] assertthat_0.2.1 ggplot2_3.3.0 xfun_0.19 eulerr_6.1.0
#> [77] xtable_1.8-4 skmeans_0.2-12 RSpectra_0.16-0 viridisLite_0.3.0
#> [81] survival_3.1-12 Polychrome_1.2.5 tibble_3.0.1 iterators_1.0.12
#> [85] AnnotationDbi_1.50.3 memoise_1.1.0 IRanges_2.22.2 cluster_2.1.0
#> [89] ellipsis_0.3.1 brew_1.0-6